bioRxiv Channel: Vanderbilt University https://biorxiv.org This feed contains articles for bioRxiv Channel "Vanderbilt University" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Extrapolating histone marks across developmental stages, tissues, and species: an enhancer prediction case study ]]> https://biorxiv.org/content/10.1101/010710v1?rss=1 John Anthony Capra 2014-10-25 doi:10.1101/010710 Cold Spring Harbor Laboratory Press 2014-10-25 <![CDATA[ Evolution of Conditional Cooperativity Between HOXA11 and FOXO1 Through Allosteric Regulation ]]> https://biorxiv.org/content/10.1101/014381v1?rss=1 Mauris C. Nnamani Soumya Ganguly Vincent J. Lynch Laura S. Mizoue Yingchun Tong Heather Darling Monika Fuxreiter Jens Meiler Gunter P. Wagner 2015-01-26 doi:10.1101/014381 Cold Spring Harbor Laboratory Press 2015-01-26 <![CDATA[ RNAseq in the mosquito maxillary palp: a little antennal RNA goes a long way ]]> https://biorxiv.org/content/10.1101/016998v1?rss=1 David C. Rinker Xiaofan Zhou Ronald Jason Pitts Patrick L. Jones Antonis Rokas LJ Zwiebel 2015-03-25 doi:10.1101/016998 Cold Spring Harbor Laboratory Press 2015-03-25 <![CDATA[ PrediXcan: Trait Mapping Using Human Transcriptome Regulation ]]> https://biorxiv.org/content/10.1101/020164v1?rss=1 Eric R Gamazon Heather E Wheeler Kaanan Shah Sahar V Mozaffari Keston Aquino-Michaels Robert J Carroll Anne E Eyler Joshua C Denny Dan L Nicolae Nancy J Cox Hae Kyung Im GTEx Consortium 2015-06-17 doi:10.1101/020164 Cold Spring Harbor Laboratory Press 2015-06-17 <![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[ Stimulus induced visual cortical networks are recapitulated by spontaneous local and inter-areal synchronization ]]> https://biorxiv.org/content/10.1101/021055v1?rss=1 Christopher Lewis Conrado Bosmann Thilo Womelsdorf Pascal Fries 2015-06-16 doi:10.1101/021055 Cold Spring Harbor Laboratory Press 2015-06-16 <![CDATA[ Avoiding accuracy-limiting pitfalls in the study of protein-ligand interactions with isothermal titration calorimetry ]]> https://biorxiv.org/content/10.1101/023796v1?rss=1 Sarah E. Boyce Joel Tellinghuisen John D. Chodera 2015-08-03 doi:10.1101/023796 Cold Spring Harbor Laboratory Press 2015-08-03 <![CDATA[ Suboptimal larval habitats modulate oviposition of the malaria vector mosquito Anopheles gambiae ]]> https://biorxiv.org/content/10.1101/027367v1?rss=1 Eunho Suh Dong-Hwan Choe Ahmed M Saveer Laurence J Zwiebel 2015-09-22 doi:10.1101/027367 Cold Spring Harbor Laboratory Press 2015-09-22 <![CDATA[ in silico Whole Genome Sequencer &amp; Analyzer (iWGS): a computational pipeline to guide the design and analysis of de novo genome sequencing studies ]]> https://biorxiv.org/content/10.1101/028134v1?rss=1 Xiaofan Zhou David Peris Jacek Kominek Cletus P Kurtzman Chris Todd Hittinger Antonis Rokas 2015-10-02 doi:10.1101/028134 Cold Spring Harbor Laboratory Press 2015-10-02 <![CDATA[ Meiotic interactors of a mitotic gene TAO3 revealed by functional analysis of its rare variant ]]> https://biorxiv.org/content/10.1101/033167v1?rss=1 Saumya Gupta Aparna Radhakrishnan Rachana Nitin Pandu Raharja-Liu Gen Lin Lars M Steinmetz Julien Gagneur Himanshu Sinha 2015-11-27 doi:10.1101/033167 Cold Spring Harbor Laboratory Press 2015-11-27 <![CDATA[ Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes ]]> https://biorxiv.org/content/10.1101/038596v1?rss=1 Kevin R Theis Nolwenn M. Dheilly Jonathan L. Klassen Robert M. Brucker John F. Baines Thomas C.G. Bosch John F. Cryan Scott F. Gilbert Charles J. Goodnight Elisabeth A. Lloyd Jan Sapp Philippe Vandenkoornhuyse Ilana Zilber-Rosenberg Eugene Rosenberg Seth R. Bordenstein 2016-02-02 doi:10.1101/038596 Cold Spring Harbor Laboratory Press 2016-02-02 <![CDATA[ Survey of the Heritability and Sparsity of Gene Expression Traits Across Human Tissues ]]> https://biorxiv.org/content/10.1101/043653v1?rss=1 Heather E Wheeler Kaanan P Shah Jonathon Brenner Tzintzuni Garcia Keston Aquino-Michaels GTEx Consortium Nancy J Cox Dan L Nicolae Hae Kyung Im 2016-03-15 doi:10.1101/043653 Cold Spring Harbor Laboratory Press 2016-03-15 <![CDATA[ Genetic predictors of gene expression associated with risk of bipolar disorder ]]> https://biorxiv.org/content/10.1101/043752v1?rss=1 Kaanan Shah Heather E Wheeler Eric R Gamazon Dan L Nicolae Nancy J Cox Hae Kyung Im 2016-03-15 doi:10.1101/043752 Cold Spring Harbor Laboratory Press 2016-03-15 <![CDATA[ Speciation by Symbiosis: The Microbiome and Behavior ]]> https://biorxiv.org/content/10.1101/045195v1?rss=1 J. Dylan Shropshire Seth R. Bordenstein 2016-03-23 doi:10.1101/045195 Cold Spring Harbor Laboratory Press 2016-03-23 <![CDATA[ Integrating tissue specific mechanisms into GWAS summary results ]]> https://biorxiv.org/content/10.1101/045260v1?rss=1 Alvaro Barbeira Scott P Dickinson Jason M Torres Eric S Torstenson Jiamao Zheng Heather E Wheeler Kaanan P Shah Todd Edwards GTEx Consortium Dan Nicolae Nancy J Cox Hae Kyung Im 2016-03-23 doi:10.1101/045260 Cold Spring Harbor Laboratory Press 2016-03-23 <![CDATA[ The mutational landscape of EGFR-, MYC-, and Kras- driven genetically-engineered mouse models of lung adenocarcinoma ]]> https://biorxiv.org/content/10.1101/048058v1?rss=1 David McFadden Katerina Politi Arjun Bhutkar Frances K Chen Xiaoling Song Mono Pirun Philip M Santiago Caroline Kim James T Platt Emily Lee Emily Hodges Adam P Rosebrock Roderick Bronson Nicholas D Socci Gregory Hannon Tyler Jacks Harold Varmus 2016-04-11 doi:10.1101/048058 Cold Spring Harbor Laboratory Press 2016-04-11 <![CDATA[ Unconscious integration of multisensory bodily inputs in the peripersonal space shapes bodily self-consciousness ]]> https://biorxiv.org/content/10.1101/048108v1?rss=1 Roy Salomon Jean Paul Noel Marta Lukowska Nathan Faivre Thomas Metzinger Andrea Serino Olaf Blanke 2016-04-11 doi:10.1101/048108 Cold Spring Harbor Laboratory Press 2016-04-11 <![CDATA[ Eukaryotic Association Module in Phage WO Genomes from Wolbachia ]]> https://biorxiv.org/content/10.1101/049049v1?rss=1 Sarah R Bordenstein Seth R Bordenstein 2016-04-16 doi:10.1101/049049 Cold Spring Harbor Laboratory Press 2016-04-16 <![CDATA[ Homeostatic responses regulate selfish mitochondrial genome dynamics in C. elegans ]]> https://biorxiv.org/content/10.1101/050930v1?rss=1 Bryan L Gitschlag Cait S Kirby David C Samuels Rama D Gangula Simon A Mallal Maulik R Patel 2016-04-29 doi:10.1101/050930 Cold Spring Harbor Laboratory Press 2016-04-29 <![CDATA[ Reduced spatial integration in the ventral visual cortex underlies face recognition deficits in developmental prosopagnosia ]]> https://biorxiv.org/content/10.1101/051102v1?rss=1 Nathaniel Witthoft Sonia Poltoratski Mai Nguyen Golijeh Golarai Alina Liberman Karen F LaRocque Mary E Smith Kalanit Grill-Spector 2016-04-29 doi:10.1101/051102 Cold Spring Harbor Laboratory Press 2016-04-29 <![CDATA[ A novel homology-based algorithm for the identification of physically linked clusters of paralogous genes ]]> https://biorxiv.org/content/10.1101/051953v1?rss=1 Juan F Ortiz Antonis Rokas 2016-05-05 doi:10.1101/051953 Cold Spring Harbor Laboratory Press 2016-05-05 <![CDATA[ The PAS domain-containing protein HeuR regulates heme uptake in Campylobacter jejuni ]]> https://biorxiv.org/content/10.1101/057042v1?rss=1 Jeremiah Johnson Jennifer Gaddy Victor DiRita 2016-06-03 doi:10.1101/057042 Cold Spring Harbor Laboratory Press 2016-06-03 <![CDATA[ Initiation of Retina Regeneration By a Conserved Mechanism of Adult Neurogenesis ]]> https://biorxiv.org/content/10.1101/057893v1?rss=1 Mahesh B Rao Dominic Didiano James G Patton 2016-06-08 doi:10.1101/057893 Cold Spring Harbor Laboratory Press 2016-06-08 <![CDATA[ Lingering representations of stimulus history at encoding influence recall organization ]]> https://biorxiv.org/content/10.1101/068353v1?rss=1 Stephanie C.Y. Chan Marissa C. Applegate Neal W Morton Sean M. Polyn Kenneth A. Norman 2016-08-11 doi:10.1101/068353 Cold Spring Harbor Laboratory Press 2016-08-11 <![CDATA[ Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data ]]> https://biorxiv.org/content/10.1101/070235v1?rss=1 Xing-Xing Shen Xiaofan Zhou Jacek Kominek Cletus P Kurtzman Chris Todd Hittinger Antonis Rokas 2016-08-18 doi:10.1101/070235 Cold Spring Harbor Laboratory Press 2016-08-18 <![CDATA[ A Machine Learning-based Framework to Identify Type 2 Diabetes through Electronic Health Records ]]> https://biorxiv.org/content/10.1101/078634v1?rss=1 Tao Zheng Wei Xie Liling Xu Xiaoying He Ya Zhang Mingrong You Gong Yang You Chen 2016-09-30 doi:10.1101/078634 Cold Spring Harbor Laboratory Press 2016-09-30 <![CDATA[ How Transcranial Magnetic Stimulation over Early Visual Cortex impacts short-term memory precision and guess rate ]]> https://biorxiv.org/content/10.1101/079178v1?rss=1 Rosanne Rademaker Vincent G van de Ven Frank Tong Alexander T Sack 2016-10-04 doi:10.1101/079178 Cold Spring Harbor Laboratory Press 2016-10-04 <![CDATA[ A global co-expression network approach for connecting genes to specialized metabolic pathways in plants ]]> https://biorxiv.org/content/10.1101/093914v1?rss=1 Wisecaver, J. H. Borowsky, A. T. Tzin, V. Jander, G. Kliebenstein, D. Rokas, A. 2016-12-14 doi:10.1101/093914 Cold Spring Harbor Laboratory Press 2016-12-14 <![CDATA[ Initiation of DNA replication requires actin dynamics and formin activity ]]> https://biorxiv.org/content/10.1101/102806v1?rss=1 Nikolaos, P. Krasinska, L. Harker, B. Urbach, S. Rossignol, M. Camasses, A. Dewar, J. Morin, N. Fisher, D. 2017-01-25 doi:10.1101/102806 Cold Spring Harbor Laboratory Press 2017-01-25 <![CDATA[ Interactions between genetic variation and cellular environment in skeletal muscle gene expression ]]> https://biorxiv.org/content/10.1101/105429v1?rss=1 Taylor, D. L. Knowles, D. A. Scott, L. J. Ramirez, A. H. Casale, F. P. Wolford, B. N. Guan, L. Varshney, A. Albanus, R. D. Parker, S. C. J. Narisu, N. Chines, P. S. Erdos, M. R. Welch, R. P. Kinnunen, L. Saramies, J. Sundvall, J. Lakka, T. A. Laakso, M. Tuomilehto, J. Koistinen, H. A. Stegle, O. Boehnke, M. Birney, E. Collins, F. S. 2017-02-03 doi:10.1101/105429 Cold Spring Harbor Laboratory Press 2017-02-03 <![CDATA[ Extensive Copy Number Variation in Fermentation-Related Genes among Saccharomyces cerevisiae Wine Strains ]]> https://biorxiv.org/content/10.1101/105502v1?rss=1 Steenwyk, J. Rokas, A. 2017-02-03 doi:10.1101/105502 Cold Spring Harbor Laboratory Press 2017-02-03 <![CDATA[ Integrative cross tissue analysis of gene expression identifies novel type 2 diabetes genes ]]> https://biorxiv.org/content/10.1101/108134v1?rss=1 Torres, J. M. Barbeira, A. N. Bonazzola, R. Morris, A. P. Shah, K. P. Wheeler, H. E. Bell, G. Cox, N. J. Im, H. K. 2017-02-13 doi:10.1101/108134 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[ Sequence properties underlying gene regulatory enhancers are conserved across mammals ]]> https://biorxiv.org/content/10.1101/110676v1?rss=1 Chen, L. Fish, A. E. Capra, J. A. 2017-02-21 doi:10.1101/110676 Cold Spring Harbor Laboratory Press 2017-02-21 <![CDATA[ Short DNA sequence patterns accurately identify broadlyactive human enhancers ]]> https://biorxiv.org/content/10.1101/111955v1?rss=1 Colbran, L. L. Chen, L. Capra, J. A. 2017-02-26 doi:10.1101/111955 Cold Spring Harbor Laboratory Press 2017-02-26 <![CDATA[ Widespread dysregulation of the circadian clock in human cancer ]]> https://biorxiv.org/content/10.1101/130765v1?rss=1 Chen, G. Hughey, J. 2017-04-25 doi:10.1101/130765 Cold Spring Harbor Laboratory Press 2017-04-25 <![CDATA[ COPI Mediates Recycling Of An Exocytic SNARE From Endosomes By Recognition Of A Ubiquitin Sorting Signal ]]> https://biorxiv.org/content/10.1101/133546v1?rss=1 Xu, P. Hankins, H. Macdonald, C. Erlinger, S. J. Frazier, M. Diab, N. S. Piper, R. C. Jackson, L. P. MacGurn, J. A. Graham, T. R. 2017-05-03 doi:10.1101/133546 Cold Spring Harbor Laboratory Press 2017-05-03 <![CDATA[ Bayesian Integrated Analysis Of Multiple Types Of Rare Variants To Infer Risk Genes For Schizophrenia And Other Neurodevelopmental Disorders ]]> https://biorxiv.org/content/10.1101/135293v1?rss=1 0.55), but low between SCZ and the NDDs ({rho} < 0.3). In depth analysis of 288 NDD genes shows highly significant protein-protein interaction (PPI) network connectivity, and functionally distinct PPI subnetworks based on pathway enrichments, single-cell RNA-seq (scRNAseq) cell types and multi-region developmental brain RNA-seq.nnConclusionsWe have extended a pipeline used in ASD studies and applied it to infer rare genetic parameters for SCZ and four NDDs. We find many new DD risk genes, supported by gene set enrichment and PPI network connectivity analyses. We find greater similarity among NDDs than between NDDs and SCZ. NDD gene subnetworks are implicated in postnatally expressed presynaptic and postsynaptic genes, and for transcriptional and post-transcriptional gene regulation in prenatal neural progenitor and stem cells. ]]> Nguyen, H. T. Dobbyn, A. Huckins, L. M. Ruderfer, D. Genovese, G. Fromer, M. Xu, X. Buxbaum, J. Hultman, C. Sklar, P. Purcell, S. M. He, X. Sullivan, P. F. Stahl, E. A. 2017-05-08 doi:10.1101/135293 Cold Spring Harbor Laboratory Press 2017-05-08 <![CDATA[ Genes Involved In Human Sialic Acid Biology Do Not Harbor Signatures Of Recent Positive Selection ]]> https://biorxiv.org/content/10.1101/137034v1?rss=1 Moon, J. M. Aronoff, D. Capra, T. Abbot, P. Rokas, A. 2017-05-11 doi:10.1101/137034 Cold Spring Harbor Laboratory Press 2017-05-11 <![CDATA[ Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets ]]> https://biorxiv.org/content/10.1101/142323v1?rss=1 Zhou, X. Shen, X.-X. Hittinger, C. T. Rokas, A. 2017-05-25 doi:10.1101/142323 Cold Spring Harbor Laboratory Press 2017-05-25 <![CDATA[ Opportunities And Obstacles For Deep Learning In Biology And Medicine ]]> https://biorxiv.org/content/10.1101/142760v1?rss=1 Ching, T. Himmelstein, D. S. Beaulieu-Jones, B. K. Kalinin, A. A. Do, B. T. Way, G. P. Ferrero, E. Agapow, P.-M. Xie, W. Rosen, G. L. Lengerich, B. J. Israeli, J. Lanchantin, J. Woloszynek, S. Carpenter, A. E. Shrikumar, A. Xu, J. Cofer, E. M. Harris, D. J. DeCaprio, D. Qi, Y. Kundaje, A. Peng, Y. Wiley, L. K. Segler, M. H. S. Gitter, A. Greene, C. S. 2017-05-28 doi:10.1101/142760 Cold Spring Harbor Laboratory Press 2017-05-28 <![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[ Refining The Accuracy Of Validated Target Identification Through Coding Variant Fine-Mapping In Type 2 Diabetes ]]> https://biorxiv.org/content/10.1101/144410v1?rss=1 1.36. Second, we used GWAS data from 50,160 T2D cases and 465,272 controls to fine-map associated coding variants in their regional context, with and without additional weighting, to account for the global enrichment of complex trait association signals in coding exons. We demonstrate convincing support (posterior probability >80% under the "annotation-weighted" model) that coding variants are causal for the association at 16 of the 40 signals (including novel signals involving POC5 p.His36Arg, ANKH p.Arg187Gln, WSCD2 p.Thr113Ile, PLCB3 p.Ser778Leu, and PNPLA3 p.Ile148Met). However, one third of coding variant association signals represent "false leads" at which naive analysis would have led to an erroneous inference regarding the effector transcript mediating the signal. Accurate identification of validated targets is dependent on correct specification of the contribution of coding and non-coding mediated mechanisms at associated loci. ]]> Mahajan, A. Morris, A. P. Rotter, J. I. McCarthy, M. I. 2017-05-31 doi:10.1101/144410 Cold Spring Harbor Laboratory Press 2017-05-31 <![CDATA[ Drivers of genetic diversity in secondary metabolic gene clusters in a fungal population ]]> https://biorxiv.org/content/10.1101/149856v1?rss=1 Lind, A. L. Wisecaver, J. H. Lameiras, C. Rodrigues, F. Goldman, G. H. Rokas, A. 2017-06-13 doi:10.1101/149856 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ Amyloid accumulation drives proteome-wide alterations in mouse models of Alzheimers disease like pathology ]]> https://biorxiv.org/content/10.1101/150623v1?rss=1 Savas, J. N. Wang, Y.-Z. DeNardo, L. A. Martinez-Bartolome, S. McClatchy, D. B. Hark, T. J. Shanks, N. F. Cozzolino, K. A. Lavallee-Adam, M. Smukowski, S. N. Park, S. K. Kelly, J. W. Koo, E. H. Nakagawa, T. Masliah, E. Ghosh, A. Yates, J. R. 2017-06-15 doi:10.1101/150623 Cold Spring Harbor Laboratory Press 2017-06-15 <![CDATA[ FUCCI tracking shows that Neurog3 levels vary with cell-cycle phase in endocrine-biased pancreatic progenitors ]]> https://biorxiv.org/content/10.1101/153700v1?rss=1 Bechard, M. E. Bankaitis, E. D. Ustione, A. Piston, D. Magnuson, M. A. Wright, C. V. E. 2017-06-21 doi:10.1101/153700 Cold Spring Harbor Laboratory Press 2017-06-21 <![CDATA[ Predicting single-cell transcription dynamics even when the central limit theorem fails ]]> https://biorxiv.org/content/10.1101/154401v1?rss=1 Munsky, B. Li, G. Fox, Z. Shepherd, D. P. Neuert, G. 2017-06-23 doi:10.1101/154401 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ Linearly changing stress environment causes cellular growth phenotype ]]> https://biorxiv.org/content/10.1101/155267v1?rss=1 Li, G. Kesler, B. K. Thiemicke, A. Rogers, D. C. Neuert, G. 2017-06-25 doi:10.1101/155267 Cold Spring Harbor Laboratory Press 2017-06-25 <![CDATA[ Unification of Countermanding and Perceptual Decision-making ]]> https://biorxiv.org/content/10.1101/158170v1?rss=1 Middlebrooks, P. G. Zandbelt, B. Logan, G. D. Palmeri, T. J. Schall, J. D. 2017-06-30 doi:10.1101/158170 Cold Spring Harbor Laboratory Press 2017-06-30 <![CDATA[ Whole genome bisulfite sequencing reveals a sparse, but robust pattern of DNA methylation in the Dictyostelium discoideum genome ]]> https://biorxiv.org/content/10.1101/166033v1?rss=1 Steenwyk, J. St. Denis, J. Dresch, J. Larochelle, D. Drewell, R. 2017-07-20 doi:10.1101/166033 Cold Spring Harbor Laboratory Press 2017-07-20 <![CDATA[ Quartet-based computations of internode certainty provide accurate and robust measures of phylogenetic incongruence ]]> https://biorxiv.org/content/10.1101/168526v1?rss=1 Zhou, X. Lutteropp, S. Czech, L. Stamatakis, A. von Looz, M. Rokas, A. 2017-07-27 doi:10.1101/168526 Cold Spring Harbor Laboratory Press 2017-07-27 <![CDATA[ Genomic dissection of bipolar disorder and schizophrenia including 28 subphenotypes ]]> https://biorxiv.org/content/10.1101/173435v1?rss=1 PGC Bipolar Disorder/Schizophrenia Working Group, Ruderfer, D. Sklar, P. Kendler, K. 2017-08-08 doi:10.1101/173435 Cold Spring Harbor Laboratory Press 2017-08-08 <![CDATA[ Proofreading-deficient coronaviruses adapt over long-term passage for increased fidelity and fitness without reversion of exoribonuclease-inactivating mutations ]]> https://biorxiv.org/content/10.1101/175562v1?rss=1 Graepel, K. Lu, X. Case, J. B. Sexton, N. R. Smith, E. C. Denison, M. R. 2017-08-11 doi:10.1101/175562 Cold Spring Harbor Laboratory Press 2017-08-11 <![CDATA[ Genome-wide Enhancer Maps Differ Significantly in Genomic Distribution, Evolution, and Function ]]> https://biorxiv.org/content/10.1101/176610v1?rss=1 Benton, M. L. Talipineni, S. C. Kostka, D. Capra, J. A. 2017-08-15 doi:10.1101/176610 Cold Spring Harbor Laboratory Press 2017-08-15 <![CDATA[ RNA editing of CAPS1 regulates synaptic vesicle organization, release and retrieval. ]]> https://biorxiv.org/content/10.1101/178202v1?rss=1 Ulbricht, R. J. Sun, S. J. DelBove, C. E. Kitko, K. E. Rehman, S. C. Wang, M. Y. Lazarenko, R. M. Zhang, Q. Emeson, R. 2017-08-18 doi:10.1101/178202 Cold Spring Harbor Laboratory Press 2017-08-18 <![CDATA[ Mouse hepatitis virus nsp14 exoribonuclease activity is required for resistance to innate immunity ]]> https://biorxiv.org/content/10.1101/182196v1?rss=1 Case, J. B. Li, Y. Elliott, R. Lu, X. Graepel, K. W. Sexton, N. R. Smith, E. C. Weiss, S. R. Denison, M. R. 2017-08-29 doi:10.1101/182196 Cold Spring Harbor Laboratory Press 2017-08-29 <![CDATA[ Microcircuitry of Performance Monitoring ]]> https://biorxiv.org/content/10.1101/187989v1?rss=1 Schall, J. D. Sajad, A. Godlove, D. C. 2017-09-12 doi:10.1101/187989 Cold Spring Harbor Laboratory Press 2017-09-12 <![CDATA[ Salient Experiences are Represented by Unique Transcriptional Signatures in the Brain ]]> https://biorxiv.org/content/10.1101/192278v1?rss=1 Mukherjee, D. Ignatowska-Jankowska, B. M. Itskovits, E. Gonzales, B. J. Turm, H. Izakson, L. Haritan, D. Bleistein, N. Cohen, C. Amit, I. Shay, T. Grueter, B. Zaslaver, A. Citri, A. 2017-09-21 doi:10.1101/192278 Cold Spring Harbor Laboratory Press 2017-09-21 <![CDATA[ Genetic validation of bipolar disorder identified by automated phenotyping using electronic health records ]]> https://biorxiv.org/content/10.1101/193011v1?rss=1 Chen, C.-Y. Lee, P. Castro, V. Minnier, J. Charney, A. Stahl, E. Ruderfer, D. Murphy, S. Gainer, V. Cai, T. Jones, I. Pato, C. Pato, M. Landen, M. Sklar, P. Perlis, R. Smoller, J. 2017-09-23 doi:10.1101/193011 Cold Spring Harbor Laboratory Press 2017-09-23 <![CDATA[ New evidence of a rhythmic priming effect that enhances grammaticality judgments in children ]]> https://biorxiv.org/content/10.1101/193961v1?rss=1 Chern, A. Tillmann, B. Vaughan, C. Gordon, R. L. 2017-09-27 doi:10.1101/193961 Cold Spring Harbor Laboratory Press 2017-09-27 <![CDATA[ Quaddles: A multidimensional 3D object set with parametrically-controlled and customizable features ]]> https://biorxiv.org/content/10.1101/194381v1?rss=1 Watson, M. R. Voloh, B. Naghizadeh, M. Womelsdorf, T. 2017-09-27 doi:10.1101/194381 Cold Spring Harbor Laboratory Press 2017-09-27 <![CDATA[ A LaeA- and BrlA-dependent cellular network governs tissue-specific secondary metabolism in the human pathogen Aspergillus fumigatus ]]> https://biorxiv.org/content/10.1101/196600v1?rss=1 AbaA>WetA transcriptional cascade. To elucidate BrlA pathway involvement in SM regulation, we examined the transcriptional and metabolic profiles of {Delta}brlA, {Delta}abaA, {Delta}wetA and wild-type strains of the human pathogen Aspergillus fumigatus. We find that BrlA, in addition to regulating production of developmental SMs, regulates vegetative SMs and the SrbA-regulated hypoxia stress response in a concordant fashion to LaeA. We further show that the transcriptional and metabolic equivalence of {Delta}brlA and {Delta}laeA is mediated by a LaeA requirement preventing heterochromatic marks in the brlA promoter. These results provide a framework for the cellular network regulating not only fungal SMs but diverse cellular processes linked to virulence of this pathogen. ]]> Lind, A. Lim, F. Y. Soukup, A. Keller, N. Rokas, A. 2017-09-30 doi:10.1101/196600 Cold Spring Harbor Laboratory Press 2017-09-30 <![CDATA[ N6-methyladenosine modification and the YTHDF2 reader protein play cell type specific roles in lytic viral gene expression during Kaposi’s sarcoma-associated herpesvirus infection ]]> https://biorxiv.org/content/10.1101/201475v1?rss=1 Hesser, C. Karijolich, J. Dominissini, D. He, C. Glaunsinger, B. A. 2017-10-11 doi:10.1101/201475 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ FLASH irradiation enhances the therapeutic index of abdominal radiotherapy in mice ]]> https://biorxiv.org/content/10.1101/2019.12.12.873414v1?rss=1 Levy, K. Natarajan, S. Wang, J. Chow, S. Eggold, J. Loo, P. Manjappa, R. Lartey, F. M. Schüler, E. Skinner, L. Rafat, M. Ko, R. Kim, A. Al Rawi, D. von Eyben, R. Dorigo, O. Casey, K. M. Graves, E. E. Bush, K. Yu, A. S. Koong, A. C. Maxim, P. G. Loo, B. W. Rankin, E. B. 2019-12-12 doi:10.1101/2019.12.12.873414 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ Phase of Firing Coding of Learning Variables across Prefrontal Cortex, Anterior Cingulate Cortex and Striatum during Feature Learning ]]> https://biorxiv.org/content/10.1101/2019.12.12.874859v1?rss=1 Voloh, B. Oemisch, M. Womelsdorf, T. 2019-12-13 doi:10.1101/2019.12.12.874859 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ RosettaGPCR: Multiple Template Homology Modeling of GPCRs with Rosetta ]]> https://biorxiv.org/content/10.1101/2019.12.13.875237v1?rss=1 Bender, B. Marlow, B. Meiler, J. 2019-12-13 doi:10.1101/2019.12.13.875237 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ Stutter: a Transient Dynamic Instability Phase that is Strongly Associated with Catastrophe ]]> https://biorxiv.org/content/10.1101/2019.12.16.878603v1?rss=1 Mahserejian, S. M. Scripture, J. P. Mauro, A. J. Lawrence, E. J. Jonasson, E. M. Murray, K. S. Li, J. Gardner, M. K. Alber, M. Zanic, M. Goodson, H. V. 2019-12-17 doi:10.1101/2019.12.16.878603 Cold Spring Harbor Laboratory Press 2019-12-17 <![CDATA[ Resolving the spatial profile of figure enhancement in human V1 through population receptive field modeling ]]> https://biorxiv.org/content/10.1101/2019.12.18.881722v1?rss=1 Poltoratski, S. Tong, F. 2019-12-19 doi:10.1101/2019.12.18.881722 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Implications of TP53 Allelic State for Genome Stability, Clinical Presentation and Outcomes in Myelodysplastic Syndromes ]]> https://biorxiv.org/content/10.1101/2019.12.19.868844v1?rss=1 Bernard, E. Nannya, Y. Hasserjian, R. P. Devlin, S. M. Tuechler, H. Medina-Martinez, J. S. Yoshizato, T. Shiozawa, Y. Saiki, R. Malcovati, L. Levine, M. F. Arango, J. E. Zhou, Y. Sole, F. Cargo, C. A. Haase, D. Creignou, M. Germing, U. Zhang, Y. Gundem, G. Sarian, A. van de Loosdrecht, A. A. Jadersten, M. Tobiasson, M. Kosmider, O. Follo, M. Y. Thol, F. Pinheiro, R. F. Santini, V. Kotsianidis, I. Boultwood, J. Santos, F. P. S. Schanz, J. Kasahara, S. Ishikawa, T. Tsurumi, H. Takaori-Kondo, A. Kiguchi, T. Polprasert, C. Bennett, J. M. Klimek, V. M. Savon 2019-12-19 doi:10.1101/2019.12.19.868844 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Molecular Basis for the Evolved Instability of a Human G-Protein Coupled Receptor ]]> https://biorxiv.org/content/10.1101/2019.12.20.884718v1?rss=1 Chamness, L. M. Zelt, N. B. Kuntz, C. P. Bender, B. J. Penn, W. D. Ziarek, J. J. Meiler, J. P. Schlebach, J. P. 2019-12-23 doi:10.1101/2019.12.20.884718 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[ Contrasting adaptations to synaptic physiology of prefrontal cortex interneuron subtypes in a mouse model of binge drinking ]]> https://biorxiv.org/content/10.1101/2020.01.05.895169v1?rss=1 Joffe, M. E. Winder, D. G. Conn, P. J. 2020-01-06 doi:10.1101/2020.01.05.895169 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ Free-water metrics in medial temporal lobe white matter tract projections relate to longitudinal cognitive decline ]]> https://biorxiv.org/content/10.1101/2020.01.06.896217v1?rss=1 Archer, D. B. Moore, E. E. Shashikumar, N. Dumitrescu, L. Pechman, K. Landman, B. Gifford, K. Jefferson, A. Hohman, T. 2020-01-07 doi:10.1101/2020.01.06.896217 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ The neural computations for stimulus presence and modal identity diverge along a shared circuit ]]> https://biorxiv.org/content/10.1101/2020.01.09.900563v1?rss=1 Tovar, D. A. Noel, J.-P. Ishizawa, Y. Patel, S. R. Eskandar, E. Wallace, M. T. 2020-01-09 doi:10.1101/2020.01.09.900563 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Topologically associating domain (TAD) boundaries stable across diverse cell types are evolutionarily constrained and enriched for heritability ]]> https://biorxiv.org/content/10.1101/2020.01.10.901967v1?rss=1 McArthur, E. Capra, J. A. 2020-01-11 doi:10.1101/2020.01.10.901967 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Distinct components of photoperiodic light are differentially encoded by the mammalian circadian clock ]]> https://biorxiv.org/content/10.1101/2020.01.14.906131v1?rss=1 Tackenberg, M. Hughey, J. McMahon, D. G. 2020-01-15 doi:10.1101/2020.01.14.906131 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Atf-6 regulates lifespan through ER-mitochondrial calcium homeostasis ]]> https://biorxiv.org/content/10.1101/2020.01.14.906693v1?rss=1 Burkewitz, K. Dutta, S. Kelley, C. A. Steinbaugh, M. Cram, E. J. Mair, W. B. 2020-01-15 doi:10.1101/2020.01.14.906693 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Genetically encoded split luciferase biosensors to measure endosome disruption in real time in live cells ]]> https://biorxiv.org/content/10.1101/2020.01.16.906180v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@11f6b8forg.highwire.dtl.DTLVardef@1ceaf34org.highwire.dtl.DTLVardef@508600org.highwire.dtl.DTLVardef@8da9c3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kilchrist, K. V. Tierney, J. W. Duvall, C. L. 2020-01-16 doi:10.1101/2020.01.16.906180 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ Registration-free Distortion Correction of Diffusion Weighted MRI ]]> https://biorxiv.org/content/10.1101/2020.01.19.911784v1?rss=1 Schilling, K. G. Blaber, J. Hansen, C. Rogers, B. Anderson, A. W. Smith, S. Kanakaraj, P. Rex, T. Resnick, S. M. Shafer, A. T. Cutting, L. Woodward, N. Zald, D. Landman, B. A. 2020-01-19 doi:10.1101/2020.01.19.911784 Cold Spring Harbor Laboratory Press 2020-01-19 <![CDATA[ Reduced function of the glutathione S-transferase S1 suppresses behavioral hyperexcitability in Drosophila expressing a mutant voltage-gated sodium channel ]]> https://biorxiv.org/content/10.1101/2020.01.21.906156v1?rss=1 Chen, H.-L. Kasuya, J. Lansdon, P. Kaas, G. A. Tang, H. Sodders, M. Kitamoto, T. 2020-01-21 doi:10.1101/2020.01.21.906156 Cold Spring Harbor Laboratory Press 2020-01-21 <![CDATA[ Cross-sectional and longitudinal associations of family income-to-needs ratio with cortical and subcortical brain volume in adolescent boys and girls ]]> https://biorxiv.org/content/10.1101/2020.01.24.918847v1?rss=1 King, L. S. Dennis, E. L. Humphreys, K. L. Thompson, P. M. Gotlib, I. H. 2020-01-25 doi:10.1101/2020.01.24.918847 Cold Spring Harbor Laboratory Press 2020-01-25 <![CDATA[ Macrophages Promote Aortic Valve Cell Calcification Through STAT3 Splicing ]]> https://biorxiv.org/content/10.1101/2020.01.24.919001v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@3ee95org.highwire.dtl.DTLVardef@24ae93org.highwire.dtl.DTLVardef@41497corg.highwire.dtl.DTLVardef@3f6c05_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Raddatz, M. Huffstater, T. Bersi, M. R. Reinfeld, B. Madden, M. Booton, S. Rathmell, K. Rathmell, J. C. Lindman, B. Madhur, M. Merryman, W. D. 2020-01-24 doi:10.1101/2020.01.24.919001 Cold Spring Harbor Laboratory Press 2020-01-24 <![CDATA[ Functional characterization of clinical isolates of the opportunistic fungal pathogen Aspergillus nidulans ]]> https://biorxiv.org/content/10.1101/2020.01.28.917278v1?rss=1 Bastos, R. W. Valero, C. Silva, L. P. Schoen, T. Drott, M. Brauer, V. Silva-Rocha, R. Lind, A. Steenwyk, J. L. Rokas, A. Rodrigues, F. Resendiz-Sharpe, A. Lagrou, K. Marcet-Houben, M. Gabaldon, T. McDonnell, E. Reid, I. Tsang, A. Oakley, B. R. Loures, F. Almeida, F. Huttenlocher, A. Keller, N. P. Ries, L. Goldman, G. H. 2020-01-29 doi:10.1101/2020.01.28.917278 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ Diverse cell stimulation kinetics identify predictive signal transduction models ]]> https://biorxiv.org/content/10.1101/2020.01.28.923755v1?rss=1 Jashnsaz, H. Fox, Z. R. Hughes, J. Li, G. Munsky, B. E. Neuert, G. 2020-01-29 doi:10.1101/2020.01.28.923755 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ Peripheral Myelin Protein 22 Preferentially Partitions into Ordered Phase Membrane Domains ]]> https://biorxiv.org/content/10.1101/2020.01.28.923771v1?rss=1 Marinko, J. T. Li, G. C. Kenworthy, A. K. Sanders, C. R. 2020-01-29 doi:10.1101/2020.01.28.923771 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ Eating breakfast and avoiding the evening snack sustains lipid oxidation ]]> https://biorxiv.org/content/10.1101/2020.01.29.923417v1?rss=1 Kelly, K. P. McGuinness, O. P. Buchowski, M. Hughey, J. P. Chen, H. Powers, J. Page, T. Johnson, C. H. 2020-01-30 doi:10.1101/2020.01.29.923417 Cold Spring Harbor Laboratory Press 2020-01-30 <![CDATA[ A Minimal Biophysical Model of Neocortical Pyramidal Cells: Implications for Frontal Cortex Microcircuitry and Field Potential Generation ]]> https://biorxiv.org/content/10.1101/2020.01.29.925180v1?rss=1 Herrera, B. Sajad, A. Woodman, G. F. Schall, J. D. Riera, J. J. 2020-01-30 doi:10.1101/2020.01.29.925180 Cold Spring Harbor Laboratory Press 2020-01-30 <![CDATA[ Matrix-targeted Nanoparticles for MMP13 RNA Interference Blocks Post-Traumatic Osteoarthritis. ]]> https://biorxiv.org/content/10.1101/2020.01.30.925321v1?rss=1 View larger version (54K): org.highwire.dtl.DTLVardef@1803795org.highwire.dtl.DTLVardef@c1254dorg.highwire.dtl.DTLVardef@78233eorg.highwire.dtl.DTLVardef@151d96f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOAbstract Figure:C_FLOATNO PTOA targeted delivery of MMP13 siRNA to block disease progressionThe top left schematic illustrates the progression (left to right) from healthy knee joint, through inflammation induction following traumatic injury, to cartilage loss and degenerative joint disease (including synovial response). Degradation of cartilage enhances inflammation, inducing a degenerative cycle (middle right). The bottom of the graphic illustrates the concept of the matrix targeted nanocarriers for enhanced retention and activity of MMP13 siRNA at sites of cartilage injury. C_FIG ]]> Bedingfield, S. K. Yu, F. Liu, D. D. Jackson, M. A. Himmel, L. E. Cho, H. Colazo, J. M. Crofford, L. J. Hasty, K. A. Duvall, C. L. 2020-01-31 doi:10.1101/2020.01.30.925321 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Selfish mitochondria exploit nutrient status across different levels of selection ]]> https://biorxiv.org/content/10.1101/2020.01.30.927202v1?rss=1 Gitschlag, B. L. Tate, A. T. Patel, M. R. 2020-01-31 doi:10.1101/2020.01.30.927202 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Leukotriene B4 licenses inflammasome activation to enhance skin host defense ]]> https://biorxiv.org/content/10.1101/2020.02.03.932129v1?rss=1 Salina, A. C. G. Brandt, S. Klopfenstein, N. Blackman, A. Byers-Glosson, N. Brodskyn, C. Tavares, N. M. Santos Da Silva, I. B. Medeiros, A. I. Serezani, C. H. 2020-02-04 doi:10.1101/2020.02.03.932129 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Energy supply per neuron is constrained by capillary density in the mouse brain ]]> https://biorxiv.org/content/10.1101/2020.02.03.932434v1?rss=1 Ventura-Antunes, L. Herculano-Houzel, S. 2020-02-03 doi:10.1101/2020.02.03.932434 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ A novel mutation in KCNK16 causing a gain-of-function in the TALK-1 potassium channel: a new cause of maturity onset diabetes of the young. ]]> https://biorxiv.org/content/10.1101/2020.02.04.929430v1?rss=1 C, p.Leu114Pro) segregating with MODY. KCNK16 is the most abundant and {beta}-cell-restricted K+ channel transcript and encodes the two-pore-domain K+ channel TALK-1. Whole-cell K+ currents in transfected HEK293 cells demonstrated drastic (312-fold increase) gain-of-function with TALK-1 Leu144Pro vs. WT, due to greater single channel activity. Glucose-stimulated cytosolic Ca2+ influx was inhibited in mouse islets expressing TALK-1 Leu114Pro (area under the curve [AUC] at 20mM glucose: Leu114Pro 60.1 vs. WT 89.1; P=0.030) and less endoplasmic reticulum calcium storage (cyclopiazonic acid-induced release AUC: Leu114Pro 17.5 vs. WT 46.8; P=0.008). TALK-1 Leu114Pro significantly blunted GSIS compared to TALK-1 WT in both mouse (52% decrease, P=0.039) and human (38% decrease, P=0.019) islets. ConclusionsOur data identify a novel MODY-associated gene, KCNK16; with a gain-of-function mutation limiting Ca2+ influx and GSIS. A gain-of-function common polymorphism in KCNK16 is associated with type 2 diabetes (T2DM); thus, our findings have therapeutic implications not only for KCNK16-associated MODY but also for T2DM. ]]> Graff, S. Johnson, S. Leo, P. Dadi, P. Nakhe, A. McInerney-Leo, A. Marshall, M. Brown, M. Jacobson, D. Duncan, E. 2020-02-04 doi:10.1101/2020.02.04.929430 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ A series of dual-reporter vectors for ratiometric analysis of protein abundance in plants ]]> https://biorxiv.org/content/10.1101/2020.02.10.939363v1?rss=1 Khosla, A. Rodriguez-Furlan, C. Kapoor, S. Van Norman, J. M. Nelson, D. C. 2020-02-12 doi:10.1101/2020.02.10.939363 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2020.02.11.941351v1?rss=1 Lopez de Maturana, E. Rodriguez, J. Alonso, L. Lao, O. Molina-Montes, E. Martin-Antoniano, I. Gomez-Rubio, P. Lawlor, R. Carrato, A. Hidalgo, M. Iglesias, M. Molero, X. Lohr, M. Michalski, C. Perea, J. O'Rorke, M. Barbera, V. Tardon, A. Farre, A. Munoz-Bellvis, L. Crnogorac-Jurcevic, T. Dominguez-Munoz, E. Gress, T. Greenhaf, W. Sharp, L. Arnes, L. Cecchini, L. Balsells, J. Costello, E. Ilzarbe, L. Kleeff, J. Kong, B. Marquez, M. Mora, J. O'Driscoll, D. Scarpa, A. Ye, W. Yu, J. Investigators, P. Garcia-Closas, M. Kogevinas, M. Rothman, N. Silverman, D. 2020-02-12 doi:10.1101/2020.02.11.941351 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Kupffer Cell Release of Platelet Activating Factor Drives Dose Limiting Toxicities of Nucleic Acid Nanocarriers ]]> https://biorxiv.org/content/10.1101/2020.02.11.944504v1?rss=1 Jackson, M. A. Patel, S. S. Yu, F. Cottam, M. A. Glass, E. B. Dollinger, B. R. Hoogenboezem, E. N. Patil, P. Liu, D. D. Kelly, I. B. Bedingfield, S. K. King, A. R. Miles, R. E. Hasty, A. M. Giorgio, T. D. Duvall, C. L. 2020-02-12 doi:10.1101/2020.02.11.944504 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Accelerated Simulations of Chemical Reaction Systems using the Stochastic Simulation Algorithm on GPUs ]]> https://biorxiv.org/content/10.1101/2020.02.14.948612v1?rss=1 Pino, J. C. Prugger, M. Lubbock, A. L. R. Harris, L. A. Lopez, C. F. 2020-02-14 doi:10.1101/2020.02.14.948612 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Rapid quantitative imaging of high intensity ultrasonic pressure fields ]]> https://biorxiv.org/content/10.1101/2020.02.15.951046v1?rss=1 Luo, H. Kusunose, J. Pinton, G. Caskey, C. F. Grissom, W. A. 2020-02-16 doi:10.1101/2020.02.15.951046 Cold Spring Harbor Laboratory Press 2020-02-16 <![CDATA[ CRISPR-mediated isogenic cell-SELEX approach for generating highly specific aptamers against native membrane proteins ]]> https://biorxiv.org/content/10.1101/2020.02.17.949768v1?rss=1 Rosch, J. C. Neal, E. H. Balikov, D. A. Rahim, M. Lippmann, E. 2020-02-17 doi:10.1101/2020.02.17.949768 Cold Spring Harbor Laboratory Press 2020-02-17 <![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[ 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[ Transcriptional control of parallel-acting pathways that remove discrete presynaptic proteins in remodeling neurons ]]> https://biorxiv.org/content/10.1101/2020.02.21.959700v1?rss=1 Miller, D. M. Fleming-Miller, T. W. Cuentas-Condori, A. Manning, L. Palumbos, S. Richmond, J. E. 2020-02-24 doi:10.1101/2020.02.21.959700 Cold Spring Harbor Laboratory Press 2020-02-24 <![CDATA[ Predicting changes in protein thermostability upon point mutation with deep 3D convolutional neural networks ]]> https://biorxiv.org/content/10.1101/2020.02.28.959874v1?rss=1 Li, B. Yang, Y. T. Capra, J. A. Gerstein, M. 2020-02-28 doi:10.1101/2020.02.28.959874 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ Genomic and phenotypic heterogeneity of clinical isolates of the human pathogens Aspergillus fumigatus, Aspergillus lentulus and Aspergillus fumigatiaffinis ]]> https://biorxiv.org/content/10.1101/2020.02.28.970384v1?rss=1 200,000 life-threatening aspergillosis infections per year worldwide are caused by Aspergillus fumigatus. Recently, molecular typing techniques have revealed that aspergillosis can also be caused by organisms that are phenotypically similar to A. fumigatus but genetically distinct, such as Aspergillus lentulus and Aspergillus fumigatiaffinis. Importantly, some of these so-called cryptic species exhibit different virulence and drug susceptibility profiles than A. fumigatus, however, our understanding of their biology and pathogenic potential has been stymied by the lack of genome sequences and phenotypic profiling. To fill this gap, we phenotypically characterized the virulence and drug susceptibility of 15 clinical strains of A. fumigatus, A. lentulus, and A. fumigatiaffinis from Spain and sequenced their genomes. We found heterogeneity in virulence and drug susceptibility across species and strains. Genes known to influence drug susceptibility (cyp51A and fks1) vary in paralog number and sequence among these species and strains and correlate with differences in drug susceptibility. Similarly, genes known to be important for virulence in A. fumigatus showed variability in number of paralogs across strains and across species. Characterization of the genomic similarities and differences of clinical strains of A. lentulus, A. fumigatiaffinis, and A. fumigatus that vary in disease-relevant traits will advance our understanding of the variance in pathogenicity between Aspergillus species and strains that are collectively responsible for the vast majority of aspergillosis infections in humans. ]]> Santos, R. A. C. Steenwyk, J. L. Rivero-Menendez, O. Mead, M. E. Silva, L. P. Bastos, R. W. Alastruey-Izquierdo, A. Goldman, G. H. Rokas, A. 2020-02-28 doi:10.1101/2020.02.28.970384 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ A computational framework to explore cellular response mechanisms from multi-omics datasets ]]> https://biorxiv.org/content/10.1101/2020.03.02.974121v1?rss=1 Pino, J. C. Lubbock, A. L. R. Harris, L. A. Gutierrez, D. B. Farrow, M. A. Muszynski, N. Tsui, T. Norris, J. L. Caprioli, R. M. Wikswo, J. P. Lopez, C. F. 2020-03-03 doi:10.1101/2020.03.02.974121 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ Phosphorylation barcode-dependent signal bias of the dopamine D1 receptor ]]> https://biorxiv.org/content/10.1101/2020.03.03.971846v1?rss=1 Kaya, A. I. Perry Hauser, N. Gurevich, V. V. Iverson, T. 2020-03-04 doi:10.1101/2020.03.03.971846 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ Symmetrically substituted dichlorophenes inhibit N-acyl-phosphatidylethanolamine phospholipase D ]]> https://biorxiv.org/content/10.1101/2020.03.05.979567v1?rss=1 Aggarwal, G. Zarrow, J. E. Mashhadi, Z. Flynn, C. R. Vinson, P. Weaver, C. D. Davies, S. S. 2020-03-05 doi:10.1101/2020.03.05.979567 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Express saccades during a countermanding task ]]> https://biorxiv.org/content/10.1101/2020.03.20.000760v1?rss=1 Errington, S. P. Schall, J. D. 2020-03-23 doi:10.1101/2020.03.20.000760 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ Nuclear envelope-vacuole contacts mitigate nuclear pore complex assembly stress ]]> https://biorxiv.org/content/10.1101/2020.03.23.001719v1?rss=1 Lord, C. Wente, S. 2020-03-23 doi:10.1101/2020.03.23.001719 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ Sexually Antagonistic Selection on Genetic Variation is Rare in Humans ]]> https://biorxiv.org/content/10.1101/2020.03.26.009670v1?rss=1 Kasimatis, K. R. Abraham, A. Ralph, P. L. Kern, A. D. Capra, J. A. Phillips, P. C. 2020-03-28 doi:10.1101/2020.03.26.009670 Cold Spring Harbor Laboratory Press 2020-03-28 <![CDATA[ Structure based virtual screening identifies novel competitive inhibitors for the sialoglycan binding protein Hsa ]]> https://biorxiv.org/content/10.1101/2020.03.27.006247v1?rss=1 Agarwal, R. Bensing, B. A. Mi, D. Vinson, P. N. Baudry, J. Iverson, T. M. Smith, J. 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Holmes, W. R. 2020-04-02 doi:10.1101/2020.04.01.020289 Cold Spring Harbor Laboratory Press 2020-04-02 <![CDATA[ Multimodal Nonlinear Optical and Thermal Imaging Platform for Label-Free Characterization of Biological Tissue ]]> https://biorxiv.org/content/10.1101/2020.04.06.023820v1?rss=1 Adams, W. R. Mehl, B. Leiser, E. Wang, M. Patton, S. Throckmorton, G. A. Jenkins, J. L. Ford, J. B. Gautam, R. Brooker, J. Jansen, E. D. Mahadevan-Jansen, A. 2020-04-07 doi:10.1101/2020.04.06.023820 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Lipid Landscape of the Human Retina and Supporting Tissues Revealed by High Resolution Imaging Mass Spectrometry ]]> https://biorxiv.org/content/10.1101/2020.04.08.029538v1?rss=1 Anderson, D. M. Messinger, J. D. Patterson, N. H. Rivera, E. S. Kotnala, A. Spraggins, J. M. Caprioli, R. M. Curcio, C. A. Schey, K. L. 2020-04-09 doi:10.1101/2020.04.08.029538 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Neuronal Modeling of Alternating Hemiplegia of Childhood Reveals Transcriptional Compensation and Replicates a Trigger-Induced Phenotype ]]> https://biorxiv.org/content/10.1101/2020.04.08.031732v1?rss=1 Snow, J. Westlake, G. Klofas, L. Jeon, S. Armstrong, L. Swoboda, K. George, A. L. Ess, K. 2020-04-10 doi:10.1101/2020.04.08.031732 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ Viral cross-linking and solid-phase purification enables discovery of ribonucleoprotein complexes on incoming RNA virus genomes ]]> https://biorxiv.org/content/10.1101/2020.04.08.032441v1?rss=1 Kim, B. Arcos, S. E. Rothamel, K. L. Ascano, M. 2020-04-09 doi:10.1101/2020.04.08.032441 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Thyroglobulin Interactome Profiling Uncovers Molecular Mechanisms of Thyroid Dyshormonogenesis ]]> https://biorxiv.org/content/10.1101/2020.04.08.032482v1?rss=1 Wright, M. T. Kouba, L. Plate, L. 2020-04-09 doi:10.1101/2020.04.08.032482 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Biosynthetic gene clusters, secondary metabolite profiles, and cards of virulence in the closest nonpathogenic relatives of Aspergillus fumigatus ]]> https://biorxiv.org/content/10.1101/2020.04.09.033902v1?rss=1 Steenwyk, J. L. Mead, M. E. Knowles, S. L. Raja, H. A. Roberts, C. D. Bader, O. Houbraken, J. Goldman, G. H. Oberlies, N. H. Rokas, A. 2020-04-10 doi:10.1101/2020.04.09.033902 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ SETD2 is an actin lysine methyltransferase ]]> https://biorxiv.org/content/10.1101/2020.04.13.034629v1?rss=1 Seervai, R. N. H. Jangid, R. K. Karki, M. Tripathi, D. N. Jung, S. Y. Kearns, S. E. Verhey, K. J. Cianfrocco, M. A. Millis, B. A. Tyska, M. J. Mason, F. M. Rathmell, W. K. Park, I. Y. Dere, R. Walker, C. L. 2020-04-14 doi:10.1101/2020.04.13.034629 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Control of mammalian brain aging by the unfolded protein response (UPR) ]]> https://biorxiv.org/content/10.1101/2020.04.13.039172v1?rss=1 Cabral Miranda, F. Tamburini, G. Martinez, G. Medinas, D. Gerakis, Y. Miedema, T. Duran-Aniotz, C. Ardilles, A. Ibaceta, C. Sabusap, C. Bermedo-Garcia, F. Adamson, S. Vitangcol, K. Huerta, H. Zhang, X. Nakamura, T. Sardi, P. Lipton, S. Kennedy, B. Cardenas, J. C. Palacios, A. Plate, L. Henriquez, J. P. Hetz, C. 2020-04-14 doi:10.1101/2020.04.13.039172 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Clinically adaptable polymer enables simultaneous spatial analysis of colonic tissues and biofilms ]]> https://biorxiv.org/content/10.1101/2020.04.15.030874v1?rss=1 Macedonia, M. C. Drewes, J. L. Markham, N. O. Simmons, A. J. Roland, J. T. Vega, P. N. Scurrah, C. R. Coffey, R. J. Shrubsole, M. J. Sears, C. L. Lau, K. S. 2020-04-17 doi:10.1101/2020.04.15.030874 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ Beyond the biosynthetic gene cluster paradigm: Genome-wide co-expression networks connect clustered and unclustered transcription factors to secondary metabolic pathways ]]> https://biorxiv.org/content/10.1101/2020.04.15.040477v1?rss=1 Kwon, M. J. Steiniger, C. Cairns, T. C. Wisecaver, J. H. Lind, A. Pohl, C. Regner, C. Rokas, A. Meyer, V. 2020-04-15 doi:10.1101/2020.04.15.040477 Cold Spring Harbor Laboratory Press 2020-04-15 <![CDATA[ Neonicotinoids Disrupt Circadian Rhythms and Sleep in Honey Bees ]]> https://biorxiv.org/content/10.1101/2020.04.15.042960v1?rss=1 Tackenberg, M. C. Giannoni-Guzman, M. A. Doll, C. A. Agosto-Rivera, J. L. Broadie, K. Moore, D. McMahon, D. G. 2020-04-16 doi:10.1101/2020.04.15.042960 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Elucidation and refinement of synthetic receptor mechanisms ]]> https://biorxiv.org/content/10.1101/2020.04.16.045039v1?rss=1 Edelstein, H. I. Donahue, P. S. Muldoon, J. J. Kang, A. K. Dolberg, T. B. Battaglia, L. M. Allchin, E. R. Hong, M. Leonard, J. N. 2020-04-18 doi:10.1101/2020.04.16.045039 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Epigenetic regulator BMI1 promotes fusion-positive rhabdomyosarcoma proliferation and constitutes a novel therapeutic target ]]> https://biorxiv.org/content/10.1101/2020.04.18.048355v1?rss=1 Shields, C. E. Potlapalli, S. Cuya-Smith, S. M. Chappell, S. K. Chen, D. Martinez, D. Pogoriler, J. Rathi, K. S. Patel, S. A. Maris, J. M. Schnepp, R. W. 2020-04-18 doi:10.1101/2020.04.18.048355 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices ]]> https://biorxiv.org/content/10.1101/2020.04.20.049999v1?rss=1 Walker, J. F. Shen, X.-X. Rokas, A. Smith, S. A. Moyroud, E. 2020-04-21 doi:10.1101/2020.04.20.049999 Cold Spring Harbor Laboratory Press 2020-04-21 <![CDATA[ Erythropoietin regulates transcription and YY1 dynamics in a pre-established chromatin architecture ]]> https://biorxiv.org/content/10.1101/2020.04.21.034116v1?rss=1 Perreault, A. A. Brown, J. D. Venters, B. J. 2020-04-22 doi:10.1101/2020.04.21.034116 Cold Spring Harbor Laboratory Press 2020-04-22 <![CDATA[ Localization of the Lens Intermediate Filament Switch by Imaging Mass Spectrometry ]]> https://biorxiv.org/content/10.1101/2020.04.21.053793v1?rss=1 Wang, Z. Ryan, D. J. Schey, K. L. 2020-04-23 doi:10.1101/2020.04.21.053793 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ A Cytoskeletal Function for PBRM1 Reading Methylated Microtubules ]]> https://biorxiv.org/content/10.1101/2020.04.21.053942v1?rss=1 Karki, M. Jangid, R. K. Seervai, R. N. H. Bertocchio, J.-P. Hotta, T. Msaouel, P. Jung, S. Y. Grimm, S. L. Coarfa, C. Weissman, B. E. Ohi, R. Verhey, K. J. Hodges, C. H. Dere, R. Park, I.-Y. Rathmell, K. W. Walker, C. L. Tripathi, D. N. 2020-04-22 doi:10.1101/2020.04.21.053942 Cold Spring Harbor Laboratory Press 2020-04-22 <![CDATA[ Human iPSC-derived cerebral organoids model features of Leigh Syndrome and reveal abnormal corticogenesis ]]> https://biorxiv.org/content/10.1101/2020.04.21.054361v1?rss=1 Romero-Morales, A. I. Rastogi, A. Temuri, H. Rasmussen, M. L. McElroy, G. S. Hsu, L. Almonacid, P. M. Millis, B. A. Chandel, N. S. Cartailler, J.-P. Gama, V. 2020-04-22 doi:10.1101/2020.04.21.054361 Cold Spring Harbor Laboratory Press 2020-04-22 <![CDATA[ Pancreatic beta cell selective deletion of mitofusins 1 and 2 (Mfn1 and Mfn2) disrupts mitochondrial architecture and abrogates glucose-stimulated insulin secretion in vivo ]]> https://biorxiv.org/content/10.1101/2020.04.22.055384v1?rss=1 five-fold decrease (p<0.0001) in plasma insulin. Mitochondrial length, glucose-induced polarisation, ATP synthesis and cytosolic Ca2+ increases were all reduced (p<0.05,p<0.01,p<0.0001) in dKO islets, and beta cell Ca2+ dynamics were suppressed in vivo (p<0.001). In contrast, oral glucose tolerance was near normal in {beta}Mfn1/2 dKO mice (p<0.05, p<0.01) and GLP-1 or GIP receptor agonists largely corrected defective GSIS from isolated islets through an EPAC-dependent signalling activation. Conclusions/interpretationMitochondrial fusion and fission cycles are thus essential in the beta cell to maintain normal glucose, but not incretin, sensing. Defects in these cycles in some forms of diabetes might therefore provide opportunities for novel incretin-based or other therapies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=180 SRC="FIGDIR/small/055384v3_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@258053org.highwire.dtl.DTLVardef@c07cborg.highwire.dtl.DTLVardef@1d3bb1forg.highwire.dtl.DTLVardef@1a1f128_HPS_FORMAT_FIGEXP M_FIG Impact of Mfn1/2 deletion on glucose and incretin stimulated-insulin secretion in beta cells. (A) In control animals, glucose is taken up by beta cells through GLUT2 and metabolised by mitochondria (elongated structure) through the citrate (TCA) cycle, leading to an increased mitochondrial proton motive force (hyperpolarised {Delta}{psi}m), accelerated ATP synthesis and O2 consumption rate (OCR). Consequently, the cytoplasmic ATP:ADP ratio rises, which causes closure of KATP channels, depolarisation of plasma membrane potential ({psi}m), opening of VDCCs and influx of cytosolic Ca2+. Elevated [Ca2+]cyt triggers a number of ATP-dependent processes including insulin secretion and improved beta-beta cell communication through connexin 36 (Cx36). (B) Following Mfn1/2 deletion (Mfn1/2 dKO), highly fragmented mitochondria were associated with reduced mitochondrial Ca2+ ([Ca2+]m) accumulation, leading to a less polarised {Delta}{psi}m, weaker OCR, lower mtDNA copy number and decreased ATP synthesis. This is expected to result in weaker {psi}m depolarisation, cytosolic Ca2+ influx and beta-beta cell connectivity due to lower expression of Cx36. Despite observing a higher number of docked insulin granules on the plasma membrane, insulin secretion was highly suppressed in these animals. This was also associated with increased beta cell death and reduced beta cell mass. (C) In response to incretins, insulin secretion is potentiated through the activation of GLP1-R and cAMP signalling involving PKA- and EPAC2-dependent pathways. Elevated [Ca2+]cyt triggers a number of ATP-dependent processes including insulin secretion and Ca2+ removal into the endoplasmic reticulum (ER).(D) In Mfn1/2 dKO cells, activation of the GLP1-R was shown to be linked with a potentiation of the EPAC2 pathway that is PKA independent, along with an increased ER Ca2+ uptake and improved beta-beta cell communication. How these amplifying signals of glucose metabolism for insulin secretion are linked with fragmented mitochondria remains unknown. Red and bold arrows represent enhanced pathways; dashed arrows represent impaired pathways. This figure was produced using illustrations from Servier Medical Art, http://smart.servier.com/ C_FIG Research in contextWhat is already known about this subject? Mitochondrial ultrastructural variations and number are altered in beta cells of human T2D patients [1]. Mice lacking Opa1, which controls mitochondrial fusion and inner membrane cristae structure, in beta cells, develop hyperglycaemia and defects in GSIS [2]. What is the key question? Is an interconnected mitochondrial network essential in primary mouse beta cells for normal insulin secretion and glucose homeostasis? What are the new findings? We generated mice with beta cell-selective, adult-restricted deletion of the mitofusin genes Mfn1 and Mfn2 and show that insulin secretion and glucose homeostasis are strongly reduced in vivo. Cytosolic and mitochondrial Ca2+ increases, {Delta}{psi}m, ATP production and beta cell connectivity are impaired in {beta}Mfn1/2 dKO animals. Incretins bypass the above defects through an exchange protein directly activated by cAMP (EPAC)-dependent signalling mechanism. How might this impact on clinical practice in the foreseeable future? 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S. Thackray, L. Diamond, M. S. Carnahan, R. H. Crowe, J. E. 2020-05-13 doi:10.1101/2020.05.12.091462 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ Evolution-guided mutagenesis of the cytoplasmic incompatibility proteins: Identifying CifAs complex functional repertoire and new essential regions in CifB ]]> https://biorxiv.org/content/10.1101/2020.05.13.093815v1?rss=1 Shropshire, J. D. Kalra, M. Bordenstein, S. R. 2020-05-14 doi:10.1101/2020.05.13.093815 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Gene Editing Reveals Obligate and Modulatory Components of the CO2 Receptor Complex in the Malaria Vector Mosquito, Anopheles coluzzii ]]> https://biorxiv.org/content/10.1101/2020.05.13.094995v1?rss=1 Liu, F. Ye, Z. Baker, A. P. Sun, H. Zwiebel, L. 2020-05-15 doi:10.1101/2020.05.13.094995 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Dengue and Zika virus infection are impaired by small molecule ER proteostasis regulator 147 in an ATF6-independent manner ]]> https://biorxiv.org/content/10.1101/2020.05.15.098624v1?rss=1 Almasy, K. M. Davies, J. P. Lisy, S. M. Tirgar, R. Tran, S. C. Plate, L. 2020-05-15 doi:10.1101/2020.05.15.098624 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Sexually dimorphic roles for the type 2 diabetes-associated C2cd4b gene in murine glucose homeostasis ]]> https://biorxiv.org/content/10.1101/2020.05.18.099200v1?rss=1 Mousavy-Gharavy, N. S. Owen, B. Millership, S. J. Chabosseau, P. Pizza, G. Martinez-Sanchez, A. Tasoez, E. Georgiadou, E. Hu, M. Fine, N. H. F. Jacobson, D. A. Dickerson, M. Idevall, O. Montoya, A. Kramer, H. Mehta, Z. Withers, D. Ninov, N. Gadue, P. Cardenas-Diaz, F. L. Cruciani-Guglielmacci, C. Magnan, C. Ibberson, M. Leclerc, I. Voz, M. Rutter, G. A. 2020-05-19 doi:10.1101/2020.05.18.099200 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ Practical gradient non-linearity correction of multi-site diffusion weighted MRI with empirical field maps ]]> https://biorxiv.org/content/10.1101/2020.05.18.102558v1?rss=1 Hansen, C. B. Rogers, B. P. Schilling, K. G. Nath, V. Blaber, J. A. Irfanoglu, O. Barnett, A. Pierpaoli, C. Anderson, A. W. Landman, B. A. 2020-05-20 doi:10.1101/2020.05.18.102558 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Nutrient sensing pathways regulating adult reproductive diapause in C. elegans ]]> https://biorxiv.org/content/10.1101/2020.05.21.108340v1?rss=1 Eustice, M. Reece, J. M. Konzman, D. Ghosh, S. Alston, J. Hansen, T. Golden, A. Hanover, J. 2020-05-21 doi:10.1101/2020.05.21.108340 Cold Spring Harbor Laboratory Press 2020-05-21 <![CDATA[ Potently neutralizing human antibodies that block SARS-CoV-2 receptor binding and protect animals ]]> https://biorxiv.org/content/10.1101/2020.05.22.111005v1?rss=1 Zost, S. J. Gilchuk, P. Case, J. B. Binshtein, E. Chen, R. E. Reidy, J. X. Trivette, A. Nargi, R. S. Sutton, R. E. Suryadevara, N. Williamson, L. E. Chen, E. C. Jones, T. Day, S. Myers, L. Hassan, A. O. Kafai, N. M. Winkler, E. S. Fox, J. M. Steinhardt, J. J. Ren, K. Loo, Y.-M. Kallewaard, N. L. Martinez, D. R. Schafer, A. Gralinski, L. E. Baric, R. S. Thackray, L. B. Diamond, M. S. Carnahan, R. H. Crowe, J. E. 2020-05-22 doi:10.1101/2020.05.22.111005 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Ebola and Marburg virus matrix layers are locally ordered assemblies of VP40 dimers ]]> https://biorxiv.org/content/10.1101/2020.05.25.114462v1?rss=1 Wan, W. Clarke, M. Norris, M. Kolesnikova, L. Koehler, A. Bornholdt, Z. Becker, S. Saphire, E. O. Briggs, J. 2020-05-25 doi:10.1101/2020.05.25.114462 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ The recent report by Liu and Zhang Claiming "No support for the adaptive hypothesis of lagging-strand encoding in bacterial genomes" is factually incorrect ]]> https://biorxiv.org/content/10.1101/2020.05.26.117366v1?rss=1 Merrikh, C. Merrikh, H. 2020-05-29 doi:10.1101/2020.05.26.117366 Cold Spring Harbor Laboratory Press 2020-05-29 <![CDATA[ Genome-wide association and function studies identify Mfd as a critical RNA polymerase co-factor at hard-to-transcribe regions ]]> https://biorxiv.org/content/10.1101/2020.05.28.121731v1?rss=1 Ragheb, M. N. Merrikh, H. 2020-05-30 doi:10.1101/2020.05.28.121731 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Two new immature and dysfunctional neutrophil cell subsets define a predictive signature of sepsis useable in clinical practice ]]> https://biorxiv.org/content/10.1101/2020.05.29.123992v1?rss=1 Meghraoui-Kheddar, A. Chousterman, B. G. Guillou, N. Barone, S. M. Granjeaud, S. Vallet, H. Corneau, A. Guessous, K. Boissonnas, A. Irish, J. M. Combadiere, C. 2020-05-31 doi:10.1101/2020.05.29.123992 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Identifying digenic disease genes using machine learning in the undiagnosed diseases network ]]> https://biorxiv.org/content/10.1101/2020.05.31.125716v1?rss=1 77%), and we further demonstrate its utility using novel digenic pairs from the recent literature. In contrast to other approaches, DiGePred also appropriately controls the number of false positives when applied in realistic clinical settings like the UDN. Finally, to facilitate the rapid screening of variant gene pairs for digenic disease potential, we freely provide the predictions of DiGePred on all human gene pairs. Our work facilitates the discovery of genetic causes for rare non-monogenic diseases by providing a means to rapidly evaluate variant gene pairs for the potential to cause digenic disease. ]]> Mukherjee, S. Cogan, J. D. Newman, J. H. Phillips, J. A. Hamid, R. Undiagnosed Diseases Network, Meiler, J. Capra, J. A. 2020-06-01 doi:10.1101/2020.05.31.125716 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ Structure and assembly of CAV1 8S complexes revealed by single particle electron microscopy ]]> https://biorxiv.org/content/10.1101/2020.06.04.133678v1?rss=1 Han, B. Porta, J. C. Hanks, J. L. Peskova, Y. Binshtein, E. Dryden, K. Claxton, D. P. Mchaourab, H. S. Karakas, E. Ohi, M. D. Kenworthy, A. K. 2020-06-05 doi:10.1101/2020.06.04.133678 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Factors Influencing Precision Medicine Knowledge and Attitudes ]]> https://biorxiv.org/content/10.1101/2020.06.04.133942v1?rss=1 Chakravarthy, R. Stallings, S. C. Williams, M. Hollister, M. Davidson, M. Canedo, J. Wilkins, C. 2020-06-04 doi:10.1101/2020.06.04.133942 Cold Spring Harbor Laboratory Press 2020-06-04 <![CDATA[ Distinct genetic pathways define pre-leukemic and compensatory clonal hematopoiesis in Shwachman-Diamond syndrome ]]> https://biorxiv.org/content/10.1101/2020.06.04.134692v1?rss=1 Kennedy, A. L. Myers, K. C. Bowman, J. Gibson, C. J. Camarda, N. D. Furutani, E. M. Muscato, G. M. Klein, R. H. Ballotti, K. Liu, S. Harris, C. E. Galvin, A. Malsch, M. Dale, D. Gansner, J. M. Nakano, T. A. Bertuch, A. Vlachos, A. Lipton, J. M. Castillo, P. Connelly, J. Churpek, J. Edwards, J. R. Hijiya, N. Ho, R. H. Hofmann, I. Huang, J. N. Keel, S. Lamble, A. Lau, B. W. Norkin, M. Stieglitz, E. Stock, W. Walkovich, K. Boettcher, S. Brendel, C. Fleming, M. D. Davies, S. M. Weller, E. A. Bahl, C. Carter, S. L. Shimamura, A. Lindsley, R. C. 2020-06-05 doi:10.1101/2020.06.04.134692 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ MCL1 dependence across MDS subtypes and dual inhibition of MCL1 and BCL2 in MISTRG6 mice ]]> https://biorxiv.org/content/10.1101/2020.06.05.133090v1?rss=1 Fischer, M. A. Song, Y. Gbyli, R. Arrate, M. P. Villaume, M. T. Childress, M. A. Smith, B. N. Stricker, T. P. Halene, S. Savona, M. R. 2020-06-06 doi:10.1101/2020.06.05.133090 Cold Spring Harbor Laboratory Press 2020-06-06 <![CDATA[ A unifying framework disentangles genetic, epigenetic, and stochastic sources of drug-response variability in an in vitro model of tumor heterogeneity ]]> https://biorxiv.org/content/10.1101/2020.06.05.136119v1?rss=1 Hayford, C. E. Tyson, D. R. Robbins, C. J. Frick, P. L. Quaranta, V. Harris, L. 2020-06-05 doi:10.1101/2020.06.05.136119 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Integrating Long-term Optogenetic Stimulation and Bioluminescence Recording to Study Neural Plasticity Induced by Circadian Entrainment ]]> https://biorxiv.org/content/10.1101/2020.06.05.136440v1?rss=1 Kim, S. McMahon, D. G. 2020-06-06 doi:10.1101/2020.06.05.136440 Cold Spring Harbor Laboratory Press 2020-06-06 <![CDATA[ Multi-ancestry Genome- and Phenome-wide Association Studies of Diverticular Disease in Electronic Health Records with Natural Language Processing enriched phenotype algorithm ]]> https://biorxiv.org/content/10.1101/2020.06.08.138735v1?rss=1 Joo, Y. Y. Pacheco, J. A. Thompson, W. K. Rasmussen-Torvik, L. Rasmussen, L. V. Lin, F. T. Andrade, M. d. Borthwick, K. M. Bottinger, E. Cagan, A. Carrell, D. S. Denny, J. C. Ellis, S. B. Gottesman, O. Linneman, J. G. Pathak, J. Peissig, P. L. Shang, N. S. Tromp, G. Veerappan, A. Smith, M. Chisholm, R. L. Gawron, A. J. Kho, A. N. Hayes, M. G. 2020-06-09 doi:10.1101/2020.06.08.138735 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Quantifying the contribution of Neanderthal introgression to the heritability of complex traits ]]> https://biorxiv.org/content/10.1101/2020.06.08.140087v1?rss=1 McArthur, E. Rinker, D. C. Capra, J. A. 2020-06-08 doi:10.1101/2020.06.08.140087 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ ClipKIT: a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference ]]> https://biorxiv.org/content/10.1101/2020.06.08.140384v1?rss=1 Steenwyk, J. L. Buida, T. J. Li, Y. Shen, X.-X. Rokas, A. 2020-06-10 doi:10.1101/2020.06.08.140384 Cold Spring Harbor Laboratory Press 2020-06-10 <![CDATA[ Helicobacter pylori diversification during chronic infection within a single host generates sub-populations with distinct phenotypes ]]> https://biorxiv.org/content/10.1101/2020.06.10.144071v1?rss=1 Jackson, L. K. Potter, B. Schneider, S. E. Fitzgibbon, M. Blair, K. Farah, H. Krishna, U. Peek, R. Bedford, T. Salama, N. R. 2020-06-10 doi:10.1101/2020.06.10.144071 Cold Spring Harbor Laboratory Press 2020-06-10 <![CDATA[ SARS-CoV-2 mRNA Vaccine Development Enabled by Prototype Pathogen Preparedness ]]> https://biorxiv.org/content/10.1101/2020.06.11.145920v1?rss=1 Corbett, K. S. Edwards, D. Leist, S. R. Abiona, O. M. Boyoglu-Barnum, S. Gillespie, R. A. Himansu, S. Schafer, A. Ziwawo, C. T. DiPiazza, A. T. Dinnon, K. H. Elbashir, S. M. Shaw, C. A. Woods, A. Fritch, E. J. Martinez, D. R. Bock, K. W. Minai, M. Nagata, B. M. Hutchinson, G. B. Bahl, K. Garcia-Dominguez, D. Ma, L. Renzi, I. Kong, W.-P. Schmidt, S. D. Wang, L. Zhang, Y. Stevens, L. J. Phung, E. Chang, L. A. Loomis, R. J. Altaras, N. E. Narayanan, E. Metkar, M. Presnyak, V. Liu, C. Louder, M. K. Shi, W. Leung, K. Yang, E. S. West, A. Gully, K. L. Wang, 2020-06-11 doi:10.1101/2020.06.11.145920 Cold Spring Harbor Laboratory Press 2020-06-11 <![CDATA[ Persistence of quantal synaptic vesicle recycling following dynamin depletion ]]> https://biorxiv.org/content/10.1101/2020.06.12.147975v1?rss=1 Kavalali, E. T. Afuwape, O. Chanaday, N. Kasap, M. Monteggia, L. M. 2020-06-12 doi:10.1101/2020.06.12.147975 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Microtubules regulate pancreatic beta cell heterogeneity via spatiotemporal control of insulin secretion hot spots ]]> https://biorxiv.org/content/10.1101/2020.06.12.148668v1?rss=1 Trogden, K. P. McKinney, H. Zhu, X. Arpag, G. Folland, T. G. Osipovich, A. B. Magnuson, M. A. Zanic, M. Gu, G. Holmes, W. R. Kaverina, I. 2020-06-13 doi:10.1101/2020.06.12.148668 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ Pandora: 4-D white matter bundle population-based atlasesderived from diffusion MRI fiber tractography ]]> https://biorxiv.org/content/10.1101/2020.06.12.148999v1?rss=1 Hansen, C. B. Yang, Q. Lyu, I. Rheault, F. Kerley, C. Chandio, B. Q. Fadnavis, S. Williams, O. Shafer, A. T. Resnick, S. M. Zald, D. H. Cutting, L. Taylor, W. D. Boyd, B. Garyfallidis, E. Anderson, A. W. Descoteaux, M. Landman, B. A. Schilling, K. 2020-06-13 doi:10.1101/2020.06.12.148999 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ Heritable Genetic Background Alters Survival and Phenotype of Mll-AF9-Induced Leukemias ]]> https://biorxiv.org/content/10.1101/2020.06.13.149310v1?rss=1 Young, K. Loberg, M. Eudy, E. Schwartz, L. Mujica, K. Trowbridge, J. 2020-06-13 doi:10.1101/2020.06.13.149310 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ Dose-dependent enhancement of motion direction discrimination with transcranial magnetic stimulation of visual cortex ]]> https://biorxiv.org/content/10.1101/2020.06.14.151118v1?rss=1 Arana, O. L. G. Palmer, H. Dannhauer, M. Hile, C. Liu, S. Hamdan, R. Brito, A. Cabeza, R. Davis, S. W. Peterchev, A. V. Sommer, M. A. Appelbaum, L. 2020-06-15 doi:10.1101/2020.06.14.151118 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Definition of a Small Core Transcriptional Circuit Regulated by AML1-ETO ]]> https://biorxiv.org/content/10.1101/2020.06.14.151159v1?rss=1 Stengel, K. R. Ellis, J. Spielman, C. L. Bomber, M. L. Hiebert, S. W. 2020-06-15 doi:10.1101/2020.06.14.151159 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Structural Determinants of Cholesterol Recognition in Helical Integral Membrane Proteins ]]> https://biorxiv.org/content/10.1101/2020.06.15.152025v1?rss=1 Marlow, B. Meiler, J. Kuenze, G. Sanders, C. Li, B. 2020-06-15 doi:10.1101/2020.06.15.152025 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Prediction of amphipathic helix - membrane interactions with Rosetta ]]> https://biorxiv.org/content/10.1101/2020.06.15.152322v1?rss=1 Gulsevin, A. Meiler, J. 2020-06-15 doi:10.1101/2020.06.15.152322 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Identification of ubiquitin Ser57 kinases regulating the oxidative stress response in yeast ]]> https://biorxiv.org/content/10.1101/2020.06.20.162883v1?rss=1 Hepowit, N. L. Pereira, K. N. Tumolo, J. M. Chazin, W. J. MacGurn, J. A. 2020-06-20 doi:10.1101/2020.06.20.162883 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ MYC regulates ribosome biogenesis and mitochondrial gene expression programs through interaction with Host Cell Factor-1 ]]> https://biorxiv.org/content/10.1101/2020.06.22.164764v1?rss=1 Popay, T. M. Wang, J. Adams, C. M. Codreanu, S. G. Sherrod, S. D. McLean, J. A. Thomas, L. R. Lorey, S. L. Machida, Y. J. Weissmiller, A. M. Eischen, C. M. Liu, Q. Tansey, W. 2020-06-23 doi:10.1101/2020.06.22.164764 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes ]]> https://biorxiv.org/content/10.1101/2020.06.23.166181v1?rss=1 Vysotskiy, M. Zhong, X. Miller-Fleming, T. W. Zhou, D. Autism Working Group of the Psychiatric Genomics Consortium, Bipolar Disorder Working Group of the Psychiatric Genomics Consortium, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Cox, N. J. Weiss, L. A. 2020-06-24 doi:10.1101/2020.06.23.166181 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Replication-transcription conflicts promote adaptive evolution ]]> https://biorxiv.org/content/10.1101/2020.06.23.167650v1?rss=1 Merrikh, H. Merrikh, C. Harris, L. Mangiameli, S. 2020-06-25 doi:10.1101/2020.06.23.167650 Cold Spring Harbor Laboratory Press 2020-06-25 <![CDATA[ The native structure of the full-length, assembled influenza A virus matrix protein, M1. ]]> https://biorxiv.org/content/10.1101/2020.06.24.168567v1?rss=1 Peukes, J. Xiong, X. Erlendsson, S. Qu, K. Wan, W. Calder, L. J. Schraidt, O. Kummer, S. Freund, S. M. V. Kräusslich, H.-G. Briggs, J. A. G. 2020-06-24 doi:10.1101/2020.06.24.168567 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Circadian photoperiod alters TREK-1 channel function and expression in dorsal raphe serotonergic neurons ]]> https://biorxiv.org/content/10.1101/2020.06.24.169532v1?rss=1 Giannoni-Guzman, M. A. Kamitakahara, A. Magalong, V. Levitt, P. McMahon, D. G. 2020-06-28 doi:10.1101/2020.06.24.169532 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ Exofacial membrane composition and lipid metabolism regulates plasma membrane P4-ATPase substrate specificity ]]> https://biorxiv.org/content/10.1101/2020.06.24.169672v1?rss=1 Roland, B. P. Jain, B. K. Graham, T. R. 2020-06-24 doi:10.1101/2020.06.24.169672 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Deep Learning for Virtual Screening: Five Reasons to Use ROC Cost Functions ]]> https://biorxiv.org/content/10.1101/2020.06.25.166884v1?rss=1 Golkov, V. Becker, A. Plop, D. T. Cuturilo, D. Davoudi, N. Mendenhall, J. Moretti, R. Meiler, J. Cremers, D. 2020-06-26 doi:10.1101/2020.06.25.166884 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Photoperiodic Effects on Monoamine Signaling & Gene Expression Throughout Development in the Serotonin & Dopamine Systems ]]> https://biorxiv.org/content/10.1101/2020.06.25.171470v1?rss=1 Siemann, J. K. Williams, P. Malik, T. N. Jackson, C. Green, N. H. Emeson, R. Levitt, P. McMahon, D. G. 2020-06-26 doi:10.1101/2020.06.25.171470 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Spatiotemporal coding in the macaque supplementary eye fields: landmark influence in the target-to-gaze transformation ]]> https://biorxiv.org/content/10.1101/2020.06.25.172031v1?rss=1 Bharmauria, V. Sajad, A. Yan, X. Wang, H. Crawford, J. D. 2020-06-29 doi:10.1101/2020.06.25.172031 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Nf2 fine-tunes proliferation and tissue alignment during closure of the optic fissure in the embryonic mouse eye ]]> https://biorxiv.org/content/10.1101/2020.06.28.176065v1?rss=1 Sun, W. R. Ramirez, S. Spiller, K. E. Zhao, Y. Fuhrmann, S. 2020-06-28 doi:10.1101/2020.06.28.176065 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ Feature Frequency Profile-based phylogenies are inaccurate ]]> https://biorxiv.org/content/10.1101/2020.06.28.176479v1?rss=1 Li, Y. David, K. T. Shen, X.-X. Steenwyk, J. L. Halanych, K. M. Rokas, A. 2020-06-30 doi:10.1101/2020.06.28.176479 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ Male-biased islet β cell dysfunction is caused by the MODY MAFA S64F variant inducing premature aging and senescence ]]> https://biorxiv.org/content/10.1101/2020.06.29.177527v1?rss=1 Walker, E. M. Tong, X. Cha, J. Guo, M. Liu, J.-H. Yu, S. Iacovazzo, D. Mauvais-Jarvis, F. M. Flanagan, S. E. Korbonits, M. Stafford, J. Jacobson, D. A. Stein, R. 2020-06-29 doi:10.1101/2020.06.29.177527 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Changes to zonular tension alters the subcellular distribution of AQP5 in regions of influx and efflux of water in the rat lens. ]]> https://biorxiv.org/content/10.1101/2020.06.29.178756v1?rss=1 Petrova, R. S. Bavana, N. Zhao, R. Schey, K. L. Donaldson, P. J. 2020-06-30 doi:10.1101/2020.06.29.178756 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ Leptin suppresses development of GLP-1 Inputs to the Paraventricular Nucleus of the Hypothalamus ]]> https://biorxiv.org/content/10.1101/2020.06.30.180513v1?rss=1 Biddinger, J. E. Lazarenko, R. M. Scott, M. M. Simerly, R. 2020-07-01 doi:10.1101/2020.06.30.180513 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ FLN-1/Filamin is required to anchor the actomyosin cytoskeleton and for global organization of sub-cellular organelles in a contractile tissue ]]> https://biorxiv.org/content/10.1101/2020.07.03.186965v1?rss=1 Kelley, C. A. Triplett, O. Mallick, S. Burkewitz, K. Mair, W. B. Cram, E. J. 2020-07-04 doi:10.1101/2020.07.03.186965 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Combinatorial transcriptional profiling of mouse and human enteric neurons identifies shared and disparate subtypes in situ. ]]> https://biorxiv.org/content/10.1101/2020.07.03.187211v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@1b41277org.highwire.dtl.DTLVardef@12856feorg.highwire.dtl.DTLVardef@1674dadorg.highwire.dtl.DTLVardef@11ca1c8_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG ]]> May-Zhang, A. A. Tycksen, E. Southard-Smith, A. N. Deal, K. K. Benthal, J. T. Buehler, D. P. Adam, M. Simmons, A. J. Monaghan, J. R. Matlock, B. K. Flaherty, D. K. Potter, S. Lau, K. S. Southard-Smith, E. M. 2020-07-04 doi:10.1101/2020.07.03.187211 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Which animals are at risk? Predicting species susceptibility to Covid-19 ]]> https://biorxiv.org/content/10.1101/2020.07.09.194563v1?rss=1 Matthew R Alexander Clara T. Schoeder Jacquelyn A. Brown Charles D. Smart Christopher W. Moth John P. Wikswo John Anthony Capra Jens Meiler Wenbiao Chen Meena S. Madhur 2020-07-10 doi:10.1101/2020.07.09.194563 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Kinetics of osmotic stress regulates a cell fate switch of cell survival ]]> https://biorxiv.org/content/10.1101/2020.07.10.197871v1?rss=1 Alexander Thiemicke Gregor Neuert 2020-07-10 doi:10.1101/2020.07.10.197871 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Hematopoietic Stem and Progenitor Cell Aging is Initiated at Middle Age Through Decline in Local Insulin-Like Growth Factor 1 (IGF1) ]]> https://biorxiv.org/content/10.1101/2020.07.11.198846v1?rss=1 Kira Young Elizabeth Eudy Rebecca Bell Matthew Loberg Tim Stearns Lars Velten Simon Haas Jennifer Trowbridge 2020-07-12 doi:10.1101/2020.07.11.198846 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ Prostaglandin E2 promotes intestinal inflammation via inhibiting microbiota-dependent regulatory T cells ]]> https://biorxiv.org/content/10.1101/2020.07.12.199513v1?rss=1 Siobhan Crittenden Marie Goepp Jolinda Pollock Calum T Robb Danielle J Smyth You Zhou Robert Andrews Victoria Tyrrell Alexander Adima Richard A OConnor Luke Davies Xue-Feng Li Hatti X Yao Gwo-Tzer Ho Xiaozhong Zheng Amil Mair Sonja Vermeren Binzhi Qian Damian James Mole Jurgen Schwarze Richard M Breyer Mark J Arends Valerie O'Donnell John P Iredale Stephen M Anderton Shuh Narumiya Rick M Maizels Adriano G Rossi Sarah E Howie Chengcan Yao 2020-07-12 doi:10.1101/2020.07.12.199513 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ Cigarette Smoke and Nicotine-Containing E-cigarette Vapor Downregulate Lung WWOX Expression Which is Associated with Increased Severity of Murine ARDS ]]> https://biorxiv.org/content/10.1101/2020.07.13.200832v1?rss=1 Zeng, Z. Chen, W. Moshensky, A. Khan, R. Alexander, L. C. Ware, L. B. Aldaz, C. M. Jacobson, J. R. Dudek, S. M. Natarajan, V. Machado, R. F. Singla, S. 2020-07-13 doi:10.1101/2020.07.13.200832 Cold Spring Harbor Laboratory Press 2020-07-13 <![CDATA[ Comparative multiplexed interactomics of SARS-CoV-2 and homologous coronavirus non-structural proteins identifies unique and shared host-cell dependencies ]]> https://biorxiv.org/content/10.1101/2020.07.13.201517v1?rss=1 Davies, J. P. Almasy, K. M. McDonald, E. F. Plate, L. 2020-07-15 doi:10.1101/2020.07.13.201517 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ ACDC: Automated Cell Detection and Counting for Time-lapse Fluorescence Microscopy ]]> https://biorxiv.org/content/10.1101/2020.07.14.202804v1?rss=1 Rundo, L. Tangherloni, A. Tyson, D. R. Betta, R. Militello, C. Spolaor, S. Nobile, M. S. Besozzi, D. Lubbock, A. L. R. Quaranta, V. Mauri, G. Lopez, C. F. Cazzaniga, P. 2020-07-16 doi:10.1101/2020.07.14.202804 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ TRPM7 is a critical regulator of pancreatic endocrine development and high-fat diet-induced β-cell proliferation. ]]> https://biorxiv.org/content/10.1101/2020.07.15.204974v1?rss=1 Altman, M. K. Schaub, C. M. Dickerson, M. T. Dadi, P. K. Graff, S. M. Galletta, T. J. Amarnath, G. Thorson, A. S. Gu, G. Jacobson, D. A. 2020-07-15 doi:10.1101/2020.07.15.204974 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ Signatures of optimal codon usage predict metabolic ecology in budding yeasts ]]> https://biorxiv.org/content/10.1101/2020.07.22.214635v1?rss=1 LaBella, A. L. Opulente, D. Steenwyk, J. L. Hittinger, C. T. Rokas, A. 2020-07-24 doi:10.1101/2020.07.22.214635 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo's law of irreversible loss ]]> https://biorxiv.org/content/10.1101/2020.07.22.216101v1?rss=1 Haase, M. A. B. Kominek, J. Opulente, D. Shen, X.-X. LaBella, A. Zhou, X. DeVirgilio, J. Hulfachor, A. Kurtzman, C. Rokas, A. Hittinger, C. T. 2020-07-24 doi:10.1101/2020.07.22.216101 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Interneuron Specific Gamma Synchronization Encodes Uncertain Cues and Prediction Errors in Lateral Prefrontal and Anterior Cingulate Cortex ]]> https://biorxiv.org/content/10.1101/2020.07.24.220319v1?rss=1 Banaie Boroujeni, K. Tiesinga, P. Womelsdorf, T. 2020-07-25 doi:10.1101/2020.07.24.220319 Cold Spring Harbor Laboratory Press 2020-07-25 <![CDATA[ Mtg16-dependent repression of E protein activity is required for early lymphopoiesis ]]> https://biorxiv.org/content/10.1101/2020.07.24.220525v1?rss=1 Acharya, P. Sampathi, S. Flaherty, D. K. Matlock, B. K. Williams, C. S. Hiebert, S. W. Stengel, K. R. 2020-07-25 doi:10.1101/2020.07.24.220525 Cold Spring Harbor Laboratory Press 2020-07-25 <![CDATA[ No evidence for basigin/CD147 as a direct SARS-CoV-2 spike binding receptor ]]> https://biorxiv.org/content/10.1101/2020.07.25.221036v1?rss=1 Shilts, J. Wright, G. J. 2020-07-26 doi:10.1101/2020.07.25.221036 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ Tet1 isoforms differentially regulate gene expression, synaptic transmission and memory in the mammalian brain. ]]> https://biorxiv.org/content/10.1101/2020.07.27.223685v1?rss=1 Greer, C. B. Wright, J. Weiss, J. D. Lazarenko, R. M. Moran, S. P. Zhu, J. Chronister, K. S. Jin, A. Y. Kennedy, A. J. Sweatt, J. D. Kaas, G. A. 2020-07-29 doi:10.1101/2020.07.27.223685 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Digital spatial profiling of coronary plaques from persons living with HIV reveals high levels of STING and CD163 in macrophage enriched regions ]]> https://biorxiv.org/content/10.1101/2020.07.28.221325v1?rss=1 View larger version (51K): org.highwire.dtl.DTLVardef@1a4757forg.highwire.dtl.DTLVardef@1e2236org.highwire.dtl.DTLVardef@582f4borg.highwire.dtl.DTLVardef@188f376_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Characterization of coronary plaques. Representative coronary plaques from three HIV-positive and three HIV-negative individuals were stained with H&E and Movat stain (A). Plaque area (m2) and % plaque stenosis were measured and calculated in 6 individuals per group (B). Statistical analysis, Mann-Whitney; ns not significant C_FIG ConclusionsIncreased inflammation within the coronary plaques of PLWH is characterized by more innate and adaptive immune cells. Higher STING expression in PLWH suggests that immune response to viral antigens within the plaque might be a driver above other stimulants. STING inhibitors are available and could be investigated as a future therapeutic target in PWH if these results are replicated with a larger number of plaques. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/221325v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@27fa00org.highwire.dtl.DTLVardef@8e4a65org.highwire.dtl.DTLVardef@1b65320org.highwire.dtl.DTLVardef@10b7c9a_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIImmunohistochemical and fluorescent stains combined with GeoMx(R) digital spatial profiling allowed for deep characterization of immune cells within intact coronary plaques and perivascular adipose tissue C_LIO_LICoronary plaques from HIV-positive persons had higher proportion of CD163+ immune cells compared to HIV-negative persons C_LIO_LIDifferential protein expression of immune-rich regions of interest within intact 5m sections of coronary plaques revealed higher levels of stimulator of interferon gamma (STING) in HIV-positive persons C_LI ]]> Wanjalla, C. N. Guo, L. Fuller, D. T. Mashayekhi, M. Bailin, S. Gabriel, C. L. Temu, T. Gong, J. Liang, Y. Virmani, R. Finn, A. V. Kalams, S. A. Mallal, S. A. Miner, J. Beckman, J. A. Koethe, J. R. 2020-07-29 doi:10.1101/2020.07.28.221325 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Identification and characterization of CD4+ T cell epitopes after Shingrix vaccination. ]]> https://biorxiv.org/content/10.1101/2020.07.29.227082v1?rss=1 Voic, H. de Vries, R. D. Sidney, J. Rubiro, P. Moore, E. Phillips, E. J. Mallal, S. Schwan, B. Weiskopf, D. Grifoni, A. Sette, A. 2020-07-29 doi:10.1101/2020.07.29.227082 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Disease-Linked Super-Trafficking of a Mutant Potassium Channel ]]> https://biorxiv.org/content/10.1101/2020.07.29.227231v1?rss=1 Huang, H. Chamness, L. M. Vanoye, C. G. Kuenze, G. Meiler, J. George, A. L. Schlebach, J. P. Sanders, C. 2020-07-29 doi:10.1101/2020.07.29.227231 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy ]]> https://biorxiv.org/content/10.1101/2020.07.31.190454v1?rss=1 Barone, S. M. Paul, A. G. A. Muehling, L. M. Lannigan, J. A. Kwok, W. W. Turner, R. B. Woodfolk, J. A. Irish, J. M. 2020-08-01 doi:10.1101/2020.07.31.190454 Cold Spring Harbor Laboratory Press 2020-08-01 <![CDATA[ Noise-robust recognition of objects by humans and deep neural networks ]]> https://biorxiv.org/content/10.1101/2020.08.03.234625v1?rss=1 Jang, H. McCormack, D. R. Tong, F. 2020-08-04 doi:10.1101/2020.08.03.234625 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Modeling the evolutionary architectures of human enhancer sequences reveals distinct origins, functions, and associations with human-trait variation ]]> https://biorxiv.org/content/10.1101/2020.08.03.235051v1?rss=1 Fong, S. L. Capra, J. A. 2020-08-03 doi:10.1101/2020.08.03.235051 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Aspergillus fumigatus G-protein coupled receptors GprM and GprJ are important for the regulation of the cell wall integrity pathway, secondary metabolite production, and virulence ]]> https://biorxiv.org/content/10.1101/2020.08.03.235119v1?rss=1 da Costa Filho, A. P. Brancini, G. T. de Castro, P. A. Ferreira, J. A. Silva, L. P. Rocha, M. C. Malavazi, I. de Moraes Pontes, J. G. Fill, T. Silva, R. Almeida, F. Steenwyk, J. L. Rokas, A. dos Reis, T. F. Ries, L. N. Goldman, G. H. 2020-08-03 doi:10.1101/2020.08.03.235119 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Changes in weak pair-wise correlations during running reshapes network state in the main olfactory bulb ]]> https://biorxiv.org/content/10.1101/2020.08.04.235382v1?rss=1 Chockanathan, u. Crosier, E. J. W. Waddle, S. Lyman, E. Gerkin, R. Padmanabhan, K. 2020-08-04 doi:10.1101/2020.08.04.235382 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Dissociation of Medial Frontal β-Bursts and Executive Control ]]> https://biorxiv.org/content/10.1101/2020.08.06.240606v1?rss=1 Errington, S. P. Woodman, G. F. Schall, J. D. 2020-08-06 doi:10.1101/2020.08.06.240606 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ Cell Programmed Nutrient Partitioning in the Tumor Microenvironment ]]> https://biorxiv.org/content/10.1101/2020.08.10.238428v1?rss=1 Reinfeld, B. I. Madden, M. Z. Wolf, M. M. Chytil, A. Bader, J. E. Patterson, A. R. Cohen, A. S. Ali, A. Do, B. T. Lewis, C. A. Muir, A. Hongo, R. A. Young, K. L. Brown, R. E. Todd, V. M. Huffstater, T. Abraham, A. O'Neil, R. T. Wilson, M. T. Xin, F. Tantawy, M. N. Merryman, W. D. Johnson, R. W. Williams, C. S. Mason, E. F. Mason, F. M. Beckermann, K. E. Vander Heiden, M. G. Manning, H. C. Rathmell, J. C. Rathmell, W. K. 2020-08-10 doi:10.1101/2020.08.10.238428 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ A combined proteomics and Mendelian randomization approach to investigate the effects of aspirin-targeted proteins on colorectal cancer ]]> https://biorxiv.org/content/10.1101/2020.08.14.239871v1?rss=1 Nounu, A. Greenhough, A. Heesom, K. J. Richmond, R. C. Zheng, J. Weinstein, S. J. Albanes, D. Baron, J. A. Hopper, J. L. Figueiredo, J. C. Newcomb, P. A. Lindor, N. M. Casey, G. Platz, E. A. Le Marchand, L. Ulrich, C. M. Li, C. I. van Duijnhoven, F. J. Gsur, A. Campbell, P. T. Moreno, V. Vodicka, P. Vodickova, L. Brenner, H. Chang-Claude, J. Hoffmeister, M. Sakoda, L. C. Slattery, M. L. Schoen, R. E. Gunter, M. J. Castellvi-Bel, S. Rok Kim, H. Kweon, S.