bioRxiv Channel: Case Western Reserve University https://biorxiv.org This feed contains articles for bioRxiv Channel "Case Western Reserve University" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Are Genetic Interactions Influencing Gene Expression Evidence for Biological Epistasis or Statistical Artifacts? ]]> https://biorxiv.org/content/10.1101/020479v1?rss=1 Alexandra Fish John A. Capra William S Bush 2015-06-05 doi:10.1101/020479 Cold Spring Harbor Laboratory Press 2015-06-05 <![CDATA[ In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River ]]> https://biorxiv.org/content/10.1101/027235v1?rss=1 Matthew Cannon James Hester Amanda Shalkhauser Ernest R Chan Kyle Logue Scott T Small David Serre 2015-09-18 doi:10.1101/027235 Cold Spring Harbor Laboratory Press 2015-09-18 <![CDATA[ QPot: An R Package for Stochastic Differential Equation Quasi-Potential Analysis ]]> https://biorxiv.org/content/10.1101/029777v1?rss=1 Christopher M. Moore Christopher R. Stieha Ben C. Nolting Maria K. Cameron Karen C. Abbott 2015-10-23 doi:10.1101/029777 Cold Spring Harbor Laboratory Press 2015-10-23 <![CDATA[ Reconstitution of CO2 regulation of SLAC1 anion channel and function of CO2-permeable PIP2;1 aquaporin as carbonic anhydrase 4 interactor ]]> https://biorxiv.org/content/10.1101/030296v1?rss=1 Cun Wang Honghong Hu Xue Qin Brian Zeise Danyun Xu Wouter-Jan Rappel Walter F Boron Julian I Schroeder 2015-11-10 doi:10.1101/030296 Cold Spring Harbor Laboratory Press 2015-11-10 <![CDATA[ Discrete step sizes of molecular motors lead to bimodal non-Gaussian velocity distributions under force ]]> https://biorxiv.org/content/10.1101/049064v1?rss=1 Huong Vu Shaon Chakrabarti Michael Hinczewski Dave Thirumalai 2016-04-18 doi:10.1101/049064 Cold Spring Harbor Laboratory Press 2016-04-18 <![CDATA[ Noise Control In Gene Regulatory Networks With Negative Feedback ]]> https://biorxiv.org/content/10.1101/049502v1?rss=1 Michael Hinczewski Dave Thirumalai 2016-04-20 doi:10.1101/049502 Cold Spring Harbor Laboratory Press 2016-04-20 <![CDATA[ Protein Collapse is Encoded in the Folded State Architecture ]]> https://biorxiv.org/content/10.1101/070920v1?rss=1 Himadri S Samanta Pavel Zhuravlev Michael Hinczewski Naoto Hori Shaon Chakrabarti Dave Thirumalai 2016-08-22 doi:10.1101/070920 Cold Spring Harbor Laboratory Press 2016-08-22 <![CDATA[ Alzheimer’s disease pathogenesis is dependent on neuronal receptor PTPσ ]]> https://biorxiv.org/content/10.1101/079806v1?rss=1 Yuanzheng Gu Yaoling Shu Angela Corona Kui Xu Allen F Yi Shannon Chen Man Luo Michel Tremblay Gary E Landreth Randy Nelson Jerry Silver Yingjie Shen 2016-10-07 doi:10.1101/079806 Cold Spring Harbor Laboratory Press 2016-10-07 <![CDATA[ Genome-wide association analyses of sleep disturbance traits identify new loci and highlight shared genetics with neuropsychiatric and metabolic traits ]]> https://biorxiv.org/content/10.1101/082792v1?rss=1 Lane, J. M. Liang, J. Vlasac, I. Anderson, S. G. Bechtold, D. A. Bowden, J. Emsley, R. Gill, S. Little, M. A. Luik, A. I. Loudon, A. Scheer, F. A. J. L. Purcell, S. M. Kyle, S. D. Lawlor, D. A. Zhu, X. Redline, S. Ray, D. W. Rutter, M. K. Saxena, R. 2016-10-24 doi:10.1101/082792 Cold Spring Harbor Laboratory Press 2016-10-24 <![CDATA[ Long-term sustained malaria control leads to inbreeding and fragmentation of Plasmodium vivax populations ]]> https://biorxiv.org/content/10.1101/100610v1?rss=1 Waltmann, A. Koepfli, C. Tessier, N. Karl, S. Darcy, A. Wini, L. Harrison, G. L. A. Barnadas, C. Jannison, C. Karunajeewa, H. Boyd, S. Whittaker, M. Kazura, J. Bahlo, M. Mueller, I. Barry, A. E. 2017-01-15 doi:10.1101/100610 Cold Spring Harbor Laboratory Press 2017-01-15 <![CDATA[ Population dynamics of mutualism and intraspecific density dependence:how θ-logistic-like density dependence affects mutualistic positive feedback ]]> https://biorxiv.org/content/10.1101/108175v1?rss=1 Moore, C. M. Catella, S. A. Abbott, K. C. 2017-02-13 doi:10.1101/108175 Cold Spring Harbor Laboratory Press 2017-02-13 <![CDATA[ Comprehensive Analysis of Constraint on the Spatial Distribution of Missense Variants in Human Protein Structures ]]> https://biorxiv.org/content/10.1101/109652v1?rss=1 Sivley, R. M. Kropski, J. Sheehan, J. Cogan, J. Dou, X. Blackwell, T. S. Phillips, J. A. Meiler, J. Bush, W. S. Capra, J. A. 2017-02-18 doi:10.1101/109652 Cold Spring Harbor Laboratory Press 2017-02-18 <![CDATA[ A common haplotype lowers SPI1 (PU.1) expression in myeloid cells and delays age at onset for Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/110957v1?rss=1 Huang, K.-l. Marcora, E. Pimenova, A. Di Narzo, A. Kapoor, M. Jin, S. C. Harari, O. Bertelsen, S. Fairfax, B. Czajkowski, J. Chouraki, V. Grenier-Boley, B. Bellenguez, C. Deming, Y. McKenzie, A. Raj, T. Renton, A. Budde, J. Smith, A. Fitzpatrick, A. Bis, J. DeStefano, A. Adams, H. Ikram, M. A. van der Lee, S. Del-Aguila, J. Fernandez, M. Ibanez, L. The International Genomics of Alzheimer's Project, The Alzheimer's Disease Neuroimaging Initiative, Sims, R. Escott-Price, V. Mayeux, R. Haines, J. Farrer, L. Pericak-Vance, M. Lambert, J. C. van Duijn, C. L 2017-02-26 doi:10.1101/110957 Cold Spring Harbor Laboratory Press 2017-02-26 <![CDATA[ The mismatch in distributions of vertebrates and the plants that they disperse ]]> https://biorxiv.org/content/10.1101/120485v1?rss=1 Dittel, J. W. Moore, C. M. Vander Wall, S. 2017-03-24 doi:10.1101/120485 Cold Spring Harbor Laboratory Press 2017-03-24 <![CDATA[ De novo BK channel mutation causes epilepsy by regulating voltage-dependent, but not calcium-dependent, activation ]]> https://biorxiv.org/content/10.1101/120543v1?rss=1 Wang, Q. K. Willemsen, M. Li, X. Poschmann, S. Chen, Q. Oundjian, N. J. Snoeijen-Schouwenaars, F. M. Kamsteeg, E.-J. 2017-03-25 doi:10.1101/120543 Cold Spring Harbor Laboratory Press 2017-03-25 <![CDATA[ Spatial Structure Of Synchronized Inhibition In The Olfactory Bulb ]]> https://biorxiv.org/content/10.1101/123695v1?rss=1 Arnson, H. A. Strowbridge, B. 2017-04-03 doi:10.1101/123695 Cold Spring Harbor Laboratory Press 2017-04-03 <![CDATA[ Burst Activation Of Dopamine Neurons Produces Prolonged Post-Burst Availability Of Actively Released Dopamine ]]> https://biorxiv.org/content/10.1101/125062v1?rss=1 20 min) of extracellular dopamine in nucleus accumbens and prefrontal cortex. This elevation is not due to spillover from the stimulation surge but depends on impulse flow-mediated dopamine release. We identified Rho-mediated internalization of dopamine transporter as a mechanism responsible for prolonged availability of actively released dopamine. These results demonstrate that phasic and tonic dopamine neurotransmission can be a continuum and may explain why both modes of signaling are critical for motivational and cognitive functions associated with dopamine. ]]> Lohani, S. Martig, A. Underhill, S. DeFrancesco, A. Roberts, M. Rinaman, L. Amara, S. Moghaddam, B. 2017-04-06 doi:10.1101/125062 Cold Spring Harbor Laboratory Press 2017-04-06 <![CDATA[ Optimal Information Transfer In Enzymatic Networks: A Field Theoretic Formulation ]]> https://biorxiv.org/content/10.1101/130112v1?rss=1 Samanta, H. Hinczewski, M. Thirumalai, D. 2017-04-24 doi:10.1101/130112 Cold Spring Harbor Laboratory Press 2017-04-24 <![CDATA[ Widespread Inter-Chromosomal Epistasis Regulates Glucose Homeostasis And Gene Expression ]]> https://biorxiv.org/content/10.1101/132175v1?rss=1 Chen, A. Yang, L. Williams, S. M. Morris, N. Buchner, D. A. 2017-05-01 doi:10.1101/132175 Cold Spring Harbor Laboratory Press 2017-05-01 <![CDATA[ Ccr4 And Pop2 Control Poly(A) Tail Length In Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/140202v1?rss=1 Balagopal, V. Bolisetty, M. Al Husaini, N. Coller, J. Graveley, B. R. 2017-05-19 doi:10.1101/140202 Cold Spring Harbor Laboratory Press 2017-05-19 <![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[ Positively Selected Enhancer Elements Endow Tumor Cells with MetastaticCompetence ]]> https://biorxiv.org/content/10.1101/155416v1?rss=1 Morrow, J. J. Bayles, I. Funnell, A. Miller, T. Saiakhova, A. Lizardo, M. Bartels, C. Kapteijn, M. Hung, S. Mendoza, A. Chee, D. Myers, J. Allen, F. Gambarotti, M. Righi, A. DiFeo, A. Rubin, B. Huang, A. Meltzer, P. Helman, L. Picci, P. Versteeg, H. Stamatoyannopoulos, J. Khanna, C. Scacheri, P. 2017-06-25 doi:10.1101/155416 Cold Spring Harbor Laboratory Press 2017-06-25 <![CDATA[ CD55 regulates self-renewal and cisplatin resistance in endometrioid tumors ]]> https://biorxiv.org/content/10.1101/155887v1?rss=1 Saygin, C. Wiechert, A. Rao, V. S. Alluru, R. Connor, E. Thiagarajan, P. S. Hale, J. S. Li, Y. Chumakova, A. Jarrar, A. Parker, Y. Lindner, D. J. Nagaraj, A. B. Kim, J. J. DiFeo, A. Abdul-Karim, F. W. Michener, C. Rose, P. G. DeBernardo, R. Mahdi, H. McCrae, K. R. Lin, F. Lathia, J. D. Reizes, O. 2017-06-27 doi:10.1101/155887 Cold Spring Harbor Laboratory Press 2017-06-27 <![CDATA[ Modulation of Ether-a-go-go related gene (ERG) current governs intrinsic persistent activity in rodent neocortical pyramidal cells ]]> https://biorxiv.org/content/10.1101/156075v1?rss=1 Cui, E. D. Strowbridge, B. 2017-06-26 doi:10.1101/156075 Cold Spring Harbor Laboratory Press 2017-06-26 <![CDATA[ Distinct epigenetic shift in a subset of Glioma CpG island methylator phenotype (G-CIMP) during tumor recurrence ]]> https://biorxiv.org/content/10.1101/156646v1?rss=1 de Souza, C. F. Sabedot, T. S. Malta, T. M. Stetson, L. Morozova, O. Sokolov, A. Laird, P. W. Wiznerowicz, M. Iavarone, A. Snyder, J. deCarvalho, A. C. Sanborn, Z. McDonald, K. L. Friedman, W. A. Tirapelli, D. Poisson, L. Mikkelsen, T. Carlotti, C. G. Kalkanis, S. N. Zenklusen, J. C. Salama, S. R. Barnholtz-Sloan, J. S. Noushmehr, H. 2017-06-28 doi:10.1101/156646 Cold Spring Harbor Laboratory Press 2017-06-28 <![CDATA[ Recapitulating bone development for tissue regeneration through engineered mesenchymal condensations and mechanical cues ]]> https://biorxiv.org/content/10.1101/157362v1?rss=1 McDermott, A. M. Herberg, S. Mason, D. E. Pearson, H. B. Dawahare, J. H. Collins, J. M. Grinstaff, M. W. Kelly, D. J. Alsberg, E. Boerckel, J. D. 2017-06-29 doi:10.1101/157362 Cold Spring Harbor Laboratory Press 2017-06-29 <![CDATA[ The RNA-binding site of poliovirus 3C protein doubles as a phosphoinositide-binding domain ]]> https://biorxiv.org/content/10.1101/172742v1?rss=1 Shengjuler, D. Chan, Y. M. Sun, S. Moustafa, I. M. Li, Z.-L. Gohara, D. W. Buck, M. Cremer, P. S. Boehr, D. D. Cameron, C. E. 2017-08-04 doi:10.1101/172742 Cold Spring Harbor Laboratory Press 2017-08-04 <![CDATA[ SPIN1 promotes tumorigenesis by blocking the uL18-MDM2-p53 pathway ]]> https://biorxiv.org/content/10.1101/177881v1?rss=1 Fang, Z. Liao, J.-M. Cao, B. Deng, J. Plummer, K. D. Liao, P. Liu, T. Zeng, S. X. Xiong, J. Lu, H. 2017-08-18 doi:10.1101/177881 Cold Spring Harbor Laboratory Press 2017-08-18 <![CDATA[ A "Tug of War" maintains a dynamic protein-membrane complex: MD simulations of C-Raf RBD-CRD bound to K-Ras4B at an anionic membrane ]]> https://biorxiv.org/content/10.1101/181347v1?rss=1 LI, Z. Srivastava, P. P. Buck, M. 2017-08-27 doi:10.1101/181347 Cold Spring Harbor Laboratory Press 2017-08-27 <![CDATA[ Inhibition of Intracellular Lipolysis Promotes Cancer Cell Adaptation to Hypoxia ]]> https://biorxiv.org/content/10.1101/181503v1?rss=1 Zhang, X. Saarinen, A. M. Hitosugi, T. Wang, Z. Wang, L. Ho, T. H. Liu, J. 2017-08-28 doi:10.1101/181503 Cold Spring Harbor Laboratory Press 2017-08-28 <![CDATA[ Collateral sensitivity is contingent on the repeatability of evolution ]]> https://biorxiv.org/content/10.1101/185892v1?rss=1 Nichol, D. Rutter, J. Bryant, C. Jeavons, P. Anderson, A. Bonomo, R. Scott, J. 2017-09-07 doi:10.1101/185892 Cold Spring Harbor Laboratory Press 2017-09-07 <![CDATA[ A simplified electronic circuit for combined single-cell stimulation and recording using loose cell-attached electrodes ]]> https://biorxiv.org/content/10.1101/191718v1?rss=1 Strowbridge, B. W. Pressler, R. T. 2017-09-20 doi:10.1101/191718 Cold Spring Harbor Laboratory Press 2017-09-20 <![CDATA[ Enhancers mapping uncovers phenotypic heterogeneity and evolution in patients with luminal breast cancer. ]]> https://biorxiv.org/content/10.1101/193771v1?rss=1 Patten, D. Corleone, G. Gyorffy, B. Erdos, E. Saiakhova, A. Goddard, K. Vingiani, A. Shousha, S. Pongor, L. S. Hadjiminas, D. Schiavon, G. Barry, P. Palmieri, C. Coombes, C. Scacheri, P. Pruneri, G. Magnani, L. 2017-09-26 doi:10.1101/193771 Cold Spring Harbor Laboratory Press 2017-09-26 <![CDATA[ Predicting cancer outcomes from histology and genomics using convolutional networks ]]> https://biorxiv.org/content/10.1101/198010v1?rss=1 Mobadersany, P. Yousefi, S. Amgad, M. Gutman, D. A. Barnholtz-Sloan, J. S. Velazquez Vega, J. E. Brat, D. J. Cooper, L. A. D. 2017-10-03 doi:10.1101/198010 Cold Spring Harbor Laboratory Press 2017-10-03 <![CDATA[ Therapeutic Targeting of 15-PGDH in Murine Idiopathic Pulmonary Fibrosis ]]> https://biorxiv.org/content/10.1101/2019.12.16.878215v1?rss=1 Smith, J. N. P. Witkin, M. D. Jogasuria, A. P. Christo, K. F. Raffay, T. M. Markowitz, S. D. Desai, A. B. 2019-12-18 doi:10.1101/2019.12.16.878215 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ Global analysis reveals complex demographic responses of mammals to climate change ]]> https://biorxiv.org/content/10.1101/2019.12.16.878348v1?rss=1 Paniw, M. James, T. Archer, C. R. Roemer, G. Levin, S. Compagnoni, A. Che-Castaldo, J. Bennett, J. M. Mooney, A. Childs, D. Z. Ozgul, A. Jones, O. R. Burns, J. H. Beckerman, A. P. Patwary, A. Sanchez-Gassen, N. Knight, T. M. Salguero-Gomez, R. 2019-12-17 doi:10.1101/2019.12.16.878348 Cold Spring Harbor Laboratory Press 2019-12-17 <![CDATA[ Contrast-enhanced ultrasound with sub-micron sized contrast agents detects insulitis and beta-cell mass decline in mouse models of type 1 diabetes ]]> https://biorxiv.org/content/10.1101/2019.12.20.885327v1?rss=1 Ramirez, D. G. Abenojar, E. Hernandez, C. Papazian, L. A. Passman, S. Pham, V. Exner, A. A. Benninger, R. K. K. 2019-12-23 doi:10.1101/2019.12.20.885327 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ Prostatic osteopontin expression is associated with symptomatic benign prostatic hyperplasia ]]> https://biorxiv.org/content/10.1101/2019.12.23.887612v1?rss=1 Popovics, P. Awadallah, W. N. Kohrt, S. Case, T. C. Miller, N. L. Ricke, E. Huang, W. Ramirez-Solano, M. Liu, Q. Vezina, C. M. Matusik, R. J. Ricke, W. A. Grabowska, M. M. 2019-12-26 doi:10.1101/2019.12.23.887612 Cold Spring Harbor Laboratory Press 2019-12-26 <![CDATA[ NFIA regulates granule recruitment and exocytosis in the adult pancreas ]]> https://biorxiv.org/content/10.1101/2019.12.24.885020v1?rss=1 Scavuzzo, M. A. Chmielowiec, J. Teaw, J. Yang, D. Hill, M. C. Waksmunski, A. R. Duraine, L. Camunas-Soler, J. Dai, X. King, J. C. Quake, S. R. MacDonald, P. E. Catic, A. Borowiak, M. 2019-12-26 doi:10.1101/2019.12.24.885020 Cold Spring Harbor Laboratory Press 2019-12-26 <![CDATA[ Human Tau Isoform Aggregation and Selective Detection of Misfolded Tau from Post-Mortem Alzheimer's Disease Brains ]]> https://biorxiv.org/content/10.1101/2019.12.31.876946v1?rss=1 Wu, L. Wang, Z. Lad, S. Dougharty, D. Madhavan, S. Marcus, M. Henderson, F. Ray, W. K. Tan, C. Siedlak, S. Li, J. Helm, R. F. Zhu, X. Bloom, G. S. Zou, W. Xu, B. 2020-01-02 doi:10.1101/2019.12.31.876946 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ Myosin X interaction with KIF13B, a crucial pathway for Netrin-1-induced axonal development ]]> https://biorxiv.org/content/10.1101/2020.01.06.896100v1?rss=1 Yu, H.-L. Peng, Y. Zhao, Y. Lan, Y.-S. Wang, B. Zhao, L. Sun, D. Pan, J.-X. Dong, Z. Mei, L. Ding, Y.-Q. Zhu, X.-J. Xiong, W.-C. 2020-01-06 doi:10.1101/2020.01.06.896100 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ TCF-1 regulates the stem-like memory potential of HIV-specific CD8+ T cells in elite controllers ]]> https://biorxiv.org/content/10.1101/2020.01.07.894535v1?rss=1 Rutishauser, R. L. Deguit, C. D. T. Hiatt, J. Blaeschke, F. Roth, T. L. Wang, L. Raymond, K. Starke, C. E. Mudd, J. C. Chen, W. Smullin, C. Matus-Nicodemos, R. Hoh, R. Krone, M. Hecht, F. M. Pilcher, C. D. Martin, J. N. Koup, R. A. Douek, D. C. Brenchley, J. M. Sekaly, R.-P. Pillai, S. K. Marson, A. Deeks, S. G. McCune, J. M. Hunt, P. W. 2020-01-08 doi:10.1101/2020.01.07.894535 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Investigating the impact of combination phage and antibiotic therapy: a modeling study ]]> https://biorxiv.org/content/10.1101/2020.01.08.899476v1?rss=1 Banuelos, S. Gulbudak, H. Horn, M. A. Huang, Q. Nandi, A. Ryu, H. Segal, R. 2020-01-09 doi:10.1101/2020.01.08.899476 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Calcium-independent astrocytic lipid release modulates neuronal activity through Kv channels ]]> https://biorxiv.org/content/10.1101/2020.01.12.903393v1?rss=1 Wang, F. Bradshaw, H. B. Jablonska, B. Pena, S. E. Xavier, J. Gong, S. Li, B. Chandler-Militello, D. Bekar, L. K. Smith, N. A. 2020-01-13 doi:10.1101/2020.01.12.903393 Cold Spring Harbor Laboratory Press 2020-01-13 <![CDATA[ Sources of Off-Target Effects of Vagus Nerve Stimulation Using the Helical Clinical Lead in Domestic Pigs ]]> https://biorxiv.org/content/10.1101/2020.01.15.907246v1?rss=1 10 mA) and human studies (<250 {micro}A). After removing muscle-generated artifacts, ENG signals with post-stimulus latencies consistent with A{delta}- and B-fibers occurred in only a small subset of animals, and these signals had similar thresholds to those that caused bradycardia. By identifying specific neuroanatomical pathways that cause off-target effects and characterizing the stimulation dose-response curves for on- and off-target effects, we hope to guide interpretation and optimization of clinical VNS. ]]> Nicolai, E. N. Settell, M. L. Knudsen, B. E. McConico, A. L. Gosink, B. A. Trevathan, J. K. Baumgart, I. W. Ross, E. K. Pelot, N. A. Grill, W. M. Gustafson, K. J. Shoffstall, A. J. Williams, J. C. Ludwig, K. A. 2020-01-15 doi:10.1101/2020.01.15.907246 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Cyclodextrin polymer coatings resist protein fouling, mammalian cell adhesion, and bacterial attachment ]]> https://biorxiv.org/content/10.1101/2020.01.16.909564v1?rss=1 Learn, G. D. Lai, E. J. von Recum, H. A. 2020-01-17 doi:10.1101/2020.01.16.909564 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ Computational estimates of mechanical constraints on cell migration through extracellular matrix ]]> https://biorxiv.org/content/10.1101/2020.01.19.912006v1?rss=1 Maxian, O. Mogilner, A. Strychalski, W. 2020-01-20 doi:10.1101/2020.01.19.912006 Cold Spring Harbor Laboratory Press 2020-01-20 <![CDATA[ A Drosophila model of oral peptide therapeutics for adult intestinal stem cell tumors ]]> https://biorxiv.org/content/10.1101/2020.01.21.913806v1?rss=1 Bajpai, A. Ahmad, Q. T. Hong-Wen Tang, H.-W. Manzar, N. Singh, V. Thakur, A. Ateeq, B. Perrimon, N. Sinha, P. 2020-01-22 doi:10.1101/2020.01.21.913806 Cold Spring Harbor Laboratory Press 2020-01-22 <![CDATA[ The Effect of Kinship in Re-identification Attacks Against Genomic Data Sharing Beacons ]]> https://biorxiv.org/content/10.1101/2020.01.30.926907v1?rss=1 Aysen, M. Ayday, E. Cicek, A. E. 2020-01-31 doi:10.1101/2020.01.30.926907 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ A large cross-ancestry meta-analysis of genome-wide association studies identifies 69 novel risk loci for primary open-angle glaucoma and includes a genetic link with Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2020.01.30.927822v1?rss=1 Gharahkhani, P. Jorgenson, E. Hysi, P. Khawaja, A. P. Pendergrass, S. Han, X. Ong, J. S. Hewitt, A. W. Segre, A. Igo, R. P. Choquet, H. Qassim, A. Josyula, N. S. Cooke Bailey, J. N. Bonnemaijer, P. Iglesias, A. Siggs, O. M. Young, T. Vitart, V. Thiadens, A. A. H. J. Karjalainen, J. Uebe, S. Melles, R. B. Nair, S. Luben, R. Simcoe, M. Amersinghe, N. Cree, A. J. Hohn, R. Poplawski, A. Chen, L. J. Cheng, C.-Y. Vithana, E. N. NEIGHBORHOOD consortium, ANZRAG consortium, Biobank Japan project, FinnGen study, UK Biobank Eye and Vision Consortium, GIGA s 2020-02-03 doi:10.1101/2020.01.30.927822 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ Engineering Selective Molecular Tethers to Enhance Suboptimal Drug Properties ]]> https://biorxiv.org/content/10.1101/2020.02.01.929356v1?rss=1 Dogan, A. B. von Recum, H. A. 2020-02-02 doi:10.1101/2020.02.01.929356 Cold Spring Harbor Laboratory Press 2020-02-02 <![CDATA[ Impact of immediate cryopreservation on the establishment of patient derived xenografts from head and neck cancer patients. ]]> https://biorxiv.org/content/10.1101/2020.02.03.930891v1?rss=1 Abel, L. Durmaz, A. Hu, R. Longhurst, C. Scott, J. G. Kimple, R. J. 2020-02-04 doi:10.1101/2020.02.03.930891 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Identifying states of collateral sensitivity during the evolution of therapeutic resistance in Ewings sarcoma ]]> https://biorxiv.org/content/10.1101/2020.02.11.943936v1?rss=1 Scarborough, J. A. McClure, E. Anderson, P. Dhawan, A. Durmaz, A. Lessnick, S. L. Hitomi, M. Scott, J. G. 2020-02-12 doi:10.1101/2020.02.11.943936 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ MCT2 Overexpression Rescues Metabolic Vulnerability and Protects Retinal Ganglion Cells in Two Models of Glaucoma ]]> https://biorxiv.org/content/10.1101/2020.02.14.950097v1?rss=1 Harun-Or-Rashid, M. Pappenhagen, N. Zubricky, R. Coughlin, L. Jassim, A. H. Inman, D. M. 2020-02-15 doi:10.1101/2020.02.14.950097 Cold Spring Harbor Laboratory Press 2020-02-15 <![CDATA[ High-throughput discovery of trafficking-deficient variants in the cardiac potassium channel KCNH2 ]]> https://biorxiv.org/content/10.1101/2020.02.17.952606v1?rss=1 Kozek, K. A. Glazer, A. M. Ng, C.-A. Blackwell, D. J. Egly, C. L. Vanags, L. R. Blair, M. A. Mitchell, D. W. Matreyek, K. A. Fowler, D. Knollmann, B. C. Vandenberg, J. I. Roden, D. M. Kroncke, B. M. 2020-02-17 doi:10.1101/2020.02.17.952606 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ Myeloid-derived suppressor cell subsets drive glioblastoma growth in a sex-specific manner ]]> https://biorxiv.org/content/10.1101/2020.02.19.954552v1?rss=1 Bayik, D. Zhou, Y. Park, C. Hong, C. Vail, D. Silver, D. J. Lauko, A. J. Roversi, G. A. Watson, D. C. Lo, A. Alban, T. J. McGraw, M. Sorensen, M. D. Grabowski, M. M. Otvos, B. Vogelbaum, M. A. Horbinski, C. M. Kristensen, B. W. Khalil, A. M. Hwang, T. H. Ahluwalia, M. S. Cheng, F. Lathia, J. 2020-02-20 doi:10.1101/2020.02.19.954552 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Genetic Variants and Functional Pathways Associated with Resilience to Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2020.02.19.954651v1?rss=1 0.42) nor associated with APOE (p-values>0.13). In single variant analyses, we observed a genome-wide significant locus among participants with normal cognition on chromosome 18 upstream of ATP8B1 (index SNP rs2571244, MAF=0.08, p=2.3x10-8). The top variant at this locus (rs2571244) was significantly associated with methylation in prefrontal cortex tissue at multiple CpG sites, including one just upstream of ATPB81 (cg19596477; p=2x10-13). Overall, this comprehensive genetic analysis of resilience implicates a putative role of vascular risk, metabolism, and mental health in protection from the cognitive consequences of neuropathology, while also providing evidence for a novel resilience gene along the bile acid metabolism pathway. Furthermore, the genetic architecture of resilience appears to be distinct from that of clinical AD, suggesting that a shift in focus to molecular contributors to resilience may identify novel pathways for therapeutic targets. ]]> Dumitrescu, L. Mahoney, E. R. Mukherjee, S. Lee, M. L. Bush, W. S. Engelman, C. D. Lu, Q. Fardo, D. W. Trittschuh, E. H. Mez, J. Kaczorowski, C. Hernandez Saucedo, H. Widaman, K. F. Buckley, R. Properzi, M. Mormina, E. Yang, H.-S. Harrison, T. Hedden, T. Nho, K. Andrews, S. J. Tommet, D. Hadad, N. Sanders, R. E. Ruderfer, D. M. Gifford, K. A. Moore, A. M. Cambronero, F. Zhong, X. Raghavan, N. S. Vardarajan, B. The Alzheimer's Disease Neuroimaging Initiative (ADNI), Alzheimer's Disease Genetics Consortium (ADGC), A4 Study Team, Pericak-Vance, M. A. Farre 2020-02-21 doi:10.1101/2020.02.19.954651 Cold Spring Harbor Laboratory Press 2020-02-21 <![CDATA[ SR-B1 uptake of HDL promotes prostate cancer proliferation and tumor progression ]]> https://biorxiv.org/content/10.1101/2020.02.24.963454v1?rss=1 Traughber, C. A. Opoku, E. Brubaker, G. Major, J. Lu, H. Lorkowski, S. W. Neumann, C. Hardaway, A. Chung, Y.-M. Gulshan, K. Sharifi, N. Brown, J. M. Smith, J. D. 2020-02-26 doi:10.1101/2020.02.24.963454 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ Genome wide-association study identifies novel loci in the Primary Open-Angle African American Glaucoma Genetics (POAAGG) study ]]> https://biorxiv.org/content/10.1101/2020.02.27.968156v1?rss=1 Gudiseva, H. V. Verma, S. S. Chavali, V. R. M. Salowe, R. Lucas, A. Collins, D. W. Rathi, S. He, J. Lee, R. Merriam, S. Bowman, A. S. mchugh, c. p. Zody, M. C. Pistilli, M. Khachatryan, N. Ebenezer, D. Windell, M. Weiner, M. Henderer, J. Ross, A. Cui, Q. N. Addis, V. Lehman, A. Miller-Ellis, E. Sankar, P. Varma, R. Williams, S. M. Ying, G.-S. Moore, J. H. Ritchie, M. D. O'Brien, J. M. 2020-02-28 doi:10.1101/2020.02.27.968156 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ Increased APOEϵ4 expression is associated with reactive A1 astrocytes and the difference in Alzheimer Disease risk from diverse ancestral backgrounds ]]> https://biorxiv.org/content/10.1101/2020.03.09.983817v1?rss=1 Griswold, A. J. Celis, K. Bussies, P. Rajabli, F. Whitehead, P. Hamilton-Nelson, K. Beecham, G. W. Dykxhoorn, D. M. Nuytemans, K. Wang, L. Gardner, O. K. Dorfsman, D. Bigio, E. H. Mesulam, M.-M. Weintraub, S. Geula, C. Gearing, M. Martinez-McGrath, E. Dalgard, C. L. Scott, W. K. Haines, J. L. Pericak-Vance, M. A. Young, J. I. Vance, J. M. 2020-03-11 doi:10.1101/2020.03.09.983817 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Small Molecule Targeting IRES Domain Inhibits Enterovirus 71 Replication via an Allosteric Mechanism that Stabilizes a Ternary Complex ]]> https://biorxiv.org/content/10.1101/2020.03.10.981167v1?rss=1 Davila-Calderon, J. Patwardhan, N. N. Chiu, L.-Y. Sugarman, A. L. Cai, Z. Penutmutchu, S. R. Li, M.-L. Brewer, G. Hargrove, A. E. Tolbert, B. S. 2020-03-11 doi:10.1101/2020.03.10.981167 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Patterns of 'Analytical Irreproducibility' in Multimodal Diseases ]]> https://biorxiv.org/content/10.1101/2020.03.22.002469v1?rss=1 Basson, A. R. Cominelli, F. Rodriguez-Palacios, A. 2020-03-25 doi:10.1101/2020.03.22.002469 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Identification of genes required for enzalutamide resistance in castration-resistant prostate cancer cells in vitro ]]> https://biorxiv.org/content/10.1101/2020.03.27.011825v1?rss=1 Kohrt, S. E. Awadallah, W. N. Phillips, R. A. Case, T. C. Jin, R. Nanda, J. S. Yu, X. Clark, P. E. Yi, Y. Matusik, R. J. Anderson, P. D. Grabowska, M. M. 2020-03-27 doi:10.1101/2020.03.27.011825 Cold Spring Harbor Laboratory Press 2020-03-27 <![CDATA[ High-resolution Structures of multiple 5-HT3AR-setron complexes reveal a novel mechanism of competitive inhibition ]]> https://biorxiv.org/content/10.1101/2020.03.30.016154v1?rss=1 Basak, S. Kumar, A. Ramsey, S. Gibbs, E. Kapoor, A. Filizola, M. Chakrapani, S. 2020-04-01 doi:10.1101/2020.03.30.016154 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ SLX4IP-mediated telomere maintenance is essential for androgen receptor-independent castration-resistant prostate cancer ]]> https://biorxiv.org/content/10.1101/2020.03.31.018846v1?rss=1 Mangosh, T. L. Awadallah, W. N. Grabowska, M. M. Taylor, D. J. 2020-04-01 doi:10.1101/2020.03.31.018846 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Ecology and molecular targets of hypermutation in the global microbiome. ]]> https://biorxiv.org/content/10.1101/2020.04.01.020958v1?rss=1 30,000 metagenome-derived DGRs, and determine that DGRs have a single evolutionary origin and a universal bias towards adenine mutations. We further identified six major lineages of DGRs, each associated with a specific ecological niche defined as a genome type, i.e. whether the DGR is encoded on a viral or cellular genome, a limited set of taxa and environments, and a distinct type of target. Finally, we leverage read mapping and metagenomic time series to demonstrate that DGRs are consistently and broadly active, and responsible for >10% of all amino acid changes in some organisms at a conservative estimate. Overall, these results highlight the strong constraints under which DGRs diversify and expand, and elucidate several distinct roles these elements play in natural communities and in shaping microbial community structure and function in our environment. ]]> Roux, S. Paul, B. G. Bagby, S. C. Allen, M. A. Attwood, G. Cavicchioli, R. Chistoserdova, L. Hallam, S. Hernandez, M. E. Hess, M. Liu, W.-T. O'Malley, M. A. Peng, X. Rich, V. I. Saleska, S. Eloe-Fadrosh, E. A. 2020-04-02 doi:10.1101/2020.04.01.020958 Cold Spring Harbor Laboratory Press 2020-04-02 <![CDATA[ Non-Canonical Targets of HIF1a Drive Cell-Type-Specific Dysfunction ]]> https://biorxiv.org/content/10.1101/2020.04.03.003632v1?rss=1 Allan, K. C. Hu, L. R. Morton, A. R. Scavuzzo, M. A. Gevorgyan, A. S. Clayton, B. L. L. Bederman, I. Hung, S. Bartels, C. F. Madhavan, M. Tesar, P. J. 2020-04-04 doi:10.1101/2020.04.03.003632 Cold Spring Harbor Laboratory Press 2020-04-04 <![CDATA[ Nonmedical Masks in Public for Respiratory Pandemics: Droplet Retention by two-layer Textile Barrier Fully Protects Germ-free Mice from Bacteria in Droplets ]]> https://biorxiv.org/content/10.1101/2020.04.06.028688v1?rss=1 600 bacterial droplet units per 56.75cm2) compared to the contamination of mice not protected by a textile (0/12 vs 6/6, Fishers exact, p<0.0001). In a second phase of the experiment with 12 germ-free mice exposed again to 10-fold more droplets remained germ-free, while 100% of mice at 180cm became colonized with a single spray (0/8 vs 4/4, Fisher exact, p=0.002). Collectively, barriers protected all mice (even with low-density textiles, heavy vs. light fabric, T-test, p=0.0028) when using textile-EDB to cover the cages (0/20 vs 10/10, Fisher exact, p<0.0001). This study demonstrated, in vivo, that widely available household textiles are 100% effective at preventing contamination of the environment and the exposed animals by microbe-carrying droplets. ]]> Rodriguez-Palacios, A. Conger, M. Cominelli, F. 2020-04-10 doi:10.1101/2020.04.06.028688 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ Inhibition of 15-PGDH Protects Mice from Immune-mediated Bone Marrow Failure ]]> https://biorxiv.org/content/10.1101/2020.04.07.030312v1?rss=1 Smith, J. N. P. Otegbeye, F. Jogasuria, A. Christo, K. F. Gerson, S. L. Markowitz, S. D. Desai, A. B. 2020-04-09 doi:10.1101/2020.04.07.030312 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Revealing heritability missed by single locus analyses by examining epistasis in mouse chromosome substitution strains ]]> https://biorxiv.org/content/10.1101/2020.04.10.034637v1?rss=1 Miller, A. K. Chen, A. Bartlett, J. Wang, L. Williams, S. Buchner, D. A. 2020-04-10 doi:10.1101/2020.04.10.034637 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ Integration of IL-2 and IL-4 Signals Coordinates Divergent Regulatory T cell Responses and Drives Therapeutic Efficacy ]]> https://biorxiv.org/content/10.1101/2020.04.14.040485v1?rss=1 Zhou, J. Y. Alvarez, C. A. Cobb, B. A. 2020-04-14 doi:10.1101/2020.04.14.040485 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates ]]> https://biorxiv.org/content/10.1101/2020.04.16.045302v1?rss=1 Damas, J. Hughes, G. M. Keough, K. C. Painter, C. A. Persky, N. S. Corbo, M. Hiller, M. Koepfli, K.-P. Pfenning, A. R. Zhao, H. Genereux, D. P. Swofford, R. Pollard, K. S. Ryder, O. A. Nweeia, M. T. Lindblad-Toh, K. Teeling, E. C. Karlsson, E. K. Lewin, H. A. 2020-04-18 doi:10.1101/2020.04.16.045302 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Cadherin-6 mediates thrombosis in vivo ]]> https://biorxiv.org/content/10.1101/2020.04.20.051045v1?rss=1 Bouck, E. G. de la Fuente, M. Zunica, E. R. Li, W. Mumaw, M. M. Nieman, M. T. 2020-04-21 doi:10.1101/2020.04.20.051045 Cold Spring Harbor Laboratory Press 2020-04-21 <![CDATA[ Pleiotropy-guided transcriptome imputation from normal and tumor tissues identifies new candidate susceptibility genes for breast and ovarian cancer ]]> https://biorxiv.org/content/10.1101/2020.04.23.043653v1?rss=1 1 Mb away from known breast and/or ovarian cancer susceptibility loci. We also identified 38 candidate breast cancer susceptibility genes and 17 candidate ovarian cancer susceptibility genes at conjunction FDR < 0.05 at known breast and/or ovarian susceptibility loci. Overlaying candidate causal risk variants identified by GWAS fine mapping onto expression prediction models for genes at known loci suggested that the association for 55% of these genes was driven by the underlying GWAS signal. SignificanceThe 22 new genes identified by our cross-cancer analysis represent promising candidates that further elucidate the role of the transcriptome in mediating germline breast and ovarian cancer risk. ]]> Kar, S. Considine, D. Tyrer, J. Plummer, J. Chen, S. Dezem, F. Barbeira, A. Rajagopal, P. Rosenow, W. Anton, F. Bodelon, C. Chang-Claude, J. Chenevix-Trench, G. deFazio, A. Doerk, T. Ekici, A. Ewing, A. Fountzilas, G. Goode, E. Hartman, M. Heitz, F. Hillemanns, P. Hogdall, E. Hogdall, C. Huzarski, T. Jensen, A. Karlan, B. Khusnutdinova, E. Kiemeney, L. Kjaer, S. Klapdor, R. Kobel, M. Li, J. Liebrich, C. May, T. Olsson, H. Permuth, J. Peterlongo, P. Radice, P. Ramus, S. Riggan, M. Saloustros, E. Simard, J. Szafron, L. Thompson, C. Vierkant, R. Winha 2020-04-24 doi:10.1101/2020.04.23.043653 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Targeting Thymidine Phosphorylase with Tipiracil Hydrochloride is a Safe and Effective Antithrombotic Therapy ]]> https://biorxiv.org/content/10.1101/2020.04.25.061234v1?rss=1 Zulfiker, A. H. M. Belcher, A. Li, O. Yue, H. Sen Gupta, A. Li, W. 2020-04-27 doi:10.1101/2020.04.25.061234 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ Robust Inference of Kinase Activity using Functional Networks ]]> https://biorxiv.org/content/10.1101/2020.05.01.062802v1?rss=1 Yilmaz, S. Ayati, M. Schlatzer, D. Cicek, A. E. Chance, M. Koyuturk, M. 2020-05-05 doi:10.1101/2020.05.01.062802 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Co-Phosphorylation Networks Reveal Subtype-Specific Signaling Modules in Breast Cancer ]]> https://biorxiv.org/content/10.1101/2020.05.04.073148v1?rss=1 Ayati, M. Chance, M. R. Koyuturk, M. 2020-05-05 doi:10.1101/2020.05.04.073148 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ The kinetic landscape of an RNA binding protein in cells ]]> https://biorxiv.org/content/10.1101/2020.05.11.089102v1?rss=1 Sharma, D. Zagore, L. L. Brister, M. M. Ye, X. Crespo-Hernández, C. E. Licatalosi, D. Jankowsky, E. 2020-05-13 doi:10.1101/2020.05.11.089102 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ Human follicular CD4 T cell function is defined by specific molecular, positional and TCR dynamic signatures. ]]> https://biorxiv.org/content/10.1101/2020.05.12.089706v1?rss=1 Padhan, K. Moysi, E. Noto, A. Chassiakos, A. Ghneim, K. Shah, S. Papaioannou, V. Fabozzi, G. Ambrozak, D. Poultsidi, A. Ioannou, M. Fenwik, C. Darko, S. Douek, D. C. Sekaly, R.-P. Pantaleo, G. Koup, R. A. Petrovas, C. 2020-05-13 doi:10.1101/2020.05.12.089706 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ Naturally acquired blocking human monoclonal antibodies to Plasmodium vivax reticulocyte binding protein 2b ]]> https://biorxiv.org/content/10.1101/2020.05.12.091900v1?rss=1 Chan, L.-J. Gandhirajan, A. Carias, L. L. Dietrich, M. H. Vadas, O. Visentin, R. Franca, C. T. Menant, S. Soldati-Favre, D. Mueller, I. King, C. L. Tham, W.-H. 2020-05-13 doi:10.1101/2020.05.12.091900 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ An autoregulatory switch in sex-specific phf7 transcription causes loss of sexual identity and tumors in the Drosophila female germline ]]> https://biorxiv.org/content/10.1101/2020.05.13.093344v1?rss=1 Smolko, A. Shapiro-Kulnane, L. Salz, H. 2020-05-15 doi:10.1101/2020.05.13.093344 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Barrett's esophagus is the precursor of all esophageal adenocarcinomas ]]> https://biorxiv.org/content/10.1101/2020.05.14.096826v1?rss=1 Curtius, K. Rubenstein, J. H. Chak, A. Inadomi, J. M. 2020-05-16 doi:10.1101/2020.05.14.096826 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Multi-ancestry genome-wide gene-sleep interactions identify novel loci for blood pressure ]]> https://biorxiv.org/content/10.1101/2020.05.29.123505v1?rss=1 Wang, H. Noordam, R. Cade, B. E. Schwander, K. Winkler, T. W. Lee, J. Sung, Y. J. Bentley, A. R. Manning, A. K. Aschard, H. Kilpelainen, T. O. Ilkov, M. Brown, M. R. Horimoto, A. R. Richard, M. Bartz, T. M. Vojinovic, D. Lim, E. Nierenberg, J. L. Liu, Y. Chitrala, K. Rankinen, T. Musani, S. K. Franceschini, N. Rauramaa, R. Alver, M. Zee, P. Harris, S. E. van der Most, P. J. Nolte, I. M. Munroe, P. B. Palmer, N. D. Kuhnel, B. Weiss, S. Wen, W. Hall, K. A. Lyytikainen, L.-P. O'Connell, J. R. Eiriksdottir, G. Launer, L. J. de Vries, P. S. Arking, D. Chen, 2020-05-31 doi:10.1101/2020.05.29.123505 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ The neural representation of force across grasp types in motor cortex of humans with tetraplegia ]]> https://biorxiv.org/content/10.1101/2020.06.01.126755v1?rss=1 Rastogi, A. Willett, F. R. Abreu, J. Crowder, D. C. Murphy, B. Memberg, W. D. Vargas-Irwin, C. E. Miller, J. P. Sweet, J. Walter, B. L. Rezaii, P. G. Stavisky, S. D. Hochberg, L. R. Shenoy, K. V. Henderson, J. M. Kirsch, R. F. Ajiboye, A. B. 2020-06-02 doi:10.1101/2020.06.01.126755 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ Complement factor C4a does not activate protease activated receptor 1 (PAR1) or PAR4 on human platelets. ]]> https://biorxiv.org/content/10.1101/2020.06.01.127662v1?rss=1 Han, X. de la Fuente, M. Nieman, M. T. 2020-06-02 doi:10.1101/2020.06.01.127662 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ Multifactorial and closed head impact traumatic brain injuries cause distinct tactile hypersensitivity profiles ]]> https://biorxiv.org/content/10.1101/2020.06.01.127944v1?rss=1 Wattiez, A.-S. Castonguay, W. C. Gaul, O. J. Waite, J. S. Schmidt, C. M. Reis, A. S. Rea, B. J. Sowers, L. P. Cintron-Perez, C. J. Vazquez-Rosa, E. Pieper, A. A. Russo, A. F. 2020-06-02 doi:10.1101/2020.06.01.127944 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ Development and Characterization of Patient-Derived Xenografts from Non-Small Cell Lung Cancer Brain Metastases ]]> https://biorxiv.org/content/10.1101/2020.06.02.130062v1?rss=1 Baschnagel, A. M. Kaushik, S. Durmaz, A. Goldstein, S. Ong, I. M. Abel, L. Clark, P. A. Leal, T. Buehler, D. Iyer, G. Scott, J. G. Kimple, R. J. 2020-06-03 doi:10.1101/2020.06.02.130062 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Density Dependent Resource Budget Model for Alternate Bearing ]]> https://biorxiv.org/content/10.1101/2020.06.15.148924v1?rss=1 Esmaeili, S. Hastings, A. Abbott, K. Machta, J. Reddy Nareddy, V. 2020-06-16 doi:10.1101/2020.06.15.148924 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ Structure of a dominant negative mutant reveals a stalled intermediate in anthrax protective antigen pore maturation ]]> https://biorxiv.org/content/10.1101/2020.06.15.152231v1?rss=1 Scott, H. Huang, W. Ganti, S. Zhang, K. Mehzabeen, N. Day, A. Battaile, K. P. Lovell, S. G. Bann, J. Taylor, D. J. 2020-06-15 doi:10.1101/2020.06.15.152231 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Combining genome-wide studies of breast, prostate, ovarian and endometrial cancers maps cross-cancer susceptibility loci and identifies new genetic associations ]]> https://biorxiv.org/content/10.1101/2020.06.16.146803v1?rss=1 1Mb from previously identified risk loci for the four cancers and an additional 23 lead variant-cancer associations were novel for one of the cancers. Bayesian models supported pleiotropic effects involving at least two cancers at 222/465 lead variants in 118/192 regions. Gene-level association analysis identified 13 shared susceptibility genes (P<2.6x10-6) in 13 regions not previously implicated in any of the four cancers and not uncovered by our variant-level meta-analysis. Several lead variants had opposite effects across cancers, including a cluster of such variants in the TP53 pathway. Fifty-four lead variants were associated with blood cell traits and suggested genetic overlaps with clonal hematopoiesis. Our study highlights the remarkable pervasiveness of pleiotropy across hormone-related cancers, further illuminating their shared genetic and mechanistic origins at variant- and gene-level resolution. ]]> Kar, S. P. Lindstroem, S. Hung, R. Lawrenson, K. Schmidt, M. O'Mara, T. Glubb, D. Tyrer, J. Schildkraut, J. Chang-Claude, J. Alsulimani, A. Anton, F. Beeghly-Fadiel, A. Bjorge, L. Bodelon, C. Brauch, H. Burghaus, S. Campa, D. Carney, M. Chen, Z. Daly, M. du Bois, A. Ekici, A. Ewing, A. Fasching, P. Flanagan, J. M. Gawelko, J. Giles, G. Hamilton, R. Harris, H. Heitz, F. Hildebrandt, M. Hillemanns, P. Huang, R.-Y. Imaz, L. Irmejs, A. Jakubowska, A. Jensen, A. John, E. Kannisto, P. Karlan, B. Khusnutdinova, E. Kiemeney, L. Kjaer, S. Klapdor, R. Kleiblo 2020-06-19 doi:10.1101/2020.06.16.146803 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Short-lived plants have stronger demographic responses to climate ]]> https://biorxiv.org/content/10.1101/2020.06.18.160135v1?rss=1 Compagnoni, A. Levin, S. Childs, D. Z. Harpole, S. Paniw, M. Romer, G. Burns, J. H. Che-Castaldo, J. Rueger, N. Kunstler, G. Bennett, J. M. Archer, R. Jones, O. R. Salguero-Gomez, R. Knight, T. M. 2020-06-20 doi:10.1101/2020.06.18.160135 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Integrating deep learning with microfluidics for biophysical classification of sickle red blood cells ]]> https://biorxiv.org/content/10.1101/2020.07.01.181545v1?rss=1 Praljak, N. Iram, S. Goreke, U. Singh, G. Hill, A. Gurkan, U. A. Hinczewski, M. 2020-07-04 doi:10.1101/2020.07.01.181545 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Detection of complex genetic architecture using two-locus population differentiation: modeling epistasis ]]> https://biorxiv.org/content/10.1101/2020.07.01.182840v1?rss=1 Huang, M. Graham, B. Zhang, G. Bartlett, J. Moore, J. Muglia, L. Williams, S. M. 2020-07-01 doi:10.1101/2020.07.01.182840 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Modeling of collaterally sensitive drug cycles, and optimization of the drug effect in the spirit of adaptive therapy ]]> https://biorxiv.org/content/10.1101/2020.07.02.184952v1?rss=1 Yoon, N. Krishnan, N. P. Scott, J. G. 2020-07-03 doi:10.1101/2020.07.02.184952 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ Vascular dimorphism ensured by regulated proteoglycan dynamics favors rapid umbilical artery closure at birth ]]> https://biorxiv.org/content/10.1101/2020.07.02.184978v1?rss=1 Nandadasa, S. Szafron, J. M. Pathak, V. Murtada, S.-I. Craft, C. M. O'Donnell, A. Norvik, C. Hughes, C. Caterson, B. Domowicz, M. S. Schwartz, N. B. Tran-Lundmark, K. Veigl, M. Sedwick, D. Philipson, E. H. Humphrey, J. D. Apte, S. S. 2020-07-03 doi:10.1101/2020.07.02.184978 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ Astroglial Calcium Signaling Encodes Sleep Need in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.07.04.187906v1?rss=1 Blum, I. D. Keles, M. F. Baz, E.-S. Han, E. Park, K. Luu, S. Issa, H. Brown, M. Ho, M. C. W. Tabuchi, M. Liu, S. Wu, M. 2020-07-05 doi:10.1101/2020.07.04.187906 Cold Spring Harbor Laboratory Press 2020-07-05 <![CDATA[ Tau conformers in FTLD-MAPT undergo liquid-liquid phase separation and perturb the nuclear envelope ]]> https://biorxiv.org/content/10.1101/2020.07.04.187997v1?rss=1 Kang, S.-G. Han, Z. Z. Daude, N. McNamara, E. Wohlgemuth, S. Safar, J. G. Mok, S.-A. Westaway, D. 2020-07-05 doi:10.1101/2020.07.04.187997 Cold Spring Harbor Laboratory Press 2020-07-05 <![CDATA[ Spatial odor discrimination in hawkmoth, Manduca sexta (L.) ]]> https://biorxiv.org/content/10.1101/2020.07.08.194126v1?rss=1 70%. The information about spatial distribution of odor stimuli is thus available to moths searching for odor sources, opening the possibility that they use both spatial and temporal odor information. ]]> P. Kalyanasundaram M. A. Willis 2020-07-10 doi:10.1101/2020.07.08.194126 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ A role for protease activated receptor type 3 (PAR3) in nociception demonstrated through development of a novel peptide agonist ]]> https://biorxiv.org/content/10.1101/2020.07.08.194373v1?rss=1 Juliet Mwirigi Moeno Kume Shayne N Hassler Ayesha Ahmad Pradipta R. Ray Changyu Jiang Alexander Chamessian Nakleh Mseeh Breya P Ludwig Benjamin D. Rivera Marvin T Nieman Thomas Van de Ven Ru-Rong Ji Gregory Dussor Scott Boitano Josef Vagner Theodore J Price 2020-07-10 doi:10.1101/2020.07.08.194373 Cold Spring Harbor Laboratory Press 2020-07-10 <![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[ A three-dimensional musculoskeletal model of the dog ]]> https://biorxiv.org/content/10.1101/2020.07.16.205856v1?rss=1 Stark, H. Fischer, M. S. Hunt, A. Young, F. Quinn, R. Andrada, E. 2020-07-16 doi:10.1101/2020.07.16.205856 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ Dynamical Ising model of spatially-coupled ecological oscillators ]]> https://biorxiv.org/content/10.1101/2020.07.17.209296v1?rss=1 Nareddy, V. R. Machta, J. Abbott, K. C. Esmaeili, S. Hastings, A. 2020-07-17 doi:10.1101/2020.07.17.209296 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Biallelic mutation of CLRN2 causes non-syndromic hearing loss in humans ]]> https://biorxiv.org/content/10.1101/2020.07.29.222828v1?rss=1 A, NM_001079827.2) segregating with the disease. Using in vitro RNA splicing analysis, we show that the CLRN2 c.494C>A mutation leads to two events: 1) the substitution of a highly conserved threonine (uncharged amino acid) to lysine (charged amino acid) at position 165, p.(Thr165Lys), and 2) aberrant splicing, with the retention of intron 2 resulting in a stop codon after 26 additional amino acids, p.(Gly146Lysfs*26). Expression studies and phenotyping of newly produced zebrafish and mouse models deficient for clarin 2 further confirm that clarin 2, expressed in the inner ear hair cells, is essential for normal organization and maintenance of the auditory hair bundles, and for hearing function. Together, our findings identify CLRN2 as a new deafness gene, which will impact future diagnosis and treatment for deaf patients. ]]> Vona, B. Mazaheri, N. Lin, S.-J. Dunbar, L. A. Maroofian, R. Azaiez, H. Booth, K. T. Vitry, S. Rad, A. Varshney, P. Fowler, B. Alagramam, K. N. Murphy, D. Shariati, G. Sedaghat, A. Houlden, H. VijayKumar, S. Smith, R. J. H. Haaf, T. El-Amraoui, A. Bowl, M. R. Varshney, G. K. Galehdari, H. 2020-07-29 doi:10.1101/2020.07.29.222828 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Antibiofilm activity of Fmoc-phenylalanine against Gram-positive and Gram-negative bacterial biofilms ]]> https://biorxiv.org/content/10.1101/2020.08.03.232629v1?rss=1 Singh, H. Gahane, A. Y. Singh, V. Ghosh, S. Thakur, A. K. 2020-08-03 doi:10.1101/2020.08.03.232629 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Plasmodium falciparum increases its investment in gametocytes in the wet season in asymptomatic individuals ]]> https://biorxiv.org/content/10.1101/2020.08.04.236950v1?rss=1 Aduma, C. O. Ogolla, S. Atieli, H. Ondigo, B. N. Lee, M.-C. Githeko, A. Dent, A. E. Kazura, J. W. Yan, G. Koepfli, C. 2020-08-05 doi:10.1101/2020.08.04.236950 Cold Spring Harbor Laboratory Press 2020-08-05 <![CDATA[ A comparison of non-magnetic and magnetic beads for measuring IgG antibodies against P. vivax antigens in a multiplexed bead-based assay using Luminex(R) technology (Bio-Plex(R)200 or MAGPIX(R)) ]]> https://biorxiv.org/content/10.1101/2020.08.10.243980v1?rss=1 Mazhari, R. Brewster, J. Fong, R. Bourke, C. Liu, Z. S. Takashima, E. Tsuboi, T. Tham, W.-H. Harbers, M. Chitnis, C. Healer, J. Ome-Kaius, M. Sattabongkot, J. Kazura, J. Robinson, L. King, C. Mueller, I. Longley, R. 2020-08-10 doi:10.1101/2020.08.10.243980 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Proteome-scale Analysis of Vertebrate Protein Thermoadaptation Modulated by Dynamic Allostery And Protein Solvation ]]> https://biorxiv.org/content/10.1101/2020.08.10.244558v1?rss=1 LI, Z. Buck, M. 2020-08-11 doi:10.1101/2020.08.10.244558 Cold Spring Harbor Laboratory Press 2020-08-11 <![CDATA[ The identity of human tissue-emigrant CD8+ T cells ]]> https://biorxiv.org/content/10.1101/2020.08.11.236372v1?rss=1 Buggert, M. Vella, L. A. Nguyen, S. Wu, V. Sekine, T. Perez-Potti, A. Maldini, C. R. Manne, S. Darko, S. Ransier, A. Kuri-Cervantes, L. Sada Japp, A. Bukh Brody, I. Ivarsson, M. A. Hertwig, L. Antel, J. P. Johnson, M. E. Okoye, A. Picker, L. J. Vahedi, G. Sparrelid, E. Llewellyn-Lacey, S. Gostick, E. Bjorkstrom, N. K. Bar-Or, A. Dori, Y. Naji, A. Canaday, D. Laufer, T. M. Wells, A. D. Price, D. Frank, I. Douek, D. Wherry, E. J. Itkin, M. G. Betts, M. R. 2020-08-11 doi:10.1101/2020.08.11.236372 Cold Spring Harbor Laboratory Press 2020-08-11 <![CDATA[ In a nutshell, a reciprocal transplant experiment reveals local adaptation and fitness trade-offs in response to urban evolution in an acorn-dwelling ant ]]> https://biorxiv.org/content/10.1101/2020.08.21.251025v1?rss=1 Martin, R. A. Chick, L. D. Garvin, M. L. Diamond, S. E. 2020-08-24 doi:10.1101/2020.08.21.251025 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ The receptor binding domain of SARS-CoV-2 spike is the key target of neutralizing antibody in human polyclonal sera. ]]> https://biorxiv.org/content/10.1101/2020.08.21.261727v1?rss=1 Steffen, T. Stone, E. T. Hassert, M. Geerling, E. Grimberg, B. T. Espino, A. M. Pantoja, P. Climent, C. Hoft, D. F. George, S. L. Sariol, C. A. Pinto, A. K. Brien, J. D. 2020-08-22 doi:10.1101/2020.08.21.261727 Cold Spring Harbor Laboratory Press 2020-08-22 <![CDATA[ Frequency shapes the quality of tactile percepts evoked through electrical stimulation of the nerves ]]> https://biorxiv.org/content/10.1101/2020.08.24.263822v1?rss=1 Graczyk, E. L. Christie, B. P. He, Q. Tyler, D. J. Bensmaia, S. J. 2020-08-24 doi:10.1101/2020.08.24.263822 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Role of channels in the oxygen permeability of red blood cells ]]> https://biorxiv.org/content/10.1101/2020.08.28.265066v1?rss=1 Zhao, P. Geyer, R. R. Salameh, A. I. Wass, A. B. Taki, S. Huffmann, D. E. Meyerson, H. J. Occhipinti, R. Moss, F. J. Boron, W. F. 2020-08-28 doi:10.1101/2020.08.28.265066 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ Pocket MUSE: an affordable, versatile and high performance fluorescence microscope using a smartphone ]]> https://biorxiv.org/content/10.1101/2020.08.28.273094v1?rss=1 Liu, Y. Rollins, A. M. Levenson, R. M. Fereidouni, F. Jenkins, M. W. 2020-08-31 doi:10.1101/2020.08.28.273094 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ INPP5D expression is associated with risk for Alzheimer's disease and induced by plaque-associated microglia ]]> https://biorxiv.org/content/10.1101/2020.08.31.276444v1?rss=1 Tsai, A. P.-Y. Lin, P. B.-C. Dong, C. Moutinho, M. Casali, B. T. Liu, Y. Lamb, B. T. Landreth, G. E. Oblak, A. L. Nho, K. 2020-08-31 doi:10.1101/2020.08.31.276444 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Privacy-Preserving and Robust Watermarking on Sequential Genome Data using Belief Propagation and Local Differential Privacy ]]> https://biorxiv.org/content/10.1101/2020.09.04.283135v1?rss=1 Oksuz, A. C. Ayday, E. Gudukbay, U. 2020-09-06 doi:10.1101/2020.09.04.283135 Cold Spring Harbor Laboratory Press 2020-09-06 <![CDATA[ Asprosin Neutralizing Antibodies as a Treatment for Metabolic Syndrome ]]> https://biorxiv.org/content/10.1101/2020.09.15.298489v1?rss=1 Mishra, I. Duerrschmid, C. Ku, Z. Xie, W. Silva, E. S. Hoffman, J. Zhang, N. An, Z. Chopra, A. 2020-09-16 doi:10.1101/2020.09.15.298489 Cold Spring Harbor Laboratory Press 2020-09-16 <![CDATA[ Baricitinib treatment resolves lower airway inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques ]]> https://biorxiv.org/content/10.1101/2020.09.16.300277v1?rss=1 Hoang, T. N. Pino, M. Boddapati, A. K. Viox, E. G. Starke, C. E. Upadhyay, A. A. Gumber, S. Busman-Sahay, K. Strongin, Z. Harper, J. L. Tharp, G. K. Pellegrini, K. L. Kirejczyk, S. Zandi, K. Tao, S. Horton, T. R. Beagle, E. N. Mahar, E. A. Lee, M. Y. Cohen, J. Jean, S. Wood, J. S. Connor-Stroud, F. Stammen, R. L. Delmas, O. M. Wang, S. Cooney, K. A. Sayegh, M. N. Wang, L. Weiskopf, D. Filev, P. D. Waggoner, J. Piantadosi, A. Kasturi, S. P. Al-Shakhshir, H. Ribeiro, S. P. Sekaly, R. P. Levit, R. D. Estes, J. D. Vanderford, T. H. Schinazi, R. F. Bosinger, 2020-09-16 doi:10.1101/2020.09.16.300277 Cold Spring Harbor Laboratory Press 2020-09-16 <![CDATA[ 15-PGDH Inhibition Activates the Splenic Niche to Promote Hematopoietic Regeneration ]]> https://biorxiv.org/content/10.1101/2020.09.17.302422v1?rss=1 Smith, J. N. P. Dawson, D. M. Christo, K. F. Jogasuria, A. P. Cameron, M. J. Antczak, M. I. Ready, J. M. Gerson, S. L. Markowitz, S. D. Desai, A. B. 2020-09-18 doi:10.1101/2020.09.17.302422 Cold Spring Harbor Laboratory Press 2020-09-18 <![CDATA[ AlzGPS: A Genome-wide Positioning Systems Platform to Catalyze Multi-omics for Alzheimer's Therapeutic Discovery ]]> https://biorxiv.org/content/10.1101/2020.09.17.302612v1?rss=1 Zhou, Y. Fang, J. Bekris, L. Kim, Y. H. Pieper, A. A. Leverenz, J. B. Cummings, J. Cheng, F. 2020-09-20 doi:10.1101/2020.09.17.302612 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ Comprehensive characterization of protein-protein interaction network perturbations by human disease mutations ]]> https://biorxiv.org/content/10.1101/2020.09.18.302588v1?rss=1 Cheng, F. Zhao, J. Wang, Y. Lu, W. Liu, Z. Zhou, Y. Martin, W. Wang, R. Huang, J. Hao, T. Yue, H. Ma, J. Hou, Y. Castrillon, J. Fang, J. Lathia, J. D. Keri, R. A. Lightstone, F. C. Antman, E. M. Rabadan, R. Hill, D. E. Eng, C. Vidal, M. Loscalzo, J. 2020-09-21 doi:10.1101/2020.09.18.302588 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ Altered lipid metabolism marks glioblastoma stem and non-stem cells in separate tumor niches ]]> https://biorxiv.org/content/10.1101/2020.09.20.304964v1?rss=1 Shakya, S. Gromovsky, A. Hale, J. Knudsen, A. Prager, B. Wallace, L. Penalva, L. O. Ivanova, P. Brown, H. A. Kristensen, B. Rich, J. Lathia, J. Brown, J. M. Hubert, C. G. 2020-09-20 doi:10.1101/2020.09.20.304964 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ Microbial metabolites of flavanols in urine are associated with enhanced anti-proliferative activity in bladder cancer cells in vitro ]]> https://biorxiv.org/content/10.1101/2020.09.22.308056v1?rss=1 Griffin, L. E. Kohrt, S. E. Rathore, A. Kay, C. D. Grabowska, M. M. Neilson, A. P. 2020-09-23 doi:10.1101/2020.09.22.308056 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Multimodal single-cell/nucleus RNA-sequencing data analysis uncovers molecular networks between disease-associated microglia and astrocytes with implications for drug repurposing in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2020.09.23.310466v1?rss=1 Xu, J. Zhang, P. Huang, Y. Bekris, L. Lathia, J. Chiang, C.