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. 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