-S. Chan, A. T. Li, L. Zheng, W. Bishop, D. T. Buchanan, D. D. Giles, G. G. Gruber, S. B. Rennert, G. 2020-08-14 doi:10.1101/2020.08.14.239871 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Single-Strand DNA Breaks Cause Replisome Disassembly ]]> https://biorxiv.org/content/10.1101/2020.08.17.254235v1?rss=1 Vrtis, K. Dewar, J. Chistol, G. Wu, A. Graham, T. Walter, J. 2020-08-17 doi:10.1101/2020.08.17.254235 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ The Role of Colony Temperature in the Entrainment of Circadian Rhythms of Honey Bee Foragers ]]> https://biorxiv.org/content/10.1101/2020.08.17.254722v1?rss=1 Giannoni Guzman, M. A. Rivera, E. Aleman-Rios, J. Melendez Moreno, A. M. Lubirel, D. Perez Ramos, M. Moore, D. Giray, T. Agosto Rivera, J. L. 2020-08-18 doi:10.1101/2020.08.17.254722 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Genetic ablation of serotonin receptor 2B improves aortic valve hemodynamics in a high-cholesterol diet mouse model ]]> https://biorxiv.org/content/10.1101/2020.08.18.255414v1?rss=1 Joll, J. E. Clark, C. Scott, C. Raddatz, M. Bersi, M. Merryman, W. D. 2020-08-18 doi:10.1101/2020.08.18.255414 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Functions of Gle1 are governed by two distinct modes of self-association ]]> https://biorxiv.org/content/10.1101/2020.08.20.259564v1?rss=1 Mason, A. C. Wente, S. R. 2020-08-21 doi:10.1101/2020.08.20.259564 Cold Spring Harbor Laboratory Press 2020-08-21 <![CDATA[ A genome-scale phylogeny of Fungi; insights into early evolution, radiations, and the relationship between taxonomy and phylogeny ]]> https://biorxiv.org/content/10.1101/2020.08.23.262857v1?rss=1 Li, Y. Steenwyk, J. L. Chang, Y. Wang, Y. James, T. Y. Stajich, J. E. Spatafora, J. W. Groenewald, M. Dunn, C. Hittinger, C. T. Shen, X.-X. Rokas, A. 2020-08-24 doi:10.1101/2020.08.23.262857 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ ELAVL1 Exclusively Couples mRNA Stability with the 3'UTRs of Interferon Stimulated Genes ]]> https://biorxiv.org/content/10.1101/2020.08.24.263418v1?rss=1 Rothamel, K. L. Arcos, S. E. Kim, B. Reasoner, C. Mukherjee, N. Ascano, M. 2020-08-24 doi:10.1101/2020.08.24.263418 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Novel cryo-electron tomography structure of Arp2/3 complex in cells reveals mechanisms of branch formation ]]> https://biorxiv.org/content/10.1101/2020.08.25.266262v1?rss=1 Faessler, F. Dimchev, G. Hodirnau, V.-V. Wan, W. Schur, F. K. 2020-08-25 doi:10.1101/2020.08.25.266262 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Transport mechanism of class-3 P4 ATPase lipid flippases ]]> https://biorxiv.org/content/10.1101/2020.08.25.266742v1?rss=1 Li, H. Bai, L. You, Q. Jain, B. K. Graham, T. R. Kovach, A. 2020-08-25 doi:10.1101/2020.08.25.266742 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Coordinated interactions between endothelial cells and macrophages in the islet microenvironment promote beta cell regeneration ]]> https://biorxiv.org/content/10.1101/2020.08.28.265728v1?rss=1 Saunders, D. C. Aamodt, K. I. Richardson, T. M. Hopkirk, A. Khan, Z. Aramandla, R. Poffenberger, G. Jenkins, R. Flaherty, D. K. Prasad, N. Levy, S. Powers, A. Brissova, M. 2020-08-30 doi:10.1101/2020.08.28.265728 Cold Spring Harbor Laboratory Press 2020-08-30 <![CDATA[ Structural analysis of the Legionella pneumophila Dot/Icm Type IV Secretion System Core Complex ]]> https://biorxiv.org/content/10.1101/2020.08.28.271460v1?rss=1 Durie, C. L. Sheedlo, M. J. Chung, J. M. Byrne, B. Su, M. Knight, T. Swanson, M. Lacy, B. Ohi, M. D. 2020-08-28 doi:10.1101/2020.08.28.271460 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ Murine intrarectal instillation of purified recombinant C. difficile toxins enables mechanistic studies of pathogenesis ]]> https://biorxiv.org/content/10.1101/2020.08.30.274738v1?rss=1 Markham, N. O. Bloch, S. C. Shupe, J. A. Laubacher, E. N. Washington, M. K. Coffey, R. J. Lacy, D. B. 2020-08-31 doi:10.1101/2020.08.30.274738 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ SARS-CoV-2 Cell Entry Factors ACE2 and TMPRSS2 are Expressed in the Pancreas but Not in Islet Endocrine Cells ]]> https://biorxiv.org/content/10.1101/2020.08.31.275719v1?rss=1 Coate, K. C. Cha, J. Shrestha, S. Wang, W. Fasolino, M. Morgan, A. Dai, C. Saunders, D. C. Aramandla, R. Jenkins, R. Kapp, M. E. Stein, R. Kaestner, K. H. Vahedi, G. Brissova, M. Powers, A. C. 2020-08-31 doi:10.1101/2020.08.31.275719 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Enhanced synaptic transmission in the extended amygdala and altered excitability in an extended amygdala to brainstem circuit in a Dravet syndrome mouse model ]]> https://biorxiv.org/content/10.1101/2020.09.01.267112v1?rss=1 Yan, W. W. Xia, M. Levitt, A. Hawkins, N. Kearney, J. A. Swanson, G. T. Chetkovich, D. Nobis, W. P. 2020-09-01 doi:10.1101/2020.09.01.267112 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Spatially-targeted proteomics of the host-pathogen interface during staphylococcal abscess formation ]]> https://biorxiv.org/content/10.1101/2020.09.01.267773v1?rss=1 Guiberson, E. Weiss, A. Ryan, D. J. Monteith, A. J. Sharman, K. Gutierrez, D. B. Perry, W. J. Caprioli, R. M. Skaar, E. P. Spraggins, J. M. 2020-09-01 doi:10.1101/2020.09.01.267773 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Cryo-EM reveals species-specific components within the Helicobacter pylori Cag type IV secretion system core complex ]]> https://biorxiv.org/content/10.1101/2020.09.01.277012v1?rss=1 Sheedlo, M. J. Chung, J. M. Sawhney, N. Durie, C. L. Cover, T. L. Ohi, M. D. Lacy, B. 2020-09-01 doi:10.1101/2020.09.01.277012 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Gains and Losses Differentially Regulate Attentional Efficacy and Learning at Low and High Attentional Load ]]> https://biorxiv.org/content/10.1101/2020.09.01.278168v1?rss=1 Banaie Boroujeni, K. Watson, M. R. Womelsdorf, T. 2020-09-02 doi:10.1101/2020.09.01.278168 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ SPECIES-DEPENDENT HETEROPHILIC AND HOMOPHILIC CADHERIN INTERACTIONS IN INTESTINAL INTERMICROVILLAR LINKS ]]> https://biorxiv.org/content/10.1101/2020.09.01.278846v1?rss=1 Gray, M. E. Modak, D. Johnson, Z. R. Tyska, M. J. Sotomayor, M. 2020-09-02 doi:10.1101/2020.09.01.278846 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ Mutagenesis of the Orco Odorant Receptor Co-receptor Impairs Olfactory Function in the Malaria Vector Anopheles coluzzii ]]> https://biorxiv.org/content/10.1101/2020.09.04.283424v1?rss=1 Sun, H. Liu, F. Ye, Z. Baker, A. P. Zwiebel, L. J. 2020-09-04 doi:10.1101/2020.09.04.283424 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ A heterologous in-cell assay for investigating intermicrovillar adhesion complex interactions and function ]]> https://biorxiv.org/content/10.1101/2020.09.06.285171v1?rss=1 Weck, M. L. Crawley, S. W. Tyska, M. J. 2020-09-07 doi:10.1101/2020.09.06.285171 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ Neuronal Odor Coding in the Larval Sensory Cone of Anopheles coluzzii: Complex Responses from a Simple System ]]> https://biorxiv.org/content/10.1101/2020.09.09.290544v1?rss=1 Sun, H. Liu, F. Baker, A. P. Zwiebel, L. 2020-09-10 doi:10.1101/2020.09.09.290544 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Transcriptomic, protein-DNA interaction, and metabolomic studies of VosA, VelB, and WetA in Aspergillus nidulans asexual spores ]]> https://biorxiv.org/content/10.1101/2020.09.09.290809v1?rss=1 Wu, M.-Y. Mead, M. E. Lee, M.-K. Neuhaus, G. F. Adpressa, D. A. Martien, J. I. Son, Y.-E. Moon, H. Amador-Noguez, D. Han, K.-H. Rokas, A. Loesgen, S. Yu, J.-H. Park, H.-S. 2020-09-10 doi:10.1101/2020.09.09.290809 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ A long-range chromatin interaction regulates SATB homeobox 1 gene expression in trophoblast stem cells ]]> https://biorxiv.org/content/10.1101/2020.09.11.294181v1?rss=1 Yu, W. Chakravarthi, V. P. Borosha, S. Ratri, A. Dalal, K. Wolfe, M. W. Starks, R. R. Tuteja, G. Rumi, M. A. K. 2020-09-11 doi:10.1101/2020.09.11.294181 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Chemical Stabilization of the HIV-1 Capsid Results in Efficient HIV-1 Reverse Transcription in vitro ]]> https://biorxiv.org/content/10.1101/2020.09.17.302315v1?rss=1 Jennings, J. Shi, J. Varadarajan, J. Jamieson, P. J. Aiken, C. 2020-09-17 doi:10.1101/2020.09.17.302315 Cold Spring Harbor Laboratory Press 2020-09-17 <![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[ Multivariate GWAS elucidates the genetic architecture of alcohol consumption and misuse, corrects biases, and reveals novel associations with disease ]]> https://biorxiv.org/content/10.1101/2020.09.21.304196v1?rss=1 Mallard, T. T. Savage, J. E. Johnson, E. C. Huang, Y. Edwards, A. C. Hottenga, J. J. Grotzinger, A. D. Gustavson, D. E. Jennings, M. V. Anokhin, A. Dick, D. M. Edenberg, H. J. Kramer, J. R. Lai, D. Meyers, J. L. Pandey, A. K. Harden, K. P. Nivard, M. G. de Geus, E. J. Boomsma, D. I. Agrawal, A. Davis, L. K. Clarke, T.-K. Palmer, A. A. Sanchez-Roige, S. 2020-09-22 doi:10.1101/2020.09.21.304196 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Hypoxia uncouples HIF gene transcription and metabolic flux in proliferating primary cells ]]> https://biorxiv.org/content/10.1101/2020.09.21.306464v1?rss=1 Copeland, C. A. Olenchock, B. A. Young, J. D. Loscalzo, J. Oldham, W. M. 2020-09-21 doi:10.1101/2020.09.21.306464 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ Insufficient Eye Tracking Data Leads to Errors in Evaluating Typical and Atypical Fixation Preferences ]]> https://biorxiv.org/content/10.1101/2020.09.21.306621v1?rss=1 Reimann, G. E. Walsh, C. Csumitta, K. McClure, P. Pereira, F. Martin, A. Ramot, M. 2020-09-22 doi:10.1101/2020.09.21.306621 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Granulosa cell genes that regulate ovarian follicle development beyond the antral stage: the role of estrogen receptor β ]]> https://biorxiv.org/content/10.1101/2020.09.25.295550v1?rss=1 Chakravarthi, V. P. Borosha, S. Ghosh, S. Roby, K. F. Wolfe, M. W. Christenson, L. Rumi, M. A. 2020-09-26 doi:10.1101/2020.09.25.295550 Cold Spring Harbor Laboratory Press 2020-09-26 <![CDATA[ Learning at variable attentional load requires cooperation between working memory, meta-learning and attention-augmented reinforcement learning ]]> https://biorxiv.org/content/10.1101/2020.09.27.315432v1?rss=1 Womelsdorf, T. Watson, M. R. Tiesinga, P. 2020-09-28 doi:10.1101/2020.09.27.315432 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Measuring effects of trainee professional development on research productivity: A cross-institutional meta-analysis ]]> https://biorxiv.org/content/10.1101/2020.09.28.316422v1?rss=1 Brandt, P. Sturzenegger Varvayanis, S. Baas, T. Bolgioni-Smith, A. Alder, J. Petrie, K. A. Dominguez, I. Brown, A. M. Stayart, C. A. Singh, H. Van Wart, A. Chow, C. S. Mathur, A. Schreiber, B. M. Fruman, D. A. Bowden, B. Holmquist, C. E. Arneman, D. Hall, J. D. Hyman, L. E. Gould, K. Chalkley, R. Brennwald, P. Layton, R. 2020-09-28 doi:10.1101/2020.09.28.316422 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ SOCS-1 inhibition of type I interferon limits Staphylococcus aureus skin host defense ]]> https://biorxiv.org/content/10.1101/2020.09.28.317107v1?rss=1 Klopsfenstein, N. Brandt, S. Castellanos, S. Serezani, C. 2020-09-28 doi:10.1101/2020.09.28.317107 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ A patient-designed tissue-engineered model of the infiltrative glioblastoma microenvironment ]]> https://biorxiv.org/content/10.1101/2020.10.02.322735v1?rss=1 Cornelison, R. C. Yuan, J. X. Tate, K. M. Petrosky, A. Beeghly, G. F. Bloomfield, M. Schwager, S. R. Berr, A. L. Cimini, D. Bafakih, F. F. Mandell, J. W. Purow, B. W. Horton, B. J. Munson, J. 2020-10-04 doi:10.1101/2020.10.02.322735 Cold Spring Harbor Laboratory Press 2020-10-04 <![CDATA[ Genome-Wide CRISPR Screen Identifies Non-Canonical NF-κB Signaling as a Potent Regulator of Density-dependent Proliferation ]]> https://biorxiv.org/content/10.1101/2020.10.02.324301v1?rss=1 Fomicheva, M. Macara, I. G. 2020-10-02 doi:10.1101/2020.10.02.324301 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Lysophosphatidic acid (LPA)-antibody (504B3)validation by free-solution assay and interferometry identifies off-target binding ]]> https://biorxiv.org/content/10.1101/2020.10.05.327122v1?rss=1 Ray, M. Kihara, Y. Bornhop, D. J. Chun, J. 2020-10-05 doi:10.1101/2020.10.05.327122 Cold Spring Harbor Laboratory Press 2020-10-05 <![CDATA[ Tractography dissection variability: what happens when 42 groups dissect 14 white matter bundles on the same dataset? ]]> https://biorxiv.org/content/10.1101/2020.10.07.321083v1?rss=1 Schilling, K. G. Rheault, F. Petit, L. Hansen, C. B. Nath, V. Yeh, F.-C. Girard, G. Barakovic, M. Rafael-Patino, J. Yu, T. Fischi-Gomez, E. Pizzolato, M. Ocampo-Pineda, M. Schiavi, S. Canales-Rodriguez, E. J. Daducci, A. Granziera, C. Innocenti, G. Thiran, J.-P. Mancini, L. Wastling, S. Cocozza, S. Petracca, M. Pontillo, G. Mancini, M. Vos, S. B. Vakharia, V. N. Duncan, J. S. Melero, H. Manzanedo, L. Sanz-Morales, E. Pena-Melian, A. Calamante, F. Attye, A. Cabeen, R. P. Korobova, L. Toga, A. W. Ambili Vijayakumari, A. Parker, D. Verma, R. Radwan, A. Sun 2020-10-08 doi:10.1101/2020.10.07.321083 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Silencing of oncogenic KRAS by mutant-selective small interfering RNA ]]> https://biorxiv.org/content/10.1101/2020.10.08.331835v1?rss=1 Papke, B. Azam, S. H. Feng, A. Y. Van Swearingen, A. E. D. Gutierrez-Ford, C. Pallan, P. S. Egli, M. Cox, A. D. Der, C. J. Pecot, C. V. 2020-10-09 doi:10.1101/2020.10.08.331835 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Automated quality control and cell identification of droplet-based single-cell data using dropkick ]]> https://biorxiv.org/content/10.1101/2020.10.08.332288v1?rss=1 Heiser, C. N. Wang, V. M. Chen, B. Hughey, J. J. Lau, K. S. 2020-10-09 doi:10.1101/2020.10.08.332288 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Clock proteins regulate spatiotemporal organization of clock genes to control circadian rhythms ]]> https://biorxiv.org/content/10.1101/2020.10.09.333732v1?rss=1 Xiao, Y. Yuan, Y. Jimenez, M. Soni, N. Yadlapalli, S. 2020-10-10 doi:10.1101/2020.10.09.333732 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ Discovery of the first selective M4 muscarinic acetylcholine receptor antagonists with in vivo anti-parkinsonian and anti-dystonic efficacy ]]> https://biorxiv.org/content/10.1101/2020.10.12.324152v1?rss=1 Moehle, M. S. Bender, A. M. Dickerson, J. W. Foster, D. J. Donsante, Y. Peng, W. Bryany, Z. K. Bridges, T. M. Chang, S. Watson, K. J. O'Neill, J. C. Engers, J. L. Peng, L. Rodriguez, A. Niswender, C. M. Lindsley, C. W. Conn, P. J. Rook, J. M. 2020-10-12 doi:10.1101/2020.10.12.324152 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ A dominant-negative variant in the dopamine transporter PDZ-binding motif is linked to parkinsonism and neuropsychiatric disease ]]> https://biorxiv.org/content/10.1101/2020.10.12.336461v1?rss=1 Herborg, F. Jensen, K. L. Tolstoy, S. Arends, N. V. Posselt, L. P. Shekar, A. Aguilar, J. Lund, V. K. Erreger, K. Rickhag, M. Lycas, M. D. Lonsdale, M. N. Rahbek-Clemmensen, T. Sorensen, A. T. Newman, A. H. Loekkegaard, A. Kjaerulff, O. Werge, T. Moeller, L. B. Matthies, H. J. Galli, A. Hjermind, L. E. Gether, U. 2020-10-12 doi:10.1101/2020.10.12.336461 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ Myofibrillar Structural Variability Underlies Contractile Function in Stem Cell-Derived Cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2020.10.13.336685v1?rss=1 Ufford, K. Friedline, S. Tong, Z. Tang, V. T. Dobbs, A. S. Tsan, Y.-C. Bielas, S. L. Liu, A. P. Helms, A. S. 2020-10-13 doi:10.1101/2020.10.13.336685 Cold Spring Harbor Laboratory Press 2020-10-13 <![CDATA[ Convergence of a common solution to broad ebolavirus neutralization by glycan cap directed human antibodies ]]> https://biorxiv.org/content/10.1101/2020.10.14.340026v1?rss=1 Murin, C. D. Gilchuk, P. Ilinykh, P. Huang, K. Kuzmina, N. Shen, X. Brunh, J. F. Brunh, A. L. Davidson, E. Doranz, B. Williamson, L. E. Copps, J. Alkutkar, T. Flyak, A. I. Bukreyev, A. Crowe, J. E. Ward, A. B. 2020-10-14 doi:10.1101/2020.10.14.340026 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Emergence of prefrontal neuron maturation properties by training recurrent neural networks in cognitive tasks ]]> https://biorxiv.org/content/10.1101/2020.10.15.339663v1?rss=1 Liu, Y. H. Zhu, J. Constantinidis, C. Zhou, X. 2020-10-16 doi:10.1101/2020.10.15.339663 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Direct visualization of epithelial microvilli biogenesis ]]> https://biorxiv.org/content/10.1101/2020.10.21.341248v1?rss=1 Gaeta, I. M. Meenderink, L. M. Postema, M. M. Cencer, C. S. Tyska, M. J. 2020-10-21 doi:10.1101/2020.10.21.341248 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Molecular determinants for α-tubulin methylation by SETD2 ]]> https://biorxiv.org/content/10.1101/2020.10.21.349365v1?rss=1 Kearns, S. Mason, F. M. Rathmell, W. K. Park, I. Y. Walker, C. Verhey, K. A. Cianfrocco, M. A. 2020-10-21 doi:10.1101/2020.10.21.349365 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Training-induced prefrontal neuronal changes transfer between tasks ]]> https://biorxiv.org/content/10.1101/2020.10.22.351197v1?rss=1 Tang, H. Riley, M. R. Singh, B. Qi, X. Blake, D. T. Constantinidis, C. 2020-10-23 doi:10.1101/2020.10.22.351197 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ A Bacterial Signaling Network Controls Antibiotic Resistance by Regulating Anaplerosis of 2-oxoglutarate ]]> https://biorxiv.org/content/10.1101/2020.10.22.351270v1?rss=1 Hurst, M. N. Beebout, C. J. Mersfelder, R. Hollingsworth, A. N. Guckes, K. R. Bermudez, T. A. Floyd, K. A. Reasoner, S. Williams, D. C. Hadjifrangiskou, M. 2020-10-23 doi:10.1101/2020.10.22.351270 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ Transcriptional silencing of ALDH2 in acute myeloid leukemia confers a dependency on Fanconi anemia proteins ]]> https://biorxiv.org/content/10.1101/2020.10.23.352070v1?rss=1 Yang, Z. Wei, Y. Wu, X. S. Iyer, S. V. Jung, M. Adelman, E. R. Klingbeil, O. Kramer, M. Demerdash, O. E. Chang, K. Goodwin, S. Hodges, E. McCombie, W. R. Figueroa, M. E. Smogorzewska, A. Vakoc, C. R. 2020-10-23 doi:10.1101/2020.10.23.352070 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ SETD2 regulates the methylation of translation elongation factor eEF1A1 in clear cell renal cell carcinoma ]]> https://biorxiv.org/content/10.1101/2020.10.26.354902v1?rss=1 Hapke, R. Venton, L. Rose, K. L. Sheng, Q. Reddy, A. Jones, A. Rathmell, W. K. Haake, S. M. 2020-10-26 doi:10.1101/2020.10.26.354902 Cold Spring Harbor Laboratory Press 2020-10-26 <![CDATA[ Microtubules and Gαo-signaling independently regulate the preferential secretion of newly synthesized insulin granules in pancreatic islet β cells ]]> https://biorxiv.org/content/10.1101/2020.10.26.354936v1?rss=1 Gu, G. Hu, R. Zhu, X. Yuan, M. Ho, K.-H. Kaverina, I. 2020-10-26 doi:10.1101/2020.10.26.354936 Cold Spring Harbor Laboratory Press 2020-10-26 <![CDATA[ Activating mGlu3 metabotropic glutamate receptors rescues schizophrenia-like cognitive deficits through metaplastic adaptations within the hippocampus. ]]> https://biorxiv.org/content/10.1101/2020.10.27.356196v1?rss=1 Dogra, S. Stansley, B. J. Xiang, Z. Qian, W. Gogliotti, R. G. Nicoletti, F. Lindsley, C. W. Niswender, C. M. Joffe, M. E. Conn, P. J. 2020-10-27 doi:10.1101/2020.10.27.356196 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ CRISPR-based knockin mutagenesis of the pioneer transcription factor FOXA1; optimization of strategies for multi-allelic proteins in cancer cells ]]> https://biorxiv.org/content/10.1101/2020.10.27.356824v1?rss=1 Li, S. Garay, J. P. Tubbs, C. A. Franco, H. 2020-10-27 doi:10.1101/2020.10.27.356824 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Rooting the animal tree of life ]]> https://biorxiv.org/content/10.1101/2020.10.27.357798v1?rss=1 Li, Y. Shen, X.-X. Evans, B. Dunn, C. W. Rokas, A. 2020-10-28 doi:10.1101/2020.10.27.357798 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ AKAP350 REGULATES CYTOSKELETON REMODELLING AND LFA-1 ORGANIZATION DURING NK CYTOLYTIC RESPONSE ]]> https://biorxiv.org/content/10.1101/2020.10.27.357970v1?rss=1 Pariani, A. P. Almada, E. Hidalgo, F. Borini-Etichetti, C. Vena, R. Favre, C. Goldenring, J. R. Larocca, M. C. 2020-10-27 doi:10.1101/2020.10.27.357970 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ PhyKIT: a UNIX shell toolkit for processing and analyzing phylogenomic data ]]> https://biorxiv.org/content/10.1101/2020.10.27.358143v1?rss=1 Steenwyk, J. L. Buida, T. J. LaBella, A. L. Li, Y. Shen, X.-X. Rokas, A. 2020-10-28 doi:10.1101/2020.10.27.358143 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Enhancing lifespan of budding yeast by pharmacological lowering of amino acid pools ]]> https://biorxiv.org/content/10.1101/2020.10.30.362459v1?rss=1 Hepowit, N. L. Macedo, J. K. A. Young, L. E. A. Liu, K. Sun, R. C. MacGurn, J. Dickson, R. C. 2020-10-30 doi:10.1101/2020.10.30.362459 Cold Spring Harbor Laboratory Press 2020-10-30 <![CDATA[ First report of an insilico study of Luciferase in Mycobacterium sp. EPa45 ]]> https://biorxiv.org/content/10.1101/2020.10.30.362764v1?rss=1 Dasgupta, R. Pradhan, A. K. Ghosh, S. 2020-11-01 doi:10.1101/2020.10.30.362764 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ CryoET structures of immature HIV Gag reveal a complete six-helix bundle and stabilizing small molecules distinct from IP6 ]]> https://biorxiv.org/content/10.1101/2020.10.31.363382v1?rss=1 Mendonca, L. Sun, D. Ning, J. Liu, J. Kotecha, A. Olek, M. Frosio, T. Fu, X. Himes, B. A. Kleinpeter, A. B. Freed, E. O. Zhou, J. Aiken, C. Zhang, P. 2020-11-01 doi:10.1101/2020.10.31.363382 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ Control of neurogenic competence in mammalian hypothalamic tanycytes. ]]> https://biorxiv.org/content/10.1101/2020.11.02.359992v1?rss=1 Yoo, S. Kim, J. Lyu, P. Hoang, T. Ma, A. Trinh, V. Dai, W. Jiang, L. Leavey, P. Won, J.-K. Park, S.-H. Qian, J. Brown, S. P. Blackshaw, S. 2020-11-02 doi:10.1101/2020.11.02.359992 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ Inflexible Updating of the Self-Other Divide During a Social Context in Autism; Psychophysical, Electrophysiological, and Neural Network Modeling Evidence ]]> https://biorxiv.org/content/10.1101/2020.11.02.364836v1?rss=1 Noel, J.-P. G. Paredes, R. Terrebonne, E. Feldman, J. I. Woynaroski, T. G. Cascio, C. J. Series, P. Wallace, M. 2020-11-03 doi:10.1101/2020.11.02.364836 Cold Spring Harbor Laboratory Press 2020-11-03 <![CDATA[ Genomic and phenotypic analysis of COVID-19-associated pulmonary aspergillosis isolates of Aspergillus fumigatus ]]> https://biorxiv.org/content/10.1101/2020.11.06.371971v1?rss=1 Steenwyk, J. L. Mead, M. E. Castro, P. A. Valero, C. Damasio, A. Santos, R. A. C. LaBella, A. L. Li, Y. Knowles, S. L. Raja, H. A. Oberlies, N. H. Zhou, X. Cornely, O. A. Fuchs, F. Koehler, P. Goldman, G. Rokas, A. 2020-11-06 doi:10.1101/2020.11.06.371971 Cold Spring Harbor Laboratory Press 2020-11-06 <![CDATA[ Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments ]]> https://biorxiv.org/content/10.1101/2020.11.09.375592v1?rss=1 Sheng, X. Ma, Z. Wu, J. Liu, H. Qiu, C. Miao, Z. Seasock, M. J. Palmer, M. Shin, M. K. Duffin, K. L. Pullen, S. S. Edwards, T. L. Hellwege, J. N. Hung, A. M. Li, M. Voight, B. Coffman, T. Brown, C. D. Susztak, K. 2020-11-10 doi:10.1101/2020.11.09.375592 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ A new microfluidic concept for successful in vitro culture of mouse embryos ]]> https://biorxiv.org/content/10.1101/2020.11.10.376160v1?rss=1 Mancini, V. McKeegan, P. Rutledge, A. C. Condreanu, S. G. Sherrod, S. D. McLean, J. A. Picton, H. M. Pensabene, V. 2020-11-10 doi:10.1101/2020.11.10.376160 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ ASCL1 represses a latent osteogenic program in small cell lung cancer in multiple cells of origin ]]> https://biorxiv.org/content/10.1101/2020.11.11.362632v1?rss=1 Olsen, R. R. Kastner, D. W. Ireland, A. S. Groves, S. M. Pozo, K. Whitney, C. P. Guthrie, M. R. Wait, S. J. Soltero, D. Witt, B. L. Quaranta, V. Johnson, J. E. Oliver, T. G. 2020-11-11 doi:10.1101/2020.11.11.362632 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ Enforced dimerization between XBP1s and ATF6f enhances the protective effects of the unfolded protein response (UPR) in models of neurodegeneration ]]> https://biorxiv.org/content/10.1101/2020.11.17.387480v1?rss=1 Vidal, R. L. Sepulveda, D. Troncoso-Escudero, P. Garcia-Huerta, P. Gonzalez, C. Plate, L. Jerez, C. Canovas, J. Rivera, C. Castillo, V. Cisternas, M. Leal, S. Martinez, A. Grandjean, J. Lashuel, H. Martin, A. J. M. Latapiat, V. Matus, S. Sardi, S. P. Wiseman, L. Hetz, C. 2020-11-18 doi:10.1101/2020.11.17.387480 Cold Spring Harbor Laboratory Press 2020-11-18 <![CDATA[ IBEX: A versatile multi-plex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues ]]> https://biorxiv.org/content/10.1101/2020.11.20.390690v1?rss=1 65 parameters in the same tissue section without physical degradation. IBEX can be employed with various types of conventional microscopes and permits use of both commercially available and user-generated antibodies in an open system to allow easy adjustment of staining panels based on ongoing marker discovery efforts. We show how IBEX can also be used with amplified staining methods for imaging strongly fixed tissues with limited epitope retention and with oligonucleotide-based staining, allowing potential cross-referencing between flow cytometry, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq), and IBEX analysis of the same tissue. To facilitate data processing, we provide an open source platform for automated registration of iterative images. IBEX thus represents a technology that can be rapidly integrated into most current laboratory workflows to achieve high content imaging to reveal the complex cellular landscape of diverse organs and tissues. Significance StatementSingle cell flow cytometry and genomic methods are rapidly increasing our knowledge of the diversity of cell types in metazoan tissues. However, suitably robust methods for placing these cells in a spatial context that reveal how their localization and putative interactions contribute to tissue physiology and pathology are still lacking. Here we provide a readily accessible pipeline (IBEX) for highly multi-plex immunofluorescent imaging that enables a fine-grained analysis of cells in their tissue context. Additionally, we describe extensions of the IBEX workflow to handle hard to image tissue preparations and a method to facilitate direct integration of the imaging data with flow cytometry and sequencing technologies. ]]> Radtke, A. J. Kandov, E. Lowekamp, B. Speranza, E. Chu, C. J. Gola, A. Thakur, N. Shih, R. Yao, L. Yaniv, Z. R. Beuschel, R. T. Kabat, J. Croteau, J. Davis, J. Hernandez, J. M. Germain, R. N. 2020-11-21 doi:10.1101/2020.11.20.390690 Cold Spring Harbor Laboratory Press 2020-11-21 <![CDATA[ Cyto-nuclear linkage disequilibrium resulting from admixture ]]> https://biorxiv.org/content/10.1101/2020.11.24.396903v1?rss=1 Fields, P. McCauley, D. E. Taylor, D. 2020-11-25 doi:10.1101/2020.11.24.396903 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ The C99 domain of the amyloid precursor protein is a disordered membrane phase-preferring protein ]]> https://biorxiv.org/content/10.1101/2020.11.25.397893v1?rss=1 Capone, R. F. Tiwari, A. Hadziselimovic, A. Peskova, Y. Hutchinson, J. M. Sanders, C. R. Kenworthy, A. K. 2020-11-25 doi:10.1101/2020.11.25.397893 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ No evidence for whole-chromosome dosage compensation or global transcriptomic expression differences in spontaneously-aneuploid mutation accumulation lines of Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2020.12.01.404830v1?rss=1 McQueary, H. C. Behringer, M. G. Chamberlin, J. Tsfoni, A. Canas, A. Demario, S. Johnson, B. S. Hall, D. W. 2020-12-02 doi:10.1101/2020.12.01.404830 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Th17-skewed inflammation due to genetic deficiency of a cadherin stress sensor ]]> https://biorxiv.org/content/10.1101/2020.12.01.406587v1?rss=1 Godsel, L. M. Roth-Carter, Q. R. Koetsier, J. L. Tsoi, L. C. Broussard, J. A. Fitz, G. N. Lloyd, S. M. Kweon, J. Huffine, A. L. Burks, H. E. Hegazy, M. Amagai, S. Harms, P. W. Johnson, J. L. Urciuoli, G. Doglio, L. T. Swindell, W. R. Awatramani, R. Sprecher, E. Bao, X. Cohen-Barak, E. Missero, C. Gudjonsson, J. E. Green, K. J. 2020-12-02 doi:10.1101/2020.12.01.406587 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Leukodystrophy resembling Vanishing White Matter Disease is recapitulated by brain-specific depletion of apoptosis regulator MCL-1 ]]> https://biorxiv.org/content/10.1101/2020.12.02.408138v1?rss=1 Cleveland, A. H. Romero, A. Alfonso Azcona, L. Herrero, M. Elroy-Stein, O. Gama, V. Gershon, T. R. 2020-12-03 doi:10.1101/2020.12.02.408138 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ A multi-task deep-learning system for predicting membrane associations and secondary structures of proteins ]]> https://biorxiv.org/content/10.1101/2020.12.02.409045v1?rss=1 LI, B. Mendenhall, J. Capra, J. A. Meiler, J. 2020-12-03 doi:10.1101/2020.12.02.409045 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ MASiVar: Multisite, Multiscanner, and Multisubject Acquisitions for Studying Variability in Diffusion Weighted Magnetic Resonance Imaging ]]> https://biorxiv.org/content/10.1101/2020.12.03.408567v1?rss=1 Cai, L. Y. Yang, Q. Kanakaraj, P. Nath, V. Newton, A. T. Edmonson, H. A. Luci, J. Conrad, B. N. Price, G. R. Hansen, C. B. Kerley, C. I. Ramadass, K. Yeh, F.-C. Kang, H. Garyfallidis, E. Descoteaux, M. Rheault, F. Schilling, K. G. Landman, B. A. 2020-12-03 doi:10.1101/2020.12.03.408567 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ De novo macrocyclic peptides for inhibiting, stabilising and probing the function of the Retromer endosomal trafficking complex ]]> https://biorxiv.org/content/10.1101/2020.12.03.410779v1?rss=1 Chen, K.-E. Guo, Q. Cui, Y. Kendall, A. K. Hill, T. A. Hall, R. J. Sacharz, J. Norwood, S. J. Xie, B. Leneva, N. Yang, Z. Ghai, R. Stroud, D. A. Fairlie, D. P. Suga, H. Jackson, L. P. Teasdale, R. D. Passioura, T. Collins, B. M. 2020-12-04 doi:10.1101/2020.12.03.410779 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ CYRI-A regulates macropinocytic cup maturation and mediates integrin uptake, limiting invasive migration ]]> https://biorxiv.org/content/10.1101/2020.12.04.411645v1?rss=1 Le, A. H. Yelland, T. Paul, N. Fort, L. Nikolaou, S. Ismail, S. Machesky, L. 2020-12-04 doi:10.1101/2020.12.04.411645 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ Granzyme B skews CD4+ T cell differentiation resulting in increased intestinal pathogenicity ]]> https://biorxiv.org/content/10.1101/2020.12.04.412056v1?rss=1 Hoek, K. Greer, M. J. Mcclanahan, K. G. Nazmi, A. Piazuelo, M. B. Wilson, K. T. Olivares-Villagomez, D. 2020-12-06 doi:10.1101/2020.12.04.412056 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Biogenesis of RNA-containing extracellular vesicles at endoplasmic reticulum membrane contact sites ]]> https://biorxiv.org/content/10.1101/2020.12.04.412379v1?rss=1 Barman, B. Ping, J. Krystofiak, E. Allen, R. Prasad, N. Vickers, K. Patton, J. G. Liu, Q. Weaver, A. M. 2020-12-05 doi:10.1101/2020.12.04.412379 Cold Spring Harbor Laboratory Press 2020-12-05 <![CDATA[ Highly Multiplexed Immunofluorescence of the Human Kidney using Co-Detection by Indexing (CODEX) ]]> https://biorxiv.org/content/10.1101/2020.12.04.412429v1?rss=1 Neumann, E. K. Rivera, E. S. Patterson, N. H. deCaestecker, M. Fogo, A. B. Caprioli, R. M. Spraggins, J. M. 2020-12-04 doi:10.1101/2020.12.04.412429 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ A protease-initiated model of wound detection ]]> https://biorxiv.org/content/10.1101/2020.12.08.415554v1?rss=1 O'Connor, J. T. Stevens, A. C. Shannon, E. K. Akbar, F. B. LaFever, K. S. Narayanan, N. Hutson, M. S. Page-McCaw, A. 2020-12-09 doi:10.1101/2020.12.08.415554 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Extracellular spreading of Wingless is required for Drosophila oogenesis ]]> https://biorxiv.org/content/10.1101/2020.12.08.416594v1?rss=1 Wang, X. LaFever, K. S. Waghmare, I. Page-McCaw, A. 2020-12-08 doi:10.1101/2020.12.08.416594 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ Unsupervised logic-based mechanism inference for network-driven biological processes ]]> https://biorxiv.org/content/10.1101/2020.12.15.422874v1?rss=1 Prugger, M. Einkemmer, L. Beik, S. P. Harris, L. A. Lopez, C. F. 2020-12-15 doi:10.1101/2020.12.15.422874 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Molecular topography of an entire nervous system ]]> https://biorxiv.org/content/10.1101/2020.12.15.422897v1?rss=1 Taylor, S. R. Santpere, G. Weinreb, A. Barrett, A. Reilly, M. B. Xu, C. Varol, E. Oikonomou, P. Glenwinkel, L. McWhirter, R. Poff, A. Basavaraju, M. Rafi, I. Yemini, E. Cook, S. J. Abrams, A. Vidal, B. Cros, C. Tavazoie, S. Sestan, N. Hammarlund, M. Hobert, O. Miller, D. M. 2020-12-16 doi:10.1101/2020.12.15.422897 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ Ventral hippocampal mossy cell hyperactivity degrades dorsal hippocampal mnemonic function via longitudinal projections ]]> https://biorxiv.org/content/10.1101/2020.12.15.422938v1?rss=1 Bauer, J. P. Rader, S. L. Joffe, M. Kwon, W. Quay, J. Zhou, C. Conn, P. J. Lewis, A. S. 2020-12-16 doi:10.1101/2020.12.15.422938 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ Analysis of Genetically Determined Gene Expression Suggests Role of Inflammatory Processes in Exfoliation Syndrome ]]> https://biorxiv.org/content/10.1101/2020.12.17.423318v1?rss=1 Hirbo, J. B. Pasutto, F. Gamazon, E. R. Evans, P. Pawar, P. Berner, D. Sealock, J. Tao, R. Straub, P. S. Konkashbaev, A. I. Breyer, M. A. Schlötzer-Schrehardt, U. Reis, A. Brantley, M. A. Khor, C. C. Joos, K. M. Cox, N. J. 2020-12-18 doi:10.1101/2020.12.17.423318 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ Glycosylation Limits Forward Trafficking of the Tetraspan Membrane Protein PMP22 ]]> https://biorxiv.org/content/10.1101/2020.12.18.423452v1?rss=1 Marinko, J. T. Wright, M. T. Heintzman, D. R. Plate, L. Sanders, C. 2020-12-20 doi:10.1101/2020.12.18.423452 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ Cross-reactive coronavirus antibodies with diverse epitope specificities and extra-neutralization functions ]]> https://biorxiv.org/content/10.1101/2020.12.20.414748v1?rss=1 Shiakolas, A. R. Kramer, K. J. Wrapp, D. Richardson, S. I. Schäfer, A. Wall, S. Wang, N. Janowska, K. Pilewski, K. A. Venkat, R. Parks, R. Manamela, N. P. Raju, N. Friedman Fechter, E. Holt, C. M. Suryadevara, N. Chen, R. E. Martinez, D. R. Nargi, R. S. Sutton, R. E. Ledgerwood, J. E. Graham, B. S. Diamond, M. S. Haynes, B. F. Acharya, P. Carnahan, R. H. Crowe, J. E. Baric, R. S. Morris, L. McLellan, J. S. Georgiev, I. S. 2020-12-20 doi:10.1101/2020.12.20.414748 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ In vivo genetic screen identifies a SLC5A3-dependent myo-inositol auxotrophy in acute myeloid leukemia ]]> https://biorxiv.org/content/10.1101/2020.12.22.424018v1?rss=1 Wei, Y. Iyer, S. Costa, S. Yang, Z. Kramer, M. Adelman, E. Klingbeil, O. Demerdash, O. Polyanskaya, S. Chang, K. Goodwin, S. Hodges, E. McCombie, W. R. Figueroa, M. Vakoc, C. 2020-12-22 doi:10.1101/2020.12.22.424018 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Creation and validation of 3D-printed head molds for stereotaxic injections of neonatal mouse brains ]]> https://biorxiv.org/content/10.1101/2020.12.22.424033v1?rss=1 Chervonski, E. Brockman, A. Khurana, R. Chen, Y. Greenberg, S. Hay, M. S. Luo, Y. Miller, J. Patelis, D. Whitney, S. K. Walker, M. Ihrie, R. A. 2020-12-22 doi:10.1101/2020.12.22.424033 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Narratives: fMRI data for evaluating models of naturalistic language comprehension ]]> https://biorxiv.org/content/10.1101/2020.12.23.424091v1?rss=1 Nastase, S. A. Liu, Y.-F. Hillman, H. Zadbood, A. Hasenfratz, L. Keshavarzian, N. Chen, J. Honey, C. J. Yeshurun, Y. Regev, M. Nguyen, M. Chang, C. H. C. Baldassano, C. Lositsky, O. Simony, E. Chow, M. A. Leong, Y. C. Brooks, P. P. Micciche, E. Choe, G. Goldstein, A. Vanderwal, T. Halchenko, Y. O. Norman, K. A. Hasson, U. 2020-12-23 doi:10.1101/2020.12.23.424091 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ Automated Biomarker Candidate Discovery in Imaging Mass Spectrometry Data Through Spatially Localized Shapley Additive Explanations ]]> https://biorxiv.org/content/10.1101/2020.12.23.424201v1?rss=1 Tideman, L. E. M. Migas, L. G. Djambazova, K. V. Patterson, N. H. Caprioli, R. M. Spraggins, J. M. Van de Plas, R. 2020-12-24 doi:10.1101/2020.12.23.424201 Cold Spring Harbor Laboratory Press 2020-12-24 <![CDATA[ The P4-ATPase Drs2 regulates the homeostasis of Atg9 ]]> https://biorxiv.org/content/10.1101/2020.12.25.417865v1?rss=1 Pazos Capell, I. Puig-Tinto, M. Cordero, J. Jimenez-Menendez, N. Abella Guerra, M. G. Duran, A. Adachi-Fernandez, E. Belmonte, C. Sabido-Bozo, S. Chinchilla, A. Tosi, S. Nezu, A. Colombelli, J. Graham, T. Yoshimori, T. Muniz, M. Hamasaki, M. Gallego, O. 2020-12-26 doi:10.1101/2020.12.25.417865 Cold Spring Harbor Laboratory Press 2020-12-26 <![CDATA[ XMAP215 promotes microtubule catastrophe by disrupting the growing microtubule end ]]> https://biorxiv.org/content/10.1101/2020.12.29.424748v1?rss=1 Farmer, V. J. Arpag, G. Hall, S. L. Zanic, M. 2020-12-29 doi:10.1101/2020.12.29.424748 Cold Spring Harbor Laboratory Press 2020-12-29 <![CDATA[ Cryo-EM structure of the yeast TREX complex and coordination with the SR-like protein Gbp2 ]]> https://biorxiv.org/content/10.1101/2021.01.04.425184v1?rss=1 Xie, Y. Clarke, B. P. Kim, Y. J. Ivey, A. L. Hill, P. S. Shi, Y. Ren, Y. 2021-01-04 doi:10.1101/2021.01.04.425184 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Optogenetic stimulation of VIPergic SCN neurons induces photoperiodic changes in the mammalian circadian clock ]]> https://biorxiv.org/content/10.1101/2021.01.04.425287v1?rss=1 Tackenberg, M. C. Hughey, J. J. McMahon, D. G. 2021-01-04 doi:10.1101/2021.01.04.425287 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ An optimized ribodepletion approach for C. elegans RNA-sequencing libraries ]]> https://biorxiv.org/content/10.1101/2021.01.04.425342v1?rss=1 Barrett, A. McWhirter, R. Taylor, S. R. Weinreb, A. Miller, D. Hammarlund, M. 2021-01-05 doi:10.1101/2021.01.04.425342 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Seeing the World Like Never Before: Human stereovision through perfect optics ]]> https://biorxiv.org/content/10.1101/2021.01.05.425427v1?rss=1 Ng, C. J. Blake, R. Banks, M. S. Tadin, D. J. Yoon, G. 2021-01-06 doi:10.1101/2021.01.05.425427 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Human colorectal pre-cancer atlas identifies distinct molecular programs underlying two major subclasses of pre-malignant tumors ]]> https://biorxiv.org/content/10.1101/2021.01.11.426044v1?rss=1 Chen, B. McKinley, E. T. Simmons, A. J. Ramirez, M. A. Zhu, X. Southard-Smith, A. N. Markham, N. O. Sheng, Q. Drewes, J. Xu, Y. Heiser, C. N. Zhou, Y. Revetta, F. Berry, L. D. Zheng, W. Washington, M. K. Cai, Q. Sears, C. L. Goldenring, J. R. Franklin, J. L. Vandekar, S. Roland, J. T. Su, T. Huh, W. J. Liu, Q. Coffey, R. J. Shrubsole, M. J. Lau, K. 2021-01-13 doi:10.1101/2021.01.11.426044 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ Mapping the Promiscuous Binding Interface of HOX-A11 with KIX by Experimentally Guided in-silico docking ]]> https://biorxiv.org/content/10.1101/2021.01.11.426190v1?rss=1 Ganguly, S. Meiler, J. Wagner, G. P. 2021-01-11 doi:10.1101/2021.01.11.426190 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Neutralizing and protective human monoclonal antibodies recognizing the N-terminaldomain of the SARS-CoV-2 spike protein ]]> https://biorxiv.org/content/10.1101/2021.01.19.427324v1?rss=1 Suryadevara, N. Shrihari, S. Gilchuk, P. VanBlargan, L. Binshtein, E. Zost, S. Nargi, R. Sutton, R. Winkler, E. S. Chen, E. C. Fouch, M. E. Davidson, E. Doranz, B. Carnahan, R. H. Thackray, L. Diamond, M. D. Crowe, J. E. 2021-01-20 doi:10.1101/2021.01.19.427324 Cold Spring Harbor Laboratory Press 2021-01-20 <![CDATA[ Diverse functions associate with trans-species polymorphisms in humans ]]> https://biorxiv.org/content/10.1101/2021.01.21.427090v1?rss=1 Velazquez-Arcelay, K. Benton, M. L. Capra, J. A. 2021-01-22 doi:10.1101/2021.01.21.427090 Cold Spring Harbor Laboratory Press 2021-01-22 <![CDATA[ A Single Cell Atlas of Lung Development ]]> https://biorxiv.org/content/10.1101/2021.01.21.427641v1?rss=1 Negretti, N. M. Plosa, E. J. Benjamin, J. T. Schuler, B. A. Habermann, A. C. Jetter, C. S. Taylor, C. J. Gulleman, P. Nichols, D. Matlock, B. K. Guttentag, S. H. Blackwell, T. S. Banovich, N. E. Kropski, J. A. Sucre, J. M. 2021-01-22 doi:10.1101/2021.01.21.427641 Cold Spring Harbor Laboratory Press 2021-01-22 <![CDATA[ Cancer Hallmarks Define a Continuum of Plastic Cell States between Small Cell Lung Cancer Archetypes ]]> https://biorxiv.org/content/10.1101/2021.01.22.427865v1?rss=1 Groves, S. M. Ireland, A. Liu, Q. Simmons, A. J. Lau, K. Iams, W. T. Tyson, D. R. Lovly, C. Oliver, T. G. Quaranta, V. 2021-01-24 doi:10.1101/2021.01.22.427865 Cold Spring Harbor Laboratory Press 2021-01-24 <![CDATA[ Microbial population dynamics and evolutionary outcomes under extreme energy-limitation ]]> https://biorxiv.org/content/10.1101/2021.01.25.428163v1?rss=1 Shoemaker, W. R. Jones, S. E. Muscarella, M. E. Behringer, M. G. Lehmkuhl, B. K. Lennon, J. T. 2021-01-26 doi:10.1101/2021.01.25.428163 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Probability-based mechanisms in biological networks with parameter uncertainty ]]> https://biorxiv.org/content/10.1101/2021.01.26.428266v1?rss=1 Ortega, O. O. Wilson, B. A. Pino, J. C. Irvin, M. W. Ildefonso, G. V. Garbett, S. P. Lopez, C. F. 2021-01-27 doi:10.1101/2021.01.26.428266 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Genetic and structural basis for recognition of SARS-CoV-2 spike protein by a two-antibody cocktail ]]> https://biorxiv.org/content/10.1101/2021.01.27.428529v1?rss=1 Dong, J. Zost, S. Greaney, A. Starr, T. N. Dingens, A. S. Chen, E. C. Chen, R. Case, B. Sutton, R. Gilchuk, P. Rodriguez, J. Armstrong, E. Gainza, C. Nargi, R. Binshtein, E. Xie, X. Zhang, X. Shi, P.-Y. Logue, J. Weston, S. McGrath, M. Frieman, M. Brady, T. Tuffy, K. Bright, H. Loo, Y.-M. McvTamney, P. Esser, M. Carnahan, R. Diamond, M. Bloom, J. Crowe, J. E. 2021-01-28 doi:10.1101/2021.01.27.428529 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Modeling mutational effects on biochemical phenotypes using convolutional neural networks: application to SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2021.01.28.428521v1?rss=1 Wang, B. Gamazon, E. R. 2021-01-28 doi:10.1101/2021.01.28.428521 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM ]]> https://biorxiv.org/content/10.1101/2021.01.28.428677v1?rss=1 Antanasijevic, A. Sewall, L. M. Cottrell, C. A. Carnathan, D. G. Jimenez, L. E. Ngo, J. T. Silverman, J. B. Groschel, B. Georgeson, E. Bhiman, J. Bastidas, R. LaBranche, C. Allen, J. D. Copps, J. Perrett, H. R. Rantalainen, K. Cannac, F. Yang, Y. R. Torrents de la Pena, A. Froes Rocha, R. Berndsen, Z. T. Baker, D. King, N. P. Sanders, R. W. Moore, J. P. Crotty, S. Crispin, M. Montefiori, D. C. Burton, D. R. Schief, W. R. Silvestri, G. Ward, A. B. 2021-01-28 doi:10.1101/2021.01.28.428677 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Generalizing about GC (hypoxia): Dys- & Dat-InformaticaComment on Germinal center B cells selectively oxidize fatty acids for energy while conducting minimal glycolysis ]]> https://biorxiv.org/content/10.1101/2021.01.28.428711v1?rss=1 Boothby, M. R. Raybuck, A. Cho, S. H. Stengel, K. Hiebert, S. W. Li, J. 2021-01-30 doi:10.1101/2021.01.28.428711 Cold Spring Harbor Laboratory Press 2021-01-30 <![CDATA[ Mutagenesis of the Ammonium Transporter AcAmt Reveals a Reproductive Role and a Novel Ammonia-Sensing Mechanism in the Malaria Vector Mosquito Anopheles coluzzii ]]> https://biorxiv.org/content/10.1101/2021.01.29.428879v1?rss=1 Ye, Z. Liu, F. Ferguson, S. T. Baker, A. P. Pitts, R. J. Zwiebel, L. 2021-01-31 doi:10.1101/2021.01.29.428879 Cold Spring Harbor Laboratory Press 2021-01-31 <![CDATA[ Trial-to-trial variability of spiking delay activity in prefrontal cortex constrains burst-coding models of working memory ]]> https://biorxiv.org/content/10.1101/2021.01.30.428962v1?rss=1 Li, D. Constantinidis, C. Murray, J. D. 2021-02-01 doi:10.1101/2021.01.30.428962 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Increased energy expenditure and protection from diet-induced obesity in mice lacking the cGMP-specific phosphodiesterase, PDE9 ]]> https://biorxiv.org/content/10.1101/2021.02.02.429406v1?rss=1 Ceddia, R. P. Liu, D. Shi, F. Mishra, S. Kass, D. A. Collins, S. 2021-02-02 doi:10.1101/2021.02.02.429406 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Balanced Input from the tRNA Prenyltransferase MiaA Controls the Stress Resistance and Virulence Potential of Extraintestinal Pathogenic Escherichia coli ]]> https://biorxiv.org/content/10.1101/2021.02.02.429414v1?rss=1 Blango, M. G. Fleming, B. A. Kincannon, W. M. Tran, A. Lewis, A. J. Russell, C. W. Zhou, Q. Baird, L. M. Brannon, J. R. Beebout, C. J. Bandarian, V. Hadjifraniskou, M. Howard, M. T. Mulvey, M. A. 2021-02-02 doi:10.1101/2021.02.02.429414 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ PDE9 Inhibition Activates PPARa to Stimulate Mitochondrial Fat Metabolism and Reduce Cardiometabolic Syndrome ]]> https://biorxiv.org/content/10.1101/2021.02.02.429442v1?rss=1 Mishra, S. Hahn, V. Sadagopan, N. Dunkerly-Eyring, B. Rodriguez, S. Sarver, D. C. Ceddia, R. P. Murphy, S. Knutsdottir, H. Jani, V. Ashok, D. Oeing, C. U. O'Rourke, B. Sharma, K. Gangoiti, J. Sears, D. D. Wong, G. W. Collins, S. Kass, D. A. 2021-02-02 doi:10.1101/2021.02.02.429442 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ MTHFD2 is a Metabolic Checkpoint Controlling Effector and Regulatory T Cell Fate and Function ]]> https://biorxiv.org/content/10.1101/2021.02.03.428939v1?rss=1 Sugiura, A. Andrejeva, G. Voss, K. Heintzman, D. R. Beier, K. L. Wolf, M. M. Greenwood, D. L. Ye, X. Shahi, S. K. Freedman, S. N. Cameron, A. M. Foerch, P. Bourne, T. Xu, X. Garcia-Canaveras, J. C. Mangalam, A. K. Rabinowitz, J. Rathmell, J. 2021-02-03 doi:10.1101/2021.02.03.428939 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/2021.02.03.429484v1?rss=1 Chen, J. Cheong, C. Lan, L. Zhou, X. Liu, J. Lu, A. Cheung, W. K. Zhang, L. 2021-02-03 doi:10.1101/2021.02.03.429484 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Leaky wiring of the brain: local cluster of coupled synapses and extracellular signal integration ]]> https://biorxiv.org/content/10.1101/2021.02.05.429974v1?rss=1 1.5 {micro}m distant to the releasing synapse. 2P-glutamate uncaging was used to quantitatively probe glutamate spread in the neuropil. Releasing [~]35000 molecules of glutamate ([~]5 vesicles) at a distance of 500 nm to a spine generated an uncaging EPSC reaching [~]30% of the quantal amplitude at synaptic AMPA-Rs. The same stimulus activated [~]70% of the quantal amplitude at NMDA-Rs and still generated clear current and calcium responses when applied at >= 2 {micro}m remote to the spine. Extracellular spread of glutamate on the sub-micrometer scale appeared cooperative and caused supra-additive activation of AMPA-Rs in a spine. These observations are not predicted by previously used models of glutamate diffusion in the neuropil. An extracellular glutamate scavenger system weakly reduced field potential responses but not the quantal amplitude, indicating that a cross-talk component regularly contributes to synaptic transmission. Our data suggest that slight synaptic crosstalk responses at AMPA receptors of [~]2-4 adjacent synapses may be common (>70 synapses for NMDA receptors). Such broadcasting of synaptic signals to very local neighborhoods could stabilize network learning performance and allow for integration of synaptic activity within the extracellular space. ]]> Dietrich, D. Matthews, E. Sun, W. McMahon, S. Döngi, M. Halka, L. Anders, S. Müller, J. A. Steinlein, P. Vana, N. van Dyk, G. Pitsch, J. Becker, A. J. Pfeifer, A. Kavalali, E. T. Lamprecht, A. Henneberger, C. Stein, V. Schoch, S. 2021-02-08 doi:10.1101/2021.02.05.429974 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ SSNA1 stabilizes dynamic microtubules and detects microtubule damage ]]> https://biorxiv.org/content/10.1101/2021.02.05.429994v1?rss=1 Lawrence, B. Arnaiz, C. Arpag, G. Zanic, M. 2021-02-06 doi:10.1101/2021.02.05.429994 Cold Spring Harbor Laboratory Press 2021-02-06 <![CDATA[ Latrophilin GPCR Signaling Mediates Synapse Formation ]]> https://biorxiv.org/content/10.1101/2021.02.10.430631v1?rss=1 Sando, R. Südhof, T. C. 2021-02-12 doi:10.1101/2021.02.10.430631 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ Bfimpute: A Bayesian factorization method to recover single-cell RNA sequencing data ]]> https://biorxiv.org/content/10.1101/2021.02.10.430649v1?rss=1 Wen, Z.-H. Langsam, J. L. Zhang, L. Shen, W. Zhou, X. 2021-02-11 doi:10.1101/2021.02.10.430649 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ Evaluating Sleep Disturbances in Children with Rare Genetic Neurodevelopmental Syndromes ]]> https://biorxiv.org/content/10.1101/2021.02.12.430633v1?rss=1 Veatch, O. J. Malow, B. A. Lee, H.-S. Knight, A. Barrish, J. O. Neul, J. L. Lane, J. B. Skinner, S. A. Kaufmann, W. E. Miller, J. L. Driscoll, D. J. Bird, L. M. Butler, M. G. Dykens, E. M. Gold, J.-A. Kimonis, V. Bacino, C. A. Tan, W.-H. Kothare, S. V. Peters, S. U. Percy, A. K. Glaze, D. G. 2021-02-15 doi:10.1101/2021.02.12.430633 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ Genomes of gut bacteria from Nasonia wasps shed light on phylosymbiosis and microbe-assisted hybrid breakdown ]]> https://biorxiv.org/content/10.1101/2021.02.13.431100v1?rss=1 Cross, K. L. Leigh, B. A. Hatmaker, E. A. Mikaelyan, A. Miller, A. K. Bordenstein, S. R. 2021-02-14 doi:10.1101/2021.02.13.431100 Cold Spring Harbor Laboratory Press 2021-02-14 <![CDATA[ Pharmacologic Therapy for Engraftment Arrhythmia Induced by Transplantation of Human Cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2021.02.15.431108v1?rss=1 Nakamura, K. Neidig, L. E. Yang, X. Weber, G. J. El-nachef, D. Tsuchida, H. Dupras, S. Kalucki, F. A. Jayabalu, A. Futakuchi-Tsuchida, A. Nakamura, D. S. Marchiano, S. Bertero, A. Robinson, M. R. Cain, K. Whittington, D. Reinecke, H. Pabon, L. Knollmann, B. C. Kattman, S. Thies, R. S. MacLellan, W. R. Murry, C. E. 2021-02-16 doi:10.1101/2021.02.15.431108 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Targeting Diacylglycerol Lipase to Reduce AlcoholConsumption ]]> https://biorxiv.org/content/10.1101/2021.02.16.431429v1?rss=1 Bedse, G. Winters, N. D. Astafyev, A. Patrick, T. A. Mahajan, V. R. Uddin, M. J. Centanni, S. W. Samuels, D. C. Marnett, L. J. Winder, D. G. Patel, S. 2021-02-17 doi:10.1101/2021.02.16.431429 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Delivery of recombinant SARS-CoV-2 envelope protein into human cells ]]> https://biorxiv.org/content/10.1101/2021.02.18.431684v1?rss=1 Hutchison, J. M. Capone, R. Luu, D. D. Hadziselimovic, A. Van Horn, W. D. Sanders, C. R. 2021-02-19 doi:10.1101/2021.02.18.431684 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Combinatorial transcription factor profiles predict mature and functional human islet α and β cells ]]> https://biorxiv.org/content/10.1101/2021.02.23.432522v1?rss=1 40,000 cells from normal human islets by scRNA-seq and stratified and {beta} cells based on combinatorial TF expression. Subpopulations of islet cells co-expressing ARX/MAFB ( cells) and MAFA/MAFB ({beta} cells) exhibited greater expression of key genes related to glucose sensing and hormone secretion relative to subpopulations expressing only one or neither TF. Moreover, all subpopulations were identified in native pancreatic tissue from multiple donors. By Patch-seq, MAFA/MAFB co-expressing {beta} cells showed enhanced electrophysiological activity. Thus, these results indicate combinatorial TF expression in islet and {beta} cells predicts highly functional, mature subpopulations. ]]> Shrestha, S. Saunders, D. C. Walker, J. T. Camunas-Soler, J. Dai, X.-Q. Haliyur, R. Aramandla, R. Poffenberger, G. Prasad, N. Bottino, R. Stein, R. Cartailler, J.-P. Parker, S. C. J. MacDonald, P. E. Levy, S. E. Powers, A. C. Brissova, M. 2021-02-24 doi:10.1101/2021.02.23.432522 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ Cortical Tension Initiates the Positive Feedback Loop Between E-cadherin and F-actin ]]> https://biorxiv.org/content/10.1101/2021.02.23.432578v1?rss=1 Yu, Q. Holmes, W. R. Thiery, J. P. Luwor, R. B. Rajagopal, V. 2021-02-24 doi:10.1101/2021.02.23.432578 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ Spatially-Resolved Proteomic Analysis of the Lens Extracellular Diffusion Barrier ]]> https://biorxiv.org/content/10.1101/2021.02.23.432581v1?rss=1 Wang, Z. Schey, K. L. 2021-02-23 doi:10.1101/2021.02.23.432581 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Power spectra reveal distinct BOLD resting-state time courses in white matter ]]> https://biorxiv.org/content/10.1101/2021.02.24.432346v1?rss=1 Li, M. Gao, Y. Ding, Z. Gore, J. C. 2021-02-25 doi:10.1101/2021.02.24.432346 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Larvae and adults exhibit contrasting patterns of immune gene expression and infection resistance in wild flour beetle populations ]]> https://biorxiv.org/content/10.1101/2021.02.24.432795v1?rss=1 Tate, A. T. Perry, A. Jent, D. G. 2021-02-25 doi:10.1101/2021.02.24.432795 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Programmatic modeling for biological systems ]]> https://biorxiv.org/content/10.1101/2021.02.26.433125v1?rss=1 Lubbock, A. L. R. Lopez, C. F. 2021-02-27 doi:10.1101/2021.02.26.433125 Cold Spring Harbor Laboratory Press 2021-02-27 <![CDATA[ Influence of basal media composition on barrier fidelity within human pluripotent stem cell-derived blood-brain barrier models ]]> https://biorxiv.org/content/10.1101/2021.03.01.433282v1?rss=1 Neal, E. Katdare, K. Shi, Y. Marinelli, N. Hagerla, K. Lippmann, E. 2021-03-01 doi:10.1101/2021.03.01.433282 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi ]]> https://biorxiv.org/content/10.1101/2021.03.01.433394v1?rss=1 Mead, M. E. Steenwyk, J. L. Silva, L. P. de Castro, P. A. Saeed, N. Hillmann, F. Goldman, G. Rokas, A. 2021-03-01 doi:10.1101/2021.03.01.433394 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ On the generalizability of diffusion MRI signal representations across acquisition parameters, sequences and tissue types: chronicles of the MEMENTO challenge. ]]> https://biorxiv.org/content/10.1101/2021.03.02.433228v1?rss=1 De Luca, A. Ianus, A. Leemans, A. Palombo, M. Shemesh, N. Zhang, H. Alexander, D. C. Nilsson, M. Froeling, M. Biessels, G.-J. Zucchelli, M. Frigo, M. Albay, E. Sedlar, S. Alimi, A. Deslauriers-Gauthier, S. Deriche, R. Fick, R. Afzali, M. Pieciak, T. Bogusz, F. Aja-Fernandez, S. Ozarslan, E. Jones, D. K. Chan, H. Jin, M. Zhang, Z. Wang, F. Nath, V. Parvathaneni, P. Morez, J. Sijbers, J. Jeurissen, B. Fadnavis, S. Endres, S. Rokem, A. Garyfallidis, E. Sanchez, I. Prchkovska, V. Rodrigues, P. Landman, B. A. Schilling, K. G. 2021-03-02 doi:10.1101/2021.03.02.433228 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Oxaliplatin Resistance in Colorectal Cancer Enhances TRAIL Sensitivity Via Death Receptor 4 Upregulation and Lipid Raft Localization ]]> https://biorxiv.org/content/10.1101/2021.03.05.434100v1?rss=1 Greenlee, J. D. Lopez Cavestany, M. Ortiz-Otero, N. Liu, K. Subramanian, T. Cagir, B. King, M. R. 2021-03-05 doi:10.1101/2021.03.05.434100 Cold Spring Harbor Laboratory Press 2021-03-05 <![CDATA[ A Kiosk Station for the Assessment of Multiple Cognitive Domains and Enrichment of Monkeys ]]> https://biorxiv.org/content/10.1101/2021.03.06.434198v1?rss=1 Womelsdorf, T. Thomas, C. Neumann, A. Watson, M. Banaie Boroujeni, K. Hassani, S. A. Parker, J. M. Hoffman, K. L. 2021-03-08 doi:10.1101/2021.03.06.434198 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Lag structure of BOLD signals within white matter in resting-state fMRI ]]> https://biorxiv.org/content/10.1101/2021.03.06.434206v1?rss=1 Guo, B. Zhou, F. Li, M. Gore, J. C. 2021-03-08 doi:10.1101/2021.03.06.434206 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Comparative host interactomes of the SARS-CoV-2 nonstructural protein 3 and human coronavirus homologs ]]> https://biorxiv.org/content/10.1101/2021.03.08.434440v1?rss=1 Almasy, K. M. Davies, J. P. Plate, L. 2021-03-08 doi:10.1101/2021.03.08.434440 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Psychomotor impairments and therapeutic implications revealed by a mutation linked with Infantile Parkinsonism-Dystonia ]]> https://biorxiv.org/content/10.1101/2021.03.09.434693v1?rss=1 Aguilar, J. I. Cheng, M. H. Font, J. Schwartz, A. C. Ledwitch, K. Duran, A. Mabry, S. J. Belovich, A. N. Zhu, Y. Carter, A. M. Shi, L. Kurian, M. A. Fenollar-Ferrer, C. Meiler, J. Ryan, R. M. Mchaourab, H. S. Bahar, I. Matthies, H. J. G. Galli, A. 2021-03-10 doi:10.1101/2021.03.09.434693 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Bruton's Tyrosine Kinase Supports Gut Mucosal Immunity and Commensal Microbiome Recognition in Autoimmune Arthritis ]]> https://biorxiv.org/content/10.1101/2021.03.10.434762v1?rss=1 Bonami, R. H. Thurman, C. E. Nyhoff, L. E. Westlake, C. S. Barron, B. B. Kendall, P. L. 2021-03-10 doi:10.1101/2021.03.10.434762 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Behavior emerges from unstructured muscle activity in response to neuromodulation ]]> https://biorxiv.org/content/10.1101/2021.03.10.434785v1?rss=1 Elliott, A. Berndt, A. Houpert, M. Roy, S. Scott, R. L. Chow, C. C. Shroff, H. White, B. 2021-03-11 doi:10.1101/2021.03.10.434785 Cold Spring Harbor Laboratory Press 2021-03-11 <![CDATA[ A single synonymous nucleotide change impacts the male-killing phenotype of prophage WO gene wmk ]]> https://biorxiv.org/content/10.1101/2021.03.11.434916v1?rss=1 Perlmutter, J. Bordenstein, S. R. Meyers, J. E. 2021-03-12 doi:10.1101/2021.03.11.434916 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Cryo-EM structure of an elusive pre-transport intermediate of the multidrug transporter BmrCD reveals modes of asymmetric drug binding ]]> https://biorxiv.org/content/10.1101/2021.03.13.435271v1?rss=1 Thaker, T. M. Mishra, S. Zhou, W. Faraldo-Gomez, J. Mchaourab, H. Tomasiak, T. M. 2021-03-14 doi:10.1101/2021.03.13.435271 Cold Spring Harbor Laboratory Press 2021-03-14 <![CDATA[ MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging ]]> https://biorxiv.org/content/10.1101/2021.03.15.435473v1?rss=1 Schapiro, D. Sokolov, A. Yapp, C. Muhlich, J. L. Hess, J. Lin, J.-R. Chen, Y.-A. Nariya, M. K. Baker, G. J. Ruokonen, J. Maliga, Z. Jacobson, C. A. Farhi, S. L. Abbondanza, D. McKinley, E. T. Betts, C. Regev, A. Coffey, R. J. Coussens, L. M. Santagata, S. Sorger, P. K. 2021-03-16 doi:10.1101/2021.03.15.435473 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Fiber tractography bundle segmentation depends on scanner effects, acquisition, diffusion sensitization, and bundle segmentation workflow ]]> https://biorxiv.org/content/10.1101/2021.03.17.435872v1?rss=1 Schilling, K. Tax, C. M. W. Rheault, F. Hansen, C. B. Yang, Q. Yeh, F.-c. Cai, L. Y. Anderson, A. W. Landman, B. A. 2021-03-19 doi:10.1101/2021.03.17.435872 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Contemporary clinical isolates of Staphylococcus aureus from pediatric osteomyelitis patients display unique characteristics in a mouse model of hematogenous osteomyelitis ]]> https://biorxiv.org/content/10.1101/2021.03.22.436444v1?rss=1 Roper, P. Eichelberger, K. Cox, L. O'Connor, L. Shao, C. Ford, C. Fritz, S. Cassat, J. Veis, D. 2021-03-22 doi:10.1101/2021.03.22.436444 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Autism_genepheno: Text mining of gene-phenotypeassociations reveals new phenotypic profiles ofautism-associated genes ]]> https://biorxiv.org/content/10.1101/2021.03.24.436848v1?rss=1 Li, S. Guo, Z. Ioffe, J. B. Hu, Y. Zhen, Y. Zhou, X. 2021-03-25 doi:10.1101/2021.03.24.436848 Cold Spring Harbor Laboratory Press 2021-03-25 <![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[ Expression of Sonic Hedgehog and Pathway Components in the Embryonic Mouse Head: Anatomical Relationships Between Regulators of Positive and Negative Feedback ]]> https://biorxiv.org/content/10.1101/2021.03.30.437697v1?rss=1 Sigulinsky, C. L. Li, X. Levine, E. M. 2021-03-31 doi:10.1101/2021.03.30.437697 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Influence of substrate stiffness on barrier function in an iPSC-derived in vitro blood-brain barrier model ]]> https://biorxiv.org/content/10.1101/2021.03.31.437924v1?rss=1 Bosworth, A. Kim, H. O'Grady, K. Richter, I. Lee, L. O'Grady, B. Lippmann, E. 2021-03-31 doi:10.1101/2021.03.31.437924 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer ]]> https://biorxiv.org/content/10.1101/2021.03.31.437984v1?rss=1 Lin, J.-R. Wang, S. Coy, S. Tyler, M. A. Yapp, C. Chen, Y.-A. Heiser, C. N. Lau, K. Santagata, S. Sorger, P. K. 2021-04-02 doi:10.1101/2021.03.31.437984 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ Accelerating Strain Engineering using Desorption Electrospray Ionization-Imaging Mass Spectrometry and Untargeted Molecular Analysis of Intact Microbial Colonies. ]]> https://biorxiv.org/content/10.1101/2021.04.01.438078v1?rss=1 Ellis, B. M. Babele, P. May, J. C. Pfleger, B. F. Young, J. D. McLean, J. A. 2021-04-02 doi:10.1101/2021.04.01.438078 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ Single-cell transcriptomics reveals a conserved metaplasia program in pancreatic injury ]]> https://biorxiv.org/content/10.1101/2021.04.09.439243v1?rss=1 Ma, Z. Lytle, N. K. Chen, B. Jyotsana, N. Weiser Novak, S. Cho, C. J. Caplan, L. Ben-Levy, O. Neininger, A. C. Burnette, D. T. Trinh, V. Q. Tan, M. C. B. Patterson, E. A. Arrojo e Drigo, R. Giraddi, R. R. Ramos, C. Means, A. L. Manor, U. Mills, J. C. Goldenring, J. R. Lau, K. Wahl, G. DelGiorno, K. E. 2021-04-11 doi:10.1101/2021.04.09.439243 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Nonclassical monocytes are prone to migrate into tumor in diffuse large B-cell lymphoma ]]> https://biorxiv.org/content/10.1101/2021.04.10.439292v1?rss=1 Le Gallou, S. Lhomme, F. Irish, J. M. Mingam, A. Pangault, C. Monvoisin, C. Ferrant, J. Azzaoui, I. Rossille, D. Bouabdallah, K. Damaj, G. Cartron, G. Godemer, P. Le Gouill, S. Casanovas, O. Molina, T. Houot, R. Lamy, T. Tarte, K. Fest, T. Roussel, M. 2021-04-11 doi:10.1101/2021.04.10.439292 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ The Hippo pathway regulates density-dependent proliferation of iPSC-derived cardiac myocytes ]]> https://biorxiv.org/content/10.1101/2021.04.12.439529v1?rss=1 Neininger, A. C. Dai, X. Liu, Q. Burnette, D. T. 2021-04-12 doi:10.1101/2021.04.12.439529 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum ]]> https://biorxiv.org/content/10.1101/2021.04.13.439724v1?rss=1 Phillips, M. A. Steenwyk, J. L. Shen, X.-X. Rokas, A. 2021-04-14 doi:10.1101/2021.04.13.439724 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ A Focal Adhesion Filament Cross-correlation Kit for fast, automated segmentation and correlation of focal adhesions and actin stress fibers in cells ]]> https://biorxiv.org/content/10.1101/2021.04.14.439781v1?rss=1 Hauke, L. Narasimhan, S. Primessnig, A. Kaverina, I. Rehfeldt, F. 2021-04-14 doi:10.1101/2021.04.14.439781 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ The allosteric activation of α7 nAChR by α-conotoxin MrIC is modified by mutations at the vestibular site ]]> https://biorxiv.org/content/10.1101/2021.04.14.439845v1?rss=1 Gulsevin, A. Papke, R. L. Stokes, C. Tran, H. N. T. Jin, A.-H. Vetter, I. Meiler, J. 2021-04-14 doi:10.1101/2021.04.14.439845 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Dendritic GABAergic inhibition controlled by Shh signaling-dependent stellate cell pool is critical for motor learning ]]> https://biorxiv.org/content/10.1101/2021.04.15.439999v1?rss=1 Li, W. Chen, L. Fleming, J. T. Brignola, E. Y. Zavalin, K. Lagrange, A. Rex, T. heiney, S. A. Wojaczynski, G. J. Medina, J. F. Chiang, C. 2021-04-15 doi:10.1101/2021.04.15.439999 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ Albumin-binding Aptamer Chimeras for Improved siRNA Bioavailability ]]> https://biorxiv.org/content/10.1101/2021.04.15.440012v1?rss=1 Rosch, J. Hoogenboezem, E. Sorets, A. Duvall, C. Lippmann, E. 2021-04-16 doi:10.1101/2021.04.15.440012 Cold Spring Harbor Laboratory Press 2021-04-16 <![CDATA[ DIETARY RESCUE OF ADULT BEHAVIORAL DEFICITS IN THE FMR1 KNOCKOUT MOUSE ]]> https://biorxiv.org/content/10.1101/2021.04.16.440191v1?rss=1 Nolan, S. O. Hodges, S. L. Binder, M. S. Smith, G. Okoh, J. T. Escobar, B. Lugo, J. N. 2021-04-18 doi:10.1101/2021.04.16.440191 Cold Spring Harbor Laboratory Press 2021-04-18 <![CDATA[ Correlated Functional Connectivity and Glucose Metabolism in Brain White Matter Revealed by Simultaneous MRI/PET ]]> https://biorxiv.org/content/10.1101/2021.04.16.440245v1?rss=1 Guo, B. Zhou, F. Li, M. Gore, J. C. Ding, Z. 2021-04-20 doi:10.1101/2021.04.16.440245 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Bacteriophage Lambda RexA and RexB Functions Assist the Transition from Lysogeny to Lytic Growth ]]> https://biorxiv.org/content/10.1101/2021.04.19.439022v1?rss=1 Thomason, L. Court, D. L. Schlitz, C. J. Court, C. Hosford, C. J. Adams, M. C. Chappie, J. S. 2021-04-19 doi:10.1101/2021.04.19.439022 Cold Spring Harbor Laboratory Press 2021-04-19 <![CDATA[ Replication timing analysis in polyploid cells reveals Rif1 uses multiple mechanisms to promote underreplication in Drosophila. ]]> https://biorxiv.org/content/10.1101/2021.04.19.440528v1?rss=1 Das, S. Caballero, M. Kolesnikova, T. Zhimulev, I. Koren, A. Nordman, J. 2021-04-19 doi:10.1101/2021.04.19.440528 Cold Spring Harbor Laboratory Press 2021-04-19 <![CDATA[ Altered Cortical Activation Associated with Mirror Overflow Driven by Non-Dominant Hand Movement in Attention-Deficit/Hyperactivity Disorder ]]> https://biorxiv.org/content/10.1101/2021.04.23.441107v1?rss=1 Luo, Y. Chen, C. Adamek, J. Crocetti, D. Mostofsky, S. Ewen, J. 2021-04-23 doi:10.1101/2021.04.23.441107 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Trypanosoma brucei Tim50 Plays a Critical Role in Cell Cycle Regulation and Parasite Infectivity ]]> https://biorxiv.org/content/10.1101/2021.04.26.441502v1?rss=1 Tripathi, A. Singha, U. K. Cooley, A. Gillyard, T. Krystofiak, E. Pratap, S. Davis, J. Chaudhuri, M. 2021-04-27 doi:10.1101/2021.04.26.441502 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Structural basis of the P4B ATPase lipid flippase activity ]]> https://biorxiv.org/content/10.1101/2021.04.28.441804v1?rss=1 Bai, L. Jain, B. K. You, Q. Duan, H. D. Graham, T. R. Li, H. 2021-04-28 doi:10.1101/2021.04.28.441804 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Ornament, armament, or toolkit? Modelling how population size drives the evolution of birdsong, a functional cultural trait ]]> https://biorxiv.org/content/10.1101/2021.04.29.442039v1?rss=1 Hudson, E. J. Creanza, N. 2021-04-30 doi:10.1101/2021.04.29.442039 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Tissue fixation effects on human retinal lipid analysis by MALDI imaging and LC-MS/MS technologies ]]> https://biorxiv.org/content/10.1101/2021.04.29.442044v1?rss=1 Kotnala, A. Anderson, D. M. Patterson, N. H. Cantrell, L. S. Messinger, J. D. Curcio, C. A. Schey, K. L. 2021-04-30 doi:10.1101/2021.04.29.442044 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Convergent antibody responses to the SARS-CoV-2 spike protein in convalescent and vaccinated individuals ]]> https://biorxiv.org/content/10.1101/2021.05.02.442326v1?rss=1 Chen, E. C. Gilchuk, P. Zost, S. J. Suryadevara, N. Winkler, E. S. Cabel, C. R. Binshtein, E. Sutton, R. E. Rodriguez, J. L. Day, S. Myers, L. Trivette, A. Williams, J. K. Davidson, E. Li, S. Doranz, B. J. Campos, S. K. Carnahan, R. H. Thorne, C. A. Diamond, M. S. Crowe, J. E. 2021-05-03 doi:10.1101/2021.05.02.442326 Cold Spring Harbor Laboratory Press 2021-05-03 <![CDATA[ The effects of predator odor (TMT) exposure and mGlu3 NAM pretreatment on lasting behavioral and molecular adaptations in the insular cortex and BNST ]]> https://biorxiv.org/content/10.1101/2021.05.07.443122v1?rss=1 Tyler, R. E. Bluitt, M. N. Engers, J. L. Lindsley, C. L. Besheer, J. 2021-05-09 doi:10.1101/2021.05.07.443122 Cold Spring Harbor Laboratory Press 2021-05-09 <![CDATA[ Galectin-anchored indoleamine 2,3-dioxygenase suppresses local inflammation ]]> https://biorxiv.org/content/10.1101/2021.05.07.443161v1?rss=1 Bracho-Sanchez, E. Rocha, F. Bedingfield, S. K. Partain, B. D. Brusko, M. A. Colazo, J. M. Fettis, M. M. Farhadi, S. A. Helm, E. Y. Koenders, K. Kwiatkowski, A. J. Macias, S. L. Restuccia, A. Wanchoo, A. Avram, D. Allen, K. D. Duvall, C. L. Wallet, S. M. Hudalla, G. A. Keselowsky, B. G. 2021-05-09 doi:10.1101/2021.05.07.443161 Cold Spring Harbor Laboratory Press 2021-05-09 <![CDATA[ Molecular basis and functional consequences of the interaction between the Base Excision Repair DNA glycosylase NEIL1 and RPA ]]> https://biorxiv.org/content/10.1101/2021.05.11.443618v1?rss=1 Le Meur, R. A. Pecen, T. J. Le Meur, K. V. Nagel, Z. D. Chazin, W. J. 2021-05-11 doi:10.1101/2021.05.11.443618 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ cAMP controls a trafficking mechanism that directs the neuron specificity and subcellular placement of electrical synapses ]]> https://biorxiv.org/content/10.1101/2021.05.12.443836v1?rss=1 Palumbos, S. Skelton, R. McWhirter, R. Mitchell, A. Swann, I. Heifner, S. Von Stetina, S. Miller, D. M. 2021-05-13 doi:10.1101/2021.05.12.443836 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ The effect of developmental pleiotropy on the evolution of immune genes in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2021.05.12.443901v1?rss=1 Ngo, T. M. Tate, A. T. 2021-05-14 doi:10.1101/2021.05.12.443901 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ Identification of mundulone and mundulone acetate as natural products with tocolytic efficacy in mono- and combination-therapy with current tocolytics ]]> https://biorxiv.org/content/10.1101/2021.05.13.444040v1?rss=1 Siricilla, S. Hansen, C. J. Rogers, J. H. Simpson, C. L. Crockett, S. L. Reese, J. Paria, B. C. Herington, J. L. 2021-05-14 doi:10.1101/2021.05.13.444040 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ Data Independent Acquisition Mass Spectrometry of the Human Lens Enhances Spatiotemporal Measurement of Fiber Cell Aging ]]> https://biorxiv.org/content/10.1101/2021.05.13.444062v1?rss=1 Cantrell, L. S. Schey, K. L. 2021-05-13 doi:10.1101/2021.05.13.444062 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ Sequence and functional characterization of a public HIV-specific antibody clonotype ]]> https://biorxiv.org/content/10.1101/2021.05.14.444191v1?rss=1 Raju, N. Qin, J. S. Fechter, E. F. Setliff, I. Georgiev, I. S. Kaldine, H. Mapengo, R. Scheepers, C. Morris, L. Janowska, K. Acharya, P. Murji, A. A. 2021-05-17 doi:10.1101/2021.05.14.444191 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Potent neutralization of SARS-CoV-2 variants of concern by an antibody with a unique genetic signature and structural mode of spike recognition ]]> https://biorxiv.org/content/10.1101/2021.05.16.444004v1?rss=1 Kramer, K. J. Johnson, N. V. Shiakolas, A. R. Suryadevara, N. Periasamy, S. Raju, N. Williams, J. K. Wrapp, D. Zost, S. J. Holt, C. M. Hsieh, C.-L. Sutton, R. E. Paulo, A. Davidson, E. Doranz, B. J. Crowe, J. E. Bukreyev, A. Carnahan, R. H. McLellan, J. S. Georgiev, I. S. 2021-05-16 doi:10.1101/2021.05.16.444004 Cold Spring Harbor Laboratory Press 2021-05-16 <![CDATA[ Glucose-dependent miR-125b is a negative regulator of β-cell function ]]> https://biorxiv.org/content/10.1101/2021.05.17.444559v1?rss=1 Cheung, R. W. S. Pizza, G. Chabosseau, P. Rolando, D. Tomas, A. Burgoyne, T. Salowka, A. Macklin, A. Cao, Y. Nguyen-Tu, M.-S. Marchetti, P. Shapiro, J. Piemonti, L. de Koning, E. J. P. Leclerc, I. Sakamoto, K. Smith, D. M. Rutter, G. A. Martinez-sanchez, A. 2021-05-17 doi:10.1101/2021.05.17.444559 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ The misleading certainty of uncertain data in biological network processes ]]> https://biorxiv.org/content/10.1101/2021.05.18.444743v1?rss=1 Irvin, M. Ramanathan, A. Lopez, C. F. 2021-05-20 doi:10.1101/2021.05.18.444743 Cold Spring Harbor Laboratory Press 2021-05-20 <![CDATA[ Genetic structure correlates with ethnolinguistic diversity in eastern and southern Africa ]]> https://biorxiv.org/content/10.1101/2021.05.19.444732v1?rss=1 Atkinson, E. G. Dalvie, S. Pichkar, Y. Kalungi, A. Majara, L. Stevenson, A. Abebe, T. Akena, D. Alemayehu, M. Ashaba, F. K. Atwoli, L. Baker, M. Chibnik, L. B. Creanza, N. Daly, M. J. Fekadu, A. Gelaye, B. Gichuru, S. Injera, W. E. James, R. Kariuki, S. M. Kigen, G. Koen, N. Koenen, K. C. Koenig, Z. Kwobah, E. Kyebuzibwa, J. Musinguzi, H. Mwema, R. M. Neale, B. M. Newman, C. P. Newton, C. R. J. C. Ongeri, L. Ramachandran, S. Ramesar, R. Shiferaw, W. Stein, D. J. Stroud, R. E. Teferra, S. Zingela, Z. Martin, A. R. NeuroGAP-Psychosis Study Team, 2021-05-19 doi:10.1101/2021.05.19.444732 Cold Spring Harbor Laboratory Press 2021-05-19 <![CDATA[ Tumor-secreted versican co-opts myeloid IKKβ during metastasis ]]> https://biorxiv.org/content/10.1101/2021.05.20.444963v1?rss=1 Spella, M. Lamort, A. S. Vreka, M. Marazioti, A. Lilis, I. Ntaliarda, G. Skiadas, G. Bouloukou, E. Giotopoulou, G. A. Pepe, M. A. Weiss, S. A. Petrera, A. Hauck, S. M. Koch, I. Lindner, M. Hatz, R. A. Behr, J. Arendt, K. A. Giopanou, I. Brunn, D. Savai, R. Jenne, D. E. Yull, F. E. Blackwell, T. Stathopoulos, G. T. 2021-05-22 doi:10.1101/2021.05.20.444963 Cold Spring Harbor Laboratory Press 2021-05-22 <![CDATA[ ROS-Degradable Polythioketal Urethane Foam Dressings to Promote Porcine Skin Wound Repair ]]> https://biorxiv.org/content/10.1101/2021.05.21.445175v1?rss=1 Patil, P. Russo, K. A. McCune, J. T. Pollins, A. C. Cottom, M. A. Dollinger, B. R. Colazo, J. M. Yu, F. Martin, J. R. Gupta, M. K. Cardwell, N. L. Davidson, J. M. Thompson, C. M. Barbul, A. Hasty, A. M. Guelcher, S. A. Duvall, C. L. 2021-05-23 doi:10.1101/2021.05.21.445175 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ Visualizing the Role of Lipid Dynamics during Infrared Neural Stimulation with Hyperspectral Stimulated Raman Scattering Microscopy ]]> https://biorxiv.org/content/10.1101/2021.05.24.444984v1?rss=1 Adams, W. R. Gautam, R. Locke, A. K. Borrachero-Conejo, A. I. Dollinger, B. R. Throckmorton, G. A. Duvall, C. Jansen, E. D. Mahadevan-Jansen, A. 2021-05-25 doi:10.1101/2021.05.24.444984 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Convolutional neural networks trained with a developmental sequence of blurry to clear images reveal core differences between face and object processing ]]> https://biorxiv.org/content/10.1101/2021.05.25.444835v1?rss=1 Jang, H. Tong, F. 2021-05-26 doi:10.1101/2021.05.25.444835 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ An infection-activated redox switch promotes tumor growth ]]> https://biorxiv.org/content/10.1101/2021.05.25.445662v1?rss=1 Kovalyova, Y. Bak, D. W. Gordon, E. M. Fung, C. Shuman, J. H. B. Cover, T. L. Amieva, M. R. Weerapana, E. Hatzios, S. K. 2021-05-25 doi:10.1101/2021.05.25.445662 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Salmonella Typhimurium uses anaerobic respiration to overcome propionate-mediated colonization resistance ]]> https://biorxiv.org/content/10.1101/2021.05.25.445690v1?rss=1 Shelton, C. D. Yoo, W. Shealy, N. G. Torres, T. P. Zieba, J. K. Calcutt, M. W. Foegeding, N. J. Kim, D. Kim, J. Ryu, S. Byndloss, M. X. 2021-05-25 doi:10.1101/2021.05.25.445690 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ The skeletal muscle circadian clock regulates sarcomere length homeostasis through titin splicing ]]> https://biorxiv.org/content/10.1101/2021.05.27.445953v1?rss=1 Riley, L. Zhang, X. Mijares, J. Hammers, D. Olafson, H. Du, P. Douglas, C. Labeit, S. T. Wang, E. Esser, K. A. 2021-05-28 doi:10.1101/2021.05.27.445953 Cold Spring Harbor Laboratory Press 2021-05-28 <![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[ A Universal Approach to Analyzing Transmission Electron Microscopy with ImageJ ]]> https://biorxiv.org/content/10.1101/2021.05.27.446036v1?rss=1 Lam, J. Biete, M. Mungai, M. AshShareef, S. Neikirk, K. Garza Lopez, E. Christensen, T. A. Salisbury, J. L. Katti, P. Glancy, B. Pereira, R. O. Abel, E. D. Hinton, A. 2021-05-29 doi:10.1101/2021.05.27.446036 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ Zones of Cellular Damage Around Pulsed-Laser Wounds ]]> https://biorxiv.org/content/10.1101/2021.05.28.446116v1?rss=1 O'Connor, J. Akbar, F. B. Hutson, M. S. Page-McCaw, A. 2021-05-28 doi:10.1101/2021.05.28.446116 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Retrosplenial and hippocampal synchrony during retrieval of old memories in macaques ]]> https://biorxiv.org/content/10.1101/2021.05.28.446142v1?rss=1 Hussin, A. T. Abbaspoor, S. Hoffman, K. L. 2021-05-28 doi:10.1101/2021.05.28.446142 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ A Family of Glycosylated Macrolides Selectively Target Energetic Vulnerabilities in Leukemia ]]> https://biorxiv.org/content/10.1101/2021.05.31.445492v1?rss=1 Reisman, B. J. Guo, H. Ramsey, H. E. Wright, M. T. Reinfeld, B. I. Ferrell, P. B. Sulikowski, G. A. Rathmell, W. K. Savona, M. R. Plate, L. Rubinstein, J. L. Bachmann, B. O. 2021-05-31 doi:10.1101/2021.05.31.445492 Cold Spring Harbor Laboratory Press 2021-05-31 <![CDATA[ Efficient discovery of potently neutralizing SARS-CoV-2 antibodies using LIBRA-seq with ligand blocking ]]> https://biorxiv.org/content/10.1101/2021.06.02.446813v1?rss=1 Shiakolas, A. R. Johnson, N. Kramer, K. J. Suryadevara, N. Wrapp, D. Periasamy, S. Pilewski, K. A. Raju, N. Nargi, R. Sutton, R. E. Walker, L. Crowe, J. E. Bukreyev, A. Carnahan, R. H. McLellan, J. S. Georgiev, I. S. 2021-06-02 doi:10.1101/2021.06.02.446813 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Elicitation of neutralizing antibody responses to HIV-1 immunization with nanoparticle vaccine platforms ]]> https://biorxiv.org/content/10.1101/2021.06.03.446978v1?rss=1 Murji, A. A. Qin, J. S. Hermanus, T. Morris, L. Georgiev, I. 2021-06-04 doi:10.1101/2021.06.03.446978 Cold Spring Harbor Laboratory Press 2021-06-04 <![CDATA[ The zinc transporter ZnuABC is critical for the virulence of Chromobacterium violaceum and contributes to diverse zinc-dependent physiological processes ]]> https://biorxiv.org/content/10.1101/2021.06.03.447022v1?rss=1 Santos, R. E. R. S. da Silva Junior, W. P. Harrison, S. A. Skaar, E. P. Chazin, W. J. da Silva Neto, J. F. 2021-06-07 doi:10.1101/2021.06.03.447022 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Caenorhabditis elegans ETR-1/CELF has broad effects on the muscle cell transcriptome, including genes that regulate translation and neuroblast migration ]]> https://biorxiv.org/content/10.1101/2021.06.08.447597v1?rss=1 Ochs, M. E. McWhirter, R. Unckless, R. Miller, D. Lundquist, E. A. 2021-06-09 doi:10.1101/2021.06.08.447597 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ Aspergillus fumigatus acetate utilisation impacts virulence traits and pathogenicity ]]> https://biorxiv.org/content/10.1101/2021.06.09.447827v1?rss=1 Ries, L. N. de Castro, P. A. Silva, L. P. Valero, C. dos Reis, T. F. Saborano, R. Duarte, I. F. Persinoti, G. F. Steenwyk, J. L. Rokas, A. Almeida, F. Costa, J. H. Fill, T. P. Sze Wah Wong, S. Aimanianda, V. Rodrigues, F. Goncales, R. A. Duarte-Oliveira, C. Carvalho, A. Goldman, G. H. 2021-06-10 doi:10.1101/2021.06.09.447827 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Cryo-EM reveals new species-specific proteins and symmetry elements in the Legionella pneumophila Dot/Icm T4SS ]]> https://biorxiv.org/content/10.1101/2021.06.18.449039v1?rss=1 Sheedlo, M. J. Durie, C. L. Chung, J. M. Chang, L. Swanson, M. Lacy, D. B. Ohi, M. D. 2021-06-18 doi:10.1101/2021.06.18.449039 Cold Spring Harbor Laboratory Press 2021-06-18 <![CDATA[ Lipid droplets protect human β cells from lipotoxic-induced stress and cell identity changes ]]> https://biorxiv.org/content/10.1101/2021.06.19.449124v1?rss=1 Tong, X. Stein, R. W. 2021-06-20 doi:10.1101/2021.06.19.449124 Cold Spring Harbor Laboratory Press 2021-06-20 <![CDATA[ Large-Scale Intrinsic Functional Brain Organization Emerges from Three Canonical Spatiotemporal Patterns ]]> https://biorxiv.org/content/10.1101/2021.06.20.448984v1?rss=1 Bolt, T. S. Nomi, J. Bzdok, D. Chang, C. Yeo, B. T. T. Uddin, L. Q. Keilholz, S. 2021-06-20 doi:10.1101/2021.06.20.448984 Cold Spring Harbor Laboratory Press 2021-06-20 <![CDATA[ Apoptotic Find-me Signals are an Essential Driver of Stem Cell Conversion To The Cardiac Lineage ]]> https://biorxiv.org/content/10.1101/2021.06.21.449262v1?rss=1 Fort, L. Gama, V. Macara, I. G. 2021-06-22 doi:10.1101/2021.06.21.449262 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Homolog of ELAC2 is a central regulator of the mitochondrial unfolded protein response ]]> https://biorxiv.org/content/10.1101/2021.06.22.449331v1?rss=1 Held, J. P. Saunders, B. R. Pereria, C. V. Patel, M. R. 2021-06-22 doi:10.1101/2021.06.22.449331 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Prevalence of white matter pathways coming into a single diffusion MRI voxel orientation: the bottleneck issue in tractography ]]> https://biorxiv.org/content/10.1101/2021.06.22.449454v1?rss=1 Schilling, K. Tax, C. M. W. Rheault, F. M. W. Landman, B. A. Anderson, A. W. Descoteaux, M. Petit, L. 2021-06-22 doi:10.1101/2021.06.22.449454 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Moving Beyond the 'CAP' of the Iceberg: Intrinsic Connectivity Networks in fMRI are Continuously Engaging and Overlapping ]]> https://biorxiv.org/content/10.1101/2021.06.23.449485v1?rss=1 Iraji, A. Faghiri, A. Fu, Z. Kochunov, P. Adhikari, B. M. Belger, A. Ford, J. M. McEwen, S. Mathalon, D. H. Pearlson, G. D. Potkin, S. G. Preda, A. Turner, J. A. Van Erp, T. G. M. Chang, C. Calhoun, V. D. 2021-06-24 doi:10.1101/2021.06.23.449485 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates ]]> https://biorxiv.org/content/10.1101/2021.06.24.449766v1?rss=1 Toth, A. Steinmeyer, S. Kannan, P. S. Gray, J. Jackson, C. Mukherjee, S. Demmert, M. Sheak, J. R. Benson, D. Kitzmiller, J. Wayman, J. A. Presicce, P. Cates, C. Rubin, R. Chetal, K. Du, Y. Miao, Y. Guo, M. Gu, M. Kalinichenko, V. V. Kallapur, S. G. Miraldi, E. R. Xu, Y. Swarr, D. T. Lewkowich, I. Salomonis, N. T. Miller, L. Sucre, J. Whitsett, J. A. Chougnet, C. Jobe, A. H. Deshmukh, H. Zacharias, W. J. 2021-06-25 doi:10.1101/2021.06.24.449766 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Nanoparticle-mediated transgene expression of insulin-like growth factor 1 in the guinea pig placenta differentially affects fetal liver gene expression depending on maternal nutrient status ]]> https://biorxiv.org/content/10.1101/2021.06.24.449769v1?rss=1 Wilson, R. Stephens, K. Lampe, K. Gupta, M. Duvall, C. Jones, H. 2021-06-25 doi:10.1101/2021.06.24.449769 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Sulfation of glycosaminoglycans depends on catalytic activity of a lithium-inhibited phosphatase ]]> https://biorxiv.org/content/10.1101/2021.06.24.449779v1?rss=1 Eisele, B. S. Luka, Z. A. Wu, A. J. Yang, F. Hale, A. T. York, J. D. 2021-06-24 doi:10.1101/2021.06.24.449779 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ A comprehensive approach for artifact-free sample preparation and assessment of mitochondrial morphology in tissue and cultured cells ]]> https://biorxiv.org/content/10.1101/2021.06.27.450055v1?rss=1 Hinton, A. Katti, P. Christensen, T. A. Mungai, M. Shao, J. Zhang, L. Trushin, S. Alghanem, A. Jaspersen, A. Geroux, R. E. Neikirk, K. Biete, M. Garza Lopez, E. Vue, Z. Beasley, H. Marshall, A. Hicsasmaz, I. Edmonds, R. A. C. Dajles, A. Koo, Y. D. Bacevac, S. Salisbury, J. L. Pereira, R. O. Glancy, B. Trushina, E. Abel, E. D. 2021-06-29 doi:10.1101/2021.06.27.450055 Cold Spring Harbor Laboratory Press 2021-06-29 <![CDATA[ Biophysical Models of PAR Cluster Transport by Cortical Flow in C. elegans Early Embryogenesis ]]> https://biorxiv.org/content/10.1101/2021.06.28.450200v1?rss=1 Zmurchok, C. Holmes, W. R. 2021-06-29 doi:10.1101/2021.06.28.450200 Cold Spring Harbor Laboratory Press 2021-06-29 <![CDATA[ Mapping of the fibrinogen-binding site on the staphylocoagulase C-terminal repeat region ]]> https://biorxiv.org/content/10.1101/2021.06.29.450373v1?rss=1 Maddur, A. A. Voehler, M. W. Panizzi, P. Meiler, J. Bock, P. E. Verhamme, I. M. 2021-07-01 doi:10.1101/2021.06.29.450373 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ Discrete Roles of the Ir76b Ionotropic Co-Receptor Impact Olfaction, Blood Feeding, and Mating in the Malaria Vector Mosquito Anopheles coluzzii ]]> https://biorxiv.org/content/10.1101/2021.07.05.451160v1?rss=1 Ye, Z. Liu, F. Sun, H. Baker, A. P. Zwiebel, L. 2021-07-06 doi:10.1101/2021.07.05.451160 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ FANCD2 directly inhibits DNA2 nuclease at stalled replication forks and acts as a RAD51 mediator in strand exchange ]]> https://biorxiv.org/content/10.1101/2021.07.08.450798v1?rss=1 Liu, W. Roubal, I. Polaczek, P. Meng, Y. Choe, W.