bioRxiv Channel: University of California, Berkeley https://biorxiv.org This feed contains articles for bioRxiv Channel "University of California, Berkeley" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Structural basis for mTORC1-dependent regulation of the lysosomal and autophagic transcription factor TFEB ]]> https://biorxiv.org/content/10.1101/2022.09.12.507619v1?rss=1 Cui, Z. Napolitano, G. de Araujo, M. E. G. Esposito, A. Monfregola, J. Huber, L. Ballabio, A. Hurley, J. H. 2022-09-12 doi:10.1101/2022.09.12.507619 Cold Spring Harbor Laboratory Press 2022-09-12 <![CDATA[ Immunological landscape of human lymph nodes during ex vivo measles virus infection ]]> https://biorxiv.org/content/10.1101/2022.09.12.507535v1?rss=1 Acklin, J. A. Patel, A. R. Horiuchi, S. Moss, A. S. Kurland, A. P. Thibault, P. Degrace, E. J. Ikegame, S. Carmichael, J. Imai, N. Ueno, H. Tweel, B. Johnson, J. R. Rosenberg, B. R. Lee, B. Lim, J. K. 2022-09-13 doi:10.1101/2022.09.12.507535 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ SPRAY-INDUCED GENE SILENCING IDENTIFIES PATHOGEN PROCESSES CONTRIBUTING TO POWDERY MILDEW PROLIFERATION ]]> https://biorxiv.org/content/10.1101/2022.09.13.507682v1?rss=1 McRae, A. G. Taneja, J. Yee, K. Shi, X. Haridas, S. LaButti, K. Singan, V. Grigoriev, I. V. Wildermuth, M. C. 2022-09-13 doi:10.1101/2022.09.13.507682 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Vowel and formant representation in human auditory speech cortex ]]> https://biorxiv.org/content/10.1101/2022.09.13.507547v1?rss=1 Oganian, Y. Bhaya-Grossman, I. Johnson, K. Chang, E. F. 2022-09-14 doi:10.1101/2022.09.13.507547 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ Kinase-independent activity of DYRK1A promotes viral entry of highly pathogenic human coronaviruses ]]> https://biorxiv.org/content/10.1101/2022.09.13.507833v1?rss=1 Strine, M. S. Cai, W. L. Wei, J. Alfajaro, M. M. Filler, R. B. Biering, S. B. Sarnik, S. Patil, A. Cervantes, K. S. Collings, C. K. DeWeirdt, P. C. Hanna, R. E. Schofield, K. Hulme, C. Konermann, S. Doench, J. G. Hsu, P. D. Kadoch, C. Yan, Q. Wilen, C. B. 2022-09-14 doi:10.1101/2022.09.13.507833 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ Organization of Upstream ESCRT Machinery at the HIV-1 Budding Site ]]> https://biorxiv.org/content/10.1101/2022.09.13.507863v1?rss=1 Hudait, A. Hurley, J. H. Voth, G. A. 2022-09-14 doi:10.1101/2022.09.13.507863 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ Development of human lateral prefrontal sulcal morphology and its relation to reasoning performance ]]> https://biorxiv.org/content/10.1101/2022.09.14.507822v1?rss=1 Willbrand, E. H. Ferrer, E. Bunge, S. A. Weiner, K. S. 2022-09-14 doi:10.1101/2022.09.14.507822 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ Dispensing with unnecessary assumptions in population genetics analysis ]]> https://biorxiv.org/content/10.1101/2022.09.12.507656v1?rss=1 Labayle, O. Tetley-Campbell, K. J. van der Laan, M. J. Ponting, C. P. Beentjes, S. V. Khamseh, A. 2022-09-15 doi:10.1101/2022.09.12.507656 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Ultraviolet radiation and dehydration stress induce overlapping transcriptional and metabolic responses in Syntrichia mosses ]]> https://biorxiv.org/content/10.1101/2022.09.14.508022v1?rss=1 Ekwealor, J. T. B. Kosina, S. M. Bowen, B. Silva, A. T. Northen, T. Oliver, M. Mishler, B. D. 2022-09-16 doi:10.1101/2022.09.14.508022 Cold Spring Harbor Laboratory Press 2022-09-16 <![CDATA[ Advanced Feedback Enhances Sensorimotor Adaptation ]]> https://biorxiv.org/content/10.1101/2022.09.14.508027v1?rss=1 Wang, T. Avraham, G. Tsay, J. Thummala, T. Ivry, R. B. 2022-09-16 doi:10.1101/2022.09.14.508027 Cold Spring Harbor Laboratory Press 2022-09-16 <![CDATA[ Rapid learning of neural circuitry from holographic ensemble stimulation enabled by model-based compressed sensing ]]> https://biorxiv.org/content/10.1101/2022.09.14.507926v1?rss=1 Triplett, M. A. Gajowa, M. Antin, B. Sadahiro, M. Adesnik, H. Paninski, L. 2022-09-17 doi:10.1101/2022.09.14.507926 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Optogenetic Instruction of Cell Fate by Temporal Patterning of Mechanobiological Signals ]]> https://biorxiv.org/content/10.1101/2022.09.14.508003v1?rss=1 Sampayo, R. G. Sakamoto, M. Kumar, S. Schaffer, D. V. 2022-09-17 doi:10.1101/2022.09.14.508003 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ DNA processing by the Kaposi's sarcoma-associated herpesvirus alkaline exonuclease SOX contributes to viral gene expression and infectious virion production ]]> https://biorxiv.org/content/10.1101/2022.09.19.508573v1?rss=1 Hartenian, E. Mendez, A. Didychuk, A. Khosla, S. Glaunsinger, B. A. 2022-09-19 doi:10.1101/2022.09.19.508573 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Eliminating Genes for a Two Component System Increases PHB Productivity in Cupriavidus basilensis 4G11 Under PHB Suppressing, Non-Stress Conditions ]]> https://biorxiv.org/content/10.1101/2022.09.19.508597v1?rss=1 Sander, K. B. Abel, A. J. Friedline, S. Sharpless, W. Skerker, J. M. B. Deutschbauer, A. Clark, D. S. Arkin, A. P. 2022-09-20 doi:10.1101/2022.09.19.508597 Cold Spring Harbor Laboratory Press 2022-09-20 <![CDATA[ Synaptic scale dopamine disruption in Huntington's Disease model mice imaged with near infrared catecholamine nanosensors ]]> https://biorxiv.org/content/10.1101/2022.09.19.508617v1?rss=1 Yang, S. J. Del Bonis-O'Donnell, J. T. Giordani, F. A. Wang, J. W.-T. Lui, A. Piekarski, D. Irrinki, A. Schaffer, D. Landry, M. P. 2022-09-21 doi:10.1101/2022.09.19.508617 Cold Spring Harbor Laboratory Press 2022-09-21 <![CDATA[ Sequential Activation and Local Unfolding Control Poly(A)-Binding Protein Condensation ]]> https://biorxiv.org/content/10.1101/2022.09.21.508844v1?rss=1 Chen, R. Kahan, D. Shangguan, J. Sachleben, J. R. Riback, J. A. Drummond, D. A. Sosnick, T. 2022-09-21 doi:10.1101/2022.09.21.508844 Cold Spring Harbor Laboratory Press 2022-09-21 <![CDATA[ A hierarchy of cell death pathways confers layered resistance to shigellosis in mice ]]> https://biorxiv.org/content/10.1101/2022.09.21.508939v1?rss=1 Roncaioli, J. L. Babirye, J. P. Chavez, R. A. Liu, F. L. Turcotte, E. A. Lee, A. Y. Lesser, C. F. Vance, R. E. 2022-09-21 doi:10.1101/2022.09.21.508939 Cold Spring Harbor Laboratory Press 2022-09-21 <![CDATA[ The logic of recurrent circuits in the primary visual cortex ]]> https://biorxiv.org/content/10.1101/2022.09.20.508739v1?rss=1 Oldenburg, I. A. Hendricks, W. D. Handy, G. Shamardani, K. Bounds, H. A. Doiron, B. Adesnik, H. 2022-09-22 doi:10.1101/2022.09.20.508739 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Host specific sensing of coronaviruses and picornaviruses by the CARD8 inflammasome ]]> https://biorxiv.org/content/10.1101/2022.09.21.508960v1?rss=1 Tsu, B. V. Agarwal, R. Gokhale, N. S. Kulsuptrakul, J. Ryan, A. P. Castro, L. K. Beierschmitt, C. M. Turcotte, E. A. Fay, E. J. Vance, R. E. Hyde, J. L. Savan, R. Mitchell, P. S. Daugherty, M. D. 2022-09-22 doi:10.1101/2022.09.21.508960 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ The Selection Landscape and Genetic Legacy of Ancient Eurasians ]]> https://biorxiv.org/content/10.1101/2022.09.22.509027v1?rss=1 1600 imputed ancient genomes 1, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify major selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported, and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in >400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic, and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, while risk alleles for diabetes and Alzheimers disease are enriched for Western Hunter-gatherer ancestry. Our results suggest that ancient selection and migration were major contributors to the distribution of phenotypic diversity in present-day Europeans. ]]> Irving-Pease, E. K. Refoyo-Martinez, A. Ingason, A. Pearson, A. Fischer, A. Barrie, W. Sjögren, K.-G. Halgren, A. S. Macleod, R. Demeter, F. Henriksen, R. A. Vimala, T. McColl, H. Vaughn, A. Speidel, L. Stern, A. J. Scorrano, G. Ramsoe, A. Schork, A. J. Rosengren, A. Zhao, L. Kristiansen, K. Sudmant, P. H. Lawson, D. J. Durbin, R. Korneliussen, T. Werge, T. Allentoft, M. E. Sikora, M. Nielsen, R. Racimo, F. Willerslev, E. 2022-09-23 doi:10.1101/2022.09.22.509027 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ A natural language fMRI dataset for voxelwise encoding models ]]> https://biorxiv.org/content/10.1101/2022.09.22.509104v1?rss=1 LeBel, A. Wagner, L. Jain, S. Adhikari-Desai, A. Gupta, B. Morgenthal, A. Tang, J. Xu, L. Huth, A. G. 2022-09-23 doi:10.1101/2022.09.22.509104 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Genetic risk for Multiple Sclerosis originated in Pastoralist Steppe populations ]]> https://biorxiv.org/content/10.1101/2022.09.23.509097v1?rss=1 Barrie, W. Yang, Y. Attfield, K. E. Irving-Pease, E. Scorrano, G. Jensen, L. T. Armen, A. P. Dimopoulos, E. A. Stern, A. Refoyo-Martinez, A. Ramsoe, A. Gaunitz, C. Demeter, F. Jorkov, M. L. S. Moller, S. B. Springborg, B. Klassen, L. Hyldgard, I. M. Wickmann, N. Vinner, L. Korneliussen, T. S. Allentoft, M. E. Sikora, M. Kristiansen, K. Rodriguez, S. Nielsen, R. Iversen, A. K. N. Lawson, D. J. Fugger, L. Willerslev, E. 2022-09-26 doi:10.1101/2022.09.23.509097 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Models of Throughput for Multi-Cell, Multi-Type Droplet Microfluidics ]]> https://biorxiv.org/content/10.1101/2022.09.23.509249v1?rss=1 Krinsman, W. E. 2022-09-26 doi:10.1101/2022.09.23.509249 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Extending Comparison Methods for Unsigned Networks to Signed Networks ]]> https://biorxiv.org/content/10.1101/2022.09.23.509251v1?rss=1 Krinsman, W. E. 2022-09-26 doi:10.1101/2022.09.23.509251 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Mapping of the bs5 and bs6 non-race-specific recessive resistances against bacterial spot of pepper ]]> https://biorxiv.org/content/10.1101/2022.09.26.509408v1?rss=1 Sharma, A. Li, J. Wente, R. Minsavage, G. V. Gill, U. S. Ortega, A. Vallejos, C. E. Hart, J. P. Staskawicz, B. J. Mazourek, M. R. Stall, R. E. Jones, J. B. Hutton, S. F. 2022-09-27 doi:10.1101/2022.09.26.509408 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Personalized transcranial alternating current stimulation improves sleep quality: Initial Findings ]]> https://biorxiv.org/content/10.1101/2022.09.26.509537v1?rss=1 Gurumoorthy, R. Ayanampudi, V. Kumar, V. Krishnan, A. Walker, M. P. Ivry, R. Knight, R. T. 2022-09-27 doi:10.1101/2022.09.26.509537 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ The promiscuous development of an unconventional Qa1b-restricted T cell population ]]> https://biorxiv.org/content/10.1101/2022.09.26.509583v1?rss=1 Manoharan Valerio, M. A. Arana, K. Guan, J. Wei Chan, S. Kurd, N. S. Lee, A. Shastri, N. Robey, E. 2022-09-27 doi:10.1101/2022.09.26.509583 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ A genome-wide CRISPR screen implicates plasma membrane asymmetry in exogenous C6-ceramide toxicity ]]> https://biorxiv.org/content/10.1101/2022.09.26.509629v1?rss=1 Morris, S. N. S. Deol, K. K. Lange, M. Olzmann, J. A. 2022-09-28 doi:10.1101/2022.09.26.509629 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Edaphic specialization onto bare, rocky outcrops as a factor in the evolution of desert angiosperms ]]> https://biorxiv.org/content/10.1101/2022.09.27.509613v1?rss=1 Lichter-Marck, I. H. Baldwin, B. G. 2022-09-28 doi:10.1101/2022.09.27.509613 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Pericytes control vascular stability and auditory spiral ganglion neuron survival ]]> https://biorxiv.org/content/10.1101/2022.09.27.509698v1?rss=1 Zhang, Y. Neng, L. Sharma, K. Hou, Z. Johnson, A. Song, J. Dabdoub, A. Shi, X. 2022-09-28 doi:10.1101/2022.09.27.509698 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Parallel evolution and cryptic diversification in the common and widespread Amazonian tree, Protium subserratum ]]> https://biorxiv.org/content/10.1101/2022.09.28.509925v1?rss=1 Misiewicz, T. M. Simmons, T. Carter, B. E. Fine, P. V. Moore, A. J. 2022-09-28 doi:10.1101/2022.09.28.509925 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Semantic reconstruction of continuous language from non-invasive brain recordings ]]> https://biorxiv.org/content/10.1101/2022.09.29.509744v1?rss=1 Tang, J. LeBel, A. Jain, S. Huth, A. G. 2022-09-29 doi:10.1101/2022.09.29.509744 Cold Spring Harbor Laboratory Press 2022-09-29 <![CDATA[ Cortical somatostatin interneuron subtypes form cell-type specific circuits ]]> https://biorxiv.org/content/10.1101/2022.09.29.510081v1?rss=1 Wu, J. S. Sevier, E. Saldi, G.-A. Yu, S. Abbott, L. Choi, D. H. Sherer, M. Qiu, Y. Shinde, A. Rizzo, D. Xu, Q. Barrera, I. Kumar, V. Marrero, G. Pörnneke, A. Huang, S. Rudy, B. Stafford, D. A. Macosko, E. Chen, F. Fishell, G. 2022-09-29 doi:10.1101/2022.09.29.510081 Cold Spring Harbor Laboratory Press 2022-09-29 <![CDATA[ Mechanisms of insertions at a DNA double-strand break ]]> https://biorxiv.org/content/10.1101/2022.09.30.509517v1?rss=1 Min, J. Zhao, J. Zagelbaum, J. Takahashi, S. Cummings, P. Schooley, A. Dekker, J. Gottesman, M. E. Rabadan, R. Gautier, J. 2022-10-01 doi:10.1101/2022.09.30.509517 Cold Spring Harbor Laboratory Press 2022-10-01 <![CDATA[ Evolution of spatial and temporal cis-regulatory divergence between marine and freshwater sticklebacks ]]> https://biorxiv.org/content/10.1101/2022.09.30.510353v1?rss=1 Mack, K. L. Square, T. A. Zhao, B. Miller, C. T. Fraser, H. B. 2022-10-01 doi:10.1101/2022.09.30.510353 Cold Spring Harbor Laboratory Press 2022-10-01 <![CDATA[ Isotope-enrichment reveals active viruses follow microbial host dynamics during rewetting of a California grassland soil ]]> https://biorxiv.org/content/10.1101/2022.09.30.510406v1?rss=1 Nicolas, A. M. Sieradzki, E. T. Pett-Ridge, J. Banfield, J. F. Taga, M. E. Firestone, M. K. Blazewicz, S. J. 2022-10-01 doi:10.1101/2022.09.30.510406 Cold Spring Harbor Laboratory Press 2022-10-01 <![CDATA[ JGI Plant Gene Atlas: An updateable transcriptome resource to improve structural annotations and functional gene descriptions across the plant kingdom ]]> https://biorxiv.org/content/10.1101/2022.09.30.510380v1?rss=1 Sreedasyam, A. Plott, C. Hossain, M. S. Lovell, J. T. Grimwood, J. Jenkins, J. W. Daum, C. Barry, K. Carlson, J. Shu, S. Phillips, J. Amirebrahimi, M. Zane, M. Wang, M. Goodstein, D. Haas, F. B. Hiss, M. Perroud, P. F. Jawdy, S. S. Hu, R. Johnson, J. Kropat, J. Gallaher, S. D. Lipzen, A. Tillman, R. Shakirov, E. V. Weng, X. Torres-Jerez, I. Weers, B. Conde, D. Pappas, M. R. Liu, L. Muchlinski, A. Jiang, H. Shyu, C. Huang, P. Sebastian, J. Laiben, C. Medlin, A. Carey, S. Carrell, A. A. Perales, M. Swaminathan, K. Allona, I. Grattapaglia, D. Cooper, E 2022-10-03 doi:10.1101/2022.09.30.510380 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ MarR-Dependent Transcriptional Regulation of mmpSL5 Induces Ethionamide Resistance in Mycobacterium abscessus ]]> https://biorxiv.org/content/10.1101/2022.10.03.510743v1?rss=1 Rodriguez, R. Campbell-Kruger, N. Gonzalez Camba, J. Berude, J. Fetterman, R. Stanley, S. 2022-10-04 doi:10.1101/2022.10.03.510743 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ A human-specific motif facilitates CARD8 inflammasome activation after HIV-1 infection ]]> https://biorxiv.org/content/10.1101/2022.10.04.510817v1?rss=1 Kulsuptrakul, J. Turcotte, E. Emerman, M. Mitchell, P. 2022-10-04 doi:10.1101/2022.10.04.510817 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ Photosynthetically active radiation is required for seedling growth promotion by volcanic dacitic tuff breccia (Azomite) ]]> https://biorxiv.org/content/10.1101/2022.10.03.510703v1?rss=1 McCue, K. F. Mehlferber, E. Reed, R. Ortiz, A. Ferrel, J. Khanna, R. 2022-10-05 doi:10.1101/2022.10.03.510703 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Effects of high temperature and heavy precipitation on drinking water quality and child hand contamination levels in rural Kenya ]]> https://biorxiv.org/content/10.1101/2022.10.04.510863v1?rss=1 Powers, J. E. Mureithi, M. Mboya, J. Campolo, J. Swarthout, J. M. Pajka, J. Null, C. Pickering, A. J. 2022-10-05 doi:10.1101/2022.10.04.510863 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ A neural model of proximity to reward ]]> https://biorxiv.org/content/10.1101/2022.10.03.510669v1?rss=1 Botros, P. Vendrell-Llopis, N. Costa, R. Carmena, J. 2022-10-06 doi:10.1101/2022.10.03.510669 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ Deep generative modeling for quantifying sample-level heterogeneity in single-cell omics ]]> https://biorxiv.org/content/10.1101/2022.10.04.510898v1?rss=1 Boyeau, P. Hong, J. Gayoso, A. Jordan, M. Azizi, E. Yosef, N. 2022-10-06 doi:10.1101/2022.10.04.510898 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ Does prefrontal connectivity during task switching help or hinder children's performance? ]]> https://biorxiv.org/content/10.1101/2022.10.04.510761v1?rss=1 Schwarze, S. A. Laube, C. Khosravani, N. Lindenberger, U. Bunge, S. Fandakova, Y. 2022-10-07 doi:10.1101/2022.10.04.510761 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Alignment, calibration, and validation of an adaptive optics scanning laser ophthalmoscope optimized for resolving human cones in the central fovea ]]> https://biorxiv.org/content/10.1101/2022.10.04.510799v1?rss=1 Moon, B. Poletti, M. Roorda, A. Tiruveedhula, P. Liu, S. H. Linebach, G. Rucci, M. Rolland, J. P. 2022-10-07 doi:10.1101/2022.10.04.510799 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Majority of the highly variable NLRs in maize share genomic location and contain additional target-binding domains ]]> https://biorxiv.org/content/10.1101/2022.10.05.510735v1?rss=1 Prigozhin, D. M. Rangavajjhala, S. Krasileva, K. V. 2022-10-07 doi:10.1101/2022.10.05.510735 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Near Infrared Nanosensors Enable Optical Imaging of Oxytocin with Selectivity over Vasopressin in Acute Mouse Brain Slices ]]> https://biorxiv.org/content/10.1101/2022.10.05.511026v1?rss=1 Navarro, N. Jeong, S. Ouassil, N. Mun, J. Leem, E. Landry, M. P. 2022-10-07 doi:10.1101/2022.10.05.511026 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ A switch in jaw form-function coupling during the evolution of mammals ]]> https://biorxiv.org/content/10.1101/2022.10.06.511001v1?rss=1 Tseng, J. Garcia-Lara, S. Flynn, J. J. Holmes, E. Rowe, T. B. Dickson, B. V. 2022-10-07 doi:10.1101/2022.10.06.511001 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ canaper: Categorical analysis of neo- and paleo-endemism in R ]]> https://biorxiv.org/content/10.1101/2022.10.06.511072v1?rss=1 Nitta, J. Laffan, S. W. Mishler, B. D. Iwasaki, W. 2022-10-07 doi:10.1101/2022.10.06.511072 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ A single amino acid change drives left- right asymmetry in Bilateria ]]> https://biorxiv.org/content/10.1101/2022.10.06.511172v1?rss=1 Truchado-Garcia, M. Perry, K. J. Cavodeassi, F. Kenny, N. J. Henry, J. Q. Grande, C. 2022-10-07 doi:10.1101/2022.10.06.511172 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Mechanisms of AGO4 slicing-enhanced RNA-directed DNA methylation ]]> https://biorxiv.org/content/10.1101/2022.10.06.511223v1?rss=1 Wang, F. Huang, H.-Y. Huang, J. Singh, J. Pikaard, C. S. 2022-10-07 doi:10.1101/2022.10.06.511223 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Cellular sources and targets of type I interferons that drive susceptibility to tuberculosis ]]> https://biorxiv.org/content/10.1101/2022.10.06.511233v1?rss=1 Kotov, D. I. Lee, O. V. Langner, C. Guillen, J. V. Peters, J. M. Moon, A. Burd, E. M. Witt, K. C. Stetson, D. B. Jaye, D. L. Bryson, B. D. Vance, R. E. 2022-10-07 doi:10.1101/2022.10.06.511233 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Crystal Structure of the kinase domain of a receptor tyrosine kinase from a choanoflagellate, Monosiga brevicollis ]]> https://biorxiv.org/content/10.1101/2022.10.07.511304v1?rss=1 Bajaj, T. Kuriyan, J. Gee, C. L. 2022-10-07 doi:10.1101/2022.10.07.511304 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Cerebellar degeneration impairs strategy discovery but not strategy recall ]]> https://biorxiv.org/content/10.1101/2022.10.07.511309v1?rss=1 Tsay, J. S. Schuck, L. Ivry, R. B. 2022-10-07 doi:10.1101/2022.10.07.511309 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Pseudomonas aeruginosa can diversify after host cell invasion to establish multiple intracellular niches ]]> https://biorxiv.org/content/10.1101/2022.10.07.511388v1?rss=1 Kumar, N. G. Nieto, V. Kroken, A. R. Jedel, E. Grosser, M. R. Hallsten, M. E. Metruccio, M. M. E. Yahr, T. L. Evans, D. J. Fleiszig, S. M. J. 2022-10-08 doi:10.1101/2022.10.07.511388 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ Drosophila epidermal cells are intrinsically mechanosensitive and drive nociceptive behavioral outputs ]]> https://biorxiv.org/content/10.1101/2022.10.07.511265v1?rss=1 Yoshino, J. Mali, S. Williams, C. Morita, T. Emerson, C. Arp, C. Sophie, M. Yin, C. The, L. Chikaya, H. Motoyoshi, M. Ishii, K. Emoto, K. Bautista, D. M. Parrish, J. Z. 2022-10-10 doi:10.1101/2022.10.07.511265 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ Elucidating the molecular programming of a nonlinear nonribosomal peptide synthetase responsible for fungal siderophore biosynthesis. ]]> https://biorxiv.org/content/10.1101/2022.10.10.511241v1?rss=1 Jenner, M. Hai, Y. Nguyen, H. H. Passmore, M. Skyrud, W. Kim, J. Garg, N. K. Zhang, W. Ogorzalek Loo, R. R. Tang, Y. 2022-10-10 doi:10.1101/2022.10.10.511241 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ Functional screens of barcoded expression libraries uncover new gene functions in carbon utilization among gut Bactereroidales ]]> https://biorxiv.org/content/10.1101/2022.10.10.511384v1?rss=1 Huang, Y. Y. Price, M. N. Hung, A. Gal-Oz, O. Ho, D. Carion, H. Deutschbauer, A. M. Arkin, A. P. 2022-10-11 doi:10.1101/2022.10.10.511384 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ A description of the genus Denitromonas nom. rev.: Denitromonas iodatirespirans sp. nov. a novel iodate-reducing bacterium and two novel perchlorate-reducing bacteria Denitromonas halophila and Denitromonas ohlonensis isolated from San Francisco Bay intertidal mudflats. ]]> https://biorxiv.org/content/10.1101/2022.10.10.511631v1?rss=1 Reyes Umana, V. M. Coates, J. 2022-10-11 doi:10.1101/2022.10.10.511631 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ wMel replacement of dengue-competent mosquitoes is robust to near-term climate change ]]> https://biorxiv.org/content/10.1101/2022.10.12.511962v1?rss=1 Vasquez, V. N. Kueppers, L. M. Rasic, G. Marshall, J. M. 2022-10-16 doi:10.1101/2022.10.12.511962 Cold Spring Harbor Laboratory Press 2022-10-16 <![CDATA[ Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes. ]]> https://biorxiv.org/content/10.1101/2022.10.14.512296v1?rss=1 Zhang, X. Li, Z. Zhang, Y. Liu, Y. Wang, J. Liu, B. Chen, Q. Wang, Q. Fu, L. Wang, P. Zhong, X. Jin, L. Chen, L. He, J. Zhao, J. Xiong, X. 2022-10-16 doi:10.1101/2022.10.14.512296 Cold Spring Harbor Laboratory Press 2022-10-16 <![CDATA[ Non-viral gene editing in utero with lipid nanoparticles complexed to mRNA ]]> https://biorxiv.org/content/10.1101/2022.10.14.512310v1?rss=1 Gao, K. Li, J. Song, H. Han, H. Wang, Y. Yin, B. Farmer, D. L. Murthy, N. Wang, A. 2022-10-16 doi:10.1101/2022.10.14.512310 Cold Spring Harbor Laboratory Press 2022-10-16 <![CDATA[ The Impact of Protein Dynamics on Residue-Residue Coevolution and Contact Prediction ]]> https://biorxiv.org/content/10.1101/2022.10.16.512436v1?rss=1 Fung, A. Koehl, A. Jagota, M. Song, Y. S. 2022-10-17 doi:10.1101/2022.10.16.512436 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Decoding of YAP levels and dynamics by pluripotency factors ]]> https://biorxiv.org/content/10.1101/2022.10.17.512504v1?rss=1 Meyer, K. Lammers, N. C. Bugaj, L. J. Garcia, H. H. Weiner, O. D. 2022-10-17 doi:10.1101/2022.10.17.512504 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ STING activation depends on ACBD3 and other phosphatidylinositol 4-phosphate-regulating proteins ]]> https://biorxiv.org/content/10.1101/2022.10.17.512580v1?rss=1 Luteijn, R. D. van Terwisga, S. R. Ver Eecke, J. E. Onia, L. Zaver, S. A. Woodward, J. J. Raulet, D. H. van Kuppeveld, F. J. 2022-10-17 doi:10.1101/2022.10.17.512580 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Ploidy modulates cell size and metabolic rate in Xenopus embryos ]]> https://biorxiv.org/content/10.1101/2022.10.17.512616v1?rss=1 Cadart, C. Bartz, J. Oaks, G. Liu, M. Heald, R. 2022-10-17 doi:10.1101/2022.10.17.512616 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs ]]> https://biorxiv.org/content/10.1101/2022.10.15.512390v1?rss=1 Chao, K.-H. Chen, P.-W. Seshia, S. A. Langmead, B. 2022-10-18 doi:10.1101/2022.10.15.512390 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Vitamin B2 enables peroxisome proliferator-activated receptor α regulation of fasting glucose availability ]]> https://biorxiv.org/content/10.1101/2022.10.16.512439v1?rss=1 Masschelin, P. M. Saha, P. Ochsner, S. A. Cox, A. R. Kim, K. H. Felix, J. B. Sharp, R. Li, X. Tan, L. Park, J. H. Wang, L. Putluri, V. Lorenzi, P. L. Nuotio-Antar, A. M. Sun, Z. Kiapparettu, B. A. Putluri, N. Moore, D. Summers, S. A. McKenna, N. J. Hartig, S. M. 2022-10-18 doi:10.1101/2022.10.16.512439 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Long-term, super-resolution HIDE imaging of the inner mitochondrial membrane in live cells with a cell-permeant lipid probe ]]> https://biorxiv.org/content/10.1101/2022.10.19.512772v1?rss=1 Zheng, S. Dadina, N. Mozumdar, D. Lesiak, L. Martinez, K. Miller, E. Schepartz, A. 2022-10-19 doi:10.1101/2022.10.19.512772 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ Loss of Linker Histone H1 in the Maternal Genome Influences DEMETER-Mediated Demethylation and Affects the Endosperm DNA Methylation Landscape ]]> https://biorxiv.org/content/10.1101/2022.10.17.512625v1?rss=1 Hsieh, T.-F. Han, Q. Hung, Y.-H. Zhang, C. Bartels, A. Rea, M. Yang, H. Park, C. Zhang, X.-Q. Fsicher, R. L. Xiao, W. 2022-10-20 doi:10.1101/2022.10.17.512625 Cold Spring Harbor Laboratory Press 2022-10-20 <![CDATA[ Diurnality shapes the visual opsin genes of colorful Neotropical frogs ]]> https://biorxiv.org/content/10.1101/2022.10.18.510514v1?rss=1 Wan, Y. C. Navarrete, M. J. O'Connell, L. A. Uricchio, L. H. Roland, A. Maan, M. E. Ron, S. R. Betancourth-Cundar, M. Pie, M. R. Howell, K. A. Richards-Zawacki, C. L. Cummings, M. E. Cannatella, D. C. Santos, J. C. Tarvin, R. D. 2022-10-21 doi:10.1101/2022.10.18.510514 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Mating activates neuroendocrine pathways signaling hunger in Drosophila females ]]> https://biorxiv.org/content/10.1101/2022.10.19.512959v1?rss=1 Laturney, M. Sterne, G. R. Scott, K. 2022-10-21 doi:10.1101/2022.10.19.512959 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Striatal dopamine synthesis and cognitive flexibility differ between hormonal contraceptive users and non-users ]]> https://biorxiv.org/content/10.1101/2022.10.20.513082v1?rss=1 Taylor, C. Furman, D. Berry, A. White, R. L. Jagust, W. J. D'Esposito, M. Jacobs, E. G. 2022-10-21 doi:10.1101/2022.10.20.513082 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Mitotic chromosomes scale to nucleo-cytoplasmic ratio and cell size in Xenopus ]]> https://biorxiv.org/content/10.1101/2022.10.20.513104v1?rss=1 Zhou, C. Y. Dekker, B. Liu, Z. Cabrera, H. Ryan, J. Dekker, J. Heald, R. 2022-10-21 doi:10.1101/2022.10.20.513104 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes ]]> https://biorxiv.org/content/10.1101/2022.10.23.513397v1?rss=1 McCully, A. L. Yao, M. L. Brower, K. Fordyce, P. M. Spormann, A. M. 2022-10-23 doi:10.1101/2022.10.23.513397 Cold Spring Harbor Laboratory Press 2022-10-23 <![CDATA[ Unsupervised Discovery of Ancestry Informative Markers and Genetic Admixture Proportions in Biobank-Scale Data Sets ]]> https://biorxiv.org/content/10.1101/2022.10.22.513294v1?rss=1 Ko, S. Chu, B. B. Peterson, D. Okenwa, C. Papp, J. C. Alexander, D. H. Sobel, E. M. Zhou, H. Lange, K. L. 2022-10-24 doi:10.1101/2022.10.22.513294 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ The trans-regulatory landscape of gene networks in plants ]]> https://biorxiv.org/content/10.1101/2022.10.23.513368v1?rss=1 Hummel, N. F. C. Zhou, A. Li, B. Markel, K. Ornelas, I. J. Shih, P. M. 2022-10-24 doi:10.1101/2022.10.23.513368 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ High Angular Resolution Susceptibility Imaging and Estimation of Fiber Orientation Distribution Functions in Primate Brain ]]> https://biorxiv.org/content/10.1101/2022.10.23.513390v1?rss=1 Gkotsoulias, D. G. Mueller, R. Jaeger, C. Schlumm, T. Mildner, T. Eichner, C. Pampel, A. Jaffe, J. Graessle, T. Alsleben, N. Chen, J. Crockford, C. Wittig, R. Liu, C. Moeller, H. E. 2022-10-24 doi:10.1101/2022.10.23.513390 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Decision and response monitoring during working memory are sequentially represented in the human insula ]]> https://biorxiv.org/content/10.1101/2022.10.25.513764v1?rss=1 Llorens, A. Bellier, L. Blenkmann, A. O. Ivanovic, J. Larsson, P. G. Lin, J. J. Endestad, T. Solbakk, A.-K. Knight, R. T. 2022-10-27 doi:10.1101/2022.10.25.513764 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Lipid homeostasis is essential for a maximal ER stress response ]]> https://biorxiv.org/content/10.1101/2022.10.27.513991v1?rss=1 Garcia, G. Zhang, H. Moreno, S. Tsui, C. K. Webster, B. M. Higuchi-Sanabria, R. Dillin, A. 2022-10-27 doi:10.1101/2022.10.27.513991 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Linking Choroid Plexus Enlargement with Plasma Analyte and Structural Phenotypes in Clinical High Risk for Psychosis: A Multisite Neuroimaging Study ]]> https://biorxiv.org/content/10.1101/2022.10.28.514160v1?rss=1 Bannai, D. Reuter, M. Hegde, R. Hoang, D. Adhan, I. Gandu, S. Pong, S. Zeng, A. Raymond, N. Zeng, V. Chung, Y. He, G. Sun, D. van Erp, T. G. M. Addington, J. Bearden, C. E. Cadenhead, K. Cornblatt, B. Mathalon, D. H. McGlashan, T. Jeffries, C. Stone, W. Tsuang, M. Walker, E. Woods, S. W. Cannon, T. D. Perkins, D. Keshavan, M. Lizano, P. 2022-10-30 doi:10.1101/2022.10.28.514160 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ Tuned Fitness Landscapes for Benchmarking Model-Guided Protein Design ]]> https://biorxiv.org/content/10.1101/2022.10.28.514293v1?rss=1 Thomas, N. Agarwala, A. Belanger, D. Song, Y. S. Colwell, L. 2022-10-30 doi:10.1101/2022.10.28.514293 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ Expanding the stdpopsim species catalog, and lessons learned forrealistic genome simulations ]]> https://biorxiv.org/content/10.1101/2022.10.29.514266v1?rss=1 Lauterbur, M. E. Cavassim, M. I. A. Gladstein, A. L. Gower, G. Pope, N. S. Tsambos, G. Adrion, J. Belsare, S. Biddanda, A. Caudill, V. Cury, J. Echevarria, I. Haller, B. C. Hasan, A. R. Huang, X. Iasi, L. N. M. Noskova, E. Obsteter, J. Pavinato, V. A. C. Pearson, A. Peede, D. Perez, M. F. Rodrigues, M. F. Smith, C. C. R. Spence, J. P. Teterina, A. Tittes, S. Unneberg, P. Vazquez, J. M. Waples, R. K. Wohns, A. W. Wong, Y. Baumdicker, F. Cartwright, R. A. Gorjanc, G. Gutenkunst, R. N. Kelleher, J. Kern, A. D. Ragsdale, A. P. Ralph, P. L. Schrider, D. R. G 2022-10-31 doi:10.1101/2022.10.29.514266 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ A bistable autoregulatory module in the developing embryo commits cells to binary fates ]]> https://biorxiv.org/content/10.1101/2022.10.31.514335v1?rss=1 Zhao, J. Perkins, M. L. Norstad, M. Garcia, H. G. 2022-11-01 doi:10.1101/2022.10.31.514335 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Genome editing in plants using the compact editor Cas{Phi} ]]> https://biorxiv.org/content/10.1101/2022.10.31.514567v1?rss=1 Li, Z. Zhong, Z. Wu, Z. Pausch, P. Al-Shayeb, B. Amerasekerae, J. Doudna, J. A. Jacobsen, S. E. 2022-11-01 doi:10.1101/2022.10.31.514567 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Independent mutation effects enable design of combinatorial protein binding mutants ]]> https://biorxiv.org/content/10.1101/2022.10.31.514613v1?rss=1 0.8). We hypothesized that the local structural dependencies surrounding a residue could be sufficient to learn these required mutation preferences, and developed an unsupervised design approach, which we term CoVES for Combinatorial Variant Effects from Structure. We show that CoVES outperforms not just model free sampling approaches but also complicated, high-capacity autoregressive neural networks in generating functional and diverse sequence variants for two example proteins. This simple, biologically-rooted model can be an effective alternative to high-capacity, out of domain models for the design of functional proteins. ]]> Ding, D. 2022-11-01 doi:10.1101/2022.10.31.514613 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Syncytin-mediated open-ended membrane tubular connections facilitate the intercellular transfer of cargos including Cas9 protein ]]> https://biorxiv.org/content/10.1101/2022.11.01.514662v1?rss=1 Zhang, C. Schekman, R. 2022-11-01 doi:10.1101/2022.11.01.514662 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Pyrophosphate-Mediated Repair of Damaged and Mismatched RNA by a Polymerase Ribozyme ]]> https://biorxiv.org/content/10.1101/2022.11.01.514781v1?rss=1 Kent, A. D. Yang, L. L. Lee, I. A. Luptak, A. 2022-11-02 doi:10.1101/2022.11.01.514781 Cold Spring Harbor Laboratory Press 2022-11-02 <![CDATA[ A Virus-Packageable CRISPR System Identifies Host Dependency Factors Across Multiple HIV-1 Strains ]]> https://biorxiv.org/content/10.1101/2022.11.03.515041v1?rss=1 Montoya, V. R. Ready, T. M. Felton, A. Fine, S. R. OhAinle, M. Emerman, M. 2022-11-04 doi:10.1101/2022.11.03.515041 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Rational Chemical Design of Molecular Glue Degraders ]]> https://biorxiv.org/content/10.1101/2022.11.04.512693v1?rss=1 Toriki, E. S. Papatzimas, J. W. Nishikawa, K. Dovala, D. McGregor, L. M. Hesse, M. J. McKenna, J. M. Tallarico, J. A. Schirle, M. Nomura, D. K. 2022-11-04 doi:10.1101/2022.11.04.512693 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Towards Environmental Control of Microbiomes ]]> https://biorxiv.org/content/10.1101/2022.11.04.515211v1?rss=1 Sharpless, W. A. Sander, K. B. Song, F. Kuehl, J. V. Arkin, A. P. 2022-11-04 doi:10.1101/2022.11.04.515211 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Integrative single-cell characterization of hypothalamus sex-differential and obesity-associated genes and regulatory elements ]]> https://biorxiv.org/content/10.1101/2022.11.06.515311v1?rss=1 Nguyen, H. P. Chan, C. S. Cintron, D. L. Sheng, R. Harshman, L. Nobuhara, M. Ushiki, A. Biellak, C. An, K. Gordon, G. M. Mifsud, F. Blake, A. Huang, E. J. Hemberg, M. Vaisse, C. Ahituv, N. 2022-11-06 doi:10.1101/2022.11.06.515311 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ Orphan quality control shapes network dynamics and gene expression ]]> https://biorxiv.org/content/10.1101/2022.11.06.515368v1?rss=1 Mark, K. G. Kolla, S. Garshott, D. Martinez-Gonzalez, B. Xu, C. Akopian, D. Haakonsen, D. L. See, S. K. Rape, M. 2022-11-06 doi:10.1101/2022.11.06.515368 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ Distinct energy-coupling factor transporter subunits enable flavin acquisition and extracytosolic trafficking for extracellular electron transfer in Listeria monocytogenes ]]> https://biorxiv.org/content/10.1101/2022.11.04.515267v1?rss=1 Rivera-Lugo, R. Huang, S. Lee, F. Meheust, R. Iavarone, A. T. Sidebottom, A. M. Oldfield, E. Portnoy, D. A. Light, S. H. 2022-11-07 doi:10.1101/2022.11.04.515267 Cold Spring Harbor Laboratory Press 2022-11-07 <![CDATA[ Periodic neglect after frontoparietal lesions provides causal evidence for rhythmic attention sampling ]]> https://biorxiv.org/content/10.1101/2022.11.07.515418v1?rss=1 Raposo, I. Szczepanski, S. Haaland, K. Endestad, T. Solbakk, A.-K. Knight, R. T. Helfrich, R. F. 2022-11-07 doi:10.1101/2022.11.07.515418 Cold Spring Harbor Laboratory Press 2022-11-07 <![CDATA[ Quantitative imaging of gene therapy delivery vehicles using CEST-NMR/MRI ]]> https://biorxiv.org/content/10.1101/2022.11.09.515733v1?rss=1 0.99, P<0.001), pH (R2=0.97, P=0.01), and viral titer per cell count (R2=0.92, P<0.001). Transition to a preclinical field strength yielded up to 11.8% CEST contrast following optimization of saturation parameters. ConclusionAAV2 viral capsids exhibit strong capacity as an endogenous CEST contrast agent and can potentially be used for monitoring and evaluation of AAV vector-mediated gene therapy protocols. ]]> Lam, B. Velasquez, M. Velasquez-Mao, A. J. Godines, K. AlGhuraibawi, W. Wendland, M. Pelton, J. G. Vandsburger, M. 2022-11-10 doi:10.1101/2022.11.09.515733 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ A new LD protein, ApoL6 disrupts the Perilipin 1-HSL interaction to inhibit lipolysis ]]> https://biorxiv.org/content/10.1101/2022.11.10.516022v1?rss=1 Wang, Y. Nguyen, H. P. Xue, P. Xie, Y. Yi, D. Lin, F. Viscarra, J. A. Ibe, N. U. Duncan, R. E. Sul, H. S. 2022-11-10 doi:10.1101/2022.11.10.516022 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ Circuit dissection and functional validation of a cross-species emotional biomarker ]]> https://biorxiv.org/content/10.1101/2022.11.11.516218v1?rss=1 Jackson, A. Cohen, J. Phensy, A. Chang, E. F. Dawes, H. Sohal, V. 2022-11-11 doi:10.1101/2022.11.11.516218 Cold Spring Harbor Laboratory Press 2022-11-11 <![CDATA[ Latch Verified Bulk-RNA Seq toolkit: a cloud-based suite of workflows for bulk RNA-seq quality control, analysis, and functional enrichment ]]> https://biorxiv.org/content/10.1101/2022.11.10.516016v1?rss=1 Le, H. G. B. H. Steenwyk, J. L. Manske, N. Smolin, M. Abdulali, A. Kamat, A. Kanchana, R. Giffin, K. Andere, A. Workman, K. 2022-11-13 doi:10.1101/2022.11.10.516016 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Serial dependence in timing at the perceptual level being modulated by working memory ]]> https://biorxiv.org/content/10.1101/2022.11.11.516083v1?rss=1 Chen, S. Wang, T. Bao, Y. 2022-11-13 doi:10.1101/2022.11.11.516083 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ An RFX transcription factor regulated ciliogenesis in the progenitors of choanoflagellates and animals ]]> https://biorxiv.org/content/10.1101/2022.11.11.515474v1?rss=1 Coyle, M. Tajima, A. Leon, F. Choksi, S. P. Yang, A. Espinoza, S. Hughes, T. R. Reiter, J. F. Booth, D. S. King, N. 2022-11-14 doi:10.1101/2022.11.11.515474 Cold Spring Harbor Laboratory Press 2022-11-14 <![CDATA[ Some like it hotter: differential thermal preferences among lizard color morphs ]]> https://biorxiv.org/content/10.1101/2022.11.11.516149v1?rss=1 Thompson, A. Kapsanaki, V. Liwanag, H. E. M. Pafilis, P. Wang, I. J. Brock, K. M. 2022-11-14 doi:10.1101/2022.11.11.516149 Cold Spring Harbor Laboratory Press 2022-11-14 <![CDATA[ It's not easy seeing green: the veridical perception of small spots ]]> https://biorxiv.org/content/10.1101/2022.11.15.516626v1?rss=1 Vanston, J. E. Boehm, A. E. Tuten, W. S. Roorda, A. 2022-11-15 doi:10.1101/2022.11.15.516626 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Subspace partitioning in human prefrontal cortex resolves cognitive interference ]]> https://biorxiv.org/content/10.1101/2022.11.16.516719v1?rss=1 Weber, J. Iwama, G. Solbakk, A.-K. Blenkmann, A. O. Larsson, P. G. Ivanovic, J. Knight, R. T. Endestad, T. Helfrich, R. 2022-11-16 doi:10.1101/2022.11.16.516719 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Auditory prediction hierarchy in the human hippocampus and amygdala ]]> https://biorxiv.org/content/10.1101/2022.11.16.516768v1?rss=1 Tzovara, A. Fedele, T. Sarnthein, J. Ledergerber, D. Lin, J. J. Knight, R. T. 2022-11-16 doi:10.1101/2022.11.16.516768 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Uptake of tumor-derived microparticles induces metabolic reprogramming of macrophages in the early metastatic lung. ]]> https://biorxiv.org/content/10.1101/2022.11.15.516217v1?rss=1 Kersten, K. You, R. Liang, S. Tharp, K. Pollack, J. Weaver, V. M. Krummel, M. F. Headley, M. B. 2022-11-17 doi:10.1101/2022.11.15.516217 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Cross-protein transfer learning substantially improves zero-shot prediction of disease variant effects ]]> https://biorxiv.org/content/10.1101/2022.11.15.516532v1?rss=1 Jagota, M. Ye, C. Rastogi, R. Albors, C. Koehl, A. Ioannidis, N. Song, Y. S. 2022-11-17 doi:10.1101/2022.11.15.516532 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Defining the Parameters to Improve Plant Regeneration with Developmental Regulators ]]> https://biorxiv.org/content/10.1101/2022.11.15.516675v1?rss=1 Nasti, R. A. Cody, J. P. Zinselmeier, M. H. Badey, N. B. Sridhar, A. Sharma, A. Maher, M. F. Blackman, B. K. A. Voytas, D. 2022-11-17 doi:10.1101/2022.11.15.516675 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Autotrophic biofilms sustained by deeply-sourced groundwater host diverse CPR bacteria implicated in sulfur and hydrogen metabolism ]]> https://biorxiv.org/content/10.1101/2022.11.17.516901v1?rss=1 Alvarado, L. E. V. Fakra, S. C. Probst, A. J. Giska, J. R. Jaffe, A. L. Oltrogge, L. M. West-Roberts, J. Rowland, J. Manga, M. Savage, D. F. Greening, C. Baker, B. J. Banfield, J. F. 2022-11-17 doi:10.1101/2022.11.17.516901 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ NMY-2, TOE-2 and PIG-1 Regulate C. elegans Asymmetric Cell Divisions ]]> https://biorxiv.org/content/10.1101/2022.11.17.516947v1?rss=1 Robinson, J. D. Teuliere, J. Yoo, S. Garriga, G. 2022-11-17 doi:10.1101/2022.11.17.516947 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Engineered molecular sensors of cell surface crowding ]]> https://biorxiv.org/content/10.1101/2022.11.18.517164v1?rss=1 Takatori, S. C. Son, S. Lee, D. Fletcher, D. A. 2022-11-20 doi:10.1101/2022.11.18.517164 Cold Spring Harbor Laboratory Press 2022-11-20 <![CDATA[ Optogenetic dissection of transcriptional repression in a multicellular organism ]]> https://biorxiv.org/content/10.1101/2022.11.20.517211v1?rss=1 Zhao, J. Lammers, N. C. Alamos, S. Kim, Y. J. Martini, G. Garcia, H. G. 2022-11-20 doi:10.1101/2022.11.20.517211 Cold Spring Harbor Laboratory Press 2022-11-20 <![CDATA[ Novel and unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments ]]> https://biorxiv.org/content/10.1101/2022.11.20.517286v1?rss=1 Zhang, C. Liu, X. Shi, L.-D. Li, J. Xiao, X. Shao, Z. Dong, X. 2022-11-21 doi:10.1101/2022.11.20.517286 Cold Spring Harbor Laboratory Press 2022-11-21 <![CDATA[ Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England ]]> https://biorxiv.org/content/10.1101/2022.11.21.517390v1?rss=1 Yu, Q. Ascensao, J. A. Okada, T. The COVID-19 Genomics UK (COG-UK) consortium, Boyd, O. Volz, E. Hallatschek, O. 2022-11-22 doi:10.1101/2022.11.21.517390 Cold Spring Harbor Laboratory Press 2022-11-22 <![CDATA[ Host translation machinery is not a barrier to phages that infect both CPR and non-CPR bacteria ]]> https://biorxiv.org/content/10.1101/2022.11.22.517103v1?rss=1 Liu, J. D. Jaffe, A. L. Chen, L. Bor, B. Banfield, J. F. 2022-11-22 doi:10.1101/2022.11.22.517103 Cold Spring Harbor Laboratory Press 2022-11-22 <![CDATA[ Taste adaptations associated with host-specialization in the specialist Drosophila sechellia ]]> https://biorxiv.org/content/10.1101/2022.11.21.517453v1?rss=1 REISENMAN, C. E. Wong, J. Vedagarbha, N. Livelo, C. Scott, K. 2022-11-23 doi:10.1101/2022.11.21.517453 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ Retinal microvascular and neuronal pathologies probed in vivo by adaptive optical two-photon fluorescence microscopy ]]> https://biorxiv.org/content/10.1101/2022.11.23.517628v1?rss=1 Zhang, Q. Yang, Y. Cao, K. J. Chen, W. Paidi, S. Xia, C.-h. Kramer, R. Gong, X. Ji, N. 2022-11-23 doi:10.1101/2022.11.23.517628 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ A model for Scc2p Stimulation of Cohesin's ATPase and its Inhibition by Acetylation of Smc3p ]]> https://biorxiv.org/content/10.1101/2022.11.23.517716v1?rss=1 Boardman, K. M. Xiang, S. Chatterjee, F. Mbonu, U. Guacci, V. A. Koshland, D. 2022-11-23 doi:10.1101/2022.11.23.517716 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ Physiological adaptation of sulfate reducing bacteria in syntrophic partnership with anaerobic methanotrophic archaea ]]> https://biorxiv.org/content/10.1101/2022.11.23.517749v1?rss=1 Murali, R. Yu, H. Speth, D. Wu, F. Metcalfe, K. S. Cremiere, A. Laso-Perez, R. Malmstrom, R. Goudeau, D. Woyke, T. Hatzenpichler, R. Chadwick, G. Orphan, V. J. 2022-11-23 doi:10.1101/2022.11.23.517749 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ Gasdermin D is the only Gasdermin that provides non-redundant protection against acute Salmonella gut infection ]]> https://biorxiv.org/content/10.1101/2022.11.24.517575v1?rss=1 Fattinger, S. A. Maurer, L. Geiser, P. Enz, U. Ganguillet, S. Gul, E. Kroon, S. Demarco, B. Furter, M. Barthel, M. Pelczar, P. Shao, F. Broz, P. Sellin, M. E. Hardt, W.-D. 2022-11-25 doi:10.1101/2022.11.24.517575 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ Evidence that SPIO Chain Formation is Essential for High-Resolution MPI ]]> https://biorxiv.org/content/10.1101/2022.11.27.518061v1?rss=1 Colson, C. Fung, K. L. B. Bryan, J. Tay, Z. W. Fellows, B. D. Sayuujya, C. Kuo, R. Chandrasekharan, P. Conolly, S. M. 2022-11-28 doi:10.1101/2022.11.27.518061 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Evolutionary dynamics of transposable elements in Magnaporthe oryzae reveal evidence of genomic transfer and key differences between rice and wheat blast pathotypes ]]> https://biorxiv.org/content/10.1101/2022.11.27.518126v1?rss=1 Nakamoto, A. A. Joubert, P. M. Krasileva, K. V. 2022-11-28 doi:10.1101/2022.11.27.518126 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Age-related decline in prefrontal glutamate predicts failure to efficiently deploy working memory in the service of learning ]]> https://biorxiv.org/content/10.1101/2022.11.28.518237v1?rss=1 Rmus, M. He, M. Baribault, B. Walsh, E. G. Festa, E. K. Collins, A. G. E. Nassar, M. R. 2022-11-29 doi:10.1101/2022.11.28.518237 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ SARS-CoV-2 Envelope-mediated Golgi pH dysregulation interferes with ERAAP retention in cells ]]> https://biorxiv.org/content/10.1101/2022.11.29.518257v1?rss=1 Vargas-Zapata, V. Geiger, K. M. Tran, D. Ma, J. Mao, X. Puschnik, A. S. Coscoy, L. 2022-11-30 doi:10.1101/2022.11.29.518257 Cold Spring Harbor Laboratory Press 2022-11-30 <![CDATA[ Translation-dependent downregulation of Cas12a mRNA by an anti-CRISPR protein ]]> https://biorxiv.org/content/10.1101/2022.11.29.518452v1?rss=1 Marino, N. D. Talaie, A. Carion, H. Zhang, Y. Silas, S. Li, Y. Bondy-Denomy, J. 2022-11-30 doi:10.1101/2022.11.29.518452 Cold Spring Harbor Laboratory Press 2022-11-30 <![CDATA[ Multiple paths towards repeated phenotypic evolution in the spiny-leg adaptive radiation (Tetragnatha; Hawaii) ]]> https://biorxiv.org/content/10.1101/2022.11.29.518358v1?rss=1 Cerca, J. Cotoras, D. D. Santander, C. G. Bieker, V. C. Hutchins, L. Morin-Lagos, J. Prada, C. F. Kennedy, S. Krehenwinkel, H. Rominger, A. Meier, J. Dimitrov, D. Struck, T. Gillespie, R. G. 2022-12-02 doi:10.1101/2022.11.29.518358 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity ]]> https://biorxiv.org/content/10.1101/2022.12.02.518885v1?rss=1 Williams, C. J. Dai, D. Tran, K. A. Monroe, J. G. P. Williams, B. P. 2022-12-03 doi:10.1101/2022.12.02.518885 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ Cell-surface targeting of fluorophores in Drosophila for rapid neuroanatomy visualization ]]> https://biorxiv.org/content/10.1101/2022.12.01.518740v1?rss=1 Kirk, M. J. Gold, A. Ravi, A. Sterne, G. R. Scott, K. Miller, E. W. 2022-12-05 doi:10.1101/2022.12.01.518740 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ A Unitary Mechanism Underlies Adaptation to Both Local and Global Environmental Statistics in Time Perception ]]> https://biorxiv.org/content/10.1101/2022.12.03.519001v1?rss=1 Wang, T. Luo, Y. Ivry, R. B. Tsay, J. Poeppel, E. Bao, Y. 2022-12-05 doi:10.1101/2022.12.03.519001 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ A highly active Burkholderia polyketoacyl-CoA thiolase for production of triacetic acid lactone ]]> https://biorxiv.org/content/10.1101/2022.12.04.519061v1?rss=1 Wang, Z. Cheong, S. Pereira, J. H. Kim, J. DeGiovanni, A. Guo, Y. Lan, G. Barcelos, C. A. Haushalter, R. Lee, T. S. Adams, P. D. Keasling, J. D. 2022-12-05 doi:10.1101/2022.12.04.519061 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ X-Chromosome Target Specificity Diverged Between Dosage Compensation Mechanisms of Two Closely Related Caenorhabditis Species ]]> https://biorxiv.org/content/10.1101/2022.12.05.519163v1?rss=1 Yang, Q. Lo, T.-W. Brejc, K. Schartner, C. Ralston, E. J. Lapidus, D. M. Meyer, B. J. 2022-12-05 doi:10.1101/2022.12.05.519163 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ Morphogenesis and development of human telencephalic organoids in the absence and presence of exogenous ECM ]]> https://biorxiv.org/content/10.1101/2022.12.06.519271v1?rss=1 Martins-Costa, C. Pham, V. Sidhaye, J. Novatchkova, M. Peer, A. Moeseneder, P. Corsini, N. S. Knoblich, J. A. 2022-12-07 doi:10.1101/2022.12.06.519271 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets ]]> https://biorxiv.org/content/10.1101/2022.12.06.519402v1?rss=1 Pipes, L. Nielsen, R. 2022-12-07 doi:10.1101/2022.12.06.519402 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Trans-cellular control of synapse properties by a cell type-specific splicing regulator ]]> https://biorxiv.org/content/10.1101/2022.12.07.519444v1?rss=1 Traunmuller, L. Schulz, J. M. Ortiz, R. Feng, H. Furlanis, E. Gomez, A. M. Schreiner, D. Bischofberger, J. Zhang, C. Scheiffele, P. 2022-12-07 doi:10.1101/2022.12.07.519444 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Attention weights accurately predict language representations in the brain ]]> https://biorxiv.org/content/10.1101/2022.12.07.519480v1?rss=1 Lamarre, M. Chen, C. Deniz, F. 2022-12-07 doi:10.1101/2022.12.07.519480 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Single cell RNA-seq in Drosophila testis reveals evolutionary trajectory of sex chromosome regulation ]]> https://biorxiv.org/content/10.1101/2022.12.07.519494v1?rss=1 Bachtrog, D. 2022-12-07 doi:10.1101/2022.12.07.519494 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Asymmetric coding of reward prediction errors in human insula and dorsomedial prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2022.12.07.519496v1?rss=1 Hoy, C. W. Quiroga-Martinez, D. R. King-Stephens, D. Laxer, K. Weber, P. Lin, J. J. Knight, R. T. 2022-12-07 doi:10.1101/2022.12.07.519496 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Controlling the bioelectrical properties of neurons with ferritin-based Magnetogenetics ]]> https://biorxiv.org/content/10.1101/2022.12.07.519516v1?rss=1 HERNANDEZ-MORALES, M. MORALES-WEIL, K. HAN, S. M. HAN, V. PEGRAM, K. BENNER, E. J. MILLER, E. W. KRAMER, R. H. LIU, C. 2022-12-07 doi:10.1101/2022.12.07.519516 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Mild SARS-CoV-2 infection results in long-lasting microbiota instability ]]> https://biorxiv.org/content/10.1101/2022.12.07.519508v1?rss=1 Upadhyay, V. Suryawanshi, R. Tasoff, P. McCavitt-Malvido, M. Kumar, G. R. Murray, V. Noecker, C. Bisanz, J. E. Hswen, Y. Ha, C. Sreekumar, B. Chen, I. P. Lynch, S. V. Ott, M. Lee, S. Turnbaugh, P. J. 2022-12-08 doi:10.1101/2022.12.07.519508 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ Transboundary hotspots associated with SARS-like coronavirus spillover risk: implications for mitigation ]]> https://biorxiv.org/content/10.1101/2022.12.08.518776v1?rss=1 Muylaert, R. L. Wilkinson, D. A. Kingston, T. D`Odorico, P. Rulli, M. C. Galli, N. John, R. S. Alviola, P. Hayman, D. T. S. 2022-12-09 doi:10.1101/2022.12.08.518776 Cold Spring Harbor Laboratory Press 2022-12-09 <![CDATA[ Insights into the evolution of herbivory from a leaf-mining, drosophilid fly ]]> https://biorxiv.org/content/10.1101/2022.12.07.519390v1?rss=1 Aguilar, J. M. Gloss, A. D. Suzuki, H. C. Verster, K. I. Singhal, M. Hoff, J. Grebenok, R. Nabity, P. D. Behmer, S. T. Whiteman, N. K. 2022-12-11 doi:10.1101/2022.12.07.519390 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Genomic data suggest parallel dental vestigialization within the xenarthran radiation ]]> https://biorxiv.org/content/10.1101/2022.12.09.519446v1?rss=1 Emerling, C. A. Gibb, G. C. Tilak, M.-K. Hughes, J. J. Kuch, M. Duggan, A. T. Poinar, H. N. Nachman, M. W. Delsuc, F. 2022-12-11 doi:10.1101/2022.12.09.519446 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Abstraction of reward context facilitates relative reward coding in dorsal and ventral anterior cingulate cortex ]]> https://biorxiv.org/content/10.1101/2022.12.10.519901v1?rss=1 Chien, J. Wallis, J. D. Rich, E. L. 2022-12-11 doi:10.1101/2022.12.10.519901 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Pseudomonas isolates from ponds populated with duckweed prevent disease caused by pathogenic Pseudomonas species ]]> https://biorxiv.org/content/10.1101/2022.12.09.519836v1?rss=1 Baggs, E. Stark, F. G. Tiersma, M. Krasileva, K. 2022-12-12 doi:10.1101/2022.12.09.519836 Cold Spring Harbor Laboratory Press 2022-12-12 <![CDATA[ Extending eco-evolutionary theory with oligomorphic dynamics ]]> https://biorxiv.org/content/10.1101/2022.12.12.520082v1?rss=1 Lion, S. Sasaki, A. Boots, M. 2022-12-14 doi:10.1101/2022.12.12.520082 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ Identification of structurally diverse FSP1 inhibitors that sensitize cancer cells to ferroptosis ]]> https://biorxiv.org/content/10.1101/2022.12.14.520445v1?rss=1 Hendricks, J. M. Doubravsky, C. Wehri, E. Li, Z. Roberts, M. A. Deol, K. Lange, M. Lasheras-Otero, I. Dixon, S. J. Bersuker, K. Schaletzky, J. Olzmann, J. A. 2022-12-14 doi:10.1101/2022.12.14.520445 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ Jaccard dissimilarity in stochastic community models based on the species-independence assumption ]]> https://biorxiv.org/content/10.1101/2022.12.13.520233v1?rss=1 Iritani, R. Ontiveros, V. L. J. Alonso, D. Capitan, J. A. Godsoe, W. Tatsumi, S. 2022-12-15 doi:10.1101/2022.12.13.520233 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Cell non-autonomous control of autophagy and metabolism by glial cells ]]> https://biorxiv.org/content/10.1101/2022.12.15.520639v1?rss=1 Metcalf, M. G. Monshietehadi, S. Sahay, A. Frakes, A. E. Durieux, J. Velichkovska, M. Mena, C. Farinas, A. Sanchez, M. Dillin, A. 2022-12-15 doi:10.1101/2022.12.15.520639 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Logging alters tropical forest structure, while conversion reduces biodiversity and functioning ]]> https://biorxiv.org/content/10.1101/2022.12.15.520573v1?rss=1 Marsh, C. J. Turner, E. C. Blonder, B. Bongalov, B. Both, S. Cruz, R. S. Elias, D. M. O. Hemprich-Bennett, D. Jotan, P. Kemp, V. Kritzler, U. H. Milne, S. Milodowski, D. T. Mitchell, S. L. Montoya Pillco, M. Nunes, M. H. Riutta, T. Robinson, S. J. B. Slade, E. M. Bernard, H. Burslem, D. F. R. P. Chung, A. Y. C. Clare, E. L. Coomes, D. A. Davies, Z. G. Edwards, D. P. Johnson, D. Kratina, P. Malhi, Y. Majalap, N. Nilus, R. Ostle, N. J. Rossiter, S. J. Struebig, M. J. Williams, M. Ewers, R. M. Lewis, O. T. Reynolds, G. Teh, Y. A. Hector, A. 2022-12-18 doi:10.1101/2022.12.15.520573 Cold Spring Harbor Laboratory Press 2022-12-18 <![CDATA[ Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements ]]> https://biorxiv.org/content/10.1101/2022.12.17.520895v1?rss=1 Wirthlin, M. E. Schmid, T. A. Elie, J. E. Zhang, X. Shvareva, V. A. Rakuljic, A. Ji, M. B. Bhat, N. S. Kaplow, I. M. Schäffer, D. E. Lawler, A. J. Annaldasula, S. Lim, B. Azim, E. Zoonomia Consortium, Meyer, W. K. Yartsev, M. M. Pfenning, A. R. 2022-12-18 doi:10.1101/2022.12.17.520895 Cold Spring Harbor Laboratory Press 2022-12-18 <![CDATA[ High-Throughput Discovery and Characterization of Viral Transcriptional Effectors in Human Cells ]]> https://biorxiv.org/content/10.1101/2022.12.16.520835v1?rss=1 Ludwig, C. H. Thurm, A. R. Morgens, D. W. Yang, K. J. Tycko, J. Bassik, M. C. Glaunsinger, B. A. Bintu, L. 2022-12-19 doi:10.1101/2022.12.16.520835 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Targeted Protein Degradation through E2 Recruitment ]]> https://biorxiv.org/content/10.1101/2022.12.19.520812v1?rss=1 Forte, N. Dovala, D. Hesse, M. J. McKenna, J. M. Tallarico, J. A. Schirle, M. Nomura, D. K. 2022-12-20 doi:10.1101/2022.12.19.520812 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Deep learning-enabled design of synthetic orthologs of a signaling protein ]]> https://biorxiv.org/content/10.1101/2022.12.21.521443v1?rss=1 Lian, X. Praljak, N. Subramanian, S. Wasinger, S. Ranganathan, R. Ferguson, A. L. 2022-12-21 doi:10.1101/2022.12.21.521443 Cold Spring Harbor Laboratory Press 2022-12-21 <![CDATA[ Genetic inactivation of the USP19 deubiquitinase regulates a-synuclein ubiquitination and inhibits accumulation of Lewy body like aggregates in mice ]]> https://biorxiv.org/content/10.1101/2022.12.21.521125v1?rss=1 Schorova, L. Bedard, N. Khayachi, A. Bolivar-Pedroso, J. Ho, H.-H. Huynh, J. Piccirelli, M. Wang, Y. Plourde, M. Luo, W. Del Cid Pellitero, E. Schlaifer, I. Ye, Y. Durcan, T. Wing, S. S. 2022-12-22 doi:10.1101/2022.12.21.521125 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Expanded Multiplexing on Sensor-Constrained Microfluidic Partitioning Systems ]]> https://biorxiv.org/content/10.1101/2022.12.23.521805v1?rss=1 Kota, P. K. Vu, H.-A. LeJeune, D. Han, M. Syed, S. Baraniuk, R. G. Drezek, R. A. 2022-12-23 doi:10.1101/2022.12.23.521805 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ ESCRT recruitment to mRNA-encoded SARS-CoV-2 spike induces virus-like particles and enhanced antibody responses ]]> https://biorxiv.org/content/10.1101/2022.12.26.521940v1?rss=1 10-fold against Omicron-based variants for three months post-boost. Thus, EABR technology enhances potency and breadth of vaccine-induced responses through antigen presentation on cell surfaces and eVLPs, enabling longer-lasting protection against SARS-CoV-2 and other viruses. ]]> Hoffmann, M. A. Yang, Z. Huey-Tubman, K. E. Cohen, A. A. Gnanapragasam, P. N. Nakatomi, L. M. Storm, K. N. Moon, W. J. Lin, P. J. Bjorkman, P. J. 2022-12-27 doi:10.1101/2022.12.26.521940 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Exceptionally versatile respiratory metabolisms drive metabolite production by diverse gut bacteria ]]> https://biorxiv.org/content/10.1101/2022.12.26.521950v1?rss=1 Little, A. S. Younker, I. T. Schechter, M. S. Meheust, R. Stemczynski, J. Scorza, K. Nol Bernardino, P. Mullowney, M. W. Sharan, D. Waligurski, E. Smith, R. Ramanswamy, R. Leiter, W. Moran, D. McMillin, M. Odenwald, M. A. Iavarone, A. T. Sidebottom, A. M. Sundararajan, A. Pamer, E. G. Eren, A. M. Light, S. H. 2022-12-27 doi:10.1101/2022.12.26.521950 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Annexin A6 mediates calcium-dependent secretion of exosomes ]]> https://biorxiv.org/content/10.1101/2022.12.28.522125v1?rss=1 Williams, J. K. Ngo, J. M. Schekman, R. 2022-12-29 doi:10.1101/2022.12.28.522125 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Origin of wiring specificity in an olfactory map: dendrite targeting of projection neurons ]]> https://biorxiv.org/content/10.1101/2022.12.28.522173v1?rss=1 Wong, K. K. L. Li, T. Fu, T.-M. Liu, G. Lyu, C. Kohani, S. Xie, Q. Luginbuhl, D. J. Upadhyayula, G. Betzig, E. Luo, L. 2022-12-29 doi:10.1101/2022.12.28.522173 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Deficiency in Galectin-3, -8, and -9 impairs immunity to chronic Mycobacterium tuberculosis infection but not acute infection with multiple intracellular pathogens ]]> https://biorxiv.org/content/10.1101/2022.12.29.522180v1?rss=1 Morrison, H. M. Craft, J. Rivera-Lugo, R. Johnson, J. R. Golovkine, G. R. Dodd, C. E. Van Dis, E. Beatty, W. L. Margolis, S. R. Repasy, T. Shaker, I. Lee, A. Y. Vance, R. E. Stanley, S. A. Krogan, N. J. Portnoy, D. A. Penn, B. H. Cox, J. S. 2022-12-29 doi:10.1101/2022.12.29.522180 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Data-driven model of glycolysis identifies the role of allostery in maintaining ATP homeostasis ]]> https://biorxiv.org/content/10.1101/2022.12.28.522046v1?rss=1 Choe, M. Einav, T. Phillips, R. Titov, D. V. 2022-12-30 doi:10.1101/2022.12.28.522046 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ Molecular characterization of nervous system organization in the hemichordate Saccoglossus kowalevskii ]]> https://biorxiv.org/content/10.1101/2023.01.02.522090v1?rss=1 Andrade Lopez, J. M. Pani, A. M. Wu, M. Gerhart, J. Lowe, C. J. 2023-01-03 doi:10.1101/2023.01.02.522090 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Metrics of Coral Microfragment Viability ]]> https://biorxiv.org/content/10.1101/2023.01.03.522625v1?rss=1 Lager, C. Perry, R. Daly, J. Page, C. Mizobe, M. Bouwmeester, J. Consiglio, A. Powell-Palm, M. J. Hagedorn, M. 2023-01-03 doi:10.1101/2023.01.03.522625 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ A Novel Protein for the Bioremediation of Gadolinium Waste ]]> https://biorxiv.org/content/10.1101/2023.01.05.522788v1?rss=1 Lee, H. D. Grady, C. J. Krell, K. Strebeck, C. Good, N. M. Martinez-Gomez, N. C. Gilad, A. 2023-01-06 doi:10.1101/2023.01.05.522788 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ High-throughput single molecule tracking identifies drug interactions and cellular mechanisms ]]> https://biorxiv.org/content/10.1101/2023.01.05.522916v1?rss=1 106 cells/day and screening > 104 compounds). We applied htSMT to measure the cellular dynamics of fluorescently tagged estrogen receptor (ER) and screened a diverse library to identify small molecules that perturbed ER function in real time. With this one experimental modality, we determined the potency, pathway selectivity, target engagement, and mechanism of action for identified hits. Kinetic htSMT experiments were capable of distinguishing between on-target and on-pathway modulators of ER signaling. Integrated pathway analysis recapitulated the network of known ER interaction partners and suggested potentially novel, kinase-mediated regulatory mechanisms. The sensitivity of htSMT revealed a new correlation between ER dynamics and the ability of ER antagonists to suppress cancer cell growth. Therefore, measuring protein motion at scale is a powerful method to investigate dynamic interactions among proteins and may facilitate the identification and characterization of novel therapeutics. ]]> McSwiggen, D. T. Liu, H. Tan, R. Agramunt Puig, S. Akella, L. B. Berman, R. Bretan, M. Chen, H. Darzacq, X. Ford, K. Godbey, R. Gonzalez, E. Hanuka, A. Heckert, A. Ho, J. J. Johnson, S. L. Kelso, R. Klammer, A. Li, J. Lin, K. Margolin, B. McNamara, P. Meyer, L. Pierce, S. E. Sule, A. Tang, Y. Anderson, D. J. Beck, H. 2023-01-06 doi:10.1101/2023.01.05.522916 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ The Cortical Representation of Language Timescales is Shared between Reading and Listening ]]> https://biorxiv.org/content/10.1101/2023.01.06.522601v1?rss=1 Chen, C. Dupre la Tour, T. Gallant, J. Klein, D. Deniz, F. 2023-01-06 doi:10.1101/2023.01.06.522601 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ H2A.X mutants exhibit enhanced DNA demethylation in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2023.01.08.523178v1?rss=1 Frost, J. M. Lee, J. Hsieh, P.-H. Lin, S. J. Min, Y. Bauer, M. Runkel, A. Cho, H.-T. Hsieh, T.-F. Choi, Y. Fischer, R. L. 2023-01-09 doi:10.1101/2023.01.08.523178 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ A Cellular Platform for Production of C4 Monomers ]]> https://biorxiv.org/content/10.1101/2023.01.09.523327v1?rss=1 Davis, M. A. Yu, V. Y. Fu, B. Wen, M. Koleski, E. J. Silverman, J. Berdan, C. A. Nomura, D. K. Chang, M. C. Y. 2023-01-10 doi:10.1101/2023.01.09.523327 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Comparing rapid rule-learning strategies in humans and monkeys ]]> https://biorxiv.org/content/10.1101/2023.01.10.523416v1?rss=1 Goudar, V. Kim, J.-W. Liu, Y. Dede, A. J. O. Jutras, M. J. Skelin, I. Ruvalcaba, M. Chang, W. Fairhall, A. L. Lin, J. J. Knight, R. T. Buffalo, E. A. Wang, X.-J. 2023-01-10 doi:10.1101/2023.01.10.523416 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Photosynthetic and water transport strategies of plants along a tropical forest aridity gradient: a test of optimality theory ]]> https://biorxiv.org/content/10.1101/2023.01.10.523419v1?rss=1 Zhang-Zheng, H. Malhi, Y. Gvozdevaite, A. Peprah, T. Boackye, M. Zieminska, K. Adu-Bredu, S. Aguirre-Gutierrez, J. Sandoval, D. Prentice, C. Oliveras, I. 2023-01-11 doi:10.1101/2023.01.10.523419 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ Let there be nightlights: the ecological role of bioluminescence in a Costa Rican mushroom ]]> https://biorxiv.org/content/10.1101/2023.01.10.523474v1?rss=1 Adams, C. A. Donald, M. L. Swearingen, C. Escudero, E. Sourell, S. Landrein, S. Seas, C. Mueller, G. Chaverri, P. 2023-01-11 doi:10.1101/2023.01.10.523474 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ Two RNA-binding proteins mediate the sorting of miR223 from mitochondria into exosomes ]]> https://biorxiv.org/content/10.1101/2023.01.11.523558v1?rss=1 Ma, L. Singh, J. Schekman, R. 2023-01-11 doi:10.1101/2023.01.11.523558 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ Pressure and ultrasound activate mechanosensitive TRAAK K+ channels through increased membrane tension ]]> https://biorxiv.org/content/10.1101/2023.01.11.523644v1?rss=1 Sorum, B. Docter, T. Panico, V. Rietmeijer, R. A. Brohawn, S. G. 2023-01-12 doi:10.1101/2023.01.11.523644 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ Selection of optimal cell lines for high-content phenotypic screening ]]> https://biorxiv.org/content/10.1101/2023.01.11.523662v1?rss=1 Heinrich, L. Kumbier, K. Li, L. Altschuler, S. Wu, L. 2023-01-12 doi:10.1101/2023.01.11.523662 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ Phenotypic and genotypic adaptation of E. coli to thermal stress is contingent on genetic background ]]> https://biorxiv.org/content/10.1101/2023.01.11.523675v1?rss=1 Batarseh, T. N. Batarseh, S. N. Rodriguez-Verdugo, A. N. Gaut, B. S. 2023-01-13 doi:10.1101/2023.01.11.523675 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ High intraspecies allelic diversity in Arabidopsis NLR immune receptors is associated with higher transcription, gene body hypomethylation, and proximity to transposable elements ]]> https://biorxiv.org/content/10.1101/2023.01.12.523861v1?rss=1 Sutherland, C. A. Prigozhin, D. M. Monroe, J. G. Krasileva, K. V. 2023-01-13 doi:10.1101/2023.01.12.523861 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Draft Genome Sequence of Pedococcus sp. Strain 5OH_020 Isolated from California Grassland Soil ]]> https://biorxiv.org/content/10.1101/2023.01.13.523987v1?rss=1 Green, M. A. Alvarez-Aponte, Z. I. Trotter, V. V. Taga, M. E. 2023-01-13 doi:10.1101/2023.01.13.523987 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Mechanistic insights into robust cardiac IKs potassium channel activation by aromatic polyunsaturated fatty acid analogues ]]> https://biorxiv.org/content/10.1101/2023.01.12.523777v1?rss=1 Bohannon, B. M. Jowais, J. J. Nyberg, L. Liin, S. I. Larsson, H. P. 2023-01-16 doi:10.1101/2023.01.12.523777 Cold Spring Harbor Laboratory Press 2023-01-16 <![CDATA[ Ribosome rescue factor PELOTA modulates translation start site choice and protein isoform levels of transcription factor C/EBPα ]]> https://biorxiv.org/content/10.1101/2023.01.16.524343v1?rss=1 Fernandez, S. G. Ferguson, L. Ingolia, N. T. 2023-01-17 doi:10.1101/2023.01.16.524343 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ Cultivation of Ulva sp. offshore the Eastern Mediterranean Sea in experimental bioreactors: seasonal growth dynamics and environmental effects ]]> https://biorxiv.org/content/10.1101/2023.01.15.524102v1?rss=1 Zollmann, M. Liberzon, A. Palatnik, R. R. Zilberman, D. Golberg, A. 2023-01-18 doi:10.1101/2023.01.15.524102 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Adaptive optical two-photon fluorescence microscopy probes cellular organization of ocular lenses in vivo ]]> https://biorxiv.org/content/10.1101/2023.01.17.524320v1?rss=1 Paidi, S. K. Zhang, Q. Yang, Y. Xia, C.-h. Ji, N. Gong, X. 2023-01-19 doi:10.1101/2023.01.17.524320 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi ]]> https://biorxiv.org/content/10.1101/2023.01.17.524442v1?rss=1 Balamurugan, C. Steenwyk, J. L. Goldman, G. H. Rokas, A. 2023-01-20 doi:10.1101/2023.01.17.524442 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Identifying Neural Signatures of Dopamine Signaling with Machine Learning ]]> https://biorxiv.org/content/10.1101/2023.01.17.524454v1?rss=1 Sorooshyari, S. Ouassil, N. Yang, S. J. Landry, M. P. 2023-01-20 doi:10.1101/2023.01.17.524454 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Predictors of sensorimotor adaption: insights from over 100,000 reaches ]]> https://biorxiv.org/content/10.1101/2023.01.18.524634v1?rss=1 Tsay, J. Asmerian, H. Germine, L. Wilmer, J. Ivry, R. B. Nakayama, K. 2023-01-20 doi:10.1101/2023.01.18.524634 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Sex chromosome evolution in beetles ]]> https://biorxiv.org/content/10.1101/2023.01.18.524646v1?rss=1 Bracewell, R. Tran, A. Chatla, K. Bachtrog, D. 2023-01-20 doi:10.1101/2023.01.18.524646 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Implicit motor adaptation and perceived hand position without proprioception: A kinesthetic error may be derived from efferent signals ]]> https://biorxiv.org/content/10.1101/2023.01.19.524726v1?rss=1 Tsay, J. S. Chandy, A. M. Chua, R. Miall, R. C. Cole, J. Farne, A. Ivry, R. B. Sarlegna, F. R. 2023-01-20 doi:10.1101/2023.01.19.524726 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Interactions between terminal RNA helices affect the stability of the Escherichia coli large ribosomal subunit ]]> https://biorxiv.org/content/10.1101/2023.01.19.524821v1?rss=1 Nissley, A. J. Kamal, T. S. Cate, J. H. 2023-01-20 doi:10.1101/2023.01.19.524821 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Rapid turnover and evolution of sex-determining regions among Sebastes rockfishes ]]> https://biorxiv.org/content/10.1101/2023.01.19.524770v1?rss=1 Sykes, N. T. B. Kolora, S. R. R. Sudmant, P. H. Owens, G. L. 2023-01-21 doi:10.1101/2023.01.19.524770 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ Fine scale sampling reveals spatial heterogeneity of rhizosphere microbiome in young Brachypodium plants ]]> https://biorxiv.org/content/10.1101/2023.01.20.524947v1?rss=1 Acharya, S. M. Yee, M. O. Diamond, S. Andeer, P. F. Baig, N. F. Aladesanmi, O. T. Northen, T. R. Banfield, J. F. Chakraborty, R. 2023-01-21 doi:10.1101/2023.01.20.524947 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ Genome expansion by a CRISPR trimmer-integrase ]]> https://biorxiv.org/content/10.1101/2023.01.23.522648v1?rss=1 Wang, J. Y. Tuck, O. T. Skopintsev, P. Soczek, K. M. Li, G. Al-Shayeb, B. Zhou, J. Doudna, J. A. 2023-01-24 doi:10.1101/2023.01.23.522648 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ Leveraging genomic redundancy to improve inference and alignment of orthologous proteins ]]> https://biorxiv.org/content/10.1101/2023.01.24.525427v1?rss=1 Singleton, M. Eisen, M. 2023-01-25 doi:10.1101/2023.01.24.525427 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Selective recruitment: Evidence for task-dependent gating of inputs to the cerebellum ]]> https://biorxiv.org/content/10.1101/2023.01.25.525395v1?rss=1 Shahshahani, L. King, M. Nettekoven, C. Ivry, R. Diedrichsen, J. 2023-01-26 doi:10.1101/2023.01.25.525395 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ Aminobenzoic acid derivatives obstruct induced fit in the catalytic center of the ribosome ]]> https://biorxiv.org/content/10.1101/2023.01.25.525534v1?rss=1 Majumdar, C. Walker, J. A. Francis, M. B. Schepartz, A. Cate, J. H. D. 2023-01-26 doi:10.1101/2023.01.25.525534 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ Single-molecule displacement mapping indicates unhindered intracellular diffusion of small (<~1 kDa) solutes ]]> https://biorxiv.org/content/10.1101/2023.01.26.525579v1?rss=1 300 m2/s. We thus show that for multiple water-soluble dyes and dye-tagged nucleotides, intracellular diffusion is dominated by vast regions of high diffusivity ~60-70% of that in vitro, up to ~250 m2/s in the fastest cases. Meanwhile, we also visualize sub-micrometer foci of substantial slowdowns in diffusion, thus underscoring the importance of spatially resolving the local diffusion behavior. Together, these results suggest that the intracellular diffusion of small solutes is only modestly scaled down by the slightly higher viscosity of the cytosol over water, but otherwise not further hindered by macromolecular crowding. We thus lift a paradoxically low speed limit for intracellular diffusion suggested by previous experiments. Abstract Graphic O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY ]]> Choi, A. A. Xiang, L. Li, W. Xu, K. 2023-01-26 doi:10.1101/2023.01.26.525579 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ Single-molecule displacement mapping unveils sign-asymmetric protein charge effects on intraorganellar diffusion ]]> https://biorxiv.org/content/10.1101/2023.01.26.525611v1?rss=1 Xiang, L. Yan, R. Chen, K. Li, W. Xu, K. 2023-01-26 doi:10.1101/2023.01.26.525611 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ Multimodal models of animal sex: breaking binaries leads to a better understanding of ecology and evolution ]]> https://biorxiv.org/content/10.1101/2023.01.26.525769v1?rss=1 McLaughlin, J. F. Brock, K. M. Gates, I. Pethkar, A. Piattoni, M. Rossi, A. Lipshutz, S. 2023-01-27 doi:10.1101/2023.01.26.525769 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Vitamin interdependencies predicted by metagenomics-informed network analyses validated in microbial community microcosms ]]> https://biorxiv.org/content/10.1101/2023.01.27.524772v1?rss=1 Hessler, T. Huddy, R. J. Sachdeva, R. Lei, S. Harrison, S. T. L. Diamond, S. Banfield, J. F. 2023-01-28 doi:10.1101/2023.01.27.524772 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ Structure and dynamics of the essential endogenous mycobacterial polyketide synthasePks13 ]]> https://biorxiv.org/content/10.1101/2023.01.27.525930v1?rss=1 Kim, S. K. Dickinson, M. S. Finer-Moore, J. S. Guan, Z. Kaake, R. M. Echeverria, I. Chen, J. Pulido, E. H. Sali, A. Krogan, N. J. Rosenberg, O. S. Stroud, R. M. 2023-01-28 doi:10.1101/2023.01.27.525930 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ Structural characterization of HIV-1 Env heterotrimers bound to one or two CD4 receptors reveals intermediate Env conformations ]]> https://biorxiv.org/content/10.1101/2023.01.27.525985v1?rss=1 Dam, K.-M. A. Fan, C. Yang, Z. Bjorkman, P. J. 2023-01-28 doi:10.1101/2023.01.27.525985 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ Perturbation Variability Does Not Influence Implicit Sensorimotor Adaptation ]]> https://biorxiv.org/content/10.1101/2023.01.27.525949v1?rss=1 Wang, T. Avraham, G. Tsay, J. S. Abram, S. J. Ivry, R. B. 2023-01-29 doi:10.1101/2023.01.27.525949 Cold Spring Harbor Laboratory Press 2023-01-29 <![CDATA[ The viral packaging motor potentiates late gene expression in Kaposi's sarcoma-associated herpesvirus ]]> https://biorxiv.org/content/10.1101/2023.01.29.526158v1?rss=1 McCollum, C. O. Didychuk, A. L. Liu, D. Murray-Nerger, L. A. Christea, I. M. Glaunsinger, B. A. 2023-01-31 doi:10.1101/2023.01.29.526158 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ A modular plasmid toolkit applied in marine Proteobacteria reveals functional insights during bacteria-stimulated metamorphosis ]]> https://biorxiv.org/content/10.1101/2023.01.31.526474v1?rss=1 Alker, A. T. Aspiras, A. E. Dunbar, T. L. Farrell, M. V. Fedoriouk, A. Jones, J. E. Mikhail, S. R. Salcedo, G. Y. Moore, B. S. Shikuma, N. J. 2023-01-31 doi:10.1101/2023.01.31.526474 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Isolating objective and subjective filling-in using the Drift Diffusion Model ]]> https://biorxiv.org/content/10.1101/2023.02.01.526391v1?rss=1 Dekel, R. Sagi, D. Zomet, A. Levi, D. M. Polat, U. 2023-02-03 doi:10.1101/2023.02.01.526391 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Large-scale brain-wide neural recording in nonhuman primates ]]> https://biorxiv.org/content/10.1101/2023.02.01.526664v1?rss=1 Trautmann, E. M. Hesse, J. K. Stine, G. Xia, R. Shude Zhu, S. O'Shea, D. J. Karsh, B. Colonell, J. Lanfranchi, F. Vyas, S. Zimnik, A. Steinemann, N. A. Wagenaar, D. A. Andrei, A. Mora Lopez, C. OCallaghan, J. M. Putzeys, J. Raducanu, B. C. Welkenhuysen, M. Churchland, M. Moore, T. Shadlen, M. N. Shenoy, K. V. Tsao, D. Dutta, B. Harris, T. 2023-02-03 doi:10.1101/2023.02.01.526664 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Adipocyte lipin 1 is positively associated with metabolic health in humans and regulates systemic metabolism in mice. ]]> https://biorxiv.org/content/10.1101/2023.02.01.526676v1?rss=1 LaPoint, A. Singer, J. M. Ferguson, D. Shew, T. M. RenKemeyer, K. Palacios, H. Field, R. Shankaran, M. Smith, G. I. Yoshino, J. He, M. Patti, G. J. Hellerstein, M. Klein, S. Brestoff, J. R. Finck, B. Lutkewitte, A. J. 2023-02-03 doi:10.1101/2023.02.01.526676 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ McrD binds asymmetrically to methyl-coenzyme M reductase improving active site accessibility during assembly ]]> https://biorxiv.org/content/10.1101/2023.02.01.526716v1?rss=1 Chadwick, G. L. Joiner, A. M. Ramesh, S. Mitchell, D. A. Nayak, D. D. 2023-02-03 doi:10.1101/2023.02.01.526716 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Streamlined and sensitive mono- and diribosome profiling in yeast and human cells ]]> https://biorxiv.org/content/10.1101/2023.02.01.526718v1?rss=1 Ferguson, L. Upton, H. E. Pimentel, S. C. Mok, A. Lareau, L. F. Collins, K. Ingolia, N. T. 2023-02-03 doi:10.1101/2023.02.01.526718 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Force transmission and SUN-KASH higher-order assembly in the LINC complex models ]]> https://biorxiv.org/content/10.1101/2023.02.02.526920v1?rss=1 Yerima, G. Domkam, N. Ornowski, J. Jahed, Z. Mofrad, M. R. K. 2023-02-03 doi:10.1101/2023.02.02.526920 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ The gag-like gene RTL8 antagonizes PEG10-mediated virus like particles in humans ]]> https://biorxiv.org/content/10.1101/2023.02.03.527044v1?rss=1 Campodonico, W. Black, H. Lau, C. Whiteley, A. M. 2023-02-04 doi:10.1101/2023.02.03.527044 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Sulcal morphology of posteromedial cortex substantially differs between humans and chimpanzees ]]> https://biorxiv.org/content/10.1101/2023.02.06.527223v1?rss=1 Willbrand, E. H. Maboudian, S. A. Kelly, J. P. Parker, B. J. Foster, B. L. Weiner, K. S. 2023-02-06 doi:10.1101/2023.02.06.527223 Cold Spring Harbor Laboratory Press 2023-02-06 <![CDATA[ Colocalization of Cancer Associated Biomarkers on Single Extracellular Vesicles for Early Cancer Detection ]]> https://biorxiv.org/content/10.1101/2023.02.07.527360v1?rss=1 Salem, D. P. Bortolin, L. T. Couvillon, A. D. Gusenleitner, D. Grosha, J. Zabrowski, I. O. Biette, K. M. Banerjee, S. Sedlak, C. R. Byrne, D. M. Hamzeh, B. F. King, M. S. Cuoco, L. T. Duff, P. A. Winn-Deen, E. S. Huang, E. K. Schekman, R. Sedlak, J. C. 2023-02-08 doi:10.1101/2023.02.07.527360 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6 ]]> https://biorxiv.org/content/10.1101/2023.01.31.525914v1?rss=1 80% efficiency. Fully sequenced replicons and infectious viral stocks can be generated in 1 and 3 weeks, respectively. By testing a series of naturally occurring viruses as well as Delta-Omicron chimeric replicons, we show that Omicron nonstructural protein 6 harbors critical attenuating mutations, which dampen viral RNA replication and reduce lipid droplet consumption. Thus, pGLUE overcomes remaining barriers to broadly study SARS-CoV-2 replication and reveals deficits in nonstructural protein function underlying Omicron attenuation. ]]> Taha, T. Y. Chen, I. P. Hayashi, J. M. Tabata, T. Walcott, K. Kimmerly, G. R. Syed, A. M. Ciling, A. Suryawanshi, R. K. Martin, H. S. Bach, B. H. Tsou, C.-L. Montano, M. Khalid, M. M. Sreekumar, B. K. Kumar, G. R. Wyman, S. Doudna, J. A. Ott, M. 2023-02-09 doi:10.1101/2023.01.31.525914 Cold Spring Harbor Laboratory Press 2023-02-09 <![CDATA[ Pumping Iron: A Multi-omics Analysis of Two Extremophilic Algae Reveals Mechanisms of Iron Economy ]]> https://biorxiv.org/content/10.1101/2023.02.09.527888v1?rss=1 Davidi, L. Gallaher, S. D. Ben-David, E. Purvine, S. O. Fillmore, T. L. Nicora, C. D. Craig, R. J. Schmollinger, S. Roje, S. Blaby-Haas, C. E. Auber, R. P. Wisecaver, J. Merchant, S. S. 2023-02-09 doi:10.1101/2023.02.09.527888 Cold Spring Harbor Laboratory Press 2023-02-09 <![CDATA[ A highly efficient human cell-free translation system ]]> https://biorxiv.org/content/10.1101/2023.02.09.527910v1?rss=1 Aleksashin, N. A. Chang, S. T.-L. Cate, J. H. 2023-02-10 doi:10.1101/2023.02.09.527910 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Unified bursting strategies in ectopic and endogenous even-skipped expression patterns ]]> https://biorxiv.org/content/10.1101/2023.02.09.527927v1?rss=1 Berrocal, A. Lammers, N. C. Garcia, H. G. Eisen, M. B. 2023-02-10 doi:10.1101/2023.02.09.527927 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ The balance of acidic and hydrophobic residues predicts acidic transcriptional activation domains from protein sequence ]]> https://biorxiv.org/content/10.1101/2023.02.10.528081v1?rss=1 Kotha, S. R. Staller, M. V. 2023-02-11 doi:10.1101/2023.02.10.528081 Cold Spring Harbor Laboratory Press 2023-02-11 <![CDATA[ Transcriptomic profiles of stress susceptibility and resilience in the amygdala and hippocampus ]]> https://biorxiv.org/content/10.1101/2023.02.08.527777v1?rss=1 Long, K. L. P. Muroy, S. E. Sorooshyari, S. Ko, M. J. Jaques, Y. Sudmant, P. H. Kaufer, D. 2023-02-12 doi:10.1101/2023.02.08.527777 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ Cognitive relevance of an evolutionarily new and variable prefrontal structure ]]> https://biorxiv.org/content/10.1101/2023.02.10.528061v1?rss=1 Willbrand, E. H. Jackson, S. Chen, S. Hathaway, C. B. Voorhies, W. I. Bunge, S. A. Weiner, K. S. 2023-02-12 doi:10.1101/2023.02.10.528061 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.02.11.528119v1?rss=1 Eichler, K. Hampel, S. Alejandro, A. Calle, S. Santana, A. Kmecova, L. Blagburn, J. M. Hoopfer, E. D. Seeds, A. M. 2023-02-12 doi:10.1101/2023.02.11.528119 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ Chemoproteomic Profiling Reveals that Anti-Cancer Natural Product Dankastatin B Covalently Targets Mitochondrial VDAC3 ]]> https://biorxiv.org/content/10.1101/2023.02.11.528139v1?rss=1 Belcher, B. P. Machicao, P. A. Tong, B. Ho, E. Friedli, J. So, B. Bui, H. Isobe, Y. Maimone, T. J. Nomura, D. K. 2023-02-12 doi:10.1101/2023.02.11.528139 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ Overcoming resolution loss due to thermal magnetic field fluctuations from phase plates in transmission electron microscopy ]]> https://biorxiv.org/content/10.1101/2023.02.12.528160v1?rss=1 Axelrod, J. J. Petrov, P. N. Zhang, J. T. Remis, J. Buijsse, B. Glaeser, R. Mueller, H. 2023-02-13 doi:10.1101/2023.02.12.528160 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ Intracellular replication of Pseudomonas aeruginosa in epithelial cells requires suppression of the caspase-4 inflammasome ]]> https://biorxiv.org/content/10.1101/2023.02.13.528260v1?rss=1 Kroken, A. R. Klein, K. A. Mitchell, P. S. Nieto, V. Jedel, E. J. Evans, D. J. Fleiszig, S. M. J. 2023-02-13 doi:10.1101/2023.02.13.528260 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ Self-organizing actin networks drive sequential endocytic protein recruitment and vesicle release on synthetic lipid bilayers ]]> https://biorxiv.org/content/10.1101/2023.02.14.528546v1?rss=1 Stoops, E. H. Ferrin, M. A. Jorgens, D. M. Drubin, D. G. 2023-02-14 doi:10.1101/2023.02.14.528546 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ Spatiotemporal dynamics of sensory neuron and Merkel-cell remodeling are decoupled during epidermal homeostasis ]]> https://biorxiv.org/content/10.1101/2023.02.14.528558v1?rss=1 Clary, R. C. Jenkins, B. A. Lumpkin, E. A. 2023-02-14 doi:10.1101/2023.02.14.528558 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ Flow augmentation from off-channel storage improves salmonid habitat and survival ]]> https://biorxiv.org/content/10.1101/2023.02.15.528508v1?rss=1 1.5 km downstream from the point of augmentation and had a marginal warming effect on stream temperature. During the wet year, both dissolved oxygen and water temperature effects were negligible. In both years, augmentation had a small but positive effect on invertebrate drift. Inter-pool movement of juvenile steelhead (Oncorhynchus mykiss) and stocked Coho Salmon (O. kisutch) increased due to augmentation during the dry summer. Flow augmentation also increased the survival probability for salmonids, with a larger effect during the dry summer (24% higher survival for Coho and 20% higher for steelhead), than during the wet summer (when no effect was observed for steelhead survival and Coho Salmon survival increased by 11%). This study indicates that appropriately designed and timed flow augmentations can improve conditions for rearing salmonids in small streams, particularly during dry years. More broadly it provides empirical evidence that efforts to restore summer streamflow in small, salmon-bearing streams can yield significant ecological benefits. ]]> Rossi, G. Obedzinski, M. Pneh, S. Pierce, S. N. Boucher, W. Flynn, K. Slaughter, W. Grantham, T. 2023-02-15 doi:10.1101/2023.02.15.528508 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ An integrated transcriptomics-functional genomics approach reveals a small RNA that modulates Bacteroides thetaiotaomicron sensitivity to tetracyclines ]]> https://biorxiv.org/content/10.1101/2023.02.16.528795v1?rss=1 Ryan, D. Bornet, E. Prezza, G. Alampalli, S. V. de Carvalho, T. F. Felchle, H. Ebbecke, T. Hayward, R. Deutschbauer, A. Barquist, L. Westermann, A. J. 2023-02-16 doi:10.1101/2023.02.16.528795 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Evolution of the ribbon-like organization of the Golgi apparatus in animal cells ]]> https://biorxiv.org/content/10.1101/2023.02.16.528797v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@17a404forg.highwire.dtl.DTLVardef@11413b4org.highwire.dtl.DTLVardef@119c036org.highwire.dtl.DTLVardef@19a512f_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG ]]> Benvenuto, G. Leone, S. Astoricchio, E. Bormke, S. Jasek, S. D'Aniello, E. Kittelmann, M. McDonald, K. Hartenstein, V. Baena, V. Escriva, H. Bertrand, S. Schierwater, B. Burkhardt, P. Ruiz-Trillo, I. Jekely, G. Ullrich-Luter, J. Luter, C. D'Aniello, S. Arnone, M. I. Ferraro, F. 2023-02-16 doi:10.1101/2023.02.16.528797 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Distinct genomic contexts predict gene presence-absence variation in different pathotypes of a fungal plant pathogen ]]> https://biorxiv.org/content/10.1101/2023.02.17.529015v1?rss=1 Joubert, P. M. Krasileva, K. V. 2023-02-17 doi:10.1101/2023.02.17.529015 Cold Spring Harbor Laboratory Press 2023-02-17 <![CDATA[ Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics ]]> https://biorxiv.org/content/10.1101/2023.02.17.528811v1?rss=1 Marinos, G. Hamerich, I. K. Debray, R. Obeng, N. Petersen, C. Taubenheim, J. Zimmermann, J. Blackburn, D. Samuel, B. S. Dierking, K. Franke, A. Laudes, M. Waschina, S. Schulenburg, H. Kaleta, C. 2023-02-18 doi:10.1101/2023.02.17.528811 Cold Spring Harbor Laboratory Press 2023-02-18 <![CDATA[ Domestic dogs maintain positive clinical, nutritional, and hematological health outcomes when fed a commercial plant-based diet for a year ]]> https://biorxiv.org/content/10.1101/2023.02.18.525405v1?rss=1 Linde, A. Lahiff, M. Krantz, A. Sharp, N. Ng, T. T. Melgarejo, T. 2023-02-21 doi:10.1101/2023.02.18.525405 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ DeepHeme: A generalizable, bone marrow classifierwith hematopathologist-level performance ]]> https://biorxiv.org/content/10.1101/2023.02.20.528987v1?rss=1 Goldgof, G. Sun, S. Cleaves, J. Wang, L. Lucas, F. Brown, L. Spectors, J. Boiocchi, L. Baik, J. Zhu, M. Ardon, O. Lu, C. Dogan, A. Goldgof, D. Carmichael, I. Prakash, S. Butte, A. 2023-02-21 doi:10.1101/2023.02.20.528987 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Tracing cancer evolution and heterogeneity using Hi-C ]]> https://biorxiv.org/content/10.1101/2023.02.20.529175v1?rss=1 Erdmann-Pham, D. D. Batra, S. S. Turkalo, T. K. Durbin, J. Blanchette, M. Yeh, I. Shain, H. Bastian, B. Song, Y. S. Rokhsar, D. S. Hockemeyer, D. 2023-02-21 doi:10.1101/2023.02.20.529175 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Ubiquinone deficiency drives reverse electron transport to disrupt hepatic metabolic homeostasis in obesity ]]> https://biorxiv.org/content/10.1101/2023.02.21.528863v1?rss=1 Goncalves, R. L. S. Wang, Z. B. Inouye, K. E. Lee, Y. G. Fu, X. Saksi, J. Rosique, C. Parlakgul, G. Arruda, A. P. Hui, T. S. Loperena, M. C. Burgess, S. C. Graupera, I. Hotamisligil, G. S. 2023-02-22 doi:10.1101/2023.02.21.528863 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ choros: correction of sequence-based biases for accurate quantification of ribosome profiling data ]]> https://biorxiv.org/content/10.1101/2023.02.21.529452v1?rss=1 Mok, A. Tunney, R. Benegas, G. Wallace, E. W. J. Lareau, L. F. 2023-02-22 doi:10.1101/2023.02.21.529452 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Multi-omic screening of invasive GBM cells in engineered biomaterials and patient biopsies reveals targetable transsulfuration pathway alterations ]]> https://biorxiv.org/content/10.1101/2023.02.23.529575v1?rss=1 Garcia, J. H. Akins, E. A. Jain, S. Wolf, K. J. Zhang, J. Choudhary, N. Lad, M. Shukla, P. Gill, S. Carson, W. Carette, L. Zheng, A. Kumar, S. Aghi, M. K. 2023-02-24 doi:10.1101/2023.02.23.529575 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Intraluminal neutrophils limit epithelium damage by reducing pathogen assault on intestinal epithelial cells during Salmonella gut infection ]]> https://biorxiv.org/content/10.1101/2023.02.23.529832v1?rss=1 Gül, E. Fattinger, S. A. Nguyen, B. D. Hausmann, A. Furter, M. Barthel, M. Sellin, M. E. Hardt, W.-D. 2023-02-24 doi:10.1101/2023.02.23.529832 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Coordinated growth of linked epithelia is mediated by the Hippo pathway ]]> https://biorxiv.org/content/10.1101/2023.02.26.530099v1?rss=1 Friesen, S. Hariharan, I. 2023-02-26 doi:10.1101/2023.02.26.530099 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ Pretraining strategies for effective promoter-driven gene expression prediction ]]> https://biorxiv.org/content/10.1101/2023.02.24.529941v1?rss=1 Reddy, A. J. Herschl, M. H. Kolli, S. Lu, A. X. Geng, X. Kumar, A. Hsu, P. D. Levine, S. Ioannidis, N. M. 2023-02-27 doi:10.1101/2023.02.24.529941 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Tipping points emerge from weak mutualism inmetacommunities ]]> https://biorxiv.org/content/10.1101/2023.02.26.530120v1?rss=1 Denk, J. Hallatschek, O. 2023-02-27 doi:10.1101/2023.02.26.530120 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life ]]> https://biorxiv.org/content/10.1101/2023.02.27.530264v1?rss=1 Meyer, M. O. Yamagami, R. Choi, S. Keating, C. D. Bevilacqua, P. C. 2023-02-27 doi:10.1101/2023.02.27.530264 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Bacteriophage-mediated lysis supports robust growth of amino acid auxotrophs ]]> https://biorxiv.org/content/10.1101/2023.02.28.530524v1?rss=1 Pherribo, G. J. Taga, M. E. 2023-03-01 doi:10.1101/2023.02.28.530524 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ A Vibrio cholerae viral satellite maximizes its spread and inhibits phage by remodeling hijacked phage coat proteins into small capsids ]]> https://biorxiv.org/content/10.1101/2023.03.01.530633v1?rss=1 Boyd, C. M. Subramanian, S. Dunham, D. T. Parent, K. N. Seed, K. D. 2023-03-01 doi:10.1101/2023.03.01.530633 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Commensal Bacteria Maintain a Qa-1b-restricted Unconventional CD8+ T Population in Gut Epithelium ]]> https://biorxiv.org/content/10.1101/2023.03.01.530600v1?rss=1 Guan, J. Manoharan Valerio, M. Peske, J. D. Park, C. Robey, E. A. Sadegh-Nasseri, S. Shastri, N. 2023-03-02 doi:10.1101/2023.03.01.530600 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Detrimental Impact of a Type VI Secretion System on Direct Interspecies Electron Transfer ]]> https://biorxiv.org/content/10.1101/2023.03.02.530876v1?rss=1 Smith, J. A. Holmes, D. E. Woodard, T. L. Li, Y. Liu, X. Wang, L.-Y. Meier, D. Schwarz, I. A. Lovley, D. R. 2023-03-02 doi:10.1101/2023.03.02.530876 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Adaptive dynamics of memory-1 strategies in the repeated donation game ]]> https://biorxiv.org/content/10.1101/2023.03.02.530745v1?rss=1 LaPorte, P. Hilbe, C. Nowak, M. 2023-03-03 doi:10.1101/2023.03.02.530745 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Probing inter-areal computations with a cellular resolution two-photon holographic mesoscope ]]> https://biorxiv.org/content/10.1101/2023.03.02.530875v1?rss=1 Abdeladim, L. Shin, H. Jagadisan, U. Ogando, M. Adesnik, H. 2023-03-03 doi:10.1101/2023.03.02.530875 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Widespread CRISPR repeat-like RNA regulatory elements in CRISPR-Cas systems ]]> https://biorxiv.org/content/10.1101/2023.03.03.530964v1?rss=1 Shmakov, S. A. Barth, Z. Makarova, K. S. Wolf, Y. I. Brover, V. Peters, J. E. Koonin, E. V. 2023-03-03 doi:10.1101/2023.03.03.530964 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Cryopreservation and revival of Hawaiian stony corals via isochoric vitrification ]]> https://biorxiv.org/content/10.1101/2023.03.05.531199v1?rss=1 Powell-Palm, M. J. Henley, E. M. Consiglio, A. N. Lager, C. Chang, B. Perry, R. Fitzgerald, K. Daly, J. Rubinsky, B. Hagedorn, M. 2023-03-06 doi:10.1101/2023.03.05.531199 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Mechanical transmission of Dengue Virus by Aedes aegypti may influence disease transmission dynamics during outbreaks ]]> https://biorxiv.org/content/10.1101/2023.03.07.531453v1?rss=1 Li, H.-H. Su, M. P. Wu, S.-C. Tsou, H.-H. Chang, M.-C. Cheng, Y.-C. Tsai, K.-N. Wang, H.-W. Chen, G.-H. Tang, C.-K. Chung, P.-J. Tsai, W.-T. Huang, L.-R. Yueh, Y. A. Chen, H.-W. Pan, C.-Y. Akbari, O. Chang, H.-H. Yu, G.-Y. Marshall, J. M. CHEN, C.-H. 2023-03-07 doi:10.1101/2023.03.07.531453 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Sex chromosome - autosome fusions in Heliconius butterflies ]]> https://biorxiv.org/content/10.1101/2023.03.06.531374v1?rss=1 Rueda-M, N. Jiggins, C. D. Pardo-Diaz, C. McMillan, W. O. McCarthy, S. Kozak, K. M. Arias, C. F. Ready, J. Durbin, R. Montejo-Kovacevich, G. Meier, J. Salazar, C. 2023-03-08 doi:10.1101/2023.03.06.531374 Cold Spring Harbor Laboratory Press 2023-03-08 <![CDATA[ Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection through aging ]]> https://biorxiv.org/content/10.1101/2023.03.06.531392v1?rss=1 T/C>A mutations, and that somatic mutations in protein coding genes exhibit signatures of negative selection. Lastly, we identify an extensive enrichment in somatic reversion mutations that "re-align" mito-nuclear ancestry within an organisms lifespan. Together, our findings demonstrate that mitochondrial genomes are a dynamically evolving subcellular population shaped by somatic mutation and selection throughout organismal lifetimes. ]]> Serrano, I. Hirose, M. H. Valentine, C. Austin, S. Schmidt, E. Pratt, G. Williams, L. Salk, J. Ibrahim, S. Sudmant, P. H. 2023-03-08 doi:10.1101/2023.03.06.531392 Cold Spring Harbor Laboratory Press 2023-03-08 <![CDATA[ Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes ]]> https://biorxiv.org/content/10.1101/2023.03.07.531504v1?rss=1 Eme, L. Tamarit, D. Caceres, E. F. Stairs, C. de Anda, V. Schon, M.-E. Seitz, K. Dombrowski, N. Lewis, W. H. Saw, J. H. Homa, F. Lombard, J. Nunoura, T. Li, W.-J. Hua, Z.-S. Chen, L.-X. Banfield, J. St. John, E. Reysenbach, A.-L. Stott, M. B. Schramm, A. Kjeldsen, K. U. Teske, A. P. Baker, B. J. Ettema, T. J. G. 2023-03-09 doi:10.1101/2023.03.07.531504 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Ophiobolin A Covalently Targets Complex IV Leading to Mitochondrial Metabolic Collapse in Cancer Cells ]]> https://biorxiv.org/content/10.1101/2023.03.09.531918v1?rss=1 Gowans, F. A. Thach, D. Q. Wang, Y. Poblano, B. E. A. Dovala, D. Tallarico, J. A. McKenna, J. M. Schirle, M. Maimone, T. J. Nomura, D. K. 2023-03-09 doi:10.1101/2023.03.09.531918 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells ]]> https://biorxiv.org/content/10.1101/2023.03.09.531939v1?rss=1 Lee, S.-Y. Cheah, J. S. Zhao, B. Xu, C. Roh, H. Kim, C. K. Cho, K. F. Udeshi, N. Carr, S. A. Ting, A. Y. 2023-03-09 doi:10.1101/2023.03.09.531939 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Ultrapotent SARS coronavirus-neutralizing single-domain antibodies that bind a conserved membrane proximal epitope of the spike ]]> https://biorxiv.org/content/10.1101/2023.03.10.531533v1?rss=1 De Cae, S. Van Molle, I. van Schie, L. Shoemaker, S. R. Deckers, J. Debeuf, N. Lameire, S. Nerinckx, W. Roose, K. Fijalkowska, D. Devos, S. Desmet, A.-S. Zavala Marchan, J. C. Venneman, T. Ghassabeh, G. H. Sedeyn, K. Ballegeer, M. Vanheerswynghels, M. De Wolf, C. Demol, H. Vanhaverbeke, P. Lonigro, C. Bockstal, V. Rinaldi, M. Abdelnabi, R. Neyts, J. Marqusee, S. Lambrecht, B. N. Callewaert, N. Remaut, H. Saelens, X. Schepens, B. 2023-03-10 doi:10.1101/2023.03.10.531533 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Enzymatic Hydroxylation of Aliphatic C-H Bonds by a Mn/Fe Cofactor ]]> https://biorxiv.org/content/10.1101/2023.03.10.532131v1?rss=1 Powell, M. M. Rao, G. Britt, R. D. Rittle, J. 2023-03-11 doi:10.1101/2023.03.10.532131 Cold Spring Harbor Laboratory Press 2023-03-11 <![CDATA[ Genomic analysis of cultivated infant microbiomes identifies Bifidobacterium 2'-fucosyllactose utilization can be facilitated by co-existing species ]]> https://biorxiv.org/content/10.1101/2023.03.10.532136v1?rss=1 Lou, Y. C. Rubin, B. E. Schoelmerich, M. C. DiMarco, K. Borges, A. L. Rovinsky, R. Song, L. Doudna, J. A. Banfield, J. F. 2023-03-11 doi:10.1101/2023.03.10.532136 Cold Spring Harbor Laboratory Press 2023-03-11 <![CDATA[ Unsupervised pattern discovery in spatial gene expression atlas reveals mouse brain regions beyond established ontology ]]> https://biorxiv.org/content/10.1101/2023.03.10.531984v1?rss=1 Cahill, R. Wang, Y. Lee, A. Zeng, H. Yu, B. Tasic, B. Abbasi-Asl, R. 2023-03-12 doi:10.1101/2023.03.10.531984 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Antigen receptor signaling and cell death resistance controls intestinal humoral response zonation. ]]> https://biorxiv.org/content/10.1101/2023.03.16.532481v1?rss=1 Raso, F. Liu, S. Willett, M. J. Barton, G. Mayer, C. T. Bannard, O. Acharya, M. Muppidi, J. Marshak-Rothstein, A. Reboldi, A. 2023-03-16 doi:10.1101/2023.03.16.532481 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae ]]> https://biorxiv.org/content/10.1101/2023.03.16.532987v1?rss=1 150 million years ago [mya]), obscuring genomic evolutionary patterns. Here, we characterized chemosensory and detoxification gene family evolution across Scaptomyza, a genus nested within Drosophila that includes a recently derived (<15 mya) herbivore lineage of mustard (Brassicales) specialists and carnation (Caryophyllaceae) specialists, and several non-herbivorous species. Comparative genomic analyses revealed that herbivorous Scaptomyza have among the smallest chemosensory and detoxification gene repertoires across 12 drosophilid species surveyed. Rates of gene turnover averaged across the herbivore clade were significantly higher than background rates in over half of the surveyed gene families. However, gene turnover was more limited along the ancestral herbivore branch, with only gustatory receptors and odorant binding proteins experiencing strong losses. The genes most significantly impacted by gene loss, duplication, or changes in selective constraint were those involved in detecting compounds associated with feeding on plants (bitter or electrophilic phytotoxins) or their ancestral diet (yeast and fruit volatiles). These results provide insight into the molecular and evolutionary mechanisms of plant-feeding adaptations and highlight strong gene candidates that have also been linked to other dietary transitions in Drosophila. ]]> Pelaez, J. N. Gloss, A. D. Goldman-Huertas, B. Kim, B. Lapoint, R. T. Pimentel-Solorio, G. Verster, K. I. Aguilar, J. M. Dittrich, A. C. N. Singhal, M. Suzuki, H. C. Matsunaga, T. Armstrong, E. E. Charboneau, J. L. M. Groen, S. C. Hembry, D. H. Ochoa, C. J. OConnor, T. K. Prost, S. Zaaijer, S. Nabity, P. D. Wang, J. Rodas, E. Liang, I. Whiteman, N. K. 2023-03-16 doi:10.1101/2023.03.16.532987 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Bioactive Natural Product Discovery via Deuterium Adduct Bioactivity Screening ]]> https://biorxiv.org/content/10.1101/2023.03.16.532988v1?rss=1 Zill, N. A. Du, Y. Marinkovich, S. Gu, D. Seidel, J. A. Zhang, W. 2023-03-17 doi:10.1101/2023.03.16.532988 Cold Spring Harbor Laboratory Press 2023-03-17 <![CDATA[ Targeted DNA integration in human cells without double-strand breaks using CRISPR RNA-guided transposases ]]> https://biorxiv.org/content/10.1101/2023.03.17.533036v1?rss=1 Lampe, G. D. King, R. T. Halpin-Healy, T. S. Klompe, S. E. Hogan, M. I. Vo, P. L. H. Tang, S. Chavez, A. Sternberg, S. H. 2023-03-18 doi:10.1101/2023.03.17.533036 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ Phyllosphere fungal diversity generates pervasive non-additive effects on plant performance ]]> https://biorxiv.org/content/10.1101/2023.03.17.533234v1?rss=1 1000% increase in productivity above the additive expectation), 2) interactions among commensal fungi were responsible for this non-additivity in diverse communities, 3) synergistic interactions were ~4 times stronger than antagonistic effects, 4) fungal diversity affected the magnitude but not frequency or direction of non-additivity, and 5) diversity affected plant performance nonlinearly with highest performance in low microbial diversity treatments. C_LIO_LIThese findings highlight the importance of interpreting plant-microbial interactions under a framework that incorporates intermicrobial interactions and non-additive outcomes to understand natural complexity. C_LI ]]> Almeida, B. K. Tran, E. Afkhami, M. E. 2023-03-21 doi:10.1101/2023.03.17.533234 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Control of meiotic entry by dual inhibition of a key mitotic transcription factor ]]> https://biorxiv.org/content/10.1101/2023.03.17.533246v1?rss=1 Su, A. J. Yendluri, S. C. Ünal, E. 2023-03-21 doi:10.1101/2023.03.17.533246 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Transgene Expression in Cultured Cells Using Unpurified Recombinant Adeno-Associated Viral Vectors ]]> https://biorxiv.org/content/10.1101/2023.03.20.533580v1?rss=1 Benyamini, B. Esbin, M. N. Whitney, O. Walther, N. Maurer, A. C. 2023-03-21 doi:10.1101/2023.03.20.533580 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ An endocytic myosin essential for plasma membrane invagination powers motility against resistance ]]> https://biorxiv.org/content/10.1101/2023.03.21.533689v1?rss=1 Pedersen, R. T. Snoberger, A. Pyrpassopoulos, S. Safer, D. Drubin, D. G. Ostap, E. M. 2023-03-22 doi:10.1101/2023.03.21.533689 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells ]]> https://biorxiv.org/content/10.1101/2023.03.22.533709v1?rss=1 Tsuchida, C. A. Brandes, N. Bueno, R. Trinidad, M. Mazumder, T. Yu, B. Hwang, B. Chang, C. Liu, J. Sun, Y. Hopkins, C. R. Parker, K. R. Qi, Y. Satpathy, A. Stadtmauer, E. Cate, J. H. D. Eyquem, J. Fraietta, J. A. June, C. H. Chang, H. Y. Ye, C. J. Doudna, J. A. 2023-03-22 doi:10.1101/2023.03.22.533709 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ Transcriptomic contributions to a modern cytoarchitectonic parcellation of the human cerebral cortex ]]> https://biorxiv.org/content/10.1101/2023.03.22.533710v1?rss=1 King, L. Weiner, K. S. 2023-03-23 doi:10.1101/2023.03.22.533710 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Targeted and selective knockout of the TLQP-21 neuropeptide unmasks its unique role in energy homeostasis ]]> https://biorxiv.org/content/10.1101/2023.03.23.532619v1?rss=1 Sahu, B. Razzoli, M. McGonigle, S. Pallais, J. P. Nguyen, M. Sadahiro, M. Jiang, C. Lin, W.-J. Kelley, K. Rodriguez, P. Mansk, R. Cero, C. Caviola, G. Palanza, P. Rao, L. Beetch, M. Alejandro, E. Sham, Y. Frontini, A. Salton, S. Bartolomucci, A. 2023-03-23 doi:10.1101/2023.03.23.532619 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia ]]> https://biorxiv.org/content/10.1101/2023.03.23.533946v1?rss=1 Paulat, N. S. Storer, J. M. Moreno-Santillan, D. D. Osmanski, A. B. Sullivan, K. A. Grimshaw, J. R. Korstian, J. Halsey, M. Garcia, C. J. Crookshanks, C. Roberts, J. Smit, A. F. Hubley, R. Rosen, J. Teeling, E. C. Vernes, S. C. Myers, E. Pippel, M. Brown, T. Hiller, M. Zoonomia Consortium, Rojas, D. Davalos, L. M. Lindblad-Toh, K. Karlsson, E. K. Ray, D. A. 2023-03-23 doi:10.1101/2023.03.23.533946 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Nuclease genes occupy boundaries of genetic exchange between bacteriophages ]]> https://biorxiv.org/content/10.1101/2023.03.23.533998v1?rss=1 10kb) of high nucleotide identity flanked by HEGs, deemed HEG islands, which we hypothesize to be mobilized by the activity of flanking HEGs. Finally, we found examples of domain swapping between phage-encoded HEGs and genes encoded by other phages and phage satellites. We anticipate that HEGs have a larger impact on the evolutionary trajectory of phages than previously appreciated and that future work investigating the role of HEGs in phage evolution will continue to highlight these observations. ]]> Barth, Z. Dunham, D. Seed, K. 2023-03-23 doi:10.1101/2023.03.23.533998 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ A Comprehensive Enumeration of the Human Proteostasis Network. 2. Components of the Autophagy-Lysosome Pathway ]]> https://biorxiv.org/content/10.1101/2023.03.22.533675v1?rss=1 The Proteostasis Consortium, Elsasser, S. Elia, L. P. Morimoto, R. I. Powers, E. T. Finley, D. Costa, B. Budron, M. Tokuno, Z. Wang, S. Iyer, R. G. Barth, B. Mockler, E. Finkbeiner, S. Gestwicki, J. E. Richardson, R. A. K. Stoeger, T. Tan, E. P. Xiao, Q. Cole, C. M. Massey, L. A. Garza, D. Kelly, J. W. Rainbolt, T. K. Chou, C.-C. Masto, V. B. Frydman, J. Nixon, R. A. 2023-03-24 doi:10.1101/2023.03.22.533675 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Role of Lactate in the Regulation of Transcriptional Activity of Breast Cancer-Related Genes and Epithelial-to-Mesenchymal Transition Proteins: A Comparison of MCF7 and MDA-MB-231 Cancer Cell Lines ]]> https://biorxiv.org/content/10.1101/2023.03.23.533060v1?rss=1 San-Millan, I. Martinez, J. L. Pickard, S. L. Yu, H. Hirsch, F. R. Brooks, G. A. Rivard, C. J. 2023-03-25 doi:10.1101/2023.03.23.533060 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Multiscale Computational Framework to Investigate Integrin Mechanosensing and Cell Adhesion ]]> https://biorxiv.org/content/10.1101/2023.03.24.533575v1?rss=1 Montes, A. R. Gutierrez, G. Buganza Tepole, A. Mofrad, M. 2023-03-25 doi:10.1101/2023.03.24.533575 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Transformations of sensory information in the brain reflect a changing definition of optimality ]]> https://biorxiv.org/content/10.1101/2023.03.24.534044v1?rss=1 Manning, T. S. Alexander, E. Cumming, B. G. DeAngelis, G. C. Huang, X. Cooper, E. A. 2023-03-25 doi:10.1101/2023.03.24.534044 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development ]]> https://biorxiv.org/content/10.1101/2023.03.24.534069v1?rss=1 Sieradzki, E. T. Nuccio, E. E. Pett-Ridge, J. Firestone, M. K. 2023-03-25 doi:10.1101/2023.03.24.534069 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Primate TRIM34 is a broadly-acting, TRIM5-dependent lentiviral restriction factor ]]> https://biorxiv.org/content/10.1101/2023.03.24.534139v1?rss=1 Twentyman, J. Khalifeh, A. Felton, A. Emerman, M. Ohainle, M. 2023-03-25 doi:10.1101/2023.03.24.534139 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Intrinsic protein disorder is insufficient to drive subnuclear clustering in embryonic transcription factors ]]> https://biorxiv.org/content/10.1101/2023.03.27.534457v1?rss=1 Hannon, C. E. Eisen, M. B. 2023-03-27 doi:10.1101/2023.03.27.534457 Cold Spring Harbor Laboratory Press 2023-03-27 <![CDATA[ A visual paired associate learning (vPAL) paradigm to study memory consolidation during sleep ]]> https://biorxiv.org/content/10.1101/2023.03.28.534494v1?rss=1 Schmidig, F. J. Geva-Sagiv, M. Falach, R. Yakim, S. Gat, Y. Sharon, O. Fried, I. Nir, Y. 2023-03-28 doi:10.1101/2023.03.28.534494 Cold Spring Harbor Laboratory Press 2023-03-28 <![CDATA[ Implantation of engineered adipocytes that outcompete tumors for resources suppresses cancer progression ]]> https://biorxiv.org/content/10.1101/2023.03.28.534564v1?rss=1 Nguyen, H. P. Sheng, R. Murray, E. Ito, Y. Bruck, M. Biellak, C. An, K. Lynce, F. Dillon, D. A. Magbanua, M. J. M. Huppert, L. A. Hammerlindl, H. Esserman, L. Rosenbluth, J. M. Ahituv, N. 2023-03-29 doi:10.1101/2023.03.28.534564 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ The Transcriptional Regulator Ume6 is a Major Driver of Early Gene Expression during Gametogenesis ]]> https://biorxiv.org/content/10.1101/2023.03.28.534652v1?rss=1 Harris, A. Ünal, E. 2023-03-29 doi:10.1101/2023.03.28.534652 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Transposon-sequencing across multiple Mycobacterium abscessus isolates reveals significant functional genomic diversity among strains ]]> https://biorxiv.org/content/10.1101/2023.03.29.534805v1?rss=1 Akusobi, C. Benghomari, B. S. Choudhery, S. Singhvi, S. Hicks, A. L. Ioerger, T. R. Rubin, E. J. 2023-03-29 doi:10.1101/2023.03.29.534805 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Splicing accuracy varies across human introns, tissues and age ]]> https://biorxiv.org/content/10.1101/2023.03.29.534370v1?rss=1 Garcia-Ruiz, S. Zhang, D. Gustavsson, E. K. Rocamora-Perez, G. Grant-Peters, M. Fairbrother-Browne, A. Reynolds, R. H. Brenton, J. W. Gil-Martinez, A. L. Chen, Z. Rio, D. C. Botia, J. A. Guelfi, S. Collado-Torres, L. Ryten, M. 2023-03-30 doi:10.1101/2023.03.29.534370 Cold Spring Harbor Laboratory Press 2023-03-30 <![CDATA[ Model-based differential sequencing analysis ]]> https://biorxiv.org/content/10.1101/2023.03.29.534803v1?rss=1 Busia, A. Listgarten, J. 2023-04-01 doi:10.1101/2023.03.29.534803 Cold Spring Harbor Laboratory Press 2023-04-01 <![CDATA[ Activation of a Vibrio cholerae CBASS anti-phage system by quorum sensing and folate depletion ]]> https://biorxiv.org/content/10.1101/2023.04.04.535582v1?rss=1 Severin, G. B. Ramliden, M. S. Ford, K. C. Van Alst, A. J. Sanath-Kumar, R. Decker, K. A. Hsueh, B. Y. Yoon, S. H. Demey, L. M. O'Hara, B. J. Rhoades, C. R. DiRita, V. J. Ng, W. L. Waters, C. M. 2023-04-04 doi:10.1101/2023.04.04.535582 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ Hierarchical TAF1-dependent co-translational assembly of the basal transcription factor TFIID ]]> https://biorxiv.org/content/10.1101/2023.04.05.535704v1?rss=1 Bernardini, A. Mukherjee, P. Scheer, E. Kamenova, I. Antonova, S. Sanchez, P. K. M. Yayli, G. Morlet, B. Timmers, H. T. M. Tora, L. 2023-04-05 doi:10.1101/2023.04.05.535704 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ Secondary Structure Detection Through Direct Nanopore RNA Sequencing ]]> https://biorxiv.org/content/10.1101/2023.04.05.535757v1?rss=1 Shaw, A. Craig, J. M. Amiri, H. Kim, J. Upton, H. E. Pimentel, S. C. Huang, J. R. Marqusee, S. Gundlach, J. H. Collins, K. Bustamante, C. J. 2023-04-05 doi:10.1101/2023.04.05.535757 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ Building pangenome graphs ]]> https://biorxiv.org/content/10.1101/2023.04.05.535718v1?rss=1 Garrison, E. Guarracino, A. Heumos, S. Villani, F. Bao, Z. Tattini, L. Hagmann, J. Vorbrugg, S. Marco-Sola, S. Kubica, C. Ashbrook, D. G. Thorell, K. Rusholme-Pilcher, R. L. Liti, G. Rudbeck, E. Nahnsen, S. Yang, Z. Moses, M. N. Nobrega, F. L. Wu, Y. Chen, H. de Ligt, J. Sudmant, P. H. Soranzo, N. Colonna, V. Williams, R. W. Prins, P. 2023-04-06 doi:10.1101/2023.04.05.535718 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Embryo-specific epigenetic mechanisms reconstitute the CHH methylation landscape during Arabidopsis embryogenesis ]]> https://biorxiv.org/content/10.1101/2023.04.06.535361v1?rss=1 Hsieh, P.-H. Frost, J. M. Choi, Y. Hsieh, T.-F. Zilberman, D. Fischer, R. L. 2023-04-08 doi:10.1101/2023.04.06.535361 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Hunger- and thirst-sensing neurons modulate a neuroendocrine network to coordinate sugar and water ingestion ]]> https://biorxiv.org/content/10.1101/2023.04.06.535891v1?rss=1 Gonzalez-Segarra, A. J. Pontes, G. Jourjine, N. Del Toro, A. Scott, K. 2023-04-08 doi:10.1101/2023.04.06.535891 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Evolution of neuronal cell classes and types in the vertebrate retina ]]> https://biorxiv.org/content/10.1101/2023.04.07.536039v1?rss=1 80% of RGCs in the human retina, subserve high-acuity vision, and were believed to be primate-specific (Berson, 2008); in contrast, the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information. ]]> Hahn, J. Monavarfeshani, A. Qiao, M. Kao, A. Kölsch, Y. Kumar, A. Kunze, V. P. Rasys, A. M. Richardson, R. Baier, H. Lucas, R. J. Li, W. Meister, M. Trachtenberg, J. T. Yan, W. Peng, Y.-R. Sanes, J. Shekhar, K. 2023-04-08 doi:10.1101/2023.04.07.536039 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Geochemical constraints on bacteriophage infectivity in terrestrial environments ]]> https://biorxiv.org/content/10.1101/2023.04.10.536276v1?rss=1 Carlson, H. K. Piya, D. Moore, M. L. Magar, R. T. Elisabeth, N. H. Deutschbauer, A. M. Arkin, A. P. Mutalik, V. K. 2023-04-10 doi:10.1101/2023.04.10.536276 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ Flowers are leakier than leaves but cheaper to build ]]> https://biorxiv.org/content/10.1101/2023.04.11.536372v1?rss=1 Roddy, A. Guilliams, M. Fine, P. Mambelli, S. Dawson, T. Simonin, K. 2023-04-12 doi:10.1101/2023.04.11.536372 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ The Impact of Stability Considerations on Genetic Fine-Mapping ]]> https://biorxiv.org/content/10.1101/2023.04.11.536456v1?rss=1 Aw, A. Jin, L. C. Ioannidis, N. Song, Y. S. 2023-04-13 doi:10.1101/2023.04.11.536456 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Kir7.1 is the physiological target for hormones and steroids that regulate uteroplacental function ]]> https://biorxiv.org/content/10.1101/2023.04.11.536476v1?rss=1 Haoui, M. Vergara, C. Lishko, P. V. 2023-04-13 doi:10.1101/2023.04.11.536476 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Flexibility and sensitivity in gene regulation out of equilibrium ]]> https://biorxiv.org/content/10.1101/2023.04.11.536490v1?rss=1 Mahdavi, S. Salmon, G. L. Daghlian, P. Garcia, H. G. Phillips, R. 2023-04-13 doi:10.1101/2023.04.11.536490 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Non-specific recognition of histone modifications by H3K9bhb antibody ]]> https://biorxiv.org/content/10.1101/2023.04.12.536655v1?rss=1 Tsusaka, T. Oses-Prieto, J. A. Lee, C. DeFelice, B. Burlingame, A. Goldberg, E. L. 2023-04-13 doi:10.1101/2023.04.12.536655 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Selenium reduction of ubiquinone via SQOR suppresses ferroptosis ]]> https://biorxiv.org/content/10.1101/2023.04.13.535674v1?rss=1 Lee, N. Park, S. J. Lange, M. Tseyang, T. Doshi, M. B. Kim, T. Song, Y. Kim, D. Greer, P. L. Olzmann, J. A. Spinelli, J. Kim, D. 2023-04-13 doi:10.1101/2023.04.13.535674 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Genome editing in the mouse brain with minimally immunogenic Cas9 RNPs ]]> https://biorxiv.org/content/10.1101/2023.04.13.536294v1?rss=1 Stahl, E. C. Sabo, J. K. Kang, M. H. Allen, R. Applegate, E. Kim, S. E. Kwon, M. Seth, A. Lemus, N. Salinas-Rios, V. Soczek, K. Trinidad, M. Vo, L. T. Jeans, C. Wozniak, A. Morris, T. Kimberlin, A. Foti, T. Savage, D. F. Doudna, J. A. 2023-04-13 doi:10.1101/2023.04.13.536294 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Mechanisms of regulation of cryptic prophage-encoded gene products in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2023.04.14.536235v1?rss=1 Ragunathan, P. T. Kim, E. N. Ma, X. Masse, E. Vanderpool, C. K. 2023-04-14 doi:10.1101/2023.04.14.536235 Cold Spring Harbor Laboratory Press 2023-04-14 <![CDATA[ Nucleus accumbens and dorsal medial striatal dopamine and neural activity are essential for action sequence performance ]]> https://biorxiv.org/content/10.1101/2023.04.17.537212v1?rss=1 Fraser, K. M. Chen, B. J. Janak, P. H. 2023-04-17 doi:10.1101/2023.04.17.537212 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Amyloplast sedimentation repolarizes LAZYs to achieve gravity sensing in plants ]]> https://biorxiv.org/content/10.1101/2023.04.17.537121v1?rss=1 Chen, J. Yu, R. Li, N. Deng, Z. Zhang, X. Zhao, Y. Qu, C. Yuan, Y. Pan, Z. Zhou, Y. Li, K. Wang, J. Chen, Z. Wang, X. Wang, X. Dong, J. Deng, X. W. Chen, H. 2023-04-18 doi:10.1101/2023.04.17.537121 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ The hagfish genome and the evolution of vertebrates ]]> https://biorxiv.org/content/10.1101/2023.04.17.537254v1?rss=1 Marletaz, F. Timoshevskaya, N. Timoshevskiy, V. Simakov, O. Parey, E. Gavriouchkina, D. Suzuki, M. Kubokawa, K. Brenner, S. Smith, J. Rokhsar, D. S. 2023-04-18 doi:10.1101/2023.04.17.537254 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ A multi-dimensional selective landscape drives adaptive divergence between and within closely related Phlox species ]]> https://biorxiv.org/content/10.1101/2023.04.18.537324v1?rss=1 Goulet-Scott, B. Farnitano, M. C. Brown, A. L. M. Hale, C. O. Blumstein, M. Hopkins, R. 2023-04-18 doi:10.1101/2023.04.18.537324 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Dynamic expectations: Behavioral and electrophysiological evidence of sub-second updates in reward predictions ]]> https://biorxiv.org/content/10.1101/2023.04.18.537382v1?rss=1 Marciano, D. Bellier, L. Mayer, I. Ruvalcaba, M. Lee, S. Hsu, M. Knight, R. T. 2023-04-18 doi:10.1101/2023.04.18.537382 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Kinetic investigation reveals an HIV-1 Nef-dependent increase in AP-2 recruitment and productivity at endocytic sites ]]> https://biorxiv.org/content/10.1101/2023.04.18.537262v1?rss=1 Iwamoto, Y. Ye, A. A. Shirazinejad, C. Hurley, J. H. Drubin, D. G. 2023-04-19 doi:10.1101/2023.04.18.537262 Cold Spring Harbor Laboratory Press 2023-04-19 <![CDATA[ BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale ]]> https://biorxiv.org/content/10.1101/2023.04.19.537435v1?rss=1 Backman, T. W. H. Schenk, C. Radivojevic, T. Ando, D. Singh, J. Czajka, J. J. Costello, Z. Keasling, J. D. Tang, Y. Akhmatskaya, E. Garcia Martin, H. 2023-04-20 doi:10.1101/2023.04.19.537435 Cold Spring Harbor Laboratory Press 2023-04-20 <![CDATA[ MmcA is an electron conduit that facilitates both intracellular and extracellular electron transport in Methanosarcina acetivorans ]]> https://biorxiv.org/content/10.1101/2023.04.20.537704v1?rss=1 Gupta, D. Chen, K. Elliott, S. J. Nayak, D. D. 2023-04-20 doi:10.1101/2023.04.20.537704 Cold Spring Harbor Laboratory Press 2023-04-20 <![CDATA[ A chromosome scale genome assembly and evaluation of mtDNA variation in the willow leaf beetle Chrysomela aeneicollis ]]> https://biorxiv.org/content/10.1101/2023.04.19.537531v1?rss=1 Bracewell, R. R. Stillman, J. Dahlhoff, E. Smeds, E. Chatla, K. Bachtrog, D. Williams, C. Rank, N. 2023-04-21 doi:10.1101/2023.04.19.537531 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Genetic basis of aposematic coloration in a mimetic radiation of poison frogs ]]> https://biorxiv.org/content/10.1101/2023.04.20.537757v1?rss=1 Linderoth, T. Aguilar-Gomez, D. White, E. Twomey, E. Stuckert, A. Bi, K. Ko, A. Graham, N. Rocha, J. L. Chang, J. MacManes, M. D. Summers, K. Nielsen, R. 2023-04-21 doi:10.1101/2023.04.20.537757 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Functional analysis of Salix purpurea genes support roles for ARR17 and GATA15 as master regulators of sex determination ]]> https://biorxiv.org/content/10.1101/2023.04.21.537837v1?rss=1 Hyden, B. Carper, D. L. Abraham, P. E. Yuan, G. Yao, T. Baumgart, L. Zhang, Y. Chen, C. O'Malley, R. Chen, J.-G. Yang, X. Hettich, R. L. Tuskan, G. A. Smart, L. B. 2023-04-21 doi:10.1101/2023.04.21.537837 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Adaptation to bile and anaerobicity limits Vibrio cholerae phage adsorption ]]> https://biorxiv.org/content/10.1101/2023.04.22.537938v1?rss=1 Netter, Z. Dunham, D. T. Seed, K. 2023-04-23 doi:10.1101/2023.04.22.537938 Cold Spring Harbor Laboratory Press 2023-04-23 <![CDATA[ Cortical Plasticity is associated with Blood-Brain-Barrier Modulation ]]> https://biorxiv.org/content/10.1101/2023.04.23.537964v1?rss=1 Swissa, E. Monsonego, U. Yang, L. T. Schori, L. Kamintsky, L. Mirloo, S. Burger, I. Uzzan, S. Patel, R. Sudmant, P. H. Prager, O. Kaufer, D. Friedman, A. 2023-04-24 doi:10.1101/2023.04.23.537964 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ Keystone competitor creates spatial patterns of biodiversity ]]> https://biorxiv.org/content/10.1101/2023.04.21.536496v1?rss=1 Ennis, K. K. Perfecto, I. Vandermeer, J. 2023-04-25 doi:10.1101/2023.04.21.536496 Cold Spring Harbor Laboratory Press 2023-04-25 <![CDATA[ Tumor cell heterogeneity drives spatial organization of the intratumoral immune response in squamous cell skin carcinoma ]]> https://biorxiv.org/content/10.1101/2023.04.25.538140v1?rss=1 Tanaka, M. Lum, L. Hu, K. H. Ledezma-Soto, C. Superville, D. A. Ng, K. M. Adams, Z. Kersten, K. H. Fong, L. Krummel, M. F. Reeves, M. Q. 2023-04-26 doi:10.1101/2023.04.25.538140 Cold Spring Harbor Laboratory Press 2023-04-26 <![CDATA[ Swi/Snf Chromatin Remodeling Regulates Transcriptional Interference and Gene Repression ]]> https://biorxiv.org/content/10.1101/2023.04.27.538572v1?rss=1 Morse, K. Swerdlow, S. Unal, E. 2023-04-27 doi:10.1101/2023.04.27.538572 Cold Spring Harbor Laboratory Press 2023-04-27 <![CDATA[ Rediversification Following Ecotype Isolation Reveals Hidden Adaptive Potential ]]> https://biorxiv.org/content/10.1101/2023.05.03.539206v1?rss=1 Ascensao, J. A. Denk, J. Lok, K. Yu, Q. Wetmore, K. M. Hallatschek, O. 2023-05-04 doi:10.1101/2023.05.03.539206 Cold Spring Harbor Laboratory Press 2023-05-04 <![CDATA[ Patterns of evolution of TRIM genes highlight the evolutionary plasticity of antiviral effectors in mammals ]]> https://biorxiv.org/content/10.1101/2023.05.03.539286v1?rss=1 Fernandes, A. P. Ohainle, M. Esteves, P. J. 2023-05-04 doi:10.1101/2023.05.03.539286 Cold Spring Harbor Laboratory Press 2023-05-04 <![CDATA[ ARID1B controls transcriptional programs of axon projection in the human corpus callosum ]]> https://biorxiv.org/content/10.1101/2023.05.04.539362v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@dd4e9aorg.highwire.dtl.DTLVardef@153a081org.highwire.dtl.DTLVardef@14e884corg.highwire.dtl.DTLVardef@d64081_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO Human callosal projection neurons are vulnerable to ARID1B haploinsufficiency. (Top) During healthy development, callosal projection neurons (CPNs) project long interhemispheric axons, forming the corpus callosum (CC) tract, which can be modeled in vitro. (Bottom) In ARID1B patients, transcriptional dysregulation of genetic programs of CC development reduces the formation of long-range projections from CPNs, causing CC agenesis in vivo and underconnectivity phenotypes in vitro. C_FIG ]]> Martins-Costa, C. Pham, V. A. Wiegers, A. Sidhaye, J. Doleschall, B. Novatchkova, M. Lendl, T. Piber, M. Peer, A. Moeseneder, P. Stuempflen, M. Chow, S. Y. A. Seidl, R. Prayer, D. Hoeftberger, R. Kasprian, G. Ikeuchi, Y. Corsini, N. Knoblich, J. A. 2023-05-04 doi:10.1101/2023.05.04.539362 Cold Spring Harbor Laboratory Press 2023-05-04 <![CDATA[ Sleep is required for neural network plasticity in the jellyfish Cassiopea ]]> https://biorxiv.org/content/10.1101/2023.05.04.538973v1?rss=1 Abrams, M. J. Zhang, L. von Emster, K. Lee, B. H. Zeigler, H. Jain, T. Jafri, A. Chen, Z. Harland, R. J. 2023-05-05 doi:10.1101/2023.05.04.538973 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ Mapping the Morphology of DNA on Carbon Nanotube-Based Sensors in Solution using X-ray Scattering Interferometry ]]> https://biorxiv.org/content/10.1101/2023.05.04.539504v1?rss=1 Rosenberg, D. J. Cunningham, F. J. Hubbard, J. D. Goh, N. S.-Y. Wang, J. W.-T. Hayman, E. B. Hura, G. L. Landry, M. P. Pinals, R. L. 2023-05-06 doi:10.1101/2023.05.04.539504 Cold Spring Harbor Laboratory Press 2023-05-06 <![CDATA[ A longitudinal single-cell therapeutic atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease ]]> https://biorxiv.org/content/10.1101/2023.05.05.539635v1?rss=1 Thomas, T. Rich-Griffin, C. Pohin, M. Friedrich, M. Aschenbrenner, D. Pakpoor, J. Jainarayanan, A. Voda, A.-I. Sanches Peres, R. Nee, E. Sathananthan, D. Kotliar, D. Turner, J. Nayar, S. Zhang, F. Jonsson, A. Brenner, M. Raychaudhuri, S. Kulicke, R. Ramsdell, D. Stransky, N. Pagliarini, R. Belecki, P. Spies, N. Wagner, A. Walsh, A. Coles, M. Jostins-Dean, L. Powrie, F. Filer, A. Travis, S. Uhlig, H. Dendrou, C. Buckley, C. 2023-05-06 doi:10.1101/2023.05.05.539635 Cold Spring Harbor Laboratory Press 2023-05-06 <![CDATA[ Critical role of down-regulated in adenoma bicarbonate transporter in linaclotide stimulated intestinal bicarbonate secretion ]]> https://biorxiv.org/content/10.1101/2023.05.05.539132v1?rss=1 Sarthi, J. B. Trumbull, A. M. Abazari, S. M. van Unen, V. Chan, J. E. Joo, N. S. Jiang, Y. Kuo, C. Sellers, Z. M. 2023-05-07 doi:10.1101/2023.05.05.539132 Cold Spring Harbor Laboratory Press 2023-05-07 <![CDATA[ Cortical cerebrovascular and metabolic perturbations in the 5xFAD mouse model of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2023.05.05.539629v1?rss=1 Jullienne, A. Szu, J. I. Quan, R. Trinh, M. V. Norouzi, T. Noarbe, B. P. Bedwell, A. A. Eldridge, K. Persohn, S. C. Territo, P. R. Obenaus, A. 2023-05-08 doi:10.1101/2023.05.05.539629 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Anatomical registration of intracranial electrodes. Robust model-based localization and deformable smooth brain-shift compensation methods ]]> https://biorxiv.org/content/10.1101/2023.05.08.539503v1?rss=1 Blenkmann, A. O. Leske, S. L. Llorens, A. Lin, J. J. Chang, E. Brunner, P. Schalk, G. Ivanovic, J. Larsson, P. G. Knight, R. T. Endestad, T. Solbakk, A.-K. 2023-05-09 doi:10.1101/2023.05.08.539503 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Transmission mode shapes host specialization of the phyllosphere microbiome ]]> https://biorxiv.org/content/10.1101/2023.05.08.539874v1?rss=1 Meyer, K. M. Muscettola, I. E. Vasconcelos, A. L. S. Sherman, J. K. Metcalf, C. J. E. Lindow, S. E. Koskella, B. 2023-05-09 doi:10.1101/2023.05.08.539874 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Linking bacterial tetrabromopyrrole biosynthesis to coral metamorphosis ]]> https://biorxiv.org/content/10.1101/2023.05.08.539906v1?rss=1 Alker, A. Farrell, M. Demko, A. Purdy, T. Adak, S. Moore, B. Sneed, J. Paul, V. Shikuma, N. J. 2023-05-09 doi:10.1101/2023.05.08.539906 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Context dependent function of the transcriptional regulator Rap1 in gene silencing and activation in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2023.05.08.539937v1?rss=1 Bondra, E. R. Rine, J. 2023-05-09 doi:10.1101/2023.05.08.539937 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ "When I talk about it, my eyes light up!" Impacts of a national laboratory internship on community college student success ]]> https://biorxiv.org/content/10.1101/2023.05.08.539924v1?rss=1 Cote, L. E. Van Doren, S. Zamora, A. N. Jaramillo Salcido, J. Law, E. W. Otero Munoz, G. Manocha, A. Flood, C. L. Baranger, A. M. 2023-05-10 doi:10.1101/2023.05.08.539924 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ Anatomical and behavioral correlates of auditory perception in developmental dyslexia ]]> https://biorxiv.org/content/10.1101/2023.05.09.539936v1?rss=1 Qi, T. Mandelli, M. L. Watson Pereira, C. L. Wellman, E. Bogley, R. Licata, A. E. Chang, E. F. Oganian, Y. Gorno-Tempini, M. L. 2023-05-10 doi:10.1101/2023.05.09.539936 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ L. pneumophila resists its self-harming metabolite HGA via secreted factors and collective peroxide scavenging ]]> https://biorxiv.org/content/10.1101/2023.05.11.540380v1?rss=1 1 hour of oxidation. While this manifests as a delay in killing within well-mixed liquid cultures, in a biofilm environment, this could provide time for HGA to diffuse away before becoming toxic. Second, HGA generates quantities of hydroperoxides that can be collectively scavenged by high-density, but not low-density cells. And third, high-density cells produce one or more secreted factors that are transiently protective from HGA. In combination, we propose that the bacteria are able to deploy HGA to generate a pool of reactive oxygen species surrounding their own biofilms, while maintaining non-toxic conditions within them. Overall, these findings help to explain how broadly toxic molecules can be used as inter-bacterial weapons. They also provide insights about why some of our current decontamination methods to control L. pneumophila are ineffective, leading to recurrent disease outbreaks. ]]> Holland, M. Farinella, D. N. Cruz-Lorenzo, E. Laubscher, M. I. Doakes, D. A. Ramos, M. A. Kubota, N. Levin, T. 2023-05-11 doi:10.1101/2023.05.11.540380 Cold Spring Harbor Laboratory Press 2023-05-11 <![CDATA[ Dysregulation of amino acid metabolism upon rapid depletion of cap-binding protein eIF4E ]]> https://biorxiv.org/content/10.1101/2023.05.11.540079v1?rss=1 Diamond, P. D. McGlincy, N. J. Ingolia, N. T. 2023-05-12 doi:10.1101/2023.05.11.540079 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ Dissociating instructive from permissive roles of brain circuits with reversible neural activity manipulations ]]> https://biorxiv.org/content/10.1101/2023.05.11.540397v1?rss=1 Bounds, H. A. Quintana, D. Brown, J. A. Wang, M. Bhatla, N. Wiegert, J. S. Adesnik, H. 2023-05-12 doi:10.1101/2023.05.11.540397 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ Foldy: a web application for interactive protein structure analysis ]]> https://biorxiv.org/content/10.1101/2023.05.11.540333v1?rss=1 Roberts, J. B. Nava, A. A. Pearson, A. N. Incha, M. R. Valencia, L. E. Ma, M. Rao, A. Keasling, J. D. 2023-05-14 doi:10.1101/2023.05.11.540333 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Spatial Tracking Across Time (ST AT ): Tracking Neurons Across In-Vivo Imaging Sessions through Optimizing Local Neighborhood Motion Consistency ]]> https://biorxiv.org/content/10.1101/2023.05.13.540658v1?rss=1 Gu, S. Mackevicius, E. L. Fee, M. S. Zhou, P. 2023-05-14 doi:10.1101/2023.05.13.540658 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Genome-wide CRISPRi knockdown to map gene essentiality landscape in coliphages {lambda} and P1 ]]> https://biorxiv.org/content/10.1101/2023.05.14.540688v1?rss=1 Mutalik, V. K. Piya, D. Nolan, N. Moore, M. L. Ramirez Hernandez, L. A. Cress, B. F. Young, R. Arkin, A. P. 2023-05-14 doi:10.1101/2023.05.14.540688 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Drosophila embryogenesis scales uniformly across temperature and developmentally diverse species ]]> https://biorxiv.org/content/10.1101/000307v1?rss=1 Steven Gregory Kuntz Michael B Eisen 2013-11-12 doi:10.1101/000307 Cold Spring Harbor Laboratory Press 2013-11-12 <![CDATA[ Design and implementation of a synthetic biomolecular concentration tracker ]]> https://biorxiv.org/content/10.1101/000448v1?rss=1 Victoria Hsiao Emmanuel LC de los Santos Weston R Whitaker John E Dueber Richard M Murray 2013-11-15 doi:10.1101/000448 Cold Spring Harbor Laboratory Press 2013-11-15 <![CDATA[ Sap flow through petioles and petioles reveals leaf-level responses to light and vapor pressure deficit in the tropical tree Tabebuia rosea (Bignoniaceae) ]]> https://biorxiv.org/content/10.1101/000711v1?rss=1 Adam Roddy Klaus Winter Todd Dawson 2013-11-19 doi:10.1101/000711 Cold Spring Harbor Laboratory Press 2013-11-19 <![CDATA[ Ancient human genomes suggest three ancestral populations for present-day Europeans ]]> https://biorxiv.org/content/10.1101/001552v1?rss=1 Iosif Lazaridis Nick Patterson Alissa Mittnik Gabriel Renaud Swapan Mallick Karola Kirsanow Peter H. Sudmant Joshua G. Schraiber Sergi Castellano Mark Lipson Bonnie Berger Christos Economou Ruth Bollongino Qiaomei Fu Kirsten Bos Susanne Nordenfelt Heng Li Cesare de Filippo Kay Prüfer Susanna Sawyer Cosimo Posth Wolfgang Haak Fredrik Hallgren Elin Fornander Nadin Rohland Dominique Delsate Michael Francken Jean-Michel Guinet Joachim Wahl George Ayodo Hamza A. Babiker Graciela Baillet Elena Balanovska Oleg Balanovsky Ramiro Barrantes Gabriel Bedoya Haim Ben-Ami Judit Bene Fouad Berrada Claudio M. 2013-12-23 doi:10.1101/001552 Cold Spring Harbor Laboratory Press 2013-12-23 <![CDATA[ Shifts in stability and control effectiveness during evolution of Paraves support aerial maneuvering hypotheses for flight origins ]]> https://biorxiv.org/content/10.1101/001750v1?rss=1 Dennis Evangelista Sharlene Cam Tony Huynh Austin Kwong Homayun Mehrabani Kyle Tse Robert Dudley 2014-01-13 doi:10.1101/001750 Cold Spring Harbor Laboratory Press 2014-01-13 <![CDATA[ Approximation to the distribution of fitness effects across functional categories in human segregating polymorphisms ]]> https://biorxiv.org/content/10.1101/002345v1?rss=1 Fernando Racimo Joshua G Schraiber 2014-02-04 doi:10.1101/002345 Cold Spring Harbor Laboratory Press 2014-02-04 <![CDATA[ Protected polymorphisms and evolutionary stability of patch-selection strategies in stochastic environments ]]> https://biorxiv.org/content/10.1101/003780v1?rss=1 Steve Evans Alexandru Hening Sebastian Schreiber 2014-04-03 doi:10.1101/003780 Cold Spring Harbor Laboratory Press 2014-04-03 <![CDATA[ Exact Reconstruction of Gene Regulatory Networks using Compressive Sensing ]]> https://biorxiv.org/content/10.1101/004242v1?rss=1 Young Hwan Chang Joe W. Gray Claire J. Tomlin 2014-04-20 doi:10.1101/004242 Cold Spring Harbor Laboratory Press 2014-04-20 <![CDATA[ Disentangling Multidimensional Spatio-Temporal Data into their Common and Aberrant Responses ]]> https://biorxiv.org/content/10.1101/004259v1?rss=1 Young Hwan Chang Jim Korkola Dhara N. Amin Mark M. Moasser Jose M. Carmena Joe W. Gray Claire J. Tomlin 2014-04-23 doi:10.1101/004259 Cold Spring Harbor Laboratory Press 2014-04-23 <![CDATA[ Gradual divergence and diversification of mammalian duplicate gene functions ]]> https://biorxiv.org/content/10.1101/004267v1?rss=1 Raquel Assis Doris Bachtrog 2014-04-17 doi:10.1101/004267 Cold Spring Harbor Laboratory Press 2014-04-17 <![CDATA[ Phylogenetic ANOVA: The Expression Variance and Evolution (EVE) model for quantitative trait evolution ]]> https://biorxiv.org/content/10.1101/004374v1?rss=1 Rori Rohlfs Rasmus Nielsen 2014-04-21 doi:10.1101/004374 Cold Spring Harbor Laboratory Press 2014-04-21 <![CDATA[ diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals ]]> https://biorxiv.org/content/10.1101/005082v1?rss=1 Paula Tataru Jasmine A. Nirody Yun S. Song 2014-05-12 doi:10.1101/005082 Cold Spring Harbor Laboratory Press 2014-05-12 <![CDATA[ Bio-inspired design of ice-retardant devices based on benthic marine invertebrates: the effect of surface texture ]]> https://biorxiv.org/content/10.1101/005470v1?rss=1 Homayun Mehrabani Neil Ray Kyle Tse Dennis Evangelista 2014-05-24 doi:10.1101/005470 Cold Spring Harbor Laboratory Press 2014-05-24 <![CDATA[ Validation of methods for Low-volume RNA-seq ]]> https://biorxiv.org/content/10.1101/006130v1?rss=1 Peter Acuña Combs Michael B Eisen 2014-06-10 doi:10.1101/006130 Cold Spring Harbor Laboratory Press 2014-06-10 <![CDATA[ Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition ]]> https://biorxiv.org/content/10.1101/006312v1?rss=1 Xiao-Yong Li Melissa Harrison Tommy Kaplan Michael Eisen 2014-06-13 doi:10.1101/006312 Cold Spring Harbor Laboratory Press 2014-06-13 <![CDATA[ Evaluation of de novo transcriptome assemblies from RNA-Seq data ]]> https://biorxiv.org/content/10.1101/006338v1?rss=1 Bo Li Nathanael Fillmore Yongsheng Bai Mike Collins James A Thomson Ron Stewart Colin Dewey 2014-06-13 doi:10.1101/006338 Cold Spring Harbor Laboratory Press 2014-06-13 <![CDATA[ The effective founder effect in a spatially expanding population ]]> https://biorxiv.org/content/10.1101/006700v1?rss=1 Benjamin Marco Peter Montgomery Slatkin 2014-06-28 doi:10.1101/006700 Cold Spring Harbor Laboratory Press 2014-06-28 <![CDATA[ Multi-locus analysis of genomic time series data from experimental evolution ]]> https://biorxiv.org/content/10.1101/006734v1?rss=1 Jonathan Terhorst Yun S. Song 2014-06-28 doi:10.1101/006734 Cold Spring Harbor Laboratory Press 2014-06-28 <![CDATA[ Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data ]]> https://biorxiv.org/content/10.1101/006742v1?rss=1 Anand Bhaskar Y.X. Rachel Wang Yun S. Song 2014-06-28 doi:10.1101/006742 Cold Spring Harbor Laboratory Press 2014-06-28 <![CDATA[ Selection of chromosomal DNA libraries using a multiplex CRISPR system in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/007310v1?rss=1 Owen W Ryan Jeffrey M Skerker Matthew J Maurer Xin Li Jordan C Tsai Snigdha Poddar Michael E Lee Will DeLoache John E Dueber Adam P Arkin Jamie Cate 2014-07-21 doi:10.1101/007310 Cold Spring Harbor Laboratory Press 2014-07-21 <![CDATA[ Ontogeny of aerial righting and wing flapping in juvenile birds ]]> https://biorxiv.org/content/10.1101/007708v1?rss=1 Dennis Evangelista Sharlene Cam Tony Huynh Igor Krivitskiy Robert Dudley 2014-08-06 doi:10.1101/007708 Cold Spring Harbor Laboratory Press 2014-08-06 <![CDATA[ Expanding xylose metabolism in yeast for plant cell wall conversion to biofuels ]]> https://biorxiv.org/content/10.1101/007807v1?rss=1 Xin Li Vivian Y Yu Yuping Lin Kulika Chomvong Raíssa Estrela Julie M Liang Elizabeth Znameroski Joanna Feehan Soo Rin Kim Yong-Su Jin N Louise Glass Jamie Cate 2014-08-09 doi:10.1101/007807 Cold Spring Harbor Laboratory Press 2014-08-09 <![CDATA[ Sensitivity of quantitative traits to mutational effects, number of loci, and population history ]]> https://biorxiv.org/content/10.1101/008540v1?rss=1 Joshua G. Schraiber Michael J. Landis 2014-08-29 doi:10.1101/008540 Cold Spring Harbor Laboratory Press 2014-08-29 <![CDATA[ The projection of a test genome onto a reference population and applications to humans and archaic hominins ]]> https://biorxiv.org/content/10.1101/008805v1?rss=1 Melinda A Yang Kelley Harris Montgomery Slatkin 2014-09-04 doi:10.1101/008805 Cold Spring Harbor Laboratory Press 2014-09-04 <![CDATA[ Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus ]]> https://biorxiv.org/content/10.1101/009134v1?rss=1 Matthew D MacManes Michael B Eisen 2014-09-15 doi:10.1101/009134 Cold Spring Harbor Laboratory Press 2014-09-15 <![CDATA[ Reticulate speciation and adaptive introgression in the Anopheles gambiae species complex ]]> https://biorxiv.org/content/10.1101/009837v1?rss=1 Jacob Crawford Michelle M. Riehle Wamdaogo M. Guelbeogo Awa Gneme N'fale Sagnon Kenneth D. Vernick Rasmus Nielsen Brian P. Lazzaro 2014-10-01 doi:10.1101/009837 Cold Spring Harbor Laboratory Press 2014-10-01 <![CDATA[ Fitting the Balding-Nichols model to forensic databases ]]> https://biorxiv.org/content/10.1101/009969v1?rss=1 Rori Rohlfs Vitor R.C. Aguiar Kirk E. Lohmueller Amanda M. Castro Alessandro C.S. Ferreira Vanessa C.O. Almeida Iuri D. Louro Rasmus Nielsen 2014-10-03 doi:10.1101/009969 Cold Spring Harbor Laboratory Press 2014-10-03 <![CDATA[ A 22,403 marker composite genetic linkage map for cassava (Manihot esculenta Crantz) derived from ten populations ]]> https://biorxiv.org/content/10.1101/010637v1?rss=1 International Cassava Genetic Map Consortium 2014-10-24 doi:10.1101/010637 Cold Spring Harbor Laboratory Press 2014-10-24 <![CDATA[ The origin and evolution of maize in the American Southwest ]]> https://biorxiv.org/content/10.1101/013540v1?rss=1 Rute R da Fonseca Bruce D Smith Nathan Wales Enrico Cappellini Pontus Skoglund Matteo Fumagalli José Alfredo Samaniego Christian Carøe María C Ávila-Arcos David E Hufnagel Thorfinn Sand Korneliussen Filipe Garrett Vieira Mattias Jakobsson Bernardo Arriaza Eske Willerslev Rasmus Nielsen Matthew B Hufford Anders Albrechtsen Jeffrey Ross-Ibarra M Thomas P Gilbert 2015-01-11 doi:10.1101/013540 Cold Spring Harbor Laboratory Press 2015-01-11 <![CDATA[ Transition densities and sample frequency spectra of diffusion processes with selection and variable population size ]]> https://biorxiv.org/content/10.1101/014639v1?rss=1 Daniel Zivkovic Matthias Steinrücken Yun S. Song Wolfgang Stephan 2015-02-02 doi:10.1101/014639 Cold Spring Harbor Laboratory Press 2015-02-02 <![CDATA[ After the games are over: life-history trade-offs drive dispersal attenuation following range expansion ]]> https://biorxiv.org/content/10.1101/014852v1?rss=1 Alex Perkins Carl Boettiger Ben Phillips 2015-02-04 doi:10.1101/014852 Cold Spring Harbor Laboratory Press 2015-02-04 <![CDATA[ Optimal Haplotype Assembly from High-Throughput Mate-Pair Reads ]]> https://biorxiv.org/content/10.1101/014993v1?rss=1 Govinda M Kamath Eren Şaşoğlu David Tse 2015-02-07 doi:10.1101/014993 Cold Spring Harbor Laboratory Press 2015-02-07 <![CDATA[ Detecting recent selective sweeps while controlling for mutation rate and background selection ]]> https://biorxiv.org/content/10.1101/018697v1?rss=1 Christian D. Huber Michael DeGiorgio Ines Hellmann Rasmus Nielsen 2015-04-30 doi:10.1101/018697 Cold Spring Harbor Laboratory Press 2015-04-30 <![CDATA[ Molecular Fossils from Microorganisms Preserved in Glacial Ice ]]> https://biorxiv.org/content/10.1101/019240v1?rss=1 P. Buford Price J. Jeffrey Morris Ryan C. Bay Ajeeth Adhikari Stephen J. Giovannoni Kevin L. Vergin 2015-05-13 doi:10.1101/019240 Cold Spring Harbor Laboratory Press 2015-05-13 <![CDATA[ Ancestral chromatin configuration constrains chromatin evolution on differentiating sex chromosomes in Drosophila ]]> https://biorxiv.org/content/10.1101/019786v1?rss=1 Qi Zhou Doris Bachtrog 2015-05-24 doi:10.1101/019786 Cold Spring Harbor Laboratory Press 2015-05-24 <![CDATA[ A Bayesian Approach for Detecting Mass-Extinction Events When Rates of Lineage Diversification Vary ]]> https://biorxiv.org/content/10.1101/020149v1?rss=1 Michael R. May Sebastian Höhna Brian R. Moore 2015-05-31 doi:10.1101/020149 Cold Spring Harbor Laboratory Press 2015-05-31 <![CDATA[ MDMA impairs response to water intake in healthy volunteers ]]> https://biorxiv.org/content/10.1101/021113v1?rss=1 Matthew J Baggott Kathleen J Garrison Jeremy R Coyle Gantt P Galloway Allan J Barnes Marilyn A Huestis John E Mendelson 2015-06-18 doi:10.1101/021113 Cold Spring Harbor Laboratory Press 2015-06-18 <![CDATA[ TESS: Bayesian inference of lineage diversification rates from (incompletely sampled) molecular phylogenies in R ]]> https://biorxiv.org/content/10.1101/021238v1?rss=1 Sebastian Höhna Michael R. May Brian R. Moore 2015-06-19 doi:10.1101/021238 Cold Spring Harbor Laboratory Press 2015-06-19 <![CDATA[ Effects of MDMA on socioemotional feelings, authenticity, and autobiographical disclosure in healthy volunteers in a controlled setting ]]> https://biorxiv.org/content/10.1101/021329v1?rss=1 Matthew J Baggott Jeremy R Coyle Jennifer D Siegrist Kathleen J Garrison Gantt P Galloway John E Mendelson 2015-06-23 doi:10.1101/021329 Cold Spring Harbor Laboratory Press 2015-06-23 <![CDATA[ Oxygen changes drive non-uniform scaling in Drosophila melanogaster embryogenesis ]]> https://biorxiv.org/content/10.1101/024208v1?rss=1 Steven Gregory Kuntz Michael B. Eisen 2015-08-12 doi:10.1101/024208 Cold Spring Harbor Laboratory Press 2015-08-12 <![CDATA[ Genome divergence and gene flow between Drosophila simulans and D. mauritiana ]]> https://biorxiv.org/content/10.1101/024711v1?rss=1 Sarah B. Kingan Anthony J. Geneva Jeffrey P. Vedanayagam Daniel Garrigan 2015-08-14 doi:10.1101/024711 Cold Spring Harbor Laboratory Press 2015-08-14 <![CDATA[ Inference of complex population histories using whole-genome sequences from multiple populations ]]> https://biorxiv.org/content/10.1101/026591v1?rss=1 Matthias Steinrücken John A. Kamm Yun S. Song 2015-09-16 doi:10.1101/026591 Cold Spring Harbor Laboratory Press 2015-09-16 <![CDATA[ Social selection parapatry in an Afrotropical sunbird ]]> https://biorxiv.org/content/10.1101/027417v1?rss=1 Jay P McEntee Joshua Penalba Chacha Werema Elia Mulungu Maneno Mbilinyi David Moyer Louis Hansen Jon Fjeldsaa Rauri C.K. Bowie 2015-09-23 doi:10.1101/027417 Cold Spring Harbor Laboratory Press 2015-09-23 <![CDATA[ Deep learning for population genetic inference ]]> https://biorxiv.org/content/10.1101/028175v1?rss=1 Sara Sheehan Yun S. Song 2015-10-02 doi:10.1101/028175 Cold Spring Harbor Laboratory Press 2015-10-02 <![CDATA[ Gene discovery for Mendelian conditions via social networking: de novo variants in KDM1A cause developmental delay and distinctive facial features ]]> https://biorxiv.org/content/10.1101/028241v1?rss=1 Jessica Chong Joon-Ho Yu Peter Lorentzen Karen Park Seema M Jamal Holly K Tabor Anita Rauch Margarita Sifuentes Saenz Eugen Boltshauser Karynne E Patterson Deborah A Nickerson University of Washington Center for Mendelian Geno Michael J Bamshad 2015-10-03 doi:10.1101/028241 Cold Spring Harbor Laboratory Press 2015-10-03 <![CDATA[ Hydraulic conductance and the maintenance of water balance in flowers ]]> https://biorxiv.org/content/10.1101/030122v1?rss=1 Adam Roddy Craig R. Brodersen Todd E. Dawson 2015-10-28 doi:10.1101/030122 Cold Spring Harbor Laboratory Press 2015-10-28 <![CDATA[ An evaluation of transcriptome-based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura) ]]> https://biorxiv.org/content/10.1101/031468v1?rss=1 200 bp), with no major reduction in coverage towards the ends of exons. We observed significant differences in the performance of blocking oligos for target enrichment and non-target depletion during captures, and observed differences in PCR duplication rates that can be attributed to the number of individuals pooled for capture reactions. We explicitly tested the effects of phylogenetic distance on capture sensitivity, specificity, and missing data, and provide a baseline estimate of expectations for these metrics based on nuclear pairwise differences among samples. We provide recommendations for transcriptome-based exon capture design based on our results, and describe multiple pipelines for data assembly and analysis. ]]> Daniel Portik Lydia Smith Ke Bi 2015-11-12 doi:10.1101/031468 Cold Spring Harbor Laboratory Press 2015-11-12 <![CDATA[ Genome-wide and single-base resolution DNA methylomes of the Sea Lamprey (Petromyzon marinus) Reveal Gradual Transition of the Genomic Methylation Pattern in Early Vertebrates ]]> https://biorxiv.org/content/10.1101/033233v1?rss=1 Zhao Zhang Gangbiao Liu Yangyun Zhou James P. B. Lloyd David W. McCauley Weiming Li Xun Gu Zhixi Su 2015-11-30 doi:10.1101/033233 Cold Spring Harbor Laboratory Press 2015-11-30 <![CDATA[ Tunable protein synthesis by transcript isoforms in human cells ]]> https://biorxiv.org/content/10.1101/035188v1?rss=1 Stephen N Floor Jennifer A Doudna 2015-12-23 doi:10.1101/035188 Cold Spring Harbor Laboratory Press 2015-12-23 <![CDATA[ Efficient Correction of the Sickle Mutation in Human Hematopoietic Stem Cells Using a Cas9 Ribonucleoprotein Complex ]]> https://biorxiv.org/content/10.1101/036236v1?rss=1 Mark DeWitt Wendy Magis Nicolas L Bray Tianjiao Wang Jennifer R Berman Fabrizia Urbinati Denise P Muñoz Donald B Kohn Mark C Walters Dana Carroll David K Martin Jacob E Corn 2016-01-15 doi:10.1101/036236 Cold Spring Harbor Laboratory Press 2016-01-15 <![CDATA[ The Effect of Anthropogenic Land Cover Change on Pollen-Vegetation Relationships in the American Midwest ]]> https://biorxiv.org/content/10.1101/037051v1?rss=1 Ellen Ruth Kujawa Simon J. Goring Andria Dawson Randy Calcote Eric Grimm Sara Hotchkiss Elizabeth A. Lynch Jason McLachlan Jeannine-Marie St-Jacques Charles Umbanhowar John W. Williams 2016-01-19 doi:10.1101/037051 Cold Spring Harbor Laboratory Press 2016-01-19 <![CDATA[ Bayesian inference of natural selection from allele frequency time series ]]> https://biorxiv.org/content/10.1101/037200v1?rss=1 Joshua Schraiber Steven N. Evans Montgomery Slatkin 2016-01-19 doi:10.1101/037200 Cold Spring Harbor Laboratory Press 2016-01-19 <![CDATA[ An open library of human kinase domain constructs for automated bacterial expression ]]> https://biorxiv.org/content/10.1101/038711v1?rss=1 Daniel L. Parton Sonya M. Hanson Lucelenie Rodríguez-Laureano Steven K. Albanese Scott Gradia Chris Jeans Markus A. Seeliger Nicholas M. Levinson John D. Chodera 2016-02-03 doi:10.1101/038711 Cold Spring Harbor Laboratory Press 2016-02-03 <![CDATA[ Quantifying pollen-vegetation relationships to reconstruct ancient forests using 19th-century forest composition and pollen data ]]> https://biorxiv.org/content/10.1101/039073v1?rss=1 Andria Dawson Christopher J. Paciorek Jason S. McLachlan Simon Goring John W. Williams Stephen T. Jackson 2016-02-09 doi:10.1101/039073 Cold Spring Harbor Laboratory Press 2016-02-09 <![CDATA[ Shannon: An Information-Optimal de Novo RNA-Seq Assembler ]]> https://biorxiv.org/content/10.1101/039230v1?rss=1 Sreeram Kannan Joseph Hui Kayvon Mazooji Lior Pachter David Tse 2016-02-09 doi:10.1101/039230 Cold Spring Harbor Laboratory Press 2016-02-09 <![CDATA[ Non-homologous DNA increases gene disruption efficiency by altering DNA repair outcomes ]]> https://biorxiv.org/content/10.1101/040212v1?rss=1 Christopher D Richardson Grahm J Ray Jacob E Corn 2016-02-18 doi:10.1101/040212 Cold Spring Harbor Laboratory Press 2016-02-18 <![CDATA[ C. elegans paraoxonase-like proteins control the functional expression of DEG/ENaC mechanosensory proteins ]]> https://biorxiv.org/content/10.1101/040337v1?rss=1 Yushu Chen Shashank Bharill Zeynep Altun Robert O'Hagan Brian Coblitz Ehud I. Isacoff Martin Chalfie 2016-02-19 doi:10.1101/040337 Cold Spring Harbor Laboratory Press 2016-02-19 <![CDATA[ Distinct stages in the recognition, sorting and packaging of proTGFα into COPII coated transport vesicles ]]> https://biorxiv.org/content/10.1101/040410v1?rss=1 Pengcheng Zhang Randy Schekman 2016-02-19 doi:10.1101/040410 Cold Spring Harbor Laboratory Press 2016-02-19 <![CDATA[ Extrusions promote engulfment and Chlamydia survival within macrophages ]]> https://biorxiv.org/content/10.1101/041079v1?rss=1 Meghan Zuck Tisha C Ellis Anthony Venida Kevin Hybiske 2016-02-23 doi:10.1101/041079 Cold Spring Harbor Laboratory Press 2016-02-23 <![CDATA[ Fast imaging of DNA motion reveals distinct sub-diffusion regimes at the site of DNA damage ]]> https://biorxiv.org/content/10.1101/042051v1?rss=1 Judith Mine-Hattab Vincent Recamier Ignacio Izeddin Rodney Rothstein Xavier Darzacq 2016-03-01 doi:10.1101/042051 Cold Spring Harbor Laboratory Press 2016-03-01 <![CDATA[ Genotyping Allelic and Copy Number Variation in the Immunoglobulin Heavy Chain Locus ]]> https://biorxiv.org/content/10.1101/042226v1?rss=1 Shishi Luo Jane A Yu Yun S. Song 2016-03-03 doi:10.1101/042226 Cold Spring Harbor Laboratory Press 2016-03-03 <![CDATA[ FastProject: A Tool for Low-Dimensional Analysis of Single-Cell RNA-Seq Data ]]> https://biorxiv.org/content/10.1101/043463v1?rss=1 David DeTomaso Nir Yosef 2016-03-12 doi:10.1101/043463 Cold Spring Harbor Laboratory Press 2016-03-12 <![CDATA[ Left-right leaf asymmetry in decussate and distichous phyllotactic systems ]]> https://biorxiv.org/content/10.1101/043869v1?rss=1 800 commonivy (Hedera helix) and >3,000 grapevine (Vitis and Ampelopsis spp.) leaf pairs and find statistical enrichment of predicted mirrored asymmetries. Our results demonstrate that left-right auxin asymmetries in models of decussate and distichous phyllotaxy successfully predict mirrored asymmetric leaf morphologies in superficially symmetric leaves. ]]> Ciera C Martinez Daniel H Chitwood Richard S Smith Neelima R Sinha 2016-03-15 doi:10.1101/043869 Cold Spring Harbor Laboratory Press 2016-03-15 <![CDATA[ Towards standard practices for sharing computer code and programs in neuroscience ]]> https://biorxiv.org/content/10.1101/045104v1?rss=1 Stephen Eglen Ben Marwick Yaroslav Halchenko Michael Hanke Shoaib Sufi Padraig Gleeson R. Angus Silver Andrew Davison Linda Lanyon Mathew Abrams Thomas Wachtler David J Willshaw Christophe Pouzat Jean-Baptiste Poline 2016-03-24 doi:10.1101/045104 Cold Spring Harbor Laboratory Press 2016-03-24 <![CDATA[ Genome-wide measurement of spatial expression in patterning mutants of Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/046128v1?rss=1 Peter A. Combs Michael B Eisen 2016-03-29 doi:10.1101/046128 Cold Spring Harbor Laboratory Press 2016-03-29 <![CDATA[ Magnetite biomineralization in Magnetospirillum magneticum is regulated by a switch-like behavior in the HtrA protease MamE ]]> https://biorxiv.org/content/10.1101/047555v1?rss=1 David M Hershey Patrick J Browne Anthony T Iavarone Joan Teyra Eun H Lee Sachdev S Sidhu Arash Komeili 2016-04-07 doi:10.1101/047555 Cold Spring Harbor Laboratory Press 2016-04-07 <![CDATA[ The effects of population size histories on estimates of selection coefficients from time-series genetic data ]]> https://biorxiv.org/content/10.1101/048355v1?rss=1 Ethan M Jewett Matthias Steinrücken Yun S. Song 2016-04-13 doi:10.1101/048355 Cold Spring Harbor Laboratory Press 2016-04-13 <![CDATA[ Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9 ]]> https://biorxiv.org/content/10.1101/048371v1?rss=1 2 s-1 upon introduction of mismatches proximal to the protospacer adjacent motif (PAM), demonstrating that mismatches encountered early during heteroduplex formation induce rapid rejection of off-target DNA. In contrast, PAM-distal mismatches up to 12 base pairs in length, which prevent DNA cleavage, still allow the formation of a stable complex (off-rate < 0.006 s-1), suggesting that extremely slow rejection could sequester Cas9-RNA, increasing the Cas9 expression level necessary for genome editing thereby aggravating off-target effects. We also observed at least two different bound FRET states that may represent distinct steps in target search and proofreading. ]]> Digvijay Singh Samuel H. Sternberg Jingyi Fei Taekjip Ha Jennifer A. Doudna 2016-04-13 doi:10.1101/048371 Cold Spring Harbor Laboratory Press 2016-04-13 <![CDATA[ Allele Surfing Promotes Microbial Adaptation from Standing Variation ]]> https://biorxiv.org/content/10.1101/049353v1?rss=1 Matti Gralka Fabian Stiewe Fred Farrell Wolfram Moebius Bartlomiej Waclaw Oskar Hallatschek 2016-04-19 doi:10.1101/049353 Cold Spring Harbor Laboratory Press 2016-04-19 <![CDATA[ Membrane tension is a key determinant of bud morphology in clathrin-mediated endocytosis ]]> https://biorxiv.org/content/10.1101/050484v1?rss=1 Julian E. Hassinger George Oster David G. Drubin Padmini Rangamani 2016-04-27 doi:10.1101/050484 Cold Spring Harbor Laboratory Press 2016-04-27 <![CDATA[ Paradoxical signaling regulates structural plasticity in dendritic spines ]]> https://biorxiv.org/content/10.1101/050492v1?rss=1 Padmini Rangamani Michael G. Levy Shahid M. Khan George Oster 2016-04-27 doi:10.1101/050492 Cold Spring Harbor Laboratory Press 2016-04-27 <![CDATA[ Reduced spatial integration in the ventral visual cortex underlies face recognition deficits in developmental prosopagnosia ]]> https://biorxiv.org/content/10.1101/051102v1?rss=1 Nathaniel Witthoft Sonia Poltoratski Mai Nguyen Golijeh Golarai Alina Liberman Karen F LaRocque Mary E Smith Kalanit Grill-Spector 2016-04-29 doi:10.1101/051102 Cold Spring Harbor Laboratory Press 2016-04-29 <![CDATA[ Data-Driven Phenotypic Categorization for Neurobiological Analyses: Beyond DSM-5 Labels ]]> https://biorxiv.org/content/10.1101/051789v1?rss=1 Nicholas Van Dam David O'Connor Enitan T Marcelle Erica J Ho Richard Cameron Craddock Russell H Tobe Vilma Gabbay James J Hudziak Francisco Xavier Castellanos Bennett L Leventhal Michael P Milham 2016-05-06 doi:10.1101/051789 Cold Spring Harbor Laboratory Press 2016-05-06 <![CDATA[ Bacteria regulate choanoflagellate development with lipid activators, inhibitors, and synergists ]]> https://biorxiv.org/content/10.1101/052399v1?rss=1 Arielle Woznica Alexandra M. Cantley Christine Beemelmanns Elizaveta Freinkman Jon Clardy Nicole King 2016-05-10 doi:10.1101/052399 Cold Spring Harbor Laboratory Press 2016-05-10 <![CDATA[ Self-driven jamming in growing microbial populations ]]> https://biorxiv.org/content/10.1101/052480v1?rss=1 Morgan Delarue Jörn Hartung Carl Schreck Pawel Gniewek Lucy Hu Stephan Herminghaus Oskar Hallatschek 2016-05-11 doi:10.1101/052480 Cold Spring Harbor Laboratory Press 2016-05-11 <![CDATA[ Excess of mutational jackpot events in growing populations due to gene surfing ]]> https://biorxiv.org/content/10.1101/053405v1?rss=1 Diana Fusco Matti Gralka Alex Anderson Jona Kayser Oskar Hallatschek 2016-05-16 doi:10.1101/053405 Cold Spring Harbor Laboratory Press 2016-05-16 <![CDATA[ Building a Web of Linked Data Resources to Advance Neuroscience Research ]]> https://biorxiv.org/content/10.1101/053934v1?rss=1 B Nolan Nichols Satrajit S Ghosh Tibor Auer Thomas J Grabowskith Camille Maumet David Keator Kilian Pohl Jean-Baptiste Poline 2016-05-24 doi:10.1101/053934 Cold Spring Harbor Laboratory Press 2016-05-24 <![CDATA[ Best Practices in Data Analysis and Sharing in Neuroimaging using MRI ]]> https://biorxiv.org/content/10.1101/054262v1?rss=1 Thomas E. Nichols Samir Das Simon B. Eickhoff Alan C. Evans Tristan Glatard Michael Hanke Nikolaus Kriegeskorte Michael P. Milham Russell A. Poldrack Jean-Baptiste Poline Erika Proal Bertrand Thirion David C. Van Essen Tonya White B. T. Thomas Yeo 2016-05-20 doi:10.1101/054262 Cold Spring Harbor Laboratory Press 2016-05-20 <![CDATA[ Long shelf-life streptavidin support-films suitable for electron microscopy of biological macromolecules ]]> https://biorxiv.org/content/10.1101/054452v1?rss=1 Bong-Gyoon Han Zoe Watson Hannah Kang Arto Pulk Kenneth Downing Jamie Cate Robert Glaeser 2016-05-20 doi:10.1101/054452 Cold Spring Harbor Laboratory Press 2016-05-20 <![CDATA[ The evolution of alternative splicing in Drosophila ]]> https://biorxiv.org/content/10.1101/054700v1?rss=1 Lauren Gibilisco Qi Zhou Shivani Mahajan Doris Bachtrog 2016-05-21 doi:10.1101/054700 Cold Spring Harbor Laboratory Press 2016-05-21 <![CDATA[ An open-hardware platform for optogenetics and photobiology ]]> https://biorxiv.org/content/10.1101/055053v1?rss=1 Karl Gerhardt Evan Olson Sebastian Castillo-Hair Lucas Hartsough Brian Landry Felix Ekness Rayka Yokoo Eric Gomez Prabha Ramakrishnan Junghae Suh David Savage Jeffrey Tabor 2016-05-24 doi:10.1101/055053 Cold Spring Harbor Laboratory Press 2016-05-24 <![CDATA[ Scanning the Horizon: challenges and solutions for neuroimaging research ]]> https://biorxiv.org/content/10.1101/059188v1?rss=1 Russell Poldrack Chris I Baker Joke Durnez Krzysztof Gorgolewski Paul M Matthews Marcus Munafo Thomas Nichols Jean-Baptiste Poline Edward Vul Tal Yarkoni 2016-06-16 doi:10.1101/059188 Cold Spring Harbor Laboratory Press 2016-06-16 <![CDATA[ High-throughput biochemical profiling reveals Cas9 off-target binding and unbinding heterogeneity ]]> https://biorxiv.org/content/10.1101/059782v1?rss=1 Evan August Boyle Johan Oscar Lennart Andreasson Lauren Mallory Chircus Samuel Henry Sternberg Michelle Jennifer Wu Chantal Katrin Guegler Jennifer Anne Doudna William James Greenleaf 2016-06-19 doi:10.1101/059782 Cold Spring Harbor Laboratory Press 2016-06-19 <![CDATA[ Periodic Non-Sinusoidal Activity Can Produce Cross-Frequency Coupling in Cortical Signals in the Absence of Functional Interaction Between Neural Sources ]]> https://biorxiv.org/content/10.1101/062190v1?rss=1 Edden M. Gerber Boaz Sadeh Andrew Ward Robert T. Knight Leon Y. Deouell 2016-07-05 doi:10.1101/062190 Cold Spring Harbor Laboratory Press 2016-07-05 <![CDATA[ A Thousand Fly Genomes: An Expanded Drosophila Genome Nexus ]]> https://biorxiv.org/content/10.1101/063537v1?rss=1 Justin B Lack Jeremy D Lange Alison B Tang Russell B Corbett-Detig John E Pool 2016-07-12 doi:10.1101/063537 Cold Spring Harbor Laboratory Press 2016-07-12 <![CDATA[ Architectures of a lipid transport systems for the bacterial outer membrane ]]> https://biorxiv.org/content/10.1101/064360v1?rss=1 Damian C Ekiert Gira Bhabha Garrett Greenan Sergey Ovchinnikov Jeffery S Cox Ronald D Vale 2016-07-18 doi:10.1101/064360 Cold Spring Harbor Laboratory Press 2016-07-18 <![CDATA[ CRISPR-Cas9 mediated mutagenesis of a DMR6 ortholog in tomato confers broad-spectrum disease resistance ]]> https://biorxiv.org/content/10.1101/064824v1?rss=1 Daniela Paula de Toledo Thomazella Quinton Brail Douglas Dahlbeck Brian J Staskawicz 2016-07-20 doi:10.1101/064824 Cold Spring Harbor Laboratory Press 2016-07-20 <![CDATA[ RNase H enables efficient repair of R-loop induced DNA damage ]]> https://biorxiv.org/content/10.1101/068742v1?rss=1 Jeremy D. Amon Douglas Koshland 2016-08-09 doi:10.1101/068742 Cold Spring Harbor Laboratory Press 2016-08-09 <![CDATA[ A functional analysis of the contribution of climatic niche divergence to adaptive radiation ]]> https://biorxiv.org/content/10.1101/069294v1?rss=1 Alex R Gunderson D. Luke Mahler Manuel Leal 2016-08-14 doi:10.1101/069294 Cold Spring Harbor Laboratory Press 2016-08-14 <![CDATA[ A Systems-Level Model Reveals That 1,2-Propanediol Utilization Microcompartments Enhance Pathway Flux Through Intermediate Sequestration. ]]> https://biorxiv.org/content/10.1101/069542v1?rss=1 Christopher M Jakobson Marilyn F. Slininger Danielle Tullman-Ercek Niall M. Mangan 2016-08-14 doi:10.1101/069542 Cold Spring Harbor Laboratory Press 2016-08-14 <![CDATA[ CH···O Interactions Are Not the Cause of Trends in Reactivity and Secondary Kinetic Isotope Effects for Enzymatic SN2 Methyl Transfer Reactions ]]> https://biorxiv.org/content/10.1101/071043v1?rss=1 Jianyu Zhang Judith P. Klinman 2016-09-01 doi:10.1101/071043 Cold Spring Harbor Laboratory Press 2016-09-01 <![CDATA[ Ohana, a tool set for population genetic analyses of admixture components ]]> https://biorxiv.org/content/10.1101/071233v1?rss=1 Jade Yu Cheng Thomas Mailund Rasmus Nielsen 2016-08-23 doi:10.1101/071233 Cold Spring Harbor Laboratory Press 2016-08-23 <![CDATA[ Range stability predicts lineage persistence in a morphologically cryptic ground squirrel species complex ]]> https://biorxiv.org/content/10.1101/073320v1?rss=1 Mark A Phuong Ke Bi Craig Moritz 2016-09-04 doi:10.1101/073320 Cold Spring Harbor Laboratory Press 2016-09-04 <![CDATA[ mTORC1 controls cytoplasmic crowding by regulating ribosome concentration ]]> https://biorxiv.org/content/10.1101/073866v1?rss=1 Delarue, M. Brittingham, G. Surovtsev, I. Kennedy, K. J. Gutierrez, I. Chung, J. Groves, J. T. Jacobs-Wagner, C. Holt, L. J. 2017-02-16 doi:10.1101/073866 Cold Spring Harbor Laboratory Press 2017-02-16 <![CDATA[ Neuroplasticity of language in left-hemisphere stroke: evidence linking subsecond electrophysiology and structural connections ]]> https://biorxiv.org/content/10.1101/075333v1?rss=1 Vitoria Piai Lars Meyer Nina F Dronkers Robert T Knight 2016-09-16 doi:10.1101/075333 Cold Spring Harbor Laboratory Press 2016-09-16 <![CDATA[ Multiple factors influence population sex ratios in the Mojave Desert moss Syntrichia caninervis ]]> https://biorxiv.org/content/10.1101/075861v1?rss=1 Jenna T. Baughman Adam C. Payton Amber E. Paasch Kirsten M. Fisher Stuart F. McDaniel 2016-09-19 doi:10.1101/075861 Cold Spring Harbor Laboratory Press 2016-09-19 <![CDATA[ ATP homeostasis underlies optimal glucose consumption by Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/076364v1?rss=1 Kulika Chomvong Daniel Benjamin Dan Nomura Jamie Cate 2016-09-21 doi:10.1101/076364 Cold Spring Harbor Laboratory Press 2016-09-21 <![CDATA[ An Electrochemistry Study of Cryoelectrolysis in Frozen Physiological Saline ]]> https://biorxiv.org/content/10.1101/077545v1?rss=1 Thomas J. Manuel Pujita Munnangi Boris Rubinsky 2016-09-26 doi:10.1101/077545 Cold Spring Harbor Laboratory Press 2016-09-26 <![CDATA[ Reproducibility and replicability of rodent phenotyping in preclinical studies ]]> https://biorxiv.org/content/10.1101/079350v1?rss=1 Neri Kafkafi Joseph Agassi Elissa J Chesler John C Crabbe Wim E Crusio David Eilam Robert Gerlai Ilan Golani Alex Gomez-Marin Ruth Heller Fuad Iraqi Iman Jaljuli Natasha A Karp Hugh Morgan George Nicholson Donald W Pfaff Helene S Richter Philip B Stark Oliver Stiedl Victoria Stodden Lisa M Tarantino Valter Tucci William Valdar Robert W Williams Hanno Wurbel Yoav Benjamini 2016-10-05 doi:10.1101/079350 Cold Spring Harbor Laboratory Press 2016-10-05 <![CDATA[ QTL-guided metabolic engineering of a complex trait ]]> https://biorxiv.org/content/10.1101/079764v1?rss=1 Matthew J Maurer Lawrence Sutardja Dominic Pinel Stefan Bauer Amanda L Muehlbauer Tyler D Ames Jeffrey M Skerker Adam P Arkin 2016-10-07 doi:10.1101/079764 Cold Spring Harbor Laboratory Press 2016-10-07 <![CDATA[ SWALO: scaffolding with assembly likelihood optimization ]]> https://biorxiv.org/content/10.1101/081786v1?rss=1 Rahman, A. Pachter, L. 2016-10-18 doi:10.1101/081786 Cold Spring Harbor Laboratory Press 2016-10-18 <![CDATA[ A simple molecular mechanism explains multiple patterns of cell-size regulation ]]> https://biorxiv.org/content/10.1101/083725v1?rss=1 Delarue, M. Weissman, D. Hallatschek, O. 2016-10-26 doi:10.1101/083725 Cold Spring Harbor Laboratory Press 2016-10-26 <![CDATA[ Minimal-assumption inference from population-genomic data ]]> https://biorxiv.org/content/10.1101/084459v1?rss=1 Weissman, D. B. Hallatschek, O. 2016-10-31 doi:10.1101/084459 Cold Spring Harbor Laboratory Press 2016-10-31 <![CDATA[ Impaired lexical selection with competing distractors: Evidence from left temporal and left prefrontal lesions ]]> https://biorxiv.org/content/10.1101/085670v1?rss=1 Piai, V. Knight, R. T. 2016-11-04 doi:10.1101/085670 Cold Spring Harbor Laboratory Press 2016-11-04 <![CDATA[ Inactivation of thermogenic UCP1 as a historical contingency in multiple placental mammal clades ]]> https://biorxiv.org/content/10.1101/086819v1?rss=1 Gaudry, M. Jastroch, M. Treberg, J. Hofreiter, M. Paijmans, J. Starett, J. Wales, N. Signore, A. Springer, M. Campbell, K. L. 2016-11-09 doi:10.1101/086819 Cold Spring Harbor Laboratory Press 2016-11-09 <![CDATA[ Statistical properties of simple random-effects models for genetic heritability ]]> https://biorxiv.org/content/10.1101/087304v1?rss=1 Steinsaltz, D. Dahl, A. Wachter, K. W. 2016-11-14 doi:10.1101/087304 Cold Spring Harbor Laboratory Press 2016-11-14 <![CDATA[ Time-resolved proteomics vs. ribosome profiling reveals translation dynamics under stress ]]> https://biorxiv.org/content/10.1101/087486v1?rss=1 Liu, T.-Y. Huang, H. H. Wheeler, D. Wells, J. A. Song, Y. S. Wiita, A. P. 2016-11-14 doi:10.1101/087486 Cold Spring Harbor Laboratory Press 2016-11-14 <![CDATA[ Persistent neural activity encoding real-time presence of visual stimuli decays along the ventral stream ]]> https://biorxiv.org/content/10.1101/088021v1?rss=1 Gerber, E. M. Golan, T. Knight, R. T. Deouell, L. Y. 2016-11-16 doi:10.1101/088021 Cold Spring Harbor Laboratory Press 2016-11-16 <![CDATA[ The Semantics of Adjective Noun Phrases in the Human Brain ]]> https://biorxiv.org/content/10.1101/089615v1?rss=1 Fyshe, A. Sudre, G. Wehbe, L. Rafidi, N. Mitchell, T. M. 2016-11-25 doi:10.1101/089615 Cold Spring Harbor Laboratory Press 2016-11-25 <![CDATA[ Identification and quantitative analysis of the major determinants of translation elongation rate variation ]]> https://biorxiv.org/content/10.1101/090837v1?rss=1 Dao Duc, K. Song, Y. S. 2016-12-01 doi:10.1101/090837 Cold Spring Harbor Laboratory Press 2016-12-01 <![CDATA[ Discovery of an autoimmunity-associated IL2RA enhancer by unbiased targeting of transcriptional activation ]]> https://biorxiv.org/content/10.1101/091843v1?rss=1 100 kilobases) surrounding two key autoimmunity risk loci, CD69 and IL2RA (interleukin-2 receptor alpha; CD25). We identified several CRISPRa responsive elements (CaREs) with stimulation-dependent enhancer activity, including an IL2RA enhancer that harbors an autoimmunity risk variant. Using engineered mouse models and genome editing of human primary T cells, we found that sequence perturbation of the disease-associated IL2RA enhancer does not block IL2RA expression, but rather delays the timing of gene activation in response to specific extracellular signals. This work develops an approach to rapidly identify functional enhancers within non-coding regions, decodes a key human autoimmunity association, and suggests a general mechanism by which genetic variation can cause immune dysfunction. ]]> Simeonov, D. R. Gowen, B. G. Boontanrart, M. Roth, T. Lee, Y. Chan, A. Nguyen, M. L. Gate, R. E. Subramaniam, M. Woo, J. M. Mitros, T. Ray, G. J. Bray, N. L. Curie, G. L. Naddaf, N. Boyer, E. Van Gool, F. Schumann, K. Daly, M. J. Fahr, K. K. Ye, C. Bluestone, J. A. Anderson, M. S. Corn, J. E. Marson, A. 2016-12-05 doi:10.1101/091843 Cold Spring Harbor Laboratory Press 2016-12-05 <![CDATA[ A Resource for Assessing Information Processing in the Developing Brain Using EEG and Eye Tracking ]]> https://biorxiv.org/content/10.1101/092213v1?rss=1 Langer, N. Ho, E. J. Alexander, L. M. Xu, H. Y. Jozanovic, R. K. Henin, S. Cohen, S. Marcelle, E. T. Parra, L. C. Milham, M. P. Kelly, S. P. 2016-12-07 doi:10.1101/092213 Cold Spring Harbor Laboratory Press 2016-12-07 <![CDATA[ Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. ]]> https://biorxiv.org/content/10.1101/095349v1?rss=1 Baillie, J. K. Bretherick, A. Haley, C. Clohisey, S. Gray, A. Barret, J. Stahl, E. Tenesa, A. Andersson, R. Brown, J. B. Faulkner, G. Lizio, M. Schaefer, U. Daub, C. Itoh, M. Kondo, N. Lassmann, T. Kawai, J. IIBDGC Consortium, FANTOM5 Consortium, Bajic, V. B. Heutink, P. Rehli, M. Kawaji, H. Sandelin, A. Suzuki, H. Satsangi, J. Wells, C. Nir, H. Freeman, T. Hayashizaki, Y. Carninci, P. Forrest, A. R. Hume, D. A. 2016-12-19 doi:10.1101/095349 Cold Spring Harbor Laboratory Press 2016-12-19 <![CDATA[ Targeted degradation of CTCF decouples local insulation of chromosome domains from higher-order genomic compartmentalization ]]> https://biorxiv.org/content/10.1101/095802v1?rss=1 nView larger version (49K):norg.highwire.dtl.DTLVardef@79c6c5org.highwire.dtl.DTLVardef@e8e61forg.highwire.dtl.DTLVardef@5c2eedorg.highwire.dtl.DTLVardef@cf7f3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Nora, E. P. Goloborodko, A. Valton, A.-L. Gibcus, J. Uebsersohn, A. Abdennur, N. Dekker, J. Mirny, L. Bruneau, B. 2016-12-21 doi:10.1101/095802 Cold Spring Harbor Laboratory Press 2016-12-21 <![CDATA[ Mechanical interactions in bacterial colonies and the surfing probability of beneficial mutations ]]> https://biorxiv.org/content/10.1101/100099v1?rss=1 Farrell, F. F. Gralka, M. Hallatschek, O. Waclaw, B. 2017-01-13 doi:10.1101/100099 Cold Spring Harbor Laboratory Press 2017-01-13 <![CDATA[ The complex origins of strigolactone signalling in land plants ]]> https://biorxiv.org/content/10.1101/102715v1?rss=1 Bythell-Douglas, R. Rothfels, C. J. Stevenson, D. W. D. Graham, S. W. Wong, G. K.-S. Nelson, D. C. Bennett, T. 2017-01-24 doi:10.1101/102715 Cold Spring Harbor Laboratory Press 2017-01-24 <![CDATA[ Composite Likelihood Method for Inferring Local Pedigrees ]]> https://biorxiv.org/content/10.1101/106492v1?rss=1 Ko, A. Nielsen, R. 2017-02-07 doi:10.1101/106492 Cold Spring Harbor Laboratory Press 2017-02-07 <![CDATA[ Measuring changes in transmission of neglected tropical diseases, malaria, and enteric pathogens from quantitative antibody levels ]]> https://biorxiv.org/content/10.1101/106708v1?rss=1 Arnold, B. van der Laan, M. J. Hubbard, A. E. Steel, C. Kubofcik, J. Hamlin, K. L. Moss, D. M. Nutman, T. B. Priest, J. W. Lammie, P. J. 2017-02-07 doi:10.1101/106708 Cold Spring Harbor Laboratory Press 2017-02-07 <![CDATA[ Recovery of genomes from metagenomes via a dereplication, aggregation, and scoring strategy ]]> https://biorxiv.org/content/10.1101/107789v1?rss=1 Sieber, C. M. K. Probst, A. J. Sharrar, A. Thomas, B. C. Hess, M. Tringe, S. G. Banfield, J. F. 2017-02-11 doi:10.1101/107789 Cold Spring Harbor Laboratory Press 2017-02-11 <![CDATA[ Parsing propagule pressure: Simulated and experimental disentanglement of introduction size and number of introductions for colonizing individuals ]]> https://biorxiv.org/content/10.1101/108324v1?rss=1 Koontz, M. J. Oldfather, M. F. Melbourne, B. A. Hufbauer, R. A. 2017-02-17 doi:10.1101/108324 Cold Spring Harbor Laboratory Press 2017-02-17 <![CDATA[ COPII-coated membranes function as transport carriers of intracellular procollagen-1 ]]> https://biorxiv.org/content/10.1101/110700v1?rss=1 Gorur, A. Yuan, L. Kenny, S. J. Baba, S. Xu, K. Schekman, R. 2017-02-21 doi:10.1101/110700 Cold Spring Harbor Laboratory Press 2017-02-21 <![CDATA[ Super-resolution microscopy reveals the three-dimensional organization of meiotic chromosome axes in intact C. elegans tissue ]]> https://biorxiv.org/content/10.1101/112599v1?rss=1 Kohler, S. Wojcik, M. Xu, K. Dernburg, A. F. 2017-02-28 doi:10.1101/112599 Cold Spring Harbor Laboratory Press 2017-02-28 <![CDATA[ Bacterial Microtubules Exhibit Polarized Growth, Mixed-Polarity Bundling, and Destabilization by GTP Hydrolysis ]]> https://biorxiv.org/content/10.1101/112987v1?rss=1 Diaz Celis, C. D. Risca, V. I. Hurtado, F. Polka, J. K. Hansen, S. D. Maturana, D. Lagos, R. Mullins, R. D. Monasterio, O. 2017-03-02 doi:10.1101/112987 Cold Spring Harbor Laboratory Press 2017-03-02 <![CDATA[ The Junction Usage Model (JUM): A method for comprehensive annotation-free differential analysis of tissue-specific global alternative pre-mRNA splicing patterns ]]> https://biorxiv.org/content/10.1101/116863v1?rss=1 Wang, Q. Rio, D. 2017-03-14 doi:10.1101/116863 Cold Spring Harbor Laboratory Press 2017-03-14 <![CDATA[ Demographic compensation does not rescue populations at a trailing range edge ]]> https://biorxiv.org/content/10.1101/117606v1?rss=1 Sheth, S. N. Angert, A. L. 2017-03-17 doi:10.1101/117606 Cold Spring Harbor Laboratory Press 2017-03-17 <![CDATA[ The Human Cell Atlas ]]> https://biorxiv.org/content/10.1101/121202v1?rss=1 Regev, A. Teichmann, S. Lander, E. S. Amit, I. Benoist, C. Birney, E. Bodenmiller, B. Campbell, P. Carninci, P. Clatworthy, M. Clevers, H. Deplancke, B. Dunham, I. Eberwine, J. Eils, R. Enard, W. Farmer, A. Fugger, L. Gottgens, B. Hacohen, N. Haniffa, M. Hemberg, M. Kim, S. K. Klenerman, P. Kriegstein, A. Lein, E. Linnarsson, S. Lundeberg, J. Majumder, P. Marioni, J. Merad, M. Mhlanga, M. Nawijn, M. Netea, M. Nolan, G. Pe'er, D. Philipakis, A. Ponting, C. P. Quake, S. R. Reik, W. Rozenblatt-Rosen, O. Sanes, J. R. Satija, R. Shumacher, T. Shalek, A. K 2017-05-08 doi:10.1101/121202 Cold Spring Harbor Laboratory Press 2017-05-08 <![CDATA[ Biosynthesis of Isonitrile Lipopeptides by Conserved Non-ribosomal Peptide Synthetase Gene Clusters in Actinobacteria ]]> https://biorxiv.org/content/10.1101/121228v1?rss=1 Harris, N. C. Sato, M. Herman, N. A. Twigg, F. Cai, W. Liu, J. Downey, J. Khalaf, R. Martin, J. Koshino, H. Zhang, W. 2017-03-27 doi:10.1101/121228 Cold Spring Harbor Laboratory Press 2017-03-27 <![CDATA[ Should A Few Null Findings Falsify Prefrontal Theories Of Conscious Perception? ]]> https://biorxiv.org/content/10.1101/122267v1?rss=1 Odegaard, B. Knight, R. T. Lau, H. 2017-03-30 doi:10.1101/122267 Cold Spring Harbor Laboratory Press 2017-03-30 <![CDATA[ Nanoscale Manipulation Of Membrane Curvature For Probing Endocytosis In Live Cells ]]> https://biorxiv.org/content/10.1101/122275v1?rss=1 Zhao, W. Hanson, L. Lou, H.-Y. Akamatsu, M. Chowdary, P. Santoro, F. Marks, J. Grassart, A. Drubin, D. Cui, Y. Cui, B. 2017-03-30 doi:10.1101/122275 Cold Spring Harbor Laboratory Press 2017-03-30 <![CDATA[ A correlation analysis framework for localization-based super-resolution microscopy ]]> https://biorxiv.org/content/10.1101/125005v1?rss=1 Schnitzbauer, J. Wang, Y. Bakalar, M. Chen, B. Nuwal, T. Zhao, S. Huang, B. 2017-06-23 doi:10.1101/125005 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ ZINB-WaVE: A general and flexible method for signal extraction from single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/125112v1?rss=1 Risso, D. Perraudeau, F. Gribkova, S. Dudoit, S. Vert, J.-P. 2017-04-06 doi:10.1101/125112 Cold Spring Harbor Laboratory Press 2017-04-06 <![CDATA[ Genomic regression of claw keratin, taste receptor and light-associated genes inform biology and evolutionary origins of snakes ]]> https://biorxiv.org/content/10.1101/127654v1?rss=1 Emerling, C. A. 2017-04-15 doi:10.1101/127654 Cold Spring Harbor Laboratory Press 2017-04-15 <![CDATA[ Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics ]]> https://biorxiv.org/content/10.1101/128843v1?rss=1 Street, K. Risso, D. Fletcher, R. B. Das, D. Ngai, J. Yosef, N. Purdom, E. Dudoit, S. 2017-04-19 doi:10.1101/128843 Cold Spring Harbor Laboratory Press 2017-04-19 <![CDATA[ A chromatin extension model for insulator function based on comparison of high-resolution chromatin conformation capture and polytene banding maps ]]> https://biorxiv.org/content/10.1101/129577v1?rss=1 Stadler, M. R. Eisen, M. B. 2017-04-21 doi:10.1101/129577 Cold Spring Harbor Laboratory Press 2017-04-21 <![CDATA[ Disabling Cas9 by an anti-CRISPR DNA mimic ]]> https://biorxiv.org/content/10.1101/129627v1?rss=1 Shing, J. Jiang, F. Liu, J.-J. Bray, N. L. Rauch, B. J. Baik, S. H. Nogales, E. Bondy-Denomy, J. Corn, J. E. Doudna, J. A. 2017-04-22 doi:10.1101/129627 Cold Spring Harbor Laboratory Press 2017-04-22 <![CDATA[ A lncRNA/Lin28/Let7 Axis Coupled To DNA Methylation Fine Tunes The Dynamics Of A Cell State Transition ]]> https://biorxiv.org/content/10.1101/131110v1?rss=1 Li, M. A. Amaral, P. P. Cheung, P. Bergmann, J. H. Kinoshita, M. Kalkan, T. Ralser, M. Robson, S. von Meyenn, F. Paramor, M. Yang, F. Chen, C. Nichols, J. Spector, D. L. Kouzarides, T. He, L. Smith, A. 2017-04-26 doi:10.1101/131110 Cold Spring Harbor Laboratory Press 2017-04-26 <![CDATA[ Dense Bicoid Hubs Accentuate Binding along the Morphogen Gradient ]]> https://biorxiv.org/content/10.1101/133124v1?rss=1 Mir, M. Reimer, A. Haines, J. E. Li, X.-Y. Stadler, M. Garcia, H. Eisen, M. E. Darzacq, X. 2017-05-01 doi:10.1101/133124 Cold Spring Harbor Laboratory Press 2017-05-01 <![CDATA[ Fronto-Parietal Interactions With Task-Evoked Functional Connectivity During Cognitive Control ]]> https://biorxiv.org/content/10.1101/133611v1?rss=1 Hwang, K. Shine, J. M. D'Esposito, M. 2017-05-03 doi:10.1101/133611 Cold Spring Harbor Laboratory Press 2017-05-03 <![CDATA[ CRISPR-Cas9 Genome Editing In Human Cells Works Via The Fanconi Anemia Pathway ]]> https://biorxiv.org/content/10.1101/136028v1?rss=1 20%) incorporation of ssODN sequences into the break site. This process is commonly referred to as homology directed repair (HDR) and here referred to as single stranded template repair (SSTR) to distinguish it from repair using a double stranded DNA donor (dsDonor). The high efficacy of SSTR makes it a promising avenue for the treatment of genetic diseases1,2, but the genetic basis of SSTR editing is still unclear, leaving its use a mostly empiric process. To determine the pathways underlying SSTR in human cells, we developed a coupled knockdown-editing screening system capable of interrogating multiple editing outcomes in the context of thousands of individual gene knockdowns. Unexpectedly, we found that SSTR requires multiple components of the Fanconi Anemia (FA) repair pathway, but does not require Rad51-mediated homologous recombination, distinguishing SSTR from repair using dsDonors. Knockdown of FA genes impacts SSTR without altering break repair by non-homologous end joining (NHEJ) in multiple human cell lines and in neonatal dermal fibroblasts. Our results establish an unanticipated and central role for the FA pathway in templated repair from single stranded DNA by human cells. Therapeutic genome editing has been proposed to treat genetic disorders caused by deficiencies in DNA repair, including Fanconi Anemia. Our data imply that patient genotype and/or transcriptome profoundly impact the effectiveness of gene editing treatments and that adjuvant treatments to bias cells towards FA repair pathways could have considerable therapeutic value. ]]> Richardson, C. D. Kazane, K. R. Feng, S. J. Bray, N. L. Schaefer, A. J. Floor, S. Corn, J. 2017-05-09 doi:10.1101/136028 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ Analysis Of Interphase Node Proteins In Fission Yeast By Quantitative And Super Resolution Fluorescence Microscopy ]]> https://biorxiv.org/content/10.1101/137794v1?rss=1 Akamatsu, M. Lin, Y. Bewersdorf, J. Pollard, T. D. 2017-05-14 doi:10.1101/137794 Cold Spring Harbor Laboratory Press 2017-05-14 <![CDATA[ Consensus and conflict among ecological forecasts of Zika virus outbreaks in the United States ]]> https://biorxiv.org/content/10.1101/138396v1?rss=1 Carlson, C. J. Dougherty, E. Boots, M. Getz, W. Ryan, S. 2017-05-16 doi:10.1101/138396 Cold Spring Harbor Laboratory Press 2017-05-16 <![CDATA[ A thermostable Cas9 with increased lifetime in human plasma ]]> https://biorxiv.org/content/10.1101/138867v1?rss=1 Harrington, L. Paez-Espino, D. Chen, J. S. Ma, E. Staahl, B. T. Kyrpides, N. C. Doudna, J. A. 2017-05-16 doi:10.1101/138867 Cold Spring Harbor Laboratory Press 2017-05-16 <![CDATA[ An Aphrodisiac Produced By Vibrio fischeri Stimulates Mating In The Closest Living Relatives Of Animals ]]> https://biorxiv.org/content/10.1101/139022v1?rss=1 Woznica, A. Gerdt, J. P. Hulett, R. Clardy, J. King, N. 2017-05-17 doi:10.1101/139022 Cold Spring Harbor Laboratory Press 2017-05-17 <![CDATA[ The Cerebellum Does More Than Sensory-Prediction-Error-Based Learning In Sensorimotor Adaptation Tasks ]]> https://biorxiv.org/content/10.1101/139337v1?rss=1 Butcher, P. A. Ivry, R. Kuo, S.-H. Rydz, D. Krakauer, J. W. Taylor, J. A. 2017-05-17 doi:10.1101/139337 Cold Spring Harbor Laboratory Press 2017-05-17 <![CDATA[ The industrial anaerobe Clostridium acetobutylicum uses polyketides to regulate butanol production and differentiation ]]> https://biorxiv.org/content/10.1101/139873v1?rss=1 Herman, N. Kim, S.-J. Li, J. S. Cai, W. Koshino, H. Zhang, W. 2017-05-18 doi:10.1101/139873 Cold Spring Harbor Laboratory Press 2017-05-18 <![CDATA[ Thirty-five experimental fisheries reveal the mechanisms of selection ]]> https://biorxiv.org/content/10.1101/141259v1?rss=1 Nussle, S. Hendry, A. P. Knapp, R. Bogan, M. Sturrock, A. Carlson, S. 2017-05-26 doi:10.1101/141259 Cold Spring Harbor Laboratory Press 2017-05-26 <![CDATA[ Association Mapping From Sequencing Reads Using K-mers ]]> https://biorxiv.org/content/10.1101/141267v1?rss=1 Rahman, A. Hallgrimsdottir, I. Eisen, M. B. Pachter, L. 2017-05-23 doi:10.1101/141267 Cold Spring Harbor Laboratory Press 2017-05-23 <![CDATA[ Experimenting with reproducibility in bioinformatics ]]> https://biorxiv.org/content/10.1101/143503v1?rss=1 Kim, Y.-M. Poline, J.-B. Dumas, G. 2017-06-20 doi:10.1101/143503 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Human PRDM9 Can Bind And Activate Promoters, And Other Zinc-Finger Proteins Associate With Reduced Recombination In cis ]]> https://biorxiv.org/content/10.1101/144295v1?rss=1 Altemose, N. Noor, N. Bitoun, E. Tumian, A. Imbeault, M. Chapman, J. R. Aricescu, A. R. Myers, S. R. 2017-05-31 doi:10.1101/144295 Cold Spring Harbor Laboratory Press 2017-05-31 <![CDATA[ On The Number Of Siblings And p-th Cousins In A Large Population Sample ]]> https://biorxiv.org/content/10.1101/145599v1?rss=1 Shchur, V. Nielsen, R. 2017-06-02 doi:10.1101/145599 Cold Spring Harbor Laboratory Press 2017-06-02 <![CDATA[ Theoretical quantification of interference in the TASEP: Application to mRNA translation shows near-optimality of termination rates ]]> https://biorxiv.org/content/10.1101/147017v1?rss=1 Dao Duc, K. Saleem, Z. H. Song, Y. S. 2017-06-07 doi:10.1101/147017 Cold Spring Harbor Laboratory Press 2017-06-07 <![CDATA[ NuMA Targets Dynein to Microtubule Minus-Ends at Mitosis ]]> https://biorxiv.org/content/10.1101/148692v1?rss=1 Hueschen, C. Kenny, S. J. Xu, K. Dumont, S. 2017-06-11 doi:10.1101/148692 Cold Spring Harbor Laboratory Press 2017-06-11 <![CDATA[ Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo ]]> https://biorxiv.org/content/10.1101/149344v1?rss=1 Stadler, M. R. Haines, J. E. Eisen, M. B. 2017-06-13 doi:10.1101/149344 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ The SMuSh pathway is essential for survival during growth-induced compressive mechanical stress ]]> https://biorxiv.org/content/10.1101/150789v1?rss=1 Delarue, M. Poterewicz, G. Hoxha, O. Choi, J. Yoo, W. Kayser, J. Holt, L. Hallatschek, O. 2017-06-16 doi:10.1101/150789 Cold Spring Harbor Laboratory Press 2017-06-16 <![CDATA[ Genome Architecture Leads a Bifurcation in Cell Identity ]]> https://biorxiv.org/content/10.1101/151555v1?rss=1 Liu, S. Chen, H. Ronquist, S. Seaman, L. Ceglia, N. Meixner, W. Muir, L. A. Chen, P.-Y. Higgins, G. Baldi, P. Smale, S. Hero, A. Rajapakse, I. 2017-06-18 doi:10.1101/151555 Cold Spring Harbor Laboratory Press 2017-06-18 <![CDATA[ Neurodegeneration-associated mutant TREM2 proteins abortively cycle between the ER and ER-Golgi intermediate compartment ]]> https://biorxiv.org/content/10.1101/154997v1?rss=1 Sirkis, D. W. Aparicio, R. E. Schekman, R. 2017-06-23 doi:10.1101/154997 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ Resident Macrophages are Locally Programmed for Silent Clearance of Apoptotic Cells ]]> https://biorxiv.org/content/10.1101/155010v1?rss=1 Roberts, A. W. Lee, B. L. Deguine, J. John, S. Shlomchik, M. Barton, G. M. 2017-06-24 doi:10.1101/155010 Cold Spring Harbor Laboratory Press 2017-06-24 <![CDATA[ Worldwide genetic variation of the IGHV and TRBV immune receptor gene families in humans ]]> https://biorxiv.org/content/10.1101/155440v1?rss=1 Luo, S. Yu, J. A. Li, H. Song, Y. S. 2017-06-26 doi:10.1101/155440 Cold Spring Harbor Laboratory Press 2017-06-26 <![CDATA[ The Drosophila Y chromosome affects heterochromatin integrity genome-wide ]]> https://biorxiv.org/content/10.1101/156000v1?rss=1 Brown, E. Bachtrog, D. 2017-06-26 doi:10.1101/156000 Cold Spring Harbor Laboratory Press 2017-06-26 <![CDATA[ The Y chromosome contributes to sex-specific aging in Drosophila ]]> https://biorxiv.org/content/10.1101/156042v1?rss=1 Brown, E. Bachtrog, D. 2017-06-26 doi:10.1101/156042 Cold Spring Harbor Laboratory Press 2017-06-26 <![CDATA[ CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing ]]> https://biorxiv.org/content/10.1101/156125v1?rss=1 Moreno-Mateos, M. A. Fernandez, J. P. Rouet, R. Lane, M. A. Vejnar, C. E. Mis, E. Khokha, M. K. Doudna, J. A. Giraldez, A. J. 2017-06-26 doi:10.1101/156125 Cold Spring Harbor Laboratory Press 2017-06-26 <![CDATA[ Widespread translational remodeling during human neuronal differentiation ]]> https://biorxiv.org/content/10.1101/156190v1?rss=1 Blair, J. D. Hockemeyer, D. Doudna, J. A. Bateup, H. S. Floor, S. N. 2017-06-26 doi:10.1101/156190 Cold Spring Harbor Laboratory Press 2017-06-26 <![CDATA[ Habitat preference of an herbivore shapes the habitat distribution of its host plant ]]> https://biorxiv.org/content/10.1101/156240v1?rss=1 Alexandre, N. M. Humphrery, P. T. Frazier, J. Gloss, A. D. Lee, J. Affeldt, H. A. Whiteman, N. K. 2017-06-27 doi:10.1101/156240 Cold Spring Harbor Laboratory Press 2017-06-27 <![CDATA[ Dynamics of the IFT Machinery at the Ciliary Tip ]]> https://biorxiv.org/content/10.1101/156844v1?rss=1 Chien, A. Shih, S. M. Bower, R. Tritschler, D. Porter, M. E. Yildiz, A. 2017-06-28 doi:10.1101/156844 Cold Spring Harbor Laboratory Press 2017-06-28 <![CDATA[ The role of traction in membrane curvature generation ]]> https://biorxiv.org/content/10.1101/157313v1?rss=1 Alimohamadi, H. Vasan, R. Hassinger, J. E. Stachowiak, J. Rangamani, P. 2017-06-29 doi:10.1101/157313 Cold Spring Harbor Laboratory Press 2017-06-29 <![CDATA[ Enhanced proofreading governs CRISPR-Cas9 targeting accuracy ]]> https://biorxiv.org/content/10.1101/160036v1?rss=1 Chen, J. S. Dagdas, Y. S. Kleinstiver, B. P. Welch, M. M. Harrington, L. B. Sternberg, S. H. Joung, J. K. Yildiz, A. Doudna, J. A. 2017-07-06 doi:10.1101/160036 Cold Spring Harbor Laboratory Press 2017-07-06 <![CDATA[ A broad role for YBX1 in defining the small non-coding RNA composition of exosomes ]]> https://biorxiv.org/content/10.1101/160556v1?rss=1 Shurtleff, M. J. Yao, J. Qin, Y. Nottingham, R. M. Temoche-Diaz, M. Schekman, R. Lambowitz, A. 2017-07-07 doi:10.1101/160556 Cold Spring Harbor Laboratory Press 2017-07-07 <![CDATA[ The origin of animal multicellularity and cell differentiation ]]> https://biorxiv.org/content/10.1101/161695v1?rss=1 Brunet, T. King, N. 2017-07-12 doi:10.1101/161695 Cold Spring Harbor Laboratory Press 2017-07-12 <![CDATA[ Synthetically Engineered Medea Gene Drive System in the Worldwide Crop Pest, D. suzukii ]]> https://biorxiv.org/content/10.1101/162255v1?rss=1 Buchman, A. Marshall, J. Ostrovski, D. Yang, T. Akbari, O. S. 2017-07-11 doi:10.1101/162255 Cold Spring Harbor Laboratory Press 2017-07-11 <![CDATA[ Spores and soil from six sides: interdisciplinarity and the environmental biology of anthrax (Bacillus anthracis) ]]> https://biorxiv.org/content/10.1101/165548v1?rss=1 Carlson, C. J. Getz, W. Kausrud, K. Cizauskas, C. Blackburn, J. Bustos Carrillo, F. A. Colwell, R. Easterday, W. R. Ganz, H. Kamath, P. Okstad, O. A. Turner, W. Kolsto, A.-B. Stenseth, N. C. 2017-07-20 doi:10.1101/165548 Cold Spring Harbor Laboratory Press 2017-07-20 <![CDATA[ Fusion detection and quantification by pseudoalignment ]]> https://biorxiv.org/content/10.1101/166322v1?rss=1 Melsted, P. Hateley, S. Joseph, I. C. Pimentel, H. Bray, N. L. Pachter, L. 2017-07-20 doi:10.1101/166322 Cold Spring Harbor Laboratory Press 2017-07-20 <![CDATA[ Dramatic expansion of microbial groups that shape the global sulfur cycle ]]> https://biorxiv.org/content/10.1101/166447v1?rss=1 Anantharaman, K. Jungbluth, S. P. Kantor, R. S. Lavy, A. Warren, L. A. Rappe, M. S. Thomas, B. C. Banfield, J. F. 2017-07-21 doi:10.1101/166447 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ Screening and directed evolution of transporters to improve xylodextrin utilization in the yeast Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/166678v1?rss=1 Zhang, C. Acosta-Sampson, L. Yu, V. Y. Cate, J. H. D. 2017-07-21 doi:10.1101/166678 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ Effective normalization for copy number variation in Hi-C data ]]> https://biorxiv.org/content/10.1101/167031v1?rss=1 Servant, N. Varoqaux, N. Heard, E. Vert, J.-P. Emmanuel, B. 2017-07-21 doi:10.1101/167031 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ Parasite mediated competition facilitates invasion ]]> https://biorxiv.org/content/10.1101/167254v1?rss=1 Yitbarek, S. 2017-07-24 doi:10.1101/167254 Cold Spring Harbor Laboratory Press 2017-07-24 <![CDATA[ Experience-dependent translational state defined by cell type-specific ribosome profiling ]]> https://biorxiv.org/content/10.1101/169425v1?rss=1 Eacker, S. M. Crawford, K. Brichta, L. Riessland, M. Ingolia, N. T. Greengard, P. Dawson, T. M. Dawson, V. L. 2017-07-28 doi:10.1101/169425 Cold Spring Harbor Laboratory Press 2017-07-28 <![CDATA[ Budding yeast Wpl1p regulates cohesin functions in cohesion, condensation and DNA repair by a common mechanism ]]> https://biorxiv.org/content/10.1101/169474v1?rss=1 Bloom, M. S. Guacci, V. Koshland, D. 2017-07-28 doi:10.1101/169474 Cold Spring Harbor Laboratory Press 2017-07-28 <![CDATA[ Identification of single pair of interneurons for bitter taste processing in the Drosophila brain ]]> https://biorxiv.org/content/10.1101/170464v1?rss=1 Bohra, A. A. Kallman, B. R. Reichert, H. R. VijayRaghavan, K. 2017-07-31 doi:10.1101/170464 Cold Spring Harbor Laboratory Press 2017-07-31 <![CDATA[ Detection of live mycobacteria with a solvatochromic trehalose probe for point-of-care tuberculosis diagnosis ]]> https://biorxiv.org/content/10.1101/171553v1?rss=1 700-fold fluorescence increase when transitioned from aqueous to hydrophobic environments. This enhancement occurs upon metabolic conversion of DMN-Tre to trehalose monomycolate and incorporation into the outer membrane. DMN-Tre labeling enabled the rapid, no-wash visualization of mycobacterial and corynebacterial species without nonspecific labeling of Gram-positive or -negative bacteria. DMN-Tre labeling was selective for live mycobacteria and was reduced by treatment with TB drugs. Lastly, DMN-Tre labeled Mtb in TB-positive sputum samples suggesting this operationally simple method may be deployable for TB diagnosis. ]]> Kamariza, M. Shieh, P. Rodriguez-Rivera, F. P. Ealand, C. S. Chu, B. Martinson, N. Kana, B. D. Bertozzi, C. R. 2017-08-02 doi:10.1101/171553 Cold Spring Harbor Laboratory Press 2017-08-02 <![CDATA[ A catch-bond drives stator mechanosensitivity in the Bacterial Flagellar Motor ]]> https://biorxiv.org/content/10.1101/174292v1?rss=1 Nord, A. L. Gachon, E. Perez-Carrasco, R. Nirody, J. A. Barducci, A. Berry, R. M. Pedaci, F. 2017-08-09 doi:10.1101/174292 Cold Spring Harbor Laboratory Press 2017-08-09 <![CDATA[ A nutrient-dependent division antagonist is regulated post-translationally by the Clp proteases in Bacillus subtilis ]]> https://biorxiv.org/content/10.1101/176222v1?rss=1 Hill, N. S. Zuke, J. D. Buske, P. J. Chien, A.-C. Levin, P. A. 2017-08-14 doi:10.1101/176222 Cold Spring Harbor Laboratory Press 2017-08-14 <![CDATA[ Modeling the emergence of antibiotic resistance in the environment: an analytical solution for the minimum selection concentration ]]> https://biorxiv.org/content/10.1101/176289v1?rss=1 Greenfield, B. K. Shaked, S. Marrs, C. F. Nelson, P. Raxter, I. Xi, C. McKone, T. E. Jolliet, O. 2017-08-15 doi:10.1101/176289 Cold Spring Harbor Laboratory Press 2017-08-15 <![CDATA[ Enhancer connectome in primary human cells reveals target genes of disease-associated DNA elements ]]> https://biorxiv.org/content/10.1101/178269v1?rss=1 Mumbach, M. R. Satpathy, A. T. Boyle, E. A. Dai, C. Gowen, B. G. Cho, S. W. Nguyen, M. L. Rubin, A. J. Granja, J. M. Kazane, K. R. Wei, Y. Nguyen, T. Greenside, P. G. Corces, M. R. Tycko, J. Simeonov, D. R. Suliman, N. Li, R. Xu, J. Flynn, R. A. Kundaje, A. Khavari, P. A. Marson, A. Corn, J. E. Quertermous, T. Greenleaf, W. J. Chang, H. Y. 2017-08-26 doi:10.1101/178269 Cold Spring Harbor Laboratory Press 2017-08-26 <![CDATA[ Behavioral and neural indices of affective coloring for neutral social stimuli ]]> https://biorxiv.org/content/10.1101/178384v1?rss=1 Grupe, D. W. Schaefer, S. M. Lapate, R. C. Schoen, A. J. Gresham, L. K. Mumford, J. A. Davidson, R. J. 2017-08-20 doi:10.1101/178384 Cold Spring Harbor Laboratory Press 2017-08-20 <![CDATA[ Role for Ribosome-Associated Complex and Stress-Seventy subfamily B (RAC-Ssb) in integral membrane protein translation ]]> https://biorxiv.org/content/10.1101/179564v1?rss=1 Acosta-Sampson, L. Döring, K. Lin, Y. Yu, V. Bukau, B. Kramer, G. Cate, J. 2017-08-22 doi:10.1101/179564 Cold Spring Harbor Laboratory Press 2017-08-22 <![CDATA[ The BMP2/4 ortholog Dpp functions as an inter-organ signal that regulates developmental timing in Drosophila ]]> https://biorxiv.org/content/10.1101/180562v1?rss=1 Setiawan, L. Woods, A. L. Hariharan, I. K. 2017-08-24 doi:10.1101/180562 Cold Spring Harbor Laboratory Press 2017-08-24 <![CDATA[ Selection-like biases emerge in population models with recurrent jackpot events ]]> https://biorxiv.org/content/10.1101/182519v1?rss=1 nView larger version (16K):norg.highwire.dtl.DTLVardef@d391e7org.highwire.dtl.DTLVardef@ff4eaorg.highwire.dtl.DTLVardef@198495aorg.highwire.dtl.DTLVardef@f7b58e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFIG. 1:C_FLOATNO A) Illustration of mutational jackpot events, first studied by Luria and Delbriick. Consider the growth of a well-mixed population of microbes starting from a single cell (ignore death). A mutation that occurs in the jth cell division will have a final frequency of about {approx} 1/j (j = 4 in the illustration) and thus a "family size" of u = N/j. Hence, the probability Pr[U > u] to reach an even larger family size U is equal to the probability {approx} j/N = 1/u that the mutation occurs prior to the nth cell division. The probability density to acquire a family size u therefore exhibits a power law tail p(u) {propto} u-2. (Our argument ignores the stochasticity in cell division events, which however does not change the power law exponent.) B) The blue line indicates the probability Pr[U > u] that the family size U of a mutation is larger than u. The largest family size u* in a sample of N jackpot events should typically be of order N because the probability of sampling an even larger event is 1/n (dashed lines). A typical n-sample, therefore, has a mean family size of order log(n), which is obtained upon truncating the family size distribution at u*. It turns out that this effect generates a selection-like bias favoring majority alleles, which is compensated by rare sampling events that favor minority alleles.nnC_FIGnnWhile extensions of the Wright-Fisher diffusion process to capture skewed offspring numbers have been formally constructed [2, 3, 14, 20], also including selection and mutations [1, 10, 11, 16, 18], we still lack explicit finite time predictions for the probability distribution of allele frequency trajectories. Our goal here is to fill this gap for the particular case of the Luria-Delbriick jackpot distribution, by characterizing the allele frequency process in such a way that it can be easily generalized, intuitively understood and integrated in time. ]]> Hallatschek, O. 2017-08-30 doi:10.1101/182519 Cold Spring Harbor Laboratory Press 2017-08-30 <![CDATA[ Water relations of Calycanthus flowers: hydraulic conductance, capacitance, and embolism resistance ]]> https://biorxiv.org/content/10.1101/182915v1?rss=1 Roddy, A. B. Simonin, K. A. McCulloh, K. A. Brodersen, C. R. Dawson, T. E. 2017-08-31 doi:10.1101/182915 Cold Spring Harbor Laboratory Press 2017-08-31 <![CDATA[ Neither pulled nor pushed: Genetic drift and front wandering uncover a new class of reaction-diffusion waves ]]> https://biorxiv.org/content/10.1101/183806v1?rss=1 Birzu, G. Hallatschek, O. Korolev, K. S. 2017-09-03 doi:10.1101/183806 Cold Spring Harbor Laboratory Press 2017-09-03 <![CDATA[ Within and across-trial dynamics of human EEG reveal cooperative interplay between reinforcement learning and working memory ]]> https://biorxiv.org/content/10.1101/184812v1?rss=1 Collins, A. Frank, M. 2017-09-05 doi:10.1101/184812 Cold Spring Harbor Laboratory Press 2017-09-05 <![CDATA[ Machine learning leveraging genomes from metagenomes identifies influential antibiotic resistance genes in the infant gut microbiome ]]> https://biorxiv.org/content/10.1101/185348v1?rss=1 Rahman, S. F. Olm, M. R. Morowitz, M. J. Banfield, J. F. 2017-09-07 doi:10.1101/185348 Cold Spring Harbor Laboratory Press 2017-09-07 <![CDATA[ Serial dependence is absent at the time of perception but increases in visual working memory ]]> https://biorxiv.org/content/10.1101/187666v1?rss=1 Bliss, D. P. Sun, J. J. D'Esposito, M. 2017-09-12 doi:10.1101/187666 Cold Spring Harbor Laboratory Press 2017-09-12 <![CDATA[ The FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis ]]> https://biorxiv.org/content/10.1101/187674v1?rss=1 Frost, J. Kim, M. Y. Park, G.-T. Hsieh, P.-H. Nakamura, M. Lin, S. Yoo, H. Choi, J. Ikeda, Y. Kinoshita, T. Choi, Y. Zilberman, D. Fischer, R. L. 2017-09-12 doi:10.1101/187674 Cold Spring Harbor Laboratory Press 2017-09-12 <![CDATA[ Controller for microfluidic large-scale integration ]]> https://biorxiv.org/content/10.1101/188615v1?rss=1 White, J. Streets, A. M. 2017-09-14 doi:10.1101/188615 Cold Spring Harbor Laboratory Press 2017-09-14 <![CDATA[ Invariant errors reveal limitations in motor correction rather than constraints on error sensitivity ]]> https://biorxiv.org/content/10.1101/189597v1?rss=1 Kim, H. Morehead, J. R. Parvin, D. Moazzezi, R. Ivry, R. 2017-09-15 doi:10.1101/189597 Cold Spring Harbor Laboratory Press 2017-09-15 <![CDATA[ Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides ]]> https://biorxiv.org/content/10.1101/190546v1?rss=1 Coradetti, S. Pinel, D. Geiselman, G. Ito, M. Mondo, S. Reilly, M. Cheng, Y.