-W. Li, L. Pieper, A. A. Leverenz, J. B. Cummings, J. Cheng, F. 2020-09-23 doi:10.1101/2020.09.23.310466 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ A mouse model of Bardet-Biedl Syndrome has impaired fear memory, which is rescued by lithium treatment ]]> https://biorxiv.org/content/10.1101/2020.10.06.322883v1?rss=1 Pak, T. K. Carter, C. S. Zhang, Q. Huang, S. C. Searby, C. Hsu, Y. Taugher, R. Vogel, T. Cychosz, C. C. Genova, R. Moreira, N. Stevens, H. Wemmie, J. Pieper, A. A. Wang, K. K. Sheffield, V. C. 2020-10-07 doi:10.1101/2020.10.06.322883 Cold Spring Harbor Laboratory Press 2020-10-07 <![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[ Elucidating the viral and host factors enabling the cross-species transmission of primate lentiviruses from simians to humans ]]> https://biorxiv.org/content/10.1101/2020.10.13.337303v1?rss=1 Tebit, D. Nickel, G. Gibson, R. Carpenter, C. Rodriguez, M. Hathaway, N. Bain, K. Reyes-Rodriguez, A. Bonogo, J. Canaday, D. McDonald, D. Bailey, J. Arts, E. 2020-10-13 doi:10.1101/2020.10.13.337303 Cold Spring Harbor Laboratory Press 2020-10-13 <![CDATA[ Septate junction proteins are required for egg elongation and border cell migration during oogenesis in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.10.19.346064v1?rss=1 Alhadyian, H. Shoaib, D. Ward, R. E. 2020-10-19 doi:10.1101/2020.10.19.346064 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ LPA/PKD-1 signaling promotes development of arteriolar niche that supports self-renewal of breast cancer stem cells and stemness ]]> https://biorxiv.org/content/10.1101/2020.10.22.351122v1?rss=1 Jiang, Y. Guo, Y. Hao, J. Guenter, R. Lathia, J. Beck, A. W. Hattaway, R. Hurst, D. Wang, Q. J. Liu, Y. Cao, Q. Krontiras, H. Chen, H. Silverstein, R. L. Ren, B. 2020-10-22 doi:10.1101/2020.10.22.351122 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ Ultrastructural view of astrocyte-astrocyte and astrocyte-synapse contacts within the hippocampus ]]> https://biorxiv.org/content/10.1101/2020.10.28.358200v1?rss=1 Kiyoshi, C. M. Aten, S. Arzola, E. P. Patterson, J. A. Taylor, A. T. Du, Y. Guiher, A. M. Philip, M. Camacho, E. G. Mediratta, D. Collins, K. Benson, E. Kidd, G. Terman, D. Zhou, M. 2020-10-28 doi:10.1101/2020.10.28.358200 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Gene-by-environment interactions in agricultural pest management: population effects on diet-Bt interactions in a caterpillar ]]> https://biorxiv.org/content/10.1101/2020.10.30.361170v1?rss=1 Deans, C. A. Sword, G. A. Behmer, S. Burkness, E. Pusztai-Carey, M. Hutchison, W. 2020-10-30 doi:10.1101/2020.10.30.361170 Cold Spring Harbor Laboratory Press 2020-10-30 <![CDATA[ Dermal EZH2 simultaneously orchestrates Wnt/β-catenin signaling dependent dermal differentiation and retinoic acid signaling dependent epidermal proliferation during murine skin development ]]> https://biorxiv.org/content/10.1101/2020.11.01.364216v1?rss=1 THULABANDU, V. Nehila, T. Ferguson, J. Atit, R. 2020-11-01 doi:10.1101/2020.11.01.364216 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ Lymphocyte-Specific Biomarkers Associated with Preterm Birth and Bronchopulmonary Dysplasia ]]> https://biorxiv.org/content/10.1101/2020.11.03.367201v1?rss=1 Bhattacharya, S. Mereness, J. Baran, A. Misra, R. Peterson, D. Ryan, R. Reynolds, A. M. Pryhuber, G. Mariani, T. J. 2020-11-04 doi:10.1101/2020.11.03.367201 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ Predicting Drug Interactions to Unassociated Biomedical Implants Using Machine Learning Techniques and Model Polymers ]]> https://biorxiv.org/content/10.1101/2020.11.10.374900v1?rss=1 Kerner, J. J. von Recum, H. 2020-11-11 doi:10.1101/2020.11.10.374900 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ Non-Invasive Plasma Glycomic and Metabolic Biomarkers of Post-treatment Control of HIV ]]> https://biorxiv.org/content/10.1101/2020.11.11.378174v1?rss=1 Giron, L. B. Palmer, C. S. Yin, X. Emmanouil, P. Damra, M. Goldman, A. R. Tang, H. Y. Johnston, R. Mounzer, K. Kostman, J. R. Tebas, P. Landay, A. Montaner, L. J. Jacobson, J. M. Li, J. Abdel-Mohsen, M. 2020-11-11 doi:10.1101/2020.11.11.378174 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ Proximity Measures as Graph Convolution Matrices for Link Prediction in Biological Networks ]]> https://biorxiv.org/content/10.1101/2020.11.14.382655v1?rss=1 Coskun, M. Koyuturk, M. 2020-11-16 doi:10.1101/2020.11.14.382655 Cold Spring Harbor Laboratory Press 2020-11-16 <![CDATA[ Genomic landscapes of canine splenic angiosarcoma (hemangiosarcoma) contain extensive heterogeneity within and between patients ]]> https://biorxiv.org/content/10.1101/2020.11.15.380048v1?rss=1 Wong, S. Ehrhart, E. Stewart, S. Zismann, V. Cawley, J. Halperin, R. Briones, N. Richter, K. Sivaprakasam, K. Perdigones, N. Contente-Cuomo, T. Facista, S. Trent, J. M. Murtaza, M. Khanna, C. Hendricks, W. P. D. 2020-11-17 doi:10.1101/2020.11.15.380048 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ Genomic analyses of high-grade neuroendocrine gynecological malignancies reveal a unique mutational landscape and therapeutic vulnerabilities ]]> https://biorxiv.org/content/10.1101/2020.11.17.387514v1?rss=1 Mahdi, H. Joehlin-Price, A. Dowlati, A. Abbas, A. 2020-11-19 doi:10.1101/2020.11.17.387514 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ Cancer cells are sensitive to wild-type IDH1 inhibition under nutrient limitation ]]> https://biorxiv.org/content/10.1101/2020.11.19.390633v1?rss=1 Vaziri-Gohar, A. Hue, J. J. Graor, H. J. Prendergast, E. Chen, V. Cassel, J. Mohammed, F. S. Abbas, A. Dukleska, K. Khokhar, I. Hajhassani, O. Zarei, M. Wang, R. Rothermel, L. D. Bederman, I. Browers, J. Getts, R. Brunengraber, H. Salvino, J. M. Brody, J. R. Winter, J. M. 2020-11-20 doi:10.1101/2020.11.19.390633 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ DNA polymerase theta suppresses mitotic crossing over ]]> https://biorxiv.org/content/10.1101/2020.11.27.400952v1?rss=1 Carvajal-Garcia, J. Crown, K. N. Ramsden, D. A. Sekelsky, J. 2020-11-27 doi:10.1101/2020.11.27.400952 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ MACE2K: A Text-Mining Tool to Extract Literature-based Evidence for Variant Interpretation using Machine Learning ]]> https://biorxiv.org/content/10.1101/2020.12.03.409094v1?rss=1 Gupta, S. Rao, S. Miglani, T. Iyer, Y. Lin, J. Saiyed, A. M. Ikwuemesi, I. McNulty, S. Thaxton, C. Madhavan, S. 2020-12-04 doi:10.1101/2020.12.03.409094 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ Leveraging Affinity Interactions to Prolong Drug Delivery of Protein Therapeutics ]]> https://biorxiv.org/content/10.1101/2020.12.03.410621v1?rss=1 View larger version (15K): org.highwire.dtl.DTLVardef@25ad06org.highwire.dtl.DTLVardef@1827b8eorg.highwire.dtl.DTLVardef@17dd798org.highwire.dtl.DTLVardef@d54d55_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Dogan, A. B. Dabkowski, K. von Recum, H. 2020-12-04 doi:10.1101/2020.12.03.410621 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures ]]> https://biorxiv.org/content/10.1101/2020.12.05.409821v1?rss=1 Zafferani, M. Haddad, C. Luo, L. Davila-Calderon, J. Yuan-Chiu, L. Shema Mugisha, C. Monaghan, A. G. Kennedy, A. A. Yesselman, J. D. Gifford, R. R. Tai, A. W. Kutluay, S. B. Li, M.-L. Brewer, G. Tolbert, B. S. Hargrove, A. E. 2020-12-06 doi:10.1101/2020.12.05.409821 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Heartbeats entrain breathing via baroreceptor-mediated modulation of expiratory activity ]]> https://biorxiv.org/content/10.1101/2020.12.09.416776v1?rss=1 Barnett, W. H. Baekey, D. M. Paton, J. F. R. Dick, T. E. Wehrwein, E. A. Molkov, Y. I. 2020-12-11 doi:10.1101/2020.12.09.416776 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ The biophysical basis of protein domain compatibility in ion channels ]]> https://biorxiv.org/content/10.1101/2020.12.09.418442v1?rss=1 Coyote-Maestas, W. Nedrud, D. Suma, A. He, Y. Matreyek, K. A. Fowler, D. M. Carnevale, V. Myers, C. L. Schmidt, D. 2020-12-10 doi:10.1101/2020.12.09.418442 Cold Spring Harbor Laboratory Press 2020-12-10 <![CDATA[ Uncovering complementary sets of variants for the prediction of quantitative phenotypes ]]> https://biorxiv.org/content/10.1101/2020.12.11.419952v1?rss=1 Yilmaz, S. Fakhouri, M. Koyuturk, M. Cicek, A. E. Tastan, O. 2020-12-12 doi:10.1101/2020.12.11.419952 Cold Spring Harbor Laboratory Press 2020-12-12 <![CDATA[ Circadian rhythms in bipolar disorder patient-derived neurons predict lithium response ]]> https://biorxiv.org/content/10.1101/2020.12.14.422616v1?rss=1 Mishra, H. K. Ying, N. M. Luis, A. Wei, H. Nguyen, M. Nakhla, T. Vandenburgh, S. Alda, M. Berrettini, W. H. Brennand, K. J. Calabrese, J. R. Coryell, W. H. Frye, M. A. Gage, F. H. Gershon, E. S. McInnis, M. G. Nievergelt, C. M. Nurnberger, J. I. Shilling, P. D. Oedegaard, K. J. Zandi, P. P. The Pharmacogenomics of Bipolar Disorder Study, Kelsoe, J. R. Welsh, D. K. McCarthy, M. J. 2020-12-15 doi:10.1101/2020.12.14.422616 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Multiple Temporal and Semantic Processes During Verbal Fluency Tasks in English-Russian Bilinguals ]]> https://biorxiv.org/content/10.1101/2020.12.14.422659v1?rss=1 Lerner, A. Crough, M. Lenio, S. Woyczynski, W. Lissemore, F. M. 2020-12-14 doi:10.1101/2020.12.14.422659 Cold Spring Harbor Laboratory Press 2020-12-14 <![CDATA[ Cryo-EM structure of amyloid fibrils formed by the entire low complexity domain of TDP-43 ]]> https://biorxiv.org/content/10.1101/2020.12.14.422689v1?rss=1 Li, Q. Babinchak, W. M. Surewicz, W. K. 2020-12-15 doi:10.1101/2020.12.14.422689 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Microbiome and Metabolome driven differentiation of TGF-β producing Tregs leads to Senescence and HIV latency ]]> https://biorxiv.org/content/10.1101/2020.12.15.422949v1?rss=1 Sekaly, R.-P. Ghneim, K. Sharma, A. A. Ribeiro, S. P. Fourati, S. Ahlers, J. Kulpa, D. Xu, X. Brehm, J. Talla, A. Arumugam, S. Darko, S. Rodriguez, B. Shive, C. Cristescu, R. Loboda, A. Balderas, R. Wang, I.-m. Hunt, P. Lamarre, D. Douek, D. Hazuda, D. Lederman, M. Deeks, S. 2020-12-15 doi:10.1101/2020.12.15.422949 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Real time, field-deployable whole genome sequencing of malaria parasites using nanopore technology ]]> https://biorxiv.org/content/10.1101/2020.12.17.423341v1?rss=1 Razook, Z. Mehra, S. Gilchhrist, B. Utama, D. Lautu-Gumal, D. Fola, A. Menard, D. Kazura, J. Laman, M. Mueller, I. Robinson, L. Bahlo, M. Barry, A. E. 2020-12-21 doi:10.1101/2020.12.17.423341 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ A higher burden of multiple sclerosis genetic risk confers an earlier onset ]]> https://biorxiv.org/content/10.1101/2020.12.18.423477v1?rss=1 Misicka, E. Davis, M. Kim, W. Brugger, S. W. Beales, J. Loomis, S. Bronson, P. G. Briggs, F. B. S. 2020-12-21 doi:10.1101/2020.12.18.423477 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ Low force unfolding of a single-domain protein by parallel pathways ]]> https://biorxiv.org/content/10.1101/2020.12.19.423596v1?rss=1 Zhuravlev, P. I. Hinczewski, M. Thirumalai, D. 2020-12-20 doi:10.1101/2020.12.19.423596 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ 15-PGDH as a Negative Regulator of Age-Related Organ Fitness ]]> https://biorxiv.org/content/10.1101/2020.12.22.424017v1?rss=1 Ho, W. J. Smith, J. N. P. Park, Y. S. Hadiono, M. Christo, K. F. Jogasuria, A. Zhang, Y. Broncano, A. V. Kasturi, L. Dawson, D. M. Gerson, S. L. Markowitz, S. D. Desai, A. B. 2020-12-22 doi:10.1101/2020.12.22.424017 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Multi-Modal Biomarkers of Cerebral Edema in Low Resolution MRI ]]> https://biorxiv.org/content/10.1101/2020.12.23.424020v1?rss=1 Tu, D. Goyal, M. S. Dworkin, J. D. Kampondeni, S. Vidal, L. Biondo-Savin, E. Juvvadi, S. Raghavan, P. Nicholas, J. Chetcuti, K. Clark, K. Satterthwaite, T. D. Yushkevich, P. Davatzikos, C. Erus, G. Postels, D. G. Taylor, T. E. Small, D. S. Shinohara, R. T. 2020-12-25 doi:10.1101/2020.12.23.424020 Cold Spring Harbor Laboratory Press 2020-12-25 <![CDATA[ In vivo visualization of pig vagus nerve 'vagotopy' using ultrasound ]]> https://biorxiv.org/content/10.1101/2020.12.24.424256v1?rss=1 Settell, M. L. Kasole, M. Skubal, A. C. Knudsen, B. E. Nicolai, E. N. Huang, C. Zhou, C. Trevathan, J. K. Pelot, N. A. Grill, W. M. Upadhye, A. Kolluru, C. Shoffstall, A. J. Williams, J. C. Suminski, A. J. Chen, S. Ludwig, K. A. 2020-12-24 doi:10.1101/2020.12.24.424256 Cold Spring Harbor Laboratory Press 2020-12-24 <![CDATA[ Computationally-efficient spatiotemporal correlation analysis super-resolves anomalous diffusion ]]> https://biorxiv.org/content/10.1101/2020.12.26.424447v1?rss=1 Yoshida, S. Schmid, W. Vo, N. Calabrase, W. Kisley, L. 2020-12-27 doi:10.1101/2020.12.26.424447 Cold Spring Harbor Laboratory Press 2020-12-27 <![CDATA[ Defective NETs Clearance contributes to sustained FXII Activation in COVID-19-associated Pulmonary Thrombo-Inflammation ]]> https://biorxiv.org/content/10.1101/2020.12.29.424644v1?rss=1 Frye, M. Englert, H. Rangaswamy, C. Deppermann, C. Sperhake, J.-P. Krisp, C. Schreier, D. Gordon, E. Konrath, S. Haddad, M. Pula, G. Mailer, R. Schlueter, H. Langer, F. Pueschel, K. Panousis, K. Stavrou, E. Maas, C. Renne, T. 2020-12-29 doi:10.1101/2020.12.29.424644 Cold Spring Harbor Laboratory Press 2020-12-29 <![CDATA[ Glycolysis downregulation is a hallmark of HIV-1 latency and sensitizes infected cells to oxidative stress ]]> https://biorxiv.org/content/10.1101/2020.12.30.424810v1?rss=1 Shytaj, I. L. Procopio, F. A. Tarek, M. Carlon-Andres, I. Tang, H.-Y. Goldman, A. R. Munshi, M. Forcato, M. Leskov, K. Ye, F. Lucic, B. Cruz, N. Singh, A. Bicciato, S. Padilla-Parra, S. Lusic, M. Diaz, R. S. Alvarez-Carbonell, D. Savarino, A. 2020-12-31 doi:10.1101/2020.12.30.424810 Cold Spring Harbor Laboratory Press 2020-12-31 <![CDATA[ Allosteric communication in Class A β-lactamases occurs via Cooperative Coupling of Loop Dynamics ]]> https://biorxiv.org/content/10.1101/2020.12.30.424904v1?rss=1 Galdadas, I. Qu, S. Oliveira, A. S. F. Olehnovics, E. Mack, A. R. Mojica, M. F. Agarwal, P. K. Tooke, C. L. Gervasio, F. L. Spencer, J. Bonomo, R. A. Mulholland, A. J. Haider, S. 2021-01-01 doi:10.1101/2020.12.30.424904 Cold Spring Harbor Laboratory Press 2021-01-01 <![CDATA[ Neuropilin-1 Assists SARS-CoV-2 Infection by Stimulating the Separation of Spike Protein Domains S1 and S2 ]]> https://biorxiv.org/content/10.1101/2021.01.06.425627v1?rss=1 Li, Z. Buck, M. 2021-01-07 doi:10.1101/2021.01.06.425627 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Molecular dynamics simulations and functional studies reveal that hBD-2 binds SARS-CoV-2 spike RBD and blocks viral entry into ACE2 expressing cells ]]> https://biorxiv.org/content/10.1101/2021.01.07.425621v1?rss=1 Zhang, L. Ghosh, S. K. Basavarajappa, S. C. Muller-Greven, J. Penfield, J. Brewer, A. Ramakrishnan, P. Buck, M. Weinberg, A. 2021-01-07 doi:10.1101/2021.01.07.425621 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Sustained IL-15 response signature predicts RhCMV/SIV vaccine efficacy ]]> https://biorxiv.org/content/10.1101/2021.01.11.426199v1?rss=1 Barrenäs, F. Hansen, S. G. Law, L. Driscoll, C. Green, R. R. Smith, E. Chang, J. Golez, I. Urion, T. Peng, X. Whitmore, L. Newhouse, D. Hughes, C. M. Morrow, D. Randall, K. T. Selseth, A. Ford, J. C. Gilbride, R. M. Randall, B. Ainslie, E. Oswald, K. Shoemaker, R. Fast, R. Bosche, W. J. Axthelm, M. K. Fukazawa, Y. Pavlakis, G. N. Felber, B. K. Fourati, S. Sekaly, R.-P. Lifson, J. D. Komorowski, J. Kosmider, E. Shao, J. Song, W. Edlefsen, P. T. Picker, L. J. Gale, M. 2021-01-11 doi:10.1101/2021.01.11.426199 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Dissecting lipid contents in the distinct regions of native retinal rod disk membranes ]]> https://biorxiv.org/content/10.1101/2021.01.11.426250v1?rss=1 Sander, C. L. Sears, A. E. Pinto, A. F. M. Choi, E. H. Kahremany, S. L. Jin, H. G. Suh, S. Pardon, E. Dong, Z. Steyaert, J. Saghatelian, A. Skowronska-Krawczyk, D. Kiser, P. D. Palczewski, K. 2021-01-11 doi:10.1101/2021.01.11.426250 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ NF-kB c-Rel is dispensable for the development but is required for the cytotoxic function of NK cells ]]> https://biorxiv.org/content/10.1101/2021.01.19.427356v1?rss=1 Vicioso, Y. Zhang, K. Ramakrishnan, P. Parameswaran, R. 2021-01-20 doi:10.1101/2021.01.19.427356 Cold Spring Harbor Laboratory Press 2021-01-20 <![CDATA[ Adipocyte lipolysis abrogates skin fibrosis in a Wnt/DPP4-dependent manner ]]> https://biorxiv.org/content/10.1101/2021.01.21.427497v1?rss=1 Jussila, A. R. Caves, E. Zhang, B. Kirti, S. Steele, M. Lei, V. Hamburg-Shields, E. Lydon, J. Ying, Y. Lafyatis, R. Rajagopalan, S. Horsley, V. Atit, R. P. 2021-01-21 doi:10.1101/2021.01.21.427497 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ The urea cycle is transcriptionally controlled by hypoxia-inducible factors ]]> https://biorxiv.org/content/10.1101/2021.01.25.428152v1?rss=1 Singh, C. Benos, A. Grenell, A. Tran, V. Hanna, D. Kannekanti, N. Anand-Apte, B. Brunengraber, H. Sears, J. 2021-01-27 doi:10.1101/2021.01.25.428152 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Cryo-EM Structure of Bacterioferritin Nanocages Provides Insight into the Bio-mineralization of Ferritins ]]> https://biorxiv.org/content/10.1101/2021.02.04.429857v1?rss=1 Jobichen, C. Ying Chong, T. Rattinam, R. Basak, S. Srinivasan, M. Pandey, K. P. Ngoc, T. B. Jian, S. Angayarkanni, J. Sivaraman, J. 2021-02-05 doi:10.1101/2021.02.04.429857 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Structure of an infectious mammalian prion ]]> https://biorxiv.org/content/10.1101/2021.02.14.431014v1?rss=1 Kraus, A. Hoyt, F. Schwartz, C. Hansen, B. Hughson, A. G. Artikis, E. Race, B. Caughey, B. 2021-02-15 doi:10.1101/2021.02.14.431014 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ Variability in scRNA-Seq analysis is mitigated by regularized or supervised approaches ]]> https://biorxiv.org/content/10.1101/2021.02.15.431268v1?rss=1 Durmaz, A. Scott, J. 2021-02-16 doi:10.1101/2021.02.15.431268 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ The role of Dectin-1 signaling in altering tumor immune microenvironment in the context of aging ]]> https://biorxiv.org/content/10.1101/2021.02.15.431361v1?rss=1 Pandiyan, P. 2021-02-17 doi:10.1101/2021.02.15.431361 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Resolving the Interactions Between Class 3 Semaphorin Receptors in Live Cells ]]> https://biorxiv.org/content/10.1101/2021.02.18.431813v1?rss=1 Christie, S. M. Hao, J. Tracy, E. Buck, M. Yu, J. S. Smith, A. W. 2021-02-18 doi:10.1101/2021.02.18.431813 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ IL-10 driven memory T cell survival and Tfh differentiation promote HIV persistence ]]> https://biorxiv.org/content/10.1101/2021.02.26.432955v1?rss=1 Pereira Ribeiro, S. Aid, M. Dupuy, F. P. Ngai Chan, C. Hultquist, J. Deleage, C. Moysi, E. Kulpa, D. A. Li, L. Xu, X. Tamilselvan, B. Tomalka, J. A. Nekorchuk, M. Busman-Sahay, K. Bordi, R. Simoneau, C. Goulet, J. P. Marconi, V. Routy, J. P. Balderas, R. Micci, L. J Howell, B. H Barouch, D. Krogan, N. J. Petrovas, C. Paiardini, M. Deeks, S. Estes, J. D. Gorman, D. J Hazuda, D. Sekaly, R.-P. 2021-02-26 doi:10.1101/2021.02.26.432955 Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ Infusion of CCR5 Gene-Edited T Cells Allows Immune Reconstitution, HIV Reservoir Decay, and Long-Term Virological Control ]]> https://biorxiv.org/content/10.1101/2021.02.28.433290v1?rss=1 Zeidan, J. Sharma, A. A. Lee, G. Raad, A. Fromentin, R. Fourati, S. Ghneim, K. Sanchez, G. P. Benne, C. Canderan, G. Procopio, F. A. Balderas, R. Monette, G. Lalezari, J. P. Heffernan, J. M. Sabbagh, L. Chomont, N. Ando, D. Deeks, S. G. Sekaly, R.-P. 2021-03-01 doi:10.1101/2021.02.28.433290 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes ]]> https://biorxiv.org/content/10.1101/2021.03.09.434592v1?rss=1 Sun, D. Sang, Z. Kim, J. Xiang, Y. Cohen, T. Belford, A. K. Huet, A. Conway, J. F. Sun, J. Taylor, D. Zhang, C. Huang, W. Shi, Y. 2021-03-10 doi:10.1101/2021.03.09.434592 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ PD-1 dependent expansion of Amphregulin+FOXP3+ cells is associated with oral immune dysfunction in HIV patients on therapy ]]> https://biorxiv.org/content/10.1101/2021.03.13.435273v1?rss=1 Pandiyan, P. 2021-03-14 doi:10.1101/2021.03.13.435273 Cold Spring Harbor Laboratory Press 2021-03-14 <![CDATA[ Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment ]]> https://biorxiv.org/content/10.1101/2021.03.15.435423v1?rss=1 Zhou, Y. Xu, J. Hou, Y. Leverenz, J. B. Kallianpur, A. Mehra, R. Liu, Y. Yu, H. Pieper, A. A. Jehi, L. Cheng, F. 2021-03-22 doi:10.1101/2021.03.15.435423 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Amotosalen is a bacterial multidrug efflux pump substrate potentially affecting its pathogen inactivation activity ]]> https://biorxiv.org/content/10.1101/2021.03.15.435562v1?rss=1 Green, A. B. Zulauf, K. E. Truelson, K. A. Chiaraviglio, L. Cui, M. Zhang, Z. Ware, M. P. Flegel, W. A. Haspel, R. L. Yu, E. W. Kirby, J. E. 2021-03-16 doi:10.1101/2021.03.15.435562 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Towards the NMR solution Structure and the Dynamics of the C-terminal Region of APOL1 and its G1, G2 Variants with a Membrane Mimetic ]]> https://biorxiv.org/content/10.1101/2021.03.16.435683v1?rss=1 Madhavan, S. M. Hansen, A. L. Cao, S. Sedor, J. R. Buck, M. 2021-03-16 doi:10.1101/2021.03.16.435683 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Effects of stochasticity on the length and behaviour of ecological transients ]]> https://biorxiv.org/content/10.1101/2021.03.25.437077v1?rss=1 Hastings, A. Abbott, K. C. Cuddington, K. Francis, T. Lai, Y.-C. Morozov, A. Petrovskii, S. Zeeman, M. L. 2021-03-26 doi:10.1101/2021.03.25.437077 Cold Spring Harbor Laboratory Press 2021-03-26 <![CDATA[ Systematic Profiling of Temperature- and Retinal-Sensitive Rhodopsin Variants by Deep Mutational Scanning ]]> https://biorxiv.org/content/10.1101/2021.03.26.437229v1?rss=1 McKee, A. G. Kuntz, C. P. Ortega, J. T. Woods, H. Roushar, F. J. Meiler, J. Jastrzebska, B. Schlebach, J. P. 2021-03-26 doi:10.1101/2021.03.26.437229 Cold Spring Harbor Laboratory Press 2021-03-26 <![CDATA[ Polymer additives to personal protective equipment can inactivate pathogens ]]> https://biorxiv.org/content/10.1101/2021.04.01.438151v1?rss=1 View larger version (15K): org.highwire.dtl.DTLVardef@c07ab2org.highwire.dtl.DTLVardef@b73e8dorg.highwire.dtl.DTLVardef@6bd8e5org.highwire.dtl.DTLVardef@6cc681_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Dogan, A. B. Dabkowski, K. E. von Recum, H. A. 2021-04-02 doi:10.1101/2021.04.01.438151 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ Conformational clamping by a membrane ligand activates the EphA2 receptor ]]> https://biorxiv.org/content/10.1101/2021.04.08.439029v1?rss=1 Westerfield, J. M. Sahoo, A. Alves, D. S. Grau, B. Cameron, A. Maxwell, M. Schuster, J. Souza, P. C. T. Mingarro, I. Buck, M. Barrera, F. N. 2021-04-09 doi:10.1101/2021.04.08.439029 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Cell Surface Multimeric Assemblies Regulate Canonical and Noncanonical EphA2 Receptor Tyrosine Kinase Signaling ]]> https://biorxiv.org/content/10.1101/2021.04.11.439330v1?rss=1 Shi, X. Lingerak, R. Herting, C. Ge, Y. Kim, S. Toth, P. Cuizon, C. Zheng, J. Chao, L. H. Sossey-Alaoui, K. Buck, M. Singh, S. Varadan, V. Himanen, J. Hambardzumyan, D. Nikolov, D. Smith, A. W. Wang, B. 2021-04-12 doi:10.1101/2021.04.11.439330 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Wnt-dependent activation of ERK mediates repression of chondrocyte fate during calvarial development. ]]> https://biorxiv.org/content/10.1101/2021.04.23.441148v1?rss=1 Ibarra, B. Machen, C. Atit, R. 2021-04-23 doi:10.1101/2021.04.23.441148 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Redefining the PTEN Promoter: Identification of Two Upstream Transcription Start Regions ]]> https://biorxiv.org/content/10.1101/2021.04.23.441162v1?rss=1 Grencewicz, D. J. Romigh, T. Thacker, S. Abbas, A. Jaini, R. Luse, D. Eng, C. 2021-04-23 doi:10.1101/2021.04.23.441162 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Sequential single cell transcriptional and protein marker profiling reveals TIGIT as a marker of CD19 CAR-T cell dysfunction in patients with non-Hodgkin lymphoma ]]> https://biorxiv.org/content/10.1101/2021.04.26.441326v1?rss=1 Jackson, Z. G. Hong, C. Schauner, R. Dropulic, B. Caimi, P. F. de Lima, M. Gupta, K. Reese, J. S. Hwang, T. H. Wald, D. N. 2021-04-27 doi:10.1101/2021.04.26.441326 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Biogenesis of P-TEFb in CD4+ T cells to reverse HIV latency is mediated by protein kinase C (PKC)-independent signaling pathways ]]> https://biorxiv.org/content/10.1101/2021.04.26.441433v1?rss=1 Mbonye, U. Leskov, K. Shukla, M. Valadkhan, S. Karn, J. 2021-04-26 doi:10.1101/2021.04.26.441433 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Liver Endothelium Microenvironment Promotes HER3-mediated Cell Survival in KRAS Wild-type and Mutant Colorectal Cancer ]]> https://biorxiv.org/content/10.1101/2021.04.27.441690v1?rss=1 Wang, R. Rathore, M. Bhattacharya, R. Fan, F. Wright, M. Wang, Z. Markowitz, S. Willis, J. Ellis, L. 2021-04-28 doi:10.1101/2021.04.27.441690 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Effects of BCG vaccination on donor unrestricted T cells in humans ]]> https://biorxiv.org/content/10.1101/2021.04.29.441927v1?rss=1 Gela, A. Murphy, M. Hadley, K. Hanekom, W. Boom, H. Johnson, J. Hoft, D. Joosten, S. Ottenhoff, T. Suliman, S. Moody, B. Lewinsohn, D. Hatherill, M. Seshadri, C. Nemes, E. Scriba, T. 2021-04-29 doi:10.1101/2021.04.29.441927 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Simple degradable cyclodextrin polyester with chelator-based crosslinker for stent-based drug delivery ]]> https://biorxiv.org/content/10.1101/2021.04.29.442054v1?rss=1 Young, K. Lord, A. E. Burkhart, G. E. Kozawa, S. K. Mu, N. von Recum, H. A. 2021-04-30 doi:10.1101/2021.04.29.442054 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Longitudinal analysis of diffuse glioma reveals cell state dynamics at recurrence associated with changes in genetics and the microenvironment ]]> https://biorxiv.org/content/10.1101/2021.05.03.442486v1?rss=1 Varn, F. S. Johnson, K. C. Wade, T. E. Malta, T. M. Sabedot, T. S. Barthel, F. P. Kim, H. Ahmed, N. Datta, I. Barnholtz-Sloan, J. S. Bakas, S. D'Angelo, F. Gan, H. K. Garofano, L. Huse, J. T. Khasraw, M. Kocakavuk, E. Migliozzi, S. Ormond, D. R. Paek, S. H. Van Meir, E. G. Walenkamp, A. M. E. Watts, C. Weller, M. Weiss, T. Wesseling, P. Stead, L. F. Poisson, L. M. Noushmehr, H. Iavarone, A. Verhaak, R. G. The GLASS Consortium, 2021-05-04 doi:10.1101/2021.05.03.442486 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Notch-Induced Endoplasmic Reticulum-Associated Degradation Governs Thymocyte β-Selection ]]> https://biorxiv.org/content/10.1101/2021.05.06.443041v1?rss=1 Chen, X. Liu, X. Yu, J. Xu, L. Umphred-Wilson, K. Peng, F. Ding, Y. Barton, B. M. Lv, X. Zhao, M. Y. Sun, S. Hong, Y. Qi, L. Adoro, S. 2021-05-07 doi:10.1101/2021.05.06.443041 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ Knowledge production and translation of science between Academia and Industry: assessing the impact of R&D in India ]]> https://biorxiv.org/content/10.1101/2021.05.08.443271v1?rss=1 Rao, V. Jenu, N. D. R. Arakeri, G. Nayar, R. C. Kumar, J. Amaral Mendes, R. 2021-05-10 doi:10.1101/2021.05.08.443271 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Intracellular Vesicle Entrapment of Nanobubble Ultrasound Contrast Agents Targeted to PSMA Promotes Prolonged Enhancement and Stability In Vivo and In Vitro ]]> https://biorxiv.org/content/10.1101/2021.05.11.443511v1?rss=1 Perera, R. Abenojar, E. Nittayacharn, P. Wang, X. Ramamurthy, G. Peiris, P. Bederman, I. Basilion, J. Exner, A. 2021-05-12 doi:10.1101/2021.05.11.443511 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ The EphB2-MYC Axis is a Major Determinant of Barrett's Pathobiology and a Therapeutic Vulnerability in Esophageal Cancer ]]> https://biorxiv.org/content/10.1101/2021.05.13.444044v1?rss=1 Venkitachalam, S. Babu, D. Ravillah, D. Katabathula, R. M. Joseph, P. Singh, S. Udhayakumar, B. Miao, Y. Martinez-Uribe, O. Hogue, J. A. Kresak, A. M. Dawson, D. LaFramboise, T. Willis, J. E. Chak, A. Garman, K. S. Blum, A. E. Varadan, V. Guda, K. 2021-05-15 doi:10.1101/2021.05.13.444044 Cold Spring Harbor Laboratory Press 2021-05-15 <![CDATA[ β-lactamase remodeling and evolution of collateral resistance in hypermutator Pseudomonas aeruginosa upon long-term antibiotic therapy ]]> https://biorxiv.org/content/10.1101/2021.05.14.444257v1?rss=1 Colque, C. A. Tomatis, P. E. Albarracin Orio, A. G. Dotta, G. Moreno, D. M. Hedemann, L. G. Hickman, R. A. Sommer Madsen, L. M. Feliziani, S. Moyano, A. M. Bonomo, R. A. Johansen, H. K. Molin, S. Vila, A. J. Smania, A. M. 2021-05-17 doi:10.1101/2021.05.14.444257 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Interplay between meropenem and human serum albumin on expression of carbapenem resistance genes and natural competence in Acinetobacter baumannii ]]> https://biorxiv.org/content/10.1101/2021.05.14.444273v1?rss=1 Pimentel, C. Le, C. Tuttobene, M. R. Subils, T. Nishimura, B. Traglia, G. M. Perez, F. Papp-Wallace, K. M. Bonomo, R. A. Tolmasky, M. Ramirez, M. S. 2021-05-18 doi:10.1101/2021.05.14.444273 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Caveolin-3 Null Mutation in Family with Barretts Esophagus and Esophageal Adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2021.05.15.444305v1?rss=1 Garman, K. S. von Furstenberg, R. Becker, T. C. Falk, G. W. Willis, J. E. Dawson, D. Guda, K. Chak, A. 2021-05-17 doi:10.1101/2021.05.15.444305 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ TLR2 on CD4+ and CD8+ T cells promotes late control of Mycobacterium tuberculosis infection ]]> https://biorxiv.org/content/10.1101/2021.05.19.444905v1?rss=1 Reba, S. Li, Q. Onwuzulike, S. Nagy, N. Parker, K. Umphred-Wilson, K. Shukla, S. Harding, C. V. Boom, W. H. E. Rojas, R. 2021-05-21 doi:10.1101/2021.05.19.444905 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ Adaptation to chronic ER stress enforces pancreatic β-cell plasticity ]]> https://biorxiv.org/content/10.1101/2021.05.24.445193v1?rss=1 Chen, C.-W. Guan, B.-J. Alzahrani, M. R. Gao, Z. Gao, L. Bracey, S. Haataja, L. Schaffer, A. E. Lee, H. Laframboise, T. Bederman, I. Arvan, P. Mathews, C. E. Gerling, I. Kaestner, K. H. Tirosh, B. Engin, F. Hatzoglou, M. 2021-05-24 doi:10.1101/2021.05.24.445193 Cold Spring Harbor Laboratory Press 2021-05-24 <![CDATA[ Ancestral diversity improves discovery and fine-mapping of genetic loci for anthropometric traits - the Hispanic/Latino Anthropometry Consortium ]]> https://biorxiv.org/content/10.1101/2021.05.27.445969v1?rss=1 60 established anthropometric loci in Hispanic/Latino populations at genome-wide significance--representing up to 30% of previously-reported index SNP anthropometric associations. Trans-ethnic meta-analysis of the three ancestries showed a small-to-moderate impact of uncorrected population stratification on the resulting effect size estimates. Our novel findings demonstrate that future studies may also benefit from leveraging differences in linkage disequilibrium patterns to discover novel loci and additional signals with less residual population stratification. ]]> Fernandez-Rhodes, L. Graff, M. Buchanan, V. L. Justice, A. E. Highland, H. M. Guo, X. Young, K. L. Adhikari, K. Allred, N. P. Below, J. E. Bradfield, J. Pereira, A. C. Glover, L. Kim, D. Lilly, A. G. Shrestha, P. Thomas, A. G. Zhang, X. Chen, M. Chiang, C. Pulit, S. Horimoto, A. Krieger, J. E. Guindo-Martinez, M. Preuss, M. Schumann, C. Smit, R. A. J. Torres-Mejia, G. Acuna-Alonzo, V. Bedoya, G. Bortolini, M.-C. Canizales-Quinteros, S. Gallo, C. Gonzalez-Jose, R. Poletti, G. Rothhammer, F. Hakonarson, H. Adler, S. G. Igo, R. Iyengar, S. Nicholas, S. B. 2021-05-29 doi:10.1101/2021.05.27.445969 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ Exogenous extracellular matrix proteins decrease cardiac fibroblast activation in stiffening microenvironment through CAPG ]]> https://biorxiv.org/content/10.1101/2021.06.05.447170v1?rss=1 Wang, X. Pierre, V. Liu, C. Senapati, S. Park, P. S.- H. Senyo, S. 2021-06-07 doi:10.1101/2021.06.05.447170 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ A PMMA bone cement composite that functions as a drug-refillable depot for localized, multi-window chemotherapeutic treatment of bone cancer ]]> https://biorxiv.org/content/10.1101/2021.06.13.448250v1?rss=1 Cyphert, E. L. Kanagasegar, N. Zhang, N. Learn, G. D. von Recum, H. A. 2021-06-13 doi:10.1101/2021.06.13.448250 Cold Spring Harbor Laboratory Press 2021-06-13 <![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[ Convergence of case-specific epigenetic alterations identify a confluence of genetic vulnerabilities tied to opioid dependence ]]> https://biorxiv.org/content/10.1101/2021.06.15.447736v1?rss=1 Corradin, O. Sallari, R. Hoang, A. T. Kassim, B. S. Ben Hutta, G. Cuoto, L. Quach, B. C. Lovrenert, K. Hays, C. Gryder, B. E. Iskhakova, M. Cates, H. Song, Y. Bartels, C. F. Hancock, D. B. Mash, D. C. Johnson, E. O. Akbarian, S. Scacheri, P. C. 2021-06-16 doi:10.1101/2021.06.15.447736 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ Cheater suppression and spite through quorum sensing ]]> https://biorxiv.org/content/10.1101/2021.06.16.448736v1?rss=1 Moffett, A. S. Thomas, P. J. Hinczewski, M. Eckford, A. W. 2021-06-16 doi:10.1101/2021.06.16.448736 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ Disturbed retinoid metabolism upon loss of rlbp1a impairs cone function and leads to subretinal lipid deposits and photoreceptor degeneration in the zebrafish retina ]]> https://biorxiv.org/content/10.1101/2021.06.18.448986v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@bd3de5org.highwire.dtl.DTLVardef@2a9420org.highwire.dtl.DTLVardef@162e7f0org.highwire.dtl.DTLVardef@697ee6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Schlegel, D. K. Ramkumar, S. von Lintig, J. Neuhauss, S. C. F. 2021-06-18 doi:10.1101/2021.06.18.448986 Cold Spring Harbor Laboratory Press 2021-06-18 <![CDATA[ Detecting global influence of transcription factor interactions on gene expression in lymphoblastoid cells using neural network models ]]> https://biorxiv.org/content/10.1101/2021.06.18.449031v1?rss=1 Patel, N. Bush, W. 2021-06-20 doi:10.1101/2021.06.18.449031 Cold Spring Harbor Laboratory Press 2021-06-20 <![CDATA[ Defining the Immune Responses for SARS-CoV-2-Human Macrophage Interactions ]]> https://biorxiv.org/content/10.1101/2021.07.07.449660v1?rss=1 Mostafa, M. Yeapuri, P. Machhi, J. Olson, K. Shahjin, F. Zhou, Y. Jingjing, L. Pandey, K. Acharya, A. Byrareddy, S. Mosley, L. Gendelman, H. 2021-07-07 doi:10.1101/2021.07.07.449660 Cold Spring Harbor Laboratory Press 2021-07-07 <![CDATA[ Single-nucleus sequencing reveals enriched expression of genetic risk factors sensitises Motor Neurons to degeneration in ALS ]]> https://biorxiv.org/content/10.1101/2021.07.12.452054v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@11237fdorg.highwire.dtl.DTLVardef@119f3ceorg.highwire.dtl.DTLVardef@d56c69org.highwire.dtl.DTLVardef@1c087e1_HPS_FORMAT_FIGEXP M_FIG Our study highlights cell type specific changes in premotor/motor cortex of sporadic ALS patients. Specifically, we identify upregulation of synaptic molecules in excitatory neurons of upper cortical layers, interestingly correlating to hyperexcitability phenotypes seen in patients. Moreover, excitatory neurons of the deeper layers of the cortex, that project to the spinal cord and are most affected by the disease, show higher levels of cellular stresses than other neuronal types. Correspondently, oligodendrocytes transition from a highly myelinating state to a more neuronally engaged state, probably to counteract stressed phenotypes seen in excitatory neurons. At the same time, microglia show a reactive state with specific upregulation of endo-lysosomal pathways. C_FIG ]]> Limone, F. Mordes, D. Couto, A. Pietilainen, O. Joseph, B. Burberry, A. Ghosh, S. D. Meyer, D. Goldman, M. Bortolin, L. Cobos, I. Therrien, M. Stevens, B. Kadiu, I. McCarroll, S. A. Eggan, K. 2021-07-13 doi:10.1101/2021.07.12.452054 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ The Burkholderia cenocepacia type VI secretion system effector TecA is a virulence factor during lung infection ]]> https://biorxiv.org/content/10.1101/2021.07.13.451912v1?rss=1 Loeven, N. A. Perault, A. I. Cotter, P. A. Hodges, C. A. Schwartzman, J. D. Hampton, T. H. Bliska, J. B. 2021-07-13 doi:10.1101/2021.07.13.451912 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ Cellular signaling beyond the Wiener-Kolmogorov limit ]]> https://biorxiv.org/content/10.1101/2021.07.15.452575v1?rss=1 Weisenberger, C. Hathcock, D. Hinczewski, M. 2021-07-16 doi:10.1101/2021.07.15.452575 Cold Spring Harbor Laboratory Press 2021-07-16 <![CDATA[ ASXL3 controls cortical neuron fate specification through extrinsic self-renewal pathways ]]> https://biorxiv.org/content/10.1101/2021.07.20.452995v1?rss=1 McGrath, B. T. Wu, P. Salvi, S. Girgla, N. Xu, C. Zhu, J. KC, R. Tsan, Y.-C. Moccia, A. Srivastava, A. Zhou, X. Bielas, S. L. 2021-07-21 doi:10.1101/2021.07.20.452995 Cold Spring Harbor Laboratory Press 2021-07-21 <![CDATA[ Regulatory start-stop elements in 5' untranslated regions pervasively modulate translation ]]> https://biorxiv.org/content/10.1101/2021.07.26.453809v1?rss=1 Rendleman, J. Mohammad, M. P. Pressler, M. Maity, S. Hronova, V. Gao, Z. Herrmannova, A. Lei, A. Allgoewer, K. Sultanov, D. Hinckley, W. E. Szkop, K. Topisirovic, I. Larsson, O. Hatzoglou, M. Valasek, L. S. Vogel, C. 2021-07-26 doi:10.1101/2021.07.26.453809 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ Using attentive gated neural networks to quantify the impact of non-coding variants on transcription factor binding affinity ]]> https://biorxiv.org/content/10.1101/2021.07.30.454350v1?rss=1 Patel, N. Bai, H. Bush, W. 2021-08-02 doi:10.1101/2021.07.30.454350 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ Genome-wide protein-DNA interaction site mapping using a double strand DNA-specific cytosine deaminase ]]> https://biorxiv.org/content/10.1101/2021.08.01.454665v1?rss=1 Gallagher, L. A. Velazquez, E. Peterson, S. B. Charity, J. C. Hsu, F. Radey, M. C. Gebhardt, M. J. de Moraes, M. H. Penewit, K. M. Kim, J. Andrade, P. A. LaFramboise, T. Salipante, S. J. de Lorenzo, V. Wiggins, P. A. Dove, S. L. Mougous, J. 2021-08-02 doi:10.1101/2021.08.01.454665 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ Inhibition of the H3K27 demethylase UTX enhances the epigenetic silencing of HIV proviruses and induces HIV-1 DNA hypermethylation but fails to permanently block HIV reactivation ]]> https://biorxiv.org/content/10.1101/2021.08.02.454353v1?rss=1 Nguyen, K. Karn, J. Kyung, W. Dobrowolski, C. Shukla, M. 2021-08-02 doi:10.1101/2021.08.02.454353 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ An Association Test of the Spatial Distribution of Rare Missense Variants within Protein Structures Improves Statistical Power of Sequencing Studies ]]> https://biorxiv.org/content/10.1101/2021.08.09.455695v1?rss=1 Jin, B. Capra, J. A. Benchek, P. Wheeler, N. R. Naj, A. C. Hamilton-Nelson, K. L. Farrell, J. J. Leung, Y. Y. Kunkle, B. W. Vardarajan, B. N. Schellenberg, G. D. Mayeux, R. Wang, L.-S. Farrer, L. A. Pericak-Vance, M. Martin, E. R. Haines, J. L. Crawford, D. C. Bush, W. S. 2021-08-10 doi:10.1101/2021.08.09.455695 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Cryo-EM structure of disease-related prion fibrils provides insights into seeding barriers ]]> https://biorxiv.org/content/10.1101/2021.08.10.455830v1?rss=1 Li, Q. Jaroniec, C. P. Surewicz, W. K. 2021-08-11 doi:10.1101/2021.08.10.455830 Cold Spring Harbor Laboratory Press 2021-08-11 <![CDATA[ Carbon Fiber Electrodes for Intracellular Recording and Stimulation ]]> https://biorxiv.org/content/10.1101/2021.08.12.456117v1?rss=1 Huan, Y. Gill, J. P. Fritzinger, J. B. Patel, P. R. Richie, J. M. della Valle, E. Weiland, J. D. Chestek, C. A. Chiel, H. J. 2021-08-13 doi:10.1101/2021.08.12.456117 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Polymer microparticles prolong delivery of the 15-PGDH inhibitor SW033291 ]]> https://biorxiv.org/content/10.1101/2021.08.15.456403v1?rss=1 View larger version (14K): org.highwire.dtl.DTLVardef@13aed1dorg.highwire.dtl.DTLVardef@1a541eaorg.highwire.dtl.DTLVardef@8a9fd5org.highwire.dtl.DTLVardef@1038a77_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Dogan, A. B. Rohner, N. A. Smith, J. N. P. Kilgore, J. A. Williams, N. S. Markowitz, S. D. von Recum, H. A. Desai, A. B. 2021-08-15 doi:10.1101/2021.08.15.456403 Cold Spring Harbor Laboratory Press 2021-08-15 <![CDATA[ Constructing Functional Networks of Phosphorylation Sites Using Co-Phosphorylation ]]> https://biorxiv.org/content/10.1101/2021.08.16.456448v1?rss=1 Ayati, M. Yilmaz, S. Chance, M. Koyuturk, M. 2021-08-16 doi:10.1101/2021.08.16.456448 Cold Spring Harbor Laboratory Press 2021-08-16 <![CDATA[ Stimulation of the Dorsal Root Ganglion using an Injectrode ]]> https://biorxiv.org/content/10.1101/2021.08.16.456553v1?rss=1 Dalrymple, A. N. Ting, J. E. Bose, R. Trevathan, J. K. Nieuwoudt, S. Lempka, S. F. Franke, M. Ludwig, K. A. Shoffstall, A. Fisher, L. E. Weber, D. J. 2021-08-17 doi:10.1101/2021.08.16.456553 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Converging evidence for differential regulatory control of APOEε4 on African versus European haplotypes ]]> https://biorxiv.org/content/10.1101/2021.08.23.457375v1?rss=1 Nuytemans, K. LipkinVasquez, M. Wang, L. Van Booven, D. Griswold, A. J. Rajabli, F. Celis, K. Oron, O. Hofmann, N. Rolati, S. Garcia-Serje, C. Zhang, S. Jin, F. Argenziano, M. Grant, S. F. Chesi, A. Brown, C. D. Young, J. I. Dykxhoorn, D. M. Pericak-Vance, M. A. Vance, J. M. 2021-08-24 doi:10.1101/2021.08.23.457375 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ IL1B loss is associated with increased AR activity in castration-resistant prostate cancer ]]> https://biorxiv.org/content/10.1101/2021.08.31.458406v1?rss=1 Awadallah, W. N. Nanda, J. S. Kohrt, S. E. Grabowska, M. M. 2021-09-01 doi:10.1101/2021.08.31.458406 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Horizontal mitochondrial transfer from the microenvironment increases glioblastoma tumorigenicity ]]> https://biorxiv.org/content/10.1101/2021.09.01.458565v1?rss=1 Watson, D. C. Bayik, D. Williford, S. E. Lauko, A. Zhou, Y. Deshpande, G. Seder, J. Mears, J. A. Cheng, F. Hjelmeland, A. B. Lathia, J. D. 2021-09-02 doi:10.1101/2021.09.01.458565 Cold Spring Harbor Laboratory Press 2021-09-02 <![CDATA[ SYS-Mut: Decoding the Functional Significance of Rare Somatic Mutations in Cancer ]]> https://biorxiv.org/content/10.1101/2021.09.03.458896v1?rss=1 Khalighi, S. Joseph, P. Babu, D. Singh, S. LaFramboise, T. Guda, K. Varadan, V. 2021-09-06 doi:10.1101/2021.09.03.458896 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Movement-Dependent Electrical Stimulation for Volitional Strengthening of Cortical Connections in Behaving Monkeys ]]> https://biorxiv.org/content/10.1101/2021.09.03.458906v1?rss=1 Moorjani, S. Walvekar, S. Fetz, E. E. Perlmutter, S. I. 2021-09-06 doi:10.1101/2021.09.03.458906 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Organization and engagement of a prefrontal-olfactory network during olfactory selective attention ]]> https://biorxiv.org/content/10.1101/2021.09.04.458996v1?rss=1 Cansler, H. L. in 't Zandt, E. E. Carlson, K. S. Khan, W. T. Ma, M. Wesson, D. W. 2021-09-06 doi:10.1101/2021.09.04.458996 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Predicting Transmembrane (TM) Domain Dimer Structures using Martini 3 ]]> https://biorxiv.org/content/10.1101/2021.09.10.459840v1?rss=1 Sahoo, A. R. Souza, P. C. T. Meng, Z. Buck, M. 2021-09-11 doi:10.1101/2021.09.10.459840 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Bioactive Hydrogel Microcapsules for Guiding Stem Cell Fate Decisions by Release and Reloading of Growth Factors ]]> https://biorxiv.org/content/10.1101/2021.09.21.461208v1?rss=1 Revzin, A. Gwon, K. Hong, H. Gonzalez-Suarez, A. M. Slama, M. Q. Choi, D. Hong, J. Baskaran, H. Stybayeva, G. Peterson, Q. P. 2021-09-24 doi:10.1101/2021.09.21.461208 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Carbapenem-Resistant Acinetobacter baumannii in US hospitals: diversification of circulating lineages and antimicrobial resistance ]]> https://biorxiv.org/content/10.1101/2021.09.21.461323v1?rss=1 Iovleva, A. V. Mustapha, M. M. Griffith, M. P. Komarow, L. Luterbach, C. Evans, D. R. Cober, E. Richter, S. S. Rydell, K. Arias, C. A. Jacob, J. T. Salata, R. A. Satlin, M. J. Wong, D. Bonomo, R. A. van Duin, D. Cooper, V. S. Van Tyne, D. Doi, Y. 2021-09-23 doi:10.1101/2021.09.21.461323 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Age of diabetes onset in the mutant proinsulin syndrome correlates with mutational impairment of protein foldability and stability ]]> https://biorxiv.org/content/10.1101/2021.09.24.461687v1?rss=1 Dhayalan, B. Chen, Y.-S. Yang, Y. Jarosinski, M. Chatterjee, D. Grabowski, R. Poordian, S. Phillips, N. F. B. Arvan, P. Ismail-Beigi, F. Weiss, M. A. 2021-09-25 doi:10.1101/2021.09.24.461687 Cold Spring Harbor Laboratory Press 2021-09-25 <![CDATA[ A neural network-based method for exhaustive cell label assignment using single cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/2021.09.25.461825v1?rss=1 Li, Z. Feng, H. 2021-09-26 doi:10.1101/2021.09.25.461825 Cold Spring Harbor Laboratory Press 2021-09-26 <![CDATA[ Distinct cell adhesion signature defines glioblastoma myeloid-derived suppressor cell subsets ]]> https://biorxiv.org/content/10.1101/2021.09.27.461995v1?rss=1 Bayik, D. Bartels, C. F. Lovrenert, K. Watson, D. Zhang, D. Kay, K. Lauko, A. Johnson, S. Lo, A. McGraw, M. Grabowski, M. Mohammadi, A. M. Veglia, F. Fan, Y. Vogelbaum, M. A. Scacheri, P. Lathia, J. 2021-09-28 doi:10.1101/2021.09.27.461995 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ Augmented Transcutaneous Stimulation Using an Injectable Electrode ]]> https://biorxiv.org/content/10.1101/2021.09.29.462482v1?rss=1 Verma, N. Graham, R. D. Mudge, J. Trevathan, J. K. Franke, M. Shoffstall, A. J. Williams, J. Dalrymple, A. N. Fisher, L. E. Weber, D. J. Lempka, S. F. Ludwig, K. A. 2021-10-01 doi:10.1101/2021.09.29.462482 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Gut Microbiome Signatures Linked to HIV-1 Reservoir Size and Viremia Control ]]> https://biorxiv.org/content/10.1101/2021.10.03.462590v1?rss=1 Borgognone, A. Noguera-Julian, M. Oriol, B. Noël-Romas, L. Ruiz-Riol, M. Guillen, Y. Parera, M. Casadella, M. Duran, C. Puertas, M. C. Catala-Moll, F. De Leon, M. Knodel, S. Birse, K. Manzardo, C. Miro, J. M. Clotet, B. Martinez-Picado, J. Molto, J. Mothe, B. Burgener, A. Brander, C. Paredes, R. 2021-10-04 doi:10.1101/2021.10.03.462590 Cold Spring Harbor Laboratory Press 2021-10-04 <![CDATA[ High-throughput Activity Assay for Screening Inhibitors of the SARS-CoV-2 Mac1 Macrodomain ]]> https://biorxiv.org/content/10.1101/2021.10.07.463234v1?rss=1 Dasovich, M. A. Zhou, J. Thomas, A. G. Goodman, J. A. McPherson, R. L. Jayabalan, A. K. Busa, V. F. Cheng, S.-J. Murphy, B. Redinger, K. R. Tsukamoto, T. Slusher, B. S. Bosch, J. Wei, J. Leung, A. 2021-10-07 doi:10.1101/2021.10.07.463234 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ Terminal selectors organize postmitotic chromatin accessibility for acquisition of serotonergic identity ]]> https://biorxiv.org/content/10.1101/2021.10.13.463782v1?rss=1 Zhang, X. L. Spencer, W. C. Tabuchi, N. Deneris, E. S. 2021-10-14 doi:10.1101/2021.10.13.463782 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ In vitro experiments and kinetic models of pollen hydration show that MSL8 is not a simple tension-gated osmoregulator ]]> https://biorxiv.org/content/10.1101/2021.10.19.464977v1?rss=1 Miller, K. Strychalski, W. Nickaeen, M. Carlsson, A. Haswell, E. 2021-10-19 doi:10.1101/2021.10.19.464977 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Chemical inhibition of pathological reactive astrocytes promotes neural protection ]]> https://biorxiv.org/content/10.1101/2021.11.03.467083v1?rss=1 Clayton, B. L. L. Kristell, J. D. Allan, K. C. Karl, M. Garrison, E. Maeno-Hikichi, Y. Sturno, A. Shick, E. Miller, R. H. Tesar, P. J. 2021-11-04 doi:10.1101/2021.11.03.467083 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Multiplex Embedding of Biological Networks Using Topological Similarity of Different Layers ]]> https://biorxiv.org/content/10.1101/2021.11.05.467392v1?rss=1 Coskun, M. Koyuturk, M. 2021-11-05 doi:10.1101/2021.11.05.467392 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ Fascicles split or merge every ~560 microns within the human cervical vagus nerve ]]> https://biorxiv.org/content/10.1101/2021.11.09.467343v1?rss=1 Upadhye, A. R. Kolluru, C. Druschel, L. Al Lababidi, L. Ahmad, S. Menendez, D. Buyukcelik, O. N. Settell, M. L. Jenkins, M. W. Wilson, D. Zhang, J. Tatsuoka, C. Grill, W. M. Pelot, N. A. Ludwig, K. Gustafson, K. J. Shoffstall, A. J. 2021-11-11 doi:10.1101/2021.11.09.467343 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Abolishing the prelamin A ZMPSTE24 cleavage site leads to progeroid phenotypes with near-normal longevity in mice ]]> https://biorxiv.org/content/10.1101/2021.11.11.465186v1?rss=1 Wang, Y. Shiladardi, K. Hsu, T. Odinammadu, K. O. Maruyama, T. Wu, W. Lin, C.-S. Damoci, C. B. Spear, E. D. Shin, J.-Y. Hsu, W. Michaelis, S. Worman, H. J. 2021-11-12 doi:10.1101/2021.11.11.465186 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ The Nerve Growth Factor IB-like Receptor Nurr1 (NR4A2) recruits CoREST transcription repressor complexes to silence HIV following proviral reactivation in microglial cells ]]> https://biorxiv.org/content/10.1101/2021.11.16.468784v1?rss=1 Ye, F. Alvarez-Carbonell, D. Nguyen, K. Valadkhan, S. Leskov, K. Garcia-Mesa, Y. Sreeram, S. Karn, J. 2021-11-16 doi:10.1101/2021.11.16.468784 Cold Spring Harbor Laboratory Press 2021-11-16 <![CDATA[ Algorithmic Parameter Estimation and Uncertainty Quantification for Hodgkin-Huxley Neuron Models ]]> https://biorxiv.org/content/10.1101/2021.11.18.469189v1?rss=1 Wang, Y. C. Sinha, N. Rudi, J. Velasco, J. Idumah, G. Powers, R. K. Heckman, C. J. Chardon, M. 2021-11-20 doi:10.1101/2021.11.18.469189 Cold Spring Harbor Laboratory Press 2021-11-20 <![CDATA[ Inferring kinetic rate constants from single-molecule FRET trajectories - a blind benchmark of kinetic analysis tools ]]> https://biorxiv.org/content/10.1101/2021.11.23.469671v1?rss=1 Götz, M. Barth, A. Bohr, S. S.- R. Börner, R. Chen, J. Cordes, T. Erie, D. A. Gebhardt, C. Hadzic, M. C. A. S. Hamilton, G. L. Hatzakis, N. S. Hugel, T. Kisley, L. Lamb, D. C. de Lannoy, C. Mahn, C. Dunukara, D. de Ridder, D. Sanabria, H. Schimpf, J. Seidel, C. A. M. Sigel, R. K. O. Sletfjerding, M. B. Thomsen, J. Vollmar, L. Wanninger, S. Weninger, K. R. Xu, P. Schmid, S. 2021-11-23 doi:10.1101/2021.11.23.469671 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids ]]> https://biorxiv.org/content/10.1101/2021.12.07.470215v1?rss=1 Ramdas, S. Judd, J. Graham, S. E. Kanoni, S. Wang, Y. Surakka, I. Wenz, B. Clarke, S. L. Chesi, A. Wells, A. Bhatti, K. F. Vedantam, S. Winkler, T. W. Locke, A. E. Marouli, E. Zajac, G. J. Wu, K.-H. H. Ntalla, I. Hui, Q. Klarin, D. Hilliard, A. T. Wang, Z. Xue, C. Thorleifsson, G. Helgadottir, A. Gudbjartsson, D. F. Holm, H. Olafsson, I. Hwang, M. Y. Han, S. Akiyama, M. Sakaue, S. Terao, C. Kanai, M. Zhou, W. Brumpton, B. M. Rasheed, H. Havulinna, A. S. Veturi, Y. Pacheco, J. A. Rosenthal, E. A. Lingren, T. Feng, Q. Kullo, I. J. Narita, A. Takayama, 2021-12-08 doi:10.1101/2021.12.07.470215 Cold Spring Harbor Laboratory Press 2021-12-08 <![CDATA[ Ureter single-cell and spatial mapping reveal cell types, architecture, and signaling networks ]]> https://biorxiv.org/content/10.1101/2021.12.22.473889v1?rss=1 Ting, A. H. Fink, E. E. Sona, S. Tran, U. Desprez, P.-E. Bradley, M. Qiu, H. Eltemamy, M. Wee, A. Wolkov, M. Nicolas, M. Min, B. Haber, G.-P. Wessely, O. H. Lee, B. H. 2021-12-23 doi:10.1101/2021.12.22.473889 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Structure of anchorless RML prion reveals motif variation between strains ]]> https://biorxiv.org/content/10.1101/2021.12.22.473909v1?rss=1 Hoyt, F. Standke, H. G. Artikis, E. Schwartz, C. L. Hansen, B. Li, K. Hughson, A. G. Manca, M. Thomas, O. R. Raymond, G. J. Baron, G. S. Caughey, B. Kraus, A. 2021-12-22 doi:10.1101/2021.12.22.473909 Cold Spring Harbor Laboratory Press 2021-12-22 <![CDATA[ Two distinct binding modes provide the RNA binding protein RbFox with extraordinary sequence specificity ]]> https://biorxiv.org/content/10.1101/2021.12.23.474020v1?rss=1 Ye, X. Yang, W. Yi, S. Zhao, Y. Yang, F. Varani, G. Jankowsky, E. 2021-12-24 doi:10.1101/2021.12.23.474020 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ Expanded ACE2 dependencies of diverse SARS-like coronavirus receptor binding domains ]]> https://biorxiv.org/content/10.1101/2021.12.25.474149v1?rss=1 Roelle, S. M. Shukla, N. Pham, A. T. Bruchez, A. M. Matreyek, K. A. 2022-01-03 doi:10.1101/2021.12.25.474149 Cold Spring Harbor Laboratory Press 2022-01-03 <![CDATA[ Super-immunity by broadly protective nanobodies to sarbecoviruses ]]> https://biorxiv.org/content/10.1101/2021.12.26.474192v1?rss=1 Xiang, Y. Huang, W. Liu, H. Sang, Z. Nambulli, S. Tubiana, J. Williams, K. L. Duprex, P. Schneidman-Duhovny, D. Wilson, I. A. Taylor, D. J. Shi, Y. 2021-12-28 doi:10.1101/2021.12.26.474192 Cold Spring Harbor Laboratory Press 2021-12-28 <![CDATA[ DRP1-mediated mitochondrial fission is essential to maintain cristae morphology and bioenergetics ]]> https://biorxiv.org/content/10.1101/2021.12.31.474637v1?rss=1 Robertson, G. L. Riffle, S. Patel, M. Marshall, A. Beasley, H. Garza-Lopez, E. Shao, J. Vue, Z. Hinton, A. Mears, J. Gama, V. 2022-01-03 doi:10.1101/2021.12.31.474637 Cold Spring Harbor Laboratory Press 2022-01-03 <![CDATA[ Noise source importance in linear stochastic models of biological systems that grow, shrink, wander, or persist ]]> https://biorxiv.org/content/10.1101/2022.01.10.475598v1?rss=1 Strang, A. Huffmyer, W. Rollins, H. Abbott, K. C. Thomas, P. J. 2022-01-11 doi:10.1101/2022.01.10.475598 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ Enhancement of RecET-mediated in vivo linear DNA assembly by a xonA mutation ]]> https://biorxiv.org/content/10.1101/2022.01.13.476211v1?rss=1 Sawitzke, J. A. Costantino, N. C. Hutchinson, E. Thomason, L. Court, D. L. 2022-01-14 doi:10.1101/2022.01.13.476211 Cold Spring Harbor Laboratory Press 2022-01-14 <![CDATA[ Encoding sensing functions into material interface for a rationally engineered integrated electrochemical liquid biopsy ]]> https://biorxiv.org/content/10.1101/2022.01.17.476350v1?rss=1 Zhang, Y. Zhu, H. Ying, Z. Gao, X. Chen, W. Zhan, Y. Feng, L. Liu, C.