-c. Caron, M. C. Sedgeman, C. A. Xi, Y. Liu, C. Wu, Q. Zheng, L. Masson, J. Y. Shen, B. Campbell, J. L. 2021-07-09 doi:10.1101/2021.07.08.450798 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ A gene coevolution network provides insight into eukaryotic cellular and genomic structure and function ]]> https://biorxiv.org/content/10.1101/2021.07.09.451830v1?rss=1 Steenwyk, J. L. Phillips, M. A. Yang, F. Date, S. S. Graham, T. berman, j. Hittinger, C. T. Rokas, A. 2021-07-10 doi:10.1101/2021.07.09.451830 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ A corollary discharge mediates saccade related inhibition of single units in mnemonic structures of the human brain ]]> https://biorxiv.org/content/10.1101/2021.07.12.450085v1?rss=1 Katz, C. N. Schjetnan, A. G. P. Patel, K. V. Barkley, V. Hoffman, K. L. Kalia, S. K. Duncan, K. Valiante, T. A. 2021-07-12 doi:10.1101/2021.07.12.450085 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Heterogeneity in the transcriptional response of the human pathogen Aspergillus fumigatus to the antifungal agent caspofungin ]]> https://biorxiv.org/content/10.1101/2021.07.15.452449v1?rss=1 Colabardini, A. C. Wang, F. Dong, Z. Pardeshi, L. Rocha, M. C. Costa, J. H. dos Reis, T. F. Brown, A. Jaber, Q. Z. Fridman, M. Fill, T. Rokas, A. Malavazi, I. Wong, K. H. Goldman, G. H. 2021-07-15 doi:10.1101/2021.07.15.452449 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ Dynamic variations of resting-state BOLD signal spectra in white matter ]]> https://biorxiv.org/content/10.1101/2021.07.15.452567v1?rss=1 Li, M. Gao, Y. Anderson, A. W. Ding, Z. Gore, J. C. 2021-07-16 doi:10.1101/2021.07.15.452567 Cold Spring Harbor Laboratory Press 2021-07-16 <![CDATA[ Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images ]]> https://biorxiv.org/content/10.1101/2021.07.16.452359v1?rss=1 Harris, C. R. McKinley, E. T. Roland, J. T. Liu, Q. Shrubsole, M. J. Lau, K. Coffey, R. J. Wrobel, J. Vandekar, S. 2021-07-16 doi:10.1101/2021.07.16.452359 Cold Spring Harbor Laboratory Press 2021-07-16 <![CDATA[ Autofluorescence microscopy as a label-free tool for renal histology and glomerular segmentation ]]> https://biorxiv.org/content/10.1101/2021.07.16.452703v1?rss=1 0.85 F1-score, and Dice-Sorensen coefficients >0.80, respectively. This workflow allowed lipids, profiled by imaging mass spectrometry, to be quantitatively associated with segmented FTUs. The segmentation masks were also used to acquire spatial transcriptomics data from collecting ducts. Consistent with previous literature, we demonstrated differing transcript expression of collecting ducts in the inner and outer medulla. ]]> Patterson, N. H. Neumann, E. K. Sharman, K. Allen, J. L. Harris, R. C. Fogo, A. B. deCaestecker, M. P. Caprioli, R. M. Van de Plas, R. Spraggins, J. M. 2021-07-18 doi:10.1101/2021.07.16.452703 Cold Spring Harbor Laboratory Press 2021-07-18 <![CDATA[ One mucosal administration of a live attenuated recombinant COVID-19 vaccine protects non-human primates from SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2021.07.16.452733v1?rss=1 Tioni, M. F. Jordan, R. Silva Pena, A. Garg, A. Wu, D. Phan, S. I. Cheng, X. Greenhouse, J. Orekov, T. Valentin, D. Kar, S. Pessaint, L. Andersen, H. Stobart, C. C. Bloodworth, M. H. Peebles, R. S. Liu, Y. Xie, X. Shi, P.-Y. Moore, M. L. Tang, R. S. 2021-07-19 doi:10.1101/2021.07.16.452733 Cold Spring Harbor Laboratory Press 2021-07-19 <![CDATA[ Granulocyte-colony stimulating factor (G-CSF) enhances cocaine effects in the nucleus accumbens via a dopamine release-based mechanism ]]> https://biorxiv.org/content/10.1101/2021.07.19.452968v1?rss=1 Brady, L. J. Erickson, K. R. Lucerne, K. E. Osman, A. Kiraly, D. D. Calipari, E. S. 2021-07-19 doi:10.1101/2021.07.19.452968 Cold Spring Harbor Laboratory Press 2021-07-19 <![CDATA[ A community-based approach to image analysis of cells, tissues and tumors ]]> https://biorxiv.org/content/10.1101/2021.07.22.451363v1?rss=1 CSBC/PS-ON Image Analysis Working Group, Vizcarra, J. C. Burlingame, E. A. Hug, C. B. Goltsev, Y. White, B. S. Tyson, D. R. Sokolov, A. 2021-07-25 doi:10.1101/2021.07.22.451363 Cold Spring Harbor Laboratory Press 2021-07-25 <![CDATA[ Using Deep Learning to Count Monarch Butterflies in Dense Clusters ]]> https://biorxiv.org/content/10.1101/2021.07.23.453502v1?rss=1 Patel, S. Kulkarni, A. Mukhopadhyay, A. Gujar, K. Roode, J. d. 2021-07-23 doi:10.1101/2021.07.23.453502 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ PiRATeMC: A highly flexible, scalable, and affordable system for obtaining high quality video recordings for behavioral neuroscience. ]]> https://biorxiv.org/content/10.1101/2021.07.23.453577v1?rss=1 Centanni, S. W. Smith, A. C. 2021-07-25 doi:10.1101/2021.07.23.453577 Cold Spring Harbor Laboratory Press 2021-07-25 <![CDATA[ Single-Cell Profiling of the Antigen-Specific Response to BNT162b2 SARS-CoV-2 RNA Vaccine ]]> https://biorxiv.org/content/10.1101/2021.07.28.453981v1?rss=1 Kramer, K. J. Wilfong, E. M. Voss, K. Barone, S. Shiakolas, A. R. Raju, N. Roe, C. E. Suryadevara, N. Walker, L. M. Wall, S. C. Paulo, A. Schaefer, S. Dahunsi, D. Westlake, C. S. Crowe, J. E. Carnahan, R. H. Rathmell, J. C. Bonami, R. H. Georgiev, I. S. Irish, J. M. 2021-07-28 doi:10.1101/2021.07.28.453981 Cold Spring Harbor Laboratory Press 2021-07-28 <![CDATA[ Differential impact of a dyskeratosis congenita mutation in TPP1 on mouse hematopoiesis and germline ]]> https://biorxiv.org/content/10.1101/2021.07.29.454392v1?rss=1 Graniel, J. V. Bisht, K. Friedman, A. White, J. Perkey, E. Vanderbeck, A. Moroz, A. Carrington, L. J. Brandstadter, J. D. Allen, F. Shami, A. N. Thomas, P. Crayton, A. Manzor, M. Mychalowych, A. Chase, J. Hammoud, S. S. Keegan, C. E. Maillard, I. Nandakumar, J. 2021-07-29 doi:10.1101/2021.07.29.454392 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Activation of M1 muscarinic receptors reduce pathology and slow progression of neurodegenerative disease. ]]> https://biorxiv.org/content/10.1101/2021.07.30.454298v1?rss=1 Dwomoh, L. Rossi, M. Scarpa, M. Khajehali, E. Molloy, C. Herzyk, P. Mistry, S. N. Bottrill, A. Sexton, P. M. Christopoulos, A. Conn, J. P. Lindsley, C. W. Bradley, S. J. Tobin, A. B. 2021-07-30 doi:10.1101/2021.07.30.454298 Cold Spring Harbor Laboratory Press 2021-07-30 <![CDATA[ Tissue-specific heteroplasmy dynamics is accompanied by a sharp drop in mtDNA copy number during development ]]> https://biorxiv.org/content/10.1101/2021.07.30.454495v1?rss=1 Tsyba, N. Patel, M. R. 2021-07-31 doi:10.1101/2021.07.30.454495 Cold Spring Harbor Laboratory Press 2021-07-31 <![CDATA[ Novel compound inhibitors of HIV-1NL4-3 Vpu ]]> https://biorxiv.org/content/10.1101/2021.07.30.454560v1?rss=1 650,000 compounds was performed to identify inhibitors that block the biological activity of Vpu. From this screen, we identified several positive hits but focused on two compounds from one structural family, SRI-41897 and SRI-42371. It was conceivable that the compounds inhibited the formation of infectious virions by targeting host cell proteins instead of Vpu directly, so we developed independent counter-screens for off target interactions of the compounds and found no off target interactions. Additionally, these compounds block Vpu-mediated modulation of CD4, BST-2/Tetherin and antibody dependent cell-mediated toxicity (ADCC). Unfortunately, both SRI-41897 and SRI-42371 were shown to be specific to the N-terminal region of NL4-3 Vpu and did not function against other, more clinically relevant, strains of Vpu. ]]> Robinson, C. A. Lyddon, T. D. Gil, H. M. Evans, D. T. Kuzmichev, Y. V. Richard, J. Finzi, A. Welbourn, S. Rasmussen, L. Nebane, N. M. Gupta, V. V. Ananthan, S. Cai, Z. Wonderlich, E. R. Augelli-Szafran, C. Bostwick, R. Ptak, R. G. Schader, S. Johnson, M. C. 2021-08-03 doi:10.1101/2021.07.30.454560 Cold Spring Harbor Laboratory Press 2021-08-03 <![CDATA[ Gene regulatory networks controlling temporal patterning, neurogenesis and cell fate specification in the mammalian retina. ]]> https://biorxiv.org/content/10.1101/2021.07.31.454200v1?rss=1 Lyu, P. Hoang, T. Santiago, C. P. Thomas, E. Timms, A. Appel, H. Gimmen, M. Le, N. Jiang, L. Kim, D. W. Chen, S. Espinoza, D. Tegler, A. Weir, K. Clark, B. Cherry, T. M. Qian, J. Blackshaw, S. 2021-08-02 doi:10.1101/2021.07.31.454200 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ Adult neuromarkers of sustained attention and working memory predict inter- and intra-individual differences in these processes in youth ]]> https://biorxiv.org/content/10.1101/2021.08.01.454530v1?rss=1 Kardan, O. Stier, A. J. Cardenas-Inigues, C. Pruin, J. C. Schertz, K. E. Deng, Y. Chamberlain, T. Meredith, W. J. Zhang, X. Bowman, J. E. Lakhtakia, T. Tindel, L. Avery, E. W. Lin, Q. Yoo, K. Chun, M. M. Berman, M. G. Rosenberg, M. D. 2021-08-02 doi:10.1101/2021.08.01.454530 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ Mitotic Spindle Positioning (MISP) is an actin bundler that selectively stabilizes the rootlets of epithelial microvilli ]]> https://biorxiv.org/content/10.1101/2021.08.02.454661v1?rss=1 Morales, E. A. Arnaiz, C. Krystofiak, E. S. Zanic, M. Tyska, M. J. 2021-08-03 doi:10.1101/2021.08.02.454661 Cold Spring Harbor Laboratory Press 2021-08-03 <![CDATA[ Transcriptome Profiles of Anopheles gambiae Harboring Natural Low-Level Plasmodium Infection Reveal Adaptive Advantages for the Mosquito ]]> https://biorxiv.org/content/10.1101/2021.08.02.454766v1?rss=1 Carr, A. L. Rinker, D. Dong, Y. Dimopoulos, G. Zwiebel, L. 2021-08-02 doi:10.1101/2021.08.02.454766 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ Rapid Prototyping of Cell Culture Microdevices Using Parylene-Coated 3D Prints ]]> https://biorxiv.org/content/10.1101/2021.08.02.454773v1?rss=1 O'Grady, B. Geuy, M. Kim, H. Balotin, K. Allchin, E. Florian, D. Bute, N. Scott, T. Lowen, G. Fricker, C. Guelcher, S. Wikswo, J. Bellan, L. Lippmann, E. 2021-08-04 doi:10.1101/2021.08.02.454773 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ St18 specifies globus pallidus projection neuron identity in MGE lineage ]]> https://biorxiv.org/content/10.1101/2021.08.03.454907v1?rss=1 Nunnelly, L. Campbell, M. Lee, D. Gu, G. Menon, V. Au, E. 2021-08-04 doi:10.1101/2021.08.03.454907 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ Crystal structure of the potato leafroll virus coat protein and implications for viral assembly ]]> https://biorxiv.org/content/10.1101/2021.08.03.454973v1?rss=1 Adams, M. C. Schiltz, C. J. Heck, M. L. Chappie, J. S. 2021-08-03 doi:10.1101/2021.08.03.454973 Cold Spring Harbor Laboratory Press 2021-08-03 <![CDATA[ A Self-Limiting Circuit Regulates Mammary Cap Cell Plasticity Through TGF-beta Signaling ]]> https://biorxiv.org/content/10.1101/2021.08.04.455067v1?rss=1 Le Guelte, A. M. Macara, I. G. 2021-08-05 doi:10.1101/2021.08.04.455067 Cold Spring Harbor Laboratory Press 2021-08-05 <![CDATA[ Transcranial Ultrasound Stimulation in Anterior Cingulate Cortex Impairs Information Sampling and Learning in Loss Contexts ]]> https://biorxiv.org/content/10.1101/2021.08.04.455080v1?rss=1 Banaie Boroujeni, K. Sigona, M. K. Treuting, R. L. Thomas, M. J. Caskey, C. F. Womelsdorf, T. 2021-08-05 doi:10.1101/2021.08.04.455080 Cold Spring Harbor Laboratory Press 2021-08-05 <![CDATA[ Opposing roles of p38α phosphorylation and arginine methylation in driving TDP-43 proteinopathy. ]]> https://biorxiv.org/content/10.1101/2021.08.04.455154v1?rss=1 Aikio, M. Wobst, H. J. Odeh, H. M. Lee, B. L. Class, B. Ollerhead, T. A. Mack, K. L. Ford, A. F. Barbieri, E. M. Cupo, R. R. Drake, L. E. Castello, N. Baral, A. Dunlop, J. Gitler, A. Javaherian, A. Finkbeiner, S. Brown, D. G. Moss, S. J. Brandon, N. J. Shorter, J. 2021-08-04 doi:10.1101/2021.08.04.455154 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ Dose-dependent dissociation of pro-cognitive effects of donepezil on attention and cognitive flexibility in rhesus monkeys ]]> https://biorxiv.org/content/10.1101/2021.08.09.455743v1?rss=1 Hassani, S. A. Lendor, S. Neumann, A. Roy, K. S. Banaie Boroujeni, K. Hoffman, K. L. Pawliszyn, J. Womelsdorf, T. 2021-08-10 doi:10.1101/2021.08.09.455743 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Regulation of gliotoxin biosynthesis and protection in Aspergillus species ]]> https://biorxiv.org/content/10.1101/2021.08.16.456458v1?rss=1 de Castro, P. A. Moraes, M. Colabardini, A. C. Horta, M. A. C. Knowles, S. L. Raja, H. A. Oberlies, N. H. Koyama, Y. Ogawa, M. Gomi, K. Steenwyk, J. L. Rokas, A. Ries, L. N. A. Goldman, G. H. 2021-08-16 doi:10.1101/2021.08.16.456458 Cold Spring Harbor Laboratory Press 2021-08-16 <![CDATA[ Strong gamma frequency oscillations in the adolescent prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2021.08.20.455686v1?rss=1 Wang, Z. Singh, B. Zhou, X. Constantinidis, C. 2021-08-22 doi:10.1101/2021.08.20.455686 Cold Spring Harbor Laboratory Press 2021-08-22 <![CDATA[ Multiomics reveals persistence of obesity-associated immune cell phenotypes in adipose tissue during weight loss and subsequent weight regain. ]]> https://biorxiv.org/content/10.1101/2021.08.20.455954v1?rss=1 Cottam, M. A. Caslin, H. L. Winn, N. C. Hasty, A. H. 2021-08-20 doi:10.1101/2021.08.20.455954 Cold Spring Harbor Laboratory Press 2021-08-20 <![CDATA[ CD4+CCR6+ T cells dominate the BCG-induced transcriptional signature ]]> https://biorxiv.org/content/10.1101/2021.08.20.457054v1?rss=1 Singhania, A. Dubelko, P. Kuan, R. Chronister, W. D. Muskat, K. Das, J. Phillips, E. J. Mallal, S. A. Seumois, G. Vijayanand, P. Sette, A. Lerm, M. Peters, B. Lindestam Arlehamn, C. S. 2021-08-20 doi:10.1101/2021.08.20.457054 Cold Spring Harbor Laboratory Press 2021-08-20 <![CDATA[ Neuron-specific coding sequences are the most highly conserved in the mammalian brain ]]> https://biorxiv.org/content/10.1101/2021.08.20.457147v1?rss=1 Xu, L. Herculano-Houzel, S. 2021-08-21 doi:10.1101/2021.08.20.457147 Cold Spring Harbor Laboratory Press 2021-08-21 <![CDATA[ Loops, TADs, Compartments, and Territories are Elastic and Robust to Dramatic Nuclear Volume Swelling ]]> https://biorxiv.org/content/10.1101/2021.08.20.457153v1?rss=1 Sanders, J. T. Golloshi, R. Terry, P. H. Nash, D. G. Xu, Y. Dekker, J. McCord, R. P. 2021-08-23 doi:10.1101/2021.08.20.457153 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ Getting the gist faster: Blurry images enhance the early temporal similarity between neural signals and convolutional neural networks ]]> https://biorxiv.org/content/10.1101/2021.08.22.451834v1?rss=1 Tovar, D. A. Grootswagers, T. Jun, J. Cha, O. Blake, R. Wallace, M. T. 2021-08-24 doi:10.1101/2021.08.22.451834 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ A Scale-Free Gradient of Cognitive Resource Disruptions in Childhood Psychopathology ]]> https://biorxiv.org/content/10.1101/2021.08.24.457554v1?rss=1 Stier, A. J. Cardenas-Iniguez, C. Kardan, O. J. Moore, T. M. Meyer, F. A. C. Rosenberg, M. D. Lahey, B. B. Berman, M. G. 2021-08-26 doi:10.1101/2021.08.24.457554 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ Characterizing stochastic cell cycle dynamics in exponential growth ]]> https://biorxiv.org/content/10.1101/2021.08.24.457569v1?rss=1 Huang, D. Lo, T. Merrikh, H. Wiggins, P. A. 2021-08-26 doi:10.1101/2021.08.24.457569 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ Neutrophil-associated responses to Vibrio cholerae infection in a natural host model ]]> https://biorxiv.org/content/10.1101/2021.08.24.457598v1?rss=1 Farr, D. A. Nag, D. Chazin, W. J. Harrison, S. A. Thummel, R. Luo, X. Raychaudhuri, S. Withey, J. H. 2021-08-25 doi:10.1101/2021.08.24.457598 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ Production and composition of group B streptococcal membrane vesicles varies across diverse lineages ]]> https://biorxiv.org/content/10.1101/2021.08.24.457602v1?rss=1 McCutcheon, C. R. Gaddy, J. Aronoff, D. M. Petroff, M. Manning, S. D. 2021-08-25 doi:10.1101/2021.08.24.457602 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ Loss of Secretory Pathway Ca2+ ATPase (SPCA1) Impairs Insulin Secretion and Reduces Autophagy in the Pancreatic Islet ]]> https://biorxiv.org/content/10.1101/2021.08.30.458203v1?rss=1 Bone, R. N. Tong, X. Weaver, S. A. Muralidharan, C. Krishnan, P. Kono, T. M. Evans-Molina, C. 2021-08-31 doi:10.1101/2021.08.30.458203 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Redox-mediated inactivation of the transcriptional repressor C3600 makes uropathogenic Escherichia coli exquisitely resistant to reactive chlorine species ]]> https://biorxiv.org/content/10.1101/2021.08.31.458474v1?rss=1 Sultana, S. LeDoux, K. Crompton, M. E. Jankiewicz, O. Morales, G. H. Johnson, C. Horbach, E. Hoffmann, K. P. KR, P. Shah, R. Anderson, G. M. Mortimer, N. T. Schmitz, J. E. Hadjifrangiskou, M. Foti, A. Dahl, J.-U. 2021-09-01 doi:10.1101/2021.08.31.458474 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ E-cadherin redistribution mediated by Clostridioides difficile toxins increases spore-association to adherens junctions ]]> https://biorxiv.org/content/10.1101/2021.09.01.458577v1?rss=1 Castro-Cordova, P. Otto-Medina, M. Lacy, B. Paredes-Sabja, D. 2021-09-01 doi:10.1101/2021.09.01.458577 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Experimental evolution of insect resistance to two pesticide classes reveals mechanistic diversity and context-dependent fitness costs ]]> https://biorxiv.org/content/10.1101/2021.09.03.458899v1?rss=1 Birnbaum, S. S. L. Schulz, N. K. E. Garrett, D. S. Tate, A. T. 2021-09-05 doi:10.1101/2021.09.03.458899 Cold Spring Harbor Laboratory Press 2021-09-05 <![CDATA[ Genome-wide association mapping of ethanol sensitivity in the Diversity Outbred mouse population ]]> https://biorxiv.org/content/10.1101/2021.09.06.459155v1?rss=1 Parker, C. C. Philip, V. Gatti, D. M. Kasparek, S. Kreuzman, A. Kuffler, L. Mansky, B. Masneuf, S. Sharif, K. Sluys, E. Taterra, D. Taylor, W. M. Thomas, M. Polesskaya, O. Palmer, A. A. Holmes, A. Chesler, E. 2021-09-06 doi:10.1101/2021.09.06.459155 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Effects of acute and repeated administration of the selective M4 PAM VU0152099 on cocaine vs. food choice in male rats ]]> https://biorxiv.org/content/10.1101/2021.09.06.459176v1?rss=1 Thomsen, M. H. Crittenden, J. R. Lindsley, C. W. Graybiel, A. M. 2021-09-06 doi:10.1101/2021.09.06.459176 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Distinct proteostasis states drive pharmacologic chaperone susceptibility for Cystic Fibrosis Transmembrane Conductance Regulator misfolding mutants ]]> https://biorxiv.org/content/10.1101/2021.09.09.459524v1?rss=1 McDonald, E. F. Sabusap, C. M. P. Kim, M. Plate, L. 2021-09-09 doi:10.1101/2021.09.09.459524 Cold Spring Harbor Laboratory Press 2021-09-09 <![CDATA[ Laminar microcircuitry of visual cortex producing attention-associated electric fields ]]> https://biorxiv.org/content/10.1101/2021.09.09.459639v1?rss=1 Westerberg, J. A. Schall, M. S. Maier, A. Woodman, G. Schall, J. D. 2021-09-11 doi:10.1101/2021.09.09.459639 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Dopamine biases sensitivity to personal goals and social influence in self-control over everyday desires ]]> https://biorxiv.org/content/10.1101/2021.09.10.459829v1?rss=1 Castrellon, J. J. Young, J. S. Dang, L. C. Smith, C. T. Cowan, R. L. Zald, D. H. Samanez-Larkin, G. R. 2021-09-11 doi:10.1101/2021.09.10.459829 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Integration of multidimensional splicing data and GWAS summary statistics for risk gene discovery ]]> https://biorxiv.org/content/10.1101/2021.09.13.460009v1?rss=1 Ji, Y. Wei, Q. Chen, R. Wang, Q. Tao, R. Li, B. 2021-09-15 doi:10.1101/2021.09.13.460009 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Microbench: Automated metadata management for systems biology benchmarking and reproducibility in Python ]]> https://biorxiv.org/content/10.1101/2021.09.14.460317v1?rss=1 Lubbock, A. L. R. Lopez, C. F. 2021-09-16 doi:10.1101/2021.09.14.460317 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ The 3D spatial constraint on 6.1 million amino acid sites in the human proteome ]]> https://biorxiv.org/content/10.1101/2021.09.15.460390v1?rss=1 80% (16,533) of human proteins. We show that the human proteome is broadly under 3D spatial constraint and that the level of spatial constraint is strongly associated with disease relevance both at the individual site level and the protein level. We demonstrate that COSMIS performs significantly better at a range of variant interpretation tasks than other population-based constraint metrics while also providing biophysical insight into the potential functional roles of constrained sites. We make our constraint maps freely available and anticipate that the structural landscape of constrained sites identified by COSMIS will facilitate interpretation of protein-coding variation in human evolution and prioritization of sites for mechanistic or functional investigation. ]]> Li, B. Roden, D. M. Capra, J. A. 2021-09-16 doi:10.1101/2021.09.15.460390 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ Dominant negative effects of SCN5A missense variants ]]> https://biorxiv.org/content/10.1101/2021.09.22.461398v1?rss=1 O'Neill, M. J. Muhammad, A. Li, B. Wada, Y. Hall, L. Solus, J. Short, L. Roden, D. M. Glazer, A. M. 2021-09-24 doi:10.1101/2021.09.22.461398 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein ]]> https://biorxiv.org/content/10.1101/2021.09.25.461776v1?rss=1 Shilts, J. Crozier, T. M. Teixeira-Silva, A. Gabaev, I. Greenwood, E. J. D. Watson, S. J. Ortmann, B. M. Gawden-Bone, C. M. Pauzaite, T. Hoffmann, M. Nathan, J. A. Pöhlmann, S. Lehner, P. J. Wright, G. J. 2021-09-25 doi:10.1101/2021.09.25.461776 Cold Spring Harbor Laboratory Press 2021-09-25 <![CDATA[ Practices for Measuring 3D Organelle Morphology and Generating Surfaces with Amira ]]> https://biorxiv.org/content/10.1101/2021.09.25.461807v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@1c40041org.highwire.dtl.DTLVardef@ecde92org.highwire.dtl.DTLVardef@10870daorg.highwire.dtl.DTLVardef@1290c3b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Garza Lopez, E. Vue, Z. Katti, P. Neikirk, K. Biete, M. Lam, J. Beasley, H. Marshall, A. Rodman, T. Christensen, T. A. Salisbury, J. L. Vang, L. Mungai, M. AshShareef, S. Murray, S. Shao, J. Streeter, J. Glancy, B. Pereira, R. O. Abel, E. D. Hinton, A. 2021-09-28 doi:10.1101/2021.09.25.461807 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ Systematic Transmission Electron Microscopy-Based Identification of Cellular Degradation Machinery ]]> https://biorxiv.org/content/10.1101/2021.09.26.461841v1?rss=1 Neikirk, K. Vue, Z. Katti, P. Shao, J. Christensen, T. A. Garza Lopez, E. Marshall, A. Palavicino-Maggio, C. Ponce, J. Alghanem, A. Vang, L. Beasley, H. Rodman, T. Mungai, M. Correia, M. Exil, V. Murray, S. Salisbury, J. L. Glancy, B. Pereira, R. O. Abel, E. D. Hinton, A. 2021-09-27 doi:10.1101/2021.09.26.461841 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ An ensemble deep learning framework to refine large deletions in linked-reads ]]> https://biorxiv.org/content/10.1101/2021.09.27.462057v1?rss=1 Hu, Y. Mangal, S. V. Zhang, L. Zhou, X. 2021-09-29 doi:10.1101/2021.09.27.462057 Cold Spring Harbor Laboratory Press 2021-09-29 <![CDATA[ MARS: a tool for haplotype-resolved population-based structural variation detection ]]> https://biorxiv.org/content/10.1101/2021.09.27.462061v1?rss=1 Zhang, L. Sidow, A. Zhou, X. 2021-09-29 doi:10.1101/2021.09.27.462061 Cold Spring Harbor Laboratory Press 2021-09-29 <![CDATA[ Transmembrane Signaling Regulates the Remodeling of the Actin Cytoskeleton:Roles of PKC and Adducin ]]> https://biorxiv.org/content/10.1101/2021.09.29.462380v1?rss=1 Shieh, B.-H. Sun, W. Ferng, D. 2021-09-30 doi:10.1101/2021.09.29.462380 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Optimized Workflow for High Spatial Resolution MALDI Imaging Mass Spectrometry ofFresh-Frozen Bone ]]> https://biorxiv.org/content/10.1101/2021.10.01.462831v1?rss=1 Good, C. J. Neumann, E. K. Butrico, C. E. Cassat, J. E. Caprioli, R. M. Spraggins, J. M. 2021-10-01 doi:10.1101/2021.10.01.462831 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data ]]> https://biorxiv.org/content/10.1101/2021.10.02.462868v1?rss=1 Steenwyk, J. L. Buida, T. J. Goncalves, C. Goltz, D. C. Morales, G. H. Mead, M. E. LaBella, A. L. Chavez, C. M. Schmitz, J. E. Hadjifrangiskou, M. Li, Y. Rokas, A. 2021-10-03 doi:10.1101/2021.10.02.462868 Cold Spring Harbor Laboratory Press 2021-10-03 <![CDATA[ Multimodal Imaging Mass Spectrometry of Murine Gastrointestinal Tract with Retained Luminal Content Shows Molecular Localization Patterns ]]> https://biorxiv.org/content/10.1101/2021.10.03.462819v1?rss=1 Guiberson, E. R. Wexler, A. G. Good, C. J. Skaar, E. P. Spraggins, J. M. Caprioli, R. M. 2021-10-03 doi:10.1101/2021.10.03.462819 Cold Spring Harbor Laboratory Press 2021-10-03 <![CDATA[ PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, andRNA polymerase pause release at select gene targets ]]> https://biorxiv.org/content/10.1101/2021.10.03.462944v1?rss=1 Zhang, S. Wang, J. Liu, Q. McDonald, W. H. Bomber, M. Layden, H. Ellis, J. Borinstein, S. Hiebert, S. W. Stengel, K. R. 2021-10-04 doi:10.1101/2021.10.03.462944 Cold Spring Harbor Laboratory Press 2021-10-04 <![CDATA[ Development of coarse-grained model for a minimal stratum corneum lipid mixture ]]> https://biorxiv.org/content/10.1101/2021.10.04.463115v1?rss=1 Shamaprasad, P. Moore, T. C. Xia, D. Iacovella, C. R. Bunge, A. L. McCabe, C. 2021-10-04 doi:10.1101/2021.10.04.463115 Cold Spring Harbor Laboratory Press 2021-10-04 <![CDATA[ Topoisomerase II poisons inhibit vertebrate DNA replication through distinct mechanisms ]]> https://biorxiv.org/content/10.1101/2021.10.12.464107v1?rss=1 Van Ravenstein, S. X. Mehta, K. P. Kavlashvili, T. Byl, J. A. Zhao, R. Osheroff, N. Cortez, D. Dewar, J. M. 2021-10-12 doi:10.1101/2021.10.12.464107 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ Replication Fork Uncoupling Causes Nascent Strand Degradation and Fork Reversal ]]> https://biorxiv.org/content/10.1101/2021.10.13.464136v1?rss=1 Kavlashvili, T. Dewar, J. M. 2021-10-13 doi:10.1101/2021.10.13.464136 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ An atlas of white matter anatomy, its variability, and reproducibility based on Constrained Spherical Deconvolution of diffusion MRI ]]> https://biorxiv.org/content/10.1101/2021.10.13.464139v1?rss=1 View larger version (52K): org.highwire.dtl.DTLVardef@18e7c79org.highwire.dtl.DTLVardef@18e2213org.highwire.dtl.DTLVardef@5f124borg.highwire.dtl.DTLVardef@1aa242c_HPS_FORMAT_FIGEXP M_FIG Graphical abstract(Top) shows the FWT pipeline for both CSTs, AF, and motor CC bundles. (Left to right) show the required input structural parcellation maps and a priori atlases for FWT and the resulting virtual dissection include/exclude VOIs. FWT provides two approaches to virtual dissection: (1) is a bundle-specific approach where streamlines are only seeded for the bundle of interest, (2) is a whole brain tractography followed by streamlines segmentation, (top right) shows output tractograms. (Middle) Group-averaged T1 and fODF images are generated from the HCP test-retest data, and FWT is applied to generate the HCP-atlas using the bundle-specific approach (1*). FWTs whole brain tracking and segmentation approach (2*) was applied to the HCP and MASSIVE dataset (right and left) and conducted model-based, and pair-wise similarity analyses and generated voxel-wise cumulative maps per bundle. FWT= Fun With Tracts, FS= FreeSurfer, MSBP= MultiScaleBrainParcellator, PD25= NIST Parkinsons histological, JHU= Johns Hopkins university, Juelich= Juelich university histological atlas, AC/PC= anterior commissure/posterior commissure) UKBB= UK Biobank, SUIT (spatially unbiased cerebellar atlas template), dMRI= diffusion magnetic resonance imaging, CSD= constrained spherical deconvolution, fODF= fiber orientation distribution function, CST= corticospinal tract, AF= arcuate fasciculus, CC= corpus callosum, HCP= human connectome project, MASSIVE= Multiple acquisitions for standardization of structural imaging validation and evaluation. C_FIG ]]> Radwan, A. M. Sunaert, S. Schilling, K. G. Descoteaux, M. Landman, B. A. Vandenbulcke, M. Theys, T. Dupont, P. Emsell, L. 2021-10-14 doi:10.1101/2021.10.13.464139 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ PRMT5 in T cells drives Th17 responses, mixed granulocytic inflammation and severe allergic airway inflammation ]]> https://biorxiv.org/content/10.1101/2021.10.13.464281v1?rss=1 Lewis, B. W. Amici, S. A. Kim, H.-Y. Shalosky, E. Khan, A. Walum, J. Gowdy, K. M. Englert, J. Porter, N. A. Grayson, M. H. Britt, R. D. Guerau-de-Arellano, M. 2021-10-14 doi:10.1101/2021.10.13.464281 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Alpha cell dysfunction in early type 1 diabetes ]]> https://biorxiv.org/content/10.1101/2021.10.15.464545v1?rss=1 Doliba, N. Rozo, A. Roman, J. Qin, W. Traum, D. Gao, L. Liu, J. Manduchi, E. Liu, C. Golson, M. Vahedi, G. Naji, A. Matschinsky, F. Atkinson, M. Powers, A. Brissova, M. Kaestner, K. H. Stoffers, D. 2021-10-16 doi:10.1101/2021.10.15.464545 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ Combining metabolomics and experimental evolution reveals key mechanisms underlying longevity differences in laboratory evolved Drosophila melanogaster populations ]]> https://biorxiv.org/content/10.1101/2021.10.16.464668v1?rss=1 Phillips, M. Arnold, K. R. Vue, Z. Beasley, H. Garza Lopez, E. Marshall, A. Morton, D. McReynolds, M. R. Barter, T. T. Hinton, A. 2021-10-17 doi:10.1101/2021.10.16.464668 Cold Spring Harbor Laboratory Press 2021-10-17 <![CDATA[ In situ architecture of the ciliary base reveals the stepwise assembly of IFT trains ]]> https://biorxiv.org/content/10.1101/2021.10.17.464685v1?rss=1 van den Hoek, H. Klena, N. Jordan, M. A. Alvarez Viar, G. Schaffer, M. Erdmann, P. S. Wan, W. Plitzko, J. M. Baumeister, W. Pigino, G. Hamel, V. Guichard, P. Engel, B. D. 2021-10-17 doi:10.1101/2021.10.17.464685 Cold Spring Harbor Laboratory Press 2021-10-17 <![CDATA[ Structural basis for activation and gating of IP3 receptors ]]> https://biorxiv.org/content/10.1101/2021.10.18.464806v1?rss=1 Schmitz, E. A. Takahashi, H. Karakas, E. 2021-10-18 doi:10.1101/2021.10.18.464806 Cold Spring Harbor Laboratory Press 2021-10-18 <![CDATA[ Triazolopyrimidines target aerobic respiration in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2021.10.18.464924v1?rss=1 Shelton, C. D. McNeil, M. B. Flint, L. Russell, D. Berube, B. Korkegian, A. Ovechkina, Y. Parish, T. 2021-10-20 doi:10.1101/2021.10.18.464924 Cold Spring Harbor Laboratory Press 2021-10-20 <![CDATA[ Extensive sequence divergence of non-coding regions between Aspergillus fumigatus, a major fungal pathogen of humans, and its relatives ]]> https://biorxiv.org/content/10.1101/2021.10.26.465918v1?rss=1 Brown, A. Mead, M. E. Steenwyk, J. L. Goldman, G. Rokas, A. 2021-10-28 doi:10.1101/2021.10.26.465918 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Altered circadian rhythms and sleep in a new Angelman Syndrome mouse model ]]> https://biorxiv.org/content/10.1101/2021.10.26.465956v1?rss=1 Shi, S. Mahoney, C. Houdek, P. Zhao, W. Anderson, M. Zhuo, X. Beaudet, A. Sumova, A. Scammell, T. Johnson, C. H. 2021-10-28 doi:10.1101/2021.10.26.465956 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Weakly migratory metastatic breast cancer cells activate fibroblasts via microvesicle-Tg2 to facilitate dissemination and metastasis ]]> https://biorxiv.org/content/10.1101/2021.10.27.466095v1?rss=1 Schwager, S. C. Hapach, L. A. Carlson, C. M. Mosier, J. A. McArdle, T. J. Wang, W. Jayathilake, A. L. Bordeleau, F. Antonyak, M. A. Cerione, R. A. Reinhart-King, C. A. 2021-10-29 doi:10.1101/2021.10.27.466095 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Eicosanoids in the pancreatic tumor microenvironment: a multicellular, multifaceted progression ]]> https://biorxiv.org/content/10.1101/2021.10.27.466097v1?rss=1 Gubbala, V. B. Jyotsana, N. Trinh, V. Q. Maurer, H. C. Naeem, R. F. Lytle, N. K. Ma, Z. Zhao, S. Lin, W. Han, H. Shi, Y. Hunter, T. singh, P. K. Olive, K. P. Tan, M. C. B. Kaech, S. M. Wahl, G. DelGiorno, K. E. 2021-10-28 doi:10.1101/2021.10.27.466097 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ R-loop mapping and characterization during Drosophila embryogenesis reveals developmental plasticity in R-loop signatures ]]> https://biorxiv.org/content/10.1101/2021.10.29.465954v1?rss=1 Munden, A. Benton, M. L. Capra, J. A. Nordman, J. 2021-10-29 doi:10.1101/2021.10.29.465954 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Resistance-guided mining of bacterial genotoxins defines a family of DNA glycosylases ]]> https://biorxiv.org/content/10.1101/2021.10.29.466481v1?rss=1 Bradley, N. P. Wahl, K. L. Steenwyk, J. L. Rokas, A. Eichman, B. F. 2021-10-30 doi:10.1101/2021.10.29.466481 Cold Spring Harbor Laboratory Press 2021-10-30 <![CDATA[ orthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees ]]> https://biorxiv.org/content/10.1101/2021.10.30.466607v1?rss=1 Steenwyk, J. L. Goltz, D. Buida, T. J. Li, Y. Shen, X.-X. Rokas, A. 2021-11-02 doi:10.1101/2021.10.30.466607 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ MTG16 (CBFA2T3) represses E protein-dependent transcription to regulate colonic secretory cell differentiation, epithelial regeneration, and tumorigenesis ]]> https://biorxiv.org/content/10.1101/2021.11.03.467178v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@21948borg.highwire.dtl.DTLVardef@9f60eeorg.highwire.dtl.DTLVardef@194b9fdorg.highwire.dtl.DTLVardef@13eb1a7_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Brown, R. E. Jacobse, J. Anant, S. A. Blunt, K. M. Chen, B. Vega, P. N. Jones, C. T. Pilat, J. M. Revetta, F. Gorby, A. H. Stengel, K. R. Choksi, Y. A. Palin, K. Piazuelo, M. B. Washington, M. K. Lau, K. S. Goettel, J. A. Hiebert, S. W. Short, S. P. Williams, C. S. 2021-11-04 doi:10.1101/2021.11.03.467178 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ The Most Widespread Phage in Animals: Genomics and Taxonomic Classification of Phage WO ]]> https://biorxiv.org/content/10.1101/2021.11.04.467296v1?rss=1 Bordenstein, S. R. Bordenstein, S. 2021-11-04 doi:10.1101/2021.11.04.467296 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ A switch in the development: microRNA arm usage screening in zebrafish suggests an important role of arm switching events in ontogenesis ]]> https://biorxiv.org/content/10.1101/2021.11.05.467297v1?rss=1 Oliveira, A. C. Bovolenta, L. A. Figueiredo, L. Patton, J. G. Pinhal, D. 2021-11-08 doi:10.1101/2021.11.05.467297 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ An active learning framework improves tumor variant interpretation ]]> https://biorxiv.org/content/10.1101/2021.11.08.467747v1?rss=1 Blee, A. M. Li, B. Pecen, T. Meiler, J. Nagel, Z. D. Capra, J. A. Chazin, W. J. 2021-11-09 doi:10.1101/2021.11.08.467747 Cold Spring Harbor Laboratory Press 2021-11-09 <![CDATA[ Learning Feedback Molecular Network Models Using Integer Linear Programming ]]> https://biorxiv.org/content/10.1101/2021.11.08.467837v1?rss=1 Ozen, M. Abdi, A. Emamian, E. S. 2021-11-10 doi:10.1101/2021.11.08.467837 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ Robust and generalizable segmentation of human functional tissue units ]]> https://biorxiv.org/content/10.1101/2021.11.09.467810v1?rss=1 Godwin, L. L. Ju, Y. Sood, N. Jain, Y. Quardokus, E. M. Bueckle, A. Longacre, T. Horning, A. M. Lin, Y. Esplin, E. D. Hickey, J. W. Snyder, M. P. Patterson, N. H. Spraggins, J. M. Borner, K. 2021-11-11 doi:10.1101/2021.11.09.467810 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ STAT1 Gain-of-Function Variants Drive Altered T Cell Prevalence, Metabolism, and Heightened IL-6 Sensitivity ]]> https://biorxiv.org/content/10.1101/2021.11.10.468135v1?rss=1 Kaviany, S. Bartkowiak, T. Dulek, D. E. Khan, Y. W. Hayes, M. J. Schaefer, S. K. Dahunsi, D. O. Connelly, J. A. Irish, J. M. Rathmell, J. C. 2021-11-12 doi:10.1101/2021.11.10.468135 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ The C. albicans virulence factor Candidalysin polymerizes in solution to form membrane pores and damage epithelial cells. ]]> https://biorxiv.org/content/10.1101/2021.11.11.468266v1?rss=1 Russell, C. M. Schaefer, K. Dixson, A. Gray, A. Pyron, R. J. Alves, D. Moore, N. Conley, E. White, T. Do, T. King, G. Barrera, F. N. 2021-11-12 doi:10.1101/2021.11.11.468266 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ Structural comparative modeling of multi-domain ΔF508 CFTR ]]> https://biorxiv.org/content/10.1101/2021.11.17.468921v1?rss=1 McDonald, E. F. Woods, H. Smith, S. Kim, M. Schoeder, C. T. Plate, L. Meiler, J. 2021-11-19 doi:10.1101/2021.11.17.468921 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Sampling the conformational landscapes of transporters and receptors with AlphaFold2 ]]> https://biorxiv.org/content/10.1101/2021.11.22.469536v1?rss=1 del Alamo, D. Sala, D. Mchaourab, H. Meiler, J. 2021-11-22 doi:10.1101/2021.11.22.469536 Cold Spring Harbor Laboratory Press 2021-11-22 <![CDATA[ Listeria monocytogenes requires cellular respiration for NAD+ regeneration and pathogenesis ]]> https://biorxiv.org/content/10.1101/2021.11.25.470024v1?rss=1 1,000-fold in a mouse infection model. Consistent with NAD+ regeneration maintaining L. monocytogenes viability and enabling immune evasion, a respiration-deficient strain exhibited elevated bacteriolysis within the host cytosol and NOX rescued this phenotype. These studies show that NAD+ regeneration, rather than oxidative phosphorylation, represents the primary role of L. monocytogenes respiration and highlight the nuanced relationship between bacterial metabolism, physiology, and pathogenesis. ]]> Rivera-Lugo, R. Deng, D. Anaya-Sanchez, A. Tejedor-Sanz, S. Reyes Ruiz, V. M. Smith, H. B. Titov, D. V. Sauer, J. D. Skaar, E. P. Ajo-Franklin, C. M. Portnoy, D. A. Light, S. H. 2021-11-25 doi:10.1101/2021.11.25.470024 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ Dysregulated Transferrin Receptor Disrupts T Cell Iron Homeostasis to Drive Inflammation in Systemic Lupus Erythematosus ]]> https://biorxiv.org/content/10.1101/2021.11.25.470053v1?rss=1 Voss, K. Young, A. Gibson-Corley, K. N. Sewell, A. E. Krystofiak, E. Bashum, J. H. Beavers, W. N. Sugiura, A. Skaar, E. P. Ormseth, M. J. Rathmell, J. 2021-11-25 doi:10.1101/2021.11.25.470053 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ A brainstem integrator for self-localization and positional homeostasis ]]> https://biorxiv.org/content/10.1101/2021.11.26.468907v1?rss=1 Yang, E. Zwart, M. F. Rubinov, M. James, B. Wei, Z. Narayan, S. Vladimirov, N. Mensh, B. D. Fitzgerald, J. E. Ahrens, M. B. 2021-11-27 doi:10.1101/2021.11.26.468907 Cold Spring Harbor Laboratory Press 2021-11-27 <![CDATA[ The Importance of Mentors and How to Handle More Than One Mentor ]]> https://biorxiv.org/content/10.1101/2021.11.29.469764v1?rss=1 Marshall, A. G. Brady, L. Palavicino-Maggio, C. Neikirk, K. Vue, Z. Beasley, H. Garza Lopez, E. Murray, S. Martinez, D. Shuler, H. Spencer, E. Morton, D. Hinton, A. 2021-12-01 doi:10.1101/2021.11.29.469764 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Using a Champion-Oriented Mindset to Overcome the Challenges of Graduate School ]]> https://biorxiv.org/content/10.1101/2021.11.29.469904v1?rss=1 Marshall, A. Palavicino-Maggio, C. Neikirk, K. Vue, Z. Beasley, H. Lopez, E. G. Murray, S. A. Martinez, D. Davis, J. Shuler, H. Spencer, E. Morton, D. Hinton, A. 2021-12-01 doi:10.1101/2021.11.29.469904 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Ubiquitination drives COPI priming and Golgi SNARE localization ]]> https://biorxiv.org/content/10.1101/2021.11.29.470439v1?rss=1 Date, S. S. Xu, P. Hepowit, N. L. Diab, N. S. Best, J. Xie, B. Du, J. Strieter, E. R. Jackson, L. P. MacGurn, J. A. Graham, T. R. 2021-11-29 doi:10.1101/2021.11.29.470439 Cold Spring Harbor Laboratory Press 2021-11-29 <![CDATA[ Modeling Alternate Conformations with Alphafold2 via Modification of the Multiple Sequence Alignment ]]> https://biorxiv.org/content/10.1101/2021.11.29.470469v1?rss=1 Stein, R. A. Mchaourab, H. 2021-11-29 doi:10.1101/2021.11.29.470469 Cold Spring Harbor Laboratory Press 2021-11-29 <![CDATA[ Structural Basis for an Unprecedented Enzymatic Alkylation in Cylindrocyclophane Biosynthesis ]]> https://biorxiv.org/content/10.1101/2021.12.02.470901v1?rss=1 Braffman, N. R. Ruskoski, T. B. Davis, K. M. Glasser, N. R. Johnson, C. Okafor, D. Boal, A. K. Balskus, E. P. 2021-12-02 doi:10.1101/2021.12.02.470901 Cold Spring Harbor Laboratory Press 2021-12-02 <![CDATA[ A remote lecture series roadmap to equity, diversity, and inclusion in STEM ]]> https://biorxiv.org/content/10.1101/2021.12.05.471284v1?rss=1 Boyle, E. A. Goldberg, G. Schmok, J. C. Burgado, J. Izidro Layng, F. Grunwald, H. A. Balotin, K. M. Cuoco, M. S. Chang, K.-C. Ecklu-Mensah, G. Arakaki, A. K. S. Ahmed, N. Garcia Arceo, X. Jagannatha, P. Pekar, J. Iyer, M. DASL Alliance, Yeo, G. W. 2021-12-07 doi:10.1101/2021.12.05.471284 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Predicting the Functional Impact of KCNQ1 Variants with Artificial Neural Networks ]]> https://biorxiv.org/content/10.1101/2021.12.06.471347v1?rss=1 Phul, S. Kuenze, G. Vanoye, C. G. Sanders, C. R. George, A. L. Meiler, J. 2021-12-09 doi:10.1101/2021.12.06.471347 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ An effective workshop on How to be an Effective Mentor for Underrepresented STEM Trainees ]]> https://biorxiv.org/content/10.1101/2021.12.06.471498v1?rss=1 Marshall, A. Vue, Z. Palavicino-Maggio, C. Spencer, E. C. Beasley, H. K. Garza Lopez, E. Conley, Z. Neikirk, K. Murray, S. A. Martinez, D. Davis, J. Brady, L. Shuler, H. D. Morton, D. Hinton, A. 2021-12-08 doi:10.1101/2021.12.06.471498 Cold Spring Harbor Laboratory Press 2021-12-08 <![CDATA[ Direct Imaging and Identification of Proteoforms up to 70 kDa from Human Tissue ]]> https://biorxiv.org/content/10.1101/2021.12.07.471638v1?rss=1 Su, P. McGee, J. P. Durbin, K. R. Hollas, M. A. R. Yang, M. Neumann, E. K. Allen, J. L. Drown, B. S. Butun, F. A. Greer, J. B. Early, B. P. Fellers, R. T. Spraggins, J. M. Laskin, J. Camarillo, J. M. Kafader, J. O. Kelleher, N. L. 2021-12-07 doi:10.1101/2021.12.07.471638 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ The Role of Mentoring in Promoting Diversity, Equity, and Inclusion in STEM Education and Research ]]> https://biorxiv.org/content/10.1101/2021.12.08.471502v1?rss=1 Marshall, A. Vue, Z. Palavicino-maggio, C. Spencer, E. C. Beasley, H. K. Garza- Lopez, E. Conley, Z. Neikirk, K. Murray, S. A. Martinez, D. Davis, J. Brady, L. J. Shuler, H. D. Morton, D. Hinton, A. 2021-12-09 doi:10.1101/2021.12.08.471502 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Heterogeneity of the GFP fitness landscape and data-driven protein design ]]> https://biorxiv.org/content/10.1101/2021.12.08.471728v1?rss=1 Gonzalez Somermeyer, L. Fleiss, A. Mishin, A. S. Bozhanova, N. G. Igolkina, A. A. Meiler, J. Alaball Pujol, M.-E. Putintseva, E. V. Sarkisyan, K. S. Kondrashov, F. 2021-12-09 doi:10.1101/2021.12.08.471728 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ 4-phenylbutyrate restored GABA uptake and reduced seizures in SLC6A1 variants-mediated disorders ]]> https://biorxiv.org/content/10.1101/2021.12.08.471799v1?rss=1 Nwosu, G. I. Mermer, F. Flamm, C. Poliquin, S. Shen, W. Rigsby, K. Kang, J. 2021-12-10 doi:10.1101/2021.12.08.471799 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ Strain variation in Clostridioides difficile toxin activity associated with genomic variation at both PaLoc and non-PaLoc loci ]]> https://biorxiv.org/content/10.1101/2021.12.08.471880v1?rss=1 Saund, K. Pirani, A. Lacy, B. Hanna, P. C. Snitkin, E. S. 2021-12-09 doi:10.1101/2021.12.08.471880 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Clonal hematopoiesis is driven by aberrant activation of TCL1A ]]> https://biorxiv.org/content/10.1101/2021.12.10.471810v1?rss=1 Weinstock, J. S. Gopakumar, J. Burugula, B. B. Uddin, M. M. Jahn, N. Belk, J. A. Daniel, B. Ly, N. Mack, T. M. Laurie, C. A. Broome, J. G. Taylor, K. D. Guo, X. Sinner, M. F. von Falkenhausen, A. S. Kaab, S. Shuldiner, A. R. O'Connell, J. R. Lewis, J. P. Boerwinkle, E. Barnes, K. C. Chami, N. Kenny, E. E. Loos, R. J. F. Fornage, M. Hou, L. Lloyd-Jones, D. M. Redline, S. Cade, B. E. Psaty, B. M. Bis, J. C. Brody, J. A. Silverman, E. K. Yun, J. H. Qiao, D. Palmer, N. D. Freedman, B. I. Bowden, D. W. Cho, M. H. DeMeo, D. L. Vasan, R. S. Johnson, A. D. Mat 2021-12-13 doi:10.1101/2021.12.10.471810 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Probing the segregation of evoked and spontaneous neurotransmission via photobleaching and recovery of a fluorescent glutamate sensor ]]> https://biorxiv.org/content/10.1101/2021.12.10.472065v1?rss=1 Wang, C. Chanaday, N. Monteggia, L. M. Kavalali, E. T. 2021-12-10 doi:10.1101/2021.12.10.472065 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ Metabolic properties of murine kidney mitochondria ]]> https://biorxiv.org/content/10.1101/2021.12.13.472400v1?rss=1 Panov, A. Mayorov, V. I. Dikalov, S. I. 2021-12-13 doi:10.1101/2021.12.13.472400 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Transcription Factor RFX3 Stabilizes Mammary Basal Cell Identity ]]> https://biorxiv.org/content/10.1101/2021.12.13.472491v1?rss=1 Macara, I. Tross, E. M. de Caestecker, C. Lau, K. 2021-12-13 doi:10.1101/2021.12.13.472491 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ RFX6-mediated dysregulation defines human β cell dysfunction in early type 2 diabetes ]]> https://biorxiv.org/content/10.1101/2021.12.16.466282v1?rss=1 Walker, J. T. Saunders, D. C. Rai, V. Dai, C. Orchard, P. Hopkirk, A. L. Reihsmann, C. V. Tao, Y. Fan, S. Shrestha, S. Varshney, A. Wright, J. J. Pettway, Y. D. Ventresca, C. Agarwala, S. Aramandla, R. Poffenberger, G. Jenkins, R. Hart, N. J. Greiner, D. L. Shultz, L. D. Bottino, R. Human Pancreas Analysis Program, Liu, J. Parker, S. C. J. Powers, A. C. Brissova, M. 2021-12-17 doi:10.1101/2021.12.16.466282 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Insights from the IronTract challenge: optimal methods for mapping brain pathways from multi-shell diffusion MRI ]]> https://biorxiv.org/content/10.1101/2021.12.17.472836v1?rss=1 Maffei, C. Girard, G. Schilling, K. Aydogan, B. Aduluru, N. Zhylka, A. Wu, Y. Mancini, M. Hamamci, A. Sarica, A. Telliac, A. Baete, S. Karimi, D. Yeh, F. Yildiz, M. Gholipour, A. Bihan-Poudec, Y. Hiba, B. Quattrone, A. Quattrone, A. Boshkovski, T. Stikov, N. Yap, P.-T. De Luca, A. Pluim, J. Leemans, A. Prabhakaran, V. Bendlin, B. B. Alexander, A. Landman, B. Canales-Rodriguez, E. Barakovic, M. Rafael-Patino, J. Yu, T. Rensonnet, G. Schiavi, S. Daducci, A. Pizzolato, M. Fischi-Gomez, E. Thiran, J.-P. Dai, G. Grisot, G. Lazovski, N. Puch, S. Ramos, M. 2021-12-19 doi:10.1101/2021.12.17.472836 Cold Spring Harbor Laboratory Press 2021-12-19 <![CDATA[ Physico-chemical principles of HDL-small RNA binding interactions. ]]> https://biorxiv.org/content/10.1101/2021.12.17.473011v1?rss=1 Michell, D. L. Allen, R. M. Cavnar, A. B. Contreras, D. M. Yu, M. Semler, E. M. Ramirez, M. A. Zhu, W. May-Zhang, L. Raby, C. A. Castleberry, M. Ifram, A. M. Carr, J. J. Terry, J. G. Scwendeman, A. Davies, S. S. Sheng, Q. Linton, M. F. Vickers, K. C. 2021-12-18 doi:10.1101/2021.12.17.473011 Cold Spring Harbor Laboratory Press 2021-12-18 <![CDATA[ Towards mechanistic models of mutational effects: Deep Learning on Alzheimer's Aβ peptide ]]> https://biorxiv.org/content/10.1101/2021.12.19.473403v1?rss=1 Wang, B. Gamazon, E. R. 2021-12-21 doi:10.1101/2021.12.19.473403 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Effectiveness and relationship between biased and unbiased measures of dopamine release and clearance ]]> https://biorxiv.org/content/10.1101/2021.12.20.473490v1?rss=1 Everett, A. C. Graul, B. E. Watts, D. B. Robinson, J. K. Espana, R. A. Siciliano, C. A. Yorgason, J. T. 2021-12-21 doi:10.1101/2021.12.20.473490 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Disruption of synaptic transmission in the Bed Nucleus of the Stria Terminalis reduces seizure-induced death in DBA/1 mice and alters brainstem E/I balance ]]> https://biorxiv.org/content/10.1101/2021.12.23.473665v1?rss=1 Xia, M. Owen, B. Chiang, J. Levitt, A. Yan, W. W. Nobis, W. P. 2021-12-24 doi:10.1101/2021.12.23.473665 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ Metabolic regulation by prostaglandin E2 impairs lung group 2 innate lymphoid cell responses ]]> https://biorxiv.org/content/10.1101/2021.12.23.474031v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@17dd2caorg.highwire.dtl.DTLVardef@199ce97org.highwire.dtl.DTLVardef@ca1f67org.highwire.dtl.DTLVardef@1d3a49f_HPS_FORMAT_FIGEXP M_FIG C_FIG Schematic of potential roles for activation of EP2 and EP4 by endogenous versus exogenous ligands in regulation of lung ILC2 immune responses. Endogenous PGE2 in the lung preferentially activates EP2 rather than EP4 to inhibit ILC2 responses and eosinophilic inflammation, and ablation of EP2 enhances lung ILC2 responses. Conversely, lung ILC2 responses are not altered by EP4 deficiency. However, they are markedly inhibited by EP4 agonism but not EP2 agonism. Mechanistically, PGE2-EP2/EP4 signaling activates the cAMP pathway which inhibits ILC2 energy metabolism, possibly through interruption of NF-{kappa}B (reported in Nagashima H, et al. Immunity 2019;51:682-695) and STAT5 signaling, leading to decline of ILC2 survival, proliferation and type 2 cytokine production. ]]> Robb, C. Zhou, Y. Felton, J. Zhang, B. Goepp, M. Jheeta, P. Smyth, D. Breyer, R. Narumiya, S. McSorley, H. Maizels, R. Schwarze, J. Rossi, A. Yao, C. 2021-12-24 doi:10.1101/2021.12.23.474031 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ Improving the computation efficiency of polygenic risk score modeling: Faster in Julia ]]> https://biorxiv.org/content/10.1101/2021.12.27.474263v1?rss=1 Faucon, A. Samaroo, J. Ge, T. Davis, L. K. Tao, R. Cox, N. J. Shuey, M. M. 2021-12-27 doi:10.1101/2021.12.27.474263 Cold Spring Harbor Laboratory Press 2021-12-27 <![CDATA[ Towards Generalizable Predictions for the Effects of Mutations on G-Protein Coupled Receptor Expression ]]> https://biorxiv.org/content/10.1101/2021.12.28.474371v1?rss=1 Kuntz, C. P. Woods, H. McKee, A. G. Zelt, N. B. Mendenhall, J. L. Meiler, J. Schlebach, J. P. 2021-12-28 doi:10.1101/2021.12.28.474371 Cold Spring Harbor Laboratory Press 2021-12-28 <![CDATA[ A transient apical extracellular matrix relays cytoskeletal patterns to shape permanent acellular ridges on the surface of adult C. elegans ]]> https://biorxiv.org/content/10.1101/2021.12.28.474392v1?rss=1 Katz, S. S. Barker, T. J. Maul-Newby, H. M. Sparacio, A. P. Nguyen, K. C. Q. Maybrun, C. L. Belfi, A. Cohen, J. D. Hall, D. H. Sundaram, M. V. Frand, A. R. 2021-12-29 doi:10.1101/2021.12.28.474392 Cold Spring Harbor Laboratory Press 2021-12-29 <![CDATA[ Tissue Registration and Exploration User Interfaces in support of a Human Reference Atlas ]]> https://biorxiv.org/content/10.1101/2021.12.30.474265v1?rss=1 Borner, K. Bueckle, A. Herr, B. W. Cross, L. E. Quardokus, E. M. Record, E. G. Ju, Y. Silverstein, J. C. Browne, K. Jain, S. Wasserfall, C. H. Jorgensen, M. L. Spraggins, J. M. Patterson, N. H. Weber, G. M. 2021-12-30 doi:10.1101/2021.12.30.474265 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ Theta- and gamma-band oscillatory uncoupling in the macaque hippocampus ]]> https://biorxiv.org/content/10.1101/2021.12.30.474585v1?rss=1 Abbaspoor, S. Hussin, A. Hoffman, K. L. 2022-01-01 doi:10.1101/2021.12.30.474585 Cold Spring Harbor Laboratory Press 2022-01-01 <![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[ Dissociating encoding of memory and salience by manipulating long-term synaptic potentiation ]]> https://biorxiv.org/content/10.1101/2022.01.04.474865v1?rss=1 Kaganovsky, K. Plitt, M. H. Yang, R. Sando, R. Giocomo, L. M. Ding, J. B. Südhof, T. C. 2022-01-04 doi:10.1101/2022.01.04.474865 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ Sleep slow-wave oscillations trigger seizures in a genetic epilepsy model of Dravet syndrome ]]> https://biorxiv.org/content/10.1101/2022.01.04.474940v1?rss=1 Catron, M. A. Howe, R. K. Besing, G.-L. K. St. John, E. K. Potesta, C. V. Gallagher, M. J. Macdonald, R. L. Zhou, C. 2022-01-05 doi:10.1101/2022.01.04.474940 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Function and constraint in enhancers with multiple evolutionary origins ]]> https://biorxiv.org/content/10.1101/2022.01.05.475150v1?rss=1 Fong, S. L. Capra, J. A. 2022-01-06 doi:10.1101/2022.01.05.475150 Cold Spring Harbor Laboratory Press 2022-01-06 <![CDATA[ Free diffusion of PI(4,5)P2 in the plasma membrane in the presence of high density effector protein complexes ]]> https://biorxiv.org/content/10.1101/2022.01.07.475414v1?rss=1 Pacheco, J. Cassidy, A. C. Zewe, J. P. Wills, R. C. Hammond, G. R. 2022-01-09 doi:10.1101/2022.01.07.475414 Cold Spring Harbor Laboratory Press 2022-01-09 <![CDATA[ Systematic analysis of human antibody response to ebolavirus glycoprotein reveals high prevalence of neutralizing public clonotypes ]]> https://biorxiv.org/content/10.1101/2022.01.12.476089v1?rss=1 Chen, E. C. Gilchuk, P. Zost, S. J. Ilinykh, P. A. Binshtein, E. Huang, K. Myers, L. Bonissone, S. Day, S. Kona, C. R. Trivette, A. Reidy, J. X. Sutton, R. E. Gainza, C. Monroig, S. Davidson, E. Saphire, E. O. Doranz, B. J. Castellana, N. Bukreyev, A. Carnahan, R. H. Crowe, J. E. 2022-01-13 doi:10.1101/2022.01.12.476089 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ An antibody targeting the N-terminal domain of SARS-CoV-2 disrupts the spike trimer ]]> https://biorxiv.org/content/10.1101/2022.01.12.476120v1?rss=1 Suryadevara, N. Shiakolas, A. VanBlargan, L. Binshtein, E. Chen, R. Case, J. B. Kramer, K. Armstrong, E. Myers, L. Trivette, A. Gainza, C. Nargi, R. Selverian, C. Davidson, E. Doranz, B. Diaz, S. Handal, L. Carnahan, R. H. Diamond, M. S. Georgiev, I. Crowe, J. E. 2022-01-13 doi:10.1101/2022.01.12.476120 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ The cytoplasmic incompatibility Cif proteins from prophage WO modify sperm genome integrity ]]> https://biorxiv.org/content/10.1101/2022.01.15.476471v1?rss=1 Kaur, R. Leigh, B. A. Ritchie, I. T. Bordenstein, S. R. 2022-01-16 doi:10.1101/2022.01.15.476471 Cold Spring Harbor Laboratory Press 2022-01-16 <![CDATA[ Identification of replication fork-associated proteins in Drosophila embryos and cultured cells using iPOND coupled to quantitative mass spectrometry ]]> https://biorxiv.org/content/10.1101/2022.01.18.476773v1?rss=1 Munden, A. Wright, M. Han, D. Tirgar, R. Plate, L. Nordman, J. 2022-01-20 doi:10.1101/2022.01.18.476773 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ The IMD and JNK pathways drive the functional integration of the immune and circulatory systems of mosquitoes ]]> https://biorxiv.org/content/10.1101/2022.01.26.477938v1?rss=1 Yan, Y. Sigle, L. T. Rinker, D. C. Estevez-Lao, T. Y. Capra, J. A. Hillyer, J. F. 2022-01-27 doi:10.1101/2022.01.26.477938 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ Three-dimensional actuation of hummingbird wings requires diverse effects from the primary flight muscles ]]> https://biorxiv.org/content/10.1101/2022.01.27.477984v1?rss=1 Agrawal, S. Tobalske, B. W. Anwar, M. Z. Luo, H. Hedrick, T. L. Cheng, B. 2022-01-28 doi:10.1101/2022.01.27.477984 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ RTEL1 and MCM10 overcome topological stress during vertebrate replication termination ]]> https://biorxiv.org/content/10.1101/2022.01.27.478093v1?rss=1 Campos, L. V. Greer, B. H. Heintzman, D. R. Kavlashvili, T. McDonald, W. H. Rose, K. L. Eichman, B. F. Dewar, J. M. 2022-01-28 doi:10.1101/2022.01.27.478093 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ JUN Regulation of Injury-induced Enhancers in Schwann Cells ]]> https://biorxiv.org/content/10.1101/2022.01.31.478565v1?rss=1 Ramesh, R. Manurung, Y. Ma, K. H. Blakely, T. Won, S. Wyatt, E. Awatramani, R. Svaren, J. 2022-02-02 doi:10.1101/2022.01.31.478565 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ Identification of cell types in multiplexed in situ images by combining protein expression and spatial information using CELESTA reveals novel spatial biology ]]> https://biorxiv.org/content/10.1101/2022.02.02.478888v1?rss=1 Zhang, W. Li, I. Reticker-Flynn, N. E. Good, Z. Chang, S. Samusik, N. Saumyaa, S. Li, Y. Zhou, X. Liang, R. Kong, C. S. Le, Q.-T. Gentles, A. J. Sunwoo, J. B. Nolan, G. P. Engleman, E. G. Plevritis, S. K. 2022-02-05 doi:10.1101/2022.02.02.478888 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ Real-time luminescence enables continuous drug-response analysis in adherent and suspension cell lines ]]> https://biorxiv.org/content/10.1101/2022.02.03.479010v1?rss=1 Wandishin, C. M. Robbins, C. J. Tyson, D. R. Harris, L. A. Quaranta, V. 2022-02-03 doi:10.1101/2022.02.03.479010 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Reward contingency gates selective cholinergic suppression of amygdala neurons ]]> https://biorxiv.org/content/10.1101/2022.02.04.479188v1?rss=1 Kimchi, E. Y. Burgos-Robles, A. Matthews, G. A. Chakoma, T. Patarino, M. Weddington, J. C. Siciliano, C. A. Yang, W. Foutch, S. Simons, R. Fong, M.-f. jing, m. Li, Y. Polley, D. B. Tye, K. M. 2022-02-05 doi:10.1101/2022.02.04.479188 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergence ]]> https://biorxiv.org/content/10.1101/2022.02.07.479462v1?rss=1 McArthur, E. Rinker, D. C. Gilbertson, E. N. Fudenberg, G. Pittman, M. Keough, K. Pollard, K. S. Capra, J. A. 2022-02-08 doi:10.1101/2022.02.07.479462 Cold Spring Harbor Laboratory Press 2022-02-08 <![CDATA[ High Fat Diet Blunts Stress-Induced Hypophagia and Activation of Glp1r Dorsal Lateral Septum Neurons in Male but not in Female Mice ]]> https://biorxiv.org/content/10.1101/2022.02.08.479553v1?rss=1 Bales, M. B. Centanni, S. W. Luchsinger, J. R. Nwaba, K. G. Paldrmic, I. M. Winder, D. G. Ayala, J. E. 2022-02-08 doi:10.1101/2022.02.08.479553 Cold Spring Harbor Laboratory Press 2022-02-08 <![CDATA[ Gi/o protein-coupled receptor inhibition of beta-cell electrical excitability and insulin secretion depends on Na+/K+ ATPase activation ]]> https://biorxiv.org/content/10.1101/2022.02.10.479802v1?rss=1 Dickerson, M. T. Dadi, P. K. Zaborska, K. E. Nakhe, A. Y. Schaub, C. M. Dobson, J. R. Wright, N. M. Lynch, J. C. Scott, C. F. Jacobson, D. A. 2022-02-10 doi:10.1101/2022.02.10.479802 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Aging and white matter microstructure and macrostructure: a longitudinal multi-site diffusion MRI study of 1,184 participants ]]> https://biorxiv.org/content/10.1101/2022.02.10.479977v1?rss=1 Schilling, K. Archer, D. B. Yeh, F.-C. Rheault, F. Cai, L. Y. Hansen, C. B. Yang, Q. Ramadass, K. Shafer, A. Resnick, S. Pechman, K. R. Gifford, K. A. Hohman, T. J. Jefferson, A. Anderson, A. W. Kang, H. Landman, B. A. 2022-02-11 doi:10.1101/2022.02.10.479977 Cold Spring Harbor Laboratory Press 2022-02-11 <![CDATA[ Modeling of protein conformational changes with Rosetta guided by limited experimental data ]]> https://biorxiv.org/content/10.1101/2022.02.14.480383v1?rss=1 Sala, D. del Alamo, D. Mchaourab, H. S. Meiler, J. 2022-02-16 doi:10.1101/2022.02.14.480383 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ Microbiota-derived aspartate drives pathogenic Enterobacteriaceae expansion in the inflamed gut ]]> https://biorxiv.org/content/10.1101/2022.02.14.480453v1?rss=1 Yoo, W. Zieba, J. K. Shealy, N. G. Torres, T. P. Thomas, J. D. Shelton, C. D. Foegeding, N. J. Olsan, E. E. Byndloss, M. X. 2022-02-15 doi:10.1101/2022.02.14.480453 Cold Spring Harbor Laboratory Press 2022-02-15 <![CDATA[ 2-Arachodonoylglycerol-mediated endocannabinoid signaling modulates mechanical hypersensitivity associated with alcohol withdrawal in mice ]]> https://biorxiv.org/content/10.1101/2022.02.15.480609v1?rss=1 Morgan, A. Adank, D. Johnson, K. Butler, E. Patel, S. 2022-02-17 doi:10.1101/2022.02.15.480609 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ Immune cell regulation in stem cell niche contacting glioblastomas. ]]> https://biorxiv.org/content/10.1101/2022.02.16.480731v1?rss=1 Bartkowiak, T. Lima, S. M. Hayes, M. J. Mistry, A. M. Sinnaeve, J. Leelatian, N. Roe, C. E. Mobley, B. C. Weaver, K. D. Thompson, R. C. Chambless, L. B. Ihrie, R. A. Irish, J. M. 2022-02-16 doi:10.1101/2022.02.16.480731 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ Lens aquaporin-5 inserts into bovine fiber cell plasma membranes through mitochondria-associated lysosome secretion ]]> https://biorxiv.org/content/10.1101/2022.02.16.480789v1?rss=1 Gletten, R. B. Cantrell, L. S. Schey, K. L. Bhattacharya, S. 2022-02-18 doi:10.1101/2022.02.16.480789 Cold Spring Harbor Laboratory Press 2022-02-18 <![CDATA[ Molecular architecture of the human caveolin-1 complex ]]> https://biorxiv.org/content/10.1101/2022.02.17.480763v1?rss=1 Porta, J. C. Han, B. Gulsevin, A. Chung, J. Peskova, Y. Connolly, S. Mchaourab, H. Meiler, J. Karakas, E. Kenworthy, A. K. Ohi, M. D. 2022-02-17 doi:10.1101/2022.02.17.480763 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ Benchmarking Peptide Structure Prediction with AlphaFold2 ]]> https://biorxiv.org/content/10.1101/2022.02.17.480937v1?rss=1 Gulsevin, A. Meiler, J. 2022-02-17 doi:10.1101/2022.02.17.480937 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ Reactive astrocytes transduce blood-brain barrier dysfunction through a TNFα-STAT3 signaling axis and secretion of alpha 1-antichymotrypsin ]]> https://biorxiv.org/content/10.1101/2022.02.21.481336v1?rss=1 Kim, H. Leng, K. Park, J. Sorets, A. Kim, S. Shostak, A. Sturgeon, S. Neal, E. McMahon, D. G. Schrag, M. Kampmann, M. Lippmann, E. 2022-02-22 doi:10.1101/2022.02.21.481336 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Domestication and lowland adaptation of coastal preceramic maize from Paredones, Peru ]]> https://biorxiv.org/content/10.1101/2022.02.23.481166v1?rss=1 Vallebueno-Estrada, M. Hernandez-Robles, G. G. Gonzalez-Orozco, E. Lopez-Valdivia, I. Tham, T. R. Sanchez, V. V. Swarts, K. Dillehay, T. D. Vielle-Calzada, J.-P. Montiel, R. 2022-02-25 doi:10.1101/2022.02.23.481166 Cold Spring Harbor Laboratory Press 2022-02-25 <![CDATA[ Detection of functional activity in brain white matter using fiber architecture informed synchrony mapping ]]> https://biorxiv.org/content/10.1101/2022.02.23.481698v1?rss=1 Zhao, Y. Gao, Y. Zu, Z. Li, M. Schilling, K. Anderson, A. Gore, J. 2022-02-24 doi:10.1101/2022.02.23.481698 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Distinct execution modes of a biochemical necroptosis model explain cell type-specific responses and variability to cell-death cues ]]> https://biorxiv.org/content/10.1101/2022.02.25.481705v1?rss=1 Ildefonso, G. V. Oliver Metzig, M. Hoffmann, A. Harris, L. A. Lopez, C. F. 2022-02-26 doi:10.1101/2022.02.25.481705 Cold Spring Harbor Laboratory Press 2022-02-26 <![CDATA[ Localizing temporal lobe seizure onset zones using deep learning on SEEG cortico-cortical evoked potentials ]]> https://biorxiv.org/content/10.1101/2022.02.28.481828v1?rss=1 Johnson, G. W. Cai, L. Y. Doss, D. J. Jiang, J. W. Negi, A. S. Narasimhan, S. Paulo, D. L. Gonzalez, H. F. Roberson, S. W. Bick, S. K. Chang, C. E. Morgan, V. L. Wallace, M. T. Englot, D. J. 2022-03-02 doi:10.1101/2022.02.28.481828 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Two Interaction Surfaces between XPA and RPA Organize the Preincision Complex in Nucleotide Excision Repair ]]> https://biorxiv.org/content/10.1101/2022.03.01.482439v1?rss=1 Kim, M. Kim, H. S. D'Souza, A. Gallagher, K. Jung, E. Topolska-Wos, A. Ogorodnik Le Meur, K. Tsai, C.-L. Tsai, M.-S. Kee, M. Tainer, J. A. Yeo, J.-E. Chazin, W. J. Scharer, O. D. 2022-03-02 doi:10.1101/2022.03.01.482439 Cold Spring Harbor Laboratory Press 2022-03-02 <![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[ Using machine learning to understand microgeographic determinants of the Zika vector, Aedes aegypti ]]> https://biorxiv.org/content/10.1101/2022.03.03.482880v1?rss=1 Alexander, J. Wilke, A. B. B. Mantero, A. Vasquez, C. Petrie, W. Kumar, N. Beier, J. C. 2022-03-03 doi:10.1101/2022.03.03.482880 Cold Spring Harbor Laboratory Press 2022-03-03 <![CDATA[ Improved mammalian retromer cryo-EM structures reveal a new assembly interface ]]> https://biorxiv.org/content/10.1101/2022.03.04.482375v1?rss=1 Kendall, A. Chandra, M. Xie, B. Wan, W. Jackson, L. P. 2022-03-04 doi:10.1101/2022.03.04.482375 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Mechanical Ventilation induced P21 in an Acute Aging Model of Lung Injury ]]> https://biorxiv.org/content/10.1101/2022.03.08.483505v1?rss=1 Gninzeko, F. J. K. Tho, C. K. Valentine, M. S. Wandling, E. N. Heise, R. L. 2022-03-08 doi:10.1101/2022.03.08.483505 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Lamin A/C mediated invaginations in the nuclear surface allow the nucleus to pass unimpeded through a dense array of fiber-like obstacles ]]> https://biorxiv.org/content/10.1101/2022.03.10.483838v1?rss=1 Katiyar, A. Zhang, J. Antani, J. D. Yu, Y. Lele, P. P. Reinhart-King, C. A. Sniadecki, N. J. Roux, K. J. Dickinson, R. B. Lele, T. P. 2022-03-11 doi:10.1101/2022.03.10.483838 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ Programming bacteria to sense environmental DNA for multiplexed pathogen detection ]]> https://biorxiv.org/content/10.1101/2022.03.10.483875v1?rss=1 Cheng, Y.-Y. Chen, Z. Cao, X. Ross, T. D. Falbel, T. G. S. Burton, B. M. Venturelli, O. S. 2022-03-11 doi:10.1101/2022.03.10.483875 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ Glucagon-like peptide-1 receptor differentially controls mossy cell activity across the dentate gyrus longitudinal axis ]]> https://biorxiv.org/content/10.1101/2022.03.14.484169v1?rss=1 Steiner, A. Owen, B. M. Bauer, J. P. Seanez, L. Kwon, S. Biddinger, J. E. Huffman, R. Ayala, J. E. Nobis, W. P. Lewis, A. S. 2022-03-17 doi:10.1101/2022.03.14.484169 Cold Spring Harbor Laboratory Press 2022-03-17 <![CDATA[ Selective V1-to-V4 communication of attended stimuli mediated by attentional effects in V1 ]]> https://biorxiv.org/content/10.1101/2022.03.14.484223v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@1cc79a7org.highwire.dtl.DTLVardef@146e6bdorg.highwire.dtl.DTLVardef@1d6bd6borg.highwire.dtl.DTLVardef@12dd663_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Katsanevaki, C. Bastos, A. M. Cagnan, H. Bosman, C. A. Friston, K. J. Fries, P. 2022-03-17 doi:10.1101/2022.03.14.484223 Cold Spring Harbor Laboratory Press 2022-03-17 <![CDATA[ Resolving the mesoscopic missing link: Biophysical modeling of EEG from cortical columns in primates ]]> https://biorxiv.org/content/10.1101/2022.03.16.484595v1?rss=1 Herrera, B. Westerberg, J. A. Schall, M. S. Maier, A. Woodman, G. F. Schall, J. D. Riera, J. J. 2022-03-18 doi:10.1101/2022.03.16.484595 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Merging of ventral fibers at adhesions drives the remodeling of cellular contractile systems in fibroblasts. ]]> https://biorxiv.org/content/10.1101/2022.03.16.484620v1?rss=1 Narasimhan, S. Holmes, W. R. Kaverina, I. 2022-03-16 doi:10.1101/2022.03.16.484620 Cold Spring Harbor Laboratory Press 2022-03-16 <![CDATA[ Allele-specific activation, enzyme kinetics, and inhibitor sensitivities of EGFR exon 19 deletion mutations in lung cancer ]]> https://biorxiv.org/content/10.1101/2022.03.16.484661v1?rss=1 V, and L747_A750>P). We demonstrate that sequence variation in ex19del alters oncogenic cell growth, dimerization propensity, and tyrosine kinase inhibitor (TKI) sensitivity. We show that in contrast to E746_A750 and E746_S752>V, the L747_A750>P variant forms highly active ligand-independent dimers. E746_S752>V displays the least TKI sensitivity among the variants tested, which enzyme kinetic analysis and TKI inhibition experiments suggest is due to increased ATP Km relative to the common E746_A750 variant. Through these analyses, we propose an expanded framework for interpreting ex19del variants and new considerations for therapeutic intervention. SignificanceEGFR mutations are detected in approximately 30% of all lung adenocarcinomas, and the most common EGFR mutation occurring in ~50% of patients is termed "exon 19 deletion" (ex19del). Despite the existence of dozens of different genomic variants comprising what is generically referred to clinically as ex19del, clinicians currently do not distinguish between ex19del variants in considering treatment options, and the differences between ex19del variants are largely unstudied in the broader scientific community. Herein, we describe functional differences between distinct EGFR ex19del variants attributable to the structural features of each variant. These findings suggest a possible explanation for observed differences in patient outcomes stratified by ex19del subtype and reinforce the need for allele-specific considerations in clinical treatment decision making. ]]> Brown, B. P. Zhang, Y. Kim, S. Finneran, P. Yan, Y. Du, Z. Kim, J. Hartzler, A. L. LeNoue-Newton, M. L. Smith, A. W. Meiler, J. Lovly, C. M. 2022-03-17 doi:10.1101/2022.03.16.484661 Cold Spring Harbor Laboratory Press 2022-03-17 <![CDATA[ Screening of hydrocarbon-stapled peptides for inhibition of calcium-triggered exocytosis ]]> https://biorxiv.org/content/10.1101/2022.03.21.484632v1?rss=1 Lai, Y. Tuvim, M. Pfuetzner, R. Esquivies, L. Zhou, Q. Czako, B. Cross, J. Jones, P. Dickey, B. Brunger, A. T. 2022-03-21 doi:10.1101/2022.03.21.484632 Cold Spring Harbor Laboratory Press 2022-03-21 <![CDATA[ 3D Reconstructions of Mouse Skeletal Muscle and Heart Muscle Reveal a Decrease in the MICOS Complex and Altered Mitochondrial Networks ]]> https://biorxiv.org/content/10.1101/2022.03.22.485341v1?rss=1 Vue, Z. Lopez, E. G. Neikirk, K. Vang, L. Beasley, H. Marshall, A. Hinton, A. 2022-03-23 doi:10.1101/2022.03.22.485341 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Examination of genome-wide ortholog variation in clinical and environmental isolates of the fungal pathogen Aspergillus fumigatus ]]> https://biorxiv.org/content/10.1101/2022.03.23.485522v1?rss=1 Horta, M. A. C. Steenwyk, J. L. Mead, M. E. dos Santos, L. H. B. Zhao, S. Gibbons, J. G. Marcet-Houben, M. Gabaldon, T. Rokas, A. Goldman, G. 2022-03-26 doi:10.1101/2022.03.23.485522 Cold Spring Harbor Laboratory Press 2022-03-26 <![CDATA[ Identifying transcription factor-bound gene activators and silencers in the chromatin accessible human genome using ATAC-STARR-seq ]]> https://biorxiv.org/content/10.1101/2022.03.25.485870v1?rss=1 Hodges, E. Hansen, T. J. 2022-03-28 doi:10.1101/2022.03.25.485870 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Serotonin Modulates an Inhibitory Input to the Central Amygdala from the Ventral Periaqueductal Gray ]]> https://biorxiv.org/content/10.1101/2022.03.28.486055v1?rss=1 Hon, O. Diberto, J. Mazzone, C. Sugam, J. Bloodgood, D. W. Hardaway, A. Husain, M. Kendra, A. McCall, N. Lopez, A. kash, t. Lowery-Gionta, E. 2022-03-29 doi:10.1101/2022.03.28.486055 Cold Spring Harbor Laboratory Press 2022-03-29 <![CDATA[ Lack of universal mutational biases in a fungal phylum ]]> https://biorxiv.org/content/10.1101/2022.03.29.486229v1?rss=1 A|T and A|T > G|C substitutions, revealed that fungal species vary in how their genome nucleotide composition is affected by neutral processes, mutational biases, and external evolutionary forces, such as selection. Whereas genome nucleotide composition is consistent with neutral expectations and is mainly driven by mutational bias in some species (e.g., Zymoseptoria tritici), the composition of others is influenced by both mutational bias and selection (e.g., H. uvarum and S. chartarum). These results highlight the variation of patterns of mutations across a fungal phylum and suggest that both neutral and selective processes shape the nucleotide composition of fungal genomes. ]]> Zheng, Q. Steenwyk, J. L. Rokas, A. 2022-03-29 doi:10.1101/2022.03.29.486229 Cold Spring Harbor Laboratory Press 2022-03-29 <![CDATA[ Behavioral and imaging analysis of Foxg1 heterozygous mice ]]> https://biorxiv.org/content/10.1101/2022.03.29.486318v1?rss=1 Erickson, K. R. Farmer, R. Merritt, J. K. Miletic Lanaghan, Z. Does, M. D. Ramadass, K. Landman, B. A. Cutting, L. E. Neul, J. L. 2022-03-30 doi:10.1101/2022.03.29.486318 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ Olfactory Sensitivity Aligns with Caste Revealing Multipotential Minors and Specialized Soldier Majors in Camponotus floridanus Ants ]]> https://biorxiv.org/content/10.1101/2022.04.01.486728v1?rss=1 Ferguson, S. T. Bakis, I. Edwards, N. D. Zwiebel, L. 2022-04-01 doi:10.1101/2022.04.01.486728 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Sub-type selective muscarinic acetylcholine receptor modulation for the treatment of parkinsonian tremor ]]> https://biorxiv.org/content/10.1101/2022.04.04.487007v1?rss=1 Bickham, K. Withers, C. P. Diedrich, A. Moehle, M. S. 2022-04-04 doi:10.1101/2022.04.04.487007 Cold Spring Harbor Laboratory Press 2022-04-04 <![CDATA[ Nuclease proteins CifA and CifB promote spermatid DNA damage associated with symbiont-induced cytoplasmic incompatibility ]]> https://biorxiv.org/content/10.1101/2022.04.04.487029v1?rss=1 Kaur, R. Shropshire, J. D. Leigh, B. A. Bordenstein, S. R. 2022-04-04 doi:10.1101/2022.04.04.487029 Cold Spring Harbor Laboratory Press 2022-04-04 <![CDATA[ Novel Bruton's Tyrosine Kinase (BTK) substrates for time-resolved luminescence assays ]]> https://biorxiv.org/content/10.1101/2022.04.05.487161v1?rss=1 Widstrom, N. Perez, M. Pratt, E. D. Heier, J. L. Blankenhorn, J. F. Breidenbach, L. Peterson, H. Parker, L. L. 2022-04-06 doi:10.1101/2022.04.05.487161 Cold Spring Harbor Laboratory Press 2022-04-06 <![CDATA[ Nucleoporins facilitate ORC loading onto chromatin ]]> https://biorxiv.org/content/10.1101/2022.04.05.487200v1?rss=1 Richards, L. Lord, C. Benton, M. L. Capra, J. A. Nordman, J. T. 2022-04-05 doi:10.1101/2022.04.05.487200 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Integrating bulk and single cell RNA-seq refines transcriptomic profiles of specific C. elegans neurons. ]]> https://biorxiv.org/content/10.1101/2022.04.05.487209v1?rss=1 Barrett, A. Varol, E. Weinreb, A. Taylor, S. R. McWhirter, R. Cros, C. Basavaraju, M. Poff, A. Tipps, J. A. Majeed, M. Vidal, B. Wang, C. Yemini, E. Bayer, E. A. Sun, H. Hobert, O. Miller, D. M. Hammarlund, M. 2022-04-08 doi:10.1101/2022.04.05.487209 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ A multiscale atlas of the molecular and cellular architecture of the human kidney ]]> https://biorxiv.org/content/10.1101/2022.04.07.487155v1?rss=1 Neumann, E. K. Patterson, N. H. Tideman, L. E. M. Migas, L. G. Colley, M. E. Farrow, M. A. Allen, J. L. Rivera, E. S. Rmer, C. E. Yang, H. Brewer, M. Sharman, K. Harris, R. C. Fogo, A. B. Gutierrez, D. B. de Caestecker, M. P. Caprioli, R. M. Van de Plas, R. Spraggins, J. M. 2022-04-07 doi:10.1101/2022.04.07.487155 Cold Spring Harbor Laboratory Press 2022-04-07 <![CDATA[ Structural insights into sodium/iodide symporter (NIS) substrate binding and specificity ]]> https://biorxiv.org/content/10.1101/2022.04.07.487502v1?rss=1 Ravera, S. Nicola, J. P. Salazar de Simone, G. Sigworth, F. J. Karakas, E. Amzel, L. M. Bianchet, M. A. Carrasco, N. 2022-04-08 doi:10.1101/2022.04.07.487502 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Multilevel selection analysis reveals diversity in selfish mitochondrial genome dynamics ]]> https://biorxiv.org/content/10.1101/2022.04.08.487647v1?rss=1 Gitschlag, B. L. Patel, M. R. 2022-04-10 doi:10.1101/2022.04.08.487647 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Multishot Tomography for High-Resolution In Situ Subtomogram Averaging. ]]> https://biorxiv.org/content/10.1101/2022.04.10.487763v1?rss=1 Khavnekar, S. Wan, W. Majumder, P. Wietrzynski, W. S. Erdmann, P. S. Plitzko, J. M. 2022-04-10 doi:10.1101/2022.04.10.487763 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Polerovirus N-terminal readthrough domain structures reveal novel molecular strategies for mitigating virus transmission by aphids ]]> https://biorxiv.org/content/10.1101/2022.04.10.487772v1?rss=1 Schiltz, C. J. Wilson, J. R. Hosford, C. J. Adams, M. C. Preising, S. E. DeBlasio, S. L. Macleod, H. J. Van Eck, J. Heck, M. L. Chappie, J. S. 2022-04-10 doi:10.1101/2022.04.10.487772 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ First crystal structure of a non-canonical amino acid linked to a paramagnetic lanthanide tag facilitates protein structure determination using NMR-derived restraints ]]> https://biorxiv.org/content/10.1101/2022.04.10.487812v1?rss=1 Okwei, E. N. N. Ganguly, S. Darling, H. L. Harp, J. M. Gulsevin, A. Coin, I. Mchaourab, H. Ledwitch, K. Kuenze, G. Meiler, J. 2022-04-11 doi:10.1101/2022.04.10.487812 Cold Spring Harbor Laboratory Press 2022-04-11 <![CDATA[ Calibration allows accurate estimation of the axonal volume fraction with diffusion MRI ]]> https://biorxiv.org/content/10.1101/2022.04.12.488014v1?rss=1 Papazoglou, S. Ashtarayeh, B. Oeschger, M. Callaghan, M. F. Does, M. D. Mohammadi, S. 2022-04-13 doi:10.1101/2022.04.12.488014 Cold Spring Harbor Laboratory Press 2022-04-13 <![CDATA[ Integrated AlphaFold2 and DEER investigation of the conformational dynamics of a pH-dependent APC antiporter ]]> https://biorxiv.org/content/10.1101/2022.04.13.488180v1?rss=1 del Alamo, D. DeSousa, L. Nair, R. M. Rahman, S. Meiler, J. Mchaourab, H. 2022-04-13 doi:10.1101/2022.04.13.488180 Cold Spring Harbor Laboratory Press 2022-04-13 <![CDATA[ Dopamine release at the time of a predicted aversive outcome causally controls the trajectory and expression of conditioned behavior ]]> https://biorxiv.org/content/10.1101/2022.04.15.488530v1?rss=1 Kutlu, M. G. Tat, J. Zachry, J. E. Calipari, E. S. 2022-04-16 doi:10.1101/2022.04.15.488530 Cold Spring Harbor Laboratory Press 2022-04-16 <![CDATA[ Tbx3 is required for mammalian retinal angiogenesis. ]]> https://biorxiv.org/content/10.1101/2022.04.20.488944v1?rss=1 Derbyshire, M. Akula, S. Wong, A. Rawlins, K. Voura, E. B. Brunken, W. J. Zuber, M. E. Moon, A. M. Viczian, A. S. 2022-04-22 doi:10.1101/2022.04.20.488944 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Scalable and model-free detection of spatial patterns and colocalization ]]> https://biorxiv.org/content/10.1101/2022.04.20.488961v1?rss=1 Liu, Q. Hsu, C.-Y. Shyr, Y. 2022-04-21 doi:10.1101/2022.04.20.488961 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ Glucagon-Like Peptide-1 Receptor Activation Stimulates PKA-Mediated Phosphorylation of Raptor and this Contributes to the Weight Loss Effects of Liraglutide ]]> https://biorxiv.org/content/10.1101/2022.04.21.489078v1?rss=1 Le, T. D. V. Liu, D. Ellis, B. J. Collins, S. Ayala, J. E. 2022-04-22 doi:10.1101/2022.04.21.489078 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ ACSS2 Regulates HIF-2α Degradation through the E3-Ubiquitin Ligase MUL1 in Clear Cell Renal Cell Carcinoma ]]> https://biorxiv.org/content/10.1101/2022.04.21.489116v1?rss=1 Bacigalupa, Z. A. Brown, W. A. Krystofiak, E. S. Wolf, M. M. Hongo, R. A. Landis, M. Amason, E. K. Beckermann, K. E. Rathmell, J. Rathmell, W. K. 2022-04-22 doi:10.1101/2022.04.21.489116 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Cultural specialization as a double-edged sword: division into specialized guilds might promote cultural complexity at the cost of higher susceptibility to cultural loss ]]> https://biorxiv.org/content/10.1101/2022.04.22.489202v1?rss=1 Ben-Oren, Y. Kolodny, O. Creanza, N. 2022-04-25 doi:10.1101/2022.04.22.489202 Cold Spring Harbor Laboratory Press 2022-04-25 <![CDATA[ MICOS Complex and Mitochondria Morphology Changes Across Aging in Cardiac Muscle ]]> https://biorxiv.org/content/10.1101/2022.04.23.489291v1?rss=1 Vue, Z. Garza Lopez, E. Neikirk, K. Vang, L. Beasley, H. Crabtree, A. Marshall, A. Murray, S. A. Hinton, A. 2022-04-24 doi:10.1101/2022.04.23.489291 Cold Spring Harbor Laboratory Press 2022-04-24 <![CDATA[ Pre-T cell receptor Self-MHC Sampling Restricts Thymocyte Dedifferentiation ]]> https://biorxiv.org/content/10.1101/2022.04.28.489872v1?rss=1 Duke-Cohan, J. S. Akitsu, A. Mallis, R. J. Messier, C. M. Lizotte, P. H. Hwang, W. Lang, M. J. Reinherz, E. L. 2022-04-29 doi:10.1101/2022.04.28.489872 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ Nuclear receptor ligand screening in an iPSC-derived in vitro blood-brain barrier model identifies new contributors to leptin transport ]]> https://biorxiv.org/content/10.1101/2022.05.03.490335v1?rss=1 Shi, Y. Kim, H. Hamann, C. A. Rhea, E. M. Brunger, J. M. Lippmann, E. S. 2022-05-03 doi:10.1101/2022.05.03.490335 Cold Spring Harbor Laboratory Press 2022-05-03 <![CDATA[ The microtubule minus end-binding protein CAMSAP2 does not regulate microtubule dynamics in primary pancreatic β-cells but facilitates insulin secretion ]]> https://biorxiv.org/content/10.1101/2022.05.05.490800v1?rss=1 Ho, K.-H. Osipovich, A. B. Jayathilake, A. L. Magnuson, M. A. Gu, G. Kaverina, I. 2022-05-05 doi:10.1101/2022.05.05.490800 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Serine Deamination as a New Acid Resistance Mechanism in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2022.05.05.490856v1?rss=1 Wiebe, M. A. Brannon, J. R. Steiner, B. D. Bamidele, A. Schrimpe-Rutledge, A. C. Codreanu, S. G. Sherrod, S. D. McLean, J. Hadjifrangiskou, M. 2022-05-06 doi:10.1101/2022.05.05.490856 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Proteome Remodeling of the Eye Lens at 50 Years Identified with Data-Independent Acquisition ]]> https://biorxiv.org/content/10.1101/2022.05.06.490936v1?rss=1 Cantrell, L. S. Schey, K. L. 2022-05-06 doi:10.1101/2022.05.06.490936 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Morphogen Directed Coordination of GPCR Activity Promotes Primary Cilium Function for Downstream Signaling ]]> https://biorxiv.org/content/10.1101/2022.05.06.490951v1?rss=1 Ansari, S. S. Dillard, M. E. Zhang, Y. Austria, M. A. Boatwright, N. Shelton, E. L. Johnson, A. Young, B. M. Rankovic, Z. Robinson, C. G. Schuetz, J. D. Ogden, S. K. 2022-05-06 doi:10.1101/2022.05.06.490951 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Independent regulation of mtDNA quantity and quality resets the mitochondrial genome in C. elegans primordial germ cells ]]> https://biorxiv.org/content/10.1101/2022.05.06.490954v1?rss=1 Schwartz, A. Z. Tsyba, N. Abdu, Y. Patel, M. R. Nance, J. 2022-05-07 doi:10.1101/2022.05.06.490954 Cold Spring Harbor Laboratory Press 2022-05-07 <![CDATA[ Protrusion growth driven by myosin-generated force ]]> https://biorxiv.org/content/10.1101/2022.05.06.490961v1?rss=1 Fitz, G. N. Weck, M. L. Bodnya, C. Perkins, O. L. Tyska, M. J. 2022-05-07 doi:10.1101/2022.05.06.490961 Cold Spring Harbor Laboratory Press 2022-05-07 <![CDATA[ Mosaic patterns of selection in genomic regions associated with diverse human traits ]]> https://biorxiv.org/content/10.1101/2022.05.08.491080v1?rss=1 900 genome-wide association studies (GWASs) and 11 evolutionary measures of sequence constraint, population differentiation, and allele age while accounting for linkage disequilibrium, allele frequency, and other potential confounders. We demonstrate that this framework yields consistent results across GWASs with variable sample sizes, numbers of trait-associated SNPs, and analytical approaches. The resulting evolutionary atlas maps diverse signatures of selection on genomic regions associated with complex human traits on an unprecedented scale. We detected positive enrichment for sequence conservation among trait-associated regions for the majority of traits (>77% of 290 high power GWASs), which was most dominant in reproductive traits. Many traits also exhibited substantial enrichment for population differentiation and recent positive selection, especially among hair, skin, and pigmentation traits. In contrast, we detected widespread negative enrichment for balancing selection (51% GWASs) and no evidence of enrichment for selection signals in regions associated with late-onset Alzheimers disease. These results support a pervasive role for negative selection on regions of the human genome that contribute to variation in complex traits, but also demonstrate where diverse modes of selection have shaped trait-associated loci. This atlas of signatures of different modes of natural selection across the diversity of available GWASs will enable exploration of the relationship between the genetic architecture and selection in the human genome. ]]> Abraham, A. LaBella, A. L. Capra, J. A. Rokas, A. 2022-05-08 doi:10.1101/2022.05.08.491080 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ Non-Invasive monitoring of normal tissue radiation damage using quantitative ultrasound spectroscopy ]]> https://biorxiv.org/content/10.1101/2022.05.10.491268v1?rss=1 Rafat, M. El Kaffas, A. Swarnakar, A. Shostak, A. Graves, E. E. 2022-05-10 doi:10.1101/2022.05.10.491268 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Transretinal migration of astrocytes and brain/spinal cord-like cells arising from transplanted human retinal organoids. ]]> https://biorxiv.org/content/10.1101/2022.05.12.491655v1?rss=1 Liu, Y. Santiago, C. Sogunro, A. Konar, G. K. Hu, M.