-F. Bauer, S. Grigoriev, I. Gladden, J. Simmons, B. Brem, R. Arkin, A. Skerker, J. 2017-09-19 doi:10.1101/190546 Cold Spring Harbor Laboratory Press 2017-09-19 <![CDATA[ RNA binding and HEPN nuclease activation are decoupled in CRISPR-Cas13a ]]> https://biorxiv.org/content/10.1101/190603v1?rss=1 Tambe, A. East-Seletsky, A. Knott, G. J. Doudna, J. A. O'Connell, M. R. 2017-09-19 doi:10.1101/190603 Cold Spring Harbor Laboratory Press 2017-09-19 <![CDATA[ Spillover effects of a combined water, sanitation, and handwashing intervention in rural Bangladesh: a randomized controlled trial ]]> https://biorxiv.org/content/10.1101/191726v1?rss=1 Benjamin-Chung, J. Amin, N. Ercumen, A. Arnold, B. F. Hubbard, A. E. Unicomb, L. Rahman, M. Luby, S. P. Colford, J. M. 2017-09-22 doi:10.1101/191726 Cold Spring Harbor Laboratory Press 2017-09-22 <![CDATA[ The neurobiology of agrammatic sentence comprehension: a lesion study ]]> https://biorxiv.org/content/10.1101/192245v1?rss=1 80% on noncanonical sentences in the sentence-picture matching task. Patients with ATL damage (n=18) also did not exhibit an agrammatic comprehension pattern. Across our entire patient sample, the lesions of patients with agrammatic comprehension patterns in either task had maximal overlap in posterior superior temporal and inferior parietal regions. Using voxel-based lesion symptom mapping (VLSM), we find that lower performances on canonical and noncanonical sentences in each task are both associated with damage to a large left superior temporal-inferior parietal network including portions of the ATL, but not Brocas area. Notably however, response bias in plausibility judgments was significantly associated with damage to inferior frontal cortex, including gray and white matter in Brocas area, suggesting that the contribution of Brocas area to sentence comprehension may be related to task-related cognitive demands. ]]> Rogalsky, C. LaCroix, A. N. Chen, K.-H. Anderson, S. W. Damasio, H. Love, T. Hickok, G. 2017-09-22 doi:10.1101/192245 Cold Spring Harbor Laboratory Press 2017-09-22 <![CDATA[ Spatially uniform establishment of chromatin accessibility in the early Drosophila embryo ]]> https://biorxiv.org/content/10.1101/195073v1?rss=1 Haines, J. E. Eisen, M. B. 2017-09-27 doi:10.1101/195073 Cold Spring Harbor Laboratory Press 2017-09-27 <![CDATA[ Force dependence of filopodia adhesion: involvement of myosin II and formins ]]> https://biorxiv.org/content/10.1101/195420v1?rss=1 Alieva, N. O. Efremov, A. K. Hu, S. Oh, D. Chen, Z. Natarajan, M. Ong, H. T. Jegou, A. Romet-Lemonne, G. Groves, J. T. Sheetz, M. P. Yan, J. Bershadsky, A. D. 2017-09-28 doi:10.1101/195420 Cold Spring Harbor Laboratory Press 2017-09-28 <![CDATA[ Brief targeted memory reactivation during the awake state enhances memory stability and benefits the weakest memories ]]> https://biorxiv.org/content/10.1101/196436v1?rss=1 Tambini, A. Berners-Lee, A. Davachi, L. 2017-09-30 doi:10.1101/196436 Cold Spring Harbor Laboratory Press 2017-09-30 <![CDATA[ Rice paddy Nitrospirae encode and express genes related to sulfate respiration: proposal of the new genus Candidatus Sulfobium ]]> https://biorxiv.org/content/10.1101/196774v1?rss=1 Zecchin, S. Mueller, R. C. Seifert, J. Stingl, U. Anantharaman, K. van Bergen, M. Cavalca, L. Pester, M. 2017-10-01 doi:10.1101/196774 Cold Spring Harbor Laboratory Press 2017-10-01 <![CDATA[ Cross-task contributions of fronto-basal ganglia circuitry in response inhibition and conflict-induced slowing ]]> https://biorxiv.org/content/10.1101/199299v1?rss=1 Jahfari, S. Ridderinkhof, K. R. Collins, A. G. E. Knapen, T. Waldorp, L. Frank, M. J. 2017-10-06 doi:10.1101/199299 Cold Spring Harbor Laboratory Press 2017-10-06 <![CDATA[ Electron microscopic evidence that Aip1 disintegrates cofilin-saturated F-actin domains in the presence of coronin ]]> https://biorxiv.org/content/10.1101/199463v1?rss=1 Tang, V. W. Nadkarni, A. V. Brieher, W. 2017-10-06 doi:10.1101/199463 Cold Spring Harbor Laboratory Press 2017-10-06 <![CDATA[ An interventional Soylent diet increases the Bacteroidetes to Firmicutes ratio in human gut microbiome communities: a randomized controlled trial ]]> https://biorxiv.org/content/10.1101/200881v1?rss=1 Hsu, R. H. McCormick, D. M. Seitz, M. L. J. Lui, L. M. Rishi, H. S. Arkin, A. P. 2017-10-13 doi:10.1101/200881 Cold Spring Harbor Laboratory Press 2017-10-13 <![CDATA[ Identification and characterization of Gypsophila paniculata color morphs in Sleeping Bear Dunes National Lakeshore, MI, USA. ]]> https://biorxiv.org/content/10.1101/201350v1?rss=1 Yang, M. L. Rice, E. Leimbach-Mas, H. Partridge, C. G. 2017-10-11 doi:10.1101/201350 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ Accurate design of translational output by a neural network model of ribosome distribution ]]> https://biorxiv.org/content/10.1101/201517v1?rss=1 Tunney, R. J. McGlincy, N. J. Graham, M. E. Naddaf, N. Pachter, L. Lareau, L. 2017-10-11 doi:10.1101/201517 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ Context-specific control of the neural dynamics of temporal attention by the human cerebellum ]]> https://biorxiv.org/content/10.1101/2019.12.12.874677v1?rss=1 Breska, A. Ivry, R. B. 2019-12-12 doi:10.1101/2019.12.12.874677 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ STING controls Herpes Simplex Virus in vivo independent of type I interferon induction ]]> https://biorxiv.org/content/10.1101/2019.12.12.874792v1?rss=1 Yamashiro, L. H. Wilson, S. C. Morrison, H. M. Karalis, V. Chung, J.-Y. J. Chen, K. J. Bateup, H. Szpara, M. L. Lee, A. Y. Cox, J. S. Vance, R. 2019-12-13 doi:10.1101/2019.12.12.874792 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ Overprecision Increases Subsequent Surprise ]]> https://biorxiv.org/content/10.1101/2019.12.13.875203v1?rss=1 Schatz, D. Moore, D. A. 2019-12-13 doi:10.1101/2019.12.13.875203 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ Simulation and Analysis of Animal Movement Paths using Numerus Model Builder ]]> https://biorxiv.org/content/10.1101/2019.12.15.876987v1?rss=1 Getz, W. Vissat, L. L. Salter, R. 2019-12-15 doi:10.1101/2019.12.15.876987 Cold Spring Harbor Laboratory Press 2019-12-15 <![CDATA[ Loss of Tsc1 from striatal direct pathway neurons impairs endocannabinoid-LTD and enhances motor routine learning ]]> https://biorxiv.org/content/10.1101/2019.12.15.877126v1?rss=1 Benthall, K. N. Cording, K. R. Agopyan-Miu, A. H. C. W. Chen, E. Y. Bateup, H. S. 2019-12-16 doi:10.1101/2019.12.15.877126 Cold Spring Harbor Laboratory Press 2019-12-16 <![CDATA[ Association of Sonic Hedgehog with the Extracellular Matrix Requires its Putative Zinc-Peptidase Activity ]]> https://biorxiv.org/content/10.1101/2019.12.17.880039v1?rss=1 Jaegers, C. Roelink, H. 2019-12-17 doi:10.1101/2019.12.17.880039 Cold Spring Harbor Laboratory Press 2019-12-17 <![CDATA[ The rise of diversity in metabolic platforms across the Candidate Phyla Radiation ]]> https://biorxiv.org/content/10.1101/2019.12.18.881540v1?rss=1 Jaffe, A. L. Castelle, C. J. Matheus Carnevali, P. B. Gribaldo, S. Banfield, J. 2019-12-19 doi:10.1101/2019.12.18.881540 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Water lily (Nymphaea thermarum) draft genome reveals variable genomic signatures of ancient vascular cambium losses ]]> https://biorxiv.org/content/10.1101/2019.12.18.881573v1?rss=1 Povilus, R. A. DaCosta, J. M. Grassa, C. Satyaki, P. R. V. Moeglein, M. Jaenisch, J. Xi, Z. Mathews, S. Gehring, M. Davis, C. C. Friedman, W. E. 2019-12-19 doi:10.1101/2019.12.18.881573 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Visual experience instructs dendrite orientation but is not required for asymmetric wiring of the retinal direction selective circuit. ]]> https://biorxiv.org/content/10.1101/2019.12.19.873364v1?rss=1 El-Quessny, M. Maanum, K. Feller, M. B. 2019-12-19 doi:10.1101/2019.12.19.873364 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Coverage-dependent bias creates the appearance of binary splicing in single cells ]]> https://biorxiv.org/content/10.1101/2019.12.19.883256v1?rss=1 Buen Abad Najar, C. F. Yosef, N. Lareau, L. F. 2019-12-20 doi:10.1101/2019.12.19.883256 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Dynamics of T cell activation mediated by eIF3 interactions with T cell receptor mRNAs ]]> https://biorxiv.org/content/10.1101/2019.12.20.885558v1?rss=1 De Silva, D. Ferguson, L. Smith, B. E. Chin, G. H. Apathy, R. A. Roth, T. L. Kudla, M. Marson, A. Ingolia, N. T. Cate, J. H. D. 2019-12-21 doi:10.1101/2019.12.20.885558 Cold Spring Harbor Laboratory Press 2019-12-21 <![CDATA[ Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment ]]> https://biorxiv.org/content/10.1101/2019.12.21.886093v1?rss=1 Roodgar, M. Good, B. H. Garud, N. R. Martis, S. Avula, M. Zhou, W. Lancaster, S. Lee, H. Babveyh, A. Nesamoney, S. Pollard, K. S. Snyder, M. P. 2019-12-23 doi:10.1101/2019.12.21.886093 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ Alteration of the premature tRNA landscape by gammaherpesvirus infection ]]> https://biorxiv.org/content/10.1101/2019.12.22.886382v1?rss=1 Glaunsinger, B. Tucker, J. M. Schaller, A. M. Willis, I. M. 2019-12-23 doi:10.1101/2019.12.22.886382 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ Olfactory receptors tuned to volatile mustard oils in drosophilid flies ]]> https://biorxiv.org/content/10.1101/2019.12.27.889774v1?rss=1 Matsunaga, T. Reisenman, C. E. Goldman-Huertas, B. Brand, P. Miao, K. Suzuki, H. Ramirez, S. R. Whiteman, N. K. 2019-12-28 doi:10.1101/2019.12.27.889774 Cold Spring Harbor Laboratory Press 2019-12-28 <![CDATA[ The conserved herpesviral kinase ORF36 activates B2 retrotransposons during murine gammaherpesvirus infection ]]> https://biorxiv.org/content/10.1101/2020.01.06.895789v1?rss=1 Schaller, A. Tucker, J. Willis, I. M. Glaunsinger, B. A. 2020-01-06 doi:10.1101/2020.01.06.895789 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ Role of the transcriptional regulator SP140 in resistance to bacterial infections via repression of type I interferons ]]> https://biorxiv.org/content/10.1101/2020.01.07.897553v1?rss=1 Ji, D. X. Witt, K. C. Kotov, D. I. Margolis, S. R. Louie, A. Chen, K. J. Dhaliwal, H. S. Lee, A. Y. Zamboni, D. S. Kramnik, I. Portnoy, D. A. Darwin, K. H. Vance, R. E. 2020-01-08 doi:10.1101/2020.01.07.897553 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ The snowmelt niche differentiates three microbial life strategies that influence soil nitrogen availability during and after winter ]]> https://biorxiv.org/content/10.1101/2020.01.10.900621v1?rss=1 Sorensen, P. Beller, H. Bill, M. Bouskill, N. Hubbard, S. Karaoz, U. Polussa, A. Steltzer, H. Wang, S. Williams, K. Wu, Y. Brodie, E. 2020-01-10 doi:10.1101/2020.01.10.900621 Cold Spring Harbor Laboratory Press 2020-01-10 <![CDATA[ Ferrosomes are iron storage organelles formed by broadly conserved gene clusters in bacteria and archaea ]]> https://biorxiv.org/content/10.1101/2020.01.10.902569v1?rss=1 Grant, C. R. Komeili, A. 2020-01-11 doi:10.1101/2020.01.10.902569 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Canopy parkour: movement ecology of post-hatch dispersal in a gliding nymphal stick insect (Extatosoma tiaratum) ]]> https://biorxiv.org/content/10.1101/2020.01.12.903724v1?rss=1 100 m within 60 minutes. Navigation toward open canopies is underpinned by negative gravitaxis, positive phototaxis, and visual responses to vertically oriented contrast patterns. Nymphal E. tiaratum also use directed jumping to cross air gaps, and respond to tactile stimulation and potential threat with a self-dropping reflex, resulting aerial descent. Post-hatch dispersal in E. tiaratum thus consists of visually mediated displacement both on vegetational structures and in the air; within the latter context, gliding is then an effective mechanism enabling recovery after predator- and perturbation-induced descent. These results further support the importance of a diurnal niche, in addition to the arboreal spatial niche, in the evolution of gliding in wingless arboreal invertebrates. Summary statementTo effectively disperse into canopies, ground-hatched stick insects use gravity and visual cues to navigate during midday, jump to cross air gaps and respond to threat or perturbation with self-dropping. ]]> Zeng, Y. Chang, S. W. Williams, J. Nguyen, L. Y.-N. Tang, J. J. Naing, M. G. Dudley, R. 2020-01-14 doi:10.1101/2020.01.12.903724 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Protein Corona Composition and Dynamics on Carbon Nanotubes in Blood Plasma and Cerebrospinal Fluid ]]> https://biorxiv.org/content/10.1101/2020.01.13.905356v1?rss=1 Pinals, R. L. Yang, D. Rosenberg, D. J. Chaudhary, T. Crothers, A. R. Iavarone, A. T. Hammel, M. Landry, M. P. 2020-01-14 doi:10.1101/2020.01.13.905356 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber ]]> https://biorxiv.org/content/10.1101/2020.01.16.907998v1?rss=1 Hagen, L. H. Brooke, C. G. Shaw, C. Norbeck, A. D. Piao, H. Arntzen, M. O. Brewer, H. Copeland, A. Isern, N. Shukla, A. Roux, S. Lombard, V. Henrissat, B. O'Malley, M. Grigoriev, I. V. Tringe, S. Mackie, R. Pasa-Tolic, L. Pope, P. B. Hess, M. 2020-01-17 doi:10.1101/2020.01.16.907998 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ T cell responses induced by attenuated flavivirus vaccination are specific and show limited cross-reactivity with other flavivirus species. ]]> https://biorxiv.org/content/10.1101/2020.01.17.911099v1?rss=1 Grifoni, A. Voic, H. Dhanda, S. K. Kidd, C. K. Brien, J. D. Buus, S. Stryhn, A. Durbin, A. P. Whitehead, S. Diehl, S. A. de Silva, A. D. Balmaseda, A. Harris, E. Weiskopf, D. Sette, A. 2020-01-20 doi:10.1101/2020.01.17.911099 Cold Spring Harbor Laboratory Press 2020-01-20 <![CDATA[ The optoretinogram reveals how human photoreceptors deform in response to light ]]> https://biorxiv.org/content/10.1101/2020.01.18.911339v1?rss=1 Pandiyan, V. P. Bertelli, A. M. Kuchenbecker, J. Boyle, K. C. Ling, T. Park, B. H. Roorda, A. Palanker, D. Sabesan, R. 2020-01-18 doi:10.1101/2020.01.18.911339 Cold Spring Harbor Laboratory Press 2020-01-18 <![CDATA[ Mechanical competition triggered by innate immune signaling drives the collective extrusion of bacterially-infected epithelial cells ]]> https://biorxiv.org/content/10.1101/2020.01.22.915140v1?rss=1 Bastounis, E. E. Alcade, F. S. Radhakrishnan, P. Engstrom, P. Gomez Benito, M. J. Welch, M. Garcia-Aznar, J. M. Theriot, J. A. 2020-01-22 doi:10.1101/2020.01.22.915140 Cold Spring Harbor Laboratory Press 2020-01-22 <![CDATA[ Metabolic and Epigenomic Regulation of Th17/Treg Balance by the Polyamine Pathway ]]> https://biorxiv.org/content/10.1101/2020.01.23.911966v1?rss=1 Wang, C. Wagner, A. Fessler, J. Avila-Pacheco, J. Karminski, J. Thakore, P. Zaghouani, S. Pierce, K. Bod, L. Schnell, A. DeTomaso, D. Ron-Harel, N. Haigis, M. Puleston, D. Pearce, E. Soleimani, M. Sobel, R. Clish, C. Regev, A. Yosef, N. Kuchroo, V. 2020-01-23 doi:10.1101/2020.01.23.911966 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ In Silico Modeling of Metabolic State in Single Th17 Cells Reveals Novel Regulators of Inflammation and Autoimmunity ]]> https://biorxiv.org/content/10.1101/2020.01.23.912717v1?rss=1 Wagner, A. Wang, C. DeTomaso, D. Avila-Pacheco, J. Zaghouani, S. Fessler, J. Akama-Garren, E. Pierce, K. Ron-Harel, N. Douglas, V. P. Haigis, M. Sobel, R. A. Clish, C. Regev, A. Kuchroo, V. K. Yosef, N. 2020-01-24 doi:10.1101/2020.01.23.912717 Cold Spring Harbor Laboratory Press 2020-01-24 <![CDATA[ Natural selection maintains species despite widespread hybridization in the desert shrub Encelia ]]> https://biorxiv.org/content/10.1101/2020.01.23.917021v1?rss=1 DiVittorio, C. D. Singhal, S. Roddy, A. Zapata, F. Ackerly, D. D. Baldwin, B. G. Brodersen, C. R. Burquez, A. Fine, P. V. Padilla Flores, M. Solis, E. Morales-Villavicencio, J. Morales-Arce, D. Kyhos, D. W. 2020-01-24 doi:10.1101/2020.01.23.917021 Cold Spring Harbor Laboratory Press 2020-01-24 <![CDATA[ Polyamine Metabolism Regulates the T Cell Epigenome Through Hypusination ]]> https://biorxiv.org/content/10.1101/2020.01.24.918094v1?rss=1 Puleston, D. J. Baixauli, F. Sanin, D. E. Villa, M. Kabat, A. Kaminski, M. M. Weiss, H. Grzes, K. Flachsmann, L. J. Field, C. S. Stanckzak, M. Schimmelpfennig, L. Hassler, F. Wang, C. Yosef, N. Kuchroo, V. K. Musa, Y. Mittler, G. Buescher, J. M. Balabanov, S. Pearce, E. J. Green, D. R. Pearce, E. L. 2020-01-25 doi:10.1101/2020.01.24.918094 Cold Spring Harbor Laboratory Press 2020-01-25 <![CDATA[ Sulcal depth in medial ventral temporal cortex predicts the location of a place-selective region in macaques, children, and adults. ]]> https://biorxiv.org/content/10.1101/2020.01.27.921346v1?rss=1 Natu, V. S. Arcaro, M. Barnett, M. A. Gomez, J. Livingstone, M. Grill-Spector, K. Weiner, K. S. 2020-01-28 doi:10.1101/2020.01.27.921346 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ Quantitative dissection of transcription in development yields evidence for transcription factor-driven chromatin accessibility ]]> https://biorxiv.org/content/10.1101/2020.01.27.922054v1?rss=1 Eck, E. Liu, J. Kazemzadeh-Atoufi, M. Ghoreishi, S. Blythe, S. A. Garcia, H. 2020-01-28 doi:10.1101/2020.01.27.922054 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ The γ-herpesviral TATA box binding protein directly interacts with RNA Polymerase II to direct late gene transcription ]]> https://biorxiv.org/content/10.1101/2020.01.28.922526v1?rss=1 Castaneda, A. F. Didychuk, A. L. Louder, R. K. McCollum, C. O. Davis, Z. H. Nogales, E. Glaunsinger, B. 2020-01-29 doi:10.1101/2020.01.28.922526 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ Connecting actin polymer dynamics across multiple scales ]]> https://biorxiv.org/content/10.1101/2020.01.28.923698v1?rss=1 Copos, C. Bannish, B. Gasior, K. Pinals, R. L. Rostami, M. Dawes, A. 2020-01-29 doi:10.1101/2020.01.28.923698 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ A unified model of species abundance, genetic diversity, and functional diversity revealsthe mechanisms structuring ecological communities ]]> https://biorxiv.org/content/10.1101/2020.01.30.927236v1?rss=1 Overcast, I. Ruffley, M. Rosindell, J. Harmon, L. Borges, P. A. V. Emerson, B. C. Etienne, R. Gillespie, R. Krehenwinkel, H. Mahler, D. L. Massol, F. Parent, C. Patino, J. Peter, B. Week, B. Wagner, C. Hickerson, M. J. Rominger, A. 2020-01-31 doi:10.1101/2020.01.30.927236 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Targeting Reactive Aldehyde Detoxification by Aldehyde Dehydrogenase 2 (ALDH2) as a Treatment Strategy for Endometriosis ]]> https://biorxiv.org/content/10.1101/2020.01.30.927376v1?rss=1 McAllister, S. Sinharoy, P. Vasu, M. 2020-01-31 doi:10.1101/2020.01.30.927376 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ TOR coordinates nucleotide availability with ribosome biogenesis in plants ]]> https://biorxiv.org/content/10.1101/2020.01.30.927418v1?rss=1 Brunkard, J. O. Busche, M. Scarpin, M. R. Hnasko, R. 2020-01-31 doi:10.1101/2020.01.30.927418 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism ]]> https://biorxiv.org/content/10.1101/2020.01.30.927905v1?rss=1 Thompson, M. G. Blake-Hedges, J. M. Pereira, J. H. Hangasky, J. A. Belcher, M. S. Moore, W. M. Barajas, J. F. Cruz-Morales, P. Washington, L. J. Haushalter, R. W. Eiben, C. B. Liu, Y. Skyrud, W. Benites, V. T. Barnum, T. P. Baidoo, E. E. Scheller, H. Marletta, M. A. Shih, P. M. Adams, P. D. Keasling, J. D. 2020-01-31 doi:10.1101/2020.01.30.927905 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ A helical assembly of human ESCRT-I scaffolds reverse-topology membrane scission ]]> https://biorxiv.org/content/10.1101/2020.01.31.927327v1?rss=1 Flower, T. G. Takahashi, Y. Hudait, A. Rose, K. Tjahjono, N. Pak, A. Yokom, A. L. Liang, X. Wang, H.-G. Bouamr, F. Voth, G. A. Hurley, J. H. 2020-02-01 doi:10.1101/2020.01.31.927327 Cold Spring Harbor Laboratory Press 2020-02-01 <![CDATA[ Aridity drives coordinated trait shifts but not decreased trait variance across the geographic range of eight Australian trees ]]> https://biorxiv.org/content/10.1101/2020.02.03.932715v1?rss=1 Anderegg, L. D. L. Loy, X. Markham, I. P. Elmer, C. M. Hovenden, J. J. HilleRisLambers, J. Mayfield, M. M. 2020-02-04 doi:10.1101/2020.02.03.932715 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Genome-resolved metagenomics and detailed geochemical speciation analyses yield new insights into microbial mercury cycling in geothermal springs ]]> https://biorxiv.org/content/10.1101/2020.02.03.933291v1?rss=1 Gionfriddo, C. Stott, M. Power, J. F. Ogorek, J. M. Krabbenhoft, D. P. Wick, R. R. Holt, K. E. Chen, L.-X. Thomas, B. C. Banfield, J. F. Moreau, J. W. 2020-02-04 doi:10.1101/2020.02.03.933291 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Silicon modulates multi-layered defense against powdery mildew in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2020.02.05.935734v1?rss=1 Wang, L. Dong, M. Zhang, Q. Wu, Y. Hu, L. Parson, J. F. Eisenstein, E. Du, X. Xiao, S. 2020-02-06 doi:10.1101/2020.02.05.935734 Cold Spring Harbor Laboratory Press 2020-02-06 <![CDATA[ Septins coordinate cell wall integrity and lipid metabolism in a sphingolipid-dependent process ]]> https://biorxiv.org/content/10.1101/2020.02.09.940718v1?rss=1 Mela, A. Momany, M. 2020-02-10 doi:10.1101/2020.02.09.940718 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ SAR1 paralogs differ biochemically in assembly of the COPII coat ]]> https://biorxiv.org/content/10.1101/2020.02.09.940833v1?rss=1 Melville, D. B. Studer, S. Schekman, R. 2020-02-10 doi:10.1101/2020.02.09.940833 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ CRISPR-Cas12a exploits R-loop asymmetry to form double strand breaks ]]> https://biorxiv.org/content/10.1101/2020.02.10.937540v1?rss=1 Kuriyan, J. Doudna, J. A. Cofsky, J. C. Karandur, D. Huang, C. Witte, I. 2020-02-10 doi:10.1101/2020.02.10.937540 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ Large Freshwater Phages with the Potential to Augment Aerobic Methane Oxidation ]]> https://biorxiv.org/content/10.1101/2020.02.13.942896v1?rss=1 90%) and affiliate phylogenetically with those of coexisting bacterial methanotrophs, and their abundance patterns correlate with the abundances of these bacteria, supporting host-phage relationships. We suggest that phage PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contribute to growth on methane. Transcriptomics data from one system showed that the phage-associated pmoC genes are actively expressed in situ. Augmentation of bacterial methane oxidation by pmoC-phages during infection could modulate the efflux of this powerful greenhouse gas into the environment. ]]> Chen, L.-X. Meheust, R. Crits-Christoph, A. McMahon, K. D. Colenbrander Nelson, T. Warren, L. A. Banfield, J. 2020-02-14 doi:10.1101/2020.02.13.942896 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Machine Boss: Rapid Prototyping of Bioinformatic Automata ]]> https://biorxiv.org/content/10.1101/2020.02.13.945071v1?rss=1 Silvestre-Ryan, J. Wang, Y. Sharma, M. Lin, S. Shen, Y. Dider, S. Holmes, I. 2020-02-14 doi:10.1101/2020.02.13.945071 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ A Bayesian nonparametric approach to super-resolution single-molecule localization ]]> https://biorxiv.org/content/10.1101/2020.02.15.950873v1?rss=1 Gabitto, M. I. Marie-Nellie, H. Pakman, A. Pataki, A. Darzacq, X. Jordan, M. 2020-02-15 doi:10.1101/2020.02.15.950873 Cold Spring Harbor Laboratory Press 2020-02-15 <![CDATA[ The interaction of crossover formation and the dynamic architecture of the synaptonemal complex during meiosis ]]> https://biorxiv.org/content/10.1101/2020.02.16.947804v1?rss=1 Köhler, S. Wojcik, M. Xu, K. Dernburg, A. 2020-02-16 doi:10.1101/2020.02.16.947804 Cold Spring Harbor Laboratory Press 2020-02-16 <![CDATA[ Genome editing enables reverse genetics of multicellular development in the choanoflagellate Salpingoeca rosetta ]]> https://biorxiv.org/content/10.1101/2020.02.18.948406v1?rss=1 Booth, D. S. King, N. 2020-02-19 doi:10.1101/2020.02.18.948406 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ The intriguing dynamics of chromatin folding and assembly ]]> https://biorxiv.org/content/10.1101/2020.02.18.953398v1?rss=1 Yang, Z. Miao, W. Mofrad, M. R. K. 2020-02-19 doi:10.1101/2020.02.18.953398 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ μCB-seq: Microfluidic cell barcoding and sequencing for high-resolution imaging and sequencing of single cells ]]> https://biorxiv.org/content/10.1101/2020.02.18.954974v1?rss=1 Chen, T. N. Gupta, A. N. Zalavadia, M. D. Streets, A. 2020-02-20 doi:10.1101/2020.02.18.954974 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Temporal and state abstractions for efficient learning, transfer and composition in humans ]]> https://biorxiv.org/content/10.1101/2020.02.20.958587v1?rss=1 Xia, L. Collins, A. G. E. 2020-02-24 doi:10.1101/2020.02.20.958587 Cold Spring Harbor Laboratory Press 2020-02-24 <![CDATA[ Biased localization of actin binding proteins by actin filament conformation ]]> https://biorxiv.org/content/10.1101/2020.02.21.959791v1?rss=1 Harris, A. R. Jreij, P. Belardi, B. Bausch, A. Fletcher, D. A. 2020-02-22 doi:10.1101/2020.02.21.959791 Cold Spring Harbor Laboratory Press 2020-02-22 <![CDATA[ Divergence, gene flow and the origin of leapfrog geographic distributions: The history of color pattern variation in Phyllobates poison-dart frogs ]]> https://biorxiv.org/content/10.1101/2020.02.21.960005v1?rss=1 Marquez, R. Linderoth, T. P. Mejía-Vargas, D. Nielsen, R. Kronforst, M. R. Amezquita, A. 2020-02-25 doi:10.1101/2020.02.21.960005 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome ]]> https://biorxiv.org/content/10.1101/2020.02.21.960377v1?rss=1 Deng, S. Caddell, D. F. Yang, J. Dahlen, L. Washington, L. Coleman-Derr, D. 2020-02-23 doi:10.1101/2020.02.21.960377 Cold Spring Harbor Laboratory Press 2020-02-23 <![CDATA[ A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming ]]> https://biorxiv.org/content/10.1101/2020.02.22.960872v1?rss=1 Ning, D. Yuan, M. Wu, L. Zhang, Y. Guo, X. Zhou, X. Yang, Y. Arkin, A. P. Firestone, M. K. Zhou, J. 2020-02-25 doi:10.1101/2020.02.22.960872 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Lower Soil Carbon Loss Due to Persistent Microbial Adaptation to Climate Warming ]]> https://biorxiv.org/content/10.1101/2020.02.23.961300v1?rss=1 Guo, X. Gao, Q. Yuan, M. Wang, G. Zhou, X. Feng, J. Shi, Z. Hale, L. Wu, L. Zhou, A. Tian, R. Liu, F. Wu, B. Chen, L. Gyo Jung, C. Niu, S. Li, D. Xu, X. Jiang, L. Escalas, A. Wu, L. He, Z. Van Nostrand, J. Ning, D. Liu, X. Yang, Y. Schuur, E. Konstantinidis, K. T. Cole, J. R. Penton, C. R. Luo, Y. Tiedje, J. Zhou, J. 2020-02-25 doi:10.1101/2020.02.23.961300 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing ]]> https://biorxiv.org/content/10.1101/2020.02.25.956771v1?rss=1 Silvestre-Ryan, J. Holmes, I. 2020-02-25 doi:10.1101/2020.02.25.956771 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Measurement error and resolution in quantitative stable isotope probing: implications for experimental design ]]> https://biorxiv.org/content/10.1101/2020.02.25.965764v1?rss=1 Sieradzki, E. T. Koch, B. J. Greenlon, A. Sachdeva, R. Malmstrom, R. R. Mau, R. L. Blazewicz, S. J. Firestone, M. K. Hofmockel, K. Schwartz, E. Hungate, B. A. Pett-Ridge, J. 2020-02-26 doi:10.1101/2020.02.25.965764 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types ]]> https://biorxiv.org/content/10.1101/2020.02.29.970558v1?rss=1 Yao, Z. Liu, H. Xie, F. Fischer, S. Adkins, R. S. Aldrige, A. I. Ament, S. A. Bartlett, A. Behrens, M. M. Van den Berge, K. Bertagnolli, D. Biancalani, T. Booeshaghi, A. S. Corrada Bravo, H. Casper, T. Colantuoni, C. Crabtree, J. Creasy, H. Crichton, K. Crow, M. Dee, N. Dougherty, E. L. Doyle, W. I. Dudoit, S. Fang, R. Felix, V. Fong, O. Giglio, M. Goldy, J. Hawrylycz, M. Bezieux, H. R. d. Herb, B. R. Hertzano, R. Hou, X. Hu, Q. Huang, Z. J. Kancherla, J. Kroll, M. Lathia, K. Li, Y. E. Lucero, J. D. Luo, C. Mahurkar, A. McMillen, D. Nadaf, N. M. Ner 2020-03-02 doi:10.1101/2020.02.29.970558 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Improving replicability in single-cell RNA-Seq cell type discovery with Dune ]]> https://biorxiv.org/content/10.1101/2020.03.03.974220v1?rss=1 Roux de Bezieux, H. Street, K. Fischer, S. Van den Berge, K. Chance, R. Risso, D. Gillis, J. Ngai, J. Purdom, E. Dudoit, S. 2020-03-04 doi:10.1101/2020.03.03.974220 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ Differential virulence contributions of the efflux transporter MexAB-OprM in Pseudomonas syringae infecting a variety of host plants ]]> https://biorxiv.org/content/10.1101/2020.03.04.959429v1?rss=1 Helmann, T. C. King, D. M. Lindow, S. E. 2020-03-05 doi:10.1101/2020.03.04.959429 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Systematic genome-wide querying of coding and non-coding functional elements in E. coli using CRISPRi ]]> https://biorxiv.org/content/10.1101/2020.03.04.975888v1?rss=1 Rishi, H. S. Toro, E. Liu, H. Wang, X. Qi, L. S. Arkin, A. P. 2020-03-05 doi:10.1101/2020.03.04.975888 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Polysome fractionation analysis reveals features important for human nonsense-mediated mRNA decay ]]> https://biorxiv.org/content/10.1101/2020.03.08.981811v1?rss=1 Lloyd, J. P. B. French, C. E. Brenner, S. E. 2020-03-09 doi:10.1101/2020.03.08.981811 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ Magnetotactic bacteria accumulate a large pool of iron distinct from their magnetite crystals ]]> https://biorxiv.org/content/10.1101/2020.03.10.986679v1?rss=1 Amor, M. Ceballos, A. Wan, J. Simon, C. P. Aron, A. T. Chang, C. Hellman, F. Komeili, A. 2020-03-13 doi:10.1101/2020.03.10.986679 Cold Spring Harbor Laboratory Press 2020-03-13 <![CDATA[ A genome-scale CRISPR interference guide library enables comprehensive phenotypic profiling in yeast ]]> https://biorxiv.org/content/10.1101/2020.03.11.988105v1?rss=1 McGlincy, N. J. Meacham, Z. A. Swain, K. Muller, R. Baum, R. Ingolia, N. 2020-03-12 doi:10.1101/2020.03.11.988105 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ A family of viral satellites manipulates invading virus gene expression and affects cholera toxin mobilization ]]> https://biorxiv.org/content/10.1101/2020.03.12.988147v1?rss=1 Barth, Z. K. Netter, Z. Angermeyer, A. Bhardwaj, P. Seed, K. 2020-03-12 doi:10.1101/2020.03.12.988147 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ Major stages of vertebrate adaptive radiation are assembled from a disparate spatiotemporal landscape ]]> https://biorxiv.org/content/10.1101/2020.03.12.988774v1?rss=1 Richards, E. J. McGirr, J. A. Wang, J. St John, M. E. Poelstra, J. W. Solano, M. J. O'Connell, D. C. Turner, B. J. Martin, C. H. 2020-03-13 doi:10.1101/2020.03.12.988774 Cold Spring Harbor Laboratory Press 2020-03-13 <![CDATA[ Efficient Generation of Isogenic Primary Human Myeloid Cells using CRISPR-Cas9 Ribonucleoproteins ]]> https://biorxiv.org/content/10.1101/2020.03.13.991414v1?rss=1 Hiatt, J. Cavero, D. A. McGregor, M. J. Gordon, D. E. Zheng, W. Budzik, J. M. Roth, T. L. Haas, K. M. Rathore, U. Meyer-Franke, A. Bouzidi, M. S. Hultquist, J. F. Wojcechowskyj, J. A. Fontaine, K. A. Pillai, S. K. Cox, J. S. Ernst, J. D. Krogan, N. J. Marson, A. 2020-03-15 doi:10.1101/2020.03.13.991414 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ The Effect of Visual Uncertainty on Implicit Motor Adaptation ]]> https://biorxiv.org/content/10.1101/2020.03.15.992008v1?rss=1 Tsay, J. S. Avraham, G. Kim, H. E. Parvin, D. E. Wang, Z. Ivry, R. B. 2020-03-17 doi:10.1101/2020.03.15.992008 Cold Spring Harbor Laboratory Press 2020-03-17 <![CDATA[ Spatial integration during active tactile sensation drives elementary shape perception ]]> https://biorxiv.org/content/10.1101/2020.03.16.994145v1?rss=1 Brown, J. Oldenburg, I. A. Telian, G. I. Griffin, S. Voges, M. Jain, V. Adesnik, H. 2020-03-18 doi:10.1101/2020.03.16.994145 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ Naturally occurring cobalamin (B12) analogs can function as cofactors for human methylmalonyl-CoA mutase ]]> https://biorxiv.org/content/10.1101/2020.03.20.997551v1?rss=1 Sokolovskaya, O. M. Plessl, T. Bailey, H. Mackinnon, S. Baumgartner, M. R. Yue, W. W. Froese, D. S. Taga, M. E. 2020-03-23 doi:10.1101/2020.03.20.997551 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ Repurposing the yeast peroxisome to compartmentalize a toxic enzyme enables improved (S)-reticuline production ]]> https://biorxiv.org/content/10.1101/2020.03.23.000851v1?rss=1 Grewal, P. S. Samson, J. A. Baker, J. J. Choi, B. Dueber, J. E. 2020-03-23 doi:10.1101/2020.03.23.000851 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ Conspicuous candidate alleles point to cis-regulatory divergence underlying rapidly evolving craniofacial phenotypes ]]> https://biorxiv.org/content/10.1101/2020.03.23.003947v1?rss=1 McGirr, J. A. Martin, C. H. 2020-03-25 doi:10.1101/2020.03.23.003947 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Function of a novel nasal protrusion for oral-shelling within an adaptive radiation of pupfishes ]]> https://biorxiv.org/content/10.1101/2020.03.23.004416v1?rss=1 St John, M. E. Dixon, K. Martin, C. H. 2020-03-26 doi:10.1101/2020.03.23.004416 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ A new sulcal landmark identifying anatomical and functional gradients in human lateral prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2020.03.24.006577v1?rss=1 Miller, J. A. Voorhies, W. I. Lurie, D. J. D'Esposito, M. Weiner, K. S. 2020-03-26 doi:10.1101/2020.03.24.006577 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ Non-neural expression of SARS-CoV-2 entry genes in the olfactory epithelium suggests mechanisms underlying anosmia in COVID-19 patients ]]> https://biorxiv.org/content/10.1101/2020.03.25.009084v1?rss=1 Brann, D. Tsukahara, T. Weinreb, C. Logan, D. W. Datta, S. R. 2020-03-27 doi:10.1101/2020.03.25.009084 Cold Spring Harbor Laboratory Press 2020-03-27 <![CDATA[ SCITO-seq: single-cell combinatorial indexed cytometry sequencing ]]> https://biorxiv.org/content/10.1101/2020.03.27.012633v1?rss=1 Hwang, B. Lee, D. S. Tamaki, W. Sun, Y. Ogorodnikov, A. Hartoularos, G. Winters, A. Song, Y. S. Chow, E. D. Spitzer, M. H. Ye, C. J. 2020-03-30 doi:10.1101/2020.03.27.012633 Cold Spring Harbor Laboratory Press 2020-03-30 <![CDATA[ CiBER-seq dissects genetic networks by quantitative CRISPRi profiling of expression phenotypes ]]> https://biorxiv.org/content/10.1101/2020.03.29.015057v1?rss=1 Muller, R. Meacham, Z. A. Ferguson, L. Ingolia, N. 2020-03-30 doi:10.1101/2020.03.29.015057 Cold Spring Harbor Laboratory Press 2020-03-30 <![CDATA[ Genome and time-of-day transcriptome of Wolffia australiana link morphological extreme minimization with un-gated plant growth ]]> https://biorxiv.org/content/10.1101/2020.03.31.018291v1?rss=1 Michael, T. P. Ernst, E. Hartwick, N. Chu, P. Bryant, D. Gilbert, S. Ortleb, S. Baggs, E. L. Sree, K. S. Appenroth, K. J. Fuchs, J. Jupe, F. Sandoval, J. P. Krasileva, K. V. Borisjuk, L. Mockler, T. C. Ecker, J. R. Martienssen, R. A. Lam, E. 2020-04-01 doi:10.1101/2020.03.31.018291 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ A Nimbolide-Based Kinase Degrader Preferentially Degrades Oncogenic BCR-ABL ]]> https://biorxiv.org/content/10.1101/2020.04.02.022541v1?rss=1 Tong, B. Spradlin, J. N. Novaes, L. F. T. Zhang, E. Hu, X. Moeller, M. Brittain, S. M. McGregor, L. M. McKenna, J. M. Tallarico, J. A. Schirle, M. Maimone, T. J. Nomura, D. K. 2020-04-03 doi:10.1101/2020.04.02.022541 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ Low-frequency neural tracking of speech envelope reflects evoked responses to acoustic edges ]]> https://biorxiv.org/content/10.1101/2020.04.02.022616v1?rss=1 Kojima, K. Oganian, Y. Cai, C. Findlay, A. Chang, E. F. Nagarajan, S. 2020-04-03 doi:10.1101/2020.04.02.022616 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ Oncogene Regulated Release of Extracellular Vesicles ]]> https://biorxiv.org/content/10.1101/2020.04.04.025726v1?rss=1 Kilinc, S. Paisner, R. Camarda, R. Momcilovic, O. Kohnz, R. A. L'Etoile, N. D. Perera, R. M. Nomura, D. M. Goga, A. 2020-04-05 doi:10.1101/2020.04.04.025726 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Adaptive actin organization counteracts elevated membrane tension to ensure robust endocytosis ]]> https://biorxiv.org/content/10.1101/2020.04.05.026559v1?rss=1 Kaplan, C. Kenny, S. J. Chen, S. Schoeneberg, J. Sitarska, E. Diz-Munoz, A. Xu, K. Drubin, D. G. 2020-04-06 doi:10.1101/2020.04.05.026559 Cold Spring Harbor Laboratory Press 2020-04-06 <![CDATA[ Natural image statistics at depth edges modulate perceptual stability ]]> https://biorxiv.org/content/10.1101/2020.04.05.026724v1?rss=1 Basgoze, Z. White, D. N. Burge, J. Cooper, E. A. 2020-04-06 doi:10.1101/2020.04.05.026724 Cold Spring Harbor Laboratory Press 2020-04-06 <![CDATA[ Cytoplasmic mRNA decay represses RNA polymerase II transcription during early apoptosis ]]> https://biorxiv.org/content/10.1101/2020.04.09.034694v1?rss=1 Duncan-Lewis, C. Hartenian, E. Glaunsinger, B. 2020-04-10 doi:10.1101/2020.04.09.034694 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ The impact of di-2-ethylhexyl phthalate on sperm fertility ]]> https://biorxiv.org/content/10.1101/2020.04.09.034835v1?rss=1 Gabelev Khasin, L. Dell Rosa, J. Petersen, N. Moeller, J. Kriegsfeld, L. J. Lishko, P. V. 2020-04-10 doi:10.1101/2020.04.09.034835 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ Accurate inference in parametric models reshapes neuroscientific interpretation and improves data-driven discovery ]]> https://biorxiv.org/content/10.1101/2020.04.10.036244v1?rss=1 Sachdeva, P. S. Livezey, J. A. Dougherty, M. E. Gu, B.-M. Berke, J. D. Bouchard, K. E. 2020-04-13 doi:10.1101/2020.04.10.036244 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments ]]> https://biorxiv.org/content/10.1101/2020.04.10.036442v1?rss=1 Chen, Z. Shaw, A. Wilson, H. Woringer, M. Darzacq, X. Marqusee, S. Wang, Q. Bustamante, C. 2020-04-11 doi:10.1101/2020.04.10.036442 Cold Spring Harbor Laboratory Press 2020-04-11 <![CDATA[ Head-mounted microendoscopic calcium imaging in dorsal premotor cortex of behaving rhesus macaque ]]> https://biorxiv.org/content/10.1101/2020.04.10.996116v1?rss=1 Bollimunta, A. Santacruz, S. R. Eaton, R. W. Xu, P. S. Morrison, J. H. Moxon, K. A. Carmena, J. M. Nassi, J. J. 2020-04-13 doi:10.1101/2020.04.10.996116 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 A ]]> https://biorxiv.org/content/10.1101/2020.04.14.036384v1?rss=1 Flores, J. A. Haddad, B. G. Dolan, K. A. Myers, J. B. Yoshioka, C. C. Copperman, J. Zuckerman, D. M. Reichow, S. L. 2020-04-15 doi:10.1101/2020.04.14.036384 Cold Spring Harbor Laboratory Press 2020-04-15 <![CDATA[ Oleic acid Induces Tissue Resident FoxP3 Regulatory T cell Lineage Stability and Suppressive Functions ]]> https://biorxiv.org/content/10.1101/2020.04.14.041525v1?rss=1 Pompura, S. L. Wagner, A. Kitz, A. LaPerche, J. Yosef, N. Dominguez-Villar, M. Hafler, D. A. 2020-04-15 doi:10.1101/2020.04.14.041525 Cold Spring Harbor Laboratory Press 2020-04-15 <![CDATA[ Structure of the lysosomal SCARF (L-SCARF) complex, an Arf GAP haploinsufficient in ALS and FTD ]]> https://biorxiv.org/content/10.1101/2020.04.15.042515v1?rss=1 Su, M.-Y. Zoncu, R. Hurley, J. H. 2020-04-15 doi:10.1101/2020.04.15.042515 Cold Spring Harbor Laboratory Press 2020-04-15 <![CDATA[ Breakage of the Oligomeric CaMKII Hub by the Regulatory Segment of the Kinase ]]> https://biorxiv.org/content/10.1101/2020.04.15.043067v1?rss=1 Karandur, D. Bhattacharyya, M. Xia, Z. Lee, Y. K. Muratcioglu, S. McAffee, D. McSpadden, E. Qiu, B. Groves, J. T. Williams, E. R. Kuriyan, J. 2020-04-16 doi:10.1101/2020.04.15.043067 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ The folding and unfolding behavior of ribonuclease H on the ribosome ]]> https://biorxiv.org/content/10.1101/2020.04.16.044867v1?rss=1 Jensen, M. K. Samelson, A. J. Steward, A. Clarke, J. Marqusee, S. 2020-04-18 doi:10.1101/2020.04.16.044867 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex ]]> https://biorxiv.org/content/10.1101/2020.04.18.048462v1?rss=1 Bhargava, H. K. Tabata, K. Byck, J. K. Hamasaki, M. Farrell, D. P. Anishchenko, I. DiMaio, F. Im, Y.-J. Yoshimori, T. Hurley, J. H. 2020-04-18 doi:10.1101/2020.04.18.048462 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ JARID2 and AEBP2 regulate PRC2 activity in the presence of H2A ubiquitination or other histone modifications ]]> https://biorxiv.org/content/10.1101/2020.04.20.049213v1?rss=1 Kasinath, V. Beck, C. Sauer, P. Poepsel, S. Kosmatka, J. Faini, M. Toso, D. Aebersold, R. Nogales, E. 2020-04-21 doi:10.1101/2020.04.20.049213 Cold Spring Harbor Laboratory Press 2020-04-21 <![CDATA[ Synonymous mutations and the molecular evolution of SARS-Cov-2 origins ]]> https://biorxiv.org/content/10.1101/2020.04.20.052019v1?rss=1 Nielsen, R. Wang, H. Pipes, L. 2020-04-21 doi:10.1101/2020.04.20.052019 Cold Spring Harbor Laboratory Press 2020-04-21 <![CDATA[ Adherens junction serves to generate cryptic lamellipodia required for collective migration of epithelial cells ]]> https://biorxiv.org/content/10.1101/2020.04.20.052118v1?rss=1 Ozawa, M. Hiver, S. Yamamoto, T. Shibata, T. Upadhyayula, S. Mimori-Kiyosue, Y. Takeichi, M. 2020-04-21 doi:10.1101/2020.04.20.052118 Cold Spring Harbor Laboratory Press 2020-04-21 <![CDATA[ Metabolic precision labeling enables selective probing of O-linked N-acetylgalactosamine glycosylation ]]> https://biorxiv.org/content/10.1101/2020.04.23.057208v1?rss=1 Debets, M. F. Tastan, O. Y. Wisnovsky, S. P. Malaker, S. A. Angelis, N. Moeckl, L. K. R. Choi, J. Flynn, H. Wagner, L. J. S. Bineva-Todd, G. Antononopoulos, A. Cioce, A. Browne, W. M. Li, Z. Briggs, D. C. Douglas, H. L. Hess, G. T. Agbay, A. J. Roustan, C. Kjaer, S. Haslam, S. M. Snijders, A. P. Bassik, M. C. Moerner, W. E. Li, V. S. W. Bertozzi, C. R. Schumann, B. 2020-04-25 doi:10.1101/2020.04.23.057208 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Ecological processes underlying the emergence of novel enzootic cycles--arboviruses in the neotropics as a case study ]]> https://biorxiv.org/content/10.1101/2020.04.24.057430v1?rss=1 Guth, S. Hanley, K. A. Althouse, B. M. Boots, M. 2020-04-29 doi:10.1101/2020.04.24.057430 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Embedded Enzyme Nanoclusters Depolymerize Polyesters via Chain-End Mediated Processive Degradation ]]> https://biorxiv.org/content/10.1101/2020.04.25.052050v1?rss=1 DelRe, C. Kwon, J. Kang, P. Ma, L. Hall, A. Ruan, Z. Zolkin, K. Li, T. Ritchie, R. O. Xu, T. 2020-04-27 doi:10.1101/2020.04.25.052050 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ Cancer-specific loss of TERT activation sensitizes glioblastoma to DNA damage ]]> https://biorxiv.org/content/10.1101/2020.04.25.061606v1?rss=1 Amen, A. M. Fellmann, C. Soczek, K. M. Ren, S. M. Lew, R. J. Knott, G. J. Park, J. E. McKinney, A. M. Mancini, A. Doudna, J. A. Costello, J. F. 2020-04-27 doi:10.1101/2020.04.25.061606 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ Coevolution of song and egg coloration: multimodal mating signals? ]]> https://biorxiv.org/content/10.1101/2020.04.26.062927v1?rss=1 Wang, S. 2020-04-28 doi:10.1101/2020.04.26.062927 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Systematic Discovery of Salmonella Phage-Host Interactions via High-Throughput Genome-Wide Screens ]]> https://biorxiv.org/content/10.1101/2020.04.27.058388v1?rss=1 Adler, B. A. Zhong, C. Liu, H. Kutter, E. Deutschbauer, A. M. Mutalik, V. K. Arkin, A. P. 2020-04-28 doi:10.1101/2020.04.27.058388 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome ]]> https://biorxiv.org/content/10.1101/2020.04.29.069278v1?rss=1 Shaiber, A. Willis, A. D. Delmont, T. O. Roux, S. Chen, L.-X. Schmid, A. C. Yousef, M. Watson, A. R. Lolans, K. Esen, O. C. Lee, S. T. Downey, N. Morrison, H. G. Dewhirst, F. Mark Welch, J. L. Eren, A. M. 2020-04-30 doi:10.1101/2020.04.29.069278 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Conservative and liberal attitudes drive polarized neural responses to political content ]]> https://biorxiv.org/content/10.1101/2020.04.30.071084v1?rss=1 Leong, Y. C. Chen, J. Willer, R. Zaki, J. 2020-05-02 doi:10.1101/2020.04.30.071084 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ The mitotic protein NuMA plays a spindle-independent role in nuclear formation and mechanics ]]> https://biorxiv.org/content/10.1101/2020.05.02.070680v1?rss=1 Serra-Marques, A. Houtekamer, R. Hintzen, D. Canty, J. T. Yildiz, A. Dumont, S. 2020-05-03 doi:10.1101/2020.05.02.070680 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ Design of 18 nm Doxorubicin-loaded 3-helix Micelles: Cellular Uptake and Cytotoxicity in Patient-derived GBM6 Cells ]]> https://biorxiv.org/content/10.1101/2020.05.04.072892v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@99c9a4org.highwire.dtl.DTLVardef@8540c1org.highwire.dtl.DTLVardef@5e7690org.highwire.dtl.DTLVardef@1b9f88a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jung, B. T. Jung, K. Lim, M. Li, M. Santos, R. Ozawa, T. Xu, T. 2020-05-05 doi:10.1101/2020.05.04.072892 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Spontaneous activity changes in large-scale cortical networks in older adults couple to distinct hemodynamic morphology ]]> https://biorxiv.org/content/10.1101/2020.05.05.079749v1?rss=1 Sitnikova, T. Hughes, J. W. Howard, C. M. Stephens, K. A. Woolrich, M. W. Salat, D. H. 2020-05-06 doi:10.1101/2020.05.05.079749 Cold Spring Harbor Laboratory Press 2020-05-06 <![CDATA[ Breakage of Hydrophobic Contacts Limits the Rate of Passive Lipid Exchange Between Membranes ]]> https://biorxiv.org/content/10.1101/2020.05.06.081562v1?rss=1 Rogers, J. R. Geissler, P. L. 2020-05-08 doi:10.1101/2020.05.06.081562 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ Efficient Estimation of Large-Scale Spatial Capture-Recapture Models ]]> https://biorxiv.org/content/10.1101/2020.05.07.081182v1?rss=1 Turek, D. Milleret, C. Ergon, T. Broseth, H. de Valpine, P. 2020-05-08 doi:10.1101/2020.05.07.081182 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ Evolution and genetic basis of the plant-penetrating ovipositor, a key adaptation in the transition to herbivory within the Drosophilidae ]]> https://biorxiv.org/content/10.1101/2020.05.07.083253v1?rss=1 Pelaez, J. N. Gloss, A. N. Ray, J. F. Whiteman, N. K. 2020-05-08 doi:10.1101/2020.05.07.083253 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ Disentangling selection on genetically correlated polygenic traits using whole-genome genealogies ]]> https://biorxiv.org/content/10.1101/2020.05.07.083402v1?rss=1 Stern, A. J. Speidel, L. Zaitlen, N. A. Nielsen, R. 2020-05-08 doi:10.1101/2020.05.07.083402 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ Joint probabilistic modeling of paired transcriptome and proteome measurements in single cells ]]> https://biorxiv.org/content/10.1101/2020.05.08.083337v1?rss=1 Gayoso, A. Steier, Z. Lopez, R. Regier, J. Nazor, K. L. Streets, A. Yosef, N. 2020-05-10 doi:10.1101/2020.05.08.083337 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Photorespiration pathways in a chemolithoautotroph ]]> https://biorxiv.org/content/10.1101/2020.05.08.083683v1?rss=1 Claassens, N. J. Scarinci, G. Fischer, A. Flamholz, A. I. Newell, W. Frielingsdorf, S. Lenz, O. Bar-Even, A. 2020-05-09 doi:10.1101/2020.05.08.083683 Cold Spring Harbor Laboratory Press 2020-05-09 <![CDATA[ TripletProt: Deep Representation Learning of Proteins based on Siamese Networks ]]> https://biorxiv.org/content/10.1101/2020.05.11.088237v1?rss=1 Nourani, E. Asgari, E. McHardy, A. C. Mofrad, M. R. K. 2020-05-12 doi:10.1101/2020.05.11.088237 Cold Spring Harbor Laboratory Press 2020-05-12 <![CDATA[ Interactions of Upstream and Downstream Promoter Regions with RNA Polymerase are Energetically Coupled and a Target of Regulation in Transcription Initiation ]]> https://biorxiv.org/content/10.1101/2020.05.13.070375v1?rss=1 Sosa, R. P. Florez-Ariza, A. F. Diaz Celis, C. Onoa, B. Cassago, A. de Oliveira, P. S. L. Portugal, R. V. Guerra, D. G. Bustamante, C. J. 2020-05-14 doi:10.1101/2020.05.13.070375 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in protein translation ]]> https://biorxiv.org/content/10.1101/2020.05.13.094508v1?rss=1 Scarpin, M. R. Leiboff, S. Brunkard, J. O. 2020-05-14 doi:10.1101/2020.05.13.094508 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ The cryo-electron microscopy structure of the human CDK-activating kinase ]]> https://biorxiv.org/content/10.1101/2020.05.13.094755v1?rss=1 Greber, B. J. Perez-Bertoldi, J. M. Lim, K. Iavarone, A. T. Toso, D. B. Nogales, E. 2020-05-13 doi:10.1101/2020.05.13.094755 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ S-phase independent silencing establishment in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2020.05.13.094888v1?rss=1 Goodnight, D. Rine, J. 2020-05-14 doi:10.1101/2020.05.13.094888 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale ]]> https://biorxiv.org/content/10.1101/2020.05.14.086363v1?rss=1 Matheus Carnevali, P. B. Lavy, A. Thomas, A. D. Crits-Christoph, A. Diamond, S. Meeheust, R. Olm, M. R. Sharrar, A. Lei, S. Dong, W. Falco, N. Bouskill, N. Newcomer, M. Nico, P. Wainwright, H. Dwivedi, D. Williams, K. H. Hubbard, S. Banfield, J. F. 2020-05-15 doi:10.1101/2020.05.14.086363 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Huge and variable diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems ]]> https://biorxiv.org/content/10.1101/2020.05.14.094862v1?rss=1 He, C. Y. Keren, R. Whittaker, M. Farag, I. F. Doudna, J. A. Cate, J. H. Banfield, J. F. 2020-05-15 doi:10.1101/2020.05.14.094862 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ StrVCTVRE: A supervised learning method to predict the pathogenicity of human structural variants. ]]> https://biorxiv.org/content/10.1101/2020.05.15.097048v1?rss=1 Sharo, A. G. Hu, Z. Brenner, S. E. 2020-05-16 doi:10.1101/2020.05.15.097048 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Label-free optical detection of bioelectric potentials using electrochromic thin films ]]> https://biorxiv.org/content/10.1101/2020.05.16.099002v1?rss=1 Alfonso, F. S. Zhou, Y. Liu, E. McGuire, A. F. Yang, Y. Kantarci, H. Li, D. Copenhaver, E. Zuchero, J. B. Muller, H. Cui, B. 2020-05-17 doi:10.1101/2020.05.16.099002 Cold Spring Harbor Laboratory Press 2020-05-17 <![CDATA[ NAIP-NLRC4-deficient mice are susceptible to shigellosis ]]> https://biorxiv.org/content/10.1101/2020.05.16.099929v1?rss=1 Mitchell, P. S. Roncaioli, J. L. Turcotte, E. A. Goers, L. Chavez, R. A. Lee, A. Y. Lesser, C. F. Rauch, I. Vance, R. E. 2020-05-17 doi:10.1101/2020.05.16.099929 Cold Spring Harbor Laboratory Press 2020-05-17 <![CDATA[ Rod signals are routed through specific Off cone bipolar cells in primate retina ]]> https://biorxiv.org/content/10.1101/2020.05.17.100982v1?rss=1 McLaughlin, A. J. Percival, K. A. Gayet-Primo, J. Puthussery, T. 2020-05-19 doi:10.1101/2020.05.17.100982 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ Skeletal muscle DNMT3A plays a necessary role in endurance exercise by regulating oxidative capacity of red muscles ]]> https://biorxiv.org/content/10.1101/2020.05.18.102400v1?rss=1 Kang, S. Villivalam, S. You, D. Ebert, S. Kim, J. Xiao, H. Palacios, H. Adams, C. 2020-05-19 doi:10.1101/2020.05.18.102400 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ The transcription factor Pou3f1 provides a new map to the glutamatergic neurons of the cerebellar nuclei ]]> https://biorxiv.org/content/10.1101/2020.05.18.102855v1?rss=1 Wu, J. P. H. Yeung, J. Wu, S.-R. Zoghbi, H. Y. Goldowitz, D. 2020-05-21 doi:10.1101/2020.05.18.102855 Cold Spring Harbor Laboratory Press 2020-05-21 <![CDATA[ Lipid Droplet Is an Ancient and Inheritable Organelle in Bacteria ]]> https://biorxiv.org/content/10.1101/2020.05.18.103093v1?rss=1 Chi, X. Ogunsade, O. O. Zhou, Z. Li, Z. Li, X. Zhang, M. Song, F. Wang, J. Hammad, M. A. Zhang, X. Zhang, S. Wan, X. Zhang, L. Zhang, C. Liu, P. 2020-05-19 doi:10.1101/2020.05.18.103093 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ The autophagy adaptor NDP52 and the FIP200 coiled-coil allosterically activate ULK1 complex membrane recruitment ]]> https://biorxiv.org/content/10.1101/2020.05.19.104315v1?rss=1 Shi, X. Chang, C. Yokom, A. L. Hurley, J. H. 2020-05-20 doi:10.1101/2020.05.19.104315 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ DNA from dried blood spots yields high quality sequences for exome analysis ]]> https://biorxiv.org/content/10.1101/2020.05.19.105304v1?rss=1 T and T>A changes were more frequent in DNA from DBS than from WB. However, this did not affect the accuracy of variant calling, with DBS samples yielding a comparable count of high quality SNVs and indels in samples with at least 50x coverage. ConclusionsOverall, DBS DNA provided exome sequencing data of sufficient quality for clinical interpretation. ]]> Sunderam, U. Adhikari, A. N. Kundu, K. Puck, J. M. Currier, R. Kwok, P.-Y. Brenner, S. E. Srinivasan, R. 2020-05-20 doi:10.1101/2020.05.19.105304 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Networks of Splice Factor Regulation by Unproductive Splicing Coupled With Nonsense Mediated mRNA Decay ]]> https://biorxiv.org/content/10.1101/2020.05.20.107375v1?rss=1 Desai, A. Hu, Z. French, C. E. Lloyd, J. P. B. Brenner, S. E. 2020-05-22 doi:10.1101/2020.05.20.107375 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ A previously uncharacterized gene in SARS-CoV-2 illuminates the functional dynamics and evolutionary origins of the COVID-19 pandemic ]]> https://biorxiv.org/content/10.1101/2020.05.21.109280v1?rss=1 Nelson, C. W. Ardern, Z. Goldberg, T. L. Meng, C. Kuo, C.-H. Ludwig, C. Kolokotronis, S.-O. Wei, X. 2020-05-22 doi:10.1101/2020.05.21.109280 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Application of Generalized Concentration Addition to Predict Mixture Effects of Glucocorticoid Receptor Ligands ]]> https://biorxiv.org/content/10.1101/2020.05.21.109439v1?rss=1 de la Rosa, R. Schlezinger, J. J. Webster, T. F. Smith, M. T. 2020-05-26 doi:10.1101/2020.05.21.109439 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Extracting the Dynamics of Behavior in Decision-Making Experiments ]]> https://biorxiv.org/content/10.1101/2020.05.21.109678v1?rss=1 Roy, N. A. Bak, J. H. The International Brain Lab, Akrami, A. Brody, C. D. Pillow, J. W. 2020-05-25 doi:10.1101/2020.05.21.109678 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ A DNA translocase operates by cycling between planarand lock-washer structures ]]> https://biorxiv.org/content/10.1101/2020.05.22.101154v1?rss=1 Castillo, J. P. Tong, A. Tafoya, S. Jardine, P. J. Bustamante, C. 2020-05-22 doi:10.1101/2020.05.22.101154 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Predicting wildlife hosts of betacoronaviruses for SARS-CoV-2 sampling prioritization ]]> https://biorxiv.org/content/10.1101/2020.05.22.111344v1?rss=1 Becker, D. Albery, G. F. Sjodin, A. R. Poisot, T. Dallas, T. Eskew, E. A. Farrell, M. J. Guth, S. Han, B. A. Simmons, N. B. Carlson, C. J. 2020-05-23 doi:10.1101/2020.05.22.111344 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ SciSight: Combining faceted navigation and research group detection for COVID-19 exploratory scientific search ]]> https://biorxiv.org/content/10.1101/2020.05.23.112284v1?rss=1 Hope, T. Portenoy, J. Vasan, K. Borchardt, J. Horvitz, E. Weld, D. S. Hearst, M. A. West, J. 2020-05-26 doi:10.1101/2020.05.23.112284 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Integrated hiPSC-based liver and heart microphysiological systems predict unsafe drug-drug interaction ]]> https://biorxiv.org/content/10.1101/2020.05.24.112771v1?rss=1 Lee-Montiel, F. T. Laemmle, A. Dumont, L. Lee, C. S. Huebsch, N. Charwat, V. Okochi, H. Hancock, M. J. Siemons, B. Bogess, S. Goswami, I. Miller, E. Willenbring, H. Healy, K. 2020-05-27 doi:10.1101/2020.05.24.112771 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism ]]> https://biorxiv.org/content/10.1101/2020.05.24.113720v1?rss=1 Nichols, R. J. LaFrance, B. Phillips, N. R. Oltrogge, L. M. Valentin-Alvarado, L. E. Bischoff, A. J. Nogales, E. Savage, D. 2020-05-25 doi:10.1101/2020.05.24.113720 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Systematic Discovery of Pseudomonad Genetic Factors Involved in Sensitivity to Tailocins ]]> https://biorxiv.org/content/10.1101/2020.05.27.113977v1?rss=1 Carim, S. Azadeh, A. L. Kazakov, A. E. Price, M. N. Walian, P. J. Chakraborty, R. Deutschbauer, A. M. Mutalik, V. K. Arkin, A. P. 2020-05-27 doi:10.1101/2020.05.27.113977 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Functional reconstitution of a bacterial CO2 concentrating mechanism in E. coli ]]> https://biorxiv.org/content/10.1101/2020.05.27.119784v1?rss=1 Flamholz, A. I. Dugan, E. Blikstad, C. Gleizer, S. Ben-Nissan, R. Amram, S. Antonovsky, N. Ravishankar, S. Noor, E. Bar-Even, A. Milo, R. Savage, D. 2020-05-27 doi:10.1101/2020.05.27.119784 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease ]]> https://biorxiv.org/content/10.1101/2020.05.28.121541v1?rss=1 Bassler, K. Fujii, W. Kapellos, T. S. Horne, A. Reiz, B. Dudkin, E. Luecken, M. Reusch, N. Osei-Sarpong, C. Warnat-Herresthal, S. Wagner, A. Bonaguro, L. Guenther, P. Pizarro, C. Schreiber, T. Becker, M. Haendler, K. Wohnhaas, C. T. Baumgartner, F. Koehler, M. Theis, H. Kraut, M. Wadsworth, M. H. Hughes, T. K. Ferreira, H. J. G. Schulte-Schrepping, J. Hinkley, E. Kaltheuner, I. H. Geyer, M. Thiele, C. Shalek, A. K. Feisst, A. Thomas, D. Dickten, H. Beyer, M. Baum, P. Yosef, N. Aschenbrenner, A. C. Ulas, T. Hasenauer, J. Theis, F. J. Skowasch, D. Schult 2020-05-30 doi:10.1101/2020.05.28.121541 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ An image resource of subdivided Drosophila GAL4-driver expression patterns for neuron-level searches ]]> https://biorxiv.org/content/10.1101/2020.05.29.080473v1?rss=1 Meissner, G. W. Dorman, Z. Nern, A. Forster, K. Gibney, T. Jeter, J. Johnson, L. He, Y. Lee, K. Melton, B. Yarbrough, B. Clements, J. Goina, C. Otsuna, H. Rokicki, K. Svirskas, R. R. Aso, Y. Card, G. M. Dickson, B. J. Ehrhardt, E. Goldammer, J. Ito, M. Korff, W. Minegishi, R. Namiki, S. Rubin, G. M. Sterne, G. Wolff, T. Malkesman, O. FlyLight Project Team, 2020-05-30 doi:10.1101/2020.05.29.080473 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Identifying drug response by combining measurements of the membrane potential, the cytosolic calcium concentration, and the extracellular potential in microphysiological systems ]]> https://biorxiv.org/content/10.1101/2020.05.29.122747v1?rss=1 Jaeger, K. H. Wall, S. Charwat, V. Healy, K. Tveito, A. 2020-05-31 doi:10.1101/2020.05.29.122747 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Towards Mycobacterium tuberculosis detection at the point-of-care: a brighter solvatochromic probe permits the detection of mycobacteria within minutes ]]> https://biorxiv.org/content/10.1101/2020.05.29.124008v1?rss=1 Kamariza, M. Keyser, S. G. L. Utz, A. Knapp, B. Ahn, G. Cambier, C. J. Chen, T. Huang, K. C. Bertozzi, C. 2020-05-30 doi:10.1101/2020.05.29.124008 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Pupil-linked arousal biases evidence accumulation towards desirable percepts during perceptual decision-making ]]> https://biorxiv.org/content/10.1101/2020.05.29.124115v1?rss=1 Leong, Y. C. Dziembaj, R. D'Esposito, M. 2020-05-31 doi:10.1101/2020.05.29.124115 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ What is an adaptive pattern of brain activity for a child? It depends on their environment ]]> https://biorxiv.org/content/10.1101/2020.05.29.124297v1?rss=1 Ellwood-Lowe, M. E. Whitfield-Gabrieli, S. Bunge, S. A. 2020-05-31 doi:10.1101/2020.05.29.124297 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ A hydraulic instability drives the cell death decision in the nematode germline ]]> https://biorxiv.org/content/10.1101/2020.05.30.125864v1?rss=1 Chartier, N. T. Mukherjee, A. Pfanzelter, J. Früthauer, S. Larson, B. T. Fritsch, A. W. Kreysing, M. Julicher, F. Grill, S. W. 2020-05-31 doi:10.1101/2020.05.30.125864 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Membrane potential regulates Hedgehog signaling and compartment boundary maintenance in the Drosophila wing disc ]]> https://biorxiv.org/content/10.1101/2020.06.02.128892v1?rss=1 Emmons-Bell, M. Yasutomi, R. Hariharan, I. K. 2020-06-02 doi:10.1101/2020.06.02.128892 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ An Hourglass Circuit Motif Transforms a Motor Program via Subcellularly Localized Calcium Signaling in Muscle ]]> https://biorxiv.org/content/10.1101/2020.06.02.129825v1?rss=1 Sando, S. R. Bhatla, N. Lee, E. L. Q. Horvitz, H. R. 2020-06-03 doi:10.1101/2020.06.02.129825 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Evolutionarily related small viral fusogens hijack distinct but modular actin nucleation pathways to drive cell-cell fusion ]]> https://biorxiv.org/content/10.1101/2020.06.03.130740v1?rss=1 Chan, K. M. C. Arthur, A. L. Morstein, J. Jin, M. Bhat, A. Schlesinger, D. Son, S. Stevens, D. A. Drubin, D. G. Fletcher, D. A. 2020-06-04 doi:10.1101/2020.06.03.130740 Cold Spring Harbor Laboratory Press 2020-06-04 <![CDATA[ Iron Supplementation Eliminates Antagonistic Interactions Between Root Associated Bacteria ]]> https://biorxiv.org/content/10.1101/2020.06.05.132704v1?rss=1 Eng, T. T. Herbert, R. A. Martinez, U. Wang, B. Chen, J. Brown, J. B. Deutschbauer, A. Bissell, M. Mortimer, J. Mukhopadhyay, A. 2020-06-05 doi:10.1101/2020.06.05.132704 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Topography of speech-related acoustic and phonological feature encoding throughout the human core and parabelt auditory cortex ]]> https://biorxiv.org/content/10.1101/2020.06.08.121624v1?rss=1 Hamilton, L. S. Oganian, Y. Chang, E. F. 2020-06-09 doi:10.1101/2020.06.08.121624 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Idiosyncratic Perception: A Link Between Acuity, Perceived Position, and Apparent Size ]]> https://biorxiv.org/content/10.1101/2020.06.09.143081v1?rss=1 Wang, Z. Murai, Y. Whitney, D. 2020-06-11 doi:10.1101/2020.06.09.143081 Cold Spring Harbor Laboratory Press 2020-06-11 <![CDATA[ High resilience of the mycorrhizal community to prescribed seasonal burnings in a Mediterranean woodland ]]> https://biorxiv.org/content/10.1101/2020.06.10.141671v1?rss=1 Livne- Luzon, S. Shemesh, H. Osem, Y. Carmel, Y. Migael, H. Avidan, Y. Tsafrir, A. Glassman, S. I. Bruns, T. D. Ovadia, O. 2020-06-12 doi:10.1101/2020.06.10.141671 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Cohesin residency determines chromatin loop patterns ]]> https://biorxiv.org/content/10.1101/2020.06.11.146902v1?rss=1 costantino, l. Hsieh, T.-H. S. Lamothe, R. Darzacq, X. D. Koshland, D. E. 2020-06-12 doi:10.1101/2020.06.11.146902 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Computational Investigation Of Blood Flow And Flow-mediated Transport In Arterial Thrombus Neighborhood ]]> https://biorxiv.org/content/10.1101/2020.06.11.147488v1?rss=1 Teeraratkul, C. Irwin, Z. Shadden, S. C. Mukherjee, D. 2020-06-12 doi:10.1101/2020.06.11.147488 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Electromechanics of lipid-modulated gating of Kv channels ]]> https://biorxiv.org/content/10.1101/2020.06.12.051482v1?rss=1 Thomas, N. Mandadapu, K. K. Agrawal, A. 2020-06-12 doi:10.1101/2020.06.12.051482 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Competitive hierarchies, antibiosis, and the distribution of bacterial life history traits in a microbiome ]]> https://biorxiv.org/content/10.1101/2020.06.15.152272v1?rss=1 Humphrey, P. T. Satterlee, T. T. Whiteman, N. K. 2020-06-15 doi:10.1101/2020.06.15.152272 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Detection of SARS-CoV-2 RNA by multiplex RT-qPCR ]]> https://biorxiv.org/content/10.1101/2020.06.16.155887v1?rss=1 500 copies / reaction) of SARS-CoV-2 RNA were consistently detected by the multiplex RT-qPCR. Our novel multiplex RT-qPCR improves upon current singleplex diagnostics by saving reagents, costs, time and labor. ]]> Kudo, E. Israelow, B. Vogels, C. Lu, P. Wyllie, A. L. Tokuyama, M. Venkataraman, A. Brackney, D. E. Ott, I. Petrone, M. Earnest, R. Lapidus, S. Muenker, C. Moore, A. Casanovas-Massana, A. Yale IMPACT Research Team, Omer, S. Dela Cruz, C. Farhadian, S. Ko, A. Grubaugh, N. Iwasaki, A. 2020-06-17 doi:10.1101/2020.06.16.155887 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Life under quartz: Hypolithic mosses in the Mojave Desert ]]> https://biorxiv.org/content/10.1101/2020.06.17.157941v1?rss=1 Ekwealor, J. T. B. Fisher, K. M. 2020-06-18 doi:10.1101/2020.06.17.157941 Cold Spring Harbor Laboratory Press 2020-06-18 <![CDATA[ Measuring the accuracy of gridded human population density surfaces: a case study in Bioko Island, Equatorial Guinea ]]> https://biorxiv.org/content/10.1101/2020.06.18.160101v1?rss=1 Fries, B. Smith, D. L. Wu, S. Dolgert, A. J. Guerra, C. A. Hay, S. I. Garcia, G. A. Smith, J. M. Oyono, J. N. M. Donfack, O. T. Nfumu, J. O. O. 2020-06-20 doi:10.1101/2020.06.18.160101 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny ]]> https://biorxiv.org/content/10.1101/2020.06.19.160630v1?rss=1 Pipes, L. Wang, H. Huelsenbeck, J. Nielsen, R. 2020-06-20 doi:10.1101/2020.06.19.160630 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Dot1L interacts with Zc3h10 to activate UCP1 transcription and promote thermogenesis ]]> https://biorxiv.org/content/10.1101/2020.06.22.154963v1?rss=1 Yi, D. Nguyen, H. P. Dinh, J. Viscarra, J. A. Xie, Y. Dempersmier, J. M. Wang, Y. Sul, H. S. 2020-06-23 doi:10.1101/2020.06.22.154963 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ Engineering a virus-like particle to display peptide insertions using an apparent fitness landscape ]]> https://biorxiv.org/content/10.1101/2020.06.23.168070v1?rss=1 Tullman-Ercek, D. Robinson, S. A. Hartman, E. C. Ikwuagwu, B. C. Francis, M. B. 2020-06-24 doi:10.1101/2020.06.23.168070 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Generation of a DAT-Flp mouse line for intersectional genetic targeting of dopamine neuron subpopulations ]]> https://biorxiv.org/content/10.1101/2020.06.24.167908v1?rss=1 Kramer, D. J. Kosillo, P. Friedmann, D. Stafford, D. Luo, L. Lee, A. Y.-F. Hockemeyer, D. Ngai, J. Bateup, H. S. 2020-06-29 doi:10.1101/2020.06.24.167908 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Synthesis of higher order feature codes through stimulus-specific supra-linear summation ]]> https://biorxiv.org/content/10.1101/2020.06.24.169359v1?rss=1 Lyall, E. H. Mossing, D. P. Pluta, S. R. Dudai, A. Adesnik, H. 2020-06-24 doi:10.1101/2020.06.24.169359 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity ]]> https://biorxiv.org/content/10.1101/2020.06.24.170084v1?rss=1 Crits-Christoph, A. Banfield, J. F. Bhattacharya, N. Song, Y. S. Olm, M. R. 2020-06-24 doi:10.1101/2020.06.24.170084 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Subsurface carbon monoxide oxidation capacity revealed through genome-resolved metagenomics of a carboxydotroph ]]> https://biorxiv.org/content/10.1101/2020.06.25.170886v1?rss=1 Mu, A. Thomas, B. C. Banfield, J. Moreau, J. W. 2020-06-25 doi:10.1101/2020.06.25.170886 Cold Spring Harbor Laboratory Press 2020-06-25 <![CDATA[ Ceramic Packaging in Neural Implants ]]> https://biorxiv.org/content/10.1101/2020.06.26.174144v1?rss=1 Shen, K. Maharbiz, M. M. 2020-06-29 doi:10.1101/2020.06.26.174144 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Structure of the Bacterial Ribosome at 2 A Resolution ]]> https://biorxiv.org/content/10.1101/2020.06.26.174334v1?rss=1 Watson, Z. L. Ward, F. R. Meheust, R. Ad, O. Schepartz, A. Banfield, J. Cate, J. H. D. 2020-06-26 doi:10.1101/2020.06.26.174334 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Genome-wide CRISPRi/a screens in human neurons link lysosomal failure to ferroptosis ]]> https://biorxiv.org/content/10.1101/2020.06.27.175679v1?rss=1 Tian, R. Abarientos, A. Hong, J. Hashemi, S. H. Yan, R. Nalls, M. A. Singleton, A. B. Faghri, F. Xu, K. Kampmann, M. 2020-06-27 doi:10.1101/2020.06.27.175679 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Perturbation robustness analyses reveal important parameters in variant interpretation pipelines ]]> https://biorxiv.org/content/10.1101/2020.06.29.173815v1?rss=1 Wang, Y. Adhikari, A. N. Sunderam, U. Kvale, M. N. Currier, R. J. Gallagher, R. C. Kwok, P.-Y. Puck, J. M. Srinivasan, R. Brenner, S. E. 2020-06-30 doi:10.1101/2020.06.29.173815 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ The UPRmt Preserves Mitochondrial Import to Extend Lifespan ]]> https://biorxiv.org/content/10.1101/2020.07.01.182980v1?rss=1 Xin, N. Durieux, J. Yang, C. Wolff, S. Kim, H.-E. Dillin, A. 2020-07-02 doi:10.1101/2020.07.01.182980 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Transcriptome analysis of alternative splicing-coupled nonsense-mediated mRNA decay in human cells reveals broad regulatory potential ]]> https://biorxiv.org/content/10.1101/2020.07.01.183327v1?rss=1 French, C. E. Wei, G. Lloyd, J. P. B. Hu, Z. Brooks, A. N. Brenner, S. E. 2020-07-02 doi:10.1101/2020.07.01.183327 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Understanding the Unique Advantage of Adolescents in Stochastic, Volatile Environments: Combining Reinforcement Learning and Bayesian Inference ]]> https://biorxiv.org/content/10.1101/2020.07.04.187971v1?rss=1 Eckstein, M. K. Master, S. L. Dahl, R. E. Wilbrecht, L. Collins, A. G. E. 2020-07-06 doi:10.1101/2020.07.04.187971 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Functional analysis of the fatty acid and alcohol metabolism of Pseudomonas putida using RB-TnSeq ]]> https://biorxiv.org/content/10.1101/2020.07.04.188060v1?rss=1 Thompson, M. Incha, M. Pearson, A. Schmidt, M. Sharpless, W. Eiben, C. Cruz-Morales, P. Blake-Hedges, J. Liu, Y. Adams, C. Haushalter, R. Krishna, R. Lichtner, P. Blank, L. M. Mukhopadhyay, A. Deutschbauer, A. Shih, P. Keasling, J. D. 2020-07-05 doi:10.1101/2020.07.04.188060 Cold Spring Harbor Laboratory Press 2020-07-05 <![CDATA[ Co-expressed subunits of dual genetic origin define a conserved supercomplex mediating essential protein import into chloroplasts ]]> https://biorxiv.org/content/10.1101/2020.07.04.188128v1?rss=1 Ramundo, S. Asakura, Y. Salomé, P. A. A. Strenkert, D. Boone, M. Mackinder, L. C. M. Takafuji, K. Dinc, E. Rahire, M. Crèvecoeur, M. Magneschi, L. Schaad, O. Hippler, M. Jonikas, M. C. Merchant, S. Nakai, M. Rochaix, J.-D. Walter, P. 2020-07-06 doi:10.1101/2020.07.04.188128 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Unlocking the Predictive Power of Heterogeneous Data to Build an Operational Dengue Forecasting System ]]> https://biorxiv.org/content/10.1101/2020.07.08.194019v1?rss=1 Carrie A Manore Geoffrey Fairchild Amanda Ziemann Nidhi Parikh Katherine Kempfert Kaitlyn Martinez Lauren Castro David Osthus Amir Siraj Jessica Conrad E Nicholas Generous Sara Del Valle 2020-07-10 doi:10.1101/2020.07.08.194019 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Intraspecies diversity reveals a subset of highly variable plant immune receptors and predicts their binding sites ]]> https://biorxiv.org/content/10.1101/2020.07.10.190785v1?rss=1 Daniil M Prigozhin Ksenia V Krasileva 2020-07-12 doi:10.1101/2020.07.10.190785 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ Whole-Proteome Tree of Arthropods: An "alignment-free" phylogeny of proteome "books" ]]> https://biorxiv.org/content/10.1101/2020.07.11.198689v1?rss=1 JaeJin Choi Byung-Ju Kim Sung-Hou Kim 2020-07-12 doi:10.1101/2020.07.11.198689 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ Impact of genetic susceptibility to multiple sclerosis on the T cell epigenome: proximal and distal effects ]]> https://biorxiv.org/content/10.1101/2020.07.11.198721v1?rss=1 Tina Roostaei Hans-Ulrich Klein Daniel Felsky Pia Kivisakk Sarah M. Connor Alexandra Kroshilina Christina Yung Yiyi Ma Belinda J. Kaskow Xiaorong Shao Brooke Rhead Jia Liu Nikolaos Patsopoulos Lisa F. Barcellos Howard L. Weiner Philip L. De Jager 2020-07-12 doi:10.1101/2020.07.11.198721 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ Chemoproteomics-Enabled Ligand Screening Yields Covalent RNF114-Based Degraders that Mimic Natural Product Function ]]> https://biorxiv.org/content/10.1101/2020.07.12.198150v1?rss=1 Mai Luo Jessica N Spradlin Scott M Brittain Jeffery M McKenna John A Tallarico Markus Schirle Thomas J Maimone Daniel K Nomura 2020-07-12 doi:10.1101/2020.07.12.198150 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ Unexpected diversity of CPR bacteria and nanoarchaea in the rare biosphere of rhizosphere-associated grassland soil ]]> https://biorxiv.org/content/10.1101/2020.07.13.194282v1?rss=1 Nicolas, A. M. Jaffe, A. L. Nuccio, E. E. Taga, M. E. Firestone, M. K. Banfield, J. F. 2020-07-13 doi:10.1101/2020.07.13.194282 Cold Spring Harbor Laboratory Press 2020-07-13 <![CDATA[ Non-additive polygenic models improve predictions of fitness traits in three eukaryote model species ]]> https://biorxiv.org/content/10.1101/2020.07.14.194407v1?rss=1 Exposito-Alonso, M. Wilton, P. Nielsen, R. 2020-07-15 doi:10.1101/2020.07.14.194407 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ The Grand Budapest Hotel: an fMRI dataset in response to a socially-rich, naturalistic movie ]]> https://biorxiv.org/content/10.1101/2020.07.14.203257v1?rss=1 Visconti di Oleggio Castello, M. Chauhan, V. Jiahui, G. Gobbini, M. I. 2020-07-14 doi:10.1101/2020.07.14.203257 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ Raf promotes dimerization of the Ras G-domain with increased allosteric connections ]]> https://biorxiv.org/content/10.1101/2020.07.15.205070v1?rss=1 Packer, M. Parker, J. A. Chung, J. K. Li, Z. Lee, Y. K. Cookis, T. Guterres, H. Alvarez, S. Hossain, M. A. Donnelly, D. P. Agar, J. N. Makowski, L. Buck, M. Groves, J. T. Mattos, C. 2020-07-15 doi:10.1101/2020.07.15.205070 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ Ultradian Rhythms in Heart Rate Variability and Distal Body TemperatureAnticipate the Luteinizing Hormone Surge Onset ]]> https://biorxiv.org/content/10.1101/2020.07.15.205450v1?rss=1 Grant, A. D. Newman, M. Kriegsfeld, L. J. 2020-07-17 doi:10.1101/2020.07.15.205450 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Re-exposure to a sensorimotor perturbation produces opposite effects on explicit and implicit learning processes ]]> https://biorxiv.org/content/10.1101/2020.07.16.205609v1?rss=1 Avraham, G. Morehead, J. R. Kim, H. E. Ivry, R. B. 2020-07-16 doi:10.1101/2020.07.16.205609 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ The risk of Xylella fastidiosa outbreaks will decrease in the Mediterranean olive-producing regions ]]> https://biorxiv.org/content/10.1101/2020.07.16.206474v1?rss=1 Godefroid, M. Morente, M. Schartel, T. Cornara, D. Purcell, A. Gallego, D. moreno lozano, A. Pereira, J. Fereres, A. 2020-07-17 doi:10.1101/2020.07.16.206474 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ A pentameric protein ring with novel architecture is required for herpesviral packaging ]]> https://biorxiv.org/content/10.1101/2020.07.16.206755v1?rss=1 Didychuk, A. L. Gates, S. N. Gardner, M. R. Strong, L. M. Martin, A. Glaunsinger, B. A. 2020-07-17 doi:10.1101/2020.07.16.206755 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Early acquisition of conserved, lineage-specific proteins currently lacking functional predictions were central to the rise and diversification of archaea ]]> https://biorxiv.org/content/10.1101/2020.07.16.207365v1?rss=1 Meheust, R. Castelle, C. J. Jaffe, A. L. Banfield, J. F. 2020-07-17 doi:10.1101/2020.07.16.207365 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Targeted Genome Editing of Bacteria Within Microbial Communities ]]> https://biorxiv.org/content/10.1101/2020.07.17.209189v1?rss=1 Rubin, B. E. Diamond, S. Cress, B. F. Crits-Christoph, A. He, C. Xu, M. Zhou, Z. Smock, D. C. Tang, K. Owens, T. K. Krishnappa, N. Sachdeva, R. Deutschbauer, A. M. Banfield, J. F. Doudna, J. A. 2020-07-17 doi:10.1101/2020.07.17.209189 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Epigenetic conflict on a degenerating Y chromosome increases mutational burden in Drosophila males ]]> https://biorxiv.org/content/10.1101/2020.07.19.210948v1?rss=1 Wei, K. H.- C. Gibilisco, L. Bachtrog, D. 2020-07-19 doi:10.1101/2020.07.19.210948 Cold Spring Harbor Laboratory Press 2020-07-19 <![CDATA[ Toxic Y chromosome: increased repeat expression and age-associated heterochromatin loss in male Drosophila with a young Y chromosome ]]> https://biorxiv.org/content/10.1101/2020.07.21.214528v1?rss=1 Nguyen, A. H. Bachtrog, D. 2020-07-22 doi:10.1101/2020.07.21.214528 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Spatial patterns in phage-Rhizobium coevolutionary interactions across regions of common bean domestication ]]> https://biorxiv.org/content/10.1101/2020.07.21.214783v1?rss=1 Van Cawenberghe, J. Santamaria, R. I. Bustos, P. Juarez, S. Ducci, M. A. Fleming, T. F. Etcheverry, A. V. Gonzalez, V. 2020-07-22 doi:10.1101/2020.07.21.214783 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Coupling between lipid miscibility and phosphotyrosine driven protein condensation at the membrane ]]> https://biorxiv.org/content/10.1101/2020.07.22.215970v1?rss=1 Chung, J. K. Huang, W. Y. C. Carbone, C. B. Nocka, L. M. Parikh, A. N. Vale, R. Groves, J. T. 2020-07-23 doi:10.1101/2020.07.22.215970 Cold Spring Harbor Laboratory Press 2020-07-23 <![CDATA[ Single-cell transcriptomics of the Drosophila wing disc reveals instructive epithelium-to-myoblast interactions ]]> https://biorxiv.org/content/10.1101/2020.07.27.222976v1?rss=1 Everetts, N. Worley, M. I. Yasutomi, R. Yosef, N. Hariharan, I. K. 2020-07-27 doi:10.1101/2020.07.27.222976 Cold Spring Harbor Laboratory Press 2020-07-27 <![CDATA[ CelLEVITAS: Label-free, rapid sorting and enrichment of live cells via magnetic levitation ]]> https://biorxiv.org/content/10.1101/2020.07.27.223917v1?rss=1 80%). This method is sensitive, does not impair cell viability during sorting, and significantly increases the input sample viability up to 7-fold. Overall, this new magnetic levitation-based sorting strategy drastically reduces the processing time to a single-step, 30-minute sorting protocol and eliminates the manual pre-processing and labeling steps that are required for traditional flow cytometry techniques. ]]> Chin, E. K. Grant, C. A. Ogut, M. G. Cai, B. Durmus, N. G. 2020-07-29 doi:10.1101/2020.07.27.223917 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Low Dose Lead Exposure Induces Alterations on Heterochromatin Hallmarks Persisting Through SH-SY5Y Cell Differentiation ]]> https://biorxiv.org/content/10.1101/2020.07.27.224246v1?rss=1 Lin, L. Xie, J. Sanchez, O. Bryan, C. Freeman, J. L. Yuan, C. 2020-07-29 doi:10.1101/2020.07.27.224246 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Distinctiveness of genes contributing to growth of Pseudomonas syringae in diverse host plant species ]]> https://biorxiv.org/content/10.1101/2020.07.28.216440v1?rss=1 Helmann, T. C. Deutschbauer, A. Lindow, S. 2020-07-28 doi:10.1101/2020.07.28.216440 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior ]]> https://biorxiv.org/content/10.1101/2020.07.29.226050v1?rss=1 Kölsch, Y. Hahn, J. Sappington, A. Stemmer, M. Fernandes, A. M. Helmbrecht, T. O. Lele, S. Butrus, S. Laurell, E. Arnold-Ammer, I. Shekhar, K. Sanes, J. Baier, H. 2020-07-29 doi:10.1101/2020.07.29.226050 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Novel therapeutic targets to mitigate early neuronal dysfunction and cognitive deficits in tauopathy ]]> https://biorxiv.org/content/10.1101/2020.07.31.229583v1?rss=1 Koren, S. A. Hamm, M. J. Cloyd, R. Fontaine, S. N. Chishti, E. Lanzillotta, C. Di Domenico, F. Seyfried, N. Duong, D. Powell, D. K. Vandsburger, M. Hartz, A. M. S. Koren, J. Axten, J. M. Laping, N. J. Abisambra, J. F. 2020-08-04 doi:10.1101/2020.07.31.229583 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Cohesin in space and time: architecture and oligomerization in vivo. ]]> https://biorxiv.org/content/10.1101/2020.07.31.229682v1?rss=1 Xiang, S. Koshland, D. 2020-07-31 doi:10.1101/2020.07.31.229682 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ Inferring Adaptive Introgression Using Hidden Markov Models ]]> https://biorxiv.org/content/10.1101/2020.08.02.232934v1?rss=1 Svedberg, J. Shchur, V. Reinman, S. Nielsen, R. Corbett-Detig, R. 2020-08-02 doi:10.1101/2020.08.02.232934 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ Efficient population modification gene-drive rescue system in the malaria mosquito Anopheles stephensi ]]> https://biorxiv.org/content/10.1101/2020.08.02.233056v1?rss=1 Adolfi, A. Gantz, V. M. Jasinskiene, N. Lee, H.-F. Hwang, K. Bulger, E. A. Ramaiah, A. Bennett, J. B. Terradas, G. Emerson, J. J. Marshall, J. M. Bier, E. James, A. A. 2020-08-02 doi:10.1101/2020.08.02.233056 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ Controlling the false discovery rate in GWAS with population structure ]]> https://biorxiv.org/content/10.1101/2020.08.04.236703v1?rss=1 Sesia, M. Bates, S. Candes, E. Marchini, J. Sabatti, C. 2020-08-04 doi:10.1101/2020.08.04.236703 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Fast and Flexible Estimation of Effective Migration Surfaces ]]> https://biorxiv.org/content/10.1101/2020.08.07.242214v1?rss=1 Marcus, J. H. Ha, W. Barber, R. F. Novembre, J. 2020-08-07 doi:10.1101/2020.08.07.242214 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ The Contributions of the Allopolyploid Parents of the Mesopolyploid Brassiceae are Evolutionarily Distinct but Functionally Compatible ]]> https://biorxiv.org/content/10.1101/2020.08.10.245258v1?rss=1 Hao, Y. Mabry, M. E. Edger, P. Freeling, M. Zheng, C. Jin, L. VanBuren, R. Colle, M. An, H. Abrahams, R. S. Qi, X. Barry, K. Daum, C. Shu, S. Schmutz, J. Sankoff, D. Barker, M. S. Lyons, E. Pires, J. C. Conant, G. C. 2020-08-12 doi:10.1101/2020.08.10.245258 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Discovery and biosynthesis of clostyrylpyrones from the obligate an-aerobe Clostridium roseum ]]> https://biorxiv.org/content/10.1101/2020.08.10.245514v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@1f24265org.highwire.dtl.DTLVardef@1e51bd7org.highwire.dtl.DTLVardef@86c761org.highwire.dtl.DTLVardef@8bd052_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Li, J. S. Du, Y. Gu, D. Cai, W. Green, A. Ng, S. Leung, A. Zhang, W. 2020-08-11 doi:10.1101/2020.08.10.245514 Cold Spring Harbor Laboratory Press 2020-08-11 <![CDATA[ A Novel Machine Learning Strategy for Prediction of Antihypertensive Peptides Derived from Food with High Efficiency ]]> https://biorxiv.org/content/10.1101/2020.08.12.248955v1?rss=1 Wang, L. Niu, D. Wang, X. Shen, Q. Xue, Y. 2020-08-13 doi:10.1101/2020.08.12.248955 Cold Spring Harbor Laboratory Press 2020-08-13 <![CDATA[ Structure of the activated Roq1 resistosome directly recognizing the pathogen effector XopQ ]]> https://biorxiv.org/content/10.1101/2020.08.13.246413v1?rss=1 Martin, R. Qi, T. Zhang, H. Liu, F. King, M. Toth, C. Nogales, E. Staskawicz, B. J. 2020-08-14 doi:10.1101/2020.08.13.246413 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Probing nanoscale diffusional heterogeneities in cellular membranes through multidimensional single-molecule and super-resolution microscopy ]]> https://biorxiv.org/content/10.1101/2020.08.14.232587v1?rss=1 106 probe molecules to achieve super-resolution topography and diffusivity mapping. We thus determine a trend that the membrane diffusivity drops with increased lipid packing order when comparing the endoplasmic reticulum (ER) membrane, plasma membrane, and nanodomains induced by cholera toxin B. Utilizing our nanoscale mapping capability, we further unveil reduced diffusivity in the ER membrane at ER-plasma membrane contact sites. By next integrating spectrally resolved single-molecule imaging, we show this localized diffusion slowdown is not due to altered lipid packing order, but may instead be attributed to local protein crowding. Our integrated multidimensional single-molecule approach thus unveils and differentiates between nanoscale diffusional heterogeneities of different origins in live-cell membranes. ]]> Yan, R. Chen, K. Xu, K. 2020-08-15 doi:10.1101/2020.08.14.232587 Cold Spring Harbor Laboratory Press 2020-08-15 <![CDATA[ Designing Sub-20 nm Nanocarriers for Small Molecule Delivery: Interplay among Structural Geometry, Assembly Energetics, and Cargo Release Kinetics ]]> https://biorxiv.org/content/10.1101/2020.08.14.245340v1?rss=1 Jung, B. Lim, M. Jung, K. Li, M. Dong, H. Dube, N. Xu, T. 2020-08-14 doi:10.1101/2020.08.14.245340 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Learned adaptive multiphoton illumination microscopy ]]> https://biorxiv.org/content/10.1101/2020.08.14.251314v1?rss=1 Pinkard, H. Baghdassarian, H. Mujal, A. Roberts, E. Hu, K. H. Friedman, D. H. Malenica, I. Shagam, T. Fries, A. Corbin, K. Krummel, M. F. Waller, L. 2020-08-15 doi:10.1101/2020.08.14.251314 Cold Spring Harbor Laboratory Press 2020-08-15 <![CDATA[ Predicting future regional tau accumulation in asymptomatic and early Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2020.08.15.252601v1?rss=1 Giorgio, J. Jagust, W. J. Baker, S. Landau, S. M. Tino, P. Kourtzi, Z. ADNI, 2020-08-17 doi:10.1101/2020.08.15.252601 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Single-Strand DNA Breaks Cause Replisome Disassembly ]]> https://biorxiv.org/content/10.1101/2020.08.17.254235v1?rss=1 Vrtis, K. Dewar, J. Chistol, G. Wu, A. Graham, T. Walter, J. 2020-08-17 doi:10.1101/2020.08.17.254235 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Transcriptional Profiling of Identified Neurons in Leech ]]> https://biorxiv.org/content/10.1101/2020.08.17.254631v1?rss=1 Heath-Heckman, E. Yoo, S. Winchell, C. Pellegrino, M. Angstadt, J. Lammardo, V. Bautista, D. M. de Miguel, F. F. Weisblat, D. A. 2020-08-19 doi:10.1101/2020.08.17.254631 Cold Spring Harbor Laboratory Press 2020-08-19 <![CDATA[ A High-Performance Genetically Encoded Fluorescent Biosensor for Imaging Physiological Peroxynitrite ]]> https://biorxiv.org/content/10.1101/2020.08.17.254771v1?rss=1 10 fold C_LIO_LIpnGFP-Ultra robustly detects peroxynitrite production in macrophages and primary glial cells C_LI ]]> Chen, Z. Zhang, S. Li, X. Ai, H. 2020-08-18 doi:10.1101/2020.08.17.254771 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ 4 β-hydroxycholesterol is a pro-lipogenic factor that promotes SREBP1c expression and activity through Liver X-receptor. ]]> https://biorxiv.org/content/10.1101/2020.08.20.256487v1?rss=1 Moldavski, O. Zushin, P.-J. H. Berdan, C. A. van Eijkeren, R. J. Jiang, X. Qian, M. Ory, D. S. Covey, D. F. Nomura, D. Stahl, A. Weiss, E. Zoncu, R. 2020-08-21 doi:10.1101/2020.08.20.256487 Cold Spring Harbor Laboratory Press 2020-08-21 <![CDATA[ Stable isotope informed genome-resolved metagenomics uncovers potential trophic interactions in rhizosphere soil ]]> https://biorxiv.org/content/10.1101/2020.08.21.262063v1?rss=1 70% complete. The complete 18S rRNA sequences of several micro-eukaryotic bacterivores and fungi were enriched in 13C. We generated several circularized bacteriophage (phage) genomes, some of which were the most labelled entities in the rhizosphere. CRISPR locus targeting connected one of these phage to a Burkholderiales host predicted to be a plant pathogen. Another highly labeled phage is predicted to replicate in a Catenulispora sp., a possible plant growth-promoting bacterium. We searched the genomes for traits known to be used in interactions involving bacteria, micro-eukaryotes and plant roots and found that heavily isotopically-labeled bacteria have the ability to modulate plant signaling hormones, possess numerous plant pathogenicity factors, and produce toxins targeting micro-eukaryotes. Overall, 13C stable isotope-informed genome-resolved metagenomics revealed that very active bacteria often have the potential for strong interactions with plants and directly established that phage can be important agents of turnover of plant-derived carbon in soil. ]]> Starr, E. P. Shi, S. Blazewicz, S. J. Koch, B. J. Probst, A. J. Hungate, B. A. Pett-Ridge, J. Firestone, M. K. Banfield, J. F. 2020-08-21 doi:10.1101/2020.08.21.262063 Cold Spring Harbor Laboratory Press 2020-08-21 <![CDATA[ Differential effects of redox conditions on the decomposition of litter and soil organic matter ]]> https://biorxiv.org/content/10.1101/2020.08.21.262246v1?rss=1 Lin, Y. Campbell, A. N. Bhattacharyya, A. Didonato, N. Thompson, A. M. Tfaily, M. Nico, P. S. Silver, W. L. Pett-Ridge, J. 2020-08-24 doi:10.1101/2020.08.21.262246 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Mutanofactin promotes bacterial adhesion and biofilm formation of cariogenic Streptococcus mutans ]]> https://biorxiv.org/content/10.1101/2020.08.22.262196v1?rss=1 Li, Z. Du, Y. Sun, J. Pan, A. Zeng, L. Maboudian, R. Burne, R. A. Qian, P.-Y. Zhang, W. 2020-08-23 doi:10.1101/2020.08.22.262196 Cold Spring Harbor Laboratory Press 2020-08-23 <![CDATA[ Structure of SARS-CoV-2 ORF8, a rapidly evolving coronavirus protein implicated in immune evasion ]]> https://biorxiv.org/content/10.1101/2020.08.27.270637v1?rss=1 Flower, T. G. Buffalo, C. Z. Hooy, R. M. Allaire, M. Ren, X. Hurley, J. H. 2020-08-27 doi:10.1101/2020.08.27.270637 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Quantitative characterization of the eukaryotic transcription cycle using live imaging and statistical inference ]]> https://biorxiv.org/content/10.1101/2020.08.29.273474v1?rss=1 Liu, J. Hansen, D. Eck, E. Kim, Y. J. Turner, M. A. Alamos, S. Garcia, H. G. 2020-08-31 doi:10.1101/2020.08.29.273474 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Exploring the evolutionary history of kinetic stability in the alpha-lytic protease family ]]> https://biorxiv.org/content/10.1101/2020.08.30.274340v1?rss=1 Nixon, C. F. Lim, S. A. Sailer, Z. R. Zheludev, I. N. Gee, C. L. Kelch, B. A. Harms, M. J. Marqusee, S. 2020-08-31 doi:10.1101/2020.08.30.274340 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Bioelectrochemical engineering analysis of formate-mediated microbial electrosynthesis ]]> https://biorxiv.org/content/10.1101/2020.08.31.275537v1?rss=1 Abel, A. J. Clark, D. S. 2020-08-31 doi:10.1101/2020.08.31.275537 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ A genetic screen identifies processes that couple oocyte maturation to proteostasis in the immortal C. elegans germ lineage ]]> https://biorxiv.org/content/10.1101/2020.08.31.276006v1?rss=1 Samaddar, M. Goudeau, J. Sanchez, M. Hall, D. H. Bohnert, K. A. Ingaramo, M. Kenyon, C. 2020-08-31 doi:10.1101/2020.08.31.276006 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ A nanocompartment containing the peroxidase DypB contributes to defense against oxidative stress in M. tuberculosis ]]> https://biorxiv.org/content/10.1101/2020.08.31.276014v1?rss=1 Lien, K. A. Nichols, R. J. Cassidy-Amstutz, C. Dinshaw, K. Knight, M. Singh, R. Eltis, L. D. Savage, D. F. Stanley, S. 2020-08-31 doi:10.1101/2020.08.31.276014 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Efficient isolation of protoplasts from rice calli with pause points and its application in transient gene expression and genome editing assays ]]> https://biorxiv.org/content/10.1101/2020.09.01.278176v1?rss=1 Poddar, S. Tanaka, J. Cate, J. H. D. Staskawicz, B. Cho, M.-J. 2020-09-02 doi:10.1101/2020.09.01.278176 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ Dysregulation of hippocampal adult-born immature neurons disrupts a brain-wide network for spatial memory ]]> https://biorxiv.org/content/10.1101/2020.09.02.273649v1?rss=1 Bao, H. Hu, Z. Lee, S.-h. Kolagani, R. Chao, T.-H. H. Luo, Y.-J. Ban, W. Sullivan, H. A. Gamero-Alameda, S. Lybrand, Z. R. Yu, Y. Hsieh, J. Wickersham, I. R. Brenner, S. E. Shih, Y.-Y. I. Song, J. 2020-09-03 doi:10.1101/2020.09.02.273649 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Identification of a novel cobamide remodeling enzyme in the beneficial human gut bacterium Akkermansia muciniphila ]]> https://biorxiv.org/content/10.1101/2020.09.02.280537v1?rss=1 Mok, K. C. Sokolovskaya, O. M. Nicolas, A. M. Hallberg, Z. Deutschbauer, A. M. Carlson, H. K. Taga, M. E. 2020-09-03 doi:10.1101/2020.09.02.280537 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals ]]> https://biorxiv.org/content/10.1101/2020.09.07.286450v1?rss=1 Tournebize, R. Chu, G. Moorjani, P. 2020-09-07 doi:10.1101/2020.09.07.286450 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ Bacteriophage uptake by Eukaryotic cell layers represents a major sink for phages during therapy ]]> https://biorxiv.org/content/10.1101/2020.09.07.286716v1?rss=1 Bichet, M. C. Chin, W. H. Richards, W. Lin, Y.-W. Avellaneda-Franco, L. Hernandez, C. A. Oddo, A. Chernyavskiy, O. Hilsenstein, V. Neild, A. Li, J. C. Voelcker, N. H. Patwa, R. Barr, J. J. 2020-09-08 doi:10.1101/2020.09.07.286716 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ Pervasive duplication of tumor suppressors in Afrotherians during the evolution of large bodies and reduced cancer risk ]]> https://biorxiv.org/content/10.1101/2020.09.10.291906v1?rss=1 Vazquez, J. M. Lynch, V. J. 2020-09-10 doi:10.1101/2020.09.10.291906 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Convergent evolution of increased urine concentrating ability in desert mammals ]]> https://biorxiv.org/content/10.1101/2020.09.11.294124v1?rss=1 L. Rocha, J. Brito, J. C. Nielsen, R. Godinho, R. 2020-09-13 doi:10.1101/2020.09.11.294124 Cold Spring Harbor Laboratory Press 2020-09-13 <![CDATA[ Quantifying cytoskeletal heterogeneity via single-cell protein-complex fractionation ]]> https://biorxiv.org/content/10.1101/2020.09.12.294801v1?rss=1 Vlassakis, J. Hansen, L. L. Higuchi-Sanabria, R. Zhou, Y. Tsui, C. K. Dillin, A. Huang, H. Herr, A. E. 2020-09-13 doi:10.1101/2020.09.12.294801 Cold Spring Harbor Laboratory Press 2020-09-13 <![CDATA[ SARS CoV-2 nucleocapsid protein forms condensates with viral genomic RNA ]]> https://biorxiv.org/content/10.1101/2020.09.14.295824v1?rss=1 Jack, A. Ferro, L. S. Trnka, M. J. Wehri, E. Nadgir, A. Costa, K. Schaletzky, J. Yildiz, A. 2020-09-14 doi:10.1101/2020.09.14.295824 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ An associative learning account of sensorimotor adaptation ]]> https://biorxiv.org/content/10.1101/2020.09.14.297143v1?rss=1 Avraham, G. Taylor, J. A. Ivry, R. B. McDougle, S. D. 2020-09-15 doi:10.1101/2020.09.14.297143 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ Discovery of SARS-CoV-2 antiviral synergy between remdesivir and approved drugs in human lung cells ]]> https://biorxiv.org/content/10.1101/2020.09.18.302398v1?rss=1 Nguyenla, X. Wehri, E. Van Dis, E. Biering, S. Yamashiro, L. H. Stroumza, J. Dugast-Darzacq, C. Graham, T. Stanley, S. Schaletzky, J. 2020-09-18 doi:10.1101/2020.09.18.302398 Cold Spring Harbor Laboratory Press 2020-09-18 <![CDATA[ Routes to Roots: Direct Evidence of Water Transport by Arbuscular Mycorrhizal Fungi to Host Plants ]]> https://biorxiv.org/content/10.1101/2020.09.21.305409v1?rss=1 Kakouridis, A. Hagen, J. A. Kan, M. P. Mambelli, S. Feldman, L. J. Herman, D. J. Pett-Ridge, J. Firestone, M. K. 2020-09-21 doi:10.1101/2020.09.21.305409 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ Distinct tooth regeneration systems deploy a conserved battery of genes ]]> https://biorxiv.org/content/10.1101/2020.09.21.305466v1?rss=1 Square, T. A. Sundaram, S. Mackey, E. J. Miller, C. T. 2020-09-21 doi:10.1101/2020.09.21.305466 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ Rickettsia parkeri Sca2 promotes dissemination in an intradermal infection mouse model ]]> https://biorxiv.org/content/10.1101/2020.09.23.310409v1?rss=1 Burke, T. P. Tran, C. J. Engstrom, P. Glasner, D. R. Espinosa, D. A. Harris, E. Welch, M. D. 2020-09-23 doi:10.1101/2020.09.23.310409 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Hybrid local and distributed coding in PMd/M1 provides separation and interaction of bilateral arm signals ]]> https://biorxiv.org/content/10.1101/2020.09.23.310664v1?rss=1 Dixon, T. C. Merrick, C. M. Wallis, J. D. Ivry, R. B. Carmena, J. M. 2020-09-23 doi:10.1101/2020.09.23.310664 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Ribosomal protein S7 ubiquitination during ER stress in yeast is associated with selective mRNA translation and stress outcome ]]> https://biorxiv.org/content/10.1101/2020.09.24.311365v1?rss=1 Matsuki, Y. Matsuo, Y. Nakano, Y. Iwasaki, S. Yoko, H. Udagawa, T. Li, S. Saeki, Y. Yoshihisa, T. Tanaka, K. Ingolia, N. Inada, T. 2020-09-25 doi:10.1101/2020.09.24.311365 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity ]]> https://biorxiv.org/content/10.1101/2020.09.25.313643v1?rss=1 May, M. R. Contreras, D. L. Sundue, M. A. Nagalingum, N. S. Looy, C. V. Rothfels, C. J. 2020-09-27 doi:10.1101/2020.09.25.313643 Cold Spring Harbor Laboratory Press 2020-09-27 <![CDATA[ Structural insights on the substrate-binding proteins of the Mycobacterium tuberculosis mammalian-cell-entry (Mce) 1 and 4 complexes ]]> https://biorxiv.org/content/10.1101/2020.09.29.317909v1?rss=1 Asthana, P. Singh, D. Pedersen, J. S. Hynönen, M. J. Sulu, R. Murthy, A. V. Laitaoja, M. Jänis, J. W. Riley, L. Venkatesan, R. 2020-09-30 doi:10.1101/2020.09.29.317909 Cold Spring Harbor Laboratory Press 2020-09-30 <![CDATA[ Evolutionarily Driven Domain Swap Alters Sigma Factor Dependence in Bacterial Signaling System ]]> https://biorxiv.org/content/10.1101/2020.09.30.321588v1?rss=1 Garber, M. E. Frank, V. Kazakov, A. E. Zhang, H. Rajeev, L. Mukhopadhyay, A. 2020-10-02 doi:10.1101/2020.09.30.321588 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ RNA-Sieve: A likelihood-based deconvolution of bulk gene expression data using single-cell references ]]> https://biorxiv.org/content/10.1101/2020.10.01.322867v1?rss=1 Erdmann-Pham, D. D. Fischer, J. Hong, J. Song, Y. S. 2020-10-02 doi:10.1101/2020.10.01.322867 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans ]]> https://biorxiv.org/content/10.1101/2020.10.01.323113v1?rss=1 Zhang, X. Witt, K. E. Ko, A. Yuan, K. Xu, S. Nielsen, R. Huerta-Sanchez, E. 2020-10-02 doi:10.1101/2020.10.01.323113 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ The price of a bit: energetic costs and the evolution of cellular signaling ]]> https://biorxiv.org/content/10.1101/2020.10.06.327700v1?rss=1 Wang, T.-L. Kuznets-Speck, B. Broderick, J. Hinczewski, M. 2020-10-07 doi:10.1101/2020.10.06.327700 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ A dense linkage map for a large repetitive genome: discovery of the sex-determining region in hybridising fire-bellied toads (Bombina bombina and B. variegata) ]]> https://biorxiv.org/content/10.1101/2020.10.06.328633v1?rss=1 Nürnberger, B. Baird, S. J. E. Cizkova, D. Bryjova, A. Mudd, A. B. Blaxter, M. Szymura, J. M. 2020-10-09 doi:10.1101/2020.10.06.328633 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ State space discovery in spatial representation circuits with persistent cohomology ]]> https://biorxiv.org/content/10.1101/2020.10.06.328773v1?rss=1 Kang, L. Xu, B. Morozov, D. 2020-10-08 doi:10.1101/2020.10.06.328773 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Pseudomonas aeruginosa Stimulates Inflammation and Enhances KSHV-Induced Cell Proliferation and Cellular Transformation through Both LPS and Flagellin ]]> https://biorxiv.org/content/10.1101/2020.10.07.330803v1?rss=1 Markazi, A. Bracci, P. McGrath, M. S. Gao, S.-J. 2020-10-08 doi:10.1101/2020.10.07.330803 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Fetal innate immunity contributes to the induction of atypical behaviors in a mouse model of maternal immune activation ]]> https://biorxiv.org/content/10.1101/2020.10.09.333815v1?rss=1 Nichols, E. K. Chuang, H.-C. Davis, M. T. Geiger, K. M. Li, R. Z. Arnold, M. L. Lin, P. M. Misra, R. Coscoy, L. Saijo, K. 2020-10-10 doi:10.1101/2020.10.09.333815 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ RNA-binding protein Elavl1/HuR is required for maintenance of cranial neural crest specification ]]> https://biorxiv.org/content/10.1101/2020.10.14.338715v1?rss=1 Hutchins, E. J. Chacon, J. Bronner, M. E. 2020-10-14 doi:10.1101/2020.10.14.338715 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Alzheimer's pathology is associated with dedifferentiation of functional memory networks in aging ]]> https://biorxiv.org/content/10.1101/2020.10.14.340075v1?rss=1 Cassady, K. Adams, J. Chen, X. Maass, A. Harrison, T. Landau, S. Baker, S. Jagust, W. 2020-10-15 doi:10.1101/2020.10.14.340075 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ MGDrivE 2: A simulation framework for gene drive systems incorporating seasonality and epidemiological dynamics ]]> https://biorxiv.org/content/10.1101/2020.10.16.343376v1?rss=1 Wu, S. L. Bennett, J. B. Sanchez C., H. M. Dolgert, A. J. Leon, T. M. Marshall, J. M. 2020-10-17 doi:10.1101/2020.10.16.343376 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ Diverse viral proteases activate the NLRP1 inflammasome ]]> https://biorxiv.org/content/10.1101/2020.10.16.343426v1?rss=1 Tsu, B. V. Beierschmitt, C. Ryan, A. P. Agarwal, R. Mitchell, P. S. Daugherty, M. D. 2020-10-17 doi:10.1101/2020.10.16.343426 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ Fundamental limits on the rate of bacterial growth ]]> https://biorxiv.org/content/10.1101/2020.10.18.344382v1?rss=1 Belliveau, N. M. Chure, G. D. Hueschen, C. L. Garcia, H. G. Kondev, J. Fisher, D. S. Theriot, J. A. Phillips, R. 2020-10-18 doi:10.1101/2020.10.18.344382 Cold Spring Harbor Laboratory Press 2020-10-18 <![CDATA[ A multimodal cell census and atlas of the mammalian primary motor cortex ]]> https://biorxiv.org/content/10.1101/2020.10.19.343129v1?rss=1 BRAIN Initiative Cell Census Network (BICCN), Adkins, R. S. Aldridge, A. I. Allen, S. Ament, S. A. An, X. Armand, E. Ascoli, G. A. Bakken, T. E. Bandrowski, A. Banerjee, S. Barkas, N. Bartlett, A. Bateup, H. S. Behrens, M. M. Berens, P. Berg, J. Bernabucci, M. Bernaerts, Y. Bertagnolli, D. Biancalani, T. Boggeman, L. Booeshaghi, A. S. Bowman, I. Bravo, H. C. Cadwell, C. R. Callaway, E. M. Carlin, B. O'Connor, C. Carter, R. Casper, T. Castanon, R. G. Castro, J. R. Chance, R. K. Chatterjee, A. Chen, H. Chun, J. Colantuoni, C. Crabtree, J. Creasy, H. Cric 2020-10-21 doi:10.1101/2020.10.19.343129 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation ]]> https://biorxiv.org/content/10.1101/2020.10.19.345207v1?rss=1 Silver, A. Perez, S. Gee, M. Xu, B. Garg, S. Will, K. Gill, A. 2020-10-19 doi:10.1101/2020.10.19.345207 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ Ceragenins and antimicrobial peptides kill bacteria through distinct mechanisms ]]> https://biorxiv.org/content/10.1101/2020.10.20.346411v1?rss=1 Mitchell, G. Silvis, M. R. Talkington, K. C. Budzik, J. M. Dodd, C. E. Paluba, J. M. Oki, E. A. Trotta, K. L. Licht, D. J. Jimenez-Morales, D. Chou, S. Savage, P. B. Gross, C. A. Marletta, M. A. Cox, J. S. 2020-10-20 doi:10.1101/2020.10.20.346411 Cold Spring Harbor Laboratory Press 2020-10-20 <![CDATA[ Mitohormesis reprograms macrophage metabolism to enforce tolerance ]]> https://biorxiv.org/content/10.1101/2020.10.20.347443v1?rss=1 View larger version (49K): org.highwire.dtl.DTLVardef@c5c03org.highwire.dtl.DTLVardef@16cd130org.highwire.dtl.DTLVardef@119b461org.highwire.dtl.DTLVardef@914ee4_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Timblin, G. A. Tharp, K. M. Ford, B. Winchester, J. M. Wang, J. Zhu, S. Khan, R. I. Louie, S. K. Iavarone, A. T. ten Hoeve, J. Nomura, D. K. Stahl, A. Saijo, K. 2020-10-21 doi:10.1101/2020.10.20.347443 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Multiple sequential prediction errors during reward processing in the human brain ]]> https://biorxiv.org/content/10.1101/2020.10.20.347740v1?rss=1 Hoy, C. W. Steiner, S. C. Knight, R. T. 2020-10-21 doi:10.1101/2020.10.20.347740 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Higher Variability in Fungi Compared to Bacteria in the Foraging Honey Bee ]]> https://biorxiv.org/content/10.1101/2020.10.20.348128v1?rss=1 Decker, L. San Juan, P. A. Warren, M. L. Duckworth, C. E. Gao, C. Fukami, T. 2020-10-21 doi:10.1101/2020.10.20.348128 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Executive modulation of brain reward systems endows goals with value ]]> https://biorxiv.org/content/10.1101/2020.10.21.348938v1?rss=1 McDougle, S. D. Ballard, I. C. Baribault, B. Bishop, S. J. Collins, A. G. E. 2020-10-22 doi:10.1101/2020.10.21.348938 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ The mechanism of motor inhibition by microtubule-associated proteins ]]> https://biorxiv.org/content/10.1101/2020.10.22.351346v1?rss=1 Ferro, L. S. Eshun-Wilson, L. Golcuk, M. Fernandes, J. Huijben, T. Gerber, E. Jack, A. Costa, K. Gur, M. Feng, Q. Nogales, E. Yildiz, A. 2020-10-23 doi:10.1101/2020.10.22.351346 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes ]]> https://biorxiv.org/content/10.1101/2020.10.22.351486v1?rss=1 Freyman, W. A. Johnson, M. G. Rothfels, C. J. 2020-10-23 doi:10.1101/2020.10.22.351486 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ Ultrasound activates mechanosensitive TRAAK K+ channels directly through the lipid membrane ]]> https://biorxiv.org/content/10.1101/2020.10.24.349738v1?rss=1 Sorum, B. Rietmeijer, R. A. Gopakumar, K. Adesnik, H. Brohawn, S. G. 2020-10-25 doi:10.1101/2020.10.24.349738 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ crispr2vec: Machine Learning Model Predicts Off-Target Cuts of CRISPR systems ]]> https://biorxiv.org/content/10.1101/2020.10.28.359885v1?rss=1 Tara Basu Trivedi, T. Boger, R. Govinda Kamath, G. Evangelopoulos, G. Cate, J. Doudna, J. Hidary, J. 2020-10-29 doi:10.1101/2020.10.28.359885 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ Metabolic flux signatures of the ER unfolded protein response in vivo reveal decreased hepatic de novo lipogenesis and mobilization of lipids from adipose tissue to liver ]]> https://biorxiv.org/content/10.1101/2020.10.29.360073v1?rss=1 Schneider, C. P. Peng, L. Yuen, S. Chang, M. Karapetyan, R. Nyangau, E. Mohammed, H. Palacios, H. Ziari, N. Joe, L. K. Frakes, A. Dillin, A. Hellerstein, M. K. 2020-10-29 doi:10.1101/2020.10.29.360073 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ Baculovirus actin-rearrangement-inducing factor ARIF-1 induces the formation of dynamic clusters of invadosome-like structures ]]> https://biorxiv.org/content/10.1101/2020.11.03.365502v1?rss=1 Lauko, D. I. Ohkawa, T. Mares, S. E. Welch, M. D. 2020-11-03 doi:10.1101/2020.11.03.365502 Cold Spring Harbor Laboratory Press 2020-11-03 <![CDATA[ Cognitive insights from evolutionarily new brain structures in prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2020.11.07.372805v1?rss=1 Voorhies, W. I. Miller, J. A. Yao, J. Bunge, S. A. Weiner, K. S. 2020-11-07 doi:10.1101/2020.11.07.372805 Cold Spring Harbor Laboratory Press 2020-11-07 <![CDATA[ Structure and variability of optogenetic responses identify the operating regime of cortex ]]> https://biorxiv.org/content/10.1101/2020.11.11.378729v1?rss=1 Palmigiano, A. Fumarola, F. Mossing, D. P. Kraynyukova, N. Adesnik, H. Miller, K. 2020-11-11 doi:10.1101/2020.11.11.378729 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution ]]> https://biorxiv.org/content/10.1101/2020.11.13.382424v1?rss=1 Roberts Kingman, G. A. Vyas, D. N. Jones, F. C. Brady, S. D. Chen, H. I. Reid, K. Millhaven, M. Bertino, T. S. Aguirre, W. E. Heins, D. C. von Hippel, F. A. Park, P. J. Kirch, M. Absher, D. Myers, R. M. Di Palma, F. Bell, M. A. Kingsley, D. M. Veeramah, K. R. 2020-11-15 doi:10.1101/2020.11.13.382424 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ COAL_PHYRE: A Composite Likelihood Method for Estimating Species Tree Parameters from Genomic Data Using Coalescent Theory ]]> https://biorxiv.org/content/10.1101/2020.11.17.387399v1?rss=1 Guerra, G. A. Nielsen, R. 2020-11-20 doi:10.1101/2020.11.17.387399 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ EcDNA hubs drive cooperative intermolecular oncogene expression ]]> https://biorxiv.org/content/10.1101/2020.11.19.390278v1?rss=1 Hung, K. L. Yost, K. E. Xie, L. Wu, S. Lange, J. T. Duffy, C. V. Kraft, K. Tang, J. Shi, Q. Rose, J. C. Corces, M. R. Granja, J. M. Li, R. Rajkumar, U. Tjian, R. Bafna, V. Mischel, P. S. Liu, Z. Chang, H. Y. 2020-11-20 doi:10.1101/2020.11.19.390278 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Lysine methylation shields an intracellular pathogen from ubiquitylation ]]> https://biorxiv.org/content/10.1101/2020.11.20.392290v1?rss=1 Engstrom, P. Burke, T. P. Iavarone, A. T. Welch, M. D. 2020-11-21 doi:10.1101/2020.11.20.392290 Cold Spring Harbor Laboratory Press 2020-11-21 <![CDATA[ Household-Level Risk Factors for Aedes aegypti Pupal Density in Guayaquil, Ecuador ]]> https://biorxiv.org/content/10.1101/2020.11.23.391938v1?rss=1 Ha, T.-A. Leon, T. M. Lalangui, K. Ponce, P. Marshall, J. M. Cevallos, V. 2020-11-23 doi:10.1101/2020.11.23.391938 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ An Examination of an Enhanced Remote Sensing Method for Agent Attribution of Forest Disturbance ]]> https://biorxiv.org/content/10.1101/2020.11.23.394221v1?rss=1 Worsham, H. M. 2020-11-23 doi:10.1101/2020.11.23.394221 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ Learning epistatic polygenic phenotypes with Boolean interactions ]]> https://biorxiv.org/content/10.1101/2020.11.24.396846v1?rss=1 Behr, M. Kumbier, K. Cordova-Palomera, A. Aguirre, M. Ashley, E. Butte, A. Arnaout, R. Brown, J. B. Preist, J. Yu, B. 2020-11-25 doi:10.1101/2020.11.24.396846 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ Sparse Epistatic Regularization of Deep Neural Networks for Inferring Fitness Functions ]]> https://biorxiv.org/content/10.1101/2020.11.24.396994v1?rss=1 Aghazadeh, A. Nisonoff, H. Ocal, O. Huang, Y. Koyluoglu, O. O. Listgarten, J. Ramchandran, K. 2020-11-25 doi:10.1101/2020.11.24.396994 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ An adaptive optics module for deep tissue multiphoton imaging in vivo ]]> https://biorxiv.org/content/10.1101/2020.11.25.397968v1?rss=1 Rodriguez, C. Chen, A. Rivera, J. A. Mohr, M. A. Liang, Y. Sun, W. Milkie, D. E. Bifano, T. G. Chen, X. Ji, N. 2020-11-26 doi:10.1101/2020.11.25.397968 Cold Spring Harbor Laboratory Press 2020-11-26 <![CDATA[ Mucosal vaccination with cyclic-di-nucleotide adjuvants induces effective T cell homing and IL-17 dependent protection against M. tuberculosis infection ]]> https://biorxiv.org/content/10.1101/2020.11.25.398651v1?rss=1 Jong, R. M. Van Dis, E. Nguyenla, X. Baltodano, A. Pastenkos, G. Xu, C. Yosef, N. McWhirter, S. Stanley, S. 2020-11-27 doi:10.1101/2020.11.25.398651 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Hybrid Hyperalignment: A single high-dimensional model of shared information embedded in cortical patterns of response and functional connectivity ]]> https://biorxiv.org/content/10.1101/2020.11.25.398883v1?rss=1 Busch, E. L. Slipski, L. Feilong, M. Guntupalli, J. S. Visconti di Oleggio Castello, M. Huckins, J. F. Nastase, S. A. Gobbini, M. I. Wager, T. D. Haxby, J. V. 2020-11-27 doi:10.1101/2020.11.25.398883 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ A phage satellite tunes inducing phage gene expression using a domesticated endonuclease to balance inhibition and virion hijacking ]]> https://biorxiv.org/content/10.1101/2020.11.28.402263v1?rss=1 Netter, Z. Boyd, C. M. Silvas, T. V. Seed, K. 2020-11-28 doi:10.1101/2020.11.28.402263 Cold Spring Harbor Laboratory Press 2020-11-28 <![CDATA[ Bi-directional Modeling Between Cross-Scale Neural Activity ]]> https://biorxiv.org/content/10.1101/2020.11.30.404244v1?rss=1 Chang, Y.-J. Chen, Y.-I. Yeh, H.-C. Carmena, J. M. Santacruz, S. R. 2020-12-02 doi:10.1101/2020.11.30.404244 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Reconstructing Squamate Biogeography in Afro-Arabia Reveals the Influence of a Complex and Dynamic Geologic Past ]]> https://biorxiv.org/content/10.1101/2020.12.01.406546v1?rss=1 Tejero-Cicuendez, H. Patton, A. H. Caetano, D. S. Smid, J. Harmon, L. J. Carranza, S. 2020-12-02 doi:10.1101/2020.12.01.406546 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Enhancement of antimicrobial diversity in situ through relaxed symbiont specificity in an insect/actinomycete partnership ]]> https://biorxiv.org/content/10.1101/2020.12.02.394189v1?rss=1 Pessotti, R. d. C. Hansen, B. L. Reaso, J. N. Ceja-Navarro, J. A. El-Hifnawi, L. Brodie, E. L. Traxler, M. F. 2020-12-03 doi:10.1101/2020.12.02.394189 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Mechanistic basis for ubiquitin modulation of a protein energy landscape ]]> https://biorxiv.org/content/10.1101/2020.12.06.414011v1?rss=1 Carroll, E. C. Latorraca, N. R. Lindner, J. M. Maguire, B. C. Pelton, J. G. Marqusee, S. 2020-12-07 doi:10.1101/2020.12.06.414011 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ A holobiont view of island biogeography: unraveling patterns driving the nascent diversification of a Hawaiian spider and its microbial associates ]]> https://biorxiv.org/content/10.1101/2020.12.07.414961v1?rss=1 Armstrong, E. Perez-Lamarque, B. Bi, K. Chen, C. Becking, L. E. Lim, J. Y. Linderoth, T. Krehenwinkel, H. Gillespie, R. 2020-12-08 doi:10.1101/2020.12.07.414961 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ Systems-informed genome mining for electroautotrophic microbial production ]]> https://biorxiv.org/content/10.1101/2020.12.07.414987v1?rss=1 50 mol/cm2/hr for microbes using the reductive tricarboxylic acid cycle. Phylogenetic analysis, validated by recapitulating experimental demonstrations of electroautotrophy, uncovered multiple probable electroautotrophic organisms and a significant number of genetically tractable strains that require heterologous expression of <5 proteins to gain electroautotrophic function. The model and analysis presented here will guide microbial engineering and reactor design for practical MES systems. ]]> Abel, A. J. Hilzinger, J. M. Arkin, A. P. Clark, D. S. 2020-12-09 doi:10.1101/2020.12.07.414987 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ A structural mechanism for the generation of biased agonism in the epidermal growth factor receptor ]]> https://biorxiv.org/content/10.1101/2020.12.08.417006v1?rss=1 Huang, Y. Ognjenovic, J. Karandur, D. Merk, A. Subramaniam, S. Kuriyan, J. 2020-12-09 doi:10.1101/2020.12.08.417006 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Systematic characterization of gene function in a photosynthetic organism ]]> https://biorxiv.org/content/10.1101/2020.12.11.420950v1?rss=1 Vilarrasa-Blasi, J. Fauser, F. Onishi, M. Ramundo, S. Patena, W. Millican, M. Osaki, J. Philp, C. Nemeth, M. Salome, P. A. Li, X. Wakao, S. Kim, R. G. Kaye, Y. Grossman, A. R. Niyogi, K. K. Merchant, S. Cutler, S. Walter, P. Dinneny, J. R. Jonikas, M. C. Jinkerson, R. E. 2020-12-11 doi:10.1101/2020.12.11.420950 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ A novel allele of SIR2 reveals a heritable intermediate state of gene silencing ]]> https://biorxiv.org/content/10.1101/2020.12.11.422089v1?rss=1 Farris, D. Saxton, D. S. Rine, J. 2020-12-11 doi:10.1101/2020.12.11.422089 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Uncovering the Structure and Function of Microbial Communities Formed During Periodic Tilling of TNT and DNT Co-Contaminated Soils ]]> https://biorxiv.org/content/10.1101/2020.12.12.420737v1?rss=1 Keshani Langroodi, S. Lan, Y. Stenuit, B. Rosen, G. Hughes, J. B. Alvarez-Cohen, L. Sales, C. M. 2020-12-14 doi:10.1101/2020.12.12.420737 Cold Spring Harbor Laboratory Press 2020-12-14 <![CDATA[ Total recall: episodic memory retrieval,choice, and memory confidence in the rat ]]> https://biorxiv.org/content/10.1101/2020.12.14.420174v1?rss=1 Joo, H. R. Liang, H. Chung, J. E. Geaghan-Breiner, C. Fan, J. L. Nachman, B. Kepecs, A. Frank, L. M. 2020-12-15 doi:10.1101/2020.12.14.420174 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62 ]]> https://biorxiv.org/content/10.1101/2020.12.14.422728v1?rss=1 Itskanov, S. Park, E. 2020-12-14 doi:10.1101/2020.12.14.422728 Cold Spring Harbor Laboratory Press 2020-12-14 <![CDATA[ Highly contiguous assemblies of 101 drosophilid genomes ]]> https://biorxiv.org/content/10.1101/2020.12.14.422775v1?rss=1 Kim, B. Y. Wang, J. Miller, D. E. Barmina, O. Delaney, E. K. Thompson, A. Comeault, A. A. Peede, D. D'Agostino, E. R. R. Pelaez, J. Aguilar, J. M. Haji, D. Matsunaga, T. Armstrong, E. E. Zych, M. Ogawa, Y. Stamenkovic-Radak, M. Jelic, M. Veselinovic, M. S. Tanaskovic, M. Eric, P. Gao, J.-j. Katoh, T. K. Toda, M. J. Watabe, H. Watada, M. Davis, J. S. Moyle, L. C. Manoli, G. Bertolini, E. Kostal, V. Hawley, R. S. Takahashi, A. Jones, C. D. Price, D. K. Whiteman, N. K. Kopp, A. Matute, D. R. Petrov, D. A. 2020-12-15 doi:10.1101/2020.12.14.422775 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Predicting compound activity from phenotypic profiles and chemical structures ]]> https://biorxiv.org/content/10.1101/2020.12.15.422887v1?rss=1 Becker, T. Yang, K. Caicedo, J. C. Wagner, B. K. Dancik, V. C. Clemons, P. C. Singh, S. Carpenter, A. E. 2020-12-16 doi:10.1101/2020.12.15.422887 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ Temporal Shifts in Antibiotic Resistance Elements Govern Virus-Pathogen Conflicts ]]> https://biorxiv.org/content/10.1101/2020.12.16.423150v1?rss=1 LeGault, K. Hays, S. G. Angermeyer, A. McKitterick, A. C. Johura, F.-t. Sultana, M. Alam, M. Seed, K. D. 2020-12-17 doi:10.1101/2020.12.16.423150 Cold Spring Harbor Laboratory Press 2020-12-17 <![CDATA[ In Vitro Safety Clinical Trial of the Cardiac Liability of Hydroxychloroquine and Azithromycin as COVID19 Polytherapy ]]> https://biorxiv.org/content/10.1101/2020.12.21.423869v1?rss=1 Healy, K. Charrez, B. charwat, v. siemons, b. Miller, E. edwards, a. finsberg, h. 2020-12-22 doi:10.1101/2020.12.21.423869 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Single Layers of Attention Suffice to Predict Protein Contacts ]]> https://biorxiv.org/content/10.1101/2020.12.21.423882v1?rss=1 Bhattacharya, N. Thomas, N. Rao, R. Daupras, J. Koo, P. Baker, D. Song, Y. S. Ovchinnikov, S. 2020-12-22 doi:10.1101/2020.12.21.423882 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Narratives: fMRI data for evaluating models of naturalistic language comprehension ]]> https://biorxiv.org/content/10.1101/2020.12.23.424091v1?rss=1 Nastase, S. A. Liu, Y.-F. Hillman, H. Zadbood, A. Hasenfratz, L. Keshavarzian, N. Chen, J. Honey, C. J. Yeshurun, Y. Regev, M. Nguyen, M. Chang, C. H. C. Baldassano, C. Lositsky, O. Simony, E. Chow, M. A. Leong, Y. C. Brooks, P. P. Micciche, E. Choe, G. Goldstein, A. Vanderwal, T. Halchenko, Y. O. Norman, K. A. Hasson, U. 2020-12-23 doi:10.1101/2020.12.23.424091 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ The distribution of waiting distances in ancestral recombination graphs and its applications ]]> https://biorxiv.org/content/10.1101/2020.12.24.424361v1?rss=1 Deng, Y. Song, Y. S. Nielsen, R. 2020-12-26 doi:10.1101/2020.12.24.424361 Cold Spring Harbor Laboratory Press 2020-12-26 <![CDATA[ Presynaptic autophagy is coupled to the synaptic vesicle cycle via ATG-9 ]]> https://biorxiv.org/content/10.1101/2020.12.28.424508v1?rss=1 Yang, S. Park, D. Manning, L. Hill, S. E. Cao, M. Xuan, Z. Gonzalez, I. Shao, L. Okeke, I. De Camilli, P. Colon-Ramos, D. 2020-12-28 doi:10.1101/2020.12.28.424508 Cold Spring Harbor Laboratory Press 2020-12-28 <![CDATA[ Genealogical structure changes as range expansions transition from pushed to pulled ]]> https://biorxiv.org/content/10.1101/2020.12.29.424763v1?rss=1 Birzu, G. Hallatschek, O. Korolev, K. S. 2020-12-30 doi:10.1101/2020.12.29.424763 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ Screening a library of FDA-approved and bioactive compounds for antiviral activity against SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.12.30.424862v1?rss=1 Biering, S. B. Van Dis, E. Wehri, E. Yamashiro, L. H. Nguyenla, X. Dugast-Darzacq, C. Graham, T. G. Stroumza, J. R. Golovkine, G. R. Roberts, A. W. Fines, D. M. Spradlin, J. N. Ward, C. C. Bajaj, T. Dovala, D. Gahmen, U. S. Bajaj, R. Fox, D. M. Ott, M. Murthy, N. Nomura, D. Schaletzky, J. Stanley, S. A. 2020-12-30 doi:10.1101/2020.12.30.424862 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ Allosteric communication in DNA polymerase clamp loaders relies on a critical hydrogen-bonded junction ]]> https://biorxiv.org/content/10.1101/2020.12.31.424921v1?rss=1 Subramanian, S. Gorday, K. Marcus, K. Orellana, M. R. Ren, P. Luo, X. R. O'Donnell, M. E. Kuriyan, J. 2021-01-02 doi:10.1101/2020.12.31.424921 Cold Spring Harbor Laboratory Press 2021-01-02 <![CDATA[ Meta-analysis of massive parallel reporter assay enables functional regulatory elements prediction ]]> https://biorxiv.org/content/10.1101/202002v1?rss=1 Kreimer, A. Yan, Z. Ahituv, N. Yosef, N. 2017-10-11 doi:10.1101/202002 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ A relative-motion method for parsing spatio-temporal behaviour of dyads using GPS relocation data ]]> https://biorxiv.org/content/10.1101/2021.01.04.425238v1?rss=1 Luisa Vissat, L. Blackburn, J. Getz, W. M. 2021-01-05 doi:10.1101/2021.01.04.425238 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Batf-mediated Epigenetic Control of Effector CD8+ T Cell Differentiation ]]> https://biorxiv.org/content/10.1101/2021.01.04.425241v1?rss=1 Tsao, H.-W. Kaminski, J. Kurachi, M. Barnitz, R. A. DiIorio, M. A. LaFleur, M. W. Ise, W. Kurosaki, T. Wherry, E. J. Haining, W. N. Yosef, N. 2021-01-04 doi:10.1101/2021.01.04.425241 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Associations between brain structure and sleep patterns across adolescent development ]]> https://biorxiv.org/content/10.1101/2021.01.05.424689v1?rss=1 Jalbrzikowski, M. Hayes, R. A. Scully, K. E. Franzen, P. L. Hasler, B. P. Siegle, G. J. Buysse, D. J. Dahl, R. E. Forbes, E. E. Ladouceur, C. D. McMakin, D. L. Ryan, N. D. Silk, J. S. Goldstein, T. R. Soehner, A. M. 2021-01-05 doi:10.1101/2021.01.05.424689 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Seeing the World Like Never Before: Human stereovision through perfect optics ]]> https://biorxiv.org/content/10.1101/2021.01.05.425427v1?rss=1 Ng, C. J. Blake, R. Banks, M. S. Tadin, D. J. Yoon, G. 2021-01-06 doi:10.1101/2021.01.05.425427 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Nonadaptive radiation of the gut microbiome in an adaptive radiation of Cyprinodon pupfishes with minor shifts for scale-eating ]]> https://biorxiv.org/content/10.1101/2021.01.06.425529v1?rss=1 Heras, J. Martin, C. 2021-01-07 doi:10.1101/2021.01.06.425529 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Wide distribution of alternatively coded Lak megaphages in animal microbiomes ]]> https://biorxiv.org/content/10.1101/2021.01.08.425732v1?rss=1 Crisci, M. A. Chen, L.-X. Devoto, A. E. Borges, A. L. Bordin, N. Sachdeva, R. Tett, A. Sharrar, A. M. Segata, N. Debenedetti, F. Bailey, M. Burt, R. Wood, R. M. Rowden, L. J. Corsini, P. M. Holmes, M. A. Lei, S. Banfield, J. F. Santini, J. M. 2021-01-08 doi:10.1101/2021.01.08.425732 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Selective modulation of population dynamics during neuroprosthetic skill learning ]]> https://biorxiv.org/content/10.1101/2021.01.08.425917v1?rss=1 Zippi, E. L. You, A. K. Ganguly, K. Carmena, J. M. 2021-01-08 doi:10.1101/2021.01.08.425917 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ AncestralClust: Clustering of Divergent Nucleotide Sequences by Ancestral Sequence Reconstruction using Phylogenetic Trees ]]> https://biorxiv.org/content/10.1101/2021.01.08.426008v1?rss=1 Pipes, L. Nielsen, R. 2021-01-09 doi:10.1101/2021.01.08.426008 Cold Spring Harbor Laboratory Press 2021-01-09 <![CDATA[ Protein family content uncovers lineage relationships and bacterial pathway maintenance mechanisms in DPANN archaea ]]> https://biorxiv.org/content/10.1101/2021.01.12.426361v1?rss=1 Castelle, C. J. Meheust, R. Jaffe, A. L. Seitz, K. Gong, X. Baker, B. J. Banfield, J. 2021-01-12 doi:10.1101/2021.01.12.426361 Cold Spring Harbor Laboratory Press 2021-01-12 <![CDATA[ satuRn: Scalable Analysis of differential Transcript Usage for bulk and single-cell RNA-sequencing applications ]]> https://biorxiv.org/content/10.1101/2021.01.14.426636v1?rss=1 Gilis, J. Vitting-Seerup, K. Van den Berge, K. Clement, L. 2021-01-16 doi:10.1101/2021.01.14.426636 Cold Spring Harbor Laboratory Press 2021-01-16 <![CDATA[ De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes ]]> https://biorxiv.org/content/10.1101/2021.01.14.426684v1?rss=1 Hufford, M. B. Seetharam, A. S. Woodhouse, M. R. Chougule, K. M. Ou, S. LIU, J. Ricci, W. A. Guo, T. Olson, A. Qiu, Y. Della Coletta, R. Tittes, S. Hudson, A. I. Marand, A. P. Wei, S. Lu, Z. Wang, B. Tello-Ruiz, M. K. Piri, R. D. Wang, N. Kim, D. w. Zeng, Y. O'Connor, C. H. Li, X. Gilbert, A. M. Baggs, E. Krasileva, K. V. Portwood, J. L. Cannon, E. K. Andorf, C. M. MANCHANDA, N. Snodgrass, S. J. Hufnagel, D. E. Jiang, Q. Pedersen, S. Syring, M. L. Kudrna, D. A. Llaca, V. Fengler, K. Schmitz, R. J. Ross-Ibarra, J. Yu, J. Gent, J. I. Hirsch, C. N. Ware 2021-01-16 doi:10.1101/2021.01.14.426684 Cold Spring Harbor Laboratory Press 2021-01-16 <![CDATA[ The human cerebellum is essential for modulating perceptual sensitivity based on temporal expectations ]]> https://biorxiv.org/content/10.1101/2021.01.15.426903v1?rss=1 Breska, A. Ivry, R. B. 2021-01-15 doi:10.1101/2021.01.15.426903 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ T cell self-reactivity during thymic development dictates the timing of positive selection ]]> https://biorxiv.org/content/10.1101/2021.01.18.427079v1?rss=1 Lutes, L. K. Steier, Z. McIntyre, L. L. Pandey, S. Kaminski, J. Hoover, A. R. Ariotti, S. Streets, A. Yosef, N. Robey, E. A. 2021-01-21 doi:10.1101/2021.01.18.427079 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ All-optical electrophysiology in hiPSC-derived neurons with synthetic voltage sensors ]]> https://biorxiv.org/content/10.1101/2021.01.18.427081v1?rss=1 Puppo, F. Sadegh, S. Trujillo, C. Thunemann, M. Campbell, E. Vandenberghe, M. Shan, X. Akkouh, I. A. Miller, E. W. Bloodgood, B. L. Silva, G. A. Dale, A. M. Einevoll, G. T. Djurovic, S. Andreassen, O. A. Muotri, A. R. Devor, A. 2021-01-19 doi:10.1101/2021.01.18.427081 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Voxelwise encoding models show that cerebellar language representations are highly conceptual ]]> https://biorxiv.org/content/10.1101/2021.01.18.427158v1?rss=1 LeBel, A. Jain, S. Huth, A. G. 2021-01-18 doi:10.1101/2021.01.18.427158 Cold Spring Harbor Laboratory Press 2021-01-18 <![CDATA[ Structure of an Hsp90-immunophilin complex reveals cochaperone recognition of the client-maturation state ]]> https://biorxiv.org/content/10.1101/2021.01.21.427690v1?rss=1 Lee, K. Thwin, A. C. Tse, E. Gates, S. N. Southworth, D. R. 2021-01-22 doi:10.1101/2021.01.21.427690 Cold Spring Harbor Laboratory Press 2021-01-22 <![CDATA[ Dynamics and turnover of memory CD8 T cell responses following yellow fever vaccination ]]> https://biorxiv.org/content/10.1101/2021.01.23.427919v1?rss=1 Zarnitsyna, V. I. Akondy, R. S. Ahmed, H. McGuire, D. J. Zarnitsyn, V. G. Moore, M. Johnson, P. L. F. Ahmed, R. Li, K. Hellerstein, M. Antia, R. 2021-01-23 doi:10.1101/2021.01.23.427919 Cold Spring Harbor Laboratory Press 2021-01-23 <![CDATA[ Dorsal color variation among subspecies of the "Oregon" Dark-eyed Junco complex ]]> https://biorxiv.org/content/10.1101/2021.01.24.427985v1?rss=1 Yang, E. T. Unitt, P. Mason, N. A. 2021-01-26 doi:10.1101/2021.01.24.427985 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Computational structural genomics unravels common folds and predicted functions in the secretome of fungal phytopathogen Magnaporthe oryzae ]]> https://biorxiv.org/content/10.1101/2021.01.25.427855v1?rss=1 Seong, K. Krasileva, K. V. 2021-01-25 doi:10.1101/2021.01.25.427855 Cold Spring Harbor Laboratory Press 2021-01-25 <![CDATA[ Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects ]]> https://biorxiv.org/content/10.1101/2021.01.26.428252v1?rss=1 Van den Berge, K. Chou, H.-J. Roux de Bezieux, H. Street, K. Risso, D. Ngai, J. Dudoit, S. 2021-01-27 doi:10.1101/2021.01.26.428252 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Imagined speech can be decoded from low- and cross-frequency features in perceptual space ]]> https://biorxiv.org/content/10.1101/2021.01.26.428315v1?rss=1 Proix, T. Delgado Saa, J. Christen, A. Martin, S. Pasley, B. N. Knight, R. T. Tian, X. Poeppel, D. Doyle, W. K. Devinsky, O. Arnal, L. H. Megevand, P. Giraud, A.-L. 2021-01-26 doi:10.1101/2021.01.26.428315 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Infant gut strain persistence is associated with maternal origin, phylogeny, and functional potential including surface adhesion and iron acquisition ]]> https://biorxiv.org/content/10.1101/2021.01.26.428340v1?rss=1 Lou, Y. C. Olm, M. R. Diamond, S. Crits-Christoph, A. Firek, B. A. Baker, R. Morowitz, M. Banfield, J. F. 2021-01-27 doi:10.1101/2021.01.26.428340 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Moving outside the lab: The viability of conducting sensorimotor learning studies online ]]> https://biorxiv.org/content/10.1101/2021.01.30.181370v1?rss=1 Tsay, J. S. Lee, A. S. Ivry, R. B. Avraham, G. 2021-02-01 doi:10.1101/2021.01.30.181370 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Evolution of the bread wheat D-subgenome and enriching it with diversity from Aegilops tauschii ]]> https://biorxiv.org/content/10.1101/2021.01.31.428788v1?rss=1 Gaurav, K. Arora, S. Silva, P. Sanchez-Martin, J. Horsnell, R. Gao, L. Brar, G. S. Widrig, V. Raupp, J. Singh, N. Wu, S. Kale, S. M. Chinoy, C. Nicholson, P. Quiroz-Chavez, J. Simmonds, J. Hayta, S. Smedley, M. A. Harwood, W. Pearce, S. Gilbert, D. Kangara, N. Gardener, C. Forner-Martinez, M. Liu, J. Yu, G. Boden, S. Pascuccci, A. Ghosh, S. Hafeez, A. N. O'Hara, T. Waites, J. Cheema, J. Steuernagel, B. Patpour, M. Justesen, A. F. Liu, S. Rudd, J. Avni, R. Sharon, A. Steiner, B. Kirana, R. P. Buerstmayr, H. Mehrabi, A. A. Nasyrova, F. Y. Chayut, N. 2021-02-01 doi:10.1101/2021.01.31.428788 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Identification of a conserved neutralizing epitope present on spike proteins from highly pathogenic coronaviruses ]]> https://biorxiv.org/content/10.1101/2021.01.31.428824v1?rss=1 Huang, Y. Nguyen, A. W. Hsieh, C.-L. Silva, R. Olaluwoye, O. S. Wilen, R. Kaoud, T. S. Azouz, L. R. Qerqez, A. N. Le, K. C. Bohanon, a. L. DiVenere, A. M. Liu, Y. Amengor, D. Dalby, K. D'Arcy, S. McLellan, J. S. Maynard, J. A. 2021-02-01 doi:10.1101/2021.01.31.428824 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ The conserved serine transporter SdaC moonlights to enable self recognition ]]> https://biorxiv.org/content/10.1101/2021.02.01.428846v1?rss=1 View larger version (14K): org.highwire.dtl.DTLVardef@17dbf8eorg.highwire.dtl.DTLVardef@ab0faeorg.highwire.dtl.DTLVardef@9289adorg.highwire.dtl.DTLVardef@8ccc89_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chittor, A. Gibbs, K. A. 2021-02-01 doi:10.1101/2021.02.01.428846 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Image denoising for fluorescence microscopy by self-supervised transfer learning ]]> https://biorxiv.org/content/10.1101/2021.02.01.429188v1?rss=1 Wang, Y. Pinkard, H. Zhou, S. Waller, L. Huang, B. 2021-02-02 doi:10.1101/2021.02.01.429188 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Spray-induced gene silencing for disease control is dependent on the efficiency of pathogen RNA uptake ]]> https://biorxiv.org/content/10.1101/2021.02.01.429265v1?rss=1 Qiao, L. Lan, C. Capriotti, L. Ah-Fong, A. Nino Sanchez, J. Hamby, R. Heller, J. Zhao, H. Glass, N. L. Judelson, H. S. Mezzetti, B. Niu, D. Jin, H. 2021-02-02 doi:10.1101/2021.02.01.429265 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Proximity-labeling reveals novel host and parasite proteins at the Toxoplasma parasitophorous vacuole membrane ]]> https://biorxiv.org/content/10.1101/2021.02.02.429490v1?rss=1 Cygan, A. M. Jean Beltran, P. M. Branon, T. C. Ting, A. Y. Carr, S. A. Boothroyd, J. C. 2021-02-03 doi:10.1101/2021.02.02.429490 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Touch-triggered bZIP translocation regulates elongation and secondary wall biosynthesis ]]> https://biorxiv.org/content/10.1101/2021.02.03.429573v1?rss=1 Coomey, J. H. MacKinnon, K. J.-M. Handakumbura, P. McCahill, I. W. Trabucco, G. M. Mazzola, J. Leblanc, N. A. Kheam, R. Hernandez-Romero, M. Barry, K. W. Liu, L. Lee, J. E. Vogel, J. P. O'Malley, R. Chambers, J. J. Hazen, S. P. 2021-02-03 doi:10.1101/2021.02.03.429573 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Horizontal transfer of microbial toxin genes to gall midge genomes ]]> https://biorxiv.org/content/10.1101/2021.02.03.429655v1?rss=1 Verster, K. I. Tarnopol, R. L. Akalu, S. M. Whiteman, N. K. 2021-02-04 doi:10.1101/2021.02.03.429655 Cold Spring Harbor Laboratory Press 2021-02-04 <![CDATA[ Somatosensory innervation of healthy human oral tissues ]]> https://biorxiv.org/content/10.1101/2021.02.03.429664v1?rss=1 Moayedi, Y. Michlig, S. Park, M. Koch, A. Lumpkin, E. A. 2021-02-05 doi:10.1101/2021.02.03.429664 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Elephant seal muscle cells adapt to sustained glucocorticoid exposure by shifting their metabolic phenotype ]]> https://biorxiv.org/content/10.1101/2021.02.05.429992v1?rss=1 Torres-Velarde, J. M. Kolora, S. R. R. Khudyakov, J. I. Crocker, D. E. Sudmant, P. H. Vazquez-Medina, J. P. 2021-02-07 doi:10.1101/2021.02.05.429992 Cold Spring Harbor Laboratory Press 2021-02-07 <![CDATA[ Structure of the human SAGA coactivator complex ]]> https://biorxiv.org/content/10.1101/2021.02.08.430339v1?rss=1 Nogales, E. Herbst, D. Esbin, M. Louder, R. K. Dugast-Darzacq, C. Dailey, G. Fang, Q. Darzacq, X. Tjian, R. 2021-02-08 doi:10.1101/2021.02.08.430339 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Programmed ER fragmentation drives selective ER inheritance and degradation in budding yeast meiosis ]]> https://biorxiv.org/content/10.1101/2021.02.12.430990v1?rss=1 Otto, G. M. Cheunkarndee, T. Leslie, J. M. Brar, G. A. 2021-02-15 doi:10.1101/2021.02.12.430990 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ Single-cell Visualization and Quantification of Trace Metals in Chlamydomonas Lysosome-Related Organelles ]]> https://biorxiv.org/content/10.1101/2021.02.12.431000v1?rss=1 Schmollinger, S. Chen, S. Strenkert, D. Hui, C. Ralle, M. Merchant, S. S. 2021-02-13 doi:10.1101/2021.02.12.431000 Cold Spring Harbor Laboratory Press 2021-02-13 <![CDATA[ StrainGE: A toolkit to track and characterize low-abundance strains in complex microbial communities ]]> https://biorxiv.org/content/10.1101/2021.02.14.431013v1?rss=1 van Dijk, L. R. Walker, B. J. Straub, T. J. Worby, C. J. Grote, A. Schreiber, H. L. Anyansi, C. Pickering, A. J. Hultgren, S. J. Manson, A. L. Abeel, T. Earl, A. M. 2021-02-16 doi:10.1101/2021.02.14.431013 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Calling differential DNA methylation at cell-type resolution: addressing misconceptions and best practices ]]> https://biorxiv.org/content/10.1101/2021.02.14.431168v1?rss=1 Rahmani, E. Jew, B. Schweiger, R. Rhead, B. Criswell, L. A. Barcellos, L. F. Eskin, E. Rosset, S. Sankararaman, S. Halperin, E. 2021-02-15 doi:10.1101/2021.02.14.431168 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ Region-specific maladaptive gray matter myelination is associated with differential susceptibility to stress-induced behavior in male rodents and humans ]]> https://biorxiv.org/content/10.1101/2021.02.15.431176v1?rss=1 Long, K. L. P. Chao, L. L. Kazama, Y. An, A. Hu, K. Y. Peretz, L. Muller, D. C. Y. Roan, V. D. Misra, R. Toth, C. E. Breton, J. M. Casazza, W. Mostafavi, S. M. Huber, B. R. Woodward, S. H. Neylan, T. C. Kaufer, D. 2021-02-15 doi:10.1101/2021.02.15.431176 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ Gender and geographical disparity in editorial boards of journals in psychology and neuroscience ]]> https://biorxiv.org/content/10.1101/2021.02.15.431321v1?rss=1 Palser, E. R. Lazerwitz, M. Fotopoulou, K. 2021-02-16 doi:10.1101/2021.02.15.431321 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Restricted nucleation and piRNA-mediated establishment of H3K9me3-dependent heterochromatin during embryogenesis in Drosophila miranda ]]> https://biorxiv.org/content/10.1101/2021.02.16.431328v1?rss=1 Wei, K. H. C. Chan, C. Bachtrog, D. 2021-02-17 doi:10.1101/2021.02.16.431328 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Probe the effect of clustering on EphA2 receptor signaling efficiency by subcellular control of ligand-receptor mobility ]]> https://biorxiv.org/content/10.1101/2021.02.16.431455v1?rss=1 Chen, Z. Oh, D. Biswas, K. H. Zaidel-Bar, R. Groves, J. T. 2021-02-17 doi:10.1101/2021.02.16.431455 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Optical Estimation of Absolute Membrane Potential Using One- and Two-Photon Fluorescence Lifetime Imaging Microscopy ]]> https://biorxiv.org/content/10.1101/2021.02.16.431491v1?rss=1 Lazzari-Dean, J. Miller, E. 2021-02-17 doi:10.1101/2021.02.16.431491 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Perceptual restoration fails to recover unconscious processing for smooth eye movements after occipital stroke ]]> https://biorxiv.org/content/10.1101/2021.02.16.431524v1?rss=1 Kwon, S. Huxlin, K. R. Mitchell, J. F. 2021-02-18 doi:10.1101/2021.02.16.431524 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ The role of genus and life span in predicting seed and vegetative trait variation and correlation in Lathyrus, Phaseolus, and Vicia (Fabaceae) ]]> https://biorxiv.org/content/10.1101/2021.02.17.431656v1?rss=1 Herron, S. A. Rubin, M. J. Albrecht, M. A. Long, Q. G. Sandoval, M. C. Miller, A. J. 2021-02-17 doi:10.1101/2021.02.17.431656 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Humans hastened the range collapse and extinction of woolly mammoth ]]> https://biorxiv.org/content/10.1101/2021.02.17.431706v1?rss=1 Fordham, D. A. Brown, S. C. Akcakaya, H. R. Brook, B. W. Haythorne, S. Manica, A. Shoemaker, K. T. Austin, J. J. Blonder, B. Pilowsky, J. Rahbek, C. Nogues-Bravo, D. 2021-02-18 doi:10.1101/2021.02.17.431706 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Opposing dominance within a color gene block is associated with maladaptive hybrid signal discordance ]]> https://biorxiv.org/content/10.1101/2021.02.18.431741v1?rss=1 de Zwaan, D. R. Mackenzie, J. Mikklesen, E. Wang, S. 2021-02-18 doi:10.1101/2021.02.18.431741 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ High Light and High Temperature Reduce Photosynthesis via Different Mechanisms in the C4 Model Setaria viridis ]]> https://biorxiv.org/content/10.1101/2021.02.20.431694v1?rss=1 Anderson, C. M. Mattoon, E. M. Zhang, N. Becker, E. McHargue, W. Yang, J. Patel, D. Dautermann, O. McAdam, S. A. M. Tarin, T. Pathak, S. Avenson, T. J. Berry, J. Braud, M. Niyogi, K. K. Wilson, M. Nusinow, D. A. Vargas, R. Czymmek, K. J. Eveland, A. L. Zhang, R. 2021-02-20 doi:10.1101/2021.02.20.431694 Cold Spring Harbor Laboratory Press 2021-02-20 <![CDATA[ A chimeric nuclease substitutes CRISPR-Cas: A phage weaponizes laterally acquired specificity to destroy subviral parasites ]]> https://biorxiv.org/content/10.1101/2021.02.21.432181v1?rss=1 Barth, Z. K. Nguyen, M. H. T. Seed, K. 2021-02-22 doi:10.1101/2021.02.21.432181 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ The Functional Significance of Bacterial Predators ]]> https://biorxiv.org/content/10.1101/2021.02.22.432408v1?rss=1 Hungate, B. A. Marks, J. C. Power, M. E. Schwartz, E. van Groenigen, K. J. Blazewicz, S. J. Chuckran, P. F. Dijkstra, P. Finley, B. K. Firestone, M. K. Foley, M. M. Greenlon, A. Hayer, M. Hofmockel, K. Koch, B. J. Mack, M. C. Mau, R. L. Miller, S. N. Morrissey, E. M. Propster, J. R. Purcell, A. M. Sieradzki, E. T. Starr, E. P. Stone, B. W. G. Terrer, C. Pett-Ridge, J. 2021-02-25 doi:10.1101/2021.02.22.432408 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Dissociable oscillatory networks support gain and loss processing in human orbitofrontal cortex ]]> https://biorxiv.org/content/10.1101/2021.02.25.432874v1?rss=1 Saez, I. Lin, J. Chang, E. F. Parvizi, J. Knight, R. T. Hsu, M. 2021-02-26 doi:10.1101/2021.02.25.432874 Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ Comprehensive Profiling of Plasma Exosomes Using Data Independent Acquisitions, New Tools for Aging Cohort Studies ]]> https://biorxiv.org/content/10.1101/2021.02.27.433188v1?rss=1 1.5-fold change). We also analyzed exosome miRNA cargo and detected 331 miRNAs. Levels of several were significantly different in young and old individuals. In addition, 88 and 17 miRNAs were unique to old and young individuals, respectively. Plasma exosome biomarkers have great potential for translational studies investigating biomarkers of aging and age-related diseases and to monitor therapeutic aging interventions. ]]> Patel, S. K. Bruderer, R. Basisty, N. Bons, J. Desprez, P.-Y. Neri, F. Reiter, L. Campisi, J. Schilling, B. 2021-02-28 doi:10.1101/2021.02.27.433188 Cold Spring Harbor Laboratory Press 2021-02-28 <![CDATA[ Hypothalamic Overexpression of Neurosecretory Protein GL Leads to Obesity in Mice ]]> https://biorxiv.org/content/10.1101/2021.03.01.433475v1?rss=1 Narimatsu, Y. Fukumura, K. Shikano, K. Iwakoshi-Ukena, E. Furumitsu, M. Bentley, G. E. Kriegsfeld, L. J. Ukena, K. 2021-03-02 doi:10.1101/2021.03.01.433475 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ A simple, cost-effective and automation-friendly direct PCR approach for bacterial community analysis ]]> https://biorxiv.org/content/10.1101/2021.03.01.433496v1?rss=1 Song, F. Kuehl, J. V. Chandran, A. Arkin, A. P. 2021-03-02 doi:10.1101/2021.03.01.433496 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Patterns of gene content and co-occurrence constrain the evolutionary path toward animal association in CPR bacteria ]]> https://biorxiv.org/content/10.1101/2021.03.03.433784v1?rss=1 Jaffe, A. L. He, C. Keren, R. Valentin-Alvarado, L. E. Munk, P. L. Bouma-Gregson, K. Amano, Y. West, P. T. Banfield, J. F. 2021-03-03 doi:10.1101/2021.03.03.433784 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ Monitoring deep-tissue oxygenation with a millimeter-scale ultrasonic implant ]]> https://biorxiv.org/content/10.1101/2021.03.05.434129v1?rss=1 Sonmezoglu, S. Fineman, J. R. Maltepe, E. Maharbiz, M. M. 2021-03-05 doi:10.1101/2021.03.05.434129 Cold Spring Harbor Laboratory Press 2021-03-05 <![CDATA[ Multiplexed Ion Beam Imaging Readout of Single-Cell Immunoblotting ]]> https://biorxiv.org/content/10.1101/2021.03.06.434187v1?rss=1 Lomeli, G. Bosse, M. Bendall, S. C. Angelo, M. Herr, A. E. 2021-03-08 doi:10.1101/2021.03.06.434187 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ A Tail Fiber Protein and a Receptor-Binding Protein Mediate ICP2 Bacteriophage Interactions with Vibrio cholerae OmpU ]]> https://biorxiv.org/content/10.1101/2021.03.08.434494v1?rss=1 Lim, A. N. W. Yen, M. Seed, K. Lazinski, D. W. Camilli, A. 2021-03-09 doi:10.1101/2021.03.08.434494 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression. ]]> https://biorxiv.org/content/10.1101/2021.03.09.433671v1?rss=1 Roux de Bezieux, H. Van den Berge, K. Street, K. N. Dudoit, S. 2021-03-10 doi:10.1101/2021.03.09.433671 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19 ]]> https://biorxiv.org/content/10.1101/2021.03.09.434529v1?rss=1 van der Wijst, M. G. P. Vazquez, S. E. Hartoularos, G. C. Bastard, P. Grant, T. Bueno, R. Lee, D. S. Greenland, J. R. Sun, Y. Perez, R. Ogorodnikov, A. Ward, A. Mann, S. A. Lynch, K. L. Yun, C. Havlir, D. V. Chamie, G. Marquez, C. Greenhouse, B. Lionakis, M. S. Norris, P. J. Dumont, L. J. Kelly, K. Zhang, P. Zhang, Q. Gervais, A. Le Voyer, T. Whatley, A. Si, Y. Byrne, A. Combes, A. J. Arkal, A. Song, Y. S. Fragiadakis, G. K. UCSF COMET consortium, Kangelaris, K. Calfee, C. S. Erle, D. J. Hendrickson, C. Krummel, M. F. Woodruff, P. G. Langelier, C. R. 2021-03-10 doi:10.1101/2021.03.09.434529 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Dynamic sampling bias and overdispersion induced by skewed offspring distributions ]]> https://biorxiv.org/content/10.1101/2021.03.09.434663v1?rss=1 Okada, T. Hallatschek, O. 2021-03-10 doi:10.1101/2021.03.09.434663 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Measurement of Volatile Compounds for Real-time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt ]]> https://biorxiv.org/content/10.1101/2021.03.11.432778v1?rss=1 Kim, J. Goldstein, A. H. Chakraborty, R. Jardine, K. J. Weber, R. Sorensen, P. O. Wang, S. Faybishenko, B. Misztal, P. Brodie, E. L. 2021-03-12 doi:10.1101/2021.03.11.432778 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Bacterial filamentation drives colony chirality ]]> https://biorxiv.org/content/10.1101/2021.03.11.434908v1?rss=1 Aranda-Díaz, A. Rodrigues, C. Grote, A. Sun, J. Schreck, C. Hallatschek, O. Souslov, A. Möbius, W. Huang, K. 2021-03-11 doi:10.1101/2021.03.11.434908 Cold Spring Harbor Laboratory Press 2021-03-11 <![CDATA[ Leakiness at the human-animal interface in Southeast Asia and implications for the spread of antibiotic resistance ]]> https://biorxiv.org/content/10.1101/2021.03.15.435134v1?rss=1 Nadimpalli, M. L. Stegger, M. Viau, R. Yith, V. de Lauzanne, A. Sem, N. Borand, L. Huynh, B.-t. Brisse, S. Passet, V. Overballe-Petersen, S. Aziz, M. Gouali, M. Jacobs, J. Phe, T. Hungate, B. A. Leshyk, V. O. Pickering, A. J. Gravey, F. Liu, C. M. Johnson, T. J. Le Hello, S. Price, L. B. 2021-03-16 doi:10.1101/2021.03.15.435134 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Pyrolyzed substrates induce aromatic compound metabolism in the post-fire fungus, Pyronema domesticum ]]> https://biorxiv.org/content/10.1101/2021.03.15.435558v1?rss=1 Fischer, M. S. Stark, F. G. Berry, T. D. Zeba, N. Whitman, T. Traxler, M. F. 2021-03-16 doi:10.1101/2021.03.15.435558 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Membrane Hydrophobicity Determines the Activation Free Energy of Passive Lipid Transport ]]> https://biorxiv.org/content/10.1101/2021.03.17.435885v1?rss=1 Rogers, J. R. Espinoza Garcia, G. Geissler, P. L. 2021-03-17 doi:10.1101/2021.03.17.435885 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Isochoric supercooled preservation and revival of human cardiac microtissues ]]> https://biorxiv.org/content/10.1101/2021.03.22.436466v1?rss=1 Powell-Palm, M. J. Charwat, V. Charrez, B. Siemons, B. A. Healy, K. E. Rubinsky, B. 2021-03-22 doi:10.1101/2021.03.22.436466 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ A non-invasive brain-machine interface via independent control of individual motor units ]]> https://biorxiv.org/content/10.1101/2021.03.22.436518v1?rss=1 Formento, E. Botros, P. Carmena, J. 2021-03-23 doi:10.1101/2021.03.22.436518 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ Root carbon interaction with soil minerals is dynamic, leaving a legacy of microbially-derived residues ]]> https://biorxiv.org/content/10.1101/2021.03.23.436628v1?rss=1 View larger version (52K): org.highwire.dtl.DTLVardef@17ce1bborg.highwire.dtl.DTLVardef@1c7c2e8org.highwire.dtl.DTLVardef@1cd0e41org.highwire.dtl.DTLVardef@162ff90_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Neurath, R. A. Pett-Ridge, J. Chu-Jacoby, I. Herman, D. J. Whitman, T. Nico, P. S. Lipton, A. S. Kyle, J. Tfaily, M. M. Thompson, A. Firestone, M. K. 2021-03-23 doi:10.1101/2021.03.23.436628 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ Characterization of transcript enrichment and detection bias in single-nuclei RNA-seq for mapping of distinct human adipocyte lineages ]]> https://biorxiv.org/content/10.1101/2021.03.24.435852v1?rss=1 Gupta, A. Shamsi, F. Altemose, N. Dorlhiac, G. F. Cypess, A. M. White, A. P. Patti, M. E. Tseng, Y.-H. Streets, A. M. 2021-03-25 doi:10.1101/2021.03.24.435852 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Genetic differentiation of Xylella fastidiosa following the introduction into Taiwan ]]> https://biorxiv.org/content/10.1101/2021.03.24.436723v1?rss=1 Castillo, A. I. Tsai, C.-W. Su, C.-C. Weng, L.-W. Lin, Y.-C. Cho, S.-T. Almeida, R. P. P. Kuo, C.-H. 2021-03-24 doi:10.1101/2021.03.24.436723 Cold Spring Harbor Laboratory Press 2021-03-24 <![CDATA[ Retinal waves but not visual experience are required for development of retinal direction selectivity maps ]]> https://biorxiv.org/content/10.1101/2021.03.25.437067v1?rss=1 Tiriac, A. Bistrong, K. Feller, M. 2021-03-26 doi:10.1101/2021.03.25.437067 Cold Spring Harbor Laboratory Press 2021-03-26 <![CDATA[ Resting-state based prediction of task-related activation in patients with disorders of consciousness ]]> https://biorxiv.org/content/10.1101/2021.03.27.436534v1?rss=1 Craig, M. M. Pappas, I. Allanson, J. Finoia, P. Williams, G. Pickard, J. D. Menon, D. Stamatakis, E. 2021-03-29 doi:10.1101/2021.03.27.436534 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ Combining evolutionary and assay-labelled data for protein fitness prediction ]]> https://biorxiv.org/content/10.1101/2021.03.28.437402v1?rss=1 Hsu, C. Nisonoff, H. Fannjiang, C. Listgarten, J. 2021-03-29 doi:10.1101/2021.03.28.437402 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time ]]> https://biorxiv.org/content/10.1101/2021.03.29.437569v1?rss=1 Williams, B. P. Bechen, L. A. Pohlmann, D. A. Gehring, M. 2021-03-29 doi:10.1101/2021.03.29.437569 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ Colonial choanoflagellate isolated from Mono Lake harbors a microbiome ]]> https://biorxiv.org/content/10.1101/2021.03.30.437421v1?rss=1 Hake, K. West, P. T. McDonald, K. L. Laundon, D. Feng, C. Burkhardt, P. Richter, D. J. Banfield, J. King, N. 2021-03-30 doi:10.1101/2021.03.30.437421 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ Antagonistic inhibitory subnetworks control cooperation and competition across cortical space ]]> https://biorxiv.org/content/10.1101/2021.03.31.437953v1?rss=1 Mossing, D. P. Veit, J. Palmigiano, A. Miller, K. D. Adesnik, H. 2021-03-31 doi:10.1101/2021.03.31.437953 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Repeated stimulation of the HPA axis alters white blood cell counts without increasing oxidative stress or inflammatory cytokines in fasting elephant seal pups ]]> https://biorxiv.org/content/10.1101/2021.03.31.437957v1?rss=1 Ensminger, D. C. Crocker, D. E. Lam, E. K. Allen, K. N. Vazquez-Medina, J. P. 2021-04-01 doi:10.1101/2021.03.31.437957 Cold Spring Harbor Laboratory Press 2021-04-01 <![CDATA[ Cobolt: Joint analysis of multimodal single-cell sequencing data ]]> https://biorxiv.org/content/10.1101/2021.04.03.438329v1?rss=1 Gong, B. Zhou, Y. Purdom, E. 2021-04-04 doi:10.1101/2021.04.03.438329 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Differential effects of cerebellar degeneration on feedforward versus feedback control across speech and reaching movements ]]> https://biorxiv.org/content/10.1101/2021.04.05.438454v1?rss=1 Parrell, B. Kim, H. Breska, A. Saxena, A. Ivry, R. 2021-04-06 doi:10.1101/2021.04.05.438454 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Tubular ERGIC (t-ERGIC): a SURF4-mediated expressway for ER-to-Golgi transport ]]> https://biorxiv.org/content/10.1101/2021.04.06.438517v1?rss=1 Yan, R. Chen, K. Xu, K. 2021-04-06 doi:10.1101/2021.04.06.438517 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Investigating the Interplay Between Affective, Phonatory and Motoric Subsystems in Autism Spectrum Disorder Using a Multimodal Dialogue Agent ]]> https://biorxiv.org/content/10.1101/2021.04.10.439293v1?rss=1 Kothare, H. Ramanarayanan, V. Roesler, O. Neumann, M. Liscombe, J. Burke, W. Cornish, A. Habberstad, D. Sakallah, A. Markuson, S. Kansara, S. Faerman, A. Bensidi-Slimane, Y. Fry, L. Portera, S. Suendermann-Oeft, D. Pautler, D. Demopoulos, C. 2021-04-11 doi:10.1101/2021.04.10.439293 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Excitation spectral microscopy for highly multiplexed fluorescence imaging and quantitative biosensing ]]> https://biorxiv.org/content/10.1101/2021.04.13.439576v1?rss=1 Chen, K. Yan, R. Xiang, L. Xu, K. 2021-04-13 doi:10.1101/2021.04.13.439576 Cold Spring Harbor Laboratory Press 2021-04-13 <![CDATA[ Structural basis for the ARF GAP activity and specificity of the C9orf72 complex ]]> https://biorxiv.org/content/10.1101/2021.04.13.439632v1?rss=1 Su, M.-Y. Fromm, S. H. Remis, J. Toso, D. Hurley, J. H. 2021-04-13 doi:10.1101/2021.04.13.439632 Cold Spring Harbor Laboratory Press 2021-04-13 <![CDATA[ Chromosome evolution and the genetic basis of agronomically important traits in greater yam ]]> https://biorxiv.org/content/10.1101/2021.04.14.439117v1?rss=1 Bredeson, J. V. Lyons, J. B. Oniyinde, I. O. Okereke, N. R. Kolade, O. Nnabue, I. Nwadili, C. O. Hribova, E. Parker, M. Nwogha, J. Shu, S. Carlson, J. Kariba, R. Muthemba, S. Knop, K. Barton, G. J. Sherwood, A. V. Lopez-Montes, A. Asiedu, R. Jamnadass, R. Muchugi, A. Goodstein, D. Egesi, C. N. Featherston, J. Asfaw, A. Simpson, G. G. Dolezel, J. Hendre, P. S. Van Deynze, A. Lava Kumar, P. Obidiegwu, J. E. Bhattacharjee, R. Rokhsar, D. S. 2021-04-15 doi:10.1101/2021.04.14.439117 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history ]]> https://biorxiv.org/content/10.1101/2021.04.14.439553v1?rss=1 Yu, H. Jamieson, A. Hulme-Beaman, A. Conroy, C. J. Knight, B. Speller, C. Al-Jarah, H. Eager, H. Trinks, A. Adikari, G. Baron, H. Böhlendorf-Arslan, B. Bohingamuwa, W. Crowther, A. Cucchi, T. Esser, K. Fleisher, J. Gidney, L. Gladilina, E. Gol'din, P. Goodman, S. Hamilton-Dyer, S. Helm, R. Hillman, J. C. Kallala, N. Kivikero, H. Kovacs, Z. E. Kunst, G. K. Kysely, R. Linderholm, A. Maraoui-Telmini, B. Morales-Muniz, A. Nabais, M. O'Connor, T. Oueslati, T. Quintana Morales, E. M. Pasda, K. Perera, J. Perera, N. Radbauer, S. Ramon, J. Rannamäe, E. Sanma 2021-04-14 doi:10.1101/2021.04.14.439553 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Aging alters the metabolic flux signature of the ER unfolded protein response in vivo in mice ]]> https://biorxiv.org/content/10.1101/2021.04.14.439896v1?rss=1 Schneider, C. P. Peng, L. Yuen, S. Halstead, J. Palacios, H. Nyangau, E. Mohammed, H. Ziari, N. Frakes, A. E. Dillin, A. Hellerstein, M. 2021-04-15 doi:10.1101/2021.04.14.439896 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ Discovery of a Covalent FEM1B Recruiter for Targeted Protein Degradation Applications ]]> https://biorxiv.org/content/10.1101/2021.04.15.439993v1?rss=1 600 E3 ligases that exist in human cells. Here, we have discovered a cysteine-reactive covalent ligand, EN106, that targets FEM1B, an E3 ligase recently discovered as the critical component of the cellular response to reductive stress. By targeting Cys186 in FEM1B, EN106 disrupts recognition of the key reductive stress substrate of FEM1B, FNIP1. We further establish that EN106 can be used as a covalent recruiter for FEM1B in TPD applications, in which we demonstrate that a PROTAC linking EN106 to the BET Bromodomain inhibitor JQ1 leads to specific FEM1B- and proteasome-dependent degradation of BRD4 in cells. Our study showcases a covalent ligand that targets a natural E3 ligase-substrate binding site and highlights the utility of covalent ligand screening in expanding the arsenal of E3 ligase recruiters that can be deployed for TPD applications. ]]> Henning, N. J. Manford, A. G. Spradlin, J. N. Brittain, S. M. McKenna, J. M. Tallarico, J. A. Schirle, M. Rape, M. Nomura, D. K. 2021-04-15 doi:10.1101/2021.04.15.439993 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ Genome-wide, bidirectional CRISPR screens identify mucins as critical host factors modulating SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2021.04.22.440848v1?rss=1 Biering, S. B. Sarnik, S. A. Wang, E. Zengel, J. R. Sathyan, V. Nguyenla, X. Van Dis, E. Catamura, C. Yamashiro, L. H. Begeman, A. Stark, J. C. Shon, D. J. Fox, D. M. Puschnik, A. S. Bertozzi, C. R. Carette, J. E. Stanley, S. A. Harris, E. Konermann, S. Hsu, P. D. 2021-04-23 doi:10.1101/2021.04.22.440848 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ A deep learning approach to neurite prediction in high throughput fluorescence imaging ]]> https://biorxiv.org/content/10.1101/2021.04.23.441035v1?rss=1 Barch, M. Cobb, M. M. Tokuno, Z. Leddy, J. Prenton, K. Manubens-Gil, L. Bellini, N. Lam, S. Kaye, J. A. Dierssen, M. Finkbeiner, S. 2021-04-26 doi:10.1101/2021.04.23.441035 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Binding mechanism of neutralizing Nanobodies targeting SARS-CoV-2 Spike Glycoprotein ]]> https://biorxiv.org/content/10.1101/2021.04.23.441186v1?rss=1 Golcuk, M. Hacisuleyman, A. Erman, B. Yildiz, A. Gur, M. 2021-04-26 doi:10.1101/2021.04.23.441186 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Mechanical phenotyping of acute promyelocytic leukemia reveals unique biomechanical responses in retinoic acid-resistant populations ]]> https://biorxiv.org/content/10.1101/2021.04.25.441378v1?rss=1 Li, B. Maslan, A. Streets, A. M. Sohn, L. L. 2021-04-26 doi:10.1101/2021.04.25.441378 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ The encapsulin from Thermatoga maritima is a flavoprotein with a symmetry matched ferritin-like cargo protein ]]> https://biorxiv.org/content/10.1101/2021.04.26.441214v1?rss=1 LaFrance, B. J. Cassidy-Amstutz, C. Nichols, R. J. Oltrogge, L. M. Nogales, E. Savage, D. F. 2021-04-26 doi:10.1101/2021.04.26.441214 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Sleep Loss Impacts the Interconnected Brain-Body-Mood Regulation of Cardiovascular Function in Humans ]]> https://biorxiv.org/content/10.1101/2021.04.27.441611v1?rss=1 Krause, A. J. Vallat, R. Ben Simon, E. Walker, M. P. 2021-04-28 doi:10.1101/2021.04.27.441611 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Robust and annotation-free analysis of isoform variation using short-read scRNA-seq data ]]> https://biorxiv.org/content/10.1101/2021.04.27.441683v1?rss=1 Benegas, G. Fischer, J. Song, Y. S. 2021-04-27 doi:10.1101/2021.04.27.441683 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ An organelle inheritance pathway during polarized cell growth ]]> https://biorxiv.org/content/10.1101/2021.04.28.441793v1?rss=1 Li, K. W. Pedersen, R. T. Lu, M. S. Drubin, D. G. 2021-04-29 doi:10.1101/2021.04.28.441793 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ scvi-tools: a library for deep probabilistic analysis of single-cell omics data ]]> https://biorxiv.org/content/10.1101/2021.04.28.441833v1?rss=1 Gayoso, A. Lopez, R. Xing, G. Boyeau, P. Wu, K. Jayasuriya, M. Mehlman, E. Langevin, M. Liu, Y. Samaran, J. Misrachi, G. Nazaret, A. Clivio, O. Xu, C. Ashuach, T. Lotfollahi, M. Svensson, V. da Veiga Beltrame, E. Talavera-Lopez, C. Pachter, L. Theis, F. J. Streets, A. Jordan, M. I. Regier, J. Yosef, N. 2021-04-29 doi:10.1101/2021.04.28.441833 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Systematic over-crediting in California's forest carbon offsets program ]]> https://biorxiv.org/content/10.1101/2021.04.28.441870v1?rss=1 Badgley, G. Freeman, J. Hamman, J. J. Haya, B. Trugman, A. T. Anderegg, W. R. L. Cullenward, D. 2021-04-29 doi:10.1101/2021.04.28.441870 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Ecological basis and genetic architecture of crypsis polymorphism in the desert clicker grasshopper (Ligurotettix coquilletti) ]]> https://biorxiv.org/content/10.1101/2021.04.29.441881v1?rss=1 O'Connor, T. K. Sandoval, M. C. Wang, J. Takenaka, R. Child, M. Hans, J. C. Whiteman, N. K. 2021-04-30 doi:10.1101/2021.04.29.441881 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Water Stress and Disruption of Mycorrhizae Induce Parallel Shifts in Phyllosphere Microbiome Composition ]]> https://biorxiv.org/content/10.1101/2021.04.29.442000v1?rss=1 Debray, R. Socolar, Y. Kaulbach, G. Guzman, A. Hernandez, C. A. Curley, R. Dhond, A. Bowles, T. Koskella, B. 2021-04-29 doi:10.1101/2021.04.29.442000 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Embryo-to-embryo variability in RNAi knockdown efficiency of dKDM5/lid in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2021.04.29.442033v1?rss=1 Albright, A. R. Eisen, M. 2021-04-29 doi:10.1101/2021.04.29.442033 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Deubiquitinase-Targeting Chimeras for Targeted Protein Stabilization ]]> https://biorxiv.org/content/10.1101/2021.04.30.441959v1?rss=1 Henning, N. J. Boike, L. Spradlin, J. N. Ward, C. C. Belcher, B. Brittain, S. M. Hesse, M. Dovala, D. McGregor, L. M. McKenna, J. M. Tallarico, J. A. Schirle, M. Nomura, D. K. 2021-04-30 doi:10.1101/2021.04.30.441959 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Low-bias ncRNA Libraries using Ordered Two-Template Relay: Serial Template Jumping by a Modified Retroelement Reverse Transcriptase ]]> https://biorxiv.org/content/10.1101/2021.04.30.442027v1?rss=1 upton, h. e. ferguson, l. Temoche-Diaz, m. m. liu, x. pimentel, s. c. ingolia, n. t. schekman, r. Collins, K. 2021-04-30 doi:10.1101/2021.04.30.442027 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Left Hemisphere Dominance for Bilateral Kinematic Encoding in the Human Brain ]]> https://biorxiv.org/content/10.1101/2021.05.01.442295v1?rss=1 Merrick, C. M. Dixon, T. C. Breska, A. Lin, J. J. Chang, E. F. King-Stephens, D. Laxer, K. D. Weber, P. B. Carmena, J. M. Knight, R. T. Ivry, R. B. 2021-05-02 doi:10.1101/2021.05.01.442295 Cold Spring Harbor Laboratory Press 2021-05-02 <![CDATA[ Soils and sediments host novel archaea with divergent monooxygenases implicated in ammonia oxidation ]]> https://biorxiv.org/content/10.1101/2021.05.03.442362v1?rss=1 Diamond, S. Lavy, A. Crits-Christoph, A. Matheus Carnevali, P. B. Sharrar, A. Williams, K. H. Banfield, J. F. 2021-05-03 doi:10.1101/2021.05.03.442362 Cold Spring Harbor Laboratory Press 2021-05-03 <![CDATA[ The dengue virus NS1 protein conveys pro-inflammatory signals by docking onto human high-density lipoproteins ]]> https://biorxiv.org/content/10.1101/2021.05.05.442454v1?rss=1 Benfrid, S. Park, K.-H. P. Dellarole, M. Voss, J. E. Tamietti, C. Pehau-Arnaudet, G. Raynal, B. Brule, S. England, P. Zhang, X. Mikhailova, A. Ungeheuer, M.-N. Petres, S. Biering, S. Harris, E. Sakuntabhai, A. Buchy, P. Duong, V. Dussart, P. Coulibaly, F. Bontems, F. Rey, F. A. Flamand, M. 2021-05-05 doi:10.1101/2021.05.05.442454 Cold Spring Harbor Laboratory Press 2021-05-05 <![CDATA[ In situ and transcriptomic identification of synapse-associated microglia in the developing zebrafish brain ]]> https://biorxiv.org/content/10.1101/2021.05.08.443268v1?rss=1 Silva, N. J. Dorman, L. C. vainchtein, i. Horneck, N. C. Molofsky, A. V. 2021-05-10 doi:10.1101/2021.05.08.443268 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Extracellular vesicles from neuronal cells promote neural induction of mESCs through cyclinD1 ]]> https://biorxiv.org/content/10.1101/2021.05.09.443321v1?rss=1 Song, L. Tian, X. Schekman, R. 2021-05-09 doi:10.1101/2021.05.09.443321 Cold Spring Harbor Laboratory Press 2021-05-09 <![CDATA[ The genetic architecture of phenotypic diversity in the betta fish (Betta splendens) ]]> https://biorxiv.org/content/10.1101/2021.05.10.443352v1?rss=1 Zhang, W. Wang, H. Brandt, D. Y. C. Hu, B. Sheng, J. Wang, M. Luo, H. Guo, S. Sheng, B. Zeng, Q. Peng, K. Zhao, D. Jian, S. Wu, D. Wang, J. van Esch, J. H. M. Shi, W. Ren, J. Nielsen, R. Hong, Y. 2021-05-10 doi:10.1101/2021.05.10.443352 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Comprehensive analysis of meiosis-derived cDNA libraries reveals gene isoforms and mitochondrial proteins important for competitive fitness ]]> https://biorxiv.org/content/10.1101/2021.05.10.443361v1?rss=1 Sing, T. L. Conlon, K. Lu, S. H. Madrazo, N. Barker, J. C. Hollerer, I. Brar, G. A. Sudmant, P. H. Ünal, E. 2021-05-10 doi:10.1101/2021.05.10.443361 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Extreme longevity of highly fecund termite queens achieved by mitochondrial and insulin upregulation without harmful lipid signatures or accumulation ]]> https://biorxiv.org/content/10.1101/2021.05.10.443390v1?rss=1 Seite, S. Harrison, M. C. Sillam-Dusses, D. Lupoli, R. Van Dooren, T. J. M. Robert, A. Poissonnier, L.-A. Lemainque, A. Renault, D. Acket, S. Andrieu, M. Viscarra, J. Sul, H. S. de Beer, Z. W. Bornberg-Bauer, E. Vasseur-Cognet, M. 2021-05-10 doi:10.1101/2021.05.10.443390 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes ]]> https://biorxiv.org/content/10.1101/2021.05.10.443470v1?rss=1 Tribble, C. M. Freyman, W. A. Lim, J. Y. Landis, M. J. Barido-Sottani, J. Kopperud, B. T. Höhna, S. May, M. R. 2021-05-11 doi:10.1101/2021.05.10.443470 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters ]]> https://biorxiv.org/content/10.1101/2021.05.10.443473v1?rss=1 Crits-Christoph, A. Diamond, S. Al-Shayeb, B. Valentin-Alvarado, L. Banfield, J. F. 2021-05-11 doi:10.1101/2021.05.10.443473 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation ]]> https://biorxiv.org/content/10.1101/2021.05.10.443517v1?rss=1 Lopez, R. Li, B. Keren-Shaul, H. Boyeau, P. Kedmi, M. Pilzer, D. Jelinski, A. David, E. Wagner, A. Addadi, Y. Jordan, M. I. Amit, I. Yosef, N. 2021-05-11 doi:10.1101/2021.05.10.443517 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ Evaluating brain parcellations using the distance controlled boundary coefficient ]]> https://biorxiv.org/content/10.1101/2021.05.11.443151v1?rss=1 Zhi, D. King, M. Diedrichsen, J. 2021-05-11 doi:10.1101/2021.05.11.443151 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ The recent evolutionary rescue of a staple crop depended on over half a century of global germplasm exchange ]]> https://biorxiv.org/content/10.1101/2021.05.11.443651v1?rss=1 Muleta, K. T. Felderhoff, T. Winans, N. Walstead, R. Charles, J. R. Armstrong, J. S. Mamidi, S. Plott, C. Vogel, J. P. Lemaux, P. G. Mockler, T. C. Grimwood, J. Schmutz, J. Pressoir, G. Morris, G. P. 2021-05-12 doi:10.1101/2021.05.11.443651 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ WASP integrates substrate topology and cell polarity to guide neutrophil migration ]]> https://biorxiv.org/content/10.1101/2021.05.12.443722v1?rss=1 Brunetti, R. M. Kockelkoren, G. Raghavan, P. Bell, G. R. R. Britain, D. Puri, N. Collins, S. R. Leonetti, M. D. Stamou, D. Weiner, O. D. 2021-05-14 doi:10.1101/2021.05.12.443722 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ Total Biosynthesis of Triacsin Featuring an N-hydroxytriazene Pharmacophore ]]> https://biorxiv.org/content/10.1101/2021.05.12.443849v1?rss=1 Del Rio Flores, A. Twigg, F. F. Du, Y. Cai, W. Aguirre, D. Q. Sato, M. Dror, M. J. Narayanamoorthy, M. Geng, J. Zill, N. A. Zhang, W. 2021-05-13 doi:10.1101/2021.05.12.443849 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ A chemically-defined growth medium to support Lactobacillus-Acetobacter community analysis ]]> https://biorxiv.org/content/10.1101/2021.05.12.443930v1?rss=1 Aumiller, K. Stevens, E. Scheffler, R. Guvener, Z. T. Tung, E. Grimaldo, A. B. Carlson, H. K. Deutschbauer, A. M. Taga, M. E. Marco, M. L. Ludington, W. B. 2021-05-14 doi:10.1101/2021.05.12.443930 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ The STING ligand 2'3'-cGAMP induces an NF-κB-dependent anti-bacterial innate immune response in the starlet sea anemone Nematostella vectensis ]]> https://biorxiv.org/content/10.1101/2021.05.13.443009v1?rss=1 Margolis, S. R. Dietzen, P. A. Hayes, B. M. Wilson, S. C. Remick, B. C. Chou, S. Vance, R. E. 2021-05-14 doi:10.1101/2021.05.13.443009 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ Height, but not binding epitope, affects the potency of synthetic TCR agonists ]]> https://biorxiv.org/content/10.1101/2021.05.13.443919v1?rss=1 Wilhelm, K. B. Morita, S. McAffee, D. B. Kim, S. O'Dair, M. K. Groves, J. T. 2021-05-16 doi:10.1101/2021.05.13.443919 Cold Spring Harbor Laboratory Press 2021-05-16 <![CDATA[ Serotonergic Neurons Translate Taste Detection into Internal Nutrient Regulation ]]> https://biorxiv.org/content/10.1101/2021.05.13.444014v1?rss=1 Yao, Z. Scott, K. 2021-05-14 doi:10.1101/2021.05.13.444014 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ Scale-dependent tipping points of bacterial colonization resistance ]]> https://biorxiv.org/content/10.1101/2021.05.13.444017v1?rss=1 Karita, Y. Limmer, D. T. Hallatschek, O. 2021-05-15 doi:10.1101/2021.05.13.444017 Cold Spring Harbor Laboratory Press 2021-05-15 <![CDATA[ Molecular diversity and lineage commitment of human interneuron progenitors ]]> https://biorxiv.org/content/10.1101/2021.05.13.444045v1?rss=1 Velmeshev, D. Chavali, M. Nowakowski, T. J. Bhade, M. Mayer, S. Goyal, N. Alvarado, B. Mancia, W. Wang, S. Speir, M. Haeussler, M. J. Rowitch, D. Alvarez-Buylla, A. Huang, E. Paredes, M. Kriegstein, A. 2021-05-14 doi:10.1101/2021.05.13.444045 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ riboviz 2: A flexible and robust ribosome profiling data analysis and visualization workflow ]]> https://biorxiv.org/content/10.1101/2021.05.14.443910v1?rss=1 Cope, A. L. Anderson, F. Favate, J. Jackson, M. Mok, A. Kurowska, A. MacKenzie, E. Shivakumar, V. Tilton, P. Winterbourne, S. M. Xue, S. Kavoussanakis, K. Lareau, L. F. Shah, P. Wallace, E. W. 2021-05-17 doi:10.1101/2021.05.14.443910 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Structural Basis for Membrane Recruitment of ATG16L1 by WIPI2 in Autophagy ]]> https://biorxiv.org/content/10.1101/2021.05.14.444175v1?rss=1 Strong, L. M. Chang, C. Boecker, A. Flower, T. G. Buffalo, C. Z. Ren, X. Stavoe, A. K. Holzbaur, E. L. F. Hurley, J. H. 2021-05-14 doi:10.1101/2021.05.14.444175 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ Evolved Bmp6 enhancer alleles drive spatial shifts in gene expression during tooth development in sticklebacks ]]> https://biorxiv.org/content/10.1101/2021.05.14.444181v1?rss=1 Stepaniak, M. D. Square, T. A. Miller, C. T. 2021-05-16 doi:10.1101/2021.05.14.444181 Cold Spring Harbor Laboratory Press 2021-05-16 <![CDATA[ An intranasal ASO therapeutic targeting SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2021.05.17.444397v1?rss=1 Zhu, C. Lee, J. Y. Woo, J. Z. Xu, L. Nguyenla, X. Yamashiro, L. H. Ji, F. Biering, S. B. Dis, E. V. Gonzalez, F. Fox, D. Rustagi, A. Pinsky, B. A. Blish, C. A. Chiu, C. Harris, E. Sadreyev, R. I. Stanley, S. Kauppinen, S. Rouskin, S. Näär, A. M. 2021-05-18 doi:10.1101/2021.05.17.444397 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ A new type of ERGIC-ERES membrane contact mediated by TMED9 and SEC12 is required for autophagosome biogenesis ]]> https://biorxiv.org/content/10.1101/2021.05.19.444771v1?rss=1 Li, S. Yan, R. Xu, J. Zhao, S. Ma, X. Sun, Q. Zhang, M. Li, Y. Liu, J.-J. G. Chen, L. Li, S. Xu, K. Ge, L. 2021-05-19 doi:10.1101/2021.05.19.444771 Cold Spring Harbor Laboratory Press 2021-05-19 <![CDATA[ Short-term elevations in glucocorticoids do not alter telomere lengths: A systematic review and meta-analysis of non-primate vertebrate studies ]]> https://biorxiv.org/content/10.1101/2021.05.19.444844v1?rss=1 Zane, L. H. Ensminger, D. C. Vazquez-Medina, J. P. 2021-05-21 doi:10.1101/2021.05.19.444844 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ Genetic isolation by distance underlies color pattern divergence in red-eyed treefrogs (Agalychnis callidryas) ]]> https://biorxiv.org/content/10.1101/2021.05.21.445051v1?rss=1 Clark, M. I. Bradburd, G. S. Akopyan, M. Vega, A. Rosenblum, E. B. Robertson, J. M. 2021-05-23 doi:10.1101/2021.05.21.445051 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ On the sparsity of fitness functions and implications for learning ]]> https://biorxiv.org/content/10.1101/2021.05.24.445506v1?rss=1 Brookes, D. H. Aghazadeh, A. Listgarten, J. 2021-05-25 doi:10.1101/2021.05.24.445506 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ The molecular mechanism of load adaptation by branched actin networks ]]> https://biorxiv.org/content/10.1101/2021.05.24.445507v1?rss=1 Li, T.-D. Bieling, P. Weichsel, J. Mullins, R. D. Fletcher, D. A. 2021-05-25 doi:10.1101/2021.05.24.445507 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Epigenetic Patterns in a Complete Human Genome ]]> https://biorxiv.org/content/10.1101/2021.05.26.443420v1?rss=1 Gershman, A. Sauria, M. E. G. Hook, P. W. Hoyt, S. Razaghi, R. Koren, S. Altemose, N. Caldas, G. V. Vollger, M. R. Logsdon, G. Rhie, A. Eichler, E. Schatz, M. O'Neill, R. J. Phillippy, A. M. Miga, K. H. Timp, W. 2021-05-27 doi:10.1101/2021.05.26.443420 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Engineering improved Cas13 effectors for targeted post-transcriptional regulation of gene expression ]]> https://biorxiv.org/content/10.1101/2021.05.26.445687v1?rss=1 Charles, E. J. Kim, S. E. Knott, G. J. Smock, D. Doudna, J. Savage, D. F. 2021-05-26 doi:10.1101/2021.05.26.445687 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ The complete sequence of a human genome ]]> https://biorxiv.org/content/10.1101/2021.05.26.445798v1?rss=1 Nurk, S. Koren, S. Rhie, A. Rautiainen, M. Bzikadze, A. V. Mikheenko, A. Vollger, M. R. Altemose, N. Uralsky, L. Gershman, A. Aganezov, S. Hoyt, S. J. Diekhans, M. Logsdon, G. A. Alonge, M. Antonarakis, S. E. Borchers, M. Bouffard, G. G. Brooks, S. Y. Caldas, G. V. Cheng, H. Chin, C.-S. Chow, W. de Lima, L. G. Dishuck, P. C. Durbin, R. Dvorkina, T. Fiddes, I. T. Formenti, G. Fulton, R. S. Fungtammasan, A. Garrison, E. Grady, P. G. S. Graves-Lindsay, T. A. Hall, I. M. Hansen, N. F. Hartley, G. A. Haukness, M. Howe, K. Hunkapiller, M. W. Jain, C. Jain, M. 2021-05-27 doi:10.1101/2021.05.26.445798 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Reconstructing unobserved cellular states from paired single-cell lineage tracing and transcriptomics data ]]> https://biorxiv.org/content/10.1101/2021.05.28.446021v1?rss=1 Ouardini, K. Lopez, R. Jones, M. G. Prillo, S. Zhang, R. Jordan, M. I. Yosef, N. 2021-05-30 doi:10.1101/2021.05.28.446021 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ Learning Rates Are Not All the Same: The Interpretation of Computational Model Parameters Depends on the Context ]]> https://biorxiv.org/content/10.1101/2021.05.28.446162v1?rss=1 Eckstein, M. K. Master, S. L. Xia, L. Dahl, R. E. Wilbrecht, L. Collins, A. G. E. 2021-05-28 doi:10.1101/2021.05.28.446162 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ A universal, open-source, high-performance tool for automated sleep staging ]]> https://biorxiv.org/content/10.1101/2021.05.28.446165v1?rss=1 Vallat, R. Walker, M. P. 2021-05-28 doi:10.1101/2021.05.28.446165 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ The N-terminal and central domains of CoV-2 nsp1 play key functional roles in suppression of cellular gene expression and preservation of viral gene expression ]]> https://biorxiv.org/content/10.1101/2021.05.28.446204v1?rss=1 Mendez, A. S. Ly, M. Gonzalez-Sanchez, A. M. Hartenian, E. Ingolia, N. Cate, J. H. Glaunsinger, B. 2021-05-28 doi:10.1101/2021.05.28.446204 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Structural basis of polyamine transport by human ATP13A2 (PARK9) ]]> https://biorxiv.org/content/10.1101/2021.05.28.446245v1?rss=1 Sim, S. I. von Bülow, S. Hummer, G. Park, E. 2021-05-28 doi:10.1101/2021.05.28.446245 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Secondary metabolism drives ecological breadth in the Xylariaceae ]]> https://biorxiv.org/content/10.1101/2021.06.01.446356v1?rss=1 Franco, M. E. E. Wisecaver, J. H. Arnold, A. E. Ju, Y.-M. Slot, J. C. Ahrendt, S. Moore, L. P. Eastman, K. E. Scott, K. Konkel, Z. Mondo, S. J. Kuo, A. Hayes, R. Haridas, S. Andreopoulos, B. Riley, R. LaButti, K. Pangilinan, J. Lipzen, A. Amirebrahimi, M. Yan, J. Adam, C. Keymanesh, K. Ng, V. Louie, K. Northen, T. Drula, E. Henrissat, B. Hsieh, H.-M. Youens-Clark, K. Lutzoni, F. Miadlikowska, J. Eastwood, D. C. Hamelin, R. C. Grigoriev, I. V. U'Ren, J. M. 2021-06-02 doi:10.1101/2021.06.01.446356 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Prepubertal ovariectomy alters dorsomedial striatum indirect pathway neuron excitability and explore/exploit balance in female mice ]]> https://biorxiv.org/content/10.1101/2021.06.01.446609v1?rss=1 Delevich, K. Hall, C. D. Wilbrecht, L. 2021-06-01 doi:10.1101/2021.06.01.446609 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ Evaluating sources of technical variability in the mechano-node-pore sensing pipeline and their effect on the reproducibility of single-cell mechanical phenotyping ]]> https://biorxiv.org/content/10.1101/2021.06.02.446242v1?rss=1 Li, B. Cotner, K. L. Liu, N. K. Hinz, S. LaBarge, M. A. Sohn, L. L. 2021-06-02 doi:10.1101/2021.06.02.446242 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Transposable element accumulation drives size differences among polymorphic Y chromosomes in Drosophila ]]> https://biorxiv.org/content/10.1101/2021.06.02.446622v1?rss=1 Nguyen, A. Bachtrog, D. 2021-06-03 doi:10.1101/2021.06.02.446622 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ Klf5 establishes bi-potential cell fate by dual regulation of ICM and TE specification genes ]]> https://biorxiv.org/content/10.1101/2021.06.02.446799v1?rss=1 Kinisu, M. Choi, Y. J. Cattoglio, C. Liu, K. Roux de Bezieux, H. Valbuena, R. Pum, N. Dudoit, S. Huang, H. Xuan, Z. Kim, S. Y. He, L. 2021-06-02 doi:10.1101/2021.06.02.446799 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Western Amazon was a center of Neotropical fish dispersal, as evidenced by the continental-wide time-stratified biogeographic analysis of the hyper-diverse Hypostomus catfish ]]> https://biorxiv.org/content/10.1101/2021.06.03.446980v1?rss=1 Jardim de Queiroz, L. Meyer, X. Cardoso, Y. P. Bahechar, I. A. Covain, R. Parente, T. E. Torrente-Vilara, G. Buckup, P. A. Montoya-Burgos, J. I. 2021-06-03 doi:10.1101/2021.06.03.446980 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ Volume growth in animal cells is cell cycle dependent and shows additive fluctuations ]]> https://biorxiv.org/content/10.1101/2021.06.03.446986v1?rss=1 Cadart, C. Piel, M. Lagomarsino, M. C. 2021-06-03 doi:10.1101/2021.06.03.446986 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ HLA Allele Imputation with Multitask Deep Convolutional Neural Network ]]> https://biorxiv.org/content/10.1101/2021.06.03.447012v1?rss=1 Chi, C. 2021-06-05 doi:10.1101/2021.06.03.447012 Cold Spring Harbor Laboratory Press 2021-06-05 <![CDATA[ Identifying charismatic bird species and traits with community science observations ]]> https://biorxiv.org/content/10.1101/2021.06.05.446577v1?rss=1 Stoudt, S. Goldstein, B. R. de Valpine, P. 2021-06-07 doi:10.1101/2021.06.05.446577 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Epitome: Predicting epigenetic events in novel cell types with multi-cell deep ensemble learning ]]> https://biorxiv.org/content/10.1101/2021.06.10.447140v1?rss=1 Morrow, A. K. Hughes, J. W. Singh, J. Joseph, A. D. Yosef, N. 2021-06-11 doi:10.1101/2021.06.10.447140 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Scalable and Automated CRISPR-Based Strain Engineering Using Droplet Microfluidics ]]> https://biorxiv.org/content/10.1101/2021.06.10.447396v1?rss=1 Iwai, K. Wehrs, M. Garber, M. Sustarich, J. Washburn, L. Costello, Z. Kim, P. W. Ando, D. Gaillard, W. R. Hillson, N. J. Adams, P. D. Mukhopadhyay, A. Martin, H. G. Singh, A. K. 2021-06-10 doi:10.1101/2021.06.10.447396 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq ]]> https://biorxiv.org/content/10.1101/2021.06.10.447896v1?rss=1 Mudge, J. M. Ruiz-Orera, J. Prensner, J. R. Brunet, M. A. Gonzalez, J. M. Magrane, M. Martinez, T. Schulz, J. F. Yang, Y. T. Alba, M. M. Baranov, P. V. Bazzini, A. Bruford, E. Martin, M. J. Carvunis, A.-R. Chen, J. Couso, J. P. Flicek, P. Frankish, A. Gerstein, M. Hubner, N. Ingolia, N. T. Menschaert, G. Ohler, U. Roucou, X. Saghatelian, A. Weissman, J. van Heesch, S. 2021-06-10 doi:10.1101/2021.06.10.447896 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Consciousness is supported by near-critical cortical electrodynamics ]]> https://biorxiv.org/content/10.1101/2021.06.10.447959v1?rss=1 Toker, D. Pappas, I. Lendner, J. D. Frohlich, J. Mateos, D. M. Muthukumaraswamy, S. Carhart-Harris, R. Paff, M. Vespa, P. M. Monti, M. M. Sommer, F. T. Knight, R. T. D'Esposito, M. 2021-06-11 doi:10.1101/2021.06.10.447959 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Principles of ecDNA random inheritance drive rapid genome change and therapy resistance in human cancers ]]> https://biorxiv.org/content/10.1101/2021.06.11.447968v1?rss=1 Lange, J. T. Chen, C. Y. Pichugin, Y. Xie, F. Tang, J. Hung, K. L. Yost, K. E. Shi, Q. Erb, M. L. Rajkumar, U. Wu, S. Swanton, C. Liu, Z. Huang, W. Chang, H. Y. Bafna, V. Henssen, A. G. Werner, B. Mischel, P. S. 2021-06-11 doi:10.1101/2021.06.11.447968 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Counterdiabatic control of biophysical processes ]]> https://biorxiv.org/content/10.1101/2021.06.13.448255v1?rss=1 Ilker, E. Güngör, O. Kuznets-Speck, B. Chiel, J. Deffner, S. Hinczewski, M. 2021-06-14 doi:10.1101/2021.06.13.448255 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ A pathogenic role for histone H3 copper reductase activity in a yeast model of Friedreich's Ataxia ]]> https://biorxiv.org/content/10.1101/2021.06.14.448268v1?rss=1 Campos, O. A. Attar, N. Mallipeddi, N. V. Cheng, C. Vogelauer, M. Schmollinger, S. Merchant, S. S. Kurdistani, S. K. 2021-06-14 doi:10.1101/2021.06.14.448268 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ The contribution of genetic and environmental effects to Bergmanns rule and Allens rule in house mice ]]> https://biorxiv.org/content/10.1101/2021.06.14.448454v1?rss=1 Ballinger, M. A. Nachman, M. W. 2021-06-15 doi:10.1101/2021.06.14.448454 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ Teaching Python for Data Science: Collaborative development of a modular & interactive curriculum ]]> https://biorxiv.org/content/10.1101/2021.06.17.448726v1?rss=1 Duda, M. Sovacool, K. L. Farzaneh, N. Nguyen, V. K. Haynes, S. E. Falk, H. Furman, K. L. Walker, L. A. Diao, R. Oneka, M. Drotos, A. C. Woloshin, A. Dotson, G. A. Kriebel, A. Meng, L. Thiede, S. N. Lapp, Z. Wolford, B. N. 2021-06-18 doi:10.1101/2021.06.17.448726 Cold Spring Harbor Laboratory Press 2021-06-18 <![CDATA[ Task-Dependent Warping of Semantic Representations During Search for Visual Action Categories ]]> https://biorxiv.org/content/10.1101/2021.06.17.448789v1?rss=1 Shahdloo, M. Celik, E. Urgen, B. A. Gallant, J. L. Cukur, T. 2021-06-17 doi:10.1101/2021.06.17.448789 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Nanopore callers for epigenetics from limited supervised data ]]> https://biorxiv.org/content/10.1101/2021.06.17.448800v1?rss=1 Yao, B. Hsu, C. Goldner, G. Michaeli, Y. Ebenstein, Y. Listgarten, J. 2021-06-17 doi:10.1101/2021.06.17.448800 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ 3D structure and in situ arrangements of CatSper channel in the sperm flagellum ]]> https://biorxiv.org/content/10.1101/2021.06.19.448910v1?rss=1 Zhao, Y. Wang, H. Wiesehoefer, C. Shah, N. B. Reetz, E. Hwang, J. Y. Huang, X. Lishko, P. V. Davies, K. M. Wennemuth, G. Nicastro, D. Chung, J.-J. 2021-06-20 doi:10.1101/2021.06.19.448910 Cold Spring Harbor Laboratory Press 2021-06-20 <![CDATA[ Supervised Learning Model Predicts Protein Adsorption to Nanotubes ]]> https://biorxiv.org/content/10.1101/2021.06.19.449132v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@bbc175org.highwire.dtl.DTLVardef@9a0b94org.highwire.dtl.DTLVardef@16e22e1org.highwire.dtl.DTLVardef@1b40a84_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pinals, R. L. Ouassil, N. Del Bonis-O'Donnell, J. T. Wang, J. W. Landry, M. P. 2021-06-20 doi:10.1101/2021.06.19.449132 Cold Spring Harbor Laboratory Press 2021-06-20 <![CDATA[ Meiotic cell cycle progression requires adaptation to a constitutive DNA damage signal ]]> https://biorxiv.org/content/10.1101/2021.06.20.449183v1?rss=1 Zhang, L. Stauffer, W. T. Ziesel, A. Wang, J. S. Yu, Z. Hollingsworth, N. M. Dernburg, A. F. 2021-06-21 doi:10.1101/2021.06.20.449183 Cold Spring Harbor Laboratory Press 2021-06-21 <![CDATA[ Oxidative stress is a potential cost of synchronous nesting in olive ridley sea turtles ]]> https://biorxiv.org/content/10.1101/2021.06.21.449061v1?rss=1 Arango, B. G. Harfush-Melendez, M. Ensminger, D. C. Lopez-Reyes, E. M. Marmolejo-Valencia, J. A. Merchant-Larios, H. Crocker, D. E. Vazquez-Medina, J. P. 2021-06-21 doi:10.1101/2021.06.21.449061 Cold Spring Harbor Laboratory Press 2021-06-21 <![CDATA[ Evaluating the cost of pharmaceutical purification for a long-duration space exploration medical foundry ]]> https://biorxiv.org/content/10.1101/2021.06.21.449300v1?rss=1 McNulty, M. J. Berliner, A. J. Negulescu, P. G. McKee, L. Hart, O. Yates, K. Arkin, A. P. Nandi, S. McDonald, K. A. 2021-06-22 doi:10.1101/2021.06.21.449300 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Climatic niche conservatism shapes the ecological assembly of Hawaiian arthropod communities ]]> https://biorxiv.org/content/10.1101/2021.06.22.449388v1?rss=1 Lim, J. Y. Patino, J. Noriyuki, S. Simmari, L. C. Gillespie, R. G. Krehenwinkel, H. 2021-06-22 doi:10.1101/2021.06.22.449388 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Directed Evolution of AAV Targeting Primate Retina by Intravitreal Injection Identifies R100, a Variant Demonstrating Robust Gene Delivery and Therapeutic Efficacy in Non-Human Primates ]]> https://biorxiv.org/content/10.1101/2021.06.24.449775v1?rss=1 Kotterman, M. A. Beliakoff, G. Croze, R. Vazin, T. Schmitt, C. Szymanski, P. Leong, M. Quezada, M. Holt, J. Barglow, K. Hassanipour, M. Schaffer, D. V. Francis, P. Kirn, D. H. 2021-06-25 doi:10.1101/2021.06.24.449775 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Efficient tagging and purification of endogenous proteins for structural studies by single particle cryo-EM ]]> https://biorxiv.org/content/10.1101/2021.06.25.449985v1?rss=1 Zhao, J. Makhija, S. Huang, B. Cheng, Y. 2021-06-25 doi:10.1101/2021.06.25.449985 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Macroscale structural changes of thylakoid architecture during high light acclimation in Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2021.06.26.450046v1?rss=1 Broderson, M. Niyogi, K. K. Iwai, M. 2021-06-27 doi:10.1101/2021.06.26.450046 Cold Spring Harbor Laboratory Press 2021-06-27 <![CDATA[ Actin force generation in vesicle formation: mechanistic insights from cryo-electron tomography ]]> https://biorxiv.org/content/10.1101/2021.06.28.450262v1?rss=1 Serwas, D. Akamatsu, M. Moayed, A. Vegesna, K. Vasan, R. Hill, J. M. Schoeneberg, J. Davies, K. M. Rangamani, P. Drubin, D. G. 2021-06-29 doi:10.1101/2021.06.28.450262 Cold Spring Harbor Laboratory Press 2021-06-29 <![CDATA[ Parallel genetic changes underlie integrated craniofacial traits in an adaptive radiation of trophic specialist pupfishes ]]> https://biorxiv.org/content/10.1101/2021.07.01.450661v1?rss=1 St John, M. E. Richards, E. Dunker, J. C. Romero, S. Martin, C. H. 2021-07-01 doi:10.1101/2021.07.01.450661 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ Adaptive introgression and de novo mutations increase access to novel fitness peaks on the fitness landscape during a vertebrate adaptive radiation ]]> https://biorxiv.org/content/10.1101/2021.07.01.450666v1?rss=1 Patton, A. H. Richards, E. Gould, K. J. Buie, L. K. Martin, C. H. 2021-07-01 doi:10.1101/2021.07.01.450666 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ High-density transposon mutagenesis in Mycobacterium abscessus identifies an essential penicillin-binding lipo-protein (PBP-lipo) involved in septal peptidoglycan synthesis and antibiotic sensitivity ]]> https://biorxiv.org/content/10.1101/2021.07.01.450732v1?rss=1 Akusobi, C. Benghomari, B. S. Wolf, I. D. Singhvi, S. Zhu, J. Ioerger, T. R. Rubin, E. J. 2021-07-01 doi:10.1101/2021.07.01.450732 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ A comparative life cycle analysis of electromicrobial production systems ]]> https://biorxiv.org/content/10.1101/2021.07.01.450744v1?rss=1 ~90% renewable energy sources. For each of the three products we consider (biomass, enzymes, and lactic acid), the H2-mediated Knallgas bacteria system achieves the lowest overall global warming potential, indicating that this EMP strategy may be best-suited for industrial efforts based on current technology. We also identify environmental hotspots and process limitations that are key sites for future engineering and research efforts for each EMP system. Our analysis demonstrates the utility of an integrated bioelectrochemical model/life cycle assessment framework in both analyzing and aiding the ecodesign of electromicrobial processes and should help guide the design of working, scalable, and sustainable systems. ]]> Abel, A. J. Adams, J. D. Clark, D. S. 2021-07-02 doi:10.1101/2021.07.01.450744 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ Diversity begets diversity through shared adaptive genetic variation: discovery of a cryptic wide-mouthed scale-eater ]]> https://biorxiv.org/content/10.1101/2021.07.01.450755v1?rss=1 Richards, E. Martin, C. H. 2021-07-02 doi:10.1101/2021.07.01.450755 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ Aspects of the Neurospora crassa sulfur starvation response are revealed by transcriptional profiling and DNA affinity purification sequencing ]]> https://biorxiv.org/content/10.1101/2021.07.01.450814v1?rss=1 Huberman, L. B. Wu, V. W. Lee, J. Daum, C. O'Malley, R. Glass, N. L. 2021-07-02 doi:10.1101/2021.07.01.450814 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ Selective sorting of microRNAs into exosomes by phase-separated YBX1 condensates ]]> https://biorxiv.org/content/10.1101/2021.07.06.451310v1?rss=1 Liu, X.-M. Ma, L. Schekman, R. 2021-07-06 doi:10.1101/2021.07.06.451310 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Multi-morph eco-evolutionary dynamics in structured populations ]]> https://biorxiv.org/content/10.1101/2021.07.08.451558v1?rss=1 Lion, S. Boots, M. Sasaki, A. 2021-07-09 doi:10.1101/2021.07.08.451558 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Pyroptosis-dependent and -independent cross-priming of CD8+ T cells by intestinal epithelial cell-derived antigen ]]> https://biorxiv.org/content/10.1101/2021.07.08.451636v1?rss=1 Deets, K. A. Nichols, R. D. Rauch, I. Vance, R. E. 2021-07-08 doi:10.1101/2021.07.08.451636 Cold Spring Harbor Laboratory Press 2021-07-08 <![CDATA[ Critical genetic program for Drosophila imaginal disc regeneration revealed by single-cell analysis ]]> https://biorxiv.org/content/10.1101/2021.07.08.451678v1?rss=1 Worley, M. I. Everetts, N. Yasutomi, R. Yosef, N. Hariharan, I. K. 2021-07-09 doi:10.1101/2021.07.08.451678 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient ]]> https://biorxiv.org/content/10.1101/2021.07.10.451524v1?rss=1 Reimer, A. Alamos, S. Westrum, C. Turner, M. A. Talledo, P. Zhao, J. Garcia, H. G. 2021-07-11 doi:10.1101/2021.07.10.451524 Cold Spring Harbor Laboratory Press 2021-07-11 <![CDATA[ Borgs are giant extrachromosomal elements with the potential to augment methane oxidation ]]> https://biorxiv.org/content/10.1101/2021.07.10.451761v1?rss=1 Al-Shayeb, B. Schoelmerich, M. C. West-Roberts, J. Valentin-Alvarado, L. E. Sachdeva, R. Mullen, S. Crits-Christoph, A. Wilkins, M. J. Williams, K. H. Doudna, J. A. Banfield, J. F. 2021-07-10 doi:10.1101/2021.07.10.451761 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ The SARS-CoV-2 spike reversibly samples an open-trimer conformation exposing novel epitopes ]]> https://biorxiv.org/content/10.1101/2021.07.11.451855v1?rss=1 Costello, S. M. Shoemaker, S. R. Hobbs, H. T. Nguyen, A. W. Hsieh, C.-L. Maynard, J. A. McLellan, J. S. Pak, J. E. Marqusee, S. 2021-07-11 doi:10.1101/2021.07.11.451855 Cold Spring Harbor Laboratory Press 2021-07-11 <![CDATA[ From telomere to telomere: the transcriptional and epigenetic state of human repeat elements ]]> https://biorxiv.org/content/10.1101/2021.07.12.451456v1?rss=1 Hoyt, S. J. Storer, J. M. Hartley, G. A. Grady, P. G. S. Gershman, A. de Lima, L. G. Limouse, C. Halabian, R. Wojenski, L. Rodriguez, M. Altemose, N. Core, L. Gerton, J. L. Makalowski, W. Olson, D. Rosen, J. Smit, A. F. A. Straight, A. F. Vollger, M. R. Wheeler, T. Schatz, M. Eichler, E. Phillippy, A. M. Timp, W. Miga, K. H. O'Neill, R. J. 2021-07-12 doi:10.1101/2021.07.12.451456 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Critical Assessment of Metagenome Interpretation - the second round of challenges ]]> https://biorxiv.org/content/10.1101/2021.07.12.451567v1?rss=1 Meyer, F. Fritz, A. Deng, Z.-L. Koslicki, D. Gurevich, A. Robertson, G. Zhu, J. Jia, H. Kola, A. Limasset, A. Kolmogorov, M. Egan, R. Rosen, G. L. Cristian, A. Zhao, Z. Gray, M. A. Nissen, J. Zeller, G. Paoli, L. Ruscheweyh, H.-J. Milanese, A. Sunagawa, S. Alser, M. Shi, L. Chen, B. Wang, Z. Wang, Z. Huang, P. You, R. Sun, F. Zhu, S. Bertrand, D. Tong, C. Li, C. Nagarajan, N. Renard, B. Malcher-Miranda, F. Piro, V. C. Chikhi, R. Vicedomini, R. Wang, Z. Thomas, A. Tremblay, J. Dabrowski, P. W. Nurk, S. Jorgensen, T. S. Willassen, N. P. Klemetsen, T 2021-07-12 doi:10.1101/2021.07.12.451567 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Complete genomic and epigenetic maps of human centromeres ]]> https://biorxiv.org/content/10.1101/2021.07.12.452052v1?rss=1 Altemose, N. Logsdon, G. Bzikadze, A. V. Sidhwani, P. Langley, S. A. Caldas, G. V. Hoyt, S. J. Uralsky, L. Ryabov, F. D. Shew, C. Sauria, M. E. G. Borchers, M. Gershman, A. Mikheenko, A. Shepelev, V. A. Dvorkina, T. Kunyavskaya, O. Vollger, M. R. Rhie, A. McCartney, A. M. Asri, M. Lorig-Roach, R. Shafin, K. Aganezov, S. Olson, D. Gomes de Lima, L. Potapova, T. Hartley, G. A. Haukness, M. Kerpedjiev, P. Gusev, F. Tigyi, K. Brooks, S. Y. Young, A. Nurk, S. Koren, S. Salama, S. Paten, B. Rogaev, E. I. Streets, A. M. Karpen, G. H. Dernburg, A. Sullivan, B. 2021-07-13 doi:10.1101/2021.07.12.452052 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ Mistreating birth-death models as priors in phylogenetic analysis compromises our ability to compare models ]]> https://biorxiv.org/content/10.1101/2021.07.12.452074v1?rss=1 May, M. R. Rothfels, C. 2021-07-12 doi:10.1101/2021.07.12.452074 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Single-cell multi-omic analysis of thymocyte development reveals NFAT as adriver of CD4/CD8 lineage commitment ]]> https://biorxiv.org/content/10.1101/2021.07.12.452119v1?rss=1 Steier, Z. McIntyre, L. L. Lutes, L. K. Huang, T.-S. Robey, E. A. Yosef, N. Streets, A. 2021-07-13 doi:10.1101/2021.07.12.452119 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ A phage parasite deploys a nicking nuclease effector to inhibit replication of its viral host ]]> https://biorxiv.org/content/10.1101/2021.07.12.452122v1?rss=1 LeGault, K. Barth, Z. DePaola, P. Seed, K. 2021-07-13 doi:10.1101/2021.07.12.452122 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ Tree-based automated machine learning to predict biogas production for anaerobic co-digestion of organic waste ]]> https://biorxiv.org/content/10.1101/2021.07.12.452124v1?rss=1 Wang, Y. Huntington, T. Scown, C. D. 2021-07-13 doi:10.1101/2021.07.12.452124 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ Neo-sex chromosome evolution shapes sex-dependent asymmetrical introgression barrier ]]> https://biorxiv.org/content/10.1101/2021.07.13.452191v1?rss=1 Wang, S. Nalley, M. J. Chatla, K. Aldaimalani, R. MacPherson, A. Wei, K. Corbett, R. Mai, D. Bachtrog, D. 2021-07-14 doi:10.1101/2021.07.13.452191 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1 ]]> https://biorxiv.org/content/10.1101/2021.07.14.452365v1?rss=1 Hsieh, T.-H. S. Cattoglio, C. Slobodyanyuk, E. Hansen, A. S. Darzacq, X. Tjian, R. 2021-07-14 doi:10.1101/2021.07.14.452365 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ Latent neural dynamics encode temporal context in speech ]]> https://biorxiv.org/content/10.1101/2021.07.15.452519v1?rss=1 Stephen, E. P. Li, Y. Metzger, S. Oganian, Y. Chang, E. F. 2021-07-16 doi:10.1101/2021.07.15.452519 Cold Spring Harbor Laboratory Press 2021-07-16 <![CDATA[ Asymmetric Arp2/3-mediated actin assembly facilitates clathrin-mediated endocytosis at stalled sites in genome-edited human stem cells. ]]> https://biorxiv.org/content/10.1101/2021.07.16.452693v1?rss=1 Jin, M. Shirazinejad, C. Wang, B. Yan, A. Schöneberg, J. Upadhyayula, S. Xu, K. Drubin, D. G. 2021-07-16 doi:10.1101/2021.07.16.452693 Cold Spring Harbor Laboratory Press 2021-07-16 <![CDATA[ Deep neural language modeling enables functional protein generation across families ]]> https://biorxiv.org/content/10.1101/2021.07.18.452833v1?rss=1 Madani, A. Krause, B. Greene, E. R. Subramanian, S. Mohr, B. P. Holton, J. M. Olmos, J. L. Xiong, C. Sun, Z. Z. Socher, R. Fraser, J. S. Naik, N. 2021-07-18 doi:10.1101/2021.07.18.452833 Cold Spring Harbor Laboratory Press 2021-07-18 <![CDATA[ Displacement statistics of unhindered single molecules show no enhanced diffusion in enzymatic reactions ]]> https://biorxiv.org/content/10.1101/2021.07.20.452795v1?rss=1 View larger version (11K): org.highwire.dtl.DTLVardef@1c78ba4org.highwire.dtl.DTLVardef@1a0c727org.highwire.dtl.DTLVardef@73027dorg.highwire.dtl.DTLVardef@a87771_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Choi, A. Park, H. Chen, K. Yan, R. Li, W. Xu, K. 2021-07-21 doi:10.1101/2021.07.20.452795 Cold Spring Harbor Laboratory Press 2021-07-21 <![CDATA[ Adolescent Development of Biological Rhythms: Estradiol Dependence and Effects of Combined Contraceptives ]]> https://biorxiv.org/content/10.1101/2021.07.20.453145v1?rss=1 Grant, A. D. Wilbrecht, L. Kriegsfeld, L. J. 2021-07-21 doi:10.1101/2021.07.20.453145 Cold Spring Harbor Laboratory Press 2021-07-21 <![CDATA[ Raptor downregulation rescues neuronal phenotypes in mouse models of Tuberous Sclerosis Complex ]]> https://biorxiv.org/content/10.1101/2021.07.21.453275v1?rss=1 Karalis, V. Caval-Holme, F. Bateup, H. S. 2021-07-23 doi:10.1101/2021.07.21.453275 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Polymer-Conjugated Carbon Nanotubes for Biomolecule Loading ]]> https://biorxiv.org/content/10.1101/2021.07.22.453422v1?rss=1 Jackson, C. T. Wang, J. W. Gonzalez-Grandio, E. Goh, N. S. Mun, J. Krishnan, S. Landry, M. P. 2021-07-23 doi:10.1101/2021.07.22.453422 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Identifying cell-state associated alternative splicing events and their co-regulation ]]> https://biorxiv.org/content/10.1101/2021.07.23.453605v1?rss=1 Buen Abad Najar, C. F. Burra, P. Yosef, N. Lareau, L. F. 2021-07-24 doi:10.1101/2021.07.23.453605 Cold Spring Harbor Laboratory Press 2021-07-24 <![CDATA[ Bats host the most virulent--but not the most dangerous--zoonotic viruses ]]> https://biorxiv.org/content/10.1101/2021.07.25.453574v1?rss=1 Guth, S. Mollentze, N. Renault, K. Streicker, D. Visher, E. Boots, M. Brook, C. E. 2021-07-26 doi:10.1101/2021.07.25.453574 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ Barcoded RH-seq illuminates the complex genetic basis of yeast thermotolerance ]]> https://biorxiv.org/content/10.1101/2021.07.26.453780v1?rss=1 Abrams, M. B. Chuong, J. N. AlZaben, F. Dubin, C. A. Skerker, J. M. Brem, R. B. 2021-07-26 doi:10.1101/2021.07.26.453780 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ Emotional context sculpts action goal representations in the lateral frontal pole ]]> https://biorxiv.org/content/10.1101/2021.07.28.453895v1?rss=1 Lapate, R. C. Ballard, I. C. Heckner, M. K. D'Esposito, M. 2021-07-29 doi:10.1101/2021.07.28.453895 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Predictive modeling reveals that higher-order cooperativity drives transcriptional repression in a synthetic developmental enhancer ]]> https://biorxiv.org/content/10.1101/2021.07.28.454075v1?rss=1 Kim, Y. J. Rhee, K. Liu, J. Jeammet, P. Turner, M. A. Small, S. Garcia, H. G. 2021-07-29 doi:10.1101/2021.07.28.454075 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Carbon nanotube biocompatibility in plants is determined by their surface chemistry ]]> https://biorxiv.org/content/10.1101/2021.07.29.454380v1?rss=1 Gonzalez-Grandio, E. Demirer, G. S. Jackson, C. T. Yang, D. Landry, M. P. 2021-07-30 doi:10.1101/2021.07.29.454380 Cold Spring Harbor Laboratory Press 2021-07-30 <![CDATA[ Neural representations of stereotype content predict social decisions ]]> https://biorxiv.org/content/10.1101/2021.08.01.454671v1?rss=1 Kobayashi, K. Kable, J. W. Hsu, M. Jenkins, A. C. 2021-08-04 doi:10.1101/2021.08.01.454671 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ Macaques preferentially attend to intermediately surprising information ]]> https://biorxiv.org/content/10.1101/2021.08.02.454786v1?rss=1 Wu, S. Blanchard, T. Meschke, E. Aslin, R. N. Hayden, B. Kidd, C. 2021-08-02 doi:10.1101/2021.08.02.454786 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ Trophic specialization on unique resources in one of the most celebrated examples of sympatric speciation, Barombi Mbo crater lake cichlids ]]> https://biorxiv.org/content/10.1101/2021.08.04.455125v1?rss=1 Galvez, J. McLean, K. Touokong, C. D. Gonwouo, L. N. Martin, C. 2021-08-06 doi:10.1101/2021.08.04.455125 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Rapid assessment of SARS-CoV-2 evolved variants using virus-like particles ]]> https://biorxiv.org/content/10.1101/2021.08.05.455082v1?rss=1 Syed, A. M. Taha, T. Y. Khalid, M. M. Tabata, T. Chen, I. P. Sreekumar, B. Chen, P.