-c. Dai, Y. 2022-01-20 doi:10.1101/2022.01.17.476350 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ PopB-PcrV Interactions are Essential for Pore Formation in the Pseudomonas aeruginosa Type III Secretion System Translocon ]]> https://biorxiv.org/content/10.1101/2022.01.21.477233v1?rss=1 Kundracik, E. C. Trichka, J. Diaz Aponte, J. E. Rietsch, A. 2022-01-22 doi:10.1101/2022.01.21.477233 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ Divergent Golgi Trafficking Limits B cell-Mediated IgG Sialylation ]]> https://biorxiv.org/content/10.1101/2022.01.25.477787v1?rss=1 Glendenning, L. M. Zhou, J. Y. Reynero, K. M. Cobb, B. A. 2022-01-28 doi:10.1101/2022.01.25.477787 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ The RNA helicase DDX39B activates FOXP3 RNA splicing to control T regulatory cell fate ]]> https://biorxiv.org/content/10.1101/2022.01.25.477795v1?rss=1 Hirano, M. Galarza-Munoz, G. Schott, G. Wang, L. Nagasawa, C. Antonia, A. L. Jain, V. Yu, X. Widen, S. G. Briggs, F. B. Gregory, S. G. Ko, D. C. Fagg, W. S. Bradrick, S. Garcia-Blanco, M. A. 2022-01-27 doi:10.1101/2022.01.25.477795 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ Plasma ST6Gal1 is Dispensable for IgG Sialylation ]]> https://biorxiv.org/content/10.1101/2022.02.01.478679v1?rss=1 Oswald, D. M. Lehoux, S. D. Zhou, J. Y. Glendenning, L. M. Cummings, R. D. Cobb, B. A. 2022-02-04 doi:10.1101/2022.02.01.478679 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Inactivating Mast Cell Function Promotes Steady-State and Regenerative Hematopoiesis ]]> https://biorxiv.org/content/10.1101/2022.02.03.479012v1?rss=1 Smith, J. N. P. Campanelli, J. Cordova, B. Broncano, A. Christo, K. F. Markowitz, S. D. Gerson, S. L. Desai, A. B. 2022-02-04 doi:10.1101/2022.02.03.479012 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Characterization of the Interaction of Nanobubble Ultrasound Contrast Agents with Human Blood Components ]]> https://biorxiv.org/content/10.1101/2022.02.11.480110v1?rss=1 Cooley, M. B. Abenojar, E. C. Wegierak, D. Sen Gupta, A. Kolios, M. C. Exner, A. A. 2022-02-14 doi:10.1101/2022.02.11.480110 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution ]]> https://biorxiv.org/content/10.1101/2022.02.24.481899v1?rss=1 Starr, T. N. Greaney, A. J. Hannon, W. W. Loes, A. N. Hauser, K. Dillen, J. R. Ferri, E. Ghez Farrell, A. Dadonaite, B. McCallum, M. Matreyek, K. A. Corti, D. Veesler, D. Snell, G. Bloom, J. D. 2022-02-26 doi:10.1101/2022.02.24.481899 Cold Spring Harbor Laboratory Press 2022-02-26 <![CDATA[ Molecular Basis for Variations in the Sensitivity of Pathogenic Rhodopsin Variants to 9-cis-Retinal ]]> https://biorxiv.org/content/10.1101/2022.03.01.482516v1?rss=1 Roushar, F. J. McKee, A. G. Kuntz, C. P. Ortega, J. T. Penn, W. D. Woods, H. Chamness, L. M. Most, V. Meiler, J. Jastrzebska, B. Schlebach, J. P. 2022-03-01 doi:10.1101/2022.03.01.482516 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ The Endoplasmic Reticulum Membrane Complex Promotes Proteostasis of GABAA Receptors ]]> https://biorxiv.org/content/10.1101/2022.03.03.482920v1?rss=1 Whittsette, A. Wang, Y.-J. Mu, T.-W. 2022-03-04 doi:10.1101/2022.03.03.482920 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Conserved Pib2 regions have distinct roles in TORC1 regulation at the vacuole ]]> https://biorxiv.org/content/10.1101/2022.03.04.483060v1?rss=1 Troutman, K. K. Varlakhanova, N. V. Tornabene, B. A. Ramachandran, R. Ford, M. G. J. 2022-03-04 doi:10.1101/2022.03.04.483060 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Newly synthesized mRNA escapes translational repression during the acute phase of the mammalian unfolded protein response ]]> https://biorxiv.org/content/10.1101/2022.03.06.483204v1?rss=1 Alzahrani, M. R. Guan, B. Zagore, L. Wu, J. Licatalosi, D. Baker, K. E. Hatzoglou, M. 2022-03-07 doi:10.1101/2022.03.06.483204 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Molecular profiling of XPO1 inhibitor and gemcitabine-nab-paclitaxel combination in cellular and LSL-Kras G12D/+; Trp53 fl/+; Pdx1-Cre (KPC) pancreatic cancer model ]]> https://biorxiv.org/content/10.1101/2022.03.08.481108v1?rss=1 Uddin, M. H. Aboukameel, A. Li, Y. Khan, H. Y. Sexton, R. E. Bannoura, S. Dyson, G. Al-Hallak, M. N. Mzannar, Y. Mohamed, A. Landesman, Y. Kim, S. Beydoun, R. Mohammad, R. M. Shields, A. F. Azmi, A. S. 2022-03-09 doi:10.1101/2022.03.08.481108 Cold Spring Harbor Laboratory Press 2022-03-09 <![CDATA[ Quantitative interactome proteomics identifies proteostasis network for GABAA receptors ]]> https://biorxiv.org/content/10.1101/2022.03.08.483512v1?rss=1 Wang, Y.-J. Di, X.-J. Mu, T. 2022-03-08 doi:10.1101/2022.03.08.483512 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ R-BIND 2.0: An Updated Database of Bioactive RNA-Targeting Small Molecules and Associated RNA Secondary Structures ]]> https://biorxiv.org/content/10.1101/2022.03.14.484334v1?rss=1 Donlic, A. Swanson, E. G. Chiu, L.-Y. Wicks, S. L. Umuhire Juru, A. Cai, Z. Kassam, K. J. Laudeman, C. Sanaba, B. Sugarman, A. Han, E. Tolbert, B. S. Hargrove, A. E. 2022-03-15 doi:10.1101/2022.03.14.484334 Cold Spring Harbor Laboratory Press 2022-03-15 <![CDATA[ Conventional polymers may unintentionally refill in vivo with unassociated drugs ]]> https://biorxiv.org/content/10.1101/2022.03.21.485180v1?rss=1 Young, K. Dogan, A. B. Hernandez, C. Exner, A. A. von Recum, H. A. 2022-03-23 doi:10.1101/2022.03.21.485180 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Multiplexed microfluidic chip for cell co-culture ]]> https://biorxiv.org/content/10.1101/2022.03.25.485382v1?rss=1 Watson, C. Liu, C. Ansari, A. Miranda, H. C. Somoza, R. A. Senyo, S. E. 2022-03-27 doi:10.1101/2022.03.25.485382 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Helical remodeling augments 5-lipoxygenase activity ]]> https://biorxiv.org/content/10.1101/2022.03.31.486615v1?rss=1 Gallegos, E. M. Reed, T. D. Mathes, F. A. Guevara, N. Neau, D. Huang, W. Newcomer, M. E. Gilbert, N. C. 2022-03-31 doi:10.1101/2022.03.31.486615 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ Actin turnover required for adhesion-independent bleb migration ]]> https://biorxiv.org/content/10.1101/2022.04.01.486735v1?rss=1 Copos, C. Strychalski, W. 2022-04-01 doi:10.1101/2022.04.01.486735 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Chromenone derivatives as novel pharmacological chaperones for retinitis pigmentosa-linked rod opsin mutants ]]> https://biorxiv.org/content/10.1101/2022.04.05.487228v1?rss=1 Ortega, J. T. McKee, A. G. Roushar, F. J. Penn, W. D. Schlebach, J. P. Jastrzebska, B. 2022-04-08 doi:10.1101/2022.04.05.487228 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Neutrophil IL-1β secretion induced by ExoS expressing Pseudomonas aeruginosa is dependent on NLRP3 and Gasdermin D ]]> https://biorxiv.org/content/10.1101/2022.04.07.487503v1?rss=1 Minns, M. Lima, T. Liboro, K. Abbondante, S. Marshall, M. Rietsch, A. Dubyak, G. Pearlman, E. 2022-04-07 doi:10.1101/2022.04.07.487503 Cold Spring Harbor Laboratory Press 2022-04-07 <![CDATA[ COVID-19 Infection and Transmission Includes Complex Sequence Diversity ]]> https://biorxiv.org/content/10.1101/2022.04.18.488717v1?rss=1 Chan, E. R. Jones, L. D. Linger, M. Kovach, J. D. Torres-Teran, M. M. Wertz, A. Donskey, C. J. Zimmerman, P. A. 2022-04-19 doi:10.1101/2022.04.18.488717 Cold Spring Harbor Laboratory Press 2022-04-19 <![CDATA[ Prediction of Kinase-Substrate Associations Using The Functional Landscape of Kinases and Phosphorylation Sites ]]> https://biorxiv.org/content/10.1101/2022.04.22.489231v1?rss=1 90%) of the identified phosphorylation sites are unknown. Knowledge of kinase-substrate associations is also mostly limited to a small number of well-studied kinases, with 20% of known kinases accounting for the phosphorylation of 87% of currently annotated sites. The scarcity of available annotations calls for the development of computational algorithms for more comprehensive and reliable prediction of kinase-substrate associations. ResultsTo broadly utilize available structural, functional, evolutionary, and contextual information in predicting kinase-substrate associations, we develop a network-based machine learning framework. Our framework integrates a multitude of data sources to characterize the landscape of functional relationships and associations among phosphosites and kinases. To construct a phosphosite-phosphosite association network, we use sequence similarity, shared biological pathways, co-evolution, co-occurrence, and co-phosphorylation of phosphosites across different biological states. To construct a kinase-kinase association network, we integrate protein-protein interactions, shared biological pathways, and membership in common kinase families. We use node embeddings computed from these heterogeneous networks to train machine learning models for predicting kinase-substrate associations. Our systematic computational experiments using the PhosphositePLUS database shows that the resulting algorithm, NetKSA, outperforms state-of-the-art algorithms and resources, including KinomeXplorer and LinkPhinder, in reliably predicting KSAs. By stratifying the ranking of kinases, NetKSA also enables annotation of phosphosites that are targeted by relatively less-studied kinases. Finally, we observe that the performance of NetKSA is robust to the choice of network embedding algorithms, while each type of network contributes valuable information that is complementary to the information provided by other networks. ConclusionRepresentation of available functional information on kinases and phosphorylation sites, along with integrative machine learning algorithms, has the potential to significantly enhance our knowledge on kinase-substrate associations. AvailabilityThe code and data are available at compbio.case.edu/NetKSA. ]]> Ayati, M. Yilmaz, S. Blasco Tavares Pereira Lopes, F. Chance, M. R. Koyuturk, M. 2022-04-22 doi:10.1101/2022.04.22.489231 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Spleen voltammetry assesses in real time norepinephrine release elicited by autonomic stimulation ]]> https://biorxiv.org/content/10.1101/2022.04.26.489592v1?rss=1 Mughrabi, I. T. Gerber, M. Jayaprakash, N. Al-Abed, Y. Zanos, S. 2022-04-28 doi:10.1101/2022.04.26.489592 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ ATP6AP2-to-MMP14, a key pathway for osteoblast to osteocyte transition ]]> https://biorxiv.org/content/10.1101/2022.04.27.489713v1?rss=1 Xiong, L. Guo, H.-H. PAN, J.-X. Ren, X. Lee, D. Mei, L. Xiong, W.-C. 2022-04-28 doi:10.1101/2022.04.27.489713 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Increased glucose availability sensitizes pancreatic cancer to chemotherapy ]]> https://biorxiv.org/content/10.1101/2022.04.29.490090v1?rss=1 Vaziri-Gohar, A. Hue, J. J. Graor, H. J. Abbas, A. Zarei, M. Hajihassani, O. Titomihelakis, G. Feczko, J. Rathore, M. Wang, R. Zarei, M. Goudarzi, M. Zhang, R. Willard, B. Zhang, L. Wang, G.-M. Tatsuoka, C. Salvino, J. M. Bederman, I. Brunengraber, H. Lyssiotis, C. A. Brody, J. R. Winter, J. M. 2022-05-01 doi:10.1101/2022.04.29.490090 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ HIV-1 Rev-RRE Functional Activity in Primary Isolates is Highly Dependent on Minimal Context-Dependent Changes in Rev ]]> https://biorxiv.org/content/10.1101/2022.04.29.490105v1?rss=1 Dzhivhuho, G. Holsey, J. O'Farrell, H. Rekosh, D. Hammmarskjold, M.-L. A. Jackson, P. E. H. 2022-04-29 doi:10.1101/2022.04.29.490105 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ Inferring Density-Dependent Population Dynamics Mechanisms through Rate Disambiguation for Logistic Birth-Death Processes ]]> https://biorxiv.org/content/10.1101/2022.05.10.491405v1?rss=1 Huynh, L. Scott, J. G. Thomas, P. J. 2022-05-11 doi:10.1101/2022.05.10.491405 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Wild-type IDH1 inhibition enhances chemotherapy response in melanoma ]]> https://biorxiv.org/content/10.1101/2022.05.13.491880v1?rss=1 Zarei, M. Hajihassani, O. Hue, J. J. Graor, H. J. Rathore, M. Vaziri-Gohar, A. Asara, J. M. Winter, J. M. Rothermel, L. D. 2022-05-14 doi:10.1101/2022.05.13.491880 Cold Spring Harbor Laboratory Press 2022-05-14 <![CDATA[ Kidney collecting duct cells make vasopressin in response to NaCl induced hypertonicity ]]> https://biorxiv.org/content/10.1101/2022.05.13.491898v1?rss=1 Arroyo, J. P. Terker, A. S. Zuchowski, Y. Watts, J. A. Bock, F. Meyer, C. Luo, W. Kapp, M. E. Gould, E. R. Hammock, E. Wilson, M. Zent, R. Zhang, M.-Z. Bhave, G. Harris, R. C. 2022-05-13 doi:10.1101/2022.05.13.491898 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Variational and phase response analysis for limit cycles with hard boundaries, with applications to neuromechanical control problems ]]> https://biorxiv.org/content/10.1101/2022.05.17.492350v1?rss=1 Wang, Y. Gill, J. P. Chiel, H. J. Thomas, P. J. 2022-05-20 doi:10.1101/2022.05.17.492350 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Membrane-Bound O-Acyltransferase 7 (MBOAT7)-Driven Lysophosphatidylinositol (LPI) Acylation in Adipocytes Contributes to Systemic Glucose Homeostasis ]]> https://biorxiv.org/content/10.1101/2022.05.19.492632v1?rss=1 T) near the gene encoding Membrane-Bound O-Acyltransferase 7 (MBOAT7) is associated with increased susceptibility to NAFLD as well as the entire spectrum of NAFLD progression. The MBOAT7 gene encodes a lipid metabolic enzyme that is capable of esterifying polyunsaturated fatty acyl-CoAs to LPI substrates to generate phosphatidylinositol (PI) lipids. We previously showed that antisense oligonucleotide (ASO)-mediated knockdown of Mboat7 in mice promoted high fat diet-induced hepatic steatosis, hyperinsulinemia, and systemic insulin resistance (Helsley et al., 2019). Thereafter, other groups showed that hepatocyte-specific genetic deletion of Mboat7 promoted striking fatty liver and NAFLD progression but does not alter insulin sensitivity, suggesting the potential for cell autonomous roles. Here, we show that MBOAT7 function in adipocytes contributes to diet-induced metabolic disturbances including hyperinsulinemia and systemic insulin resistance. The expression of Mboat7 in white adipose tissue closely correlates with diet-induced obesity across a panel of [~]100 inbred strains of mice fed a high fat/high sucrose diet. Moreover, adipocyte-specific genetic deletion of Mboat7 is sufficient to promote hyperinsulinemia, systemic insulin resistance, and mild fatty liver. Unlike in the liver, where Mboat7 plays a relatively minor role in maintaining arachidonic acid (AA)-containing PI pools, Mboat7 is the major source of AA-containing PI pools in adipose tissue. Our data demonstrate that MBOAT7 is a critical regulator of adipose tissue PI homeostasis, and adipocyte MBOAT7-driven PI biosynthesis is closely linked to hyperinsulinemia and insulin resistance in mice. ]]> Massey, W. Varadharajan, V. Banerjee, R. Brown, A. L. Horak, A. J. Hohe, R. C. Chan, E. R. Pan, C. Zhang, R. Allende, D. S. Lusis, A. J. Brown, J. M. 2022-05-19 doi:10.1101/2022.05.19.492632 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Spatially selective stimulation of the pig vagus nerve to modulate target effect versus side effect ]]> https://biorxiv.org/content/10.1101/2022.05.19.492726v1?rss=1 Blanz, S. L. Musselman, E. D. Settell, M. L. Knudsen, B. E. Nicolai, E. N. Trevathan, J. K. Verner, R. S. Begnaud, J. Suminski, A. J. Williams, J. C. Shoffstall, A. J. Grill, W. M. Pelot, N. A. Ludwig, K. A. 2022-05-20 doi:10.1101/2022.05.19.492726 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Surveying non-visual arrestins reveals allosteric interactions between functional sites ]]> https://biorxiv.org/content/10.1101/2022.05.20.492847v1?rss=1 Seckler, J. M. Robinson, E. N. Lewis, S. J. Grossfield, A. 2022-05-21 doi:10.1101/2022.05.20.492847 Cold Spring Harbor Laboratory Press 2022-05-21 <![CDATA[ Sickle red blood cell derived extracellular vesicles activate endothelial cells and enhance sickle red cell adhesion mediated by von Willebrand factor ]]> https://biorxiv.org/content/10.1101/2022.05.25.492883v1?rss=1 An, R. Man, Y. Cheng, K. Zhang, T. Chen, C. Kucukal, E. Wulftange, W. Goreke, U. Bode, A. Nayak, L. Vercellotti, G. M. Belcher, J. D. Little, J. A. Gurkan, U. A. 2022-05-25 doi:10.1101/2022.05.25.492883 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Opto-MASS: a high-throughput engineering platform for genetically encoded fluorescentsensors enabling all optical in vivo detection of monoamines and neuropeptides ]]> https://biorxiv.org/content/10.1101/2022.06.01.494241v1?rss=1 Rappleye, M. Gordon-Fennel, A. Castro, D. C. Matarasso, A. K. Zamorano, C. A. Wait, S. J. Lee, J. D. Siebart, J. D. Suko, A. Smith, N. C. Muster, J. Matreyek, K. A. Fowler, D. M. Stuber, G. D. Bruchas, M. R. Berndt, A. 2022-06-02 doi:10.1101/2022.06.01.494241 Cold Spring Harbor Laboratory Press 2022-06-02 <![CDATA[ Linking physiology to ecosystem function: how vulnerable are different functional groups to climate change? ]]> https://biorxiv.org/content/10.1101/2022.06.07.495062v1?rss=1 da Silva, C. R. B. Beaman, J. E. Youngblood, J. Kellermann, V. Diamond, S. E. 2022-06-11 doi:10.1101/2022.06.07.495062 Cold Spring Harbor Laboratory Press 2022-06-11 <![CDATA[ Detecting sources of immune activation and viral rebound in HIV infection ]]> https://biorxiv.org/content/10.1101/2022.06.08.495415v1?rss=1 Wietgrefe, S. Duan, L. Anderson, J. Marques, G. Sanders, M. Cummins, N. W. Badley, A. D. Dobrowolski, C. Karn, J. Pagliuzza, A. Chomont, N. Sannier, G. Dube, M. Kaufmann, D. E. Zuck, P. Wu, G. Howell, B. Reilly, C. Herschhorn, A. Schacker, T. Haase, A. T. 2022-06-11 doi:10.1101/2022.06.08.495415 Cold Spring Harbor Laboratory Press 2022-06-11 <![CDATA[ Small molecule mediated stabilization of PP2A modulates the Homologous Recombination pathway and potentiates DNA damage-induced cell death ]]> https://biorxiv.org/content/10.1101/2022.06.10.495657v1?rss=1 Avelar, R. Armstrong, A. Carvette, G. Puleo, N. Gupta, R. Colina, J. Joseph, P. Sobeck, A. O'Connor, C. Gandhi, A. Dziubinski, M. Ma, D. Waggoner, S. Zanotti, K. Nagel, C. Resnick, K. Singh, S. Thomas, D. Skala, S. Zhang, J. Narla, G. DiFeo, A. 2022-06-12 doi:10.1101/2022.06.10.495657 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Fitness seascapes facilitate the prediction of therapy resistance under time-varying selection ]]> https://biorxiv.org/content/10.1101/2022.06.10.495696v1?rss=1 King, E. S. Pelesko, J. Maltas, J. A. Owen, S. J. Dolson, E. Scott, J. G. 2022-06-12 doi:10.1101/2022.06.10.495696 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Sex-specific niche signaling contributes to sexual dimorphism following stem cell transplantation ]]> https://biorxiv.org/content/10.1101/2022.06.13.495897v1?rss=1 Smith, J. N. P. Cordova, B. A. Richardson, B. Christo, K. F. Campanelli, J. Broncano, A. V. Chen, J. Lee, J. Cameron, S. J. Lathia, J. D. Goodman, W. A. Cameron, M. J. Desai, A. B. 2022-06-16 doi:10.1101/2022.06.13.495897 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ MicroRNA-27a is essential for bone remodeling by modulating p62-mediated osteoclast signaling ]]> https://biorxiv.org/content/10.1101/2022.06.13.495939v1?rss=1 Hsu, W. Wang, S. Maruyama, E. O. Martinez, J. Hsu, T. Wu, W. Maruyama, T. 2022-06-17 doi:10.1101/2022.06.13.495939 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Brain-Controlled Electrical Stimulation Restores Continuous Finger Function ]]> https://biorxiv.org/content/10.1101/2022.06.15.496349v1?rss=1 Nason-Tomaszewski, S. R. Mender, M. J. Kennedy, E. Lambrecht, J. M. Kilgore, K. L. Chiravuri, S. Ganesh Kumar, N. Kung, T. A. Willsey, M. S. Chestek, C. A. Patil, P. G. 2022-06-17 doi:10.1101/2022.06.15.496349 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Probing the biophysical constraints of SARS-CoV-2 spike N-terminal domain using deep mutational scanning ]]> https://biorxiv.org/content/10.1101/2022.06.20.496903v1?rss=1 Ouyang, W. O. Tan, T. J. C. Lei, R. Song, G. Kieffer, C. Andrabi, R. Matreyek, K. A. Wu, N. C. 2022-06-21 doi:10.1101/2022.06.20.496903 Cold Spring Harbor Laboratory Press 2022-06-21 <![CDATA[ Enhancers of human and rodent oligodendrocyte formation predominantly induce cholesterol precursor accumulation ]]> https://biorxiv.org/content/10.1101/2022.06.21.497032v1?rss=1 Sax, J. Hershman, S. Hubler, Z. Allimuthu, D. Elitt, M. S. Bederman, I. Adams, D. J. 2022-06-24 doi:10.1101/2022.06.21.497032 Cold Spring Harbor Laboratory Press 2022-06-24 <![CDATA[ Liver Endothelium Microenvironment Promotes HER3-mediated Cell Growth in Pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2022.06.24.497507v1?rss=1 Zhang, W. Wright, M. Rathore, M. Zarei, M. Vaziri-Gohar, A. Winter, J. Brody, J. Wang, R. 2022-06-28 doi:10.1101/2022.06.24.497507 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ Diet prevents the expansion of segmented filamentous bacteria and ileo-colonic inflammation in a model of Crohn's disease ]]> https://biorxiv.org/content/10.1101/2022.07.06.498810v1?rss=1 Metwaly, A. Jovic, J. Waldschmitt, N. Khaloian, S. Heimes, H. Haecker, D. Hammoudi, N. Le Bourhis, L. Mayorgas, A. Siebert, K. Basic, M. Schwerd, T. Allez, M. Panes, J. Salas, A. Bleich, A. Zeissig, S. Schnupf, P. Cominelli, F. Haller, D. 2022-07-06 doi:10.1101/2022.07.06.498810 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ Single-cell CD8+ dynamics in PLWH uncover the depletion of TIGIT+ memory HIV-1-specific cells during long-term ART ]]> https://biorxiv.org/content/10.1101/2022.07.13.499924v1?rss=1 Blanch-Lombarte, O. Ouchi, D. Jimenez-Moyano, E. Carabelli, J. Marin, M. A. Penya, R. Pelletier, A. Talla, A. Sharma, A. Dalmau, J. Santos, J. R. Sekaly, R.-P. A. Clotet, B. Prado, J. G. 2022-07-14 doi:10.1101/2022.07.13.499924 Cold Spring Harbor Laboratory Press 2022-07-14 <![CDATA[ Stabilization of a Protein by a Single Halogen-Based Aromatic Amplifier ]]> https://biorxiv.org/content/10.1101/2022.07.25.501420v1?rss=1 Hage, K. E. Phillips, N. B. Chen, Y.-S. Dhayalan, B. Whittaker, J. Carr, K. Whittaker, L. Phillips, M. H. Ismail-Beigi, F. Meuwly, M. Weiss, M. A. 2022-07-25 doi:10.1101/2022.07.25.501420 Cold Spring Harbor Laboratory Press 2022-07-25 <![CDATA[ BRAFV600E expression in thyrocytes causes recruitment of immunosuppressive STABILIN-1 macrophages ]]> https://biorxiv.org/content/10.1101/2022.07.27.501733v1?rss=1 Spourquet, C. Delcorte, O. Lemoine, P. Dauguet, N. Loriot, A. Achouri, Y. Hollmen, M. Jalkanen, S. Huaux, F. Lucas, S. Van Meerbeeck, P. Knauf, J. Fagin, J. A. Dessy, C. Mourad, M. Henriet, P. Tyteca, D. Marbaix, E. Pierreux, C. E. 2022-07-29 doi:10.1101/2022.07.27.501733 Cold Spring Harbor Laboratory Press 2022-07-29 <![CDATA[ Surgical techniques and tips for a reliable murine model of primary and metastatic pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2022.07.30.502136v1?rss=1 Hue, J. J. Zarei, M. Graor, H. J. Hajihassani, O. Katayama, E. S. Loftus, A. W. Vaziri-Gohar, A. Winter, J. M. 2022-08-02 doi:10.1101/2022.07.30.502136 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Recovery of forearm and fine digit function after chronic spinal cord injury by simultaneous blockade of inhibitory matrix CSPG production and the receptor PTPσ. ]]> https://biorxiv.org/content/10.1101/2022.08.01.502398v1?rss=1 Milton, A. Silver, D. J. Kwok, J. C. F. McClellan, J. Warren, P. M. Silver, J. 2022-08-03 doi:10.1101/2022.08.01.502398 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Coordinated cadherin functions sculpt respiratory motor circuit connectivity ]]> https://biorxiv.org/content/10.1101/2022.08.02.502511v1?rss=1 Vagnozzi, A. N. Moore, M. T. Lin, M. Brozost, E. M. KC, R. Agarwal, A. Lindsay, S. Duan, X. Zampieri, N. Landmesser, L. T. Philippidou, P. 2022-08-04 doi:10.1101/2022.08.02.502511 Cold Spring Harbor Laboratory Press 2022-08-04 <![CDATA[ The Translation Initiation Factor Homolog, eif4e1c, Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration ]]> https://biorxiv.org/content/10.1101/2022.08.15.502524v1?rss=1 Rao, A. Lyu, B. Lubbertozzi, A. Jahan, I. Tedeschi, F. Jankowsky, E. Carstens, B. C. Poss, K. D. Baskin, K. Goldman, J. A. 2022-08-15 doi:10.1101/2022.08.15.502524 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Sex-specific T cell exhaustion drives differential immune responses in glioblastoma ]]> https://biorxiv.org/content/10.1101/2022.08.17.503211v1?rss=1 Lee, J. Nicosia, M. Silver, D. J. Li, C. Bayik, D. Watson, D. C. Lauko, A. Johnson, S. McGraw, M. Grabowski, M. Kish, D. Desai, A. Goodman, W. Cameron, S. Okada, H. Valujskikh, A. Fairchild, R. L. Ahluwalia, M. S. Lathia, J. D. 2022-08-18 doi:10.1101/2022.08.17.503211 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ Boolean modeling of mechanosensitive Epithelial to Mesenchymal Transition and its reversal ]]> https://biorxiv.org/content/10.1101/2022.08.29.505701v1?rss=1 Sullivan, E. Harris, M. Bhatnagar, A. Guberman, E. Zonfa, I. Ravasz Regan, E. 2022-09-01 doi:10.1101/2022.08.29.505701 Cold Spring Harbor Laboratory Press 2022-09-01 <![CDATA[ Receptor binding domain (RBD) antibodies contribute more to SARS-CoV-2 neutralization when target cells express high levels of ACE2 ]]> https://biorxiv.org/content/10.1101/2022.08.29.505713v1?rss=1 Farrell, A. G. Dadonaite, B. Greaney, A. J. Eguia, R. Loes, A. N. Francko, N. M. Logue, J. Carreno, J. M. Abbad, A. Chu, H. Y. Matreyek, K. A. Bloom, J. D. 2022-08-30 doi:10.1101/2022.08.29.505713 Cold Spring Harbor Laboratory Press 2022-08-30 <![CDATA[ Safeguarding Drosophila female germ cell identity depends on an H3K9me3 mini domain guided by a ZAD zinc finger protein ]]> https://biorxiv.org/content/10.1101/2022.09.04.506543v1?rss=1 Shapiro-Kulnane, L. Salz, H. K. 2022-09-04 doi:10.1101/2022.09.04.506543 Cold Spring Harbor Laboratory Press 2022-09-04 <![CDATA[ The cytidine deaminase APOBEC3G drives cancer mutagenesis and clonal evolution in bladder cancer ]]> https://biorxiv.org/content/10.1101/2022.09.05.503899v1?rss=1 Liu, W. Newhall, K. P. Khani, F. Barlow, L. Nguyen, D. Gu, L. Eng, K. Bhinder, B. Uppal, M. Recapet, C. Sboner, A. Ross, S. R. Elemento, O. Chelico, L. Faltas, B. M. 2022-09-05 doi:10.1101/2022.09.05.503899 Cold Spring Harbor Laboratory Press 2022-09-05 <![CDATA[ Reduction of the HIV-1 reservoir in T cells from persons with HIV-1 on suppressive antiretroviral therapy using expanded natural killer cells ex vivo ]]> https://biorxiv.org/content/10.1101/2022.09.05.506592v1?rss=1 Checkley Luttge, M. A. LUTTGE, B. G. Dobrowolski, C. Wald, D. N. McMahon, D. Haidar, G. Sobolewski, M. D. Enick, P. N. Cyktor, J. Mellors, J. W. Karn, J. 2022-09-06 doi:10.1101/2022.09.05.506592 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ Mechanisms of mRNA processing defects in inherited THOC6 intellectual disability syndrome ]]> https://biorxiv.org/content/10.1101/2022.09.06.506502v1?rss=1 Werren, E. A. LaForce, G. R. Srivastava, A. Perillo, D. R. Johnson, K. Berger, B. Baris, S. Regan, S. L. Pfennig, C. D. de Munnik, S. Pfundt, R. Hebbar, M. Jimenez-Heredia, R. Karakoc-Aydiner, E. Ozen, A. Dmytrus, J. Krolo, A. Corning, K. Prijoles, E. Louie, R. Lebel, R. Le, T.-L. Gordon, C. Girish, K. M. Boztug, K. Shukla, A. Bielas, S. L. Schaffer, A. E. 2022-09-07 doi:10.1101/2022.09.06.506502 Cold Spring Harbor Laboratory Press 2022-09-07 <![CDATA[ Cryo-EM of prion strains from the same genotype of host identifies conformational determinants ]]> https://biorxiv.org/content/10.1101/2022.09.19.508587v1?rss=1 Hoyt, F. Alam, P. Artikis, E. Schwartz, C. L. Hughson, A. G. Race, B. Baune, C. Raymond, G. J. Baron, G. S. Kraus, A. Caughey, B. 2022-09-19 doi:10.1101/2022.09.19.508587 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Peroxisome biogenesis initiated by protein phase separation ]]> https://biorxiv.org/content/10.1101/2022.09.20.508718v1?rss=1 Ravindran, R. Bacellar, I. O. L. Castellanos-Girouard, X. Zhang, Z. Kisley, L. Michnick, S. W. 2022-09-21 doi:10.1101/2022.09.20.508718 Cold Spring Harbor Laboratory Press 2022-09-21 <![CDATA[ Comprehensive characterization of multi-omic landscapes between gut-microbiota metabolites and the G-protein-coupled receptors in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2022.09.20.508759v1?rss=1 Qiu, Y. Hou, Y. Zhou, Y. Xu, J. Bykova, M. Leverenz, J. B. Pieper, A. P. Nussinov, R. Caldwell, J. Z. K. Brown, M. Cheng, F. 2022-09-22 doi:10.1101/2022.09.20.508759 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Allelic Transcription Factor binding shape transcriptional kinetics in human cell lines ]]> https://biorxiv.org/content/10.1101/2022.09.21.508743v1?rss=1 Jin, B. Feng, H. Bush, W. 2022-09-22 doi:10.1101/2022.09.21.508743 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ A Haptoglobin (HP) Structural Variant Alters the Effect of APOE Alleles on Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2022.09.22.508749v1?rss=1 Bai, H. Naj, A. C. Benchek, P. Dumitrescu, L. Hohman, T. Hamilton-Nelson, K. Kallianpur, A. R. Griswold, A. J. Vardarajan, B. Martin, E. R. Beecham, G. Below, J. E. Schellenberg, G. D. Mayeux, R. Farrer, L. Pericak-Vance, M. A. Haines, J. L. Bush, W. S. 2022-09-23 doi:10.1101/2022.09.22.508749 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ High-throughput identification of prefusion-stabilizing mutations in SARS-CoV-2 spike ]]> https://biorxiv.org/content/10.1101/2022.09.24.509341v1?rss=1 Tan, T. J. C. Mou, Z. Lei, R. Ouyang, W. O. Yuan, M. Song, G. Andrabi, R. Wilson, I. A. Kieffer, C. Dai, X. Matreyek, K. A. Wu, N. C. 2022-09-26 doi:10.1101/2022.09.24.509341 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Integrated Model of the Vertebrate Augmin Complex ]]> https://biorxiv.org/content/10.1101/2022.09.26.509603v1?rss=1 Travis, S. M. Mahon, B. P. Huang, W. Ma, M. Rale, M. J. Kraus, J. S. Taylor, D. Zhang, R. Petry, S. 2022-09-27 doi:10.1101/2022.09.26.509603 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Specific connectivity optimizes learning in thalamocortical loops ]]> https://biorxiv.org/content/10.1101/2022.09.27.509618v1?rss=1 Lakshminarasimhan, K. Xie, M. Cohen, J. D. Sauerbrei, B. Hantman, A. W. Litwin-Kumar, A. Escola, S. 2022-09-28 doi:10.1101/2022.09.27.509618 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Omnigenic epistasis regulates complex trait heritability ]]> https://biorxiv.org/content/10.1101/2022.09.28.509932v1?rss=1 Miller, A. K. Pan, C. Lusis, A. J. Crawford, D. C. Williams, S. M. Buchner, D. A. 2022-09-28 doi:10.1101/2022.09.28.509932 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Asynchronous haltere input impairs wing and gaze control in Drosophila ]]> https://biorxiv.org/content/10.1101/2022.09.29.509061v1?rss=1 Rauscher, M. J. Fox, J. L. 2022-09-30 doi:10.1101/2022.09.29.509061 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Microbiota-dependent histone butyrylation in the mammalian intestine ]]> https://biorxiv.org/content/10.1101/2022.09.29.510184v1?rss=1 Gates, L. A. Reis, B. S. Lund, P. J. Paul, M. R. Leboeuf, M. Nadeem, Z. Carroll, T. S. Garcia, B. Mucida, D. Allis, C. D. 2022-09-30 doi:10.1101/2022.09.29.510184 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Serotonergic Modulation of Spinal Circuitry Restores Motor Function after Chronic Spinal Cord Injury ]]> https://biorxiv.org/content/10.1101/2022.10.04.510858v1?rss=1 Walvekar, S. Robinson, R. B. Chadwick, H. M. Burch, R. M. Ding, H. Perlmutter, S. I. Moorjani, S. 2022-10-07 doi:10.1101/2022.10.04.510858 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Characterizing Aerosol Generating Procedures with Background Oriented Schlieren ]]> https://biorxiv.org/content/10.1101/2022.10.05.511018v1?rss=1 Howard, N. S. Alrefaie, A. Mejia, N. A. Ugbeye, T. Schmidt, B. E. 2022-10-06 doi:10.1101/2022.10.05.511018 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ A general theory for the dynamics of social populations: Within-group density dependence and between-group processes. ]]> https://biorxiv.org/content/10.1101/2022.10.07.511281v1?rss=1 Lerch, B. A. Abbott, K. C. 2022-10-07 doi:10.1101/2022.10.07.511281 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ kimma: flexible linear mixed effects modeling with kinship for RNA-seq data ]]> https://biorxiv.org/content/10.1101/2022.10.10.508946v1?rss=1 Dill-McFarland, K. A. Mitchell, K. Batchu, S. Segnitz, R. M. Benson, B. Janczyk, T. Cox, M. S. Mayanja-Kizza, H. A. Boom, W. H. Benchek, P. Stein, C. Hawn, T. R. Altman, M. C. 2022-10-11 doi:10.1101/2022.10.10.508946 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Data Descriptor: Human whole exome genotype data for Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2022.10.11.511653v1?rss=1 30. Our new strategy for processing these diversely generated WES samples has shown to generate high-quality data. The improved ability to combine data sequenced in different batches benefits the whole genomics research community. The WES data are accessible to the scientific community via https://dss.niagads.org/. ]]> Leung, Y. Y. Naj, A. C. Chou, Y.-F. Valladares, O. Wheeler, N. Lin, H. Gangadharan, P. Qu, L. Clark, K. Cantwell, L. Nicaretta, H. the Alzheimer's Disease Sequencing Project, Seshadri, S. Brkanac, Z. Cruchaga, C. Pericak-Vance, M. A. Mayeux, R. Kuzma, A. B. Lee, W.-P. Bush, W. S. DeStefano, A. L. Martin, E. Schellenberg, G. D. Wang, L.-S. 2022-10-13 doi:10.1101/2022.10.11.511653 Cold Spring Harbor Laboratory Press 2022-10-13 <![CDATA[ Enriching Biomedical Knowledge for Low-resource Language Through Translation ]]> https://biorxiv.org/content/10.1101/2022.10.11.511776v1?rss=1 Phan, L. Dang, T. Tran, H. Phan, V. Chau, L. D. Trinh, T. H. 2022-10-14 doi:10.1101/2022.10.11.511776 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ MR1-restricted T cell clonotypes are associated with 'resistance' to M.tuberculosis infection ]]> https://biorxiv.org/content/10.1101/2022.10.12.511825v1?rss=1 Cross, D. L. Layton, E. D. Yu, K. K. Smith, M. T. Aguilar, M. S. Li, S. Mayanja-Kizza, H. Stein, C. M. Boom, W. H. Hawn, T. R. Bradley, P. Newell, E. Seshadri, C. 2022-10-13 doi:10.1101/2022.10.12.511825 Cold Spring Harbor Laboratory Press 2022-10-13 <![CDATA[ Development of novel cytoprotective small compounds inhibiting mitochondria-dependent apoptosis ]]> https://biorxiv.org/content/10.1101/2022.10.12.511987v1?rss=1 Matsuyama, S. Matsuyama, M. Ortega, J. Fedorov, Y. Scott-McKean, J. Muller-Greven, J. Buck, M. Adams, D. Jastrzebska, B. Greenlee, W. 2022-10-12 doi:10.1101/2022.10.12.511987 Cold Spring Harbor Laboratory Press 2022-10-12 <![CDATA[ Are under-studied proteins under-represented? How to fairly evaluate link prediction algorithms in network biology ]]> https://biorxiv.org/content/10.1101/2022.10.13.511953v1?rss=1 Yilmaz, S. Yorgancioglu, K. Koyuturk, M. 2022-10-17 doi:10.1101/2022.10.13.511953 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Searching across-cohort relatives via encrypted genotype regression ]]> https://biorxiv.org/content/10.1101/2022.10.18.512407v1?rss=1 Zhang, Q.-X. Liu, T. Guo, X. Zhen, J. Bao, K. Yang, M.-y. Khederzadeh, S. Zhou, F. Han, X. Zheng, Q. Jia, P. Ding, X. He, M. Zou, X. Zhang, H. He, J. Zhu, X. Zou, Y. Lu, S. Lu, D. Chen, H. Zeng, C. Liu, F. Zheng, H.-F. Liu, S. Xu, H. Chen, G.-B. 2022-10-21 doi:10.1101/2022.10.18.512407 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ The NQR pathway regulates the immunomodulatory function of Bacteroides thetaiotaomicron ]]> https://biorxiv.org/content/10.1101/2022.10.21.513251v1?rss=1 Engelhart, M. J. Glowacki, R. W. Harding, C. V. Martens, E. C. Ahern, P. P. 2022-10-22 doi:10.1101/2022.10.21.513251 Cold Spring Harbor Laboratory Press 2022-10-22 <![CDATA[ Hsp47 Promotes Biogenesis of Multi-subunit Neuroreceptors in the Endoplasmic Reticulum ]]> https://biorxiv.org/content/10.1101/2022.10.24.513629v1?rss=1 Wang, Y.-J. Di, X.-J. Han, D.-Y. Nashmi, R. Henderson, B. J. Moss, F. J. Mu, T.-W. 2022-10-26 doi:10.1101/2022.10.24.513629 Cold Spring Harbor Laboratory Press 2022-10-26 <![CDATA[ Gating interactions steer loop conformational changes in the active site of the L1 metallo-β-lactamase ]]> https://biorxiv.org/content/10.1101/2022.10.25.513716v1?rss=1 Zhao, Z. Shen, X. Chen, S. Gu, J. Wang, H. Mojica, M. F. Samanta, M. Bhowmik, D. Vila, A. J. Bonomo, R. A. Haider, S. 2022-10-27 doi:10.1101/2022.10.25.513716 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ TRPA1 activation in non-sensory supporting cells contributes to regulation of cochlear sensitivity after acoustic trauma ]]> https://biorxiv.org/content/10.1101/2022.10.30.514409v1?rss=1 Velez-Ortega, A. C. Stepanyan, R. Edelmann, S. E. Torres-Gallego, S. Park, C. Marinkova, D. A. Nowacki, J. S. Sinha, G. P. Frolenkov, G. I. 2022-11-01 doi:10.1101/2022.10.30.514409 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Allosteric inhibition of the epidermal growth factor receptor through disruption of transmembrane interactions ]]> https://biorxiv.org/content/10.1101/2022.10.31.514582v1?rss=1 Rybak, J. A. Sahoo, A. R. Kim, S. Pyron, R. J. Pitts, S. B. Guleryuz, S. Smith, A. W. Buck, M. Barrera, F. N. 2022-11-01 doi:10.1101/2022.10.31.514582 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Size-Dependent Transport of Cerebrospinal Fluid Tracers in Mouse Brain Observed by Dynamic Contrast-Enhanced MRI ]]> https://biorxiv.org/content/10.1101/2022.11.03.515111v1?rss=1 Zhu, Y. Wang, G. Kolluru, C. Gu, Y. Gao, H. Zhang, J. Wang, Y. Wilson, D. L. Zhu, X. Flask, C. A. Yu, X. 2022-11-04 doi:10.1101/2022.11.03.515111 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Heterozygous Inversion Breakpoints Suppress Meiotic Crossovers by Altering Recombination Repair Outcomes ]]> https://biorxiv.org/content/10.1101/2022.11.09.515852v1?rss=1 Li, H. Berent, E. Hadjipanteli, S. Galey, M. Miller, D. E. Crown, K. N. 2022-11-09 doi:10.1101/2022.11.09.515852 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ Modeling multiphage-bacteria kinetics to predict phage therapy potency and longevity ]]> https://biorxiv.org/content/10.1101/2022.11.11.516137v1?rss=1 Yu, Z. Luong, T. Banuelos, S. Sue, A. Horn, M. A. Ryu, H. Roach, D. R. Segal, R. Huang, Q. 2022-11-11 doi:10.1101/2022.11.11.516137 Cold Spring Harbor Laboratory Press 2022-11-11 <![CDATA[ Catch bonds in sickle cell disease: shear-enhanced adhesion of red blood cells to laminin ]]> https://biorxiv.org/content/10.1101/2022.11.12.515898v1?rss=1 Goreke, U. Iram, S. Singh, G. Dominguez-Medina, S. Man, Y. Bode, A. An, R. Little, J. A. Wirth, C. L. Hinczewski, M. Gurkan, U. A. 2022-11-13 doi:10.1101/2022.11.12.515898 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Somatic Loss of the Y Chromosome and Alzheimer's Disease Risk ]]> https://biorxiv.org/content/10.1101/2022.11.14.516433v1?rss=1 Palmer, E. L. Benchek, P. Wheeler, N. R. Smeiszek, S. Naj, A. C. Haines, J. L. Pericak-Vance, M. A. Forsberg, L. A. Cukier, H. N. Song, Y. Bush, W. 2022-11-16 doi:10.1101/2022.11.14.516433 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Autism-specific PTEN p.I135L mutation and an autism genetic background combine to dysregulate cortical neurogenesis ]]> https://biorxiv.org/content/10.1101/2022.11.15.516317v1?rss=1 Fu, S. Bury, L. A. Eum, J. Wynshaw-Boris, A. 2022-11-16 doi:10.1101/2022.11.15.516317 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Temporal chromatin accessibility changes define transcriptional states essential for osteosarcoma metastasis ]]> https://biorxiv.org/content/10.1101/2022.11.15.516627v1?rss=1 Pontius, W. D. Hong, E. S. Faber, Z. J. Gray, J. Peacock, C. Bayles, I. Lovrenert, K. Bartels, C. F. Scacheri, P. C. 2022-11-17 doi:10.1101/2022.11.15.516627 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Cellular Maturation of Oligodendrocytes is Governed by Transient Gene Melting ]]> https://biorxiv.org/content/10.1101/2022.11.17.516981v1?rss=1 Allan, K. C. Miller, T. E. Morton, A. R. Scavuzzo, M. A. Elitt, M. S. Clayton, B. L. Hu, L. R. Vrabic, J. K. Olsen, H. E. Factor, D. C. Henninger, J. E. Young, R. A. Lin, C. Y. Scacheri, P. C. Tesar, P. J. 2022-11-18 doi:10.1101/2022.11.17.516981 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ Design and validation of an exposure system for efficient inter-animal SARS-CoV-2 airborne transmission in Syrian hamsters ]]> https://biorxiv.org/content/10.1101/2022.11.18.517035v1?rss=1 Kuehl, P. J. Dearing, J. Werts, A. Cox, J. Irshad, H. Barrett, E. G. Tucker, S. Langel, S. N. 2022-11-18 doi:10.1101/2022.11.18.517035 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ gtexture: Haralick texture analysis for graphs and its application to biological networks ]]> https://biorxiv.org/content/10.1101/2022.11.21.517417v1?rss=1 Barker-Clarke, R. J. Scott, J. G. Weaver, D. 2022-11-24 doi:10.1101/2022.11.21.517417 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ High-throughput Approaches to Uncover Synergistic Drug Combinations in Leukemia ]]> https://biorxiv.org/content/10.1101/2022.11.29.518409v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@1e85ef9org.highwire.dtl.DTLVardef@b3369eorg.highwire.dtl.DTLVardef@1c6d705org.highwire.dtl.DTLVardef@14ec6b2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chory, E. J. Wang, M. Ceribelli, M. Michalowska, A. M. Golas, S. Beck, E. Klumpp-Thomas, C. Chen, L. McKnight, C. Itkin, Z. Divakaran, S. Bradner, J. Khan, J. Gryder, B. E. Thomas, C. J. Stanton, B. Z. 2022-12-02 doi:10.1101/2022.11.29.518409 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Fractions strategy differences in those born extremely preterm ]]> https://biorxiv.org/content/10.1101/2022.12.06.519175v1?rss=1 Carr, S. Babinchak, W. M. Istrate, A. Martyn-Dow, B. Wang, G. Chen, W. Fondran, J. Zhang, J. Wein, M. Yoon, S. Y. Birnbaum, A. Roth, E. Gross, C. Minich, N. Thompson, L. Kim, W. H. Stern, Y. Nosarti, C. Taylor, H. G. Tatsuoka, C. 2022-12-06 doi:10.1101/2022.12.06.519175 Cold Spring Harbor Laboratory Press 2022-12-06 <![CDATA[ Hypo-responsiveness of human alveolar macrophages to IFN-γ is not due to attenuated STAT1 signaling ]]> https://biorxiv.org/content/10.1101/2022.12.07.519298v1?rss=1 Thiel, B. A. Lundberg, K. C. Schlatzer, D. Jarvela, J. Li, Q. Shaw, R. Beckloff, S. E. Chance, M. R. Boom, W. H. A. Silver, R. F. Bebek, G. 2022-12-07 doi:10.1101/2022.12.07.519298 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Transcriptional Responses of Cancer Cells to Heat Shock-Inducing Stimuli Involve Amplification of Robust HSF1 Binding ]]> https://biorxiv.org/content/10.1101/2022.12.14.519647v1?rss=1 Ghosh Dastidar, S. De Kumar, B. Lauckner, B. Parrello, D. Perley, D. Vlasenok, M. Tyagi, A. Koney-Kwaku Koney, N. Abbas, A. Nechaev, S. 2022-12-15 doi:10.1101/2022.12.14.519647 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Mechanical regulation of retinal vascular inflammation and degeneration in diabetic retinopathy ]]> https://biorxiv.org/content/10.1101/2022.12.18.520943v1?rss=1 Chandrakumar, S. Santiago Tierno, I. Agarwal, M. Lessieur, E. M. Du, Y. Tang, J. Kiser, J. Yang, X. Kern, T. S. Ghosh, K. 2022-12-19 doi:10.1101/2022.12.18.520943 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Decorrelation Time Mapping as an Analysis Tool for Nanobubble-Based Contrast Enhanced Ultrasound Imaging ]]> https://biorxiv.org/content/10.1101/2022.12.21.521428v1?rss=1 Wegierak, D. Cooley, M. B. Perera, R. Wultange, W. J. Gurkan, U. Kolios, M. C. Exner, A. A. 2022-12-22 doi:10.1101/2022.12.21.521428 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ MOPD I patient-derived cerebral organoids model microcephaly showing premature neurogenesis due to disrupted mitotic spindle orientation. ]]> https://biorxiv.org/content/10.1101/2022.12.29.520610v1?rss=1 A mutation and compared them to isogenic organoids obtained from iPSCs expressing wild-type U4atac snRNA, using immunostaining and 10X Genomics single-cell RNA sequencing. In our MOPD I organoids, we observed: a) reduced proliferation accompanied by premature neurogenesis depleting the neuro-progenitor pool due to an increased frequency of horizontal cell divisions in the ventricular zone; b) reduced numbers of intermediate progenitor and outer radial glial cells in the outer sub-ventricular zone; and c) defective radial neuronal migration, which is critical for cortical expansion in humans. Our findings therefore provide insight into MOPD I cellular pathogenesis and underline the value of these cerebral organoids as model systems for human neurodevelopmental disorders. ]]> Singh, J. Daniels, N. J. Pirozzi, F. Wynshaw-Boris, A. Lopez-Gonzalez, R. Padgett, R. A. 2022-12-29 doi:10.1101/2022.12.29.520610 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Loss of PTPMT1 limits mitochondrial utilization of carbohydrates and leads to muscle atrophy and heart failure ]]> https://biorxiv.org/content/10.1101/2023.01.09.523031v1?rss=1 Zheng, H. Li, Q. Li, S. Li, Z. Brotto, M. Weiss, D. Prosdocimo, D. Xu, C. Reddy, A. Puchowicz, M. Zhao, X. Weitzmann, M. N. Jain, M. K. Qu, C.-K. 2023-01-09 doi:10.1101/2023.01.09.523031 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ MRBEE: A novel bias-corrected multivariable Mendelian Randomization method ]]> https://biorxiv.org/content/10.1101/2023.01.10.523480v1?rss=1 Lorincz-Comi, N. J. Yang, Y. Li, G. Zhu, X. 2023-01-12 doi:10.1101/2023.01.10.523480 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ Reinforcement Learning informs optimal treatmentstrategies to limit antibiotic resistance. ]]> https://biorxiv.org/content/10.1101/2023.01.12.523765v1?rss=1 Weaver, D. T. Maltas, J. Scott, J. G. 2023-01-12 doi:10.1101/2023.01.12.523765 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ A standard protocol to report discrete stage-structured demographic information ]]> https://biorxiv.org/content/10.1101/2023.01.13.523871v1?rss=1 Gascoigne, S. J. L. Rolph, S. Sankey, D. Nidadavolu, N. Stell Picman, A. S. Hernandez, C. M. Philpott, M. E. R. Salam, A. Bernard, C. Fenollosa, E. Jun Lee, Y. McLean, J. Hetti Achchige Perera, S. Spacey, O. G. Kajin, M. Vinton, A. C. Archer, C. R. Burns, J. H. Buss, D. L. Caswell, H. Che-Castaldo, J. P. Childs, D. Z. Capdevila, P. Compagnoni, A. Crone, E. Ezard, T. H. G. Hodgson, D. Knight, T. M. Jones, O. R. Jongejans, E. McDonald, J. Tenhumberg, B. Thomas, C. C. Tyre, A. J. Ramula, S. Stott, I. Tremblay, R. L. Wilson, P. Vaupel, J. W. Salguero-Gomez, R 2023-01-16 doi:10.1101/2023.01.13.523871 Cold Spring Harbor Laboratory Press 2023-01-16 <![CDATA[ Apical expansion of calvarial osteoblasts and suture patency is dependent on graded fibronectin cues ]]> https://biorxiv.org/content/10.1101/2023.01.16.524278v1?rss=1 Feng, X. Molteni, H. Gregory, M. Lanza, J. Polsani, N. Wyetzner, R. Hawkins, M. B. Holmes, G. Hopyan, S. Harris, M. Atit, R. 2023-01-16 doi:10.1101/2023.01.16.524278 Cold Spring Harbor Laboratory Press 2023-01-16 <![CDATA[ Catenin signaling controls phrenic motor neuron development and function during a narrow temporal window ]]> https://biorxiv.org/content/10.1101/2023.01.18.524559v1?rss=1 Vagnozzi, A. N. Moore, M. T. Lopez de Boer, R. Agarwal, A. Zampieri, N. Landmesser, L. T. Philippidou, P. 2023-01-19 doi:10.1101/2023.01.18.524559 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Targeting sterol regulatory element binding proteins (SREBPs) activation lowers intraocular pressure by halting its mechanosensing function in the trabecular meshwork ]]> https://biorxiv.org/content/10.1101/2023.02.05.527136v1?rss=1 Wang, T. Soundararajan, A. Rabinowitz, J. Jaiswal, A. Osborne, T. Pattabiraman, P. P. 2023-02-05 doi:10.1101/2023.02.05.527136 Cold Spring Harbor Laboratory Press 2023-02-05 <![CDATA[ Pervasive environmental chemicals impair oligodendrocyte development ]]> https://biorxiv.org/content/10.1101/2023.02.10.528042v1?rss=1 Cohn, E. F. Clayton, B. L. L. Madhavan, M. Yacoub, S. Federov, Y. Paul-Friedman, K. Shafer, T. J. Tesar, P. 2023-02-12 doi:10.1101/2023.02.10.528042 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ TRAF4 is crucial for the propagation of ST2+ memory Th2 cells in IL-33-mediated type 2 airway inflammation ]]> https://biorxiv.org/content/10.1101/2023.02.11.528093v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@18a8f48org.highwire.dtl.DTLVardef@1c4e29corg.highwire.dtl.DTLVardef@f98f72org.highwire.dtl.DTLVardef@38aacb_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Xiao, J. Chen, X. Liu, W. Qian, W. Bulek, K. Hong, L. Miller-Little, W. Li, X. Liu, C. 2023-02-12 doi:10.1101/2023.02.11.528093 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ LRG1 is a novel ligand of HER3 and promotes metastatic colorectal cancer growth ]]> https://biorxiv.org/content/10.1101/2023.02.18.529070v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@1a84299org.highwire.dtl.DTLVardef@1ac6654org.highwire.dtl.DTLVardef@1723260org.highwire.dtl.DTLVardef@4970a8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Rathore, M. Wang, R. 2023-02-18 doi:10.1101/2023.02.18.529070 Cold Spring Harbor Laboratory Press 2023-02-18 <![CDATA[ Single-strand mismatch and damage patterns revealed by single-molecule DNA sequencing ]]> https://biorxiv.org/content/10.1101/2023.02.19.526140v1?rss=1 Liu, M. H. Costa, B. Choi, U. Bandler, R. Lassen, E. M. Gronska-Peski, M. Schwing, A. K. Murphy, Z. R. Rosenkjaer, D. Picciotto, S. Bianchi, V. Stengs, L. Edwards, M. Loh, C. Truong, T. K. Brand, R. Pastinen, T. Wagner, J. R. Skytte, A.-B. Tabori, U. Shoag, J. E. Evrony, G. D. 2023-02-19 doi:10.1101/2023.02.19.526140 Cold Spring Harbor Laboratory Press 2023-02-19 <![CDATA[ Enterovirus Evolution Reveals the Mechanism of an RNA-Targeted Antiviral and Determinants of Viral Replication ]]> https://biorxiv.org/content/10.1101/2023.02.20.529064v1?rss=1 Davila-Calderon, J. Li, M.-L. Penumutchu, S. Haddad, C. Malcolm, L. Hargrove, A. E. Brewer, G. Tolbert, B. S. 2023-02-20 doi:10.1101/2023.02.20.529064 Cold Spring Harbor Laboratory Press 2023-02-20 <![CDATA[ Spatial and Amplitude Dynamics of Neurostimulation: Insights from the Acute Intrahippocampal Kainate Seizure Mouse Model ]]> https://biorxiv.org/content/10.1101/2023.03.07.531440v1?rss=1 Foutz, T. J. Rensing, N. Han, L. Durand, D. M. Wong, M. 2023-03-09 doi:10.1101/2023.03.07.531440 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Spinal Cord Stimulation using time-dynamic pulses achieves faster and longer reversal of allodynia compared to tonic pulses in a rat model of neuropathic pain ]]> https://biorxiv.org/content/10.1101/2023.03.07.531522v1?rss=1 Edhi, M. Zhu, C. Jeong, K.-S. Rogness, V. Esteller, R. Saab, C. Y. 2023-03-10 doi:10.1101/2023.03.07.531522 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Crosstalkr: An open-source R package to facilitatedrug target identification. ]]> https://biorxiv.org/content/10.1101/2023.03.07.531526v1?rss=1 Weaver, D. T. Scott, J. G. 2023-03-10 doi:10.1101/2023.03.07.531526 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Naturally acquired and Vaccine-induced Human Monoclonal Antibodies to Plasmodium vivax Duffy Binding Protein Inhibit Invasion of Plasmodium knowlesi (PvDBPOR) Transgenic Parasites ]]> https://biorxiv.org/content/10.1101/2023.03.07.531647v1?rss=1 Watson, Q. D. Carias, L. Malachin, A. Redinger, K. R. Bosch, J. Bardelli, M. Moon, R. W. Draper, S. J. Zimmerman, P. A. King, C. L. 2023-03-09 doi:10.1101/2023.03.07.531647 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Evolutionary constraint and innovation across hundreds of placental mammals ]]> https://biorxiv.org/content/10.1101/2023.03.09.531574v1?rss=1 Christmas, M. J. Kaplow, I. M. Genereux, D. P. Dong, M. X. Hughes, G. M. Li, X. Sullivan, P. F. Hindle, A. G. Andrews, G. Armstrong, J. C. Bianchi, M. Breit, A. M. Diekhans, M. Fanter, C. Foley, N. M. Goodman, D. B. Goodman, L. Keough, K. C. Kirilenko, B. Kowalczyk, A. Lawless, C. Lind, A. L. Meadows, J. R. S. Moreira, L. R. Redlich, R. W. Ryan, L. Swofford, R. Valenzuela, A. Wagner, F. Wallerman, O. Brown, A. R. Damas, J. Fan, K. Gatesy, J. Grimshaw, J. Johnson, J. Kozyrev, S. V. Lawler, A. J. Marinescu, V. D. Morrill, K. M. Osmanski, A. Paulat, N. S. 2023-03-09 doi:10.1101/2023.03.09.531574 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Fitness seascapes promote genetic heterogeneity through spatiotemporally distinct mutant selection windows ]]> https://biorxiv.org/content/10.1101/2023.03.09.531899v1?rss=1 King, E. S. Pierce, B. Hinczewski, M. Scott, J. G. 2023-03-11 doi:10.1101/2023.03.09.531899 Cold Spring Harbor Laboratory Press 2023-03-11 <![CDATA[ Live-trapping of rodents in urban green spaces across Los Angeles ]]> https://biorxiv.org/content/10.1101/2023.03.13.531394v1?rss=1 Friscia, A. R. Helman, S. Maloney, M. Molina-Echavarria, A. K. Nugen, S. Punjabi, N. Tweedt, I. Lynch, J. 2023-03-15 doi:10.1101/2023.03.13.531394 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Masking, maintenance and mimicry: the interplay of cell-intrinsic and cell-extrinsic effects in evolutionary games ]]> https://biorxiv.org/content/10.1101/2023.03.15.532871v1?rss=1 Barker-Clarke, R. J. Gray, J. Tadele, D. scott, j. Hinczewski, M. 2023-03-16 doi:10.1101/2023.03.15.532871 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Draft genome assembly of the ancient tetraploid orphan legume marama bean (Tylosema esculentum) with PacBio HiFi data ]]> https://biorxiv.org/content/10.1101/2023.03.16.532621v1?rss=1 Li, J. Cullis, C. 2023-03-17 doi:10.1101/2023.03.16.532621 Cold Spring Harbor Laboratory Press 2023-03-17 <![CDATA[ Standardizing and applying a mating-based whole-genome simulation approach reveals caution in using chromosome-level PCA and kinship estimates ]]> https://biorxiv.org/content/10.1101/2023.03.16.532885v1?rss=1 13,000). We provide an application example that uses whole-genome simulation to underscore the importance of whole-genome quality control (QC) statistics, such as principal component analysis (PCA) and kinship estimates, compared to the chromosome-level ones. Results of the application indicate instability and bias in the chromosome-level QC statistics. Overall, our approach represents a valuable tool for genetics research that can assist in the evaluation and validation of genetic analyses, and people should avoid chromosome-level QC statistics. ]]> Cui, Z. Schumacher, F. 2023-03-16 doi:10.1101/2023.03.16.532885 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Frequency-dependent ecological interactions increase the prevalence and shape the distribution of pre-existing drug resistance ]]> https://biorxiv.org/content/10.1101/2023.03.16.533001v1?rss=1 Maltas, J. Tadele, D. S. Durmaz, A. McFarland, C. D. Hinczewski, M. Scott, J. G. 2023-03-16 doi:10.1101/2023.03.16.533001 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Intra-Host Mutation Rate of Acute SARS-CoV-2 Infection During the Initial Pandemic Wave ]]> https://biorxiv.org/content/10.1101/2023.03.24.534062v1?rss=1 0.25 vs wtNSP-14. Patients with immune comorbidities had higher mutation rate at all allele frequencies. DiscussionIntra-host SARS-CoV-2 mutation rates are substantially higher than those reported through population analysis. Virus strains with altered NSP-14 have accelerated mutation rate at low AF. Immunosuppressed patients have elevated mutation rate at all AF. Understanding intra-host virus evolution will aid in current and future pandemic modeling. ]]> El Haddad, K. Adhikari, T. M. Zheng, T. Cheng, Y.-W. Leng, X. Zhang, X. Rhoads, D. Ko, J. Worley, S. Li, J. Rubin, B. Esper, F. 2023-03-25 doi:10.1101/2023.03.24.534062 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Comparative Analysis of Tylosema esculentum Mitochondrial DNA Revealed Two Distinct Genome Structures ]]> https://biorxiv.org/content/10.1101/2023.03.27.534440v1?rss=1 Li, J. Cullis, C. A. 2023-03-29 doi:10.1101/2023.03.27.534440 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Bioenergetic costs and the evolution of noise regulation by microRNAs ]]> https://biorxiv.org/content/10.1101/2023.03.28.534633v1?rss=1 Ilker, E. Hinczewski, M. 2023-03-29 doi:10.1101/2023.03.28.534633 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Targeting wild-type IDH1 enhances chemosensitivity in pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2023.03.29.534596v1?rss=1 Zarei, M. Hajihassani, O. Hue, J. J. Graor, H. J. Rothermel, L. D. Winter, J. M. 2023-03-29 doi:10.1101/2023.03.29.534596 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Adapting the endoplasmic reticulum proteostasis rescues epilepsy-associated NMDA receptor variants ]]> https://biorxiv.org/content/10.1101/2023.04.01.535233v1?rss=1 Zhang, P.-P. Benske, T. M. Paton, J. C. Paton, A. W. Mu, T. Wang, Y.