-W. McNally, M. M. Lu, Y. Li, Z. Agakishiev, D. Hadyniak, S. Hussey, K. Creamer, T. J. Orzolek, L. D. Teng, D. Qian, J. Jiang, Z. Johnston, R. J. Blackshaw, S. Singh, M. S. 2022-05-13 doi:10.1101/2022.05.12.491655 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ The 5-LOX/COX-2 cross-over metabolite, hemiketal E2, enhances VEGFR2 activation and promotes angiogenesis ]]> https://biorxiv.org/content/10.1101/2022.05.13.491890v1?rss=1 Nakashima, F. Gimenez-Bastida, J. A. Luis, P. B. Presley, S. H. Boer, R. E. Chiusa, M. Shibata, T. Sulikowski, G. A. Pozzi, A. Schneider, C. 2022-05-13 doi:10.1101/2022.05.13.491890 Cold Spring Harbor Laboratory Press 2022-05-13 <![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[ The ClpP Peptidase Forcefully Grips Protein Substrates ]]> https://biorxiv.org/content/10.1101/2022.05.14.491966v1?rss=1 Walker, S. D. Olivares, A. O. 2022-05-15 doi:10.1101/2022.05.14.491966 Cold Spring Harbor Laboratory Press 2022-05-15 <![CDATA[ A comprehensive investigation of statistical and machine learning approaches for predicting complex human diseases on genomic variants ]]> https://biorxiv.org/content/10.1101/2022.05.16.492056v1?rss=1 Wang, C. Zhang, J. Zhou, X. Zhang, L. 2022-05-18 doi:10.1101/2022.05.16.492056 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Mammary Tissue-Derived Extracellular Matrix Hydrogels Reveal the Role of the Irradiated Microenvironment in Breast Cancer Recurrence ]]> https://biorxiv.org/content/10.1101/2022.05.16.492117v1?rss=1 Zhu, T. Alves, S. M. Adamo, A. Wen, X. Corn, K. C. Shostak, A. Shaub, N. D. Hacker, B. C. D'Amore, A. Bardhan, R. Rafat, M. 2022-05-16 doi:10.1101/2022.05.16.492117 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ Radiation-Induced Metabolic Reprogramming of Fibroblasts Regulates the Breast Cancer Microenvironment ]]> https://biorxiv.org/content/10.1101/2022.05.17.492249v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@181680aorg.highwire.dtl.DTLVardef@d58a1forg.highwire.dtl.DTLVardef@15f04eforg.highwire.dtl.DTLVardef@13cf5f9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Corn, K. C. Britto, L. S. Ivanova, Y. I. Mohamed, Y. K. Rafat, M. 2022-05-18 doi:10.1101/2022.05.17.492249 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Substrate adhesion determines migration during mesenchymal cell condensation in chondrogenesis ]]> https://biorxiv.org/content/10.1101/2022.05.17.492260v1?rss=1 Casanellas, I. Jiang, H. David, C. M. Vida, Y. Perez-Inestrosa, E. Samitier, J. Lagunas, A. 2022-05-18 doi:10.1101/2022.05.17.492260 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Effect of pressure insole sampling frequency on peak force accuracy during running ]]> https://biorxiv.org/content/10.1101/2022.05.18.492523v1?rss=1 Elstub, L. J. Grohowski, L. M. Wolf, D. N. Owen, M. K. Noehren, B. Zelik, K. E. 2022-05-20 doi:10.1101/2022.05.18.492523 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Modeling clonal evolution and oncogenic dependency in vivo in the context of hematopoietic transformation ]]> https://biorxiv.org/content/10.1101/2022.05.18.492524v1?rss=1 Bowman, R. L. Dunbar, A. Mishra, T. Xiao, W. Waarts, M. R. Fernandez Maestre, I. Eisman, S. E. Cai, L. Cai, S. F. Sanchez Vela, P. Mowla, S. Martinez Benitez, A. R. Park, Y. Csete, I. S. Krishnan, A. Lee, D. Boorady, N. Potts, C. R. Jenkins, M. T. Carroll, M. P. Meyer, S. E. Miles, L. A. Ferrell, P. B. Trowbridge, J. J. Levine, R. L. 2022-05-18 doi:10.1101/2022.05.18.492524 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Resolution doubling in light-sheet microscopy via oblique plane structured illumination ]]> https://biorxiv.org/content/10.1101/2022.05.19.492671v1?rss=1 Chen, B. Chang, B.-J. Roudot, P. Zhou, F. Sapoznik, E. Marlar-Pavey, M. Hayes, J. Brown, P. Zeng, C.-W. Lambert, T. Friedman, J. R. Zhang, C.-L. Burnette, D. T. Shepherd, D. P. Dean, K. M. Fiolka, R. P. 2022-05-20 doi:10.1101/2022.05.19.492671 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Sphingolipid depletion inhibits bulk endocytosis while triggering selective clearance of the methionine transporter Mup1 ]]> https://biorxiv.org/content/10.1101/2022.05.20.492841v1?rss=1 Hepowit, N. L. Moon, B. J. Dickson, R. C. MacGurn, J. A. 2022-05-20 doi:10.1101/2022.05.20.492841 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Aspergillus fumigatus FhdA transcription factor is important for mitochondrial activity and codon usage regulation during the caspofungin paradoxical effect ]]> https://biorxiv.org/content/10.1101/2022.05.21.492902v1?rss=1 Colabardini, A. C. van Rhijn, N. LaBella, A. L. Valero, C. Wang, F. Dineen, L. Rokas, A. Goldman, G. H. 2022-05-25 doi:10.1101/2022.05.21.492902 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Structural characterization of a breast cancer-associated mutation in caveolin-1 ]]> https://biorxiv.org/content/10.1101/2022.05.23.493104v1?rss=1 Han, B. Gulsevin, A. Connolly, S. Wang, T. Porta, J. Tiwari, A. Deng, A. Chang, L. Peskova, Y. Mchaourab, H. Karakas, E. Ohi, M. D. Meiler, J. Kenworthy, A. K. 2022-05-23 doi:10.1101/2022.05.23.493104 Cold Spring Harbor Laboratory Press 2022-05-23 <![CDATA[ An interaction between betaprime-COP and the ArfGAP, Glo3, maintains post-Golgi cargo recycling ]]> https://biorxiv.org/content/10.1101/2022.05.25.493481v1?rss=1 Xie, B. Guillem, C. Jung, C. Kendall, A. K. Date, S. Best, J. T. Graham, T. R. Jackson, L. P. 2022-05-26 doi:10.1101/2022.05.25.493481 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ G protein βγ subunits bind to and inhibit the function of multiple Qa- and Qb,c-SNARE isoforms. ]]> https://biorxiv.org/content/10.1101/2022.05.30.494040v1?rss=1 Zurawski, Z. Huynh, S. Kaya, A. Hyde, K. Hamm, H. E. Alford, S. 2022-05-30 doi:10.1101/2022.05.30.494040 Cold Spring Harbor Laboratory Press 2022-05-30 <![CDATA[ Molecular simulations reveal a mechanism for enhanced allosteric coupling between voltage-sensor and pore domains in KCNQ1 explaining its activation by ML277 ]]> https://biorxiv.org/content/10.1101/2022.05.31.494217v1?rss=1 Kuenze, G. Vanoye, C. G. Wilkinson, M. C. Desai, R. R. Adusumilli, S. Sanders, C. R. George, A. L. Meiler, J. 2022-05-31 doi:10.1101/2022.05.31.494217 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Short superficial white matter and aging: a longitudinal multi-site study of 1,293 subjects and 2,711 sessions ]]> https://biorxiv.org/content/10.1101/2022.06.06.494720v1?rss=1 Schilling, K. G. Archer, D. B. Yeh, F.-C. Rheault, F. Cai, L. Y. Shafer, A. Resnick, S. M. Hohman, T. Jefferson, A. Anderson, A. W. Kang, H. Landman, B. A. 2022-06-06 doi:10.1101/2022.06.06.494720 Cold Spring Harbor Laboratory Press 2022-06-06 <![CDATA[ Feedforward attentional selection in sensory cortex ]]> https://biorxiv.org/content/10.1101/2022.06.06.495037v1?rss=1 Westerberg, J. A. Schall, J. D. Woodman, G. F. Maier, A. 2022-06-09 doi:10.1101/2022.06.06.495037 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Abasic site ring opening and DNA-protein crosslink reversal by the SRAP protein YedK ]]> https://biorxiv.org/content/10.1101/2022.06.07.495154v1?rss=1 Paulin, K. A. Cortez, D. Eichman, B. F. 2022-06-07 doi:10.1101/2022.06.07.495154 Cold Spring Harbor Laboratory Press 2022-06-07 <![CDATA[ Overall patterns of eye-specific retino-geniculo-cortical projections to layers III, IV and VI in primary visual cortex of the prosimian galago, and correlation with cytochrome oxidase blobs. ]]> https://biorxiv.org/content/10.1101/2022.06.08.495376v1?rss=1 Olavarria, J. F. Qi, H. Takahata, T. Kaas, J. H. 2022-06-12 doi:10.1101/2022.06.08.495376 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Along-tract quantification of resting-state BOLD hemodynamic response functions in white matter ]]> https://biorxiv.org/content/10.1101/2022.06.09.495555v1?rss=1 Schilling, K. Li, M. Rheault, F. Ding, Z. Anderson, A. W. Kang, H. Landman, B. A. Gore, J. C. 2022-06-12 doi:10.1101/2022.06.09.495555 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Reovirus efficiently reassorts genome segments during coinfection and superinfection ]]> https://biorxiv.org/content/10.1101/2022.06.09.495584v1?rss=1 Thoner, T. W. Meloy, M. M. Long, J. M. Diller, J. R. Slaughter, J. C. Ogden, K. M. 2022-06-10 doi:10.1101/2022.06.09.495584 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Lipid transport by Candida albicans Dnf2 is required for hyphal growth and virulence ]]> https://biorxiv.org/content/10.1101/2022.06.10.495726v1?rss=1 Jain, B. K. Wagner, A. S. Reynolds, T. B. Graham, T. R. 2022-06-11 doi:10.1101/2022.06.10.495726 Cold Spring Harbor Laboratory Press 2022-06-11 <![CDATA[ Hotspot of de novo telomere addition stabilizes linear amplicons in yeast grown in sulfate-limiting conditions ]]> https://biorxiv.org/content/10.1101/2022.06.12.495855v1?rss=1 Hoerr, R. E. Eng, A. Payen, C. DiRienzi, S. C. Raghuraman, M. K. Dunham, M. J. Brewer, B. J. Friedman, K. L. 2022-06-15 doi:10.1101/2022.06.12.495855 Cold Spring Harbor Laboratory Press 2022-06-15 <![CDATA[ Trem2 deficiency does not worsen metabolic function in diet-induced obese mice ]]> https://biorxiv.org/content/10.1101/2022.06.13.495953v1?rss=1 Winn, N. C. Wolf, E. M. Garcia, J. N. Hasty, A. H. 2022-06-16 doi:10.1101/2022.06.13.495953 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ SERCA2 regulates proinsulin processing and processing enzyme maturation in the pancreatic β cell ]]> https://biorxiv.org/content/10.1101/2022.06.13.495980v1?rss=1 Iida, H. Kono, T. M. Lee, C.-C. Krishnan, P. Arvin, M. C. Weaver, S. A. Jarvela, T. S. Bone, R. N. Tong, X. Arvan, P. Lindberg, I. Evans-Molina, C. 2022-06-17 doi:10.1101/2022.06.13.495980 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Correlations between behavior and neuronal responses in the cochlear nucleus (CN) and inferior colliculus (IC) of behaving monkeys ]]> https://biorxiv.org/content/10.1101/2022.06.15.496306v1?rss=1 Mackey, C. A. Dylla, M. Bohlen, P. Hrnicek, A. Mayfield, J. M. Ramachandran, R. 2022-06-17 doi:10.1101/2022.06.15.496306 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Schedule-dependent production of stereotyped sequences of actions ]]> https://biorxiv.org/content/10.1101/2022.06.16.496442v1?rss=1 Follman, E. G. Chevee, M. Kim, C. J. Johnson, A. R. Tat, J. Calipari, E. S. 2022-06-17 doi:10.1101/2022.06.16.496442 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Theropod dinosaurs had primate-like numbers of telencephalic neurons ]]> https://biorxiv.org/content/10.1101/2022.06.20.496834v1?rss=1 Herculano-Houzel, S. 2022-06-21 doi:10.1101/2022.06.20.496834 Cold Spring Harbor Laboratory Press 2022-06-21 <![CDATA[ Mammals, birds and non-avian reptiles have signature proportions of numbers of neurons across their brain structures: Numbers of neurons increased differently with endothermy in birds and mammals ]]> https://biorxiv.org/content/10.1101/2022.06.20.496835v1?rss=1 Herculano-Houzel, S. 2022-06-21 doi:10.1101/2022.06.20.496835 Cold Spring Harbor Laboratory Press 2022-06-21 <![CDATA[ The Interictal Suppression Hypothesis in Focal Epilepsy: Electrographic and Structural Evaluation ]]> https://biorxiv.org/content/10.1101/2022.06.27.497765v1?rss=1 Johnson, G. W. Doss, D. J. Morgan, V. L. Shless, J. S. Paulo, D. L. Kang, H. Bick, S. K. Roberson, S. W. Wallace, M. T. Englot, D. J. 2022-06-30 doi:10.1101/2022.06.27.497765 Cold Spring Harbor Laboratory Press 2022-06-30 <![CDATA[ Nucleotide excision repair is universally mutagenic and transcription-associated ]]> https://biorxiv.org/content/10.1101/2022.06.28.497968v1?rss=1 Carvajal-Garcia, J. Samadpour, A. N. Viera, A. J. H. Merrikh, H. 2022-06-28 doi:10.1101/2022.06.28.497968 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ IL-15 superagonist N-803 enhances IFNγ production and alters the trafficking of MAIT cells in SIV+ macaques ]]> https://biorxiv.org/content/10.1101/2022.06.28.498052v1?rss=1 Ellis-Connell, A. Balgeman, A. J. Kannal, N. M. Hansen Chaimson, K. Batchenkova, A. Safrit, J. T. O'Connor, S. L. 2022-07-01 doi:10.1101/2022.06.28.498052 Cold Spring Harbor Laboratory Press 2022-07-01 <![CDATA[ DNA methylation is a widespread mechanism of light-induced circadian clock period plasticity ]]> https://biorxiv.org/content/10.1101/2022.06.30.498269v1?rss=1 Kim, S. McMahon, D. G. 2022-07-02 doi:10.1101/2022.06.30.498269 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Weight cycling induces innate immune memory in adipose tissue macrophages ]]> https://biorxiv.org/content/10.1101/2022.07.02.498553v1?rss=1 Caslin, H. L. Cottam, M. A. Pinon, J. M. Boney, L. Y. Hasty, A. H. 2022-07-03 doi:10.1101/2022.07.02.498553 Cold Spring Harbor Laboratory Press 2022-07-03 <![CDATA[ Deep learning segmentation of the nucleus basalis of Meynert on 3T MRI ]]> https://biorxiv.org/content/10.1101/2022.07.02.498556v1?rss=1 Doss, D. J. Johnson, G. W. Narasimhan, S. Jiang, J. W. Gonzalez, H. F. J. Paulo, D. L. Lucas, A. Davis, K. A. Chang, C. Morgan, V. L. Constantinidis, C. Dawant, B. M. Englot, D. J. 2022-07-05 doi:10.1101/2022.07.02.498556 Cold Spring Harbor Laboratory Press 2022-07-05 <![CDATA[ Distinct Tumor Necrosis Factor Alpha Receptors Dictate Stem Cell Fitness Versus Lineage Output in Dnmt3a-Mutant Clonal Hematopoiesis ]]> https://biorxiv.org/content/10.1101/2022.07.03.498502v1?rss=1 SanMiguel, J. M. Eudy, E. Loberg, M. A. Young, K. A. Mistry, J. J. Schwartz, L. S. Stearns, T. Challen, G. A. Trowbridge, J. J. 2022-07-03 doi:10.1101/2022.07.03.498502 Cold Spring Harbor Laboratory Press 2022-07-03 <![CDATA[ Corticostriatal Beta Power Changes Associated with Cognitive Function in Parkinsons Disease ]]> https://biorxiv.org/content/10.1101/2022.07.07.499165v1?rss=1 Paulo, D. L. Qian, H. Subramanian, D. Johnson, G. W. Hett, K. Kao, C. Roy, N. Dhima, K. Claassen, D. O. Bick, S. K. 2022-07-10 doi:10.1101/2022.07.07.499165 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Disruption of flour beetle microbiota limits experimentally evolved immune priming response, but not pathogen resistance ]]> https://biorxiv.org/content/10.1101/2022.07.11.499528v1?rss=1 Prakash, A. Agashe, D. Khan, I. 2022-07-12 doi:10.1101/2022.07.11.499528 Cold Spring Harbor Laboratory Press 2022-07-12 <![CDATA[ Template-free prediction of a new protein fold and oligomeric assembly by Alphafold2 ]]> https://biorxiv.org/content/10.1101/2022.07.12.499809v1?rss=1 Gulsevin, A. Han, B. Porta, J. C. Mchaourab, H. Meiler, J. Kenworthy, A. K. 2022-07-13 doi:10.1101/2022.07.12.499809 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Genomic and phenotypic trait variation of the opportunistic human pathogen Aspergillus flavus and its non-pathogenic close relatives ]]> https://biorxiv.org/content/10.1101/2022.07.12.499845v1?rss=1 Hatmaker, E. A. Rangel-Grimaldo, M. Raja, H. A. Knowles, S. L. Pourhadi, H. Fuller, K. Adams, E. M. Lightfoot, J. D. Bastos, R. Goldman, G. H. Oberlies, N. H. Rokas, A. 2022-07-13 doi:10.1101/2022.07.12.499845 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Antigenic mapping and functional characterization of human New World hantavirus neutralizing antibodies ]]> https://biorxiv.org/content/10.1101/2022.07.19.500579v1?rss=1 Engdahl, T. B. Binshtein, E. Brocato, R. L. Kuzmina, N. A. A. Principe, L. M. Kwilas, S. A. Kim, R. K. Chapman, N. S. Porter, M. S. Guardado-Calvo, P. Rey, F. A. Handal, L. S. Diaz, S. M. Zagol-Ikapitte, I. A. Reidy, J. X. Trivette, A. Bukreyev, A. Hooper, J. W. Crowe, J. E. 2022-07-20 doi:10.1101/2022.07.19.500579 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Superficial white matter across the lifespan: volume, thickness, change, and relationship with cortical features ]]> https://biorxiv.org/content/10.1101/2022.07.20.500818v1?rss=1 Schilling, K. Archer, D. B. Rheault, F. Lyu, I. Huo, Y. Cai, L. Y. Bunge, S. Weiner, K. S. Gore, J. C. Anderson, A. W. Landman, B. A. 2022-07-21 doi:10.1101/2022.07.20.500818 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Unified Tumor Growth Mechanisms from Multimodel Inference and Dataset Integration ]]> https://biorxiv.org/content/10.1101/2022.07.22.500696v1?rss=1 Beik, S. P. Harris, L. A. Kochen, M. A. Sage, J. Quaranta, V. Lopez, C. F. 2022-07-23 doi:10.1101/2022.07.22.500696 Cold Spring Harbor Laboratory Press 2022-07-23 <![CDATA[ From multi-omics data to the cancer druggable genediscovery: a novel machine learning-based approach ]]> https://biorxiv.org/content/10.1101/2022.07.24.501277v1?rss=1 Yang, H. Gan, L. Chen, R. Li, D. Zhang, J. Wang, Z. 2022-07-24 doi:10.1101/2022.07.24.501277 Cold Spring Harbor Laboratory Press 2022-07-24 <![CDATA[ Irradiated Mammary Spheroids Elucidate Mechanisms of Macrophage-Mediated Breast Cancer Recurrence ]]> https://biorxiv.org/content/10.1101/2022.07.24.501296v1?rss=1 Hacker, B. C. Herman, D. C. Lin, E. J. Questell, A. M. Hedges, R. J. Rafat, M. 2022-07-24 doi:10.1101/2022.07.24.501296 Cold Spring Harbor Laboratory Press 2022-07-24 <![CDATA[ Female investment in terminal reproduction or somatic maintenance depends on infection dose ]]> https://biorxiv.org/content/10.1101/2022.07.25.501224v1?rss=1 Schulz, N. K. E. Stewart, C. M. Tate, A. T. 2022-07-25 doi:10.1101/2022.07.25.501224 Cold Spring Harbor Laboratory Press 2022-07-25 <![CDATA[ Structure of a LRRC8 chimera with physiologically relevant properties reveals heptameric assembly and pore-blocking lipids ]]> https://biorxiv.org/content/10.1101/2022.07.28.501913v1?rss=1 Takahashi, H. Yamada, T. Denton, J. S. Strange, K. Karakas, E. 2022-07-28 doi:10.1101/2022.07.28.501913 Cold Spring Harbor Laboratory Press 2022-07-28 <![CDATA[ Pleiotropy promotes the evolution of inducible immune responses in a model of host-pathogen coevolution ]]> https://biorxiv.org/content/10.1101/2022.08.02.502467v1?rss=1 Martin, R. A. Tate, A. T. 2022-08-03 doi:10.1101/2022.08.02.502467 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Psychometric and subcortical neurometric measures of temporal discrimination in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2022.08.05.502987v1?rss=1 Mackey, C. A. Hauser, S. Schoenhaut, A. M. Temghare, N. Ramachandran, R. 2022-08-06 doi:10.1101/2022.08.05.502987 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ Targeting Epsins to Inhibit FGF Signaling while Potentiating TGF-β Signaling Constrains Endothelial-to-Mesenchymal-Transition in Atherosclerosis ]]> https://biorxiv.org/content/10.1101/2022.08.09.503324v1?rss=1 Dong, Y. Wang, B. Du, M. Zhu, B. Cui, K. Chan, K. Cowan, D. B. Bhattacharjee, S. Shan, D. Wong, S. Bischoff, J. Linton, M. F. Chen, H. 2022-08-09 doi:10.1101/2022.08.09.503324 Cold Spring Harbor Laboratory Press 2022-08-09 <![CDATA[ Targeting Epsins by nanotherapy regulates lipid metabolism and promotes 1 ABCG1-mediated cholesterol efflux to fortify atheroma regression ]]> https://biorxiv.org/content/10.1101/2022.08.09.503334v1?rss=1 Cui, K. Gao, X. Wang, B. Wu, H. Dong, Y. Xiao, Y. Jiang, X. Malovichko, M. V. Li, K. Chan, K. Shan, D. Peng, Q. Lu, Y. W. Zhu, B. Wong, S. Cowan, D. B. Linton, M. F. Srivastava, S. Shi, J. Chen, K. F. Chen, H. 2022-08-09 doi:10.1101/2022.08.09.503334 Cold Spring Harbor Laboratory Press 2022-08-09 <![CDATA[ The high-resolution in vivo measurement of replication fork velocity and pausing ]]> https://biorxiv.org/content/10.1101/2022.08.13.503874v1?rss=1 Huang, D. Johnson, A. E. Sim, B. S. Lo, T. Merrikh, H. Wiggins, P. A. 2022-08-14 doi:10.1101/2022.08.13.503874 Cold Spring Harbor Laboratory Press 2022-08-14 <![CDATA[ Cellular Mechanisms Underlying Embryonic Retinal Waves ]]> https://biorxiv.org/content/10.1101/2022.08.14.503889v1?rss=1 Voufo, C. Chen, A. Q. Smith, B. E. Feller, M. B. Tiriac, A. 2022-08-15 doi:10.1101/2022.08.14.503889 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Helicobacter pylori vacuolating cytotoxin A exploits human endosomes for intracellular activation ]]> https://biorxiv.org/content/10.1101/2022.08.22.504206v1?rss=1 Palframan, S. L. Mahmud, M. T. Tan, K. S. Grinter, R. Xin, V. Dunstan, R. A. Micati, D. Kerr, G. McMurrick, P. J. Smith, A. Abud, H. Nguyen, T. N. Lazarou, M. Kleifeld, O. Lithgow, T. Cover, T. L. Gabriel, K. Gorrell, R. J. Kwok, T. 2022-08-23 doi:10.1101/2022.08.22.504206 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ Mechanistic Deep Learning Framework on Cell Traits Derived from Single-Cell Mass Cytometry Data ]]> https://biorxiv.org/content/10.1101/2022.08.22.504669v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@10e35cborg.highwire.dtl.DTLVardef@1edc8ecorg.highwire.dtl.DTLVardef@220726org.highwire.dtl.DTLVardef@35916_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wang, B. Zinkel, S. S. Gamazon, E. R. 2022-08-29 doi:10.1101/2022.08.22.504669 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Mucosal gene expression in response to SARS-CoV-2 is associated with early viral load. ]]> https://biorxiv.org/content/10.1101/2022.08.23.504908v1?rss=1 80% of the genome from 85% of the samples from symptomatic COVID-19 adults. The respiratory virome was dominated by SARS-CoV-2, with limited co-detection of common respiratory viruses i.e., only the human Rhinovirus (HRV) being identified in 6% of the samples. We observed a significant positive correlation between SARS-CoV-2 viral load and interferon signaling (OAS2, OAS3, IFIT1, UPS18, ISG15, ISG20, IFITM1, and OASL), chemokine signaling (CXCL10 and CXCL11), and adaptive immune system (IFITM1, CD300E, and SIGLEC1) genes in symptomatic, mild-to-moderate COVID-19 adults, when adjusted for age, sex and race. Interestingly, the expression levels of most of these genes plateaued at a CT value of ~25. Overall, our data shows that early nasal mucosal immune response to SARS-CoV-2 infection is viral load dependent, which potentially could modify COVID-19 outcomes. AUTHOR SUMMARYSeveral prior studies have shown that SARS-CoV-2 viral load can predict the likelihood of disease spread and severity. A higher detectable SARS-CoV-2 plasma viral load was associated with worse respiratory disease severity. However, the relationship between SARS-CoV-2 viral load and airway mucosal gene expression and immune response remains elusive. We profiled the nasal mucosal transcriptome from nasal samples collected from adults infected with SARS-CoV-2 during Spring 2020 with mild-to-moderate symptoms using a comprehensive metatranscriptomics method. We observed a positive correlation between SARS-CoV-2 viral load with interferon signaling, chemokine signaling, and adaptive immune system in adults with COVID-19. Our data suggest that early nasal mucosal immune response to SARS-CoV-2 infection was viral load-dependent and may modify COVID-19 outcomes. ]]> Rajagopala, S. V. Strickland, B. A. Pakala, S. B. Kimura, K. S. Shilts, M. H. Rosas-Salazar, C. Brown, H. M. Freeman, M. H. Wessinger, B. C. Gupta, V. Phillips, E. Mallal, S. A. Turner, J. H. Das, S. R. 2022-08-23 doi:10.1101/2022.08.23.504908 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ MyD88-Dependent Signaling Drives Toll-Like Receptor-Induced Trained Immunity in Macrophages ]]> https://biorxiv.org/content/10.1101/2022.08.23.504963v1?rss=1 Owen, A. M. Luan, L. Burelbach, K. R. McBride, M. A. Stothers, C. L. Boykin, O. A. Sivanesam, K. Schaedel, J. F. Patil, T. K. Wang, J. Hernandez, A. Patil, N. K. Sherwood, E. R. Bohannon, J. K. 2022-08-24 doi:10.1101/2022.08.23.504963 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi ]]> https://biorxiv.org/content/10.1101/2022.08.23.505037v1?rss=1 Hugaboom, M. Hatmaker, E. A. LaBella, A. L. Rokas, A. 2022-08-26 doi:10.1101/2022.08.23.505037 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ MicroRNA-218 instructs proper assembly of hippocampal networks ]]> https://biorxiv.org/content/10.1101/2022.08.24.505085v1?rss=1 Taylor, S. Kobayashi, M. Vilella, A. Tiwari, D. Zolboot, N. Hartzell, A. Girgiss, C. Abaci, Y. De Sanctis, C. Bellenchi, G. C. Darnell, R. B. Gross, C. Zoli, M. Berg, D. K. Lippi, G. 2022-08-25 doi:10.1101/2022.08.24.505085 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Interpretable Chirality-Aware Graph Neural Network forQuantitative Structure Activity Relationship Modeling in Drug Discovery ]]> https://biorxiv.org/content/10.1101/2022.08.24.505155v1?rss=1 Liu, Y. Wang, Y. Vu, O. T. Moretti, R. Bodenheimer, B. Meiler, J. Derr, T. 2022-08-26 doi:10.1101/2022.08.24.505155 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ A mathematical model of calcium signals around laser-induced epithelial wounds ]]> https://biorxiv.org/content/10.1101/2022.08.24.505161v1?rss=1 Stevens, A. C. O'Connor, J. T. Pumford, A. D. Page-McCaw, A. Hutson, M. S. 2022-08-25 doi:10.1101/2022.08.24.505161 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Multiple polarity kinases inhibit phase separation of F-BAR protein Cdc15 and antagonize cytokinetic ring assembly in fission yeast ]]> https://biorxiv.org/content/10.1101/2022.08.26.505417v1?rss=1 Bhattacharjee, R. Hall, A. Mangione, M. C. Igarashi, M. G. Roberts-Galbraith, R. H. Chen, J.-S. Vavylonis, D. Gould, K. 2022-08-26 doi:10.1101/2022.08.26.505417 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ FAVOR: Functional Annotation of Variants Online Resource and Annotator for Variation across the Human Genome ]]> https://biorxiv.org/content/10.1101/2022.08.28.505582v1?rss=1 Zhou, H. Arapoglou, T. Li, X. Li, Z. Zheng, X. Moore, J. E. Asok, A. Kumar, S. Blue, E. E. Buyske, S. Cox, N. Felsenfeld, A. Gerstein, M. Kenny, E. Li, B. Matise, T. Philippakis, A. Rehm, H. Sofia, H. J. Neale, B. Snyder, G. Weng, Z. Sunyaev, S. Lin, X. 2022-08-29 doi:10.1101/2022.08.28.505582 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Alignment, Segmentation and Neighborhood Analysis in Cyclic Immunohistochemistry Data Using CASSATT ]]> https://biorxiv.org/content/10.1101/2022.08.29.504975v1?rss=1 Brockman, A. Khurana, R. Bartkowiak, T. Thomas, P. L. Sivagnanam, S. Betts, C. B. Coussens, L. M. Lovly, C. Irish, J. M. Ihrie, R. A. 2022-08-29 doi:10.1101/2022.08.29.504975 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Cardiomyocyte alpha-1A adrenergic receptors mitigate post-infarct remodeling and mortality by constraining necroptosis ]]> https://biorxiv.org/content/10.1101/2022.08.29.505687v1?rss=1 Zhang, J. Sandroni, P. B. Huang, W. Oswalt, L. Smith, A. J. Ash, T. Lee, S.-H. Shih, Y.-Y. I. Huang, H.-Y. S. Myagmar, B.-E. Schisler, J. C. Jensen, B. C. 2022-08-29 doi:10.1101/2022.08.29.505687 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Exercise performance is not improved in mice with skeletal muscle deletion of natriuretic peptide clearance receptor ]]> https://biorxiv.org/content/10.1101/2022.08.30.505918v1?rss=1 Jia, B. Hasse, A. Shi, F. Collins, S. 2022-09-02 doi:10.1101/2022.08.30.505918 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Porcn is essential for growth and invagination of the mammalian optic cup ]]> https://biorxiv.org/content/10.1101/2022.09.01.506058v1?rss=1 Fuhrmann, S. Ramirez, S. Abouda, M. M. Campbell, C. D. 2022-09-02 doi:10.1101/2022.09.01.506058 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Cardiovascular Hemodynamics in Mice with Tumor Necrosis Factor Receptor - Associated Factor 2 Mediated Cytoprotection in the Heart ]]> https://biorxiv.org/content/10.1101/2022.09.03.506447v1?rss=1 Marshall, A. G. Neikirk, K. Vue, Z. Beasley, H. K. Garza-Lopez, E. Vang, L. Barongan, T. Evans, Z. Anudokem, J. Pham, T. T. Gomez, J. A. Exil, V. Dai, D.-F. Entman, M. L. Taffet, G. E. Hinton, A. Reddy, A. K. 2022-09-06 doi:10.1101/2022.09.03.506447 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ Time-Resolved Interactome Profiling Deconvolutes Secretory Protein Quality Control Dynamics ]]> https://biorxiv.org/content/10.1101/2022.09.04.506558v1?rss=1 Wright, M. T. Timalsina, B. Lopez, V. A. G. Plate, L. 2022-09-05 doi:10.1101/2022.09.04.506558 Cold Spring Harbor Laboratory Press 2022-09-05 <![CDATA[ NUDT6, the Antisense Protein of FGF2 Gene, Plays a Depressogenic Role by Promoting Inflammation and Suppressing Neurogenesis without Altering FGF2 Signaling ]]> https://biorxiv.org/content/10.1101/2022.09.05.506638v1?rss=1 Uzay, B. Hokelekli, F. O. Yilmaz, M. Esen, E. C. Basar, K. Bahadir-Varol, A. Ayhan, Y. Dalkara, T. Eren-Kocak, E. 2022-09-06 doi:10.1101/2022.09.05.506638 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ Discovery of an alternate mechanism for the inhibition of particulate guanylyl cyclases by the natriuretic peptide 'clearance' receptor ]]> https://biorxiv.org/content/10.1101/2022.09.06.506848v1?rss=1 Liu, D. Ceddia, R. P. Zhang, W. Fang, H. Collins, S. P. 2022-09-07 doi:10.1101/2022.09.06.506848 Cold Spring Harbor Laboratory Press 2022-09-07 <![CDATA[ Analysis of transcriptome datasets reveals involvement of epithelial-mesenchymal transition genes in small cell lung cancer phenotypic plasticity ]]> https://biorxiv.org/content/10.1101/2022.09.09.507376v1?rss=1 Groves, S. M. Panchy, N. Tyson, D. R. Harris, L. A. Quaranta, V. Hong, T. 2022-09-11 doi:10.1101/2022.09.09.507376 Cold Spring Harbor Laboratory Press 2022-09-11 <![CDATA[ Modeling effects of inter-group contact on links between population size and cultural complexity ]]> https://biorxiv.org/content/10.1101/2022.09.11.507470v1?rss=1 Ben-Oren, Y. Strassberg, S. S. Hovers, E. Kolodny, O. Creanza, N. 2022-09-13 doi:10.1101/2022.09.11.507470 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Functional impairment of the Lateral Geniculate Nucleus in Multiple Sclerosis ]]> https://biorxiv.org/content/10.1101/2022.09.12.506825v1?rss=1 Sardaripour, N. Asadi, M. Moghaddam, H. A. Khadem, A. Rajimehr, R. 2022-09-14 doi:10.1101/2022.09.12.506825 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ OPA1 Downregulation in Skeletal Muscle Induces MERC formation in an ATF4-Dependent Manner ]]> https://biorxiv.org/content/10.1101/2022.09.12.507669v1?rss=1 Hinton, A. Katti, P. Mungai, M. Hall, D. Koval, O. Shao, J. Vue, Z. Christensen, T. A. Lopez, E. G. Rostami, R. Neikirk, K. Lam, J. Alghanem, A. Ponce, J. Hicsasmaz, I. Streeter, J. Schickling, B. Bacevac, S. Grueter, C. Marshall, A. Beasley, H. K. DoKoo, Y. Bodine, S. Nava, N. G. R. Quintana, A. Trushina, E. Weatherford, E. Murray, S. A. Salisbury, J. Song, L.-S. Grumbach, I. Exil, V. Pereira, R. O. Glancy, B. Abel, E. D. 2022-09-15 doi:10.1101/2022.09.12.507669 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ SynBOLD-DisCo: Synthetic BOLD images for distortion correction of fMRI without additional calibration scans ]]> https://biorxiv.org/content/10.1101/2022.09.13.507794v1?rss=1 Yu, T. Cai, L. Y. Morgan, V. L. Goodale, S. E. Englot, D. J. Chang, C. E. Landman, B. A. Schilling, K. G. 2022-09-15 doi:10.1101/2022.09.13.507794 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Genetic Disruption of System xc- Mediated Glutamate Release from Astrocytes Increases Negative-Outcome Behaviors While Preserving Basic Brain Function in Rat ]]> https://biorxiv.org/content/10.1101/2022.09.14.504799v1?rss=1 Hess, E. M. Kassel, S. N. Simandl, G. Raddatz, N. J. Hurley, M. M. Grzybowski, M. Klotz, J. Geurts, A. Liu, Q.-s. Choi, S. Twining, R. C. Baker, D. 2022-09-17 doi:10.1101/2022.09.14.504799 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Differences in self-reported benefits for student-artist versus faculty experiences in a virtual artist-in-residence program. ]]> https://biorxiv.org/content/10.1101/2022.09.14.507965v1?rss=1 Cuevas, S. Liu, Q. Qian, H. Joffe, M. E. Calvitti, K. Schladt, M. Skaar, E. P. Oliver, K. H. 2022-09-17 doi:10.1101/2022.09.14.507965 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Pseudocontact shift NMR data obtained from a non-canonical amino acid-linked lanthanide tag improves integral membrane protein structure prediction ]]> https://biorxiv.org/content/10.1101/2022.09.14.507970v1?rss=1 Ledwitch, K. V. Kuenze, G. Larochelle, K. Okwei, E. N. N. Pankewitz, L. Ganguly, S. Darling, H. L. Coin, I. Meiler, J. 2022-09-15 doi:10.1101/2022.09.14.507970 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Illuminating histidine phosphorylation in the pancreatic tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2022.09.15.508158v1?rss=1 Hunter, T. Wahl, G. Lytle, N. DelGiorno, K. E. Shi, Y. Kaech, S. Naeem, R. Luhtala, N. Hollingsworth, M. 2022-09-17 doi:10.1101/2022.09.15.508158 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ The histone chaperone NASP maintains H3-H4 reservoirs in the early Drosophila embryo ]]> https://biorxiv.org/content/10.1101/2022.09.16.508322v1?rss=1 Tirgar, R. Davies, J. Plate, L. Nordman, J. T. 2022-09-18 doi:10.1101/2022.09.16.508322 Cold Spring Harbor Laboratory Press 2022-09-18 <![CDATA[ Prefrontal neuronal dynamics in the absence of task execution ]]> https://biorxiv.org/content/10.1101/2022.09.16.508324v1?rss=1 Pu, S. Dang, W. Qi, X. Constantinidis, C. 2022-09-19 doi:10.1101/2022.09.16.508324 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Genetic, clinical underpinnings of subtle early brain change along Alzheimer's dimensions ]]> https://biorxiv.org/content/10.1101/2022.09.16.508329v1?rss=1 WEN, J. Yang, Z. Nasrallah, I. Cui, Y. Erus, G. Srinivasan, D. Abdulkadir, A. Mamourian, E. Hwang, G. Singh, A. Bergman, M. Bao, J. Varol, E. Zhou, Z. Boquet-Pujadas, A. Chen, J. Toga, A. W. Saykin, A. J. Hohman, T. Thompson, P. Villeneuve, S. Gollub, R. Sotiras, A. Wittfeld, K. Grabe, H. Tosun, D. Bilgel, M. An, Y. Marcus, D. LaMontagne, P. J. Heckbert, S. Austin, T. Launer, L. Espeland, M. Masters, C. Maruff, P. Fripp, J. Johnson, S. C. Morris, j. Albert, M. Nick, R. Resnick, S. M. Ferrucci, L. Fan, Y. Mohamad, H. Wolk, D. Shen, L. Shou, H. Dav 2022-09-19 doi:10.1101/2022.09.16.508329 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ CD73 generated extracellular adenosine promotes resolution of neutrophil-mediated tissue injury and restrains metaplasia in pancreatitis ]]> https://biorxiv.org/content/10.1101/2022.09.17.508367v1?rss=1 View larger version (61K): org.highwire.dtl.DTLVardef@ecae66org.highwire.dtl.DTLVardef@adea9dorg.highwire.dtl.DTLVardef@5f50corg.highwire.dtl.DTLVardef@11b2256_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> O'Brien, B. J. Faraoni, E. Y. Strickland, L. N. Ma, Z. Mota, V. Y. Mota, S. Y. Chen, X. Mills, T. Eltzschig, H. K. DelGiorno, K. E. Bailey-Lundberg, J. M. 2022-09-17 doi:10.1101/2022.09.17.508367 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Nanoparticle-mediated Targeting of the Fusion Gene RUNX1/ETO in t(8;21)-positive Acute Myeloid Leukaemia ]]> https://biorxiv.org/content/10.1101/2022.09.21.508893v1?rss=1 Issa, H. Swart, L. Rasouli, M. Ashtiani, M. Nakjang, S. jyotsana, n. Schuschel, K. Heuser, M. Blair, H. Heidenreich, O. 2022-09-21 doi:10.1101/2022.09.21.508893 Cold Spring Harbor Laboratory Press 2022-09-21 <![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[ CLASP2 facilitates dynamic actin filament organization along the microtubule lattice ]]> https://biorxiv.org/content/10.1101/2022.09.22.509100v1?rss=1 Rodgers, N. C. Lawrence, E. J. Sawant, A. V. Efimova, N. Gonzalez-Vasquez, G. Hickman, T. T. Kaverina, I. Zanic, M. 2022-09-23 doi:10.1101/2022.09.22.509100 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Subtle cultural boundaries reinforce genetic structure in England ]]> https://biorxiv.org/content/10.1101/2022.09.23.509228v1?rss=1 Pichkar, Y. Creanza, N. 2022-09-23 doi:10.1101/2022.09.23.509228 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Acquired secondary HER2 mutations enhance HER2/MAPK signaling and promote resistance to HER2 kinase inhibition in HER2-mutant breast cancer ]]> https://biorxiv.org/content/10.1101/2022.09.23.509246v1?rss=1 Marin, A. Mamun, A. A. Akamatsu, H. Ye, D. Sudhan, d. R. Brown, B. P. Eli, L. Marcelain, K. Meiler, J. Arteaga, C. L. Hanker, A. B. 2022-09-25 doi:10.1101/2022.09.23.509246 Cold Spring Harbor Laboratory Press 2022-09-25 <![CDATA[ The Effect of P2X7 Antagonism on Subcortical Spread of Optogenetically-Triggered Cortical Spreading Depression and Neuroinflammation ]]> https://biorxiv.org/content/10.1101/2022.09.26.509535v1?rss=1 Uzay, B. Demir, B. D. Ozcan, S. Y. Kocak, E. E. Yemisci, M. Ozdemir, Y. G. Dalkara, T. Karatas, H. 2022-09-27 doi:10.1101/2022.09.26.509535 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ A small molecule that inhibits the evolution of antibiotic resistance ]]> https://biorxiv.org/content/10.1101/2022.09.26.509600v1?rss=1 Johnson, A. E. Bracey, H. Viera, A. J. H. Carvajal-Garcia, J. Simsek, E. N. Kim, K. Merrikh, H. 2022-09-26 doi:10.1101/2022.09.26.509600 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Biochemical identification of a nuclear coactivator protein required for AtrR-dependent gene regulation in Aspergillus fumigatus ]]> https://biorxiv.org/content/10.1101/2022.09.26.509624v1?rss=1 Paul, S. Ror, S. McDonald, W. H. Moye-Rowley, W. S. 2022-09-28 doi:10.1101/2022.09.26.509624 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics ]]> https://biorxiv.org/content/10.1101/2022.09.27.509640v1?rss=1 Vuckovic, Z. Wang, J. Pham, V. Mobbs, J. I. Belousoff, M. J. Bhattarai, A. Burger, W. A. C. Thompson, G. Yeasmin, M. Leach, K. van der Westhuizen, E. T. Khajehali, E. Liang, Y.-L. Glukhova, A. Wootten, D. Lindsley, C. W. Tobin, A. Sexton, P. Danev, R. Valant, C. Miao, Y. Christopoulos, A. Thal, D. M. 2022-09-28 doi:10.1101/2022.09.27.509640 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Active antennal movements in Drosophila tune wind encoding ]]> https://biorxiv.org/content/10.1101/2022.09.30.510392v1?rss=1 Suver, M. P. Medina, A. M. Nagel, K. I. 2022-10-02 doi:10.1101/2022.09.30.510392 Cold Spring Harbor Laboratory Press 2022-10-02 <![CDATA[ A ubiquitous spectrolaminar motif of local field potential power across the primate cortex ]]> https://biorxiv.org/content/10.1101/2022.09.30.510398v1?rss=1 Mendoza-Halliday, D. Major, A. J. Lee, N. Lichtenfeld, M. Carlson, B. Mitchell, B. Meng, P. D. Xiong, Y. Westerberg, J. A. Maier, A. Desimone, R. Miller, E. K. Bastos, A. M. 2022-10-03 doi:10.1101/2022.09.30.510398 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ Cortical Contributions to Medial Frontal β-Bursts during Executive Control ]]> https://biorxiv.org/content/10.1101/2022.10.04.510901v1?rss=1 Errington, S. P. Westerberg, J. A. Woodman, G. F. Schall, J. D. 2022-10-07 doi:10.1101/2022.10.04.510901 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ M1 selective muscarinic allosteric modulation enhances cognitive flexibility and effective salience in nonhuman primates ]]> https://biorxiv.org/content/10.1101/2022.10.05.511029v1?rss=1 Hassani, S.-A. A. Neumann, A. Russell, J. Jones, C. K. Womelsdorf, T. 2022-10-07 doi:10.1101/2022.10.05.511029 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Preparing future STEM faculty nationwide through flexible teaching professional development ]]> https://biorxiv.org/content/10.1101/2022.10.06.511090v1?rss=1 Goldberg, B. Bruff, D. Greenler, R. Barnicle, K. Green, N. Campbell, L. Laursen, S. Ford, M. Serafini, A. Mack, C. Carley, T. Maimone, C. Campa, H. 2022-10-11 doi:10.1101/2022.10.06.511090 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Epithelial Outgrowth Through Mesenchymal Rings Drives Alveologenesis ]]> https://biorxiv.org/content/10.1101/2022.10.06.511160v1?rss=1 Negretti, N. M. Son, Y. Crooke, P. Plosa, E. J. Benjamin, J. T. Jetter, C. S. Bunn, C. Mignemi, N. Marini, J. Hackett, A. N. Ransom, M. Nichols, D. Guttentag, S. H. Pua, H. H. Blackwell, T. S. Zacharias, W. Frank, D. B. Kozub, J. A. Mahadevan-Jansen, A. Kropski, J. A. Wright, C. V. E. Millis, B. Sucre, J. M. S. 2022-10-10 doi:10.1101/2022.10.06.511160 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ Engaging in word recognition elicits highly specific modulations in visual cortex ]]> https://biorxiv.org/content/10.1101/2022.10.10.511419v1?rss=1 White, A. L. Kay, K. Tang, K. A. Yeatman, J. D. 2022-10-11 doi:10.1101/2022.10.10.511419 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Extracellular vesicles from non-neuroendocrine SCLC cells promote adhesion and survival of neuroendocrine SCLC cells ]]> https://biorxiv.org/content/10.1101/2022.10.12.511984v1?rss=1 Jimenez, L. Stolzenbach, V. Ozawa, P. M. M. Ramirez-Solano, M. A. Liu, Q. Sage, J. Weaver, A. 2022-10-13 doi:10.1101/2022.10.12.511984 Cold Spring Harbor Laboratory Press 2022-10-13 <![CDATA[ Smaller total and subregional cerebellar volumes in posttraumatic stress disorder: a mega-analysis by the ENIGMA-PGC PTSD workgroup ]]> https://biorxiv.org/content/10.1101/2022.10.13.512111v1?rss=1 Huggins, A. A. Baird, C. L. Briggs, M. Laskowitz, S. Fouda, S. Haswell, C. C. Sun, D. Salminen, L. E. Jahanshad, N. Thomopoulos, S. I. Veltman, D. J. Frijling, J. L. Olff, M. van Zuiden, M. Koch, S. B. J. Nawijn, L. Wang, L. Zhu, Y. Li, G. Stein, D. J. Ipser, J. Seedat, S. du Plessis, S. van den Heuvel, L. L. Suarez-Jimenez, B. Zhu, X. Kim, Y. He, X. Zilcha-Mano, S. Lazarov, A. Neria, Y. Stevens, J. S. Ressler, K. J. Jovanovic, T. van Rooij, S. J. H. Fani, N. Hudson, A. R. Mueller, S. C. Sierk, A. Manthey, A. Walter, H. Daniels, J. K. Schmahl, C. Herz 2022-10-17 doi:10.1101/2022.10.13.512111 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Automatic mechanistic inference from large families of Boolean models generated by Monte Carlo Tree Search ]]> https://biorxiv.org/content/10.1101/2022.10.13.512151v1?rss=1 Glazer, B. Lifferth, J. T. Lopez, C. F. 2022-10-17 doi:10.1101/2022.10.13.512151 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Elucidation of Global Trends in the Effects of VX-661 and VX-445 on the Expression of Clinical CFTR Variants ]]> https://biorxiv.org/content/10.1101/2022.10.14.512300v1?rss=1 McKee, A. G. McDonald, E. F. Penn, W. D. Kuntz, C. P. Noguera, K. Chamness, L. M. Roushar, F. J. Meiler, J. Oliver, K. E. Plate, L. Schlebach, J. P. 2022-10-15 doi:10.1101/2022.10.14.512300 Cold Spring Harbor Laboratory Press 2022-10-15 <![CDATA[ Generalized strategy for engineering mammalian cell-compatible RNA-based biosensors from random sequence libraries ]]> https://biorxiv.org/content/10.1101/2022.10.18.512695v1?rss=1 Allchin, E. Rosch, J. Kim, H. Lippmann, E. 2022-10-18 doi:10.1101/2022.10.18.512695 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Temporal Application of Lysyl Oxidase during Hierarchical Collagen Fiber Formation Differentially Effects Mechanics in Engineered Tissues ]]> https://biorxiv.org/content/10.1101/2022.10.18.512696v1?rss=1 Bates, M. Troop, L. Brown, M. E. Puetzer, J. L. 2022-10-21 doi:10.1101/2022.10.18.512696 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Rosetta 's Predictive Ability for Low-Affinity Ligand Binding in Fragment-Based Drug Discovery ]]> https://biorxiv.org/content/10.1101/2022.10.18.512794v1?rss=1 Okwei, E. Smith, S. Bender, B. J. Allison, B. Ganguly, S. Geanes, A. Zhang, X. Ledwitch, K. Meiler, J. 2022-10-19 doi:10.1101/2022.10.18.512794 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ Species-specific roles for the MAFA and MAFB transcription factors in regulatingislet β cell identity ]]> https://biorxiv.org/content/10.1101/2022.10.20.512880v1?rss=1 Cha, J. Tong, X. Walker, E. M. Dahan, T. Cochrane, V. Ashe, S. Russell, R. Osipovich, A. B. Mawla, A. M. Guo, M. Liu, J.-h. Huising, M. O. Magnuson, M. A. Hebrok, M. Dor, Y. Stein, R. 2022-10-21 doi:10.1101/2022.10.20.512880 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Career Self-Efficacy Disparities in Underrepresented Biomedical Scientist Trainees ]]> https://biorxiv.org/content/10.1101/2022.10.21.512368v1?rss=1 Chatterjee, D. Jacob, G. A. Sturzenegger Varvayanis, S. Wefes, I. Chalkley, R. Nogueira, A. T. Fuhrmann, C. Varadarajan, J. Hubbard, N. M. Gaines, C. H. Layton, R. L. Chaudhary, S. 2022-10-21 doi:10.1101/2022.10.21.512368 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Computationally restoring the potency of a clinical antibody against SARS-CoV-2 Omicron subvariants ]]> https://biorxiv.org/content/10.1101/2022.10.21.513237v1?rss=1 Desautels, T. A. Arrildt, K. T. Zemla, A. T. Lau, E. Y. Zhu, F. Ricci, D. Cronin, S. Zost, S. Binshtein, E. Scheaffer, S. M. Engdahl, T. B. Chen, E. Goforth, J. W. Vashchenko, D. Nguyen, S. Weilhammer, D. R. Lo, J. K.-Y. Rubinfeld, B. Saada, E. A. Weisenberger, T. Lee, T.-H. Whitener, B. Case, J. B. Ladd, A. Silva, M. S. Haluska, R. M. Grzesiak, E. A. Bates, T. W. Petersen, B. K. Thackray, L. B. Segelke, B. W. Lillo, A. M. Sundaram, S. Diamond, M. S. Crowe, J. E. Carnahan, R. H. Faissol, D. M. 2022-10-24 doi:10.1101/2022.10.21.513237 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Clustering of CaV1.3 L-type calcium channels by Shank3 ]]> https://biorxiv.org/content/10.1101/2022.10.21.513252v1?rss=1 Yang, Q. Perfitt, T. L. Quay, J. Hu, L. Colbran, R. J. 2022-10-22 doi:10.1101/2022.10.21.513252 Cold Spring Harbor Laboratory Press 2022-10-22 <![CDATA[ SETD2 safeguards the genome against isochromosome formation ]]> https://biorxiv.org/content/10.1101/2022.10.25.513694v1?rss=1 Mason, F. Kounlavong, E. S. Tebeje, A. T. Dahiya, R. Guess, T. Vlach, L. Norris, S. R. Lovejoy, C. A. Dere, R. Ohi, R. Ly, P. Walker, C. L. Rathmell, W. K. 2022-10-26 doi:10.1101/2022.10.25.513694 Cold Spring Harbor Laboratory Press 2022-10-26 <![CDATA[ A contamination focused approach for optimizing thesingle-cell RNA-seq experiment ]]> https://biorxiv.org/content/10.1101/2022.10.25.513758v1?rss=1 Arceneaux, D. Chen, Z. Simmons, A. Heiser, C. N. Southard-Smith, A. N. Brenan, M. Yang, Y. Chen, B. Xu, Y. Choi, E. Campbell, J. D. Liu, Q. Lau, K. 2022-10-27 doi:10.1101/2022.10.25.513758 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Salt-inducible kinase inhibition promotes the adipocyte thermogenic program and adipose tissue browning ]]> https://biorxiv.org/content/10.1101/2022.10.27.514130v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@ce743org.highwire.dtl.DTLVardef@122f339org.highwire.dtl.DTLVardef@18e3013org.highwire.dtl.DTLVardef@1f65311_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractsC_FLOATNO C_FIG ObjectiveNorepinephrine stimulates the adipose tissue thermogenic program through a {beta}-adrenergic receptor ({beta}AR) - cyclic adenosine monophosphate (cAMP) - protein kinase A (PKA) signaling cascade. We discovered that a noncanonical activation of the mechanistic target of rapamycin complex 1 (mTORC1) by PKA is required for the {beta}AR-stimulation of adipose tissue browning. However, the downstream events triggered by PKA-phosphorylated mTORC1 activation that drive this thermogenic response are not well understood. MethodsWe used a proteomic approach of Stable Isotope Labeling by/with Amino acids in Cell culture (SILAC) to characterize the global protein phosphorylation profile in brown adipocytes treated with the {beta}AR agonist. We identified salt-inducible kinase 3 (SIK3) as a candidate mTORC1 substrate and further tested the effect of SIK3 deficiency or SIK inhibition on the thermogenic gene expression program in brown adipocytes and in mouse adipose tissue. ResultsSIK3 interacts with RAPTOR, the defining component of the mTORC1 complex, and is phosphorylated at Ser884 in a rapamycin-sensitive manner. Pharmacological SIK inhibition by a pan-SIK inhibitor (HG-9-91-01) in brown adipocytes increases basal Ucp1 gene expression and restores its expression upon blockade of either mTORC1 or PKA. Short-hairpin RNA (shRNA) knockdown of Sik3 augments, while overexpression of SIK3 suppresses, Ucp1 gene expression in brown adipocytes. The regulatory PKA phosphorylation domain of SIK3 is essential for its inhibition. CRISPR-mediated Sik3 deletion in brown adipocytes increases type IIa histone deacetylase (HDAC) activity and enhances the expression of genes involved in thermogenesis such as Ucp1, Pgc1, and mitochondrial OXPHOS complex protein. We further show that HDAC4 interacts with PGC1 after {beta}AR stimulation and reduces lysine acetylation in PGC1. Finally, a SIK inhibitor well-tolerated in vivo (YKL-05-099) can stimulate the expression of thermogenesis-related genes and browning of mouse subcutaneous adipose tissue. ConclusionsTaken together, our data reveal that SIK3, with the possible contribution of other SIKs, functions as a phosphorylation switch for {beta}-adrenergic activation to drive the adipose tissue thermogenic program and indicates that more work to understand the role of the SIKs is warranted. Our findings also suggest that maneuvers targeting SIKs could be beneficial for obesity and related cardiometabolic disease. ]]> Shi, F. de Fatima Silva, F. Liu, D. Turk, C. Kruger, M. Collins, S. 2022-10-28 doi:10.1101/2022.10.27.514130 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Autism-related behavioral phenotypes of three Camk2a mutant mouse lines with reduced CaMKIIalpha expression and/or activity ]]> https://biorxiv.org/content/10.1101/2022.10.28.514232v1?rss=1 Thomas, J. R. Spiess, K. L. Colbran, R. J. 2022-10-28 doi:10.1101/2022.10.28.514232 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Routing States Transition During Oscillatory Bursts and Attention States ]]> https://biorxiv.org/content/10.1101/2022.10.29.514374v1?rss=1 Banaie Boroujeni, K. Womelsdorf, T. 2022-10-30 doi:10.1101/2022.10.29.514374 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ The neuropeptidergic connectome of C. elegans ]]> https://biorxiv.org/content/10.1101/2022.10.30.514396v1?rss=1 Sanchez, L. R. Watteyne, J. Sun, H. Fernandez, R. Taylor, S. Weinreb, A. Hammarlund, M. Miller, D. Hobert, O. Beets, I. Vertes, P. Schafer, W. 2022-10-31 doi:10.1101/2022.10.30.514396 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ Mosaic chromosomal alterations in blood across ancestries via whole-genome sequencing ]]> https://biorxiv.org/content/10.1101/2022.11.07.515222v1?rss=1 Auer, P. L. Jakubek, Y. A. Zhou, Y. Stilp, A. M. Bacon, J. Wong, J. Mitchell, B. Lewis, J. Boerwinkle, E. Loos, R. J. F. Preuss, M. Barnes, K. Pankratz, N. Fornage, M. Redline, S. Psaty, B. M. Bis, J. C. Silverman, E. Cho, M. Yun, J. Ramachandran, V. Mathias, R. A. Taub, M. Peyser, P. A. Smith, J. A. Kardia, S. Arnett, D. North, K. E. Raffield, L. M. Carson, A. Doyle, M. Rich, S. Rotter, J. Guo, X. Cox, N. Mack, T. Chasman, D. Machiela, M. Ozcan, Z. Conomos, M. Li, Y. Desai, P. Bick, A. Reiner, A. P. Scheet, P. 2022-11-08 doi:10.1101/2022.11.07.515222 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ EV Fingerprinting: Resolving extracellular vesicle heterogeneity using multi-parametric flow cytometry ]]> https://biorxiv.org/content/10.1101/2022.11.10.515864v1?rss=1 von Lersner, A. K. Fernandes, F. C. L. Ozawa, P. M. M. Vagner, T. Lima, S. M. Sung, B. H. Wehbe, M. Franze, K. Wilson, J. T. Irish, J. M. Weaver, A. Di Vizio, D. Zijlstra, A. 2022-11-11 doi:10.1101/2022.11.10.515864 Cold Spring Harbor Laboratory Press 2022-11-11 <![CDATA[ A Junction-Dependent Mechanism Drives Mammary Cell Intercalation for Ductal Elongation ]]> https://biorxiv.org/content/10.1101/2022.11.11.516046v1?rss=1 Pfannenstein, A. Macara, I. G. 2022-11-13 doi:10.1101/2022.11.11.516046 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ PD-1 is induced on tumor-associated macrophages in obesity to directly restrain anti-tumor immunity ]]> https://biorxiv.org/content/10.1101/2022.11.12.515348v1?rss=1 Bader, J. E. Wolf, M. M. Madden, M. Z. Reinfeld, B. I. Arner, E. N. Hathaway, E. S. Steiner, K. K. Needle, G. A. Landis, M. D. Cottam, M. A. Ye, X. Christofides, A. Boussiotis, V. A. Haake, S. M. Beckermann, K. E. Rathmell, W. K. Hasty, A. H. Rathmell, J. C. 2022-11-12 doi:10.1101/2022.11.12.515348 Cold Spring Harbor Laboratory Press 2022-11-12 <![CDATA[ Toxin-mediated downregulation of absorptive ion transporters NHE3, DRA, and SGLT1 in the colon contributes to diarrhea associated with Clostridioides difficile infection. ]]> https://biorxiv.org/content/10.1101/2022.11.12.516162v1?rss=1 View larger version (69K): org.highwire.dtl.DTLVardef@e6e23corg.highwire.dtl.DTLVardef@ed6bborg.highwire.dtl.DTLVardef@33adcaorg.highwire.dtl.DTLVardef@d6e359_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Peritore-Galve, F. C. Kaji, I. Smith, A. Walker, L. M. Shupe, J. A. Dudeja, P. K. Goldenring, J. R. Lacy, D. B. 2022-11-13 doi:10.1101/2022.11.12.516162 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Subset-specific mitochondrial and DNA damage shapes T cell responses to fever and inflammation ]]> https://biorxiv.org/content/10.1101/2022.11.14.516478v1?rss=1 Heintzman, D. Elasy, J. H. Chi, C. Ye, X. Krystoviak, E. Khan, W. Olson, L. M. Jones, A. Voss, K. Patterson, A. Sugiura, A. Mason, F. M. Hong, H. Bass, L. E. Beier, K. L. Deng, W. Lyssiotis, C. A. Bick, A. G. Rathmell, W. K. Rathmell, J. 2022-11-15 doi:10.1101/2022.11.14.516478 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Design principles of caveolins across metazoa and beyond ]]> https://biorxiv.org/content/10.1101/2022.11.15.516482v1?rss=1 Han, B. Wilson, L. F. L. Gulsevin, A. Meiler, J. Karakas, E. Kenworthy, A. K. 2022-11-16 doi:10.1101/2022.11.15.516482 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Characterizing the landscape of gene expression variance in humans ]]> https://biorxiv.org/content/10.1101/2022.11.15.516646v1?rss=1 Wolf, S. Melo, D. Garske, K. M. Pallares, L. F. Ayroles, J. F. 2022-11-17 doi:10.1101/2022.11.15.516646 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Potently neutralizing human monoclonal antibodies against the zoonotic pararubulavirus Sosuga virus ]]> https://biorxiv.org/content/10.1101/2022.11.17.516973v1?rss=1 Parrington, H. M. Kose, N. Armstrong, E. Handal, L. S. Diaz, S. Reidy, J. X. Dong, J. Stewart-Jones, G. B. E. Shrivastava-Ranjan, P. Jain, S. Albarino, C. G. Carnahan, R. H. Crowe, J. E. 2022-11-17 doi:10.1101/2022.11.17.516973 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ GBMdeconvoluteR accurately infers proportions of neoplastic and immune cell populations from bulk glioblastoma transcriptomics data ]]> https://biorxiv.org/content/10.1101/2022.11.19.517187v1?rss=1 Ajaib, S. A. Lodha, D. Pollock, S. Hemmings, G. Finetti, M. Gusnanto, A. Chakrabarty, A. Ismail, A. Wilson, E. Varn, F. S. Hunter, B. Filby, A. Brockman, A. S. McDonald, D. Verhaak, R. Ihrie, R. A. Stead, L. F. 2022-11-20 doi:10.1101/2022.11.19.517187 Cold Spring Harbor Laboratory Press 2022-11-20 <![CDATA[ Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus ]]> https://biorxiv.org/content/10.1101/2022.11.22.517304v1?rss=1 Steenwyk, J. L. Balamurugan, C. Raja, H. A. Goncalves, C. Li, N. Martin, F. Berman, J. Oberlies, N. H. Gibbons, J. G. Goldman, G. H. Geiser, D. M. Hibbett, D. S. Rokas, A. 2022-11-24 doi:10.1101/2022.11.22.517304 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ CYRI-B mediated macropinocytosis drives metastasis via lysophosphatidic acid receptor uptake ]]> https://biorxiv.org/content/10.1101/2022.11.23.517689v1?rss=1 Nikolaou, S. Juin, A. Whitelaw, J. A. Paul, N. R. Fort, L. Nixon, C. Spence, H. J. Bryson, S. Machesky, L. M. 2022-11-24 doi:10.1101/2022.11.23.517689 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Chromatin activity identifies differential gene regulation across human ancestries ]]> https://biorxiv.org/content/10.1101/2022.11.25.517959v1?rss=1 Pettie, K. P. Mumbach, M. Lea, A. J. Ayroles, J. Chang, H. Y. Kasowski, M. Fraser, H. B. 2022-11-25 doi:10.1101/2022.11.25.517959 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ The Epithelial Na+ Channel UNC-8 promotes an endocytic mechanism that recycles presynaptic components from old to new boutons in remodeling neurons ]]> https://biorxiv.org/content/10.1101/2022.11.29.518248v1?rss=1 Cuentas-Condori, A. Chen, S. Krout, M. Gallick, K. Tipps, J. Flautt, L. Richmond, J. E. E. Miller, D. M. 2022-12-01 doi:10.1101/2022.11.29.518248 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Hyperglycemia increases the severity of Staphylococcus aureus osteomyelitis and influences bacterial genes required for survival in bone. ]]> https://biorxiv.org/content/10.1101/2022.11.30.518635v1?rss=1 Butrico, C. E. Klopfenstein, N. B. Green, E. R. Johnson, J. R. Peck, S. H. Ibberson, C. Serezani, C. H. Cassat, J. E. 2022-12-01 doi:10.1101/2022.11.30.518635 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Mutated cells mediate distinct inflammatory responses in clonal hematopoiesis ]]> https://biorxiv.org/content/10.1101/2022.12.01.518580v1?rss=1 Heimlich, J. B. Bhat, P. Parker, A. C. Jenkins, M. T. Vlasschaert, C. Ulloa, J. Potts, C. R. Olson, S. Silver, A. J. Ahmad, A. Sharber, B. Brown, D. Hu, N. van Galen, P. Savona, M. R. Bick, A. G. Ferrell, P. B. 2022-12-03 doi:10.1101/2022.12.01.518580 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ CLASPs stabilize the intermediate state between microtubule growth and catastrophe ]]> https://biorxiv.org/content/10.1101/2022.12.03.518990v1?rss=1 Lawrence, E. J. Chatterjee, S. Zanic, M. 2022-12-04 doi:10.1101/2022.12.03.518990 Cold Spring Harbor Laboratory Press 2022-12-04 <![CDATA[ Cultural signatures of punctuated environmental change: measuring the effects of population-wide stress on song distribution in dark-eyed juncos and song sparrows ]]> https://biorxiv.org/content/10.1101/2022.12.03.519005v1?rss=1 Snyder, K. T. Sellers, M. L. Creanza, N. 2022-12-04 doi:10.1101/2022.12.03.519005 Cold Spring Harbor Laboratory Press 2022-12-04 <![CDATA[ Non-Canonical Functions of a Mutant TSC2 Protein in Mitotic Division ]]> https://biorxiv.org/content/10.1101/2022.12.07.519401v1?rss=1 Chalkley, M.-B. L. Mersfelder, R. B. Sundberg, M. Armstrong, L. Sahin, M. Ihrie, R. A. Ess, K. 2022-12-07 doi:10.1101/2022.12.07.519401 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Disrupted RNA editing in beta cells mimics early stage type 1 diabetes ]]> https://biorxiv.org/content/10.1101/2022.12.08.519618v1?rss=1 Knebel, E. Peleg, S. Dai, C. Cohen-Fultheim, R. Glaser, B. Levanon, E. Powers, A. Klochendler, A. Dor, Y. 2022-12-10 doi:10.1101/2022.12.08.519618 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ Bulk and Mosaic Deletions of Egfr Reveal Regionally Defined Gliogenesis in the Developing Mouse Forebrain ]]> https://biorxiv.org/content/10.1101/2022.12.10.519926v1?rss=1 Zhang, X. Xiao, G. Johnson, C. A. Cai, Y. Horowitz, Z. Mennicke, C. Coffey, R. Haider, M. Threadgill, D. W. Eliscu, R. Oldham, M. C. Greenbaum, A. C. Ghashghaei, H. T. 2022-12-11 doi:10.1101/2022.12.10.519926 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Multimodal Imaging-Based Classification of PTSD Using Data-Driven Computational Approaches: A Multisite Big Data Study from the ENIGMA-PGC PTSD Consortium ]]> https://biorxiv.org/content/10.1101/2022.12.12.519838v1?rss=1 Zhu, X. Kim, Y. Ravid, O. He, X. Suarez-Jimenez, B. Zilcha-Mano, S. Lazarov, A. Lee, S. Abdallah, C. G. Angstadt, M. Averill, C. L. Baird, C. L. Baugh, L. A. Blackford, J. U. Bomyea, J. Bruce, S. E. Bryant, R. A. Cao, Z. Choi, K. Cisler, J. Cotton, A. S. Daniels, J. K. Davenport, N. D. Davidson, R. J. DeBellis, M. D. Dennis, E. L. Densmore, M. deRoon-Cassini, T. Disner, S. G. El Hage, W. Etkin, A. Fani, N. Fercho, K. A. Fitzgerald, J. Forster, G. L. Frijling, J. L. Geuze, E. Gonenc, A. Gordon, E. M. Gruber, S. Grupe, D. W. Guenette, J. P. Haswell, C. C 2022-12-13 doi:10.1101/2022.12.12.519838 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Adaptation of a transmitted/founder simian-human immunodeficiency virus for enhanced replication in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2022.12.12.520031v1?rss=1 Bauer, A. Lindemuth, E. Joy, J. Marino, F. E. Docken, S. S. Krause, R. Mallick, S. McCormick, K. Holt, C. Georgiev, I. Felber, B. K. Keele, B. F. Veazey, R. Davenport, M. P. Li, H. Shaw, G. Bar, K. J. 2022-12-12 doi:10.1101/2022.12.12.520031 Cold Spring Harbor Laboratory Press 2022-12-12 <![CDATA[ A High-Throughput Screen Reveals the Structure-Activity Relationship of the Antimicrobial Lasso Peptide Ubonodin ]]> https://biorxiv.org/content/10.1101/2022.12.13.520261v1?rss=1 Thokkadam, A. Do, T. Ran, X. Brynildsen, M. Yang, Z. J. Link, A. J. 2022-12-13 doi:10.1101/2022.12.13.520261 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Differential adenine methylation analysis reveals increased variability in 6mA in the absence of methyl-directed mismatch repair ]]> https://biorxiv.org/content/10.1101/2022.12.14.520158v1?rss=1 Stone, C. J. Boyer, G. F. Behringer, M. G. 2022-12-14 doi:10.1101/2022.12.14.520158 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ COVID-19 Associated Pulmonary Aspergillosis isolates are genomically diverse but similar to each other in their responses to infection-relevant stresses ]]> https://biorxiv.org/content/10.1101/2022.12.14.520265v1?rss=1 Mead, M. E. Alves de Castro, P. Steenwyk, J. B. Gangneux, J.-P. Hoenigl, M. Prattes, J. Rautemaa-Richardson, R. Guegan, H. Moore, C. B. Lass-Floerl, C. Reizine, F. Valero, C. van Rhijn, N. Bromley, M. J. Rokas, A. Goldman, G. H. Gago, S. 2022-12-15 doi:10.1101/2022.12.14.520265 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Cross-tissue patterns of DNA hypomethylation reveal genetically distinct histories of cell development ]]> https://biorxiv.org/content/10.1101/2022.12.15.520535v1?rss=1 80% of CpG sites are stably methylated, tens of thousands of discrete CpG loci form hypomethylated regions (HMRs). Because they lack DNAme, HMRs are considered transcriptionally permissive, but not all HMRs actively regulate genes. Unlike promoter HMRs, a subset of non-coding HMRs is cell-type specific and enriched for tissue specific gene regulatory functions. Our data further argues not only that HMR establishment is an important step in enforcing cell identity, but also that complex HMR patterns are functionally instructive to gene regulation. To understand the significance of non-coding HMRs, we systematically dissected HMR patterns across diverse human cell types and developmental timepoints, including embryonic, fetal, and adult tissues. Unsupervised clustering of 102,390 distinct HMRs revealed that levels of HMR specificity reflects a developmental hierarchy supported by enrichment of stage-specific transcription factors and gene ontologies. Using a pseudo-time course of development from embryonic stem cells to adult stem and mature hematopoietic cells, we find that most HMRs observed in differentiated cells (~70-75%) are established at early developmental stages and accumulate as development progresses. HMRs that arise during differentiation frequently (~35%) establish near existing HMRs ([≤] 6kb away), leading to the formation of HMR clusters associated with stronger enhancer activity. Using SNP-based partitioned heritability from GWAS summary statistics across diverse traits and clinical lab values, we discovered that genetic contribution to trait heritability is enriched within HMRs. Moreover, the contribution of heritability to cell-relevant traits increases with both increasing developmental specificity and HMR clustering, supporting the role of distinct HMR subsets in regulating normal cell function. Altogether, our findings reveal that HMRs can predict cellular phenotypes by providing genetically distinct historical records of a cells journey through development. AUTHOR SUMMARYStudies aiming to understand the relationship between DNA methylation patterns and phenotypic outcomes have focused largely on individual differentially methylated regions without consideration of combinatorial changes that drive phenotypes. In non-disease contexts, most of the human genome is stably methylated, except for thousands of discrete DNA hypomethylated regions (HMRs) coinciding with gene regulatory elements. Here, we comprehensively characterize HMR relationships both within and between developmentally diverse cell types to understand the functional significance of complex HMR patterns. We show that levels of HMR specificity across cell-types captures time-point specific branchpoints of development. Our analysis further reveals that HMRs form clusters in proximity to cell identity genes and are associated with stronger gene enhancer activity. This is a wide-spread phenomenon and only a very small subset of HMR clusters is explained by overlapping super-enhancer annotations. Partitioned heritability revealed the functional significance of different HMR patterns linked to specific phenotypic outcomes and indicates a quantitative relationship between HMR patterns and complex trait heritability. Altogether, our findings reveal that HMRs can predict cellular phenotypes by providing genetically distinct historical records of a cells journey through development, ultimately providing novel insights into how DNA hypo-methylation mediates genome function. ]]> Scott, T. J. Hansen, T. J. McArthur, E. Hodges, E. 2022-12-16 doi:10.1101/2022.12.15.520535 Cold Spring Harbor Laboratory Press 2022-12-16 <![CDATA[ LIQ HD (Lick Instance Quantifier Home cage Device): An open-source tool for recording undisturbed two-bottle drinking behavior in a home cage environment ]]> https://biorxiv.org/content/10.1101/2022.12.16.520661v1?rss=1 Petersen, N. Adank, D. N. Raghavan, R. Winder, D. G. Doyle, M. A. 2022-12-17 doi:10.1101/2022.12.16.520661 Cold Spring Harbor Laboratory Press 2022-12-17 <![CDATA[ LRRK2 Kinase Activity Regulates Parkinson's Disease-Relevant Lipids at the Lysosome ]]> https://biorxiv.org/content/10.1101/2022.12.19.521070v1?rss=1 Maloney, M. T. Wang, X. Ghosh, R. Andrews, S. V. Maciuca, R. Masoud, S. T. Caprioli, R. M. Chen, J. Chiu, C.-L. Davis, S. S. Ho, A. C.-N. Nguyen, H. N. Propson, N. E. Reyzer, M. L. Davis, O. B. Deen, M. C. Zhu, S. Di Paolo, G. Vocadlo, D. J. Estrada, A. A. de Vicente, J. Lewcock, J. W. Arguello, A. Suh, J. H. Huntwork-Rodriguez, S. Henry, A. G. 2022-12-19 doi:10.1101/2022.12.19.521070 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ An Open-Source Rodent Chronic EEG Array System with High Density MXene-Based Skull Surface Electrodes ]]> https://biorxiv.org/content/10.1101/2022.12.28.522126v1?rss=1 Ding, L. Patel, A. Shankar, S. Driscoll, N. Zhou, C. rex, T. S. Vitale, F. Gallagher, M. J. 2022-12-29 doi:10.1101/2022.12.28.522126 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Liver Fibroblast Growth Factor 21 (FGF21) is Required for the Full Anorectic Effect of the Glucagon-Like Peptide-1 Receptor Agonist Liraglutide in Male Mice fed High Carbohydrate Diets ]]> https://biorxiv.org/content/10.1101/2023.01.03.522509v1?rss=1 Le, T. D. V. Fathi, P. Watters, A. B. Ellis, B. J. Bozadjieva-Kramer, N. Perez, M. B. Sullivan, A. I. Rose, J. P. Baggio, L. L. Koehler, J. Brown, J. L. Bales, M. B. Nwaba, K. G. Campbell, J. E. Drucker, D. J. Potthoff, M. J. Seeley, R. J. Ayala, J. E. 2023-01-04 doi:10.1101/2023.01.03.522509 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ Bivalent mRNA vaccine improves antibody-mediated neutralization of many SARS-CoV-2 Omicron lineage variants ]]> https://biorxiv.org/content/10.1101/2023.01.08.523127v1?rss=1 Jiang, N. Wang, L. Hatta, M. Feng, C. Currier, M. Lin, X. Hossain, J. Cui, D. Mann, B. R. Kovacs, N. A. Wang, W. Atteberry, G. Wilson, M. Chau, R. Lacek, K. A. Paden, C. R. Hassell, N. Rambo-Martin, B. Barnes, J. R. Kondor, R. J. Self, W. H. Rhoads, J. P. Baughman, A. Chappell, J. D. Shapiro, N. I. Gibbs, K. W. Hager, D. N. Lauring, A. S. Surie, D. McMorrow, M. L. Thornburg, N. J. Wentworth, D. E. Zhou, B. 2023-01-09 doi:10.1101/2023.01.08.523127 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ Associative white matter tracts selectively predict sensorimotor learning ]]> https://biorxiv.org/content/10.1101/2023.01.10.523345v1?rss=1 Vinci-Booher, S. McDonald, D. Berquist, E. Pestilli, F. 2023-01-10 doi:10.1101/2023.01.10.523345 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ The QseB response regulator imparts tolerance to positively charged antibiotics by controlling metabolism and minor changes to LPS ]]> https://biorxiv.org/content/10.1101/2023.01.10.523522v1?rss=1 Hurst, M. N. Beebout, C. J. Hollingsworth, A. Guckes, K. R. Purcell, A. B. Bermudez, T. Williams, D. Trent, M. S. Hadjifrangiskou, M. 2023-01-11 doi:10.1101/2023.01.10.523522 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ Independent regulation of Z-lines and M-linesduring sarcomere assembly in cardiac myocytesrevealed by the automatic image analysis software sarcApp ]]> https://biorxiv.org/content/10.1101/2023.01.11.523681v1?rss=1 Neininger-Castro, A. C. Hayes, J. B. Sanchez, Z. C. Taneja, N. Fenix, A. M. Moparthi, S. Vassilopoulos, S. Burnette, D. T. 2023-01-12 doi:10.1101/2023.01.11.523681 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ Damage-induced senescent immune cells regulate regeneration of the zebrafish retina ]]> https://biorxiv.org/content/10.1101/2023.01.16.524296v1?rss=1 Konar, G. J. Flickinger, Z. R. Sharma, S. P. Vallone, K. T. Lyon, C. E. Doshier, C. C. Lyon, W. D. Patton, J. G. 2023-01-16 doi:10.1101/2023.01.16.524296 Cold Spring Harbor Laboratory Press 2023-01-16 <![CDATA[ Adaptations to water stress and pastoralism in the Turkana of northwest Kenya ]]> https://biorxiv.org/content/10.1101/2023.01.17.524066v1?rss=1 Lea, A. J. Caldas, I. V. Garske, K. M. Echwa, J. Gurven, M. Handley, C. Kahumbu, J. Kamau, J. Kinyua, P. Lotukoi, F. Lopurudoi, A. Lowasa, S. Mallarino, R. Martins, D. Messer, P. W. Miano, C. Muhoya, B. Peng, J. Phung, T. Rabinowitz, J. D. Roichman, A. Siford, R. Stone, A. Taravella-Oill, A. M. Mathew, S. Wilson, M. A. Ayroles, J. F. 2023-01-19 doi:10.1101/2023.01.17.524066 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi ]]> https://biorxiv.org/content/10.1101/2023.01.17.524442v1?rss=1 Balamurugan, C. Steenwyk, J. L. Goldman, G. H. Rokas, A. 2023-01-20 doi:10.1101/2023.01.17.524442 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Measurable fields to spikes causality and its dependence on cortical layer and area. ]]> https://biorxiv.org/content/10.1101/2023.01.17.524451v1?rss=1 Akella, S. Bastos, A. M. Miller, E. K. Principe, J. C. 2023-01-20 doi:10.1101/2023.01.17.524451 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Extensive characterization of a Williams Syndrome murine model shows Gtf2ird1-mediated rescue of select sensorimotor tasks, but no effect on enhanced social behavior ]]> https://biorxiv.org/content/10.1101/2023.01.18.523029v1?rss=1 Dougherty, J. D. Nygaard, K. R. Maloney, S. E. Swift, R. G. McCullough, K. B. Wagner, R. E. Fass, S. B. Garbett, K. Mirnics, K. Veenstra-VanderWeele, J. 2023-01-18 doi:10.1101/2023.01.18.523029 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ A Unified Physiological Process Links Global Patterns of Functional MRI, Respiratory Activity, and Autonomic Signaling ]]> https://biorxiv.org/content/10.1101/2023.01.19.524818v1?rss=1 Bolt, T. S. Wang, S. Nomi, J. S. Setton, R. Gold, B. Frederick, B. Spreng, R. N. Keilholz, S. Uddin, L. Chang, C. 2023-01-20 doi:10.1101/2023.01.19.524818 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Detecting cultural evolution in a songbird species using community-science data and computational modeling ]]> https://biorxiv.org/content/10.1101/2023.01.23.525255v1?rss=1 Pichkar, Y. Searfoss, A. M. Creanza, N. 2023-01-23 doi:10.1101/2023.01.23.525255 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Functional Overlap of Inborn Errors of Immunity and Metabolism Genes Define T Cell Immunometabolic Vulnerabilities ]]> https://biorxiv.org/content/10.1101/2023.01.24.525419v1?rss=1 Patterson, A. R. Needle, G. A. Sugiura, A. Chi, C. Steiner, K. K. Fisher, E. L. Robertson, G. L. Bodnya, C. Markle, J. G. Gama, V. Rathmell, J. C. 2023-01-24 doi:10.1101/2023.01.24.525419 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ Small Molecule Activation of NAPE-PLD Enhances Efferocytosis by Macrophages ]]> https://biorxiv.org/content/10.1101/2023.01.25.525554v1?rss=1 Zarrow, J. E. Alli-Oluwafuyi, A.-M. Youwakim, C. M. Kim, K. Jenkins, A. N. Suero, I. C. Jones, M. R. Mashhadi, Z. Mackie, K. P. Waterson, A. G. Doran, A. C. Sulikowski, G. A. Davies, S. S. 2023-01-25 doi:10.1101/2023.01.25.525554 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Cannabidiol sensitizes TRPV2 channels to activation by 2-APB ]]> https://biorxiv.org/content/10.1101/2023.01.27.525817v1?rss=1 40% sequence identity with TRPV2 are also activated by 2-APB and CBD, but we only find a strong sensitizing effect of CBD on the response of mouse TRPV3 to 2-APB. Mutations at non-conserved positions between rTRPV2 and rTRPV1 in either the pore domain or the CBD sites failed to confer strong sensitization by CBD in mutant rTRPV1 channels. Together, our results indicate that CBD-dependent sensitization of TRPV2 channels engages multiple channel regions and possibly involves more than one CBD and 2-APB sites. The remarkably robust effect of CBD on TRPV2 and TRPV3 channels offers a promising new tool to both understand and overcome one of the major roadblocks in the study of these channels - their resilience to activation. ]]> Gochman, A. Tan, X. Bae, C. Chen, H. Swartz, K. J. Jara-Oseguera, A. 2023-01-27 doi:10.1101/2023.01.27.525817 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Robust biomarker discovery through multiplatform multiplex image analysis of breast cancer clinical cohorts ]]> https://biorxiv.org/content/10.1101/2023.01.31.525753v1?rss=1 Eng, J. R. Bucher, E. Hu, Z. Sanders, M. Chakravarthy, B. Pietenpol, J. A. Gibbs, S. L. Chin, K. 2023-02-03 doi:10.1101/2023.01.31.525753 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Consensus tissue domain detection in spatial -omics data using MILWRM ]]> https://biorxiv.org/content/10.1101/2023.02.02.526900v1?rss=1 Kaur, H. Heiser, C. N. McKinley, E. T. Antunes, L. V. Harris, C. R. Roland, J. T. Shrubsole, M. J. Coffey, R. J. Lau, K. Vandekar, S. N. 2023-02-03 doi:10.1101/2023.02.02.526900 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Neanderthal Introgression Shaped Human Circadian Traits ]]> https://biorxiv.org/content/10.1101/2023.02.03.527061v1?rss=1 Velazquez-Arcelay, K. Colbran, L. L. McArthur, E. Brand, C. M. Siemann, J. K. McMahon, D. G. Capra, J. A. 2023-02-04 doi:10.1101/2023.02.03.527061 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Elexacaftor/VX-445-mediated CFTR interactome remodeling reveals differential correction driven by mutation-specific translational dynamics ]]> https://biorxiv.org/content/10.1101/2023.02.04.527134v1?rss=1 Kim, M. McDonald, E. F. Sabusap, C. M. P. Timalsina, B. Joshi, D. Hong, J. S. Rab, A. Sorscher, E. J. Plate, L. 2023-02-04 doi:10.1101/2023.02.04.527134 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ IQGAP2 regulates blood-brain barrier immune dynamics ]]> https://biorxiv.org/content/10.1101/2023.02.07.527394v1?rss=1 Katdare, K. Kjar, A. O'Brown, N. Neal, E. Sorets, A. Shostak, A. Mlouk, K. Kim, H. Horner, K. Schrag, M. Megason, S. Lippmann, E. 2023-02-08 doi:10.1101/2023.02.07.527394 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ Oxidized phospholipid oxPAPC induces a Th1-like phenotype in regulatory T cells and inhibits their protective function in atherosclerosis ]]> https://biorxiv.org/content/10.1101/2023.02.08.527689v1?rss=1 Appleton, B. D. Palmer, S. A. Smith, H. Stephens, L. E. Major, A. S. 2023-02-11 doi:10.1101/2023.02.08.527689 Cold Spring Harbor Laboratory Press 2023-02-11 <![CDATA[ Androgen Signaling Restricts Glutaminolysis to Drive Sex-Specific Th17 Metabolism ]]> https://biorxiv.org/content/10.1101/2023.02.10.527741v1?rss=1 Chowdhury, N. U. Cephus, J.-Y. Madden, M. Z. Wolf, M. M. Chi, C. Sugiura, A. Stier, M. T. Voss, K. Ye, X. Kuehnle, S. N. Scales, K. Gandhi, V. D. Guzy, R. D. Cahill, K. N. Sperling, A. I. Peebles, R. S. Rathmell, J. Newcomb, D. C. 2023-02-13 doi:10.1101/2023.02.10.527741 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ Fixation Before Dissociation Using a Deep Eutectic Solvent Preserves In Vivo States and Phospho-Signaling in Single-Cell Sequencing ]]> https://biorxiv.org/content/10.1101/2023.02.13.528370v1?rss=1 Fortmann, S. D. Frey, B. F. Hanumanthu, V. S. Liu, S. Goldsborough, A. Kilchrist, K. V. Ferrell, P. B. Weaver, C. T. Grant, M. B. Welner, R. S. 2023-02-13 doi:10.1101/2023.02.13.528370 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans ]]> https://biorxiv.org/content/10.1101/2023.02.14.528376v1?rss=1 50% of trans differences and trace how cis changes can produce cascades of trans changes. Overall, we find that most divergent elements (67%) experienced changes in both cis and trans, revealing a substantial role for trans divergence--alone and together with cis changes--to regulatory differences between species. ]]> Hansen, T. J. Fong, S. Capra, J. A. Hodges, E. 2023-02-15 doi:10.1101/2023.02.14.528376 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Dephosphorylation of 4EBP1/2 Induces Prenatal Neural Stem Cell Quiescence ]]> https://biorxiv.org/content/10.1101/2023.02.14.528513v1?rss=1 Geben, L. C. Brockman, A. A. Chalkley, M. B. L. Sweet, S. R. Gallagher, J. E. Scheuing, A. L. Simerly, R. B. Ess, K. C. Irish, J. M. Ihrie, R. A. 2023-02-15 doi:10.1101/2023.02.14.528513 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Whole-brain, gray and white matter time-locked functional signal changes with simple tasks and model-free analysis ]]> https://biorxiv.org/content/10.1101/2023.02.14.528557v1?rss=1 Schilling, K. Li, M. Rheault, F. Gao, Y. Cai, L. Y. Zhao, Y. Xu, L. Ding, Z. Anderson, A. W. Landman, B. A. Gore, J. C. 2023-02-14 doi:10.1101/2023.02.14.528557 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ Structural Optimization of siRNA Conjugates for Albumin Binding Achieves Effective MCL1-Targeted Cancer Therapy ]]> https://biorxiv.org/content/10.1101/2023.02.14.528574v1?rss=1 Hoogenboezem, E. Patel, S. S. Cavnar, A. Lo, J. Babb, L. Francini, N. Patil, P. Colazo, J. Michell, D. L. Sanchez, V. McCune, J. Ma, J. DeJulius, C. Lee, L. Rosch, J. Allen, R. Stokes, L. Hill, J. Vickers, K. Cook, R. Duvall, C. 2023-02-15 doi:10.1101/2023.02.14.528574 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Low Gut Microbial Diversity Augments Estrogen-driven Pulmonary Fibrosis in Female-Predominant Interstitial Lung Disease ]]> https://biorxiv.org/content/10.1101/2023.02.15.528630v1?rss=1 Chioma, O. S. Mallott, E. Bandhi, B. S. Wiggins, Z. Langford, M. Lancaster, A. W. Gelbard, A. Wu, H. Johnson, J. Lancaster, L. Wilfong, E. Crofford, L. J. Montgomery, C. Van Kaer, L. Bordenstein, S. Newcomb, D. Drake, W. 2023-02-15 doi:10.1101/2023.02.15.528630 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Citizenship status and career self-efficacy: An intersectional study of biomedical trainees in the United States ]]> https://biorxiv.org/content/10.1101/2023.02.19.526477v1?rss=1 Chatterjee, D. Nogueira, A. T. Wefes, I. Chalkley, R. Sturzenegger Varvayanis, S. Fuhrmann, C. N. Varadarajan, J. Jacob, G. A. Gaines, C. H. Hubbard, N. M. Chaudhary, S. Layton, R. L. 2023-02-21 doi:10.1101/2023.02.19.526477 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ CXCR2 expression during melanoma tumorigenesis controls transcriptional programs that facilitate tumor growth ]]> https://biorxiv.org/content/10.1101/2023.02.22.529548v1?rss=1 Yang, J. Bergdorf, K. Yan, C. Luo, W. Chen, S.-C. Ayers, D. Liu, Q. Liu, X. Boothby, M. R. Groves, S. M. Oleskie, A. Zhang, X. Maeda, D. Zebala, J. Quaranta, V. Richmond, A. 2023-02-22 doi:10.1101/2023.02.22.529548 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Sensitivity to outcome devaluation in operant tasks is better predicted by food restriction level than reinforcement training schedule in mice ]]> https://biorxiv.org/content/10.1101/2023.02.23.529699v1?rss=1 Chevee, M. Kim, C. J. Crow, N. Follman, E. G. Calipari, E. S. 2023-02-23 doi:10.1101/2023.02.23.529699 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Effects of pasteurization on osteopontin levels in human breastmilk and pasteurized breastmilk products ]]> https://biorxiv.org/content/10.1101/2023.02.24.529945v1?rss=1 McClanahan, K. G. Reese, J. Weitkemp, J.-H. Olivares-Villagomez, D. 2023-02-26 doi:10.1101/2023.02.24.529945 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ Convolutional-recurrent neural networks approximate diffusion tractography from T1-weighted MRI and associated anatomical context ]]> https://biorxiv.org/content/10.1101/2023.02.25.530046v1?rss=1 Cai, L. Y. Lee, H. H. Newlin, N. R. Kerley, C. I. Kanakaraj, P. Yang, Q. Johnson, G. W. Moyer, D. Schilling, K. G. Rheault, F. Landman, B. A. 2023-02-27 doi:10.1101/2023.02.25.530046 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Directing Protein Design Choices by Per-Residue Energy Breakdown Analysis with an Interactive Web Application ]]> https://biorxiv.org/content/10.1101/2023.02.27.530287v1?rss=1 Engelberger, F. Zakary, J. D. Kuenze, G. 2023-02-28 doi:10.1101/2023.02.27.530287 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ Jedi-1/MEGF12-mediated phagocytosis controls the pro-neurogenic properties of microglia in the ventricular-subventricular zone ]]> https://biorxiv.org/content/10.1101/2023.03.03.531012v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@16b9785org.highwire.dtl.DTLVardef@a8be50org.highwire.dtl.DTLVardef@66b726org.highwire.dtl.DTLVardef@1825d8b_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThe engulfment receptor Jedi-1 is expressed by microglia in the neonatal ventricular-subventricular zone (V-SVZ) neurogenic niche. C_LIO_LIJedi-1 knockout microglia have decreased engulfment ability, resulting in accumulation of dead cells in the V-SVZ. C_LIO_LILoss of Jedi-1 leads to a neuroinflammatory phenotype in microglia that is characteristic of neurodegenerative and age-associated microglia. C_LIO_LIMicroglial-specific loss of Jedi-1 reduces neurogenesis, which is rescued in vivo by inhibition of interleukin-1{beta} signaling. C_LI ]]> Morrison, V. E. Houpert, M. G. Trapani, J. B. Brockman, A. Kingsley, P. J. Katdare, K. A. Layden, H. M. Nguena-Jones, G. N. Trevisan, A. J. Maguire-Zeiss, K. A. Marnett, L. J. Bix, G. Ihrie, R. A. Carter, B. D. 2023-03-07 doi:10.1101/2023.03.03.531012 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Acute alcohol and chronic drinking bidirectionally regulate the excitability of prefrontal cortex vasoactive intestinal peptide interneurons ]]> https://biorxiv.org/content/10.1101/2023.03.07.531614v1?rss=1 Thompson, S. M. Ferranti, A. S. Joffe, M. E. 2023-03-10 doi:10.1101/2023.03.07.531614 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Adhesion-based capture stabilizes nascent microvilli at epithelial cell junctions ]]> https://biorxiv.org/content/10.1101/2023.03.08.531705v1?rss=1 Cencer, C. S. Silverman, J. B. Meenderink, L. Krystofiak, E. Millis, B. A. Tyska, M. J. 2023-03-09 doi:10.1101/2023.03.08.531705 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ LRRC8A anion channels modulate vasodilation via association with Myosin Phosphatase Rho Interacting Protein (MPRIP) ]]> https://biorxiv.org/content/10.1101/2023.03.08.531807v1?rss=1 Choi, H. Miller, M. R. Nguyen, H.-N. Rohrbough, J. C. Koch, S. R. Boatwright, N. Yarboro, M. T. Sah, R. McDonald, H. Reese, J. J. Stark, R. J. Lamb, F. S. 2023-03-11 doi:10.1101/2023.03.08.531807 Cold Spring Harbor Laboratory Press 2023-03-11 <![CDATA[ Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors ]]> https://biorxiv.org/content/10.1101/2023.03.09.530832v1?rss=1 Heiser, C. N. Simmons, A. J. Revetta, F. McKinley, E. T. Ramirez-Solano, M. A. Wang, J. Shao, J. Ayers, G. D. Wang, Y. Glass, S. E. Kaur, H. Rolong, A. Chen, B. Vega, P. N. Drewes, J. L. Saleh, N. Vandekar, S. Jones, A. L. Washington, M. K. Roland, J. T. Sears, C. L. Liu, Q. Shrubsole, M. J. Coffey, R. J. Lau, K. S. 2023-03-12 doi:10.1101/2023.03.09.530832 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ The fission yeast cytokinetic ring component Fic1 promotes septum formation ]]> https://biorxiv.org/content/10.1101/2023.03.13.532462v1?rss=1 Rossi, A. M. Bohnert, K. A. Gould, K. L. 2023-03-14 doi:10.1101/2023.03.13.532462 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Molecular mechanisms of functional impairment for active site mutations in glucose-6-phosphatase catalytic subunit 1 linked to glycogen storage disease type 1a. ]]> https://biorxiv.org/content/10.1101/2023.03.13.532485v1?rss=1 Sinclair, M. Stein, R. A. Sheehan, J. Hawes, E. M. O'Brien, R. M. Tajkhorshid, E. Claxton, D. P. 2023-03-15 doi:10.1101/2023.03.13.532485 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ A mechanistic model of primer synthesis from catalytic structures of DNA polymerase α-primase ]]> https://biorxiv.org/content/10.1101/2023.03.16.533013v1?rss=1 Mullins, E. A. Salay, L. E. Durie, C. L. Jackman, J. E. Ohi, M. D. Chazin, W. J. Eichman, B. F. 2023-03-16 doi:10.1101/2023.03.16.533013 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ A comprehensive map of hotspots of de novo telomere addition in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2023.03.20.533556v1?rss=1 Ngo, K. Gittens, T. H. Gonzalez, D. I. Hatmaker, E. A. Plotkin, S. Engle, M. Friedman, G. A. Goldin, M. Hoerr, R. E. Eichman, B. F. Rokas, A. Benton, M. L. Friedman, K. L. 2023-03-23 doi:10.1101/2023.03.20.533556 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Microbial short-chain fatty acids regulate drug seeking and transcriptional control in a model of cocaine seeking ]]> https://biorxiv.org/content/10.1101/2023.03.22.533834v1?rss=1 Meckel, K. R. Simpson, S. Godino, A. Peck, E. G. George, O. Calipari, E. S. Hofford, R. S. Kiraly, D. 2023-03-24 doi:10.1101/2023.03.22.533834 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Golgi organization is a determinant of stem cell function in the small intestine ]]> https://biorxiv.org/content/10.1101/2023.03.23.533814v1?rss=1 Scharaw, S. Sola Carvajal, A. Belevich, I. Webb, A. T. Das, S. Andersson, S. Pentinmikko, N. Villablanca, E. J. Goldenring, J. R. Jokitalo, E. Coffey, R. J. Katajisto, P. 2023-03-24 doi:10.1101/2023.03.23.533814 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ MutationExplorer - a webserver for mutation of proteins and 3D visualization of energetic impacts ]]> https://biorxiv.org/content/10.1101/2023.03.23.533926v1?rss=1 Philipp, M. Moth, C. W. Ristic, N. Tiemann, J. K. S. Seufert, F. Meiler, J. Hildebrand, P.