-Y. Hayashi, J. M. Soczek, K. M. Ott, M. Doudna, J. A. 2021-08-05 doi:10.1101/2021.08.05.455082 Cold Spring Harbor Laboratory Press 2021-08-05 <![CDATA[ Voltage imaging in Drosophila using a hybrid chemical-genetic rhodamine voltage reporter ]]> https://biorxiv.org/content/10.1101/2021.08.05.455279v1?rss=1 Kirk, M. Benlian, B. Han, Y. Gold, A. Ravi, A. Deal, P. Molina, R. Drobizhev, M. Dickman, D. Scott, K. Miller, E. 2021-08-06 doi:10.1101/2021.08.05.455279 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Classification and genetic targeting of cell types in the primary taste and premotor center of the Drosophila brain ]]> https://biorxiv.org/content/10.1101/2021.08.06.455433v1?rss=1 Sterne, G. R. Otsuna, H. Dickson, B. J. Scott, K. 2021-08-08 doi:10.1101/2021.08.06.455433 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ Surveying the global landscape of post-transcriptional regulators ]]> https://biorxiv.org/content/10.1101/2021.08.09.455688v1?rss=1 Reynaud, K. McGeachy, A. M. Noble, D. Meacham, Z. A. Ingolia, N. 2021-08-09 doi:10.1101/2021.08.09.455688 Cold Spring Harbor Laboratory Press 2021-08-09 <![CDATA[ Vision is Required for Cell Type Specification in the Visual Cortex ]]> https://biorxiv.org/content/10.1101/2021.08.10.455824v1?rss=1 Cheng, S. Butrus, S. Xu, V. Sagireddy, S. Tan, L. Shekhar, K. Zipursky, S. L. 2021-08-10 doi:10.1101/2021.08.10.455824 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Dynamics and impacts of transposable element proliferation during the Drosophila nasuta species group radiation ]]> https://biorxiv.org/content/10.1101/2021.08.12.456169v1?rss=1 Wei, K. Mai, D. Chatla, K. Bachtrog, D. 2021-08-13 doi:10.1101/2021.08.12.456169 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Single-nucleus RNA-sequencing in pre-cellularization Drosophila melanogaster embryos ]]> https://biorxiv.org/content/10.1101/2021.08.13.456172v1?rss=1 Albright, A. R. Stadler, M. R. Eisen, M. 2021-08-13 doi:10.1101/2021.08.13.456172 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ A cooperative network at the nuclear envelope counteracts LINC-mediated forces during oogenesis in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.08.13.456272v1?rss=1 Liu, C. Lung, Z. Wang, J. S. Wu, F. Dernburg, A. F. 2021-08-13 doi:10.1101/2021.08.13.456272 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Severe inbreeding and gene loss in the historical and extant population of the critically endangered Devils Hole pupfish ]]> https://biorxiv.org/content/10.1101/2021.08.13.456274v1?rss=1 Tian, D. Turner, B. J. Martin, C. H. 2021-08-14 doi:10.1101/2021.08.13.456274 Cold Spring Harbor Laboratory Press 2021-08-14 <![CDATA[ Structures of Tweety Homolog Proteins TTYH2 and TTYH3 reveal a Ca2+-dependent switch from intra- to inter-membrane dimerization ]]> https://biorxiv.org/content/10.1101/2021.08.15.456437v1?rss=1 Li, B. Hoel, C. M. Brohawn, S. G. 2021-08-16 doi:10.1101/2021.08.15.456437 Cold Spring Harbor Laboratory Press 2021-08-16 <![CDATA[ Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription ]]> https://biorxiv.org/content/10.1101/2021.08.16.456551v1?rss=1 Chong, S. Graham, T. G. W. Dugast-Darzacq, C. Dailey, G. M. Darzacq, X. Tjian, R. 2021-08-17 doi:10.1101/2021.08.16.456551 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Playing with FiRE: A genome resolved view of the soil microbiome responses to high severity forest wildfire ]]> https://biorxiv.org/content/10.1101/2021.08.17.456416v1?rss=1 Nelson, A. R. Narrowe, A. B. Rhoades, C. C. Fegel, T. S. Daly, R. A. Roth, H. K. Chu, R. K. Amundson, K. K. Geonczy, S. E. Emerson, J. B. Young, R. B. Steindorff, A. S. Mondo, S. J. Grigoriev, I. V. Salamov, A. Borch, T. Wilkins, M. J. 2021-08-17 doi:10.1101/2021.08.17.456416 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Chlamydomonas ATX1 is essential for Cu distribution towards the secretory pathway and maintenance of biomass in conditions demanding cupro-enzyme dependent metabolic pathways ]]> https://biorxiv.org/content/10.1101/2021.08.18.456897v1?rss=1 Pham, K. L. J. Schmollinger, S. Merchant, S. S. Strenkert, D. 2021-08-18 doi:10.1101/2021.08.18.456897 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ Machine learning enables discovery of DNA-carbon nanotube sensors for serotonin ]]> https://biorxiv.org/content/10.1101/2021.08.20.457145v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@9e1a2corg.highwire.dtl.DTLVardef@1c84e68org.highwire.dtl.DTLVardef@1939d1eorg.highwire.dtl.DTLVardef@30424e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kelich, P. Jeong, S. Navarro, N. Adams, J. Sun, X. Zhao, H. Landry, M. P. Vukovic, L. 2021-08-20 doi:10.1101/2021.08.20.457145 Cold Spring Harbor Laboratory Press 2021-08-20 <![CDATA[ Eliminating Aedes aegypti from its southern margin in Australia: insights from genomic data and simulation modeling ]]> https://biorxiv.org/content/10.1101/2021.08.21.457232v1?rss=1 99%) was predicted in both towns, and complete elimination was predicted in 35% of simulations in one town. Without tank removal, however, IIT led to a moderate suppression (61-93%) even with a 40:1 ratio of released IIT males to local males. Moreover, with a ratio of >20:1, Wolbachia establishment was predicted when the sorting error was >10-7. Our conservative estimates of intervention outcomes inform the planning of Ae. aegypti elimination in the region, and offer insight into the effective combinations of conventional and novel control tools, particularly for vulnerable mosquito populations at range margins. SignificanceAfter decades of range stagnation in Australia, the Aedes aegypti mosquito is expanding southward, approaching the most-densely-populated areas of Queensland. Using population genomics and simulation modeling of elimination campaigns, we show that Australias southernmost populations of this disease vector are genetically isolated and could be eliminated with moderate releases of incompatible Wolbachia-infected males if major larval breeding sites (non-compliant rainwater tanks) are removed first. The risk of Wolbachia establishment for this approach is low, and so is the risk of quick mosquito re-invasion. Our conservative estimates of intervention outcomes inform the planning of Ae. aegypti elimination in the region, and offer new insight into the benefits of combining conventional and novel control tools, particularly for mosquito populations at range margins. ]]> Rasic, G. Filipovic, I. Wu, S. L. Leon, T. M. Bennett, J. B. Sanchez Castellanos, H. M. Marshall, J. M. Trewin, B. 2021-08-22 doi:10.1101/2021.08.21.457232 Cold Spring Harbor Laboratory Press 2021-08-22 <![CDATA[ Belowground allocation and dynamics of recently fixed plant carbon in a California annual grassland soil ]]> https://biorxiv.org/content/10.1101/2021.08.23.457405v1?rss=1 Fossum, C. Estera-Molina, K. Yuan, M. Herman, D. Chu-Jacoby, I. Nico, P. Morrison, K. Pett-Ridge, J. Firestone, M. K. 2021-08-24 doi:10.1101/2021.08.23.457405 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ The Chloroflexi supergroup is metabolically diverse and representatives have novel genes for non-photosynthesis based CO2 fixation ]]> https://biorxiv.org/content/10.1101/2021.08.23.457424v1?rss=1 West-Roberts, J. A. Matheus Carnevali, P. B. Scholmerich, M. C. Al-Shayeb, B. Thomas, A. Sharrar, A. M. He, C. Y. Chen, L.-X. Lavy, A. Keren, R. Amano, Y. Banfield, J. 2021-08-24 doi:10.1101/2021.08.23.457424 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ Effective Ensemble of Deep Neural Networks Predicts Neural Responses to Naturalistic Videos ]]> https://biorxiv.org/content/10.1101/2021.08.24.457581v1?rss=1 Yang, H. Zhang, S. Wu, Y. Li, Y. Gu, S. 2021-08-27 doi:10.1101/2021.08.24.457581 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Host-associated microbial diversity in New Zealand cicadas uncovers elevational structure and replacement of obligate bacterial endosymbionts by Ophiocordyceps fungal pathogens ]]> https://biorxiv.org/content/10.1101/2021.08.24.457591v1?rss=1 Haji, D. Vailionis, J. Stukel, M. Gordon, E. R. Lemmon, E. Lemmon, A. McCutcheon, J. P. Simon, C. 2021-08-27 doi:10.1101/2021.08.24.457591 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Synergistic Enzyme Mixtures to Realize Near-Complete Depolymerization in Biodegradable Polymer/Additive Blends ]]> https://biorxiv.org/content/10.1101/2021.08.25.457667v1?rss=1 95% to less than 50%, causing formation of highly crystalline plastic pieces including microplastics. By synergizing both random chain scission and processive depolymerization, it is feasible to navigate morphological changes in polymer/additive blends and to achieve near complete depolymerization. The random scission enzymes in the amorphous domains create new chain ends that are subsequently bound and depolymerized by processive enzymes. Present studies further highlight the importance to consider host polymer morphological effects on the reactions catalyzed by embedded catalytic species. ]]> DelRe, C. Chang, B. Jayapurna, I. Hall, A. Wang, A. Zolkin, K. Xu, T. 2021-08-27 doi:10.1101/2021.08.25.457667 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Plucking a string or playing a G? Degree of choice abstraction impacts human reinforcement learning ]]> https://biorxiv.org/content/10.1101/2021.08.25.457707v1?rss=1 Rmus, M. Zou, A. Collins, A. G. E. 2021-08-27 doi:10.1101/2021.08.25.457707 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Exploring dimensions of biodiversity in Japanese ferns ]]> https://biorxiv.org/content/10.1101/2021.08.26.457744v1?rss=1 300,000 specimen records. We combined this with a phylogeny and functional traits to analyze taxonomic, phylogenetic, and functional diversity, and modeled biodiversity metrics in response to environmental factors and reproductive mode. Hierarchical clustering was used to delimit bioregions. Conservation status and threats were assessed by comparing the overlap of significantly diverse grid-cells with conservation zones and range maps of native Japanese deer. ResultsTaxonomic richness was highest at mid-latitudes. Phylogenetic and functional diversity and phylogenetic endemism were highest in small southern islands. Relative phylogenetic and functional diversity were high at high and low latitudes, and low at mid-latitudes. Grid-cells were grouped into three (phylogenetic) or four (taxonomic) major bioregions. Temperature and apomixis were identified as drivers of biodiversity patterns. Conservation status was generally high for grid-cells with significantly high biodiversity, but the threat due to herbivory by deer was greater for taxonomic richness than other metrics. ConclusionsOur integrative approach reveals previously undetected patterns and drivers of biodiversity in the ferns of Japan. Future conservation efforts should recognize that threats can vary by biodiversity metric and consider multiple multiple metrics when establishing conservation priorities. ]]> Nitta, J. Mishler, B. D. Iwasaki, W. Ebihara, A. 2021-08-28 doi:10.1101/2021.08.26.457744 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Dissociating the Neural Correlates of Planning and Executing Hierarchical Task Sets ]]> https://biorxiv.org/content/10.1101/2021.08.26.457791v1?rss=1 Cookson, S. L. Schumacher, E. H. 2021-08-28 doi:10.1101/2021.08.26.457791 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Efficient decoding of large-scale neural population responses with Gaussian-process multiclass regression ]]> https://biorxiv.org/content/10.1101/2021.08.26.457795v1?rss=1 Greenidge, C. D. Scholl, B. Yates, J. Pillow, J. W. 2021-08-28 doi:10.1101/2021.08.26.457795 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Redesigning the Eterna100 for the Vienna 2 folding engine ]]> https://biorxiv.org/content/10.1101/2021.08.26.457839v1?rss=1 Koodli, R. V. Rudolfs, B. Wayment-Steele, H. K. Eterna Structure Designers, Das, R. 2021-08-28 doi:10.1101/2021.08.26.457839 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Crossover patterning through kinase-regulated condensation and coarsening of recombination nodules ]]> https://biorxiv.org/content/10.1101/2021.08.26.457865v1?rss=1 Zhang, L. Stauffer, W. Zwicker, D. Dernburg, A. 2021-08-27 doi:10.1101/2021.08.26.457865 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Multimodal measurements of phototoxicity in nonlinear optical microscopy ]]> https://biorxiv.org/content/10.1101/2021.08.27.457929v1?rss=1 Zhang, X. Dorlhiac, G. Landry, M. Streets, A. 2021-08-28 doi:10.1101/2021.08.27.457929 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ The brain uses invariant dynamics to generalize outputs across movements ]]> https://biorxiv.org/content/10.1101/2021.08.27.457931v1?rss=1 Athalye, V. R. Khanna, P. Gowda, S. Orsborn, A. L. Costa, R. M. Carmena, J. M. 2021-08-28 doi:10.1101/2021.08.27.457931 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Binary outcomes of enhancer activity underlie stable random monoallelic expression ]]> https://biorxiv.org/content/10.1101/2021.08.27.457979v1?rss=1 Kissiov, D. U. Ethell, A. Chen, S. Wolf, N. K. Zhang, C. Dang, S. M. Jo, Y. Madsen, K. N. Paranjpe, I. D. Lee, A. Y. Chim, B. Raulet, D. 2021-08-28 doi:10.1101/2021.08.27.457979 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ DNA damage signaling regulates cohesin stabilization and promotes meiotic chromosome axis morphogenesis ]]> https://biorxiv.org/content/10.1101/2021.08.28.458025v1?rss=1 Yu, Z. Dernburg, A. F. 2021-08-28 doi:10.1101/2021.08.28.458025 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Mutationathon: towards standardization in estimates of pedigree-based germline mutation rates ]]> https://biorxiv.org/content/10.1101/2021.08.30.458162v1?rss=1 Bergeron, L. A. Besenbacher, S. Turner, T. N. Versoza, C. J. Wang, R. Price, A. L. Armstrong, E. Riera, M. Carlson, J. Chen, H.-y. Hahn, M. W. Harris, K. Kleppe, A. S. L. N. M. Lopez-Nandam, E. H. Moorjani, P. Pfeifer, S. P. Tiley, G. P. Yoder, A. D. Zhang, G. Schierup, M. H. 2021-08-31 doi:10.1101/2021.08.30.458162 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Long-term incubation of lake water enables genomic sampling of consortia involving Planctomycetes and Candidate Phyla Radiation bacteria ]]> https://biorxiv.org/content/10.1101/2021.09.01.458585v1?rss=1 300 kbp genome and several predicted to infect Planctomycetes. Together, our analyses suggest that freshwater Planctomycetes may act as hubs for interaction networks that include symbiotic CPR bacteria and phages. ]]> Jaffe, A. L. Fuster, M. Schoelmerich, M. C. Chen, L.-X. Colombet, J. Billard, H. Sime-Ngando, T. Banfield, J. 2021-09-01 doi:10.1101/2021.09.01.458585 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Three new Cenomanian conifers from El Chango (Chiapas, Mexico) offer a snapshot of the geographic mosaic of the Mesozoic conifer decline ]]> https://biorxiv.org/content/10.1101/2021.09.01.458614v1?rss=1 Gonzalez-Ramirez, I. Cevallos-Ferriz, S. R. Rothfels, C. 2021-09-03 doi:10.1101/2021.09.01.458614 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Molecular Organization of the Early Stages of Nucleosome Phase Separation Visualized by Cryo-Electron Tomography ]]> https://biorxiv.org/content/10.1101/2021.09.01.458650v1?rss=1 Zhang, M. Diaz-Celis, C. D. Onoa, B. Canari-Chumpitaz, C. Requejo, K. I. Liu, J. Vien, M. Nogales, E. Ren, G. Bustamante, C. 2021-09-02 doi:10.1101/2021.09.01.458650 Cold Spring Harbor Laboratory Press 2021-09-02 <![CDATA[ Excitatory neurotransmission activates compartmentalized calcium transients in Müller glia without affecting lateral process motility ]]> https://biorxiv.org/content/10.1101/2021.09.02.458760v1?rss=1 Tworig, J. M. Coate, C. Feller, M. B. 2021-09-03 doi:10.1101/2021.09.02.458760 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Emergent intra-pair sex differences and behavioral coordination in pair bonded prairie voles ]]> https://biorxiv.org/content/10.1101/2021.09.03.458892v1?rss=1 Brusman, L. E. Protter, D. S. W. Fultz, A. C. Paulson, M. U. Chapel, G. D. Elges, I. O. Cameron, R. T. Beery, A. K. Donaldson, Z. R. 2021-09-06 doi:10.1101/2021.09.03.458892 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Unearthing modes of climatic adaptation in underground storage organs across Liliales ]]> https://biorxiv.org/content/10.1101/2021.09.03.458928v1?rss=1 Tribble, C. M. May, M. R. Jackson-Gain, A. Zenil-Ferguson, R. Specht, C. D. Rothfels, C. J. 2021-09-05 doi:10.1101/2021.09.03.458928 Cold Spring Harbor Laboratory Press 2021-09-05 <![CDATA[ Recruitment of an ancient branching program to suppress carpel development in maize flowers ]]> https://biorxiv.org/content/10.1101/2021.09.03.458935v1?rss=1 Klein, H. Gallagher, J. P. Demesa-Arevalo, E. Abraham-Juarez, M. J. Heeney, M. Feil, R. Lunn, J. E. Xiao, Y. Chuck, G. S. Whipple, C. J. Jackson, D. Bartlett, M. E. 2021-09-04 doi:10.1101/2021.09.03.458935 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep ]]> https://biorxiv.org/content/10.1101/2021.09.07.458675v1?rss=1 Chen, Z. Xu, Y.-X. Xie, X.-L. Wang, D.-F. Aguilar-Gomez, D. Liu, G.-J. Li, X. Esmailizadeh, A. Rezaei, V. Kantanen, J. Ammosov, I. Nosrati, M. Periasamy, K. Coltman, D. W. Lenstra, J. A. Nielsen, R. A. Li, M.-h. 2021-09-09 doi:10.1101/2021.09.07.458675 Cold Spring Harbor Laboratory Press 2021-09-09 <![CDATA[ Deep learning of Cas13 guide activity from high-throughput gene essentiality screening ]]> https://biorxiv.org/content/10.1101/2021.09.14.460134v1?rss=1 Wei, J. Lotfy, P. Faizi, K. Kitano, H. Hsu, P. D. Konermann, S. 2021-09-14 doi:10.1101/2021.09.14.460134 Cold Spring Harbor Laboratory Press 2021-09-14 <![CDATA[ 3D Microenvironment-Specific Mechanosensing Regulates Neural Stem Cell Lineage Commitment ]]> https://biorxiv.org/content/10.1101/2021.09.15.460399v1?rss=1 Baek, J. Lopez, P. A. Lee, S. Kim, T.-S. Kumar, S. Schaffer, D. V. 2021-09-16 doi:10.1101/2021.09.15.460399 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ Acidity and sulfur oxidation intermediate concentrations controlled by O2-driven partitioning of sulfur oxidizing bacteria in a mine tailings impoundment ]]> https://biorxiv.org/content/10.1101/2021.09.16.460096v1?rss=1 Whaley-Martin, K. J. Chen, L.-X. Colebrander Nelson, T. Gordon, J. Kantor, R. Twible, L. E. Marshall, S. Rossi, L. Bessette, B. Baron, C. Apte, S. Banfield, J. Warren, L. A. 2021-09-16 doi:10.1101/2021.09.16.460096 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis ]]> https://biorxiv.org/content/10.1101/2021.09.16.460328v1?rss=1 View larger version (49K): org.highwire.dtl.DTLVardef@1f849b6org.highwire.dtl.DTLVardef@1af655borg.highwire.dtl.DTLVardef@274baaorg.highwire.dtl.DTLVardef@1d8af02_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sun, D. A. Patel, N. H. 2021-09-18 doi:10.1101/2021.09.16.460328 Cold Spring Harbor Laboratory Press 2021-09-18 <![CDATA[ Exploring neural correlates of behavioral and academic resilience among children in poverty ]]> https://biorxiv.org/content/10.1101/2021.09.16.460710v1?rss=1 Ellwood-Lowe, M. E. Irving, C. N. Bunge, S. A. 2021-09-22 doi:10.1101/2021.09.16.460710 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ A specific eIF4A paralog facilitates LARP1-mediated translation repression during mTORC1 inhibition ]]> https://biorxiv.org/content/10.1101/2021.09.18.460932v1?rss=1 Shichino, Y. Mito, M. Kashiwagi, K. Takahashi, M. Ito, T. Ingolia, N. T. Iwasaki, S. 2021-09-19 doi:10.1101/2021.09.18.460932 Cold Spring Harbor Laboratory Press 2021-09-19 <![CDATA[ A Two-tiered Functional Screen Identifies Herpesviral Transcriptional Modifiers and their Essential Domains ]]> https://biorxiv.org/content/10.1101/2021.09.20.460982v1?rss=1 Morgens, D. W. Nandakumar, D. Didychuk, A. L. Yang, K. J. Glaunsinger, B. 2021-09-22 doi:10.1101/2021.09.20.460982 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ SCONCE: A method for profiling Copy Number Alterations in Cancer Evolution using Single Cell Whole Genome Sequencing ]]> https://biorxiv.org/content/10.1101/2021.09.23.461581v1?rss=1 Hui, S. Nielsen, R. 2021-09-24 doi:10.1101/2021.09.23.461581 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Evaluating the reliability, validity, and utility of overlapping networks: Implications for cognitive control ]]> https://biorxiv.org/content/10.1101/2021.09.28.462232v1?rss=1 Cookson, S. L. D'Esposito, M. 2021-09-30 doi:10.1101/2021.09.28.462232 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Blood variation implicates respiratory limits on elevational ranges of Andean birds ]]> https://biorxiv.org/content/10.1101/2021.09.30.462673v1?rss=1 Linck, E. B. Williamson, J. Bautista, E. Beckman, E. Benham, P. M. DuBay, S. G. Flores, L. M. Gadek, C. R. Johnson, A. B. Jones, M. R. Nunez-Zapata, J. Quinonez, A. Schmitt, C. J. Susanibar, D. Tiravanti C, J. Verde-Guerra, K. Wright, N. A. Valqui, T. Storz, J. F. Witt, C. C. 2021-10-01 doi:10.1101/2021.09.30.462673 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Direct brain recordings reveal continuous encoding of structure in random stimuli ]]> https://biorxiv.org/content/10.1101/2021.10.01.462295v1?rss=1 Fuhrer, J. Glette, K. Ivanovic, J. Larsson, P. G. Bekinschtein, T. A. Kochen, S. Knight, R. T. Torresen, J. Solbakk, A.-K. S. Endestad, T. E. Blenkmann, A. 2021-10-03 doi:10.1101/2021.10.01.462295 Cold Spring Harbor Laboratory Press 2021-10-03 <![CDATA[ Transferability of Geometric Patterns from Protein Self-Interactions to Protein-Ligand Interactions ]]> https://biorxiv.org/content/10.1101/2021.10.01.462692v1?rss=1 Koehl, A. Jagota, M. Erdmann-Pham, D. D. Fung, A. Song, Y. S. 2021-10-01 doi:10.1101/2021.10.01.462692 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ A mycobacterial glycine-rich protein governs actin-based motility ]]> https://biorxiv.org/content/10.1101/2021.10.01.462822v1?rss=1 Hill, N. S. Welch, M. D. 2021-10-01 doi:10.1101/2021.10.01.462822 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Increased remodeling and impaired adaption to endurance exercise in desminopathy ]]> https://biorxiv.org/content/10.1101/2021.10.03.462939v1?rss=1 Mossakowski, A. A. Langer, H. T. Bizieff, A. Avey, A. M. Zbinden-Foncea, H. Hellerstein, M. Baar, K. 2021-10-03 doi:10.1101/2021.10.03.462939 Cold Spring Harbor Laboratory Press 2021-10-03 <![CDATA[ Robust T cell activation requires an eIF3-driven burst in T cell receptor translation ]]> https://biorxiv.org/content/10.1101/2021.10.04.463005v1?rss=1 DeSilva, D. Ferguson, L. Chin, G. Smith, B. Apathy, R. Roth, T. Blaeschke, F. Kudla, M. Marson, A. Ingolia, N. T. Cate, J. H. 2021-10-04 doi:10.1101/2021.10.04.463005 Cold Spring Harbor Laboratory Press 2021-10-04 <![CDATA[ Chromatin changes in PIF-regulated genes parallel their rapid transcriptional response to light ]]> https://biorxiv.org/content/10.1101/2021.10.04.463089v1?rss=1 Gonzalez-Grandio, E. Alamos, S. Zhang, Y. Dalton-Roesler, J. Niyogi, K. K. Garcia, H. G. Quail, P. H. 2021-10-05 doi:10.1101/2021.10.04.463089 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ Multifunctional Cre-dependent transgenic mice for high-precision all-optical interrogation of neural circuits ]]> https://biorxiv.org/content/10.1101/2021.10.05.463223v1?rss=1 Bounds, H. A. Sadahiro, M. Hendricks, W. D. Gajowa, M. Oldenburg, I. A. Gopakumar, K. Quintana, D. Daigle, T. Zeng, H. Adesnik, H. 2021-10-07 doi:10.1101/2021.10.05.463223 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ Evolutionary sweeps of subviral parasites and their phage host bring unique parasite variants and disappearance of a phage CRISPR-Cas system ]]> https://biorxiv.org/content/10.1101/2021.10.07.463549v1?rss=1 Angermeyer, A. Hays, S. Nguyen, M. Johura, F.-t. Sultana, M. Alam, M. Seed, K. 2021-10-07 doi:10.1101/2021.10.07.463549 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ CRISPR-Cas9-mediated knockout of CYP79D1 and CYP79D2 in cassava attenuates toxic cyanogen production ]]> https://biorxiv.org/content/10.1101/2021.10.08.462827v1?rss=1 Gomez, M. A. Berkoff, K. C. Gill, B. K. Iavarone, A. T. Lieberman, S. E. Ma, J. M. Schultink, A. Wyman, S. K. Chauhan, R. D. Taylor, N. J. Staskawicz, B. J. Cho, M.-J. Rokhsar, D. S. Lyons, J. B. 2021-10-08 doi:10.1101/2021.10.08.462827 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ Widespread distribution of collagens and collagen-associated domains in eukaryotes ]]> https://biorxiv.org/content/10.1101/2021.10.08.463732v1?rss=1 Linden, T. A. King, N. 2021-10-10 doi:10.1101/2021.10.08.463732 Cold Spring Harbor Laboratory Press 2021-10-10 <![CDATA[ Structural basis of mitochondrial protein import by the TIM complex ]]> https://biorxiv.org/content/10.1101/2021.10.10.463828v1?rss=1 Sim, S. I. Chen, Y. Park, E. 2021-10-11 doi:10.1101/2021.10.10.463828 Cold Spring Harbor Laboratory Press 2021-10-11 <![CDATA[ Phage-encoded ribosomal protein S21 expression is linked to late stage phage replication ]]> https://biorxiv.org/content/10.1101/2021.10.11.463225v1?rss=1 Chen, L.-X. Jaffe, A. L. Borges, A. L. Penev, P. Nelson, T. C. Warren, L. A. Banfield, J. 2021-10-11 doi:10.1101/2021.10.11.463225 Cold Spring Harbor Laboratory Press 2021-10-11 <![CDATA[ The Evolution of Host Specialization in an Insect Pathogen ]]> https://biorxiv.org/content/10.1101/2021.10.11.463986v1?rss=1 Visher, E. Uricchio, L. Bartlett, L. DeNamur, N. Yarcan, A. Alhassani, D. Boots, M. 2021-10-12 doi:10.1101/2021.10.11.463986 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ Frugivore gut passage increases seed germination: an updated meta-analysis ]]> https://biorxiv.org/content/10.1101/2021.10.12.462022v1?rss=1 Rogers, H. S. Cavazos, B. R. Gawel, A. M. Karnish, A. T. Ray, C. A. Rose, E. Thierry, H. Fricke, E. C. 2021-10-13 doi:10.1101/2021.10.12.462022 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ The extrachromosomal circular DNAs of the rice blast pathogen Magnaporthe oryzae contain a wide variety of LTR retrotransposons, genes, and effectors ]]> https://biorxiv.org/content/10.1101/2021.10.12.464130v1?rss=1 Joubert, P. M. Krasileva, K. V. 2021-10-13 doi:10.1101/2021.10.12.464130 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ AUG-3387, a Human-Derived Monoclonal Antibody Neutralizes SARS-CoV-2 Variants and Reduces Viral Load from Therapeutic Treatment of Hamsters In Vivo ]]> https://biorxiv.org/content/10.1101/2021.10.12.464150v1?rss=1 Emig, C. J. Mena, M. A. Henry, S. J. Vitug, A. Ventura, C. J. Fox, D. Nguyenla, X. H. Xu, H. Moon, C. Sahakijjpijarn, S. Kuehl, P. J. Revelli, D. Cui, Z. Williams, R. O. Christensen, D. J. 2021-10-13 doi:10.1101/2021.10.12.464150 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Sex Differences in Pubertal Circadian and Ultradian Rhythmic Development Under Naturalistic Conditions ]]> https://biorxiv.org/content/10.1101/2021.10.15.464452v1?rss=1 Grant, A. D. Wilbrecht, L. Kriegsfeld, L. J. 2021-10-16 doi:10.1101/2021.10.15.464452 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ Diversity and evolution of nitric oxide reduction ]]> https://biorxiv.org/content/10.1101/2021.10.15.464467v1?rss=1 Hemp, J. Murali, R. Pace, L. A. Sanford, R. A. Hatzenpichler, R. Ward, L. Lingappa, U. Fischer, W. W. Gennis, R. B. 2021-10-15 doi:10.1101/2021.10.15.464467 Cold Spring Harbor Laboratory Press 2021-10-15 <![CDATA[ Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs ]]> https://biorxiv.org/content/10.1101/2021.10.18.464293v1?rss=1 Bredeson, J. V. Mudd, A. B. Medina-Ruiz, S. Mitros, T. Smith, O. K. Miller, K. E. Lyons, J. B. Batra, S. S. Park, J. Berkoff, K. C. Plott, C. Grimwood, J. Schmutz, J. Aguirre-Figueroa, G. Khokha, M. K. Lane, M. Philipp, I. Laslo, M. Hanken, J. Kerdivel, G. Buisine, N. Sachs, L. M. Buchholz, D. R. Kwon, T. Smith-Parker, H. Gridi-Papp, M. Ryan, M. J. Denton, R. D. Malone, J. H. Wallingford, J. B. Straight, A. F. Heald, R. Hockemeyer, D. Harland, R. M. Rokhsar, D. S. 2021-10-18 doi:10.1101/2021.10.18.464293 Cold Spring Harbor Laboratory Press 2021-10-18 <![CDATA[ A patatin-like phospholipase mediates Rickettsia parkeri escape from host membranes ]]> https://biorxiv.org/content/10.1101/2021.10.21.465009v1?rss=1 Borgo, G. M. Burke, T. P. Tran, C. J. Lo, N. T. N. Engström, P. Welch, M. D. 2021-10-21 doi:10.1101/2021.10.21.465009 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ Use-dependent biases primarily originate from a contaminated motor plan ]]> https://biorxiv.org/content/10.1101/2021.10.21.465112v1?rss=1 Tsay, J. S. Kim, H. E. Saxena, A. Parvin, D. E. Verstynen, T. V. Ivry, R. B. 2021-10-22 doi:10.1101/2021.10.21.465112 Cold Spring Harbor Laboratory Press 2021-10-22 <![CDATA[ Diversification of multipotential postmitotic mouse retinal ganglion cell precursors into discrete types ]]> https://biorxiv.org/content/10.1101/2021.10.21.465277v1?rss=1 Shekhar, K. Whitney, I. E. Butrus, S. Peng, Y.-R. Sanes, J. R. 2021-10-21 doi:10.1101/2021.10.21.465277 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ A positively Tuned Voltage Indicator Reveals Electrical Correlates of Calcium Activity in the Brain ]]> https://biorxiv.org/content/10.1101/2021.10.21.465345v1?rss=1 Evans, S. W. Shi, D. Chavarha, M. Plitt, M. H. Taxidis, J. Madruga, B. Van Keulen, S. C. Pang, M. Su, S. Hwang, F.-J. Zhang, G. Reese, A. Pradhan, L. Fan, J. L. Lee, S. Liu, Y. Suomivuori, C.-M. Jiang, D. Negrean, A. Wang, S. Ji, N. Clandinin, T. Dror, R. Bi, G. G. Makinson, C. D. Golshani, P. Giocomo, L. M. Losonczy, A. Ding, J. B. Lin, M. Z. 2021-10-23 doi:10.1101/2021.10.21.465345 Cold Spring Harbor Laboratory Press 2021-10-23 <![CDATA[ Single-particle tracking of dynein identifies PP2A B55/SUR-6 as a cell cycle regulator of cortical force generation ]]> https://biorxiv.org/content/10.1101/2021.10.22.465443v1?rss=1 Edwards, G. A. Linehan, J. B. Boudreau, V. Maddox, P. S. 2021-10-23 doi:10.1101/2021.10.22.465443 Cold Spring Harbor Laboratory Press 2021-10-23 <![CDATA[ The endoplasmic reticulum adopts two distinct tubule forms ]]> https://biorxiv.org/content/10.1101/2021.10.26.465969v1?rss=1 Wang, B. Zhao, Z. Xiong, M. Yan, R. Xu, K. 2021-10-26 doi:10.1101/2021.10.26.465969 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors ]]> https://biorxiv.org/content/10.1101/2021.10.27.466110v1?rss=1 Chen, Y. Cattoglio, C. Dailey, G. Zhu, Q. Tjian, R. Darzacq, X. 2021-10-28 doi:10.1101/2021.10.27.466110 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Reproduction, seasonal morphology, and juvenile growth in three Malagasy fruit bats ]]> https://biorxiv.org/content/10.1101/2021.10.28.466299v1?rss=1 Andrianiaina, A. Andry, S. Gentles, A. Guth, S. Heraud, J.-M. Ranaivoson, H. C. Ravelomanantsoa, N. A. F. Treuer, T. Brook, C. E. 2021-10-29 doi:10.1101/2021.10.28.466299 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Impact of Protein Identity on Tumor-Associated Antigen Uptake into Infiltrating Immune Cells: A Comparison of Different Fluorescent Proteins as Model Antigens ]]> https://biorxiv.org/content/10.1101/2021.10.30.464602v1?rss=1 Yi, R. Chen, E. Roberts, E. W. Krummel, M. F. Serwas, N. K. 2021-11-02 doi:10.1101/2021.10.30.464602 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Explaining heterogeneity in medial entorhinal cortex with task-driven neural networks ]]> https://biorxiv.org/content/10.1101/2021.10.30.466617v1?rss=1 Nayebi, A. Attinger, A. Campbell, M. G. Hardcastle, K. Low, I. I. C. Mallory, C. S. Mel, G. C. Sorscher, B. Williams, A. H. Ganguli, S. Giocomo, L. M. Yamins, D. L. K. 2021-11-02 doi:10.1101/2021.10.30.466617 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Machine learning-based library design improves packaging and diversity of adeno-associated virus (AAV) libraries ]]> https://biorxiv.org/content/10.1101/2021.11.02.467003v1?rss=1 ZHU, D. Brookes, D. H. Busia, A. Carneiro, A. Fannjiang, C. Popova, G. Shin, D. Chang, E. F. Nowakowski, T. J. Listgarten, J. Schaffer, D. V. 2021-11-04 doi:10.1101/2021.11.02.467003 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Sulcal depth in prefrontal cortex: A novel predictor of working memory performance ]]> https://biorxiv.org/content/10.1101/2021.11.03.467157v1?rss=1 Yao, J. K. Voorhies, W. I. Miller, J. A. Weiner, K. S. Bunge, S. A. 2021-11-04 doi:10.1101/2021.11.03.467157 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Thymic macrophages consist of two populations with distinct localization and origin ]]> https://biorxiv.org/content/10.1101/2021.11.04.467238v1?rss=1 Zhou, T.-A. Hsu, H.-P. Tu, Y.-H. Lin, C.-Y. Chen, N.-J. Tsai, J.-W. Robey, E. A. Huang, H.-C. Hsu, C.-L. Dzhagalov, I. L. 2021-11-04 doi:10.1101/2021.11.04.467238 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ CALDERA: Finding all significant de Bruijn subgraphs for bacterial GWAS ]]> https://biorxiv.org/content/10.1101/2021.11.05.467462v1?rss=1 Roux de Bezieux, H. Lima, L. Perraudeau, F. Mary, A. Dudoit, S. Jacob, L. 2021-11-05 doi:10.1101/2021.11.05.467462 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ Discovery of a carbonic anhydrase-Rubisco supercomplex within the alpha-carboxysome ]]> https://biorxiv.org/content/10.1101/2021.11.05.467472v1?rss=1 Blikstad, C. Dugan, E. J. Laughlin, T. G. Liu, M. D. Shoemaker, S. R. Remis, J. P. Savage, D. F. 2021-11-05 doi:10.1101/2021.11.05.467472 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ Large-scale discovery of recombinases for integrating DNA into the human genome ]]> https://biorxiv.org/content/10.1101/2021.11.05.467528v1?rss=1 Durrant, M. G. Fanton, A. Tycko, J. Hinks, M. Chandrasekaran, S. Perry, N. T. Schaepe, J. Du, P. P. Bintu, L. Bassik, M. C. Bhatt, A. S. Hsu, P. D. 2021-11-06 doi:10.1101/2021.11.05.467528 Cold Spring Harbor Laboratory Press 2021-11-06 <![CDATA[ Dopamine neuron morphology and output are differentially controlled by mTORC1 and mTORC2 ]]> https://biorxiv.org/content/10.1101/2021.11.07.467637v1?rss=1 Kosillo, P. Ahmed, K. M. Roberts, B. M. Cragg, S. J. Bateup, H. S. 2021-11-07 doi:10.1101/2021.11.07.467637 Cold Spring Harbor Laboratory Press 2021-11-07 <![CDATA[ CRISPR-Cas9 mediated nuclear transport and genomic integration of nanostructured genes in human primary cells ]]> https://biorxiv.org/content/10.1101/2021.11.08.467750v1?rss=1 Lin Shiao, E. Pfeifer, W. G. Shy, B. R. Doost, M. S. Chen, E. Vykunta, V. S. Hamilton, J. R. Stahl, E. C. Lopez, D. M. Espinoza, C. R. S. Dejanov, A. E. Lew, R. J. Poirer, M. G. Marson, A. Castro, C. E. Doudna, J. A. 2021-11-09 doi:10.1101/2021.11.08.467750 Cold Spring Harbor Laboratory Press 2021-11-09 <![CDATA[ Individual differences in frontoparietal plasticity in humans ]]> https://biorxiv.org/content/10.1101/2021.11.08.467831v1?rss=1 Boroshok, A. L. Park, A. T. Fotiadis, P. Velasquez, G. H. Tooley, U. A. Simon, K. R. Forde, J. C. P. Delgado Reyes, L. M. Tisdall, M. D. Bassett, D. S. Cooper, E. A. Mackey, A. P. 2021-11-10 doi:10.1101/2021.11.08.467831 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ Structural Basis for pH-Gating of the K+ Channel TWIK1 at the Selectivity Filter ]]> https://biorxiv.org/content/10.1101/2021.11.09.467928v1?rss=1 Turney, T. S. Li, V. Brohawn, S. G. 2021-11-11 doi:10.1101/2021.11.09.467928 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Large cells activate global protein degradation to maintain cell size homeostasis ]]> https://biorxiv.org/content/10.1101/2021.11.09.467936v1?rss=1 Liu, S. Tan, C. Melo-Gavin, C. Mark, K. G. Ginzberg, M. B. Blutrich, R. Patel, N. Rape, M. Kafri, R. 2021-11-11 doi:10.1101/2021.11.09.467936 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Vaccinia virus D10 has broad decapping activity that is regulated by mRNA splicing ]]> https://biorxiv.org/content/10.1101/2021.11.10.468017v1?rss=1 Ly, M. Burgess, H. M. Mohr, I. Glaunsinger, B. A. 2021-11-10 doi:10.1101/2021.11.10.468017 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ Phylogenetic diversity of two common Trypanosoma cruzi lineages in the Southwestern United States ]]> https://biorxiv.org/content/10.1101/2021.11.10.468115v1?rss=1 Flores-Lopez, C. A. Mitchell, E. A. Reisenman, C. E. Sarkar, S. Williamson, P. C. Machado, C. A. 2021-11-12 doi:10.1101/2021.11.10.468115 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ An optimized ChIP-Seq framework for profiling of histone modifications in Chromochloris zofingiensis ]]> https://biorxiv.org/content/10.1101/2021.11.11.468265v1?rss=1 Strenkert, D. Mingay, M. Schmollinger, S. Chen, C. O'Malley, R. C. Merchant, S. S. 2021-11-13 doi:10.1101/2021.11.11.468265 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ A de novo matrix for macroscopic living materials from bacteria ]]> https://biorxiv.org/content/10.1101/2021.11.12.468079v1?rss=1 Molinari, S. Tesoriero, R. F. Li, D. Sridhar, S. Cai, R. Soman, J. Ryan, K. R. Ashby, P. D. Ajo-Franklin, C. 2021-11-12 doi:10.1101/2021.11.12.468079 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ A Multi-Omics and Bioenergetics Longitudinal Aging Dataset in Primary Human Fibroblasts with Mitochondrial Perturbations ]]> https://biorxiv.org/content/10.1101/2021.11.12.468448v1?rss=1 Sturm, G. Monzel, A. S. Karan, K. R. Michelson, J. Ware, S. A. Cardenas, A. Lin, J. Bris, C. Santhanam, B. Murphy, M. P. Levine, M. E. Horvath, S. Belsky, D. W. Wang, S. Procaccio, V. Kaufman, B. A. Hirano, M. Picard, M. 2021-11-13 doi:10.1101/2021.11.12.468448 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ Evaluation of methods for the inference of ancestral recombination graphs ]]> https://biorxiv.org/content/10.1101/2021.11.15.468686v1?rss=1 Y C Brandt, D. Wei, X. Deng, Y. Vaughn, A. H. Nielsen, R. 2021-11-17 doi:10.1101/2021.11.15.468686 Cold Spring Harbor Laboratory Press 2021-11-17 <![CDATA[ Structures of the Cyanobacterial Phycobilisome ]]> https://biorxiv.org/content/10.1101/2021.11.15.468712v1?rss=1 Sauer, P. V. Dominguez-Martin, M. A. Kirst, H. Sutter, M. Bina, D. Greber, B. J. Nogales, E. Polivka, T. Kerfeld, C. A. 2021-11-15 doi:10.1101/2021.11.15.468712 Cold Spring Harbor Laboratory Press 2021-11-15 <![CDATA[ Rigid DNA nanotube tethers suppress high frequency noise in dual-trap optical tweezers systems ]]> https://biorxiv.org/content/10.1101/2021.11.15.468716v1?rss=1 Shaw, A. Satija, R. De la Matta, E. A. d. M. Marqusee, S. Bustamante, C. 2021-11-16 doi:10.1101/2021.11.15.468716 Cold Spring Harbor Laboratory Press 2021-11-16 <![CDATA[ Structure of the Quenched Cyanobacterial OCP-Phycobilisome Complex ]]> https://biorxiv.org/content/10.1101/2021.11.15.468719v1?rss=1 Dominguez-Martin, M. A. Sauer, P. V. Sutter, M. Kirst, H. Bina, D. Greber, B. J. Nogales, E. Polivka, T. Kerfeld, C. A. 2021-11-15 doi:10.1101/2021.11.15.468719 Cold Spring Harbor Laboratory Press 2021-11-15 <![CDATA[ Microglia do not restrict SARS-CoV-2 replication following infection of the central nervous system of K18-hACE2 transgenic mice ]]> https://biorxiv.org/content/10.1101/2021.11.15.468761v1?rss=1 Olivarria, G. M. Cheng, Y. Pachow, C. Hohsfield, L. A. Smith-Geater, C. Miramontes, R. Wu, J. Burns, M. S. Tsourmas, K. I. Stocksdale, J. Manlapaz, C. Furman, S. Yong, W. H. Teijaro, J. Edwards, R. A. Green, K. Thompson, L. M. Lane, T. 2021-11-17 doi:10.1101/2021.11.15.468761 Cold Spring Harbor Laboratory Press 2021-11-17 <![CDATA[ Tissue-specific impacts of aging and genetics on gene expression patterns in humans ]]> https://biorxiv.org/content/10.1101/2021.11.16.468753v1?rss=1 Yamamoto, R. Chung, R. Vazquez, J. M. Sheng, H. Steinberg, P. Ioannidis, N. Sudmant, P. H. 2021-11-19 doi:10.1101/2021.11.16.468753 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Not so fast: Limited validity of deep convolutional neural networks as in silico models for human naturalistic face processing ]]> https://biorxiv.org/content/10.1101/2021.11.17.469009v1?rss=1 Jiahui, G. Feilong, M. Visconti di Oleggio Castello, M. Nastase, S. A. Haxby, J. V. Gobbini, M. I. 2021-11-19 doi:10.1101/2021.11.17.469009 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ PURC v2.0: a program for improved sequence inference for polyploid phylogenetics and other manifestations of the multiple-copy problem ]]> https://biorxiv.org/content/10.1101/2021.11.18.468666v1?rss=1 Schafran, P. W. Li, F.-W. W. Rothfels, C. 2021-11-19 doi:10.1101/2021.11.18.468666 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Cryo-EM structures of the channelrhodopsin ChRmine in lipid nanodiscs ]]> https://biorxiv.org/content/10.1101/2021.11.21.469454v1?rss=1 Tucker, K. Sridharan, S. Adesnik, H. Brohawn, S. G. 2021-11-22 doi:10.1101/2021.11.21.469454 Cold Spring Harbor Laboratory Press 2021-11-22 <![CDATA[ Theoretical Guarantees for Phylogeny Inference from Single-Cell Lineage Tracing ]]> https://biorxiv.org/content/10.1101/2021.11.21.469464v1?rss=1 Wang, R. Zhang, R. Y. Khodaverdian, A. Yosef, N. 2021-11-22 doi:10.1101/2021.11.21.469464 Cold Spring Harbor Laboratory Press 2021-11-22 <![CDATA[ Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2021.11.25.469980v1?rss=1 Brothers, M. Rine, J. 2021-11-25 doi:10.1101/2021.11.25.469980 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ Listeria monocytogenes requires cellular respiration for NAD+ regeneration and pathogenesis ]]> https://biorxiv.org/content/10.1101/2021.11.25.470024v1?rss=1 1,000-fold in a mouse infection model. Consistent with NAD+ regeneration maintaining L. monocytogenes viability and enabling immune evasion, a respiration-deficient strain exhibited elevated bacteriolysis within the host cytosol and NOX rescued this phenotype. These studies show that NAD+ regeneration, rather than oxidative phosphorylation, represents the primary role of L. monocytogenes respiration and highlight the nuanced relationship between bacterial metabolism, physiology, and pathogenesis. ]]> Rivera-Lugo, R. Deng, D. Anaya-Sanchez, A. Tejedor-Sanz, S. Reyes Ruiz, V. M. Smith, H. B. Titov, D. V. Sauer, J. D. Skaar, E. P. Ajo-Franklin, C. M. Portnoy, D. A. Light, S. H. 2021-11-25 doi:10.1101/2021.11.25.470024 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ OxPhos Dysfunction Causes Hypermetabolism and Reduces Lifespan in Cells and in Patients with Mitochondrial Diseases ]]> https://biorxiv.org/content/10.1101/2021.11.29.470428v1?rss=1 Sturm, G. Karan, K. R. Santhanham, B. S. Taivassalo, T. Bris, C. Duplaga, S. A. Cross, M. Towheed, A. Higgins-Chen, A. T. McManus, M. J. Cardenas, A. Lin, J. Epel, E. S. Rahman, S. Vissing, J. Grassi, B. Levine, M. Horvath, S. Haller, R. G. Lenaers, G. Wallace, D. C. Tavazoie, S. Procaccio, V. Kaufman, B. A. Seifert, E. Hirano, M. Monzel, A. Picard, M. 2021-11-30 doi:10.1101/2021.11.29.470428 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Remote sensing reveals multi-decadal losses of tree cover in California driven by increasing fire disturbance and climate stress ]]> https://biorxiv.org/content/10.1101/2021.11.30.470651v1?rss=1 Wang, J. A. Randerson, J. T. Goulden, M. L. Knight, C. Battles, J. B. 2021-12-01 doi:10.1101/2021.11.30.470651 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Ligand-induced changes in dynamics mediate long-range allostery in the lac repressor ]]> https://biorxiv.org/content/10.1101/2021.11.30.470682v1?rss=1 Glasgow, A. Hobbs, H. T. Perry, Z. R. Marqusee, S. Kortemme, T. 2021-12-01 doi:10.1101/2021.11.30.470682 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ A naturally DNase-free CRISPR-Cas12c enzyme silences gene expression ]]> https://biorxiv.org/content/10.1101/2021.12.06.471469v1?rss=1 Huang, C. J. Adler, B. A. Doudna, J. A. 2021-12-06 doi:10.1101/2021.12.06.471469 Cold Spring Harbor Laboratory Press 2021-12-06 <![CDATA[ Drosophila gustatory projections are segregated by taste modality and connectivity ]]> https://biorxiv.org/content/10.1101/2021.12.08.471796v1?rss=1 Engert, S. Sterne, G. R. Harris, D. T. Scott, K. 2021-12-09 doi:10.1101/2021.12.08.471796 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Electrically Controlling and Optically Observing the Membrane Potential of Supported Lipid Bilayers ]]> https://biorxiv.org/content/10.1101/2021.12.10.472087v1?rss=1 Yudovich, S. Marzouqe, A. Kantorovitsch, J. Teblum, E. Chen, T. Enderlein, J. Miller, E. W. Weiss, S. 2021-12-10 doi:10.1101/2021.12.10.472087 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ SARS-CoV-2 Spike triggers barrier dysfunction and vascular leak via integrins and TGF-β signaling ]]> https://biorxiv.org/content/10.1101/2021.12.10.472112v1?rss=1 Biering, S. B. Tramontini Gomes de Sousa, F. Tjang, L. V. Pahmeier, F. Ruan, R. Blanc, S. F. Patel, T. S. Worthington, C. M. Glasner, D. R. Castillo-Rojas, B. Servellita, V. Lo, N. T. Wong, M. P. Warnes, C. M. Sandoval, D. R. Clausen, T. M. Santos, Y. A. Ortega, V. Aguilar-Carreno, H. Esko, J. D. Chiu, C. Y. Pak, J. E. Beatty, P. R. Harris, E. 2021-12-13 doi:10.1101/2021.12.10.472112 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Dynamics of CTCF and cohesin mediated chromatin looping revealed by live-cell imaging ]]> https://biorxiv.org/content/10.1101/2021.12.12.472242v1?rss=1 Gabriele, M. Brandao, H. B. Grosse-Holz, S. Jha, A. Dailey, G. M. Cattoglio, C. Hsieh, T.-H. S. Mirny, L. Zechner, C. Hansen, A. S. 2021-12-13 doi:10.1101/2021.12.12.472242 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ A two-component protein condensate of EGFR and Grb2 regulates Ras activation at the membrane ]]> https://biorxiv.org/content/10.1101/2021.12.12.472247v1?rss=1 Lin, C.-W. Nocka, L. M. Stinger, B. DeGrandchamp, J. Lew, N. Alvarez, S. Phan, H. Kondo, Y. Kuriyan, J. Groves, J. T. 2021-12-12 doi:10.1101/2021.12.12.472247 Cold Spring Harbor Laboratory Press 2021-12-12 <![CDATA[ Spatially distributed computation in cortical circuits ]]> https://biorxiv.org/content/10.1101/2021.12.13.472322v1?rss=1 Gepshtein, S. Pawar, A. Kwon, S. Savelev, S. Albright, T. D. 2021-12-14 doi:10.1101/2021.12.13.472322 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ Generative Language Modeling for Antibody Design ]]> https://biorxiv.org/content/10.1101/2021.12.13.472419v1?rss=1 Shuai, R. W. Ruffolo, J. A. Gray, J. J. 2021-12-14 doi:10.1101/2021.12.13.472419 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ Proximity-assisted photoactivation (PAPA): Detecting molecular interactions in live-cell single-molecule imaging ]]> https://biorxiv.org/content/10.1101/2021.12.13.472508v1?rss=1 Graham, T. G. W. Ferrie, J. J. Dailey, G. M. Tjian, R. Darzacq, X. 2021-12-15 doi:10.1101/2021.12.13.472508 Cold Spring Harbor Laboratory Press 2021-12-15 <![CDATA[ A salvaging strategy enables stable metabolite provisioning among free-living bacteria ]]> https://biorxiv.org/content/10.1101/2021.12.14.472564v1?rss=1 Gude, S. Pherribo, G. J. Taga, M. E. 2021-12-14 doi:10.1101/2021.12.14.472564 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ Evolution of stickleback spines through independent cis-regulatory changes at HOXDB ]]> https://biorxiv.org/content/10.1101/2021.12.14.472698v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@8e6675org.highwire.dtl.DTLVardef@e89e13org.highwire.dtl.DTLVardef@1e1f1dcorg.highwire.dtl.DTLVardef@cdb6f8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wucherpfennig, J. I. Howes, T. R. Au, J. N. Au, E. H. Roberts Kingman, G. A. Brady, S. D. Herbert, A. L. Reimchen, T. E. Bell, M. A. Lowe, C. B. Dalziel, A. C. Kingsley, D. M. 2021-12-15 doi:10.1101/2021.12.14.472698 Cold Spring Harbor Laboratory Press 2021-12-15 <![CDATA[ Self-consistent migration puts tight constraintson the spatio-temporal organization ofspecies-rich metacommunities ]]> https://biorxiv.org/content/10.1101/2021.12.14.472702v1?rss=1 Denk, J. Hallatschek, O. 2021-12-16 doi:10.1101/2021.12.14.472702 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Pseudomonas response regulators produced in an E. coli heterologous expression host exhibit host-derived post-translational phosphorylation ]]> https://biorxiv.org/content/10.1101/2021.12.14.472705v1?rss=1 Garber, M. E. Fregoso, R. Lake, J. Kakouridis, A. Mukhopadhyay, A. 2021-12-15 doi:10.1101/2021.12.14.472705 Cold Spring Harbor Laboratory Press 2021-12-15 <![CDATA[ One of these morphs is not like the others: orange morphs exhibit different escape behavior than other morphs in a color polymorphic lizard ]]> https://biorxiv.org/content/10.1101/2021.12.14.472706v1?rss=1 Brock, K. M. Madden, I. E. 2021-12-16 doi:10.1101/2021.12.14.472706 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Discrete LAT condensates encode antigen information from single pMHC:TCR binding events ]]> https://biorxiv.org/content/10.1101/2021.12.16.472676v1?rss=1 McAffee, D. B. O'Dair, M. K. Lin, J. J. Low-Nam, S. T. Wilhelm, K. B. Kim, S. Morita, S. Groves, J. T. 2021-12-16 doi:10.1101/2021.12.16.472676 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Genomic characteristics of recently recognized Vibrio cholerae El Tor lineages associated with cholera in Bangladesh, 1991-2017 ]]> https://biorxiv.org/content/10.1101/2021.12.16.473094v1?rss=1 Monir, M. M. Hossain, T. Morita, M. Ohnishi, M. Johura, F.-t. Sultana, M. Monira, S. Ahmed, T. Thomson, N. Watanabe, H. Huq, A. Colwell, R. R. Seed, K. D. Alam, M. 2021-12-17 doi:10.1101/2021.12.16.473094 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ CRISPR/Cas9 knockout of EPFL10 reduces stomatal density while maintaining photosynthesis and enhancing water conservation in rice ]]> https://biorxiv.org/content/10.1101/2021.12.21.473329v1?rss=1 Karavolias, N. Patel, D. Seong, K. Tjahjadi, M. Gueorguieva, G.-A. Tanaka, J. Dahlbeck, D. Cho, M.-J. Niyogi, K. K. Staskawicz, B. J. 2021-12-23 doi:10.1101/2021.12.21.473329 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Applying computer vision to digitised natural history collections for climate change research: temperature-size responses in British butterflies ]]> https://biorxiv.org/content/10.1101/2021.12.21.473511v1?rss=1 180,000 specimens). Mothra automatically detects the specimen in the image, sets the scale, measures wing features (e.g., forewing length), determines the orientation of the specimen (pinned ventrally or dorsally), and identifies the sex. We pair these measurements and meta-data with temperature records to test how adult size varies with temperature during the immature stages of species and to assess patterns of sexual-size dimorphism across species and families. C_LIO_LIMothra accurately measures the forewing lengths of butterfly specimens and compared to manual baseline measurements, Mothra accurately determines sex and forewing lengths of butterfly specimens. Females are the larger sex in most species and an increase in adult body size with warm monthly temperatures during the late larval stages is the most common temperature size response. These results confirm suspected patterns and support hypotheses based on recent studies using a smaller dataset of manually measured specimens. C_LIO_LIWe show that CV can be a powerful tool to efficiently and accurately extract phenotypic data from a very large collection of digital NHCs. In the future, CV will become widely applied to digital NHC collections to advance ecological and evolutionary research and to accelerate the use of NHCs for biotic response to global change research. C_LI ]]> Wilson, R. J. de Siqueira, A. F. Brooks, S. J. Price, B. W. Simon, L. M. van der Walt, S. J. Fenberg, P. B. 2021-12-22 doi:10.1101/2021.12.21.473511 Cold Spring Harbor Laboratory Press 2021-12-22 <![CDATA[ Comprehensive Fitness Landscape of a Multi-Geometry Protein Capsid Informs Machine Learning Models of Assembly ]]> https://biorxiv.org/content/10.1101/2021.12.21.473721v1?rss=1 Brauer, D. D. Santiago, C. B. Merz, Z. N. McCarthy, E. Tullman-Ercek, D. Francis, M. B. 2021-12-23 doi:10.1101/2021.12.21.473721 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Fasting Induces a Highly Resilient Deep Quiescent State in Muscle Stem Cells via Ketone Body Signaling ]]> https://biorxiv.org/content/10.1101/2022.01.04.474961v1?rss=1 Benjamin, D. I. Both, P. I. Benjamin, J. S. Nutter, C. W. Tan, J. H. Kang, J. I. Machado, L. A. Klein, J. D. D. Morree, A. d. Kim, S. I. Liu, L. I. Dulay, H. Feraboli, L. Louie, S. M. Nomura, D. K. Rando, T. A. 2022-01-04 doi:10.1101/2022.01.04.474961 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ A Saturation-Mutagenesis Analysis of the Interplay Between Stability and Activation in Ras ]]> https://biorxiv.org/content/10.1101/2022.01.06.475190v1?rss=1 Hidalgo, F. Nocka, L. M. Shah, N. H. Gorday, K. Latorraca, N. R. Bandaru, P. Templeton, S. Lee, D. Karandur, D. Pelton, J. G. Marqusee, S. Wemmer, D. Kuriyan, J. 2022-01-06 doi:10.1101/2022.01.06.475190 Cold Spring Harbor Laboratory Press 2022-01-06 <![CDATA[ Temperature-dependent genetics of thermotolerance between yeast species ]]> https://biorxiv.org/content/10.1101/2022.01.11.475859v1?rss=1 Abrams, M. B. Brem, R. B. 2022-01-12 doi:10.1101/2022.01.11.475859 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Ionophore-stimulation promotes re-organization of the invasion machinery of Toxoplasma gondii ]]> https://biorxiv.org/content/10.1101/2022.01.12.476068v1?rss=1 Segev-Zarko, L.-a. Dahlberg, P. D. Sun, S. Y. Pelt, D. M. Sethian, J. A. Chiu, W. Boothroyd, J. C. 2022-01-12 doi:10.1101/2022.01.12.476068 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Distinct Inhibitory Pathways Control Velocity and Directional Tuning in the Retina ]]> https://biorxiv.org/content/10.1101/2022.01.13.476257v1?rss=1 Summers, M. T. Feller, M. B. 2022-01-17 doi:10.1101/2022.01.13.476257 Cold Spring Harbor Laboratory Press 2022-01-17 <![CDATA[ The C-terminal domain of SEC-10 is fundamental for exocyst function, Spitzenkorper organization and cell morphogenesis in Neurospora crassa. ]]> https://biorxiv.org/content/10.1101/2022.01.14.475644v1?rss=1 Figueroa-Melendez, A. Martinez-Nunez, L. Rico-Ramirez, A. M. Martinez-Andrade, J. M. Munson, M. Riquelme, M. 2022-01-14 doi:10.1101/2022.01.14.475644 Cold Spring Harbor Laboratory Press 2022-01-14 <![CDATA[ Population genomic evidence of selection on structural variants in a natural hybrid zone ]]> https://biorxiv.org/content/10.1101/2022.01.14.476419v1?rss=1 100,000 SVs segregating within or between the two hybridizing species. SVs and SNPs exhibited similar levels of genetic differentiation between species, with the exception of inversions, which were more differentiated. We detected credible variation in patterns of introgression among SV loci in the hybrid zone, with 562 of 1419 ancestry-informative SVs exhibiting genomic clines that deviating from null expectations based on genome-average ancestry. Overall, hybrids exhibited a directional shift towards Jackson Hole Lycaeides ancestry at SV loci, consistent with the hypothesis that these loci experienced more selection on average then SNP loci. Surprisingly, we found that deletions, rather than inversions, showed the highest skew towards excess introgression from Jackson Hole Lycaeides. Excess Jackson Hole Lycaeides ancestry in hybrids was also especially pronounced for Z-linked SVs and inversions containing many genes. In conclusion, our results show that SVs are ubiquitous and suggest that SVs in general, but especially deletions, might contribute disproportionately to hybrid fitness and thus (partial) reproductive isolation. ]]> Zhang, L. Chaturvedi, S. Nice, C. Lucas, L. Gompert, Z. 2022-01-15 doi:10.1101/2022.01.14.476419 Cold Spring Harbor Laboratory Press 2022-01-15 <![CDATA[ Metabolomic, photoprotective, and photosynthetic acclimatory responses to post-flowering drought in sorghum ]]> https://biorxiv.org/content/10.1101/2022.01.14.476420v1?rss=1 Baker, c. Patel, D. Cole, B. J. Ching, L. G. Dautermann, O. Kelikian, A. C. Allison, C. Pedraza, J. Sievert, J. Bilbao, A. Lee, J.-Y. Kim, Y.-M. Kyle, J. E. Bloodsworth, K. J. Paurus, V. Hixson, K. K. Hutmacher, R. Dahlberg, J. Lemaux, P. Niyogi, K. K. 2022-01-15 doi:10.1101/2022.01.14.476420 Cold Spring Harbor Laboratory Press 2022-01-15 <![CDATA[ Using strain-resolved analysis to identify contamination in metagenomics data ]]> https://biorxiv.org/content/10.1101/2022.01.16.476537v1?rss=1 Lou, Y. C. Hoff, J. Olm, M. R. West-Roberts, J. Diamond, S. Firek, B. A. Morowitz, M. J. Banfield, J. F. 2022-01-17 doi:10.1101/2022.01.16.476537 Cold Spring Harbor Laboratory Press 2022-01-17 <![CDATA[ Reconstructing the spatiotemporal patterns of admixture during the European Holocene using a novel genomic dating method ]]> https://biorxiv.org/content/10.1101/2022.01.18.476710v1?rss=1 Chintalapati, M. Patterson, N. Moorjani, P. 2022-01-20 doi:10.1101/2022.01.18.476710 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Fam49b dampens TCR signal strength to regulate survival of positively selected thymocytes ]]> https://biorxiv.org/content/10.1101/2022.01.18.476719v1?rss=1 Park, C.-S. Guan, J. Rhee, P. Gonzalez, F. Coscoy, L. Robey, E. A. Shastri, N. Sadegh-Nasseri, S. 2022-01-18 doi:10.1101/2022.01.18.476719 Cold Spring Harbor Laboratory Press 2022-01-18 <![CDATA[ A local translation program regulates centriole amplification in the airway epithelium ]]> https://biorxiv.org/content/10.1101/2022.01.18.476821v1?rss=1 Liu, H. Li, H. Jiang, Z. Jin, S. Song, R. Yang, Y. Li, J. Huang, J. Zhang, X. Dong, X. Que, J. Mori, M. Fritzler, M. J. He, L. Cardoso, W. V. Lu, J. 2022-01-20 doi:10.1101/2022.01.18.476821 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Oxygen availability drives blood traits and the cell number-size tradeoff across Andean hummingbirds ]]> https://biorxiv.org/content/10.1101/2022.01.18.476833v1?rss=1 Williamson, J. L. Linck, E. B. Bautista, E. Smiley, A. McGuire, J. A. Dudley, R. Witt, C. C. 2022-01-21 doi:10.1101/2022.01.18.476833 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Identification of a biosynthetic gene cluster encoding a novel lanthanide chelator in Methylorubrum extorquens AM1 ]]> https://biorxiv.org/content/10.1101/2022.01.19.476857v1?rss=1 Zytnick, A. M. Good, N. M. Barber, C. C. Phi, M. T. Gutenthaler, S. M. Zhang, W. Daumann, L. J. Martinez-Gomez, N. C. 2022-01-20 doi:10.1101/2022.01.19.476857 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Implicit adaptation is modulated by the relevance of feedback ]]> https://biorxiv.org/content/10.1101/2022.01.19.476924v1?rss=1 Parvin, D. E. Dang, K. V. Stover, A. R. Ivry, R. B. Morehead, R. 2022-01-21 doi:10.1101/2022.01.19.476924 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Engineered bacterial swarm patterns as spatial records of environmental inputs ]]> https://biorxiv.org/content/10.1101/2022.01.20.477106v1?rss=1 Doshi, A. Shaw, M. Tonea, R. Moon, S. Doshi, A. Laine, A. Guo, J. Danino, T. 2022-01-21 doi:10.1101/2022.01.20.477106 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ The Retinal Basis of Photoaversion in Neonatal Mice ]]> https://biorxiv.org/content/10.1101/2022.01.20.477130v1?rss=1 Caval-Holme, F. Aranda, M. Quaen Chen, A. Tiriac, A. Zhang, Y. Smith, B. Birnbaumer, L. Schmidt, T. M. Feller, M. 2022-01-22 doi:10.1101/2022.01.20.477130 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ High-throughput suppressor screens unveil functional convergence of single-gene lysis proteins ]]> https://biorxiv.org/content/10.1101/2022.01.20.477139v1?rss=1 Adler, B. A. Chamakura, K. Carion, H. Krog, J. Deutschbauer, A. M. Young, R. F. Mutalik, V. K. Arkin, A. P. 2022-01-20 doi:10.1101/2022.01.20.477139 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Caulobacter requires anionic sphingolipids and deactivation of fur to lose lipid A ]]> https://biorxiv.org/content/10.1101/2022.01.20.477143v1?rss=1 Zik, J. J. Yoon, S. H. Guan, Z. Skidmore, G. S. Gudoor, R. R. Davies, K. M. Deutschbauer, A. M. Goodlett, D. R. Klein, E. A. Ryan, K. R. 2022-01-21 doi:10.1101/2022.01.20.477143 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Quantitative proteomics of the CDK9 interactome reveals a novel function of the HSP90-CDC37-P-TEFb complex for BETi-induced HIV-1 latency reactivation ]]> https://biorxiv.org/content/10.1101/2022.01.20.477160v1?rss=1 Wang, C. Pan, Z. He, Y. Zhang, Z. Liu, R. Xue, Y. Zhou, Q. Gao, X. 2022-01-21 doi:10.1101/2022.01.20.477160 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ A draft genome assembly for the heterozygous wild tomato Solanum habrochaites highlights haplotypic structural variations of intracellular immune receptors ]]> https://biorxiv.org/content/10.1101/2022.01.21.477156v1?rss=1 Seong, K. Lunde, C. Seo, E. Li, M. Krasileva, K. Staskawicz, B. 2022-01-23 doi:10.1101/2022.01.21.477156 Cold Spring Harbor Laboratory Press 2022-01-23 <![CDATA[ Widespread transposon co-option in the Caenorhabditis germline regulatory network ]]> https://biorxiv.org/content/10.1101/2022.01.21.477252v1?rss=1 Carelli, F. N. Cerrato, C. Dong, Y. Appert, A. Dernburg, A. Ahringer, J. 2022-01-23 doi:10.1101/2022.01.21.477252 Cold Spring Harbor Laboratory Press 2022-01-23 <![CDATA[ Rubisco forms a lattice inside alpha-carboxysomes ]]> https://biorxiv.org/content/10.1101/2022.01.24.477598v1?rss=1 Metskas, L. A. Ortega, D. R. Oltrogge, L. M. Blikstad, C. Laughlin, T. Savage, D. Jensen, G. J. 2022-01-25 doi:10.1101/2022.01.24.477598 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Metabolic strategies shared by basement residents of the Lost City hydrothermal field ]]> https://biorxiv.org/content/10.1101/2022.01.25.477282v1?rss=1 Brazelton, W. J. McGonigle, J. M. Motamedi, S. Pendleton, H. L. Twing, K. I. Miller, B. C. Lowe, W. J. Hoffman, A. M. Prator, C. A. Chadwick, G. L. Anderson, R. E. Thomas, E. Butterfield, D. A. Aquino, K. A. Früh-Green, G. L. Schrenk, M. O. Lang, S. Q. 2022-01-25 doi:10.1101/2022.01.25.477282 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Robust, versatile DNA FISH probes for chromosome-specific repeats in Caenorhabditis elegans and Pristionchus pacificus ]]> https://biorxiv.org/content/10.1101/2022.01.25.477430v1?rss=1 Adilardi, R. S. Dernburg, A. F. 2022-01-28 doi:10.1101/2022.01.25.477430 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Reconstitution of muscle cell microtubule organization in vitro ]]> https://biorxiv.org/content/10.1101/2022.01.26.477920v1?rss=1 Heald, R. Nadkarni, A. 2022-01-27 doi:10.1101/2022.01.26.477920 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ A wheat kinase and immune receptor form the host-specificity barrier against the blast fungus ]]> https://biorxiv.org/content/10.1101/2022.01.27.477927v1?rss=1 Arora, S. Steed, A. Goddard, R. Gaurav, K. O'Hara, T. Schoen, A. Rawat, N. Elkot, A. F. Chinoy, C. Nicholson, M. H. Asuke, S. Steuernagel, B. Yu, G. Awal, R. Forner-Martinez, M. Wingen, L. Baggs, E. Clarke, J. Krasileva, K. V. Tosa, Y. Jones, J. D. G. Tiwari, V. K. Wulff, B. B. H. Nicholson, P. 2022-01-28 doi:10.1101/2022.01.27.477927 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Unconventional secretion of α-synuclein mediated by palmitoylated DNAJC5 oligomers ]]> https://biorxiv.org/content/10.1101/2022.01.27.477991v1?rss=1 Wu, S. Sirkis, D. W. Schekman, R. 2022-01-27 doi:10.1101/2022.01.27.477991 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ Shade-induced transcription of PIF-Direct-Target Genes precedes H3K4-trimethylation chromatin modifications ]]> https://biorxiv.org/content/10.1101/2022.01.27.478074v1?rss=1 Calderon, R. H. Dalton-Roesler, J. Zhang, Y. Quail, P. H. 2022-01-28 doi:10.1101/2022.01.27.478074 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Encoding and decoding analysis of music perception using intracranial EEG ]]> https://biorxiv.org/content/10.1101/2022.01.27.478085v1?rss=1 Bellier, L. Llorens, A. Marciano, D. Schalk, G. Brunner, P. Knight, R. T. Pasley, B. N. 2022-01-28 doi:10.1101/2022.01.27.478085 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Glia of C. elegans coordinate the heat shock response independent of the neuronal thermosensory circuit and serotonin ]]> https://biorxiv.org/content/10.1101/2022.01.31.478522v1?rss=1 Gildea, H. K. Frankino, P. A. Tronnes, S. U. Pender, C. L. Choi, H. O. Hunter, T. D. Cheung, S. S. Frakes, A. E. Sukarto, E. Dillin, A. 2022-01-31 doi:10.1101/2022.01.31.478522 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ Genomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineages ]]> https://biorxiv.org/content/10.1101/2022.02.01.478673v1?rss=1 Oliveira, G. Vogels, C. B. F. Zolfaghari, A. Saraf, S. Klitting, R. Weger-Lucarelli, J. Ontiveros, C. O. Agarwal, R. Leon, K. P. Tsetsarkin, K. A. Harris, E. Ebel, G. D. Wohl, S. Grubaugh, N. D. Andersen, K. G. 2022-02-02 doi:10.1101/2022.02.01.478673 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ Distinct silencer states determine epigenetic states of heterochromatin ]]> https://biorxiv.org/content/10.1101/2022.02.01.478725v1?rss=1 Saxton, D. S. Rine, J. 2022-02-03 doi:10.1101/2022.02.01.478725 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Quantifying the Adaptive Potential of a Nascent Bacterial Community ]]> https://biorxiv.org/content/10.1101/2022.02.03.475969v1?rss=1 Ascensao, J. A. Wetmore, K. M. Good, B. H. Arkin, A. P. Hallatschek, O. 2022-02-05 doi:10.1101/2022.02.03.475969 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ Analysis of altered pre-mRNA splicing patterns caused by a mutation in the RNA binding protein hnRNPA1 linked to amyotrophic lateral sclerosis ]]> https://biorxiv.org/content/10.1101/2022.02.03.479052v1?rss=1 Rio, D. C. Lee, Y. J. 2022-02-04 doi:10.1101/2022.02.03.479052 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Friction-driven membrane scission by the human ESCRT-III proteins CHMP1B and IST1 ]]> https://biorxiv.org/content/10.1101/2022.02.03.479062v1?rss=1 Cada, A. K. Remec Pavlin, M. Castillo, J. P. Tong, A. B. Larsen, K. P. Ren, X. Yokom, A. L. Tsai, F.-C. Bassereau, P. Bustamante, C. J. Hurley, J. H. 2022-02-04 doi:10.1101/2022.02.03.479062 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Deep sequencing of yeast and mouse tRNAs and tRNA fragments using OTTR ]]> https://biorxiv.org/content/10.1101/2022.02.04.479139v1?rss=1 Gustafsson, T. Galan, C. Yu, T. Upton, H. Ferguson, L. Kaymak, E. Weng, Z. Collins, K. Rando, O. 2022-02-04 doi:10.1101/2022.02.04.479139 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Genome-wide identification of fitness determinants in the Xanthomonas campestris bacterial pathogen during early stages of plant infection ]]> https://biorxiv.org/content/10.1101/2022.02.07.479439v1?rss=1 Luneau, J. S. Baudin, M. Quiroz-Monnens, T. Carrere, S. Bouchez, O. Jardinaud, M.-F. Gris, C. Francois, J. Ray, J. Torralba, B. Arlat, M. Lewis, J. D. Deutschbauer, A. M. Lauber, E. Noël, L. D. Boulanger, A. 2022-02-07 doi:10.1101/2022.02.07.479439 Cold Spring Harbor Laboratory Press 2022-02-07 <![CDATA[ Historical contingency drives compensatory evolution and rare reversal of phage resistance ]]> https://biorxiv.org/content/10.1101/2022.02.10.479996v1?rss=1 Debray, R. De Luna, N. Koskella, B. 2022-02-13 doi:10.1101/2022.02.10.479996 Cold Spring Harbor Laboratory Press 2022-02-13 <![CDATA[ In vivo calcium imaging identifies functionally and molecularly distinct subsets of tongue-innervating mechanosensory neurons ]]> https://biorxiv.org/content/10.1101/2022.02.11.480171v1?rss=1 Moayedi, Y. Xu, S. Obayashi, S. K. Hoffman, B. U. Gerling, G. J. Lumpkin, E. A. 2022-02-14 doi:10.1101/2022.02.11.480171 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Saccharibacteria harness light energy using Type-1 rhodopsins that may rely on retinal sourced from microbial hosts ]]> https://biorxiv.org/content/10.1101/2022.02.13.480300v1?rss=1 Jaffe, A. L. Konno, M. Kawasaki, Y. Kataoka, C. Beja, O. Kandori, H. Inoue, K. Banfield, J. 2022-02-14 doi:10.1101/2022.02.13.480300 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Nitric oxide signaling controls collective contractions in a colonial choanoflagellate ]]> https://biorxiv.org/content/10.1101/2022.02.14.480389v1?rss=1 Reyes-Rivera, J. Wu, Y. Guthrie, B. G. H. Marletta, M. A. King, N. Brunet, T. 2022-02-14 doi:10.1101/2022.02.14.480389 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Highly efficient generation of isogenic pluripotent stem cell models using prime editing ]]> https://biorxiv.org/content/10.1101/2022.02.15.480601v1?rss=1 Li, H. Busquets, O. Verma, Y. Syed, K. M. Kutnowski, N. Pangilinan, G. R. Gilbert, L. Bateup, H. Rio, D. C. Hockemeyer, D. Soldner, F. 2022-02-15 doi:10.1101/2022.02.15.480601 Cold Spring Harbor Laboratory Press 2022-02-15 <![CDATA[ Phosphoregulation of DSB-1 mediates control of meiotic double-strand break activity ]]> https://biorxiv.org/content/10.1101/2022.02.16.480793v1?rss=1 Guo, H. Stamper, E. L. Sato-Carlton, A. Shimazoe, M. A. Li, X. Zhang, L. Stevens, L. Tam, K. J. Dernburg, A. F. Carlton, P. M. 2022-02-17 doi:10.1101/2022.02.16.480793 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ Noninvasive sampling for comparisons of wildlife microbiomes may be more reliable than sampling trapped animals ]]> https://biorxiv.org/content/10.1101/2022.02.17.480865v1?rss=1 Turjeman, S. Pekarsky, S. Corl, A. Kamath, P. L. Getz, W. M. Bowie, R. C. Markin, Y. Nathan, R. 2022-02-19 doi:10.1101/2022.02.17.480865 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Close-kin mark-recapture methods to estimate demographic parameters of mosquitoes ]]> https://biorxiv.org/content/10.1101/2022.02.19.481126v1?rss=1 Sharma, Y. Bennett, J. B. Rasic, G. Marshall, J. M. 2022-02-22 doi:10.1101/2022.02.19.481126 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Cobalamin riboswitches are broadly sensitive to corrinoid cofactors to enable an efficient gene regulatory strategy ]]> https://biorxiv.org/content/10.1101/2022.02.20.481237v1?rss=1 Kennedy, K. J. Widner, F. J. Sokolovskaya, O. M. Innocent, V. L. Procknow, R. R. Mok, K. C. Taga, M. E. 2022-02-22 doi:10.1101/2022.02.20.481237 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Multiple bumps can enhance robustness to noise in continuous attractor networks ]]> https://biorxiv.org/content/10.1101/2022.02.22.481545v1?rss=1 Wang, R. Kang, L. 2022-02-25 doi:10.1101/2022.02.22.481545 Cold Spring Harbor Laboratory Press 2022-02-25 <![CDATA[ Human septins in cells organize as octamer-based filaments mediating actin-membrane anchoring ]]> https://biorxiv.org/content/10.1101/2022.02.23.481653v1?rss=1 Martins, C. S. Taveneau, C. Castro-Linares, G. Baibakov, M. Buzhinsky, N. Eroles, M. Milanovic, V. Iv, F. Bouillard, L. Llewellyn, A. Gomes, M. Belhabib, M. Kuzmic, M. Verdier-Pinard, P. Lee, S. Badache, A. Kumar, S. Chandre, C. Brasselet, S. Rico, F. Rossier, O. Koenderink, G. H. Wenger, J. Cabantous, S. Mavrakis, M. 2022-02-24 doi:10.1101/2022.02.23.481653 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Plasma membrane protrusions mediate host cell-cell fusion induced by Burkholderia thailandensis ]]> https://biorxiv.org/content/10.1101/2022.02.24.481536v1?rss=1 Kostow, N. Welch, M. 2022-02-24 doi:10.1101/2022.02.24.481536 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Hominoid-specific sulcal variability is related to face perception ability ]]> https://biorxiv.org/content/10.1101/2022.02.28.482330v1?rss=1 Parker, B. J. Voorhies, W. I. Guo, J. Miller, J. A. Willbrand, E. Hallock, T. Furl, N. Garrido, L. Duchaine, B. Weiner, K. S. 2022-03-01 doi:10.1101/2022.02.28.482330 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Presence or absence of a prefrontal sulcus is linked to reasoning performance during child development ]]> https://biorxiv.org/content/10.1101/2022.03.02.482563v1?rss=1 Willbrand, E. H. Voorhies, W. I. Yao, J. K. Weiner, K. S. Bunge, S. A. 2022-03-03 doi:10.1101/2022.03.02.482563 Cold Spring Harbor Laboratory Press 2022-03-03 <![CDATA[ Discovery of Potent Pyrazoline-Based Covalent SARS-CoV-2 Main Protease Inhibitors ]]> https://biorxiv.org/content/10.1101/2022.03.05.483025v1?rss=1 Moon, P. Boike, L. Dovala, D. Henning, N. J. Knapp, M. Spradlin, J. N. Ward, C. C. Wolleb, H. Zammit, C. M. Fuller, D. Blake, G. Murphy, J. P. Wang, F. Lu, Y. Moquin, S. A. Tandeske, L. Hesse, M. J. McKenna, J. M. Tallarico, J. Schirle, M. Toste, F. D. Nomura, D. K. 2022-03-07 doi:10.1101/2022.03.05.483025 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Engineering of Sr33 and Sr50 plant immune receptors to alter recognition specificity and autoactivity ]]> https://biorxiv.org/content/10.1101/2022.03.05.483131v1?rss=1 Tamborski, J. Seong, K. Liu, F. Staskawicz, B. Krasileva, K. 2022-03-06 doi:10.1101/2022.03.05.483131 Cold Spring Harbor Laboratory Press 2022-03-06 <![CDATA[ Bessel-droplet foci enable high-resolution and high-contrast volumetric imaging of synapses and circulation in the brain in vivo ]]> https://biorxiv.org/content/10.1101/2022.03.05.483143v1?rss=1 Chen, W. Zhang, Q. Natan, R. G. Fan, J. Ji, N. 2022-03-06 doi:10.1101/2022.03.05.483143 Cold Spring Harbor Laboratory Press 2022-03-06 <![CDATA[ LanA (Language Atlas): A probabilistic atlas for the language network based on fMRI data from >800 individuals ]]> https://biorxiv.org/content/10.1101/2022.03.06.483177v1?rss=1 Lipkin, B. Tuckute, G. Affourtit, J. Small, H. Mineroff, Z. Kean, H. Jouravlev, O. Rakocevic, L. Pritchett, B. Siegelman, M. Hoeflin, C. Pongos, A. Blank, I. Shruhl, M. K. Ivanova, A. Shannon, S. Sathe, A. Hoffmann, M. Nieto-Castanon, A. Fedorenko, E. 2022-03-07 doi:10.1101/2022.03.06.483177 800 individuals]]> Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Taste quality interactions and transformations in a sensorimotor circuit ]]> https://biorxiv.org/content/10.1101/2022.03.06.483180v1?rss=1 Shiu, P. K. Sterne, G. R. Engert, S. Dickson, B. Scott, K. 2022-03-07 doi:10.1101/2022.03.06.483180 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Molecular conflicts disrupting centromere assembly contribute to Xenopus hybrid inviability ]]> https://biorxiv.org/content/10.1101/2022.03.06.483208v1?rss=1 Kitaoka, M. Smith, O. K. Straight, A. F. Heald, R. 2022-03-07 doi:10.1101/2022.03.06.483208 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Reconstitution of Kinetochore and Microtubule Dynamics Reveals a Role for a Kinesin-8 in Establishing End-on Attachments ]]> https://biorxiv.org/content/10.1101/2022.03.07.483312v1?rss=1 Torvi, J. R. Wong, J. Serwas, D. Moayed, A. Drubin, D. G. Barnes, G. 2022-03-08 doi:10.1101/2022.03.07.483312 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Not optimal, just noisy: the geometry of correlated variability leads to highly suboptimal sensory coding ]]> https://biorxiv.org/content/10.1101/2022.03.08.483488v1?rss=1 Livezey, J. A. Sachdeva, P. S. Dougherty, M. E. Summers, M. T. Bouchard, K. E. 2022-03-09 doi:10.1101/2022.03.08.483488 Cold Spring Harbor Laboratory Press 2022-03-09 <![CDATA[ Altered excitatory and inhibitory neuronal subpopulation parameters are distinctly associated with tau and amyloid in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2022.03.09.483594v1?rss=1 Ranasinghe, K. Verma, P. Cai, C. Xie, X. Kudo, K. Gao, X. Lerner, H. Mizuiri, D. Strom, A. Iaccarino, L. La Joie, R. Miller, B. L. Gorno-Tempini, M. L. Rankin, K. P. Jagust, W. J. Vossel, K. Rabinovici, G. Raj, A. Nagarajan, S. 2022-03-10 doi:10.1101/2022.03.09.483594 Cold Spring Harbor Laboratory Press 2022-03-10 <![CDATA[ Dissecting neural computations of the human auditory pathway using deep neural networks for speech ]]> https://biorxiv.org/content/10.1101/2022.03.14.484195v1?rss=1 Li, Y. Anumanchipalli, G. K. Mohamed, A. Lu, J. Wu, J. Chang, E. F. 2022-03-15 doi:10.1101/2022.03.14.484195 Cold Spring Harbor Laboratory Press 2022-03-15 <![CDATA[ Decorating chromatin for enhanced genome editing using CRISPR-Cas9 ]]> https://biorxiv.org/content/10.1101/2022.03.15.484540v1?rss=1 Chen, E. Lin Shiao, E. Doost, M. S. Doudna, J. A. 2022-03-16 doi:10.1101/2022.03.15.484540 Cold Spring Harbor Laboratory Press 2022-03-16 <![CDATA[ Topological action potentials in engineered tissues ]]> https://biorxiv.org/content/10.1101/2022.03.16.484369v1?rss=1 Ori, H. Duque Ramirez, M. Hayward, R. F. Tian, H. Ortiz, G. Cohen, A. E. 2022-03-18 doi:10.1101/2022.03.16.484369 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Ratiometric Sensing of Redox Environments Inside Individual Carboxysomes Trapped in Solution ]]> https://biorxiv.org/content/10.1101/2022.03.17.484789v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@1fccfacorg.highwire.dtl.DTLVardef@a639b6org.highwire.dtl.DTLVardef@116fff6org.highwire.dtl.DTLVardef@fe95fd_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Carpenter, W. B. Lavania, A. A. Borden, J. S. Oltrogge, L. M. Perez, D. D. Dahlberg, P. D. Savage, D. F. Moerner, W. E. 2022-03-19 doi:10.1101/2022.03.17.484789 Cold Spring Harbor Laboratory Press 2022-03-19 <![CDATA[ Spatial turnover of soil viral populations and genotypes overlain by cohesive responses to moisture in grasslands ]]> https://biorxiv.org/content/10.1101/2022.03.24.485562v1?rss=1 =90% of the viromes), which tended to exhibit significant negative correlations between genomic similarity of their predominant allelic variants and distance. Although spatial turnover was also observed in the bacterial and archaeal communities from the same soils, the signal was dampened relative to the viromes, suggesting differences in assembly drivers at local scales for viruses and their microbial hosts and/or differences in the temporal scales captured by viromes and total DNA. Despite the overwhelming spatial signal, vOTUs responsive to a decrease in soil moisture were significantly enriched in a predicted protein-sharing subnetwork of 326 vOTUs linked to 191 known actinobacteriophages, suggesting a genomically cohesive viral response to soil moisture evocative of environmental filtering, potentially by way of actinobacterial hosts. Overall, soil viral ecological processes appear to be highly constrained in space and tightly coupled to the heterogeneous, dynamic soil environment and thus fundamentally different from those of their well-mixed and more thoroughly studied marine counterparts. ]]> Santos-Medellin, C. Estera-Molina, K. Yuan, M. Pett-Ridge, J. Firestone, M. K. Emerson, J. B. 2022-03-24 doi:10.1101/2022.03.24.485562 Cold Spring Harbor Laboratory Press 2022-03-24 <![CDATA[ HPCA1 is required for systemic ROS and calcium cell-to-cell signaling and plant acclimation to stress ]]> https://biorxiv.org/content/10.1101/2022.03.24.485694v1?rss=1 Fichman, Y. Zandalinas, S. I. Peck, S. C. Luan, S. Mittler, R. 2022-03-27 doi:10.1101/2022.03.24.485694 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Combinatorial interactions of Hox genes establish appendage diversity of the amphipod crustacean Parhyale hawaiensis ]]> https://biorxiv.org/content/10.1101/2022.03.25.485717v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@16bfc85org.highwire.dtl.DTLVardef@8f859eorg.highwire.dtl.DTLVardef@8d7892org.highwire.dtl.DTLVardef@1e6c9f0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jarvis Alberstat, E. Chung, K. Sun, D. A. Ray, S. Patel, N. H. 2022-03-27 doi:10.1101/2022.03.25.485717 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Distinct regulation of Hox genes by Polycomb Group genes in a crustacean ]]> https://biorxiv.org/content/10.1101/2022.03.27.485719v1?rss=1 View larger version (59K): org.highwire.dtl.DTLVardef@7508a7org.highwire.dtl.DTLVardef@18b0c2dorg.highwire.dtl.DTLVardef@1cc602corg.highwire.dtl.DTLVardef@bdf7fc_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sun, D. A. Takahashi, Y. Chang, R. J. Patel, N. H. 2022-03-28 doi:10.1101/2022.03.27.485719 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Genomic demography of world's ethnic groups and their genomic identity between two individuals ]]> https://biorxiv.org/content/10.1101/2022.03.28.486119v1?rss=1 Kim, B.-J. Choi, J. Kim, S.-H. 2022-03-30 doi:10.1101/2022.03.28.486119 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ In vitro reconstitution of calcium-dependent recruitment of the human ESCRT machinery in lysosomal membrane repair ]]> https://biorxiv.org/content/10.1101/2022.03.30.486420v1?rss=1 Shukla, S. Larsen, K. P. Ou, C. Rose, K. Hurley, J. H. 2022-03-30 doi:10.1101/2022.03.30.486420 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles ]]> https://biorxiv.org/content/10.1101/2022.03.30.486467v1?rss=1 Olm, M. R. Dahan, D. Carter, M. M. Merrill, B. D. Yu, B. Jain, S. Meng, X. D. Tripathi, S. Wastyk, H. Neff, N. Holmes, S. Sonnenburg, E. D. Jha, A. R. Sonnenburg, J. L. 2022-04-02 doi:10.1101/2022.03.30.486467 Cold Spring Harbor Laboratory Press 2022-04-02 <![CDATA[ Characterization of EDS1-independent plant defense responses against bacterial pathogens using Duckweed/Pseudomonas pathosystems ]]> https://biorxiv.org/content/10.1101/2022.03.31.486129v1?rss=1 Baggs, E. L. Tiersma, M. B. Abramsom, B. W. Michael, T. Krasileva, K. V. 2022-04-01 doi:10.1101/2022.03.31.486129 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Microenvironmental engineering improves the self-organization of patterned microvascular networks ]]> https://biorxiv.org/content/10.1101/2022.04.04.487052v1?rss=1 Cabral, K. A. Srivastava, V. Coyle, M. C. Stashko, C. Weaver, V. Gartner, Z. J. 2022-04-05 doi:10.1101/2022.04.04.487052 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ EcoFun-MAP: An Ecological Function Oriented Metagenomic Analysis Pipeline ]]> https://biorxiv.org/content/10.1101/2022.04.05.481366v1?rss=1 Shi, Z. J. Xiao, N. Ning, D. Tian, R. Zhang, P. Curtis, D. Van Nostrand, J. D. Wu, L. Hazen, T. C. Rocha, A. M. He, Z. Arkin, A. P. Firestone, M. K. Zhou, J. 2022-04-08 doi:10.1101/2022.04.05.481366 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Structural and biochemical basis of FANCI-FANCD2 interdependent ubiquitination ]]> https://biorxiv.org/content/10.1101/2022.04.07.487446v1?rss=1 Lemonidis, K. Rennie, M. L. Arkinson, C. Chaugule, V. K. Clarke, M. Streetley, J. Walden, H. 2022-04-07 doi:10.1101/2022.04.07.487446 Cold Spring Harbor Laboratory Press 2022-04-07 <![CDATA[ Restoration of high-sensitivity patterned vision in motion with an engineered light-gated G protein-coupled receptor ]]> https://biorxiv.org/content/10.1101/2022.04.07.487476v1?rss=1 Holt, A. Berry, M. Lo, J. Donthamsetti, P. Visel, M. Broichhagen, J. Flannery, J. G. Isacoff, E. Y. 2022-04-09 doi:10.1101/2022.04.07.487476 Cold Spring Harbor Laboratory Press 2022-04-09 <![CDATA[ Functionally and structurally distinct fusiform face area(s) in over 1000 participants ]]> https://biorxiv.org/content/10.1101/2022.04.08.487562v1?rss=1 1000) group of participants are still lacking. To fill this gap, we quantified structural, functional, and connectivity features of fusiform face-selective regions in 1080 participants in the Human Connectome Project (HCP). After manually defining over 4,000 fusiform face-selective regions, we report five main findings. First, 68.94% of hemispheres have two cortically separate regions (pFus-faces/FFA-1 and mFus-faces/FFA-2). Second, in 26.48% of hemispheres, pFus-faces/FFA-1 and mFus-faces/FFA-2 are spatially contiguous, yet functionally and structurally distinct. Third, pFus-faces/FFA-1 is more face-selective than mFus-faces/FFA-2, and the two regions have distinct functional connectivity fingerprints. Fourth, pFus-faces/FFA-1 is cortically thinner and more heavily myelinated than mFus-faces/FFA-2. Fifth, face-selective patterns and functional connectivity fingerprints of each region were more similar in monozygotic than dizygotic twins and more so than structural gradients. As we share our areal definitions with the field, future studies can explore how structural and functional features of these regions will inform theories regarding how visual categories are represented in the brain. ]]> Chen, X. Liu, X. Parker, B. J. Zhen, Z. Weiner, K. S. 2022-04-10 doi:10.1101/2022.04.08.487562 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ A cross-sectional study of the commercial plant-based landscape across the US, UK and Canada. ]]> https://biorxiv.org/content/10.1101/2022.04.08.487708v1?rss=1 15g protein, 60% had <10%kcal from saturated fat; 29% had >10g fibre per meal; 86% had <1000mg sodium. At restaurants, meat-based main meals were significantly higher in protein and sodium compared to vegetarian and vegan meals. The meat-based options were also significantly higher in saturated fat than the vegan but not vegetarian options. We conclude that plant-based items tend to be lower in saturated fat and sodium than their meat-based counterparts but improvements are needed to optimise their nutritional composition. ]]> Guess, N. Klatt, K. Wei, D. Williamson, E. Ulgenalp, I. Trinidade, O. Kusaslan, E. Yilidrim, A. Gowers, C. Guard, R. Mills, C. 2022-04-11 doi:10.1101/2022.04.08.487708 Cold Spring Harbor Laboratory Press 2022-04-11 <![CDATA[ From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology ]]> https://biorxiv.org/content/10.1101/2022.04.08.487709v1?rss=1 Pandey, A. Incer, I. Sangiovanni-Vincentelli, A. Murray, R. M. 2022-04-11 doi:10.1101/2022.04.08.487709 Cold Spring Harbor Laboratory Press 2022-04-11 <![CDATA[ The RNA-RNA interactome between a phage and its satellite virus reveals a small RNA differentially regulates gene expression across both genomes ]]> https://biorxiv.org/content/10.1101/2022.04.08.487710v1?rss=1 Dunham, D. T. Angermeyer, A. Seed, K. 2022-04-08 doi:10.1101/2022.04.08.487710 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Improvement of Gene Delivery and Mutation Efficiency in the CRISPR-Cas9 Wheat (Triticum aestivum L.) Genomics System via Biolistics ]]> https://biorxiv.org/content/10.1101/2022.04.09.487748v1?rss=1 Tanaka, J. Minkenberg, B. Poddar, S. Staskawicz, B. Cho, M.-J. 2022-04-10 doi:10.1101/2022.04.09.487748 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Learning inverse folding from millions of predicted structures ]]> https://biorxiv.org/content/10.1101/2022.04.10.487779v1?rss=1 Hsu, C. Verkuil, R. Liu, J. Lin, Z. Hie, B. Sercu, T. Lerer, A. Rives, A. 2022-04-10 doi:10.1101/2022.04.10.487779 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Ribosome stalling during selenoprotein translation exposes a ferroptosis vulnerability in cancer ]]> https://biorxiv.org/content/10.1101/2022.04.11.487892v1?rss=1 Li, Z. Ferguson, L. Deol, K. K. Roberts, M. A. Magtanong, L. Bassik, M. C. Dixon, S. J. Ingolia, N. Olzmann, J. 2022-04-11 doi:10.1101/2022.04.11.487892 Cold Spring Harbor Laboratory Press 2022-04-11 <![CDATA[ Interpreting the pervasive observation of U-shaped Site Frequency Spectra ]]> https://biorxiv.org/content/10.1101/2022.04.12.488084v1?rss=1 Freund, F. Kerdoncuff, E. Matuszewski, S. Lapierre, M. Hildebrandt, M. Jensen, J. D. Ferretti, L. Lambert, A. Sackton, T. B. Achaz, G. 2022-04-13 doi:10.1101/2022.04.12.488084 Cold Spring Harbor Laboratory Press 2022-04-13 <![CDATA[ Defining tertiary sulci in lateral prefrontal cortex in chimpanzees using human predictions ]]> https://biorxiv.org/content/10.1101/2022.04.12.488091v1?rss=1 Hathaway, C. Voorhies, W. I. Sathishkumar, N. Mittal, C. Yao, J. K. Miller, J. A. Parker, B. Weiner, K. S. 2022-04-13 doi:10.1101/2022.04.12.488091 Cold Spring Harbor Laboratory Press 2022-04-13 <![CDATA[ Assignment of structural transitions during mechanical unwrapping of nucleosomes and their disassembly products ]]> https://biorxiv.org/content/10.1101/2022.04.13.488252v1?rss=1 Diaz-Celis, C. D. Canari-Chumpitaz, C. Sosa, R. P. Castillo, J. P. Zhang, M. Cheng, E. Chen, A. Vien, M. Kim, J. Onoa, B. Bustamante, C. J. 2022-04-14 doi:10.1101/2022.04.13.488252 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ Meiotic Nuclear Pore Complex Remodeling Provides Key Insights into Nuclear Basket Organization ]]> https://biorxiv.org/content/10.1101/2022.04.14.488376v1?rss=1 King, G. A. Wettstein, R. Varberg, J. M. Chetlapalli, K. Walsh, M. E. Gillet, L. Hernandez-Armenta, C. Beltrao, P. Aebersold, R. Jaspersen, S. L. Matos, J. Unal, E. 2022-04-15 doi:10.1101/2022.04.14.488376 Cold Spring Harbor Laboratory Press 2022-04-15 <![CDATA[ Prescribed fire selects for a pyrophilous soil subcommunity in a northern California mixed conifer forest. ]]> https://biorxiv.org/content/10.1101/2022.04.15.488482v1?rss=1 Fischer, M. S. Patel, N. J. de Lorimier, P. J. Traxler, M. F. 2022-04-16 doi:10.1101/2022.04.15.488482 Cold Spring Harbor Laboratory Press 2022-04-16 <![CDATA[ Vision-dependent and -independent molecular maturation of mouse retinal ganglion cells ]]> https://biorxiv.org/content/10.1101/2022.04.20.488897v1?rss=1 Whitney, I. Butrus, S. Dyer, M. A. Rieke, F. Sanes, J. Shekhar, K. 2022-04-20 doi:10.1101/2022.04.20.488897 Cold Spring Harbor Laboratory Press 2022-04-20 <![CDATA[ Candidatus Nealsonbacteria (OD1) in a methanogenic benzene-degrading enrichment culture is likely an ectosymbiotic biomass recycler ]]> https://biorxiv.org/content/10.1101/2022.04.20.488981v1?rss=1 Chen, X. Molenda, O. Brown, C. T. Toth, C. R. A. Guo, S. Luo, F. Howe, J. Nesbo, C. L. He, C. Montabana, E. A. Cate, J. H. D. Banfield, J. F. Edwards, E. A. 2022-04-21 doi:10.1101/2022.04.20.488981 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ McaA and McaB control the dynamic positioning of a bacterial magnetic organelle ]]> https://biorxiv.org/content/10.1101/2022.04.21.485668v1?rss=1 Wan, J. Monteil, C. L. Taoka, A. Ernie, G. Park, K. Amor, M. Taylor-Cornejo, E. Lefevre, C. T. Komeili, A. 2022-04-21 doi:10.1101/2022.04.21.485668 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ A natural variation-based screen in mouse cells reveals USF2 as a regulator of the DNA damage response and cellular senescence ]]> https://biorxiv.org/content/10.1101/2022.04.21.489100v1?rss=1 Kang, T. Moore, E. C. Kopania, E. King, C. Schilling, B. Campisi, J. Good, J. Brem, R. 2022-04-23 doi:10.1101/2022.04.21.489100 Cold Spring Harbor Laboratory Press 2022-04-23 <![CDATA[ Saturation mutagenesis of a predicted ancestral Syk-family kinase ]]> https://biorxiv.org/content/10.1101/2022.04.24.489292v1?rss=1 Hobbs, H. T. Shah, N. H. Shoemaker, S. R. Amacher, J. F. Marqusee, S. Kuriyan, J. 2022-04-24 doi:10.1101/2022.04.24.489292 Cold Spring Harbor Laboratory Press 2022-04-24 <![CDATA[ Blood-brain barrier dysfunction promotes astrocyte senescence through albumin-induced TGFβ signaling activation ]]> https://biorxiv.org/content/10.1101/2022.04.25.489438v1?rss=1 Preininger, M. Zaytseva, D. Lin, J. M. Kaufer, D. 2022-04-28 doi:10.1101/2022.04.25.489438 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Molecular Determinants of Tissue Specificity of Flavivirus Nonstructural Protein 1 Interaction with Endothelial Cells ]]> https://biorxiv.org/content/10.1101/2022.04.28.489972v1?rss=1 Lo, N. T. Roodsari, S. Tin, N. R. Biering, S. B. Harris, E. 2022-04-29 doi:10.1101/2022.04.28.489972 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ Comparative computational structural genomics highlights divergent evolution of fungal effectors ]]> https://biorxiv.org/content/10.1101/2022.05.02.490317v1?rss=1 Seong, K. Krasileva, K. 2022-05-02 doi:10.1101/2022.05.02.490317 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Population Genomics of Stone Age Eurasia ]]> https://biorxiv.org/content/10.1101/2022.05.04.490594v1?rss=1 1,600 ancient humans. Our analyses revealed a Great Divide genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers (HGs) were highly genetically differentiated east and west of this zone, and the impact of the neolithisation was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacements of HGs in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, while east of the Urals relatedness remained high until [~]4,000 BP, consistent with persistence of localised HG groups. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive but we demonstrate that HGs from the Middle Don region contributed ancestry to them. Yamnaya-groups later admixed with individuals associated with the Globular Amphora Culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a Neolithic steppe cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations. ]]> Allentoft, M. E. Sikora, M. Refoyo-Martinez, A. Irving-Pease, E. K. Fischer, A. Barrie, W. Ingason, A. Stenderup, J. Sjögren, K.-G. Pearson, A. Sousa da Mota, B. Paulsson, B. S. Halgren, A. S. Schjellerup Jorkov, M. L. Demeter, F. Novosolov, M. Macleod, R. Sorensen, L. Nielsen, P. O. Henriksen, R. A. Vimala, T. McColl, H. Margaryan, A. Ilardo, M. Vaughn, A. Mortensen, M. F. Nielsen, A. B. Hede, M. U. Rasmussen, P. Vinner, L. Renaud, G. Stern, A. J. Trolle Jensen, T. Z. Johannsen, N. N. Schroeder, H. Scorrano, G. Ramsoe, A. Skorobogatov, A. Schork, A. J. 2022-05-05 doi:10.1101/2022.05.04.490594 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Feature-space selection with banded ridge regression ]]> https://biorxiv.org/content/10.1101/2022.05.05.490831v1?rss=1 Dupre la Tour, T. Eickenberg, M. Gallant, J. L. 2022-05-05 doi:10.1101/2022.05.05.490831 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ A task-general connectivity model reveals variation in convergence of cortical inputs to functional regions of the cerebellum ]]> https://biorxiv.org/content/10.1101/2022.05.07.490946v1?rss=1 King, M. Shahshahani, L. 2022-05-08 doi:10.1101/2022.05.07.490946 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ Evolution avoids a pathological stabilizing interaction in the immune protein S100A9 ]]> https://biorxiv.org/content/10.1101/2022.05.09.490804v1?rss=1 Harman, J. L. Reardon, P. N. Costello, S. M. Warren, G. D. Phillips, S. R. Connor, P. J. Marqusee, S. Harms, M. J. 2022-05-09 doi:10.1101/2022.05.09.490804 Cold Spring Harbor Laboratory Press 2022-05-09 <![CDATA[ Rapid learning with highly localized synaptic plasticity ]]> https://biorxiv.org/content/10.1101/2022.05.09.491102v1?rss=1 Masse, N. Y. Rosen, M. C. Tsao, D. Y. Freedman, D. J. 2022-05-10 doi:10.1101/2022.05.09.491102 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ JBrowse Jupyter: A Python interface to JBrowse 2 ]]> https://biorxiv.org/content/10.1101/2022.05.11.491552v1?rss=1 Martinez, T. D. J. Hershberg, E. Guo, E. Stevens, G. J. Diesh, C. Xie, P. Bridge, C. Cain, S. Haw, R. Buels, R. M. Stein, L. D. Holmes, I. H. 2022-05-16 doi:10.1101/2022.05.11.491552 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ SCONCE2: jointly inferring single cell copy number profiles and tumor evolutionary distances ]]> https://biorxiv.org/content/10.1101/2022.05.12.491742v1?rss=1 Hui, S. Nielsen, R. 2022-05-13 doi:10.1101/2022.05.12.491742 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Human REM sleep controls neural excitability in support of memory formation ]]> https://biorxiv.org/content/10.1101/2022.05.13.491801v1?rss=1 Lendner, J. D. Mander, B. A. Schuh-Hofer, S. Schmidt, H. Knight, R. T. Walker, M. P. Lin, J. J. Helfrich, R. F. 2022-05-15 doi:10.1101/2022.05.13.491801 Cold Spring Harbor Laboratory Press 2022-05-15 <![CDATA[ Site pleiotropy of a stickleback tooth and fin enhancer ]]> https://biorxiv.org/content/10.1101/2022.05.13.491895v1?rss=1 Rowley, A. J. Square, T. A. Miller, C. T. 2022-05-14 doi:10.1101/2022.05.13.491895 Cold Spring Harbor Laboratory Press 2022-05-14 <![CDATA[ In situ cryo-electron tomography reveals the asymmetric architecture of mammalian sperm axonemes ]]> https://biorxiv.org/content/10.1101/2022.05.15.492011v1?rss=1 Chen, Z. Greenan, G. A. Shiozaki, M. Liu, Y. Skinner, W. M. Zhao, X. Zhao, S. Yan, R. Guo, C. Yu, Z. Lishko, P. V. Agard, D. A. Vale, R. D. 2022-05-16 doi:10.1101/2022.05.15.492011 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ In-vivo detection of cyclic-di-AMP in Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/2022.05.16.492224v1?rss=1 Chatterjee, S. S. Mukkayyan, N. Poon, R. Sander, P. Hammond, M. Lai, L.-Y. Zubair-Nizami, Z. 2022-05-17 doi:10.1101/2022.05.16.492224 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ Borg tandem repeats undergo rapid evolution and are under strong selection to create new intrinsically disordered regions in proteins ]]> https://biorxiv.org/content/10.1101/2022.05.18.492195v1?rss=1 Schoelmerich, M. C. Sachdeva, R. Waldburger, L. West-Roberts, J. Banfield, J. 2022-05-19 doi:10.1101/2022.05.18.492195 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Chemoproteomics-Enabled Discovery of a Covalent Molecular Glue Degrader Targeting NF-κB ]]> https://biorxiv.org/content/10.1101/2022.05.18.492542v1?rss=1 King, E. A. Cho, Y. Dovala, D. McKenna, J. M. Tallarico, J. A. Schirle, M. Nomura, D. K. 2022-05-18 doi:10.1101/2022.05.18.492542 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat ]]> https://biorxiv.org/content/10.1101/2022.05.23.493093v1?rss=1 Hooy, R. M. Iwamoto, Y. Tudorica, D. Ren, X. Hurley, J. H. 2022-05-23 doi:10.1101/2022.05.23.493093 Cold Spring Harbor Laboratory Press 2022-05-23 <![CDATA[ G protein-coupled receptor 151 regulates glucose metabolism and hepatic gluconeogenesis ]]> https://biorxiv.org/content/10.1101/2022.05.25.493489v1?rss=1 Bielczyk-Maczynska, E. Zhao, M. Zushin, P.-J. H. Schnurr, T. M. Kim, H.-J. Li, J. Nallagatla, P. Sangwung, P. Park, C. Cornn, C. Stahl, A. Svensson, K. J. Knowles, J. W. 2022-05-28 doi:10.1101/2022.05.25.493489 Cold Spring Harbor Laboratory Press 2022-05-28 <![CDATA[ DLPFC-tDCS unable to modulate mind-wandering propensity nor underlying functional or effective brain connectivity. ]]> https://biorxiv.org/content/10.1101/2022.05.26.493632v1?rss=1 Coulborn, S. Fernandez-Espejo, D. 2022-05-29 doi:10.1101/2022.05.26.493632 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ An Empirical Bayes Method for Differential Expression Analysis of Single Cells with Deep Generative Models ]]> https://biorxiv.org/content/10.1101/2022.05.27.493625v1?rss=1 Boyeau, P. Regier, J. Gayoso, A. Jordan, M. I. Lopez, R. Yosef, N. 2022-05-29 doi:10.1101/2022.05.27.493625 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Evolutionary rescue is promoted in compact cellular populations ]]> https://biorxiv.org/content/10.1101/2022.05.27.493727v1?rss=1 Aif, S. Appold, N. Kampman, L. Hallatschek, O. Kayser, J. 2022-05-28 doi:10.1101/2022.05.27.493727 Cold Spring Harbor Laboratory Press 2022-05-28 <![CDATA[ CELL-E: Biological zero-shot text-to-image synthesis for protein localization prediction ]]> https://biorxiv.org/content/10.1101/2022.05.27.493774v1?rss=1 Khwaja, E. Song, Y. S. Huang, B. 2022-05-29 doi:10.1101/2022.05.27.493774 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Charting a narrow course for direct electron uptake-facilitated electromicrobial production ]]> https://biorxiv.org/content/10.1101/2022.05.28.493842v1?rss=1 48 mA/cm2 to reach parity with the H2- mediated system. Because this is currently only practical with a gas diffusion electrode (GDE) architecture, we developed a physical model of the proposed bio-GDE and used it to determine the conditions that a microbial catalyst would experience in a reactor. Our analysis demonstrates that unavoidable inefficiencies in the reactor (e.g., kinetic overpotentials and Ohmic losses) require additional energy input, increasing the breakeven current density to [~]91 mA/cm2. At this current density, the microbial catalyst would need to withstand a pH >10.4 and a total salinity >18.8%. Because currently-known electroautotrophs are not adapted to such extreme conditions, we discuss potential improvements to reactor design that may alleviate these challenges, and consider the implications these results have on the engineerability and feasibility of direct electron uptake-based EMP. ]]> Abel, A. J. Adams, J. D. Hilzinger, J. M. Arkin, A. P. 2022-05-29 doi:10.1101/2022.05.28.493842 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Mapping the temporal transcriptional landscape of human white and brown adipogenesis using single-nuclei RNA-seq ]]> https://biorxiv.org/content/10.1101/2022.05.30.494007v1?rss=1 Gupta, A. Shamsi, F. Patti, M. E. Tseng, Y.-H. Streets, A. M. 2022-05-30 doi:10.1101/2022.05.30.494007 Cold Spring Harbor Laboratory Press 2022-05-30 <![CDATA[ Lis1 binding regulates force-induced detachment of cytoplasmic dynein from microtubules ]]> https://biorxiv.org/content/10.1101/2022.06.02.494578v1?rss=1 Kusakci, E. Htet, Z. M. Gillies, J. P. Reck-Peterson, S. L. Yildiz, A. 2022-06-03 doi:10.1101/2022.06.02.494578 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Dose-dependent nuclear delivery and transcriptional repression with a cell-penetrant MeCP2 ]]> https://biorxiv.org/content/10.1101/2022.06.03.494754v1?rss=1 Zhang, X. Zoltek, M. Mozumdar, D. Schepartz, A. 2022-06-04 doi:10.1101/2022.06.03.494754 Cold Spring Harbor Laboratory Press 2022-06-04 <![CDATA[ Emergent Programmable Behavior and Chaos in Dynamically Driven Active Filaments ]]> https://biorxiv.org/content/10.1101/2022.06.05.494577v1?rss=1 Krishnamurthy, D. Prakash, M. 2022-06-05 doi:10.1101/2022.06.05.494577 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ A phage weaponizes a satellite recombinase to subvert viral restriction ]]> https://biorxiv.org/content/10.1101/2022.06.08.495392v1?rss=1 Nguyen, M. Netter, Z. Angermeyer, A. Seed, K. 2022-06-09 doi:10.1101/2022.06.08.495392 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Human sperm TMEM95 binds eggs and facilitates membrane fusion ]]> https://biorxiv.org/content/10.1101/2022.06.10.495573v1?rss=1 Tang, S. Lu, Y. Skinner, W. M. Sanyal, M. Lishko, P. V. Ikawa, M. Kim, P. S. 2022-06-10 doi:10.1101/2022.06.10.495573 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Microfluidics-free single-cell genomics with templated emulsification ]]> https://biorxiv.org/content/10.1101/2022.06.10.495582v1?rss=1 Clark, I. C. Fontanez, K. M. Meltzer, R. H. Xue, Y. Hayford, C. May-Zhang, A. D'Amato, C. Osman, A. Zhang, J. Q. Hettige, P. Delley, C. L. Weisgerber, D. W. Replogle, J. M. Jost, M. Phong, K. T. Kennedy, V. E. Peretz, C. A. C. Kim, E. A. Song, S. Karlon, W. Weissman, J. S. Smith, C. C. Gartner, Z. J. Abate, A. 2022-06-13 doi:10.1101/2022.06.10.495582 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ Structure of SARS-CoV-2 M protein in lipid nanodiscs ]]> https://biorxiv.org/content/10.1101/2022.06.12.495841v1?rss=1 Dolan, K. A. Dutta, M. Kern, D. M. Kotecha, A. Voth, G. A. Brohawn, S. G. 2022-06-13 doi:10.1101/2022.06.12.495841 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ CellScape: Protein structure visualization with vector graphics cartoons ]]> https://biorxiv.org/content/10.1101/2022.06.14.495869v1?rss=1 Silvestre-Ryan, J. Fletcher, D. A. Holmes, I. 2022-06-16 doi:10.1101/2022.06.14.495869 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ The Chlamydomonas Genome Project, version 6: reference assemblies for mating type plus and minus strains reveal extensive structural mutation in the laboratory ]]> https://biorxiv.org/content/10.1101/2022.06.16.496473v1?rss=1 80% of filled gaps are within genes. We used Iso-Seq and deep RNA-seq datasets to improve structural annotations, and updated gene symbols and textual annotation of functionally characterized genes via extensive curation. We discovered that the cell wall-less classical reference strain CC-503 exhibits genomic instability potentially caused by deletion of RECQ3 helicase, with major structural mutations identified that affect >100 genes. We therefore present the CC-4532 assembly as the primary reference, although this strain also carries unique structural mutations and is experiencing rapid proliferation of a Gypsy retrotransposon. We expect all laboratory strains to harbor gene-disrupting mutations, which should be considered when interpreting and comparing experimental results across laboratories and over time. Collectively, the resources presented here herald a new era of Chlamydomonas genomics and will provide the foundation for continued research in this important reference. ]]> Craig, R. J. Gallaher, S. D. Shu, S. Salomé, P. Jenkins, J. W. Blaby-Haas, C. E. Purvine, S. O. O'Donnell, S. Barry, K. Grimwood, J. Strenkert, D. Kropat, J. Daum, C. Yoshinaga, Y. Goodstein, D. M. Vallon, O. Schmutz, J. Merchant, S. S. 2022-06-16 doi:10.1101/2022.06.16.496473 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Estimating population split times and migration rates from historical effective population sizes ]]> https://biorxiv.org/content/10.1101/2022.06.17.496540v1?rss=1 Shchur, V. Yoshihara Caldeira Brandt, D. Ilina, A. Nielsen, R. 2022-06-17 doi:10.1101/2022.06.17.496540 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Timing and causes of the evolution of the germline mutation spectrum in humans ]]> https://biorxiv.org/content/10.1101/2022.06.17.496622v1?rss=1 TTC mutations in Europeans and novel signals of divergence in C>G and T>A mutation rates among population samples. We also find a significant difference between groups sampled in and outside of Africa, in old T>C polymorphisms that predate the out-of-Africa migration. This surprising signal is driven by TpG>CpG mutations, and stems in part from mis-polarized CpG transitions, which are more likely to undergo recurrent mutations. Finally, by relating the mutation spectrum of polymorphisms to parental age effects on de novo mutations, we show that plausible changes in the generation time cannot explain the patterns observed for different mutation types jointly. Thus, other factors--genetic modifiers or environmental exposures--must have had a non-negligible impact on the human mutation landscape. ]]> Gao, Z. Zhang, Y. Przeworski, M. Moorjani, P. 2022-06-18 doi:10.1101/2022.06.17.496622 Cold Spring Harbor Laboratory Press 2022-06-18 <![CDATA[ Structure of the GOLD-domain seven-transmembrane helix protein family member TMEM87A ]]> https://biorxiv.org/content/10.1101/2022.06.20.496907v1?rss=1 Hoel, C. M. Zhang, L. Brohawn, S. G. 2022-06-20 doi:10.1101/2022.06.20.496907 Cold Spring Harbor Laboratory Press 2022-06-20 <![CDATA[ Nutrient and moisture limitation reveal keystone metabolites that link switchgrass rhizosphere metabolome and microbiome dynamics ]]> https://biorxiv.org/content/10.1101/2022.06.20.496911v1?rss=1 Baker, N. R. Zhalnina, K. Yuan, M. Herman, D. Ceja-Navarro, J. Sasse, J. Jordan, J. S. Bowen, B. P. Wu, L. Fossum, C. Chew, A. Fu, Y. Saha, M. Zhou, J. Pett-Ridge, J. Northen, T. Firestone, M. 2022-06-21 doi:10.1101/2022.06.20.496911 Cold Spring Harbor Laboratory Press 2022-06-21 <![CDATA[ Linking microenvironment modification to species interactions and demography in an alpine plant community ]]> https://biorxiv.org/content/10.1101/2022.06.21.497097v1?rss=1 Ray, C. A. Kapas, R. E. Opedal, O. H. Blonder, B. W. 2022-06-26 doi:10.1101/2022.06.21.497097 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Trajectories for the evolution of bacterial CO2-concentrating mechanisms ]]> https://biorxiv.org/content/10.1101/2022.06.21.497102v1?rss=1 Flamholz, A. I. Dugan, E. J. Panich, J. Desmarais, J. J. Oltrogge, L. M. Fischer, W. W. Singer, S. W. Savage, D. F. 2022-06-22 doi:10.1101/2022.06.21.497102 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ VPS13A and VPS13C influence lipid droplet abundance ]]> https://biorxiv.org/content/10.1101/2022.06.21.497109v1?rss=1 Chen, S. Roberts, M. A. Chen, C.-Y. Markmiller, S. Wei, H.-G. Yeo, G. W. Granneman, J. G. Olzmann, J. A. Ferro-Novick, S. 2022-06-23 doi:10.1101/2022.06.21.497109 Cold Spring Harbor Laboratory Press 2022-06-23 <![CDATA[ Evolution of Carbon Isotope Fractionation in Cyanobacteria ]]> https://biorxiv.org/content/10.1101/2022.06.22.497258v1?rss=1 >1 Ga. This strain, nicknamed ANC, grows in ambient pCO2 and displays larger {varepsilon}p values than WT, despite having a much smaller {varepsilon}Rubisco (17.23 {+/-} 0.61{per thousand} vs. 25.18 {+/-} 0.31{per thousand} respectively). Measuring both enzymatic and biomass fractionation revealed a surprising result--ANC {varepsilon}p exceeded ANC {varepsilon}Rubisco in all conditions tested, contradicting prevailing models of cyanobacterial carbon isotope fractionation. However, these models were corrected by accounting for cyanobacterial physiology, notably the CO2 concentrating mechanism (CCM). Our model suggested that additional fractionating processes like powered inorganic carbon uptake systems contribute to {varepsilon}p, and this effect is exacerbated in ANC. Understanding the evolution of rubisco and the CCM is therefore critical for interpreting the carbon isotope record. Large fluctuations in that record may reflect the evolving efficiency of carbon fixing metabolisms in addition to changes in atmospheric CO2. Significance StatementEarth scientists rely on chemical fossils like the carbon isotope record to derive ancient atmospheric CO2 concentrations, but interpretation of this record is calibrated using modern organisms. We tested this assumption by measuring the carbon isotope fractionation of a reconstructed ancestral rubisco enzyme (>1 billion years old) in vivo and in vitro. Our results contradicted prevailing models of carbon flow in Cyanobacteria, but our data could be rationalized if light-driven uptake of CO2 is taken into account. Our study showed that the carbon isotope record tracks both the evolution of photosynthesis physiology as well as changes in atmospheric CO2, highlighting the value of considering both evolution and physiology for comparative biological approaches to understanding Earths history. ]]> Wang, R. Z. Nichols, R. J. Liu, A. K. Flamholz, A. I. Banda, D. M. Savage, D. F. Eiler, J. M. Shih, P. M. Fischer, W. W. 2022-06-23 doi:10.1101/2022.06.22.497258 Cold Spring Harbor Laboratory Press 2022-06-23 <![CDATA[ To share or not to share? iEEG evidence for state-dependent inequity encoding in the human OFC ]]> https://biorxiv.org/content/10.1101/2022.06.23.497432v1?rss=1 Marciano, D. Staveland, B. R. Lin, J. J. Saez, I. Hsu, M. Knight, R. T. 2022-06-26 doi:10.1101/2022.06.23.497432 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ A novel meiotic protein required for homolog pairing and regulation of synapsis in C. elegans ]]> https://biorxiv.org/content/10.1101/2022.06.24.496392v1?rss=1 Kim, H. J. Dernburg, A. F. 2022-06-27 doi:10.1101/2022.06.24.496392 Cold Spring Harbor Laboratory Press 2022-06-27 <![CDATA[ A moonlighting function of a chitin polysaccharide monooxygenase, CWR-1, in allorecognition in Neurospora crassa ]]> https://biorxiv.org/content/10.1101/2022.06.26.497659v1?rss=1 Glass, N. L. Detomasi, T. C. Rico Ramirez, A. M. Sayler, R. I. Goncalves, A. P. Marletta, M. A. 2022-06-29 doi:10.1101/2022.06.26.497659 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Induced CD45 Proximity Potentiates Natural Killer Cell Receptor Antagonism ]]> https://biorxiv.org/content/10.1101/2022.06.27.497842v1?rss=1 Ren, J. Jo, Y. Picton, L. Su, L. Raulet, D. Garcia, K. C. 2022-06-30 doi:10.1101/2022.06.27.497842 Cold Spring Harbor Laboratory Press 2022-06-30 <![CDATA[ Structural basis for FLCN RagC GAP activation in MiT-TFE substrate-selective mTORC1 regulation ]]> https://biorxiv.org/content/10.1101/2022.06.28.498039v1?rss=1 Jansen, R. M. Peruzzo, R. Fromm, S. A. Yokom, A. L. Zoncu, R. Hurley, J. H. 2022-06-29 doi:10.1101/2022.06.28.498039 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Early phyllosphere microbial associations impact plant reproductive success ]]> https://biorxiv.org/content/10.1101/2022.06.30.498294v1?rss=1 Mehlferber, E. C. McCue, K. F. Debray, R. Kaulbach, G. Ferrel, J. E. C. Khanna, R. Koskella, B. 2022-07-02 doi:10.1101/2022.06.30.498294 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ HT-SIP: A semi-automated Stable Isotope Probing pipeline identifies interactions in the hyphosphere of arbuscular mycorrhizal fungi ]]> https://biorxiv.org/content/10.1101/2022.07.01.498377v1?rss=1 Nuccio, E. E. Blazewicz, S. J. Lafler, M. Campbell, A. N. Kakouridis, A. Kimbrel, J. A. Wollard, J. Vyshenska, D. Riley, R. Tomatsu, A. Hestrin, R. Malmstrom, R. Firestone, M. K. Pett-Ridge, J. 2022-07-02 doi:10.1101/2022.07.01.498377 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Competing constraints shape the non-equilibrium limits of cellular decision making ]]> https://biorxiv.org/content/10.1101/2022.07.01.498451v1?rss=1 Lammers, N. C. Flamholz, A. Garcia, H. G. 2022-07-03 doi:10.1101/2022.07.01.498451 Cold Spring Harbor Laboratory Press 2022-07-03 <![CDATA[ Cerebral perfusion in post-stroke aphasia and its relation to residual language abilities ]]> https://biorxiv.org/content/10.1101/2022.07.01.498516v1?rss=1 Ivanova, M. V. Pappas, I. Inglis, B. Pracar, A. Herron, T. J. Baldo, J. V. Kayser, A. S. D'Esposito, M. Dronkers, N. F. 2022-07-05 doi:10.1101/2022.07.01.498516 Cold Spring Harbor Laboratory Press 2022-07-05 <![CDATA[ Mapping protein-DNA interactions with DiMeLo-seq ]]> https://biorxiv.org/content/10.1101/2022.07.03.498618v1?rss=1 Maslan, A. Altemose, N. Mishra, R. Marcus, J. Brennan, L. D. Sundararajan, K. Karpen, G. Straight, A. F. Streets, A. M. 2022-07-05 doi:10.1101/2022.07.03.498618 Cold Spring Harbor Laboratory Press 2022-07-05 <![CDATA[ A parasitic fungus employs mutated eIF4A to survive on rocaglate-synthesizing Aglaia plants ]]> https://biorxiv.org/content/10.1101/2022.07.04.498659v1?rss=1 Chen, M. Kumakura, N. Muller, R. Shichino, Y. Nishimoto, M. Mito, M. Gan, P. Ingolia, N. T. Shirasu, K. Ito, T. Iwasaki, S. 2022-07-04 doi:10.1101/2022.07.04.498659 Cold Spring Harbor Laboratory Press 2022-07-04 <![CDATA[ Murine gammaherpesvirus 68 ORF45 stimulates B2 retrotransposon and pre-tRNA activation in a manner dependent on mitogen-activated protein kinase (MAPK) signaling ]]> https://biorxiv.org/content/10.1101/2022.07.09.499448v1?rss=1 Lari, A. Glaunsinger, B. A. 2022-07-10 doi:10.1101/2022.07.09.499448 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Structural basis for ATG9A recruitment to the ULK1 complex in mitophagy initiation ]]> https://biorxiv.org/content/10.1101/2022.07.12.499634v1?rss=1 Ren, X. Nguyen, T. N. Lam, W. K. Buffalo, C. Z. Lazarou, M. Yokom, A. L. Hurley, J. H. 2022-07-13 doi:10.1101/2022.07.12.499634 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Molecular recording of calcium signaling via calcium-dependent protein proximity labeling ]]> https://biorxiv.org/content/10.1101/2022.07.14.500122v1?rss=1 Kim, J. W. Yong, A. J. H. Dawson, T. M. Dawson, V. L. Jan, Y.-N. Ingolia, N. T. 2022-07-14 doi:10.1101/2022.07.14.500122 Cold Spring Harbor Laboratory Press 2022-07-14 <![CDATA[ Rare Ribosomal RNA Sequences from Archaea Stabilize the Bacterial Ribosome ]]> https://biorxiv.org/content/10.1101/2022.07.15.499945v1?rss=1 Nissley, A. J. Penev, P. I. Watson, Z. L. Banfield, J. Cate, J. H. 2022-07-16 doi:10.1101/2022.07.15.499945 Cold Spring Harbor Laboratory Press 2022-07-16 <![CDATA[ Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq ]]> https://biorxiv.org/content/10.1101/2022.07.15.500120v1?rss=1 Sunshine, S. Puschnik, A. S. Replogle, J. M. Laurie, M. T. Liu, J. Zha, B. S. Nunez, J. K. Byrum, J. R. McMorrow, A. H. Frieman, M. B. Winkler, J. Qiu, X. Rosenberg, O. S. Leonetti, M. D. Ye, C. J. Weissman, J. S. DeRisi, J. L. Hein, M. Y. 2022-07-17 doi:10.1101/2022.07.15.500120 Cold Spring Harbor Laboratory Press 2022-07-17 <![CDATA[ Variable impact of geochemical gradients on the functional potential of bacteria, archaea, and phages from the permanently stratified Lac Pavin ]]> https://biorxiv.org/content/10.1101/2022.07.18.500538v1?rss=1 Jaffe, A. L. Bardot, C. Le Jeune, A.-H. Liu, J. Colombet, J. Perriere, F. Billard, H. Castelle, C. J. Lehours, A.-C. Banfield, J. 2022-07-19 doi:10.1101/2022.07.18.500538 Cold Spring Harbor Laboratory Press 2022-07-19 <![CDATA[ Cas9+ conditionally immortalized neutrophil progenitors as a tool for genome wide CRISPR screening for neutrophil differentiation and function ]]> https://biorxiv.org/content/10.1101/2022.07.19.500665v1?rss=1 Jong, R. M. Ching, K. Garelis, N. E. Zilinskas, A. Nguyenla, X. Rawal, S. Hill, B. Luckie, B. Shallow, L. Cox, J. S. Barton, G. Stanley, S. 2022-07-20 doi:10.1101/2022.07.19.500665 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ GO Bench: Shared-hub for Universal Benchmarking of Machine Learning-Based Protein Functional Annotations ]]> https://biorxiv.org/content/10.1101/2022.07.19.500685v1?rss=1 Dickson, A. M. Asgari, E. McHardy, A. C. Mofrad, M. R. K. 2022-07-20 doi:10.1101/2022.07.19.500685 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Superficial white matter across the lifespan: volume, thickness, change, and relationship with cortical features ]]> https://biorxiv.org/content/10.1101/2022.07.20.500818v1?rss=1 Schilling, K. Archer, D. B. Rheault, F. Lyu, I. Huo, Y. Cai, L. Y. Bunge, S. Weiner, K. S. Gore, J. C. Anderson, A. W. Landman, B. A. 2022-07-21 doi:10.1101/2022.07.20.500818 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ A dolabralexin-deficient mutant provides insight into specialized diterpenoid metabolism in maize (Zea mays). ]]> https://biorxiv.org/content/10.1101/2022.07.21.500061v1?rss=1 Murphy, K. M. Dowd, T. Khalil, A. Char, S. N. Yang, B. Endelman, B. J. Shih, P. M. Topp, C. N. Schmelz, E. A. Zerbe, P. 2022-07-22 doi:10.1101/2022.07.21.500061 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Flexible selection of task-relevant features through across-area population gating ]]> https://biorxiv.org/content/10.1101/2022.07.21.500962v1?rss=1 Barbosa, J. Proville, R. Rodgers, C. C. Ostojic, S. Boubenec, Y. 2022-07-22 doi:10.1101/2022.07.21.500962 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Cortical surface electrical potentials are composed of multiple bandlimited frequency components, including high-gamma ]]> https://biorxiv.org/content/10.1101/2022.07.22.501176v1?rss=1 Livezey, J. A. Hwang, A. Usovich, K. Dougherty, M. Chang, E. F. Bouchard, K. E. 2022-07-23 doi:10.1101/2022.07.22.501176 Cold Spring Harbor Laboratory Press 2022-07-23 <![CDATA[ Wireless Measurements Using Electrical Impedance Spectroscopy to Monitor Fracture Healing ]]> https://biorxiv.org/content/10.1101/2022.07.23.501237v1?rss=1 Fukase, N. Duke, V. R. Lin, M. C. Stake, I. K. Huard, M. Huard, J. Marmor, M. T. Maharbiz, M. M. Ehrhart, N. P. Bahney, C. S. Herfat, S. T. 2022-07-23 doi:10.1101/2022.07.23.501237 Cold Spring Harbor Laboratory Press 2022-07-23 <![CDATA[ The ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles ]]> https://biorxiv.org/content/10.1101/2022.07.30.502157v1?rss=1 Schreiber, J. M. Boix, C. A. Lee, J. w. Li, H. Guan, Y. Chang, C.-C. Chang, J.-C. Hawkins-Hooker, A. Schoelkopf, B. Schweikert, G. Rojas Carulla, M. Canakoglu, A. Guzzo, F. Nanni, L. Masseroli, M. Carman, M. J. Pinoli, P. Hong, C. Yip, K. Y. Spence, J. P. Batra, S. S. Song, Y. S. Mahony, S. Zhang, Z. Tan, W. Shen, Y. Sun, Y. Shi, M. Adrian, J. Sandstrom, R. S. Farrell, N. Halow, J. M. Lee, K. Jiang, L. Yang, X. Epstein, C. B. Strattan, J. S. Snyder, M. P. Kellis, M. Noble, W. S. Kundaje, A. B. 2022-08-02 doi:10.1101/2022.07.30.502157 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Structural basis for assembly and lipid-mediated gating of LRRC8A:C volume-regulated anion channels ]]> https://biorxiv.org/content/10.1101/2022.07.31.502239v1?rss=1 Kern, D. M. Bleier, J. Mukherjee, S. Hill, J. M. Kossiakoff, A. A. Isacoff, E. Y. Brohawn, S. G. 2022-08-02 doi:10.1101/2022.07.31.502239 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ NF-κB inhibitor alpha has a cross-variant role during SARS-CoV-2 infection in ACE2-overexpressing human airway organoids ]]> https://biorxiv.org/content/10.1101/2022.08.02.502100v1?rss=1 Simoneau, C. R. Chen, P.-Y. Xing, G. X. Khalid, M. M. Meyers, N. L. Hayashi, J. M. Taha, T. Y. Leon, K. E. Ashuach, T. Fontaine, K. A. Rodriguez, L. Joehnk, B. Walcott, K. Vasudevan, S. Fang, X. Maishan, M. Schultz, S. Roose, J. Matthay, M. A. Sil, A. Arjomandi, M. Yosef, N. Ott, M. 2022-08-02 doi:10.1101/2022.08.02.502100 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Addictions may be driven by competition-induced microbiome dysbiosis ]]> https://biorxiv.org/content/10.1101/2022.08.02.502262v1?rss=1 Lewin-Epstein, O. Jaques, Y. Feldman, M. W. Kaufer, D. Hadany, L. 2022-08-02 doi:10.1101/2022.08.02.502262 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Representation of sustained visual experience by time-invariant distributed neural patterns ]]> https://biorxiv.org/content/10.1101/2022.08.02.502469v1?rss=1 Vishne, G. Gerber, E. M. Knight, R. T. Deouell, L. Y. 2022-08-04 doi:10.1101/2022.08.02.502469 Cold Spring Harbor Laboratory Press 2022-08-04 <![CDATA[ Multi-areal neural dynamics encode human decision making ]]> https://biorxiv.org/content/10.1101/2022.08.05.502992v1?rss=1 Overton, J. A. Moxon, K. A. Stickle, M. P. Peters, L. M. Lin, J. J. Chang, E. F. Knight, R. T. Hsu, M. Saez, I. 2022-08-06 doi:10.1101/2022.08.05.502992 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ A common mechanism of Sec61 translocon inhibition by small molecules ]]> https://biorxiv.org/content/10.1101/2022.08.11.503542v1?rss=1 Itskanov, S. Wang, L. Junne, T. Sherriff, R. Xiao, L. Blanchard, N. Shi, W. Q. Forsyth, C. Hoepfner, D. Spiess, M. Park, E. 2022-08-11 doi:10.1101/2022.08.11.503542 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells ]]> https://biorxiv.org/content/10.1101/2022.08.12.503709v1?rss=1 Gayoso, A. Weiler, P. Lotfollahi, M. Klein, D. Hong, J. Streets, A. M. Theis, F. J. Yosef, N. 2022-08-15 doi:10.1101/2022.08.12.503709 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Cantilever-based in vivo measurements in the early Drosophila embryo reveal adiabatic elastic response on developmentally relevant time scales ]]> https://biorxiv.org/content/10.1101/2022.08.12.503803v1?rss=1 Cheikh, M. I. Tchoufag, J. Dean, K. Bhaduri, S. Zhang, C. Mandadapu, K. K. Doubrovinski, K. 2022-08-14 doi:10.1101/2022.08.12.503803 Cold Spring Harbor Laboratory Press 2022-08-14 <![CDATA[ Cellular Mechanisms Underlying Embryonic Retinal Waves ]]> https://biorxiv.org/content/10.1101/2022.08.14.503889v1?rss=1 Voufo, C. Chen, A. Q. Smith, B. E. Feller, M. B. Tiriac, A. 2022-08-15 doi:10.1101/2022.08.14.503889 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Leaf side determines the relative importance of dispersal versus host filtering in the phyllosphere microbiome ]]> https://biorxiv.org/content/10.1101/2022.08.16.504148v1?rss=1 Smets, W. Chock, M. K. Walsh, C. M. Vanderburgh, C. Q. Kau, E. Lindow, S. E. Fierer, N. Koskella, B. 2022-08-17 doi:10.1101/2022.08.16.504148 Cold Spring Harbor Laboratory Press 2022-08-17 <![CDATA[ Dodecaploid Xenopus longipes provides insight into the emergence of size scaling relationships during development ]]> https://biorxiv.org/content/10.1101/2022.08.16.504201v1?rss=1 Miller, K. Cadart, C. Heald, R. 2022-08-17 doi:10.1101/2022.08.16.504201 Cold Spring Harbor Laboratory Press 2022-08-17 <![CDATA[ Methylglyoxal-derived hydroimidazolone, MG-H1, increases food intake by altering tyramine signaling via the GATA transcription factor ELT-3 in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2022.08.18.504374v1?rss=1 Muthaiyan Shanmugam, M. Chaudhuri, J. Sellegounder, D. Sahu, A. K. Guha, S. Chamoli, M. Hodge, B. Roberts, C. Lithgow, G. Sarpong, R. Kapahi, P. 2022-08-19 doi:10.1101/2022.08.18.504374 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ Within-host adaptation alters priority effects within the phyllosphere microbiome ]]> https://biorxiv.org/content/10.1101/2022.08.19.504580v1?rss=1 Debray, R. Conover, A. Zhang, X. Dewald-Wang, E. A. Koskella, B. 2022-08-20 doi:10.1101/2022.08.19.504580 Cold Spring Harbor Laboratory Press 2022-08-20 <![CDATA[ Engineering Pseudomonas putida KT2440 for chain length tailored free fatty acid and oleochemical production ]]> https://biorxiv.org/content/10.1101/2022.08.20.504671v1?rss=1 Valencia, L. E. Incha, M. R. Schmidt, M. Pearson, A. N. Thompson, M. G. Roberts, J. Mehling, M. Yin, K. Sun, N. Oka, A. Shih, P. M. Blank, L. M. Gladden, J. Keasling, J. D. 2022-08-21 doi:10.1101/2022.08.20.504671 Cold Spring Harbor Laboratory Press 2022-08-21 <![CDATA[ DNA language models are powerful zero-shot predictors of non-coding variant effects ]]> https://biorxiv.org/content/10.1101/2022.08.22.504706v1?rss=1 Benegas, G. Batra, S. S. Song, Y. S. 2022-08-23 doi:10.1101/2022.08.22.504706 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ Murine cytomegalovirus downregulates ERAAP and induces an unconventional T cell response to self ]]> https://biorxiv.org/content/10.1101/2022.08.23.504566v1?rss=1 Geiger, K. Manoharan, M. Coombs, R. Park, C.-s. Lee, A. Shastri, N. Robey, E. Coscoy, L. 2022-08-23 doi:10.1101/2022.08.23.504566 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ Exploring masses and internal mass distributions of single carboxysomes in free solution using fluorescence and interferometric scattering in an anti-Brownian trap ]]> https://biorxiv.org/content/10.1101/2022.08.23.505029v1?rss=1 View larger version (21K): org.highwire.dtl.DTLVardef@18e9f99org.highwire.dtl.DTLVardef@900912org.highwire.dtl.DTLVardef@4398baorg.highwire.dtl.DTLVardef@1dff103_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lavania, A. A. Carpenter, W. B. Oltrogge, L. M. Perez, D. Borden, J. S. Savage, D. F. Moerner, W. E. 2022-08-25 doi:10.1101/2022.08.23.505029 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Cell type-programmable genome editing with enveloped delivery vehicles ]]> https://biorxiv.org/content/10.1101/2022.08.24.505004v1?rss=1 Hamilton, J. R. Chen, E. Perez, B. S. Sandoval Espinoza, C. R. Doudna, J. A. 2022-08-24 doi:10.1101/2022.08.24.505004 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ Stimulation of the catalytic activity of the tyrosine kinase Btk by the adaptor protein Grb2 ]]> https://biorxiv.org/content/10.1101/2022.08.25.505243v1?rss=1 Nocka, L. M. Groves, J. T. Kuriyan, J. 2022-08-25 doi:10.1101/2022.08.25.505243 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Dosage differences in 12-OXOPHYTODIENOATE REDUCTASE genes modulate wheat primary root growth ]]> https://biorxiv.org/content/10.1101/2022.08.25.505338v1?rss=1 Gabay, G. Wang, H. Zhang, J. Moriconi, J. Burguener, G. F. Howell, T. R. Lukaszewski, A. Staskawicz, B. Cho, M.-J. Tanaka, J. Fahima, T. Ke, H. Dehesh, K. Zhang, G.-L. Gou, J.-Y. Hamberg, M. Santa Maria, G. Dubcovsky, J. 2022-08-26 doi:10.1101/2022.08.25.505338 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Parallel CRISPR-Cas9 screens reveal mechanisms of PLIN2 and lipid droplet regulation ]]> https://biorxiv.org/content/10.1101/2022.08.27.505556v1?rss=1 Roberts, M. A. Deol, K. K. Lange, M. Leto, D. E. Mathiowetz, A. J. Stevenson, J. Hashemi, S. H. Morgens, D. W. Easter, E. Heydari, K. Nalls, M. A. Bassik, M. C. Kampmann, M. Kopito, R. R. Faghri, F. Olzmann, J. A. 2022-08-28 doi:10.1101/2022.08.27.505556 Cold Spring Harbor Laboratory Press 2022-08-28 <![CDATA[ Environmentally robust cis-regulatory changes underlie rapid climatic adaptation ]]> https://biorxiv.org/content/10.1101/2022.08.29.505745v1?rss=1 Ballinger, M. A. Mack, K. L. Durkin, S. M. Riddell, E. A. Nachman, M. W. 2022-09-01 doi:10.1101/2022.08.29.505745 Cold Spring Harbor Laboratory Press 2022-09-01 <![CDATA[ X chromosome dosage drives statin-induced dysglycemia and mitochondrial dysfunction ]]> https://biorxiv.org/content/10.1101/2022.08.29.505759v1?rss=1 Zhang, P. Munier, J. J. Vergnes, L. Wiese, C. B. Link, J. C. Abbasi, F. Ronquillo, E. Munoz, A. Kuang, Y.-L. Liu, M. Sanchez, G. Oni-Orisan, A. Iribarren, C. McPhaul, M. J. Nomura, D. K. Knowles, J. W. Krauss, R. M. Medina, M. W. Reue, K. 2022-09-01 doi:10.1101/2022.08.29.505759 Cold Spring Harbor Laboratory Press 2022-09-01 <![CDATA[ Rejection of inappropriate synaptic partners mediated by transcellular FLRT2-UNC5 signaling ]]> https://biorxiv.org/content/10.1101/2022.08.29.505771v1?rss=1 Prigge, C. L. Sharma, A. Dembla, M. El-Quessny, M. Kozlowski, C. Paisley, C. E. Johnson, T. Della Santina, L. Feller, M. Kay, J. N. 2022-08-30 doi:10.1101/2022.08.29.505771 Cold Spring Harbor Laboratory Press 2022-08-30 <![CDATA[ Coenzyme A governs proinflammatory macrophage metabolism ]]> https://biorxiv.org/content/10.1101/2022.08.30.505732v1?rss=1 Timblin, G. A. Tharp, K. M. Hoeve, J. t. Baydemir, I. Khantwal, C. Farahzad, J. N. Dominguez-Andres, J. Vance, R. E. Weaver, V. M. 2022-09-02 doi:10.1101/2022.08.30.505732 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Negative allosteric modulation of the glucagon receptor by RAMP2 ]]> https://biorxiv.org/content/10.1101/2022.08.30.505955v1?rss=1 Krishna Kumar, K. O'Brien, E. Habrian, C. Latorraca, N. R. Wang, H. Tuneew, I. Montabana, E. Marqusee, S. Hilger, D. Isacoff, E. Y. Mathiesen, J. M. Kobilka, B. K. 2022-08-31 doi:10.1101/2022.08.30.505955 Cold Spring Harbor Laboratory Press 2022-08-31 <![CDATA[ Systematic Engineering of Virus-Like Particles to Identify Self-Assembly Rules for Shifting Particle Size ]]> https://biorxiv.org/content/10.1101/2022.08.31.506130v1?rss=1 Ikwuagwu, B. Hartman, E. Mills, C. Tullman-Ercek, D. 2022-09-03 doi:10.1101/2022.08.31.506130 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Ventral temporal and posteromedial sulcal morphology in autism spectrum disorder ]]> https://biorxiv.org/content/10.1101/2022.09.01.506213v1?rss=1 Benitez, J. A. R. Kannan, S. Hastings, W. Parker, B. Willbrand, E. Weiner, K. S. 2022-09-02 doi:10.1101/2022.09.01.506213 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Improved Genome Editing by an Engineered CRISPR-Cas12a ]]> https://biorxiv.org/content/10.1101/2022.09.02.506401v1?rss=1 Ma, E. Chen, K. Shi, H. Stahl, E. C. Adler, B. A. Liu, J. Zhou, K. Ye, J. Doudna, J. A. 2022-09-02 doi:10.1101/2022.09.02.506401 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Chorography and conformational dynamism of the Soluble Human Fibrinogen in solution ]]> https://biorxiv.org/content/10.1101/2022.09.05.506423v1?rss=1 Sen, M. Hudson, N. E. Offenbacher, A. R. Iavarone, A. T. Nguyen, Q. Ray, K. Popovic, G. Manandhar, P. Pinelo, J. E. E. 2022-09-05 doi:10.1101/2022.09.05.506423 Cold Spring Harbor Laboratory Press 2022-09-05 <![CDATA[ Characterizing Cone Spectral Classification by Optoretinography ]]> https://biorxiv.org/content/10.1101/2022.09.07.507027v1?rss=1 Pandiyan, V. P. Schleufer, S. Slezak, E. Fong, J. Upadhyay, R. Roorda, A. Ng, R. Sabesan, R. 2022-09-10 doi:10.1101/2022.09.07.507027 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ The evolution of host resistance to a virus is determined by resources, historical contingency, and time scale ]]> https://biorxiv.org/content/10.1101/2022.09.08.507185v1?rss=1 Visher, E. Mahjoub, H. Soufi, K. Pascual, N. Hoang, V. Bartlett, L. J. Roberts, K. E. Meaden, S. Boots, M. 2022-09-10 doi:10.1101/2022.09.08.507185 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Stimulating microtubule growth is not the essential function of the microtubule polymerase Stu2 ]]> https://biorxiv.org/content/10.1101/2022.09.09.507218v1?rss=1 Carrier, J. S. Torvi, J. R. Jenson, E. Jones, C. Gangadharan, B. Geyer, E. A. Rice, L. Lagesse, B. Barnes, G. Miller, M. P. 2022-09-10 doi:10.1101/2022.09.09.507218 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid-membrane contacts ]]> https://biorxiv.org/content/10.1101/2022.09.10.507427v1?rss=1 Rogers, J. R. Geissler, P. L. 2022-09-11 doi:10.1101/2022.09.10.507427 Cold Spring Harbor Laboratory Press 2022-09-11 <![CDATA[ Treatment of prostate cancer with CD46 targeted 225Ac alpha particle radioimmunotherapy ]]> https://biorxiv.org/content/10.1101/2022.10.13.512165v1?rss=1 Bidkar, A. P. Wang, S. Bobba, K. N. Chan, E. Bidlingmaier, S. Egusa, E. A. Peter, R. Ali, U. Meher, N. Wadhwa, A. Dhrona, S. Beckford-Vera, D. Su, Y. Tang, R. Zhang, L. He, J. Wilson, D. M. Aggarwal, R. VanBrocklin, H. F. Seo, Y. Chou, J. Liu, B. Flavell, R. R. 2022-10-14 doi:10.1101/2022.10.13.512165 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ The complete sequence of a human Y chromosome ]]> https://biorxiv.org/content/10.1101/2022.12.01.518724v1?rss=1 Rhie, A. Nurk, S. Cechova, M. Hoyt, S. J. Taylor, D. J. Altemose, N. Hook, P. W. Koren, S. Rautiainen, M. Alexandrov, I. A. Allen, J. Asri, M. Bzikadze, A. V. Chen, N.-C. Chin, C.-S. Diekhans, M. Flicek, P. Formenti, G. Fungtammasan, A. Garcia Giron, C. Garrison, E. Gershman, A. Gerton, J. Grady, P. G. Guarracino, A. Haggerty, L. Halabian, R. Hansen, N. F. Harris, R. Hartley, G. A. Harvey, W. T. Haukness, M. Heinz, J. Hourlier, T. Hubley, R. M. Hunt, S. E. Hwang, S. Jain, M. Kesharwani, R. K. Lewis, A. P. Li, H. Logsdon, G. A. Lucas, J. K. Makalowski, 2022-12-01 doi:10.1101/2022.12.01.518724 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ CherryML: Scalable Maximum Likelihood Estimation of Phylogenetic Models ]]> https://biorxiv.org/content/10.1101/2022.12.21.521328v1?rss=1 Prillo, S. Deng, Y. Boyeau, P. Li, X. Chen, P.-Y. Song, Y. S. 2022-12-22 doi:10.1101/2022.12.21.521328 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ FAZ assembly in bloodstream form Trypanosoma brucei requires kinesin KIN-E ]]> https://biorxiv.org/content/10.1101/2022.12.22.521263v1?rss=1 Albisetti, A. C. Douglas, R. L. Welch, M. D. 2022-12-22 doi:10.1101/2022.12.22.521263 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ A central helical fulcrum in eIF2B coordinates allosteric regulation of Integrated Stress Response signaling ]]> https://biorxiv.org/content/10.1101/2022.12.22.521453v1?rss=1 Lawrence, R. Shoemaker, S. Deal, A. Sangwan, S. Anand, A. Wang, L. Marqusee, S. Walter, P. 2022-12-22 doi:10.1101/2022.12.22.521453 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ The Warburg Effect is the result of faster ATP production by glycolysis than respiration ]]> https://biorxiv.org/content/10.1101/2022.12.28.522160v1?rss=1 Kukurugya, M. A. Titov, D. V. 2022-12-29 doi:10.1101/2022.12.28.522160 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Effect of Nivolumab therapy on Metastatic Lung Cancer in Human Microbiome ]]> https://biorxiv.org/content/10.1101/2023.01.03.522679v1?rss=1 Kubba, R. Nguyen, S. Borneman, J. Pai, R. Evans, R. J. 2023-01-04 doi:10.1101/2023.01.03.522679 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ Altered hierarchical auditory predictive processing after lesions to the orbitofrontal cortex ]]> https://biorxiv.org/content/10.1101/2023.01.04.521570v1?rss=1 Asko, O. Blenkmann, A. O. Leske, S. L. Foldal, M. D. Llorens, A. Funderud, I. Meling, T. Knight, R. T. Endestad, T. Solbakk, A.-K. 2023-01-04 doi:10.1101/2023.01.04.521570 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ Critical assessment of E. coli genome-scale metabolic model with high-throughput mutant fitness data ]]> https://biorxiv.org/content/10.1101/2023.01.05.522875v1?rss=1 Bernstein, D. B. Akkas, B. Price, M. N. Arkin, A. P. 2023-01-05 doi:10.1101/2023.01.05.522875 Cold Spring Harbor Laboratory Press 2023-01-05 <![CDATA[ Crystal Structures of Inhibitor-Bound Main Protease from Delta- and Gamma-Coronaviruses ]]> https://biorxiv.org/content/10.1101/2023.02.01.526623v1?rss=1 Zvornicanin, S. N. Shaqra, A. M. Huang, Q. Y. Ornelas, E. Moghe, M. Knapp, M. Moquin, S. Dovala, D. Schiffer, C. A. Kurt Yilmaz, N. 2023-02-02 doi:10.1101/2023.02.01.526623 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ OH 89: A newly described ~1.8-million-year-old hominid clavicle from Olduvai Gorge ]]> https://biorxiv.org/content/10.1101/2023.02.02.526656v1?rss=1 Taylor, C. Masao, F. Njau, J. N. Songita, A. V. Hlusko, L. J. 2023-02-02 doi:10.1101/2023.02.02.526656 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ Cysteine: an ancestral Cu binding ligand in green algae? ]]> https://biorxiv.org/content/10.1101/2023.03.15.532757v1?rss=1 Strenkert, D. Schmollinger, S. Hu, Y. Hofmann, C. Holbrook, K. Liu, H. W. Purvine, S. O. Nicora, C. D. Chen, S. Lipton, M. S. Northen, T. R. Clemens, S. Merchant, S. S. 2023-03-15 doi:10.1101/2023.03.15.532757 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ The Generation and Propagation of the Human Alpha Rhythm ]]> https://biorxiv.org/content/10.1101/202564v1?rss=1 Halgren, M. Devinsky, O. Doyle, W. K. Bastuji, H. Rey, M. Mak-McCully, R. Chauvel, P. Ulbert, I. Fabo, D. Wittner, L. Heit, G. Eskandar, E. Mandell, A. Cash, S. S. 2017-11-18 doi:10.1101/202564 Cold Spring Harbor Laboratory Press 2017-11-18 <![CDATA[ A population phylogenetic view of mitochondrial heteroplasmy ]]> https://biorxiv.org/content/10.1101/204479v1?rss=1 Wilton, P. Zaidi, A. Makova, K. Nielsen, R. 2017-10-17 doi:10.1101/204479 Cold Spring Harbor Laboratory Press 2017-10-17 <![CDATA[ Programmable RNA recognition using a CRISPR-associated Argonaute ]]> https://biorxiv.org/content/10.1101/208041v1?rss=1 Lapinaite, A. Doudna, J. A. Cate, J. 2017-10-23 doi:10.1101/208041 Cold Spring Harbor Laboratory Press 2017-10-23 <![CDATA[ Dynamic and Selective Low-Complexity Domain Interactions Revealed by Live-Cell Single-Molecule Imaging ]]> https://biorxiv.org/content/10.1101/208710v1?rss=1 Chong, S. Dugast-Darzacq, C. Liu, Z. Dong, P. Dailey, G. Banala, S. Lavis, L. Darzacq, X. Tjian, R. 2017-10-25 doi:10.1101/208710 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ Massive Factorial Design Untangles Coding Sequences Determinants Of Translation Efficacy ]]> https://biorxiv.org/content/10.1101/208801v1?rss=1 Cambray, G. Guimaraes, J. C. Arkin, A. P. 2017-10-25 doi:10.1101/208801 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ Massive Phenotypic Measurements Reveal Complex Physiological Consequences Of Differential Translation Efficacies ]]> https://biorxiv.org/content/10.1101/209098v1?rss=1 Arkin, A. P. Cambray, G. 2017-10-25 doi:10.1101/209098 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ Synergism between a simple sugar and a small intrinsically disordered protein mitigate the lethal stresses of severe water loss ]]> https://biorxiv.org/content/10.1101/209163v1?rss=1 Kim, S. X. Camdere, G. Hu, X. Koshland, D. Tapia, H. 2017-10-25 doi:10.1101/209163 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ Simultaneous CRISPR/Cas9-mediated editing of cassava eIF4E isoforms nCBP-1 and nCBP-2 confers elevated resistance to cassava brown streak disease ]]> https://biorxiv.org/content/10.1101/209874v1?rss=1 Gomez, M. A. Lin, Z.-J. D. Moll, T. Luebbert, C. Chauhan, R. D. Vijayaraghavan, A. Renninger, K. Beyene, G. Taylor, N. J. Carrington, J. C. Staskawicz, B. J. Bart, R. 2017-10-27 doi:10.1101/209874 Cold Spring Harbor Laboratory Press 2017-10-27 <![CDATA[ Effects of Spatial Heterogeneity on Transmission Potential in Vectorial-Contact Networks: A Comparison of Three Aedes aegypti Control Strategies ]]> https://biorxiv.org/content/10.1101/210450v1?rss=1 Sanchez C., H. M. Marshall, J. M. Wu, S. L. Vallejo, E. E. 2017-10-28 doi:10.1101/210450 Cold Spring Harbor Laboratory Press 2017-10-28 <![CDATA[ Combinatorial Drug Discovery in Nanoliter Droplets ]]> https://biorxiv.org/content/10.1101/210492v1?rss=1 Kulesa, A. Kehe, J. Hurtado, J. Tawde, P. Blainey, P. C. 2017-10-28 doi:10.1101/210492 Cold Spring Harbor Laboratory Press 2017-10-28 <![CDATA[ Evolutionary dynamics of bacteria in the gut microbiome within and across hosts ]]> https://biorxiv.org/content/10.1101/210955v1?rss=1 Garud, N. R. Good, B. H. Hallatschek, O. Pollard, K. S. 2017-10-30 doi:10.1101/210955 Cold Spring Harbor Laboratory Press 2017-10-30 <![CDATA[ The effect of strong purifying selection on genetic diversity ]]> https://biorxiv.org/content/10.1101/211557v1?rss=1 Cvijovic, I. Good, B. H. Desai, M. M. 2017-10-30 doi:10.1101/211557 Cold Spring Harbor Laboratory Press 2017-10-30 <![CDATA[ Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially processed plant derived carbon ]]> https://biorxiv.org/content/10.1101/211649v1?rss=1 Starr, E. P. Shi, S. Blazewicz, S. J. Probst, A. J. Herman, D. J. Firestone, M. A. Banfield, J. F. 2017-10-31 doi:10.1101/211649 Cold Spring Harbor Laboratory Press 2017-10-31 <![CDATA[ The ancestral animal genetic toolkit revealed by diverse choanoflagellate transcriptomes ]]> https://biorxiv.org/content/10.1101/211789v1?rss=1 Richter, D. Fozouni, P. Eisen, M. King, N. 2017-12-10 doi:10.1101/211789 Cold Spring Harbor Laboratory Press 2017-12-10 <![CDATA[ Lessons from simple marine models on the bacterial regulation of eukaryotic development ]]> https://biorxiv.org/content/10.1101/211797v1?rss=1 Woznica, A. King, N. 2017-10-31 doi:10.1101/211797 Cold Spring Harbor Laboratory Press 2017-10-31 <![CDATA[ Inferring the evolutionary reduction of corm lobation in Isoëtes using Bayesian model-averaged ancestral state reconstruction ]]> https://biorxiv.org/content/10.1101/212316v1?rss=1 Freund, F. Freyman, W. Rothfels, C. 2017-11-01 doi:10.1101/212316 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Population Differentiation at the HLA Genes ]]> https://biorxiv.org/content/10.1101/214668v1?rss=1 Brandt, D. Y. C. Cesar, J. Goudet, J. Meyer, D. 2017-11-06 doi:10.1101/214668 Cold Spring Harbor Laboratory Press 2017-11-06 <![CDATA[ Non-invasive measurement of mRNA decay reveals translation initiation as the major determinant of mRNA stability ]]> https://biorxiv.org/content/10.1101/214775v1?rss=1 Chan, L. Y. Mugler, C. F. Heinrich, S. Vallotton, P. Weis, K. 2017-11-07 doi:10.1101/214775 Cold Spring Harbor Laboratory Press 2017-11-07 <![CDATA[ Spontaneous eye blink rate and dopamine synthesis capacity: Preliminary evidence for an absence of positive correlation ]]> https://biorxiv.org/content/10.1101/215178v1?rss=1 Sescousse, G. Ligneul, R. van Holst, R. J. Janssen, L. K. de Boer, F. Janssen, M. Berry, A. S. Jagust, W. J. Cools, R. 2017-11-17 doi:10.1101/215178 Cold Spring Harbor Laboratory Press 2017-11-17 <![CDATA[ Prefrontal cortex regulates amygdala response to threat in trait anxiety ]]> https://biorxiv.org/content/10.1101/215699v1?rss=1 Ironside, M. Browning, M. Ansari, T. Harvey, C. Sekyi-Djan, M. Bishop, S. Harmer, C. O'Shea, J. 2017-11-07 doi:10.1101/215699 Cold Spring Harbor Laboratory Press 2017-11-07 <![CDATA[ Multiplexed temporally focused light shaping for high-resolutionmulti-cell targeting ]]> https://biorxiv.org/content/10.1101/216135v1?rss=1 Accanto, N. Tanese, D. Ronzitti, E. Molinier, C. Newman, Z. L. Wyart, C. Isacoff, E. Papagiakoumou, E. Emiliani, V. 2017-11-08 doi:10.1101/216135 Cold Spring Harbor Laboratory Press 2017-11-08 <![CDATA[ Microbiome-by-ethanol interactions impact Drosophila melanogaster fitness and physiology ]]> https://biorxiv.org/content/10.1101/217240v1?rss=1 Chandler, J. A. Innocent, L. V. Yang, J. L. Eisen, M. B. Ludington, W. B. 2017-11-09 doi:10.1101/217240 Cold Spring Harbor Laboratory Press 2017-11-09 <![CDATA[ Anti-phage islands force their target phage to directly mediate island excision and spread ]]> https://biorxiv.org/content/10.1101/218164v1?rss=1 McKitterick, A. C. Seed, K. 2017-11-11 doi:10.1101/218164 Cold Spring Harbor Laboratory Press 2017-11-11 <![CDATA[ Sex differences in the genetic architecture of obsessive-compulsive disorder ]]> https://biorxiv.org/content/10.1101/219170v1?rss=1 Khramtsova, E. A. Heldman, R. Derks, E. M. Yu, D. TS/OCD Psychiatric Genomics Disorders Workgroup, Davis, L. K. Stranger, B. E. 2017-11-21 doi:10.1101/219170 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ Suboptimal eye movements for seeing fine details ]]> https://biorxiv.org/content/10.1101/220319v1?rss=1 Agaoglu, M. N. Sheehy, C. K. Tiruveedhula, P. Roorda, A. Chung, S. T. L. 2017-11-16 doi:10.1101/220319 Cold Spring Harbor Laboratory Press 2017-11-16 <![CDATA[ Origin and evolution of the nuclear auxin response system ]]> https://biorxiv.org/content/10.1101/220731v1?rss=1 Mutte, S. Kato, H. Rothfels, C. Melkonian, M. Wong, G. K.-S. Weijers, D. 2017-11-16 doi:10.1101/220731 Cold Spring Harbor Laboratory Press 2017-11-16 <![CDATA[ The polygenic basis of an ancient divergence in yeast thermotolerance ]]> https://biorxiv.org/content/10.1101/220913v1?rss=1 Weiss, C. Roop, J. I. Hackley, R. Chuong, J. Grigoriev, I. V. Arkin, A. P. Skerker, J. M. Brem, R. B. 2017-11-17 doi:10.1101/220913 Cold Spring Harbor Laboratory Press 2017-11-17 <![CDATA[ Flex ddG: Rosetta ensemble-based estimation of changes in protein-protein binding affinity upon mutation ]]> https://biorxiv.org/content/10.1101/221689v1?rss=1 Barlow, K. A. O Conchuir, S. Thompson, S. Suresh, P. Lucas, J. E. Heinonen, M. Kortemme, T. 2017-11-17 doi:10.1101/221689 Cold Spring Harbor Laboratory Press 2017-11-17 <![CDATA[ Mechanochemical Coupling and Bi-Phasic Force-Velocity Dependence in the Ultra-Fast Ring ATPase SpoIIIE ]]> https://biorxiv.org/content/10.1101/224022v1?rss=1 Liu, N. Chistol, G. Cui, Y. Bustamante, C. 2017-11-22 doi:10.1101/224022 Cold Spring Harbor Laboratory Press 2017-11-22 <![CDATA[ Rapid evolution of gained essential developmental functions of a young gene via interactions with other essential genes ]]> https://biorxiv.org/content/10.1101/226936v1?rss=1 Lee, Y. C. G. Ventura, I. M. Rice, G. R. Chen, D.-Y. Long, M. 2017-11-30 doi:10.1101/226936 Cold Spring Harbor Laboratory Press 2017-11-30 <![CDATA[ CRISPR-Cas12a target binding unleashes single-stranded DNase activity ]]> https://biorxiv.org/content/10.1101/226993v1?rss=1 Chen, J. S. Ma, E. Harrington, L. B. Tian, X. Doudna, J. A. 2017-11-29 doi:10.1101/226993 Cold Spring Harbor Laboratory Press 2017-11-29 <![CDATA[ Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans ]]> https://biorxiv.org/content/10.1101/227660v1?rss=1 Steinrücken, M. Spence, J. P. Kamm, J. A. Wieczorek, E. Song, Y. S. 2017-12-01 doi:10.1101/227660 Cold Spring Harbor Laboratory Press 2017-12-01 <![CDATA[ Accurate Determination of Bacterial Abundances in Human Metagenomes Using Full-length 16S Sequencing Reads ]]> https://biorxiv.org/content/10.1101/228619v1?rss=1 Perraudeau, F. Dudoit, S. Bullard, J. H. 2017-12-04 doi:10.1101/228619 Cold Spring Harbor Laboratory Press 2017-12-04 <![CDATA[ Three-way clustering of multi-tissue multi-individual gene expression data using constrained tensor decomposition ]]> https://biorxiv.org/content/10.1101/229245v1?rss=1 Wang, M. Fischer, J. Song, Y. S. 2017-12-05 doi:10.1101/229245 Cold Spring Harbor Laboratory Press 2017-12-05 <![CDATA[ Integrated analysis of anatomical and electrophysiological human intracranial data ]]> https://biorxiv.org/content/10.1101/230912v1?rss=1 Stolk, A. Griffin, S. van der Meij, R. Dewar, C. Saez, I. Lin, J. J. Piantoni, G. Schoffelen, J.-M. Knight, R. T. Oostenveld, R. 2017-12-08 doi:10.1101/230912 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ Reconciling persistent and dynamic hypotheses of working memory coding in prefrontal cortex ]]> https://biorxiv.org/content/10.1101/231506v1?rss=1 Cavanagh, S. E. Towers, J. P. Wallis, J. D. Hunt, L. T. Kennerley, S. W. 2017-12-14 doi:10.1101/231506 Cold Spring Harbor Laboratory Press 2017-12-14 <![CDATA[ A fungal pathogen that robustly manipulates the behavior of Drosophila melanogaster in the laboratory ]]> https://biorxiv.org/content/10.1101/232140v1?rss=1 Elya, C. Lok, T. C. Spencer, Q. E. McCausland, H. Eisen, M. B. 2017-12-10 doi:10.1101/232140 Cold Spring Harbor Laboratory Press 2017-12-10 <![CDATA[ Pivotal roles of PCNA loading and unloading on heterochromatin function ]]> https://biorxiv.org/content/10.1101/232181v1?rss=1 Janke, R. King, G. Kupiec, M. Rine, J. 2017-12-11 doi:10.1101/232181 Cold Spring Harbor Laboratory Press 2017-12-11 <![CDATA[ On negative heritability and negative estimates of heritability ]]> https://biorxiv.org/content/10.1101/232843v1?rss=1 Steinsaltz, D. Dahl, A. Wachter, K. W. 2017-12-13 doi:10.1101/232843 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ Geometry of the sample frequency spectrum and the perils of demographic inference ]]> https://biorxiv.org/content/10.1101/233908v1?rss=1 Rosen, Z. Bhaskar, A. Roch, S. Song, Y. S. 2017-12-13 doi:10.1101/233908 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ The tortoise and the hare: interactions between reinforcement learning and working memory. ]]> https://biorxiv.org/content/10.1101/234724v1?rss=1 Collins, A. G. 2017-12-15 doi:10.1101/234724 Cold Spring Harbor Laboratory Press 2017-12-15 <![CDATA[ Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq ]]> https://biorxiv.org/content/10.1101/235382v1?rss=1 Cole, M. B. Risso, D. Wagner, A. DeTomaso, D. Ngai, J. Purdom, E. Dudoit, S. Yosef, N. 2017-12-16 doi:10.1101/235382 Cold Spring Harbor Laboratory Press 2017-12-16 <![CDATA[ A general method to predict the effect of single amino acid substitutions on enzyme catalytic activity ]]> https://biorxiv.org/content/10.1101/236265v1?rss=1 Lin, Y.-H. Huang, C. L. V. Ho, C. Shatsky, M. Kirsch, J. F. 2017-12-19 doi:10.1101/236265 Cold Spring Harbor Laboratory Press 2017-12-19 <![CDATA[ Quantifying biases in test-negative studies of vaccine effectiveness ]]> https://biorxiv.org/content/10.1101/237503v1?rss=1 Lewnard, J. A. Tedijanto, C. A. Cowling, B. J. Lipsitch, M. 2017-12-22 doi:10.1101/237503 Cold Spring Harbor Laboratory Press 2017-12-22 <![CDATA[ 50 Hz volumetric functional imaging with continuously adjustable depth of focus ]]> https://biorxiv.org/content/10.1101/240069v1?rss=1 Lu, R. Taminoto, M. Koyama, M. Ji, N. 2017-12-28 doi:10.1101/240069 Cold Spring Harbor Laboratory Press 2017-12-28 <![CDATA[ Synchronous diversification of Sulawesi’s iconic artiodactyls driven by recent geological events ]]> https://biorxiv.org/content/10.1101/241448v1?rss=1 Frantz, L. Rudzinski, A. Mansyursyah Surya Nugraha, A. Evin, A. Burton, J. Hulme-Beaman, A. Linderholm, A. Barnett, R. Vega, R. Irving-Pease, E. Haile, J. Allen, R. Leus, K. Shephard, J. Hillyer, M. Gillemot, S. van den Hurk, J. Ogle, S. Atofanei, C. Thomas, M. Johansson, F. Mustari, A. Williams, J. Mohamad, K. Damayanti, C. Wiryadi, I. Obbles, D. Day, H. Yasin, M. Meker, S. McGuire, J. Evans, B. von Rintelen, T. Ho, S. Searle, J. Kitchener, A. Macdonald, A. Shaw, D. Hall, R. Galbusera, P. Larson, G. 2018-01-04 doi:10.1101/241448 Cold Spring Harbor Laboratory Press 2018-01-04 <![CDATA[ Identification of an arabinopyranosyltransferase from Physcomitrella patens involved in the synthesis of the hemicellulose xyloglucan ]]> https://biorxiv.org/content/10.1101/241521v1?rss=1 Zhu, L. Dama, M. Pauly, M. 2017-12-31 doi:10.1101/241521 Cold Spring Harbor Laboratory Press 2017-12-31 <![CDATA[ Uncovering temporal structure in hippocampal output patterns ]]> https://biorxiv.org/content/10.1101/242594v1?rss=1 Maboudi, K. Ackermann, E. Pfeiffer, B. E. Foster, D. J. Diba, K. Kemere, C. 2018-01-04 doi:10.1101/242594 Cold Spring Harbor Laboratory Press 2018-01-04 <![CDATA[ Observing the Cell in Its Native State: Imaging Subcellular Dynamics in Multicellular Organisms ]]> https://biorxiv.org/content/10.1101/243352v1?rss=1 Liu, T.-l. Upadhyayula, S. Milkie, D. E. Singh, V. Wang, K. Swinburne, I. A. Mosaliganti, K. R. Collin, Z. M. Hiscock, T. W. Shea, J. Kohrman, A. Q. Medwig, T. N. Dambournet, D. Forster, R. Cunniff, B. Ruan, Y. Yashiro, H. Scholpp, S. Meyerowitz, E. M. Hockemeyer, D. Drubin, D. G. Martin, B. L. Matus, D. Q. Koyama, M. Megason, S. G. Kirchhausen, T. Betzig, E. 2018-01-08 doi:10.1101/243352 Cold Spring Harbor Laboratory Press 2018-01-08 <![CDATA[ Spatial gradient in activity within the insula reflects dissociable neural mechanisms underlying context-dependent advantageous and disadvantageous inequity aversion ]]> https://biorxiv.org/content/10.1101/243428v1?rss=1 Gao, X. Yu, H. Saez, I. Blue, P. R. Zhu, L. Hsu, M. Zhou, X. 2018-01-05 doi:10.1101/243428 Cold Spring Harbor Laboratory Press 2018-01-05 <![CDATA[ Visualization of PRC2-Dinucleosome Interactions Leading to Epigenetic Repression ]]> https://biorxiv.org/content/10.1101/245134v1?rss=1 Poepsel, S. Kasinath, V. Nogales, E. 2018-01-08 doi:10.1101/245134 Cold Spring Harbor Laboratory Press 2018-01-08 <![CDATA[ Quantum chemistry reveals the thermodynamic principles of redoxbiochemistry ]]> https://biorxiv.org/content/10.1101/245365v1?rss=1 Jinich, A. Flamholz, A. Ren, H. Kim, S.-J. Sanchez-Lengeling, B. Cotton, C. A. R. Noor, E. Aspuru-Guzik, A. Bar-Even, A. 2018-01-09 doi:10.1101/245365 Cold Spring Harbor Laboratory Press 2018-01-09 <![CDATA[ Loop Assembly: a simple and open system for recursive fabrication of DNA circuits ]]> https://biorxiv.org/content/10.1101/247593v1?rss=1 Pollak, B. Cerda, A. Delmans, M. Alamos, S. Moyano, T. West, A. Gutierrez, R. A. Patron, N. Federici, F. Haseloff, J. 2018-01-15 doi:10.1101/247593 Cold Spring Harbor Laboratory Press 2018-01-15 <![CDATA[ Baculovirus AC102 is a nucleocapsid protein that is crucial for nuclear actin polymerization and nucleocapsid morphogensis ]]> https://biorxiv.org/content/10.1101/248278v1?rss=1 Hepp, S. E. Borgo, G. M. Ticau, S. Ohkawa, T. Welch, M. D. 2018-01-19 doi:10.1101/248278 Cold Spring Harbor Laboratory Press 2018-01-19 <![CDATA[ Homologous recombination and transposon propagation shapes the population structure of an organism from the deep subsurface with minimal metabolism ]]> https://biorxiv.org/content/10.1101/249516v1?rss=1 Probst, A. J. Banfield, J. F. 2018-01-17 doi:10.1101/249516 Cold Spring Harbor Laboratory Press 2018-01-17 <![CDATA[ Observation weights to unlock bulk RNA-seq tools for zero inflation and single-cell applications ]]> https://biorxiv.org/content/10.1101/250126v1?rss=1 Van den Berge, K. Perraudeau, F. Soneson, C. Love, M. I. Risso, D. Vert, J.-P. Robinson, M. D. Dudoit, S. Clement, L. 2018-01-18 doi:10.1101/250126 Cold Spring Harbor Laboratory Press 2018-01-18 <![CDATA[ Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy ]]> https://biorxiv.org/content/10.1101/250241v1?rss=1 90% drove expression patterns. We achieved 86.7% precision on a genome-wide scan, with an estimated recall of at least 98%, indicating high accuracy and completeness in annotating this class of functional elements.nnSignificance StatementWe demonstrate a high accuracy method for predicting enhancers genome wide with > 85% precision as validated by transgenic reporter assays in Drosophila embryos. This is the first time such accuracy has been achieved in a metazoan system, allowing us to predict with high-confidence 1640 enhancers, 916 of which are novel. The predicted enhancers are demarcated by heterogeneous collections of epigenetic marks; many strong enhancers are free from classical indicators of activity, including H3K27ac, but are bound by key transcription factors. H3K27ac, often used as a one-dimensional predictor of enhancer activity, is an uninformative parameter in our data. ]]> Arbel, H. Fisher, W. W. Hammonds, A. S. Wan, K. H. Park, S. Weiszmann, R. Keranen, S. Henriquez, C. Solari, O. S. Bickel, P. J. Biggin, M. Celniker, S. E. Brown, J. B. 2018-01-18 doi:10.1101/250241 Cold Spring Harbor Laboratory Press 2018-01-18 <![CDATA[ Size-dependent segregation controls macrophage phagocytosis of antibody-opsonized targets ]]> https://biorxiv.org/content/10.1101/250373v1?rss=1 10 nm from the target surface. Increasing antigen height allows for co-localization of Fc receptors and the inhibitory phosphatase CD45 at the cell-cell interface, which reduces Fc receptor phosphorylation, and inhibits phagocytosis. Our work shows that close contact between macrophage and target cell is a requirement for efficient phagocytosis, suggesting that therapeutic antibodies should target short antigens in order to trigger Fc receptor activation through size-dependent physical segregation. ]]> Bakalar, M. H. Joffe, A. M. Schmid, E. Son, S. Podolski, M. Fletcher, D. A. 2018-01-19 doi:10.1101/250373 Cold Spring Harbor Laboratory Press 2018-01-19 <![CDATA[ Fine-tuning of substrate preferences of the Src-family kinase Lck revealed through a high-throughput specificity screen ]]> https://biorxiv.org/content/10.1101/250753v1?rss=1 Shah, N. H. Löbel, M. Weiss, A. Kuriyan, J. 2018-01-19 doi:10.1101/250753 Cold Spring Harbor Laboratory Press 2018-01-19 <![CDATA[ The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000 ]]> https://biorxiv.org/content/10.1101/254797v1?rss=1 Dudchenko, O. Shamim, M. S. Batra, S. Durand, N. C. Musial, N. T. Mostofa, R. Pham, M. Glenn St Hilaire, B. Yao, W. Stamenova, E. Hoeger, M. Nyquist, S. K. Korchina, V. Pletch, K. Flanagan, J. P. Tomaszewicz, A. McAloose, D. Perez Estrada, C. Novak, B. J. Omer, A. D. Aiden, E. L. 2018-01-28 doi:10.1101/254797 Cold Spring Harbor Laboratory Press 2018-01-28 <![CDATA[ Spindle assembly in egg extracts of the Marsabit clawed frog, Xenopus borealis ]]> https://biorxiv.org/content/10.1101/254979v1?rss=1 Kitaoka, M. Heald, R. Gibeaux, R. 2018-01-27 doi:10.1101/254979 Cold Spring Harbor Laboratory Press 2018-01-27 <![CDATA[ MicroPheno: Predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples ]]> https://biorxiv.org/content/10.1101/255018v1?rss=1 Asgari, E. Garakani, K. McHardy, A. C. Mofrad, M. R. K. 2018-01-28 doi:10.1101/255018 Cold Spring Harbor Laboratory Press 2018-01-28 <![CDATA[ Identification of transcriptional signatures for cell types from single-cell RNA-Seq ]]> https://biorxiv.org/content/10.1101/258566v1?rss=1 Ntranos, V. Yi, L. Melsted, P. Pachter, L. 2018-02-01 doi:10.1101/258566 Cold Spring Harbor Laboratory Press 2018-02-01 <![CDATA[ Convergent evolution of gene expression in two high-toothed stickleback populations ]]> https://biorxiv.org/content/10.1101/259499v1?rss=1 Hart, J. C. Ellis, N. A. Eisen, M. B. Miller, C. T. 2018-02-03 doi:10.1101/259499 Cold Spring Harbor Laboratory Press 2018-02-03 <![CDATA[ mRNA expression-mediated gene repression in human cells ]]> https://biorxiv.org/content/10.1101/264721v1?rss=1 Hollerer, I. Barker, J. C. Jorgensen, V. Tresenrider, A. Dugast-Darzacq, C. Darzacq, X. Chan, L. Y. Tjian, R. Ünal, E. Brar, G. A. 2018-02-13 doi:10.1101/264721 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ MethCP: Differentially Methylated Region Detection with Change Point Models ]]> https://biorxiv.org/content/10.1101/265116v1?rss=1 Gong, B. Purdom, E. 2018-02-13 doi:10.1101/265116 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ Selective activation of alternative MYC core promoters by Wnt-responsive enhancers ]]> https://biorxiv.org/content/10.1101/266387v1?rss=1 Bardales, J. A. Wieser, E. Kawaji, H. Murakawa, Y. Darzacq, X. 2018-03-05 doi:10.1101/266387 Cold Spring Harbor Laboratory Press 2018-03-05 <![CDATA[ A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks ]]> https://biorxiv.org/content/10.1101/267211v1?rss=1 Chan, J. Perrone, V. Spence, J. P. Jenkins, P. A. Mathieson, S. Song, Y. S. 2018-02-18 doi:10.1101/267211 Cold Spring Harbor Laboratory Press 2018-02-18 <![CDATA[ Collective motion conceals fitness differences in crowded cellular populations ]]> https://biorxiv.org/content/10.1101/267286v1?rss=1 Kayser, J. Schreck, C. Gralka, M. Fusco, D. Hallatschek, O. 2018-02-18 doi:10.1101/267286 Cold Spring Harbor Laboratory Press 2018-02-18 <![CDATA[ TRPV4 is the temperature-sensitive ion channel of human sperm ]]> https://biorxiv.org/content/10.1101/268409v1?rss=1 Mundt, N. Spehr, M. Lishko, P. V. 2018-02-20 doi:10.1101/268409 Cold Spring Harbor Laboratory Press 2018-02-20 <![CDATA[ Multimodal on-axis platform for all-optical electrophysiology with near-infrared probes in human stem-cell-derived cardiomyocytes ]]> https://biorxiv.org/content/10.1101/269258v1?rss=1 Klimas, A. Ortiz, G. Boggess, S. Miller, E. W. Entcheva, E. 2018-02-21 doi:10.1101/269258 Cold Spring Harbor Laboratory Press 2018-02-21 <![CDATA[ An Integrin-Independent Kaposi’s Sarcoma-Associated Herpesvirus Infection Mechanism ]]> https://biorxiv.org/content/10.1101/270108v1?rss=1 TerBush, A. A. Hafkamp, F. Hartenian, E. Lee, H. J. Glaunsinger, B. A. Coscoy, L. 2018-02-22 doi:10.1101/270108 Cold Spring Harbor Laboratory Press 2018-02-22 <![CDATA[ Serial Dependence in Position Perception Occurs at the Time of Perception ]]> https://biorxiv.org/content/10.1101/270272v1?rss=1 Manassi, M. Liberman, A. Kosovicheva, A. Zhang, K. Whitney, D. 2018-02-25 doi:10.1101/270272 Cold Spring Harbor Laboratory Press 2018-02-25 <![CDATA[ Deep mutational analysis reveals functional trade-offs in the sequences of EGFR autophosphorylation sites ]]> https://biorxiv.org/content/10.1101/273516v1?rss=1 Cantor, A. J. Shah, N. H. Kuriyan, J. 2018-02-28 doi:10.1101/273516 Cold Spring Harbor Laboratory Press 2018-02-28 <![CDATA[ The ecology of the Drosophila-yeast mutualism in wineries ]]> https://biorxiv.org/content/10.1101/273839v1?rss=1 Quan, A. S. Eisen, M. B. 2018-02-28 doi:10.1101/273839 Cold Spring Harbor Laboratory Press 2018-02-28 <![CDATA[ Atlastins mediate selective autophagy of the endoplasmic reticulum ]]> https://biorxiv.org/content/10.1101/274530v1?rss=1 Liang, A. Lingeman, E. Ahmed, S. Corn, J. 2018-03-01 doi:10.1101/274530 Cold Spring Harbor Laboratory Press 2018-03-01 <![CDATA[ In vitro transcribed guide RNAs trigger an innate immune response via the RIG-I pathway ]]> https://biorxiv.org/content/10.1101/275669v1?rss=1 Weinert, B. Shin, J. Zelin, E. Pestal, K. Corn, J. E. 2018-03-03 doi:10.1101/275669 Cold Spring Harbor Laboratory Press 2018-03-03 <![CDATA[ A streamlined method for transposon mutagenesis of Rickettsia parkeri yields numerous mutations that impact infection ]]> https://biorxiv.org/content/10.1101/277160v1?rss=1 Lamason, R. L. Kafai, N. M. Welch, M. D. 2018-03-08 doi:10.1101/277160 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ Capturing diverse microbial sequence with comprehensive and scalable probe design ]]> https://biorxiv.org/content/10.1101/279570v1?rss=1 Siddle, K. J. Metsky, H. C. Gladden-Young, A. Qu, J. Yang, D. K. Brehio, P. Goldfarb, A. Piantadosi, A. Wohl, S. Lin, A. E. Barnes, K. G. Tully, D. C. Hennigan, S. Barbosa-Lima, G. Vieira, Y. R. Paul, L. M. Tan, A. L. Garcia, K. F. Parham, L. A. Odia, I. Eromon, P. Folarin, O. A. Goba, A. Viral Hemorrhagic Fever Consortium, Simon-Loriere, E. Hensley, L. Balmaseda, A. Harris, E. Allen, T. M. Runstadler, J. A. Smole, S. Bozza, F. A. Souza, T. M. Isern, S. Michael, S. F. Lorenzana, I. Gehrke, L. Bosch, I. Ebel, G. Happi, C. Grant, D. Park, D. J. Gnirke, 2018-03-12 doi:10.1101/279570 Cold Spring Harbor Laboratory Press 2018-03-12 <![CDATA[ clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets ]]> https://biorxiv.org/content/10.1101/280545v1?rss=1 Risso, D. Purvis, L. Fletcher, R. Das, D. Ngai, J. Dudoit, S. Purdom, E. 2018-03-12 doi:10.1101/280545 Cold Spring Harbor Laboratory Press 2018-03-12 <![CDATA[ Spatial summation in the human fovea: the effect of optical aberrations and fixational eye movements ]]> https://biorxiv.org/content/10.1101/283119v1?rss=1 Tuten, W. S. Cooper, R. F. Tiruveedhula, P. Dubra, A. Roorda, A. Cottaris, N. P. Brainard, D. H. Morgan, J. I. W. 2018-03-15 doi:10.1101/283119 Cold Spring Harbor Laboratory Press 2018-03-15 <![CDATA[ Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA ]]> https://biorxiv.org/content/10.1101/283812v1?rss=1 Welkie, D. G. Rubin, B. E. Chang, Y.-G. Diamond, S. Rifkin, S. A. LiWang, A. Golden, S. S. 2018-03-17 doi:10.1101/283812 Cold Spring Harbor Laboratory Press 2018-03-17 <![CDATA[ NRG1 is required for the function of the TIR-NLR immune receptors Roq1 and RPP1 in Nicotiana benthamiana ]]> https://biorxiv.org/content/10.1101/284471v1?rss=1 Staskawicz, B. Qi, T. Schultink, A. Cho, M.-J. Pham, J. 2018-03-18 doi:10.1101/284471 Cold Spring Harbor Laboratory Press 2018-03-18 <![CDATA[ Orbitofrontal cortex, dorsolateral prefrontal cortex, and hippocampus represent the magnitude of event saliency ]]> https://biorxiv.org/content/10.1101/285718v1?rss=1 Jafarpour, A. Griffin, S. Lin, J. J. Knight, R. T. 2018-03-21 doi:10.1101/285718 Cold Spring Harbor Laboratory Press 2018-03-21 <![CDATA[ Efficiently inferring the demographic history of many populations with allele count data ]]> https://biorxiv.org/content/10.1101/287268v1?rss=1 Kamm, J. A. Terhorst, J. Durbin, R. Song, Y. S. 2018-03-23 doi:10.1101/287268 Cold Spring Harbor Laboratory Press 2018-03-23 <![CDATA[ Asymmetrically Positioned Flagellar Control Units Regulate Human Sperm Rotation ]]> https://biorxiv.org/content/10.1101/290122v1?rss=1 Miller, M. Kenny, S. Mannowetz, N. Mansell, S. Wojcik, M. Mendoza, S. Zucker, R. Xu, K. Lishko, P. V. 2018-03-27 doi:10.1101/290122 Cold Spring Harbor Laboratory Press 2018-03-27 <![CDATA[ Probing the Acyl Carrier Protein-Enzyme Interactions within Terminal Alkyne Biosynthetic Machinery ]]> https://biorxiv.org/content/10.1101/291195v1?rss=1 Su, M. Zhu, X. Zhang, W. 2018-03-29 doi:10.1101/291195 Cold Spring Harbor Laboratory Press 2018-03-29 <![CDATA[ Geometry-dependent instabilities in electrically excitable tissues ]]> https://biorxiv.org/content/10.1101/291617v1?rss=1 McNamara, H. M. Dodson, S. Huang, Y.-L. Miller, E. W. Sandstede, B. Cohen, A. E. 2018-04-02 doi:10.1101/291617 Cold Spring Harbor Laboratory Press 2018-04-02 <![CDATA[ Using a System’s Equilibrium Behavior to Reduce Its Energy Dissipation in Non-Equilibrium Processes ]]> https://biorxiv.org/content/10.1101/291989v1?rss=1 Tafoya, S. Large, S. Liu, S. Bustamante, C. Sivak, D. 2018-03-30 doi:10.1101/291989 Cold Spring Harbor Laboratory Press 2018-03-30 <![CDATA[ Bayesian Inference for a Generative Model of Transcriptome Profiles from Single-cell RNA Sequencing ]]> https://biorxiv.org/content/10.1101/292037v1?rss=1 Lopez, R. Regier, J. Cole, M. B. Jordan, M. Yosef, N. 2018-03-30 doi:10.1101/292037 Cold Spring Harbor Laboratory Press 2018-03-30 <![CDATA[ The Genomic Formation of South and Central Asia ]]> https://biorxiv.org/content/10.1101/292581v1?rss=1 Narasimhan, V. M. Patterson, N. J. Moorjani, P. Lazaridis, I. Mark, L. Mallick, S. Rohland, N. Bernardos, R. Kim, A. M. Nakatsuka, N. Olalde, I. Coppa, A. Mallory, J. Moiseyev, V. Monge, J. Olivieri, L. M. Adamski, N. Broomandkhoshbacht, N. Candilio, F. Cheronet, O. Culleton, B. J. Ferry, M. Fernandes, D. Gamarra, B. Gaudio, D. Hajdinjak, M. Harney, E. Harper, T. K. Keating, D. Lawson, A.-M. Michel, M. Novak, M. Oppenheimer, J. Rai, N. Sirak, K. Slon, V. Stewardson, K. Zhang, Z. Akhatov, G. Bagashev, A. N. Baitanayev, B. Bonora, G. L. Chikisheva, T. D 2018-03-31 doi:10.1101/292581 Cold Spring Harbor Laboratory Press 2018-03-31 <![CDATA[ Directional selection limits ecological diversification and promotes ecological tinkering during the competition for substitutable resources ]]> https://biorxiv.org/content/10.1101/292821v1?rss=1 Good, B. H. Martis, S. Hallatschek, O. 2018-03-31 doi:10.1101/292821 Cold Spring Harbor Laboratory Press 2018-03-31 <![CDATA[ Microbial diversity and metabolic potential in cyanotoxin producing cyanobacterial mats throughout a river network ]]> https://biorxiv.org/content/10.1101/294421v1?rss=1 Bouma-Gregson, K. Olm, M. R. Probst, A. J. Anantharaman, K. Power, M. E. Banfield, J. F. 2018-04-03 doi:10.1101/294421 Cold Spring Harbor Laboratory Press 2018-04-03 <![CDATA[ CagY-dependent regulation of type IV secretion in Helicobacter pylori is associated with alterations in integrin binding ]]> https://biorxiv.org/content/10.1101/294769v1?rss=1 Skoog, E. Morikis, V. A. Martin, M. E. Foster, G. A. Cai, L. P. Hansen, L. M. Li, B. Gaddy, J. A. Simon, S. Solnick, J. V. 2018-04-04 doi:10.1101/294769 Cold Spring Harbor Laboratory Press 2018-04-04 <![CDATA[ Telomere length set point regulation in human pluripotent stem cells critically depends on the shelterin protein TPP1 ]]> https://biorxiv.org/content/10.1101/298778v1?rss=1 Boyle, J. M. Hennick, K. M. Regalado, S. G. Vogan, J. Zhang, X. Collins, K. Hockemeyer, D. 2018-04-10 doi:10.1101/298778 Cold Spring Harbor Laboratory Press 2018-04-10 <![CDATA[ Spatial soft sweeps: patterns of adaptation in populations with long-range dispersal ]]> https://biorxiv.org/content/10.1101/299453v1?rss=1 Paulose, J. Hermisson, J. Hallatschek, O. 2018-04-11 doi:10.1101/299453 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ Parameterizing neural power spectra ]]> https://biorxiv.org/content/10.1101/299859v1?rss=1 Haller, M. Donoghue, T. Peterson, E. Varma, P. Sebastian, P. Gao, R. Noto, T. Knight, R. T. Shestyuk, A. Voytek, B. 2018-04-11 doi:10.1101/299859 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ Trypanosomes have divergent kinesin-2 proteins that function differentially in IFT, cell division, and motility ]]> https://biorxiv.org/content/10.1101/301127v1?rss=1 Douglas, R. L. Haltiwanger, B. M. Wu, H. Jeng, R. L. Mancuso, J. Cande, W. Z. Welch, M. D. 2018-04-13 doi:10.1101/301127 Cold Spring Harbor Laboratory Press 2018-04-13 <![CDATA[ Controlled cycling and quiescence enables homology directed repair in engraftment-enriched adult hematopoietic stem and progenitor cells ]]> https://biorxiv.org/content/10.1101/301176v1?rss=1 Shin, J. Wyman, S. K. DeWitt, M. A. Bray, N. L. Vu, J. Corn, J. 2018-04-13 doi:10.1101/301176 Cold Spring Harbor Laboratory Press 2018-04-13 <![CDATA[ Retracing the Hawaiian silversword radiation despite phylogenetic, biogeographic, and paleogeographic uncertainty ]]> https://biorxiv.org/content/10.1101/301887v1?rss=1 Landis, M. J. Freyman, W. A. Baldwin, B. G. 2018-04-17 doi:10.1101/301887 Cold Spring Harbor Laboratory Press 2018-04-17 <![CDATA[ Design and analysis of a Proportional-Integral-Derivative controller with biological molecules ]]> https://biorxiv.org/content/10.1101/303545v1?rss=1 Chevalier, M. Gomez-Schiavon, M. Ng, A. El-Samad, H. 2018-04-18 doi:10.1101/303545 Cold Spring Harbor Laboratory Press 2018-04-18 <![CDATA[ Myelinated inhibitory axons in human neocortex ]]> https://biorxiv.org/content/10.1101/306480v1?rss=1 Micheva, K. D. Chang, E. F. Nana, A. L. Seeley, W. W. Ting, J. T. Cobbs, C. Lein, E. Smith, S. J. Weinberg, R. J. Madison, D. V. 2018-04-23 doi:10.1101/306480 Cold Spring Harbor Laboratory Press 2018-04-23 <![CDATA[ Isonitrile Formation by a Non-heme Iron(II)-dependent Oxidase/Decarboxylase ]]> https://biorxiv.org/content/10.1101/308460v1?rss=1 Harris, N. C. Born, D. A. Cai, W. Huang, Y. Martin, J. Khalaf, R. Drennan, C. L. Zhang, W. 2018-04-25 doi:10.1101/308460 Cold Spring Harbor Laboratory Press 2018-04-25 <![CDATA[ Disturbance macroecology: integrating disturbance ecology and macroecology in different-age post-fire stands of a closed-cone pine forest as a case study ]]> https://biorxiv.org/content/10.1101/309419v1?rss=1 Newman, E. A. Wilber, M. Q. Kopper, K. E. Moritz, M. A. Falk, D. A. McKenzie, D. Harte, J. 2018-04-28 doi:10.1101/309419 Cold Spring Harbor Laboratory Press 2018-04-28 <![CDATA[ Claudin-4 Reconstituted in Unilamellar Vesicles is Sufficient to Form Tight Interfaces that Partition Membrane Proteins ]]> https://biorxiv.org/content/10.1101/309856v1?rss=1 Belardi, B. Son, S. Vahey, M. D. Wang, J. Hou, J. Fletcher, D. A. 2018-04-27 doi:10.1101/309856 Cold Spring Harbor Laboratory Press 2018-04-27 <![CDATA[ Redox fluctuations control the coupled cycling of iron and carbon in tropical forest soils ]]> https://biorxiv.org/content/10.1101/312108v1?rss=1 nView larger version (23K):norg.highwire.dtl.DTLVardef@add07borg.highwire.dtl.DTLVardef@15269bforg.highwire.dtl.DTLVardef@19ca034org.highwire.dtl.DTLVardef@1d9d793_HPS_FORMAT_FIGEXP M_FIG Toc Art C_FIG ]]> Bhattacharyya, A. Campbell, A. N. Tfaily, M. M. Lin, Y. Silver, W. L. Nico, P. S. Pett-Ridge, J. 2018-05-01 doi:10.1101/312108 Cold Spring Harbor Laboratory Press 2018-05-01 <![CDATA[ Optical alignment device for two-photon microscopy ]]> https://biorxiv.org/content/10.1101/312207v1?rss=1 Galinanes, G. Marchand, P. J. Turcotte, R. Pellat, S. Ji, N. Huber, D. 2018-05-01 doi:10.1101/312207 Cold Spring Harbor Laboratory Press 2018-05-01 <![CDATA[ Differential contributions of subthalamic beta rhythms and neural noise to Parkinson motor symptoms ]]> https://biorxiv.org/content/10.1101/312819v1?rss=1 Martin, S. Iturrate, I. Chavarriaga, R. Leeb, R. Sobolewski, A. Li, A. M. Zaldivar, J. Peciu-Florianu, I. Pralong, E. Castro-Jimenez, M. Benninger, D. Vingerhoets, F. Knight, R. T. Bloch, J. Millan, J. d. R. 2018-05-02 doi:10.1101/312819 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Analysis of 19 Highly Conserved Vibrio cholerae Bacteriophages Isolated from Environmental and Patient Sources Over a Twelve-Year Period ]]> https://biorxiv.org/content/10.1101/313346v1?rss=1 Angermeyer, A. Das, M. M. Singh, D. V. Seed, K. D. 2018-05-02 doi:10.1101/313346 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Early transcriptional responses after dengue vaccination mirror the response to natural infection and predict neutralizing antibody titers ]]> https://biorxiv.org/content/10.1101/314377v1?rss=1 200 versus 21 post-vaccination; 3,210 versus 286 transcripts with significant fold-change), but shared gene modules were induced in the same sequence. The abundance of 131 transcripts on days 8 and 9 post-vaccination was strongly correlated with NAb titers measured 6 weeks post-vaccination.nnConclusionsLAV dengue vaccination elicits early transcriptional responses that mirror those found in symptomatic natural infection and provide candidate early markers of protection against DENV infection.nnClinical Trial Registration Number: NCT00831012 (available at clinicaltrials.gov)nnSummary: Interferon- and cell cycle-associated gene transcript abundance levels in the peripheral blood of dengue vaccine recipients on days 8 and 9 post-vaccination were associated with dengue neutralizing antibody titers on day 42, and mirrored responses in primary dengue infection, suggesting the possibility of predicting protective immunity. ]]> Popper, S. J. Strouts, F. R. Lindow, J. C. Cheng, H. K. Montoya, M. Balmaseda, A. Durbin, A. P. Whitehead, S. S. Harris, E. Kirkpatrick, B. D. Relman, D. A. 2018-05-06 doi:10.1101/314377 Cold Spring Harbor Laboratory Press 2018-05-06 <![CDATA[ Evidence of a Novel Vitivirus in Grapevine cv Riesling ]]> https://biorxiv.org/content/10.1101/314674v1?rss=1 Debat, H. J. Zavallo, D. Gomez-Talquenca, S. Asurmendi, S. 2018-05-04 doi:10.1101/314674 Cold Spring Harbor Laboratory Press 2018-05-04 <![CDATA[ Estrogen Signaling in Arcuate Kiss1 Neurons Suppresses a Sex-Dependent Circuit That Promotes Dense Strong Bones in Female Mice ]]> https://biorxiv.org/content/10.1101/315283v1?rss=1 Herber, C. B. Krause, W. C. Wang, L. Bayrer, J. R. Li, A. Schmitz, M. Fields, A. Ford, B. Reid, M. S. Nomura, D. K. Nissenson, R. A. Correa, S. Ingraham, H. A. 2018-05-05 doi:10.1101/315283 Cold Spring Harbor Laboratory Press 2018-05-05 <![CDATA[ Structural basis for selective stalling of human ribosome nascent chain complexes by a drug-like molecule ]]> https://biorxiv.org/content/10.1101/315325v1?rss=1 Li, W. McClure, K. Montabana, E. Liras, S. Dullea, R. Cate, J. 2018-05-05 doi:10.1101/315325 Cold Spring Harbor Laboratory Press 2018-05-05 <![CDATA[ Highly Multiplexed Single-Cell RNA-seq for Defining Cell Population and Transcriptional Spaces ]]> https://biorxiv.org/content/10.1101/315333v1?rss=1 Gehring, J. Park, J. H. Chen, S. Thomson, M. Pachter, L. 2018-05-05 doi:10.1101/315333 Cold Spring Harbor Laboratory Press 2018-05-05 <![CDATA[ Orthogonal regulation of ferritin translation by human eIF3 and the iron response proteins ]]> https://biorxiv.org/content/10.1101/316299v1?rss=1 Pulos, M. C. Srole, D. N. McSwiggen, D. T. Ingolia, N. T. Cate, J. 2018-05-08 doi:10.1101/316299 Cold Spring Harbor Laboratory Press 2018-05-08 <![CDATA[ Functional degradation: a mechanism of NLRP1 inflammasome activation by diverse pathogen enzymes ]]> https://biorxiv.org/content/10.1101/317834v1?rss=1 Sandstrom, A. Mitchell, P. S. Goers, L. Mu, E. W. Lesser, C. F. Vance, R. E. 2018-05-09 doi:10.1101/317834 Cold Spring Harbor Laboratory Press 2018-05-09 <![CDATA[ Site specific target binding controls RNA cleavage efficiency by the Kaposi’s sarcoma-associated herpesvirus endonuclease SOX ]]> https://biorxiv.org/content/10.1101/320929v1?rss=1 Mendez, A. S. Vogt, C. Bohne, J. Glaunsinger, B. A. 2018-05-13 doi:10.1101/320929 Cold Spring Harbor Laboratory Press 2018-05-13 <![CDATA[ A high-density carbon fiber neural recording array technology ]]> https://biorxiv.org/content/10.1101/320937v1?rss=1 Massey, T. L. Santacruz, S. R. Hou, J. F. Pister, K. S. Carmena, J. M. Maharbiz, M. M. 2018-05-13 doi:10.1101/320937 Cold Spring Harbor Laboratory Press 2018-05-13 <![CDATA[ Kaposi’s sarcoma-associated herpesvirus ORF68 is a DNA binding protein required for viral genome cleavage and packaging ]]> https://biorxiv.org/content/10.1101/322719v1?rss=1 Gardner, M. R. Glaunsinger, B. A. 2018-05-15 doi:10.1101/322719 Cold Spring Harbor Laboratory Press 2018-05-15 <![CDATA[ Rampant cryptic sex chromosome drive in Drosophila ]]> https://biorxiv.org/content/10.1101/324368v1?rss=1 Bachtrog, D. Ellison, C. Leonard, C. Landeen, E. Gibilisco, L. Phadnis, N. 2018-05-16 doi:10.1101/324368 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ When parasites are selected to kill the young ]]> https://biorxiv.org/content/10.1101/324632v1?rss=1 Iritani, R. Visher, E. Boots, M. 2018-05-20 doi:10.1101/324632 Cold Spring Harbor Laboratory Press 2018-05-20 <![CDATA[ Common Neural Code for Reward and Information Value ]]> https://biorxiv.org/content/10.1101/324665v1?rss=1 Kobayashi, K. Hsu, M. 2018-05-17 doi:10.1101/324665 Cold Spring Harbor Laboratory Press 2018-05-17 <![CDATA[ De novo assembly of a young Drosophila Y chromosome using Single-Molecule sequencing and Chromatin Conformation capture ]]> https://biorxiv.org/content/10.1101/324673v1?rss=1 100Mb of the recently formed highly repetitive neo-Y chromosome. While Y chromosome evolution is typically characterized by global sequence loss and shrinkage, the neo-Y increased in size by almost 3-fold, due to the accumulation of repetitive sequences. Our high-quality assembly allows us to reconstruct the chromosomal events that have led to the unusual sex chromosome karyotype in D. miranda, including the independent de novo formation of a pair of sex chromosomes at two distinct time points, or the reversion of a former Y chromosome to an autosome. ]]> Mahajan, S. Wei, K. Nalley, M. Gibilisco, L. Bachtrog, D. 2018-05-21 doi:10.1101/324673 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ Overlooked roles of DNA damage and maternal age in generating human germline mutations ]]> https://biorxiv.org/content/10.1101/327098v1?rss=1 Gao, Z. Moorjani, P. Amster, G. Przeworski, M. 2018-05-21 doi:10.1101/327098 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ Hydrogen-based metabolism - An ancestral trait in lineages sibling to the Cyanobacteria ]]> https://biorxiv.org/content/10.1101/328856v1?rss=1 Matheus Carnevali, P. B. Schulz, F. Castelle, C. J. Kantor, R. Shih, P. Sharon, I. Santini, J. Olm, M. Amano, Y. Thomas, B. C. Anantharaman, K. Burstein, D. Becraft, E. D. Stepanauskas, R. Woyke, T. Banfield, J. F. 2018-05-25 doi:10.1101/328856 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Low fidelity assembly of influenza A virus promotes escape from host cells ]]> https://biorxiv.org/content/10.1101/332650v1?rss=1 Vahey, M. D. Fletcher, D. A. 2018-05-28 doi:10.1101/332650 Cold Spring Harbor Laboratory Press 2018-05-28 <![CDATA[ Tracing a proteins folding pathway over evolutionary time using ancestral sequence reconstruction and hydrogen exchange ]]> https://biorxiv.org/content/10.1101/334607v1?rss=1 Lim, S. A. Bolin, E. R. Marqusee, S. 2018-05-30 doi:10.1101/334607 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ Nucleotide-pair encoding of 16S rRNA sequences for host phenotype and biomarker detection ]]> https://biorxiv.org/content/10.1101/334722v1?rss=1 Asgari, E. Münch, P. C. Lesker, T. R. McHardy, A. C. Mofrad, M. R. K. 2018-05-30 doi:10.1101/334722 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ Binary transcriptional control of pattern formation in development ]]> https://biorxiv.org/content/10.1101/335919v1?rss=1 Lammers, N. C. Galstyan, V. Reimer, A. Medin, S. A. Wiggins, C. H. Garcia, H. G. 2018-05-31 doi:10.1101/335919 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ A geometric attractor mechanism for self-organization of entorhinal grid modules ]]> https://biorxiv.org/content/10.1101/338087v1?rss=1 Kang, L. Balasubramanian, V. 2018-06-04 doi:10.1101/338087 Cold Spring Harbor Laboratory Press 2018-06-04 <![CDATA[ Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics ]]> https://biorxiv.org/content/10.1101/342006v1?rss=1 Shelton, A. N. Seth, E. C. Mok, K. C. Han, A. W. Jackson, S. N. Haft, D. R. Taga, M. E. 2018-06-08 doi:10.1101/342006 Cold Spring Harbor Laboratory Press 2018-06-08 <![CDATA[ A robust method for transfection in choanoflagellates illuminates their cell biology and the ancestry of animal septins ]]> https://biorxiv.org/content/10.1101/343111v1?rss=1 Booth, D. Middleton, H. King, N. 2018-06-09 doi:10.1101/343111 Cold Spring Harbor Laboratory Press 2018-06-09 <![CDATA[ Whole-genome analysis of introgression between the spotted owl and barred owl (Strix occidentalis and Strix varia, respectively; Aves: Strigidae) in western North America ]]> https://biorxiv.org/content/10.1101/343202v1?rss=1 Hanna, Z. R. Dumbacher, J. P. Bowie, R. C. K. Henderson, J. B. Wall, J. D. 2018-06-11 doi:10.1101/343202 Cold Spring Harbor Laboratory Press 2018-06-11 <![CDATA[ Whole-genome sequences suggest long term declines of spotted owl (Strix occidentalis) (Aves: Strigiformes: Strigidae) populations in California ]]> https://biorxiv.org/content/10.1101/343434v1?rss=1 Hanna, Z. R. Dumbacher, J. P. Bowie, R. C. K. Wall, J. D. 2018-06-11 doi:10.1101/343434 Cold Spring Harbor Laboratory Press 2018-06-11 <![CDATA[ Probabilistic variable-length segmentation of protein sequences for discriminative motif mining (DiMotif)and sequence embedding (ProtVecX) ]]> https://biorxiv.org/content/10.1101/345843v1?rss=1 Asgari, E. McHardy, A. Mofrad, M. R. K. 2018-06-13 doi:10.1101/345843 Cold Spring Harbor Laboratory Press 2018-06-13 <![CDATA[ Nominally non-responsive frontal and sensory cortical cells encode task-relevant variables via ensemble consensus-building ]]> https://biorxiv.org/content/10.1101/347617v1?rss=1 Insanally, M. N. Carcea, I. Field, R. E. Rodgers, C. C. DePasquale, B. Rajan, K. DeWeese, M. R. Albanna, B. F. Froemke, R. C. 2018-06-14 doi:10.1101/347617 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ A small single-domain protein folds through the same pathway on- and off- the ribosome ]]> https://biorxiv.org/content/10.1101/347864v1?rss=1 Guinn, E. J. Tian, P. Shin, M. Best, R. B. Marqusee, S. 2018-06-15 doi:10.1101/347864 Cold Spring Harbor Laboratory Press 2018-06-15 <![CDATA[ MGDrivE: A modular simulation framework for the spread of gene drives through spatially-explicit mosquito populations ]]> https://biorxiv.org/content/10.1101/350488v1?rss=1 Sanchez C., H. M. Wu, S. L. Bennett, J. B. Marshall, J. M. 2018-06-19 doi:10.1101/350488 Cold Spring Harbor Laboratory Press 2018-06-19 <![CDATA[ Modulating long-range energetics via helix stabilization: a case study using T4 lysozyme ]]> https://biorxiv.org/content/10.1101/353649v1?rss=1 Rosemond, S. N. Hamadani, K. M. Cate, J. H. D. Marqusee, S. 2018-06-22 doi:10.1101/353649 Cold Spring Harbor Laboratory Press 2018-06-22 <![CDATA[ Kluyveromyces marxianus as a robust synthetic biology platform host ]]> https://biorxiv.org/content/10.1101/353680v1?rss=1 Cernak, P. Estrela, R. Poddar, S. Skerker, J. Cheng, Y.-F. Carlson, A. Chen, B. Glynn, V. Furlan, M. Ryan, O. Donnelly, M. Arkin, A. P. Taylor, J. Cate, J. 2018-06-22 doi:10.1101/353680 Cold Spring Harbor Laboratory Press 2018-06-22 <![CDATA[ Scrublet: computational identification of cell doublets in single-cell transcriptomic data ]]> https://biorxiv.org/content/10.1101/357368v1?rss=1 Wolock, S. L. Lopez, R. Klein, A. M. 2018-07-09 doi:10.1101/357368 Cold Spring Harbor Laboratory Press 2018-07-09 <![CDATA[ Differences in the path to exit the ribosome across the three domains of life ]]> https://biorxiv.org/content/10.1101/357970v1?rss=1 Dao Duc, K. Batra, S. S. Bhattacharya, N. Cate, J. H. D. Song, Y. S. 2018-06-28 doi:10.1101/357970 Cold Spring Harbor Laboratory Press 2018-06-28 <![CDATA[ Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale ]]> https://biorxiv.org/content/10.1101/358572v1?rss=1 Krehenwinkel, H. Pomerantz, A. Henderson, J. B. Kennedy, S. R. Lim, J. Y. Swamy, V. Shoobridge, J. D. Patel, N. H. Gillespie, R. G. Prost, S. 2018-06-29 doi:10.1101/358572 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Fst between archaic and present-day samples ]]> https://biorxiv.org/content/10.1101/362053v1?rss=1 Ortega-Del Vecchyo, D. Slatkin, M. 2018-07-04 doi:10.1101/362053 Cold Spring Harbor Laboratory Press 2018-07-04 <![CDATA[ Intrinsic rewards modulate sensorimotor adaptation ]]> https://biorxiv.org/content/10.1101/363606v1?rss=1 Kim, H. Parvin, D. Ivry, R. 2018-07-06 doi:10.1101/363606 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ Smart bone plates can monitor fracture healing ]]> https://biorxiv.org/content/10.1101/366039v1?rss=1 Lin, M. C. Hu, D. Marmor, M. Herfat, S. T. Bahney, C. S. Maharbiz, M. M. 2018-07-10 doi:10.1101/366039 Cold Spring Harbor Laboratory Press 2018-07-10 <![CDATA[ Inversion and computational maturation of drug response using human stem cell derived cardiomyocytes in microphysiological systems ]]> https://biorxiv.org/content/10.1101/366617v1?rss=1 Tveito, A. Jaeger, K. H. Huebsch, N. Charrez, B. Edwards, A. G. Wall, S. Healy, K. E. 2018-07-10 doi:10.1101/366617 Cold Spring Harbor Laboratory Press 2018-07-10 <![CDATA[ Feasibility of Functional MRI at Ultralow Magnetic Field via Changes in Cerebral Blood Volume ]]> https://biorxiv.org/content/10.1101/366955v1?rss=1 Buckenmaier, K. Pedersen, A. SanGiorgio, P. Scheffler, K. Clarke, J. Inglis, B. 2018-07-11 doi:10.1101/366955 Cold Spring Harbor Laboratory Press 2018-07-11 <![CDATA[ Apparent thinning of visual cortex during childhood is associated with myelination, not pruning ]]> https://biorxiv.org/content/10.1101/368274v1?rss=1 Natu, V. S. Gomez, J. Barnett, M. Jeska, B. Kirilina, E. Jaeger, C. Zhen, Z. Cox, S. Weiner, K. S. Weiskopf, N. Grill-Spector, K. 2018-07-13 doi:10.1101/368274 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ FleN contributes to heterogeneous swimming at high temperatures in Pseudomonas syringae ]]> https://biorxiv.org/content/10.1101/372060v1?rss=1 Hockett, K. L. Lindow, S. E. 2018-07-20 doi:10.1101/372060 Cold Spring Harbor Laboratory Press 2018-07-20 <![CDATA[ Information-rich localization microscopy through machine learning ]]> https://biorxiv.org/content/10.1101/373878v1?rss=1 Kim, T. Moon, S. Xu, K. 2018-07-22 doi:10.1101/373878 Cold Spring Harbor Laboratory Press 2018-07-22 <![CDATA[ Cortical Column and Whole Brain Imaging of Neural Circuits with Molecular Contrast and Nanoscale Resolution ]]> https://biorxiv.org/content/10.1101/374140v1?rss=1 Gao, R. Asano, S. M. Upadhyayula, S. Pisarev, I. Milkie, D. E. Liu, T.-L. Singh, V. Graves, A. Huynh, G. H. Zhao, Y. Bogovic, J. Colonell, J. Ott, C. M. Zugates, C. Tappan, S. Rodriguez, A. Mosaliganti, K. R. Megason, S. G. Lippincott-Schwartz, J. Hantman, A. Rubin, G. M. Kirchhausen, T. Saalfeld, S. Aso, Y. Boyden, E. S. Betzig, E. 2018-07-23 doi:10.1101/374140 Cold Spring Harbor Laboratory Press 2018-07-23 <![CDATA[ A method for genome editing in the anaerobic magnetotactic bacterium Desulfovibrio magneticus RS-1 ]]> https://biorxiv.org/content/10.1101/375410v1?rss=1 Grant, C. R. Rahn-Lee, L. LeGault, K. N. Komeili, A. 2018-07-24 doi:10.1101/375410 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ Human posterior parietal cortex responds to visual stimuli as early as peristriate occipital cortex ]]> https://biorxiv.org/content/10.1101/377887v1?rss=1 Regev, T. I. Winawer, J. Gerber, E. M. Knight, R. T. Deouell, L. Y. 2018-07-26 doi:10.1101/377887 Cold Spring Harbor Laboratory Press 2018-07-26 <![CDATA[ Benchmarking Time-Series Data Discretization on Inference Methods ]]> https://biorxiv.org/content/10.1101/378620v1?rss=1 Li, Y. Jann, T. Vera-Licona, P. 2018-08-01 doi:10.1101/378620 Cold Spring Harbor Laboratory Press 2018-08-01 <![CDATA[ An actuated neural probe architecture for reducing gliosis-induced recording degradation ]]> https://biorxiv.org/content/10.1101/380006v1?rss=1 Massey, T. L. Kuo, L. S. Fan, J. L. Maharbiz, M. M. 2018-07-30 doi:10.1101/380006 Cold Spring Harbor Laboratory Press 2018-07-30 <![CDATA[ Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: Insights from a natural arms-race ]]> https://biorxiv.org/content/10.1101/381962v1?rss=1 McKitterick, A. LeGault, K. Angermeyer, A. Alam, M. Seed, K. 2018-08-01 doi:10.1101/381962 Cold Spring Harbor Laboratory Press 2018-08-01 <![CDATA[ Carbon monoxide, a retrograde messenger generated in post-synaptic mushroom body neurons evokes local dopamine release ]]> https://biorxiv.org/content/10.1101/382127v1?rss=1 Ueno, K. Morstein, J. Ofusa, K. Naganos, S. Suzuki-Sawano, E. Minegishi, A. Kitagishi, H. Chang, C. Horiuchi, J. Saitoe, M. 2018-08-01 doi:10.1101/382127 Cold Spring Harbor Laboratory Press 2018-08-01 <![CDATA[ Individual differences in dopamine are associated with reward discounting in clinical groups but not in healthy adults ]]> https://biorxiv.org/content/10.1101/383810v1?rss=1 Castrellon, J. J. Seaman, K. L. Crawford, J. L. Young, J. S. Smith, C. T. Dang, L. C. Hsu, M. Cowan, R. L. Zald, D. H. Samanez-Larkin, G. R. 2018-08-02 doi:10.1101/383810 Cold Spring Harbor Laboratory Press 2018-08-02 <![CDATA[ 3D Tissue elongation via ECM stiffness-cued junctional remodeling ]]> https://biorxiv.org/content/10.1101/384958v1?rss=1 Chen, D.-Y. Crest, J. Streichan, S. J. Bilder, D. 2018-08-06 doi:10.1101/384958 Cold Spring Harbor Laboratory Press 2018-08-06 <![CDATA[ Condensin controls mitotic chromosome stiffness and stability without forming a structurally contiguous scaffold ]]> https://biorxiv.org/content/10.1101/384982v1?rss=1 Marko, J. Biggs, R. Sun, M. Hornick, J. 2018-08-04 doi:10.1101/384982 Cold Spring Harbor Laboratory Press 2018-08-04 <![CDATA[ MEMS-Actuated Carbon Fiber Microelectrode for Neural Recording ]]> https://biorxiv.org/content/10.1101/385153v1?rss=1 Zoll, R. S. Schindler, C. B. Massey, T. L. Drew, D. S. Maharbiz, M. M. Pister, K. S. J. 2018-08-05 doi:10.1101/385153 Cold Spring Harbor Laboratory Press 2018-08-05 <![CDATA[ Lateral gene transfer shapes the distribution of RuBisCO among Candidate Phyla Radiation bacteria and DPANN archaea ]]> https://biorxiv.org/content/10.1101/386292v1?rss=1 Jaffe, A. L. Castelle, C. J. Dupont, C. L. Banfield, J. F. 2018-08-07 doi:10.1101/386292 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ AICM: A Genuine Framework for Correcting Inconsistency Between Large Pharmacogenomics Datasets ]]> https://biorxiv.org/content/10.1101/386896v1?rss=1 Hu, Z. T. Ye, Y. Newbury, P. Huang, H. Chen, B. 2018-08-07 doi:10.1101/386896 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ Data-adaptive pipeline for filtering and normalizing metabolomics data. ]]> https://biorxiv.org/content/10.1101/387365v1?rss=1 Schiffman, C. Petrick, L. Perttula, K. Yano, Y. Carlsson, H. Whitehead, T. Metayer, C. Hayes, J. Edmands, W. M. B. Rappaport, S. Dudoit, S. 2018-08-08 doi:10.1101/387365 Cold Spring Harbor Laboratory Press 2018-08-08 <![CDATA[ Dub-seq: dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits ]]> https://biorxiv.org/content/10.1101/387399v1?rss=1 Mutalik, V. K. Novichkov, P. S. Price, M. N. Owens, T. K. Callaghan, M. Carim, S. Deutschbauer, A. M. Arkin, A. P. 2018-08-08 doi:10.1101/387399 Cold Spring Harbor Laboratory Press 2018-08-08 <![CDATA[ Measuring Illumina Size Bias Using REcount: A Novel Method for Highly Accurate Quantification of Engineered Genetic Constructs ]]> https://biorxiv.org/content/10.1101/388108v1?rss=1 Gohl, D. M. Becker, A. Johnson, D. Anderson, S. Billstein, B. McDevitt, S. L. Beckman, K. B. 2018-08-09 doi:10.1101/388108 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ A speech envelope landmark for syllable encoding in human superior temporal gyrus ]]> https://biorxiv.org/content/10.1101/388280v1?rss=1 Oganian, Y. Chang, E. F. 2018-08-09 doi:10.1101/388280 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ Interleukin-1 receptor antagonist mediates type I interferon-driven susceptibility to Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/389288v1?rss=1 Ji, D. X. Chen, K. J. Mukaida, N. Kramnik, I. Darwin, K. H. Vance, R. E. 2018-08-10 doi:10.1101/389288 Cold Spring Harbor Laboratory Press 2018-08-10 <![CDATA[ Structures of the substrate-engaged 26S proteasome reveal the mechanisms for ATP hydrolysis-driven translocation ]]> https://biorxiv.org/content/10.1101/393223v1?rss=1 de la Pena, A. H. Goodall, E. A. Gates, S. N. Lander, G. C. Martin, A. 2018-08-16 doi:10.1101/393223 Cold Spring Harbor Laboratory Press 2018-08-16 <![CDATA[ The global distribution of Bacillus anthracis and associated anthrax risk to humans, livestock, and wildlife ]]> https://biorxiv.org/content/10.1101/394023v1?rss=1 Carlson, C. J. Kracalik, I. Ross, N. Alexander, K. Hugh-Jones, M. E. Fegan, M. Elkin, B. Epp, T. Shury, T. Bagirova, M. Getz, W. M. Blackburn, J. K. 2018-08-19 doi:10.1101/394023 Cold Spring Harbor Laboratory Press 2018-08-19 <![CDATA[ An Automated Behavioral Apparatus to Assess Distal Forelimb Function in Non-Human Primates ]]> https://biorxiv.org/content/10.1101/396572v1?rss=1 Totten, D. Novik, L. Christe, K. Lemoy, M.-J. Roberts, J. Carmena, J. Morecraft, R. Ganguly, K. 2018-08-22 doi:10.1101/396572 Cold Spring Harbor Laboratory Press 2018-08-22 <![CDATA[ Speaker-normalized vowel representations in the human auditory cortex ]]> https://biorxiv.org/content/10.1101/397026v1?rss=1 Sjerps, M. J. Fox, N. P. Johnson, K. Chang, E. F. 2018-08-22 doi:10.1101/397026 Cold Spring Harbor Laboratory Press 2018-08-22 <![CDATA[ Single-cell transcriptomics identifies drivers of local inflammation in multiple sclerosis ]]> https://biorxiv.org/content/10.1101/403527v1?rss=1 Schafflick, D. Cole, M. Hartlehnert, M. Lautwein, T. Buscher, K. Wolbert, J. Meuth, S. G. Stettner, M. Kleinschnitz, C. Kuhlmann, T. Gross, C. C. Wiendl, H. Yosef, N. Meyer zu Horste, G. 2018-08-29 doi:10.1101/403527 Cold Spring Harbor Laboratory Press 2018-08-29 <![CDATA[ Formation of periodic pigment spots by the reaction-diffusion mechanism ]]> https://biorxiv.org/content/10.1101/403600v1?rss=1 Ding, B. Patterson, E. L. Holalu, S. Li, J. Johnson, G. A. Stanley, L. E. Greenlee, A. B. Peng, F. Bradshaw, H. D. Blackman, B. K. Yuan, Y.-W. 2018-08-30 doi:10.1101/403600 Cold Spring Harbor Laboratory Press 2018-08-30 <![CDATA[ Sleep and Motor Control by a Basal Ganglia Circuit ]]> https://biorxiv.org/content/10.1101/405324v1?rss=1 Liu, D. Ma, C. Zheng, W. Yao, Y. Dan, Y. 2018-09-02 doi:10.1101/405324 Cold Spring Harbor Laboratory Press 2018-09-02 <![CDATA[ TANGO1 and SEC12 are co-packaged with procollagen I to facilitate the generation of large COPII carriers ]]> https://biorxiv.org/content/10.1101/406348v1?rss=1 Yuan, L. Kenny, S. J. Hemmati, J. Xu, K. Schekman, R. 2018-08-31 doi:10.1101/406348 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ Temperature-responsive competitive inhibition of CRISPR-Cas9 ]]> https://biorxiv.org/content/10.1101/407718v1?rss=1 Jiang, F. Liu, J.-J. Osuna, B. A. Xu, M. Berry, J. D. Rauch, B. J. Nogales, E. Bondy-Denomy, J. Doudna, J. A. 2018-09-03 doi:10.1101/407718 Cold Spring Harbor Laboratory Press 2018-09-03 <![CDATA[ Social integration predicts mitochondrial DNA copy number in rhesus macaques ]]> https://biorxiv.org/content/10.1101/408849v1?rss=1 Debray, R. Snyder-Mackler, N. Kohn, J. Wilson, M. Barreiro, L. Tung, J. 2018-09-06 doi:10.1101/408849 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ Unc93b1 recruits Syntenin-1 to dampen TLR7 signaling and prevent autoimmunity ]]> https://biorxiv.org/content/10.1101/409862v1?rss=1 Majer, O. Liu, B. Krogan, N. Barton, G. 2018-09-05 doi:10.1101/409862 Cold Spring Harbor Laboratory Press 2018-09-05 <![CDATA[ An essential checkpoint for TLR9 signaling is release from 1 Unc93b1 in endosomes ]]> https://biorxiv.org/content/10.1101/410092v1?rss=1 Majer, O. Woo, B. Liu, B. Van Dis, E. Barton, G. 2018-09-05 doi:10.1101/410092 Cold Spring Harbor Laboratory Press 2018-09-05 <![CDATA[ Fast temporal dynamics and causal relevance of face processing in the human temporal cortex ]]> https://biorxiv.org/content/10.1101/416214v1?rss=1 Schrouff, J. V. Raccah, O. Baek, S. Rangarajan, V. Salehi, S. Mourao-Miranda, J. Helili, Z. Daitch, A. L. Parvizi, J. 2018-09-14 doi:10.1101/416214 Cold Spring Harbor Laboratory Press 2018-09-14 <![CDATA[ Different capsid-binding patterns of the β-herpesvirus-specific tegument protein pp150 (pM32/pUL32) in murine and human cytomegaloviruses ]]> https://biorxiv.org/content/10.1101/420604v1?rss=1 Liu, W. Zhou, H. Dai, X. Jih, J. Yu, X. Liu, F. Mei, Y. Chan, K. Trang, P. Balogun, R. 2018-09-18 doi:10.1101/420604 Cold Spring Harbor Laboratory Press 2018-09-18 <![CDATA[ Serotype association with neonatal invasive potential, disease manifestation, and clinical outcome in group B Streptococcus: A Bayesian analysis ]]> https://biorxiv.org/content/10.1101/421412v1?rss=1 Lewnard, J. A. Cowley, L. A. 2018-09-20 doi:10.1101/421412 Cold Spring Harbor Laboratory Press 2018-09-20 <![CDATA[ Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock ]]> https://biorxiv.org/content/10.1101/423368v1?rss=1 Lavy, A. Geller McGrath, D. Matheus Carnevali, P. B. Wan, J. Dong, W. Tokunaga, T. Thomas, B. C. Williams, K. H. Hubbard, S. Banfield, J. F. 2018-09-21 doi:10.1101/423368 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ A Multi-Domain Task Battery Reveals Functional Boundaries in the Human Cerebellum ]]> https://biorxiv.org/content/10.1101/423509v1?rss=1 King, M. Hernandez-Castillo, C. R. Poldrack, R. R. Ivry, R. Diedrichsen, J. 2018-09-21 doi:10.1101/423509 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ Molecular basis of human asparagine synthetase inhibitor specificity ]]> https://biorxiv.org/content/10.1101/428508v1?rss=1 Zhu, W. Radadiya, A. Bisson, C. Nordin, B. Baumann, P. Imasaki, T. Wenzel, S. Sedelnikova, S. Berry, A. Nomanbhoy, T. Kozarich, J. Jin, Y. Takagi, Y. Rice, D. Richards, N. 2018-09-29 doi:10.1101/428508 Cold Spring Harbor Laboratory Press 2018-09-29 <![CDATA[ Industrial bees: when agricultural intensification doesn’t impact local disease prevalence ]]> https://biorxiv.org/content/10.1101/428656v1?rss=1 Bartlett, L. J. Rozins, C. Brosi, B. J. Delaplane, K. S. de Roode, J. C. White, A. Wilfert, L. Boots, M. 2018-09-28 doi:10.1101/428656 Cold Spring Harbor Laboratory Press 2018-09-28 <![CDATA[ A high-resolution map of non-crossover events in mice reveals impacts of genetic diversity on meiotic recombination ]]> https://biorxiv.org/content/10.1101/428987v1?rss=1 Li, R. Bitoun, E. Altemose, N. Davies, R. W. Davies, B. Myers, S. R. 2018-09-27 doi:10.1101/428987 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ Managing Marek’s disease in the egg industry ]]> https://biorxiv.org/content/10.1101/431304v1?rss=1 Rozins, C. Day, T. Greenhalgh, S. 2018-10-04 doi:10.1101/431304 Cold Spring Harbor Laboratory Press 2018-10-04 <![CDATA[ Dengue antigenic relationships predict evolutionary dynamics ]]> https://biorxiv.org/content/10.1101/432054v1?rss=1 Bell, S. M. Katzelnick, L. Bedford, T. 2018-10-02 doi:10.1101/432054 Cold Spring Harbor Laboratory Press 2018-10-02 <![CDATA[ In vivo selection for corrected β-globin alleles after CRISPR/Cas9 editing in human sickle hematopoietic stem cells enhances therapeutic potential ]]> https://biorxiv.org/content/10.1101/432716v1?rss=1 Magis, W. DeWitt, M. A. Wyman, S. K. Vu, J. T. Heo, S.-J. Shao, S. J. Hennig, F. Romero, Z. G. Campo-Fernandez, B. McNeill, M. Rettig, G. R. Sun, Y. Lau, P. J. Wang, Y. Behlke, M. A. Kohn, D. B. Boffelli, D. Walters, M. C. Corn, J. E. Martin, D. I. K. 2018-10-03 doi:10.1101/432716 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ High local mutual information drives the response in the human language network ]]> https://biorxiv.org/content/10.1101/436204v1?rss=1 Mollica, F. Siegelman, M. Diachek, E. Piantadosi, S. T. Mineroff, Z. Futrell, R. Fedorenko, E. 2018-10-08 doi:10.1101/436204 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ Harnessing the Anti-Cancer Natural Product Nimbolide for Targeted Protein Degradation ]]> https://biorxiv.org/content/10.1101/436998v1?rss=1 Spradlin, J. N. Hu, X. Ward, C. C. Brittain, S. M. Ou, L. Bussiere, D. E. Thomas, J. R. Tallarico, J. A. McKenna, J. M. Schirle, M. Maimone, T. J. Nomura, D. K. 2018-10-15 doi:10.1101/436998 Cold Spring Harbor Laboratory Press 2018-10-15 <![CDATA[ Covalent Ligand Screening Uncovers a RNF4 E3 Ligase Recruiter for Targeted Protein Degradation Applications ]]> https://biorxiv.org/content/10.1101/439125v1?rss=1 Ward, C. C. Kleinman, J. I. Chung, C. Y. S. Kim, K. Petri, Y. Lee, P. S. Thomas, J. R. Tallarico, J. A. McKenna, J. M. Schirle, M. Nomura, D. K. 2018-10-16 doi:10.1101/439125 Cold Spring Harbor Laboratory Press 2018-10-16 <![CDATA[ The key parameters that govern translation efficiency ]]> https://biorxiv.org/content/10.1101/440693v1?rss=1 Erdmann-Pham, D. D. Dao Duc, K. Song, Y. S. 2018-10-11 doi:10.1101/440693 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Elevated de novo fatty acid biosynthesis gene expression promotes melanoma cell survival and drug resistance ]]> https://biorxiv.org/content/10.1101/441303v1?rss=1 Wu, S. Naar, A. 2018-10-11 doi:10.1101/441303 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ The ULK1-FBXW5-SEC23B nexus controls autophagy ]]> https://biorxiv.org/content/10.1101/441923v1?rss=1 Pagano, M. Jeong, Y.-T. Simoneschi, D. Keegan, S. Melville, D. Adler, N. Saraf, A. Florens, L. Washburn, M. P. Cavasotto, C. Fenyö, D. Cuervo, A. M. Rossi, M. 2018-10-12 doi:10.1101/441923 Cold Spring Harbor Laboratory Press 2018-10-12 <![CDATA[ Cryo-EM structures of the DCPIB-inhibited volume-regulated anion channel LRRC8A in lipid nanodiscs ]]> https://biorxiv.org/content/10.1101/442459v1?rss=1 Kern, D. M. Oh, S. Hite, R. K. Brohawn, S. G. 2018-10-14 doi:10.1101/442459 Cold Spring Harbor Laboratory Press 2018-10-14 <![CDATA[ Hopanoid composition mediates bacterial ethanol tolerance ]]> https://biorxiv.org/content/10.1101/443473v1?rss=1 50 genome copies per cell), we found that disruptions of essential hopanoid biosynthesis (hpn) genes in Z. mobilis act as genetic knockdowns, reliably modulating the abundance of different hopanoid species. Using a set of hpn transposon mutants, we demonstrate that both reduced hopanoid content and modified hopanoid head group composition mediate growth and survival in ethanol. In contrast, the amount of hopanoids, but not their polar group composition, contributes to fitness at low pH. Spectroscopic analysis of model membranes showed that hopanoids protect against several ethanol-driven phase transitions in membrane structure, including lipid interdigitation and bilayer dissolution. We propose that hopanoids act through a combination of hydrophobic and inter-lipid hydrogen bonding interactions to stabilize bacterial membranes against solvent stress.nnGraphical abstractnnO_FIG O_LINKSMALLFIG WIDTH=196 HEIGHT=200 SRC="FIGDIR/small/443473v2_ufig1.gif" ALT="Figure 1">nView larger version (57K):norg.highwire.dtl.DTLVardef@119f9adorg.highwire.dtl.DTLVardef@5701bcorg.highwire.dtl.DTLVardef@330bfaorg.highwire.dtl.DTLVardef@1574d44_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Budin, I. Brenac, L. Baidoo, E. Keasling, J. D. 2018-10-15 doi:10.1101/443473 Cold Spring Harbor Laboratory Press 2018-10-15 <![CDATA[ A normalized template matching method for improving spike detection in extracellular voltage recordings ]]> https://biorxiv.org/content/10.1101/445585v1?rss=1 Laboy-Juarez, K. Ahn, S. Feldman, D. E. 2018-10-17 doi:10.1101/445585 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Processing of grassland soil C-N compounds into soluble and volatile molecules is depth stratified and mediated by genomically novel bacteria and archaea ]]> https://biorxiv.org/content/10.1101/445817v1?rss=1 Diamond, S. Andeer, P. Li, Z. Crits-Christoph, A. Burstein, D. Anantharaman, K. Lane, K. R. Thomas, B. C. Pan, C. Northen, T. Banfield, J. F. 2018-10-17 doi:10.1101/445817 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Loss of the Heparan Sulfate Proteoglycan Glypican5 facilitates long range Shh signaling. ]]> https://biorxiv.org/content/10.1101/448621v1?rss=1 Guo, W. Roelink, H. 2018-10-19 doi:10.1101/448621 Cold Spring Harbor Laboratory Press 2018-10-19 <![CDATA[ Candidate Phyla Radiation Roizmanbacteria from hot springs have novel, unexpectedly abundant, and potentially alternatively functioning CRISPR-Cas systems ]]> https://biorxiv.org/content/10.1101/448639v1?rss=1 Chen, L.