-J. 2023-04-02 doi:10.1101/2023.04.01.535233 Cold Spring Harbor Laboratory Press 2023-04-02 <![CDATA[ ALDH2 dysfunction accelerates ESCC pathogenesis ]]> https://biorxiv.org/content/10.1101/2023.04.03.534985v1?rss=1 Flashner, S. Shimonosono, M. Matsuura, N. Ohashi, S. Klein-Szanto, A. J. Diehl, J. A. Chen, C.-H. Nakagawa, H. 2023-04-05 doi:10.1101/2023.04.03.534985 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ Computational ranking-assisted identification of Plexin-B2 in homotypic and heterotypic clustering of circulating tumor cells in breast cancer metastasis ]]> https://biorxiv.org/content/10.1101/2023.04.10.536233v1?rss=1 Schuster, E. J. Dashzeveg, N. K. Jia, Y. Golam, K. Zhang, T. Hoffman, A. D. Zhang, Y. Zheng, C. Ramos, E. K. Taftaf, R. El-Shennawy, L. Scholten, D. Adorno-Cruz, V. Reduzzi, C. Xu, R. Siziopikou, K. P. Plantanias, L. C. Shah, A. Gradishar, W. Cristofanilli, M. Tsai, C.-F. Shi, T. Liu, H. Kitata, R. B. Spahija, S. 2023-04-12 doi:10.1101/2023.04.10.536233 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ FGF-21 Conducts a Liver-Brain-Kidney Axis to Promote Renal Cell Carcinoma ]]> https://biorxiv.org/content/10.1101/2023.04.12.536558v1?rss=1 Li, Z. Zhang, X. Zhu, W. Zhang, C. Sadak, K. Halberstam, A. A. Brown, J. R. Perry, C. J. Bunn, A. Braun, D. A. Adeniran, A. Lee, S. Wang, A. Perry, R. J. 2023-04-13 doi:10.1101/2023.04.12.536558 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Pharmacological chaperones restore proteostasis of epilepsy-associated GABAA receptor variants ]]> https://biorxiv.org/content/10.1101/2023.04.18.537383v1?rss=1 Wang, Y.-J. Seibert, H. Ahn, L. Y. Schaffer, A. E. Mu, T.-W. 2023-04-19 doi:10.1101/2023.04.18.537383 Cold Spring Harbor Laboratory Press 2023-04-19 <![CDATA[ COVID-19 and silent hypoxemia in a minimal closed-loop model of the respiratory rhythm generator ]]> https://biorxiv.org/content/10.1101/2023.04.19.536507v1?rss=1 Diekman, C. O. Thomas, P. J. Wilson, C. G. 2023-04-19 doi:10.1101/2023.04.19.536507 Cold Spring Harbor Laboratory Press 2023-04-19 <![CDATA[ Tension sensing by FAK governs nuclear mechanotransduction, endothelial transcriptome and fate ]]> https://biorxiv.org/content/10.1101/2023.04.24.538195v1?rss=1 Akhter, M. Z. Yazbeck, P. Tauseef, M. Anwar, M. Hossen, F. Datta, S. Vellingiri, V. Joshi, J. C. Srivastava, N. Lenzini, S. Zhou, G. Lee, J. Jain, M. K. Shin, J.-W. Mehta, D. 2023-04-26 doi:10.1101/2023.04.24.538195 Cold Spring Harbor Laboratory Press 2023-04-26 <![CDATA[ Behavioral Paradigm for the Evaluation of Stimulation-Evoked Somatosensory Perception Thresholds in Rats ]]> https://biorxiv.org/content/10.1101/2023.05.04.537848v1?rss=1 Smith, T. J. Wu, Y. Cheon, C. Khan, A. A. Srinivasan, H. Capadona, J. R. Cogan, S. F. Pancrazio, J. J. Engineer, C. T. Hernandez-Reynoso, A. G. 2023-05-05 doi:10.1101/2023.05.04.537848 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ Oncogenic reactivation of young L1s is a hallmark of colon cancer ]]> https://biorxiv.org/content/10.1101/2023.05.17.541189v1?rss=1 Neu, D. Hung, S. Bartels, C. F. Faber, Z. J. Lovrenert, K. Pontius, W. D. Morgan, L. Chakraborty, M. Liao, W. Chin, D. Hong, E. S. Gray, J. Moreno, V. Kalady, M. Peters, U. Gryder, B. Sallari, R. C. Scacheri, P. C. 2023-05-21 doi:10.1101/2023.05.17.541189 Cold Spring Harbor Laboratory Press 2023-05-21 <![CDATA[ Mesenchymal stem cells ameliorate inflammation in an experimental model of Crohn's disease via the mesentery ]]> https://biorxiv.org/content/10.1101/2023.05.22.541829v1?rss=1 Dave, M. Dev, A. Somoza, R. A. Zhao, N. Viswanath, S. Mina, P. R. Chirra, P. Obmann, V. C. Mahabeleshwar, G. H. Menghini, P. Johnson, B. D. Nolta, J. A. Soto, C. Osme, A. Khuat, L. T. Murphy, W. Caplan, A. I. Cominelli, F. 2023-05-24 doi:10.1101/2023.05.22.541829 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ The Structural Role of N170 in Substrate-assisted Deacylation in KPC-2 β-Lactamase ]]> https://biorxiv.org/content/10.1101/2023.05.22.541848v1?rss=1 Parwana, D. Gu, J. Wang, Q. Bethel, C. Marshall, E. K. Hujer, A. M. Bonomo, R. A. Haider, S. 2023-05-24 doi:10.1101/2023.05.22.541848 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Enhanced Annotation of CD45RA to Distinguish T cell Subsets in Single Cell RNA-seq via Machine Learning ]]> https://biorxiv.org/content/10.1101/2023.05.23.541821v1?rss=1 Ran, R. Brubaker, D. K. 2023-05-24 doi:10.1101/2023.05.23.541821 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Detailed Survey of an in-vitro Intestinal Epithelium Model by Single-Cell Transcriptomics ]]> https://biorxiv.org/content/10.1101/2023.05.23.541940v1?rss=1 Ran, R. Munoz, J. Jena, S. Green, L. Brubaker, D. 2023-05-23 doi:10.1101/2023.05.23.541940 Cold Spring Harbor Laboratory Press 2023-05-23 <![CDATA[ A single cell transcriptomic fingerprint of stressed premature, imbalanced differentiation of embryonic stem cells. ]]> https://biorxiv.org/content/10.1101/2023.05.23.541952v1?rss=1 Ruden, X. Singh, A. Marben, T. Tang, W. Awonuga, A. Ruden, D. M. Puscheck, E. Feng, H. Rappolee, D. 2023-05-25 doi:10.1101/2023.05.23.541952 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ How NINJ1 mediates plasma membrane rupture and why NINJ2 cannot ]]> https://biorxiv.org/content/10.1101/2023.05.31.543175v1?rss=1 Sahoo, B. Mou, Z. Liu, W. Dubyak, G. Dai, X. 2023-06-01 doi:10.1101/2023.05.31.543175 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ The basis of antigenic operon fragmentation in Bacteroidota and commensalism ]]> https://biorxiv.org/content/10.1101/2023.06.02.543472v1?rss=1 Bank, N. C. Singh, V. Grubb, B. McCourt, B. Burberry, A. Roberts, K. D. Rodriguez-Palacios, A. 2023-06-02 doi:10.1101/2023.06.02.543472 Cold Spring Harbor Laboratory Press 2023-06-02 <![CDATA[ Predicting genetically regulated gene expression on the X chromosome ]]> https://biorxiv.org/content/10.1101/2023.06.06.543877v1?rss=1 0.05) within the cis-regulatory window were used to train tissue-specific models of each gene. We apply the best models in both tissues to sex-stratified summary statistics from a meta-analysis of Alzheimers disease Genetics Consortium (ADGC) studies to identify AD-related genes on the X chromosome. ResultsAcross different model parameters, sample sex, and tissue types, we modeled the expression of 217 genes (95 genes in blood and 135 genes in brain cortex). The average model R2 was 0.12 (range from 0.03 to 0.34). We also compared sex-stratified and sex-combined models on the X chromosome. We further investigated genes that escaped X chromosome inactivation (XCI) to determine if their genetic regulation patterns were distinct. We found ten genes associated with AD at p < 0.05, with only ARMCX6 in female brain cortex (p = 0.008) nearing the significance threshold after adjusting for multiple testing ( = 0.002). ConclusionsWe optimized the expression prediction of X chromosome genes, applied these models to sex-stratified AD GWAS summary statistics, and identified one putative AD risk gene, ARMCX6. ]]> Zhang, X. Below, J. Kunkle, B. W. Martin, E. Naj, A. C. Bush, W. 2023-06-08 doi:10.1101/2023.06.06.543877 Cold Spring Harbor Laboratory Press 2023-06-08 <![CDATA[ Enteric glial hub cells coordinate intestinal motility ]]> https://biorxiv.org/content/10.1101/2023.06.07.544052v1?rss=1 Scavuzzo, M. A. Letai, K. C. Maeno-Hikichi, Y. Wulftange, W. J. Shah, I. K. Rameshbabu, J. S. Tomar, A. Shick, H. E. Shah, A. K. Xiong, Y. Cohn, E. F. Allan, K. C. Tesar, P. J. 2023-06-09 doi:10.1101/2023.06.07.544052 Cold Spring Harbor Laboratory Press 2023-06-09 <![CDATA[ Structural basis of CMKLR1 signaling induced by chemerin9 ]]> https://biorxiv.org/content/10.1101/2023.06.09.544295v1?rss=1 Zhang, C. Zhang, X. Weiss, T. Cheng, M. H. Chen, S. Ambrosius, C. K. Czerniak, A. S. Li, K. Feng, M. Bahar, I. Beck-Sickinger, A. G. 2023-06-10 doi:10.1101/2023.06.09.544295 Cold Spring Harbor Laboratory Press 2023-06-10 <![CDATA[ Platelet-Localized ST6Gal1 Does Not Impact IgG Sialylation ]]> https://biorxiv.org/content/10.1101/2023.06.15.545133v1?rss=1 Glendenning, L. M. Zhou, J. Y. Kukan, E. N. Gao, C. Cummings, R. D. Joshi, S. Whiteheart, S. W. Cobb, B. A. 2023-06-15 doi:10.1101/2023.06.15.545133 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ FLOWERING LOCUS C drives delayed flowering in Arabidopsis grown and selected at elevated CO2 ]]> https://biorxiv.org/content/10.1101/2023.06.15.545149v1?rss=1 Henderson-Carter, A. L. Kinmonth-Schultz, H. Hileman, L. Ward, J. K. 2023-06-15 doi:10.1101/2023.06.15.545149 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ Neuronal lineage tracing from progenitors in human cortical organoids reveals novel mechanisms of human neuronal production, diversity, and disease ]]> https://biorxiv.org/content/10.1101/2023.06.17.545314v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@da0038org.highwire.dtl.DTLVardef@44997dorg.highwire.dtl.DTLVardef@1b90ff2org.highwire.dtl.DTLVardef@c5dbcd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphic AbstractC_FLOATNO C_FIG ]]> Bury, L. A. D. Fu, S. Wynshaw-Boris, A. 2023-06-17 doi:10.1101/2023.06.17.545314 Cold Spring Harbor Laboratory Press 2023-06-17 <![CDATA[ Neuronal Ndst1 depletion accelerates prion protein clearance and slows neurodegeneration in prion infection ]]> https://biorxiv.org/content/10.1101/2023.06.19.545528v1?rss=1 Aguilar Calvo, P. Malik, A. Sandoval, D. Barback, C. Orru, C. Standke, H. Thomas, O. Dwyer, C. Pizzo, D. Bapat, J. Soldau, K. Ogawa, R. Riley, M. Nilsson, P. kraus, a. caughey, b. Iliff, J. Esko, J. Vera, D. Sigurdson, C. J. 2023-06-20 doi:10.1101/2023.06.19.545528 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ Oligosaccharide production and signaling correlate with delayed flowering in an Arabidopsis genotype grown and selected in high ]]> https://biorxiv.org/content/10.1101/2023.06.19.545630v1?rss=1 Kinmonth-Schultz, H. Walker, S. M. Bingol, K. Hoyt, D. W. Kim, Y.-M. Markillie, L. M. Mitchell, H. D. Nicora, C. D. Taylor, R. Ward, J. K. 2023-06-20 doi:10.1101/2023.06.19.545630 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ Prothrombin Knockdown Protects Podocytes and Reduces Proteinuria in Glomerular Disease ]]> https://biorxiv.org/content/10.1101/2023.06.20.544360v1?rss=1 Waller, A. P. Wolfgang, K. J. Abdelghani, E. Stevenson, Z. S. Muralidharan, K. Wilkie, T. K. Smoyer, W. E. Nieman, M. T. Kerlin, B. A. 2023-06-23 doi:10.1101/2023.06.20.544360 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Structural Basis for Regulated Assembly of the Mitochondrial Fission GTPase Drp1 ]]> https://biorxiv.org/content/10.1101/2023.06.22.546081v1?rss=1 Rochon, K. Bauer, B. L. Roethler, N. A. Buckley, Y. Su, C.-C. Huang, W. Ramachandran, R. Stoll, M. S. K. Yu, E. W. Taylor, D. J. Mears, J. A. 2023-06-22 doi:10.1101/2023.06.22.546081 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Tessellation Of Artificial Touch Via Microstimulation Of Human Somatosensory Cortex ]]> https://biorxiv.org/content/10.1101/2023.06.23.545425v1?rss=1 Greenspon, C. M. Shelchkova, N. D. Valle, G. Hobbs, T. Berger-Wolf, E. I. Hutchison, B. C. Dogruoz, E. Jordan, P. M. Verbarschott, C. Callier, T. Sobinov, A. Okorokova, E. V. Prasad, D. He, Q. Liu, F. Miller, J. P. Lee, R. C. Satzer, D. Gonzalez-Martinez, J. Warnke, P. Miller, L. E. Boninger, M. L. Ajiboye, B. B. Graczyk, E. L. Downey, J. E. Collinger, J. Hatsopoulos, N. Gaunt, R. Bensmaia, S. J. 2023-06-26 doi:10.1101/2023.06.23.545425 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Stochastic Model of Alzheimer's Disease Progression Using Two-State Markov Chains ]]> https://biorxiv.org/content/10.1101/2023.06.29.547071v1?rss=1 Parks, M. E. 2023-07-01 doi:10.1101/2023.06.29.547071 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ IgG sialylation occurs via the FcRn-mediated recycling pathway in endothelial cells ]]> https://biorxiv.org/content/10.1101/2023.06.30.547255v1?rss=1 Glendenning, L. M. Reynero, K. M. Kukan, E. N. Long, M. D. Cobb, B. A. 2023-07-02 doi:10.1101/2023.06.30.547255 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Stem-loop induced ribosome queuing in the uORF2/ATF4 overlap fine-tunes stress-induced human ATF4 translational control ]]> https://biorxiv.org/content/10.1101/2023.07.12.548609v1?rss=1 Smirnova, A. M. Hronova, V. Gunisova, S. Mohammad, M. P. Petrackova, D. Halada, P. Rendelman, J. Coufal, S. Herrmannova, A. Beznoskova, P. Jendruchova, K. Hatzoglou, M. Vogel, C. Valasek, L. S. 2023-07-12 doi:10.1101/2023.07.12.548609 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ Phosphorylation modulates estrogen receptor disorder by altering long-range hydrophobic interactions ]]> https://biorxiv.org/content/10.1101/2023.07.14.548966v1?rss=1 Du, Z. Wang, H. Wu, C. Buck, M. Zheng, W. Hansen, A. L. Kao, H.-Y. Yang, S. 2023-07-15 doi:10.1101/2023.07.14.548966 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ Self-assembling Gn head ferritin nanoparticle vaccine provides full protection from lethal challenge of Dabie Bandavirus in aged ferrets ]]> https://biorxiv.org/content/10.1101/2023.07.19.549761v1?rss=1 4 years old)-dependent DBV infection and pathogenesis that fully recapitulates human clinical manifestation. To protect the aged population from DBV-induced SFTS, vaccine should carry robust immunogenicity with high safety profile. Previous studies have shown that glycoproteins Gn/Gc are the most effective antigens for inducing both neutralizing antibody (NAb)- and T cell-mediated immunity and, thereby, protection. Here, we report the development of a protein subunit vaccine with 24-mer self-assembling ferritin (FT) nanoparticle to present DBV Gn head region (GnH) for enhanced immunogenicity. Anion exchange chromatography and size exclusion chromatography readily purified the GnH-FT nanoparticles to homogeneity with structural integrity. Mice immunized with GnH-FT nanoparticles induced robust NAb response and T-cell immunity against DBV Gn. Furthermore, aged ferrets immunized with GnH-FT nanoparticles were fully protected from DBV challenge without SFTS symptoms such as body weight loss, thrombocytopenia, leukopenia, and fatality. This study demonstrates that DBV GnH-FT nanoparticles provide an efficient vaccine efficacy in mouse and aged ferret models and should be an outstanding vaccine candidate targeted for the aged population against fatal DBV infection. ImportanceDabie Bandavirus (DBV) is an emerging tick-borne virus that causes Severe Fever with Thrombocytopenia Syndrome (SFTS) in infected patients. Human SFTS symptoms progress from fever, fatigue, and muscle pain to the depletion of white blood cells and platelets with fatality rates up to 30%. The recent spread of its vector tick to over 20 states in the United States increases the potential for outbreaks of the SFTS beyond the East Asia. Thus, the development of vaccine to control this rapidly emerging virus is a high priority. In this study, we applied self-assembling ferritin (FT) nanoparticle to enhance the immunogenicity of viral Gn head domain as a vaccine target. Mice immunized with the GnH-FT nanoparticle vaccine induced potent antibody responses and cellular immunity. Immunized aged-ferrets were fully protected from the lethal challenge of DBV. Our study describes the GnH-FT nanoparticle vaccine candidate that provides protective immunity against the emerging DBV infection. ]]> Jung, J. U. Kim, D. Kim, E. Kim, S. Chung, Y. Cho, S.-D. Choi, Y. Lai, C.-J. Dai, X. Kang, S. Kwak, M.-J. Cha, I. Liu, Z. Choi, Y. Park, S.-H. Choi, Y. K. Kim, S. 2023-07-19 doi:10.1101/2023.07.19.549761 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Identification and Characterization of Calcium Binding Protein, Spermatid Associated 1 (CABS1) in Selected Human Tissues and Fluids ]]> https://biorxiv.org/content/10.1101/2023.07.21.550040v1?rss=1 Reyes-Serratos, E. Santos, J. R. L. Puttagunta, L. Lewis, S. Watanabe, M. Gonshor, A. Buck, R. Befus, A. D. Marcet-Palacios, M. 2023-07-21 doi:10.1101/2023.07.21.550040 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ Blood pressure pulsations modulate olfactory bulb neuronal activity via mechanosensitive ion channels ]]> https://biorxiv.org/content/10.1101/2023.07.27.550787v1?rss=1 Jammal, L. Bitzenhofer, S. H. Hanganu-Opatz, I. L. Dutschmann, M. Egger, V. 2023-07-28 doi:10.1101/2023.07.27.550787 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ The mRNACalc web server accounts for the hypochromicity of modified nucleosides and enables the accurate quantification of nucleoside-modified mRNA. ]]> https://biorxiv.org/content/10.1101/2023.07.27.550903v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@1a9e310org.highwire.dtl.DTLVardef@7a67aforg.highwire.dtl.DTLVardef@2d28f9org.highwire.dtl.DTLVardef@dcffd5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Finol, E. Krul, S. E. Hoehn, S. J. Crespo-Hernandez, C. E. 2023-07-27 doi:10.1101/2023.07.27.550903 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Local climate change velocities explain multidirectional range shifts in a North American butterfly assemblage ]]> https://biorxiv.org/content/10.1101/2023.07.31.551397v1?rss=1 da Silva, C. R. B. Diamond, S. E. 2023-08-02 doi:10.1101/2023.07.31.551397 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Patient iPSC models reveal glia-intrinsic phenotypes in multiple sclerosis ]]> https://biorxiv.org/content/10.1101/2023.08.01.551553v1?rss=1 Clayton, B. L. L. Barbar, L. Sapar, M. Rusielewicz, T. Kalpana, K. Migliori, B. The NYSCF Global Stem Cell Array, Paull, D. Brenner, K. Moroziewicz, D. Sand, I. K. Casaccia, P. Tesar, P. J. Fossati, V. 2023-08-02 doi:10.1101/2023.08.01.551553 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Benchmarking combined informatics approaches for virus discovery: Caution is needed when combining in silico identification methods ]]> https://biorxiv.org/content/10.1101/2023.08.07.552334v1?rss=1 Hegarty, B. Riddell, J. Bastien, G. E. Langenfeld, K. Lindback, M. Saini, J. S. Wing, A. Zhang, J. Duhaime, M. 2023-08-08 doi:10.1101/2023.08.07.552334 Cold Spring Harbor Laboratory Press 2023-08-08 <![CDATA[ Exploring Temporal and Sex-Linked Dysregulation in Alzheimer's Disease Phospho-Proteome ]]> https://biorxiv.org/content/10.1101/2023.08.15.553056v1?rss=1 Yilmaz, S. Lopes, F. B. T. P. Schlatzer, D. Wang, R. Qi, X. Koyuturk, M. Chance, M. 2023-08-17 doi:10.1101/2023.08.15.553056 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Targeting CD19-positive lymphomas with the antibody-drug conjugate (ADC) loncastuximab tesirine: preclinical evidence as single agent and as combinatorial approach ]]> https://biorxiv.org/content/10.1101/2023.08.17.553668v1?rss=1 Tarantelli, C. Wald, D. Munz, N. Spriano, F. Bruscaggin, A. Cannas, E. Cascione, L. Gaudio, E. Arribas, A. J. Manjappa, S. Golino, G. Scalise, L. Zucca, E. Stathis, A. Van Berkel, P. H. Rossi, D. Caimi, P. F. Zammarchi, F. Bertoni, F. 2023-08-18 doi:10.1101/2023.08.17.553668 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ Structural basis for the ligand recognition and signaling of free fatty acid receptors ]]> https://biorxiv.org/content/10.1101/2023.08.20.553924v1?rss=1 Zhang, X. Guseinov, A. A. Jenkins, L. Li, K. Tikhonova, I. Milligan, G. Zhang, C. 2023-08-21 doi:10.1101/2023.08.20.553924 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Making Proteomics Accessible: RokaiXplorer for interactive analysis of phospho-proteomic data ]]> https://biorxiv.org/content/10.1101/2023.08.22.553639v1?rss=1 Yılmaz, S. Lopes, F. B. T. P. Schlatzer, D. Ayati, M. Chance, M. R. Koyutürk, M. 2023-08-25 doi:10.1101/2023.08.22.553639 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ Reprogramming of breast tumor-associated macrophages with modulation of arginine metabolism ]]> https://biorxiv.org/content/10.1101/2023.08.22.554238v1?rss=1 Fernando, V. Zheng, X. Sharma, V. Furuta, S. 2023-08-22 doi:10.1101/2023.08.22.554238 Cold Spring Harbor Laboratory Press 2023-08-22 <![CDATA[ Protection of β2GPI Deficient Mice from Thrombosis Reflects a Defect in PAR3-facilitated Platelet Activation ]]> https://biorxiv.org/content/10.1101/2023.08.23.554547v1?rss=1 Kulkarni, P. P. Alluri, R. K. Godwin, M. Forbes, G. L. Merkulova, A. Vijay, A. Palihati, M. Kundu, S. Shim, Y. J. Schmaier, A. H. Holinstat, M. Cameron, S. J. McCrae, K. R. 2023-08-25 doi:10.1101/2023.08.23.554547 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ Large-scale annotated dataset for cochlear hair cell detection and classification ]]> https://biorxiv.org/content/10.1101/2023.08.30.553559v1?rss=1 Buswinka, C. J. Rosenberg, D. B. Simikyan, R. G. Osgood, R. T. Fernandez, K. Nitta, H. Hayashi, Y. Liberman, L. W. Nguyen, E. Yildiz, E. Kim, J. Jarysta, A. Renauld, J. Wesson, E. Thapa, P. Bordiga, P. McMurtry, N. Llamas, J. Kitcher, S. R. Lopez-Porras, A. I. Cui, R. Behnammanesh, G. Bird, J. E. Ballesteros, A. Velez-Ortega, A. C. Edge, A. S. Deans, M. Gnedeva, K. Shrestha, B. R. Manor, U. Zhao, B. Ricci, A. J. Tarchini, B. Basch, M. Stepanyan, R. S. Landegger, L. D. Rutherford, M. Liberman, M. C. Walters, B. J. Kros, C. Richardson, G. P. Cunningham, L 2023-09-01 doi:10.1101/2023.08.30.553559 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Dysregulation of γδ intraepithelial lymphocytes precedes Crohn's disease-like ileitis ]]> https://biorxiv.org/content/10.1101/2023.08.31.555710v1?rss=1 Xu, W. Golovchenko, N. B. Fong, A. Achi, S. Bucar, E. B. Vidmar, K. J. Zhang, L. Frey, M. R. Prinz, I. Pizarro, T. T. Kollias, G. Edelblum, K. L. 2023-09-03 doi:10.1101/2023.08.31.555710 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Efficient ultrasound-mediated drug delivery to orthotopic liver tumors: Direct comparison of doxorubicin-loaded nanobubbles and microbubbles ]]> https://biorxiv.org/content/10.1101/2023.09.01.555196v1?rss=1 Nittayacharn, P. A. Abenojar, E. Cooley, M. B. Berg, F. Counil, C. Sojahrood, A. Khan, M. S. Yang, C. Berndl, E. Golczak, M. Kolios, M. Exner, A. 2023-09-05 doi:10.1101/2023.09.01.555196 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ A heterochromatin domain forms gradually at a new telomere and is highly dynamic at stable telomeres ]]> https://biorxiv.org/content/10.1101/211565v1?rss=1 Wang, J. Eisenstatt, J. R. Audry, J. Cornelius, K. Shaughnessy, M. Berkner, K. L. Runge, K. W. 2017-11-09 doi:10.1101/211565 Cold Spring Harbor Laboratory Press 2017-11-09 <![CDATA[ Genomic Locus Modulating Corneal Thickness in the Mouse Identifies POU6F2 as a Potential Risk of Developing Glaucoma ]]> https://biorxiv.org/content/10.1101/212605v1?rss=1 King, R. Struebing, F. L. Li, Y. Wang, J. Koch, A. A. Bailey, J. C. Gharahkhan, P. MacGregor, S. Allingham, R. R. Hauser, M. A. Wiggs, J. L. Geisert, E. E. 2017-11-01 doi:10.1101/212605 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Genomic Loci Modulating Retinal Ganglion Cell Death Following Elevated IOP in the Mouse ]]> https://biorxiv.org/content/10.1101/212753v1?rss=1 Struebing, F. L. King, R. Li, Y. Bailey, J. C. NEIGHBORHOOD Consortium, Wiggs, J. Geisert, E. E. 2017-11-01 doi:10.1101/212753 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Robustness of early warning signals for catastrophic and non-catastrophic transitions ]]> https://biorxiv.org/content/10.1101/218297v1?rss=1 Dutta, P. S. Sharma, Y. Abbott, K. 2017-11-12 doi:10.1101/218297 Cold Spring Harbor Laboratory Press 2017-11-12 <![CDATA[ Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal ]]> https://biorxiv.org/content/10.1101/223081v1?rss=1 Jeong, C. Witonsky, D. B. Basnyat, B. Neupane, M. Beall, C. M. Childs, G. Craig, S. R. Novembre, J. Di Rienzo, A. 2017-11-23 doi:10.1101/223081 Cold Spring Harbor Laboratory Press 2017-11-23 <![CDATA[ VarExp: Estimating variance explained by Genome-Wide GxE summary statistics ]]> https://biorxiv.org/content/10.1101/224634v1?rss=1 Laville, V. Bentley, A. Prive, F. Zhu, X. Gauderman, W. Winkler, T. Province, M. Rao, D. Aschard, H. CHARGE Gene-Lifestyle Interactions Working Group, 2017-11-24 doi:10.1101/224634 Cold Spring Harbor Laboratory Press 2017-11-24 <![CDATA[ Sex-specific genome-wide association study in glioma identifies new risk locus at 3p21.31 in females, and finds sex-differences in risk at 8q24.21 ]]> https://biorxiv.org/content/10.1101/229112v1?rss=1 Ostrom, Q. T. Kinnersley, B. Wrensch, M. R. Eckel-Passow, J. E. Armstrong, G. Rice, T. Chen, Y. Wiencke, J. K. McCoy, L. S. Hansen, H. M. Amos, C. I. Bernstein, J. L. Claus, E. B. Il'yasova, D. Johansen, C. Lachance, D. H. Lai, R. K. Merrell, R. T. Olson, S. H. Sadetzki, S. Schildkraut, J. M. Shete, S. Rubin, J. B. Lathia, J. D. Berens, M. E. Andersson, U. Rajaraman, P. Chanock, S. J. Linet, M. S. Wang, Z. Yeager, M. Houlston, R. S. Jenkins, R. B. Melin, B. Bondy, M. L. Barnholtz-Sloan, J. S. 2017-12-18 doi:10.1101/229112 Cold Spring Harbor Laboratory Press 2017-12-18 <![CDATA[ A cortical pathway modulates sensory input into the olfactory striatum ]]> https://biorxiv.org/content/10.1101/235291v1?rss=1 White, K. A. Zhang, Y.-F. Zhang, Z. Bhattarai, J. P. Moberly, A. H. in 't Zandt, E. Mi, H. Jia, X. Fuccillo, M. V. Xu, F. Ma, M. Wesson, D. W. 2017-12-16 doi:10.1101/235291 Cold Spring Harbor Laboratory Press 2017-12-16 <![CDATA[ Sex-specific gene and pathway modeling of inherited glioma risk ]]> https://biorxiv.org/content/10.1101/235408v1?rss=1 Ostrom, Q. T. Coleman, W. Huang, W. Rubin, J. B. Lathia, J. D. Berens, M. E. Speyer, G. Liao, P. Wrensch, M. R. Eckel-Passow, J. E. Armstrong, G. Rice, T. Wiencke, J. K. McCoy, L. S. Hansen, H. M. Amos, C. I. Bernstein, J. L. Claus, E. B. Il'yasova, D. Johansen, C. Lachance, D. H. Lai, R. K. Merrell, R. T. Olson, S. H. Sadetzki, S. Schildkraut, J. M. Shete, S. Houlston, R. S. Jenkins, R. B. Andersson, U. Rajaraman, P. Chanock, S. J. Linet, M. S. Wang, Z. Yeager, M. Melin, B. Bondy, M. L. Barnholtz-Sloan, J. S. 2017-12-18 doi:10.1101/235408 Cold Spring Harbor Laboratory Press 2017-12-18 <![CDATA[ Selective attention controls olfaction in rodents ]]> https://biorxiv.org/content/10.1101/236331v1?rss=1 Carlson, K. S. Gadziola, M. A. Dauster, E. S. Wesson, D. W. 2017-12-18 doi:10.1101/236331 Cold Spring Harbor Laboratory Press 2017-12-18 <![CDATA[ The PTPRT pseudo-phosphatase domain is a denitrase ]]> https://biorxiv.org/content/10.1101/238980v1?rss=1 Zhao, Y. Zhao, S. Hao, Y. Wang, B. Zhang, P. Feng, X. Chen, Y. Song, J. Mieyal, J. Markowitz, S. Ewing, R. Conlon, R. Miyagi, M. Wang, Z. 2017-12-22 doi:10.1101/238980 Cold Spring Harbor Laboratory Press 2017-12-22 <![CDATA[ Genome-wide association meta-analysis of PR interval identifies 47 novel loci associated with atrial and atrioventricular electrical activity ]]> https://biorxiv.org/content/10.1101/241489v1?rss=1 van Setten, J. Brody, J. A. Jamshidi, Y. Swenson, B. R. Butler, A. M. Campbell, H. Del Greco, F. M. Evans, D. S. Gibson, Q. Gudbjartsson, D. F. Kerr, K. F. Krijthe, B. P. Lyytikainen, L.-P. Muller, C. Muller-Nurasyid, M. Nolte, I. M. Padmanabhan, S. Ritchie, M. D. Robino, A. Smith, A. V. Steri, M. Tanaka, T. Teumer, A. Trompet, S. Ulivi, S. Verweij, N. Yin, X. Arnar, D. O. Asselbergs, F. W. Bader, J. S. Barnard, J. Bis, J. Blankenberg, S. Boerwinkle, E. Bradford, Y. Buckley, B. M. Chung, M. K. Crawford, D. den Hoed, M. Denny, J. Dominiczak, A. F. Ehret, 2018-01-17 doi:10.1101/241489 Cold Spring Harbor Laboratory Press 2018-01-17 <![CDATA[ Pattern, Pathways and Dynamics of EphA2 SAM and SHIP2 SAM Heterodimer Association Revealed by All-Atom Molecular Dynamics Simulation ]]> https://biorxiv.org/content/10.1101/241810v1?rss=1 LI, Z. Buck, M. 2018-01-02 doi:10.1101/241810 Cold Spring Harbor Laboratory Press 2018-01-02 <![CDATA[ Environmental and evolutionary drivers of the modular gene regulatory network underlying phenotypic plasticity for stress resistance in the nematode Caenorhabditis remanei ]]> https://biorxiv.org/content/10.1101/243758v1?rss=1 Sikkink, K. L. Reynolds, R. M. Ituarte, C. M. Cresko, W. A. Phillips, P. C. 2018-01-05 doi:10.1101/243758 Cold Spring Harbor Laboratory Press 2018-01-05 <![CDATA[ Neuron-specific cTag-CLIP reveals cell-specific diversity of functional RNA regulation in the brain ]]> https://biorxiv.org/content/10.1101/244905v1?rss=1 Saito, Y. Yuan, Y. Zucker-Scharff, I. Fak, J. J. Tajima, Y. Licatalosi, D. D. Darnell, R. B. 2018-01-08 doi:10.1101/244905 Cold Spring Harbor Laboratory Press 2018-01-08 <![CDATA[ Easy Hi-C: A simple efficient protocol for 3D genome mapping in small cell populations ]]> https://biorxiv.org/content/10.1101/245688v1?rss=1 Lu, L. Liu, X. Peng, J. Li, Y. Jin, F. 2018-01-10 doi:10.1101/245688 Cold Spring Harbor Laboratory Press 2018-01-10 <![CDATA[ Engineering of a Polydisperse Small Heat-Shock Protein Reveals Conserved Motifs of Oligomer Plasticity ]]> https://biorxiv.org/content/10.1101/247288v1?rss=1 Mishra, S. Chandler, S. A. Williams, D. Claxton, D. P. Koteiche, H. A. Stewart, P. L. Benesch, J. L. P. Mchaourab, H. S. 2018-01-12 doi:10.1101/247288 Cold Spring Harbor Laboratory Press 2018-01-12 <![CDATA[ CoPhosK: A Method for Comprehensive Kinase Substrate Annotation Using Co-phosphorylation Analysis ]]> https://biorxiv.org/content/10.1101/251009v1?rss=1 Ayati, M. Wiredja, D. Schlatzer, D. Maxwell, S. Li, M. Koyuturk, M. Chance, M. 2018-03-04 doi:10.1101/251009 Cold Spring Harbor Laboratory Press 2018-03-04 <![CDATA[ H3K9 methylation maintains female identity in Drosophila germ cells through repression of the spermatogenesis program ]]> https://biorxiv.org/content/10.1101/259473v1?rss=1 Smolko, A. Shapiro-Kulnane, L. Salz, H. 2018-02-02 doi:10.1101/259473 Cold Spring Harbor Laboratory Press 2018-02-02 <![CDATA[ Dazl regulates germ cell survival through a network of polyA proximal mRNA interactions ]]> https://biorxiv.org/content/10.1101/273292v1?rss=1 Zagore, L. L. Sweet, T. J. Hannigan, M. M. Weyn-Vanhentenryck, S. M. Zhang, C. Licatalosi, D. D. 2018-02-28 doi:10.1101/273292 Cold Spring Harbor Laboratory Press 2018-02-28 <![CDATA[ egtplot: A Python Package for 3-Strategy Evolutionary Games ]]> https://biorxiv.org/content/10.1101/300004v1?rss=1 Mirzaev, I. Williamson, D. Scott, J. G. 2018-04-12 doi:10.1101/300004 Cold Spring Harbor Laboratory Press 2018-04-12 <![CDATA[ In Vitro and In Vivo activity of a novel catheter lock solution against bacterial and fungal biofilms ]]> https://biorxiv.org/content/10.1101/300145v1?rss=1 Chandra, J. Long, L. Isham, N. Mukherjee, P. K. DiSciullo, G. Appelt, K. Ghannoum, M. A. 2018-04-13 doi:10.1101/300145 Cold Spring Harbor Laboratory Press 2018-04-13 <![CDATA[ Translation elongation and mRNA stability are coupled through the ribosomal A-site ]]> https://biorxiv.org/content/10.1101/300467v1?rss=1 Hanson, G. Alhusaini, N. Morris, N. Sweet, T. Coller, J. 2018-04-12 doi:10.1101/300467 Cold Spring Harbor Laboratory Press 2018-04-12 <![CDATA[ Community origins and regional differences in plasmid-mediated fluoroquinolone resistant Enterobacteriaceae infections in children ]]> https://biorxiv.org/content/10.1101/301457v1?rss=1 5 times more likely to have PMFQR-Ent infections than those in the reference region, while residence in Central Chicago was associated with a 97% decreased risk. Other demographic, comorbidity, invasive-device, antibiotic use, or healthcare differences were not found.nnConclusionsThe strong association of infection with MDROs showing FQR with patient residence rather than with traditional risk factors suggests that the community environment is a major contributor to spread of these pathogens in children. ]]> Logan, L. K. Medernach, R. L. Rispens, J. R. Marshall, S. H. Hujer, A. M. Domitrovic, T. N. Rudin, S. D. Zheng, X. Qureshi, N. K. Konda, S. Hayden, M. Weinstein, R. A. Bonomo, R. A. 2018-04-16 doi:10.1101/301457 Cold Spring Harbor Laboratory Press 2018-04-16 <![CDATA[ Cdc23/Mcm10 Primase Generates the Lagging Strand-Specific Ribonucleotide Imprint in Fission Yeast ]]> https://biorxiv.org/content/10.1101/303180v1?rss=1 Singh, J. Singh, B. Bisht, K. K. Upadhyay, U. Kushwaha, A. C. Nanda, J. S. Srivastava, S. Klar, A. J. 2018-04-17 doi:10.1101/303180 Cold Spring Harbor Laboratory Press 2018-04-17 <![CDATA[ Unraveling the mechanism of the cadherin-catenin-actin catch bond ]]> https://biorxiv.org/content/10.1101/306761v1?rss=1 Adhikari, S. Moran, J. Weddle, C. Hinczewski, M. 2018-04-23 doi:10.1101/306761 Cold Spring Harbor Laboratory Press 2018-04-23 <![CDATA[ Oscillatory cortical forces promote three dimensional cell intercalations that shape the mandibular arch ]]> https://biorxiv.org/content/10.1101/309120v1?rss=1 Tao, H. Zhu, M. Lau, K. Whitley, O. Samani, M. Xiao, X. Chen, X. X. Hahn, N. A. Liu, W. Valencia, M. Wu, M. Wang, X. Fenelon, K. D. Pasiliao, C. C. Hu, D. Wu, J. Spring, S. Ferguson, J. Karuana, E. P. Henkelman, R. M. Dunn, A. Huang, H. Ho, H.-Y. H. Atit, R. Goyal, S. Sun, Y. Hopyan, S. 2018-04-26 doi:10.1101/309120 Cold Spring Harbor Laboratory Press 2018-04-26 <![CDATA[ Global immune fingerprinting in glioblastoma reveals immune-suppression signatures associated with prognosis ]]> https://biorxiv.org/content/10.1101/309807v1?rss=1 Alban, T. J. Alvarado, A. G. Sorensen, M. D. Bayik, D. Volovetz, J. Serbinowski, E. Mulkearn-Hubert, E. Maksim, S. Hale, J. S. Onzi, G. R. McGraw, M. Huang, P. Grabowski, M. M. Wathen, C. A. Radivoyevitch, T. Kornblum, H. I. Kristensen, B. W. Vogelbaum, M. A. Lathia, J. D. 2018-04-27 doi:10.1101/309807 Cold Spring Harbor Laboratory Press 2018-04-27 <![CDATA[ A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection ]]> https://biorxiv.org/content/10.1101/311696v1?rss=1 Fourati, S. Talla, A. Mahmoudian, M. Burkhart, J. G. Klen, R. Henao, R. Aydin, Z. Yeung, K. Y. Ahsen, M. E. Almugbel, R. Jahandideh, S. Liang, X. Nordling, T. E. M. Shiga, M. Stanescu, A. Vogel, R. The Respiratory Viral DREAM Challenge Consortium, Pandey, G. Chiu, C. McClain, M. T. Woods, C. W. Ginsburg, G. S. Elo, L. L. Tsalik, E. L. Mangravite, L. M. Sieberts, S. K. 2018-04-30 doi:10.1101/311696 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Quality Control and Integration of Genotypes from Two Calling Pipelines for Whole Genome Sequence Data in the Alzheimer’s Disease Sequencing Project ]]> https://biorxiv.org/content/10.1101/318857v1?rss=1 Naj, A. C. Lin, H. Vardarajan, B. N. White, S. Lancour, D. Ma, Y. Schmidt, M. Sun, F. Butkiewicz, M. Bush, W. S. Kunkle, B. W. Malamon, J. Amin, N. Choi, S. H. Hamilton-Nelson, K. L. van der Lee, S. J. Gupta, N. Koboldt, D. C. Saad, M. Wang, B. Nato, A. Q. Sohi, H. K. Kuzma, A. Alzheimer's Disease Sequencing Project (ADSP), Wang, L.-S. Cupples, L. A. van Duijn, C. Seshadri, S. Schellenberg, G. D. Boerwinkle, E. Bis, J. C. Dupuis, J. Salerno, W. J. Wijsman, E. M. Martin, E. DeStefano, A. L. 2018-05-11 doi:10.1101/318857 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ K-Ras G-domain binding with signaling lipid phosphoinositides: PIP2 association, orientation, function ]]> https://biorxiv.org/content/10.1101/324210v1?rss=1 Cao, S. Chung, S. Kim, S. Li, Z. Manor, D. Buck, M. 2018-05-16 doi:10.1101/324210 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Metastable contacts and structural disorder in the estrogen receptor transactivation domain ]]> https://biorxiv.org/content/10.1101/332205v1?rss=1 Peng, Y. Cao, S. Kiselar, J. Xiao, X. Hsien, A. Chen, Y. Shi, W. Jiang, W. Yang, L. Chance, M. Surewicz, W. Buck, M. Yang, S. 2018-05-28 doi:10.1101/332205 Cold Spring Harbor Laboratory Press 2018-05-28 <![CDATA[ Modeling the growth of organisms validates a general relation between metabolic costs and natural selection ]]> https://biorxiv.org/content/10.1101/358440v1?rss=1 Ilker, E. Hinczewski, M. 2018-06-29 doi:10.1101/358440 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Non-adhesive alginate hydrogels support growth of pluripotent stem cell-derived intestinal organoids ]]> https://biorxiv.org/content/10.1101/364885v1?rss=1 Capeling, M. M. Czerwinski, M. Huang, S. Tsai, Y.-H. Wu, A. Nagy, M. S. Juliar, B. Song, Y. Sundaram, N. Takayama, S. Alsberg, E. Helmrath, M. Putnam, A. J. Spence, J. R. 2018-07-08 doi:10.1101/364885 Cold Spring Harbor Laboratory Press 2018-07-08 <![CDATA[ Occidiofungin, an actin binding antifungal with in vivo efficacy in a vulvovaginal candidiasis infection ]]> https://biorxiv.org/content/10.1101/368720v1?rss=1 Ravichandran, A. Geng, M. Hull, K. G. Romo, D. Lu, S.-E. Albee, A. Nutter, C. Gordon, D. Ghannoum, M. A. Lockless, S. W. Smith, L. 2018-07-13 doi:10.1101/368720 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ Static stability predicts the continuum of interleg coordination patterns in Drosophila ]]> https://biorxiv.org/content/10.1101/374272v1?rss=1 Szczecinski, N. S. Bockemuhl, T. Chockley, A. S. Buschges, A. 2018-07-23 doi:10.1101/374272 Cold Spring Harbor Laboratory Press 2018-07-23 <![CDATA[ Quantifying the effects of head movement on magnetic resonance spectroscopy estimates of gamma-aminobutyric acid ]]> https://biorxiv.org/content/10.1101/381699v1?rss=1 Cui, E. D. Maddock, R. J. Buonocore, M. H. Ozturk, M. Yoon, J. H. 2018-07-31 doi:10.1101/381699 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ The role of sodium channels in sudden unexpected death in pediatrics ]]> https://biorxiv.org/content/10.1101/383562v1?rss=1 Rochtus, A. M. Goldstein, R. D. Holm, I. A. Brownstein, C. A. Perez-Palma, E. Lal, D. Poduri, A. 2018-08-02 doi:10.1101/383562 Cold Spring Harbor Laboratory Press 2018-08-02 <![CDATA[ Integrative analyses of multi-tissue Hi-C and eQTL data demonstrate close spatial proximity between eQTLs and their target genes ]]> https://biorxiv.org/content/10.1101/392266v1?rss=1 Yu, J. Hu, M. Li, C. 2018-08-14 doi:10.1101/392266 Cold Spring Harbor Laboratory Press 2018-08-14 <![CDATA[ Age of onset in genetic prion disease and the design of preventive clinical trials ]]> https://biorxiv.org/content/10.1101/401406v1?rss=1 Minikel, E. V. Vallabh, S. M. Orseth, M. C. Brandel, J.-P. Haik, S. Laplanche, J.-L. Zerr, I. Parchi, P. Capellari, S. Safar, J. Kenny, J. Fong, J. C. Takada, L. T. Ponto, C. Hermann, P. Knipper, T. Stehmann, C. Kitamoto, T. Ae, R. Hamaguchi, T. Sanjo, N. Tsukamoto, T. Mizusawa, H. Collins, S. J. Chiesa, R. Roiter, I. de Pedro-Cuesta, J. Calero, M. Geschwind, M. D. Yamada, M. Nakamura, Y. Mead, S. 2018-08-29 doi:10.1101/401406 Cold Spring Harbor Laboratory Press 2018-08-29 <![CDATA[ Mismatch-repair signature mutations activate gene enhancers across colorectal cancer epigenomes ]]> https://biorxiv.org/content/10.1101/411264v1?rss=1 Hung, S. Saiakhova, A. Faber, Z. Bartels, C. F. Neu, D. Bayles, I. Ojo, E. Hong, E. S. Pontius, W. D. Morton, A. R. Liu, R. Kalady, M. F. Wald, D. N. Markowitz, S. Scacheri, P. C. 2018-09-07 doi:10.1101/411264 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ Imaging breast cancer using a dual-ligand nanochain particle ]]> https://biorxiv.org/content/10.1101/411728v1?rss=1 Covarrubias, G. Cha, A. Rahmy, A. Lorkowski, M. Perera, V. Erokwu, B. O. Flask, C. Peiris, P. M. Schiemann, W. P. Karathanasis, E. 2018-09-07 doi:10.1101/411728 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ Critical role of miR-10b in BRafV600E dependent anchorage independent growth and invasion of melanoma cells ]]> https://biorxiv.org/content/10.1101/413476v1?rss=1 Datar, I. Kalpana, G. de la Serna, I. Trumbly, R. Choi, J. Yeung, K. C. 2018-09-10 doi:10.1101/413476 Cold Spring Harbor Laboratory Press 2018-09-10 <![CDATA[ Human Migration and the Spread of the Nematode Parasite Wuchereria bancrofti ]]> https://biorxiv.org/content/10.1101/421248v1?rss=1 Small, S. T. Labbe, F. Coulibaly, Y. I. Nutman, T. B. King, C. L. Serre, D. Zimmerman, P. A. 2018-09-19 doi:10.1101/421248 Cold Spring Harbor Laboratory Press 2018-09-19 <![CDATA[ Human IFNε: Spaciotemporal expression, hormone regulation and innate immunity in the female reproductive tract ]]> https://biorxiv.org/content/10.1101/445007v1?rss=1 Bourke, N. M. Achilles, S. L. Huang, S. U. Cumming, H. E. Papageorgio, I. Gearing, L. J. Thakore, S. Mangan, N. E. Mesiano, S. Hertzog, P. J. 2018-10-16 doi:10.1101/445007 Cold Spring Harbor Laboratory Press 2018-10-16 <![CDATA[ Imaging Oxysterols in Mouse Brain by On-Tissue Derivatisation-Robotic Liquid Micro-Extraction Surface Analysis-Liquid Chromatography Mass Spectrometry ]]> https://biorxiv.org/content/10.1101/450973v1?rss=1 Griffiths, W. J. Yutuc, E. Angelini, R. Baumert, M. Mast, N. Pikuleva, I. Newton, J. Clench, M. R. Howell, O. Wang, Y. 2018-10-23 doi:10.1101/450973 Cold Spring Harbor Laboratory Press 2018-10-23 <![CDATA[ Shared heritability and functional enrichment across six solid cancers ]]> https://biorxiv.org/content/10.1101/453480v1?rss=1 Jiang, X. Finucane, H. Schumacher, F. Schmit, S. Tyrer, J. Han, Y. Michailidou, K. Lesseur, C. Kuchenbaecker, K. Dennis, J. Conti, D. Casey, G. Gaude, M. Huyghe, J. Albanes, D. Aldrich, M. Andrew, A. Andrulis, I. Anton-Culver, H. Antoniou, A. Antonenkova, N. Arnold, S. Aronson, K. Arun, B. Bandera, E. Barkardottir, R. Barnes, D. Batra, J. Beckmann, M. Benitez, J. Benlloch, S. Berchuck, A. Berndt, S. Bickeboller, H. Bien, S. Blomqvist, C. Boccia, S. Bogdanova, N. Bojesen, S. Bolla, M. Brauch, H. Brenner, H. Brenton, J. Brook, M. Brunet, J. Brunnstrom 2018-10-25 doi:10.1101/453480 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Genome-wide association analysis of excessive daytime sleepiness identifies 42 loci that suggest phenotypic subgroups ]]> https://biorxiv.org/content/10.1101/454561v1?rss=1 Wang, H. Lane, J. M. Jones, S. E. Dashti, H. S. Ollila, H. Wood, A. R. van Hees, V. T. Brumpton, B. Winsvold, B. S. Kantojarvi, K. Cade, B. E. Sofer, T. Song, Y. Patel, K. Anderson, S. G. Bechtold, D. A. Bowden, J. Emsley, R. Kyle, S. D. Little, M. A. Loudon, A. S. Scheer, F. A. Purcell, S. M. Richmond, R. C. Spiegelhalder, K. Tyrrell, J. Zhu, X. Kristiansson, K. Sulkava, S. Paunio, T. Hveem, K. Nielsen, J. B. Willer, C. J. Zwart, J.-A. Strand, L. B. Frayling, T. M. Ray, D. Lawlor, D. A. Rutter, M. K. Weedon, M. N. Redline, S. Saxena, R. 2018-10-26 doi:10.1101/454561 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ Largest genome-wide association study for PTSD identifies genetic risk loci in European and African ancestries and implicates novel biological pathways ]]> https://biorxiv.org/content/10.1101/458562v1?rss=1 Nievergelt, C. M. Maihofer, A. X. Klengel, T. Atkinson, E. G. Chen, C.-Y. Choi, K. W. Coleman, J. R. I. Dalvie, S. Duncan, L. E. Logue, M. W. Provost, A. Ratanatharathorn, A. Stein, M. B. Torres, K. Aiello, A. E. Almli, L. M. Amstadter, A. B. Andersen, S. B. Andreassen, O. A. Arbisi, P. A. Ashley-Koch, A. E. Austin, S. B. Avdibegovic, E. Babic, D. Baekvad-Hansen, M. Baker, D. G. Beckham, J. C. Bierut, L. J. Bisson, J. I. Boks, M. P. Bolger, E. A. Borglum, A. D. Bradley, B. Brashear, M. Breen, G. Bryant, R. A. Bustamante, A. C. Bybjerg-Grauholm, J. Calabres 2018-11-01 doi:10.1101/458562 Cold Spring Harbor Laboratory Press 2018-11-01 <![CDATA[ Efficient GFP-labeling and analysis of spermatogenic cells using the IRG transgene and flow cytometry ]]> https://biorxiv.org/content/10.1101/465286v1?rss=1 Zagore, L. L. Akesson, C. C. Licatalosi, D. D. 2018-11-08 doi:10.1101/465286 Cold Spring Harbor Laboratory Press 2018-11-08 <![CDATA[ Age but not disease progression defines CD4+ and CD8+ T stem cell memory levels in human retroviral infections: contrasting effects of HTLV-1 and HIV-1 ]]> https://biorxiv.org/content/10.1101/473363v1?rss=1 400% increase in elderly HTLV-1 infected individuals (>60 years). A significant correlation between age and TSCM signature genes was validated at the transcriptome level in an independent cohort. CD8+ but not CD4+ TSCM were significantly decreased in untreated HIV-1 infection. Unexpectedly, CD8+ TSCM recovery upon successful antiretroviral treatment was essentially complete (92.2{+/-}11.0%) in younger (<45 years) individuals, but significantly lower (37.3{+/-}6.1%) in older (>45 years) individuals (p=0.0003).nnConclusionIn HTLV-1 infection, an age-dependent accumulation of CD4+ and CD8+ TSCM points towards a possible protective role of CD8 TSCM in the elderly against leukemic but not neuroinflammatory disease. HIV-1-infected individuals lose their ability to restore CD8+ TSCM levels upon successful antiretroviral therapy at later age (>45 years), which might eventually lead to immunological failure and decreased vaccine efficacy. ]]> Menezes, S. M. Leal, F. E. Pereira Ribeiro, S. Dierckx, T. Roederer, M. SenGupta, D. Nixon, D. Van Weyenbergh, J. 2018-11-19 doi:10.1101/473363 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Development and validation of serological markers for detecting recent exposure to Plasmodium vivax infection ]]> https://biorxiv.org/content/10.1101/481168v1?rss=1 Longley, R. J. White, M. T. Takashima, E. Brewster, J. Morita, M. Harbers, M. Robinson, L. J. Matsuura, F. Liu, S.-J. Li-Wai-Suen, C. S. N. Tham, W.-H. Healer, J. Huon, C. Chitnis, C. E. Nguitragool, W. Monteiro, W. M. Proietti, C. Doolan, D. L. Ding, X. C. Gonzalez, I. J. Kazura, J. Lacerda, M. Sattabongkot, J. Tsuboi, T. Mueller, I. 2018-11-30 doi:10.1101/481168 Cold Spring Harbor Laboratory Press 2018-11-30 <![CDATA[ Mutations In PIK3C2A Cause Syndromic Short Stature, Skeletal Abnormalities, and Cataracts Associated With Ciliary Dysfunction ]]> https://biorxiv.org/content/10.1101/488411v1?rss=1 Tiosano, D. Baris Feldman, H. Chen, A. Hitzert, M. M. Schueler, M. Gulluni, F. Wiesener, A. Bergua, A. Mory, A. Copeland, B. Gleeson, J. G. Rump, P. van Meer, H. Sival, D. A. Haucke, V. Kriwinsky, J. Knaup, K. X. Reis, A. Hauer, N. N. Hirsch, E. Roepman, R. Pfundt, R. Thiel, C. T. Wiesener, M. S. Aslanyan, M. G. Buchner, D. A. 2018-12-07 doi:10.1101/488411 Cold Spring Harbor Laboratory Press 2018-12-07 <![CDATA[ Codon usage and amino acid identity are major determinants of mRNA stability in humans ]]> https://biorxiv.org/content/10.1101/488676v1?rss=1 Forrest, M. E. Narula, A. Sweet, T. J. Arango, D. Hanson, G. Ellis, J. Oberdoerffer, S. Coller, J. Rissland, O. S. 2018-12-07 doi:10.1101/488676 Cold Spring Harbor Laboratory Press 2018-12-07 <![CDATA[ Bone-Inspired Microarchitectured Materials with Enhanced Fatigue Life ]]> https://biorxiv.org/content/10.1101/494633v1?rss=1 Torres, A. M. Trikanad, A. A. Aubin, C. A. Lambers, F. M. Luna, M. Rimnac, C. M. Zavattieri, P. D. Hernandez, C. 2018-12-13 doi:10.1101/494633 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ PTBP2-dependent alternative splicing regulates protein transport and mitochondria morphology in post-meiotic germ cells. ]]> https://biorxiv.org/content/10.1101/497461v1?rss=1 Hannigan, M. M. Fujioka, H. Brett-Morris, A. Mears, J. A. Licatalosi, D. D. 2018-12-15 doi:10.1101/497461 Cold Spring Harbor Laboratory Press 2018-12-15 <![CDATA[ Neural ensemble dynamics in dorsal motor cortex during speech in people with paralysis ]]> https://biorxiv.org/content/10.1101/505487v1?rss=1 Stavisky, S. D. Willett, F. R. Murphy, B. A. Rezaii, P. Memberg, W. D. Miller, J. P. Kirsch, R. F. Hochberg, L. R. Ajiboye, A. B. Shenoy, K. V. Henderson, J. M. 2018-12-30 doi:10.1101/505487 Cold Spring Harbor Laboratory Press 2018-12-30 <![CDATA[ Therapeutic suppression of proteolipid protein rescues Pelizaeus-Merzbacher Disease in mice ]]> https://biorxiv.org/content/10.1101/508192v1?rss=1 Elitt, M. S. Barbar, L. Shick, H. E. Powers, B. E. Maeno-Hikitchi, Y. Madhavan, M. Allan, K. C. Nawash, B. S. Nevin, Z. S. Olsen, H. E. Hitomi, M. LePage, D. F. Jiang, W. Conlon, R. A. Rigo, F. Tesar, P. J. 2018-12-31 doi:10.1101/508192 Cold Spring Harbor Laboratory Press 2018-12-31 <![CDATA[ Duffy Antigen Expression in Erythroid Bone Marrow Precursor Cells of Genotypically Duffy Negative Individuals ]]> https://biorxiv.org/content/10.1101/508481v1?rss=1 Dechavanne, C. Dechavanne, S. Metral, S. Roeper, B. Krishnan, S. Fong, R. Bennett, S. Carias, L. Chen, E. Salinas, N. D. Ghosh, A. Tolia, N. H. Woost, P. G. Jacobberger, J. J. Colin, Y. Gamain, B. King, C. L. Zimmerman, P. A. 2018-12-31 doi:10.1101/508481 Cold Spring Harbor Laboratory Press 2018-12-31 <![CDATA[ Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli ]]> https://biorxiv.org/content/10.1101/511402v1?rss=1 Davies, T. J. Stoesser, N. Sheppard, A. E. Abuoun, M. Fowler, P. W. Swann, J. Quan, P. Griffiths, D. Vaughan, A. Morgan, M. Phan, H. T. T. Jeffery, K. J. Andersson, M. Ellington, M. Ekelund, O. Mathers, A. Bonomo, R. Woodford, N. Crook, D. W. Peto, T. E. Anjum, M. Walker, A. S. 2019-01-07 doi:10.1101/511402 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ Discovery of a redox-thiol switch regulating cellular energy metabolism ]]> https://biorxiv.org/content/10.1101/520411v1?rss=1 Gao, X.-H. Li, L. Parisien, M. Mcleod, M. Wu, J. Bederman, I. Gao, Z. Krokowski, D. Chirieleison, S. M. Diatchenko, L. Abbott, D. Yee, V. Hoppel, C. Kibbey, R. Holyoak, T. Willard, B. Arvan, P. Hatzoglou, M. 2019-01-14 doi:10.1101/520411 Cold Spring Harbor Laboratory Press 2019-01-14 <![CDATA[ Novel Insights into Malaria Vector Surveillance in Madagascar Using a Quadrant Enabled Screen Trap (QUEST) and Bloodmeal Detection Assay for Regional Transmission (BLOODART) ]]> https://biorxiv.org/content/10.1101/530758v1?rss=1 Tedrow, R. E. Rakotomanga, T. Nepomichene, T. Ratovonjato, J. Ratsimbasoa, A. Svenson, G. J. Zimmerman, P. 2019-01-25 doi:10.1101/530758 Cold Spring Harbor Laboratory Press 2019-01-25 <![CDATA[ MmpL3 is a lipid transporter that binds trehalose monomycolate and phosphatidylethanolamine ]]> https://biorxiv.org/content/10.1101/531160v1?rss=1 Su, C.-C. Klenotic, P. Bolla, J. R. Purdy, G. Robinson, C. Yu, E. 2019-01-26 doi:10.1101/531160 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Effectiveness of a mobile antiretroviral pharmacy and HIV care intervention on the continuum of HIV care in rural Uganda ]]> https://biorxiv.org/content/10.1101/533950v1?rss=1 5km from the hospital were provided the option to participate. For each hospital, we identified 4 health centres in the catchment area to serve as site for the mobile pharmacy. Each site was visited once a month to provide ART refills, adherence counseling and treatment of other illnesses. We measured patient waiting time, adherence and viral load suppression before and after the intervention. ResultsWe conducted baseline assessment among 292 patients at the two hospitals. The mean waiting time at Kitagata Hospital changed from 4.48 hours before the intervention but increased to 4.76 hours after the intervention (p=0.13). The proportion of patients who missed an ART dose in the last 30 days dropped from 20% at baseline to 8.5% at 12 months after the intervention (p=0.009). The proportion of patients with detectable viral load from 19.9% to 7.4% after the intervention (p=0.001). ConclusionsOur study has showed that a mobile pharmacy intervention in rural Uganda is feasible and resulted in improvement in adherence and viral load suppression. Although it did not reduce patient waiting time at the clinic, we recommend a scale-up of this intervention in rural areas where patients face challenges of transportation to the clinic. ]]> Bajunirwe, F. Ayebazibwe, N. Mulogo, E. Eng, M. McGrath, J. Kaawa-Mafigiri, D. Mugyenyi, P. Sethi, A. K. 2019-01-29 doi:10.1101/533950 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ GIT2 is dispensable for normal learning and memory function due to a predominant brain GIT2 splice variant that evades GIT/PIX complexes. ]]> https://biorxiv.org/content/10.1101/538223v1?rss=1 Toth, K. Martyn, A. C. Bastrikova, N. Kim, W. Rodriguiz, R. M. Ahmed, U. Schmalzigaug, R. Dudek, S. M. Wetsel, W. C. Premont, R. T. 2019-02-01 doi:10.1101/538223 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ Competition and immune selection of multi-strain Plasmodium falciparum malaria ]]> https://biorxiv.org/content/10.1101/539676v1?rss=1 Gurarie, D. 2019-02-03 doi:10.1101/539676 Cold Spring Harbor Laboratory Press 2019-02-03 <![CDATA[ Facilitating Replication and Reproducibility in Team Science: the 'projects' R Package ]]> https://biorxiv.org/content/10.1101/540542v1?rss=1 Krieger, N. I. Perzynski, A. T. Dalton, J. E. Northeast Ohio Cohort for Atherosclerotic Risk Estimation (NEOCARE) investigative team, 2019-02-04 doi:10.1101/540542 Cold Spring Harbor Laboratory Press 2019-02-04 <![CDATA[ Deep proteomic analysis of Dnmt1 mutant/hypomorphic colorectal cancer cells reveals dys-regulation of Epithelial-Mesenchymal Transition and subcellular re-localization of Beta-Catenin ]]> https://biorxiv.org/content/10.1101/547737v1?rss=1 Bowler, E. Smith-Vidal, A. Lester, A. Bell, J. Wang, Z. Bell, C. Wang, Y. Divecha, N. Skipp, P. Ewing, R. M. 2019-02-13 doi:10.1101/547737 Cold Spring Harbor Laboratory Press 2019-02-13 <![CDATA[ Malignant liver cancers have distinct myeloid-derived suppressor cell signatures ]]> https://biorxiv.org/content/10.1101/554600v1?rss=1 Bayik, D. Serbinowski, E. Lauko, A. Roversi, G. A. Acevedo-Moreno, L.-A. Lanigan, C. Orujov, M. Silver, D. J. Brown, J. M. Allende, D. S. Aucejo, F. N. Lathia, J. D. 2019-02-19 doi:10.1101/554600 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ Multi-ancestry analysis of gene-sleep interactions in 126,926 individuals identifies multiple novel blood lipid loci that contribute to our understanding of sleep-associated adverse blood lipid profile ]]> https://biorxiv.org/content/10.1101/559393v1?rss=1 Noordam, R. Bos, M. M. Wang, H. Winkler, T. W. Bentley, A. R. Kilpeläinen, T. de Vries, P. S. Sung, Y. J. Schwander, K. Cabe, B. E. Manning, A. Aschard, H. Brown, M. R. Chen, H. Franceschini, N. Musani, S. K. Richard, M. Vojinovic, D. Aslibekyan, S. Bartz, T. M. de las Fuentes, L. Feitosa, M. Horimoto, A. R. Ilkov, M. Kho, M. Kraja, A. Li, C. Lim, E. Liu, Y. Mook-Kanamori, D. O. Rankinen, T. Tajuddin, S. M. van der Spek, A. Wang, Z. Marten, J. Laville, V. Alver, M. Evangelou, E. Graff, M. E. He, M. Kühnel, B. Lyytikäinen, L.-P. Marques-Vidal, P. No 2019-02-25 doi:10.1101/559393 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ Combinatorial morphogenetic and mechanical cues to mimic bone development for defect repair ]]> https://biorxiv.org/content/10.1101/561837v1?rss=1 Herberg, S. McDermott, A. M. Dang, P. N. Alt, D. S. Tang, R. Dawahare, J. H. Varghai, D. Shin, J.