-W. Stein, A. Wiegreffe, D. Staritzbichler, R. 2023-03-25 doi:10.1101/2023.03.23.533926 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ A role for N6-methyldeoxyadenosine in C. elegans mitochondrial genome regulation ]]> https://biorxiv.org/content/10.1101/2023.03.27.534452v1?rss=1 Grub, L. K. Held, J. P. Hansen, T. J. Schaffner, S. H. Canter, M. R. Malagise, E. M. Patel, M. R. 2023-03-29 doi:10.1101/2023.03.27.534452 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ BRWD3 promotes KDM5 degradation to maintain H3K4 methylation levels ]]> https://biorxiv.org/content/10.1101/2023.03.28.534572v1?rss=1 Han, D. Schaffner, S. Davies, J. P. Benton, M. L. Plate, L. Nordman, J. 2023-03-28 doi:10.1101/2023.03.28.534572 Cold Spring Harbor Laboratory Press 2023-03-28 <![CDATA[ Sox11 is enriched in myogenic progenitors but dispensable for development and regeneration of skeletal muscle. ]]> https://biorxiv.org/content/10.1101/2023.03.30.534956v1?rss=1 Oprescu, S. N. Baumann, N. Chen, X. Sun, Q. Zhao, Y. Yue, F. Wang, H. Kuang, S. 2023-04-01 doi:10.1101/2023.03.30.534956 Cold Spring Harbor Laboratory Press 2023-04-01 <![CDATA[ Data-driven structural analysis of Small Cell Lung Cancer transcription factor networksuggests potential subtype regulators and transition pathways ]]> https://biorxiv.org/content/10.1101/2023.04.01.535226v1?rss=1 Ozen, M. Lopez, C. F. 2023-04-03 doi:10.1101/2023.04.01.535226 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ The adhesion GPCRs CELSR1-3 and LPHN3 engage G proteins via distinct activation mechanisms ]]> https://biorxiv.org/content/10.1101/2023.04.02.535287v1?rss=1 Bui, D. L. H. Roach, A. Li, J. Bandekar, S. J. Orput, E. Raghavan, R. Arac, D. Sando, R. 2023-04-03 doi:10.1101/2023.04.02.535287 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Immune Profiling of Dermatologic Adverse Events from Checkpoint Blockade using Tissue Cyclic Immunofluorescence ]]> https://biorxiv.org/content/10.1101/2023.04.03.535435v1?rss=1 Maliga, Z. Kim, D. Y. Bui, A.-T. N. Lin, J.-R. Dewan, A. K. Murphy, G. F. Nirmal, A. J. Lian, C. G. Sorger, P. K. LeBoeuf, N. R. 2023-04-05 doi:10.1101/2023.04.03.535435 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ Implementation considerations for deep learning with diffusion MRI streamline tractography ]]> https://biorxiv.org/content/10.1101/2023.04.03.535465v1?rss=1 Cai, L. Y. Lee, H. H. Newlin, N. R. Kim, M. E. Moyer, D. Rheault, F. Schilling, K. G. Landman, B. A. 2023-04-06 doi:10.1101/2023.04.03.535465 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Interplay between Nrf2 and αB-crystallin in the lens and heart of zebrafish under proteostatic stress ]]> https://biorxiv.org/content/10.1101/2023.04.04.535454v1?rss=1 Mchaourab, H. S. park, j. MacGavin, S. Niederbrach, L. 2023-04-04 doi:10.1101/2023.04.04.535454 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ Comparing chromatin contact maps at scale: methods and insights ]]> https://biorxiv.org/content/10.1101/2023.04.04.535480v1?rss=1 Gunsalus, L. M. McArthur, E. Gjoni, K. Kuang, S. Pittman, M. Capra, J. A. Pollard, K. S. 2023-04-04 doi:10.1101/2023.04.04.535480 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ Prelimbic neuron calcium activity predicts perceived hedonic value across drinking solutions and ethanol dependent states in mice ]]> https://biorxiv.org/content/10.1101/2023.04.04.535635v1?rss=1 Rinker, J. A. Hoffman, M. Knapp, J. Wukitsch, T. J. Kutlu, M. G. Calipari, E. S. McMahan, C. S. Baker, G. H. Woodward, J. J. Mulholland, P. J. 2023-04-06 doi:10.1101/2023.04.04.535635 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Histone Deacetylases (HDACs) maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and non-coding loci ]]> https://biorxiv.org/content/10.1101/2023.04.06.535398v1?rss=1 Kelly, R. Stengel, K. Chandru, A. Johnson, L. Hiebert, S. W. Cowley, S. M. 2023-04-06 doi:10.1101/2023.04.06.535398 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Differential Expression of Gluconeogenesis-Related Transcripts in a Freshwater Zooplankton Model Organism Suggests a Role of the Cori Cycle in Hypoxia Tolerance ]]> https://biorxiv.org/content/10.1101/2023.04.06.535910v1?rss=1 Yampolsky, L. Y. Malek, M. Kilaru, A. Behera, J. 2023-04-07 doi:10.1101/2023.04.06.535910 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ Development of human hippocampal subfield microstructure and relation to associative inference ]]> https://biorxiv.org/content/10.1101/2023.04.07.536066v1?rss=1 Vinci-Booher, S. Schlichting, M. Preston, A. Pestilli, F. 2023-04-09 doi:10.1101/2023.04.07.536066 Cold Spring Harbor Laboratory Press 2023-04-09 <![CDATA[ tCFS: A new 'CFS tracking' paradigm reveals uniform suppression depth regardless of target complexity or salience ]]> https://biorxiv.org/content/10.1101/2023.04.17.537110v1?rss=1 Alais, D. Coorey, J. Blake, R. Davidson, M. J. 2023-04-17 doi:10.1101/2023.04.17.537110 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Integrating Expert Knowledge with Deep Learning Improves QSAR Models for CADD Modeling ]]> https://biorxiv.org/content/10.1101/2023.04.17.537185v1?rss=1 Liu, Y. Moretti, R. Wang, Y. Bodenheimer, B. Derr, T. Meiler, J. 2023-04-18 doi:10.1101/2023.04.17.537185 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Age-dependent ventilator-induced lung injury: Mathematical modeling, experimental data, and statistical analysis ]]> https://biorxiv.org/content/10.1101/2023.04.20.537614v1?rss=1 Hay, Q. Grubb, C. Minucci, S. Valentine, M. S. Van Mullekom, J. Heise, R. L. Reynolds, A. M. 2023-04-21 doi:10.1101/2023.04.20.537614 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Effects of repeated developmental GLP-1R agonist exposure on adult behavior and hippocampal structure in mice ]]> https://biorxiv.org/content/10.1101/2023.04.21.537724v1?rss=1 Cerroni, C. Steiner, A. Seanez, L. Kwon, S. Lewis, A. S. 2023-04-21 doi:10.1101/2023.04.21.537724 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ SARS-CoV-2 Nonstructural Proteins 3 and 4 tune the Unfolded Protein Response ]]> https://biorxiv.org/content/10.1101/2023.04.22.537917v1?rss=1 Davies, J. P. Sivadas, A. Keller, K. R. Wojcikiewicz, R. J. Plate, L. 2023-04-24 doi:10.1101/2023.04.22.537917 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ Frontal-midline oscillations index the evolution of spatial memory during active navigation ]]> https://biorxiv.org/content/10.1101/2023.04.22.537940v1?rss=1 Du, Y. K. Liang, M. McAvan, A. S. Wilson, R. C. Ekstrom, A. D. 2023-04-23 doi:10.1101/2023.04.22.537940 Cold Spring Harbor Laboratory Press 2023-04-23 <![CDATA[ Distinct blood CD3+ CD14+ T Cell-Monocyte complexes harbor HIV and are dynamic, glucose-dependent, and increased in individuals with glucose intolerance ]]> https://biorxiv.org/content/10.1101/2023.04.24.538020v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@fdc324org.highwire.dtl.DTLVardef@168fc4org.highwire.dtl.DTLVardef@138a9a0org.highwire.dtl.DTLVardef@1087108_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LICirculating CD3+ CD14+ T cell-monocyte complexes are higher in individuals with diabetes. C_LIO_LICD3+ CD14+ T cell-monocytes complexes comprise a heterogenous group of functional and dynamic cell-cell interactions. C_LIO_LIThe proportion of CD3+ CD14+ T cell-monocyte complexes is positively associated with fasting blood glucose and negatively with plasma IL-10 levels and CD4+ T regulatory cells. C_LIO_LICD3+ CD14+ T cell-monocyte complexes are metabolically flexible and can utilize both glycolysis and oxidative phosphorylation for their energy requirements. C_LIO_LIIn persons with treated HIV, CD3+ CD14+ T cell-monocytes have more detectable HIV DNA than circulating CD4+ T cells alone. C_LI ]]> Wanjalla, C. N. Simmons, J. Oakes, J. Zhang, X. Nochowivz, C. Priest, S. Bailin, S. S. Watten, C. M. Mashayekhi, M. Beasley, H. K. Wang, J. Meenderink, L. M. Sheng, Q. Stolze, J. Gangula, R. Chopra, A. Gabriel, C. L. Temu, T. Pakala, S. Wilfong, E. M. Gianella, S. Phillips, E. J. Harrison, D. G. Hinton, A. Kalams, S. A. Mallal, S. A. Koethe, J. R. 2023-04-26 doi:10.1101/2023.04.24.538020 Cold Spring Harbor Laboratory Press 2023-04-26 <![CDATA[ A Nanoparticle RIG-I Agonist for Cancer Immunotherapy ]]> https://biorxiv.org/content/10.1101/2023.04.25.537919v1?rss=1 Wang-Bishop, L. Wehbe, M. Pastora, L. E. Yang, J. Garland, K. M. Becker, K. W. Carson, C. S. Gibson-Corley, K. N. Ulkoski, D. Krishnamurthy, V. Fedorova, O. Richmond, A. Pyle, A. M. Wilson, J. T. 2023-04-25 doi:10.1101/2023.04.25.537919 Cold Spring Harbor Laboratory Press 2023-04-25 <![CDATA[ Turicibacterales protect mice from severe Citrobacter rodentium infection ]]> https://biorxiv.org/content/10.1101/2023.04.25.538270v1?rss=1 Hoek, K. L. McClanahan, K. G. Latour, Y. L. Shealy, N. Piazuelo, M. B. Vallance, B. A. Byndloss, M. X. Olivares-Villagomez, D. Wilson, K. T. 2023-04-25 doi:10.1101/2023.04.25.538270 Cold Spring Harbor Laboratory Press 2023-04-25 <![CDATA[ Membrane binding of endocytic myosin-1s is inhibited by a class of ankyrin repeat proteins ]]> https://biorxiv.org/content/10.1101/2023.04.26.538419v1?rss=1 Willet, A. H. Ren, L. Chen, J.-S. Gould, K. 2023-04-27 doi:10.1101/2023.04.26.538419 Cold Spring Harbor Laboratory Press 2023-04-27 <![CDATA[ Fission yeast CK1 promotes DNA double-strand break repair through both homologous recombination and non-homologous end joining ]]> https://biorxiv.org/content/10.1101/2023.04.27.538600v1?rss=1 Cullati, S. N. Zhang, E. Shan, Y. Guillen, R. X. Chen, J.-S. Navarrete-Perea, J. Elmore, Z. C. Ren, L. Gygi, S. P. Gould, K. L. 2023-04-28 doi:10.1101/2023.04.27.538600 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Mitotic spindle positioning protein (MISP) is an actin bundler that senses ADP-actin and binds near the pointed ends of filaments ]]> https://biorxiv.org/content/10.1101/2023.05.05.539649v1?rss=1 Morales, E. A. Tyska, M. J. 2023-05-06 doi:10.1101/2023.05.05.539649 Cold Spring Harbor Laboratory Press 2023-05-06 <![CDATA[ Dark nanodiscs as a model membrane for evaluating membrane protein thermostability by differential scanning fluorimetry ]]> https://biorxiv.org/content/10.1101/2023.05.08.539917v1?rss=1 Selvasingh, J. A. McDonald, E. F. Mckinney, J. R. Ledwitch, K. V. Meiler, J. 2023-05-09 doi:10.1101/2023.05.08.539917 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Near-field potentials index local neural computations more accurately than population spiking ]]> https://biorxiv.org/content/10.1101/2023.05.11.540026v1?rss=1 Tovar, D. A. Westerberg, J. A. Cox, M. A. Dougherty, K. Wallace, M. Bastos, A. M. Maier, A. 2023-05-12 doi:10.1101/2023.05.11.540026 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ Cryo-electron tomography reveals postsynaptic nanoblocks in excitatory synapses for transcellular alignment ]]> https://biorxiv.org/content/10.1101/2023.05.12.540562v1?rss=1 Sun, R. Wilson, L. Haider, M. Alten, B. Zhou, Z. Wang, X. Zhou, Q. 2023-05-13 doi:10.1101/2023.05.12.540562 Cold Spring Harbor Laboratory Press 2023-05-13 <![CDATA[ Pathogenic bacteria experience pervasive RNA polymerase backtracking during infection ]]> https://biorxiv.org/content/10.1101/2023.05.12.540596v1?rss=1 Browning, K. R. Merrikh, H. 2023-05-12 doi:10.1101/2023.05.12.540596 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ Defining Mitochondrial Cristae Morphology Changes Induced by Aging in Brown Adipose Tissue ]]> https://biorxiv.org/content/10.1101/2023.05.12.540609v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@96099borg.highwire.dtl.DTLVardef@50b4f4org.highwire.dtl.DTLVardef@983092org.highwire.dtl.DTLVardef@19ceb9b_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO Overview of serial block facing-scanning electron microscopy (SBF-SEM) workflow, data segmentation, and 3D analysis of mitochondria using Amira software for murine interscapular BAT. C_FIG ]]> Crabtree, A. Neikirk, K. Marshall, A. Vang, L. Stephens, D. Shao, B. Garza-Lopez, E. Lam, J. Rodriguez, B. Mungai, M. Stanley, J. Dean, D. Gaddy, J. Scudese, E. Sweetwyne, M. Davis, J. Zaganjor, E. Murray, S. Katti, P. Damo, S. Vue, Z. Hinton, A. 2023-05-14 doi:10.1101/2023.05.12.540609 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Amyloid-β exposed astrocytes induce iron transport from endothelial cells at the blood-brain barrier by altering the ratio of apo- and holo-transferrin ]]> https://biorxiv.org/content/10.1101/2023.05.15.540795v1?rss=1 Baringer, S. L. Lukacher, A. S. Palsa, K. Kim, H. Lippmann, E. S. Spiegelman, V. S. Simpson, I. A. Connor, J. R. 2023-05-17 doi:10.1101/2023.05.15.540795 Cold Spring Harbor Laboratory Press 2023-05-17 <![CDATA[ The role of learned song in the evolution and speciation of Eastern and Spotted towhees ]]> https://biorxiv.org/content/10.1101/2023.05.15.540821v1?rss=1 Leon Du'Mottuchi, X. Creanza, N. 2023-05-16 doi:10.1101/2023.05.15.540821 Cold Spring Harbor Laboratory Press 2023-05-16 <![CDATA[ Leveraging longitudinal diffusion MRI data to quantify differences in white matter microstructural decline in normal and abnormal aging ]]> https://biorxiv.org/content/10.1101/2023.05.17.541182v1?rss=1 Archer, D. B. Schilling, K. Shashikumar, N. Jasodanand, V. Moore, E. Pechman, K. Bilgel, M. Beason-Held, L. An, Y. Shafer, A. Ferrucci, L. Risacher, S. L. Gifford, K. Landman, B. Landman, B. A. Jefferson, A. Saykin, A. J. Resnick, S. M. Hohman, T. Alzheimer's Disease Neuroimaging Initiative, 2023-05-18 doi:10.1101/2023.05.17.541182 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Folding of the cerebellar cortex is clade-specific in form, but universal in degree ]]> https://biorxiv.org/content/10.1101/2023.05.17.541232v1?rss=1 York, A. R. Sherwood, C. C. Manger, P. R. Kaas, J. H. Mota, B. Herculano-Houzel, S. 2023-05-18 doi:10.1101/2023.05.17.541232 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Myeloid Cell-Derived IL1β Contributes to Pulmonary Vascular Remodeling in Heart Failure with Preserved Ejection Fraction ]]> https://biorxiv.org/content/10.1101/2023.05.18.541302v1?rss=1 Agrawal, V. Kropski, J. A. Gokey, J. J. Kobeck, E. Murphy, M. B. Murray, K. T. Fortune, N. L. Moore, C. S. Meoli, D. F. Monahan, K. Su, Y. R. Blackwell, T. Gupta, D. K. Talati, M. H. Carrier, E. J. West, J. D. Hemnes, A. R. 2023-05-18 doi:10.1101/2023.05.18.541302 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Calorie Restriction Outperforms Bariatric Surgery in a Murine Model of Obesity and Triple-Negative Breast Cancer ]]> https://biorxiv.org/content/10.1101/2023.05.19.541484v1?rss=1 Coleman, M. F. Camp, K. K. McFarlane, T. L. Doerstling, S. S. Khatib, S. A. Rezeli, E. T. Lewis, A. G. Pfeil, A. J. Smith, L. A. Fouladi, F. Gong, W. Glenny, E. M. Parker, J. S. Milne, G. L. Carroll, I. M. Fodor, A. A. Seeley, R. Hursting, S. D. 2023-05-22 doi:10.1101/2023.05.19.541484 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Optimizing In Situ Proximity Ligation Assays for Mitochondria, ER, or MERC Markers in Skeletal Muscle Tissue and Cells ]]> https://biorxiv.org/content/10.1101/2023.05.20.541599v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@1021ce7org.highwire.dtl.DTLVardef@1b78f8borg.highwire.dtl.DTLVardef@31030corg.highwire.dtl.DTLVardef@1bf0afa_HPS_FORMAT_FIGEXP M_FIG C_FIG O_TBL View this table: org.highwire.dtl.DTLVardef@169ba8corg.highwire.dtl.DTLVardef@566b30org.highwire.dtl.DTLVardef@197330dorg.highwire.dtl.DTLVardef@198ca7borg.highwire.dtl.DTLVardef@158b80_HPS_FORMAT_FIGEXP M_TBL C_TBL ]]> Stephens, D. C. Crabtree, A. Beasley, H. K. Garza-Lopez, E. Neikirk, K. Mungai, M. Vang, L. Vue, Z. Vue, N. Marshall, A. G. Turner, K. Shao, J.-q. Murray, S. A. Gaddy, J. A. Wanjalla, C. Davis, J. Damo, S. M. Hinton, A. 2023-05-22 doi:10.1101/2023.05.20.541599 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Components of Isolated Skeletal Muscle Differentiated Through Antibody Validation ]]> https://biorxiv.org/content/10.1101/2023.05.20.541600v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@165b34dorg.highwire.dtl.DTLVardef@1de9976org.highwire.dtl.DTLVardef@12d3cfeorg.highwire.dtl.DTLVardef@ff660c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Stephens, D. C. Mungai, M. Crabtree, A. Beasley, H. K. Garza-Lopez, E. Vang, L. Neikirk, K. Vue, Z. Vue, N. Marshall, A. G. Turner, K. Shao, J.-q. Sarker, B. Murray, S. A. Gaddy, J. A. Davis, J. Damo, S. M. Hinton, A. 2023-05-22 doi:10.1101/2023.05.20.541600 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Creating Optimal Conditions for OPA1 isoforms by Western Blot in Muscle Tissue ]]> https://biorxiv.org/content/10.1101/2023.05.20.541601v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@1dc254dorg.highwire.dtl.DTLVardef@150d3eorg.highwire.dtl.DTLVardef@186ed2org.highwire.dtl.DTLVardef@13cc3a_HPS_FORMAT_FIGEXP M_FIG C_FIG O_TBL View this table: org.highwire.dtl.DTLVardef@1c518ceorg.highwire.dtl.DTLVardef@df826borg.highwire.dtl.DTLVardef@1eb5bf8org.highwire.dtl.DTLVardef@e324e6org.highwire.dtl.DTLVardef@8baedc_HPS_FORMAT_FIGEXP M_TBL C_TBL Method SummarySamples for western blot analysis are isolated from lysed cells, loaded onto a gel, and ran using optimized conditions to better isolate OPA1 isoforms. Samples are transferred to a membrane for incubation and protein detection using OPA1 antibodies. ]]> Stephens, D. C. Crabtree, A. Beasley, H. K. Garza-Lopez, E. Mungai, M. Neikirk, K. Vang, L. Vue, Z. Vue, N. Marshall, A. G. Turner, K. Shao, J.-q. Murray, S. A. Gaddy, J. A. Wanjalla, C. Davis, J. Damo, S. M. Hinton, A. 2023-05-22 doi:10.1101/2023.05.20.541601 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Ablation of Sam50 is associated with fragmentation and alterations in metabolism in human myotubes ]]> https://biorxiv.org/content/10.1101/2023.05.20.541602v1?rss=1 Vue, Z. Vang, C. Neikirk, K. Garza-Lopez, E. Shao, J.-q. Mungai, M. Vang, L. Beasley, H. K. Marshall, A. G. Crabtree, A. Stephens, D. C. McReynolds, M. Murray, S. A. Katti, P. Gaddy, J. A. Damo, S. M. Hinton, A. 2023-05-22 doi:10.1101/2023.05.20.541602 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Mapping Niche-specific Two-Component System Requirements in Uropathogenic Escherichia coli ]]> https://biorxiv.org/content/10.1101/2023.05.23.541942v1?rss=1 75% of urinary tract infections (UTIs) worldwide. UTIs are most prevalent among people assigned female at birth, with the vagina becoming colonized by UPEC in addition to the gut and the bladder. In the bladder, adherence to the urothelium triggers E. coli invasion of bladder cells and an intracellular pathogenic cascade. Intracellular E. coli are safely hidden from host neutrophils, competition from the microbiota, and antibiotics that kill extracellular E. coli. To survive in these intimately connected, yet physiologically diverse niches E. coli must rapidly coordinate metabolic and virulence systems in response to the distinct stimuli encountered in each environment. We hypothesized that specific TCSs allow UPEC to sense these diverse environments encountered during infection with built-in redundant safeguards. Here, we created a library of isogenic TCS deletion mutants that we leveraged to map distinct TCS contributions to infection. We identify - for the first time - a comprehensive panel of UPEC TCSs that are critical for infection of the genitourinary tract and report that the TCSs mediating colonization of the bladder, kidneys, or vagina are distinct. IMPORTANCEWhile two-component system (TCS) signaling has been investigated at depth in model strains of E. coli, there have been no studies to elucidate - at a systems level - which TCSs are important during infection by pathogenic Escherichia coli. Here, we report the generation of a markerless TCS deletion library in a uropathogenic E. coli (UPEC) isolate that can be leveraged for dissecting the role of TCS signaling in different aspects of pathogenesis. We use this library to demonstrate, for the first time in UPEC, that niche-specific colonization is guided by distinct TCS groups. ]]> Brannon, J. R. Reasoner, S. Bermudez, T. Dunigan, T. L. Wiebe, M. A. Beebout, C. J. Ross, T. L. Bamidele, A. Hadjifrangiskou, M. 2023-05-23 doi:10.1101/2023.05.23.541942 Cold Spring Harbor Laboratory Press 2023-05-23 <![CDATA[ Growth factor-free, peptide-functionalized gelatin hydrogel promotes arteriogenesis and attenuates tissue damage in a murine model of critical limb ischemia ]]> https://biorxiv.org/content/10.1101/2023.05.24.542150v1?rss=1 Curry, C. W. Sturgeon, S. M. O'Grady, B. J. Yates, A. K. Kjar, A. Paige, H. A. Mowery, L. S. Katdare, K. A. Patel, R. V. Mlouk, K. Stiefbold, M. R. Vafaie-Partin, S. Kawabata, A. McKee, R. M. Moore-Lotridge, S. Hawkes, A. Kusunose, J. Gibson-Corley, K. N. Schmeckpeper, J. Schoenecker, J. G. Caskey, C. F. Lippmann, E. S. 2023-05-25 doi:10.1101/2023.05.24.542150 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Influence of Fast-Spiking Prefrontal Neurons on Working Memory Behavior ]]> https://biorxiv.org/content/10.1101/2023.05.28.542641v1?rss=1 Chung, S. Mozumder, R. Li, S. Constantinidis, C. 2023-05-30 doi:10.1101/2023.05.28.542641 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter ]]> https://biorxiv.org/content/10.1101/2023.05.29.541986v1?rss=1 Tang, Q. Sinclair, M. Hasdemir, H. Stein, R. A. Karakas, E. Tajkhorshid, E. Mchaourab, H. 2023-05-29 doi:10.1101/2023.05.29.541986 Cold Spring Harbor Laboratory Press 2023-05-29 <![CDATA[ Study design features that improve effect sizes in cross-sectional and longitudinal brain-wide association studies ]]> https://biorxiv.org/content/10.1101/2023.05.29.542742v1?rss=1 Kang, K. Seidlitz, J. Bethlehem, R. A. I. Schildcrout, J. Tao, R. Xiong, J. Jones, M. T. Lifespan Brain Chart Consortium, 3R-BRAIN, AIBL, Alzheimers Disease Neuroimaging Initiative, Alzheimers Disease Repository Without Borders Investigators, CALM Team, CCNP, COBRE, cVEDA, Harvard Aging Brain Study, IMAGEN, POND, The PREVENT-AD Research Group, Alexander-Bloch, A. Vandekar, S. 2023-06-01 doi:10.1101/2023.05.29.542742 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Albumin-binding RNAi Conjugate for Carrier Free Treatment of Arthritis ]]> https://biorxiv.org/content/10.1101/2023.05.31.542971v1?rss=1 Colazo, J. M. Hoogenboezem, E. N. Shah, V. Yu, F. Lo, J. H. Sorets, A. G. Francini, N. Cho, H. Michell, D. L. Vickers, K. C. Gibson-Corley, K. N. Hasty, K. A. Crofford, L. Cook, R. S. Duvall, C. L. 2023-06-04 doi:10.1101/2023.05.31.542971 Cold Spring Harbor Laboratory Press 2023-06-04 <![CDATA[ After wounding, a G-protein coupled receptor restores tension to epithelial cells in a dynamic inward-traveling wave ]]> https://biorxiv.org/content/10.1101/2023.05.31.543122v1?rss=1 Han, I. Nassar, L. S. Page-McCaw, A. Hutson, M. S. 2023-06-03 doi:10.1101/2023.05.31.543122 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ Eosinophils exert direct and indirect anti-tumorigenic effects in the development of esophageal squamous cell carcinoma ]]> https://biorxiv.org/content/10.1101/2023.06.01.543287v1?rss=1 Jacobse, J. Aziz, Z. Sun, L. Chaparro, J. Pilat, J. M. Kwag, A. Buendia, M. Wimbiscus, M. Nasu, M. Saito, T. Mine, S. Orita, H. Revetta, F. Short, S. Washington, M. K. Hiremath, G. Gibson, M. Coburn, L. A. Koyama, T. Goettel, J. Williams, C. Choksi, Y. A. 2023-06-05 doi:10.1101/2023.06.01.543287 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ The impact of common variants on gene expression in the human brain: from RNA to protein to schizophrenia risk ]]> https://biorxiv.org/content/10.1101/2023.06.04.543603v1?rss=1 Liang, Q. Jiang, Y. Shieh, A. W. Zhou, D. Chen, R. Wang, F. Xu, M. Wang, X. Pinto, D. Wang, Y. Cheng, L. Vadukapuram, R. Zhang, C. Grennan, K. Giase, G. The PsychENCODE Consortium, White, K. P. Peng, J. Li, B. Liu, C. Chen, C. Wang, S. H. 2023-06-05 doi:10.1101/2023.06.04.543603 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ DNA methylation signatures of early life adversity are exposure-dependent in wild baboons ]]> https://biorxiv.org/content/10.1101/2023.06.05.542485v1?rss=1 Anderson, J. A. Lin, D. Lea, A. J. Johnston, R. A. Voyles, T. Akinyi, M. Y. Archie, E. Alberts, S. C. Tung, J. 2023-06-05 doi:10.1101/2023.06.05.542485 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ The proprotein convertase BLI-4 promotes collagen secretion during assembly of the Caenorhabditis elegans cuticle ]]> https://biorxiv.org/content/10.1101/2023.06.06.542650v1?rss=1 Birnbaum, S. K. Cohen, J. D. Belfi, A. Murray, J. I. Adams, J. R. G. Chisholm, A. D. Sundaram, M. V. 2023-06-07 doi:10.1101/2023.06.06.542650 Cold Spring Harbor Laboratory Press 2023-06-07 <![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[ Arrest of mouse preterm labor until term delivery by combination therapy with atosiban and mundulone, a natural product with tocolytic efficacy ]]> https://biorxiv.org/content/10.1101/2023.06.06.543921v1?rss=1 day 19, 4-5 days post-mifepristone exposure) without any visible maternal and fetal consequences. Collectively, these studies provide a strong foundation for the future development of mundulone as a stand-alone single- and/or combination-tocolytic therapy for management of PL. ]]> Siricilla, S. Hansen, C. J. Rogers, J. H. De, D. Simpson, C. L. Waterson, A. G. Sulikowski, G. A. Crockett, S. L. Boatwright, N. Reese, J. J. Paria, B. C. Newton, J. M. Herington, J. L. 2023-06-08 doi:10.1101/2023.06.06.543921 Cold Spring Harbor Laboratory Press 2023-06-08 <![CDATA[ Minimum entropy framework identifies a novel class of genomic functional elements and reveals regulatory mechanisms at human disease loci ]]> https://biorxiv.org/content/10.1101/2023.06.11.544507v1?rss=1 Betti, M. J. Aldrich, M. Gamazon, E. R. 2023-06-12 doi:10.1101/2023.06.11.544507 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ Thermal proteome profiling of breast cancer cells reveals proteasomal activation by CDK4/6 inhibitor palbociclib ]]> https://biorxiv.org/content/10.1101/202770v1?rss=1 Miettinen, T. P. Peltier, J. Hartlova, A. Gierlinski, M. Jansen, V. M. Trost, M. Bjorklund, M. 2017-10-13 doi:10.1101/202770 Cold Spring Harbor Laboratory Press 2017-10-13 <![CDATA[ Genetic analysis of de novo variants reveals sex differences in complex and isolated congenital diaphragmatic hernia and indicates MYRF as a candidate gene ]]> https://biorxiv.org/content/10.1101/206037v1?rss=1 Qi, H. Yu, L. Zhou, X. Kitaygorodsky, A. Wynn, J. Zhu, N. Aspelund, G. Lim, F. Y. Crombleholme, T. Cusick, R. Azarow, K. Danko, M. E. Chung, D. Warner, B. W. Mychaliska, G. B. Potoka, D. Wagner, A. J. ElFiky, M. Wilson, J. M. High, F. A. Longoni, M. Donahoe, P. Chung, W. K. Shen, Y. 2017-10-19 doi:10.1101/206037 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata ]]> https://biorxiv.org/content/10.1101/207746v1?rss=1 Wang, M. Fu, H. Shen, X.-X. Ruan, R. Pun, N. Xu, J. Li, H. Rokas, A. 2017-10-31 doi:10.1101/207746 Cold Spring Harbor Laboratory Press 2017-10-31 <![CDATA[ Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies ]]> https://biorxiv.org/content/10.1101/212357v1?rss=1 1400 binary phenotypes, we show that SAIGE can efficiently analyze large sample data, controlling for unbalanced case-control ratios and sample relatedness. ]]> Zhou, W. Nielsen, J. B. Fritsche, L. G. Dey, R. Elvestad, M. B. Wolford, B. B. LeFaive, J. Lin, M. Hveem, K. Kang, H. M. Abecasis, G. R. Willer, C. J. Lee, S. 2017-11-01 doi:10.1101/212357 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Functional categories in macaque frontal eye field ]]> https://biorxiv.org/content/10.1101/212589v1?rss=1 Lowe, K. Schall, J. D. 2017-11-01 doi:10.1101/212589 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Neural mechanisms of speed-accuracy tradeoff of visual search: Saccade vigor, targeting errors, superior colliculus and frontal eye field ]]> https://biorxiv.org/content/10.1101/212621v1?rss=1 Reppert, T. Servant, M. Heitz, R. Schall, J. D. 2017-11-01 doi:10.1101/212621 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Prefrontal control of visual distraction ]]> https://biorxiv.org/content/10.1101/212720v1?rss=1 Cosman, J. Woodman, G. Schall, J. D. 2017-11-01 doi:10.1101/212720 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Evidence for loss and adaptive reacquisition of alcoholic fermentation in an early-derived fructophilic yeast lineage ]]> https://biorxiv.org/content/10.1101/213686v1?rss=1 Goncalves, C. Wisecaver, J. H. Salema-Oom, M. Leandro, M. J. Shen, X.-X. Peris, D. Hittinger, C. T. Rokas, A. Goncalves, P. 2017-11-03 doi:10.1101/213686 Cold Spring Harbor Laboratory Press 2017-11-03 <![CDATA[ Prevention and reversion of pancreatic tumorigenesis through a differentiation-based mechanism ]]> https://biorxiv.org/content/10.1101/221986v1?rss=1 Krah, N. M. Yugawa, D. Straley, J. Wright, C. V. E. MacDonald, R. J. Murtaugh, L. C. 2017-11-19 doi:10.1101/221986 Cold Spring Harbor Laboratory Press 2017-11-19 <![CDATA[ High Throughput Functional Evaluation of KCNQ1 Decrypts Variants of Unknown Significance ]]> https://biorxiv.org/content/10.1101/223206v1?rss=1 Vanoye, C. Desai, R. Fabre, K. Potet, F. DeKeyser, J.-M. Macaya, D. Meiler, J. Sanders, C. George, A. 2017-11-21 doi:10.1101/223206 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ Assessing the genetic effect mediated through gene expression from summary eQTL and GWAS data ]]> https://biorxiv.org/content/10.1101/223263v1?rss=1 Barfield, R. Feng, H. Gusev, A. Wu, L. Zheng, W. Pasaniuc, B. Kraft, P. 2017-11-21 doi:10.1101/223263 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ Mutations in RPL3L and MYZAP increase risk of atrial fibrillation ]]> https://biorxiv.org/content/10.1101/223578v1?rss=1 Thorolfsdottir, R. B. Sveinbjornsson, G. Sulem, P. Jonsson, S. Halldorsson, G. Melsted, P. Ivarsdottir, E. V. Davidsson, O. B. Kristjansson, R. B. Thorleifsson, G. Helgadottir, A. Gretarsdottir, S. Norddahl, G. Rajamani, S. Torfason, B. Valgardsson, A. S. Sverrisson, J. T. Tragante, V. Asselbergs, F. W. Roden, D. M. Darbar, D. Pedersen, T. R. Sabatine, M. S. Lochen, M.-L. Halldorsson, B. V. Jonsdottir, I. Arnar, D. O. Thorsteinsdottir, U. Gudbjartsson, D. F. Holm, H. Stefansson, K. 2017-11-21 doi:10.1101/223578 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ Mechanisms of KCNQ1 Channel Dysfunction in Long QT Syndrome Involving Voltage Sensor Domain Mutations ]]> https://biorxiv.org/content/10.1101/231845v1?rss=1 Huang, H. Kuenze, G. Smith, J. Taylor, K. C. Duran, A. M. Hadziselimovic, A. Meiler, J. Vanoye, C. George, A. Sanders, C. 2017-12-10 doi:10.1101/231845 Cold Spring Harbor Laboratory Press 2017-12-10 <![CDATA[ Copy number variation in fungi and its implications for wine yeast genetic diversity and adaptation ]]> https://biorxiv.org/content/10.1101/233122v1?rss=1 Steenwyk, J. Rokas, A. 2017-12-12 doi:10.1101/233122 Cold Spring Harbor Laboratory Press 2017-12-12 <![CDATA[ iterativeWGCNA: iterative refinement to improve module detection from WGCNA co-expression networks ]]> https://biorxiv.org/content/10.1101/234062v1?rss=1 Greenfest-Allen, E. Cartailler, J.-P. Magnuson, M. A. Stoeckert, C. J. 2017-12-14 doi:10.1101/234062 Cold Spring Harbor Laboratory Press 2017-12-14 <![CDATA[ Muscle specific stress fibers give rise to sarcomeres and are mechanistically distinct from stress fibers in non-muscle cells ]]> https://biorxiv.org/content/10.1101/235424v1?rss=1 Feinx, A. M. Taneja, N. Neininger, A. C. Visetsouk, M. R. Nixon, B. R. Manalo, A. E. Becker, J. R. Crawley, S. W. Bader, D. M. Tyska, M. J. Gutzman, J. H. Burnette, D. T. 2017-12-18 doi:10.1101/235424 Cold Spring Harbor Laboratory Press 2017-12-18 <![CDATA[ Formation of retinal direction-selective circuitry initiated by starburst amacrine cell homotypic contact ]]> https://biorxiv.org/content/10.1101/235978v1?rss=1 Ray, T. A. Roy, S. Kozlowski, C. Wang, J. Cafaro, J. Hulbert, S. Wright, C. V. E. Field, G. D. Kay, J. N. 2017-12-18 doi:10.1101/235978 Cold Spring Harbor Laboratory Press 2017-12-18 <![CDATA[ A memory element imposes epigenetic behavior on intrinsically labile RNAi-induced heterochromatin spread. ]]> https://biorxiv.org/content/10.1101/237479v1?rss=1 Greenstein, R. A. Jones, S. K. Spivey, E. C. Rybarski, J. R. Finkelstein, I. Al-Sady, B. 2017-12-21 doi:10.1101/237479 Cold Spring Harbor Laboratory Press 2017-12-21 <![CDATA[ Bioinformatic analysis of endogenous and exogenous small RNAs on lipoproteins ]]> https://biorxiv.org/content/10.1101/246900v1?rss=1 85% of sRNAs in liver, bile, and urine, a significant advance compared to existing software. Results suggest that the majority of sRNAs on lipoproteins are non-host sRNAs derived from bacterial sources in the microbiome and environment, specifically rRNA-derived sRNAs from Proteobacteria. Collectively, TIGER facilitated novel discoveries of lipoprotein and biofluid sRNAs and has tremendous applicability for the field of extracellular RNA. ]]> Allen, R. M. Zhao, S. Ramirez-Solano, M. A. Michell, D. L. Wang, Y. Shyr, Y. Sethupathy, P. Linton, M. F. Graf, G. A. Sheng, Q. Vickers, K. C. 2018-01-11 doi:10.1101/246900 Cold Spring Harbor Laboratory Press 2018-01-11 <![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[ A simple genetic basis for managing maternally transmitted symbionts ]]> https://biorxiv.org/content/10.1101/256909v1?rss=1 Funkhouser-Jones, L. J. van Opstal, E. J. Sharma, A. Bordenstein, S. R. 2018-02-01 doi:10.1101/256909 Cold Spring Harbor Laboratory Press 2018-02-01 <![CDATA[ Focal adhesion kinase regulates early steps of myofibrillogenesis in cardiomyocytes ]]> https://biorxiv.org/content/10.1101/261248v1?rss=1 Taneja, N. Neininger, A. C. Bersi, M. R. Merryman, W. D. Burnette, D. T. 2018-02-07 doi:10.1101/261248 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ FGF activity asymmetrically regulates the timing of habenular neurogenesis in a Nodal-dependent manner ]]> https://biorxiv.org/content/10.1101/261834v1?rss=1 Dean, B. J. Gamse, J. T. Wu, S.-Y. 2018-02-07 doi:10.1101/261834 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ Multisensory perception reflects individual differences in processing temporal correlations ]]> https://biorxiv.org/content/10.1101/264457v1?rss=1 Nidiffer, A. Diederich, A. Ramachandran, R. Wallace, M. T. 2018-02-13 doi:10.1101/264457 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ Differences In Neural Activity, But Not Behavior, Across Social Contexts In Guppies, Poecilia reticulata ]]> https://biorxiv.org/content/10.1101/265736v1?rss=1 Fischer, E. K. Westrick, S. E. Hartsough, L. Hoke, K. L. 2018-02-14 doi:10.1101/265736 Cold Spring Harbor Laboratory Press 2018-02-14 <![CDATA[ Feature Specific Prediction Errors and Surprise across Macaque Fronto-Striatal Circuits during Attention and Learning ]]> https://biorxiv.org/content/10.1101/266205v1?rss=1 Oemisch, M. Westendorff, S. Azimi, M. Hassani, S. A. Ardid, S. Tiesinga, P. Womelsdorf, T. 2018-02-15 doi:10.1101/266205 Cold Spring Harbor Laboratory Press 2018-02-15 <![CDATA[ Significant shared heritability underlies suicide attempt and clinically predicted probability of attempting suicide ]]> https://biorxiv.org/content/10.1101/266411v1?rss=1 Ruderfer, D. M. Walsh, C. G. Aquirre, M. W. Ribeiro, J. D. Franklin, J. C. Rivas, M. A. 2018-02-15 doi:10.1101/266411 Cold Spring Harbor Laboratory Press 2018-02-15 <![CDATA[ Most calbindin-immunoreactive neurons, but few calretinin-immunoreactive neurons, express the m1 acetylcholine receptor in the middle temporal visual area of the macaque monkey ]]> https://biorxiv.org/content/10.1101/271924v1?rss=1 Coppola, J. J. Disney, A. A. 2018-02-27 doi:10.1101/271924 Cold Spring Harbor Laboratory Press 2018-02-27 <![CDATA[ Variations in neuromodulatory chemical signatures define compartments in macaque cortex ]]> https://biorxiv.org/content/10.1101/272849v1?rss=1 Ward, N. J. Zinke, W. Coppola, J. J. Disney, A. A. 2018-02-27 doi:10.1101/272849 Cold Spring Harbor Laboratory Press 2018-02-27 <![CDATA[ A 3D model of human skeletal muscle innervated with stem cell-derived motor neurons enables epsilon-subunit targeted myasthenic syndrome studies ]]> https://biorxiv.org/content/10.1101/275545v1?rss=1 Afshar Bakooshli, M. Lippmann, E. S. Mulcahy, B. Tung, K. Pegoraro, E. Ahn, H. Ginsberg, H. Zhen, M. Ashton, R. S. Gilbert, P. M. 2018-03-02 doi:10.1101/275545 Cold Spring Harbor Laboratory Press 2018-03-02 <![CDATA[ YES1 amplification: a mechanism of acquired resistance to EGFR inhibitors identified by transposon mutagenesis and clinical genomics ]]> https://biorxiv.org/content/10.1101/275974v1?rss=1 Fan, P.-D. Narzisi, G. Jayaprakash, A. D. Venturini, E. Robine, N. Smibert, P. Germer, S. Yu, H. A. Jordan, E. J. Paik, P. K. Janjigian, Y. Y. Chaft, J. E. Wang, L. Jungbluth, A. A. Middha, S. Spraggon, L. Qiao, H. Lovly, C. M. Kris, M. G. Riely, G. J. Politi, K. Varmus, H. Ladanyi, M. 2018-03-16 doi:10.1101/275974 Cold Spring Harbor Laboratory Press 2018-03-16 <![CDATA[ Microtubule minus-end aster organization is driven by processive HSET-tubulin clusters ]]> https://biorxiv.org/content/10.1101/278481v1?rss=1 Norris, S. R. Jung, S. Singh, P. Strothman, C. E. Erwin, A. L. Ohi, M. D. Zanic, M. Ohi, R. 2018-03-08 doi:10.1101/278481 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ Disabling Gβγ SNARE interaction in transgenic mice disrupts GPCR-mediated presynaptic inhibition leading to physiological and behavioral phenotypes. ]]> https://biorxiv.org/content/10.1101/280347v1?rss=1 Zurawski, Z. Thompson Gray, A. D. Brady, L. J. Page, B. Church, E. Harris, N. A. Dohn, M. R. Yim, Y. Y. Hyde, K. Mortlock, D. P. Winder, D. G. Alford, S. Jones, C. K. Hamm, H. E. 2018-03-11 doi:10.1101/280347 Cold Spring Harbor Laboratory Press 2018-03-11 <![CDATA[ Prosody perception in children: studying individual differences with novel brain and behavioral approaches ]]> https://biorxiv.org/content/10.1101/281998v1?rss=1 View larger version (68K): org.highwire.dtl.DTLVardef@7a4ca2org.highwire.dtl.DTLVardef@13d41c6org.highwire.dtl.DTLVardef@a9652borg.highwire.dtl.DTLVardef@130eb6a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Myers, B. Vaughan, C. Soman, U. Blain, S. Korsnack, K. Camarata, S. Gordon, R. 2018-03-14 doi:10.1101/281998 Cold Spring Harbor Laboratory Press 2018-03-14 <![CDATA[ Disrupted structure and aberrant function of CHIP mediates the loss of motor and cognitive function in preclinical models of cerebellar CHIPopathy ]]> https://biorxiv.org/content/10.1101/283192v1?rss=1 Shi, C.-h. Rubel, C. Soss, S. E. Sanchez-Hodge, R. Zhang, S. Stevens, D. A. McDonough, H. Page, R. C. Chazin, W. Patterson, C. Mao, C.-y. Willis, M. S. Luo, H.-Y. Tang, M.-b. Du, P. Wang, Y.-h. Hu, Z.-w. Xu, Y.-M. Schisler, J. 2018-03-15 doi:10.1101/283192 Cold Spring Harbor Laboratory Press 2018-03-15 <![CDATA[ Genome wide association analysis identifies genetic variants associated with reproductive variation across domestic dog breeds and uncovers links to domestication ]]> https://biorxiv.org/content/10.1101/285791v1?rss=1 Phillips, J. B. Smith, S. A. Johnson, M. L. Abbot, P. Capra, J. A. Rokas, A. 2018-03-20 doi:10.1101/285791 Cold Spring Harbor Laboratory Press 2018-03-20 <![CDATA[ Regulation of DVL2 ubiquitylation by USP9X biases participation in canonical or non-canonical WNT signalling ]]> https://biorxiv.org/content/10.1101/289595v1?rss=1 Nielsen, C. P. Jernigan, K. K. MacGurn, J. A. 2018-03-27 doi:10.1101/289595 Cold Spring Harbor Laboratory Press 2018-03-27 <![CDATA[ HDAC11 Suppresses the Thermogenic Program of Adipose Tissue via BRD2 ]]> https://biorxiv.org/content/10.1101/292011v1?rss=1 Bagchi, R. A. Ferguson, B. S. Stratton, M. S. Hu, T. Cavasin, M. A. Sun, L. Lin, Y.-H. Liu, D. Londono, P. Song, K. Pino, M. F. Sparks, L. M. Smith, S. R. Scherer, P. E. Collins, S. Seto, E. McKinsey, T. A. 2018-03-30 doi:10.1101/292011 Cold Spring Harbor Laboratory Press 2018-03-30 <![CDATA[ A systematic review of social contact surveys to inform transmission models of close contact infections ]]> https://biorxiv.org/content/10.1101/292235v1?rss=1 Hoang, T. V. Coletti, P. Melegaro, A. Wallinga, J. Grijalva, C. Edmunds, J. Beutels, P. Hens, N. 2018-03-31 doi:10.1101/292235 Cold Spring Harbor Laboratory Press 2018-03-31 <![CDATA[ CagY-dependent regulation of type IV secretion in Helicobacter pylori is associated with alterations in integrin binding ]]> https://biorxiv.org/content/10.1101/294769v1?rss=1 Skoog, E. Morikis, V. A. Martin, M. E. Foster, G. A. Cai, L. P. Hansen, L. M. Li, B. Gaddy, J. A. Simon, S. Solnick, J. V. 2018-04-04 doi:10.1101/294769 Cold Spring Harbor Laboratory Press 2018-04-04 <![CDATA[ Confidence Analysis of DEER Data and its Structural Interpretation with Ensemble-Biased Metadynamics ]]> https://biorxiv.org/content/10.1101/299941v1?rss=1 Hustedt, E. J. Martinelli, F. Stein, R. A. Faraldo-Gomez, J. Mchaourab, H. 2018-04-11 doi:10.1101/299941 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ A single prophage WO gene rescues cytoplasmic incompatibility in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/300269v1?rss=1 Shropshire, J. D. On, J. Layton, E. M. Zhou, H. Bordenstein, S. R. 2018-04-13 doi:10.1101/300269 Cold Spring Harbor Laboratory Press 2018-04-13 <![CDATA[ Mass Action Kinetic Model of Apoptosis by TRAIL-Functionalized Leukocytes ]]> https://biorxiv.org/content/10.1101/300400v1?rss=1 Lederman, E. King, M. 2018-04-12 doi:10.1101/300400 Cold Spring Harbor Laboratory Press 2018-04-12 <![CDATA[ Intrinsic cooperativity potentiates parallel cis-regulatory evolution ]]> https://biorxiv.org/content/10.1101/301234v1?rss=1 Sorrells, T. R. Johnson, A. N. Howard, C. J. Britton, C. S. Fowler, K. R. Feigerle, J. T. Weil, P. A. Johnson, A. D. 2018-04-14 doi:10.1101/301234 Cold Spring Harbor Laboratory Press 2018-04-14 <![CDATA[ Population level rhythms in human skin: implications for circadian medicine ]]> https://biorxiv.org/content/10.1101/301820v1?rss=1 Wu, G. Ruben, M. Schmidt, R. Francey, L. Smith, D. Anafi, R. Hughey, J. Tasseff, R. Sherrill, J. Oblong, J. Mills, K. Hogenesch, J. 2018-04-16 doi:10.1101/301820 Cold Spring Harbor Laboratory Press 2018-04-16 <![CDATA[ integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth ]]> https://biorxiv.org/content/10.1101/302612v1?rss=1 Eidem, H. R. Steenwyk, J. L. Wisecaver, J. H. Capra, J. A. Abbot, P. Rokas, A. 2018-04-17 doi:10.1101/302612 Cold Spring Harbor Laboratory Press 2018-04-17 <![CDATA[ Loading of piperlongumine to liposomes after complexation with β-cyclodextrin and its effect on viability of colon and prostate cancer cells ]]> https://biorxiv.org/content/10.1101/314161v1?rss=1 Jayawardana, K. W. Jyotsana, N. Zhang, Z. King, M. 2018-05-03 doi:10.1101/314161 Cold Spring Harbor Laboratory Press 2018-05-03 <![CDATA[ Genetic determinants of risk and survival in pulmonary arterial hypertension ]]> https://biorxiv.org/content/10.1101/317164v1?rss=1 16 years versus 8 years), compared to patients homozygous for the alternative allele.nnInterpretationWe have found that common genetic variation at loci in HLA-DPA1/DPB1 and an enhancer near SOX17 are associated with PAH. Impairment of Sox17 function may be more common in PAH than suggested by rare mutations in SOX17. Allelic variation at HLA-DPB1 stratifies PAH patients for survival following diagnosis, with implications for future therapeutic trial design.nnFundingUK NIHR, BHF, UK MRC, Dinosaur Trust, NIH/NHLBI, ERS, EMBO, Wellcome Trust, EU, AHA, ACClinPharm, Netherlands CVRI, Dutch Heart Foundation, Dutch Federation of UMC, Netherlands OHRD and RNAS, German DFG, German BMBF, APH Paris, Inserm, Universite Paris-Sud, and French ANR. ]]> Rhodes, C. Batai, K. Bleda, M. Haimel, M. Southgate, L. Germain, M. Pauciulo, M. Hadinnapola, C. Girerd, B. Arora, A. Knight, J. Hanscombe, K. Karnes, J. Kaakinen, M. Gall, H. Ulrich, A. Harbaum, L. Aman, J. Cebola, I. Ferrer, J. NIHR BioResource Rare Diseases Consortium, UK PAH Cohort Study Consortium, US PAH Biobank Consortium, Ahmad, F. Amouyel, P. Archer, S. Argula, R. Austin, E. Badesch, D. Bakshi, S. Barnett, C. Benza, R. Bhatt, N. Bogaard, H. Burger, C. Chakinala, M. Church, C. Coghlan, J. Condliffe, R. Corris, P. Danesino, C. Debette, S. 2018-05-16 doi:10.1101/317164 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Amycomicin: a potent and specific antibiotic discovered with a targeted interaction screen ]]> https://biorxiv.org/content/10.1101/317362v1?rss=1 Pishchany, G. Mevers, E. Ndousse-Fetter, S. Horvath, D. J. Paludo, C. R. Silva-Junior, E. A. Koren, S. Skaar, E. P. Clardy, J. Kolter, R. 2018-05-08 doi:10.1101/317362 Cold Spring Harbor Laboratory Press 2018-05-08 <![CDATA[ Binocular Integration Manifests as a Transient Spiking Increase Followed by Selective Suppression in Primary Visual Cortex ]]> https://biorxiv.org/content/10.1101/318667v1?rss=1 Cox, M. A. Dougherty, K. Westerberg, J. Schall, M. Maier, A. 2018-05-10 doi:10.1101/318667 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Expression and purification of a functional heteromeric GABAA receptor for structural studies ]]> https://biorxiv.org/content/10.1101/318832v1?rss=1 Claxton, D. P. Gouaux, E. 2018-05-09 doi:10.1101/318832 Cold Spring Harbor Laboratory Press 2018-05-09 <![CDATA[ Binocular modulation of monocular V1 neurons ]]> https://biorxiv.org/content/10.1101/320218v1?rss=1 Dougherty, K. Cox, M. A. Westerberg, J. Maier, A. 2018-05-11 doi:10.1101/320218 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Adaptation of Intracortical Signaling Concurs with Enhanced Encoding Efficiency ]]> https://biorxiv.org/content/10.1101/320226v1?rss=1 Westerberg, J. Cox, M. A. Dougherty, K. Maier, A. 2018-05-11 doi:10.1101/320226 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Relief of the Dma1-mediated checkpoint requires Dma1 autoubiquitination and dynamic localization ]]> https://biorxiv.org/content/10.1101/322214v1?rss=1 Jones, C. M. Chen, J.-S. Johnson, A. E. Elmore, Z. C. Cullati, S. N. Beckley, J. Gould, K. L. 2018-05-14 doi:10.1101/322214 Cold Spring Harbor Laboratory Press 2018-05-14 <![CDATA[ Glucocorticoid Regulation of Ependymal Glia and Regenerative Potential after Spinal Cord Injury ]]> https://biorxiv.org/content/10.1101/328781v1?rss=1 Nelson, C. M. Lee, H. B. Krug, R. G. Kamalova, A. Madigan, N. N. Clark, K. J. Lennon, V. A. Windebank, A. J. Henley, J. R. 2018-05-25 doi:10.1101/328781 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Unperturbed Expression Bias of Imprinted Genes in Schizophrenia ]]> https://biorxiv.org/content/10.1101/329748v1?rss=1 Gulyas-Kovacs, A. Keydar, I. Xia, E. Fromer, M. Hoffman, G. Ruderfer, D. Consortium, C. Sachidanandam, R. Chess, A. 2018-05-24 doi:10.1101/329748 Cold Spring Harbor Laboratory Press 2018-05-24 <![CDATA[ Contemporary circulating enterovirus D68 strains show differential viral entry and replication in human neuronal cells ]]> https://biorxiv.org/content/10.1101/331116v1?rss=1 Brown, D. M. Hixon, A. M. Oldfield, L. M. Zhang, Y. Novotny, M. Wang, W. Das, S. R. Shabman, R. S. Tyler, K. L. Scheuermann, R. H. 2018-05-25 doi:10.1101/331116 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Conservation and Divergence in the Asexual Sporulation Gene Regulatory Network Across a Genus of Filamentous Fungi ]]> https://biorxiv.org/content/10.1101/331868v1?rss=1 Wu, M.-Y. Mead, M. E. Lee, M.-K. Kim, S. C. Rokas, A. Yu, J.-H. 2018-05-27 doi:10.1101/331868 Cold Spring Harbor Laboratory Press 2018-05-27 <![CDATA[ Quantitative assessment of cell population diversity in single-cell landscapes ]]> https://biorxiv.org/content/10.1101/333393v1?rss=1 Liu, Q. Herring, C. A. Sheng, Q. Ping, J. Simmons, A. J. Chen, B. Banerjee, A. Gu, G. Coffey, R. J. Shyr, Y. Lau, K. S. 2018-05-30 doi:10.1101/333393 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ Using Topic Modeling via Non-negative Matrix Factorization to Identify Relationships between Genetic Variants and Disease Phenotypes: A Case Study of Lipoprotein(a) (LPA) ]]> https://biorxiv.org/content/10.1101/335745v1?rss=1 Zhao, J. Feng, Q. Wu, P. Warner, J. L. Denny, J. C. Wei, W.-Q. 2018-05-31 doi:10.1101/335745 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ Diagnostic algorithms to study post-concussion syndrome using electronic health records: validating a method to capture an important patient population ]]> https://biorxiv.org/content/10.1101/336560v1?rss=1 Dennis, J. Yengo-Kahn, A. Kirby, P. Solomon, G. S. Cox, N. Zuckerman, S. L. 2018-06-04 doi:10.1101/336560 Cold Spring Harbor Laboratory Press 2018-06-04 <![CDATA[ Cryo-EM structure of the benzodiazepine-sensitive α1β1γ2 heterotrimeric GABAA receptor in complex with GABA illuminates mechanism of receptor assembly and agonist binding ]]> https://biorxiv.org/content/10.1101/337659v1?rss=1 Phulera, S. Zhu, H. Yu, J. Claxton, D. Yoder, N. Yoshioka, C. Gouaux, E. 2018-06-03 doi:10.1101/337659 Cold Spring Harbor Laboratory Press 2018-06-03 <![CDATA[ Targeted Molecular Dynamics Simulations Suggest Direct Ligand Competition as a Plausible Efflux Inhibition Mechanism in the Multidrug Resistance Pump AcrB. ]]> https://biorxiv.org/content/10.1101/339242v1?rss=1 Vieira da Silva Junior, L. Almeida da Silva, P. E. Machado, K. S. Dutra, N. Lybrand, T. P. 2018-06-05 doi:10.1101/339242 Cold Spring Harbor Laboratory Press 2018-06-05 <![CDATA[ Gut Microbiota Diversity across Ethnicities in the United States ]]> https://biorxiv.org/content/10.1101/342915v1?rss=1 Brooks, A. W. Priya, S. Blekhman, R. Bordenstein, S. R. 2018-06-08 doi:10.1101/342915 Cold Spring Harbor Laboratory Press 2018-06-08 <![CDATA[ Saracatinib and Dasatinib Fail To Prevent Heritable Pulmonary Arterial Hypertension ]]> https://biorxiv.org/content/10.1101/345447v1?rss=1 D'Amico, R. Gladson, S. Shay, S. Copeland, C. West, J. 2018-06-12 doi:10.1101/345447 Cold Spring Harbor Laboratory Press 2018-06-12 <![CDATA[ Large-scale transcriptome-wide association study identifies new prostate cancer risk regions ]]> https://biorxiv.org/content/10.1101/345736v1?rss=1 Mancuso, N. Gayther, S. Gusev, A. Zheng, W. Penney, K. L. the PRACTICAL consortium, CRUK, BPC3, CAPS, PEGASUS, Kote-Jarai, Z. Eeles, R. Freedman, M. Haiman, C. Pasaniuc, B. 2018-06-14 doi:10.1101/345736 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ Rif1 inhibits replication fork progression and controls DNA copy number in Drosophila ]]> https://biorxiv.org/content/10.1101/346650v1?rss=1 Munden, A. Rong, Z. Gangula, R. Mallal, S. Nordman, J. T. 2018-06-13 doi:10.1101/346650 Cold Spring Harbor Laboratory Press 2018-06-13 <![CDATA[ Validation of an automated segmentation algorithm for lower leg MR images, applied to sodium quantification ]]> https://biorxiv.org/content/10.1101/348136v1?rss=1 Greer, J. Wang, P. Deger, S. M. Alsouqi, A. Ikizler, T. A. Titze, J. M. Rogers, B. P. 2018-06-15 doi:10.1101/348136 Cold Spring Harbor Laboratory Press 2018-06-15 <![CDATA[ Exocyst Dynamics During Vesicle Tethering and Fusion ]]> https://biorxiv.org/content/10.1101/354449v1?rss=1 Ahmed, S. M. Nishida-Fukuda, H. Li, Y. McDonald, W. H. Gradinaru, C. Macara, I. 2018-06-22 doi:10.1101/354449 Cold Spring Harbor Laboratory Press 2018-06-22 <![CDATA[ Genome-wide maps of distal gene regulatory regions active in the human placenta ]]> https://biorxiv.org/content/10.1101/364026v1?rss=1 Zhang, J. Simonti, C. N. Capra, J. A. 2018-07-06 doi:10.1101/364026 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ Transgenic Zebrafish Models Reveal Distinct Molecular Mechanisms for Cataract-linked alphaA-Crystallin Mutants ]]> https://biorxiv.org/content/10.1101/364125v1?rss=1 Wu, S.-Y. Zou, P. Mishra, S. Mchaourab, H. S. 2018-07-08 doi:10.1101/364125 Cold Spring Harbor Laboratory Press 2018-07-08 <![CDATA[ Learning from Longitudinal Data in Electronic Health Record and Genetic Data to Improve Cardiovascular Event Prediction ]]> https://biorxiv.org/content/10.1101/366682v1?rss=1 Zhao, J. Feng, Q. Wu, P. Lupu, R. Wilke, R. A. Wells, Q. S. Denny, J. Wei, W.-Q. 2018-07-11 doi:10.1101/366682 Cold Spring Harbor Laboratory Press 2018-07-11 <![CDATA[ Multiscale Adaptive Gabor Expansion (MAGE): Improved Detection of Transient Oscillatory Burst Amplitude and Phase ]]> https://biorxiv.org/content/10.1101/369116v1?rss=1 Canolty, R. T. Womelsdorf, T. 2018-07-13 doi:10.1101/369116 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ Asymmetric effective connectivity between primate anterior cingulate and lateral prefrontal cortex revealed by electrical microstimulation. ]]> https://biorxiv.org/content/10.1101/369488v1?rss=1 Nacher, V. Hassani, S. A. Womelsdorf, T. 2018-07-14 doi:10.1101/369488 Cold Spring Harbor Laboratory Press 2018-07-14 <![CDATA[ Double Dissociation of Nicotinic alpha-7 and alpha-4/beta-2 Sub-receptor Agonists for Enhancing Learning and Attentional Filtering of Distraction ]]> https://biorxiv.org/content/10.1101/369496v1?rss=1 Azimi, M. Oemisch, M. Womelsdorf, T. 2018-07-14 doi:10.1101/369496 Cold Spring Harbor Laboratory Press 2018-07-14 <![CDATA[ A robust phylogenomic timetree for biotechnologically and medically important fungi from Aspergillaceae (Eurotiomycetes, Ascomycota) ]]> https://biorxiv.org/content/10.1101/370429v1?rss=1 1,000 known species, mostly in the genera Aspergillus and Penicillium. Several species are used in the food, biotechnology, and drug industries (e.g., Aspergillus oryzae, Penicillium camemberti), while others are dangerous human and plant pathogens (e.g., Aspergillus fumigatus, Penicillium digitatum). To infer a robust phylogeny and pinpoint poorly resolved branches and their likely underlying contributors, we used 81 genomes spanning the diversity of Aspergillus and Penicillium to construct a 1,668-gene data matrix. Phylogenies of the nucleotide and amino acid versions of this full data matrix as well as of five additional 834-gene data matrices constructed by subsampling the top 50% of genes according to different criteria associated with strong phylogenetic signal were generated using three different maximum likelihood schemes (i.e., gene-partitioned, unpartitioned, and coalescence). Examination of the topological agreement among these 36 phylogenies and measures of internode certainty identified 12 / 78 (15.4%) bipartitions that were incongruent and pinpoint the likely underlying contributing factors (incomplete lineage sorting, hybridization or introgression, and reconstruction artifacts associated with poor taxon sampling). Relaxed molecular clock analyses suggest that Aspergillaceae likely originated in the lower Cretaceous and the Aspergillus and Penicillium genera in the upper Cretaceous. Our results shed light on the ongoing debate on Aspergillus systematics and taxonomy and provide a robust evolutionary and temporal framework for comparative genomic analyses in Aspergillaceae. More broadly, our approach provides a general template for phylogenomic identification of resolved and contentious branches in densely genome-sequenced lineages across the tree of life. ]]> Steenwyk, J. L. Shen, X.-X. Lind, A. L. Goldman, G. G. Rokas, A. 2018-07-16 doi:10.1101/370429 Cold Spring Harbor Laboratory Press 2018-07-16 <![CDATA[ Programmatic Detection of Diploid-Triploid Mixoploidy via Whole Genome Sequencing ]]> https://biorxiv.org/content/10.1101/371468v1?rss=1 Holt, J. M. Birch, C. L. Brown, D. M. Cogan, J. Hamid, R. Dorrani, N. Herzog, M. R. Lee, H. Martinez, J. Undiagnosed Diseases Network, Dipple, K. Vilain, E. Phillips, J. Worthey, E. A. 2018-07-18 doi:10.1101/371468 Cold Spring Harbor Laboratory Press 2018-07-18 <![CDATA[ The GRE Over the Entire Range of Scores Lacks Predictive Ability for PhD Outcomes in the Biomedical Sciences ]]> https://biorxiv.org/content/10.1101/373225v1?rss=1 Sealy, L. Saunders, C. Blume, J. Chalkley, R. 2018-07-20 doi:10.1101/373225 Cold Spring Harbor Laboratory Press 2018-07-20 <![CDATA[ Identification and characterization of yeast and human glycosphingolipid flippases ]]> https://biorxiv.org/content/10.1101/373712v1?rss=1 Roland, B. P. Naito, T. Best, J. T. Arnaiz-Yepez, C. Takatsu, H. Yu, R. J. Shin, H.-W. Graham, T. R. 2018-07-21 doi:10.1101/373712 Cold Spring Harbor Laboratory Press 2018-07-21 <![CDATA[ Adaptor protein Bbc1 regulates localization of Wsp1 and Vrp1 during endocytic actin patch assembly ]]> https://biorxiv.org/content/10.1101/389015v1?rss=1 40 known yeast endocytic proteins with distinct spatial and temporal localizations and functions; however, it is still unclear how these proteins work together to drive endocytosis. We used quantitative live cell imaging to determine the function of the uncharacterized S. pombe protein Bbc1. We discovered Myo1 interacts with and recruits Bbc1 to sites of endocytosis. Bbc1 competes with verprolin Vrp1 for Myo1 binding, thus releasing Vrp1 and its binding partner Wsp1 from Myo1. Normally Myo1 remains at the base of the endocytic invagination and Vrp1-Wsp1 internalize with the endocytic vesicle; however, in the absence of Bbc1, a portion of Vrp1-Wsp1 remains with Myo1 at the base of the invagination and endocytic invaginations are twice as long. We propose that Bbc1 disrupts a transient Myo1-Vrp1-Wsp1 interaction and limits Arp2/3 complex-nucleation of actin branches at the plasma membrane. ]]> MacQuarrie, C. D. Mangione, M. Carroll, R. James, M. Gould, K. L. Sirotkin, V. 2018-08-09 doi:10.1101/389015 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ Nonsteroidal anti-inflammatory drugs alter the microbiota and exacerbate Clostridium difficile colitis while dysregulating the inflammatory response ]]> https://biorxiv.org/content/10.1101/391607v1?rss=1 Maseda, D. Zackular, J. P. Trindade, B. Kirk, L. Crofford, L. J. Schloss, P. D. Roxas, J. L. Viswanathan, V. K. Vedantam, G. Rogers, L. M. Washington, M. K. Skaar, E. P. Aronoff, D. M. 2018-08-14 doi:10.1101/391607 Cold Spring Harbor Laboratory Press 2018-08-14 <![CDATA[ Context triggers the retrieval of long-term memories into working memory to guide attention ]]> https://biorxiv.org/content/10.1101/401216v1?rss=1 Itthipuripat, S. Woodman, G. F. 2018-09-10 doi:10.1101/401216 Cold Spring Harbor Laboratory Press 2018-09-10 <![CDATA[ Antimicrobial Susceptibility Testing of Chlamydophila pneumoniae: Pilot Study for Alternative Methods that Address the Complex Chlamydial Life Cycle ]]> https://biorxiv.org/content/10.1101/403295v1?rss=1 Stratton, C. W. Stewart, L. S. Alvarez-Macias, s. McHenry, R. Chappell, J. D. 2018-08-29 doi:10.1101/403295 Cold Spring Harbor Laboratory Press 2018-08-29 <![CDATA[ Sex-Specific Protection Against Diet-Induced Non-Alcoholic Fatty Liver Disease in TRPV1 Null Mice ]]> https://biorxiv.org/content/10.1101/403881v1?rss=1 Connell, P. J. Bratz, I. N. Andrei, S. R. Eusebio, L. DelloStritto, D. J. Fahmy, J. N. Ferrell, J. M. Pathak, P. Chiang, J. Y. L. Damron, D. S. 2018-08-30 doi:10.1101/403881 Cold Spring Harbor Laboratory Press 2018-08-30 <![CDATA[ Large-scale genome-wide association meta-analysis of endometriosis reveals 13 novel loci and genetically-associated comorbidity with other pain conditions ]]> https://biorxiv.org/content/10.1101/406967v1?rss=1 Rahmioglu, N. Banasik, K. Christofidou, P. Danning, R. Galarneau, G. Giri, A. MacGregor, S. Mortlock, S. Sapkota, Y. Schork, A. J. Sobalska-Kwapis, M. Stefansdottir, L. Turman, C. Oimari, O. Adachi, S. Andrews, S. Arnadottir, R. Burgdorf, K. S. Campbell, A. Cheuk, C. S. Clementi, C. Cook, J. De Vivio, I. DiVasta, A. Dorien, O. Edwards, T. Fontanillas, P. Fung, J. N. Geirsson, R. T. Girling, J. Harris, H. R. Holdsworth-Carson, S. Houshdaran, S. Hu-Seliger, T. Jarvelin, M.-R. Kepka, E. Kulig, B. Laufer, M. R. Law, M. Low, S.-K. Mangino, M. Marciniak, B. 2018-09-07 doi:10.1101/406967 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ Trans-ethnic genome-wide association study provides insight into effector genes and molecular mechanisms for kidney function and highlights a causal effect on kidney-specific disease aetiologies ]]> https://biorxiv.org/content/10.1101/420273v1?rss=1 Morris, A. P. Le, T. H. Wu, H. Akbarov, A. van der Most, P. P. Mahajan, A. Hemani, G. Gaulton, K. J. Nadkarni, G. Valladares-Salgado, A. Wacher-Rodarte, N. Mychaleckyj, J. C. Dueker, N. D. Guo, X. Hai, Y. Haessler, J. Kamatani, Y. Stilp, A. Zhu, G. Cook, J. P. Arnlov, J. Blanton, S. H. de Borst, M. Bottinger, E. P. Buchanan, T. A. Charchar, F. J. Damman, J. Eales, J. M. Gharavi, A. G. Giedraitis, V. Heath, A. C. Ipp, E. Kiryluk, K. Kubo, M. Larsson, A. Lindgren, C. Lu, Y. Madden, P. A. Kramer, H. J. Montgomery, G. W. Papanicolaou, G. J. Raffel, L. J. S 2018-09-18 doi:10.1101/420273 Cold Spring Harbor Laboratory Press 2018-09-18 <![CDATA[ NATF (Native And Tissue-specific Fluorescence): A strategy for bright, tissue-specific GFP labeling of native proteins. ]]> https://biorxiv.org/content/10.1101/426205v1?rss=1 He, S. Cuentas-Condori, A. Miller, D. M. 2018-09-25 doi:10.1101/426205 Cold Spring Harbor Laboratory Press 2018-09-25 <![CDATA[ Characterizing the pathogenic, genomic, and chemical traits of Aspergillus fischeri, the closest sequenced relative of the major human fungal pathogen Aspergillus fumigatus ]]> https://biorxiv.org/content/10.1101/430728v1?rss=1 Mead, M. E. Knowles, S. L. Raja, H. A. Beattie, S. R. Kowalski, C. H. Steenwyk, J. L. Silva, L. P. Chiaratto, J. Ries, L. N. Goldman, G. H. Cramer, R. A. Oberlies, N. H. Rokas, A. 2018-09-29 doi:10.1101/430728 Cold Spring Harbor Laboratory Press 2018-09-29 <![CDATA[ Actin dynamics drive microvillar motility and clustering during brush border assembly ]]> https://biorxiv.org/content/10.1101/432294v1?rss=1 Meenderink, L. M. Tyska, M. J. 2018-10-05 doi:10.1101/432294 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ Crystallographic and kinetic analyses of human IPMK reveal disordered domains modulate ATP binding and kinase activity. ]]> https://biorxiv.org/content/10.1101/434308v1?rss=1 Seacrist, C. D. Blind, R. D. 2018-10-03 doi:10.1101/434308 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ USE: An integrative suite for temporally-precise psychophysical experiments in virtual environments ]]> https://biorxiv.org/content/10.1101/434944v1?rss=1 Watson, M. R. Voloh, B. Thomas, C. J. Womelsdorf, T. 2018-10-05 doi:10.1101/434944 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ Initiation of droxidopa during hospital admission for management of refractory neurogenic orthostatic hypotension in severely ill patients ]]> https://biorxiv.org/content/10.1101/437319v1?rss=1 McDonell, K. E. Preheim, B. A. Diedrich, A. Muldowney, J. A. S. Peltier, A. C. Robertson, D. Biaggioni, I. Shibao, C. A. 2018-10-08 doi:10.1101/437319 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ Interactions of medial and lateral prefrontal cortex in hierarchical predictive coding ]]> https://biorxiv.org/content/10.1101/439927v1?rss=1 Alexander, W. H. Womelsdorf, T. 2018-10-10 doi:10.1101/439927 Cold Spring Harbor Laboratory Press 2018-10-10 <![CDATA[ Streptococcus agalactiae induces placental macrophages to release extracellular traps loaded with tissue remodeling enzymes via an oxidative-burst-dependent mechanism ]]> https://biorxiv.org/content/10.1101/440685v1?rss=1 Doster, R. S. Sutton, J. Rogers, L. M. Aronoff, D. M. Gaddy, J. 2018-10-11 doi:10.1101/440685 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Differential generation of saccade, fixation and image onset event-related potentials in the human mesial temporal lobe ]]> https://biorxiv.org/content/10.1101/442855v1?rss=1 Katz, C. Patel, K. Talakoub, O. Groppe, D. Hoffman, K. Valiante, T. A. 2018-10-14 doi:10.1101/442855 Cold Spring Harbor Laboratory Press 2018-10-14 <![CDATA[ On statistical tests of functional connectome fingerprinting ]]> https://biorxiv.org/content/10.1101/443556v1?rss=1 Wang, Z. Sair, H. Crainiceanu, C. Lindquist, M. Landman, B. A. Resnick, S. Vogelstein, J. T. Caffo, B. S. 2018-10-15 doi:10.1101/443556 Cold Spring Harbor Laboratory Press 2018-10-15 <![CDATA[ Identification of essential regulatory elements in the human genome ]]> https://biorxiv.org/content/10.1101/444562v1?rss=1 telenti, a. Wells, A. C. Heckerman, D. Torkamani, A. Ren, B. di Iulio, J. 2018-10-16 doi:10.1101/444562 Cold Spring Harbor Laboratory Press 2018-10-16 <![CDATA[ Functionally Coherent Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling and Oncogenic Notch ]]> https://biorxiv.org/content/10.1101/455709v1?rss=1 Overton, I. M. Sims, A. H. Owen, J. A. Heale, B. Ford, M. J. Lubbock, A. L. R. Pairo-Castineira, E. Essafi, A. 2018-10-29 doi:10.1101/455709 Cold Spring Harbor Laboratory Press 2018-10-29 <![CDATA[ White Matter Microstructure Correlates of General and Specific Second-Order Factors of Psychopathology ]]> https://biorxiv.org/content/10.1101/459396v1?rss=1 Hinton, K. E. Lahey, B. B. Villalta-Gil, V. Meyer, F. A. C. Burgess, L. L. Chodes, L. K. Applegate, B. Van Hulle, C. A. Landman, B. A. Zald, D. H. 2018-11-01 doi:10.1101/459396 Cold Spring Harbor Laboratory Press 2018-11-01 <![CDATA[ Respiratory heterogeneity shapes biofilm formation and host colonization in uropathogenic Escherichia coli ]]> https://biorxiv.org/content/10.1101/460311v1?rss=1 Beebout, C. J. Eberly, A. R. werby, S. H. Reasoner, S. Brannon, J. R. De, S. Fitzgerald, M. J. Huggins, M. M. Clayton, D. B. Cegelski, L. Hadjifrangiskou, M. 2018-11-02 doi:10.1101/460311 Cold Spring Harbor Laboratory Press 2018-11-02 <![CDATA[ The evolutionary advantage of cultural memory on heterogeneous contact networks ]]> https://biorxiv.org/content/10.1101/466524v1?rss=1 Carja, O. Creanza, N. 2018-11-09 doi:10.1101/466524 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ Novel genes for autism implicate both excitatory and inhibitory cell lineages in risk ]]> https://biorxiv.org/content/10.1101/484113v1?rss=1 Satterstrom, F. K. Kosmicki, J. A. Wang, J. Breen, M. De Rubeis, S. An, J.-Y. Peng, M. Collins, R. L. Grove, J. Klei, L. Stevens, C. Reichert, J. Mulhern, M. Artomov, M. Gerges, S. Sheppard, B. Xu, X. Bhaduri, A. Norman, U. Brand, H. Schwartz, G. Nguyen, R. Guerrero, E. Dias, C. Aleksic, B. Anney, R. J. Barbosa, M. Bishop, S. Brusco, A. Bybjerg-Grauholm, J. Carracedo, A. Chan, M. C. Y. Chiocchetti, A. Chung, B. Coon, H. Cuccaro, M. Curro, A. Dalla Bernardina, B. Doan, R. Domenici, E. Dong, S. Fallerini, C. Fernandez-Prieto, M. Ferrero, G. B. Freitag, 2018-11-30 doi:10.1101/484113 Cold Spring Harbor Laboratory Press 2018-11-30 <![CDATA[ Tractography Reproducibility Challenge with Empirical Data (TraCED): The 2017 ISMRM Diffusion Study Group Challenge ]]> https://biorxiv.org/content/10.1101/484543v1?rss=1 0.88. Reproducibility is high within these top 5 submissions when assessed across sessions or across scanners. However, it can be directly attributed to containment of smaller volume tracts in larger volume tracts. This holds true for the top five submissions where they are contained in a specific order. While most algorithms are contained in an ordering there are some outliers.nnConclusionThe different methods clearly result in fundamentally different tract structures at the more conservative specificity choices (i.e., volumetrically smaller tractograms). The data and challenge infrastructure remain available for continued analysis and provide a platform for comparison. ]]> Nath, V. Schilling, K. Parvathaneni, P. Hainline, A. E. Huo, Y. Blaber, J. A. Rowe, M. Rodrigues, P. Prckovska, V. Aydogan, B. Sun, W. Shi, Y. Parker, W. Ismail, A. A. O. Verma, R. Cabeen, R. P. Toga, A. W. Newton, A. T. Wasserthal, J. Neher, P. Maier-Hein, K. H. Savini, G. Palesi, F. Kaden, E. Wu, Y. Feng, Y. He, J. Barakovic, M. Romascano, D. Rafael-Pinto, J. Frigo, M. Girard, G. Daducci, A. Thiran, J.-P. Paquette, M. Rheault, F. M. Sidhu, J. Lebel, C. Leemans, A. Descoteaux, M. Dyrby, T. Kang, H. Landman, B. A. 2018-12-03 doi:10.1101/484543 Cold Spring Harbor Laboratory Press 2018-12-03 <![CDATA[ Netrin/UNC-6 triggers actin assembly and non-muscle myosin activity to drive dendrite retraction in the self-avoidance response. ]]> https://biorxiv.org/content/10.1101/492769v1?rss=1 Sundararajan, L. Smith, C. Watson, J. Millis, B. Tyska, M. Miller, D. 2018-12-10 doi:10.1101/492769 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Deconvoluting Stress-Responsive Proteostasis Signaling Pathways for Pharmacologic Activation using Targeted RNA-sequencing ]]> https://biorxiv.org/content/10.1101/499046v1?rss=1 Grandjean, J. M. D. Plate, L. Morimoto, R. I. Bollong, M. J. Powers, E. T. Wiseman, R. L. 2018-12-17 doi:10.1101/499046 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ Antigen receptor control of methionine metabolism in T cells ]]> https://biorxiv.org/content/10.1101/499095v1?rss=1 Sinclair, L. V. Howden, A. J. Brenes-Murillo, A. J. Spinelli, L. Hukelmann, J. L. Macintyre, A. N. Liu, X. Thomson, S. Taylor, P. M. Rathmell, J. C. Locasale, J. W. Lamond, A. I. Cantrell, D. A. 2018-12-18 doi:10.1101/499095 Cold Spring Harbor Laboratory Press 2018-12-18 <![CDATA[ The Genomic Geography and Evolution of Clusters of Tandemly Duplicated Genes in the Human and Mammal Genomes ]]> https://biorxiv.org/content/10.1101/504498v1?rss=1 Ortiz, J. F. Rokas, A. 2018-12-21 doi:10.1101/504498 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ Elongated cells drive morphogenesis in a surface-wrapped finite element model of germband retraction ]]> https://biorxiv.org/content/10.1101/504548v1?rss=1 McCleery, W. T. Veldhuis, J. H. Brodland, G. W. Bennett, M. E. Hutson, M. S. 2018-12-21 doi:10.1101/504548 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ The impact of natural selection on the evolution and function of placentally expressed galectins ]]> https://biorxiv.org/content/10.1101/505339v1?rss=1 Ely, Z. A. Moon, J. M. Sliwoski, G. R. Sangha, A. K. Shen, X.-X. LaBella, A. L. Meiler, J. Capra, J. A. Rokas, A. 2018-12-23 doi:10.1101/505339 Cold Spring Harbor Laboratory Press 2018-12-23 <![CDATA[ Small Cell Lung Cancer subtypes identified by systems-level modeling of transcription factor networks ]]> https://biorxiv.org/content/10.1101/506402v1?rss=1 Wooten, D. Maddox, S. Tyson, D. Liu, Q. Lim, J. S. Sage, J. Quaranta, V. 2018-12-26 doi:10.1101/506402 Cold Spring Harbor Laboratory Press 2018-12-26 <![CDATA[ Genetic risk for major depressive disorder and loneliness in gender-specific associations with coronary artery disease ]]> https://biorxiv.org/content/10.1101/512541v1?rss=1 Dennis, J. Sealock, J. Levinson, R. T. Farber-Eger, E. Franco, J. Fong, S. Straub, P. Hucks, D. Linton, M. F. Song, W.-L. Fontanillas, P. Elson, S. L. Ruderfer, D. Abdellaoui, A. Sanchez-Roige, S. Palmer, A. A. Boomsma, D. I. Cox, N. Chen, G. Mosley, J. D. Wells, Q. S. Davis, L. 2019-01-05 doi:10.1101/512541 Cold Spring Harbor Laboratory Press 2019-01-05 <![CDATA[ Signal integration and information transfer in an allosterically regulated network ]]> https://biorxiv.org/content/10.1101/518514v1?rss=1 Shockley, E. Rouzer, C. A. Marnett, L. J. Deeds, E. J. Lopez, C. F. 2019-01-11 doi:10.1101/518514 Cold Spring Harbor Laboratory Press 2019-01-11 <![CDATA[ IL-10-producing B cells are enriched in murine pericardial adipose tissues and ameliorate the outcome of acute myocardial infarction ]]> https://biorxiv.org/content/10.1101/520742v1?rss=1 Van Kaer, L. Wu, L. Dalal, R. Cao, C. Postoack, J. L. Zhang, Q. Wang, Z. Lal, H. 2019-01-23 doi:10.1101/520742 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Isogenic human iPSC pairs reveal a neuronal subtype-specific and genetic background-independent mechanism of SCN1A epilepsy ]]> https://biorxiv.org/content/10.1101/524835v1?rss=1 Xie, Y. Ng, N. N. Safrina, O. S. Ramos, C. M. Ess, K. C. Schwartz, P. H. Smith, M. A. O'Dowd, D. K. 2019-01-18 doi:10.1101/524835 Cold Spring Harbor Laboratory Press 2019-01-18 <![CDATA[ Scavenging of reactive dicarbonyls with 2-hydroxybenzylamine reduces atherosclerosis in hypercholesterolemic Ldlr-/- mice ]]> https://biorxiv.org/content/10.1101/524884v1?rss=1 Tao, H. Huang, J. Yancey, P. G. Ding, L. Zhang, Y. Blakemore, J. L. Amarnath, V. Oates, J. A. Roberts, L. J. Davies, S. S. Linton, M. F. 2019-01-18 doi:10.1101/524884 Cold Spring Harbor Laboratory Press 2019-01-18 <![CDATA[ Reactive Dicarbonyl Scavenging Effectively Reduces MPO-Mediated Oxidation of HDL and Preserves HDL Atheroprotective Functions ]]> https://biorxiv.org/content/10.1101/528026v1?rss=1 Huang, J. Yancey, P. G. Tao, H. Borja, M. Loren, S. E. Kon, V. Davies, S. S. Linton, M. F. 2019-01-23 doi:10.1101/528026 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Visualization and analysis of high-throughput in vitro dose-response datasets with Thunor ]]> https://biorxiv.org/content/10.1101/530329v1?rss=1 Lubbock, A. L. R. Harris, L. A. Quaranta, V. Tyson, D. R. Lopez, C. F. 2019-01-25 doi:10.1101/530329 Cold Spring Harbor Laboratory Press 2019-01-25 <![CDATA[ CADHERIN-11 BLOCKADE REDUCES INFLAMMATION DRIVEN FIBROTIC REMODELING AND IMPROVES OUTCOMES AFTER MYOCARDIAL INFARCTION ]]> https://biorxiv.org/content/10.1101/533000v1?rss=1 Schroer, A. Bersi, M. Clark, C. Zhang, Q. Sanders, L. Hatzopoulos, A. Force, T. Majka, S. Lal, H. Merryman, W. D. 2019-01-29 doi:10.1101/533000 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Neanderthal introgression reintroduced functional alleles lost in the human out of Africa bottleneck ]]> https://biorxiv.org/content/10.1101/533257v1?rss=1 Rinker, D. C. Simonti, C. McArthur, E. Shaw, D. Hodges, E. Capra, J. A. 2019-01-29 doi:10.1101/533257 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Signatures of recent positive selection in enhancers across 41 human tissues ]]> https://biorxiv.org/content/10.1101/534461v1?rss=1 Moon, J. M. Capra, J. A. Abbot, P. Rokas, A. 2019-01-29 doi:10.1101/534461 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Multi-Neuromodulator Measurements across Fronto-Striatal Network Areas of the Behaving Macaque using Solid-Phase Microextraction ]]> https://biorxiv.org/content/10.1101/534651v1?rss=1 Hassani, S.-A. Lendor, S. Boyaci, E. Pawliszyn, J. Womelsdorf, T. 2019-01-30 doi:10.1101/534651 Cold Spring Harbor Laboratory Press 2019-01-30 <![CDATA[ An actin-based protrusion originating from a podosome-enrichedregion initiates macrophage fusion ]]> https://biorxiv.org/content/10.1101/538314v1?rss=1 Faust, J. J. Balabiyev, A. Heddleston, J. M. Podolnikova, N. P. Baluch, D. P. Chew, T.-L. Ugarova, T. 2019-02-04 doi:10.1101/538314 Cold Spring Harbor Laboratory Press 2019-02-04 <![CDATA[ Impaired M-current in KCNQ2 Encephalopathy Evokes Dyshomeostatic Modulation of Excitability ]]> https://biorxiv.org/content/10.1101/538371v1?rss=1 Simkin, D. Searl, T. J. Piyevsky, B. N. Forrest, M. Williams, L. A. Joshi, V. Zhang, H. Ryan, S. J. Schwake, M. Robertson, G. L. Penzes, P. Laux, L. C. McManus, O. B. Dempsey, G. T. Millichap, J. J. George, A. L. Kiskinis, E. 2019-02-01 doi:10.1101/538371 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ Trans-generational transcriptomic response to natural variation in host plant toxicity and insecticides in a specialist insect. ]]> https://biorxiv.org/content/10.1101/541904v1?rss=1 Birnbaum, S. S. L. Abbot, P. 2019-02-05 doi:10.1101/541904 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Optical Metabolic Imaging of Heterogeneous Drug Response in Pancreatic Cancer Patient Organoids ]]> https://biorxiv.org/content/10.1101/542167v1?rss=1 Sharick, J. T. Walsh, C. M. Sprackling, C. M. Pasch, C. A. Parikh, A. A. Matkowskyj, K. A. Deming, D. A. Skala, M. C. 2019-02-06 doi:10.1101/542167 Cold Spring Harbor Laboratory Press 2019-02-06 <![CDATA[ Extensive loss of cell cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts ]]> https://biorxiv.org/content/10.1101/546366v1?rss=1 Steenwyk, J. L. Opulente, D. Kominek, J. Shen, X.-X. Zhou, X. LaBella, A. L. Bradley, N. P. Eichman, B. F. Cadez, N. Libkind, D. DeVirgilio, J. Hulfachor, A. B. Kurtzman, C. P. Hittinger, C. T. Rokas, A. 2019-02-11 doi:10.1101/546366 Cold Spring Harbor Laboratory Press 2019-02-11 <![CDATA[ A rare variant on a common risk haplotype of HFE causes increased risk of hereditary hemochromatosis ]]> https://biorxiv.org/content/10.1101/547471v1?rss=1 Glazer, A. M. Bastarache, L. Hall, L. Short, L. Shields, T. Kroncke, B. M. Denny, J. C. Roden, D. M. 2019-02-12 doi:10.1101/547471 Cold Spring Harbor Laboratory Press 2019-02-12 <![CDATA[ Characterization of single gene copy number variants in schizophrenia ]]> https://biorxiv.org/content/10.1101/550863v1?rss=1 Szatkiewicz, J. Fromer, M. Nonneman, R. Ancalade, N. Johnson, J. Stahl, E. Rees, E. Bergen, S. Hultman, C. Kirov, G. O'Donovan, M. Owen, M. Holmans, P. Sklar, P. Sullivan, P. Purcell, S. Crowley, J. Ruderfer, D. 2019-02-15 doi:10.1101/550863 Cold Spring Harbor Laboratory Press 2019-02-15 <![CDATA[ Neuronal L-Type Calcium Channel Signaling to the Nucleus Requires a Novel CaMKIIα-Shank3 Interaction ]]> https://biorxiv.org/content/10.1101/551648v1?rss=1 Perfitt, T. L. Wang, X. Stephenson, J. R. Nakagawa, T. Colbran, R. J. 2019-02-16 doi:10.1101/551648 Cold Spring Harbor Laboratory Press 2019-02-16 <![CDATA[ Hippocampal and neocortical oscillations are tuned to behavioral state in freely-behaving macaques ]]> https://biorxiv.org/content/10.1101/552877v1?rss=1 Talakoub, O. Sayegh, P. F. Womelsdorf, T. Zinke, W. Fries, P. Lewis, C. M. Hoffman, K. L. 2019-02-18 doi:10.1101/552877 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ 3D computational models explain muscle activation patterns and energetic functions of internal structures in fish swimming ]]> https://biorxiv.org/content/10.1101/556126v1?rss=1 Ming, T. Jin, B. Song, J. Luo, H. Du, R. Ding, Y. 2019-02-20 doi:10.1101/556126 Cold Spring Harbor Laboratory Press 2019-02-20 <![CDATA[ Cardiolipin-dependent Properties of Model Mitochondrial Membranes from Molecular Dynamics Simulations ]]> https://biorxiv.org/content/10.1101/557744v1?rss=1 Wilson, B. A. Ramanathan, A. Lopez, C. F. 2019-02-22 doi:10.1101/557744 Cold Spring Harbor Laboratory Press 2019-02-22 <![CDATA[ Modeling cell shape diversity arising from complex Rho GTPase dynamics ]]> https://biorxiv.org/content/10.1101/561373v1?rss=1 Zmurchok, C. Holmes, W. R. 2019-02-26 doi:10.1101/561373 Cold Spring Harbor Laboratory Press 2019-02-26 <![CDATA[ Ticks Home in on Body Heat: A New Understanding of Ectoparasite Host-Seeking and Repellent Action ]]> https://biorxiv.org/content/10.1101/564179v1?rss=1 Carr, A. L. Salgado, V. 2019-02-28 doi:10.1101/564179 Cold Spring Harbor Laboratory Press 2019-02-28 <![CDATA[ Mortality among adults living with HIV treated for tuberculosis based on positive, negative, or no bacteriologic test results for tuberculosis: the IeDEA consortium ]]> https://biorxiv.org/content/10.1101/571000v1?rss=1 Humphrey, J. M. Mpofu, P. Pettit, A. C. Musick, B. Carter, E. J. Messou, E. Marcy, O. Crabtree-Ramirez, B. Yotebieng, M. Anastos, K. Sterling, T. R. Yiannoutsos, C. Diero, L. Wools-Kaloustian, K. See S8 Table, 2019-03-08 doi:10.1101/571000 Cold Spring Harbor Laboratory Press 2019-03-08 <![CDATA[ A Bayesian method using sparse data to estimate penetrance of disease-associated genetic variants ]]> https://biorxiv.org/content/10.1101/571158v1?rss=1 Kroncke, B. Smith, D. Glazer, A. M. Roden, D. M. Blume, J. D. 2019-03-07 doi:10.1101/571158 Cold Spring Harbor Laboratory Press 2019-03-07 <![CDATA[ pHluo_M153R-CD63, a bright, versatile live cell reporter of exosome secretion and uptake, reveals pathfinding behavior of migrating cells ]]> https://biorxiv.org/content/10.1101/577346v1?rss=1 Sung, B. H. Pelletier, R. J. Weaver, A. M. 2019-03-14 doi:10.1101/577346 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ Analysis of Genetically Regulated Gene Expression identifies a trauma type specific PTSD gene, SNRNP35 ]]> https://biorxiv.org/content/10.1101/581124v1?rss=1 Huckins, L. M. Breen, M. S. Chatzinakos, C. Hartmann, J. Klengel, T. da Silva Almeida, A. C. Dobbyn, A. Girdhar, K. Hoffman, G. E. Klengel, C. Logue, M. Lori, A. Morrison, F. G. Nguyen, H. T. Park, Y. Ruderfer, D. Sloofman, L. van Rooij, S. J. PTSD Working Group of the Psychiatric Genomics Con, Baker, D. Chen, C.-Y. Cox, N. Duncan, L. Geyer, M. A. Glatt, S. Im, H. K. Maihofer, A. Risbrough, V. B. Smoller, J. W. Stein, D. J. Yehuda, R. Liberzon, I. Koenen, K. C. Jovanovic, T. Kellis, M. Miller, M. W. Bacanu, S.-A. Nievergelt, C. Buxbaum, J. D. Sklar, P. 2019-03-19 doi:10.1101/581124 Cold Spring Harbor Laboratory Press 2019-03-19 <![CDATA[ Protein fold prediction using simulated DEER distance distributions and decay traces ]]> https://biorxiv.org/content/10.1101/581181v1?rss=1 del Alamo, D. Tessmer, M. Stein, R. A. Feix, J. B. Mchaourab, H. S. Meiler, J. 2019-03-18 doi:10.1101/581181 Cold Spring Harbor Laboratory Press 2019-03-18 <![CDATA[ Microtubules Regulate Spatial Localization and Availability of Insulin Granules in Pancreatic Beta Cells. ]]> https://biorxiv.org/content/10.1101/581330v1?rss=1 Bracey, K. M. Ho, K.-H. Yampolsky, D. Gu, G. Kaverina, I. Holmes, W. 2019-03-18 doi:10.1101/581330 Cold Spring Harbor Laboratory Press 2019-03-18 <![CDATA[ The TMEM106B rs1990621 protective variant is also associated with increased neuronal proportion ]]> https://biorxiv.org/content/10.1101/583286v1?rss=1 Li, Z. Farias, F. G. Dube, U. Del Aguila, J. L. L. Mihindukulasuriya, K. A. Fernandez, M.-V. V. Ibanez, L. Budde, J. P. Wang, F. Lake, A. M. Robles, Y. Perez, J. Yang, C. Bradley, J. Davenport, R. Bergmann, K. Benitez, B. A. A. Dougherty, J. D. Harari, O. Cruchaga, C. 2019-03-20 doi:10.1101/583286 Cold Spring Harbor Laboratory Press 2019-03-20 <![CDATA[ Leveraging non-human primate multisensory neurons and circuits in assessing consciousness theory ]]> https://biorxiv.org/content/10.1101/584516v1?rss=1 Noel, J.-P. Ishizawa, Y. Patel, S. Eskandar, E. Wallace, M. 2019-03-21 doi:10.1101/584516 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Trans-endothelial insulin transport is impaired in skeletal muscle capillaries of obese male mice. ]]> https://biorxiv.org/content/10.1101/585372v1?rss=1 Williams, I. M. McClatchey, P. M. Bracy, D. P. Bonner, J. S. Valenzuela, F. A. Wasserman, D. H. 2019-03-21 doi:10.1101/585372 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Identification and characterization of OmpT-like proteases in uropathogenic Escherichia coli clinical isolates ]]> https://biorxiv.org/content/10.1101/594564v1?rss=1 Desloges, I. Taylor, J. A. Leclerc, J.-M. Brannon, J. R. Portt, A. Spencer, J. D. Dewar, K. Marczynski, G. T. Manges, A. Gruenheid, S. Le Moual, H. Thomassin, J.-L. 2019-04-04 doi:10.1101/594564 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ Dendritic spines on GABAergic neurons respond to cholinergic signaling in the Caenorhabditis elegans motor circuit. ]]> https://biorxiv.org/content/10.1101/598714v1?rss=1 Cuentas-Condori, A. A. Mulcahy, B. He, S. Palumbos, S. Zhen, M. Miller, D. M. 2019-04-05 doi:10.1101/598714 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ Genome-wide analyses indirectly implicate miRNA regulatory mechanisms in Obsessive-compulsive Disorder psychopathology ]]> https://biorxiv.org/content/10.1101/601401v1?rss=1 McGregor, N. W. O'Connell, K. S. Davis, L. Mathews, C. Lochner, C. Stein, D. 2019-04-07 doi:10.1101/601401 Cold Spring Harbor Laboratory Press 2019-04-07 <![CDATA[ Innate CD8aa+ cells and osteopontin promote ILC1-like intraepithelial lymphocyte homeostasis and intestinal inflammation ]]> https://biorxiv.org/content/10.1101/606616v1?rss=1 Olivares-Villagomez, D. Nazmi, A. Hoek, K. Greer, M. Piazuelo, M. B. Minato, N. 2019-04-11 doi:10.1101/606616 Cold Spring Harbor Laboratory Press 2019-04-11 <![CDATA[ Variation and selection on codon usage bias across an entire subphylum ]]> https://biorxiv.org/content/10.1101/608042v1?rss=1 LaBella, A. L. Opulente, D. Steenwyk, J. L. Hittinger, C. T. Rokas, A. 2019-04-13 doi:10.1101/608042 Cold Spring Harbor Laboratory Press 2019-04-13 <![CDATA[ Inhibiting fibroblast aggregation in skin wounds unlocks developmental pathway to regeneration ]]> https://biorxiv.org/content/10.1101/608075v1?rss=1 Seifert, A. W. Cook, A. B. Shaw, D. 2019-04-13 doi:10.1101/608075 Cold Spring Harbor Laboratory Press 2019-04-13 <![CDATA[ Machine learning predicts rapid relapse of triple negative breast cancer ]]> https://biorxiv.org/content/10.1101/613604v1?rss=1 2 years).nnPatients and MethodsWe identified 453 primary TNBCs from three publicly-available datasets and characterized each as rrTNBc, lrTNBC, or no relapse (nrTNBC: no relapse/death with at least 5 years follow-up). We compiled primary tumor clinical and multi-omic data, including transcriptome (n=453), copy number alterations (CNAs; n=317), and mutations in 171 cancer-related genes (n=317), then calculated published gene expression and immune signatures.nnResultsPatients with rrTNBC were higher stage at diagnosis (Chi-square p<0.0001) while lrTNBC were more likely to be non-basal PAM50 subtype (Chi-square p=0.03). Among 125 expression signatures, five immune signatures were significantly higher in nrTNBCs while lrTNBC were enriched for eight estrogen/luminal signatures (all FDR p<0.05). There was no significant difference in tumor mutation burden or percent genome altered across the groups. Among mutations, only TP53 mutations were significantly more frequent in rrTNBC compared to lrTNBC (Fisher exact FDR p=0.009). To develop an optimal classifier, we used 77 significant clinical and omic features to evaluate six modeling approaches encompassing simple, machine learning, and artificial neural network (ANN). Support vector machine outperformed other models with average receiver-operator characteristic area under curve >0.75.nnConclusionsWe provide a new approach to define TNBCs based on timing of relapse. We identify distinct clinical and genomic features that can be incorporated into machine learning models to predict rapid relapse of TNBC. ]]> Zhang, Y. Nock, W. Wyse, M. Weber, Z. Adams, E. Stockard, S. Tallman, D. Asad, S. Winer, E. P. Lin, N. U. Cherian, M. Lustberg, M. Ramaswamy, B. Sardesai, S. Vandeusen, J. Williams, N. Wesolowski, R. Stover, D. G. 2019-04-21 doi:10.1101/613604 Cold Spring Harbor Laboratory Press 2019-04-21 <![CDATA[ The Molecular Basis for Nestmate Recognition in the Eusocial Ant Camponotus floridanus ]]> https://biorxiv.org/content/10.1101/614719v1?rss=1 Ferguson, S. T. Park, K. Y. Ruff, A. Zwiebel, L. J. 2019-04-22 doi:10.1101/614719 Cold Spring Harbor Laboratory Press 2019-04-22 <![CDATA[ An antisense oligonucleotide leads to suppressed transcriptional elongation of Hdac2 and long-term memory enhancement ]]> https://biorxiv.org/content/10.1101/618116v1?rss=1 Greer, C. B. Poplawski, S. Garbett, K. A. McMahan, R. L. Kordasiewicz, H. B. Zhao, H. Kennedy, A. J. Goleva, S. B. Sanders, T. H. Motley, T. Swayze, E. E. Ecker, D. J. Michael, T. P. Sweatt, D. 2019-04-24 doi:10.1101/618116 Cold Spring Harbor Laboratory Press 2019-04-24 <![CDATA[ Fitness barriers limit reversion of a proofreading-deficient coronavirus ]]> https://biorxiv.org/content/10.1101/618249v1?rss=1 Graepel, K. W. Agostini, M. L. Lu, X. Sexton, N. R. Denison, M. R. 2019-04-26 doi:10.1101/618249 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Selective Influence and Sequential Operations: A Research Strategy for Visual Search ]]> https://biorxiv.org/content/10.1101/619726v1?rss=1 Lowe, K. A. Reppert, T. R. Schall, J. 2019-04-26 doi:10.1101/619726 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Neural correlates of cardiac interoceptive accuracy across development: implications for social symptoms in autism spectrum disorders ]]> https://biorxiv.org/content/10.1101/630343v1?rss=1 Failla, M. D. Bryant, L. K. Heflin, B. H. Mash, L. E. Schauder, K. Davis, S. Gerdes, M. B. Weitlauf, A. S. Rogers, B. P. Cascio, C. J. 2019-05-07 doi:10.1101/630343 Cold Spring Harbor Laboratory Press 2019-05-07 <![CDATA[ Non-autonomous induction of epithelial lineage infidelity and hyperplasia by DNA damage ]]> https://biorxiv.org/content/10.1101/630954v1?rss=1 Seldin, L. Macara, I. G. 2019-05-08 doi:10.1101/630954 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Multiplex RNA single molecule FISH of inducible mRNAs in single yeast cells ]]> https://biorxiv.org/content/10.1101/631622v1?rss=1 Li, G. Neuert, G. 2019-05-09 doi:10.1101/631622 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ High risk glioblastoma cells revealed by machine learning and single cell signaling profiles ]]> https://biorxiv.org/content/10.1101/632208v1?rss=1 Leelatian, N. Sinnaeve, J. Mistry, A. M. Barone, S. M. Diggins, K. E. Greenplate, A. R. Weaver, K. D. Thompson, R. C. Chambless, L. B. Mobley, B. C. Ihrie, R. A. Irish, J. M. 2019-05-10 doi:10.1101/632208 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Generating kinetic environments to study dynamic cellular processes in single cells ]]> https://biorxiv.org/content/10.1101/632687v1?rss=1 Thiemicke, A. Jashnsaz, H. Li, G. Neuert, G. 2019-05-09 doi:10.1101/632687 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Automated cell boundary and 3D nuclear segmentation of cells in suspension ]]> https://biorxiv.org/content/10.1101/632711v1?rss=1 Kesler, B. Li, G. Thiemicke, A. Venkat, R. Neuert, G. 2019-05-09 doi:10.1101/632711 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ 4-oxo-2-nonenal Adducts In HDL Are Elevated In Familial Hypercholesterolemia: Identification Of Modified Sites And Functional Consequences ]]> https://biorxiv.org/content/10.1101/635458v1?rss=1 3 mol ONE per 10 mol apoA-I (0.3 eq), which is 100-fold lower than HNE but comparable to the potent protein crosslinker, isolevuglandin. ONE-modified HDL partially inhibited the ability of HDL to protect against LPS-induced TNF and IL-1{beta} mRNA expression in murine macrophages. At 3 eq., ONE dramatically decreased the ability of apoA-I to exchange from HDL, from ~46.5% to only ~18.4% (P<0.001). Surprisingly, ONE-modification of HDL or apoA-I did not alter macrophage cholesterol efflux capacity. LC/MS/MS analysis showed modification of Lys12, Lys23, Lys96, and Lys226 of apoA-I by ONE-ketoamide adducts. Compared to other dicarbonyl scavengers, pentylpyridoxamine (PPM) was most efficacious at blocking ONE-induced protein crosslinking in HDL. Our studies show that ONE HDL adducts are elevated in FH who have severe hypercholesterolemia and atherosclerosis and causes HDL dysfunction. We demonstrate the use of PPM in preferentially scavenging ONE in biological systems. ]]> May-Zhang, L. S. Yermalitsky, V. Melchior, J. T. Morris, J. Tallman, K. A. Borja, M. S. Pleasent, T. Amarnath, V. Yancey, P. G. Davidson, W. S. Linton, M. F. Davies, S. S. 2019-05-12 doi:10.1101/635458 Cold Spring Harbor Laboratory Press 2019-05-12 <![CDATA[ Precise tuning of cortical contractility regulates cell shape during cytokinesis ]]> https://biorxiv.org/content/10.1101/635615v1?rss=1 Taneja, N. Bersi, M. R. Baillargeon, S. Fenix, A. M. Cooper, J. A. Gama, V. Merryman, W. D. Ohi, R. Burnette, D. T. 2019-05-13 doi:10.1101/635615 Cold Spring Harbor Laboratory Press 2019-05-13 <![CDATA[ Structural state recognition facilitates tip tracking of EB1 at growing microtubule ends in cells ]]> https://biorxiv.org/content/10.1101/636092v1?rss=1 Reid, T. A. Coombes, C. Mukherjee, S. Goldblum, R. White, K. Parmar, S. McClellan, M. Zanic, M. Courtemanche, N. Gardner, M. K. 2019-05-13 doi:10.1101/636092 Cold Spring Harbor Laboratory Press 2019-05-13 <![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[ Staphylococcus aureus infects osteoclasts and replicates intracellularly ]]> https://biorxiv.org/content/10.1101/638528v1?rss=1 Roper, P. Krauss, J. Ballard, A. Shih, C.