-X. Al-Shayeb, B. Meheust, R. Li, W.-J. Doudna, J. A. Banfield, J. F. 2018-10-22 doi:10.1101/448639 Cold Spring Harbor Laboratory Press 2018-10-22 <![CDATA[ The population history of northeastern Siberia since the Pleistocene ]]> https://biorxiv.org/content/10.1101/448829v1?rss=1 Sikora, M. Pitulko, V. Sousa, V. Allentoft, M. E. Vinner, L. Rasmussen, S. Margaryan, A. de Barros Damgaard, P. de la Fuente Castro, C. Renaud, G. Yang, M. Fu, Q. Dupanloup, I. Giampoudakis, K. Bravo Nogues, D. Rahbek, C. Kroonen, G. Peyrot, M. McColl, H. Vasilyev, S. Veselovskaya, E. Gerasimova, M. Pavlova, E. Chasnyk, V. Nikolskiy, P. Grebenyuk, P. Fedorchenko, A. Lebedintsev, A. Malyarchuk, B. Meldgaard, M. Martiniano, R. Arppe, L. Palo, J. Sundell, T. Mannermaa, K. Putkonen, M. Alexandersen, V. Primeau, C. Mahli, R. Sjögren, K.-G. Kristiansen, K. W 2018-10-22 doi:10.1101/448829 Cold Spring Harbor Laboratory Press 2018-10-22 <![CDATA[ A comparison of visual features used by humans and machines to classify wildlife ]]> https://biorxiv.org/content/10.1101/450189v1?rss=1 Miao, Z. Gaynor, K. M. Wang, J. Liu, Z. Muellerklein, O. Norouzzadeh, M. S. McInturff, A. Bowie, R. C. K. Nathon, R. Yu, S. X. Getz, W. M. 2018-10-22 doi:10.1101/450189 Cold Spring Harbor Laboratory Press 2018-10-22 <![CDATA[ Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolism ]]> https://biorxiv.org/content/10.1101/450254v1?rss=1 Thompson, M. G. Blake-Hedges, J. M. Cruz-Morales, P. Barajas, J. F. Curran, S. C. Harris, N. C. Benites, V. T. Gin, J. W. Eiben, C. B. Sharpless, W. A. Krishna, R. N. Baidoo, E. Petzold, C. J. Arkin, A. P. Deutschbauer, A. M. Keasling, J. D. 2018-10-22 doi:10.1101/450254 Cold Spring Harbor Laboratory Press 2018-10-22 <![CDATA[ An Accessible Continuous-Culture Turbidostat for Pooled Analysis of Complex Libraries ]]> https://biorxiv.org/content/10.1101/450536v1?rss=1 McGeachy, A. M. Meacham, Z. A. Ingolia, N. 2018-10-26 doi:10.1101/450536 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ Massive gene amplification on a recently formed Drosophila Y chromosome ]]> https://biorxiv.org/content/10.1101/451005v1?rss=1 Bachtrog, D. Mahajan, S. 2018-10-24 doi:10.1101/451005 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ Tunable Transcriptional Interference at the Endogenous Alcohol Dehydrogenase Gene Locus in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/452649v1?rss=1 Jorgensen, V. Chen, J. Vander Wende, H. Harris, D. Wong-Deyrup, S. W. Chen, Y. Rangan, P. Brar, G. A. Sawyer, E. M. Chan, L. Y. Ünal, E. 2018-10-24 doi:10.1101/452649 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ Transcriptome profiling of pathogen-specific CD4 T cells identifies T-cell-intrinsic caspase-1 as an important regulator of Th17 differentiation ]]> https://biorxiv.org/content/10.1101/452763v1?rss=1 Gao, Y. Deason, K. Jain, A. Irizarry-Caro, R. A. Dozmorov, I. Rauch, I. Wakeland, E. K. Pasare, C. 2018-10-25 doi:10.1101/452763 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Proximity RNA labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules ]]> https://biorxiv.org/content/10.1101/454066v1?rss=1 Padron, A. Iwasaki, S. Ingolia, N. 2018-10-25 doi:10.1101/454066 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds ]]> https://biorxiv.org/content/10.1101/454843v1?rss=1 Xu, L.-h. Auer, G. Peona, V. Suh, A. Deng, Y. Feng, S.-h. Zhang, G.-j. Blom, M. Christidis, L. Prost, S. Irestedt, M. Zhou, Q. 2018-10-29 doi:10.1101/454843 Cold Spring Harbor Laboratory Press 2018-10-29 <![CDATA[ The more you know: Investigating why adults get a bigger memory boost from semantic congruency than children ]]> https://biorxiv.org/content/10.1101/456624v1?rss=1 Wang, W.-C. Ghetti, S. Brod, G. Bunge, S. A. 2018-10-30 doi:10.1101/456624 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ Human APOBEC3G prevents emergence of infectious endogenous retrovirus in mice ]]> https://biorxiv.org/content/10.1101/457937v1?rss=1 Treger, R. Tokuyama, M. Dong, H. Ross, S. R. Kong, Y. Iwasaki, A. 2018-10-31 doi:10.1101/457937 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ Modeling neural tuning in human ventral temporal cortex predicts the perception of visual ambiguity ]]> https://biorxiv.org/content/10.1101/460337v1?rss=1 Rosenke, M. Davidenko, N. Grill-Spector, K. Weiner, K. S. 2018-11-02 doi:10.1101/460337 Cold Spring Harbor Laboratory Press 2018-11-02 <![CDATA[ Prey’s traits mediate a neotropical toad diet ]]> https://biorxiv.org/content/10.1101/464511v1?rss=1 McElroy, M. T. Donoso, D. A. A. 2018-11-07 doi:10.1101/464511 Cold Spring Harbor Laboratory Press 2018-11-07 <![CDATA[ Prawn aquaculture as a method for schistosomiasis control and poverty alleviation: a win-win approach to address a critical infectious disease of poverty ]]> https://biorxiv.org/content/10.1101/465195v1?rss=1 Hoover, C. M. Sokolow, S. H. Kemp, J. Sanchirico, J. N. Lund, A. J. Jones, I. Higginson, T. Riveau, G. Savaya-Alkalay, A. Coyle, S. Wood, C. L. Micheli, F. Casagrandi, R. Mari, L. Gatto, M. Rinaldo, A. Perez-Saez, J. Rohr, J. R. Sagi, A. Remais, J. V. De Leo, G. A. 2018-11-09 doi:10.1101/465195 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ The DeepTune framework for modeling and characterizing neurons in visual cortex area V4 ]]> https://biorxiv.org/content/10.1101/465534v1?rss=1 Abbasi-Asl, R. Chen, Y. Bloniarz, A. Oliver, M. Willmore, B. D. B. Gallant, J. L. Yu, B. 2018-11-09 doi:10.1101/465534 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria ]]> https://biorxiv.org/content/10.1101/465690v1?rss=1 Probst, A. J. Elling, F. J. Castelle, C. J. Zhu, Q. Elvert, M. Birarda, G. Holman, H.-Y. Lane, K. R. Ladd, B. Ryan, M. C. Woyke, T. Hinrichs, K.-U. Banfield, J. F. 2018-11-08 doi:10.1101/465690 Cold Spring Harbor Laboratory Press 2018-11-08 <![CDATA[ Anti-NMDA receptor encephalitis in mice induced by active immunization with conformationally-stabilized holoreceptors ]]> https://biorxiv.org/content/10.1101/467902v1?rss=1 Jones, B. E. Tovar, K. R. Goehring, A. Okada, N. J. Gouaux, E. Westbrook, G. L. 2018-11-10 doi:10.1101/467902 Cold Spring Harbor Laboratory Press 2018-11-10 <![CDATA[ Open Humans: A platform for participant-centered research and personal data exploration ]]> https://biorxiv.org/content/10.1101/469189v1?rss=1 Greshake Tzovaras, B. Arvai, K. Dulaney, M. Estrada-Galinanes, V. Gunderson, B. Head, T. Lewis, D. Nov, O. Shaer, O. Bobe, J. Price Ball, M. 2018-11-14 doi:10.1101/469189 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq ]]> https://biorxiv.org/content/10.1101/469635v1?rss=1 Wienert, B. Wyman, S. K. Richardson, C. D. Yeh, C. D. Akcakaya, P. Porritt, M. J. Morlock, M. Vu, J. T. Kazane, K. R. Watry, H. L. Judge, L. M. Conklin, B. R. Maresca, M. Corn, J. E. 2018-11-14 doi:10.1101/469635 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ Revisiting tradeoffs in Rubisco kinetic parameters ]]> https://biorxiv.org/content/10.1101/470021v1?rss=1 Flamholz, A. Prywes, N. Moran, U. Davidi, D. Bar-On, Y. Oltrogge, L. Savage, D. Milo, R. 2018-11-14 doi:10.1101/470021 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ A non-canonical arm of UPRER mediates longevity through ER remodeling and lipophagy. ]]> https://biorxiv.org/content/10.1101/471177v1?rss=1 Daniele, J. R. Higuchi-Sanabria, R. Ramachandran, V. Sanchez, M. Durieux, J. Tronnes, S. U. Paul, J. W. Esping, D. J. Monshietehadi, S. Metcalf, M. G. Dillin, A. 2018-11-15 doi:10.1101/471177 Cold Spring Harbor Laboratory Press 2018-11-15 <![CDATA[ Immuno-proteomic interrogation of dengue infection reveals novel HLA haplotype-specific MHC-I antigens ]]> https://biorxiv.org/content/10.1101/471821v1?rss=1 Swaminathan, K. Olsson, N. Lund, P. J. Marceau, C. D. Wagar, L. E. Tian, Y. Sidney, J. Weiskopf, D. Majzoub, K. deSilva, A. D. Harris, E. Davis, M. M. Sette, A. Carette, J. E. Elias, J. E. 2018-11-19 doi:10.1101/471821 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Single-cell whole-brain imaging and network analysis provide evidence of the three-stage hypothesis of addiction ]]> https://biorxiv.org/content/10.1101/471847v1?rss=1 Kimbrough, A. Lurie, D. J. Collazo, A. Kreifeldt, M. Sidhu, H. D'Esposito, M. Contet, C. George, O. 2018-11-21 doi:10.1101/471847 Cold Spring Harbor Laboratory Press 2018-11-21 <![CDATA[ A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase ]]> https://biorxiv.org/content/10.1101/473983v1?rss=1 Sun, S. Weile, J. Verby, M. Cote, A. G. Wu, Y. Fotiadou, I. Kitaygorodsky, J. Rine, J. Jesina, P. Kozich, V. Roth, F. P. 2018-11-19 doi:10.1101/473983 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Neural Signatures of Prediction Errors in a Decision-making Task are Modulated by Action Execution Failures ]]> https://biorxiv.org/content/10.1101/474361v1?rss=1 McDougle, S. D. Butcher, P. A. Parvin, D. Mushtaq, F. Niv, Y. Ivry, R. B. Taylor, J. A. 2018-11-20 doi:10.1101/474361 Cold Spring Harbor Laboratory Press 2018-11-20 <![CDATA[ Genome-wide screening reveals a novel class of carbonic anhydrase-like inorganic carbon transporters in chemoautotrophic bacteria ]]> https://biorxiv.org/content/10.1101/476713v1?rss=1 Desmarais, J. J. Flamholz, A. I. Blikstad, C. Dugan, E. J. Laughlin, T. G. Oltrogge, L. M. Wetmore, K. Wang, J. Y. Savage, D. F. 2018-11-22 doi:10.1101/476713 Cold Spring Harbor Laboratory Press 2018-11-22 <![CDATA[ A serum-free and insulin-supplemented cell culture medium ensures fatty acid synthesis gene activation in cancer cells ]]> https://biorxiv.org/content/10.1101/479964v1?rss=1 Wu, S. Naar, A. M. 2018-11-29 doi:10.1101/479964 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ Double Stranded DNA Damage and Genome Editing Trigger Ribosome Remodeling and Translational Shutdown ]]> https://biorxiv.org/content/10.1101/486704v1?rss=1 Riepe, C. Zelin, E. Wyman, S. K. Nguyen, D. N. Liang, J. R. Frankino, P. A. Meacham, Z. A. Vu, J. T. Marson, A. Ingolia, N. T. Corn, J. E. 2018-12-05 doi:10.1101/486704 Cold Spring Harbor Laboratory Press 2018-12-05 <![CDATA[ An archaeal symbiont-host association from the deep terrestrial subsurface ]]> https://biorxiv.org/content/10.1101/486977v1?rss=1 Schwank, K. Bornemann, T. L. V. Dombrowski, N. Spang, A. Banfield, J. F. Probst, A. 2018-12-05 doi:10.1101/486977 Cold Spring Harbor Laboratory Press 2018-12-05 <![CDATA[ Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila ]]> https://biorxiv.org/content/10.1101/488569v1?rss=1 Bachtrog, D. Ellison, C. 2018-12-05 doi:10.1101/488569 Cold Spring Harbor Laboratory Press 2018-12-05 <![CDATA[ TgCentrin2 is required for invasion and replication in the human parasite Toxoplasma gondii ]]> https://biorxiv.org/content/10.1101/491316v1?rss=1 Leung, J. M. Liu, J. Wetzel, L. A. Hu, K. 2018-12-12 doi:10.1101/491316 Cold Spring Harbor Laboratory Press 2018-12-12 <![CDATA[ Joint Estimation of Pedigrees and Effective Population Size Using Markov Chain Monte Carlo ]]> https://biorxiv.org/content/10.1101/492678v1?rss=1 Ko, A. Nielsen, R. 2018-12-10 doi:10.1101/492678 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Environmental disorder can tip the population genetics of range expansions ]]> https://biorxiv.org/content/10.1101/494955v1?rss=1 Gralka, M. Hallatschek, O. 2018-12-13 doi:10.1101/494955 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ cGAMP signaling controls a transient surface-associated lifestyle ]]> https://biorxiv.org/content/10.1101/495150v1?rss=1 Hallberg, Z. F. Chan, C. H. Wright, T. A. Kranzusch, P. J. Doxzen, K. W. Park, J. J. Bond, D. Hammond, M. C. 2018-12-12 doi:10.1101/495150 Cold Spring Harbor Laboratory Press 2018-12-12 <![CDATA[ The clarifying role of time series data in the population genetics of HIV ]]> https://biorxiv.org/content/10.1101/495275v1?rss=1 Feder, A. F. Pennings, P. S. Petrov, D. A. 2018-12-13 doi:10.1101/495275 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Enhancer priming enables fast and sustained transcriptional responses to Notch signaling ]]> https://biorxiv.org/content/10.1101/497651v1?rss=1 Falo-Sanjuan, J. Lammers, N. C. Garcia, H. G. Bray, S. 2018-12-15 doi:10.1101/497651 Cold Spring Harbor Laboratory Press 2018-12-15 <![CDATA[ A high-throughput fluorescence-based assay for the detection of petroleum hydrocarbon degrading bacteria ]]> https://biorxiv.org/content/10.1101/498345v1?rss=1 French, K. E. Terry, N. 2018-12-17 doi:10.1101/498345 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ Timed inhibition of CDC7 increases CRISPR-Cas9 mediated templated repair ]]> https://biorxiv.org/content/10.1101/500462v1?rss=1 Wienert, B. Feng, S. J. Locke, M. Nguyen, D. N. Wyman, S. K. Kazane, K. R. MARSON, A. Richardson, C. D. Corn, J. E. 2018-12-19 doi:10.1101/500462 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Exploration of Anti-Yo and Anti-Hu paraneoplastic neurological disorders by PhIP-Seq reveals a highly restricted pattern of antibody epitopes ]]> https://biorxiv.org/content/10.1101/502187v1?rss=1 O'Donovan, B. D. Mandel-Brehm, C. Vazquez, S. E. Liu, J. Parent, A. V. Anderson, M. S. Kassimatis, T. Zekeridou, A. Hauser, S. L. Pittock, S. J. Chow, E. Wilson, M. R. DeRisi, J. L. 2018-12-20 doi:10.1101/502187 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ The Caenorhabditis elegans HAM-1 protein modifies G protein signaling and membrane extension to reverse the polarity of asymmetric cell division ]]> https://biorxiv.org/content/10.1101/504787v1?rss=1 Teuliere, J. Garriga, G. 2018-12-21 doi:10.1101/504787 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ Crustaceans as hosts of parasites throughout the Phanerozoic ]]> https://biorxiv.org/content/10.1101/505495v1?rss=1 Klompmaker, A. A. Robins, C. M. Portell, R. W. De Angeli, A. 2018-12-31 doi:10.1101/505495 Cold Spring Harbor Laboratory Press 2018-12-31 <![CDATA[ PTBP1 mRNA isoforms and regulation of their translation ]]> https://biorxiv.org/content/10.1101/509174v1?rss=1 Arake de Tacca, L. M. Pulos, M. C. Floor, S. N. Cate, J. 2018-12-31 doi:10.1101/509174 Cold Spring Harbor Laboratory Press 2018-12-31 <![CDATA[ Effects of water, sanitation, handwashing and nutritional interventions on soil-transmitted helminth infections in young children: a cluster-randomized controlled trial in rural Bangladesh ]]> https://biorxiv.org/content/10.1101/512509v1?rss=1 1.5 billion people. Mass drug administration (MDA) reduces infection; however, drug resistance is emerging and reinfection occurs rapidly. We conducted a randomized controlled trial in Bangladesh (WASH Benefits, NCT01590095) to assess whether water, sanitation, hygiene and nutrition interventions, alone and combined, reduce STH in a setting with ongoing MDA. Methodology/Principal FindingsWe randomized clusters of pregnant women into water treatment, sanitation, handwashing, combined water+sanitation+handwashing (WSH), nutrition, nutrition+WSH (N+WSH) or control arms. After 2.5 years of intervention, we enumerated STH infections in children aged 2-12 years with Kato-Katz. We estimated intention-to-treat intervention effects on infection prevalence and intensity. Participants and field staff were not blinded; laboratory technicians and data analysts were blinded. In 2012-2013, we randomized 5551 women in 720 clusters. In 2015-2016, we enrolled 7795 children of 4102 available women for STH follow-up and collected stool from 7187. Prevalence among controls was 36.8% for A. lumbricoides, 9.2% for hookworm and 7.5% for T. trichiura. Most infections were low-intensity. Compared to controls, the water intervention reduced hookworm (prevalence ratio [PR]=0.69 (0.50, 0.95), prevalence difference [PD]=-2.83 (-5.16, -0.50)) but did not affect other STH. Sanitation improvements reduced T. trichiura (PR=0.71 (0.52, 0.98), PD=-2.17 (-4.03, -0.38)), had a similar borderline effect on hookworm and no effect on A. lumbricoides. Handwashing and nutrition interventions did not reduce any STH. WSH and N+WSH reduced hookworm prevalence by 29-33% (2-3 percentage points) and marginally reduced A. lumbricoides. Effects on infection intensity were similar. Conclusions/SignificanceIn a low-intensity infection setting with MDA, we found modest but sustained hookworm reduction from water treatment, sanitation and combined WSH interventions. Interventions more effectively reduced STH species with no persistent environmental reservoirs. Our findings highlight waterborne transmission for hookworm and suggest that water treatment and sanitation improvements can augment MDA programs to interrupt STH transmission. Author summarySoil-transmitted helminths (STH) infect >1.5 billion people worldwide. Mass-administration of deworming drugs is the cornerstone of global strategy for STH control but treated individuals often rapidly get reinfected and there is also concern about emerging drug resistance. Interventions to treat drinking water, wash hands at critical times and isolate human feces from the environment through improved sanitation could reduce STH transmission by reducing the spread of ova from the feces of infected individuals into the environment and subsequently to new hosts, while nutrition improvements could reduce host susceptibility to infection. Existing evidence on the effect of these interventions on STH is scarce. In a setting with ongoing mass-drug administration, we assessed the effect of individual and combined water, sanitation, handwashing and nutrition interventions on STH infection in children. Approximately 2.5 years after delivering interventions, we found reductions in STH infection from water treatment and sanitation interventions; there was no reduction from the handwashing and nutrition interventions. While the reductions were modest in magnitude compared to cure rates achieved by deworming drugs, they indicated sustained reduction in environmental transmission. The reductions were more pronounced for STH species that do not have persistent environmental reservoirs. These findings suggest that water treatment and sanitation interventions can augment mass-drug administration programs in striving toward elimination of STH. ]]> Ercumen, A. Benjamin-Chung, J. Arnold, B. F. Lin, A. Hubbard, A. E. Stewart, C. Rahman, Z. Parvez, S. M. Unicomb, L. Rahman, M. Haque, R. Colford, J. M. Luby, S. P. 2019-01-12 doi:10.1101/512509 Cold Spring Harbor Laboratory Press 2019-01-12 <![CDATA[ Integrating Quality of Life and Survival Outcomes Cardiovascular Clinical Trials: Results from the PARTNER Trial ]]> https://biorxiv.org/content/10.1101/513895v1?rss=1 Spertus, J. Hatfield, L. A. Cohen, D. J. Arnold, S. V. Ho, M. Jones, P. G. Leon, M. Zuckerman, B. Spertus, J. A. 2019-01-12 doi:10.1101/513895 Cold Spring Harbor Laboratory Press 2019-01-12 <![CDATA[ Heparan sulfate expression on B cells modulates IgM expression in aged mice and steady-state plasma cells ]]> https://biorxiv.org/content/10.1101/514588v1?rss=1 Trujillo, D. L. Jarousse, N. Coscoy, L. 2019-01-14 doi:10.1101/514588 Cold Spring Harbor Laboratory Press 2019-01-14 <![CDATA[ Optical determination of absolute membrane potential ]]> https://biorxiv.org/content/10.1101/519736v1?rss=1 Lazzari-Dean, J. R. Gest, A. M. M. Miller, E. 2019-01-14 doi:10.1101/519736 Cold Spring Harbor Laboratory Press 2019-01-14 <![CDATA[ Enteropathogen seroepidemiology among children in low-resource settings ]]> https://biorxiv.org/content/10.1101/522920v1?rss=1 Arnold, B. F. Martin, D. L. Juma, J. Mkocha, H. Ochieng, J. B. Cooley, G. M. Omore, R. Goodhew, E. B. Morris, J. F. Costantini, V. Vinje, J. Lammie, P. J. Priest, J. W. 2019-01-18 doi:10.1101/522920 Cold Spring Harbor Laboratory Press 2019-01-18 <![CDATA[ Multiple selection signatures in farmed Atlantic salmon adapted to different environments across Hemispheres ]]> https://biorxiv.org/content/10.1101/525550v1?rss=1 Lopez, M.-E. Linderoth, T. Norris, A. Lhorente, J.-P. Neira, R. Yanez, J. M. 2019-01-20 doi:10.1101/525550 Cold Spring Harbor Laboratory Press 2019-01-20 <![CDATA[ DNA methylation and histone H1 cooperatively repress transposable elements and aberrant intragenic transcripts ]]> https://biorxiv.org/content/10.1101/527523v1?rss=1 Choi, J. Lyons, D. B. Kim, Y. Moore, J. D. Zilberman, D. 2019-01-27 doi:10.1101/527523 Cold Spring Harbor Laboratory Press 2019-01-27 <![CDATA[ A metabolic dependency for host isoprenoids in the obligate intracellular pathogen Rickettsia parkeri underlies a sensitivity for the statin class of host-targeted therapeutics ]]> https://biorxiv.org/content/10.1101/528018v1?rss=1 Ahyong, V. Berdan, C. A. Nomura, D. K. Welch, M. D. 2019-01-23 doi:10.1101/528018 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Environmental Consistency Modulation of Error Sensitivity During Motor Adaptation is Explicitly Controlled ]]> https://biorxiv.org/content/10.1101/528752v1?rss=1 Avraham, G. Keizman, M. Shmuelof, L. 2019-01-23 doi:10.1101/528752 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Functional potential of bacterial strains in the premature infant gut microbiome is associated with gestational age ]]> https://biorxiv.org/content/10.1101/530139v1?rss=1 Rahman, S. F. Olm, M. R. Morowitz, M. J. Banfield, J. F. 2019-01-24 doi:10.1101/530139 Cold Spring Harbor Laboratory Press 2019-01-24 <![CDATA[ Macrocyclic colibactin induces DNA double-strand breaks via copper-mediated oxidative cleavage ]]> https://biorxiv.org/content/10.1101/530204v1?rss=1 Li, Z.-R. Li, J. Cai, W. Lai, J. McKinnie, S. Zhang, W.-P. Moore, B. Zhang, W. Qian, P.-Y. 2019-01-24 doi:10.1101/530204 Cold Spring Harbor Laboratory Press 2019-01-24 <![CDATA[ Hand-hygiene mitigation strategies against globaldisease spreading through the air transportationnetwork ]]> https://biorxiv.org/content/10.1101/530618v1?rss=1 Nicolaides, C. Avraam, D. Cueto-Felgueroso, L. Gonzalez, M. C. Juanes, R. 2019-01-26 doi:10.1101/530618 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Dose-specific effectiveness of 7- and 13-valent pneumococcal conjugate vaccines against vaccine-serotype Streptococcus pneumoniae colonization: a matched, case-control study ]]> https://biorxiv.org/content/10.1101/532085v1?rss=1 Lewnard, J. A. Givon-Lavi, N. Dagan, R. 2019-02-01 doi:10.1101/532085 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations ]]> https://biorxiv.org/content/10.1101/532168v1?rss=1 Spence, J. P. Song, Y. S. 2019-01-28 doi:10.1101/532168 Cold Spring Harbor Laboratory Press 2019-01-28 <![CDATA[ Harmonization and Annotation of Single-cell Transcriptomics data with Deep Generative Models ]]> https://biorxiv.org/content/10.1101/532895v1?rss=1 Xu, C. Lopez, R. Mehlman, E. Regier, J. Jordan, M. I. Yosef, N. 2019-01-29 doi:10.1101/532895 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Accumulation of Rare Coding Variants in Genes Implicated in Risk of Human Cleft Lip with or without Cleft Palate ]]> https://biorxiv.org/content/10.1101/533208v1?rss=1 Marini, N. Asrani, K. Yang, W. Rine, J. Shaw, G. 2019-01-29 doi:10.1101/533208 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Global proteomic profiling of primary macrophages during M. tuberculosis infection identifies TAX1BP1 as a mediator of autophagy targeting ]]> https://biorxiv.org/content/10.1101/534917v1?rss=1 Budzik, J. M. Garelis, N. E. Repasy, T. Roberts, A. W. Popov, L. Parry, T. J. Jiminez-Morales, D. Swaney, D. Johnson, J. R. Krogan, N. J. Cox, J. S. 2019-01-31 doi:10.1101/534917 Cold Spring Harbor Laboratory Press 2019-01-31 <![CDATA[ Variation in assembly stoichiometry in non-metazoan homologs of the hub domain of Ca2+/Calmodulin-dependent protein kinase II ]]> https://biorxiv.org/content/10.1101/536094v1?rss=1 McSpadden, E. D. Xia, Z. Chi, C. C. Susa, A. C. Shah, N. H. Gee, C. L. Williams, E. R. Kuriyan, J. 2019-01-31 doi:10.1101/536094 Cold Spring Harbor Laboratory Press 2019-01-31 <![CDATA[ Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance in a model gut microbiota ]]> https://biorxiv.org/content/10.1101/538132v1?rss=1 Aranda-Diaz, A. Obadia, B. Thomsen, T. Hallberg, Z. F. Guvener, Z. T. Huang, K. C. Ludington, W. B. 2019-02-01 doi:10.1101/538132 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ Differential gene expression and the importance of regulatory ncRNAs in acidophilic microorganisms ]]> https://biorxiv.org/content/10.1101/538918v1?rss=1 80% in the archaea G-plasma and Ferroplasma Type II. High gene expression by G-plasma and the Leptospirillum Group II UBA strain correlated with extremely acidic conditions, whereas high transcriptional expression of Leptospirillum Group III and Leptospirillum Group II 5way-CG strain occurred under higher pH and lower temperature. While expression of CRISPR Cas genes occurs on the sense strand, expression of the CRISPR loci occurs on the antisense strand in the Leptospirilli. A novel riboswitch associated with the biosynthetic pathway for the osmolyte ectoine was upregulated when each specific Leptospirillum Group II strain was growing under the conditions most favorable for it. Newly described ncRNAs associated with CO dehydrogenase (CODH) suggest regulation of expression of CODH as a CO sensor in mature biofilms in the Leptospirilli. Results reveal the ways in which environmental conditions shape transcriptional profiles of organisms growing in acidophilic microbial communities and highlight the significance of ncRNAs in regulating gene expression. IMPORTANCEMicroorganisms play important roles in environmental acidification and in metal-recovery based bioleaching processes. Therefore, characterizing how actively growing microbial communities respond to different environments is key to understanding their role in those processes. Microorganisms express their genes, both coding and non-coding, differently depending on environmental factors, thus evaluating community expression profiles inform about the ecology of actively growing microorganisms. Here we used community transcriptomic analyses to characterize gene expression profiles from biofilm communities growing under extremely acidic conditions. Results expand our knowledge of how acidophilic microorganisms respond to changes in their environment and provide insight into possible gene regulation mechanisms. ]]> Aliaga Goltsman, D. S. Hauser, L. Dasari, M. Thomas, B. C. BANFIELD, J. F. 2019-02-02 doi:10.1101/538918 Cold Spring Harbor Laboratory Press 2019-02-02 <![CDATA[ SLC19A1 is a cyclic dinucleotide transporter ]]> https://biorxiv.org/content/10.1101/539767v1?rss=1 Luteijn, R. Zaver, S. Gowen, B. G. Wyman, S. Garelis, N. Onia, L. McWhirter, S. Katibah, G. Corn, J. Woodward, J. Raulet, D. 2019-02-04 doi:10.1101/539767 Cold Spring Harbor Laboratory Press 2019-02-04 <![CDATA[ Single-cell determination of iron content in magnetotactic bacteria: implications for the iron biogeochemical cycle ]]> https://biorxiv.org/content/10.1101/541953v1?rss=1 Amor, M. Tharaud, M. Gelabert, A. Komeili, A. 2019-02-05 doi:10.1101/541953 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Fast and scalable genome-wide inference of local tree topologies from large number of haplotypes based on tree consistent PBWT data structure ]]> https://biorxiv.org/content/10.1101/542035v1?rss=1 Shchur, V. Ziganurova, L. Durbin, R. 2019-02-06 doi:10.1101/542035 Cold Spring Harbor Laboratory Press 2019-02-06 <![CDATA[ Kilohertz in vivo imaging of neural activity ]]> https://biorxiv.org/content/10.1101/543058v1?rss=1 Wu, J. liang, Y. Hsu, C.-L. Chavarha, M. Evans, S. Shi, D. Lin, M. Tsia, K. Ji, N. 2019-02-06 doi:10.1101/543058 Cold Spring Harbor Laboratory Press 2019-02-06 <![CDATA[ Horizontal transfer of prokaryotic cytolethal distending toxin B genes to eukaryotes ]]> https://biorxiv.org/content/10.1101/544197v1?rss=1 40 million years ago and encode a protein that retains ancestral DNase activity. This phage-derived toxin has been domesticated by diverse insects and we hypothesize that it is used as a defensive weapon against parasitoid wasps. One Sentence SummaryWe report horizontal transfer of the gene cytolethal distending toxin B, which encodes a DNase, into eukaryotic genomes from bacteriophage. SignificanceCytolethal distending toxins (CDTs) are secreted by diverse pathogenic bacterial species to kill animal cells. The cdtB subunit enters cell nuclei, damaging the DNA and leading to mitotic arrest and apoptosis. In the pea aphid, a bacterial endosymbiont provides protection against wasp attack, possibly via cdtB. We discovered that this same endosymbiont-encoded lineage of cdtB was transferred to the genomes of Diptera and Hemiptera species and retains ancestral DNase activity. This is the first report of cdtB outside of bacteria or phages. A toxin that first evolved to kill eukaryotic cells has been co-opted by insects, potentially to their benefit. ]]> Verster, K. I. Wisecaver, J. H. Duncan, R. P. Karageorgi, M. Gloss, A. D. Armstrong, E. Price, D. K. Menon, A. R. Ali, Z. M. Whiteman, N. K. 2019-02-08 doi:10.1101/544197 Cold Spring Harbor Laboratory Press 2019-02-08 <![CDATA[ Ohana: detecting selection in multiple populations by modelling ancestral admixture components ]]> https://biorxiv.org/content/10.1101/546408v1?rss=1 Cheng, J. Y. Racimo, F. Nielsen, R. 2019-02-14 doi:10.1101/546408 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ Optogenetic control reveals differential promoter interpretation of transcription factor nuclear translocation dynamics ]]> https://biorxiv.org/content/10.1101/548255v1?rss=1 Chen, S. Y. Osimiri, L. C. Chevalier, M. W. Bugaj, L. J. Ng, A. H. Stewart-Ornstein, J. Neves, L. T. El-Samad, H. 2019-02-13 doi:10.1101/548255 Cold Spring Harbor Laboratory Press 2019-02-13 <![CDATA[ Parthenolide Covalently Targets and Inhibits Focal Adhesion Kinase in Breast Cancer Cells ]]> https://biorxiv.org/content/10.1101/550806v1?rss=1 Berdan, C. A. Ho, R. Lehtola, H. S. To, M. Hu, X. Huffman, T. R. Petri, Y. Altobelli, C. R. Demeulenaere, S. G. Olzmann, J. A. Maimone, T. J. Nomura, D. 2019-02-14 doi:10.1101/550806 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ Changes in anterior and posterior hippocampus differentially predict item-space, item-time, and item-item memory improvement ]]> https://biorxiv.org/content/10.1101/551705v1?rss=1 Lee, J. K. Fandakova, Y. Johnson, E. G. Cohen, N. Bunge, S. A. Ghetti, S. 2019-02-15 doi:10.1101/551705 Cold Spring Harbor Laboratory Press 2019-02-15 <![CDATA[ Functional characterization of genes mediating cell wall metabolism and responses to plant cell wall integrity impairment ]]> https://biorxiv.org/content/10.1101/552893v1?rss=1 Engelsdorf, T. Kjaer, L. Gigli-Bisceglia, N. Vaahtera, L. Bauer, S. Miedes, E. Wormit, A. James, L. Chairam, I. Molina, A. Hamann, T. 2019-02-19 doi:10.1101/552893 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ Adaptive introgression during environmental change can weaken reproductive isolation ]]> https://biorxiv.org/content/10.1101/553230v1?rss=1 Owens, G. L. Samuk, K. 2019-02-18 doi:10.1101/553230 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ A global synthesis reveals biodiversity-mediated benefits for crop production ]]> https://biorxiv.org/content/10.1101/554170v1?rss=1 Dainese, M. Martin, E. A. Aizen, M. Albrecht, M. Bartomeus, I. Bommarco, R. Carvalheiro, L. G. Chaplin-Kramer, R. Gagic, V. Garibaldi, L. A. Ghazoul, J. Grab, H. Jonsson, M. Karp, D. S. Kennedy, C. M. Kleijn, D. Kremen, C. Landis, D. A. Letourneau, D. K. Marini, L. Poveda, K. Rader, R. Smith, H. G. Tscharntke, T. Andersson, G. K. S. Badenhausser, I. Baensch, S. Bezerra, A. D. M. Bianchi, F. J. J. A. Boreux, V. Bretagnolle, V. Caballero-Lopez, B. Cavigliasso, P. Cetkovic, A. Chacoff, N. P. Classen, A. Cusser, S. Silva e Silva, F. D. d. de Groot, G. A. Dude 2019-02-20 doi:10.1101/554170 Cold Spring Harbor Laboratory Press 2019-02-20 <![CDATA[ New factors for protein transport identified by a genome-wide CRISPRi screen in mammalian cells ]]> https://biorxiv.org/content/10.1101/556746v1?rss=1 Bassaganyas, L. Popa, S. J. Horlbeck, M. Ashok, A. Stewart, S. E. Butnaru, C. M. Brouwers, N. Heydari, K. Ripoche, J. Weissman, J. Schekman, R. Malhotra, V. Moreau, K. Villeneuve, J. 2019-02-21 doi:10.1101/556746 Cold Spring Harbor Laboratory Press 2019-02-21 <![CDATA[ Glutarate metabolism in Pseudomonas putida is regulated by two distinct glutarate sensing transcription factors ]]> https://biorxiv.org/content/10.1101/557751v1?rss=1 Thompson, M. G. Cruz-Morales, P. Krishna, R. N. Blake-Hedges, J. M. Incha, M. R. Keasling, J. D. 2019-02-22 doi:10.1101/557751 Cold Spring Harbor Laboratory Press 2019-02-22 <![CDATA[ Mechanochemical coupling and junctional forces during collective cell migration ]]> https://biorxiv.org/content/10.1101/558452v1?rss=1 Bui, J. Conway, D. E. Heise, R. L. Weinberg, S. H. 2019-02-22 doi:10.1101/558452 Cold Spring Harbor Laboratory Press 2019-02-22 <![CDATA[ Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria that may stimulate TLR4 receptors ]]> https://biorxiv.org/content/10.1101/558676v1?rss=1 Olm, M. R. Bhattacharya, N. Crits-Christoph, A. Firek, B. A. Baker, R. Song, Y. S. Morowitz, M. J. Banfield, J. F. 2019-02-22 doi:10.1101/558676 Cold Spring Harbor Laboratory Press 2019-02-22 <![CDATA[ Super-resolution displacement mapping of unbound single molecules reveals nanoscale heterogeneities in intracellular diffusivity ]]> https://biorxiv.org/content/10.1101/559484v1?rss=1 Xiang, L. Chen, K. Yan, R. Li, W. Xu, K. 2019-02-25 doi:10.1101/559484 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ The genome and mRNA transcriptome of the cosmopolitan calanoid copepod Acartia tonsa Dana improve the understanding of copepod genome size evolution ]]> https://biorxiv.org/content/10.1101/560102v1?rss=1 Jorgensen, T. S. Petersen, B. Jepsen, P. M. van Someren Greve, H. Hestbjerg Hansen, L. Hansen, B. W. 2019-02-25 doi:10.1101/560102 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ A genome-wide screen for ER autophagy highlights key roles of mitochondrial metabolism and ER- resident UFMylation ]]> https://biorxiv.org/content/10.1101/561001v1?rss=1 Liang, J. R. Lingeman, E. Luong, T. Ahmed, S. Nguyen, T. Olzmann, J. Corn, J. E. 2019-02-25 doi:10.1101/561001 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ Left Ventricular Chamber Shape During Vena Caval Occlusion: Improved MRI-based Measurement of the End-Systolic Pressure-Volume Relationship in Normal Sheep ]]> https://biorxiv.org/content/10.1101/562017v1?rss=1 Giao, D. M. Wang, Y. Rojas, R. Takaba, K. Badathala, A. Spaulding, K. A. Soon, G. Zhang, Y. Wang, V. Y. Heraldsson, H. Liu, J. Saloner, D. Ge, L. Guccione, J. M. Wallace, A. W. Ratcliffe, M. B. 2019-02-26 doi:10.1101/562017 Cold Spring Harbor Laboratory Press 2019-02-26 <![CDATA[ Replay as wavefronts and theta sequences as bump oscillations in a grid cell attractor network ]]> https://biorxiv.org/content/10.1101/565440v1?rss=1 Kang, L. DeWeese, M. R. 2019-03-01 doi:10.1101/565440 Cold Spring Harbor Laboratory Press 2019-03-01 <![CDATA[ Genetic drift in range expansions is very sensitive to density feedback in dispersal and growth ]]> https://biorxiv.org/content/10.1101/565986v1?rss=1 Birzu, G. Matin, S. Hallatschek, O. Korolev, K. 2019-03-05 doi:10.1101/565986 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Bioelectrical signaling via domain wall migration ]]> https://biorxiv.org/content/10.1101/570440v1?rss=1 McNamara, H. M. Salegame, R. Al Tanoury, Z. Xu, H. Begum, S. Ortiz, G. Pourquie, O. Cohen, A. E. 2019-03-08 doi:10.1101/570440 Cold Spring Harbor Laboratory Press 2019-03-08 <![CDATA[ A Bayesian framework for inferring the influence of sequence context on single base modifications ]]> https://biorxiv.org/content/10.1101/571646v1?rss=1 Ling, G. Miller, D. Nielsen, R. Stern, A. 2019-03-09 doi:10.1101/571646 Cold Spring Harbor Laboratory Press 2019-03-09 <![CDATA[ Clades of huge phage from across Earth’s ecosystems ]]> https://biorxiv.org/content/10.1101/572362v1?rss=1 Al-Shayeb, B. Sachdeva, R. Chen, L.-X. Ward, F. Munk, P. Devoto, A. Castelle, C. J. Olm, M. R. Bouma-Gregson, K. Amano, Y. He, C. Meheust, R. Brooks, B. Thomas, A. Lavy, A. Matheus-Carnevali, P. Sun, C. Goltsman, D. Borton, M. A. Nelson, T. C. Kantor, R. Jaffe, A. L. Keren, R. Farag, I. F. Lei, S. Finstad, K. Amundson, R. Anantharaman, K. Zhou, J. Probst, A. J. Power, M. E. Tringe, S. G. Li, W.-J. Wrighton, K. Harrison, S. Morowitz, M. Relman, D. A. Doudna, J. A. Lehours, A.-C. Warren, L. Cate, J. H. Santini, J. M. Banfield, J. F. 2019-03-11 doi:10.1101/572362 Cold Spring Harbor Laboratory Press 2019-03-11 <![CDATA[ Convergent gene loss in aquatic plants predicts new components of plant immunity and drought response ]]> https://biorxiv.org/content/10.1101/572560v1?rss=1 Baggs, E. L. Thanki, A. S. O'Grady, R. Schudoma, C. Haerty, W. Krasileva, K. V. 2019-03-11 doi:10.1101/572560 Cold Spring Harbor Laboratory Press 2019-03-11 <![CDATA[ Evolutionary dynamics in structured populations under strong population genetic forces ]]> https://biorxiv.org/content/10.1101/579854v1?rss=1 Feder, A. F. Pennings, P. S. Hermisson, J. Petrov, D. A. 2019-03-16 doi:10.1101/579854 Cold Spring Harbor Laboratory Press 2019-03-16 <![CDATA[ Separations-Encoded Microparticles For Single-Cell Western Blotting ]]> https://biorxiv.org/content/10.1101/580233v1?rss=1 Gumuscu, B. Herr, A. 2019-03-16 doi:10.1101/580233 Cold Spring Harbor Laboratory Press 2019-03-16 <![CDATA[ Structural color in Junonia butterflies evolves by tuning scale lamina thickness ]]> https://biorxiv.org/content/10.1101/584532v1?rss=1 Thayer, R. C. Allen, F. I. Patel, N. H. 2019-03-21 doi:10.1101/584532 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ 3.1A structure of yeast RNA polymerase II elongation complex stalled at a cyclobutane pyrimidine dimer lesion solved using streptavidin affinity grids ]]> https://biorxiv.org/content/10.1101/585547v1?rss=1 Lahiri, I. Xu, J. Han, B. G. Oh, J. Wang, D. DiMaio, F. Leschziner, A. E. 2019-03-22 doi:10.1101/585547 Cold Spring Harbor Laboratory Press 2019-03-22 <![CDATA[ Endosymbiotic bacteria are prevalent and diverse in agricultural spiders ]]> https://biorxiv.org/content/10.1101/586750v1?rss=1 White, J. A. Styer, A. Rosenwald, L. C. Curry, M. M. Welch, K. D. Athey, K. J. Chapman, E. G. 2019-03-24 doi:10.1101/586750 Cold Spring Harbor Laboratory Press 2019-03-24 <![CDATA[ Whisker map organization in somatosensory cortex of awake, behaving mice ]]> https://biorxiv.org/content/10.1101/587634v1?rss=1 Wang, H. C. LeMessurier, A. M. Feldman, D. E. 2019-03-24 doi:10.1101/587634 Cold Spring Harbor Laboratory Press 2019-03-24 <![CDATA[ Human Foveal Cone Photoreceptor Topography and its Dependence on Eye Length ]]> https://biorxiv.org/content/10.1101/589135v1?rss=1 Wang, Y. Bensaid, N. Tiruveedhula, P. Ma, J. Ravikumar, S. Roorda, A. 2019-03-27 doi:10.1101/589135 Cold Spring Harbor Laboratory Press 2019-03-27 <![CDATA[ An approximate full-likelihood method for inferring selection and allele frequency trajectories from DNA sequence data ]]> https://biorxiv.org/content/10.1101/592675v1?rss=1 Stern, A. J. Wilton, P. R. Nielsen, R. 2019-03-28 doi:10.1101/592675 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ A likelihood method for estimating present-day human contamination in ancient DNA samples using low-depth haploid chromosome data ]]> https://biorxiv.org/content/10.1101/594481v1?rss=1 Moreno-Mayar, J. V. Korneliussen, T. S. Albrechtsen, A. Dalal, J. Renaud, G. Nielsen, R. Malaspinas, A.-S. 2019-03-31 doi:10.1101/594481 Cold Spring Harbor Laboratory Press 2019-03-31 <![CDATA[ Drosophila female-specific brain neuron elicits persistent position- and direction-selective male-like social behaviors ]]> https://biorxiv.org/content/10.1101/594960v1?rss=1 Wu, Y. Bidaye, S. Mahringer, D. 2019-03-31 doi:10.1101/594960 Cold Spring Harbor Laboratory Press 2019-03-31 <![CDATA[ Unusual metabolism and hypervariation in the genome of a Gracilibacteria (BD1-5) from an oil degrading community ]]> https://biorxiv.org/content/10.1101/595074v1?rss=1 Sieber, C. M. K. Paul, B. G. Castelle, C. J. Hu, P. Tringe, S. G. Valentine, D. L. Andersen, G. L. Banfield, J. F. 2019-04-01 doi:10.1101/595074 Cold Spring Harbor Laboratory Press 2019-04-01 <![CDATA[ Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil ]]> https://biorxiv.org/content/10.1101/597468v1?rss=1 Starr, E. P. Nuccio, E. E. Pett-Ridge, J. Banfield, J. F. Firestone, M. K. 2019-04-04 doi:10.1101/597468 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ Suppression of unwanted CRISPR/Cas9 editing by co-administration of catalytically inactivating truncated guide RNAs ]]> https://biorxiv.org/content/10.1101/597849v1?rss=1 Rose, J. C. Popp, N. A. Richardson, C. D. Stephany, J. J. Mathieu, J. Wei, C. T. Corn, J. E. Maly, D. J. Fowler, D. M. 2019-04-03 doi:10.1101/597849 Cold Spring Harbor Laboratory Press 2019-04-03 <![CDATA[ Tuning the affinity of tandem calponin homology domains ]]> https://biorxiv.org/content/10.1101/598359v1?rss=1 Harris, A. R. Belardi, B. Jreij, P. Wei, K. Bausch, A. Fletcher, D. A. 2019-04-04 doi:10.1101/598359 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ A polygenic risk score for breast cancer in U.S. Latinas and Latin-American women ]]> https://biorxiv.org/content/10.1101/598730v1?rss=1 Shieh, Y. Fejerman, L. Lott, P. C. Marker, K. Sawyer, S. D. Hu, D. Huntsman, S. Torres, J. Echeverry, M. Bohorquez, M. E. Martinez-Chequer, J. C. Polanco-Echeverry, G. Estrada-Florez, A. P. Haiman, C. A. John, E. M. Kushi, L. H. Torres-Mejia, G. Viadaurre, T. Weitzel, J. N. Casavilco Zambrano, S. Carvajal-Carmona, L. G. Ziv, E. Neuhausen, S. L. 2019-04-12 doi:10.1101/598730 Cold Spring Harbor Laboratory Press 2019-04-12 <![CDATA[ Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles ]]> https://biorxiv.org/content/10.1101/598821v1?rss=1 Cho, Y. S. Jun, J. Kim, J. A. Kim, H.-M. Chung, O. Kang, S.-G. Park, J.-Y. Kim, H.-J. Kim, S. Kim, H.-J. Jang, J.-h. Na, K.-J. Kim, J. Park, S. G. Lee, H.-Y. Manica, A. Mindell, D. P. Puchs, J. Edwards, J. S. Weber, J. A. Witt, C. C. Yeo, J.-H. Kim, S. Bhak, J. 2019-04-05 doi:10.1101/598821 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ RNAi screen reveals a role for PACSIN2 and caveolins during bacterial cell-to-cell spread ]]> https://biorxiv.org/content/10.1101/599795v1?rss=1 Sanderlin, A. Vondrak, C. Scricco, A. Fedrigo, I. Ahyong, V. Lamason, R. 2019-04-04 doi:10.1101/599795 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ Second messengers and divergent HD-GYP enzymes regulate 3’,3’-cGAMP signaling ]]> https://biorxiv.org/content/10.1101/600031v1?rss=1 Wright, T. A. Jiang, L. Park, J. J. Anderson, W. A. Chen, G. Hallberg, Z. F. Nan, B. Hammond, M. C. 2019-04-05 doi:10.1101/600031 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ Consistent bacterial responses to land use change across the tropics ]]> https://biorxiv.org/content/10.1101/600924v1?rss=1 Petersen, I. A. Meyer, K. M. Bohannan, B. J. M. 2019-04-07 doi:10.1101/600924 Cold Spring Harbor Laboratory Press 2019-04-07 <![CDATA[ Meiotic cellular rejuvenation is coupled to nuclear remodeling in budding yeast ]]> https://biorxiv.org/content/10.1101/602433v1?rss=1 Ünal, E. King, G. A. Goodman, J. S. Chetlapalli, K. Schick, J. G. Jorgens, D. M. McDonald, K. L. 2019-04-08 doi:10.1101/602433 Cold Spring Harbor Laboratory Press 2019-04-08 <![CDATA[ Multiplex serologic testing within a cross-sectional lymphatic filariasis sentinel site survey in coastal Kenya reveals community-level differences in IgG antibody responses to parasitic diseases and vaccines ]]> https://biorxiv.org/content/10.1101/604181v1?rss=1 Njenga, S. M. Kanyi, H. M. Arnold, B. F. Matendechero, H. S. Onsongo, J. K. Won, K. Y. Priest, J. W. 2019-04-19 doi:10.1101/604181 Cold Spring Harbor Laboratory Press 2019-04-19 <![CDATA[ Human Aging DNA Methylation Signatures are Conserved but Accelerated in Cultured Fibroblasts ]]> https://biorxiv.org/content/10.1101/605295v1?rss=1 nView larger version (60K):norg.highwire.dtl.DTLVardef@101e4f2org.highwire.dtl.DTLVardef@15df049org.highwire.dtl.DTLVardef@4a704dorg.highwire.dtl.DTLVardef@112f970_HPS_FORMAT_FIGEXP M_FIG Graphical AbstractnnC_FIG ]]> Sturm, G. Cardenas, A. Bind, M.-A. Horvath, S. Wang, S. Wang, Y. Hagg, S. Hirano, M. Picard, M. 2019-04-10 doi:10.1101/605295 Cold Spring Harbor Laboratory Press 2019-04-10 <![CDATA[ Confinement and reversibility of threshold-dependent gene drive systems in spatially-explicit Aedes aegypti populations ]]> https://biorxiv.org/content/10.1101/607267v1?rss=1 Sanchez C., H. M. Bennett, J. B. Wu, S. L. Rasic, G. Akbari, O. S. Marshall, J. M. 2019-04-12 doi:10.1101/607267 Cold Spring Harbor Laboratory Press 2019-04-12 <![CDATA[ 2’, 3’, 4’-trihydroxychalcone is an Estrogen Receptor Ligand Which Modulates the Activity of 17β-estradiol ]]> https://biorxiv.org/content/10.1101/607275v1?rss=1 Herber, C. Quirit, J. Firestone, G. Krois, C. 2019-04-13 doi:10.1101/607275 Cold Spring Harbor Laboratory Press 2019-04-13 <![CDATA[ Hypotonic stress induces fast, reversible degradation of the vimentin cytoskeleton via intracellular calcium release ]]> https://biorxiv.org/content/10.1101/607416v1?rss=1 Pan, L. Zhang, P. Hu, F. Yan, R. He, M. Li, W. Xu, J. Xu, K. 2019-04-13 doi:10.1101/607416 Cold Spring Harbor Laboratory Press 2019-04-13 <![CDATA[ Benchmarking of alignment-free sequence comparison methods ]]> https://biorxiv.org/content/10.1101/611137v1?rss=1 Zielezinski, A. Girgis, H. Z. Bernard, G. Leimeister, C.-A. Tang, K. Dencker, T. Lau, A. K. Roehling, S. Choi, J. Waterman, M. S. Comin, M. Kim, S.-H. Vinga, S. Almeida, J. S. Chan, C. X. James, B. Sun, F. Morgenstern, B. Karlowski, W. M. 2019-04-16 doi:10.1101/611137 Cold Spring Harbor Laboratory Press 2019-04-16 <![CDATA[ Niche differentiation is spatially and temporally regulated in the rhizosphere ]]> https://biorxiv.org/content/10.1101/611863v1?rss=1 Nuccio, E. E. Starr, E. Karaoz, U. Brodie, E. L. Zhou, J. Tringe, S. Malmstrom, R. R. Woyke, T. Banfield, J. F. Firestone, M. K. Pett-Ridge, J. 2019-04-18 doi:10.1101/611863 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Distinct mechanisms of microRNA sorting into cancer cell-derived extracellular vesicle subtypes ]]> https://biorxiv.org/content/10.1101/612069v1?rss=1 Temoche-Diaz, M. M. Shurtleff, M. J. Nottingham, R. M. Yao, J. Fadadu, R. P. Lambowitz, A. M. Schekman, R. 2019-04-17 doi:10.1101/612069 Cold Spring Harbor Laboratory Press 2019-04-17 <![CDATA[ A microfabricated, 3D-sharpened silicon shuttle for insertion of flexible electrode arrays through dura mater into brain ]]> https://biorxiv.org/content/10.1101/614685v1?rss=1 Joo, H. R. Fan, J. L. Chen, S. Pebbles, J. A. Liang, H. Chung, J. E. Yorita, A. M. Tooker, A. C. Tolosa, V. M. Geaghan-Breiner, C. Roumis, D. K. Liu, D. F. Haque, R. Frank, L. M. 2019-04-26 doi:10.1101/614685 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ RNA transcribed from heterochromatic simple-tandem repeats are required for male fertility and histone-protamine exchange in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/617175v1?rss=1 Mills, W. K. Lee, Y. C. G. Kochendoerfer, A. M. Dunleavy, E. M. Karpen, G. H. 2019-04-24 doi:10.1101/617175 Cold Spring Harbor Laboratory Press 2019-04-24 <![CDATA[ Insect herbivory reshapes a native leaf microbiome ]]> https://biorxiv.org/content/10.1101/620716v1?rss=1 Humphrey, P. T. Whiteman, N. K. 2019-04-26 doi:10.1101/620716 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Distentangling the systems contributing to changes in learning during adolescence ]]> https://biorxiv.org/content/10.1101/622860v1?rss=1 Master, S. L. Eckstein, M. K. Gotlieb, N. Dahl, R. Wilbrecht, L. Collins, A. G. 2019-04-30 doi:10.1101/622860 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ Trajectory-based differential expression analysis for single-cell sequencing data ]]> https://biorxiv.org/content/10.1101/623397v1?rss=1 Van den Berge, K. Roux de Bezieux, H. Street, K. Saelens, W. Cannoodt, R. Saeys, Y. Dudoit, S. Clement, L. 2019-05-02 doi:10.1101/623397 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Kinesin-1 and dynein use distinct mechanisms to bypass obstacles ]]> https://biorxiv.org/content/10.1101/624056v1?rss=1 Ferro, L. S. Can, S. Turner, M. A. Elshenawy, M. M. Yildiz, A. 2019-04-30 doi:10.1101/624056 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ A role for phagocytosis in inducing cell death during thymocyte negative selection ]]> https://biorxiv.org/content/10.1101/624148v1?rss=1 Kurd, N. S. Lutes, L. K. Yoon, J. Dzhagalov, I. L. Hoover, A. Robey, E. A. 2019-04-30 doi:10.1101/624148 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ The metabolic response of Pseudomonas taiwanensis to NADH dehydrogenase deficiency ]]> https://biorxiv.org/content/10.1101/624536v1?rss=1 Nies, S. C. Dinger, R. Chen, Y. Wordofa, G. G. Kristensen, M. Schneider, K. Büchs, J. Petzold, C. J. Keasling, J. D. Blank, L. Ebert, B. E. 2019-05-02 doi:10.1101/624536 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ An Electrophysiological Marker of Arousal Level in Humans ]]> https://biorxiv.org/content/10.1101/625210v1?rss=1 Lendner, J. D. Helfrich, R. F. Mander, B. A. Romundstad, L. Lin, J. J. Walker, M. P. Larsson, P. G. Knight, R. T. 2019-05-02 doi:10.1101/625210 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Pseudomonas syringae Increases Water Availability in Leaf Microenvironments via Production of Hygroscopic Syringafactin ]]> https://biorxiv.org/content/10.1101/626630v1?rss=1 Hernandez, M. N. Lindow, S. E. 2019-05-03 doi:10.1101/626630 Cold Spring Harbor Laboratory Press 2019-05-03 <![CDATA[ Comparison of multi-parallel qPCR and Kato-Katz for detection of soil-transmitted helminth infection among children in rural Bangladesh ]]> https://biorxiv.org/content/10.1101/629501v1?rss=1 Benjamin-Chung, J. Pilotte, N. Ercumen, A. Grant, J. R. Maasch, J. R. M. A. Gonzales, A. M. Abrams, B. P. Ester, A. C. Arnold, B. F. Rahman, M. Haque, R. Hubbard, A. E. Luby, S. P. Williams, S. A. Colford, J. M. 2019-05-10 doi:10.1101/629501 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Integrating exposure knowledge and serum suspect screening as a new approach to biomonitoring: An application in firefighters and office workers ]]> https://biorxiv.org/content/10.1101/630848v1?rss=1 Grashow, R. Bessonneau, V. Gerona, R. R. Wang, A. Trowbridge, J. Lin, T. Buren, H. Rudel, R. A. Morello-Frosch, R. 2019-05-10 doi:10.1101/630848 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Operations Research Methods for Estimating the Population Size of Neuron Types ]]> https://biorxiv.org/content/10.1101/633313v1?rss=1 Attili, S. M. Mackesey, S. Ascoli, G. 2019-05-09 doi:10.1101/633313 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Electrocorticographic dissociation of alpha and beta rhythmic activity in the human sensorimotor system ]]> https://biorxiv.org/content/10.1101/636241v1?rss=1 Stolk, A. Brinkman, L. Vansteensel, M. J. Aarnoutse, E. Leijten, F. S. S. Dijkerman, C. H. Knight, R. T. de Lange, F. P. Toni, I. 2019-05-12 doi:10.1101/636241 Cold Spring Harbor Laboratory Press 2019-05-12 <![CDATA[ Cofactor selectivity in methylmalonyl-CoA mutase, a model cobamide-dependent enzyme ]]> https://biorxiv.org/content/10.1101/637140v1?rss=1 Sokolovskaya, O. M. Mok, K. C. Park, J. D. Tran, J. L. A. Quanstrom, K. A. Taga, M. E. 2019-05-15 doi:10.1101/637140 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ Genome-wide identification of Pseudomonas syringae genes required for competitive fitness during colonization of the leaf surface and apoplast ]]> https://biorxiv.org/content/10.1101/637496v1?rss=1 Helmann, T. C. Deutschbauer, A. M. Lindow, S. E. 2019-05-20 doi:10.1101/637496 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Resolving the 3D landscape of transcription-linked mammalian chromatin folding ]]> https://biorxiv.org/content/10.1101/638775v1?rss=1 Hsieh, T.-H. S. Slobodyanyuk, E. Hansen, A. S. Cattoglio, C. Rando, O. J. Tjian, R. Darzacq, X. 2019-05-17 doi:10.1101/638775 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Structural basis for tetherin antagonism as a barrier to zoonotic lentiviral transmission ]]> https://biorxiv.org/content/10.1101/638890v1?rss=1 Buffalo, C. Z. Sturzel, C. Heusinger, E. Kmiec, D. Kirchhoff, F. Hurley, J. Ren, X. 2019-05-16 doi:10.1101/638890 Cold Spring Harbor Laboratory Press 2019-05-16 <![CDATA[ Prepubertal gonadectomy reveals sex differences in approach-avoidance behavior in adult mice ]]> https://biorxiv.org/content/10.1101/638916v1?rss=1 Delevich, K. Hall, C. Boivin, J. R. Piekarski, D. Zhang, Y. Wilbrecht, L. 2019-05-28 doi:10.1101/638916 Cold Spring Harbor Laboratory Press 2019-05-28 <![CDATA[ Genome replication dynamics of a bacteriophage and its satellite reveal strategies for parasitism and viral restriction ]]> https://biorxiv.org/content/10.1101/639039v1?rss=1 Barth, Z. Silvas, T. Angermeyer, A. Seed, K. 2019-05-17 doi:10.1101/639039 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier ]]> https://biorxiv.org/content/10.1101/641506v1?rss=1 Chen, Z. Gabizon, R. Bustamante, C. Yao, T. Lee, A. Diaz-Celis, C. Koslover, E. F. Brown, A. I. Song, A. 2019-05-17 doi:10.1101/641506 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Graphene-enabled, spatially controlled electroporation of adherent cells for live-cell super-resolution microscopy ]]> https://biorxiv.org/content/10.1101/642868v1?rss=1 Moon, S. Li, W. Xu, K. 2019-05-27 doi:10.1101/642868 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Consistent metagenome-derived metrics verify and define bacterial species boundaries ]]> https://biorxiv.org/content/10.1101/647511v1?rss=1 Olm, M. R. Crits-Christoph, A. Diamond, S. Lavy, A. Matheus Carnevali, P. B. Banfield, J. F. 2019-05-24 doi:10.1101/647511 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Ecological and genomic attributes of novel bacterial taxa that thrive in subsurface soil horizons ]]> https://biorxiv.org/content/10.1101/647651v1?rss=1 Brewer, T. E. Aronson, E. L. Arogyaswamy, K. Billings, S. A. Botthoff, J. K. Campbell, A. N. Dove, N. C. Fairbanks, D. Gallery, R. E. Hart, S. Kaye, J. King, G. M. Logan, G. Lohse, K. A. Maltz, M. R. Mayorga, E. O'Neill, C. Owens, S. Packman, A. I. Pett-Ridge, J. Plante, A. F. Richter, D. D. Silver, W. L. Yang, W. H. Fierer, N. 2019-05-24 doi:10.1101/647651 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Peptide Arrays of Three Collections of Human Sera from Patients Infected with Mosquito-Borne Viruses ]]> https://biorxiv.org/content/10.1101/650796v1?rss=1 Martinez Viedma, M. d. P. Kose, N. Parham, L. Balmaseda, A. Kuan, G. E. Lorenzana, I. Harris, E. Crowe, J. E. Pickett, B. E. 2019-05-26 doi:10.1101/650796 Cold Spring Harbor Laboratory Press 2019-05-26 <![CDATA[ The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens ]]> https://biorxiv.org/content/10.1101/653105v1?rss=1 Zhou, N. Jiang, Y. Bergquist, T. R. Lee, A. J. Kacsoh, B. Z. Crocker, A. W. Lewis, K. A. Georghiou, G. Nguyen, H. N. Hamid, M. N. Davis, L. The Critical Assessment of Function Annotation, Rost, B. Brenner, S. E. Orengo, C. A. Jeffery, C. J. Bosco, G. D. Hogan, D. A. Martin, M. J. O'Donovan, C. Mooney, S. D. Greene, C. S. Radivojac, P. Friedberg, I. 2019-05-29 doi:10.1101/653105 Cold Spring Harbor Laboratory Press 2019-05-29 <![CDATA[ Neutrophils promote CXCR3-dependent itch in the development of atopic dermatitis ]]> https://biorxiv.org/content/10.1101/653873v1?rss=1 Walsh, C. M. Hill, R. Z. Schwendinger-Schreck, J. Deguine, J. Brock, E. C. Kucirek, N. Rifi, Z. Wei, J. Gronert, K. Brem, R. B. Barton, G. M. Bautista, D. M. 2019-05-31 doi:10.1101/653873 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Augmenting biologging with supervised machine learning to study in situ behavior of the medusa Chrysaora fuscescens ]]> https://biorxiv.org/content/10.1101/657684v1?rss=1 Fannjiang, C. Mooney, T. A. Cones, S. Mann, D. Shorter, K. A. Katija, K. 2019-06-03 doi:10.1101/657684 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Light-regulated collective contractility in a multicellular choanoflagellate ]]> https://biorxiv.org/content/10.1101/661009v1?rss=1 Brunet, T. Larson, B. Linden, T. Vermeij, M. McDonald, K. L. King, N. 2019-06-06 doi:10.1101/661009 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Analysis of meiosis in Pristionchus pacificus reveals plasticity in homolog pairing and synapsis within the nematode lineage ]]> https://biorxiv.org/content/10.1101/662049v1?rss=1 Rillo-Bohn, R. Adilardi, R. Avsaroglu, B. Stevens, L. Kohler, S. Bayes, J. Wang, C. Lin, S. Baskevitch, K. Dernburg, A. 2019-06-05 doi:10.1101/662049 Cold Spring Harbor Laboratory Press 2019-06-05 <![CDATA[ Adaptation of Mycobacterium tuberculosis to biofilm growth is genetically linked to drug tolerance ]]> https://biorxiv.org/content/10.1101/663369v1?rss=1 Richards, J. P. Cai, W. Zill, N. A. Zhang, W. Ojha, A. K. 2019-06-06 doi:10.1101/663369 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Optogenetic control of Wnt signaling for modeling early embryogenic patterning with human pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/665695v1?rss=1 500-fold) using an optoWnt optogenetic system, drove broad transcriptional changes and mesendoderm differentiation of human ESCs at high efficiency (>95% cells). Furthermore, activating Wnt signaling in subpopulations of ESCs in 2D and 3D cultures induced cell self-organization and morphogenesis reminiscent of human gastrulation, including changes in cell migration and epithelial to mesenchymal transition. Our findings thus reveal an instructive role for Wnt in directing cell patterning in this ESC model for gastrulation. ]]> Repina, N. A. Bao, X. Zimmermann, J. A. Joy, D. A. Kane, R. S. Schaffer, D. V. 2019-06-10 doi:10.1101/665695 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Quickly fading afterimages: hierarchical adaptations in human perception ]]> https://biorxiv.org/content/10.1101/666198v1?rss=1 Klinger, M. E. Kell, C. A. Nikolic, D. 2019-06-10 doi:10.1101/666198 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ The genomic basis of evolved virus resistance is dependent on environmental resources ]]> https://biorxiv.org/content/10.1101/666404v1?rss=1 Roberts, K. Meaden, S. Sharpe, S. Kay, S. Doyle, T. Wilson, D. Bartlett, L. J. Paterson, S. Boots, M. 2019-06-11 doi:10.1101/666404 Cold Spring Harbor Laboratory Press 2019-06-11 <![CDATA[ Telophase correction refines division orientation in stratified epithelia ]]> https://biorxiv.org/content/10.1101/668244v1?rss=1 Lough, K. J. Byrd, K. M. Descovich, C. P. Spitzer, D. C. Bergman, A. J. Beaudoin, G. M. Reichardt, L. F. Williams, S. E. 2019-06-13 doi:10.1101/668244 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Chemical precision glyco-mutagenesis by glycosyltransferase engineering in living cells ]]> https://biorxiv.org/content/10.1101/669861v1?rss=1 Schumann, B. Malaker, S. A. Wisnovsky, S. P. Debets, M. F. Agbay, A. J. Fernandez, D. Wagner, L. J. S. Lin, L. Choi, J. Fox, D. M. Peh, J. Gray, M. A. Pedram, K. Kohler, J. J. Mrksich, M. Bertozzi, C. R. 2019-06-13 doi:10.1101/669861 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Phase separation of TAZ compartmentalizes the transcription machinery to promote gene expression ]]> https://biorxiv.org/content/10.1101/671230v1?rss=1 Wu, T. Lu, Y. Gutman, O. Lu, H. Zhou, Q. Henis, Y. I. Luo, K. 2019-06-14 doi:10.1101/671230 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ Viral satellites exploit phage proteins to escape degradation of the bacterial host chromosome ]]> https://biorxiv.org/content/10.1101/671271v1?rss=1 McKitterick, A. Hays, S. Alam, M. Seed, K. 2019-06-14 doi:10.1101/671271 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ Wide distribution of phage that infect freshwater SAR11 bacteria ]]> https://biorxiv.org/content/10.1101/672428v1?rss=1 Chen, L.-X. Zhao, Y. McMahon, K. D. Mori, J. F. Jessen, G. L. Nelson, T. C. Warren, L. A. Banfield, J. F. 2019-06-15 doi:10.1101/672428 Cold Spring Harbor Laboratory Press 2019-06-15 <![CDATA[ A mechanical model reveals that non-axisymmetric buckling lowers the energy barrier associated with membrane neck constriction ]]> https://biorxiv.org/content/10.1101/672485v1?rss=1 Vasan, R. Rudraraju, S. Akamatsu, M. Garikipati, K. Rangamani, P. 2019-06-15 doi:10.1101/672485 Cold Spring Harbor Laboratory Press 2019-06-15 <![CDATA[ High Throughput Evolution of Near Infrared Serotonin Nanosensors ]]> https://biorxiv.org/content/10.1101/673152v1?rss=1 Jeong, S. Yang, D. Beyene, A. G. Best, A. Landry, M. 2019-06-18 doi:10.1101/673152 Cold Spring Harbor Laboratory Press 2019-06-18 <![CDATA[ Phylogeny of Paullinia L. (Paullinieae: Sapindaceae), a diverse genus of lianas with rapid fruit evolution ]]> https://biorxiv.org/content/10.1101/673988v1?rss=1 Chery, J. G. Acevedo-Rodriguez, P. Rothfels, C. J. Specht, C. D. 2019-06-19 doi:10.1101/673988 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Genome-wide and enzymatic analysis reveals efficient D-galacturonic acid metabolism in the basidiomycete yeast Rhodosporidium toruloides ]]> https://biorxiv.org/content/10.1101/675652v1?rss=1 Protzko, R. J. Hach, C. A. Coradetti, S. T. Hackhofer, M. A. Magosch, S. Thieme, N. Arkin, A. P. Skerker, J. M. Dueber, J. E. Benz, J. P. 2019-06-21 doi:10.1101/675652 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Choice suppression through opponent but not independent function of the striatal indirect pathway ]]> https://biorxiv.org/content/10.1101/675850v1?rss=1 Delevich, K. Hoshal, B. D. Collins, A. G. E. Wilbrecht, L. 2019-06-19 doi:10.1101/675850 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Engineered illumination devices for optogenetic control of cellular signaling dynamics ]]> https://biorxiv.org/content/10.1101/675892v1?rss=1 Repina, N. A. McClave, T. Bao, X. Kane, R. S. Schaffer, D. V. 2019-06-19 doi:10.1101/675892 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Evaluating Protein Transfer Learning with TAPE ]]> https://biorxiv.org/content/10.1101/676825v1?rss=1 Rao, R. Bhattacharya, N. Thomas, N. Duan, Y. Chen, X. Canny, J. Abbeel, P. Song, Y. S. 2019-06-20 doi:10.1101/676825 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ EpiSort: Enumeration of cell types using targeted bisulfite sequencing ]]> https://biorxiv.org/content/10.1101/677211v1?rss=1 Aran, D. Dover, R. S. Lundy, K. E. Leipold, M. D. Xuhuai, J. McDevitt, S. L. Davis, M. M. Butte, A. J. 2019-06-21 doi:10.1101/677211 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Accurate assembly of the olive baboon (Papio anubis) genome using long-read and Hi-C data ]]> https://biorxiv.org/content/10.1101/678771v1?rss=1 Batra, S. S. Levy-Sakin, M. Robinson, J. Guillory, J. Durinck, S. Kwok, P.-Y. Cox, L. A. Seshagiri, S. Song, Y. S. Wall, J. D. 2019-06-24 doi:10.1101/678771 Cold Spring Harbor Laboratory Press 2019-06-24 <![CDATA[ Principles of self-organization and load adaptation by the actin cytoskeleton during clathrin-mediated endocytosis ]]> https://biorxiv.org/content/10.1101/678797v1?rss=1 Akamatsu, M. Vasan, R. Serwas, D. Ferrin, M. Rangamani, P. Drubin, D. G. 2019-06-21 doi:10.1101/678797 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Cell-in-the-loop pattern formation with optogenetically emulated cell-to-cell signaling ]]> https://biorxiv.org/content/10.1101/679597v1?rss=1 Perkins, M. L. Benzinger, D. Arcak, M. Khammash, M. 2019-06-22 doi:10.1101/679597 Cold Spring Harbor Laboratory Press 2019-06-22 <![CDATA[ POL30 alleles in Saccharomyces cerevisiae reveal complexities of the cell cycle and ploidy on heterochromatin assembly ]]> https://biorxiv.org/content/10.1101/679829v1?rss=1 Brothers, M. Rine, J. 2019-06-22 doi:10.1101/679829 Cold Spring Harbor Laboratory Press 2019-06-22 <![CDATA[ Consciousness & Brain Functional Complexity in Propofol Anaesthesia ]]> https://biorxiv.org/content/10.1101/680447v1?rss=1 Varley, T. Luppi, A. Pappas, I. Naci, L. Adapa, R. Owen, A. Menon, D. Stamatakis, E. 2019-07-02 doi:10.1101/680447 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Activity-Based Ratiometric FRET Probe Reveals Oncogene-Driven Changes in Labile Copper Pools Induced by Altered Glutathione Metabolism ]]> https://biorxiv.org/content/10.1101/682047v1?rss=1 Chung, C. Y.-S. Posimo, J. M. Lee, S. Tsang, T. Davis, J. M. Brady, D. C. Chang, C. J. 2019-06-24 doi:10.1101/682047 Cold Spring Harbor Laboratory Press 2019-06-24 <![CDATA[ Prevalence of antimicrobial resistance genes and integrons in commensal Gram-negative bacteria in a college community ]]> https://biorxiv.org/content/10.1101/683524v1?rss=1 Rubin, J. Mussio, K. Xu, Y. Suh, J. W. Riley, L. 2019-06-27 doi:10.1101/683524 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Genome-wide transposon screen of a Pseudomonas syringae mexB mutant reveals the substrates of efflux transporters ]]> https://biorxiv.org/content/10.1101/684605v1?rss=1 Helmann, T. C. Ongsarte, C. L. Lam, J. Deutschbauer, A. M. Lindow, S. E. 2019-07-02 doi:10.1101/684605 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Alpha/Beta Hydrolase Domain-Containing Protein 2 regulates the rhythm of follicular maturation and estrous stages of the female reproductive cycle ]]> https://biorxiv.org/content/10.1101/684951v1?rss=1 Bjoerkgren, I. Chung, D. H. Mendoza, S. Gabelev-Khasin, L. Modzelewski, A. He, L. Lishko, P. V. 2019-06-27 doi:10.1101/684951 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ BSU1 family phosphatases mediate Flagellin-FLS2 signaling through a specific phosphocode. ]]> https://biorxiv.org/content/10.1101/685610v1?rss=1 Park, C. H. Youn, J.-H. Xu, S.-L. Kim, J.-G. Bi, Y. Xu, N. Mudgett, M. B. Kim, S.-K. Kim, T.-W. Wang, Z.-Y. 2019-06-27 doi:10.1101/685610 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Hotspot prioritizations show sensitivity to data type ]]> https://biorxiv.org/content/10.1101/685735v1?rss=1 Norman, K. E. A. White, E. P. 2019-06-28 doi:10.1101/685735 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Specific lid-base contacts in the 26S proteasome control the conformational switching required for substrate engagement and degradation ]]> https://biorxiv.org/content/10.1101/687921v1?rss=1 Greene, E. R. Goodall, E. A. de la Pena, A. H. Matyskiela, M. E. Lander, G. C. Martin, A. 2019-07-02 doi:10.1101/687921 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Non-axisymmetric shapes of biological membranes from locally induced curvature ]]> https://biorxiv.org/content/10.1101/688127v1?rss=1 Omar, Y. A. D. Sahu, A. Sauer, R. A. Mandadapu, K. K. 2019-07-01 doi:10.1101/688127 Cold Spring Harbor Laboratory Press 2019-07-01 <![CDATA[ Explicit strategies in force field adaptation ]]> https://biorxiv.org/content/10.1101/694430v1?rss=1 Schween, R. McDougle, S. D. Hegele, M. Taylor, J. A. 2019-07-07 doi:10.1101/694430 Cold Spring Harbor Laboratory Press 2019-07-07 <![CDATA[ The Neural Basis of Predictive Pursuit ]]> https://biorxiv.org/content/10.1101/694604v1?rss=1 Yoo, S. B. M. Tu, J. C. Piantadosi, S. Hayden, B. Y. 2019-08-24 doi:10.1101/694604 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Soil bacterial populations are shaped by recombination and gene-specific selection across a meadow ]]> https://biorxiv.org/content/10.1101/695478v1?rss=1 Crits-Christoph, A. Olm, M. Diamond, S. Bouma-Gregson, K. Banfield, J. F. 2019-07-08 doi:10.1101/695478 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Massively parallel kinetic profiling of natural and engineered CRISPR nucleases ]]> https://biorxiv.org/content/10.1101/696393v1?rss=1 Jones, S. K. Hawkins, J. A. Johnson, N. V. Jung, C. Hu, K. Rybarski, J. R. Chen, J. S. Doudna, J. A. Press, W. H. Finkelstein, I. J. 2019-07-09 doi:10.1101/696393 Cold Spring Harbor Laboratory Press 2019-07-09 <![CDATA[ New genotype invasion of dengue virus serotype 1 drove massive outbreak in Guangzhou, China ]]> https://biorxiv.org/content/10.1101/697052v1?rss=1 Jing, Q. Wu, S. He, Z. Yuan, L. Ma, M. Bai, Z. Jiang, L. Marshall, J. Lu, J. Yang, Z. 2019-07-09 doi:10.1101/697052 Cold Spring Harbor Laboratory Press 2019-07-09 <![CDATA[ Inflammasome-mediated antagonism of type I interferon enhances Rickettsia pathogenesis ]]> https://biorxiv.org/content/10.1101/697573v1?rss=1 Burke, T. P. Engström, P. Chavez, R. A. Fonbuena, J. A. Vance, R. E. Welch, M. D. 2019-07-11 doi:10.1101/697573 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ VolcanoFinder: genomic scans for adaptive introgression ]]> https://biorxiv.org/content/10.1101/697987v1?rss=1 Setter, D. Mousset, S. Cheng, X. Nielsen, R. DeGiorgio, M. Hermisson, J. 2019-07-11 doi:10.1101/697987 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ HBMITool: a user-friendly software for labeling Human Brain Microscopy Images ]]> https://biorxiv.org/content/10.1101/699215v1?rss=1 Wang, H. Grinberg, L. T. Alegro, M. 2019-07-11 doi:10.1101/699215 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Identification, characterization, and application of a highly sensitive lactam biosensor from Pseudomonas putida ]]> https://biorxiv.org/content/10.1101/700484v1?rss=1 1000x more sensitive to exogenous ligand than previously reported sensors. Manipulating the expression of the sensor oplR (PP_3516) substantially altered the sensing parameters, with various vectors showing Kd values ranging from 700 nM (79.1 g/L) to 1.2 mM (135.6 mg/L). Our most sensitive construct was able to detect in vivo production of caprolactam above background at ~6 g/L. The high sensitivity and range of OplR is a powerful tool towards the development of novel routes to the biological synthesis of caprolactam. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/700484v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@ff5b8corg.highwire.dtl.DTLVardef@d365aaorg.highwire.dtl.DTLVardef@b79b18org.highwire.dtl.DTLVardef@27732f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Thompson, M. G. Pearson, A. N. Barajas, J. F. Cruz-Morales, P. Sedaghatian, N. Costello, Z. Garber, M. E. Incha, M. R. Valencia, L. E. Baidoo, E. Martin, H. G. Mukhopadhyay, A. Keasling, J. D. 2019-07-16 doi:10.1101/700484 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ DeepPrime2Sec: Deep Learning for Protein Secondary Structure Prediction from the Primary Sequences ]]> https://biorxiv.org/content/10.1101/705426v1?rss=1 Asgari, E. Poerner, N. McHardy, A. Mofrad, M. 2019-07-18 doi:10.1101/705426 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ Phazolicin - a Novel Thiazole/Oxazole-Modified Peptide Inhibiting the Bacterial Ribosome in a Species-Specific Way. ]]> https://biorxiv.org/content/10.1101/705970v1?rss=1 Travin, D. Y. Watson, Z. L. Metelev, M. Ward, F. R. Osterman, I. A. Khven, I. M. Khabibullina, N. F. Serebryakova, M. Mergaert, P. Polikanov, Y. S. Cate, J. H. D. Severinov, K. 2019-07-18 doi:10.1101/705970 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ μDamID: a microfluidic approach for imaging and sequencing protein-DNA interactions in single cells ]]> https://biorxiv.org/content/10.1101/706903v1?rss=1 Altemose, N. Maslan, A. Lai, A. White, J. A. Streets, A. M. 2019-07-18 doi:10.1101/706903 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ α-carboxysome formation is mediated by the multivalent and disordered protein CsoS2 ]]> https://biorxiv.org/content/10.1101/708164v1?rss=1 Oltrogge, L. M. Chaijarasphong, T. Chen, A. W. Bolin, E. R. Marqusee, S. Savage, D. F. 2019-07-19 doi:10.1101/708164 Cold Spring Harbor Laboratory Press 2019-07-19 <![CDATA[ Super-resolution microscopy unveils FIP200-scaffolded, cup-shaped organization of mammalian autophagic initiation machinery ]]> https://biorxiv.org/content/10.1101/712828v1?rss=1 Kenny, S. Chen, X. Ge, L. Xu, K. 2019-07-31 doi:10.1101/712828 Cold Spring Harbor Laboratory Press 2019-07-31 <![CDATA[ The mechanosensitive ion channel TRAAK is localized to the mammalian node of Ranvier ]]> https://biorxiv.org/content/10.1101/713990v1?rss=1 Brohawn, S. G. Wang, W. Schwarz, J. R. Handler, A. Campbell, E. B. MacKinnon, R. 2019-07-25 doi:10.1101/713990 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ Endocytic Clathrin Coats Develop Curvature at Early Stages of Their Formation ]]> https://biorxiv.org/content/10.1101/715219v1?rss=1 Willy, N. Ferguson, J. Silahli, S. Cakez, C. Hasan, F. Chang, H. Travesset, A. Li, S. Zandi, R. Li, D. Betzig, E. Cocucci, E. Kural, C. 2019-07-26 doi:10.1101/715219 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ Mitochondrial dysfunction is signaled to the integrated stress response by OMA1, DELE1 and HRI ]]> https://biorxiv.org/content/10.1101/715896v1?rss=1 Guo, X. Aviles, G. Liu, Y. Tian, R. Unger, B. A. Lin, Y.-H. T. Wiita, A. P. Xu, K. Correia, M. A. Kampmann, M. 2019-07-26 doi:10.1101/715896 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ Ecological divergence in sympatry causes gene misregulation in hybrids ]]> https://biorxiv.org/content/10.1101/717025v1?rss=1 McGirr, J. Martin, C. 2019-07-28 doi:10.1101/717025 Cold Spring Harbor Laboratory Press 2019-07-28 <![CDATA[ High Resolution Imaging Mass Spectrometry of Bacterial Microcolonies at Ecological Scales ]]> https://biorxiv.org/content/10.1101/717066v1?rss=1 Pessotti, R. d. C. Hansen, B. L. Zacharia, V. M. Polyakov, D. Traxler, M. F. 2019-07-28 doi:10.1101/717066 Cold Spring Harbor Laboratory Press 2019-07-28 <![CDATA[ A chimeric Japanese encephalitis vaccine protects against lethal yellow fever virus infection without inducing neutralizing antibodies ]]> https://biorxiv.org/content/10.1101/717181v1?rss=1 Mishra, N. Boudewijns, R. Schmid, M. A. Marques, R. E. Sharma, S. Neyts, J. Dallmeier, K. 2019-07-28 doi:10.1101/717181 Cold Spring Harbor Laboratory Press 2019-07-28 <![CDATA[ Grazer behavior can regulate large-scale patterns of community states ]]> https://biorxiv.org/content/10.1101/722215v1?rss=1 Karatayev, V. A. Baskett, M. L. Kushner, D. J. Shears, N. T. Caselle, J. E. Boettiger, C. 2019-08-01 doi:10.1101/722215 Cold Spring Harbor Laboratory Press 2019-08-01 <![CDATA[ Individual differences in model-based planning are linked to the ability to infer latent structure ]]> https://biorxiv.org/content/10.1101/723072v1?rss=1 Rmus, M. Ritz, H. Hunter, L. E. Bornstein, A. M. Shenhav, A. 2019-08-02 doi:10.1101/723072 Cold Spring Harbor Laboratory Press 2019-08-02 <![CDATA[ Microbial extracellular polysaccharide production and aggregate stability controlled by Switchgrass (Panicum virgatum) root biomass and soil water potential ]]> https://biorxiv.org/content/10.1101/724195v1?rss=1 Sher, Y. Baker, N. R. Herman, D. J. Fossum, C. Hale, L. Zhang, X.-X. Nuccio, E. E. Saha, M. C. Zhou, J. Pett-Ridge, J. Firestone, M. K. 2019-08-05 doi:10.1101/724195 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ On the distribution of tract lengths during adaptive introgression ]]> https://biorxiv.org/content/10.1101/724815v1?rss=1 Shchur, V. Svedberg, J. Medina, P. Corbett-Detig, R. Nielsen, R. 2019-08-05 doi:10.1101/724815 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ JMJD6 Cleaves MePCE to Release P-TEFb ]]> https://biorxiv.org/content/10.1101/725853v1?rss=1 Zhang, G. Lee, S. Liu, H. Hill, R. Hong, X. Liu, X. Crawford, F. Zhang, Q. Kingsley, M. Chen, Z. Lengeling, A. Bernet, K. Marrack, P. Kappler, J. Hansen, K. Zhou, Q. Li, C.-Y. 2019-08-05 doi:10.1101/725853 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ NeuroGPU, software for NEURON modeling in GPU-based hardware ]]> https://biorxiv.org/content/10.1101/727560v1?rss=1 Ben-Shalom, R. Athreya, N. S. Cross, C. Sanghevi, H. Korngreen, A. Bender, K. J. 2019-08-06 doi:10.1101/727560 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ Inferring neuronal ionic conductances from membrane potentials using CNNs ]]> https://biorxiv.org/content/10.1101/727974v1?rss=1 Ben-Shalom, R. Balewski, J. Siththaranjan, A. Baratham, V. Kyoung, H. Kim, K. G. Bender, K. J. Bouchard, K. E. 2019-08-06 doi:10.1101/727974 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ Conserved CxnC motifs in Kaposi’s sarcoma-associated herpesvirus ORF66 are required for viral late gene expression and mediate its interaction with ORF34 ]]> https://biorxiv.org/content/10.1101/728139v1?rss=1 Didychuk, A. L. Castaneda, A. F. Kushnir, L. O. Huang, C. Glaunsinger, B. A. 2019-08-08 doi:10.1101/728139 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ Allosteric activation of the nitric oxide receptor soluble guanylate cyclase mapped by cryo-electron microscopy ]]> https://biorxiv.org/content/10.1101/729418v1?rss=1 Horst, B. G. Yokom, A. L. Rosenberg, D. J. Morris, K. L. Hammel, M. Hurley, J. H. Marletta, M. A. 2019-08-08 doi:10.1101/729418 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ Computational evidence for hierarchically-structured reinforcement learning in humans ]]> https://biorxiv.org/content/10.1101/731752v1?rss=1 Eckstein, M. K. Collins, A. G. E. 2019-08-10 doi:10.1101/731752 Cold Spring Harbor Laboratory Press 2019-08-10 <![CDATA[ Can individual and integrated water, sanitation, and handwashing interventions reduce fecal contamination in the household environment? Evidence from the WASH Benefits cluster-randomized trial in rural Kenya ]]> https://biorxiv.org/content/10.1101/731992v1?rss=1 Pickering, A. Swarthout, J. Mureithi, M. Mboya, J. Arnold, B. F. Wolfe, M. Dentz, H. Lin, A. Arnold, C. Rao, G. Stewart, C. Ram, P. K. Clasen, T. Colford, J. Null, C. 2019-08-12 doi:10.1101/731992 Cold Spring Harbor Laboratory Press 2019-08-12 <![CDATA[ Unexpected sound omissions are signaled in human posterior superior temporal gyrus: an intracranial study ]]> https://biorxiv.org/content/10.1101/733212v1?rss=1 Fonken, Y. M. Mukerji, A. Jimenez, R. Lin, J. Brunner, P. Schalk, G. Knight, R. T. 2019-08-14 doi:10.1101/733212 Cold Spring Harbor Laboratory Press 2019-08-14 <![CDATA[ Dynamic turnover of centromeres drives karyotype evolution in Drosophila ]]> https://biorxiv.org/content/10.1101/733527v1?rss=1 Bracewell, R. Chatla, K. Nalley, M. J. Bachtrog, D. 2019-08-27 doi:10.1101/733527 Cold Spring Harbor Laboratory Press 2019-08-27 <![CDATA[ Direct comparison of clathrin-mediated endocytosis in budding and fission yeast reveals conserved and evolvable features ]]> https://biorxiv.org/content/10.1101/733543v1?rss=1 Sun, Y. Schoeneberg, J. Chen, S. Jiang, T. Kaplan, C. Xu, K. Pollard, T. Drubin, D. G. 2019-08-13 doi:10.1101/733543 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Defects in the assembly of ribosomes selected for β-amino acid incorporation ]]> https://biorxiv.org/content/10.1101/733584v1?rss=1 Ward, F. R. Watson, Z. L. Ad, O. Schepartz, A. Cate, J. H. D. 2019-08-13 doi:10.1101/733584 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ A Canal-Associated Neuron cAMP signalling pathway that regulates C. elegans larval development ]]> https://biorxiv.org/content/10.1101/733618v1?rss=1 Chien, J. Wolf, F. W. Grosche, S. Yosef, N. Garriga, G. Morck, C. 2019-08-15 doi:10.1101/733618 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Megacities as drivers of national outbreaks: the role of holiday travel in the spread of infectious diseases ]]> https://biorxiv.org/content/10.1101/737379v1?rss=1 Mahmud, A. S. Kabir, M. I. Engo-Monsen, K. Tahmina, S. Riaz, B. K. Hossain, M. A. Khanom, F. Rahman, M. M. Rahman, M. K. Sharmin, M. Hossain, D. M. Yasmin, S. Ahmed, M. M. Lusha, M. A. F. Buckee, C. O. 2019-08-16 doi:10.1101/737379 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ Linking microbial communities to ecosystem functions: what we can learn from genotype-phenotype mapping in organisms ]]> https://biorxiv.org/content/10.1101/740373v1?rss=1 Morris, A. H. Meyer, K. M. Bohannan, B. J. 2019-08-20 doi:10.1101/740373 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ Cytoplasmic mRNA decay factors modulate RNA polymerase II processivity in 5’ and 3’ gene regions in yeast ]]> https://biorxiv.org/content/10.1101/741058v1?rss=1 Fischer, J. Song, Y. S. Yosef, N. di Iulio, J. Churchman, L. S. Choder, M. 2019-08-23 doi:10.1101/741058 Cold Spring Harbor Laboratory Press 2019-08-23 <![CDATA[ Impact of crowding on the diversity of expanding populations ]]> https://biorxiv.org/content/10.1101/743534v1?rss=1 Schreck, C. F. Fusco, D. Karita, Y. Martis, S. Kayser, J. Duvernoy, M.-C. Hallatschek, O. 2019-08-22 doi:10.1101/743534 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Systematic identification of engineered methionines and oxaziridines for efficient, stable, and site-specific antibody bioconjugation ]]> https://biorxiv.org/content/10.1101/748160v1?rss=1 Elledge, S. K. Tran, H. L. Christian, A. H. Steri, V. Hann, B. Toste, F. D. Chang, C. J. Wells, J. A. 2019-08-28 doi:10.1101/748160 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ Defective cell death of distinct microglial subsets contributes to ADHD-like behavior in mice ]]> https://biorxiv.org/content/10.1101/749390v1?rss=1 Chuang, H.-C. Nichols, E. K. Rauch, I. Chang, W.-C. Misra, R. Lin, P. M. Kitaoka, M. Vance, R. E. Saijo, K. 2019-08-30 doi:10.1101/749390 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ Whole Genome Tree of Life: Deep Burst of Organism Diversity ]]> https://biorxiv.org/content/10.1101/756155v1?rss=1 Choi, J. Kim, S.-H. 2019-09-05 doi:10.1101/756155 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Surprising spatiotemporal stability and frequency-independence across multiple fitness peaks driving adaptive radiation in the wild ]]> https://biorxiv.org/content/10.1101/756908v1?rss=1 Martin, C. H. Gould, K. Bocklage, C. 2019-09-06 doi:10.1101/756908 Cold Spring Harbor Laboratory Press 2019-09-06 <![CDATA[ Causes and consequences of facultative sea crossing in a soaring migrant ]]> https://biorxiv.org/content/10.1101/758102v1?rss=1 Becciu, P. Rotics, S. Horvitz, N. Kaatz, M. Fiedler, W. Zurell, D. Flack, A. Jeltsch, F. Wikelski, M. Nathan, R. Sapir, N. 2019-09-08 doi:10.1101/758102 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ Exploratory movement analysis and report building with R package stmove ]]> https://biorxiv.org/content/10.1101/758987v1?rss=1 Seidel, D. P. Dougherty, E. R. Getz, W. 2019-09-09 doi:10.1101/758987 Cold Spring Harbor Laboratory Press 2019-09-09 <![CDATA[ Epigenetic memory independent of symmetric histone inheritance ]]> https://biorxiv.org/content/10.1101/760801v1?rss=1 Saxton, D. S. Rine, J. 2019-09-08 doi:10.1101/760801 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ A viral fusogen hijacks the actin cytoskeleton to drive cell-cell fusion ]]> https://biorxiv.org/content/10.1101/761502v1?rss=1 10 nm) ectodomains that undergo conformational changes to bring apposing membranes in close contact prior to fusion. Here we report that a viral fusogen with a short (<2 nm) ectodomain, the reptilian orthoreovirus p14, accomplishes the same task by hijacking the actin cytoskeleton. We show that the cytoplasmic domain of p14 triggers N-WASP-mediated assembly of a branched actin network, directly coupling local force generation with a short membrane-disruptive ectodomain. This work reveals that overcoming energetic barriers to cell-cell fusion does not require conformational changes of tall fusogens but can instead be driven by harnessing the host cytoskeleton.nnImpact StatementA viral fusogen drives cell-cell fusion by hijacking the actin machinery to directly couple actin assembly with a short fusogenic ectodomain. ]]> Chan, K. M. C. Son, S. Schmid, E. M. Fletcher, D. A. 2019-09-08 doi:10.1101/761502 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ Factors that influence the thymic selection of CD8αα intraepithelial lymphocytes ]]> https://biorxiv.org/content/10.1101/761601v1?rss=1 Kurd, N. S. Hoover, A. Yoon, J. Weist, B. M. Robey, E. A. 2019-09-12 doi:10.1101/761601 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ The theory and practice of measuring broad-range recombination rate from marker selected pools ]]> https://biorxiv.org/content/10.1101/762575v1?rss=1 Wei, K. H.- C. Mantha, A. Bachtrog, D. 2019-09-08 doi:10.1101/762575 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ A simple pyrocosm for studying soil microbial response to fire reveals a rapid, massive response by Pyronema species ]]> https://biorxiv.org/content/10.1101/763169v1?rss=1 Bruns, T. D. Chung, J. A. Carver, A. A. Glassman, S. 2019-09-09 doi:10.1101/763169 Cold Spring Harbor Laboratory Press 2019-09-09 <![CDATA[ Aquatic Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have novel nitrogenase-like gene clusters ]]> https://biorxiv.org/content/10.1101/765248v1?rss=1 Banfield, J. F. Meheust, R. He, C. Farag, I. Castelle, C. J. Chen, L.-X. Matheus Carnevali, P. B. Hug, L. A. Amano, Y. 2019-09-11 doi:10.1101/765248 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ Evolution of herbivory remodels a Drosophila genome ]]> https://biorxiv.org/content/10.1101/767160v1?rss=1 400 million years ago (mya) spurred the diversification of plant-feeding (herbivorous) insects and triggered an ongoing chemical co-evolutionary arms race. Because ancestors of most herbivorous insects first colonized plants >200 mya, the sands of time have buried evidence of how their genomes changed with their diet. We leveraged the serendipitous intersection of two genetic model systems: a close relative of yeast-feeding fruit fly (Drosophila melanogaster), the "wasabi fly" (Scaptomyza flava), that evolved to consume mustard plants including Arabidopsis thaliana. The yeast-to-mustard dietary transition remodeled the flys gene repertoire for sensing and detoxifying chemicals. Although many genes were lost, some underwent duplications that encode the most efficient detoxifying enzymes against mustard oils known from animals. ]]> Gloss, A. D. Nelson Dittrich, A. C. Lapoint, R. T. Goldman Huertas, B. Verster, K. I. Pelaez, J. L. Nelson, A. D. L. Aguilar, J. Armstrong, E. Charboneau, J. L. M. Groen, S. C. Hembry, D. H. Ochoa, C. J. O'Connor, T. K. Prost, S. Suzuki, H. C. Zaaijer, S. Nabity, P. D. Whiteman, N. K. 2019-09-12 doi:10.1101/767160 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Taxonomically and metabolically distinct microbial communities with depth and across a hillslope to riparian zone transect ]]> https://biorxiv.org/content/10.1101/768572v1?rss=1 Lavy, A. Matheus Carnevali, P. B. Keren, R. Bill, M. Wan, J. Tokunaga, T. K. Williams, K. H. Hubbard, S. S. Banfield, J. F. 2019-09-14 doi:10.1101/768572 Cold Spring Harbor Laboratory Press 2019-09-14 <![CDATA[ Activation of specific mushroom body output neurons inhibits proboscis extension and feeding behavior ]]> https://biorxiv.org/content/10.1101/768960v1?rss=1 Chia, J. Scott, K. 2019-09-13 doi:10.1101/768960 Cold Spring Harbor Laboratory Press 2019-09-13 <![CDATA[ Muntjac chromosome evolution and architecture ]]> https://biorxiv.org/content/10.1101/772343v1?rss=1 Mudd, A. B. Bredeson, J. V. Baum, R. Hockemeyer, D. Rokhsar, D. S. 2019-09-18 doi:10.1101/772343 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ The transcriptional co-repressor CtBP is a negative regulator of growth that antagonizes the Yorkie and JNK/AP-1 pathways ]]> https://biorxiv.org/content/10.1101/772533v1?rss=1 Sumabat, T. M. Worley, M. I. Pellock, B. J. Bosch, J. A. Hariharan, I. K. 2019-09-18 doi:10.1101/772533 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Flexible cobamide metabolism in Clostridioides (Clostridium) difficile 630 Δerm ]]> https://biorxiv.org/content/10.1101/772582v1?rss=1 Shelton, A. N. Lyu, X. Taga, M. E. 2019-09-19 doi:10.1101/772582 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Perceptual metacognition of human faces is causally supported by function of the lateral prefrontal cortex ]]> https://biorxiv.org/content/10.1101/772632v1?rss=1 Lapate, R. C. Samaha, J. Rokers, B. Postle, B. R. Davidson, R. J. 2019-09-20 doi:10.1101/772632 Cold Spring Harbor Laboratory Press 2019-09-20 <![CDATA[ A CLN6-CLN8 complex recruits lysosomal enzymes at the ER for Golgi transfer ]]> https://biorxiv.org/content/10.1101/773804v1?rss=1 Bajaj, L. di Ronza, A. Zheng, P. Eblimit, A. Pal, R. Sharma, J. Roman, D. Collette, J. R. Sifers, R. N. Jung, S. Y. Chen, R. Schekman, R. Sardiello, M. 2019-09-18 doi:10.1101/773804 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ A tale of winglets: evolution of flight morphology in stick insects ]]> https://biorxiv.org/content/10.1101/774067v1?rss=1 Zeng, Y. O'Maley, C. Singhal, S. Rahim, F. Park, S. Chen, X. Dudley, R. 2019-09-19 doi:10.1101/774067 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Spatial whitening in the retina may be necessary for V1 to learn a sparse representation of natural scenes ]]> https://biorxiv.org/content/10.1101/776799v1?rss=1 Dodds, E. M. Livezey, J. A. DeWeese, M. R. 2019-09-20 doi:10.1101/776799 Cold Spring Harbor Laboratory Press 2019-09-20 <![CDATA[ A distinct population of L6 neurons in mouse V1 mediate cross-callosal communication ]]> https://biorxiv.org/content/10.1101/778019v1?rss=1 Liang, Y. Sun, W. Lu, R. Chen, M. Ji, N. 2019-09-22 doi:10.1101/778019 Cold Spring Harbor Laboratory Press 2019-09-22 <![CDATA[ Comparison of BOLD and CBV using 3D EPI and 3D GRASE for cortical layer fMRI at 7T. ]]> https://biorxiv.org/content/10.1101/778142v1?rss=1 Beckett, A. J. Dadakova, T. Townsend, J. Huber, L. Park, S. Feinberg, D. A. 2019-09-23 doi:10.1101/778142 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ Using Parsimony-Guided Tree Proposals to Accelerate Convergence in Bayesian Phylogenetic Inference ]]> https://biorxiv.org/content/10.1101/778571v1?rss=1 Zhang, C. Huelsenbeck, J. P. Ronquist, F. 2019-09-23 doi:10.1101/778571 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ Adaptive Tree Proposals for Bayesian Phylogenetic Inference ]]> https://biorxiv.org/content/10.1101/783597v1?rss=1 Meyer, X. 2019-09-26 doi:10.1101/783597 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Evolution of NLR resistance genes with non-canonical N-terminal domains in wild tomato species ]]> https://biorxiv.org/content/10.1101/786194v1?rss=1 Seong, K. Seo, E. Li, M. Staskawicz, B. 2019-09-28 doi:10.1101/786194 Cold Spring Harbor Laboratory Press 2019-09-28 <![CDATA[ Improved computational identification of drug response using optical measurements of human stem cell derived cardiomyocytes in microphysiological systems ]]> https://biorxiv.org/content/10.1101/787390v1?rss=1 Jaeger, K. H. Charwat, V. Charrez, B. Finsberg, H. Maleckar, M. M. Wall, S. Healy, K. Tveito, A. 2019-10-01 doi:10.1101/787390 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ No statistical evidence for an effect of CCR5-Δ32 on lifespan in the UK Biobank cohort ]]> https://biorxiv.org/content/10.1101/787986v1?rss=1 Maier, R. M. Akbari, A. Wei, X. Patterson, N. Nielsen, R. J. Reich, D. E. 2019-10-02 doi:10.1101/787986 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology ]]> https://biorxiv.org/content/10.1101/790097v1?rss=1 Wu, S. L. Sanchez, H. M. Henry, J. M. Citron, D. T. Zhang, Q. Compton, K. E. Liang, B. Verma, A. Cummings, D. A. T. Le Menach, A. Scott, T. W. Wilson, A. L. Lindsay, S. W. Moyes, C. L. Hancock, P. A. Russell, T. L. Burkot, T. R. Marshall, J. M. Kiware, S. Reiner, R. C. Smith, D. L. 2019-10-01 doi:10.1101/790097 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Massive haplotypes underlie ecotypic differentiation in sunflowers ]]> https://biorxiv.org/content/10.1101/790279v1?rss=1 Todesco, M. Owens, G. L. Bercovich, N. Legare, J.-S. Soudi, S. Burge, D. O. Huang, K. Ostevik, K. L. Drummond, E. B. M. Imerovski, I. Lande, K. Pascual, M. A. Cheung, W. Staton, S. E. Munos, S. Nielsen, R. Donovan, L. A. Burke, J. M. Yeaman, S. Rieseberg, L. H. 2019-10-02 doi:10.1101/790279 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Dominant Vibrio cholerae phage exhibits lysis inhibition sensitive to disruption by a defensive phage satellite ]]> https://biorxiv.org/content/10.1101/790493v1?rss=1 Hays, S. G. Seed, K. 2019-10-02 doi:10.1101/790493 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Stereo In-Line Holographic Digital Microscope ]]> https://biorxiv.org/content/10.1101/790535v1?rss=1 Zimmerman, T. Antipac, N. Elnatan, D. Murru, A. Biswas, S. Pastore, V. P. Bonani, M. Waller, L. Fung, J. Fenu, G. Bianco, S. 2019-10-02 doi:10.1101/790535 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ A Joint Model of RNA Expression and Surface Protein Abundance in Single Cells ]]> https://biorxiv.org/content/10.1101/791947v1?rss=1 Gayoso, A. Lopez, R. Steier, Z. R. Regier, J. Streets, A. M. Yosef, N. 2019-10-07 doi:10.1101/791947 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Deep Generative Models for Detecting Differential Expression in Single Cells ]]> https://biorxiv.org/content/10.1101/794289v1?rss=1 Boyeau, P. Lopez, R. Regier, J. Gayoso, A. Jordan, M. I. Yosef, N. 2019-10-04 doi:10.1101/794289 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ Detecting Zero-Inflated Genes in Single-Cell Transcriptomics Data ]]> https://biorxiv.org/content/10.1101/794875v1?rss=1 Clivio, O. Lopez, R. Regier, J. Gayoso, A. Jordan, M. I. Yosef, N. 2019-10-07 doi:10.1101/794875 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Ratiometric bioluminescent sensors towards in vivo imaging of bacterial signaling ]]> https://biorxiv.org/content/10.1101/798140v1?rss=1 Dippel, A. B. Anderson, W. A. Park, J. H. Yildiz, F. H. Hammond, M. C. 2019-10-08 doi:10.1101/798140 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Cryo-EM structure of the mitochondrial protein-import channel TOM complex from Saccharomyces cerevisiae. ]]> https://biorxiv.org/content/10.1101/798371v1?rss=1 Tucker, K. Park, E. 2019-10-08 doi:10.1101/798371 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Numerous post-translational modifications of RNA polymerase II subunit Rpb4 link transcription to post-transcriptional mechanisms ]]> https://biorxiv.org/content/10.1101/798603v1?rss=1 Richard, S. Gross, L. Fischer, J. Bendalak, K. Ziv, T. Urim, S. Choder, M. 2019-10-10 doi:10.1101/798603 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Phenotypic differences in reversible attachment behavior reveal distinct P. aeruginosa surface colonization strategies ]]> https://biorxiv.org/content/10.1101/798843v1?rss=1 Lee, C. K.-m. Vachier, J. de Anda, J. zhao, k. Baker, A. Bennett, R. R. Armbruster, C. R. Lewis, K. A. Tarnopol, R. L. Lomba, C. J. Hogan, D. A. Parsek, M. R. O'Toole, G. A. Golestanian, R. Wong, G. C. L. 2019-10-10 doi:10.1101/798843 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Native and invasive populations of the ectomycorrhizal death cap Amanita phalloides are highly sexual but dispersal limited ]]> https://biorxiv.org/content/10.1101/799254v1?rss=1 Golan, J. J. Adams, C. Cross, H. Elmore, H. Gardes, M. Glassman, S. I. Goncalves, S. Hess, J. I. Richard, F. Wang, Y.-W. Wolfe, B. Pringle, A. 2019-10-09 doi:10.1101/799254 Cold Spring Harbor Laboratory Press 2019-10-09 <![CDATA[ Potent CRISPR-Cas9 inhibitors from Staphylococcus genomes ]]> https://biorxiv.org/content/10.1101/799403v1?rss=1 Watters, K. E. Shivram, H. Fellmann, C. Lew, R. J. McMahon, B. Doudna, J. A. 2019-10-09 doi:10.1101/799403 Cold Spring Harbor Laboratory Press 2019-10-09 <![CDATA[ Inference of Single-Cell Phylogenies from Lineage Tracing Data ]]> https://biorxiv.org/content/10.1101/800078v1?rss=1 Jones, M. G. Khodaverdian, A. Quinn, J. J. Chan, M. M. Hussmann, J. A. Wang, R. Xu, C. Weissman, J. S. Yosef, N. 2019-10-10 doi:10.1101/800078 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ From sectors to speckles: The impact of long range migration on gene surfing ]]> https://biorxiv.org/content/10.1101/803189v1?rss=1 Paulose, J. Hallatschek, O. 2019-10-13 doi:10.1101/803189 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ Cryo-EM structure of the potassium-chloride cotransporter KCC4 in lipid nanodiscs ]]> https://biorxiv.org/content/10.1101/805267v1?rss=1 Brohawn, S. G. Kern, D. M. Reid, M. S. 2019-10-14 doi:10.1101/805267 Cold Spring Harbor Laboratory Press 2019-10-14 <![CDATA[ A weak link with actin organizes tight junctions to control epithelial permeability ]]> https://biorxiv.org/content/10.1101/805689v1?rss=1 Belardi, B. Hamkins-Indik, T. Harris, A. R. Fletcher, D. A. 2019-10-16 doi:10.1101/805689 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ 3D projection electrophoresis for single-cell immunoblotting ]]> https://biorxiv.org/content/10.1101/805770v1?rss=1 2.5 cells/s (70X faster than serial sampling) and perform 25 immunoblots/mm2 device area (>10X increase over previous immunoblots). A straightforward device for parallel single-cell immunoblotting, projection electrophoresis promises to advance integration of protein-level profiles into the emerging single-cell atlas of genomic and transcriptomic profiles. ]]> Grist, S. M. Mourdoukoutas, A. P. Herr, A. E. 2019-10-16 doi:10.1101/805770 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Phytotransferrin endocytosis mediates a direct cell surface-to-chloroplast iron trafficking axis in marine diatoms ]]> https://biorxiv.org/content/10.1101/806539v1?rss=1 Turnsek, J. Brunson, J. K. Deerinck, T. J. Obornik, M. Horak, A. Bielinski, V. A. Allen, A. E. 2019-10-16 doi:10.1101/806539 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Soil microbial communities associated with giant sequoia: How does the world’s largest tree affect some of the world’s smallest organisms? ]]> https://biorxiv.org/content/10.1101/807040v1?rss=1 Carey, C. J. Glassman, S. I. Bruns, T. D. Aronson, E. L. Hart, S. C. 2019-10-17 doi:10.1101/807040 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Challenging conventional wisdom on the evolution of resistance to multi-drug HIV treatment: Lessons from data and modeling. ]]> https://biorxiv.org/content/10.1101/807560v1?rss=1 Feder, A. F. Harper, K. N. Pennings, P. S. 2019-10-17 doi:10.1101/807560 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Accurate and Complete Genomes from Metagenomes ]]> https://biorxiv.org/content/10.1101/808410v1?rss=1 Chen, L.-X. Anantharaman, K. Shaiber, A. Eren, A. M. Banfield, J. F. 2019-10-17 doi:10.1101/808410 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Heterogeneous synaptic weighting improves neural coding in the presence of common noise ]]> https://biorxiv.org/content/10.1101/811364v1?rss=1 Sachdeva, P. S. Livezey, J. A. DeWeese, M. R. 2019-10-21 doi:10.1101/811364 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Roq1 confers resistance to Xanthomonas, Pseudomonas syringae and Ralstonia solanacearum in tomato ]]> https://biorxiv.org/content/10.1101/813758v1?rss=1 Thomas, N. C. Hendrich, C. G. Gill, U. S. Allen, C. Hutton, S. F. Schultink, A. 2019-10-21 doi:10.1101/813758 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ A highly homogeneous expansion microscopy polymer composed of tetrahedron-like monomers ]]> https://biorxiv.org/content/10.1101/814111v1?rss=1 Gao, R. Yu, C.-C. Gao, L. Piatkevich, K. D. Neve, R. L. Upadhyayula, S. Boyden, E. S. 2019-10-22 doi:10.1101/814111 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Manumycin Polyketides Act as Molecular Glues Between UBR7 and P53 to Impair Breast Cancer Pathogenicity ]]> https://biorxiv.org/content/10.1101/814285v1?rss=1 Isobe, Y. Okumura, M. White, R. McGregor, L. M. McKenna, J. M. Tallarico, J. A. Schirle, M. Maimone, T. J. Nomura, D. K. 2019-10-22 doi:10.1101/814285 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Emergence of opposite neurons in a firing-rate model of multisensory integration ]]> https://biorxiv.org/content/10.1101/814483v1?rss=1 Chau, H. Y. Zhang, W.-H. Lee, T. S. 2019-10-22 doi:10.1101/814483 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ What would it take to describe the global diversity of parasites? ]]> https://biorxiv.org/content/10.1101/815902v1?rss=1 Carlson, C. J. Phillips, A. J. Dallas, T. A. Alexander, L. W. Bansal, S. 2019-10-23 doi:10.1101/815902 Cold Spring Harbor Laboratory Press 2019-10-23 <![CDATA[ Flexible Modulation of Neural Variance Facilitates Neuroprosthetic Skill Learning ]]> https://biorxiv.org/content/10.1101/817346v1?rss=1 You, A. K. Liu, B. Singhal, A. Gowda, S. Moorman, H. Orsborn, A. Ganguly, K. Carmena, J. M. 2019-10-24 doi:10.1101/817346 Cold Spring Harbor Laboratory Press 2019-10-24 <![CDATA[ Bacterial secondary metabolite biosynthetic potential in soil varies with phylum, depth, and vegetation type ]]> https://biorxiv.org/content/10.1101/818815v1?rss=1 Sharrar, A. Crits-Christoph, A. Meheust, R. Diamond, S. Starr, E. Banfield, J. 2019-10-25 doi:10.1101/818815 Cold Spring Harbor Laboratory Press 2019-10-25 <![CDATA[ Regenerative capacity in Drosophila imaginal discs is controlled by damage-responsive, maturity-silenced enhancers ]]> https://biorxiv.org/content/10.1101/820605v1?rss=1 Harris, R. E. Stinchfield, M. J. Nystrom, S. L. McKay, D. J. Hariharan, I. K. 2019-10-28 doi:10.1101/820605 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ Bacterial metabolism rescues the inhibition of intestinal drug absorption by food and drug additives ]]> https://biorxiv.org/content/10.1101/821132v1?rss=1 Zou, L. Spanogiannopoulos, P. Chien, H.-C. Pieper, L. M. Cai, W. Khuri, N. Pottel, J. Vora, B. Ni, Z. Tsakalozou, E. Zhang, W. Shoichet, B. K. Giacomini, K. M. Turnbaugh, P. J. 2019-10-28 doi:10.1101/821132 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ Prevalence of beta-lactam drug-resistance genes in commensal Escherichia coli contaminating ready-to-eat lettuce ]]> https://biorxiv.org/content/10.1101/824516v1?rss=1 Liao, N. Rubin, J. Hu, Y. Ramirez, H. A. Araujo Borges, C. Zhou, B. Zhang, Y. Zhang, R. Jiang, J. Riley, L. W. 2019-10-30 doi:10.1101/824516 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ TRIM14 is a key regulator of the type I interferon response during Mycobacterium tuberculosis infection ]]> https://biorxiv.org/content/10.1101/828533v1?rss=1 Hoffpauir, C. T. Bell, S. L. West, K. O. Jing, T. Odio-Torres, S. Cox, J. S. West, A. P. Li, P. Patrick, K. L. Watson, R. O. 2019-11-02 doi:10.1101/828533 Cold Spring Harbor Laboratory Press 2019-11-02 <![CDATA[ Matrix Inversion and Subset Selection (MISS): A novel pipeline for quantitative mapping of diverse cell types across the murine brain ]]> https://biorxiv.org/content/10.1101/833566v1?rss=1 Torok, J. Mezias, C. Maia, P. Raj, A. 2019-11-07 doi:10.1101/833566 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Cargo licenses maturation of stalled endocytic sites through a regulatory checkpoint ]]> https://biorxiv.org/content/10.1101/834523v1?rss=1 Pedersen, R. T. Hassinger, J. E. Marchando, P. Drubin, D. G. 2019-11-08 doi:10.1101/834523 Cold Spring Harbor Laboratory Press 2019-11-08 <![CDATA[ Design of Ceramic Packages for Acoustically Coupled Implantable Medical Devices ]]> https://biorxiv.org/content/10.1101/836312v1?rss=1 Shen, K. Maharbiz, M. M. 2019-11-11 doi:10.1101/836312 Cold Spring Harbor Laboratory Press 2019-11-11 <![CDATA[ Exploring High-Dimensional Biological Data with Sparse Contrastive Principal Component Analysis ]]> https://biorxiv.org/content/10.1101/836650v1?rss=1 Boileau, P. Hejazi, N. S. Dudoit, S. 2019-11-09 doi:10.1101/836650 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Surface Modification Effects on Single-Walled Carbon Nanotubes for Multimodal Optical Applications ]]> https://biorxiv.org/content/10.1101/837278v1?rss=1 Chio, L. Pinals, R. L. Goh, N. S. Murali, A. Landry, M. P. 2019-11-12 doi:10.1101/837278 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ ULK complex organization in autophagy by a C-shaped FIP200 N-terminal domain dimer ]]> https://biorxiv.org/content/10.1101/840009v1?rss=1 Shi, X. Yokom, A. L. Wang, C. Young, L. N. Youle, R. J. Hurley, J. H. 2019-11-12 doi:10.1101/840009 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Integrated Genomic Analysis Reveals Key Features of Long Undecoded Transcript Isoform (LUTI)-based Gene Repression ]]> https://biorxiv.org/content/10.1101/843458v1?rss=1 Tresenrider, A. Jorgensen, V. Chia, M. Liao, H. van Werven, F. Unal, E. 2019-11-15 doi:10.1101/843458 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Ubiquitination modulates a protein energy landscape site-specifically with consequences for proteasomal degradation ]]> https://biorxiv.org/content/10.1101/843631v1?rss=1 Carroll, E. C. Greene, E. R. Martin, A. Marqusee, S. 2019-11-15 doi:10.1101/843631 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ A comparison of humans and baboons suggests germline mutation rates do not track cell divisions ]]> https://biorxiv.org/content/10.1101/844910v1?rss=1 Wu, F. L. Strand, A. Ober, C. Wall, J. D. Moorjani, P. Przeworski, M. 2019-11-16 doi:10.1101/844910 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ Comparative transcriptomics of a monocotyledonous geophyte reveals shared molecular mechanisms of underground storage organ formation. ]]> https://biorxiv.org/content/10.1101/845602v1?rss=1 Tribble, C. M. Martinez-Gomez, J. Alzate-Guarin, F. Rothfels, C. J. Specht, C. D. 2019-11-17 doi:10.1101/845602 Cold Spring Harbor Laboratory Press 2019-11-17 <![CDATA[ Emergence of opposite neurons in a decentralized firing-rate model of multisensory integration ]]> https://biorxiv.org/content/10.1101/845743v1?rss=1 Niu, X. Chau, H. Y. Lee, T. S. Zhang, W.-H. 2019-11-17 doi:10.1101/845743 Cold Spring Harbor Laboratory Press 2019-11-17 <![CDATA[ Chromosome-level assembly of Drosophila bifasciata reveals important karyotypic transition of the X chromosome ]]> https://biorxiv.org/content/10.1101/847558v1?rss=1 Bracewell, R. Tran, A. Chatla, K. Bachtrog, D. 2019-11-20 doi:10.1101/847558 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Signal to Noise Ratio as a Cross-Platform Metric for Intraoperative Fluorescence Imaging ]]> https://biorxiv.org/content/10.1101/847863v1?rss=1 Gharia, A. Philip Papageorgiou, E. P. Giverts, S. D. Park, C. Anwar, M. 2019-11-20 doi:10.1101/847863 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Complex evolutionary history of the Y chromosome in flies of the Drosophila obscura species group ]]> https://biorxiv.org/content/10.1101/848804v1?rss=1 Bracewell, R. Bachtrog, D. 2019-11-21 doi:10.1101/848804 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Convergence and divergence in anti-predator displays: A novel approach to quantitative behavioural comparison in Neotropical snakes ]]> https://biorxiv.org/content/10.1101/849703v1?rss=1 Davis Rabosky, A. R. Moore, T. Y. Sanchez-Paredes, C. M. Westeen, E. P. Larson, J. G. Sealey, B. A. Balinski, B. A. 2019-11-21 doi:10.1101/849703 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Synergistic cues from diverse bacteria enhance multicellular development in a choanoflagellate ]]> https://biorxiv.org/content/10.1101/851824v1?rss=1 Ireland, E. V. Woznica, A. King, N. 2019-11-22 doi:10.1101/851824 Cold Spring Harbor Laboratory Press 2019-11-22 <![CDATA[ Machine Learning Predicts New Anti-CRISPR Proteins ]]> https://biorxiv.org/content/10.1101/854950v1?rss=1 Eitzinger, S. Asif, A. Watters, K. E. Iavarone, A. T. Knott, G. J. Doudna, J. A. Minhas, F. u. A. A. 2019-11-29 doi:10.1101/854950 Cold Spring Harbor Laboratory Press 2019-11-29 <![CDATA[ Whole genome sequences of 23 species from the Drosophila montium species group (Diptera: Drosophilidae): A resource for testing evolutionary hypotheses ]]> https://biorxiv.org/content/10.1101/861005v1?rss=1 Bronski, M. J. Martinez, C. C. Weld, H. A. Eisen, M. B. 2019-12-02 doi:10.1101/861005 Cold Spring Harbor Laboratory Press 2019-12-02 <![CDATA[ A yeast platform for high-level synthesis of natural and unnatural tetrahydroisoquinoline alkaloids ]]> https://biorxiv.org/content/10.1101/863506v1?rss=1 Pyne, M. E. Kevvai, K. Grewal, P. S. Narcross, L. Choi, B. Bourgeois, L. Dueber, J. E. Martin, V. J. 2019-12-05 doi:10.1101/863506 Cold Spring Harbor Laboratory Press 2019-12-05 <![CDATA[ Abundant expression of maternal siRNAs is a conserved feature of seed development ]]> https://biorxiv.org/content/10.1101/866806v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@68de55org.highwire.dtl.DTLVardef@dca8eaorg.highwire.dtl.DTLVardef@d5d489org.highwire.dtl.DTLVardef@74824a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Grover, J. W. Burgess, D. G. Kendall, T. Baten, A. Pokhrel, S. King, G. J. Meyers, B. C. Freeling, M. Mosher, R. A. 2019-12-06 doi:10.1101/866806 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Distinct activities of Scrib module proteins organize epithelial polarity ]]> https://biorxiv.org/content/10.1101/866863v1?rss=1 Khoury, M. J. Bilder, D. 2019-12-06 doi:10.1101/866863 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Controlling the speed and trajectory of evolution with counterdiabatic driving ]]> https://biorxiv.org/content/10.1101/867143v1?rss=1 Iram, S. Dolson, E. Chiel, J. Pelesko, J. Krishnan, N. Güngör, O. Kuznets-Speck, B. Deffner, S. Ilker, E. Scott, J. G. Hinczewski, M. 2019-12-06 doi:10.1101/867143 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ The neural representation of emotion is high-dimensional, categorical, and distributed across transmodal brain regions ]]> https://biorxiv.org/content/10.1101/872192v1?rss=1 Horikawa, T. Cowen, A. S. Keltner, D. Kamitani, Y. 2019-12-11 doi:10.1101/872192 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ Population diversification in a yeast metabolic program promotes anticipation of environmental shifts ]]> https://biorxiv.org/content/10.1101/002907v1?rss=1 Ophelia S Venturelli Ignacio Zuleta Richard M Murray Hana El-Samad 2014-02-21 doi:10.1101/002907 Cold Spring Harbor Laboratory Press 2014-02-21 <![CDATA[ Exploring the spatially explicit predictions of the Maximum Entropy Theory of Ecology ]]> https://biorxiv.org/content/10.1101/003657v1?rss=1 Daniel McGlinn Xiao Xiao Justin Kitzes Ethan P White 2014-03-30 doi:10.1101/003657 Cold Spring Harbor Laboratory Press 2014-03-30 <![CDATA[ Non-respiratory functions of Saccharomyces cerevisiae mitochondria are required for optimal attractiveness to Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/007336v1?rss=1 Kelly M Schiabor Allison S Quan Michael Eisen 2014-07-21 doi:10.1101/007336 Cold Spring Harbor Laboratory Press 2014-07-21 <![CDATA[ Understanding Admixture Fractions ]]> https://biorxiv.org/content/10.1101/008078v1?rss=1 Mason Liang Rasmus Nielsen 2014-08-16 doi:10.1101/008078 Cold Spring Harbor Laboratory Press 2014-08-16 <![CDATA[ FinisherSC : A repeat-aware tool for upgrading de-novo assembly using long reads ]]> https://biorxiv.org/content/10.1101/010215v1?rss=1 Ka Kit Lam Kurt LaButti Asif Khalak David Tse 2014-10-14 doi:10.1101/010215 Cold Spring Harbor Laboratory Press 2014-10-14 <![CDATA[ Recent evolution of the mutation rate and spectrum in Europeans ]]> https://biorxiv.org/content/10.1101/010314v1?rss=1 Kelley Harris 2014-10-14 doi:10.1101/010314 Cold Spring Harbor Laboratory Press 2014-10-14 <![CDATA[ A Hidden Markov Model for Investigating Recent Positive Selection through Haplotype Structure ]]> https://biorxiv.org/content/10.1101/011247v1?rss=1 Hua Chen Jody Hey Montgomery Slatkin 2014-11-08 doi:10.1101/011247 Cold Spring Harbor Laboratory Press 2014-11-08 <![CDATA[ Shrinkage of dispersion parameters in the binomial family, with application to differential exon skipping ]]> https://biorxiv.org/content/10.1101/012823v1?rss=1 Sean Ruddy Marla Johnson Elizabeth Purdom 2014-12-16 doi:10.1101/012823 Cold Spring Harbor Laboratory Press 2014-12-16 <![CDATA[ Do Read Errors Matter for Genome Assembly? ]]> https://biorxiv.org/content/10.1101/014399v1?rss=1 Ilan Shomorony Thomas Courtade David Tse 2015-01-26 doi:10.1101/014399 Cold Spring Harbor Laboratory Press 2015-01-26 <![CDATA[ GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown roots systems ]]> https://biorxiv.org/content/10.1101/016931v1?rss=1 Rubén Rellán-Álvarez Guillaume Lobet Heike Lindner Pierre-Luc M Pradier Jose Sebastian Muh-Ching Yee Yu Geng Charlotte Trontin Therese LaRue Amanda Schrager Lavelle Cara H Haney Rita Nieu Julin N Maloof John P Vogel José R Dinneny 2015-03-30 doi:10.1101/016931 Cold Spring Harbor Laboratory Press 2015-03-30 <![CDATA[ A Novel Mechanism for Color Vision: Pupil Shape and Chromatic Aberration Can Provide Spectral Discrimination for Color Blind Organisms. ]]> https://biorxiv.org/content/10.1101/017756v1?rss=1 Alexander L Stubbs Christopher W Stubbs 2015-04-09 doi:10.1101/017756 Cold Spring Harbor Laboratory Press 2015-04-09 <![CDATA[ Sequencing of 15,622 gene-bearing BACs reveals new features of the barley genome ]]> https://biorxiv.org/content/10.1101/018978v1?rss=1 María Muñoz-Amatriaín Stefano Lonardi MingCheng Luo Kavitha Madishetty Jan Svensson Matthew Moscou Steve Wanamaker Tao Jiang Andris Kleinhofs Gary Muehlbauer Roger Wise Nils Stein Yaqin Ma Edmundo Rodriguez Dave Kudrna Prasanna R Bhat Shiaoman Chao Pascal Condamine Shane Heinen Josh Resnik Rod Wing Heather N Witt Matthew Alpert Marco Beccuti Serdar Bozdag Francesca Cordero Hamid Mirebrahim Rachid Ounit Yonghui Wu Frank You Jie Zheng Hana Šimková Jaroslav Doležel Jane Grimwood Jeremy Schmutz Denisa Duma Lothar Altschmied Tom Blake Phil Bregitzer Laurel Cooper Muharrem Dilbirligi Anders Falk Lei 2015-05-05 doi:10.1101/018978 Cold Spring Harbor Laboratory Press 2015-05-05 <![CDATA[ Clustering of mRNA-Seq data for detection of alternative splicing patterns ]]> https://biorxiv.org/content/10.1101/021733v1?rss=1 Marla Johnson Elizabeth Purdom 2015-06-30 doi:10.1101/021733 Cold Spring Harbor Laboratory Press 2015-06-30 <![CDATA[ Joint estimation of contamination, error and demography for nuclear DNA from ancient humans ]]> https://biorxiv.org/content/10.1101/022285v1?rss=1 3X), we find we can recover accurate estimates of all these parameters, even when the contamination rate is as high as 50%. ]]> Fernando Racimo Gabriel Renaud Montgomery Slatkin 2015-07-10 doi:10.1101/022285 Cold Spring Harbor Laboratory Press 2015-07-10 <![CDATA[ Genomic DNA transposition induced by human PGBD5 ]]> https://biorxiv.org/content/10.1101/023887v1?rss=1 Anton Henssen Elizabeth Henaff Eileen Jiang Amy R Eisenberg Julianne R Carson Camila Villasante Mondira Ray Eric Still Melissa Burns Jorge Gandara Cedric Feschotte Christopher E. Mason Alex Kentsis 2015-08-03 doi:10.1101/023887 Cold Spring Harbor Laboratory Press 2015-08-03 <![CDATA[ Isolation-By-Distance-and-Time in a stepping-stone model ]]> https://biorxiv.org/content/10.1101/024133v1?rss=1 Nicolas Duforet-Frebourg Montgomery Slatkin 2015-08-07 doi:10.1101/024133 Cold Spring Harbor Laboratory Press 2015-08-07 <![CDATA[ Using Ancient Samples in Projection Analysis ]]> https://biorxiv.org/content/10.1101/025015v1?rss=1 Melinda A Yang Montgomery Slatkin 2015-08-20 doi:10.1101/025015 Cold Spring Harbor Laboratory Press 2015-08-20 <![CDATA[ SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates, and effective population sizes ]]> https://biorxiv.org/content/10.1101/029736v1?rss=1 Matthias Steinrücken Ethan M Jewett Yun S Song 2015-10-23 doi:10.1101/029736 Cold Spring Harbor Laboratory Press 2015-10-23 <![CDATA[ The Genetic Cost of Neanderthal Introgression ]]> https://biorxiv.org/content/10.1101/030387v1?rss=1 Kelley Harris Rasmus Nielsen 2015-10-30 doi:10.1101/030387 Cold Spring Harbor Laboratory Press 2015-10-30 <![CDATA[ Hybrid Systems Modeling for (Cancer) Systems Biology ]]> https://biorxiv.org/content/10.1101/035022v1?rss=1 Roel I.J. Dobbe Claire J. Tomlin 2015-12-23 doi:10.1101/035022 Cold Spring Harbor Laboratory Press 2015-12-23 <![CDATA[ Fast and accurate single-cell RNA-Seq analysis by clustering of transcript-compatibility counts ]]> https://biorxiv.org/content/10.1101/036863v1?rss=1 Vasilis Ntranos Govinda M. Kamath Jesse Zhang Lior Pachter David N. Tse 2016-01-15 doi:10.1101/036863 Cold Spring Harbor Laboratory Press 2016-01-15 <![CDATA[ Local joint testing improves power and identifies missing heritability in association studies ]]> https://biorxiv.org/content/10.1101/040089v1?rss=1 Brielin C Brown Alkes Price Nikolaos Patsopoulos Noah Zaitlen 2016-02-18 doi:10.1101/040089 Cold Spring Harbor Laboratory Press 2016-02-18 <![CDATA[ Y-box protein 1 is required to sort microRNAs into exosomes in cells and in a cell-free reaction ]]> https://biorxiv.org/content/10.1101/040238v1?rss=1 Matthew Shurtleff Kate V. Karfilis Morayma Temoche-Diaz Sayaka Ri Randy Schekman 2016-02-19 doi:10.1101/040238 Cold Spring Harbor Laboratory Press 2016-02-19 <![CDATA[ An ecological assessment of the pandemic threat of Zika virus ]]> https://biorxiv.org/content/10.1101/040386v1?rss=1 Colin Carlson Eric Dougherty Wayne Getz 2016-02-19 doi:10.1101/040386 Cold Spring Harbor Laboratory Press 2016-02-19 <![CDATA[ BIGMAC : Breaking Inaccurate Genomes and Merging Assembled Contigs for long read metagenomic assembly ]]> https://biorxiv.org/content/10.1101/045690v1?rss=1 Ka Kit Lam Richard Hall Alicia Clum Satish Rao 2016-03-29 doi:10.1101/045690 Cold Spring Harbor Laboratory Press 2016-03-29 <![CDATA[ k-BOOM: A Bayesian approach to ontology structure inference, with applications in disease ontology construction ]]> https://biorxiv.org/content/10.1101/048843v1?rss=1 Christopher J Mungall Sebastian Koehler Peter Robinson Ian Holmes Melissa Haendel 2016-04-15 doi:10.1101/048843 Cold Spring Harbor Laboratory Press 2016-04-15 <![CDATA[ Cortical rhythms are modulated by respiration ]]> https://biorxiv.org/content/10.1101/049007v1?rss=1 Detlef H Heck Samuel S McAfee Yu Liu Abbas Babajani-Feremi Roozbeh Rezaie Walter J Freeman James W Wheless Andrew C Papanicolaou Miklos Ruszinko Robert Kozma 2016-04-16 doi:10.1101/049007 Cold Spring Harbor Laboratory Press 2016-04-16 <![CDATA[ Arabidopsis cobra protein binds to glucan chains with higher affinity than to cellulose ]]> https://biorxiv.org/content/10.1101/050427v1?rss=1 Nadav Sorek Chris Somerville 2016-04-26 doi:10.1101/050427 Cold Spring Harbor Laboratory Press 2016-04-26 <![CDATA[ Stable host gene expression in the gut of adult Drosophila melanogaster with different bacterial mono-associations ]]> https://biorxiv.org/content/10.1101/053512v1?rss=1 Carolyn Elya Vivian Zhang Will Ludington Michael B Eisen 2016-05-15 doi:10.1101/053512 Cold Spring Harbor Laboratory Press 2016-05-15 <![CDATA[ Parvalbumin interneuron dysfunction in a thalamus - prefrontal cortex circuit in Disc1 deficiency mice ]]> https://biorxiv.org/content/10.1101/054759v1?rss=1 Kristen Delevich Hanna Jaaro-Peled Mario Penzo Akira Sawa Bo Li 2016-05-21 doi:10.1101/054759 Cold Spring Harbor Laboratory Press 2016-05-21 <![CDATA[ Could a neuroscientist understand a microprocessor? ]]> https://biorxiv.org/content/10.1101/055624v1?rss=1 Eric Jonas Konrad Kording 2016-05-26 doi:10.1101/055624 Cold Spring Harbor Laboratory Press 2016-05-26 <![CDATA[ Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation ]]> https://biorxiv.org/content/10.1101/055921v1?rss=1 Fabiana M Duarte Nicholas J Fuda Dig B Mahat Leighton J Core Michael Guertin John T Lis 2016-05-27 doi:10.1101/055921 Cold Spring Harbor Laboratory Press 2016-05-27 <![CDATA[ The Lair: A resource for exploratory analysis of published RNA-Seq data ]]> https://biorxiv.org/content/10.1101/056200v1?rss=1 Harold Pimentel Pascal Sturmfels Nicolas Bray Pall Melsted Lior Pachter 2016-05-31 doi:10.1101/056200 Cold Spring Harbor Laboratory Press 2016-05-31 <![CDATA[ Modular non-repeating codes for DNA storage ]]> https://biorxiv.org/content/10.1101/057448v1?rss=1 Ian Holmes 2016-06-07 doi:10.1101/057448 Cold Spring Harbor Laboratory Press 2016-06-07 <![CDATA[ In situ replication rates for uncultivated bacteria in microbial communities ]]> https://biorxiv.org/content/10.1101/057992v1?rss=1 Christopher T Brown Matthew R Olm Brian C Thomas Jillian F Banfield 2016-06-16 doi:10.1101/057992 Cold Spring Harbor Laboratory Press 2016-06-16 <![CDATA[ Differential analysis of RNA-Seq incorporating quantification uncertainty ]]> https://biorxiv.org/content/10.1101/058164v1?rss=1 Harold J Pimentel Nicolas Bray Suzette Puente Páll Melsted Lior Pachter 2016-06-10 doi:10.1101/058164 Cold Spring Harbor Laboratory Press 2016-06-10 <![CDATA[ HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution ]]> https://biorxiv.org/content/10.1101/062117v1?rss=1 Govinda M Kamath Ilan Shomorony Fei Xia Thomas A Courtade David N Tse 2016-07-05 doi:10.1101/062117 Cold Spring Harbor Laboratory Press 2016-07-05 <![CDATA[ Prober: A general toolkit for analyzing sequencing-based ‘toeprinting’ assays ]]> https://biorxiv.org/content/10.1101/063107v1?rss=1 Bo Li Akshay Tambe Sharon Aviran Lior Pachter 2016-07-10 doi:10.1101/063107 Cold Spring Harbor Laboratory Press 2016-07-10 <![CDATA[ A hidden Markov model approach for simultaneously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy ]]> https://biorxiv.org/content/10.1101/064238v1?rss=1 Russell Corbett-Detig Rasmus Nielsen 2016-07-15 doi:10.1101/064238 Cold Spring Harbor Laboratory Press 2016-07-15 <![CDATA[ An introduction to linear stability analysis for deciphering spatial patterns in signaling networks ]]> https://biorxiv.org/content/10.1101/065474v1?rss=1 Jasmine Nirody Padmini Rangamani 2016-07-23 doi:10.1101/065474 Cold Spring Harbor Laboratory Press 2016-07-23 <![CDATA[ The genome of the crustacean Parhyale hawaiensis: a model for animal development, regeneration, immunity and lignocellulose digestion ]]> https://biorxiv.org/content/10.1101/065789v1?rss=1 Damian Kao Alvina G Lai Evangelia Stamataki Silvana Rosic Nikolaos Konstantinides Erin Jarvis Alessia Di Donfrancesco Natalia Pouchkina-Stantcheva Marie Semon Marco Grillo Heather Bruce Suyash Kumar Igor Siwanowicz Andy Le Andrew Lemire Michael Eisen Cassandra Extavour William Browne Carsten Wolff Michalis Averof Nipam H Patel Peter Sarkies Anastasios Pavlopoulos Aziz Aboobaker 2016-07-25 doi:10.1101/065789 Cold Spring Harbor Laboratory Press 2016-07-25 <![CDATA[ A Dynamic Mode of Mitotic Bookmarking by Transcription Factors ]]> https://biorxiv.org/content/10.1101/066464v1?rss=1 Sheila S Teves Luye An Anders S Hansen Liangqi Xie Xavier Darzacq Robert Tjian 2016-07-28 doi:10.1101/066464 Cold Spring Harbor Laboratory Press 2016-07-28 <![CDATA[ A rodent model of social rejection ]]> https://biorxiv.org/content/10.1101/066993v1?rss=1 Haozhe Shan Inbal Ben-Ami Bartal Peggy Mason 2016-07-31 doi:10.1101/066993 Cold Spring Harbor Laboratory Press 2016-07-31 <![CDATA[ How the AFF1/4 scaffold recruits the elongation factor ELL2 to promote HIV-1 proviral transcription ]]> https://biorxiv.org/content/10.1101/068262v1?rss=1 Shiqian Qi Zichong Li Ursula Schulze-Gahmen Goran Stjepanovic Qiang Zhou James Hurley 2016-08-06 doi:10.1101/068262 Cold Spring Harbor Laboratory Press 2016-08-06 <![CDATA[ Molecular mechanisms of substrate-controlled ring dynamics and sub-stepping in a nucleic-acid dependent hexameric motor ]]> https://biorxiv.org/content/10.1101/069559v1?rss=1 Nathan D. Thomsen Michael R. Lawson Lea B. Witkowsky Song Qu James M. Berger 2016-08-16 doi:10.1101/069559 Cold Spring Harbor Laboratory Press 2016-08-16 <![CDATA[ Ligand-induced and small molecule control of substrate loading in a hexameric helicase ]]> https://biorxiv.org/content/10.1101/069773v1?rss=1 Michael R. Lawson Kevin Dyer James M. Berger 2016-08-16 doi:10.1101/069773 Cold Spring Harbor Laboratory Press 2016-08-16 <![CDATA[ Ordinary Differential Equations in Cancer Biology ]]> https://biorxiv.org/content/10.1101/071134v1?rss=1 Margaret P Chapman Claire J. Tomlin 2016-08-23 doi:10.1101/071134 Cold Spring Harbor Laboratory Press 2016-08-23 <![CDATA[ Network Identification Methods ]]> https://biorxiv.org/content/10.1101/071217v1?rss=1 Young Hwan Chang Claire Tomlin 2016-08-23 doi:10.1101/071217 Cold Spring Harbor Laboratory Press 2016-08-23 <![CDATA[ Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways ]]> https://biorxiv.org/content/10.1101/072439v1?rss=1 Lynn Yi Harold Pimentel Lior Pachter 2016-08-30 doi:10.1101/072439 Cold Spring Harbor Laboratory Press 2016-08-30 <![CDATA[ Targeted reconstruction of T cell receptor sequence from single cell RNA-sequencing links CDR3 length to T cell differentiation state ]]> https://biorxiv.org/content/10.1101/072744v1?rss=1 Shaked Afik Kathleen B Yates Kevin Bi Samuel Darko Jernej Godec Ulrike Gerdemann Leo Swadling Daniel C Douek Paul Klenerman Eleanor J Barnes Arlene H Sharpe W. Nicholas Haining Nir Yosef 2016-08-31 doi:10.1101/072744 Cold Spring Harbor Laboratory Press 2016-08-31 <![CDATA[ A Numerus Population Viability and Harvesting Analyses Web App ]]> https://biorxiv.org/content/10.1101/074492v1?rss=1 Wayne Getz Oliver C Muellerklein Richard Salter Colin Carlson Andrew Lyons Dana Paige Seidel 2016-09-10 doi:10.1101/074492 Cold Spring Harbor Laboratory Press 2016-09-10 <![CDATA[ A compound that directly and selectively stalls PCSK9 translation ]]> https://biorxiv.org/content/10.1101/083097v1?rss=1 Lintner, N. McClure, K. Petersen, D. Londregan, A. Piotrowski, D. Wei, L. Xiao, J. Bolt, M. Loria, P. Maguire, B. Geoghegan, K. Huang, A. Rolph, T. Liras, S. Doudna, J. Dullea, R. Cate, J. 2016-10-25 doi:10.1101/083097 Cold Spring Harbor Laboratory Press 2016-10-25 <![CDATA[ Engineering Genetically-Encoded Mineralization and Magnetism via Directed Evolution ]]> https://biorxiv.org/content/10.1101/085233v1?rss=1 Liu, X. L. Lopez, P. A. Giessen, T. W. Giles, M. Way, J. C. Silver, P. A. 2016-11-02 doi:10.1101/085233 Cold Spring Harbor Laboratory Press 2016-11-02 <![CDATA[ Selection on the FADS region in Europeans ]]> https://biorxiv.org/content/10.1101/086439v1?rss=1 Buckley, M. T. Racimo, F. Allentoft, M. E. Karoline, M. K. Jonsson, A. Huang, H. Hormozdiari, F. Sikora, M. Marnetto, D. Eskin, E. Jorgensen, M. E. Grarup, N. Pedersen, O. Hansen, T. Kraft, P. Willerslev, E. Nielsen, R. 2016-11-08 doi:10.1101/086439 Cold Spring Harbor Laboratory Press 2016-11-08 <![CDATA[ Overcoming evolved resistance to population-suppressing homing-based gene drives ]]> https://biorxiv.org/content/10.1101/088427v1?rss=1 Marshall, J. Buchman, A. Sanchez C., H. M. Akbari, O. S. 2016-11-17 doi:10.1101/088427 Cold Spring Harbor Laboratory Press 2016-11-17 <![CDATA[ Monolayer-crystal streptavidin support films provide an internal standard of cryo-EM image quality ]]> https://biorxiv.org/content/10.1101/091355v1?rss=1 Han, B.-G. Watson, Z. L. Cate, J. H. D. Glaeser, R. M. 2016-12-03 doi:10.1101/091355 Cold Spring Harbor Laboratory Press 2016-12-03 <![CDATA[ Historian: accurate reconstruction of ancestral sequences and evolutionary rates ]]> https://biorxiv.org/content/10.1101/093161v1?rss=1 Holmes, I. H. 2016-12-11 doi:10.1101/093161 Cold Spring Harbor Laboratory Press 2016-12-11 <![CDATA[ BioMake: a GNU Make-compatible utility for declarative workflow management ]]> https://biorxiv.org/content/10.1101/093245v1?rss=1 Holmes, I. H. Mungall, C. J. 2016-12-12 doi:10.1101/093245 Cold Spring Harbor Laboratory Press 2016-12-12 <![CDATA[ CTCF and Cohesin Regulate Chromatin Loop Stability with Distinct Dynamics ]]> https://biorxiv.org/content/10.1101/093476v1?rss=1 Hansen, A. S. Pustova, I. Cattoglio, C. Tjian, R. Darzacq, X. 2016-12-12 doi:10.1101/093476 Cold Spring Harbor Laboratory Press 2016-12-12 <![CDATA[ Mechanism of Nuclear Movements in a Multinucleated Cell ]]> https://biorxiv.org/content/10.1101/095695v1?rss=1 Gibeaux, R. Politi, A. Philippsen, P. Nedelec, F. 2016-12-20 doi:10.1101/095695 Cold Spring Harbor Laboratory Press 2016-12-20 <![CDATA[ The DOE Systems Biology Knowledgebase (KBase) ]]> https://biorxiv.org/content/10.1101/096354v1?rss=1 Arkin, A. P. Stevens, R. L. Cottingham, R. W. Maslov, S. Henry, C. S. Dehal, P. Ware, D. Perez, F. Harris, N. L. Canon, S. Sneddon, M. W. Henderson, M. L. Riehl, W. J. Gunter, D. Murphy-Olson, D. Chan, S. Kamimura, R. T. Brettin, T. S. Meyer, F. Chivian, D. Weston, D. J. Glass, E. M. Davison, B. H. Kumari, S. Allen, B. H. Baumohl, J. Best, A. A. Bowen, B. Brenner, S. E. Bun, C. C. Chandonia, J.-M. Chia, J.-M. Colasanti, R. Conrad, N. Davis, J. J. DeJongh, M. Devoid, S. Dietrich, E. Drake, M. M. Dubchak, I. Edirisinghe, J. N. Fang, G. Faria, J. P. Fryb 2016-12-22 doi:10.1101/096354 Cold Spring Harbor Laboratory Press 2016-12-22 <![CDATA[ Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens ]]> https://biorxiv.org/content/10.1101/100867v1?rss=1 Linck, E. B. Hanna, Z. Sellas, A. Dumbacher, J. P. 2017-01-16 doi:10.1101/100867 Cold Spring Harbor Laboratory Press 2017-01-16 <![CDATA[ Tracking multiple genomic elements using correlative CRISPR imaging and sequential DNA FISH ]]> https://biorxiv.org/content/10.1101/101444v1?rss=1 Guan, J. Liu, H. Shi, X. Feng, S. Huang, B. 2017-01-18 doi:10.1101/101444 Cold Spring Harbor Laboratory Press 2017-01-18 <![CDATA[ Metagenomic Next-Generation Sequencing Detects Pulmonary Pathogens in Hematopoietic Cellular Transplant Patients with Acute Respiratory Illnesses ]]> https://biorxiv.org/content/10.1101/102798v1?rss=1 Langelier, C. Zinter, M. S. Kalantar, K. Yank, G. A. Christenson, S. Odonovan, B. White, C. Wilson, M. R. Sapru, A. Dvorak, C. C. Miller, S. Chiu, C. Y. DeRisi, J. L. 2017-01-24 doi:10.1101/102798 Cold Spring Harbor Laboratory Press 2017-01-24 <![CDATA[ Joint estimation of relatedness coefficients and allele frequencies from ancient samples ]]> https://biorxiv.org/content/10.1101/103903v1?rss=1 Theunert, C. Racimo, F. Slatkin, M. 2017-01-28 doi:10.1101/103903 Cold Spring Harbor Laboratory Press 2017-01-28 <![CDATA[ Neural Encoding of Auditory Features during Music Perception and Imagery: Insight into the Brain of a Piano Player ]]> https://biorxiv.org/content/10.1101/106617v1?rss=1 Martin, S. Mikutta, C. Leonard, M. K. Hungate, D. Koelsch, S. Chang, E. F. Millan, J. d. R. Knight, R. T. Pasley, B. N. 2017-02-07 doi:10.1101/106617 Cold Spring Harbor Laboratory Press 2017-02-07 <![CDATA[ Engineered shell proteins confer improved encapsulated pathway behavior in a bacterial microcompartment ]]> https://biorxiv.org/content/10.1101/106716v1?rss=1 nView larger version (26K):norg.highwire.dtl.DTLVardef@1f69a12org.highwire.dtl.DTLVardef@fd5560org.highwire.dtl.DTLVardef@1f01d6aorg.highwire.dtl.DTLVardef@11b442c_HPS_FORMAT_FIGEXP M_FIG TOC Abstract Graphic C_FIG ]]> Slininger Lee, M. F. Jakobson, C. M. Tullman-Ercek, D. 2017-02-07 doi:10.1101/106716 Cold Spring Harbor Laboratory Press 2017-02-07 <![CDATA[ dRep: A tool for fast and accurate genome de-replication that enables tracking of microbial genotypes and improved genome recovery from metagenomes ]]> https://biorxiv.org/content/10.1101/108142v1?rss=1 Olm, M. R. Brown, C. T. Brooks, B. Banfield, J. F. 2017-02-13 doi:10.1101/108142 Cold Spring Harbor Laboratory Press 2017-02-13 <![CDATA[ Identifying a TFIID interactome via integrated biochemical and high-throughput proteomic studies ]]> https://biorxiv.org/content/10.1101/111682v1?rss=1 Liu, W.-L. Song, L. Dailey, G. Piasecka, A. Coleman, R. A. 2017-08-10 doi:10.1101/111682 Cold Spring Harbor Laboratory Press 2017-08-10 <![CDATA[ Impulse model-based differential expression analysis of time course sequencing data ]]> https://biorxiv.org/content/10.1101/113548v1?rss=1 Fischer, D. S. Theis, F. J. Yosef, N. 2017-03-05 doi:10.1101/113548 Cold Spring Harbor Laboratory Press 2017-03-05 <![CDATA[ WTFgenes: What's The Function of these genes? Static sites for model-based gene set analysis ]]> https://biorxiv.org/content/10.1101/114785v1?rss=1 Mungall, C. Holmes, I. 2017-03-07 doi:10.1101/114785 Cold Spring Harbor Laboratory Press 2017-03-07 <![CDATA[ Identifiers for the 21st century:How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data ]]> https://biorxiv.org/content/10.1101/117812v1?rss=1 McMurry, J. Juty, N. Blomberg, N. Burdett, A. Conlin, T. Conte, N. Courtot, M. Deck, J. Dumontier, M. Fellows, D. Gonzalez-Beltran, A. Gormanns, P. Grethe, J. Hastings, J. Hermjakob, H. Heriche, J.-K. Ison, J. Jimenez, R. Jupp, S. Kunze, J. Laibe, C. Le Novere, N. Malone, J. R. Martin, M.-J. McEntyre, J. Morris, C. Muilu, J. Mueller, W. Rocca-Serra, P. Sansone, S.-A. Sariyar, M. Snoep, J. Stanford, N. J. Soiland-Reyes, S. Swainston, N. Washington, N. Williams, A. Wimalaratne, S. Winfree, L. Wolstencroft, K. Goble, C. Mungall, C. Haendel, M. Parkinson, 2017-03-20 doi:10.1101/117812 Cold Spring Harbor Laboratory Press 2017-03-20 <![CDATA[ Regulatory remodeling in the allo-tetraploid frog Xenopus laevis ]]> https://biorxiv.org/content/10.1101/120212v1?rss=1 Elurbe, D. M. Paranjpe, S. S. Georgiou, G. van Kruijsbergen, I. Bogdanovic, O. Gibeaux, R. Heald, R. Lister, R. Huynen, M. A. van Heeringen, S. J. Veenstra, G. J. C. 2017-03-24 doi:10.1101/120212 Cold Spring Harbor Laboratory Press 2017-03-24 <![CDATA[ STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq ]]> https://biorxiv.org/content/10.1101/120295v1?rss=1 Haas, B. Dobin, A. Stransky, N. Li, B. Yang, X. Tickle, T. Bankapur, A. Ganote, C. Doak, T. Pochet, N. Sun, J. Wu, C. Gingeras, T. Regev, A. 2017-03-24 doi:10.1101/120295 Cold Spring Harbor Laboratory Press 2017-03-24 <![CDATA[ A Conformational Checkpoint Between DNA Binding And Cleavage By CRISPR-Cas9 ]]> https://biorxiv.org/content/10.1101/122242v1?rss=1 Dagdas, Y. S. Chen, J. S. Sternberg, S. H. Doudna, J. A. Yildiz, A. 2017-03-30 doi:10.1101/122242 Cold Spring Harbor Laboratory Press 2017-03-30 <![CDATA[ Estimating The Extinction Date Of The Thylacine Accounting For Unconfirmed Sightings ]]> https://biorxiv.org/content/10.1101/123331v1?rss=1 Carlson, C. J. Bond, A. L. Burgio, K. R. 2017-04-03 doi:10.1101/123331 Cold Spring Harbor Laboratory Press 2017-04-03 <![CDATA[ Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering ]]> https://biorxiv.org/content/10.1101/124271v1?rss=1 Higgins, S. Ouonkap Yimga, S. Savage, D. 2017-04-04 doi:10.1101/124271 Cold Spring Harbor Laboratory Press 2017-04-04 <![CDATA[ A Versatile Compressed Sensing Scheme For Faster And Less Phototoxic 3D Fluorescence Microscopy ]]> https://biorxiv.org/content/10.1101/125815v1?rss=1 Woringer, M. Darzacq, X. Zimmer, C. Mir, M. 2017-04-10 doi:10.1101/125815 Cold Spring Harbor Laboratory Press 2017-04-10 <![CDATA[ Just above chance: is it harder to decode information from human prefrontal cortex BOLD signals? ]]> https://biorxiv.org/content/10.1101/127324v1?rss=1 Bhandari, A. Gagne, C. Badre, D. 2017-04-13 doi:10.1101/127324 Cold Spring Harbor Laboratory Press 2017-04-13 <![CDATA[ Light Guided In-vivo Activation of Innate Immune Cells with Photocaged TLR 2/6 Agonist ]]> https://biorxiv.org/content/10.1101/128942v1?rss=1 Ryu, K. A. McGonnigal, B. Moore, T. Mancini, R. J. Esser-Kahn, A. P. 2017-04-20 doi:10.1101/128942 Cold Spring Harbor Laboratory Press 2017-04-20 <![CDATA[ Independent pseudogenization of CYP2J19 in penguins, owls and kiwis implicates gene in red carotenoid synthesis ]]> https://biorxiv.org/content/10.1101/130468v1?rss=1 Emerling, C. A. 2017-04-25 doi:10.1101/130468 Cold Spring Harbor Laboratory Press 2017-04-25 <![CDATA[ Use antibiotics in cell culture with caution: genome-wide identification ofantibiotic-induced changes in gene expression and regulation ]]> https://biorxiv.org/content/10.1101/130484v1?rss=1 Ryu, A. H. Eckalbar, W. L. Kreimer, A. Yosef, N. Ahituv, N. 2017-04-25 doi:10.1101/130484 Cold Spring Harbor Laboratory Press 2017-04-25 <![CDATA[ Network Reconstruction And Systems Analysis Of Plant Cell Wall Deconstruction By Neurospora crassa ]]> https://biorxiv.org/content/10.1101/133165v1?rss=1 Samal, A. Craig, J. P. Coradetti, S. T. Benz, J. P. Eddy, J. A. Price, N. D. Glass, N. L. 2017-05-02 doi:10.1101/133165 Cold Spring Harbor Laboratory Press 2017-05-02 <![CDATA[ Sex Differentiation In Grayling (Salmonidae) Goes Through An All-Male Stage And Is Delayed In Genetic Males Who Instead Grow Faster ]]> https://biorxiv.org/content/10.1101/135194v1?rss=1 Maitre, D. Selmoni, O. M. Uppal, A. Marques da Cunha, L. Wilkins, L. G. E. Roux, J. Mobley, K. B. Knorr, S. Robinson-Rechavi, M. Wedekind, C. 2017-05-08 doi:10.1101/135194 Cold Spring Harbor Laboratory Press 2017-05-08 <![CDATA[ Sex-Specific Changes In Gene Expression And Delayed Sex Differentiation In Response To Estrogen Pollution In Grayling (Salmonidae) ]]> https://biorxiv.org/content/10.1101/135210v1?rss=1 Selmoni, O. M. Maitre, D. Roux, J. Wilkins, L. G. E. Marques da Cunha, L. Vermeirssen, E. Knorr, S. Robinson-Rechavi, M. Wedekind, C. 2017-05-09 doi:10.1101/135210 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ Duplication And Sub/Neofunctionalization Of malvolio, An Insect Homolog Of Nramp, In The Subsocial Beetle Nicrophorus vespilloides ]]> https://biorxiv.org/content/10.1101/135590v1?rss=1 Mehlferber, E. C. Benowitz, K. M. Roy-Zokan, E. M. McKinney, E. C. Cunningham, C. B. Moore, A. J. 2017-05-09 doi:10.1101/135590 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ Barcode identification for single cell genomics ]]> https://biorxiv.org/content/10.1101/136242v1?rss=1 Tambe, A. Pachter, L. 2017-05-09 doi:10.1101/136242 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ The Multiple Sclerosis Genomic Map: Role of peripheral immune cells and resident microglia in susceptibility ]]> https://biorxiv.org/content/10.1101/143933v1?rss=1 - International Multiple Sclerosis Genetics Consorti, Patsopoulos, N. Baranzini, S. E. Santaniello, A. Shoostari, P. Cotsapas, C. Wong, G. Beecham, A. H. James, T. Replogle, J. Vlachos, I. McCabe, C. Pers, T. Brandes, A. White, C. Keenan, B. Cimpean, M. Winn, P. Panteliadis, I.-P. Robbins, A. Andlauer, T. F. M. Zarzycki, O. Dubois, B. Goris, A. Bach Sondergaard, H. Sellebjerg, F. Soelberg Sorensen, P. Ullum, H. Wegner Thoerner, L. Saarela, J. Cournu-Rebeix, I. Damotte, V. Fontaine, B. Guillot-Noel, L. Lathrop, M. Vukusik, S. Berthele, A. Biberacher, V. B 2017-07-13 doi:10.1101/143933 Cold Spring Harbor Laboratory Press 2017-07-13 <![CDATA[ Stochastic Simulation Of Dopamine Neuromodulation For Implementation Of Fluorescent Neurochemical Probes In The Striatal Extracellular Space ]]> https://biorxiv.org/content/10.1101/144436v1?rss=1 Beyene, A. McFarlane, I. R. Pinals, R. Landry, M. 2017-05-31 doi:10.1101/144436 Cold Spring Harbor Laboratory Press 2017-05-31 <![CDATA[ Molecular Recognition of Dopamine with Dual Near Infrared Excitation-Emission Two-Photon Microscopy ]]> https://biorxiv.org/content/10.1101/145912v1?rss=1 Del Bonis-O'Donnell, J. T. Page, R. H. Beyene, A. G. Tindall, E. G. McFarlane, I. R. Landry, M. P. 2017-06-04 doi:10.1101/145912 Cold Spring Harbor Laboratory Press 2017-06-04 <![CDATA[ Evidence for a causal link between left posterior alpha-beta power decreases and context-driven word production. ]]> https://biorxiv.org/content/10.1101/150748v1?rss=1 Piai, V. Rommers, J. Knight, R. T. 2017-06-15 doi:10.1101/150748 Cold Spring Harbor Laboratory Press 2017-06-15 <![CDATA[ simExTargId: An R package for real-time LC-MS metabolomic data analysis, instrument failure/drift notification and MS2 target identification ]]> https://biorxiv.org/content/10.1101/151159v1?rss=1 Edmands, W. M. B. Rappaport, S. M. 2017-06-16 doi:10.1101/151159 Cold Spring Harbor Laboratory Press 2017-06-16 <![CDATA[ Evolutionary proteomics uncovers ciliary signaling components ]]> https://biorxiv.org/content/10.1101/153437v1?rss=1 Sigg, M. A. Menchen, T. Johnson, J. Lee, C. Choksi, S. P. Garcia, G. Busengdal, H. Dougherty, G. Pennekamp, P. Werner, C. Rentzsch, F. Krogan, N. Wallingford, J. B. Omran, H. Reiter, J. F. 2017-06-22 doi:10.1101/153437 Cold Spring Harbor Laboratory Press 2017-06-22 <![CDATA[ Rhodosporidium toruloides: A new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts ]]> https://biorxiv.org/content/10.1101/154872v1?rss=1 Yaegashi, J. Kirby, J. Ito, M. Sun, J. Dutta, T. Mirsiaghi, M. Sundstrom, E. Rodriguez, A. Baidoo, E. Tanjore, D. Pray, T. Sale, K. Singh, S. Keasling, J. Simmons, B. Singer, S. Magnuson, J. Arkin, A. Skerker, J. Gladden, J. 2017-06-23 doi:10.1101/154872 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ Nuclease escape elements protect messenger RNA against cleavage by multiple viral endonucleases ]]> https://biorxiv.org/content/10.1101/155457v1?rss=1 Muller, M. Glaunsinger, B. A. 2017-06-26 doi:10.1101/155457 Cold Spring Harbor Laboratory Press 2017-06-26 <![CDATA[ Column subset selection for single-cell RNA-Seq clustering ]]> https://biorxiv.org/content/10.1101/159079v1?rss=1 McCurdy, S. Ntranos, V. Pachter, L. 2017-07-03 doi:10.1101/159079 Cold Spring Harbor Laboratory Press 2017-07-03 <![CDATA[ Tissue Folding by Mechanical Compaction of the Mesenchyme ]]> https://biorxiv.org/content/10.1101/164020v1?rss=1 Hughes, A. J. Miyazaki, H. Coyle, M. C. Zhang, J. Laurie, M. T. Chu, D. Vavrusova, Z. Schneider, R. A. Klein, O. D. Gartner, Z. J. 2017-07-15 doi:10.1101/164020 Cold Spring Harbor Laboratory Press 2017-07-15 <![CDATA[ Spatial and temporal distribution of genome divergence among California populations of Aedes aegypti. ]]> https://biorxiv.org/content/10.1101/166629v1?rss=1 Lee, Y. Collier, T. C. Conner, W. R. Hanemaaijer, M. J. Smartt, C. T. Slatkin, M. Chiu, J. C. Lanzaro, G. C. Mulligan, F. S. Cornel, A. J. 2017-07-20 doi:10.1101/166629 Cold Spring Harbor Laboratory Press 2017-07-20 <![CDATA[ Diversity of translation initiation mechanisms across bacterial species is driven by environmental conditions and growth demands ]]> https://biorxiv.org/content/10.1101/167429v1?rss=1 Hockenberry, A. J. Stern, A. J. Amaral, L. A. Jewett, M. C. 2017-07-23 doi:10.1101/167429 Cold Spring Harbor Laboratory Press 2017-07-23 <![CDATA[ A cross-validation-based approach for delimiting reliable home range estimates ]]> https://biorxiv.org/content/10.1101/168021v1?rss=1 Dougherty, E. R. Carlson, C. J. Blackburn, J. K. Getz, W. M. 2017-07-25 doi:10.1101/168021 Cold Spring Harbor Laboratory Press 2017-07-25 <![CDATA[ Remodeling of ER-exit sites initiates a membrane supply pathway forautophagosome biogenesis ]]> https://biorxiv.org/content/10.1101/168518v1?rss=1 Ge, L. Zhang, M. Kenny, S. Liu, D. Maeda, M. Saito, K. Marthur, A. Xu, K. Schekman, R. 2017-07-25 doi:10.1101/168518 Cold Spring Harbor Laboratory Press 2017-07-25 <![CDATA[ A compartmentalized, self-extinguishing signaling network mediates crossover control in meiosis ]]> https://biorxiv.org/content/10.1101/168948v1?rss=1 Zhang, L. Koehler, S. Rillo-Bohn, R. Dernburg, A. F. 2017-07-26 doi:10.1101/168948 Cold Spring Harbor Laboratory Press 2017-07-26 <![CDATA[ Genome-reconstruction for eukaryotes from complex natural microbial communities ]]> https://biorxiv.org/content/10.1101/171355v1?rss=1 West, P. T. Probst, A. J. Grigoriev, I. V. Thomas, B. C. Banfield, J. F. 2017-08-01 doi:10.1101/171355 Cold Spring Harbor Laboratory Press 2017-08-01 <![CDATA[ Spot-On: robust model-based analysis of single-particle tracking experiments ]]> https://biorxiv.org/content/10.1101/171983v1?rss=1 Hansen, A. S. Woringer, M. Grimm, J. B. Lavis, L. D. Tjian, R. Darzacq, X. 2017-08-03 doi:10.1101/171983 Cold Spring Harbor Laboratory Press 2017-08-03 <![CDATA[ Climate change drives uncertain global shifts in potential distribution and seasonal risk of Aedes-transmitted viruses ]]> https://biorxiv.org/content/10.1101/172221v1?rss=1 Ryan, S. J. Carlson, C. J. Mordecai, E. A. Johnson, L. R. 2017-08-04 doi:10.1101/172221 Cold Spring Harbor Laboratory Press 2017-08-04 <![CDATA[ ShhN-mediated activation of Smo in the absence of Ptch1/2 function ]]> https://biorxiv.org/content/10.1101/172429v1?rss=1 Casillas, C. Roelink, H. 2017-08-04 doi:10.1101/172429 Cold Spring Harbor Laboratory Press 2017-08-04 <![CDATA[ SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site ]]> https://biorxiv.org/content/10.1101/176073v1?rss=1 Zhang, L. Martini, G. Rube, H. T. Kribelbauer, J. F. Rastogi, C. FitzPatrick, V. D. Houtman, J. C. Bussemaker, H. J. Pufall, M. A. 2017-08-14 doi:10.1101/176073 Cold Spring Harbor Laboratory Press 2017-08-14 <![CDATA[ Evolution of mechanisms that control mating in Drosophila males ]]> https://biorxiv.org/content/10.1101/177337v1?rss=1 Ahmed, O. M. Shah, N. M. Stern, D. L. Davis, G. W. Pollard, K. S. Parthasarathy, S. Avila-Herrera, A. Tun, K. M. Serpa, P. H. Peng, J. Knapp, J.-M. 2017-08-16 doi:10.1101/177337 Cold Spring Harbor Laboratory Press 2017-08-16 <![CDATA[ Nanoparticle-Guided Biomolecule Delivery for Transgene Expression and Gene Silencing in Mature Plants ]]> https://biorxiv.org/content/10.1101/179549v1?rss=1 Demirer, G. S. Chang, R. Zhang, H. Chio, L. Landry, M. P. 2017-08-22 doi:10.1101/179549 Cold Spring Harbor Laboratory Press 2017-08-22 <![CDATA[ A role for the Smc3 hinge domain in the maintenance of sister chromatid cohesion ]]> https://biorxiv.org/content/10.1101/179788v1?rss=1 Robison, B. Guacci, V. Koshland, D. 2017-08-23 doi:10.1101/179788 Cold Spring Harbor Laboratory Press 2017-08-23 <![CDATA[ Cryo-EM shows how dynactin recruits two dyneins for faster movement ]]> https://biorxiv.org/content/10.1101/183160v1?rss=1 Urnavicius, L. Lau, C. K. Elshenawy, M. M. Morales-Rios, E. Motz, C. Yildiz, A. Carter, A. P. 2017-08-31 doi:10.1101/183160 Cold Spring Harbor Laboratory Press 2017-08-31 <![CDATA[ Associations between memory traces emerge in a generic neural circuit model through STDP ]]> https://biorxiv.org/content/10.1101/188938v1?rss=1 Pokorny, C. Ison, M. J. Rao, A. Legenstein, R. Papadimitriou, C. Maass, W. 2017-09-14 doi:10.1101/188938 Cold Spring Harbor Laboratory Press 2017-09-14 <![CDATA[ Real-time DNA barcoding in a remote rainforest using nanopore sequencing ]]> https://biorxiv.org/content/10.1101/189159v1?rss=1 99% in less than 24 hours after collecting specimens. In addition, we generated sequence information at Universidad Tecnologica Indoamerica in Quito for the recently re-discovered Jambato toad Atelopus ignescens, which was thought to be extinct for 28 years, a rare species of blind snake Trilepida guayaquilensis, and two undescribed species of Dipsas snakes. In this study we establish how mobile laboratories and nanopore sequencing can help to accelerate species identification in remote areas (especially for species that are difficult to diagnose based on characters of external morphology), be applied to local research facilities in developing countries, and rapidly generate information for species that are rare, endangered and undescribed, which can potentially aid in conservation efforts. ]]> Pomerantz, A. Penafiel, N. Arteaga, A. Bustamante, L. Pichardo, F. Coloma, L. A. Barrio-Amoros, C. L. Salazar-Valenzuela, D. Prost, S. 2017-09-15 doi:10.1101/189159 Cold Spring Harbor Laboratory Press 2017-09-15 <![CDATA[ The Role Of Circle Of Willis Anatomy Variations In Cardio-embolic Stroke - A Patient-specific Simulation Based Study. ]]> https://biorxiv.org/content/10.1101/190579v1?rss=1 Mukherjee, D. Jani, N. D. Narvid, J. Shadden, S. C. 2017-09-20 doi:10.1101/190579 Cold Spring Harbor Laboratory Press 2017-09-20 <![CDATA[ Modeling Epidemics: A Primer and Numerus Software Implementation ]]> https://biorxiv.org/content/10.1101/191601v1?rss=1 Getz, W. M. Salter, R. Muellerklein, O. Yoon, H. S. Tallam, K. 2017-09-22 doi:10.1101/191601 Cold Spring Harbor Laboratory Press 2017-09-22 <![CDATA[ The Parasite Extinction Assessment & Red List: an open-source, online biodiversity database for neglected symbionts ]]> https://biorxiv.org/content/10.1101/192351v1?rss=1 Carlson, C. J. Muellerklein, O. C. Phillips, A. J. Burgio, K. R. Castaldo, G. Cizauskas, C. A. Cumming, G. S. Dallas, T. A. Dona, J. Harris, N. Jovani, R. Miao, Z. Proctor, H. Yoon, H. S. Getz, W. M. 2017-09-21 doi:10.1101/192351 Cold Spring Harbor Laboratory Press 2017-09-21 <![CDATA[ Nasal and aerosol shedding of infectious influenza virus - a community based study ]]> https://biorxiv.org/content/10.1101/194985v1?rss=1 5 m and fine <5 m fractions) on days 1 to 3 post symptom onset. We assessed viral RNA copy number for all samples and cultured NP swabs and fine aerosols. We recovered infectious virus from 52 (39%) of the fine aerosols and 150 (89%) of the NP swabs with valid cultures. The geometric mean RNA copy numbers were 3.8x104/30-min fine, 1.2x104/30-min coarse aerosol sample, and 8.2x108 per NP swab. Fine and coarse aerosol viral RNA was positively associated with body mass index (fine p<0.05, coarse p<0.10) and number of coughs (fine p<0.001, coarse p<0.01) and negatively associated with increasing days since symptom onset (fine p<0.05 to p<0.01, coarse p<0.10) in adjusted models. Fine aerosol viral RNA was also positively associated with having influenza vaccination for both the current and prior season (p<0.01). NP swab viral RNA was positively associated with upper respiratory symptoms (p<0.01) and negatively associated with age (p<0.01) but was not significantly associated with fine or coarse aerosol viral RNA or their predictors. Sneezing was rare, and sneezing and coughing were not necessary for infectious aerosol generation. Our observations suggest that influenza infection in the upper and lower airways are compartmentalized and independent.nnSignificanceLack of human data on influenza virus aerosol shedding fuels debate over the importance of airborne transmission. We provide overwhelming evidence that humans generate infectious aerosols and quantitative data to improve mathematical models of transmission and public health interventions. We show that sneezing is rare and not important for, and that coughing is not required for influenza virus aerosolization. Our findings, that upper and lower airway infection are independent and that fine particle exhaled aerosols reflect infection in the lung, open a new pathway for understanding the human biology of influenza infection and transmission. Our observation of an association between repeated vaccination and increased viral aerosol generation demonstrated the power of our method, but needs confirmation. ]]> Yan, J. Grantham, M. Pantelic, J. Bueno de Mesquita, P. J. Albert, B. Liu, F. Ehrman, S. Milton, D. K. EMIT Consortium, 2017-09-29 doi:10.1101/194985 Cold Spring Harbor Laboratory Press 2017-09-29 <![CDATA[ Effects of anthropogenic wildfire activity in low elevation Pacific island vegetation communities in French Polynesia ]]> https://biorxiv.org/content/10.1101/196352v1?rss=1 Newman, E. A. Winkler, C. A. Hembry, D. H. 2017-09-30 doi:10.1101/196352 Cold Spring Harbor Laboratory Press 2017-09-30 <![CDATA[ A multi-modal approach to decomposing standard neuropsychological test performance: Symbol Search ]]> https://biorxiv.org/content/10.1101/200998v1?rss=1 Langer, N. Ho, E. J. Pedroni, A. Alexander, L. M. Marcelle, E. T. Schuster, K. Milham, M. P. Kelly, S. P. 2017-10-11 doi:10.1101/200998 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ N6-methyladenosine modification and the YTHDF2 reader protein play cell type specific roles in lytic viral gene expression during Kaposi’s sarcoma-associated herpesvirus infection ]]> https://biorxiv.org/content/10.1101/201475v1?rss=1 Hesser, C. Karijolich, J. Dominissini, D. He, C. Glaunsinger, B. A. 2017-10-11 doi:10.1101/201475 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ Heterogeneity and targeted therapy-induced adaptations in lung cancer revealed by longitudinal single-cell RNA sequencing ]]> https://biorxiv.org/content/10.1101/2019.12.08.868828v1?rss=1 Maynard, A. McCoach, C. E. Rotow, J. K. Harris, L. Haderk, F. Kerr, L. D. Yu, E. A. Schenk, E. L. Tan, W. Zee, A. Tan, M. Gui, P. Lea, T. Wu, W. Urisman, A. Jones, K. Sit, R. Kolli, P. K. Seeley, E. Gesthalter, Y. Le, D. D. Yamauchi, K. A. Naeger, D. M. Thomas, N. J. Gupta, A. Gonzalez, M. Do, H. Tan, L. Gomez-Sjoberg, R. Gubens, M. Jahan, T. Kratz, J. R. Jablons, D. Neff, N. Doebele, R. C. Weissman, J. Blakely, C. M. Darmanis, S. Bivona, T. G. 2019-12-13 doi:10.1101/2019.12.08.868828 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ An Alignment-free Method for Phylogeny Estimation using Maximum Likelihood ]]> https://biorxiv.org/content/10.1101/2019.12.13.875526v1?rss=1 Zahin, T. Abrar, M. H. Rahman, M. Tasnim, T. Bayzid, M. S. Rahman, A. 2019-12-13 doi:10.1101/2019.12.13.875526 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ Molecular basis of CTCF binding polarity in genome folding ]]> https://biorxiv.org/content/10.1101/2019.12.13.876177v1?rss=1 Nora, E. P. Caccianini, L. Fudenberg, G. Kameswaran, V. Nagle, A. Uebersohn, A. So, K. Hajj, B. Le Saux, A. Coulon, A. Mirny, L. A. Pollard, K. S. Dahan, M. Bruneau, B. G. 2019-12-14 doi:10.1101/2019.12.13.876177 Cold Spring Harbor Laboratory Press 2019-12-14 <![CDATA[ OLGenie: Estimating Natural Selection to Predict Functional Overlapping Genes ]]> https://biorxiv.org/content/10.1101/2019.12.14.876607v1?rss=1 Nelson, C. W. Ardern, Z. Wei, X. 2019-12-15 doi:10.1101/2019.12.14.876607 Cold Spring Harbor Laboratory Press 2019-12-15 <![CDATA[ Don't Dismiss Logistic Regression: The Case for Sensible Extraction of Interactions in the Era of Machine Learning ]]> https://biorxiv.org/content/10.1101/2019.12.15.877134v1?rss=1 Levy, J. J. O'Malley, J. 2019-12-16 doi:10.1101/2019.12.15.877134 Cold Spring Harbor Laboratory Press 2019-12-16 <![CDATA[ Contrast-Enhanced, Molecular Imaging of Vascular Inflammation in the Mouse Model by Simultaneous PET/MRI ]]> https://biorxiv.org/content/10.1101/2019.12.16.878652v1?rss=1 Du, S. Ng, T. House, A. Tang, T. Zheng, L. Tu, C. Peake, J. Espiritu, I. Ma, K.-L. Pinkerton, K. Jacobs, R. Louie, A. 2019-12-17 doi:10.1101/2019.12.16.878652 Cold Spring Harbor Laboratory Press 2019-12-17 <![CDATA[ Genetic variation of Aedes aegypti populations from Ecuador ]]> https://biorxiv.org/content/10.1101/2019.12.17.875591v1?rss=1 Cevallos, V. Benitez, A. Coloma, J. Carrazco, A. Wang, C. Holecheck, S. Quiroga, C. Castillo, A. Tillis, B. Ponce, P. 2019-12-18 doi:10.1101/2019.12.17.875591 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ Phf15, a novel transcriptional repressor regulating inflammation in mouse microglia ]]> https://biorxiv.org/content/10.1101/2019.12.17.879940v1?rss=1 Saijo, K. Muroy, S. E. Timblin, G. A. Preininger, M. K. Cedillo, P. 2019-12-18 doi:10.1101/2019.12.17.879940 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ A PI3K-WIPI2 positive feedback loop allosterically activates LC3 lipidation in autophagy ]]> https://biorxiv.org/content/10.1101/2019.12.18.880591v1?rss=1 Fracchiolla, D. Chang, C. Hurley, J. H. Martens, S. 2019-12-18 doi:10.1101/2019.12.18.880591 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ New Tools for Genetically Targeting Myeloid Populations in the Central Nervous System ]]> https://biorxiv.org/content/10.1101/2019.12.20.885244v1?rss=1 McKinsey, G. L. Lizama, C. O. Keown-Lang, A. E. Niu, A. Chee, E. Santander, N. Arnold, T. D. 2019-12-23 doi:10.1101/2019.12.20.885244 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ Citrullination regulates wound responses and tissue regeneration in zebrafish ]]> https://biorxiv.org/content/10.1101/2019.12.27.889378v1?rss=1 Huttenlocher, A. Golenberg, N. Squirrell, J. Bennin, D. RIndy, J. Pistono, P. Eliceiri, K. Shelef, M. Kang, J. 2019-12-27 doi:10.1101/2019.12.27.889378 Cold Spring Harbor Laboratory Press 2019-12-27 <![CDATA[ The Ocular Glymphatic Clearance System ]]> https://biorxiv.org/content/10.1101/2019.12.29.889873v1?rss=1 Wang, X. Lou, N. Eberhardt, A. Kusk, P. Xu, Q. Forstera, B. Peng, S. Yang, Y. Shi, M. Xavier, A. L. R. Erturk, A. Libby, R. T. Chen, L. Thrane, A. S. Nedergaard, M. 2019-12-30 doi:10.1101/2019.12.29.889873 Cold Spring Harbor Laboratory Press 2019-12-30 <![CDATA[ Molecular height measurement by cell surface optical profilometry (CSOP) ]]> https://biorxiv.org/content/10.1101/2019.12.31.892075v1?rss=1 Son, S. Takatori, S. Belardi, B. Podolski, M. Bakalar, M. H. Fletcher, D. A. 2020-01-01 doi:10.1101/2019.12.31.892075 Cold Spring Harbor Laboratory Press 2020-01-01 <![CDATA[ Near-chromosome level genome assembly of the fruit pest Drosophila suzukii using long-read sequencing ]]> https://biorxiv.org/content/10.1101/2020.01.02.892844v1?rss=1 Paris, M. Boyer, R. Jaenichen, R. Wolf, J. B. W. Karageorgi, M. Green, J. Cagnon, M. Parinello, H. Estoup, A. Gautier, M. Gompel, N. Prud'homme, B. 2020-01-02 doi:10.1101/2020.01.02.892844 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ Overexpression of Thalassiosira pseudonana violaxanthin de-epoxidase-like 2 (VDL2) increases fucoxanthin while stoichiometrically reducing diadinoxanthin cycle pigment abundance ]]> https://biorxiv.org/content/10.1101/2020.01.06.896316v1?rss=1 Gaidarenko, O. Mills, D. W. Vernet, M. Hildebrand, M. 2020-01-07 doi:10.1101/2020.01.06.896316 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ Preliminary Evaluation of the Utility of Deep Generative Histopathology Image Translation at a Mid-Sized NCI Cancer Center ]]> https://biorxiv.org/content/10.1101/2020.01.07.897801v1?rss=1 Levy, J. J. Jackson, C. R. Sriharan, A. Christensen, B. Vaickus, L. J. 2020-01-08 doi:10.1101/2020.01.07.897801 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Enhanced triacylglycerol (TAG) and protein accumulation in transgenic diatom Thalassiosira pseudonana with altered photosynthetic pigmentation ]]> https://biorxiv.org/content/10.1101/2020.01.07.897850v1?rss=1 Gaidarenko, O. Yee, D. P. Hildebrand, M. 2020-01-08 doi:10.1101/2020.01.07.897850 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Bright and tunable far-red chemigenetic indicators ]]> https://biorxiv.org/content/10.1101/2020.01.08.898783v1?rss=1 Deo, C. Abdelfattah, A. S. Bhargava, H. K. Berro, A. J. Falco, N. Moeyaert, B. Chupanova, M. Lavis, L. D. Schreiter, E. R. 2020-01-09 doi:10.1101/2020.01.08.898783 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Silencing of Mu elements in maize involves distinct populations of small RNAs and distinct patterns of DNA methylation ]]> https://biorxiv.org/content/10.1101/2020.01.09.900282v1?rss=1 Burgess, D. Zhao, M. Kim, S. Y. Lisch, D. 2020-01-09 doi:10.1101/2020.01.09.900282 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy ]]> https://biorxiv.org/content/10.1101/2020.01.10.902478v1?rss=1 Maniates-Selvin, J. T. Hildebrand, D. G. C. Graham, B. J. Kuan, A. T. Thomas, L. A. Nguyen, T. Buhmann, J. Azevedo, A. W. Shanney, B. L. Funke, J. Tuthill, J. C. Lee, W.-C. A. 2020-01-11 doi:10.1101/2020.01.10.902478 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Size-Based Dominance Hierarchy In One Of Two Sympatric Cryptic Pacific Skinks (Emoia impar And Emoia cyanura) ]]> https://biorxiv.org/content/10.1101/2020.01.11.902866v1?rss=1 Hallsten, M. E. 2020-01-14 doi:10.1101/2020.01.11.902866 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Antisense targeting of decoy exons can reduce intron retention and increase protein expression in human erythroblasts ]]> https://biorxiv.org/content/10.1101/2020.01.13.902544v1?rss=1 1kb). Splicing reporter studies have shown that decoy splice sites are essential for activity, suggesting that decoys act by engaging intron-terminal splice sites and competing with cross-intron interactions required for intron excision. The decoy model predicts that antisense oligonucleotides blocking decoy splice sites in endogenous pre-mRNA should increase productive gene expression by reducing IR. Indeed, we now demonstrate that targeting a decoy 5' splice site in the O-GlcNAc transferase (OGT) gene reduced IR from [~]80% to [~]20% in primary human erythroblasts, accompanied by increases in spliced OGT RNA and OGT protein expression. The remaining OGT IR was refractory to antisense treatment and might be mediated by independent mechanism(s). In contrast, other retained introns were strongly dependent on decoy function, since IR was nearly eliminated by antisense targeting of 5' splice sites. Genes in the latter group encode the widely expressed splicing factor (SF3B1), and the erythroid-specific structural protein, alpha-spectrin (SPTA1). These results show that modulating decoy exon function can dramatically alter IR, and suggest that dynamic regulation of decoy exons could be a mechanism to fine tune gene expression post-transcriptionally in many cell types. ]]> Parra, M. Zhang, W. Vu, J. DeWitt, M. A. Conboy, J. G. 2020-01-14 doi:10.1101/2020.01.13.902544 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Sponge Physioecology On Moorea, French Polynesia: Local Distribution And Filtration Efficiency Of Lamellodysidea Under Varying Temperatures ]]> https://biorxiv.org/content/10.1101/2020.01.14.906990v1?rss=1 Leveque-Eichhorn, L. 2020-01-15 doi:10.1101/2020.01.14.906990 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ ATF4 mediates fetal globin upregulation in response to reduced β-globin ]]> https://biorxiv.org/content/10.1101/2020.01.15.905943v1?rss=1 Boontanrart, M. Y. Stehli, G. Banovic, M. Schroeder, M. Wyman, S. Lew, R. Bordi, M. Gowen, B. DeWitt, M. Corn, J. E. 2020-01-15 doi:10.1101/2020.01.15.905943 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ RNA-dependent structures of the RNA-binding loop in the flavivirus NS3 helicase ]]> https://biorxiv.org/content/10.1101/2020.01.15.907725v1?rss=1 Davidson, R. B. Hendrix, J. Geiss, B. J. McCullagh, M. 2020-01-15 doi:10.1101/2020.01.15.907725 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Dissociable neural systems support the learning and transfer of hierarchical control structure ]]> https://biorxiv.org/content/10.1101/2020.01.16.909978v1?rss=1 Eichenbaum, A. Scimeca, J. D'Esposito, M. 2020-01-17 doi:10.1101/2020.01.16.909978 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ A standardized and reproducible method to measure decision-making in mice ]]> https://biorxiv.org/content/10.1101/2020.01.17.909838v1?rss=1 The International Brain Laboratory Aguillon, V. Angelaki, D. Bayer, H. M. Bonacchi, N. Carandini, M. Cazettes, F. Churchland, A. K. Chapuis, G. Dan, Y. Dewitt, E. Faulkner, M. Hamish, F. Haetzel, L. Hausser, M. Hofer, S. Hu, F. Khanal, A. Krasniak, C. Laranjeira, I. Mainen, Z. Meijer, G. Miska, N. Mrsic-Flogel, T. Noel, J.-P. Pan Vazquez, A. Sanders, J. Socha, K. Terry, R. Urai, A. Vergara, H. M. Wells, M. Wilson, C. Witten, I. Wool, L. Zador, A. 2020-01-17 doi:10.1101/2020.01.17.909838 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ InStrain enables population genomic analysis from metagenomic data and rigorous detection of identical microbial strains ]]> https://biorxiv.org/content/10.1101/2020.01.22.915579v1?rss=1 1,000 fecal metagenomes from newborn premature infants and find that siblings share significantly more strains than unrelated infants, although identical twins share no more strains than fraternal siblings. Infants born via cesarean section harbored Klebsiella with significantly higher nucleotide diversity than infants delivered vaginally, potentially reflecting acquisition from hospital versus maternal microbiomes. Genomic loci showing diversity within an infant included variants found in other infants, possibly reflecting inoculation from diverse hospital-associated sources. InStrain can be applied to any metagenomic dataset for microdiversity analysis and rigorous strain comparison. ]]> Olm, M. R. Crits-Christoph, A. Bouma-Gregson, K. Firek, B. Morowitz, M. Banfield, J. 2020-01-23 doi:10.1101/2020.01.22.915579 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Evolution of vertebrate gill covers via shifts in an ancient Pou3f3 enhancer ]]> https://biorxiv.org/content/10.1101/2020.01.27.918193v1?rss=1 430 mya and subsequent modifications may thus have contributed to the acquisition and diversification of gill covers and respiratory strategies during gnathostome evolution. ]]> Barske, L. Fabian, P. Hirschberger, C. Jandzik, D. Square, T. A. Xu, P. Nelson, N. Yu, H. V. Medeiros, D. M. Gillis, A. Crump, G. 2020-01-28 doi:10.1101/2020.01.27.918193 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ Wide-vergence, multi-spectral adaptive optics scanning laser ophthalmoscope with diffraction-limited illumination and collection ]]> https://biorxiv.org/content/10.1101/2020.01.29.924969v1?rss=1 Mozaffari, S. LaRocca, F. Jaedicke, V. Tiruveedhula, P. Roorda, A. 2020-01-31 doi:10.1101/2020.01.29.924969 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Characterization of an ECF56-family sigma factor from Streptomyces venezuelae reveals a highly conserved regulome ]]> https://biorxiv.org/content/10.1101/2020.01.30.927608v1?rss=1 Thompson, M. G. Zargar, A. Cruz-Morales, P. De Rond, T. Chang, S. Pearson, A. N. Goyal, G. Barajas, J. F. Blake-Hedges, J. M. Phelan, R. M. Reyes-Umana, V. Hernandez, A. C. Hillson, N. J. Shih, P. M. Keasling, J. D. 2020-01-31 doi:10.1101/2020.01.30.927608 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Cytoprotection by a naturally occurring variant of ATP5G1 in Arctic ground squirrels ]]> https://biorxiv.org/content/10.1101/2020.01.31.929018v1?rss=1 Singhal, N. S. Bai, M. Lee, E. M. Luo, S. Cook, K. R. Ma, D. K. 2020-01-31 doi:10.1101/2020.01.31.929018 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ G-baToN: a versatile cell-cell interaction reporter system. ]]> https://biorxiv.org/content/10.1101/2020.02.01.929877v1?rss=1 Tang, R. Murray, C. W. Linde, I. Kramer, N. J. Tsai, M. K. Chen, L. Cai, H. Gitler, A. D. Engleman, E. Winslow, M. M. 2020-02-02 doi:10.1101/2020.02.01.929877 Cold Spring Harbor Laboratory Press 2020-02-02 <![CDATA[ An unusual MHC molecule generates protective CD8+ T cell responses to chronic infection ]]> https://biorxiv.org/content/10.1101/2020.02.03.932848v1?rss=1 Tsitsiklis, A. Bangs, D. J. Lutes, L. L. Chan, S.-W. Geiger, K. Modzelewski, A. J. Labarta-Bajo, L. Zuniga, E. I. Robey, E. A. 2020-02-04 doi:10.1101/2020.02.03.932848 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ GENVISAGE: Rapid Identification of Discriminative and Explainable Feature Pairs for Genomic Analysis ]]> https://biorxiv.org/content/10.1101/2020.02.05.935411v1?rss=1 Huang, S. Blatti, C. Sinha, S. Parameswaran, A. 2020-02-05 doi:10.1101/2020.02.05.935411 Cold Spring Harbor Laboratory Press 2020-02-05 <![CDATA[ Integrating smFRET, SAXS and NMR data to infer structural ensembles of an intrinsically-disordered protein ]]> https://biorxiv.org/content/10.1101/2020.02.05.935890v1?rss=1 Gomes, G.-N. W. Krzeminski, M. Martin, E. Mittag, T. Head-Gordon, T. Forman-Kay, J. Gradinaru, C. 2020-02-06 doi:10.1101/2020.02.05.935890 Cold Spring Harbor Laboratory Press 2020-02-06 <![CDATA[ Identifying Informative Gene Modules Across Modalities of Single Cell Genomics ]]> https://biorxiv.org/content/10.1101/2020.02.06.937805v1?rss=1 DeTomaso, D. Yosef, N. 2020-02-07 doi:10.1101/2020.02.06.937805 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Diverse Arctic lake sediment microbiota shape methane emission temperature sensitivity ]]> https://biorxiv.org/content/10.1101/2020.02.08.934661v1?rss=1 Emerson, J. B. Varner, R. K. Wik, M. Parks, D. H. Neumann, R. B. Johnson, J. E. Singleton, C. M. Woodcroft, B. J. Tollerson, R. Owusu-Dommey, A. Binder, M. Freitas, N. L. Crill, P. M. Saleska, S. R. Tyson, G. W. Rich, V. I. 2020-02-10 doi:10.1101/2020.02.08.934661 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ Binding affinity and conformational preferences influence kinetic stability of short oligonucleotides on carbon nanotubes ]]> https://biorxiv.org/content/10.1101/2020.02.08.939918v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@6483e6org.highwire.dtl.DTLVardef@10f9e60org.highwire.dtl.DTLVardef@66c8c3org.highwire.dtl.DTLVardef@68ff4_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Alizadehmojarad, A. Zhou, X. Beyene, A. G. Chacon, K. Sung, Y. Landry, M. P. Vukovic, L. 2020-02-10 doi:10.1101/2020.02.08.939918 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ Plasticity in gene expression facilitates invasion of the desert environment in house mice ]]> https://biorxiv.org/content/10.1101/2020.02.10.939231v1?rss=1 Bittner, N. K. J. Mack, K. L. Nachman, M. W. 2020-02-11 doi:10.1101/2020.02.10.939231 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ Single mosquito metatranscriptomics recovers mosquito species, blood meal sources, and microbial cargo, including viral dark matter ]]> https://biorxiv.org/content/10.1101/2020.02.10.942854v1?rss=1 Batson, J. Kistler, A. Dudas, G. Li, L. Ratnasari, K. Haas-Stapleton, E. Logan, P. Retallack, H. 2020-02-13 doi:10.1101/2020.02.10.942854 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Mechanics regulate human embryonic stem cell self-organization to specify mesoderm ]]> https://biorxiv.org/content/10.1101/2020.02.10.943076v1?rss=1 View larger version (61K): org.highwire.dtl.DTLVardef@e21aaeorg.highwire.dtl.DTLVardef@45c41forg.highwire.dtl.DTLVardef@4ee902org.highwire.dtl.DTLVardef@a3837d_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG HighlightsO_LISubstrates that enhance cell-cell adhesion promote hESC self-organization C_LIO_LITissue nodes exhibiting high tension are predisposed to gastrulation induction C_LIO_LIColony geometry dictates the localization of tension nodes to specify mesoderm C_LIO_LITension activates {beta}-catenin and stimulates Wnt signaling to induce mesoderm C_LI In BriefEngineered substrates that promote cell-cell adhesion and reconstitute epiblast tissue organization facilitate "gastrulation-like" morphogenesis in cultured hESCs. Tissue geometries that foster localized regions of high cell-cell tension potentiate BMP4-dependent mesoderm specification by enhancing phosphorylation and nuclear translocation of {beta}-catenin to promote Wnt signaling. ]]> Muncie, J. M. Ayad, N. M. E. Lakins, J. N. Weaver, V. M. 2020-02-11 doi:10.1101/2020.02.10.943076 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ Inflammation promotes tumor aggression by stimulating stromal cell-dependent collagen crosslinking and stromal stiffening ]]> https://biorxiv.org/content/10.1101/2020.02.13.948141v1?rss=1 Maller, O. Drain, A. P. Barrett, A. S. Borgquist, S. Ruffell, B. Thanh, P. T. Gruosso, T. Kuasne, H. Lakins, J. N. Acerbi, I. Barnes, J. M. Nemkov, T. Chauhan, A. Gruenberg, J. Nasir, A. Bjarnadottir, O. Werb, Z. Kabos, P. Hwang, E. S. Park, M. Coussens, L. M. Nelson, A. C. Hansen, K. C. Weaver, V. M. 2020-02-13 doi:10.1101/2020.02.13.948141 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Disadvantages of writing, reading, publishing and presenting scientific papers caused by the dominance of the English language in science: The case of Colombian Ph.D. in biological sciences ]]> https://biorxiv.org/content/10.1101/2020.02.15.949982v1?rss=1 Ramirez-Castaneda, V. 2020-02-19 doi:10.1101/2020.02.15.949982 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Assessing trait driver theory along abiotic gradients in a tropical plant communities ]]> https://biorxiv.org/content/10.1101/2020.02.15.950139v1?rss=1 Lourenco, J. Newman, E. A. Enquist, B. J. Dias Milanez, C. R. Thomaz, L. D. 2020-02-19 doi:10.1101/2020.02.15.950139 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ High-throughput mapping of the phage resistance landscape in E. coli ]]> https://biorxiv.org/content/10.1101/2020.02.15.951020v1?rss=1 Mutalik, V. K. Adler, B. A. Rishi, H. S. Piya, D. Zhong, C. Koskella, B. Calendar, R. Novichkov, P. Price, M. N. Deutschbauer, A. M. Arkin, A. P. 2020-02-16 doi:10.1101/2020.02.15.951020 Cold Spring Harbor Laboratory Press 2020-02-16 <![CDATA[ Genomic variation and population histories of spotted (Strix occidentalis) and barred (S. varia) owls ]]> https://biorxiv.org/content/10.1101/2020.02.18.954685v1?rss=1 Fujito, N. T. Hanna, Z. R. Levy-Sakin, M. Bowie, R. C. K. Kwok, P.-Y. Dumbacher, J. P. Wall, J. D. 2020-02-19 doi:10.1101/2020.02.18.954685 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Promoter keyholes enable specific and persistent multi-gene expression programs in primary T cells without genome modification ]]> https://biorxiv.org/content/10.1101/2020.02.19.956730v1?rss=1 Wilken, M. S. Ciarlo, C. Pearl, J. Bloom, J. Schanzer, E. Liao, H. Boyken, S. E. Van Biber, B. Queitsch, K. Heberlein, G. Federation, A. Acosta, R. Vong, S. Otterman, E. Dunn, D. Wang, H. Zrazhevskey, P. Nandakumar, V. Bates, D. Sandstrom, R. Chen, Z. Urnov, F. D. Baker, D. Funnell, A. Green, S. Stamatoyannopoulos, J. A. 2020-02-20 doi:10.1101/2020.02.19.956730 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Genome-scale metabolic rewiring to achieve predictable titers rates and yield of a non-native product at scale ]]> https://biorxiv.org/content/10.1101/2020.02.21.954792v1?rss=1 Banerjee, D. Eng, T. T. Lau, A. K. Wang, B. Sasaki, Y. Herbert, R. A. Chen, Y. Liu, Y. Prahl, J.-P. Singan, V. R. Tanjore, D. Petzold, C. J. Keasling, J. D. Mukhopadhyay, A. 2020-02-24 doi:10.1101/2020.02.21.954792 Cold Spring Harbor Laboratory Press 2020-02-24 <![CDATA[ Intracranial recordings demonstrate medial temporal lobe engagement in visual search in humans ]]> https://biorxiv.org/content/10.1101/2020.02.29.971341v1?rss=1 Slama, K. Jimenez, R. Saha, S. King-Stephens, D. Laxer, K. D. Weber, P. B. Endestad, T. Larsson, P. G. Solbakk, A.-K. Lin, J. J. Knight, R. T. 2020-03-03 doi:10.1101/2020.02.29.971341 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ Parallel organization of cerebellar pathways to sensorimotor, associative, and modulatory forebrain ]]> https://biorxiv.org/content/10.1101/2020.03.06.979153v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@1bead0corg.highwire.dtl.DTLVardef@1531de2org.highwire.dtl.DTLVardef@1cf02f6org.highwire.dtl.DTLVardef@1cb6774_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pisano, T. J. Dhanerawala, Z. M. Kislin, M. Bakshinskaya, D. Engel, E. A. Lee, J. de Oude, N. L. Umadevi Venkataraju, K. Verpeut, J. L. Boele, H.-J. Wang, S. S.- H. 2020-03-08 doi:10.1101/2020.03.06.979153 Cold Spring Harbor Laboratory Press 2020-03-08 <![CDATA[ Mechanosensing through direct binding of tensed F-actin by LIM domains ]]> https://biorxiv.org/content/10.1101/2020.03.06.979245v1?rss=1 Sun, X. Phua, D. Y. Z. Axiotakis, L. Smith, M. A. Blankman, E. Gong, R. Cail, R. C. Espinosa de los Reyes, S. Beckerle, M. C. Waterman, C. M. Alushin, G. M. 2020-03-07 doi:10.1101/2020.03.06.979245 Cold Spring Harbor Laboratory Press 2020-03-07 <![CDATA[ Cytoskeletal tension forces mitohormesis ]]> https://biorxiv.org/content/10.1101/2020.03.06.979583v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@1ecdaceorg.highwire.dtl.DTLVardef@1112c32org.highwire.dtl.DTLVardef@6c99a1org.highwire.dtl.DTLVardef@1da1e5f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Tharp, K. M. Higuchi-Sanabria, R. Timblin, G. Garzon-Coral, C. Ford, B. Schneider, C. Muncie, J. M. Stashko, C. Daniele, J. Frankino, P. Manoli, S. Shao, H. Gestwicki, J. Hellerstein, M. Nomura, D. K. Saijo, K. Dunn, A. Dillin, A. Weaver, V. M. 2020-03-07 doi:10.1101/2020.03.06.979583 Cold Spring Harbor Laboratory Press 2020-03-07 <![CDATA[ Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta ]]> https://biorxiv.org/content/10.1101/2020.03.16.987719v1?rss=1 Bilcke, G. Van den Berge, K. De Decker, S. Bonneure, E. Poulsen, N. Bulankova, P. Osuna-Cruz, C. M. Dickenson, J. Sabbe, K. Pohnert, G. Vandepoele, K. Mangelinckx, S. Clement, L. De Veylder, L. Vyverman, W. 2020-03-18 doi:10.1101/2020.03.16.987719 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ A single mechanism for global and selective response inhibition under the influence of motor preparation ]]> https://biorxiv.org/content/10.1101/2020.03.16.993261v1?rss=1 Raud, L. Huster, R. Ivry, R. B. Labruna, L. Messel, M. S. Greenhouse, I. 2020-03-18 doi:10.1101/2020.03.16.993261 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ Conversion of marginal land into switchgrass conditionally accrues soil carbon and reduces methane consumption ]]> https://biorxiv.org/content/10.1101/2020.03.18.997304v1?rss=1 Bates, C. T. Escalas, A. Kuang, J. Hale, L. Wang, Y. Herman, D. Nuccio, E. E. Wang, X. Fu, Y. Tian, R. Wang, G. Ning, D. Yang, Y. Wu, L. Pett-Ridge, J. Saha, M. Craven, K. Firestone, M. K. Zhou, J. 2020-03-20 doi:10.1101/2020.03.18.997304 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ PathFlow-MixMatch for Whole Slide Image Registration: An Investigation of a Segment-Based Scalable Image Registration Method ]]> https://biorxiv.org/content/10.1101/2020.03.22.002402v1?rss=1 Levy, J. J. Jackson, C. R. Haudenschild, C. C. Christensen, B. C. Vaickus, L. J. 2020-03-24 doi:10.1101/2020.03.22.002402 Cold Spring Harbor Laboratory Press 2020-03-24 <![CDATA[ FcRn, but not FcgRs, drives maternal-fetal transplacental transport of human IgGantibodies ]]> https://biorxiv.org/content/10.1101/2020.03.22.999243v1?rss=1 Borghi, S. Bournazos, S. Thulin, N. Li, C. Gajewski, A. Sherwood, R. Zhang, S. Harris, E. Jagannathan, P. Wang, L.-X. Ravetch, J. V. Wang, T. T. 2020-03-25 doi:10.1101/2020.03.22.999243 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics and proteomics ]]> https://biorxiv.org/content/10.1101/2020.03.23.004093v1?rss=1 West, P. T. Peters, S. L. Olm, M. R. Yu, F. B. Lou, Y. C. Firek, B. A. Baker, R. Johnson, A. D. Morowitz, M. J. Hettich, R. L. Banfield, J. F. 2020-03-25 doi:10.1101/2020.03.23.004093 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Structure of the ForT/PRPP complex uncovers the mechanism of C-C bond formation in C-nucleotide antibiotic biosynthesis ]]> https://biorxiv.org/content/10.1101/2020.03.26.009662v1?rss=1 View larger version (12K): org.highwire.dtl.DTLVardef@1817d54org.highwire.dtl.DTLVardef@4b3558org.highwire.dtl.DTLVardef@19b248eorg.highwire.dtl.DTLVardef@7d0c62_HPS_FORMAT_FIGEXP M_FIG C_FIG A new class of enzymes catalyse C-C bond formation by irreversible CO2 and pyrophosphate production. ]]> Gao, S. Radadiya, A. Li, W. Liu, H. Zhu, W. de Crecy-Lagard, V. Richards, N. Naismith, J. 2020-03-30 doi:10.1101/2020.03.26.009662 Cold Spring Harbor Laboratory Press 2020-03-30 <![CDATA[ The Hoja loca1 Mutant and AUX/1 IAA Function in Maize ]]> https://biorxiv.org/content/10.1101/2020.03.27.012211v1?rss=1 Richardson, A. Sluis, A. Hake, S. 2020-03-29 doi:10.1101/2020.03.27.012211 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ Biallelic variants in the RNA exosome gene EXOSC5 are associated with developmental delays, short stature, cerebellar hypoplasia and motor weakness ]]> https://biorxiv.org/content/10.1101/2020.04.01.839274v1?rss=1 Slavotinek, A. Misceo, D. Htun, S. Mathisen, L. Frengen, E. Foreman, M. Hurtig, J. E. Enyenihi, L. Sterrett, M. C. Leung, S. W. Schneidman-Duhovny, D. Estrada-Veras, J. I. Duncan, J. L. Xia, V. Beleford, D. Si, Y. Douglas, G. Treidene, H. E. van Hoof, A. Fasken, M. B. Corbett, A. H. 2020-04-02 doi:10.1101/2020.04.01.839274 Cold Spring Harbor Laboratory Press 2020-04-02 <![CDATA[ IDseq - An Open Source Cloud-based Pipeline and Analysis Service for Metagenomic Pathogen Detection and Monitoring ]]> https://biorxiv.org/content/10.1101/2020.04.07.030551v1?rss=1 Kalantar, K. L. Carvalho, T. de Bourcy, C. F. A. Dimitrov, B. Dingle, G. Egger, R. Han, J. Holmes, O. B. Juan, Y. King, R. Kislyuk, A. Mariano, M. Reyenoso, L. V. Rissato Cruz, D. Sheu, J. Tang, J. Wang, J. Zhang, M. A. Zhong, E. Ahyong, V. Lay, S. Chea, S. Bohl, J. A. Manning, J. E. Tato, C. M. DeRisi, J. L. 2020-04-09 doi:10.1101/2020.04.07.030551 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Transcriptome analysis of the zebrafish atoh7-/- mutant, lakritz, highlights Atoh7-dependent genetic networks with potential implications for human eye diseases ]]> https://biorxiv.org/content/10.1101/2020.04.09.033704v1?rss=1 Covello, G. Rossello, F. J. Filosi, M. Gajardo, F. Duchemin, A.-L. Tremonti, B. F. Eichenlaub, M. Polo, J. M. Powell, D. Ngai, J. Allende, M. L. Domenici, E. Ramialison, M. Poggi, L. 2020-04-10 doi:10.1101/2020.04.09.033704 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ An empirical comparison of univariate versus multivariate methods for the analysis of brain-behavior mapping ]]> https://biorxiv.org/content/10.1101/2020.04.13.039958v1?rss=1 Ivanova, M. V. Herron, T. J. Dronkers, N. F. Baldo, J. V. 2020-04-14 doi:10.1101/2020.04.13.039958 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ A faster implementation of association mapping from k-mers ]]> https://biorxiv.org/content/10.1101/2020.04.14.040675v1?rss=1 Mehrab, Z. Mobin, J. Tahmid, I. A. Rahman, A. 2020-04-14 doi:10.1101/2020.04.14.040675 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Continuous lineage recording reveals rapid, multidirectional metastasis in a lung cancer xenograft model in mouse ]]> https://biorxiv.org/content/10.1101/2020.04.16.045245v1?rss=1 Quinn, J. J. Jones, M. G. Okimoto, R. A. Yosef, N. Bivona, T. G. Weissman, J. S. 2020-04-17 doi:10.1101/2020.04.16.045245 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ CeMbio - The C. elegans microbiome resource ]]> https://biorxiv.org/content/10.1101/2020.04.22.055426v1?rss=1 Dirksen, P. Assie, A. Zimmermann, J. Zhang, F. Tietje, A.-M. Marsh, S. A. Felix, M.-A. Shapira, M. Kaleta, C. Schulenburg, H. Samuel, B. S. 2020-04-24 doi:10.1101/2020.04.22.055426 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Parental population range expansion before secondary contact promotes heterosis ]]> https://biorxiv.org/content/10.1101/2020.04.28.066308v1?rss=1 MacPherson, A. Wang, S. Yamaguchi, R. Reiseberg, L. Otto, S. 2020-04-30 doi:10.1101/2020.04.28.066308 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Thiocyanate and organic carbon inputs drive convergent selection for specific autotrophic Afipia and Thiobacillus strains within complex microbiomes ]]> https://biorxiv.org/content/10.1101/2020.04.29.067207v1?rss=1 Huddy, R. J. Sachdeva, R. Kadzinga, F. Kantor, R. Harrison, S. T. L. Banfield, J. F. 2020-04-30 doi:10.1101/2020.04.29.067207 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Continuous Reports of Sensed Hand Position During Sensorimotor Adaptation ]]> https://biorxiv.org/content/10.1101/2020.04.29.068197v1?rss=1 Tsay, J. S. Parvin, D. E. Ivry, R. B. 2020-04-30 doi:10.1101/2020.04.29.068197 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Heritability of visual cortex architecture and perception ]]> https://biorxiv.org/content/10.1101/2020.05.04.077545v1?rss=1 View larger version (77K): org.highwire.dtl.DTLVardef@ceacd6org.highwire.dtl.DTLVardef@b51604org.highwire.dtl.DTLVardef@b860f8org.highwire.dtl.DTLVardef@e67398_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Alvarez, I. Finlayson, N. J. Ei, S. de Haas, B. Greenwood, J. A. Schwarzkopf, D. S. 2020-05-05 doi:10.1101/2020.05.04.077545 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Meta-Align: A Novel HMM-based Algorithm for Pairwise Alignment of Error-Prone Sequencing Reads ]]> https://biorxiv.org/content/10.1101/2020.05.11.087676v1?rss=1 TOMII, K. Kumar, S. Zhi, D. Brenner, S. E. 2020-05-12 doi:10.1101/2020.05.11.087676 Cold Spring Harbor Laboratory Press 2020-05-12 <![CDATA[ A bimodular PKS platform that expands the biological design space ]]> https://biorxiv.org/content/10.1101/2020.05.14.096743v1?rss=1 Zargar, A. Valencia, L. Wang, J. Chang, S. Werts, M. Wong, A. Benites, V. Baidoo, E. Katz, L. Keasling, J. D. 2020-05-16 doi:10.1101/2020.05.14.096743 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Homology-guided identification of a conserved motif linking the antiviral functions of IFITM3 to its oligomeric state ]]> https://biorxiv.org/content/10.1101/2020.05.14.096891v1?rss=1 Rahman, K. Coomer, C. A. Majdoul, S. Ding, S. Padilla-Parra, S. Compton, A. A. 2020-05-16 doi:10.1101/2020.05.14.096891 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Peptide YY: a novel Paneth cell antimicrobial peptide that maintains fungal commensalism ]]> https://biorxiv.org/content/10.1101/2020.05.15.096875v1?rss=1 Pierre, J. F. La Torre, D. Sidebottom, A. Kambal, A. Zhu, X. Tao, Y. Cham, C. M. Wang, L. Harris, K. G. Zaborina, O. Alverdy, J. C. Witchley, J. Noble, S. M. Chang, E. B. 2020-05-16 doi:10.1101/2020.05.15.096875 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Widening the bottleneck: Heterologous expression, purification, and characterization of the Ktedonobacter racemifer minimal type II polyketide synthase in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2020.05.18.102780v1?rss=1 Klein, J. G. Wu, Y. Kokona, B. Charkoudian, L. K. 2020-05-21 doi:10.1101/2020.05.18.102780 Cold Spring Harbor Laboratory Press 2020-05-21 <![CDATA[ Gbx2 identifies two amacrine cell subtypes with distinct molecular, morphological, and physiological properties ]]> https://biorxiv.org/content/10.1101/2020.05.19.104307v1?rss=1 Kerstein, P. C. Leffler, J. Sivyer, B. Taylor, W. R. Wright, K. M. 2020-05-20 doi:10.1101/2020.05.19.104307 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Selective inhibition of human translation by a drug-like compound that traps terminated protein nascent chains on the ribosome ]]> https://biorxiv.org/content/10.1101/2020.05.20.106807v1?rss=1 Li, W. Chang, S. T.- L. Ward, F. R. Cate, J. H. D. 2020-05-22 doi:10.1101/2020.05.20.106807 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Chromosome-level reference genome of the European wasp spider Argiope bruennichi: a resource for studies on range expansion and evolutionary adaptation ]]> https://biorxiv.org/content/10.1101/2020.05.21.103564v1?rss=1 Sheffer, M. M. Hoppe, A. Krehenwinkel, H. Uhl, G. Kuss, A. W. Jensen, L. Jensen, C. Gillespie, R. G. Hoff, K. J. Prost, S. 2020-05-22 doi:10.1101/2020.05.21.103564 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Compromised nuclear envelope integrity drives tumor cell invasion ]]> https://biorxiv.org/content/10.1101/2020.05.22.110122v1?rss=1 Nader, G. Aguera-Gonzalez, S. Routet, F. Gratia, M. Maurin, M. Cancila, V. Cadart, C. Gentili, M. Yamada, A. Lodillinsky, C. Lagoutte, E. Villard, C. Viovy, J.-L. Tripodo, C. Scita, G. Manel, N. Chavrier, P. Piel, M. 2020-05-23 doi:10.1101/2020.05.22.110122 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ Choanoflagellates and the ancestry of neurosecretory vesicles ]]> https://biorxiv.org/content/10.1101/2020.05.24.111997v1?rss=1 Gohde, R. Nauman, B. Laundon, D. Imig, C. McDonald, K. L. Cooper, B. H. Varoqueaux, F. Fasshauer, D. Burkhardt, P. 2020-05-27 doi:10.1101/2020.05.24.111997 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Coupling between slow-waves and sharp-wave ripples organizes distributed neural activity during sleep in humans ]]> https://biorxiv.org/content/10.1101/2020.05.24.113480v1?rss=1 Skelin, I. Zhang, H. Zheng, J. Ma, S. Mander, B. A. Kim Mcmanus, O. Vadera, S. Knight, R. T. McNaughton, B. L. Lin, J. J. 2020-05-25 doi:10.1101/2020.05.24.113480 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Comparative analysis of macrophage post-translational modifications during intracellular bacterial pathogen infection ]]> https://biorxiv.org/content/10.1101/2020.05.27.116772v1?rss=1 Johnson, J. R. Parry, T. Repasy, T. Geiger, K. M. Verschueren, E. Budzik, J. M. Jimenez-Morales, D. Newton, B. W. Powell, E. Coscoy, L. Portnoy, D. A. Krogan, N. J. Cox, J. S. 2020-05-27 doi:10.1101/2020.05.27.116772 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ mbkmeans: fast clustering for single cell data using mini-batch k-means ]]> https://biorxiv.org/content/10.1101/2020.05.27.119438v1?rss=1 Hicks, S. C. Liu, R. Ni, Y. Purdom, E. Risso, D. 2020-05-27 doi:10.1101/2020.05.27.119438 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Novel Vβ specific germline contacts shape an elite controller T cell response ]]> https://biorxiv.org/content/10.1101/2020.05.31.102566v1?rss=1 Wang, Y. Tsitsiklis, A. Gao, W. Chu, H. H. Zhang, Y. Li, W. Wong, W. K. Deane, C. M. Neau, D. Slansky, J. Thomas, P. G. Robey, E. A. Dai, S. 2020-06-01 doi:10.1101/2020.05.31.102566 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ Balancing signal and photoperturbation in multiphoton light-sheet microscopy by optimizing laser pulse frequency ]]> https://biorxiv.org/content/10.1101/2020.06.02.130377v1?rss=1 Maioli, V. Boniface, A. Mahou, P. Ferrer Ortas, J. Abdeladim, L. Beaurepaire, E. Supatto, W. 2020-06-03 doi:10.1101/2020.06.02.130377 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014 ]]> https://biorxiv.org/content/10.1101/2020.06.05.098590v1?rss=1 Huong, N. Q. Nga, N. T. T. Long, N. V. Luu, B. D. Latinne, A. Pruvot, M. Phuong, N. T. Quang, L. T. V. Hung, V. V. Lan, N. T. Hoa, N. T. Minh, P. Q. Diep, N. T. Tung, N. Ky, V. D. Roberton, S. I. Thuy, H. B. Long, N. V. Gilbert, M. Wicker, L. Mazet, J. A. K. Johnson, C. K. Goldstein, T. Tremeau-Bravard, A. Ontiveros, V. Joly, D. O. Walzer, C. Fine, A. E. Olson, S. H. 2020-06-09 doi:10.1101/2020.06.05.098590 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Enhanced production of taxadiene in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2020.06.08.139600v1?rss=1 Nowrouzi, B. Li, R. Walls, L. E. d'Espaux, L. Malci, K. Liang, L. Jonguitud Borrego, N. Lerma Escalera, A. I. Morones-Ramirez, J. R. Keasling, J. D. Rios Solis, L. 2020-06-08 doi:10.1101/2020.06.08.139600 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ Development of genetic tools for the thermophilic filamentous fungus Thermoascus aurantiacus ]]> https://biorxiv.org/content/10.1101/2020.06.09.143198v1?rss=1 Gabriel, R. Prinz, J. Jecmenica, M. Romero-Vazquez, C. Chou, P. Harth, S. Floerl, L. Curran, L. Oostlander, A. Matz, L. Fritsche, S. Gorman, J. Schuerg, T. Fleissner, A. Singer, S. W. 2020-06-11 doi:10.1101/2020.06.09.143198 Cold Spring Harbor Laboratory Press 2020-06-11 <![CDATA[ Extensive individual differences of category information in ventral temporal cortex in the congenitally blind ]]> https://biorxiv.org/content/10.1101/2020.06.14.151092v1?rss=1 Rosenke, M. van den Hurk, J. Margalit, E. Op de Beeck, H. P. grill-spector, k. Weiner, K. S. 2020-06-14 doi:10.1101/2020.06.14.151092 Cold Spring Harbor Laboratory Press 2020-06-14 <![CDATA[ The ATPase mechanism of myosin 15, the molecular motor mutated in DFNB3 deafness ]]> https://biorxiv.org/content/10.1101/2020.06.17.155424v1?rss=1 Jiang, F. Takagi, Y. Shams, A. Heissler, S. M. Friedman, T. B. Sellers, J. R. Bird, J. E. 2020-06-19 doi:10.1101/2020.06.17.155424 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs ]]> https://biorxiv.org/content/10.1101/2020.06.17.156554v1?rss=1 Kern, D. M. Sorum, B. Hoel, C. M. Sridharan, S. Remis, J. P. Toso, D. B. Brohawn, S. G. 2020-06-18 doi:10.1101/2020.06.17.156554 Cold Spring Harbor Laboratory Press 2020-06-18 <![CDATA[ Identification and characterization of centromeric sequences in Xenopus laevis ]]> https://biorxiv.org/content/10.1101/2020.06.23.167643v1?rss=1 Smith, O. K. Limouse, C. Fryer, K. A. Teran, N. A. Sundararajan, K. Heald, R. Straight, A. F. 2020-06-24 doi:10.1101/2020.06.23.167643 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ A flagellate-to-amoeboid switch in the closest living relatives of animals ]]> https://biorxiv.org/content/10.1101/2020.06.26.171736v1?rss=1 Brunet, T. Albert, M. Roman, W. Spitzer, D. King, N. 2020-06-28 doi:10.1101/2020.06.26.171736 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ Three-dimensional Multi-site Random Access Photostimulation (3D-MAP) ]]> https://biorxiv.org/content/10.1101/2020.06.28.176503v1?rss=1 Adesnik, H. Waller, L. Pegard, N. Xue, Y. 2020-06-29 doi:10.1101/2020.06.28.176503 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Approximation of Indel Evolution by Differential Calculus of Finite State Automata ]]> https://biorxiv.org/content/10.1101/2020.06.29.178764v1?rss=1 Holmes, I. 2020-06-30 doi:10.1101/2020.06.29.178764 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ Convergence in light transmission properties of transparent wing areas in clearwing mimetic butterflies ]]> https://biorxiv.org/content/10.1101/2020.06.30.180612v1?rss=1 Pinna, C. S. Vilbert, M. Borenztajn, S. Daney de Marcillac, W. Piron-Prunier, F. Pomerantz, A. F. Patel, N. H. Berthier, S. Andraud, C. Gomez, D. Elias, M. 2020-07-02 doi:10.1101/2020.06.30.180612 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Galectin-8 senses phagosomal damage and recruits selective autophagy adapter TAX1BP1 to control Mycobacterium tuberculosis infection in macrophages ]]> https://biorxiv.org/content/10.1101/2020.06.30.180877v1?rss=1 Bell, S. L. Lopez, K. L. Cox, J. S. Patrick, K. L. Watson, R. O. 2020-07-01 doi:10.1101/2020.06.30.180877 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ SWR1-independent association of H2A.Z to the LINC complex promotes meiotic chromosome motion ]]> https://biorxiv.org/content/10.1101/2020.06.30.181016v1?rss=1 Gonzalez-Arranz, S. Gardner, J. M. Yu, Z. Patel, N. J. Heldrich, J. Santos, B. Carballo, J. A. Jaspersen, S. Hochwagen, A. San-Segundo, P. A. 2020-07-01 doi:10.1101/2020.06.30.181016 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Transcriptomic and morphological response of SIM-A9 mouse microglia to carbon nanotube neuro-sensors ]]> https://biorxiv.org/content/10.1101/2020.06.30.181420v1?rss=1 Yang, D. Yang, S. J. Del Bonis-O'Donnell, J. T. Pinals, R. L. Landry, M. P. 2020-07-01 doi:10.1101/2020.06.30.181420 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Phosphoregulation of HORMA domain protein HIM-3 promotes asymmetric synaptonemal complex disassembly in meiotic prophase in C. elegans ]]> https://biorxiv.org/content/10.1101/2020.07.01.182063v1?rss=1 Sato-Carlton, A. Nakamura-Tabuchi, C. Li, X. Boog, H. Lehmer, M. K. Rosenberg, S. C. Barroso, C. Martinez-Perez, E. Corbett, K. D. Carlton, P. M. 2020-07-01 doi:10.1101/2020.07.01.182063 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Developmental, cellular, and biochemical basis of transparency in the glasswing butterfly Greta oto ]]> https://biorxiv.org/content/10.1101/2020.07.02.183590v1?rss=1 Pomerantz, A. F. Siddique, R. H. Cash, E. I. Kishi, Y. Pinna, C. Hammar, K. Gomez, D. Elias, M. Patel, N. H. 2020-07-02 doi:10.1101/2020.07.02.183590 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ A Large-Scale Internal Validation Study of Unsupervised Virtual Trichrome Staining Technologies on Non-alcoholic Steatohepatitis Liver Biopsies ]]> https://biorxiv.org/content/10.1101/2020.07.03.187237v1?rss=1 Levy, J. Azizgolshani, N. Andersen, M. Suriawinata, A. A. Liu, X. Lisovsky, M. Ren, B. Christensen, B. Vaickus, L. J. 2020-07-04 doi:10.1101/2020.07.03.187237 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Multiple Haplotype Reconstruction from Allele Frequency Data ]]> https://biorxiv.org/content/10.1101/2020.07.09.191924v1?rss=1 Marta Pelizzola Merle Behr Housen Li Axel Munk Andreas Futschik 2020-07-10 doi:10.1101/2020.07.09.191924 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Differential Contributions of Static and Time-Varying Functional Connectivity to Human Behavior ]]> https://biorxiv.org/content/10.1101/2020.07.14.203273v1?rss=1 Eichenbaum, A. Pappas, I. Lurie, D. Cohen, J. R. D'Esposito, M. 2020-07-15 doi:10.1101/2020.07.14.203273 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance ]]> https://biorxiv.org/content/10.1101/2020.07.14.203604v1?rss=1 99% query coverage, >99% identity) identified as integrated in the genomes of specific Pseudomonas, Acidovorax and Castellaniella strains, resulting in very high-confidence host assignments. Lastly, 21 of these viruses encoded putative auxiliary metabolite genes for metal and antibiotic resistance, which might drive their infection cycles and/or provide selective advantage to infected hosts. Exploring the groundwater virome provides a necessary foundation for integration of viruses into ecosystem models where they act as key players in microbial adaption to environmental stress. ImportanceTo our knowledge, this is the first study to identify the bacteriophage distribution in a groundwater ecosystem shedding light on their prevalence and distribution across metal-contaminated and background sites. Our study is uniquely based on selective sequencing of solely the extrachromosomal elements of a microbiome followed by analysis for viral signatures, thus establishing a more focused approach for phage identifications. Using this method, we detect several novel phage genera along with those previously established. Our approach of using the whole genome sequences of hundreds of bacterial isolates from the same site enabled us to make host assignments with high confidence, several at strain levels. Certain phage-encoded genes suggest they provide an environment-specific selective advantage to their bacterial hosts. Our study lays the foundation for future research on directed phage isolations using specific bacterial host strains to further characterize groundwater phages, their lifecycles, and its effects on groundwater microbiome and biogeochemistry. ]]> Kothari, A. Roux, S. Zhang, H. Prieto, A. Soneja, D. Chandonia, J.-M. Spencer, S. J. Wu, X. Altenburg, S. Fields, M. W. Deutschbauer, A. M. Arkin, A. P. Alm, E. J. Chakraborty, R. Mukhopadhyay, A. 2020-07-15 doi:10.1101/2020.07.14.203604 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ Automated and accurate segmentation of leaf venation networks via deep learning ]]> https://biorxiv.org/content/10.1101/2020.07.19.206631v1?rss=1 700 leaves representing 50 southeast Asian plant families. Ensembles of 6 independently trained CNNs were used to segment networks from larger leaf regions (~100 mm2). Segmented networks were analysed using hierarchical loop decomposition to extract a range of statistics describing scale transitions in vein and areole geometry. C_LIO_LIThe CNN approach gave a precision-recall harmonic mean of 94.5% {+/-} 6%, outperforming other current network extraction methods, and accurately described the widths, angles, and connectivity of veins. Multi-scale statistics then enabled identification of previously-undescribed variation in network architecture across species. C_LIO_LIWe provide a LeafVeinCNN software package to enable multi-scale quantification of leaf vein networks, facilitating comparison across species and exploration of the functional significance of different leaf vein architectures. C_LI ]]> Xu, H. Blonder, B. Jodra, M. Malhi, Y. Fricker, M. 2020-07-19 doi:10.1101/2020.07.19.206631 Cold Spring Harbor Laboratory Press 2020-07-19 <![CDATA[ Irradiance modulates thermal niche in a previously undescribed low-light and cold-adapted nano-diatom ]]> https://biorxiv.org/content/10.1101/2020.07.21.210047v1?rss=1 Kling, J. D. Kelly, K. J. Pei, S. Rynearson, T. A. Hutchins, D. A. 2020-07-21 doi:10.1101/2020.07.21.210047 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Repulsive expansion dynamics in colony growth and patterning ]]> https://biorxiv.org/content/10.1101/2020.07.21.213611v1?rss=1 Cao, Y. Neu, J. Meldgin, D. R. Lu, T. You, L. 2020-07-21 doi:10.1101/2020.07.21.213611 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Spatial phylogenetics of butterflies in relation to environmental drivers and angiosperm diversity across North America ]]> https://biorxiv.org/content/10.1101/2020.07.22.216119v1?rss=1 Earl, C. Belitz, M. W. Laffan, S. W. Barve, V. Barve, N. Soltis, D. E. Allen, J. M. Soltis, P. S. Mishler, B. D. Kawahara, A. Y. Guralnick, R. P. 2020-07-24 doi:10.1101/2020.07.22.216119 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Structural mechanism for amino acid-dependent Rag GTPase switching by SLC38A9 ]]> https://biorxiv.org/content/10.1101/2020.07.28.225524v1?rss=1 Fromm, S. Lawrence, R. E. Hurley, J. H. 2020-07-29 doi:10.1101/2020.07.28.225524 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Genetically-encoded fluorescent biosensor for rapid detection of protein expression ]]> https://biorxiv.org/content/10.1101/2020.07.30.229633v1?rss=1 30 min that causes delays in real-time detection of protein expression. Here, we engineer a genetically-encoded fluorescent biosensor to enable detection of protein expression within seconds in live cells. This sensor for transiently-expressed proteins (STEP) is based on a fully matured but dim green fluorescent protein in which pre-existing fluorescence increases 11-fold in vivo following the specific and rapid binding of a protein tag (Kd 120 nM, kon 1.7 x 105 M-1s-1). In live E. coli cells, our STEP biosensor enables detection of protein expression twice as fast as the use of standard fluorescent protein fusions. Our biosensor opens the door to the real-time study of short-timescale processes in research model animals with high spatiotemporal resolution. ]]> Eason, M. G. Pandelieva, A. T. Mayer, M. M. Khan, S. T. Garcia, H. G. Chica, R. A. 2020-07-30 doi:10.1101/2020.07.30.229633 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ Antibody:CD47 ratio regulates macrophage phagocytosis through competitive receptor phosphorylation ]]> https://biorxiv.org/content/10.1101/2020.07.31.231779v1?rss=1 Suter, E. C. Schmid, E. M. Voets, E. Francica, B. Fletcher, D. A. 2020-08-02 doi:10.1101/2020.07.31.231779 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ Topological Feature Extraction and Visualization of Whole Slide Images using Graph Neural Networks ]]> https://biorxiv.org/content/10.1101/2020.08.01.231639v1?rss=1 Levy, J. Haudenschild, C. Bar, C. Christensen, B. Vaickus, L. 2020-08-03 doi:10.1101/2020.08.01.231639 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ NPC1-mTORC1 signaling Couples Cholesterol Sensing to Organelle Homeostasis and is a Targetable Pathway in Niemann-Pick type C ]]> https://biorxiv.org/content/10.1101/2020.08.02.233254v1?rss=1 Davis, O. B. Shin, H. R. Lim, C.