-Y. McMillan, A. Dikina, A. He, F. Lee, Y. B. Cheng, Y. Umemori, K. Wong, P. C. Park, H. Boerckel, J. D. Alsberg, E. 2019-02-26 doi:10.1101/561837 Cold Spring Harbor Laboratory Press 2019-02-26 <![CDATA[ Computational Design of Myristoylated Cell Penetrating Peptides Targeting Oncogenic K-Ras.G12D at the Effector Binding Membrane Interface ]]> https://biorxiv.org/content/10.1101/565945v1?rss=1 Li, Z. Buck, M. 2019-03-03 doi:10.1101/565945 Cold Spring Harbor Laboratory Press 2019-03-03 <![CDATA[ Ciliary Genes arl13b, ahi1 and cc2d2a Differentially Modify Expression of Visual Acuity Phenotypes but do not Enhance Retinal Degeneration due to Mutation of cep290 in Zebrafish ]]> https://biorxiv.org/content/10.1101/569822v1?rss=1 Perkins, B. Lessieur, E. Song, P. Nivar, G. Piccillo, E. Fogerty, J. Rozic, R. 2019-03-06 doi:10.1101/569822 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ Evolution, not transgenerational plasticity, explains the divergence of acorn ant thermal tolerance across an urban-rural temperature cline ]]> https://biorxiv.org/content/10.1101/571521v1?rss=1 Martin, R. A. Chick, L. D. Yilmaz, A. R. Diamond, S. E. 2019-03-09 doi:10.1101/571521 Cold Spring Harbor Laboratory Press 2019-03-09 <![CDATA[ Kindlin-3 Mutation in Mesenchymal Stem Cells Results in Enhanced Chondrogenesis ]]> https://biorxiv.org/content/10.1101/578690v1?rss=1 Kerr, B. Shi, L. Jinnah, A. Willey, J. Lennon, D. Caplan, A. Byzova, T. 2019-03-15 doi:10.1101/578690 Cold Spring Harbor Laboratory Press 2019-03-15 <![CDATA[ ITGA2 is a target of miR-206 promoting cancer stemness and lung metastasis through enhanced ACLY and CCND1 expression in triple negative breast cancer ]]> https://biorxiv.org/content/10.1101/583062v1?rss=1 Adorno-Cruz, V. Hoffmann, A. D. Liu, X. Wray, B. Keri, R. A. Liu, H. 2019-03-19 doi:10.1101/583062 Cold Spring Harbor Laboratory Press 2019-03-19 <![CDATA[ A Truly Injectable Neural Stimulation Electrode Made From an In-Body Curing Polymer/Metal Composite ]]> https://biorxiv.org/content/10.1101/584995v1?rss=1 Trevathan, J. K. Baumgart, I. Nicolai, E. N. Gosink, B. A. Asp, A. J. Settell, M. L. Polaconda, S. R. Malerick, K. Brodnick, S. K. Zeng, W. Knudsen, B. E. McConico, A. L. Sanger, Z. Lee, J. H. Aho, J. M. Suminski, A. J. Ross, E. K. Lujan, J. L. Weber, D. J. Williams, J. C. Franke, M. Ludwig, K. A. Shoffstall, A. J. 2019-03-21 doi:10.1101/584995 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Phospho-tuning immunity through Denisovan, modern human, and mouse TNFAIP3 gene variants ]]> https://biorxiv.org/content/10.1101/589507v1?rss=1 Zammit, N. W. Siggs, O. M. Gray, P. Horikawa, K. Daley, S. R. Langley, D. B. Cultrone, D. Malle, E. K. Walters, S. N. Villanueva, J. E. Warren, J. Russell, A. Cowley, M. J. Gayevskiy, V. Dinger, M. E. Loetsch, C. King, C. Brink, R. Zahra, D. Chaudhri, G. Karupiah, G. Whittle, B. Roots, C. Bertram, E. Yamada, M. Jeelall, Y. Enders, A. Clifton, B. E. Mabbitt, P. D. Jackson, C. J. Watson, S. R. Jenne, C. N. Lanier, L. L. Wiltshire, T. Spitzer, M. H. Nolan, G. P. Schmitz, F. Aderem, A. Porebski, B. T. Buckle, A. M. Abbott, D. W. Ziegler, J. B. Craig, M. E. 2019-03-27 doi:10.1101/589507 Cold Spring Harbor Laboratory Press 2019-03-27 <![CDATA[ Domain-specific quantification of prion protein in cerebrospinal fluid by targeted mass spectrometry ]]> https://biorxiv.org/content/10.1101/591487v1?rss=1 Minikel, E. V. Kuhn, E. Cocco, A. R. Vallabh, S. M. Hartigan, C. R. Reidenbach, A. G. Safar, J. G. Raymond, G. J. McCarthy, M. D. O'Keefe, R. Llorens, F. Zerr, I. Capellari, S. Parchi, P. Schreiber, S. L. Carr, S. A. 2019-04-01 doi:10.1101/591487 Cold Spring Harbor Laboratory Press 2019-04-01 <![CDATA[ APOL1-G0 protects podocytes in a mouse model of HIV-associated nephropathy ]]> https://biorxiv.org/content/10.1101/598557v1?rss=1 Bruggeman, L. A. Wu, Z. Luo, L. Madhavan, S. Drawz, P. E. Thomas, D. B. Barisoni, L. O'Toole, J. F. Sedor, J. R. 2019-04-05 doi:10.1101/598557 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ Living cell-only bioink and photocurable supporting medium for printing and generation of engineered tissues with complex geometries ]]> https://biorxiv.org/content/10.1101/611525v1?rss=1 Jeon, O. Lee, Y. B. Jeong, H. Lee, S. J. Alsberg, E. 2019-04-17 doi:10.1101/611525 Cold Spring Harbor Laboratory Press 2019-04-17 <![CDATA[ A neural system for encoding odor-reward associations which influences approach behaviors ]]> https://biorxiv.org/content/10.1101/617902v1?rss=1 Gadziola, M. A. Stetzik, L. A. Milton, A. J. Arakawa, K. Wesson, D. W. 2019-04-26 doi:10.1101/617902 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Updated Database and Evolutionary Dynamics of U12-Type Introns ]]> https://biorxiv.org/content/10.1101/620658v1?rss=1 Moyer, D. Larue, G. E. Hershberger, C. E. Roy, S. W. Padgett, R. A. 2019-05-05 doi:10.1101/620658 Cold Spring Harbor Laboratory Press 2019-05-05 <![CDATA[ APOL1 is not expressed in proximal tubules and is not filtered ]]> https://biorxiv.org/content/10.1101/623918v1?rss=1 Blessing, N. A. Wu, Z. Madhavan, S. Shin, M. K. Hoek, M. Sedor, J. R. O'Toole, J. F. Bruggeman, L. A. 2019-05-02 doi:10.1101/623918 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Bubble Trouble: Conquering Microbubble Limitations in Contrast Enhanced Ultrasound Imaging by Nature-Inspired Ultrastable Echogenic Nanobubbles ]]> https://biorxiv.org/content/10.1101/633578v1?rss=1 de Leon, A. Perera, R. Hernandez, C. Cooley, M. Jung, O. Jeganathan, S. Abenojar, E. Fishbein, G. Jafari Sojahrood, A. Emerson, C. Stewart, P. Kolios, M. Exner, A. 2019-05-09 doi:10.1101/633578 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Real Time Ultrasound Molecular Imaging of Prostate Cancer with PSMA-targeted Nanobubbles ]]> https://biorxiv.org/content/10.1101/634444v1?rss=1 Perera, R. H. De Leon, A. Wang, X. Wang, Y. Ramamurthy, G. Peiris, P. Abenojar, E. Basilion, J. P. Exner, A. A. 2019-05-10 doi:10.1101/634444 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Do available protein 3D structures reflect human genetic and functional diversity? ]]> https://biorxiv.org/content/10.1101/637744v1?rss=1 Sliwoski, G. Patel, N. Sivley, R. M. Sanders, C. R. Meiler, J. Bush, W. S. Capra, J. A. 2019-05-17 doi:10.1101/637744 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Kaposi sarcoma-associated herpesvirus infection in HIV patients: potential role of HIV-associated extracellular vesicles ]]> https://biorxiv.org/content/10.1101/640532v1?rss=1 Jin, G. Chen, L. Feng, Z. Yuan, G. Reinthal, B. Ye, F. 2019-05-16 doi:10.1101/640532 Cold Spring Harbor Laboratory Press 2019-05-16 <![CDATA[ The calcium channel subunit α2δ-3 organizes synapses via a novel activity-dependent, autocrine BMP signaling pathway ]]> https://biorxiv.org/content/10.1101/640664v1?rss=1 Hoover, K. M. Gratz, S. J. Herrmann, K. A. Qi, N. Liu, A. Perry-Richardson, J. J. Vanderzalm, P. J. O'Connor-Giles, K. M. Broihier, H. T. 2019-05-16 doi:10.1101/640664 Cold Spring Harbor Laboratory Press 2019-05-16 <![CDATA[ Whole-Genome Association Analyses of Sleep-disordered Breathing Phenotypes in the NHLBI TOPMed Program ]]> https://biorxiv.org/content/10.1101/652966v1?rss=1 Cade, B. E. Lee, J. Sofer, T. Wang, H. Zhang, M. Chen, H. Gharib, S. A. Gottlieb, D. J. Guo, X. Lane, J. M. Liang, J. Lin, X. Mei, H. Patel, S. R. Purcell, S. M. Saxena, R. Shah, N. A. Evans, D. S. Hanis, C. L. Hillman, D. R. Mukherjee, S. Palmer, L. J. Stone, K. L. Tranah, G. J. NHLBI Trans-Omics for Precision Medicine (TOPMed), Abecasis, G. Boerwinkle, E. Correa, A. Cupples, L. A. Kaplan, R. C. Nickerson, D. A. North, K. E. Psaty, B. M. Rotter, J. I. Rich, S. S. Tracy, R. P. Vasan, R. S. Wilson, J. G. Zhu, X. Redline, S. TOPMed Sleep Working Group, 2019-06-03 doi:10.1101/652966 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ DeepKinZero: Zero-Shot Learning for Predicting Kinase-Phosphosite Associations Involving Understudied Kinases ]]> https://biorxiv.org/content/10.1101/670638v1?rss=1 Deznabi, I. Arabaci, B. Koyuturk, M. Tastan, O. 2019-06-13 doi:10.1101/670638 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Class of antiretroviral drugs and anemia risk in the current treatment era ]]> https://biorxiv.org/content/10.1101/674549v1?rss=1 Harding, B. N. Whitney, B. M. Nance, R. M. Crane, H. M. Burkholder, G. Moore, R. D. Mathews, W. C. Eron, J. J. Hunt, P. W. Volberding, P. Rodriguez, B. Mayer, K. H. Saag, M. S. Kitahata, M. M. Heckbert, S. R. Delaney, J. A. C. 2019-06-21 doi:10.1101/674549 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Drosophila Aop imposes a delay on E(spl)-mediated repression of Ato during R8 specification. ]]> https://biorxiv.org/content/10.1101/678169v1?rss=1 Majot, A. T. Jozwick, L. M. Bishop, C. P. Bidwai, A. P. 2019-06-20 doi:10.1101/678169 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ Nuclear factor I/B increases in prostate cancer to support androgen receptor activation ]]> https://biorxiv.org/content/10.1101/684472v1?rss=1 Nanda, J. S. Awadallah, W. N. Kohrt, S. E. Popovics, P. Cates, J. M. M. Mirosevich, J. Clark, P. E. Giannico, G. A. Grabowska, M. M. 2019-06-27 doi:10.1101/684472 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Deficiency in Bhlhe40 impairs resistance to H. polygyrus bakeri and reveals novel Csf2rb-dependent regulation of anti-helminth immunity ]]> https://biorxiv.org/content/10.1101/687541v1?rss=1 Jarjour, N. N. Bradstreet, T. R. Schwarzkopf, E. A. Cook, M. E. Lai, C.-W. Huang, S. C.-C. Taneja, R. Stappenbeck, T. S. Van Dyken, S. J. Urban, J. F. Edelson, B. T. 2019-07-02 doi:10.1101/687541 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Causal associations between potentially modifiable risk factors and the Alzheimer’s phenome: A Mendelian randomization study ]]> https://biorxiv.org/content/10.1101/689752v1?rss=1 Andrews, S. J. Marcora, E. Goate, A. M. 2019-07-02 doi:10.1101/689752 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Tumor cell phenotype and heterogeneity differences in IDH1 mutant vs wild-type gliomas ]]> https://biorxiv.org/content/10.1101/690297v1?rss=1 Berens, M. Sood, A. Barnholtz-Sloan, J. Graf, J. F. Cho, S. Kim, S. Kiefer, J. Byron, S. A. Halperin, R. F. Nasser, S. Adkins, J. Cuyugan, L. Devine, K. Ostrom, Q. Couce, M. Wolansky, L. McDonough, E. Schyberg, S. Dinn, S. Sloan, A. E. Prados, M. Phillips, J. J. Nelson, S. J. Liang, W. S. Rusu, M. Zavodszky, M. Ginty, F. 2019-07-02 doi:10.1101/690297 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Temporal changes in genetic admixture are linked to heterozygosity and health diagnoses in humans ]]> https://biorxiv.org/content/10.1101/697581v1?rss=1 Mautz, B. S. Hellwege, J. Li, C. Xu, Y. Zhang, S. Denny, J. C. Roden, D. McGregor, T. L. Velez Edwards, D. R. Edwards, T. L. 2019-07-11 doi:10.1101/697581 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Oral tenofovir disoproxil fumarate/emtricitabine for HIV pre-exposure prophylaxis increases expression of type I/III interferon-stimulated factors in the gastrointestinal tract but not in the blood ]]> https://biorxiv.org/content/10.1101/701961v1?rss=1 Hughes, S. M. Levy, C. N. Calienes, F. Stekler, J. D. Pandey, U. Vojtech, L. Berard, A. R. Birse, K. Noel-Romas, L. Richardson, B. Golden, J. Cartwright, M. Collier, A. C. Stevens, C. E. Curlin, M. E. Holtz, T. H. Mugo, N. Irungu, E. Katabira, E. Muwonge, T. Lama, J. R. Baeten, J. M. Burgener, A. Lingappa, J. R. McElrath, M. J. Mackelprang, R. McGowan, I. Cranston, R. D. Cameron, M. J. Hladik, F. 2019-07-13 doi:10.1101/701961 Cold Spring Harbor Laboratory Press 2019-07-13 <![CDATA[ TWO-SIGMA: a novel TWO-component SInGle cell Model-based Association method for single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/709238v1?rss=1 Van Buren, E. Hu, M. Weng, C. Jin, F. Li, Y. Wu, D. Li, Y. 2019-07-22 doi:10.1101/709238 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Vaccine-induced ICOS+CD38+ cTfh are sensitive biosensors of age-related changes in inflammatory pathways ]]> https://biorxiv.org/content/10.1101/711911v1?rss=1 Herati, R. S. Silva, L. V. Vella, L. A. Muselman, A. Alanio, C. Bengsch, B. Kurupati, R. Kannan, S. Manne, S. Kossenkov, A. Canaday, D. Doyle, S. Ertl, H. Schmader, K. Wherry, E. J. 2019-07-24 doi:10.1101/711911 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Genomic Influences on Self-Reported Childhood Maltreatment ]]> https://biorxiv.org/content/10.1101/717314v1?rss=1 Dalvie, S. Maihofer, A. X. Coleman, J. R. Bradley, B. Breen, G. Brick, L. A. Chen, C.-Y. Choi, K. W. Duncan, L. E. Guffanti, G. Haas, M. Harnal, S. Liberzon, I. Nugent, N. R. Provost, A. C. Ressler, K. J. Torres, K. Amstadter, A. B. Austin, S. B. Baker, D. G. Bolger, E. A. Bryant, R. A. Calabrese, J. R. Delahanty, D. L. Farrer, L. A. Feeny, N. C. Flory, J. D. Forbes, D. Galea, S. Gautam, A. Gelernter, J. Hammamieh, R. Jett, M. Junglen, A. G. Kaufman, M. L. Kessler, R. C. Khan, A. Kranzler, H. R. Lebois, L. A. Marmar, C. Mavissakalian, M. R. McFarlane, A 2019-07-28 doi:10.1101/717314 Cold Spring Harbor Laboratory Press 2019-07-28 <![CDATA[ Assessment of Polygenic Architecture and Risk Prediction based on Common Variants Across Fourteen Cancers ]]> https://biorxiv.org/content/10.1101/723825v1?rss=1 Zhang, Y. Wilcox, A. N. Zhang, H. Choudhury, P. P. Easton, D. F. Milne, R. L. Simard, J. Hall, P. Michailidou, K. Dennis, J. Schmidt, M. K. Chang-Claude, J. Gharahkhani, P. Whiteman, D. Campbell, P. T. Hoffmeister, M. Jenkins, M. Peters, U. Hsu, L. Gruber, S. B. Casey, G. Schmit, S. L. O'Mara, T. A. Spurdle, A. B. Thompson, D. J. Tomlinson, I. Vivo, I. D. Landi, M. T. Law, M. H. Iles, M. M. Demenais, F. Kumar, R. MacGregor, S. Bishop, D. T. Ward, S. V. Bondy, M. L. Houlston, R. Wiencke, J. K. Melin, B. Barnholtz-Sloan, J. Kinnersley, B. Wrensch, M. R. 2019-08-09 doi:10.1101/723825 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ Using QSAR for predictions in drug delivery ]]> https://biorxiv.org/content/10.1101/727172v1?rss=1 Rivera-Delgado, E. Xin, A. von Recum, H. 2019-08-06 doi:10.1101/727172 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ A low-cost, open source, self-contained bacterial EVolutionary biorEactor (EVE) ]]> https://biorxiv.org/content/10.1101/729434v1?rss=1 Gopalakrishnan, V. Krishnan, N. P. McClure, E. Pelesko, J. Guo, D. Williamson, D. F. K. Webster, N. Ecker, D. Nichol, D. Scott, J. G. 2019-08-09 doi:10.1101/729434 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ Haplotype genetic score analysis in 10,734 mother/infant pairs reveals complex maternal and fetal genetic effects underlying the associations between maternal phenotypes, birth outcomes and adult phenotypes ]]> https://biorxiv.org/content/10.1101/737106v1?rss=1 Chen, J. Bacelis, J. Navais, P. S. Srivastava, A. Juodakis, J. Rouse, A. Hallman, M. Teramo, K. Melbye, M. Feenstra, B. Freathy, R. M. Davey-Smith, G. Lawlor, D. A. Murray, J. C. Williams, S. M. Jacobsson, B. Muglia, L. J. Zhang, G. 2019-08-15 doi:10.1101/737106 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Extradomain-B Fibronectin is a molecular marker of invasive breast cancer cells ]]> https://biorxiv.org/content/10.1101/743500v1?rss=1 Lu, Z.-R. Vaidya, A. Wang, H. Qian, V. 2019-08-22 doi:10.1101/743500 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Robust Hi-C chromatin loop maps in human neurogenesis and brain tissues at high-resolution ]]> https://biorxiv.org/content/10.1101/744540v1?rss=1 LU, L. Liu, X. Huang, W.-K. Giusti-Rodriguez, P. Cui, J. Zhang, S. Xu, W. Wen, Z. Ma, S. Rosen, J. D. Xu, Z. Bartels, C. Riki Kawaguchi, R. Hu, M. Scacheri, P. Rong, Z. Li, Y. Sullivan, P. F. Song, H. Ming, G.-l. Li, Y. Jin, F. 2019-08-22 doi:10.1101/744540 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ JAM-A functions as a female microglial tumor suppressor in glioblastoma ]]> https://biorxiv.org/content/10.1101/761445v1?rss=1 Turaga, S. M. Silver, D. J. Bayik, D. Paouri, E. Borjini, N. Peng, S. Naik, U. Keri, R. A. Connor, J. R. Barnholtz-Sloan, J. Rubin, J. B. Berens, M. Davalos, D. Lathia, J. 2019-09-08 doi:10.1101/761445 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ Physical activity and risks of breast and colorectal cancer: A Mendelian randomization analysis ]]> https://biorxiv.org/content/10.1101/762484v1?rss=1 Papadimitriou, N. Dimou, N. Tsilidis, K. K. Banbury, B. Martin, R. Lewis, S. Kazmi, N. Robinson, T. M. Albanes, D. Aleksandrova, K. Berndt, S. I. Bishop, D. T. Brenner, H. Buchanan, D. D. Bueno-de-Mesquita, B. Campbell, P. T. Castellvi-Bel, S. Chan, A. T. Chang-Claude, J. Ellingjord-Dale, M. Figueiredo, J. C. Gallinger, S. J. Giles, G. G. Giovannucci, E. Gruber, S. B. Gsur, A. Hampe, J. Hampel, H. Harlid, S. Harrison, T. A. Hoffmeister, M. Hopper, J. L. Hsu, L. Huerta, J. M. Huyghe, J. R. Jenkins, M. A. Keku, T. O. Kuhn, T. La Vecchia, C. Le Marchand, L. 2019-09-09 doi:10.1101/762484 Cold Spring Harbor Laboratory Press 2019-09-09 <![CDATA[ Interaction between host genes and M. tuberculosis lineage can affect tuberculosis severity: evidence for co-evolution ]]> https://biorxiv.org/content/10.1101/769448v1?rss=1 McHenry, M. L. Bartlett, J. Igo, R. P. Wampande, E. Bencheck, P. Mayanja-Kizza, H. Fluegge, K. Hall, N. B. Gagneux, S. Tishkoff, S. Wejse, C. Sirugo, G. Boom, W. H. Joloba, M. Williams, S. M. Stein, C. 2019-09-14 doi:10.1101/769448 Cold Spring Harbor Laboratory Press 2019-09-14 <![CDATA[ Deep Mutational Scan of a cardiac sodium channel voltage sensor ]]> https://biorxiv.org/content/10.1101/773887v1?rss=1 Glazer, A. M. Kroncke, B. M. Matreyek, K. A. Yang, T. Wada, Y. Shields, T. Salem, J.-E. Fowler, D. M. Roden, D. 2019-09-18 doi:10.1101/773887 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Understanding artificial mouse-microbiome heterogeneity and six actionable themes to increase study power ]]> https://biorxiv.org/content/10.1101/778043v1?rss=1 Basson, A. R. LaSalla, A. Lam, G. Kulpins, D. Moen, E. L. Sundrud, M. Miyoshi, J. Ilic, S. Theriault, B. R. Cominelli, F. Rodriguez-Palacios, A. 2019-09-25 doi:10.1101/778043 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Scaffold-free human mesenchymal stem cell construct geometry regulates long bone regeneration ]]> https://biorxiv.org/content/10.1101/785386v1?rss=1 Herberg, S. Varghai, D. Alt, D. S. Dang, P. N. Park, H. Cheng, Y. Shin, J.-Y. Dikina, A. D. Boerckel, J. D. Rolle, M. W. Alsberg, E. 2019-09-30 doi:10.1101/785386 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ Role of Proinsulin Self-Association in Mutant INS gene-induced Diabetes of Youth ]]> https://biorxiv.org/content/10.1101/786970v1?rss=1 Liu, M. Arvan, P. Sun, J. Xiong, Y. Li, X. Haataja, L. Chen, W. Mir, S. A. Madley, R. Larkin, D. Anjum, A. Dhayalan, B. Rege, N. K. Wickramasinghe, N. D. Weiss, M. A. Itkin-Ansari, P. Kaufman, R. J. Ostrov, D. A. 2019-10-01 doi:10.1101/786970 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Mechanisms of activation and desensitization of full-length glycine receptor in membranes ]]> https://biorxiv.org/content/10.1101/788695v1?rss=1 kumar, A. Basak, S. Rao, S. Gicheru, Y. Mayer, M. L. Sansom, M. Chakrapani, S. 2019-09-30 doi:10.1101/788695 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ Bioinformatic analysis of brain-specific miRNAs for identification of candidate traumatic brain injury blood biomarkers. ]]> https://biorxiv.org/content/10.1101/794321v1?rss=1 Smothers, C. G. Winkelman, C. O'Connell, G. C. 2019-10-07 doi:10.1101/794321 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Clonal interference patterns shift during range expansion ]]> https://biorxiv.org/content/10.1101/794867v1?rss=1 Scott, J. G. Krishnan, N. 2019-10-06 doi:10.1101/794867 Cold Spring Harbor Laboratory Press 2019-10-06 <![CDATA[ Plexin-Bs enhance their GAP activity with a novel activation switchloop ]]> https://biorxiv.org/content/10.1101/796748v1?rss=1 LI, Z. Greven, J. M. Kim, S. Tamagnone, L. Buck, M. 2019-10-08 doi:10.1101/796748 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Affinity-based polymers provide long-term immunotherapeutic drug delivery across particle size ranges optimal for macrophage targeting ]]> https://biorxiv.org/content/10.1101/802801v1?rss=1 Rohner, N. A. Purdue, L. von Recum, H. A. 2019-10-13 doi:10.1101/802801 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ Expression and purification of Protease Activated Receptor 4 (PAR4) and analysis with histidine hydrogen deuterium exchange. ]]> https://biorxiv.org/content/10.1101/804427v1?rss=1 0.01) in t1/2 values observed for four histidine residues (His180, His229, His240, and His380) demonstrating that these regions have decreased solvent accessibility upon thrombin treatment. In agreement, thrombin cleaved PAR4 also was resistant to thermolysin digestion. In contrast, activation with the PAR4 agonist peptide was digested at the same rate as apo PAR4. Further analysis showed the C-terminus is protected in thrombin activated PAR4 compared to uncleaved or agonist peptide treated PAR4. The studies described here are the first to examine the tethered ligand activation mechanism for a PAR family member using biophysically and shed light on the overall conformational changes that follow activation of PARs by a protease. ]]> de le Fuente, M. Han, X. Miyagi, M. Nieman, M. T. 2019-10-16 doi:10.1101/804427 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Dillenia indica fruit extract has Glucose and Cholesterol Lowering effects ]]> https://biorxiv.org/content/10.1101/804815v1?rss=1 KHAN, S. Bhowmik, A. Rhaman, S. B. Gan, S. H. Rokeya, B. 2019-10-14 doi:10.1101/804815 Cold Spring Harbor Laboratory Press 2019-10-14 <![CDATA[ Monitoring Plasmodium falciparum and Plasmodium vivax using microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea ]]> https://biorxiv.org/content/10.1101/817320v1?rss=1 Kattenberg, J. H. Razook, Z. Keo, R. Jennison, C. Lautu, D. Fola, A. A. Ome-Kaius, M. Barnadas, C. Siba, P. M. Felger, I. Kazura, J. Mueller, I. Robinson, L. J. Barry, A. E. 2019-10-24 doi:10.1101/817320 Cold Spring Harbor Laboratory Press 2019-10-24 <![CDATA[ Genomic and functional gene studies suggest a key role of beta-carotene oxygenase 1 like (bco1l) gene in salmon flesh color. ]]> https://biorxiv.org/content/10.1101/821652v1?rss=1 Helgeland, H. Sodeland, M. Zoric, N. Torgersen, J. S. Grammes, F. von Lintig, J. Moen, T. Kjoglum, S. Lien, S. Vage, D. I. 2019-10-29 doi:10.1101/821652 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ Combination antibiotic delivery in PMMA provides sustained broad-spectrum antimicrobial activity and allows for post-implantation refilling ]]> https://biorxiv.org/content/10.1101/832402v1?rss=1 Cyphert, E. L. Lu, C.-y. Marques, D. W. Learn, G. D. von Recum, H. A. 2019-11-06 doi:10.1101/832402 Cold Spring Harbor Laboratory Press 2019-11-06 <![CDATA[ Nonthermal plasma treatment of polymers modulates biological fouling but can cause material embrittlement ]]> https://biorxiv.org/content/10.1101/842260v1?rss=1 Learn, G. D. Lai, E. J. Wilson, E. J. von Recum, H. A. 2019-11-15 doi:10.1101/842260 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ STRESS-INDUCED GENETIC CHANGE IN FLAX REVEALS GENOME VARIATION MECHANISM ]]> https://biorxiv.org/content/10.1101/843763v1?rss=1 Li, X. 2019-11-15 doi:10.1101/843763 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ FtsW exhibits distinct processive movements driven by either septal cell wall synthesis or FtsZ treadmilling in E. coli ]]> https://biorxiv.org/content/10.1101/850073v1?rss=1 Yang, X. McQuillen, R. Lyv, Z. Phillips-Mason, P. De La Cruz, A. McCausland, J. W. Liang, H. DeMeester, K. E. Grimes, C. L. de Boer, P. Xiao, J. 2019-11-21 doi:10.1101/850073 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Network potential identifies therapeutic miRNA cocktails in Ewings Sarcoma ]]> https://biorxiv.org/content/10.1101/854695v1?rss=1 Weaver, D. T. Pishas, K. I. Williamson, D. Scarborough, J. Lessnick, S. L. Dhawan, A. Scott, J. G. 2019-11-27 doi:10.1101/854695 Cold Spring Harbor Laboratory Press 2019-11-27 <![CDATA[ The Ccr4-Not complex monitors the translating ribosome for codon optimality ]]> https://biorxiv.org/content/10.1101/854810v1?rss=1 Buschauer, R. Matsuo, Y. Chen, Y.-H. Alhusaini, N. Sweet, T. Sugiyama, T. Ikeuchi, K. Cheng, J. Matsuki, Y. Gilmozzi, A. Berninghausen, O. Becker, T. Coller, J. Inada, T. Beckmann, R. 2019-11-25 doi:10.1101/854810 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Functional Vagotopy in the Cervical Vagus Nerve of the Domestic Pig: Implications for Vagus Nerve Stimulation ]]> https://biorxiv.org/content/10.1101/856989v1?rss=1 Settell, M. L. Knudsen, B. E. Dingle, A. M. McConico, A. L. Nicolai, E. N. Trevathan, J. K. Ross, E. K. Pelot, N. A. Grill, W. M. Gustafson, K. J. Shoffstall, A. J. Williams, J. C. Zeng, W. Poore, S. O. Populin, L. C. Suminski, A. J. Ludwig, K. A. 2019-11-27 doi:10.1101/856989 Cold Spring Harbor Laboratory Press 2019-11-27 <![CDATA[ Predicting cancer origins with a DNA methylation-based deep neural network model ]]> https://biorxiv.org/content/10.1101/860171v1?rss=1 Zheng, C. Xu, R. 2019-11-29 doi:10.1101/860171 Cold Spring Harbor Laboratory Press 2019-11-29 <![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[ Using nonthermal plasma treatment to improve quality and durability of hydrophilic coatings on hydrophobic polymer surfaces ]]> https://biorxiv.org/content/10.1101/868885v1?rss=1 Learn, G. D. Lai, E. J. von Recum, H. A. 2019-12-08 doi:10.1101/868885 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ SQANTI: extensive characterization of long read transcript sequences for quality control in full-length transcriptome identification and quantification ]]> https://biorxiv.org/content/10.1101/118083v1?rss=1 Tardaguila, M. de la Fuente, L. Marti, C. Pereira, C. del Risco, H. Ferrell, M. Mellado, M. Macchietto, M. Verheggen, K. Edelmann, M. Ezkurdia, I. Vazquez, J. Tress, M. Mortazavi, A. Martens, L. Rodriguez-Navarro, S. Moreno, V. Conesa, A. 2017-03-18 doi:10.1101/118083 Cold Spring Harbor Laboratory Press 2017-03-18 <![CDATA[ Molecular Dynamics Simulations Of Membrane Deformation Induced By The Amphiphilic Helices Of Epsin, Sar1p And Arf1 ]]> https://biorxiv.org/content/10.1101/140970v1?rss=1 Li, Z.-L. Ding, H.-M. 2017-05-23 doi:10.1101/140970 Cold Spring Harbor Laboratory Press 2017-05-23 <![CDATA[ Glioblastoma myeloid-derived suppressor cell subsets express differential macrophage migration inhibitory factor receptor profiles that can be targeted to reduce immune suppression ]]> https://biorxiv.org/content/10.1101/2019.12.19.882555v1?rss=1 Alban, T. Bayik, D. Otvos, B. Rabljenovic, A. Leng, L. Jia-shiun, L. Roversi, G. Lauko, A. Momin, A. Mohammadi, A. M. Peereboom, D. M. Ahluwalia, M. S. Matsuda, K. Yun, K. Bucala, R. Vogelbaum, M. A. Lathia, J. 2019-12-20 doi:10.1101/2019.12.19.882555 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Melanopsin Carboxy-terminus Phosphorylation Plasticity and Bulk Negative Charge, not Strict Site Specificity, Achieves Phototransduction Deactivation ]]> https://biorxiv.org/content/10.1101/2020.01.09.900050v1?rss=1 Valdez-Lobez, J. C. Gulati, S. Ortiz, E. A. Palczewski, K. Robinson, P. 2020-01-11 doi:10.1101/2020.01.09.900050 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Compartmentalization of enhanced biomolecular interactions for high-throughput drug screening in test tubes ]]> https://biorxiv.org/content/10.1101/2020.01.19.911149v1?rss=1 Zhou, M. Li, W. Li, J. Xie, L. Wu, R. Wang, L. Fu, S. Su, W. Hu, J. Wang, J. Li, P. 2020-01-20 doi:10.1101/2020.01.19.911149 Cold Spring Harbor Laboratory Press 2020-01-20 <![CDATA[ Membrane-Bound O-Acyltransferase 7 (MBOAT7) is a Key Regulator of Glycolysis in Clear Cell Renal Carcinoma. ]]> https://biorxiv.org/content/10.1101/2020.02.10.942458v1?rss=1 Neumann, C. K. A. Massey, W. Orabi, D. Zhang, R. Silver, D. J. Lathia, J. D. Brown, J. M. 2020-02-11 doi:10.1101/2020.02.10.942458 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ Learning to Control the Brain through Adaptive Closed-Loop Patterned Stimulation ]]> https://biorxiv.org/content/10.1101/2020.03.14.992198v1?rss=1 Tafazoli, S. MacDowell, C. J. Che, Z. Letai, K. C. Steinhardt, C. Buschman, T. J. 2020-03-16 doi:10.1101/2020.03.14.992198 Cold Spring Harbor Laboratory Press 2020-03-16 <![CDATA[ Motor neurons involved in fine motor control are labeled by tracing Atoh1-lineage neurons in the spinal cord ]]> https://biorxiv.org/content/10.1101/2020.03.20.000588v1?rss=1 Ogujiofor, O. W. Pop, I. V. Espinosa, F. Durodoye, R. O. Viacheslavov, M. L. Jarvis, R. Landy, M. A. Fishell, G. Machold, R. P. Lai, H. C. 2020-03-20 doi:10.1101/2020.03.20.000588 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Amantadine disrupts lysosomal gene expression; potential therapy for COVID19 ]]> https://biorxiv.org/content/10.1101/2020.04.05.026187v1?rss=1 Smieszek, S. Przychodzen, B. Polymeropoulos, M. H. 2020-04-05 doi:10.1101/2020.04.05.026187 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact ]]> https://biorxiv.org/content/10.1101/2020.05.10.087312v1?rss=1 Chiasson, M. A. Rollins, N. J. Stephany, J. J. Sitko, K. A. Matreyek, K. A. Verby, M. Sun, S. Roth, F. DeSloover, D. Marks, D. S. Rettie, A. E. Fowler, D. M. 2020-05-10 doi:10.1101/2020.05.10.087312 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Molecular Basis of Far-red Sensing in Cyanobacteriochrome ]]> https://biorxiv.org/content/10.1101/2020.06.02.130930v1?rss=1 Bandara, S. Rockwell, N. C. Zeng, X. Ren, Z. Wang, C. Shin, H. Martin, S. Moreno, M. Lagarias, J. C. Yang, X. 2020-06-03 doi:10.1101/2020.06.02.130930 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Title: Acetylcholine regulates pulmonary inflammation and facilitates the transition from active immunity to tissue repair during respiratory viral infection ]]> https://biorxiv.org/content/10.1101/2020.07.02.184226v1?rss=1 Horkowitz, A. P. Schwartz, A. V. Alvarez, C. A. Herrera, E. B. Thoman, M. L. Chatfield, D. A. Osborn, K. G. Feuer, R. George, U. Z. Phillips, J. A. 2020-07-02 doi:10.1101/2020.07.02.184226 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Clinical characteristics and primary management of patients diagnosed with prostate cancer between 2015 and 2019 at the Uganda Cancer Institute ]]> https://biorxiv.org/content/10.1101/2020.07.09.194936v1?rss=1 Paul Katongole Obondo J. Sande Mulumba Yusuf Moses Joloba Steven J Reynolds Nixon Niyonzima 2020-07-09 doi:10.1101/2020.07.09.194936 Cold Spring Harbor Laboratory Press 2020-07-09 <![CDATA[ The PopN gate-keeper complex acts on the ATPase PscN to regulate the T3SS secretion switch from early to middle substrates in Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2020.07.28.224923v1?rss=1 View larger version (15K): org.highwire.dtl.DTLVardef@1e6803corg.highwire.dtl.DTLVardef@1ed155aorg.highwire.dtl.DTLVardef@14faf6org.highwire.dtl.DTLVardef@1685ec8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ngo, T. D. Perdu, C. Jneid, B. Ragno, M. Novion Ducassou, J. Kraut, A. Coute, Y. Stopford, C. Attree, I. Rietsch, A. Faudry, E. 2020-07-29 doi:10.1101/2020.07.28.224923 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Preclinical modeling of surgery and steroid therapy for glioblastoma reveals changes in immunophenotype that are associated with tumor growth and outcome ]]> https://biorxiv.org/content/10.1101/2020.08.12.248443v1?rss=1 Otvos, B. Alban, T. J. Grabowski, M. M. Bayik, D. Mulkearns-Hubert, E. E. Radivoyevitch, T. Rabljenovic, a. Johnson, S. Androjna, C. Mohammadi, A. M. Barnett, G. Ahluwalia, M. S. Vogelbaum, M. A. Fecci, P. E. Lathia, J. D. 2020-08-12 doi:10.1101/2020.08.12.248443 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Supraphysiological testosterone induces ferroptosis and activates NF-kappaB mediated immune pathways in prostate cancer through nucleophagy ]]> https://biorxiv.org/content/10.1101/2020.09.10.286252v1?rss=1 Mendonca, J. Kumar, R. Owoyemi, O. Boyapati, K. Thomas, N. Kanacharoen, S. Coffey, M. Topiwala, D. Gomes, C. Ozbek, B. Jones, T. Rosen, M. Dong, L. Wiens, S. Brennen, W. N. Isaacs, J. De Marzo, A. M. Markowski, M. Antonarakis, E. S. Qian, D. Pienta, K. Pardoll, D. Carducci, M. Denmeade, S. Kachhap, S. 2020-09-10 doi:10.1101/2020.09.10.286252 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Dose dependent evolutionary game dynamics modulate competitive release in cancer therapy ]]> https://biorxiv.org/content/10.1101/2020.09.18.303966v1?rss=1 Farrokhian, N. Maltas, J. Ellsworth, P. Durmaz, A. Dinh, M. Hitomi, M. Kaznatcheev, A. Marusyk, A. Scott, J. G. 2020-09-20 doi:10.1101/2020.09.18.303966 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ A selectable, plasmid-based system to generate CRISPR/Cas9 gene edited and knock-in mosquito cell lines ]]> https://biorxiv.org/content/10.1101/2020.10.09.333641v1?rss=1 Rozen-Gagnon, K. Yi, S. Jacobson, E. Novack, S. Rice, C. M. 2020-10-10 doi:10.1101/2020.10.09.333641 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ TMEM41B is a pan-flavivirus host factor ]]> https://biorxiv.org/content/10.1101/2020.10.09.334128v1?rss=1 Hoffmann, H.- H. Schneider, W. M. Rozen-Gagnon, K. Miles, L. A. Schuster, F. Razooky, B. Jacobson, E. Wu, X. Yi, S. Rudin, C. M. MacDonald, M. R. McMullan, L. K. Poirier, J. T. Rice, C. M. 2020-10-10 doi:10.1101/2020.10.09.334128 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ Adaptive translational pausing is a hallmark of the cellular response to severe environmental stress ]]> https://biorxiv.org/content/10.1101/2020.10.10.334375v1?rss=1 Jobava, R. Mao, Y. Guan, B.-J. Krokowski, D. Shu, E. Chukwurah, E. Wu, J. Gao, Z. Zagore, L. L. Merrick, W. C. Zhang, Y. Qi, X. Jankowsky, E. Topisirovic, I. Licatalosi, D. D. Qian, S.-B. Hatzoglou, M. 2020-10-10 doi:10.1101/2020.10.10.334375 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ Diverse Changes in Microglia Morphology and Axonal Pathology Over One Year after Mild Traumatic Brain Injury in Pigs ]]> https://biorxiv.org/content/10.1101/2020.10.16.343103v1?rss=1 Grovola, M. R. Paleologos, N. Brown, D. P. Tran, N. Wofford, K. Harris, J. Browne, K. Wolf, J. Cullen, D. K. Duda, J. E. 2020-10-17 doi:10.1101/2020.10.16.343103 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ A Novel Surgical Method for Continuous Intra-Portal Infusion of Gut Microbial Metabolites in Mice ]]> https://biorxiv.org/content/10.1101/2020.10.29.360628v1?rss=1 Orabi, D. Osborn, L. J. Fung, K. Aucejo, F. Choucair, I. DeLucia, B. Wang, Z. Claesen, J. Brown, J. M. 2020-10-29 doi:10.1101/2020.10.29.360628 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ A Fast Lysine Cross-linker DOPA Enables Mass Spectrometry Analyses of Protein Unfolding and Weak Protein-protein Interactions ]]> https://biorxiv.org/content/10.1101/2020.11.05.369280v1?rss=1 Wang, J.-H. Tang, Y.-L. Jain, R. Xiao, F. Gong, Z. Zhou, Y. Tan, D. Li, Q. Dong, X. Liu, S.-Q. Tang, C. Huang, N. Ye, K. Dong, M.-Q. Lei, X. 2020-11-05 doi:10.1101/2020.11.05.369280 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Augmenting Flexibility: Mutual Inhibition Between Inhibitory Neurons Expands Functional Diversity ]]> https://biorxiv.org/content/10.1101/2020.11.08.371179v1?rss=1 Liu, B. White, A. J. Lo, C.-C. 2020-11-09 doi:10.1101/2020.11.08.371179 Cold Spring Harbor Laboratory Press 2020-11-09 <![CDATA[ The Nuclear Pore Complex consists of two independent scaffolds ]]> https://biorxiv.org/content/10.1101/2020.11.13.381947v1?rss=1 Regmi, S. G. Lee, H. Kaufhold, R. Fichtman, B. Chen, S. Aksenova, V. Turcotte, E. Harel, A. Arnaoutov, A. Dasso, M. 2020-11-14 doi:10.1101/2020.11.13.381947 Cold Spring Harbor Laboratory Press 2020-11-14 <![CDATA[ Gut Microbe-Targeted Choline Trimethylamine Lyase Inhibition Improves Obesity Via Rewiring of Host Circadian Rhythms ]]> https://biorxiv.org/content/10.1101/2020.12.04.411546v1?rss=1 Schugar, R. C. Gliniak, C. M. Helsley, R. N. Brown, A. L. Burrows, A. Finney, C. Fung, K. K. Allen, F. M. Ferguson, D. Gromovsky, A. D. Neumann, C. McMillan, A. Buffa, J. A. Anderson, J. T. Mehrabian, M. Goudarzi, M. Willard, B. Mak, T. D. Armstrong, A. R. Swanson, G. Keshavarzian, A. Garcia-Garcia, J. C. Wang, Z. Lusis, A. J. Hazen, S. L. Brown, J. M. 2020-12-06 doi:10.1101/2020.12.04.411546 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Putative Pseudolysogeny-Dependent Phage Gene Implicated in the Superinfection Resistance of Cutibacterium acnes ]]> https://biorxiv.org/content/10.1101/2020.12.15.422974v1?rss=1 Wottrich, S. Mendonca, S. Safarpour, C. Nguyen, C. Marinelli, L. J. Modlin, R. L. Moberg Parker, J. 2020-12-16 doi:10.1101/2020.12.15.422974 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ Male sex and age biases viral burden, viral shedding, and type 1 and 2 interferon responses during SARS-CoV-2 infection in ferrets ]]> https://biorxiv.org/content/10.1101/2021.01.12.426381v1?rss=1 Francis, M. Richardson, B. McNeil, M. Rioux, M. Foley, M. Ge, A. Pechous, R. Kindrachuk, J. Cameron, C. Richardson, C. Lew, J. Cameron, M. Gerdts, V. Falzarano, D. Kelvin, A. A. A. 2021-01-12 doi:10.1101/2021.01.12.426381 Cold Spring Harbor Laboratory Press 2021-01-12 <![CDATA[ Targeting primary and metastatic uveal melanoma with a G protein inhibitor ]]> https://biorxiv.org/content/10.1101/2021.01.16.426957v1?rss=1 Onken, M. D. Makepeace, C. M. Kaltenbronn, K. M. Choi, J. Hernandez-Aya, L. Weilbaecher, K. N. Piggott, K. D. Rao, P. K. Yuede, C. M. Dixon, A. J. Osei-Owusu, P. Cooper, J. A. Blumer, K. J. 2021-01-17 doi:10.1101/2021.01.16.426957 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Microenvironment Impacts the Molecular Architecture and Interactivity of Resident Cells in Marmoset Brain ]]> https://biorxiv.org/content/10.1101/2021.01.25.426385v1?rss=1 5 times more WM volume and complexity than mouse, identifies novel WM-glia subtypes and their contributions to different neurological disorders. A companion Callithrix jacchus Primate Cell Atlas (CjPCA) is available through an online portal https://cjpca.ninds.nih.gov to facilitate data exploration. ]]> Lin, J.-P. Kelly, H. M. Song, Y. Kawaguchi, R. Geschwind, D. Jacobson, S. Reich, D. S. 2021-01-27 doi:10.1101/2021.01.25.426385 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ L-WNK1 is required for BK channel activation in intercalated cells ]]> https://biorxiv.org/content/10.1101/2021.01.26.428162v1?rss=1 Ray, E. C. Carrisoza, R. Al-Bataineh, M. Marciszyn, A. L. Nkashama, L. Chen, J. C. Winfrey, A. Flores, D. Wu, P. Wang, W. C. wang, c.-l. Subramanya, A. R. Kleyman, T. R. Satlin, L. M. 2021-01-27 doi:10.1101/2021.01.26.428162 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Development of spike receptor-binding domain nanoparticle as a vaccine candidate against SARS-CoV-2 infection in ferrets ]]> https://biorxiv.org/content/10.1101/2021.01.28.428743v1?rss=1 Kim, Y.-I. Kim, D. Yu, K.-M. Seo, H. D. Lee, S.-A. Casel, M. A. B. Jang, S.-G. Kim, S. Jung, W. Lai, C.-J. Choi, Y. K. Jung, J. U. 2021-01-29 doi:10.1101/2021.01.28.428743 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ Molecular basis for Ras suppressor-1 recruitment to focal adhesions and stabilization of consensus adhesome complex ]]> https://biorxiv.org/content/10.1101/2021.02.19.432017v1?rss=1 Fukuda, K. Lu, F. Qin, J. 2021-02-19 doi:10.1101/2021.02.19.432017 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Kidney-Specific WNK1 Amplifies NCC Responsiveness to Potassium Imbalance ]]> https://biorxiv.org/content/10.1101/2021.03.12.435046v1?rss=1 Boyd-Shiwarski, C. R. Beacham, R. T. Griffiths, S. E. Shiwarski, D. J. Knoell, S. A. Nkashama, L. J. Querry, K. E. Marciszyn, A. L. Huang, C.-L. Stocker, S. D. Subramanya, A. R. 2021-03-12 doi:10.1101/2021.03.12.435046 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Osteoblast-Specific Wnt Secretion is Required for Skeletal Homeostasis and Loading-Induced Bone Formation in Adult Mice ]]> https://biorxiv.org/content/10.1101/2021.03.30.437737v1?rss=1 Lawson, L. Y. Brodt, M. D. Migotsky, N. Chermside-Scabbo, C. Palaniappan, R. Silva, M. J. 2021-03-30 doi:10.1101/2021.03.30.437737 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ Distortion Discovery: A Framework to Model, Spot and Explain Tumor Heterogeneity and Mitigate its Negative Impact on Cancer Risk Assessment ]]> https://biorxiv.org/content/10.1101/2021.04.28.441787v1?rss=1 Elmansy, D. F. 2021-04-29 doi:10.1101/2021.04.28.441787 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Scalable Clustering with Supervised Linkage Methods ]]> https://biorxiv.org/content/10.1101/2021.08.01.454697v1?rss=1 Anibal, J. Day, A. Bahadiroglu, E. O'Neill, L. Phan, L. Peltekian, A. Erez, A. Kaplan, M. Altan-Bonnet, G. Mehta, P. 2021-08-02 doi:10.1101/2021.08.01.454697 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ Engineering site-selective incorporation of fluorine into natural product analogs ]]> https://biorxiv.org/content/10.1101/2021.08.09.455754v1?rss=1 Sirirungruang, S. Ad, O. Privalsky, T. M. Ramesh, S. Sax, J. L. Dong, H. Baidoo, E. E. Amer, B. Khosla, C. Chang, M. C. 2021-08-10 doi:10.1101/2021.08.09.455754 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Repair of Noise-Induced Damage to Stereocilia F-actin Cores is Facilitated by XIRP2 ]]> https://biorxiv.org/content/10.1101/2021.08.10.455815v1?rss=1 Wagner, E. L. Im, J.-S. Nakahata, M. I. Imbery, T. E. Li, S. Chen, D. B. Noy, Y. Archer, D. W. Xu, W. Hashisaki, G. T. Avraham, K. B. Shin, J.-B. 2021-08-10 doi:10.1101/2021.08.10.455815 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Intercellular crosstalk regulating ARRB2/RARRES1 is involved in transition from fibrosis to cancer ]]> https://biorxiv.org/content/10.1101/2021.09.08.458161v1?rss=1 Schierwagen, R. Dietrich, P. Heinzen, J. Klein, S. Uschner, F. E. Ortiz, C. Tyc, O. Torres, S. Hieber, C. Kraus, N. Premont, R. T. Gruenewald, L. D. Poisson, J. Ratou, P.-E. Kristiansen, G. Gracia-Sancho, J. Poglitsch, M. Ludwig-Portugall, I. Walther, T. Trautwein, C. Abdullah, Z. Muench, C. Welsch, C. Fernandez, M. Zeuzem, S. Moreau, R. Helllerbrand, C. Rombouts, K. Kastenmueller, W. Diehl, A. M. Trebicka, J. 2021-09-08 doi:10.1101/2021.09.08.458161 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ Chicken Auditory Supporting Cells Express Interferon Response Genes during Regeneration towards Nascent Sensory Hair Cells In Vivo ]]> https://biorxiv.org/content/10.1101/2021.09.21.461299v1?rss=1 Janesick, A. S. Scheibinger, M. Benkafadar, N. Kirti, S. Heller, S. 2021-09-24 doi:10.1101/2021.09.21.461299 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Vpr shapes the proviral landscape and polyclonal HIV-1 reactivation patterns in cultured cells ]]> https://biorxiv.org/content/10.1101/2021.10.08.463623v1?rss=1 Atindaana, E. Emery, S. Burnett, C. Pitcher, J. Kidd, J. M. Telesnitsky, A. 2021-10-08 doi:10.1101/2021.10.08.463623 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ Cholesterol and sphingomyelin are critical for Fcγ receptor-mediated phagocytosis of Cryptococcus neoformans by macrophages ]]> https://biorxiv.org/content/10.1101/2021.11.02.466923v1?rss=1 Bryan, A. M. You, J. K. Li, G. Kim, J. Singh, A. Morstein, J. Trauner, D. Pereira de Sa, N. Normile, T. G. Farnoud, A. M. London, E. Del Poeta, M. 2021-11-02 doi:10.1101/2021.11.02.466923 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Loss of Zfp335 triggers cGAS/STING-dependent apoptosis of post-β selection pre-T cells ]]> https://biorxiv.org/content/10.1101/2021.12.03.471158v1?rss=1 Ratiu, J. J. Wang, Q. Mehta, N. Harnois, M. J. DiPalma, D. Wellford, S. Roy, S. Contreras, A. Wiest, D. Zhuang, Y. 2021-12-03 doi:10.1101/2021.12.03.471158 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ SerpinB3 drives cancer stem cell survival in glioblastoma ]]> https://biorxiv.org/content/10.1101/2021.12.21.473663v1?rss=1 Lauko, A. Volovetz, J. Turaga, S. M. Bayik, D. Watson, D. C. Silver, D. J. Mitchell, K. Mulkearns-Hubert, E. Desai, K. Midha, M. Hao, J. McCortney, K. Steffens, A. Naik, U. Ahluwalia, M. S. Bao, S. Horbinski, C. Yu, J. Lathia, J. D. 2021-12-22 doi:10.1101/2021.12.21.473663 Cold Spring Harbor Laboratory Press 2021-12-22 <![CDATA[ VRK1 is a Paralog Synthetic Lethal Target in VRK2-methylated Glioblastoma ]]> https://biorxiv.org/content/10.1101/2021.12.30.474571v1?rss=1 Shields, J. A. Meier, S. R. Bandi, M. Dam Ferdinez, M. Engel, J. L. Mulkearns-Hubert, E. E. Hajdari, N. Mitchell, K. Zhang, W. Zhao, S.-c. Zhang, M. Tjin Tham Sjin, R. Wilker, E. Lathia, J. Andersen, J. Chen, Y. Li, F. Weber, B. Huang, A. Emmanuel, N. 2022-01-01 doi:10.1101/2021.12.30.474571 Cold Spring Harbor Laboratory Press 2022-01-01 <![CDATA[ An in vitro neurogenetics platform for precision disease modeling in the mouse ]]> https://biorxiv.org/content/10.1101/2022.01.21.477242v1?rss=1 CORTES, D. E. ESCUDERO, M. MITRA, A. KORGAN, A. C. EDWARDS, A. O'CONNELL, K. M. S. Reinholdt, L. G. PERA, M. F. 2022-01-21 doi:10.1101/2022.01.21.477242 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ N-phosphonacetyl-L-aspartate enhances type I interferon anti-viral responses through activation of non-canonical NOD2 signaling ]]> https://biorxiv.org/content/10.1101/2022.02.08.479597v1?rss=1 Ponti, A. K. Zangara, M. T. O'Connor, C. Johnson, E. E. McDonald, C. 2022-02-08 doi:10.1101/2022.02.08.479597 Cold Spring Harbor Laboratory Press 2022-02-08 <![CDATA[ CD81 partners with CD44 in promoting exosome biogenesis, tumor cluster formation, and lung metastasis in triple negative breast cancer ]]> https://biorxiv.org/content/10.1101/2022.02.23.481674v1?rss=1 80% of human circulating tumor cells (CTCs) and specifically enriched in clustered CTCs along with CD44 isolated from breast cancer patients. Mimicking the phenotypes of CD44 deficiency, loss of CD81 also inhibits tumor cluster aggregation, tumorigenesis, and lung metastasis of triple negative breast cancer (TNBC), supporting the clinical significance of CD81 in association with patient outcomes. Our study highlights the novel role of CD81 and its partnership with CD44 in cancer exosomes, self-renewal, CTC clustering, and metastasis initiation of TNBC. ]]> Ramos, E. K. Tsai, C.-F. Dashzeveg, N. K. Jia, Y. Cao, Y. Manu, M. Taftaf, R. Hoffmann, A. D. El-Shennawy, L. Gritsenko, M. A. Adorno-Cruz, V. Schuster, E. J. Scholten, D. Patel, D. Liu, X. Patel, P. Wray, B. Zhang, Y. Zhang, S. Moore, R. J. Schipma, M. J. Liu, T. Tokars, V. L. Cristofanilli, M. Shi, T. Shen, Y. Liu, H. 2022-02-25 doi:10.1101/2022.02.23.481674 Cold Spring Harbor Laboratory Press 2022-02-25 <![CDATA[ The MIF SNP rs755622 is a germline determinant of tumor immune activation in Glioblastoma ]]> https://biorxiv.org/content/10.1101/2022.03.07.483365v1?rss=1 Alban, T. Grabowski, M. M. Otvos, B. Watson, D. B. Zalavadia, A. Makarav, V. Troike, K. M. McGraw, M. Rabljenovic, A. Lauko, A. Neumann, C. K. A. Roversi, G. Waite, K. Cioffi, G. Patil, N. Tran, T. McCortney, K. Steffens, A. Diaz, M. Brown, J. M. Egan, K. Horbinski, C. Barnholtz-sloan, J. Vogelbaum, M. Bucala, R. Chan, T. Ahluwalia, M. Lathia, J. 2022-03-08 doi:10.1101/2022.03.07.483365 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Chemokine Receptor 1 and its associated immune pathway are downregulated in SF3B1MT blood and non-blood cancers ]]> https://biorxiv.org/content/10.1101/2022.03.31.485699v1?rss=1 20% of the significantly upregulated genes in the SF3B1K700E ES lines have immune functions. Thus, SF3B1 may have an additional role in proper expression of immune genes in appropriate cell types. In striking contrast, we found that published RNA-seq data from SF3B1 blood (MDS, CLL, AML) and non-blood (BRCA, UVM) cancers exhibited the opposite, downregulation of a multitude of immune pathways with 7 of the pathways shared among all 5 of the SF3B1 cancers. One of these pathways, "leukocyte migration", is the 1st reported pathway shared among all splicing factor cancers, including the 5 SF3B1 cancers and MDS associated with U2AF1, SRSF2 and ZRSR2. Importantly, we identified CCR1, which is in the leukocyte migration pathway as the only shared downregulated gene in the 5 SF3B1 cancers and in U2AF1MT MDS. We conclude that downregulation of CCR1 and its associated immune pathway may play a key role in pathogenesis of these splicing factor cancers and are thus potential therapeutic targets. ]]> Dastpak, M. Kim, H. Paraggio, C. L. Leonard, C. E. Yin, S. Chi, B. Nassar, K. W. Rowe, R. G. Hou, Z. Zhang, J. Cohn, E. F. Yang, N. Marion, W. Zhang, Y. Daley, G. Q. Reed, R. 2022-03-31 doi:10.1101/2022.03.31.485699 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ Structural and Dynamic Effects of PTEN C-terminal Tail Phosphorylation ]]> https://biorxiv.org/content/10.1101/2022.04.16.488508v1?rss=1 Smith, I. N. Dawson, J. E. Krieger, J. M. Thacker, S. Bahar, I. Eng, C. 2022-04-16 doi:10.1101/2022.04.16.488508 Cold Spring Harbor Laboratory Press 2022-04-16 <![CDATA[ An intranasal stringent response vaccine targeting dendritic cells as a novel adjunctive therapy against tuberculosis ]]> https://biorxiv.org/content/10.1101/2022.04.19.488816v1?rss=1 Karanika, S. Gordy, J. Neupane, P. KARANTANOS, T. Castillo, J. Quijada, D. Comstock, K. Sandhu, A. Hui, Y. Ayeh, S. Tasneen, R. Krug, S. Danchik, C. Wang, T. Schill, C. Markham, R. t. Karakousis, P. 2022-04-19 doi:10.1101/2022.04.19.488816 Cold Spring Harbor Laboratory Press 2022-04-19 <![CDATA[ Evolutionarily conserved effects of Notch signaling drive intestinal graft-versus-host disease in mice and non-human primates ]]> https://biorxiv.org/content/10.1101/2022.04.23.488844v1?rss=1 Tkachev, V. Vanderbeck, A. Perkey, E. Furlan, S. N. McGuckin, C. Gomez Atria, D. Gerdemann, U. Rui, X. Lane, J. Hunt, D. J. Zheng, H. Colonna, L. Hoffman, M. Yu, A. Kelly, S. Allman, A. Burbach, B. Shimizu, Y. Panoskaltsis-Mortari, A. Chen, G. Carpenter, S. Harari, O. Kuhnert, F. Thurston, G. Blazar, B. R. Kean, L. S. Maillard, I. 2022-04-27 doi:10.1101/2022.04.23.488844 Cold Spring Harbor Laboratory Press 2022-04-27 <![CDATA[ Exogenous DNA upregulates DUOX2 expression and function in human pancreatic cancer cells by activating the cGAS-STING signaling pathway ]]> https://biorxiv.org/content/10.1101/2022.05.14.491678v1?rss=1 Wang, S. L. Wu, Y. Konate, M. Lu, J. Antony, S. Meitzler, J. L. Jiang, G. Dahan, I. Juhasz, A. Diebold, B. Roy, K. Doroshow, J. H. 2022-05-14 doi:10.1101/2022.05.14.491678 Cold Spring Harbor Laboratory Press 2022-05-14 <![CDATA[ Amyloid-β seeding effects are dependent on the presence of knock-in genes in the AppNL-G-F mice. ]]> https://biorxiv.org/content/10.1101/2022.05.28.492382v1?rss=1 Lacoursiere, S. G. Westaway, D. Safar, J. Mohajerani, M. H. Sutherland, R. J. 2022-05-29 doi:10.1101/2022.05.28.492382 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Micropatterned Organoids Enable Modeling of the Earliest Stages of Human Cardiac Vascularization ]]> https://biorxiv.org/content/10.1101/2022.07.08.499233v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@17b265org.highwire.dtl.DTLVardef@1c1113eorg.highwire.dtl.DTLVardef@531c18org.highwire.dtl.DTLVardef@596bd2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Abilez, O. J. Yang, H. Tian, L. Wilson, K. D. Lyall, E. H. Shen, M. Bhoi, R. Zhuge, Y. Jia, F. Wo, H. T. Zhou, G. Guan, Y. Aldana, B. Obal, D. Peltz, G. Zarins, C. K. Wu, J. C. 2022-07-10 doi:10.1101/2022.07.08.499233 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Evaluating limitations of quantitative metagenomics with synthetic dsDNA and ssDNA standards ]]> https://biorxiv.org/content/10.1101/2022.07.08.499345v1?rss=1 Langenfeld, K. Hegarty, B. Vidaurri, S. Crossette, E. Duhaime, M. B. Wigginton, K. 2022-07-10 doi:10.1101/2022.07.08.499345 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome ]]> https://biorxiv.org/content/10.1101/2022.07.25.501461v1?rss=1 100-fold, while the remaining strains are largely unaffected. In single-strain dropout communities (i.e., a strain swap within the niche), Cs and Ch reach the same relative abundance and dehydroxylate bile acids to a similar extent. However, the effect on strains in other niches differs markedly: Clostridium sporogenes increases >1000-fold in the {Delta}Cs but not {Delta}Ch dropout, reshaping the pool of microbiome-derived phenylalanine metabolites. Thus, strains that are functionally redundant within a niche can have widely varying impacts outside the niche, and a strain swap can ripple through the community in an unpredictable manner, resulting in a large impact on an unrelated community-level phenotype. Mice colonized by the {Delta}Cs{Delta}Ch community show decreased liver steatosis relative to those colonized by the {Delta}Ch community, demonstrating that a single strain from the microbiome can have a substantive impact on host physiology. Our work opens the door to the mechanistic studies of the role of an individual strain on community ecology and host physiology. ]]> Wang, M. Osborn, L. J. Jain, S. Meng, X. Weakley, A. Yan, J. Massey, W. Venkateshwari, V. Horak, A. J. Banerjee, R. Allende, D. S. Chan, R. Hajjar, A. Dimas, A. Zhao, A. Nagashima, K. Cheng, A. Higginbottom, S. K. Brown, J. M. Fischbach, M. A. 2022-07-25 doi:10.1101/2022.07.25.501461 Cold Spring Harbor Laboratory Press 2022-07-25 <![CDATA[ Cellular, Molecular, and Enzymatic Signatures ofThrombi are Vascular Bed-Dependent ]]> https://biorxiv.org/content/10.1101/2022.08.11.503688v1?rss=1 Bender, M. Aggarwal, A. Mix, D. Godwin, M. Guntupalli, S. Nanjundappa, A. Tefera, L. Haddadin, I. Bhandari, R. Tong, M. Baldwin, W. Faurchild, R. Gomes, M. Campbell, J. Schumick, D. Cameron, S. 2022-08-12 doi:10.1101/2022.08.11.503688 Cold Spring Harbor Laboratory Press 2022-08-12 <![CDATA[ Myeloid-cell-specific role of Gasdermin D in promoting lung cancer progression in mice. ]]> https://biorxiv.org/content/10.1101/2022.08.22.504854v1?rss=1 Traughber, c. deshpande, G. neupane, k. Khan, M. McMullen, M. R. Swaidani, S. Opoku, E. Muppals, S. Smith, J. Nagy, L. Gulshan, K. 2022-08-22 doi:10.1101/2022.08.22.504854 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ A genome-wide atlas of recurrent repeat expansions in human cancer ]]> https://biorxiv.org/content/10.1101/2022.08.24.505159v1?rss=1 Erwin, G. S. Gursoy, G. Al-Abri, R. Suriyaprakash, A. Dolzhenko, E. Zhu, K. Hoerner, C. R. White, S. M. Ramirez, L. Vadlakonda, A. Vadlakonda, A. von Kraut, K. Park, J. Brannon, C. M. Sumano, D. A. Kirtikar, R. A. Erwin, A. A. Metzner, T. J. Yuen, R. K. C. Fan, A. C. Leppert, J. T. Eberle, M. A. Gerstein, M. Snyder, M. P. 2022-08-24 doi:10.1101/2022.08.24.505159 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ A pan-variant mRNA-LNP T cell vaccine protects HLA transgenic mice from mortality after infection with SARS-CoV-2 Beta ]]> https://biorxiv.org/content/10.1101/2022.09.23.509206v1?rss=1 Carter, B. Huang, P. Liu, G. Liang, Y. Lin, P. J. C. Peng, B.-H. McKay, L. Dimitrakakis, A. Hsu, J. Tat, V. Saenkham-Huntsinger, P. Chen, J. Kaseke, C. Gaiha, G. D. Xu, Q. Griffiths, A. Tam, Y. K. Tseng, C.-T. K. Gifford, D. K. 2022-09-26 doi:10.1101/2022.09.23.509206 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Novel Biosensor Identifies Ruxolitinib as a Potent and Cardioprotective CaMKII Inhibitor ]]> https://biorxiv.org/content/10.1101/2022.09.24.509320v1?rss=1 Reyes Gaido, O. E. Granger, J. M. Nkashama, L. J. Lin, B. L. Long, A. Mesubi, O. O. Schole, K. L. Terrillion, C. E. Liu, J. O. Luczak, E. D. Anderson, M. E. 2022-09-24 doi:10.1101/2022.09.24.509320 Cold Spring Harbor Laboratory Press 2022-09-24 <![CDATA[ A deficiency screen of the 3rd chromosome for dominant modifiers of the Drosophila ER integral membrane protein, Jagunal ]]> https://biorxiv.org/content/10.1101/2022.10.26.513935v1?rss=1 Ascencio, G. de Cruz, M. A. Abuel, J. Alvarado, S. Arriaga, Y. Conrad, E. A. Castro, A. Eichelberger, K. Galvan, L. Gundy, G. Inojoza, J. A. Jimenez, A. D. Lu, N. T. Lugar, C. Marania, R. Mendsaikhan, T. Ortega, J. Nand, N. Rodrigues, N. S. Shabazz, K. Tam, C. Valenciano, E. Hayzelden, C. Eritano, A. S. Riggs, B. 2022-10-28 doi:10.1101/2022.10.26.513935 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Ancestry-related differences in chromatin accessibility and gene expression of APOE4 are associated with Alzheimer disease risk ]]> https://biorxiv.org/content/10.1101/2022.10.27.514114v1?rss=1 Celis, K. Muniz Moreno, M. D. Rajabli, F. Whitehead, P. Hamilton-Nelson, K. Dykxhoorn, D. M. Nuytemans, K. Wang, L. Dalgard, C. L. Flanagan, M. Weintraub, S. Geula, C. Gearing, M. Bennett, D. A. Schuck, T. Jin, F. Pericak-Vance, M. A. Griswold, A. J. Young, J. I. Vance, J. M. 2022-10-28 doi:10.1101/2022.10.27.514114 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Axon guidance pathways modulate neurotoxicity of ALS-associated UBQLN2 ]]> https://biorxiv.org/content/10.1101/2022.10.31.514355v1?rss=1 Kim, S. H. Nichols, K. D. Anderson, E. N. Liu, Y. Ramesh, N. Jia, W. Kuerbis, C. J. Scalf, M. Smith, L. M. Pandey, U. B. Tibbetts, R. S. 2022-11-01 doi:10.1101/2022.10.31.514355 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Impaired HIV-specific T-cell responses in HIV and S. mansoni coinfected Ugandans. ]]> https://biorxiv.org/content/10.1101/2022.11.01.514652v1?rss=1 Obuku, A. E. Sharma, A. A. Rukundo, A. Odong, M. Auma, B. Serwanga, J. S. Nkangi, R. Nakitto, Z. Joloba, M. Pantaleo, G. Kaleebu, P. Sekaly, R. P. 2022-11-01 doi:10.1101/2022.11.01.514652 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Rescue of neuropsychiatric phenotypes in a mouse model of 16p11.2 duplication syndrome by genetic correction of an epilepsy network hub ]]> https://biorxiv.org/content/10.1101/2022.11.09.515866v1?rss=1 Forrest, M. P. Dos Santos, M. Piguel, N. H. Wang, Y. Z. Yoon, S. Bagchi, V. A. Hawkins, N. A. Dionisio, L. E. Simkin, D. Martin-de-Saavedra, M. D. Gao, R. Horan, K. E. George, A. L. LeDoux, M. Kearney, J. A. Savas, J. Penzes, P. 2022-11-09 doi:10.1101/2022.11.09.515866 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ An international scholastic network to generate LexA enhancer-trap lines for Drosophila ]]> https://biorxiv.org/content/10.1101/2022.11.24.517565v1?rss=1 Kim, E. S. Rajan, A. Chang, K. Gulick, C. English, E. Nakada, S. Beard, C. O'Connor, S. Mastroianni, S. Downey, E. Feigenbaum, M. Tolentino, C. Pace, A. Khan, M. Moon, S. DiPrima, J. Syed, A. Lin, F. Govindarajan, S. Abukhadra, Y. Bacon, I. Beckerle, J. Bloomfield, O. Cho, S. Esi Donkor, N. Garberg, L. Harrington, A. Hoang, M. Lawani, N. Noori, A. Park, E. Parsons, E. Oravitan, P. Chen, M. Molina, C. Richmond, C. Reddi, A. Huang, J. Shugrue, C. Coviello, R. Unver, S. Indelicarto, M. Islamovic, E. McIlroy, R. Yang, A. Hamad, M. Griffin, E. Ahmed, Z 2022-11-25 doi:10.1101/2022.11.24.517565 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ The RNA-binding protein Adad1 is necessary for germ cell maintenance and meiosis in zebrafish ]]> https://biorxiv.org/content/10.1101/2022.12.21.521539v1?rss=1 Islam, K. N. Ajao, A. Henke, K. Siegfried, K. R. 2022-12-22 doi:10.1101/2022.12.21.521539 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Characterization and Applications of Evoked Responses During Epidural Electrical Stimulation ]]> https://biorxiv.org/content/10.1101/2023.01.10.523453v1?rss=1 Verma, N. Romanauski, B. Lam, D. Lujan, L. Blanz, S. Ludwig, K. Lempka, S. Knudsen, B. Nishiyama, Y. Hao, J. Park, H.