-C. Fitzpatrick, J. Cassat, J. Ng, P. Y. Pavlos, N. Veis, D. 2019-05-14 doi:10.1101/638528 Cold Spring Harbor Laboratory Press 2019-05-14 <![CDATA[ Group B rotavirus encodes a functional fusion-associated small transmembrane (FAST) protein ]]> https://biorxiv.org/content/10.1101/639070v1?rss=1 Diller, J. R. Parrington, H. M. Patton, J. T. Ogden, K. M. 2019-05-15 doi:10.1101/639070 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ Mammalian retromer is an adaptable scaffold for cargo sorting from endosomes ]]> https://biorxiv.org/content/10.1101/639575v1?rss=1 Kendall, A. K. Xie, B. Xu, P. Wang, J. Burcham, R. Frazier, M. N. Binshtein, E. Wei, H. Graham, T. R. Nakagawa, T. Jackson, L. P. 2019-05-15 doi:10.1101/639575 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ Extensive Transcriptional and Translational Regulation Occur During the Maturation of Malaria Parasite Sporozoites ]]> https://biorxiv.org/content/10.1101/642298v1?rss=1 Lindner, S. E. Swearingen, K. E. Shears, M. J. Walker, M. P. Vrana, E. N. Hart, K. J. Minns, A. M. Sinnis, P. Moritz, R. L. Kappe, S. H. 2019-05-20 doi:10.1101/642298 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Peptide Arrays of Three Collections of Human Sera from Patients Infected with Mosquito-Borne Viruses ]]> https://biorxiv.org/content/10.1101/650796v1?rss=1 Martinez Viedma, M. d. P. Kose, N. Parham, L. Balmaseda, A. Kuan, G. E. Lorenzana, I. Harris, E. Crowe, J. E. Pickett, B. E. 2019-05-26 doi:10.1101/650796 Cold Spring Harbor Laboratory Press 2019-05-26 <![CDATA[ TractEM: Fast Protocols for Whole Brain Deterministic Tractography-Based White Matter Atlas ]]> https://biorxiv.org/content/10.1101/651935v1?rss=1 Bayrak, R. G. Schilling, K. G. Greer, J. M. Hansen, C. B. Greer, C. M. Blaber, J. A. Williams, O. Beason-Held, L. L. Resnick, S. M. Rogers, B. P. Landman, B. A. 2019-05-30 doi:10.1101/651935 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ Multi-ethnic genome-wide association study of decomposed cardioelectric phenotypes illustrates strategies to identify and characterize evidence of shared genetic effects for complex traits ]]> https://biorxiv.org/content/10.1101/654012v1?rss=1 Baldassari, A. R. Avery, C. L. Highland, H. M. Arking, D. R. Buyske, S. Darbar, D. Gondalia, R. Graff, M. R. Guo, X. R. Heckbert, S. R. Hindorff, L. A. Hodonsky, C. J. Ida Chen, Y.-D. Kaplan, R. C. Peters, U. Post, W. Reiner, A. P. Shohet, R. V. Sotoodehnia, N. Tao, R. Taylor, K. D. Yao, J. D. Kenny, E. D. Lin, H. J. Soliman, E. Z. Whitsel, E. A. North, K. E. Kooperberg, C. Rotters, j. Seyerle, A. A. 2019-05-31 doi:10.1101/654012 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Epidermal Growth Factor signaling acts directly and through a sedation neuron to depolarizes a sleep-active neuron following cellular stress ]]> https://biorxiv.org/content/10.1101/656512v1?rss=1 Konietzka, J. Fritz, M. Spiri, S. McWhirter, R. Leha, A. Palumbos, S. Steuer Costa, W. Oranth, A. Gottschalk, A. Miller, D. Hajnal, A. Bringmann, H. 2019-06-03 doi:10.1101/656512 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Interactive Multiresolution Visualization of Cellular Network Processes ]]> https://biorxiv.org/content/10.1101/659367v1?rss=1 Ortega, O. O. Lopez, C. F. 2019-06-04 doi:10.1101/659367 Cold Spring Harbor Laboratory Press 2019-06-04 <![CDATA[ Autophosphorylation of the CK1 kinase domain regulates enzyme activity and function ]]> https://biorxiv.org/content/10.1101/660548v1?rss=1 Cullati, S. N. Chen, J.-S. Gould, K. L. 2019-06-05 doi:10.1101/660548 Cold Spring Harbor Laboratory Press 2019-06-05 <![CDATA[ Resting-state \"Physiological Networks\" ]]> https://biorxiv.org/content/10.1101/660787v1?rss=1 Chen, J. Lewis, L. Chang, C. Fultz, N. Ohringer, N. Rosen, B. Polimeni, J. 2019-06-06 doi:10.1101/660787 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ PARP1 as a biomarker for early detection and intraoperative tumor delineation in epithelial cancers - first-in-human results ]]> https://biorxiv.org/content/10.1101/663385v1?rss=1 95% sensitivity and specificity without terminal processing. PARPi-FL imaging can be integrated into clinical workflows, potentially providing instantaneous assessment of the presence or absence of microscopic disease at the surgical margin. Additionally, we showed first-in-human PARPi-FL imaging in oral cancer. In aggregate, our preclinical and clinical studies have the unifying goal of verifying the clinical value of PARPi-FL-based optical imaging for early detection and intraoperative margin assignment. ]]> Kossatz, S. Pirovano, G. Demetrio De Souza Franca, P. Strome, A. L. Sunny, S. P. Karassawa Zanoni, D. Mauguen, A. Carney, B. Brand, C. Shah, V. Ramanajinappa, R. D. Hedne, N. Birur, P. Sihag, S. Ghossein, R. A. Gonen, M. Strome, M. Suresh, A. Molena, D. Kuriakose, M. A. Patel, S. G. Reiner, T. 2019-06-14 doi:10.1101/663385 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ Targeting the Cx43 Carboxyl Terminal H2 Domain Preserves Left Ventricular Function Following Ischemia-Reperfusion Injury ]]> https://biorxiv.org/content/10.1101/668509v1?rss=1 Jiang, J. Palatinus, J. A. He, H. Iyyathurai, J. Jourdan, J. L. Hoagland, D. Bultynck, G. Wang, Z. Zhang, Z. Schey, K. Poelzing, S. McGowan, F. X. Gourdie, R. G. 2019-06-12 doi:10.1101/668509 Cold Spring Harbor Laboratory Press 2019-06-12 <![CDATA[ Osteopontin promotes survival of intestinal intraepithelial lymphocytes and protect against colitis ]]> https://biorxiv.org/content/10.1101/669432v1?rss=1 Nazmi, A. Greer, M. Hoek, K. L. Piazuelo, M. B. Weitkamp, J.-H. Olivares-Villagomez, D. 2019-06-13 doi:10.1101/669432 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Sequential Operations Revealed by Serendipitous Feature Selectivity in Frontal Eye Field ]]> https://biorxiv.org/content/10.1101/683144v1?rss=1 Lowe, K. A. Schall, J. D. 2019-06-27 doi:10.1101/683144 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ A Consensus Framework Unifies Multi-Drug Synergy Metrics ]]> https://biorxiv.org/content/10.1101/683433v1?rss=1 Wooten, D. J. Meyer, C. T. Quaranta, V. Lopez, C. F. 2019-06-27 doi:10.1101/683433 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ A quantitative framework for evaluating single-cell data structure preservation by dimensionality reduction techniques ]]> https://biorxiv.org/content/10.1101/684340v1?rss=1 Heiser, C. N. Lau, K. S. 2019-06-27 doi:10.1101/684340 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Identification of type 2 diabetes loci in 433,540 East Asian individuals ]]> https://biorxiv.org/content/10.1101/685172v1?rss=1 240 loci associated with type 2 diabetes (T2D), however most loci have been identified in analyses of European-ancestry individuals. To examine T2D risk in East Asian individuals, we meta-analyzed GWAS data in 77,418 cases and 356,122 controls. In the main analysis, we identified 298 distinct association signals at 178 loci, and across T2D association models with and without consideration of body mass index and sex, we identified 56 loci newly implicated in T2D predisposition. Common variants associated with T2D in both East Asian and European populations exhibited strongly correlated effect sizes. New associations include signals in/near GDAP1, PTF1A, SIX3, ALDH2, a microRNA cluster, and genes that affect muscle and adipose differentiation. At another locus, eQTLs at two overlapping T2D signals act through two genes, NKX6-3 and ANK1, in different tissues. Association studies in diverse populations identify additional loci and elucidate disease genes, biology, and pathways.nnType 2 diabetes (T2D) is a common metabolic disease primarily caused by insufficient insulin production and/or secretion by the pancreatic {beta} cells and insulin resistance in peripheral tissues1. Most genetic loci associated with T2D have been identified in populations of European (EUR) ancestry, including a recent meta-analysis of genome-wide association studies (GWAS) of nearly 900,000 individuals of European ancestry that identified >240 loci influencing the risk of T2D2. Differences in allele frequency between ancestries affect the power to detect associations within a population, particularly among variants rare or monomorphic in one population but more frequent in another3,4. Although smaller than studies in European populations, a recent T2D meta-analysis in almost 200,000 Japanese individuals identified 28 additional loci4. The relative contributions of different pathways to the pathophysiology of T2D may also differ between ancestry groups. For example, in East Asian (EAS) populations, T2D prevalence is greater than in European populations among people of similar body mass index (BMI) or waist circumference5. We performed the largest meta-analysis of East Asian individuals to identify new genetic associations and provide insight into T2D pathogenesis. ]]> Spracklen, C. N. Horikoshi, M. Kim, Y. J. Lin, K. Bragg, F. Moon, S. Suzuki, K. Tam, C. Tabara, Y. Kwak, S.-H. Takeuchi, F. Long, J. Lim, V. Chai, J.-F. Chen, C.-H. Nakatochi, M. Yao, J. Choi, H. S. Iyengar, A. K. Perrin, H. J. Brotman, S. M. van de Bunt, M. Gloyn, A. L. Below, J. L. Boehnke, M. Bowden, D. W. Chambers, J. C. Mahajan, A. McCarthy, M. I. Ng, M. C. Petty, L. E. Zhang, W. Morris, A. P. Adair, L. S. Bian, Z. Chan, J. Chang, L.-C. Chee, M.-L. Chen, Y.-D. I. Chen, Y.-T. Chen, Z. Chuang, L.-M. Du, S. Gordon-Larsen, P. Gross, M. Guo, X. Guo 2019-06-28 doi:10.1101/685172 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ PACSIN2-dependent apical endocytosis regulates the morphology of epithelial microvilli ]]> https://biorxiv.org/content/10.1101/686816v1?rss=1 Postema, M. M. Grega-Larson, N. E. Meenderink, L. M. Tyska, M. J. 2019-06-28 doi:10.1101/686816 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Spin{infty} an improved miniaturized spinning bioreactor for the generation of human cerebral organoids from pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/687095v1?rss=1 Romero-Morales, A. I. O'Grady, B. J. Balotin, K. M. Bellan, L. M. Lippmann, E. S. Gama, V. 2019-07-06 doi:10.1101/687095 Cold Spring Harbor Laboratory Press 2019-07-06 <![CDATA[ A novel multidimensional reinforcement task in mice elucidates sex-specific behavioral strategies ]]> https://biorxiv.org/content/10.1101/690750v1?rss=1 Kutlu, M. G. Zachry, J. E. Brady, L. J. Melugin, P. R. Sanders, C. Tat, J. Johnson, A. R. Thibeault, K. Lopez, A. J. Calipari, E. S. 2019-07-02 doi:10.1101/690750 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Topological stress is responsible for the detrimental outcomes of head-on replication-transcription conflicts ]]> https://biorxiv.org/content/10.1101/691188v1?rss=1 Lang, K. S. Merrikh, H. 2019-07-02 doi:10.1101/691188 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Phytochromes measure photoperiod in Brachypodium ]]> https://biorxiv.org/content/10.1101/697169v1?rss=1 Gao, M. Geng, F. Klose, C. Staudt, A.-M. Huang, H. Nguyen, D. Lan, H. Mockler, T. C. Nusinow, D. A. Hiltbrunner, A. Schaefer, E. Wigge, P. A. Jaeger, K. E. 2019-07-09 doi:10.1101/697169 Cold Spring Harbor Laboratory Press 2019-07-09 <![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[ Migratory divides coincide with species barriers across replicated avian hybrid zones above the Tibetan Plateau ]]> https://biorxiv.org/content/10.1101/698597v1?rss=1 Scordato, E. S. C. Smith, C. C. S. Semenov, G. A. Liu, Y. Wilkins, M. R. Liang, W. Rubtsov, A. Sundev, G. Koyama, K. Turbek, S. P. Wunder, M. B. Stricker, C. A. Safran, R. J. 2019-07-11 doi:10.1101/698597 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Urgency, Leakage, and the Relative Nature of Information Processing in Decision Making ]]> https://biorxiv.org/content/10.1101/706291v1?rss=1 Trueblood, J. S. Heathcote, A. Evans, N. Holmes, W. 2019-07-18 doi:10.1101/706291 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ Probabilistic Assessment of Nerve Regeneration with Diffusion MRI: Validation in Rat Models of Peripheral Nerve Trauma ]]> https://biorxiv.org/content/10.1101/707646v1?rss=1 Manzanera Esteve, I. V. Farinas, A. F. Pollins, A. C. Nussenbaum, M. E. Cardwell, N. L. Kang, H. Does, M. D. Thayer, W. P. Dortch, R. D. 2019-07-19 doi:10.1101/707646 Cold Spring Harbor Laboratory Press 2019-07-19 <![CDATA[ Functional annotation of rare structural variation in the human brain ]]> https://biorxiv.org/content/10.1101/711754v1?rss=1 Han, L. Zhao, X. Benton, M. L. Perumal, T. Collins, R. Hoffman, G. Johnson, J. Sloofman, L. Wang, H. Consortium, C. Brennand, K. Brand, H. Sieberts, S. Marenco, S. Peters, M. Lipska, B. Roussos, P. Capra, J. Talkowski, M. Ruderfer, D. 2019-07-23 doi:10.1101/711754 Cold Spring Harbor Laboratory Press 2019-07-23 <![CDATA[ A Clinical Phenotyping Algorithm to Identify Cases of Chronic Obstructive Pulmonary Disease in Electronic Health Records ]]> https://biorxiv.org/content/10.1101/716779v1?rss=1 Martucci, V. L. Liu, N. Kerchberger, V. E. Osterman, T. J. Torstenson, E. Richmond, B. Aldrich, M. 2019-07-28 doi:10.1101/716779 Cold Spring Harbor Laboratory Press 2019-07-28 <![CDATA[ Yersiniabactin producing AIEC promote inflammation-associated fibrosis in gnotobiotic Il10-/- mice ]]> https://biorxiv.org/content/10.1101/723148v1?rss=1 Ellermann, M. Gharaibeh, R. Fulbright, L. Dogan, B. Moore, L. N. Broberg, C. A. Lopez, L. R. Rothemich, A. M. Herzog, J. Rogala, A. Gordon, I. O. Rieder, F. Brouwer, C. R. Simpson, K. W. Jobin, C. Sartor, R. B. Arthur, J. C. 2019-08-02 doi:10.1101/723148 Cold Spring Harbor Laboratory Press 2019-08-02 <![CDATA[ Genetic Background Dominates Fibrotic Aortic Remodeling During Angiotensin-Induced Hypertension in Mice ]]> https://biorxiv.org/content/10.1101/727800v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@e9f1d9org.highwire.dtl.DTLVardef@104e221org.highwire.dtl.DTLVardef@19a00bforg.highwire.dtl.DTLVardef@1a70cd5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Spronck, B. Caulk, A. W. Ramachandra, A. B. Murtada, S.-I. Rojas, A. He, C.-S. Bersi, M. R. Tellides, G. Humphrey, J. D. 2019-08-15 doi:10.1101/727800 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Development of an N-Cadherin Biofunctionalized Hydrogel to Support the Formation of Synaptically Connected Neural Networks ]]> https://biorxiv.org/content/10.1101/729079v1?rss=1 O'Grady, B. J. Balotin, K. M. Bosworth, A. M. McClatchey, P. M. Weinstein, R. M. Gupta, M. Poole, K. S. Bellan, L. M. Lippmann, E. S. 2019-08-08 doi:10.1101/729079 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ Crystal structure of the M5 muscarinic acetylcholine receptor ]]> https://biorxiv.org/content/10.1101/730622v1?rss=1 Vuckovic, Z. Gentry, P. R. Berizzi, A. E. Hirata, K. Varghese, S. Thompson, G. van der Westhuizen, E. T. Burger, W. A. C. Rahmani, R. Valant, C. Langmead, C. J. Lindsley, C. W. Baell, J. Tobin, A. B. Sexton, P. M. Christopoulos, A. Thal, D. M. 2019-08-14 doi:10.1101/730622 Cold Spring Harbor Laboratory Press 2019-08-14 <![CDATA[ Primary complex motor stereotypies are associated with de novo damaging DNA coding mutations that identify candidate risk genes and biological pathways ]]> https://biorxiv.org/content/10.1101/730952v1?rss=1 Fernandez, T. V. Williams, Z. P. Kline, T. Rajendran, S. Augustine, F. Wright, N. Sullivan, C. A. W. Olfson, E. Abdallah, S. B. Liu, W. Hoffman, E. J. Gupta, A. R. Singer, H. S. 2019-08-13 doi:10.1101/730952 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Identification of execution modes in the extrinsic apoptosis signaling network via Bayesian inference methods ]]> https://biorxiv.org/content/10.1101/732396v1?rss=1 Kochen, M. A. Lopez, C. F. 2019-08-12 doi:10.1101/732396 Cold Spring Harbor Laboratory Press 2019-08-12 <![CDATA[ Expression profiling of the mature C. elegans nervous system by single-cell RNA-Sequencing ]]> https://biorxiv.org/content/10.1101/737577v1?rss=1 90% of the individual neuron classes in the C. elegans nervous system, an ensemble of neurons for which both the anatomy and connectivity are uniquely defined at single cell resolution. We generated single cell transcriptomes for 52,412 neurons that resolve as clusters corresponding to 109 of the canonical 118 neuron classes in the mature hermaphrodite nervous system. Detailed analysis revealed molecular signatures that further subdivide identified classes into specific neuronal subtypes. Notably, neuropeptide-related genes are often differentially expressed between subtypes of the given neuron class which points to distinct functional characteristics. All of these data are publicly available at our website (http://www.cengen.org) and can be interrogated at the web application SCeNGEA (https://cengen.shinyapps.io/SCeNGEA). We expect that this gene expression catalog will spur the goal of delineating the underlying mechanisms that define the developmental lineage, detailed anatomy, synaptic connectivity and function of each type of C. elegans neuron. ]]> Taylor, S. R. Santpere, G. Reilly, M. Glenwinkel, L. Poff, A. McWhirter, R. Xu, C. Weinreb, A. Basavaraju, M. Cook, S. J. Barrett, A. Abrams, A. Vidal, B. Cros, C. Rafi, I. Sestan, N. Hammarlund, M. Hobert, O. Miller, D. M. 2019-08-16 doi:10.1101/737577 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ Selective enhancement of object representations through multisensory integration ]]> https://biorxiv.org/content/10.1101/740555v1?rss=1 Tovar, D. A. Murray, M. M. Wallace, M. T. 2019-08-20 doi:10.1101/740555 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ Multi-State Design of Flexible Proteins Predicts Sequences Optimal for Conformational Change ]]> https://biorxiv.org/content/10.1101/741454v1?rss=1 Sauer, M. F. Sevy, A. M. Crowe, J. E. Meiler, J. 2019-08-20 doi:10.1101/741454 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ Aquila_stLFR: assembly based variant calling package for stLFR and hybrid assembly for linked-reads ]]> https://biorxiv.org/content/10.1101/742239v1?rss=1 Zhou, X. Zhang, L. Fang, X. Liu, Y. Dill, D. L. Sidow, A. 2019-08-21 doi:10.1101/742239 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ MCL-1 inhibition by selective BH3 mimetics disrupts mitochondrial dynamics in iPSC-derived cardiomyocytes ]]> https://biorxiv.org/content/10.1101/743922v1?rss=1 Rasmussen, M. L. Taneja, N. Neininger, A. C. Wang, L. Shi, L. Knollmann, B. C. Burnette, D. T. Gama, V. 2019-08-22 doi:10.1101/743922 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ PLD3 is a neuronal lysosomal phospholipase D associated with β-amyloid plaques and cognitive function in Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/746222v1?rss=1 Nackenoff, A. G. Hohman, T. J. Neuner, S. M. Akers, C. S. Weitzel, N. C. Shostak, A. Ferguson, S. Bennett, D. A. Schneider, J. A. Jefferson, A. L. Kaczorowski, C. C. Schrag, M. S. 2019-08-24 doi:10.1101/746222 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Stimulus-specific information flow across the canonical cortical microcircuit ]]> https://biorxiv.org/content/10.1101/753368v1?rss=1 Tovar, D. A. Westerberg, J. A. Cox, M. A. Dougherty, K. Carlson, T. Wallace, M. T. Maier, A. 2019-09-03 doi:10.1101/753368 Cold Spring Harbor Laboratory Press 2019-09-03 <![CDATA[ Single-cell RNA-sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/753806v1?rss=1 Habermann, A. C. Gutierrez, A. J. Bui, L. T. Yahn, S. L. Winters, N. I. Calvi, C. L. Peter, L. M. Chung, M.-I. Taylor, C. J. Jetter, C. Raju, L. Roberson, J. Ding, G. Wood, L. Sucre, J. M. Richmond, B. W. Serezani, A. P. McDonnell, W. J. Mallal, S. B. Bacchetta, M. J. Loyd, J. E. Shaver, C. M. Ware, L. B. Bremner, R. Walia, R. Blackwell, T. S. Banovich, N. E. Kropski, J. A. 2019-09-06 doi:10.1101/753806 Cold Spring Harbor Laboratory Press 2019-09-06 <![CDATA[ The role of early acoustic experience in song discrimination ]]> https://biorxiv.org/content/10.1101/756445v1?rss=1 Hudson, E. J. Creanza, N. Shizuka, D. 2019-09-06 doi:10.1101/756445 Cold Spring Harbor Laboratory Press 2019-09-06 <![CDATA[ The CRY1 tail controls circadian timing by regulating its association with CLOCK:BMAL1 ]]> https://biorxiv.org/content/10.1101/758714v1?rss=1 Parico, G. C. G. Perez, I. Fribourgh, J. L. Hernandez, B. N. Lee, H.-W. Partch, C. L. 2019-09-05 doi:10.1101/758714 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Cigarette Smoke Exposure Impairs β-Cell Function Through Activation of Oxidative Stress and Ceramide Accumulation ]]> https://biorxiv.org/content/10.1101/761007v1?rss=1 Tong, X. Chaudhry, Z. Lee, C.-C. Bone, R. N. Kanojia, S. Maddatu, J. Sohn, P. Robertson, M. Petrache, I. Evans-Molina, C. Kono, T. 2019-09-08 doi:10.1101/761007 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ Application of long-interval paired-pulse transcranial magnetic stimulation to motion-sensitive visual cortex does not lead to changes in motion perception ]]> https://biorxiv.org/content/10.1101/766428v1?rss=1 Gamboa, O. L. Brito, A. Abzug, Z. M. DArbeloff, T. Beynel, L. Wing, E. A. Dannhauer, M. Palmer, H. Hilbig, S. A. Crowell, C. A. Donaldson, R. Cabeza, R. Davis, S. W. Peterchev, A. V. Sommer, M. A. Appelbaum, L. G. 2019-09-12 doi:10.1101/766428 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Evidence that vertical transmission of the vaginal microbiota can persist into adolescence ]]> https://biorxiv.org/content/10.1101/768598v1?rss=1 Bassis, C. M. Bullock, K. A. Sack, D. E. Saund, K. Pirani, A. Snitkin, E. S. Alaniz, V. I. Quint, E. H. Young, V. B. Bell, J. 2019-09-16 doi:10.1101/768598 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ Neural Mechanisms for Executive Control of Speed-Accuracy Tradeoff ]]> https://biorxiv.org/content/10.1101/773549v1?rss=1 Reppert, T. Heitz, R. P. Schall, J. D. 2019-09-18 doi:10.1101/773549 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Sequence and Structural Determinants of Ligand-dependent Alternating Access of a MATE Transporter ]]> https://biorxiv.org/content/10.1101/773572v1?rss=1 7) and the substrate rhodamine 6G stabilizes an outward-facing (OF) conformation. PfMATE isomerization between outward-facing and inward-facing conformations is driven by protonation of a previously unidentified intracellular glutamate residue that is critical for drug resistance. Our results can be framed in a mechanistic model of transport that addresses central aspects of ligand coupling and alternating access. ]]> Jagessar, K. L. Claxton, D. P. Stein, R. A. Mchaourab, H. S. 2019-09-18 doi:10.1101/773572 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Myt Transcription Factors prevent stress-response gene over-activation to enable postnatal pancreatic β cell proliferation and function ]]> https://biorxiv.org/content/10.1101/773846v1?rss=1 Hu, R. Walker, E. Xu, Y. Huan, C. Erickson, G. Golovin, A. Yang, X. Brissova, M. Balamurugan, A. Wright, C. Li, Y. Stein, R. Gu, G. 2019-09-18 doi:10.1101/773846 Cold Spring Harbor Laboratory Press 2019-09-18 <![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[ A post-processing algorithm for building longitudinal medication dose data from extracted medication information using natural language processing from electronic health records ]]> https://biorxiv.org/content/10.1101/775015v1?rss=1 McNeer, E. Beck, C. Weeks, H. L. Williams, M. L. Choi, L. 2019-09-19 doi:10.1101/775015 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Commensal-derived succinate enhances tuft cell specification and suppresses ileal inflammation ]]> https://biorxiv.org/content/10.1101/776724v1?rss=1 Banerjee, A. Herring, C. A. Kim, H. Chen, B. Simmons, A. J. Southard-Smith, A. N. White, J. R. Ramirez Solano, M. A. Scoville, E. A. Liu, Q. Washington, M. K. Lau, K. S. 2019-09-20 doi:10.1101/776724 Cold Spring Harbor Laboratory Press 2019-09-20 <![CDATA[ The mitochondrial Ca2+ uniporter MCU is required for normal glucose-stimulated insulin secretion in vitro and in vivo ]]> https://biorxiv.org/content/10.1101/781161v1?rss=1 Haythorne, E. Georgiadou, E. Dickerson, M. Lopez Noriega, L. Pullen, T. J. da Silva Xavier, G. Davis, S. Martinez-Sanchez, A. Semplici, F. Rizzuto, R. McGinty, J. A. French, P. M. Cane, M. C. Jacobson, D. A. Leclerc, I. Rutter, G. A. 2019-09-25 doi:10.1101/781161 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ An optimized procedure for robust volitional drug intake in mice ]]> https://biorxiv.org/content/10.1101/786616v1?rss=1 Lopez, A. J. Johnson, A. R. Kunnath, A. J. Zachry, J. E. Thibeault, K. C. Kutlu, M. G. Siciliano, C. A. Calipari, E. S. 2019-09-30 doi:10.1101/786616 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ The GTEx Consortium atlas of genetic regulatory effects across human tissues ]]> https://biorxiv.org/content/10.1101/787903v1?rss=1 Aguet, F. Barbeira, A. N. Bonazzola, R. Brown, A. Castel, S. E. Jo, B. Kasela, S. Kim-Hellmuth, S. Liang, Y. Oliva, M. Parsana, P. E. Flynn, E. Fresard, L. Gaamzon, E. R. Hamel, A. R. He, Y. Hormozdiari, F. Mohammadi, P. Munoz-Aguirre, M. Park, Y. Saha, A. Segrc, A. V. Strober, B. J. Wen, X. Wucher, V. Das, S. Garrido-Martin, D. Gay, N. R. Handsaker, R. E. Hoffman, P. J. Kashin, S. Kwong, A. Li, X. MacArthur, D. Rouhana, J. M. Stephens, M. Todres, E. Vinuela, A. Wang, G. Zou, Y. The GTEx Consortium, Brown, C. D. Cox, N. Dermitzakis, E. Engelhardt, 2019-10-03 doi:10.1101/787903 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ Thickness of deep layers in the fusiform face area predicts face recognition ]]> https://biorxiv.org/content/10.1101/788216v1?rss=1 McGugin, R. W. Newton, A. T. Tamber-Rosenau, B. Tomarken, A. Gauthier, I. 2019-10-02 doi:10.1101/788216 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Natural variation in the contribution of microbial density to inducible immune dynamics ]]> https://biorxiv.org/content/10.1101/788281v1?rss=1 Jent, D. G. Perry, A. Critchlow, J. T. Tate, A. T. 2019-10-01 doi:10.1101/788281 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Machine and deep learning single-cell segmentation and quantification of multi-dimensional tissue images ]]> https://biorxiv.org/content/10.1101/790162v1?rss=1 McKinley, E. T. Roland, J. T. Franklin, J. L. Macedonia, M. C. Vega, P. N. Shin, S. Coffey, R. J. Lau, K. 2019-10-02 doi:10.1101/790162 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Integration of eye-centered and landmark-centered codes in frontal eye field gaze responses ]]> https://biorxiv.org/content/10.1101/791236v1?rss=1 Bharmauria, V. Sajad, A. Li, J. Yan, X. Wang, H. Crawford, J. D. 2019-10-02 doi:10.1101/791236 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Selectivity and engineering of the sialoglycan-binding spectrum in Siglec-like adhesins ]]> https://biorxiv.org/content/10.1101/796912v1?rss=1 Bensing, B. Loukachevitch, L. V. Agarwal, R. Yamakawa, I. Luong, K. Hadadianpour, A. Yu, H. Fialkowski, K. Castro, M. Wawrzak, Z. Chen, X. Baudry, J. Smith, J. Sullam, P. Iverson, T. M. 2019-10-07 doi:10.1101/796912 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Measuring anesthetic resistance in Drosophila by VAAPR ]]> https://biorxiv.org/content/10.1101/797209v1?rss=1 Petersen, E. N. Clowes, K. R. Hansen, S. B. 2019-10-10 doi:10.1101/797209 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Palmitate induces apoptotic cell death and inflammasome activation in human placental macrophages ]]> https://biorxiv.org/content/10.1101/799718v1?rss=1 Rogers, L. Serezani, C. H. Eastman, A. Hasty, A. Englund-Ogge, L. Jacobsson, B. Vickers, K. Aronoff, D. M. 2019-10-10 doi:10.1101/799718 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Biased M1 positive allosteric modulators reveal novel role of phospholipase D in M1-dependent rodent cortical plasticity ]]> https://biorxiv.org/content/10.1101/806943v1?rss=1 Moran, S. P. Xiang, Z. Doyle, C. A. Maksymetz, J. Lv, X. Faltin, S. Niswender, C. M. Rook, J. M. Lindsley, C. W. Conn, P. J. 2019-10-16 doi:10.1101/806943 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Chipper: Open-source software for semi-automated segmentation and analysis of birdsong and other natural sounds ]]> https://biorxiv.org/content/10.1101/807974v1?rss=1 Searfoss, A. M. Pino, J. C. Creanza, N. 2019-10-17 doi:10.1101/807974 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Plasma-derived exosomal analysis and deconvolution enables prediction and tracking of melanoma checkpoint blockade response ]]> https://biorxiv.org/content/10.1101/809699v1?rss=1 Shi, A. Kasumova, G. G. Michaud, W. A. Cintolo-Gonzalez, J. Ohmura, J. F. Mehta, A. Chien, I. Frederick, D. T. Cohen, S. Plana, D. Johnson, D. Flaherty, K. T. Sullivan, R. J. Kellis, M. Boland, G. M. 2019-10-18 doi:10.1101/809699 Cold Spring Harbor Laboratory Press 2019-10-18 <![CDATA[ Drug-tolerant idling melanoma cells exhibit theory-predicted metabolic low-low phenotype ]]> https://biorxiv.org/content/10.1101/809889v1?rss=1 Jia, D. Paudel, B. Hayford, C. E. Hardeman, K. Levine, H. Onuchic, J. N. Quaranta, V. 2019-10-17 doi:10.1101/809889 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Orexin signaling in GABAergic lateral habenula neurons modulates aggressive behavior ]]> https://biorxiv.org/content/10.1101/811265v1?rss=1 Flanigan, M. Aleyasin, H. Li, L. Burnett, C. J. Chan, K. LeClair, K. Lucas, E. Matikainen-Ankney, B. Janssen, W. Takahashi, A. Menard, C. Pfau, M. Golden, S. Bouchard, S. Calipari, E. S. Nestler, E. J. DiLeone, R. Yamanaka, A. Huntley, G. Clem, R. Russo, S. 2019-10-21 doi:10.1101/811265 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Optimal Design of Single-Cell Experiments within Temporally Fluctuating Environments ]]> https://biorxiv.org/content/10.1101/812479v1?rss=1 Fox, Z. R. Neuert, G. Munsky, B. 2019-10-21 doi:10.1101/812479 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Widespread dose-dependent effects of RNA expression and splicing on complex diseases and traits ]]> https://biorxiv.org/content/10.1101/814350v1?rss=1 Barbeira, A. N. Bonazzola, R. Gamazon, E. R. Liang, Y. Park, Y. Kim-Hellmuth, S. Wang, G. Jiang, Z. Zhou, D. Hormozdiari, F. Liu, B. Rao, A. Hamel, A. R. Pividori, M. D. Aguet, F. GTEx GWAS Working Group, Bastarache, L. Jordan, D. M. Verbanck, M. Do, R. GTEx Consortium, Stephens, M. Ardlie, K. McCarthy, M. Montgomery, S. B. Segre, A. Brown, C. D. Lappalainen, T. Wen, X. Im, H. K. 2019-10-22 doi:10.1101/814350 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Accounting for diverse evolutionary forces reveals the mosaic nature of selection on genomic regions associated with human preterm birth ]]> https://biorxiv.org/content/10.1101/816827v1?rss=1 LaBella, A. L. Abraham, A. Pichkar, Y. Fong, S. L. Zhang, G. Muglia, L. J. Abbot, P. Capra, J. A. Rokas, A. 2019-10-24 doi:10.1101/816827 Cold Spring Harbor Laboratory Press 2019-10-24 <![CDATA[ Disruption of Redox Balance Enhances the Effects of BRAF-inhibition in Melanoma Cells ]]> https://biorxiv.org/content/10.1101/818989v1?rss=1 Paudel, B. Lewis, J. E. Hardeman, K. N. Hayford, C. E. Robbins, C. J. Codreanu, S. G. Sherrod, S. D. McLean, J. A. Kemp, M. L. Quaranta, V. 2019-10-28 doi:10.1101/818989 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ Adaptive Spike-Artifact Removal from Local Field Potentials Uncovers Prominent Beta and Gamma Band Neuronal Synchronization ]]> https://biorxiv.org/content/10.1101/820571v1?rss=1 Banaie Boroujeni, K. Tiesinga, P. Womelsdorf, T. 2019-10-28 doi:10.1101/820571 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ GLP-1 Notch - LAG-1 CSL control of the germline stem cell fate is mediated by transcriptional targets lst-1 and sygl-1 ]]> https://biorxiv.org/content/10.1101/825232v1?rss=1 Schedl, T. Chen, J. Mohammad, A. Pazdernik, N. Huang, H. Bowman, B. Tycksen, E. 2019-10-31 doi:10.1101/825232 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Recurrent loss of abaA, a master regulator of asexual development in filamentous fungi, correlates with changes in genomic and morphological traits ]]> https://biorxiv.org/content/10.1101/829465v1?rss=1 Mead, M. E. Borowsky, A. T. Joehnk, B. Steenwyk, J. L. Shen, X.-X. Sil, A. Rokas, A. 2019-11-04 doi:10.1101/829465 Cold Spring Harbor Laboratory Press 2019-11-04 <![CDATA[ DRAMS: A Tool to Detect and Re-Align Mixed-up Samples for Integrative Studies of Multi-omics Data ]]> https://biorxiv.org/content/10.1101/831537v1?rss=1 Jiang, Y. Giase, G. Grennan, K. Shieh, A. W. Xia, Y. Han, L. Wang, Q. Wei, Q. Chen, R. Liu, S. White, K. P. Chen, C. Li, B. Liu, C. 2019-11-06 doi:10.1101/831537 Cold Spring Harbor Laboratory Press 2019-11-06 <![CDATA[ Dual indexed design of in-Drop single-cell RNA-seq libraries improves sequencing quality and throughput ]]> https://biorxiv.org/content/10.1101/835488v1?rss=1 Southard-Smith, A. N. Simmons, A. J. Chen, B. Jones, A. L. Ramirez-Solano, M. A. Vega, P. N. Scurrah, C. R. Zhao, Y. Brenan, M. J. Xuan, J. Porter, E. B. Chen, X. Brenan, C. J. H. Liu, Q. Quigley, L. N. M. Lau, K. N. 2019-11-08 doi:10.1101/835488 Cold Spring Harbor Laboratory Press 2019-11-08 <![CDATA[ Unravelling the genetic architecture of musical rhythm ]]> https://biorxiv.org/content/10.1101/836197v1?rss=1 Niarchou, M. Sathirapongsasuti, J. F. Jacoby, N. Bell, E. McArthur, E. Straub, P. The 23andMe Research Team, McAuley, J. D. Capra, J. A. Ullen, F. Creanza, N. Mosing, M. A. Hinds, D. Davis, L. K. Gordon, R. L. 2019-11-09 doi:10.1101/836197 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Cell-type Specific Learning of Attentional Gating in Primate Striatum ]]> https://biorxiv.org/content/10.1101/837740v1?rss=1 Banaie Boroujeni, K. Hassani, S.-A. Oemisch, M. Womelsdorf, T. 2019-11-11 doi:10.1101/837740 Cold Spring Harbor Laboratory Press 2019-11-11 <![CDATA[ Elevated polygenic burden for ASD is associated with the broad autism phenotype ]]> https://biorxiv.org/content/10.1101/838375v1?rss=1 Nayar, K. Sealock, J. M. Maltman, N. Bush, L. Cook, E. H. Davis, L. K. Losh, M. 2019-11-12 doi:10.1101/838375 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ A/T/N polygenic risk score for cognitive decline in old age ]]> https://biorxiv.org/content/10.1101/838847v1?rss=1 Moore, A. M. Filshtein, T. J. Dumitrescu, L. Harrati, A. Elahi, F. Mormino, E. C. Deming, Y. Kunkle, B. W. Mungas, D. M. Hedden, T. Apostolova, L. G. Saykin, A. J. Chasioti, D. Lu, Q. Dennis, J. Sealock, J. Davis, L. K. Fardo, D. W. Buckley, R. Hohman, T. J. 2019-11-12 doi:10.1101/838847 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Rapid Recalibration of Peri-Personal Space; Psychophysical, Electrophysiological, and Neural Network Modeling Evidence ]]> https://biorxiv.org/content/10.1101/842690v1?rss=1 Noel, J.-P. Bertoni, T. Terrebonne, E. Pellencin, E. Herbelin, B. Cascio, C. Blanke, O. Magosso, E. Wallace, M. Serino, A. 2019-11-16 doi:10.1101/842690 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ Human pseudoislet system enables detection of differences in G-protein-coupled-receptor signaling pathways between α and β cells ]]> https://biorxiv.org/content/10.1101/842989v1?rss=1 Walker, J. T. Haliyur, R. Nelson, H. A. Ishahak, M. Poffenberger, G. Aramandla, R. Reihsmann, C. Luchsinger, J. R. Saunders, D. C. Wang, P. Garcia-Ocana, A. Bottino, R. Agarwal, A. Powers, A. C. Brissova, M. 2019-11-14 doi:10.1101/842989 Cold Spring Harbor Laboratory Press 2019-11-14 <![CDATA[ Neural correlates of goal-directed and non-goal-directed movements ]]> https://biorxiv.org/content/10.1101/843011v1?rss=1 Sendhilnathan, N. Basu, D. Goldberg, M. E. Schall, J. D. Murthy, A. 2019-11-15 doi:10.1101/843011 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Tet2 negatively regulates memory fidelity ]]> https://biorxiv.org/content/10.1101/843581v1?rss=1 Zengeler, K. E. Gettens, C. P. Smith, H. C. Caron, M. M. Zhang, X. Howard, A. H. Boitnott, A. R. Gogliettino, A. R. Reda, A. Malachowsky, B. G. Zhong, C. Song, H. Kaas, G. A. Kennedy, A. J. 2019-11-25 doi:10.1101/843581 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Structural characterization of an intermediate reveals a unified mechanism for the CLC Cl-/H+ transport cycle ]]> https://biorxiv.org/content/10.1101/857136v1?rss=1 Chavan, T. S. Cheng, R. C. Jiang, T. Mathews, I. I. Stein, R. A. Koehl, A. Mchaourab, H. S. Tajkhorshid, E. Maduke, M. 2019-11-27 doi:10.1101/857136 Cold Spring Harbor Laboratory Press 2019-11-27 <![CDATA[ High-throughput reclassification of SCN5A variants ]]> https://biorxiv.org/content/10.1101/858175v1?rss=1 Glazer, A. M. Wada, Y. Li, B. Muhammad, A. Kalash, O. R. O'neill, M. J. Shields, T. Hall, L. Short, L. Blair, M. A. Kroncke, B. M. Capra, J. A. Roden, D. M. 2019-11-29 doi:10.1101/858175 Cold Spring Harbor Laboratory Press 2019-11-29 <![CDATA[ Machine learning on drug-specific data to predict small molecule teratogenicity ]]> https://biorxiv.org/content/10.1101/860627v1?rss=1 Challa, A. P. Beam, A. L. Shen, M. Peryea, T. Lavieri, R. R. Lippmann, E. S. Aronoff, D. M. 2019-11-30 doi:10.1101/860627 Cold Spring Harbor Laboratory Press 2019-11-30 <![CDATA[ LEARNING AND INTERPRETING THE GENE REGULATORY GRAMMAR IN A DEEP LEARNING FRAMEWORK ]]> https://biorxiv.org/content/10.1101/864058v1?rss=1 Capra, J. A. Chen, L. 2019-12-03 doi:10.1101/864058 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ Gliotoxin, a known virulence factor in the major human pathogen Aspergillus fumigatus, is also biosynthesized by the non-pathogenic relative A. fischeri ]]> https://biorxiv.org/content/10.1101/868745v1?rss=1 Knowles, S. L. Mead, M. E. Pereira Silva, L. Raja, H. A. Steenwyk, J. L. Goldman, G. H. Rokas, A. Oberlies, N. H. 2019-12-08 doi:10.1101/868745 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ Rif1 functions in a tissue-specific manner to control replication timing through its PP1-binding motif ]]> https://biorxiv.org/content/10.1101/870451v1?rss=1 Armstrong, R. L. Das, S. Hill, C. A. Duronio, R. J. Nordman, J. T. 2019-12-09 doi:10.1101/870451 Cold Spring Harbor Laboratory Press 2019-12-09 <![CDATA[ Revealing missing isoforms encoded in the human genome by integrating genomic, transcriptomic and proteomic data ]]> https://biorxiv.org/content/10.1101/012112v1?rss=1 Zhiqiang Hu Hamish S. Scott Guangrong Qin Guangyong Zheng Xixia Chu Lu Xie David L. Adelson Bergithe E. Oftedal Parvalthy Venugopal Milena Barbic Christopher N. Hahn Bing Zhang Xiaojing Wang Nan Li Chaochun Wei 2014-12-04 doi:10.1101/012112 Cold Spring Harbor Laboratory Press 2014-12-04 <![CDATA[ Computing the Internode Certainty and related measures from partial gene trees. ]]> https://biorxiv.org/content/10.1101/022053v1?rss=1 Kassian Kobert Leonidas Salichos Antonis Rokas Alexandros Stamatakis 2015-07-06 doi:10.1101/022053 Cold Spring Harbor Laboratory Press 2015-07-06 <![CDATA[ The Great Migration and African-American genomic diversity ]]> https://biorxiv.org/content/10.1101/029173v1?rss=1 Soheil Baharian Maxime Barakatt Christopher R Gignoux Suyash Shringarpure Jacob Errington William J Blot Carlos D Bustamante Eimear E Kenny Scott M Williams Melinda C Aldrich Simon Gravel 2015-10-15 doi:10.1101/029173 Cold Spring Harbor Laboratory Press 2015-10-15 <![CDATA[ An Ancestry Based Approach for Detecting Interactions ]]> https://biorxiv.org/content/10.1101/036640v1?rss=1 Danny Park Itamar Eskin Eun Yong Kang Eric R Gamazon Celeste Eng Christopher R Gignoux Joshua M Galanter Esteban Burchard Chun J Ye Hugues Aschard Eleazar Eskin Eran Halperin Noah Zaitlen 2016-01-13 doi:10.1101/036640 Cold Spring Harbor Laboratory Press 2016-01-13 <![CDATA[ SNP-based heritability estimation: measurement noise, population stratification and stability ]]> https://biorxiv.org/content/10.1101/040055v1?rss=1 Eric R Gamazon Danny S Park 2016-02-18 doi:10.1101/040055 Cold Spring Harbor Laboratory Press 2016-02-18 <![CDATA[ Quantification of Focal Outflow Enhancement using Differential Canalograms ]]> https://biorxiv.org/content/10.1101/044503v1?rss=1 Ralitsa T. Loewen Eric N. Brown Gordon Scott Hardik Parikh Joel S. Schuman Nils A Loewen 2016-03-18 doi:10.1101/044503 Cold Spring Harbor Laboratory Press 2016-03-18 <![CDATA[ Rare copy number variants in NRXN1 and CNTN6 increase risk for Tourette syndrome ]]> https://biorxiv.org/content/10.1101/062471v1?rss=1 Alden Y Huang Dongmei Yu Lea K Davis Jae-Hoon Sul Fotis Tsetsos Vasily Ramensky Ivette Zelaya Eliana Marisa Ramos Lisa Osiecki Jason A Chen Lauren M McGrath Cornelia Illmann Paul Sandor Cathy L Barr Marco Grados Harvey S Singer Markus M Noethen Johannes Hebebrand Robert A King Yves Dion Guy Rouleau Cathy L Budman Christel Depienne Yulia Worbe Andreas Hartmann Kirsten R Muller-Vahl Manfred Stuhrmann Harald Aschauer Mara Stamenkovic Monika Schloegelhofer Anastasios Konstantinidis Gholson L Lyon William M McMahon Csaba Barta Zsanett Tarnok Peter Nagy James R Batterson Renata Rizzo Danielle C Cath 2016-07-08 doi:10.1101/062471 Cold Spring Harbor Laboratory Press 2016-07-08 <![CDATA[ Neuroendocrine Modulation Sustains the C. elegans Forward Motor State ]]> https://biorxiv.org/content/10.1101/065235v1?rss=1 Maria A. Lim Jyothsna Chitturi Valeriya Laskova Jun Meng Daniel Findeis Anne Wiekenberg Ben Mulcahy Linjiao Luo Yan Li Yangning Lu Wesley Hung Yixin Qu Chi-Yip Ho Douglas Holmyard Ni Ji Rebecca WcWhirter Aravinthan D. T. Samuel David Miller Ralf Schnabel John Calarco Mei Zhen 2016-07-23 doi:10.1101/065235 Cold Spring Harbor Laboratory Press 2016-07-23 <![CDATA[ Monitoring the circadian clock in human blood using personalized machine learning ]]> https://biorxiv.org/content/10.1101/066126v1?rss=1 Jacob J Hughey 2016-07-31 doi:10.1101/066126 Cold Spring Harbor Laboratory Press 2016-07-31 <![CDATA[ Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis ]]> https://biorxiv.org/content/10.1101/071696v1?rss=1 Marcin J Skwark Nicholas J Croucher Santeri Puranen Claire Chewapreecha Maiju Pesonen Yingying Xu Paul Turner Simon R Harris Julian Parkhill Stephen D Bentley Erik Aurell Jukka Corander 2016-08-25 doi:10.1101/071696 Cold Spring Harbor Laboratory Press 2016-08-25 <![CDATA[ Distant regulatory effects of genetic variation in multiple human tissues ]]> https://biorxiv.org/content/10.1101/074419v1?rss=1 Brian Jo Yuan He Benjamin J Strober Princy Parsana Francois Aguet Andrew A Brown Stephane E Castel Eric R Gamazon Ariel Gewirtz Genna Gliner Buhm Han Amy Z He Eun Yong Kang Ian C McDowell Xiao Li Pejman Mohammadi Christine B Peterson Gerald Quon Ashis Saha Ayellet V Segre Jae Hoon Sul Timothy J Sullivan Kristin G Ardlie Christopher D Brown Donald F Conrad Nancy J Cox Emmanouil T Dermitzakis Eleazar Eskin Manolis Kellis Tuuli Lappalainen Chiara Sabatti GTEx Consortium Barbara E Engelhardt Alexis Battle 2016-09-09 doi:10.1101/074419 Cold Spring Harbor Laboratory Press 2016-09-09 <![CDATA[ Local genetic effects on gene expression across 44 human tissues ]]> https://biorxiv.org/content/10.1101/074450v1?rss=1 Francois Aguet Andrew A Brown Stephane Castel Joe R Davis Pejman Mohammadi Ayellet V Segre Zachary Zappala Nathan S Abell Laure Fresard Eric R Gamazon Ellen Gelfand Machael J Gloudemans Yuan He Farhad Hormozdiari Xiao Li Xin Li Boxiang Liu Diego Garrido-Martin Halit Ongen John J Palowitch YoSon Park Christine B Peterson Gerald Quon Stephan Ripke Andrey A Shabalin Tyler C Shimko Benjamin J Strober Timothy J Sullivan Nicole A Teran Emily K Tsang Hailei Zhang Yi-Hui Zhou Alexis Battle Carlos D Bustamonte Nancy J Cox Barbara E Engelhardt Eleazar Eskin Gad Getz Manolis Kellis Gen Li Daniel G MacArt 2016-09-09 doi:10.1101/074450 Cold Spring Harbor Laboratory Press 2016-09-09 <![CDATA[ Genomic analyses for age at menarche identify 389 independent signals and indicate BMI-independent effects of puberty timing on cancer susceptibility ]]> https://biorxiv.org/content/10.1101/076794v1?rss=1 Felix Day Deborah Thompson Hannes Helgason Daniel Chasman Hilary Finucane Patrick Sulem Katherine Ruth Sean Whalen Abhishek Sarkar Eva Albrecht Elisabeth Altmaier Marzyeh Amini Caterina Barbieri Thibaud Boutin Archie Campbell Ellen Demerath Ayush Giri Chunyan He Jouke Hottenga Robert Karlsson Ivana Kolcic Po-Ru Loh Kathryn Lunetta Massimo Mangino Brumat Marco Gerorge McMahon Sarah Medland Ilja Nolte Raymond Noordam Teresa Nutile Lavinia Paternoster Natalia Perjakova Eleonora Porcu Lynda Rose Katharina Schraut Ayellet Segre Albert Smith Lisette Stolk Alexander Teumer Irene Andrulis Stefania Ban 2016-09-23 doi:10.1101/076794 Cold Spring Harbor Laboratory Press 2016-09-23 <![CDATA[ Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset ]]> https://biorxiv.org/content/10.1101/077248v1?rss=1 Michael R. Shirts Christoph Klein Jason M. Swails Jian Yin Michael K. Gilson David L. Mobley David A. Case Ellen D. Zhong 2016-09-25 doi:10.1101/077248 Cold Spring Harbor Laboratory Press 2016-09-25 <![CDATA[ Genome-Wide Association Study Reveals First Locus for Anorexia Nervosa and Metabolic Correlations ]]> https://biorxiv.org/content/10.1101/088815v1?rss=1 Duncan, L. Yilmaz, Z. Walters, R. Goldstein, J. Antilla, V. Bulik-Sullivan, B. Ripke, S. Adan, R. Alfredsson, L. Ando, T. Andreassen, O. Aschauer, H. Baker, J. Barrett, J. Bencko, V. Bergen, A. Berrettini, W. Birgegard, A. Boni, C. Boraska Perica, V. Brandt, H. Bughardt, R. Carlberg, L. Cassina, M. Cesta, C. Cichon, S. Clementi, M. Cohen-Woods, S. Coleman, J. Cone, R. Courtet, P. Crawford, S. Crow, S. Crowley, J. Danner, U. Davis, O. de Zaan, M. Dedoussis, G. Degortes, D. DeSocio, J. Dick, D. Dikeos, D. Dina, C. Ding, B. Dmitrzak-Weglarz, M. Docampo 2016-11-25 doi:10.1101/088815 Cold Spring Harbor Laboratory Press 2016-11-25 <![CDATA[ Expanding the language network: Domain-specific hippocampal recruitment during high-level linguistic processing ]]> https://biorxiv.org/content/10.1101/091900v1?rss=1 Blank, I. Duff, M. C. Brown-Schmidt, S. Fedorenko, E. 2016-12-06 doi:10.1101/091900 Cold Spring Harbor Laboratory Press 2016-12-06 <![CDATA[ Defects of myelination are common pathophysiology in syndromic and idiopathic autism spectrum disorders ]]> https://biorxiv.org/content/10.1101/128124v1?rss=1 Phan, B. N. Page, S. C. Campbell, M. N. Bohlen, J. F. Thaxton, C. L. Simon, J. M. Burke, E. E. Shin, J. H. Kennedy, A. J. Sweatt, J. D. Philpot, B. D. Jaffe, A. E. Maher, B. J. 2017-04-18 doi:10.1101/128124 Cold Spring Harbor Laboratory Press 2017-04-18 <![CDATA[ Co-localization of Conditional eQTL and GWAS Signatures in Schizophrenia ]]> https://biorxiv.org/content/10.1101/129429v1?rss=1 0.8), including six loci with co-localization of conditional eQTL. Our co-localization analyses support previously reported genes and identify novel genes for schizophrenia risk, and provide specific hypotheses for their functional follow-up. ]]> Dobbyn, A. Huckins, L. M. Boocock, J. Sloofman, L. G. Glicksberg, B. S. Giambartolomei, C. Hoffman, G. Perumal, T. Girdhar, K. Jiang, Y. Ruderfer, D. M. Kramer, R. S. Pinto, D. the CommonMind Consortium, Akbarian, S. Roussos, P. Domenici, E. Devlin, B. Sklar, P. Stahl, E. A. Sieberts, S. K. 2017-04-25 doi:10.1101/129429 Cold Spring Harbor Laboratory Press 2017-04-25 <![CDATA[ Meta-analysis of Cytometry Data Reveals Racial Differences in Immune Cells ]]> https://biorxiv.org/content/10.1101/130948v1?rss=1 Hu, Z. Jujjavarapu, C. Hughey, J. J. Andorf, S. Gherardini, P. F. Spitzer, M. H. Dunn, P. Thomas, C. G. Campbell, J. Wiser, J. Nolan, G. P. Bhattacharya, S. Butte, A. J. 2017-06-09 doi:10.1101/130948 Cold Spring Harbor Laboratory Press 2017-06-09 <![CDATA[ Exact Topological Inference For Paired Brain Networks Via Persistent Homology ]]> https://biorxiv.org/content/10.1101/140533v1?rss=1 Chung, M. K. Villalta-Gil, V. Lee, H. Rathouz, P. J. Lahey, B. B. Zald, D. H. 2017-05-22 doi:10.1101/140533 Cold Spring Harbor Laboratory Press 2017-05-22 <![CDATA[ Olfactory Receptors Are Required For Social Behavior And Neural Plasticity In Ants, As Evidenced By CRISPR-Mediated Gene Knockout ]]> https://biorxiv.org/content/10.1101/142232v1?rss=1 Yan, H. Opachaloemphan, C. Mancini, G. Yang, H. Gallitto, M. Mlejnek, J. Haight, K. Ghaninia, M. Huo, L. Leibholz, A. Slone, J. Zhou, X. Traficante, M. Penick, C. A. Dolezal, K. Gokhale, K. Stevens, K. Fetter-Pruneda, I. Bonasio, R. Zwiebel, L. J. Berger, S. Liebig, J. Reinberg, D. Desplan, C. 2017-05-25 doi:10.1101/142232 Cold Spring Harbor Laboratory Press 2017-05-25 <![CDATA[ Large Meta-Analysis Provides Evidence For An Association Of Serum Vitamin D With Pulmonary Function ]]> https://biorxiv.org/content/10.1101/144717v1?rss=1 Xu, J. Bartz, T. M. Chittoor, G. Eiriksdottir, G. Manichaikul, A. W. Sun, F. Terzikhan, N. Zhou, X. Booth, S. L. Brusselle, G. G. de Boer, I. H. Fornage, M. Frazier-Wood, A. C. Graff, M. Gudnason, V. Harris, T. B. Hofman, A. Hou, R. Houston, D. K. Jacobs, D. R. Kritchevsky, S. B. Latourelle, J. Lemaitre, R. N. Lutsey, P. L. O'Connor, G. Oelsner, E. C. Pankow, J. S. Psaty, B. M. Rohde, R. R. Rich, S. S. Rotter, J. I. Smith, L. J. Stricker, B. H. Voruganti, V. S. Wang, T. J. Zillikens, M. C. Barr, R. G. Dupuis, J. Gharib, S. A. Lahousse, L. London, S. J. 2017-06-02 doi:10.1101/144717 Cold Spring Harbor Laboratory Press 2017-06-02 <![CDATA[ Genetics of the Research Domain Criteria (RDoC): genome-wide association study of delay discounting ]]> https://biorxiv.org/content/10.1101/146936v1?rss=1 Sanchez-Roige, S. Fontanillas, P. Elson, S. L. - The 23andMe Research Team, Pandit, A. Schmidt, E. Forster, J. Abecasis, G. R. Gray, J. C. de Wit, H. Davis, L. K. MacKillop, J. Palmer, A. A. 2017-06-07 doi:10.1101/146936 Cold Spring Harbor Laboratory Press 2017-06-07 <![CDATA[ Genome-wide association study of Alcohol Use Disorder Identification Test (AUDIT) scores in 20,328 research participants of European ancestry ]]> https://biorxiv.org/content/10.1101/147397v1?rss=1 Sanchez-Roige, S. Fontanillas, P. Elson, S. L. - the 23andMe Research Team, Gray, J. C. de Wit, H. Davis, L. K. MacKillop, J. Palmer, A. A. 2017-06-15 doi:10.1101/147397 Cold Spring Harbor Laboratory Press 2017-06-15 <![CDATA[ Harmonization of cortical thickness measurements across scanners and sites ]]> https://biorxiv.org/content/10.1101/148502v1?rss=1 Fortin, J.-P. Cullen, N. Sheline, Y. I. Taylor, W. D. Aselcioglu, I. Adams, P. Cooper, C. Fava, M. McGrath, P. J. McInnis, M. Parsey, R. V. Phillips, M. L. Trivedi, M. H. Weissman, M. M. Shinohara, R. T. 2017-06-10 doi:10.1101/148502 Cold Spring Harbor Laboratory Press 2017-06-10 <![CDATA[ Automated collection of pathogen-specific diagnostic data for real-time syndromic epidemiological studies ]]> https://biorxiv.org/content/10.1101/157156v1?rss=1 Meyers, L. Ginocchio, C. C. Faucett, A. N. Nolte, F. S. Gesteland, P. H. Leber, A. Janowiak, D. Donovan, V. Dien Bard, J. Spitzer, S. Stellrecht, K. A. Salimnia, H. Selvarangan, R. Juretschko, S. Daly, J. A. Wallentine, J. C. Lindsey, K. Moore, F. Reed, S. L. Aguero-Rosenfeld, M. Fey, P. D. Storch, G. A. Melnick, S. J. Cook, C. V. Nelson, R. K. Jones, J. D. Scarpino, S. V. Althouse, B. M. Ririe, K. M. Malin, B. A. Poritz, M. A. 2017-07-31 doi:10.1101/157156 Cold Spring Harbor Laboratory Press 2017-07-31 <![CDATA[ Polygenic selection underlies evolution of human brain structure and behavioral traits ]]> https://biorxiv.org/content/10.1101/164707v1?rss=1 Beiter, E. R. Khramtsova, E. A. van der Merwe, C. Chimusa, E. R. Simonti, C. Stein, J. Thompson, P. Fisher, S. Stein, D. J. Capra, J. A. Knowles, J. A. Stranger, B. E. Davis, L. K. 2017-09-09 doi:10.1101/164707 Cold Spring Harbor Laboratory Press 2017-09-09 <![CDATA[ Evolutionary genetics of cytoplasmic incompatibility genes cifA and cifB in prophage WO of Wolbachia ]]> https://biorxiv.org/content/10.1101/180075v1?rss=1 Lindsey, A. R. I. Rice, D. W. Bordenstein, S. R. Brooks, A. W. Bordenstein, S. R. Newton, I. L. G. 2017-08-24 doi:10.1101/180075 Cold Spring Harbor Laboratory Press 2017-08-24 <![CDATA[ Transcriptional signatures of schizophrenia in hiPSC-derived NPCs and neurons are concordant with signatures from post mortem adult brains ]]> https://biorxiv.org/content/10.1101/185546v1?rss=1 Hoffman, G. E. Hartley, B. J. Flaherty, E. Ladran, I. Gochman, P. Ruderfer, D. Stahl, E. A. Rapoport, J. Sklar, P. Brennand, K. J. 2017-09-07 doi:10.1101/185546 Cold Spring Harbor Laboratory Press 2017-09-07 <![CDATA[ Exome chip meta-analysis elucidates the genetic architecture of rare coding variants in smoking and drinking behavior ]]> https://biorxiv.org/content/10.1101/187658v1?rss=1 Liu, D. J. Brazel, D. M. Turcot, V. Zhan, X. Gong, J. Barnes, D. R. Bertelsen, S. Chou, Y.-L. Erzurumluoglu, A. M. Faul, J. D. Haessler, J. Hammerschlag, A. R. Hsu, C. Kapoor, M. Lai, D. Le, N. de Leeuw, C. A. Loukola, A. Mangino, M. Melbourne, C. A. Pistis, G. Qaiser, B. Rohde, R. Shao, Y. Stringham, H. Wetherill, L. Zhao, W. Agrawal, A. Beirut, L. Chen, C. Eaton, C. B. Goate, A. Haiman, C. Heath, A. Iacono, W. G. Martin, N. G. Polderman, T. J. CHD Exome+ Consortium, Consortium for Genetics of Smoking Behavior, Reiner, A. Rice, J. Schlessinger, D. 2017-09-12 doi:10.1101/187658 Cold Spring Harbor Laboratory Press 2017-09-12 <![CDATA[ Genetic Diversity Turns a New PAGE in Our Understanding of Complex Traits ]]> https://biorxiv.org/content/10.1101/188094v1?rss=1 Wojcik, G. Graff, M. Nishimura, K. K. Tao, R. Haessler, J. Gignoux, C. R. Highland, H. M. Patel, Y. M. Sorokin, E. P. Avery, C. L. Belbin, G. M. Bien, S. A. Cheng, I. Hodonsky, C. J. Huckins, L. M. Jeff, J. Justice, A. E. Kocarnik, J. M. Lim, U. Lin, B. M. Lu, Y. Nelson, S. C. Park, S.-S. L. Preuss, M. H. Richard, M. A. Schurmann, C. Setiawan, V. W. Vahi, K. Vishnu, A. Verbanck, M. Walker, R. Young, K. L. Zubair, N. Ambite, J. L. Boerwinkle, E. Bottinger, E. Bustamante, C. D. Caberto, C. Conomos, M. P. Deelman, E. Do, R. Doheny, K. Fernandez-Rhodes, L. 2017-09-15 doi:10.1101/188094 Cold Spring Harbor Laboratory Press 2017-09-15 <![CDATA[ Genetic analysis of over one million people identifies 535 novel loci for blood pressure. ]]> https://biorxiv.org/content/10.1101/198234v1?rss=1 Evangelou, E. Warren, H. R. Mosen-Ansorena, D. Mifsud, B. Pazoki, R. Gao, H. Ntritsos, G. Dimou, N. Cabrera, C. P. Karaman, I. Ng, F. L. Evangelou, M. Witkowska, K. Tzanis, E. Hellwege, J. N. Giri, A. Velez Edwards, D. R. Sun, Y. V. Cho, K. Gaziano, J. M. Wilson, P. W. F. Tsao, P. S. Kovesdy, C. P. Esko, T. Magi, R. Milani, L. Almgren, P. Boutin, T. Debette, S. Ding, J. Giulianini, F. Holliday, E. G. Jackson, A. U. Li-Gao, R. Lin, W.-Y. Luan, J. Mangino, M. Oldmeadow, C. Prins, B. Qian, Y. Sargurupremraj, M. Shah, N. Surendran, P. Theriault, S. Verwe 2017-10-11 doi:10.1101/198234 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ Staphylococcal Enterotoxin C promotes Staphylococcus aureus Infective Endocarditis Independent of Superantigen Activity ]]> https://biorxiv.org/content/10.1101/2019.12.13.875633v1?rss=1 Kinney, K. J. Tran, P. M. Gibson-Corley, K. N. Forsythe, A. N. Kulhankova, K. Salgado-Pabon, W. 2019-12-13 doi:10.1101/2019.12.13.875633 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ In vivo studies of glucagon secretion by human islets transplanted in mice ]]> https://biorxiv.org/content/10.1101/2019.12.15.876920v1?rss=1 Tellez, K. Hang, Y. Gu, X. Stein, R. W. Kim, S. K. 2019-12-15 doi:10.1101/2019.12.15.876920 Cold Spring Harbor Laboratory Press 2019-12-15 <![CDATA[ Levonorgestrel modulates innate immune activation in human endocervical epithelium and monocytes during Chlamydia trachomatis infection ]]> https://biorxiv.org/content/10.1101/2019.12.16.878710v1?rss=1 Eastman, A. J. Liu, S. Bell, J. D. 2019-12-18 doi:10.1101/2019.12.16.878710 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ Insula Functional Connectivity in Schizophrenia ]]> https://biorxiv.org/content/10.1101/2019.12.16.878827v1?rss=1 Sheffield, J. M. Rogers, B. P. Blackford, J. U. Heckers, S. Woodward, N. D. 2019-12-18 doi:10.1101/2019.12.16.878827 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ Chop/Ddit3 depletion in β-cells alleviates ER stress and corrects hepatic steatosis ]]> https://biorxiv.org/content/10.1101/2020.01.02.893271v1?rss=1 Yong, J. Parekh, V. P. Nayak, J. Chen, Z. Lebeaupin, C. Zhang, J. Prakash, T. P. Murray, S. Guo, S. Ayala, J. E. Satin, L. S. Kaufman, R. J. 2020-01-03 doi:10.1101/2020.01.02.893271 Cold Spring Harbor Laboratory Press 2020-01-03 <![CDATA[ The Latent Genetic Structure of Impulsivity and its Relation to Internalizing Psychopathology ]]> https://biorxiv.org/content/10.1101/2020.01.07.897231v1?rss=1 Gustavson, D. E. Friedman, N. P. Fontanillas, P. Elson, S. L. the 23andMe Research Team, Palmer, A. A. Sanchez-Roige, S. 2020-01-08 doi:10.1101/2020.01.07.897231 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Single-cell metabolic analysis by mass cytometry reveals distinct transitional states of CD8 T cell differentiation ]]> https://biorxiv.org/content/10.1101/2020.01.21.911545v1?rss=1 Levine, L. S. Hiam, K. J. Marquez, D. M. Tenvooren, I. Contreras, D. C. Rathmell, J. C. Spitzer, M. H. 2020-01-22 doi:10.1101/2020.01.21.911545 Cold Spring Harbor Laboratory Press 2020-01-22 <![CDATA[ Granulocyte-Colony Stimulating Factor reduces cocaine-seeking and downregulates glutamatergic synaptic proteins in medial prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2020.02.17.949990v1?rss=1 Hofford, R. S. Euston, T. J. Wilson, R. S. Meckel, K. R. Peck, E. G. Godino, A. Landry, J. A. Calipari, E. S. Lam, T. T. Kiraly, D. D. 2020-02-18 doi:10.1101/2020.02.17.949990 Cold Spring Harbor Laboratory Press 2020-02-18 <![CDATA[ Anxiety and the neurobiology of uncertain threat anticipation ]]> https://biorxiv.org/content/10.1101/2020.02.25.964734v1?rss=1 Hur, J. Smith, J. F. DeYoung, K. A. Anderson, A. S. Kuang, J. Kim, H. C. Tillman, R. M. Kuhn, M. Fox, A. S. Shackman, A. J. 2020-02-26 doi:10.1101/2020.02.25.964734 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ Evidence for modulation of EEG microstate sequence by vigilance level ]]> https://biorxiv.org/content/10.1101/2020.02.26.966150v1?rss=1 Krylova, M. Alizadeh, S. Izyurov, I. Teckentrup, V. Chang, C. van der Meer, J. N. Erb, M. Kroemer, N. Koenig, T. Walter, M. Jamalabadi, H. 2020-02-27 doi:10.1101/2020.02.26.966150 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ Mycobacterium tuberculosis Rv0991c is a redox-regulated molecular chaperone ]]> https://biorxiv.org/content/10.1101/2020.03.05.980086v1?rss=1 Becker, S. H. Ulrich, K. Dhabaria, A. Ueberheide, B. Beavers, W. N. Skaar, E. P. Iyer, L. M. Aravind, L. Jakob, U. Darwin, K. H. 2020-03-07 doi:10.1101/2020.03.05.980086 Cold Spring Harbor Laboratory Press 2020-03-07 <![CDATA[ Chromatin-Bound PARP1 Correlates with Upregulation of Inflammatory Genes in Response to Long-Term Treatment with Veliparib ]]> https://biorxiv.org/content/10.1101/2020.03.08.982785v1?rss=1 Alvarado-Cruz, I. Mahmoud, M. Khan, M. Zhao, S. Oeck, S. Meas, R. Clairmont, K. Quintana, V. Zhu, Y. Porciuncula, A. Wyatt, H. Ma, S. Shyr, Y. Kong, Y. LoRusso, P. M. Laverty, D. Nagel, Z. D. Schalper, K. A. Krauthammer, M. Sweasy, J. B. 2020-03-09 doi:10.1101/2020.03.08.982785 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ High-Dimensional mass cytometry analysis reveals systemic immune perturbations in paediatric cancer influenced by age ]]> https://biorxiv.org/content/10.1101/2020.03.09.983288v1?rss=1 8 years old) had decreased naive CD4 and CD8 T-cells with concomitant increases in effector memory and T effector memory RA-revertant (TEMRA) T-cells. These immunological changes in pediatric cancer patients are relevant to the better understanding of how cancers diagnosed in childhood interact with systemic immunity and could inform the development and application of effective immune-modulating therapies in the pediatric population. One Sentence SummaryHigh dimensional analysis of systemic immunity in pediatric cancer patients reveals clinically relevant immune changes in NK and T-cells that vary with patient age. ]]> Syrimi, E. Irish, J. Khan, N. Willcox, B. Willcox, C. Murray, P. Haigh, T. Masand, N. Zuo, J. Barone, S. Kearns, P. Taylor, G. S. 2020-03-10 doi:10.1101/2020.03.09.983288 Cold Spring Harbor Laboratory Press 2020-03-10 <![CDATA[ Sprouty2 limits intestinal tuft and goblet cell numbers through GSK3β-mediated restriction of epithelial IL-33. ]]> https://biorxiv.org/content/10.1101/2020.03.09.984369v1?rss=1 Schumacher, M. A. Hsieh, J. J. Liu, C. Y. Appel, K. L. Waddell, A. Almohazey, D. Katada, K. Bernard, J. K. Bucar, E. B. Gadeock, S. Maselli, K. M. Washington, M. K. Grikscheit, T. C. Warburton, D. Rosen, M. J. Frey, M. R. 2020-03-11 doi:10.1101/2020.03.09.984369 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ ODELAM: Rapid sequence-independent detection of drug resistance in clinical isolates of Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2020.03.17.995480v1?rss=1 Herricks, T. Donczew, M. Mast, F. Rustad, T. Morrison, R. Sterling, T. R. Sherman, D. Aitchison, J. D. 2020-03-19 doi:10.1101/2020.03.17.995480 Cold Spring Harbor Laboratory Press 2020-03-19 <![CDATA[ An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 and multiple endemic, epidemic and bat coronavirus ]]> https://biorxiv.org/content/10.1101/2020.03.19.997890v1?rss=1 Sheahan, T. P. Sims, A. C. Zhou, S. Hill, C. Leist, S. R. Schaefer, A. Agostini, M. Pruijssers, A. Brown, A. J. Bluemling, G. Natchus, M. Saindane, M. Kolykhalov, A. Painter, G. Swanstrom, R. Dinnon, K. Graham, R. Harcourt, J. Tamin, A. Thornburg, N. J. Montgomery, S. A. Chappell, J. Denison, M. Baric, R. S. 2020-03-20 doi:10.1101/2020.03.19.997890 Cold Spring Harbor Laboratory Press 2020-03-20 <![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[ Analysis of female song provides insight into the evolution of dimorphism in a widely studied songbird ]]> https://biorxiv.org/content/10.1101/2020.03.28.013433v1?rss=1 Wilkins, M. R. Odom, K. J. Benedict, L. Safran, R. J. 2020-03-30 doi:10.1101/2020.03.28.013433 Cold Spring Harbor Laboratory Press 2020-03-30 <![CDATA[ Risperidone-induced changes in DNA methylation from peripheral blood in first-episode schizophrenia parallel neuroimaging and cognitive phenotype ]]> https://biorxiv.org/content/10.1101/2020.03.31.018283v1?rss=1 Hu, M. Xia, Y. Zong, X. Sweeney, J. A. Bishop, J. R. Giase, G. Li, B. Rubin, L. H. Chen, X. Wang, Y. Kunney, L. Li, Z. He, Y. Liu, C. Chen, C. Chen, X. Tang, J. 2020-04-02 doi:10.1101/2020.03.31.018283 Cold Spring Harbor Laboratory Press 2020-04-02 <![CDATA[ Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence ]]> https://biorxiv.org/content/10.1101/2020.04.10.029454v1?rss=1 Leary, S. Gaudieri, S. Chopra, A. Pakala, S. Alves, E. John, M. Das, S. Mallal, S. Phillips, P. J. 2020-04-11 doi:10.1101/2020.04.10.029454 Cold Spring Harbor Laboratory Press 2020-04-11 <![CDATA[ Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells ]]> https://biorxiv.org/content/10.1101/2020.04.19.049254v1?rss=1 Muus, C. Luecken, M. D. Eraslan, G. Waghray, A. Heimberg, G. Sikkema, L. Kobayashi, Y. Vaishnav, E. D. Subramanian, A. Smillie, C. Jagadeesh, K. Duong, E. T. Fiskin, E. Torlai Triglia, E. Ansari, M. Cai, P. Lin, B. Buchanan, J. Chen, S. Shu, J. Haber, A. L. Chung, H. Montoro, D. T. Adams, T. Aliee, H. Allon, S. J. Andrusivova, Z. Angelidis, I. Ashenberg, O. Bassler, K. Becavin, C. Benhar, I. Bergenstrahle, J. Bergenstrahle, L. Bolt, L. Braun, E. Bui, L. T. Chaffin, M. Chichelnitskiy, E. Chiou, J. Conlon, T. M. Cuoco, M. S. Deprez, M. Fischer, D. S. G 2020-04-20 doi:10.1101/2020.04.19.049254 Cold Spring Harbor Laboratory Press 2020-04-20 <![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[ Peptidoglycan editing provides immunity to Acinetobacter baumannii during bacterial warfare ]]> https://biorxiv.org/content/10.1101/2020.04.23.058008v1?rss=1 Le, N.-H. Peters, K. Espaillat, A. Sheldon, J. R. Gray, J. Di Venanzio, G. Lopez, J. Djahanschiri, B. Mueller, E. A. Hennon, S. W. Levin, P. A. Ebersberger, I. Skaar, E. P. Cava, F. Vollmer, W. Feldman, M. F. 2020-04-25 doi:10.1101/2020.04.23.058008 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Remdesivir potently inhibits SARS-CoV-2 in human lung cells and chimeric SARS-CoV expressing the SARS-CoV-2 RNA polymerase in mice. ]]> https://biorxiv.org/content/10.1101/2020.04.27.064279v1?rss=1 Pruijssers, A. J. George, A. S. Schäfer, A. Leist, S. R. Gralinski, L. E. Dinnon, K. H. Yount, B. L. Agostini, M. L. Stevens, L. J. Chappell, J. D. Lu, X. Hughes, T. M. Gully, K. L. Martinez, D. R. Brown, A. J. Graham, R. L. Perry, J. K. Du Pont, V. Pitts, J. Ma, B. Babusis, D. Murakami, E. Feng, J. Y. Bilello, J. P. Porter, D. P. Cihlar, T. Baric, R. S. Denison, M. R. Sheahan, T. P. 2020-04-27 doi:10.1101/2020.04.27.064279 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis ]]> https://biorxiv.org/content/10.1101/2020.04.30.071217v1?rss=1 Xu, C. Fisher, D. Rankovic, S. Li, W. Dick, R. Runge, B. Zadorozhnyi, R. Ahn, J. Aiken, C. Polenova, T. Engelman, A. Ambrose, Z. Rousso, I. Perilla, J. R. 2020-05-01 doi:10.1101/2020.04.30.071217 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ Integrated technology platform for accelerated discovery of antiviral antibody therapeutics ]]> https://biorxiv.org/content/10.1101/2020.05.12.090944v1?rss=1 100 individual Zika virus (ZIKV) specific human mAbs, assessed their function, identified 29 broadly-neutralizing mAbs, and verified therapeutic potency of lead candidates with antibody-encoding mRNA formulation and/or IgG protein delivery in mice and nonhuman primates. Our work provides a roadmap for the rapid antibody discovery programs against viral pathogens of global concern. ]]> Gilchuk, P. Bombardi, R. G. Erasmus, J. H. Tan, Q. Nargi, R. S. Soto, C. Abbink, P. Suscovich, T. J. Dunellin, L. A. Khandhar, A. Archer, J. Liang, J. Fouch, M. E. Davidson, E. Doranz, B. Jones, T. Larson, E. Ertel, S. Granger, B. Fuerte-Stone, J. Roy, V. Broge, T. Linnekin, T. C. Linde, C. H. Gorman, M. J. Nkolola, J. Alter, G. Reed, S. G. Barouch, D. H. Diamond, M. S. Crowe, J. E. Van Hoeven, N. Thackray, L. Carnahan, R. H. 2020-05-14 doi:10.1101/2020.05.12.090944 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Multilayer modelling and analysis of the humantranscriptome ]]> https://biorxiv.org/content/10.1101/2020.05.21.109082v1?rss=1 Azevedo, T. Dimitri, G. M. Lio, P. Gamazon, E. R. 2020-05-25 doi:10.1101/2020.05.21.109082 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Age-related expression of SARS-CoV-2 priming protease TMPRSS2 in the developing lung ]]> https://biorxiv.org/content/10.1101/2020.05.22.111187v1?rss=1 Schuler, B. A. Habermann, A. C. Plosa, E. J. Taylor, C. J. Jetter, C. S. Kapp, M. E. Benjamin, J. Gulleman, P. Nichols, D. S. Braunstein, L. Z. Koval, M. H. Guttentag, S. H. Blackwell, T. S. Vanderbilt COVID-19 Consortium Cohort, Webber, S. A. Banovich, N. Kropski, J. A. Sucre, J. M. HCA Lung Biological Network, 2020-05-23 doi:10.1101/2020.05.22.111187 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ Motor corollary discharge activates layer six circuits in the auditory cortex ]]> https://biorxiv.org/content/10.1101/2020.05.28.121459v1?rss=1 Clayton, K. K. Williamson, R. S. Watanabe, Y. Hancock, K. E. Tasaka, G.-i. Mizrahi, A. Hackett, T. Polley, D. B. 2020-05-30 doi:10.1101/2020.05.28.121459 Cold Spring Harbor Laboratory Press 2020-05-30 <![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[ Reovirus σ1 conformational flexibility modulates the efficiency of host cell attachment ]]> https://biorxiv.org/content/10.1101/2020.06.09.143594v1?rss=1 Diller, J. R. Halloran, S. R. Koehler, M. dos Santos Natividade, R. Alsteens, D. Stehle, T. Dermody, T. S. Ogden, K. M. 2020-06-12 doi:10.1101/2020.06.09.143594 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Heart Slice Culture System Reliably Demonstrates Clinical Drug-Related Cardiotoxicity ]]> https://biorxiv.org/content/10.1101/2020.06.12.148197v1?rss=1 Miller, J. M. Meki, M. H. Ou, Q. George, S. A. Gams, A. Abouleisa, R. R. E. Tang, X.-L. Ahern, B. M. Giridharan, G. A. El-Baz, A. Hill, B. G. Satin, J. Conklin, D. J. Moslehi, J. Bolli, R. Ribeiro, A. J. S. Efimov, I. R. Mohamed, T. M. A. 2020-06-13 doi:10.1101/2020.06.12.148197 Cold Spring Harbor Laboratory Press 2020-06-13 <![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[ Dynamics of altruistic fluid transport in egg development ]]> https://biorxiv.org/content/10.1101/2020.06.16.155606v1?rss=1 Imran Alsous, J. Romeo, N. Jackson, J. Mason, F. Dunkel, J. Martin, A. 2020-06-17 doi:10.1101/2020.06.16.155606 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Identification of a critical horseshoe-shaped region in the nsp5 (Mpro, 3CLpro) protease interdomain loop (IDL) of coronavirus mouse hepatitis virus (MHV) ]]> https://biorxiv.org/content/10.1101/2020.06.18.160671v1?rss=1 Nick, B. C. Pandya, M. C. Lu, X. Franke, M. E. Callahan, S. M. Hasik, E. F. Berthrong, S. T. Denison, M. R. Stobart, C. C. 2020-06-19 doi:10.1101/2020.06.18.160671 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Does rhythmic priming improve grammatical processing in Hungarian-speaking children with and without Developmental Language Disorder? ]]> https://biorxiv.org/content/10.1101/2020.06.19.162347v1?rss=1 Ladanyi, E. Lukacs, A. Gervain, J. 2020-06-21 doi:10.1101/2020.06.19.162347 Cold Spring Harbor Laboratory Press 2020-06-21 <![CDATA[ Robust, flexible, and scalable tests for Hardy-Weinberg Equilibrium across diverse ancestries ]]> https://biorxiv.org/content/10.1101/2020.06.23.167759v1?rss=1 Kwong, A. NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Blackwell, T. W. TOPMed Analysis Working Group, LeFaive, J. de Andrade, M. Barnard, J. Barnes, K. C. Blangero, J. Boerwinkle, E. Burchard, E. G. Cade, B. E. Chasman, D. Chen, H. Conomos, M. Cupples, L. A. Ellinor, P. T. Eng, C. Gao, Y. Guo, X. Irvin, M. R. Kelly, T. Kim, W. Kooperberg, C. Lubitz, S. A. Mak, A. C. Y. Manichaikul, A. W. Mathias, R. A. Montasser, M. E. Montgomery, C. G. Musani, S. Palmer, N. D. Peloso, G. Qiao, D. Reiner, A. P. Roden, D. M. Shoemaker, M. B. Smith, J. A 2020-06-24 doi:10.1101/2020.06.23.167759 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ periscope: sub-genomic RNA identification in SARS-CoV-2 ARTIC Network Nanopore Sequencing Data ]]> https://biorxiv.org/content/10.1101/2020.07.01.181867v1?rss=1 Parker, M. D. Lindsey, B. B. Leary, S. Gaudieri, S. Chopra, A. Wyles, M. Angyal, A. Green, L. R. Parsons, P. Tucker, R. M. Brown, R. Groves, D. Johnson, K. Carrilero, L. Heffer, J. Partridge, D. Evans, C. Razza, M. Keeley, A. J. Smith, N. Wang, D. Mallal, S. de Silva, T. I. 2020-07-01 doi:10.1101/2020.07.01.181867 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Genetic architecture of host proteins interacting with SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.07.01.182709v1?rss=1 Pietzner, M. Wheeler, E. Carrasco-Zanini, J. Raffler, J. Kerrison, N. D. Oerton, E. Auyeung, V. P. W. Luan, J. Finan, C. Casas, J. P. Ostroff, R. Williams, S. A. Kastenmüller, G. Ralser, M. Gamazon, E. G. Wareham, N. J. Hingorani, A. D. Langenberg, C. 2020-07-01 doi:10.1101/2020.07.01.182709 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Directed evolution reveals the mechanism of HitRS signal transduction in Bacillus anthracis ]]> https://biorxiv.org/content/10.1101/2020.07.03.185868v1?rss=1 Skaar, E. P. Pi, H. Chu, M. Ivan, S. Latario, C. Toth, A. Carlin, S. Hillebrand, G. Lin, H. Reppart, J. Stauff, D. L. 2020-07-03 doi:10.1101/2020.07.03.185868 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ Antagonistic epistasis of Hnf4a and FoxO1 networks through enhancer interactionsin beta-cell function ]]> https://biorxiv.org/content/10.1101/2020.07.04.187864v1?rss=1 Kuo, T. Du, W. Miyachi, Y. Dadi, P. K. Jacobson, D. A. Accili, D. 2020-07-05 doi:10.1101/2020.07.04.187864 Cold Spring Harbor Laboratory Press 2020-07-05 <![CDATA[ INTS13 Mutations Causing a Developmental Ciliopathy Disrupt Integrator Complex Assembly ]]> https://biorxiv.org/content/10.1101/2020.07.20.209130v1?rss=1 Mascibroda, L. G. Shboul, M. Elrod, N. D. Colleaux, L. Hamamy, H. Huang, K.-L. Peart, N. J. Singh, M. K. Lee, H. Merriman, B. Jodoin, J. N. Lee, L. A. Al-Rawashdeh, B. Ababneh, O. El-Khateeb, M. Fathalla, R. Escande-Beillard, N. Nelson, S. F. Wu, Y. Tong, L. Kenney, L. J. Russell, W. K. Amiel, J. Reversade, B. Wagner, E. J. 2020-07-21 doi:10.1101/2020.07.20.209130 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Siderophore-mediated zinc acquisition enhances enterobacterial colonization of the inflamed gut. ]]> https://biorxiv.org/content/10.1101/2020.07.20.212498v1?rss=1 Zhi, H. Behnsen, J. Aron, A. Subramanian, V. Liu, J. Gerner, R. Petras, D. Green, K. Price, S. Camacho, J. Hillman, H. Tjokrosurjo, J. Montaldo, N. Hoover, E. Treacy-Abarca, S. Gilston, B. Skaar, E. Chazin, W. Garneau-Tsodikova, S. Lawrenz, M. Perry, R. Nuccio, S.-P. Dorrestein, P. Raffatellu, M. 2020-07-21 doi:10.1101/2020.07.20.212498 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Neuron-intrinsic NF-κB Signaling Mediates Reovirus Virulence ]]> https://biorxiv.org/content/10.1101/2020.08.05.238220v1?rss=1 Dermody, T. Pruijssers, A. J. Taylor, G. M. Brigleb, P. Shang, P. Urbanek, K. Brwon, J. 2020-08-06 doi:10.1101/2020.08.05.238220 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ A DNA-origami nuclear pore mimic reveals nuclear entry mechanisms of HIV-1 capsid ]]> https://biorxiv.org/content/10.1101/2020.08.10.245522v1?rss=1 Shen, Q. Xu, C. Jang, S. Xiong, Q. Devarkar, S. Tian, T. Bedwell, G. Tripler, T. Hu, Y. Yuan, S. Temple, J. Shi, J. Aiken, C. Engelman, A. Perilla, J. R. Lusk, C. P. Lin, C. Xiong, Y. 2020-08-11 doi:10.1101/2020.08.10.245522 Cold Spring Harbor Laboratory Press 2020-08-11 <![CDATA[ The risks of using the chi-square periodogram to estimate the period of biological rhythms ]]> https://biorxiv.org/content/10.1101/2020.08.14.251512v1?rss=1 Tackenberg, M. C. Hughey, J. J. 2020-08-15 doi:10.1101/2020.08.14.251512 Cold Spring Harbor Laboratory Press 2020-08-15 <![CDATA[ The Role of Temperature on the Development of Circadian Rhythms in Honey Bee Workers ]]> https://biorxiv.org/content/10.1101/2020.08.17.254557v1?rss=1 Giannoni-Guzman, M. A. Aleman-Rios, J. Melendez Moreno, A. M. Diaz Hernandez, G. Perez Torres, M. Lubriel, D. Giray, T. Agosto Rivera, J. L. 2020-08-18 doi:10.1101/2020.08.17.254557 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Shift work dynamics and division of labor: honeybee foraging and fanning tasks ]]> https://biorxiv.org/content/10.1101/2020.08.17.254755v1?rss=1 Giannoni Guzman, M. A. Giray, T. Agosto Rivera, J. L. 2020-08-18 doi:10.1101/2020.08.17.254755 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Modular metabolite assembly in C. elegans lysosome-related organelles ]]> https://biorxiv.org/content/10.1101/2020.08.22.262956v1?rss=1 View larger version (42K): org.highwire.dtl.DTLVardef@6e83cborg.highwire.dtl.DTLVardef@18e9302org.highwire.dtl.DTLVardef@1557670org.highwire.dtl.DTLVardef@1d2ca50_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Le, H. H. Wrobel, C. J. Cohen, S. M. Yu, J. Park, H. Helf, M. J. Curtis, B. J. Rodrigues, P. R. Sternberg, P. W. Schroeder, F. C. 2020-08-24 doi:10.1101/2020.08.22.262956 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Tissue specificity-aware TWAS (TSA-TWAS) framework identifies novel associations with metabolic, immunologic, and virologic traits in HIV-positive adults ]]> https://biorxiv.org/content/10.1101/2020.08.31.273458v1?rss=1 Li, B. Veturi, Y. Verma, A. Bradford, Y. Daar, E. S. Gulick, R. M. Riddler, S. A. Robbins, G. K. Lennox, J. L. Haas, D. W. Ritchie, M. D. 2020-09-01 doi:10.1101/2020.08.31.273458 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ BrainPhys neuronal medium optimized for imaging and optogenetics in vitro ]]> https://biorxiv.org/content/10.1101/2020.09.02.276535v1?rss=1 Zabolocki, M. McCormack, K. van den Hurk, M. Milky, B. Shoubridge, A. Adams, R. Tran, J. Mahadevan-Jansen, A. Reineck, P. Thomas, J. Hutchinson, M. R. Mark, C. Anonuevo, A. Chew, L. H. Hirst, A. J. Lee, V. M. Knock, E. Bardy, C. 2020-09-03 doi:10.1101/2020.09.02.276535 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ pmparser and PMDB: resources for large-scale, open studies of the biomedical literature ]]> https://biorxiv.org/content/10.1101/2020.09.07.285924v1?rss=1 Schoenbachler, J. L. Hughey, J. J. 2020-09-09 doi:10.1101/2020.09.07.285924 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ A simple permutation-based test of intermodal correspondence ]]> https://biorxiv.org/content/10.1101/2020.09.10.285049v1?rss=1 Weinstein, S. M. Vandekar, S. N. Adebimpe, A. Tapera, T. M. Robert-Fitzgerald, T. Gur, R. C. Gur, R. E. Raznahan, A. Satterthwaite, T. D. Alexander-Bloch, A. F. Shinohara, R. T. 2020-09-11 doi:10.1101/2020.09.10.285049 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition ]]> https://biorxiv.org/content/10.1101/2020.09.10.292078v1?rss=1 Greaney, A. J. Starr, T. N. Gilchuk, P. Zost, S. J. Binshtein, E. Loes, A. N. Hilton, S. K. Huddleston, J. Eguia, R. Crawford, K. H. Dingens, A. S. Nargi, R. S. Sutton, R. E. Suryadevara, N. Rothlauf, P. W. Liu, Z. Whelan, S. P. Carnahan, R. H. Crowe, J. E. Bloom, J. D. 2020-09-10 doi:10.1101/2020.09.10.292078 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ PreQual: An automated pipeline for integrated preprocessing and quality assurance of diffusion weighted MRI images ]]> https://biorxiv.org/content/10.1101/2020.09.14.260240v1?rss=1 Cai, L. Y. Yang, Q. Hansen, C. B. Nath, V. Ramadass, K. Johnson, G. W. Conrad, B. N. Boyd, B. D. Begnoche, J. P. Beason-Held, L. L. Shafer, A. T. Resnick, S. M. Taylor, W. D. Price, G. R. Morgan, V. L. Rogers, B. P. Schilling, K. G. Landman, B. A. 2020-09-15 doi:10.1101/2020.09.14.260240 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ Sequence-dependent mechanics of collagen reflect its structural and functional organization ]]> https://biorxiv.org/content/10.1101/2020.09.27.315929v1?rss=1 Al-Shaer, A. Lyons, A. Ishikawa, Y. Hudson, B. G. Boudko, S. Forde, N. R. 2020-09-28 doi:10.1101/2020.09.27.315929 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Helicobacter pylori accelerates KRAS-dependent gastric dysplasia ]]> https://biorxiv.org/content/10.1101/2020.10.06.328518v1?rss=1 O'Brien, V. P. Koehne, A. Dubrulle, J. Rodriguez, A. Leverich, C. Kong, P. Campbell, J. Pierce, R. Goldenring, J. Choi, E. Salama, N. 2020-10-06 doi:10.1101/2020.10.06.328518 Cold Spring Harbor Laboratory Press 2020-10-06 <![CDATA[ High contrast probe cleavage detection on porous silicon biosensors via quantum dot labeled DNA probes ]]> https://biorxiv.org/content/10.1101/2020.10.07.330589v1?rss=1 Dubrovsky, M. Layouni, R. Bao, M. Chung, H. Du, K. Boriskina, S. V. Weiss, S. M. Vermeulen, D. 2020-10-08 doi:10.1101/2020.10.07.330589 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Racial and ethnic imbalance in neuroscience reference lists and intersections with gender ]]> https://biorxiv.org/content/10.1101/2020.10.12.336230v1?rss=1 Bertolero, M. A. Dworkin, J. D. David, S. U. Lloreda, C. L. Srivastava, P. Stiso, J. Zhou, D. Dzirasa, K. Fair, D. A. Kaczkurkin, A. N. Marlin, B. J. Shohamy, D. Uddin, L. Q. Zurn, P. Bassett, D. S. 2020-10-12 doi:10.1101/2020.10.12.336230 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ Genetic Landscape of Gullah African Americans ]]> https://biorxiv.org/content/10.1101/2020.10.12.336347v1?rss=1 Zimmerman, K. D. Schurr, T. G. Chen, W.-M. Nayak, U. Mychaleckyj, J. C. Quet, Q. Moultrie, L. H. Divers, J. Keene, K. L. Kamen, D. L. Gilkeson, G. S. Hunt, K. J. Spruill, I. J. Fernandes, J. K. Aldrich, M. Reich, D. E. Garvey, W. T. Langefeld, C. D. Sale, M. M. Ramos, P. S. 2020-10-13 doi:10.1101/2020.10.12.336347 Cold Spring Harbor Laboratory Press 2020-10-13 <![CDATA[ Reovirus RNA recombination is sequence directed and generates internally deleted defective genome segments during passage ]]> https://biorxiv.org/content/10.1101/2020.10.19.346031v1?rss=1 Smith, S. C. Gribble, J. Diller, J. R. Wiebe, M. A. Thoner, T. W. Denison, M. R. Ogden, K. M. 2020-10-19 doi:10.1101/2020.10.19.346031 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ Single-cell RNA-sequencing reveals dysregulation of molecular programs associated with SARS-CoV-2 severity and outcomes in patients with chronic lung disease ]]> https://biorxiv.org/content/10.1101/2020.10.20.347187v1?rss=1 Bui, L. T. Winters, N. I. Chung, M.-I. Joseph, C. Gutierrez, A. J. Habermann, A. C. Adams, T. S. Schupp, J. C. Poli, S. Peter, L. M. Taylor, C. J. Blackburn, J. B. Richmond, B. W. Nicholson, A. G. Rassl, D. Wallace, W. A. Rosas, I. O. Jenkins, R. G. Kaminski, N. Kropski, J. A. Banovich, N. E. Human Cell Atlas Lung Biological Network, 2020-10-20 doi:10.1101/2020.10.20.347187 Cold Spring Harbor Laboratory Press 2020-10-20 <![CDATA[ Integrated Single Cell Atlas of Endothelial Cells of the Human Lung ]]> https://biorxiv.org/content/10.1101/2020.10.21.347914v1?rss=1 Schupp, J. C. Adams, T. S. Cosme, C. Brickman Raredon, M. S. Omote, N. Poli, S. Rose, K.-A. Manning, E. Sauler, M. DeIuliis, G. Ahangari, F. Neumark, N. Yuan, Y. Habermann, A. C. Gutierrez, A. J. Bui, L. T. Meyer, K. B. Nawijn, M. C. Teichmann, S. A. Banovich, N. Kropski, J. A. Niklason, L. E. Pe'er, D. Yan, X. Homer, R. Rosas, I. O. Kaminski, N. 2020-10-22 doi:10.1101/2020.10.21.347914 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ Amplification of potential thermogenetic mechanisms in cetacean brains ]]> https://biorxiv.org/content/10.1101/2020.10.23.352138v1?rss=1 Manger, P. R. Patzke, N. Spocter, M. Bhagwandin, A. Karlsson, K. Bertelsen, M. Alagaili, A. Bennett, N. Mohammed, O. Herculano-Houzel, S. Hof, P. Fuxe, K. 2020-10-23 doi:10.1101/2020.10.23.352138 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ Chronic BDNF simultaneously inhibits and unmasks superficial dorsal horn neuronal activity ]]> https://biorxiv.org/content/10.1101/2020.11.02.364786v1?rss=1 Alles, S. R. A. Odem, M. A. Lu, V. B. Cassidy, R. M. Smith, P. A. 2020-11-02 doi:10.1101/2020.11.02.364786 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ SARS-CoV-2 Infects Human Engineered Heart Tissues and Models COVID-19 Myocarditis ]]> https://biorxiv.org/content/10.1101/2020.11.04.364315v1?rss=1 Bailey, A. L. Dmytrenko, O. Greenberg, L. Bredemeyer, A. L. Ma, P. Liu, J. Penna, V. Lai, L. Winkler, E. S. Sviben, S. Brooks, E. Nair, A. P. Heck, K. A. Rali, A. S. Simpson, L. Saririan, M. Hobohm, D. Stump, W. T. Fitzpatrick, J. A. Xie, X. Shi, P.