-Y. Wu, E. Y. Kukurugya, M. Maher, C. F. Perera, R. M. Ordonez, P. Zoncu, R. 2020-08-02 doi:10.1101/2020.08.02.233254 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ An MRI protocol for anatomical and functional evaluation of the California sea lion brain ]]> https://biorxiv.org/content/10.1101/2020.08.02.233429v1?rss=1 Cook, P. Hoard, V. Dolui, S. Frederick, B. Redfern, R. Dennison, S. Halaska, B. Bloom, J. Kruse-Elliott, K. Whitmer, E. Trumbull, E. Berns, G. Detre, J. D'Esposito, M. Gulland, F. Reichmuth, C. Johnson, S. Field, C. Inglis, B. 2020-08-03 doi:10.1101/2020.08.02.233429 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Intestinal infection results in impaired lung innate immunity to secondary respiratory infection. ]]> https://biorxiv.org/content/10.1101/2020.08.03.235457v1?rss=1 Trivedi, S. Grossmann, A. H. Jensen, O. Cody, M. J. Warren, K. J. Yost, C. C. Leung, D. T. 2020-08-04 doi:10.1101/2020.08.03.235457 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ H3 K27M and EZHIP impede H3K27-methylation spreading by inhibiting allosterically stimulated PRC2 ]]> https://biorxiv.org/content/10.1101/2020.08.05.236737v1?rss=1 Jain, S. U. Rashoff, A. Q. Krabbenhoft, S. D. Hoelper, D. Do, T. J. Gibson, T. J. Lundgren, S. M. Bondra, E. R. Deshmukh, S. Harutyunyan, A. S. Juretic, N. Jabado, N. Harrison, M. Lewis, P. W. 2020-08-05 doi:10.1101/2020.08.05.236737 Cold Spring Harbor Laboratory Press 2020-08-05 <![CDATA[ Deep reinforcement learning for modeling human locomotion control in neuromechanical simulation ]]> https://biorxiv.org/content/10.1101/2020.08.11.246801v1?rss=1 Song, S. Kidzinski, Łukasz Peng, X. B. Ong, C. Hicks, J. L. Levine, S. Atkeson, C. Delp, S. 2020-08-12 doi:10.1101/2020.08.11.246801 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Investigation of Capsule-Inspired Neural Network Approaches for DNA Methylation ]]> https://biorxiv.org/content/10.1101/2020.08.14.251306v1?rss=1 Levy, J. Chen, Y. Azizgolshani, N. Petersen, C. L. Titus, A. J. Moen, E. L. Vaickus, L. J. Salas, L. A. Christensen, B. 2020-08-14 doi:10.1101/2020.08.14.251306 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Deuteration improves small-molecule fluorophores ]]> https://biorxiv.org/content/10.1101/2020.08.17.250027v1?rss=1 Grimm, J. B. Xie, L. Casler, J. C. Patel, R. Tkachuk, A. N. Choi, H. Lippincott-Schwartz, J. Brown, T. A. Glick, B. S. Liu, Z. Lavis, L. D. 2020-08-17 doi:10.1101/2020.08.17.250027 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Development of a pan-neuronal genetic driver in Aedes aegypti mosquitoes ]]> https://biorxiv.org/content/10.1101/2020.08.22.262527v1?rss=1 Zhao, Z. Tian, D. McBride, C. S. 2020-08-22 doi:10.1101/2020.08.22.262527 Cold Spring Harbor Laboratory Press 2020-08-22 <![CDATA[ Single nucleus analysis of Arabidopsis seeds reveals new cell types and imprinting dynamics ]]> https://biorxiv.org/content/10.1101/2020.08.25.267476v1?rss=1 Picard, C. L. Povilus, R. A. Williams, B. P. Gehring, M. 2020-08-25 doi:10.1101/2020.08.25.267476 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Rest is Required to Learn an Appetitively-Reinforced Operant Task in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.08.28.272047v1?rss=1 Wiggin, T. D. Hsiao, Y.-Y. Liu, J. B. Huber, R. Griffith, L. C. 2020-08-30 doi:10.1101/2020.08.28.272047 Cold Spring Harbor Laboratory Press 2020-08-30 <![CDATA[ Proximity labeling at non-centrosomal microtubule-organizing centers reveals VAB-10B and WDR-62 as distinct microtubule regulators ]]> https://biorxiv.org/content/10.1101/2020.08.29.272369v1?rss=1 Sanchez, A. D. Branon, T. C. Cote, L. E. Papagiannakis, A. Liang, X. Shen, K. Jacobs-Wagner, C. Ting, A. Y. Feldman, J. L. 2020-08-29 doi:10.1101/2020.08.29.272369 Cold Spring Harbor Laboratory Press 2020-08-29 <![CDATA[ Live imaging and biophysical modeling support a button-based mechanism of somatic homolog pairing in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.08.30.265108v1?rss=1 Child, M. B. Bateman, J. R. Jahangiri, A. Reimer, A. Lammers, N. C. Sabouni, N. Villamarin, D. McKenzie-Smith, G. C. Johnson, J. E. Jost, D. Garcia, H. G. 2020-08-31 doi:10.1101/2020.08.30.265108 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Quantitative imaging of RNA polymerase II activity in plants reveals the single-cell basis of tissue-wide transcriptional dynamics ]]> https://biorxiv.org/content/10.1101/2020.08.30.274621v1?rss=1 Alamos, S. Reimer, A. Niyogi, K. K. Garcia, H. G. 2020-08-31 doi:10.1101/2020.08.30.274621 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Molecular and evolutionary mechanisms of yeast thermotolerance ]]> https://biorxiv.org/content/10.1101/2020.08.31.275453v1?rss=1 Abrams, M. B. Dubin, C. A. AlZaben, F. Bravo, J. Joubert, P. M. Weiss, C. V. Brem, R. B. 2020-09-01 doi:10.1101/2020.08.31.275453 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Engineering high-yield biopolymer secretion creates an extracellular protein matrix for living materials ]]> https://biorxiv.org/content/10.1101/2020.08.31.276303v1?rss=1 Charrier, M. Orozco-Hidalgo, M. T. Tjahjono, N. Li, D. Molinari, S. Ryan, K. R. Ashby, P. D. Rad, B. Ajo-Franklin, C. 2020-09-01 doi:10.1101/2020.08.31.276303 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Genome-wide identification of tomato xylem sap fitness factors for Ralstonia pseudosolanacearum and Ralstonia syzygii ]]> https://biorxiv.org/content/10.1101/2020.08.31.276741v1?rss=1 Georgoulis, S. J. Shalvarjian, K. E. Helmann, T. C. Hamilton, C. D. Carlson, H. Deutschbauer, A. M. Lowe-Power, T. M. 2020-09-01 doi:10.1101/2020.08.31.276741 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ miR-200 deficiency promotes lung cancer metastasis by activating cancer-associated fibroblasts ]]> https://biorxiv.org/content/10.1101/2020.09.02.276550v1?rss=1 Xue, B. Chuang, C.-H. Prosser, H. M. Fuziwara, C. S. Chan, C. Sahasrabudhe, N. Kühn, M. Wu, Y. Chen, J. Biton, A. Chen, C. Wilkinson, J. E. McManus, M. T. Bradley, A. Winslow, M. M. Su, B. He, L. 2020-09-03 doi:10.1101/2020.09.02.276550 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Developmental plasticity of texture discrimination following early vision loss in the marsupial Monodelphis domestica ]]> https://biorxiv.org/content/10.1101/2020.09.05.284554v1?rss=1 Ramamurthy, D. L. Dodson, H. K. Krubitzer, L. A. 2020-09-05 doi:10.1101/2020.09.05.284554 Cold Spring Harbor Laboratory Press 2020-09-05 <![CDATA[ Chromosome-level Genome Assembly of a Regenerable Maize Inbred Line A188 ]]> https://biorxiv.org/content/10.1101/2020.09.09.289611v1?rss=1 Lin, G. He, C. Zheng, J. Koo, D.-H. Le, H. Zheng, H. Tamang, T. M. Lin, J. Liu, Y. Zhao, M. Hao, Y. McFarland, F. Wang, B. Qin, Y. Tang, H. McCarty, D. R. Wei, H. Cho, M.-J. Park, S. Kaeppler, H. Kaeppler, S. Liu, Y. Springer, N. M. Schnable, P. S. Wang, G. White, F. F. Liu, S. 2020-09-10 doi:10.1101/2020.09.09.289611 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ A non-canonical EZH2 function sensitizes solid tumors to genotoxic stress ]]> https://biorxiv.org/content/10.1101/2020.09.11.291534v1?rss=1 LIAO, Y. Chen, C.-H. Shah, N. Xiao, T. Feit, A. Yang, M. Cai, C. Gao, S. Xue, P. Liu, Z. Xu, H. Lee, J. Li, W. Mei, S. Pierre, R. S. Shu, S. Fei, T. Duarte, M. Zhao, J. Bradner, J. E. Polyak, K. Kantoff, P. W. Long, H. Balk, S. W. Liu, S. X. Brown, M. Xu, K. 2020-09-11 doi:10.1101/2020.09.11.291534 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Wild flies hedge their thermal preference bets in response to seasonal fluctuations ]]> https://biorxiv.org/content/10.1101/2020.09.16.300731v1?rss=1 Akhund-Zade, J. Yoon, D. Bangerter, A. Polizos, N. Campbell, M. K. Soloshenko, A. Zhang, T. Wice, E. Albright, A. Narayanan, A. Schmidt, P. Saltz, J. Ayroles, J. Klein, M. Bergland, A. de Bivort, B. 2020-09-20 doi:10.1101/2020.09.16.300731 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ Critical Interactions Between the SARS-CoV-2 Spike Glycoprotein and the Human ACE2 Receptor ]]> https://biorxiv.org/content/10.1101/2020.09.21.305490v1?rss=1 Taka, E. Yilmaz, S. Z. Golcuk, M. Kilinc, C. Aktas, U. Yildiz, A. Gur, M. 2020-09-21 doi:10.1101/2020.09.21.305490 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ Internal checkpoint regulates T cell neoantigen reactivity and susceptibility to PD1 blockade ]]> https://biorxiv.org/content/10.1101/2020.09.24.306571v1?rss=1 Palmer, D. C. Webber, B. R. Patel, Y. Johnson, M. J. Kariya, C. M. Lahr, W. S. Parkhurst, M. R. Gartner, J. J. Prickett, T. D. Lowery, F. J. Kishton, R. J. Gurusamy, D. Franco, Z. Vodnala, S. K. Diers, M. D. Wolf, N. K. Slipek, N. J. McKenna, D. H. Sumstad, D. Viney, L. Henley, T. Burckstummer, T. Baker, O. Hu, Y. Yan, C. Meerzaman, D. Padhan, K. Lo, W. Malekzadeh, P. Jia, L. Deniger, D. C. Patel, S. J. Robbins, P. F. McIvor, R. S. Choudhry, M. Rosenberg, S. A. Moriarity, B. S. Restifo, N. P. 2020-09-25 doi:10.1101/2020.09.24.306571 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Dscam1 promotes blood cell survival in Drosophila melanogaster through a dual role in blood cells and neurons ]]> https://biorxiv.org/content/10.1101/2020.09.26.314997v1?rss=1 Ouyang, D. Xiao, X. Mase, A. Li, G. Corcoran, S. Wang, F. Brueckner, K. 2020-09-26 doi:10.1101/2020.09.26.314997 Cold Spring Harbor Laboratory Press 2020-09-26 <![CDATA[ GHB confers neuroprotection by stabilizing the CaMKIIα hub domain ]]> https://biorxiv.org/content/10.1101/2020.09.28.310474v1?rss=1 Leurs, U. Klein, A. B. McSpadden, E. D. Griem-Krey, N. Solbak, S. M. Houlton, J. Villumsen, I. S. Vogensen, S. B. Hamborg, L. Gauger, S. J. Palmelund, L. B. Larsen, A. S. G. Shehata, M. A. Kelstrup, C. D. Olsen, J. V. Bach, A. Burnie, R. O. Kerr, D. S. Gowing, E. K. Teurlings, S. M. W. Chi, C. C. Gee, C. L. Frolund, B. Kornum, B. R. van Woerden, G. M. Clausen, R. P. Kuriyan, J. Clarkson, A. N. Wellendorph, P. 2020-09-28 doi:10.1101/2020.09.28.310474 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Effect of sanitation improvements on soil-transmitted helminth eggs in courtyard soil from rural Bangladesh: Evidence from a cluster-randomized controlled trial ]]> https://biorxiv.org/content/10.1101/2020.09.29.318097v1?rss=1 Kwong, L. Sen, D. Islam, S. Shahriar, S. Benjamin-Chung, J. Arnold, B. F. Hubbard, A. Parvez, S. M. Unicomb, L. Rahman, M. Colford, J. M. Luby, S. P. Ercumen, A. 2020-09-29 doi:10.1101/2020.09.29.318097 Cold Spring Harbor Laboratory Press 2020-09-29 <![CDATA[ ToxVec: Deep Language Model-Based Representation Learning for Venom Peptide Classification ]]> https://biorxiv.org/content/10.1101/2020.09.29.319046v1?rss=1 Ahmadi, M. Jahed-Motlagh, M. R. Asgari, E. Torkaman Rahmani, A. McHardy, A. C. 2020-10-01 doi:10.1101/2020.09.29.319046 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Arabidopsis ACINUS is O-glycosylated and regulates transcription and alternative splicing of regulators of reproductive transitions ]]> https://biorxiv.org/content/10.1101/2020.10.01.322347v1?rss=1 Bi, Y. Deng, Z. Ni, W. Shrestha, R. Savage, D. Hartwig, T. Patil, S. Hong, S. H. Oses-Prieto, J. A. Li, K. H. Quail, P. H. Burlingame, A. xu, S.-L. Wang, Z.-Y. 2020-10-01 doi:10.1101/2020.10.01.322347 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Proton-Dependent Inhibition, Inverted Voltage Activation, and Slow Gating of CLC-0 Chloride Channel ]]> https://biorxiv.org/content/10.1101/2020.10.02.323352v1?rss=1 Chen, T.-Y. Kwon, H. C. Yu, Y. Fairclough, R. H. 2020-10-02 doi:10.1101/2020.10.02.323352 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Interpretable multi-timescale models for predicting fMRI responses to continuous natural speech ]]> https://biorxiv.org/content/10.1101/2020.10.02.324392v1?rss=1 Jain, S. Vo, V. A. Mahto, S. LeBel, A. Turek, J. S. Huth, A. G. 2020-10-02 doi:10.1101/2020.10.02.324392 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Individual differences in proprioception predict the extent of implicit sensorimotor adaptation ]]> https://biorxiv.org/content/10.1101/2020.10.03.324855v1?rss=1 Tsay, J. S. Kim, H. E. Parvin, D. E. Strover, A. R. Ivry, R. B. 2020-10-03 doi:10.1101/2020.10.03.324855 Cold Spring Harbor Laboratory Press 2020-10-03 <![CDATA[ Variable optical properties of light-harvesting complex II revisited ]]> https://biorxiv.org/content/10.1101/2020.10.05.312405v1?rss=1 Iwai, M. Chen, J.-J. Park, S. Yoneda, Y. Schmid, E. M. Fletcher, D. A. Fleming, G. R. Niyogi, K. K. 2020-10-07 doi:10.1101/2020.10.05.312405 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ A hierarchical point process model for spatial capture-recapture data ]]> https://biorxiv.org/content/10.1101/2020.10.06.325035v1?rss=1 Zhang, W. Chipperfield, J. D. Illian, J. B. Dupont, P. Milleret, C. de Valpine, P. Bischof, R. 2020-10-08 doi:10.1101/2020.10.06.325035 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Screening of Cultivars for Tissue Culture Response and Establishment of Genetic Transformation in a High-yielding and Disease-resistant Cultivar of Theobroma cacao ]]> https://biorxiv.org/content/10.1101/2020.10.07.327486v1?rss=1 Jones, J. Zhang, E. Tucker, D. Rietz, D. Dahlbeck, D. Gomez, M. Garcia, C. Marelli, J.-P. Livingstone, D. Schnell, R. Staskawicz, B. Cho, M.-J. 2020-10-08 doi:10.1101/2020.10.07.327486 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Optical spike detection and connectivity analysis with a far-red voltage-sensitive fluorophore reveals changes to network connectivity in development and disease ]]> https://biorxiv.org/content/10.1101/2020.10.09.332270v1?rss=1 Walker, A. Raliski, B. Karbasi, K. Zhang, P. Sanders, K. Miller, E. 2020-10-10 doi:10.1101/2020.10.09.332270 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ Imaging voltage in complete neuronal networks within patterned microislands reveals preferential wiring of excitatory hippocampal neurons ]]> https://biorxiv.org/content/10.1101/2020.10.09.332304v1?rss=1 Walker, A. Raliski, B. Nguyen, D. V. Karbasi, K. Zhang, P. Sanders, K. Miller, E. 2020-10-10 doi:10.1101/2020.10.09.332304 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ Single cell transcriptome analysis defines novel heterogeneity within the pancreatic ductal tree ]]> https://biorxiv.org/content/10.1101/2020.10.12.336784v1?rss=1 Hendley, A. M. Rao, A. A. Leonhardt, L. Ashe, S. Smith, J. A. Giacometti, S. Peng, X. L. Jiang, H. Berrios, D. Pawlak, M. Li, L. Y. Lee, J. Collisson, E. A. Anderson, M. Fragiadakis, G. K. Yeh, J. J. Chun, J. Y. Kim, G. E. Weaver, V. M. Hebrok, M. 2020-10-12 doi:10.1101/2020.10.12.336784 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ CaBagE: a Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing ]]> https://biorxiv.org/content/10.1101/2020.10.13.337253v1?rss=1 Wallace, A. Sasani, T. Swanier, J. Gates, B. Greenland, J. Pedersen, B. Varley, K. Quinlan, A. R. 2020-10-13 doi:10.1101/2020.10.13.337253 Cold Spring Harbor Laboratory Press 2020-10-13 <![CDATA[ Coping with darkness: The adaptive response of marine picocyanobacteria to repeated light energy deprivation ]]> https://biorxiv.org/content/10.1101/2020.10.15.341503v1?rss=1 Coe, A. Biller, S. Thomas, E. Boulias, K. Bliem, C. Arellano, A. Dooley, K. Rasmussen, A. N. LeGault, K. O'Keefe, T. J. Greer, E. L. Chisholm, S. W. 2020-10-15 doi:10.1101/2020.10.15.341503 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Behavioral and genomic sensory adaptations underlying the pest activity of Drosophila suzukii ]]> https://biorxiv.org/content/10.1101/2020.10.15.341594v1?rss=1 Durkin, S. M. Chakraborty, M. Abrieux, A. Lewald, K. M. Gadau, A. Svetec, N. Peng, J. Kopyto, M. Chiu, J. C. Emerson, J. J. Zhao, L. 2020-10-15 doi:10.1101/2020.10.15.341594 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ EfgA is a conserved formaldehyde sensor that halts bacterial translation in response to elevated formaldehyde ]]> https://biorxiv.org/content/10.1101/2020.10.16.343392v1?rss=1 Bazurto, J. Nayak, D. D. Ticak, T. Davlieva, M. Lee, J. A. Lambert, L. B. Benski, O. J. Quates, C. J. Johnson, J. L. Patel, J. S. Ytreberg, F. M. Shamoo, Y. Marx, C. J. 2020-10-17 doi:10.1101/2020.10.16.343392 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ Structural coordination between active sites of a Cas6-reverse transcriptase-Cas1--Cas2 CRISPR integrase complex ]]> https://biorxiv.org/content/10.1101/2020.10.18.344481v1?rss=1 Wang, J. Y. Hoel, C. M. Al-Shayeb, B. Banfield, J. F. Brohawn, S. G. Doudna, J. A. 2020-10-19 doi:10.1101/2020.10.18.344481 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules ]]> https://biorxiv.org/content/10.1101/2020.10.19.344077v1?rss=1 Shams, A. Higgins, S. A. Fellmann, C. Laughlin, T. J. Oakes, B. L. Lew, R. Lukarska, M. Arnold, M. Staahl, B. Doudna, J. A. Savage, D. 2020-10-19 doi:10.1101/2020.10.19.344077 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ Contact-dependent traits in Pseudomonas syringae B728a ]]> https://biorxiv.org/content/10.1101/2020.10.20.346825v1?rss=1 Hernandez, M. N. Lindow, S. 2020-10-21 doi:10.1101/2020.10.20.346825 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ TaqMan Array Cards enable monitoring of diverse enteric pathogens across environmental and host reservoirs ]]> https://biorxiv.org/content/10.1101/2020.10.27.356642v1?rss=1 Lappan, R. Henry, R. Chown, S. L. Luby, S. P. Higginson, E. Bata, L. Jirapanjawat, T. Schang, C. Openshaw, J. J. O'Toole, J. Lin, A. Tela, A. Wong, T. H. F. French, M. A. Brown, R. R. Leder, K. Greening, C. McCarthy, D. 2020-10-27 doi:10.1101/2020.10.27.356642 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ The mutability of demographic noise in microbial range expansions ]]> https://biorxiv.org/content/10.1101/2020.10.27.357483v1?rss=1 Yu, Q. Gralka, M. Duvernoy, M.-C. Sousa, M. Harpak, A. Hallatschek, O. 2020-10-28 doi:10.1101/2020.10.27.357483 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Bacterial microcompartments linked to the flavin-based extracellular electron transfer drives anaerobic ethanolamine utilization in Listeria monocytogenes ]]> https://biorxiv.org/content/10.1101/2020.10.27.358424v1?rss=1 Zeng, Z. Boeren, S. Bhandula, V. Light, S. Smid, E. J. Notebaart, R. A. Abee, T. 2020-10-28 doi:10.1101/2020.10.27.358424 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ The scales and signatures of climate adaptation by the Arabidopsis transcriptome ]]> https://biorxiv.org/content/10.1101/2020.10.28.358325v1?rss=1 Colicchio, J. M. Akman, M. Blackman, B. K. 2020-10-28 doi:10.1101/2020.10.28.358325 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ An integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients ]]> https://biorxiv.org/content/10.1101/2020.11.01.362269v1?rss=1 The NeuroLINCS Consortium, Ornelas, L. Gomez, E. Panther, L. Frank, A. Lei, S. Mandefro, B. Banuelos, M. G. Shelley, B. Kaye, J. A. Lima, L. Wyman, S. Lim, R. G. Wu, J. Stocksdale, J. Casale, M. Dardov, V. Matlock, A. Venkatraman, V. Holewenski, R. Milani, P. Adam, M. Wassie, B. T. Cheng, A. Coyne, A. N. Daigle, J. G. Li, J. Yang, S. Cox, V. Wilhelm, M. Lloyd, T. E. Hayes, L. Pham, J. Escalante-Chong, R. Lenail, A. Sachs, K. Patel-Murray, N. L. Ramamoorthy, D. Thompson, T. G. NYGC ALS Consortium, Finkbeiner, S. Fraenkel, E. Rothstein, J. D. Sareen 2020-11-01 doi:10.1101/2020.11.01.362269 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ Estimating latent positions of actors using Neural Networks in R with GCN4R ]]> https://biorxiv.org/content/10.1101/2020.11.02.364935v1?rss=1 Levy, J. Bobak, C. A. Christensen, B. Vaickus, L. J. O'Malley, A. J. 2020-11-05 doi:10.1101/2020.11.02.364935 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Discovering subgenomes of octoploid strawberry with repetitive sequences ]]> https://biorxiv.org/content/10.1101/2020.11.04.330431v1?rss=1 Session, A. M. Rokhsar, D. S. 2020-11-05 doi:10.1101/2020.11.04.330431 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Bioarchaeological sex prediction from central Italy using generalized low rank imputation for cross-validated metric craniodental supervised ensemble machine learning with missing data ]]> https://biorxiv.org/content/10.1101/2020.11.04.368894v1?rss=1 Muzzall, E. 2020-11-05 doi:10.1101/2020.11.04.368894 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Non-canonical odor coding ensures unbreakable mosquito attraction to humans ]]> https://biorxiv.org/content/10.1101/2020.11.07.368720v1?rss=1 Younger, M. A. Herre, M. Ehrlich, A. R. Gong, Z. Gilbert, Z. N. Rahiel, S. Matthews, B. J. Vosshall, L. B. 2020-11-08 doi:10.1101/2020.11.07.368720 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ Drought shifts sorghum root metabolite and microbiome profiles and enriches the stress response factor pipecolic acid ]]> https://biorxiv.org/content/10.1101/2020.11.08.373399v1?rss=1 Caddell, D. F. Louie, K. Bowen, B. Sievert, J. A. Hollingsworth, J. Dahlberg, J. Purdom, E. F. Northen, T. Coleman-Derr, D. 2020-11-09 doi:10.1101/2020.11.08.373399 Cold Spring Harbor Laboratory Press 2020-11-09 <![CDATA[ Evolution of the genetic architecture of local adaptations under genetic rescue is determined by mutational load and polygenicity ]]> https://biorxiv.org/content/10.1101/2020.11.09.374413v1?rss=1 Zhang, Y. Stern, A. J. Nielsen, R. 2020-11-09 doi:10.1101/2020.11.09.374413 Cold Spring Harbor Laboratory Press 2020-11-09 <![CDATA[ A longitudinal study of E. coli lineages and antimicrobial resistance in Ecuadorian children ]]> https://biorxiv.org/content/10.1101/2020.11.09.375931v1?rss=1 Calderon, D. Cardenas, P. A. Graham, J. Trueba, G. 2020-11-11 doi:10.1101/2020.11.09.375931 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ Precise Estimation of In Vivo Protein Turnover Rates ]]> https://biorxiv.org/content/10.1101/2020.11.10.377440v1?rss=1 O'Brien, J. Narayan, V. Wong, Y. L. Seitzer, P. Sandoval, C. Haste, N. Smith, M. Rad, R. Gaun, A. Baker, A. Kukurugya, M. Martin-McNulty, B. Zhang, C. Kolumam, G. Sidrauski, C. Jojic, V. McAllister, F. Bennett, B. Buffenstein, R. 2020-11-11 doi:10.1101/2020.11.10.377440 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ The Nuclear Pore Complex consists of two independent scaffolds ]]> https://biorxiv.org/content/10.1101/2020.11.13.381947v1?rss=1 Regmi, S. G. Lee, H. Kaufhold, R. Fichtman, B. Chen, S. Aksenova, V. Turcotte, E. Harel, A. Arnaoutov, A. Dasso, M. 2020-11-14 doi:10.1101/2020.11.13.381947 Cold Spring Harbor Laboratory Press 2020-11-14 <![CDATA[ Degradation of mixed-linkage (1,3;1,4)-β-D-glucan in maize is mediated by the CAL1 licheninase ]]> https://biorxiv.org/content/10.1101/2020.11.16.385146v1?rss=1 Kraemer, F. J. Lunde, C. Koch, M. Kuhn, B. M. Ruehl, C. Brown, P. Hoffmann, P. Göhre, V. Hake, S. Pauly, M. Ramirez, V. 2020-11-18 doi:10.1101/2020.11.16.385146 Cold Spring Harbor Laboratory Press 2020-11-18 <![CDATA[ A Hybrid Cellular and Heterogeneous Catalyst Strategy for the Production of Olefins from Glucose ]]> https://biorxiv.org/content/10.1101/2020.11.17.387563v1?rss=1 Wang, Z. Q. Song, H. Hara, N. Park, D. S. Kumar, G. Min, Y. Dauenhauer, P. J. Chang, M. C. Y. 2020-11-18 doi:10.1101/2020.11.17.387563 Cold Spring Harbor Laboratory Press 2020-11-18 <![CDATA[ A conserved strategy for inducing appendage regeneration ]]> https://biorxiv.org/content/10.1101/2020.11.21.392720v1?rss=1 Abrams, M. J. Tan, F. H. Basinger, T. Heithe, M. L. Li, Y. Raffiee, M. Leahy, P. Dabiri, J. O. Gold, D. A. Goentoro, L. A. 2020-11-22 doi:10.1101/2020.11.21.392720 Cold Spring Harbor Laboratory Press 2020-11-22 <![CDATA[ 3D Adaptive Optical Nanoscopy for Thick Specimen Imaging at sub-50 nm Resolution ]]> https://biorxiv.org/content/10.1101/2020.11.25.398958v1?rss=1 Hao, X. Allgeyer, E. S. Antonello, J. Watters, K. Gerdes, J. A. Schroeder, L. K. Bottanelli, F. Zhao, J. Kidd, P. Lessard, M. D. Rothman, J. E. Cooley, L. Biederer, T. Booth, M. J. Bewersdorf, J. 2020-11-27 doi:10.1101/2020.11.25.398958 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ EpitopeVec: Linear Epitope Prediction Using DeepProtein Sequence Embeddings ]]> https://biorxiv.org/content/10.1101/2020.11.26.395830v1?rss=1 Bahai, A. Asgari, E. Mofrad, M. Kloetgen, A. McHardy, A. C. 2020-11-26 doi:10.1101/2020.11.26.395830 Cold Spring Harbor Laboratory Press 2020-11-26 <![CDATA[ Multielectrode Cortical Stimulation Selectively Induces Unidirectional Wave Propagation in Biophysical/Neural Model ]]> https://biorxiv.org/content/10.1101/2020.11.28.402289v1?rss=1 Halgren, A. S. Siegel, Z. Golden, R. Bazhenov, M. 2020-11-29 doi:10.1101/2020.11.28.402289 Cold Spring Harbor Laboratory Press 2020-11-29 <![CDATA[ Characterization of genetic diversity and population structure within Staphylococcus chromogenes by multilocus sequence Typing ]]> https://biorxiv.org/content/10.1101/2020.11.30.403683v1?rss=1 Huebner, R. Mugabi, R. Hetesy, G. Fox, L. De Vliegher, S. De Visscher, A. Barlow, J. W. Sensabaugh, G. 2020-11-30 doi:10.1101/2020.11.30.403683 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ u-track 3D: measuring and interrogating intracellular dynamics in three dimensions. ]]> https://biorxiv.org/content/10.1101/2020.11.30.404814v1?rss=1 Roudot, P. Legant, W. R. Zou, Q. Dean, K. M. Welf, E. S. David, A. F. Gerlich, D. W. Fiolka, R. P. Betzig, E. Danuser, G. 2020-12-01 doi:10.1101/2020.11.30.404814 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Versatile labeling and detection ofendogenous proteins using tag-assistedsplit enzyme complementation ]]> https://biorxiv.org/content/10.1101/2020.12.01.407072v1?rss=1 Makhija, S. Brown, D. Bourke, S. Wang, Y. Zhou, S. Rudlaff, R. Cheloor-Kovilakam, R. Huang, B. 2020-12-02 doi:10.1101/2020.12.01.407072 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ THE DYNAMIC INTERPLAY BETWEEN HOMEODOMAIN TRANSCRIPTION FACTORS AND CHROMATIN ENVIRONMENT REGULATES PRONEURAL FACTOR OUTCOMES ]]> https://biorxiv.org/content/10.1101/2020.12.02.398677v1?rss=1 Ang, C. E. Olmos, V. Zhou, B. Lee, Q. Y. Sinha, R. Narayanaswamy, A. Mall, M. Chesnov, K. Sudhof, T. C. Wernig, M. 2020-12-02 doi:10.1101/2020.12.02.398677 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Modeling Changes in Probabilistic Reinforcement Learning during Adolescence ]]> https://biorxiv.org/content/10.1101/2020.12.02.407932v1?rss=1 Xia, L. Master, S. L. Eckstein, M. K. Baribault, B. Dahl, R. E. Wilbrecht, L. Collins, A. G. E. 2020-12-02 doi:10.1101/2020.12.02.407932 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Structural basis of FANCD2 deubiquitination by USP1-UAF1 ]]> https://biorxiv.org/content/10.1101/2020.12.05.412924v1?rss=1 Rennie, M. L. Arkinson, C. Chaugule, V. K. Toth, R. Walden, H. 2020-12-06 doi:10.1101/2020.12.05.412924 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Genetic Encoding of Three Distinct Noncanonical Amino Acids Using Reprogrammed Initiator and Nonsense Codons ]]> https://biorxiv.org/content/10.1101/2020.12.07.415521v1?rss=1 View larger version (15K): org.highwire.dtl.DTLVardef@10e7ebdorg.highwire.dtl.DTLVardef@a2c26dorg.highwire.dtl.DTLVardef@18ab3aborg.highwire.dtl.DTLVardef@119cf87_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Tharp, J. M. Vargas-Rodriguez, O. Schepartz, A. Söll, D. 2020-12-08 doi:10.1101/2020.12.07.415521 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ Coiled coil control of diverse EGFR functions ]]> https://biorxiv.org/content/10.1101/2020.12.10.419739v1?rss=1 Mozumdar, D. Quach, K. Doerner, A. Schepartz, A. 2020-12-11 doi:10.1101/2020.12.10.419739 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ FeRIC-based magnetogenetics: evaluation of methods and protocols in in vitro models ]]> https://biorxiv.org/content/10.1101/2020.12.10.419911v1?rss=1 HERNANDEZ-MORALES, M. Han, V. Kramer, R. H. Liu, C. 2020-12-11 doi:10.1101/2020.12.10.419911 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Non-cell autonomous inhibition of the Shh pathway due to impaired cholesterol biosynthesis requires Ptch1/2 ]]> https://biorxiv.org/content/10.1101/2020.12.10.420588v1?rss=1 Jaegers, C. E. Roelink, H. 2020-12-11 doi:10.1101/2020.12.10.420588 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ A gene regulatory network critical for axillary bud dormancy directly controlled by Arabidopsis BRANCHED1 ]]> https://biorxiv.org/content/10.1101/2020.12.14.394403v1?rss=1 van Es, S. W. Munoz-Gasca, A. Romero-Campero, F. J. Gonzalez-Grandio, E. de los Reyes, P. Tarancon, C. van Dijk, A. D. J. van Esse, W. Angenent, G. C. Immink, R. Cubas, P. 2020-12-15 doi:10.1101/2020.12.14.394403 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Juvenile exposure to acute traumatic stress leads to long-lasting alterations in grey matter myelination in adult female but not male rats ]]> https://biorxiv.org/content/10.1101/2020.12.14.422686v1?rss=1 Breton, J. M. Barraza, M. Hu, K. Y. Frias, S. J. Long, K. L. P. Kaufer, D. 2020-12-15 doi:10.1101/2020.12.14.422686 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Transcription of protease and chitinase genes provides a window onto macromolecular organic nitrogen decomposition in soil ]]> https://biorxiv.org/content/10.1101/2020.12.14.422732v1?rss=1 Sieradzki, E. T. Nuccio, E. E. Pett-Ridge, J. Firestone, M. K. 2020-12-14 doi:10.1101/2020.12.14.422732 Cold Spring Harbor Laboratory Press 2020-12-14 <![CDATA[ Transformer protein language models are unsupervised structure learners ]]> https://biorxiv.org/content/10.1101/2020.12.15.422761v1?rss=1 Rao, R. M. Meier, J. Sercu, T. Ovchinnikov, S. Rives, A. 2020-12-15 doi:10.1101/2020.12.15.422761 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Methane-derived carbon flow through host-virus trophic networks in soil ]]> https://biorxiv.org/content/10.1101/2020.12.16.423115v1?rss=1 Lee, S. Sieradzki, E. T. Nicolas, A. M. Firestone, M. K. Hazard, C. Nicol, G. W. 2020-12-16 doi:10.1101/2020.12.16.423115 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ Hippocampal neurons construct a map of an abstract value space ]]> https://biorxiv.org/content/10.1101/2020.12.17.423272v1?rss=1 Knudsen, E. B. Wallis, J. D. 2020-12-17 doi:10.1101/2020.12.17.423272 Cold Spring Harbor Laboratory Press 2020-12-17 <![CDATA[ Principled simulation of agent-based models in epidemiology ]]> https://biorxiv.org/content/10.1101/2020.12.21.423765v1?rss=1 Wu, S. L. Dolgert, A. J. Lewnard, J. A. Marshall, J. M. Smith, D. L. 2020-12-21 doi:10.1101/2020.12.21.423765 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ CRISPR-based functional genomics in human dendritic cells ]]> https://biorxiv.org/content/10.1101/2020.12.22.423985v1?rss=1 93% across >300 genes. Using this method, we perform genetic screens in moDCs, identifying mechanisms by which DCs tune responses to lipopolysaccharides from the human microbiome. In addition, we reveal donor-specific responses to lipopolysaccharides, underscoring the importance of assessing immune phenotypes in donor-derived cells, and identify genes that control this specificity, highlighting the potential of our method to pinpoint determinants of inter-individual variation in immune responses. Our work sets the stage for a systematic dissection of the immune signaling at the host-microbiome interface and for targeted engineering of DCs for neoantigen vaccination. ]]> Jost, M. Jacobson, A. N. Hussmann, J. A. Cirolia, G. Fischbach, M. Weissman, J. S. 2020-12-22 doi:10.1101/2020.12.22.423985 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ The Diversity and Evolution of Microbial Dissimilatory Phosphite Oxidation ]]> https://biorxiv.org/content/10.1101/2020.12.28.424620v1?rss=1 Ewens, S. D. Gomberg, A. Barnum, T. Borton, M. Carlson, H. Wrighton, K. Coates, J. 2020-12-28 doi:10.1101/2020.12.28.424620 Cold Spring Harbor Laboratory Press 2020-12-28 <![CDATA[ Genetic and phylogenetic analysis of dissimilatory iodate-reducing bacteria identifies potential niches across the world's oceans ]]> https://biorxiv.org/content/10.1101/2020.12.28.424624v1?rss=1 Reyes-Umana, V. Henning, Z. Lee, K. Barnum, T. Coates, J. 2020-12-29 doi:10.1101/2020.12.28.424624 Cold Spring Harbor Laboratory Press 2020-12-29 <![CDATA[ The size of helical pitch is important for microtubule plus end dynamic instability ]]> https://biorxiv.org/content/10.1101/2020.12.29.424770v1?rss=1 Liu, C. Prahl, L. He, Y. Wang, Y. Zhu, R. Mao, Y. 2020-12-30 doi:10.1101/2020.12.29.424770 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ Lysosomal retargeting of Myoferlin mitigates membrane stress to enable pancreatic cancer growth ]]> https://biorxiv.org/content/10.1101/2021.01.04.425106v1?rss=1 Gupta, S. Yano, J. A. Htwe Htwe, H. Shin, H. R. Cakir, Z. Ituarte, T. Wen, K. W. Kim, G. E. Zoncu, R. Dawson, D. W. Perera, R. M. 2021-01-04 doi:10.1101/2021.01.04.425106 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Proton receptors regulate synapse-specific reconsolidation in the amygdala ]]> https://biorxiv.org/content/10.1101/2021.01.04.425235v1?rss=1 Koffman, E. E. Kruse, C. M. Singh, K. Naghavi, F. N. Egbo, J. A. Boateng, S. Houdi, M. B. Lin, B. Debiec, J. Du, J. 2021-01-05 doi:10.1101/2021.01.04.425235 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Identifying low risk insecticides to address both food shortages and the biocontrol of human schistosomiasis ]]> https://biorxiv.org/content/10.1101/2021.01.05.425425v1?rss=1 Haggerty, C. Delius, B. Jouanard, N. Ndao, P. D. De Leo, G. A. Lund, A. J. Lopez-Carr, D. Remais, J. V. Riveau, G. Sokolow, S. H. Rohr, J. R. 2021-01-06 doi:10.1101/2021.01.05.425425 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Crystallographic molecular replacement using an in silico-generated search model of SARS-CoV-2 ORF8 ]]> https://biorxiv.org/content/10.1101/2021.01.05.425441v1?rss=1 Flower, T. G. Hurley, J. H. 2021-01-05 doi:10.1101/2021.01.05.425441 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Widespread bacterial protein flavinylation in functionally distinct extracytosolic redox biochemistries ]]> https://biorxiv.org/content/10.1101/2021.01.07.425746v1?rss=1 Méheust, R. Huang, S. Rivera-Lugo, R. Banfield, J. Light, S. H. 2021-01-07 doi:10.1101/2021.01.07.425746 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ A simple Agrobacterium-mediated stable transformation technique for the hornwort model Anthoceros agrestis ]]> https://biorxiv.org/content/10.1101/2021.01.07.425778v1?rss=1 Frangedakis, E. Waller, M. Nishiyama, T. Tsukaya, H. Xu, X. Yue, Y. Tjahjadi, M. Gunadi, A. Van Eck, J. Li, F.-W. Szovenyi, P. Sakakibara, K. 2021-01-07 doi:10.1101/2021.01.07.425778 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Reconstitution of cargo-induced LC3 lipidation in mammalian selective autophagy ]]> https://biorxiv.org/content/10.1101/2021.01.08.425958v1?rss=1 Chang, C. Shi, X. Jensen, L. Yokom, A. L. Fracchiolla, D. Martens, S. Hurley, J. H. 2021-01-09 doi:10.1101/2021.01.08.425958 Cold Spring Harbor Laboratory Press 2021-01-09 <![CDATA[ Characterization of 475 novel, putative small RNAs (sRNAs) in Carbon-starved Salmonella enterica serovar typhimurium ]]> https://biorxiv.org/content/10.1101/2021.01.11.426214v1?rss=1 Houserova, D. M. Dahmer, D. J. Amin, S. V. King, V. M. Barnhill, E. C. Huang, Y. Zambrano, M. E. Dean, M. A. crucello, a. Aria, K. M. Spector, M. P. Borchert, G. M. 2021-01-11 doi:10.1101/2021.01.11.426214 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Community RNA-Seq: Multi-kingdom responses to living versus decaying root inputs in soil ]]> https://biorxiv.org/content/10.1101/2021.01.12.426429v1?rss=1 Nuccio, E. E. Nguyen, N. H. Nunes da Rocha, U. Mayali, X. Bougoure, J. Weber, P. Brodie, E. L. Firestone, M. K. Pett-Ridge, J. 2021-01-13 doi:10.1101/2021.01.12.426429 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ Molecular programs of fibrotic change in aging human lung ]]> https://biorxiv.org/content/10.1101/2021.01.18.427195v1?rss=1 Lee, J. Islam, M. N. Boostanpour, K. Aran, D. Christenson, S. Matthay, M. A. Eckalbar, W. DePianto, D. J. Arron, J. R. Magee, L. Bhattacharya, S. Matsumoto, R. Kubota, M. Farber, D. L. Bhattacharya, J. Wolters, P. J. Bhattacharya, M. 2021-01-19 doi:10.1101/2021.01.18.427195 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ The impact of antigenic escape on the evolution of virulence ]]> https://biorxiv.org/content/10.1101/2021.01.19.427227v1?rss=1 Sasaki, A. Lion, S. boots, M. 2021-01-19 doi:10.1101/2021.01.19.427227 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Correlates of Sleep and Arousal via Matrix Methods ]]> https://biorxiv.org/content/10.1101/2021.01.20.427445v1?rss=1 de Lecea, L. Sorooshyari, S. 2021-01-21 doi:10.1101/2021.01.20.427445 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ How to align arthropod legs ]]> https://biorxiv.org/content/10.1101/2021.01.20.427514v1?rss=1 Bruce, H. S. 2021-01-21 doi:10.1101/2021.01.20.427514 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Low photorespiratory capacity is sufficient to block photosynthetic capacity acclimation in high light ]]> https://biorxiv.org/content/10.1101/2021.01.20.427534v1?rss=1 Baker, C. R. Niyogi, K. K. Alonso, A. P. Cocuron, J. C. 2021-01-21 doi:10.1101/2021.01.20.427534 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Induction of a colitogenic phenotype in Th1 cells depends on IL-23R signaling ]]> https://biorxiv.org/content/10.1101/2021.01.24.426445v1?rss=1 Pawlak, M. DeTomaso, D. Meyer zu Horste, G. Lee, Y. Nyman, J. Dionne, D. Wang, C. Wallrapp, A. Burkett, P. R. Riesenfeld, S. J. Anderson, A. C. Regev, A. Xavier, R. J. Yosef, N. Kuchroo, V. K. 2021-01-26 doi:10.1101/2021.01.24.426445 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Prior dengue immunity enhances Zika virus infection of the maternal-fetal interface in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2021.01.25.428184v1?rss=1 Crooks, C. M. Weiler, A. M. Rybarczyk, S. L. Bliss, M. I. Jaeger, A. S. Murphy, M. E. Simmons, H. A. Mejia, A. Fritsch, M. K. Hayes, J. M. Eickhoff, J. C. Mitzey, A. M. Razo, E. Braun, K. M. Brown, E. A. Yamamoto, K. Shepherd, P. M. Possell, A. Weaver, K. Antony, K. M. Morgan, T. K. Newman, C. M. Dudley, D. M. Schultz-Darken, N. Peterson, E. Katzelnick, L. C. Balmaseda, A. Harris, E. OConnor, D. H. Mohr, E. L. Golos, T. G. Friedrich, T. C. Aliota, M. T. 2021-01-26 doi:10.1101/2021.01.25.428184 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Deep Proteome Profiling of Human Mammary Epithelia at Lineage and Age Resolution ]]> https://biorxiv.org/content/10.1101/2021.02.02.429276v1?rss=1 9,000 total proteins, and >15,000 phosphopeptides, from normal primary human mammary epithelia at lineage resolution from ten women ranging in age from 19 to 68. Data were quality controlled, and results were biologically validated with cell-based assays. Age-dependent protein signatures were identified using differential expression analyses and weighted protein co-expression network analyses. Up-regulation of basal markers in luminal cells, including KRT14 and AXL, were a prominent consequence of aging. PEAK1 was identified as an age-dependent signaling kinase in luminal cells, which revealed a potential age-dependent vulnerability for targeted ablation. Correlation analyses between transcriptome and proteome revealed age-associated loss of proteostasis regulation. Protein expression and phosphorylation changes in the aging breast epithelium identify potential therapeutic targets for reducing breast cancer susceptibility. ]]> Hinz, S. Manousopoulou, A. Miyano, M. Sayaman, R. W. Aguilera, K. Y. Todhunter, M. E. Lopez, J. C. Sohn, L. L. Wang, L. D. LaBarge, M. A. 2021-02-02 doi:10.1101/2021.02.02.429276 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Disentangling the effects of climate change, landscape heterogeneity, and scale on phenological metrics ]]> https://biorxiv.org/content/10.1101/2021.02.05.429398v1?rss=1 Newman, E. A. Breckheimer, I. K. Park, D. S. 2021-02-08 doi:10.1101/2021.02.05.429398 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ An Incrementally Updatable and Scalable System for Large-Scale Sequence Search using LSM Trees ]]> https://biorxiv.org/content/10.1101/2021.02.05.429839v1?rss=1 Almodaresi, F. Khan, J. Madaminov, S. Pandey, P. Ferdman, M. Johnson, R. Patro, R. 2021-02-08 doi:10.1101/2021.02.05.429839 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Bacterium-Enabled Transient Gene Activation by Artificial Transcription Factor for Resolving Gene Regulation in Maize ]]> https://biorxiv.org/content/10.1101/2021.02.05.429970v1?rss=1 Zhao, M. Peng, Z. Qin, Y. Zhang, L. Tian, B. Chen, Y. Liu, Y. Lin, G. Zheng, H. He, C. Lv, K. Trick, H. N. Liu, Y. Cho, M.-J. Park, S. Wei, H. Zheng, J. White, F. F. Liu, S. 2021-02-08 doi:10.1101/2021.02.05.429970 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Molecular and structural mechanisms of ZZ domain-mediated cargo recognition by autophagy receptor Nbr1 ]]> https://biorxiv.org/content/10.1101/2021.02.07.430097v1?rss=1 Wang, Y.-Y. Zhang, J. Liu, X.-M. Dong, M.-Q. Ye, K. Du, L.-L. 2021-02-07 doi:10.1101/2021.02.07.430097 Cold Spring Harbor Laboratory Press 2021-02-07 <![CDATA[ Optimized CRISPR tools and site-directed transgenesis in Culex quinquefasciatus mosquitoes for gene drive development. ]]> https://biorxiv.org/content/10.1101/2021.02.10.430702v1?rss=1 Feng, X. Lopez Del Amo, V. Mameli, E. Lee, M. Bishop, A. L. Perrimon, N. Gantz, V. M. 2021-02-11 doi:10.1101/2021.02.10.430702 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ MSA Transformer ]]> https://biorxiv.org/content/10.1101/2021.02.12.430858v1?rss=1 Rao, R. Liu, J. Verkuil, R. Meier, J. Canny, J. F. Abbeel, P. Sercu, T. Rives, A. 2021-02-15 doi:10.1101/2021.02.12.430858 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ Dynamic Representation of the Subjective Value of Information ]]> https://biorxiv.org/content/10.1101/2021.02.12.431038v1?rss=1 Kobayashi, K. Lee, S. Filipowicz, A. L. S. McGaughey, K. D. Kable, J. W. Nassar, M. R. 2021-02-16 doi:10.1101/2021.02.12.431038 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2021.02.17.431526v1?rss=1 Wakao, S. Shih, P. M. Guan, K. Schackwitz, W. Ye, J. Shih, R. Chovatia, M. Sharma, A. Martin, J. Wei, C.-L. Niyogi, K. K. 2021-02-18 doi:10.1101/2021.02.17.431526 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Glioblastoma remodeling of neural circuits in the human brain decreases survival ]]> https://biorxiv.org/content/10.1101/2021.02.18.431915v1?rss=1 Krishna, S. Choudhury, A. Seo, K. Ni, L. Kakaizada, S. Lee, A. Aabedi, A. Cao, C. Sudharshan, R. Egladyous, A. Almeida, N. Venkatesh, H. Findlay, A. Nagarajan, S. Raleigh, D. Brang, D. Monje, M. Hervey-Jumper, S. 2021-02-19 doi:10.1101/2021.02.18.431915 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Parallel Characterization of cis-Regulatory Elements for Multiple Genes UsingCRISPRpath ]]> https://biorxiv.org/content/10.1101/2021.02.19.431931v1?rss=1 Ren, X. Wang, M. Li, B. Jamieson, K. Zheng, L. Jones, I. R. Li, B. Takagi, M. A. Lee, J. Maliskova, L. Tam, T. W. Yu, M. Hu, R. Lee, L. Abnousi, A. Li, G. Li, Y. Hu, M. Ren, B. Wang, W. Shen, Y. 2021-02-19 doi:10.1101/2021.02.19.431931 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Outcomes of Progranulin Gene Therapy in the Retina are Dependent on Time of Delivery ]]> https://biorxiv.org/content/10.1101/2021.02.24.432570v1?rss=1 Zin, E. A. Han, D. Tran, J. Morrison-Welch, N. Visel, M. Kuronen, M. Flannery, J. G. 2021-02-25 doi:10.1101/2021.02.24.432570 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ The CCL2 Chemokine Promotes Early Seeding of the Latent HIV Reservoir ]]> https://biorxiv.org/content/10.1101/2021.02.25.432826v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@8d6da8org.highwire.dtl.DTLVardef@11a3a1corg.highwire.dtl.DTLVardef@dd05dborg.highwire.dtl.DTLVardef@ab84e6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Packard, T. Schwarzer, R. Herzig, E. Rao, D. Luo, X. Egedal, J. Hsiao, F. Widera, M. Hultquist, J. F. Grimmett, Z. W. Messer, R. J. Krogan, N. J. Deeks, S. Roan, N. R. Dittmer, U. Hasenkrug, K. J. Greene, W. C. 2021-02-25 doi:10.1101/2021.02.25.432826 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ A unicellular walker embodies a finite state machine ]]> https://biorxiv.org/content/10.1101/2021.02.26.433123v1?rss=1 Larson, B. T. Garbus, J. Pollack, J. B. Marshall, W. F. 2021-02-27 doi:10.1101/2021.02.26.433123 Cold Spring Harbor Laboratory Press 2021-02-27 <![CDATA[ Small molecule SWELL1-LRRC8 complex induction improves glycemic control and nonalcoholic fatty liver disease in murine Type 2 diabetes ]]> https://biorxiv.org/content/10.1101/2021.02.28.432901v1?rss=1 Gunasekar, S. K. Xie, L. Chheda, P. R. Kang, C. Kern, D. M. My-Ta, C. Kumar, A. Maurer, J. M. Gerber, E. E. Grzesik, W. J. Elliot-Hudson, M. Zhang, Y. Kulkarni, C. A. Samuel, I. Smith, J. K. Nau, P. Imai, Y. Sheldon, R. D. Taylor, E. B. Lerner, D. J. Norris, A. W. Brohawn, S. G. Kerns, R. Sah, R. 2021-03-02 doi:10.1101/2021.02.28.432901 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Synthetic algal-bacteria consortia for space-efficient microalgal growth in a simple hydrogel system ]]> https://biorxiv.org/content/10.1101/2021.03.01.433490v1?rss=1 Martin, N. Bernat, T. Dinasquet, J. Stofko, A. Damon, A. Deheyn, D. Azam, F. Smith, J. Davey, M. P. Smith, A. G. Vignolini, S. Wangpraseurt, D. 2021-03-02 doi:10.1101/2021.03.01.433490 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ A H3K9me2-Binding Protein AGDP3 Limits DNA Methylation and Transcriptional Gene Silencing in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2021.03.08.434320v1?rss=1 Zhou, X. Wei, M. Nie, W. Xi, Y. Du, X. Tang, K. Peng, L. Zheng, Q. Satheesh, V. Luo, J. Wang, Y. Liu, R. Yang, Z. Zhong, Y. An, G.-Y. Zhu, J.-K. Du, J. Lei, M. 2021-03-08 doi:10.1101/2021.03.08.434320 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Efficient graphene oxide coating improves cryo-EM sample preparation and data collection from tilted grids ]]> https://biorxiv.org/content/10.1101/2021.03.08.434344v1?rss=1 Patel, A. B. Toso, D. Litvak, A. Nogales, E. 2021-03-08 doi:10.1101/2021.03.08.434344 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ RS-FISH: Precise, interactive and scalable smFISH spot detection using Radial Symmetry ]]> https://biorxiv.org/content/10.1101/2021.03.09.434205v1?rss=1 Bahry, E. Breimann, L. Epstein, L. Kolyvanov, K. Harrington, K. Lionnet, T. Preibisch, S. 2021-03-09 doi:10.1101/2021.03.09.434205 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Massively parallel reporter perturbation assay uncovers temporal regulatory architecture during neural differentiation ]]> https://biorxiv.org/content/10.1101/2021.03.12.435197v1?rss=1 Kreimer, A. Ashuach, T. Inoue, F. Khodaverdian, A. Yosef, N. Ahituv, N. 2021-03-12 doi:10.1101/2021.03.12.435197 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ RNA-BINDING PROTEINS DIRECT MYOGENIC CELL FATE DECISIONS ]]> https://biorxiv.org/content/10.1101/2021.03.14.435333v1?rss=1 Wheeler, J. R. Whitney, O. N. Vogler, T. O. Nguyen, E. D. Pawlikowski, B. Lester, E. Cutler, A. Elston, T. Dalla Betta, N. Parker, K. R. Yost, K. Vogel, H. Rando, T. A. Chang, H. Y. Johnson, A. M. Parker, R. Olwin, B. B. 2021-03-14 doi:10.1101/2021.03.14.435333 Cold Spring Harbor Laboratory Press 2021-03-14 <![CDATA[ Nanoparticle Cellular Internalization is Not Required for RNA Delivery to Mature Plant Leaves ]]> https://biorxiv.org/content/10.1101/2021.03.17.435888v1?rss=1 Zhang, H. Goh, N. S. Wang, J. Demirer, G. S. Butrus, S. Park, S.-J. Landry, M. P. 2021-03-19 doi:10.1101/2021.03.17.435888 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Gold nanocluster mediated delivery of siRNA to intact plant cells for efficient gene knockdown ]]> https://biorxiv.org/content/10.1101/2021.03.17.435890v1?rss=1 Zhang, H. Cao, Y. Xu, D. Goh, N. S. Demirer, G. S. Landry, M. P. Yang, P. 2021-03-17 doi:10.1101/2021.03.17.435890 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ An fMRI-based brain marker predicts individual differences in delay discounting ]]> https://biorxiv.org/content/10.1101/2021.03.18.435969v1?rss=1 Koban, L. Lee, S. Schelski, D. S. Simon, M.-C. Lerman, C. Weber, B. Kable, J. W. Plassmann, H. 2021-03-19 doi:10.1101/2021.03.18.435969 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Joint effects of genes underlying a temperature specialization tradeoff in yeast ]]> https://biorxiv.org/content/10.1101/2021.03.18.436093v1?rss=1 AlZaben, F. Chuong, J. N. Abrams, M. B. Brem, R. B. 2021-03-19 doi:10.1101/2021.03.18.436093 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ A species-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for preimplantation development ]]> https://biorxiv.org/content/10.1101/2021.03.24.436683v1?rss=1 Modzelewski, A. J. Shao, W. Chen, J. Lee, A. Qi, X. Noon, M. Tjokro, K. Sales, G. Biton, A. Speed, T. Xuan, Z. Wang, T. Risso, D. He, L. 2021-03-25 doi:10.1101/2021.03.24.436683 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING ]]> https://biorxiv.org/content/10.1101/2021.03.24.436770v1?rss=1 Marin, W. Dandekar, R. Augusto, D. G. Yusufali, T. Heyn, B. Hofmann, J. Lange, V. Sauter, J. Norman, P. J. Hollenbach, J. A. 2021-03-24 doi:10.1101/2021.03.24.436770 Cold Spring Harbor Laboratory Press 2021-03-24 <![CDATA[ RNA polymerase II depletion from the inactive X chromosome territory is not mediated by physical compartmentalization. ]]> https://biorxiv.org/content/10.1101/2021.03.26.437188v1?rss=1 Collombet, S. Rall, I. Dugast-Darzacq, C. Heckert, A. Halavatyi, A. le Saux, A. Dailey, G. Darzacq, X. Heard, E. 2021-03-27 doi:10.1101/2021.03.26.437188 Cold Spring Harbor Laboratory Press 2021-03-27 <![CDATA[ Sulfate adenylyl transferase kinetics and mechanisms of metabolic inhibitors of microbial sulfate respiration ]]> https://biorxiv.org/content/10.1101/2021.03.29.436835v1?rss=1 Carlson, H. K. Youngblut, M. D. Redford, S. A. Williamson, A. J. Coates, J. 2021-03-29 doi:10.1101/2021.03.29.436835 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ Coupling brain cerebrovascular oscillations and CSF flow during wakefulness: An fMRI study ]]> https://biorxiv.org/content/10.1101/2021.03.29.437406v1?rss=1 Yang, H.-C. S. Inglis, B. Talavage, T. M. Vijayakrishnan Nair, V. Yao, J. F. Fitzgerald, B. Schwichtenberg, A. J. Tong, Y. 2021-03-30 doi:10.1101/2021.03.29.437406 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ OpenCell: proteome-scale endogenous tagging enables the cartography of human cellular organization ]]> https://biorxiv.org/content/10.1101/2021.03.29.437450v1?rss=1 Cho, N. H. Cheveralls, K. C. Brunner, A.-D. Kim, K. Michaelis, A. C. Raghavan, P. Kobayashi, H. Savy, L. Li, J. Y. Canaj, H. Kim, J. Y. S. Setwart, E. M. Gnann, C. McCarthy, F. Cabrera, J. P. Brunetti, R. M. Chhun, B. B. Dingle, G. Hein, M. Y. Huang, B. Mehta, S. B. Weissman, J. S. Gomez-Sjoberg, R. Itzhak, D. N. Royer, L. A. Mann, M. Leonetti, M. D. 2021-03-29 doi:10.1101/2021.03.29.437450 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ Time-varying Dynamic Network Model For Dynamic Resting State Functional Connectivity in fMRI and MEG imaging ]]> https://biorxiv.org/content/10.1101/2021.04.01.438060v1?rss=1 Jiang, F. Jin, H. Bao, Y. Xie, X. Cummings, J. Raj, A. Nagarajan, S. 2021-04-02 doi:10.1101/2021.04.01.438060 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ Diverse ATPase proteins in mobilomes constitute a large potential sink for prokaryotic host ATP ]]> https://biorxiv.org/content/10.1101/2021.04.01.438130v1?rss=1 Shim, H. Shivram, H. Lei, S. Doudna, J. A. Banfield, J. 2021-04-01 doi:10.1101/2021.04.01.438130 Cold Spring Harbor Laboratory Press 2021-04-01 <![CDATA[ High performance microbial opsins for spatially and temporally precise perturbations of large neuronal networks ]]> https://biorxiv.org/content/10.1101/2021.04.01.438134v1?rss=1 Sridharan, S. Gajowa, M. Ogando, M. B. Jagadisan, U. Abdeladim, L. Sadahiro, M. Bounds, H. Hendricks, W. D. Gopakumar, K. Tayler, I. Oldenburg, I. A. Brohawn, S. G. Adesnik, H. 2021-04-05 doi:10.1101/2021.04.01.438134 Cold Spring Harbor Laboratory Press 2021-04-05 <![CDATA[ Design considerations for workflow management systems use in production genomics research and the clinic ]]> https://biorxiv.org/content/10.1101/2021.04.03.437906v1?rss=1 Ahmed, A. E. Allen, J. Bhat, T. Burra, P. Fliege, C. E. Hart, S. N. Heldenbrand, J. R. Hudson, M. E. Istanto, D. D. Kalmbach, M. T. Kapraun, G. D. Kendig, K. I. Kendzior, M. C. Klee, E. W. Mattson, N. Ross, C. A. Sharif, S. M. Venkatakrishnan, R. Fadlelmola, F. M. Mainzer, L. S. 2021-04-05 doi:10.1101/2021.04.03.437906 Cold Spring Harbor Laboratory Press 2021-04-05 <![CDATA[ An Engineered Contact Lens for Passive and Sustained Release of Lifitegrast, an Anti-Dry Eye Syndrome Drug ]]> https://biorxiv.org/content/10.1101/2021.04.10.439289v1?rss=1 View larger version (75K): org.highwire.dtl.DTLVardef@1049076org.highwire.dtl.DTLVardef@a83fceorg.highwire.dtl.DTLVardef@1f52c4borg.highwire.dtl.DTLVardef@12f0ead_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mu, C. Lee, V. Liu, Y. Han, Y. marriott, g. 2021-04-11 doi:10.1101/2021.04.10.439289 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Measuring salivary cortisol in wild carnivores ]]> https://biorxiv.org/content/10.1101/2021.04.11.438354v1?rss=1 Montgomery, T. M. Greenberg, J. R. Gunson, J. L. John, K. Laubach, Z. M. Nonnamaker, E. Person, E. S. Rogers, H. Ronis, E. Smale, L. Steinfield, K. Strong, R. Holekamp, K. E. Beehner, J. C. 2021-04-12 doi:10.1101/2021.04.11.438354 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Molecular determinants of phase separation for Drosophila DNA replication licensing factors ]]> https://biorxiv.org/content/10.1101/2021.04.12.439485v1?rss=1 Parker, M. W. Kao, J. A. Huang, A. T. Berger, J. M. Botchan, M. R. 2021-04-12 doi:10.1101/2021.04.12.439485 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Visual detection of binary, ternary, and quaternary protein-protein interactions in fission yeast by Pil1 co-tethering assay ]]> https://biorxiv.org/content/10.1101/2021.04.13.439745v1?rss=1 Yu, Z.-Q. Liu, X.-M. Zhao, D. Xu, D.-D. Du, L.-L. 2021-04-14 doi:10.1101/2021.04.13.439745 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Fixational Eye Movements Depend on Task and Target ]]> https://biorxiv.org/content/10.1101/2021.04.14.439841v1?rss=1 Bowers, N. R. Gautier, J. Lin, S. Roorda, A. 2021-04-14 doi:10.1101/2021.04.14.439841 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Sonicated fibrils of huntingtin exon-1 preferentially seed neurons and produce toxic assemblies ]]> https://biorxiv.org/content/10.1101/2021.04.16.440200v1?rss=1 Chongtham, A. Isas, J. M. Pandey, N. K. Rawat, A. Yoo, J. H. Mastro, T. L. Kennedy, M. Langen, R. Khoshnan, A. 2021-04-18 doi:10.1101/2021.04.16.440200 Cold Spring Harbor Laboratory Press 2021-04-18 <![CDATA[ Thalamocortical mechanisms regulating the relationship between transient beta events and human tactile perception ]]> https://biorxiv.org/content/10.1101/2021.04.16.440210v1?rss=1 Law, R. Pugliese, S. Shin, H. Sliva, D. D. Lee, S. Neymotin, S. Moore, C. Jones, S. R. 2021-04-18 doi:10.1101/2021.04.16.440210 Cold Spring Harbor Laboratory Press 2021-04-18 <![CDATA[ Evidence for a Nuclear Role for Drosophila Dlg as a Regulator of the NURF Complex ]]> https://biorxiv.org/content/10.1101/2021.04.18.440284v1?rss=1 Sharp, K. A. Khoury, M. J. Wirtz-Peitz, F. Bilder, D. 2021-04-18 doi:10.1101/2021.04.18.440284 Cold Spring Harbor Laboratory Press 2021-04-18 <![CDATA[ Highly task-specific and distributed neural connectivity in working memory revealed by single-trial decoding in mice and humans ]]> https://biorxiv.org/content/10.1101/2021.04.20.440621v1?rss=1 Strahnen, D. Kapanaiah, S. K. T. Bygrave, A. M. Liss, B. Bannerman, D. M. Akam, T. Grewe, B. F. Johnson, E. L. Kätzel, D. 2021-04-21 doi:10.1101/2021.04.20.440621 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Sentinel cells enable genetic detection of SARS-CoV-2 Spike protein ]]> https://biorxiv.org/content/10.1101/2021.04.20.440678v1?rss=1 Weinberg, Z. Y. Hilburger, C. E. Kim, M. Cao, L. Khalid, M. M. Elmes, S. Diwanji, D. Hernandez, E. Lopez, J. Schaefer, K. Smith, A. M. Zhou, F. QCRG Structural Biology Consortium, Kumar, G. R. Ott, M. Baker, D. El-Samad, H. 2021-04-20 doi:10.1101/2021.04.20.440678 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Modeling intracranial electrodes ]]> https://biorxiv.org/content/10.1101/2021.04.28.441828v1?rss=1 Blenkmann, A. O. Solbakk, A.-K. Ivanovic, J. Larsson, P. G. Knight, R. T. Endestad, T. 2021-04-29 doi:10.1101/2021.04.28.441828 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ PeakVI: A Deep Generative Model for Single Cell Chromatin Accessibility Analysis ]]> https://biorxiv.org/content/10.1101/2021.04.29.442020v1?rss=1 Ashuach, T. Reidenbach, D. A. Gayoso, A. Yosef, N. 2021-04-30 doi:10.1101/2021.04.29.442020 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Recovering mixtures of fast diffusing states from short single particle trajectories ]]> https://biorxiv.org/content/10.1101/2021.05.03.442482v1?rss=1 Heckert, A. B. Dahal, L. Tjian, R. Darzacq, X. 2021-05-04 doi:10.1101/2021.05.03.442482 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Cold survival and its molecular mechanisms in a locally adapted nematode population ]]> https://biorxiv.org/content/10.1101/2021.05.10.443188v1?rss=1 Wang, W. Flury, A. G. Garrison, J. L. Brem, R. B. 2021-05-10 doi:10.1101/2021.05.10.443188 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Repeated origins, gene flow, and allelic interactions of herbicide resistance mutations in a widespread agricultural weed ]]> https://biorxiv.org/content/10.1101/2021.05.10.443516v1?rss=1 Kreiner, J. M. Sandler, G. Stern, A. J. Tranel, P. J. Weigel, D. Stinchcombe, J. R. Wright, S. I. 2021-05-10 doi:10.1101/2021.05.10.443516 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Syntrophic H2 production enhances the performance of primarily acetate-supplemented reactors treating sulphate contaminated solutions ]]> https://biorxiv.org/content/10.1101/2021.05.12.443249v1?rss=1 Hessler, T. Harrison, S. T. L. Banfield, J. F. Huddy, R. J. 2021-05-12 doi:10.1101/2021.05.12.443249 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ Uncoupling of Chromatin Assembly from DNA Replication in Sciara Reveals a Domain of Postreplicative Immature Chromatin ]]> https://biorxiv.org/content/10.1101/2021.05.12.443896v1?rss=1 Urnov, F. D. Scheer, U. Zentgraf, H. Smith, H. S. Gerbi, S. A. 2021-05-12 doi:10.1101/2021.05.12.443896 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ STING mediates immune responses in a unicellular choanoflagellate ]]> https://biorxiv.org/content/10.1101/2021.05.13.443778v1?rss=1 Woznica, A. Kumar, A. Sturge, C. R. Xing, C. King, N. Pfeiffer, J. K. 2021-05-14 doi:10.1101/2021.05.13.443778 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ A toolbox for efficient proximity-dependent biotinylation in zebrafish embryos ]]> https://biorxiv.org/content/10.1101/2021.05.16.444353v1?rss=1 Rosenthal, S. M. Misra, T. Abdouni, H. Branon, T. C. Ting, A. Y. Scott, I. C. Gingras, A.-C. 2021-05-17 doi:10.1101/2021.05.16.444353 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Quantitative reverse transcription PCR assay to detect pyrethroid resistance in Culex mosquitoes ]]> https://biorxiv.org/content/10.1101/2021.05.18.444631v1?rss=1 Hager, K. Gaona, E. Kistler, A. Ratnasiri, K. Retallack, H. Barretto, M. Wheeler, S. Hoover, C. M. Haas-Stapleton, E. J. 2021-05-18 doi:10.1101/2021.05.18.444631 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Cortical Representations of Concrete and Abstract Concepts in Language Combine Visual and Linguistic Representations ]]> https://biorxiv.org/content/10.1101/2021.05.19.444701v1?rss=1 Tang, J. LeBel, A. Huth, A. G. 2021-05-19 doi:10.1101/2021.05.19.444701 Cold Spring Harbor Laboratory Press 2021-05-19 <![CDATA[ VIP neurons desynchronize cortical assemblies ]]> https://biorxiv.org/content/10.1101/2021.05.20.444979v1?rss=1 Veit, J. Mossing, D. P. Adesnik, H. 2021-05-20 doi:10.1101/2021.05.20.444979 Cold Spring Harbor Laboratory Press 2021-05-20 <![CDATA[ Cap-dependent translation initiation monitored in living cells ]]> https://biorxiv.org/content/10.1101/2021.05.21.445166v1?rss=1 Gandin, V. English, B. P. Freeman, M. Leroux, L.-P. Preibisch, S. Walpita, D. Jaramillo, M. Singer, R. H. 2021-05-22 doi:10.1101/2021.05.21.445166 Cold Spring Harbor Laboratory Press 2021-05-22 <![CDATA[ A ratiometric dual color luciferase reporter for fast characterization of transcriptional regulatory elements ]]> https://biorxiv.org/content/10.1101/2021.05.26.443018v1?rss=1 Gonzalez-Grandio, E. Demirer, G. S. Ma, W. Brady, S. M. Landry, M. P. 2021-05-27 doi:10.1101/2021.05.26.443018 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ A Universal Approach to Analyzing Transmission Electron Microscopy with ImageJ ]]> https://biorxiv.org/content/10.1101/2021.05.27.446036v1?rss=1 Lam, J. Biete, M. Mungai, M. AshShareef, S. Neikirk, K. Garza Lopez, E. Christensen, T. A. Salisbury, J. L. Katti, P. Glancy, B. Pereira, R. O. Abel, E. D. Hinton, A. 2021-05-29 doi:10.1101/2021.05.27.446036 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ Molecular characterization of inversion breakpoints in the Drosophila nasuta species group ]]> https://biorxiv.org/content/10.1101/2021.06.01.446624v1?rss=1 Mai, D. Bachtrog, D. 2021-06-01 doi:10.1101/2021.06.01.446624 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ A unifying mechanism governing inter-brain neural relationship during social interactions ]]> https://biorxiv.org/content/10.1101/2021.06.02.446694v1?rss=1 Zhang, W. Yartsev, M. M. 2021-06-02 doi:10.1101/2021.06.02.446694 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Extremely bright, near-IR emitting spontaneously blinking fluorophores enable ratiometric multicolor nanoscopy in live cells ]]> https://biorxiv.org/content/10.1101/2021.06.02.446776v1?rss=1 Tyson, J. Hu, K. Zheng, S. Kidd, P. Dadina, N. Chu, L. Toomre, D. Bewersdorf, J. Schepartz, A. 2021-06-02 doi:10.1101/2021.06.02.446776 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Physical basis for distinct basal and mechanically-gated activity of the human K+ channel TRAAK ]]> https://biorxiv.org/content/10.1101/2021.06.04.447000v1?rss=1 Rietmeijer, R. A. Sorum, E. Li, B. Brohawn, S. G. 2021-06-06 doi:10.1101/2021.06.04.447000 Cold Spring Harbor Laboratory Press 2021-06-06 <![CDATA[ Retinoic acid exerts sexually dimorphic effects over muscle energy metabolism and function ]]> https://biorxiv.org/content/10.1101/2021.06.04.447134v1?rss=1 30%. Rdh10+/- male GM had impaired electron transport chain activity, and a 60% reduction in fasting ATP. The share of oxidative fibers increased, as did expression of the myogenic transcription factors Myog and Myf5. Centralized nuclei increased 5-fold in fibers--indicating muscle malady or repair. In Rdh10+/- female GM, RA decreased only 17%, due to a 1.8-fold increase in the estrogen-induced retinol dehydrogenase, Dhrs9. Rdh10+/- female GM did not amass TAG, increase oxidative fibers, decrease Glut1 mRNA or glucose, nor increase centralized nuclei. Expression of Myog and Myf5 decreased. Electron transport chain activity increased, elevating fasting ATP >3-fold. Thus, small decreases in skeletal muscle RA affect whole body energy use, insulin resistance and adiposity, in part through estrogen-related sexual dimorphic effects on mitochondria function. ]]> Zhao, Y. Vuckovic, M. Yoo, H. S. Fox, N. Rodriguez, A. McKessy, K. Napoli, J. L. 2021-06-04 doi:10.1101/2021.06.04.447134 Cold Spring Harbor Laboratory Press 2021-06-04 <![CDATA[ Unified classification of mouse retinal ganglion cells using function, morphology, and gene expression ]]> https://biorxiv.org/content/10.1101/2021.06.10.447922v1?rss=1 Goetz, J. Jessen, Z. F. Jacobi, A. Mani, A. Cooler, S. Greer, D. Kadri, S. Segal, J. Shekhar, K. Sanes, J. Schwartz, G. 2021-06-11 doi:10.1101/2021.06.10.447922 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Ovule siRNAs methylate and silence protein-coding genes in trans ]]> https://biorxiv.org/content/10.1101/2021.06.10.447945v1?rss=1 Burgess, D. Chow, H. T. Grover, J. W. Freeling, M. Mosher, R. A. 2021-06-10 doi:10.1101/2021.06.10.447945 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Metabolomic analysis of diverse mice reveals hepatic arginase-1 as source of plasma arginase in Plasmodium chabaudi infection ]]> https://biorxiv.org/content/10.1101/2021.06.11.448167v1?rss=1 Davis, N. M. Lissner, M. M. Massis, L. M. Richards, C. L. Chevee, V. Gupta, A. S. Gherardini, F. C. Monack, D. M. Schneider, D. S. 2021-06-13 doi:10.1101/2021.06.11.448167 Cold Spring Harbor Laboratory Press 2021-06-13 <![CDATA[ Harnessing methylotrophs as a bacterial platform to reduce adverse effects of the use of the heavy lanthanide gadolinium in magnetic resonance imaging ]]> https://biorxiv.org/content/10.1101/2021.06.12.448192v1?rss=1 Good, N. M. Lee, H. Hawker, E. R. Gilad, A. Martinez-Gomez, N. C. 2021-06-12 doi:10.1101/2021.06.12.448192 Cold Spring Harbor Laboratory Press 2021-06-12 <![CDATA[ The atypical RNA-binding protein TAF15 regulates dorsoanterior neural development through diverse mechanisms in Xenopus tropicalis. ]]> https://biorxiv.org/content/10.1101/2021.06.14.041913v1?rss=1 DeJong, C. S. Dichmann, D. S. Exner, C. R. T. Xu, Y. Harland, R. M. 2021-06-14 doi:10.1101/2021.06.14.041913 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ Oxytocin receptor antagonism during song tutoring in zebra finches reduces preference for and learning of the tutor's song ]]> https://biorxiv.org/content/10.1101/2021.06.16.448133v1?rss=1 Pilgeram, N. R. Baran, N. M. Bhise, A. Davis, M. T. Kim, E. Rodriguez-Saltos, C. A. Lee, S. Maney, D. L. 2021-06-16 doi:10.1101/2021.06.16.448133 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ PLEKHA5, PLEKHA6 and PLEKHA7 bind to PDZD11 to target the Menkes ATPase ATP7A to the cell periphery and regulate copper homeostasis ]]> https://biorxiv.org/content/10.1101/2021.06.17.448791v1?rss=1 Citi, S. Sluysmans, S. Mean, I. Xiao, T. Boukhatemi, A. Ferreira, F. Jond, L. Chang, C. J. 2021-06-17 doi:10.1101/2021.06.17.448791 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Distinct Processing of Sensory Prediction Error and Task Error during Motor Learning ]]> https://biorxiv.org/content/10.1101/2021.06.20.449180v1?rss=1 Tsay, J. Haith, A. Ivry, R. B. Kim, H. E. 2021-06-20 doi:10.1101/2021.06.20.449180 Cold Spring Harbor Laboratory Press 2021-06-20 <![CDATA[ Genetic code expansion in the engineered organism Vmax X2: High yield and exceptional fidelity ]]> https://biorxiv.org/content/10.1101/2021.06.22.449487v1?rss=1 Santiago, S. Ad, O. Shah, B. Zhang, Z. Zhang, X. Chatterjee, A. Schepartz, A. 2021-06-22 doi:10.1101/2021.06.22.449487 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Aberrant FGF signaling promotes granule neuron precursor expansion in SHH subgroup infantile medulloblastoma ]]> https://biorxiv.org/content/10.1101/2021.06.23.449636v1?rss=1 Yabut, O. R. Gomez, H. Arela, J. Castillo, J. G. Ngo, T. Pleasure, S. J. 2021-06-24 doi:10.1101/2021.06.23.449636 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Polygenic variation in sexual investment across an ephemerality gradient in Daphnia pulex ]]> https://biorxiv.org/content/10.1101/2021.06.23.449662v1?rss=1 Barnard-Kubow, K. B. Becker, D. Murray, C. S. Porter, R. Gutierrez, G. Erickson, P. A. Nunez, J. C. B. Voss, E. Suryamohan, K. Ratan, A. Beckerman, A. Bergland, A. O. 2021-06-24 doi:10.1101/2021.06.23.449662 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Genetic basis and dual adaptive role of floral pigmentation in sunflowers ]]> https://biorxiv.org/content/10.1101/2021.06.26.449999v1?rss=1 Todesco, M. Bercovich, N. Kim, A. Imerovski, I. Owens, G. L. Dorado Ruiz, O. Holalu, S. V. Madilao, L. L. Jahani, M. Legare, J.-S. Blackman, B. K. Rieseberg, L. H. 2021-06-27 doi:10.1101/2021.06.26.449999 Cold Spring Harbor Laboratory Press 2021-06-27 <![CDATA[ A role for worm cutl-24 in background- and parent-of-origin-dependent ER stress resistance ]]> https://biorxiv.org/content/10.1101/2021.07.01.450736v1?rss=1 Wang, W. Brem, R. B. Garrison, J. Flury, A. 2021-07-01 doi:10.1101/2021.07.01.450736 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ Loss of GdpP function in Staphylococcus aureus leads to β-lactam tolerance and enhanced evolution of β-lactam resistance ]]> https://biorxiv.org/content/10.1101/2021.07.02.449101v1?rss=1 Poon, R. Basuino, L. Satishkumar, N. Chatterjee, A. Mukkayyan, N. Buggeln, E. Huang, L. Nair, V. Argudin, M. A. Datta, S. K. Chambers, H. F. Chatterjee, S. S. 2021-07-02 doi:10.1101/2021.07.02.449101 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ Accurately positioning functional residues with robotics-inspired computational protein design ]]> https://biorxiv.org/content/10.1101/2021.07.02.450934v1?rss=1 Krivacic, C. Kundert, K. Pan, X. Pache, R. A. Liu, L. O Conchuir, S. Jeliazkov, J. R. Gray, J. J. Thompson, M. C. Fraser, J. S. Kortemme, T. 2021-07-03 doi:10.1101/2021.07.02.450934 Cold Spring Harbor Laboratory Press 2021-07-03 <![CDATA[ DiMeLo-seq: a long-read, single-molecule method for mappingprotein-DNA interactions genome-wide ]]> https://biorxiv.org/content/10.1101/2021.07.06.451383v1?rss=1 Altemose, N. Maslan, A. Smith, O. K. Sundararajan, K. Brown, R. R. Detweiler, A. M. Neff, N. Miga, K. H. Straight, A. F. Streets, A. 2021-07-07 doi:10.1101/2021.07.06.451383 Cold Spring Harbor Laboratory Press 2021-07-07 <![CDATA[ Language models enable zero-shot prediction of the effects of mutations on protein function ]]> https://biorxiv.org/content/10.1101/2021.07.09.450648v1?rss=1 Meier, J. Rao, R. Verkuil, R. Liu, J. Sercu, T. Rives, A. 2021-07-10 doi:10.1101/2021.07.09.450648 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ Photoprotective qH in Arabidopsis occurs in the light-harvesting complex II trimer ]]> https://biorxiv.org/content/10.1101/2021.07.09.450705v1?rss=1 Bru, P. Steen, C. J. Park, S. Amstutz, C. L. Sylak-Glassman, E. J. Leuenberger, M. Lam, L. Longoni, F. Fleming, G. R. Niyogi, K. K. Malnoë, A. 2021-07-10 doi:10.1101/2021.07.09.450705 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ Myosin-driven Nucleation of Actin Filaments Drives Stereocilia Development Critical for Hearing ]]> https://biorxiv.org/content/10.1101/2021.07.09.451618v1?rss=1 Moreland, Z. G. Jiang, F. Aguilar, C. Barzik, M. Gong, R. Shams, A. Faaborg-Andersen, C. Werth, J. C. Harley, R. Sutton, D. C. Cole, S. M. Parker, A. Morse, S. Wilson, E. Takagi, Y. Sellers, J. R. Brown, S. D. Friedman, T. B. Alushin, G. M. Bowl, M. R. Bird, J. E. 2021-07-10 doi:10.1101/2021.07.09.451618 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ Structural basis for tunable control of actin dynamics by myosin-15 in mechanosensory stereocilia ]]> https://biorxiv.org/content/10.1101/2021.07.09.451843v1?rss=1 Gong, R. Jiang, F. Moreland, Z. G. Reynolds, M. J. Espinosa de los Reyes, S. Gurel, P. S. Shams, A. Bowl, M. R. Bird, J. E. Alushin, G. M. 2021-07-10 doi:10.1101/2021.07.09.451843 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ Probing remdesivir nucleotide analogue insertion to SARS-CoV-2 RNA dependent RNA polymerase in viral replication ]]> https://biorxiv.org/content/10.1101/2021.07.12.452099v1?rss=1 Romero, M. E. Long, C. La Rocco, D. Keerthi, A. M. Xu, D. Yu, J. 2021-07-13 doi:10.1101/2021.07.12.452099 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ ECM dimensionality tunes actin tension to modulate the endoplasmic reticulum and spheroid phenotype ]]> https://biorxiv.org/content/10.1101/2021.07.14.452329v1?rss=1 Kai, F. Ou, G. Tourdot, R. W. Stashko, C. Gaietta, G. Swift, M. F. Volkmann, N. Long, A. F. Han, Y. Huang, H. H. Northey, J. J. Leidal, A. M. Viasnoff, V. Bryant, D. M. Guo, W. Wiita, A. P. Guo, M. Dumont, S. Hanein, D. Radhakrishnan, R. Weaver, V. M. 2021-07-14 doi:10.1101/2021.07.14.452329 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ Plumage balances camouflage and thermoregulation in Horned Larks (Eremophila alpestris) ]]> https://biorxiv.org/content/10.1101/2021.07.15.452373v1?rss=1 Mason, N. A. Riddell, E. Romero, F. Cicero, C. Bowie, R. C. K. 2021-07-15 doi:10.1101/2021.07.15.452373 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ Induced Membrane Curvature Bypasses Clathrin's Essential Endocytic Function ]]> https://biorxiv.org/content/10.1101/2021.07.15.452420v1?rss=1 Cail, R. C. Shirazinejad, C. R. Drubin, D. G. 2021-07-15 doi:10.1101/2021.07.15.452420 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ Differences in the dynamics of the tandem-SH2 modules of the Syk and ZAP-70 tyrosine kinases ]]> https://biorxiv.org/content/10.1101/2021.07.20.453126v1?rss=1 Hobbs, H. T. Shah, N. H. Badroos, J. M. Gee, C. L. Marqusee, S. Kuriyan, J. 2021-07-20 doi:10.1101/2021.07.20.453126 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ Manipulation of RNA Polymerase III by Herpes Simplex Virus-1 ]]> https://biorxiv.org/content/10.1101/2021.07.21.453214v1?rss=1 Dremel, S. E. Sivrich, F. L. Tucker, J. M. Glaunsinger, B. A. DeLuca, N. A. 2021-07-23 doi:10.1101/2021.07.21.453214 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Evolution of Learning in Technology Adoption: The case of the U.S. Soybean Seed Industry. ]]> https://biorxiv.org/content/10.1101/2021.07.22.453433v1?rss=1 Ilin, C. Shi, G. 2021-07-23 doi:10.1101/2021.07.22.453433 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Toxin breakdown does not preclude the potential for defensive toxin use in a fruit fly ]]> https://biorxiv.org/content/10.1101/2021.07.23.453507v1?rss=1 Douglas, T. E. Beskid, S. G. Gernand, C. E. Nirtaut, B. E. Tamsil, K. E. Fitch, R. W. Tarvin, R. D. 2021-07-24 doi:10.1101/2021.07.23.453507 Cold Spring Harbor Laboratory Press 2021-07-24 <![CDATA[ Stabilizing selection shapes variation in phenotypic plasticity ]]> https://biorxiv.org/content/10.1101/2021.07.29.454146v1?rss=1 100 D. pulex strains originating from a natural population in the UK. We found low genetic diversity for morphological defenses among genetically diverse clones upon predation risk exposure. The strongest reduction in genetic variation was observed in areas of greatest phenotypic plasticity, which we interpret as evidence of stabilizing selection. By assessing among-clone variance in clonally related, field derived strains, we contrasted mutational variation (Vm) to standing variation (Vg). We found that Vg/Vm is lowest in areas of greatest plasticity. These data strongly suggest that stabilizing selection operates directly on phenotypic plasticity, providing a rare glimpse into the evolution of fitness related traits in natural populations. ]]> Becker, D. Barnard-Kubow, K. Porter, R. Edwards, A. Voss, E. Beckerman, A. P. Bergland, A. O. 2021-07-29 doi:10.1101/2021.07.29.454146 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning ]]> https://biorxiv.org/content/10.1101/2021.07.29.454330v1?rss=1 Lu, A. X. Lu, A. X. Pritisanac, I. Zarin, T. Forman-Kay, J. D. Moses, A. M. 2021-07-30 doi:10.1101/2021.07.29.454330 Cold Spring Harbor Laboratory Press 2021-07-30 <![CDATA[ Mitochondrial TRAK adaptors coordinate dynein and kinesin motility ]]> https://biorxiv.org/content/10.1101/2021.07.30.454553v1?rss=1 Canty, J. T. Hensley, A. Yildiz, A. 2021-07-31 doi:10.1101/2021.07.30.454553 Cold Spring Harbor Laboratory Press 2021-07-31 <![CDATA[ Social selectivity and social motivation in voles ]]> https://biorxiv.org/content/10.1101/2021.07.30.454556v1?rss=1 Beery, A. K. Lopez, S. A. Blandino, K. L. Lee, N. S. Bourdon, N. S. Ahern, T. H. 2021-07-31 doi:10.1101/2021.07.30.454556 Cold Spring Harbor Laboratory Press 2021-07-31 <![CDATA[ Mixed Effects Machine Learning Models for Colon Cancer Metastasis Prediction using Spatially Localized Immuno-Oncology Markers ]]> https://biorxiv.org/content/10.1101/2021.08.01.454649v1?rss=1 Levy, J. Bobak, C. Nasir-Moin, M. Veziroglu, E. M. Palisoul, S. M. Barney, R. E. Salas, L. A. Christensen, B. C. Tsongalis, G. J. Vaickus, L. J. 2021-08-02 doi:10.1101/2021.08.01.454649 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ GEPSi: A Python Library to Simulate GWAS Phenotype Data ]]> https://biorxiv.org/content/10.1101/2021.08.04.455085v1?rss=1 Reidenbach, D. A. Lal, A. Slim, L. Mosafi, O. Israeli, J. 2021-08-06 doi:10.1101/2021.08.04.455085 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ The lesser Pacific striped octopus, Octopus chierchiae: an emerging laboratory model for the study of octopuses ]]> https://biorxiv.org/content/10.1101/2021.08.04.455148v1?rss=1 Grearson, A. G. Dugan, A. Sakmar, T. Dolen, G. Gire, D. H. Sivitilli, D. M. Niell, C. Caldwell, R. L. Wang, Z. Y. Grasse, B. 2021-08-06 doi:10.1101/2021.08.04.455148 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Automated tracking reveals the social network of beach mice and their burrows ]]> https://biorxiv.org/content/10.1101/2021.08.07.455531v1?rss=1 Bedford, N. L. Gable, J. T. Hu, C. K. Wooldridge, T. B. Sokolov, N. A. Lassance, J.-M. Hoekstra, H. E. 2021-08-08 doi:10.1101/2021.08.07.455531 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ Inhibiting retinoic acid mitigates vision loss in a mouse model of retinal degeneration ]]> https://biorxiv.org/content/10.1101/2021.08.09.455683v1?rss=1 Telias, M. Sit, K. Frozenfar, D. Smith, B. Misra, A. Goard, M. J. Kramer, R. H. 2021-08-10 doi:10.1101/2021.08.09.455683 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Engineering site-selective incorporation of fluorine into natural product analogs ]]> https://biorxiv.org/content/10.1101/2021.08.09.455754v1?rss=1 Sirirungruang, S. Ad, O. Privalsky, T. M. Ramesh, S. Sax, J. L. Dong, H. Baidoo, E. E. Amer, B. Khosla, C. Chang, M. C. 2021-08-10 doi:10.1101/2021.08.09.455754 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Gut bacteria regulate the pathogenesis of Huntington's disease in Drosophila ]]> https://biorxiv.org/content/10.1101/2021.08.12.456124v1?rss=1 Chongtham, A. Yoo, J. H. Chin, T. M. Akingbesote, N. D. Huda, A. Khoshnan, A. 2021-08-13 doi:10.1101/2021.08.12.456124 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Structural transitions in the GTP cap visualized by cryo-EM of catalytically inactive microtubules ]]> https://biorxiv.org/content/10.1101/2021.08.13.456308v1?rss=1 LaFrance, B. J. Roostalu, J. Henkin, G. Greber, B. J. Zhang, R. Normanno, D. McCollum, C. Surrey, T. Nogales, E. 2021-08-13 doi:10.1101/2021.08.13.456308 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Mapping the genetic landscape of biomineralization in Magnetospirillum magneticum AMB-1 with RB-Tnseq ]]> https://biorxiv.org/content/10.1101/2021.08.13.456315v1?rss=1 McCausland, H. C. Wetmore, K. M. Arkin, A. P. Komeili, A. 2021-08-13 doi:10.1101/2021.08.13.456315 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Columnar localization and laminar origin of cortical surface electrical potentials ]]> https://biorxiv.org/content/10.1101/2021.08.16.456540v1?rss=1 Baratham, V. L. Dougherty, M. E. Ledochowitsch, P. Maharbiz, M. M. Bouchard, K. 2021-08-17 doi:10.1101/2021.08.16.456540 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Identification of INSR protein structural differences in Diabetes Mellitus type 2 subjects from protein sequences ]]> https://biorxiv.org/content/10.1101/2021.08.17.456584v1?rss=1 Carroll, P. H. 2021-08-17 doi:10.1101/2021.08.17.456584 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Bridge Category Models: Development of Bayesian Modelling Procedures to Account for Bridge Ordinal Ratings for Disease Staging ]]> https://biorxiv.org/content/10.1101/2021.08.17.456726v1?rss=1 Levy, J. Bobak, C. A. Azizgolshani, N. Andersen, M. J. Suriawinata, A. Liu, X. Lisovsky, M. Ren, B. Christensen, B. Vaickus, L. O'Malley, J. 2021-08-18 doi:10.1101/2021.08.17.456726 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ Ubiquitin modulates 26S proteasome conformational dynamics and promotes substrate degradation ]]> https://biorxiv.org/content/10.1101/2021.08.18.456915v1?rss=1 Jonsson, E. Htet, Z. M. Bard, J. A. M. Dong, K. C. Martin, A. 2021-08-19 doi:10.1101/2021.08.18.456915 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Course-based Undergraduate Research Module for Enzyme Discovery Using Protein Structure Prediction ]]> https://biorxiv.org/content/10.1101/2021.08.19.456875v1?rss=1 Kelz, J. I. Takahashi, G. R. Safizadeh, F. Farahmand, V. Crosby, M. G. Uribe, J. L. Kim, S. H. Sprague-Piercy, M. A. Diessner, E. M. Norton-Baker, B. Damo, S. M. Martin, R. W. Kadandale, P. 2021-08-20 doi:10.1101/2021.08.19.456875 Cold Spring Harbor Laboratory Press 2021-08-20 <![CDATA[ MultiVI: deep generative model for the integration of multi-modal data ]]> https://biorxiv.org/content/10.1101/2021.08.20.457057v1?rss=1 Ashuach, T. Gabitto, M. I. Jordan, M. I. Yosef, N. 2021-08-20 doi:10.1101/2021.08.20.457057 Cold Spring Harbor Laboratory Press 2021-08-20 <![CDATA[ Membrane Constriction by ESCRT-III Proteins Induces Structural Lipid Bilayer Asymmetries ]]> https://biorxiv.org/content/10.1101/2021.08.24.457428v1?rss=1 Moss, F. R. Lincoff, J. Tucker, M. Mohammed, A. Grabe, M. Frost, A. 2021-08-25 doi:10.1101/2021.08.24.457428 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ The B.1.427/1.429 (epsilon) SARS-CoV-2 variants are more virulent than ancestral B.1 (614G) in Syrian hamsters ]]> https://biorxiv.org/content/10.1101/2021.08.25.457626v1?rss=1 Carroll, T. Fox, D. van Doremalen, N. Ball, E. Morris, M. K. Sotomayor-Gonzalez, A. Servellita, V. Rustagi, A. Yinda, C. K. Fritts, L. Port, J. R. Ma, Z.-M. Holbrook, M. Schulz, J. Blish, C. A. Hanson, C. Chiu, C. Y. Munster, V. Stanley, S. Miller, C. J. 2021-08-25 doi:10.1101/2021.08.25.457626 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes ]]> https://biorxiv.org/content/10.1101/2021.08.26.457843v1?rss=1 Borges, A. L. Lou, Y. C. Sachdeva, R. Al-Shayeb, B. Jaffe, A. L. Lei, S. Santini, J. M. Banfield, J. F. 2021-08-26 doi:10.1101/2021.08.26.457843 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ Edible fire buffers: mitigation of wildfire with multifunctional landscapes ]]> https://biorxiv.org/content/10.1101/2021.08.30.458294v1?rss=1 Fu, X. Lidar, A. Kantar, M. B. Raghavan, B. 2021-09-01 doi:10.1101/2021.08.30.458294 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Structure and RNA template requirements of Arabidopsis RNA-DEPENDENT RNA POLYMERASE 2 ]]> https://biorxiv.org/content/10.1101/2021.08.31.458351v1?rss=1 Fukudome, A. Singh, J. Mishra, V. Reddem, E. Martinez-Marquez, F. Wenzel, S. Yan, R. Shiozaki, M. Yu, Z. Wang, J. C.-Y. Takagi, Y. Pikaard, C. 2021-08-31 doi:10.1101/2021.08.31.458351 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Sex differences in the reward value of familiar mates in prairie voles ]]> https://biorxiv.org/content/10.1101/2021.09.01.458610v1?rss=1 Vahaba, D. M. Halstead, E. R. Donaldson, Z. Ahern, T. H. Beery, A. K. 2021-09-03 doi:10.1101/2021.09.01.458610 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Community science designed ribosomes with beneficial phenotypes ]]> https://biorxiv.org/content/10.1101/2021.09.05.458952v1?rss=1 Kruger, A. Watkins, A. M. Wellington-Oguri, R. Romano, J. Kofman, C. DeFoe, A. Kim, Y. Anderson-Lee, J. Fisker, E. Townley, J. Eterna participants, d'Aquino, A. E. Das, R. Jewett, M. C. 2021-09-06 doi:10.1101/2021.09.05.458952 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ CRISPR-Cas9 bends and twists DNA to read its sequence ]]> https://biorxiv.org/content/10.1101/2021.09.06.459219v1?rss=1 Cofsky, J. C. Soczek, K. M. Knott, G. J. Nogales, E. Doudna, J. A. 2021-09-07 doi:10.1101/2021.09.06.459219 Cold Spring Harbor Laboratory Press 2021-09-07 <![CDATA[ Methylothon: a versatile course-based high school research experience in microbiology and bioinformatics-- with pink bacteria ]]> https://biorxiv.org/content/10.1101/2021.09.08.459370v1?rss=1 Jones, P. A. Frischer, D. Mueller, S. Le, T. Schwanes, A. Govindaraju, A. Shalvarjian, K. E. Leducq, J.-B. Marx, C. J. Martinez-Gomez, N. C. Lee, J. A. 2021-09-09 doi:10.1101/2021.09.08.459370 Cold Spring Harbor Laboratory Press 2021-09-09 <![CDATA[ Probing neuropeptide volume transmission in vivo by a novel all-optical approach ]]> https://biorxiv.org/content/10.1101/2021.09.10.459853v1?rss=1 Xiong, H. Lacin, E. Ouyang, H. Naik, A. Xu, X. Xie, C. Youn, J. Kumar, K. Kern, T. Aisenberg, E. Kircher, D. Li, X. Zasadzinski, J. A. Mateo, C. Kleinfeld, D. Hrabetova, S. Slesinger, P. Qin, Z. 2021-09-11 doi:10.1101/2021.09.10.459853 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Convergent patterns of gene expression and protein evolution associated with adaptation to desert environments in rodents ]]> https://biorxiv.org/content/10.1101/2021.09.10.459863v1?rss=1 Bittner, N. K. J. Mack, K. L. Nachman, M. W. 2021-09-11 doi:10.1101/2021.09.10.459863 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Cold shock induces a terminal investment reproductive response in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.09.11.459896v1?rss=1 Gulyas, L. Powell, J. R. 2021-09-11 doi:10.1101/2021.09.11.459896 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Accumulation of auranofin in white adipose tissues lowers leptin levels and exerts anti-diabetic effects ]]> https://biorxiv.org/content/10.1101/2021.09.11.459899v1?rss=1 Cox, A. R. Masschelin, P. M. Saha, P. Felix, J. B. Sharp, R. Lian, Z. Xia, Y. Chernis, N. Bader, D. A. Kim, K. H. Li, X. Yoshino, J. Li, X. Sun, Z. Wu, H. Coarfa, C. Moore, D. D. Klein, S. Sun, K. Hartig, S. M. 2021-09-12 doi:10.1101/2021.09.11.459899 Cold Spring Harbor Laboratory Press 2021-09-12 <![CDATA[ PhyloVision: Interactive Software for Integrated Analysis of Single-Cell Transcriptomic and PhylogeneticData ]]> https://biorxiv.org/content/10.1101/2021.09.13.460142v1?rss=1 Jones, M. G. Rosen, Y. Yosef, N. 2021-09-13 doi:10.1101/2021.09.13.460142 Cold Spring Harbor Laboratory Press 2021-09-13 <![CDATA[ Land use, macroecology, and the accuracy of the Maximum Entropy Theory of Ecology: A case study of Azorean arthropods ]]> https://biorxiv.org/content/10.1101/2021.09.14.460355v1?rss=1 Brush, M. J. Matthews, T. Borges, P. A. V. Harte, J. 2021-09-17 doi:10.1101/2021.09.14.460355 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ Long-term Motor Learning in the Wild with High Volume Video Game Data ]]> https://biorxiv.org/content/10.1101/2021.09.15.460516v1?rss=1 Listman, J. B. Tsay, J. Kim, H. E. Mackey, W. E. Heeger, D. J. 2021-09-17 doi:10.1101/2021.09.15.460516 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ Genome wide profiling of histone H3 lysine 4 methylation during the Chlamydomonas cell cycle reveals stable and dynamic properties of lysine 4 trimethylation at gene promoters and near ubiquitous lysine 4 monomethylation ]]> https://biorxiv.org/content/10.1101/2021.09.19.460975v1?rss=1 Strenkert, D. Yildirim, A. Yan, J. Yoshinaga, Y. Pellegrini, M. O'Malley, R. C. Merchant, S. S. Umen, J. G. 2021-09-20 doi:10.1101/2021.09.19.460975 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ Improved antibody structure prediction by deep learning of side chain conformations ]]> https://biorxiv.org/content/10.1101/2021.09.22.461349v1?rss=1 Akpinaroglu, D. Ruffolo, J. A. Mahajan, S. P. Gray, J. J. 2021-09-22 doi:10.1101/2021.09.22.461349 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea ]]> https://biorxiv.org/content/10.1101/2021.09.25.461819v1?rss=1 Chadwick, G. L. Skennerton, C. T. Laso-Perez, R. Leu, A. O. Speth, D. R. Yu, H. Morgan-Lang, C. Hatzenpichler, R. Goudeau, D. Malmstrom, R. Brazelton, W. J. Woyke, T. Hallam, S. J. Tyson, G. W. Wegener, G. Boetius, A. Orphan, V. J. 2021-09-26 doi:10.1101/2021.09.25.461819 Cold Spring Harbor Laboratory Press 2021-09-26 <![CDATA[ Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome ]]> https://biorxiv.org/content/10.1101/2021.09.27.462052v1?rss=1 Meyer, K. M. Porch, R. Muscettola, I. E. Vasconcelos, A. L. S. Sherman, J. K. Metcalf, C. J. E. Lindow, S. E. Koskella, B. 2021-09-29 doi:10.1101/2021.09.27.462052 Cold Spring Harbor Laboratory Press 2021-09-29 <![CDATA[ Variation in the response to malaria in Diversity Outbred mice ]]> https://biorxiv.org/content/10.1101/2021.09.29.462483v1?rss=1 Gupta, A. S. Chevee, V. Kirosingh, A. S. Davis, N. M. Schneider, D. S. 2021-09-30 doi:10.1101/2021.09.29.462483 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Induction of autotetraploidy and microbiome associations mediate differential responses to pathogens ]]> https://biorxiv.org/content/10.1101/2021.10.01.462589v1?rss=1 Mehlferber, E. C. Song, M. J. Pelaez, J. N. Jaenisch, J. Coate, J. E. Koskella, B. Rothfels, C. J. 2021-10-01 doi:10.1101/2021.10.01.462589 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Targeting ON-bipolar cells by AAV gene therapy stably reverses LRIT3-congenital stationary night blindness ]]> https://biorxiv.org/content/10.1101/2021.10.04.462588v1?rss=1 Miyadera, K. Santana, E. Roszak, K. Iffrig, S. Visel, M. Iwabe, S. Boyd, R. F. Bartoe, J. T. Sato, Y. Gray, A. Ripolles Garcia, A. Dufour, V. L. Byrne, L. C. Flannery, J. G. Beltran, W. A. Aguirre, G. D. 2021-10-04 doi:10.1101/2021.10.04.462588 Cold Spring Harbor Laboratory Press 2021-10-04 <![CDATA[ A mitochondrial electron transport chain with atypical subunit composition confers oxygen sensitivity to a mammalian chemoreceptor ]]> https://biorxiv.org/content/10.1101/2021.10.04.463079v1?rss=1 Timon-Gomez, A. Scharr, A. L. Wong, N. Y. Ni, E. Roy, A. Liu, M. Chau, J. Lampert, J. L. Hireed, H. Kim, N. S. Jan, M. Gupta, A. R. Day, R. W. Gardner, J. M. Wilson, R. J. Barrientos, A. Chang, A. J. 2021-10-05 doi:10.1101/2021.10.04.463079 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ Local conjugation of auxin by the GH3 amido synthetases is required for normaldevelopment of roots and flowers in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2021.10.04.463114v1?rss=1 Guo, R. Hu, Y. Aoi, Y. Hira, H. Ge, C. Dai, X. Kasahara, H. Zhao, Y. 2021-10-05 doi:10.1101/2021.10.04.463114 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ Boundary domain genes were recruited to suppress bract growth and promote branching in maize ]]> https://biorxiv.org/content/10.1101/2021.10.05.463134v1?rss=1 Xiao, Y. Guo, J. Dong, Z. Richardson, A. Patterson, E. Mangrum, S. Bybee, S. Bertolini, E. Bartlett, M. Chuck, G. Eveland, A. L. Scanlon, M. J. Whipple, C. 2021-10-05 doi:10.1101/2021.10.05.463134 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ Identification of a novel modulator of the actin cytoskeleton, mitochondria, nutrient metabolism and lifespan in yeast ]]> https://biorxiv.org/content/10.1101/2021.10.07.463535v1?rss=1 Sing, C. N. Garcia, E. J. Lipkin, T. Huckaba, T. Tsang, C. A. Coughlin, A. Yang, E. J. Boldogh, I. R. Higuchi-Sanabria, R. Pon, L. 2021-10-07 doi:10.1101/2021.10.07.463535 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ VIP interneurons in mouse whisker S1 exhibit sensory and action-related signals during goal-directed behavior ]]> https://biorxiv.org/content/10.1101/2021.10.08.463283v1?rss=1 Ramamurthy, D. L. Chen, A. Huang, P. C. Bharghavan, P. Krishna, G. Casale, K. Feldman, D. E. 2021-10-08 doi:10.1101/2021.10.08.463283 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ Mutagenesis-visualization: analysis of site saturation mutagenesis datasets in Python ]]> https://biorxiv.org/content/10.1101/2021.10.08.463725v1?rss=1 Hidalgo, F. Templeton, S. Olavaria Gallegos, C. Wang, J. 2021-10-09 doi:10.1101/2021.10.08.463725 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution ]]> https://biorxiv.org/content/10.1101/2021.10.12.464111v1?rss=1 Yang, D. Jones, M. G. Naranjo, S. Rideout, W. M. Min, K. H. J. Ho, R. Wu, W. Replogle, J. M. Page, J. L. Quinn, J. J. Horns, F. Qiu, X. Chen, M. Z. Freed-Pastor, W. A. McGinnis, C. S. Patterson, D. M. Gartner, Z. J. Chow, E. D. Bivona, T. G. Chan, M. M. Yosef, N. Jacks, T. Weissman, J. S. 2021-10-13 doi:10.1101/2021.10.12.464111 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman ]]> https://biorxiv.org/content/10.1101/2021.10.23.465204v1?rss=1 Petti, S. Bhattacharya, N. Rao, R. Dauparas, J. Thomas, N. Zhou, J. Rush, A. M. Koo, P. K. Ovchinnikov, S. 2021-10-24 doi:10.1101/2021.10.23.465204 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ Fast and parallel nanoscale 3D tracking of heterogeneous mammalian chromatin dynamics ]]> https://biorxiv.org/content/10.1101/2021.10.24.465625v1?rss=1 Gustavsson, A.-K. Ghosh, R. P. Petrov, P. N. Liphardt, J. T. Moerner, W. E. 2021-10-24 doi:10.1101/2021.10.24.465625 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ Hepatitis C Virus Infects and Perturbs Liver Stem Cells ]]> https://biorxiv.org/content/10.1101/2021.10.26.465357v1?rss=1 Meyers, N. L. Ashuach, T. Lyons, D. E. Simoneau, C. R. Erickson, A. L. Nguyen, T. T. Bouhaddou, M. Khalid, M. M. Taha, T. Y. Natarajan, V. Baron, J. L. Neff, N. Zanini, F. Mahmoudi, T. Quake, S. R. Krogan, N. J. Cooper, S. L. McDevitt, T. C. Yosef, N. Ott, M. 2021-10-26 doi:10.1101/2021.10.26.465357 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Estimating the Inter- and Intra-Rater Reliability for NASH Fibrosis Staging in the Presence of Bridge Ordinal Ratings with Hierarchical Bridge Category Models ]]> https://biorxiv.org/content/10.1101/2021.10.27.466144v1?rss=1 Levy, J. Bobak, C. Azizgolshani, N. Liu, X. Ren, B. Lisovsky, M. Suriawinata, A. Christensen, B. O'Malley, J. Vaickus, L. 2021-10-28 doi:10.1101/2021.10.27.466144 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Metacognition, cortical thickness, and tauopathy in aging ]]> https://biorxiv.org/content/10.1101/2021.10.27.466146v1?rss=1 Zhuang, K. Chen, X. Baker, S. L. Jagust, W. J. 2021-10-29 doi:10.1101/2021.10.27.466146 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Genetic features of persistently antimicrobial drug-susceptible extraintestinal pathogenic Escherichia coli pandemic sequence type 95 ]]> https://biorxiv.org/content/10.1101/2021.10.28.466352v1?rss=1 Allegretti, Y. H. Yamaji, R. Adams-Sapper, S. Riley, L. W. 2021-10-29 doi:10.1101/2021.10.28.466352 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Elevated Hoxb5b expands vagal neural crest pool and blocks enteric neuronal development in zebrafish ]]> https://biorxiv.org/content/10.1101/2021.10.28.466356v1?rss=1 Howard, A. G. A. Nguyen, A. C. Tworig, J. Ravisankar, P. Singleton, E. W. Li, C. Kotzur, G. Waxman, J. S. Uribe, R. A. 2021-10-29 doi:10.1101/2021.10.28.466356 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Diverse operant control of different motor cortex populations during learning ]]> https://biorxiv.org/content/10.1101/2021.10.29.466535v1?rss=1 Vendrell-Llopis, N. Fang, C. Qu, A. J. Costa, R. M. Carmena, J. M. 2021-11-02 doi:10.1101/2021.10.29.466535 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ A new tripartite landmark in posterior cingulate cortex ]]> https://biorxiv.org/content/10.1101/2021.10.30.466521v1?rss=1 Willbrand, E. H. Parker, B. J. Voorhies, W. I. Miller, J. A. Lyu, I. Hallock, T. Aponik-Gremillion, L. Bunge, S. Foster, B. L. Weiner, K. S. 2021-11-02 doi:10.1101/2021.10.30.466521 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Bacterial growth in multicellular aggregates leads to the emergence of complex lifecycles ]]> https://biorxiv.org/content/10.1101/2021.11.01.466752v1?rss=1 Schwartzman, J. A. Ebrahimi, A. Chadwick, G. Sato, Y. Orphan, V. Cordero, O. X. 2021-11-01 doi:10.1101/2021.11.01.466752 Cold Spring Harbor Laboratory Press 2021-11-01 <![CDATA[ Powerful synergistic effects of a STING agonist and an IL-2 superkine in cancer immunotherapy against MHC I-deficient and MHC I+ tumors ]]> https://biorxiv.org/content/10.1101/2021.11.02.465022v1?rss=1 Wolf, N. K. Blaj, C. Picton, L. Snyder, G. Zhang, L. Nicolai, C. J. Ndubaku, C. O. McWhirter, S. M. Garcia, K. C. Raulet, D. H. 2021-11-02 doi:10.1101/2021.11.02.465022 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells ]]> https://biorxiv.org/content/10.1101/2021.11.04.467237v1?rss=1 Lensch, S. Herschl, M. H. Ludwig, C. H. Sinha, J. Hinks, M. M. Mukund, A. Fujimori, T. Bintu, L. 2021-11-04 doi:10.1101/2021.11.04.467237 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Rapid ecological and evolutionary divergence during a poleward range expansion ]]> https://biorxiv.org/content/10.1101/2021.11.04.467261v1?rss=1 Sheffer, M. M. Zander, L. Schulze, B. Mouginot, P. Naef, T. Kreyling, J. Gillespie, R. G. Hoff, K. J. Prost, S. Krehenwinkel, H. Uhl, G. 2021-11-04 doi:10.1101/2021.11.04.467261 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Single-Cell Multiomics Defines Tolerogenic Extrathymic Aire-Expressing Populations with Unique Homology to Thymic Epithelium ]]> https://biorxiv.org/content/10.1101/2021.11.05.467513v1?rss=1 Wang, J. Lareau, C. A. Bautista, J. L. Gupta, A. R. Sandor, K. Germino, J. Yin, Y. Arvedson, M. P. Reeder, G. C. Cramer, N. T. Xie, F. Ntranos, V. Satpathy, A. T. Anderson, M. S. Gardner, J. M. 2021-11-06 doi:10.1101/2021.11.05.467513 Cold Spring Harbor Laboratory Press 2021-11-06 <![CDATA[ FLIP: Benchmark tasks in fitness landscape inference for proteins ]]> https://biorxiv.org/content/10.1101/2021.11.09.467890v1?rss=1 Dallago, C. Mou, J. Johnston, K. E. Wittmann, B. Bhattacharya, N. Goldman, S. L. Madani, A. Yang, K. K. 2021-11-11 doi:10.1101/2021.11.09.467890 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Transcriptomic plasticity and symbiont shuffling underpin Pocillopora acclimatization across heat-stress regimes in the Pacific Ocean ]]> https://biorxiv.org/content/10.1101/2021.11.12.468330v1?rss=1 Armstrong, E. J. Le-Hoang, J. Carradec, Q. Aury, J.-M. Noel, B. Poulain, J. Belser, C. Da Silva, C. Wincker, P. Tara Pacific Consortium, 2021-11-12 doi:10.1101/2021.11.12.468330 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ A Cryptic K48 Ubiquitin Chain Binding Site on UCH37 is Required for its Role in Proteasomal Degradation ]]> https://biorxiv.org/content/10.1101/2021.11.15.468727v1?rss=1 Du, J. Babik, S. Li, Y. Deol, K. K. Eyles, S. J. Fejzo, J. Tonelli, M. Strieter, E. 2021-11-15 doi:10.1101/2021.11.15.468727 Cold Spring Harbor Laboratory Press 2021-11-15 <![CDATA[ Complementary population codes in the dorsal and ventral hippocampus during associative learning ]]> https://biorxiv.org/content/10.1101/2021.11.16.468862v1?rss=1 Biane, J. S. Ladow, M. A. Stefanini, F. Boddu, S. P. Fan, A. Hassan, S. Dundar, N. Apodaca-Montano, D. L. Woods, N. I. Khierbek, M. A. 2021-11-18 doi:10.1101/2021.11.16.468862 Cold Spring Harbor Laboratory Press 2021-11-18 <![CDATA[ kTMP: A New Non-invasive Magnetic Induction Method to Modulate Cortical Excitability. ]]> https://biorxiv.org/content/10.1101/2021.11.17.465477v1?rss=1 Labruna, L. Merrick, C. Inglis, B. Ivry, R. B. Sheltraw, D. 2021-11-19 doi:10.1101/2021.11.17.465477 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Edaphic controls on genome size and GC content of bacteria in soil microbial communities ]]> https://biorxiv.org/content/10.1101/2021.11.17.469016v1?rss=1 Chuckran, P. F. Flagg, C. Propster, J. Rutherford, W. A. Sieradzki, E. T. Blazewicz, S. J. Hungate, B. A. Pett-Ridge, J. A. Schwartz, E. Dijkstra, P. 2021-11-19 doi:10.1101/2021.11.17.469016 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Awake ripples enhance emotional memory encoding in the human brain ]]> https://biorxiv.org/content/10.1101/2021.11.17.469047v1?rss=1 Zhang, H. Skelin, I. Ma, S. Paff, M. Yassa, M. A. Knight, R. T. Lin, J. J. 2021-11-19 doi:10.1101/2021.11.17.469047 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Joint estimation of selection intensity and mutation rate under balancing selection withapplications to HLA ]]> https://biorxiv.org/content/10.1101/2021.11.18.469194v1?rss=1 Slatkin, M. 2021-11-19 doi:10.1101/2021.11.18.469194 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ In vitro and in vivo CRISPR-Cas9 screens reveal drivers of aging in neural stem cells of the brain ]]> https://biorxiv.org/content/10.1101/2021.11.23.469762v1?rss=1 Ruetz, T. J. Kashiwagi, C. M. Morton, B. Yeo, R. W. Leeman, D. S. Morgens, D. W. Tsui, C. K. Li, A. Bassik, M. C. Brunet, A. 2021-11-23 doi:10.1101/2021.11.23.469762 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ Host Species is Linked to Pathogen Genotype for the Amphibian Chytrid Fungus (Batrachochytrium dendrobatidis) ]]> https://biorxiv.org/content/10.1101/2021.11.24.469827v1?rss=1 Byrne, A. Q. Waddle, A. W. Saenz, V. Ohmer, M. Jaeger, J. R. Richards-Zawacki, C. L. Voyles, J. Rosenblum, E. B. 2021-11-24 doi:10.1101/2021.11.24.469827 Cold Spring Harbor Laboratory Press 2021-11-24 <![CDATA[ The DOMINO web-server for active module identification analysis ]]> https://biorxiv.org/content/10.1101/2021.11.25.469692v1?rss=1 Levi, H. Rahmanian, N. Elkon, R. Shamir, R. 2021-11-25 doi:10.1101/2021.11.25.469692 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ Pontin/Reptin-associated complexes differentially impact plant development and viral pathology ]]> https://biorxiv.org/content/10.1101/2021.11.29.470430v1?rss=1 Chatterjee, S. Xu, M. Shemyakina, E. M. Brunkard, J. O. 2021-11-30 doi:10.1101/2021.11.29.470430 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Adolescent rats extend help to outgroup members, highlighting a neural network for group identity categorization. ]]> https://biorxiv.org/content/10.1101/2021.11.29.470434v1?rss=1 Breton, J. Eisner, J. S. Gandhi, V. S. Musick, N. Zhang, A. Long, K. L. P. Perloff, O. S. Hu, K. Y. Pham, C. M. Lalchandani, P. Barraza, M. K. Kantor, B. Kaufer, D. Ben-Ami Bartal, I. 2021-12-01 doi:10.1101/2021.11.29.470434 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Differential EDS1 requirement for cell death activities of plant TIR-domain proteins ]]> https://biorxiv.org/content/10.1101/2021.11.29.470438v1?rss=1 Lapin, D. Johanndrees, O. Baggs, E. Uhlmann, C. Locci, F. Laessle, H. L. Melkonian, K. Kaeufer, K. Dongus, J. A. Nakagami, H. Krasileva, K. V. Parker, J. E. 2021-11-30 doi:10.1101/2021.11.29.470438 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Structured connectivity in the cerebellum enables noise-resilient pattern separation ]]> https://biorxiv.org/content/10.1101/2021.11.29.470455v1?rss=1 Nguyen, T. M. Thomas, L. A. Rhoades, J. L. Ricchi, I. Yuan, X. C. Sheridan, A. Hildebrand, D. G. Funke, J. Regehr, W. G. Lee, W.-C. A. 2021-11-30 doi:10.1101/2021.11.29.470455 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ The Evolutionary Dynamics of Hyperparasites ]]> https://biorxiv.org/content/10.1101/2021.12.01.470853v1?rss=1 Northrup, G. R. Parratt, S. R. Rozins, C. Laine, A.-L. Boots, M. 2021-12-03 doi:10.1101/2021.12.01.470853 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ A Substrate-triggered μ-Peroxodiiron(III) Intermediate in the 4-Choro-L-Lysine-Fragmenting Heme-Oxygenase-like Diiron Oxidase (HDO) BesC: Substrate Dissociation from, and C4 Targeting by, the Intermediate ]]> https://biorxiv.org/content/10.1101/2021.12.02.471016v1?rss=1 McBride, M. J. Nair, M. A. Sil, D. Slater, J. W. Neugebauer, M. E. Chang, M. Boal, A. Krebs, C. Bollinger, J. M. 2021-12-03 doi:10.1101/2021.12.02.471016 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ Kinetic frustration by limited bond availability controls the LAT protein condensation phase transition on membranes ]]> https://biorxiv.org/content/10.1101/2021.12.05.471009v1?rss=1 Sun, S. GrandPre, T. Limmer, D. T. Groves, J. T. 2021-12-06 doi:10.1101/2021.12.05.471009 Cold Spring Harbor Laboratory Press 2021-12-06 <![CDATA[ Genetic conversion of a split-drive into a full-drive element ]]> https://biorxiv.org/content/10.1101/2021.12.05.471291v1?rss=1 Terradas, G. Bennett, J. B. Li, Z. Marshall, J. M. Bier, E. 2021-12-06 doi:10.1101/2021.12.05.471291 Cold Spring Harbor Laboratory Press 2021-12-06 <![CDATA[ The Omicron Variant Increases the Interactions of SARS-CoV-2 Spike Glycoprotein with ACE2 ]]> https://biorxiv.org/content/10.1101/2021.12.06.471377v1?rss=1 Golcuk, M. Yildiz, A. Gur, M. 2021-12-07 doi:10.1101/2021.12.06.471377 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Chlorine redox chemistry is not rare in biology ]]> https://biorxiv.org/content/10.1101/2021.12.08.471835v1?rss=1 Barnum, T. P. Coates, J. D. 2021-12-08 doi:10.1101/2021.12.08.471835 Cold Spring Harbor Laboratory Press 2021-12-08 <![CDATA[ Seeing the future: predictive control in neural models of ocular accommodation ]]> https://biorxiv.org/content/10.1101/2021.12.09.471909v1?rss=1 Read, J. C. A. Kaspiris-Rousellis, C. Wood, T. Wu, B. Vlaskamp, B. N. S. Schor, C. M. 2021-12-10 doi:10.1101/2021.12.09.471909 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ Nitrogen metabolism in Pseudomonas putida: functional analysis using random barcode transposon sequencing ]]> https://biorxiv.org/content/10.1101/2021.12.09.472016v1?rss=1 Schmidt, M. Pearson, A. N. Incha, M. R. Thompson, M. G. Baidoo, E. E. K. Kakumanu, R. Mukhopadhyay, A. Shih, P. M. Deutschbauer, A. M. Blank, L. M. Keasling, J. D. 2021-12-09 doi:10.1101/2021.12.09.472016 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Prolyl-hydroxylase inhibitor-induced regeneration of alveolar bone and soft tissue in a mouse model of ligature-induced periodontitis ]]> https://biorxiv.org/content/10.1101/2021.12.14.472623v1?rss=1 Zebrowitz, E. Kajikawa, T. Bedelbaeva, K. Bollinger, S. Zhang, Y. Sarfatti, D. Cheng, J. Messersmith, P. B. Hajishengallis, G. Heber-Katz, E. 2021-12-16 doi:10.1101/2021.12.14.472623 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Semantic representations during language comprehension are affected by context ]]> https://biorxiv.org/content/10.1101/2021.12.15.472839v1?rss=1 Deniz, F. Tseng, C. Wehbe, L. Gallant, J. L. 2021-12-16 doi:10.1101/2021.12.15.472839 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq ]]> https://biorxiv.org/content/10.1101/2021.12.16.473013v1?rss=1 2.5 million human cells and present a framework to power biological discovery with the resulting genotype-phenotype map. We use transcriptional phenotypes to predict the function of poorly-characterized genes, uncovering new regulators of ribosome biogenesis (including CCDC86, ZNF236, and SPATA5L1), transcription (C7orf26), and mitochondrial respiration (TMEM242). In addition to assigning gene function, single-cell transcriptional phenotypes allow for in-depth dissection of complex cellular phenomena - from RNA processing to differentiation. We leverage this ability to systematically identify the genetic drivers and consequences of aneuploidy and to discover an unanticipated layer of stress-specific regulation of the mitochondrial genome. Our information-rich genotype-phenotype map reveals a multidimensional portrait of gene function and cellular behavior. ]]> Replogle, J. M. Saunders, R. A. Pogson, A. N. Hussmann, J. A. Lenail, A. Guna, A. Mascibroda, L. Wagner, E. J. Adelman, K. Bonnar, J. L. Jost, M. Norman, T. M. Weissman, J. S. 2021-12-17 doi:10.1101/2021.12.16.473013 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ IFN-γ-independent control of M. tuberculosis requires CD4 T cell-derived GM-CSF and activation of HIF-1α ]]> https://biorxiv.org/content/10.1101/2021.12.16.473015v1?rss=1 Van Dis, E. Morrison, H. M. Fines, D. M. Babirye, J. P. McCann, L. H. Rawal, S. Cox, J. S. Stanley, S. A. 2021-12-16 doi:10.1101/2021.12.16.473015 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Well-Lit: A programmable and customizable assistant for manual multi-well plate pipetting ]]> https://biorxiv.org/content/10.1101/2021.12.17.473010v1?rss=1 Gomez-Sjöberg, R. Cabrera, J. P. Cote, A. 2021-12-20 doi:10.1101/2021.12.17.473010 Cold Spring Harbor Laboratory Press 2021-12-20 <![CDATA[ MicroRNA-like snoRNA-derived RNAs (sdRNAs) promote castration resistant prostate cancer ]]> https://biorxiv.org/content/10.1101/2021.12.17.473174v1?rss=1 Coley, A. B. Stahly, A. N. Kasukurthi, M. V. Barchie, A. A. Hutcheson, S. B. Houserova, D. Huang, Y. Watters, B. C. King, V. M. Dean, M. A. Roberts, J. T. DeMeis, J. D. McInnis, C. H. Godang, N. L. Wright, R. M. Haider, D. F. Piracha, N. B. Brown, C. L. Ijaz, Z. M. Li, S. Xi, Y. McDonald, O. G. Huang, J. Borchert, G. M. 2021-12-20 doi:10.1101/2021.12.17.473174 Cold Spring Harbor Laboratory Press 2021-12-20 <![CDATA[ Proprioceptive Re-alignment drives Implicit Sensorimotor Adaptation ]]> https://biorxiv.org/content/10.1101/2021.12.21.473747v1?rss=1 Tsay, J. S. Kim, H. E. Haith, A. M. Ivry, R. B. 2021-12-23 doi:10.1101/2021.12.21.473747 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Interplay between LHCSR proteins and state transitions governs the NPQ response in intact cells of Chlamydomonas during light fluctuations. ]]> https://biorxiv.org/content/10.1101/2021.12.31.474662v1?rss=1 Steen, C. Burlacot, A. Short, A. Niyogi, K. K. Fleming, G. 2022-01-02 doi:10.1101/2021.12.31.474662 Cold Spring Harbor Laboratory Press 2022-01-02 <![CDATA[ Low vision impairs implicit sensorimotor adaptation in response to small errors, but not large errors ]]> https://biorxiv.org/content/10.1101/2022.01.03.474829v1?rss=1 Tsay, J. S. Tan, S. Chu, M. Ivry, R. B. Cooper, E. A. 2022-01-04 doi:10.1101/2022.01.03.474829 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ Encoding of speech in convolutional layers and the brain stem based on language experience ]]> https://biorxiv.org/content/10.1101/2022.01.03.474864v1?rss=1 Begus, G. Zhou, A. Zhao, C. 2022-01-04 doi:10.1101/2022.01.03.474864 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ Redirecting RiPP biosynthetic enzymes to proteins and backbone-modified substrates ]]> https://biorxiv.org/content/10.1101/2022.01.05.475141v1?rss=1 Walker, J. A. Hamlish, N. Tytla, A. Brauer, D. D. Francis, M. B. Schepartz, A. 2022-01-06 doi:10.1101/2022.01.05.475141 Cold Spring Harbor Laboratory Press 2022-01-06 <![CDATA[ Validation that human microbiome phages use alternative genetic coding with TAG stop read as Q ]]> https://biorxiv.org/content/10.1101/2022.01.06.475225v1?rss=1 Peters, S. Borges, A. L. Giannone, R. J. Morowitz, M. Banfield, J. Hettich, R. 2022-01-06 doi:10.1101/2022.01.06.475225 Cold Spring Harbor Laboratory Press 2022-01-06 <![CDATA[ Predicting patient treatment response and resistance via single-cell transcriptomics of their tumors ]]> https://biorxiv.org/content/10.1101/2022.01.11.475728v1?rss=1 Sinha, S. vegesna, R. Dhruba, S. R. Wu, W. Kerr, D. L. Stroganov, O. V. Grishagin, I. Aldape, K. D. Blakely, C. M. Jiang, P. Thomas, C. J. Bivona, T. G. Schaffer, A. A. Ruppin, E. 2022-01-12 doi:10.1101/2022.01.11.475728 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ A Longitudinal Study of Dominant E. coli Lineages and Antimicrobial Resistance in the Gut of Children Living in an Upper Middle-income Country ]]> https://biorxiv.org/content/10.1101/2022.01.11.475974v1?rss=1 Trueba, G. Calderon, D. Cardenas, P. A. Prado, M. B. Graham, J. 2022-01-12 doi:10.1101/2022.01.11.475974 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Characterizing Potential Tetrodotoxin Resistance in Domain IV of the Voltage-Gated Sodium Channel Nav1.4 of Pacific Chorus Frogs, Pseudacris regilla ]]> https://biorxiv.org/content/10.1101/2022.01.22.475505v1?rss=1 Montana, K. O. Ramirez Castaneda, V. Tarvin, R. D. 2022-01-23 doi:10.1101/2022.01.22.475505 Cold Spring Harbor Laboratory Press 2022-01-23 <![CDATA[ Crystal structure of an RNA/DNA strand exchange junction ]]> https://biorxiv.org/content/10.1101/2022.01.24.477483v1?rss=1 Cofsky, J. C. Knott, G. J. Gee, C. L. Doudna, J. A. 2022-01-24 doi:10.1101/2022.01.24.477483 Cold Spring Harbor Laboratory Press 2022-01-24 <![CDATA[ Human sialomucin CD164 is an essential entry factor for lymphocytic choriomeningitis virus ]]> https://biorxiv.org/content/10.1101/2022.01.24.477570v1?rss=1 Liu, J. Knopp, K. A. Rackaityte, E. Wang, C. Y. Laurie, M. T. Sunshine, S. Puschnik, A. S. DeRisi, J. 2022-01-25 doi:10.1101/2022.01.24.477570 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ A high-throughput approach to identify reproductive toxicants among environmental chemicals using an in vivo evaluation of gametogenesis in budding yeast Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2022.01.25.477777v1?rss=1 Kumar, R. Oke, A. Rockmill, B. de Cruz, M. Verduzco, R. Madeira, X. W. Abrahamsson, D. Robinson, J. Allard, P. Woodruff, T. Fung, J. 2022-01-28 doi:10.1101/2022.01.25.477777 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ An Archaea-Specific c-type Cytochrome Maturation Machinery is Crucial for Methanogenesis in Methanosarcina acetivorans ]]> https://biorxiv.org/content/10.1101/2022.01.26.477811v1?rss=1 Nayak, D. D. Gupta, D. Shalvarjian, K. E. 2022-01-26 doi:10.1101/2022.01.26.477811 Cold Spring Harbor Laboratory Press 2022-01-26 <![CDATA[ Identifying systematic variation at the single-cell level by leveraging low-resolution population-level data ]]> https://biorxiv.org/content/10.1101/2022.01.27.478115v1?rss=1 Rahmani, E. Jordan, M. I. Yosef, N. 2022-01-28 doi:10.1101/2022.01.27.478115 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ A widespread group of large plasmids in methanotrophic Methanoperedens archaea ]]> https://biorxiv.org/content/10.1101/2022.02.01.478723v1?rss=1 Schoelmerich, M. C. Ouboter, H. T. Sachdeva, R. Penev, P. Amano, Y. West-Roberts, J. A. Welte, C. U. Banfield, J. F. 2022-02-01 doi:10.1101/2022.02.01.478723 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ SKN-1 is a metabolic surveillance factor that monitors amino acid catabolism to control stress resistance ]]> https://biorxiv.org/content/10.1101/2022.02.03.479044v1?rss=1 Frankino, P. A. Siddiqi, T. F. Bolas, T. Bar-Ziv, R. Gildea, H. K. Zhang, H. Higuchi-Sanabria, R. Dillin, A. 2022-02-03 doi:10.1101/2022.02.03.479044 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Substrate topology and cognate immunity modulate antibacterial toxicity of Tae cell wall hydrolases ]]> https://biorxiv.org/content/10.1101/2022.02.15.480620v1?rss=1 Radkov, A. Sapiro, A. Flores, S. Henderson, C. Saunders, H. Kim, R. Massa, S. Thompson, S. Mateusiak, C. Biboy, J. Zhao, Z. Starita, L. M. Hatleberg, W. Vollmer, W. Russell, A. B. Simorre, J.-P. Anthony-Cahill, S. Brzovic, P. Hayes, B. Chou, S. 2022-02-16 doi:10.1101/2022.02.15.480620 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ Randomized gates eliminate bias in sort-seq assays ]]> https://biorxiv.org/content/10.1101/2022.02.17.480881v1?rss=1 Trippe, B. L. Huang, B. DeBenedictis, E. A. Coventry, B. Bhattacharya, N. Yang, K. K. Baker, D. Crawford, L. 2022-02-19 doi:10.1101/2022.02.17.480881 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Self-organization of songbird neural sequences during social isolation ]]> https://biorxiv.org/content/10.1101/2022.02.18.480996v1?rss=1 Mackevicius, E. L. Gu, S. Denisenko, N. Fee, M. 2022-02-18 doi:10.1101/2022.02.18.480996 Cold Spring Harbor Laboratory Press 2022-02-18 <![CDATA[ Data-Driven Flow-Map Models for Data-Efficient Discovery of Dynamics and Fast Uncertainty Quantification of Biological and Biochemical Systems ]]> https://biorxiv.org/content/10.1101/2022.02.19.481146v1?rss=1 Makrygiorgos, G. Berliner, A. J. Shi, F. Clark, D. S. Arkin, A. P. Mesbah, A. 2022-02-22 doi:10.1101/2022.02.19.481146 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Tyrosine phosphorylation of mitofusin 2 regulates endoplasmic reticulum-mitochondria tethering ]]> https://biorxiv.org/content/10.1101/2022.02.21.481295v1?rss=1 Zhang, P. Ford, K. Sung, J. H. Moeller, J. Suzuki, Y. Polina, I. Tachibana, T. Kusakari, Y. Cypress, M. W. Chaput, I. Drenkova, K. Landherr, M. Adaniya, S. M. Mishra, J. Mende, U. Jhun, B. S. O-Uchi, J. 2022-02-21 doi:10.1101/2022.02.21.481295 Cold Spring Harbor Laboratory Press 2022-02-21 <![CDATA[ Coursing hyenas and stalking lions: the potential for inter- and intraspecific interactions ]]> https://biorxiv.org/content/10.1101/2022.02.23.481665v1?rss=1 Barker, N. A. Joubert, F. G. Kasaona, M. Shatumbu, G. Stowbunenko, V. Alexander, K. A. Slotow, R. Getz, W. M. 2022-02-24 doi:10.1101/2022.02.23.481665 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ FtsH Protease Inactivation Allows Accumulation of Aberrant Photosystem II in a Chlamydomonas Rubredoxin Mutant ]]> https://biorxiv.org/content/10.1101/2022.02.24.481860v1?rss=1 Calderon, R. H. de Vitry, C. Wollman, F.-A. Niyogi, K. K. 2022-02-26 doi:10.1101/2022.02.24.481860 Cold Spring Harbor Laboratory Press 2022-02-26 <![CDATA[ Construction of a constitutively active type III secretion system for heterologous protein secretion ]]> https://biorxiv.org/content/10.1101/2022.02.24.481905v1?rss=1 Liang, J. M. Burdette, L. A. Wong, H. T. Tullman-Ercek, D. 2022-02-25 doi:10.1101/2022.02.24.481905 Cold Spring Harbor Laboratory Press 2022-02-25 <![CDATA[ Orthogonal synthetases for polyketide precursors ]]> https://biorxiv.org/content/10.1101/2022.02.28.482149v1?rss=1 Schepartz, A. Fricke, R. Swenson, C. Roe, L. T. Hamlish, N. Ad, O. Smaga, S. Gee, C. L. 2022-03-01 doi:10.1101/2022.02.28.482149 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Reconstructing the ancestral vertebrate brain using a lamprey neural cell type atlas ]]> https://biorxiv.org/content/10.1101/2022.02.28.482278v1?rss=1 Lamanna, F. Hervas-Sotomayor, F. Oel, A. P. Jandzik, D. Sobrido-Camean, D. Martik, M. L. Green, S. A. Brüning, T. Mössinger, K. Schmidt, J. Schneider, C. Sepp, M. Murat, F. Smith, J. J. Bronner, M. E. Rodicio, M. C. Barreiro-Iglesias, A. Meulemans Medeiros, D. Arendt, D. Kaessmann, H. 2022-03-01 doi:10.1101/2022.02.28.482278 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Individually unique, fixed body patterns of Octopus chierchiae allow for photo-identification in long-term studies ]]> https://biorxiv.org/content/10.1101/2022.03.01.482473v1?rss=1 Liu, B. Song, L. Kelkar, S. Ramji, A. Caldwell, R. 2022-03-01 doi:10.1101/2022.03.01.482473 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Neovascularization and the recruitment of CD31+ cells from the bone marrow are unique under regenerative but not wound repair conditions ]]> https://biorxiv.org/content/10.1101/2022.03.02.482660v1?rss=1 Bedelbaevak, K. Zhang, Y. Azlanukov, A. Gourevitch, D. V. Strehin, I. Messersmith, P. Heber-Katz, E. 2022-03-04 doi:10.1101/2022.03.02.482660 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Mouse Genomic Associations with Ex Vivo Sensitivity to Simulated Space Radiation ]]> https://biorxiv.org/content/10.1101/2022.03.03.482929v1?rss=1 Cekanaviciute, E. Tran, D. Nguyen, H. Lopez Macha, A. Pariset, E. Langley, S. Babbi, G. Malkani, S. Penninckx, S. Schisler, J. C. Tin, N. Karpen, G. Costes, S. V. 2022-03-05 doi:10.1101/2022.03.03.482929 Cold Spring Harbor Laboratory Press 2022-03-05 <![CDATA[ Estimating spatially variable and density-dependent survival using open-population spatial capture-recapture models ]]> https://biorxiv.org/content/10.1101/2022.03.04.482982v1?rss=1 Milleret, C. Dey, S. Dupont, P. Turek, D. de Valpine, P. Bischof, R. 2022-03-06 doi:10.1101/2022.03.04.482982 Cold Spring Harbor Laboratory Press 2022-03-06 <![CDATA[ Mycorrhizal fungi stabilize bacterial growth and diversity in water-limited soils ]]> https://biorxiv.org/content/10.1101/2022.03.05.483112v1?rss=1 Hestrin, R. Kan, M. Lafler, M. Wollard, J. Kimbrel, J. Ray, P. Blazewicz, S. J. Stuart, R. Craven, K. D. Firestone, M. K. Nuccio, E. E. Pett-Ridge, J. 2022-03-07 doi:10.1101/2022.03.05.483112 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Do lanthanide-dependent microbial metabolisms drive the release of REEs from weathered granites? ]]> https://biorxiv.org/content/10.1101/2022.03.08.483559v1?rss=1 Voutsinos, M. Y. West-Roberts, J. A. Sachdeva, R. Moreau, J. W. Banfield, J. F. 2022-03-09 doi:10.1101/2022.03.08.483559 Cold Spring Harbor Laboratory Press 2022-03-09 <![CDATA[ Implicit sensorimotor adaptation is preserved in Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2022.03.11.484047v1?rss=1 Tsay, J. S. Najafi, T. Schuck, L. Wang, T. Ivry, R. B. 2022-03-14 doi:10.1101/2022.03.11.484047 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Comprehensive phylogenomics of Methylobacterium reveals four evolutionary distinct groups and underappreciated phyllosphere diversity. ]]> https://biorxiv.org/content/10.1101/2022.03.12.484109v1?rss=1 Leducq, J.-B. Sneddon, D. Santos, M. Condrain-Morel, D. Bourret, G. Martinez-Gomez, N. C. Lee, J. A. Foster, J. A. Shapiro, B. J. Kembel, S. W. Sullivan, J. Marx, C. J. 2022-03-13 doi:10.1101/2022.03.12.484109 Cold Spring Harbor Laboratory Press 2022-03-13 <![CDATA[ Evidence-based calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for clinical use of PP3/BP4 criteria ]]> https://biorxiv.org/content/10.1101/2022.03.17.484479v1?rss=1 Pejaver, V. Byrne, A. B. Feng, B.-J. Pagel, K. A. Mooney, S. D. Karchin, R. O'Donnell-Luria, A. Harrison, S. M. Tavtigian, S. V. Greenblatt, M. S. Biesecker, L. G. Radivojac, P. Brenner, S. E. ClinGen Sequence Variant Interpretation Working Group, 2022-03-19 doi:10.1101/2022.03.17.484479 Cold Spring Harbor Laboratory Press 2022-03-19 <![CDATA[ Sparse coding models predict a spectral bias in the development of primary visual cortex (V1) receptive fields ]]> https://biorxiv.org/content/10.1101/2022.03.17.484705v1?rss=1 Ligeralde, A. DeWeese, M. 2022-03-19 doi:10.1101/2022.03.17.484705 Cold Spring Harbor Laboratory Press 2022-03-19 <![CDATA[ Coenzyme Q regulates UCP1 expression and thermogenesis through the integrated stress responses ]]> https://biorxiv.org/content/10.1101/2022.03.18.484957v1?rss=1 Chang, C.-F. Gunawan, A. L. Zushin, P.-J. H. Timblin, G. A. Bertholet, A. M. Wang, B. Saijo, K. Kirichok, Y. Stahl, A. 2022-03-19 doi:10.1101/2022.03.18.484957 Cold Spring Harbor Laboratory Press 2022-03-19 <![CDATA[ Liguleless narrow and narrow odd dwarf act in overlapping pathways to regulate maize development & physiology ]]> https://biorxiv.org/content/10.1101/2022.03.20.485070v1?rss=1 Abraham-Juarez, M. J. Busche, M. Anderson, A. A. Lunde, C. Winders, J. Christensen, S. A. Hunter, C. T. Hake, S. Brunkard, J. O. 2022-03-21 doi:10.1101/2022.03.20.485070 Cold Spring Harbor Laboratory Press 2022-03-21 <![CDATA[ An E3 ligase network engages GCN1 to promote elongation factor-1α degradation on stalled ribosomes ]]> https://biorxiv.org/content/10.1101/2022.03.21.485216v1?rss=1 Oltion, K. Carelli, J. D. Yang, T. See, S. K. Wang, H.-Y. Kampmann, M. Taunton, J. 2022-03-22 doi:10.1101/2022.03.21.485216 Cold Spring Harbor Laboratory Press 2022-03-22 <![CDATA[ Distinct gene programs underpinning 'disease tolerance' and 'resistance' in influenza virus infection ]]> https://biorxiv.org/content/10.1101/2022.03.22.485254v1?rss=1 Cohn, O. Yankovitz, G. Peshes-Yaloz, N. Steuerman, Y. Frishberg, A. Brandes, R. Mandelboim, M. R. Hamilton, J. Hagai, T. Amit, I. G. Netea, M. Hacohen, N. A. Iraqi, F. Bacharach, E. Gat-Viks, I. 2022-03-22 doi:10.1101/2022.03.22.485254 Cold Spring Harbor Laboratory Press 2022-03-22 <![CDATA[ From neural border to migratory stage: A comprehensive single cell roadmap of the timing and regulatory logic driving cranial and vagal neural crest emergence ]]> https://biorxiv.org/content/10.1101/2022.03.23.485460v1?rss=1 Kotov, A. Alkobtawi, M. Seal, S. Kappes, V. Medina Ruiz, S. Arbes, H. Harland, R. Peshkin, L. Monsoro-Burq, A. H. 2022-03-23 doi:10.1101/2022.03.23.485460 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ RNA-targeting CRISPR-Cas13 Provides Broad-spectrum Phage Immunity ]]> https://biorxiv.org/content/10.1101/2022.03.25.485874v1?rss=1 Adler, B. A. Hessler, T. Cress, B. F. Mutalik, V. K. Barrangou, R. K. Banfield, J. Doudna, J. A. 2022-03-26 doi:10.1101/2022.03.25.485874 Cold Spring Harbor Laboratory Press 2022-03-26 <![CDATA[ Endothelial Caspase-9 Promotes Glial Changes, Inflammation, and Contrast Sensitivity Decline in Retinal Vascular Injury ]]> https://biorxiv.org/content/10.1101/2022.03.30.486450v1?rss=1 Ortiz, C. C. Neal, A. Avrutsky, M. Choi, M. Smart, J. Lawson, J. Troy, C. M. 2022-03-30 doi:10.1101/2022.03.30.486450 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes ]]> https://biorxiv.org/content/10.1101/2022.03.30.486478v1?rss=1 Merrill, B. D. Carter, M. M. Olm, M. R. Dahan, D. Tripathi, S. Spencer, S. P. Yu, F. B. Jain, S. Neff, N. Jha, A. R. Sonnenburg, E. D. Sonnenburg, J. L. 2022-03-31 doi:10.1101/2022.03.30.486478 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ Temporal and Spatial Resolution of a Protein Quake that Activates Hydrogen Tunneling in Soybean Lipoxygenase ]]> https://biorxiv.org/content/10.1101/2022.03.31.486235v1?rss=1 Zaragoza, J. P. Offenbacher, A. R. Hu, S. Gee, C. L. Firestein, Z. M. Minnetian, N. Deng, Z. Fan, F. Iavarone, A. T. Klinman, J. P. 2022-04-01 doi:10.1101/2022.03.31.486235 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Death-seq identifies regulators of cell death and senolytic therapies ]]> https://biorxiv.org/content/10.1101/2022.04.01.486768v1?rss=1 Colville, A. Liu, J.-Y. Thomas, S. Ishak, H. D. Zhou, R. Klein, J. D. D. Morgens, D. W. Goshayeshi, A. Salvi, J. S. Yao, D. Spees, K. Bassik, M. C. Rando, T. A. 2022-04-03 doi:10.1101/2022.04.01.486768 Cold Spring Harbor Laboratory Press 2022-04-03 <![CDATA[ NSMCE2, a Novel Super-Enhancer Regulated Gene, is Linked to Poor Prognosis and Therapy Resistance in Breast Cancer ]]> https://biorxiv.org/content/10.1101/2022.04.01.486781v1?rss=1 Di Benedetto, C. Oh, J. Choidhery, Z. Shi, W. Valdes, G. Betancur, P. 2022-04-03 doi:10.1101/2022.04.01.486781 Cold Spring Harbor Laboratory Press 2022-04-03 <![CDATA[ In Utero Activation of NK Cells in Congenital CMV Infection ]]> https://biorxiv.org/content/10.1101/2022.04.04.487059v1?rss=1 Vaaben, A. V. Levan, J. Nguyen, C. B. T. Callaway, P. C. Prahl, M. Warrier, L. Nankya, F. Musinguzi, K. Kakuru, A. Muhindo, M. K. Dorsey, G. Kamya, M. R. Feeney, M. E. 2022-04-05 doi:10.1101/2022.04.04.487059 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Impact of temperature and time on DNA-free Cas9-ribonucleoprotein mediated gene editing in wheat protoplasts and immature embryos ]]> https://biorxiv.org/content/10.1101/2022.04.05.487229v1?rss=1 Poddar, S. Tanaka, J. Running, K. L. D. Kariyawasam, G. K. Faris, J. Friesen, T. Cho, M.-J. Cate, J. H. Staskawicz, B. 2022-04-06 doi:10.1101/2022.04.05.487229 Cold Spring Harbor Laboratory Press 2022-04-06 <![CDATA[ Cryo-EM reveals a mechanism of USP1 inhibition through a cryptic binding site ]]> https://biorxiv.org/content/10.1101/2022.04.06.487267v1?rss=1 Rennie, M. L. Arkinson, C. Chaugule, V. K. Walden, H. 2022-04-06 doi:10.1101/2022.04.06.487267 Cold Spring Harbor Laboratory Press 2022-04-06 <![CDATA[ SOX9 binds TCFs to mediate Wnt/β catenin target gene activation ]]> https://biorxiv.org/content/10.1101/2022.04.06.487337v1?rss=1 Ramakrishnan, A.-B. Burby, P. E. Adiga, K. Cadigan, K. M. 2022-04-08 doi:10.1101/2022.04.06.487337 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ A Spiking Neural Network Model for the Control of Oscillatory Phase Differences Between Multiple Brain Areas ]]> https://biorxiv.org/content/10.1101/2022.04.08.487667v1?rss=1 Canolty, R. T. Stimberg, M. T. 2022-04-10 doi:10.1101/2022.04.08.487667 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Radioactive Contamination in Feral Dogs in the Chernobyl Exclusion Zone: Population Body-Burden Survey and Implications for Human Radiation Exposure ]]> https://biorxiv.org/content/10.1101/2022.04.12.487820v1?rss=1 Hecla, J. Kambarian, E. Tubbs, R. McKinley, C. Berliner, A. J. Russell, K. Spatola, G. Chertok, J. Braun, W. Hank, N. Marquette, C. Betz, J. Paik, T. Chenery, M. Cagan, A. Willis, C. Mousseau, T. 2022-04-13 doi:10.1101/2022.04.12.487820 Cold Spring Harbor Laboratory Press 2022-04-13 <![CDATA[ Causal contributions of the domain-general (Multiple Demand) and the language-selective brain networks to perceptual and semantic challenges in speech comprehension ]]> https://biorxiv.org/content/10.1101/2022.04.12.487989v1?rss=1 MacGregor, L. J. Gilbert, R. A. Balewski, Z. Mitchell, D. J. Erzinclioglu, S. W. Rodd, J. M. Duncan, J. Fedorenko, E. Davis, M. H. 2022-04-12 doi:10.1101/2022.04.12.487989 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ Is It A Barrel? General Features of Transmembrane Beta Barrels from a Large Database ]]> https://biorxiv.org/content/10.1101/2022.04.13.488089v1?rss=1 240,000 unrelated to previously structurally-resolved OMPs. We identify ten types of OMPs in our database. The largest types signal sequence--used for targeting the membrane-insertion machinery--varies by phylogenetic class. All other types of OMPs do not have a related signal sequence, raising new questions of how these proteins fold. Our web-accessible database will allow for further exploration of the varieties of outer membrane proteins to uncover new targets for controlling antibiotic resistance. ]]> Montezano, D. Bernstein, R. Copeland, M. Slusky, J. S. 2022-04-13 doi:10.1101/2022.04.13.488089 Cold Spring Harbor Laboratory Press 2022-04-13 <![CDATA[ Dcifer: an IBD-based method to calculate genetic distance between polyclonal infections ]]> https://biorxiv.org/content/10.1101/2022.04.14.488406v1?rss=1 Gerlovina, I. Gerlovin, B. Rodriguez-Barraquer, I. Greenhouse, B. 2022-04-15 doi:10.1101/2022.04.14.488406 Cold Spring Harbor Laboratory Press 2022-04-15 <![CDATA[ Early dosage compensation of zygotically-expressed genes in Drosophila melanogaster is mediated through a post-transcriptional regulatory mechanism ]]> https://biorxiv.org/content/10.1101/2022.04.25.489409v1?rss=1 Blake, V. M. Eisen, M. 2022-04-26 doi:10.1101/2022.04.25.489409 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ Geographic Name Resolution Service: A tool for the standardization and indexing of world political division names, with applications to species distribution modeling ]]> https://biorxiv.org/content/10.1101/2022.04.25.489424v1?rss=1 270 million species occurrences, only 1.9%, representing just 6% of occurrences, matched exactly to GADM political divisions in their original form. The GNRS was able to resolve, completely or in part, 92% of the remaining 378,568 political division names, or 86% of the full biodiversity occurrence dataset. In an assessment of geocoordinate accuracy for >239 million species occurrences, resolution of political divisions by the GNRS enabled detection of an order of magnitude more errors and an order of magnitude more error-free occurrences. By providing a novel solution to a major data quality impediment, the GNRS liberates a tremendous amount of biodiversity data for quantitative biodiversity research. The GNRS runs as a web service and can be accessed via an API, an R package, and a web-based graphical user interface. Its modular architecture is easily integrated into existing data validation workflows. ]]> Boyle, B. L. Maitner, B. S. Barbosa, G. G. C. Sajja, R. K. Feng, X. Merow, C. Newman, E. A. Park, D. S. Roehrdanz, P. R. Enquist, B. J. 2022-04-25 doi:10.1101/2022.04.25.489424 Cold Spring Harbor Laboratory Press 2022-04-25 <![CDATA[ A Feed-forward Pathway Drives LRRK2 kinaseMembrane Recruitment and Apparent Activation ]]> https://biorxiv.org/content/10.1101/2022.04.25.489459v1?rss=1 Vides, E. G. Adhikari, A. Lis, P. Purlyte, E. Shumate, J. L. Lasso, E. S. Dhekne, H. S. Alessi, D. R. Pfeffer, S. R. 2022-04-25 doi:10.1101/2022.04.25.489459 Cold Spring Harbor Laboratory Press 2022-04-25 <![CDATA[ Relative abundance data can misrepresent heritability of the microbiome ]]> https://biorxiv.org/content/10.1101/2022.04.26.489345v1?rss=1 Bruijning, M. Ayroles, J. F. Henry, L. P. Koskella, B. Meyer, K. M. Metcalf, C. J. E. 2022-04-26 doi:10.1101/2022.04.26.489345 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ A fast machine-learning-guided primer design pipeline for selective whole genome amplification ]]> https://biorxiv.org/content/10.1101/2022.04.27.489632v1?rss=1 Yu, J. A. Oppler, Z. J. Mitchell, M. W. Song, Y. S. Brisson, D. 2022-04-28 doi:10.1101/2022.04.27.489632 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Minimal functional domains of the core polarity regulator Dlg ]]> https://biorxiv.org/content/10.1101/2022.04.29.490107v1?rss=1 Khoury, M. J. Bilder, D. 2022-05-02 doi:10.1101/2022.04.29.490107 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Quantitative stable-isotope probing (qSIP) with metagenomics links microbial physiology and activity to soil moisture in Mediterranean-climate grassland ecosystems ]]> https://biorxiv.org/content/10.1101/2022.05.02.490339v1?rss=1 Greenlon, A. Sieradzki, E. T. Zablocki, O. Koch, B. J. Foley, M. M. Kimbrel, J. A. Hungate, B. A. Blazewicz, S. J. Nuccio, E. E. Sun, C. L. Chew, A. Mancilla, C.-J. Sullivan, M. B. Firestone, M. K. Pett-Ridge, J. Banfield, J. F. 2022-05-02 doi:10.1101/2022.05.02.490339 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Quantification of cell penetrating peptide mediated delivery of proteins in plant leaves ]]> https://biorxiv.org/content/10.1101/2022.05.03.490515v1?rss=1 Wang, J. W.-T. Goh, N. S.-Y. Lien, E. S. Gonzalez-Grandio, E. Landry, M. P. 2022-05-04 doi:10.1101/2022.05.03.490515 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Membrane curvature sensing and stabilization by the autophagic LC3 lipidation machinery ]]> https://biorxiv.org/content/10.1101/2022.05.03.490522v1?rss=1 Jensen, L. E. Rao, S. Schuschnig, M. Cada, A. K. Martens, S. Hummer, G. Hurley, J. H. 2022-05-04 doi:10.1101/2022.05.03.490522 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ A synthetic tear protein resolves dry eye through promoting corneal nerve regeneration. ]]> https://biorxiv.org/content/10.1101/2022.05.07.491018v1?rss=1 Efraim, Y. Chen, F. Y. T. Cheong, K. N. Gaylord, E. A. McNamara, N. A. Knox, S. M. 2022-05-07 doi:10.1101/2022.05.07.491018 Cold Spring Harbor Laboratory Press 2022-05-07 <![CDATA[ Multimodal disease transmission as a limiting factor for the spatial extent of a host plant ]]> https://biorxiv.org/content/10.1101/2022.05.11.491512v1?rss=1 Uricchio, L. H. Bruns, E. Hood, M. Boots, M. Antonovics, J. 2022-05-11 doi:10.1101/2022.05.11.491512 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Systemic coagulopathy drives host lethality in a new Drosophila tumor model ]]> https://biorxiv.org/content/10.1101/2022.05.11.491522v1?rss=1 Hsi, T.-C. Ong, K. Sepers, J. J. Kim, J. Bilder, D. 2022-05-11 doi:10.1101/2022.05.11.491522 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ AGS3 antagonizes LGN to balance oriented cell divisions and cell fate choices in mammalian epidermis ]]> https://biorxiv.org/content/10.1101/2022.05.20.492864v1?rss=1 Descovich, C. P. Lough, K. J. Jena, A. Wu, J. J. Yom, J. Spitzer, D. C. Uppalapati, M. Kedziora, K. M. Williams, S. E. 2022-05-20 doi:10.1101/2022.05.20.492864 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Oncogenic KRAS alters splicing factor phosphorylation and alternative splicing in lung cancer ]]> https://biorxiv.org/content/10.1101/2022.05.20.492866v1?rss=1 Lo, A. McSharry, M. Berger, A. 2022-05-20 doi:10.1101/2022.05.20.492866 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Rates and spectra of de novo structural mutation in Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2022.05.23.493040v1?rss=1 Lopez-Cortegano, E. Craig, R. Chebib, J. Balogun, E. J. Keightley, P. D. 2022-05-23 doi:10.1101/2022.05.23.493040 Cold Spring Harbor Laboratory Press 2022-05-23 <![CDATA[ Multiplexed microfluidic platform for stem-cell derived pancreatic islet β cells ]]> https://biorxiv.org/content/10.1101/2022.05.23.493153v1?rss=1 Goswami, I. de Klerk, E. Carnese, P. Hebrok, M. Healy, K. 2022-05-23 doi:10.1101/2022.05.23.493153 Cold Spring Harbor Laboratory Press 2022-05-23 <![CDATA[ Impact of Shelterin Complex on Telomere Accessibility ]]> https://biorxiv.org/content/10.1101/2022.05.24.493289v1?rss=1 Shiekh, S. Jack, A. Mustafa, G. Kodikara, S. G. Gyawali, P. Hoque, M. E. Yildiz, A. Balci, H. 2022-05-25 doi:10.1101/2022.05.24.493289 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Short tandem repeats bind transcription factors to tune eukaryotic gene expression ]]> https://biorxiv.org/content/10.1101/2022.05.24.493321v1?rss=1 Horton, C. A. Alexandari, A. M. Hayes, M. G. B. Marklund, E. Schaepe, J. M. Aditham, A. K. Shah, N. Shrikumar, A. A. Afek, A. Greenleaf, W. J. Gordan, R. Zeitlinger, J. Kundaje, A. Fordyce, P. M. 2022-05-25 doi:10.1101/2022.05.24.493321 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ IDPConformerGenerator: A Flexible Software Suite for Sampling Conformational Space of Disordered Protein States ]]> https://biorxiv.org/content/10.1101/2022.05.28.493726v1?rss=1 Teixeira, J. M. C. Liu, Z. H. Namini, A. Li, J. Vernon, R. M. Krzeminski, M. Shamandy, A. A. Zhang, O. Haghighatlari, M. Yu, L. Head-Gordon, T. Forman-Kay, J. D. 2022-05-29 doi:10.1101/2022.05.28.493726 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Uncovering Hidden Enhancers Through Unbiased In Vivo Testing ]]> https://biorxiv.org/content/10.1101/2022.05.29.493901v1?rss=1 Mannion, B. J. Osterwalder, M. Tran, S. Plajzer-Frick, I. Novak, C. S. Afzal, V. Akiyama, J. A. Barton, S. Beckman, E. Garvin, T. H. Godfrey, P. Godoy, J. Hunter, R. D. Kato, M. Kosicki, M. Kronshage, A. H. Lee, E. A. Meky, E. M. Pham, Q. T. von Maydell, K. Zhu, Y. Lopez-Rios, J. Dickel, D. E. Visel, A. Pennacchio, L. A. 2022-05-30 doi:10.1101/2022.05.29.493901 Cold Spring Harbor Laboratory Press 2022-05-30 <![CDATA[ The Effect of Perturbation Variability on Sensorimotor Adaptation Does Not Require an Implicit Memory of Errors ]]> https://biorxiv.org/content/10.1101/2022.05.30.493844v1?rss=1 Wang, T. Avraham, G. Tsay, J. Ivry, R. 2022-05-31 doi:10.1101/2022.05.30.493844 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ MEBOCOST: Metabolic Cell-Cell Communication Modeling by Single Cell Transcriptome ]]> https://biorxiv.org/content/10.1101/2022.05.30.494067v1?rss=1 Zheng, R. Zhang, Y. Tsuji, T. Zhang, L. Tseng, Y.-H. Chen, K. 2022-05-31 doi:10.1101/2022.05.30.494067 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Towards generalizable prediction of antibody thermostability using machine learning on sequence and structure features ]]> https://biorxiv.org/content/10.1101/2022.06.03.494724v1?rss=1 Harmalkar, A. Rao, R. M. Honer, J. Deisting, W. Anlahr, J. Hoenig, A. Czwikla, J. Sienz-Widmann, E. Rau, D. Rice, A. Riley, T. P. Li, D. Catterall, H. B. Tinberg, C. E. Gray, J. J. Wei, K. Y. 2022-06-04 doi:10.1101/2022.06.03.494724 Cold Spring Harbor Laboratory Press 2022-06-04 <![CDATA[ Arabidopsis MLO4 Functions as a Ca2+ Channel Essential for Mechanosensing in Root Tips ]]> https://biorxiv.org/content/10.1101/2022.06.05.494847v1?rss=1 Zhang, Z. Sun, Y. Lu, P. Feng, C. Niu, Q. Lin, G. Kong, D. Liu, L. Luan, S. Li, L. HOU, C. 2022-06-05 doi:10.1101/2022.06.05.494847 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ Modeling the Diverse Effects of Divisive Normalization on Noise Correlations ]]> https://biorxiv.org/content/10.1101/2022.06.08.495145v1?rss=1 Weiss, O. Bounds, H. A. Adesnik, H. Coen-Cagli, R. 2022-06-10 doi:10.1101/2022.06.08.495145 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Dynamic Phaeodactylum tricornutum Exometabolites Shape Surrounding Bacterial Communities ]]> https://biorxiv.org/content/10.1101/2022.06.08.495228v1?rss=1 Brisson, V. Swink, C. Kimbrel, J. Mayali, X. Samo, T. Kosina, S. M. Thelen, M. Northen, T. R. Stuart, R. K. 2022-06-08 doi:10.1101/2022.06.08.495228 Cold Spring Harbor Laboratory Press 2022-06-08 <![CDATA[ Beyond winglets: evolution of flight-related morphology in stick insects (Phasmatodea) ]]> https://biorxiv.org/content/10.1101/2022.06.09.495408v1?rss=1 Zeng, Y. Park, S. Gonzales, C. Rahim, F. Dudley, R. 2022-06-12 doi:10.1101/2022.06.09.495408 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Spatial variation in population genomic responses to over a century of anthropogenic change within a tidal marsh songbird ]]> https://biorxiv.org/content/10.1101/2022.06.10.495648v1?rss=1 Benham, P. Walsh, J. Bowie, R. C. K. 2022-06-12 doi:10.1101/2022.06.10.495648 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Multiple memory systems for efficient temporal order memory ]]> https://biorxiv.org/content/10.1101/2022.06.10.495702v1?rss=1 Jafarpour, A. Lin, J. J. Knight, R. T. Buffalo, E. A. 2022-06-13 doi:10.1101/2022.06.10.495702 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ Running modulates primate and rodent visual cortex via common mechanism but quantitatively distinct implementation ]]> https://biorxiv.org/content/10.1101/2022.06.13.495712v1?rss=1 Liska, J. P. Rowley, D. P. Nguyen, T. T. K. Muthmann, J.-O. Butts, D. A. Yates, J. L. Huk, A. C. 2022-06-14 doi:10.1101/2022.06.13.495712 Cold Spring Harbor Laboratory Press 2022-06-14 <![CDATA[ Precise Transcript Targeting by CRISPR-Csm Complexes ]]> https://biorxiv.org/content/10.1101/2022.06.20.496908v1?rss=1 Colognori, D. Trinidad, M. Doudna, J. A. 2022-06-20 doi:10.1101/2022.06.20.496908 Cold Spring Harbor Laboratory Press 2022-06-20 <![CDATA[ Abundant Phenotypic Parallelism, Incomplete Lineage Sorting, and Introgression in Open-Habitat Chats ]]> https://biorxiv.org/content/10.1101/2022.06.21.496980v1?rss=1 Alaei Kakhki, N. Schweizer, M. Lutgen, D. Bowie, R. C. K. Shirihai, H. Suh, A. Schielzeth, H. Burri, R. 2022-06-25 doi:10.1101/2022.06.21.496980 Cold Spring Harbor Laboratory Press 2022-06-25 <![CDATA[ Metabolic traits and the niche of bulk soil bacteria in a Mediterranean grassland ]]> https://biorxiv.org/content/10.1101/2022.06.21.497019v1?rss=1 Zhalnina, K. White, R. A. de Raad, M. Deng, K. Nicora, C. D. Karaoz, U. Pett-Ridge, J. Firestone, M. Lipton, M. S. Northen, T. Brodie, E. L. 2022-06-22 doi:10.1101/2022.06.21.497019 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ Large-scale genetic screens identify BET-1 as a cytoskeleton regulator promoting actin health and lifespan. ]]> https://biorxiv.org/content/10.1101/2022.06.22.497249v1?rss=1 Garcia, G. Bar-Ziv, R. Dutta, N. Moaddeli, D. Averbukh, M. Torres, T. C. Alcala, A. Tsui, C. K. Moehle, E. A. Shalem, O. Thorwald, M. Higuchi-Sanabria, R. 2022-06-22 doi:10.1101/2022.06.22.497249 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ Early life tolerance depends on a subset of specialized dendritic cells and is reinforced by the skin microbiota ]]> https://biorxiv.org/content/10.1101/2022.06.23.497363v1?rss=1 Weckel, A. A. Dhariwala, M. O. Ly, K. Ojewumi, O. T. Riggs, J. B. Gonzalez, J. R. Dwyer, L. R. Okoro, J. N. Leech, J. M. Bacino, M. S. Cho, G. D. merana, G. Anandasabapathy, N. Kumamoto, Y. O. Scharschmidt, T. C. 2022-06-26 doi:10.1101/2022.06.23.497363 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Proteome-wide antigenic profiling in Ugandan cohorts identifies associations between age, exposure intensity, and responses to repeat-containing antigens in Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2022.06.24.497532v1?rss=1 Raghavan, M. Kalantar, K. L. Duarte, E. Teyssier, N. Takahashi, S. Kung, A. F. Rajan, J. V. Rek, J. Tetteh, K. K. A. Drakeley, C. Ssewanyana, I. Rodriguez-Barraquer, I. Greenhouse, B. DeRisi, J. L. 2022-06-26 doi:10.1101/2022.06.24.497532 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Use of a ubiquitous gene-editing tool in budding yeast causes off-target repression of neighboring gene protein synthesis ]]> https://biorxiv.org/content/10.1101/2022.06.27.497784v1?rss=1 Powers, E. N. Llacsahuanga Allcca, L. Doron-Mandel, E. Kim Kim, J. Jovanovic, M. Brar, G. A. 2022-06-29 doi:10.1101/2022.06.27.497784 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Extravascular spaces are reservoirs of antigenic diversity in Trypanosoma brucei infection ]]> https://biorxiv.org/content/10.1101/2022.06.27.497797v1?rss=1 Beaver, A. Crilly, N. P. Hakim, J. Zhang, B. Bobb, B. Rijo-Ferreira, F. Figueiredo, L. M. Mugnier, M. R. 2022-06-27 doi:10.1101/2022.06.27.497797 Cold Spring Harbor Laboratory Press 2022-06-27 <![CDATA[ Meiotic resetting of the cellular Sod1 pool is driven by protein aggregation, degradation, and transient LUTI-mediated repression ]]> https://biorxiv.org/content/10.1101/2022.06.28.498006v1?rss=1 Wende, H. M. V. Gopi, M. Onyundo, M. Medrano, C. Adanlawo, T. Brar, G. A. 2022-06-29 doi:10.1101/2022.06.28.498006 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Functional succession of actively growing soil microorganisms during rewetting is shaped by precipitation history ]]> https://biorxiv.org/content/10.1101/2022.06.28.498032v1?rss=1 Sieradzki, E. T. Greenlon, A. Nicolas, A. M. Firestone, M. K. Pett-Ridge, J. Blazewicz, S. J. Banfield, J. 2022-06-29 doi:10.1101/2022.06.28.498032 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Paracrine signaling by pancreatic delta cells determines the glycemic set point in mice ]]> https://biorxiv.org/content/10.1101/2022.06.29.496132v1?rss=1 Huang, J. L. Lee, S. Pourhosseinzadeh, M. S. Krämer, N. Guillen, J. V. Cinque, N. H. Aniceto, P. A. Koike, S. Huising, M. O. 2022-07-02 doi:10.1101/2022.06.29.496132 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Life history strategies and niches of soil bacteria emerge from interacting thermodynamic, biophysical, and metabolic traits ]]> https://biorxiv.org/content/10.1101/2022.06.29.498137v1?rss=1 Marschmann, G. L. Tang, J. Zhalnina, K. Karaoz, U. Cho, H. Le, B. Pett-Ridge, J. Brodie, E. L. 2022-07-02 doi:10.1101/2022.06.29.498137 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Acetaminophen production in the edible, filamentous cyanobacterium Arthrospira platensis ]]> https://biorxiv.org/content/10.1101/2022.06.30.498297v1?rss=1 Hilzinger, J. M. Freidline, S. Sivanandan, D. Cheng, Y.-F. Yamazaki, S. Clark, D. S. Skerker, J. M. Arkin, A. P. 2022-07-02 doi:10.1101/2022.06.30.498297 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Signatures of contextual interference in implicit sensorimotor adaptation ]]> https://biorxiv.org/content/10.1101/2022.07.03.498608v1?rss=1 Tsay, J. S. Irving, C. Ivry, R. B. 2022-07-04 doi:10.1101/2022.07.03.498608 Cold Spring Harbor Laboratory Press 2022-07-04 <![CDATA[ Epidermal threads reveal the origin of hagfish slime ]]> https://biorxiv.org/content/10.1101/2022.07.06.499062v1?rss=1 Zeng, Y. Plachetzki, D. C. Nieders, K. Campbell, H. Cartee, M. Guillen, K. Fudge, D. 2022-07-07 doi:10.1101/2022.07.06.499062 Cold Spring Harbor Laboratory Press 2022-07-07 <![CDATA[ Predicting and prioritizing species coexistence: learning outcomes via experiments ]]> https://biorxiv.org/content/10.1101/2022.07.07.499099v1?rss=1 Blonder, B. W. Godoy, O. 2022-07-07 doi:10.1101/2022.07.07.499099 Cold Spring Harbor Laboratory Press 2022-07-07 <![CDATA[ Directed Shortest Walk on Temporal Graphs ]]> https://biorxiv.org/content/10.1101/2022.07.08.499368v1?rss=1 0. Lastly, we develop an integer linear program to solve a generalized version of TCSW, and demonstrate its ability to reach optimality with instances of the human protein interaction network. ConclusionWe demonstrate that when extending the shortest walk problem in computational biology to account for multiple ordered conditions, the problem not only becomes hard to solve, but hard to approximate, a limitation which we address via a new solver. From this narrow definition of TCSW, we relax the constraint of time consistency within the shortest walk, deriving a direct relationship between hardness of approximation and the allowable step size in our walk between time conditioned networks. Lastly we briefly explore a variety of alternative formulations for this problem, providing insight into both tractable and intractable variants. AvailabilityOur solver for the general k-Time Condition Shortest Walk problem is available at https://github.com/YosefLab/temporal_condition_shortest_walk ]]> Khodaverdian, A. Yosef, N. 2022-07-10 doi:10.1101/2022.07.08.499368 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Temporal single cell atlas of non-neuronal retinal cells reveals dynamic, coordinated multicellular responses to central nervous system injury ]]> https://biorxiv.org/content/10.1101/2022.07.10.499469v1?rss=1 Benhar, I. Ding, J. Yan, W. Whitney, I. E. Jacobi, A. Sud, M. Burgin, G. Shekhar, K. Tran, N. M. Wang, C. He, Z. Sanes, J. R. Regev, A. 2022-07-10 doi:10.1101/2022.07.10.499469 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Longitudinal Urine Metabolic Profiling and Gestational Age Prediction in Pregnancy ]]> https://biorxiv.org/content/10.1101/2022.07.10.499478v1?rss=1 Chen, S. Shen, X. Liang, L. Avina, M. Zackriah, H. Jelliffe-Pawlowski, L. Rand, L. Snyder, M. 2022-07-10 doi:10.1101/2022.07.10.499478 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Liquid-liquid phase separation recapitulates the thermodynamics and kinetics of heterochromatin formation ]]> https://biorxiv.org/content/10.1101/2022.07.11.499635v1?rss=1 Tortora, M. M. Brennan, L. Karpen, G. Jost, D. 2022-07-11 doi:10.1101/2022.07.11.499635 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Maximizing CRISPRi efficacy and accessibility with dual-sgRNA libraries and optimal effectors ]]> https://biorxiv.org/content/10.1101/2022.07.13.499814v1?rss=1 Replogle, J. M. Bonnar, J. L. Pogson, A. N. Liem, C. R. Maier, N. K. Ding, Y. Russell, B. J. Wang, X. Leng, K. Guna, A. Norman, T. M. Pak, R. A. Ramos, D. M. Ward, M. E. Gilbert, L. A. Kampmann, M. Weissman, J. S. Jost, M. 2022-07-13 doi:10.1101/2022.07.13.499814 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Probing the KRas Switch II Groove by Fluorine NMR Spectroscopy ]]> https://biorxiv.org/content/10.1101/2022.07.15.500267v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@2fe99corg.highwire.dtl.DTLVardef@19223bdorg.highwire.dtl.DTLVardef@1686090org.highwire.dtl.DTLVardef@19b9d05_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Peacock, D. M. Kelly, M. J. S. Shokat, K. M. 2022-07-16 doi:10.1101/2022.07.15.500267 Cold Spring Harbor Laboratory Press 2022-07-16 <![CDATA[ AGO2 silences mobile transposons in the nucleus of quiescent cells ]]> https://biorxiv.org/content/10.1101/2022.07.17.500356v1?rss=1 Sala, L. Chandrasekhar, S. Cosby, R. L. La Rocca, G. Macfarlan, T. Awasthi, P. Chari, R. Kruhlak, M. Vidigal, J. A. 2022-07-17 doi:10.1101/2022.07.17.500356 Cold Spring Harbor Laboratory Press 2022-07-17 <![CDATA[ Combined oral vaccination with niche competition can generate sterilizing immunity against entero-pathogenic bacteria ]]> https://biorxiv.org/content/10.1101/2022.07.20.498444v1?rss=1 Lentsch, V. Woller, A. Moresi, C. Fattinger, S. A. Aslani, S. Hardt, W.-D. Loverdo, C. Diard, M. Slack, E. 2022-07-20 doi:10.1101/2022.07.20.498444 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ The dual role of a multi-heme cytochrome in methanogenesis: MmcA is important for energy conservation and carbon metabolism in Methanosarcina acetivorans ]]> https://biorxiv.org/content/10.1101/2022.07.20.500911v1?rss=1 Nayak, D. D. Gupta, D. Downing, B. 2022-07-21 doi:10.1101/2022.07.20.500911 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Deep self-supervised learning for biosynthetic gene cluster detection and product classification ]]> https://biorxiv.org/content/10.1101/2022.07.22.500861v1?rss=1 Rios-Martinez, C. Bhattacharya, N. Amini, A. P. Crawford, L. Yang, K. K. 2022-07-23 doi:10.1101/2022.07.22.500861 Cold Spring Harbor Laboratory Press 2022-07-23 <![CDATA[ Oxytocin receptor is not required for social attachment in prairie voles ]]> https://biorxiv.org/content/10.1101/2022.07.22.501192v1?rss=1 Berendzen, K. M. Sharma, R. Alvarado, M. Wei, Y. Rogers, F. D. Seelke, A. Simmons, T. C. Bond, J. Larios, R. D. Sherman, M. Parthasarathy, S. Espineda, I. Knoedler, J. R. Beery, A. Bales, K. L. Shah, N. M. Manoli, D. S. 2022-07-23 doi:10.1101/2022.07.22.501192 Cold Spring Harbor Laboratory Press 2022-07-23 <![CDATA[ A widely distributed gene cluster compensates for uricase loss in hominids ]]> https://biorxiv.org/content/10.1101/2022.07.24.501321v1?rss=1 Liu, Y. Jarman, J. B. Low, Y. S. Huang, S. Chen, H. Defeo, M. E. Sekiba, K. Hou, B.-H. Ganesan, C. Pao, A. C. Gombar, S. Dodd, D. 2022-07-25 doi:10.1101/2022.07.24.501321 Cold Spring Harbor Laboratory Press 2022-07-25 <![CDATA[ JBrowse 2: A modular genome browser with views of synteny and structural variation ]]> https://biorxiv.org/content/10.1101/2022.07.28.501447v1?rss=1 Diesh, C. Stevens, G. J. Xie, P. Martinez, T. D. J. Hershberg, E. A. Leung, A. Guo, E. Dider, S. Zhang, J. Bridge, C. Hogue, G. Duncan, A. Morgan, M. Flores, T. Bimber, B. N. Haw, R. Cain, S. Buels, R. M. Stein, L. D. Holmes, I. 2022-07-31 doi:10.1101/2022.07.28.501447 Cold Spring Harbor Laboratory Press 2022-07-31 <![CDATA[ Basolateral amygdala and orbitofrontal cortex, but not dorsal hippocampus, are necessary for the control of reward-seeking by occasion setters ]]> https://biorxiv.org/content/10.1101/2022.07.28.501885v1?rss=1 Fraser, K. M. Janak, P. H. 2022-08-01 doi:10.1101/2022.07.28.501885 Cold Spring Harbor Laboratory Press 2022-08-01 <![CDATA[ Dually targeted proteins regulate proximity between peroxisomes and partner organelles ]]> https://biorxiv.org/content/10.1101/2022.07.29.501968v1?rss=1 Stehlik, T. Bittner, E. Lam, J. Dimitrov, L. Schöck, I. Harberding, J. Heymons, N. Schuldiner, M. Zalckvar, E. Bölker, M. Schekman, R. Freitag, J. 2022-07-31 doi:10.1101/2022.07.29.501968 Cold Spring Harbor Laboratory Press 2022-07-31 <![CDATA[ Characterization, Comparison, and Optimization of Lattice Light Sheets ]]> https://biorxiv.org/content/10.1101/2022.07.30.502108v1?rss=1 Ruan, X. Liu, G. Milkie, D. E. Gorlitz, F. Mueller, M. Hercule, W. Kililea, A. Betzig, E. Upadhyayula, S. 2022-07-30 doi:10.1101/2022.07.30.502108 Cold Spring Harbor Laboratory Press 2022-07-30 <![CDATA[ Optogenetic control of RelA reveals effect of transcription factor dynamics on downstream gene expression ]]> https://biorxiv.org/content/10.1101/2022.08.03.502739v1?rss=1 Osimiri, L. C. Bonny, A. R. Takagishi, S. R. Luecke, S. Riehs, N. Hoffmann, A. El-Samad, H. 2022-08-05 doi:10.1101/2022.08.03.502739 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Dissecting the contributions of tumor heterogeneity on metastasis at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2022.08.04.502697v1?rss=1 Winkler, J. Tan, W. Diadhiou, C. M. M. McGinnis, C. S. Abbasi, A. Hasnain, S. Durney, S. Atamaniuc, E. Superville, D. Awni, L. Lee, J. V. Hinrichs, J. H. Hein, M. Y. Borja, M. Detweiler, A. Liu, S.-Y. Nanjaraj, A. Sitarama, V. Rugo, H. S. Neff, N. Gartner, Z. J. Pisco, A. O. Goga, A. Darmanis, S. Werb, Z. 2022-08-05 doi:10.1101/2022.08.04.502697 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Mitochondrial uncouplers impair human sperm motility without altering ATP content ]]> https://biorxiv.org/content/10.1101/2022.08.04.502752v1?rss=1 Skinner, W. M. Petersen, N. T. Unger, B. Tang, S. Tabarsi, E. Lamm, J. Jalalian, L. Smith, J. Bertholet, A. M. Xu, K. Kirichok, Y. Lishko, P. 2022-08-05 doi:10.1101/2022.08.04.502752 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Kinesin-1, -2 and -3 motors use family-specific mechanochemical strategies to effectively compete with dynein during bidirectional transport ]]> https://biorxiv.org/content/10.1101/2022.08.04.502809v1?rss=1 Gicking, A. M. Ma, T.-C. Feng, Q. Jiang, R. Badieyan, S. Cianfrocco, M. A. Hancock, W. O. 2022-08-05 doi:10.1101/2022.08.04.502809 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Regioselective control of biocatalytic C-H activation and halogenation ]]> https://biorxiv.org/content/10.1101/2022.08.04.502814v1?rss=1 Kissman, E. N. Neugebauer, M. E. Sumida, K. H. Swenson, C. V. Sambold, N. A. Marchand, J. A. Millar, D. C. Chang, M. C. Y. 2022-08-05 doi:10.1101/2022.08.04.502814 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Plant species within Streptanthoid Complex associate with distinct microbial communities that shift to be more similar under drought ]]> https://biorxiv.org/content/10.1101/2022.08.05.502885v1?rss=1 Igwe, A. N. Pearse, I. Aguilar, J. M. Strauss, S. Y. Vannette, R. L. 2022-08-06 doi:10.1101/2022.08.05.502885 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ Nanomolar inhibition of SARS-CoV-2 infection by an unmodified peptide targeting the pre-hairpin intermediate of the spike protein ]]> https://biorxiv.org/content/10.1101/2022.08.11.503553v1?rss=1 Yang, K. Wang, C. Kreutzberger, A. J. B. Ojha, R. Kuivanen, S. Couoh-Cardel, S. Muratcioglu, S. Eisen, T. J. White, K. I. Held, R. G. Subramanian, S. Marcus, K. Pfuetzner, R. A. Esquivies, L. Doyle, C. A. Kuriyan, J. Vapalahti, O. Balistreri, G. Kirchhausen, T. Brunger, A. T. 2022-08-11 doi:10.1101/2022.08.11.503553 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates ]]> https://biorxiv.org/content/10.1101/2022.08.13.503842v1?rss=1 Watson, Z. Knudson, I. Ward, F. R. Miller, S. J. Cate, J. H. Schepartz, A. Abramyan, A. M. 2022-08-13 doi:10.1101/2022.08.13.503842 Cold Spring Harbor Laboratory Press 2022-08-13 <![CDATA[ From Prediction to Action: Dissociable Roles of Ventral Tegmental Area and Substantia Nigra Dopamine Neurons in Instrumental Reinforcement ]]> https://biorxiv.org/content/10.1101/2022.08.15.501890v1?rss=1 Fraser, K. M. Pribut, H. J. Janak, P. H. Keiflin, R. 2022-08-15 doi:10.1101/2022.08.15.501890 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Modulation of xanthophyll cycle impacts biomass productivity in the marine microalga Nannochloropsis ]]> https://biorxiv.org/content/10.1101/2022.08.16.504082v1?rss=1 Perin, G. Bellan, A. Lyska, D. Niyogi, K. K. Morosinotto, T. 2022-08-16 doi:10.1101/2022.08.16.504082 Cold Spring Harbor Laboratory Press 2022-08-16 <![CDATA[ Allosteric Inhibition of the T Cell Receptor by a Designed Membrane Ligand ]]> https://biorxiv.org/content/10.1101/2022.08.19.503518v1?rss=1 Ye, Y. Morita, S. Groves, J. T. Barrera, F. N. 2022-08-20 doi:10.1101/2022.08.19.503518 Cold Spring Harbor Laboratory Press 2022-08-20 <![CDATA[ A Mesp1-dependent developmental breakpoint in transcriptional and epigenomic specification of early cardiac precursors ]]> https://biorxiv.org/content/10.1101/2022.08.22.504863v1?rss=1 Krup, A. L. Winchester, S. Ranade, S. Agrawal, A. Devine, W. P. Sinha, T. Choudhary, K. Dominguez, M. Thomas, R. Black, B. L. Srivastava, D. Bruneau, B. 2022-08-22 doi:10.1101/2022.08.22.504863 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ A dynamic sequence of visual processing initiated by gaze shifts ]]> https://biorxiv.org/content/10.1101/2022.08.23.504847v1?rss=1 Parker, P. R. L. Martins, D. M. Leonard, E. S. P. Casey, N. M. Sharp, S. L. Abe, E. T. T. Smear, M. C. Yates, J. L. Mitchell, J. F. Niell, C. M. 2022-08-25 doi:10.1101/2022.08.23.504847 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Gene amplification mutations originate prior to selective stress in Acinetobacter baylyi ]]> https://biorxiv.org/content/10.1101/2022.08.23.504990v1?rss=1 Reams, A. B. Herrmann, J. A. Koprowska, A. Winters, T. J. Villanueva, N. Nikityuk, V. D. Pek, F. Reis, E. M. Dominguez, C. Z. Davis, D. McPherson, E. Rocco, S. R. Recendez, C. Difuntorum, S. M. Faeth, K. Lopez, M. D. Awwad, H. M. Ghobashy, R. A. Cappiello, L. Neidle, E. L. Quinones-Soto, S. 2022-08-24 doi:10.1101/2022.08.23.504990 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ Human anti-ACE2 monoclonal antibodies as pan-sarbecovirus prophylactic agents ]]> https://biorxiv.org/content/10.1101/2022.08.24.505169v1?rss=1 Zhang, F. Jenkins, J. de Carvalho, R. V. H. Nakandakari-Higa, S. Chen, T. Abernathy, M. E. Nyakatura, E. Andrew, D. Lebedeva, I. V. Lorenz, I. C. Hoffmann, H.- H. Rice, C. M. Victora, G. D. Barnes, C. O. Hatziioannou, T. Bieniasz, P. D. 2022-08-24 doi:10.1101/2022.08.24.505169 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ Jagged1 overexpression on T cells induces thymic regulatory T cells leading to thymic involution ]]> https://biorxiv.org/content/10.1101/2022.08.25.504005v1?rss=1 Kritikou, J. Sanchez-Pascual, I. Munoz-Miranda, J. P. Vashist, N. Wagner, A. K. Zhang, X. M. Assarsson, E. Dominguez-Villar, M. Yagita, H. Garcia-Cozar, F. Riese, P. Harris, R. A. Ljunggrean, H.-G. Chambers, B. 2022-08-25 doi:10.1101/2022.08.25.504005 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ A megaprotein-based molecular bridge critical for lipid trafficking and cold resilience ]]> https://biorxiv.org/content/10.1101/2022.08.25.505359v1?rss=1 Wang, C. Wang, B. Pandey, T. Long, Y. Zhang, J. Oh, F. Sima, J. Guo, R. Liu, Y. K. Zhang, C. Mukherjee, S. Bassik, M. C. Lin, W. Deng, H. Vale, G. McDonald, J. G. Shen, K. Ma, D. K. 2022-08-26 doi:10.1101/2022.08.25.505359 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Combined single-sample metabolomics and RNAseq reveals a hepatic pyrimidine metabolic response to acute viral infection ]]> https://biorxiv.org/content/10.1101/2022.08.26.505340v1?rss=1 Madaj, Z. B. Dahabieh, M. S. Kamalumpundi, V. Muhire, B. Pettinga, D. J. Siwicki, R. A. Ellis, A. E. Isaguirre, C. Escobar Galvis, M. L. DeCamp, L. Jones, R. G. Givan, S. A. Adams, M. Sheldon, R. D. 2022-08-26 doi:10.1101/2022.08.26.505340 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ A small molecule screen reveals the essentiality of p38 kinase for choanoflagellate cell proliferation ]]> https://biorxiv.org/content/10.1101/2022.08.26.505350v1?rss=1 Rutaganira, F. U. N. Scopton, A. P. Dar, A. King, N. 2022-08-27 doi:10.1101/2022.08.26.505350 Cold Spring Harbor Laboratory Press 2022-08-27 <![CDATA[ Deep surveys of transcriptional modules with Massive Associative Kbiclustering (MAK) ]]> https://biorxiv.org/content/10.1101/2022.08.26.505372v1?rss=1 Joachimiak, M. P. Tuglus, C. Salamzade, R. van der Laan, M. Arkin, A. P. 2022-08-26 doi:10.1101/2022.08.26.505372 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Extending Conway's Game of Life ]]> https://biorxiv.org/content/10.1101/2022.08.30.505937v1?rss=1 p{sigma}U then a cell in state{sigma} at location (i, j) respectively stays in state{sigma} , progresses to state{sigma} + 1, or dies. In this paper, we illustrate some of the properties of such games of life with three, four and six states, identifying still-life, oscillator, glider and replicator pattern sequences. We also examine the long term behavior of patterns arising from random and regular (stripped diagonals) starting configurations, as well as set-piece motifs. Most importantly, we introduce two freely downloadable, Numerus runtime alterable model platforms (Numerus RAMPs) that can be used to simulate the three and four state GoLs discussed in this paper, and provide a guide on how these RAMPs can be used to explore the behavior of our GoLs. ]]> Getz, W. M. Salter, R. M. 2022-09-02 doi:10.1101/2022.08.30.505937 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ A two-compartment system for subfreezing temperatures preservation of large volumes of organic matter in an isochoric system ]]> https://biorxiv.org/content/10.1101/2022.08.31.506083v1?rss=1 Nastase, G. Botea, F. Beschea, G. A. Campean, S. I. Barcu, A. Popescu, I. Rubinsky, B. Serban, A. 2022-09-03 doi:10.1101/2022.08.31.506083 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Divergent microbial traits influence the transformation of living versus dead root inputs to soil carbon ]]> https://biorxiv.org/content/10.1101/2022.09.02.506384v1?rss=1 Sokol, N. Foley, M. Blazewicz, S. J. Battacharyya, A. Estera-Molina, K. Firestone, M. K. Greenlon, A. Hungate, B. A. Kimbrel, J. Liquet, J. Lafler, M. Marple, M. Nico, P. Slessarev, E. Pett-Ridge, J. 2022-09-03 doi:10.1101/2022.09.02.506384 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Rad51-mediated interhomolog recombination during budding yeast meiosis is promoted by the meiotic recombination checkpoint and the conserved Pif1 helicase ]]> https://biorxiv.org/content/10.1101/2022.09.05.506590v1?rss=1 Ziesel, A. Weng, Q. Ahuja, J. S. Bhattacharya, A. Dutta, R. Cheng, E. Börner, G. V. Lichten, M. Hollingsworth, N. M. 2022-09-06 doi:10.1101/2022.09.05.506590 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ Bayesian inference of admixture graphs on Native American and Arctic populations ]]> https://biorxiv.org/content/10.1101/2022.09.06.506725v1?rss=1 Nielsen, S. V. Vaughn, A. Leppälä, K. Landis, M. J. Mailund, T. Nielsen, R. 2022-09-06 doi:10.1101/2022.09.06.506725 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ Actin-driven protrusions generate rapid long-range membrane tension propagation in cells ]]> https://biorxiv.org/content/10.1101/2022.09.07.507005v1?rss=1 De Belly, H. Yan, S. Borja da Rocha, H. Ichbiah, S. Town, J. P. Turlier, H. Bustamante, C. J. Weiner, O. D. 2022-09-08 doi:10.1101/2022.09.07.507005 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Activity in primate visual cortex is minimally driven by spontaneous movements ]]> https://biorxiv.org/content/10.1101/2022.09.08.507006v1?rss=1 Thalluri, B. C. Kang, I. Lazere, A. Quinn, K. R. Kaliss, N. Yates, J. Butts, D. A. Nienborg, H. 2022-09-10 doi:10.1101/2022.09.08.507006 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ A membrane-associated light harvesting model is enabled by functionalized assemblies of gene-doubled TMV proteins ]]> https://biorxiv.org/content/10.1101/2022.09.08.507180v1?rss=1 Dai, J. Wilhelm, K. B. Bischoff, A. J. Pereira, J. H. Dedeo, M. T. Garcia-Almedina, D. M. Adams, P. D. Groves, J. T. Francis, M. B. 2022-09-10 doi:10.1101/2022.09.08.507180 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Mechanism of small molecule inhibition of Plasmodium falciparum myosin A informs antimalarial drug design ]]> https://biorxiv.org/content/10.1101/2022.09.09.507123v1?rss=1 Moussaoui, D. Robblee, J. P. Auguin, D. Fisher, F. Fagnant, P. M. MacFarlane, J. E. Schaletzky, J. Wehri, E. Mueller-Dieckmann, C. Baum, J. Robert-Paganin, J. Trybus, K. Houdusse, A. 2022-09-09 doi:10.1101/2022.09.09.507123 Cold Spring Harbor Laboratory Press 2022-09-09 <![CDATA[ Identification of KNX-002, a novel inhibitor of Toxoplasma motility targeting the Class XIV myosin, TgMyoA ]]> https://biorxiv.org/content/10.1101/2022.09.09.507210v1?rss=1 Kelsen, A. Kent, R. S. Snyder, A. K. Wehri, E. Bishop, S. J. Stadler, R. V. Powell, C. Rompikuntal, P. K. Boulanger, M. J. Warshaw, D. M. Westwood, N. J. Schaletzky, J. Ward, G. E. 2022-09-09 doi:10.1101/2022.09.09.507210 Cold Spring Harbor Laboratory Press 2022-09-09 <![CDATA[ Cik1 and Vik1 Accessory Proteins Confer Distinct Functions to the Kinesin-14, Kar3 ]]> https://biorxiv.org/content/10.1101/2022.09.09.507361v1?rss=1 Bergman, Z. J. Wong, J. J. Drubin, D. Barnes, G. 2022-09-10 doi:10.1101/2022.09.09.507361 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Trajectory classification method for anchored molecular motor-biopolymer interactions in the C. elegans first mitosis. ]]> https://biorxiv.org/content/10.1101/2022.09.11.507465v1?rss=1 Linehan, J. B. Edwards, A. Boudreau, V. Maddox, P. 2022-09-11 doi:10.1101/2022.09.11.507465 Cold Spring Harbor Laboratory Press 2022-09-11 <![CDATA[ IL-10 suppresses T cell expansion while promoting tissue-resident memory cell formation during SARS-CoV-2 infection in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2022.09.13.507852v1?rss=1 Nelson, C. E. Foreman, T. W. Kauffman, K. D. Sakai, S. Fleegle, J. D. Gomez, F. NIAID/DIR Tuberculosis Imaging Program, Le Nouen, C. Liu, X. Burdette, T. L. Garza, N. L. Lafont, B. A. P. Brooks, K. Arlehamn, C. S. L. Weiskopf, D. Sette, A. Hickman, H. D. Buchhholz, U. J. Johnson, R. F. Brenchley, J. M. Via, L. E. Barber, D. L. 2022-09-13 doi:10.1101/2022.09.13.507852 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Modulation of tooth regeneration through opposing responses to Wnt and BMP signals in teleosts ]]> https://biorxiv.org/content/10.1101/2022.10.01.510447v1?rss=1 Square, T. A. Mackey, E. J. Chen, Z. Z. Sundaram, S. Miller, C. T. 2022-10-02 doi:10.1101/2022.10.01.510447 Cold Spring Harbor Laboratory Press 2022-10-02 <![CDATA[ ULTRAFAST STRUCTURAL CHANGES DIRECT THE FIRST MOLECULAR EVENTS OF VISION ]]> https://biorxiv.org/content/10.1101/2022.10.14.511948v1?rss=1 Gruhl, T. Weinert, T. Rodrigues, M. Milne, C. J. Ortolani, G. Nass, K. Nango, E. Sen, S. Johnson, P. J. Cirelli, C. Furrer, A. Mous, S. Skopintsev, P. James, D. Dworkowski, F. Bath, P. Kekilli, D. Ozerov, D. Tanaka, R. Glover, H. Bacellar, C. Brunle, S. Casadei, C. M. Diethelm, A. D. Gashi, D. Gotthard, G. Guixa-Gonzalez, R. Joti, Y. Kabanova, V. Knopp, G. Lesca, E. Ma, P. Martiel, I. Muhle, J. Owada, S. Pamula, F. Sarabi, D. Tejero, O. Tsai, C.-J. Varma, N. Wach, A. Boutet, S. Tono, K. Nogly, P. Deupi, X. Iwata, S. Neutze, R. Standfuss, J. Scher 2022-10-14 doi:10.1101/2022.10.14.511948 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ ATGL is differentially required for adipocyte FABP4 secretion in vivo and ex vivo ]]> https://biorxiv.org/content/10.1101/2022.10.14.512277v1?rss=1 Prentice, K. J. Lee, A. Cedillo, P. Inouye, K. E. Ertunc, M. E. Lee, G. Y. Hotamisligil, G. S. 2022-10-17 doi:10.1101/2022.10.14.512277 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ First superferromagnetic remanence characterization and scan optimization for super-resolution Magnetic Particle Imaging ]]> https://biorxiv.org/content/10.1101/2022.11.08.515719v1?rss=1 Fung, K. L. B. Colson, C. Bryan, J. Saayujya, C. Mokkarala-Lopez, J. Hartley, A. Yousuf, K. Kuo, R. Lu, Y. Fellows, B. D. Chandrasekharan, P. Conolly, S. M. 2022-11-09 doi:10.1101/2022.11.08.515719 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus ]]> https://biorxiv.org/content/10.1101/2022.11.22.517304v1?rss=1 Steenwyk, J. L. Balamurugan, C. Raja, H. A. Goncalves, C. Li, N. Martin, F. Berman, J. Oberlies, N. H. Gibbons, J. G. Goldman, G. H. Geiser, D. M. Hibbett, D. S. Rokas, A. 2022-11-24 doi:10.1101/2022.11.22.517304 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Computational modeling reveals latent components of mouse behavior in the sucrose preference test ]]> https://biorxiv.org/content/10.1101/2022.11.30.518425v1?rss=1 Verharen, J. P. H. de Jong, J. W. Zhu, Y. Lammel, S. 2022-12-01 doi:10.1101/2022.11.30.518425 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Mcr-dependent methanogenesis in Archaeoglobaceae enriched from a terrestrial hot spring ]]> https://biorxiv.org/content/10.1101/2022.12.01.518715v1?rss=1 Buessecker, S. Chadwick, G. Quan, M. E. Hedlund, B. Dodsworth, J. A. Dekas, A. E. 2022-12-01 doi:10.1101/2022.12.01.518715 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Sex-biased Yap1 oncogene function ]]> https://biorxiv.org/content/10.1101/2022.12.21.521494v1?rss=1 Abdelfattah, N. Natarajan, S. Maldonado, J. Tran, H. N. McMinimy, R. Borland, H. Chen, S.-h. Camargo, F. Olson, J. George, J. Yun, K. 2022-12-22 doi:10.1101/2022.12.21.521494 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Potential for Methanosarcina to contribute to uranium reduction during acetate-promoted groundwater bioremediation ]]> https://biorxiv.org/content/10.1101/202242v1?rss=1 Holmes, D. E. Orelana, R. Giloteaux, L. Wang, L.-Y. Shrestha, P. M. Williams, K. Lovley, D. R. Rotaru, A.-E. 2017-10-12 doi:10.1101/202242 Cold Spring Harbor Laboratory Press 2017-10-12 <![CDATA[ A comprehensive rRNA variation atlas in health and disease ]]> https://biorxiv.org/content/10.1101/2023.01.30.526360v1?rss=1 Rothschild, D. Susanto, T. T. Spence, J. P. Genuth, N. R. Sinnott-Armstrong, N. Pritchard, J. K. Barna, M. 2023-02-02 doi:10.1101/2023.01.30.526360 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ Multi-input drug-controlled switches of mammalian gene expression based on engineered nuclear hormone receptors ]]> https://biorxiv.org/content/10.1101/2023.02.01.526549v1?rss=1 Kretschmer, S. Perry, N. Zhang, Y. Kortemme, T. 2023-02-01 doi:10.1101/2023.02.01.526549 Cold Spring Harbor Laboratory Press 2023-02-01 <![CDATA[ From Policy to Practice: Tracking an Open Science Funding Initiative ]]> https://biorxiv.org/content/10.1101/2023.02.27.530238v1?rss=1 Ratan, K. McIntosh, S. Shah, H. V. Lewis, M. Dumanis, S. B. Vines, T. H. Schekman, R. Riley, E. A. U. 2023-02-28 doi:10.1101/2023.02.27.530238 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ Identification of a pharmaceutical biostasis inducer that slows metabolism in multiple vertebrates that do not hibernate ]]> https://biorxiv.org/content/10.1101/2023.02.27.530270v1?rss=1 Sperry, M. M. Charrez, B. Fotowat, H. Gardner, E. Pilobello, K. Izadifar, Z. Lin, T. Kuelker, A. Kaki, S. Lewandowski, M. Lightbown, S. Martinez, R. Marquez, S. Sesay, A. Shcherbina, K. Takeda, T. Andrijauskaite, K. Cisneros, E. Lopez, R. Cano, I. Maxwell, Z. Veraza, R. Bunegin, L. Percival, T. J. Yracheta, J. Pena, J. J. Wood, D. M. Homas, Z. T. Hinshaw, C. J. Cox-Hinshaw, J. Parry, O. G. Sleeter, J. J. Weitzel, E. Levin, M. Super, M. Novak, R. Ingber, D. E. 2023-02-28 doi:10.1101/2023.02.27.530270 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ A phylogeny-informed characterization of global tetrapod traits addresses data gaps and biases ]]> https://biorxiv.org/content/10.1101/2023.03.04.531098v1?rss=1 Moura, M. R. Ceron, K. Guedes, J. J. M. Sica, Y. V. Catenazzi, A. Werneck, F. Toledo, L. F. Jetz, W. 2023-03-06 doi:10.1101/2023.03.04.531098 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ DRMY1 promotes robust morphogenesis by sustaining translation of a hormone signaling protein ]]> https://biorxiv.org/content/10.1101/2023.04.07.536060v1?rss=1 Kong, S. Zhu, M. Scarpin, M. R. Pan, D. Jia, L. Martinez, R. E. Alamos, S. Vadde, V. L. Garcia, H. G. Qian, S.-B. Brunkard, J. O. Roeder, A. H. K. 2023-04-07 doi:10.1101/2023.04.07.536060 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ Novel discovery of a lymphatic bridge connecting Schlemm's canal to limbal and conjunctival lymphatic pathway ]]> https://biorxiv.org/content/10.1101/2023.04.26.538479v1?rss=1 Yang, Y. Shi, M. Li, G. Shen, L. Chen, L. 2023-04-28 doi:10.1101/2023.04.26.538479 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ An Oxidative Pathway of Deoxyribose Catabolism ]]> https://biorxiv.org/content/10.1101/205583v1?rss=1 Ray, J. Price, M. N. Iavarone, A. T. Carlson, H. K. Ryan, E. M. Malmstrom, R. R. Arkin, A. P. Deutschbauer, A. M. 2017-10-18 doi:10.1101/205583 Cold Spring Harbor Laboratory Press 2017-10-18 <![CDATA[ DNA-stabilized silver nanoclusters as specific, ratiometric fluorescent dopamine sensors ]]> https://biorxiv.org/content/10.1101/205591v1?rss=1 Del Bonis-O'Donnell, J. T. Thakrar, A. Wain Hirschberg, J. Vong, D. Queenan, B. N. Fygenson, D. Pennathur, S. 2017-10-18 doi:10.1101/205591 Cold Spring Harbor Laboratory Press 2017-10-18 <![CDATA[ Specific hippocampal representations are linked to generalized cortical representations in memory. ]]> https://biorxiv.org/content/10.1101/207142v1?rss=1 Yu, J. Y. Liu, D. F. Loback, A. Grossrubatscher, I. Frank, L. M. 2017-10-21 doi:10.1101/207142 Cold Spring Harbor Laboratory Press 2017-10-21 <![CDATA[ Lineage and stage-specific expressed CYCD7;1 coordinates the single symmetric division that creates stomatal guard cells ]]> https://biorxiv.org/content/10.1101/207837v1?rss=1 Weimer, A. K. Matos, J. L. Dewitte, W. Murray, J. Bergmann, D. C. 2017-10-23 doi:10.1101/207837 Cold Spring Harbor Laboratory Press 2017-10-23 <![CDATA[ Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data ]]> https://biorxiv.org/content/10.1101/209676v1?rss=1 Köksal, A. S. Beck, K. Cronin, D. R. McKenna, A. Camp, N. D. Srivastava, S. MacGilvray, M. E. Bodik, R. Wolf-Yadlin, A. Fraenkel, E. Fisher, J. Gitter, A. 2017-10-26 doi:10.1101/209676 Cold Spring Harbor Laboratory Press 2017-10-26 <![CDATA[ Heritable plant phenotypes track light and herbivory levels at fine spatial scales ]]> https://biorxiv.org/content/10.1101/210765v1?rss=1 Humphrey, P. Gloss, A. D. Frazier, J. Nelson-Dittrich, A. C. Faries, S. Whiteman, N. K. 2017-10-29 doi:10.1101/210765 Cold Spring Harbor Laboratory Press 2017-10-29 <![CDATA[ Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles ]]> https://biorxiv.org/content/10.1101/217950v1?rss=1 Brown, C. T. Xiong, W. Olm, M. R. Thomas, B. C. Baker, R. Firek, B. Morowitz, M. J. Hettich, R. L. Banfield, J. F. 2017-11-10 doi:10.1101/217950 Cold Spring Harbor Laboratory Press 2017-11-10 <![CDATA[ iterative Random Forests to discover predictive and stable high order interactions ]]> https://biorxiv.org/content/10.1101/222299v1?rss=1 Basu, S. Kumbier, K. Brown, J. B. Yu, B. 2017-11-20 doi:10.1101/222299 Cold Spring Harbor Laboratory Press 2017-11-20 <![CDATA[ The preprophase band-associated kinesin-14 OsKCH2 is a processive minus-end-directed microtubule motor ]]> https://biorxiv.org/content/10.1101/232652v1?rss=1 Tseng, K.-F. Wang, P. Lee, Y.-R. J. Bowen, J. Gicking, A. M. Guo, L. Liu, B. Qiu, W. 2017-12-11 doi:10.1101/232652 Cold Spring Harbor Laboratory Press 2017-12-11 <![CDATA[ High-dimensional microbiome interactions shape host fitness ]]> https://biorxiv.org/content/10.1101/232959v1?rss=1 Gould, A. L. Zhang, V. Lamberti, L. Jones, E. W. Obadia, B. Gavryushkin, A. Carlson, J. M. Beerenwinkel, N. Ludington, W. B. 2017-12-12 doi:10.1101/232959 Cold Spring Harbor Laboratory Press 2017-12-12 <![CDATA[ S1PR3 mediates inflammatory pain and itch via distinct TRP channel-dependent pathways ]]> https://biorxiv.org/content/10.1101/235614v1?rss=1 Hill, R. Z. Morita, T. Brem, R. B. Bautista, D. M. 2017-12-16 doi:10.1101/235614 Cold Spring Harbor Laboratory Press 2017-12-16 <![CDATA[ The signaling lipid sphingosine 1-phosphate regulates mechanical pain ]]> https://biorxiv.org/content/10.1101/236778v1?rss=1 Hill, R. Z. Hoffman, B. Morita, T. Campos, S. M. Lumpkin, E. A. Brem, R. B. Bautista, D. M. 2017-12-19 doi:10.1101/236778 Cold Spring Harbor Laboratory Press 2017-12-19 <![CDATA[ Going through the motions: incorporating movement analyses into disease research ]]> https://biorxiv.org/content/10.1101/237891v1?rss=1 Dougherty, E. R. Seidel, D. P. Carlson, C. J. Speigel, O. Getz, W. M. 2017-12-22 doi:10.1101/237891 Cold Spring Harbor Laboratory Press 2017-12-22 <![CDATA[ Competitive release from native range does not predict invasive success of a globally dominant exotic ant species ]]> https://biorxiv.org/content/10.1101/239277v1?rss=1 Yitbarek, S. Perfecto, I. Vandermeer, J. 2017-12-24 doi:10.1101/239277 Cold Spring Harbor Laboratory Press 2017-12-24 <![CDATA[ An ordered pattern of Ana2 phosphorylation by Plk4 is required for centriole assembly ]]> https://biorxiv.org/content/10.1101/240374v1?rss=1 McLamarrah, T. A. Buster, D. W. Galletta, B. J. Boese, C. J. Ryniawec, J. M. Hollingsworth, N. A. Byrnes, A. E. Brownlee, C. W. Slep, K. C. Rusan, N. M. Rogers, G. C. 2017-12-28 doi:10.1101/240374 Cold Spring Harbor Laboratory Press 2017-12-28 <![CDATA[ A Multi-layer, Self-aligning Hydrogel Micro-molding Process Offering a Fabrication Route to Perfusable 3D In-Vitro Microvasculature ]]> https://biorxiv.org/content/10.1101/242156v1?rss=1 Heidari, H. Taylor, H. 2018-01-02 doi:10.1101/242156 Cold Spring Harbor Laboratory Press 2018-01-02 <![CDATA[ Listeria monocytogenes InlP interacts with afadin and facilitates basement membrane crossing ]]> https://biorxiv.org/content/10.1101/242222v1?rss=1 Faralla, C. Bastounis, E. E. Ortega, F. E. Light, S. H. Rizzuto, G. Nocadello, S. Anderson, W. F. Robbins, J. R. Theriot, J. A. Bakardjiev, A. I. 2018-01-05 doi:10.1101/242222 Cold Spring Harbor Laboratory Press 2018-01-05 <![CDATA[ Protein-coding variation and introgression of regulatory alleles drive plumage pattern diversity in the rock pigeon ]]> https://biorxiv.org/content/10.1101/242552v1?rss=1 Vickrey, A. Bruders, R. Kronenberg, Z. Mackey, E. Bohlender, R. J. Maclary, E. Osborne, E. J. Johnson, K. P. Huff, C. D. Yandell, M. Shapiro, M. 2018-01-05 doi:10.1101/242552 Cold Spring Harbor Laboratory Press 2018-01-05 <![CDATA[ Insect wings and body wall evolved from ancient leg segments ]]> https://biorxiv.org/content/10.1101/244541v1?rss=1 Bruce, H. S. Patel, N. H. 2018-01-09 doi:10.1101/244541 Cold Spring Harbor Laboratory Press 2018-01-09 <![CDATA[ Causal contribution and dynamical encoding in the striatum during evidence accumulation ]]> https://biorxiv.org/content/10.1101/245316v1?rss=1 Yartsev, M. M. Hanks, T. D. Yoon, A. M. Brody, C. D. 2018-01-10 doi:10.1101/245316 Cold Spring Harbor Laboratory Press 2018-01-10 <![CDATA[ Latin Americans show wide-spread Converso ancestry and the imprint of local Native ancestry on physical appearance ]]> https://biorxiv.org/content/10.1101/252155v1?rss=1 Chacon-Duque, J. C. Adhikari, K. Fuentes-Guajardo, M. Mendoza-Revilla, J. Acuna-Alonzo, V. Barquera Lozano, R. Quinto-Sanchez, M. Gomez-Valdes, J. Everardo Martinez, P. Villamil-Ramirez, H. Hunemeier, T. Ramallo, V. Silva de Cerqueira, C. C. Hurtado, M. Villegas, V. Granja, V. Villena, M. Vasquez, R. Llop, E. Sandoval, J. R. Salazar-Granara, A. A. Parolin, M.-L. Sandoval, K. Penaloza-Espinosa, R. I. Rangel-Villalobos, H. Winkler, C. Klitz, W. Bravi, C. Molina, J. Corach, D. Barrantes, R. Gomes, V. Resende, C. Gusmao, L. Amorim, A. Xue, Y. Dugoujon, J.-M. Mo 2018-01-23 doi:10.1101/252155 Cold Spring Harbor Laboratory Press 2018-01-23 <![CDATA[ Transcriptomic analyses reveal tissue-specific selection on genes related to apoptotic processes in the subterranean rodent, Ctenomys sociabilis ]]> https://biorxiv.org/content/10.1101/256875v1?rss=1 Lang, A. Kordonowy, L. Lacey, E. MacManes, M. 2018-01-30 doi:10.1101/256875 Cold Spring Harbor Laboratory Press 2018-01-30 <![CDATA[ A stable mode of bookmarking by TBP recruits RNA Polymerase II to mitotic chromosomes ]]> https://biorxiv.org/content/10.1101/257451v1?rss=1 Teves, S. S. An, L. Bhargava-Shah, A. Xie, L. Darzacq, X. Tjian, R. 2018-01-31 doi:10.1101/257451 Cold Spring Harbor Laboratory Press 2018-01-31 <![CDATA[ Activity of Antimicrobial Peptides Decreases with Increased Cell Membrane Crossing Free Energy Cost ]]> https://biorxiv.org/content/10.1101/258863v1?rss=1 Zou, R. Zhu, X. Tu, Y. Wu, J. Landry, M. P. 2018-02-01 doi:10.1101/258863 Cold Spring Harbor Laboratory Press 2018-02-01 <![CDATA[ Sensations from a single M-cone depend on the activity of surrounding S-cones ]]> https://biorxiv.org/content/10.1101/260653v1?rss=1 Schmidt, B. P. Sabesan, R. Tuten, W. S. Neitz, J. Roorda, A. 2018-02-09 doi:10.1101/260653 Cold Spring Harbor Laboratory Press 2018-02-09 <![CDATA[ Using movement data to estimate contact rates in a simulated environmentally-transmitted disease system ]]> https://biorxiv.org/content/10.1101/261198v1?rss=1 Dougherty, E. R. Seidel, D. P. Carlson, C. J. Getz, W. M. 2018-02-07 doi:10.1101/261198 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ ATP-dependent force generation and membrane scission by ESCRT-III and Vps4 ]]> https://biorxiv.org/content/10.1101/262170v1?rss=1 Schoeneberg, J. Yan, S. Righini, M. Remec Pavlin, M. Lee, I.-H. Carlson, L.-A. Bahrami, A. H. Goldman, D. H. Ren, X. Hummer, G. Bustamante, C. Hurley, J. 2018-02-07 doi:10.1101/262170 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ Structure of the 30S ribosomal decoding complex at ambient temperature ]]> https://biorxiv.org/content/10.1101/262972v1?rss=1 Dao, E. H. Poitevin, F. Sierra, R. G. Gati, C. Rao, Y. Ciftci, H. I. Aksit, F. McGurk, A. Obrinski, T. Mgbam, P. Hayes, B. de Lichtenberg, C. Pardo-Avila, F. Corsepius, N. Zhang, L. Seaberg, M. Hunter, M. S. Liang, M. Koglin, J. E. Wakatsuki, S. Demirci, H. 2018-02-10 doi:10.1101/262972 Cold Spring Harbor Laboratory Press 2018-02-10 <![CDATA[ A Hierarchical Anti-Hebbian Network Model for the Formation of Spatial Cells in Three-Dimensional Space ]]> https://biorxiv.org/content/10.1101/264366v1?rss=1 Soman, K. Chakravarthy, S. Yartsev, M. 2018-02-13 doi:10.1101/264366 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ Somatic nicotinic acetylcholine receptors control the activity of dopamine neurons and reward-related behaviors. ]]> https://biorxiv.org/content/10.1101/266163v1?rss=1 Durand-de Cuttoli, R. Mondoloni, S. Marti, F. Lemoine, D. Naude, J. d'Izarny-Gargas, T. Pons, S. Maskos, U. Trauner, D. Kramer, R. H. Faure, P. Mourot, A. 2018-02-15 doi:10.1101/266163 Cold Spring Harbor Laboratory Press 2018-02-15 <![CDATA[ Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome ]]> https://biorxiv.org/content/10.1101/266700v1?rss=1 Goltsman, D. S. A. Sun, C. L. Proctor, D. M. DiGiulio, D. B. Robaczewska, A. Thomas, B. C. Shaw, G. M. Stevenson, D. K. Holmes, S. P. Banfield, J. F. Relman, D. A. 2018-02-18 doi:10.1101/266700 Cold Spring Harbor Laboratory Press 2018-02-18 <![CDATA[ DeepLoco: Fast 3D Localization Microscopy Using Neural Networks ]]> https://biorxiv.org/content/10.1101/267096v1?rss=1 Boyd, N. Jonas, E. Babcock, H. P. Recht, B. 2018-02-16 doi:10.1101/267096 Cold Spring Harbor Laboratory Press 2018-02-16 <![CDATA[ Subset-based genomic prediction provides insights into the genetic architecture of free amino acid levels in dry Arabidopsis thaliana seeds ]]> https://biorxiv.org/content/10.1101/272047v1?rss=1 Bird, K. A. Turner, S. D. Beissinger, T. M. Angelovici, R. 2018-02-26 doi:10.1101/272047 Cold Spring Harbor Laboratory Press 2018-02-26 <![CDATA[ A novel xenograft model reveals invasive mesenchymal transition and ineffective angiogenic response during the evolution of resistance to anti-angiogenic therapy ]]> https://biorxiv.org/content/10.1101/272328v1?rss=1 Jahangiri, A. Chen, W. Chandra, A. Nguyen, A. Weiss, J. Wolf, K. Lin, G. Rick, J. Sidorov, M. Flanigan, P. Yagnik, G. Carbonell, W. S. Kumar, S. Aghi, M. K. 2018-02-28 doi:10.1101/272328 Cold Spring Harbor Laboratory Press 2018-02-28 <![CDATA[ The Hedgehog signaling domain was acquired from a prokaryote. ]]> https://biorxiv.org/content/10.1101/276295v1?rss=1 Roelink, H. 2018-03-08 doi:10.1101/276295 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ HIV-1 Nefs are cargo-sensitive AP-1 trimerization switches in tetherin and MHC-I downregulation ]]> https://biorxiv.org/content/10.1101/276733v1?rss=1 Morris, K. L. Buffalo, C. Z. Sturzel, C. M. Heusinger, E. Kirchhoff, F. Ren, X. Hurley, J. H. 2018-03-05 doi:10.1101/276733 Cold Spring Harbor Laboratory Press 2018-03-05 <![CDATA[ Bacteriophage cooperation suppresses CRISPR-Cas3 and Cas9 immunity ]]> https://biorxiv.org/content/10.1101/279141v1?rss=1 Bacteria utilize CRISPR-Cas adaptive immune systems for protection from bacteriophages (phages), and some phages produce anti-CRISPR (Acr) proteins that inhibit immune function. Despite thorough mechanistic and structural information for some Acr proteins, how they are deployed and utilized by a phage during infection is unknown. Here, we show that Acr production does not guarantee phage replication, but instead, infections fail when phage population numbers fall below a critical threshold. Failing infections can be rescued by related phages that act as Acr donors, demonstrating that infections succeed if a sufficient Acr dose is contributed to a single cell by multiple phage genomes. The production of Acr proteins by phage genomes that fail to replicate leave the cell immunosuppressed, which predisposes the cell for successful infection by other phages in the population. This "cooperative" phage mechanism for CRISPR-Cas inhibition demonstrates inter-virus cooperation that may also manifest in other host-parasite interactions. ]]> Borges, A. L. Zhang, J. Y. Rollins, M. Osuna, B. A. Wiedenheft, B. Bondy-Denomy, J. 2018-03-08 doi:10.1101/279141 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ Zika Virus Outbreak, Barbados, 2015 - 2016 ]]> https://biorxiv.org/content/10.1101/279182v1?rss=1 Ryan, S. J. Lippi, C. A. Carlson, C. J. Stewart-Ibarra, A. M. Borbor Cordova, M. J. Romero, M. M. Cox, S.-A. Mahon, R. Trotman, A. Rollock, L. Gittens-St. Hilaire, M. King, D. Daniel, S. 2018-03-09 doi:10.1101/279182 Cold Spring Harbor Laboratory Press 2018-03-09 <![CDATA[ Characterization of Diverse Homoserine Lactone Synthases in Escherichia coli ]]> https://biorxiv.org/content/10.1101/279349v1?rss=1 Daer, R. Barrett, C. Melendez, E. L. Wu, J. Tekel, S. Xu, J. Dennison, B. Muller, R. Haynes, K. A. 2018-03-09 doi:10.1101/279349 Cold Spring Harbor Laboratory Press 2018-03-09 <![CDATA[ Spatial extinction date estimation: a novel method for reconstructing spatiotemporal patterns of extinction and identifying potential zones of rediscovery ]]> https://biorxiv.org/content/10.1101/279679v1?rss=1 Carlson, C. J. Burgio, K. R. Dallas, T. A. Bond, A. L. 2018-03-11 doi:10.1101/279679 Cold Spring Harbor Laboratory Press 2018-03-11 <![CDATA[ Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community ]]> https://biorxiv.org/content/10.1101/280438v1?rss=1 Gomez-Consarnau, L. Sachdeva, R. Gifford, S. M. Cutter, L. S. Fuhrman, J. Sanudo-Wilhelmy, S. A. Moran, M. A. 2018-03-12 doi:10.1101/280438 Cold Spring Harbor Laboratory Press 2018-03-12 <![CDATA[ Estimation of population divergence times from SNP data and a test for treeness ]]> https://biorxiv.org/content/10.1101/281881v1?rss=1 Theunert, C. Slatkin, M. 2018-03-14 doi:10.1101/281881 Cold Spring Harbor Laboratory Press 2018-03-14 <![CDATA[ A network of MAP-Kinase pathways and transcription factors regulates cell-to-cell communication and cell wall integrity in Neurospora crassa ]]> https://biorxiv.org/content/10.1101/281931v1?rss=1 Glass, N. L. Fischer, M. S. Wu, V. W. Lee, J. E. O'Malley, R. C. 2018-03-13 doi:10.1101/281931 Cold Spring Harbor Laboratory Press 2018-03-13 <![CDATA[ Switch-like activation of Bruton’s tyrosine kinase by membrane-mediated dimerization ]]> https://biorxiv.org/content/10.1101/284000v1?rss=1 Chung, J. K. Nocka, L. M. Wang, Q. Kadlecek, T. A. Weiss, A. Kuriyan, J. Groves, J. T. 2018-03-17 doi:10.1101/284000 Cold Spring Harbor Laboratory Press 2018-03-17 <![CDATA[ Conservation and Divergence of YODA MAPKKK Function in Regulation of Grass Epidermal Patterning ]]> https://biorxiv.org/content/10.1101/287433v1?rss=1 Abrash, E. Anleu Gil, M. X. Matos, J. L. Bergmann, D. C. 2018-03-23 doi:10.1101/287433 Cold Spring Harbor Laboratory Press 2018-03-23 <![CDATA[ Low-Cost Touchscreen Driven Programmable Dual Syringe Pump for Life Science Applications ]]> https://biorxiv.org/content/10.1101/288290v1?rss=1 Garcia, V. E. Liu, J. DeRisi, J. 2018-03-25 doi:10.1101/288290 Cold Spring Harbor Laboratory Press 2018-03-25 <![CDATA[ Oblique plane single-molecule localization microscopy for thick samples ]]> https://biorxiv.org/content/10.1101/289686v1?rss=1 Kim, J. Wojcik, M. Wang, Y. Xu, K. Zhang, X. 2018-03-27 doi:10.1101/289686 Cold Spring Harbor Laboratory Press 2018-03-27 <![CDATA[ Global changes in mRNA abundance drive differential shuttling of RNA binding proteins, linking cytoplasmic RNA degradation to transcription ]]> https://biorxiv.org/content/10.1101/295972v1?rss=1 Gilbertson, S. Federspiel, J. D. Hartenian, E. Cristea, I. M. Glaunsinger, B. 2018-04-06 doi:10.1101/295972 Cold Spring Harbor Laboratory Press 2018-04-06 <![CDATA[ A 3D Topographical Model of Parenchymal Infiltration and Perivascular Invasion in Glioblastoma ]]> https://biorxiv.org/content/10.1101/298240v1?rss=1 Wolf, K. J. Lee, S. Kumar, S. 2018-04-09 doi:10.1101/298240 Cold Spring Harbor Laboratory Press 2018-04-09 <![CDATA[ Connectivity Problems on Heterogeneous Graphs ]]> https://biorxiv.org/content/10.1101/300012v1?rss=1 0, and that this bound is tight. Moving beyond the worst case, we explore a special set of instances where the reference graph grows monotonically between conditions, and show that this problem admits substantially improved approximation algorithms. We also developed an integer linear programming solver for the general problem and demonstrate its ability to reach optimality with instances from the human protein interaction network.nnConclusionOur results demonstrate that in contrast to most connectivity problems studied in computational biology, accounting for multiplicity of biological conditions adds considerable complexity, which we propose to address with a new solver. Importantly, our results extend to several network connectivity problems that are commonly used in computational biology, such as Prize-Collecting Steiner Tree, and provide insight into the theoretical guarantees for their applications in a multiple condition setting.nnAvailabilityOur solver for the general condition Steiner network problem is available at https://github.com/YosefLab/condition_connectivity_problems ]]> Wu, J. Khodaverdian, A. Weitz, B. Yosef, N. 2018-04-13 doi:10.1101/300012 Cold Spring Harbor Laboratory Press 2018-04-13 <![CDATA[ Stress relaxation in epithelial monolayers is controlled by actomyosin ]]> https://biorxiv.org/content/10.1101/302158v1?rss=1 Khalilgharibi, N. Fouchard, J. Asadipour, N. Yonis, A. Harris, A. Mosaffa, P. Fujita, Y. Kabla, A. Baum, B. Munoz, J. J. Miodownik, M. Charras, G. 2018-04-16 doi:10.1101/302158 Cold Spring Harbor Laboratory Press 2018-04-16 <![CDATA[ Dynamics of ion fluxes between neurons, astrocytes and the extracellular space during neurotransmission ]]> https://biorxiv.org/content/10.1101/305706v1?rss=1 Rouach, N. Dao Duc, K. Sibille, J. Holcman, D. 2018-04-20 doi:10.1101/305706 Cold Spring Harbor Laboratory Press 2018-04-20 <![CDATA[ Estimating the timing of multiple admixture pulses during local ancestry inference. ]]> https://biorxiv.org/content/10.1101/314617v1?rss=1 Medina, P. Thornlow, B. Nielsen, R. Corbett-Detig, R. 2018-05-08 doi:10.1101/314617 Cold Spring Harbor Laboratory Press 2018-05-08 <![CDATA[ The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms ]]> https://biorxiv.org/content/10.1101/315689v1?rss=1 Brooks, B. Olm, M. R. Firek, B. A. Baker, R. Geller-McGrath, D. Reimer, S. R. Soenjoyo, K. R. Yip, J. S. Dahan, D. Thomas, B. C. Morowitz, M. J. Banfield, J. F. 2018-05-07 doi:10.1101/315689 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ Increased excitation-inhibition ratio stabilizes synapse and circuit excitability in four autism mouse models. ]]> https://biorxiv.org/content/10.1101/317693v1?rss=1 Antoine, M. W. Schnepel, P. Langberg, T. Feldman, D. E. 2018-05-09 doi:10.1101/317693 Cold Spring Harbor Laboratory Press 2018-05-09 <![CDATA[ The spectral identity of foveal cones is preserved in hue perception ]]> https://biorxiv.org/content/10.1101/317750v1?rss=1 Schmidt, B. P. Boehm, A. E. Foote, K. G. Roorda, A. 2018-05-09 doi:10.1101/317750 Cold Spring Harbor Laboratory Press 2018-05-09 <![CDATA[ CDK19 is a Regulator of Triple-Negative Breast Cancer Growth ]]> https://biorxiv.org/content/10.1101/317776v1?rss=1 Hsieh, R. W. Kuo, A. H. Scheeren, F. A. Zarnegar, M. A. Sikandar, S. S. Antony, J. Heitink, L. S. Periyakoil, D. Kalisky, T. Sim, S. Qian, D. Malhotra, S. V. Somlo, G. Dirbas, F. M. Jadhav, A. Newman, A. M. Clarke, M. F. 2018-05-10 doi:10.1101/317776 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Strain-level overlap between infant and hospital fungal microbiomes revealed through de novo assembly of eukaryotic genomes from metagenomes ]]> https://biorxiv.org/content/10.1101/324566v1?rss=1 Olm, M. R. West, P. T. Brooks, B. Firek, B. A. Baker, R. Morowitz, M. J. Banfield, J. F. 2018-05-17 doi:10.1101/324566 Cold Spring Harbor Laboratory Press 2018-05-17 <![CDATA[ Nucleo-cytoplasmic trafficking regulates nuclear surface area during nuclear organogenesis ]]> https://biorxiv.org/content/10.1101/326140v1?rss=1 Boudreau, V. Hazel, J. Sellinger, J. K. Chen, P. Manakova, K. Radzyminski, R. Garcia, H. G. Allard, J. Gatlin, J. Maddox, P. S. 2018-05-18 doi:10.1101/326140 Cold Spring Harbor Laboratory Press 2018-05-18 <![CDATA[ Revealing biases in the sampling of ecological interaction networks ]]> https://biorxiv.org/content/10.1101/328245v1?rss=1 de Aguiar, M. Newman, E. A. Pires, M. M. Yeakel, J. D. Hembry, D. H. Boettinger, C. Burkle, L. A. Gravel, D. Guimaraes, P. R. O'Donnell, J. L. Poisot, T. Fortin, M.-J. Ecological Network Dynamics Working Group at the National Institute for Mathematical and Biological, 2018-05-22 doi:10.1101/328245 Cold Spring Harbor Laboratory Press 2018-05-22 <![CDATA[ Taxonomy, phylogeny and biogeography of African spurfowls (Galliformes, Phasianidae, Coturnicinae, Pternistis spp.) ]]> https://biorxiv.org/content/10.1101/329243v1?rss=1 Crowe, T. M. Mandiwana-Neudani, T. G. Little, R. M. Bowie, R. C. K. N/A, 2018-05-23 doi:10.1101/329243 Cold Spring Harbor Laboratory Press 2018-05-23 <![CDATA[ A synthesis of mapping experiments reveals extensive genomic structural diversity in the Mimulus guttatus species complex ]]> https://biorxiv.org/content/10.1101/330159v1?rss=1 Flagel, L. Blackman, B. K. Fishman, L. Monnahan, P. J. Sweigart, A. Kelly, J. K. 2018-05-24 doi:10.1101/330159 Cold Spring Harbor Laboratory Press 2018-05-24 <![CDATA[ Biological capacities clearly define a major subdivision in Domain Bacteria ]]> https://biorxiv.org/content/10.1101/335083v1?rss=1 Meheust, R. Burstein, D. Castelle, C. J. Banfield, J. F. 2018-05-30 doi:10.1101/335083 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ CRISPR-Cas9 interrogation of a putative fetal globin repressor in human erythroid cells. ]]> https://biorxiv.org/content/10.1101/335729v1?rss=1 Chung, J. E. Magis, W. Vu, J. Heo, S.-J. Wartiovaara, K. Walters, M. C. Kurita, R. Nakamura, Y. Boffelli, D. Martin, D. I. Corn, J. E. Dewitt, M. A. 2018-05-31 doi:10.1101/335729 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ Leveraging pathogen community distributions to understand outbreak and emergence potential ]]> https://biorxiv.org/content/10.1101/336065v1?rss=1 Dallas, T. A. Carlson, C. J. Poisot, T. 2018-05-31 doi:10.1101/336065 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ Integrating Host Response and Unbiased Microbe Detection for Lower Respiratory Tract Infection Diagnosis in Critically Ill Adults ]]> https://biorxiv.org/content/10.1101/341149v1?rss=1 Langelier, C. Kalantar, K. L. Moazed, F. Wilson, M. R. Crawford, E. Deiss, T. Belzer, A. Bolourchi, S. Caldera, S. Fung, M. Jauregui, A. Malcolm, K. Lyden, A. Khan, L. Vessel, K. Quan, J. Zinter, M. Chiu, C. Y. Chow, E. D. Wilson, J. Miller, S. Matthay, M. A. Pollard, K. S. Christenson, S. Calfee, C. S. DeRisi, J. L. 2018-06-11 doi:10.1101/341149 Cold Spring Harbor Laboratory Press 2018-06-11 <![CDATA[ Ultralarge Modulation of Single Wall Carbon Nanotube Fluorescence Mediated by Neuromodulators Adsorbed on Arrays of Oligonucleotide Rings ]]> https://biorxiv.org/content/10.1101/351627v1?rss=1 Beyene, A. G. Alizadehmojarad, A. A. Dorlhiac, G. Streets, A. M. Kral, P. Vukovic, L. Landry, M. P. 2018-06-20 doi:10.1101/351627 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Imaging Striatal Dopamine Release Using a Non-Genetically Encoded Near-Infrared Fluorescent Catecholamine Nanosensor ]]> https://biorxiv.org/content/10.1101/356543v1?rss=1 Beyene, A. G. Delevich, K. Del Bonis ODonnell, J. T. Piekarski, D. J. Lin, W. C. Thomas, A. W. Yang, S. J. Kosillo, P. Yang, D. Wilbrecht, L. Landry, M. P. 2018-07-03 doi:10.1101/356543 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Megaphage infect Prevotella and variants are widespread in gut microbiomes ]]> https://biorxiv.org/content/10.1101/356790v1?rss=1 540 kb in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phage. We refer to these as Lak phage. CRISPR spacer targeting indicates that the Lak phage infect bacteria of the genus Prevotella. We manually curated to completion 15 distinct Lak phage genomes recovered from metagenomes. The genomes display several interesting features, including use of an alternative genetic code, large intergenic regions that are highly expressed, and up to 35 putative tRNAs, some of which contain enigmatic introns. Different individuals have distinct phage genotypes, and shifts in variant frequencies over consecutive sampling days reflect changes in relative abundance of phage sub-populations. Recent homologous recombination has resulted in extensive genome admixture of nine baboon Lak phage populations. We infer that Lak phage are widespread in gut communities that contain Prevotella species, especially in individuals in the developing world, and conclude that megaphage, with fascinating and underexplored biology, may be common but largely overlooked components of human and animal gut microbiomes. ]]> Devoto, A. E. Santini, J. M. Olm, M. R. Anantharaman, K. Munk, P. Tung, J. Archie, E. A. Turnbaugh, P. J. Seed, K. D. Blekhman, R. Aarestrup, F. M. Thomas, B. C. Banfield, J. F. 2018-06-27 doi:10.1101/356790 Cold Spring Harbor Laboratory Press 2018-06-27 <![CDATA[ Single-embryo and single-blastomere immunoblotting reports protein expression heterogeneity in early-stage preimplantation embryos ]]> https://biorxiv.org/content/10.1101/357731v1?rss=1 Rosas, E. Modzelewski, A. J. He, L. Herr, A. E. 2018-06-28 doi:10.1101/357731 Cold Spring Harbor Laboratory Press 2018-06-28 <![CDATA[ Deconvolution of substrate processing by the 26S proteasome reveals a selective kinetic gateway to degradation ]]> https://biorxiv.org/content/10.1101/359695v1?rss=1 Bard, J. A. Bashore, C. Dong, K. C. Martin, A. 2018-06-30 doi:10.1101/359695 Cold Spring Harbor Laboratory Press 2018-06-30 <![CDATA[ The return to water in ancestral Xenopus was accompanied by a novel mechanisms for producing and shaping vocal signals ]]> https://biorxiv.org/content/10.1101/360255v1?rss=1 Kwong-Brown, U. Tobias, M. L. Elias, D. O. Hall, I. C. Elemans, C. P. H. Kelley, D. B. 2018-07-03 doi:10.1101/360255 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Mango: Distributed Visualization for Genomic Analysis ]]> https://biorxiv.org/content/10.1101/360842v1?rss=1 Morrow, A. K. He, G. Z. Nothaft, F. A. Paschall, J. Yosef, N. Joseph, A. D. 2018-07-03 doi:10.1101/360842 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ A smartphone-based tool for rapid, portable, and automated wide-field retinal imaging ]]> https://biorxiv.org/content/10.1101/364265v1?rss=1 Kim, T. Myers, F. Reber, C. Loury, P. Loumou, P. Webster, D. Echanique, C. Li, P. Davila, J. Maamari, R. Switz, N. Keenan, J. Woodward, M. Paulus, Y. Margolis, T. Fletcher, D. 2018-07-07 doi:10.1101/364265 Cold Spring Harbor Laboratory Press 2018-07-07 <![CDATA[ Expression reflects population structure ]]> https://biorxiv.org/content/10.1101/364448v1?rss=1 Brown, B. C. Bray, N. L. Pachter, L. 2018-07-08 doi:10.1101/364448 Cold Spring Harbor Laboratory Press 2018-07-08 <![CDATA[ Massively parallel characterization of regulatory dynamics during neural induction ]]> https://biorxiv.org/content/10.1101/370452v1?rss=1 Inoue, F. Kreimer, A. Ashuach, T. Ahituv, N. Yosef, N. 2018-07-16 doi:10.1101/370452 Cold Spring Harbor Laboratory Press 2018-07-16 <![CDATA[ Architectural Features of 3D Genome Organization Revealed by Counting CTCF and Cohesin Molecules ]]> https://biorxiv.org/content/10.1101/370650v1?rss=1 Cattoglio, C. Pustova, I. Ho, J. J. Inouye, C. J. Dailey, G. M. Darzacq, X. Tjian, R. Hansen, A. S. 2018-07-17 doi:10.1101/370650 Cold Spring Harbor Laboratory Press 2018-07-17 <![CDATA[ Entomophthovirus: An insect-derived iflavirus that infects a behavior manipulating fungal pathogen of dipterans ]]> https://biorxiv.org/content/10.1101/371526v1?rss=1 Coyle, M. C. Elya, C. N. Bronski, M. J. Eisen, M. B. 2018-07-18 doi:10.1101/371526 Cold Spring Harbor Laboratory Press 2018-07-18 <![CDATA[ Transient DNA Binding Induces RNA Polymerase II Compartmentalization During Herpesviral Infection Distinct From Phase Separation ]]> https://biorxiv.org/content/10.1101/375071v1?rss=1 McSwiggen, D. T. Hansen, A. S. Marie-Nelly, H. Teves, S. Heckert, A. B. Dugast-Darzacq, C. Hao, Y. Umemoto, K. K. Tjian, R. Darzacq, X. 2018-07-23 doi:10.1101/375071 Cold Spring Harbor Laboratory Press 2018-07-23 <![CDATA[ A Metagenomic Comparison of Tracheal Aspirate and Mini-Bronchial Alveolar Lavage for Assessment of Respiratory Microbiota ]]> https://biorxiv.org/content/10.1101/375360v1?rss=1 Kalantar, K. Moazed, F. Christenson, S. Wilson, J. Deiss, T. Belzer, A. Vessell, K. Jauregui, A. Boulourchi, S. DeRisi, J. L. Calfee, C. Langelier, C. 2018-07-24 doi:10.1101/375360 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ Predicting HIV Incidence in the SEARCH Trial: A Mathematical Modelling Study ]]> https://biorxiv.org/content/10.1101/376244v1?rss=1 Jewell, B. L. Bershteyn, A. 2018-07-25 doi:10.1101/376244 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ Developmental Regulation of an Organelle Tether Coordinates Mitochondrial Remodeling in Meiosis ]]> https://biorxiv.org/content/10.1101/376509v1?rss=1 Unal, E. Sawyer, E. Joshi, P. Berchowitz, L. 2018-07-24 doi:10.1101/376509 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ 3D-printable tools for developmental biology: Improving embryo injection and screening techniques through 3D-printing technology ]]> https://biorxiv.org/content/10.1101/376657v1?rss=1 Truchado-Garcia, M. Harland, R. M. Abrams, M. J. 2018-07-25 doi:10.1101/376657 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ Tsc1-mTOR signaling controls the structure and function of midbrain dopamine neurons ]]> https://biorxiv.org/content/10.1101/376814v1?rss=1 Kosillo, P. Doig, N. Agopyan-Miu, A. Ahmed, K. Conyers, L. Threlfell, S. Magill, P. Bateup, H. 2018-07-25 doi:10.1101/376814 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ SymSim: simulating multi-faceted variability in single cell RNA sequencing ]]> https://biorxiv.org/content/10.1101/378646v1?rss=1 Zhang, X. Xu, C. Yosef, N. 2018-07-28 doi:10.1101/378646 Cold Spring Harbor Laboratory Press 2018-07-28 <![CDATA[ Stabilizing Obligatory Non-native Intermediates Along Co-transcriptional Folding Trajectories of SRP RNA Affects Cell Viability ]]> https://biorxiv.org/content/10.1101/378745v1?rss=1 Fukuda, S. Yan, S. Komi, Y. Sun, M. Gabizon, R. Bustamante, C. 2018-07-27 doi:10.1101/378745 Cold Spring Harbor Laboratory Press 2018-07-27 <![CDATA[ Computationally Reconstructing Cotranscriptional RNA Folding Pathways from Experimental Data Reveals Rearrangement of Non-Native Folding Intermediates ]]> https://biorxiv.org/content/10.1101/379222v1?rss=1 Yu, A. M. Gasper, P. M. Strobel, E. J. Watters, K. E. Chen, A. A. Lucks, J. B. 2018-07-28 doi:10.1101/379222 Cold Spring Harbor Laboratory Press 2018-07-28 <![CDATA[ Glycosyltransferase homologs prevent promiscuous cell aggregation and promote multicellular development in the choanoflagellate S. rosetta ]]> https://biorxiv.org/content/10.1101/384453v1?rss=1 Wetzel, L. Levin, T. Hulett, R. E. Chan, D. King, G. Aldayafleh, R. Booth, D. Sigg, M. A. King, N. 2018-08-04 doi:10.1101/384453 Cold Spring Harbor Laboratory Press 2018-08-04 <![CDATA[ Etiology of fever in Ugandan children: identification of microbial pathogens using metagenomic next-generation sequencing and IDseq, a platform for unbiased metagenomic analysis ]]> https://biorxiv.org/content/10.1101/385005v1?rss=1 Ramesh, A. Nakielny, S. Hsu, J. Kyohere, M. Byaruhanga, O. de Bourcy, C. Egger, R. Dimitrov, B. Juan, Y.