-J. Ross, E. Lavrov, I. Zhang, M. 2023-01-11 doi:10.1101/2023.01.10.523453 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ Structural Plasticity of GABAergic Pallidothalamic Terminals in MPTP-treated Parkinsonian Monkeys: A 3D Electron Microscopic Analysis ]]> https://biorxiv.org/content/10.1101/2023.04.05.535706v1?rss=1 Masilamoni, G. J. Kelly, H. Swain, A. Pare, J.-F. Villalba, R. Smith, Y. 2023-04-06 doi:10.1101/2023.04.05.535706 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ How individual P. aeruginosa cells with diverse stator distributions collectively form a heterogeneous macroscopic swarming population ]]> https://biorxiv.org/content/10.1101/2023.04.10.536285v1?rss=1 de Anda, J. Kuchma, S. Webster, S. S. Boromand, A. Lewis, K. A. Lee, C. Contreras, M. Medeiros Pereira, V. F. Hogan, D. A. O'Hern, C. O'Toole, G. A. Wong, G. C. L. 2023-04-10 doi:10.1101/2023.04.10.536285 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ LOCC: a novel visualization and scoring of cutoffs for continuous variables ]]> https://biorxiv.org/content/10.1101/2023.04.11.536461v1?rss=1 View larger version (17K): org.highwire.dtl.DTLVardef@1712bc2org.highwire.dtl.DTLVardef@efd579org.highwire.dtl.DTLVardef@1a8236borg.highwire.dtl.DTLVardef@1ad78ea_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Luo, G. Letterio, J. 2023-04-12 doi:10.1101/2023.04.11.536461 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ The initiation and maintenance of CHH methylation and its effects on gene expression are unique in maize ]]> https://biorxiv.org/content/10.1101/2023.04.15.537008v1?rss=1 Liu, B. Wang, D. Liang, C. Wang, J. Lisch, D. Zhao, M. 2023-04-17 doi:10.1101/2023.04.15.537008 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ A core Nrf2 gene set defined through comprehensive transcriptomic analysis predicts drug resistance and poor multi-cancer prognosis ]]> https://biorxiv.org/content/10.1101/2023.04.20.537691v1?rss=1 Luo, G. Kumar, H. Alridge, K. Rieger, S. Jiang, E. Chan, E. R. Soliman, A. Mahdi, H. Letterio, J. J. 2023-04-21 doi:10.1101/2023.04.20.537691 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ OPERANT REFLEX CONDITIONING SIMULATION ENVIRONMENT REVEALS EFFECTS OF FEEDBACK PARAMETERS ]]> https://biorxiv.org/content/10.1101/2023.05.26.542391v1?rss=1 Kim, K. Oblak, E. Manella, K. Sulzer, J. 2023-05-26 doi:10.1101/2023.05.26.542391 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Dicarboxylic acid supplementation protects from acute kidney injury via stimulation of renal peroxisomal activity ]]> https://biorxiv.org/content/10.1101/2023.05.31.543068v1?rss=1 Barbosa, A. C. S. Pfister, K. E. Chiba, T. Bons, J. Rose, J. Burton, J. B. King, C. D. O'Broin, A. Young, V. Zhang, B. Sivakama, B. Schmidt, A. V. Uhlean, R. Schilling, B. Goetzman, E. S. Sims-Lucas, S. 2023-06-04 doi:10.1101/2023.05.31.543068 Cold Spring Harbor Laboratory Press 2023-06-04 <![CDATA[ Specification and survival of post-metamorphic branchiomeric neurons in the hindbrain of a non-vertebrate chordate. ]]> https://biorxiv.org/content/10.1101/2023.06.16.545305v1?rss=1 Gigante, E. D. Piekarz, K. M. Gurgis, A. Cohen, L. Razy-Krajka, F. Popsuj, S. Ali, H. S. Mohana Sundaram, S. Stolfi, A. 2023-06-18 doi:10.1101/2023.06.16.545305 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Glycoprotein VI is Critical for the Detection and Progression of Abdominal Aortic Aneurysms ]]> https://biorxiv.org/content/10.1101/2023.07.02.547361v1?rss=1 Benson, T. W. Pike, M. M. Spuzzillo, A. Hicks, S. M. Pham, M. Mix, D. S. Brunner, S. I. Wadding-Lee, C. A. Conrad, K. A. Russell, H. M. Jennings, C. Coughlin, T. M. Aggarwal, A. Lyden, S. Mani, K. Bjorck, M. Wanhainen, A. Bhandari, R. Lipworth, L. Robinson-Cohen, C. Caputo, F. J. Shim, S. Edwards, T. L. Tranter, M. Gardiner, E. E. Mackman, N. Cameron, S. J. Owens, A. P. 2023-07-05 doi:10.1101/2023.07.02.547361 Cold Spring Harbor Laboratory Press 2023-07-05 <![CDATA[ Liquid channels within B. subtilis biofilms allow the escape of trapped clones and population rescue ]]> https://biorxiv.org/content/10.1101/2023.07.20.549970v1?rss=1 Krishnan, N. Knight, J. Ruiz Pestana, L. Fusco, D. 2023-07-24 doi:10.1101/2023.07.20.549970 Cold Spring Harbor Laboratory Press 2023-07-24 <![CDATA[ XRN1 deletion induces PKR-dependent cell lethality in interferon-activated cancer cells ]]> https://biorxiv.org/content/10.1101/2023.08.01.551488v1?rss=1 Zou, T. Zhou, M. Gupta, A. Zhuang, P. Fishbein, A. R. Wei, H. Y. Zhang, Z. Cherniack, A. D. Meyerson, M. 2023-08-03 doi:10.1101/2023.08.01.551488 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ TLR2 Regulates Hair Follicle Cycle and Regeneration via BMP Signaling. ]]> https://biorxiv.org/content/10.1101/2023.08.14.553236v1?rss=1 Xiong, L. Zhevlakova, I. West, X. Z. Gao, D. Murtazina, R. Horak, A. Brown, J. M. Molokotina, I. Podrez, E. A. Byzova, T. V. 2023-08-16 doi:10.1101/2023.08.14.553236 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ Structural and functional vascular dysfunction within brain metastases is linked to pembrolizumab inefficacy ]]> https://biorxiv.org/content/10.1101/2023.08.25.554868v1?rss=1 Kim, A. E. Lou, K. W. Giobbie-Hurder, A. Chang, K. Gidwani, M. Hoebel, K. Patel, J. Cleveland, M. Singh, P. Bridge, C. Ahmed, S. R. Bearce, B. Liu, W. Fuster-Garcia, E. Lee, E. Lin, N. U. Overmoyer, B. Wen, P. Y. Nayak, L. Cohen, J. Dietrich, J. Eichler, A. Heist, R. Krop, I. Lawrence, D. Ligibel, J. Tolaney, S. Mayer, E. Winer, E. Perrino, C. M. Summers, E. J. Mahar, M. Oh, K. Shih, H. Cahill, D. Rosen, B. R. Yen, Y.-F. Kalpathy-Cramer, J. Martinez-Lage, M. Sullivan, R. J. Brastianos, P. K. Emblem, K. Gerstner, E. R. 2023-08-28 doi:10.1101/2023.08.25.554868 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Dark selection for JAK/STAT-inhibitor resistance in chronic myelomonocytic leukemia ]]> https://biorxiv.org/content/10.1101/211151v1?rss=1 Kaznatcheev, A. Grimes, D. R. Vander Velde, R. Cannataro, V. L. Baratchart, E. Dhawan, A. Liu, L. Myroshnychenko, D. Taylor-King, J. P. Yoon, N. Padron, E. Marusyk, A. Basanta, D. 2017-10-30 doi:10.1101/211151 Cold Spring Harbor Laboratory Press 2017-10-30 <![CDATA[ Clinically Important sex differences in GBM biology revealed by analysis of male and female imaging, transcriptome and survival data ]]> https://biorxiv.org/content/10.1101/232744v1?rss=1 Yang, W. Warrington, N. M. Taylor, S. J. Carrasco, E. Singleton, K. W. Wu, N. Lathia, J. D. Berens, M. E. Kim, A. H. Barnholtz-Sloan, J. S. Swanson, K. R. Luo, J. Rubin, J. B. 2017-12-12 doi:10.1101/232744 Cold Spring Harbor Laboratory Press 2017-12-12 <![CDATA[ How Do Telomeres Block Checkpoint Activation? ]]> https://biorxiv.org/content/10.1101/251389v1?rss=1 Runge, K. Audry, J. Wang, J. Eisenstatt, J. Sanders, S. L. Berkner, K. L. 2018-01-22 doi:10.1101/251389 Cold Spring Harbor Laboratory Press 2018-01-22 <![CDATA[ Meta-analysis of genetic association with diagnosed Alzheimer’s disease identifies novel risk loci and implicates Abeta, Tau, immunity and lipid processing ]]> https://biorxiv.org/content/10.1101/294629v1?rss=1 60 years) is the most prevalent dementia in the elderly1, and risk is partially driven by genetics2. Many of the loci responsible for this genetic risk were identified by genome-wide association studies (GWAS)3-8. To identify additional LOAD risk loci, the we performed the largest GWAS to date (89,769 individuals), analyzing both common and rare variants. We confirm 20 previous LOAD risk loci and identify four new genome-wide loci (IQCK, ACE, ADAM10, and ADAMTS1). Pathway analysis of these data implicates the immune system and lipid metabolism, and for the first time tau binding proteins and APP metabolism. These findings show that genetic variants affecting APP and A{beta} processing are not only associated with early-onset autosomal dominant AD but also with LOAD. Analysis of AD risk genes and pathways show enrichment for rare variants (P = 1.32 x 10-7) indicating that additional rare variants remain to be identified. ]]> Kunkle, B. W. Grenier-Boley, B. Sims, R. Bis, J. C. Naj, A. C. Boland, A. Vronskaya, M. van der Lee, S. J. Amlie-Wolf, A. Bellenguez, C. Frizatti, A. Chouraki, V. Alzheimer's Disease Genetics Consortium (ADGC), European Alzheimer's Disease Initiative (EADI), Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium (CHARGE), Genetic and Environmental Risk in Alzheimer's Disease Consortium (GERAD/PERADES), Schmidt, H. Hakonarson, H. Munger, R. Schmidt, R. Farrer, L. A. Van Broeckhoven, C. O'Donovan, M. C. Destefano, A. L. Jones, L. Haines, J. L 2018-04-04 doi:10.1101/294629 Cold Spring Harbor Laboratory Press 2018-04-04 <![CDATA[ Prion protein quantification in cerebrospinal fluid as a tool for prion disease drug development ]]> https://biorxiv.org/content/10.1101/295063v1?rss=1 Vallabh, S. M. Nobuhara, C. K. Llorens, F. Zerr, I. Parchi, P. Capellari, S. Kuhn, E. Klickstein, J. Safar, J. Nery, F. Swoboda, K. Schreiber, S. L. Geschwind, M. D. Zetterberg, H. Arnold, S. E. Minikel, E. V. 2018-04-04 doi:10.1101/295063 Cold Spring Harbor Laboratory Press 2018-04-04 <![CDATA[ Marginal Effects of Systemic CCR5 Blockade with Maraviroc on Oral Simian Immunodeficiency Virus Transmission to Infant Macaques ]]> https://biorxiv.org/content/10.1101/299206v1?rss=1 Brocca-Cofano, E. Xu, C. Wetzel, K. Cottrell, M. Policicchio, B. Raehtz, K. Ma, D. Dunsmore, T. Haret-Richter, G. Musaitif, K. Keele, B. F. Kashuba, A. D. Collman, R. Pandrea, I. Apetrei, C. 2018-04-11 doi:10.1101/299206 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ Structural insights on TRPV5 gating by endogenous modulators ]]> https://biorxiv.org/content/10.1101/338798v1?rss=1 Hughes, T. E. T. Pumroy, R. A. Fluck, E. C. Huynh, K. W. Samanta, A. Molugu, S. Zhou, Z. H. Moiseenkova-Bell, V. Y. 2018-06-05 doi:10.1101/338798 Cold Spring Harbor Laboratory Press 2018-06-05 <![CDATA[ Distinct roles and requirements for Ras pathway signaling in visceral versus somatic muscle founder specification ]]> https://biorxiv.org/content/10.1101/347526v1?rss=1 Zhou, Y. Popadowski, S. E. Deustchman, E. Halfon, M. S. 2018-06-14 doi:10.1101/347526 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ The Clinical and Molecular Epidemiology of CTX-M-9 Group Producing Enterobacteriaceae infections in children ]]> https://biorxiv.org/content/10.1101/416016v1?rss=1 Logan, L. K. Medernach, R. L. Domitrovic, T. N. Rispens, J. R. Hujer, A. M. Qureshi, N. K. Marshall, S. H. Nguyen, D. C. Rudin, S. D. Zheng, X. Weinstein, R. A. Bonomo, R. A. 2018-09-20 doi:10.1101/416016 Cold Spring Harbor Laboratory Press 2018-09-20 <![CDATA[ lncDIFF: a novel distribution-free method for differential expression analysis of long non-coding RNA ]]> https://biorxiv.org/content/10.1101/420562v1?rss=1 Li, Q. Yu, X. Chaudhary, R. Slebos, R. J. Chung, C. H. Wang, X. 2018-09-18 doi:10.1101/420562 Cold Spring Harbor Laboratory Press 2018-09-18 <![CDATA[ Inhibition of nucleotide synthesis mediates replicative senescence of human mammary epithelial cells ]]> https://biorxiv.org/content/10.1101/423665v1?rss=1 Delfarah, A. Parrish, S. Yang, J. Seo, F. Li, S. Wang, P. Graham, N. 2018-09-21 doi:10.1101/423665 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ Evolutionary exploitation of PD-L1 expression in hormone receptor positive breast cancer ]]> https://biorxiv.org/content/10.1101/454447v1?rss=1 West, J. Park, D. Harmon, C. Williamson, D. Ashcroft, P. Maestrini, D. Ardaseva, A. Bravo, R. Sahoo, P. Khong, H. Luddy, K. Robertson-Tessi, M. 2018-10-26 doi:10.1101/454447 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ Multiscale causal network models of Alzheimer’s disease identify VGF as a key regulator of disease ]]> https://biorxiv.org/content/10.1101/458430v1?rss=1 Beckmann, N. D. Lin, W.-J. Wang, M. Cohain, A. T. Wang, P. Ma, W. Wang, Y.-C. Jiang, C. Audrain, M. Comella, P. Hariharan, S. P. Belbin, G. M. Levey, A. I. Seyfried, N. T. Dammer, E. B. Duong, D. Lah, J. J. Haure-Mirande, J.-V. Shackleton, B. Charney, A. W. Kenny, E. Zhu, J. Haroutunian, V. Katsel, P. Gandy, S. Tu, Z. Ehrlich, M. Zhang, B. Salton, S. R. Schadt, E. E. 2018-11-04 doi:10.1101/458430 Cold Spring Harbor Laboratory Press 2018-11-04 <![CDATA[ Resistance to ALK targeting therapies as a gradual Darwinian adaptation to inhibitor specific selective pressures ]]> https://biorxiv.org/content/10.1101/504837v1?rss=1 Vander Velde, R. Yoon, N. Marusyk, V. Dhawan, A. Balynska, O. Desai, B. Peral, D. Myroshnychenko, D. Poleszhuk, J. Liu, K. Mian, O. Abazeed, M. Haura, E. Scott, J. Marusyk, A. 2018-12-25 doi:10.1101/504837 Cold Spring Harbor Laboratory Press 2018-12-25 <![CDATA[ Molecular mechanism of TRPV2 channel modulation by cannabidiol ]]> https://biorxiv.org/content/10.1101/521880v1?rss=1 Pumroy, R. A. Samanta, A. Liu, Y. Hughes, T. E. T. Zhao, S. Yudin, Y. Huynh, K. W. Zhou, Z. H. Rohacs, T. Han, S. Moiseenkova-Bell, V. Y. 2019-01-16 doi:10.1101/521880 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ \"Self-inactivating\" rabies viruses are just first-generation, ΔG rabies viruses ]]> https://biorxiv.org/content/10.1101/550640v1?rss=1 Matsuyama, M. Jin, L. Lavin, T. K. Sullivan, H. A. Hou, Y. Lea, N. E. Pruner, M. T. Dam Ferdinez, M. L. Wickersham, I. R. 2019-02-18 doi:10.1101/550640 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ Stag1 and Stag2 regulate cell fate decisions in hematopoiesis through non-redundant topological control ]]> https://biorxiv.org/content/10.1101/581868v1?rss=1 Viny, A. D. Bowman, R. L. Liu, Y. Lavallee, V.-P. Redlich, S. E. Xiao, W. Durham, B. H. Navitski, A. Park, J. Braunstein, S. Azizi, E. Witkin, M. Baslan, T. Ott, C. J. Pe'er, D. Dekker, J. Koche, R. Levine, R. L. 2019-03-18 doi:10.1101/581868 Cold Spring Harbor Laboratory Press 2019-03-18 <![CDATA[ Adaptive substitutions underlying cardiac glycoside insensitivity in insects exhibit epistasis in vivo. ]]> https://biorxiv.org/content/10.1101/621185v1?rss=1 Taverner, A. M. Yang, L. Barile, Z. J. Becky, L. Peng, J. Pinharanda, A. Rao, A. Roland, B. P. Talsma, A. D. Wei, D. Petschenka, G. Palladino, M. J. Andolfatto, P. 2019-04-28 doi:10.1101/621185 Cold Spring Harbor Laboratory Press 2019-04-28 <![CDATA[ Mycobacterium tuberculosis infection boosts B cell responses to unrelated pathogens ]]> https://biorxiv.org/content/10.1101/680058v1?rss=1 Kimuda, S. G. Andia-Biraro, I. Sebina, I. Egesa, M. Nalwoga, A. Smith, S. G. Ssentalo Bagaya, B. Levin, J. Elliott, A. Raynes, J. G. Cose, S. 2019-06-25 doi:10.1101/680058 Cold Spring Harbor Laboratory Press 2019-06-25 <![CDATA[ LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility ]]> https://biorxiv.org/content/10.1101/751958v1?rss=1 Moon, H. M. Hippenmeyer, S. Luo, L. Wynshaw-Boris, A. 2019-08-30 doi:10.1101/751958 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ B cell Compartmentalisation in Blood and Cerebrospinal Fluid of HIV- Infected Ugandans with Cryptococcal Meningitis ]]> https://biorxiv.org/content/10.1101/759092v1?rss=1 Okurut, S. Meya, D. B. Olobo, J. Bohjanen, P. R. Bwanga, F. Eller, M. A. Boulware, D. Huppler Hullsiek, K. Pratap, H. Manabe, Y. C. Palmer, B. Janoff, E. Jallow, F. 2019-09-06 doi:10.1101/759092 Cold Spring Harbor Laboratory Press 2019-09-06 <![CDATA[ DAF-16 and SMK-1 contribute to innate immunity during adulthood in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/761312v1?rss=1 McHugh, D. R. Koumis, E. Schlaubitz-Garcia, M. Bennani, S. Regan, P. Patel, P. Youngman, M. J. 2019-09-08 doi:10.1101/761312 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ A Brain to Spine Interface for Transferring Artificial Sensory Information ]]> https://biorxiv.org/content/10.1101/807735v1?rss=1 Yadav, A. P. Li, D. Nicolelis, M. A. L. 2019-10-17 doi:10.1101/807735 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ A synthetic approach reveals a highly sensitive maize auxin response circuit ]]> https://biorxiv.org/content/10.1101/844100v1?rss=1 Ramos Baez, R. Buckley, Y. Yu, H. Chen, Z. Gallavotti, A. Nemhauser, J. Moss, B. L. 2019-11-19 doi:10.1101/844100 Cold Spring Harbor Laboratory Press 2019-11-19 <![CDATA[ Determination of secretory granule maturation times in pancreatic islet beta-cells by serial block face scanning electron microscopy ]]> https://biorxiv.org/content/10.1101/865683v1?rss=1 Rao, A. McBride, E. L. Zhang, G. Cai, T. Notkins, A. L. Aronova, M. A. Leapman, R. D. 2019-12-05 doi:10.1101/865683 Cold Spring Harbor Laboratory Press 2019-12-05 <![CDATA[ Seeding Activity of Skin Misfolded Tau as a Novel Biomarker for Tauopathies ]]> https://biorxiv.org/content/10.1101/2023.09.07.556724v1?rss=1 Wang, Z. Wu, L. Gerasimenko, M. Gilliland, T. Shah, Z. S. A. Gunzler, S. A. Donadio, V. Liguori, R. Xu, B. Zou, W. 2023-09-09 doi:10.1101/2023.09.07.556724 Cold Spring Harbor Laboratory Press 2023-09-09 <![CDATA[ Reduced S-nitrosylation of TGFβ1 elevates its binding affinity towards the receptor and promotes fibrogenic signaling in the breast ]]> https://biorxiv.org/content/10.1101/2023.09.07.556714v1?rss=1 Letson, J. Furuta, S. 2023-09-10 doi:10.1101/2023.09.07.556714 Cold Spring Harbor Laboratory Press 2023-09-10 <![CDATA[ Contrasting Effects of SARS-CoV-2 Vaccination vs. Infection on Antibody and TCR Repertoires ]]> https://biorxiv.org/content/10.1101/2023.09.08.556703v1?rss=1 Braun, J. Hill, E. D. Contreras, E. Yasuda, M. Morgan, A. Ditelberg, S. Winter, E. Callahan, C. Mazzoni, G. Kirmaier, A. Mirebrahim, H. Asgharian, H. Telman, D. Collier, A.-R. Y. Barouch, D. H. Riedel, S. Dutta, S. Rubelt, F. Arnaout, R. 2023-09-11 doi:10.1101/2023.09.08.556703 Cold Spring Harbor Laboratory Press 2023-09-11 <![CDATA[ magpie: a power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing ]]> https://biorxiv.org/content/10.1101/2023.09.08.556896v1?rss=1 Guo, Z. Duan, D. Tang, W. Zhu, J. Bush, W. S. Zhang, L. Zhu, X. Jin, F. Feng, H. 2023-09-12 doi:10.1101/2023.09.08.556896 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ HIV co-infection is associated with reduced Mycobacterium tuberculosis transmissibility in sub-Saharan Africa ]]> https://biorxiv.org/content/10.1101/2023.09.12.557301v1?rss=1 Windels, E. M. Wampande, E. M. Joloba, M. L. Boom, W. H. Goig, G. A. Cox, H. Hella, J. Borrell, S. Gagneux, S. Brites, D. Stadler, T. 2023-09-13 doi:10.1101/2023.09.12.557301 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Ultrasound-Mediated Drug-free Theranostics for Treatment of Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2023.09.13.555594v1?rss=1 Perera, R. H. Berg, F. M. Abenojar, E. C. Nittayacharn, P. Kim, Y. Wang, X. Basilion, J. P. Exner, A. A. 2023-09-14 doi:10.1101/2023.09.13.555594 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ simmr: An open-source tool to perform simulations in Mendelian Randomization ]]> https://biorxiv.org/content/10.1101/2023.09.11.556975v1?rss=1 Lorincz-Comi, N. J. Yang, Y. Zhu, X. 2023-09-15 doi:10.1101/2023.09.11.556975 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Magnetically Powered Microwheel Thrombolysis of Occlusive Thrombi in Zebrafish ]]> https://biorxiv.org/content/10.1101/2023.09.11.557256v1?rss=1 Pontius, M. H. H. Ku, C.-J. Osmond, M. J. Disharoon, D. Liu, Y. Marr, D. W. M. Neeves, K. B. Shavit, J. A. 2023-09-15 doi:10.1101/2023.09.11.557256 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Developmental priming of cancer susceptibility ]]> https://biorxiv.org/content/10.1101/2023.09.12.557446v1?rss=1 Panzeri, I. Fagnocchi, L. Apostle, S. Tompkins, M. Wolfrum, E. Madaj, Z. Hostetter, G. Liu, Y. Schaefer, K. Yang, C.-H. Bergsma, A. Drougard, A. Dror, E. PERMUTE, Chandler, D. Schramek, D. Triche, T. J. Pospisilik, J. A. 2023-09-15 doi:10.1101/2023.09.12.557446 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Exponentially decreasing exposure of antigen generates anti-inflammatory T-cell responses ]]> https://biorxiv.org/content/10.1101/2023.09.15.558014v1?rss=1 Esrafili, A. Kupfer, J. Thumsi, A. JAGGARAPU, M. Suresh, A. Talitckii, A. Khodaei, T. Swaminathan, S. Mantri, S. Peet, M. Acharya, A. 2023-09-17 doi:10.1101/2023.09.15.558014 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Bacterial Efflux Pump Modulators Prevent Bacterial Growth in Macrophages and Under Broth Conditions that Mimic the Host Environment ]]> https://biorxiv.org/content/10.1101/2023.09.20.558466v1?rss=1 Allgood, S. C. Su, C.-C. Crooks, A. L. Meyer, C. T. Zhou, B. Betterton, M. D. Barbachyn, M. R. Yu, E. W. Detweiler, C. S. 2023-09-20 doi:10.1101/2023.09.20.558466 Cold Spring Harbor Laboratory Press 2023-09-20 <![CDATA[ Computational modeling of dorsal root ganglion stimulation using an Injectrode ]]> https://biorxiv.org/content/10.1101/2023.09.20.558675v1?rss=1 Bhowmick, S. Graham, R. D. Verma, N. Trevathan, J. K. Franke, M. Nieuwoudt, S. Fisher, L. E. Shoffstall, A. J. Weber, D. J. Ludwig, K. A. Lempka, S. 2023-09-22 doi:10.1101/2023.09.20.558675 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Tenofovir Activation is Diminished in the Brain and Liver of Creatine Kinase Brain-Type Knockout Mice ]]> https://biorxiv.org/content/10.1101/2023.09.25.559370v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@1f8d26aorg.highwire.dtl.DTLVardef@be3d8corg.highwire.dtl.DTLVardef@1bab6d0org.highwire.dtl.DTLVardef@1381293_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Eberhard, C. D. Mosher, E. P. Bumpus, N. N. Orsburn, B. C. 2023-09-26 doi:10.1101/2023.09.25.559370 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition ]]> https://biorxiv.org/content/10.1101/2023.09.26.559521v1?rss=1 Vollger, M. R. Korlach, J. Eldred, K. C. Swanson, E. Underwood, J. G. Munson, K. M. Cheng, Y.-H. H. Ranchalis, J. Mao, Y. Blue, E. E. Schwarze, U. Saunders, C. T. Wenger, A. M. Allworth, A. Chanprasert, S. Duerden, B. L. Glass, I. Horike-Pyne, M. Kim, M. Leppig, K. A. McLaughlin, I. J. Ogawa, J. Rosenthal, E. A. Sheppeard, S. Sherman, S. M. Strohbehn, S. Yuen, A. L. Reh, T. A. Byers, P. H. Bamshad, M. J. Hisama, F. M. Jarvik, G. P. Sancak, Y. Dipple, K. M. Stergachis, A. B. 2023-09-27 doi:10.1101/2023.09.26.559521 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Evidence of antigenic drift in the fusion machinery core of SARS-CoV-2 spike ]]> https://biorxiv.org/content/10.1101/2023.09.27.559757v1?rss=1 Tan, T. J. C. Odle, A. Lei, R. Matreyek, K. A. Perlman, S. Wong, L.-Y. R. Wu, N. C. 2023-09-28 doi:10.1101/2023.09.27.559757 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ imply: improving cell-type deconvolution accuracy using personalized reference profiles ]]> https://biorxiv.org/content/10.1101/2023.09.27.559579v1?rss=1 Meng, G. Pan, Y. Tang, W. Zhang, L. Cui, Y. Schumacher, F. Wang, M. Wang, R. He, S. Krischer, J. Li, Q. Feng, H. 2023-09-29 doi:10.1101/2023.09.27.559579 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life ]]> https://biorxiv.org/content/10.1101/2023.10.02.560517v1?rss=1 1Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family. ]]> Kim, B. Y. Gellert, H. R. Church, S. H. Suvorov, A. Anderson, S. S. Barmina, O. Beskid, S. G. Comeault, A. A. Crown, K. N. Diamond, S. E. Dorus, S. Fujichika, T. Hemker, J. A. Hrcek, J. Kankare, M. Katoh, T. Magnacca, K. N. Martin, R. A. Matsunaga, T. Medeiros, M. J. Miller, D. E. Pitnick, S. Simoni, S. Steenwinkel, T. E. Schiffer, M. Syed, Z. A. Takahashi, A. Wei, K. H.-C. Yokoyama, T. Eisen, M. B. Kopp, A. Matute, D. Obbard, D. J. O'Grady, P. M. Price, D. K. Toda, M. J. Werner, T. Petrov, D. A. 2023-10-02 doi:10.1101/2023.10.02.560517 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ The SAM Domain of EphA2 Inhibits Ligand-Independent Clustering and Activation ]]> https://biorxiv.org/content/10.1101/2023.10.05.561050v1?rss=1 Shi, X. Lingerak, R. Shrestha, P. Buck, M. Wang, B. Smith, A. W. 2023-10-06 doi:10.1101/2023.10.05.561050 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Traumatic brain injury disrupts state-dependent functional cortical connectivity in a mouse model ]]> https://biorxiv.org/content/10.1101/2023.10.06.560776v1?rss=1 Bottom-Tanzer, S. Corella, S. Meyer, J. Sommer, M. Bolanos, L. Murphy, T. Quinones, S. Heiney, S. Shtrahman, M. Whalen, M. Oren, R. Higley, M. J. Cardin, J. A. Noubary, F. Armbruster, M. Dulla, C. 2023-10-06 doi:10.1101/2023.10.06.560776 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Motion Blur Microscopy ]]> https://biorxiv.org/content/10.1101/2023.10.08.561435v1?rss=1 Goreke, U. Gonzales, A. Shipley, B. Man, Y. Wulftange, W. An, R. Hinczewski, M. Gurkan, U. A. 2023-10-10 doi:10.1101/2023.10.08.561435 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Do bed bugs transmit human viruses, or do humans transmit bed bug viruses? A worldwide survey of the bed bug RNA virosphere ]]> https://biorxiv.org/content/10.1101/2023.10.20.563367v1?rss=1 Walt, H. K. King, J. G. Sheele, J. M. Meyer, F. Pietri, J. Hoffmann, F. G. 2023-10-23 doi:10.1101/2023.10.20.563367 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Molecular regulation of PPARγ/RXRα signaling by the novel cofactor ZFP407 ]]> https://biorxiv.org/content/10.1101/2023.10.25.563939v1?rss=1 Ockunzzi, J. Buchner, D. A. Charrier, A. Ghanta, S. V. 2023-10-26 doi:10.1101/2023.10.25.563939 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ Mapping RNA-Protein Interactions with Subcellular Resolution Using Colocalization CLIP ]]> https://biorxiv.org/content/10.1101/2023.10.26.563984v1?rss=1 Yi, S. Singh, S. S. Rozen-Gagnon, K. Luna, J. M. 2023-10-26 doi:10.1101/2023.10.26.563984 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ A Toxoplasma gondii O-glycosyltransferase that modulates bradyzoite cyst wall rigidity is structurally and functionally distinct from host homologues ]]> https://biorxiv.org/content/10.1101/2023.10.26.564164v1?rss=1 Kumar, P. Tomita, T. Gerken, T. A. Ballard, C. J. Lee, Y. S. Weiss, L. M. Samara, N. L. 2023-10-26 doi:10.1101/2023.10.26.564164 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ Modeling the dynamics of actin and myosin during bleb stabilization ]]> https://biorxiv.org/content/10.1101/2023.10.26.564082v1?rss=1 Asante-Asamani, E. O. Dalton, M. Brazill, D. Strychalski, W. 2023-10-27 doi:10.1101/2023.10.26.564082 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants ]]> https://biorxiv.org/content/10.1101/2023.11.03.565292v1?rss=1 Gygi, J. P. Maguire, C. Patel, R. K. Shinde, P. Konstorum, A. Shannon, C. P. Xu, L. Hoch, A. Jayavelu, N. IMPACC Network, Haddad, E. K. Reed, E. F. Kraft, M. McComsey, G. A. Metcalf, J. Ozonoff, A. Esserman, D. Cairns, C. B. Rouphael, N. Bosinger, S. E. Kim-Schulze, S. Krammer, F. Rosen, L. B. Bakel, H. Wilson, M. Eckalbar, W. Maecker, H. Langelier, C. R. Steen, H. Altman, M. C. Montgomery, R. R. Levy, O. Melamed, E. Pulendran, B. Arce, J. Smolen, K. K. Fragiadakis, G. K. Becker, P. M. Augustine, A. D. Sekaly, R. P. Ehrlich, L. I. R. Fourati, S. Pete 2023-11-06 doi:10.1101/2023.11.03.565292 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ An output-null signature of inertial load in motor cortex ]]> https://biorxiv.org/content/10.1101/2023.11.06.565869v1?rss=1 Kirk, E. A. Hope, K. T. Sober, S. J. Sauerbrei, B. A. 2023-11-07 doi:10.1101/2023.11.06.565869 Cold Spring Harbor Laboratory Press 2023-11-07 <![CDATA[ UNSEG: unsupervised segmentation of cells and their nuclei in complex tissue samples ]]> https://biorxiv.org/content/10.1101/2023.11.13.566842v1?rss=1 Kochetov, B. Bell, P. Garcia, P. S. Shalaby, A. S. Raphael, R. Raymond, B. Leibowitz, B. J. Schoedel, K. Brand, R. M. Brand, R. E. Yu, J. Zhang, L. Diergaarde, B. Schoen, R. E. Singhi, A. Uttam, S. 2023-11-15 doi:10.1101/2023.11.13.566842 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Tumor cell-derived spermidine promotes a pro-tumorigenic immune microenvironment in glioblastoma via CD8+ T cell inhibition ]]> https://biorxiv.org/content/10.1101/2023.11.14.567048v1?rss=1 Kay, K. Lee, J. Hong, E. S. Beilis, J. Dayal, S. Wesley, E. R. Mitchell, S. Wang, S. Z. Silver, D. J. Volovetz, J. Johnson, S. McGraw, M. Grabowski, M. M. Lu, T. Freytag, L. Narayana, V. Freytag, S. Best, S. A. Whittle, J. R. Wang, Z. Reizes, O. Yu, J. S. Hazen, S. L. Brown, J. M. Bayik, D. Lathia, J. 2023-11-16 doi:10.1101/2023.11.14.567048 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Pathogenicity Prediction of GABAA Receptor Missense Variants ]]> https://biorxiv.org/content/10.1101/2023.11.14.567135v1?rss=1 Wang, Y.-J. Vu, G. H. Mu, T. 2023-11-16 doi:10.1101/2023.11.14.567135 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Differential responses of primary neuron-secreted MCP-1 and IL-9 to type 2 diabetes and Alzheimer's disease-associated metabolites ]]> https://biorxiv.org/content/10.1101/2023.11.17.567595v1?rss=1 Ball, B. K. Kuhn, M. K. Fleeman, R. M. Proctor, E. A. Brubaker, D. K. 2023-11-17 doi:10.1101/2023.11.17.567595 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ SARS-CoV-2 monoclonal antibody treatment followed by vaccination shifts human memory B cell epitope recognition suggesting antibody feedback ]]> https://biorxiv.org/content/10.1101/2023.11.21.567575v1?rss=1 Coelho, C. H. Bloom, N. Ramirez, S. I. Parikh, U. M. Heaps, A. Sieg, S. F. Greninger, A. Ritz, J. Moser, C. Eron, J. J. Currier, J. S. Klekotka, P. Wohl, D. A. Daar, E. S. Li, J. Hughes, M. D. Chew, K. W. Smith, D. M. Crotty, S. Accelerating COVID-19 Therapeutic Interventions and Vaccines: 2/A5401 (ACTIV-2/A5401) Study Team, 2023-11-22 doi:10.1101/2023.11.21.567575 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ The evolution of diverse antimicrobial responses in vancomycin-intermediate Staphylococcus aureus and its therapeutic implications ]]> https://biorxiv.org/content/10.1101/2023.11.30.569373v1?rss=1 Crozier, D. Gray, J. M. Maltas, J. A. Bonomo, R. A. Card, K. J. Scott, J. G. 2023-12-01 doi:10.1101/2023.11.30.569373 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ A Mouse Model of the Protease Activated Receptor 4 (PAR4) Pro310Leu Variant has Reduced Platelet Reactivity ]]> https://biorxiv.org/content/10.1101/2023.12.01.569075v1?rss=1 Han, X. Knauss, E. A. de la Fuente, M. Li, W. Conlon, R. A. LePage, D. F. Jiang, W. Renna, S. A. McKenzie, S. E. Nieman, M. T. 2023-12-01 doi:10.1101/2023.12.01.569075 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Mesenchymal Wnts are required for morphogenetic movements of calvarial osteoblasts during apical expansion ]]> https://biorxiv.org/content/10.1101/2023.12.05.570300v1?rss=1 Polsani, N. Yung, T. Thomas, E. C. Phung-Rojas, M. Gupta, I. Denker, J. Feng, X. Ibarra, B. Hopyan, S. Atit, R. 2023-12-05 doi:10.1101/2023.12.05.570300 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Synergistic Effects of Sulopenem in Combination with Cefuroxime or Durlobactam against Mycobacterium abscessus ]]> https://biorxiv.org/content/10.1101/2023.12.15.571879v1?rss=1 Dousa, K. M. Shin, E. Kurz, S. G. Plummer, M. Nantongo, M. Bethel, C. R. Taracila, M. A. Nguyen, D. C. Kreiswith, B. N. Daley, C. L. Remy, K. E. Holland, S. Bonomo, R. A. 2023-12-15 doi:10.1101/2023.12.15.571879 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Genome organization in double-stranded DNA viruses observed by cryoET ]]> https://biorxiv.org/content/10.1101/2023.12.15.571939v1?rss=1 Chen, M. Sahoo, B. Mou, Z. Song, X. Tsai, T. Dai, X. 2023-12-16 doi:10.1101/2023.12.15.571939 Cold Spring Harbor Laboratory Press 2023-12-16 <![CDATA[ Deciphering the co-evolutionary dynamics of L2 β-lactamases via Deep learning ]]> https://biorxiv.org/content/10.1101/2024.01.14.575584v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@1db15forg.highwire.dtl.DTLVardef@168043eorg.highwire.dtl.DTLVardef@1eebb96org.highwire.dtl.DTLVardef@5d8019_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Zhu, Y. Gu, J. Zhao, Z. Chan, A. W. E. Mojica, M. F. Hujer, A. M. Bonomo, R. A. Haider, S. 2024-01-14 doi:10.1101/2024.01.14.575584 Cold Spring Harbor Laboratory Press 2024-01-14 <![CDATA[ Temporal Dynamics of Cyanobacterial Bloom Community Composition and Toxin Production from Urban Lakes ]]> https://biorxiv.org/content/10.1101/2024.02.07.579333v1?rss=1 Maurer, J. A. Kim, A. M. Oblie, N. Hefferan, S. Xie, H. Slitt, A. Jenkins, B. D. Bertin, M. J. 2024-02-10 doi:10.1101/2024.02.07.579333 Cold Spring Harbor Laboratory Press 2024-02-10 <![CDATA[ LDL-Binding IL-10 Reduces Vascular Inflammation in Atherosclerotic Mice ]]> https://biorxiv.org/content/10.1101/2024.03.04.582839v1?rss=1 Volpatti, L. R. Norton de Matos, S. Borjas, G. Reda, J. Watkins, E. A. Zhou, Z. Nguyen, M. Solanki, A. Fang, Y. Hubbell, J. A. 2024-03-06 doi:10.1101/2024.03.04.582839 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Cell-state dependent regulation of PPARγ signaling by ZBTB9 in adipocytes ]]> https://biorxiv.org/content/10.1101/2024.03.04.583402v1?rss=1 Xu, X. Charrier, A. Congrove, S. Buchner, D. A. 2024-03-06 doi:10.1101/2024.03.04.583402 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Sarm1 is not necessary for activation of neuron-intrinsic growth programs yet required for the Schwann cell repair response and peripheral nerve regeneration. ]]> https://biorxiv.org/content/10.1101/2024.03.04.583374v1?rss=1 Schmitd, L. B. Hafner, H. Ward, A. Adib, E. A. Biscola, N. P. Kohen, R. Patel, M. Williamson, R. E. Desai, E. Bennett, J. Saxman, G. Athaiya, M. Wilborn, D. Shumpert, J. Zhao, X.-F. Kawaguchi, R. Geschwind, D. H. Hoke, A. Shrager, P. Collins, C. A. Havton, L. A. Kalinski, A. L. Giger, R. J. 2024-03-08 doi:10.1101/2024.03.04.583374 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ DR5 disulfide bonding as a sensor and effector of protein folding stress ]]> https://biorxiv.org/content/10.1101/2024.03.04.583390v1?rss=1 Law, M. E. Dulloo, Z. M. Eggleston, S. R. Takacs, G. P. Alexandrow, G. M. Wang, M. Su, H. Forsyth, B. A. Chiang, C.-W. Sharma, A. Kanumuri, S. R. R. Guryanova, O. A. Harrison, J. K. Tirosh, B. Castellano, R. K. Law, B. K. 2024-03-07 doi:10.1101/2024.03.04.583390 Cold Spring Harbor Laboratory Press 2024-03-07 <![CDATA[ To prosper, live long: understanding the sources of reproductive skew and extreme reproductive success in structured populations ]]> https://biorxiv.org/content/10.1101/2024.03.07.583934v1?rss=1 Snyder, R. E. Ellner, S. P. 2024-03-09 doi:10.1101/2024.03.07.583934 Cold Spring Harbor Laboratory Press 2024-03-09 <![CDATA[ A low-footprint, fluorescence-based bacterial time-kill assay for estimating dose-dependent cell death dynamics ]]> https://biorxiv.org/content/10.1101/2024.03.08.584154v1?rss=1 King, E. S. Stacey, A. E. Jacob, S. G. 2024-03-09 doi:10.1101/2024.03.08.584154 Cold Spring Harbor Laboratory Press 2024-03-09 <![CDATA[ Analysis of meiotic recombination in Drosophila simulans shows heterozygous inversions do not cause an interchromosomal effect ]]> https://biorxiv.org/content/10.1101/2024.03.09.584235v1?rss=1 Man, B. Kim, E. Vadlakonda, A. Stern, D. L. Crown, N. 2024-03-12 doi:10.1101/2024.03.09.584235 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ miR-644a is a tumor cell-intrinsic mediator of sex bias in glioblastoma ]]> https://biorxiv.org/content/10.1101/2024.03.11.584443v1?rss=1 Hong, E. S. Wang, S. Z. Ponti, A. K. Hajdari, N. Lee, J. Mulkearns-Hubert, E. E. Volovetz, J. Kay, K. E. Lathia, J. Dhawan, A. 2024-03-12 doi:10.1101/2024.03.11.584443 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Flies tune the sensitivity of their multifunctional gyroscope. ]]> https://biorxiv.org/content/10.1101/2024.03.13.583703v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@1296750org.highwire.dtl.DTLVardef@13dc425org.highwire.dtl.DTLVardef@185de0org.highwire.dtl.DTLVardef@1bb38de_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Verbe, A. Lea, K. M. Fox, J. L. Dickerson, B. H. 2024-03-14 doi:10.1101/2024.03.13.583703 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Toward generalizable phenotype prediction from single-cell morphology representations ]]> https://biorxiv.org/content/10.1101/2024.03.13.584858v1?rss=1 Tomkinson, J. Kern, R. Mattson, C. Way, G. P. 2024-03-13 doi:10.1101/2024.03.13.584858 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ A high-throughput zebrafish screen identifies novel candidate treatments for Kaposiform Lymphangiomatosis (KLA) ]]> https://biorxiv.org/content/10.1101/2024.03.21.586124v1?rss=1 Bassi, I. Jabali, A. Farag, N. Egozi, S. Moshe, N. Leichner, G. S. Geva, P. Levin, L. Barzilai, A. Avivi, C. Long, J. Otterstrom, J. J. Paran, Y. Barr, H. Yaniv, K. Greenberger, S. 2024-03-25 doi:10.1101/2024.03.21.586124 Cold Spring Harbor Laboratory Press 2024-03-25 <![CDATA[ Pathological C-terminal phosphomimetic substitutions alter the mechanism of liquid-liquid phase separation of TDP-43 low complexity domain ]]> https://biorxiv.org/content/10.1101/2024.03.21.586202v1?rss=1 Haider, R. Shipley, B. E. Surewicz, K. Hinczewski, M. Surewicz, W. K. 2024-03-27 doi:10.1101/2024.03.21.586202 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Rodent Gut Bacteria Coexisting with an Insect Gut Virus in Parasitic Cysts: Metagenomic Evidence of Microbial Translocation and Co-adaptation in Spatially-Confined Niches ]]> https://biorxiv.org/content/10.1101/2024.03.22.585885v1?rss=1 Ammar, A. Singh, V. Ilic, S. Samiksha, F. Marsh, A. Rodriguez-Palacios, A. 2024-03-23 doi:10.1101/2024.03.22.585885 Cold Spring Harbor Laboratory Press 2024-03-23 <![CDATA[ Analysis Pipeline to Quantify Uterine Gland Structural Variations ]]> https://biorxiv.org/content/10.1101/2024.03.24.586502v1?rss=1 Khan, S. Alessio, A. Arora, R. 2024-03-27 doi:10.1101/2024.03.24.586502 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Distinct Motor Map Characteristics for Biceps and Triceps Muscles in Persons with Chronic Tetraplegia: Implications for Arm Function ]]> https://biorxiv.org/content/10.1101/2024.03.27.585546v1?rss=1 Liu, J. Olaughlin, K. Forrest, G. F. Arora, T. Nemunaitis, G. Cunningham, D. Kirshblum, S. Pundik, S. Baker, K. Bryden, A. Kilgore, K. Bethoux, F. Wang, X. Henzel, M. K. Brihmat, N. Bayram, M. B. Plow, E. B. 2024-03-29 doi:10.1101/2024.03.27.585546 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Network medicine informed multi-omics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis ]]> https://biorxiv.org/content/10.1101/2024.03.27.586949v1?rss=1 Yu, M. Dutta, R. Trapp, B. Pieper, A. A. Cheng, F. 2024-03-30 doi:10.1101/2024.03.27.586949 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Exhaustion profile on classical monocytes after LPS stimulation in patients with Crohn's disease. ]]> https://biorxiv.org/content/10.1101/2024.03.28.587307v1?rss=1 Oliveira, L. P. Xavier, R. G. Nora, C. C. Mangueira, C. L. Rosseto, E. A. Aloia, T. Gil, J. Z. Scavanini Neto, A. Lopes, F. B. Carvalho, K. I. 2024-03-29 doi:10.1101/2024.03.28.587307 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Cross-correlation increases sampling in diffusion-based super-resolution optical fluctuation imaging ]]> https://biorxiv.org/content/10.1101/2024.04.01.587586v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@12eb1beorg.highwire.dtl.DTLVardef@975a95org.highwire.dtl.DTLVardef@bc1589org.highwire.dtl.DTLVardef@29d5bf_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Antarasen, J. Wellnitz, B. Kramer, S. N. Chatterjee, S. Kisley, L. 2024-04-02 doi:10.1101/2024.04.01.587586 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ CINner: modeling and simulation of chromosomal instability in cancer at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2024.04.03.587939v1?rss=1 Dinh, K. N. Vazquez-Garcia, I. Chan, A. Malhotra, R. Weiner, A. Mcpherson, A. Tavare, S. 2024-04-03 doi:10.1101/2024.04.03.587939 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ The Structure of the Drp1 Lattice on Membrane ]]> https://biorxiv.org/content/10.1101/2024.04.04.588123v1?rss=1 Peng, R. Rochon, K. Stagg, S. Mears, J. A. 2024-04-04 doi:10.1101/2024.04.04.588123 Cold Spring Harbor Laboratory Press 2024-04-04 <![CDATA[ A new leaf sensing organ in a predatory insect group, the praying mantises (Mantodea) ]]> https://biorxiv.org/content/10.1101/2024.04.14.589444v1?rss=1 Brannoch, S. K. Katzke, J. Taylor, D. S. Economo, E. P. Ogawa, Y. Narendra, A. Svenson, G. J. Martin, J. P. 2024-04-17 doi:10.1101/2024.04.14.589444 Cold Spring Harbor Laboratory Press 2024-04-17 <![CDATA[ Lipid Nanoparticle-Associated Inflammation is Triggered by Sensing of Endosomal Damage: Engineering Endosomal Escape without Side Effects ]]> https://biorxiv.org/content/10.1101/2024.04.16.589801v1?rss=1 Omo-Lamai, S. Wang, Y. Patel, M. N. Essien, E.-o. Shen, M. Majumder, A. Espy, C. Wu, J. Channer, B. Tobin, M. P. Murali, S. Papp, T. E. Maheshwari, R. Wang, L. Chase, L. S. Zamora, M. E. Arral, M. L. Marcos-Contreras, O. A. Myerson, J. W. Hunter, C. A. Tsourkas, A. Muzykantov, V. Brodsky, I. E. Shin, S. Whitehead, K. A. Gaskill, P. Discher, D. Parhiz, H. Brenner, J. S. 2024-04-18 doi:10.1101/2024.04.16.589801 Cold Spring Harbor Laboratory Press 2024-04-18 <![CDATA[ KIRA6 is an effective and versatile mast cell inhibitor of IgE-mediated activation ]]> https://biorxiv.org/content/10.1101/2024.04.18.589885v1?rss=1 Wilhelm, T. Wunderle, V. Boukeileh, S. Gossen, J. Margreiter, M. A. Sakurov, R. Capellmann, S. Schwoerer, M. Ahmed, N. Bronneberg, G. Arock, M. Martin, C. Schubert, T. Levi-Schaffer, F. Rossetti, G. Tirosh, B. Huber, M. 2024-04-21 doi:10.1101/2024.04.18.589885 Cold Spring Harbor Laboratory Press 2024-04-21 <![CDATA[ Droplet Hi-C for Fast and Scalable Profiling of Chromatin Architecture in Single Cells ]]> https://biorxiv.org/content/10.1101/2024.04.18.590148v1?rss=1 Chang, L. Xie, Y. Taylor, B. Wang, Z. Sun, J. Tan, T. R. Bejar, R. Chen, C. C. Furnari, F. B. Hu, M. Ren, B. 2024-04-22 doi:10.1101/2024.04.18.590148 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ In situ cell condensation-based cartilage tissue engineering via immediately implantable high-density stem cell core and rapidly degradable shell microgels ]]> https://biorxiv.org/content/10.1101/2024.04.20.590385v1?rss=1 Lee, S. J. Jeon, O. Lee, Y. B. Alt, D. S. Ding, A. Tang, R. Alsberg, E. 2024-04-25 doi:10.1101/2024.04.20.590385 Cold Spring Harbor Laboratory Press 2024-04-25 <![CDATA[ Re-examination of the taxonomic status of the Antarctic Pseudomonas syringae Lz4W isolate and proposal to rename it as a novel species Pseudomonas cryophila sp. nov. ]]> https://biorxiv.org/content/10.1101/2024.04.22.590509v1?rss=1 Ray, M. K. Pandiyan, A. Sahu, B. 2024-04-22 doi:10.1101/2024.04.22.590509 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ Metabolic immaturity of newborns and breast milk bile acids are the central determinants of heightened neonatal vulnerability to norovirus diarrhea ]]> https://biorxiv.org/content/10.1101/2024.05.01.592031v1?rss=1 Peiper, A. M. Morales, J. Phophi, L. Hu, Z. Phillips, M. Williams, C. G. Subramanian, S. Cross, M. Iyer, N. Nguyen, Q. Newsome, R. C. Jobin, C. Langel, S. N. Becker-Dreps, S. Tan, X.-D. Dawson, P. A. Helm, E. W. Bucardo, F. Karst, S. M. 2024-05-01 doi:10.1101/2024.05.01.592031 Cold Spring Harbor Laboratory Press 2024-05-01 <![CDATA[ HER4 is a high affinity dimerization partner for all EGFR/HER/ErbB-family proteins ]]> https://biorxiv.org/content/10.1101/2024.05.03.592409v1?rss=1 Singh, P. K. Kim, S. Smith, A. W. 2024-05-06 doi:10.1101/2024.05.03.592409 Cold Spring Harbor Laboratory Press 2024-05-06 <![CDATA[ Protocols for circulating neutrophil depletion in neonatal C57/Bl6 mice ]]> https://biorxiv.org/content/10.1101/2024.05.06.592835v1?rss=1 Mukherjee, D. Satyavolu, S. Thomas, A. Li, Y. Nayak, L. 2024-05-10 doi:10.1101/2024.05.06.592835 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Collagen I is a critical organizer of scarring and CNS regeneration failure ]]> https://biorxiv.org/content/10.1101/2024.05.07.592424v1?rss=1 Bi, Y. Duan, W. Silver, J. 2024-05-08 doi:10.1101/2024.05.07.592424 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Clinicogenomic characterization of inflammatory breast cancer ]]> https://biorxiv.org/content/10.1101/2024.05.07.592972v1?rss=1 Priedigkeit, N. Harrison, B. Shue, R. Hughes, M. E. Li, Y. Kirkner, G. J. Spurr, L. F. Remolano, M. C. Strauss, S. Files, J. Feeney, A.-M. Grant, L. Mohammed-Abreu, A. Garrido-Castro, A. Sousa, R. B. Bychkovsky, B. Nakhlis, F. Bellon, J. R. King, T. A. Winer, E. P. Lindeman, N. Johnson, B. E. Sholl, L. Dillon, D. Overmoyer, B. Tolaney, S. M. Cherniack, A. Lin, N. U. Lynce, F. 2024-05-10 doi:10.1101/2024.05.07.592972 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Intracranial substrates of meditation-induced neuromodulation in amygdala and hippocampus ]]> https://biorxiv.org/content/10.1101/2024.05.10.593445v1?rss=1 Maher, C. Tortolero, L. Cummins, D. Saad, A. Young, J. J. Nunez Martinez, L. Schulman, Z. Marcuse, L. Waters, A. Mayberg, H. Davidson, R. J. Saez, I. Panov, F. 2024-05-10 doi:10.1101/2024.05.10.593445 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Mitochondrial dysfunction heightens the integrated stress response to drive ALS pathogenesis ]]> https://biorxiv.org/content/10.1101/2024.05.13.594000v1?rss=1 Landry, C. A. Costanzo, J. Neto, M. M. Zatz, M. Schaffer, A. E. Hatzoglou, M. Muotri, A. R. Miranda, H. C. 2024-05-14 doi:10.1101/2024.05.13.594000 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Amyloid beta glycation leads to neuronal mitochondrial dysfunction and Alzheimers pathogenesis through VDAC1-dependent mtDNA efflux ]]> https://biorxiv.org/content/10.1101/2024.05.14.594173v1?rss=1 Akhter, F. Akhter, A. Schiff, H. Maffei, A. Zhu, X. DOUGLAS, J. Zhao, Z. Zhu, D. 2024-05-14 doi:10.1101/2024.05.14.594173 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Epidural Spinal Cord Recordings (ESRs): Sources of Artifact in Stimulation Evoked Compound Action Potentials ]]> https://biorxiv.org/content/10.1101/2024.05.17.594739v1?rss=1 Deshmukh, A. Settell, M. L. Cheng, K. L. Knudsen, B. Trevathan, J. K. LaLuzerne, M. Blanz, S. Skubal, A. Verma, N. Romanauski, B. Brucker-Hahn, M. Lam, D. Lavrov, I. Suminski, A. Weber, D. Fisher, L. Lempka, S. Shoffstall, A. Park, H. Ross Ellison, E. Zhang, M. Ludwig, K. 2024-05-17 doi:10.1101/2024.05.17.594739 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ epiTCR-KDA: Knowledge Distillation model on Dihedral Angles for TCR-peptide prediction ]]> https://biorxiv.org/content/10.1101/2024.05.18.594806v1?rss=1 Pham, M.-D. N. Su, C. T.-T. Nguyen, T.-N. Nguyen, H.-N. Nguyen, D. D. A. Giang, H. Nguyen, D.-T. Phan, M.-D. Nguyen, V. 2024-05-21 doi:10.1101/2024.05.18.594806 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Ultra-stable insulin-glucagon fusion protein exploits an endogenous hepatic switch to mitigate hypoglycemic risk ]]> https://biorxiv.org/content/10.1101/2024.05.20.594997v1?rss=1 Varas, N. Grabowski, R. Jarosinski, M. A. Tai, N. Herzog, R. I. Ismail-Beigi, F. Yang, Y. Cherrington, A. D. Weiss, M. A. 2024-05-21 doi:10.1101/2024.05.20.594997 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ An Unbiased Proteomic Platform for Activity-based Arginylation Profiling ]]> https://biorxiv.org/content/10.1101/2024.06.01.596974v1?rss=1 Lin, Z. Xie, Y. Gongora, J. Liu, X. Zahn, E. Palai, B. B. Ramirez, D. Searfoss, R. Vitorino, F. N. Dann, G. P. Zhao, C. Han, X. Mactaggart, B. Lan, X. Fu, D. Greenberg, L. Zhang, Y. Lavine, K. J. Greenberg, M. J. Lyu, D. Kashina, A. S. Garcia, B. A. 2024-06-02 doi:10.1101/2024.06.01.596974 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Time-division multiplexing (TDM) sequence removes bias in T2 estimation and relaxation-diffusion measurements ]]> https://biorxiv.org/content/10.1101/2024.06.03.597138v1?rss=1 map and on average 3.5x larger bias in the covariance between relaxation-diffusion coefficients. ConclusionOur analysis demonstrates that TDM provides a more accurate estimation of relaxation-diffusion measurements while accelerating the acquisitions by a factor of 2 to 3. ]]> Liu, Q. Gagoski, B. Shaik, I. A. Westin, C.-F. Wilde, E. A. Schneider, W. Bilgic, B. Grissom, W. Nielsen, J.-F. Zaitsev, M. Rathi, Y. Ning, L. 2024-06-03 doi:10.1101/2024.06.03.597138 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Metastasis-initiating osteosarcoma subpopulations establish paracrine interactions with both lung and tumor cells to create a metastatic niche ]]> https://biorxiv.org/content/10.1101/2024.06.09.597967v1?rss=1 Reinecke, J. B. Saraf, A. Hinckley, J. Gross, A. C. Le Pommellette, H. Jimenez Garcia, L. Cam, M. Cannon, M. V. Vatelle, S. Gryder, B. E. Dries, R. B. Roberts, R. D. 2024-06-10 doi:10.1101/2024.06.09.597967 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ An optimized and robust workflow for quantifying the canonical histone ubiquitination marks H2AK119ub and H2BK120ub by LC-MS/MS ]]> https://biorxiv.org/content/10.1101/2024.06.11.596744v1?rss=1 Lopes, M. Lund, P. Garcia, B. 2024-06-13 doi:10.1101/2024.06.11.596744 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Neuropathologically-directed profiling of PRNP somatic and germline variants in sporadic human prion disease ]]> https://biorxiv.org/content/10.1101/2024.06.25.600668v1?rss=1 5,000X across the PRNP coding region and analyzed for variants using MosaicHunter. An allele mixing experiment showed positive detection of variants in bulk DNA at a variant allele fraction (VAF) as low as 0.2%. We observed multiple polymorphic germline variants among individuals in our cohort. However, we did not identify bona fide somatic variants in sCJD, including across multiple affected regions in H-sCJD, nor in control individuals. Beyond our stringent variant-identification pipeline, we also analyzed VAFs from raw sequencing data, and observed no evidence of prion disease enrichment for the known germline pathogenic variants P102L, D178N, and E200K. The lack of PRNP pathogenic somatic mutations in H-sCJD or the broader cohort of sCJD suggests that clonal somatic mutations may not play a major role in sporadic prion disease. With H-sCJD representing a focal presentation of neurodegeneration, this serves as a test of the potential role of clonal somatic mutations in genes known to cause familial neurodegeneration. ]]> McDonough, G. A. Cheng, Y. Morillo, K. Doan, R. N. Kenny, C. J. Foutz, A. Kim, C. Cohen, M. L. Appleby, B. S. Walsh, C. A. Safar, J. G. Huang, A. Y. Miller, M. B. 2024-06-29 doi:10.1101/2024.06.25.600668 Cold Spring Harbor Laboratory Press 2024-06-29 <![CDATA[ IgM plays a prominent role in naturally acquired immunity against Plasmodium falciparum gametocytes ]]> https://biorxiv.org/content/10.1101/2024.06.30.601434v1?rss=1 Chan, J.-A. Lisboa-Pinto, A. Lu, S. Harris, A. Dixon, M. W. Thomas, A. Drew, D. R. Jayakrishnan, N. Larcher, K. Naghizadeh, M. Opi, D. H. Reiling, L. Theisen, M. Chelimo, K. Kaius-Ome, M. Mantila, D. Laman, M. Robinson, L. Mueller, I. King, C. L. Dent, A. Kazura, J. Beeson, J. 2024-07-02 doi:10.1101/2024.06.30.601434 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Connexin 43 drives glioblastoma cancer stem cell phenotypes through a WNK lysine-deficient protein kinase 1-c-MYC signaling axis ]]> https://biorxiv.org/content/10.1101/2024.07.01.601549v1?rss=1 Mulkearns-Hubert, E. E. Hajdari, N. Hong, E. S. Jacobs, A. P. Kay, K. E. Wang, S. Z. Silver, D. J. Hubert, C. G. Lathia, J. D. 2024-07-03 doi:10.1101/2024.07.01.601549 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ BATF2 is a regulator of interferon-gamma signaling in astrocytes during neuroinflammation ]]> https://biorxiv.org/content/10.1101/2024.07.10.602938v1?rss=1 Tinkey, R. A. Smith, B. C. Habean, M. L. Williams, J. L. 2024-07-16 doi:10.1101/2024.07.10.602938 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Determining potential immunomodulatory drug efficacy in sepsis using ELISpot ]]> https://biorxiv.org/content/10.1101/2024.07.10.602970v1?rss=1 Walton, A. H. Mazer, M. B. Remy, K. E. Davitt, E. B. Griffith, T. S. Gould, R. W. Badovinac, V. P. Brakenridge, S. C. Drewry, A. M. Loftus, T. J. Efron, P. A. Moldawer, L. L. Caldwell, C. C. Hotchkiss, R. S. 2024-07-16 doi:10.1101/2024.07.10.602970 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Endomucin knockout leads to delayed retinal vascular development and reduced ocular pathological neovascularization ]]> https://biorxiv.org/content/10.1101/2024.07.16.603729v1?rss=1 Hu, Z. Cano, I. Lennikov, A. Wild, M. Gupta, U. Ng, E. Y. S. D'Amore, P. 2024-07-19 doi:10.1101/2024.07.16.603729 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Systematic Analysis of Human Colorectal Cancer scRNA-seq Revealed Limited Pro-tumoral IL-17 Production Potential in Gamma Delta T Cells ]]> https://biorxiv.org/content/10.1101/2024.07.18.604156v1?rss=1 Ran, R. Trapecar, M. Brubaker, D. 2024-07-19 doi:10.1101/2024.07.18.604156 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ γ-aminobutyric acid receptor B signaling drives glioblastoma in females in an immune-dependent manner ]]> https://biorxiv.org/content/10.1101/2024.07.18.603996v1?rss=1 Pathak, A. Palasalava, S. Knott, M. V. Colon, B. Ciervo, E. Zhou, Y. Mitchell, J. Pumar, O. T. Wong, H. K. A. Zhang, L. Susic, N. Shah, K. H. Kay, K. Chin, D. Johnson, S. Cheng, F. Lyssiotis, C. A. Watson, D. C. Ceccarelli, M. Shah, A. Wahl, D. Lathia, J. Bayik, D. 2024-07-22 doi:10.1101/2024.07.18.603996 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ A Ketogenic Diet Sensitizes Pancreatic Cancer to Inhibition of Glutamine Metabolism ]]> https://biorxiv.org/content/10.1101/2024.07.19.604377v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@1ebeefforg.highwire.dtl.DTLVardef@97e2ceorg.highwire.dtl.DTLVardef@1ab45c3org.highwire.dtl.DTLVardef@1713540_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical Abstract Description: Mechanistic rationale for combining a ketogenic diet and glutamine metabolism inhibitors. The combination of low glucose from a ketogenic diet and pharmacologic glutamine inhibition impairs nutrient input to mitochondria, reducing cancer growth. ]]> Hajihassani, O. Zarei, M. Roichman, A. Loftus, A. Boutros, C. Hue, J. J. Naji, P. Boyer, J. A. Tahhan, S. Gallagher, P. Beegan, W. Choi, J. Lei, S. Kim, C. Rathore, M. Nakazzi, F. Shah, I. Lebo, K. Cheng, H. Mudigonda, A. Alibeckoff, S. Ji, K. Graor, H. J. Miyagi, M. Vaziri-Gohar, A. Brunengraber, H. Wang, R. Lund, P. Rothermel, L. D. Rabinowitz, J. D. Winter, J. M. 2024-07-23 doi:10.1101/2024.07.19.604377 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma ]]> https://biorxiv.org/content/10.1101/2024.07.23.604673v1?rss=1 Tandukar, B. Deivendran, D. Chen, L. Cruz-Pacheco, N. Sharma, H. Xu, A. Bandari, A. K. Chen, D. George, C. Marty, A. Cho, R. J. Cheng, J. Saylor, D. Gerami, P. Arron, S. T. Bastian, B. C. Shain, A. H. 2024-07-24 doi:10.1101/2024.07.23.604673 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Sepsis-induced NET formation requires MYD88 but is independent of GSDMD and PAD4 ]]> https://biorxiv.org/content/10.1101/2024.07.29.605563v1?rss=1 Renne, T. Englert, H. Rangaswamy, C. Divivier, M. Göbel, J. Hermans-Borgmeyer, I. Borgmeyer, U. Mowen, K. A. Beerens, M. Frye, M. Mailer, R. K. Gelderblom, M. Stavrou, E. Preston, R. J. Schneider, S. W. Fuchs, T. A. 2024-07-30 doi:10.1101/2024.07.29.605563 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ A biofilm-tropic Pseudomonas aeruginosa bacteriophage uses the exopolysaccharide Psl as receptor ]]> https://biorxiv.org/content/10.1101/2024.08.12.607380v1?rss=1 Walton, B. Abbodante, S. Marshall, M. E. Dobruchowska, J. M. Alvi, A. Gallagher, L. A. Vallikat, N. Zhang, Z. Wozniak, D. J. Yu, E. W. Boons, G.