-Y. Hinson, J. T. Gi, W.-T. Schmidt, C. Leuschner, F. Lin, C.-Y. Diamond, M. S. Greenberg, M. J. Lavine, K. J. 2020-11-05 doi:10.1101/2020.11.04.364315 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Combined assessment of MHC binding and antigen expression improves T cell epitope predictions ]]> https://biorxiv.org/content/10.1101/2020.11.09.375204v1?rss=1 Kosaloglu-Yalcin, Z. Lee, J. Nielsen, M. Greenbaum, J. Schoenberger, S. P. Miller, A. Kim, Y. J. Sette, A. Peters, B. 2020-11-10 doi:10.1101/2020.11.09.375204 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ Polygenic transcriptome risk scores improve portability of polygenic risk scores across ancestries ]]> https://biorxiv.org/content/10.1101/2020.11.12.373647v1?rss=1 Liang, Y. Pividori, M. Manichaikul, A. Palmer, A. A. Cox, N. J. Wheeler, H. E. Im, H. K. 2020-11-13 doi:10.1101/2020.11.12.373647 Cold Spring Harbor Laboratory Press 2020-11-13 <![CDATA[ Disentangling genetic feature selection and aggregation in transcriptome-wide association studies ]]> https://biorxiv.org/content/10.1101/2020.11.19.390617v1?rss=1 Cao, C. Kwok, D. Li, Q. He, J. Guo, X. Zhang, Q. Long, Q. 2020-11-20 doi:10.1101/2020.11.19.390617 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ The Erythropoietin Receptor Stimulates Rapid Cycling and Formation of Larger Red Cells During Mouse and Human Erythropoiesis ]]> https://biorxiv.org/content/10.1101/2020.11.30.404780v1?rss=1 Hidalgo, D. Bejder, J. Pop, R. Gellatly, K. Scalf, S. M. Eastman, A. E. Chen, J.-J. Zhu, J. L. Heuberger, J. A. A. C. Guo, S. Koury, M. J. Nordsborg, N. B. Socolovsky, M. 2020-11-30 doi:10.1101/2020.11.30.404780 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ Phospholipid Metabolism Is Associated with HIV Rebound Upon Treatment Interruption ]]> https://biorxiv.org/content/10.1101/2020.12.09.418814v1?rss=1 Giron, L. B. Papasavvas, E. Yin, X. Goldman, A. Tang, H.-Y. Palmer, C. Landay, A. L. Li, J. Z. Koethe, J. Mounzer, K. C. Kostman, J. Liu, Q. Montaner, L. J. Abdel-Mohsen, M. 2020-12-10 doi:10.1101/2020.12.09.418814 Cold Spring Harbor Laboratory Press 2020-12-10 <![CDATA[ Human neutralizing antibodies against SARS-CoV-2 require intact Fc effector functions and monocytes for optimal therapeutic protection ]]> https://biorxiv.org/content/10.1101/2020.12.28.424554v1?rss=1 Winkler, E. S. Gilchuk, P. Yu, J. Bailey, A. L. Chen, R. E. Zost, S. J. Jang, H. Huang, Y. Allen, J. D. Case, J. B. Sutton, R. E. Carnahan, R. H. Darling, T. L. Boon, A. C. M. Mack, M. Head, R. D. Ross, T. M. Crowe, J. E. Diamond, M. 2020-12-28 doi:10.1101/2020.12.28.424554 Cold Spring Harbor Laboratory Press 2020-12-28 <![CDATA[ Statistical and machine learning models for classification of human wear and delivery days in accelerometry data ]]> https://biorxiv.org/content/10.1101/2020.12.31.424867v1?rss=1 Moore, R. Archer, K. R. Choi, L. 2021-01-04 doi:10.1101/2020.12.31.424867 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Canonical features of human antibodies recognizing the influenza hemagglutinin trimer interface ]]> https://biorxiv.org/content/10.1101/2020.12.31.424868v1?rss=1 Zost, S. J. Dong, J. Gilchuk, I. M. Gilchuk, P. Thornburg, N. J. Bangaru, S. Kose, N. Finn, J. A. Bombardi, R. Soto, C. Nargi, R. S. Irving, R. P. Suryadevara, N. Westover, J. B. Carnahan, R. H. Turner, H. L. Li, S. Ward, A. B. Crowe, J. E. 2021-01-03 doi:10.1101/2020.12.31.424868 Cold Spring Harbor Laboratory Press 2021-01-03 <![CDATA[ Multiplatform Integrative Analyses of Immunosuppressive Signatures in Cortisol-secreting Adrenocortical Carcinoma ]]> https://biorxiv.org/content/10.1101/2021.01.14.426712v1?rss=1 Baechle, J. J. Hanna, D. N. Konjeti, S. R. Rathmell, J. C. Rathmell, W. K. Baregamian, N. 2021-01-16 doi:10.1101/2021.01.14.426712 Cold Spring Harbor Laboratory Press 2021-01-16 <![CDATA[ HIV-1 uncoating occurs via a series of rapid biomechanical changes in the core related to individual stages of reverse transcription ]]> https://biorxiv.org/content/10.1101/2021.01.16.426924v1?rss=1 Rankovic, S. Deshpande, A. Harel, S. Aiken, C. Rousso, I. 2021-01-17 doi:10.1101/2021.01.16.426924 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ MAESTRO affords 'breadth and depth' for mutation testing ]]> https://biorxiv.org/content/10.1101/2021.01.22.427323v1?rss=1 Gydush, G. Nguyen, E. Bae, J. H. Rhoades, J. Reed, S. C. Shea, D. Xiong, K. Liu, R. Blewett, T. Yu, F. Leong, K. W. Choudhury, A. D. Stover, D. G. Tolaney, S. M. Krop, I. E. Love, J. C. Parsons, H. A. Makrigiorgos, G. M. Golub, T. R. Adalsteinsson, V. A. 2021-01-24 doi:10.1101/2021.01.22.427323 Cold Spring Harbor Laboratory Press 2021-01-24 <![CDATA[ A systematic analysis of genetically regulated differences in gene expression and the role of co-expression networks across 16 psychiatric disorders and substance use phenotypes ]]> https://biorxiv.org/content/10.1101/2021.01.28.428688v1?rss=1 Gerring, Z. F. Thorp, J. G. Gamazon, E. Derks, E. M. 2021-01-30 doi:10.1101/2021.01.28.428688 Cold Spring Harbor Laboratory Press 2021-01-30 <![CDATA[ Neptune: An environment for the delivery of genomic medicine ]]> https://biorxiv.org/content/10.1101/2021.01.29.428608v1?rss=1 Venner, E. Yi, V. Murdock, D. R. Kalla, S. E. Wu, T.-J. Sabo, A. Li, S. Meng, Q. Tian, X. Murugan, M. Cohen, M. Kovar, C. Wei, W.-Q. Chung, W. Weng, C. Weisner, G. Jarvik, G. Muzny, D. M. Gibbs, R. 2021-02-01 doi:10.1101/2021.01.29.428608 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Genomic Considerations for FHIR; eMERGE Implementation Lessons ]]> https://biorxiv.org/content/10.1101/2021.01.31.429037v1?rss=1 Murugan, M. Babb, L. J. Taylor, C. O. Rasmussen, L. V. Freimuth, R. R. Venner, E. Yan, F. Yi, V. Granite, S. J. Zouk, H. Aronson, S. J. Power, K. Fedotov, A. Crosslin, D. R. Fasel, D. Jarvik, G. P. Hakonarson, H. Bangash, H. Kullo, I. J. Connolly, J. J. Nestor, J. G. Caraballo, P. J. Wei, W. Wiley, K. Rehm, H. L. Gibbs, R. A. 2021-02-01 doi:10.1101/2021.01.31.429037 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Role of transmembrane spanning domain 1 in cystic fibrosis transmembrane conductance regulator folding ]]> https://biorxiv.org/content/10.1101/2021.02.02.428178v1?rss=1 Patrick, A. E. Millen, L. Thomas, P. J. 2021-02-02 doi:10.1101/2021.02.02.428178 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Oxidant-Resistant LRRC8A/C Anion Channels Support Superoxide Production by Nox1 ]]> https://biorxiv.org/content/10.1101/2021.02.03.429614v1?rss=1 Rohrbough, J. Choi, H. Nguyen, H.-N. Dikalova, A. Lamb, F. S. 2021-02-03 doi:10.1101/2021.02.03.429614 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ On the robustness of inference of association with the gut microbiota in stool, swab and mucosal tissue samples ]]> https://biorxiv.org/content/10.1101/2021.02.04.429844v1?rss=1 Sun, S. Zhu, X. Huang, X. Murff, H. J. Ness, R. M. Seidner, D. L. Sorgen, A. Blakley, I. Yu, C. Dai, Q. Azcarate-Peril, M. A. Shrubsole, M. J. Fodor, A. A. 2021-02-05 doi:10.1101/2021.02.04.429844 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Diet-dependent Natriuretic Peptide Receptor C expression in adipose tissue is mediated by PPARγ via long-range distal enhancers ]]> https://biorxiv.org/content/10.1101/2021.02.09.430332v1?rss=1 Shi, F. Simandi, Z. Nagy, L. Collins, S. 2021-02-11 doi:10.1101/2021.02.09.430332 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ Multiplatform Computational Analysis of Mast Cells in Adrenocortical Carcinoma Tumor Microenvironment ]]> https://biorxiv.org/content/10.1101/2021.02.09.430462v1?rss=1 Baechle, J. J. Hanna, D. N. Konjeti, S. R. Rathmell, J. C. Rathmell, W. K. Baregamian, N. 2021-02-11 doi:10.1101/2021.02.09.430462 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ Hotspot ESR1 mutations are multimodal and contextual drivers of breast cancer metastasis ]]> https://biorxiv.org/content/10.1101/2021.02.10.430701v1?rss=1 Li, Z. Wu, Y. Yates, M. E. Tasdemir, N. Bahreini, A. Chen, J. Levine, K. M. Priedigkeit, N. M. Ali, S. Buluwela, L. Arnesen, S. Gertz, J. Richer, J. K. Troness, B. El-Ashry, D. Zhang, Q. Gerratana, L. Zhang, Y. Cristofanilli, M. Montanez, M. A. Sundd, P. Wallace, C. T. Watkins, S. C. Zhu, L. Tseng, G. Wagle, N. Carroll, J. Jank, P. Denkert, C. Karsten, M. M. Blohmer, J. Park, B. H. Lucas, P. C. Atkinson, J. M. Lee, A. V. Oesterreich, S. 2021-02-11 doi:10.1101/2021.02.10.430701 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ Shared long-term and short-term memory representational formats in occipital and parietal cortex ]]> https://biorxiv.org/content/10.1101/2021.02.16.431528v1?rss=1 Vo, V. A. Sutterer, D. W. Foster, J. J. Sprague, T. C. Awh, E. Serences, J. T. 2021-02-16 doi:10.1101/2021.02.16.431528 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Functional cooperativity mediated by rationally selected combinations of human monoclonal antibodies targeting the henipavirus receptor binding protein ]]> https://biorxiv.org/content/10.1101/2021.02.17.431743v1?rss=1 Doyle, M. P. Kose, N. Borisevich, V. Binshtein, E. Amaya, M. Nagel, M. Annand, E. J. Armstrong, E. Bombardi, R. Dong, J. Schey, K. L. Broder, C. C. Zeitlin, L. Kuang, E. Bornholdt, Z. West, B. Geisbert, T. W. Cross, R. W. Crowe, J. E. 2021-02-18 doi:10.1101/2021.02.17.431743 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Altered Sub-Genomic RNA Expression in SARS-CoV-2 B.1.1.7 Infections ]]> https://biorxiv.org/content/10.1101/2021.03.02.433156v1?rss=1 CAT, D3L) creating a transcription regulatory-like sequence complementary to a region 3 of the genomic leader. These findings provide a unique insight into the biology of B.1.1.7 and support monitoring of sgRNA profiles in sequence data to evaluate emerging potential variants of concern. One Sentence SummaryThe recently emerged and more transmissible SARS-CoV-2 lineage B.1.1.7 shows greater subgenomic RNA expression in clinical infections and enhanced expression of a noncanonical subgenomic RNA near ORF9b. ]]> Parker, M. D. Lindsey, B. B. Shah, D. R. Hsu, S. Keeley, A. J. Partridge, D. G. Leary, S. Cope, A. State, A. Johnson, K. Ali, N. Raghei, R. Heffer, J. Smith, N. Zhang, P. Gallis, M. Louka, S. F. Whiteley, M. Foulkes, B. H. Christou, S. Wolverson, P. Pohare, M. Hansford, S. E. Green, L. R. Evans, C. Raza, M. Wang, D. Gaudieri, S. Mallal, S. The COVID-19 Genomics UK (COG-UK) consortium, de Silva, T. I. 2021-03-03 doi:10.1101/2021.03.02.433156 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures ]]> https://biorxiv.org/content/10.1101/2021.03.03.433815v1?rss=1 Li, J. Jia, C. Lu, Q. Hungate, B. A. Dijkstra, P. Wang, S. Wu, C. Chen, S. Li, D. Shim, H. 2021-03-04 doi:10.1101/2021.03.03.433815 Cold Spring Harbor Laboratory Press 2021-03-04 <![CDATA[ mTOR-activating mutations in RRAGD cause kidney tubulopathy and cardiomyopathy (KICA) syndrome ]]> https://biorxiv.org/content/10.1101/2021.03.11.434334v1?rss=1 Schlingmann, K. P. Jouret, F. Shen, K. Nigam, A. Arjona, F. J. Dafinger, C. Houillier, P. Jones, D. P. Kleinerueschkamp, F. Oh, J. Godefroid, N. Eltan, M. Guran, T. Burtey, S. Parotte, M.-C. Koenig, J. Braun, A. Bos, C. Ibars Serra, M. Rehmann, H. Zwartkruis, F. J. T. Renkema, K. Y. Klingel, K. Schulze-Bahr, E. Schermer, B. Bergmann, C. Altmueller, J. Thiele, H. Beck, B. B. Dahan, K. Sabatini, D. Libau, M. C. Vargas-Poussou, R. Knoers, N. V. A. M. Konrad, M. de Baaij, J. H. F. 2021-03-12 doi:10.1101/2021.03.11.434334 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Anxiety-related frontocortical activity is associated with dampened stressor reactivity in the real world ]]> https://biorxiv.org/content/10.1101/2021.03.17.435791v1?rss=1 10,000 momentary assessments of emotional experience--to demonstrate that individuals showing greater activation in a cingulo-opercular circuit during an anxiety-eliciting laboratory paradigm experience lower levels of stressor-dependent distress in their daily lives (n=202-208). Extended amygdala activation was not significantly related to momentary negative affect. These observations provide a framework for understanding the neurobiology of negative affect in the laboratory and in the real world. STATEMENT OF RELEVANCEAnxiety, sadness, and other negative emotions are hallmarks of the human condition. When extreme, they contribute to a variety of adverse outcomes--from physical and mental illness to divorce and premature death--pointing to the need to develop a better understanding of the underlying brain circuitry. Recent work has begun to reveal the neural systems governing negative affect, but the relevance of these tantalizing laboratory discoveries to the real world has remained unclear. Here we used a combination of brain imaging and smartphone-based survey techniques to show that individuals marked by greater activation in a cingulo-opercular circuit during an anxiety-promoting laboratory paradigm tend to experience diminished distress in response to everyday stressors. These observations provide new insights into the brain systems most relevant to moment-by-moment fluctuations in negative mood, underscoring the importance of more recently evolved cortical association areas. ]]> Hur, J. Kuhn, M. Grogans, S. E. Anderson, A. S. Islam, S. Kim, H. C. Tillman, R. M. Fox, A. S. Smith, J. F. DeYoung, K. A. Shackman, A. J. 2021-03-17 doi:10.1101/2021.03.17.435791 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Genomics-informed insights into microbial degradation of N,N-dimethylformamide ]]> https://biorxiv.org/content/10.1101/2021.03.18.435917v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@e46e1dorg.highwire.dtl.DTLVardef@f93887org.highwire.dtl.DTLVardef@1ee5ce8org.highwire.dtl.DTLVardef@15a529_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Li, J. Dijkstra, P. Lu, Q. Wang, S. Chen, S. Li, D. Wang, Z. Jia, Z. Wang, L. Shim, H. 2021-03-18 doi:10.1101/2021.03.18.435917 Cold Spring Harbor Laboratory Press 2021-03-18 <![CDATA[ Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks ]]> https://biorxiv.org/content/10.1101/2021.04.04.438423v1?rss=1 Koehler Leman, J. Lyskov, S. Lewis, S. Adolf-Bryfogle, J. Alford, R. F. Barlow, K. Ben-Aharon, Z. Farrell, D. Fell, J. Hansen, W. A. Harmalkar, A. Jeliazkov, J. Krys, J. D. Kuenze, G. Ljubetic, A. Loshbaugh, A. L. Maguire, J. Moretti, R. Mulligan, V. K. Nguyen, P. T. OConchuir, S. Roy Burman, S. S. Smith, S. T. Teets, F. Tiemann, J. K. Watkins, A. Woods, H. Yachnin, B. J. Bahl, C. D. Bailey-Kellogg, C. Baker, D. Das, R. DiMaio, F. Khare, S. D. Kortemme, T. Labonte, J. W. Lindorff-Larsen, K. Meiler, J. Schief, W. Schueler-Furman, O. Siegel, J. Stein, A. 2021-04-05 doi:10.1101/2021.04.04.438423 Cold Spring Harbor Laboratory Press 2021-04-05 <![CDATA[ Heterogenous impairment of α-cell function in type 2 diabetes is linked to cell maturation state ]]> https://biorxiv.org/content/10.1101/2021.04.08.435504v1?rss=1 Dai, X.-Q. Camunas-Soler, J. Briant, L. J. dos Santos, T. Spigelman, A. F. Walker, E. M. Arrojo e Drigo, R. Bautista, A. Jones, R. C. Lyon, J. Nie, A. Smith, N. Manning Fox, J. E. Kim, S. K. Rorsman, P. Stein, R. W. Quake, S. R. MacDonald, P. E. 2021-04-08 doi:10.1101/2021.04.08.435504 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) ]]> https://biorxiv.org/content/10.1101/2021.04.22.436044v1?rss=1 Schatz, M. C. Philippakis, A. A. Afgan, E. Banks, E. Carey, V. J. Carroll, R. J. Culotti, A. Ellrott, K. Goecks, J. Grossman, R. L. Hall, I. Hansen, K. D. Lawson, J. Leek, J. T. O'Donnell Luria, A. Mosher, S. Morgan, M. Nekrutenko, A. O'Connor, B. D. Osborn, K. Paten, B. Patterson, C. Tan, F. J. Overby Taylor, C. Vessio, J. Waldron, L. D. Wang, T. Wuichet, K. AnVIL Team, 2021-04-23 doi:10.1101/2021.04.22.436044 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Lhx2 is a progenitor-intrinsic modulator of Sonic Hedgehog signaling during early retinal neurogenesis ]]> https://biorxiv.org/content/10.1101/2021.04.24.441277v1?rss=1 Li, X. Gordon, P. J. Gaynes, J. A. Fuller, A. W. Ringuette, R. Santiago, C. P. Wallace, V. A. Blackshaw, S. Li, P. LEVINE, E. M. 2021-04-26 doi:10.1101/2021.04.24.441277 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ A potently neutralizing anti-SARS-CoV-2 antibody inhibits variants of concern by binding a highly conserved epitope ]]> https://biorxiv.org/content/10.1101/2021.04.26.441501v1?rss=1 VanBlargan, L. Adams, L. Liu, Z. Chen, R. E. Gilchuk, P. Raju, S. Smith, B. Zhao, H. Case, J. B. Winkler, E. S. Whitener, B. Droit, L. Aziati, I. Shi, P.-Y. Creanga, A. Pegu, A. Handley, S. Wang, D. Boon, A. Crowe, J. E. Whelan, S. P. J. Fremont, D. Diamond, M. 2021-04-26 doi:10.1101/2021.04.26.441501 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Protective pan-ebolavirus combination therapy by two multifunctional human antibodies ]]> https://biorxiv.org/content/10.1101/2021.05.02.442324v1?rss=1 Gilchuk, P. Murin, C. D. Cross, R. W. Ilinykh, P. A. Huang, K. Kuzmina, N. Borisevich, V. Agans, K. N. Geisbert, J. B. Carnahan, R. H. Nargi, R. S. Sutton, R. E. Suryadevara, N. Zost, S. J. Bombardi, R. G. Bukreyev, A. Geisbert, T. W. Ward, A. B. Crowe, J. E. 2021-05-02 doi:10.1101/2021.05.02.442324 Cold Spring Harbor Laboratory Press 2021-05-02 <![CDATA[ Rare copy number variants (CNVs) and breast cancer risk ]]> https://biorxiv.org/content/10.1101/2021.05.20.444828v1?rss=1 Dennis, J. Tyrer, J. P. Walker, L. C. Michailidou, K. Dorling, L. Bolla, M. K. Wang, Q. Ahearn, T. U. Andrulis, I. L. Anton-Culver, H. Antonenkova, N. N. Arndt, V. Aronson, K. J. Beane Freeman, L. E. Beckmann, M. W. Behrens, S. Benitez, J. Bermisheva, M. Bogdanova, N. V. Bojesen, S. E. Brenner, H. Castelao, J. E. Chang-Claude, J. Chenevix-Trench, G. Clarke, C. L. Collaborators, N. Collee, J. M. Consortium, C. Couch, F. J. Cox, A. Cross, S. S. Czene, K. Devilee, P. Dork, T. Dossus, L. Eliassen, A. H. Eriksson, M. Evans, D. G. Fasching, P. A. Figueroa, J. 2021-05-21 doi:10.1101/2021.05.20.444828 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ Leveraging a founder population to identify novel rare-population genetic determinants of lipidome ]]> https://biorxiv.org/content/10.1101/2021.05.21.445208v1?rss=1 Montasser, M. E. Aslibekyan, S. Srinivasasainagendra, V. Tiwari, H. K. Patki, A. Bagheri, M. Perry, J. A. Ryan, K. A. Arnett, D. K. Beitelshees, A. L. Irvin, M. R. O'Connell, J. R. 2021-05-23 doi:10.1101/2021.05.21.445208 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ Anal skin-like epithelium mediates colonic wound healing ]]> https://biorxiv.org/content/10.1101/2021.06.02.446836v1?rss=1 Liu, C. Y. Girish, N. Gomez, M. L. Dube, P. E. Washington, M. K. Simons, B. D. Polk, D. B. 2021-06-03 doi:10.1101/2021.06.02.446836 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ Selective pharmaceutical inhibition of PARP14 mitigates allergen-induced IgE and mucus overproduction in a mouse model of pulmonary allergic response ]]> https://biorxiv.org/content/10.1101/2021.06.05.447208v1?rss=1 Eddie, A. M. Schenkel, L. B. Swinger, K. K. Molina, J. R. Kunii, K. Raybuck, A. L. Keilhack, H. Niepel, M. Peebles, R. S. Boothby, M. R. Cho, S. H. 2021-06-07 doi:10.1101/2021.06.05.447208 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Brain charts for the human lifespan ]]> https://biorxiv.org/content/10.1101/2021.06.08.447489v1?rss=1 Bethlehem, R. A. I. Seidlitz, J. White, S. R. Vogel, J. W. Anderson, K. M. Adamson, C. Adler, S. Alexopoulos, G. S. Anagnostou, E. Areces-Gonzalez, A. Astle, D. E. Auyeung, B. Ayub, M. Ball, G. Baron-Cohen, S. Beare, R. Bedford, S. A. Benegal, V. Beyer, F. Bin Bae, J. Blangero, J. Blesa Cabez, M. Boardman, J. P. Borzage, M. Bosch-Bayard, J. F. Bourke, N. Calhoun, V. D. Chakravarty, M. M. Chen, C. Chertavian, C. Chetelat, G. Chong, Y. S. Cole, J. H. Corvin, A. Courchesne, E. Crivello, F. Cropley, V. L. Crosbie, J. Crossley, N. Delarue, M. Desrivieres, S. 2021-06-10 doi:10.1101/2021.06.08.447489 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Rapid simultaneous acquisition of macromolecular tissue volume, susceptibility, and relaxometry maps ]]> https://biorxiv.org/content/10.1101/2021.06.08.447552v1?rss=1 Yu, F. F. Huang, S. Y. Kumar, A. Witzel, T. Liao, C. Duval, T. Cohen-Adad, J. Bilgic, B. 2021-06-09 doi:10.1101/2021.06.08.447552 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ Stratum Lacunosum-moleculare Interneurons of the Hippocampus Coordinate Memory Encoding and Retrieval ]]> https://biorxiv.org/content/10.1101/2021.06.11.448103v1?rss=1 Guo, J. Oliveros, H. C. Oh, S. J. Liang, B. Li, Y. Kavalali, E. T. Lin, D.-T. Xu, W. 2021-06-12 doi:10.1101/2021.06.11.448103 Cold Spring Harbor Laboratory Press 2021-06-12 <![CDATA[ Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy ]]> https://biorxiv.org/content/10.1101/2021.06.15.448495v1?rss=1 10% on at least one day). Unsupervised learning was then applied to hierarchically organize VRVs by spatiotemporal patterns and identify VRV-haplotypes. Finally, homology modelling was performed to gain insight into potential impact of VRVs on Spike protein structure. We identified 90 VRVs, 71 of which have not previously been observed in a VOI/VOC, and 35 of which have emerged recently and are durably present. Our analysis identifies 17 VRVs [~]91 days earlier than their first corresponding VOI/VOC publication. Unsupervised learning revealed eight VRV-haplotypes of 4 VRVs or more, suggesting two emerging strains (B1.1.222 and B.1.234). Structural modeling supported potential functional impact of the D1118H and L452R mutations. The SLS approach equally monitors all Spike residues over time, independently of existing phylogenic classifications, and is complementary to existing genomic surveillance methods. ]]> Zhao, L. P. Lybrand, T. P. Gilbert, P. B. Hawn, T. R. Schiffer, J. T. Stamatatos, L. Payne, T. H. Carpp, L. Geraghty, D. E. Jerome, K. R. 2021-06-15 doi:10.1101/2021.06.15.448495 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ Human NAIP/NLRC4 and NLRP3 inflammasomes detect Salmonella type III secretion system activities to restrict intracellular bacterial replication ]]> https://biorxiv.org/content/10.1101/2021.06.17.448811v1?rss=1 Naseer, N. Egan, M. Reyes Ruiz, V. Brodsky, I. Shin, S. 2021-06-17 doi:10.1101/2021.06.17.448811 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Kidney organoids: A system to study human basement membrane assembly in health and disease ]]> https://biorxiv.org/content/10.1101/2021.06.27.450067v1?rss=1 Morais, M. R. Tian, P. Lawless, C. Murtuza-Baker, S. Hopkinson, L. Woods, S. Mironov, A. Long, D. A. Gale, D. Zorn, T. M. Zent, R. Lennon, R. 2021-06-29 doi:10.1101/2021.06.27.450067 Cold Spring Harbor Laboratory Press 2021-06-29 <![CDATA[ Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms ]]> https://biorxiv.org/content/10.1101/2021.07.05.450786v1?rss=1 Pividori, M. Lu, S. Li, B. Su, C. Johnson, M. E. Wei, W.-Q. Feng, Q. Namjou, B. Kiryluk, K. Kullo, I. Luo, Y. Sullivan, B. D. Skarke, C. Ritchie, M. D. Grant, S. F. A. Greene, C. S. 2021-07-06 doi:10.1101/2021.07.05.450786 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Reversal of the renal hyperglycemic memory by targeting sustained tubular p21 expression ]]> https://biorxiv.org/content/10.1101/2021.07.05.450846v1?rss=1 Al-Dabet, M. M. Shahzad, K. Elwakiel, A. Sulaj, A. Kopf, S. Bock, F. Gadi, I. Zimmermann, S. Rana, R. Krishnan, S. Gupta, D. Nazir, S. Baber, R. Scholz, M. Geffers, R. Mertens, P. R. Nawroth, P. P. Griffin, J. Dockendorff, C. Kohli, S. Isermann, B. 2021-07-05 doi:10.1101/2021.07.05.450846 Cold Spring Harbor Laboratory Press 2021-07-05 <![CDATA[ Tracing the evolution of human gene regulation and its association with shifts in environment ]]> https://biorxiv.org/content/10.1101/2021.07.05.451164v1?rss=1 Colbran, L. L. Johnson, M. R. Mathieson, I. Capra, J. A. 2021-07-05 doi:10.1101/2021.07.05.451164 Cold Spring Harbor Laboratory Press 2021-07-05 <![CDATA[ A Massively Parallel Trafficking Assay Accurately Predicts Loss of Channel Function in KCNH2 Variants ]]> https://biorxiv.org/content/10.1101/2021.07.10.451881v1?rss=1 Ng, C. A. Ullah, R. Farr, J. Hill, A. P. Kozek, K. A. Vanags, L. R. Mitchell, D. W. Kroncke, B. M. Vandenberg, J. I. 2021-07-11 doi:10.1101/2021.07.10.451881 Cold Spring Harbor Laboratory Press 2021-07-11 <![CDATA[ The Murine Neuronal Receptor NgR1 Is Dispensable for Reovirus Pathogenesis ]]> https://biorxiv.org/content/10.1101/2021.07.22.453368v1?rss=1 Aravamudhan, P. Guzman-Cardozo, C. Urbanek, K. Welsh, O. Konopka-Anstadt, J. Sutherland, D. M. Dermody, T. S. 2021-07-22 doi:10.1101/2021.07.22.453368 Cold Spring Harbor Laboratory Press 2021-07-22 <![CDATA[ The human neuronal receptor NgR1 bridges reovirus capsid proteins to initiate infection ]]> https://biorxiv.org/content/10.1101/2021.07.23.453469v1?rss=1 Sutherland, D. M. Strebl, M. Koehler, M. Welsh, O. L. Yu, X. Hu, L. dos Santos Natividade, R. Knowlton, J. J. Taylor, G. M. Moreno, R. Woerz, P. Lonergan, Z. L. Aravamudhan, P. Guzman-Cardozo, C. Alsteens, D. Wang, Z. Prasad, B. Stehle, T. Dermody, T. S. 2021-07-24 doi:10.1101/2021.07.23.453469 Cold Spring Harbor Laboratory Press 2021-07-24 <![CDATA[ Mutated in Colorectal Cancer (MCC): a centrosomal protein that relocalizes to the ncMTOC during intestinal cell differentiation ]]> https://biorxiv.org/content/10.1101/2021.07.27.453941v1?rss=1 Tomaz, L. B. Liu, B. A. Ong, S. L. M. Tan, E. K. M, M. Tolwinski, N. S. Williams, C. S. Gingras, A.-C. Leushacke, M. Dunn, N. R. 2021-07-27 doi:10.1101/2021.07.27.453941 Cold Spring Harbor Laboratory Press 2021-07-27 <![CDATA[ Arap1 Loss Causes RPE Phagocytic Dysfunction and Subsequent Photoreceptor Death ]]> https://biorxiv.org/content/10.1101/2021.08.09.455745v1?rss=1 Shao, A. Jacobo Lopez, A. Chen, J. Tham, A. Javier, S. Quiroz, A. Frick, S. Levine, E. M. Lloyd, K. C. K. Leonard, B. C. Murphy, C. J. Glaser, T. M. Moshiri, A. 2021-08-10 doi:10.1101/2021.08.09.455745 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ microRNA Expression Levels Change in Neonatal Patients During and After Exposure to Cardiopulmonary Bypass ]]> https://biorxiv.org/content/10.1101/2021.08.13.454953v1?rss=1 Hsieh, L. Tu, L. Paquette, A. G. Kibiryeva, N. Marshall, J. Bittel, D. O'Brien, J. Vickers, K. Pastuszko, P. Nigam, V. 2021-08-13 doi:10.1101/2021.08.13.454953 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Single-cell transcriptomic assessment of cellular phenotype stability in human precision-cut lung slices ]]> https://biorxiv.org/content/10.1101/2021.08.19.457016v1?rss=1 Winters, N. I. Taylor, C. J. Jetter, C. S. Camarata, J. E. Gutierrez, A. J. Bui, L. T. Gokey, J. J. Bacchetta, M. Banovich, N. E. Sucre, J. M. S. Kropski, J. A. 2021-08-19 doi:10.1101/2021.08.19.457016 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ CRISPRi screens in human astrocytes elucidate regulators of distinct inflammatory reactive states ]]> https://biorxiv.org/content/10.1101/2021.08.23.457400v1?rss=1 Leng, K. Rooney, B. Kim, H. Xia, W. Koontz, M. Krawczyk, M. Zhang, Y. Ullian, E. M. Fancy, S. P. J. Schrag, M. S. Lippmann, E. S. Kampmann, M. 2021-08-24 doi:10.1101/2021.08.23.457400 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ HIV-1 Mutants that Escape the Cytotoxic T-Lymphocytes are Defective in Viral DNA Integration ]]> https://biorxiv.org/content/10.1101/2021.08.29.458043v1?rss=1 Balasubramaniam, M. Thapa, S. Davids, B.-O. Bryer, A. Xu, C. Shi, J. Aiken, C. Pandhare, J. Perilla, J. R. Dash, C. 2021-08-29 doi:10.1101/2021.08.29.458043 Cold Spring Harbor Laboratory Press 2021-08-29 <![CDATA[ Targeting metabolic adaptations in the breast cancer liver metastatic niche using dietary approaches to improve endocrine therapy efficacy ]]> https://biorxiv.org/content/10.1101/2021.09.07.458711v1?rss=1 Zuo, Q. Mogol, A. N. Liu, Y.-J. Casiano, A. S. Chien, C. Drnevich, J. Imir, O. B. Kulkoyluoglu-Cotul, E. Park, N. H. Shapiro, D. J. Park, B. H. Ziegler, Y. Katzenellenbogen, B. S. Aranda, E. O'Neill, J. D. Raghavendra, A. S. Tripathy, D. Madak-Erdogan, Z. 2021-09-07 doi:10.1101/2021.09.07.458711 Cold Spring Harbor Laboratory Press 2021-09-07 <![CDATA[ Symbiotic bacterial community of Drosophila melanogaster changes with nutritional modifications of the diet but can alleviate negative effects on larval phenotypes ]]> https://biorxiv.org/content/10.1101/2021.09.07.458894v1?rss=1 Bombin, A. Cunneely, O. Bombin, S. Eickman, K. Ruesy, A. Cowan, R. Myers, A. Su, M. Mosley, J. D. Ferguson, J. Reed, L. K. 2021-09-07 doi:10.1101/2021.09.07.458894 Cold Spring Harbor Laboratory Press 2021-09-07 <![CDATA[ SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells ]]> https://biorxiv.org/content/10.1101/2021.09.15.460381v1?rss=1 Wang, Y. Yen, F. S. Zhu, X. G. Timson, R. C. Weber, R. Xing, C. Liu, Y. Allwein, B. Luo, H. Yeh, H.-W. Heissel, S. Unlu, G. Gamazon, E. R. Kharas, M. G. Hite, R. Birsoy, K. 2021-09-16 doi:10.1101/2021.09.15.460381 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ Intestinal epithelial IPMK protects mice from experimental colitis via governing colonic tuft cell development ]]> https://biorxiv.org/content/10.1101/2021.09.15.460418v1?rss=1 Park, S. E. Jung, J. W. Lee, S.-H. Park, S. J. Ryu, J. Oh, S. K. Fang, S. Kim, S. 2021-09-17 doi:10.1101/2021.09.15.460418 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ Epigenetic Remodeling by Vitamin C Potentiates the Differentiation of Mouse and Human Plasma Cells ]]> https://biorxiv.org/content/10.1101/2021.09.15.460473v1?rss=1 Chen, H.-Y. Almonte-Loya, A. Lay, F.-Y. Johnson, E. Gonzalez-Avalos, E. Yin, J. Ma, Q. Wozniak, D. J. Harrison, F. E. Lio, C.-W. J. 2021-09-17 doi:10.1101/2021.09.15.460473 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ Emotion Down- and Up-Regulation Act on Spatially Distinct Brain Areas:Interoceptive Regions to Calm Down and Other Affective Regions to Amp Up ]]> https://biorxiv.org/content/10.1101/2021.09.20.461138v1?rss=1 Min, J. Nashiro, K. Yoo, H. J. Cho, C. Nasseri, P. Bachman, S. L. Porat, S. Thayer, J. F. Chang, C. Lee, T.-h. Mather, M. 2021-09-23 doi:10.1101/2021.09.20.461138 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Protective transfer: Maternal passive immunization with a rotavirus-neutralizing dimeric IgA protects against rotavirus disease in suckling neonates ]]> https://biorxiv.org/content/10.1101/2021.09.21.461116v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@1af34dcorg.highwire.dtl.DTLVardef@1b78cb2org.highwire.dtl.DTLVardef@1760a62org.highwire.dtl.DTLVardef@a3cea2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Langel, S. N. Steppe, J. T. Chang, J. Travieso, T. Webster, H. Otero, C. Williamson, L. Crowe, J. E. Greenberg, H. Wu, H. Hornik, C. Mansouri, K. Edward, R. Stalls, V. Acharya, P. Blasi, M. Permar, S. R. 2021-09-23 doi:10.1101/2021.09.21.461116 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Glucosyltransferase-dependent and independent effects of Clostridioides difficile toxins during infection ]]> https://biorxiv.org/content/10.1101/2021.09.22.460915v1?rss=1 Peritore-Galve, F. C. Shupe, J. A. Cave, R. J. Washington, M. K. Kuehne, S. A. Lacy, D. B. 2021-09-23 doi:10.1101/2021.09.22.460915 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Reovirus infection is regulated by NPC1 and endosomal cholesterol homeostasis ]]> https://biorxiv.org/content/10.1101/2021.09.27.462002v1?rss=1 Ortega Gonzalez, P. Taylor, G. M. Jangra, R. Tenorio Vela, R. Fernandez de Castro Martin, I. Mainou, B. Orchard, R. Wilen, C. B. Brigleb, P. A. Sojati, J. Chandran, K. Risco, C. Dermody, T. S. 2021-09-28 doi:10.1101/2021.09.27.462002 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ A combination of two human neutralizing antibodies prevents SARS-CoV-2 infection in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2021.09.27.462074v1?rss=1 Cobb, R. R. Nkolola, J. Gilchuk, P. Chandrashekar, A. House, R. V. Earnhart, C. G. Dorsey, N. M. Hopkins, S. A. Snow, D. M. Chen, R. E. VanBlargan, L. A. Hechenblaickner, M. Hoppe, B. Collins, L. Tomic, M. T. Nonet, G. H. Hackett, K. Slaughter, J. C. Diamond, M. S. Carnahan, R. H. Barouch, D. H. Crowe, J. E. 2021-09-29 doi:10.1101/2021.09.27.462074 Cold Spring Harbor Laboratory Press 2021-09-29 <![CDATA[ Structural mapping of antibody landscapes to human betacoronavirus spike proteins ]]> https://biorxiv.org/content/10.1101/2021.09.30.462459v1?rss=1 Bangaru, S. Antanasijevic, A. Kose, N. Sewall, L. M. Jackson, A. M. Suryadevara, N. Zhan, X. Torres, J. L. Copps, J. Torrents de la Pena, A. Crowe, J. E. Ward, A. B. 2021-10-01 doi:10.1101/2021.09.30.462459 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Age-related change in task-evoked amygdala-prefrontal circuitry: a multiverse approach with an accelerated longitudinal cohort aged 4-22 years ]]> https://biorxiv.org/content/10.1101/2021.10.08.463601v1?rss=1 Bloom, P. A. VanTieghem, M. Gabard-Durnam, L. Gee, D. G. Flannery, J. Caldera, C. Goff, B. Telzer, E. H. Humphreys, K. L. Fareri, D. S. Shapiro, M. Algharazi, S. Bolger, N. Aly, M. Tottenham, N. 2021-10-09 doi:10.1101/2021.10.08.463601 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ Obesity influences composition of salivary and fecal microbiota and impacts the interactions between bacterial taxa ]]> https://biorxiv.org/content/10.1101/2021.10.12.464168v1?rss=1 Bombin, A. Mosley, J. D. Yan, S. Bombin, S. Ferguson, J. F. 2021-10-13 doi:10.1101/2021.10.12.464168 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ A kinesin-1 variant reveals motor-induced microtubule damage in cells ]]> https://biorxiv.org/content/10.1101/2021.10.19.464974v1?rss=1 Budaitis, B. G. Badieyan, S. Yue, Y. Blasius, T. L. Reinemann, D. N. Lang, M. J. Cianfrocco, M. A. Verhey, K. J. 2021-10-20 doi:10.1101/2021.10.19.464974 Cold Spring Harbor Laboratory Press 2021-10-20 <![CDATA[ Translating outcomes from the clinical setting to preclinical models: chronic pain and functionality in chronic musculoskeletal pain ]]> https://biorxiv.org/content/10.1101/2021.10.27.466137v1?rss=1 Lenert, M. E. Gomez, R. Lane, B. T. Dailey, D. L. Vance, C. G. T. Rakel, B. A. Crofford, L. J. Sluka, K. A. Merriwether, E. N. Burton, M. D. 2021-10-29 doi:10.1101/2021.10.27.466137 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ WY14643 Increases Herpesvirus Replication Independent of PPARα Expression and Inhibits IFNβ Production ]]> https://biorxiv.org/content/10.1101/2021.10.29.466551v1?rss=1 Tao, L. Dryden, P. Lowe, A. Wang, G. Dozmorov, I. Chang, T. Reese, T. A. 2021-11-02 doi:10.1101/2021.10.29.466551 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Dysconnectivity between auditory-cognitive network associated with auditory GABA and glutamate levels in presbycusis patients ]]> https://biorxiv.org/content/10.1101/2021.10.31.466279v1?rss=1 Li, N. Ma, W. Ren, F. Li, X. Li, F. Zong, W. Wu, L. Dai, Z. Hui, S. C. N. Edden, R. A. E. Li, M. Gao, F. 2021-11-03 doi:10.1101/2021.10.31.466279 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ LRH-1/NR5A2 regulates the PTGS2-PGE2-PTGER1 signalling axis contributing to islet survival and antidiabetic actions of the agonist BL001 ]]> https://biorxiv.org/content/10.1101/2021.11.02.466895v1?rss=1 Martin Vazquez, E. Cobo_Vuilleumier, N. Araujo Legido, R. Nola, E. Lopez Bermudo, L. Crespo, A. Romero-Zerbo, S. Y. Garcia-Fernandez, M. Martin Montalvo, A. Rojas, A. Ferrer, J. Comaills, V. Bermudez-Silva, F. J. Gannon, M. Martin, F. Lorenzo, P. I. Gauthier, B. R. 2021-11-04 doi:10.1101/2021.11.02.466895 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels ]]> https://biorxiv.org/content/10.1101/2021.11.04.467311v1?rss=1 Lea, A. J. Peng, J. Ayroles, J. J. 2021-11-04 doi:10.1101/2021.11.04.467311 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Molecular signature of postmortem lung tissue from COVID-19 patients suggests distinct trajectories driving mortality ]]> https://biorxiv.org/content/10.1101/2021.11.08.467705v1?rss=1 Budhraja, A. Basu, A. Gheware, A. Abhilash, D. Rajagopala, S. Pakala, S. Sumit, M. Ray, A. Arulselvi, S. Mathur, P. Nambirajan, A. Kumar, S. Gupa, R. Wig, N. Trikha, A. Guleria, R. Sarkar, C. Gupta, I. Jain, D. 2021-11-08 doi:10.1101/2021.11.08.467705 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ Club cells are the primary source of pIgR in small airways ]]> https://biorxiv.org/content/10.1101/2021.11.10.467794v1?rss=1 Blackburn, J. B. Schaff, J. A. Gutor, S. Du, R.-H. Nichols, D. Sherrill, T. Gutierrez, A. J. Xin, M. K. Wickersham, N. Zhang, Y. Holtzman, M. J. Ware, L. B. Lee, J. W. Banovich, N. E. Kropski, J. A. Polosukhin, V. V. Blackwell, T. S. Richmond, B. W. 2021-11-11 doi:10.1101/2021.11.10.467794 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ WebSeq: A Genomic Data Analytics Platform for Monogenic Disease Discovery ]]> https://biorxiv.org/content/10.1101/2021.11.16.460500v1?rss=1 Agarwal, M. Ghimire, K. Cogan, J. D. Undiagnosed Disease Network, Markle, J. 2021-11-19 doi:10.1101/2021.11.16.460500 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Differential neutralization and inhibition of SARS-CoV-2 variants by antibodies elicited by COVID-19 mRNA vaccines ]]> https://biorxiv.org/content/10.1101/2021.11.24.469906v1?rss=1 Wang, L. Kainulainen, M. H. Jiang, N. Di, H. Bonenfant, G. Mills, L. Currier, M. Shrivastava-Ranjan, P. Calderon, B. M. Sheth, M. Mann, B. R. Hossain, J. Lin, X. Lester, S. Pusch, E. Jones, J. Cui, D. Chatterjee, P. Jenks, H. M. Morantz, E. Larson, G. Hatta, M. Harcourt, J. Tamin, A. Lin, Y. Tao, Y. Zhao, K. Lacek, K. Burroughs, A. Wong, T. Tong, S. Barnes, J. R. Tenforde, M. W. Self, W. H. Shapiro, N. I. Exline, M. C. Files, D. C. Gibbs, K. W. Hager, D. N. Patel, M. Laufer Halpin, A. S. McMullan, L. K. Lee, J. S. Spiropoulou, C. F. Thornburg, N. J. 2021-11-30 doi:10.1101/2021.11.24.469906 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Similarities Between Bacterial GAD and Human GAD65:Implications in Gut Mediated Autoimmune Type 1 Diabetes ]]> https://biorxiv.org/content/10.1101/2021.11.29.470330v1?rss=1 Westley, M. Richardson, T. Bedi, S. Jia, B. Brinkman, F. S. L. Saab, H. 2021-11-29 doi:10.1101/2021.11.29.470330 Cold Spring Harbor Laboratory Press 2021-11-29 <![CDATA[ Neutralization Fingerprinting Technology for Characterizing Polyclonal Antibody Responses to Dengue Vaccines ]]> https://biorxiv.org/content/10.1101/2021.12.02.467518v1?rss=1 Raju, N. Zhan, X. Das, S. Karwal, L. Dean, H. Crowe, J. E. Carnahan, R. H. Georgiev, I. 2021-12-03 doi:10.1101/2021.12.02.467518 Cold Spring Harbor Laboratory Press 2021-12-03 <![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[ Genetic Sex Validation for Sample Tracking in Clinical Testing ]]> https://biorxiv.org/content/10.1101/2021.12.13.470986v1?rss=1 Hu, J. Korchina, V. Zouk, H. Harden, M. V. Murdock, D. Alyssa Macbeth, A. Harrison, S. M. Lennon, N. Kovar, C. Balasubramanian, A. Zhang, L. Chandanavelli, G. Pasham, D. Rowley, R. Wiley, K. Smith, M. E. Gordon, A. Jarvik, G. P. Sleiman, P. Kelly, M. A. Bland, S. T. Murugan, M. Venner, E. Boerwinkle, E. the eMERGE III consortium, Prows, C. Mahanta, L. Rehm, H. L. Gibbs, R. A. Muzny, D. M. 2021-12-17 doi:10.1101/2021.12.13.470986 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ A calibrated functional patch clamp assay to enhance clinical variant interpretation in KCNH2-related long QT syndrome ]]> https://biorxiv.org/content/10.1101/2021.12.13.472492v1?rss=1 Jiang, C. Richardson, E. Farr, J. Hill, A. P. Ullah, R. Kroncke, B. M. Harrison, S. M. Thomson, K. L. Ingles, J. Vandenberg, J. I. Ng, C. A. 2021-12-15 doi:10.1101/2021.12.13.472492 Cold Spring Harbor Laboratory Press 2021-12-15 <![CDATA[ An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by several therapeutic monoclonal antibodies ]]> https://biorxiv.org/content/10.1101/2021.12.15.472828v1?rss=1 VanBlargan, L. A. Errico, J. M. Halfmann, P. Zost, S. J. Crowe, J. E. Purcell, L. A. Kawaoka, Y. Corti, D. Fremont, D. H. Diamond, M. 2021-12-17 doi:10.1101/2021.12.15.472828 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Optimized phylogenetic clustering of HIV-1 sequence data for public health applications ]]> https://biorxiv.org/content/10.1101/2022.01.14.476062v1?rss=1 Chato, C. Feng, Y. Ruan, Y. Xing, H. Herbeck, J. Kalish, M. Poon, A. 2022-01-18 doi:10.1101/2022.01.14.476062 Cold Spring Harbor Laboratory Press 2022-01-18 <![CDATA[ Distinct genetic determinants and mechanisms of SARS-CoV-2 resistance to remdesivir ]]> https://biorxiv.org/content/10.1101/2022.01.25.477724v1?rss=1 6 million publicly available nsp12-RdRp consensus sequences in the absence of RDV selection. The results define genetic and biochemical pathways to RDV resistance and emphasize the need for additional studies to define the potential for emergence of these or other RDV resistance mutations in various clinical settings. One Sentence SummarySARS-CoV-2 develops in vitro resistance to remdesivir by distinct and complementary mutations and mechanisms in the viral polymerase ]]> Stevens, L. J. Pruijssers, A. J. Lee, H. W. Gordon, C. J. Tchesnokov, E. P. Gribble, J. George, A. S. Hughes, T. M. Lu, X. Li, J. Perry, J. K. Porter, D. P. Cihlar, T. Sheahan, T. P. Baric, R. S. Gotte, M. Denison, M. R. 2022-01-29 doi:10.1101/2022.01.25.477724 Cold Spring Harbor Laboratory Press 2022-01-29 <![CDATA[ Feedback in the β-catenin destruction complex imparts bistability and cellular memory ]]> https://biorxiv.org/content/10.1101/2022.01.28.478206v1?rss=1 Cantoria, M. J. Alizadeh, E. Ravi, J. Bunnag, N. Kettenbach, A. N. Ahmed, Y. Paek, A. L. Tyson, J. J. Doubrovinski, K. Lee, E. Thorne, C. A. 2022-01-29 doi:10.1101/2022.01.28.478206 Cold Spring Harbor Laboratory Press 2022-01-29 <![CDATA[ Three Distinct Transcriptional Profiles of Monocytes Correlate with Disease Activity in SSc Patients ]]> https://biorxiv.org/content/10.1101/2022.01.29.477568v1?rss=1 Makinde, H.-K. M. Dunn, J. L. M. Gadhvi, G. Carns, M. Aren, K. Chung, A. H. Muhammad, L. N. Song, J. Cuda, C. M. Dominguez, S. Pandolfino, J. E. Dematte D'Amico, J. E. Budinger, G. S. Assassi, S. Frech, T. Khanna, D. Shaeffer, A. Perlman, H. Hinchcliff, M. Winter, D. R. 2022-02-02 doi:10.1101/2022.01.29.477568 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ A heterogeneous drug tolerant persister state in BRAF-mutant melanoma is characterized by ion channel dysregulation and susceptibility to ferroptosis ]]> https://biorxiv.org/content/10.1101/2022.02.03.479045v1?rss=1 Hayford, C. E. Stauffer, P. E. Baleami, B. Paudel, B. B. Tyson, D. R. Al'Khafaji, A. Johnson, K. E. Harris, L. A. Brock, A. Quaranta, V. 2022-02-05 doi:10.1101/2022.02.03.479045 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ Interactions between evolved pesticide resistance and pesticide exposure on immunity against pathogens ]]> https://biorxiv.org/content/10.1101/2022.02.04.479151v1?rss=1 Birnbaum, S. S. L. Schulz, N. K. Tate, A. T. 2022-02-04 doi:10.1101/2022.02.04.479151 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Increased H3K27 trimethylation contributes to cone survival in a mouse model of cone dystrophy ]]> https://biorxiv.org/content/10.1101/2022.02.07.479069v1?rss=1 Miller, A. L. Fuller-Carter, P. I. Masarini, K. Samardzija, M. Carter, K. W. Rashwan, R. Brunet, A. A. Chopra, A. Ram, R. Grimm, C. Ueffing, M. Carvalho, L. S. Trifunovic, D. 2022-02-09 doi:10.1101/2022.02.07.479069 Cold Spring Harbor Laboratory Press 2022-02-09 <![CDATA[ The Genetic and Evolutionary Basis of Gene Expression Variation in East Africans ]]> https://biorxiv.org/content/10.1101/2022.02.16.480765v1?rss=1 Kelly, D. E. Ramdas, S. Ma, R. Rawlings-Goss, R. A. Grant, G. R. Ranciaro, A. Hirbo, J. B. Beggs, W. Yeager, M. Chanock, S. Nyambo, T. B. Omar, S. A. Meskel, D. W. Belay, G. Li, H. Brown, C. D. Tishkoff, S. A. 2022-02-16 doi:10.1101/2022.02.16.480765 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ Voxel-wise Intermodal Coupling Analysis of Two or More Modalities using Local Covariance Decomposition ]]> https://biorxiv.org/content/10.1101/2022.02.19.481070v1?rss=1 Hu, F. Weinstein, S. M. Baller, E. B. Valcarcel, A. M. Adebimpe, A. Raznahan, A. Roalf, D. R. Robert-Fitzgerald, T. E. Gonzenbach, V. Gur, R. C. Gur, R. E. Vandekar, S. Detre, J. A. Linn, K. A. Alexander-Bloch, A. Satterthwaite, T. D. Shinohara, R. T. 2022-02-22 doi:10.1101/2022.02.19.481070 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Isolation of a potently neutralizing and protective human monoclonal antibody targeting yellow fever virus ]]> https://biorxiv.org/content/10.1101/2022.02.28.482437v1?rss=1 Crowe, J. E. Doyle, M. Genualdi, J. R. Bailey, A. Kose, N. Gainza, C. Rodriguez, J. Reeder, K. M. Nelson, C. A. Jethva, P. N. Sutton, R. E. Bombardi, R. G. Gross, M. Julander, J. G. Fremont, D. H. Diamond, M. 2022-03-01 doi:10.1101/2022.02.28.482437 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Periventricular nodular heterotopia is functionally coupled with the neocortex during resting and task states ]]> https://biorxiv.org/content/10.1101/2022.03.03.482573v1?rss=1 Gao, Y. Chen, G. Teng, P. Zhang, X. Fang, F. Englot, D. J. Luan, G. Wang, X. Wang, Q. 2022-03-04 doi:10.1101/2022.03.03.482573 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Lrig3 restricts the size of the colon stem cell compartment ]]> https://biorxiv.org/content/10.1101/2022.03.08.483523v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@244c29org.highwire.dtl.DTLVardef@1045457org.highwire.dtl.DTLVardef@13d4134org.highwire.dtl.DTLVardef@83db4e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Stevenson, J. M. Sayegh, R. Pedicino, N. Pellitier, N. A. Wheeler, T. M. Bechard, M. E. Huh, W. J. Coffey, R. J. Zemper, A. E. 2022-03-09 doi:10.1101/2022.03.08.483523 Cold Spring Harbor Laboratory Press 2022-03-09 <![CDATA[ Recombinant annexin A6 promotes membrane repair in a stem cell derived-cardiomyocyte model of dystrophic cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2022.03.09.483528v1?rss=1 Fullenkamp, D. E. Willis, A. B. Curtin, J. L. Amaral, A. P. Harris, S. I. Burridge, P. W. Demonbreun, A. R. McNally, E. M. 2022-03-11 doi:10.1101/2022.03.09.483528 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ An integrated cell atlas of the human lung in health and disease ]]> https://biorxiv.org/content/10.1101/2022.03.10.483747v1?rss=1 Sikkema, L. Strobl, D. C. Zappia, L. Madissoon, E. Markov, N. S. Zaragosi, L.-E. Ansari, M. Arguel, M.-J. Apperloo, L. Becavin, C. Berg, M. Chichelnitskiy, E. Chung, M.-i. Collin, A. Gay, A. C. Hooshiar Kashani, B. Jain, M. Kapellos, T. Kole, T. M. Mayr, C. H. Papen, von, M. Peter, L. Ramirez-Suastegui, C. Schniering, J. Taylor, C. J. Walzthoeni, T. Xu, C. Bui, L. T. Donno, de, C. Dony, L. Guo, M. Gutierrez, A. J. Heumos, L. Huang, N. Ibarra, I. L. Jackson, N. D. Kadur Lakshminarasimha Murthy, P. Lotfollahi, M. Tabib, T. Talavera-Lopez, C. Travaglini, K. 2022-03-11 doi:10.1101/2022.03.10.483747 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ Functional Assays Reclassify Suspected Splice-Altering Variants of Uncertain Significance in Mendelian Channelopathies ]]> https://biorxiv.org/content/10.1101/2022.03.14.484344v1?rss=1 O'Neill, M. J. Wada, Y. Hall, L. D. Mitchell, D. W. Glazer, A. M. Roden, D. M. 2022-03-17 doi:10.1101/2022.03.14.484344 Cold Spring Harbor Laboratory Press 2022-03-17 <![CDATA[ A Unique Cellular Organization of Human Distal Airways and Its Disarray in Chronic Obstructive Pulmonary Disease ]]> https://biorxiv.org/content/10.1101/2022.03.16.484543v1?rss=1 Rustam, S. Hu, Y. Mahjour, S. B. Rendeiro, A. F. Ravichandran, H. Randell, S. H. Richmond, B. Polosukhin, V. Kropski, J. A. Blackwell, T. S. d'Ovidio, F. Martinez, F. J. Elemento, O. Shaykhiev, R. 2022-03-16 doi:10.1101/2022.03.16.484543 Cold Spring Harbor Laboratory Press 2022-03-16 <![CDATA[ Resilience of S309 and AZD7442 monoclonal antibody treatments against infection by SARS-CoV-2 Omicron lineage strains ]]> https://biorxiv.org/content/10.1101/2022.03.17.484787v1?rss=1 Case, J. B. Mackin, S. Errico, J. Chong, Z. Madden, E. A. Guarino, B. Schmid, M. A. Rosenthal, K. Ren, K. Jung, A. Droit, L. Handley, S. A. Halfmann, P. J. Kawaoka, Y. Crowe, J. E. Fremont, D. H. Virgin, H. W. Loo, Y.-M. Esser, M. T. Purcell, L. A. Corti, D. Diamond, M. S. 2022-03-18 doi:10.1101/2022.03.17.484787 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ A Single-Cell Molecular Atlas of White Adipose Tissue Shows Differences in Myeloid and Lymphoid Cell Polarization in Type 2 Diabetes and HIV Infection ]]> https://biorxiv.org/content/10.1101/2022.03.21.484794v1?rss=1 Bailin, S. S. Kropski, J. A. Gangula, R. D. Hannah, L. Simmons, J. D. Mashayekhi, M. Ye, F. Fan, R. Chopra, A. Ramesh, R. Mallal, S. Warren, C. M. Kalams, S. A. Gabriel, C. L. Wanjalla, C. N. Koethe, J. R. 2022-03-23 doi:10.1101/2022.03.21.484794 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces ]]> https://biorxiv.org/content/10.1101/2022.03.30.486421v1?rss=1 Peris, D. Ubbelohde, E. J. Kuang, M. C. Kominek, J. Langdon, Q. K. Adams, M. Koshalek, J. A. Hulfachor, A. B. Opulente, D. A. Hall, D. J. Hyma, K. Fay, J. C. Leducq, J.-B. Charron, G. Landry, C. R. Libkind, D. Goncalves, C. Goncalves, P. Sampaio, J. P. Wang, Q.-M. Bai, F.-Y. Wrobel, R. L. Hittinger, C. T. 2022-04-01 doi:10.1101/2022.03.30.486421 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Distinct regions of H. pylori's bactofilin regulate protein interactions to control cell shape ]]> https://biorxiv.org/content/10.1101/2022.04.05.487110v1?rss=1 Sichel, S. R. Bratton, B. P. Salama, N. 2022-04-05 doi:10.1101/2022.04.05.487110 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Electrophysiological normative responses to emotional, neutral, and cigarette-related images. ]]> https://biorxiv.org/content/10.1101/2022.04.11.487896v1?rss=1 Versace, F. Sambuco, N. Deweese, M. M. Cinciripini, P. M. 2022-04-12 doi:10.1101/2022.04.11.487896 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ IL-17A controls CNS autoimmunity by regulating gut microbiota and inducing regulatory T cells ]]> https://biorxiv.org/content/10.1101/2022.04.22.489206v1?rss=1 Shahi, S. K. Ghimire, S. Jensen, S. N. Lehman, P. Borcherding, N. Gibson-Corley, K. Ganesan, S. M. Karandikar, N. J. Mangalam, A. K. 2022-04-22 doi:10.1101/2022.04.22.489206 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Spatially-enhanced clusterwise inference for testing and localizing intermodal correspondence ]]> https://biorxiv.org/content/10.1101/2022.04.25.489462v1?rss=1 Weinstein, S. M. Vandekar, S. N. Baller, E. B. Tu, D. Adebimpe, A. Tapera, T. M. Gur, R. C. Gur, R. E. Detre, J. A. Raznahan, A. Alexander-Bloch, A. F. Satterthwaite, T. D. Shinohara, R. Park, J. Y. 2022-04-26 doi:10.1101/2022.04.25.489462 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ A CXCL12 morphogen gradient uncovers lung endothelial heterogeneity and promotes distal vascular growth ]]> https://biorxiv.org/content/10.1101/2022.04.30.490096v1?rss=1 Chandrasekaran, P. Negretti, N. M. Sivakumar, A. Peers de Nieuburgh, M. Wang, J. Michki, N. S. Chaudhry, F. N. Wen, H. Kaur, S. Lu, M. Zepp, J. A. Young, L. R. Sucre, J. M. S. Frank, D. B. 2022-05-01 doi:10.1101/2022.04.30.490096 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Cooperative RNA degradation stabilizes intermediate epithelial-mesenchymal states and supports phenotypic continuum ]]> https://biorxiv.org/content/10.1101/2022.05.10.491398v1?rss=1 Nordick, B. Park, M. C.-Y. Quaranta, V. Hong, T. 2022-05-10 doi:10.1101/2022.05.10.491398 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Genome assembly and analysis of the flavonoid and phenylpropanoid biosynthetic pathways in Fingerroot ginger (Boesenbergia rotunda) ]]> https://biorxiv.org/content/10.1101/2022.05.11.491478v1?rss=1 Taheri, S. Teo, C. H. Heslop-Harrison, J. Schwarzacher, T. Tan, Y. S. Wee, W. Y. Khalid, N. Biswas, M. K. Mutha, N. V. R. Mohd-Yusof, Y. Gan, H. M. Harikrishna, J. A. 2022-05-11 doi:10.1101/2022.05.11.491478 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Whole-brain computation of cognitive versus acoustic errors in music ]]> https://biorxiv.org/content/10.1101/2022.05.17.492262v1?rss=1 Bonetti, L. Carlomagno, F. Kliuchko, M. Gold, B. P. Palva, S. Haumann, N. T. Tervaniemi, M. Huotilainen, M. Vuust, P. Brattico, E. 2022-05-18 doi:10.1101/2022.05.17.492262 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Myriocin remodels sphingolipids and modulates proteostasis networks to enhance longevity ]]> https://biorxiv.org/content/10.1101/2022.05.20.492522v1?rss=1 Hepowit, N. L. Blalock, E. Lee, S. MacGurn, J. A. Dickson, R. C. 2022-05-20 doi:10.1101/2022.05.20.492522 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Computational epitope mapping of class I fusion proteins using Bayes classification ]]> https://biorxiv.org/content/10.1101/2022.05.23.493016v1?rss=1 Fischer, M. F. S. Crowe, J. E. Meiler, J. 2022-05-24 doi:10.1101/2022.05.23.493016 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ SMAD4 suppresses colitis-associated carcinoma through inhibition of CCL20/CCR6-mediated inflammation ]]> https://biorxiv.org/content/10.1101/2022.05.25.492945v1?rss=1 Hanna, D. N. Marincola-Smith, P. Novitskiy, S. V. Washington, M. K. Zi, J. Weaver, C. J. Hamaamen, J. A. Lewis, K. B. Zhu, J. Yang, J. Liu, Q. Beauchamp, R. D. Means, A. L. 2022-05-25 doi:10.1101/2022.05.25.492945 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Polygenic Transcriptome Risk Scores Can Translate Genetic Results Between Species ]]> https://biorxiv.org/content/10.1101/2022.06.03.494719v1?rss=1 Santhanam, N. Sanchez-Roige, S. Liang, Y. Chitre, A. Munro, D. Chen, D. Cheng, R. Gao, J. George, A. M. Gileta, A. Holl, K. Hughson, A. King, C. P. Lamparelli, A. C. Martin, C. D. Martinez, A. G. Mi, S. St. Pierre, C. L. Tripi, J. Wang, T. Chen, H. Flagel, S. Ishiwari, K. Meyer, P. Saba, L. Woods, L. S. Polesskaya, O. Palmer, A. A. Im, H. K. 2022-06-05 doi:10.1101/2022.06.03.494719 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants ]]> https://biorxiv.org/content/10.1101/2022.06.07.495133v1?rss=1 Aref, L. Bastarache, L. Hughey, J. 2022-06-09 doi:10.1101/2022.06.07.495133 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Regulated extracellular matrix trafficking shapes cell growth during cartilage morphogenesis ]]> https://biorxiv.org/content/10.1101/2022.06.08.495337v1?rss=1 Levic, D. S. Unlu, G. Melville, D. B. Knapik, E. W. 2022-06-10 doi:10.1101/2022.06.08.495337 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Codon optimization, not gene content, predicts XYLose metabolism in budding yeasts ]]> https://biorxiv.org/content/10.1101/2022.06.10.495693v1?rss=1 Nalabothu, R. L. Fisher, K. J. LaBella, A. L. Meyer, T. A. Opulente, D. A. Wolters, J. F. Rokas, A. Hittinger, C. T. 2022-06-13 doi:10.1101/2022.06.10.495693 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ Transcriptional Cartography Integrates Multiscale Biology of the Human Cortex ]]> https://biorxiv.org/content/10.1101/2022.06.13.495984v1?rss=1 Wagstyl, K. Adler, S. Seidlitz, J. Vandekar, S. Mallard, T. T. Dear, R. DeCasien, A. R. Satterthwaite, T. T. Liu, S. Vertes, P. E. Shinohara, R. T. Alexander-Bloch, A. Geschwind, D. H. Raznahan, A. 2022-06-14 doi:10.1101/2022.06.13.495984 Cold Spring Harbor Laboratory Press 2022-06-14 <![CDATA[ The unfolded protein response transcription factor XBP1s ameliorates Alzheimer`s disease by improving synaptic function and proteostasis ]]> https://biorxiv.org/content/10.1101/2022.06.21.496869v1?rss=1 Duran Aniotz, C. Rivera Krstulovic, C. Poblete, N. Ardiles, A. O. Diaz Hung, M. L. Sabusap, C. M. P. Gerakis, Y. Cabral Miranda, F. Diaz, J. Fuentealba, M. Munoz, E. Espinosa, S. Matinez, G. Quiroz, G. Tamburini, G. Medinas, D. B. Contreras, D. Lourenco, M. V. Ribeiro, F. C. Ferreira, S. T. Rozas, C. Morales, B. Plate, L. Gonzalez Billault, C. Palacios, A. G. Hetz, C. 2022-06-23 doi:10.1101/2022.06.21.496869 Cold Spring Harbor Laboratory Press 2022-06-23 <![CDATA[ RyR2 inhibition with dantrolene is antiarrhythmic, antifibrotic, and improves cardiac function in chronic ischemic heart disease ]]> https://biorxiv.org/content/10.1101/2022.06.24.496861v1?rss=1 Schmeckpeper, J. D. Kim, K. George, S. A. Blackwell, D. J. Brennan, J. A. Efimov, I. R. Knollmann, B. C. 2022-06-28 doi:10.1101/2022.06.24.496861 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ Ageing leads to nonspecific antimicrobial peptide responses in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2022.06.25.497570v1?rss=1 Shit, B. Prakash, A. Sarkar, S. Vale, P. F. Khan, I. 2022-06-28 doi:10.1101/2022.06.25.497570 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ Battle for the histones: a secreted bacterial sirtuin from Campylobacter jejuni activates neutrophils and induces inflammation during infection ]]> https://biorxiv.org/content/10.1101/2022.07.19.497369v1?rss=1 Callahan, S. M. Hancock, T. J. Doster, R. S. Parker, C. B. Wakim, M. E. Gaddy, J. A. Johnson, J. G. 2022-07-20 doi:10.1101/2022.07.19.497369 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Group 3 Innate Lymphoid Cells are regulated by WASP in a microbiota-dependent manner ]]> https://biorxiv.org/content/10.1101/2022.07.19.500438v1?rss=1 Biswas, A. Redhu, N. S. Nandy, A. Kang, Y. H. Field, M. Kelly, R. Konnikova, L. Goettel, J. Tsou, A. Horwitz, B. Snapper, S. 2022-07-20 doi:10.1101/2022.07.19.500438 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Epinephrine inhibits PI3K alpha via the Hippo kinases. ]]> https://biorxiv.org/content/10.1101/2022.07.19.500601v1?rss=1 Lin, T.-Y. Ramsamooj, S. Liberatore, K. Lantier, L. Vasan, N. Karukurichi, K. Hwang, S.-K. Kesicki, E. A. Kastenhuber, E. R. Wiederhold, T. Yaron, T. M. Zhu, M. Ma, Y. Paddock, M. N. Zhang, G. Hopkins, B. D. McGuinness, O. Schwartz, R. E. Cantley, L. C. Johnson, J. L. Goncalves, M. D. 2022-07-20 doi:10.1101/2022.07.19.500601 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Multi-ancestry GWAS of major depression aids locus discovery, fine-mapping, gene prioritisation, and causal inference ]]> https://biorxiv.org/content/10.1101/2022.07.20.500802v1?rss=1 Meng, X. Navoly, G. Giannakopoulou, O. DL, D. Koller, D. Pathak, G. Koen, N. Lin, K. Renteria, M. Feng, Y. Gaziano, J. M. Stein, D. Zar, H. Campbell, M. van Heel, D. Trivedi, B. Finer, S. McQuillin, A. Bass, N. Chundru, V. K. Martin, H. Huang, Q. Q. Valkovskaya, M. Kuo, P.-H. Chen, H.-C. Tsai, S.-J. Liu, Y.-L. Kendler, K. Peterson, R. Cai, N. Fang, Y. Sen, S. Scott, L. Burmeister, M. Loos, R. Preuss, M. Actkins, K. Davis, L. Uddin, M. Wani, A. Wildman, D. Ursano, R. Kessler, R. Kanai, M. Okada, Y. Sakaue, S. Rabinowitz, J. Maher, B. Uhl, G. Eato 2022-07-21 doi:10.1101/2022.07.20.500802 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Integrative analysis of a large real-world cohort of small cell lung cancer identifies distinct genetic subtypes and insights into histological transformation ]]> https://biorxiv.org/content/10.1101/2022.07.27.501738v1?rss=1 Sivakumar, S. Moore, J. A. Montesion, M. Sharaf, R. Lin, D. I. Fleischmann, Z. Ebot, E. M. Newberg, J. Mills, J. M. Hedge, P. S. Frampton, G. M. Sage, J. Lovly, C. M. 2022-07-29 doi:10.1101/2022.07.27.501738 Cold Spring Harbor Laboratory Press 2022-07-29 <![CDATA[ Global Protein-Turnover Quantification in Escherichia coli Reveals Cytoplasmic Recycling under Nitrogen-Limitation ]]> https://biorxiv.org/content/10.1101/2022.08.01.502339v1?rss=1 Gupta, M. Johnson, A. Cruz, E. Costa, E. Guest, R. L. Li, S. H.-J. Hart, E. M. Nguyen, T. Stadlmeier, M. Bratton, B. P. Silhavy, T. J. Wingreen, N. S. Gitai, Z. Wuhr, M. 2022-08-03 doi:10.1101/2022.08.01.502339 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Single cell transcriptomics uncovers a non-autonomous Tbx1-dependent genetic program controlling cardiac neural crest cell deployment and progression ]]> https://biorxiv.org/content/10.1101/2022.08.01.502391v1?rss=1 De Bono, C. Liu, Y. Ferrena, A. Valentine, A. Zheng, D. Morrow, B. 2022-08-02 doi:10.1101/2022.08.01.502391 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ The asthma gut microbiota influences lung inflammation in gnotobiotic mice ]]> https://biorxiv.org/content/10.1101/2022.08.09.502549v1?rss=1 Wilson, N. G. Hernandez-Leyva, A. Rosen, A. L. Jaeger, N. McDonough, R. T. Santiago-Borges, J. Lint, M. A. Rosen, T. R. Tomera, C. P. Bacharier, L. B. Swamidass, S. J. Kau, A. L. 2022-08-09 doi:10.1101/2022.08.09.502549 Cold Spring Harbor Laboratory Press 2022-08-09 <![CDATA[ Group B streptococcal membrane vesicles induce proinflammatory cytokine production and are sensed in an NLRP3 inflammasome-dependent mechanism in human macrophages ]]> https://biorxiv.org/content/10.1101/2022.08.10.503555v1?rss=1 McCutcheon, C. R. Gaddy, J. Aronoff, D. M. Manning, S. D. Petroff, M. G. 2022-08-12 doi:10.1101/2022.08.10.503555 Cold Spring Harbor Laboratory Press 2022-08-12 <![CDATA[ Sex inclusion in transcriptome studies of daily rhythms ]]> https://biorxiv.org/content/10.1101/2022.08.18.504312v1?rss=1 Obodo, D. Outland, E. H. Hughey, J. 2022-08-18 doi:10.1101/2022.08.18.504312 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ Single-nuclear RNA sequencing of endomyocardial biopsies identifies persistence of donor-recipient chimerism with distinct signatures in severe cardiac allograft vasculopathy ]]> https://biorxiv.org/content/10.1101/2022.08.24.504346v1?rss=1 Amancherla, K. Qin, J. Hulke, M. L. Pfeiffer, R. D. Agrawal, V. Sheng, Q. Xu, Y. Schlendorf, K. H. Lindenfeld, J. Shah, R. V. Freedman, J. E. Tucker, N. R. Moslehi, J. J. 2022-08-26 doi:10.1101/2022.08.24.504346 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ The seeker R package: simplified fetching and processing of transcriptome data ]]> https://biorxiv.org/content/10.1101/2022.08.30.505820v1?rss=1 Schoenbachler, J. L. Hughey, J. J. 2022-09-01 doi:10.1101/2022.08.30.505820 Cold Spring Harbor Laboratory Press 2022-09-01 <![CDATA[ Taxonomic and metagenomic analyses define the development of the microbiota in the chick ]]> https://biorxiv.org/content/10.1101/2022.08.30.505967v1?rss=1 Bogomolnaya, L. M. Talamantes, M. Rocha, J. Nagarajan, A. Zhu, W. Spiga, L. Winter, M. G. Konganti, K. Adams, L. G. Winter, S. Andrews-Polymenis, H. L. 2022-08-31 doi:10.1101/2022.08.30.505967 Cold Spring Harbor Laboratory Press 2022-08-31 <![CDATA[ The Phenotype-Genotype Reference Map: Improving biobank data science through replication. ]]> https://biorxiv.org/content/10.1101/2022.09.07.506932v1?rss=1 Bastarache, L. Delozier, S. B. Pandit, A. He, J. Lewis, A. Annis, A. C. LeFaive, J. Denny, J. C. Carroll, R. J. Hughey, J. J. Zawistowski, M. Peterson, J. F. 2022-09-08 doi:10.1101/2022.09.07.506932 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Oncogenic signals prime cancer cells for toxic cell growth during a G1 cell cycle arrest ]]> https://biorxiv.org/content/10.1101/2022.09.08.506962v1?rss=1 Foy, R. Crozier, L. Pareri, A. U. Park, B. H. Saurin, A. T. 2022-09-08 doi:10.1101/2022.09.08.506962 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics ]]> https://biorxiv.org/content/10.1101/2022.09.25.509219v1?rss=1 Zhang, D. Lape, R. Shaikh, S. A. Kohegyi, B. K. Watson, J. F. Cais, O. Nakagawa, T. Greger, I. H. 2022-09-26 doi:10.1101/2022.09.25.509219 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Improving stem cell-derived pancreatic islets using single-cell multiome-inferred regulomes ]]> https://biorxiv.org/content/10.1101/2022.09.25.509355v1?rss=1 Zhu, H. Wang, G. Nguyen-Ngoc, K.-V. Kim, D. Miller, M. Goss, G. Kovsky, J. Harrington, A. R. Saunders, D. Melton, R. Powers, A. C. Preissl, S. Spagnoli, F. M. Gaulton, K. J. Sander, M. 2022-09-26 doi:10.1101/2022.09.25.509355 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Transposase N-terminal phosphorylation and asymmetric transposon ends inhibit piggyBac transposition in mammalian cells ]]> https://biorxiv.org/content/10.1101/2022.09.26.509586v1?rss=1 Luo, W. Hickman, A. Genzor, P. Ghirlando, R. Furman, C. M. Menshikh, A. Haase, A. D. Dyda, F. Wilson, M. H. 2022-09-26 doi:10.1101/2022.09.26.509586 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Prostaglandin E2 production is required for phagocyte CXCR2-mediated skin host defense in obese hyperglycemic mice. ]]> https://biorxiv.org/content/10.1101/2022.10.02.510554v1?rss=1 Klopsfenstein, N. Hibbs, K. Blackman, A. Serezani, C. 2022-10-05 doi:10.1101/2022.10.02.510554 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Epigenetics of post-operative delirium: A genome-wide DNA methylation study of neurosurgery patients ]]> https://biorxiv.org/content/10.1101/2022.10.04.510706v1?rss=1 Yamanashi, T. Crutchley, K. J. Wahba, N. E. Nagao, T. Marra, P. S. Akers, C. C. Sullivan, E. J. Iwata, M. Howard, M. A. Cho, H. R. Kawasaki, H. Hughes, C. G. Pandharipande, P. P. Hefti, M. M. Shinozaki, G. 2022-10-07 doi:10.1101/2022.10.04.510706 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Integrative genetic analysis identifies FLVCR1 as an essential component of choline transport in mammals ]]> https://biorxiv.org/content/10.1101/2022.10.05.509986v1?rss=1 Kenny, T. C. Khan, A. Son, Y. Yue, L. Heissel, S. Gamazon, E. R. Alwaseem, H. Hite, R. K. Birsoy, K. 2022-10-05 doi:10.1101/2022.10.05.509986 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Improving polygenic risk prediction in admixed populations by explicitly modeling ancestral-specific effects via GAUDI ]]> https://biorxiv.org/content/10.1101/2022.10.06.511219v1?rss=1 Sun, Q. Rowland, B. T. Chen, J. Mikhaylova, A. V. Avery, C. Peters, U. Lundin, J. Matise, T. Buyske, S. Tao, R. Mathias, R. A. Reiner, A. P. Auer, P. L. Cox, N. J. Kooperberg, C. Thornton, T. Raffield, L. M. Li, Y. 2022-10-08 doi:10.1101/2022.10.06.511219 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ A Novel Mouse Model that Recapitulates the Heterogeneity of Human Triple Negative Breast Cancer ]]> https://biorxiv.org/content/10.1101/2022.10.07.511231v1?rss=1 Doha, Z. O. Wang, X. Calistri, N. Eng, J. Daniel, C. J. Ternes, L. Kim, E. N. Pelz, C. Munks, M. Betts, C. Kirchberger, N. Kwon, S. Bucher, E. Li, X. Waugh, T. Pietenpol, J. A. Sanders, M. E. Mills, G. B. Chin, K. Chang, Y. H. Coussens, L. M. Gray, J. W. Heiser, L. Sears, R. C. 2022-10-07 doi:10.1101/2022.10.07.511231 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Streptococcus agalactiae npx is required for survival in human placental macrophages and full virulence in a model of ascending vaginal infection during pregnancy ]]> https://biorxiv.org/content/10.1101/2022.10.20.513045v1?rss=1 Gaddy, J. 2022-10-20 doi:10.1101/2022.10.20.513045 Cold Spring Harbor Laboratory Press 2022-10-20 <![CDATA[ Development and Validation of the Vanderbilt PRS-KS, an Instrument to Quantify Polygenic Risk Score Knowledge ]]> https://biorxiv.org/content/10.1101/2022.10.26.513776v1?rss=1 0.70. The Vanderbilt PRS-KS significantly correlated with genetic knowledge and applied PRS knowledge (r=0.55, r=0.29), and graduate-level healthcare students had significantly higher scores compared to the representative sample (p<0.01). ConclusionsThe Vanderbilt PRS-KS is a rigorously validated measure to quantify PRS knowledge. ]]> Stubbs, D. Hooker, G. Le, Y. Richter, L. Bick, A. 2022-10-27 doi:10.1101/2022.10.26.513776 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Single-cell transcriptomic atlas reveals increased regeneration in diseased human inner ears ]]> https://biorxiv.org/content/10.1101/2022.10.29.514378v1?rss=1 Wang, T. Ling, A. H. Billings, S. E. Hosseini, D. K. Vaisbuch, Y. Kim, G. S. Atkinson, P. J. Sayyid, Z. N. Aaron, K. A. Wagh, D. Pham, N. Scheibinger, M. Ishiyama, A. Santa Maria, P. Blevins, N. H. Jackler, R. K. Heller, S. Lopez, I. A. Grillet, N. Jan, T. A. Cheng, A. G. 2022-10-31 doi:10.1101/2022.10.29.514378 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ Inhibition of the BMP pathway suppresses tumor growth via downregulation of EGFR in MEK/ERK-dependent colorectal cancer ]]> https://biorxiv.org/content/10.1101/2022.11.01.514643v1?rss=1 Shimizu, S. Kondo, J. Onuma, K. Ota, K. Kamada, M. Harada, Y. Tanaka, Y. Adachi Nakazawa, M. Tamada, Y. Okuno, Y. Kawada, K. Obama, K. Coffey, R. J. Fujiwara, Y. Inoue, M. 2022-11-02 doi:10.1101/2022.11.01.514643 Cold Spring Harbor Laboratory Press 2022-11-02 <![CDATA[ Ketamine induces multiple individually distinct whole-brain functional connectivity signatures ]]> https://biorxiv.org/content/10.1101/2022.11.01.514692v1?rss=1 Moujaes, F. Ji, J. L. Rahmati, M. Burt, J. Schleifer, C. H. Adkinson, B. Savic, A. Santamauro, N. Tamayo, Z. Diehl, C. Kolobaric, A. Flynn, M. Rieser, N. M. Fonteneau, C. Camarro, T. Xu, J. Cho, Y. Repovs, G. Fineberg, S. Morgan, P. Seifritz, E. Vollenweider, F. X. Krystal, J. Murray, J. D. Preller, K. H. Anticevic, A. 2022-11-01 doi:10.1101/2022.11.01.514692 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ CauloKO: an ordered transposon mutant library in Caulobacter crescentus ]]> https://biorxiv.org/content/10.1101/2022.11.02.514973v1?rss=1 Moore, G. M. Ramos, J. G. Bratton, B. P. Gitai, Z. 2022-11-03 doi:10.1101/2022.11.02.514973 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ A new method for quantifying APT and NOE(-3.5) using chemical exchange saturation transfer with double saturation powers (DSP-CEST) ]]> https://biorxiv.org/content/10.1101/2022.11.13.516305v1?rss=1 Zhao, Y. Sun, C. Zu, Z. 2022-11-13 doi:10.1101/2022.11.13.516305 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Increased Pyramidal and VIP Neuronal Excitability in Primary Auditory Cortex Directly Correlates with Tinnitus Behavior ]]> https://biorxiv.org/content/10.1101/2022.11.22.517379v1?rss=1 Ghimire, M. Cai, R. Ling, L. Brownell, K. A. Hackett, T. A. Llano, D. A. Caspary, D. M. 2022-11-23 doi:10.1101/2022.11.22.517379 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ Cloud gazing: demonstrating paths for unlocking the value of cloud genomics through cross-cohort analysis ]]> https://biorxiv.org/content/10.1101/2022.11.29.518423v1?rss=1 Deflaux, N. Selvaraj, M. S. Condon, H. R. Mayo, K. Haidermota, S. Basford, M. A. Lunt, C. Philippakis, A. A. Roden, D. M. Denny, J. C. Musick, A. Collins, R. Allen, N. Effingham, M. Glazer, D. Natarajan, P. Bick, A. G. 2022-12-02 doi:10.1101/2022.11.29.518423 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ DNA methylation at the suppressor of cytokine signaling 3 (SOCS3) gene influences height in childhood ]]> https://biorxiv.org/content/10.1101/2022.11.30.514849v1?rss=1 Issarapu, P. Arumalla, M. Elliott, H. R. Nongmaithem, S. S. Alagu, S. Betts, M. Sajjadi, S. Kessler, N. J. Bayyana, S. Mansuri, S. R. Derakhshan, M. V, K. G. Shrestha, S. K, K. Gravio, C. D. Sahariah, S. A. Sanderson, E. Relton, C. Ward, K. A. Moore, S. E. Prentice, A. M. Lillycrop, K. A. Fall, C. H. D. Silver, M. J. Chandak, G. R. 2022-12-01 doi:10.1101/2022.11.30.514849 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Biasing AlphaFold2 to predict GPCRs and Kinases with user-defined functional or structural properties ]]> https://biorxiv.org/content/10.1101/2022.12.11.519936v1?rss=1 Sala, D. Meiler, J. 2022-12-11 doi:10.1101/2022.12.11.519936 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ The gut metagenome harbors metabolic and antibiotic resistance signatures of moderate-to-severe asthma ]]> https://biorxiv.org/content/10.1101/2023.01.03.522677v1?rss=1 Wilson, N. G. Hernandez-Leyva, A. Schwartz, D. J. Bacharier, L. B. Kau, A. 2023-01-04 doi:10.1101/2023.01.03.522677 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ Targets and cross-reactivity of human T cell recognition of Common Cold Coronaviruses ]]> https://biorxiv.org/content/10.1101/2023.01.04.522794v1?rss=1 67%. However, despite sequence conservation, limited cross-reactivity was observed in the case of sarbecoCoV (50% of instances), indicating that previous CoV exposure to viruses phylogenetically closer to this subgenera is a contributing factor in determining cross-reactivity. Overall, these results provided critical insights in the development of future pan-CoV vaccines. ]]> Tarke, A. Zhang, Y. Methot, N. Narowski, T. N. Phillips, E. Mallal, S. Frazier, A. Filaci, G. Weiskopf, D. Dan, J. M. Lakshmanane, P. Scheuermann, R. H. Sette, A. Grifoni, A. 2023-01-05 doi:10.1101/2023.01.04.522794 Cold Spring Harbor Laboratory Press 2023-01-05 <![CDATA[ AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics ]]> https://biorxiv.org/content/10.1101/2023.01.15.524135v1?rss=1 Mongia, A. Saunders, D. Wang, Y. Brissova, M. Powers, A. C. Kaestner, K. H. Vahedi, G. Naji, A. Schwartz, G. Faryabi, R. B. 2023-01-18 doi:10.1101/2023.01.15.524135 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ A single amino acid polymorphism in natural Metchnikowin alleles of Drosophila results in systemic immunity and life history tradeoffs ]]> https://biorxiv.org/content/10.1101/2023.01.16.524277v1?rss=1 Perlmutter, J. I. Chapman, J. R. Wilkinson, M. C. Nevarez-Saenz, I. Unckless, R. L. 2023-01-19 doi:10.1101/2023.01.16.524277 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Ferroptosis Promotes Pulmonary Hypertension ]]> https://biorxiv.org/content/10.1101/2023.01.19.524721v1?rss=1 Vogel, N. T. Annis, J. Prisco, S. Kazmirczak, F. Brittain, E. L. Prins, K. 2023-01-20 doi:10.1101/2023.01.19.524721 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Androgen aggravates aortic aneurysms via suppressing PD-1 in mice ]]> https://biorxiv.org/content/10.1101/2023.01.22.525073v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@2e8406org.highwire.dtl.DTLVardef@1dde495org.highwire.dtl.DTLVardef@c9f42eorg.highwire.dtl.DTLVardef@be2799_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mu, X. Liu, S. Wang, Z. Jiang, K. McClintock, T. S. Stromberg, A. Villasante-Tezanos, A. Lee, E. S. Curci, J. A. Gong, M. C. Guo, Z. 2023-01-22 doi:10.1101/2023.01.22.525073 Cold Spring Harbor Laboratory Press 2023-01-22 <![CDATA[ Age differences in spatial memory are mitigated during naturalistic navigation ]]> https://biorxiv.org/content/10.1101/2023.01.23.525279v1?rss=1 Hill, P. F. McAvan, A. S. Garren, J. D. Grilli, M. D. Barnes, C. A. Ekstrom, A. D. 2023-01-24 doi:10.1101/2023.01.23.525279 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ Therapy Development for Microvillus Inclusion Disease using Patient-derived Enteroids ]]> https://biorxiv.org/content/10.1101/2023.01.28.526036v1?rss=1 Kalashyan, M. Raghunathan, K. Oller, H. Bayer, M.-T. Jimenez, L. Roland, J. T. Kolobova, E. Hagen, S. J. Goldsmith, J. D. Shub, M. D. Goldenring, J. R. Kaji, I. Thiagarajah, J. R. 2023-01-29 doi:10.1101/2023.01.28.526036 Cold Spring Harbor Laboratory Press 2023-01-29 <![CDATA[ Molecular and cellular mechanisms by which cardiac sympathetic denervation prevents heart failure and sudden cardiac arrest ]]> https://biorxiv.org/content/10.1101/2023.01.29.526082v1?rss=1 DeMazumder, D. Joshi, P. O'Rourke, B. Estes, S. Dey, S. 2023-01-31 doi:10.1101/2023.01.29.526082 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Ryanodine receptor inhibition improves cardiac repolarization reserve and contractile function and prevents sudden arrhythmic death in failing hearts. ]]> https://biorxiv.org/content/10.1101/2023.01.29.526151v1?rss=1 Joshi, P. Estes, S. DeMazumder, D. Knollmann, B. C. Dey, S. 2023-01-31 doi:10.1101/2023.01.29.526151 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants ]]> https://biorxiv.org/content/10.1101/2023.01.31.526505v1?rss=1 Einson, J. Glinos, D. Boerwinkle, E. Castaldi, P. Darbar, D. de Andrade, M. Ellinor, P. Fornage, M. Gabriel, S. Germer, S. Gibbs, R. Hersh, C. Johnsen, J. Kaplan, R. Konkle, B. Kooperberg, C. Nassir, R. Loos, R. J. F. Meyers, D. A. Mitchell, B. D. Psaty, B. Vasan, R. S. Rich, S. S. Rienstra, M. Rotter, J. I. Saferali, A. Shoemaker, M. B. Silverman, E. Smith, A. V. Mohammadi, P. Castel, S. E. Iossifov, I. Lappalainen, T. 2023-01-31 doi:10.1101/2023.01.31.526505 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ LimoRhyde2: genomic analysis of biological rhythms based on effect sizes ]]> https://biorxiv.org/content/10.1101/2023.02.02.526897v1?rss=1 Obodo, D. Outland, E. H. Hughey, J. J. 2023-02-03 doi:10.1101/2023.02.02.526897 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Assignment of molecular origins of NOE signal at -3.5 ppm in the brain ]]> https://biorxiv.org/content/10.1101/2023.02.03.526979v1?rss=1 Zhao, Y. Zu, Z. 2023-02-04 doi:10.1101/2023.02.03.526979 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Neuroticism/negative emotionality is associated with increased reactivity to uncertain threat in the bed nucleus of the stria terminalis, not the amygdala ]]> https://biorxiv.org/content/10.1101/2023.02.09.527767v1?rss=1 Grogans, S. E. Hur, J. Barstead, M. G. Anderson, A. S. Islam, S. Kim, H. C. Kuhn, M. Tillman, R. M. Fox, A. S. Smith, J. F. DeYoung, K. A. Shackman, A. J. 2023-02-10 doi:10.1101/2023.02.09.527767 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Redox Regulation of m6A Methyltransferase METTL3 in Human β-cells Controls the Innate Immune Response in Type 1 Diabetes ]]> https://biorxiv.org/content/10.1101/2023.02.16.528701v1?rss=1 De Jesus, D. F. Zhang, Z. Brown, N. K. Li, X. Gaffrey, M. J. Kahraman, S. Wei, J. Hu, J. Basile, G. Xiao, L. Rana, T. M. Mathews, C. E. Powers, A. C. Atkinson, M. A. Eizirik, D. L. Dhe-Paganon, S. Parent, A. V. Qian, W.-J. He, C. Kulkarni, R. N. 2023-02-16 doi:10.1101/2023.02.16.528701 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Pulmonary osteoclast-like cells in silica induced pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/2023.02.17.528996v1?rss=1 Hasegawa, Y. Franks, J. M. Tanaka, Y. Uehara, Y. Read, D. F. Williams, C. Srivatsan, S. Pitstick, L. B. Nikolaidis, N. M. Shaver, C. M. Wu, H. Gardner, J. C. Osterburg, A. R. Yu, J. J. Kopras, E. J. Teitelbaum, S. L. Wikenheiser-Brokamp, K. A. Trapnell, C. McCormack, F. X. 2023-02-18 doi:10.1101/2023.02.17.528996 Cold Spring Harbor Laboratory Press 2023-02-18 <![CDATA[ The immune regulation and epidemiological consequences of immune priming in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.02.22.529244v1?rss=1 Prakash, A. Fenner, F. Shit, B. Salminen, T. S. Monteith, K. M. Khan, I. Vale, P. F. 2023-02-23 doi:10.1101/2023.02.22.529244 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Post-Translational Modification Impact on MHC Peptide Binding and TCR Engagement ]]> https://biorxiv.org/content/10.1101/2023.03.02.530810v1?rss=1 Kelly, J. J. Pires, M. 2023-03-03 doi:10.1101/2023.03.02.530810 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Small volume blood-brain barrier opening in macaques with a 1 MHz ultrasound phased array ]]> https://biorxiv.org/content/10.1101/2023.03.02.530815v1?rss=1 Manuel, T. J. Sigona, M. K. Phipps, M. A. Kusonose, J. Luo, H. Yang, P.-F. Newton, A. T. Gore, J. C. Grissom, W. Chen, L. M. Caskey, C. F. 2023-03-02 doi:10.1101/2023.03.02.530815 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Hepatic stellate cells maintain liver homeostasis through paracrine neurotrophin-3 signaling ]]> https://biorxiv.org/content/10.1101/2023.03.03.531042v1?rss=1 Trinh, V. Q.-H. Lee, T.-F. Lemoinne, S. Ray, K. C. Ybanez, M. D. Tsuchida, T. Carter, J. K. Agudo, J. Brown, B. D. Akat, K. M. Friedman, S. L. Lee, Y. A. 2023-03-04 doi:10.1101/2023.03.03.531042 Cold Spring Harbor Laboratory Press 2023-03-04 <![CDATA[ The MYO1B and MYO5B motor proteins and the SNX27 sorting nexin regulate membrane mucin MUC17 trafficking in enterocytes ]]> https://biorxiv.org/content/10.1101/2023.03.06.530313v1?rss=1 Jäverfelt, S. Hellsen, G. Kaji, I. Goldenring, J. R. Pelaseyed, T. 2023-03-07 doi:10.1101/2023.03.06.530313 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function ]]> https://biorxiv.org/content/10.1101/2023.03.07.531534v1?rss=1 Okhovat, M. VanCampen, J. Lima, A. C. Nevonen, K. Layman, C. E. Ward, S. Herrera, J. Stendahl, A. M. Yang, R. Harshman, L. Li, W. Sheng, R. R. Mao, Y. Fedorov, L. Ndjamen, B. Vigh-Conrad, K. A. Matthews, I. R. Easow, S. A. Chan, D. K. Jan, T. A. Eichler, E. E. Rugonyi, S. Conrad, D. F. Ahituv, N. Carbone, L. 2023-03-07 doi:10.1101/2023.03.07.531534 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Extended regulation interface coupled to the allosteric network and disease mutations in the PP2A-B56 delta holoenzyme ]]> https://biorxiv.org/content/10.1101/2023.03.09.530109v1?rss=1 Wu, C.-G. Balakrishnan, V. K. Parihar, P. S. Konovolov, K. Chen, Y.-C. Merrill, R. A. Wei, H. Carragher, B. Sundaresan, R. Cui, Q. Wadzinski, B. E. Swingle, M. R. Musiyenko, A. Honkanen, R. Suzuki, A. Strack, S. Huang, X. Xing, Y. 2023-03-09 doi:10.1101/2023.03.09.530109 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Learning about neurodiversity from parents - auditory gestalt perception of prelinguistic vocalisations ]]> https://biorxiv.org/content/10.1101/2023.03.13.532450v1?rss=1 Zhang, D. Lang, S. Wilken, B. Einspieler, C. Neul, J. L. Boelte, S. Holzinger, D. Freilinger, M. Poustka, L. Sigafoos, J. Marschik, P. B. 2023-03-15 doi:10.1101/2023.03.13.532450 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Cell type-specific and disease-associated eQTL in the human lung ]]> https://biorxiv.org/content/10.1101/2023.03.17.533161v1?rss=1 Natri, H. M. Del Azodi, C. B. Peter, L. Taylor, C. J. Chugh, S. Kendle, R. Chung, M.-i. Flaherty, D. K. Matlock, B. K. Calvi, C. L. Blackwell, T. S. Ware, L. B. Bacchetta, M. Walia, R. Shaver, C. M. Kropski, J. A. McCarthy, D. J. Banovich, N. E. 2023-03-21 doi:10.1101/2023.03.17.533161 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ ZCCHC17 modulates neuronal RNA splicing and supports cognitive resilience in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2023.03.21.533654v1?rss=1 Bartosch, A. M. W. Youth, E. H. H. Hansen, S. Kaufman, M. E. Xiao, H. Koo, S. Y. Ashok, A. Sivakumar, S. Soni, R. K. Dumitrescu, L. C. Lam, T. G. Ropri, A. S. Lee, A. J. Klein, H.-U. Vardarajan, B. N. Bennett, D. A. J. Young-Pearse, T. De Jager, P. L. Hohman, T. J. Sproul, A. A. Teich, A. F. 2023-03-21 doi:10.1101/2023.03.21.533654 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Multiple rotavirus species encode fusion-associated small transmembrane (FAST) proteins with cell type-specific activity ]]> https://biorxiv.org/content/10.1101/2023.04.07.536061v1?rss=1 Veletanlic, V. Sartalamacchia, K. Diller, J. R. Ogden, K. M. 2023-04-08 doi:10.1101/2023.04.07.536061 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Immunoproteasomal Processing of Isolevuglandin Adducts in Hypertension ]]> https://biorxiv.org/content/10.1101/2023.04.10.536054v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@1fc2367org.highwire.dtl.DTLVardef@787fcforg.highwire.dtl.DTLVardef@10f09f2org.highwire.dtl.DTLVardef@561978_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG Isolevuglandins (isoLGs) are lipid aldehydes that form in the presence of reactive oxygen species (ROS) and drive immune activation. We found that isoLG-adducts are presented within the context of major histocompatibility complexes (MHC-I) by an immunoproteasome dependent mechanism. Pharmacologic inhibition of LMP7, the chymotrypsin subunit of the immunoproteasome, attenuates hypertension and tissue inflammation in the angiotensin II (Ang II) model of hypertension. Genetic loss of function of all immunoproteasome subunits or conditional deletion of LMP7 in dendritic cell (DCs) or endothelial cells (ECs) attenuated hypertension, reduced aortic T cell infiltration, and reduced isoLG-adduct MHC-I interaction. Furthermore, isoLG adducts structurally resemble double-stranded DNA and contribute to the activation of STING in ECs. These studies define a critical role of the immunoproteasome in the processing and presentation of isoLG-adducts. Moreover they define a role of LMP7 as a regulator of T cell activation and tissue infiltration in hypertension. ]]> de la Visitacion, N. Chen, W. Krishnan, J. Van Beusecum, J. P. Amarnath, V. Hennen, E. M. Zhao, S. Saleem, M. Ao, M. Harrison, D. G. Patrick, D. M. 2023-04-12 doi:10.1101/2023.04.10.536054 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Estimating heritability explained by local ancestry and evaluating stratification bias in admixture mapping from summary statistics ]]> https://biorxiv.org/content/10.1101/2023.04.10.536252v1?rss=1 Chan, T. F. Rui, X. Conti, D. V. Fornage, M. Graff, M. Haessler, J. Haiman, C. Highland, H. M. Jung, S. Y. Kenny, E. Kooperberg, C. Le Marchland, L. North, K. E. Tao, R. Wojcik, G. Gignoux, C. R. PAGE Consortium, Chiang, C. W. Mancuso, N. 2023-04-10 doi:10.1101/2023.04.10.536252 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ Transcriptome Complexity Disentangled: A Regulatory Elements Approach ]]> https://biorxiv.org/content/10.1101/2023.04.17.537241v1?rss=1 Asiaee, A. Abrams, Z. B. Coombes, K. R. 2023-04-18 doi:10.1101/2023.04.17.537241 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Repetitive Sulfur Dioxide Exposure in Mice Models Post-Deployment Respiratory Syndrome ]]> https://biorxiv.org/content/10.1101/2023.05.15.540867v1?rss=1 Gutor, S. S. Salinas, R. I. Nichols, D. S. Bazzano, J. M. R. Han, W. Gokey, J. J. Vasiukov, G. West, J. D. Newcomb, D. C. Dikalova, A. E. Richmond, B. W. Dikalov, S. I. Blackwell, T. S. Polosukhin, V. V. 2023-05-18 doi:10.1101/2023.05.15.540867 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ DNA methylation-environment interactions in the human genome ]]> https://biorxiv.org/content/10.1101/2023.05.19.541437v1?rss=1 Johnston, R. A. Aracena, K. A. Barreiro, L. B. Lea, A. J. Tung, J. 2023-05-19 doi:10.1101/2023.05.19.541437 Cold Spring Harbor Laboratory Press 2023-05-19 <![CDATA[ Unique interactions and functions of the mitochondrial small Tims in Trypanosoma brucei ]]> https://biorxiv.org/content/10.1101/2023.05.29.542777v1?rss=1 800 kDa) and co-fractionated with TbTim17. Altogether, our results demonstrated that TbTim13 is a part of the TbTIM complex and the smaller complexes of the small TbTims likely interact with the larger complex dynamically. Therefore, relative to other eukaryotes, the architecture and function of the small TbTim complexes are specific in T. brucei. ]]> Quinones Guillen, L. S. Gonzalez, F. S. Darden, C. Khan, M. Tripathi, A. Smith, J. Cooley, A. Paromov, V. Davis, J. Misra, S. Chaudhuri, M. 2023-05-31 doi:10.1101/2023.05.29.542777 Cold Spring Harbor Laboratory Press 2023-05-31 <![CDATA[ IL-22 promotes acute kidney injury through activation of the DNA damage response and cell death in proximal tubule cells ]]> https://biorxiv.org/content/10.1101/2023.06.08.544134v1?rss=1 Taguchi, K. Sugahara, S. Elias, B. C. Pabla, N. S. Canaud, G. Brooks, C. R. 2023-06-08 doi:10.1101/2023.06.08.544134 Cold Spring Harbor Laboratory Press 2023-06-08 <![CDATA[ Concerted epithelial and stromal changes during progression of Barrett's Esophagus to invasive adenocarcinoma exposed by multi-scale, multi-omics analysis ]]> https://biorxiv.org/content/10.1101/2023.06.08.544265v1?rss=1 View larger version (62K): org.highwire.dtl.DTLVardef@64c375org.highwire.dtl.DTLVardef@15c6ef2org.highwire.dtl.DTLVardef@177dee0org.highwire.dtl.DTLVardef@c945e7_HPS_FORMAT_FIGEXP M_FIG Graphical AbstractTo obtain a comprehensive picture of the coordinated changes in epithelial, stromal and immune compartments during development of Barretts-associated esophageal adenocarcinoma, patient-matched samples corresponding to various phases of disease progression were collected from 12 patients, each of which had at a given time point lesions at multiple stages progression (matched-normal, metaplasia, dysplasia, and carcinoma). Matched "normal" gastric tissues were also collected. These sample were analyzed by single cell RNA-sequencing (scRNAseq) for single-cell resolution transcriptomics and Copy Number Variant (CNV), by proteomics for extracellular matrix (ECM) proteins, by Atomic Force Microscopy (AFM for tissue stiffness and by CODEX spatial proteomics imaging The integrative multi-omics analysis exposed drastic alterations in cell type composition and shifts in cell states in all three compartments. A large subpopulation of fibroblasts absent in the normal esophagus and characteristic of dysplasia and adenocarcinoma sample, that based on markers would indeed be considered cancer associated fibroblasts (CAF), appeared already in the metaplastic phase. This fibroblast subpopulation had transcriptomes virtually indistinguishable with fibroblasts of the cancer free gastric epithelium in these patients C_FIG ]]> Strasser, M. Gibbs, D. L. Gascard, P. Bons, J. Hickey, J. W. Schürch, C. M. Tan, Y. Black, S. Chu, P. Ozkan, A. Basisty, N. Sangwan, V. Rose, J. Shah, S. Camilleri-Broet, S. Fiset, P.