-F. Sheu, J. Wang, J. Kalantar, K. Langelier, C. Ruel, T. Mpimbaza, A. Wilson, M. R. Rosenthal, P. J. DeRisi, J. L. 2018-08-04 doi:10.1101/385005 Cold Spring Harbor Laboratory Press 2018-08-04 <![CDATA[ Open-Source Food: Nutrition, Toxicology, and Availability of Wild Edible Greens in the East Bay ]]> https://biorxiv.org/content/10.1101/385864v1?rss=1 Stark, P. Miller, D. Carlson, T. de Vasquez, K. R. 2018-08-06 doi:10.1101/385864 Cold Spring Harbor Laboratory Press 2018-08-06 <![CDATA[ Voxelwise encoding models with non-spherical multivariate normal priors ]]> https://biorxiv.org/content/10.1101/386318v1?rss=1 Nunez-Elizalde, A. O. Huth, A. G. Gallant, J. L. 2018-08-09 doi:10.1101/386318 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ Reconstructing B cell receptor sequences from short-read single cell RNA-sequencing with BRAPeS ]]> https://biorxiv.org/content/10.1101/389999v1?rss=1 Afik, S. Yosef, N. 2018-08-10 doi:10.1101/389999 Cold Spring Harbor Laboratory Press 2018-08-10 <![CDATA[ There and back again: metagenome-assembled genomes provide new insights into two thermal pools in Kamchatka, Russia ]]> https://biorxiv.org/content/10.1101/392308v1?rss=1 Wilkins, L. Ettinger, C. Jospin, G. Eisen, J. A. 2018-08-15 doi:10.1101/392308 Cold Spring Harbor Laboratory Press 2018-08-15 <![CDATA[ Global climate changes will lead to regionally divergent trajectories for ectomycorrhizal communities in North American Pinaceae forests ]]> https://biorxiv.org/content/10.1101/393009v1?rss=1 Steidinger, B. Bhatnagar, J. Vilgalys, R. Taylor, J. Bruns, T. Peay, K. G. 2018-08-16 doi:10.1101/393009 Cold Spring Harbor Laboratory Press 2018-08-16 <![CDATA[ Distinct higher-order thalamic circuits channel parallel streams of visual information in mice ]]> https://biorxiv.org/content/10.1101/395244v1?rss=1 Bennett, C. Gale, S. D. Garrett, M. E. Newton, M. L. Callaway, E. M. Murphy, G. J. Olsen, S. R. 2018-08-18 doi:10.1101/395244 Cold Spring Harbor Laboratory Press 2018-08-18 <![CDATA[ Xenopus hybrids provide insight into cell and organism size control ]]> https://biorxiv.org/content/10.1101/395814v1?rss=1 Gibeaux, R. Miller, K. Acker, R. Kwon, T. Heald, R. 2018-08-20 doi:10.1101/395814 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ Epigallocatechin-3-gallate yield in different temperature gradients in green tea (Camellia sinensis) brewing ]]> https://biorxiv.org/content/10.1101/396234v1?rss=1 Hsieh, M.-h. Hsieh, M.-j. Wu, C.-R. Peng, W.-h. Hsieh, M.-t. Hsieh, C.-c. 2018-08-20 doi:10.1101/396234 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ Sexual conflict in self-fertile hermaphrodites: reproductive differences among species, and between individuals versus cohorts, in the leech genus Helobdella (Lophotrochozoa; Annelida; Clitellata; Hirudinida; Glossiphoniidae) ]]> https://biorxiv.org/content/10.1101/401901v1?rss=1 Iyer, R. G. Rogers, D. V. Winchell, C. J. Weisblat, D. A. 2018-09-05 doi:10.1101/401901 Cold Spring Harbor Laboratory Press 2018-09-05 <![CDATA[ The interaction between ORF18 and ORF30 is required for late gene transcription in Kaposi’s sarcoma-associated herpesvirus ]]> https://biorxiv.org/content/10.1101/401976v1?rss=1 Castaneda, A. F. Glaunsinger, B. A. 2018-08-28 doi:10.1101/401976 Cold Spring Harbor Laboratory Press 2018-08-28 <![CDATA[ Estimation of Rearrangement Break Rates Across the Genome ]]> https://biorxiv.org/content/10.1101/402933v1?rss=1 Hann-Soden, C. Holmes, I. Taylor, J. W. 2018-08-29 doi:10.1101/402933 Cold Spring Harbor Laboratory Press 2018-08-29 <![CDATA[ Functional Interpretation of Single-Cell Similarity Maps ]]> https://biorxiv.org/content/10.1101/403055v1?rss=1 DeTomaso, D. Jones, M. Subramaniam, M. Ashuach, T. Ye, C. J. Yosef, N. 2018-08-29 doi:10.1101/403055 Cold Spring Harbor Laboratory Press 2018-08-29 <![CDATA[ The effects of fixational tremor on the retinal image ]]> https://biorxiv.org/content/10.1101/403964v1?rss=1 Bowers, N. R. Boehm, A. E. Roorda, A. 2018-08-30 doi:10.1101/403964 Cold Spring Harbor Laboratory Press 2018-08-30 <![CDATA[ CHEMOMETRIC APPROACHES FOR DEVELOPING INFRARED NANOSENSORS TO IMAGE ANTHRACYCLINES ]]> https://biorxiv.org/content/10.1101/407650v1?rss=1 Del Bonis-O Donnell, J. T. Pinals, R. Jeong, S. Thakrar, A. Wolfinger, R. Landry, M. P. 2018-09-04 doi:10.1101/407650 Cold Spring Harbor Laboratory Press 2018-09-04 <![CDATA[ Versatile Multi-Detector Scheme for Adaptive Optics Scanning Laser Ophthalmoscopy ]]> https://biorxiv.org/content/10.1101/408526v1?rss=1 Mozaffari, S. Jaedicke, V. LaRocca, F. Tiruveedhula, P. Roorda, A. 2018-09-06 doi:10.1101/408526 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ Behavioral Analysis of Substrate Texture Preference in a Leech, Helobdella austinensis ]]> https://biorxiv.org/content/10.1101/409755v1?rss=1 Kim, R. C. Le, D. Ma, K. Heath-Heckman, E. A. C. Whitehorn, N. Kristan, W. B. Weisblat, D. A. 2018-09-05 doi:10.1101/409755 Cold Spring Harbor Laboratory Press 2018-09-05 <![CDATA[ A versatile platform strain for high-fidelity multiplex genome editing ]]> https://biorxiv.org/content/10.1101/410001v1?rss=1 Egbert, R. G. Rishi, H. S. Adler, B. A. McCormick, D. M. Toro, E. Gill, R. T. Arkin, A. P. 2018-09-06 doi:10.1101/410001 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies ]]> https://biorxiv.org/content/10.1101/412924v1?rss=1 0.4). Furthermore, even for rats obtained from the same vendor, there was strong population structure across breeding facilities and even between rooms at the same facility. We performed multiple separate GWAS by fitting a linear mixed model that accounted population structure and using meta-analysis to jointly analyze all cohorts. Our study examined Pavlovian conditioned approach (PavCA) behavior, which assesses the propensity for rats to attribute incentive salience to reward-associated cues. We identified 46 significant associations for the various metrics used to define PavCA. The surprising degree of population structure among SD rats from different sources has important implications for their use in both genetic and non-genetic studies. Author SummaryOutbred Sprague Dawley rats are among the most commonly used rats for neuroscience, physiology and pharmacological research; in the year 2020, 4,188 publications contained the keyword "Sprague Dawley". Rats identified as "Sprague Dawley" are sold by several commercial vendors, including Charles River Laboratories and Harlan Sprague Dawley Inc. (now Envigo). Despite their widespread use, little is known about the genetic diversity of SD. We genotyped more than 4,000 SD rats, which we used for a genome-wide association study (GWAS) and to characterize genetic differences between SD rats from Charles River Laboratories and Harlan. Our analysis revealed extensive population structure both between and within vendors. The GWAS for Pavlovian conditioned approach (PavCA) identified a number of genome-wide significant loci for that complex behavioral trait. Our results demonstrate that, despite sharing an identical name, SD rats that are obtained from different vendors are very different. Future studies should carefully define the exact source of SD rats being used and may exploit their genetic diversity for genetic studies of complex traits. ]]> Gileta, A. F. Fitzpatrick, C. J. Chitre, A. S. St. Pierre, C. L. Joyce, E. V. Maguire, R. J. McLeod, A. M. Gonzales, N. M. Williams, A. E. Morrow, J. D. Robinson, T. E. Flagel, S. B. Palmer, A. A. 2018-09-10 doi:10.1101/412924 Cold Spring Harbor Laboratory Press 2018-09-10 <![CDATA[ Lessons learned when looking for non-neutral ecological processes in the built environment: the bacterial and fungal microbiota of shower tiles ]]> https://biorxiv.org/content/10.1101/413773v1?rss=1 Adams, R. I. Lymperopoulou, D. 2018-09-11 doi:10.1101/413773 Cold Spring Harbor Laboratory Press 2018-09-11 <![CDATA[ Novel childhood experience suggests eccentricity drives organization of human visual cortex ]]> https://biorxiv.org/content/10.1101/415729v1?rss=1 Gomez, J. Barnett, M. Grill-Spector, K. 2018-09-13 doi:10.1101/415729 Cold Spring Harbor Laboratory Press 2018-09-13 <![CDATA[ The Synergistic Effect of Antioxidant Interaction between Luteolin and Chlorogenic Acid in Lonicera japonica ]]> https://biorxiv.org/content/10.1101/418319v1?rss=1 Hsieh, M.-H. Hsieh, M.-j. Wu, C.-R. Peng, W.-H. Hsieh, M.-T. Hsieh, C.-C. 2018-09-14 doi:10.1101/418319 Cold Spring Harbor Laboratory Press 2018-09-14 <![CDATA[ Environmental oscillations favor the evolution of adaptive transgenerational plasticity ]]> https://biorxiv.org/content/10.1101/426007v1?rss=1 Colicchio, J. Herman, J. J. 2018-09-25 doi:10.1101/426007 Cold Spring Harbor Laboratory Press 2018-09-25 <![CDATA[ GIGANTEA promotes sorghum flowering by stimulating floral activator gene expression ]]> https://biorxiv.org/content/10.1101/427492v1?rss=1 Harmon, F. G. Chen, J. Xin, Z. 2018-09-29 doi:10.1101/427492 Cold Spring Harbor Laboratory Press 2018-09-29 <![CDATA[ The nuclear RNAi factor, NRDE2, prevents the accumulation of DNA damage during mitosis in stressful growth conditions ]]> https://biorxiv.org/content/10.1101/428250v1?rss=1 Asuni, A. Venkataramanan, S. Suzuki, A. Floor, S. N. Goga, A. L'Etoile, N. 2018-09-27 doi:10.1101/428250 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ Structural basis for substrate gripping and translocation by the ClpB AAA+ disaggregase ]]> https://biorxiv.org/content/10.1101/428458v1?rss=1 Rizo, A. N. Lin, J. Gates, S. N. Tse, E. Bart, S. M. Castellano, L. M. DiMaio, F. Shorter, J. Southworth, D. R. 2018-09-26 doi:10.1101/428458 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ Herbarium records reveal early flowering in response to warming in the southern hemisphere ]]> https://biorxiv.org/content/10.1101/432765v1?rss=1 Daru, B. H. Kling, M. M. Meineke, E. K. van Wyk, A. E. E. 2018-10-02 doi:10.1101/432765 Cold Spring Harbor Laboratory Press 2018-10-02 <![CDATA[ Suppressor of Fused controls the proliferation of postnatal neural stem and precursor cells via a Gli3-dependent mechanism ]]> https://biorxiv.org/content/10.1101/438705v1?rss=1 Gomez, H. G. Castillo, J. G. Noguchi, H. Aguilar, D. Pleasure, S. J. Yabut, O. R. 2018-10-09 doi:10.1101/438705 Cold Spring Harbor Laboratory Press 2018-10-09 <![CDATA[ Tropical arboreal ants form dominance hierarchies over nesting resources in agroecosystems ]]> https://biorxiv.org/content/10.1101/442632v1?rss=1 Yitbarek, S. Philpott, S. M. 2018-10-13 doi:10.1101/442632 Cold Spring Harbor Laboratory Press 2018-10-13 <![CDATA[ Tactile enrichment drives emergence of functional columns and improves sensory coding in L2/3 of mouse S1 ]]> https://biorxiv.org/content/10.1101/447508v1?rss=1 LeMessurier, A. M. Feldman, D. E. 2018-10-18 doi:10.1101/447508 Cold Spring Harbor Laboratory Press 2018-10-18 <![CDATA[ On-ratio PDMS bonding for multilayer microfluidic device fabrication ]]> https://biorxiv.org/content/10.1101/450544v1?rss=1 Lai, A. Altemose, N. White, J. A. Streets, A. M. 2018-10-23 doi:10.1101/450544 Cold Spring Harbor Laboratory Press 2018-10-23 <![CDATA[ The architecture of cell differentiation in choanoflagellates and sponge choanocytes ]]> https://biorxiv.org/content/10.1101/452185v1?rss=1 Laundon, D. Larson, B. McDonald, K. King, N. Burkhardt, P. 2018-10-29 doi:10.1101/452185 Cold Spring Harbor Laboratory Press 2018-10-29 <![CDATA[ Directed evolution of split APEX peroxidase ]]> https://biorxiv.org/content/10.1101/452888v1?rss=1 Han, Y. Martell, J. Branon, T. Boassa, D. Shechner, D. Ellisman, M. Ting, A. 2018-10-25 doi:10.1101/452888 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Suppressor of Fused controls perinatal expansion and quiescence of future dentate adult neural stem cells ]]> https://biorxiv.org/content/10.1101/454751v1?rss=1 Pleasure, S. J. Noguchi, H. Castillo, J. G. Nakashima, K. 2018-10-27 doi:10.1101/454751 Cold Spring Harbor Laboratory Press 2018-10-27 <![CDATA[ Complementary subnetworks of cortical somatostatin interneurons ]]> https://biorxiv.org/content/10.1101/456574v1?rss=1 Naka, A. Shababo, B. Snyder, B. Egladyous, A. Sridharan, S. Paninski, L. Adesnik, H. 2018-10-30 doi:10.1101/456574 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ Cellular response to small molecules that selectively stall protein synthesis by the ribosome ]]> https://biorxiv.org/content/10.1101/461624v1?rss=1 Liaud, N. Horlbeck, M. A. Gilbert, L. A. Gjoni, K. Weissman, J. S. Cate, J. 2018-11-04 doi:10.1101/461624 Cold Spring Harbor Laboratory Press 2018-11-04 <![CDATA[ adductomicsR: A package for detection and quantification of protein adducts from mass spectra of tryptic digests ]]> https://biorxiv.org/content/10.1101/463331v1?rss=1 Hayes, J. L. Edmands, W. M. Yano, Y. Grigoryan, H. Schiffman, C. Dudoit, S. Rappaport, S. 2018-11-06 doi:10.1101/463331 Cold Spring Harbor Laboratory Press 2018-11-06 <![CDATA[ Strategies For Efficient Genome Editing Using CRISPR-Cas9 ]]> https://biorxiv.org/content/10.1101/465252v1?rss=1 Meyer, B. J. Farboud, B. Severson, A. 2018-11-07 doi:10.1101/465252 Cold Spring Harbor Laboratory Press 2018-11-07 <![CDATA[ Shifts in microbial transcription patterns prior to onset of Necrotizing enterocolitis may indicate low oxygen levels in the gut ]]> https://biorxiv.org/content/10.1101/466417v1?rss=1 Sher, Y. Olm, M. R. Raveh-Sadka, T. Brown, C. T. Sher, R. Firek, B. Baker, R. Morowitz, M. Banfield, J. 2018-11-09 doi:10.1101/466417 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ A New Method to Correct for Habitat Filtering in Microbial Correlation Networks ]]> https://biorxiv.org/content/10.1101/467365v1?rss=1 Brisson, V. Schmidt, J. Northen, T. R. Vogel, J. P. Gaudin, A. 2018-11-09 doi:10.1101/467365 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ Refining interaction search through signed iterative Random Forests ]]> https://biorxiv.org/content/10.1101/467498v1?rss=1 Kumbier, K. Basu, S. Brown, J. B. Celniker, S. Yu, B. 2018-11-11 doi:10.1101/467498 Cold Spring Harbor Laboratory Press 2018-11-11 <![CDATA[ The Drosophila pioneer factor Zelda modulates the nuclear microenvironment of a Dorsal target enhancer to potentiate transcriptional output ]]> https://biorxiv.org/content/10.1101/471029v1?rss=1 Yamada, S. Whitney, P. H. Huang, S.-K. Eck, E. C. Garcia, H. G. Rushlow, C. A. 2018-11-15 doi:10.1101/471029 Cold Spring Harbor Laboratory Press 2018-11-15 <![CDATA[ Transient activation of the UPRER is an essential step in the acquisition of pluripotency during reprogramming ]]> https://biorxiv.org/content/10.1101/472787v1?rss=1 Simic, M. Moehle, E. Schinzel, R. Lorbeer, F. Jullie, D. Halloran, J. Heydari, K. Sanchez, M. Hockemeyer, D. Dillin, A. 2018-11-17 doi:10.1101/472787 Cold Spring Harbor Laboratory Press 2018-11-17 <![CDATA[ Long-term balancing selection drives evolution of immunity genes in Capsella ]]> https://biorxiv.org/content/10.1101/477612v1?rss=1 Koenig, D. Hagmann, J. Li, R. Bemm, F. Slotte, T. Nueffer, B. Wright, S. Weigel, D. 2018-11-26 doi:10.1101/477612 Cold Spring Harbor Laboratory Press 2018-11-26 <![CDATA[ Intelligible speech synthesis from neural decoding of spoken sentences ]]> https://biorxiv.org/content/10.1101/481267v1?rss=1 Anumanchipalli, G. K. Chartier, J. Chang, E. F. 2018-11-29 doi:10.1101/481267 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ Coherence-based spectro-spatial fillters for stimulus features prediction from electrocorticographic recordings. ]]> https://biorxiv.org/content/10.1101/481572v1?rss=1 Delgado Saa, J. F. Christen, A. Martin, S. Pasley, B. N. Knight, R. T. Giraud, A.-L. 2018-11-28 doi:10.1101/481572 Cold Spring Harbor Laboratory Press 2018-11-28 <![CDATA[ Transverse chromatic offsets with pupil displacements in the human eye: Sources of variability and methods for real-time correction ]]> https://biorxiv.org/content/10.1101/484386v1?rss=1 Boehm, A. E. Privitera, C. M. Schmidt, B. P. Roorda, A. 2018-12-02 doi:10.1101/484386 Cold Spring Harbor Laboratory Press 2018-12-02 <![CDATA[ Auditory deviance detection in the human insula: An intracranial EEG study ]]> https://biorxiv.org/content/10.1101/487306v1?rss=1 Blenkmann, A. O. Collavini, S. Lubell, J. Llorens, A. Funderud, I. Ivanovic, J. Larson, P. G. Meling, T. R. Bekinschtein, T. Kochen, S. Endestad, T. Knight, R. T. Solbakk, A.-K. 2018-12-04 doi:10.1101/487306 Cold Spring Harbor Laboratory Press 2018-12-04 <![CDATA[ Anacapa Toolkit: an environmental DNA toolkit for processing multilocus metabarcode datasets ]]> https://biorxiv.org/content/10.1101/488627v1?rss=1 Curd, E. E. Gold, Z. Kandlikar, G. Gomer, J. Ogden, M. O'Connell, T. Pipes, L. Schweizer, T. Rabichow, L. Lin, M. Shi, B. Barber, P. Kraft, N. Wayne, R. Meyer, R. S. 2018-12-07 doi:10.1101/488627 Cold Spring Harbor Laboratory Press 2018-12-07 <![CDATA[ The dynamic association of SPO11-1 with conformational changes of meiotic axial elements in maize ]]> https://biorxiv.org/content/10.1101/489278v1?rss=1 Ronceret, A. Golubovskaya, I. Ku, J.-C. Lee, D. H. Timofejeva, L. Angoa, A. K. G. Kao, Y.-H. Kremling, K. Williams-Carrier, R. Meeley, R. Barkan, A. Cande, W. Z. Wang, C.-J. R. 2018-12-06 doi:10.1101/489278 Cold Spring Harbor Laboratory Press 2018-12-06 <![CDATA[ Cryo-Electron tomography 3D structure and nanoscale model of Arabidopsis thaliana cell wall ]]> https://biorxiv.org/content/10.1101/492140v1?rss=1 Sarkar, P. Kowalczyk, M. Apte, S. Yap, E. G. Das, J. Adams, P. D. Bajaj, C. Guindos, P. Auer, M. 2018-12-10 doi:10.1101/492140 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Invariant neural responses for sensory categories revealed by the time-varying information for communication calls ]]> https://biorxiv.org/content/10.1101/492546v1?rss=1 Elie, J. E. Theunissen, F. E. 2018-12-10 doi:10.1101/492546 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ A genome-wide haploid genetic screen for essential factors in vaccinia virus infection identifies TMED10 as regulator of macropinocytosis ]]> https://biorxiv.org/content/10.1101/493205v1?rss=1 Luteijn, R. D. van Diemen, F. R. Blomen, V. A. Boer, I. G. Manikam Sadasivam, S. van Kuppevelt, T. Drexler, I. Brummelkamp, T. R. Lebbink, R. J. Wiertz, E. J. 2018-12-11 doi:10.1101/493205 Cold Spring Harbor Laboratory Press 2018-12-11 <![CDATA[ Human visual cortex is organized along two genetically opposed hierarchical gradients with unique developmental and evolutionary origins ]]> https://biorxiv.org/content/10.1101/495143v1?rss=1 Gomez, J. Zhen, Z. Weiner, K. 2018-12-13 doi:10.1101/495143 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Identifying the Biosynthetic Gene Cluster for Triacsins with an N-hydroxytriazene Moiety ]]> https://biorxiv.org/content/10.1101/495424v1?rss=1 Twigg, F. F. Cai, W. Huang, W. Liu, J. Sato, M. Perez, T. Geng, J. Dror, M. Montanez, I. Tong, T. Lee, H. Zhang, W. 2018-12-13 doi:10.1101/495424 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ An RNA-binding region regulates CTCF clustering and chromatin looping ]]> https://biorxiv.org/content/10.1101/495432v1?rss=1 Hansen, A. S. Hsieh, T.-H. S. Cattoglio, C. Pustova, I. Darzacq, X. Tjian, R. 2018-12-13 doi:10.1101/495432 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Guided nuclear exploration increases CTCF target search efficiency ]]> https://biorxiv.org/content/10.1101/495457v1?rss=1 Hansen, A. S. Amitai, A. Cattoglio, C. Tjian, R. Darzacq, X. 2018-12-13 doi:10.1101/495457 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Disease and introgression explain the long-lasting contact zone of Modern Humans and Neanderthals and its eventual destabilization ]]> https://biorxiv.org/content/10.1101/495515v1?rss=1 Greenbaum, G. Getz, W. M. Rosenberg, N. A. Feldman, M. W. Hovers, E. Kolodny, O. 2018-12-13 doi:10.1101/495515 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Twinkle is not the mitochondrial DNA replicative helicase in C. elegans, but may have alternate mitochondrial functions ]]> https://biorxiv.org/content/10.1101/497305v1?rss=1 Henderson, H. R. Liliya, E. Suomalainen, A. Dillin, A. 2019-02-20 doi:10.1101/497305 Cold Spring Harbor Laboratory Press 2019-02-20 <![CDATA[ Electrostatic-assemblies of single-walled carbon nanotubes and sequence-tunable peptoid polymers detect a lectin protein and its target sugars ]]> https://biorxiv.org/content/10.1101/500611v1?rss=1 Chio, L. Del Bonis-O'Donnell, J. T. Kline, M. Kim, J.-H. McFarlane, I. R. Zuckermann, R. N. Landry, M. 2018-12-20 doi:10.1101/500611 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ Microbiome and Antimicrobial Resistance Gene Dynamics in International Travelers ]]> https://biorxiv.org/content/10.1101/506394v1?rss=1 Langelier, C. Graves, M. Kalantar, K. L. Caldera, S. Durrant, R. Fisher, M. Backman, R. Tanner, W. DeRisi, J. Leung, D. 2018-12-26 doi:10.1101/506394 Cold Spring Harbor Laboratory Press 2018-12-26 <![CDATA[ Assessing the bioenergy potential of grassland biomass from conservation areas in England ]]> https://biorxiv.org/content/10.1101/506709v1?rss=1 French, K. 2018-12-27 doi:10.1101/506709 Cold Spring Harbor Laboratory Press 2018-12-27 <![CDATA[ Identification of TTN as a novel candidate gene for atrioventricular block in a Chinese pedigree by whole-exome sequencing ]]> https://biorxiv.org/content/10.1101/506824v1?rss=1 A (p.N16429K), in the titin (TTN, NM_001267550.2) gene in all 5 affected family members, but not in the unaffected family members. The point mutation is predicted to be functionally deleterious by in-silico software tools. Our finding was further supported by the conservative analysis across species.nnConclusionBased on this study, TTN was identified as a potential novel candidate gene for autosomal dominant AVB; this study expands the mutational spectrum of TTN gene and is the first to implicate TTN mutations as AVB disease causing in a Chinese pedigree. ]]> Li, W. Liu, G. Yang, Z. Chen, W. Yang, P. Xu, J. Miao, L. Yu, Q. Guo, J. Xu, H. Liu, F. Sun, Y. Huang, H. Peng, Z. Sun, J. 2018-12-27 doi:10.1101/506824 Cold Spring Harbor Laboratory Press 2018-12-27 <![CDATA[ Recording of \"sonic attacks\" on U.S. diplomats in Cuba spectrally matches the echoing call of a Caribbean cricket ]]> https://biorxiv.org/content/10.1101/510834v1?rss=1 Stubbs, A. L. Montealegre-Z, F. 2019-01-04 doi:10.1101/510834 Cold Spring Harbor Laboratory Press 2019-01-04 <![CDATA[ Apollo: Democratizing genome annotation ]]> https://biorxiv.org/content/10.1101/512376v1?rss=1 Dunn, N. Unni, D. Munoz-Torres, M. Munoz-Torres, M. Harris, N. Yao, E. Rasche, H. Holmes, I. Elsik, C. Lewis, S. 2019-01-04 doi:10.1101/512376 Cold Spring Harbor Laboratory Press 2019-01-04 <![CDATA[ Influenza A virus surface proteins are organized to help penetrate host mucus ]]> https://biorxiv.org/content/10.1101/512467v1?rss=1 Vahey, M. D. Fletcher, D. A. 2019-01-04 doi:10.1101/512467 Cold Spring Harbor Laboratory Press 2019-01-04 <![CDATA[ Effects of α-tubulin acetylation on microtubule structure and stability ]]> https://biorxiv.org/content/10.1101/516591v1?rss=1 Eshun-Wilson, L. Zhang, R. Portran, D. Nachury, M. Toso, D. Lohr, T. Vendruscolo, M. Bonomi, M. Fraser, J. Nogales, E. 2019-01-09 doi:10.1101/516591 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ Microtubules are necessary for proper Reticulon localization during mitosis ]]> https://biorxiv.org/content/10.1101/516773v1?rss=1 Bergman, Z. Diaz, U. Sims, A. Riggs, B. 2019-01-10 doi:10.1101/516773 Cold Spring Harbor Laboratory Press 2019-01-10 <![CDATA[ The CUL5 ubiquitin ligase complex mediates resistance to CDK9 and MCL1 inhibitors in lung cancer cells ]]> https://biorxiv.org/content/10.1101/518555v1?rss=1 Corn, J. E. Kabir, S. Cidado, J. Andersen, C. Dick, C. Lin, P.-C. Mitros, T. Ma, H. Baik, S. H. Belmonte, M. Drew, L. 2019-01-11 doi:10.1101/518555 Cold Spring Harbor Laboratory Press 2019-01-11 <![CDATA[ A 3D-printed hand-powered centrifuge for molecular biology ]]> https://biorxiv.org/content/10.1101/519835v1?rss=1 Byagathvalli, G. Pomerantz, A. Sinha, S. Standeven, J. Bhamla, M. S. 2019-01-16 doi:10.1101/519835 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ Direct synthesis of EM-visible gold nanoparticles on genetically encoded tags for single-molecule visualization in cells ]]> https://biorxiv.org/content/10.1101/520999v1?rss=1 Jiang, Z. Jin, X. Li, Y. Liu, S. Liu, X.-M. Wang, Y.-Y. Zhao, P. Cai, X. Liu, Y. Tang, Y. Sun, X. Liu, Y. Hu, Y. Li, M. Cai, G. Qi, X. Chen, S. Du, L.-L. He, W. 2019-01-17 doi:10.1101/520999 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ Spatial summation of individual cones in human color vision ]]> https://biorxiv.org/content/10.1101/521492v1?rss=1 Schmidt, B. Boehm, A. E. Tuten, W. S. Roorda, A. 2019-01-15 doi:10.1101/521492 Cold Spring Harbor Laboratory Press 2019-01-15 <![CDATA[ Excessive deliberation in social anxiety ]]> https://biorxiv.org/content/10.1101/522433v1?rss=1 Hunter, L. E. Meer, E. A. Gillan, C. M. Hsu, M. Daw, N. D. 2019-01-17 doi:10.1101/522433 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ Maximum entropy models elucidate the contribution of metabolic traits to patterns of community assembly ]]> https://biorxiv.org/content/10.1101/526764v1?rss=1 Bertram, J. Newman, E. A. Dewar, R. 2019-01-22 doi:10.1101/526764 Cold Spring Harbor Laboratory Press 2019-01-22 <![CDATA[ MPRAnalyze - A statistical framework for Massively Parallel Reporter Assays ]]> https://biorxiv.org/content/10.1101/527887v1?rss=1 Ashuach, T. Fischer, D. S. Kreimer, A. Ahituv, N. Theis, F. J. Yosef, N. 2019-01-23 doi:10.1101/527887 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Planning Face, Hand, and Leg Movements: Anatomical Constraints on Preparatory Inhibition. ]]> https://biorxiv.org/content/10.1101/529107v1?rss=1 Labruna, L. Tischler, C. Cazares, C. Greenhouse, I. Duque, J. Lebon, F. Ivry, R. B. 2019-01-26 doi:10.1101/529107 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Accurate prediction of bacterial two-component signaling with a deep recurrent neural network ORAKLE ]]> https://biorxiv.org/content/10.1101/532721v1?rss=1 Balewski, J. Hallberg, Z. 2019-01-28 doi:10.1101/532721 Cold Spring Harbor Laboratory Press 2019-01-28 <![CDATA[ Increased Replication Rates of Dissimilatory Nitrogen-Reducing Bacteria Leads to Decreased Anammox Reactor Performance ]]> https://biorxiv.org/content/10.1101/534925v1?rss=1 Keren, R. Lawrence, J. Zhuang, W.-Q. Jenkins, D. Banfield, J. F. Alvarez-Cohen, L. Zhou, L. Yu, K. 2019-01-30 doi:10.1101/534925 Cold Spring Harbor Laboratory Press 2019-01-30 <![CDATA[ Blood-brain barrier dysfunction in aging induces hyper-activation of TGF-beta signaling and chronic yet reversible neural dysfunction ]]> https://biorxiv.org/content/10.1101/537431v1?rss=1 Senatorov, V. V. Friedman, A. R. Milikovsky, D. Z. Ofer, J. Saar-Ashkenazy, R. Charbash, A. Jahan, N. Chin, G. Mihaly, E. Lin, J. M. Ramsay, H. J. Moghbel, A. Preininger, M. K. Eddings, C. R. Harrison, H. V. Patel, R. Shen, Y. Ghanim, H. Sheng, H. Veksler, R. Sudmant, P. Becker, A. Hart, B. Rogawski, M. Dillin, A. Friedman, A. Kaufer, D. 2019-02-01 doi:10.1101/537431 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ Chemosymbiotic bivalves contribute to the nitrogen budget of seagrass ecosystems ]]> https://biorxiv.org/content/10.1101/537746v1?rss=1 Cardini, U. Bartoli, M. Lee, R. Luecker, S. Mooshammer, M. Polzin, J. Weber, M. Petersen, J. 2019-02-05 doi:10.1101/537746 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Alzheimer's disease clinical variants show distinct regional patterns of neurofibrillary tangle accumulation ]]> https://biorxiv.org/content/10.1101/538496v1?rss=1 IV. ResultsPatients diagnosed with logopenic primary progressive aphasia showed significantly higher NFT density in the superior temporal gyrus relative to patients diagnosed with Alzheimer-type dementia (p = 0.0091), while patients with corticobasal syndrome showed significantly higher NFT density in the primary motor cortex (p = 0.0205). Hierarchical clustering identified three discrete clusters of patients characterized respectively by low overall NFT burden (n = 18), high overall burden (n = 30), and cortical-predominant burden (n = 24). A regionally specific effect was observed for visuospatial ability; higher NFT density in the angular gyrus ({beta} = - 0.0921, p = 0.0099) and in the CA1 sector of the hippocampus ({beta} = -0.0735, p = 0.0380) was significantly associated with more severe visuospatial dysfunction, modulated by age of death. ConclusionsOur results suggest domain-specific functional consequences of regional NFT accumulation. In particular, we observed focal aggregation of NFT density in clinically relevant regions among different clinical AD variants. Continued work to map the regionally specific clinical consequences of tau accumulation presents an opportunity to increase understanding of disease mechanisms underlying atypical clinical manifestations. ]]> Petersen, C. Nolan, A. L. de Paula Franca Resende, E. Ehrenberg, A. J. Spina, S. Miller, B. L. Seeley, W. Miller, Z. Grinberg, L. 2019-02-02 doi:10.1101/538496 Cold Spring Harbor Laboratory Press 2019-02-02 <![CDATA[ DNA Nanostructures Coordinate Gene Silencing in Mature Plants ]]> https://biorxiv.org/content/10.1101/538678v1?rss=1 Zhang, H. Demirer, G. S. Zhang, H. Ye, T. Goh, N. S. Aditham, A. J. Cunningham, F. J. Fan, C. Landry, M. 2019-02-02 doi:10.1101/538678 Cold Spring Harbor Laboratory Press 2019-02-02 <![CDATA[ Identifying Drug Sensitivity Subnetworks with NETPHLIX ]]> https://biorxiv.org/content/10.1101/543876v1?rss=1 Kim, Y.-A. Sarto Basso, R. Wojtowicz, D. Hochbaum, D. S. Vandin, F. Przytycka, T. M. 2019-02-08 doi:10.1101/543876 Cold Spring Harbor Laboratory Press 2019-02-08 <![CDATA[ Multiplexed CRISPR-Cas9 based genome editing of Rhodosporidium toruloides ]]> https://biorxiv.org/content/10.1101/545426v1?rss=1 Otoupal, P. B. Ito, M. Arkin, A. P. Magnuson, J. K. Gladden, J. M. Skerker, J. M. 2019-02-10 doi:10.1101/545426 Cold Spring Harbor Laboratory Press 2019-02-10 <![CDATA[ Single cell profiling of the VMH reveals a sexually dimorphic regulatory node of energy expenditure ]]> https://biorxiv.org/content/10.1101/549725v1?rss=1 van Veen, J. E. Kammel, L. G. Bunda, P. C. Shum, M. Reid, M. S. Park, J. W. Zhang, Z. Massa, M. G. Arneson, D. Hrncir, H. Liesa, M. Arnold, A. P. Yang, X. Correa, S. M. 2019-02-14 doi:10.1101/549725 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ Species dispersal mediates opposing influences of a branching network on genetic variation in a metapopulation ]]> https://biorxiv.org/content/10.1101/550194v1?rss=1 Chiu, M.-C. Li, B. Nukazawa, K. Carvajal, T. Watanabe, K. 2019-02-14 doi:10.1101/550194 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ An integrative approach identifies direct targets of the late viral transcription complex and an expanded promoter recognition motif in Kaposi's sarcoma-associated herpesvirus ]]> https://biorxiv.org/content/10.1101/550772v1?rss=1 Nandakumar, D. Glaunsinger, B. 2019-02-15 doi:10.1101/550772 Cold Spring Harbor Laboratory Press 2019-02-15 <![CDATA[ Evolutionary dynamics of phage resistance in bacterial biofilms ]]> https://biorxiv.org/content/10.1101/552265v1?rss=1 Simmons, M. Bond, M. C. Drescher, K. Bucci, V. Nadell, C. D. 2019-02-17 doi:10.1101/552265 Cold Spring Harbor Laboratory Press 2019-02-17 <![CDATA[ A Bayesian Approach for Estimating Branch-Specific Speciation and Extinction Rates ]]> https://biorxiv.org/content/10.1101/555805v1?rss=1 Hoehna, S. Freyman, W. A. Nolen, Z. Huelsenbeck, J. May, M. R. Moore, B. R. 2019-02-20 doi:10.1101/555805 Cold Spring Harbor Laboratory Press 2019-02-20 <![CDATA[ Nanoparticle-mediated transformation expands horizon of organism engineering ]]> https://biorxiv.org/content/10.1101/559252v1?rss=1 French, K. E. 2019-02-24 doi:10.1101/559252 Cold Spring Harbor Laboratory Press 2019-02-24 <![CDATA[ Communication between distinct subunit interfaces of the cohesin complex promotes its topological entrapment of DNA. ]]> https://biorxiv.org/content/10.1101/559492v1?rss=1 Guacci, V. A. Chatterjee, F. Robison, B. Koshland, D. 2019-02-24 doi:10.1101/559492 Cold Spring Harbor Laboratory Press 2019-02-24 <![CDATA[ Nanotubes effectively deliver siRNA to intact plant cells and protect siRNA against nuclease degradation ]]> https://biorxiv.org/content/10.1101/564427v1?rss=1 Demirer, G. S. Zhang, H. Goh, N. S. Chang, R. Landry, M. P. 2019-03-01 doi:10.1101/564427 Cold Spring Harbor Laboratory Press 2019-03-01 <![CDATA[ Structural basis of the differential binding of engineered knottins 2.5F and 2.5D to integrins αVβ3 and α5β1 ]]> https://biorxiv.org/content/10.1101/565358v1?rss=1 van Agthoven, J. F. Shams, H. Cochran, F. V. Alonso, J. L. Kintzing, J. R. Grakami, K. Xiong, J.-P. Mofrad, M. R. Cochran, J. R. Arnaout, M. A. 2019-03-01 doi:10.1101/565358 Cold Spring Harbor Laboratory Press 2019-03-01 <![CDATA[ Arabidopsis phytochelatin synthase 1, but not phytochelatin synthesis, functions in extracellular defense against multiple fungal pathogens ]]> https://biorxiv.org/content/10.1101/568113v1?rss=1 Hematy, K. Lim, M. Cherk, C. Bednarek, P. Pislewska-Bednarek, M. Sanchez-Rodriguez, C. Stein, M. Fuchs, R. Klapprodt, C. Lipka, V. Molina, A. Grill, E. Schulze-Lefert, P. Somerville, S. 2019-03-05 doi:10.1101/568113 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Network-based approaches elucidate differences within APOBEC and clock-like signatures in breast cancer ]]> https://biorxiv.org/content/10.1101/568568v1?rss=1 Kim, Y.-A. Wojtowicz, D. Sarto Basso, R. Sason, I. Robinson, W. Hochbaum, D. S. Leiserson, M. D. M. Sharan, R. Vandin, F. Przytycka, T. M. 2019-03-05 doi:10.1101/568568 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Hydrology-informed metapopulation modeling of liver fluke transmission in the Lawa Lake complex of northeast Thailand ]]> https://biorxiv.org/content/10.1101/569913v1?rss=1 Leon, T. M. Plermkamon, V. Kuntiyawichai, K. Sripa, B. Spear, R. C. 2019-03-06 doi:10.1101/569913 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation ]]> https://biorxiv.org/content/10.1101/577478v1?rss=1 Kelmer Sacramento, E. Kirkpatrick, J. M. Mazzetto, M. Di Sanzo, S. Caterino, C. Sanguanini, M. Papaevgeniou, N. Lefaki, M. Childs, D. Bagnoli, S. Terzibasi Tozzini, E. Bartolome, A. Romanov, N. Baumgart, M. Huber, W. Chondrogianni, N. Vendruscolo, M. Cellerino, A. Ori, A. 2019-03-16 doi:10.1101/577478 Cold Spring Harbor Laboratory Press 2019-03-16 <![CDATA[ The \"sewing machine\" for minimally invasive neural recording ]]> https://biorxiv.org/content/10.1101/578542v1?rss=1 Hanson, T. L. Diaz-Botia, C. A. Kharazia, V. Maharbiz, M. M. Sabes, P. N. 2019-03-14 doi:10.1101/578542 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ Unbiased metagenomic sequencing for pediatric meningitis in Bangladesh reveals neuroinvasive Chikungunya virus outbreak and other unrealized pathogens ]]> https://biorxiv.org/content/10.1101/579532v1?rss=1 99% identical to each other and to a Bangladeshi strain only previously recognized to cause systemic illness in 2017. CHIKV qPCR of all remaining stored CSF samples from children who presented with idiopathic meningitis in 2017 at the same hospital (n=472) revealed 17 additional CHIKV meningitis cases. Orthogonal molecular confirmation of each mNGS-identified infection, case-based clinical data, and follow-up of patients substantiated the key findings.nnUsing mNGS, we obtained a microbiological diagnosis for 40% of idiopathic meningitis cases and identified a previous unappreciated pediatric CHIKV meningitis outbreak. Case-control CSF mNGS surveys can complement conventional diagnostic methods to identify etiologies of meningitis and facilitate informed policy decisions. ]]> Saha, S. Ramesh, A. Kalantar, K. L. Malaker, R. Hasanuzzaman, M. Khan, L. M. Mayday, M. Y. Sajib, M. S. I. Li, L. M. Langelier, C. Rahman, H. Crawford, E. D. Tato, C. M. Islam, M. Juan, Y.-F. Bourcy, C. d. Dimitrov, B. Wang, J. Tang, J. Sheu, J. Egger, R. Carvalho, T. R. D. Wilson, M. R. Saha, S. DeRisi, J. 2019-03-15 doi:10.1101/579532 Cold Spring Harbor Laboratory Press 2019-03-15 <![CDATA[ Male recombination produced multiple geographically restricted neo-Y chromosome haplotypes of varying ages that correlate with onset of neo-Y decay in Drosophila albomicans ]]> https://biorxiv.org/content/10.1101/580118v1?rss=1 Wei, K. H.-C. Bachtrog, D. 2019-03-16 doi:10.1101/580118 Cold Spring Harbor Laboratory Press 2019-03-16 <![CDATA[ Diverse commensal E. coli clones and plasmids disseminate antimicrobial resistance genes in domestic animals and children in a semi-rural community in Ecuador ]]> https://biorxiv.org/content/10.1101/581967v1?rss=1 Salinas, L. Cardenas, P. A. Johnson, T. J. Vasco, K. Graham, J. Trueba, G. 2019-03-20 doi:10.1101/581967 Cold Spring Harbor Laboratory Press 2019-03-20 <![CDATA[ Live-cell Imaging Analysis of Antimycin-Type Depsipeptides via Bioorthogonal Stimulated Raman Scattering Microscopy ]]> https://biorxiv.org/content/10.1101/583252v1?rss=1 Seidel, J. A. Miao, Y. Porterfield, W. Cai, W. Zhu, X. Kim, S.-J. Hu, F. Bhattarai-Kline, S. Min, W. Zhang, W. 2019-03-21 doi:10.1101/583252 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Xrn1 activity broadly represses RNA polymerase II occupancy at mammalian but not viral promoters during herpesvirus infection ]]> https://biorxiv.org/content/10.1101/585984v1?rss=1 Hartenian, E. Glaunsinger, B. 2019-03-26 doi:10.1101/585984 Cold Spring Harbor Laboratory Press 2019-03-26 <![CDATA[ DNA-scaffolded biomaterials enable modular and tunable control of cell-based cancer immunotherapies ]]> https://biorxiv.org/content/10.1101/587105v1?rss=1 Huang, X. Williams, J. Z. Chang, R. Li, Z. Gai, E. Patterson, D. M. Yu, W. Lim, W. A. Desai, T. A. 2019-03-23 doi:10.1101/587105 Cold Spring Harbor Laboratory Press 2019-03-23 <![CDATA[ Structure-function analysis of ZAR1 immune receptor reveals key molecular interactions for activity ]]> https://biorxiv.org/content/10.1101/592824v1?rss=1 Baudin, M. Schreiber, K. J. Martin, E. C. Petrescu, A. J. Lewis, J. 2019-03-29 doi:10.1101/592824 Cold Spring Harbor Laboratory Press 2019-03-29 <![CDATA[ De novo design of proteins with two isoenergetic but structurally divergent ground states ]]> https://biorxiv.org/content/10.1101/597161v1?rss=1 Wei, K. Y. Moschidi, D. Bick, M. J. Nerli, S. McShan, A. C. Carter, L. P. Huang, P.-S. Fletcher, D. A. Sgourakis, N. G. Boyken, S. E. Baker, D. 2019-04-04 doi:10.1101/597161 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ Halyos: A patient-facing visual EHR interface for longitudinal risk awareness ]]> https://biorxiv.org/content/10.1101/597583v1?rss=1 Mataraso, S. Socrates, V. Lekschas, F. Gehlenborg, N. 2019-04-12 doi:10.1101/597583 Cold Spring Harbor Laboratory Press 2019-04-12 <![CDATA[ PyMethylProcess - highly parallelized preprocessing for DNA methylation array data ]]> https://biorxiv.org/content/10.1101/604496v1?rss=1 Levy, J. J. Titus, A. J. Salas, L. A. Christensen, B. 2019-04-12 doi:10.1101/604496 Cold Spring Harbor Laboratory Press 2019-04-12 <![CDATA[ Biomarker Localization, Analysis, Visualization, Extraction, and Registration (BLAzER) Workflow for Research and Clinical Brain PET Applications ]]> https://biorxiv.org/content/10.1101/608323v1?rss=1 0.97, p < 0.001) with high inter-operator reproducibility for both (ICC > 0.97) and nearly identical dichotomization as amyloid-positive or -negative (2 discrepant cases out of 127). Comparing FS vs. NR segmentation with BLAzER, the global SUVRs were strongly correlated for global amyloid-PET (r = 0.9841, p < 0.001), but were systematically higher (4% on average) with NR, likely due to more inclusion of white matter, which has high florbetapir binding.nnConclusionsBLAzER provides an efficient workflow for regional brain PET quantification. FDA-cleared components and the ability to visualize registration reduce barriers between research and clinical applications. ]]> Raman, F. Grandhi, S. Murchison, C. F. Kennedy, R. E. Landau, S. Roberson, E. D. McConathy, J. Alzheimer's Disease Neuroimaging Initiative, 2019-04-13 doi:10.1101/608323 Cold Spring Harbor Laboratory Press 2019-04-13 <![CDATA[ Reconstructing the transcriptional ontogeny of maize and sorghum supports an inverse hourglass model of inflorescence development ]]> https://biorxiv.org/content/10.1101/616235v1?rss=1 Leiboff, S. Hake, S. 2019-04-23 doi:10.1101/616235 Cold Spring Harbor Laboratory Press 2019-04-23 <![CDATA[ Water storage and irrigation practices associated with cannabis production drive seasonal patterns of water extraction and use in Northern California watersheds ]]> https://biorxiv.org/content/10.1101/618934v1?rss=1 Dillis, C. McIntee, C. Grantham, T. Butsic, V. Le, L. Grady, K. 2019-04-25 doi:10.1101/618934 Cold Spring Harbor Laboratory Press 2019-04-25 <![CDATA[ Reevaluation of the RNA binding properties of the Tetrahymena thermophila telomerase reverse transcriptase N-terminal domain ]]> https://biorxiv.org/content/10.1101/621573v1?rss=1 Palka, C. Deshpande, A. P. Stone, M. D. Collins, K. 2019-04-29 doi:10.1101/621573 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ treeSeg: Testing for Dependence on Tree Structures ]]> https://biorxiv.org/content/10.1101/622811v1?rss=1 Behr, M. Ansari, M. A. Munk, A. Holmes, C. 2019-04-30 doi:10.1101/622811 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ A new class of disordered elements controls DNA replication through initiator self-assembly ]]> https://biorxiv.org/content/10.1101/623058v1?rss=1 Parker, M. W. Bell, M. Mir, M. Kao, J. A. Darzacq, X. Botchan, M. R. Berger, J. M. M. 2019-04-29 doi:10.1101/623058 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ The Catalytic Core of DEMETER Guides Active DNA Demethylation in Arabidopsis ]]> https://biorxiv.org/content/10.1101/623843v1?rss=1 Zhang, C. Hung, Y.-H. Zhang, X.-Q. Zhang, D. Frost, J. M. Liu, F. Xiao, W. Iyer, L. M. Aravind, L. Huh, J. H. Fischer, R. L. Hsieh, T.-F. 2019-05-01 doi:10.1101/623843 Cold Spring Harbor Laboratory Press 2019-05-01 <![CDATA[ Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection ]]> https://biorxiv.org/content/10.1101/627794v1?rss=1 Morella, N. M. Weng, F. C.-H. Joubert, P. M. Metcalf, C. J. E. Lindow, S. Koskella, B. 2019-05-05 doi:10.1101/627794 Cold Spring Harbor Laboratory Press 2019-05-05 <![CDATA[ Single-cell analysis of EphA clustering phenotypes to probe cancer cell heterogeneity ]]> https://biorxiv.org/content/10.1101/635102v1?rss=1 Ravasio, A. Myaing, M. Z. Chia, S. Arora, A. Sathe, A. Cao, E. Y. Bertocchi, C. Sharma, A. Arasi, B. Chung, V. Y. Green, A. C. Tan, T. Z. Chen, Z. Ong, H. T. Iyer, N. G. Huang, R. Y. DasGupta, R. Groves, J. T. Viasnoff, V. 2019-05-10 doi:10.1101/635102 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Rare microbes from diverse Earth biomes dominate community activity ]]> https://biorxiv.org/content/10.1101/636373v1?rss=1 Sachdeva, R. Campbell, B. J. Heidelberg, J. F. 2019-05-16 doi:10.1101/636373 Cold Spring Harbor Laboratory Press 2019-05-16 <![CDATA[ Fighting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics ]]> https://biorxiv.org/content/10.1101/643676v1?rss=1 0.9) sensitivity and predictive values, where the relative contribution of the different categories of biomarkers strongly depended on the antibiotic. For all drugs except for ciprofloxacin, gene expression information substantially improved diagnostic performance. Our results pave the way for the development of a molecular resistance profiling tool that reliably predicts antimicrobial susceptibility based on genomic and transcriptomic markers. The implementation of a molecular susceptibility test system in routine clinical microbiology diagnostics holds promise to provide earlier and more detailed information on antibiotic resistance profiles of bacterial pathogens and thus could change how physicians treat bacterial infections. ]]> Khaledi, A. Weimann, A. Schniederjans, M. Asgari, E. Kuo, T.-H. Oliver, A. Cabot, G. Kola, A. Gastmeier, P. Hogardt, M. Jonas, D. Mofrad, M. Bremges, A. McHardy, A. C. Haeussler, S. 2019-05-24 doi:10.1101/643676 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Exploring Contextual Interference in Implicit and Explicit Motor Learning ]]> https://biorxiv.org/content/10.1101/644211v1?rss=1 Dang, K. Parvin, D. Ivry, R. 2019-05-20 doi:10.1101/644211 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Computational design of a modular protein sense/response system ]]> https://biorxiv.org/content/10.1101/648485v1?rss=1 Glasgow, A. A. Huang, Y.-M. Mandell, D. J. Thompson, M. Ritterson, R. Loshbaugh, A. L. Pellegrino, J. Krivacic, C. Pache, R. A. Barlow, K. A. Ollikainen, N. Jeon, D. Kelly, M. J. S. Fraser, J. S. Kortemme, T. 2019-05-24 doi:10.1101/648485 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ High-throughput smFRET analysis of freely diffusing nucleic acid molecules and associated proteins ]]> https://biorxiv.org/content/10.1101/651869v1?rss=1 Segal, M. Ingargiola, A. Lerner, E. Chung, S. White, J. A. Streets, A. M. Weiss, S. Michalet, X. 2019-05-27 doi:10.1101/651869 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ A New Role for Telomerase in Promoting Meiotic Homolog Pairing Fidelity ]]> https://biorxiv.org/content/10.1101/654376v1?rss=1 Smith, D. L. Oke, A. Pollard, M. Anderson, C. M. Zhuge, T. Yam, P. Gromova, T. Conant, K. Chu, D. Patel, N. Gonzalez, F. Stoddard, C. Burgess, S. M. Hochwagen, A. Marshall, W. F. Blackburn, E. Fung, J. C. 2019-05-30 doi:10.1101/654376 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ Biophysical principles of choanoflagellate self-organization ]]> https://biorxiv.org/content/10.1101/659698v1?rss=1 Larson, B. T. Ruiz-Herrero, T. Lee, S. Kumar, S. Mahadevan, L. King, N. 2019-06-04 doi:10.1101/659698 Cold Spring Harbor Laboratory Press 2019-06-04 <![CDATA[ Host engineering for improved valerolactam production in Pseudomonas putida ]]> https://biorxiv.org/content/10.1101/660795v1?rss=1 Thompson, M. Valencia, L. E. Blake-Hedges, J. Cruz-Morales, P. Velasquez, A. Pearson, A. Sermeno, L. Sharpless, W. Benites, V. Chen, Y. Baidoo, E. Petzold, C. J. Deutschbauer, A. Keasling, J. D. 2019-06-06 doi:10.1101/660795 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Kindlin Assists Talin to Promote Integrin Activation ]]> https://biorxiv.org/content/10.1101/662163v1?rss=1 Haydari, Z. Shams, H. Jahed, Z. Mofrad, M. R. K. 2019-06-06 doi:10.1101/662163 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ A yeast optogenetic toolkit (yOTK) for gene expression control in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/663393v1?rss=1 An-adirekkun, J. Stewart, C. J. Geller, S. H. Patel, M. T. Melendez, J. Oakes, B. L. Noyes, M. B. McClean, M. 2019-06-16 doi:10.1101/663393 Cold Spring Harbor Laboratory Press 2019-06-16 <![CDATA[ Why evolve reliance on the microbiome for timing of ontogeny? ]]> https://biorxiv.org/content/10.1101/665182v1?rss=1 Metcalf, C. J. E. Henry, L. P. Rebolleda-Gomez, M. Koskella, B. 2019-06-10 doi:10.1101/665182 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Protective microbiomes can limit the evolution of host pathogen defense ]]> https://biorxiv.org/content/10.1101/665265v1?rss=1 Metcalf, C. J. Koskella, B. 2019-06-10 doi:10.1101/665265 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Estimating abundance with interruptions in data collection using open population spatial capture-recapture models ]]> https://biorxiv.org/content/10.1101/671461v1?rss=1 Milleret, C. Dupont, P. Chipperfield, J. Turek, D. Broseth, H. Gimenez, O. de Valpine, P. Bischof, R. 2019-06-14 doi:10.1101/671461 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements ]]> https://biorxiv.org/content/10.1101/672238v1?rss=1 Karin, B. R. Gamble, T. Jackman, T. R. 2019-06-15 doi:10.1101/672238 Cold Spring Harbor Laboratory Press 2019-06-15 <![CDATA[ Rapid range shifts in African Anopheles mosquitoes over the last century ]]> https://biorxiv.org/content/10.1101/673913v1?rss=1 Carlson, C. J. Bannon, E. Mendenhall, E. Newfield, T. Bansal, S. 2019-06-19 doi:10.1101/673913 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Split-gene drive system provides flexible application for safe laboratory investigation and potential field deployment ]]> https://biorxiv.org/content/10.1101/684597v1?rss=1 Lopez del Amo, V. Bishop, A. L. Sanchez C., H. M. Bennett, J. B. Feng, X. Marshall, J. M. Bier, E. Gantz, V. M. 2019-06-27 doi:10.1101/684597 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Graphene Quantum Dot Oxidation Governs Noncovalent Biopolymer Adsorption ]]> https://biorxiv.org/content/10.1101/684670v1?rss=1 Jeong, S. Pinals, R. L. Dharmadhikari, B. Song, H. Kalluri, A. Debnath, D. Qi, W. Ham, M.-H. Patra, P. Landry, M. 2019-06-27 doi:10.1101/684670 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ In vitro prototyping and rapid optimization of biosynthetic enzymes for cellular design ]]> https://biorxiv.org/content/10.1101/685768v1?rss=1 Karim, A. S. Dudley, Q. M. Juminaga, A. Yuan, Y. Crowe, S. A. Heggestad, J. T. Abdalla, T. Grubbe, W. Rasor, B. Coar, D. Torculas, M. Krein, M. Liew, F. Quattlebaum, A. Jensen, R. O. Stuart, J. Simpson, S. D. Köpke, M. Jewett, M. C. 2019-06-28 doi:10.1101/685768 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Lis1 activates dynein motility by pairing it with dynactin ]]> https://biorxiv.org/content/10.1101/685826v1?rss=1 ElShenawy, M. Kusakci, E. Volz, S. Baumbach, J. Bullock, S. L. Yildiz, A. 2019-06-28 doi:10.1101/685826 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ MethylNet: A Modular Deep Learning Approach to Methylation Prediction ]]> https://biorxiv.org/content/10.1101/692665v1?rss=1 Levy, J. J. Titus, A. J. Petersen, C. L. Chen, D. Salas, L. A. Christensen, B. C. 2019-07-04 doi:10.1101/692665 Cold Spring Harbor Laboratory Press 2019-07-04 <![CDATA[ Within-host dynamics of virulent viruses in bat reservoirs for emerging zoonotic disease ]]> https://biorxiv.org/content/10.1101/696195v1?rss=1 Brook, C. E. Boots, M. Chandran, K. Dobson, A. P. Drosten, C. Graham, A. L. Grenfell, B. Müller, M. A. Ng, M. Wang, L.-F. van Leeuwen, A. 2019-07-08 doi:10.1101/696195 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Mapping Vector Field of Single Cells ]]> https://biorxiv.org/content/10.1101/696724v1?rss=1 Qiu, X. Zhang, Y. Yang, D. Hosseinzadeh, S. Wang, L. Yuan, R. Xu, S. Ma, Y. Replogle, J. Darmanis, S. Xing, J. Weissman, J. 2019-07-09 doi:10.1101/696724 Cold Spring Harbor Laboratory Press 2019-07-09 <![CDATA[ JBrowse Connect: A server API to connect JBrowse instances and users ]]> https://biorxiv.org/content/10.1101/699504v1?rss=1 Holmes, I. Buels, R. Yao, E. Sen, T. Stein, L. 2019-07-11 doi:10.1101/699504 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Population genomics of the Viking world ]]> https://biorxiv.org/content/10.1101/703405v1?rss=1 Margaryan, A. Lawson, D. J. Sikora, M. Racimo, F. Rasmussen, S. Moltke, I. Cassidy, L. Jorsboe, E. Ingason, A. Pedersen, M. W. Korneliussen, T. S. Wilhelmson, H. Bus, M. M. de Barros Damgaard, P. Martiniano, R. Renaud, G. Bherer, C. Moreno-Mayar, J. V. Fotakis, A. K. Allen, M. Molak, M. Cappellini, E. Scorrano, G. Buzhilova, A. Fox, A. M. Albrechtsen, A. Schutz, B. Skar, B. Arcini, C. A. Falys, C. G. Hedenstierna-Jonson, C. Blaszczyk, D. Pezhemsky, D. Turner-Walker, G. Gestsdottir, H. Lundstrom, I. Gustin, I. Mainland, I. Potekhina, I. Muntoni, I. M. Che 2019-07-17 doi:10.1101/703405 Cold Spring Harbor Laboratory Press 2019-07-17 <![CDATA[ Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses ]]> https://biorxiv.org/content/10.1101/705632v1?rss=1 Marine, R. L. Magana, L. C. Castro, C. J. Zhao, K. Montmayeur, A. Schmidt, A. Diez-Valcarce, M. Ng, T. F. F. Vinje, J. Burns, C. C. Nix, W. A. Rota, P. A. Oberste, M. S. 2019-07-17 doi:10.1101/705632 Cold Spring Harbor Laboratory Press 2019-07-17 <![CDATA[ Diffusive Flux Analysis of Tumor Vascular Permeability for 3-Helix-Micelles in Comparison to Other Nanoparticles ]]> https://biorxiv.org/content/10.1101/708263v1?rss=1 nView larger version (26K):norg.highwire.dtl.DTLVardef@5981e5org.highwire.dtl.DTLVardef@5ef928org.highwire.dtl.DTLVardef@137edceorg.highwire.dtl.DTLVardef@dd9b17_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG ]]> Lim, M. Dharmaraj, V. Gong, B. Xu, T. 2019-07-23 doi:10.1101/708263 Cold Spring Harbor Laboratory Press 2019-07-23 <![CDATA[ RNA Polymerase II CTD phosphatase Rtr1 prevents premature transcription termination ]]> https://biorxiv.org/content/10.1101/708727v1?rss=1 Fox, M. J. Victorino, J. F. Smith-Kinnaman, W. R. Peck Justice, S. A. Gao, H. Boyd, A. K. Zimmerly, M. A. Chan, R. R. Hunter, G. O. Liu, Y. Mosley, A. L. 2019-07-19 doi:10.1101/708727 Cold Spring Harbor Laboratory Press 2019-07-19 <![CDATA[ Diverse temporal dynamics of repetition suppression revealed by intracranial recordings in human ventral temporal cortex ]]> https://biorxiv.org/content/10.1101/711523v1?rss=1 Rangarajan, V. Jacques, C. Knight, R. Weiner, K. Grill-Spector, K. 2019-07-23 doi:10.1101/711523 Cold Spring Harbor Laboratory Press 2019-07-23 <![CDATA[ Facile discovery of isonitrile natural products via tetrazine based click reactions ]]> https://biorxiv.org/content/10.1101/711853v1?rss=1 Huang, Y. Cai, W. Del Rio Flores, A. Twiff, F. F. Zhang, W. 2019-07-26 doi:10.1101/711853 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ Fungal seed pathogens of wild chili peppers possess multiple mechanisms to tolerate capsaicinoids ]]> https://biorxiv.org/content/10.1101/712711v1?rss=1 Adams, C. A. Zimmerman, K. Fenstermacher, K. Thompson, M. G. Skyrud, W. Behie, S. W. Pringle, A. 2019-07-24 doi:10.1101/712711 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Spontaneous polyploids and antimutators compete during the evolution of mutator cells ]]> https://biorxiv.org/content/10.1101/718163v1?rss=1 Tracy, M. Lee, M. Hearn, B. Dowsett, I. Thurber, L. Loo, J. Loeb, A. M. Preston, K. Tuncel, M. Ghodsian, N. Bode, A. Tang, T. Herr, A. J. 2019-07-30 doi:10.1101/718163 Cold Spring Harbor Laboratory Press 2019-07-30 <![CDATA[ Evolution of conserved noncoding sequences in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/727669v1?rss=1 Yocca, A. Lu, Z. Schmitz, R. J. Freeling, M. Edger, P. 2019-08-06 doi:10.1101/727669 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ IRG1 and iNOS act redundantly with other interferon gamma induced factors to restrict intracellular replication of Legionella pneumophila. ]]> https://biorxiv.org/content/10.1101/731182v1?rss=1 Price, J. V. Russo, D. Ji, D. X. Chavez, R. A. DiPeso, L. Lee, A. Y.-F. Coers, J. Vance, R. 2019-08-10 doi:10.1101/731182 Cold Spring Harbor Laboratory Press 2019-08-10 <![CDATA[ Conjugation-dependent \"gene drives\" harness indigenous bacteria for bioremediation ]]> https://biorxiv.org/content/10.1101/735886v1?rss=1 French, K. E. Zhou, Z. Terry, N. 2019-08-19 doi:10.1101/735886 Cold Spring Harbor Laboratory Press 2019-08-19 <![CDATA[ Structural control of regioselectivity in an unusual bacterial acyl-CoA dehydrogenase ]]> https://biorxiv.org/content/10.1101/736256v1?rss=1 Blake-Hedges, J. M. Henrique Pereira, J. Cruz-Morales, P. Thompson, M. G. Barajas, J. F. Chen, J. Krishna, R. N. Chan, L. J. G. Nimlos, D. Alonso-Martinez, C. Chen, Y. Gin, J. W. Katz, L. Petzold, C. J. Adams, P. D. Keasling, J. D. 2019-08-15 doi:10.1101/736256 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ How squirrels protect their caches: Location, conspicuousness during caching, and proximity to kin influence cache lifespan ]]> https://biorxiv.org/content/10.1101/738237v1?rss=1 Delgado, M. M. Jacobs, L. F. 2019-08-16 doi:10.1101/738237 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ Extradomain-B Fibronectin is a molecular marker of invasive breast cancer cells ]]> https://biorxiv.org/content/10.1101/743500v1?rss=1 Lu, Z.-R. Vaidya, A. Wang, H. Qian, V. 2019-08-22 doi:10.1101/743500 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Ocular hypertension drives remodeling of AMPA receptors in select populations of retinal ganglion cells ]]> https://biorxiv.org/content/10.1101/743559v1?rss=1 Sladek, A. L. Nawy, S. 2019-10-04 doi:10.1101/743559 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ Leveraging host metabolism for bisdemethoxycurcumin production in Pseudomonas putida ]]> https://biorxiv.org/content/10.1101/753889v1?rss=1 Incha, M. R. Thompson, M. G. Blake-Hedges, J. M. Pearson, A. N. Schmidt, M. Deutschbauer, A. Keasling, J. D. 2019-08-31 doi:10.1101/753889 Cold Spring Harbor Laboratory Press 2019-08-31 <![CDATA[ Loss of a novel striated muscle-enriched mitochondrial protein Coq10a enhances postnatal cardiac hypertrophic growth ]]> https://biorxiv.org/content/10.1101/755793v1?rss=1 Hirose, K. Chang, S. Yu, H. Wang, J. Barca, E. Chen, X. Khyeam, S. Tajima, K. Yoneshiro, T. Kajimura, S. Quinzii, C. M. Hu, G. Huang, G. N. 2019-09-03 doi:10.1101/755793 Cold Spring Harbor Laboratory Press 2019-09-03 <![CDATA[ Suppression of p53 response by targeting p53-Mediator binding with a stapled peptide ]]> https://biorxiv.org/content/10.1101/757401v1?rss=1 Allen, B. L. Quach, K. Levandowski, C. B. Rubin, J. D. Read, T. Dowell, R. D. Schepartz, A. Taatjes, D. J. 2019-09-04 doi:10.1101/757401 Cold Spring Harbor Laboratory Press 2019-09-04 <![CDATA[ Structural Pathway for Allosteric Activation of the Autophagic PI 3-Kinase Complex I ]]> https://biorxiv.org/content/10.1101/758797v1?rss=1 Young, L. N. Goerdeler, F. Hurley, J. H. 2019-09-05 doi:10.1101/758797 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Corona exchange dynamics on carbon nanotubes by multiplexed fluorescence monitoring ]]> https://biorxiv.org/content/10.1101/761296v1?rss=1 Pinals, R. L. Yang, D. Lui, A. Cao, W. Landry, M. P. 2019-09-08 doi:10.1101/761296 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ A single-cell and single-nucleus RNA-seq toolbox for fresh and frozen human tumors ]]> https://biorxiv.org/content/10.1101/761429v1?rss=1 Slyper, M. Porter, C. B. M. Ashenberg, O. Waldman, J. Drokhlyansky, E. Wakiro, I. Smillie, C. Smith-Rosario, G. Wu, J. Dionne, D. Vigneau, S. Jane-Valbuena, J. Napolitano, S. Su, M.-J. Patel, A. G. Karlstrom, A. Gritsch, S. Nomura, M. Waghray, A. Gohil, S. H. Tsankov, A. M. Jerby-Arnon, L. Cohen, O. Klughammer, J. Rosen, Y. Gould, J. Li, B. Nguyen, L. Wu, C. J. Izar, B. Haq, R. Hodi, F. S. Yoon, C. H. Hata, A. N. Baker, S. J. Suva, M. L. Bueno, R. Stover, E. H. Matulonis, U. A. Clay, M. R. Dyer, M. A. Collins, N. B. Wagle, N. Rotem, A. Johnson, B. E. 2019-09-12 doi:10.1101/761429 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Two distinct trophectoderm lineage stem cells from human pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/762542v1?rss=1 Mischler, A. Karakis, V. Mahinthakumar, J. Carberry, C. San Miguel, A. Rager, J. Fry, R. Rao, B. M. 2019-09-08 doi:10.1101/762542 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ The response of Pseudomonas putida to a complex lignolysate ]]> https://biorxiv.org/content/10.1101/764399v1?rss=1 Park, M.-R. Chen, Y. Thompson, M. G. Benites, V. Fong, B. Petzold, C. J. Baidoo, E. E. K. Gladden, J. Adams, P. D. Keasling, J. D. Simmons, B. A. Singer, S. 2019-09-10 doi:10.1101/764399 Cold Spring Harbor Laboratory Press 2019-09-10 <![CDATA[ Native plasmid-encoded mercury resistance genes are functional and demonstrate natural transformation in environmental bacterial isolates ]]> https://biorxiv.org/content/10.1101/764415v1?rss=1 Kothari, A. Soneja, D. Tang, A. Carlson, H. K. Deutschbauer, A. M. Mukhopadhyay, A. 2019-09-10 doi:10.1101/764415 Cold Spring Harbor Laboratory Press 2019-09-10 <![CDATA[ New mutant mouse models clarify the role of NAIPs, phosphorylation, NLRP3, and tumors in NLRC4 inflammasome activation ]]> https://biorxiv.org/content/10.1101/765313v1?rss=1 Tenthorey, J. Chavez, R. A. Thompson, T. W. Deets, K. A. Vance, R. E. Rauch, I. 2019-09-18 doi:10.1101/765313 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Coordinate Enhancer Reprogramming by GATA3 and AP1 Promotes Phenotypic Plasticity to Achieve Breast Cancer Endocrine Resistance ]]> https://biorxiv.org/content/10.1101/767871v1?rss=1 Bi, M. Zhang, Z. Wang, H. Xue, P. Hernandez, K. Fu, X. De angelis, C. Gao, Z. Ruan, J. Jin, V. Wang, Q. Marangoni, E. Huang, T. H.-M. Chen, L. Glass, C. K. Li, W. Schiff, R. Liu, Z. 2019-09-16 doi:10.1101/767871 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ Deviations from Hardy Weinberg Equilibrium at CCR5-Δ32 in Large Sequencing Data Sets ]]> https://biorxiv.org/content/10.1101/768390v1?rss=1 Wei, X. Nielsen, R. 2019-09-14 doi:10.1101/768390 Cold Spring Harbor Laboratory Press 2019-09-14 <![CDATA[ Testing Finch’s hypothesis: the role of organismal modularity on the escape from actuarial senescence ]]> https://biorxiv.org/content/10.1101/771378v1?rss=1 Bernard, C. Compagnoni, A. Salguero-Gomez, R. 2019-09-18 doi:10.1101/771378 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Definition of alleles and altered regulatory motifs across Cas9-edited cell populations ]]> https://biorxiv.org/content/10.1101/775361v1?rss=1 Ehmsen, K. T. Knuesel, M. T. Martinez, D. Asahina, M. Aridomi, H. Yamamoto, K. R. 2019-09-19 doi:10.1101/775361 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Novel compartmental models of infectious disease transmission ]]> https://biorxiv.org/content/10.1101/777250v1?rss=1 Greenhalgh, S. Rozins, C. 2019-09-20 doi:10.1101/777250 Cold Spring Harbor Laboratory Press 2019-09-20 <![CDATA[ Identification of a parasitic symbiosis between respiratory metabolisms in the biogeochemical chlorine cycle ]]> https://biorxiv.org/content/10.1101/781625v1?rss=1 Barnum, T. Cheng, Y. Hill, K. Lucas, L. Carlson, H. Coates, J. D. 2019-09-25 doi:10.1101/781625 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Sex and pubertal status influence dendritic spine density onto frontal cortiocostriatal projection neurons ]]> https://biorxiv.org/content/10.1101/787408v1?rss=1 Delevich, K. Okada, N. J. Rahane, A. Zhang, Z. Hall, C. D. Wilbrecht, L. 2019-09-30 doi:10.1101/787408 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ A high-content screen profiles cytotoxic microRNAs in pediatric and adult glioblastoma cells and identifies miR-1300 as a potent inducer of cytokinesis failure ]]> https://biorxiv.org/content/10.1101/789438v1?rss=1 Boissinot, M. King, H. Adams, M. Higgins, J. Ward, T. A. Steele, L. P. Tams, D. Morton, R. Polson, E. da Silva, B. Droop, A. P. Hayes, J. L. Martin, H. Laslo, P. Morrison, E. E. Tomlinson, D. C. Wurdak, H. Bond, J. Lawler, S. E. Short, S. C. 2019-10-01 doi:10.1101/789438 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Micro-scale fluid behavior during cryo-EM sample blotting ]]> https://biorxiv.org/content/10.1101/791285v1?rss=1 Armstrong, M. Han, B.-G. Gomez, S. Turner, J. Fletcher, D. A. Glaeser, R. M. 2019-10-02 doi:10.1101/791285 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ A quantitative narrative on movement, disease and patch exploitation in nesting agent groups ]]> https://biorxiv.org/content/10.1101/791400v1?rss=1 Getz, W. M. Salter, R. Tallam, K. 2019-10-03 doi:10.1101/791400 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ Replacement of microglia by monocyte-derived macrophages prevents long-term memory deficits after therapeutic irradiation ]]> https://biorxiv.org/content/10.1101/794354v1?rss=1 Feng, X. Chen, D. Gupta, S. Boosalis, Z. Liu, S. Gupta, N. Rosi, S. 2019-10-07 doi:10.1101/794354 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Stable and dynamic representations of value in the prefrontal cortex ]]> https://biorxiv.org/content/10.1101/794685v1?rss=1 Enel, P. Wallis, J. Rich, E. 2019-10-07 doi:10.1101/794685 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Gene balance predicts transcriptional responses immediately following ploidy change in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/795328v1?rss=1 Potter, B. I. Song, M. J. Doyle, J. J. Coate, J. E. 2019-10-07 doi:10.1101/795328 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Two brain pathways initiate distinct forward walking programs in Drosophila ]]> https://biorxiv.org/content/10.1101/798439v1?rss=1 Bidaye, S. S. Laturney, M. Chang, A. K. Liu, Y. Bockemuhl, T. Buschges, A. Scott, K. 2019-10-08 doi:10.1101/798439 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Establishment of chromatin accessibility by the conserved transcription factor Grainy head is developmentally regulated ]]> https://biorxiv.org/content/10.1101/798454v1?rss=1 Nevil, M. Gibson, T. J. Bartolutti, C. Iyengar, A. Harrison, M. M. 2019-10-08 doi:10.1101/798454 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Diversification of metazoan Kexin-like proprotein convertases: insights from the leech Helobdella ]]> https://biorxiv.org/content/10.1101/802215v1?rss=1 Tao, W.-Y. Cheng, Y.-C. Song, M. H. Weisblat, D. A. Kuo, D.-H. 2019-10-13 doi:10.1101/802215 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement ]]> https://biorxiv.org/content/10.1101/804534v1?rss=1 Patel, A. B. Moore, C. M. Greber, B. J. Luo, J. Ranish, J. Nogales, E. 2019-10-16 doi:10.1101/804534 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Chemoinformatic-guided engineering of polyketide synthases ]]> https://biorxiv.org/content/10.1101/805671v1?rss=1 Zargar, A. Lal, R. Valencia, L. Wang, J. Backman, T. Cruz-Morales, P. Kothari, A. Werts, M. Wong, A. Bailey, C. B. Loubat, A. Liu, Y. Benites, V. Chang, S. Hernandez, A. C. Barajas, J. F. Thompson, M. Barcelos, C. Anayah, R. Garcia-Martin, H. Mukhopadhyay, A. Baidoo, E. E. Katz, L. Keasling, J. D. 2019-10-16 doi:10.1101/805671 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Cdc42 GTPase regulates ESCRTs in nuclear envelope sealing and ER remodeling ]]> https://biorxiv.org/content/10.1101/808436v1?rss=1 Lu, M. Drubin, D. G. 2019-10-17 doi:10.1101/808436 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Rapid multicomponent bioluminescence imaging via substrate unmixing ]]> https://biorxiv.org/content/10.1101/811026v1?rss=1 Rathbun, C. M. Ionkina, A. A. Yao, Z. Jones, K. A. Porterfield, W. B. Prescher, J. A. 2019-10-21 doi:10.1101/811026 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Drivers of plant traits and forest functional composition in coastal plant communities of the Atlantic Forest ]]> https://biorxiv.org/content/10.1101/812339v1?rss=1 Lourenco, J. Newman, E. A. Ventura, J. A. Milanez, C. R. D. Thomaz, L. D. Wandekoken, D. T. Enquist, B. J. 2019-10-21 doi:10.1101/812339 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Opposing transcriptomic gradients explain orthogonal maps in human visual areas ]]> https://biorxiv.org/content/10.1101/812560v1?rss=1 Zhen, Z. Gomez, J. Weiner, K. S. 2019-10-21 doi:10.1101/812560 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Robust, automated sleep scoring by a compact neural network with distributional shift correction ]]> https://biorxiv.org/content/10.1101/813345v1?rss=1 Barger, Z. Frye, C. G. Liu, D. Dan, Y. Bouchard, K. E. 2019-10-21 doi:10.1101/813345 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ A hierarchical framework for segmenting movement paths ]]> https://biorxiv.org/content/10.1101/819763v1?rss=1 Getz, W. M. 2019-10-25 doi:10.1101/819763 Cold Spring Harbor Laboratory Press 2019-10-25 <![CDATA[ Atomic structures determined from digitally defined nanocrystalline regions ]]> https://biorxiv.org/content/10.1101/820274v1?rss=1 Gallagher-Jones, M. J. Bustillo, K. C. Ophus, C. Richards, L. S. Ciston, J. Lee, S. Minor, A. M. Rodriguez, J. A. 2019-10-29 doi:10.1101/820274 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ TSA-Seq 2.0 reveals both conserved and variable chromosomal distances to nuclear speckles ]]> https://biorxiv.org/content/10.1101/824433v1?rss=1 Zhang, L. Zhang, Y. Chen, Y. Gholamalamdari, O. Ma, J. Belmont, A. S. 2019-10-30 doi:10.1101/824433 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ A cryo-tomography-based volumetric model of the actin core of mouse vestibular hair cell stereocilia lacking plastin 1 ]]> https://biorxiv.org/content/10.1101/825737v1?rss=1 Song, J. Patterson, R. Krey, J. F. Hao, S. Wang, L. Ng, B. Sazzed, S. Kovacs, J. Wriggers, W. He, J. Barr-Gillespie, P. G. Auer, M. G. 2019-10-31 doi:10.1101/825737 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Correction of missing-wedge artifacts in filamentous tomograms by template-based constrained deconvolution ]]> https://biorxiv.org/content/10.1101/827006v1?rss=1 Kovacs, J. Song, J. H. Auer, M. He, J. Wriggers, W. R. 2019-11-01 doi:10.1101/827006 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ Unraveling Why We Sleep: Quantitative Analysis Reveals Abrupt Transition from Neural Reorganization to Repair in Early Development ]]> https://biorxiv.org/content/10.1101/827212v1?rss=1 Cao, J. Herman, A. B. West, G. B. Poe, G. Savage, V. M. 2019-11-01 doi:10.1101/827212 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ Density dependence and a colonization rule predict spatial patterning ]]> https://biorxiv.org/content/10.1101/827238v1?rss=1 Brush, M. J. Harte, J. 2019-11-01 doi:10.1101/827238 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ Inferring punctuated evolution in the learned songs of African sunbirds ]]> https://biorxiv.org/content/10.1101/828459v1?rss=1 McEntee, J. P. Zhelezov, G. Werema, C. Najar, N. Penalba, J. V. Mulungu, E. Mbilinyi, M. Karimi, S. Chumakova, L. Burleigh, J. G. Bowie, R. C. K. 2019-11-01 doi:10.1101/828459 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ mir-71 mediates age-dependent opposing contributions of the stress activated kinase KGB-1 in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/835355v1?rss=1 Ruediger, C. Shapira, M. 2019-11-08 doi:10.1101/835355 Cold Spring Harbor Laboratory Press 2019-11-08 <![CDATA[ Aurora B-dependent Ndc80 Degradation Regulates Kinetochore Composition in Meiosis ]]> https://biorxiv.org/content/10.1101/836668v1?rss=1 Chen, J. Liao, A. Powers, E. N. Liao, H. Kohlstaedt, L. A. Evans, R. Holly, R. M. Kim Kim, J. Jovanovic, M. Unal, E. 2019-11-09 doi:10.1101/836668 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Tuberculosis resistance acquisition in space and time: an analysis of globally diverse M. tuberculosis whole genome sequences ]]> https://biorxiv.org/content/10.1101/837096v1?rss=1 20 years).nnCountries with lower gross wealth indices were found to have more recent resistance acquisition to the drug rifampicin. Based on the resistance patterns identified in our study we estimate that commercial diagnostic tests vary considerably in sensitivity for second-line resistance diagnosis by country.nnImplications of all available evidenceThe longevity of resistant MTB in many parts of the world emphasizes its fitness for transmission and its continued threat to public health. The association between country wealth and recent resistance acquisition emphasizes the need for continued investment in TB care delivery and surveillance programs. Geographically relevant diagnostics that take into account a countrys unique distribution of resistance are necessary. ]]> Ektefaie, Y. Dixit, A. Freschi, L. Farhat, M. R. 2019-11-11 doi:10.1101/837096 Cold Spring Harbor Laboratory Press 2019-11-11 <![CDATA[ Structural modularity of the XIST ribonucleoprotein complex ]]> https://biorxiv.org/content/10.1101/837229v1?rss=1 Lu, Z. Guo, J. K. Wei, Y. Dou, D. R. Zarnegar, B. Ma, Q. Li, R. Zhao, Y. Liu, F. Choudhry, H. Khavari, P. A. Chang, H. 2019-11-24 doi:10.1101/837229 Cold Spring Harbor Laboratory Press 2019-11-24 <![CDATA[ Feasibility analysis of semiconductor voltage nanosensors for neuronal membrane potential sensing ]]> https://biorxiv.org/content/10.1101/838342v1?rss=1 Ludwig, A. Serna, P. Morgenstein, L. Yang, G. Bar-Elli, O. Ortiz, G. Miller, E. Oron, D. Grupi, A. Weiss, S. Triller, A. 2019-11-12 doi:10.1101/838342 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Non-stem progenitors enable coordinated changes in gut epithelial cell-type composition ]]> https://biorxiv.org/content/10.1101/840371v1?rss=1 Sanman, L. E. Chen, I. W. Bieber, J. M. Steri, V. Hann, B. Wu, L. F. Altschuler, S. J. 2019-11-13 doi:10.1101/840371 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum ]]> https://biorxiv.org/content/10.1101/841288v1?rss=1 Dennis, A. B. Ballesteros, G. I. Robin, S. Schrader, L. Bast, J. Berghöfer, J. Beukeboom, L. Belghazi, M. Bretaudeau, A. Büllesbach, J. Cash, E. Colinet, D. Dumas, Z. Falabella, P. gatti, j.-l. Geuverink, E. Gibson, J. D. Hertäg, C. Hartmann, S. Jacquin-Joly, E. Lammers, M. Lavandero, B. I. Lindenbaum, I. Massardier-Galata, L. Meslin, C. Montagne, N. Pak, N. Poirie, M. Salvia, R. Smith, C. R. Tagu, D. Tares, S. Vogel, H. Schwander, T. Simon, J.-C. Figueroa, C. C. Vorburger, C. Legeai, F. Gadau, J. 2019-11-14 doi:10.1101/841288 Cold Spring Harbor Laboratory Press 2019-11-14 <![CDATA[ Developmental transcriptomic analysis of the cave-dwelling crustacean, Asellus aquaticus ]]> https://biorxiv.org/content/10.1101/845990v1?rss=1 Gross, J. B. Sun, D. A. Carlson, B. M. Brodo-Abo, S. Protas, M. 2019-11-17 doi:10.1101/845990 Cold Spring Harbor Laboratory Press 2019-11-17 <![CDATA[ Oxidative and non-oxidative active turnover of genomic methylcytosine in distinct pluripotent states ]]> https://biorxiv.org/content/10.1101/846584v1?rss=1 Spada, F. Schiffers, S. Kirchner, A. Zhang, Y. Kosmatchev, O. Korytiakova, E. Rahimoff, R. Ebert, C. Carell, T. 2019-11-18 doi:10.1101/846584 Cold Spring Harbor Laboratory Press 2019-11-18 <![CDATA[ In vivo directed evolution of AAV in the primate retina ]]> https://biorxiv.org/content/10.1101/847459v1?rss=1 Byrne, L. C. Day, T. P. Visel, M. Fortuny, C. Dalkara, D. Merigan, W. H. Schaffer, D. V. Flannery, J. G. 2019-11-20 doi:10.1101/847459 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Flexible linkers in CaMKII control the balance between activating and inhibitory autophosphorylation ]]> https://biorxiv.org/content/10.1101/848044v1?rss=1 Bhattacharyya, M. Lee, Y. K. Muratcioglu, S. Qiu, B. Nyayapati, P. Schulman, H. Groves, J. T. Kuriyan, J. 2019-11-20 doi:10.1101/848044 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ THE SPATIAL REGULATION OF CONDENSIN ACTIVITY IN CHROMOSOME CONDENSATION ]]> https://biorxiv.org/content/10.1101/849273v1?rss=1 Lamothe, R. Costantino, L. Koshland, D. 2019-11-20 doi:10.1101/849273 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Distinct Processing of Selection and Execution Errors in Neural Signatures of Outcome Monitoring ]]> https://biorxiv.org/content/10.1101/853317v1?rss=1 Mushtaq, F. McDougle, S. D. Craddock, M. P. Parvin, D. Brookes, J. Schaefer, A. Mon-Williams, M. Taylor, J. A. Ivry, R. B. 2019-11-25 doi:10.1101/853317 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Genome editing to model and reverse a prevalent mutation associated with myeloproliferative neoplasms ]]> https://biorxiv.org/content/10.1101/855452v1?rss=1 Baik, R. Wyman, S. K. Kabir, S. Corn, J. E. 2019-11-26 doi:10.1101/855452 Cold Spring Harbor Laboratory Press 2019-11-26 <![CDATA[ Stable isotope composition of feathers help track the migratory patterns of Sharp-shinned Hawks (Accipiter striatus) along Western Flyways of North America ]]> https://biorxiv.org/content/10.1101/856278v1?rss=1 Wommack, E. Marrack, L. Mambelli, S. Hull, J. Dawson, T. 2019-11-26 doi:10.1101/856278 Cold Spring Harbor Laboratory Press 2019-11-26 <![CDATA[ Statistically-estimated tree biomass, stem density, and basal area for the upper Midwestern United States at the time of Euro-American settlement ]]> https://biorxiv.org/content/10.1101/856526v1?rss=1 Paciorek, C. J. Cogbill, C. V. Peters, J. A. Goring, S. J. Williams, J. W. Mladenoff, D. J. Dawson, A. McLachlan, J. S. 2019-12-02 doi:10.1101/856526 Cold Spring Harbor Laboratory Press 2019-12-02 <![CDATA[ Nanotopography enhances dynamic remodeling of tight junction proteins through cytosolic complexes ]]> https://biorxiv.org/content/10.1101/858118v1?rss=1 Huang, X. Shi, X. Hansen, M. E. Nemeth, C. L. Celli, A. Huang, B. Mauro, T. Koval, M. Desai, T. 2019-11-28 doi:10.1101/858118 Cold Spring Harbor Laboratory Press 2019-11-28 <![CDATA[ A minimal CRISPR-Cas3 system for genome engineering ]]> https://biorxiv.org/content/10.1101/860999v1?rss=1 Csorgo, B. Leon, L. M. Chau-Ly, I. J. Vasquez-Rifo, A. Berry, J. D. Mahendra, C. Crawford, E. Lewis, J. D. Bondy-Denomy, J. 2019-12-03 doi:10.1101/860999 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ kRISP-meR: A Reference-free Guide-RNA Design Tool for CRISPR/Cas9 ]]> https://biorxiv.org/content/10.1101/869115v1?rss=1 Hera, M. R. Rahman, A. Rahman, A. 2019-12-08 doi:10.1101/869115 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ The direction of local adaptation on pathogen exploitation rates reverses with environmental context ]]> https://biorxiv.org/content/10.1101/2023.05.12.540593v1?rss=1 Visher, E. Ali, A. Barajas, J. Masud, S. McBride, A. Ramos, E. Sui, M. Villalobos-Heredia, C. Walzer, N. White, P. S. Boots, M. 2023-05-15 doi:10.1101/2023.05.12.540593 Cold Spring Harbor Laboratory Press 2023-05-15 <![CDATA[ Predictive and Interpretable: Combining Artificial Neural Networks and Classic Cognitive Models to Understand Human Learning and Decision Making ]]> https://biorxiv.org/content/10.1101/2023.05.17.541226v1?rss=1 Eckstein, M. K. Summerfield, C. Daw, N. D. Miller, K. J. 2023-05-17 doi:10.1101/2023.05.17.541226 Cold Spring Harbor Laboratory Press 2023-05-17 <![CDATA[ Concurrent measurement of O2 and isoprene production during photosynthesis: pros, cons, and metabolic implications ]]> https://biorxiv.org/content/10.1101/2023.05.15.540825v1?rss=1 Som, S. Gallo, L. B. Sunder, A. Demus, J. Domingues, T. F. Wistrom, C. M. Gu, L. Tcherkez, G. G. B. Jardine, K. 2023-05-18 doi:10.1101/2023.05.15.540825 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Carrion converging: Skull shape is predicted by feeding ecology in vultures ]]> https://biorxiv.org/content/10.1101/2023.05.17.541171v1?rss=1 Steinfield, K. R. Felice, R. N. Kirchner, M. E. Knapp, A. 2023-05-18 doi:10.1101/2023.05.17.541171 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ p300 Is an Obligate Integrator of Combinatorial Transcription Factor Inputs ]]> https://biorxiv.org/content/10.1101/2023.05.18.541220v1?rss=1 Ferrie, J. J. Karr, J. P. Graham, T. G. Dailey, G. M. Zhang, G. Tjian, R. Darzacq, X. 2023-05-18 doi:10.1101/2023.05.18.541220 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Covalent Targeting of Glutamate Cysteine Ligase to Inhibit Glutathione Synthesis ]]> https://biorxiv.org/content/10.1101/2023.05.18.541312v1?rss=1 Zhang, L. Tang, M. Tao, X. Shao, Q. Thomas, V. Shimizu, S. Kasano, M. Ishikawa, Y. Inukai, T. Nomura, D. K. 2023-05-18 doi:10.1101/2023.05.18.541312 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Engineering 3D neuronal networks with directional endogenous neuronal plasticity pathways ]]> https://biorxiv.org/content/10.1101/2023.05.17.540876v1?rss=1 Pagan Diaz, G. J. Kilacarslan, E. A. Wester, M. Rahman, S. Aydin, O. Gapinske, L. Kim, Y. Buoros, D. Saif, M. T. A. Bashir, R. 2023-05-19 doi:10.1101/2023.05.17.540876 Cold Spring Harbor Laboratory Press 2023-05-19 <![CDATA[ Benzylisoquinoline alkaloid production in yeast via norlaudanosoline improves selectivity and yield ]]> https://biorxiv.org/content/10.1101/2023.05.19.541502v1?rss=1 Martin, V. Narcross, L. Pyne, M. E. Kevvai, K. Siu, K.-H. Dueber, J. E. 2023-05-20 doi:10.1101/2023.05.19.541502 Cold Spring Harbor Laboratory Press 2023-05-20 <![CDATA[ Commonly used Bayesian diversification-rate models produce biologically meaningful differences on empirical phylogenies ]]> https://biorxiv.org/content/10.1101/2023.05.17.541228v1?rss=1 Martinez-Gomez, J. Song, M. J. Tribble, C. M. Kopperud, B. T. Höhna, S. Freyman, W. A. Specht, C. D. Rothfels, C. J. 2023-05-21 doi:10.1101/2023.05.17.541228 Cold Spring Harbor Laboratory Press 2023-05-21 <![CDATA[ Cynipid wasps systematically reprogram host metabolism and restructure cell walls in developing galls ]]> https://biorxiv.org/content/10.1101/2023.05.22.540048v1?rss=1 Markel, K. Novak, V. Bowen, B. Tian, Y. Chen, Y.-C. Sirirungruang, S. Zhou, A. Louie, K. Northen, T. Eudes, A. Scheller, H. Shih, P. 2023-05-23 doi:10.1101/2023.05.22.540048 Cold Spring Harbor Laboratory Press 2023-05-23 <![CDATA[ Demographic consequences of an extreme heatwave are mitigated by spatial heterogeneity in an annual monkeyflower ]]> https://biorxiv.org/content/10.1101/2023.05.23.541340v1?rss=1 96% of seedlings from geographically-local populations. Some populations from hotter and drier environments had higher fitness, however others from comparable environments performed poorly. Observational studies of local natural populations drastically differed in the consequences of the heatwave - one population was completely extirpated and nearly half had a >50% decrease in fitness. However, a few populations had greater fitness during the heatwave year. Differences in mortality corresponded to the impact of the heatwave on soil moisture - retention of soil moisture throughout the heatwave led to greater survivorship. Our results suggest that not all populations experience the same intensity or degree of mortality during extreme events and such heterogeneity could be important for genetic rescue or to facilitate the distribution of adaptive variants throughout the region. ]]> McDonald, L. M. Scharnagl, A. Turcu, A. K. Patterson, C. M. Kooyers, N. J. 2023-05-23 doi:10.1101/2023.05.23.541340 Cold Spring Harbor Laboratory Press 2023-05-23 <![CDATA[ Evolutionary rescue and reintroduction of resistant frogs allows recovery in the presence of a lethal fungal disease ]]> https://biorxiv.org/content/10.1101/2023.05.22.541534v1?rss=1 Knapp, R. A. Wilber, M. Q. Byrne, A. Q. Joseph, M. B. Smith, T. C. Rothstein, A. P. Grasso, R. L. Rosenblum, E. B. 2023-05-24 doi:10.1101/2023.05.22.541534 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Effects of focused ultrasound in a "clean" mouse model of ultrasonic neuromodulation ]]> https://biorxiv.org/content/10.1101/2023.05.22.541780v1?rss=1 Guo, H. Salahshoor, H. Wu, D. Yoo, S. Sato, T. Tsao, D. Shapiro, M. 2023-05-24 doi:10.1101/2023.05.22.541780 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ The phycobilisome linker protein ApcG interacts with photosystem II and regulates energy transfer to photosystem I in Synechocystis sp. PCC 6803 ]]> https://biorxiv.org/content/10.1101/2023.05.22.541798v1?rss=1 espinoza-corral, R. Iwai, M. Zavrel, T. Lechno-Yossef, S. Sutter, M. Cerveny, J. Niyogi, K. K. Kerfeld, C. 2023-05-24 doi:10.1101/2023.05.22.541798 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Differential Contribution of Sensorimotor Cortex and Subthalamic Nucleus to Unimanual and Bimanual Hand Movements ]]> https://biorxiv.org/content/10.1101/2023.05.23.542003v1?rss=1 Merrick, C. M. Doyle, O. N. Gallegos, N. E. Irwin, Z. T. Olson, J. W. Gonzalez, C. L. Knight, R. T. Ivry, R. B. Walker, H. C. 2023-05-24 doi:10.1101/2023.05.23.542003 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Neuroanatomical and functional dissociations between variably present anterior lateral prefrontal sulci ]]> https://biorxiv.org/content/10.1101/2023.05.25.542301v1?rss=1 Willbrand, E. H. Bunge, S. A. Weiner, K. S. 2023-05-25 doi:10.1101/2023.05.25.542301 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Bayesian target optimisation for high-precision holographic optogenetics ]]> https://biorxiv.org/content/10.1101/2023.05.25.542307v1?rss=1 Triplett, M. A. Gajowa, M. Adesnik, H. Paninski, L. 2023-05-25 doi:10.1101/2023.05.25.542307 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Sorgoleone degradation by sorghum-associated bacteria; an opportunity for enforcing plant growth promotion ]]> https://biorxiv.org/content/10.1101/2023.05.26.542311v1?rss=1 Oda, Y. Elmore, J. R. Nelson, W. C. Wilson, A. Farris, Y. Shrestha, R. Garcia, C. F. Pettinga, D. Ogden, A. J. Baldino, H. Alexander, W. G. Deutschbauer, A. Hurtado, C. V. McDermott, J. E. Guss, A. M. Coleman-Derr, D. McClure, R. Harwood, C. S. Egbert, R. 2023-05-26 doi:10.1101/2023.05.26.542311 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Self-Assembly of a Repeatable DNA Nanohinge System Supporting Higher Order Structure Formation ]]> https://biorxiv.org/content/10.1101/2023.05.26.542516v1?rss=1 Law, M. Sushams, C. Mackay, D. Nguyen, S. Nicholas, R. Tsai, M. R. G. Rajkumar, E. Inaba, F. Maheden, K. Abdi, I. Ho, J. C. H. Kieft, B. Hallam, S. J. 2023-05-26 doi:10.1101/2023.05.26.542516 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Nde1 is a Biphasic Regulator of the Dynein Activation Pathway ]]> https://biorxiv.org/content/10.1101/2023.05.26.542537v1?rss=1 Zhao, Y. Oten, S. Yildiz, A. 2023-05-26 doi:10.1101/2023.05.26.542537 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Reference-free multiplexed single-cell sequencing identifies genetic modifiers of the human immune response ]]> https://biorxiv.org/content/10.1101/2023.05.29.542756v1?rss=1 Hartoularos, G. C. Si, Y. Zhang, F. C. Kathail, P. Lee, D. Ogorodnikov, A. Sun, Y. Song, Y. S. Kang, H. M. Ye, C. J. 2023-06-01 doi:10.1101/2023.05.29.542756 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Visualizing scRNA-Seq Data at Population Scale with GloScope ]]> https://biorxiv.org/content/10.1101/2023.05.29.542786v1?rss=1 Wang, H. Torous, W. Gong, B. Purdom, E. 2023-06-01 doi:10.1101/2023.05.29.542786 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ COBRA improves the quality of viral genomes assembled from metagenomes ]]> https://biorxiv.org/content/10.1101/2023.05.30.542503v1?rss=1 Chen, L. Banfield, J. F. 2023-06-01 doi:10.1101/2023.05.30.542503 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Foveal RGCs develop abnormal calcium dynamics weeks after photoreceptor ablation ]]> https://biorxiv.org/content/10.1101/2023.05.30.542908v1?rss=1 Xu, Z. Kunala, K. Murphy, P. Puthussery, T. McGregor, J. E. 2023-06-01 doi:10.1101/2023.05.30.542908 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Distinct neural representations during a brain-machine interface and manual reaching task in motor cortex, prefrontal cortex, and striatum ]]> https://biorxiv.org/content/10.1101/2023.05.31.542532v1?rss=1 Zippi, E. L. Shvartsman, G. F. Vendrell-Llopis, N. Wallis, J. D. Carmena, J. M. 2023-06-01 doi:10.1101/2023.05.31.542532 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex ]]> https://biorxiv.org/content/10.1101/2023.06.01.543278v1?rss=1 Chen, M. H. Ren, X. Cook, A. S. I. Hurley, J. H. 2023-06-01 doi:10.1101/2023.06.01.543278 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Defined synthetic microbial communities colonize and benefit field-grown sorghum ]]> https://biorxiv.org/content/10.1101/2023.05.30.542977v1?rss=1 Fonseca Garcia, C. Wilson, A. Elmore, J. R. Pettinga, D. McClure, R. Atim, J. Pedraza, J. Hutmacher, R. Egbert, R. Coleman-Derr, D. 2023-06-02 doi:10.1101/2023.05.30.542977 Cold Spring Harbor Laboratory Press 2023-06-02 <![CDATA[ TPPP Forms Liquid Condensates and Aggregates in Multiple System Atrophy ]]> https://biorxiv.org/content/10.1101/2023.05.31.542915v1?rss=1 Kemal, S. Richardson, H. S. McAlear, T. S. Kopach, A. Nowacki, J. C. Li, Y. Bechstedt, S. Fu, M.-m. 2023-06-03 doi:10.1101/2023.05.31.542915 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ Phylodynamics Uncovers the Transmission of Antibiotic-Resistant Escherichia coli between Canines and Humans in an Urban Environment ]]> https://biorxiv.org/content/10.1101/2023.06.01.543064v1?rss=1 Walas, N. Müller, N. F. Parker, E. Henderson, A. Capone, D. Brown, J. Barker, T. Graham, J. P. 2023-06-03 doi:10.1101/2023.06.01.543064 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ Deep-learning Based Pathological Assessment of Frozen Procurement Kidney Biopsies Predicts Graft Loss and Guides Organ Utilization: A Large-scale Retrospective Study ]]> https://biorxiv.org/content/10.1101/2023.05.31.543098v1?rss=1 Yi, Z. Xi, C. Menon, M. C. Cravedi, P. Tedla, F. Soto, A. Sun, Z. Liu, K. Zhang, J. Wei, C. Chen, M. Wang, W. Veremis, B. Garcia-barros, M. Kumar, A. Haakinson, D. Brody, R. Gallon, L. O'Connell, P. Naesens, M. Shapiro, R. Colvin, R. Ward, S. Salem, F. Zhang, W. 2023-06-04 doi:10.1101/2023.05.31.543098 Cold Spring Harbor Laboratory Press 2023-06-04 <![CDATA[ dsRID: Editing-free in silico identification of dsRNA region using long-read RNA-seq data ]]> https://biorxiv.org/content/10.1101/2023.06.02.543466v1?rss=1 Yamamoto, R. Liu, Z. Choundhury, M. Xiao, X. 2023-06-05 doi:10.1101/2023.06.02.543466 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Discovery of a new craniofacial gene influencing adaptive phenotypes in a non-model pupfish radiation ]]> https://biorxiv.org/content/10.1101/2023.06.02.543513v1?rss=1 Palominos, M. F. Muhl, V. Richards, E. J. Martin, C. H. 2023-06-05 doi:10.1101/2023.06.02.543513 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Recurrent pattern completion drives the neocortical representation of sensory inference ]]> https://biorxiv.org/content/10.1101/2023.06.05.543698v1?rss=1 Shin, H. Ogando, M. B. Abdeladim, L. Durand, S. Belski, H. Cabasco, H. Loefler, H. Bawany, A. Hardcastle, B. Wilkes, J. Nguyen, K. Suarez, L. Johnson, T. Han, W. Ouellette, B. Grasso, C. Swapp, J. Ha, V. Young, A. Caldejon, S. Williford, A. Groblewski, P. Olsen, S. Kiselycznyk, C. Lecoq, J. Adesnik, H. 2023-06-07 doi:10.1101/2023.06.05.543698 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ A novel, precise and high-throughput technology for viroid detection in cannabis (MFDetectTM) ]]> https://biorxiv.org/content/10.1101/2023.06.05.543818v1?rss=1 Fernandez i Marti, A. Parungao, M. Selimotic, B. Farrar, G. Seyler, T. Anand, A. Ahmad, R. 2023-06-07 doi:10.1101/2023.06.05.543818 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ The Mechanism and Energetics of the Dynein Priming Stroke ]]> https://biorxiv.org/content/10.1101/2023.06.10.544469v1?rss=1 Golcuk, M. Yilmaz, S. Z. Yildiz, A. Gur, M. 2023-06-11 doi:10.1101/2023.06.10.544469 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ An Enterobacteriaceae bloom in aging animals is restrained by the gut microbiome ]]> https://biorxiv.org/content/10.1101/2023.06.13.544815v1?rss=1 Choi, R. Bodkhe, R. Pees, B. Kim, D. J. Berg, M. Monnin, D. Cho, J. Narayan, V. Deller, E. Shapira, M. 2023-06-14 doi:10.1101/2023.06.13.544815 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem ]]> https://biorxiv.org/content/10.1101/2023.06.13.544848v1?rss=1 Lin, H.-H. Torres, M. Adams, C. A. Andeer, P. F. Owens, T. K. Zhalnina, K. Jabusch, L. K. Carlson, H. K. Kuehl, J. V. Deutschbauer, A. M. Northen, T. R. Glass, L. Mortimer, J. C. 2023-06-14 doi:10.1101/2023.06.13.544848 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ Participant-derived cell line transcriptomic analyses and mouse studies reveal a role for ZNF335 in plasma cholesterol statin response ]]> https://biorxiv.org/content/10.1101/2023.06.14.544860v1?rss=1 Theusch, E. Ting, F. Y. Qin, Y. Stevens, K. Naidoo, D. King, S. M. Yang, N. Orr, J. Han, B. Y. Cyster, J. G. Chen, Y.-D. I. Rotter, J. I. Krauss, R. M. Medina, M. W. 2023-06-15 doi:10.1101/2023.06.14.544860 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ The AusTraits Plant Dictionary ]]> https://biorxiv.org/content/10.1101/2023.06.16.545047v1?rss=1 Wenk, E. H. Sauquet, H. Gallagher, R. V. Brownlee, R. Boettiger, C. Coleman, D. Yang, S. Auld, T. Barrett, R. L. Brodribb, T. Choat, B. Dun, L. Ellsworth, D. Gosper, C. Guja, L. Jordan, G. J. Breton, T. Leigh, A. Irving, P. Medlyn, B. Nolan, R. Ooi, M. Sommerville, K. D. Vesk, P. White, M. Wright, I. J. Falster, D. S. 2023-06-18 doi:10.1101/2023.06.16.545047 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities ]]> https://biorxiv.org/content/10.1101/2023.06.18.545353v1?rss=1 Knecht, A. Sirias, D. Utter, D. R. Gibbs, K. A. 2023-06-18 doi:10.1101/2023.06.18.545353 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Physiological phenotypes differ among color morphs in introduced populations of the common wall lizard, Podarcis muralis ]]> https://biorxiv.org/content/10.1101/2023.06.17.545449v1?rss=1 Amer, A. Spears, S. Vaughn, P. L. Colwell, C. Livingston, E. H. McQueen, W. Schill, A. Reichard, D. Gangloff, E. J. Brock, K. M. 2023-06-21 doi:10.1101/2023.06.17.545449 Cold Spring Harbor Laboratory Press 2023-06-21 <![CDATA[ Dynamic noise estimation: A generalized method for modeling noise in sequential decision-making behavior ]]> https://biorxiv.org/content/10.1101/2023.06.19.545524v1?rss=1 Li, J.-J. Shi, C. Li, L. Collins, A. 2023-06-22 doi:10.1101/2023.06.19.545524 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Predicting the impact of rare variants on RNA splicing in CAGI6 ]]> https://biorxiv.org/content/10.1101/2023.06.20.545093v1?rss=1 Lord, J. Jaramillo Oquendo, C. Wai, H. A. Douglas, A. G. L. Bunyan, D. J. Wang, Y. Hu, Z. Zeng, Z. Danis, D. Katsonis, P. Williams, A. Lichtarge, O. Chang, Y. Bagnall, R. D. Mount, S. M. Matthiasardottir, B. Lin, C. van Overeem Hansen, T. Leman, R. Martins, A. Houdayer, C. Krieger, S. Bakolitsa, C. Peng, Y. Kamandula, A. Radivojac, P. Baralle, D. 2023-06-22 doi:10.1101/2023.06.20.545093 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Soil carbon mineralization and microbial community dynamics in response to PyOM addition ]]> https://biorxiv.org/content/10.1101/2023.06.21.545992v1?rss=1 Zeba, N. Berry, T. D. Fischer, M. S. Traxler, M. F. Whitman, T. 2023-06-22 doi:10.1101/2023.06.21.545992 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Tiny Earth CURE improves student persistence in science ]]> https://biorxiv.org/content/10.1101/2023.06.21.543782v1?rss=1 Miller, S. Aldana, C. C. Du, W. Lee, H. Maldonado, N. Sandoval, P. Vong, J. Young, G. Handelsman, J. Broderick, N. A. Hernandez, P. R. Estrada, M. 2023-06-23 doi:10.1101/2023.06.21.543782 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Microbiome remodeling through bacterial competition and host behavior enables rapid adaptation to environmental toxins. ]]> https://biorxiv.org/content/10.1101/2023.06.21.545768v1?rss=1 Kim, D. J. Perez-Carrascal, O. M. DeSousa, C. Jung, D. K. Bohley, S. Wijaya, L. Trang, K. Khoury, S. E. Shapira, M. 2023-06-23 doi:10.1101/2023.06.21.545768 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Fine-tuning Protein Embeddings for GeneralizableAnnotation Propagation ]]> https://biorxiv.org/content/10.1101/2023.06.22.546084v1?rss=1 Dickson, A. M. Mofrad, M. R. K. 2023-06-24 doi:10.1101/2023.06.22.546084 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ The unique microbial diversity, community composition and networks of Pacific Islander endocervical and vaginal microbiomes in the presence or absence of Chlamydia trachomatis infection using metagenomic shotgun sequencing ]]> https://biorxiv.org/content/10.1101/2023.06.23.546186v1?rss=1 Bommana, S. Hu, Y. Kama, M. Wang, R. Kodimerla, R. Jijakli, K. Read, T. Dean, D. 2023-06-24 doi:10.1101/2023.06.23.546186 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ Alternative splicing and environmental adaptation in house mice ]]> https://biorxiv.org/content/10.1101/2023.06.23.546335v1?rss=1 Manahan, D. N. Nachman, M. W. 2023-06-24 doi:10.1101/2023.06.23.546335 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ The microenvironment dictates glycocalyx construction and immune surveillance ]]> https://biorxiv.org/content/10.1101/2023.06.23.546317v1?rss=1 Tharp, K. Park, S. Timblin, G. A. Richards, A. Berg, J. Twells, N. Riley, N. M. Peltan, E. Shon, D. J. Stevenson, E. Tsui, C. K. Palomba, F. Lefebvre, A. E. Soens, R. Ayad, N. ten Hoeve-Scott, J. Healy, K. Digman, M. Dillin, A. Bertozzi, C. Mahal, L. K. Swaney, D. Cantor, J. R. Paszek, M. Weaver, V. 2023-06-25 doi:10.1101/2023.06.23.546317 Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ Dysregulation of Neuroprotective Lipoxin Pathway in Astrocytes in Response to Cytokines and Ocular Hypertension ]]> https://biorxiv.org/content/10.1101/2023.06.22.546157v1?rss=1 Karnam, S. Maurya, S. Ng, E. Choudhary, A. Thobani, A. Flanagan, J. G. Gronert, K. 2023-06-26 doi:10.1101/2023.06.22.546157 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ A cytokinetic ring-driven cell rotation achieves Hertwig's rule in early development ]]> https://biorxiv.org/content/10.1101/2023.06.23.546115v1?rss=1 Middelkoop, T. C. Neipel, J. Cornell, C. E. Naumann, R. Pimpale, L. G. Julicher, F. Grill, S. W. 2023-06-26 doi:10.1101/2023.06.23.546115 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ TOMM40 and TOMM22 of the Translocase Outer Mitochondrial Membrane Complex rescue statin-impaired mitochondrial dynamics, morphology, and mitophagy in skeletal myotubes ]]> https://biorxiv.org/content/10.1101/2023.06.24.546411v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@1845842org.highwire.dtl.DTLVardef@1be8a26org.highwire.dtl.DTLVardef@5fd618org.highwire.dtl.DTLVardef@1e0f523_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yang, N. V. Rogers, S. Guerra, R. Pagliarini, D. J. Theusch, E. Krauss, R. M. 2023-06-26 doi:10.1101/2023.06.24.546411 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Genetic dissection of regulation by a repressing and novel activating corrinoid riboswitch enables engineering of synthetic riboswitches ]]> https://biorxiv.org/content/10.1101/2023.06.26.546531v1?rss=1 Procknow, R. R. Kennedy, K. J. Kluba, M. Rodriguez, L. J. Taga, M. E. 2023-06-26 doi:10.1101/2023.06.26.546531 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ MGSurvE: A framework to optimize trap placement for genetic surveillance of mosquito population ]]> https://biorxiv.org/content/10.1101/2023.06.26.546301v1?rss=1 Sanchez Castellanos, H. M. Smith, D. L. Marshall, J. M. 2023-06-27 doi:10.1101/2023.06.26.546301 Cold Spring Harbor Laboratory Press 2023-06-27 <![CDATA[ Reference genome of the bicolored carpenter ant, Camponotus vicinus ]]> https://biorxiv.org/content/10.1101/2023.06.26.546281v1?rss=1 Ward, P. S. Cash, E. I. Ferger, K. Escalona, M. Sahasrabudhe, R. Miller, C. Toffelmier, E. Fairbairn, C. Seligmann, W. Shaffer, H. B. Tsutsui, N. D. 2023-06-28 doi:10.1101/2023.06.26.546281 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ The evolution and mutational robustness of chromatin accessibility in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.06.26.546587v1?rss=1 Khodursky, S. Zheng, E. B. Svetec, N. Durkin, S. M. Benjamin, S. Gadau, A. Wu, X. Zhao, L. 2023-06-28 doi:10.1101/2023.06.26.546587 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ Variations in Homoeologous Dosage and Epigenomics Mark the Early Evolution of Synthetic Brassica Tetraploids ]]> https://biorxiv.org/content/10.1101/2023.06.27.543697v1?rss=1 Zhang, K. Yang, Y. Zhang, L. Cui, Y. Wu, J. Liang, J. Li, X. Zhang, L. Zhang, X. Zhang, Y. Guo, Z. Chen, S. Freeling, M. Wang, X. Cheng, F. 2023-06-28 doi:10.1101/2023.06.27.543697 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ Implicit reward-based motor learning ]]> https://biorxiv.org/content/10.1101/2023.06.27.546738v1?rss=1 van Mastrigt, N. M. Tsay, J. S. Wang, T. Avraham, G. Abram, S. J. van der Kooij, K. Smeets, J. Ivry, R. B. 2023-06-28 doi:10.1101/2023.06.27.546738 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ Enabling AI in Synthetic Biology through Construction File Specification ]]> https://biorxiv.org/content/10.1101/2023.06.28.546630v1?rss=1 Ataii, N. Bakshi, S. Chen, Y. Fernandez, M. Scheftel, Z. Shao, Z. Tou, C. J. Vega, M. Wang, Y. Zhang, H. Zhao, Z. Anderson, J. C. 2023-06-28 doi:10.1101/2023.06.28.546630 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ Characterization of a phyllosphere methylotroph community isolated with lanthanides ]]> https://biorxiv.org/content/10.1101/2023.06.28.546956v1?rss=1 Govindaraju, A. Friel, C. A. Good, N. M. Wayne, K. S. Martinez-Gomez, N. C. 2023-06-28 doi:10.1101/2023.06.28.546956 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ Encoding and context-dependent control of reward consumption within the central nucleus of the amygdala ]]> https://biorxiv.org/content/10.1101/2023.06.28.546936v1?rss=1 Fraser, K. M. Kim, T. H. Castro, M. Drieu, C. Padovan-Hernandez, Y. Chen, B. J. Pat, F. Ottenheimer, D. J. Janak, P. H. 2023-06-30 doi:10.1101/2023.06.28.546936 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Tuberculosis susceptibility in genetically diverse mice reveals functional diversity of neutrophils ]]> https://biorxiv.org/content/10.1101/2023.06.29.547125v1?rss=1 Ravesloot-Chavez, M. M. Van Dis, E. Fox, D. Nguyenla, X. H. Rawal, S. L. Ballinger, M. A. Thomas, H. Kotov, D. I. Vance, R. Nachman, M. Stanley, S. 2023-06-30 doi:10.1101/2023.06.29.547125 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Personal transcriptome variation is poorly explained by current genomic deep learning models ]]> https://biorxiv.org/content/10.1101/2023.06.30.547100v1?rss=1 Huang, C. Shuai, R. Baokar, P. Chung, R. Rastogi, R. Kathail, P. Ioannidis, N. M. 2023-06-30 doi:10.1101/2023.06.30.547100 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Defining overlooked structures reveals new associations between cortex and cognition in aging and Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2023.06.29.546558v1?rss=1 Maboudian, S. A. Willbrand, E. H. Jagust, W. J. Weiner, K. S. 2023-07-01 doi:10.1101/2023.06.29.546558 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ Cranes soar on thermal updrafts behind cold fronts as they migrate across the sea ]]> https://biorxiv.org/content/10.1101/2023.06.29.547013v1?rss=1 Pekarsky, S. Shohami, D. Horvitz, N. Bowie, R. C. K. Kamath, P. Markin, Y. Getz, W. Nathan, R. 2023-07-01 doi:10.1101/2023.06.29.547013 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ The importance of input sequence set to consensus-derived proteins and their relationship to reconstructed ancestral proteins ]]> https://biorxiv.org/content/10.1101/2023.06.29.547063v1?rss=1 Nixon, C. Lim, S. A. Sternke, M. Barrick, D. Harms, M. J. Marqusee, S. 2023-07-01 doi:10.1101/2023.06.29.547063 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ Genome size evolution and phenotypic correlates in the poison frog family Dendrobatidae ]]> https://biorxiv.org/content/10.1101/2023.06.30.547273v1?rss=1 Douglas, T. E. Marquez, R. Holmes, V. R. D. Johnston, J. S. Tarvin, R. D. 2023-07-02 doi:10.1101/2023.06.30.547273 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Small extracellular vesicles promote stiffness-mediated metastasis ]]> https://biorxiv.org/content/10.1101/2023.07.01.545937v1?rss=1 View larger version (42K): org.highwire.dtl.DTLVardef@1be1dbdorg.highwire.dtl.DTLVardef@928710org.highwire.dtl.DTLVardef@1e14e9borg.highwire.dtl.DTLVardef@efdb7f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sneider, A. Liu, Y. Starich, B. Du, W. Marar, C. Faqih, N. Ciotti, G. E. Kim, J. H. Krishnan, S. Ibrahim, S. Igboko, M. Locke, A. Lewis, D. M. Hong, H. Karl, M. Vij, R. Russo, G. C. Nair, P. R. Gomez-de-Mariscal, E. Habibi, M. Munoz-Barrutia, A. Gu, L. Eisinger-Mathason, T. S. K. Wirtz, D. 2023-07-02 doi:10.1101/2023.07.01.545937 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Chemical alkylation of Asp12 enables mutant selective targeting of K-Ras(G12D) ]]> https://biorxiv.org/content/10.1101/2023.07.01.547359v1?rss=1 Zhang, Z. Zheng, Q. Guiley, K. Z. Shokat, K. 2023-07-02 doi:10.1101/2023.07.01.547359 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Hypoxia blunts angiogenic signaling and upregulates the antioxidant system in elephant seal endothelial cells ]]> https://biorxiv.org/content/10.1101/2023.07.01.547248v1?rss=1 Allen, K. Torres-Velarde, J. M. Vazquez, J. M. Moreno-Santillan, D. D. Sudmant, P. H. Vazquez-Medina, J. P. 2023-07-03 doi:10.1101/2023.07.01.547248 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Non-destructive real-time monitoring of underground root development with distributed fiber optic sensing ]]> https://biorxiv.org/content/10.1101/2023.07.03.547481v1?rss=1 Tei, M. Soma, F. Barbieri, E. Uga, Y. Kawahito, Y. 2023-07-03 doi:10.1101/2023.07.03.547481 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Evolutionary origin, population diversity, and diagnostics for a cryptic hybrid pathogen ]]> https://biorxiv.org/content/10.1101/2023.07.03.547508v1?rss=1 Steenwyk, J. L. Knowles, S. L. Bastos, R. Balamurugan, C. Rinker, D. Mead, M. E. Roberts, C. D. Raja, H. A. Li, Y. Colabardini, A. C. Castro, P. A. Reis, T. F. Canovas, D. Sanchez, R. L. Lagrou, K. Torrado, E. Rodrigues, F. Oberlies, N. H. Zhou, X. Goldman, G. Rokas, A. 2023-07-03 doi:10.1101/2023.07.03.547508 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Baited reconstruction with 2D template matching for high-resolution structure determination in vitro and in vivo without template bias ]]> https://biorxiv.org/content/10.1101/2023.07.03.547552v1?rss=1 Lucas, B. A. Himes, B. A. Grigorieff, N. 2023-07-03 doi:10.1101/2023.07.03.547552 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ A Brain-Wide Map of Neural Activity during Complex Behaviour ]]> https://biorxiv.org/content/10.1101/2023.07.04.547681v1?rss=1 International Brain Lab, Benson, B. Benson, J. Birman, D. Bonacchi, N. Carandini, M. Catarino, J. A. Chapuis, G. A. Churchland, A. K. Dan, Y. Dayan, P. DeWitt, E. E. Engel, T. A. Fabbri, M. Faulkner, M. Fiete, I. R. Findling, C. Freitas-Silva, L. Gercek, B. Harris, K. D. Hausser, M. Hofer, S. B. Hu, F. Hubert, F. Huntenburg, J. M. Khanal, A. Krasniak, C. Langdon, C. Lau, P. Y. P. Mainen, Z. F. Meijer, G. T. Miska, N. J. Mrsic-Flogel, T. D. Noel, J.-P. Nylund, K. Pan-Vazquez, A. Pouget, A. Rossant, C. Roth, N. Schaeffer, R. Schartner, M. Shi, Y. Socha 2023-07-04 doi:10.1101/2023.07.04.547681 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ Brain-wide representations of prior information in mouse decision-making ]]> https://biorxiv.org/content/10.1101/2023.07.04.547684v1?rss=1 Findling, C. Hubert, F. International Brain Laboratory, Acerbi, L. Benson, B. Benson, J. Birman, D. Bonacchi, N. Carandini, M. Catarino, J. A. Chapuis, G. A. Churchland, A. K. Dan, Y. DeWitt, E. E. Engel, T. A. Fabbri, M. Faulkner, M. Fiete, I. R. Freitas-Silva, L. Gercek, B. Harris, K. D. Hausser, M. Hofer, S. B. Hu, F. Huntenburg, J. M. Khanal, A. Krasniak, C. Langdon, C. Latham, P. E. Lau, P. Y. P. Meijer, G. T. Miska, N. J. Mrsic-Flogel, T. D. Noel, J.-P. Nylund, K. Paninski, L. Pan-Vazquez, A. Pillow, J. Rossant, C. Roth, N. Schaeffer, R. Schartn 2023-07-04 doi:10.1101/2023.07.04.547684 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ A Cerebellar Population Coding Model for Sensorimotor Learning ]]> https://biorxiv.org/content/10.1101/2023.07.04.547720v1?rss=1 Wang, T. Ivry, R. B. 2023-07-04 doi:10.1101/2023.07.04.547720 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ Affinity hierarchies underlie the co-assembly of nucleolar and heterochromatin condensates in Drosophila embryos ]]> https://biorxiv.org/content/10.1101/2023.07.06.547894v1?rss=1 Rajshekar, S. Adame-Arana, O. Bajpai, G. Lin, K. Colmenares, S. Safran, S. Karpen, G. H. 2023-07-08 doi:10.1101/2023.07.06.547894 Cold Spring Harbor Laboratory Press 2023-07-08 <![CDATA[ α-carboxysome size is controlled by the disordered scaffold protein CsoS2 ]]> https://biorxiv.org/content/10.1101/2023.07.07.548173v1?rss=1 100 nm and >300 megadaltons. Although many of the protein interactions driving the assembly process have been determined, it remains unknown how size and composition are precisely controlled. Here we show that the size of -carboxysomes is controlled by the disordered scaffolding protein CsoS2. CsoS2 contains two classes of related peptide repeats which bind to the shell in a distinct fashion, and our data indicate that size is controlled by the relative number of these interactions. We propose an energetic and structural model wherein the two repeat classes bind at the junction of shell hexamers but differ in their preferences for the shell contact angles, and thus the local curvature. In total, this model suggests that a set of specific and repeated interactions between CsoS2 and shell proteins collectively achieve the large size and monodispersity of -carboxysomes. ]]> Oltrogge, L. M. Chen, A. W. Chaijarasphong, T. Turnsek, J. B. Savage, D. F. 2023-07-08 doi:10.1101/2023.07.07.548173 Cold Spring Harbor Laboratory Press 2023-07-08 <![CDATA[ Coding and non-coding elements comprise a regulatory network controlling transcription in Kaposi's sarcoma-associated herpesvirus ]]> https://biorxiv.org/content/10.1101/2023.07.08.548212v1?rss=1 Morgens, D. W. Gulyas, L. Souza, A. S. Glaunsinger, B. A. 2023-07-08 doi:10.1101/2023.07.08.548212 Cold Spring Harbor Laboratory Press 2023-07-08 <![CDATA[ Conserved and repetitive motifs in an intrinsically disordered protein drive α-carboxysome assembly ]]> https://biorxiv.org/content/10.1101/2023.07.08.548221v1?rss=1 Turnsek, J. B. Oltrogge, L. M. Savage, D. F. 2023-07-08 doi:10.1101/2023.07.08.548221 Cold Spring Harbor Laboratory Press 2023-07-08 <![CDATA[ Artificial Tactile Stimulation Provides Haptic Cuing in Force Field Adaptation ]]> https://biorxiv.org/content/10.1101/2023.07.08.548191v1?rss=1 Avraham, C. Avraham, G. Nisky, I. 2023-07-10 doi:10.1101/2023.07.08.548191 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ Machine Learning identifies conserved traits that influence lifespan and healthspan responses to dietary restriction ]]> https://biorxiv.org/content/10.1101/2023.07.09.548232v1?rss=1 Hilsabeck, T. A. Wilson, K. A. Narayan, V. P. Carrera, E. Brem, R. B. Campisi, J. A. Kapahi, P. 2023-07-10 doi:10.1101/2023.07.09.548232 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ Signatures of Jamming in the Cellular Potts Model ]]> https://biorxiv.org/content/10.1101/2023.07.10.548321v1?rss=1 Devanny, A. J. Lee, D. J. Kampman, L. Kaufman, L. J. 2023-07-11 doi:10.1101/2023.07.10.548321 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Genomic characterization of Pseudomonas syringae pv. syringae from Callery pear and the efficiency of associated phages in disease protection ]]> https://biorxiv.org/content/10.1101/2023.07.11.545637v1?rss=1 Holtappels, D. Abelson, S. A. Nouth, S. C. Rickus, G. E. J. Giller, J. P. Koskella, B. 2023-07-11 doi:10.1101/2023.07.11.545637 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral-associated organic matter ]]> https://biorxiv.org/content/10.1101/2023.07.11.548626v1?rss=1 20 atom%). Mapping 13C-enriched metagenome-assembled genomes to total ASVs showed at least 92 bacteria and archaea were significantly 13C-enriched. C_LIO_LIOur results illustrate the quantitative impact of hyphal C transport on the formation of potentially protective SOM pools and indicate microbial roles in the AMF hyphosphere soil food web. C_LI ]]> Kakouridis, A. Yuan, M. Nuccio, E. E. Hagen, J. A. Fossum, C. A. Moore, M. L. Estera-Molina, K. Nico, P. S. Weber, P. K. Pett-Ridge, J. Firestone, M. K. 2023-07-11 doi:10.1101/2023.07.11.548626 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Multidimensional super-resolution microscopy unveils nanoscale surface aggregates in the aging of FUS condensates ]]> https://biorxiv.org/content/10.1101/2023.07.12.548239v1?rss=1 He, C. Wu, C. Y. Li, W. Xu, K. 2023-07-12 doi:10.1101/2023.07.12.548239 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ Cortical timescales and the modular organization of structural and functional brain networks ]]> https://biorxiv.org/content/10.1101/2023.07.12.548751v1?rss=1 Lurie, D. J. Pappas, I. D'Esposito, M. T. 2023-07-12 doi:10.1101/2023.07.12.548751 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ Radial glia control microglial differentiation via integrin avb8-dependent trans-activation of TGFB1 ]]> https://biorxiv.org/content/10.1101/2023.07.13.548459v1?rss=1 McKinsey, G. L. Santander, N. Zhang, X. Kleemann, K. Katewa, A. Tran, L. Conant, K. Barraza, M. Lizama, C. O. Koo, H. J. Lee, H. Mukherjee, D. Paidassi, H. Anton, E. S. Atabai, K. Sheppard, D. Butovsky, O. Arnold, T. D. 2023-07-13 doi:10.1101/2023.07.13.548459 Cold Spring Harbor Laboratory Press 2023-07-13 <![CDATA[ Truncated protein isoforms generate diversity of protein localization and function in yeast ]]> https://biorxiv.org/content/10.1101/2023.07.13.548938v1?rss=1 Higdon, A. L. Won, N. H. Brar, G. A. 2023-07-14 doi:10.1101/2023.07.13.548938 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ Direct, quantitative, and comprehensive analysis of tRNA acylation using intact tRNA liquid-chromatography mass-spectrometry ]]> https://biorxiv.org/content/10.1101/2023.07.14.549096v1?rss=1 Fricke, R. Knudson, I. Schepartz, A. 2023-07-14 doi:10.1101/2023.07.14.549096 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ Removing direct photocurrent artifacts in optogenetic connectivity mapping data via constrained matrix factorization ]]> https://biorxiv.org/content/10.1101/2023.07.13.548849v1?rss=1 Antin, B. Sadahiro, M. Gajowa, M. Triplett, M. A. Adesnik, H. Paninski, L. 2023-07-15 doi:10.1101/2023.07.13.548849 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ Tissue tension permits β-catenin phosphorylation to drive mesoderm specification in human embryonic stem cells. ]]> https://biorxiv.org/content/10.1101/2023.07.14.549074v1?rss=1 Ayad, N. M. E. Lakins, J. N. Ghagre, A. Ehrlicher, A. J. Weaver, V. M. 2023-07-15 doi:10.1101/2023.07.14.549074 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ Distinct senescence mechanisms restrain progression of dysplastic nevi ]]> https://biorxiv.org/content/10.1101/2023.07.14.548818v1?rss=1 Lorbeer, F. K. Rieser, G. Goel, A. Wang, M. Oh, A. Yeh, I. Bastian, B. C. Hockemeyer, D. 2023-07-16 doi:10.1101/2023.07.14.548818 Cold Spring Harbor Laboratory Press 2023-07-16 <![CDATA[ The importance of habitat type and historical fire regimes in arthropod community response following large-scale wildfires ]]> https://biorxiv.org/content/10.1101/2023.07.17.548903v1?rss=1 Holmquist, A. J. Markelz, R. C. Martinez, C. C. Gillespie, R. G. 2023-07-17 doi:10.1101/2023.07.17.548903 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ Bimodality in Ras signaling originates from processivity of the Ras activator SOS without classic kinetic bistability ]]> https://biorxiv.org/content/10.1101/2023.07.17.549263v1?rss=1 Lee, A. A. Kim, N. H. Alvarez, S. Ren, H. DeGrandchamp, J. B. Lew, L. N. Groves, J. T. 2023-07-17 doi:10.1101/2023.07.17.549263 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ Conservation and divergence of regulatory architecture in nitrate-responsive plant gene circuits ]]> https://biorxiv.org/content/10.1101/2023.07.17.549299v1?rss=1 Bian, C. Demirer, G. S. Oz, M. T. Cai, Y. Witham, S. Mason, G. A. Shen, R. Ahn, J. Gaudinier, A. Brady, S. Patron, N. 2023-07-17 doi:10.1101/2023.07.17.549299 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ Three-step docking by WIPI2, ATG16L1 and ATG3 delivers LC3 to the phagophore ]]> https://biorxiv.org/content/10.1101/2023.07.17.549391v1?rss=1 Rao, S. Strong, L. M. Ren, X. Skulsuppaisarn, M. Lazarou, M. Hurley, J. H. Hummer, G. 2023-07-17 doi:10.1101/2023.07.17.549391 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ Stem cell transcriptional profiles from mouse subspecies reveal cis-regulatory evolution at ribosomal large-subunit genes ]]> https://biorxiv.org/content/10.1101/2023.07.18.549406v1?rss=1 Simon, N. M. Kim, Y. Bautista, D. M. Dutton, J. R. Brem, R. B. 2023-07-18 doi:10.1101/2023.07.18.549406 Cold Spring Harbor Laboratory Press 2023-07-18 <![CDATA[ Model connectivity: leveraging the power of encoding models to overcome the limitations of functional connectivity ]]> https://biorxiv.org/content/10.1101/2023.07.17.549356v1?rss=1 Meschke, E. X. Visconti di Oleggio Castello, M. Dupre la Tour, T. Gallant, J. L. 2023-07-19 doi:10.1101/2023.07.17.549356 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Evolving Membrane-Associated Accessory Protein Variants for Improved Adeno-Associated Virus Production ]]> https://biorxiv.org/content/10.1101/2023.07.18.549400v1?rss=1 Schieferecke, A. J. Lee, H. Chen, A. Kilaru, V. Williams, J. K. Schaffer, D. V. 2023-07-19 doi:10.1101/2023.07.18.549400 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ A Cell Cycle-Dependent Ferroptosis Sensitivity Switch Governed by EMP2 ]]> https://biorxiv.org/content/10.1101/2023.07.19.549715v1?rss=1 Rodencal, J. Kim, N. Li, V. He, A. Lange, M. He, J. Tarangelo, A. Schafer, Z. T. Olzmann, J. Sage, J. Long, J. Z. Dixon, S. J. 2023-07-19 doi:10.1101/2023.07.19.549715 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data ]]> https://biorxiv.org/content/10.1101/2023.07.20.549584v1?rss=1 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms role in ecology and human health. ]]> Zuffa, S. Schmid, R. Bauermeister, A. P. Gomes, P. W. Caraballo-Rodriguez, A. M. El Abiead, Y. Aron, A. T. Gentry, E. C. Zemlin, J. Meehan, M. J. Avalon, N. E. Cichewicz, R. H. Buzun, E. Carrillo Terrazas, M. Hsu, C.-Y. Oles, R. Vasquez Ayala, A. Zhao, J. Chu, H. Kuijpers, M. C. M. Jackrel, S. L. Tugizimana, F. Nephali, L. P. Dubery, I. A. Madala, N. E. Moreira, E. A. Costa-Lotufo, L. V. Lopes, N. P. Rezende-Teixeira, P. Jimenez, P. C. Rimal, B. Patterson, A. D. Traxler, M. F. Pessotti, R. d. C. Alvarado-Villalobos, D. Tamayo-Castillo, G. Chaverri, P. Escud 2023-07-20 doi:10.1101/2023.07.20.549584 Cold Spring Harbor Laboratory Press 2023-07-20 <![CDATA[ Five inhibitory receptors display distinct vesicular distributions in T cells ]]> https://biorxiv.org/content/10.1101/2023.07.21.550019v1?rss=1 Lu, J. Veler, A. Simonetti, B. Raj, T. Chou, P. H. Cross, S. J. Phillips, A. M. Ruan, X. J. Huynh, L. Dowsey, A. W. Ye, D. Murphy, R. F. Verkade, P. Cullen, P. J. Wuelfing, C. 2023-07-22 doi:10.1101/2023.07.21.550019 Cold Spring Harbor Laboratory Press 2023-07-22 <![CDATA[ Characterization and diversification of AraC/XylS family regulators guided by transposon sequencing ]]> https://biorxiv.org/content/10.1101/2023.07.21.550116v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@fb1ee2org.highwire.dtl.DTLVardef@a88f1dorg.highwire.dtl.DTLVardef@4bbd5borg.highwire.dtl.DTLVardef@7cdbfc_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pearson, A. N. Incha, M. R. Ho, C. Schmidt, M. Roberts, J. B. Nava, A. A. Keasling, J. D. 2023-07-22 doi:10.1101/2023.07.21.550116 Cold Spring Harbor Laboratory Press 2023-07-22 <![CDATA[ Glial-derived mitochondrial signals impact neuronal proteostasis and aging. ]]> https://biorxiv.org/content/10.1101/2023.07.20.549924v1?rss=1 Bar-Ziv, R. Dutta, N. Hruby, A. Sukarto, E. Henderson, H. R. Durieux, J. Tronnes, S. U. Averbukh, M. Alcala, A. Ahmad, Q. Bolas, T. Perez, J. Dishart, J. G. Vega, M. Garcia, G. Higuchi-Sanabria, R. Dillin, A. 2023-07-23 doi:10.1101/2023.07.20.549924 Cold Spring Harbor Laboratory Press 2023-07-23 <![CDATA[ Early-life stress triggers long-lasting organismal resilience and longevity via tetraspanin ]]> https://biorxiv.org/content/10.1101/2023.07.25.550452v1?rss=1 Jiang, W. I. Belly, H. D. Wang, B. K. Wong, A. Kim, M. Oh, F. DeGeorge, J. Huang, X. Guang, S. Weiner, O. K. Ma, D. K. 2023-07-25 doi:10.1101/2023.07.25.550452 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Extensive and diverse lanthanide-dependent metabolism in the ocean ]]> https://biorxiv.org/content/10.1101/2023.07.25.550467v1?rss=1 Voutsinos, M. Y. Banfield, J. F. McClelland, H.-L. O. 2023-07-25 doi:10.1101/2023.07.25.550467 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Microglia Regulate Sleep via Calcium-Dependent Modulation of Norepinephrine Transmission ]]> https://biorxiv.org/content/10.1101/2023.07.24.550176v1?rss=1 Ma, C. Li, B. Silverman, D. Ding, X. Li, A. Xiao, C. Huang, G. Worden, K. Muroy, S. Chen, W. Xu, Z. Tso, C. F. Huang, Y. Zhang, Y. Luo, Q. Saijo, K. Dan, Y. 2023-07-26 doi:10.1101/2023.07.24.550176 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Identification of Late Pleistocene and Holocene fossil lizards from Hall's Cave and a primer on morphological variation in North American lizard skulls ]]> https://biorxiv.org/content/10.1101/2023.07.25.549934v1?rss=1 Ledesma, D. T. Scarpetta, S. G. Jacisin, J. J. Meza, A. Kemp, M. E. 2023-07-26 doi:10.1101/2023.07.25.549934 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Lariat debranching by RNA DEBRANCHING ENZYME 1 depends on SICKLE in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2023.07.25.550414v1?rss=1 Kovak, E. E. Marshall, C. M. Molinari, M. D. C. Nepomuceno, A. L. Harmon, F. G. 2023-07-26 doi:10.1101/2023.07.25.550414 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Leishmania major-induced alteration of host cellular and systemic copper homeostasis drives the fate of infection ]]> https://biorxiv.org/content/10.1101/2023.07.25.550461v1?rss=1 Paul, R. Chakrabarty, A. Dey, S. Samanta, S. Pandey, R. Maji, S. Pezacki, A. T. Chang, C. J. Datta, R. Gupta, A. 2023-07-26 doi:10.1101/2023.07.25.550461 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Local Disordered Region Sampling (LDRS) for Ensemble Modeling of Proteins with Experimentally Undetermined or Low Confidence Prediction Segments ]]> https://biorxiv.org/content/10.1101/2023.07.25.550520v1?rss=1 Liu, Z. H. Teixeira, J. M. C. Zhang, O. Tsangaris, T. E. Li, J. Gradinaru, C. C. Head-Gordon, T. Forman-Kay, J. D. 2023-07-27 doi:10.1101/2023.07.25.550520 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ DCLRE1B/hSNM1B (Apollo) is not acutely required for human pluripotent stem cell survival ]]> https://biorxiv.org/content/10.1101/2023.07.29.551071v1?rss=1 Bartke, R. Hockemeyer, D. 2023-07-30 doi:10.1101/2023.07.29.551071 Cold Spring Harbor Laboratory Press 2023-07-30 <![CDATA[ Spatial Omics Driven Crossmodal Pretraining Applied to Graph-based Deep Learning for Cancer Pathology Analysis ]]> https://biorxiv.org/content/10.1101/2023.07.30.551187v1?rss=1 Azher, Z. Fatemi, M. Lu, Y. Srinivasan, G. Diallo, A. Christensen, B. Salas, L. Kolling, F. Perreard, L. Palisoul, S. Vaickus, L. Levy, J. 2023-07-31 doi:10.1101/2023.07.30.551187 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ Potential to Enhance Large Scale Molecular Assessments of Skin Photoaging through Virtual Inference of Spatial Transcriptomics from Routine Staining ]]> https://biorxiv.org/content/10.1101/2023.07.30.551188v1?rss=1 Srinivasan, G. Davis, M. LeBoeuf, M. Fatemi, M. Azher, Z. Lu, Y. Diallo, A. Montivero, M. Kolling, F. Perrard, L. Salas, L. Christensen, B. Palisoul, S. Tsongalis, G. Vaickus, L. Preum, S. Levy, J. 2023-08-01 doi:10.1101/2023.07.30.551188 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ Iron rescues glucose-mediated photosynthesis repression during lipid accumulation in the green alga Chromochloris zofingiensis ]]> https://biorxiv.org/content/10.1101/2023.07.31.551119v1?rss=1 Jeffers, T. L. Purvine, S. O. Nicora, C. D. McCombs, R. M. Upadhyaya, S. L. Stroumza, A. Whang, K. Gallaher, S. D. Dohnalkova, A. Merchant, S. Lipton, M. Niyogi, K. K. Roth, M. S. 2023-08-01 doi:10.1101/2023.07.31.551119 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires ]]> https://biorxiv.org/content/10.1101/2023.08.01.549754v1?rss=1 Schoelmerich, M. C. Ly, L. West-Roberts, J. Shi, L.-D. Shen, C. Malvankar, N. Taib, N. Gribaldo, S. Woodcroft, B. J. Al-Shayeb, B. Dai, X. Mozsary, C. Hickey, S. He, C. Beaulaurier, J. A. Juul, S. Sachdeva, R. Banfield, J. 2023-08-01 doi:10.1101/2023.08.01.549754 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ Tissue-specific and cis-regulatory changes underlie parallel, adaptive gene expression evolution in house mice ]]> https://biorxiv.org/content/10.1101/2023.08.01.551413v1?rss=1 Durkin, S. Ballinger, M. A. Nachman, M. W. 2023-08-01 doi:10.1101/2023.08.01.551413 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ Jointly modeling deep mutational scans identifies shifted mutational effects among SARS-CoV-2 spike homologs ]]> https://biorxiv.org/content/10.1101/2023.07.31.551037v1?rss=1 1,000-fold in the impact of the same mutation on spike-mediated viral infection across spikes from different SARS-CoV-2 variants. Overall, our work establishes a general approach for comparing sets of DMS experiments to identify biologically important shifts in mutational effects. Significance StatementAmino-acid mutations to a protein have effects that can shift as the protein evolves or is put under new selective pressure. The effects of amino-acid mutations to a specific protein under a defined selective pressure can be measured by deep mutational scanning experiments. Here, we devise an approach to quantify shifts in mutational effects between experiments performed on different homologs (i.e. variants) of the same protein, or on the same protein selected under different conditions. We use this approach to compare experiments performed on three homologs of SARS-CoV-2 spike, identifying mutations that have shifted in their effect on spike-mediated viral infection by >1,000 fold across SARS-CoV-2 variants. ]]> Haddox, H. K. Galloway, J. G. Dadonaite, B. Bloom, J. D. Matsen, F. A. DeWitt, W. S. 2023-08-02 doi:10.1101/2023.07.31.551037 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Methanotrophic Methanoperedens archaea host diverse and interacting extrachromosomal elements ]]> https://biorxiv.org/content/10.1101/2023.08.02.551345v1?rss=1 Shi, L.-D. West-Roberts, J. Schoelmerich, M. C. Penev, P. I. Chen, L. Amano, Y. Lei, S. Sachdeva, R. Banfield, J. F. 2023-08-02 doi:10.1101/2023.08.02.551345 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ A force-sensitive mutation reveals a spindle assembly checkpoint-independent role for dynein in anaphase progression ]]> https://biorxiv.org/content/10.1101/2023.08.03.551815v1?rss=1 Salvador-Garcia, D. Jin, L. Hensley, A. Golcuk, M. Gallaud, E. Chaaban, S. Port, F. Vagnoni, A. Planelles-Herrero, V. J. McClintock, M. A. Derivery, E. Carter, A. P. Giet, R. Gur, M. Yildiz, A. Bullock, S. L. 2023-08-04 doi:10.1101/2023.08.03.551815 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ A Bright, Photostable Dye that Enables Multicolor, Time Lapse, and Super-Resolution Imaging of Acidic Organelles ]]> https://biorxiv.org/content/10.1101/2023.08.04.552058v1?rss=1 Lesiak, L. Dadina, N. Zheng, S. Schelvis, M. Schepartz, A. 2023-08-04 doi:10.1101/2023.08.04.552058 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ The cell adhesion molecule Echinoid promotes tissue survival and separately restricts tissue overgrowth in Drosophila imaginal discs ]]> https://biorxiv.org/content/10.1101/2023.08.04.552072v1?rss=1 Spitzer, D. C. Sun, W. Y. Rodriguez-Vargas, A. Hariharan, I. K. 2023-08-06 doi:10.1101/2023.08.04.552072 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ Infant gut bacteriophage strain persistence during the first three years of life ]]> https://biorxiv.org/content/10.1101/2023.08.07.552389v1?rss=1 Lou, Y. C. Chen, L. Borges, A. L. West-Roberts, J. A. Firek, B. A. Morowitz, M. Banfield, J. 2023-08-08 doi:10.1101/2023.08.07.552389 Cold Spring Harbor Laboratory Press 2023-08-08 <![CDATA[ DeltaAI: Semi-Autonomous Tissue Grossing Measurements and Recommendations using Neural Radiance Fields for Rapid, Complete Intraoperative Histological Assessment of Tumor Margins ]]> https://biorxiv.org/content/10.1101/2023.08.07.552349v1?rss=1 Suvarna, A. Vempati, R. Chacko, R. Srinivasan, G. Lu, Y. Hunt, B. Torres, V. Samkoe, K. Davis, M. Fu, L. Christensen, B. Vaickus, L. LeBoeuf, M. Levy, J. 2023-08-09 doi:10.1101/2023.08.07.552349 Cold Spring Harbor Laboratory Press 2023-08-09 <![CDATA[ Open-source milligram-scale, four channel, automated protein purification system ]]> https://biorxiv.org/content/10.1101/2023.08.09.552685v1?rss=1 Puccinelli, R. R. Sama, S. S. Worthington, C. M. Puschnik, A. S. Pak, J. E. Gomez-Sjoberg, R. 2023-08-10 doi:10.1101/2023.08.09.552685 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes ]]> https://biorxiv.org/content/10.1101/2023.08.09.552727v1?rss=1 Yoon, P. H. Skopintsev, P. Shi, H. Chen, L.-X. Adler, B. A. Al-Shimary, M. Craig, R. J. Li, Z. Amerasekera, J. Trinidad, M. Nisonoff, H. Chen, K. Lahiri, A. Boger, R. Jacobsen, S. Banfield, J. F. Doudna, J. A. 2023-08-10 doi:10.1101/2023.08.09.552727 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ Mycobacterial formation of intracellular lipid inclusions is a dynamic process associated with rapid replication ]]> https://biorxiv.org/content/10.1101/2023.08.10.552809v1?rss=1 Fines, D. M. Schichnes, D. Knight, M. Anaya-Sanchez, A. Thuong, N. T. T. Cox, J. S. Stanley, S. 2023-08-10 doi:10.1101/2023.08.10.552809 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ Temperature variation drives coordinated scaling of temporal and dynamic features of transcription in embryonic development ]]> https://biorxiv.org/content/10.1101/2023.08.09.552666v1?rss=1 Martini, G. Garcia, H. G. 2023-08-11 doi:10.1101/2023.08.09.552666 Cold Spring Harbor Laboratory Press 2023-08-11 <![CDATA[ Local interneurons in the murine visual thalamus have diverse receptive fields and can provide feature selective inhibition to relay cells. ]]> https://biorxiv.org/content/10.1101/2023.08.10.549394v1?rss=1 Gorin, A. S. Miao, Y. Ahn, S. Suresh, V. Su, Y. Ciftcioglu, U. M. Sommer, F. T. Hirsch, J. A. 2023-08-12 doi:10.1101/2023.08.10.549394 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ Targeted Protein Degradation through Recruitment of the CUL4A Complex Adaptor Protein DDB1 ]]> https://biorxiv.org/content/10.1101/2023.08.11.553046v1?rss=1 Meyers, M. Cismoski, S. Panidapu, A. Chie-Leon, B. Nomura, D. K. 2023-08-12 doi:10.1101/2023.08.11.553046 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ Flexible regulation of representations on a drifting manifold enables long-term stable complex neuroprosthetic control ]]> https://biorxiv.org/content/10.1101/2023.08.11.551770v1?rss=1 NATRAJ, N. Seko, S. Abiri, R. Yan, H. Graham, Y. Tu-Chan, A. Chang, E. F. Ganguly, K. 2023-08-14 doi:10.1101/2023.08.11.551770 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Does urbanization lead to parallel demographic shifts across the world in a cosmopolitan plant? ]]> https://biorxiv.org/content/10.1101/2023.08.14.552623v1?rss=1 Caizergues, A. E. Santangelo, J. S. Ness, R. W. Angeoletto, F. Anstett, D. N. Anstett, J. Baena-Diaz, F. Carlen, E. J. Chaves, J. A. Comerford, M. S. Dyson, K. Falahati-Anbaran, M. Fellowes, M. D. E. Hodgins, K. A. Hood, G. R. Iniguez-Armijos, C. Kooyers, N. J. Lazaro-Lobo, A. Moles, A. T. Munshi-South, J. Paule, J. Porth, I. M. Santiago-Rosario, L. Y. Stack Whitney, K. Tack, A. J. M. Johnson, M. T. J. 2023-08-14 doi:10.1101/2023.08.14.552623 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Two-way feedback between chromatin compaction and histone modification state explains S. cerevisiae heterochromatin bistability ]]> https://biorxiv.org/content/10.1101/2023.08.12.552948v1?rss=1 Movilla Miangolarra, A. Saxton, D. S. Yan, Z. Rine, J. Howard, M. 2023-08-15 doi:10.1101/2023.08.12.552948 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Phosphorylation of a Cleaved Tau Proteoform at a Single Residue Inhibits Binding to the E3 Ubiquitin Ligase, CHIP ]]> https://biorxiv.org/content/10.1101/2023.08.16.553575v1?rss=1 Nadel, C. M. Wucherer, K. Oehler, A. Thwin, A. C. Basu, K. Callahan, M. D. Southworth, D. R. Mordes, D. A. Craik, C. S. Gestwicki, J. E. 2023-08-16 doi:10.1101/2023.08.16.553575 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ Decoding reveals the neural representation of held and manipulate musical thoughts ]]> https://biorxiv.org/content/10.1101/2023.08.15.553456v1?rss=1 Quiroga-Martinez, D. R. Fernandez-Rubio, G. Bonetti, L. Achyutuni, K. G. Tzovara, A. Knight, R. T. Vuust, P. 2023-08-17 doi:10.1101/2023.08.15.553456 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Surface-active antibiotic production is a multifunctional adaptation for postfire microbes ]]> https://biorxiv.org/content/10.1101/2023.08.17.553728v1?rss=1 Liu, M. D. Du, Y. Koupaei, S. K. Kim, N. R. Zhang, W. Traxler, M. F. 2023-08-17 doi:10.1101/2023.08.17.553728 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair ]]> https://biorxiv.org/content/10.1101/2023.08.17.553567v1?rss=1 O'Meara, M. J. Rapala, J. R. Nichols, C. B. Alexandre, C. Billmyre, R. B. Steenwyk, J. L. Alspaugh, J. A. O'Meara, T. R. 2023-08-18 doi:10.1101/2023.08.17.553567 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ Enlarged Perivascular Spaces are Associated with White Matter Injury, Brain Atrophy, Cognitive Decline and Markers of Inflammation in an Autosomal Dominant Vascular Neurodegenerative Disease (CADASIL) ]]> https://biorxiv.org/content/10.1101/2023.08.17.553732v1?rss=1 Karvelas, N. Oh, B. Wang, E. Cobigo, Y. Tsuei, T. Fitzsimons, S. Ehrenberg, A. Geschwind, M. Schwartz, D. Kramer, J. Ferguson, A. R. Miller, B. L. Silbert, L. Rosen, H. Elahi, F. M. 2023-08-19 doi:10.1101/2023.08.17.553732 Cold Spring Harbor Laboratory Press 2023-08-19 <![CDATA[ Graduate student mentorship as a target for diversifying the biological sciences ]]> https://biorxiv.org/content/10.1101/2023.08.18.553806v1?rss=1 Debray, R. Dewald-Wang, E. A. Ennis, K. 2023-08-19 doi:10.1101/2023.08.18.553806 Cold Spring Harbor Laboratory Press 2023-08-19 <![CDATA[ Consensus prediction of cell type labels with popV ]]> https://biorxiv.org/content/10.1101/2023.08.18.553912v1?rss=1 Ergen, C. Xing, G. Xu, C. Jayasuriya, M. McGeever, E. Pisco, A. O. Streets, A. M. Yosef, N. 2023-08-21 doi:10.1101/2023.08.18.553912 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Regulatory variation controlling architectural pleiotropy in maize ]]> https://biorxiv.org/content/10.1101/2023.08.19.553731v1?rss=1 Bertolini, E. Rice, B. R. Braud, M. Yang, J. Hake, S. Strable, J. Lipka, A. E. Eveland, A. L. 2023-08-21 doi:10.1101/2023.08.19.553731 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Plasticity drives geographic variation and trait coordination in blue oak drought physiology ]]> https://biorxiv.org/content/10.1101/2023.08.20.553748v1?rss=1 Anderegg, L. D. L. Skelton, R. P. Diaz, J. Papper, P. Ackerly, D. D. Dawson, T. D. L. 2023-08-21 doi:10.1101/2023.08.20.553748 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Differential neural mechanisms underlie cortical gating of visual spatial attention mediated by alpha-band oscillations ]]> https://biorxiv.org/content/10.1101/2023.08.21.553303v1?rss=1 Yang, X. Fiebelkorn, I. C. Jensen, O. Knight, R. T. Kastner, S. 2023-08-22 doi:10.1101/2023.08.21.553303 Cold Spring Harbor Laboratory Press 2023-08-22 <![CDATA[ Olfaction regulates peripheral mitophagy and mitochondrial function ]]> https://biorxiv.org/content/10.1101/2023.08.21.554156v1?rss=1 Dishart, J. G. Pender, C. Shen, K. Zhang, H. Ly, M. Webb, M. Dillin, A. G. 2023-08-22 doi:10.1101/2023.08.21.554156 Cold Spring Harbor Laboratory Press 2023-08-22 <![CDATA[ Age-dependent extinction and the neutral theory of biodiversity ]]> https://biorxiv.org/content/10.1101/2023.08.23.554417v1?rss=1 Saulsbury, J. G. Parins-Fukuchi, C. T. Wilson, C. J. Reitan, T. Liow, L. H. 2023-08-24 doi:10.1101/2023.08.23.554417 Cold Spring Harbor Laboratory Press 2023-08-24 <![CDATA[ A phylogenetic approach to explore the Aspergillus fumigatus conidial surface-associated proteome and its role in pathogenesis ]]> https://biorxiv.org/content/10.1101/2023.08.22.553365v1?rss=1 Valero, C. Pinzan, C. F. de Castro, P. A. van Rhijn, N. Earle, K. Liu, H. Horta, M. A. C. Kniemeyer, O. Krüger, T. Pschibul, A. Coemert, D. N. Heinekamp, T. Brakhage, A. A. Steenwyk, J. L. Mead, M. E. Rokas, A. Filler, S. G. da Rosa-Garzon, N. G. Cabral, H. Deljabe, E. Bromley, M. J. Angeli, C. B. Palmisano, G. Ibrahim, A. S. Gago, S. dos Reis, T. F. Goldman, G. H. 2023-08-26 doi:10.1101/2023.08.22.553365 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ A deep learning phenotyping method for genetic analysis of 3D micro-CT data ]]> https://biorxiv.org/content/10.1101/2023.08.24.554725v1?rss=1 Karshenas, A. Linderoth, T. P. Zatha, R. RusuWa, B. Durbin, R. 2023-08-26 doi:10.1101/2023.08.24.554725 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum ]]> https://biorxiv.org/content/10.1101/2023.08.28.551515v1?rss=1 Haase, M. A. B. Steenwyk, J. L. Boeke, J. D. 2023-08-28 doi:10.1101/2023.08.28.551515 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Brain-Derived CCN3 Is An Osteoanabolic Hormone That Sustains Bone in Lactating Females ]]> https://biorxiv.org/content/10.1101/2023.08.28.554707v1?rss=1 Babey, M. E. Krause, W. C. Herber, C. B. Chen, K. Nikkannen, J. Rodriquez, R. Zhang, X. Castro-Navarro, F. Wang, Y. Villeda, S. Lance, N. E. Scheller, E. L. Chan, C. K. F. Ambrosi, T. H. Ingraham, H. A. 2023-08-28 doi:10.1101/2023.08.28.554707 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Tau fibrils induce nanoscale membrane damage and nucleate cytosolic tau at lysosomes ]]> https://biorxiv.org/content/10.1101/2023.08.28.555157v1?rss=1 Rose, K. Jepson, T. Shukla, S. Maya-Romero, A. Kampmann, M. Xu, K. Hurley, J. H. 2023-08-28 doi:10.1101/2023.08.28.555157 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ A RAB7A Phosphoswitch Coordinates Rubicon Homology Protein Regulation of PINK1/Parkin-Dependent Mitophagy ]]> https://biorxiv.org/content/10.1101/2023.08.28.555228v1?rss=1 Tudorica, D. A. Basak, B. L. F. Cordova, A. P. Khuu, G. Rose, K. Lazarou, M. Holzbaur, E. Hurley, J. H. 2023-08-29 doi:10.1101/2023.08.28.555228 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Step-wise activation of a Family C GPCR ]]> https://biorxiv.org/content/10.1101/2023.08.29.555158v1?rss=1 Kumar, K. K. Wang, H. Habrian, C. Latorraca, N. R. Xu, J. O'Brien, E. S. Zhang, C. Montabana, E. Koehl, A. Marqusee, S. Isacoff, E. Y. Kobilka, B. K. 2023-08-30 doi:10.1101/2023.08.29.555158 Cold Spring Harbor Laboratory Press 2023-08-30 <![CDATA[ Foodscapes for Salmon and Other Mobile Consumers in River Networks ]]> https://biorxiv.org/content/10.1101/2023.08.30.555604v1?rss=1 Rossi, G. Bellmore, J. R. Armstrong, J. B. Jeffres, C. Naman, S. M. Carlson, S. M. Grantham, T. E. Kaylor, M. J. White, S. Katz, J. Power, M. E. 2023-09-01 doi:10.1101/2023.08.30.555604 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Uncovering the mosaic evolution of carnivoran skeletal systems ]]> https://biorxiv.org/content/10.1101/2023.09.03.556127v1?rss=1 Law, C. J. Hlusko, L. J. Tseng, J. 2023-09-04 doi:10.1101/2023.09.03.556127 Cold Spring Harbor Laboratory Press 2023-09-04 <![CDATA[ Scalable bio-platform to recover critical metals fromcomplex waste sources ]]> https://biorxiv.org/content/10.1101/2023.09.02.556034v1?rss=1 Good, N. M. Kang-Yun, C. S. Su, M. Z. Zytnick, A. M. Vu, H. N. Grace, J. M. Nguyen, H. H. Park, D. M. Skovran, E. Fan, M. Martinez-Gomez, N. C. 2023-09-06 doi:10.1101/2023.09.02.556034 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Deep learning enables accurate soft tissue deformation estimation in vivo ]]> https://biorxiv.org/content/10.1101/2023.09.04.556266v1?rss=1 Huff, R. D. Houghton, F. Earl, C. C. Ghajar-Rahimi, E. Dogra, I. Yu, D. Harris-Adamson, C. Goergen, C. J. O'Connell, G. D. 2023-09-06 doi:10.1101/2023.09.04.556266 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ DropBlot: single-cell western blotting of chemically fixed cancer cells ]]> https://biorxiv.org/content/10.1101/2023.09.04.556277v1?rss=1 Liu, Y. Herr, A. E. 2023-09-06 doi:10.1101/2023.09.04.556277 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Causal Genetic Loci for a Motivated Behavior Spectrum Harbor Psychiatric Risk Genes ]]> https://biorxiv.org/content/10.1101/2023.09.06.556529v1?rss=1 Xu, J. Casanave, R. Chitre, A. S. Wang, Q. Nguyen, K.-M. Blake, C. Wagle, M. Cheng, R. Polesskaya, O. Palmer, A. A. Guo, S. 2023-09-06 doi:10.1101/2023.09.06.556529 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Context-dependent decision-making in the primate hippocampal-prefrontal circuit ]]> https://biorxiv.org/content/10.1101/2023.09.08.556931v1?rss=1 Elston, T. W. Wallis, J. D. 2023-09-09 doi:10.1101/2023.09.08.556931 Cold Spring Harbor Laboratory Press 2023-09-09 <![CDATA[ Reciprocal inflammatory signals establish profibrotic cross-feeding metabolism ]]> https://biorxiv.org/content/10.1101/2023.09.06.556606v1?rss=1 Yadav, P. Gomez Ortega, J. Chang, K.-C. Pan, S. Biswas, N. Nilsson, J. Yin, X. Bhattacharyya, A. Boostanpour, K. Tsukui, T. Sheppard, D. Li, B. Maishan, M. Taenaka, H. Matthay, M. Muramatsu, R. Naser, M. Molofsky, A. B. Wolters, P. J. Abate, A. R. Tharp, K. Bhattacharya, M. 2023-09-10 doi:10.1101/2023.09.06.556606 Cold Spring Harbor Laboratory Press 2023-09-10 <![CDATA[ MGDrivE 3: A decoupled vector-human framework for epidemiological simulation of mosquito genetic control tools and their surveillance ]]> https://biorxiv.org/content/10.1101/2023.09.09.556958v1?rss=1 Mondal, A. Sanchez C., H. M. Marshall, J. M. 2023-09-12 doi:10.1101/2023.09.09.556958 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Systematic identification of transcriptional activator domains from non-transcription factor proteins in plants and yeast ]]> https://biorxiv.org/content/10.1101/2023.09.12.557247v1?rss=1 800 non-transcription factor genes in both species, and experimentally validated that 89% of proteins contained fragments capable of activating transcription in yeast. Peptides with similar sequence composition show a broad range of activities, which is explained by the arrangement of key amino acids. We also annotated hundreds of nuclear proteins with activation domains as putative coactivators; many of which have never been ascribed any function in plants. Furthermore, our library contains >250 non-nuclear proteins containing peptides with activation domain function across both eukaryotic lineages, suggesting that there are unknown biological roles of these peptides beyond transcription. Finally, we identify and validate short, universal eukaryotic activation domains that activate transcription in both yeast and plants with comparable or stronger performance to state-of-the-art activation domains. Overall, our dual host screen provides a blueprint on how to systematically discover novel genetic parts for synthetic biology that function across a wide diversity of eukaryotes. Significance StatementActivation domains promote transcription and play a critical role in regulating gene expression. Although the mapping of activation domains from transcription factors has been carried out in previous genome-wide screens, their occurrence in non-transcription factors has been less explored. We utilize an activation domain predictor to mine the entire proteomes of Arabidopsis thaliana and Saccharomyces cerevisiae for new activation domains on non-transcription factor proteins. We validate peptides derived from >750 non-transcription factor proteins capable of activating transcription, discovering many potentially new coactivators in plants. Importantly, we identify novel genetic parts that can function across both species, representing unique synthetic biology tools. ]]> Hummel, N. Markel, K. Stefani, J. Staller, M. V. Shih, P. 2023-09-12 doi:10.1101/2023.09.12.557247 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Ancient origin of the rod bipolar cell pathway in the vertebrate retina ]]> https://biorxiv.org/content/10.1101/2023.09.12.557433v1?rss=1 Hellevik, A. M. Mardoum, P. Hahn, J. Kolsch, Y. D'Orazi, F. D. Suzuki, S. C. Godinho, L. Lawrence, O. Rieke, F. Shekhar, K. Sanes, J. R. Baier, H. Baden, T. Wong, R. O. Yoshimatsu, T. 2023-09-13 doi:10.1101/2023.09.12.557433 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses ]]> https://biorxiv.org/content/10.1101/2023.09.13.557537v1?rss=1 Tagirdzhanova, G. Scharnagl, K. Yan, X. Talbot, N. J. 2023-09-13 doi:10.1101/2023.09.13.557537 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Syntrichia ruralis: Emerging model moss genome reveals a conserved and previously unknown regulator of desiccation in flowering plants ]]> https://biorxiv.org/content/10.1101/2023.09.12.557352v1?rss=1 Zhang, X. Ekwealor, J. T. B. Silva, A. T. Yu, L. Jones, A. K. Mishle, B. D. Nelson, A. Oliver, M. J. 2023-09-15 doi:10.1101/2023.09.12.557352 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ maskNMF: A denoise-sparsen-detect approach for extracting neural signals from dense imaging data ]]> https://biorxiv.org/content/10.1101/2023.09.14.557777v1?rss=1 Pasarkar, A. P. Kinsella, I. Zhou, P. Wu, M. M. Pan, D. Fan, J. L. Wang, Z. Abdeladim, L. Peterka, D. S. Adesnik, H. Ji, N. Paninski, L. 2023-09-15 doi:10.1101/2023.09.14.557777 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Artificial neural networks for model identification and parameter estimation in computational cognitive models ]]> https://biorxiv.org/content/10.1101/2023.09.14.557793v1?rss=1 Rmus, M. Pan, T.-F. Xia, L. Collins, A. G. E. 2023-09-15 doi:10.1101/2023.09.14.557793 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Small molecule correctors divert CFTR-F508del from ERAD by stabilizing sequential folding states ]]> https://biorxiv.org/content/10.1101/2023.09.15.556420v1?rss=1 Riepe, C. Wachalska, M. Deol, K. K. Amaya, A. K. Porteus, M. H. Olzmann, J. Kopito, R. R. 2023-09-16 doi:10.1101/2023.09.15.556420 Cold Spring Harbor Laboratory Press 2023-09-16 <![CDATA[ The Pex6 N1 domain is required for Pex15 binding and proper assembly with Pex1 ]]> https://biorxiv.org/content/10.1101/2023.09.15.557798v1?rss=1 Ali, B. A. Judy, R. M. Chowdhury, S. Jacobsen, N. K. Castanzo, D. T. Carr, K. L. Richardson, C. D. Lander, G. C. Martin, A. Gardner, B. M. 2023-09-16 doi:10.1101/2023.09.15.557798 Cold Spring Harbor Laboratory Press 2023-09-16 <![CDATA[ The association between cortical gyrification and sleep in adolescents and young adults. ]]> https://biorxiv.org/content/10.1101/2023.09.15.557966v1?rss=1 Lima Santos, J. P. Hayes, R. Franzen, P. L. Goldstein, T. R. Hasler, B. P. Buysse, D. J. Siegle, G. J. Dahl, R. E. Forbes, E. E. Ladouceur, C. D. McMakin, D. L. Ryan, N. D. Silk, J. S. Jalbrzikowski, M. Soehner, A. 2023-09-16 doi:10.1101/2023.09.15.557966 Cold Spring Harbor Laboratory Press 2023-09-16 <![CDATA[ Diverse signatures of convergent evolution in cacti-associated yeasts ]]> https://biorxiv.org/content/10.1101/2023.09.14.557833v1?rss=1 Goncalves, C. Harrison, M.-C. Steenwyk, J. L. Opulente, D. A. LaBella, A. L. Wolters, J. F. Zhou, X. Shen, X.-X. Groenewald, M. Hittinger, C. T. Rokas, A. 2023-09-17 doi:10.1101/2023.09.14.557833 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Surprising Features of Nuclear Receptor Interaction Networks Revealed by Live Cell Single Molecule Imaging ]]> https://biorxiv.org/content/10.1101/2023.09.16.558083v1?rss=1 Dahal, L. Graham, T. G. W. Dailey, G. M. Heckert, A. B. Tjian, R. Darzacq, X. 2023-09-17 doi:10.1101/2023.09.16.558083 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ A proposed function for the red body of Nannochloropsis in the formation of the recalcitrant cell wall polymer, algaenan ]]> https://biorxiv.org/content/10.1101/2023.09.17.558137v1?rss=1 Gee, C. W. Andersen-Ranberg, J. Rosen, R. Z. Jorgens, D. Grob, P. Holman, H.-Y. Niyogi, K. K. 2023-09-17 doi:10.1101/2023.09.17.558137 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Genome-wide Characterization of Diverse Bacteriophages Enabled by RNA-Binding CRISPRi ]]> https://biorxiv.org/content/10.1101/2023.09.18.558157v1?rss=1 Adler, B. A. Al-Shimary, M. J. Patel, J. R. Ambruster, E. Colognori, D. Charles, E. J. Miller, K. V. Lahiri, A. Trinidad, M. Boger, R. Nomburg, J. Beurnier, S. Cui, M. L. Barrangou, R. Mutalik, V. K. Schoeniger, J. S. Pogliano, J. A. Savage, D. F. Doudna, J. A. Cress, B. F. 2023-09-18 doi:10.1101/2023.09.18.558157 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ An Evaluation of Representational Similarity Analysis for Model Selection and Assessment in Computational Neuroscience ]]> https://biorxiv.org/content/10.1101/2023.09.18.558316v1?rss=1 Chen, L. 2023-09-18 doi:10.1101/2023.09.18.558316 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ Double-Strand Break Repair Pathways Differentially Affect Processing and Transduction by Dual AAV Vectors ]]> https://biorxiv.org/content/10.1101/2023.09.19.558438v1?rss=1 Maurer, A. C. Benyamini, B. Fan, V. B. Whitney, O. N. Dailey, G. M. Darzacq, X. Weitzman, M. D. Tjian, R. 2023-09-19 doi:10.1101/2023.09.19.558438 Cold Spring Harbor Laboratory Press 2023-09-19 <![CDATA[ Plant-based production of diverse human milk oligosaccharides ]]> https://biorxiv.org/content/10.1101/2023.09.18.558286v1?rss=1 Barnum, C. R. Paviani, B. Couture, G. Masarweh, C. Chen, Y. Huang, Y.-P. Mills, D. A. Lebrilla, C. B. Barile, D. Yang, M. Shih, P. 2023-09-20 doi:10.1101/2023.09.18.558286 Cold Spring Harbor Laboratory Press 2023-09-20 <![CDATA[ Sex Chromosomes and Gonads Shape the Sex-Biased Transcriptomic Landscape in Tlr7-Mediated Demyelination During Aging ]]> https://biorxiv.org/content/10.1101/2023.09.19.558439v1?rss=1 Lopez-Lee, C. Kodama, L. Fan, L. Wong, M. Y. Foxe, N. R. Ijaz, L. Yu, F. Ye, P. Zhu, J. Norman, K. Torres, E. R. Kim, R. Mousa, G. A. Dubal, D. Liddelow, S. Luo, W. Gan, L. 2023-09-21 doi:10.1101/2023.09.19.558439 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ A genome-scale Opisthokonta tree of life: toward phylogenomic resolution of ancient divergences ]]> https://biorxiv.org/content/10.1101/2023.09.20.556338v1?rss=1 Liu, H. Steenwyk, J. L. Zhou, X. Schultz, D. T. Kocot, K. M. Shen, X.-X. Rokas, A. Li, Y. 2023-09-21 doi:10.1101/2023.09.20.556338 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection ]]> https://biorxiv.org/content/10.1101/2023.09.20.558163v1?rss=1 Armbruster, E. Lee, J. Hutchings, J. VanderWal, A. Enustun, E. Adler, B. Aindow, A. Deep, A. Rodriguez, Z. Morgan, C. Ghassemian, M. Charles, E. Cress, B. Savage, D. Doudna, J. Pogliano, K. Corbett, K. Villa, E. Pogliano, J. 2023-09-21 doi:10.1101/2023.09.20.558163 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Into the Wild: A novel wild-derived inbred strain resource expands the genomic and phenotypic diversity of laboratory mouse models ]]> https://biorxiv.org/content/10.1101/2023.09.21.558738v1?rss=1 90% of 1119 surveyed traits and expand the range of phenotypic diversity captured in classical inbred strain panels alone. Taken together, our work introduces a novel wild-derived inbred mouse strain resource that will enable new discoveries in basic and preclinical research. These strains are currently available through The Jackson Laboratory Repository under laboratory code NachJ. ]]> Dumont, B. L. Gatti, D. M. Ballinger, M. A. Lin, D. Phifer-Rixey, M. Sheehan, M. J. Suzuki, T. Wooldridge, L. K. Opoku Frempong, H. Churchill, G. A. Lutz, C. M. Rosenthal, N. White, J. K. Nachman, M. 2023-09-21 doi:10.1101/2023.09.21.558738 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ The Inflammasome Pathway is Activated by Dengue Virus Non-structural Protein 1 and is Protective During Dengue Virus Infection ]]> https://biorxiv.org/content/10.1101/2023.09.21.558875v1?rss=1 Wong, M. P. Juan, E. Y. Chelluri, S. S. Wang, P. Pahmeier, F. Castillo-Rojas, B. Blanc, S. F. Biering, S. B. Vance, R. E. Harris, E. 2023-09-21 doi:10.1101/2023.09.21.558875 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Multi-signal regulation of the GSK-3β homolog Rim11 governs meiosis entry in yeast ]]> https://biorxiv.org/content/10.1101/2023.09.21.558844v1?rss=1 Kociemba, J. Joergensen, A. C. S. Tadic, N. Harris, A. Sideri, T. Chan, W. Y. Ibrahim, F. Unal, E. Skehel, M. Shahrezaei, V. Arguello-Miranda, O. van Werven, F. J. 2023-09-22 doi:10.1101/2023.09.21.558844 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Targeted hypermutation of putative antigen sensors in multicellular bacteria ]]> https://biorxiv.org/content/10.1101/2023.09.22.558884v1?rss=1 Dore, H. Eisenberg, A. R. Junkins, E. N. Ganesh, A. Cordero, O. X. Paul, B. G. Valentine, D. L. O'Malley, M. A. Wilbanks, E. G. 2023-09-22 doi:10.1101/2023.09.22.558884 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ A phage nucleus-associated RNA-binding protein is required for jumbo phage infection ]]> https://biorxiv.org/content/10.1101/2023.09.22.559000v1?rss=1 Enustun, E. Armbruster, E. G. Lee, J. Zhang, S. Yee, B. A. Gu, Y. Deep, A. Naritomi, J. T. Liang, Q. Aigner, S. Adler, B. A. Cress, B. F. Doudna, J. A. Chaikeeratisak, V. Cleveland, D. W. Ghassemian, M. Yeo, G. W. Pogliano, J. Corbett, K. D. 2023-09-22 doi:10.1101/2023.09.22.559000 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ The MUC19 gene in Denisovans, Neanderthals, and Modern Humans: An Evolutionary History of Recurrent Introgression and Natural Selection ]]> https://biorxiv.org/content/10.1101/2023.09.25.559202v1?rss=1 Villanea, F. A. Peede, D. Kaufman, E. J. Anorve-Garibay, V. Dillon, K. E. W. Zeloni, R. Marnetto, d. Moorjani, P. Jay, F. Valdmanis, P. N. Avila-Arcos, M. C. Huerta-Sanchez, E. 2023-09-25 doi:10.1101/2023.09.25.559202 Cold Spring Harbor Laboratory Press 2023-09-25 <![CDATA[ Topography influences diurnal and seasonal microclimate fluctuations in hilly terrain environments of coastal California ]]> https://biorxiv.org/content/10.1101/2023.09.22.559081v1?rss=1 12 km2) comprised of mixed evergreen-deciduous woodland vegetation typical of California coastal ranges. We investigated the effect of topography and tree cover on site-to-site variation in near-surface temperatures using a combination of multiple linear regression and multivariate techniques. Sites in topographically depressed areas (e.g., valley bottoms) exhibited larger seasonal and diurnal variation. Elevation (at 10 m resolution) was found to be the primary driver of daily and seasonal variations, in addition to local topographic features that measure how depressed a site is compared to the surrounding area, canopy cover and northness. The elevation effect on seasonal mean temperatures was inverted, reflecting large-scale cold-air pooling in the study region, with elevated minimum and mean temperature at higher elevations. Additionally, several of our sites showed considerable buffering (dampened diurnal and seasonal temperature fluctuations) compared to average regional conditions measured by weather station. Results from this study help inform efforts to extrapolate temperature records across large landscapes and have the potential to improve our ecological understanding of fine-scale seasonal climate variation in coastal range environments. ]]> John, A. Olden, J. D. Oldfather, M. F. Kling, M. M. Ackerly, D. D. 2023-09-26 doi:10.1101/2023.09.22.559081 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Neural circuit mechanisms underlying context-specific halting in Drosophila. ]]> https://biorxiv.org/content/10.1101/2023.09.25.559438v1?rss=1 Sapkal, N. Mancini, N. Kumar, D. S. Spiller, N. Murakami, K. Vitelli, G. Bargeron, B. Maier, K. Eichler, K. Jefferis, G. S. X. E. Shiu, P. Sterne, G. R. Bidaye, S. S. 2023-09-27 doi:10.1101/2023.09.25.559438 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Mapping the biochemical landscape of rubisco ]]> https://biorxiv.org/content/10.1101/2023.09.27.559826v1?rss=1 99% of single amino acid mutants across CO2 concentrations, we inferred enzyme velocity and CO2 affinity for thousands of substitutions. We identified many highly conserved positions that tolerate mutation and rare mutations that improve CO2 affinity. These data suggest that non-trivial kinetic improvements are readily accessible and provide a comprehensive sequence-to-function mapping for enzyme engineering efforts. ]]> Prywes, N. Phillips, N. R. Oltrogge, L. M. de Pins, B. Cowan, A. E. Taylor-Kearney, L. J. Chang, H. A. Hall, L. N. Bhatt, A. Shih, P. Milo, R. Savage, D. F. 2023-09-27 doi:10.1101/2023.09.27.559826 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Deep Variational Autoencoders for Population Genetics ]]> https://biorxiv.org/content/10.1101/2023.09.27.558320v1?rss=1 Geleta, M. Mas Montserrat, D. Giro-i-Nieto, X. Ioannidis, A. G. 2023-09-28 doi:10.1101/2023.09.27.558320 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ Structural pathway for class III PI 3-kinase activation by the myristoylated GTP-binding pseudokinase VPS15 ]]> https://biorxiv.org/content/10.1101/2023.09.28.559894v1?rss=1 Cook, A. S. I. Chen, M. H. Ren, X. Rao, S. Garcia, S. N. Claveras Cabezudo, A. Iavarone, A. T. Hummer, G. Hurley, J. H. 2023-09-28 doi:10.1101/2023.09.28.559894 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ HybriSeq: Probe-based Device-free Single-cell RNA Profiling ]]> https://biorxiv.org/content/10.1101/2023.09.27.559406v1?rss=1 Foyt, D. Brown, D. Zhou, S. Huang, B. 2023-09-29 doi:10.1101/2023.09.27.559406 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Hierarchical VAEs provide a normative account of motion processing in the primate brain ]]> https://biorxiv.org/content/10.1101/2023.09.27.559646v1?rss=1 Vafaii, H. Yates, J. L. Butts, D. A. 2023-09-29 doi:10.1101/2023.09.27.559646 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Best practices for perturbation MPRA--a computational evaluation framework of sequence design strategies ]]> https://biorxiv.org/content/10.1101/2023.09.27.559768v1?rss=1 Liu, J. Ashuach, T. Inoue, F. Ahituv, N. Yosef, N. Kreimer, A. 2023-09-29 doi:10.1101/2023.09.27.559768 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ A conserved class of viral RNA structures regulate translation reinitiation through dynamic ribosome interactions ]]> https://biorxiv.org/content/10.1101/2023.09.29.560040v1?rss=1 Sherlock, M. Langeberg, C. Segar, K. Kieft, J. S. 2023-09-29 doi:10.1101/2023.09.29.560040 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Degraded tactile coding in the Cntnap2 mouse model of autism ]]> https://biorxiv.org/content/10.1101/2023.09.29.560240v1?rss=1 WANG, H. C. Feldman, D. 2023-09-30 doi:10.1101/2023.09.29.560240 Cold Spring Harbor Laboratory Press 2023-09-30 <![CDATA[ Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes ]]> https://biorxiv.org/content/10.1101/2023.09.30.560311v1?rss=1 Sauer, P. V. Cupellini, L. Sutter, M. Bondanza, M. Dominguez Martin, M. A. Kirst, H. Bina, D. Koh, A. F. Kotecha, A. Greber, B. J. Nogales, E. Polivka, T. Mennucci, B. Kerfeld, C. A. 2023-09-30 doi:10.1101/2023.09.30.560311 Cold Spring Harbor Laboratory Press 2023-09-30 <![CDATA[ Rhythmic lipid and gene expression responses to chilling in panicoid grasses ]]> https://biorxiv.org/content/10.1101/2023.09.29.560160v1?rss=1 Kenchanmane Raju, S. K. Zhang, Y. Mahboub, S. Ngu, D. Qiu, Y. Harmon, F. Schnable, J. C. Roston, R. L. 2023-10-02 doi:10.1101/2023.09.29.560160 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life ]]> https://biorxiv.org/content/10.1101/2023.10.02.560517v1?rss=1 1Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family. ]]> Kim, B. Y. Gellert, H. R. Church, S. H. Suvorov, A. Anderson, S. S. Barmina, O. Beskid, S. G. Comeault, A. A. Crown, K. N. Diamond, S. E. Dorus, S. Fujichika, T. Hemker, J. A. Hrcek, J. Kankare, M. Katoh, T. Magnacca, K. N. Martin, R. A. Matsunaga, T. Medeiros, M. J. Miller, D. E. Pitnick, S. Simoni, S. Steenwinkel, T. E. Schiffer, M. Syed, Z. A. Takahashi, A. Wei, K. H.-C. Yokoyama, T. Eisen, M. B. Kopp, A. Matute, D. Obbard, D. J. O'Grady, P. M. Price, D. K. Toda, M. J. Werner, T. Petrov, D. A. 2023-10-02 doi:10.1101/2023.10.02.560517 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Predicting the effect of CRISPR-Cas9-based epigenome editing ]]> https://biorxiv.org/content/10.1101/2023.10.03.560674v1?rss=1 Batra, S. S. Cabrera, A. Spence, J. P. Hilton, I. Song, Y. S. 2023-10-03 doi:10.1101/2023.10.03.560674 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Backbone extension acyl rearrangements enable cellular synthesis of proteins with internal β2-peptide linkages ]]> https://biorxiv.org/content/10.1101/2023.10.03.560714v1?rss=1 Schepartz, A. Roe, L. Schissel, C. K. Dover, T. L. Shah, B. Hamlish, N. X. Zheng, S. Dilworth, D. A. Wong, N. Zhang, Z. Chatterjee, A. Francis, M. B. Miller, S. J. 2023-10-03 doi:10.1101/2023.10.03.560714 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ MOIRE: A software package for the estimation of allele frequenciesand effective multiplicity of infection from polyallelic data ]]> https://biorxiv.org/content/10.1101/2023.10.03.560769v1?rss=1 Murphy, M. Greenhouse, B. 2023-10-05 doi:10.1101/2023.10.03.560769 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Four-dimensional quantitative analysis of cell plate development using lattice light sheet microscopy identifies robust transition points between growth phases ]]> https://biorxiv.org/content/10.1101/2023.10.03.560767v1?rss=1 Sinclair, R. M. Wang, M. Jawaid, M. Z. Aaron, J. Rossetti, B. Wait, E. McDonald, K. Cox, D. heddleston, J. Wilkop, T. Drakakaki, G. 2023-10-06 doi:10.1101/2023.10.03.560767 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ CASTER: Direct species tree inference from whole-genome alignments ]]> https://biorxiv.org/content/10.1101/2023.10.04.560884v1?rss=1 Zhang, C. Nielsen, R. Mirarab, S. 2023-10-06 doi:10.1101/2023.10.04.560884 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Differential Requirement for Dimerization of the Membrane-Binding PH-TH Module of BTK in B cells and T cells ]]> https://biorxiv.org/content/10.1101/2023.10.05.561114v1?rss=1 Eisen, T. J. Ghaffari-Kashani, S. Weiss, A. Kuriyan, J. 2023-10-06 doi:10.1101/2023.10.05.561114 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Regional specialization, polyploidy, and seminal fluid transcripts in the Drosophila female reproductive tract ]]> https://biorxiv.org/content/10.1101/2023.10.05.561141v1?rss=1 Thayer, R. C. Polston, E. S. Xu, J. Begun, D. J. 2023-10-06 doi:10.1101/2023.10.05.561141 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ A Flat Protein Complex Shapes Rough ER Membrane Sheets ]]> https://biorxiv.org/content/10.1101/2023.10.06.559866v1?rss=1 Sawyer, E. M. Jensen, L. E. Meehl, J. B. Larsen, K. P. Petito, D. A. Hurley, J. H. Voeltz, G. K. 2023-10-06 doi:10.1101/2023.10.06.559866 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ LRRK2 kinase inhibition reverses G2019S mutation-dependent effects on tau pathology spread ]]> https://biorxiv.org/content/10.1101/2023.10.06.561190v1?rss=1 Lubben, N. Brynildsen, J. K. Leyns, C. E. G. Webb, C. M. Li, H. L. Changolkar, L. Zhang, B. Meymand, E. O'Reilly, M. Madaj, Z. DeWeerd, D. Fell, M. J. Lee, V. M. Y. Bassett, D. S. Henderson, M. X. 2023-10-06 doi:10.1101/2023.10.06.561190 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ CELL-E 2: Translating Proteins to Pictures and Back with a Bidirectional Text-to-Image Transformer ]]> https://biorxiv.org/content/10.1101/2023.10.05.561066v1?rss=1 Khwaja, E. Song, Y. S. Agarunov, A. Huang, B. 2023-10-07 doi:10.1101/2023.10.05.561066 Cold Spring Harbor Laboratory Press 2023-10-07 <![CDATA[ Deep mutational scanning of CYP2C19 reveals a substrate specificity-abundance tradeoff ]]> https://biorxiv.org/content/10.1101/2023.10.06.561250v1?rss=1 Boyle, G. E. Sitko, K. Galloway, J. G. Haddox, H. K. Bianchi, A. H. Dixon, A. Thomson, R. E. S. Garge, R. K. Rettie, A. E. Rubin, A. F. Geck, R. C. Gillam, E. M. J. DeWitt, W. S. Matsen, F. A. Fowler, D. M. 2023-10-08 doi:10.1101/2023.10.06.561250 Cold Spring Harbor Laboratory Press 2023-10-08 <![CDATA[ Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom ]]> https://biorxiv.org/content/10.1101/2023.10.09.561603v1?rss=1 Krishna, R. Wang, J. Ahern, W. Sturmfels, P. Venkatesh, P. Kalvet, I. Lee, G. R. Morey-Burrows, F. S. Anishchenko, I. Humphreys, I. R. McHugh, R. Vafeados, D. Li, X. Sutherland, G. A. Hitchcock, A. Hunter, C. N. Baek, M. DiMaio, F. Baker, D. 2023-10-09 doi:10.1101/2023.10.09.561603 Cold Spring Harbor Laboratory Press 2023-10-09 <![CDATA[ A red-emitting carborhodamine for monitoring and measuring membrane potential ]]> https://biorxiv.org/content/10.1101/2023.10.06.561080v1?rss=1 Gest, A. M. M. Lazzari-Dean, J. R. Ortiz, G. Yaeger-Weiss, S. K. Boggess, S. C. Miller, E. W. 2023-10-10 doi:10.1101/2023.10.06.561080 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Do calcium channel blockers applied to cardiomyocytes cause increased channel expression resulting in reduced efficacy? ]]> https://biorxiv.org/content/10.1101/2023.10.09.561500v1?rss=1 Jaeger, K. H. Charwat, V. Wall, S. Healy, K. E. Tveito, A. 2023-10-11 doi:10.1101/2023.10.09.561500 Cold Spring Harbor Laboratory Press 2023-10-11 <![CDATA[ GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction ]]> https://biorxiv.org/content/10.1101/2023.10.10.561776v1?rss=1 Benegas, G. Albors, C. Aw, A. J. Ye, C. Song, Y. S. 2023-10-11 doi:10.1101/2023.10.10.561776 Cold Spring Harbor Laboratory Press 2023-10-11 <![CDATA[ Programmable delivery of fluoxetine via wearable bioelectronics for wound healing in vivo ]]> https://biorxiv.org/content/10.1101/2023.10.10.561754v1?rss=1 Li, H. Yang, H.-y. Asefifeyzabadi, N. Baniya, P. Zlobina, K. Hsieh, H.-C. Nguyen, T. Hernandez, C. Carrion, H. Tebyani, M. Selberg, J. Gomez, M. Teodorescu, M. Lopez, A. M. Gallegos, A. Zhu, K. Recendez, C. Luo, L. Alhamo, M. A. Norouzi, N. Soulika, A. M. Levin, M. Zhao, M. Isseroff, R. R. Rolandi, M. 2023-10-13 doi:10.1101/2023.10.10.561754 Cold Spring Harbor Laboratory Press 2023-10-13 <![CDATA[ Activation of automethylated PRC2 by dimerization on chromatin ]]> https://biorxiv.org/content/10.1101/2023.10.12.562141v1?rss=1 Sauer, P. V. Pavlenko, E. Cookis, T. Zirden, L. C. Renn, J. Singhal, A. Hunold, P. Hoehne, M. N. van Ray, O. Haensel-Hertsch, R. Sanbonmatsu, K. Y. Nogales, E. Poepsel, S. 2023-10-13 doi:10.1101/2023.10.12.562141 Cold Spring Harbor Laboratory Press 2023-10-13 <![CDATA[ Genetically refactored Agrobacterium-mediated transformation ]]> https://biorxiv.org/content/10.1101/2023.10.13.561914v1?rss=1 Thompson, M. Kirkpatrick, L. D. Geiselman, G. M. Waldburger, L. M. Pearson, A. N. Szarzanowicz, M. Vuu, K. M. Markel, K. Hummel, N. F. Suazo, D. D. Tahmin, C. Cui, R. Liu, S. Cevallos, J. Pannu, H. Liu, D. Gin, J. W. Chen, Y. Petzold, C. J. Gladden, J. Keasling, J. D. Chang, J. H. Weisberg, A. J. Shih, P. M. 2023-10-13 doi:10.1101/2023.10.13.561914 Cold Spring Harbor Laboratory Press 2023-10-13 <![CDATA[ EEG spectral attractors identify a geometric core of resting brain activity ]]> https://biorxiv.org/content/10.1101/2023.10.13.562264v1?rss=1 Pourdavood, P. Jacob, M. 2023-10-13 doi:10.1101/2023.10.13.562264 Cold Spring Harbor Laboratory Press 2023-10-13 <![CDATA[ Chlorophyll to Zeaxanthin Energy Transfer in Non-Photochemical Quenching: An Exciton Annihilation-free Transient Absorption Study ]]> https://biorxiv.org/content/10.1101/2023.10.11.561813v1?rss=1 Lee, T.-Y. Lam, L. Patel-Tupper, D. Roy, P. P. Ma, S. A. Lucas-DeMott, A. Karavolias, N. G. Niyogi, K. K. Fleming, G. R. 2023-10-14 doi:10.1101/2023.10.11.561813 Cold Spring Harbor Laboratory Press 2023-10-14 <![CDATA[ Effects of isochoric freezing on quality characteristics of raw bovine milk ]]> https://biorxiv.org/content/10.1101/2023.10.12.562068v1?rss=1 Maida, A. Bilbao-Sainz, C. Karman, A. Takeoka, G. Powell-Palm, M. J. Rubinsky, B. 2023-10-14 doi:10.1101/2023.10.12.562068 Cold Spring Harbor Laboratory Press 2023-10-14 <![CDATA[ Listeria monocytogenes utilizes glutathione and limited inorganic sulfur compounds as a source of essential L-cysteine ]]> https://biorxiv.org/content/10.1101/2023.10.16.562582v1?rss=1 Berude, J. Kennouche, P. Reniere, M. L. Portnoy, D. A. 2023-10-16 doi:10.1101/2023.10.16.562582 Cold Spring Harbor Laboratory Press 2023-10-16 <![CDATA[ GUANinE v0.9: Benchmark Datasets for Genomic AISequence-to-Function Models ]]> https://biorxiv.org/content/10.1101/2023.10.12.562113v1?rss=1 Robson, E. S. Ioannidis, N. M. 2023-10-17 doi:10.1101/2023.10.12.562113 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Regulated Cleavage and Relocation of FERONIA Control Immunity in Arabidopsis Roots ]]> https://biorxiv.org/content/10.1101/2023.10.16.562456v1?rss=1 Yu, F. Chen, J. Qiang, X. Liu, H. Xu, F. Wang, L. Jiang, L. Li, C. Wang, B. Luan, S. Wu, D. Zhou, F. 2023-10-17 doi:10.1101/2023.10.16.562456 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Development of covalent chemogenetic K2P channel activators ]]> https://biorxiv.org/content/10.1101/2023.10.15.561774v1?rss=1 Deal, P. E. Lee, H. Mondal, A. Lolicato, M. Furtado de Mandonca, P. R. Black, H. El-Hilali, X. Bryant, C. Isacoff, E. Y. Renslo, A. Minor, D. L. 2023-10-18 doi:10.1101/2023.10.15.561774 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ Polinton-like Viruses Associated with Entomopoxviruses Provide Insight into Replicon Evolution ]]> https://biorxiv.org/content/10.1101/2023.10.16.562556v1?rss=1 Barth, Z. K. Hicklin, I. Theze, J. Takatsuka, J. Nakai, M. Herniou, E. A. Brown, A. M. Aylward, F. O. 2023-10-18 doi:10.1101/2023.10.16.562556 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ Multicolor on-chip fluorescence microscopy for real-time surgical guidance ]]> https://biorxiv.org/content/10.1101/2023.10.16.562247v1?rss=1 Roschelle, M. L. Rabbani, R. Papageorgiou, E. Zhang, H. Cooperberg, M. Stohr, B. A. Niknejad, A. Anwar, M. 2023-10-19 doi:10.1101/2023.10.16.562247 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Mechanism and cellular function of direct membrane binding by the ESCRT and ERES-associated Ca2+-sensor ALG-2 ]]> https://biorxiv.org/content/10.1101/2023.10.17.562764v1?rss=1 Shukla, S. Chen, W. Rao, S. Yang, S. Ou, C. Larsen, K. P. Hummer, G. Hanson, P. I. Hurley, J. H. 2023-10-19 doi:10.1101/2023.10.17.562764 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Encoding of melody in the human auditory cortex ]]> https://biorxiv.org/content/10.1101/2023.10.17.562771v1?rss=1 Sankaran, N. Leonard, M. K. Theunissen, F. E. Chang, E. F. 2023-10-19 doi:10.1101/2023.10.17.562771 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Adaptive capacity of a DNA polymerase clamp-loader ATPase complex ]]> https://biorxiv.org/content/10.1101/2023.10.18.562948v1?rss=1 Subramanian, S. Zhang, W. Nimkar, S. Kamel, M. O'Donnell, M. E. Kuriyan, J. 2023-10-19 doi:10.1101/2023.10.18.562948 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ UPL3 Promotes BZR1 Degradation, Growth Arrest, and Seedling Survival under Starvation Stress in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2023.10.18.562997v1?rss=1 Zhang, Z. Zhang, H. Gonzalez, E. Grismer, T. Xu, S.-L. Wang, Z.-Y. 2023-10-19 doi:10.1101/2023.10.18.562997 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Integrin-like adhesin CglD confers traction and stabilizes bacterial focal adhesions involved in myxobacterial gliding motility ]]> https://biorxiv.org/content/10.1101/2023.10.19.562135v1?rss=1 Jolivet, N. Y. Han, E. Belgrave, A. M. Saïdi, F. Koushki, N. Lemon, D. J. Faure, L. M. Fleuchot, B. Mahanta, U. Jiang, H. Sharma, G. Fiche, J.-B. Bratton, B. P. Diallo, M. Nan, B. Zusman, D. R. Sudre, G. Garza, A. Nollmann, M. Ehrlicher, A. J. Theodoly, O. Shaevitz, J. W. Mignot, T. Islam, S. T. 2023-10-19 doi:10.1101/2023.10.19.562135 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Distinct function of Chlamydomonas CTRA-CTR transporters in Cu assimilation and intracellular mobilization ]]> https://biorxiv.org/content/10.1101/2023.10.19.563170v1?rss=1 Strenkert, D. Schmollinger, S. Paruthiyil, S. Brown, B. C. Green, S. Shafer, C. M. Salome, P. A. Nelson, H. Blaby-Haas, C. E. Moseley, J. L. Merchant, S. S. 2023-10-19 doi:10.1101/2023.10.19.563170 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Discovery of two archaeal GDGT lipid modifying enzymes reveals diverse microbes capable of H-GDGT biosynthesis and modification ]]> https://biorxiv.org/content/10.1101/2023.10.20.563219v1?rss=1 Garcia, A. A. Chadwick, G. L. Welander, P. V. 2023-10-21 doi:10.1101/2023.10.20.563219 Cold Spring Harbor Laboratory Press 2023-10-21 <![CDATA[ Multiplexed CRISPR/Cas9 mutagenesis of rice PSBS1 non-coding sequences for transgene-free overexpression ]]> https://biorxiv.org/content/10.1101/2023.10.20.563333v1?rss=1 Patel-Tupper, D. Kelikian, A. Leipertz, A. Maryn, N. Tjahjadi, M. Karavolias, N. G. Cho, M.-J. Niyogi, K. K. 2023-10-21 doi:10.1101/2023.10.20.563333 Cold Spring Harbor Laboratory Press 2023-10-21 <![CDATA[ Exploiting the Cullin E3 Ligase Adaptor Protein SKP1 for Targeted Protein Degradation ]]> https://biorxiv.org/content/10.1101/2023.10.20.563371v1?rss=1 Hong, S. H. Osa, A. Wertz, I. E. Nomura, D. 2023-10-21 doi:10.1101/2023.10.20.563371 Cold Spring Harbor Laboratory Press 2023-10-21 <![CDATA[ Recombinase Polymerase Amplification Assay for the Field Detection of Mal Secco Disease by Plenodomus tracheiphilus ]]> https://biorxiv.org/content/10.1101/2023.10.21.563392v1?rss=1 Rovetto, E. I. Garbelotto, M. Moricca, S. Amato, M. La Spada, F. Cacciola, S. O. 2023-10-21 doi:10.1101/2023.10.21.563392 Cold Spring Harbor Laboratory Press 2023-10-21 <![CDATA[ Germline novelty through recurrent copy-number, protein, and regulatory evolution of the synaptonemal complex ]]> https://biorxiv.org/content/10.1101/2023.10.20.563324v1?rss=1 Wei, K. H. Chang, C.-H. Chatla, K. Krishnapura, A. Appiah, S. P. Zhang, J. Unckless, R. L. Blumenstiel, J. Bachtrog, D. 2023-10-24 doi:10.1101/2023.10.20.563324 Cold Spring Harbor Laboratory Press 2023-10-24 <![CDATA[ Combinatorial CRISPR screens and lectin microarrays identify novel glycosylation regulators ]]> https://biorxiv.org/content/10.1101/2023.10.23.563662v1?rss=1 Tsui, C. K. Twells, N. Doan, E. Brooks, J. Kulepa, A. Webster, B. Mahal, L. K. Dillin, A. 2023-10-24 doi:10.1101/2023.10.23.563662 Cold Spring Harbor Laboratory Press 2023-10-24 <![CDATA[ Pulmonary Ventilation Analysis Using 1H Ultra-Short Echo Time (UTE) Lung MRI: A Reproducibility Study ]]> https://biorxiv.org/content/10.1101/2023.10.22.563196v1?rss=1 Tan, F. Zhu, X. Chan, M. Deveshwar, N. Willmering, M. M. Lustig, M. Larson, P. E. Z. 2023-10-25 doi:10.1101/2023.10.22.563196 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ Identification of intestinal mediators of Caenorhabditis elegans DBL-1/BMP immune signaling shaping gut microbiome composition ]]> https://biorxiv.org/content/10.1101/2023.10.26.564221v1?rss=1 Trang, K. Pees, B. Karimzadegan, S. Bodkhe, R. Hammond, S. Shapira, M. 2023-10-27 doi:10.1101/2023.10.26.564221 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Chemically induced proximity reveals mechanotransduction of a meiotic checkpoint at the nuclear envelope ]]> https://biorxiv.org/content/10.1101/2023.10.28.564506v1?rss=1 Liu, C. Dernburg, A. F. 2023-10-28 doi:10.1101/2023.10.28.564506 Cold Spring Harbor Laboratory Press 2023-10-28 <![CDATA[ Evaluating ChatGPT as an Agent for Providing Genetic Education ]]> https://biorxiv.org/content/10.1101/2023.10.25.564074v1?rss=1 Walton, N. Graceffo, S. Sutherland, N. Kozel, B. Danford, C. McGrath, S. 2023-10-29 doi:10.1101/2023.10.25.564074 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ Distinct rich and diverse clubs regulate coarse and fine binocular disparity processing: Evidence from stereoscopic task-based fMRI ]]> https://biorxiv.org/content/10.1101/2023.10.25.564094v1?rss=1 Lohia, K. Soans, R. S. Saxena, R. Mahajan, K. Gandhi, T. K. 2023-10-30 doi:10.1101/2023.10.25.564094 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ Retinoic acid-dependent loss of synaptic output from bipolar cells impairs visual information processing in inherited retinal degeneration. ]]> https://biorxiv.org/content/10.1101/2023.10.29.564225v1?rss=1 Ganzen, L. Yadav, S. C. Wei, M. Ma, H. Nawy, S. Kramer, R. 2023-10-30 doi:10.1101/2023.10.29.564225 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ A Latent Activated Olfactory Stem Cell State Revealed by Single Cell Transcriptomic and Epigenomic Profiling ]]> https://biorxiv.org/content/10.1101/2023.10.26.564041v1?rss=1 Van den Berge, K. Chou, H.-J. Kunda, D. Risso, D. Street, K. Purdom, E. Dudoit, S. Ngai, J. Heavner, W. E. 2023-10-31 doi:10.1101/2023.10.26.564041 Cold Spring Harbor Laboratory Press 2023-10-31 <![CDATA[ Remarkably high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery. ]]> https://biorxiv.org/content/10.1101/2023.10.26.564301v1?rss=1 Benham, P. Cicero, C. Escalona, M. Beraut, E. Fairbairn, C. Marimuthu, M. P. A. Nguyen, O. Sahasrabudhe, R. King, B. L. Thomas, W. K. Kovach, A. I. Nachman, M. W. Bowie, R. C. K. 2023-10-31 doi:10.1101/2023.10.26.564301 Cold Spring Harbor Laboratory Press 2023-10-31 <![CDATA[ Structure-Aware Annotation of Leucine-rich Repeat Domains ]]> https://biorxiv.org/content/10.1101/2023.10.27.562987v1?rss=1 Xu, B. Cerbu, A. Lim, D. Tralie, C. J. Krasileva, K. 2023-11-01 doi:10.1101/2023.10.27.562987 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Immunosuppression is a conserved driver of tuberculosis susceptibility ]]> https://biorxiv.org/content/10.1101/2023.10.27.564420v1?rss=1 Kotov, D. I. Lee, O. V. Ji, D. X. Jaye, D. L. Suliman, S. Gabay, C. Vance, R. E. 2023-11-01 doi:10.1101/2023.10.27.564420 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Desiccated cyanobacteria serve as efficient plasmid DNA carrier in space flight ]]> https://biorxiv.org/content/10.1101/2023.10.31.564425v1?rss=1 Kakouridis, A. Diamond, S. Eng, T. Mills, H. J. Gamez-Holzhaus, O. Summers, M. L. Garcia-Pichel, F. Mukhopadhyay, A. 2023-11-01 doi:10.1101/2023.10.31.564425 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Effects of Gene Dosage and Development on Subcortical Nuclei Volumes in Individuals with 22q11.2 Copy Number Variations ]]> https://biorxiv.org/content/10.1101/2023.10.31.564553v1?rss=1 Schleifer, C. H. O'Hora, K. P. Fung, H. Xu, J. Robinson, T.-A. Wu, A. S. Kushan-Wells, L. Ching, C. R. K. Bearden, C. E. 2023-11-01 doi:10.1101/2023.10.31.564553 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Covalent Degrader of the Oncogenic Transcription Factor β-Catenin ]]> https://biorxiv.org/content/10.1101/2023.10.31.565018v1?rss=1 Gowans, F. A. Forte, N. Hatcher, J. Wang, Y. Poblano, B. E. A. Wertz, I. E. Nomura, D. K. 2023-11-01 doi:10.1101/2023.10.31.565018 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Across two continents: the genomic basis of environmental adaptation in house mice (Mus musculus domesticus) from the Americas ]]> https://biorxiv.org/content/10.1101/2023.10.30.564674v1?rss=1 Gutierrez Guerrero, Y. T. Phifer-Rixey, M. Nachman, M. W. 2023-11-02 doi:10.1101/2023.10.30.564674 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Development of Corynebacterium glutamicum as a monoterpene production platform ]]> https://biorxiv.org/content/10.1101/2023.10.31.565027v1?rss=1 Luckie, B. A. Kashyap, M. Pearson, A. N. Chen, Y. Liu, Y. Valencia, L. E. Romero, A. C. Hudson, G. A. Tao, X. B. Wu, B. Petzold, C. J. Keasling, J. D. 2023-11-02 doi:10.1101/2023.10.31.565027 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Chromosome-level genome assemblies of two hemichordates provide new insights into deuterostome origin and chromosome evolution ]]> https://biorxiv.org/content/10.1101/2023.11.01.564642v1?rss=1 Lin, C.-Y. Marletaz, F. Perez-Posada, A. Martinez Garcia, P. M. Schloissnig, S. Peluso, P. Conception, G. T. Bump, P. Chen, Y.-C. Chou, C. Lin, C.-Y. Fan, T.-P. Tsai, C.-T. Gomez Skarmeta, J. L. Tena, J. J. Lowe, C. J. Rank, D. R. Rokhsar, D. S. Yu, J.-K. Su, Y.-H. 2023-11-02 doi:10.1101/2023.11.01.564642 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Targeting editing of tomato SPEECHLESS cis-regulatory regions generates plants with altered stomatal density in response to changing climate conditions ]]> https://biorxiv.org/content/10.1101/2023.11.02.564550v1?rss=1 Nir, I. Budrys, A. Smoot, N. K. Erberich, J. Bergmann, D. 2023-11-02 doi:10.1101/2023.11.02.564550 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Jasmonic acid and methyl jasmonate attenuate neuroinflammation via crosstalk with the prostaglandin E2/receptor EP2 signaling axis ]]> https://biorxiv.org/content/10.1101/2023.10.31.564983v1?rss=1 Ward, E. L. 2023-11-03 doi:10.1101/2023.10.31.564983 Cold Spring Harbor Laboratory Press 2023-11-03 <![CDATA[ Design rules for efficient endosomal escape ]]> https://biorxiv.org/content/10.1101/2023.11.03.565388v1?rss=1 Zoltek, M. Vazquez-Maldonado, A. L. Zhang, X. Dadina, N. Lesiak, L. Schepartz, A. 2023-11-04 doi:10.1101/2023.11.03.565388 Cold Spring Harbor Laboratory Press 2023-11-04 <![CDATA[ Molecular Forecasting of Domoic Acid during a Pervasive Toxic Diatom Bloom ]]> https://biorxiv.org/content/10.1101/2023.11.02.565333v1?rss=1 Brunson, J. K. Thukral, M. Ryan, J. P. Anderson, C. R. Kolody, B. C. James, C. C. Chavez, F. P. Leaw, C. P. Rabines, A. J. Venepally, P. Zheng, H. Kudela, R. M. Smith, G. J. Moore, B. S. Allen, A. E. 2023-11-05 doi:10.1101/2023.11.02.565333 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Microscale visualization of cellular features in adult macaque visual cortex ]]> https://biorxiv.org/content/10.1101/2023.11.02.565381v1?rss=1 Balaram, P. Takasaki, K. T. Hellevik, A. Tandukar, J. Turschak, E. MacLennan, B. Ouellette, N. Torres, R. Laughland, C. Gliko, O. Seshamani, S. Perlman, E. Taormina, M. Peterson, E. Juneau, Z. Potekhina, L. Glaser, A. Chandrashekar, J. Logsdon, M. Cao, K. Dylla, C. Hatanaka, G. Chatterjee, S. Ting, J. T. Vumbaco, D. Waters, J. T. Bair, W. Tsao, D. Gao, R. Reid, R. C. 2023-11-05 doi:10.1101/2023.11.02.565381 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Calibrated Identification of Feature Dependencies in Single-cell Multiomics ]]> https://biorxiv.org/content/10.1101/2023.11.03.565520v1?rss=1 Boyeau, P. Bates, S. Ergen, C. Jordan, M. Yosef, N. 2023-11-05 doi:10.1101/2023.11.03.565520 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ An injectable in situ crosslinkable platform for ultra-long-acting delivery of hydrophilic therapeutics ]]> https://biorxiv.org/content/10.1101/2023.11.04.565631v1?rss=1 Lee, S. Zhao, S. Chen, X. Zhu, L. Joseph, J. Agus, E. Barooj, S. Mary, H. B. Shah, P. Slaughter, K. Cheung, K. Luo, J. N. Gao, J. Lee, D. Karp, J. Joshi, N. 2023-11-05 doi:10.1101/2023.11.04.565631 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Contexts facilitate dynamic value encoding in the mesolimbic dopamine system ]]> https://biorxiv.org/content/10.1101/2023.11.05.565687v1?rss=1 Fraser, K. M. Collins, V. L. Wolff, A. R. Ottenheimer, D. J. Bornhoft, K. N. Pat, F. Chen, B. J. Janak, P. H. Saunders, B. T. 2023-11-05 doi:10.1101/2023.11.05.565687 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Revisiting the Briggs ancient DNA damage model: a fast regression method to estimate postmortem damage ]]> https://biorxiv.org/content/10.1101/2023.11.06.565746v1?rss=1 Zhao, L. Henriksen, R. A. Ramsoe, A. D. Nielsen, R. Korneliussen, T. S. 2023-11-06 doi:10.1101/2023.11.06.565746 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Coordinated differentiation of human intestinal organoids with functional enteric neurons and vasculature ]]> https://biorxiv.org/content/10.1101/2023.11.06.565830v1?rss=1 Childs, C. J. Poling, H. M. Chen, K. Tsai, Y.-H. Wu, A. Sweet, C. W. Vallie, A. Eiken, M. K. Huang, S. Schreiner, R. Xiao, Z. Conchola, A. S. Anderman, M. F. Holloway, E. M. Singh, A. Giger, R. Mahe, M. M. Walton, K. D. Loebel, C. Helmrath, M. A. Rafii, S. Spence, J. R. 2023-11-06 doi:10.1101/2023.11.06.565830 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Covalent 14-3-3 Molecular Glues and Heterobifunctional Molecules Against Nuclear Transcription Factors and Regulators ]]> https://biorxiv.org/content/10.1101/2023.11.06.565850v1?rss=1 Shao, Q. Duong, T. N. Park, I. Nomura, D. K. 2023-11-06 doi:10.1101/2023.11.06.565850 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Contact-Inhibited ERK Signaling is Determined by Cellular-Resolution Western Blotting ]]> https://biorxiv.org/content/10.1101/2023.11.06.565857v1?rss=1 Zhang, Y. Naguro, I. Ryuno, H. Herr, A. 2023-11-06 doi:10.1101/2023.11.06.565857 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Single cell transcriptional profiling of benign prostatic hyperplasia reveals a progenitor-like luminal epithelial cell state within an inflammatory microenvironment ]]> https://biorxiv.org/content/10.1101/2023.11.06.565375v1?rss=1 Unno, R. Akutagawa, J. Song, H. Hui, K. Chen, Y.-A. Pham, J. Yang, H. Huang, F. W. Chi, T. 2023-11-07 doi:10.1101/2023.11.06.565375 Cold Spring Harbor Laboratory Press 2023-11-07 <![CDATA[ Incorporation of multiple beta 2-backbones into a protein invivo using an orthogonal aminoacyl-tRNA synthetase ]]> https://biorxiv.org/content/10.1101/2023.11.07.565973v1?rss=1 Hamlish, N. Abramyan, A. Schepartz, A. 2023-11-08 doi:10.1101/2023.11.07.565973 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Integrated multi-omics single cell atlas of the human retina ]]> https://biorxiv.org/content/10.1101/2023.11.07.566105v1?rss=1 Li, J. Wang, J. Ibarra, I. L. Cheng, X. Luecken, M. D. Lu, J. Monavarfeshani, A. Yan, W. Zheng, Y. Zuo, Z. Colborn, S. L. Z. Cortez, B. S. Owen, L. A. Tran, N. M. Shekhar, K. Sanes, J. R. Stout, J. T. Chen, S. Li, Y. DeAngelis, M. M. Theis, F. J. Chen, R. 2023-11-08 doi:10.1101/2023.11.07.566105 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Minimization of the E. coli ribosome, aided and optimized by community science ]]> https://biorxiv.org/content/10.1101/2023.11.09.566451v1?rss=1 Tangpradabkul, T. Palo, M. Z. Townley, J. Hsu, K. B. Eterna Participants, Smaga, S. Das, R. Schepartz, A. 2023-11-10 doi:10.1101/2023.11.09.566451 Cold Spring Harbor Laboratory Press 2023-11-10 <![CDATA[ eIF3 engages with 3'-UTR termini of highly translated mRNAs in neural progenitor cells ]]> https://biorxiv.org/content/10.1101/2023.11.11.566681v1?rss=1 Mestre-Fos, S. Ferguson, L. Trinidad, M. I. Ingolia, N. Cate, J. H. D. 2023-11-11 doi:10.1101/2023.11.11.566681 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ GENTANGLE: integrated computational design of gene entanglements ]]> https://biorxiv.org/content/10.1101/2023.11.09.565696v1?rss=1 Marti, J. M. Hsu, C. Rochereau, C. Blazejewski, T. Nisonoff, H. Leonard, S. P. Kang-Yun, C. S. Chlebek, J. L. Ricci, D. P. Park, D. M. Wang, H. H. Listgarten, J. Jiao, Y. Allen, J. E. 2023-11-13 doi:10.1101/2023.11.09.565696 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Disrupted sleep-wake regulation in the MCI-Park mouse model of Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2023.11.09.566376v1?rss=1 Summa, K. C. Jiang, P. Gonzalez-Rodriguez, P. Huang, X. Lin, X. Vitaterna, M. H. Dan, Y. Surmeier, D. J. Turek, F. W. 2023-11-13 doi:10.1101/2023.11.09.566376 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Comparative mutant analyses reveal a novel mechanism of ARF regulation in land plants ]]> https://biorxiv.org/content/10.1101/2023.11.09.566459v1?rss=1 Prigge, M. J. Morffy, N. De Neve, A. Szutu, W. Juarez, M. J. A. Johnson, K. Do, N. Lavy, M. Hake, S. Strader, L. Estelle, M. Richardson, A. E. 2023-11-13 doi:10.1101/2023.11.09.566459 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Nucleus accumbens dopamine release reflects Bayesian inference during instrumental learning ]]> https://biorxiv.org/content/10.1101/2023.11.10.566306v1?rss=1 Qu, A. J. Tai, L.-H. Hall, C. D. Tu, E. M. Eckstein, M. K. Mischanchuk, K. Lin, W. C. Chase, J. B. MacAskill, A. F. Collins, A. G. E. Gershman, S. J. Wilbrecht, L. 2023-11-13 doi:10.1101/2023.11.10.566306 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Optical segmentation-based compressed readout of neuronal voltage dynamics ]]> https://biorxiv.org/content/10.1101/2023.11.10.566599v1?rss=1 Choi, M. M. Kim, S. Ko, G. Kang, I. Tian, H. Fan, L. Z. Li, Y. Cohen, A. E. Wu, J. Dai, Q. 2023-11-13 doi:10.1101/2023.11.10.566599 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Testing of putative antiseizure drugs in a preclinical Dravet syndrome zebrafish model ]]> https://biorxiv.org/content/10.1101/2023.11.11.566723v1?rss=1 Whyte-Fagundes, P. Vance, A. Carroll, A. Figueroa, F. Manukyan, C. Baraban, S. C. 2023-11-15 doi:10.1101/2023.11.11.566723 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Lung and liver editing by lipid nanoparticle delivery of a stable CRISPR-Cas9 RNP ]]> https://biorxiv.org/content/10.1101/2023.11.15.566339v1?rss=1 100X greater than those induced by the native GeoCas9 enzyme. Furthermore, iGeoCas9 RNP:LNP complexes edited a variety of cell lines and induced homology-directed repair (HDR) in cells receiving co-delivered single-stranded DNA (ssDNA) templates. Using tissue-selective LNP formulations, we observed genome editing of 35-56% efficiency in the liver or lungs of mice that received intravenous injections of iGeoCas9 RNP:LNPs. In particular, iGeoCas9 complexed to acid-degradable LNPs edited lung tissue in vivo with an average of 35% efficiency, a significant improvement over editing efficiencies observed previously using viral or non-viral delivery strategies. These results show that thermostable Cas9 RNP:LNP complexes are a powerful alternative to mRNA:LNP delivery vehicles, expanding the therapeutic potential of genome editing. ]]> Chen, K. Han, H. Zhao, S. Xu, B. Yin, B. Trinidad, M. Burgstone, B. W. Murthy, N. Doudna, J. A. 2023-11-15 doi:10.1101/2023.11.15.566339 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Engineering self-deliverable ribonucleoproteins for genome editing in the brain ]]> https://biorxiv.org/content/10.1101/2023.11.15.567251v1?rss=1 Chen, K. Stahl, E. C. Kang, M. H. Xu, B. Allen, R. Trinidad, M. Doudna, J. A. 2023-11-15 doi:10.1101/2023.11.15.567251 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Olfaction foraging in visually oriented tropical arboreal ants Oecophylla smaragdina: Implications for insect predation studies using artificial sentinel prey ]]> https://biorxiv.org/content/10.1101/2023.11.14.566109v1?rss=1 Yan, L. Kagame, S. P. Liu, Y. Mizuno, T. Nakamura, A. 2023-11-16 doi:10.1101/2023.11.14.566109 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ De novo Design of Peptides that Bind Specific Conformers of α-Synuclein ]]> https://biorxiv.org/content/10.1101/2023.11.14.567090v1?rss=1 Wallace, H. Yang, H. Tan, S. K. Pan, H. Yang, R. Xu, J. Jo, H. Condello, C. Polizzi, N. DeGrado, W. 2023-11-16 doi:10.1101/2023.11.14.567090 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Identification of a putative rhamnogalacturonan-II CMP-beta-Kdo transferase through a callus-based gene editing method which overcomes embryo lethality. ]]> https://biorxiv.org/content/10.1101/2023.11.15.567147v1?rss=1 Zhang, Y. Sharma, D. Liang, Y. Downs, N. Dolman, F. Thorne, K. Pereira, J. H. Adams, P. D. Scheller, H. O'Neill, M. Urbanowicz, B. R. Mortimer, J. C. 2023-11-16 doi:10.1101/2023.11.15.567147 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Reversible histone deacetylase activity catalyzes lysine acylation ]]> https://biorxiv.org/content/10.1101/2023.11.17.567549v1?rss=1 Tsusaka, T. Najar, M. A. Schwarz, B. Bohrnsen, E. Oses-Prieto, J. A. Lee, C. Burlingame, A. L. Bosio, C. M. Burslem, G. M. Goldberg, E. L. 2023-11-17 doi:10.1101/2023.11.17.567549 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ JUN mRNA Translation Regulation is Mediated by Multiple 5' UTR and Start Codon Features ]]> https://biorxiv.org/content/10.1101/2023.11.17.567602v1?rss=1 Gonzalez-Sanchez, A. M. Castellanos-Silva, E. A. Diaz-Figueroa, G. Cate, J. H. D. 2023-11-17 doi:10.1101/2023.11.17.567602 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Environment-independent distribution of mutational effects emerges from microscopic epistasis ]]> https://biorxiv.org/content/10.1101/2023.11.18.567655v1?rss=1 Ardell, S. Martsul, A. Johnson, M. S. Kryazhimskiy, S. 2023-11-18 doi:10.1101/2023.11.18.567655 Cold Spring Harbor Laboratory Press 2023-11-18 <![CDATA[ An engineered glioblastoma model yields novel macrophage-secreted drivers of invasion ]]> https://biorxiv.org/content/10.1101/2023.11.18.567683v1?rss=1 Akins, E. A. Wilkins, D. Aghi, M. Kumar, S. 2023-11-18 doi:10.1101/2023.11.18.567683 Cold Spring Harbor Laboratory Press 2023-11-18 <![CDATA[ Public Health Response to Pan-Resistant Pseudomonas aeruginosa Sequence Type 309 with Tandem Guiana Extended Spectrum Beta Lactamases Genetic Characterization and In Vivo Efficacy Assessment using Translational Murine Model. ]]> https://biorxiv.org/content/10.1101/2023.11.17.567598v1?rss=1 Lloyd, T. Gill, C. M. Aquino Herrera, J. Heaton, D. Shemsu, M. Trivedi, K. K. Gorzalski, A. Bender, M. Pandori, M. Varghese, V. Nicolau, D. P. 2023-11-20 doi:10.1101/2023.11.17.567598 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ Rhizonet: Image Segmentation for Plant Root in Hydroponic Ecosystem ]]> https://biorxiv.org/content/10.1101/2023.11.20.565580v1?rss=1 Ushizima, D. Sordo, Z. Andeer, P. Sethian, J. Northen, T. 2023-11-21 doi:10.1101/2023.11.20.565580 Cold Spring Harbor Laboratory Press 2023-11-21 <![CDATA[ Hippocampal place code plasticity in CA1 requires postsynaptic membrane fusion ]]> https://biorxiv.org/content/10.1101/2023.11.20.567978v1?rss=1 Plitt, M. H. Kaganovsky, K. Südhof, T. C. Giocomo, L. M. 2023-11-21 doi:10.1101/2023.11.20.567978 Cold Spring Harbor Laboratory Press 2023-11-21 <![CDATA[ Effects of deafening on vocal production learning in the Egyptian fruit-bat ]]> https://biorxiv.org/content/10.1101/2023.11.21.568126v1?rss=1 Elie, J. E. Muroy, S. E. Genzel, D. Na, T. Beyer, L. A. Swiderski, D. L. Raphael, Y. Yartsev, M. M. 2023-11-21 doi:10.1101/2023.11.21.568126 Cold Spring Harbor Laboratory Press 2023-11-21 <![CDATA[ Winging it: Unveiling how hummingbirds alter their flying kinematics during molt. ]]> https://biorxiv.org/content/10.1101/2023.11.21.568135v1?rss=1 Diaz-Salazar, A. F. Garzon-Agudelo, F. Smiley, A. Cadena, C. D. Rico-Guevara, A. 2023-11-22 doi:10.1101/2023.11.21.568135 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Asgard archaea modulate potential methanogenesis substrates in wetland soil ]]> https://biorxiv.org/content/10.1101/2023.11.21.568159v1?rss=1 Valentin-Alvarado, L. E. Appler, K. E. De Anda, V. Schoelmerich, M. C. West-Roberts, J. Kivenson, V. Crits-Christoph, A. Ly, L. Sachdeva, R. Savage, D. F. Baker, B. J. Banfield, J. F. 2023-11-22 doi:10.1101/2023.11.21.568159 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Giant genes are rare but implicated in cell wall degradation by predatory bacteria ]]> https://biorxiv.org/content/10.1101/2023.11.21.568195v1?rss=1 30,000 aa occur in bacterial phyla such as Firmicutes and Actinobacteria, they are most common in ca. Omnitrophota, ultra small bacteria that adopt predatory lifestyles. All full length giant genes encode numerous transmembrane regions and most encode divergent secA DEAD helicase domains. In silico structural prediction of protein subregions was required to identify domains in unannotated protein segments, and revealed putative domains implicated in attachment and carbohydrate degradation. Many giant genes in new complete and near-complete Omnitrophota genomes occur in close proximity to genes homologous to type II secretion systems as well as carbohydrate import systems. This, in combination with the domain content, suggests that many bacterial giant proteins enable prey adhesion and cell wall digestion during bacterial predation. ]]> West-Roberts, J. A. Valentin Alvarado, L. E. Mullen, S. Sachdeva, R. Smith, J. Hug, L. A. Gregoire, D. Liu, W. Lin, T.-Y. Husain, G. Amano, Y. Ly, L. Banfield, J. 2023-11-22 doi:10.1101/2023.11.21.568195 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ The doublecortin-family kinase ZYG-8/DCLK1 regulates motor activity to achieve proper force balance in C. elegans acentrosomal spindles ]]> https://biorxiv.org/content/10.1101/2023.11.22.568242v1?rss=1 Czajkowski, E. R. Divekar, N. S. Wignall, S. M. 2023-11-22 doi:10.1101/2023.11.22.568242 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Assembly reactions of SARS-CoV-2 nucleocapsid protein with nucleic acid ]]> https://biorxiv.org/content/10.1101/2023.11.22.568361v1?rss=1 Zhao, H. Syed, A. M. Khalid, M. M. Nguyen, A. Ciling, A. Wu, D. Yau, W.-M. Srinivasan, S. Esposito, D. Doudna, J. A. Piszczek, G. Ott, M. Schuck, P. 2023-11-23 doi:10.1101/2023.11.22.568361 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ Codon optimality modulates protein output by tuning translation initiation ]]> https://biorxiv.org/content/10.1101/2023.11.27.568910v1?rss=1 Lyons, E. F. Devanneaux, L. C. Muller, R. Y. Freitas, A. V. Meacham, Z. A. McSharry, M. V. Trinh, V. N. Rogers, A. J. Ingolia, N. T. Lareau, L. F. 2023-11-28 doi:10.1101/2023.11.27.568910 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ DNA Double-Strand Break Movement in Heterochromatin Depends on the Drosophila Histone Acetyltransferase Gcn5. ]]> https://biorxiv.org/content/10.1101/2023.11.30.569406v1?rss=1 Kendek, A. Sandron, A. Lambooij, J.-P. Colmenares, S. U. Sobrevals Alcaraz, P. van Es, R. Pociunaite, S. M. Gooijers, I. de Groot, L. Karpen, G. Janssen, A. 2023-11-30 doi:10.1101/2023.11.30.569406 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ Digital telomere measurement by long-read sequencing distinguishes healthy aging from disease ]]> https://biorxiv.org/content/10.1101/2023.11.29.569263v1?rss=1 Sanchez, S. E. Gu, J. Golla, A. Martin, A. Shomali, W. Hockemeyer, D. Savage, S. Artandi, S. 2023-12-01 doi:10.1101/2023.11.29.569263 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Editing cis-regulatory elements towards generating rice stomatal morphological variation for adaptation to broad and dynamic environments ]]> https://biorxiv.org/content/10.1101/2023.11.29.569268v1?rss=1 Karavolias, N. G. Patel-Tupper, D. Cruz, A. G. Litvak, L. Lieberman, S. E. Tjahjadi, M. Niyogi, K. K. Cho, M.-J. Staskawicz, B. 2023-12-01 doi:10.1101/2023.11.29.569268 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes ]]> https://biorxiv.org/content/10.1101/2023.11.30.569198v1?rss=1 100 great ape individuals. These reference assemblies are expected to inform human evolution and conservation genetics of nonhuman apes, all of which are endangered species. ]]> Makova, K. D. Pickett, B. D. Harris, R. S. Hartley, G. A. Cechova, M. Pal, K. Nurk, S. Yoo, D. Li, Q. Hebbar, P. McGrath, B. C. Antonacci, F. Aubel, M. Biddanda, A. Borchers, M. Bornberg, E. Bouffard, G. G. Brooks, S. Y. Carbone, L. Carrel, L. Carroll, A. Chang, P.-C. Chin, C.-S. Cook, D. E. Craig, S. J. C. de Gennaro, L. Diekhans, M. Dutra, A. Garcia, G. H. Grady, P. G. S. Green, R. E. Haddad, D. Hallast, P. Harvey, W. T. Hickey, G. Hillis, D. A. Hoyt, S. J. Jeong, H. Kamali, K. Pond, S. L. K. LaPolice, T. M. Lee, C. Lewis, A. P. Loh, Y.-H. E. Maste 2023-12-01 doi:10.1101/2023.11.30.569198 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Bidirectional Energy Flow in the Photosystem II Supercomplex ]]> https://biorxiv.org/content/10.1101/2023.11.30.569278v1?rss=1 Leonardo, C. Yang, S.