-J. Pearlman, E. Rietsch, A. 2024-08-12 doi:10.1101/2024.08.12.607380 Cold Spring Harbor Laboratory Press 2024-08-12 <![CDATA[ Abnormal activation of the mineralocorticoid receptor in the aldosterone-sensitive distal nephron contributes to fructose-induced salt-sensitive hypertension ]]> https://biorxiv.org/content/10.1101/2024.08.19.608663v1?rss=1 Zhang, R. Shi, S. Jadhav, D. A. Kim, N. Brostek, A. Forester, B. R. Shukla, R. Qu, C. Kramer, B. Garvin, J. L. Kleyman, T. R. Gonzalez-Vicente, A. 2024-08-20 doi:10.1101/2024.08.19.608663 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ A Novel Combinatorial Approach Integrating Experimental and Computational Analysis of Antioxidant Activity: Evaluating Catechin and L-Ascorbic Acid in Serum ]]> https://biorxiv.org/content/10.1101/2024.08.22.609135v1?rss=1 Chandra, R. Rasool, A. Chidi, C. Rigaut, S. Carty, S. Soubra-Ghaoui, C. 2024-08-23 doi:10.1101/2024.08.22.609135 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ Bronchopulmonary Dysplasia with Pulmonary Hypertension Associates with Loss of Semaphorin Signaling and Functional Decrease in FOXF1 Expression ]]> https://biorxiv.org/content/10.1101/2024.08.27.609955v1?rss=1 Shirazi, S. P. Negretti, N. M. Jetter, C. S. Sharkey, A. L. Garg, S. Kapp, M. E. Wilkins, D. Fortier, G. Mallapragada, S. Banovich, N. Wright, C. V. E. Frank, D. B. Kropski, J. A. Sucre, J. M. S. 2024-08-28 doi:10.1101/2024.08.27.609955 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Rapid synthesis and screening of natively paired antibodies against influenza hemagglutinin stem via oPool+ display ]]> https://biorxiv.org/content/10.1101/2024.08.30.610421v1?rss=1 300 uncommon influenza hemagglutinin (HA) antibodies against 9 HA variants through 16 different screens. Over 5,000 binding tests were performed in 3-5 days with further scaling potential. Follow-up structural analysis of two HA stem antibodies revealed the previously unknown versatility of IGHD3-3 gene segment in recognizing the HA stem. Overall, this study established an experimental platform that not only accelerate antibody characterization, but also enable unbiased discovery of antibody molecular signatures. ]]> Ouyang, W. O. Lv, H. Liu, W. Mou, Z. Lei, R. Pholcharee, T. Wang, Y. Dailey, K. E. Gopal, A. B. Choi, D. Ardagh, M. R. Talmage, L. Rodriguez, L. A. Dai, X. Wu, N. C. 2024-08-30 doi:10.1101/2024.08.30.610421 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Deep mutational scanning of the human insulin receptor ectodomain to inform precision therapy for insulin resistance ]]> https://biorxiv.org/content/10.1101/2024.09.07.611782v1?rss=1 Aslanzadeh, V. Brierley, G. V. Kumar, R. Cubuk, H. Vigouroux, C. Matreyek, K. A. Kudla, G. Semple, R. K. 2024-09-08 doi:10.1101/2024.09.07.611782 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ A blended genome and exome sequencing method captures genetic variation in an unbiased, high-quality, and cost-effective manner ]]> https://biorxiv.org/content/10.1101/2024.09.06.611689v1?rss=1 53,000 samples from the Populations Underrepresented in Mental Illness Associations Studies (PUMAS) Project, which included participants across African, African American, and Latin American populations. We evaluated the accuracy of BGE imputed genotypes against raw genotype calls from the Illumina Global Screening Array. All PUMAS cohorts had R2 concordance [≥]95% among SNPs with MAF[≥]1%, and never fell below [≥]90% R2 for SNPs with MAF<1%. Furthermore, concordance rates among local ancestries within two recently admixed cohorts were consistent among SNPs with MAF[≥]1%, with only minor deviations in SNPs with MAF<1%. We also benchmarked the discovery capacity of BGE to access protein-coding copy number variants (CNVs) against deep whole genome data, finding that deletions and duplications spanning at least 3 exons had a positive predicted value of [~]90%. Our results demonstrate BGE scalability and efficacy in capturing SNPs, indels, and CNVs in the human genome at 28% of the cost of deep whole-genome sequencing. BGE is poised to enhance access to genomic testing and empower genomic discoveries, particularly in underrepresented populations. ]]> Boltz, T. A. Chu, B. B. Liao, C. Sealock, J. M. Ye, R. Majara, L. Fu, J. M. Service, S. Zhan, L. Medland, S. E. Chapman, S. B. Rubinacci, S. DeFelice, M. Grimsby, J. L. Abebe, T. Alemayehu, M. Ashaba, F. K. Atkinson, E. G. Bigdeli, T. Bradway, A. B. Brand, H. Chibnik, L. B. Fekadu, A. Gatzen, M. Gelaye, B. Gichuru, S. Gildea, M. L. Hill, T. C. Huang, H. Hubbard, K. M. Injera, W. E. James, R. Joloba, M. Kachulis, C. Kalmbach, P. R. Kamulegeya, R. Kigen, G. Kim, S. Koen, N. Kwobah, E. K. Kyebuzibwa, J. Lee, S. Lennon, N. J. Lind, P. A. Lopera-Maya, E. 2024-09-09 doi:10.1101/2024.09.06.611689 Cold Spring Harbor Laboratory Press 2024-09-09 <![CDATA[ Inhibition of glutaminase elicits senolysis in therapy-induced senescent melanoma cells. ]]> https://biorxiv.org/content/10.1101/2024.09.12.612728v1?rss=1 Kim, J. Brunetti, B. Kumar, A. Mangla, A. Honda, K. Yoshida, A. 2024-09-17 doi:10.1101/2024.09.12.612728 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ Incorporating buccal mass planar mechanics and anatomical features improves neuromechanical modeling of Aplysia feeding behavior ]]> https://biorxiv.org/content/10.1101/2024.09.17.613591v1?rss=1 Bennington, M. J. Liao, A. S. Sukhnandan, R. Kundu, B. Rogers, S. M. Gill, J. P. McManus, J. M. Sutton, G. P. Chiel, H. J. Webster-Wood, V. A. 2024-09-19 doi:10.1101/2024.09.17.613591 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Safeguarding Privacy in Genome Research: A Comprehensive Framework for Authors ]]> https://biorxiv.org/content/10.1101/2024.09.20.614092v1?rss=1 Ghasemian, M. Gerido, L. H. Ayday, E. 2024-09-24 doi:10.1101/2024.09.20.614092 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Heterogeneous Kinetics of Nanobubble Ultrasound Contrast Agent and Angiogenic Signaling in Head and Neck Cancer ]]> https://biorxiv.org/content/10.1101/2024.09.22.614362v1?rss=1 Van Court, B. Ciccaglione, M. Neupert, B. Knitz, M. W. Maroney, S. P. Nguyen, D. Abdelazeem, K. N. M. Exner, A. A. Saviola, A. J. Benninger, R. K. P. Karam, S. D. 2024-09-24 doi:10.1101/2024.09.22.614362 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Skeletal Metastasis of Prostate Cancer Is Augmented by Activation of EphA2 Noncanonical Signaling and Ligand-Deficient Bone Microenvironment ]]> https://biorxiv.org/content/10.1101/2024.09.25.615079v1?rss=1 Wang, B. Lingerak, R. Petty, A. Shi, X. Kim, S. Lin, H. Hsieh, J.-T. Tang, D. Stiles, B. Wald, D. Varambally, S. Chinnaiyan, A. M. Lee, Z. Morrissey, C. 2024-09-27 doi:10.1101/2024.09.25.615079 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Distinct neuroendocrine subtypes predict treatment-induced neuroendocrine prostate cancer prognosis and provide clues for personalized treatment ]]> https://biorxiv.org/content/10.1101/2024.09.28.615561v1?rss=1 Hong, Y.-C. Tsai, C.-H. Tze-Yun, H. Hsu, C.-S. Peng, Y.-C. Chen, W. Huang, W. J. Lin, T.-P. Chang, P.-C. 2024-09-30 doi:10.1101/2024.09.28.615561 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Sex differences in colonic inflammation are driven by epithelial-specific expression of estrogen receptor alpha ]]> https://biorxiv.org/content/10.1101/2024.09.28.615598v1?rss=1 Pereda, G. A. Kocinski, A. D. Broncano, A. V. McNeer, S. K. Raymond, M. L. Ziats, N. P. Breau, K. A. Burclaff, J. Magness, S. T. Goodman, W. A. 2024-09-30 doi:10.1101/2024.09.28.615598 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Sex differences in the clinical manifestation of autosomal dominant frontotemporal dementia ]]> https://biorxiv.org/content/10.1101/2024.10.01.614851v1?rss=1 Memel, M. Staffaroni, A. Ilan-Gala, I. Garcia Castro, J. Kornak, J. Tartaglia, C. Saloner, R. VandeBunte, A. Paolillo, E. Cadwallader, C. Chen, C. Gorno-Tempini, M. L. Mandelli, M. Apostolova, L. Graff-Radford, N. Litvan, I. Bayram, E. Pressman, P. Miyagawa, T. Mackenzie, I. Goldman, J. Darby, R. Appleby, B. Petrucelli, L. Gendron, T. Heuer, H. Forseberg, L. Rojas, J. Boeve, B. Brushaber, N. Domoto-Reilly, K. Ghoshal, N. Lapid, M. Pascual, B. Lee, S. Ramos, E. Ramanan, V. Rademakers, R. Rascovsky, K. Pantelyat, A. Masdeu, J. Snyder, A. Boxer, A. Rosen 2024-10-03 doi:10.1101/2024.10.01.614851 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Novel murine model of human astrovirus infection reveals a cardiovascular tropism ]]> https://biorxiv.org/content/10.1101/2024.10.03.616429v1?rss=1 10-fold in heart tissue or serum samples from Rag1 or Stat1 knockout mice, demonstrating the role of both adaptive and innate immunity in the response to VA1 infection. Based on the in vivo tropisms, we also tested cardiac-derived primary cells and determined that VA1 can replicate in human cardiac microvascular and coronary artery endothelial cells, suggesting a novel cardiovascular tropism in human cells. This novel in vivo model of a human-infecting astrovirus enables further characterization of viral pathogenesis and reveals a new cardiovascular tropism of astroviruses. Author SummaryAstroviruses typically cause viral diarrhea in humans but can also cause serious infections of the brain. Previously, the methods available to study how these viruses lead to invasive infections were limited. Here, we describe the first system to study human-infecting astroviruses using mice. We demonstrate that mice are susceptible to astrovirus VA1, a strain that commonly infects humans and has been linked to fatal brain infections. The virus infected heart tissue and was associated with inflammation. When mice with impaired immune systems were infected with VA1, they were found to have higher amounts of virus in their hearts and blood. Linking back to human health, we also found that VA1 can infect cells derived from human blood vessels of the heart. This model will enable us to better understand how astroviruses cause disease and how the immune system responds to infection. Our findings also suggest that astroviruses could be linked to cardiovascular diseases, including in humans. In the future, we can develop interventions that will prevent and treat astrovirus infections in humans. ]]> Owen, M. C. Zhou, Y. Dudley, H. Feehley, T. Hahn, A. Yokoyama, C. C. Axelrod, M. L. Lin, C.-Y. Wang, D. Janowski, A. B. 2024-10-03 doi:10.1101/2024.10.03.616429 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Neuropeptide-dependent spike time precision and plasticity in circadian output neurons ]]> https://biorxiv.org/content/10.1101/2024.10.06.616871v1?rss=1 Chong, B. Kumar, V. Nguyen, D. L. Hopkins, M. A. Spera, L. K. Paul, E. M. Hutson, A. N. Tabuchi, M. 2024-10-07 doi:10.1101/2024.10.06.616871 Cold Spring Harbor Laboratory Press 2024-10-07 <![CDATA[ A Method for Electrical Stimulus Artifact Removal Exploiting Neural Refractoriness: Validation by Contrasting Cathodic and Anodic Stimulation ]]> https://biorxiv.org/content/10.1101/2024.10.06.616879v1?rss=1 Nakhmani, A. Block, J. Awad, M. Olson, J. Smith, R. J. Bentley, N. J. Holland, M. T. Brinkerhoff, S. A. Gonzalez, C. L. Moffitt, M. Walker, H. C. 2024-10-07 doi:10.1101/2024.10.06.616879 Cold Spring Harbor Laboratory Press 2024-10-07 <![CDATA[ Computational Microbiome Pharmacology Analysis Elucidates the Anti-Cancer Potential of Vaginal Microbes and Metabolites ]]> https://biorxiv.org/content/10.1101/2024.10.10.616351v1?rss=1 Lawore, D. C. Jena, S. Berard, A. R. Birse, K. Lamont, A. Mackelprang, R. D. Noel-Romas, L. Perner, M. Hou, X. Irungu, E. Mugo, N. Knodel, S. Muwonge, T. R. Katabira, E. Hughes, S. M. Levy, C. Calienes, F. L. Baeten, J. M. Celum, C. Hladik, F. Lingappa, J. R. Burgener, A. D. Green, L. N. Brubaker, D. K. 2024-10-11 doi:10.1101/2024.10.10.616351 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Mice with Reduced PAR4 Reactivity show Decreased Venous Thrombosis and Platelet Procoagulant Activity ]]> https://biorxiv.org/content/10.1101/2024.10.14.617127v1?rss=1 Knauss, E. A. Guci, J. Luc, N. Disharoon, D. Huang, G. H. Sen Gupta, A. Nieman, M. T. 2024-10-17 doi:10.1101/2024.10.14.617127 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Gut bacteria-derived succinate induces enteric nervous system regeneration ]]> https://biorxiv.org/content/10.1101/2024.10.15.618589v1?rss=1 Aydin, B. Mamede, I. Cardoso, J. Deere, J. Alvarez, Y. Qiao, S. Sharma, V. P. Scavuzzo, M. A. Donaldson, G. P. Guo, C.-J. Mucida, D. 2024-10-18 doi:10.1101/2024.10.15.618589 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Methylation Clocks Do Not Predict Age or Alzheimer's Disease Risk Across Genetically Admixed Individuals ]]> https://biorxiv.org/content/10.1101/2024.10.16.618588v1?rss=1 Cruz-Gonzalez, S. Gu, E. Gomez, L. Mews, M. Vance, J. M. Cuccaro, M. L. Cornejo-Olivas, M. R. Feliciano-Astacio, B. E. Byrd, G. S. Haines, J. L. Pericak-Vance, M. A. Griswold, A. J. Bush, W. S. Capra, J. A. 2024-10-18 doi:10.1101/2024.10.16.618588 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum ]]> https://biorxiv.org/content/10.1101/2024.10.17.618979v1?rss=1 Vereau Gorbitz, D. Schwarz, C. McMullen, J. G. Ceron-Romero, M. Doyle, R. T. Lau, J. A. Whitaker, R. J. Vanderpool, C. K. Heath, K. 2024-10-22 doi:10.1101/2024.10.17.618979 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ African origin haplotype protective for Alzheimer's disease in APOEϵ4 carriers: exploring potential mechanisms ]]> https://biorxiv.org/content/10.1101/2024.10.24.619909v1?rss=1 Bertholim-Nasciben, L. Nuytemans, K. Van Booven, D. Rajabli, F. Moura, S. Ramirez, A. M. Dykxhoorn, D. M. Wang, L. Scott, W. K. Davis, D. D. Vontell, R. T. McInerney, K. F. Cuccaro, M. L. Byrd, G. S. Haines, J. L. Gearing, M. Adams, L. D. Pericak-Vance, M. A. ADSP (Alzheimers Disease Sequencing Project), Young, J. I. Griswold, A. J. Vance, J. M. 2024-10-27 doi:10.1101/2024.10.24.619909 Cold Spring Harbor Laboratory Press 2024-10-27 <![CDATA[ A Reinforcement Learning-based Approach for Dynamic Privacy Protection in Genomic Data Sharing Beacons ]]> https://biorxiv.org/content/10.1101/2024.10.28.620587v1?rss=1 Poorghaffar Aghdam, M. Shukueian Tabrizi, S. Ayoz, K. Ayday, E. Sav, S. Cicek, A. E. 2024-10-31 doi:10.1101/2024.10.28.620587 Cold Spring Harbor Laboratory Press 2024-10-31 <![CDATA[ Functionally Important Residues from Graph Analysis of Coevolved Dynamic couplings ]]> https://biorxiv.org/content/10.1101/2024.10.30.621065v1?rss=1 Xu, M. Dantu, S. C. Garnett, J. A. Bonomo, R. A. Pandini, A. Haider, S. 2024-11-02 doi:10.1101/2024.10.30.621065 Cold Spring Harbor Laboratory Press 2024-11-02 <![CDATA[ Axonal injury signaling is restrained by a spared synaptic branch ]]> https://biorxiv.org/content/10.1101/2024.11.07.622420v1?rss=1 Smithson, L. J. Zang, J. L. Junginger, L. Waller, T. J. Reilly-Jankowiak, L. Khan, S. Li, Y. Cai, D. Collins, C. A. 2024-11-07 doi:10.1101/2024.11.07.622420 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ Multi-omic latent variable data integration reveals multicellular structure pathways associated with resistance to tuberculin skin test (TST)/interferon gamma release assay (IGRA) conversion in Uganda ]]> https://biorxiv.org/content/10.1101/2024.11.05.622020v1?rss=1 Cox, M. S. Dill-McFarland, K. A. Simmons, J. D. Benchek, P. Mayanja-Kizza, H. Boom, W. H. Stein, C. M. Hawn, T. R. 2024-11-08 doi:10.1101/2024.11.05.622020 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ How do body size and habitat fragmentation influence extinction in lizards? A long-term case study on artificial islands in the Brazilian Cerrado ]]> https://biorxiv.org/content/10.1101/2024.11.05.622112v1?rss=1 Miranda, R. B. Abbott, K. C. Martin, R. A. Brandao, R. A. 2024-11-08 doi:10.1101/2024.11.05.622112 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Basal cell of origin resolves neuroendocrine-tuft lineage plasticity in cancer ]]> https://biorxiv.org/content/10.1101/2024.11.13.623500v1?rss=1 Ireland, A. S. Hawgood, S. B. Xie, D. A. Barbier, M. W. Lucas-Randolph, S. Tyson, D. R. Zuo, L. Y. Witt, B. L. Govindan, R. Dowlati, A. Moser, J. C. Puri, S. Rudin, C. M. Chan, J. M. Elliott, A. Oliver, T. G. 2024-11-15 doi:10.1101/2024.11.13.623500 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Cerebellar white matter development is regulated by fractalkine-dependent microglia phagocytosis of oligodendrocyte progenitor cells ]]> https://biorxiv.org/content/10.1101/2024.11.15.620441v1?rss=1 Chappell, M. K. Shelestak, J. Irfan, M. Shelestak, E. Nemes-Baran, A. D. Mey, G. M. DeSilva, T. M. 2024-11-17 doi:10.1101/2024.11.15.620441 Cold Spring Harbor Laboratory Press 2024-11-17 <![CDATA[ Neural correlates of kinematic features of passive finger movement revealed by univariate and multivariate fMRI analyses ]]> https://biorxiv.org/content/10.1101/2024.11.20.624514v1?rss=1 Pamplona, G. S. P. Sulzer, J. Beldzik, E. Lambercy, O. Ionta, S. Gassert, R. Lewis-Peacock, J. A. 2024-11-21 doi:10.1101/2024.11.20.624514 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Unraveling SARS-CoV-2 Host-Response Heterogeneity through Longitudinal Molecular Subtyping ]]> https://biorxiv.org/content/10.1101/2024.11.22.624784v1?rss=1 Wang, K. Nie, Y. Maguire, C. Syphurs, C. Sheen, H. Karoly, M. Lapp, L. Gygi, J. P. Jayavelu, N. D. Patel, R. K. Hoch, A. IMPACC Network, Corry, D. Kheradmand, F. McComsey, G. A. Fernandez-Sesma, A. Simon, V. Metcalf, J. P. Agudelo Higuita, N. I. Messer, W. B. David, M. M. Nadeau, K. C. Kraft, M. Bime, C. Schaenman, J. Erle, D. Calfee, C. S. Atkinson, M. A. Brackenridge, S. C. Hafler, D. A. Shaw, A. C. Rahman, A. Hough, C. L. Geng, L. N. Ozonoff, A. Haddad, E. K. Reed, E. F. Bakel, H. v. Kim-Schulze, S. H. Krammer, F. Wilson, M. Eckalbar, W. Bosinger, 2024-11-25 doi:10.1101/2024.11.22.624784 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Elucidating the dynamics of Integrin αIIb3 from native platelet membranes by cryo-EM with build and retrieve method ]]> https://biorxiv.org/content/10.1101/2024.11.27.625729v1?rss=1 Han, X. Zhang, Z. Su, C.-c. Lyu, M. Miyagi, M. Yu, E. W. Nieman, M. T. 2024-11-27 doi:10.1101/2024.11.27.625729 Cold Spring Harbor Laboratory Press 2024-11-27 <![CDATA[ GABRA1 frameshift variants impair GABAA receptor proteostasis ]]> https://biorxiv.org/content/10.1101/2024.11.28.625971v1?rss=1 Williams, M. P. Wang, Y.-J. Kang, J.-Q. Mu, T. 2024-11-29 doi:10.1101/2024.11.28.625971 Cold Spring Harbor Laboratory Press 2024-11-29 <![CDATA[ Cell-Cell Fusion in NSCLC Confers a Fitness Benefit Under Drug Selection ]]> https://biorxiv.org/content/10.1101/2024.12.02.626399v1?rss=1 Shultes, P. V. Tadele, D. S. Durmaz, A. Weaver, D. T. Barker-Clarke, R. Dinh, M. N. Liu, S. Alemu, E. A. Rayner, S. Scott, J. G. 2024-12-02 doi:10.1101/2024.12.02.626399 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ ST6GAL1-mediated sialyl linkage switching in tumor-associated macrophages drives cancer-promoting nanotubes carrying α2,6-sialylation in anti-inflammatory cells ]]> https://biorxiv.org/content/10.1101/2024.11.28.625934v1?rss=1 Dipta, P. Bansal, N. Sumer-Bayraktar, Z. Chien, A. Ugonotti, J. Chau, T. H. Anugraham, M. Kolarich, D. Tirosh, B. Kawahara, R. Thaysen-Andersen, M. 2024-12-03 doi:10.1101/2024.11.28.625934 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Two distinct durable human class-switched memory B cell populations are induced by vaccination and infection ]]> https://biorxiv.org/content/10.1101/2024.11.29.624972v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@169c77forg.highwire.dtl.DTLVardef@1a872f5org.highwire.dtl.DTLVardef@1360cforg.highwire.dtl.DTLVardef@38d7ed_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Perugino, C. Liu, H. Feldman, J. Marbourg, J. Guy, T. Hui, A. Ingram, N. Liebaert, J. Chaudhary, N. Tao, W. Jacob-Dolan, C. Hauser, B. M. Mian, Z. Nathan, A. Zhao, Z. Kaseke, C. Tano-Menka, R. Getz, M. Senjobe, F. Berrios, C. Ofoman, O. Manickas-Hill, Z. Wesemann, D. Lemieux, J. Goldberg, M. B. Nundel, K. Moormann, A. M. Marshak-Rothstein, A. Larocque, R. Ryan, E. Iafrate, A. J. Lingwood, D. Gaiha, G. Charles, R. Balazs, A. B. Pandit, A. Naranbhai, V. Schmidt, A. Pillai, S. 2024-12-04 doi:10.1101/2024.11.29.624972 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ Vaccines for immunological defense against traumatic brain injury ]]> https://biorxiv.org/content/10.1101/2024.12.02.626331v1?rss=1 Acharya, A. P. Stabenfeldt, S. E. 2024-12-05 doi:10.1101/2024.12.02.626331 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Tokenvizz: GraphRAG-Inspired Tokenization Tool for Genomic Data Discovery and Visualization ]]> https://biorxiv.org/content/10.1101/2024.12.03.626631v1?rss=1 Oguztuzun, C. Gao, Z. Xu, R. 2024-12-06 doi:10.1101/2024.12.03.626631 Cold Spring Harbor Laboratory Press 2024-12-06 <![CDATA[ High KIR diversity in Uganda and Botswana children living with HIV ]]> https://biorxiv.org/content/10.1101/2024.12.03.626612v1?rss=1 John, M. Kyobe, S. Amujal, M. Katagirya, E. Diphoko, T. Sebetso, G. Mwesigwa, S. Mboowa, G. Retshabile, G. Williams, L. Mogomotsi, M. Mlotshwa, B. Jjingo, D. kateete, D. P. Joloba, M. Mardon, G. Hanchard, N. Hollenbach, J. A. 2024-12-07 doi:10.1101/2024.12.03.626612 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ UltimateSynth: MRI Physics for Pan-Contrast AI ]]> https://biorxiv.org/content/10.1101/2024.12.05.627056v1?rss=1 Adams, R. Zhao, W. Hu, S. Lyu, W. Huynh, K. M. Ahmad, S. Ma, D. Yap, P.-T. 2024-12-10 doi:10.1101/2024.12.05.627056 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ Personalizing chemotherapy drug selection using a novel transcriptomic chemogram ]]> https://biorxiv.org/content/10.1101/2024.12.17.628754v1?rss=1 Lin-Rahardja, K. Scarborough, J. Scott, J. G. 2024-12-20 doi:10.1101/2024.12.17.628754 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ PRLX-93936 and BMS-214662 are cytotoxic molecular glues that leverage TRIM21 to degrade nucleoporins ]]> https://biorxiv.org/content/10.1101/2024.12.18.629219v1?rss=1 Scemama de Gialluly, M. A. Allen, A. R. Hayes, E. H. Zhuang, P. Goldfarb, R. B. Farrar, A. N. Fedorov, Y. Adams, D. J. 2024-12-21 doi:10.1101/2024.12.18.629219 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ Regulation of epigenetics and chromosome structure by human ORC2 ]]> https://biorxiv.org/content/10.1101/2024.12.18.629220v1?rss=1 Su, Z. Tian, M. Shibata, E. Shibata, Y. Yang, T. Wang, Z. Jin, F. Zang, C. Dutta, A. 2024-12-21 doi:10.1101/2024.12.18.629220 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ Inverted topologies in sequential fitness landscapes enable evolutionary control ]]> https://biorxiv.org/content/10.1101/2024.12.29.630702v1?rss=1 Chen, P. Krishnan, N. Stacy, A. Weaver, D. T. Barker-Clarke, R. Hinczewski, M. Maltas, J. A. Scott, J. G. 2024-12-30 doi:10.1101/2024.12.29.630702 Cold Spring Harbor Laboratory Press 2024-12-30 <![CDATA[ Rev-RRE activity modulates HIV-1 replication and latency reactivation: Implications for viral persistence and cure strategies ]]> https://biorxiv.org/content/10.1101/2025.01.06.631466v1?rss=1 Dzhivhuho, G. A. Jackson, P. E. H. Honeycutt, E. S. Mesquita, F. d. S. Huang, J. Hammarskjold, M.-L. Rekosh, D. 2025-01-06 doi:10.1101/2025.01.06.631466 Cold Spring Harbor Laboratory Press 2025-01-06 <![CDATA[ RhCMV Expands CCR5 Memory T Cells and promotes SIV reservoir seeding in the Gut Mucosa ]]> https://biorxiv.org/content/10.1101/2025.01.06.631163v1?rss=1 Perdios, C. Suresh Babu, N. Coleman, C. D. Brown, A. T. Mostrom, M. J. Allers, C. Doyle-Meyers, L. Fennessey, C. M. Keele, B. F. Kaur, A. Freeman, M. L. Mudd, J. C. 2025-01-08 doi:10.1101/2025.01.06.631163 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ Mitoxantrone inhibits and downregulates ERα through binding at the DBD-LBD interface ]]> https://biorxiv.org/content/10.1101/2025.01.07.631371v1?rss=1 Wang, H. Luo, Y. Artham, S. Wang, Q. Peng, Y. Yun, Z. Li, X. Wu, C. Liu, Z. Weber-Bonk, K. L. Pai, C.-P. Cao, Y. Yue, J. Park, S. Keri, R. A. Geng, L. McDonnell, D. P. Kao, H.-Y. Yang, S. 2025-01-08 doi:10.1101/2025.01.07.631371 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ Cholesterol-Dependent Dimerization and Conformational Dynamics of EphA2 Receptors: Insights from Coarse-Grained and All-Atom Simulations ]]> https://biorxiv.org/content/10.1101/2025.01.07.631553v1?rss=1 Sahoo, A. R. Bhattarai, N. Buck, M. 2025-01-10 doi:10.1101/2025.01.07.631553 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ Susceptibility of bovine respiratory and mammary epithelial cells to avian and mammalian derived clade 2.3.4.4b H5N1 highly pathogenic avian influenza viruses ]]> https://biorxiv.org/content/10.1101/2025.01.09.632235v1?rss=1 Meliopoulos, V. A. Cherry, S. Smith, M. Sharp, B. Brigleb, P. H. Roubidoux, E. K. Livingston, B. Morris, D. R. Ripperger, T. Baker, P. Gragg, S. Dimitrov, K. M. Langel, S. Schultz-Cherry, S. 2025-01-10 doi:10.1101/2025.01.09.632235 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ A GluN2B disease-associated variant promotes degradation of NMDA receptors via autophagy ]]> https://biorxiv.org/content/10.1101/2025.01.12.632651v1?rss=1 Benske, T. M. Williams, M. P. Zhang, P.-P. Palumbo, A. J. Mu, T. 2025-01-13 doi:10.1101/2025.01.12.632651 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Cytosolic transport of citrate protects nutrient-austere pancreatic cancer from ferroptosis ]]> https://biorxiv.org/content/10.1101/2025.01.15.633097v1?rss=1 Kneebone, A. Lindaur, K. Abbas, A. Cassel, J. Graff, S. Abood, G. Ding, X. Small, W. Tatsuoka, C. Sidoli, S. Salvino, J. M. Vaziri-Gohar, A. 2025-01-17 doi:10.1101/2025.01.15.633097 Cold Spring Harbor Laboratory Press 2025-01-17 <![CDATA[ Single-cell digital twins identify drug targets and repurposable medicine in Alzheimers disease ]]> https://biorxiv.org/content/10.1101/2025.01.14.633081v1?rss=1 Ren, Y. Hu, M. Li, Y. E. Pieper, A. A. Cummings, J. Cheng, F. 2025-01-20 doi:10.1101/2025.01.14.633081 Cold Spring Harbor Laboratory Press 2025-01-20 <![CDATA[ Dynamic activity of Erg promotes aging of the hematopoietic system ]]> https://biorxiv.org/content/10.1101/2025.01.23.634563v1?rss=1 Yano, M. Sugden, W. Wang, D. Badalamenti, B. Cote, P. Chin, D. Goldstein, J. George, S. Rodrigues-Luiz, G. F. da Rocha, E. L. Li, H. North, T. Gryder, B. Rowe, G. 2025-01-23 doi:10.1101/2025.01.23.634563 Cold Spring Harbor Laboratory Press 2025-01-23 <![CDATA[ Impact of infusion conditions and anesthesia on CSF tracer dynamics in mouse brain ]]> https://biorxiv.org/content/10.1101/2025.01.21.634133v1?rss=1 Zhu, Y. Zhu, J. Ni, C. Chen, A. Li, L. Gao, Y. Shoffstall, A. J. Yu, X. 2025-01-24 doi:10.1101/2025.01.21.634133 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Ultra-deep sequencing of somatic mutations induced by a maize transposon ]]> https://biorxiv.org/content/10.1101/2025.01.22.634239v1?rss=1 Scherer, J. Hinczewski, M. Nelms, B. 2025-01-24 doi:10.1101/2025.01.22.634239 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Lambda N as a model substrate for studying the mechanism of Escherichia coli ATP-dependent protease Lon as a regulatory enzyme. ]]> https://biorxiv.org/content/10.1101/2025.01.24.634763v1?rss=1 Castro, M. Lee, S. Lee, I. 2025-01-25 doi:10.1101/2025.01.24.634763 Cold Spring Harbor Laboratory Press 2025-01-25 <![CDATA[ Comprehensive mutational characterization of the calcium-sensing STIM1 EF-hand reveals residues essential for structure and function ]]> https://biorxiv.org/content/10.1101/2025.01.23.634525v1?rss=1 Kamath, N. D. Matreyek, K. A. 2025-01-26 doi:10.1101/2025.01.23.634525 Cold Spring Harbor Laboratory Press 2025-01-26 <![CDATA[ The Pseudomonas aeruginosa T3SS can contribute to traversal of an in situ epithelial multilayer independently of the T3SS needle ]]> https://biorxiv.org/content/10.1101/2025.01.28.635263v1?rss=1 Jedel, E. Schator, D. Kumar, N. G. Sullivan, A. B. Rietsch, A. Evans, D. J. Fleiszig, S. M. J. 2025-01-29 doi:10.1101/2025.01.28.635263 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ Development of itaconate polymer microparticles for intracellular regulation of pro-inflammatory macrophage activation ]]> https://biorxiv.org/content/10.1101/2025.01.30.635692v1?rss=1 Woodworth, K. E. Froom, Z. S. C. S. Osborne, N. D. Rempe, C. N. Wheeler, B. Medd, K. Callaghan, N. I. Qian, H. Acharya, A. P. Charron, C. Huyer, L. D. 2025-02-05 doi:10.1101/2025.01.30.635692 Cold Spring Harbor Laboratory Press 2025-02-05 <![CDATA[ Cryo-EM structures reveal the PP2A-B55α and Eya3 interaction that can be disrupted by a peptide inhibitor ]]> https://biorxiv.org/content/10.1101/2025.02.04.636346v1?rss=1 Shi, S. Li, X. Alderman, C. Huang, W. Wick, L. Foulon, N. Rossi, J. Hu, W. Cui, S. Zheng, H. Taylor, D. J. Ford, H. L. Zhao, R. 2025-02-05 doi:10.1101/2025.02.04.636346 Cold Spring Harbor Laboratory Press 2025-02-05 <![CDATA[ The conserved N-terminal SANT1-binding domain (SBD) of EZH2 Regulates PRC2 Activity ]]> https://biorxiv.org/content/10.1101/2025.02.04.636462v1?rss=1 Patriotis, A. L. Soto-Feliciano, Y. Barrows, D. Khan, L. Leboeuf, M. Lund, P. Marunde, M. R. Djomo, A. Keogh, M.-C. Carroll, T. Garcia, B. Soshnev, A. A. Allis, C. D. 2025-02-05 doi:10.1101/2025.02.04.636462 Cold Spring Harbor Laboratory Press 2025-02-05 <![CDATA[ Fatty Acid Transport Protein-2 (FATP2) Inhibition Enhances Glucose Tolerance through α-Cell-mediated GLP-1 Secretion ]]> https://biorxiv.org/content/10.1101/2025.01.31.635976v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@190c799org.highwire.dtl.DTLVardef@203076org.highwire.dtl.DTLVardef@14dbf26org.highwire.dtl.DTLVardef@140869e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Khan, S. Gaivin, R. J. Liu, Z. Li, V. Samuels, I. Son, J. Osei-Owusu, P. Garvin, J. L. Accili, D. Schelling, J. R. 2025-02-06 doi:10.1101/2025.01.31.635976 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ Rumenomics: Evaluation of rumen metabolites from healthy sheep identifies differentially produced metabolites across sex, age, and weight ]]> https://biorxiv.org/content/10.1101/2025.02.05.636747v1?rss=1 Munoz-Briones, J. Ball, B. K. Jena, S. Lescun, T. B. Chan, D. D. Brubaker, D. K. 2025-02-08 doi:10.1101/2025.02.05.636747 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Lineage plasticity of the integrated stress response is a hallmark of cancer evolution. ]]> https://biorxiv.org/content/10.1101/2025.02.10.637516v1?rss=1 Diao, S. Zou, J. Y. Wang, S. Ghaddar, N. Chan, J. E. Kim, H. Poulain, N. Koumenis, C. Hatzoglou, M. Walter, P. Sonenberg, N. Le Quesne, J. Tammela, T. Koromilas, A. E. 2025-02-13 doi:10.1101/2025.02.10.637516 Cold Spring Harbor Laboratory Press 2025-02-13 <![CDATA[ Mobile genetic elements that shape microbial diversity and functions inthawing permafrost soils ]]> https://biorxiv.org/content/10.1101/2025.02.12.637893v1?rss=1 Guo, J. Aroney, S. Dominguez-Huerta, G. Smith, D. Vik, D. Ansah, C. O. Pratama, A. A. Solonenko, S. Tian, F. Howard-Varona, C. Zhong, Z. Fofana, A. Smith, G. Hodgkins, S. B. Cronin, D. EMERGE Field Teams 2010-2019, EMERGE Coordinators, Woodcroft, B. J. Tyson, G. W. Rich, V. I. Sullivan, M. B. Roux, S. Bagby, S. C. 2025-02-13 doi:10.1101/2025.02.12.637893 Cold Spring Harbor Laboratory Press 2025-02-13 <![CDATA[ Identification of a multi-omics factor predictive of long COVID in the IMPACC study ]]> https://biorxiv.org/content/10.1101/2025.02.12.637926v1?rss=1 500 hospitalized COVID-19 patients in the IMPACC cohort to identify a multi-omics "recovery factor". IMPACC participants who experienced LC had lower recovery factor scores compared to participants without LC. Biologic characterization revealed increased levels of plasma proteins associated with inflammation, elevated transcriptional signatures of heme metabolism, and decreased androgenic steroids in LC patients. The recovery factor was also associated with altered circulating immune cell frequencies. Notably, recovery factor scores were predictive of LC occurrence in patients as early as hospital admission, irrespective of acute disease severity. Thus, the recovery factor identifies patients at risk of LC early after SARS-CoV-2 infection and reveals LC biomarkers and potential treatment targets. ]]> Gabernet, G. Maciuch, J. Gygi, J. P. Moore, J. F. Hoch, A. Syphurs, C. Chu, T. Jayavelu, N. D. Corry, D. B. Kheradmand, F. Baden, L. R. Sekaly, R.-P. McComsey, G. A. Haddad, E. K. Cairns, C. B. Rouphael, N. Fernandez-Sesma, A. Simon, V. Metcalf, J. P. Agudelo Higuita, N. I. Hough, C. L. Messer, W. B. Davis, M. M. Nadeau, K. C. Pulendran, B. Kraft, M. Bime, C. Reed, E. F. Schaenman, J. Erle, D. J. Calfee, C. S. Atkinson, M. A. Brackenridge, S. C. Melamed, E. Shaw, A. C. Hafler, D. A. Ozonoff, A. Bosinger, S. E. Eckalbar, W. Maecker, H. T. Kim-Schulze, S. 2025-02-14 doi:10.1101/2025.02.12.637926 Cold Spring Harbor Laboratory Press 2025-02-14 <![CDATA[ SLICK: A Sandwich-LIke Culturing Kit for in situ Cryo-ET Sample Preparation ]]> https://biorxiv.org/content/10.1101/2025.02.14.638381v1?rss=1 Li, Q. Zhang, L. Xu, Q. Zhang, P. Zhu, S. 2025-02-16 doi:10.1101/2025.02.14.638381 Cold Spring Harbor Laboratory Press 2025-02-16 <![CDATA[ Targeting the ClpP-αSynuclein Interaction with a Decoy Peptide to Mitigate Neuropathology in Parkinson's Disease Models ]]> https://biorxiv.org/content/10.1101/2025.02.16.638540v1?rss=1 Hu, D. Sun, X. Qi, X. 2025-02-21 doi:10.1101/2025.02.16.638540 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ Computational Translation of Mouse Models of Osteoarthritis Predicts Human Disease ]]> https://biorxiv.org/content/10.1101/2025.02.23.639777v1?rss=1 Frost, M. R. Ball, B. K. Pendyala, M. Douglas, S. R. Brubaker, D. K. Chan, D. D. 2025-02-28 doi:10.1101/2025.02.23.639777 Cold Spring Harbor Laboratory Press 2025-02-28 <![CDATA[ Restoration of ovarian endocrine function with encapsulated immune isolated human ovarian xenograft in ovariectomized mice ]]> https://biorxiv.org/content/10.1101/2025.02.27.640622v1?rss=1 Brunette, M. Wall, M. Sinko, D. Machlin, J. Blevins, G. Leo, M. Ta, A. Ray, B. Cascalho, M. Padmanabhan, V. Shikanov, A. 2025-03-03 doi:10.1101/2025.02.27.640622 Cold Spring Harbor Laboratory Press 2025-03-03 <![CDATA[ Mechanism of CO2 and NH3 Transport through Human Aquaporin 1: Evidence for Parallel CO2 Pathways ]]> https://biorxiv.org/content/10.1101/2025.02.28.640247v1?rss=1 Musa-Aziz, R. Geyer, R. R. Moss, F. J. Boron, W. F. 2025-03-03 doi:10.1101/2025.02.28.640247 Cold Spring Harbor Laboratory Press 2025-03-03 <![CDATA[ Three-dimensional tissue platform co-laid with native collagen fibers and cells for phenotypic screening of stem cell interactions ]]> https://biorxiv.org/content/10.1101/2025.02.28.640824v1?rss=1 Tang, R. Ding, A. Fu, C. Umerori, K. Rivera, M. Alt, D. S. Carmean, C. M. Li, L. Eppell, S. Wynshaw-Boris, A. Alsberg, E. 2025-03-06 doi:10.1101/2025.02.28.640824 Cold Spring Harbor Laboratory Press 2025-03-06 <![CDATA[ Role of channels in the O2 permeabilityof murine red blood cells. I. Stopped-flow and hematological studies ]]> https://biorxiv.org/content/10.1101/2025.03.05.639948v1?rss=1 Zhao, P. Moss, F. J. Occhipinti, R. Geyer, R. R. Huffmann, D. E. Meyerson, H. J. Boron, W. F. 2025-03-10 doi:10.1101/2025.03.05.639948 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Role of channels in the O2 permeability of murine red blood cells II. Morphological and proteomic studies ]]> https://biorxiv.org/content/10.1101/2025.03.05.639962v1?rss=1 Moss, F. J. Zhao, P. Salameh, A. I. Taki, S. Wass, A. B. Jacobberger, J. W. Huffman, D. E. Meyerson, H. J. Occhipinti, R. Boron, W. F. 2025-03-10 doi:10.1101/2025.03.05.639962 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Alternative polyadenylation regulates human urothelial differentiation ]]> https://biorxiv.org/content/10.1101/2025.03.03.641311v1?rss=1 Le, N. B. Sona, S. Santo, B. Schweickart, R. A. Kochat, V. Padron, W. Rai, K. Lee, S.-H. Yi, J. M. Wessely, O. Lee, B. H. Ting, A. H. 2025-03-11 doi:10.1101/2025.03.03.641311 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Missense variants in GABAA receptor beta2 subunit disrupt receptor biogenesis and cause loss of function ]]> https://biorxiv.org/content/10.1101/2025.03.09.642292v1?rss=1 C), I246T (c. 737T>C), and I299S (c. 896T>G). HEK293T cells exogenously expressing these {beta}2 variants exhibited significantly reduced GABA-induced peak chloride current, indicating their loss of function. However, the four {beta}2 EAVs differed in the degree of proteostasis deficiencies, including increased ER retention, compromised assembly, decreased protein stability, and reduced trafficking and surface expression, with Q209F210delinsH and R240T variants leading to the most severe degradation. Collectively, these results indicate that these epilepsy-linked variants have debilitating effects on the early biogenesis of the {beta}2 subunit, causing misfolding, aggregation, and rapid degradation before it can be assembled with other subunits and transported to the plasma membrane. Overall, our work offers crucial mechanistic insight into how specific {beta}2 missense variants impact the proteostasis maintenance of GABAARs, which could facilitate the development of effective therapeutics for genetic epilepsy by targeting trafficking-deficient GABAAR variants. ]]> Chen, X. Wang, Y.-J. Mu, T. 2025-03-11 doi:10.1101/2025.03.09.642292 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Autism risk genes converge on PBX1 to govern neural cell growth ]]> https://biorxiv.org/content/10.1101/2025.03.12.642693v1?rss=1 Fu, S. Wynshaw-Boris, A. 2025-03-13 doi:10.1101/2025.03.12.642693 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Single-Cell Analysis Reveals Tissue-Specific T Cell Adaptation and Clonal Distribution Across the Human Gut-Liver-Blood Axis ]]> https://biorxiv.org/content/10.1101/2025.03.11.642626v1?rss=1 Ran, R. Uslu, M. Siddiqui, M. F. Brubaker, D. Trapecar, M. 2025-03-14 doi:10.1101/2025.03.11.642626 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ The denitrosylase SCoR2 controls cardioprotective metabolic reprogramming ]]> https://biorxiv.org/content/10.1101/2025.03.12.642752v1?rss=1 View larger version (51K): org.highwire.dtl.DTLVardef@72bfbborg.highwire.dtl.DTLVardef@189cbc4org.highwire.dtl.DTLVardef@1a0cc51org.highwire.dtl.DTLVardef@1c61004_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Grimmett, Z. W. Zhang, R. Zhou, H.-L. Chen, Q. Miller, D. Qian, Z. Lin, J. Kalra, R. Gross, S. Koch, W. J. Premont, R. T. Stamler, J. S. 2025-03-14 doi:10.1101/2025.03.12.642752 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Computation model predicts Rho GTPase function with the Plexin Transmembrane receptor GAP activity on Rap1b via dynamic allosteric changes ]]> https://biorxiv.org/content/10.1101/2025.03.13.643120v1?rss=1 Bhattarai, N. Morrison, L. Gomes, A. F. Savage, P. Sahoo, A. R. Buck, M. 2025-03-15 doi:10.1101/2025.03.13.643120 Cold Spring Harbor Laboratory Press 2025-03-15 <![CDATA[ Replicative selfish genetic elements are driving rapid pathogenic adaptation of Enterococcus faecium ]]> https://biorxiv.org/content/10.1101/2025.03.16.643550v1?rss=1 Grieshop, M. P. Behr, A. A. Bowden, S. Lin, J. D. Molari, M. Reynolds, G. Z. Brooks, E. F. Doyle, B. Rodriguez-Nava, G. Salinas, J. L. Banaei, N. Bhatt, A. S. 2025-03-16 doi:10.1101/2025.03.16.643550 Cold Spring Harbor Laboratory Press 2025-03-16 <![CDATA[ In Vivo Multiplexed Modeling Reveals Diverse Roles of the TBX2 Subfamily and Egr1 in Ras-Driven Lung Adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2025.03.15.642187v1?rss=1 Khalil, A. Dinh, T. Parks, M. Obeng, R. Gryder, B. Kersak, A. Wang, Y. Maltas, J. Bedrock, M. Wei, X. Faber, Z. Rahm, M. Scott, J. LaFramboise, T. Wang, Z. McFarland, C. D. 2025-03-17 doi:10.1101/2025.03.15.642187 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ Comparative Metabolomic Analysis of Vaginal Microbiota in Planktonic and Biofilm States Unveils Species-Specific Metabolic Signatures ]]> https://biorxiv.org/content/10.1101/2025.03.21.644638v1?rss=1 Jena, S. Lawore, D. C. Green, L. N. Brubaker, D. 2025-03-21 doi:10.1101/2025.03.21.644638 Cold Spring Harbor Laboratory Press 2025-03-21 <![CDATA[ Inherent Specificity and Mutational Sensitivity as Quantitative Metrics for RBP Binding ]]> https://biorxiv.org/content/10.1101/2025.03.28.646018v1?rss=1 Yi, S. Singh, S. S. Ye, X. Krishna, R. Jankowsky, E. Luna, J. M. 2025-04-01 doi:10.1101/2025.03.28.646018 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Cathepsin Z is a conserved susceptibility factor underlying tuberculosis severity ]]> https://biorxiv.org/content/10.1101/2025.04.01.644622v1?rss=1 Meade, R. K. Adefisayo, O. O. Gontijo, M. T. P. Harris, S. J. Pyle, C. J. Wilburn, K. M. Ecker, A. M. V. Hughes, E. J. Garcia, P. D. Ivie, J. McHenry, M. L. Benchek, P. H. Mayanja-Kizza, H. Neff, J. L. Ko, D. C. Stout, J. E. Stein, C. M. Hawn, T. R. Tobin, D. M. Smith, C. M. 2025-04-01 doi:10.1101/2025.04.01.644622 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Pre-Clinical Evaluation of a Novel Immunomodulator: a potential immunotherapy for coronaviral disease ]]> https://biorxiv.org/content/10.1101/2025.04.01.646433v1?rss=1 Lee, I. Desai, A. Berdis, A. J. Patil, A. Xu, Y. Pozza-Adams, K. 2025-04-02 doi:10.1101/2025.04.01.646433 Cold Spring Harbor Laboratory Press 2025-04-02 <![CDATA[ Mapping the spatial architecture of glioblastoma from core to edge delineates niche-specific tumor cell states and intercellular interactions ]]> https://biorxiv.org/content/10.1101/2025.04.04.647096v1?rss=1 Khan, S. M. Wang, A. Z. Desai, R. R. McCornack, C. R. Sun, R. Dahiya, S. M. Foltz-Stringfellow, J. Sherpa, N. D. Leavitt, L. West, T. R. Wang, A. F. Krbanjevic, A. Choi, B. D. Leuthardt, E. C. Patel, B. Charest, A. Kim, A. H. Dunn, G. P. Petti, A. A. 2025-04-04 doi:10.1101/2025.04.04.647096 Cold Spring Harbor Laboratory Press 2025-04-04 <![CDATA[ Transcriptional downregulation of rhodopsin is associated with desensitization of rods to light-induced damage in a murine model of retinitis pigmentosa. ]]> https://biorxiv.org/content/10.1101/2025.04.03.646684v1?rss=1 Takita, S. Harikrishnan, H. Miyagi, M. Imanishi, Y. 2025-04-05 doi:10.1101/2025.04.03.646684 Cold Spring Harbor Laboratory Press 2025-04-05 <![CDATA[ Phenylhydrazone-based Endoplasmic Reticulum Proteostasis Regulator Compounds with Enhanced Biological Activity ]]> https://biorxiv.org/content/10.1101/2025.04.04.646800v1?rss=1 Kline, G. M. Boinon, L. Guerrero, A. Kutseikin, S. Cruz, G. Williams, M. P. Paxman, R. J. Balch, W. E. Kelly, J. W. Mu, T. Wiseman, L. 2025-04-05 doi:10.1101/2025.04.04.646800 Cold Spring Harbor Laboratory Press 2025-04-05 <![CDATA[ Pyruvate kinase deficiency links metabolic perturbations to neurodegeneration and axonal protection ]]> https://biorxiv.org/content/10.1101/2025.04.04.647282v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@1bba464org.highwire.dtl.DTLVardef@25bdd2org.highwire.dtl.DTLVardef@1d12611org.highwire.dtl.DTLVardef@1a3d96_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Waller, T. J. Collins, C. A. Dus, M. 2025-04-05 doi:10.1101/2025.04.04.647282 Cold Spring Harbor Laboratory Press 2025-04-05 <![CDATA[ Mechanism of clinically relevant neurosecretory and metabolic impairment in Alzheimers and identification of engineered nanotherapy ]]> https://biorxiv.org/content/10.1101/2025.04.09.647859v1?rss=1 Shang, Y. Cho, W. J. Munj, S. A. Jena, S. G. Arslanturk, S. Patil, S. R. Qi, X. Jena, B. P. 2025-04-10 doi:10.1101/2025.04.09.647859 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Gut Microbe-Derived N-Acyl Serinol Lipids Shape Host Postprandial Metabolic Homeostasis ]]> https://biorxiv.org/content/10.1101/2025.04.11.648385v1?rss=1 Dutta, S. Mahen, K. K. Massey, W. J. Varadharajan, V. Burrows, A. Horak, A. J. Mrdjen, M. Mouannes, N. Orabi, D. Osborn, L. Grubb, T. Hohe, R. Banerjee, R. Uppin, V. Laungani, D. Hamilton, G. Ye, X. Sangwan, N. Dwidar, M. Hajjar, A. Willard, B. Martin, M. Guetschow, E. Westcott, P. Wang, Z. Hazen, S. L. Brown, J. M. 2025-04-17 doi:10.1101/2025.04.11.648385 Cold Spring Harbor Laboratory Press 2025-04-17 <![CDATA[ 15-PGDH inhibition promotes hematopoietic recovery and enhances HSC function during aging ]]> https://biorxiv.org/content/10.1101/2025.04.11.648417v1?rss=1 View larger version (18K): org.highwire.dtl.DTLVardef@1952ad9org.highwire.dtl.DTLVardef@30169aorg.highwire.dtl.DTLVardef@11bec0corg.highwire.dtl.DTLVardef@2617c8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chaudhary, R. Cordova, B. A. Hong, M. Klein, B. R. Contreras, L. A. Rashmil, R. Goshevski, F. Smith, J. N. Taylor, D. Pieper, A. A. Markowitz, S. D. Desai, A. B. 2025-04-17 doi:10.1101/2025.04.11.648417 Cold Spring Harbor Laboratory Press 2025-04-17 <![CDATA[ Enhanced delivery of lipid nanoparticle-based immunotherapy by modulating the tumor tissue stiffness using ultrasound-activated nanobubbles ]]> https://biorxiv.org/content/10.1101/2025.04.13.648512v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@da7fborg.highwire.dtl.DTLVardef@8f5f27org.highwire.dtl.DTLVardef@b002f6org.highwire.dtl.DTLVardef@19265da_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Bhalotia, A. Nittayacharn, P. Mehta, M. Iyer, A. Hutchinson, D. W. Cheplyansky, A. Takizawa, K. Nidhiry, A. Gopalakrishnan, R. Kosmides, T. Exner, A. A. Karathanasis, E. 2025-04-19 doi:10.1101/2025.04.13.648512 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ Kinocilia of Vestibular Hair Cells: Bridging Structural and Functional Traits of Primary and Motile Cilia ]]> https://biorxiv.org/content/10.1101/2025.04.16.647417v1?rss=1 Xu, Z. Tavakoli, A. Kulasooriya, S. Liu, H. Tu, S. Bloom, C. Li, Y. Zuo, J. Tao, L. Kachar, B. He, D. Z. Z. 2025-04-21 doi:10.1101/2025.04.16.647417 Cold Spring Harbor Laboratory Press 2025-04-21 <![CDATA[ Isolation and characterization of TayeBlu, a novel bacteriophage of Azotobacter vinelandii ]]> https://biorxiv.org/content/10.1101/2025.04.23.650044v1?rss=1 Akanbi, T. M. Labat, M. Sun, T. Smith, D. A. Bagby, S. C. 2025-04-23 doi:10.1101/2025.04.23.650044 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Increasing Stemness Drives Prostate Cancer Progression, Plasticity, Therapy Resistance and Poor Patient Survival ]]> https://biorxiv.org/content/10.1101/2025.04.27.650697v1?rss=1 Liu, X. Cortes, E. Ji, Y. Zhao, K. Ho, J. Liu, Y. S. Davicioni, E. Feng, F. Y. Alumkal, J. J. Spratt, D. E. Sweeney, C. J. Yu, H. Hu, Q. Cheng, Z. Zhang, D. Chatta, G. Nastiuk, K. L. Goodrich, D. W. Rycaj, K. Jamroze, A. Kirk, J. S. Puzanov, I. Liu, S. Wang, J. Tang, D. G. 2025-04-30 doi:10.1101/2025.04.27.650697 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Kozak sequence libraries for characterizing transgenes across expression levels ]]> https://biorxiv.org/content/10.1101/2025.04.28.651141v1?rss=1 Shukla, N. Kamath, N. D. Snell, J. C. Bruchez, A. M. Matreyek, K. A. 2025-04-30 doi:10.1101/2025.04.28.651141 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ HIV infection in microglia leads to senescence, triggering activation of neurotoxicity pathways ]]> https://biorxiv.org/content/10.1101/2025.05.08.651477v1?rss=1 Mason, S. J. Sreeram, S. Niazi, F. Leskov, K. Levine, A. D. Karn, J. Valadkhan, S. 2025-05-08 doi:10.1101/2025.05.08.651477 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Personalized Gut-Liver Microphysiological System Maps Donor-Specific Tissue Resident Immunity and Reveals a Conserved Metabolic Crosstalk ]]> https://biorxiv.org/content/10.1101/2025.05.05.652244v1?rss=1 Uslu, M. Ran, R. Siddiqui, M. F. Liang, J. Raechal, L. Dogsa, M. Perrot, C. Lieberman, L. A. Brubaker, D. K. Trapecar, M. 2025-05-10 doi:10.1101/2025.05.05.652244 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ In vivo tracking of CAR-T cells in tumors via nanobubble-based contrastenhanced ultrasound ]]> https://biorxiv.org/content/10.1101/2025.05.06.651695v1?rss=1 Durig, D. Franklin, J. Perera, R. Jackson, Z. Vasanna, H. Kolios, M. Wald, D. Exner, A. A. 2025-05-10 doi:10.1101/2025.05.06.651695 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ A Mechanism Based Pharmacokinetic/Pharmacodynamic Analysis of Polymyxin B-Based Combination Therapy Against Carbapenem-Resistant Klebsiella pneumoniae Isolates with Diverse Phenotypic and Genotypic Resistance Mechanisms ]]> https://biorxiv.org/content/10.1101/2025.05.06.652358v1?rss=1 73% reduction in area under the bacterial load-versus-time curve for four isolates. The triple combination showed 67.7% reduction in non-carbapenamase producing isolate. This study demonstrates that a low dosing regimen of PMB can produce synergistic effects in combination therapy and might be effective in managing infections caused by CRKP, including PMB resistant isolates. Author summaryAntimicrobial resistance is a major concern in treating infectious diseases. CRKP bacterial isolates are resistant to most of the novel antimicrobial agents. One of the primary resistant mechanisms is restricting the permeability of drugs to the site of action. Polymyxin B, an antimicrobial agent, disrupts the bacterial outer membrane, enhancing the permeability of other drugs. When using combination therapy with polymyxin B, selecting drugs with different mechanisms of action is crucial to enhance synergistic effects and improve treatment efficacy. In our study we chose to evaluate the efficacy of meropenem and fosfomycin in double and triple combination therapies. Mechanism based models (MBMs) are the strongest tool to analyse the time course bacterial load data. Our study provides insights into applying available phenotypic and genotypic information to refine and enhance the accuracy of MBMs. Final model simulations revealed that low exposure of polymyxin B below the nephrotoxic threshold was sufficient to produce synergistic effects when combined with fosfomycin and meropenem. Additionally, we found that polymyxin B combination with fosfomycin was more effective compared to meropenem in treating CRKP. ]]> Mahadevan, R. Garcia, E. Sharma, R. Qiu, H. Elsheikh, A. Parambi, R. Abboud, C. S. Pasteran, F. Ramirez, M. S. Kaye, K. S. Bonomo, R. A. Rao, G. G. 2025-05-10 doi:10.1101/2025.05.06.652358 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ APOE genotype confers context dependent neurovascular vulnerability in immune-vascularized human forebrain organoids ]]> https://biorxiv.org/content/10.1101/2025.05.08.652864v1?rss=1 Fang, H. Liao, X. Bullen, C. K. Pu, R. Wang, H. Condoleo, J. Cheat, S. Chen, X. Zhang, Y. Zhang, S. Huo, D. Lissit, K. Yang, A. Jarvis, K. Neifert, S. Huang, Y. Bishai, W. Jain, S. K. Dawson, T. Dawson, V. L. Xu, J. 2025-05-10 doi:10.1101/2025.05.08.652864 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ Short chain fatty acids regulate the chromatin landscape and distinct gene expression changes in human colorectal cancer cells ]]> https://biorxiv.org/content/10.1101/2025.05.07.652677v1?rss=1 Kabir, T. Connamacher, C. A. Nadeem, Z. Paul, M. R. Smutny, M. R. Lawler, Z. K. Djomo, A. M. Carroll, T. Gates, L. A. 2025-05-13 doi:10.1101/2025.05.07.652677 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ H3K79 methylation and H3K36 tri-methylation synergistically regulate gene expression in pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2025.05.08.652740v1?rss=1 Cooke, E. W. Zeng, C. Nur, S. M. Jia, Y. Huang, A. Chen, J. Gao, P. CHEN, F. X. Jin, F. Cao, K. 2025-05-13 doi:10.1101/2025.05.08.652740 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Large Language Models Can Extract Metadata for Annotation of Human Neuroimaging Publications ]]> https://biorxiv.org/content/10.1101/2025.05.13.653828v1?rss=1 Turner, M. D. Appaji, A. Ar Rakib, N. Golnari, P. Rajasekar, A. K. Rathnam K V, A. Sahoo, S. S. Wang, Y. Wang, L. Turner, J. A. 2025-05-14 doi:10.1101/2025.05.13.653828 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ PML1-Mediated Feedforward Loop Through PI3K and MAPK Axes Drives Endocrine Resistance ]]> https://biorxiv.org/content/10.1101/2025.05.15.653365v1?rss=1 Wang, H. Yun, Z. Cao, Y. Li, X. Liu, Z. Pai, C.-P. Wu, C. Yue, J. Lin, G. Cai, J. Willard, B. Yang, S. Keri, R. A. Schiemann, W. P. Diehl, J. A. Kao, H.-Y. 2025-05-16 doi:10.1101/2025.05.15.653365 Cold Spring Harbor Laboratory Press 2025-05-16 <![CDATA[ DJ-1 deficiency and aging: dual drivers of retinal mitochondrial dysfunction. ]]> https://biorxiv.org/content/10.1101/2025.05.19.654941v1?rss=1 Upadhyay, M. Sturgis, J. Bhattacharyya, S. Jiang, K. Hagstrom, S. A. Bonilha, V. L. 2025-05-21 doi:10.1101/2025.05.19.654941 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Single-Cell Analysis of Meningiomas Reveals Mutation-Associated Tumor and Immune Cell Gene Expression Programs ]]> https://biorxiv.org/content/10.1101/2025.05.21.655421v1?rss=1 Maldonado, J. A. Mashimo, B. L. Wang, A. Z. Desai, R. Khan, S. M. Sherpa, N. D. Anzaldua-Campos, M. I. Zipfel, G. J. Kim, A. H. Dowling, J. L. Leuthardt, E. C. Osbun, J. W. Vellimana, A. K. Chicoine, M. R. Dunn, G. P. Petti, A. A. 2025-05-24 doi:10.1101/2025.05.21.655421 Cold Spring Harbor Laboratory Press 2025-05-24 <![CDATA[ Repurposing Romidepsin for Osteosarcoma: Screening FDA-Approved Oncology Drugs with Three-Dimensional Osteosarcoma Spheroids ]]> https://biorxiv.org/content/10.1101/2025.05.22.654354v1?rss=1 Seiden, E. E. Richardson, S. Everitt, L. A. Knafler, G. J. Kinsella, G. P. Walker, A. L. Whiteside, V. A. Buschbach, J. D. Gandhi, D. A. Saadatzadeh, M. R. Wurtz, L. D. Getty, P. J. Padgett, S. L. Gamblin, R. M. Childress, M. O. Fulkerson, C. M. Pollok, K. E. Collier, C. D. Greenfield, E. M. 2025-05-24 doi:10.1101/2025.05.22.654354 Cold Spring Harbor Laboratory Press 2025-05-24 <![CDATA[ Prevalence of sympathetic fibers within the rat cervical vagus, and functional consequence on physiological effects mediated by vagus nerve stimulation (VNS). ]]> https://biorxiv.org/content/10.1101/2025.05.21.655349v1?rss=1 Deshmukh, A. Chen, R. C.-H. Chin, J. Knudsen, B. Trevathan, J. Shoffstall, A. Ludwig, K. 2025-05-27 doi:10.1101/2025.05.21.655349 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Not all alloantibodies are created equal: IgG glycosylation and severity of antibody-mediated rejection in kidney transplantation ]]> https://biorxiv.org/content/10.1101/2025.05.28.656600v1?rss=1 Noble, J. Glendenning, L. M. Dard, C. Bourdin, A. Carlson, G. C. Cobb, B. A. Cravedi, P. 2025-05-30 doi:10.1101/2025.05.28.656600 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Doxycycline Release From Cyclodextrin Oligomer-Containing Collagen Gels ]]> https://biorxiv.org/content/10.1101/2025.05.28.656660v1?rss=1 Trout, E. Palomo, L. von Recum, H. A. Eppell, S. J. 2025-06-01 doi:10.1101/2025.05.28.656660 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ A missense mutation in Muc2 promotes gut microbiome- and metabolome-dependent colitis-associated tumorigenesis. ]]> https://biorxiv.org/content/10.1101/2025.05.31.657160v1?rss=1 Verna, G. De Santis, S. Islam, B. Sommella, E. M. Licastro, D. Zhang, L. De Almeida Celio, F. Merciai, F. Caponigro, V. Campiglia, P. Pizarro, T. T. Chieppa, M. Cominelli, F. 2025-06-03 doi:10.1101/2025.05.31.657160 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ TGF-β serves as a critical signaling determinant of liver progenitor cell fate and function ]]> https://biorxiv.org/content/10.1101/2025.06.04.657336v1?rss=1 Tong, C. Lin, T. Wang, H. La Torre, C. D. Liu, H. Shao, C. Hammad, S. Liebe, R. Ebert, M. P. Ding, H. Dooley, S. Weng, H.