-J. Orcutt, K. Iwai, M. Arsenault, E. A. Fleming, G. R. 2023-12-01 doi:10.1101/2023.11.30.569278 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ CO2 Reduction by the Iron Nitrogenase Competes with N2 Fixation Under Physiological Conditions ]]> https://biorxiv.org/content/10.1101/2023.11.30.569367v1?rss=1 Oehlmann, N. N. Schmidt, F. V. Herzog, M. Goldman, A. L. Rebelein, J. G. 2023-12-01 doi:10.1101/2023.11.30.569367 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Double-strand breaks in facultative heterochromatin require specific movements and chromatin changes for efficient repair ]]> https://biorxiv.org/content/10.1101/2023.12.01.569547v1?rss=1 Wensveen, M. R. Dixit, A. A. Colmenares, S. U. Janssen, A. 2023-12-01 doi:10.1101/2023.12.01.569547 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ ConvexML: Scalable and accurate inference of single-cell chronograms from CRISPR/Cas9 lineage tracing data ]]> https://biorxiv.org/content/10.1101/2023.12.03.569785v1?rss=1 Prillo, S. Ravoor, A. Yosef, N. Song, Y. S. 2023-12-03 doi:10.1101/2023.12.03.569785 Cold Spring Harbor Laboratory Press 2023-12-03 <![CDATA[ High yield, low magnesium flexizyme reactions in a water-ice eutectic phase ]]> https://biorxiv.org/content/10.1101/2023.12.03.569792v1?rss=1 Davisson, J. Alejo, J. Blank, M. Kalb, E. Prasad, A. Knudson, I. Schepartz, A. Engelhart, A. E. Adamala, K. P. 2023-12-03 doi:10.1101/2023.12.03.569792 Cold Spring Harbor Laboratory Press 2023-12-03 <![CDATA[ Adaptive algorithms for shaping behavior ]]> https://biorxiv.org/content/10.1101/2023.12.03.569774v1?rss=1 Tong, W. L. Iyer, A. Murthy, V. N. Reddy, G. 2023-12-05 doi:10.1101/2023.12.03.569774 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Towards A Wireless Image Sensor for Real-Time Fluorescence Microscopy in Cancer Therapy ]]> https://biorxiv.org/content/10.1101/2023.12.03.569779v1?rss=1 Rabbani, R. Najafiaghdam, H. Roschelle, M. L. Papageorgiou, E. P. Zhao, B. R. Ghanbari, M. M. Muller, R. Stojanovic, V. Anwar, M. 2023-12-05 doi:10.1101/2023.12.03.569779 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Quantitative Modeling of the Short-Term Response to Nitrogen Availability that Coordinates Early Events in Lateral Root Initiation ]]> https://biorxiv.org/content/10.1101/2023.12.05.570292v1?rss=1 Gaudinier, A. Van den Broeck, L. Moreno-Risueno, M. Rodriguez-Mendina, J. Sozzani, R. Brady, S. 2023-12-06 doi:10.1101/2023.12.05.570292 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ Rapid, concerted switching of the neural code in inferotemporal cortex ]]> https://biorxiv.org/content/10.1101/2023.12.06.570341v1?rss=1 Shi, Y. Bi, D. Hesse, J. K. Lanfranchi, F. F. Chen, S. Tsao, D. Y. 2023-12-06 doi:10.1101/2023.12.06.570341 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ Glial swip-10 expression controls systemic mitochondrial function, oxidative stress, and neuronal viability via copper ion homeostasis ]]> https://biorxiv.org/content/10.1101/2023.12.06.570462v1?rss=1 Rodriguez, P. Kalia, V. Gibson, C. L. Gichi, Z. Rajoo, A. Matier, C. D. Pezacki, A. T. Xiao, T. Carvelli, L. Chang, C. J. Miller, G. W. Khamoui, A. V. Boerner, J. Blakely, R. D. 2023-12-08 doi:10.1101/2023.12.06.570462 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ A Fluorescence-Based Sensor for Calibrated Measurement of Protein Kinase Stability in Live Cells ]]> https://biorxiv.org/content/10.1101/2023.12.07.570636v1?rss=1 Paul, J. W. Muratcioglu, S. Kuriyan, J. 2023-12-08 doi:10.1101/2023.12.07.570636 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Large-Scale Information Retrieval and Correction of Noisy Pharmacogenomic Datasets through Residual Thresholded Deep Matrix Factorization ]]> https://biorxiv.org/content/10.1101/2023.12.07.570723v1?rss=1 Hu, Z. T. Yu, Y. Chen, R. Yeh, S.-J. Chen, B. Huang, H. 2023-12-08 doi:10.1101/2023.12.07.570723 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ WRN Inhibition Leads to its Chromatin-Associated Degradation Via the PIAS4-RNF4-p97/VCP Axis ]]> https://biorxiv.org/content/10.1101/2023.12.08.570895v1?rss=1 Rodriguez Perez, F. Natwick, D. E. Schiff, L. Huey, M. McSwiggen, D. Heckert, A. Ortega, J. Loo, M. Miranda, R. Morrison, H. M. Butler, R. Cheng, K. Filbin, J. Gonzalez, E. Rand, M. Tang, Y. Ho, J. J. Zhang, Z. Anderson, D. J. Bashore, C. Basham, S. 2023-12-09 doi:10.1101/2023.12.08.570895 Cold Spring Harbor Laboratory Press 2023-12-09 <![CDATA[ Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species ]]> https://biorxiv.org/content/10.1101/2023.12.09.570939v1?rss=1 Kust, A. Zorz, J. Paniker, C. C. Bouma-Gregson, K. Krishnappa, N. Banfield, J. F. Diamond, S. 2023-12-10 doi:10.1101/2023.12.09.570939 Cold Spring Harbor Laboratory Press 2023-12-10 <![CDATA[ Torques within and outside the human spindle balance twist at anaphase ]]> https://biorxiv.org/content/10.1101/2023.12.10.570990v1?rss=1 Neahring, L. He, Y. Cho, N. H. Liu, G. Fernandes, J. Rux, C. J. Nakos, K. Subramanian, R. Upadhyayula, S. Yildiz, A. Dumont, S. 2023-12-10 doi:10.1101/2023.12.10.570990 Cold Spring Harbor Laboratory Press 2023-12-10 <![CDATA[ Lanthanide Cathodophores for Multicolor Electron Microscopy ]]> https://biorxiv.org/content/10.1101/2023.12.11.570835v1?rss=1 Abdul Rehman, S. Conway, J. B. Nichols, A. Soucy, E. R. Dee, A. Stevens, K. Merminod, S. MacNaughton, I. Curtis, A. Prigozhin, M. B. 2023-12-12 doi:10.1101/2023.12.11.570835 Cold Spring Harbor Laboratory Press 2023-12-12 <![CDATA[ Utilizing Non-Invasive Prenatal Test Sequencing Data Resource for Human Genetic Investigation ]]> https://biorxiv.org/content/10.1101/2023.12.11.570976v1?rss=1 Liu, S. Huang, S. Liu, Y. Gu, Y. Lin, X. Zhu, H. Liu, H. Xu, Z. Cheng, S. Lan, X. Li, L. Chen, G.-B. Li, H. Xu, X. Nielsen, R. Davies, R. Albrechtsen, A. Qiu, X. Jin, X. 2023-12-12 doi:10.1101/2023.12.11.570976 Cold Spring Harbor Laboratory Press 2023-12-12 <![CDATA[ The importance of the location of the N-terminus in successful protein folding in vivo and in vitro ]]> https://biorxiv.org/content/10.1101/2023.12.11.571183v1?rss=1 Dall, N. R. Mendonca, C. A. T. F. Torres Vera, H. L. Marqusee, S. 2023-12-12 doi:10.1101/2023.12.11.571183 Cold Spring Harbor Laboratory Press 2023-12-12 <![CDATA[ Glioma Cells Secrete Collagen VI to Facilitate Invasion ]]> https://biorxiv.org/content/10.1101/2023.12.12.571198v1?rss=1 Cha, J. Ding, E. A. Carvalho, E. M. Fowler, A. Aghi, M. K. Kumar, S. 2023-12-12 doi:10.1101/2023.12.12.571198 Cold Spring Harbor Laboratory Press 2023-12-12 <![CDATA[ Sporadic phage defense in epidemic Vibrio cholerae mediated by the toxin-antitoxin system DarTG is countered by a phage-encoded antitoxin mimic ]]> https://biorxiv.org/content/10.1101/2023.12.14.571748v1?rss=1 Patel, K. Seed, K. 2023-12-15 doi:10.1101/2023.12.14.571748 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Substrate-interacting pore loops of two ATPase subunits determine the degradation efficiency of the 26S proteasome ]]> https://biorxiv.org/content/10.1101/2023.12.14.571752v1?rss=1 Martin, A. Lopez-Alfonzo, E. M. Saurabh, A. Zarafshan, S. Presse, S. 2023-12-15 doi:10.1101/2023.12.14.571752 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Covalent Attachment of Horseradish Peroxidase to Single-Walled Carbon Nanotubes for Hydrogen Peroxide Detection ]]> https://biorxiv.org/content/10.1101/2023.12.14.571773v1?rss=1 Ledesma, F. Nishitani, S. Cunningham, F. J. Hubbard, J. D. Yim, D. Lui, A. Chio, L. Murali, A. Landry, M. P. 2023-12-15 doi:10.1101/2023.12.14.571773 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9 ]]> https://biorxiv.org/content/10.1101/2023.12.14.571777v1?rss=1 100-fold higher genome editing levels. Cryo-EM structures of the wildtype and improved GeoCas9 (iGeoCas9) enzymes reveal extended contacts between the WED domain of iGeoCas9 and DNA substrates. Biochemical analysis shows that iGeoCas9 accelerates DNA unwinding to capture substrates under the magnesium-restricted conditions typical of mammalian but not bacterial cells. These findings enabled rational engineering of other Cas9 orthologs to enhance genome editing levels, pointing to a general strategy for editing enzyme improvement. Together, these results uncover a new role for the Cas9 WED domain in DNA unwinding and demonstrate how accelerated target unwinding dramatically improves Cas9-induced genome editing activity. ]]> Eggers, A. R. Chen, K. Soczek, K. M. Tuck, O. T. Doherty, E. E. Thornton, B. W. Xu, B. Trinidad, M. I. Doudna, J. A. 2023-12-15 doi:10.1101/2023.12.14.571777 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Structure-conditioned masked language models for protein sequence design generalize beyond the native sequence space ]]> https://biorxiv.org/content/10.1101/2023.12.15.571823v1?rss=1 Akpinaroglu, D. Seki, K. Guo, A. Zhu, E. Kelly, M. J. Kortemme, T. 2023-12-15 doi:10.1101/2023.12.15.571823 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Powdery mildew infection induces a non-canonical route to storage lipid formation at the expense of host thylakoid lipids to fuel its spore production ]]> https://biorxiv.org/content/10.1101/2023.12.15.571944v1?rss=1 Jaenisch, J. Xue, H. Schlapfer, J. McGarrigle, E. R. Louie, K. B. Northen, T. Wildermuth, M. C. 2023-12-16 doi:10.1101/2023.12.15.571944 Cold Spring Harbor Laboratory Press 2023-12-16 <![CDATA[ TRPM8-dependent shaking in mammals and birds ]]> https://biorxiv.org/content/10.1101/2023.12.27.573364v1?rss=1 Selescu, T. Bivoleanu, R.-A. Iodi Carstens, M. Manolache, A. Caragea, V.-M. Hutanu, D.-E. Meerupally, R. Wei, E. T. Carstens, E. Zimmermann, K. Babes, A. 2023-12-27 doi:10.1101/2023.12.27.573364 Cold Spring Harbor Laboratory Press 2023-12-27 <![CDATA[ Genetically encoded tool for manipulation of Δ{Psi}m identifies the latter as the driver of integrative stress response induced by ATP Synthase dysfunction ]]> https://biorxiv.org/content/10.1101/2023.12.27.573435v1?rss=1 Choe, M. Titov, D. V. 2023-12-27 doi:10.1101/2023.12.27.573435 Cold Spring Harbor Laboratory Press 2023-12-27 <![CDATA[ The Statistical Building Blocks of Animal Movement Simulations ]]> https://biorxiv.org/content/10.1101/2023.12.27.573450v1?rss=1 Getz, W. M. Salter, R. Sethi, V. Cain, S. Nathan, R. Spiegel, O. Toledo, S. 2023-12-27 doi:10.1101/2023.12.27.573450 Cold Spring Harbor Laboratory Press 2023-12-27 <![CDATA[ Hippocampal sequences span experience relative to rewards ]]> https://biorxiv.org/content/10.1101/2023.12.27.573490v1?rss=1 Sosa, M. Plitt, M. H. Giocomo, L. M. 2023-12-28 doi:10.1101/2023.12.27.573490 Cold Spring Harbor Laboratory Press 2023-12-28 <![CDATA[ Interplay between Two Paralogous Human Silencing Hub (HuSH) Complexes in Regulating LINE-1 Element Silencing ]]> https://biorxiv.org/content/10.1101/2023.12.28.573526v1?rss=1 Jensvold, Z. D. Christenson, A. E. Flood, J. R. Lewis, P. W. 2023-12-28 doi:10.1101/2023.12.28.573526 Cold Spring Harbor Laboratory Press 2023-12-28 <![CDATA[ Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae ]]> https://biorxiv.org/content/10.1101/2023.12.30.573743v1?rss=1 Rakibova, Y. Dunham, D. T. Seed, K. D. Freddolino, L. 2024-01-01 doi:10.1101/2023.12.30.573743 Cold Spring Harbor Laboratory Press 2024-01-01 <![CDATA[ Image processing tools for petabyte-scale light sheet microscopy data ]]> https://biorxiv.org/content/10.1101/2023.12.31.573734v1?rss=1 Ruan, X. Mueller, M. Liu, G. Görlitz, F. Fu, T.-M. Milkie, D. E. Lillvis, J. Killilea, A. Betzig, E. Upadhyayula, S. 2024-01-01 doi:10.1101/2023.12.31.573734 Cold Spring Harbor Laboratory Press 2024-01-01 <![CDATA[ Dbp1 is a low performance paralog of RNA helicase Ded1 that drives impaired translation and heat stress response ]]> https://biorxiv.org/content/10.1101/2024.01.12.575095v1?rss=1 Powers, E. N. Reynaud, K. Sousa, C. Kuwayama, N. Jovanovic, M. Ingolia, N. Brar, G. A. 2024-01-14 doi:10.1101/2024.01.12.575095 Cold Spring Harbor Laboratory Press 2024-01-14 <![CDATA[ Sterol O-acyltransferase (SOAT/ACAT) activity is required to form cholesterol crystals in hepatocyte lipid droplets ]]> https://biorxiv.org/content/10.1101/2024.01.20.576345v1?rss=1 Bairos, J. A. Njoku, U. Zafar, M. Akl, M. G. Li, L. Parlakgul, G. Arruda, A. P. Widenmaier, S. B. 2024-01-21 doi:10.1101/2024.01.20.576345 Cold Spring Harbor Laboratory Press 2024-01-21 <![CDATA[ CLSTN3B enhances adipocyte lipid droplet structure and function via endoplasmic reticulum contact ]]> https://biorxiv.org/content/10.1101/2024.01.20.576491v1?rss=1 Zhang, C. Ye, M. Melikov, K. Yang, D. Dias do Vale, G. Mcdonald, J. Eckert, K. Lin, M.-J. Zeng, X. 2024-01-21 doi:10.1101/2024.01.20.576491 Cold Spring Harbor Laboratory Press 2024-01-21 <![CDATA[ Alpha phase-coding supports feature binding during working memory maintenance ]]> https://biorxiv.org/content/10.1101/2024.01.21.576561v1?rss=1 Pagnotta, M. F. Santo-Angles, A. Temudo, A. Barbosa, J. Compte, A. D'Esposito, M. Sreenivasan, K. K. 2024-01-22 doi:10.1101/2024.01.21.576561 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Can't carve air, can't weave names: Plant species used in Colombian artisan crafts are not equally assessed for vulnerability at the international and national level ]]> https://biorxiv.org/content/10.1101/2024.01.24.573691v1?rss=1 Hernandez, K. V. Andrade-Rivas, F. Zapata, F. Batista, N. Cardenas-Navarrete, A. Davila Arenas, A. Herrera-R, G. A. Langhans, K. E. Levey, D. Neill, A. Nguyen, O. Ocampo-Penuela, N. Sanchez Lopez, S. Echeverri, A. 2024-01-26 doi:10.1101/2024.01.24.573691 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ Bridge RNAs direct modular and programmable recombination of target and donor DNA ]]> https://biorxiv.org/content/10.1101/2024.01.24.577089v1?rss=1 Durrant, M. G. Perry, N. T. Pai, J. J. Jangid, A. R. Athukoralage, J. S. Hiraizumi, M. McSpedon, J. P. Pawluk, A. Nishimasu, H. Konermann, S. Hsu, P. D. 2024-01-26 doi:10.1101/2024.01.24.577089 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ Yellow and oxidation-resistant derivatives of a monomeric superfolder GFP ]]> https://biorxiv.org/content/10.1101/2024.01.25.577236v1?rss=1 Valbuena, F. M. Krahn, A. H. Tokamov, S. A. Greene, A. C. Fehon, R. G. Glick, B. S. 2024-01-26 doi:10.1101/2024.01.25.577236 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ Scarcity of fixed carbon transfer in a model microbial phototroph-heterotroph interaction ]]> https://biorxiv.org/content/10.1101/2024.01.26.577492v1?rss=1 Dupuis, S. Lingappa, U. F. Mayali, X. Sindermann, E. S. Chastain, J. L. Weber, P. K. Stuart, R. Merchant, S. S. 2024-01-27 doi:10.1101/2024.01.26.577492 Cold Spring Harbor Laboratory Press 2024-01-27 <![CDATA[ Cytosolic bacterial pathogens activate TLR pathways in tumors that synergistically enhance STING agonist cancer therapies ]]> https://biorxiv.org/content/10.1101/2024.01.30.578087v1?rss=1 80% of mice after a single dose. Small molecule TLR agonists also synergistically enhanced the anti-tumor activity of STING agonists. The anti-tumor effects were diminished in Rag2-deficient mice and upon CD8 T cell depletion. Mice cured from combination therapy developed immunity to cancer rechallenge that was superior to STING agonist monotherapy. Together, these data provide a framework for enhancing the efficacy of microbial cancer therapies and small molecule innate immune agonists, via the co-activation of STING and TLRs. ]]> Danielson, M. Nicolai, C. J. Vo, T. T. Wolf, N. Burke, T. P. 2024-02-02 doi:10.1101/2024.01.30.578087 Cold Spring Harbor Laboratory Press 2024-02-02 <![CDATA[ The ubiquitin ligase HUWE1 enhances WNT signaling by antagonizing destruction complex-mediated beta-catenin degradation and through a mechanism independent of beta-catenin stability ]]> https://biorxiv.org/content/10.1101/2024.02.02.578552v1?rss=1 McKenna, J. K. Wu, Y. Sonkusre, P. Lebensohn, A. M. 2024-02-02 doi:10.1101/2024.02.02.578552 Cold Spring Harbor Laboratory Press 2024-02-02 <![CDATA[ Reducing stomatal density by expression of a synthetic EPF increases leaf intrinsic water use efficiency and reduces plant water use in a C4 crop ]]> https://biorxiv.org/content/10.1101/2024.02.01.578512v1?rss=1 Ferguson, J. N. Schmuker, P. Dmitrieva, A. Quach, T. Zhang, T. Ge, Z. Nersesian, N. Sato, S. Clemente, T. Leakey, A. 2024-02-03 doi:10.1101/2024.02.01.578512 Cold Spring Harbor Laboratory Press 2024-02-03 <![CDATA[ Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface ]]> https://biorxiv.org/content/10.1101/2024.02.03.578758v1?rss=1 Goff, J. L. Szink, E. G. Durrence, K. L. Lui, L. M. Nielsen, T. N. Kuehl, J. V. Hunt, K. A. Chandonia, J.-M. Huang, J. Thorgersen, M. P. Poole, F. L. Stahl, D. A. Chakraborty, R. Deutschbauer, A. M. Arkin, A. P. Adams, M. W. W. 2024-02-04 doi:10.1101/2024.02.03.578758 Cold Spring Harbor Laboratory Press 2024-02-04 <![CDATA[ MAGIC matrices: freeform bioprinting materials to support complex and reproducible organoid morphogenesis ]]> https://biorxiv.org/content/10.1101/2024.02.01.578324v1?rss=1 Graham, A. J. Khoo, M. W. L. Srivastava, V. Viragova, S. Parekh, K. Morley, C. D. Bird, M. Lebel, P. Kumar, S. Klein, O. D. Gomez-Sjoberg, R. Gartner, Z. J. 2024-02-05 doi:10.1101/2024.02.01.578324 Cold Spring Harbor Laboratory Press 2024-02-05 <![CDATA[ Defining the mechanisms and properties of post-transcriptional regulatory disordered regions by high-throughput functional profiling ]]> https://biorxiv.org/content/10.1101/2024.02.01.578453v1?rss=1 Lobel, J. H. Ingolia, N. T. 2024-02-05 doi:10.1101/2024.02.01.578453 Cold Spring Harbor Laboratory Press 2024-02-05 <![CDATA[ Improving rice drought tolerance through host-mediated microbiome selection ]]> https://biorxiv.org/content/10.1101/2024.02.03.578672v1?rss=1 Styer, A. Pettinga, D. Caddell, D. F. Coleman-Derr, D. 2024-02-05 doi:10.1101/2024.02.03.578672 Cold Spring Harbor Laboratory Press 2024-02-05 <![CDATA[ A TBX5-dependent compartment boundary patterns the cardiac interventricular septum ]]> https://biorxiv.org/content/10.1101/2024.02.05.578995v1?rss=1 Kathiriya, I. S. Dominguez, M. H. Rao, K. S. Muncie-Vasic, J. M. Devine, W. P. Hu, K. M. Hota, S. K. Garay, B. I. Quintero, D. Goyal, P. Matthews, M. N. Thomas, R. Sukonnik, T. Miguel-Perez, D. Winchester, S. Brower, E. F. Forjaz, A. Wu, P.-H. Wirtz, D. Kiemen, A. L. Bruneau, B. G. 2024-02-05 doi:10.1101/2024.02.05.578995 Cold Spring Harbor Laboratory Press 2024-02-05 <![CDATA[ Global diversity, recurrent evolution, and recent selection on amylase structural haplotypes in humans ]]> https://biorxiv.org/content/10.1101/2024.02.07.579378v1?rss=1 10,000-fold the SNP mutation rate, whereas AMY2B gene duplications share a single origin. Using a pangenome graph-based approach to infer structural haplotypes across thousands of humans, we identify extensively duplicated haplotypes present at higher frequencies in modern day populations with traditionally agricultural diets. Leveraging 533 ancient human genomes we find that duplication-containing haplotypes (i.e. haplotypes with more amylase gene copies than the ancestral haplotype) have increased in frequency more than seven-fold over the last 12,000 years providing evidence for recent selection in West Eurasians. Together, our study highlights the potential impacts of the agricultural revolution on human genomes and the importance of long-read sequencing in identifying signatures of selection at structurally complex loci. ]]> Bolognini, D. Halgren, A. S. Lou, R. N. Raveane, A. Rocha, J. Guarracino, A. Soranzo, N. Chin, J. Garrison, E. Sudmant, P. H. 2024-02-09 doi:10.1101/2024.02.07.579378 Cold Spring Harbor Laboratory Press 2024-02-09 <![CDATA[ Structural basis for the inhibition of PRC2 by active transcription histone posttranslational modifications ]]> https://biorxiv.org/content/10.1101/2024.02.09.579730v1?rss=1 Cookis, T. Lydecker, A. Sauer, P. V. Kasinath, V. Nogales, E. 2024-02-10 doi:10.1101/2024.02.09.579730 Cold Spring Harbor Laboratory Press 2024-02-10 <![CDATA[ The ChAHP chromatin remodelling complex regulates neurodevelopmental disorder risk genes to scale the production of neocortical layers ]]> https://biorxiv.org/content/10.1101/2024.02.12.579820v1?rss=1 Clemot-Dupont, S. Fernandes, J. A. L. Larrigan, S. Sun, X. Medisetti, S. Stanley, R. El Hankouri, Z. Joshi, S. V. Picketts, D. J. Shekhar, K. Mattar, P. 2024-02-13 doi:10.1101/2024.02.12.579820 Cold Spring Harbor Laboratory Press 2024-02-13 <![CDATA[ iSCORE-PD: an isogenic stem cell collection to research Parkinson Disease ]]> https://biorxiv.org/content/10.1101/2024.02.12.579917v1?rss=1 G/FS, SYNJ1 R258Q/FS, VPS13C A444P/FS, VPS13C W395C/FS, GBA1 IVS2+1/FS). All mutations were introduced into a fully characterized and sequenced female human embryonic stem cell (hESC) line (WIBR3; NIH approval number NIHhESC-10-0079) using different genome editing techniques. To ensure the genetic integrity of these cell lines, we implemented rigorous quality controls, including whole-genome sequencing of each line. Our analysis of the genetic variation in this cell line collection revealed that while genome editing, particularly using CRISPR/Cas9, can introduce rare off-target mutations, the predominant source of genetic variants arises from routine cell culture and are fixed in cell lines during clonal isolation. The observed genetic variation was minimal compared to that typically found in patient-derived iPSC experiments and predominantly affected non-coding regions of the genome. Importantly, our analysis outlines strategies for effectively managing genetic variation through stringent quality control measures and careful experimental design. This systematic approach ensures the high quality of our stem cell collection, highlights advantages of prime editing over conventional CRISPR/Cas9 methods and provides a roadmap for the generation of gene-edited hPSC collections at scale in an academic setting. Our iSCORE-PD collection represents an easily accessible and valuable platform to study PD, which can be used by investigators to understand the molecular pathophysiology of PD in a human cellular setting. ]]> Busquets, O. Li, H. Syed, K. M. Jerez, P. A. Dunnack, J. Bu, R. L. Verma, Y. Pangilinan, G. R. Martin, A. Straub, J. Du, Y. Simon, V. M. Poser, S. Bush, Z. Diaz, J. Sahagun, A. Gao, J. Hernandez, D. Levine, K. S. Booth, E. O. Bateup, H. Rio, D. Hockemeyer, D. Blauwendraat, C. Soldner, F. 2024-02-13 doi:10.1101/2024.02.12.579917 Cold Spring Harbor Laboratory Press 2024-02-13 <![CDATA[ PSAP-genomic-regions: a method leveraging population data to prioritize coding and non-coding variants in whole genome sequencing for rare disease diagnosis ]]> https://biorxiv.org/content/10.1101/2024.02.13.580050v1?rss=1 Ogloblinsky, M.-S. Bocher, O. Aloui, C. Leutenegger, A.-L. Ozisik, O. Baudot, A. Tournier-Lasserve, E. Castillo-Madeen, H. Lewinsohn, D. Conrad, D. F. Genin, E. Marenne, G. 2024-02-13 doi:10.1101/2024.02.13.580050 Cold Spring Harbor Laboratory Press 2024-02-13 <![CDATA[ Identification of retinal tau oligomers, citrullinated tau, and other tau isoforms in early and advanced AD and relations to disease status ]]> https://biorxiv.org/content/10.1101/2024.02.13.579999v1?rss=1 Shi, H. Mirzaei, N. Koronyo, Y. Davis, M. R. Robinson, E. Braun, G. M. Jallow, O. Rentsendorj, A. Ramanujan, V. K. Fert-Bober, J. Kramerov, A. A. Ljubimov, A. V. Schneider, L. S. Tourtellotte, W. G. Hawes, D. Schneider, J. A. Black, K. L. Kayed, R. Selenica, M.-L. B. Lee, D. C. Fuchs, D.-T. Koronyo-Hamaoui, M. 2024-02-16 doi:10.1101/2024.02.13.579999 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ Striatal Dopamine Can Enhance Learning, Both Fast and Slow, and Also Make it Cheaper ]]> https://biorxiv.org/content/10.1101/2024.02.14.580392v1?rss=1 Westbrook, A. van den Bosch, R. Hofmans, L. Papadopetraki, D. Maatta, J. I. Collins, A. G. E. Frank, M. J. Cools, R. 2024-02-17 doi:10.1101/2024.02.14.580392 Cold Spring Harbor Laboratory Press 2024-02-17 <![CDATA[ 50,000 years of Evolutionary History of India: Insights from ~2,700 Whole Genome Sequences ]]> https://biorxiv.org/content/10.1101/2024.02.15.580575v1?rss=1 Kerdoncuff, E. Skov, L. Patterson, N. Zhao, W. Lueng, Y. Y. Schellenberg, G. D. Smith, J. A. Dey, S. Ganna, A. Dey, A. Kardia, S. L. R. Lee, J. Moorjani, P. 2024-02-17 doi:10.1101/2024.02.15.580575 Cold Spring Harbor Laboratory Press 2024-02-17 <![CDATA[ Gammaherpesvirus infection alters transfer RNA splicing and triggers tRNA cleavage ]]> https://biorxiv.org/content/10.1101/2024.02.16.580780v1?rss=1 Manning, A. C. Bashir, M. M. Jimenez, A. C. Upton, H. E. Collins, K. Lowe, T. M. Tucker, J. M. 2024-02-17 doi:10.1101/2024.02.16.580780 Cold Spring Harbor Laboratory Press 2024-02-17 <![CDATA[ Transgenesis enables mapping of segmental ganglia in the leech Helobdella austinensis ]]> https://biorxiv.org/content/10.1101/2024.02.14.580271v1?rss=1 Kuo, D.-H. Szczupak, L. Weisblat, D. Portiansky, E. Winchell, C. Lee, J.-R. Tsai, F.-Y. 2024-02-18 doi:10.1101/2024.02.14.580271 Cold Spring Harbor Laboratory Press 2024-02-18 <![CDATA[ High-resolution single particle imaging at 100-200 keV with the Gatan Alpine direct electron detector. ]]> https://biorxiv.org/content/10.1101/2024.02.14.580363v1?rss=1 Chan, L. M. Courteau, B. J. Maker, A. Wu, M. Basanta, B. Mehmood, H. Bulkley, D. Joyce, D. Lee, B. C. Mick, S. Gulati, S. Lander, G. C. Verba, K. A. 2024-02-18 doi:10.1101/2024.02.14.580363 Cold Spring Harbor Laboratory Press 2024-02-18 <![CDATA[ Expression of a mammalian RNA demethylase increases flower number and floral stem branching in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2024.02.15.580558v1?rss=1 Markel, K. Waldburger, L. M. Shih, P. 2024-02-19 doi:10.1101/2024.02.15.580558 Cold Spring Harbor Laboratory Press 2024-02-19 <![CDATA[ Heat Stable and Intrinsically Sterile Liquid Protein Formulations ]]> https://biorxiv.org/content/10.1101/2024.02.19.581015v1?rss=1 Lawanprasert, A. Pimcharoen, S. Singh, H. Vargas, M. G. Dewan, A. Kirimanjeswara, G. S. Medina, S. 2024-02-22 doi:10.1101/2024.02.19.581015 Cold Spring Harbor Laboratory Press 2024-02-22 <![CDATA[ DCAF16-Based Covalent Handle for the Rational Design of Monovalent Degraders ]]> https://biorxiv.org/content/10.1101/2024.02.20.580683v1?rss=1 Lim, M. Do Cong, T. Orr, L. M. Toriki, E. S. Kile, A. C. Papatzimas, J. W. Lee, E. Nomura, D. K. 2024-02-22 doi:10.1101/2024.02.20.580683 Cold Spring Harbor Laboratory Press 2024-02-22 <![CDATA[ Asiatic acid improves mitochondrial function, activates antioxidant response in the mouse brain and improves cognitive function in beta-amyloid overexpressing mice. ]]> https://biorxiv.org/content/10.1101/2024.02.21.581270v1?rss=1 Varada, S. Chamberlin, S. R. Bui, L. Brandes, M. S. Gladen-Kolarksy, N. Harris, C. J. Hack, W. Brumbach, B. H. Quinn, J. F. Gray, N. E. 2024-02-22 doi:10.1101/2024.02.21.581270 Cold Spring Harbor Laboratory Press 2024-02-22 <![CDATA[ Survival of tardigrades (Hypsibius exemplaris) to subzero temperatures depends on exposure intensity, duration, and ice-nucleation--as shown by large-scale mortality dye-based assays ]]> https://biorxiv.org/content/10.1101/2024.02.28.582259v1?rss=1 Lyons, A. M. Roberts, K. T. Williams, C. M. 2024-03-02 doi:10.1101/2024.02.28.582259 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ Assessing the impact of Brd2 depletion on chromatin compartmentalization ]]> https://biorxiv.org/content/10.1101/2024.03.02.583085v1?rss=1 Athreya, A. Xie, L. Tjian, R. Zhang, B. Liu, Z. J. 2024-03-06 doi:10.1101/2024.03.02.583085 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Prevalent fast evolution of genes involved in heterochromatin functions ]]> https://biorxiv.org/content/10.1101/2024.03.03.583199v1?rss=1 Lin, L. Huang, Y. McIntyre, J. Chang, C.-H. Colmenares, S. S. Lee, G. Y. C. 2024-03-06 doi:10.1101/2024.03.03.583199 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Molecular mechanism of α-latrotoxin action ]]> https://biorxiv.org/content/10.1101/2024.03.06.583760v1?rss=1 Klink, B. U. Alavizargar, A. Subramaniam, K. K. Chen, M. Heuer, A. Gatsogiannis, C. 2024-03-06 doi:10.1101/2024.03.06.583760 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Deep Plasma Proteome Profiling by Modulating Single Nanoparticle Protein Corona with Small Molecules ]]> https://biorxiv.org/content/10.1101/2024.03.06.582595v1?rss=1 Ashkarran, A. A. Gharibi, H. Modaresi, S. M. Sayadi, M. Jafari, M. Lin, Z. Ritz, D. Kakhniashvili, D. Sun, L. Landry, M. P. Dibavar, A. S. Mahmoudi, M. 2024-03-08 doi:10.1101/2024.03.06.582595 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ An array of Zymoseptoria tritici effectors suppress plant immune responses ]]> https://biorxiv.org/content/10.1101/2024.03.12.584321v1?rss=1 Thynne, E. Ali, H. Seong, K. Abukhalaf, M. Guerreiro, M. A. Flores-Nunez, V. M. Hansen, R. Salman, M. Rudd, J. J. Kanyuka, K. Krasileva, K. V. Kettles, G. J. Stukenbrock, E. H. 2024-03-13 doi:10.1101/2024.03.12.584321 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Functional genetics reveals modulators of anti-microtubule drug sensitivity ]]> https://biorxiv.org/content/10.1101/2024.03.12.584469v1?rss=1 Su, K.-C. Radul, E. Maier, N. K. Tsang, M.-J. Goul, C. S. Moodie, B. Keys, H. R. Cheeseman, I. M. 2024-03-13 doi:10.1101/2024.03.12.584469 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Bayesian inference of state feedback control parameters for fo perturbation responses in cerebellar ataxia ]]> https://biorxiv.org/content/10.1101/2024.03.12.584554v1?rss=1 Gaines, J. L. Kim, K. S. Parrell, B. Ramanarayanan, V. Pongos, A. L. Nagarajan, S. S. Houde, J. F. 2024-03-14 doi:10.1101/2024.03.12.584554 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Versatile roles of protein flavinylation in bacterial extracyotosolic electron transfer ]]> https://biorxiv.org/content/10.1101/2024.03.13.584918v1?rss=1 Huang, S. Meheust, R. Barquera, B. Light, S. H. 2024-03-14 doi:10.1101/2024.03.13.584918 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Throat color polymorphism is related to differences in aggression in the Aegean wall lizard ]]> https://biorxiv.org/content/10.1101/2024.03.14.585063v1?rss=1 Mandavilli, D. S. Wang, I. J. Brock, K. M. 2024-03-14 doi:10.1101/2024.03.14.585063 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Robust and Accurate Bayesian Inference of Genome-Wide Genealogies for Large Samples ]]> https://biorxiv.org/content/10.1101/2024.03.16.585351v1?rss=1 Deng, Y. Nielsen, R. Song, Y. S. 2024-03-16 doi:10.1101/2024.03.16.585351 Cold Spring Harbor Laboratory Press 2024-03-16 <![CDATA[ A numbers game: Mosquito-based arbovirus surveillance in two distinct geographic regions of Latin America ]]> https://biorxiv.org/content/10.1101/2024.03.15.585246v1?rss=1 Mojica, J. Arevalo, V. Juarez, J. G. Galarza, X. Gonzalez, K. Carrazco-Montalvo, A. Suazo, H. Harris, E. Coloma, J. Ponce, P. Balmaseda, A. Cevallos, V. 2024-03-19 doi:10.1101/2024.03.15.585246 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Characterization of the murine spine for spaceflight studies ]]> https://biorxiv.org/content/10.1101/2024.03.17.585438v1?rss=1 Lim, S. Veres, J. E. Almeida, E. A. O'Connell, G. 2024-03-19 doi:10.1101/2024.03.17.585438 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Metric Ion Classification (MIC): A deep learning tool for assigning ions and waters in cryo-EM and x-ray crystallography structures ]]> https://biorxiv.org/content/10.1101/2024.03.18.585639v1?rss=1 Shub, L. Liu, W. Skiniotis, G. Keiser, M. J. Robertson, M. J. 2024-03-19 doi:10.1101/2024.03.18.585639 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Evidence for the key roles of the Pseudomonas syringae mobilome in shaping biotic interactions ]]> https://biorxiv.org/content/10.1101/2024.03.19.585818v1?rss=1 Holtappels, D. Rickus, G. J. E. Morgan, T. de Rezende, R. R. Koskella, B. Alfenas-Zerbini, P. 2024-03-20 doi:10.1101/2024.03.19.585818 Cold Spring Harbor Laboratory Press 2024-03-20 <![CDATA[ A human commons cell atlas reveals cell type specificity for OAS1 isoforms ]]> https://biorxiv.org/content/10.1101/2024.03.23.586412v1?rss=1 Galvez-Merchan, A. Booeshaghi, A. S. Pachter, L. 2024-03-24 doi:10.1101/2024.03.23.586412 Cold Spring Harbor Laboratory Press 2024-03-24 <![CDATA[ Paraneoplastic renal dysfunction in fly cancer models driven by inflammatory activation of stem cells ]]> https://biorxiv.org/content/10.1101/2024.03.21.586173v1?rss=1 Kwok, S. H. Liu, Y. Bilder, D. Kim, J. 2024-03-25 doi:10.1101/2024.03.21.586173 Cold Spring Harbor Laboratory Press 2024-03-25 <![CDATA[ Algorithms for a Commons Cell Atlas ]]> https://biorxiv.org/content/10.1101/2024.03.23.586413v1?rss=1 Booeshaghi, A. S. Galvez-Merchan, A. Pachter, L. 2024-03-26 doi:10.1101/2024.03.23.586413 Cold Spring Harbor Laboratory Press 2024-03-26 <![CDATA[ The Genomes of Nematode-Trapping Fungi Provide Insights into the Origin and Diversification of Fungal Carnivorism ]]> https://biorxiv.org/content/10.1101/2024.03.21.586190v1?rss=1 Fan, Y. Du, M. Zhang, W. Deng, W. Yang, E. Wang, S. Yan, L. Zhang, L. Kang, S. Steenwyk, J. L. An, Z. Liu, X. Xiang, M. 2024-03-27 doi:10.1101/2024.03.21.586190 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Mutation of negative regulatory gene CEHC1 encoding an FBXO3 protein results in normoxic expression of HYDA genes in Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2024.03.22.586359v1?rss=1 Sun, X. LaVoie, M. Lefebvre, P. Gallaher, S. D. Glaesener, A. G. Strenkert, D. Mehta, R. Merchant, S. S. Silflow, C. D. 2024-03-27 doi:10.1101/2024.03.22.586359 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Honoring the Afro-Colombian musical culture with the naming of Epipedobates sp. nov. (Anura: Dendrobatidae), a frog from the Pacific rainforests ]]> https://biorxiv.org/content/10.1101/2024.03.23.586415v1?rss=1 Betancourth-Cundar, M. Rios-Orjuela, J. C. Crawford, A. J. Cannatella, D. C. Tarvin, R. D. 2024-03-27 doi:10.1101/2024.03.23.586415 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Mixed clonal-aggregative multicellularity entrained by extreme salinity fluctuations in a close relative of animals ]]> https://biorxiv.org/content/10.1101/2024.03.25.586565v1?rss=1 Ros-Rocher, N. Reyes-Rivera, J. Foroughijabbari, Y. Combredet, C. Larson, B. T. Coyle, M. C. Houtepen, E. A. T. Vermeij, M. J. A. King, N. Brunet, T. 2024-03-27 doi:10.1101/2024.03.25.586565 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ The inflammatory microenvironment of the lung at the time of infection governs innate control of SARS-CoV-2 replication ]]> https://biorxiv.org/content/10.1101/2024.03.27.586885v1?rss=1 Baker, P. J. Bohrer, A. C. Castro, E. Amaral, E. P. Snow-Smith, M. Torres-Juarez, F. Gould, S. T. Queiroz, A. T. Fukutani, E. R. Jordan, C. M. Khillan, J. S. Cho, K. Barber, D. L. Andrade, B. B. Johnson, R. F. Hilligan, K. L. Mayer-Barber, K. D. 2024-03-27 doi:10.1101/2024.03.27.586885 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ py_ped_sim - A flexible forward genetic simulator for complex family pedigree analysis ]]> https://biorxiv.org/content/10.1101/2024.03.25.586501v1?rss=1 Guardado, M. A. Perez, C. Campana, S. Chavez-Rojas, B. Magana, J. Jackson, S. Samperio, E. Syas, K. Hernandez, S. Hernandez, R. Zavala, E. Rohlfs, R. 2024-03-29 doi:10.1101/2024.03.25.586501 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Integration of CTCF Loops, Methylome, and Transcriptome in Differentiating LUHMES as a Model for Imprinting Dynamics of the 15q11-q13 Locus in Human Neurons ]]> https://biorxiv.org/content/10.1101/2024.03.26.586689v1?rss=1 Fugon, O. J. G. Sharifi, O. Heath, N. G. Soto, D. C. Gomez, J. A. Yasui, D. H. Mendiola, A. J. P. O'Geen, H. Beitnere, U. Tomkova, M. Haghani, V. Dillon, G. Segal, D. J. LaSalle, J. 2024-03-29 doi:10.1101/2024.03.26.586689 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Multispecies interactions and the community context of the evolution of virulence ]]> https://biorxiv.org/content/10.1101/2024.03.29.587402v1?rss=1 Evensen, C. White, A. Boots, M. 2024-03-30 doi:10.1101/2024.03.29.587402 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Soft skeletons transmit force with variable gearing ]]> https://biorxiv.org/content/10.1101/2024.03.28.587271v1?rss=1 Ellers, O. Ellers, K.-I. Johnson, A. S. Po, T. Heydari, S. Kanso, E. McHenry, M. J. 2024-03-31 doi:10.1101/2024.03.28.587271 Cold Spring Harbor Laboratory Press 2024-03-31 <![CDATA[ Isolation and Characterization of a Halomonas Species for Non-Axenic Growth-Associated Production of Bio-Polyesters from Sustainable Feedstocks ]]> https://biorxiv.org/content/10.1101/2024.03.28.587248v1?rss=1 Woo, S.-G. Averesch, N. J. Berliner, A. J. Deutzmann, J. S. Payne, V. E. Chatterjee, S. Criddle, C. S. 2024-04-02 doi:10.1101/2024.03.28.587248 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Cryo-EM Structures Reveal Tau Filaments from Down Syndrome Adopt Alzheimer's Disease Fold ]]> https://biorxiv.org/content/10.1101/2024.04.02.587507v1?rss=1 Ghosh, U. Tse, E. Shi, M. Yang, H. Wang, F. Merz, G. E. Prusiner, S. B. Southworth, D. R. Condello, C. 2024-04-03 doi:10.1101/2024.04.02.587507 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Increased EZH2 function in regulatory T cells promotes their capacity to suppress autoimmunity by driving effector differentiation prior to activation ]]> https://biorxiv.org/content/10.1101/2024.04.05.588284v1?rss=1 Peeters, J. Silveria, S. Ozdemir, M. Ramachandran, S. DuPage, M. 2024-04-10 doi:10.1101/2024.04.05.588284 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ Life Histories and Study Duration matter less than Prior Knowledge of Vital Rates to Inverse Integral Projection Models ]]> https://biorxiv.org/content/10.1101/2024.04.06.588423v1?rss=1 Bernard, C. D. Bonsall, M. B. Salguero-Gomez, R. 2024-04-10 doi:10.1101/2024.04.06.588423 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ Tick-borne flavivirus exoribonuclease-resistant RNAs contain a 'double loop' structure ]]> https://biorxiv.org/content/10.1101/2024.04.14.589432v1?rss=1 Kieft, J. S. Langeberg, C. J. Szucs, M. J. Sherlock, M. E. Vicens, Q. 2024-04-14 doi:10.1101/2024.04.14.589432 Cold Spring Harbor Laboratory Press 2024-04-14 <![CDATA[ Robust self-supervised denoising of voltage imaging data using CellMincer ]]> https://biorxiv.org/content/10.1101/2024.04.12.589298v1?rss=1 Wang, B. Ma, T. Chen, T. Nguyen, T. Crouse, E. Fleming, S. J. Walker, A. S. Valakh, V. Nehme, R. Miller, E. W. Farhi, S. L. Babadi, M. 2024-04-15 doi:10.1101/2024.04.12.589298 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ Label-free structural imaging of plant roots and microbes using third- harmonic generation microscopy ]]> https://biorxiv.org/content/10.1101/2024.04.13.589377v1?rss=1 Pan, D. Rivera, J. A. Kim, P. Miao, M. Tyml, T. Rodriguez, C. Wang, B. Yoshikuni, Y. Elisabeth, N. H. Northen, T. Vogel, J. P. Ji, N. 2024-04-16 doi:10.1101/2024.04.13.589377 Cold Spring Harbor Laboratory Press 2024-04-16 <![CDATA[ Jumbo phages possess independent synthesis and utilization systems of NAD+ ]]> https://biorxiv.org/content/10.1101/2024.04.18.590177v1?rss=1 200 kbp, contain some unique genes for successful reproduction in their bacterial hosts. Due to complex and massive genomes analogous to those of small-celled bacteria, how do jumbo phages complete their life cycle remain largely undefined. In this study, we assembled 668 high-quality jumbo phage genomes from over 15 TB of intestinal metagenomic data from 955 samples of five animal species (cow, sheep, pig, horse, and deer). Within them, we obtained a complete genome of 716 kbp in length, which is the largest phage genome so far reported in the gut environments. Interestingly, 174 out of the 668 jumbo phages were found to encode all genes required for synthesis of NAD+ by the salvage pathway or Preiss-Handler pathway, referred as NAD-jumbo phage. Besides synthesis genes of NAD+, these NAD-jumbo phages also encode at least 15 types of NAD+-consuming enzyme genes involved in DNA replication, DNA repair, and counterdefense, suggesting that these phages not only have the capacity to synthesize NAD+ but also redirect NAD+ metabolism towards phage propagation need in hosts. Phylogenetic analysis and environmental survey indicated NAD-jumbo phages are widely present in the Earths ecosystems, including the human gut, lakes, salt ponds, mine tailings, and seawater. In summary, this study expands our understanding of the diversity and survival strategies of phages, and in-depth study of the NAD-jumbo phages is crucial for understanding their role in ecological regulation. ]]> Li, C. Liu, K. Gu, C. Li, M. Zhou, P. Chen, L. Sun, S. Li, X. Wang, L. Ni, W. Li, M. Hu, S. 2024-04-19 doi:10.1101/2024.04.18.590177 Cold Spring Harbor Laboratory Press 2024-04-19 <![CDATA[ A Role for Cross-linking Proteins in Actin Filament Network Organization and Force Generation ]]> https://biorxiv.org/content/10.1101/2024.04.19.590161v1?rss=1 Hill, J. M. Cai, S. Carver, M. D. Drubin, D. G. 2024-04-20 doi:10.1101/2024.04.19.590161 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ ATM and 53BP1 regulate alternative end joining-mediated V(D)J recombination ]]> https://biorxiv.org/content/10.1101/2024.04.25.591195v1?rss=1 Wang, J. Sadeghi, C. Le, L. V. Le Bouteiller, M. Frock, R. L. 2024-04-25 doi:10.1101/2024.04.25.591195 Cold Spring Harbor Laboratory Press 2024-04-25 <![CDATA[ Recent adaptation in an imperiled salmonid revealed by museum genomics ]]> https://biorxiv.org/content/10.1101/2024.04.25.590849v1?rss=1 Sharo, A. G. Supple, M. A. Cabrera, R. Seligmann, W. E. Sacco, S. Columbus, C. D. Pearse, D. E. Shapiro, B. Garza, J. C. 2024-04-28 doi:10.1101/2024.04.25.590849 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ An shRNA screen in primary human beta cells identifies the serotonin 1F receptor as a negative regulator of survival during transplant ]]> https://biorxiv.org/content/10.1101/2024.05.01.591950v1?rss=1 Lee, R. A. Chopra, D. G. Nguyen, V. Huang, X.-P. Zhang, Y. Shariati, K. Yiv, N. Schugar, R. Annes, J. Roth, B. L. Ku, G. 2024-05-03 doi:10.1101/2024.05.01.591950 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Genetic variants associated with cell-type-specific intra-individual gene expression variability reveal new mechanisms of genome regulation ]]> https://biorxiv.org/content/10.1101/2024.05.05.592598v1?rss=1 Powell, J. E. Xue, A. Yazar, S. Alquicira, J. Cuomo, A. Senabouth, A. Gordon, G. Kathail, P. Ye, J. Hewitt, A. 2024-05-07 doi:10.1101/2024.05.05.592598 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ The carnivoran adaptive landscape reveals trade-offs among functional traits in the skull, appendicular, and axial skeleton ]]> https://biorxiv.org/content/10.1101/2024.05.06.592620v1?rss=1 Law, C. Hlusko, L. Tseng, J. 2024-05-08 doi:10.1101/2024.05.06.592620 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ The kinetics and optimality of influenza A virus locomotion ]]> https://biorxiv.org/content/10.1101/2024.05.06.592729v1?rss=1 Agarwal, S. Veytsman, B. Fletcher, D. Huber, G. 2024-05-09 doi:10.1101/2024.05.06.592729 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ The vibriophage-encoded inhibitor OrbA abrogates BREX-mediated defense through the ATPase BrxC ]]> https://biorxiv.org/content/10.1101/2024.05.09.593382v1?rss=1 Oshiro, R. Dunham, D. Seed, K. 2024-05-09 doi:10.1101/2024.05.09.593382 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ The potential impacts of vector host species fidelity on zoonotic arbovirus transmission ]]> https://biorxiv.org/content/10.1101/2024.05.08.593124v1?rss=1 Sulaimon, T. A. Wood, A. J. Bonsall, M. B. Boots, M. Lord, J. S. 2024-05-10 doi:10.1101/2024.05.08.593124 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Near infrared fluorescent nanosensors for high spatiotemporal oxytocin imaging ]]> https://biorxiv.org/content/10.1101/2024.05.10.593556v1?rss=1 Adams, J. Komatsu, N. Navarro, N. P. Leem, E. Sun, X. Zhao, J. Arias-Soto, O. Landry, M. 2024-05-10 doi:10.1101/2024.05.10.593556 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Acceleration of genome rearrangement in clitellate annelids ]]> https://biorxiv.org/content/10.1101/2024.05.12.593736v1?rss=1 Schultz, D. T. Heath-Heckman, E. A. C. Winchell, C. J. Kuo, D.-H. T. Yu, Y.-s. Oberauer, F. Kocot, K. Cho, S.-J. Simakov, O. Weisblat, D. A. 2024-05-14 doi:10.1101/2024.05.12.593736 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Replay without sharp wave ripples in a spatial memory task. ]]> https://biorxiv.org/content/10.1101/2024.05.13.593931v1?rss=1 Widloski, J. Foster, D. 2024-05-14 doi:10.1101/2024.05.13.593931 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Cortical Dynamics during Contour Integration ]]> https://biorxiv.org/content/10.1101/2024.05.13.594033v1?rss=1 He, D. Yang, A. Coates, D. R. Ogmen, H. Chung, S. T. 2024-05-14 doi:10.1101/2024.05.13.594033 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Circadian rhythms mediate malaria transmission potential ]]> https://biorxiv.org/content/10.1101/2024.05.14.594221v1?rss=1 Bento, I. Parrington, B. Pascual, R. Goldberg, A. S. Wang, E. Liu, H. Zelle, M. Takahashi, J. S. Elias, J. E. Mota, M. M. Rijo-Ferreira, F. 2024-05-14 doi:10.1101/2024.05.14.594221 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ The nitrogen-fixing fern Azolla has a complex microbiome characterized by multiple modes of transmission ]]> https://biorxiv.org/content/10.1101/2024.05.20.592813v1?rss=1 Song, M. J. Li, F.-W. Freund, F. Tribble, C. M. Toffelmier, E. Miller, C. Shaffer, H. B. Rothfels, C. 2024-05-20 doi:10.1101/2024.05.20.592813 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ Transcriptional control of central T cell tolerance by NR4A family nuclear receptors ]]> https://biorxiv.org/content/10.1101/2024.05.19.594881v1?rss=1 Nielsen, H. V. Mueller, J. L. Hiwa, R. Yang, L. Proekt, I. Rackaityte, E. Aylard, D. Scharer, C. D. Anderson, M. Au-Yeung, B. B. Zikherman, J. 2024-05-21 doi:10.1101/2024.05.19.594881 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Tau pathology leads to lonely non-traveling slow waves that mediate human memory impairment ]]> https://biorxiv.org/content/10.1101/2024.05.22.595043v1?rss=1 Sharon, O. Chen, X. Dude, J. Shah, V. D. Ju, Y.-E. S. Jagust, W. J. Walker, M. P. 2024-05-22 doi:10.1101/2024.05.22.595043 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ Metabolic engineering of yeast for de novo production of kratom monoterpene indole alkaloids ]]> https://biorxiv.org/content/10.1101/2024.05.22.595370v1?rss=1 Holtz, M. Rago, D. Nedermark, I. Hansson, F. G. Lehka, B. J. Hansen, L. G. Marcussen, N. E. J. Veneman, W. J. Ahonen, L. Wungsintaweekul, J. Dirks, R. P. Acevedo-Rocha, C. G. Zhang, J. Keasling, J. D. Jensen, M. K. 2024-05-22 doi:10.1101/2024.05.22.595370 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation ]]> https://biorxiv.org/content/10.1101/2024.05.22.595375v1?rss=1 DeGroat, W. Inoue, F. Ashuach, T. Yosef, N. Ahituv, N. Kreimer, A. 2024-05-23 doi:10.1101/2024.05.22.595375 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Antibodies targeting Crimean-Congo hemorrhagic fever virus GP38 limit vascular leak and viral spread ]]> https://biorxiv.org/content/10.1101/2024.05.23.595578v1?rss=1 Pahmeier, F. Monticelli, S. R. Feng, X. Hjorth, C. K. Wang, A. Kuehne, A. I. Bakken, R. R. Batchelor, T. G. Lee, S. E. Middlecamp, M. Stuart, L. Abelson, D. M. McLellan, J. S. Biering, S. B. Herbert, A. S. Chandran, K. Harris, E. 2024-05-23 doi:10.1101/2024.05.23.595578 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ An acidic loop in the FHA domain of the yeast meiosis-specific kinase Mek1 interacts with a specific motif in a subset of Mek1 substrates ]]> https://biorxiv.org/content/10.1101/2024.05.24.595751v1?rss=1 Weng, Q. Wan, L. Straker, G. C. Deegan, T. D. Duncker, B. P. Neiman, A. M. Luk, E. Hollingsworth, N. M. 2024-05-25 doi:10.1101/2024.05.24.595751 Cold Spring Harbor Laboratory Press 2024-05-25 <![CDATA[ Heartbeat perception is causally linked to frontal delta oscillations ]]> https://biorxiv.org/content/10.1101/2024.05.25.595873v1?rss=1 Haslacher, D. Reber, P. Cavallo, A. Rosenthal, A. Pangratz, E. Beck, A. Romanczuk Seiferth, N. Nikulin, V. Villringer, A. Soekadar, S. 2024-05-26 doi:10.1101/2024.05.25.595873 Cold Spring Harbor Laboratory Press 2024-05-26 <![CDATA[ Plant hormone manipulation impacts salt spray tolerance, which preempts herbivory as a driver of local adaptation in the yellow monkeyflower, Mimulus guttatus ]]> https://biorxiv.org/content/10.1101/2024.05.23.595619v1?rss=1 Toll, K. Blanchard, M. Scharnagl, A. Lowry, D. Holeski, L. 2024-05-28 doi:10.1101/2024.05.23.595619 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ New isolates refine the ecophysiology of the Roseobacter CHAB-I-5 lineage ]]> https://biorxiv.org/content/10.1101/2024.05.28.596239v1?rss=1 Lanclos, V. C. Feng, X. Cheng, C. Yang, M. Hider, C. J. Coelho, J. T. Kojima, C. Y. Barnes, S. J. Cleveland, C. Xie, M. Zhao, Y. Luo, H. Thrash, J. C. 2024-05-28 doi:10.1101/2024.05.28.596239 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ Chromatin profiling identifies putative dual roles for H3K27me3 in regulating transposons and cell type specific genes in choanoflagellates ]]> https://biorxiv.org/content/10.1101/2024.05.28.596151v1?rss=1 Gahan, J. M. Helfrich, L. W. Wetzel, L. A. Bhanu, N. V. Yuan, Z.-F. Garcia, B. A. Klose, R. Booth, D. S. 2024-05-30 doi:10.1101/2024.05.28.596151 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Balanced bidirectional optogenetics reveals the causal impact of cortical temporal dynamics in sensory perception ]]> https://biorxiv.org/content/10.1101/2024.05.30.596706v1?rss=1 Quintana, D. Bounds, H. A. Veit, J. Adesnik, H. 2024-05-30 doi:10.1101/2024.05.30.596706 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Interference underlies attenuation upon relearning in sensorimotor adaptation ]]> https://biorxiv.org/content/10.1101/2024.05.27.596118v1?rss=1 Avraham, G. Ivry, R. B. 2024-06-01 doi:10.1101/2024.05.27.596118 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Targeting complement C3a receptor resolves mitochondrial hyperfusion and subretinal microglial activation in progranulin-deficient frontotemporal dementia ]]> https://biorxiv.org/content/10.1101/2024.05.29.595206v1?rss=1 Tan, L. X. Oertel, F. C. Cheng, A. Cobigo, Y. Keihani, A. Bennett, D. Abdelhak, A. Montes, S. C. Chapman, M. Chen, R. Cordano, C. Ward, M. Casaletto, K. Kramer, J. Rosen, H. H. Boxer, A. L. Miller, B. L. Green, A. Elahi, F. Lakkaraju, A. 2024-06-01 doi:10.1101/2024.05.29.595206 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Lepidopteran scale cells derive from sensory organ precursors through a canonical lineage ]]> https://biorxiv.org/content/10.1101/2024.05.31.596873v1?rss=1 Loh, L. S. DeMarr, K. A. Heryanto, C. Tsimba, M. Berrio, A. Patel, N. H. Martin, A. Wray, G. A. McMillan, W. O. Hanly, J. J. 2024-06-01 doi:10.1101/2024.05.31.596873 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Caldas meets Janzen: Thermal regimes of montane plants and implications for global patterns of speciation ]]> https://biorxiv.org/content/10.1101/2024.05.28.596313v1?rss=1 Sanchez, A. Quintero, I. Pedraza, S. S. Bonilla, D. A. Lohmann, L. G. Cadena, D. Zapata, F. 2024-06-02 doi:10.1101/2024.05.28.596313 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Retracing the horizontal transfer of a novel innate immune factor in Drosophila ]]> https://biorxiv.org/content/10.1101/2024.05.29.596511v1?rss=1 Tarnopol, R. L. Tamsil, J. A. Cinege, G. Ha, J. H. Verster, K. I. Abraham, E. Magyar, L. B. Kim, B. Y. Bernstein, S. L. Lipinszki, Z. Ando, I. Whiteman, N. K. 2024-06-02 doi:10.1101/2024.05.29.596511 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Electromigration of Charged Analytes Through Immiscible Fluids in Multiphasic Electrophoresis ]]> https://biorxiv.org/content/10.1101/2024.05.29.596534v1?rss=1 100% decrease in injection dispersion. Our theoretical predictions were experimentally validated by comparing the electrotransfer regimes of three different mineral oil samples. We show that lowering the oil viscosity to 0.0039 Pa{middle dot}s results in an injection regime similar to that of the absence of an oil layer. Additionally, we measure the migration distance and show that average electromigration velocity over the transit duration is inversely proportional to the viscosity of an interleaving oil layer. Understanding of the impact of electrotransfer of charged species across multiple immiscible fluid layers on peak dispersion informs the design of multiphasic electrophoresis systems. ]]> Herr, A. Liu, Y. Islam, M. N. 2024-06-02 doi:10.1101/2024.05.29.596534 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ A physical model for M1-mediated influenza A virus assembly ]]> https://biorxiv.org/content/10.1101/2024.06.01.594783v1?rss=1 Peukes, J. Dmitrieff, S. Nedelec, F. J. Briggs, J. A. G. 2024-06-02 doi:10.1101/2024.06.01.594783 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Transcription factor binding site divergence across maize inbred lines drives transcriptional and phenotypic variation ]]> https://biorxiv.org/content/10.1101/2024.05.31.596834v1?rss=1 Galli, M. Chen, Z. Ghandour, T. Chaudhry, A. Gregory, J. Li, M. Zhang, X. Dong, Y. Song, G. Walley, J. Chuck, G. Whipple, C. J. Kaeppler, H. F. Huang, S.-s. C. Gallavotti, A. 2024-06-03 doi:10.1101/2024.05.31.596834 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Robust virtual staining of landmark organelles ]]> https://biorxiv.org/content/10.1101/2024.05.31.596901v1?rss=1 Liu, Z. Hirata Miyasaki, E. Pradeep, S. Rahm, J. V. Foley, C. Chandler, T. Ivanov, I. E. Woosley, H. O. Lao, T. Balasubramanian, A. Liu, C. Leonetti, M. D. Arias, C. Jacobo, A. Mehta, S. B. 2024-06-03 doi:10.1101/2024.05.31.596901 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Cataract-prone variants of γD-crystallin populate a conformation with a partially unfolded N-terminal domain under native conditions ]]> https://biorxiv.org/content/10.1101/2024.06.01.596973v1?rss=1 Volz, S. Malone, J. R. Guseman, A. J. Gronenborn, A. M. Marqusee, S. 2024-06-03 doi:10.1101/2024.06.01.596973 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Tracking the genetic diversity of SARS-CoV-2 variants in Nicaragua throughout the COVID-19 Pandemic ]]> https://biorxiv.org/content/10.1101/2024.06.03.596876v1?rss=1 Vasquez Aleman, G. Cerpas, C. G. Juarez, J. Moreira, H. Arguello, S. Coloma, J. Harris, E. Gordon, A. N. Bennett, S. Balmaseda, A. 2024-06-04 doi:10.1101/2024.06.03.596876 Cold Spring Harbor Laboratory Press 2024-06-04 <![CDATA[ A paradoxical misperception of relative motion ]]> https://biorxiv.org/content/10.1101/2024.06.04.596708v1?rss=1 D'Angelo, J. C. Tiruveedhula, P. Weber, R. J. Arathorn, D. W. Roorda, A. 2024-06-06 doi:10.1101/2024.06.04.596708 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Spatial localization of hippocampal replay requires dopamine signaling ]]> https://biorxiv.org/content/10.1101/2024.06.04.597435v1?rss=1 Kleinman, M. R. Foster, D. 2024-06-06 doi:10.1101/2024.06.04.597435 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Haptic perception is contingent to hemispaces, not to hands ]]> https://biorxiv.org/content/10.1101/2024.06.04.597475v1?rss=1 Hartcher-O'Brien, J. Terekhov, A. V. Hayward, V. 2024-06-06 doi:10.1101/2024.06.04.597475 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria ]]> https://biorxiv.org/content/10.1101/2024.06.07.597961v1?rss=1 Zhang, P. Roque, B. Romero, P. Shapiro, N. Eloe-Fadrosh, E. Kebreab, E. Diamond, S. Hess, M. 2024-06-07 doi:10.1101/2024.06.07.597961 Cold Spring Harbor Laboratory Press 2024-06-07 <![CDATA[ Critical assessment of missense variant effect predictors on disease-relevant variant data ]]> https://biorxiv.org/content/10.1101/2024.06.06.597828v1?rss=1 Rastogi, R. Chung, R. Li, S. Li, C. Lee, K. Woo, J. Kim, D.-W. Keum, C. Babbi, G. Martelli, P. L. Savojardo, C. Casadio, R. Chennen, K. Weber, T. Poch, O. Ancien, F. Cia, G. Pucci, F. Raimondi, D. Vranken, W. Rooman, M. Marquet, C. Olenyi, T. Rost, B. Andreoletti, G. Kamandula, A. Peng, Y. Bakolitsa, C. Mort, M. Cooper, D. N. Bergquist, T. Pejaver, V. Liu, X. Radivojac, P. Brenner, S. E. Ioannidis, N. M. 2024-06-08 doi:10.1101/2024.06.06.597828 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ CLCC1 promotes hepatic neutral lipid flux and nuclear pore complex assembly ]]> https://biorxiv.org/content/10.1101/2024.06.07.597858v1?rss=1 Mathiowetz, A. J. Meymand, E. S. Deol, K. K. Parlakgul, G. Lange, M. Pang, S. P. Roberts, M. A. Torres, E. F. Jorgens, D. M. Zalpuri, R. Kang, M. Boone, C. Zhang, Y. Morgens, D. W. Tso, E. Zhou, Y. Talukdar, S. Levine, T. Ku, G. Arruda, A. P. Olzmann, J. 2024-06-08 doi:10.1101/2024.06.07.597858 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Reversible kink instability drives ultrafast jumping in nematodes and soft robots ]]> https://biorxiv.org/content/10.1101/2024.06.07.598012v1?rss=1 Kumar, S. Tiwari, I. M. Ortega-Jimenez, V. R. Dillman, A. He, D. Hu, Y. Bhamla, M. S. 2024-06-10 doi:10.1101/2024.06.07.598012 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Spontaneous emergence of alternating hippocampal theta sequences in a simple 2D adaptation model. ]]> https://biorxiv.org/content/10.1101/2024.06.10.598313v1?rss=1 Widloski, J. Foster, D. 2024-06-10 doi:10.1101/2024.06.10.598313 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Chromatin enables precise and scalable gene regulation with factors of limited specificity ]]> https://biorxiv.org/content/10.1101/2024.06.13.598840v1?rss=1 Perkins, M. L. Crocker, J. Tkacik, G. 2024-06-16 doi:10.1101/2024.06.13.598840 Cold Spring Harbor Laboratory Press 2024-06-16 <![CDATA[ Phylogenomics of the North American Desert Radiation Linanthus (Polemoniaceae) Reveals Mixed Trait Lability and No Single Geographic Mode of Speciation ]]> https://biorxiv.org/content/10.1101/2024.06.13.598867v1?rss=1 Anghel, I. G. Smith, L. Lichter-Marck, I. H. Zapata, F. 2024-06-17 doi:10.1101/2024.06.13.598867 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Reconfiguration of the visual code and retinal cell type complement in closely related diurnal and nocturnal mice ]]> https://biorxiv.org/content/10.1101/2024.06.14.598659v1?rss=1 Allen, A. E. Hahn, J. Richarson, R. Pantiru, A. Mouland, J. Bano-Otalora, B. Monavarfeshani, A. Yan, W. Williams, C. Wynne, J. Rodgers, J. Milosavljevic, N. Orlowska-Feuer, P. Storchi, R. Sanes, J. R. Shekhar, K. Lucas, R. J. 2024-06-17 doi:10.1101/2024.06.14.598659 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ VASCilia (Vision Analysis StereoCilia): A Napari Plugin for Deep Learning-Based 3D Analysis of Cochlear Hair Cell Stereocilia Bundles ]]> https://biorxiv.org/content/10.1101/2024.06.17.599381v1?rss=1 Kassim, Y. M. Rosenberg, D. B. Renero, A. Das, S. Rahman, S. Al Shammaa, I. Salim, S. Huang, Z. Huang, K. Ninoyu, Y. Friedman, R. A. Indzhykulian, A. A. Manor, U. 2024-06-17 doi:10.1101/2024.06.17.599381 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Designing Cell-Type-Specific Promoter Sequences Using Conservative Model-Based Optimization ]]> https://biorxiv.org/content/10.1101/2024.06.23.600232v1?rss=1 Reddy, A. J. Geng, X. Herschl, M. H. Kolli, S. Kumar, A. Hsu, P. D. Levine, S. Ioannidis, N. M. 2024-06-23 doi:10.1101/2024.06.23.600232 Cold Spring Harbor Laboratory Press 2024-06-23 <![CDATA[ TOMM40 regulates hepatocellular and plasma lipid metabolism via an LXR-dependent pathway ]]> https://biorxiv.org/content/10.1101/2024.06.27.600910v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@17b0c8forg.highwire.dtl.DTLVardef@17599aaorg.highwire.dtl.DTLVardef@1bb6ab2org.highwire.dtl.DTLVardef@15a035f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yang, N. V. Chao, J. Y. Garton, K. A. Tran, T. King, S. Orr, J. Oei, J. H. Kang, M. Zalpuri, R. Jorgens, D. M. Konchadi, P. Chorba, J. S. Theusch, E. Krauss, R. M. 2024-06-29 doi:10.1101/2024.06.27.600910 Cold Spring Harbor Laboratory Press 2024-06-29 <![CDATA[ Motor adaptation is reduced by symbolic compared to sensory feedback ]]> https://biorxiv.org/content/10.1101/2024.06.28.601293v1?rss=1 Chen, Y. Abram, S. J. Ivry, R. B. Tsay, J. S. 2024-07-01 doi:10.1101/2024.06.28.601293 Cold Spring Harbor Laboratory Press 2024-07-01 <![CDATA[ TEtrimmer: a novel tool to automate the manual curation of transposable elements ]]> https://biorxiv.org/content/10.1101/2024.06.27.600963v1?rss=1 QIAN, J. Xue, H. Ou, S. Storer, J. M. Fuertauer, L. Wildermuth, M. C. Kusch, S. Panstruga, R. 2024-07-02 doi:10.1101/2024.06.27.600963 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Unveiling the Family of Optimal Accelerations in Minimax Optimization and Fixed-Point Algorithms ]]> https://biorxiv.org/content/10.1101/2024.06.29.601352v1?rss=1 Bartlett, P. Li, C. J. Wu, J. Yu, B. 2024-07-02 doi:10.1101/2024.06.29.601352 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Simulating 500 million years of evolution with a language model ]]> https://biorxiv.org/content/10.1101/2024.07.01.600583v1?rss=1 Hayes, T. Rao, R. Akin, H. Sofroniew, N. J. Oktay, D. Lin, Z. Verkuil, R. Tran, V. Q. Deaton, J. Wiggert, M. Badkundri, R. Shafkat, I. Gong, J. Derry, A. Molina, R. S. Thomas, N. Khan, Y. A. Mishra, C. Kim, C. Bartie, L. J. Nemeth, M. Hsu, P. D. Sercu, T. Candido, S. Rives, A. 2024-07-02 doi:10.1101/2024.07.01.600583 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Multiplatform molecular profiling and functional genomic screens identify prognostic signatures and mechanisms underlying MEK inhibitor response in somatic NF1 mutant glioblastoma ]]> https://biorxiv.org/content/10.1101/2024.07.01.601334v1?rss=1 Pan, S. Mirchia, K. Payne, E. Liu, S. J. Al-Adli, N. Peeran, Z. Shukla, P. Young, J. S. Gupta, R. Wu, J. Pak, J. Seo, K. Ozawa, T. Na, B. Reddy, A. T. Braunstein, S. E. Phillips, J. J. Chang, S. Solomon, D. A. Perry, A. Raleigh, D. R. Berger, M. S. Abate, A. R. Vasudevan, H. N. 2024-07-03 doi:10.1101/2024.07.01.601334 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ Differential Aging Effects on Implicit and Explicit Sensorimotor Learning ]]> https://biorxiv.org/content/10.1101/2024.07.02.601091v1?rss=1 Cisneros, E. Karny, S. Ivry, R. B. Tsay, J. S. 2024-07-04 doi:10.1101/2024.07.02.601091 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ Multivariate analysis of multimodal brain structure predicts individual differences in risk and intertemporal preference ]]> https://biorxiv.org/content/10.1101/2024.07.04.602046v1?rss=1 Bergstrom, F. Schu, G. Lee, S. Lerman, C. Kable, J. W. 2024-07-08 doi:10.1101/2024.07.04.602046 Cold Spring Harbor Laboratory Press 2024-07-08 <![CDATA[ The WAVE complex forms linear arrays at negative membrane curvature to instruct lamellipodia formation. ]]> https://biorxiv.org/content/10.1101/2024.07.08.600855v1?rss=1 Wu, M. Marchando, P. Meyer, K. Tang, Z. Woolfson, D. N. Weiner, O. D. 2024-07-08 doi:10.1101/2024.07.08.600855 Cold Spring Harbor Laboratory Press 2024-07-08 <![CDATA[ Current genomic deep learning models display decreased performance in cell type specific accessible regions ]]> https://biorxiv.org/content/10.1101/2024.07.05.602265v1?rss=1 Kathail, P. Shuai, R. W. Chung, R. Ye, C. J. Loeb, G. Ioannidis, N. M. 2024-07-10 doi:10.1101/2024.07.05.602265 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ The West African lungfish secretes a living cocoon during aestivation with uncertain antimicrobial function ]]> https://biorxiv.org/content/10.1101/2024.07.05.602297v1?rss=1 Palominos, M. F. Bharadwaj, R. Tralka, C. Trang, K. Aka, D. Alami, M. Andrews, D. Bartlett, B. Golde, C. Liu, J. Le-Pedroza, M. Perrot, R. Seiter, B. Sparrow, C. Shapira, M. Martin, C. H. 2024-07-10 doi:10.1101/2024.07.05.602297 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Basement membrane patterning by spatial deployment of a secretion-regulating protease ]]> https://biorxiv.org/content/10.1101/2024.07.06.602330v1?rss=1 Ku, H.-Y. Bilder, D. 2024-07-10 doi:10.1101/2024.07.06.602330 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Hypersensitivity of the vimentin cytoskeleton to net-charge states and Coulomb repulsion ]]> https://biorxiv.org/content/10.1101/2024.07.08.602555v1?rss=1 Unger, B. Wu, C. Y. Choi, A. He, C. Xu, K. 2024-07-11 doi:10.1101/2024.07.08.602555 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Acute rapamycin treatment reveals novel mechanisms of behavioral, physiological, and functional dysfunction in a maternal inflammation mouse model of autism and sensory over-responsivity ]]> https://biorxiv.org/content/10.1101/2024.07.08.602602v1?rss=1 Le Belle, J. E. Condro, M. Cepeda, C. Oikonomou, K. D. Tessema, K. Dudley, L. Schoenfield, J. Kawaguchi, R. Geschwind, D. Silva, A. J. Zhang, Z. Shokat, K. Harris, N. G. Kornblum, H. I. 2024-07-11 doi:10.1101/2024.07.08.602602 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Optical Fibers Functionalized with Single-Walled Carbon Nanotubes for Flexible Fluorescent Catecholamine Detection ]]> https://biorxiv.org/content/10.1101/2024.07.09.602792v1?rss=1 Klinger, M. E. Miller, R. A. Wilbrecht, L. Landry, M. P. 2024-07-11 doi:10.1101/2024.07.09.602792 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Physical activity modulates early visual response and improves target detection in humans ]]> https://biorxiv.org/content/10.1101/2024.07.10.602924v1?rss=1 Weischner, T. Che, X. Schmid, P. R. Reichert, C. Scholz, A. Knight, R. T. Duerschmid, S. 2024-07-16 doi:10.1101/2024.07.10.602924 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Peptide-enabled ribonucleoprotein delivery for CRISPR engineering (PERC) in primary human immune cells and hematopoietic stem cells ]]> https://biorxiv.org/content/10.1101/2024.07.14.603391v1?rss=1 Sahu, S. Castro, M. Muldoon, J. J. Asija, K. Wyman, S. K. Krishnappa, N. Eyquem, J. Nguyen, D. N. Wilson, R. C. 2024-07-16 doi:10.1101/2024.07.14.603391 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Single-molecule live-cell RNA imaging with CRISPR-Csm ]]> https://biorxiv.org/content/10.1101/2024.07.14.603457v1?rss=1 Xia, C. Colognori, D. Jiang, X. Xu, K. Doudna, J. A. 2024-07-16 doi:10.1101/2024.07.14.603457 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Sequence-specific targeting of intrinsically disordered protein regions ]]> https://biorxiv.org/content/10.1101/2024.07.15.603480v1?rss=1 Wu, K. Jiang, H. Hicks, D. R. Liu, C. Muratspahic, E. Ramelot, T. A. Liu, Y. McNally, K. Gaur, A. Coventry, B. Chen, W. Bera, A. K. Kang, A. Gerben, S. Lamb, M. Y.-L. Murray, A. Li, X. Kennedy, M. A. Yang, W. Schober, G. Brierley, S. M. Gelb, M. H. Montelione, G. T. Derivery, E. Baker, D. 2024-07-16 doi:10.1101/2024.07.15.603480 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Perturbed pediatric serum metabolome in mild and severe dengue disease ]]> https://biorxiv.org/content/10.1101/2024.07.16.603788v1?rss=1 Soma, P. S. Gullberg, R. C. Graham, B. Islam, M. N. Balmaseda, A. Blair, C. D. Beaty, B. Belisle, J. T. Harris, E. Perera, R. 2024-07-19 doi:10.1101/2024.07.16.603788 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Reward history guides attentional selection in whisker somatosensory (S1) cortex ]]> https://biorxiv.org/content/10.1101/2024.07.17.603927v1?rss=1 Ramamurthy, D. Rodriguez, L. Cen, C. Li, S. Chen, A. Feldman, D. E. 2024-07-21 doi:10.1101/2024.07.17.603927 Cold Spring Harbor Laboratory Press 2024-07-21 <![CDATA[ Self-avoidance dominates the selection of hippocampal replay ]]> https://biorxiv.org/content/10.1101/2024.07.18.604185v1?rss=1 Mallory, C. S. Widloski, J. Foster, D. J. 2024-07-21 doi:10.1101/2024.07.18.604185 Cold Spring Harbor Laboratory Press 2024-07-21 <![CDATA[ Advances in Estimating Level-1 Phylogenetic Networks from Unrooted SNPs ]]> https://biorxiv.org/content/10.1101/2024.07.19.604386v1?rss=1 Warnow, T. Tabatabaee, Y. Evans, S. N. 2024-07-23 doi:10.1101/2024.07.19.604386 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Synapse protein signatures in cerebrospinal fluid and plasma predict cognitive maintenance versus decline in Alzheimers disease ]]> https://biorxiv.org/content/10.1101/2024.07.22.604680v1?rss=1 Oh, H. S.-H. Urey, D. Y. Karlsson, L. Zhu, Z. Shen, Y. Farinas, A. Timsina, J. Guldner, I. H. Morshed, N. Yang, C. Western, D. Ali, M. Le Guen, Y. Trelle, A. Herukka, S.-K. Rauramaa, T. Hiltunen, M. Lipponen, A. Luikku, A. J. Poston, K. L. Mormino, E. Wagner, A. D. Wilson, E. N. Channappa, D. Leinonen, V. Stevens, B. Ehrenberg, A. J. Zetterberg, H. Bennett, D. A. Franzmeier, N. Hansson, O. Cruchaga, C. Wyss-Coray, T. 2024-07-23 doi:10.1101/2024.07.22.604680 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Mechanism-guided engineering of a minimal biological particle for genome editing ]]> https://biorxiv.org/content/10.1101/2024.07.23.604809v1?rss=1 Ngo, W. Peukes, J. T. Baldwin, A. Xue, Z. W. Hwang, S. Stickels, R. R. Lin, Z. Satpathy, A. Wells, J. A. Schekman, R. Nogales, E. Doudna, J. A. 2024-07-24 doi:10.1101/2024.07.23.604809 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Eco-evolutionary dynamics of pathogen immune-escape: deriving a population-level phylodynamic curve ]]> https://biorxiv.org/content/10.1101/2024.07.23.604819v1?rss=1 Nielsen, B. F. Saad-Roy, C. M. Metcalf, C. J. E. Viboud, C. Grenfell, B. T. 2024-07-24 doi:10.1101/2024.07.23.604819 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae. ]]> https://biorxiv.org/content/10.1101/2024.07.24.605010v1?rss=1 Duenas, M. A. Craig, R. J. Gallaher, S. D. Moseley, J. L. Merchant, S. S. 2024-07-25 doi:10.1101/2024.07.24.605010 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ Spindle morphology changes between meiosis and mitosis driven by CK2 regulation of the Ran pathway ]]> https://biorxiv.org/content/10.1101/2024.07.25.605073v1?rss=1 Cantwell, H. Nguyen, H. Kettenbach, A. Heald, R. 2024-07-25 doi:10.1101/2024.07.25.605073 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ Eco-evolutionary consequences of selective exploitation on metapopulations illustrated with Atlantic salmon ]]> https://biorxiv.org/content/10.1101/2024.07.25.605173v1?rss=1 Lamarins, A. Carlson, S. M. Prevost, E. Satterthwaite, W. H. Buoro, M. 2024-07-25 doi:10.1101/2024.07.25.605173 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ In vivo analysis of the relationship between CP26 and qE-type NPQ via higher-order Arabidopsis cp26 mutants ]]> https://biorxiv.org/content/10.1101/2024.07.26.605339v1?rss=1 Kromdijk, J. Walter, J. Patel-Tupper, D. Lam, L. Ma, A. Taylor, G. Fleming, G. Niyogi, K. K. 2024-07-26 doi:10.1101/2024.07.26.605339 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ Proteomic Profiling Reveals Age-Related Changes in Transporter Proteins in the Human Blood-Brain Barrier ]]> https://biorxiv.org/content/10.1101/2024.07.26.604313v1?rss=1 Zhou, X. Azimi, M. Handin, N. Riselli, A. Vora, B. Chun, E. Yee, S. W. Artursson, P. Giacomini, K. M. 2024-07-27 doi:10.1101/2024.07.26.604313 Cold Spring Harbor Laboratory Press 2024-07-27 <![CDATA[ Active Learning-Assisted Directed Evolution ]]> https://biorxiv.org/content/10.1101/2024.07.27.605457v1?rss=1 Yang, J. Lal, R. G. Bowden, J. C. Astudillo, R. Hameedi, M. A. Kaur, S. Hill, M. Yue, Y. Arnold, F. H. 2024-07-28 doi:10.1101/2024.07.27.605457 Cold Spring Harbor Laboratory Press 2024-07-28 <![CDATA[ The nuclear-cytoplasmic ratio controls the cell cycle period in compartmentalized frog egg extract ]]> https://biorxiv.org/content/10.1101/2024.07.28.605512v1?rss=1 Pineros, L. Frolov, N. Ruiz-Reynes, D. Van Eynde, A. Cavin-Meza, G. J. Heald, R. Gelens, L. 2024-07-29 doi:10.1101/2024.07.28.605512 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Nonenzymatic, prebiotic aminoacylation couples chirality of RNA and protein ]]> https://biorxiv.org/content/10.1101/2024.07.29.605638v1?rss=1 Davisson, J. A. Kalb, E. M. Knudson, I. J. Schepartz, A. Engelhart, A. E. Adamala, K. 2024-07-29 doi:10.1101/2024.07.29.605638 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Complete sequencing of ape genomes ]]> https://biorxiv.org/content/10.1101/2024.07.31.605654v1?rss=1 Yoo, D. Rhie, A. Hebbar, P. Antonacci, F. Logsdon, G. A. Solar, S. J. Antipov, D. Pickett, B. D. Safonova, Y. Montinaro, F. Luo, Y. Malukiewicz, J. Storer, J. M. Lin, J. Sequeira, A. N. Mangan, R. J. Hickey, G. Anez, G. M. Balachandran, P. Bankevich, A. Beck, C. R. Biddanda, A. Borchers, M. Bouffard, G. G. Brannan, E. Brooks, S. Y. Carbone, L. Carrel, L. Chan, A. P. Crawford, J. Diekhans, M. Engelbrecht, E. Feschotte, C. Formenti, G. Garcia, G. H. Gennaro, L. d. Gilbert, D. Green, R. E. Guarracino, A. Gupta, I. Haddad, D. Han, J. Harris, R. S. Hartley 2024-07-31 doi:10.1101/2024.07.31.605654 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Discrete protein condensation events govern calcium signal dynamics in T cells ]]> https://biorxiv.org/content/10.1101/2024.07.31.606035v1?rss=1 Morita, S. O'Dair, M. K. Groves, J. T. 2024-07-31 doi:10.1101/2024.07.31.606035 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Perceived and observed biases within scientific communities: a case study in movement ecology ]]> https://biorxiv.org/content/10.1101/2024.07.29.605602v1?rss=1 Shaw, A. K. Fouda, L. Mezzini, S. Kim, D. Chatterjee, N. Wolfson, D. Abrahms, B. Attias, N. Beardsworth, C. E. Beltran, R. Binning, S. A. Blincow, K. M. Chan, Y.-C. Fronhofer, E. A. Hegemann, A. Hurme, E. R. Iannarilli, F. Kellner, J. B. McCoy, K. D. Rafiq, K. Saastamoinen, M. Sequeira, A. M. M. Serota, M. W. Sumasgutner, P. Tao, Y. Torstenson, M. Yanco, S. W. Beck, K. B. Bertram, M. G. Beumer, L. T. Bradaric, M. Clermont, J. Ellis-Soto, D. Faltusova, M. Fieberg, J. Hall, R. J. Kolzsch, A. Lai, S. Lee-Cruz, L. Loretto, M.-C. Loveridge, A. Michelangeli, 2024-08-02 doi:10.1101/2024.07.29.605602 Cold Spring Harbor Laboratory Press 2024-08-02 <![CDATA[ Prevalence of the Calvin-Benson-Bassham cycle in chemolithoautotrophic psychrophiles and the potential for cold-adapted Rubisco ]]> https://biorxiv.org/content/10.1101/2024.08.01.606197v1?rss=1 Harrison, K. Rapp, J. Z. Jaffe, A. L. Deming, J. W. Young, J. 2024-08-02 doi:10.1101/2024.08.01.606197 Cold Spring Harbor Laboratory Press 2024-08-02 <![CDATA[ Activated Interferon Signaling Suppresses Age-Dependent Liver Cancer ]]> https://biorxiv.org/content/10.1101/2024.07.31.606057v1?rss=1 Havas, A. Lande, K. Rajesh, A. Evensen, K. G. Varanasi, S. K. Shang, L. Schmidt, E. Lee, J. Kim, K. Teneche, M. G. Hoffmann, F. LaPorte, M. Davis, A. Grier, A. Reisz, J. A. Tharp, K. Gandhi, A. Lei, X. Proulx, J. Miller, K. N. Sacco, A. Shadel, G. S. Niedernhofer, L. Feng, G.-S. D'Alesssandro, A. Kaech, S. Williams, A. Adams, P. D. 2024-08-03 doi:10.1101/2024.07.31.606057 Cold Spring Harbor Laboratory Press 2024-08-03 <![CDATA[ Field conditions greatly modify a major growth-defense tradeoff in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2024.08.15.607984v1?rss=1 Lundberg, D. S. Kersten, S. Mehmetoglu Boz, E. Pramoj Na Ayutthaya, P. Zhu, W. Poersch, K. Yuan, W. Swartz, S. Müller, D. Bezrukov, I. Harvest Team, Weigel, D. 2024-08-15 doi:10.1101/2024.08.15.607984 Cold Spring Harbor Laboratory Press 2024-08-15 <![CDATA[ Multipartite complexity of the lichen symbiosis revealed by metagenome and transcriptome analysis of Xanthoria parietina ]]> https://biorxiv.org/content/10.1101/2024.08.16.608140v1?rss=1 Tagirdzhanova, G. Scharnagl, K. Sahu, N. Yan, X. Bucknell, A. Bentham, A. R. Jegousse, C. Ament-Velasquez, S. L. Brännström, I. O. Johannesson, H. MacLean, D. Talbot, N. J. 2024-08-17 doi:10.1101/2024.08.16.608140 Cold Spring Harbor Laboratory Press 2024-08-17 <![CDATA[ Seeing the Future: Anticipatory Eye Gaze as a Marker of Memory ]]> https://biorxiv.org/content/10.1101/2024.08.14.607869v1?rss=1 Yamin, D. Schmidig, F. J. Sharon, O. Nadu, Y. Nir, J. Ranganath, C. Nir, Y. 2024-08-19 doi:10.1101/2024.08.14.607869 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Insect size responses to climate changes vary across elevations according to seasonal timing ]]> https://biorxiv.org/content/10.1101/2024.08.15.608059v1?rss=1 Nufio, C. Sheffer, M. Smith, J. Troutman, M. Bawa, S. Taylor, E. Schoville, S. Williams, C. Buckley, L. 2024-08-19 doi:10.1101/2024.08.15.608059 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ The glycolytic reaction PGAM unexpectedly restrains Th17 pathogenicity and Th17-dependent autoimmunity ]]> https://biorxiv.org/content/10.1101/2024.08.18.607992v1?rss=1 Wang, C. Wagner, A. Fessler, J. DeTomaso, D. Zaghouani, S. Zhou, Y. Pierce, K. Sobel, R. A. Clish, C. Yosef, N. Kuchroo, V. K. 2024-08-19 doi:10.1101/2024.08.18.607992 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Protection of the Telomeric Junction by the Shelterin Complex ]]> https://biorxiv.org/content/10.1101/2024.08.18.608453v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@a58e79org.highwire.dtl.DTLVardef@12cb172org.highwire.dtl.DTLVardef@135bf40org.highwire.dtl.DTLVardef@19f3fe4_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Shiekh, S. Feldt, D. Jack, A. Kodikara, S. Alfehaid, J. Pasha, S. Yildiz, A. Balci, H. 2024-08-19 doi:10.1101/2024.08.18.608453 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Network influence determines the impact of cortical ensembles on stimulus detection ]]> https://biorxiv.org/content/10.1101/2024.08.18.608496v1?rss=1 Bounds, H. A. Adesnik, H. 2024-08-19 doi:10.1101/2024.08.18.608496 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Dissecting the oncogenic mechanisms of POT1 cancer mutations through deep scanning mutagenesis ]]> https://biorxiv.org/content/10.1101/2024.08.19.608636v1?rss=1 Martin, A. Schabort, J. Bartke-Croughan, R. Tran, S. Preetham, A. Lu, R. Ho, R. Gao, J. Jenkins, S. Boyle, J. Ghanim, G. E. Jagota, M. Song, Y. S. Li, H. Hockemeyer, D. 2024-08-19 doi:10.1101/2024.08.19.608636 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Validation of a Microfluidic Device Prototype for Cancer Detection and Identification: Circulating Tumor Cells Classification Based on Cell Trajectory Analysis Leveraging Cell-Based Modeling and Machine Learning ]]> https://biorxiv.org/content/10.1101/2024.08.19.608572v1?rss=1 Rejuan, R. Aulisa, E. Li, W. Thompson, T. Kumar, S. Canic, S. Wang, Y. 2024-08-20 doi:10.1101/2024.08.19.608572 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ The Rickettsia actin-based motility effectors RickA and Sca2 contribute differently to cell-to-cell spread and pathogenicity ]]> https://biorxiv.org/content/10.1101/2024.08.20.608656v1?rss=1 Tran, C. J. Zubair-Nizami, Z. B. Langohr, I. M. Welch, M. D. 2024-08-20 doi:10.1101/2024.08.20.608656 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ A toolbox of FRET-based c-di-GMP biosensors and its FRET-To-Sort application for genome-wide mapping of the second messenger regulatory network ]]> https://biorxiv.org/content/10.1101/2024.08.21.609041v1?rss=1 Wang, L. Malengo, G. Medeiros, A. S. Chen, X. Teteneva, N. Gonzalez, S. S. Hammond, M. Sourjik, V. 2024-08-21 doi:10.1101/2024.08.21.609041 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Olfactory receptor coexpression and co-option in the dengue mosquito ]]> https://biorxiv.org/content/10.1101/2024.08.21.608847v1?rss=1 Adavi, E. D. dos Anjos, V. L. Kotb, S. Metz, H. C. Tian, D. Zhao, Z. Zung, J. L. Rose, N. H. McBride, C. S. 2024-08-22 doi:10.1101/2024.08.21.608847 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ GeneDrive.jl: A decision tool to optimize vector-borne disease management planning under climate change ]]> https://biorxiv.org/content/10.1101/2024.08.23.609480v1?rss=1 Vasquez, V. N. Mordecai, E. A. Anthoff, D. 2024-08-26 doi:10.1101/2024.08.23.609480 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Single-molecule diffusivity quantification in Xenopus egg extracts elucidates physicochemical properties of the cytoplasm ]]> https://biorxiv.org/content/10.1101/2024.08.24.609541v1?rss=1 Choi, A. Zhou, C. Y. Tabo, A. Heald, R. Xu, K. 2024-08-26 doi:10.1101/2024.08.24.609541 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ AI-based Prediction of Protein Corona Composition on DNA Nanostructures ]]> https://biorxiv.org/content/10.1101/2024.08.25.609594v1?rss=1 Huzar, J. Coreas, R. Landry, M. P. Tikhomirov, G. 2024-08-26 doi:10.1101/2024.08.25.609594 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Neuronal heterogeneity in the medial septum and diagonal band of Broca: classes and continua ]]> https://biorxiv.org/content/10.1101/2024.08.27.609593v1?rss=1 Kuhn, F. Mocellin, P. Pupe, S. Cembrowski, M. S. Remy, S. 2024-08-28 doi:10.1101/2024.08.27.609593 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Marine spatial planning to enhance coral adaptive potential ]]> https://biorxiv.org/content/10.1101/2024.08.27.609972v1?rss=1 Forrest, D. L. McManus, L. C. Tekwa, E. W. Schindler, D. E. Colton, M. A. Webster, M. M. Fox, H. E. Essington, T. E. Palumbi, S. R. Mumby, P. J. DeFilippo, L. Schill, S. R. Pollock, F. J. Pinsky, M. 2024-08-28 doi:10.1101/2024.08.27.609972 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining ]]> https://biorxiv.org/content/10.1101/2024.08.27.610007v1?rss=1 Prillo, S. An, K. Wu, W. Kristanto, I. Jones, M. G. Song, Y. S. Yosef, N. 2024-08-28 doi:10.1101/2024.08.27.610007 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Reconstitution of BNIP3/NIX-mediated autophagy reveals two pathways and hierarchical flexibility of the initiation machinery ]]> https://biorxiv.org/content/10.1101/2024.08.28.609967v1?rss=1 Adriaenssens, E. Schaar, S. Cooke, A. S. I. Stuke, J. F. M. Sawa-Makarska, J. Nguyen, T. N. Ren, X. Schuschnig, M. Romanov, J. Khuu, G. Lazarou, M. Hummer, G. Hurley, J. H. Martens, S. 2024-08-28 doi:10.1101/2024.08.28.609967 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Brain Charts for the Rhesus Macaque Lifespan ]]> https://biorxiv.org/content/10.1101/2024.08.28.610193v1?rss=1 Alldritt, S. Ramirez, J. S. B. Vos de Wael, R. Bethlehem, R. Seidlitz, J. Wang, Z. Nenning, K.-H. Esper, N. B. Smallwood, J. Franco, A. R. Byeon, K. Alexander-Bloch, A. Messinger, A. Chen, A. Thiele, A. Weiss, A. R. Shmuel, A. Fox, A. Tusche, A. Brambrink, A. M. Falchier, A. Hiba, B. Jarraya, B. Jung, B. Butler, B. Russ, B. E. Howell, B. R. Drzewiecki, C. M. Guedj, C. Schwiedrzik, C. M. Amiez, C. Wilson, C. R. E. Klink, C. Kroenke, C. Constantinidis, C. Garin, C. M. Poirier, C. Gale, D. J. Leopold, D. A. Rudko, D. A. Amaral, D. G. Tsao, D. Cook, D. J. 2024-08-30 doi:10.1101/2024.08.28.610193 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ De novo design of Ras isoform selective binders ]]> https://biorxiv.org/content/10.1101/2024.08.29.610300v1?rss=1 Zhang, J. Z. Li, X. Liu, C. Jiang, H. Wu, K. Baker, D. 2024-08-30 doi:10.1101/2024.08.29.610300 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Deciphering regulation of FOXP3 expression in human conventional T cells ]]> https://biorxiv.org/content/10.1101/2024.08.30.610436v1?rss=1 Umhoefer, J. M. Arce, M. M. Dajani, R. Belk, J. A. Mowery, C. T. Nguyen, V. Gowen, B. G. Simeonov, D. R. Curie, G. L. Corn, J. E. Chang, H. Y. Marson, A. 2024-09-02 doi:10.1101/2024.08.30.610436 Cold Spring Harbor Laboratory Press 2024-09-02 <![CDATA[ Spatial Heterogeneity of Climate Fluctuations Shapes Ecological Processes and Community Dynamics in Riverine Invertebrates Across a Landscape ]]> https://biorxiv.org/content/10.1101/2024.08.30.610482v1?rss=1 Lin, X. Wan, J. Luo, Q. Cai, Q. Chiu, M.-C. Resh, V. H. 2024-09-02 doi:10.1101/2024.08.30.610482 Cold Spring Harbor Laboratory Press 2024-09-02 <![CDATA[ A hybrid approach to invertebrate biomonitoring using computer vision and DNA metabarcoding ]]> https://biorxiv.org/content/10.1101/2024.09.02.610558v1?rss=1 Blair, J. D. Weiser, M. D. Siler, C. D. Kaspari, M. Smith, S. N. McLaughlin, J. F. Marshall, K. E. 2024-09-03 doi:10.1101/2024.09.02.610558 Cold Spring Harbor Laboratory Press 2024-09-03 <![CDATA[ Decoupling Coldness and Softness in Tactile Wetness Perception Using Tunable Hydrogels ]]> https://biorxiv.org/content/10.1101/2024.09.03.611060v1?rss=1 Becerra, L. L. Root, N. Clark, A. Rafeedi, T. Brown, W. Chen, A. X. Qie, Y. Blau, R. Miller, J. Kapadia, K. Ng, T. N. Rouw, R. Lipomi, D. J. 2024-09-05 doi:10.1101/2024.09.03.611060 Cold Spring Harbor Laboratory Press 2024-09-05 <![CDATA[ Calpains Orchestrate Secretion of Annexin-containing Microvesicles during Membrane Repair ]]> https://biorxiv.org/content/10.1101/2024.09.05.611512v1?rss=1 Williams, J. K. Ngo, J. M. Murugupandiyan, A. Croall, D. E. Hartzell, H. C. Schekman, R. 2024-09-07 doi:10.1101/2024.09.05.611512 Cold Spring Harbor Laboratory Press 2024-09-07 <![CDATA[ Fuzzy ripple artifact in high resolution fMRI: identification, cause, and mitigation ]]> https://biorxiv.org/content/10.1101/2024.09.04.611294v1?rss=1 Huber, L. Stirnberg, R. Morgan, A. T. Feinberg, D. Ehses, P. Gulban, O. F. Koiso, K. Gephart, I. Swegle, S. Wardle, S. G. Persichetti, A. Beckett, A. Stoecker, T. Boulant, N. Poser, B. Bandettini, P. 2024-09-09 doi:10.1101/2024.09.04.611294 Cold Spring Harbor Laboratory Press 2024-09-09 <![CDATA[ High-quality peptide evidence for annotating non-canonical open reading frames as human proteins ]]> https://biorxiv.org/content/10.1101/2024.09.09.612016v1?rss=1 Deutsch, E. W. Kok, L. W. Mudge, J. M. Ruiz-Orera, J. Fierro-Monti, I. Sun, Z. Abelin, J. G. Alba, M. M. Aspden, J. L. Bazzini, A. A. Bruford, E. Brunet, M. A. Calviello, L. Carr, S. A. Carvunis, A.-R. Chothani, S. Clauwaert, J. Dean, K. Faridi, P. Frankish, A. Hubner, N. Ingolia, N. Magrane, M. Martin, M. J. Martinez, T. F. Menschaert, G. Ohler, U. Orchard, S. Rackham, O. Roucou, X. Slavoff, S. A. Valen, E. Wacholder, A. C. Weissman, J. S. Wu, W. Xie, Z. Choudhary, J. Bassani-Sternberg, M. Vizcaino, J. A. Ternette, N. Moritz, R. L. Prensner, J. van He 2024-09-09 doi:10.1101/2024.09.09.612016 Cold Spring Harbor Laboratory Press 2024-09-09 <![CDATA[ Exploring the sequence and structural determinants of the energy landscape from thermodynamically stable and kinetically trapped subtilisins: ISP1 and SbtE ]]> https://biorxiv.org/content/10.1101/2024.09.08.611919v1?rss=1 Hood, M. R. Marqusee, S. 2024-09-10 doi:10.1101/2024.09.08.611919 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ Optimized expansion microscopy reveals species-specific spindle microtubule organization in Xenopus egg extracts ]]> https://biorxiv.org/content/10.1101/2024.09.11.612005v1?rss=1 Guilloux, G. Kitaoka, M. Mocaer, K. Heichette, C. Duchesne, L. Heald, R. Pecot, T. Gibeaux, R. 2024-09-11 doi:10.1101/2024.09.11.612005 Cold Spring Harbor Laboratory Press 2024-09-11 <![CDATA[ Identification of Proteins Influencing CRISPR-Associated Transposases for Enhanced Genome Editing ]]> https://biorxiv.org/content/10.1101/2024.09.11.612086v1?rss=1 View larger version (13K): org.highwire.dtl.DTLVardef@12609e5org.highwire.dtl.DTLVardef@53a128org.highwire.dtl.DTLVardef@794e63org.highwire.dtl.DTLVardef@9835f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Song, L. Alker, A. T. P. Oromi-Bosch, A. Swartz, S. E. Martinson, J. N. V. Arora, J. Wang, A. M. Rovinsky, R. Smith, S. J. Pierce, E. C. Deutschbauer, A. M. Doudna, J. A. Cress, B. F. Rubin, B. E. 2024-09-11 doi:10.1101/2024.09.11.612086 Cold Spring Harbor Laboratory Press 2024-09-11 <![CDATA[ Synapse-to-synapse plasticity variability balanced to generate input-wide constancy of transmitter release ]]> https://biorxiv.org/content/10.1101/2024.09.11.612562v1?rss=1 Aghi, K. Schultz, R. Newman, Z. L. Mendonca, P. Bakshinska, D. Isacoff, E. Y. 2024-09-12 doi:10.1101/2024.09.11.612562 Cold Spring Harbor Laboratory Press 2024-09-12 <![CDATA[ Context-Seq: CRISPR-Cas9 Targeted Nanopore Sequencing for Transmission Dynamics of Antimicrobial Resistance ]]> https://biorxiv.org/content/10.1101/2024.09.12.612745v1?rss=1 Fuhrmeister, E. R. Kim, S. Mairal, S. A. McCormack, C. Chieng, B. Swarthout, J. M. Paulos, A. H. Njenga, S. M. Pickering, A. J. 2024-09-12 doi:10.1101/2024.09.12.612745 Cold Spring Harbor Laboratory Press 2024-09-12 <![CDATA[ Attentional Information Routing in The Human Brain ]]> https://biorxiv.org/content/10.1101/2024.09.11.612548v1?rss=1 Boroujeni, K. B. Helfrich, R. F. Fiebelkorn, I. C. Bentley, N. Lin, J. J. Knight, R. T. Kastner, S. 2024-09-15 doi:10.1101/2024.09.11.612548 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Mindfulness-based Neurofeedback: A Systematic Review of EEG and fMRI studies ]]> https://biorxiv.org/content/10.1101/2024.09.12.612669v1?rss=1 Treves, I. N. Greene, K. D. Bajwa, Z. Wool, E. Kim, N. Bauer, C. C. Bloom, P. A. Pagliaccio, D. Zhang, J. Whitfield-Gabrieli, S. Auerbach, R. P. 2024-09-15 doi:10.1101/2024.09.12.612669 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Spatial microenvironments tune immune response dynamics in the Drosophila larval fat body ]]> https://biorxiv.org/content/10.1101/2024.09.12.612587v1?rss=1 Schlomann, B. H. Pai, T.-W. Sandhu, J. Ferrer Imbert, G. Graham, T. G. W. Garcia, H. G. 2024-09-16 doi:10.1101/2024.09.12.612587 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ The global spectrum of tree crown architecture ]]> https://biorxiv.org/content/10.1101/2024.09.14.613032v1?rss=1 500,000 globally distributed trees, we explored how climate, disturbance, competition, functional traits, and evolutionary history constrain the height, crown size and shape of the worlds tree species. We found that variation in height scaling relationships was primarily controlled by water availability and light competition. Conversely, crown width was predominantly shaped by exposure to wind and fire, while also covarying with other functional traits related to mechanical stability and photosynthesis. Additionally, several plant lineages had crown architectures that defy their environments, such as the exceedingly slender dipterocarps of Southeast Asia, or the extremely wide crowns of legumes in African savannas. Our study charts the global spectrum of tree crown architectural types. It provides a roadmap for integrating crown architecture with vegetation models and remote sensing observations, so that we may better understand the processes that shape the 3D structure of woody ecosystems. ]]> Jucker, T. Fischer, F. Chave, J. Coomes, D. Caspersen, J. Ali, A. Panzou, G. Feldpausch, T. Falster, D. Usoltsev, V. Jackson, T. Adu-Bredu, S. Alves, L. Aminpour, M. Angoboy, I. Anten, N. Antin, C. Askari, Y. Munoz, R. Ayyappan, N. Banin, L. Barbier, N. Battles, J. Beeckman, H. Bocko, Y. Bond-Lamberty, B. Bongers, F. Bowers, S. Breugel, M. Chantrain, A. Chaudhary, R. Dai, J. Dalponte, M. Dimobe, K. Domec, J.-C. Doucet, J.-L. Dupuy-Rada, J. Duursma, R. Enriquez, M. Ewijk, K. Farfan-Rios, W. Fayolle, A. Ferretti, M. Forni, E. Forrester, D. Gilani, H. 2024-09-17 doi:10.1101/2024.09.14.613032 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ A dopaminergic basis of behavioral control ]]> https://biorxiv.org/content/10.1101/2024.09.17.613524v1?rss=1 Ballard, I. C. Furman, D. J. Berry, A. S. White, R. L. Jagust, W. J. Kayser, A. S. D'Esposito, M. 2024-09-17 doi:10.1101/2024.09.17.613524 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ Lateral prefrontal cortex controls interplay between working memory and actions ]]> https://biorxiv.org/content/10.1101/2024.09.17.613601v1?rss=1 Kiyonaga, A. Miller, J. D'Esposito, M. 2024-09-18 doi:10.1101/2024.09.17.613601 Cold Spring Harbor Laboratory Press 2024-09-18 <![CDATA[ Molecular Magnetic Resonance Imaging of Dysregulated Zinc Secretion Detects Early Pancreatic Ductal Adenocarcinoma Lesions and Response to KRASG12D Inhibitor Treatment ]]> https://biorxiv.org/content/10.1101/2024.09.15.613145v1?rss=1 Jordan, V. C. Sojoodi, M. Moloudi, F. Pagan, P. G. Jin, M. Pantazopoulos, P. French, E. Weigand-Whittier, J. Rotile, N. Tavallai, M. Hallin, J. Ramsay, I. Gale, E. M. Barrett, S. Bardeesy, N. Qadan, M. Tanabe, K. Caravan, P. 2024-09-19 doi:10.1101/2024.09.15.613145 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Lateralized cerebellar connectivity differentiates auditory pathways in echolocating and non-echolocating whales ]]> https://biorxiv.org/content/10.1101/2024.09.18.609772v1?rss=1 Flem, S. A. Berns, G. Inglis, B. Niederhut, D. Montie, E. Deacon, T. Miller, K. L. Tyack, P. Cook, P. F. 2024-09-19 doi:10.1101/2024.09.18.609772 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Role of copper during microglial inflammation ]]> https://biorxiv.org/content/10.1101/2024.09.18.613750v1?rss=1 Craciun, L. Muroy, S. E. Saijo, K. 2024-09-19 doi:10.1101/2024.09.18.613750 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Calibration of additional computational tools expands ClinGen recommendation options for variant classification with PP3/BP4 criteria ]]> https://biorxiv.org/content/10.1101/2024.09.17.611902v1?rss=1 Bergquist, T. Stenton, S. L. Nadeau, E. A. W. Byrne, A. B. Greenblatt, M. S. Harrison, S. M. Tavtigian, S. V. O'Donnell-Luria, A. Biesecker, L. G. Radivojac, P. Brenner, S. E. Pejaver, V. ClinGen Sequence Variant Interpretation Working Group, 2024-09-21 doi:10.1101/2024.09.17.611902 Cold Spring Harbor Laboratory Press 2024-09-21 <![CDATA[ Physiologically based demographic model/GIS analyses of thirteen invasive species in Africa: why the biology matters ]]> https://biorxiv.org/content/10.1101/2024.09.17.613432v1?rss=1 Gutierrez, A. P. Ponti, L. Neteler, M. Cure, J. R. Kenmore, P. E. Simmons, G. 2024-09-21 doi:10.1101/2024.09.17.613432 Cold Spring Harbor Laboratory Press 2024-09-21 <![CDATA[ Truncated Complement Factor H Y402 Gene Therapy Cures C3 Glomerulonephritis ]]> https://biorxiv.org/content/10.1101/2024.09.17.613471v1?rss=1 Chew, L. A. Grigsby, D. Hester, C. G. Amason, J. McPherson, W. K. Flynn, E. J. Visel, M. Flannery, J. G. Bowes Rickman, C. 2024-09-21 doi:10.1101/2024.09.17.613471 Cold Spring Harbor Laboratory Press 2024-09-21 <![CDATA[ A novel method for characterizing cell-cell interactions at single-cell resolution reveals unique signatures in blood T cell-monocyte complexes during infection ]]> https://biorxiv.org/content/10.1101/2024.09.20.612103v1?rss=1 View larger version (17K): org.highwire.dtl.DTLVardef@f90023org.highwire.dtl.DTLVardef@178007corg.highwire.dtl.DTLVardef@167e53corg.highwire.dtl.DTLVardef@1faff48_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kang, N. Chawla, A. Hillman, H. Tippalagama, R. Kim, C. Mikulski, Z. Seumois, G. Vijayanand, P. Scriba, T. J. De Silva, A. D. Balmaseda, A. Harris, E. Weiskopf, D. Sette, A. Lindestam Arlehman, C. Peters, B. Burel, J. G. 2024-09-23 doi:10.1101/2024.09.20.612103 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ Quantifying Data Distortion in Bar Graphs in Biological Research ]]> https://biorxiv.org/content/10.1101/2024.09.20.609464v1?rss=1 Lin, T.-J. Landry, M. P. 2024-09-24 doi:10.1101/2024.09.20.609464 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Small mammals and their burrows shape the distribution of Coccidioides in soils: a long-term ecological experiment ]]> https://biorxiv.org/content/10.1101/2024.09.21.613892v1?rss=1 Head, J. R. Camponuri, S. K. Weaver, A. K. Montoya, L. Lee, E. Radosevich, M. T. Jones, I. Wagner, R. Bhattachan, A. Campbell, G. Keeney, N. Collender, P. A. Heaney, A. K. Couper, L. Colvin, K. A. Larios, L. Bean, W. T. Taylor, J. Remais, J. V. 2024-09-24 doi:10.1101/2024.09.21.613892 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Super-enhancer profiling reveals ThPOK/ZBTB7B, a CD4+ cell lineage commitment factor, as a master regulator that restricts breast cancer cells to a luminal non-migratory phenotype ]]> https://biorxiv.org/content/10.1101/2024.09.21.614267v1?rss=1 Arcuschin, C. D. Kahrizi, K. Sayaman, R. W. DiBenedetto, C. Shen, Y. Salaberry, P. J. Zakroui, O. Schwarzer, C. Scapozza, A. Betancur, P. Saba, J. D. Coppe, J.-P. Barcellos-Hoff, M. H. Kappes, D. van 't Veer, L. Schor, I. E. Munoz, D. P. 2024-09-24 doi:10.1101/2024.09.21.614267 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ A curated collection of transcriptome datasets to study the transcriptional response in blood and nasal samples following viral respiratory inoculation and vaccination ]]> https://biorxiv.org/content/10.1101/2024.09.23.614262v1?rss=1 Lan, Z. Zhang, T. Zhang, Y. Sun, X. Liu, C. Liu, P. Tang, M. Fu, M. Hagood, J. S. Pickles, R. J. Zou, F. Zheng, X. 2024-09-24 doi:10.1101/2024.09.23.614262 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Comprehensive proteolytic profiling of Aedes aegypti mosquito midgut extracts: Unraveling the blood meal protein digestion system ]]> https://biorxiv.org/content/10.1101/2024.09.23.614410v1?rss=1 O'Donoghue, A. J. Lui, C. Simington, C. J. Montermoso, S. Moreno-Galvez, E. Serafim, M. S. M. Burata, O. E. Lucero, R. M. Nguyen, J. T. Fong, D. Tran, K. Millan, N. Gallimore, J. M. Parungao, K. A. Fong, J. Suzuki, B. M. Jiang, Z. Isoe, J. Rascon, A. A. 2024-09-24 doi:10.1101/2024.09.23.614410 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ A toolbox for ablating excitatory and inhibitory synapses ]]> https://biorxiv.org/content/10.1101/2024.09.23.614589v1?rss=1 Bareghamyan, A. Deng, C. Daoudi, S. Nawy, S. Lu, X. Zhang, W. Campbell, R. E. Kramer, R. Chenoweth, D. M. Arnold, D. B. 2024-09-24 doi:10.1101/2024.09.23.614589 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Surface delivery quantification reveals distinct trafficking efficiencies among clustered protocadherin isoforms ]]> https://biorxiv.org/content/10.1101/2024.09.23.614616v1?rss=1 May, E. J. Gaudet, R. 2024-09-24 doi:10.1101/2024.09.23.614616 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ nSMase2-mediated exosome secretion shapes the tumor microenvironment to immunologically support pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2024.09.23.614610v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@b6e6d1org.highwire.dtl.DTLVardef@1ebb41eorg.highwire.dtl.DTLVardef@17e4275org.highwire.dtl.DTLVardef@3d31f1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hendley, A. M. Ashe, S. Urano, A. Ng, M. Phu, T. A. Peng, X. L. Luan, C. Finger, A.-M. Jang, G. H. Kerper, N. R. Berrios, D. I. Jin, D. Lee, J. Riahi, I. R. Gbenedio, O. M. Chung, C. Roose, J. Yeh, J. J. Gallinger, S. Biankin, A. V. OKane, G. M. Ntranos, V. Chang, D. Dawson, D. W. Kim, G. E. Weaver, V. M. Raffai, R. L. Hebrok, M. 2024-09-25 doi:10.1101/2024.09.23.614610 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Fine-tuning sequence-to-expression models onpersonal genome and transcriptome data ]]> https://biorxiv.org/content/10.1101/2024.09.23.614632v1?rss=1 Rastogi, R. Reddy, A. J. Chung, R. Ioannidis, N. M. 2024-09-25 doi:10.1101/2024.09.23.614632 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Oxytocin receptor controls distinct components of pair bonding and development in prairie voles ]]> https://biorxiv.org/content/10.1101/2024.09.25.613753v1?rss=1 Sharma, R. Berendzen, K. M. Everitt, A. Wang, B. Williams, G. Wang, S. Quine, K. Larios, R. D. Long, K. L. P. Hoglen, N. Sulaman, B. A. Heath, M. C. Sherman, M. Kinkel, M. Cai, A. Galo, D. Caamal, L. C. Goodwin, N. L. Beery, A. Bales, K. L. Pollard, K. S. Willsey, A. J. Manoli, D. S. 2024-09-26 doi:10.1101/2024.09.25.613753 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Rewilding alters mouse epigenetic aging ]]> https://biorxiv.org/content/10.1101/2024.09.25.615023v1?rss=1 Zipple, M. N. Zhao, I. Kuo, D. C. Lee, S. M. Sheehan, M. J. Zhou, W. 2024-09-27 doi:10.1101/2024.09.25.615023 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Novel color vision assessment tool: AIM Color Detection and Discrimination ]]> https://biorxiv.org/content/10.1101/2024.09.26.615300v1?rss=1 He, J. Skerswetat, J. Bex, P. J. 2024-09-27 doi:10.1101/2024.09.26.615300 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Characterizing the soil microbial community associated with the fungal pathogen Coccidioides immitis ]]> https://biorxiv.org/content/10.1101/2024.09.27.615053v1?rss=1 Radosevich, M. T. Head, J. R. Couper, L. Weaver, A. K. Camponuri, S. K. Montoya, L. Taylor, J. Remais, J. V. 2024-09-28 doi:10.1101/2024.09.27.615053 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ The Human Neural Cell Atlas of Zika Infection in developing human brain tissue: viralpathogenesis, innate immunity, and lineage reprogramming ]]> https://biorxiv.org/content/10.1101/2024.09.27.615512v1?rss=1 Stokes, C. Whitmore, L. Moreno, D. Malhotra, K. Tisoncik-Go, J. Tran, E. Wren, N. Glass, I. Birth Defects Research Laboratory, Young, J. E. Gale, M. 2024-09-30 doi:10.1101/2024.09.27.615512 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ TRACKing Tandem Repeats: a customizable pipeline for identification and cross-species comparisons ]]> https://biorxiv.org/content/10.1101/2024.09.27.615531v1?rss=1 de Lima Adam, C. Rocha, J. L. Sudmant, P. H. Rohlfs, R. 2024-09-30 doi:10.1101/2024.09.27.615531 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Diploid assembly of the Mexican lime genome reveals extensive heterozygosity ]]> https://biorxiv.org/content/10.1101/2024.09.30.615868v1?rss=1 Leichty, A. Thomson, J. Massaro, I. 2024-10-01 doi:10.1101/2024.09.30.615868 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Sporadic distribution of a new archaeal genetic code with all TAG codons as pyrrolysine ]]> https://biorxiv.org/content/10.1101/2024.09.30.615893v1?rss=1 View larger version (42K): org.highwire.dtl.DTLVardef@f363a5org.highwire.dtl.DTLVardef@112f061org.highwire.dtl.DTLVardef@63ad59org.highwire.dtl.DTLVardef@9eddb_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kivenson, V. Peters, S. L. Borrel, G. Kivenson, A. Roe, L. T. Hamlish, N. X. Fadhlaoui, K. Schepartz, A. Gribaldo, S. Hettich, R. Banfield, J. 2024-10-02 doi:10.1101/2024.09.30.615893 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Efficient Coding in Motor Planning ]]> https://biorxiv.org/content/10.1101/2024.09.30.615975v1?rss=1 Wang, T. Fang, Y. Whitney, D. 2024-10-02 doi:10.1101/2024.09.30.615975 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ A previously reported bottleneck in human ancestry 900 kya is likely a statistical artifact ]]> https://biorxiv.org/content/10.1101/2024.10.01.615851v1?rss=1 Deng, Y. Nielsen, R. Song, Y. S. 2024-10-02 doi:10.1101/2024.10.01.615851 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Rapid two-step target capture ensures efficient CRISPR-Cas9-guided genome editing ]]> https://biorxiv.org/content/10.1101/2024.10.01.616117v1?rss=1 Shi, H. Al-Sayyad, N. Wasko, K. Trinidad, M. I. Doherty, E. E. Vohra, K. Boger, R. S. Colognori, D. Cofsky, J. C. Skopintsev, P. Bryant, Z. Doudna, J. A. 2024-10-02 doi:10.1101/2024.10.01.616117 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Autophosphorylation of the oncogenic protein TEL-ABL confers resistance to the allosteric ABL inhibitor asciminib ]]> https://biorxiv.org/content/10.1101/2024.10.02.616342v1?rss=1 2000-fold less potent against TEL-ABL than BCR-ABL in cell-growth assays. This is surprising because the ABL components of the two fusion proteins, including the asciminib binding sites, have identical sequence. We deleted a short helical segment in the ABL kinase domain that closes over asciminib when it is bound. This deletion results in asciminib resistance in BCR-ABL, but has no effect on TEL-ABL, suggesting that the native autoinhibitory mechanism that asciminib engages in BCR-ABL is disrupted in TEL-ABL. We show, using mammalian cell expression and single-molecule microscopy, that BCR-ABL is mainly dimeric while TEL-ABL forms higher-order oligomers. Oligomerization can promote trans-autophosphorylation of ABL, and we find that a regulatory phosphorylation site in the SH3 domain of ABL (Tyr 89) is highly phosphorylated in TEL-ABL. This phosphorylation is expected to disassemble the autoinhibited conformation of ABL, thereby preventing asciminib binding. We show that TEL-ABL is intrinsically susceptible to inhibition by asciminib, but that increased phosphorylation results in resistance. Our results demonstrate that different ABL fusion proteins can have dramatically different responses to allosteric inhibitors due to differential phosphorylation. One Sentence SummaryWhen TEL-ABL is phosphorylated, it is insensitive to asciminib. However, when TEL-ABL is dephosphorylated by a phosphatase, asciminib sensitivity is restored. ]]> Muratcioglu, S. Eide, C. A. Gorday, K. Sumpena, E. Zuo, W. Groves, J. T. Druker, B. J. Kuriyan, J. 2024-10-02 doi:10.1101/2024.10.02.616342 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ New Statistical Metric for Robust Target Detection in Cryo-EM Using 2DTM ]]> https://biorxiv.org/content/10.1101/2024.10.01.616095v1?rss=1 Zhang, K. Cossio, P. Rangan, A. V. Lucas, B. A. Grigorieff, N. 2024-10-03 doi:10.1101/2024.10.01.616095 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Decreased hippocampal neurite density in middle-aged/aging adults following prenatal exposure to higher levels of maternal inflammation ]]> https://biorxiv.org/content/10.1101/2024.10.01.616156v1?rss=1 Mohyee, R. A. Elliott, B. L. Pike, M. R. Smith, E. Kring, A. M. Olson, I. R. Breen, E. C. Cohn, B. A. Cirillo, P. M. Krigbaum, N. Y. Olino, T. M. D'Esposito, M. Cogan, A. B. Patwardan, B. P. Ellman, L. M. 2024-10-03 doi:10.1101/2024.10.01.616156 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Multi-laboratory Study Establishes Reproducible Methods for Plant-Microbiome Research in Fabricated Ecosystems ]]> https://biorxiv.org/content/10.1101/2024.10.02.615924v1?rss=1 Novak, V. Andeer, P. F. King, E. Calabria, J. Fitzpatrick, C. Kelm, J. M. Wippel, K. Kosina, S. M. Daum, C. Zane, M. Yadav, A. Chen, M. Russ, D. Adams, C. A. Owens, T. K. Lee, B. Ding, Y. Sordo, Z. Chakraborty, R. Roux, S. Deutschbauer, A. M. Ushizima, D. Zengler, K. Arsova, B. Dangl, J. Schulze-Lefert, P. Watt, M. Vogel, J. Northen, T. R. 2024-10-03 doi:10.1101/2024.10.02.615924 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Tissue-specific transcriptomics uncovers novel craniofacial genes underlying jaw divergence in specialist pupfishes ]]> https://biorxiv.org/content/10.1101/2024.10.02.616385v1?rss=1 Palominos, M. F. Muhl, V. Martin, C. H. 2024-10-03 doi:10.1101/2024.10.02.616385 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Dissecting autonomous enzyme variability in single cells ]]> https://biorxiv.org/content/10.1101/2024.10.03.616530v1?rss=1 Gnann, C. Cesnik, A. Sigaeva, A. Le, T. Sariyar, S. Mahdessian, D. Schutten, R. Raghavan, P. Leonetti, M. D. Lindskog, C. Uhlen, M. Axelsson, U. Lundberg, E. 2024-10-04 doi:10.1101/2024.10.03.616530 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Estimating wingbeat frequency on hummingbirds by using a no-labeling learning computer vision approach ]]> https://biorxiv.org/content/10.1101/2024.10.04.616678v1?rss=1 Bastidas-Rodriguez, M. X. Fernandes, A. M. Espejo Uribe, M. J. Abaunza, D. Roncancio, J. S. Gutierrez Zamora, E. A. Florez Pai, C. Smiley, A. Hurme, K. M. Clark, C. J. Rico-Guevara, A. 2024-10-05 doi:10.1101/2024.10.04.616678 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ Cholinergic regulation of sleep in the upside-down jellyfish Cassiopea ]]> https://biorxiv.org/content/10.1101/2024.10.04.616757v1?rss=1 Abrams, M. J. Ohdera, A. H. Francis, D. A. Donayre, O. Chen, H. Lu, K. Y. Harland, R. M. 2024-10-05 doi:10.1101/2024.10.04.616757 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ A shared code for perceiving and imagining objects in human ventral temporal cortex ]]> https://biorxiv.org/content/10.1101/2024.10.05.616828v1?rss=1 Wadia, V. S. Reed, C. M. Chung, J. M. Bateman, L. M. Mamelak, A. N. Rutishauser, U. Tsao, D. Y. 2024-10-06 doi:10.1101/2024.10.05.616828 Cold Spring Harbor Laboratory Press 2024-10-06 <![CDATA[ Odorant receptors tuned to isothiocyanates in Drosophila melanogaster and their evolutionary expansion in herbivorous relatives ]]> https://biorxiv.org/content/10.1101/2024.10.08.617316v1?rss=1 Matsunaga, T. Reisenman, C. E. Goldman-Huertas, B. M. Rajshekar, S. Suzuki, H. C. Tadres, D. Wong, J. Louis, M. Ramirez, S. R. Whiteman, N. K. 2024-10-11 doi:10.1101/2024.10.08.617316 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Activity in the peripheral representation within primate V1 is substantially modulated during running ]]> https://biorxiv.org/content/10.1101/2024.10.10.617723v1?rss=1 Rowley, D. P. Huk, A. C. Yates, J. L. 2024-10-11 doi:10.1101/2024.10.10.617723 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Extensive longevity and DNA virus-driven adaptation in nearctic Myotis bats ]]> https://biorxiv.org/content/10.1101/2024.10.10.617725v1?rss=1 Vazquez, J. M. Lauterbur, M. E. Mottaghinia, S. Bucci, M. Fraser, D. Gray-Sandoval, G. Gaucherand, L. Haidar, Z. R. Han, M. Kohler, W. Lama, T. M. Lecorf, A. Maesen, S. McMillan, D. Li, S. Lo, J. Rey, C. Capel, S. L. Singer, M. Slocum, K. Thomas, W. Debelak Tyburec, J. Santos Villa, S. G. Miller, R. Buchalski, M. Vazquez-Medina, J. P. Pfeffer, S. Etienne, L. Enard, D. Sudmant, P. H. 2024-10-11 doi:10.1101/2024.10.10.617725 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ A Suite of Foundation Models Captures the Contextual Interplay Between Codons ]]> https://biorxiv.org/content/10.1101/2024.10.10.617568v1?rss=1 Naghipourfar, M. Chen, S. Howard, M. Macdonald, C. Saberi, A. Hagen, T. Mofrad, M. Coyote-Maestas, W. Goodarzi, H. 2024-10-13 doi:10.1101/2024.10.10.617568 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ Quiescent cell re-entry is limited by macroautophagy-induced lysosomal damage ]]> https://biorxiv.org/content/10.1101/2024.10.11.617892v1?rss=1 Murley, A. Popovici, A. Hu, X. S. Lund, A. Wickham, K. Durieux, J. Joe, L. Koronyo, E. Dillin, A. 2024-10-13 doi:10.1101/2024.10.11.617892 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ CandyCollect: An Open-Microfluidic Device for the Direct Capture and Enumeration of Salivary-Extracellular Vesicles ]]> https://biorxiv.org/content/10.1101/2024.10.09.617508v1?rss=1 Pierce, C. Suryoraharjo, K. Robertson, I. H. Su, X. Hatchett, D. B. Shin, A. Adams, K. N. Berthier, E. Thongpang, S. Ogata, A. Theberge, A. B. Sohn, L. L. 2024-10-14 doi:10.1101/2024.10.09.617508 Cold Spring Harbor Laboratory Press 2024-10-14 <![CDATA[ PhenoVision: A framework for automating and delivering research-ready plant phenology data from field images ]]> https://biorxiv.org/content/10.1101/2024.10.10.617505v1?rss=1 Dinnage, R. Grady, E. Neal, N. Deck, J. Denny, E. Walls, R. Seltzer, C. Guralnick, R. Li, D. 2024-10-14 doi:10.1101/2024.10.10.617505 Cold Spring Harbor Laboratory Press 2024-10-14 <![CDATA[ Reactive Oxygen Detoxification Contributes to Mycobacterium abscessus Antibiotic Survival ]]> https://biorxiv.org/content/10.1101/2024.10.13.618103v1?rss=1 Bates, N. A. Rodriguez, R. Drwich, R. Ray, A. Stanley, S. A. Penn, B. H. 2024-10-15 doi:10.1101/2024.10.13.618103 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ TRENDY: Gene Regulatory Network Inference Enhanced by Transformer ]]> https://biorxiv.org/content/10.1101/2024.10.14.618189v1?rss=1 Tian, X. Patel, Y. Wang, Y. 2024-10-16 doi:10.1101/2024.10.14.618189 Cold Spring Harbor Laboratory Press 2024-10-16 <![CDATA[ An analysis of RNA quality metrics in human brain tissue ]]> https://biorxiv.org/content/10.1101/2024.10.14.618253v1?rss=1 Tian, J. Lam, T. Ross, S. Ciener, B. Leskinen, S. Sivakumar, S. Bennett, D. A. Menon, V. McKhann, G. M. Runnels, A. Teich, A. 2024-10-17 doi:10.1101/2024.10.14.618253 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Representations of stimulus meaning in the hippocampus ]]> https://biorxiv.org/content/10.1101/2024.10.14.618280v1?rss=1 Biane, J. S. Ladow, M. A. Fan, A. Choi, H. S. Zhou, L. Z. Hassan, S. Apodaca-Montano, D. L. Kwon, A. O. Bratsch-Prince, J. X. Kheirbek, M. A. 2024-10-17 doi:10.1101/2024.10.14.618280 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Epigenetic and 3D genome reprogramming during the aging of human hippocampus ]]> https://biorxiv.org/content/10.1101/2024.10.14.618338v1?rss=1 Zemke, N. Lee, S. Mamde, S. Yang, B. Berchtold, N. Garduno, M. Indralingam, H. Bartosik, W. Lau, P. Dong, K. Yang, A. Tani, Y. Chen, C. Zeng, Q. Ajith, V. Tong, L. Seng, C. Li, D. Wang, T. Xu, X. Ren, B. 2024-10-17 doi:10.1101/2024.10.14.618338 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ HP1a promotes chromatin liquidity and drives spontaneous heterochromatin compartmentalization ]]> https://biorxiv.org/content/10.1101/2024.10.18.618981v1?rss=1 Brennan, L. D. Kim, H.-K. Colmenares, S. Ego, T. Kumar, A. Safran, S. Ryu, J.-K. Karpen, G. 2024-10-18 doi:10.1101/2024.10.18.618981 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Resolving an unconventional non-photochemical quenching signature at the light-to-dark transition ]]> https://biorxiv.org/content/10.1101/2024.10.17.618902v1?rss=1 Lam, L. Patel-Tupper, D. Lam, H. E. Steen, C. J. Ma, A. Ma, S. A. Leipertz, A. Lee, T.-Y. Fleming, G. Niyogi, K. K. 2024-10-21 doi:10.1101/2024.10.17.618902 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ Academic Success and Mental Health: The Paradox of Frontoparietal-Default Mode Network Coupling among Children Facing Poverty ]]> https://biorxiv.org/content/10.1101/2024.10.18.619123v1?rss=1 Pacheco, S. Bunge, S. A. Ellwood-Lowe, M. E. 2024-10-22 doi:10.1101/2024.10.18.619123 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Correlating Disordered Activation Domain Ensembles with Gene Expression Levels ]]> https://biorxiv.org/content/10.1101/2024.10.19.619222v1?rss=1 Flores, E. Camacho, A. Cuevas-Zepeda, E. McCoy, M. B. Yu, F. Staller, M. V. Sukenik, S. 2024-10-22 doi:10.1101/2024.10.19.619222 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Understanding the development of enzalutamide resistance based on a functional single-cell approach ]]> https://biorxiv.org/content/10.1101/2024.10.20.619319v1?rss=1 Xue, C. Ko, H.-K. Shi, K. Pittsenbarger, J. Dao, L. V. Shi, K. Libmann, M. Geng, H. Qian, D. Z. 2024-10-22 doi:10.1101/2024.10.20.619319 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Genetic diversity loss in the Anthropocene will continue long after habitat destruction ends ]]> https://biorxiv.org/content/10.1101/2024.10.21.619096v1?rss=1 Mualim, K. S. Spence, J. P. Weiss, C. L. Selmoni, O. Lin, M. Exposito-Alonso, M. 2024-10-22 doi:10.1101/2024.10.21.619096 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Human Satellite 3 DNA encodes megabase-scale transcription factor binding platforms ]]> https://biorxiv.org/content/10.1101/2024.10.22.616524v1?rss=1 Franklin, J. M. Dubocanin, D. Chittenden, C. Barillas, A. G. Lee, R. J. Ghosh, R. P. Gerton, J. L. Guan, K.-L. Altemose, N. 2024-10-23 doi:10.1101/2024.10.22.616524 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Variable Presence of an Evolutionarily New Brain Structure is Related to Trait Impulsivity ]]> https://biorxiv.org/content/10.1101/2024.10.23.619912v1?rss=1 Willbrand, E. H. Maboudian, S. A. Elliott, M. V. Kellerman, G. M. Johnson, S. L. Weiner, K. S. 2024-10-24 doi:10.1101/2024.10.23.619912 Cold Spring Harbor Laboratory Press 2024-10-24 <![CDATA[ The deubiquitinase Rpn11 functions as an allosteric ubiquitin sensor to promote substrate engagement by the 26S proteasome ]]> https://biorxiv.org/content/10.1101/2024.10.24.620116v1?rss=1 Htet, Z. M. Dong, K. C. Martin, A. 2024-10-24 doi:10.1101/2024.10.24.620116 Cold Spring Harbor Laboratory Press 2024-10-24 <![CDATA[ Too dim, too bright, and just right: Systems analysis of the Chlamydomonas diurnal program upon acclimation to light stress and limitation ]]> https://biorxiv.org/content/10.1101/2024.10.22.618525v1?rss=1 Dupuis, S. Ojeda, V. Gallaher, S. D. Purvine, S. O. Glaesener, A. G. Ponce, R. Nicora, C. D. Bloodsworth, K. Lipton, M. S. Niyogi, K. K. Iwai, M. Merchant, S. S. 2024-10-25 doi:10.1101/2024.10.22.618525 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ The genome assembly of the duckweed fern, Azolla caroliniana ]]> https://biorxiv.org/content/10.1101/2024.10.22.619683v1?rss=1 Song, M. J. Li, F.-W. Freund, F. Escalona, M. Toffelmier, E. Miller, C. Shaffer, H. B. Nguyen, O. Marimuthu, M. P. A. Chumchim, N. Tribble, C. Fairbairn, C. W. Seligmann, W. Rothfels, C. J. 2024-10-25 doi:10.1101/2024.10.22.619683 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Identification of immunogenic and cross-reactive chikungunya virus-specific CD4+ T cell epitopes in chronic chikungunya viral arthritic disease in humans ]]> https://biorxiv.org/content/10.1101/2024.10.22.619717v1?rss=1 Agarwal, R. Ha, C. Cortes, F. H. Lee, Y. Martinez-Perez, A. Galvez, R. Castillo, I. Balmaseda, A. Harris, E. Romero-Vivas, C. M. Lakshmanane, P. Falconar, A. K. Grifoni, A. Sette, A. Weiskopf, D. 2024-10-25 doi:10.1101/2024.10.22.619717 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Biocultural vulnerability of traditional crops in the Indian Trans Himalaya ]]> https://biorxiv.org/content/10.1101/2024.10.22.619747v1?rss=1 Jaggi, H. Anand, A. Solari, K. A. Echeverri, A. Tobge, R. Tsewang, T. Suryawanshi, K. Tuljapurkar, S. D. 2024-10-25 doi:10.1101/2024.10.22.619747 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Learning antibody sequence constraints from allelic inclusion ]]> https://biorxiv.org/content/10.1101/2024.10.22.619760v1?rss=1 Jagota, M. Hsu, C. Mazumder, T. Sung, K. DeWitt, W. S. Listgarten, J. Matsen, F. A. Ye, C. J. Song, Y. S. 2024-10-25 doi:10.1101/2024.10.22.619760 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Imaging synaptic density in ageing and Alzheimer's Disease with -SynVesT-1 ]]> https://biorxiv.org/content/10.1101/2024.10.23.619941v1?rss=1 Giorgio, J. Soleimani-Meigooni, D. N. Janabi, M. Baker, S. Chen, X. Toueg, T. N. Weimer, R. Zinnhardt, B. Green, A. Rabinovici, G. D. Jagust, W. 2024-10-26 doi:10.1101/2024.10.23.619941 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ Motor Clustering Enhances Kinesin-driven Vesicle Transport ]]> https://biorxiv.org/content/10.1101/2024.10.23.619892v1?rss=1 Jiang, R. Feng, Q. Nong, D. Kang, Y. J. Sept, D. Hancock, W. O. 2024-10-27 doi:10.1101/2024.10.23.619892 Cold Spring Harbor Laboratory Press 2024-10-27 <![CDATA[ CRISPR-enabled control of gene expression sets the isotopic composition of microbial methane ]]> https://biorxiv.org/content/10.1101/2024.10.28.620722v1?rss=1 Gropp, J. Bill, M. Lloyd, M. Stein, R. Nayak, D. D. Stolper, D. A. 2024-10-28 doi:10.1101/2024.10.28.620722 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Phosphorylation of HP1/Swi6 relieves competition with Suv39/Clr4 on nucleosomes and enables H3K9 trimethyl spreading. ]]> https://biorxiv.org/content/10.1101/2024.10.25.620326v1?rss=1 Kennedy, D. R. Lemiere, J. Tan, C. Simental, E. Braxton, J. Maxwell, R. A. Amine, A. A. Al-Sady, B. 2024-10-29 doi:10.1101/2024.10.25.620326 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ A multi-subunit autophagic capture complex facilitates degradation of ER stalled MHC-I in pancreatic cancer. ]]> https://biorxiv.org/content/10.1101/2024.10.27.620516v1?rss=1 Berquez, M. Li, A. L. Luy, M. A. Venida, A. C. O'Loughlin, T. Rademaker, G. Barpanda, A. Hu, J. Yano, J. Wiita, A. Gilbert, L. A. Bruno, P. M. Perera, R. M. 2024-10-29 doi:10.1101/2024.10.27.620516 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ A mitochondrial redox switch licenses the onset of morphogenesis in animals ]]> https://biorxiv.org/content/10.1101/2024.10.28.620733v1?rss=1 Kahlin, U. Dalla Ricca, F. Pillai, S. J. Olivetta, M. Tharp, K. M. Jao, L.-E. Dudin, O. McDonald, K. L. Aydogan, M. G. 2024-10-29 doi:10.1101/2024.10.28.620733 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Genomic Analysis of Progenitors in Viral Infection Implicates Glucocorticoids as Suppressors of Plasmacytoid Dendritic Cell Generation ]]> https://biorxiv.org/content/10.1101/2024.10.28.620771v1?rss=1 Jo, Y. Greene, T. T. Zhang, K. Chiale, C. Fang, Z. Dallari, S. Marooki, N. Wang, W. Zuniga, E. I. 2024-10-30 doi:10.1101/2024.10.28.620771 Cold Spring Harbor Laboratory Press 2024-10-30 <![CDATA[ The adolescent frontal cortex shows stronger population-level encoding of information than the adult during a putative sensitive period ]]> https://biorxiv.org/content/10.1101/2024.10.31.621384v1?rss=1 Klinger, M. Wang, H. Tai, L.-H. Qu, A. J. Murphy, M. Wilbrecht, L. 2024-11-01 doi:10.1101/2024.10.31.621384 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Detection of airborne Coccidioides spores using lightweight portable air samplers affixed to uncrewed aircraft systems in California's Central Valley ]]> https://biorxiv.org/content/10.1101/2024.10.28.620741v1?rss=1 Radosevich, M. T. Dobson, S. Weaver, A. K. Lampman, P. T. A. Kollath, D. R. Couper, L. Campbell, G. Taylor, J. Remais, J. V. Kobziar, L. Markwiese, J. Head, J. R. 2024-11-02 doi:10.1101/2024.10.28.620741 Cold Spring Harbor Laboratory Press 2024-11-02 <![CDATA[ Switch of TIR signaling by a Ca2+ sensor activates ADR1 recognition of pRib-AMP-EDS1-PAD4 for stomatal immunity ]]> https://biorxiv.org/content/10.1101/2024.10.29.620780v1?rss=1 Wang, H. Tan, J. Cui, X. Bai, Y. Gao, S. Staskawicz, B. Song, S. Yan, C. Qi, T. 2024-11-02 doi:10.1101/2024.10.29.620780 Cold Spring Harbor Laboratory Press 2024-11-02 <![CDATA[ SOQ1 functions as a methionine sulfoxide reductase in the chloroplast lumen for regulation of photoprotective qH in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2024.11.01.621559v1?rss=1 Hao, J. Johansson, A. Svensson Fall, J. Duan, J. Hertle, A. P. Brooks, M. D. Niyogi, K. K. Yoshida, K. Hisabori, T. Malnoe, A. 2024-11-02 doi:10.1101/2024.11.01.621559 Cold Spring Harbor Laboratory Press 2024-11-02 <![CDATA[ Many transcription factor families have evolutionarily conserved binding motifs in plants ]]> https://biorxiv.org/content/10.1101/2024.10.31.621407v1?rss=1 Zenker, S. Wulf, D. Meierhenrich, A. Viehöver, P. Becker, S. Eisenhut, M. Stracke, R. Weisshaar, B. Bräutigam, A. 2024-11-03 doi:10.1101/2024.10.31.621407 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Site-specific DNA insertion into the human genome with engineered recombinases ]]> https://biorxiv.org/content/10.1101/2024.11.01.621560v1?rss=1 Fanton, A. Bartie, L. J. Martins, J. Q. Tran, V. Q. Goudy, L. Durrant, M. G. Wei, J. Pawluk, A. Konermann, S. Marson, A. Gilbert, L. A. Hsu, P. D. 2024-11-03 doi:10.1101/2024.11.01.621560 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Methylglyoxal is an antibacterial effector produced by macrophages during infection ]]> https://biorxiv.org/content/10.1101/2024.11.03.621721v1?rss=1 Anaya-Sanchez, A. Berry, S. B. Espich, S. Zilinskas, A. Tran, P. M. Agudelo, C. Samani, H. Darwin, K. H. Portnoy, D. A. Stanley, S. 2024-11-03 doi:10.1101/2024.11.03.621721 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Prolonged low flows and non-native fish operate additively to alter insect emergence in mountain streams ]]> https://biorxiv.org/content/10.1101/2024.11.03.621706v1?rss=1 Evangelista, C. Buoro, M. Leathers, K. Tronel, T. Carlson, S. Ruhi, A. 2024-11-04 doi:10.1101/2024.11.03.621706 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ Molecular Signatures of Resilience to Alzheimer's Disease in Neocortical Layer 4 Neurons ]]> https://biorxiv.org/content/10.1101/2024.11.03.621787v1?rss=1 Dharshini, S. A. P. Sanz-Ros, J. Pan, J. Tang, W. Vallejo, K. Otero-Garcia, M. Cobos, I. 2024-11-04 doi:10.1101/2024.11.03.621787 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ Type IV pili-associated secretion of a biofilm matrix protein from Clostridium perfringens that forms intermolecular isopeptide bonds ]]> https://biorxiv.org/content/10.1101/2024.11.04.621531v1?rss=1 25 kD. To determine if the T4P-associated genes comprise a Gram-positive TTSS, the secretome of mutants lacking type IV pilins were examined and a single protein, a von Willebrand A domain containing protein, BsaC (CPE0517), was identified as being dependent on pilin PilA3 for secretion. The bsaC gene is in an operon with genes encoding a SipW signal peptidase and two putative biofilm matrix proteins BsaA and BsaB, both of which have remote homology to Bacillus subtilis biofilm protein TasA. Since BsaA forms long oligomers that are secreted, we analyzed BsaA monomer interactions with de novo modeling. These models projected that the monomers formed isopeptide bonds as part of a donor strand exchange process, in which an N-terminal disordered loop of one monomer intercalates into a beta sheet structure of an adjacent monomer and reforms into a beta sheet with subsequent isopeptide bond formation. Mutations in residues predicted to form the isopeptide bonds led to loss of oligomerization, supporting an exchange and lock mechanism. Phylogenetic analysis showed the BsaA family of proteins are widespread among bacteria and archaea but only a subset is predicted to form isopeptide bonds. ImportanceFor bacteria to secrete folded proteins to the environment, they have to overcome the physical barriers of an outer membrane in Gram-negative bacteria and the thick peptidoglycan layer in Gram-positive bacteria. One mechanism to do this is the use of a Type II secretion system in Gram-negative bacteria, which has a structure similar to type IV pili and is modeled to act as a piston that pumps folded proteins through the outer membrane to the environment. Clostridium perfringens, like all or most all of the clostridia, has type IV pili and, in fact, has two sets of pilus-associated genes. Here we present evidence that C. perfringens uses one set of pilus genes to secrete a biofilm associated protein and may be responsible for secreting the main biofilm protein, BsaA. We show that BsaA monomers are, unlike most other biofilm matrix proteins, linked by intermolecular isopeptide bonds, enhancing the physical strength of BsaA fibers. ]]> Kivimaki, S. E. Dempsey, S. Tani, J. M. Camper, C. Hicklin, I. K. Blaby-Haas, C. E. Brown, A. M. Melville, S. 2024-11-04 doi:10.1101/2024.11.04.621531 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ Microbes display broad diversity in cobamide preferences ]]> https://biorxiv.org/content/10.1101/2024.11.04.621602v1?rss=1 Mok, K. C. Sokolovskaya, O. M. Deutschbauer, A. C. Carlson, H. K. Taga, M. E. 2024-11-04 doi:10.1101/2024.11.04.621602 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ Antigen-Specific T Cell Receptor Discovery for Treating Progressive Multifocal Leukoencephalopathy ]]> https://biorxiv.org/content/10.1101/2024.11.04.621904v1?rss=1 Gupta, S. Martinov, T. Thelen, A. Sunahara, M. Mureli, S. Vazquez, A. Gerdts, J. Dandekar, R. Cortese, I. Fouassier, C. Schanzer, E. Urnov, F. D. Marson, A. Shy, B. R. Greenberg, P. D. Wilson, M. R. 2024-11-04 doi:10.1101/2024.11.04.621904 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ Direct lipid interactions control SARS-CoV-2 M protein conformational dynamics and virus assembly ]]> https://biorxiv.org/content/10.1101/2024.11.04.620124v1?rss=1 Dutta, M. Dolan, K. A. Amiar, S. Bass, E. J. Sultana, R. Voth, G. A. Stahelin, R. V. Brohawn, S. G. 2024-11-05 doi:10.1101/2024.11.04.620124 Cold Spring Harbor Laboratory Press 2024-11-05 <![CDATA[ Aging drives a program of DNA methylation decay in plant organs ]]> https://biorxiv.org/content/10.1101/2024.11.04.621941v1?rss=1 Dai, D. Chen, K. Tao, J. Williams, B. P. 2024-11-05 doi:10.1101/2024.11.04.621941 Cold Spring Harbor Laboratory Press 2024-11-05 <![CDATA[ Tomato roots exhibit distinct, development-specific responses to bacterial-derived peptides ]]> https://biorxiv.org/content/10.1101/2024.11.04.621969v1?rss=1 Leuschen-Kohl, R. L. Roberts, R. Stevens, D. M. Zhang, N. Buchanan, S. Pilkey, B. Coaker, G. Iyer-Pascuzzi, A. S. 2024-11-05 doi:10.1101/2024.11.04.621969 Cold Spring Harbor Laboratory Press 2024-11-05 <![CDATA[ An algal nutrient-replete, optimized medium for fast growth and high triacylglycerol accumulation ]]> https://biorxiv.org/content/10.1101/2024.11.07.622501v1?rss=1 Jeffers, T. L. McCombs, R. Schmollinger, S. Merchant, S. S. Niyogi, K. K. Roth, M. S. 2024-11-08 doi:10.1101/2024.11.07.622501 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Transmembrane coupling accelerates the growth of liquid-like protein condensates ]]> https://biorxiv.org/content/10.1101/2024.11.07.622512v1?rss=1 Lee, Y. Yuan, F. Cabriales, J. L. Stachowiak, J. C. 2024-11-08 doi:10.1101/2024.11.07.622512 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Polyhydroxybutyrate production in freshwater SAR11 (LD12) ]]> https://biorxiv.org/content/10.1101/2024.11.08.622676v1?rss=1 Bennett, B. D. Meier, D. A. Lanclos, V. C. Asrari, H. Coates, J. D. Thrash, J. C. 2024-11-08 doi:10.1101/2024.11.08.622676 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ The development of aperiodic neural activity in the human brain ]]> https://biorxiv.org/content/10.1101/2024.11.08.622714v1?rss=1 Cross, Z. R. Gray, S. M. Dede, A. J. O. Rivera, Y. M. Yin, Q. Vahidi, P. Rau, E. M. B. Cyr, C. Holubecki, A. M. Asano, E. Lin, J. J. McManus, O. K. Sattar, S. Saez, I. Girgis, F. King-Stephens, D. Weber, P. B. Laxer, K. D. Schuele, S. U. Rosenow, J. M. Wu, J. Y. Kam, S. K. Raskin, J. S. Chang, E. F. Shaikhouni, A. Brunner, P. Roland, J. L. Braga, R. M. Knight, R. T. Ofen, N. Johnson, E. L. 2024-11-09 doi:10.1101/2024.11.08.622714 Cold Spring Harbor Laboratory Press 2024-11-09 <![CDATA[ Structural landscape of AAA+ ATPase motor states in the substrate-degrading human 26S proteasome reveals conformation-specific binding of TXNL1 ]]> https://biorxiv.org/content/10.1101/2024.11.08.622731v1?rss=1 Martin, A. Arkinson, C. Gee, C. L. Zhang, Z. Dong, K. 2024-11-09 doi:10.1101/2024.11.08.622731 Cold Spring Harbor Laboratory Press 2024-11-09 <![CDATA[ Mutant RIT1 cooperates with YAP to drive an EMT-like lung cancer state ]]> https://biorxiv.org/content/10.1101/2024.11.11.623044v1?rss=1 Rominger, M. C. Gupta, S. Moorthi, S. McSharry, M. Kamlapurkar, S. O'Brien, S. Waldum, A. Lo, A. Duke, F. Lowe, A. Cromwell, E. Glabman, R. Koehne, A. Berger, A. 2024-11-12 doi:10.1101/2024.11.11.623044 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Structures of vertebrate R2 retrotransposon complexes during target-primed reverse transcription and after second strand nicking ]]> https://biorxiv.org/content/10.1101/2024.11.11.623112v1?rss=1 Thawani, A. Rodriguez-Vargas, A. Treeck, B. V. Hassan, N. T. Adelson, D. L. Nogales, E. Collins, K. 2024-11-12 doi:10.1101/2024.11.11.623112 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Sulfur-species in Zinc-specific Condylar Zones of a Rat Temporomandibular Joint ]]> https://biorxiv.org/content/10.1101/2024.11.11.623079v1?rss=1 Lee, B. H. Yang, Z. Ho, T. J. Wang, Y. Tamura, N. Webb, S. Bone, S. Ho, S. P. 2024-11-14 doi:10.1101/2024.11.11.623079 Cold Spring Harbor Laboratory Press 2024-11-14 <![CDATA[ Force transmission through the inner kinetochore is enhanced by centromeric DNA sequences ]]> https://biorxiv.org/content/10.1101/2024.11.13.623448v1?rss=1 Miedlar, E. Hamilton, G. E. Witus, S. R. Gonske, S. J. Riffle, M. Zelter, A. Klevit, R. E. Asbury, C. L. Dimitrova, Y. N. Davis, T. N. 2024-11-14 doi:10.1101/2024.11.13.623448 Cold Spring Harbor Laboratory Press 2024-11-14 <![CDATA[ Biomarkers of recovery: characterizing trophic flow following ecological restoration ]]> https://biorxiv.org/content/10.1101/2024.11.14.623625v1?rss=1 Spindel, N. B. Galloway, A. W. E. Schram, J. B. McNeill, D. G. Bellis, V. S. K. Guujaaw, N. Yakgujanaas, J. Thompson, M. Lee, L. C. Okamoto, D. K. 2024-11-15 doi:10.1101/2024.11.14.623625 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Categorical and semantic perception of the meaning of call-types in zebra finches ]]> https://biorxiv.org/content/10.1101/2024.11.14.623689v1?rss=1 Elie, J. E. de Witasse-Thezy, A. Thomas, L. Malit, B. Theunissen, F. E. 2024-11-15 doi:10.1101/2024.11.14.623689 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Ultrafast elastocapillary fans control agile maneuvering in ripple bugs and robots ]]> https://biorxiv.org/content/10.1101/2024.11.15.623609v1?rss=1 Ortega-Jimenez, V. Kim, D. Kumar, S. Kim, C. Koh, J.-s. Bhamla, M. S. 2024-11-15 doi:10.1101/2024.11.15.623609 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Structural basis for growth factor and nutrient signal integration on the lysosomal membrane by mTORC1 ]]> https://biorxiv.org/content/10.1101/2024.11.15.623810v1?rss=1 Cui, Z. Esposito, A. Napolitano, G. Ballabio, A. Hurley, J. H. 2024-11-15 doi:10.1101/2024.11.15.623810 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Occurrence of Aneuploidy Across the Range of Coast Redwood (Sequoia sempervirens) ]]> https://biorxiv.org/content/10.1101/2024.11.19.624336v1?rss=1 Nikolaeva, A. S. Santangelo, J. Smith, L. Dodd, R. Nielsen, R. 2024-11-21 doi:10.1101/2024.11.19.624336 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ UPR deficiency in budding yeast reveals a trade-off between ER folding capacity and maintenance of euploidy ]]> https://biorxiv.org/content/10.1101/2024.11.22.624941v1?rss=1 Bartolutti, C. Kim, A. J. Brar, G. 2024-11-24 doi:10.1101/2024.11.22.624941 Cold Spring Harbor Laboratory Press 2024-11-24 <![CDATA[ Structure and mechanism of the RalGAP tumor suppressor complex ]]> https://biorxiv.org/content/10.1101/2024.11.25.625123v1?rss=1 Rasche, R. Klink, B. U. Apken, L. H. Michalke, E. Chen, M. Oeckinghaus, A. Gatsogiannis, C. Kuemmel, D. 2024-11-25 doi:10.1101/2024.11.25.625123 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Dynamic regulation of the oxidative stress response by the E3 ligase TRIP12 ]]> https://biorxiv.org/content/10.1101/2024.11.25.625235v1?rss=1 Ingersoll, A. J. McCloud, D. M. Hu, J. Y. Rape, M. 2024-11-25 doi:10.1101/2024.11.25.625235 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Assembly and lipid-gating of LRRC8A:D volume-regulated anion channels ]]> https://biorxiv.org/content/10.1101/2024.11.24.625074v1?rss=1 Lurie, A. Kern, D. M. Henn, K. Brohawn, S. G. 2024-11-26 doi:10.1101/2024.11.24.625074 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ De novo assembled databases enable species-specific protein-based stable isotope probing of microbiomes without prior knowledge of the community composition ]]> https://biorxiv.org/content/10.1101/2024.11.25.625156v1?rss=1 Klaes, S. White, C. Alvarez-Cohen, L. Adrian, L. Ding, C. 2024-11-26 doi:10.1101/2024.11.25.625156 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Programmable epigenome editing by transient delivery of CRISPR epigenome editor ribonucleoproteins ]]> https://biorxiv.org/content/10.1101/2024.11.26.625496v1?rss=1 Nunez, J. K. Xu, D. Besselink, S. Ramadoss, G. N. Dierks, P. H. Lubin, J. P. Pattali, R. K. Brim, J. I. Christenson, A. E. Colias, P. J. Ornelas, I. J. Nguyen, C. D. Chasins, S. E. Conklin, B. R. 2024-11-27 doi:10.1101/2024.11.26.625496 Cold Spring Harbor Laboratory Press 2024-11-27 <![CDATA[ Arterial endothelial deletion of Alk1 causes epistaxis and cerebral microhemorrhage with aberrant arteries and defective smooth muscle coverage. ]]> https://biorxiv.org/content/10.1101/2024.11.25.622742v1?rss=1 Zhang, X. Jacobs, K. A. Raygor, K. P. Li, S. Li, J. Wang, R. A. 2024-11-28 doi:10.1101/2024.11.25.622742 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Genome Organization with CUT and Tag (GO-CaT) identifies substructure and maturation of lamina-associated domains in neurons of the developing human brain ]]> https://biorxiv.org/content/10.1101/2024.11.27.625786v1?rss=1 Zhang, C. Gil, E. Ahanger, S. H. Li, M. Wang, L. Li, J. Kriegstein, A. Lim, D. 2024-11-28 doi:10.1101/2024.11.27.625786 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Mapping essential somatic hypermutations in a CD4-binding site bNAb informs HIV-1 vaccine design ]]> https://biorxiv.org/content/10.1101/2024.11.26.625503v1?rss=1 Dam, K.-M. A. Gristick, H. B. Li, Y. E. Yang, Z. Gnanapragasam, P. N. P. West, A. P. Seaman, M. S. Bjorkman, P. J. 2024-11-29 doi:10.1101/2024.11.26.625503 Cold Spring Harbor Laboratory Press 2024-11-29 <![CDATA[ Structural and functional insights into activation and regulation of the dynein-dynactin-NuMA complex ]]> https://biorxiv.org/content/10.1101/2024.11.26.625568v1?rss=1 Aslan, M. Cho, N. H. d'Amico, E. A. Taheri, A. Zhao, Y. Zhong, X. Blaauw, M. Carter, A. P. Dumont, S. Yildiz, A. 2024-11-29 doi:10.1101/2024.11.26.625568 Cold Spring Harbor Laboratory Press 2024-11-29 <![CDATA[ Benchmarking concentration and direct extraction methods for wastewater-based surveillance of eight human respiratory viruses: implications for rapid application to novel pathogens ]]> https://biorxiv.org/content/10.1101/2024.11.27.625007v1?rss=1 Jiang, M. Nguyen, A. Kane, S. R. Borucki, M. K. Kantor, R. S. Nelson, K. L. 2024-11-29 doi:10.1101/2024.11.27.625007 Cold Spring Harbor Laboratory Press 2024-11-29 <![CDATA[ NuMA mechanically reinforces the spindle independently of its partner dynein ]]> https://biorxiv.org/content/10.1101/2024.11.29.622360v1?rss=1 Cho, N. H. Aslan, M. Yildiz, A. Dumont, S. 2024-12-01 doi:10.1101/2024.11.29.622360 Cold Spring Harbor Laboratory Press 2024-12-01 <![CDATA[ Coordinated organic and inorganic nitrogen transformations fuel soil microbial blooms and increase nitrogen retention during snowmelt ]]> https://biorxiv.org/content/10.1101/2024.11.30.626193v1?rss=1 Sorensen, P. Karaoz, U. Beller, H. R. Bill, M. Bouskill, N. J. Banfield, J. F. Chu, R. K. Hoyt, D. W. Eder, E. Eloe-Fadrosh, E. Sharrar, A. M. Tfaily, M. Toyoda, J. Tolic, N. Wang, S. Wong, A. Williams, K. H. Zhong, Y. Brodie, E. L. 2024-12-01 doi:10.1101/2024.11.30.626193 Cold Spring Harbor Laboratory Press 2024-12-01 <![CDATA[ Ancient genomics support deep divergence between Eastern and Western Mediterranean Indo-European languages ]]> https://biorxiv.org/content/10.1101/2024.12.02.626332v1?rss=1 Yediay, F. E. Kroonen, G. Sabatini, S. Frei, K. M. Frank, A. B. Pinotti, T. Wigman, A. Thorso, R. Vimala, T. McColl, H. Moutafi, I. Altinkaya, I. Ramsoe, A. Gaunitz, C. Renaud, G. Mederos Martin, A. Demeter, F. Scorrano, G. Canci, A. Fischer, P. Duyar, I. Serhal, C. Varzari, A. Turkteki, M. O'Shea, J. Rahmstorf, L. Polat, G. Atamturk, D. Vinner, L. Omura, S. Matsumura, K. Cao, J. Valeur Seersholm, F. Morillo Leon, J. M. Voutsaki, S. Orgeolet, R. Burke, B. Herrmann, N. P. Recchia, G. Corazza, S. Borgna, E. Cipolloni Sampo, M. Trucco, F. Pajuelo Pando, 2024-12-02 doi:10.1101/2024.12.02.626332 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ The molecular basis of integrated stress response silencing ]]> https://biorxiv.org/content/10.1101/2024.12.02.626349v1?rss=1 Yang, Z. Haakonsen, D. Heider, M. Witus, S. R. Zelter, A. Beschauner, T. MacCoss, M. J. Rape, M. 2024-12-02 doi:10.1101/2024.12.02.626349 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ RCVT: a novel diagnostic to quantify compositional biases among taxa for phylogenomics ]]> https://biorxiv.org/content/10.1101/2024.11.28.625917v1?rss=1 Steenwyk, J. L. Buida, T. J. 2024-12-03 doi:10.1101/2024.11.28.625917 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Rebuilding the autoimmune-damaged corneal stroma through topical lubrication ]]> https://biorxiv.org/content/10.1101/2024.11.29.626078v1?rss=1 Efraim, Y. Chen, F. Y. T. Niknezhad, S. V. Pham, D. Cheong, K. N. An, L. Sinada, H. McNamara, N. A. Knox, S. 2024-12-03 doi:10.1101/2024.11.29.626078 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Expanding the HP1a-binding consensus and molecular grammar for heterochromatin assembly ]]> https://biorxiv.org/content/10.1101/2024.12.03.626544v1?rss=1 Colmenares, S. U. Tsukamoto, S. Karpen, G. Mofrad, M. Brennan, L. D. Hickmann, C. 2024-12-04 doi:10.1101/2024.12.03.626544 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ Contact Lens Wear Alters Transcriptional Responses to Pseudomonas aeruginosa in Both the Corneal Epithelium and the Bacteria ]]> https://biorxiv.org/content/10.1101/2024.12.03.626720v1?rss=1 Kumar, N. G. Grosser, M. R. Wan, S. J. Schator, D. Ahn, E. Jedel, E. Nieto, V. Evans, D. J. Fleiszig, S. M. J. 2024-12-04 doi:10.1101/2024.12.03.626720 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ PITHD1: An Endogenous Inhibitor of the 26S Proteasome During Cellular Dormancy ]]> https://biorxiv.org/content/10.1101/2024.12.04.626795v1?rss=1 Amann, S. J. Dong, K. Roehsner, J. Krall, D. Grishkovskaya, I. Kotisch, H. Schleiffer, A. Roitinger, E. Pauli, A. Martin, A. Haselbach, D. 2024-12-04 doi:10.1101/2024.12.04.626795 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ Generating All-Atom Protein Structure from Sequence-Only Training Data ]]> https://biorxiv.org/content/10.1101/2024.12.02.626353v1?rss=1 Lu, A. X. Yan, W. Robinson, S. A. Yang, K. K. Gligorijevic, V. Cho, K. Bonneau, R. Abbeel, P. Frey, N. 2024-12-05 doi:10.1101/2024.12.02.626353 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Perception of Temperature Even in the Absence of Actual Change is Sufficient to Drive Transgenerational Epigenetic Inheritance ]]> https://biorxiv.org/content/10.1101/2024.12.02.626416v1?rss=1 Teichman, G. Sela, M. Ewe, C. K. Rieger, I. Anava, S. Mor, Y. Szanto, P. Meyer, D. H. Doron, H. Shachar, O. Pechuk, V. Gingold, H. Oren-Suissa, M. McGee, M. Shapira, M. Schumacher, B. Rechavi, O. 2024-12-05 doi:10.1101/2024.12.02.626416 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Target cell tension regulates macrophage trogocytosis ]]> https://biorxiv.org/content/10.1101/2024.12.02.626490v1?rss=1 Cornell, C. E. Chorlay, A. Krishnamurthy, D. Martin, N. R. Baldauf, L. Fletcher, D. A. 2024-12-05 doi:10.1101/2024.12.02.626490 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Conservation of function without conservation of amino acid sequence in intrinsically disordered transcriptional activation domains ]]> https://biorxiv.org/content/10.1101/2024.12.03.626510v1?rss=1 LeBlanc, C. J. Stefani, J. Soriano, M. Lam, A. Zintel, M. A. Kotha, S. R. Chase, E. Pimentel-Solorio, G. Vunnum, A. Flug, K. L. Fultineer, A. T. Hummel, N. Staller, M. V. 2024-12-05 doi:10.1101/2024.12.03.626510 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ DNA tensiometer reveals catch-bond detachment kinetics of kinesin-1, -2 and -3 ]]> https://biorxiv.org/content/10.1101/2024.12.03.626575v1?rss=1 kinesin-2 > kinesin-1. However, in reconstituted kinesin-dynein pairs vitro, all three kinesin families compete nearly equally well against dynein. Modeling and experiments have confirmed that vertical forces inherent to the large trapping beads enhance kinesin-1 dissociation rates. In vivo, vertical forces are expected to range from negligible to dominant, depending on cargo and microtubule geometries. To investigate the detachment and reattachment kinetics of kinesin-1, 2 and 3 motors against loads oriented parallel to the microtubule, we created a DNA tensiometer comprising a DNA entropic spring attached to the microtubule on one end and a motor on the other. Kinesin dissociation rates at stall were slower than detachment rates during unloaded runs, and the complex reattachment kinetics were consistent with a weakly-bound slip state preceding detachment. Kinesin-3 behaviors under load suggested that long KIF1A run lengths result from the concatenation of multiple short runs connected by diffusive episodes. Stochastic simulations were able to recapitulate the load-dependent detachment and reattachment kinetics for all three motors and provide direct comparison of key transition rates between families. These results provide insight into how kinesin-1, -2 and -3 families transport cargo in complex cellular geometries and compete against dynein during bidirectional transport. ]]> Noell, C. R. Ma, T.-C. Jiang, R. McKinley, S. A. Hancock, W. O. 2024-12-05 doi:10.1101/2024.12.03.626575 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Predictable modulation of plant root development using engineered cytokinin regulators ]]> https://biorxiv.org/content/10.1101/2024.12.06.627221v1?rss=1 Rattan, R. Alamos, S. Szarzanowicz, M. Markel, K. Shih, P. M. 2024-12-06 doi:10.1101/2024.12.06.627221 Cold Spring Harbor Laboratory Press 2024-12-06 <![CDATA[ Cannabinoid inhibition of mechanosensitive K+ channels ]]> https://biorxiv.org/content/10.1101/2024.12.09.627564v1?rss=1 Docter, T. Sorum, B. Deshmane, R. Doubravsky, C. Brohawn, S. G. 2024-12-10 doi:10.1101/2024.12.09.627564 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ Scaling ecological niches from individuals to populations and beyond ]]> https://biorxiv.org/content/10.1101/2024.12.06.627157v1?rss=1 Lu, M. Yanco, S. Carlson, B. Winner, K. Cohen, J. Ellis Soto, D. Sharma, S. Rogers, W. Jetz, W. 2024-12-11 doi:10.1101/2024.12.06.627157 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ OrthoHMM: Improved Inference of Ortholog Groups using Hidden Markov Models ]]> https://biorxiv.org/content/10.1101/2024.12.07.627370v1?rss=1 Steenwyk, J. L. Buida, T. J. Rokas, A. King, N. 2024-12-12 doi:10.1101/2024.12.07.627370 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Oncogenic RAS Induces a Distinctive Form of Non-Canonical Autophagy Mediated by the P38-ULK1-PI4KB Axis ]]> https://biorxiv.org/content/10.1101/2024.12.10.627736v1?rss=1 Ge, L. Wang, X. Li, S. Lin, S. Han, Y. Zhan, T. Huang, Z. Wang, J. Li, Y. Deng, H. Zhang, M. Du, F. 2024-12-12 doi:10.1101/2024.12.10.627736 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Single cell transcriptomics of X-ray irradiated Drosophila wing discs reveals heterogeneity related to cell-cycle status and cell location ]]> https://biorxiv.org/content/10.1101/2024.12.10.627868v1?rss=1 Cruz, J. Sun, W. Y. Verbeke, A. Hariharan, I. K. 2024-12-12 doi:10.1101/2024.12.10.627868 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Fe starvation induces a second LHCI tetramer to photosystem I in green algae ]]> https://biorxiv.org/content/10.1101/2024.12.11.624522v1?rss=1 Liu, H. W. Khera, R. Grob, P. Gallaher, S. D. Purvine, S. O. Nicora, C. D. Lipton, M. Niyogi, K. K. Nogales, E. Iwai, M. Merchant, S. 2024-12-12 doi:10.1101/2024.12.11.624522 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ MetaBiome: A Multiscale Model Integrating Agent-Based Modeling and Metabolic Networks Reveals Spatial Regulation in Mucosal Microbial Communities ]]> https://biorxiv.org/content/10.1101/2024.12.11.628036v1?rss=1 Aminian-Dehkordi, J. Dickson, A. M. Valiei, A. Mofrad, M. 2024-12-12 doi:10.1101/2024.12.11.628036 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Deep profiling of plant stress biomarkers following bacterial pathogen infection with protein corona based nano-omics ]]> https://biorxiv.org/content/10.1101/2024.12.12.627884v1?rss=1 Coreas, R. Sridhar, N. Lin, T.-J. Squire, H. J. Voke, E. Landry, M. P. 2024-12-13 doi:10.1101/2024.12.12.627884 Cold Spring Harbor Laboratory Press 2024-12-13 <![CDATA[ Leucine Aminopeptidase LyLAP enables lysosomal degradation of membrane proteins ]]> https://biorxiv.org/content/10.1101/2024.12.13.628212v1?rss=1 Jain, A. Heremans, I. Rademaker, G. Detomasi, T. Rohweder, P. Anderson, D. Zhang, J. Hernandez, G. Gupta, S. von Linde, T. Lange, M. Spacci, M. Citron, Y. Olzmann, J. Dawson, D. Craik, C. Bommer, G. Perera, R. M. Zoncu, R. 2024-12-14 doi:10.1101/2024.12.13.628212 Cold Spring Harbor Laboratory Press 2024-12-14 <![CDATA[ Tax1bp1 enhances bacterial virulence and promotes inflammatory responses during Mycobacterium tuberculosis infection of alveolar macrophages ]]> https://biorxiv.org/content/10.1101/2024.12.16.628616v1?rss=1 Chin, J. Abeydeera, N. Repasy, T. Rivera-Lugo, R. Mitchell, G. Nguyen, V. Q. Zheng, W. Richards, A. Swaney, D. L. Krogan, N. J. Ernst, J. D. Cox, J. S. Budzik, J. M. 2024-12-16 doi:10.1101/2024.12.16.628616 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Spatial Phylogenetics with Continuous Data: an Application to California Bryophytes ]]> https://biorxiv.org/content/10.1101/2024.12.16.628580v1?rss=1 Kling, M. M. Gonzalez-Ramirez, I. S. Carter, B. Borokini, I. Mishler, B. D. 2024-12-20 doi:10.1101/2024.12.16.628580 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Predictive Modeling of Gene Expression and Localization of DNA Binding Site Using Deep Convolutional Neural Networks ]]> https://biorxiv.org/content/10.1101/2024.12.17.629042v1?rss=1 Karshenas, A. Roschinger, T. Garcia, H. 2024-12-20 doi:10.1101/2024.12.17.629042 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ DTPSP: A Deep Learning Framework for Optimized Time Point Selection in Time-Series Single-Cell Studies ]]> https://biorxiv.org/content/10.1101/2024.12.18.629276v1?rss=1 Hijazin, M. Shi, P. Wang, J. Ding, J. 2024-12-20 doi:10.1101/2024.12.18.629276 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ The active subset of grassland soil microbiomes changes with soil depth, water availability and prominently features predatory bacteria and episymbionts ]]> https://biorxiv.org/content/10.1101/2024.12.19.629468v1?rss=1 20 cm) across both ecosystems. Active Saccharibacteria unexpectedly encode nucleotide synthesis genes that enabled isotope incorporation while growing in shallow Angelo soils over all time periods. In contrast to predicted episymbiotic lifestyles of Saccharibacteria, other highly active bacteria are predicted predators. Obligately predatory Pseudobdellovibrio are active in intermediate depth Hopland soils whereas bacteria of the order Haliangiales are active in shallow Angelo soils. Supporting predatory lifestyles of Haliangiales, we used in silico structure prediction to assemble a large protein complex that we identify as a contractile injection system. Overall, the results indicate the potential for active carbon turnover in deep grassland soil and strong seasonal changes in the active members of microbial communities, despite relatively minor shifts in community composition. ]]> Penev, P. I. Estera-Molina, K. Allen, G. M. Sachdeva, R. Lei, S. Law, K. K. Hoff, J. Blazewicz, S. J. Pett-Ridge, J. Banfield, J. F. 2024-12-20 doi:10.1101/2024.12.19.629468 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ The cell biology and genome of Stentor pyriformis, a giant cell that embeds symbiotic algae in a microtubule meshwork ]]> https://biorxiv.org/content/10.1101/2024.12.19.629502v1?rss=1 Boudreau, v. Albright, A. R. Gerbich, T. Fadero, T. Yan, V. Larson, B. Lucas-DeMott, A. Yung, J. Moulin, S. Descovich, C. P. Slabodnick, M. M. Burlacot, A. Wang, J. Niyogi, K. K. Marshall, W. F. 2024-12-21 doi:10.1101/2024.12.19.629502 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ Neuronal representation of the decisional reference point in monkeys ]]> https://biorxiv.org/content/10.1101/2024.12.20.629801v1?rss=1 Nguyen, D. Rich, E. L. Wallis, J. D. Louie, K. Glimcher, P. W. 2024-12-21 doi:10.1101/2024.12.20.629801 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ A biologically-inspired hierarchical convolutional energy model predicts V4 responses to natural videos ]]> https://biorxiv.org/content/10.1101/2024.12.16.628781v1?rss=1 Gallant, J. L. Oliver, M. Winter, M. Eickenberg, M. Dupre la Tour, T. 2024-12-22 doi:10.1101/2024.12.16.628781 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Mapping the Genetic Architecture of the Adaptive Integrated Stress Response in S. cerevisiae ]]> https://biorxiv.org/content/10.1101/2024.12.19.629525v1?rss=1 Baum, R. Kim, J. Muller, R. Y. Ingolia, N. 2024-12-22 doi:10.1101/2024.12.19.629525 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Haplotype editing with CRISPR/Cas9 as a therapeutic approach for dominant-negative missense mutations in NEFL ]]> https://biorxiv.org/content/10.1101/2024.12.20.629813v1?rss=1 Dua, P. H. Simon, B. M. Marley, C. B. Feliciano, C. M. Watry, H. L. Steury, D. Abraham, A. Gilbertson, E. N. Ramey, G. D. Capra, J. A. Conklin, B. R. Judge, L. M. 2024-12-22 doi:10.1101/2024.12.20.629813 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Short activation domains control chromatin association of transcription factors ]]> https://biorxiv.org/content/10.1101/2024.12.20.629816v1?rss=1 Fan, V. Darzacq, X. Staller, M. V. 2024-12-22 doi:10.1101/2024.12.20.629816 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ The biophysical mechanism of mitochondrial pearling ]]> https://biorxiv.org/content/10.1101/2024.12.21.629509v1?rss=1 Sturm, G. Hake, K. Lefebvre, A. E. Y. T. Rux, C. J. Ivanova, D. Millett-Sikking, A. Tharp, K. M. Rao, B. Closser, M. Waite, A. Precido-Lopez, M. Dumont, S. Lu, W. Manley, S. Landoni, J. C. Marshall, W. F. 2024-12-22 doi:10.1101/2024.12.21.629509 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Pearling Drives Mitochondrial DNA Nucleoid Distribution ]]> https://biorxiv.org/content/10.1101/2024.12.21.629917v1?rss=1 Landoni, J. C. Lycas, M. D. Macuada, J. Jaccard, R. Obara, C. J. Moore, A. S. Ben Nejma, S. Hoffman, D. Lippincott-Schwartz, J. Marshall, W. Sturm, G. Manley, S. 2024-12-22 doi:10.1101/2024.12.21.629917 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Spatiotemporal photocatalytic proximity labeling proteomics reveals ligand-activated extracellular and intracellular EGFR neighborhoods ]]> https://biorxiv.org/content/10.1101/2024.12.21.629933v1?rss=1 Lin, Z. Ngo, W. Chou, Y.-T. Wu, H. Susa, K. J. Jun, Y.-w. Bivona, T. G. Doudna, J. A. Wells, J. A. 2024-12-22 doi:10.1101/2024.12.21.629933 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Overexpression of Xanthophyll Cycle Genes Leads to Faster NPQ Acclimation in the C4 Monocot Setaria viridis ]]> https://biorxiv.org/content/10.1101/2024.12.23.630197v1?rss=1 Stone, W. D. Acosta-Gamboa, L. Kang, X. zhang, f. Owens, L. Li, L. Thielen, P. M. Jander, G. Gore, M. A. Lawton, T. J. 2024-12-25 doi:10.1101/2024.12.23.630197 Cold Spring Harbor Laboratory Press 2024-12-25 <![CDATA[ Open-source cell culture automation system with integrated cell counting for passaging microplate cultures ]]> https://biorxiv.org/content/10.1101/2024.12.27.629034v1?rss=1 Courville, G. Vaid, S. Toruno, A. Lebel, P. Cabrera, J. Raghavan, P. Jacobsen, A. Bell, G. R. Leonetti, M. D. Gomez-Sjöberg, R. 2024-12-27 doi:10.1101/2024.12.27.629034 Cold Spring Harbor Laboratory Press 2024-12-27 <![CDATA[ Human precentral gyrus neurons link speech sequences from listening to speaking ]]> https://biorxiv.org/content/10.1101/2024.12.27.630563v1?rss=1 Xu, D. Chung, J. E. Greicius, Q. R. Metzger, S. L. Zhang, Y. Leonard, M. K. Chang, E. F. 2024-12-28 doi:10.1101/2024.12.27.630563 Cold Spring Harbor Laboratory Press 2024-12-28 <![CDATA[ Nde1 Promotes Lis1 Binding to Full-Length Autoinhibited Human Dynein-1 ]]> https://biorxiv.org/content/10.1101/2024.12.30.630764v1?rss=1 Yang, J. Zhao, Y. Chai, P. Yildiz, A. Zhang, K. 2024-12-30 doi:10.1101/2024.12.30.630764 Cold Spring Harbor Laboratory Press 2024-12-30 <![CDATA[ scRepertoire 2: Enhanced and Efficient Toolkit for Single-Cell Immune Profiling ]]> https://biorxiv.org/content/10.1101/2024.12.31.630854v1?rss=1 Yang, Q. Safina, K. R. Borcherding, N. 2024-12-31 doi:10.1101/2024.12.31.630854 Cold Spring Harbor Laboratory Press 2024-12-31 <![CDATA[ Circuit dynamics of approach-avoidance conflict in humans ]]> https://biorxiv.org/content/10.1101/2024.12.31.630927v1?rss=1 Staveland, B. R. Oberschulte, J. Kim-McManus, O. Willie, J. T. Brunner, P. Dastjerdi, M. Lin, J. J. Hsu, M. Knight, R. T. 2025-01-01 doi:10.1101/2024.12.31.630927 Cold Spring Harbor Laboratory Press 2025-01-01 <![CDATA[ CD38 expression by neonatal human naïve CD4+ T cells shapes their distinct metabolic state and high regulatory T cell potential ]]> https://biorxiv.org/content/10.1101/2025.01.02.631038v1?rss=1 Dwyer, L. R. Clancy, S. Gouirand, V. Chien, C. Rogers, E. E. Oltman, S. P. Jelliffe-Pawlowski, L. L. Lynch, S. V. Wagner, A. Combes, A. J. Scharschmidt, T. C. 2025-01-02 doi:10.1101/2025.01.02.631038 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Identifying a next-generation antimalarial trioxolane in a landscape of artemisinin partial resistance ]]> https://biorxiv.org/content/10.1101/2025.01.02.631109v1?rss=1 Klope, M. T. Talukder, P. Blank, B. R. Chelebieva, S. Chen, J. Fontaine, S. D. Gonciarz, R. L. Jaishankar, P. Lee, G. J. Legac, J. Mathur, V. Narayan, A. Okitwi, M. Orena, S. Settineri, N. S. Tapia, J. Taremwa, Y. Tumwebaze, P. K. Vinod, A. Burrows, J. N. Rosenthal, P. J. Cooper, R. A. Renslo, A. R. 2025-01-03 doi:10.1101/2025.01.02.631109 Cold Spring Harbor Laboratory Press 2025-01-03 <![CDATA[ An arginine switch drives the stepwise activation of β-arrestin ]]> https://biorxiv.org/content/10.1101/2025.01.05.631353v1?rss=1 Ji, J. S. Yun, Y. Stepniewski, T. Yoon, H.-J. Min, K. Park, J. Y. Chung, C. Chung, K. Y. Selent, J. Lee, H. H. 2025-01-05 doi:10.1101/2025.01.05.631353 Cold Spring Harbor Laboratory Press 2025-01-05 <![CDATA[ Physiological and molecular impairment of PV circuit homeostasis in mouse models of autism ]]> https://biorxiv.org/content/10.1101/2025.01.08.632056v1?rss=1 Monday, H. R. Nieto, A. M. Yohannes, S. A. Luxu, S. Wong, K. W. Bolio, F. E. Feldman, D. 2025-01-09 doi:10.1101/2025.01.08.632056 Cold Spring Harbor Laboratory Press 2025-01-09 <![CDATA[ Nonlinear effects of temperature on mosquito parasite infection across a large geographic climate gradient ]]> https://biorxiv.org/content/10.1101/2025.01.07.631804v1?rss=1 Farner, J. E. Lyberger, K. P. Couper, L. I. Cruz-Loya, M. Mordecai, E. A. 2025-01-10 doi:10.1101/2025.01.07.631804 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ Pillar arrays as tunable interfacial barriers for microphysiological systems ]]> https://biorxiv.org/content/10.1101/2025.01.08.632020v1?rss=1 Goswami, I. Kim, Y. Neiman, G. Siemons, B. Velazquez, J. I. Yazgan, K. Ng, T. Healy, K. 2025-01-13 doi:10.1101/2025.01.08.632020 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Viscoelastic HyA Hydrogel Promotes Recovery of Muscle Quality and Vascularization in a Murine Model of Delayed Rotator Cuff Repair ]]> https://biorxiv.org/content/10.1101/2025.01.08.632047v1?rss=1 Pfaff, M. R. Wague, A. Davies, M. Killaars, A. R. Ning, D. Garcia, S. Nguyen, A. Nuthalapati, P. Liu, M. Liu, X. Feeley, B. T. Healy, K. E. 2025-01-13 doi:10.1101/2025.01.08.632047 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Modification of Non-photochemical Quenching Pathways in the C4 Model Plant Setaria viridis Revealed Shared and Unique Photoprotection Mechanisms as Compared to C3 Plants ]]> https://biorxiv.org/content/10.1101/2025.01.12.632622v1?rss=1 Milburn, G. Morris, C. M. Kosola, E. Patel-Tupper, D. Liu, J. Pham, D. H. Acosta-Gamboa, L. Stone, W. D. Pardi, S. Hillman, K. McHargue, W. E. Becker, E. Kang, X. Sumner, J. Bailey, C. Thielen, P. M. Jander, G. Kane, C. N. McAdam, S. A. M. Lawton, T. J. Nusinow, D. A. Zhang, F. Gore, M. A. Cheng, J. Niyogi, K. K. Zhang, R. 2025-01-15 doi:10.1101/2025.01.12.632622 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Kinking and buckling instability in growing bacterial chains ]]> https://biorxiv.org/content/10.1101/2025.01.12.632655v1?rss=1 McMahon, S. G. Neu, J. Chen, J. 2025-01-15 doi:10.1101/2025.01.12.632655 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Misophonia Symptoms Severity is Attributed to Impaired Flexibility and Heightened Rumination ]]> https://biorxiv.org/content/10.1101/2025.01.13.632542v1?rss=1 Black, V. Allen, J. Aazh, H. Johnson, S. L. Erfanian, M. 2025-01-15 doi:10.1101/2025.01.13.632542 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Overcoming Fluorescence Loss in mEOS-based AAA+ Unfoldase Reporters Through Covalent Linkage ]]> https://biorxiv.org/content/10.1101/2025.01.14.633048v1?rss=1 Walter, I. Smith, B. Castanzo, D. Wohlever, M. L. 2025-01-15 doi:10.1101/2025.01.14.633048 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Monitoring monomer-specific acyl-tRNA levels in cells with PARTI ]]> https://biorxiv.org/content/10.1101/2025.01.14.633079v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@f3b8a0org.highwire.dtl.DTLVardef@de400dorg.highwire.dtl.DTLVardef@13f17faorg.highwire.dtl.DTLVardef@13f2c0f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pressimone, M. A. Schissel, C. K. Goss, I. H. Swenson, C. V. Schepartz, A. 2025-01-15 doi:10.1101/2025.01.14.633079 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Genetic changes linked to two different syndromic forms of autism enhance reinforcement learning in adolescent male but not female mice ]]> https://biorxiv.org/content/10.1101/2025.01.15.633099v1?rss=1 Chase, J. Li, J.-J. Lin, W. C. Tai, L.-H. Collins, A. G. E. Wilbrecht, L. 2025-01-15 doi:10.1101/2025.01.15.633099 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ CPI-Pred: A deep learning framework for predicting functional parameters of compound-protein interactions ]]> https://biorxiv.org/content/10.1101/2025.01.16.633372v1?rss=1 Xu, Z. Barghout, R. A. Wu, J. Garg, D. Song, Y. S. Mahadevan, R. 2025-01-21 doi:10.1101/2025.01.16.633372 Cold Spring Harbor Laboratory Press 2025-01-21 <![CDATA[ Identification of regions required for allelic specificity at the cell wall remodeling allorecognition checkpoint in Neurospora crassa ]]> https://biorxiv.org/content/10.1101/2025.01.17.633681v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@7e150org.highwire.dtl.DTLVardef@1596b00org.highwire.dtl.DTLVardef@1800a37org.highwire.dtl.DTLVardef@11ea8d4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG ]]> Rico-Ramirez, A. M. Glass, N. L. 2025-01-22 doi:10.1101/2025.01.17.633681 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Autism-Associated Genes and Neighboring lncRNAs Converge on Key Gene Regulatory Networks ]]> https://biorxiv.org/content/10.1101/2025.01.20.634000v1?rss=1 Andersen, R. Talukdar, M. Sakamoto, T. Song, J. H. Qian, X. Lee, S. Delgado, R. N. Zhao, S. Eichfeld, G. Harms, J. Walsh, C. A. 2025-01-22 doi:10.1101/2025.01.20.634000 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Protein corona formed on lipid nanoparticles compromises delivery efficiency of mRNA cargo ]]> https://biorxiv.org/content/10.1101/2025.01.20.633942v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@2fef29org.highwire.dtl.DTLVardef@fe7613org.highwire.dtl.DTLVardef@1f9de01org.highwire.dtl.DTLVardef@15e5237_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Voke, E. Arral, M. Squire, H. J. Lin, T.-J. Coreas, R. Lui, A. Iavarone, A. T. Pinals, R. L. Whitehead, K. A. Landry, M. 2025-01-24 doi:10.1101/2025.01.20.633942 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ WASTER: Practical de novo phylogenomics from low-coverage short reads ]]> https://biorxiv.org/content/10.1101/2025.01.20.633983v1?rss=1 Zhang, C. Nielsen, R. 2025-01-24 doi:10.1101/2025.01.20.633983 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Single-cell differential detergent fractionation for detection of cytokeratin 8 proteoforms ]]> https://biorxiv.org/content/10.1101/2025.01.21.634008v1?rss=1 Khartchenko, A. F. Lam, T. Herr, A. 2025-01-24 doi:10.1101/2025.01.21.634008 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ The microbiome of Calasterella californica is shaped mostly by the genetics of the host thalli ]]> https://biorxiv.org/content/10.1101/2025.01.23.634585v1?rss=1 Gonzalez-Ramirez, I. Song, M. J. Mishler, B. D. 2025-01-24 doi:10.1101/2025.01.23.634585 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Lipidomic Analysis Reveals Drug-Induced Lipoxins in Glaucoma Treatment ]]> https://biorxiv.org/content/10.1101/2025.01.24.634771v1?rss=1 D, M. M. Maurya, S. Ho, J. Livne-Bar, I. Chan, D. Buys, Y. Sit, M. Trope, G. FLANAGAN, J. gronert, k. Sivak, J. M. 2025-01-27 doi:10.1101/2025.01.24.634771 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ From Local Interactions to Global Patterns: An Analysis of Silk Density in Spider Webs ]]> https://biorxiv.org/content/10.1101/2025.01.26.634972v1?rss=1 Lin, F. Nagel, K. M. Lee, S. Jiang, J. Yang, G. Chang, P. Li, S. Sheu, N. 2025-01-27 doi:10.1101/2025.01.26.634972 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ Non-Visual Light Sensing Enhances Behavioral Memory and Drives Gene Expression in C. elegans ]]> https://biorxiv.org/content/10.1101/2025.01.27.634647v1?rss=1 Ji, Z. Wang, B. Liu, J. Chandra, R. K. Yang, W. Long, Y. Egan, M. L'Etoile, N. Ma, D. K. 2025-01-28 doi:10.1101/2025.01.27.634647 Cold Spring Harbor Laboratory Press 2025-01-28 <![CDATA[ The Interplay of Furin Cleavage and D614G in Modulating SARS-CoV-2 Spike Protein Dynamics ]]> https://biorxiv.org/content/10.1101/2025.01.27.635166v1?rss=1 Shoemaker, S. R. Luo, M. Dam, K.-M. A. Pak, J. E. Hoffmann, M. A. G. Marqusee, S. 2025-01-28 doi:10.1101/2025.01.27.635166 Cold Spring Harbor Laboratory Press 2025-01-28 <![CDATA[ Identification of Scaffold Specific Energy Transfer Networks in the Enthalpic Activation of Orotidine 5'-Monophosphate Decarboxylase ]]> https://biorxiv.org/content/10.1101/2025.01.29.635545v1?rss=1 Dubey, P. Somani, A. Lin, J. Iavarone, A. T. Klinman, J. P. 2025-01-29 doi:10.1101/2025.01.29.635545 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ Capturing dynamic phage-pathogen coevolution by clinical surveillance ]]> https://biorxiv.org/content/10.1101/2025.01.29.635557v1?rss=1 Mathur, Y. Boyd, C. Farnham, J. MONIR, M. M. Islam, M. T. Sultana, M. Ahmed, T. Alam, M. Seed, K. 2025-01-29 doi:10.1101/2025.01.29.635557 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ SRS microscopy identifies inhibition of vitellogenesis as a mediator of lifespan extension by caloric restriction in C. elegans ]]> https://biorxiv.org/content/10.1101/2025.01.31.636008v1?rss=1 60%, but their combination has no additional effect on lifespan, suggesting that CR extends the lifespan of C. elegans in part by inhibiting vitellogenesis. The extensive dataset of more than 12,000 images stitched into over 350 whole-animal SRS images of C. elegans at different ages and subjected to different longevity intervention will be a valuable resource for researchers interested in aging. ]]> Yang, B. Manifold, B. Han, W. DeSousa, C. Zhu, W. Streets, A. M. Titov, D. V. 2025-02-03 doi:10.1101/2025.01.31.636008 Cold Spring Harbor Laboratory Press 2025-02-03 <![CDATA[ Generating functional plasmid origins with OriGen ]]> https://biorxiv.org/content/10.1101/2025.02.03.636306v1?rss=1 Irvine, J. Arora, J. Martinson, J. N. V. Patel, J. R. Hasham, S. I. Cress, B. F. Rubin, B. E. 2025-02-04 doi:10.1101/2025.02.03.636306 Cold Spring Harbor Laboratory Press 2025-02-04 <![CDATA[ Avid lysosomal acidification in fibroblasts of the Mediterranean mouse Mus spretus ]]> https://biorxiv.org/content/10.1101/2025.02.05.636718v1?rss=1 Sui, M. Teh, J. Fort, K. A. Shaw, D. E. Sudmant, P. H. Koide, T. Good, J. Vazquez, J. M. Brem, R. B. 2025-02-07 doi:10.1101/2025.02.05.636718 Cold Spring Harbor Laboratory Press 2025-02-07 <![CDATA[ Museum genomics reveals temporal genetic stasis and global genetic diversity in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2025.02.06.636844v1?rss=1 Lopez, L. Lang, P. L. M. Marciniak, S. Kistler, L. Latorre, S. M. Haile, A. Vasquez Cerda, E. Gamba, D. Xu, Y. Woods, P. Yifru, M. Kerby, J. McKay, J. K. Oakley, C. G. Agren, J. Wondimu, T. Bulafu, C. Perry, G. H. Burbano, H. A. Lasky, J. R. 2025-02-07 doi:10.1101/2025.02.06.636844 Cold Spring Harbor Laboratory Press 2025-02-07 <![CDATA[ Consumer resilience suppresses the recovery of overgrazed ecosystems ]]> https://biorxiv.org/content/10.1101/2025.02.04.636488v1?rss=1 Spindel, N. B. Galloway, A. W. E. Schram, J. B. Mcneill, G. D. Bellis, S. K. V. Guujaaw, N. Yakgujanaas, J. Pontier, O. Thompson, M. Lee, L. C. Okamoto, D. 2025-02-08 doi:10.1101/2025.02.04.636488 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Multitask deep learning for the emulation and calibration of an agent-based malaria transmission model ]]> https://biorxiv.org/content/10.1101/2025.02.05.636692v1?rss=1 Mondal, A. Anirudh, R. Selvaraj, P. 2025-02-08 doi:10.1101/2025.02.05.636692 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Somatic mutations distinguish melanocyte subpopulations in human skin ]]> https://biorxiv.org/content/10.1101/2025.02.07.637114v1?rss=1 Tandukar, B. Deivendran, D. Chen, L. Bahrani, N. Weier, B. Sharma, H. Cruz-Pacheco, N. Hu, M. Marks, K. Zitnay, R. G. Bandari, A. K. Nekoonam, R. Yeh, I. Judson-Torres, R. Shain, A. H. 2025-02-08 doi:10.1101/2025.02.07.637114 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Natural Variation in Photoprotection: Rapid NPQ Kinetics in Ferns ]]> https://biorxiv.org/content/10.1101/2025.02.07.637181v1?rss=1 Maryn, N. Chaparro, A. Short, A. Fleming, G. R. Niyogi, K. K. 2025-02-08 doi:10.1101/2025.02.07.637181 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Cross-membrane cooperation among bacteria can facilitate intracellular pathogenesis ]]> https://biorxiv.org/content/10.1101/2025.02.09.637186v1?rss=1 Schator, D. Kumar, N. G. Chong, S. J. U. Jung, T. K. Jedel, E. Smith, B. Evans, D. J. Fleiszig, S. M. J. 2025-02-09 doi:10.1101/2025.02.09.637186 Cold Spring Harbor Laboratory Press 2025-02-09 <![CDATA[ Discovery of widespread activating mutations in a compact RNA-guided endonuclease ]]> https://biorxiv.org/content/10.1101/2025.02.11.637750v1?rss=1 Thornton, B. W.-L. Weissman, R. F. Tran, R. V. Duong, B. T. Rodriguez, J. E. Terrace, C. I. Groover, E. D. Park, J.-U. Tartaglia, J. Doudna, J. A. Savage, D. 2025-02-12 doi:10.1101/2025.02.11.637750 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Circuit-Based Understanding of Fine Spatial Scale Clustering of Orientation Tuning in Mouse Visual Cortex ]]> https://biorxiv.org/content/10.1101/2025.02.11.637768v1?rss=1 20 {micro}m) are irregularly and randomly organized, while neuron pairs that are extremely close (< 20 {micro}m) have strongly correlated orientation tuning, indicating a narrow yet strong spatially clustered organization of orientation preference, which we term micro-clustered organization. Exploring a circuit-based model of recurrently coupled mouse V1 we derived two key predictions for the micro-cluster: spatially localized recurrent connections over a comparable narrow spatial scale, and common relative spatial spreads of balanced excitation and inhibition in the network over broad spatial scales. These predictions are validated by both anatomical and optogenetic-based physiological circuit mapping experiments. Altogether, our work takes an important step in building a circuit-based theory of visual processing in mouse V1 over spatial scales that are often ignored, yet contain powerful synaptic interactions. ]]> Yu, P. Yang, Y. Gozel, O. Oldenburg, I. Dipoppa, M. Rossi, F. Miller, K. Adesnik, H. Ji, N. Doiron, B. 2025-02-13 doi:10.1101/2025.02.11.637768 Cold Spring Harbor Laboratory Press 2025-02-13 <![CDATA[ Neural dynamics of proactive and reactive cognitive control in medial and lateral prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2025.02.12.637987v1?rss=1 Khan, A. U. Hoy, C. W. Anderson, K. L. Piai, V. King-Stephens, D. Laxer, K. D. Weber, P. Lin, J. J. Knight, R. T. Bentley, J. N. 2025-02-13 doi:10.1101/2025.02.12.637987 Cold Spring Harbor Laboratory Press 2025-02-13 <![CDATA[ Dual process impairments in reinforcement learning and working memory systems underlie learning deficits in physiological anxiety ]]> https://biorxiv.org/content/10.1101/2025.02.14.638024v1?rss=1 Senta, J. Bishop, S. J. Collins, A. G. E. 2025-02-14 doi:10.1101/2025.02.14.638024 Cold Spring Harbor Laboratory Press 2025-02-14 <![CDATA[ Covalent Destabilizing Degrader of AR and AR-V7 in Androgen-Independent Prostate Cancer Cells ]]> https://biorxiv.org/content/10.1101/2025.02.12.637117v1?rss=1 Zammit, C. M. Nadel, C. Lin, Y. Koirala, S. Potts, P. R. Nomura, D. K. 2025-02-16 doi:10.1101/2025.02.12.637117 Cold Spring Harbor Laboratory Press 2025-02-16 <![CDATA[ Biochemical and structural basis of Dicer helicase function unveiled by resurrecting ancient proteins ]]> https://biorxiv.org/content/10.1101/2025.02.15.638221v1?rss=1 Aderounmu, A. Maus-Conn, J. Consalvo, C. D. Shen, P. S. Bass, B. L. 2025-02-16 doi:10.1101/2025.02.15.638221 Cold Spring Harbor Laboratory Press 2025-02-16 <![CDATA[ A subset of conserved phagocytic genes are likely used for the intracellular theft of cnidarian stinging organelles in nudibranch gastropods ]]> https://biorxiv.org/content/10.1101/2025.02.13.637864v1?rss=1 Goodheart, J. A. Fiorenza, R. Rio, R. Lopez-Anido, R. N. Martin, N. J. Herrlinger, T. J. Tarvin, R. D. Lyons, D. C. 2025-02-17 doi:10.1101/2025.02.13.637864 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ Infections in the Atlantic Blue Crab Callinectes sapidus (Rathbun, 1896) in coastal Adriatic and Aegean sea, and Atlantic Iberian coast ]]> https://biorxiv.org/content/10.1101/2025.02.14.637520v1?rss=1 Schott, E. Scepanovic, M. B. Lucic, J. M. Pares, O. Zhao, M. Hrabar, J. Glamuzina, L. Pecarevic, M. Grdan, S. Encarnacao, J. P. d. S. Morais, P. Cetkovic, I. Glamuzina, B. 2025-02-17 doi:10.1101/2025.02.14.637520 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ RB-TnSeq elucidates dicarboxylic acid specific catabolism in β-proteobacteria for improved plastic monomer upcycling ]]> https://biorxiv.org/content/10.1101/2025.02.21.639450v1?rss=1 Pearson, A. N. Lynch, J. M. Ho, C. N. Hudson, G. A. Roberts, J. B. Menasalvas, J. Vilchez, A. A. Incha, M. R. Schmidt, M. Mukhopadhyay, A. Deutschbauer, A. M. Thompson, M. G. Shih, P. Keasling, J. D. 2025-02-21 doi:10.1101/2025.02.21.639450 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ A vectorial code for semantics in human hippocampus ]]> https://biorxiv.org/content/10.1101/2025.02.21.639601v1?rss=1 Franch, M. Mickiewicz, E. A. Belanger, J. Chericoni, A. Chavez, A. G. Katlowitz, K. Mathura, R. Bartoli, E. Kemmer, S. Piantadosi, S. T. Provenza, N. Watrous, A. Sheth, S. Hayden, B. 2025-02-23 doi:10.1101/2025.02.21.639601 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ Local variations in L/M ratio influence the detection and color naming of small spots ]]> https://biorxiv.org/content/10.1101/2025.02.19.639104v1?rss=1 Greene, M. J. Pandiyan, V. P. Sabesan, R. Tuten, W. S. 2025-02-24 doi:10.1101/2025.02.19.639104 Cold Spring Harbor Laboratory Press 2025-02-24 <![CDATA[ A network of coiled-coil and actin-like proteins controls the cellular organization of magnetosome organelles in deep-branching magnetotactic bacteria ]]> https://biorxiv.org/content/10.1101/2025.02.24.639979v1?rss=1 Russell, V. V. Iavarone, A. T. Ozyamak, E. Grant, C. Komeili, A. 2025-02-24 doi:10.1101/2025.02.24.639979 Cold Spring Harbor Laboratory Press 2025-02-24 <![CDATA[ Electrostatics facilitate mid-air host attachment in parasitic jumping nematodes ]]> https://biorxiv.org/content/10.1101/2025.02.20.639345v1?rss=1 Ran, R. Burton, J. C. Ortega-Jimenez, V. M. 2025-02-26 doi:10.1101/2025.02.20.639345 Cold Spring Harbor Laboratory Press 2025-02-26 <![CDATA[ pholidosis: an R package to compare biological surface patterns ]]> https://biorxiv.org/content/10.1101/2025.02.23.639543v1?rss=1 Krone, I. W. 2025-02-28 doi:10.1101/2025.02.23.639543 Cold Spring Harbor Laboratory Press 2025-02-28 <![CDATA[ mTORC1 activation drives astrocyte reactivity in cortical tubers and brain organoid models of TSC ]]> https://biorxiv.org/content/10.1101/2025.02.28.640914v1?rss=1 Li, T. L. Blair, J. D. Yoo, T. Grant, G. A. Hockemeyer, D. Porter, B. E. Bateup, H. S. 2025-03-05 doi:10.1101/2025.02.28.640914 Cold Spring Harbor Laboratory Press 2025-03-05 <![CDATA[ Morphogenesis and morphometry of brain folding patterns across species ]]> https://biorxiv.org/content/10.1101/2025.03.05.641692v1?rss=1 Yin, S. Liu, C. Choi, G. P. T. Jung, Y. Heuer, K. Toro, R. Mahadevan, L. 2025-03-10 doi:10.1101/2025.03.05.641692 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ FACED 2.0 enables large-scale voltage and calcium imaging in vivo ]]> https://biorxiv.org/content/10.1101/2025.03.06.641784v1?rss=1 Zhong, J. Natan, R. G. Zhang, Q. Wong, J. S. J. Miehl, C. Bose, K. Lu, X. St-Pierre, F. Guo, S. Doiron, B. Tsia, K. K. Ji, N. 2025-03-10 doi:10.1101/2025.03.06.641784 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Poxvirus attack of anti-viral defense pathways unleashes an effector-triggered NF-κB response ]]> https://biorxiv.org/content/10.1101/2025.03.04.641538v1?rss=1 Remick, B. C. Mao, J. Q. Manford, A. G. Gutierrez-Jensen, A. D. Wagner, A. Rape, M. McFadden, G. Rahman, M. M. Gaidt, M. M. Vance, R. E. 2025-03-11 doi:10.1101/2025.03.04.641538 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Robust and Adaptive Non-Parametric Tests for Detecting General Distributional Shifts in Gene Expression ]]> https://biorxiv.org/content/10.1101/2025.03.06.641952v1?rss=1 Zhou, F. Aw, A. J. Erdmann-Pham, D. D. Fischer, J. Song, Y. S. 2025-03-11 doi:10.1101/2025.03.06.641952 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Brainstem circuit for sickness-induced sleep ]]> https://biorxiv.org/content/10.1101/2025.03.09.642181v1?rss=1 Darmohray, D. Yao, Y. Sima, J. Chen, C.-H. Silverman, D. Chen, C. Dan, Y. 2025-03-11 doi:10.1101/2025.03.09.642181 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Subliminal risk influences subjective value in the ventromedial prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2025.03.11.642695v1?rss=1 1 or 0 points depending on probability cue). The risky reward was either 2 or 5 points, varying across trials. In some trials the probability cue was absent (replaced by a random distractor) and the probability to win the risky reward was 50%. When probability cues were unseen, they did not influence choice, as value-maximizing choice (d) was not greater than chance, but they did influence reaction time in both experiments. Consistent with SV integration, the BOLD signal in aVS and vmPFC was higher for both conscious rewards (high > low) and subliminal probabilities (high > low) and could not be explained by subliminal salience (cue present > absent). Moreover, multivariate pattern similarity between conscious rewards and subliminal probabilities in vmPFC suggest integration into an abstract value representation. Additionally, we found brain-wide subliminal probability and salience effects. Taken together, these results suggest that conscious awareness is not necessary for probability to be integrated with conscious rewards to form an abstract "common currency" SV representation in vmPFC. Additionally, brain-wide subliminal probability and salience effects suggests information can have "global access" without conscious awareness. ]]> Fernandes, P. Lee, S. Kable, J. W. Seidel, P. Almeida, J. Eriksson, J. de Sousa, B. Bergstrom, F. 2025-03-13 doi:10.1101/2025.03.11.642695 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ DiMeLo-cito: a one-tube protocol for mapping protein-DNA interactions reveals CTCF bookmarking in mitosis ]]> https://biorxiv.org/content/10.1101/2025.03.11.642717v1?rss=1 Gamarra, N. Chittenden, C. Sundararajan, K. Schwartz, J. P. Lundqvist, S. Robles, D. Dixon-Luinenburg, O. Marcus, J. Maslan, A. Franklin, J. M. Streets, A. Straight, A. F. Altemose, N. 2025-03-14 doi:10.1101/2025.03.11.642717 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Microtubule-dependent cell polarity regulates skin-resident macrophage phagocytosis and directed cell migration ]]> https://biorxiv.org/content/10.1101/2025.03.13.642867v1?rss=1 Peterman, E. Murphy, A. Swinburne, I. Megason, S. Rasmussen, J. P. 2025-03-15 doi:10.1101/2025.03.13.642867 Cold Spring Harbor Laboratory Press 2025-03-15 <![CDATA[ transfactor: Transcription factor activity estimation via probabilistic gene expression deconvolution ]]> https://biorxiv.org/content/10.1101/2025.03.19.644088v1?rss=1 Van den Berge, K. Bickel, P. J. Dudoit, S. 2025-03-19 doi:10.1101/2025.03.19.644088 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ Gyral crowns contribute to the cortical infrastructure of human face processing ]]> https://biorxiv.org/content/10.1101/2025.03.20.644439v1?rss=1 Willbrand, E. H. Kelly, J. P. Chen, X. Zhen, Z. Jiahui, G. Duchaine, B. Weiner, K. S. 2025-03-21 doi:10.1101/2025.03.20.644439 Cold Spring Harbor Laboratory Press 2025-03-21 <![CDATA[ A GENERALIZED PROTEIN DESIGN ML MODEL ENABLESGENERATION OF FUNCTIONAL DE NOVO PROTEINS ]]> https://biorxiv.org/content/10.1101/2025.03.21.644400v1?rss=1 Riley, T. P. Matusovsky, O. Parsa, M. S. Kalantari, P. Naderi, I. Azimian, K. Wei, K. Y. 2025-03-22 doi:10.1101/2025.03.21.644400 Cold Spring Harbor Laboratory Press 2025-03-22 <![CDATA[ Aromatic acid metabolism in Methylobacterium extorquens reveals interplay between methylotrophic and heterotrophic pathways ]]> https://biorxiv.org/content/10.1101/2025.03.22.644763v1?rss=1 Govindaraju, A. M. Martinez-Gomez, N. C. 2025-03-23 doi:10.1101/2025.03.22.644763 Cold Spring Harbor Laboratory Press 2025-03-23 <![CDATA[ Mosquito Dispersal in Context ]]> https://biorxiv.org/content/10.1101/2025.03.22.642900v1?rss=1 Sanchez Castellanos, H. M. Wu, S. L. Henry, J. M. Guerra, C. A. Galick, D. S. Garcia, G. Marshall, J. M. Smith, D. L. 2025-03-25 doi:10.1101/2025.03.22.642900 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Temporal fMRI Dynamics Map Dopamine Physiology ]]> https://biorxiv.org/content/10.1101/2025.03.24.645022v1?rss=1 Ballard, I. Pappas, I. Furman, D. J. Berry, A. S. Frederick, B. d. White, R. L. Kayser, A. S. Jagust, W. J. D'Esposito, M. 2025-03-26 doi:10.1101/2025.03.24.645022 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Where are they now? Academic and career trajectories of national laboratory STEM internship alumni from community colleges, compared to those from universities ]]> https://biorxiv.org/content/10.1101/2025.03.24.645145v1?rss=1 Cote, L. E. Zamora, A. N. Jaramillo Salcido, J. Van Doren, S. Manocha, A. Otero Munoz, G. Law, E. W. Baranger, A. M. 2025-03-26 doi:10.1101/2025.03.24.645145 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Rare Jackpot Individuals Drive Rapid Adaptation in Threespine Stickleback ]]> https://biorxiv.org/content/10.1101/2025.03.25.642177v1?rss=1 Kwakye, A. Reid, K. Wund, M. A. Heins, D. C. Bell, M. A. Veeramah, K. R. 2025-03-26 doi:10.1101/2025.03.25.642177 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Directed evolution expands CRISPR-Cas12a genome editing capacity ]]> https://biorxiv.org/content/10.1101/2025.03.26.645588v1?rss=1 Ma, E. Chen, K. Shi, H. Wasko, K. M. Esain-Garcia, I. Trinidad, M. I. Zhou, K. Ye, J. Doudna, J. A. 2025-03-26 doi:10.1101/2025.03.26.645588 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Assessing the combined performance of supervised learning and spike-in constructs for bias correction in eDNA metabarcoding ]]> https://biorxiv.org/content/10.1101/2025.03.25.645285v1?rss=1 Chang, J. Nielsen, R. 2025-03-28 doi:10.1101/2025.03.25.645285 Cold Spring Harbor Laboratory Press 2025-03-28 <![CDATA[ A miniature CRISPR-Cas10 enzyme confers immunity by an inverse signaling pathway ]]> https://biorxiv.org/content/10.1101/2025.03.28.646030v1?rss=1 Doherty, E. E. Adler, B. A. Yoon, P. H. Hsieh, K. Loi, K. Armbuster, E. G. Lahiri, A. Bolling, C. S. Wilcox, X. E. Akkati, A. Iavarone, A. T. Pogliano, J. Doudna, J. A. 2025-03-30 doi:10.1101/2025.03.28.646030 Cold Spring Harbor Laboratory Press 2025-03-30 <![CDATA[ Barrier-Free Microhabitats: Self-Organized Seclusion in Microbial Communities ]]> https://biorxiv.org/content/10.1101/2025.03.26.645601v1?rss=1 Slepukhin, V. Peris-Yague, V. Westendorf, C. Koch, B. Hallatschek, O. 2025-03-31 doi:10.1101/2025.03.26.645601 Cold Spring Harbor Laboratory Press 2025-03-31 <![CDATA[ The third alpha helix of plant homeoproteins are generally cell-penetrating to plant cells ]]> https://biorxiv.org/content/10.1101/2025.04.01.646723v1?rss=1 Squire, H. J. Wang, J. W.-T. Landry, M. P. 2025-04-02 doi:10.1101/2025.04.01.646723 Cold Spring Harbor Laboratory Press 2025-04-02 <![CDATA[ Paired Analyses of Nuclear Protein Targets and Genomic DNA by Single-Cell Western Blot and Single-Cell PCR ]]> https://biorxiv.org/content/10.1101/2025.03.29.646125v1?rss=1 View larger version (17K): org.highwire.dtl.DTLVardef@168541corg.highwire.dtl.DTLVardef@69ff17org.highwire.dtl.DTLVardef@ea4fa1org.highwire.dtl.DTLVardef@111daad_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gomez Martinez, A. E. Lam, T. Herr, A. 2025-04-03 doi:10.1101/2025.03.29.646125 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Improving interpretability of transcription factor binding models with DNA shape features ]]> https://biorxiv.org/content/10.1101/2025.04.01.646034v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@b648b6org.highwire.dtl.DTLVardef@15fa931org.highwire.dtl.DTLVardef@15d0d31org.highwire.dtl.DTLVardef@d212e_HPS_FORMAT_FIGEXP M_FIG C_FIG Schematic overview of the DeepShape model. One-hot encoded sequence, and five DNA shape attributes--minor groove width (MGW), helical twist (HelT), propeller twist (ProT), roll, and electrostatic potential (EP)--are input separately to sequence and shape branches of the model, each processed through two convolutional layers and subsequently concatenated for further processing through additional convolutional layers. ]]> Keivanfar, R. L. Yang, F. Pollard, K. S. Ioannidis, N. M. 2025-04-03 doi:10.1101/2025.04.01.646034 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Excitation Spectral Phasor Microscopy (ExSPM) unveils spatiotemporal heterogeneities in polarity of intracellular lipid droplets ]]> https://biorxiv.org/content/10.1101/2025.04.03.647137v1?rss=1 Liu, J. He, Y. Yan, R. Yan, J. Wang, R. Zhang, Z. Xia, J. Kireev, I. Xu, K. Chen, K. 2025-04-05 doi:10.1101/2025.04.03.647137 Cold Spring Harbor Laboratory Press 2025-04-05 <![CDATA[ How Nasal Cavity Structure Influences Empty Nose Syndrome Severity: A CFD-Based Analysis ]]> https://biorxiv.org/content/10.1101/2025.04.04.645990v1?rss=1 RUMIANO, A. Dinh, T. 2025-04-09 doi:10.1101/2025.04.04.645990 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ Force-insensitive myosin-I enhances endocytosis robustness through actin network-scale collective ratcheting ]]> https://biorxiv.org/content/10.1101/2025.04.04.647278v1?rss=1 Ferrin, M. A. Pedersen, R. T. Drubin, D. G. Akamatsu, M. 2025-04-09 doi:10.1101/2025.04.04.647278 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ SpeedyTrack: Direct microsecond wide-field single-molecule tracking and super-resolution mapping via CCD vertical shift ]]> https://biorxiv.org/content/10.1101/2025.04.07.647376v1?rss=1 30 timepoints, permitting trajectory analysis to quantify diffusion coefficients up to 1,000 {micro}m2/s. Concurrent acquisition of single-molecule diffusion trajectories and Forster resonance energy transfer (FRET) time traces further elucidates conformational dynamics and binding states for diffusing molecules. Moreover, with a temporally patterned vertical shifting scheme, we deconvolve the spatial and temporal information to map long, fast single-molecule trajectories at the super-resolution level, thus resolving the diffusion mode of a fluorescent protein in live cells with nanoscale resolution. While these demonstrated capabilities substantially outperform existing approaches, SpeedyTrack further stands out for its simplicity by directly working off the built-in functionalities of EM-CCDs without the need to modify existing optics or electronics. We thus provide a facile solution to the microsecond tracking/imaging of single molecules and their super-resolution mapping in the wide field. ]]> Steves, M. A. Xu, K. 2025-04-10 doi:10.1101/2025.04.07.647376 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Restoration of urban salmon habitat has limited effects on a key ecosystem function ]]> https://biorxiv.org/content/10.1101/2025.04.11.648418v1?rss=1 Wik, A. R. Little, C. J. 2025-04-11 doi:10.1101/2025.04.11.648418 Cold Spring Harbor Laboratory Press 2025-04-11 <![CDATA[ Warm waters undermine cryptic female choice ]]> https://biorxiv.org/content/10.1101/2025.04.10.648287v1?rss=1 Kustra, M. C. Alissa, L. M. Rogers, M. M. Molinari, M. M. Stiver, K. A. Marsh-Rollo, S. Hellmann, J. K. Alonzo, S. H. 2025-04-16 doi:10.1101/2025.04.10.648287 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ Seasonal brain regeneration and chromosome instability are linked to selection on DNA repair in Sorex araneus ]]> https://biorxiv.org/content/10.1101/2025.04.11.648246v1?rss=1 Thomas, W. R. Lama, T. M. Moreno-Santillan, D. Farre, M. Baldoni, C. Abueg, L. Balacco, J. Fedrigo, O. Formenti, G. Jain, N. Mountcastle, J. Tilley, T. Tracey, A. Ray, D. A. Dechmann, D. K. N. von Elverfeldt, D. Nieland, J. Corthals, A. P. Jarvis, E. Davalos, L. M. 2025-04-17 doi:10.1101/2025.04.11.648246 Cold Spring Harbor Laboratory Press 2025-04-17 <![CDATA[ G protein-coupled receptor diversity and evolution in the closest living relatives of Metazoa ]]> https://biorxiv.org/content/10.1101/2025.04.15.649019v1?rss=1 Garcia De Las Bayonas, A. King, N. 2025-04-17 doi:10.1101/2025.04.15.649019 Cold Spring Harbor Laboratory Press 2025-04-17 <![CDATA[ Write and read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing. ]]> https://biorxiv.org/content/10.1101/2025.04.14.648727v1?rss=1 Bertocchi, U. Grunwald, A. Goldner, G. Eitan, E. Avraham, S. Deek, J. Michaeli, Y. Yao, B. Listgarten, J. Simpson, J. T. Timp, W. Ebenstein, Y. 2025-04-19 doi:10.1101/2025.04.14.648727 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ Feature-tuned synaptic inputs to somatostatin interneurons drive context-dependent processing ]]> https://biorxiv.org/content/10.1101/2025.04.16.649203v1?rss=1 Hendricks, W. D. Sadahiro, M. Mossing, D. P. Veit, J. Adesnik, H. 2025-04-19 doi:10.1101/2025.04.16.649203 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ OpenIrisDPI: An Open-Source Digital Dual Purkinje Image Eye Tracker for Visual Neuroscience ]]> https://biorxiv.org/content/10.1101/2025.04.18.649589v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@596dd2org.highwire.dtl.DTLVardef@139027borg.highwire.dtl.DTLVardef@1d1e526org.highwire.dtl.DTLVardef@11b321c_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIOpenIrisDPI is a new open-source eye tracking system. C_LIO_LIOpenIrisDPI tracks the pupil, corneal reflection, & fourth Purkinje image at 500 Hz. C_LIO_LIDual Purkinje image-based eye tracking is more precise than pupilbased tracking. C_LIO_LIDPI improves receptive field characterization of LGN neurons in fixating macaques. C_LI ]]> Ressmeyer, R. A. Otero-Millan, J. Horwitz, G. D. Yates, J. 2025-04-19 doi:10.1101/2025.04.18.649589 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ Cell-type-specific transposable element demethylation and TAD remodeling in the aging mouse brain ]]> https://biorxiv.org/content/10.1101/2025.04.21.648266v1?rss=1 Zeng, Q. Tian, W. Klein, A. Bartlett, A. Liu, H. Nery, J. R. Castanon, R. G. Osteen, J. Johnson, N. Wang, W. Ding, W. Chen, H. Altshul, J. Kenworthy, M. Valadon, C. Owens, W. Wu, Z. Amaral, M. L. Song, Y. Baez-Becerra, C. T. Cho, S. Chen, C. Willier, J. Cao, S. Rink, J. Lee, J. Barcoma, A. Arzavala, J. Emerson, N. Lu, Y. R. Ren, B. Behrens, M. M. Ecker, J. R. 2025-04-21 doi:10.1101/2025.04.21.648266 Cold Spring Harbor Laboratory Press 2025-04-21 <![CDATA[ Exogenous Thyroxine Increases Cardiac Nrf2-TRX in Insulin Resistant OLETF Rats ]]> https://biorxiv.org/content/10.1101/2025.04.16.649239v1?rss=1 Mendez, D. A. Hernandez Garcia, J. Sonanez-Organis, J. G. Hernandez Garcia, M. Vazquez-Anaya, G. Nishiyama, A. Vazquez-Medina, J. P. Ortiz, R. M. 2025-04-23 doi:10.1101/2025.04.16.649239 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Horizontal saccade bias results from combination of saliency anisotropies and egocentric biases ]]> https://biorxiv.org/content/10.1101/2025.04.21.648827v1?rss=1 Reeves, S. M. Otero-Millan, J. 2025-04-24 doi:10.1101/2025.04.21.648827 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains captures global and local expression variation ]]> https://biorxiv.org/content/10.1101/2025.04.21.649844v1?rss=1 Rebboah, E. Weber, R. Abdollahzadeh, E. Swarna, N. P. Sullivan, D. K. Trout, D. Reese, F. Liang, H. Y. Filimban, G. Mahdipour, P. Duffield, M. Mojaverzargar, R. Taghizadeh, E. Fattahi, N. Mojgani, N. Zhang, H. Loving, R. K. Carilli, M. Booeshaghi, A. S. Kawauchi, S. Hallgrimsdottir, I. B. Williams, B. A. MacGregor, G. Pachter, L. Wold, B. Mortazavi, A. 2025-04-24 doi:10.1101/2025.04.21.649844 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Assemblies of long-read metagenomes suffer from diverse errors ]]> https://biorxiv.org/content/10.1101/2025.04.22.649783v1?rss=1 Trigodet, F. Sachdeva, R. Banfield, J. F. Eren, A. M. 2025-04-24 doi:10.1101/2025.04.22.649783 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ DCAF16-Based Covalent Degradative Handles for the Modular Design of Degraders ]]> https://biorxiv.org/content/10.1101/2025.04.25.650514v1?rss=1 Orr, L. M. Tomlinson, S. J. Grupe, H. R. Lim, M. Ho, E. Yilmaz, H. Zhou, G. Leon, B. Olzmann, J. A. Nomura, D. K. 2025-04-29 doi:10.1101/2025.04.25.650514 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ The status of human goal-directed actions after manipulations of the action-outcome contingency ]]> https://biorxiv.org/content/10.1101/2025.04.26.650713v1?rss=1 Perez, O. D. Merlo, E. Oh, S. Arenas, J. Dickinson, A. 2025-04-30 doi:10.1101/2025.04.26.650713 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Small molecule bioactivity benchmarks are often well-predicted by counting cells ]]> https://biorxiv.org/content/10.1101/2025.04.27.650853v1?rss=1 Seal, S. Dee, W. Shah, A. Zhang, A. Titterton, K. Cabrera, A. A. Boiko, D. Beatson, A. Puigvert, J. C. Singh, S. Spjuth, O. Bender, A. Carpenter, A. E. 2025-04-30 doi:10.1101/2025.04.27.650853 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Constitutive Androstane Receptor induces Ribonucleotide Reductase-M2 expression and maintains hepatocyte ploidy in mice ]]> https://biorxiv.org/content/10.1101/2025.04.29.651109v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@5e41faorg.highwire.dtl.DTLVardef@3db897org.highwire.dtl.DTLVardef@21dd53org.highwire.dtl.DTLVardef@1497b64_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Asokaumar, A. Mathur, B. Chou, A. Cronologia, B. Alencastro, F. Wheeler, L. Mathews, C. K. Moore, D. D. Duncan, A. W. Anakk, S. 2025-05-02 doi:10.1101/2025.04.29.651109 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ Chromatix: a differentiable, GPU-accelerated wave-optics library ]]> https://biorxiv.org/content/10.1101/2025.04.29.651152v1?rss=1 Deb, D. Both, G.-J. Bezzam, E. Kohli, A. Yang, S. Chaware, A. Allier, C. Cai, C. Anderberg, G. Eybposh, M. H. Schneider, M. C. Heintzmann, R. Rivera-Sanchez, F. A. Simmerer, C. Meng, G. Tormes-Vaquerano, J. Han, S. Shanmugavel, S. C. Maruvada, T. Yang, X. Kim, Y. Diederich, B. Joo, C. Waller, L. Durr, N. J. Pegard, N. C. La Riviere, P. J. Horstmeyer, R. Chowdhury, S. Turaga, S. C. 2025-05-02 doi:10.1101/2025.04.29.651152 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ The Optimal Retinal Locus for High-Resolution Vision in Space and Time ]]> https://biorxiv.org/content/10.1101/2025.04.30.650879v1?rss=1 Gautier, J. Bowers, N. R. Banks, M. S. Roorda, A. 2025-05-06 doi:10.1101/2025.04.30.650879 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ Heterchronic shifts in a timing-keeping microRNA are associated with multiple instances of neoteny in plants ]]> https://biorxiv.org/content/10.1101/2025.04.30.651569v1?rss=1 Leichty, A. R. Poethig, R. S. 2025-05-07 doi:10.1101/2025.04.30.651569 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Ectodysplasin overexpression reveals spatiotemporally dynamic tooth formation competency in stickleback and zebrafish ]]> https://biorxiv.org/content/10.1101/2025.05.01.651241v1?rss=1 Chen, Z. Z. Narayanan, S. N. Stagliano, L. M. Huynh, P. Q. Sundaram, S. Mackey, E. J. Miller, C. T. Square, T. A. 2025-05-07 doi:10.1101/2025.05.01.651241 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Landscape genomics and demography of California Azolla ]]> https://biorxiv.org/content/10.1101/2025.05.02.651959v1?rss=1 Song, M. J. Tribble, C. M. Gonzalez-Ramirez, I. Freund, F. Li, F.-W. Rothfels, C. J. 2025-05-08 doi:10.1101/2025.05.02.651959 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Associations between floor material and E. coli contamination in rural Bangladeshi households ]]> https://biorxiv.org/content/10.1101/2025.05.07.652756v1?rss=1 Tazin, S. Islam, M. Pickering, A. J. Kwong, L. H. Mertens, A. Niven, C. Arnold, B. F. Hubbard, A. E. Alam, M. Sen, D. Islam, S. Rahman, M. Unicomb, L. Luby, S. P. Benjamin-Chung, J. Ercumen, A. 2025-05-08 doi:10.1101/2025.05.07.652756 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Leveraging a synthetic biology approach to enhance BCG-mediated expansion of Vγ9Vδ2 T cells ]]> https://biorxiv.org/content/10.1101/2025.05.05.651767v1?rss=1 63 mycobacterial species, which revealed that isoprenoid biosynthetic genes are not found in gene clusters or operons across all the 356 surveyed genomes. This analysis also revealed pair biases of isoprenoid biosynthesis genes frequently found in close proximity. In our engineering attempts, we found that simply overexpressing the rate-limiting gene in the pathway was toxic to the bacterium. Thus, we generated synthetic loci with the goal of specifically overproducing HMBPP, and tested the ability of these engineered strains to induce human V{gamma}9V{delta}2 expansion in an in vitro stimulation assay. We found that BCG expressing a rationally-designed, synthetic MEP locus did not enhance V{gamma}9V{delta}2 T cell expansion over the wild-type vaccine strain, suggesting that ectopic expression of multiple MEP genes may result in feedback inhibition of the pathway. However we found that overexpression of the HMBPP synthase GcpE alone potently induced V{gamma}9V{delta}2 T cell expansion and did not result in downregulation of other pathway genes, presenting a successful strategy to accumulate HMBPP and overcome feedback inhibition in this pathway. While much remains to be done to ultimately develop a more efficacious vaccine, our data present a promising system to improve upon the BCG platform. To our knowledge, this is the first work to attempt reengineering of the MEP pathway in BCG to improve vaccine efficacy. ]]> Qabar, C. M. Waldburger, L. Keasling, J. D. Portnoy, D. A. M. Cox, J. S. 2025-05-09 doi:10.1101/2025.05.05.651767 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Lineage-Specific Evolution, Structural Diversity, and Activity of R2 Retrotransposons in Animals ]]> https://biorxiv.org/content/10.1101/2025.05.05.652312v1?rss=1 Hassan, N. T. Van Treeck, B. Rodriguez-Vargas, A. Sheppard, A. E. Adelson, D. L. Collins, K. 2025-05-09 doi:10.1101/2025.05.05.652312 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Micron-scale, liquid-liquid phase separation in ternary lipid membranes containing DPPE ]]> https://biorxiv.org/content/10.1101/2025.05.08.652930v1?rss=1 Goetz, G. J. Naomi, S. Madrigal, A. M. Chang, C. L. A. Cornell, C. E. Keller, S. L. 2025-05-09 doi:10.1101/2025.05.08.652930 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Separable global and local beta burst dynamics in motor cortex of primates ]]> https://biorxiv.org/content/10.1101/2025.05.05.652217v1?rss=1 Khanna, P. farrokhi, b. Choi, H. Griffin, S. Heimbuch, I. Novik, L. Thiesen, K. Morrison, J. H. Morecraft, R. Ganguly, K. 2025-05-10 doi:10.1101/2025.05.05.652217 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ The bivalent epigenetic regulator ULTRAPETALA1 promotes the Arabidopsis floral transition via recruitment of Polycomb histone methyltransferases for H3K27me3 deposition at the FLC locus ]]> https://biorxiv.org/content/10.1101/2025.05.06.652514v1?rss=1 Xing, Q. Shemyakina, E. Tian, J. Strotmann, V. I. Anwar, A. Li, X. Xiong, Y. Yang, T. Zheng, Y. Pu, L. Stahl, Y. Mueller-Xing, R. Fletcher, J. C. 2025-05-11 doi:10.1101/2025.05.06.652514 Cold Spring Harbor Laboratory Press 2025-05-11 <![CDATA[ An IMPDH2 variant associated with neurodevelopmental disorder disrupts purine biosynthesis and somitogenesis ]]> https://biorxiv.org/content/10.1101/2025.05.09.652712v1?rss=1 O'Neill, A. G. McCartney, M. E. Wheeler, G. M. Patel, J. H. Sanchez-Ramirez, G. Kollman, J. M. Wills, A. E. 2025-05-11 doi:10.1101/2025.05.09.652712 Cold Spring Harbor Laboratory Press 2025-05-11 <![CDATA[ Neurochemical imaging reveals changes in dopamine dynamics with photoperiod in a seasonally social vole species ]]> https://biorxiv.org/content/10.1101/2025.05.11.652581v1?rss=1 Mun, J. Power, K. C. Beery, A. K. Landry, M. P. 2025-05-12 doi:10.1101/2025.05.11.652581 Cold Spring Harbor Laboratory Press 2025-05-12 <![CDATA[ Mycobacterium tuberculosis suppresses protective Th17 responses during infection through multiple mechanisms ]]> https://biorxiv.org/content/10.1101/2025.05.08.652811v1?rss=1 Zilinskas, A. Balakhmet, A. Fox, D. Ni, H. M. Agudelo, C. Samani, H. Stanley, S. A. 2025-05-13 doi:10.1101/2025.05.08.652811 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Composition, growth, succession, and function in the Cladophora microbiome: insights from quantitative Stable Isotope Probing and NanoSIMS imaging ]]> https://biorxiv.org/content/10.1101/2025.05.12.652736v1?rss=1 Fitzpatrick, R. M. Hungate, B. A. Power, M. E. Schwartz, E. Hayer, M. Samo, T. Weber, P. Pett-Ridge, J. Foley, M. Marks, J. C. 2025-05-13 doi:10.1101/2025.05.12.652736 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Novel Fluorescent and Photoconvertible Fusions Reveal Dorsal Activator Dynamics ]]> https://biorxiv.org/content/10.1101/2025.05.12.653543v1?rss=1 Turner, M. A. Gravina, N. M. Moretti, B. Dima, S. S. Martini, G. Reeves, G. T. Garcia, H. 2025-05-13 doi:10.1101/2025.05.12.653543 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Organic carbon oxidation state shapes fermentative methanogenic microbiomes and controls greenhouse gas fluxes ]]> https://biorxiv.org/content/10.1101/2025.05.12.653603v1?rss=1 Hu, R. Aronson, H. S. Weaver, M. E. Price, M. N. Larowe, D. E. Liang, Y. Deutschbauer, A. M. Coates, J. D. Carlson, H. K. 2025-05-13 doi:10.1101/2025.05.12.653603 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ A generative language model decodes contextual constraints on codon choice for mRNA design ]]> https://biorxiv.org/content/10.1101/2025.05.13.653614v1?rss=1 Faizi, M. Sakharova, H. Lareau, L. F. 2025-05-13 doi:10.1101/2025.05.13.653614 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Alternative Splicing in TRPA1 Drives Sensory Adaptation to Electrophiles in Drosophilids ]]> https://biorxiv.org/content/10.1101/2025.05.09.653172v1?rss=1 Suzuki, H. C. Saito, C. T. Rajshekar, S. Sokabe, T. Haji, D. Groen, S. C. Pelaez, J. N. Matsunaga, T. Takemoto, A. S. Tanaka, K. M. Takahashi, A. Tominaga, M. Saito, S. Whiteman, N. K. 2025-05-14 doi:10.1101/2025.05.09.653172 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ A defined growth medium for trace metal limitation studies in Auxenochlorella sp. (UTEX 250-A) during mixotrophic growth with glucose. ]]> https://biorxiv.org/content/10.1101/2025.05.09.653207v1?rss=1 Camacho, D. J. Moseley, J. L. Merchant, S. S. 2025-05-14 doi:10.1101/2025.05.09.653207 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Multiplexed profiling of transcriptional regulators in plant cells ]]> https://biorxiv.org/content/10.1101/2025.05.12.653590v1?rss=1 Alamos, S. Waldburger, L. Dee, A. Owens, L. Rattan, R. Ong, S. Shih, P. 2025-05-14 doi:10.1101/2025.05.12.653590 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Megabase-scale human genome rearrangement with programmable bridge recombinases ]]> https://biorxiv.org/content/10.1101/2025.05.14.653916v1?rss=1 Perry, N. T. Bartie, L. J. Katrekar, D. Gonzalez, G. A. Durrant, M. G. Pai, J. J. Fanton, A. Hiraizumi, M. Ricci-Tam, C. Nishimasu, H. Konermann, S. Hsu, P. D. 2025-05-14 doi:10.1101/2025.05.14.653916 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Spatial close-kin mark-recapture methods to estimate dispersal parameters and barrier strength for mosquitoes ]]> https://biorxiv.org/content/10.1101/2025.05.11.653364v1?rss=1 Marshall, J. M. Yang, S. Bennett, J. B. Filipovic, I. Rasic, G. 2025-05-15 doi:10.1101/2025.05.11.653364 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ ngsAMOVA: A Probabilistic Framework for Analysis of Molecular Variance, dXY and Neighbor-Joining Trees with Low Depth Sequencing Data ]]> https://biorxiv.org/content/10.1101/2025.05.12.653431v1?rss=1 Altinkaya, I. Zhao, L. Nielsen, R. Korneliussen, T. S. 2025-05-15 doi:10.1101/2025.05.12.653431 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Nucleosome positioning and sensitivity suggest novel functional organization of the purple sea urchin (Strongylocentrotus purpuratus) genome ]]> https://biorxiv.org/content/10.1101/2025.05.12.653534v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@c724dforg.highwire.dtl.DTLVardef@45c163org.highwire.dtl.DTLVardef@19b6043org.highwire.dtl.DTLVardef@1ccf475_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Munstermann, M. J. Benoit, J. M. Karelitz, S. E. Arambarri, L. N. Dennis, J. H. Okamoto, D. K. 2025-05-15 doi:10.1101/2025.05.12.653534 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ RNA polymerase III transcription-associated polyadenylation promotes the accumulation of noncoding retrotransposons during infection ]]> https://biorxiv.org/content/10.1101/2025.05.14.654096v1?rss=1 Lari, A. Shah, S. B. Mao, X. Sanghrajka, P. Karijolich, J. Lareau, L. F. Glaunsinger, B. A. 2025-05-16 doi:10.1101/2025.05.14.654096 Cold Spring Harbor Laboratory Press 2025-05-16 <![CDATA[ Oxytocin receptor absence reduces selectivity in peer relationships and alters neurochemical release dynamics in prairie voles ]]> https://biorxiv.org/content/10.1101/2025.05.15.654128v1?rss=1 Black, A. M. Komatsu, N. Zhao, J. Taskey, S. R. Serrano, N. S. Sharma, R. Manoli, D. S. Landry, M. P. Beery, A. 2025-05-16 doi:10.1101/2025.05.15.654128 Cold Spring Harbor Laboratory Press 2025-05-16 <![CDATA[ Distinct Sox9 single-molecule dynamics characterize adult differentiation and fetal-like reprogrammed states in intestinal organoids ]]> https://biorxiv.org/content/10.1101/2025.05.16.654343v1?rss=1 Walther, N. Anantakrishnan, S. Dailey, G. M. Maurer, A. C. Cattoglio, C. 2025-05-17 doi:10.1101/2025.05.16.654343 Cold Spring Harbor Laboratory Press 2025-05-17 <![CDATA[ Diploid gametes in maize by mutation of A-Type cyclins: a step towards apomeiosis and synthetic apomixis. ]]> https://biorxiv.org/content/10.1101/2025.05.16.654085v1?rss=1 Skinner, D. J. Gaikwad, A. H. Fenner, J. A. Green, J. Cho, M.-J. Kelliher, T. Sundaresan, V. 2025-05-19 doi:10.1101/2025.05.16.654085 Cold Spring Harbor Laboratory Press 2025-05-19 <![CDATA[ Sustained Glucose Turnover Flux Distinguishes Cancer Cachexia from Nutrient Limitation ]]> https://biorxiv.org/content/10.1101/2025.05.15.654370v1?rss=1 Kwon, Y. Y. Liang, Y. Gomez-Jenkins, M. Ahmed, M. Jiang, G. Hsiang, J. Lewis, D. Janowitz, T. Goncalves, M. D. White, E. Hui, S. 2025-05-20 doi:10.1101/2025.05.15.654370 Cold Spring Harbor Laboratory Press 2025-05-20 <![CDATA[ Interpreting biochemical text with language models:a machine learning framework for reaction extraction and cheminformatic validation ]]> https://biorxiv.org/content/10.1101/2025.05.15.654376v1?rss=1 Lim, D. Badrinarayanan, S. Sterling, K. C. Rajesh, G. Mistry, E. Yang, D. Lee, M. Hsu, K. B. Manjrekar, M. Areff, C. Xie, P. Kristanto, I. A. Chandran, A. Anderson, J. C. 2025-05-20 doi:10.1101/2025.05.15.654376 Cold Spring Harbor Laboratory Press 2025-05-20 <![CDATA[ Matters arising: Forced Symmetry Artifacts in a Prohibitin Complex Structure ]]> https://biorxiv.org/content/10.1101/2025.05.16.653159v1?rss=1 Herrmann, E. Rose, K. M. Hurley, J. H. 2025-05-20 doi:10.1101/2025.05.16.653159 Cold Spring Harbor Laboratory Press 2025-05-20 <![CDATA[ Specialist Generalist Trade Offs in Microbial Growth Rates Across Soil Habitats ]]> https://biorxiv.org/content/10.1101/2025.05.20.655198v1?rss=1 Foley, M. Sokol, N. Stone, B. Blazewicz, S. J. Estera-Molina, K. Greenlon, A. Hayer, M. Kimbrel, J. Pett-Ridge, J. Hungate, B. A. 2025-05-20 doi:10.1101/2025.05.20.655198 Cold Spring Harbor Laboratory Press 2025-05-20 <![CDATA[ Absence of testes at puberty impacts functional development of nigrostriatal but not mesoaccumbal dopamine terminals in a wild-derived mouse ]]> https://biorxiv.org/content/10.1101/2025.05.16.654596v1?rss=1 Mun, J. Jackson, S. C. Prounis, G. Phumsatitpong, C. Motahari, N. Kriegsfeld, L. Landry, M. P. Wilbrecht, L. 2025-05-21 doi:10.1101/2025.05.16.654596 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Frontostriatal salience network expands as executive networks contract in Obsessive-Compulsive Disorder ]]> https://biorxiv.org/content/10.1101/2025.05.21.654808v1?rss=1 Vaghi, M. M. Norgaard, M. Shim, S. Rios, J. A. H. Bissett, P. G. Rodriguez, C. I. Poldrack, R. A. 2025-05-21 doi:10.1101/2025.05.21.654808 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Endosome transcriptomics reveal trafficking of Cajal bodies into multivesicular bodies ]]> https://biorxiv.org/content/10.1101/2025.05.22.655499v1?rss=1 Singh, J. Williams, J. K. Elliott, Q. Jhawar, R. Ferguson, L. Collins, K. Schekman, R. 2025-05-22 doi:10.1101/2025.05.22.655499 Cold Spring Harbor Laboratory Press 2025-05-22 <![CDATA[ Viral infection induces oxylipin chemical signaling at the end of a summer upwelling bloom: implications for carbon cycling. ]]> https://biorxiv.org/content/10.1101/2025.05.18.654734v1?rss=1 Edwards, B. R. Thamatrakoln, K. Kranzler, C. F. Ossolinski, J. Fredricks, H. Johnson, M. D. Krause, J. W. Bidle, K. D. Van Mooy, B. 2025-05-23 doi:10.1101/2025.05.18.654734 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Ancient convergence with prokaryote defense and recent adaptations to lentiviruses in primates characterize the ancestral immune factors SAMD9s ]]> https://biorxiv.org/content/10.1101/2025.05.19.654893v1?rss=1 Legrand, A. Demeure, R. Chantharath, A. Rey, C. Baltenneck, J. Gilchrist, C. L. Rocha, J. L. Loyer, C. Picard, L. Cimarelli, A. Steinegger, M. Rousset, F. Sudmant, P. Etienne, L. 2025-05-23 doi:10.1101/2025.05.19.654893 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Primitive Molecular Buffering by Low-Multivalency Coacervates ]]> https://biorxiv.org/content/10.1101/2025.05.22.655649v1?rss=1 Choi, S. Liu, S. Meyer, M. O. Bevilacqua, P. C. Keating, C. D. 2025-05-27 doi:10.1101/2025.05.22.655649 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Groundwater and phenology data reveal vulnerability of riparian trees to drought ]]> https://biorxiv.org/content/10.1101/2025.05.23.654357v1?rss=1 Mohammadi, R. M. Dawson, T. E. Tiedeman, C. R. Stella, J. Ruhi, A. 2025-05-28 doi:10.1101/2025.05.23.654357 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Prolonged fasting and glucocorticoid exposure drive dynamic DNA methylation in elephant seals ]]> https://biorxiv.org/content/10.1101/2025.05.23.654932v1?rss=1 Gibson, E. F. Torres-Velarde, J. M. Ensminger, D. C. Moreno-Santillan, D. D. Crocker, D. E. Vazquez-Medina, J. P. 2025-05-28 doi:10.1101/2025.05.23.654932 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ COVID-19 induces persistent transcriptional changes in adipose tissue that are not associated with Long COVID ]]> https://biorxiv.org/content/10.1101/2025.05.23.655815v1?rss=1 DeLine-Caballero, S. Ratnasiri, K. Chen, H. Sahagun, S. J. Mangalanathan, U. M. Barnard, T. R. Turk, N. Yang, J. Saini, N. Ayhan, E. M. Memetimin, H. Finlin, B. S. Licht, Z. Kern, P. A. Emery, I. Leeman, B. Edelstein, G. E. Costa, S. Choi, A. Licht, J. Z. Rosen, C. McLaughlin, T. Blish, C. A. 2025-05-28 doi:10.1101/2025.05.23.655815 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Drought reduces formation, but enhances persistence, of mineral-associated organic matter in a grassland soil ]]> https://biorxiv.org/content/10.1101/2025.05.23.655838v1?rss=1 Sokol, N. Foley, M. Blazewicz, S. J. Didonato, N. Estera-Molina, K. Firestone, M. K. Greenlon, A. Hungate, B. A. Kew, W. Pasa-Tolic, L. Slessarev, E. Pett-Ridge, J. 2025-05-28 doi:10.1101/2025.05.23.655838 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Development of Second-Generation Acyl Silane Photoaffinity Probes for Cellular Chemoproteomic Profiling ]]> https://biorxiv.org/content/10.1101/2025.05.24.655972v1?rss=1 Page, A. C. S. Orr, L. M. Meyers, M. L. Belcher, B. P. Coffey, T. G. Scholz, S. O. Cismoski, S. Nomura, D. Toste, F. D. 2025-05-28 doi:10.1101/2025.05.24.655972 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Double strand breaks drive toxicity in Huntington's disease mice with or without somatic expansion. ]]> https://biorxiv.org/content/10.1101/2025.05.27.654663v1?rss=1 Polyzos, A. A. Yoo, J. H. Cheong, A. Blagec, L. Nagel, Z. D. McMurray, C. T. 2025-05-28 doi:10.1101/2025.05.27.654663 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Effects of sexual dimorphism and estrous cycle on C. difficile infections prophylaxis in two rodent models ]]> https://biorxiv.org/content/10.1101/2025.05.21.655361v1?rss=1 Phan, J. R. Washington, M. Do, D. M. Mata, T. V. Niamba, M. Heredia, E. Soriano, R. Hassan, C. Cross, C. L. Abel-Santos, E. 2025-05-30 doi:10.1101/2025.05.21.655361 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Genome-wide CRISPR screens identify PTGES3 as a novel AR modulator ]]> https://biorxiv.org/content/10.1101/2025.05.29.656244v1?rss=1 Li, H. Melnyk, J. E. Fu, B. X. H. Shrestha, R. Zhang, M. Sjostrom, M. Feng, S. Anderson, J. Han, W. Chesner, L. N. Shin, H. J. Farsh, T. Suarez, H. J. Nath, S. Chou, J. Das, R. Egusa, E. A. Calvert, M. Kishishita, A. Barpanda, A. Zhu, J. Maheshwari, A. Chen, W. S. Alshalalfa, M. Winters, A. Hua, J. T. Liu, T. Davicioni, E. Wiita, A. P. Stohr, B. A. Siddiqui, J. Huang, B. Small, E. J. Shokat, K. M. Nelson, P. Quigley, D. A. Wasmuth, E. V. Gilbert, L. A. Feng, F. Y. 2025-05-30 doi:10.1101/2025.05.29.656244 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ KODA: Agentic Framework for Microbiome Drug Target Discovery ]]> https://biorxiv.org/content/10.1101/2025.05.27.656480v1?rss=1 Aminian-Dehkordi, J. Parsa, M. S. Naghipourfar, M. Mofrad, M. 2025-06-01 doi:10.1101/2025.05.27.656480 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Detection of astrocyte epigenetic memory in in vitro systems, experimental autoimmune encephalomyelitis and multiple sclerosis samples ]]> https://biorxiv.org/content/10.1101/2025.05.30.657119v1?rss=1 Quintana, F. J. Li, Z. Faust Akl, C. Lee, J.-H. Piester, G. Antel, J. Rothhammer, V. Wheeler, M. A. Prat, A. Clark, I. C. 2025-06-03 doi:10.1101/2025.05.30.657119 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Microbial dispersal from surrounding vegetation influences phyllosphere microbiome assembly of corn and soybean ]]> https://biorxiv.org/content/10.1101/2025.05.31.657201v1?rss=1 Meyer, K. M. Lindow, S. E. 2025-06-03 doi:10.1101/2025.05.31.657201 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ scVIVA: a probabilistic framework for representation of cells and their environments in spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.06.01.657182v1?rss=1 Levy, N. Ingelfinger, F. Bakulin, A. Cinnirella, G. Boyeau, P. Nadler, B. Ergen, C. Yosef, N. 2025-06-03 doi:10.1101/2025.06.01.657182 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Kinetic Proofreading through Parallel Reactions on a Single T Cell Receptor ]]> https://biorxiv.org/content/10.1101/2025.06.01.657268v1?rss=1 Morita, S. Groves, J. T. 2025-06-03 doi:10.1101/2025.06.01.657268 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Replaying germinal center evolution on a quantified affinity landscape ]]> https://biorxiv.org/content/10.1101/2025.06.02.656870v1?rss=1 DeWitt, W. S. S. Vora, A. A. Araki, T. Galloway, J. G. Alkutkar, T. Bortolatto, J. Castro, T. B. Dumm, W. Jennings-Schaffer, C. Jia, T. Mesin, L. Ozorowski, G. Pae, J. Ralph, D. K. Bloom, J. D. Nourmohammad, A. Song, Y. S. Ward, A. Starr, T. N. Matsen, F. A. Victora, G. D. 2025-06-05 doi:10.1101/2025.06.02.656870 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ Genome-Bench: A Scientific Reasoning Benchmark from Real-World Expert Discussions ]]> https://biorxiv.org/content/10.1101/2025.06.02.657538v1?rss=1 Yin, M. Qu, Y. Liu, D. Yang, L. Cong, L. Wang, M. 2025-06-05 doi:10.1101/2025.06.02.657538 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ The Immunophenotype and Proviral Landscape of HIV-infected CD4 T Cells During Antiretroviral Therapy ]]> https://biorxiv.org/content/10.1101/2025.06.05.657210v1?rss=1 Delley, C. L. Shah, S. Joslin, K. M. Park, Y. P. Busch, M. P. Stone, M. Demaree, B. Deeks, S. G. Boritz, E. A. Abate, A. R. Clark, I. C. 2025-06-05 doi:10.1101/2025.06.05.657210 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ A discontinuity in motion perception during fixational drift ]]> https://biorxiv.org/content/10.1101/2025.06.02.657265v1?rss=1 D'Angelo, J. C. Tiruveedhula, P. Weber, R. J. Arathorn, D. W. Otero-Millan, J. Roorda, A. 2025-06-06 doi:10.1101/2025.06.02.657265 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ An improved model for prediction of de novo designed proteins with diverse geometries ]]> https://biorxiv.org/content/10.1101/2025.06.02.657515v1?rss=1 Orr, B. Crilly, S. E. Akpinaroglu, D. Zhu, E. Keiser, M. J. Kortemme, T. 2025-06-06 doi:10.1101/2025.06.02.657515 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ RNA-seq reveals transcriptomic differences in circadian-related genes of the choroid plexus in a preclinical chronic migraine model. ]]> https://biorxiv.org/content/10.1101/2025.06.03.657705v1?rss=1 1) were identified. GO, KEGG, and Reactome enrichment analyses evaluated circadian gene expression changes. ResultsO_LINTG group showed reduced basal and NTG-induced pain thresholds on days 1, 5, and 9. C_LIO_LIFemales had more upregulated genes (MT2A, SLC7A11), males upregulated ZBTB16, S100A8. SLC7A11, SCG2, GRIA1 showed inverse regulation (up in females, down in males). C_LIO_LICircadian gene expression altered: 10 genes upregulated (e.g., SERPINE1, MAPK9, ATF4), 13 downregulated (e.g., PER2, DBP, EZH2). Sex-specific differences: females (FBXL12, GPR157), males (NKX2-1, ATF4, CLOCK). C_LIO_LIGO/KEGG analyses revealed significant enrichment of circadian rhythm-related pathways, insulin resistance, and inflammatory response processes, with sex-specific differences: females showed HIF-1 signaling and hemoglobin-related pathways, while males exhibited arachidonic acid and leukotriene production. C_LI ConclusionCP transcriptomics in the rat migraine model revealed sex-specific gene regulation, with females upregulating antioxidant genes (MT2A, SLC7A11) and males upregulating inflammatory factors (ZBTB16, S100A8), alongside circadian disruption (e.g., SERPINE1 upregulated, PER2 downregulated). Pathway analyses indicate enriched circadian rhythms, HIF-1 signaling (females), inflammatory processes (males), lipid metabolism (PPAR), and heme signaling, highlighting sex-specific and circadian targets for migraine therapy. ]]> Woldeamanuel, Y. W. Xia, C. Ding, S. Fonteh, A. Arakaki, X. 2025-06-06 doi:10.1101/2025.06.03.657705 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Mechanical force locally damages, remodels and stabilizes the lattice of spindle microtubules ]]> https://biorxiv.org/content/10.1101/2025.06.05.657915v1?rss=1 Rux, C. J. Chong, M. K. Myers, S. Cho, N. H. Dumont, S. 2025-06-06 doi:10.1101/2025.06.05.657915 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Biological Processes as Exploratory Dynamics ]]> https://biorxiv.org/content/10.1101/2025.06.06.657857v1?rss=1 Kondev, J. Kirschner, M. W. Garcia, H. G. Salmon, G. Phillips, R. 2025-06-09 doi:10.1101/2025.06.06.657857 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Low-density lipoprotein receptor-targeting chimeras for membrane protein degradation and enhanced drug delivery ]]> https://biorxiv.org/content/10.1101/2025.06.06.658366v1?rss=1 Zhao, F. Wu, Y. Schaefer, K. Zhang, Y. Miao, K. Yao, Z. Ganjave, S. D. Kumru, K. Peters-Clarke, T. M. Inague, A. Olzmann, J. A. Leung, K. K. Wells, J. A. 2025-06-09 doi:10.1101/2025.06.06.658366 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ The phonology of sperm whale coda vowels ]]> https://biorxiv.org/content/10.1101/2025.06.09.658556v1?rss=1 Begus, G. Dabkowski, M. Sprouse, R. Gruber, D. Gero, S. 2025-06-10 doi:10.1101/2025.06.09.658556 Cold Spring Harbor Laboratory Press 2025-06-10 <![CDATA[ Purification of post-transcriptionally modified tRNAs for enhanced cell-free translation systems ]]> https://biorxiv.org/content/10.1101/2025.06.10.658963v1?rss=1 Kalb, E. Alejo, J. Dias-Fields, L. Knudson, I. Davisson, J. Maldonado, E. Chattrakun, K. Lin, S. Schepartz, A. Zhang, S. Blanchard, S. Engelhart, A. E. Adamala, K. P. 2025-06-10 doi:10.1101/2025.06.10.658963 Cold Spring Harbor Laboratory Press 2025-06-10 <![CDATA[ Multi-selective RAS(ON) Inhibition Targets Oncogenic RAS Mutations and Overcomes RAS/MAPK-Mediated Resistance to FLT3 and BCL2 Inhibitors in Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/2025.06.10.658786v1?rss=1 Popescu, B. Jones, M. F. Piao, M. Tran, E. Koh, A. Lomeli, I. Peretz, C. A. C. Murad, N. Abelson, S. Morales, C. Rivera, J. M. Pikman, Y. Cheng, M. L. Logan, A. C. Stieglitz, E. Smith, C. C. 2025-06-14 doi:10.1101/2025.06.10.658786 Cold Spring Harbor Laboratory Press 2025-06-14 <![CDATA[ Reversible Antagonism of Dopamine D1 Receptor using a Photoswitchable Remotely Tethered Ligand ]]> https://biorxiv.org/content/10.1101/2025.06.10.658926v1?rss=1 Hetzler, B. E. Donthamsetti, P. C. Wolesensky, R. M. Stanley, C. Isacoff, E. Trauner, D. 2025-06-15 doi:10.1101/2025.06.10.658926 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Quantifying Misuse of Color in Biological Research ]]> https://biorxiv.org/content/10.1101/2025.06.12.659203v1?rss=1 Lin, T.-J. Hillman, K. Kim, L. Garg, M. Duong, M. Landry, M. P. 2025-06-15 doi:10.1101/2025.06.12.659203 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer ]]> https://biorxiv.org/content/10.1101/2025.06.15.659774v1?rss=1 Koblan, L. W. Yost, K. E. Zheng, P. Colgan, W. N. Jones, M. G. Yang, D. Kumar, A. Sandhu, J. Schnell, A. Sun, D. Ergen, C. Saunders, R. A. Zhuang, X. Allen, W. E. Yosef, N. Weissman, J. S. 2025-06-15 doi:10.1101/2025.06.15.659774 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ A Multimodal Adaptive Optical Microscope For In Vivo Imaging from Molecules to Organisms ]]> https://biorxiv.org/content/10.1101/2025.06.02.657494v1?rss=1 Fu, T.-M. Liu, G. Milkie, D. E. Ruan, X. Gorlitz, F. Shi, Y. Ferro, V. Divekar, N. S. Wang, W. York, H. M. Kilic, V. Mueller, M. Liang, Y. Daugird, T. A. Gacha-Garay, M. J. Larkin, K. A. Adikes, R. C. Harrison, N. Shirazinejad, C. Williams, S. Nourse, J. L. Sheu, S.-H. Gao, L. Li, T. Mondal, C. Achour, K. Hercule, W. Stabley, D. Emmerich, K. Dong, P. Drubin, D. Liu, Z. J. Clapham, D. Mumm, J. S. Koyama, M. Killilea, A. Bravo-Cordero, J. J. Keene, C. D. Luo, L. Kirchhausen, T. Pathak, M. M. Arumugam, S. Nunez, J. K. Gao, R. G. Matus, D. Q. Martin, B. 2025-06-16 doi:10.1101/2025.06.02.657494 Cold Spring Harbor Laboratory Press 2025-06-16 <![CDATA[ Causes and consequences of experimental variation in Nicotiana benthamiana transient expression ]]> https://biorxiv.org/content/10.1101/2025.06.12.659391v1?rss=1 Tang, S. N. Szarzanowicz, M. Lanctot, A. Sirirungruang, S. Kirkpatrick, L. D. Drako, K. Alamos, S. Cheng, A. Waldburger, L. M. Liu, S. Thompson, M. Shih, P. 2025-06-16 doi:10.1101/2025.06.12.659391 Cold Spring Harbor Laboratory Press 2025-06-16 <![CDATA[ Genome editing of phylogenetically distinct bacteria using portable retron-mediated recombineering ]]> https://biorxiv.org/content/10.1101/2025.06.16.660010v1?rss=1 Gonzalez-Delgado, A. Bonillo-Lopez, L. Johnson, M. S. Knoedlseder, N. Ko, C.-C. Lekbach, Y. Oh, J.-H. Selvakumar, H. Wold, M. C. Yu, Z. Aragon, V. Gralnick, J. A. Guell, M. Hatfull, G. Keitz, B. K. Koskella, B. Mutalik, V. K. van Pijkeren, J. P. Shipman, S. 2025-06-17 doi:10.1101/2025.06.16.660010 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Small Extra-Large GTPase-like proteins influence rhizobial symbiosis in Lotus japonicus ]]> https://biorxiv.org/content/10.1101/2025.06.18.660248v1?rss=1 Washington, L. J. Yoshino, T. Malagoli Franzon, T. Vera, V. Scheller, H. V. 2025-06-23 doi:10.1101/2025.06.18.660248 Cold Spring Harbor Laboratory Press 2025-06-23 <![CDATA[ Clade V MLO proteins are bona fide host susceptibility factors required for powdery mildew pathogenesis in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2025.06.18.660284v1?rss=1 Bloodgood, D. Zhang, Q. Li, P. Wu, Y. Pan, M. Zhou, C. Hsu, A. Zhang, J. Panstrgua, R. Kessler, S. He, P. Shan, L. Wei, C.-I. Xiao, S. 2025-06-23 doi:10.1101/2025.06.18.660284 Cold Spring Harbor Laboratory Press 2025-06-23 <![CDATA[ Attention is all you need (in the brain): semantic contextualization in human hippocampus ]]> https://biorxiv.org/content/10.1101/2025.06.23.661103v1?rss=1 Katlowitz, K. Belanger, J. L. Ismail, T. Chavez, A. G. Chericoni, A. Franch, M. C. Mickiewicz, E. A. Mathura, R. K. Paulo, D. Bartoli, E. Piantadosi, S. T. Provenza, N. R. Watrous, A. J. Sheth, S. A. Hayden, B. Y. 2025-06-24 doi:10.1101/2025.06.23.661103 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ EVODEX: A Mechanistic Framework for Extracting, Structuring, and Predicting Enzymatic Reactivity ]]> https://biorxiv.org/content/10.1101/2025.06.19.660615v1?rss=1 Conceicao, L. L. Lin, H. Tai, D. Xue, G. Zhang, H. Zhang, C. Anderson, J. C. 2025-06-25 doi:10.1101/2025.06.19.660615 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ De novo designed bright, hyperstable rhodamine binders for fluorescence microscopy ]]> https://biorxiv.org/content/10.1101/2025.06.24.661379v1?rss=1 Chen, Y. Yserentant, K. Hong, K. Kuang, Y. Bhowmick, A. Charles-Orszag, A. Lord, S. J. Lu, L. Hou, K. Mann, S. I. Grimm, J. B. Lavis, L. D. Mullins, R. D. DeGrado, W. F. Huang, B. 2025-06-25 doi:10.1101/2025.06.24.661379 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Anterior cingulate folding pattern is altered in autism spectrum disorder ]]> https://biorxiv.org/content/10.1101/2025.06.24.661411v1?rss=1 Willbrand, E. H. Maboudian, S. A. Ludwig, J. J. Weiner, K. S. 2025-06-26 doi:10.1101/2025.06.24.661411 Cold Spring Harbor Laboratory Press 2025-06-26 <![CDATA[ Harnessing fusion of genome-edited human stem cells to rapidly screen for novel protein functions in vivo ]]> https://biorxiv.org/content/10.1101/2025.06.25.661608v1?rss=1 Smith, S. L. Iwamoto, Y. Manimaran, A. Drubin, D. G. 2025-06-27 doi:10.1101/2025.06.25.661608 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Intratumoral Treg ablation is sufficient to mediate tumor control systemically without autoimmunity ]]> https://biorxiv.org/content/10.1101/2025.06.26.661765v1?rss=1 Bockman, A. Gittins, B. Zhang, C. Hung, J. Moreno Ayala, M. Saddier Axe, D. Weist, B. M. DuPage, M. 2025-06-30 doi:10.1101/2025.06.26.661765 Cold Spring Harbor Laboratory Press 2025-06-30 <![CDATA[ XoxF and the Calvin-Benson Cycle Mediate Lanthanide-Dependent Growth on Methanol in Bradyrhizobium and Sinorhizobium ]]> https://biorxiv.org/content/10.1101/2025.06.30.662339v1?rss=1 Mineo, C. R. Jiang, J. Martinez-Gomez, N. C. 2025-06-30 doi:10.1101/2025.06.30.662339 Cold Spring Harbor Laboratory Press 2025-06-30 <![CDATA[ Uncovering smooth structures in single-cell data with PCS-guided neighbor embeddings ]]> https://biorxiv.org/content/10.1101/2025.06.27.661958v1?rss=1 Ma, R. Li, X. Hu, J. Yu, B. 2025-07-02 doi:10.1101/2025.06.27.661958 Cold Spring Harbor Laboratory Press 2025-07-02 <![CDATA[ Multi-season analysis reveals hundreds of drought-responsive genes in sorghum ]]> https://biorxiv.org/content/10.1101/2025.06.27.662006v1?rss=1 Cole, B. Zhang, W. Shi, J. Wang, H. Baker, C. Varoquaux, N. Hollingsworth, J. Hutmacher, R. Dahlberg, J. Pierroz, G. Barry, K. W. Singan, V. Yoshinaga, Y. Daum, C. Zane, M. Blow, M. OMalley, R. Shu, S. Jenkins, J. W. Lovell, J. T. Schmutz, J. Taylor, J. W. Coleman-Derr, D. Visel, A. Lemaux, P. G. Purdom, E. Vogel, J. P. 2025-07-02 doi:10.1101/2025.06.27.662006 Cold Spring Harbor Laboratory Press 2025-07-02 <![CDATA[ Activation of the impaired NAMPT/SIRT7/SOD2 axis restores alveolar progenitor cell homeostasis in idiopathic pulmonary fibrosis and reverses pulmonary fibrosis in mice ]]> https://biorxiv.org/content/10.1101/2025.06.30.662456v1?rss=1 Zhang, X. Liu, X. Qiao, Y. Rabata, A. Liu, N. Yao, C. Parimon, T. Chen, D. Chen, P. Stripp, B. Gardell, S. J. Jiang, D. Noble, P. Liang, C. J. 2025-07-03 doi:10.1101/2025.06.30.662456 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ The accessory protein CvnF8 modulates histidine kinase activity in an Actinobacterial G protein system in Streptomyces coelicolor ]]> https://biorxiv.org/content/10.1101/2025.07.03.663114v1?rss=1 Cantu Morin, L. M. Dekoninck, K. Min, K.-Y. Traxler, M. F. 2025-07-04 doi:10.1101/2025.07.03.663114 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Lesions in the cerebellum impact cross-modal temporal predictions ]]> https://biorxiv.org/content/10.1101/2025.07.04.663130v1?rss=1 Criscuolo, A. Knolle, F. Schwartze, M. Schröger, E. Ivry, R. Kotz, S. A. 2025-07-04 doi:10.1101/2025.07.04.663130 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ TOMM40 Knockdown in Macrophages Inhibits Oxidized LDL-induced NLRP3 Activation and Promotes LXR-β Mediated Cholesterol Transporter Gene Expression ]]> https://biorxiv.org/content/10.1101/2025.07.01.662675v1?rss=1 Chelluri, S. S. Yang, N. V. Theusch, E. Krauss, R. M. 2025-07-05 doi:10.1101/2025.07.01.662675 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ Cholesterol Metabolism in a Murine Model of Vertical Sleeve Gastrectomy ]]> https://biorxiv.org/content/10.1101/2025.07.03.659993v1?rss=1 Whang, E. Ferrari, A. Kennelly, J. P. Gao, Y. Xiao, X. Jarrett, K. Bedard, A. de Aguiar Vallim, T. Q. Tontonoz, P. 2025-07-07 doi:10.1101/2025.07.03.659993 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ mRNABench: A curated benchmark for mature mRNA property and function prediction ]]> https://biorxiv.org/content/10.1101/2025.07.05.662870v1?rss=1 Shi, R. Dalal, T. Fradkin, P. Koyyalagunta, D. Chhabria, S. Jung, A. Tam, C. L. Ceyhan, D. Lin, J. Laverty, K. U. Baali, I. Wang, B. Morris, Q. 2025-07-08 doi:10.1101/2025.07.05.662870 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ Selective disruption of lipid peroxide homeostasis in intratumoral regulatory T cells by targeting FSP1 enhances cancer immunity ]]> https://biorxiv.org/content/10.1101/2025.07.06.663397v1?rss=1 Castillo, J. G. Olzmann, J. DuPage, M. Silveria, S. Sauquet, A. Schirokauer, L. Hendricks, J. Sul, H. S. 2025-07-10 doi:10.1101/2025.07.06.663397 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ Decoding Lymphangioleiomyomatosis (LAM) Niche Environment via Integrative Analysis of Single Cell Multiomics and Spatial Transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.07.07.663390v1?rss=1 Chen, K. Zhao, S. Guo, M. Reza, H. Wagner, A. Cakar, A. C. Jiang, C. Zhang, E. Green, J. Martin, E. Wikenheiser-Brokamp, K. Perl, A.-K. T. Sinner, D. I. Yu, J. J. Xu, Y. 2025-07-10 doi:10.1101/2025.07.07.663390 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ Advancing FAIR Data Management through AI-Assisted Curation of Morphological Data Matrices ]]> https://biorxiv.org/content/10.1101/2025.07.08.663621v1?rss=1 Jariwala, S. Long-Fox, B. L. Berardini, T. Z. 2025-07-11 doi:10.1101/2025.07.08.663621 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ Multi-omic mapping of Drosophila protein secretomes reveals tissue-specific origins and inter-organ trafficking ]]> https://biorxiv.org/content/10.1101/2025.07.09.659702v1?rss=1 Bosch, J. A. Beltran, P. M. J. Cavers, C. LaGraff, J. T. Melanson, R. Singh, A. Chen, W. Hu, Y. Tattikota, S. G. Liu, Y. Hashmi, Y. Asara, J. M. Branon, T. Ting, A. Y. Carr, S. A. Perrimon, N. 2025-07-11 doi:10.1101/2025.07.09.659702 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ Dynamic Modulation of Beta-Band Oscillations in the LGN and Their Role in Visual Processing ]]> https://biorxiv.org/content/10.1101/2025.07.08.663741v1?rss=1 Alitto, H. J. Sanchez, A. N. Alexander, P. C. Usrey, W. M. 2025-07-12 doi:10.1101/2025.07.08.663741 Cold Spring Harbor Laboratory Press 2025-07-12 <![CDATA[ The mevalonate pathway of isoprenoid biosynthesis supports metabolic flexibility in Mycobacterium marinum ]]> https://biorxiv.org/content/10.1101/2025.07.11.664281v1?rss=1 Qabar, C. Baidoo, E. E. Akyuz Turumtay, E. Qayum, T. Keasling, J. D. Madigan, C. Portnoy, D. A. Cox, J. S. 2025-07-14 doi:10.1101/2025.07.11.664281 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ mamp-ml: A deep learning approach to epitope immunogenicity in plants ]]> https://biorxiv.org/content/10.1101/2025.07.11.664399v1?rss=1 Stevens, D. M. Yang, D. Liang, T. J. Li, T. Vega, B. Coaker, G. Krasileva, K. 2025-07-15 doi:10.1101/2025.07.11.664399 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ One of these things is not like the others: Theta, beta, & ERP dynamics of mismatch detection ]]> https://biorxiv.org/content/10.1101/2025.07.11.664390v1?rss=1 Yarbrough, J. B. Shi, L. Chattopadhyay, K. Knight, R. T. Johnson, E. L. 2025-07-17 doi:10.1101/2025.07.11.664390 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Developmental Immunotoxicity of Low-dose Inorganic Arsenic Reprograms Macrophages Inducing Tumor-promoting Phenotypes ]]> https://biorxiv.org/content/10.1101/2025.07.14.663593v1?rss=1 Illingworth, E. J. Sanchez, S. S. Rychlik, K. A. Kleensang, A. Lopez-Cecetaite, G. A. Rodriguez Steube, M. C. Mathur, A. Sadhukhan, P. Medina-Cleghorn, D. A. Nomura, D. Smith, M. T. Hoque, M. O. Sille, F. C. M. 2025-07-18 doi:10.1101/2025.07.14.663593 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Long-fuse evolution of carnivoran skeletal phenomes through the Cenozoic ]]> https://biorxiv.org/content/10.1101/2025.07.14.664737v1?rss=1 Law, C. Hlusko, L. Tseng, J. 2025-07-18 doi:10.1101/2025.07.14.664737 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Covariance-Based MD Simulation Analysis Pinpoints Nanobody Attraction and Repulsion Sites on SARS-CoV-2 Omicron Spike Protein ]]> https://biorxiv.org/content/10.1101/2025.07.18.665531v1?rss=1 8 s of all-atom molecular dynamics (MD) simulations of 13 Nbs (H11-D4, H11-H4, Huo-H3, MR17, NB21, NM1230, RE5D06, SB14, SB23, SB45, Ty1, VHH-E, WNB2) bound to the Omicron RBD to characterize binding-pose stability and interfacial dynamics. Principal-component analysis of MD trajectories yields binding-pose free-energy landscapes: most Nbs occupy single dominant basins yet often deviate from WTbound poses (orientation shifts), whereas NB21 and SB14 show pose plasticity. Using our covariance-matrix-based interaction-mapping method, we map stabilizing versus destabilizing residue-residue couplings and classify the underlying attractive interactions (salt bridges, hydrogen bonds, hydrophobic contacts) and repulsive interactions (like-charge repulsion or polarity mismatches). Attractive contacts converge on recurrent hydrophobic "anchor" patches on the receptor-binding motif (RBM) ([~]V445-G456 and [~]F490-Y501) alongside binder-specific, complementarity-determining-region (CDR)-shaped interactions. Omicron substitutions rewire contact networks, shift binding orientations, and can introduce unfavorable repulsion, directly at mutation sites (e.g., E484A) or indirectly via mutation-driven reorientation, weakening binding. Mutation-induced repulsion reshapes correlated interfacial motions and reduces interfacial stability, providing a mechanistic basis for diminished binding robustness of multiple Nbs that were effective against WT and/or earlier variants. Low-speed steered MD pulling (AFM comparable) of ACE2 and selected Nbs shows lower unbinding work for Nbs than ACE2 ([~]16-42 vs [~]45 kcal/mol), with NM1230 and SB23 most mechanically robust. These Nb-RBD interaction fingerprints pinpoint epitope-specific determinants and mutation-induced clash sites, providing a blueprint for structure-guided CDR engineering of Nbs with sustained potency against ongoing SARS-CoV-2 evolution. ]]> Golcuk, M. Abu-Juam, F. E. Basturk, D. Gursel, A. D. Buran, C. X. Metin-Akkaya, R. Yildiz, A. Gur, M. 2025-07-18 doi:10.1101/2025.07.18.665531 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ A morphological comparison of the caudal rami of the superior temporal sulcus in humans, chimpanzees, and other great apes ]]> https://biorxiv.org/content/10.1101/2025.07.16.665137v1?rss=1 Sathishkumar, R. N. Willbrand, E. H. Nanayakkara, P. Voorhies, W. I. Tsai, Y.-H. Gagnant, T. Hopkins, W. D. Sherwood, C. C. Weiner, K. S. 2025-07-21 doi:10.1101/2025.07.16.665137 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Reduced Model-Based Control in Gambling Disorder Despite Intact Neural Value and Task Structure Representations ]]> https://biorxiv.org/content/10.1101/2025.07.18.665478v1?rss=1 Brands, A. M. Knauth, K. Mathar, D. Lee, S. Kuzmanovic, B. Tittgemeyer, M. Peters, J. 2025-07-23 doi:10.1101/2025.07.18.665478 Cold Spring Harbor Laboratory Press 2025-07-23 <![CDATA[ Mono-mix strategy enables comparative proteomics of a cross-kingdom microbial symbiosis ]]> https://biorxiv.org/content/10.1101/2025.07.22.666210v1?rss=1 Dupuis, S. Lingappa, U. F. Purvine, S. O. Chiang, L. Gallaher, S. D. Nicora, C. D. Lipton, M. S. Merchant, S. S. 2025-07-26 doi:10.1101/2025.07.22.666210 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ Illusory tilt does not induce optostatic torsion ]]> https://biorxiv.org/content/10.1101/2025.07.23.666363v1?rss=1 Girum, M. Otero-Millan, J. 2025-07-28 doi:10.1101/2025.07.23.666363 Cold Spring Harbor Laboratory Press 2025-07-28 <![CDATA[ Whole-genome analyses point to new candidate genes underlying aestivation in amphibians ]]> https://biorxiv.org/content/10.1101/2025.07.24.666600v1?rss=1 Ochoa-Ochoa, L. M. Tarvin, R. D. 2025-07-29 doi:10.1101/2025.07.24.666600 Cold Spring Harbor Laboratory Press 2025-07-29 <![CDATA[ Saturated lipid stress attenuates mitochondrial genome synthesis in human cells ]]> https://biorxiv.org/content/10.1101/2025.07.28.667051v1?rss=1 Boone, C. Judge, S. Shami, A. Danna, B. Ball, A. Waingankar, T. P. Saqub, H. Divakaruni, A. S. Lewis, S. C. 2025-07-29 doi:10.1101/2025.07.28.667051 Cold Spring Harbor Laboratory Press 2025-07-29 <![CDATA[ Can you trust your reconstructed lineage tree? A homoplasy-based approach for irreversible evolution ]]> https://biorxiv.org/content/10.1101/2025.07.27.667007v1?rss=1 Zilber, P. Prillo, S. Yosef, N. Nadler, B. 2025-07-30 doi:10.1101/2025.07.27.667007 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ Minimal Impact of Low Vision on Explicit Sensorimotor Adaptation ]]> https://biorxiv.org/content/10.1101/2025.07.29.667489v1?rss=1 Cipleu, M. Padmanabhan, S. Cooper, E. Tsay, J. S. 2025-07-30 doi:10.1101/2025.07.29.667489 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ Assessing cellular metabolic dynamics with NAD(P)H fluorescence polarization imaging ]]> https://biorxiv.org/content/10.1101/2025.07.28.667273v1?rss=1 Zipfel, W. R. Ling, L. Crowley, J. C. Fischbach, C. Estroff, L. A. Williams, R. Shimpi, A. A. Tan, M. L. Kunitake, J. 2025-07-31 doi:10.1101/2025.07.28.667273 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ A plant immune receptor mediates tritrophic interactions by linking caterpillar detection to predator recruitment ]]> https://biorxiv.org/content/10.1101/2025.07.29.667524v1?rss=1 Palacios, N. G. Grof-Tisza, P. Behnken, B. Arce, C. M. Wu, D. Chaparro, A. F. Schmelz, E. A. Turlings, T. C. J. Benrey, B. Steinbrenner, A. D. 2025-08-01 doi:10.1101/2025.07.29.667524 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Engineered lignin composition in Brachypodium distachyon modulates the root-associated microbiome ]]> https://biorxiv.org/content/10.1101/2025.07.30.667798v1?rss=1 Priya, S. Lin, H.-H. Menon, S. Downs, N. Andeer, P. F. Tian, Y. Kosina, S. M. Ding, Y. Eudes, A. Northen, T. Mukhopadhyay, A. Mortimer, J. C. 2025-08-01 doi:10.1101/2025.07.30.667798 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Efficient uniform sampling explains non-uniform memory of narrative stories ]]> https://biorxiv.org/content/10.1101/2025.07.31.667952v1?rss=1 Mu, J. Preston, A. R. Huth, A. G. 2025-08-01 doi:10.1101/2025.07.31.667952 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Impacts of changing ocean circulation, temperature, and food supply on larval recruitment of purple sea urchins in Southern California: A biophysical modeling study ]]> https://biorxiv.org/content/10.1101/2025.07.30.667731v1?rss=1 Simons, R. Okamoto, D. 2025-08-02 doi:10.1101/2025.07.30.667731 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Feature-specific inhibitory connectivity augments the accuracy of cortical representations ]]> https://biorxiv.org/content/10.1101/2025.08.02.668307v1?rss=1 Ogando, M. Abdeladim, L. Sit, K. K. Shin, H. Sridharan, S. Gopakumar, K. Adesnik, H. 2025-08-03 doi:10.1101/2025.08.02.668307 Cold Spring Harbor Laboratory Press 2025-08-03 <![CDATA[ Protein language models reveal evolutionary constraints on synonymous codon choice ]]> https://biorxiv.org/content/10.1101/2025.08.05.668603v1?rss=1 Sakharova, H. Lareau, L. F. 2025-08-05 doi:10.1101/2025.08.05.668603 Cold Spring Harbor Laboratory Press 2025-08-05 <![CDATA[ Developing future resilience from signatures of adaptation across the sorghum pangenome ]]> https://biorxiv.org/content/10.1101/2025.08.01.667986v1?rss=1 Morris, G. P. Harder, A. M. Healey, A. L. McLaughlin, C. M. Rice, B. R. Cruet-Burgos, C. Jenkins, J. W. Rifkin, J. Shu, S. Spiekerman, J. J. VanGessel, C. J. Agnew, E. Audebert, A. Barry, K. Baxter, I. Beurier, G. Boston, L. B. Boyles, R. E. Brady, S. M. Bunting, V. Chaparro, J. Courtney, C. Dembele, J. S. B. Deshpande, S. Diatta, C. Eck, N. Eveland, A. Faye, J. M. Fonceka, D. Gano, B. de Gracia Coquerel, M. Goodstein, D. Grimwood, J. Hudson, M. Kholova, J. Johnson, K. Johnson, K. K. Kawa, D. Kouressy, M. Kresovich, S. Lee, S. Lemaux, P. Lowery, R. Lu 2025-08-06 doi:10.1101/2025.08.01.667986 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ Vitamin B2 metabolism promotes FSP1 stability to prevent ferroptosis ]]> https://biorxiv.org/content/10.1101/2025.08.05.668752v1?rss=1 Deol, K. K. Harris, C. A. Tomlinson, S. J. Doubravsky, C. E. Mathiowetz, A. J. Olzmann, J. A. 2025-08-06 doi:10.1101/2025.08.05.668752 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ GHIST 2024: The 1st Genomic History Inference Strategies Tournament ]]> https://biorxiv.org/content/10.1101/2025.08.05.668560v1?rss=1 Struck, T. J. Vaughn, A. H. Daigle, A. Ray, D. D. Noskova, E. Sequeira, J. J. Antonets, S. Alekseevskaya, E. Grigoreva, E. Raines, E. McMaster, E. S. Kovacs, T. G. L. Ragsdale, A. P. Moreno-Estrada, A. Lotterhos, K. E. Siepel, A. Gutenkunst, R. N. 2025-08-11 doi:10.1101/2025.08.05.668560 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ STARComm Scalably Detects Emergent Modules of Spatial Cell-Cell Communication in Inflammation and Cancer. ]]> https://biorxiv.org/content/10.1101/2025.08.07.669133v1?rss=1 14million cells across 8 cancers, STARComm revealed 24 conserved and tumor-specific MCIMs, including a fibro-immune module with targetable axes linked to immune exclusion and immunotherapy resistance. In chronic graft-versus-host disease, STARComm identified three salivary gland MCIMs predictive of patient death and two druggable axes (CXCL12-CXCR4, CCL5-SDC4), both with FDA-approved therapeutics. STARComm demonstrated that peripheral tissue profiling can forecast fatality nearly 3 years in advance using minor salivary glands. By enabling scalable biomarker discovery, drug targeting, and spatially resolved precision profiling, STARComm bridges the gap between spatial biology and clinical translation, advancing the field of spatial medicine. SUMMARYDespite major advances in spatial biology, no framework has yet linked spatially resolved intercellular communication networks, independent of cell types, to clinical outcomes in human disease. Here, we present STARComm, a scalable method that identifies Multicellular Interaction MCIMs (MCIMs). Applying STARComm to minor salivary gland biopsies from patients with chronic graft-versus-host disease (GVHD), we identify MCIMs that not only distinguish healthy from diseased tissue but also stratify patient survival. High-risk MCIMs are enriched for actionable immune and stromal pathways, including those targetable with existing therapies. These findings establish the first outcome-linked spatial communication framework in any human disease and highlight the translational potential of oral tissues as minimally invasive platforms for real-time immune diagnostics, prognostic modeling, and therapeutic screening. ]]> Huynh, K. Matuck, B. F. de Souza, D. Zhang, X. Fatobene, G. Soares Junior, L. A. V. Ferraz da Silva, L. F. Rocha, V. Byrd, K. Liu, J. 2025-08-11 doi:10.1101/2025.08.07.669133 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ Dehydration promotes intracellular lipid synthesis and accumulation ]]> https://biorxiv.org/content/10.1101/2025.08.07.669190v1?rss=1 Carty, J. S. Selvasingh, J. Zuchowski, Y. Nam, H.-J. Penalva, C. Nanayakkara, G. Jennings, E. Q. Voss, K. Adame, E. T. Tossberg, J. Yap, W. S. Melzer, M. Viquez, O. McCall, A. S. Piotrowski, E. R. Bessho, R. Cao, S. Leaptrot, K. Schrimpe-Rutledge, A. C. Codreanu, S. G. Sherrod, S. D. McLean, J. A. Trapani, J. B. Cottam, M. A. Wan, M. Shrivastava, D. Delker, D. A. Wilson, M. H. Hassenour, C. M. Lantier, L. Chernova, I. Young, J. D. Haase, V. H. Medina, J.-P. V. Kosma, D. K. Kim, P. Cartailler, J. P. Zhang, M. Zent, R. Harris,, R. C. Watts, J. A. Terker, 2025-08-11 doi:10.1101/2025.08.07.669190 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ MechanoAge, a machine learning platform to identify individuals susceptible to breast cancer based on mechanical properties of single cells ]]> https://biorxiv.org/content/10.1101/2025.08.08.668946v1?rss=1 Hinz, S. Grondal, S. M. Miyano, M. Lopez, J. C. Cotner, K. L. Thomsen, T. Chen, C. Hester, E. J. Yee, L. D. Seewaldt, V. E. Lorens, J. B. Sohn, L. L. LaBarge, M. A. 2025-08-12 doi:10.1101/2025.08.08.668946 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ High frequency broadband activity detected noninvasively in infants distinguishes wake from sleep states ]]> https://biorxiv.org/content/10.1101/2025.08.08.668962v1?rss=1 sleep effect with a mean reliability of 60% when using at least 50 seconds of data per state. These findings establish that noninvasive HFB detection in infants is not only possible at sites where the skull has not fully developed, but sufficiently robust to enable systematic investigation of early cognitive development. ]]> Holubecki, A. M. Yarbrough, J. B. Rangarajan, V. Kuperman, R. Knight, R. T. Johnson, E. L. 2025-08-12 doi:10.1101/2025.08.08.668962 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Global monitoring of wildlife mortality through participatory science in near-real time ]]> https://biorxiv.org/content/10.1101/2025.08.08.669145v1?rss=1 Ellis Soto, D. Taylor, L. U. Edson, E. Hill, A. Schell, C. J. Boettiger, C. Johnson, R. F. 2025-08-12 doi:10.1101/2025.08.08.669145 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Global and local origins of trial-to-trial spike count variability in visual cortex ]]> https://biorxiv.org/content/10.1101/2025.08.08.669442v1?rss=1 Li, A. Lu, Z. Ladd, A. Matveev, P. Shea-Brown, E. Steinmetz, N. A. 2025-08-12 doi:10.1101/2025.08.08.669442 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Exploring the deletion landscape of S. aureus Cas9 with SABER ]]> https://biorxiv.org/content/10.1101/2025.08.12.669962v1?rss=1 Plebanek, A. J. Oltrogge, L. M. Terrace, C. I. Lukarska, M. Khoury, M. Savage, D. 2025-08-12 doi:10.1101/2025.08.12.669962 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Glycopolymers stabilize protein folding and protein-protein interactions via enthalpic interactions ]]> https://biorxiv.org/content/10.1101/2025.08.11.669795v1?rss=1 Richter, S. M. Brook, N. Guseman, A. 2025-08-13 doi:10.1101/2025.08.11.669795 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ Fly wounds and tumors restrict macrophages via a matrix degradation-moderating protease inhibitor ]]> https://biorxiv.org/content/10.1101/2025.08.12.669954v1?rss=1 Adiga, K. Sakai, Y. Nawabi, M. Mendez-Lopez, S. Hsi, T.-C. Bilder, D. 2025-08-15 doi:10.1101/2025.08.12.669954 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Genetically encoded tool for manipulation of ATP/ADP ratio in human cells ]]> https://biorxiv.org/content/10.1101/2025.08.12.670003v1?rss=1 Ekvik, A. E. Kober, M. M. Titov, D. V. 2025-08-15 doi:10.1101/2025.08.12.670003 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Distributed theta networks support the control of working memory: Evidence from scalp and intracranial EEG ]]> https://biorxiv.org/content/10.1101/2025.08.14.670214v1?rss=1 Shi, L. Chattopadhyay, K. Gray, S. M. Yarbrough, J. B. King-Stephens, D. Saez, I. Girgis, F. Shaikhouni, A. Schuele, S. U. Rosenow, J. M. Asano, E. Kim-McManus, O. Sattar, S. Knight, R. T. Johnson, E. L. 2025-08-15 doi:10.1101/2025.08.14.670214 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Single-dye, transfection-free FLIM multiplexing via bioorthogonal chemistry ]]> https://biorxiv.org/content/10.1101/2025.08.13.670148v1?rss=1 Dadina, N. Kwon, J. H. Lesiak, L. Zheng, S. Zoltek, M. Brauer, D. Schepartz, A. 2025-08-16 doi:10.1101/2025.08.13.670148 Cold Spring Harbor Laboratory Press 2025-08-16 <![CDATA[ Adaptive radiation along ecological and morphological lines of least resistance in Cyprinodon pupfishes ]]> https://biorxiv.org/content/10.1101/2025.08.13.670168v1?rss=1 Martin, C. H. Zapata, A. A. Paredes, R. G. C. Cortes, F. Hernandez, S. G. Kustra, M. Mar-Silva, A. F. Mex, F. Palominos, M. F. Tralka, C. Badillo-Aleman, M. Schmitter-Soto, J. J. Martinez, C. Arroyave, J. Gracida-Juarez, C. 2025-08-16 doi:10.1101/2025.08.13.670168 Cold Spring Harbor Laboratory Press 2025-08-16 <![CDATA[ Layer-by-Layer Nanoparticle Outer Polyion Impacts Protein Corona Formation ]]> https://biorxiv.org/content/10.1101/2025.08.13.670086v1?rss=1 View larger version (50K): org.highwire.dtl.DTLVardef@18a2a66org.highwire.dtl.DTLVardef@1e5b755org.highwire.dtl.DTLVardef@676af2org.highwire.dtl.DTLVardef@19e3b34_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Dacoba, T. Douglas-Green, S. A. Murthy, B. Restrepo, A. D. Strom, Z. Billingsley, M. Pryor, M. Hammond, P. T. 2025-08-18 doi:10.1101/2025.08.13.670086 Cold Spring Harbor Laboratory Press 2025-08-18 <![CDATA[ Comparative analysis reveals distinct actin-based motility mechanisms in divergent Rickettsia species ]]> https://biorxiv.org/content/10.1101/2025.08.14.669974v1?rss=1 Bacher, M. C. Choe, J. E. Jiang, J. Welch, M. D. 2025-08-18 doi:10.1101/2025.08.14.669974 Cold Spring Harbor Laboratory Press 2025-08-18 <![CDATA[ Machine-learning strategy for high error tolerance in image-based digital molecular assays ]]> https://biorxiv.org/content/10.1101/2025.08.14.670347v1?rss=1 McAffee, D. B. Hu, Q. Arnob, A. Wu, H.-J. Groves, J. T. 2025-08-18 doi:10.1101/2025.08.14.670347 Cold Spring Harbor Laboratory Press 2025-08-18 <![CDATA[ Bivalent mRNA booster encoding virus-like particles elicits potent polyclass RBD antibodies in pre-vaccinated mice ]]> https://biorxiv.org/content/10.1101/2025.08.18.670983v1?rss=1 Fan, C. Cohen, A. A. Dam, K.-M. A. Rorick, A. V. Priso Fils, A.-C. I. Yang, Z. Gnanapragasam, P. N. Segovia, L. N. Huey-Tubman, K. E. Moon, W. J. Lin, P. J. Bjorkman, P. J. Hoffmann, M. A. 2025-08-19 doi:10.1101/2025.08.18.670983 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ Cortical thickness changes precede high levels of amyloid by at least seven years ]]> https://biorxiv.org/content/10.1101/2025.08.14.670398v1?rss=1 Roe, J. M. Jagust, W. J. Landua, S. M. Harrison, T. M. Grydeland, H. Slivka, M. Alatorre-Warren, J.-L. Garrido, P. F. Sorensen, O. Grodem, E. O. Ward, T. J. Leonardsen, E. H. Fladby, T. Bjornerud, A. Walhovd, K. B. Fjell, A. M. Vidal-Pineiro, D. Wang, Y. 2025-08-20 doi:10.1101/2025.08.14.670398 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ Regulated development of cannibalistic supergiant cells ]]> https://biorxiv.org/content/10.1101/2025.08.19.671124v1?rss=1 Larson, B. T. Giannotti, D. Mtawali, M. Lord, S. J. Boscaro, V. Keeling, P. J. 2025-08-20 doi:10.1101/2025.08.19.671124 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ Frequency-dependent fitness effects are ubiquitous ]]> https://biorxiv.org/content/10.1101/2025.08.18.670924v1?rss=1 Ascensao, J. A. Abedi, K. D. Prasad, A. N. Hallatschek, O. 2025-08-21 doi:10.1101/2025.08.18.670924 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Divergent viral phosphodiesterases for immune signaling evasion ]]> https://biorxiv.org/content/10.1101/2025.08.21.671373v1?rss=1 Doherty, E. E. Nomburg, J. E. Adler, B. A. Lopez, S. Hsieh, K. Price, N. Blount, N. Doudna, J. A. 2025-08-21 doi:10.1101/2025.08.21.671373 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ CRISPR-Cas13d-mediated targeting of a context-specific essential gene enables selective elimination of uveal melanoma ]]> https://biorxiv.org/content/10.1101/2025.08.21.671629v1?rss=1 97% of uveal melanoma cells while sparing healthy cells, including retinal pigment epithelial cells. This approach outperformed conventional Cas9 and siRNA methods in potency without inducing permanent genomic alterations. Our findings establish a RNA-targeting therapeutic for uveal melanoma and a framework for Cas13d-based interventions against broad "undruggable" cancers. ]]> Stauber, D. Sosnick, L. Ma, Y. Pimcharoen, S. Lawanprasert, A. Murthy, N. Myung, D. Qi, L. S. 2025-08-21 doi:10.1101/2025.08.21.671629 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Maximum water stress is decoupled from climate, traits and growth in a xeric oak ]]> https://biorxiv.org/content/10.1101/2025.08.22.666972v1?rss=1 Anderegg, L. D. L. Skelton, R. P. Diaz, J. Papper, P. Lovegreen, P. Trugman, A. T. Ackerly, D. D. Dawson, T. 2025-08-23 doi:10.1101/2025.08.22.666972 Cold Spring Harbor Laboratory Press 2025-08-23 <![CDATA[ Plasma membrane accessible cholesterol is regulated by ACC1 and lipid droplets ]]> https://biorxiv.org/content/10.1101/2025.08.21.671640v1?rss=1 Kinnebrew, M. Wijesinghe, K. M. Kim, C.-w. Schad, E. O. Li, S. Chen, S. Takeshima, E. Khandwala, C. B. Tillo, D. Lebensohn, A. M. Olzmann, J. A. Rohatgi, R. 2025-08-26 doi:10.1101/2025.08.21.671640 Cold Spring Harbor Laboratory Press 2025-08-26 <![CDATA[ Lithosyntrophy: Obligate syntrophy in a phosphite-oxidizing, methanogenic culture ]]> https://biorxiv.org/content/10.1101/2025.08.26.672485v1?rss=1 Aronson, H. Weaver, M. E. Hu, R. Lanclos, V. C. Rapp, J. D. Iavarone, A. T. Carlson, H. K. Coates, J. D. 2025-08-26 doi:10.1101/2025.08.26.672485 Cold Spring Harbor Laboratory Press 2025-08-26 <![CDATA[ Robust fluorescent labeling and tracking of endogenous non-repetitive genomic loci ]]> https://biorxiv.org/content/10.1101/2025.08.22.671818v1?rss=1 Raterink, A. Ghosh, R. P. Yang, L. Shi, Q. Nguyen, M. K. Hilton, I. B. Liphardt, J. T. Gustavsson, A.-K. 2025-08-27 doi:10.1101/2025.08.22.671818 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Detection of Echinococcus multilocularis in coyotes in Washington State, USA highlights need for increased global wildlife surveillance ]]> https://biorxiv.org/content/10.1101/2025.08.26.672275v1?rss=1 Hentati, Y. Reese, E. Curran, C. C. Miller, E. M. Diaz-Morales, D. M. Kreling, S. E. S. Verocai, G. G. Prugh, L. R. Schell, C. J. Wood, C. L. 2025-08-27 doi:10.1101/2025.08.26.672275 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Prior contact lens wear reduces susceptibility of the superficially-injured cornea to bacterial adhesion ]]> https://biorxiv.org/content/10.1101/2025.08.27.672703v1?rss=1 Yang, Y. Flandrin, O. Abboud, S. Jedel, E. Evans, D. J. Fleiszig, S. M. J. 2025-08-27 doi:10.1101/2025.08.27.672703 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Beyond species means - the intraspecific contribution to global wood density variation ]]> https://biorxiv.org/content/10.1101/2025.08.25.671896v1?rss=1 0.08 g cm-3; single-measurement R2 = 0.59). We recommend (i) systematic within-species sampling for local applications, and (ii) expanded taxonomic coverage combined with integrative models for robust estimates across ecological scales. ]]> Fischer, F. J. Chave, J. Zanne, A. Jucker, T. Fajardo, A. Fayolle, A. de Lima, R. A. F. Vieilledent, G. Beeckman, H. Hubau, W. De Mil, T. Wallenus, D. Aldana, A. M. Alvarez-Davila, E. Alves, L. F. Apgaua, D. M. G. Arcanjo, F. Bastin, J.-F. Bilous, A. Birnbaum, P. Blyshchyk, V. Borah, J. Boukili, V. Camarero, J. J. Casas, L. Gatti, R. C. Chambers, J. Q. Fabiano, E. C. Choat, B. Conti, G. Cornwell, W. Dar, J. A. Das, A. K. Dobler, M. Dougabka, D. Edwards, D. P. Evans, R. Falster, D. Fearnside, P. Flores, O. Fyllas, N. Gerard, J. Goodman, R. C. Guibal, D 2025-08-28 doi:10.1101/2025.08.25.671896 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ A global map of wood density ]]> https://biorxiv.org/content/10.1101/2025.08.25.671920v1?rss=1 Fischer, F. J. Chave, J. Zanne, A. Jucker, T. Fajardo, A. Fayolle, A. de Lima, R. A. F. Vieilledent, G. Beeckman, H. Hubau, W. De Mil, T. Wallenus, D. Aldana, A. M. Alvarez-Davila, E. Alves, L. F. Apgaua, D. M. G. Arcanjo, F. Bastin, J.-F. Bilous, A. Birnbaum, P. Blyshchyk, V. Borah, J. Boukili, V. Camarero, J. J. Casas, L. Cazzolla Gatti, R. Chambers, J. Q. Chimbioputo Fabiano, E. Choat, B. Cifuentes, E. Conti, G. Coomes, D. Cornwell, W. Dar, J. A. Das, A. K. Dobler, M. Dougabka, D. Edwards, D. P. Eggli, U. Evans, R. Falster, D. Fearnside, P. Flores, 2025-08-28 doi:10.1101/2025.08.25.671920 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ The Kaposi's sarcoma-associated herpesvirus TBP mimic uses a non-canonical DNA binding mode to promote viral late gene transcription ]]> https://biorxiv.org/content/10.1101/2025.08.25.672222v1?rss=1 Llacsahuanga Allcca, L. E. Didychuk, A. L. Rodriguez-Vargas, A. Glaunsinger, B. 2025-08-29 doi:10.1101/2025.08.25.672222 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ Leopard-EM: An extensible 2DTM package to accelerate in situ structural biology ]]> https://biorxiv.org/content/10.1101/2025.08.26.672452v1?rss=1 Giammar, M. D. Dickerson, J. L. Hall, L. N. Lucas, B. A. 2025-08-29 doi:10.1101/2025.08.26.672452 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ Enhanced Processivity and Collective Force Production of Kinesins at Low Radial Forces ]]> https://biorxiv.org/content/10.1101/2025.08.27.672644v1?rss=1 Hensley, A. M. Yildiz, A. 2025-08-31 doi:10.1101/2025.08.27.672644 Cold Spring Harbor Laboratory Press 2025-08-31 <![CDATA[ Repeated Viewing of a Narrative Movie Changes Event Timescales in The Brain ]]> https://biorxiv.org/content/10.1101/2025.08.27.672403v1?rss=1 Al-Zahli, N. Aly, M. Baldassano, C. 2025-09-01 doi:10.1101/2025.08.27.672403 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ Light on its feet: Acclimation to high and low diurnal light is flexible in Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2025.08.28.672467v1?rss=1 Dupuis, S. Chastain, J. L. Han, G. Zhong, V. Gallaher, S. D. Nicora, C. D. Purvine, S. O. Lipton, M. S. Niyogi, K. K. Iwai, M. Merchant, S. S. 2025-09-02 doi:10.1101/2025.08.28.672467 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ Unique and conserved endoplasmic reticulum stress responses in neuroendocrine cells ]]> https://biorxiv.org/content/10.1101/2025.08.29.672971v1?rss=1 Rodriguez-dos-Santos, K. Roy, G. Geisinger, A. Somalraju, S. Johnson, T. S. Kalwat, M. A. 2025-09-02 doi:10.1101/2025.08.29.672971 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ Epigenetically regulated p53 activity maintains intestinal regulatory T cell identity to prevent inflammation ]]> https://biorxiv.org/content/10.1101/2025.08.29.673118v1?rss=1 Silveria, S. Peeters, J. G. Vickery, J. Veronezi, G. M. Ramachandran, S. DuPage, M. 2025-09-03 doi:10.1101/2025.08.29.673118 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Atypical developmental remodeling of dopamine neurons involves AKT-GSK3β signaling and glia-mediated axon degeneration ]]> https://biorxiv.org/content/10.1101/2025.08.29.673168v1?rss=1 Zhang, X. Chen, W. Wang, Y. Tu, X. Zhang, X. Davis, R. L. Jan, L. Y. Jan, Y. N. 2025-09-03 doi:10.1101/2025.08.29.673168 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Cysteine reactivity profiling identifies host regulators of Mycobacterium tuberculosis replication in human macrophages ]]> https://biorxiv.org/content/10.1101/2025.08.30.673236v1?rss=1 Neff, J. DeMeester, K. E. Parraga, P. K. Suciu, R. Dix, M. Simon, G. Gianakopoulos, M. A. Melillo, B. Cravatt, B. F. Shiloh, M. U. 2025-09-03 doi:10.1101/2025.08.30.673236 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Functional imaging of hippocampal layers using VASO and BOLD on the Next Generation (NexGen) 7T Scanner ]]> https://biorxiv.org/content/10.1101/2025.08.29.673151v1?rss=1 Häkkinen, S. Beckett, A. Walker, E. Huber, L. Feinberg, D. A. 2025-09-04 doi:10.1101/2025.08.29.673151 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Natural variation in expression of a plant immune receptor mediates elicitor sensitivity ]]> https://biorxiv.org/content/10.1101/2025.09.03.674063v1?rss=1 Behnken, B. George, W. Chaparro, A. F. Kloss-Schmidt, A. Steinbrenner, A. D. 2025-09-04 doi:10.1101/2025.09.03.674063 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Nutrient-Sensing Nuclear Receptor PPARα Controls Liver Proteostasis ]]> https://biorxiv.org/content/10.1101/2025.09.01.673563v1?rss=1 Kim, J. Bains, N. Maddox, K. G. Hwang, J. G. Margolis, J. Q. Jiang, J. Fantini, F. Jung, S. Y. Choi, J. M. Ziari, N. Mohammed, H. Hellerstein, M. Arruda, A. P. Choi, S. Kim, K. H. Moore, D. 2025-09-05 doi:10.1101/2025.09.01.673563 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Ectomesenchymal identity emerges via relief of Twist1transcript destabilization ]]> https://biorxiv.org/content/10.1101/2025.09.02.673848v1?rss=1 Busby, L. C. Patrick, J. R. Lyons, L. W. Martik, M. L. 2025-09-05 doi:10.1101/2025.09.02.673848 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ HuD controls widespread RNA stability to drive neuronal activity-dependent responses ]]> https://biorxiv.org/content/10.1101/2025.09.05.674581v1?rss=1 Duffy, E. E. Patop, I. Kalaora, S. Assad, E. G. Koren, S. A. Traunmüller, L. Krüttner, S. Pajarillo, N. S. Finander, B. Barsdale, Z. Macias, M. M. Feng, M. Y. Paulo, J. A. Griffith, E. C. Kalish, B. T. Gygi, S. P. Churchman, L. S. Greenberg, M. E. 2025-09-06 doi:10.1101/2025.09.05.674581 Cold Spring Harbor Laboratory Press 2025-09-06 <![CDATA[ Seeing the forest and the trees: a workflow for automatic acquisition of ultra-high resolution drone photos of tropical forest canopies to support botanical and ecological studies ]]> https://biorxiv.org/content/10.1101/2025.09.02.673753v1?rss=1 Laliberte, E. Caron-Guay, A. Le Falher, V. Tougas, G. Muller-Landau, H. C. Rivas-Torres, G. Walla, T. R. Baudchon, H. Hernandez, M. Buenano, A. Weber, A. Chambers, J. Q. Inuma, J. C. Arauz, F. Valdes, J. Hernandez, A. Brassfield, D. Sergio, P. Vasquez, V. Simonetti, A. Marra, D. M. Vasconcelos, C. Vaca, J. F. Rivadeneyra, G. Illanes, J. Salagaje-Muela, L. A. Gualinga, J. 2025-09-07 doi:10.1101/2025.09.02.673753 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Heterochronic myeloid cell replacement reveals the local brain environment as key driver of microglia aging ]]> https://biorxiv.org/content/10.1101/2025.09.02.673859v1?rss=1 Gizowski, C. Popova, G. Shin, H. Mader, M. M. Craft, W. Kong, W. Shibuya, Y. Wranik, B. J. Fu, Y. C. Depp, C. Lin, T. D. Martin-McNulty, B. Yoo, Y. Tai, P.-H. Hingerl, M. Leung, K. Atkins, M. Fong, N. Jogran, D. Wendorff, A. Hendrickson, D. Gillich, A. Chang, A. Stevens, B. Wernig, M. Hahn, O. 2025-09-07 doi:10.1101/2025.09.02.673859 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Human-mouse cross-species comparison identifies common and unique aspects of intestinal mesenchyme development ]]> https://biorxiv.org/content/10.1101/2025.09.03.674033v1?rss=1 Johnson, K. Dong, X. Xiao, Z. Islam, H. Anderman, M. F. Glass, I. Spence, J. R. Walton, K. D. 2025-09-07 doi:10.1101/2025.09.03.674033 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Enhancer-driven random gene overexpression (ERGO): a method to study gene function in Chlamydomonas ]]> https://biorxiv.org/content/10.1101/2025.09.05.674469v1?rss=1 Lihanova, Y. Craig, R. J. Pribbernow, M. Goss, R. Sasso, S. 2025-09-07 doi:10.1101/2025.09.05.674469 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ The biosynthetic gene cluster landscape of the oral microbiome across health and dental caries ]]> https://biorxiv.org/content/10.1101/2025.09.04.674288v1?rss=1 5000 that could distinguish healthy and dental caries samples in the metatranscriptomic dataset, which demonstrated that BGCs could be predictive markers of disease. This analysis emphasizes the importance of high-quality metagenomic and metatranscriptomic datasets to resolve BGC expression patterns and to guide discovery of metabolites relevant to oral health and disease. ]]> Yao, M. L. Lin, P. Hua, K. Zhang, W. 2025-09-08 doi:10.1101/2025.09.04.674288 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ TDP-43 loss of function drives aberrant splicing in Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2025.09.04.673943v1?rss=1 500 post-mortem human brain samples from individuals with and without PD to show that splicing alterations are frequently detected. Differentially spliced genes were significantly more enriched for those causally-implicated in both PD and ALS than genes that were differentially expressed. Furthermore, we observed a strong association between these splicing alterations and dysfunction of the RNA-binding protein (RBP), TAR DNA-binding protein 43 (TDP-43). Strikingly, genes and exon junctions affected by TDP-43 knockdown overlapped significantly with those dysregulated across brain regions in PD. In brains from individuals with the LRRK2 c.6055G>A (p.G2019S) mutation, the most common genetic cause of PD, we also observed significant enrichment of TDP-43-dependent splicing changes. This finding was corroborated in human pluripotent stem cell-derived midbrain dopaminergic neurons and a LRRK2 p.G2019S knock-in mouse model, where reduced nuclear TDP-43 levels evidenced the well-recognised loss-of-function mechanism contributing to splicing dysregulation. By leveraging our RNA-based analyses we predicted TDP-43-dependent novel peptide sequences and validated their existence within human LRRK2 mutation mDNs, while also demonstrating an overall loss of protein and mRNA expression in mis-spliced genes. Collectively, our findings reveal that PD is marked by extensive splicing dysregulation dependent on TDP-43, making TDP-43 a promising new therapeutic target in PD. ]]> Brenton, J. W. Follett, J. Nirujogi, R. Toomey, C. E. Lopez-Garcia, P. Evans, J. R. Lee, Y. J. Syed, K. M. Rocamora Perez, G. Fairbrother-Browne, A. D'Sa, K. Grant-Peters, M. Lachica, J. Hicks, A. R. Wagen, A. Z. O'Callaghan, B. Macpherson, H. Montgomery, K.-a. Busquets, O. Reynolds, R. H. Garcia Ruiz, S. Cao, T. Chen, Z. Plun-Favreau, H. Wong, P. C. Farrer, M. Lashley, T. Soldner, F. Hockemeyer, D. Alessi, D. Wood, N. W. Hardy, J. Rio, D. C. Jaunmuktane, Z. Gustavsson, E. K. Gandhi, S. Ryten, M. 2025-09-09 doi:10.1101/2025.09.04.673943 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ Human shields alter antipredator behavior in Guenther's dik-dik (Madoqua guentheri) ]]> https://biorxiv.org/content/10.1101/2025.09.07.674752v1?rss=1 Owino, R. O. Hawkins, I. Noordermeer, I. Rodriguez, M. M. Stanton, L. A. Goheen, J. R. Alston, J. M. 2025-09-10 doi:10.1101/2025.09.07.674752 Cold Spring Harbor Laboratory Press 2025-09-10 <![CDATA[ CytoVI: Deep generative modeling of antibody-based single cell technologies ]]> https://biorxiv.org/content/10.1101/2025.09.07.674699v1?rss=1 Ingelfinger, F. Levy, N. Ergen, C. Bakulin, A. Becker, A. Boyeau, P. Kim, M. Ditz, D. Dirks, J. Maaskola, J. Wertheimer, T. Zeiser, R. Widmer, C. C. Amit, I. Yosef, N. 2025-09-12 doi:10.1101/2025.09.07.674699 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ CRISPR epi-editing reveals regulatory crosstalk between alternative promoters and splicing in Neurexin isoform expression ]]> https://biorxiv.org/content/10.1101/2025.09.10.675405v1?rss=1 Hsiao, Y. Y. Gomez, A. M. 2025-09-13 doi:10.1101/2025.09.10.675405 Cold Spring Harbor Laboratory Press 2025-09-13 <![CDATA[ Distinct Implicit Contributions to Action Selection and Action Execution in Sensorimotor Adaptation ]]> https://biorxiv.org/content/10.1101/2025.09.12.675892v1?rss=1 Wang, T. Lam, T. Taylor, J. A. Ivry, R. B. 2025-09-13 doi:10.1101/2025.09.12.675892 Cold Spring Harbor Laboratory Press 2025-09-13 <![CDATA[ Active learning enables discovery of transcriptional activators across fungal evolutionary space ]]> https://biorxiv.org/content/10.1101/2025.09.12.675635v1?rss=1 Waldburger, L. Nisonoff, H. Zintel, M. Kirkpatrick, L. D. Lam, A. Lanclos, N. Keasling, J. D. Staller, M. V. Shih, P. M. 2025-09-14 doi:10.1101/2025.09.12.675635 Cold Spring Harbor Laboratory Press 2025-09-14 <![CDATA[ Estimating Historical Food Web Variation in Chesapeake Bay Using Isotope Variation in Museum Fish Specimens ]]> https://biorxiv.org/content/10.1101/2025.09.09.674953v1?rss=1 Schumm, M. P. Bemis, K. E. Parenti, L. R. Okamoto, D. K. 2025-09-15 doi:10.1101/2025.09.09.674953 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ Design principles of a membrane-spanning ubiquitin ligase ]]> https://biorxiv.org/content/10.1101/2025.09.11.675358v1?rss=1 Williams, C. Nocka, L. M. Hedger, G. Parashara, P. Pardon, E. Latorraca, N. R. Pusapati, G. V. Lartey, D. Gao, L. Milenkovic, L. Chalk, R. Steyaert, J. Marqusee, S. Carrique, L. Bazan, J. F. Rouse, S. L. Kong, J. H. Siebold, C. Rohatgi, R. 2025-09-16 doi:10.1101/2025.09.11.675358 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Allosteric Disordering of eIF2B Regulates the Integrated Stress Response ]]> https://biorxiv.org/content/10.1101/2025.09.11.675390v1?rss=1 Dalwadi, U. Subramanian, A. Deal, A. Conrad, J. Venkatesh, M. Boone, M. Egea, P. He, L. Jain, N. Lee, J. Liu, Y. Reineke, L. Saito, K. Talledge, N. Toutkoushian, H. Le Vasseur, M. Zappa, F. de Groot, R. Acosta-Alvear, D. Arthur, C. Nunnari, J. Costa-Mattioli, M. Crawford, J. van Kuppeveld, F. J. M. Croll, T. Walter, P. Frost, A. 2025-09-16 doi:10.1101/2025.09.11.675390 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ PAQman: reference-free ensemble evaluation of long-read eukaryotic genome assemblies ]]> https://biorxiv.org/content/10.1101/2025.09.11.675652v1?rss=1 O'Donnell, S. Li, N. Steenwyk, J. L. Geiser, D. Martin, F. N. Gluck-Thaler, E. 2025-09-16 doi:10.1101/2025.09.11.675652 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Single-Nucleus Analysis of Human White Adipose Tissue Reveals Adipocyte Subsets with Distinct Metabolic Profiles ]]> https://biorxiv.org/content/10.1101/2025.09.14.673351v1?rss=1 Efthymiou, V. Ghosh, A. Kodani, S. D. Caubit, X. Fasano, L. Ali, W. Poulos, L. S. Camara, H. Gupta, A. Belaidouni, Y. Booeshaghi, S. A. Yang, S. Rastogi, R. Shamsi, F. Vernon, A. Streets, A. M. Tseng, Y.-H. Patti, M. E. 2025-09-16 doi:10.1101/2025.09.14.673351 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ The Hippocampus Rapidly Integrates Sequence Representations During Novel Multistep Predictions ]]> https://biorxiv.org/content/10.1101/2025.09.15.676324v1?rss=1 Tarder-Stoll, H. Baldassano, C. Aly, M. 2025-09-16 doi:10.1101/2025.09.15.676324 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ The Annotated Blueprint: Integrated Functional Genomic Resources for a Model Tetraploid Wheat Triticum turgidum cv. Kronos ]]> https://biorxiv.org/content/10.1101/2025.09.12.675711v1?rss=1 Seong, K. Kumar, R. Prigozhin, D. M. Lunde, C. M. Cherubino Ribeiro, T. H. Belanger, S. Hsieh, J.-W. A. Tang, M. Meyers, B. C. Krasileva, K. 2025-09-17 doi:10.1101/2025.09.12.675711 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Membrane potential and feedback dynamics regulate CatSper-mediated progesterone signaling in human sperm ]]> https://biorxiv.org/content/10.1101/2025.09.14.675619v1?rss=1 Kierzek, M. Fridman, D. Biagioni, C. Miller, E. Kaupp, U. B. Brenker, C. Strünker, T. 2025-09-17 doi:10.1101/2025.09.14.675619 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Subfoveal scotomas trigger fine-scale fixation reorganization: insights from retinal imaging and retinal-contingent stimulation ]]> https://biorxiv.org/content/10.1101/2025.09.17.674062v1?rss=1 Moon, B. Clark, A. M. Prahalad, K. S. Roorda, A. Tiruveedhula, P. Harmening, W. M. Gutnikov, A. Jenks, S. K. Kapisthalam, S. Rucci, M. Rolland, J. P. Poletti, M. 2025-09-17 doi:10.1101/2025.09.17.674062 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Lipoxin B4 Mitigates TRPV4-Activated Muller Cell Gliosis During Ocular Hypertension ]]> https://biorxiv.org/content/10.1101/2025.09.17.673801v1?rss=1 Kumar, M. Karnam, S. Maurya, S. Nagireddy, R. FLANAGAN, J. gronert, k. 2025-09-19 doi:10.1101/2025.09.17.673801 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Model-based and model-free valuation signals in the human brain vary markedly in their relationship to individual differences in behavioral control ]]> https://biorxiv.org/content/10.1101/2025.09.17.676398v1?rss=1 Ding, W. Cockburn, J. Simon, J. P. Johri, A. Cho, S. J. Oh, S. Feusner, J. D. Tadayonnejad, R. O'Doherty, J. P. 2025-09-19 doi:10.1101/2025.09.17.676398 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Overlooked neuroanatomical markers of face processing and developmental prosopagnosia in posteromedial cortex ]]> https://biorxiv.org/content/10.1101/2025.09.18.677204v1?rss=1 Kelly, J. P. Willbrand, E. H. Chen, X. Maboudian, S. A. Parker, B. J. Jiahui, G. Garrido, L. Zhen, Z. Duchaine, B. Weiner, K. S. 2025-09-19 doi:10.1101/2025.09.18.677204 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Perinatal Lead (Pb) Exposure Increases Mouse Embryonic Weight and Alters Neuronal Gene Expression ]]> https://biorxiv.org/content/10.1101/2025.09.18.677210v1?rss=1 Perera, B. P. U. Li, M. Tapaswi, A. Pan, J. Wang, D. Goswami, T. Morgan, R. K. Bakulski, K. M. Goodrich, J. M. Sartor, M. A. Dolinoy, D. C. Colacino, J. A. 2025-09-20 doi:10.1101/2025.09.18.677210 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Developing and Benchmarking One Health Genomic Surveillance Tools for Influenza A Virus in Wastewater ]]> https://biorxiv.org/content/10.1101/2025.09.19.676942v1?rss=1 Jiang, M. Wang, L.-W. Thissen, J. B. Nelson, K. L. Pipes, L. Kantor, R. S. 2025-09-20 doi:10.1101/2025.09.19.676942 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Discovery of circulating cell-free DNA 5hmC biomarkers for peritoneal metastasis in colorectal and appendiceal cancer ]]> https://biorxiv.org/content/10.1101/2025.09.18.676945v1?rss=1 Malina, Y. F. Gao, L. Dhiman, A. West-Szymanski, D. C. Berger, Y. Cui, X.-L. Zhang, Z. Rivas, M. Dougherty, U. Ye, C. Kwesi, A. Deng, Z. Reddy, B. Witmer, H. D. D. Hsu, P. J. He, C. Zhang, W. Bissonnette, M. Turaga, K. 2025-09-21 doi:10.1101/2025.09.18.676945 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Interpretable biophysical neural networks of transcriptional activation domains separate roles of protein abundance and coactivator binding ]]> https://biorxiv.org/content/10.1101/2025.09.19.677413v1?rss=1 LeBlanc, C. J. Agarwal, P. Demaray, J. Hu, G. Zintel, M. Lam, A. Castro Hernandez, J. E. Staller, M. V. 2025-09-21 doi:10.1101/2025.09.19.677413 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Repressed expression of nucleoporins and importins impairs plant defense against an infectious noncoding RNA ]]> https://biorxiv.org/content/10.1101/2025.09.19.677415v1?rss=1 Wang, Y. Fang, Y. Merritt, B. A. Liu, B. Gu, Y. Mou, Z. Wang, Y. Hao, J. 2025-09-21 doi:10.1101/2025.09.19.677415 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models ]]> https://biorxiv.org/content/10.1101/2025.09.21.677619v1?rss=1 Ye, C. Benegas, G. Albors, C. Li, J. C. Prillo, S. Fields, P. D. Clarke, B. Song, Y. S. 2025-09-21 doi:10.1101/2025.09.21.677619 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Establishing a continuum of cell types in the visual cortex ]]> https://biorxiv.org/content/10.1101/2025.09.22.677893v1?rss=1 Yoo, J. Xie, F. Butrus, S. Xu, R. Tan, Z. Gorzek, R. Mirshahidi, P. Tring, E. Suresh, S. Kim, J. Fleishman, G. Tan, L. Ringach, D. Trachtenberg, J. Xu, X. Zipursky, S. L. Shekhar, K. Jain, S. 2025-09-22 doi:10.1101/2025.09.22.677893 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland ]]> https://biorxiv.org/content/10.1101/2025.09.23.678135v1?rss=1 Hernandez, L. K. DiDonato, N. Pasa-Tolic, L. Chuckran, P. F. Firestone, M. K. Sieradzki, E. T. Yuan, M. Estera-Molina, K. Kimbrel, J. Dijkstra, P. Banfield, J. F. Pett-Ridge, J. Blazewicz, S. J. 2025-09-23 doi:10.1101/2025.09.23.678135 Cold Spring Harbor Laboratory Press 2025-09-23 <![CDATA[ AMICI: Attention Mechanism Interpretation of Cell-cell Interactions ]]> https://biorxiv.org/content/10.1101/2025.09.22.677860v1?rss=1 Hong, J. Desai, K. Nguyen, T. D. Nazaret, A. Levy, N. Ergen, C. Plitas, G. Azizi, E. 2025-09-24 doi:10.1101/2025.09.22.677860 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ Phylogenetically diverse introgression drives subtle population structure in Pacific rockfishes ]]> https://biorxiv.org/content/10.1101/2025.09.23.678143v1?rss=1 Sykes, N. T. B. Lou, R. N. Siegle, M. R. Sudmant, P. H. Larson, W. Owens, G. L. 2025-09-25 doi:10.1101/2025.09.23.678143 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Genetic landscape of DNMT3A R882H reveals mechanism of aberrant oligomerization ]]> https://biorxiv.org/content/10.1101/2025.09.24.678339v1?rss=1 Garcia, E. M. Lavidor, O. R. Raval, S. Lue, N. Z. Liang, J. K. McFadden, M. Hwang, D. D. Zepeda, M. U. Chen, L. W. Carr, S. A. Papanastasiou, M. Liau, B. B. 2025-09-25 doi:10.1101/2025.09.24.678339 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Optimized Lipid Extraction and Hybrid Annotation Pipeline for Individual Chitinous Mesozooplankton Using UPLC-HRMS ]]> https://biorxiv.org/content/10.1101/2025.09.24.678324v1?rss=1 Hwang, J. Edwards, B. 2025-09-26 doi:10.1101/2025.09.24.678324 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ Atlas of Lysosomal Aging Reveals a Molecular Clock of Storage Disorder-Associated Metabolites ]]> https://biorxiv.org/content/10.1101/2025.09.25.678303v1?rss=1 Puszynska, A. M. Nguyen, T. P. Cangelosi, A. L. Armani, A. Roberts, J. M. Singh, K. A. Cameron, J. C. Tseyang, T. Liu, G. Y. Lai, S. Sprenger, H.-G. Yang, J. Colgan, W. N. Kedir, J. F. Kajderowicz, K. M. Esantsi, T. K. Lu, Y. R. Waite, M. Kunchok, T. Lewis, C. A. Schulte, F. Bell, G. W. Sabatini, D. M. Weissman, J. S. 2025-09-26 doi:10.1101/2025.09.25.678303 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ Joint Mapping of Chromatin Accessibility and Targeted Proteomics in HER2-expressing Breast Cancer Systems ]]> https://biorxiv.org/content/10.1101/2025.09.25.678463v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@673263org.highwire.dtl.DTLVardef@11d28c5org.highwire.dtl.DTLVardef@15fa336org.highwire.dtl.DTLVardef@1d4426b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Fomitcheva Khartchenko, A. Lam, T. Goldhammer, N. Bont, M. Warhadpande, S. Rosenbluth, J. Herr, A. 2025-09-27 doi:10.1101/2025.09.25.678463 Cold Spring Harbor Laboratory Press 2025-09-27 <![CDATA[ Inflammatory reprogramming of human brain endothelial cells compromises blood-brain barrier integrity in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.09.26.678918v1?rss=1 Pinals, R. L. Islam, M. R. King, O. Choi, A. Kang, E. Nakano, M. Tuyeras, A. Naomi, M. T. Ngo, A. P. Jiang, A. Truong, N. Agbas, E. Lozano Cruz, C. F. Staab, C. Ko, T. Bennett, D. A. Stanton, A. E. Langer, R. Tsai, L.-H. 2025-09-28 doi:10.1101/2025.09.26.678918 Cold Spring Harbor Laboratory Press 2025-09-28 <![CDATA[ Brawn before bite in endemic Asian mammals after the end-Cretaceous extinction ]]> https://biorxiv.org/content/10.1101/2025.09.24.678280v1?rss=1 Tseng, Z. J. Li, Q. Ting, S. 2025-09-29 doi:10.1101/2025.09.24.678280 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Genome-wide screen in Mycobacterium tuberculosis infected macrophages reveals innate regulation of antibacterial mediators by IRF2 ]]> https://biorxiv.org/content/10.1101/2025.09.26.678671v1?rss=1 Roberts, A. W. Del Cid, L. N. Garelis, N. E. Cox, J. S. 2025-09-29 doi:10.1101/2025.09.26.678671 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Computational design of pH-sensitive binders ]]> https://biorxiv.org/content/10.1101/2025.09.29.678932v1?rss=1 Ahn, G. Coventry, B. Sadre, S. Haefner, E. Hu, J. Van, M. Huang, B. Sappington, I. W. Broerman, A. J. Lichtenstein, M. Glögl, M. Goreshnik, I. Vafeados, D. Baker, D. 2025-09-29 doi:10.1101/2025.09.29.678932 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Concept Learning Builds Behaviourally Relevant Attentional Templates ]]> https://biorxiv.org/content/10.1101/2025.09.29.679121v1?rss=1 Gumus, M. Lee, Z. Z. Y. Mack, M. L. 2025-10-01 doi:10.1101/2025.09.29.679121 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ TOR inhibition drives accumulation of amino acids through transcriptional activation in algae ]]> https://biorxiv.org/content/10.1101/2025.09.29.679311v1?rss=1 Upadhyaya, S. Kosina, S. M. Hixson, K. Schepmoes, A. Mewalal, R. Zhang, Y. O'Malley, R. C. Baumgart, L. Blaby, I. K. Lipton, M. S. Northen, T. Niyogi, K. K. Roth, M. S. 2025-10-01 doi:10.1101/2025.09.29.679311 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ A single-cell transcriptomic atlas of inner ear morphogenesis in zebrafish ]]> https://biorxiv.org/content/10.1101/2025.09.30.679639v1?rss=1 Swinburne, I. A. Munjal, A. A. Kukreja, K. Williams, S. Kawanishi, T. O'Brown, N. Ishimatsu, K. Klein, A. M. Megason, S. 2025-10-01 doi:10.1101/2025.09.30.679639 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Measuring serotonin binding to its receptors via charge transfer to ANAP ]]> https://biorxiv.org/content/10.1101/2025.10.01.679840v1?rss=1 Brado, O. G. Hawkins, A. T. Hill, A. D. Puljung, M. C. 2025-10-03 doi:10.1101/2025.10.01.679840 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Slow change blindness from serial dependence ]]> https://biorxiv.org/content/10.1101/2025.10.02.679619v1?rss=1 Frey, H. G. Whitney, D. 2025-10-03 doi:10.1101/2025.10.02.679619 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Distinct laminar origins of high-gamma and low-frequency ECoG signals revealed by optogenetics ]]> https://biorxiv.org/content/10.1101/2025.10.02.680142v1?rss=1 Garderes, P.-M. Feldman, D. E. Bouchard, K. E. 2025-10-03 doi:10.1101/2025.10.02.680142 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Microclimatic Effects on Functional Traits of Arctostaphylos crustacea ssp. crustacea in Alameda County, California, USA ]]> https://biorxiv.org/content/10.1101/2025.10.03.680375v1?rss=1 Hsiao, L. 2025-10-06 doi:10.1101/2025.10.03.680375 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Preselection CD4+CD8+ thymocytes modulate TCR responsiveness following TCRβ selection ]]> https://biorxiv.org/content/10.1101/2025.10.03.680384v1?rss=1 Kim, E. Aylard, D. A. Steier, Z. Ortiz, D. Choi, J. Chen, S. Streets, A. M. Yosef, N. Robey, E. 2025-10-06 doi:10.1101/2025.10.03.680384 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Leveraging WNT Hyperactivation to Kill Colorectal Cancer While Rejuvenating Healthy Intestine. ]]> https://biorxiv.org/content/10.1101/2025.10.05.680591v1?rss=1 Eng, G. Braverman, J. Gala, M. Yilmaz, O. H. 2025-10-06 doi:10.1101/2025.10.05.680591 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ ANTIDOTE: A Metadata-Driven Neural Network for Improving CryoEM 3-D Particle Sorting ]]> https://biorxiv.org/content/10.1101/2025.10.06.680814v1?rss=1 Berkeley, R. F. Cook, B. D. Ji, D. Foroughi, A. He, Y. Bachochin, M. J. Herzik, M. A. 2025-10-06 doi:10.1101/2025.10.06.680814 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Controlled Delivery of a Neurotrophic Factor in the Adult Mouse Brain Using Engineered Microglia ]]> https://biorxiv.org/content/10.1101/2025.10.06.680702v1?rss=1 Hofland, R. J. Gronska-Peski, M. Nobuta, H. Buitrago, N. Malhotra, K. Hebert, J. M. Goncalves, J. T. 2025-10-07 doi:10.1101/2025.10.06.680702 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ A microfluidics-based platform enables discovery of gametogenicrejuvenation factors in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2025.10.07.681065v1?rss=1 Spiri, S. Sing, T. L. Phung, N. Y. Goodman, J. Unal, E. Brar, G. A. 2025-10-08 doi:10.1101/2025.10.07.681065 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Environmental DNA Reveals Reykjavik's Human and Ecological History ]]> https://biorxiv.org/content/10.1101/2025.10.08.681091v1?rss=1 Kjaer, K. H. Ruter, A. H. Menendez-Serra, M. Vogel, N. A. Ramsoe, A. D. Farnsworth, W. R. Siggaard-Andersen, M.-L. Huang, Z. Korneliussen, T. S. Sand, K. K. Prohaska, A. Vinner, L. Stenderup, J. Sikora, M. Ingolfsson, O. Einarsson, B. F. Erlendsson, E. Petersen, J. Ilsoe, P. C. Guthmundsdottir, E. R. Einarsson, A. Eiriksson, J. AEGIS Consortium, Sonderborg, F. M. Hamerlik, L. Riddell, S. J. Vesteinsson, O. Wörmer, L. Richardson, K. Larsen, N. K. Sistiaga, A. Dockter, C. Jorgensen, M. E. Waugh, R. Schreiber, M. Russell, J. R. Hedley, P. E. Bayer, M. Maca 2025-10-08 doi:10.1101/2025.10.08.681091 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Co-option of lysosomal machinery shapes the symbiosis supporting coral reefs ]]> https://biorxiv.org/content/10.1101/2025.10.09.679812v1?rss=1 Maruyama, S. Henderson, C. F. Swinhoe, N. Kowalewski, G. P. Meier, E. K. Engelke, T. R. Cleves, P. A. 2025-10-09 doi:10.1101/2025.10.09.679812 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ Uncovering Design and Assembly Rules for mRNA-DNA Origami ]]> https://biorxiv.org/content/10.1101/2025.10.09.681283v1?rss=1 Wang, J. Y. Huzar, J. Kim, M. Ryu, T. Lomeli, N. R. Delcassian, D. Kim, D.-N. Tikhomirov, G. 2025-10-09 doi:10.1101/2025.10.09.681283 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ Ex Vivo Expanded Regulatory T Cells Inhibit AAA Progression by Limiting CD4+ and CD8+ T Cell Accumulation in Aortic Tissue ]]> https://biorxiv.org/content/10.1101/2025.10.08.681290v1?rss=1 Dasari, C. Lopez, J. L. Shawyan Jan, M. Shaligram, S. Lin, P.-Y. Levy-Lambert, D. Huang, A. G. Lizama Valenzuela, C. Hadley, P. Tang, Q. Oskowitz, A. 2025-10-10 doi:10.1101/2025.10.08.681290 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ Sensorimotor Theta Oscillations Coordinate Speech Movements ]]> https://biorxiv.org/content/10.1101/2025.10.09.681482v1?rss=1 Norman, Y. Frank, L. M. Chang, E. F. 2025-10-10 doi:10.1101/2025.10.09.681482 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ Spatially patterned cytoskeletal organization shapes astrocyte branch complexity ]]> https://biorxiv.org/content/10.1101/2025.10.10.681734v1?rss=1 Wynne, M. E. Barclay, W. E. Gopal, D. Bergstrom, J. J. Ho, L. T. Lopez, E. A. Nogales, E. Fu, M.-m. 2025-10-12 doi:10.1101/2025.10.10.681734 Cold Spring Harbor Laboratory Press 2025-10-12 <![CDATA[ A human arteriovenous differentiation roadmap reveals vein developmental mechanisms and vascular effects of viruses ]]> https://biorxiv.org/content/10.1101/2025.10.11.681838v1?rss=1 Ang, L. T. Zheng, S. L. Liu, K. J. Masaltseva, A. Winters, J. von Creytz, I. Jha, S. K. Yin, Q. Qian, C. Xiong, X. Dailamy, A. Xi, E. Alcocer, J. C. Sorensen, D. W. She, R. Smolyar, K. Szumska, D. Nornes, S. Martin, R. M. Lesch, B. J. Restrepo, N. K. Sun, W. Weissman, J. S. Lickert, H. Porteus, M. P. Skylar-Scott, M. A. Mosimann, C. Sumanas, S. De Val, S. Prescott, J. B. Red-Horse, K. Loh, K. M. 2025-10-12 doi:10.1101/2025.10.11.681838 Cold Spring Harbor Laboratory Press 2025-10-12 <![CDATA[ A telomere-to-telomere map of somatic mutation burden and functional impact in cancer ]]> https://biorxiv.org/content/10.1101/2025.10.10.681725v1?rss=1 Sohn, M.-H. Dubocanin, D. Vollger, M. R. Kwon, Y. Minkina, A. Munson, K. M. Hart, S. F. Ranchalis, J. E. Parmalee, N. L. Sedeno-Cortes, A. E. Ou, J. Au, N. Y. Bohaczuk, S. Carroll, B. Frazar, C. D. Harvey, W. T. Hoekzema, K. Huang, M.-F. Jacques, C. N. Jensen, D. M. Kolar, J. T. Lee, R. Lin, J. Loy, K. Mack, T. Mao, Y. Pham, M. M. Ryke, E. Smith, J. D. Sutherlin, L. Swanson, E. G. Weiss, J. M. SMaHT Assembly Working Group, Carvalho, C. Coorens, T. H. Harris, K. Wei, C.-L. Eichler, E. E. Altemose, N. Bennett, J. T. Stergachis, A. B. 2025-10-13 doi:10.1101/2025.10.10.681725 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Transcriptional regulation of disease-relevant microglial activation programs ]]> https://biorxiv.org/content/10.1101/2025.10.12.681832v1?rss=1 McQuade, A. Mishra, R. Hagan, V. Liang, W. Colias, P. Castillo, V. C. Lubin, J. Haage, V. Marshe, V. Fujita, M. Gomes, L. Ta, T. Teter, O. Chasins, S. E. De Jager, P. L. Nunez, J. K. Kampmann, M. 2025-10-13 doi:10.1101/2025.10.12.681832 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ A compressed code for memory discrimination ]]> https://biorxiv.org/content/10.1101/2025.10.12.681901v1?rss=1 Zhou, D. Noh, S. M. Harhen, N. C. Banavar, N. V. Kirwan, C. B. Yassa, M. A. Bornstein, A. M. 2025-10-13 doi:10.1101/2025.10.12.681901 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ A Population-scale Single-cell Spatial Transcriptomic Atlas of the Human Cortex ]]> https://biorxiv.org/content/10.1101/2025.10.13.681959v1?rss=1 Han, L. Liu, Z. Wang, L. Liu, Y. Wei, Y. Ma, J. He, Y. Zuo, Y. Fang, J. Yang, H. Zou, X. Wu, Z. Wang, M. Liu, W. Gao, L. Liu, Y. Song, X. Zhang, Y. S. Lei, J. Li, H. Li, L. An, Y. Jin, B. Zhong, Y. Chai, Q. Tao, Q. Tan, X. Lin, Y. Zhang, R. Wang, S. Chang, M. Yang, B. Chen, M. Mi, L. Zhuang, L. Yuan, N. Li, C. Huang, T. Li, X. Liu, C. Sun, Y. Chen, L. Liu, L. Xu, X. Li, C. Guo, H. Li, H. Poo, M. Gan, W.-B. Yao, J. Yuan, W. Liu, S. Shen, Z. Mao, Y. Wei, W. 2025-10-14 doi:10.1101/2025.10.13.681959 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Extreme weather risk shrinks range size estimates and alters biodiversity predictions ]]> https://biorxiv.org/content/10.1101/2025.10.13.682097v1?rss=1 Cohen, J. Ellis-Soto, D. La Sorte, F. Sharma, S. Jetz, W. 2025-10-14 doi:10.1101/2025.10.13.682097 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ MAIT cells induced by engineered Listeria exhibit antibacterial and antitumor activity ]]> https://biorxiv.org/content/10.1101/2025.10.13.682223v1?rss=1 Rivera-Lugo, R. Castillo, J. G. Lobanovska, M. Tang, E. Anaya-Sanchez, A. Espich, S. Stanley, S. A. DuPage, M. Portnoy, D. A. 2025-10-14 doi:10.1101/2025.10.13.682223 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Intrinsic errors in mitochondrial translation trigger a decline in cell fitness. ]]> https://biorxiv.org/content/10.1101/2025.10.13.682189v1?rss=1 Bal, G. L. Ng, K. Y. Berzell, E. Akpinar, A. Ekvik, A. Koludarova, L. Naddafi, S. Raths, C. Vane-Tempest, T. VanPortfliet, J. O'Keefe, S. Najumudeen, A. Nyman, T. A. Stewart, J. West, P. Battersby, B. J. 2025-10-15 doi:10.1101/2025.10.13.682189 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Biosynthesis of minimal C-phycocyanin chromophore assemblies in E. coli provides a platform to dissect protein-mediated tuning of exciton transfer ]]> https://biorxiv.org/content/10.1101/2025.10.13.682215v1?rss=1 Zhuang, D. L. Chuang, D. S. Velez, A. B. Gao, K. B. Velilla, S. M. Sweeny, M. Chen, J. A. Niyogi, K. K. Iwai, M. Francis, M. B. 2025-10-15 doi:10.1101/2025.10.13.682215 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Genome-wide DNA bridging by H-NS reshapes the stationary phase nucleoid and transcriptional landscape ]]> https://biorxiv.org/content/10.1101/2025.10.14.682352v1?rss=1 Way, L. E. Dai, X. Wiesler, E. E. McCarthy, L. A. Ren, Z. Hardy, G. G. Fuller, D. E. H. Hossain, L. Meyer, A. S. Abbondanzieri, E. A. Biteen, J. S. Wang, X. 2025-10-15 doi:10.1101/2025.10.14.682352 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Mutualism in disguise? Isotopic evidence for nutrient transfer from a carnivorous pitcher plant to its insect prey ]]> https://biorxiv.org/content/10.1101/2025.10.16.682955v1?rss=1 Armitage, D. W. Conover, A. Saunders, K. M. 2025-10-17 doi:10.1101/2025.10.16.682955 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ The impacts of almond pollination on honeybee viral dynamics ]]> https://biorxiv.org/content/10.1101/2025.10.17.678657v1?rss=1 Sokolov, N. A. Northrup, G. R. Wilfert, L. Boots, M. 2025-10-17 doi:10.1101/2025.10.17.678657 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ All-atom protein design via SE(3) flow matching with ProteinZen ]]> https://biorxiv.org/content/10.1101/2025.10.18.683228v1?rss=1 Li, A. J. Kortemme, T. 2025-10-18 doi:10.1101/2025.10.18.683228 Cold Spring Harbor Laboratory Press 2025-10-18 <![CDATA[ Accessing rare bacterial biosphere of soil through culturing: a comparative study of culture media effectiveness integrated with metataxonomics ]]> https://biorxiv.org/content/10.1101/2025.10.20.683382v1?rss=1 agricultural > forest, but the community isolated from forest soil contained a higher proportion of rare taxa. SEM, characterized by its low nutrient content and chemical composition resembling that of soil, proved to be the most effective, yielding higher colony-forming unit counts, greater overall and rare richness, and recovering a more taxonomically diverse rare community. The rare community retrieved by SEM was dominated by non-spore-forming taxa, in contrast to the other media, including diluted R2A. Culturing revealed a unique fraction of culturable taxa, representing ~17% of the culture-independent community on average, likely members of the rare biosphere that escape detection in metabarcoding analyses. SEM was also the medium that best captured this fraction. Our study demonstrates that low-nutrient, soil-like media such as SEM are powerful tools for accessing and characterizing the rare soil biosphere, complementing metabarcoding and providing isolates to explore the ecological and functional significance of rare taxa. ]]> Siles, J. A. Terry, N. 2025-10-20 doi:10.1101/2025.10.20.683382 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Brain Dynamics of Mental Manipulation ]]> https://biorxiv.org/content/10.1101/2025.10.20.683458v1?rss=1 30 Hz) and slower (< 30 Hz) dynamics in primary and secondary auditory areas, suggesting a decrease in local excitability. Second, there is a distributed increase in oscillatory synchrony (6-10 Hz), which predicts imagery vividness and task performance. This evidence points to a key role of local excitability and inter-areal synchrony in the manipulation of thought. ]]> Quiroga-Martinez, D. R. He, T. Fernandez-Rubio, G. Bonetti, L. Blenkmann, A. O. Endestad, T. Solbakk, A.-K. Meling, T. R. Fabricius, M. E. McManus, O. K. Willie, J. T. Brunner, P. Dastjerdi, M. Lin, J. Knight, R. 2025-10-21 doi:10.1101/2025.10.20.683458 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Investigating Overflow Metabolism in Heterotrophic Cultures of the Green Alga Chromochloris zofingiensis ]]> https://biorxiv.org/content/10.1101/2025.10.20.683564v1?rss=1 Meagher, M. F. Camacho, D. Gallaher, S. Merchant, S. Boyle, N. 2025-10-21 doi:10.1101/2025.10.20.683564 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Identification of radical SAM enzymes responsible for the methylation and desaturation of archaeal lipids and an AttH hydratase mediating hydroxy-GDGT biosynthesis ]]> https://biorxiv.org/content/10.1101/2025.10.20.683597v1?rss=1 Garcia, A. A. Chadwick, G. Nayak, D. D. Welander, P. V. 2025-10-21 doi:10.1101/2025.10.20.683597 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ JAK1/2 Inhibition Delays Cachexia and Improves Survival through Increased Food Intake ]]> https://biorxiv.org/content/10.1101/2025.10.21.683287v1?rss=1 Dantas, E. C. Murthy, A. Kim, J. Ahmed, T. Ahmed, M. Perrier, T. Ramsamooj, S. Nathoo, I. Kniess Debarba, L. Lima Queiroz, A. Li, S. Ersoy, B. Ferrer, M. Goldstein, I. C. Gao, J. Lam, T. Nagler, M. Malbari, M. Altorki, N. Cararo Lopes, E. Gomez Jenkins, M. Das, T. Jamal-Hanjani, M. White, E. Janowitz, T. Goncalves, M. 2025-10-22 doi:10.1101/2025.10.21.683287 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Separating selection from mutation in antibody language models ]]> https://biorxiv.org/content/10.1101/2025.10.21.683652v1?rss=1 Matsen, F. A. Dumm, W. Sung, K. Johnson, M. M. Rich, D. Starr, T. Song, Y. S. Fukuyama, J. Haddox, H. K. 2025-10-22 doi:10.1101/2025.10.21.683652 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Targeted Transcriptional Repression by Induced Proximity ]]> https://biorxiv.org/content/10.1101/2025.10.22.680877v1?rss=1 90% inhibition of AR transcriptional activity in androgen-independent prostate cancer cells with locus-specific gene repression. We further show that TRACERs can be modularly reprogrammed to recruit alternative repressors, including PRC2. Collectively, these findings establish TRACERs as a generalizable modality to pharmacologically silence undruggable transcription factors through targeted epigenetic reprogramming, offering a powerful new strategy for treating cancers refractory to existing therapies. ]]> Stieger, C. E. Chen, X. Dovala, D. Wu, F. Pizzato, N. McKenna, J. Johannessen, C. Fodor, B. Schirle, M. Nomura, D. K. 2025-10-22 doi:10.1101/2025.10.22.680877 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Benchmarking remote sensing methods to capture plant functional diversity from space ]]> https://biorxiv.org/content/10.1101/2025.10.22.683881v1?rss=1 Pacheco-Labrador, J. Gomarasca, U. Pabon-Moreno, D. E. Li, W. Migliavacca, M. Jung, M. Duveiller, G. 2025-10-23 doi:10.1101/2025.10.22.683881 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Direct identification of de novo mobile element insertions from single molecule sequencing of human sperm ]]> https://biorxiv.org/content/10.1101/2025.10.25.684559v1?rss=1 Li, S. Aston, K. Gleeson, J. G. Quinlan, A. Yang, X. Sudmant, P. H. 2025-10-26 doi:10.1101/2025.10.25.684559 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ A20 restriction of nitric oxide production restores macrophage bioenergetic balance ]]> https://biorxiv.org/content/10.1101/2025.10.26.684676v1?rss=1 Ma, A. Chan, M.-P. Advincula, R. Achacoso, P. Grossman, E. Nomura, D. Malynn, B. 2025-10-27 doi:10.1101/2025.10.26.684676 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Natural variation in regulatory code revealed through Bayesian analysis of plant pan-genomes and pan-transcriptomes ]]> https://biorxiv.org/content/10.1101/2025.10.27.684862v1?rss=1 Wei, W. Wu, X. Sutherland, C. A. Lin, Y. Lunde, C. Exposito-Alonso, M. Krasileva, K. 2025-10-28 doi:10.1101/2025.10.27.684862 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ Faf1 accelerates p97-mediated protein unfolding by promoting ubiquitin engagement ]]> https://biorxiv.org/content/10.1101/2025.10.27.684972v1?rss=1 Liao, Z. Arkinson, C. Martin, A. 2025-10-28 doi:10.1101/2025.10.27.684972 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ Structure-Aware Mapping of Disease-Relevant Missense Variation in Nuclear Pore complex Genes ]]> https://biorxiv.org/content/10.1101/2025.10.27.684907v1?rss=1 Yekeh Yazdandoost, F. Parsa, M. S. 2025-10-29 doi:10.1101/2025.10.27.684907 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ Dynamic PD-L1 Regulation Shapes Tumor Immune Escape andResponse to Immunotherapy ]]> https://biorxiv.org/content/10.1101/2025.10.28.685116v1?rss=1 Pell, B. Kalizhanova, A. Tursynkozha, A. Dengi, D. Kuang, Y. Kashkynbayev, A. 2025-10-29 doi:10.1101/2025.10.28.685116 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ Stimulation with ECoG electrodes modulates cortical activity and sensory processing in the awake mouse brain ]]> https://biorxiv.org/content/10.1101/2025.10.28.685211v1?rss=1 Ji, N. Fan, J. L. Lee, K. Tchoe, Y. Ganji, M. Vatsyayan, R. Yoon, H. Y. Garrett, J. Dayeh, S. A. Halgren, E. 2025-10-30 doi:10.1101/2025.10.28.685211 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Deterministic DNA barcoding using vacuum-driven loading of free oligonucleotides to microwell arrays ]]> https://biorxiv.org/content/10.1101/2025.10.29.684720v1?rss=1 Baranowska, P. Lam, T. Herr, A. E. 2025-10-30 doi:10.1101/2025.10.29.684720 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Engineered orthogonal translation systems from metagenomic libraries expand the genetic code ]]> https://biorxiv.org/content/10.1101/2025.10.30.685624v1?rss=1 200 tRNAs, test >1,250 combinations of aaRS:tRNA pairs, and identify the AP1 TrpRS:tRNATrpUCA as an orthogonal pair that natively encodes tryptophan at the UGA codon. We demonstrate that the AP1 TrpRS:tRNATrpUCA is highly active in cell-free and cellular contexts. We then use Ochre, a genomically recoded Escherichia coli strain that lacks UAG and UGA codons, to engineer an AP1 TrpRS variant capable of 5-hydroxytryptophan incorporation at an open UGA codon. We anticipate that our strategy of integrating metagenomic bioprospecting with cell-free screening and cell-based engineering will accelerate the discovery and optimization of orthogonal translation systems for genetic code expansion. ]]> Seki, K. Nguyen, M. T. A. Penev, P. I. Isaacs, F. J. Banfield, J. F. Jewett, M. C. 2025-10-30 doi:10.1101/2025.10.30.685624 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Cohesin Acetylation and ATPase Activity Control Cohesion and Loop Architecture through Distinct Mechanisms ]]> https://biorxiv.org/content/10.1101/2025.10.30.685539v1?rss=1 Costantino, L. Ye, T. Boardman, K. Xiang, S. Luo, J. Mu, Y. Ma, W. Koshland, D. 2025-10-31 doi:10.1101/2025.10.30.685539 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Glycolytic ATP production enables rapid mammalian cell growth ]]> https://biorxiv.org/content/10.1101/2025.10.30.685682v1?rss=1 Kukurugya, M. A. Zhang, S. Ha, B. T. Ekvik, A. E. Titov, D. V. 2025-10-31 doi:10.1101/2025.10.30.685682 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Principal Components Analysis fails to recover phylogenetic structure in hominins ]]> https://biorxiv.org/content/10.1101/2025.10.31.685754v1?rss=1 Raskin, L. Y. Seselj, M. Bitarello, B. D. Stroustrup, S. Li, J. K. Huelsenbeck, J. 2025-10-31 doi:10.1101/2025.10.31.685754 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ A unifying model of LAT condensates in reconstitution experiments ]]> https://biorxiv.org/content/10.1101/2025.10.31.685772v1?rss=1 Omar, Y. A. D. Sun, S. Kardar, M. Groves, J. T. Chakraborty, A. K. 2025-11-01 doi:10.1101/2025.10.31.685772 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ TOMM40 suppression promotes neuronal cholesterol imbalance and molecular and behavioral phenotypes of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.10.31.685963v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@e3e3e2org.highwire.dtl.DTLVardef@1861f67org.highwire.dtl.DTLVardef@77a813org.highwire.dtl.DTLVardef@1bb9a83_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yang, N. V. Wang, S. Li, B. Simms, J. Dinh, L. Huang, A. Oei, J. H. Yassine, H. N. Krauss, R. M. 2025-11-01 doi:10.1101/2025.10.31.685963 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ Rapid generation of ventral A9-like dopaminergic neurons from patterned iPSCs ]]> https://biorxiv.org/content/10.1101/2025.10.31.685897v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@1d83eb3org.highwire.dtl.DTLVardef@1fc7fa5org.highwire.dtl.DTLVardef@2033e3org.highwire.dtl.DTLVardef@2e8fa3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chaplot, K. Zhang, L. Wessman, J. Rivera, M. Wang, Z. Wang, F. Duan, X. England, P. M. Clark, I. C. Ullian, E. M. 2025-11-02 doi:10.1101/2025.10.31.685897 Cold Spring Harbor Laboratory Press 2025-11-02 <![CDATA[ Dynamical memory underlies prolonged plasmid persistence after transient antibiotic treatment ]]> https://biorxiv.org/content/10.1101/2025.10.31.685803v1?rss=1 Zhou, Z. Weiss, A. Yao, Z. Chen, X. Lok, K. Son, H.-i. You, L. 2025-11-03 doi:10.1101/2025.10.31.685803 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ T cell costimulatory and inhibitory signals differentially modulate LAT condensate nucleation propensity after TCR ligation ]]> https://biorxiv.org/content/10.1101/2025.11.01.685673v1?rss=1 Choi, S. Kim, S. Tijam, J. R. Eisen, T. J. Morita, S. McAffee, D. B. Groves, J. T. 2025-11-03 doi:10.1101/2025.11.01.685673 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Design of Tissue-Selective PROTACs Through Recruiting E3 Ligase Scaffolding Protein MAGEA11 ]]> https://biorxiv.org/content/10.1101/2025.11.03.686228v1?rss=1 Jacobsen, I. E. Shi, R. Scholtz, C. R. Pomerantz, W. C. K. Georg, G. I. 2025-11-03 doi:10.1101/2025.11.03.686228 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Quorum sensing antiactivators constrain Pseudomonas aeruginosa RhlR activity ]]> https://biorxiv.org/content/10.1101/2025.10.31.685934v1?rss=1 Sridhar, V. Smalley, N. E. Dandekar, A. A. Asfahl, K. L. 2025-11-04 doi:10.1101/2025.10.31.685934 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Identification of distinct cDC2 subpopulations that direct microbiota-specific T cell differentiation ]]> https://biorxiv.org/content/10.1101/2025.11.04.686414v1?rss=1 Carroll, S. L. Ly, A. Liu, A. K. Canesso, M. C. C. Victora, G. D. Mucida, D. Barton, G. M. 2025-11-05 doi:10.1101/2025.11.04.686414 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Diversity-driven biochemical survey reveals dimeric structural origin of rubisco ]]> https://biorxiv.org/content/10.1101/2025.11.05.686826v1?rss=1 Kehl, A. J. Taylor-Kearney, L. Jaffe, A. L. Pereira, J. H. Lee, J. Hammel, M. Waldburger, L. Yeow, C. Alvarado, L. V. Adams, P. D. Banfield, J. Siegel, J. B. Prywes, N. Shih, P. M. 2025-11-05 doi:10.1101/2025.11.05.686826 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Bronsted-basic small molecules activate GTP hydrolysis in Ras Q61 mutants ]]> https://biorxiv.org/content/10.1101/2025.11.04.686643v1?rss=1 Wang, Y. Chen, S. Wu, Y. Cao, Y. Shi, Z. Norinskiy, M. A. Wang, C. Celik, H. Zhang, Z. 2025-11-06 doi:10.1101/2025.11.04.686643 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Direct Optical Quantification of Chain Collapse, Reduced Dielectric, and Water Release Driving Protein Phase Separation ]]> https://biorxiv.org/content/10.1101/2025.11.04.686660v1?rss=1 Perets, E. A. Spies, J. A. Cheong, J. H. Shi, L. Asamoto, D. K. Holehouse, A. S. Kim, J. E. Min, W. Neu, J. Yan, E. C. Y. 2025-11-06 doi:10.1101/2025.11.04.686660 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Revisiting the Evolution of Lactase Persistence: Insights from South Asian Genomes ]]> https://biorxiv.org/content/10.1101/2025.11.05.686799v1?rss=1 T, is widespread across South Asia, exhibiting clinal variation along north-south and east-west gradients. Ancient DNA analysis reveals that this variant first appeared in South Asia during the historical and medieval periods through Steppe pastoralist-related gene flow. Interestingly, unlike in other worldwide populations, the LP prevalence is almost entirely explained by Steppe ancestry--not selection--in most contemporary South Asians. A notable exception is the only two pastoralist groups, Toda in South India and Gujjar in Pakistan, that have unexpectedly high frequencies of-13.910*T, comparable to estimates in Northern Europeans. By performing local ancestry inference, we find significant enrichment for Steppe pastoralist ancestry around the LCT locus in these two geographically-distant pastoralist groups, indicative of strong selection. Together, these findings highlight the complex role of ancestry and natural selection in shaping the prevalence of lactase persistence on the subcontinent. ]]> Kerdoncuff, E. Marohn, M. Cramer, N. Dey, S. Kardia, S. Thangaraj, K. Segurel, L. Dey, A. B. Lee, J. Moorjani, P. 2025-11-06 doi:10.1101/2025.11.05.686799 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Detection of five viruses commonly implicated with Bovine Respiratory Disease using loop-mediated isothermal amplification ]]> https://biorxiv.org/content/10.1101/2025.11.06.687045v1?rss=1 Davidson, J. L. Maruthumuthu, M. K. Kamel, M. Mohan, S. Pascual-Garrigos, A. Dextre, A. Centeno-Delphia, R. E. Boerman, J. Pillai, D. Koziol, J. Ault, A. Schoonmaker, J. P. Johnson, T. A. Verma, M. S. 2025-11-07 doi:10.1101/2025.11.06.687045 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ Retinal ganglion cell input to superior colliculus encodes salient information ]]> https://biorxiv.org/content/10.1101/2025.11.06.687035v1?rss=1 Borges, K. Xian, Q. Lu, R. Liang, Y. Haley, S. Nigam, S. Ji, N. 2025-11-08 doi:10.1101/2025.11.06.687035 Cold Spring Harbor Laboratory Press 2025-11-08 <![CDATA[ Reconstitution of multistep recruitment of ULK1 to membranes in autophagy ]]> https://biorxiv.org/content/10.1101/2025.11.07.687251v1?rss=1 Duan, Y. Lu, Y. Paul, S. Betz, J. Wilhelm, L. P. Cook, A. S. I. Ren, X. Adriaenssens, E. Martens, S. Ganley, I. Hummer, G. Hurley, J. H. 2025-11-09 doi:10.1101/2025.11.07.687251 Cold Spring Harbor Laboratory Press 2025-11-09 <![CDATA[ Integrated analysis of multimodal long-read epigenetic assays ]]> https://biorxiv.org/content/10.1101/2025.11.09.687458v1?rss=1 Marcus, J. Dixon-Luinenburg, O. Gamarra, N. Schwartz, J. P. Rozenwald, M. Maslan, A. Urnov, F. Straight, A. F. Altemose, N. Ioannidis, N. M. Streets, A. 2025-11-09 doi:10.1101/2025.11.09.687458 Cold Spring Harbor Laboratory Press 2025-11-09 <![CDATA[ Challenges in predicting chromatin accessibility differences between species ]]> https://biorxiv.org/content/10.1101/2025.11.09.687449v1?rss=1 Stephen, A. Z. M. Raje, A. Sestili, H. H. Wirthlin, M. E. Lawler, A. J. Brown, A. R. Stauffer, W. R. Pfenning, A. R. Kaplow, I. M. 2025-11-10 doi:10.1101/2025.11.09.687449 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Magnetosome organelles are organized through interactions between McaA and McaB that alter the dynamics of the bacterial actin-like protein MamK ]]> https://biorxiv.org/content/10.1101/2025.11.10.687720v1?rss=1 Ra, Y. Pan, Y. Chen, T. Y. Dixon, K. Taoka, A. Komeili, A. 2025-11-10 doi:10.1101/2025.11.10.687720 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ eIF2B Selectively Anchors and Activates Mutant KRAS ]]> https://biorxiv.org/content/10.1101/2025.11.10.686860v1?rss=1 View larger version (21K): org.highwire.dtl.DTLVardef@1f50934org.highwire.dtl.DTLVardef@2f55b9org.highwire.dtl.DTLVardef@1a51e39org.highwire.dtl.DTLVardef@1634aac_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIeIF2B interacts with mutant KRAS and SOS at the plasma membrane (PM). C_LIO_LIThe eIF2B:SOS complex promotes the GTP-bound active state of mutant KRAS. C_LIO_LIeIF2B enhances the translation of B4GALT5 mRNA, encoding a key enzyme of glycosphingolipid (GSL) biosynthesis. C_LIO_LIUpregulation of the GSL metabolites, ganglioside GM3 and sulfatide SM4, remodels PM lipid composition to facilitate eIF2B:SOS:KRAS complex formation and mutant KRAS nanoclustering. C_LIO_LIThrough its interaction with SOS and stimulation of GSL synthesis, eIF2B selectively activates mutant KRAS at the PM among RAS isoforms. C_LIO_LIeIF2B is required for the development of mKRAS-driven lung adenocarcinoma in mice. C_LIO_LIeIF2B is a marker of poor prognosis in mutant KRAS-driven cancers. C_LI ]]> Kim, H. Diao, S. Cho, K.-J. Lee, H.-R. Liu, J. Egea, P. Pantsar, T. Kurki, M. Ghaddar, N. Wang, S. Zou, J. Y. Amiri, M. Gannaban, R. Hancock, J. F. Rice, K. M. Deng, Q. Sasaki, A. Asara, J. M. Tripathi, B. Lowy, D. Lawrence, R. Hatzoglou, M. Azpilcueta-Nicolas, C. R. Lumb, J.-P. Columbus, J. Turbyville, T. J. Marshall, C. B. Ikura, M. Groves, J. T. Sonenberg, N. Walter, P. Koromilas, A. E. 2025-11-12 doi:10.1101/2025.11.10.686860 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Spinal cord regeneration deploys cell-type specific developmental and non-developmental strategies to restore neuron diversity ]]> https://biorxiv.org/content/10.1101/2025.11.10.687703v1?rss=1 Angell Swearer, A. Perkowski, S. B. Husain, I. Figueiredo, T. A. McCartney, M. Wills, A. E. 2025-11-12 doi:10.1101/2025.11.10.687703 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Metabolic zonation and characterization of tissue slices with spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.11.11.687271v1?rss=1 Etxezarreta Arrastoa, O. Pirona, A.-C. Wagner, A. Yosef, N. 2025-11-12 doi:10.1101/2025.11.11.687271 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Bioplastic Production Potential of Azospira suillum PS: Growth-Associated PHB Production Under Aerobic and Anaerobic Conditions ]]> https://biorxiv.org/content/10.1101/2025.11.12.688118v1?rss=1 Meier, D. A. O. Glazer, B. Lanclos, V. C. Carlson, H. K. Coates, J. D. 2025-11-12 doi:10.1101/2025.11.12.688118 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Effects of biological fixation methods on stimulated Raman scattering microscopy signal ]]> https://biorxiv.org/content/10.1101/2025.11.11.687741v1?rss=1 Ceconello, C. Han, W. Manifold, B. Polli, D. Streets, A. M. 2025-11-13 doi:10.1101/2025.11.11.687741 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Class-I myosin responds to change in membrane tension during clathrin-mediated endocytosis in human induced pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2025.11.12.688091v1?rss=1 Smith, S. L. Zhan, T. Li, W. De Belly, H. Zhang, Q. Xu, K. Weiner, O. Drubin, D. G. 2025-11-13 doi:10.1101/2025.11.12.688091 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Random barcode transposon-site sequencing in Mycobacterium tuberculosis reveals the functions of uncharacterized genes ]]> https://biorxiv.org/content/10.1101/2025.11.13.688195v1?rss=1 Dinshaw, K. Lien, K. Knight, M. Ounkap, S. Liu, H. Savage, D. Carlson, H. Deutschbauer, A. Stanley, S. A. 2025-11-13 doi:10.1101/2025.11.13.688195 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ FOXA1 mutations co-opt nascent transcription factor networks in partnership with androgen receptor to enhance prostate tumorigenicity ]]> https://biorxiv.org/content/10.1101/2025.11.13.688263v1?rss=1 Ladewig, E. Nazir, A. Park, T. Fan, V. B. Cao, Z. Hawk, J. Kelly, L. Tjian, R. Leslie, C. S. Sawyers, C. 2025-11-14 doi:10.1101/2025.11.13.688263 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Acute Myeloid Leukemia Relapse after Bromodomain Inhibitor Treatment or Chemotherapy is Characterized by Myc-Ras Transcriptional Remodeling ]]> https://biorxiv.org/content/10.1101/2025.11.13.688312v1?rss=1 Huang, B. J. D'Souza, J. Batingana, A. R. Harris, M. D. Wang, X. Hwang, E. Wandler, A. M. Burgess, M. R. Li, Q. Meshinchi, S. Bollag, G. Shannon, K. 2025-11-14 doi:10.1101/2025.11.13.688312 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Surviving phage attack dynamically regulates bacterial immunity to defeat counterdefenses ]]> https://biorxiv.org/content/10.1101/2025.11.13.688357v1?rss=1 Oshiro, R. Dunham, D. Gill, C. Chouldjian, A. Piya, D. Mutalik, V. K. Seed, K. 2025-11-14 doi:10.1101/2025.11.13.688357 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Modulating MyoD1 dosage activates alternate cell fate beyond myogenic differentiation ]]> https://biorxiv.org/content/10.1101/2025.11.13.688391v1?rss=1 Whitney, O. N. Dailey, G. M. McKenna, J. K. Darzacq, X. Tjian, R. 2025-11-14 doi:10.1101/2025.11.13.688391 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Climate warming and urbanization may expand dengue transmission risk in California ]]> https://biorxiv.org/content/10.1101/2025.11.14.688544v1?rss=1 Couper, L. Sipin, T. J. Sambado, S. Rennie, Z. Shanebeck, K. M. Lyberger, K. P. Collender, P. P. A. Ngo, V. Remais, J. V. MacDonald, A. J. 2025-11-16 doi:10.1101/2025.11.14.688544 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ MLT-11 is necessary for C. elegans embryogenesis and conserved sequences play distinct roles in cuticle structure ]]> https://biorxiv.org/content/10.1101/2025.11.14.688552v1?rss=1 Ragle, J. M. Turzo, A. Jackson, A. Vo, A. A. Pham, V. T. Daly, K. Clancy, J. C. Levenson, M. T. Lee, A. D. Ward, J. D. 2025-11-16 doi:10.1101/2025.11.14.688552 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ Persistent trade-offs balance competition and colonization across centuries ]]> https://biorxiv.org/content/10.1101/2025.11.16.688059v1?rss=1 Backman, T. Cui, J. Caullireau, E. Bleak, E. Bezrukov, I. Girardi, P. Hawks, A. Lasky, J. R. Latorre, S. M. Erberich, J. M. Lopez, L. Neumann, M. Perkins, A. M. Symeonidi, E. Azadi, P. Horvath, M. P. Muszynski, A. Lang, P. L. M. Karasov, T. L. Burbano, H. A. 2025-11-16 doi:10.1101/2025.11.16.688059 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ Overcoming the eIF2α Brake in Human Cell-Derived Translation Systems ]]> https://biorxiv.org/content/10.1101/2025.11.16.688697v1?rss=1 Aleksashin, N. A. Shelke, R. R. Yin, T. Cate, J. H. D. 2025-11-16 doi:10.1101/2025.11.16.688697 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ MORPH2DIAG: Automated Structural MRI Preprocessing and Tissue Segmentation for Interpretable Machine and Deep Learning-Based Neuroanatomical Classification ]]> https://biorxiv.org/content/10.1101/2025.11.16.688711v1?rss=1 Bangera, S. C. Pospisil, L. Bengtsson, T. 2025-11-17 doi:10.1101/2025.11.16.688711 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ A chromosome-level genome assembly of a vernal pool specialist amphibian, the Western Spadefoot, Spea hammondii ]]> https://biorxiv.org/content/10.1101/2025.11.16.688715v1?rss=1 Thompsky, B. Beraut, E. Cooper, R. D. Escalona, M. Espinoza, R. E. Fisher, R. N. Miller, C. Nguyen, O. Sacco, S. Sahasrabudhe, R. Seligmann, W. E. Tofflemier, E. Wang, I. J. Shaffer, H. B. 2025-11-17 doi:10.1101/2025.11.16.688715 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Model of ocular surface ion and water transport predicts efficacy of dry eye therapeutics targeting epithelial transport and tear fluid dynamics ]]> https://biorxiv.org/content/10.1101/2025.11.17.688783v1?rss=1 Verma, V. Lindgren, E. S. Levin, M. H. Cil, O. Tradtrantip, L. Yan, R. Pasricha, N. D. Verkman, A. S. 2025-11-17 doi:10.1101/2025.11.17.688783 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Structure and mechanism of microtubule stabilization and motor regulation by MAP9 ]]> https://biorxiv.org/content/10.1101/2025.11.17.688911v1?rss=1 Cetin, B. Taheri, A. Golcuk, M. Monroy, B. Y. Fernandes, J. Ori-McKenney, K. M. Gur, M. Nogales, E. Yildiz, A. 2025-11-17 doi:10.1101/2025.11.17.688911 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Parallel and non-parallel features of adaptive radiation in Yucatan pupfishes ]]> https://biorxiv.org/content/10.1101/2025.11.17.688971v1?rss=1 Kustra, M. C. Tian, D. Palominos, M. F. Guo, F. Chau, D. Golwala, O. Chan, H. Alvarez Zapata, A. Cetz Paredes, R. G. Cortes Sanchez, F. X. Hernandez, S. G. Mar-Silva, A. F. Mex, F. Tralka, C. Badillo-Aleman, M. Schmitter-Soto, J. J. Gracida-Juarez, C. A. Martinez, C. M. Arroyave, J. Martin, C. H. 2025-11-18 doi:10.1101/2025.11.17.688971 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ Binary vector origin predictably determines Agrobacterium-mediated transformation outcome across eukaryotic kingdom ]]> https://biorxiv.org/content/10.1101/2025.11.18.688525v1?rss=1 Szarzanowicz, M. Busche, M. Dai, Z. Lapp, N. Geiselman, G. Jia, J. Waldburger, L. Liang, Y. Yuan, G. Duong, R. Hillson, N. Brunkard, J. O. Simmons, B. A. Gladden, J. Kim, J. Thompson, M. Shih, P. 2025-11-18 doi:10.1101/2025.11.18.688525 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ Dengue Virus NS1 Binds Ephrin B1 to Trigger Endothelial Dysfunction ]]> https://biorxiv.org/content/10.1101/2025.11.19.689067v1?rss=1 Pahmeier, F. Hammond, S. R. Flory, C. Feng, X. Lee, S. E. Jimenez-Posada, E. V. Duarte, E. M. Cardona-Ospina, J. A. Ball, A. H. Lee, N. E. Leung, K. Tjang, L. V. Beatty, P. R. Biering, S. B. Scaturro, P. Harris, E. 2025-11-19 doi:10.1101/2025.11.19.689067 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ RNA switch model for localization and translation of the myelin basic protein mRNA ]]> https://biorxiv.org/content/10.1101/2025.11.19.689361v1?rss=1 Topkar, V. V. Wu, V. Ho, L. T. Ambiel, N. Valenzuela, A. Yoshimura, K. Zuchero, J. B. Fu, M.-m. Das, R. 2025-11-20 doi:10.1101/2025.11.19.689361 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ Force-responsive symmetric cell divisions orient stomata along global tissue axes ]]> https://biorxiv.org/content/10.1101/2025.11.19.689402v1?rss=1 Hartman, K. S. Lopez, B. Y. Gonzalez, J. H. Goetz, M. E. Cleveland, A. Muroyama, A. 2025-11-20 doi:10.1101/2025.11.19.689402 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ Diverse infection models demonstrate robust resistance of Mycobacterium tuberculosis to innate immunity ]]> https://biorxiv.org/content/10.1101/2025.11.20.687493v1?rss=1 100,000 CFU) of Lp from the lung within a few days. However, pre-infection with Lp only modestly reduced Mtb CFU compared to mice infected with only Mtb, indicating that Mtb can robustly replicate even in the presence of a strong innate inflammatory response. We performed single-cell RNA-sequencing on myeloid cells from mice either infected with Mtb alone or mice primed with Lp. We found that Lp priming before Mtb infection induced measurable changes in myeloid cells responding to Mtb, but these changes had little effect on innate control of Mtb. Together, these data demonstrate the robust resistance of Mtb to innate immune clearance under diverse experimental conditions. ]]> Fairgrieve, M. R. Brydon, E. C. Chavez, R. A. Kotov, D. I. Vance, R. 2025-11-20 doi:10.1101/2025.11.20.687493 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ A Modular Toolkit For Theophylline-Dependent Synthetic Auxotrophs Via Riboswitch-Gated Essential Genes ]]> https://biorxiv.org/content/10.1101/2025.11.20.689564v1?rss=1 Gonzalez-Lopez, C. Overly, A. Singh, S. Huang, C. Lopez, G. 2025-11-21 doi:10.1101/2025.11.20.689564 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Tom70-mediated mitochondria-nuclear envelope contacts regulate nuclear pore complex inheritance during gametogenesis ]]> https://biorxiv.org/content/10.1101/2025.11.20.689567v1?rss=1 Ruediger, C. T. Styler, B. S. Sawyer, E. S. Spiri, S. King, G. A. Walsh, M. E. Brar, G. A. Jorgens, D. M. Ünal, E. 2025-11-21 doi:10.1101/2025.11.20.689567 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Exome Sequencing and Allele Dosage Analysis of Coast Redwood, a Hexaploid Conifer, Identifies a Major Population Break South of San Francisco Bay ]]> https://biorxiv.org/content/10.1101/2025.11.20.689601v1?rss=1 Nikolaeva, A. S. Santangelo, J. Smith, L. Dodd, R. Nielsen, R. 2025-11-21 doi:10.1101/2025.11.20.689601 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Increased mannosylation of extracellular vesicles in Long COVID plasma provides a potential therapeutic target for Galanthus nivalis agglutinin (GNA) affinity resin ]]> https://biorxiv.org/content/10.1101/2025.11.21.689519v1?rss=1 Pesqueira Sanchez, M. A. de Necochea Campion, R. Dalhuisen, T. Fehrman, E. A. Chhabra, P. S. Kelly, J. D. Martin, J. N. Deeks, S. G. Henrich, T. J. Peluso, M. J. LaRosa, S. P. 2025-11-21 doi:10.1101/2025.11.21.689519 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ SPRINT-MS: A high-throughput platform for identifying protein-protein interactions using pooled IP-MS and sparse signal recovery. ]]> https://biorxiv.org/content/10.1101/2025.11.21.689547v1?rss=1 Street, L. A. Majumdar, M. Rothamel, K. L. Gogus, E. Brar, G. A. Yeo, G. W. Rube, T. Jovanovic, M. 2025-11-21 doi:10.1101/2025.11.21.689547 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Observations of anisotropic paramagnetic and diamagnetic susceptibility in the primate brain ]]> https://biorxiv.org/content/10.1101/2025.11.21.689628v1?rss=1 Chen, J. Gkotsoulias, D. G. Jaffe, J. E. Grassle, T. Jaeger, C. Gone Bi, Z. B. Crockford, C. Wittig, R. Moeller, H. E. Liu, C. 2025-11-22 doi:10.1101/2025.11.21.689628 Cold Spring Harbor Laboratory Press 2025-11-22 <![CDATA[ NK2R signaling governs intestinal lipid mobilization and mucosal inflammation ]]> https://biorxiv.org/content/10.1101/2025.11.21.689675v1?rss=1 Perez, P. Liu, C.-C. Ferrari, A. Littlejohn, N. K. Kennelly, J. P. Robinson, E. Nguyen-Tran, V. T. B. Athanacio, J. Joesph, S. B. Amso, Z. Tontonoz, P. Srinivasan, S. 2025-11-23 doi:10.1101/2025.11.21.689675 Cold Spring Harbor Laboratory Press 2025-11-23 <![CDATA[ Machine Learning Analysis of the Human Initiator Reveals New Insights into the Interrelationships between the TATA box, Initiator, and DPR ]]> https://biorxiv.org/content/10.1101/2025.11.21.689830v1?rss=1 Rhyne-Carrigg, T. E. Vo ngoc, L. Medrano, C. Gillespie, K. E. Kadonaga, J. T. 2025-11-24 doi:10.1101/2025.11.21.689830 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Determining gene specificity from multivariate single-cell RNA sequencing data ]]> https://biorxiv.org/content/10.1101/2025.11.21.689845v1?rss=1 Swarna, N. P. Booeshaghi, A. S. Rebboah, E. Gordon, M. G. Kathail, P. Li, T. Alvarez, M. Ye, C. J. Wold, B. J. Mortazavi, A. Pachter, L. 2025-11-24 doi:10.1101/2025.11.21.689845 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Histones and nucleoid-associated proteins in Methanosarcina acetivorans mediate recovery from stress and stasis ]]> https://biorxiv.org/content/10.1101/2025.11.24.690127v1?rss=1 Nayak, D. D. Baskevitch, A. 2025-11-24 doi:10.1101/2025.11.24.690127 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ AlphaFlex: Ensembles of the human proteome representing disordered regions ]]> https://biorxiv.org/content/10.1101/2025.11.24.690279v1?rss=1 Liu, Z. H. Zhang, O. De Castro, S. Sun, K. Ghafouri, H. Attafi, O. A. Fawzi, N. L. Tosatto, S. C. E. Monzon, A. M. Moses, A. M. Head-Gordon, T. Forman-Kay, J. D. 2025-11-25 doi:10.1101/2025.11.24.690279 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Distributed activity in the human posterior putamen distinguishes goal-directed from habitual control in humans ]]> https://biorxiv.org/content/10.1101/2025.11.26.690863v1?rss=1 Johri, A. Kluen, L. M. Gera, R. Man, V. Perez, O. D. Simon, J. P. Ding, W. Fransen, A. Cho, S. Oh, S. Cockburn, J. Feusner, J. Tadayon-Nejad, R. O'Doherty, J. 2025-11-28 doi:10.1101/2025.11.26.690863 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Efficient in vivo mammalian neuron editing using peptide-mediated CRISPR enzyme delivery ]]> https://biorxiv.org/content/10.1101/2025.11.26.690638v1?rss=1 Manohar, B. D. Travis, M. Munjal, V. Baehr, C. M. Rahnama, L. M. A. Hyung Kang, M. Haddad, R. F. Asija, K. Noel, E. A. Peddireddy, N. Chouhan, R. S. Sharma, R. Wyman, S. K. Krishnappa, N. Killebrew, D. A. Hua Li, S. Snow, K. J. Byrne, A. K. Boosani, C. S. Otero, P. A. Bringas, J. R. O'Brien, A. A. Rocco, M. T. Zimmerly, M. P. Gray, I. Sran, G. K. Patel, M. I. Seidensticker, E. F. Saville, E. Gaitan, Y. Schmelzle, A. L. Subramanyam, P. N. B. Samaranch, L. Green, J. A. Wells, K. D. Ehrenberg, A. J. Murray, S. A. Clelland, C. D. Murthy, N. Lonser, R. R. Had 2025-11-29 doi:10.1101/2025.11.26.690638 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Uncovering senescent fibroblast heterogeneity connects DNA damage response to idiopathic pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/2025.11.26.690792v1?rss=1 Hughes, J.-W. B. Pujari, A. Sandholm, A. Croll, D. Monk, L. B. Joshua, I. Butterfield, R. Horton, C. Schneider, K. Senchyna, F. Brown, I. Coelho, A. L. Ho, T.-C. Deguchi, H. Le Saux, C. J. Deinhardt-Emmer, S. Ellerby, L. M. Vitari, A. Furman, D. Hogoboam, C. M. Laslavic, A. Desprez, P.-Y. Quarta, M. Campisi, J. 2025-11-30 doi:10.1101/2025.11.26.690792 Cold Spring Harbor Laboratory Press 2025-11-30 <![CDATA[ Bioenergetic responses to β-adrenergic stimulation in beige adipocyte depend on actomyosin driven forces ]]> https://biorxiv.org/content/10.1101/2025.11.26.690550v1?rss=1 He, Y. Ling, L. Dempsey, G. Kalindjian, N. Verghese, Z. A. Chen, E. Liparulo, I. Cho, I. Tran, V. Kumar, S. Stahl, A. 2025-12-01 doi:10.1101/2025.11.26.690550 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Interpretable Thermodynamic Score-based Classification of Relaxation Excursions ]]> https://biorxiv.org/content/10.1101/2025.11.26.690838v1?rss=1 Kuznets-Speck, B. Jung, J. Pholraksa, P. Zhong, A. Schwartz, L. Prashnani, E. Vaikuntanathan, S. Goyal, Y. 2025-12-01 doi:10.1101/2025.11.26.690838 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Induced ubiquitination bypasses canonical ERAD to drive ER protein degradation ]]> https://biorxiv.org/content/10.1101/2025.11.28.691080v1?rss=1 Tomlinson, S. J. Johnson, S. L. Kroskrity, A. H. Hu, Y. Deol, K. K. Zhang, C. Y. Harris, C. A. Nomura, D. K. Olzmann, J. A. 2025-12-01 doi:10.1101/2025.11.28.691080 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ A model of transcriptional bursting dynamics based on coupling between chromatin and enhancer states ]]> https://biorxiv.org/content/10.1101/2025.11.29.691276v1?rss=1 Axelrod, O. Binshtok, U. Gebelein, B. Garcia, H. Sprinzak, D. 2025-12-01 doi:10.1101/2025.11.29.691276 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Semi-supervised Retrieval of Functional Residues Through the Integration of Protein Language Models and Gene Ontology Data ]]> https://biorxiv.org/content/10.64898/2025.11.28.691208v1?rss=1 Dickson, A. M. Mouline, S. Tamadon, A. Mofrad, M. 2025-12-02 doi:10.64898/2025.11.28.691208 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Disentangling Superpositions: Interpretable Brain Encoding Model with Sparse Concept Atoms ]]> https://biorxiv.org/content/10.64898/2025.11.29.691321v1?rss=1 Zeng, A. Gallant, J. 2025-12-02 doi:10.64898/2025.11.29.691321 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Advancing High-Resolution 7T Diffusion MRI: Evaluating Phase-Encoding Correction Strategies for Distortion Correction from Basic to Four-Way Acquisitions ]]> https://biorxiv.org/content/10.64898/2025.12.01.687254v1?rss=1 Schilling, K. G. Beckett, A. J. S. Amandola, M. Walker, E. B. Feinberg, D. A. Bunge, S. A. Vu, A. T. 2025-12-03 doi:10.64898/2025.12.01.687254 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ A foundation model for microbial growth dynamics ]]> https://biorxiv.org/content/10.64898/2025.12.01.691707v1?rss=1 Holmes, Z. A. Shyti, I. Hoffman, A. L. Duncker, K. E. Ma, H. R. Zhou, Z. Lee, D. Maddamsetti, R. Kim, K. Simsek, E. Hamrick, G. S. Son, H. Villalobos, C. A. Lu, J. Ha, Y. Shende, A. R. Yao, Z. Liu, S. Shapiro, D. M. Kholina, K. Davis, H. Baig, Y. Wu, F. Wang, S. Wang, X. Chatterjee, P. Lynch, M. D. Lopatkin, A. J. David, L. A. Chory, E. You, L. 2025-12-03 doi:10.64898/2025.12.01.691707 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Reciprocal interactions between EMT and BMP signalling drive collective cell invasion. ]]> https://biorxiv.org/content/10.64898/2025.12.02.691808v1?rss=1 View larger version (64K): org.highwire.dtl.DTLVardef@1ae1e78org.highwire.dtl.DTLVardef@526260org.highwire.dtl.DTLVardef@b892f1org.highwire.dtl.DTLVardef@1b74815_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Takahashi, Y. Neaverson, A. Busby, L. Twarowski, F. Camacho de la Macorra, C. Serrano Najera, G. Steventon, B. 2025-12-04 doi:10.64898/2025.12.02.691808 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ High-throughput screening reveals mechanisms of environmental control of germination in a fungal thermophile ]]> https://biorxiv.org/content/10.64898/2025.12.04.692316v1?rss=1 Ogunyewo, O. Fleming, K. Morris, M. Fort, K. Huberman, L. B. Brem, R. B. 2025-12-04 doi:10.64898/2025.12.04.692316 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ Androgen receptor contributes to radioresistance through DNA repair and autophagy in AR-positive prostate cancer cells ]]> https://biorxiv.org/content/10.64898/2025.12.03.690226v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@3f713corg.highwire.dtl.DTLVardef@1233a11org.highwire.dtl.DTLVardef@1b94e5eorg.highwire.dtl.DTLVardef@c8338c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kudo, K.-i. Feng, Q. Chosco, M. I. Anzules, J. M. Huang, Z. Achanta, K. Wenning, L. Mohan, J. Rhee, J.-W. Mohebnasab, M. Sadimin, E. Wang, Z. V. Li, Y. R. 2025-12-05 doi:10.64898/2025.12.03.690226 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Structural Basis of Human Kinetochore-Microtubule Coupling by the Ndc80 and Ska Complexes ]]> https://biorxiv.org/content/10.64898/2025.12.06.692780v1?rss=1 Zhou, J. Zhao, Y. Yildiz, A. Nogales, E. 2025-12-07 doi:10.64898/2025.12.06.692780 Cold Spring Harbor Laboratory Press 2025-12-07 <![CDATA[ Visual Semantic Encoding and Identification of Naturalistic Movies via High-Density Diffuse Optical Tomography ]]> https://biorxiv.org/content/10.64898/2025.12.03.692158v1?rss=1 Fehner, W. Fogarty, M. Tang, J. Wilhelm, D. Bajracharya, A. Markow, Z. E. Hines, A. M. Trobaugh, J. W. Huth, A. G. Culver, J. P. 2025-12-08 doi:10.64898/2025.12.03.692158 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ High-efficiency, transgene-free plant genome editing by viral delivery of an engineered TnpB ]]> https://biorxiv.org/content/10.64898/2025.12.05.692691v1?rss=1 Nagalakshmi, U. Rodriguez, J. E. Nguyen, T. Weissman, R. F. Thornton, B. W. Savage, D. F. Dinesh-Kumar, S. P. 2025-12-09 doi:10.64898/2025.12.05.692691 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Stable Inheritance of Transgene and Yellow Fluorescent Protein Gene Expression in Progeny of Transgenic Cacao (Theobroma cacao) Plants ]]> https://biorxiv.org/content/10.64898/2025.12.09.692773v1?rss=1 Austin, G. Jones, J. Stevens, A. Zhang, E. Thompson, T. Gomez, M. Vrla, G. Oh, Y. Marelli, J.-P. Jones, C. Staskawicz, B. Cho, M.-J. 2025-12-09 doi:10.64898/2025.12.09.692773 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ GUANinE v1.1 Reveals Complementarity of Supervised and Genomic Language Models ]]> https://biorxiv.org/content/10.64898/2025.12.06.692772v1?rss=1 robson, e. s. Ioannidis, N. M. 2025-12-10 doi:10.64898/2025.12.06.692772 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Y-linked editors for invasive rodent control ]]> https://biorxiv.org/content/10.64898/2025.12.08.693037v1?rss=1 Verma, P. Akbari, O. S. Marshall, J. M. 2025-12-11 doi:10.64898/2025.12.08.693037 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Proteasome activator Blm10 maintains cellular proteostatic balance and gamete quality in budding yeast ]]> https://biorxiv.org/content/10.64898/2025.12.08.693079v1?rss=1 Reyes, M. C. Ramos-Ortiz, D. R. Cheng, J. A. Spiri, S. Doron-Mandel, E. Kim Kim, J. Ma, Y. Jovanovic, M. Martin, A. Brar, G. A. 2025-12-11 doi:10.64898/2025.12.08.693079 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Comparing Multislice Simulations of MD Simulations with CryoEM Exposes Membrane Prediction Errors ]]> https://biorxiv.org/content/10.64898/2025.12.09.693260v1?rss=1 Mohammed, A. Lincoff, J. Natale, A. Ophus, C. Grabe, M. Frost, A. Moss, F. R. 2025-12-11 doi:10.64898/2025.12.09.693260 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Perturbational single-cell profiling of patient tumors defines lineage- and context-specific programs of innate immune resistance ]]> https://biorxiv.org/content/10.64898/2025.12.09.693245v1?rss=1 Perry, C. J. Frey, A. Fei, Y. Wang, J. Costa, P. Nassar, A. H. Ghadermarzi, S. Levine, D. Tong, W. Wei, J. Koda, A. Mackie, M. He, M. Nie, Y. Clulo, K. Ouerghi, F. Dumit, T. C. Yaskolko, M. Ding, M. Caldera, A. Kyrysyuk, O. Lum, L. Allen, J. W. Guo, W. Naqash, A. R. Elliott, A. Vanderwalde, A. Capelletti, M. Adeyelu, T. Barry, S. T. Hugaboom, M. Bacchiocchi, A. Kluger, H. M. Bosenberg, M. Iwasaki, A. Braun, D. A. Clune, J. van Dijk, D. Olino, K. Ishizuka, J. 2025-12-12 doi:10.64898/2025.12.09.693245 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Machine learning-based prediction of human structural variation and characterization of associated sequence determinants ]]> https://biorxiv.org/content/10.64898/2025.12.09.693295v1?rss=1 90% AUROC) which can be further improved in an ensemble. The predictive ability of these models demonstrates that SV-prone regions can be accurately inferred from sequence context. Model interpretability techniques reveal key genomic contributors to SVs, including effects of sequence motifs such as microhomology and non-canonical DNA structures, as well as the presence of SV hotspots. We find that different classes of SVs exhibit distinct sequence determinants, with transposable elements and inversions displaying particularly unique signatures. Moreover, predicted SV probability correlates with allele frequency and gene functional constraint, indicating the potential utility of the model for variant effect prediction. These findings demonstrate that machine learning models trained on local sequence features can identify unstable genomic regions and provide a framework for quantifying SV susceptibility and SV variant effects in personalized genomics. ]]> Lim, D. Lou, R. N. Ioannidis, N. M. Sudmant, P. H. 2025-12-12 doi:10.64898/2025.12.09.693295 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Discovery of Non-Degradative Covalent Molecular Glues for Transcriptional Reprogramming ]]> https://biorxiv.org/content/10.64898/2025.12.12.694031v1?rss=1 Duong, T. N. Pandji, E. Shao, Q. Nomura, D. K. 2025-12-14 doi:10.64898/2025.12.12.694031 Cold Spring Harbor Laboratory Press 2025-12-14 <![CDATA[ Degraded sensory coding in a mouse model of Scn2a-related disorder and its rescue by CRISPRa gene activation ]]> https://biorxiv.org/content/10.64898/2025.12.13.694145v1?rss=1 Vandemark, K. Monday, H. R. Rodriguez, L. Zhao, M. Lee, M. Ahituv, A. Satapathy, A. Page, N. F. An, K. Hamada, E. C. Ahituv, N. Bender, K. J. Feldman, D. E. 2025-12-14 doi:10.64898/2025.12.13.694145 Cold Spring Harbor Laboratory Press 2025-12-14 <![CDATA[ Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells ]]> https://biorxiv.org/content/10.64898/2025.12.14.692434v1?rss=1 Jung, H. Devant, P. Ching, C. Ota, M. Hamilton, J. Steinhart, Z. Ngo, W. Sandoval, L. Jung, J. H. Xu, D. An, M. Urs, E. Chen, P. A. Allain, V. Tada, T. Nunez, J. K. Landau, N. R. Liu, D. R. Eyquem, J. Doudna, J. A. Marson, A. Carnevale, J. 2025-12-14 doi:10.64898/2025.12.14.692434 Cold Spring Harbor Laboratory Press 2025-12-14 <![CDATA[ Octopamine instructs head direction plasticity ]]> https://biorxiv.org/content/10.64898/2025.12.11.693783v1?rss=1 Plitt, M. H. Turner-Evans, D. B. Co, J. C. Layden, A. Eddison, M. Ray, R. P. Jayaraman, V. Fisher, Y. E. 2025-12-15 doi:10.64898/2025.12.11.693783 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ δ2-Protocadherins organize parallel indirect basal ganglia circuits ]]> https://biorxiv.org/content/10.64898/2025.12.13.694147v1?rss=1 Hoshina, N. Boeckers, J. M. Johnson-Venkatesh, E. M. Hoshina, M. Matsumoto, K. Das, A. Rally, V. R. Sant, J. Inoue, T. Umemori, H. 2025-12-15 doi:10.64898/2025.12.13.694147 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Multiparametric Assessment of TNNI3 Variant Phenotypes in Human iPSC-Cardiomyocytes Correlates with Disease Severity in Patients ]]> https://biorxiv.org/content/10.64898/2025.12.13.691658v1?rss=1 Staudt, D. W. Tran, P. P. Floyd, B. Dunn, K. Han, D. Carhuamaca, X. Serrano, R. Hnatiuk, A. P. Bang, S. Parikh, V. N. Ashley, E. A. Mercola, M. 2025-12-16 doi:10.64898/2025.12.13.691658 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Translational Downregulation of 5' TOP mRNAs During T Cell Exhaustion ]]> https://biorxiv.org/content/10.64898/2025.12.15.694525v1?rss=1 Pledger, E. S. Ambavaram, N. Ferguson, L. Cate, J. H. D. 2025-12-16 doi:10.64898/2025.12.15.694525 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ A map of the cortical functional network mediating naturalistic navigation ]]> https://biorxiv.org/content/10.64898/2025.12.16.694742v1?rss=1 Zhang, T. Meschke, E. X. Gallant, J. 2025-12-17 doi:10.64898/2025.12.16.694742 Cold Spring Harbor Laboratory Press 2025-12-17 <![CDATA[ Self-renewal of neuronal mitochondria through asymmetric division ]]> https://biorxiv.org/content/10.64898/2025.12.17.694973v1?rss=1 Waingankar, T. P. Zurita, C. Lang, A. E. Vuong, C. Shami, A. Bautista, D. M. Drerup, K. Lewis, S. C. 2025-12-18 doi:10.64898/2025.12.17.694973 Cold Spring Harbor Laboratory Press 2025-12-18 <![CDATA[ The Goldilocks effect drives plant diversification on middle-aged Hawaiian islands ]]> https://biorxiv.org/content/10.64898/2025.12.16.694722v1?rss=1 Lichter-Marck, I. Swiston, S. K. Mendes, F. K. May, M. R. Neupane, S. Baldwin, B. G. Wood, K. Ronsted, N. Wagner, W. L. Zapata, F. Landis, M. J. 2025-12-19 doi:10.64898/2025.12.16.694722 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ Identification of novel ubiquitin receptors on the 26S proteasome by photo-crosslinking mass spectrometry ]]> https://biorxiv.org/content/10.64898/2025.12.19.695558v1?rss=1 Martin, A. MacRae, N. S. Dong, K. C. Harimoto, H. 2025-12-20 doi:10.64898/2025.12.19.695558 Cold Spring Harbor Laboratory Press 2025-12-20 <![CDATA[ Excitatory nicotinic signaling drives action potential bursting in dopaminergic axons ]]> https://biorxiv.org/content/10.64898/2025.12.19.695584v1?rss=1 Kramer, P. F. Yanez, A. Clever, F. Zhang, R. Khaliq, Z. M. 2025-12-21 doi:10.64898/2025.12.19.695584 Cold Spring Harbor Laboratory Press 2025-12-21 <![CDATA[ OCTRON - a general purpose segmentation and tracking pipeline for behavioral experiments ]]> https://biorxiv.org/content/10.64898/2025.12.20.695663v1?rss=1 Jacobsen, R. I. van Eekelen, N. M. Humphrey, L. Renton, J. van Rooij, E. Rivera, J. Arenas, O. M. Lumpkin, E. A. Maccuro, S. Buresch, K. C. Seuntjens, E. Obenhaus, H. A. 2025-12-23 doi:10.64898/2025.12.20.695663 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado ]]> https://biorxiv.org/content/10.64898/2025.12.22.695989v1?rss=1 Groh, J. S. dos Santos, M. F. S. de Dios, E. A. Ackerman, G. Solares, E. Focht, E. Seymour, D. Gaut, B. S. Arpaia, M. L. Coop, G. 2025-12-24 doi:10.64898/2025.12.22.695989 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ Concreteness shapes semantic representations in bilingual brains ]]> https://biorxiv.org/content/10.64898/2025.12.23.696243v1?rss=1 Lamarre, M. Gong, X. L. Chen, C. Deniz, F. 2025-12-24 doi:10.64898/2025.12.23.696243 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ Recruitment of Fpt1 to tRNA genes requires TFIIIB and the N-terminal TPR array of TFIIIC subunit {tau}131 ]]> https://biorxiv.org/content/10.64898/2025.12.24.695929v1?rss=1 van Breugel, M. E. Seifert-Davila, W. Bakker, M. J. Meeussen, J. V. W. Hoogvliet, I. A. Novell Cardona, M. van Welsem, T. Ammerlaan, D. Baudin, F. Celie, P. Lenstra, T. L. Mueller, C. W. van Leeuwen, F. 2025-12-26 doi:10.64898/2025.12.24.695929 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Homology of the dark cells of Paleozoic liverworts with the specialized oil body cells of modern liverworts (Marchantiophyta) ]]> https://biorxiv.org/content/10.64898/2025.12.24.696392v1?rss=1 Tremblay, S. Mercadal, J. 2025-12-26 doi:10.64898/2025.12.24.696392 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Evidence for an ancient master sex determination gene in Hymenoptera ]]> https://biorxiv.org/content/10.64898/2025.12.24.696408v1?rss=1 Velasquez, S. M. Walker, I. J. McClure, T. A. Pineda, L. I. S. Gerard, M. Russell, V. V. Camaya, P. A. Campbell, G. D. J. Fernandes, N. V. Flowers, A. Raymond, A. N. Rico, S. S. Taylor, A. Velazquez, R. C. Kramer, A. Condon, C. J. Corbett-Detig, R. Brelsford, A. Anderson, N. Roy, S. W. 2025-12-26 doi:10.64898/2025.12.24.696408 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Neuropathologically validated MRI to tau PET synthesis via Covariate-modulated attention networks ]]> https://biorxiv.org/content/10.64898/2025.12.27.696668v1?rss=1 Borhi, M. Lyu, R. Q. Jagust, W. J. Wang, J. Giorgio, J. 2025-12-27 doi:10.64898/2025.12.27.696668 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ Type 2 diabetes Reprograms Bone Marrow Hematopoiesis and Dysregulates Immune Signaling in Response to Stroke ]]> https://biorxiv.org/content/10.64898/2025.12.29.696958v1?rss=1 Zhang, H. Gu, W. Yu, K. Tu, C.-L. Chang, W. Liu, J. 2025-12-30 doi:10.64898/2025.12.29.696958 Cold Spring Harbor Laboratory Press 2025-12-30 <![CDATA[ Differential retinoic acid responses across testicular development in vitro ]]> https://biorxiv.org/content/10.64898/2025.12.30.696417v1?rss=1 Hansen, B. C. Hatem, S. A. Huang, L. Amory, J. K. Faustman, E. M. Kelly, E. J. 2025-12-31 doi:10.64898/2025.12.30.696417 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Adeno-associated viruses (AAVs) induce dose-dependent neonatal ventriculomegaly following intracerebroventricular administration ]]> https://biorxiv.org/content/10.64898/2025.12.30.697113v1?rss=1 Liu, L. L. Noguera, A. Humphries, R. Zhou, B. Fame, R. M. 2025-12-31 doi:10.64898/2025.12.30.697113 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Quenching corrinoid-based interactions in a model bacterial coculture. ]]> https://biorxiv.org/content/10.64898/2025.12.31.697204v1?rss=1 Hallberg, Z. F. Alvarez-Aponte, Z. I. Gaudinier, A. Taga, M. E. 2026-01-01 doi:10.64898/2025.12.31.697204 Cold Spring Harbor Laboratory Press 2026-01-01 <![CDATA[ When exploration replaces storage: how eye movements shape visual working memory ]]> https://biorxiv.org/content/10.64898/2026.01.04.697560v1?rss=1 Qais, R. Knight, R. Yuval-Greenberg, S. 2026-01-04 doi:10.64898/2026.01.04.697560 Cold Spring Harbor Laboratory Press 2026-01-04 <![CDATA[ Convergence of Cortical and Thalamic Origins of Free Behavior Modulation of Mouse Primary Visual Cortex ]]> https://biorxiv.org/content/10.64898/2026.01.07.698022v1?rss=1 Yu, P. Yoon, H. Y. A. Yang, Y. Xu, Y. Gozel, O. Tian, G. J. Ji, N. Doiron, B. 2026-01-08 doi:10.64898/2026.01.07.698022 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Architecting cis-regulation to quantitatively tune gene expression in cereals ]]> https://biorxiv.org/content/10.64898/2026.01.08.698005v1?rss=1 30,000 CRISPR-like mutations-deletions, substitutions, and motif insertions-across entire native promoters and 5' untranslated regions (UTRs) of three photosynthesis genes: PsbS, Raf1, and SBPase. We find that gene expression is most tunable within a [~]500 base pair core promoter region, where mutational effects are reproducible across biological replicates and predictive of protein output. Within these regions, we identify compact deletions and motif insertions that strongly increase protein production (>30-fold relative to wild type), exceeding the performance of transgenic enhancer elements. Mutation-effect relationships are gene-specific, highlighting the need for tailored regulatory maps. Our results establish a high-throughput strategy for cis-regulatory fine-mapping that enables crop improvements via minimal, precise, and non-transgenic gene edits. ]]> Groover, E. D. Ding, D. Wang, F. Z. Benegas, G. Rivera, J. Schwartz, S. Chen, S. Moubarak, M. F. Georgieva, V. Lemaux, P. G. Staskawicz, B. Niyogi, K. K. Song, Y. S. Savage, D. 2026-01-08 doi:10.64898/2026.01.08.698005 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Statistical Atlas-Based Surrogate Model of Biventricular Wall Mechanics ]]> https://biorxiv.org/content/10.64898/2026.01.07.697811v1?rss=1 97%, demonstrating good fidelity to the simulated ground truth. This approach may enable accurate prediction of ventricular wall mechanics without computationally expensive finite element analysis, offering a more feasible method for rapid, subject-specific cardiac modeling. ]]> Robles, A. Konanur, R. Qi, A. Finsberg, H. Sundnes, J. McCulloch, A. D. 2026-01-09 doi:10.64898/2026.01.07.697811 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ Stepwise DNA unwinding gates TnpB genome-editing activity ]]> https://biorxiv.org/content/10.64898/2026.01.09.698545v1?rss=1 Zhou, Z. Saffarian-Deemyad, I. Shi, H. Weiss, T. ur-Rehman, M. M. Vohra, K. Skopintsev, P. Yoon, P. H. Trinidad, M. I. Langeberg, C. J. Kamalu, M. Amerasekera, J. Doherty, E. E. Aris, K. D. P. Al-Sayyad, N. Thornton, B. W. Weissman, R. F. Wasko, K. M. Esain-Garcia, I. DeTurk, E. C. Savage, D. F. Jacobsen, S. E. Bryant, Z. Doudna, J. A. 2026-01-09 doi:10.64898/2026.01.09.698545 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ Overcoming steric inhibition of antibody-dependent phagocytosiswith tall adhesions ]]> https://biorxiv.org/content/10.64898/2026.01.09.698749v1?rss=1 Joffe, A. M. Chorlay, A. Huzar, J. Hasnain, J. Geissler, P. L. Fletcher, D. A. 2026-01-10 doi:10.64898/2026.01.09.698749 Cold Spring Harbor Laboratory Press 2026-01-10 <![CDATA[ Molecular signatures and cellular responses underlying hypoxic adaptation in sea turtles ]]> https://biorxiv.org/content/10.64898/2026.01.09.698755v1?rss=1 Arango, B. G. Selleghin-Veiga, G. Moreno-Santillan, D. D. Ensminger, D. C. Vazquez, J. M. Tarvin, R. Nery, M. Godard-Codding, C. Vazquez-Medina, J. P. 2026-01-10 doi:10.64898/2026.01.09.698755 Cold Spring Harbor Laboratory Press 2026-01-10 <![CDATA[ A robust human airway organoid platform enables scalable expansion and trajectory mapping of pulmonary neuroendocrine cells ]]> https://biorxiv.org/content/10.64898/2026.01.10.698835v1?rss=1 Candeli, N. den Hartigh, L. Hou, N. Marco, A. Sanchez-Villacana, J. A. Garcia-Gonzales, A. Gandhi, S. L. Sgualdino, F. Miller, A. J. Spence, J. de Sousa Lopes, S. C. McFaline-Figueroa, J. L. Clevers, H. Dayton, T. L. 2026-01-12 doi:10.64898/2026.01.10.698835 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ Lactate-Driven Heterogeneity of Immune Checkpoint Expression in Breast and Lung Cancer Cell Lines ]]> https://biorxiv.org/content/10.64898/2026.01.11.698903v1?rss=1 San-Millan, I. Martinez, J. Pickard, S. L. Hirsch, F. R. Rivard, C. J. Brooks, G. A. 2026-01-12 doi:10.64898/2026.01.11.698903 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ Estimate of the mutation rate in the endangered Devils Hole pupfish provides support for the drift-barrier hypothesis at an outlying extreme ]]> https://biorxiv.org/content/10.64898/2026.01.11.698928v1?rss=1 Tian, D. Kerdoncuff, E. Wilson, K. Feuerbacher, O. Schwemm, M. R. Gumm, J. Moorjani, P. Martin, C. H. 2026-01-12 doi:10.64898/2026.01.11.698928 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ Designing AI-programmable therapeutics with the EDEN family of foundation models ]]> https://biorxiv.org/content/10.64898/2026.01.12.699009v1?rss=1 View larger version (59K): org.highwire.dtl.DTLVardef@1e23e28org.highwire.dtl.DTLVardef@5ef3a2org.highwire.dtl.DTLVardef@1cd32b8org.highwire.dtl.DTLVardef@bd0345_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Munsamy, G. Ayres, G. Greco, C. Kam, K. Minto-Cowcher, G. St John, J. Bohnuud, T. Bakalar, M. Chow, W. Pecoraro, R. D.T. Torres, M. Kollasch, A. Leung, M. Sirelkhatim, H. Farina, F. McGinnis, C. Sridhar, S. Anderson, D. Oteri, F. Takhibakhshi, A. Dona, J. Shimko, T. Steenbeke, C. Papadopoulos, A. Krolick, M. Spoendlin, F. Gupta, P. Kumar, S. Bara, A. Wilber, J. Ferruz, N. Rvachoc, T. Wang, F. Cao, H. Lee, H.-S. Mehta, J. Chaleil, R. Pereno, V. Potti, S. Emerson, C. Dew, R. T. Yang, K. K. Nguyen, E. Tadimeti, N. Banfield, J. Frame, A. Bolton, E. Ru 2026-01-12 doi:10.64898/2026.01.12.699009 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ An engineered nanobody inhibitor for molecular-to-circuit control of opioid receptor function ]]> https://biorxiv.org/content/10.64898/2026.01.12.698943v1?rss=1 Valbret, Z. Lamothe-Molina, P. L. Papadogkonaki, S. Koehl, A. Arafiles, J. V. V. Shapiro Tuchman, Z. Fisher, N. M. Radoux-Mergault, A. Canziani, A. Huang, G. Von Zastrow, M. Kosloff, M. Hackenberger, C. P. Manglik, A. Patriarchi, T. Stoeber, M. 2026-01-14 doi:10.64898/2026.01.12.698943 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Adapting a two-photon scanning microscope for simultaneous single-photon imaging of an infrared dopamine sensor ]]> https://biorxiv.org/content/10.64898/2026.01.13.699388v1?rss=1 Tarchick, M. Caval-Holme, F. Smith, B. Mocellin, P. Landry, M. P. Komatsu, N. Feller, M. 2026-01-14 doi:10.64898/2026.01.13.699388 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Client distribution between Chlamydomonas FDX1 and FDX2 in carbon, nitrogen and sulfur assimilation ]]> https://biorxiv.org/content/10.64898/2026.01.14.699543v1?rss=1 Schmollinger, S. Kusi-Appiah, G. Villegas, D. Stainbrook, S. O'Halloran, T. V. Strenkert, D. 2026-01-15 doi:10.64898/2026.01.14.699543 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ Urban soils along the Kern River and Los Gatos Creek are hotspots for Coccidioides in the San Joaquin Valley of California ]]> https://biorxiv.org/content/10.64898/2026.01.15.698504v1?rss=1 Wagner, R. Radosevich, M. T. Montoya, L. Remais, J. V. Taylor, J. 2026-01-16 doi:10.64898/2026.01.15.698504 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ Mitigating Bias in Spatial Transcriptomic Pipelines via Human Feedback ]]> https://biorxiv.org/content/10.64898/2026.01.15.699786v1?rss=1 Boyeau, P. Bates, S. Ergen, C. Jordan, M. I. Yosef, N. 2026-01-16 doi:10.64898/2026.01.15.699786 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ A family of archaeal hibernation factors that bind in tandem and protect ribosomes in dormant cells ]]> https://biorxiv.org/content/10.64898/2026.01.19.700200v1?rss=1 Nissley, A. J. Williams, M. C. Shulgina, Y. Kivimae, R. W. Nayak, D. D. Cate, J. H. D. 2026-01-19 doi:10.64898/2026.01.19.700200 Cold Spring Harbor Laboratory Press 2026-01-19 <![CDATA[ Evaluating the reliability of functional near-infrared spectroscopy data in the context of a reasoning paradigm ]]> https://biorxiv.org/content/10.64898/2026.01.16.699971v1?rss=1 Kelly, P. G. Bortfeld, H. Joyner, K. Bunge, S. 2026-01-20 doi:10.64898/2026.01.16.699971 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Memory erasure by dopamine-gated retrospective learning ]]> https://biorxiv.org/content/10.64898/2026.01.17.700100v1?rss=1 Jeong, H. Zsembik, L. Farouq, F. Chakraborty, R. Belur, N. Zhou, M. Sanders, A. D. Wang, S. X. Srinivasan, A. Cox, S. M. L. Garr, E. Brooke, S. Janak, P. H. Leyton, M. Chen, R. Namboodiri, V. M. K. 2026-01-21 doi:10.64898/2026.01.17.700100 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Sequence models conditioned on splicing factor expression predict splicing in unseen tissues ]]> https://biorxiv.org/content/10.64898/2026.01.20.700496v1?rss=1 Reddy, A. J. Sudmant, P. H. Ioannidis, N. M. 2026-01-21 doi:10.64898/2026.01.20.700496 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Hierarchical Reconfiguration of Neurocognitive Task Set Representations Mediates Cognitive Flexibility ]]> https://biorxiv.org/content/10.64898/2026.01.20.700694v1?rss=1 Leach, S. C. Chen, X. Hwang, K. 2026-01-21 doi:10.64898/2026.01.20.700694 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Comparative genomics of Tandem Repeat variation in apes ]]> https://biorxiv.org/content/10.64898/2026.01.20.700717v1?rss=1 de Lima Adam, C. Rocha, J. L. Sudmant, P. H. Rohlfs, R. 2026-01-21 doi:10.64898/2026.01.20.700717 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Linking genomic and phenotypic traits to interaction outcomes in a synthetic phyllosphere community ]]> https://biorxiv.org/content/10.64898/2026.01.16.699983v1?rss=1 Batarseh, T. N. Collado, J. O. Mehlferber, E. C. Alvarez-Navarrete, R. M. Wagner, F. J. Koskella, B. N. 2026-01-22 doi:10.64898/2026.01.16.699983 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Strong sustained type I IFN signaling acts cell intrinsically to impair IFNγ responses and cause tuberculosis susceptibility ]]> https://biorxiv.org/content/10.64898/2026.01.19.700487v1?rss=1 Fattinger, S. A. Chavez, R. A. Witt, K. C. Parisi, B. Rodriguez, J. J. Turcotte, E. A. Brydon, E. C. Fairgrieve, M. R. Dhaliwal, H. Lee, A. Y. Kotov, D. I. Vance, R. E. 2026-01-22 doi:10.64898/2026.01.19.700487 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Histone 3 lysine 9 dimethylation by the G9a-GLP heterodimer requires intranucleosomal product reading ]]> https://biorxiv.org/content/10.64898/2026.01.21.700667v1?rss=1 Yousefi, F. Simental, E. A. Du, Y. Whedon, S. D. Trnka, M. J. Darling, D. Jia, S. Panning, B. Cole, P. A. Halic, M. Al-Sady, B. 2026-01-22 doi:10.64898/2026.01.21.700667 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Jumbo circular extrachromosomal elements of methane-oxidizing archaea with variably extensive metabolic and defense gene repertoires ]]> https://biorxiv.org/content/10.64898/2026.01.21.700959v1?rss=1 200 kbp ("jumbo") genomes. Here, we report circular, jumbo ECEs with genomes of up to 535 kbp in length that associate with anaerobic methane-oxidizing Methanoperedens archaea. Notably, a 409-kbp genome related to jumbo ECEs is integrated into a subset of the [~]4.2 Mbp Methanoperedens chromosomes at the tRNA-Asp genes. This represents the largest integrative element in Archaea and supports the jumbo ECE - host association. Multiple genome alignment and phylogenetic analyses suggest that the large sizes were developed by extensive DNA acquisition from Methanoperedens. The newly identified ECEs encode, and in some cases express, metabolic genes such as tetrahydromethanopterin S-methyltransferase exclusively involved in methane oxidation, and genes for nitrogen and sulfur compound transformations. Also encoded are defense systems, some of which are absent in hosts, such as hybrid Type I/Type III-A CRISPR-Cas systems. In contrast to viruses and plasmids, they have host-like replication machinery and occur at stable copy ratios of 1.44 {+/-} 0.24 : 1 to the host. Overall, our results reveal a spectrum of jumbo ECEs of Methanoperedens, ranging from plasmid-like to minichromosome-like. ]]> Shi, L.-D. Kolody, B. C. Wang, S. Valentin-Alvarado, L. E. Lei, S. Sachdeva, R. Banfield, J. F. 2026-01-22 doi:10.64898/2026.01.21.700959 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Federated single-cell QTL meta-analysis reveals novel disease mechanisms ]]> https://biorxiv.org/content/10.64898/2026.01.20.700519v1?rss=1 Kaptijn, D. Michielsen, L. Neavin, D. Ripoll-Cladellas, A. Alquicira-Hernandez, J. E. Korshevniuk, M. Lee, J. T. H. Oelen, R. Vochteloo, M. Warmerdam, R. Ando, Y. Ban, M. Bayaraa, O. Berg, M. van Blokland, I. Considine, D. Dieng, M. M. Edahiro, R. Gordon, M. G. Groot, H. E. van der Harst, P. Heinig, M. Hon, C.-C. Idaghdour, Y. Kathail, P. de Klein, N. Li, W. Li, Y. Losert, C. Manikanda, V. Moody, J. Naeem, H. Mokrab, Y. Nawijn, M. C. Netea, M. Niewold, J. Okada, Y. Sawcer, S. Soulama, I. Stegle, O. Tsepilov, Y. Park, W.-Y. Rajagopalan, D. Shahin, T. 2026-01-23 doi:10.64898/2026.01.20.700519 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Efficient transgene-free multiplexed genome editing via viral delivery of an engineered TnpB. ]]> https://biorxiv.org/content/10.64898/2026.01.23.700382v1?rss=1 Weiss, T. Kamalu, M. Shi, H. Wirnowski, G. Ingelsson, A. Amerasekera, J. Vohra, K. Trinidad, M. I. Li, Z. Freitas, E. Steinmetz, N. Ambrose, C. Chen, K. Doudna, J. A. Jacobsen, S. E. 2026-01-23 doi:10.64898/2026.01.23.700382 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Supported membrane assay probes PLCγ1 activity in LAT condensates ]]> https://biorxiv.org/content/10.64898/2026.01.23.701188v1?rss=1 DeGrandchamp, J. B. Rajesh, S. V. Lew, L. J. N. Groves, J. T. 2026-01-25 doi:10.64898/2026.01.23.701188 Cold Spring Harbor Laboratory Press 2026-01-25 <![CDATA[ The evolution of genetic drift over 50,000 generations ]]> https://biorxiv.org/content/10.64898/2026.01.25.701616v1?rss=1 Ascensao, J. A. Yu, Q. Hallatschek, O. 2026-01-27 doi:10.64898/2026.01.25.701616 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Coupling high-throughput protease enzymology with viral replication reveals biochemical constraints of viral fitness ]]> https://biorxiv.org/content/10.64898/2026.01.27.702130v1?rss=1 400 variants. Integration with viral replication and in-cell cleavage assays reveals that variants with altered substrate specificity fail to support replication, suggesting imbalanced polyprotein processing as a constraint on viral fitness. More broadly, these data can enable mechanistically grounded modeling of protease sequence-property relationships and inform strategies for pharmacological modulation beyond active-site inhibition. ]]> Aidlen, D. Vo, W. V. T. Young, N. J. Rosecrans, J. Kurianowicz, A. Chuo, S.-W. Asper, G. P. R. Anderson, D. Posner, J. A. Muir, D. F. Freitas, N. Ott, M. Craik, C. S. Taha, T. Y. Pinney, M. M. 2026-01-28 doi:10.64898/2026.01.27.702130 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ Divergent Electrophysiological Responses in the Human Hippocampus During Verbal Memory Processing ]]> https://biorxiv.org/content/10.64898/2026.01.28.702353v1?rss=1 50 Hz), and low-frequency (LFA 1-8 Hz) activity. A nearly equal number of sites showed no changes in ripple rate but increased LFA power and a delayed response-locked decrease in HFA power. More importantly, both successful encoding as well as recognition of remembered words were strongly associated with the coordination of the timing of LFA and HFA increases across the two clusters of responsive HPC sites. Using direct cortical electrical stimulations, we confirmed overlapping, but partially distinct, cortical connections to the functionally distinct HPC clusters. Our findings suggest a mesoscale mosaic functional organization within the human HPC where adjacent sites with divergent electrophysiological responses may have specialized roles during verbal memory processing. More importantly, our findings suggest that successful human memory depends on the coordination of the timing of low and high frequency local fields generated across these functionally divergent neuronal population sites. ]]> Huang, W. Quabs, J. T. Lyu, D. Staalduinen, E. K. v. Pantis, S. Marais, O. Stieger, J. Liang, E. Deutsch, G. He, Z. Buch, V. P. Parvizi, J. 2026-01-29 doi:10.64898/2026.01.28.702353 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ A highly conserved two-gene operon is crucial for lipoarabinomannan localization, pathogenesis, and cell envelope function in Mycobacterium abscessus ]]> https://biorxiv.org/content/10.64898/2026.01.29.702501v1?rss=1 Campbell-Kruger, N. Balakhmet, A. Stanley, S. 2026-01-29 doi:10.64898/2026.01.29.702501 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ Global population structures and demographic history of Suillus luteus, a pine co-introduced ectomycorrhizal fungus associated with exotic forestry and invasion. ]]> https://biorxiv.org/content/10.64898/2026.01.27.699563v1?rss=1 Ke, Y.-H. Bazzicalupo, A. Ruytinx, J. Lofgren, L. A. Bruns, T. D. Branco, S. Looney, B. P. Hirose, D. Tedersoo, L. Peintner, U. Rojas, J. A. Liao, H.-L. Plett, J. M. Anderson, I. Lipzen, A. M. Kuo, A. Barry, K. W. Grigoriev, I. Hoeksema, J. D. Nguyen, N. H. Kennedy, P. Vilgalys, R. 2026-01-30 doi:10.64898/2026.01.27.699563 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ A genetically encoded ionic-stress sensor reveals protons as a sleep driver ]]> https://biorxiv.org/content/10.64898/2026.01.27.702131v1?rss=1 Ji, Z. Liu, J. Wang, B. Wei, S. Bian, Y. Zeng, W. Chung, C.-I. Ma, Z. Zhang, J. Shu, X. Ma, D. K. 2026-01-30 doi:10.64898/2026.01.27.702131 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Volume EM reveals three-dimensional architecture of the desmosome in epithelial cells and tissue models ]]> https://biorxiv.org/content/10.64898/2026.01.27.702185v1?rss=1 Bharathan, N. K. Giang, W. Chen, E. Zimmer, S. E. Lhamo, S. Jorgens, D. M. Inman, J. L. Mennella, V. Auer, M. Kowalczyk, A. P. 2026-01-30 doi:10.64898/2026.01.27.702185 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Methionine metabolism and the NOP2 methyltransferase are essential for MYC-Driven liver tumorigenesis. ]]> https://biorxiv.org/content/10.64898/2026.01.28.702329v1?rss=1 Lin, S. Berdan, C. Sandy, M. Lu, X. Ramani, V. Nomura, D. Chen, X. Lee, J. V. Goga, A. 2026-01-30 doi:10.64898/2026.01.28.702329 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ H4K20me3 and CTCF act reciprocally at TAD boundaries to regulate cell state transitions ]]> https://biorxiv.org/content/10.64898/2026.01.29.702647v1?rss=1 Atai, K. Mitra, M. Bohn, E. Hu, R. Corvalan, A. Jelinek, D. Voisin, L. Ambrus, A. Sarathy, K. Sparks, W. M. Bonitto, K. Dunkwu, A. Coller, H. A. 2026-01-30 doi:10.64898/2026.01.29.702647 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Quantitative muscle color as a proxy for structural and functional characteristics during muscle remodeling in Gryllus lineaticeps ]]> https://biorxiv.org/content/10.64898/2026.01.29.702701v1?rss=1 Laturney, M. Martins, L. Diaz, T. Lo, E. Uen, N. Williams, C. M. 2026-01-30 doi:10.64898/2026.01.29.702701 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Analysis of the assembly, stabilization and maturation of the multiphasic TAZ biomolecular condensates ]]> https://biorxiv.org/content/10.64898/2026.01.29.702607v1?rss=1 Shapira, K. E. Zhu, Q. Grig, E. Chen, X. Jing, Y. Li, X. D. Wolfenson, H. Henis, Y. I. Luo, K. 2026-02-02 doi:10.64898/2026.01.29.702607 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Science should be machine-readable ]]> https://biorxiv.org/content/10.64898/2026.01.30.702911v1?rss=1 Booeshaghi, A. S. Luebbert, L. Pachter, L. 2026-02-02 doi:10.64898/2026.01.30.702911 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Evaluating the applicability of kinship analyses for sedimentary ancient DNA datasets ]]> https://biorxiv.org/content/10.64898/2026.02.02.703194v1?rss=1 Cohen, P. Johnson, S. Zavala, E. I. Moorjani, P. Slon, V. 2026-02-02 doi:10.64898/2026.02.02.703194 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ LUCas: Light-Uncaged Cas13a using photocleavable interfering guide RNAs ]]> https://biorxiv.org/content/10.64898/2026.02.02.700737v1?rss=1 Ng, C. F. Krishnamurthy, D. Dextre, A. Chorlay, A. Ott, M. Fletcher, D. A. 2026-02-04 doi:10.64898/2026.02.02.700737 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Retinal waves shape starburst amacrine cell dendrite development through a direction-selective dendritic computation ]]> https://biorxiv.org/content/10.64898/2026.02.02.701812v1?rss=1 Pitcher, M. N. Gonzales, A. S. B. Habib, R. Feller, M. B. 2026-02-04 doi:10.64898/2026.02.02.701812 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Nested birth-death processes are competitive with parameter-heavy neural networks as time-dependent models of protein evolution ]]> https://biorxiv.org/content/10.64898/2026.02.02.702952v1?rss=1 Large, A. Holmes, I. 2026-02-04 doi:10.64898/2026.02.02.702952 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Comparison of environmental DNA and bulk DNA metabarcoding for assessing terrestrial arthropod diversity across three habitat types on Guam ]]> https://biorxiv.org/content/10.64898/2026.02.02.703366v1?rss=1 Banerjee, P. Al-Bayer, S. Calaor, J. Weber, S. Graham, N. C. Andersen, J. P. Economo, E. Kennedy, S. Krehenwinkel, H. Gillespie, R. Roderick, G. Rogers, H. P. Puliafico, K. 2026-02-04 doi:10.64898/2026.02.02.703366 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Structural basis for curvature generation and functional specialization in spirochete flagella ]]> https://biorxiv.org/content/10.64898/2026.02.04.703737v1?rss=1 Troman, L. Paul, B. Kim, J. Fenno, J. C. Goetting-Minesky, M. P. Reynolds, E. C. Banfield, J. Veith, P. D. Ghosal, D. 2026-02-04 doi:10.64898/2026.02.04.703737 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Dorsal skin biopsies: A non-lethal sampling method for studying amphibians, including the highly endangered Harlequin frogs (Bufonidae: Atelopus) ]]> https://biorxiv.org/content/10.64898/2026.02.04.703782v1?rss=1 Navarrete Mendez, M. J. Riera, A. B. Q. Teran-Valdez, A. Naydenova, E. Coloma, L. A. Tarvin, R. D. 2026-02-06 doi:10.64898/2026.02.04.703782 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ Stereoselective methyl-swapping demonstrates target specificity of cognitive enhancer ]]> https://biorxiv.org/content/10.64898/2026.02.04.700910v1?rss=1 Boone, M. Dalwadi, U. Deal, A. Zhu, P. J. Croll, T. I. Yamazaki, M. Prescott, K. Minopoli, R. Biscocho, I. Wang, J. Lee, D. J. Arthur, C. P. Laughlin, T. G. Zhou, H. Klope, M. T. Egea, P. F. Schoof, M. Lawrence, R. Renslo, A. R. Costa-Mattioli, M. Frost, A. Walter, P. 2026-02-07 doi:10.64898/2026.02.04.700910 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ Token Alignment for Verifying LLM-Extracted Text ]]> https://biorxiv.org/content/10.64898/2026.02.06.704502v1?rss=1 Booeshaghi, A. S. Streets, A. M. 2026-02-10 doi:10.64898/2026.02.06.704502 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ In vivo aberration measurement and correction for ultrafast FACED two-photon fluorescence microscopy of the brain ]]> https://biorxiv.org/content/10.64898/2026.02.06.704504v1?rss=1 Zhu, J. Natan, R. Zhong, J. Kang, I. Ji, N. 2026-02-10 doi:10.64898/2026.02.06.704504 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ A mechanism-aware stoichiometry platform resolves functional viral thresholds and induces antiviral hypersensitivity ]]> https://biorxiv.org/content/10.64898/2026.02.09.704886v1?rss=1 Clinger, G. Durden, H. Daurelle, A. Preece, B. Peppel, W. Gallegos, R. Waheed, A. A. Bohn, N. MacArthur, B. Petersen, A. Yildiz, A. Freed, E. O. Saffarian, S. 2026-02-10 doi:10.64898/2026.02.09.704886 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ CAZyme domain architectures suggest fine-scale functional differentiation among anaerobic fungi and bacteria during lignocellulose conversion to volatile fatty acids ]]> https://biorxiv.org/content/10.64898/2026.02.09.704939v1?rss=1 Lawson, C. E. Howard, J. P. Lankiewicz, T. Brown, J. B. Singer, S. Garcia Martin, H. O'Malley, M. A. 2026-02-10 doi:10.64898/2026.02.09.704939 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ Inference of admixture in dogs from whole genome sequences ]]> https://biorxiv.org/content/10.64898/2026.02.09.704954v1?rss=1 Kislik, G. Moore, G. Rubbi, L. Pellegrini, M. 2026-02-10 doi:10.64898/2026.02.09.704954 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ Telomere length of both parents contribute to heritable POT1 cancer-predisposition syndrome ]]> https://biorxiv.org/content/10.64898/2026.02.09.704652v1?rss=1 Martin, A. Lu, R. Blake, A. Nichols, K. E. Sanchez, S. E. Artandi, S. E. Sharma, R. Hockemeyer, D. 2026-02-11 doi:10.64898/2026.02.09.704652 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ Phthalate exposure induces inflammatory signaling and alters mitochondrial respiration in marine mammal and human cells ]]> https://biorxiv.org/content/10.64898/2026.02.09.704935v1?rss=1 Piotrowski, E. R. Lam, E. K. Moreno-Santillan, D. D. Allen, K. N. Crocker, D. E. Goksoyr, A. E. Vazquez-Medina, J. P. 2026-02-11 doi:10.64898/2026.02.09.704935 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ SHANK3-CAMSAP2 interaction links synapses to dendritic microtubule organisation in PV neurons ]]> https://biorxiv.org/content/10.64898/2026.02.10.705051v1?rss=1 Hacker, D. Lee, S. Hecht-Bucher, M. Lee, S. Lamborelle, C. Doil, A. N. Fanutza, T. Brueckner, A. M. Yoo, T. Ramirez-Rios, S. Smaczniak, C. Kaufmann, K. Dekkers, D. H. W. Demmers, J. A. A. Moutin, M.-J. Kim, E. Mikhaylova, M. 2026-02-11 doi:10.64898/2026.02.10.705051 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ In Vivo Cardiac Prime Editing Corrects the Pathogenic Mutation and Rescues Cardiomyopathy Phenotypes in a Novel Humanized RBM20 Mouse Model ]]> https://biorxiv.org/content/10.64898/2026.02.10.705148v1?rss=1 Liang, W. Rollosson, L. M. Easter, E. Zhou, H. Dee-Hoskins, C. Greer-Short, A. Hoey, T. Lombardi, L. M. Ivey, K. N. Cheng, Z. 2026-02-12 doi:10.64898/2026.02.10.705148 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ Tracking Transgenes with Color: RUBY as a Visual Marker in CRISPR-Edited Mutant Plants in Two Triticum Species ]]> https://biorxiv.org/content/10.64898/2026.02.10.705172v1?rss=1 Kumar, R. Palayur, A. Lunde, C. Krasileva, K. Milner, M. J. 2026-02-12 doi:10.64898/2026.02.10.705172 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ Shared somatosensory-motor neural population dynamics track motor recovery after stroke ]]> https://biorxiv.org/content/10.64898/2026.02.10.705199v1?rss=1 Heimbuch, I. S. Khanna, P. Novik, L. Morecraft, R. J. Ganguly, K. 2026-02-12 doi:10.64898/2026.02.10.705199 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ scAmp analyzes focal gene amplifications at single-cell resolution ]]> https://biorxiv.org/content/10.64898/2026.02.14.705928v1?rss=1 Jones, M. G. Weiser, N. E. Hung, K. L. Yan, X. Agarwal, S. Luebeck, J. Gnanasekar, A. Howitt, B. E. Curtis, E. J. Yu, K. Rose, J. C. Kraft, K. Amiri, V. V. P. Satpathy, L. Bafna, V. Mischel, P. S. Chang, H. Y. 2026-02-15 doi:10.64898/2026.02.14.705928 Cold Spring Harbor Laboratory Press 2026-02-15 <![CDATA[ Cellular Chemical Dynamics Governing Signal Transduction and Adaptive Gene Expression: Beyond Classical Kinetics ]]> https://biorxiv.org/content/10.64898/2026.02.13.705865v1?rss=1 Kim, J. Kim, S. Jang, S. Park, S. J. Song, S. Jeung, K. Jung, G. Y. Kim, J.-H. Koh, H. R. Sung, J. 2026-02-18 doi:10.64898/2026.02.13.705865 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Diet-Microbiome Analysis in a Healthy Cohort Reveals Potential Role of Intestinal Microbiota in Metabolism ]]> https://biorxiv.org/content/10.64898/2026.02.17.706416v1?rss=1 Trang, K. T. Gulick, D. A. Truell, J. Tian, J. Bodkhe, R. Hiseni, P. Gravdal, K. Kirubakaran, T. G. Casen, C. Singh, R. Ziegler, T. R. Reimer, R. A. Kraft, C. S. 2026-02-20 doi:10.64898/2026.02.17.706416 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Visual semantic tuning across the cortex shifts between tasks ]]> https://biorxiv.org/content/10.64898/2026.02.19.706797v1?rss=1 Zhang, T. Gallant, J. 2026-02-20 doi:10.64898/2026.02.19.706797 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Representations of semantic relations in the human cerebral cortex ]]> https://biorxiv.org/content/10.64898/2026.02.19.706815v1?rss=1 Chen, C. Gong, X. L. Deniz, F. Klein, D. Gallant, J. 2026-02-20 doi:10.64898/2026.02.19.706815 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Deep models of protein evolution in time generate realistic evolutionary trajectories and functional proteins ]]> https://biorxiv.org/content/10.64898/2026.02.19.706898v1?rss=1 Koehl, A. Prillo, S. Liu, M. Xiong, J. Weng, L. Savage, D. F. Song, Y. S. 2026-02-20 doi:10.64898/2026.02.19.706898 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Induction and regulation of a reversible form of suspended animation in C. elegans ]]> https://biorxiv.org/content/10.64898/2026.02.19.706910v1?rss=1 Liu, J. Wang, B. Catrow, J. L. Pearce, Q. Ji, Z. Yang, S. W. Balakrishnan, A. Cox, J. Ma, D. K. 2026-02-20 doi:10.64898/2026.02.19.706910 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination ]]> https://biorxiv.org/content/10.64898/2026.02.21.707213v1?rss=1 300 kilobases) in the human gut microbiome, which we term Hodors. Hodors encode conserved replication, partitioning, and type IV secretion systems, together with a complex surface-associated gene module. A subset of Hodors harbor complete, intact prophage genomes, and closely related prophages are detected across phylogenetically distant Bacillota lineages, including both Bacilli and Clostridia. Further analysis indicates that Hodor-associated prophages can exist as extracellular particles and demonstrate their transcriptional activity. Our findings support a model in which conjugative megaplasmids act as composite mobile platforms that disseminate prophage genomes across bacterial lineages, providing a mechanistic explanation for the widespread occurrence of closely related prophages in phylogenetically distant gut bacteria and effectively decoupling lysogenic host range from infective host range. ]]> Yuan, L. Qin, Y. West-Roberts, J. Anantharaman, K. Wang, H. Zou, Y. Duan, Y. Camargo, A. P. Koonin, E. V. Chen, L. 2026-02-22 doi:10.64898/2026.02.21.707213 Cold Spring Harbor Laboratory Press 2026-02-22 <![CDATA[ Metabolic stress reveals widespread accumulation of cap-unmethylated RNAs ]]> https://biorxiv.org/content/10.64898/2026.02.23.707474v1?rss=1 Xing, Z. Freitas, A. V. Sutter, B. M. Dang, N. K. Ingolia, N. T. Tu, B. P. 2026-02-24 doi:10.64898/2026.02.23.707474 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ Targeted knockout of CYP79A1 reduces cyanogenic potential in grain sorghum ]]> https://biorxiv.org/content/10.64898/2026.02.23.707491v1?rss=1 Groover, E. D. Shen, J. Aregawi, K. Li, S. Schwartz, S. Staskawicz, B. Lemaux, P. G. Savage, D. F. 2026-02-24 doi:10.64898/2026.02.23.707491 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ Automated localization of calling birds with small passive acoustic arrays in complex soundscapes ]]> https://biorxiv.org/content/10.64898/2026.02.23.707497v1?rss=1 Eisen, M. B. Brown, P. O. Sanz-Matias, A. 2026-02-24 doi:10.64898/2026.02.23.707497 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ Title: Optogenetic WNT signaling drives germ layer self-organization in a human gastruloid model ]]> https://biorxiv.org/content/10.64898/2026.02.23.707602v1?rss=1 Schaffer, D. V. Johnson, H. J. McMullin, D. M. Zimmermann, J. Kim, C. Repina, N. Bhalerao, R. Nowakowski, T. 2026-02-25 doi:10.64898/2026.02.23.707602 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ Neural Control of Autonomic Arousal During Threat Anticipation Revealed by High-Resolution Cardiac Contractility ]]> https://biorxiv.org/content/10.64898/2026.02.23.707545v1?rss=1 Stasiak, J. E. Wang, J. Dundon, N. M. Rizor, E. J. Barandon, P. L. Villanueva, C. M. Babenko, V. Li, T. L. Sabugo, K. M. Grafton, S. T. Lapate, R. C. 2026-02-26 doi:10.64898/2026.02.23.707545 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Divergent Biological Consequences of APOE Isoforms Across Industrialized and Non-Industrial Environments ]]> https://biorxiv.org/content/10.64898/2026.02.24.706846v1?rss=1 Watowich, M. M. Petersen, R. Brassington, L. Arner, A. Rodenberg, G. Huat, T. B. T. A. T. B. Tam, K. L. Schellenberg, E. Sayed, I. b. M. John, E. Kahumbu, J. Muhoya, B. Gurven, M. Trumble, B. C. Njeru, S. N. Martins, D. Ayroles, J. F. Lim, Y. A. L. Venkataraman, V. v. Wallace, I. Kraft, T. S. Lea, A. J. 2026-02-26 doi:10.64898/2026.02.24.706846 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Activation of PPARγ redirects fibro-adipogenic progenitors to replace ectopic bone with fat in models of fibrodysplasia ossificans progressiva and trauma-induced heterotopic ossification ]]> https://biorxiv.org/content/10.64898/2026.02.26.708276v1?rss=1 Koirala, P. Chen, Z. Hanumantharao, S. N. Siegel, A. E. Liu, C. Williams, Z. Sekhon, H. Maridas, D. Mishina, Y. Rosen, V. Agarwal, S. 2026-03-02 doi:10.64898/2026.02.26.708276 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ Computational modelling of natural cell-to-cell heterogeneity reveals key parameters that control the diversity of human pancreatic islet β-cell excitability in response to glucose ]]> https://biorxiv.org/content/10.64898/2026.02.27.708039v1?rss=1 Goswami, I. Koepke, J. Baghelani, M. Macdonald, P. E. Kravets, V. Light, P. E. Edwards, A. G. 2026-03-02 doi:10.64898/2026.02.27.708039 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ Orca vowels and consonants: convergent spectral structures across cetacean and human speech ]]> https://biorxiv.org/content/10.64898/2026.02.27.708287v1?rss=1 Begus, G. Holt, M. Wright, B. Gruber, D. F. 2026-03-02 doi:10.64898/2026.02.27.708287 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ Contrastive Alignment of Expression and Copy Number Highlights Dosage-Insensitive Genes in Cancer ]]> https://biorxiv.org/content/10.64898/2026.03.01.708901v1?rss=1 Goswami, G. Xu, D. Park, H. J. 2026-03-03 doi:10.64898/2026.03.01.708901 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Medulloblastoma-Associated KBTBD4 Mutations Disrupt PP2A-A Orphan Quality Control ]]> https://biorxiv.org/content/10.64898/2026.03.02.709011v1?rss=1 Baur, R. Schneider, L. A. Sathe, G. Lunardi, T. Schneider, J. Krebs, A.-S. Silva, J. C. Haakonsen, D. L. Waszak, S. M. Lingner, J. Ciulli, A. Rape, M. Thoma, N. H. 2026-03-03 doi:10.64898/2026.03.02.709011 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Rapid residual bead quantification for cell therapy manufacturing using Raman spectroscopy ]]> https://biorxiv.org/content/10.64898/2026.03.02.709071v1?rss=1 Morales, M. Ravichandran, S. Badawy, S. Tadesse, L. F. 2026-03-04 doi:10.64898/2026.03.02.709071 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Recovering signatures of archaic introgression using ancestral recombination graphs ]]> https://biorxiv.org/content/10.64898/2026.03.03.709416v1?rss=1 Zhang, Y. Biddanda, A. Johnson, S. A. O'Dushlaine, C. Moorjani, P. 2026-03-04 doi:10.64898/2026.03.03.709416 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ A Novel Pilus System in Candidate Phyla Radiation Bacteria ]]> https://biorxiv.org/content/10.64898/2026.03.03.709456v1?rss=1 Troman, L. A. Kim, J. Rose, J. J. A. Johnson, M. Banfield, J. F. Petrovski, S. Ghosal, D. 2026-03-04 doi:10.64898/2026.03.03.709456 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ An Optimized RNF126-Targeting Covalent Handle for Molecular Glue Degraders ]]> https://biorxiv.org/content/10.64898/2026.03.06.709959v1?rss=1 Modi, A. Toriki, E. S. Stieger, C. E. Lau, E. A. Song, C. Chew, A. Tsao, A. Nishikawa, K. McKenna, J. Nomura, D. K. 2026-03-07 doi:10.64898/2026.03.06.709959 Cold Spring Harbor Laboratory Press 2026-03-07 <![CDATA[ Tubulin C-terminal tails are pH sensors that regulate microtubule function ]]> https://biorxiv.org/content/10.64898/2026.03.06.710195v1?rss=1 Whited, A. M. DeLear, P. Thomas, E. C. Allen, J. Ferrer-Imbert, G. Acharya, N. Castaneda, C. A. Sept, D. Moore, J. K. Hough, L. E. 2026-03-08 doi:10.64898/2026.03.06.710195 Cold Spring Harbor Laboratory Press 2026-03-08 <![CDATA[ The extreme diversity of retinal amacrine cells has deep evolutionary roots ]]> https://biorxiv.org/content/10.64898/2026.03.07.710289v1?rss=1 Tommasini, D. Monavarfeshani, A. Dinesh, V. Hahn, J. Tangeman, J. Marre, O. Blackshaw, S. Puthussery, T. Sanes, J. Shekhar, K. 2026-03-09 doi:10.64898/2026.03.07.710289 Cold Spring Harbor Laboratory Press 2026-03-09 <![CDATA[ Differential impacts of fall versus spring prescribed burns on microbial biomass, richness, and composition in young mixed conifer forests ]]> https://biorxiv.org/content/10.64898/2026.03.09.710622v1?rss=1 Zhilik, B. B. Pulido Barriga, M. F. Homyak, P. M. York, R. A. Glassman, S. I. 2026-03-10 doi:10.64898/2026.03.09.710622 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Shape Factor Analysis as a Quantitative Framework for Assessing Spheroid and Organoid Morphology and Invasiveness ]]> https://biorxiv.org/content/10.64898/2026.03.10.710632v1?rss=1 Schutrum, B. E. Deng, J. Kim, J. H. Gao, A. Hur, E. Crowley, J. C. Ling, L. Pirtz, M. G. Ralston, C. Q. Nikitin, A. Y. Fischbach, C. 2026-03-12 doi:10.64898/2026.03.10.710632 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ Spt5's central KOW domains and the Pol II Stalk Collaborate to Regulate Chromatin and 3'-End Processing ]]> https://biorxiv.org/content/10.64898/2026.03.09.710576v1?rss=1 Morton, Z. A. Doody, M. J. Naik, N. Paniagua, N. Delahunty, C. Yates, J. R. Bustamante, C. J. Hartzog, G. A. 2026-03-13 doi:10.64898/2026.03.09.710576 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Hyperface: a naturalistic fMRI dataset for investigating human face processing ]]> https://biorxiv.org/content/10.64898/2026.03.11.711073v1?rss=1 Visconti di Oleggio Castello, M. Jiahui, G. Feilong, M. de Villemejane, M. Haxby, J. V. Gobbini, M. I. 2026-03-13 doi:10.64898/2026.03.11.711073 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Dynamin-2 promotes Atg9A retrieval from phagophores during autophagy. ]]> https://biorxiv.org/content/10.64898/2026.03.11.711183v1?rss=1 van der Bliek, A. M. Caliri, A. Martorell Riera, A. Saha, A. Kolitsida, P. Iriondo Martinez, C. Itskanov, S. Steffen, J. Koehler, C. M. 2026-03-13 doi:10.64898/2026.03.11.711183 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Human auditory cortex preferentially tracks speech over music without explicit attention ]]> https://biorxiv.org/content/10.64898/2026.03.12.710296v1?rss=1 Agravat, R. Desai, M. Field, A. M. Georges, S. Leisawitz, J. Foox, G. Asghar, S. Clarke, D. Tyler-Kabara, E. C. Iqbal, M. O. Watrous, A. J. Anderson, A. E. Weiner, H. L. Hamilton, L. S. 2026-03-13 doi:10.64898/2026.03.12.710296 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Stage-dependent biotic interactions may not be important for stochastic competitive dynamics with little variation in stage structure ]]> https://biorxiv.org/content/10.64898/2026.03.13.711558v1?rss=1 Lee, J. Y. Blonder, B. Ray, C. A. Hernandez, C. Salguero-Gomez, R. 2026-03-13 doi:10.64898/2026.03.13.711558 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Abundance-activity decoupling in sulfur-cycling bacteria reflects viral infection types in meromictic lakes ]]> https://biorxiv.org/content/10.64898/2026.03.13.711613v1?rss=1 Walker, J. R. Varona, N. S. Wallace, B. A. Aguilar, A. O'Beirne, M. D. Werne, J. P. Luque, A. Gilhooly, W. P. Bosco-Santos, A. Silveira, C. B. 2026-03-13 doi:10.64898/2026.03.13.711613 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Antarctic marine microplastics reveals environmental persistence and rapid evolution of Candida auris ]]> https://biorxiv.org/content/10.64898/2026.03.13.711634v1?rss=1 van Rhijn, N. Gan, E. Hepo-oja, P. Wang, X. Li, J. Duggan, S. Firer, D. Alsharqi, L. Gifford, H. Steenwyk, J. L. Brackin, A. P. Abdolrasouli, A. Borman, A. M. Cuomo, C. A. Fisher, M. C. Armstrong-James, D. Farrer, R. A. Usher, J. Rhodes, J. 2026-03-13 doi:10.64898/2026.03.13.711634 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ A strong start for sustained success: inclusivity through a national group mentorship program for first-year graduate students ]]> https://biorxiv.org/content/10.64898/2026.03.12.710679v1?rss=1 Labra, S. R. Tornini, V. A. Rodriguez Salazar, M. P. Cossio, D. M. Gelpi, R. A. Rubio Perez, B. E. Rodriguez, Y. M. Leana-Sandoval, G. Hernandez, K. Goldman, O. V. Fernandez, R. W. 2026-03-15 doi:10.64898/2026.03.12.710679 Cold Spring Harbor Laboratory Press 2026-03-15 <![CDATA[ Mapping frog genomic diversity on a continental scale ]]> https://biorxiv.org/content/10.64898/2026.03.13.711368v1?rss=1 Barrow, L. N. McDaniels, C. X. Bishop, A. P. Amador, L. Wiley, D. L. F. Eberle, C. M. Mason, N. M. Rosario Sanchez, E. O. Giermakowski, J. T. Hoffman, E. A. Jongsma, G. F. M. Michelsohn, M. J. Nava Martinez, M. Omlor, K. N. Rivera, S. R. Torres Lopez, A. S. Warwick, A. R. Webster, K. C. 2026-03-17 doi:10.64898/2026.03.13.711368 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Beyond Neural Noise: Critical Dynamics Predict Slower Reaction Times in Adults With and Without ADHD ]]> https://biorxiv.org/content/10.64898/2026.03.13.711705v1?rss=1 DallaVecchia, A. Zink, N. O'Connell, S. R. Betts, S. S. Noah, S. Hillberg, A. Oliva, M. T. Reid, R. C. Cohen, M. S. Simpson, G. V. Karalunas, S. L. Calhoun, V. D. Lenartowicz, A. 2026-03-17 doi:10.64898/2026.03.13.711705 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Preferential formation of NUP98-KDM5A condensates at specific H3K4me3-rich loci drives leukemogenic gene expression ]]> https://biorxiv.org/content/10.64898/2026.03.16.712262v1?rss=1 Berrocal, A. Sandoval, J. E. Khetan, N. Ma, A. Wang, T. Moore, C. Narlikar, G. J. Li, H. Galonic Fujimori, D. Huang, B. 2026-03-17 doi:10.64898/2026.03.16.712262 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Component A2 is a redox-sensitive archaeal ATPase activated by methyl-coenzyme M reductase ]]> https://biorxiv.org/content/10.64898/2026.03.18.712670v1?rss=1 Adler, S. A. Nayak, D. D. 2026-03-18 doi:10.64898/2026.03.18.712670 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Development and assessment of tailored illustrations to enhance community understandings of genetics topics ]]> https://biorxiv.org/content/10.64898/2026.03.17.711941v1?rss=1 Arner, A. M. McCabe, T. C. Seyler, A. Zamri, S. N. A/P Tan Boon Huat, T. B. T. Tam, K. L. Kinyua, P. John, E. Ngoci Njeru, S. Lim, Y. A. Gurven, M. Nicholas, C. Ayroles, J. Venkataraman, V. v. Kraft, T. S. Wallace, I. J. Lea, A. J. 2026-03-19 doi:10.64898/2026.03.17.711941 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ Metabolic adaptation to maternal hyperglycemia via ACLY-dependent acetyl-CoA production drives epigenetic remodeling and dysregulated placental development ]]> https://biorxiv.org/content/10.64898/2026.03.17.712507v1?rss=1 Liu, M. Jin, K. QI, S. Chen, D. Han, Y. Xu, W. Wen, C. Wen, H. Liu, Y. He, B. Lin, X. 2026-03-20 doi:10.64898/2026.03.17.712507 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Simultaneous broad protection against Ebola Sudan, Marburg and Lassa viruses conferred by a DNA primed MVA-vectored multivalent vaccine ]]> https://biorxiv.org/content/10.64898/2026.03.18.712579v1?rss=1 Kobasa, D. Pfranger, M. Krause, N. Fedosyuk, S. Wiegand, L. Jordan, I. Sandig, V. Leupold, C. Asbach, B. Storisteanu, D. Kalender, A. Scheer, L. Brenner, D. Prevost, J. Tailor, N. Vendramelli, R. Warner, B. Truong, T. Parthasarathy, S. Holbrook, J. Carnell, G. Sujit, S. B. Ashokan, S. Chan, A. Whittaker, C. Ugwu, C. Happi, C. Frost, S. Kinsley, R. Safronetz, D. Wagner, R. Heeney, J. L. 2026-03-20 doi:10.64898/2026.03.18.712579 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Structural basis of receptor retro-translocation in peroxisomal protein import ]]> https://biorxiv.org/content/10.64898/2026.03.18.712702v1?rss=1 Dempsey, N. W. M. Wang, L. Gao, N. Zhao, K. Cope, J. Park, E. 2026-03-20 doi:10.64898/2026.03.18.712702 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ BioReason-Pro: Advancing Protein Function Prediction with Multimodal Biological Reasoning ]]> https://biorxiv.org/content/10.64898/2026.03.19.712954v1?rss=1 Fallahpour, A. Seyed-Ahmadi, A. Idehpour, P. Ibrahim, O. Gupta, P. Naimer, J. Zhu, K. Shah, A. Ma, S. Adduri, A. Güloglu, T. Liu, N. Cui, H. Jain, A. de Castro, M. Fallahpour, A. Cembellin-Prieto, A. Stiles, J. S. Nemcko, F. Nevue, A. A. Moon, H. C. Sosnick, L. Markham, O. Duan, H. Lee, M. Y. Y. Salvador, A. F. M. Maddison, C. J. Thaiss, C. A. Ricci-Tam, C. Plosky, B. S. Burke, D. P. Hsu, P. D. Goodarzi, H. Wang, B. 2026-03-20 doi:10.64898/2026.03.19.712954 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Revealing the benefit of eye motion for acuity under emulated cone loss ]]> https://biorxiv.org/content/10.64898/2026.03.19.712913v1?rss=1 Doyle, H. K. Fong, J. Ng, R. Roorda, A. 2026-03-23 doi:10.64898/2026.03.19.712913 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ Rational reduction of a sorghum SynCom that preserves growth promotion reveals flavonoid-mediated plant microbe interactions ]]> https://biorxiv.org/content/10.64898/2026.03.20.709941v1?rss=1 Pettinga, D. Fonseca-Garcia, C. Krause, G. Ploemacher, H. Wheeler, T. Clendinen, C. S. Handakumbura, P. Egbert, R. Coleman-Derr, D. 2026-03-23 doi:10.64898/2026.03.20.709941 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ Ca2+ influx through ER-plasma membrane contacts is required for brown fat thermogenesis and metabolic health ]]> https://biorxiv.org/content/10.64898/2026.03.20.712802v1?rss=1 Zhou, J. Dogan, C. Artico, L. L. Rodrigues Santos, K. Hakam, S. Kim, T. Xu, V. Lapenta, K. Kang, M. Jorgens, D. M. Widenmaier, S. Parlakgul, G. Arruda, A. P. 2026-03-23 doi:10.64898/2026.03.20.712802 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ Mueller glia-vasculature interactions in the developing retina ]]> https://biorxiv.org/content/10.64898/2026.03.23.713726v1?rss=1 Monshietehadi, S. Garcia, A. J. Smith, B. E. Tarchick, M. Conley, A. Abhayaratne, K. Feller, M. 2026-03-25 doi:10.64898/2026.03.23.713726 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Point cloud local ancestry inference (PCLAI): continuous coordinate-based ancestry along the genome ]]> https://biorxiv.org/content/10.64898/2026.03.23.713813v1?rss=1 Geleta, M. Mas Montserrat, D. Ioannidis, N. M. Ioannidis, A. G. 2026-03-25 doi:10.64898/2026.03.23.713813 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Chiral methionine oxidation reagents reveal stereospecific proteome modifications ]]> https://biorxiv.org/content/10.64898/2026.03.24.713977v1?rss=1 Gonzalez-Valero, A. Page, A. C. S. Bertoch, J. M. Alsarhan, F. Kim, J. Alazali, A. A. Srinivas, R. R. Xie, X. Reeves, A. G. Skakuj, K. Coffey, T. G. Virgil, S. C. Nafie, J. He, D. Dao, N. Gunawan, A. L. Dukor, R. Stahl, A. Toste, F. D. Chang, C. J. 2026-03-26 doi:10.64898/2026.03.24.713977 Cold Spring Harbor Laboratory Press 2026-03-26 <![CDATA[ Apical Localization of RNA Polymerases Modulate Transcription Dynamics and Supercoiling Domains Revealed by Cryo-ET ]]> https://biorxiv.org/content/10.64898/2026.03.25.714350v1?rss=1 Zhang, M. Canari-Chumpitaz, C. Liu, J. Onoa, B. de Cleir, S. Cheng, E. Requejo, K. I. Bustamante, C. 2026-03-26 doi:10.64898/2026.03.25.714350 Cold Spring Harbor Laboratory Press 2026-03-26 <![CDATA[ IDPForge: Deep Learning of Proteins with Global and Local Regions of Disorder ]]> https://biorxiv.org/content/10.64898/2026.03.25.714313v1?rss=1 De Castro, S. Zhang, O. Liu, Z. H. Forman-Kay, J. D. Head-Gordon, T. 2026-03-27 doi:10.64898/2026.03.25.714313 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Complex benthic habitats retain larvae sinking in response to soluble cues: field study of coral reefs in wave-driven flow ]]> https://biorxiv.org/content/10.64898/2026.03.25.714321v1?rss=1 Koehl, M. A. R. Hadfield, M. G. 2026-03-27 doi:10.64898/2026.03.25.714321 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Metagenomic strain-resolved DNA modification patterns link extrachromosomal genetic elements to host strains ]]> https://biorxiv.org/content/10.64898/2026.03.27.714056v1?rss=1 1,000 isolate and mock microbiome datasets. Illustrating the approach, we identified 315 strain-resolved, non-redundant ECE-host linkages in environmental and human metagenomes. In infant gut microbiomes, a chromosomal inversion in Enterococcus faecalis alters host and associated plasmid methylation motifs simultaneously. Overall, MODIFI solves a major bottleneck in DNA modification analysis and provides a foundational tool for understanding microbial epigenomics. ]]> Wang, S. Guitor, A. K. Valentin-Alvarado, L. E. Garner, R. Zhang, P. Yan, M. Shi, L.-D. Schoelmerich, M. C. Steininger, H. M. Portik, D. M. Zhang, S. Wilkinson, J. E. Lynch, S. Morowitz, M. J. Hess, M. Diamond, S. Banfield, J. F. Sachdeva, R. 2026-03-28 doi:10.64898/2026.03.27.714056 Cold Spring Harbor Laboratory Press 2026-03-28 <![CDATA[ Single-Molecule Methods to Investigate Mechanisms of Transcription by RNA Polymerase of Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.64898/2026.03.27.714832v1?rss=1 Lin, W. Herrera-Asmat, O. Tong, A. B. Kong, T. Bustamante, C. 2026-03-28 doi:10.64898/2026.03.27.714832 Cold Spring Harbor Laboratory Press 2026-03-28 <![CDATA[ A Conserved Metabolic Oxidative Axis Underlies Immune Cell Cryo-vulnerability ]]> https://biorxiv.org/content/10.64898/2026.03.26.714376v1?rss=1 Mo, Z. Yang, H. Zhang, M. Cao, H. Wang, L. Tao, K. Chen, X. Tian, C. Han, C. Bustamante, C. Liu, Z. Wang, J. 2026-03-29 doi:10.64898/2026.03.26.714376 Cold Spring Harbor Laboratory Press 2026-03-29 <![CDATA[ The diploid reference genome of a human embryonic stem cell line ]]> https://biorxiv.org/content/10.64898/2026.03.26.714432v1?rss=1 Pacar, I. Ungaro, M. T. Chen, Y. Dallali, H. Medico, J. A. Hebbar, P. Diekhaus, M. Di Tommaso, E. Geleta, M. Chan, P. P. Lowe, T. M. Balacco, J. Jain, N. Ackerman, F. Mochi, M. Ioannidis, A. G. Sawarkar, N. Diaz, K. Krishna Sudhakar, K. Powell, J. E. Jain, M. Rosa, A. Croft, G. F. Tanzer, A. Jarvis, E. D. Formenti, G. Salama, S. R. Giunta, S. 2026-03-30 doi:10.64898/2026.03.26.714432 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Linking genotype to longevity under genealogical discordance in Sebastes rockfishes ]]> https://biorxiv.org/content/10.64898/2026.03.26.714443v1?rss=1 Mo, Y. K. Sudmant, P. H. Hahn, M. W. 2026-03-30 doi:10.64898/2026.03.26.714443 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Genetic encoding of climate-responsive stomatal developmental plasticity in tomato ]]> https://biorxiv.org/content/10.64898/2026.03.27.714625v1?rss=1 Nir, I. Budrys, A. Suraev, D. PRODJINOTO, H. Erberich, J. Tirnover, J. Zafrir, E. Kutcher, Y. Smoot, N. K. Bergmann, D. 2026-03-30 doi:10.64898/2026.03.27.714625 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes ]]> https://biorxiv.org/content/10.64898/2026.03.29.711974v1?rss=1 Kramer, A. M. Zhang, A. Ayala, N. de Sanctis, B. Karim, L. M. Hinrichs, A. S. Walia, S. Turakhia, Y. Corbett-Detig, R. 2026-03-30 doi:10.64898/2026.03.29.711974 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ DNA demethylation suppresses a state of enhanced cellular pluripotency and regeneration competence in Arabidopsis. ]]> https://biorxiv.org/content/10.64898/2026.03.27.714943v1?rss=1 Smoot, N. K. Zeng, Y. Hochman, R. M. Williams, B. P. 2026-03-31 doi:10.64898/2026.03.27.714943 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Local interaction networks reconstructed from global biodiversity data improve pollinator restoration decision making ]]> https://biorxiv.org/content/10.64898/2026.03.30.715389v1?rss=1 Baiotto, T. Cosma, C. Cheung, Y. Y. J. Narango, D. Woodard, J. McCarville, P. Echeverri, A. Horne, G. Wood, E. Williams, N. M. Seltmann, K. C. Fleri, J. R. Owens, A. Lequerica Tamara, M. Boren, A. Doneski, S. Guralnick, R. P. Li, D. Guzman, L. M. 2026-04-01 doi:10.64898/2026.03.30.715389 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Estimation of chloroplast macromolecular complex copy numbers and subunit stoichiometries during the Chlamydomonas reinhardtii cell cycle ]]> https://biorxiv.org/content/10.64898/2026.03.30.715394v1?rss=1 Schmollinger, S. Strenkert, D. Purvine, S. O. Nicora, C. D. Soubeyrand, E. Basset, G. J. Merchant, S. 2026-04-01 doi:10.64898/2026.03.30.715394 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Temporal AI model predicts drivers of cell state trajectories across human aging ]]> https://biorxiv.org/content/10.64898/2026.03.30.715396v1?rss=1 Gomez Ortega, J. Nadadur, R. D. Kunitomi, A. Kothen-Hill, S. Wagner, J. U. G. Kurtoglu, S. D. Kim, B. Reid, M. M. Lu, T. Washizu, K. Zanders, L. Chen, H. Zhang, Y. Ancheta, S. Lichtarge, S. Johnson, W. A. Thompson, C. Phan, D. M. Combes, A. J. Yang, A. C. Tadimeti, N. Dimmeler, S. Yamanaka, S. Alexanian, M. Theodoris, C. V. 2026-04-01 doi:10.64898/2026.03.30.715396 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Mapping the mammalian dark metabolome by in vivo isotope tracing ]]> https://biorxiv.org/content/10.64898/2026.03.31.713900v1?rss=1 MacArthur, M. R. Raeber, J. Lu, W. Qiang, H. Schueppert, A. V. Ayres, L. B. Cordova, R. A. Neinast, M. D. Leiva, E. Pham, V. N. AbuSalim, J. E. Jankowski, C. S. R. Samarah, L. Z. Roichman, A. Peace, C. G. Ivanov, D. G. Renzo, G. L. Oschmann, A. M. Ayroles, J. F. Mitchell, S. J. Xing, X. Olszewski, K. Kim, H. Rabinowitz, J. Skinnider, M. 2026-04-02 doi:10.64898/2026.03.31.713900 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ Chromosomal rearrangements 1 and sequence similarity drivepreferential allosyndetic introgression from a wild relative into wheat ]]> https://biorxiv.org/content/10.64898/2026.03.31.715614v1?rss=1 Ye, H. Zhang, Q. Chotewutmontri, P. Mandal, S. N. Niu, Z. Long, Y. Shen, J. Whetten, R. B. Li, G. Jin, Y. Gale, S. Friesen, T. L. Peters Haugrud, A. Xu, X. Faris, J. Yang, S. Cowger, C. Chen, J. Cai, X. Zhang, X. Luan, S. Gu, Y. Klindworth, D. L. Xu, S. S. 2026-04-02 doi:10.64898/2026.03.31.715614 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ Enabling the prediction of phage receptor specificity from genome data ]]> https://biorxiv.org/content/10.64898/2026.04.02.716166v1?rss=1 Moriniere, L. Noonan, A. J. C. Kazakov, A. Pena, M. Svab, M. Rivera-Lopez, E. O. Maucourt, F. Johnson, M. S. Roux, S. Koskella, B. Deutschbauer, A. M. Dudley, E. G. Mutalik, V. K. Arkin, A. P. 2026-04-02 doi:10.64898/2026.04.02.716166 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ CRISPR/Cas9-mutagenesis reveals that varying dependence on HSF1 is associated with differences in coral heat tolerance ]]> https://biorxiv.org/content/10.64898/2026.04.01.714264v1?rss=1 Swinhoe, N. Tinoco, A. Sarfati, D. N. Henderson, C. F. Kowalewski, G. P. Meier, E. K. Urban, J. M. Maruyama, S. Lawrence, E. C. Hulett, R. E. Engelke, T. R. Craggs, J. Bay, L. K. Cleves, P. A. 2026-04-03 doi:10.64898/2026.04.01.714264 Cold Spring Harbor Laboratory Press 2026-04-03 <![CDATA[ Human TBC1 domain-containing kinase is a class I multidomain pseudokinase ]]> https://biorxiv.org/content/10.64898/2026.04.02.716191v1?rss=1 Maurya, S. Cheek, L. E. Iavarone, A. T. Zhu, W. 2026-04-03 doi:10.64898/2026.04.02.716191 Cold Spring Harbor Laboratory Press 2026-04-03 <![CDATA[ DNA damage drives a unique, Alzheimer's disease-relevant senescent state in neurons ]]> https://biorxiv.org/content/10.64898/2026.04.02.716205v1?rss=1 Hughes, J.-W. B. Sandholm, A. Croll, D. Senchyna, F. Schneider, K. Butterfield, R. McHugh, T. L. M. Brown, I. Deguchi, H. Hilsabeck, T. A. U. Mak, S. Wilson, K. A. Davtyan, H. Blurton-Jones, M. Herdy, J. Higuchi-Sanabria, R. Gage, F. H. Furman, D. Ellerby, L. M. Desprez, P.-Y. Campisi, J. 2026-04-03 doi:10.64898/2026.04.02.716205 Cold Spring Harbor Laboratory Press 2026-04-03 <![CDATA[ Repurposing anti-phage defenses to differentially arrest the viral lifecycle reveals the regulatory logic of a parasitic satellite ]]> https://biorxiv.org/content/10.64898/2026.04.03.716414v1?rss=1 Bagdatli, S. T. Seed, K. 2026-04-04 doi:10.64898/2026.04.03.716414 Cold Spring Harbor Laboratory Press 2026-04-04 <![CDATA[ Expanding the scope of redox-balance growth coupling techniques with a carbon cofeeding strategy ]]> https://biorxiv.org/content/10.64898/2026.04.01.713023v1?rss=1 Cowan, A. E. Cawthon, B. Hillers, M. Perea, S. Grabovac, M. Stanton, A. Saleh, S. Gin, J. Chen, Y. Petzold, C. J. Keasling, J. D. 2026-04-05 doi:10.64898/2026.04.01.713023 Cold Spring Harbor Laboratory Press 2026-04-05 <![CDATA[ Methanol-specific methyltransferase isozymes have large carbon kinetic isotope effects that impact methane isotopic signatures ]]> https://biorxiv.org/content/10.64898/2026.04.02.716163v1?rss=1 Gropp, J. Stolper, D. A. Nayak, D. D. 2026-04-06 doi:10.64898/2026.04.02.716163 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ DrugPlayGround: Benchmarking Large Language Models and Embeddings for Drug Discovery ]]> https://biorxiv.org/content/10.64898/2026.04.04.716470v1?rss=1 Liu, T. Jiang, S. Zhang, F. Sun, K. Head-Gordon, T. Zhao, H. 2026-04-07 doi:10.64898/2026.04.04.716470 Cold Spring Harbor Laboratory Press 2026-04-07 <![CDATA[ Septins regulate cytokinesis and multicellular development in the closest living relatives of animals ]]> https://biorxiv.org/content/10.64898/2026.04.05.716596v1?rss=1 Carver, M. King, N. 2026-04-07 doi:10.64898/2026.04.05.716596 Cold Spring Harbor Laboratory Press 2026-04-07 <![CDATA[ Gut microbiome-dependent IL-1 signaling is a mediator of ACVR1R206H-driven heterotopic ossification ]]> https://biorxiv.org/content/10.64898/2026.04.05.716562v1?rss=1 95% of FOP patients harbor the ACVR1R206H mutation, patients exhibit significant variability in disease progression, suggesting a role of environmental drivers. Here, we identify the gut microbiome as a regulator of inflammation-driven HO in FOP. Metagenomic profiling of cohabitating FOP/unaffected sibling pairs revealed a pathogenic gut microbiome profile in FOP patients (Bray-Curtis, p < 0.05). In Pdgfr-Cre/Acvr1R206H (FOP) mice, gut microbiome ablation by antibiotics reduced spontaneous HO formation (47.4% reduction, p < 0.05) and reduced plasma IL-1 pathway activity. IL-1{beta} blockade in FOP mice suppressed trauma-induced HO formation. These findings identify a gut microbiome-IL-1-HO axis with modifiable targets for developing treatments for HO and related inflammatory conditions. One Sentence SummaryAntibiotic disruption of the gut microbiome reduces HO in FOP mice via an IL-1 mediated pathway. ]]> Herzog, H. M. Fang, C. Lam, L. Jin, K. Zamarioli, A. Dinh, E. Gupta, C. L. Sharma, A. Moody, T. Pierce, J. L. Hohl, M. S. Takimoto, S. W. Lyalina, S. Wentworth, K. L. Yu, K. Lu, V. F. Isadora Mamikunian, I. Hunt, N. K. Lynch, S. Pollard, K. S. Hernandez, C. J. Perrien, D. S. Hsiao, E. C. 2026-04-08 doi:10.64898/2026.04.05.716562 Cold Spring Harbor Laboratory Press 2026-04-08 <![CDATA[ Decoding concept representations in aphasia after stroke ]]> https://biorxiv.org/content/10.64898/2026.04.07.717076v1?rss=1 Tang, J. Millanski, C. Chen, A. Wauters, L. D. Anders, J. Shamapant, S. Wilson, S. M. Huth, A. G. Henry, M. 2026-04-08 doi:10.64898/2026.04.07.717076 Cold Spring Harbor Laboratory Press 2026-04-08