-L. 2025-06-05 doi:10.1101/2025.06.04.657336 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ Astrocyte reprogramming drives tumor progression and chemotherapy resistance in agent-based models of breast cancer brain metastases ]]> https://biorxiv.org/content/10.1101/2025.06.05.654750v1?rss=1 Kaur, R. Barker-Clarke, R. Dhawan, A. 2025-06-06 doi:10.1101/2025.06.05.654750 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ DDX3X acts as a selective dual switch regulator of mRNA translation in acute ER stress ]]> https://biorxiv.org/content/10.1101/2025.06.08.658532v1?rss=1 Shawky, A.-E.-M. A. Scarboro, A. Mick, J. Dondeti, M. Avanzino, K. Simintiras, C. Hatzoglou, M. Vourekas, A. 2025-06-09 doi:10.1101/2025.06.08.658532 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Murine peritoneal macrophages undergo female-specific remodeling with aging ]]> https://biorxiv.org/content/10.1101/2025.06.11.659200v1?rss=1 Lu, R. J. Chen, S. Kim, M. Sampathkumar, N. K. Lee, E. H. Christensen, A. Wang, E. E. Lau, I. Y. Parihar, S. Ravikumar, C. K. Jung, J. Brown, S. B. Xu, A. Alvarenga, J. L. Mehalko, K. Lee, C. D. Goodridge, H. S. Benayoun, B. A. 2025-06-17 doi:10.1101/2025.06.11.659200 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Cortical sculpting of a rhythmic motor program ]]> https://biorxiv.org/content/10.1101/2025.06.20.660772v1?rss=1 Kirk, E. A. Cai, K. Sauerbrei, B. A. 2025-06-21 doi:10.1101/2025.06.20.660772 Cold Spring Harbor Laboratory Press 2025-06-21 <![CDATA[ Structures of MmpL complexes reveal the assembly and mechanism of this family of transporters ]]> https://biorxiv.org/content/10.1101/2025.06.22.660944v1?rss=1 Zhang, Z. Maharjan, R. Gregor, W. D. Klenotic, P. A. Yu, E. W. 2025-06-22 doi:10.1101/2025.06.22.660944 Cold Spring Harbor Laboratory Press 2025-06-22 <![CDATA[ Neuromechanical Simulation with NEURON and MuJoCo ]]> https://biorxiv.org/content/10.1101/2025.06.17.660217v1?rss=1 Fietkiewicz, C. Tran, L. McDougal, R. Jackson, C. Quinn, R. D. Chiel, H. J. Thomas, P. J. 2025-06-26 doi:10.1101/2025.06.17.660217 Cold Spring Harbor Laboratory Press 2025-06-26 <![CDATA[ DrugLM: A Unified Framework to Enhance Drug-Target Interaction Predictions by Incorporating Textual Embeddings via Language Models ]]> https://biorxiv.org/content/10.1101/2025.07.09.657250v1?rss=1 Li, T. Fang, Z. Zhang, X. Tang, K. Chen, H. Jiang, Z. Zhao, T. Xu, R. Cheng, F. Li, X. Li, J. 2025-07-11 doi:10.1101/2025.07.09.657250 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ Using spatial statistics to infer game-theoretic interactions in an agent-based model of cancer cells ]]> https://biorxiv.org/content/10.1101/2025.07.09.664005v1?rss=1 Leither, S. Strobl, M. Scott, J. G. Dolson, E. 2025-07-15 doi:10.1101/2025.07.09.664005 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ Controlling treatment toxicity in ovarian cancer to prime the patient for tumor extinction therapy ]]> https://biorxiv.org/content/10.1101/2025.07.10.664235v1?rss=1 50%), most eventually succumb to their disease due to high recurrence rates, acquired resistance, and cumulative toxicity. This report summarizes work from the 12th IMO Workshop in which we explored an alternative "extinction therapy" strategy for frontline treatment of HGSOC. Inspired by ecological principles, this multi-strike approach aims to eradicate tumors not through a singular "magic bullet" but through a series of therapies after standard frontline treatment when the tumor is still, and perhaps most, vulnerable. We present a framework leveraging mathematical modeling (MM) to develop personalized multi-strike protocols for HGSOC. Key contributions include: 1) An "IMOme" score using liquid biopsy data to assess patient-specific hematopoietic toxicity risk, guiding the timing and selection of subsequent therapies, 2) MM strategies to design effective lowdose combinations of targeted agents to achieve synthetic lethality while managing toxicity, and 3) A MM framework to analyze the interplay between chemotherapy, gut microbiome toxicity, and immunotherapy, demonstrating how mitigating microbiome damage could enhance immune response. Overall, the computational approaches presented herein aim to support the design of personalized, multi-strike regimens in the frontline setting that proactively target tumor extinction while managing toxicity, ultimately seeking to deliver cures for patients with HGSOC. ]]> Gallagher, K. Sousa, R. S. Gatenbee, C. D. Schenck, R. Chen, P. Citak, T. Leither, S. Mazzacurati, L. Xella, A. Zhou, Z. Lemanne, D. Rodriguez, P. George, E. Strobl, M. A. R. 2025-07-16 doi:10.1101/2025.07.10.664235 Cold Spring Harbor Laboratory Press 2025-07-16 <![CDATA[ Improving causal effect estimation in multi-ancestry multivariable Mendelian randomization with transfer learning ]]> https://biorxiv.org/content/10.1101/2025.07.11.664423v1?rss=1 Yang, Y. Zhu, X. 2025-07-17 doi:10.1101/2025.07.11.664423 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Cell type-specific master metabolic regulators of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.07.11.664443v1?rss=1 Qiu, Y. Hou, Y. Wetzel, L. Caldwell, J. Z. K. Zhu, X. Pieper, A. A. Liu, T. Cheng, F. 2025-07-17 doi:10.1101/2025.07.11.664443 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Oral microbial signatures of head and neck cancer patients highlight diverse longitudinal patterns of oral mucositis severity ]]> https://biorxiv.org/content/10.1101/2025.07.15.665024v1?rss=1 Kodikara, S. Mao, J. San Valentin, E. M. D. Do, K.-A. Reyes-Gibby, C. Le Cao, K.-A. 2025-07-18 doi:10.1101/2025.07.15.665024 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Selective life-long suppression of an odor processing channel in response to critical period experience ]]> https://biorxiv.org/content/10.1101/2025.07.18.665601v1?rss=1 Leier, H. C. Jonaitis, J. Foden, A. J. Wilkov, A. J. Ross, A. E. Van der Linden Costello, P. Broihier, H. T. Dacks, A. M. 2025-07-20 doi:10.1101/2025.07.18.665601 Cold Spring Harbor Laboratory Press 2025-07-20 <![CDATA[ Distinct antibody-based signatures and functionality distinguish latent and active pediatric tuberculosis ]]> https://biorxiv.org/content/10.1101/2025.07.21.665984v1?rss=1 Nziza, N. Jung, W. Chen, T. Deng, Y. Franken, K. L. Ottenhoff, T. H. M. Kiguli, S. Lewinsohn, D. Boom, W. H. Mayanja-Kizza, H. Nsereko, M. Fortune, S. M. Stein, C. McNamara, R. Alter, G. Lancioni, C. L. 2025-07-24 doi:10.1101/2025.07.21.665984 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Metabolic dysfunction promoted by mitochondrial DNA mutation burden drives retinal degeneration ]]> https://biorxiv.org/content/10.1101/2025.07.30.667736v1?rss=1 Sturgis, J. Jiang, K. Hagstrom, S. Moorthy, M. Bonilha, V. L. 2025-07-31 doi:10.1101/2025.07.30.667736 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Loss of NRMT1 allows expression of multiple differentiation pathways and alters transcription of secreted proteins in C2C12 myoblasts ]]> https://biorxiv.org/content/10.1101/2025.07.29.667488v1?rss=1 Tooley, J. G. Zhou, G. Forster, J. Jones, C. Tedeschi, F. Tooley, C. E. S. 2025-08-01 doi:10.1101/2025.07.29.667488 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ A sustained Hox program delineates brainstem neurons essential for breathing ]]> https://biorxiv.org/content/10.1101/2025.08.01.668179v1?rss=1 Moore, M. T. Lin, M. Vagnozzi, A. N. Lopez de Boer, R. Brozost, E. M. Jeannotte, L. Lindsay, S. Philippidou, P. 2025-08-01 doi:10.1101/2025.08.01.668179 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Comprehensive Transcriptomic and Epigenomic Insights into Environmental Toxicant Exposures: The TaRGET II Resource ]]> https://biorxiv.org/content/10.1101/2025.07.28.667191v1?rss=1 Zhang, B. A. Miao, B. Fu, S. Coarfa, C. Kumar, R. Kuntala, P. K. Park, B. Colacino, J. A. Svobada, L. K. Shao, W. Xing, X. Li, D. Liu, S. Hamanaka, R. B. Lalancette, C. Sartor, M. A. Krapp, C. Crawford, G. E. Patisaul, H. B. Wiltshire, T. Aylor, D. L. Biswal, S. Mutlu, G. M. Rajagopalan, S. Tang, W.-Y. Dolinoy, D. C. Wang, T. Bartolomei, M. S. Walker, C. L. Grimm, S. L. Ruiz-Echartea, E. Katz, T. Jangid, R. 2025-08-02 doi:10.1101/2025.07.28.667191 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ The Lipid Hydrolase ABHD6 is a Therapeutic Target in Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD)-Related Hepatocellular Carcinoma ]]> https://biorxiv.org/content/10.1101/2025.07.29.667509v1?rss=1 Orabi, D. Massey, W. Fung, K. Varadharajan, V. Ramachandiran, I. Banerjee, R. Silver, D. J. Osborn, L. J. Brown, A. L. Marshall, S. Ferguson, D. Cao, S. Schugar, R. C. Finney, C. Neumann, C. Burrows, A. C. Horak, A. J. Pathak, P. Helsley, R. N. Bulfon, D. Zimmermann, R. Leung, Y. H. Madiraju, S. R. M. Prentki, M. Lee, R. G. Mullick, A. E. Zergeeva, O. Dasarathy, S. Lee, Z. Allende, D. S. Aucejo, F. Lathia, J. D. Brown, J. M. 2025-08-02 doi:10.1101/2025.07.29.667509 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ EphA2 and Ephrin-A1 Use the Same Interface for Both in cis and in trans Interactions That Regulate Distinct Cell Signaling and Function ]]> https://biorxiv.org/content/10.1101/2025.07.31.667925v1?rss=1 Kim, S. Toth, P. Wang, W. Seiradake, E. Shi, X. Wang, B. 2025-08-02 doi:10.1101/2025.07.31.667925 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Platelets drive immune suppression and glioblastoma growth in a sex-dependent manner via PAR4 signaling ]]> https://biorxiv.org/content/10.1101/2025.08.06.668464v1?rss=1 Sloan, A. R. Bukenya, G. Aggarwal, A. Lee, J. Rosoff, D. Alban, T. Juric, I. Silver, D. J. Tacj, L. Navadgi, T. Tannish, G. Yuan, X. Coker, J. Scalise, A. Rajasekar, B. Vincenti, A. Mulkearns-Hubert, E. E. Horbinski, C. Sloan, A. E. Hubert, C. G. Luo, J. Rubin, J. B. Stavrou, E. X. Lohoff, F. W. Nieman, M. T. Sangwan, N. Chan, T. Khorana, A. A. Dhawan, A. Cameron, S. Lathia, J. 2025-08-08 doi:10.1101/2025.08.06.668464 Cold Spring Harbor Laboratory Press 2025-08-08 <![CDATA[ Context-Dependent miRNA Regulatory Landscapes in Breast Cancer Uncovered by Network Community Structure ]]> https://biorxiv.org/content/10.1101/2025.08.07.669176v1?rss=1 Newby, E. Davis, E. Dhawan, A. 2025-08-11 doi:10.1101/2025.08.07.669176 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ Inhibition of KDEL receptors remodels the tumor microenvironment for robust T cell independent tumor regression ]]> https://biorxiv.org/content/10.1101/2025.08.07.669177v1?rss=1 Tirosh, B. Pattanayak, S. P. Wang, H. Willard, B. Chan, T. Merrick, W. C. Lu, Z.-R. 2025-08-11 doi:10.1101/2025.08.07.669177 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules ]]> https://biorxiv.org/content/10.1101/2025.08.11.669689v1?rss=1 Cheng, A. P. Rusinek, I. Sossin, A. Widman, A. J. Meiri, E. Krieger, G. Hirschberg, O. Tov, D. S. Gilad, S. Jaimovich, A. Barad, O. Avaylon, S. Rajagopalan, S. Potenski, C. Prieto, T. Yuan, D. J. Furatero, R. Runnels, A. Costa, B. M. Shoag, J. E. Al Assaad, M. Sigouros, M. Manohar, J. King, A. Wilkes, D. Otilano, J. Malbari, M. S. Elemento, O. Mosquera, J. M. Altorki, N. K. Saxena, A. Callahan, M. K. Robine, N. Germer, S. Evrony, G. Faltas, B. M. Landau, D. A. 2025-08-14 doi:10.1101/2025.08.11.669689 Cold Spring Harbor Laboratory Press 2025-08-14 <![CDATA[ Systemic Metabolic Rewiring in a Mouse Model of Left Ventricular Hypertrophy ]]> https://biorxiv.org/content/10.1101/2025.08.13.670184v1?rss=1 Schmidt, A. V. Thambadurai, T. D'annibale, O. Bharathi, S. Wood, T. Goetzman, E. S. Stelzer, J. E. 2025-08-18 doi:10.1101/2025.08.13.670184 Cold Spring Harbor Laboratory Press 2025-08-18 <![CDATA[ Mathematical Foundations of Beta Diversity: Why Common Metrics Fail in Microbiome Analysis ]]> https://biorxiv.org/content/10.1101/2025.08.14.670326v1?rss=1 Zhu, Z. Zhang, Y. Li, W. Greenacre, M. Satabdi, S. Shi, Y. Zhang, L. 2025-08-20 doi:10.1101/2025.08.14.670326 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ Finding ancestry-specific chromatin architecture in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.08.19.671054v1?rss=1 Xu, W. Wang, L. LU, L. Liu, X. Rajabli, F. Celis, K. Gearing, M. Bennett, D. A. Flanagan, M. Weintraub, S. Geula, C. Schuck, T. Williams, S. Dykxhoorn, D. M. Griswold, A. J. Pericak-Vance, M. A. Young, J. Jin, F. Vance, J. M. 2025-08-20 doi:10.1101/2025.08.19.671054 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ Fine scale structural information substantially improves multivariate regression model for mRNA in-vial degradation prediction ]]> https://biorxiv.org/content/10.1101/2025.08.15.670605v1?rss=1 Yi, S. Ali, S. Jadeja, Y. Davis, J. W. Metkar, M. 2025-08-21 doi:10.1101/2025.08.15.670605 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ N-acetylcarnosine attenuates age-associated declines in multi-organ systems to improve survival ]]> https://biorxiv.org/content/10.1101/2025.08.19.671148v1?rss=1 Miranda, E. R. Shahtout, J. L. Watanabe, S. Spaas, J. Milam, N. Y. Neiswanger, G. Werbner, B. Stuart, D. Mookherjee, S. Wilson, J. Judge, M. Goh, I. Y. Slater, T. Gallop, M. R. Hu, G. Karasawa, T. Landers, J. K. Rainbow, B. O'Connor, K. T. Black, N. J. Lan, H. Nikolova, L. S. Li, Y. Davey, C. F. Cox, J. E. Boudina, S. Karner, C. M. Harasymowicz, N. S. Ramkumar, N. Symons, J. D. Chaix, A. Long, J. Z. Drummond, M. J. Funai, K. 2025-08-22 doi:10.1101/2025.08.19.671148 Cold Spring Harbor Laboratory Press 2025-08-22 <![CDATA[ MCA: A Multicellular analysis Calcium Imaging toolbox for ImageJ ]]> https://biorxiv.org/content/10.1101/2025.08.19.671108v1?rss=1 Hageter, J. DelGaudio, A. Leathery, M. Johnson, B. Raupp, T. Holcomb, J. Trevino, A. F. Jonitis, J. Bridi, M. S. Dacks, A. Horstick, E. J. 2025-08-23 doi:10.1101/2025.08.19.671108 Cold Spring Harbor Laboratory Press 2025-08-23 <![CDATA[ Dental topography and diet in marsupials and comparisons with primates ]]> https://biorxiv.org/content/10.1101/2025.08.29.673041v1?rss=1 de Vries, D. Gao, A. Croft, D. A. Brown, G. Burkart, N. Connell, A. Gahan, E. Spinks, E. Beck, R. M. D. 2025-09-04 doi:10.1101/2025.08.29.673041 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ BOGO: A Proteome-Wide Gene Overexpression Platform for Discovering Rational Cancer Combination Therapies ]]> https://biorxiv.org/content/10.1101/2025.09.02.673780v1?rss=1 View larger version (56K): org.highwire.dtl.DTLVardef@19d5d7dorg.highwire.dtl.DTLVardef@64f7eborg.highwire.dtl.DTLVardef@d08b75org.highwire.dtl.DTLVardef@173c448_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG Cancer drug resistance remains a major barrier to durable treatment success, often leading to relapse despite advances in precision oncology. While combination therapies are being increasingly investigated, such as chemotherapy with small molecule inhibitors, predicting drug response and identifying rational drug combinations based on resistance mechanisms remain major challenges. Therefore, a proteome-wide, single-gene overexpression screening platform is essential for guiding rational therapy selection. Here, we present BOGO (Bxb1-landing pad human ORFeome-integrated system for a proteome-wide Gene Overexpression), a robust, scalable, and reproducible screening platform that enables single-copy, site-specific integration and overexpression of [~]19,000 human open across cancer cell models. Using BOGO, we identified drug-specific response drivers for 16 chemotherapeutic agents and integrated clinical datasets to uncover proliferation and resistance-associated genes with prognostic potential. Drug response similarity networks revealed both shared and unique mechanisms, highlighting key pathways such as autophagy, apoptosis, and Wnt signaling, and notable resistance-associated genes including BCL2, POLD2, and TRADD. In particular, we proposed a synergistic combination of the BCL2 family inhibitor ABT-263 (Navitoclax(R)) and the DNA analog TAS-102 (Lonsurf(R)), which revealed that lysosomal modulation is a key mechanism driving DNA analog resistance. This combination therapy selectively enhanced cytotoxicity in colorectal and pancreatic cancer cells in vitro, and demonstrated therapeutic benefit in vivo in both cell line-derived xenograft (CDX) and patient-derived xenograft (PDX) models. Together, these findings establish BOGO as a powerful gene overexpression perturbation platform for systematically identifying chemoresistance and chemosensitization drivers, and for discovering rational combination therapies. Its scalability and reproducibility position BOGO as a broadly applicable tool for functional genomics and therapeutic discovery beyond cancer resistance. ]]> Jo, K. B. Alruwaili, M. M. Kim, D.-E. Koh, Y. Kim, H. You, K. Kim, J.-S. Sane, S. Guo, Y. Wright, J. P. Lim, H. J. Naranjo, M. N. Cote, A. G. Roth, F. P. Hill, D. E. Choi, J.-H. Lee, H. Matreyek, K. A. Farh, K. K.- H. Park, J.-E. Kim, H. Bakin, A. V. Kim, D.-K. 2025-09-07 doi:10.1101/2025.09.02.673780 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Disrupted Lipid Homeostasis as a Pathogenic Mechanism in ABCA7-Associated Alzheimers Disease Risk ]]> https://biorxiv.org/content/10.1101/2025.09.03.673792v1?rss=1 Pericak-Vance, M. A. Nam, Y. DeRosa, B. A. Ramirez, A. M. Ayele, B. A. Whitehead, P. G. Adams, L. D. Golightly, C. G. Starks, T. D. Laverde-Paz, J. Cukier, H. N. Akinyemi, R. Sarfo, F. Akpalu, A. Cuccaro, M. L. Williams, S. Caban-Holt, A. Reitz, C. Haines, J. L. Goldie, B. S. Rajabli, F. Dykxhoorn, D. M. Young, J. I. Vance, J. M. 2025-09-07 doi:10.1101/2025.09.03.673792 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Individual olfactory channels shape distinct parameters of sleep architecture ]]> https://biorxiv.org/content/10.1101/2025.09.11.675654v1?rss=1 Cook, O. M. Pursley, B. T. Pauls, G. Roeder, S. Aites, I. A. Coates, K. E. Dacks, A. M. 2025-09-11 doi:10.1101/2025.09.11.675654 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Thermophysiology or resource availability: What shapes the post-flooding abundance of lizard species across artificial islands in a Neotropical biome? ]]> https://biorxiv.org/content/10.1101/2025.09.12.675825v1?rss=1 Miranda, R. B. Deme, G. G. Brandao, R. A. 2025-09-17 doi:10.1101/2025.09.12.675825 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Rethinking the Estrogen Receptor Beta Dominance Hypothesis in Endometriosis: Insights from Single Cell RNA Sequencing Meta-analysis ]]> https://biorxiv.org/content/10.1101/2025.09.15.676330v1?rss=1 Heath, A. E. Zuend, C. F. Goodman, W. A. Koyuturk, M. Brubaker, D. 2025-09-18 doi:10.1101/2025.09.15.676330 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Exploring the Effect of LED-to-Photodetector Spacing on Subcutaneous Photoplethysmography for Continuous Blood Pressure Measurement ]]> https://biorxiv.org/content/10.1101/2025.09.15.676386v1?rss=1 Cabal, D. Nguyen, B. Green, D. B. Kilgore, K. Thakkar, V. Fu, M. J. Majerus, S. J. A. 2025-09-18 doi:10.1101/2025.09.15.676386 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Efineptakin alfa (NT-I7) improves overall survival and induces tertiary lymphoid structures in murine lung tumors ]]> https://biorxiv.org/content/10.1101/2025.09.15.676444v1?rss=1 Dinh, T. Lee, J. Islam, S. Nanda, N. Bjelivuk, D. Andrews, D. Zhang, J. Mani, N. L. Zhou, J. Wolfarth, A. A. Choi, D. Ahmed, R. Skitzki, J. Fang, D. Guo, W. Wang, Z. Obeng, R. 2025-09-18 doi:10.1101/2025.09.15.676444 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Screening of a kinase library in human Huntington disease iPSC derived striatal precursor neurons reveals a neuroprotective effect of PKC alpha and PKC beta1 inhibition ]]> https://biorxiv.org/content/10.1101/2025.09.18.677178v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@256d6org.highwire.dtl.DTLVardef@1931e7borg.highwire.dtl.DTLVardef@1b6598borg.highwire.dtl.DTLVardef@b0bbb5_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIHD patient-derived iPSC-based striatal precursor neurons (ISPNs) were used to screen and identify neuroprotective compounds. C_LIO_LIThe PKC-/{beta}1 inhibitor GO6976 rescues HD ISPNs from mutant huntingtin (HTT)-induced toxicity. C_LIO_LIThe phosphorylation of PKC-/{beta}1 is elevated in HD cell and tissues, and PKC-/{beta}1 interact with both wild-type and mutant huntingtin. C_LIO_LIOverexpression of PKC-/{beta}1 is toxic to HD ISPNs, while its knockdown protects the neurons. C_LI ]]> Jiang, M. Shi, T. Miryala, R. Rodriguez, M. Wang, R. Sultania, R. Guttman, L. Johnston, J. Li, Y. Cui, A. Belkas, K. Xue, Y. Um, Y. Yuan, A. Holland, C. Troncoso, J. C. Duan, W. Ratovitski, T. Smith, W. Ross, C. A. 2025-09-19 doi:10.1101/2025.09.18.677178 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Leveraging Experimental Evolution to Extract Predictive Collateral Drug Response Signatures in Ewings Sarcoma ]]> https://biorxiv.org/content/10.1101/2025.09.19.677399v1?rss=1 Lin-Rahardja, K. Canavan, E. Scott, J. G. 2025-09-21 doi:10.1101/2025.09.19.677399 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Lipodystrophy and recovery are mediated by the Wnt/lipogenesis axis during skin fibrosis. ]]> https://biorxiv.org/content/10.1101/2025.09.24.678215v1?rss=1 Madhavan, S. R. Moore, P. Varshney, R. Ma, Q. Montegut, M. Klatt, K. Parameswaran, R. Rudolph, M. C. Atit, R. 2025-09-25 doi:10.1101/2025.09.24.678215 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ CRISPR/Cas9 screenings reveal the role of STX1A and CDK1 in Cathepsin G entering and killing colorectal cancer cells ]]> https://biorxiv.org/content/10.1101/2025.09.24.678097v1?rss=1 Wang, Y. Rozen, V. Dinh, T. Li, H. Li, Y. Wang, Z. 2025-09-26 doi:10.1101/2025.09.24.678097 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ Structures redefine the mechanism of action for tetracyclines ]]> https://biorxiv.org/content/10.1101/2025.09.25.678686v1?rss=1 Devarkar, S. C. Lomakin, I. B. Wang, J. Grada, A. Bunick, C. G. 2025-09-26 doi:10.1101/2025.09.25.678686 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ NK cell allorecognition shapes reprogramming of neutrophils infiltrating heart allografts ]]> https://biorxiv.org/content/10.1101/2025.09.28.679079v1?rss=1 Koritzinsky, E. H. Keslar, K. S. Fairchild, R. L. Basu, J. 2025-09-30 doi:10.1101/2025.09.28.679079 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ Fluid-structure Interaction Simulation of the Cerebrovascular Circulation: Immersed Boundary versus Arbitrary Lagrangian Eulerian Mesh Formulations ]]> https://biorxiv.org/content/10.1101/2025.09.28.679107v1?rss=1 McCune, M. P. Thomeer, D. E. Davison, M. A. Rashidi, M. Moore, N. Z. 2025-09-30 doi:10.1101/2025.09.28.679107 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ The Effects of DMSO Cryopreservation on the Biomechanics and Histology of Human Cerebrovascular Tissue ]]> https://biorxiv.org/content/10.1101/2025.09.29.679363v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@1d8cc51org.highwire.dtl.DTLVardef@4ddcd6org.highwire.dtl.DTLVardef@1dd94f1org.highwire.dtl.DTLVardef@5d99bf_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> McCune, M. P. Davison, M. A. Thiyagarajah, N. Thomeer, D. E. Albabish, W. Owusu-Ansah, M. Moore, N. 2025-10-01 doi:10.1101/2025.09.29.679363 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Retinoic acid production via the ray-finned fish gene beta-carotene oxygenase 1-like is essential for juvenile development ]]> https://biorxiv.org/content/10.1101/2025.09.30.679646v1?rss=1 Krupa, L. S. Villamayor, P. R. Bandara, S. Zhang, Y. Palmiotti, A. von Lintig, J. Bendesky, A. 2025-10-04 doi:10.1101/2025.09.30.679646 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ Adaptive Disruption of Carotenoid Metabolism in Cavefish via Loss of Beta-carotene oxygenase 2a (Bco2a) ]]> https://biorxiv.org/content/10.1101/2025.10.06.680734v1?rss=1 Perez Guerra, D. Bandara, S. Leal, F. von Lintig, J. Riddle, M. 2025-10-06 doi:10.1101/2025.10.06.680734 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ The Legionella effector RidL promotes mitochondrial fragmentation through phosphorylation activation of the large GTPase Drp1 ]]> https://biorxiv.org/content/10.1101/2025.10.07.680855v1?rss=1 Katic, A. Vittori, E. Halter, S. Steiner, K. Swart, A. L. Radiom, M. Garcia-Rodriguez, F.-J. Jaggi, T. Li, X. Mears, J. Buchrieser, C. Escoll, P. Panse, V. G. Hilbi, H. 2025-10-09 doi:10.1101/2025.10.07.680855 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ Systematic elucidation and pharmacologic targeting on non-oncogene dependencies in imatinib-resistant gastrointestinal stromal tumor ]]> https://biorxiv.org/content/10.1101/2025.10.12.681609v1?rss=1 Mundi, P. S. Grunn, A. Kojadinovic, A. Karan, C. Realubit, R. Caescu, I. C. Hibshoosh, H. Aburi, M. Alvarez, M. J. Ingham, M. Evans, D. Rothschild, S. Schwartz, G. K. Califano, A. 2025-10-14 doi:10.1101/2025.10.12.681609 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Targeting Endothelial PERK Accelerates Lymphoid Regeneration by Enhancing DLL4-NOTCH3 Signaling at the Pre-B Niche ]]> https://biorxiv.org/content/10.1101/2025.10.15.682539v1?rss=1 Zou, B. Chen, Q. Zheng, J. Ma, Y. Myers, J. Shang, Y. Huang, M. Christensen, P. Adoro, S. Tang, C.-h. A. Hu, C.-C. Pingali, S. R. K. Xin, W. Chan, K. S. Wong, S. T. C. Zu, Y. Jafar-Nejad, H. Zhou, L. 2025-10-15 doi:10.1101/2025.10.15.682539 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Synthesis and Characterization of ICG-based Near-infrared Photoacoustic Contrast Agents ]]> https://biorxiv.org/content/10.1101/2025.10.18.683226v1?rss=1 Hanafi, M. Giammanco, G. Singh, S. Ronzier, E. Laliwala, A. Wegierak, D. Abenojar, E. C. NITTAYACHARN, P. Exner, A. A. Chitnis, P. V. Veneziano, R. 2025-10-19 doi:10.1101/2025.10.18.683226 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ A simple theory to explain super-additivity of highly similar drug combinations ]]> https://biorxiv.org/content/10.1101/2025.10.27.684841v1?rss=1 Weed-Nichols, E. Seckler, J. M. Getsy, P. M. Lewis, S. J. Grossfield, A. 2025-10-27 doi:10.1101/2025.10.27.684841 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Ultra-High Field 31P functional Magnetic Resonance Spectroscopy Reveals NAD+ Dynamics in Brain Energy Metabolism during Visual Stimulation. ]]> https://biorxiv.org/content/10.1101/2025.11.02.686085v1?rss=1 Kaiser, A. Anvari Vind, F. Duarte, J. M. N. Jelescu, I. O. Lin, Y. Yu, X. Widmaier, M. Wenz, D. Xin, L. 2025-11-03 doi:10.1101/2025.11.02.686085 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Derivation of functional early gestation decidual natural killer cell subtypes from induced pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2025.11.03.685424v1?rss=1 View larger version (56K): org.highwire.dtl.DTLVardef@9b182dorg.highwire.dtl.DTLVardef@507037org.highwire.dtl.DTLVardef@f73238org.highwire.dtl.DTLVardef@1021ce0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cheung, V. C. DaCosta, C. Jaimez, J. Arora, H. Caron, C. Slamecka, J. Fierro, M. Meads, M. Fisch, K. Morey, R. E. Pant, D. Kaufman, D. S. Horii, M. Bui, J. D. Parast, M. M. 2025-11-05 doi:10.1101/2025.11.03.685424 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Multi-ancestry Transcriptome-Wide Association Study Reveals Shared and Population-Specific Genetic Effects in Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2025.11.03.686160v1?rss=1 0.8), including established AD loci (BIN1, PTK2B, DMPK) with consistent effects across populations. Importantly, at BIN1 we fine-mapped regulatory variants associated with gene expression and AD risk beyond the GWAS index SNP--most notably rs11682128, which is only in modest LD with rs6733839 (r^2{approx}0.34)--demonstrating that multi-population TWAS can implicate additional functional variants not captured by single-SNP GWAS signals. We also discovered a novel association between COG4 expression and AD in NHW, implicating Golgi apparatus function. Using independent SuShiE-derived models from TOPMed MESA (PBMC), several associations replicated directionally across ancestries, with statistical significance most evident in NHW. Our results show that multi-population fine-mapping improves eQTL resolution and TWAS interpretability, reveals regulatory variants beyond GWAS index SNPs, and underscores the need to expand non-European AD cohorts to resolve shared and population-specific mechanisms. ]]> Sun, X. Mews, M. Wheeler, N. R. Benchek, P. Gu, T. Gomez, L. Ray, N. Reitz, C. Naj, A. C. Below, J. E. Tosto, G. Cornejo-Olivas, M. Byrd, G. S. Feliciano-Astacio, B. E. Celis, K. Rajabli, F. Kunkle, B. W. Pericak-Vance, M. A. Haines, J. L. Griswold, A. J. Bush, W. S. 2025-11-05 doi:10.1101/2025.11.03.686160 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Lightweight open-source fine-tuning of SAM2 enables domain-specific microscopy segmentation ]]> https://biorxiv.org/content/10.1101/2025.11.08.687405v1?rss=1 Bhat, E. Selvan, S. Okekenwa, S. Dechkounian, Z. Lin, V. Nakano, M. Saha, M. Song, Y. 2025-11-10 doi:10.1101/2025.11.08.687405 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ eIF2B Selectively Anchors and Activates Mutant KRAS ]]> https://biorxiv.org/content/10.1101/2025.11.10.686860v1?rss=1 View larger version (21K): org.highwire.dtl.DTLVardef@1f50934org.highwire.dtl.DTLVardef@2f55b9org.highwire.dtl.DTLVardef@1a51e39org.highwire.dtl.DTLVardef@1634aac_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIeIF2B interacts with mutant KRAS and SOS at the plasma membrane (PM). C_LIO_LIThe eIF2B:SOS complex promotes the GTP-bound active state of mutant KRAS. C_LIO_LIeIF2B enhances the translation of B4GALT5 mRNA, encoding a key enzyme of glycosphingolipid (GSL) biosynthesis. C_LIO_LIUpregulation of the GSL metabolites, ganglioside GM3 and sulfatide SM4, remodels PM lipid composition to facilitate eIF2B:SOS:KRAS complex formation and mutant KRAS nanoclustering. C_LIO_LIThrough its interaction with SOS and stimulation of GSL synthesis, eIF2B selectively activates mutant KRAS at the PM among RAS isoforms. C_LIO_LIeIF2B is required for the development of mKRAS-driven lung adenocarcinoma in mice. C_LIO_LIeIF2B is a marker of poor prognosis in mutant KRAS-driven cancers. C_LI ]]> Kim, H. Diao, S. Cho, K.-J. Lee, H.-R. Liu, J. Egea, P. Pantsar, T. Kurki, M. Ghaddar, N. Wang, S. Zou, J. Y. Amiri, M. Gannaban, R. Hancock, J. F. Rice, K. M. Deng, Q. Sasaki, A. Asara, J. M. Tripathi, B. Lowy, D. Lawrence, R. Hatzoglou, M. Azpilcueta-Nicolas, C. R. Lumb, J.-P. Columbus, J. Turbyville, T. J. Marshall, C. B. Ikura, M. Groves, J. T. Sonenberg, N. Walter, P. Koromilas, A. E. 2025-11-12 doi:10.1101/2025.11.10.686860 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Micro-CT Analysis of a Needle to Nerve Approach for Interfascicular Peripheral Nerve Stimulation in Porcine Nerves ]]> https://biorxiv.org/content/10.1101/2025.11.19.687256v1?rss=1 0.707), with no evidence of angular clustering in any single direction. On average, nearest neighbor distances between contacts measured 2256.26{+/-}1760.28 {micro}m in 3D and 730.71 {+/-}564.83 {micro}m transversely, with implants spanning 10.3 {+/-} 4.3 mm along length of nerve. The angle of wire trajectory into the nerve was correlated with fascicle traversal, with steeper angles of insertion associated with more instances of fascicle traversal. Histological analysis corroborated the fascicular borders and wire placements found on micro-CT and demonstrated perineurium integrity. SignificanceInterfascicular implantation can reliably access both central and distributed regions of the nerve, while not being confined to a single plane, enabling access to regions which have been historically challenging to stimulate effectively. The observed nearest-neighbor transverse spacing between contacts is within the range of reported ideal values for selective activation. The MiiNS placement characteristics show its potential as an effective peripheral nerve interface alternative which achieves distributed contact placement, including in the center of the nerve volume, while remaining predominantly outside of the perineurium. ]]> Randolph, M. A. Marcu, V. I. Tsiptsis, C. Shoffstall, A. J. Baskin, J. Z. Tyler, D. J. 2025-11-20 doi:10.1101/2025.11.19.687256 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ B-cell activating factor plays a critical role in CAR-T cell-associated cytokine release syndrome ]]> https://biorxiv.org/content/10.1101/2025.11.22.689920v1?rss=1 View larger version (18K): org.highwire.dtl.DTLVardef@187a0edorg.highwire.dtl.DTLVardef@1566904org.highwire.dtl.DTLVardef@896b5org.highwire.dtl.DTLVardef@1de5db6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Parameswaran, R. Fritz, C. Metheny, L. Wald, D. N. Caimi, P. 2025-11-25 doi:10.1101/2025.11.22.689920 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Upregulation of MAM by C99 disrupts ACSL4 activity and phospholipid homeostasis in Alzheimer disease. ]]> https://biorxiv.org/content/10.1101/2025.11.25.690197v1?rss=1 Montesinos, J. Yun, T. Salomon-Cruz, I. D. Agudelo-castrillon, S. Uceda, M. Ferrer, A. C. Anton-Barros, C. Gomez-lopez, N. Agrawal, R. R. Larrea, D. Velasco, K. R. Fernandez-Bernal, A. Benitez, E. Zhu, X. Schon, E. A. Cardona-Gomez, G. P. Area-Gomez, E. 2025-11-29 doi:10.1101/2025.11.25.690197 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Development of a New Approach Method to Monitor and Modify Caffeine Metabolism Correlated to CYP1A2 Expression ]]> https://biorxiv.org/content/10.1101/2025.11.27.691042v1?rss=1 Chen, X. Miyagi, M. Tochtrop, G. P. 2025-11-30 doi:10.1101/2025.11.27.691042 Cold Spring Harbor Laboratory Press 2025-11-30 <![CDATA[ ACSS2 mediates prenatal alcohol exposure-related morphological and behavioral phenotypes ]]> https://biorxiv.org/content/10.1101/2025.11.26.690774v1?rss=1 Dodson, K. M. Periandri, E. M. Yadav, A. Lopes, M. Barfield, A. J. Ola, A. de Luna Vitorino, F. N. Cearlock, C. Garcia, B. A. Hill, C. Maloney, S. E. Egervari, G. 2025-12-01 doi:10.1101/2025.11.26.690774 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Structural Basis of Inhibition and Desensitization in Heteromeric Kainate Receptors ]]> https://biorxiv.org/content/10.64898/2025.12.02.691905v1?rss=1 Tajima, N. Zhou, C. Segura-Covarrubias, G. Hoffman, A. M. 2025-12-04 doi:10.64898/2025.12.02.691905 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ Guidance receptor-mediated mechanocompliance of GBM cells facilitates immune-silent invasion ]]> https://biorxiv.org/content/10.64898/2025.12.03.692092v1?rss=1 Kang, S. Alves, C. J. Tao, H. Kolsteeg, C. Sadia, S. Zhang, J. Fisher, J. Dixon, A. Tsankova, N. M. Ramakrishnan, A. Shen, L. Friedel, R. H. Zou, H. 2025-12-06 doi:10.64898/2025.12.03.692092 Cold Spring Harbor Laboratory Press 2025-12-06 <![CDATA[ Genomic and Transcriptomic Landscapes of MEN1-Wild-Type Low-Grade Metastatic Pancreatic NETs Uncover Key Oncogenic Drivers and Targetable Pathways ]]> https://biorxiv.org/content/10.64898/2025.12.07.692731v1?rss=1 Uddin, M. H. Mahdi, Z. Muqbil, I. Herring, B. R. Bart, R. J. Khan, H. Y. Li, Y. Aboukameel, A. Bannoura, S. F. Jimenez, H. Johansen, A. Al-Hallak, M. N. Azar, I. Mohamed, A. Hadid, T. Vaishampayan, N. Shi, Y. Wan, Y. Ong, V. Dyson, G. Beydoun, R. Tobon, M. Beal, E. W. Chen, H. Shields, A. F. Philip, P. A. Beebe-Dimmer, J. Mohammad, R. M. Pasche, B. C. El-Rayes, B. E.-R. F. Azmi, A. S. 2025-12-10 doi:10.64898/2025.12.07.692731 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ The effect of environmental enrichment on social dominance and welfare in a cichlid fish ]]> https://biorxiv.org/content/10.64898/2025.12.11.693693v1?rss=1 Chamily, F. A. Vanderklok, B. R. Buzinski, O. D. Ketterl, C. Hager, Z. D. Oldfield, R. G. Kelty, J. D. Dijkstra, P. D. 2025-12-14 doi:10.64898/2025.12.11.693693 Cold Spring Harbor Laboratory Press 2025-12-14 <![CDATA[ Alpha hemolysin polymorphisms in methicillin-resistant Staphylococcus aureus clinical isolates regulate ADAM10-dependent neutrophil IL-1 beta secretion ]]> https://biorxiv.org/content/10.64898/2025.12.13.694139v1?rss=1 Liboro, K. Chau, J. T. Begando, J. Abbodante, S. Lackner, A. Marshall, M. E. Sun, Y. Ly, N. Dubyak, G. R. Gilmore, M. McNulty, R. Andre, C. Pearlman, E. S. 2025-12-14 doi:10.64898/2025.12.13.694139 Cold Spring Harbor Laboratory Press 2025-12-14 <![CDATA[ From Dimerization to Signaling: Molecular Dynamics Insights into EphA1 and EphA2 Isoform Specificity ]]> https://biorxiv.org/content/10.64898/2025.12.23.696317v1?rss=1 Sahoo, A. R. Bhattarai, N. Buck, M. 2025-12-25 doi:10.64898/2025.12.23.696317 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ Multivalent Nanobodies for Potent and Broad Neutralization of Staphylococcus aureus Toxins ]]> https://biorxiv.org/content/10.64898/2025.12.24.696403v1?rss=1 Kim, Y. J. Walton, N. R. Huang, W. Lee, M. Xiang, Y. Sang, Z. Sussman, C. Moore, S. Taylor, D. J. Chen, K. Hook, J. L. McCormick, J. K. Shi, Y. 2025-12-25 doi:10.64898/2025.12.24.696403 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ Stabilising selection and ecological trade-offs underpin coexistence in a tropical flora ]]> https://biorxiv.org/content/10.64898/2025.12.31.697164v1?rss=1 Niissalo, M. A. Lim, J. Y. Ngiam, J. J. Rajaraman, S. Choo, L. M. Jong, J. J. Y. Ngo, K. M. Leong, F. W. S. Lum, S. K. Y. Beentje, H. J. Buerki, S. Callmander, M. W. Chen, J. Chua, M. S. E. De Kok, R. P. J. De Wilde-Duyfjes, B. E. E. Duistermaat, H. Esser, H.-J. Fleck, S. Ganesan, S. K. Gardner, E. M. Hughes, M. Koh, S. L. Leong, P. K. F. Leong-Skornickova, J. Lindsay, S. Low, Y. W. Lua, H. K. Neo, L. Pannell, C. M. Puglisi, C. Rodda, M. L. Savinov, I. A. Seah, W. W. Simpson, D. A. Strijk, J. S. Thomas, D. C. Turner, I. M. van Welzen, P. C. Wilkie, P. Wo 2025-12-31 doi:10.64898/2025.12.31.697164 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ PREP-aring is worth it: Success of the Case Western Reserve University Post-baccalaureate Research Education Program and its Scholars ]]> https://biorxiv.org/content/10.64898/2025.12.30.697004v1?rss=1 Crawford, D. C. Vazquez-Hidalgo, E. Lou, H. 2026-01-02 doi:10.64898/2025.12.30.697004 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Neural Mechanisms of Mixed Speech and Grasp Representation in Sensorimotor Cortices ]]> https://biorxiv.org/content/10.64898/2026.01.02.697428v1?rss=1 Foli, C. Conlan, E. C. Memberg, W. D. Bhat, P. Graczyk, E. L. Johnson, T. R. Taylor, D. M. Herring, E. Z. Sweet, J. A. Ajiboye, A. B. 2026-01-03 doi:10.64898/2026.01.02.697428 Cold Spring Harbor Laboratory Press 2026-01-03 <![CDATA[ Consumption of processed foods impairs memory function through dietary advanced glycation end-products ]]> https://biorxiv.org/content/10.64898/2026.01.07.698065v1?rss=1 Hayes, A. M. R. Klug, M. E. Sharma, M. Kao, A. E. Sun, S. Lopez Gonzalez, E. D. J. Zhu, H. Dent, J. C. Clark, R. J. Sell, D. R. Nelson, D. Monnier, V. M. Tsan, L. Rea, J. J. Ahuja, A. Tanios, N. Gianatiempo, I. Shanmugam, M. V. Park, Y. Yu, K. B. Hsiao, E. Y. Schier, L. A. Fodor, A. A. Woodruff, T. M. Shuck, S. C. Gati, C. Herring, B. E. Coughlan, M. T. Kanoski, S. E. 2026-01-08 doi:10.64898/2026.01.07.698065 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Polymer of methyl malonic acid suppress inflammation by downregulating IL-2 through ROS overproduction ]]> https://biorxiv.org/content/10.64898/2026.01.11.698915v1?rss=1 Pathak, S. Jaggrapu, M. M. C. S. Khodaei, T. Thumsi, A. Joseph, J. Acharya, A. P. 2026-01-12 doi:10.64898/2026.01.11.698915 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ Integrative Single-cell and Spatial Transcriptomic Analysis of Osteosarcoma Reveals Conserved and Distinct Ecosystems Across Sites and Species ]]> https://biorxiv.org/content/10.64898/2026.01.13.698472v1?rss=1 Budhathoki, Y. Cannon, M. V. McEachron, T. A. Patel, A. G. Gust, M. J. Modiano, J. F. Ammons, D. T. Cronise, K. E. Dries, R. Gryder, B. E. Regan, D. P. Gardner, H. L. Roberts, R. D. Sarver, A. L. Macchietto, M. G. 2026-01-14 doi:10.64898/2026.01.13.698472 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Selection for targeted therapy resistance leads to an indirect selection for higher phenotypic plasticity and enhanced evolvability to orthogonal stressors ]]> https://biorxiv.org/content/10.64898/2026.01.13.699073v1?rss=1 Bjornberg, A. Xierali, A. Froid, M. Clarke, R. B. Maltas, J. Vander Velde, R. Riffas, J. Gryder, B. Scott, J. Bassanta, D. Anderson, A. R. A. Turati, V. A. Marusyk, A. 2026-01-14 doi:10.64898/2026.01.13.699073 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Motor Intention Drives Corticospinal Facilitation during Interception Planning ]]> https://biorxiv.org/content/10.64898/2026.01.13.699289v1?rss=1 McCurdy, J. R. Jarvis, B. Whitman, E. Ariga, K. Khan, A. Barany, D. A. 2026-01-14 doi:10.64898/2026.01.13.699289 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ RasGRP1 agonists stimulate P-TEFb biogenesis via MEK-ERK-mTORC1 signaling to reverse HIV latency with minimal CD4 downregulation ]]> https://biorxiv.org/content/10.64898/2026.01.14.699500v1?rss=1 Mbonye, U. Bellomo, A. Elhalem, E. Donadio, L. G. Yang, M. Donner, A. Comin, M. J. Karn, J. 2026-01-15 doi:10.64898/2026.01.14.699500 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ Characterization of novel cytoplasmic roles for the N-terminal methyltransferase NRMT1 ]]> https://biorxiv.org/content/10.64898/2026.01.17.700099v1?rss=1 Tooley, J. G. Zhou, G. Obeidat, S. Arbel, A. Jones, C. Tedeschi, F. Schaner Tooley, C. 2026-01-18 doi:10.64898/2026.01.17.700099 Cold Spring Harbor Laboratory Press 2026-01-18 <![CDATA[ The heat-ramp method to study regulated cell death in a pathogenic yeastCryptococcus neoformans ]]> https://biorxiv.org/content/10.64898/2026.01.19.700367v1?rss=1 Kulkarni, M. Liu, Y. Cheng, Q. Zhu, C. Kuhn, K. Shen, A. Jin, B. Casadevall, A. Lamb, H. M. Stolp, Z. D. Hardwick, J. M. 2026-01-19 doi:10.64898/2026.01.19.700367 Cold Spring Harbor Laboratory Press 2026-01-19 <![CDATA[ Deep Plasma Proteomics Coupled with Functional Genomics Reveals Drivers of Parkinson's Disease Progression and Levodopa Response ]]> https://biorxiv.org/content/10.64898/2026.01.19.699565v1?rss=1 Kim, J.-s. Jeong, C. Kim, S. Kim, H. Lee, S. Jo, K. B. Luo, W. Shlaifer, I. Ha, S. H. Sane, S. Woo, K. A. Lee, E. Chae, S. Cote, A. G. Seo, J. Park, G. Sahni, N. Choi, J.-H. Park, J.-H. Hill, D. E. Lee, H. Matreyek, K. A. Kairs, S. N. Tsu, B. L. Kim, S. Barnes, C. A. Trempe, J.-F. Rak, J. Shin, J. H. Durcan, T. M. Yoon, K.-J. Kim, D.-K. Kim, H.-J. 2026-01-22 doi:10.64898/2026.01.19.699565 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Neuronal microscale biophysical instability mediates macroscale network dynamics shaping pathological manifestations ]]> https://biorxiv.org/content/10.64898/2026.01.20.697254v1?rss=1 Kumar, V. Sanchez Franco, V. M. Ferry, F. S. Xie, Y. Hutson, A. N. Zhang, Y. J. Daniels, S. D. Nguyen, D. L. Spera, L. K. Snyder, E. M. Knauss, A. Sudhakar, S. L. Duan, G. Y. Paul, E. M. Tabuchi, M. 2026-01-22 doi:10.64898/2026.01.20.697254 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Bayesian rhythmic model for jointly detecting circadian biomarkers and predicting molecular circadian time in human post-mortem brain transcriptome ]]> https://biorxiv.org/content/10.64898/2026.01.21.700905v1?rss=1 Xue, X. Wang, H. Zhu, Z. Guan, Y. Seney, M. L. Zhang, L. Tseng, G. C. 2026-01-23 doi:10.64898/2026.01.21.700905 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ The Unexpected Visibility of the SARS-CoV-2 Nucleocapsid Protein Reveals a Hidden Route of Surface Trafficking. ]]> https://biorxiv.org/content/10.64898/2026.01.24.701458v1?rss=1 Osuagwu, A. McCausland, J. King, C. L. 2026-01-26 doi:10.64898/2026.01.24.701458 Cold Spring Harbor Laboratory Press 2026-01-26 <![CDATA[ Correction of multiple splicing mutations associated with CFTR exon 18 using a single exon-specific U1 snRNA ]]> https://biorxiv.org/content/10.64898/2026.01.30.702834v1?rss=1 Lou, H. Elsner Pacheco, A. G. Betts, J. M. Hao, S. Callejas, H. Mader, K. McKinney, A. Conlon, R. A. Drumm, M. L. 2026-02-02 doi:10.64898/2026.01.30.702834 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Resolving Conformational Heterogeneity in IntrinsicallyDisordered Proteins via Experimentally Guided Multi-Replica Simulations ]]> https://biorxiv.org/content/10.64898/2026.01.29.702558v1?rss=1 Yang, W. Yang, S. Zheng, W. 2026-02-03 doi:10.64898/2026.01.29.702558 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Structural Mechanisms of SAMD9 Autoinhibition and Pathogenic Dysregulation ]]> https://biorxiv.org/content/10.64898/2026.02.02.703423v1?rss=1 Mou, Z. Zhang, F. Morales, M. Sahoo, B. Dai, X. Xiang, Y. 2026-02-03 doi:10.64898/2026.02.02.703423 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Hog1/p38 and ZAKα drive Shwachman-Diamond syndrome and provide targets to improve cell growth ]]> https://biorxiv.org/content/10.64898/2026.02.05.703873v1?rss=1 Kawashima, N. Prasad, N. Tedeschi, F. Mehta, H. Saito, N. Jones, C. Chen, X. Hristodor, A. M. Zhou, G. Luna, J. Cipolli, M. Bezzerri, V. Corey, S. 2026-02-08 doi:10.64898/2026.02.05.703873 Cold Spring Harbor Laboratory Press 2026-02-08 <![CDATA[ Expanding CyanoHAB Monitoring: New Micropeptins and Generalizable MS/MS Workflows for the Annotation of Cyanopeptide Classes ]]> https://biorxiv.org/content/10.64898/2026.02.07.704577v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@1849d1eorg.highwire.dtl.DTLVardef@16729a8org.highwire.dtl.DTLVardef@1dffe58org.highwire.dtl.DTLVardef@b36a52_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Xia, R. Ahn, L. Burkhauser, M. Youngs, R. Bertin, M. J. 2026-02-09 doi:10.64898/2026.02.07.704577 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Metaplastic neuronal state transition regulates species-specific interoceptive processing in Drosophila ]]> https://biorxiv.org/content/10.64898/2026.02.07.702027v1?rss=1 Brann, A. M. Nguyen, D. L. Zarjetskiy, A. N. Pokaleva, N. Paul, E. M. Tabuchi, M. 2026-02-10 doi:10.64898/2026.02.07.702027 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ Enhanced Hi-C Capture Analysis reveals complex regulatory architecture at the PICALM-EED locus for Alzheimer Disease ]]> https://biorxiv.org/content/10.64898/2026.02.14.705927v1?rss=1 Nasciben, L. B. Wang, l. Xu, W. Ramirez, A. Moura, S. Lu, L. Liu, X. Rajabli, F. Celis, K. Gearing, M. Bennett, D. Weintraub, S. Geula, C. Schuck, T. Nuytemans, K. Scott, W. Dykxhoorn, D. PERICAK-VANCE, M. A. Young, J. Griswold, A. Jin, F. Vance, J. M. 2026-02-17 doi:10.64898/2026.02.14.705927 Cold Spring Harbor Laboratory Press 2026-02-17 <![CDATA[ Chemical interactions in polyethylene glycol-induced condensates lead to an anomalous FRET response from a flexible linker-fluorescent protein crowding sensor ]]> https://biorxiv.org/content/10.64898/2026.02.16.706251v1?rss=1 Mohapatra, A. Antarasen, J. Latham, D. R. Barilla, M. A. Davis, C. M. Kisley, L. 2026-02-18 doi:10.64898/2026.02.16.706251 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Altering dosage of meiotic crossover-associated RING finger proteins affects crossover number and interference in Drosophila ]]> https://biorxiv.org/content/10.64898/2026.02.18.706578v1?rss=1 Frantz, E. Santa Rosa, P. McMahan, S. Sekelsky, J. 2026-02-19 doi:10.64898/2026.02.18.706578 Cold Spring Harbor Laboratory Press 2026-02-19 <![CDATA[ rRNA Expansion Segments Mediate Ribosome Dimerization as a Conserved Stress Response ]]> https://biorxiv.org/content/10.64898/2026.02.21.707218v1?rss=1 Jiang, W. Chen, C. Wang, X. Huang, W. Taylor, D. Chen, Z. Xie, J. Su, Z. Taylor, D. Hatzoglou, M. Guo, Q. 2026-02-22 doi:10.64898/2026.02.21.707218 Cold Spring Harbor Laboratory Press 2026-02-22 <![CDATA[ Bradykinin Contributes to Vasogenic Edema in Murine Experimental Cerebral Malaria ]]> https://biorxiv.org/content/10.64898/2026.02.23.704410v1?rss=1 Pinheiro, A. d. S. Teixeira, D. E. 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R. Selhuber-Unkel, C. Kappelmann-Fenzl, M. Bosserhoff, A. Tobar, N. Leal-Egana, A. 2026-03-03 doi:10.64898/2026.02.28.708725 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Early electrical stimulation promotes functional recovery after volumetric muscle loss ]]> https://biorxiv.org/content/10.64898/2026.03.01.708642v1?rss=1 Gershanok, S. Behre, A. Jin, R. Vinokurova, S. Blount, J. Garg, R. Ersoz, A. Wang, L. Jo, S. Ranke, D. Kulkarni, M. Cohen-Karni, D. Feinberg, A. W. Weber, D. Brown, B. Cohen-Karni, T. 2026-03-03 doi:10.64898/2026.03.01.708642 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Conformational signatures of native ligand and pharmacochaperone binding in rhodopsin ]]> https://biorxiv.org/content/10.64898/2026.03.03.709294v1?rss=1 Pashandi, Z. Ortega, J. T. Miyagi, M. Golczak, M. Jastrzebska, B. 2026-03-05 doi:10.64898/2026.03.03.709294 Cold Spring Harbor Laboratory Press 2026-03-05 <![CDATA[ Pseudomonas aeruginosa Exotoxin A is not essential for corneal disease severity or bacterial survival ]]> https://biorxiv.org/content/10.64898/2026.03.10.710780v1?rss=1 Begando, J. Dubyak, G. Rietsch, A. Pearlman, E. 2026-03-10 doi:10.64898/2026.03.10.710780 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Route of Adenovirus Type 5-Vectored Influenza Vaccination Shapes Systemic and Mucosal Immunity in a Maternal-Neonatal Pig Model ]]> https://biorxiv.org/content/10.64898/2026.03.12.711389v1?rss=1 Langel, S. N. Byrne, J. J. Leal, D. Williams, A. Sirisereewan, C. Meritet, D. Rahe, M. C. Watanabe, T. T. N. Compton, S. Rajao, D. Ferreira, J. B. Tucker, S. Crisci, E. 2026-03-13 doi:10.64898/2026.03.12.711389 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Stochastic Evolutionary Control in Heterogeneous Populations ]]> https://biorxiv.org/content/10.64898/2026.03.12.711493v1?rss=1 Chen, P. Pachter, J. A. Scott, J. G. Hinczewski, M. 2026-03-13 doi:10.64898/2026.03.12.711493 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ stMCP: Spatial Transcriptomics with a Model Context Protocol Server ]]> https://biorxiv.org/content/10.64898/2026.03.11.710153v1?rss=1 Smith, J. J. Wang, X. McPheeters, M. Widjaja-Adhi, M. A. Littleton, S. Saban, D. Golczak, M. Jenkins, M. W. 2026-03-14 doi:10.64898/2026.03.11.710153 Cold Spring Harbor Laboratory Press 2026-03-14 <![CDATA[ Proteomic analysis reveals shared biological pathways linking acrolein to biomolecular changes in the acute phase of rat spinal cord injury ]]> https://biorxiv.org/content/10.64898/2026.03.11.711153v1?rss=1 Stingel, R. L. Ball, B. K. Sun, S. Brubaker, D. K. Shi, R. 2026-03-14 doi:10.64898/2026.03.11.711153 Cold Spring Harbor Laboratory Press 2026-03-14 <![CDATA[ Human frontal eye field and eyelid motor area revisited with electrical cortical stimulation and electrode co-registration ]]> https://biorxiv.org/content/10.64898/2026.03.12.711460v1?rss=1 Fumuro, T. Bulacio, J. C. Bingaman, W. E. Ikeda, A. Shibasaki, H. Luders, H. O. Nair, D. R. Matsumoto, R. 2026-03-16 doi:10.64898/2026.03.12.711460 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ Selective regulation of transsynaptic alignment and postsynaptic assembly by a novel NCAM family synaptic adhesion molecule ]]> https://biorxiv.org/content/10.64898/2026.03.13.710942v1?rss=1 Van der Linden Costello, P. Wennerberg, M. N. Rydbom, J. A. Gratz, S. Fennema, L. F. O'Connor-Giles, K. M. Broihier, H. T. 2026-03-16 doi:10.64898/2026.03.13.710942 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ In-Situ ssDNA Isolation from dsDNA Sources as a Streamlined Pathway to DNA Origami Assembly and Testing ]]> https://biorxiv.org/content/10.64898/2026.03.19.709872v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@f7ada7org.highwire.dtl.DTLVardef@a9bab8org.highwire.dtl.DTLVardef@121b695org.highwire.dtl.DTLVardef@5a1dea_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ruiz, E. O. Neyra, K. Lopez, D. Chen, R.-W. Paramasamy, D. Bizjak, Q. Halley, P. D. Wei, Y. Sotomayor, M. Poirier, M. G. Mathur, D. Castro, C. E. Pfeifer, W. G. 2026-03-23 doi:10.64898/2026.03.19.709872 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ Metaplastic sleep regulation in Drosophila determined by microscale circadian neural dynamics ]]> https://biorxiv.org/content/10.64898/2026.03.21.713346v1?rss=1 Hutson, A. N. Zarjetskiy, A. N. Zhang, Y. J. Pokaleva, N. Paul, E. M. Xie, Y. Chong, B. Sanchez Franco, V. M. Zukowski, L. H. Faulk, E. E. Walker, J. A. Brown, A. M. Nguyen, D. L. Ferry, F. S. Snyder, E. M. Tabuchi, M. 2026-03-24 doi:10.64898/2026.03.21.713346 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Cross-Species Translation Enhances the Use of Mouse Models for Translatability and Drug Discovery in Late-Onset Alzheimer's Disease ]]> https://biorxiv.org/content/10.64898/2026.03.21.713391v1?rss=1 Park, J. H. Yu, J. Lucey, B. P. Brubaker, D. K. 2026-03-24 doi:10.64898/2026.03.21.713391 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ MLL3/4 methyltransferases regulate the differentiation of pluripotent stem cells via cellular respiration ]]> https://biorxiv.org/content/10.64898/2026.03.24.713976v1?rss=1 Nur, S. M. Jia, Y. Ye, M. Lepak, C. A. Ben-Sahra, I. Cao, K. 2026-03-26 doi:10.64898/2026.03.24.713976 Cold Spring Harbor Laboratory Press 2026-03-26 <![CDATA[ Ultrasound Activated Nanobubbles Induce Durable Systemic Antitumor Immunity ]]> https://biorxiv.org/content/10.64898/2026.03.25.714247v1?rss=1 View larger version (56K): org.highwire.dtl.DTLVardef@15d307eorg.highwire.dtl.DTLVardef@11ac7e0org.highwire.dtl.DTLVardef@138541aorg.highwire.dtl.DTLVardef@119aae0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Bhalotia, A. Nittayacharn, P. Hutchinson, D. W. Cheplyansky, A. Takizawa, K. H. Nidhiry, A. Hariharan, S. Novak, A. Iyer, A. Mehta, M. Kosmides, T. Perera, R. Hwang, I. M. Exner, A. A. Karathanasis, E. 2026-03-27 doi:10.64898/2026.03.25.714247 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ eSIG-Net: Accurate prediction of single-mutation induced perturbations on protein interactions using a language model ]]> https://biorxiv.org/content/10.64898/2026.03.27.714913v1?rss=1 Pan, X. Shrawat, A. Raghavan, S. Dong, C. Yang, Y. Li, Z. Zheng, W. J. Eckhardt, S. G. Wu, E. Fuxman Bass, J. I. Jarosz, D. F. Chen, S. McGrail, D. J. Sheynkman, G. M. Huang, J. H. Sahni, N. Yi, S. S. 2026-03-31 doi:10.64898/2026.03.27.714913 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ SPTBN2 promotes an immunosuppressive tumor microenvironment and cross-resistance to anti-cancer therapies ]]> https://biorxiv.org/content/10.64898/2026.03.30.715365v1?rss=1 Bui, Q. T. Basavaraja, R. Dhamdhere, M. R. Holczbauer, A. Paruzzo, L. Guruprasad, P. Scaglione, M. Tang, Y. Sun, Y. Beiting, D. P. Nash, E. K. Fazelinia, H. Spruce, L. Wang, A. Tan, K. Guo, W. Conn, C. S. Fan, Y. Koumenis, C. Spiegelman, V. S. Rui, H. Diehl, J. A. Atherton, M. J. Stanger, B. Bailis, W. Ruella, M. Fuchs, S. 2026-04-01 doi:10.64898/2026.03.30.715365 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ When feeling is better than seeing: Adult Zebrafish Ignore Wide-Field Optic-Flow in Laminar, but not Turbulent Hydrodynamic Environments. ]]> https://biorxiv.org/content/10.64898/2026.03.30.715425v1?rss=1 Dave, S. Liao, J. C. 2026-04-01 doi:10.64898/2026.03.30.715425 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ The Computational and Neural Basis of Zero-Shot Control in Dynamic Pursuit ]]> https://biorxiv.org/content/10.64898/2026.03.30.715455v1?rss=1 Kim, D. Lee, J. J. Hayden, B. Y. Yoo, S. B. M. 2026-04-01 doi:10.64898/2026.03.30.715455 Cold Spring Harbor Laboratory Press 2026-04-01