-O. Bertos, N. Berube, J. Djambazian, H. Li, R. Oikonomopoulos, S. Fels-Elliott, D. R. Vernovsky, S. Shimshoni, E. Collyar, D. Russell, A. Ragoussis, I. Stachler, M. Goldenring, J. R. McDonald, S. Ingber, D. E. Schilling, B. Nolan, G. P. Tlsty, T. D. Huang, S. Ferri, L. L. 2023-06-11 doi:10.1101/2023.06.08.544265 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ An atlas of genetic variation for linking pathogen-induced cellular traits to human disease ]]> https://biorxiv.org/content/10.1101/202325v1?rss=1 Wang, L. Pittman, K. J. Barker, J. R. Salinas, R. E. Stanaway, I. B. Carroll, R. J. Balmat, T. Ingham, A. Gopalakrishnan, A. M. Gibbs, K. D. Antonia, A. L. The eMERGE Network, Heitman, J. Lee, S. C. Jarvick, G. P. Denny, J. C. Delong, M. R. Valdivia, R. H. Crosslin, D. R. Ko, D. C. 2017-10-16 doi:10.1101/202325 Cold Spring Harbor Laboratory Press 2017-10-16 <![CDATA[ Clingen Cancer Somatic Working Group: standardizing and democratizing access to cancer molecular diagnostic data to drive translational research ]]> https://biorxiv.org/content/10.1101/212225v1?rss=1 50 academic and industry based cancer research organizations, we developed the Minimal Variant Level Data (MVLD) framework to standardize reporting and interpretation of drug associated alterations (5). We are currently involved in collaborative efforts to align the MVLD framework with parallel, complementary sequence variants interpretation clinical guidelines from the Association of Molecular Pathologists (AMP) for clinical labs (6). In order to truly democratize access to MolDx data for care and research needs, these standards must be harmonized to support sharing of clinical cancer variants. Here we describe the processes and methods developed within the ClinGens Somatic WG in collaboration with over 60 cancer care and research organizations as well as CLIA-certified, CAP-accredited clinical testing labs to develop standards for cancer variant interpretation and sharing. ]]> Madhavan, S. Ritter, D. Micheel, C. Rao, S. Roy, A. Sonkin, D. McCoy, M. Griffith, M. Griffith, O. L. McGarvey, P. Kulkarni, S. The Clingen Somatic Working Group, 2017-11-01 doi:10.1101/212225 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ CalR: A Web-based Analysis Tool for Indirect Calorimetry Experiments ]]> https://biorxiv.org/content/10.1101/213967v1?rss=1 nView larger version (34K):norg.highwire.dtl.DTLVardef@c27058org.highwire.dtl.DTLVardef@15dbe84org.highwire.dtl.DTLVardef@1870019org.highwire.dtl.DTLVardef@17a17c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mina, A. I. LeClair, R. A. LeClair, K. B. Cohen, D. E. Lantier, L. Banks, A. S. 2017-11-04 doi:10.1101/213967 Cold Spring Harbor Laboratory Press 2017-11-04 <![CDATA[ Sex differences in the genetic architecture of obsessive-compulsive disorder ]]> https://biorxiv.org/content/10.1101/219170v1?rss=1 Khramtsova, E. A. Heldman, R. Derks, E. M. Yu, D. TS/OCD Psychiatric Genomics Disorders Workgroup, Davis, L. K. Stranger, B. E. 2017-11-21 doi:10.1101/219170 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ Gene expression imputation across multiple brain regions reveals schizophrenia risk throughout development. ]]> https://biorxiv.org/content/10.1101/222596v1?rss=1 Huckins, L. M. Dobbyn, A. Ruderfer, D. Hoffman, G. Wang, W. Pardinas, A. F. Rajagopal, V. M. Als, T. D. Hoang, H. T. Girdhar, K. Boocock, J. Roussos, P. Fromer, M. Kramer, R. Domenici, E. Gamazon, E. Purcell, S. CommonMind Consortium, Schizophrenia Working Group of the Psychiatric Gen, iPSYCH-GEMS Schizophrenia Working Group, Demontis, D. Borglum, A. Walters, J. O'Donovan, M. Sullivan, P. F. Owen, M. Devlin, B. Sieberts, S. K. Cox, N. Im, H. K. Sklar, P. Stahl, E. A. 2017-11-21 doi:10.1101/222596 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ Transcriptomic Imputation of Bipolar Disorder and Bipolar subtypes reveals 29 novel associated genes ]]> https://biorxiv.org/content/10.1101/222786v1?rss=1 Huckins, L. Dobbyn, A. McFadden, W. Wang, W. Ruderfer, D. Hoffman, G. Rajagopal, V. Nguyen, H. T. Roussos, P. Fromer, M. Kramer, R. Domenici, E. Gamazon, E. CommonMind Consortium, Bipolar Disorder Working Group of the Psychiatric, iPSYCH Consortium, Demontis, D. Borglum, A. Devlin, B. Sieberts, S. K. Cox, N. Im, H. K. Sklar, P. Stahl, E. A. 2017-11-21 doi:10.1101/222786 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ quanTIseq: quantifying immune contexture of human tumors ]]> https://biorxiv.org/content/10.1101/223180v1?rss=1 Finotello, F. Mayer, C. Plattner, C. Laschober, G. Rieder, D. Hackl, H. Krogsdam, A. Posch, W. Wilflingseder, D. Sopper, S. Jsselsteijn, M. Johnsons, D. Xu, Y. Wang, Y. Sanders, M. E. Estrada, M. V. Ericsson-Gonzalez, P. Balko, J. de Miranda, N. F. Trajanoski, Z. 2017-11-22 doi:10.1101/223180 Cold Spring Harbor Laboratory Press 2017-11-22 <![CDATA[ Systems genetics identifies modifiers of Alzheimer’s disease risk and resilience ]]> https://biorxiv.org/content/10.1101/225714v1?rss=1 Neuner, S. M. Hohman, T. J. Richholt, R. Bennett, D. A. Schneider, J. A. De Jager, P. L. Huentelman, M. J. O'Connell, K. M. S. Kaczorowski, C. C. 2017-11-27 doi:10.1101/225714 Cold Spring Harbor Laboratory Press 2017-11-27 <![CDATA[ Examination of the Shared Genetic Basis of Anorexia Nervosa and Obsessive-Compulsive Disorder ]]> https://biorxiv.org/content/10.1101/231076v1?rss=1 Yilmaz, Z. Halvorsen, M. Bryois, J. Yu, D. Eating Disorders Working Group of the PGC, Tourette Syndrome/OCD Working Group of the PGC, Thornton, L. M. Zerwas, S. Micali, N. Moessner, R. Burton, C. L. Zai, G. Erdman, L. Kas, M. J. Arnold, P. D. Davis, L. K. Knowles, J. A. Breen, G. Scharf, J. M. Nestadt, G. Mathews, C. A. Bulik, C. M. Mattheisen, M. Crowley, J. J. 2017-12-08 doi:10.1101/231076 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ Genome-wide association analysis of lifetime cannabis use (N=184,765) identifies new risk loci, genetic overlap with mental health, and a causal influence of schizophrenia on cannabis use ]]> https://biorxiv.org/content/10.1101/234294v1?rss=1 Pasman, J. A. Verweij, K. J. H. Gerring, Z. Stringer, S. Sanchez-Roige, S. Treur, J. L. Abdellaoui, A. Nivard, M. G. Baselmans, B. M. L. Ong, J.-S. Ip, H. F. van der Zee, M. D. Bartels, M. Day, F. R. Fontanillas, P. Elson, S. L. the 23andMe Research Team, de Wit, H. Davis, L. K. MacKillop, J. International Cannabis Consortium, Derringer, J. L. Branje, S. J. T. Hartman, C. A. Heath, A. C. van Lier, P. A. C. Madden, P. A. F. Magi, R. Meeus, W. Montgomery, G. W. Oldehinkel, A. J. Pausova, Z. Ramos-Quiroga, J. A. Paus, T. Ribases, M. Kaprio, J. Boks, M. P. M 2018-01-08 doi:10.1101/234294 Cold Spring Harbor Laboratory Press 2018-01-08 <![CDATA[ AP-4 vesicles unmasked by organellar proteomics to reveal their cargo and machinery ]]> https://biorxiv.org/content/10.1101/235226v1?rss=1 Davies, A. K. Itzhak, D. N. Edgar, J. R. Archuleta, T. L. Hirst, J. Jackson, L. P. Robinson, M. S. Borner, G. H. H. 2017-12-18 doi:10.1101/235226 Cold Spring Harbor Laboratory Press 2017-12-18 <![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[ Audio-tactile and peripersonal space processing around the trunk in human parietal and temporal cortex: an intracranial EEG study ]]> https://biorxiv.org/content/10.1101/249078v1?rss=1 Bernasconi, F. Noel, J.-P. Park, H. Faivre, N. Seeck, M. Spinelli, L. Schaller, K. Blanke, O. Serino, A. 2018-01-18 doi:10.1101/249078 Cold Spring Harbor Laboratory Press 2018-01-18 <![CDATA[ Genetic meta-analysis identifies 10 novel loci and functional pathways for Alzheimer’s disease risk ]]> https://biorxiv.org/content/10.1101/258533v1?rss=1 Jansen, I. Savage, J. Watanabe, K. Bryois, J. Williams, D. Steinberg, S. Sealock, J. Karlsson, I. Hagg, S. Athanasiu, L. Voyle, N. Proitsi, P. Witoelar, A. Stringer, S. Aarsland, D. Almdahl, I. Andersen, F. Bergh, S. Bettella, F. Bjornsson, S. Braekhus, A. Brathen, G. de Leeuw, C. Desikan, R. Djurovic, S. Dumitrescu, L. Fladby, T. Homan, T. Jonsson, P. Rongve, A. Saltvedt, I. Sando, S. Selbak, G. Skene, N. Snaedal, J. Stordal, E. Ulstein, I. Wang, Y. White, L. Hjerling-Leffler, J. Sullivan, P. van der Flier, W. Dobson, R. Davis, L. Stefansson, H. St 2018-02-20 doi:10.1101/258533 Cold Spring Harbor Laboratory Press 2018-02-20 <![CDATA[ Identifying tissues implicated in Anorexia Nervosa using Transcriptomic Imputation ]]> https://biorxiv.org/content/10.1101/265017v1?rss=1 Huckins, L. M. Dobbyn, A. McFadden, W. Ruderfer, D. Wang, W. Gamazon, E. R. Leppa, V. Eating Disorders working group of the Psychiatric Genomics Consortium (PGC-ED), Devlin, B. Sieberts, S. K. Cox, N. Im, H. K. Breen, G. Sklar, P. Bulik, C. Stahl, E. A. 2018-02-14 doi:10.1101/265017 Cold Spring Harbor Laboratory Press 2018-02-14 <![CDATA[ LimoRhyde: a flexible approach for differential analysis of rhythmic transcriptome data ]]> https://biorxiv.org/content/10.1101/283622v1?rss=1 Hughey, J. J. 2018-03-16 doi:10.1101/283622 Cold Spring Harbor Laboratory Press 2018-03-16 <![CDATA[ Low frequency and rare coding variation contributes to multiple sclerosis risk ]]> https://biorxiv.org/content/10.1101/286617v1?rss=1 230 identified by genome-wide association studies (Patsopoulos et al., 2017). Multiple strands of evidence suggest that the majority of the remaining heritability is also due to the additive effects of individual variants, rather than epistatic interactions between these variants, or mutations exclusive to individual families. Here, we show in 68,379 cases and controls that as much as 5% of this heritability is explained by low-frequency variation in gene coding sequence. We identify four novel genes driving MS risk independently of common variant signals, which highlight a key role for regulatory T cell homeostasis and regulation, IFN{gamma} biology and NF{kappa}B signaling in MS pathogenesis. As low-frequency variants do not show substantial linkage disequilibrium with other variants, and as coding variants are more interpretable and experimentally tractable than non-coding variation, our discoveries constitute a rich resource for dissecting the pathobiology of MS. ]]> International Multiple Sclerosis Genetics Consortium, Mitrovic, M. Patsopoulos, N. Beecham, A. Dankowski, T. Goris, A. Dubois, B. Dhooghe, M.-B. Lemmens, R. Van Damme, P. Fitzgerald, K. Bach Sondergaard, H. Sellebjerg, F. Sorensen, P. S. Ullum, H. Wegner Thoerner, L. Werge, T. Saarela, J. Cournu-Rebeix, I. Damotte, V. Fontaine, B. Guillot-Noel, L. Lathrop, M. Vukusik, S. Gourraud, P.-A. Andlauer, T. Pongratz, V. Buck, D. Gasperi, C. Graetz, C. Bayas, A. Heesen, C. Kumpfel, T. Linker, R. Paul, F. Stangel, M. Tackenberg, B. Then Bergh, F. Warnke, C. Wiend 2018-03-23 doi:10.1101/286617 Cold Spring Harbor Laboratory Press 2018-03-23 <![CDATA[ Large-Scale Genome-Wide Meta Analysis of Polycystic Ovary Syndrome Suggests Shared Genetic Architecture for Different Diagnosis Criteria. ]]> https://biorxiv.org/content/10.1101/290502v1?rss=1 Day, F. Karaderi, T. Jones, M. R. Meun, C. He, C. Drong, A. Kraft, P. Lin, N. Huang, H. Broer, L. Magi, R. Saxena, R. Laisk-Podar, T. Urbanek, M. Hayes, G. M. Thorleifsson, G. Fernandez-Tajes, J. Mahajan, A. Mullin, B. H. Stuckey, B. G. A. Spector, T. D. Wilson, S. G. Goodarzi, M. O. Davis, L. Obermeyer-Pietsch, B. Uitterlinden, A. G. Anttila, V. Neale, B. M. Jarvelin, M.-R. Fauser, B. Kowalska, I. Visser, J. A. Anderson, M. Ong, K. Stener-Victorin, E. Ehrmann, D. Legro, R. S. Salumets, A. McCarthy, M. I. Morin-Papunen, L. Thorsteinsdottir, U. Stefansso 2018-03-28 doi:10.1101/290502 Cold Spring Harbor Laboratory Press 2018-03-28 <![CDATA[ UNC-6/Netrin and its Receptors UNC-5 and UNC-40/DCC Control Growth Cone Polarity, Microtubule Accumulation, and Protrusion ]]> https://biorxiv.org/content/10.1101/294215v1?rss=1 Gujar, M. R. Sundararajan, L. Stricker, A. M. Lundquist, E. A. 2018-04-03 doi:10.1101/294215 Cold Spring Harbor Laboratory Press 2018-04-03 <![CDATA[ Timing Determines Tuning: a Rapid Spatiotemporal Transformation in Superior Colliculus Neurons During Reactive Gaze Shifts. ]]> https://biorxiv.org/content/10.1101/302125v1?rss=1 Sadeh, M. Sajad, A. Wang, H. Yan, X. Crawford, J. D. 2018-04-16 doi:10.1101/302125 Cold Spring Harbor Laboratory Press 2018-04-16 <![CDATA[ Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1 ]]> https://biorxiv.org/content/10.1101/306282v1?rss=1 Xu, K. Acharya, P. Kong, R. Cheng, C. Chuang, G.-Y. Liu, K. Louder, M. K. O Dell, S. Rawi, R. Sastry, M. Shen, C.-H. Zhang, B. Zhou, T. Asokan, M. Bailer, R. T. Chambers, M. Chen, X. Choi, C. W. Dandey, V. P. Doria-Rose, N. A. Druz, A. Eng, E. T. Farney, S. K. Foulds, K. E. Geng, H. Georgiev, I. S. Gorman, J. Hill, K. R. Jafari, A. J. Kwon, Y. D. Lai, Y.-T. Lemmin, T. McKee, K. Ohr, T. Y. Ou, L. Peng, D. Rowshan, A. P. Sheng, Z. Todd, J.-P. Tsybovsky, Y. Viox, E. G. Wang, Y. Wei, H. Yang, Y. Zhou, A. F. Chen, R. Yang, L. Scorpio, D. G. McDermott, 2018-04-23 doi:10.1101/306282 Cold Spring Harbor Laboratory Press 2018-04-23 <![CDATA[ Decoding Selective Attention to Context Memory: An Aging Study ]]> https://biorxiv.org/content/10.1101/324384v1?rss=1 Powell, P. S. Strunk, J. James, T. Polyn, S. Duarte, A. 2018-05-16 doi:10.1101/324384 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Genome-wide association analysis identifies 27 novel loci associated with uterine leiomyomata revealing common genetic origins with endometriosis ]]> https://biorxiv.org/content/10.1101/324905v1?rss=1 Gallagher, C. S. Makinen, N. Harris, H. R. Uimari, O. Cook, J. P. Shigesi, N. Rahmioglu, N. Ferreira, T. Velez-Edwards, D. R. Edwards, T. L. Ruhioglu, Z. Day, F. Becker, C. M. Karhunen, V. Martikainen, H. Jarvelin, M.-R. Cantor, R. M. Ridker, P. M. Terry, K. L. Buring, J. E. Gordon, S. D. Medland, S. E. Montgomery, G. W. Nyholt, D. R. Hinds, D. A. Tung, J. Y. the 23andMe Research team, Perry, J. R. B. Lind, P. A. Painter, J. N. Martin, N. G. Morris, A. P. Chasman, D. I. Missmer, S. Zondervan, K. T. Morton, C. C. 2018-05-18 doi:10.1101/324905 Cold Spring Harbor Laboratory Press 2018-05-18 <![CDATA[ Visualizing APP trafficking and processing reveals its association with neuronal membrane cholesterol ]]> https://biorxiv.org/content/10.1101/328419v1?rss=1 DelBove, C. Strothman, C. Huang, H. Sanders, C. Zhang, Q. 2018-05-22 doi:10.1101/328419 Cold Spring Harbor Laboratory Press 2018-05-22 <![CDATA[ Adiposity-Independent Effects of Aging on Insulin Sensitivity and Clearance in Humans and Mice ]]> https://biorxiv.org/content/10.1101/333997v1?rss=1 Ehrhardt, N. Cui, J. Dagdeviren, S. Saengnipanthkul, S. Goodridge, H. S. Kim, J. K. Lantier, L. Guo, X. Chen, Y.-D. I. Raffel, L. J. Buchanan, T. A. Hsueh, W. A. Rotter, J. I. Goodarzi, M. O. Peterfy, M. 2018-05-30 doi:10.1101/333997 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ Notch Controls Multiple Pancreatic Cell Fate Regulators Through Direct Hes1-mediated Repression ]]> https://biorxiv.org/content/10.1101/336305v1?rss=1 de Lichtenberg, K. H. Seymour, P. A. Jorgensen, M. C. Kim, Y.-H. Grapin-Botton, A. Magnuson, M. Nakic, N. Ferrer, J. Serup, P. 2018-06-01 doi:10.1101/336305 Cold Spring Harbor Laboratory Press 2018-06-01 <![CDATA[ Molecular basis for the evolution of species-specific hemoglobin capture by pathogenic Staphylococcus ]]> https://biorxiv.org/content/10.1101/339705v1?rss=1 Choby, J. E. Buechi, H. B. Farrand, A. J. Skaar, E. P. Barber, M. F. 2018-06-07 doi:10.1101/339705 Cold Spring Harbor Laboratory Press 2018-06-07 <![CDATA[ Pulling the covers in electronic health records for an association study with self-reported sleep behaviors ]]> https://biorxiv.org/content/10.1101/341552v1?rss=1 Rhoades, S. D. Bastarache, L. Denny, J. C. Hughey, J. J. 2018-06-09 doi:10.1101/341552 Cold Spring Harbor Laboratory Press 2018-06-09 <![CDATA[ Kinesin Binding Protein (KBP) buffers the activity of Kif18A and Kif15 in mitosis to ensure accurate chromosome segregation ]]> https://biorxiv.org/content/10.1101/343046v1?rss=1 Malaby, H. Dumas, M. Ohi, R. Stumpff, J. 2018-06-08 doi:10.1101/343046 Cold Spring Harbor Laboratory Press 2018-06-08 <![CDATA[ Identification of Novel Common Breast Cancer Risk Variants in Latinas at the 6q25 Locus ]]> https://biorxiv.org/content/10.1101/343806v1?rss=1 Hoffman, J. Fejerman, L. Hu, D. Hunstman, S. Li, M. John, E. Torres-Mejia, G. Kushi, L. Ding, Y. C. Weitzel, J. Neuhausen, S. Lott, P. COLUMBUS Consortium, Echeverry, M. Carvajal-Carmona, L. Burchard, E. Eng, C. Long, J. Zheng, W. Olopade, O. Huo, D. Haiman, C. Ziv, E. 2018-06-11 doi:10.1101/343806 Cold Spring Harbor Laboratory Press 2018-06-11 <![CDATA[ PROTEIN-CODING VARIANTS IMPLICATE NOVEL GENES RELATED TO LIPID HOMEOSTASIS CONTRIBUTING TO BODY FAT DISTRIBUTION ]]> https://biorxiv.org/content/10.1101/352674v1?rss=1 Justice, A. E. Karaderi, T. Highland, H. M. Young, K. L. Graff, M. Lu, Y. Turcot, V. Auer, P. L. Fine, R. S. Guo, X. Schurmann, C. Lempradl, A. Marouli, E. Mahajan, A. Winkler, T. W. Locke, A. E. Medina-Gomez, C. Esko, T. Vedantam, S. Giri, A. Lo, K. S. Alfred, T. Mudgal, P. Ng, M. C. Heard-Costa, N. C. Feitosa, M. F. Manning, A. K. Willems, S. M. Sivapalaratnam, S. Abecasis, G. Alam, D. S. Allison, M. Amouyel, P. Arzumanyan, Z. Balkau, B. Bastarache, L. Bergmann, S. Bielak, L. F. Blüher, M. Boehnke, M. Boeing, H. Boerwinkle, E. Böger, 2018-06-30 doi:10.1101/352674 Cold Spring Harbor Laboratory Press 2018-06-30 <![CDATA[ Differential regional decline in dopamine receptor availability across adulthood: Linear and nonlinear effects of age ]]> https://biorxiv.org/content/10.1101/358200v1?rss=1 Seaman, K. L. Juarez, E. J. Smith, C. Dang, L. C. Castrellon, J. Burgess, L. L. San Juan, M. D. Kundzicz, P. M. Cowan, R. L. Zald, D. H. Samanez-Larkin, G. 2018-06-29 doi:10.1101/358200 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ GWAS of QRS Duration Identifies New Loci Specific to Hispanic/Latino Populations ]]> https://biorxiv.org/content/10.1101/363457v1?rss=1 Swenson, B. Louie, T. Lin, H. J. Mendez-Gairldez, R. Below, J. E. Laurie, C. C. Kerr, K. F. Highland, H. Thornton, T. A. Ryckman, K. K. Kooperberg, C. Soliman, E. Z. Seyerle, A. A. Guo, X. Taylor, K. D. Yao, J. Heckbert, S. R. Darbar, D. Petty, L. E. McKnight, B. Cheng, S. Bello, N. A. Whitsel, E. A. Hanis, C. L. Nalls, M. A. Evans, D. S. Rotter, J. I. Sofer, T. Avery, C. Sotoodehnia, N. 2018-07-06 doi:10.1101/363457 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants ]]> https://biorxiv.org/content/10.1101/366856v1?rss=1 Wagner, A. H. Walsh, B. Mayfield, G. Tamborero, D. Sonkin, D. Krysiak, K. Deu Pons, J. Duren, R. Gao, J. McMurry, J. Patterson, S. Del Vecchio Fitz, C. Sezerman, O. U. Warner, J. Rieke, D. T. Aittokallio, T. Cerami, E. Ritter, D. Schriml, L. M. Haendel, M. Raca, G. Madhavan, S. Baudis, M. Beckmann, J. S. Dienstmann, R. Chakravarty, D. Li, X. S. Mockus, S. M. Elemento, O. Schultz, N. Lopez-Bigas, N. Lawler, M. Goecks, J. Griffith, M. Griffith, O. L. Margolin, A. 2018-07-11 doi:10.1101/366856 Cold Spring Harbor Laboratory Press 2018-07-11 <![CDATA[ Growth Factor Independent 1 is a tumor suppressor gene in colorectal cancer ]]> https://biorxiv.org/content/10.1101/370585v1?rss=1 Chen, M.-S. Lo, Y.-H. Chen, X. Williams, C. Donnelly, J. Criss, Z. Patel, S. Butkus, J. Shroyer, N. 2018-07-16 doi:10.1101/370585 Cold Spring Harbor Laboratory Press 2018-07-16 <![CDATA[ Applying Inter-rater Reliability to Improve Consistency in Classifying PhD Career Outcomes ]]> https://biorxiv.org/content/10.1101/370783v1?rss=1 Stayart, C. A. Brandt, P. Brown, A. Hutto, T. Layton, R. Petrie, K. A. Flores-Kim, E. N. Pena, C. G. Fuhrmann, C. N. Monsalve, G. C. 2018-07-19 doi:10.1101/370783 Cold Spring Harbor Laboratory Press 2018-07-19 <![CDATA[ Quantitative Interactome Proteomics Reveals a Molecular Basis for ATF6-Dependent Regulation of a Destabilized Amyloidogenic Protein ]]> https://biorxiv.org/content/10.1101/381525v1?rss=1 Plate, L. Rius, B. Nguyen, B. Genereux, J. Kelly, J. W. Wiseman, R. L. 2018-07-31 doi:10.1101/381525 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ Individual differences in dopamine are associated with reward discounting in clinical groups but not in healthy adults ]]> https://biorxiv.org/content/10.1101/383810v1?rss=1 Castrellon, J. J. Seaman, K. L. Crawford, J. L. Young, J. S. Smith, C. T. Dang, L. C. Hsu, M. Cowan, R. L. Zald, D. H. Samanez-Larkin, G. R. 2018-08-02 doi:10.1101/383810 Cold Spring Harbor Laboratory Press 2018-08-02 <![CDATA[ Reconciling fMRI and EEG indices of attentional modulations in human visual cortex ]]> https://biorxiv.org/content/10.1101/391193v1?rss=1 Itthipuripat, S. Sprague, T. Serences, J. 2018-08-13 doi:10.1101/391193 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ Limits to anatomical accuracy of diffusion tractography using modern approaches ]]> https://biorxiv.org/content/10.1101/392571v1?rss=1 Schilling, K. G. Nath, V. Hansen, C. Parvathaneni, P. Blaber, J. Gao, Y. Neher, P. Aydogan, D. B. Shi, Y. Ocampo-Pineda, M. Schiavi, S. Daducci, A. Girard, G. Barakovic, M. Rafael-Patino, J. Romascano, D. Rensonnet, G. Pizzolato, M. Bates, A. Fischi, E. Thiran, J.-P. Canales-Rodriguez, E. J. Huang, C. Zhu, H. Zhong, L. Cabeen, R. Toga, A. W. Rheault, F. Theaud, G. Houde, J.-C. Sidhu, J. Chamberland, M. Westin, C.-F. Dyrby, T. B. Verma, R. Rathi, Y. Irfanoglu, M. O. Thomas, C. Pierpaoli, C. Descoteaux, M. Anderson, A. W. Landman, B. A. 2018-08-16 doi:10.1101/392571 Cold Spring Harbor Laboratory Press 2018-08-16 <![CDATA[ Protein-Ligand Docking with Protein-based and Ligand-based Structure Activity Relationships ]]> https://biorxiv.org/content/10.1101/394874v1?rss=1 Fu, D. Y. Meiler, J. 2018-08-18 doi:10.1101/394874 Cold Spring Harbor Laboratory Press 2018-08-18 <![CDATA[ Eukaryotic acquisition of a bacterial operon ]]> https://biorxiv.org/content/10.1101/399394v1?rss=1 Kominek, J. Doering, D. T. Opulente, D. A. Shen, X.-X. Zhou, X. DeVirgilio, J. Hulfachor, A. B. Kurtzman, C. P. Rokas, A. Hittinger, C. T. 2018-08-24 doi:10.1101/399394 Cold Spring Harbor Laboratory Press 2018-08-24 <![CDATA[ Cross-cancer pleiotropic associations with lung cancer risk in African Americans ]]> https://biorxiv.org/content/10.1101/405035v1?rss=1 Jones, C. C. Bradford, Y. Amos, C. I. Blot, W. J. Chanock, S. J. Harris, C. C. Schwartz, A. G. Spitz, M. R. Wiencke, J. K. Wrensch, M. R. Wu, X. Aldrich, M. C. 2018-08-31 doi:10.1101/405035 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ Contribution of rare copy number variants to bipolar disorder risk is limited to schizoaffective cases ]]> https://biorxiv.org/content/10.1101/406215v1?rss=1 Charney, A. W. Stahl, E. A. Green, E. K. Chen, C.-Y. Moran, J. L. Chambert, K. Belliveau, R. A. Forty, L. Gordon-Smith, K. Lee, P. H. Bromet, E. J. Buckley, P. F. Escamilla, M. A. Fanous, A. H. Fochtmann, L. J. Lehrer, D. S. Malaspina, D. Marder, S. R. Morley, C. P. Nicolini, H. Perkins, D. O. Rakofsky, J. J. Rapaport, M. H. Medeiros, H. Sobell, J. L. Backlund, L. Bergen, S. E. Jureus, A. Schalling, M. Lichtenstein, P. Knowles, J. A. Burdick, K. E. Jones, I. Jones, L. A. Hultman, C. A. Perlis, R. Purcell, S. M. McCarroll, S. A. Pato, C. N. Pato, M. T. Di 2018-09-03 doi:10.1101/406215 Cold Spring Harbor Laboratory Press 2018-09-03 <![CDATA[ Prioritizing risk genes for neurodevelopmental disorders using pathway information ]]> https://biorxiv.org/content/10.1101/410100v1?rss=1 0.95), 6 of which replicate in an independent whole-genome sequencing study. In addition, 30/40 genes are novel genes. We found that epilepsy genes had high protein-protein interaction (PPI) network connectivity, and show specific expression during human brain development. Some of the top prioritized EPI genes were connected to a PPI subnetwork of immune genes and show specific expression in prenatal microglia. We also identified multiple enriched drug-target gene sets for EPI which included immunostimulants as well as known antiepileptics. Immune biology was supported specifically by case-control variants from familial epilepsies rather than do novo mutations in generalized encephalitic epilepsy. ]]> Nguyen, H. T. Dobbyn, A. Charney, A. Bryois, J. Skene, N. G. Huckins, L. M. Wang, W. Ruderfer, D. M. Xu, X. Fromer, M. Purcell, S. M. Verhage, M. Smit, A. B. Hjerling-Leffler, J. Buxbaum, J. Pinto, D. He, X. Sullivan, P. F. Stahl, E. A. 2018-09-09 doi:10.1101/410100 Cold Spring Harbor Laboratory Press 2018-09-09 <![CDATA[ Gut microbial compositions mirror caste-specific diets in a major lineage of eusocial insects ]]> https://biorxiv.org/content/10.1101/418954v1?rss=1 Otani, S. Zhukova, M. Abdoulaye Kone, N. da Costa, R. R. Mikaelyan, A. Sapountzis, P. Poulsen, M. 2018-09-16 doi:10.1101/418954 Cold Spring Harbor Laboratory Press 2018-09-16 <![CDATA[ The speed-accuracy tradeoff reveals flexible access to accumulating sensory evidence during human decision making ]]> https://biorxiv.org/content/10.1101/420430v1?rss=1 Nelli, S. Itthipuripat, S. Rungratsameetaweemana, N. Serences, J. 2018-09-17 doi:10.1101/420430 Cold Spring Harbor Laboratory Press 2018-09-17 <![CDATA[ Penetrance and pleiotropy of polygenic risk scores for schizophrenia in 90,000 patients across three healthcare systems ]]> https://biorxiv.org/content/10.1101/421164v1?rss=1 Zheutlin, A. B. Dennis, J. Restrepo, N. Straub, P. Ruderfer, D. Castro, V. M. Chen, C.-Y. Kirchner, H. L. Chabris, C. F. Davis, L. K. Smoller, J. W. 2018-09-18 doi:10.1101/421164 Cold Spring Harbor Laboratory Press 2018-09-18 <![CDATA[ High local mutual information drives the response in the human language network ]]> https://biorxiv.org/content/10.1101/436204v1?rss=1 Mollica, F. Siegelman, M. Diachek, E. Piantadosi, S. T. Mineroff, Z. Futrell, R. Fedorenko, E. 2018-10-08 doi:10.1101/436204 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ Potent anti-influenza H7 human monoclonal antibody induces separation of hemagglutinin receptor binding head domains ]]> https://biorxiv.org/content/10.1101/436642v1?rss=1 Turner, H. L. Pallesen, J. Lang, S. Bangaru, S. Urata, S. Li, S. Cottrell, C. A. Bowman, C. A. Crowe, J. E. Wilson, I. A. Ward, A. B. 2018-10-05 doi:10.1101/436642 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ Histologically derived fiber response functions for diffusion MRI vary across white matter fibers - an ex vivo validation study in the squirrel monkey brain ]]> https://biorxiv.org/content/10.1101/438978v1?rss=1 Schilling, K. G. Gao, Y. Stepniewska, I. Janve, V. Landman, B. A. Anderson, A. W. 2018-10-09 doi:10.1101/438978 Cold Spring Harbor Laboratory Press 2018-10-09 <![CDATA[ Longitudinal Visual Analytics for Unpacking the Cancer Journey ]]> https://biorxiv.org/content/10.1101/444356v1?rss=1 Yuan, Z. Finan, S. Warner, J. Savova, G. Hochheiser, H. 2018-10-16 doi:10.1101/444356 Cold Spring Harbor Laboratory Press 2018-10-16 <![CDATA[ Calculating the Effects of Autism Risk Gene Variants on Dysfunction of Biological Processes Identifies Clinically-Useful Information ]]> https://biorxiv.org/content/10.1101/449819v1?rss=1 Veatch, O. J. Mazzotti, D. R. Sutcliffe, J. S. Schultz, R. T. Abel, T. Tunc, B. Assouline, S. G. Brodkin, E. S. Michaelson, J. J. Nickl-Jockschat, T. Warren, Z. E. Malow, B. A. Pack, A. I. 2018-10-22 doi:10.1101/449819 Cold Spring Harbor Laboratory Press 2018-10-22 <![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[ Sub-diffusive dynamics lead to depleted particle densities near cellular borders ]]> https://biorxiv.org/content/10.1101/458224v1?rss=1 Holmes, W. 2018-10-31 doi:10.1101/458224 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ Chronic intermittent ethanol and acute stress similarly modulate BNST CRF neuron activity via noradrenergic signaling ]]> https://biorxiv.org/content/10.1101/458349v1?rss=1 Snyder, A. E. Winder, D. G. Silberman, Y. 2018-10-31 doi:10.1101/458349 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ Genetic variants related to antihypertensive targets inform drug efficacy and side effects ]]> https://biorxiv.org/content/10.1101/460543v1?rss=1 Gill, D. Georgakis, M. K. Koskeridis, F. Jiang, L. Feng, Q. Wei, W.-Q. Theodoratou, E. Elliott, P. Denny, J. C. Malik, R. Evangelou, E. Dehghan, A. Dichgans, M. Tzoulaki, I. 2018-11-05 doi:10.1101/460543 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ Developing and Evaluating Mappings of ICD-10 and ICD-10-CM codes to Phecodes ]]> https://biorxiv.org/content/10.1101/462077v1?rss=1 75% of ICD-10-CM and ICD-10 codes to PheCodes. Of the unique codes observed in the VUMC (ICD-10-CM) and UKBB (ICD-10) cohorts, >90% were mapped to PheCodes. We observed 70-75% reproducibility for chronic diseases and <10% for an acute disease. A PheWAS with a lipoprotein(a) (LPA) genetic variant, rs10455872, using the ICD-9-CM and ICD-10-CM maps replicated two genotype-phenotype associations with similar effect sizes: coronary atherosclerosis (ICD-9-CM: P < .001, OR = 1.60 vs. ICD-10-CM: P < .001, OR = 1.60) and with chronic ischemic heart disease (ICD-9-CM: P < .001, OR = 1.5 vs. ICD-10-CM: P < .001, OR = 1.47).nnConclusionsThis study introduces the initial "beta" versions of ICD-10 and ICD-10-CM to PheCode maps that will enable researchers to leverage accumulated ICD-10 and ICD-10-CM data for high-throughput PheWAS in the EHR. ]]> Wu, P. Gifford, A. Meng, X. Li, X. Campbell, H. Varley, T. Zhao, J. Bastarache, L. Denny, J. C. Theodoratou, E. Wei, W.-Q. 2018-11-05 doi:10.1101/462077 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ The association between weight at birth and breast cancer risk revisited using Mendelian randomisation ]]> https://biorxiv.org/content/10.1101/464115v1?rss=1 Kar, S. P. Andrulis, I. L. Brenner, H. Burgess, S. Chang-Claude, J. Considine, D. Doerk, T. Evans, D. G. R. Gago-Dominguez, M. Giles, G. G. Hartman, M. Huo, D. Kaaks, R. Li, J. Lophatananon, A. Margolin, S. Milne, R. L. Muir, K. R. Olsson, H. Punie, K. Radice, P. Simard, J. Tamimi, R. M. Van Nieuwenhuysen, E. Wendt, C. Wei, Z. Pharoah, P. D. P. 2018-11-09 doi:10.1101/464115 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ The association between low-density lipoprotein cholesterol predicted by HMGCR genetic variants and breast cancer risk may be mediated by body mass index ]]> https://biorxiv.org/content/10.1101/464446v1?rss=1 Kar, S. P. Brenner, H. Giles, G. G. Huo, D. Milne, R. L. Rennert, G. Simard, J. Zheng, W. Burgess, S. Pharoah, P. D. P. 2018-11-09 doi:10.1101/464446 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ Biobank-wide association scan identifies risk factors for late-onset Alzheimer’s disease and endophenotypes ]]> https://biorxiv.org/content/10.1101/468306v1?rss=1 Yan, D. Hu, B. Darst, B. F. Mukherjee, S. Kunkle, B. W. Deming, Y. Dumitrescu, L. Wang, Y. Naj, A. Kuzma, A. Zhao, Y. Kang, H. Johnson, S. C. Cruchaga, C. Hohman, T. J. Crane, P. Engelman, C. D. Alzheimer's Disease Genetics Consortium, Lu, Q. 2018-11-12 doi:10.1101/468306 Cold Spring Harbor Laboratory Press 2018-11-12 <![CDATA[ Evaluating causal associations between previously reported risk factors and epithelial ovarian cancer: a Mendelian randomization analysis ]]> https://biorxiv.org/content/10.1101/472696v1?rss=1 Yarmolinsky, J. Relton, C. L. Lophatananon, A. Muir, K. Menon, U. Gentry-Maharaj, A. Walther, A. Zheng, J. Fasching, P. Zheng, W. Woo, Y. L. Chang-Claude, J. Modugno, F. Park, S. K. Kim, B.-G. Choi, J.-Y. Park, B. Davey Smith, G. Martin, R. Lewis, S. 2018-11-19 doi:10.1101/472696 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ On Using Local Ancestry to Characterize the Genetic Architecture of Human Phenotypes: Genetic Regulation of Gene Expression in Multiethnic or Admixed Populations as a Model ]]> https://biorxiv.org/content/10.1101/483107v1?rss=1 Zhong, Y. Perera, M. A. Gamazon, E. R. 2018-11-29 doi:10.1101/483107 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ Activation of intracellular transport by relieving KIF1C autoinhibition ]]> https://biorxiv.org/content/10.1101/488049v1?rss=1 Siddiqui, N. Bachmann, A. Zwetsloot, A. J. Hussain, H. Roth, D. Kaverina, I. Straube, A. 2018-12-06 doi:10.1101/488049 Cold Spring Harbor Laboratory Press 2018-12-06 <![CDATA[ Longitudinal prediction of outcome in idiopathic pulmonary fibrosis using automated CT analysis ]]> https://biorxiv.org/content/10.1101/493544v1?rss=1 Jacob, J. Bartholmai, B. J. van Moorsel, C. H. M. Rajagopalan, S. Devaraj, A. van Es, H. W. Moua, T. van Beek, F. T. Clay, R. Veltkamp, M. Kokosi, M. de Lauretis, A. Judge, E. P. Burd, T. Peikert, T. Karwoski, R. Maldonado, F. Renzoni, E. Maher, T. M. Altmann, A. Wells, A. U. 2018-12-13 doi:10.1101/493544 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Reliability of the correlative triad among aging, dopamine D2-like receptor availability, and cognition ]]> https://biorxiv.org/content/10.1101/494765v1?rss=1 Juarez, E. J. Castrellon, J. J. Green, M. A. Crawford, J. L. Seaman, K. L. Smith, C. T. Dang, L. C. Matuskey, D. Morris, E. D. Cowan, R. L. Zald, D. H. Samanez-Larkin, G. R. 2018-12-13 doi:10.1101/494765 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Simphony: simulating large-scale, rhythmic data ]]> https://biorxiv.org/content/10.1101/497859v1?rss=1 Singer, J. M. Fu, D. Y. Hughey, J. J. 2018-12-17 doi:10.1101/497859 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ Inhibition of miR-22-3p reduces kidney disease associated with systemic lupus erythematosus ]]> https://biorxiv.org/content/10.1101/512848v1?rss=1 Michell, D. L. Faust, A. Moore, J. L. Appleton, B. D. Ormseth, M. Ramirez-Solano, M. Sheng, Q. Solus, J. F. Stein, C. M. Vickers, K. C. Major, A. S. 2019-01-07 doi:10.1101/512848 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ Hip circumduction is not a compensation for reduced knee flexion angle during gait ]]> https://biorxiv.org/content/10.1101/520684v1?rss=1 Akbas, T. Prajapati, S. Ziemnicki, D. Tamma, P. Gross, S. Sulzer, J. 2019-01-15 doi:10.1101/520684 Cold Spring Harbor Laboratory Press 2019-01-15 <![CDATA[ Fine-mapping of 150 breast cancer risk regions identifies 178 high confidence target genes ]]> https://biorxiv.org/content/10.1101/521054v1?rss=1 Fachal, L. Aschard, H. Beesley, J. Barnes, D. Allen, J. Kar, S. Pooley, K. Dennis, J. Michailidou, K. Turman, C. Soucy, P. Lemacon, A. Lush, M. Tyrer, J. Ghoussaini, M. Moradi Marjaneh, M. Jiang, X. Agata, S. Aittomaki, K. Alonso, M. R. Andrulis, I. Anton-Culver, H. Antonenkova, N. Arason, A. Arndt, V. Aronson, K. Arun, B. Auber, B. Auer, P. Azzollini, J. Balmana, J. Barkardottir, R. Barrowdale, D. Beeghly-Fadiel, A. Benitez, J. Bermisheva, M. Bialkowska, K. Blanco, A. Blomqvist, C. Blot, W. Bogdanova, N. Bojesen, S. Bolla, M. Bonanni, B. Borg, A. B 2019-01-15 doi:10.1101/521054 Cold Spring Harbor Laboratory Press 2019-01-15 <![CDATA[ Scavenging dicarbonyls with 5'-O-pentyl-pyridoxamine improves insulin sensitivity and reduces atherosclerosis through modulating inflammatory Ly6Chi monocytosis and macrophage polarization ]]> https://biorxiv.org/content/10.1101/529339v1?rss=1 Huang, J. Yancey, P. G. May-Zhang, L. Tao, H. Zhang, Y. Ding, L. Oates, J. A. Amarnath, V. Roberts, J. L. Davies, S. S. Linton, M. F. 2019-02-02 doi:10.1101/529339 Cold Spring Harbor Laboratory Press 2019-02-02 <![CDATA[ Requirement for TRanslocon-Associated Protein (TRAP) α in insulin biogenesis ]]> https://biorxiv.org/content/10.1101/531491v1?rss=1 Li, X. Itani, O. A. Haataja, L. Dumas, K. J. Yang, J. Cha, J. Flibotte, S. Shih, H.-J. Xu, J. Qi, L. Arvan, P. Liu, M. Hu, P. J. 2019-01-26 doi:10.1101/531491 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Machine Learning Methods to Identify Genetic Correlates of Radiation-Associated Contralateral Breast Cancer in the WECARE Study ]]> https://biorxiv.org/content/10.1101/547422v1?rss=1 1 Gy to the contralateral breast. A previously reported algorithm, preconditioned random forest regression, was applied to predict the risk of developing RCBC. The resulting model produced an area under the curve of 0.62 (p=0.04) on hold-out validation data. The biological analysis identified the cyclic AMP-mediated signaling and Ephrin-A as significant biological correlates, which were previously shown to influence cell survival after radiation in an ATM-dependent manner. The key connected genes and proteins that are identified in this analysis were previously identified as relevant to breast cancer, radiation response, or both. In summary, machine learning/bioinformatics methods applied to genome-wide genotyping data have great potential to reveal plausible biological correlates associated with the risk of RCBC. ]]> Lee, S. Liang, X. Woods, M. Reiner, A. Thomas, D. Concannon, P. Bernstein, L. Lynch, C. Boice, J. Deasy, J. Bernstein, J. Oh, J. H. 2019-02-12 doi:10.1101/547422 Cold Spring Harbor Laboratory Press 2019-02-12 <![CDATA[ The yeast Art1 arrestin domain contains disordered insertions that regulate its localization and activity ]]> https://biorxiv.org/content/10.1101/553677v1?rss=1 Baile, M. G. Guiney, E. L. Sanford, E. J. MacGurn, J. A. Smolka, M. B. Emr, S. D. 2019-02-18 doi:10.1101/553677 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ Sox6: A new modulator of renin expression during physiological conditions ]]> https://biorxiv.org/content/10.1101/556118v1?rss=1 Saleem, M. Hodgkinson, C. P. Contreras, E. W. Xiao, L. Gimenez-Bastida, J. A. Foss, J. Payne, A. J. Mirotsou, M. Gama, V. Dzau, V. J. Gomez, J. A. 2019-02-20 doi:10.1101/556118 Cold Spring Harbor Laboratory Press 2019-02-20 <![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[ Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program ]]> https://biorxiv.org/content/10.1101/563866v1?rss=1 400 million single-nucleotide and insertion/deletion variants were detected by alignment with the reference genome. Additional novel variants are detectable through assembly of unmapped reads and customized analysis in highly variable loci. Among the >400 million variants detected, 97% have frequency <1% and 46% are singletons. These rare variants provide insights into mutational processes and recent human evolutionary history. The nearly complete catalog of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and non-coding sequence variants to phenotypic variation. Furthermore, combining TOPMed haplotypes with modern imputation methods improves the power and extends the reach of nearly all genome-wide association studies to include variants down to ~0.01% in frequency. ]]> Taliun, D. Harris, D. N. Kessler, M. D. Carlson, J. Szpiech, Z. A. Torres, R. Gagliano Taliun, S. A. Corvelo, A. Gogarten, S. M. Min Kang, H. Pitsillides, A. N. LeFaive, J. Lee, S.-b. Tian, X. Browning, B. L. Das, S. Emde, A.-K. Clarke, W. E. Loesch, D. P. Shetty, A. C. Blackwell, T. W. Wong, Q. Aguet, F. Albert, C. Alonso, A. Ardlie, K. G. Aslibekyan, S. Auer, P. L. Barnard, J. Barr, R. G. Becker, L. C. Beer, R. L. Benjamin, E. J. Bielak, L. F. Blangero, J. Boehnke, M. Bowden, D. W. Brody, J. A. Burchard, E. G. Cade, B. E. Casella, J. F. Chalazan, B. L 2019-03-06 doi:10.1101/563866 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ Signatures of divergent antimalarial treatment responses in peripheral blood from infants and adults in Malawi ]]> https://biorxiv.org/content/10.1101/564757v1?rss=1 18 years old), we assessed blood cytokine levels and characterized monocyte and dendritic cell frequencies at two timepoints: acute infection, and four weeks post antimalarial treatment. We modeled the effects of age group, sex, and timepoint, and evaluated the role of these factors on infection and treatment outcomes. ResultsRegardless of treatment timepoint, in our population age was significantly associated with overall blood hemoglobin, which was higher in adults, and plasma nitric oxide, IL-10, and TNF- levels, which were higher in infants. We found a significant effect of age on the hemoglobin treatment response, whereby after treatment, levels increased in infants and decreased in adults. Furthermore, we observed significant age-specific effects on treatment response for overall parasite load, IFN-{gamma} and IL-12(p40), and these effects were sex-dependent. We uncovered significant age effects on the overall levels and treatment response of myeloid dendritic cell frequencies. In addition, within each age group, we found continuous age effects on gametocyte levels (Pfs16), TNF-, and nitric oxide. ConclusionsIn a clinical study of infants and adults experiencing natural malaria infection and receiving antimalarial treatment, we identified age-specific signatures of infection and treatment responses in peripheral blood. We describe host markers that may indicate, and potentially mediate, differential post-treatment outcomes for malaria in infants versus adults. ]]> Maurizio, P. L. Fuseini, H. Tegha, G. Hosseinipour, M. De Paris, K. 2019-03-01 doi:10.1101/564757 Cold Spring Harbor Laboratory Press 2019-03-01 <![CDATA[ Value-driven attentional capture enhances distractor representations in early visual cortex ]]> https://biorxiv.org/content/10.1101/567354v1?rss=1 Itthipuripat, S. Vo, V. A. Sprague, T. C. Serences, J. 2019-03-04 doi:10.1101/567354 Cold Spring Harbor Laboratory Press 2019-03-04 <![CDATA[ Graphene nanoflakes for acute manipulation of membrane cholesterol and transmembrane signaling ]]> https://biorxiv.org/content/10.1101/581942v1?rss=1 Kitko, K. E. Hong, T. Lazarenko, R. M. Montenegro-Burke, R. J. Shah, A. T. Zhang, Y. Raghunathan, K. Kenworthy, A. K. Skala, M. C. McLean, J. A. Xu, Y.-Q. Zhang, Q. 2019-03-18 doi:10.1101/581942 Cold Spring Harbor Laboratory Press 2019-03-18 <![CDATA[ A distinct class of bursting neurons with strong gamma synchronization and stimulus selectivity in monkey V1 ]]> https://biorxiv.org/content/10.1101/583955v1?rss=1 Onorato, I. Neuenschwander, S. Hoy, J. Lima, B. Rocha, K.-S. Broggini, A. C. Uran, C. Spyropoulos, G. Womelsdorf, T. Fries, P. Niell, C. Singer, W. Vinck, M. 2019-03-21 doi:10.1101/583955 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Recovery of trait heritability from whole genome sequence data ]]> https://biorxiv.org/content/10.1101/588020v1?rss=1 Wainschtein, P. Jain, D. P. Yengo, L. Zheng, Z. TOPMed Anthropometry Working Group, Trans-Omics for Precision Medicine Consortium, Cupples, L. A. Shadyab, A. H. McKnight, B. Shoemaker, B. M. Mitchell, B. D. Psaty, B. M. Kooperberg, C. Roden, D. Darbar, D. Arnett, D. K. Regan, E. A. Boerwinkle, E. Rotter, J. I. Allison, M. A. McDonald, M.-L. N. Chung, M. K. Smith, N. L. Ellinor, P. T. Vasan, R. S. Mathias, R. A. Rich, S. S. Heckbert, S. R. Redline, S. Guo, X. Chen, Y.-D. I. Liu, C.-T. Andrade, M. d. Yanek, L. R. Albert, C. M. Hernandez, R. D. McGarvey, S. 2019-03-25 doi:10.1101/588020 Cold Spring Harbor Laboratory Press 2019-03-25 <![CDATA[ A Gene Co-expression Network-based Analysis of Multiple Brain Tissues Reveals Novel Genes and Molecular Pathways Underlying Major Depression ]]> https://biorxiv.org/content/10.1101/591693v1?rss=1 Gerring, Z. F. Derks, E. Major Depressive Disorder Working Group of the Psy, Gamazon, E. 2019-03-28 doi:10.1101/591693 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ A missense variant in Mitochondrial Amidoxime Reducing Component 1 gene and protection against liver disease ]]> https://biorxiv.org/content/10.1101/594523v1?rss=1 Emdin, C. A. Haas, M. Khera, A. V. Aragam, K. Chaffin, M. Jiang, L. Wei, W.-Q. Feng, Q. Karjalainen, J. Havulinna, A. Kiiskinen, T. Bick, A. Ardissino, D. Wilson, J. G. Schunkert, H. McPherson, R. Watkins, H. Elosua, R. Bown, M. J. Samani, N. J. Baber, U. Erdmann, J. Gupta, N. Danesh, J. Saleheen, D. Daly, M. Denny, J. Gabriel, S. Kathiresan, S. 2019-03-31 doi:10.1101/594523 Cold Spring Harbor Laboratory Press 2019-03-31 <![CDATA[ Protein structure prediction using sparse NOE and RDC restraints with Rosetta in CASP13 ]]> https://biorxiv.org/content/10.1101/597724v1?rss=1 45) and in three cases high-resolution models were achieved (RMSD <3.5 [A]). We also show that a meta-approach applying iterative Rosetta+NMR refinement on server-predicted models which employed non-NMR-contacts and structural templates leads to substantial improvement in model quality. Integrating these data-assisted refinement strategies with innovative non-data-assisted approaches which became possible in CASP13 such as high precision contact prediction will in the near future enable structure determination for large proteins that are outside of the realm of conventional NMR. ]]> Kuenze, G. Meiler, J. 2019-04-03 doi:10.1101/597724 Cold Spring Harbor Laboratory Press 2019-04-03 <![CDATA[ Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints ]]> https://biorxiv.org/content/10.1101/597872v1?rss=1 Kuenze, G. Bonneau, R. Koehler Leman, J. Meiler, J. 2019-04-03 doi:10.1101/597872 Cold Spring Harbor Laboratory Press 2019-04-03 <![CDATA[ Cox regression increases power to detect genotype-phenotype associations in genomic studies using the electronic health record ]]> https://biorxiv.org/content/10.1101/599910v1?rss=1 Hughey, J. J. Rhoades, S. D. Fu, D. Y. Bastarache, L. Denny, J. C. Chen, Q. 2019-04-05 doi:10.1101/599910 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ Not just one p: Multivariate GWAS of psychiatric disorders and their cardinal symptoms reveal two dimensions of cross-cutting genetic liabilities ]]> https://biorxiv.org/content/10.1101/603134v1?rss=1 Mallard, T. T. Karlsson Linner, R. Okbay, A. Grotzinger, A. D. de Vlaming, R. Meddens, S. F. W. Tucker-Drob, E. M. Kendler, K. Keller, M. C. Koellinger, P. D. Harden, K. P. 2019-04-09 doi:10.1101/603134 Cold Spring Harbor Laboratory Press 2019-04-09 <![CDATA[ Coupling metastasis to pH sensing G Protein-coupled receptor-68 through first in class inhibitor identified in an in vivo chemical genetic screen ]]> https://biorxiv.org/content/10.1101/612549v1?rss=1 Williams, C. H. Thayer, T. Keyesr, B. Wani, M. Wells, Q. Hong, C. C. 2019-04-17 doi:10.1101/612549 Cold Spring Harbor Laboratory Press 2019-04-17 <![CDATA[ A Phenome-wide Mendelian Randomisation study on genetically determined serum urate levels in UK Biobank cohort ]]> https://biorxiv.org/content/10.1101/630293v1?rss=1 Li, X. Meng, X. He, Y. Spiliopoulou, A. Timofeeva, M. Wei, W.-Q. Gifford, A. Yang, T. Varley, T. Tzoulaki, I. Joshi, P. Denny, J. C. Mckeigue, P. Campbell, H. Theodoratou, E. 2019-05-10 doi:10.1101/630293 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Dietary restriction improves fitness of ageing parents but reduces fitness of their offspring ]]> https://biorxiv.org/content/10.1101/632026v1?rss=1 Mautz, B. Lind, M. Maklakov, A. 2019-05-08 doi:10.1101/632026 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Immune-mediated genetic pathways resulting in pulmonary function impairment increase lung cancer susceptibility ]]> https://biorxiv.org/content/10.1101/635318v1?rss=1 Kachuri, L. Johansson, M. Rashkin, S. R. Graff, R. E. Bosse, Y. Manem, V. Caporaso, N. E. Landi, M. T. Christiani, D. C. Vineis, P. Liu, G. Scelo, G. Zaridze, D. Shete, S. S. Albanes, D. Aldrich, M. C. Tardon, A. Rennert, G. Chen, C. Goodman, G. E. Doherty, J. A. Bickeboller, H. Field, J. K. Davies, M. P. Teare, M. D. Kiemeney, L. A. Bojesen, S. E. Haugen, A. Zienolddiny, S. Lam, S. Le Marchand, L. Cheng, I. Schabath, M. B. Duell, E. J. Andrew, A. S. Manjer, J. Lazarus, P. Arnold, S. McKay, J. D. Emami, N. C. Warkentin, M. T. Brhane, Y. Obeidat, M. Ma 2019-05-11 doi:10.1101/635318 Cold Spring Harbor Laboratory Press 2019-05-11 <![CDATA[ High throughput Characterization of KCNB1 variants Associated with Developmental and Epileptic Encephalopathy ]]> https://biorxiv.org/content/10.1101/637041v1?rss=1 Kang, S. K. Vanoye, C. G. Misra, S. N. Echevarria, D. M. Calhoun, J. D. O'Connor, J. B. Fabre, K. L. McKnight, D. Demmer, L. Goldenberg, P. Grote, L. E. Thiffault, I. Saunders, C. Strauss, K. A. Torkamani, A. van der Smagt, J. van Gassen, K. Carson, R. P. Diaz, J. Leon, E. Jacher, J. E. Hannibal, M. C. Litwin, J. Friedman, N. R. Schreiber, A. Lynch, B. Poduri, A. Marsh, E. D. Goldberg, E. M. Millichap, J. J. George, A. L. Kearney, J. 2019-05-14 doi:10.1101/637041 Cold Spring Harbor Laboratory Press 2019-05-14 <![CDATA[ Public health in genetic spaces: a statistical framework to optimize cluster-based outbreak detection ]]> https://biorxiv.org/content/10.1101/639997v1?rss=1 50). These results demonstrate that one cannot rely on historical precedence or convention to configure genetic clustering methods for public health applications. Our framework not only provides an objective procedure to optimize a clustering method, but can also be used for variable selection in forecasting new cases. ]]> Chato, C. Poon, A. 2019-05-17 doi:10.1101/639997 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Rapid phenotypic and metabolomic domestication of wild Penicillium molds on cheese ]]> https://biorxiv.org/content/10.1101/647172v1?rss=1 Bodinaku, I. Shaffer, J. Connors, A. Steenwyk, J. Kastman, E. Rokas, A. Robbat, A. Wolfe, B. 2019-05-23 doi:10.1101/647172 Cold Spring Harbor Laboratory Press 2019-05-23 <![CDATA[ Upgraded molecular models of the human KCNQ1 potassium channel ]]> https://biorxiv.org/content/10.1101/648634v1?rss=1 Kuenze, G. Duran, A. M. Woods, H. Brewer, K. R. McDonald, E. F. Vanoye, C. G. George, A. L. Sanders, C. R. Meiler, J. 2019-05-24 doi:10.1101/648634 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ The methyl cycle is a conserved regulator of biological clocks. ]]> https://biorxiv.org/content/10.1101/653667v1?rss=1 Fustin, J.-M. Ye, S. Rakers, C. Versteven, M. Cargill, S. J. Tamai, K. T. Xu, Y. Jabbur, M. L. Kojima, R. Lamberti, M. L. Whitmore, D. Stanewsky, R. Kageyama, R. Matsuo, T. Yoshioka-Kobayashi, K. Golombek, D. A. Johnson, C. H. van Ooijen, G. Okamura, H. 2019-05-29 doi:10.1101/653667 Cold Spring Harbor Laboratory Press 2019-05-29 <![CDATA[ Entorhinal velocity signals reflect environmental geometry ]]> https://biorxiv.org/content/10.1101/671222v1?rss=1 Munn, R. G. K. Mallory, C. S. Hardcastle, K. Chetkovich, D. M. Giocomo, L. M. 2019-06-14 doi:10.1101/671222 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ Genome-wide association study provides new insights into the genetic architecture and pathogenesis of heart failure ]]> https://biorxiv.org/content/10.1101/682013v1?rss=1 Shah, S. Henry, A. Roselli, C. Lin, H. Sveinbjörnsson, G. Fatemifar, G. Hedman, A. K. Wilk, J. B. Morley, M. P. Chaffin, M. D. Helgadottir, A. Verweij, N. Dehghan, A. Almgren, P. Anderson, C. Aragam, K. G. Ärnlöv, J. Backman, J. D. Biggs, M. L. Bloom, H. L. Brandimarto, J. Broad AF Investigators, Brown, M. R. Buckbinder, L. Carey, D. J. Regeneron Genetics Center, Chasman, D. I. Chen, X. Chen, X. Chung, J. Chutkow, W. Cook, J. P. Delgado, G. E. Denaxas, S. Doney, A. S. Dörr, M. Dudley, S. C. Dunn, M. E. EchoGen Consortium, Engström, G. Esko, T. 2019-07-10 doi:10.1101/682013 Cold Spring Harbor Laboratory Press 2019-07-10 <![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[ Releasing a preprint is associated with more attention and citations ]]> https://biorxiv.org/content/10.1101/699652v1?rss=1 Fu, D. Y. Hughey, J. J. 2019-07-13 doi:10.1101/699652 Cold Spring Harbor Laboratory Press 2019-07-13 <![CDATA[ Gclc deletion in surface-ectoderm tissues induces microphthalmia ]]> https://biorxiv.org/content/10.1101/700591v1?rss=1 Thompson, B. Chen, Y. Philippe, J. Anderson, D. Prakash, J. G. Davidson, E. Apostolopoulos, N. Schey, K. Katsanis, N. Orlicky, D. J. Thompson, D. Vasiliou, V. 2019-07-13 doi:10.1101/700591 Cold Spring Harbor Laboratory Press 2019-07-13 <![CDATA[ Multi-ancestry GWAS of the electrocardiographic PR interval identifies 210 loci underlying cardiac conduction ]]> https://biorxiv.org/content/10.1101/712398v1?rss=1 Ntalla, I. Weng, L.-C. Cartwright, J. H. Hall, A. Sveinbjornsson, G. Tucker, N. R. Seung Young, C. Chaffin, M. D. Roselli, C. Barnes, M. R. Mifsud, B. Warren, H. R. Hayward, C. Marten, J. Cranley, J. J. Concas, M. P. Gasparini, P. Boutin, T. Kolcic, I. Polasek, O. Rudan, I. Araujo, N. M. Lima-Costa, M. F. Ribeiro, A. L. P. Souza, R. P. Tarazona-Santos, E. Giedraitis, V. Ingelsson, E. Mahajan, A. Morris, A. P. Del Greco M., F. Foco, L. Gogele, M. Hicks, A. A. Cook, J. P. Lind, L. Lindgren, C. M. Sundstrom, J. Nelson, C. P. Riaz, M. B. Samani, N. J. Sinag 2019-07-24 doi:10.1101/712398 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ A small membrane protein critical to both the offensive and defensive capabilities of Staphylococcus aureus. ]]> https://biorxiv.org/content/10.1101/712737v1?rss=1 Massey, R. C. Duggan, S. Laabei, M. Alnahari, A. O'Brien, E. Lacey, K. Bacon, L. Heesom, K. Fu, C.-L. Otto, M. Skaar, E. McLoughlin, R. 2019-07-24 doi:10.1101/712737 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Nanocatalytic activity of clean-surfaced, faceted nanocrystalline gold enhances remyelination in animal models of multiple sclerosis ]]> https://biorxiv.org/content/10.1101/712919v1?rss=1 Robinson, A. P. Zhang, J. Z. Titus, H. E. Karl, M. Merzliakov, M. Dorfman, A. R. Karlik, S. Stewart, M. G. Watt, R. K. Facer, B. D. Facer, J. D. Christian, N. D. Ho, K. Hotchkin, M. T. Mortenson, M. G. Miller, R. H. Miller, S. D. 2019-07-23 doi:10.1101/712919 Cold Spring Harbor Laboratory Press 2019-07-23 <![CDATA[ A polygenic and phenotypic risk prediction for Polycystic Ovary Syndrome evaluated by Phenome-wide association studies ]]> https://biorxiv.org/content/10.1101/714113v1?rss=1 Joo, Y. Y. Actkins, K. Pacheco, J. A. Basile, A. O. Carroll, R. Crosslin, D. R. Day, F. Denny, J. C. Velez Edwards, D. R. Hakonarson, H. Harley, J. B. Hebbring, S. J. Ho, K. Jarvik, G. P. Jones, M. Karderi, T. Mentch, F. D. Meun, C. Namjou, B. Pendergrass, S. Ritchie, M. D. Stanaway, I. B. Urbanek, M. Walunas, T. L. Smith, M. Chisholm, R. L. International PCOS Consortium, Kho, A. N. Davis, L. Hayes, M. G. 2019-07-24 doi:10.1101/714113 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Positive allosteric modulation of metabotropic glutamate receptor 5 modulates Akt and GSK3β signaling in vivo ]]> https://biorxiv.org/content/10.1101/718700v1?rss=1 Johnson, K. A. Conn, P. J. 2019-07-30 doi:10.1101/718700 Cold Spring Harbor Laboratory Press 2019-07-30 <![CDATA[ Mesolimbic dopamine D2 receptors and neural representations of subjective value ]]> https://biorxiv.org/content/10.1101/718858v1?rss=1 Castrellon, J. J. Young, J. S. Dang, L. C. Cowan, R. L. Zald, D. H. Samanez-Larkin, G. R. 2019-08-01 doi:10.1101/718858 Cold Spring Harbor Laboratory Press 2019-08-01 <![CDATA[ Effects of the copper IUD on composition of the vaginal microbiota in the olive baboon ]]> https://biorxiv.org/content/10.1101/720185v1?rss=1 Eastman, A. J. Sack, D. Chai, D. Bassis, C. M. Carter, K. A. Young, V. B. Bergin, I. L. Bell, J. D. 2019-07-31 doi:10.1101/720185 Cold Spring Harbor Laboratory Press 2019-07-31 <![CDATA[ Characterization of Genetic and Phenotypic Heterogeneity of Obstructive Sleep Apnea Using Electronic Health Records ]]> https://biorxiv.org/content/10.1101/724443v1?rss=1 Veatch, O. J. Bauer, C. R. Josyula, N. S. Mazzotti, D. R. Keenan, B. T. Bagai, K. Malow, B. A. Robishaw, J. D. Pack, A. I. Pendergrass, S. A. 2019-08-05 doi:10.1101/724443 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ WikiMedMap: Expanding the Phenotyping Mapping Toolbox Using Wikipedia ]]> https://biorxiv.org/content/10.1101/727792v1?rss=1 Sulieman, L. Wu, P. Denny, J. Bastarache, L. 2019-08-06 doi:10.1101/727792 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ Meta-analysis of problematic alcohol use in 435,563 individuals identifies 29 risk variants and yields insights into biology, pleiotropy and causality ]]> https://biorxiv.org/content/10.1101/738088v1?rss=1 Zhou, H. Sealock, J. M. Sanchez-Roige, S. Clarke, T.-K. Levey, D. Cheng, Z. Li, B. Polimanti, R. Kember, R. L. Smith, R. V. Thygesen, J. H. Morgan, M. Y. Atkinson, S. R. Thursz, M. R. Nyegaard, M. Mattheisen, M. Borglum, A. D. Johnson, E. C. the VA Million Veteran Program, Justice, A. C. Palmer, A. A. McQuillin, A. Davis, L. K. Edenberg, H. J. Agrawal, A. Kranzler, H. R. Gelernter, J. 2019-08-16 doi:10.1101/738088 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ The domain-general multiple demand (MD) network does not support core aspects of language comprehension: a large-scale fMRI investigation ]]> https://biorxiv.org/content/10.1101/744094v1?rss=1 Diachek, E. Blank, I. A. Siegelman, M. Fedorenko, E. 2019-08-22 doi:10.1101/744094 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Novel genetic determinants of telomere length from a multi-ethnic analysis of 75,000 whole genome sequences in TOPMed ]]> https://biorxiv.org/content/10.1101/749010v1?rss=1 1 independent signal. Fine-mapping at OBFC1 indicated the independent signals colocalized with cell-type specific eQTLs for OBFC1 (STN1). We further identified two novel genes, DCLRE1B (SNM1B) and PARN, using a multi-variant gene-based approach. ]]> Taub, M. A. Weinstock, J. S. Iyer, K. R. Yanek, L. R. Conomos, M. P. NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Reiner, A. P. Mathias, R. A. 2019-09-04 doi:10.1101/749010 Cold Spring Harbor Laboratory Press 2019-09-04 <![CDATA[ Membrane composition influences the conformation and function of the dopamine transporter in vivo ]]> https://biorxiv.org/content/10.1101/755819v1?rss=1 Fong, W. M. Erreger, K. Choi, S. J. Reddy, I. Johnson, C. W. Mosharov, E. V. Javitch, J. A. Galli, A. Yamamoto, A. 2019-09-05 doi:10.1101/755819 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Cross-disorder GWAS meta-analysis for Attention Deficit/Hyperactivity Disorder, Autism Spectrum Disorder, Obsessive Compulsive Disorder, and Tourette Syndrome ]]> https://biorxiv.org/content/10.1101/770222v1?rss=1 0.9). Gene-based GWAS meta-analysis across ADHD, ASD, OCD, and TS identified 21 genes significantly associated under Bonferroni correction. Out of those, 15 could not be identified as significantly associated based on the individual disorder GWAS dataset, indicating increased power in the cross-disorder comparisons. Cross-disorder tissue-specificity analysis implicates the Hypothalamus-Pituitary-Adrenal axis (stress response) as possibly underlying shared pathophysiology across ADHD, ASD, OCD, and TS. Our work highlights genetic variants and genes that may contribute to overlapping neurobiology across the four studied disorders and highlights the value of re-defining the framework for the study across this spectrum of highly comorbid disorders, by using transdiagnostic approaches. ]]> Yang, Z. Wu, H. Lee, P. H. Tsetsos, F. Davis, L. K. Yu, D. Lee, S. H. Dalsgaard, S. D. Haavik, J. Barta, C. Zayats, T. Eapen, V. Wray, N. R. Devlin, B. Daly, M. Neale, B. Borglum, A. Crowley, J. J. Scharf, J. Mathews, C. A. Faraone, S. V. Franke, B. Mattheisen, M. Smoller, J. W. Paschou, P. 2019-09-16 doi:10.1101/770222 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ The proton pump inhibitor omeprazole does not promote Clostridium difficile colonization in a murine model ]]> https://biorxiv.org/content/10.1101/775411v1?rss=1 Tomkovich, S. T. Lesniak, N. A. Li, Y. Bishop, L. Fitzgerald, M. J. Schloss, P. D. 2019-09-19 doi:10.1101/775411 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ An Inter-Species Translation Model Implicates Integrin Signaling in Infliximab-Resistant Colonic Crohn’s Disease ]]> https://biorxiv.org/content/10.1101/776666v1?rss=1 Brubaker, D. K. Kumar, M. P. Vega, P. N. Southard-Smith, A. N. Simmons, A. J. Scoville, E. A. Coburn, L. A. Wilson, K. T. Lau, K. S. Lauffenburger, D. A. 2019-09-23 doi:10.1101/776666 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses ]]> https://biorxiv.org/content/10.1101/778605v1?rss=1 Zhang, H. Ahearn, T. Lecarpentier, J. Barnes, D. Beesley, J. Qi, G. Jiang, X. O'Mara, T. A. Zhao, N. Bolla, M. K. Dunning, A. M. Dennis, J. Wang, Q. Abu Ful, Z. Aittomaki, K. Andrulis, I. L. Anton-Culver, H. Arndt, V. Aronson, K. J. Arun, B. K. Auer, P. L. Azzollini, J. Barrowdale, D. Becher, H. Beckmann, M. W. Behrens, S. Benitez, J. Bermisheva, M. Bialkowska, K. Blanco, A. Blomqvist, C. Bogdanova, N. V. Bojesen, S. E. Bonanni, B. Bondavalli, D. Borg, A. Brauch, H. Brenner, H. Briceno, I. Broeks, A. Brucker, S. Y. Bruning, T. Burwinkel, B. Buys, S. 2019-09-24 doi:10.1101/778605 Cold Spring Harbor Laboratory Press 2019-09-24 <![CDATA[ Neurocognitive and Functional Heterogeneity in Depressed Youth ]]> https://biorxiv.org/content/10.1101/778878v1?rss=1 Baller, E. B. Kaczkurkin, A. N. Sotiras, A. Adebimpe, A. Bassett, D. S. Calkins, M. E. Cui, Z. Gur, R. E. Gur, R. C. Linn, K. A. Moore, T. Roalf, D. R. Varol, E. Wolf, D. H. Xia, C. H. Davatzikos, C. Satterthwaite, T. D. 2019-09-23 doi:10.1101/778878 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ Inherited Causes of Clonal Hematopoiesis of Indeterminate Potential in TOPMed Whole Genomes ]]> https://biorxiv.org/content/10.1101/782748v1?rss=1 Bick, A. G. Weinstock, J. Nandakumar, S. K. Fulco, C. P. Leventhal, M. J. Bao, E. L. Nasser, J. Zekavat, S. M. Szeto, M. D. Laurie, C. Taub, M. Mitchell, B. Barnes, K. Moscati, A. Fornage, M. Redline, S. Psaty, B. M. Silverman, E. Weiss, S. Palmer, N. Ramachandran, V. Burchard, E. Kardia, S. He, J. Kaplan, R. Smith, N. L. Arnett, D. Schwartz, D. Correa, A. de Andrade, M. Guo, X. Konkle, B. A. Custer, B. Peralta, J. Gui, H. Meyers, D. McGarvey, S. T. Chen, I. Shoemaker, M. B. Peyser, P. A. Broome, J. Gogarten, S. Wang, F. F. Wong, Q. Montasser, M. Da 2019-09-27 doi:10.1101/782748 Cold Spring Harbor Laboratory Press 2019-09-27 <![CDATA[ Single-cell time-series mapping of cell fate trajectories reveals an expanded developmental potential for human PSC-derived distal lung progenitors ]]> https://biorxiv.org/content/10.1101/782896v1?rss=1 Hurley, K. Ding, J. Villacorta-Martin, C. Herriges, M. J. Jacob, A. Vedaie, M. Alysandratos, K. D. Sun, Y. L. Lin, C. Werder, R. B. Wilson, A. A. Mithal, A. Mostoslavsky, G. Caballero, I. S. Guttentag, S. H. Ahangari, F. Kaminski, N. Rodriguez- Fraticelli, A. Camargo, F. Bar-Joseph, Z. Kotton, D. 2019-09-26 doi:10.1101/782896 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Comprehensive palmitoyl-proteomic analysis identifies distinct protein signatures for large and small cancer-derived extracellular vesicles ]]> https://biorxiv.org/content/10.1101/787499v1?rss=1 Mariscal, J. Vagner, T. Kim, M. Zhou, B. Chin, A. Zandian, M. Freeman, M. R. You, S. Zijlstra, A. Yang, W. Di Vizio, D. 2019-10-02 doi:10.1101/787499 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Phylogeographic and phylodynamic approaches to epidemiological hypothesis testing ]]> https://biorxiv.org/content/10.1101/788059v1?rss=1 Dellicour, S. Lequime, S. Vrancken, B. Gill, M. S. Bastide, P. Gangavarapu, K. Matteson, N. Tan, Y. du Plessis, L. Fisher, A. A. Nelson, M. I. Gilbert, M. Suchard, M. A. Grubaugh, N. D. Andersen, K. G. Pybus, O. G. Lemey, P. 2019-10-01 doi:10.1101/788059 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Fine-tuning Polygenic Risk Scores with GWAS Summary Statistics ]]> https://biorxiv.org/content/10.1101/810713v1?rss=1 Zhao, Z. Yi, Y. Wu, Y. Zhong, X. Lin, Y. Hohman, T. J. Fletcher, J. Lu, Q. 2019-10-18 doi:10.1101/810713 Cold Spring Harbor Laboratory Press 2019-10-18 <![CDATA[ Failure to engage the TPJ-pSTS during naturalistic scene processing in schizophrenia ]]> https://biorxiv.org/content/10.1101/828988v1?rss=1 Patel, G. H. Arkin, S. C. Ruiz-Betancourt, D. Plaza, F. I. Mirza, S. A. Vieira, D. J. Strauss, N. E. Klim, C. C. Sanchez-Pena, J. P. Bartel, L. P. Grinband, J. Martinez, A. Berman, R. A. Ochsner, K. N. Leopold, D. A. Javitt, D. C. 2019-11-02 doi:10.1101/828988 Cold Spring Harbor Laboratory Press 2019-11-02 <![CDATA[ PhenomeXcan: Mapping the genome to the phenome through the transcriptome ]]> https://biorxiv.org/content/10.1101/833210v1?rss=1 0.1). We successfully replicate associations from PheWAS Catalog (AUC=0.61) and OMIM (AUC=0.64). We provide examples of (a) finding novel and underreported genome-to-phenome associations, (b) exploring complex gene-trait clusters within PhenomeXcan, (c) studying phenome-to-phenome relationships between common and rare diseases via further integration of PhenomeXcan with ClinVar, and (d) evaluating potential therapeutic targets. PhenomeXcan (phenomexcan.org) broadens access to complex genomic and transcriptomic data and empowers translational researchers. One-Sentence SummaryPhenomeXcan is a gene-based resource of gene-trait associations with biological context that supports translational research. ]]> Pividori, M. Rajagopal, P. S. Barbeira, A. N. Liang, Y. Melia, O. Bastarache, L. Park, Y. The GTEx Consortium, Wen, X. Im, H. K. 2019-11-06 doi:10.1101/833210 Cold Spring Harbor Laboratory Press 2019-11-06 <![CDATA[ A big-data approach to understanding metabolic rate and response to obesity in laboratory mice ]]> https://biorxiv.org/content/10.1101/839076v1?rss=1 Corrigan, J. K. Ramachandran, D. He, Y. Palmer, C. Jurczak, M. J. Li, B. Friedline, R. H. Kim, J. K. Ramsey, J. J. Lantier, L. McGuinness, O. P. Banks, A. S. Mouse Metabolic Phenotyping Center Energy Balance Working Group, 2019-11-12 doi:10.1101/839076 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ The Degree Distribution of Human Brain Functional Connectivity is Generalized Pareto: A Multi-Scale Analysis ]]> https://biorxiv.org/content/10.1101/840066v1?rss=1 Zucca, R. Arsiwalla, X. D. Le, H. Rubinov, M. Gurgui, A. Verschure, P. 2019-11-13 doi:10.1101/840066 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ An Integrative Network-based Analysis Reveals Gene Networks, Biological Mechanisms, and Novel Drug Targets in Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/853580v1?rss=1 Gerring, Z. F. Gamazon, E. R. White, A. Derks, E. M. 2019-11-24 doi:10.1101/853580 Cold Spring Harbor Laboratory Press 2019-11-24 <![CDATA[ Genomics of Human Respiratory Syncytial Virus Vaccine Attenuation ]]> https://biorxiv.org/content/10.1101/862185v1?rss=1 Junier, T. Kaiser, L. Chaturvedi, N. Fellay, J. 2019-12-02 doi:10.1101/862185 Cold Spring Harbor Laboratory Press 2019-12-02 <![CDATA[ Maternal Obesity and Western-style Diet Impair Fetal and Juvenile Offspring Skeletal Muscle Insulin-Stimulated Glucose Transport in Nonhuman Primates ]]> https://biorxiv.org/content/10.1101/864082v1?rss=1 Campodonico-Burnett, W. Hetrick, B. Wesolowski, S. R. Schenk, S. Takahashi, D. L. Dean, T. A. Sullivan, E. L. Kievit, P. Gannon, M. Aagaard-Tillery, K. Friedman, J. E. McCurdy, C. E. 2019-12-03 doi:10.1101/864082 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ Inhibition of Retinoic Acid Signaling in Proximal Tubular Epithelial cells Protects against Acute Kidney Injury by Enhancing Kim-1-dependent Efferocytosis ]]> https://biorxiv.org/content/10.1101/2023.06.15.545113v1?rss=1 View larger version (18K): org.highwire.dtl.DTLVardef@140ba6borg.highwire.dtl.DTLVardef@8f02f0org.highwire.dtl.DTLVardef@10a123eorg.highwire.dtl.DTLVardef@33b564_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yang, M. Lopez, L. N. Brewer, M. Delgado, R. D. Menshikh, A. A. Clouthier, K. A. Zhu, Y. Vanichapol, T. Yang, H. Harris, R. Gewin, L. Brooks, C. R. Davidson, A. de Caestecker, M. 2023-06-15 doi:10.1101/2023.06.15.545113 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ HIV-1 resistance to islatravir/tenofovir combination therapy in wild-type or NRTI resistant strains of diverse HIV-1 subtypes ]]> https://biorxiv.org/content/10.1101/2023.06.18.545484v1?rss=1 Cilento, M. A. Wen, X. Reeve, A. B. Snyder, A. Ukah, O. Carrillo, C. M. Smith, C. P. Edwards, K. Wahoski, C. C. Kitzler, D. R. Kodama, E. N. Mitsuya, H. Parniak, M. Tedbury, P. R. Sarafianos, S. G. 2023-06-18 doi:10.1101/2023.06.18.545484 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Single-neuron and population measures of neuronal activity in working memory tasks ]]> https://biorxiv.org/content/10.1101/2023.06.18.545508v1?rss=1 Mozumder, R. Constantinidis, C. 2023-06-20 doi:10.1101/2023.06.18.545508 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ Drug Resistance without a cost? Common and uncommon routes to fosfomycin resistance in Uropathogenic Escherichia coli ]]> https://biorxiv.org/content/10.1101/2023.06.20.545750v1?rss=1 75% of urinary tract infections (UTIs), fosfomycin enters the cell primarily through UhpT, which transports glucose-6-phosphate (G6P) glycolysis intermediate into the cell. Mutations in uhpT lead to fosfomycin resistance and have been identified during antimicrobial susceptibility testing (AST) in non-susceptible inner colonies that form within the zone of inhibition. However, EUCAST and CLSI guidelines differ in how to read fosfomycin AST when such resistant colonies arise. Work from our lab and others demonstrated that glycolysis is dispensable during acute UTI. Moreover, G6P is scarce in urine, prompting us to test the hypothesis that uhp mutations may not impart a fitness cost to the pathogen. We report that loss of uhp indeed does not impair UPEC pathogenesis and that clinical isolates exist that lack the uhp locus altogether. Analysis of non-susceptible inner colonies revealed a suite of novel genes involved in fosfomycin resistance. One of them is PykF that converts PEP to pyruvate during glycolysis. Single deletions of pykF or its anaerobic homolog pykA do not attenuate UPEC. Based on our data, we raise the alarm that multiple routes lead to fosfomycin resistance and do not affect pathogenesis and propose that the current EUCAST and CLSI guidelines unify into how they evaluate fosfomycin AST. IMPORTANCEWhile fosfomycin resistance is rare, the observation of non-susceptible subpopulations among clinical Escherichia coli isolates is a common phenomenon during antimicrobial susceptibility testing (AST) in American and European clinical labs. Previous evidence suggests that mutations eliciting this phenotype are of high biological cost to the pathogen during infection, leading to current recommendations of neglecting non-susceptible colonies during AST. Here we report that the most common route to fosfomycin resistance, as well as novel routes described in this work do not impair virulence in uropathogenic E. coli, the major cause of urinary tract infections, suggesting a re-evaluation of current susceptibility guidelines is warranted. ]]> Bermudez, T. Brannon, J. R. Dudipala, N. Reasoner, S. Morales, G. H. Wiebe, M. A. Cecala, M. Beebout, C. J. Amir, O. Hadjifrangiskou, M. 2023-06-20 doi:10.1101/2023.06.20.545750 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ The MODY-associated TALK-1 L114P mutation causes islet α-cell overactivity and β-cell inactivity resulting in transient neonatal diabetes and glucose dyshomeostasis in adults ]]> https://biorxiv.org/content/10.1101/2023.06.20.545631v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@19031e9org.highwire.dtl.DTLVardef@1bccc49org.highwire.dtl.DTLVardef@803e1org.highwire.dtl.DTLVardef@36c584_HPS_FORMAT_FIGEXP M_FIG Graphical Summary C_FIG ]]> Nakhe, A. Y. Dadi, P. K. Kim, J. Shrestha, S. Cartailler, J.-P. Sampson, L. Magnuson, M. A. Jacobson, D. A. 2023-06-21 doi:10.1101/2023.06.20.545631 Cold Spring Harbor Laboratory Press 2023-06-21 <![CDATA[ Genomic and ecological factors shaping specialism and generalism across an entire subphylum ]]> https://biorxiv.org/content/10.1101/2023.06.19.545611v1?rss=1 Opulente, D. A. LaBella, A. L. Harrison, M.-C. Wolters, J. F. Liu, C. Li, Y. Kominek, J. Steenwyk, J. L. Stoneman, H. R. VanDenAvond, J. Miller, C. R. Langdon, Q. K. Silva, M. Goncalves, C. Ubbelohde, E. J. Li, Y. Buh, K. V. Jarzyna, M. Haase, M. A. B. Rosa, C. A. Cadez, N. Libkind, D. DeVirgilio, J. H. Hulfachor, A. B. Kurtzman, C. P. Sampaio, J. P. Goncalves, P. Zhou, X. Shen, X.-X. Groenewald, M. Rokas, A. Hittinger, C. T. 2023-06-22 doi:10.1101/2023.06.19.545611 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Polysulfide Nanoparticles Ameliorate Ischaemia Reperfusion Injury in Renal Transplantation and Improve Kidney Function Post-Transplantation ]]> https://biorxiv.org/content/10.1101/2023.06.21.545864v1?rss=1 Stone, J. P. D'Arcy, R. Geraghty, A. Amin, K. Montero-Fernandez, A. Dabare, D. Ghibaudi, M. Francini, N. Coradello, G. Bramhall, J. Galwey, N. W. Ruseva, M. Tirelli, N. Fildes, J. 2023-06-22 doi:10.1101/2023.06.21.545864 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ RyR2 Binding of an Antiarrhythmic Cyclic Depsipeptide Mapped Using Confocal Fluorescence Lifetime Detection of FRET ]]> https://biorxiv.org/content/10.1101/2023.06.22.546083v1?rss=1 Seflova, J. Schwarz, J. A. Smith, A. N. Svensson, B. Blackwell, D. J. Phillips, T. A. Nikolaienko, R. Bovo, E. Rebbeck, R. T. Zima, A. V. Thomas, D. D. Van Petegem, F. Knollmann, B. C. Johnston, J. N. Robia, S. L. Cornea, R. L. 2023-06-22 doi:10.1101/2023.06.22.546083 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Epithelial Yap/Taz are required for functional alveolar regeneration following acute lung injury ]]> https://biorxiv.org/content/10.1101/2023.06.22.545997v1?rss=1 DiGiovanni, G. T. Han, W. Sherrill, T. Taylor, C. J. Nichols, D. S. Geis, N. M. Singha, U. K. Calvi, C. L. McCall, A. S. Dixon, M. M. Lui, Y. Jang, J.-H. Gutor, S. S. Polosukhin, V. V. Blackwell, T. S. Kropski, J. A. Gokey, J. J. 2023-06-23 doi:10.1101/2023.06.22.545997 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Alterations in Cardiovascular and Cerebral Pulse Wave Velocity in 5XFAD Murine Model of Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2023.06.22.546154v1?rss=1 Marshall, A. G. Neikirk, K. Barongan, T. Shao, B. Crabtree, A. Stephens, D. C. Vue, Z. Beasley, H. K. Garza-Lopez, E. Scudese, E. Damo, S. M. Gomez, J. A. Taffet, G. Hinton, A. Reddy, A. K. 2023-06-25 doi:10.1101/2023.06.22.546154 Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ Wound-Induced Syncytia Outpace Mononucleate Neighbors during Drosophila Wound Repair ]]> https://biorxiv.org/content/10.1101/2023.06.25.546442v1?rss=1 White, J. S. Su, J. J. Ruark, E. M. Hua, J. Hutson, M. S. Page-McCaw, A. 2023-06-26 doi:10.1101/2023.06.25.546442 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Glucose-stimulated KIF5B-driven microtubule sliding organizes microtubule networks in pancreatic beta cells ]]> https://biorxiv.org/content/10.1101/2023.06.25.546468v1?rss=1 Bracey, K. Noguchi, P. Edwards, C. Cario, A. Gu, G. Kaverina, I. 2023-06-26 doi:10.1101/2023.06.25.546468 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Iron acquisition by a commensal bacterium modifies host nutritional immunity during Salmonella infection ]]> https://biorxiv.org/content/10.1101/2023.06.25.546471v1?rss=1 Spiga, L. Fansler, R. T. Perera, Y. R. Shealy, N. G. Munneke, M. J. Torres, T. P. David, H. Lemoff, A. Ran, X. Richardson, K. L. Pudlo, N. Martens, E. C. Yang, Z. J. Skaar, E. P. Byndloss, M. X. Chazin, W. J. Zhu, W. 2023-06-26 doi:10.1101/2023.06.25.546471 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Cortical Origin of Theta Error Signals ]]> https://biorxiv.org/content/10.1101/2023.06.27.546752v1?rss=1 Herrera, B. Sajad, A. Errington, S. P. Schall, J. D. Diaz, J. R. 2023-06-30 doi:10.1101/2023.06.27.546752 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ XPA tumor variants lead to defects in NER that sensitize cells to cisplatin ]]> https://biorxiv.org/content/10.1101/2023.06.29.547124v1?rss=1 Blee, A. M. Gallagher, K. S. Kim, H.-S. Kim, M. Troll, C. R. D'Souza, A. Park, J. Neufer, P. D. Schärer, O. D. Chazin, W. J. 2023-07-01 doi:10.1101/2023.06.29.547124 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ Larvicidal activity of the photosensitive insecticides, methylene blue and rose bengal, in Aedes aegypti and Anopheles gambiae mosquitoes ]]> https://biorxiv.org/content/10.1101/2023.06.30.547250v1?rss=1 Meier, C. J. Hillyer, J. F. 2023-07-01 doi:10.1101/2023.06.30.547250 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ Substrate displacement of CK1 C-termini regulates kinase specificity ]]> https://biorxiv.org/content/10.1101/2023.06.30.547285v1?rss=1 Cullati, S. N. Akizuki, K. Chen, J.-S. Gould, K. N. 2023-07-01 doi:10.1101/2023.06.30.547285 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ A machine learning toolbox for the analysis of sharp-wave ripples reveal common features across species ]]> https://biorxiv.org/content/10.1101/2023.07.02.547382v1?rss=1 Navas-Olive, A. Rubio, A. Abbaspoor, S. Hoffman, K. L. de la Prida, L. M. 2023-07-03 doi:10.1101/2023.07.02.547382 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Evolutionary origin, population diversity, and diagnostics for a cryptic hybrid pathogen ]]> https://biorxiv.org/content/10.1101/2023.07.03.547508v1?rss=1 Steenwyk, J. L. Knowles, S. L. Bastos, R. Balamurugan, C. Rinker, D. Mead, M. E. Roberts, C. D. Raja, H. A. Li, Y. Colabardini, A. C. Castro, P. A. Reis, T. F. Canovas, D. Sanchez, R. L. Lagrou, K. Torrado, E. Rodrigues, F. Oberlies, N. H. Zhou, X. Goldman, G. Rokas, A. 2023-07-03 doi:10.1101/2023.07.03.547508 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ ent-Verticilide B1 inhibits type 2 ryanodine receptor channels and is antiarrhythmic in Casq2-/- mice ]]> https://biorxiv.org/content/10.1101/2023.07.03.547578v1?rss=1 Gochman, A. Do, T. Q. Kim, K. Schwarz, J. A. Thorpe, M. P. Blackwell, D. J. Smith, A. N. Akers, W. S. Cornea, R. L. Laver, D. L. Johnston, J. N. Knollmann, B. C. 2023-07-03 doi:10.1101/2023.07.03.547578 Cold Spring Harbor Laboratory Press 2023-07-03 <![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[ The pathogenic T42A mutation in SHP2 rewires interaction specificity and enhances signaling ]]> https://biorxiv.org/content/10.1101/2023.07.10.548257v1?rss=1 van Vlimmeren, A. E. Voleti, R. Chartier, C. A. Jiang, Z. Karandur, D. Shah, N. H. 2023-07-10 doi:10.1101/2023.07.10.548257 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ A Size Filter Regulates Apical Protein Sorting ]]> https://biorxiv.org/content/10.1101/2023.07.13.548868v1?rss=1 de Caestecker, C. Macara, I. 2023-07-13 doi:10.1101/2023.07.13.548868 Cold Spring Harbor Laboratory Press 2023-07-13 <![CDATA[ Validation of human telomere length trans-ancestry meta-analysis association signals identifies POP5 and KBTBD6 as novel human telomere length regulation genes ]]> https://biorxiv.org/content/10.1101/2023.07.12.548702v1?rss=1 Keener, R. Chhetri, S. B. Connelly, C. J. Taub, M. A. Conomos, M. P. Weinstock, J. S. Ni, B. Strober, B. J. Aslibekyan, S. Auer, P. L. Barwick, L. Becker, L. C. Blangero, J. Bleecker, E. R. Brody, J. A. Cade, B. E. Celedon, J. C. Chang, Y.-C. Cupples, L. A. Custer, B. Freedman, B. I. Gladwin, M. T. Heckbert, S. R. Hou, L. Irvin, M. R. Isasi, C. R. Johnsen, J. M. Kenny, E. E. Kooperberg, C. Minster, R. L. Nekhai, S. Pankratz, N. Peyser, P. A. Rotter, J. I. Taylor, K. D. Telen, M. J. Wu, B. Yanek, L. R. Yang, I. V. Albert, C. Arnett, D. K. Ashley-Koch, A. 2023-07-14 doi:10.1101/2023.07.12.548702 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ From goal to outcome: analyzing the progression of biomedical sciences PhD careers in a longitudinal study using an expanded taxonomy ]]> https://biorxiv.org/content/10.1101/2023.07.13.548881v1?rss=1 Brown, A. M. Meyers, L. C. Varadarajan, J. Ward, N. J. Cartailler, J.-P. Chalkley, R. G. Gould, K. L. Petrie, K. A. 2023-07-14 doi:10.1101/2023.07.13.548881 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ An expression-directed linear mixed model (edLMM) discovering low-effect genetic variants ]]> https://biorxiv.org/content/10.1101/2023.07.13.548939v1?rss=1 Li, Q. Bian, J. Qian, Y. Kossinna, P. Gordon, P. M. Zhou, X. Guo, X. Yan, J. Wu, J. Long, Q. 2023-07-15 doi:10.1101/2023.07.13.548939 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ Tepsin binds LC3B to promote ATG9A export and delivery at the cell periphery ]]> https://biorxiv.org/content/10.1101/2023.07.18.549521v1?rss=1 Wallace, N. S. Gadbery, J. E. Cohen, C. I. Kendall, A. K. Jackson, L. P. 2023-07-18 doi:10.1101/2023.07.18.549521 Cold Spring Harbor Laboratory Press 2023-07-18 <![CDATA[ Natural disaster alters the adaptive benefits of sociality ]]> https://biorxiv.org/content/10.1101/2023.07.17.549328v1?rss=1 Testard, C. Shergold, C. Acevedo-Ithier, A. Hart, J. Negron-Del Valle, J. Philips, D. Watowich, M. Montague, M. Snyder-Mackler, N. J. Higham, J. Platt, M. Brent, L. J. 2023-07-19 doi:10.1101/2023.07.17.549328 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Nucleus accumbens core single cell ensembles bidirectionally respond to experienced versus observed aversive events ]]> https://biorxiv.org/content/10.1101/2023.07.17.549364v1?rss=1 Dinckol, O. Zachry, J. E. Kutlu, M. G. 2023-07-19 doi:10.1101/2023.07.17.549364 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Discovery of post-translationally modified self-peptides that promote hypertension ]]> https://biorxiv.org/content/10.1101/2023.07.18.549523v1?rss=1 Bloodworth, N. Chen, W. Patrick, D. Palubinsky, A. Phillips, E. Roeth, D. Kalkum, M. Mallal, S. Davies, S. S. Ao, M. Moretti, R. Meiler, J. Harrison, D. G. 2023-07-19 doi:10.1101/2023.07.18.549523 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Age and Task Modulate Olfactory Sensitivity in the Florida Carpenter Ant Camponotus floridanus ]]> https://biorxiv.org/content/10.1101/2023.07.18.549561v1?rss=1 Ferguson, S. T. Bakis, I. Edwards, N. D. Zwiebel, L. J. 2023-07-19 doi:10.1101/2023.07.18.549561 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Analysis of small EV proteomes reveals unique functional protein networks regulated by VAP-A ]]> https://biorxiv.org/content/10.1101/2023.07.18.549588v1?rss=1 Barman, B. Ramirez, M. Liu, Q. Weaver, A. 2023-07-19 doi:10.1101/2023.07.18.549588 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Analysis of Drosophila and mouse mutants reveals that Peroxidasin is required for tissue mechanics and full viability ]]> https://biorxiv.org/content/10.1101/2023.07.19.549730v1?rss=1 Peebles, K. E. LaFever, K. S. Page-McCaw, P. S. Colon, S. Wang, D. Stricker, A. M. Ferrell, N. Bhave, G. Page-McCaw, A. 2023-07-19 doi:10.1101/2023.07.19.549730 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Commentary on Pang et al. (2023) Nature ]]> https://biorxiv.org/content/10.1101/2023.07.20.549785v1?rss=1 Faskowitz, J. Moyer, D. Handwerker, D. Gonzalez-Castillo, J. Bandettini, P. Jbabdi, S. Betzel, R. 2023-07-22 doi:10.1101/2023.07.20.549785 Cold Spring Harbor Laboratory Press 2023-07-22 <![CDATA[ Machine learning illuminates how diet influences the evolution of yeast galactose metabolism ]]> https://biorxiv.org/content/10.1101/2023.07.20.549758v1?rss=1 Harrison, M.-C. Ubbelohde, E. J. LaBella, A. L. Opulente, D. A. Wolters, J. F. Zhou, X. Shen, X.-X. Groenewald, M. Hittinger, C. T. Rokas, A. 2023-07-23 doi:10.1101/2023.07.20.549758 Cold Spring Harbor Laboratory Press 2023-07-23 <![CDATA[ Addressing persistent challenges in digital image analysis of cancerous tissues ]]> https://biorxiv.org/content/10.1101/2023.07.21.548450v1?rss=1 Prabhakaran, S. Yapp, C. Baker, G. J. Beyer, J. Chang, Y. H. Creason, A. L. Krueger, R. Muhlich, J. Patterson, N. H. Sidak, K. Sudar, D. Taylor, A. J. Ternes, L. Troidl, J. Yubin, X. Sokolov, A. Tyson, D. R. Participants of the Cell Imaging Hackathon 2022, 2023-07-24 doi:10.1101/2023.07.21.548450 Cold Spring Harbor Laboratory Press 2023-07-24 <![CDATA[ Characterization of Pik1 function in fission yeast reveals its conserved role in lipid synthesis and not cytokinesis ]]> https://biorxiv.org/content/10.1101/2023.07.24.550375v1?rss=1 Willet, A. H. Turner, L. A. Park, J. S. Ren, L. Snider, C. E. Gould, K. L. 2023-07-24 doi:10.1101/2023.07.24.550375 Cold Spring Harbor Laboratory Press 2023-07-24 <![CDATA[ Hummingbirds use wing inertial effects to improve maneuverability ]]> https://biorxiv.org/content/10.1101/2023.07.21.550104v1?rss=1 Haque, M. N. Cheng, B. Tobalske, B. W. Luo, H. 2023-07-25 doi:10.1101/2023.07.21.550104 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Human Plasma Proteomic Profile of Clonal Hematopoiesis ]]> https://biorxiv.org/content/10.1101/2023.07.25.550557v1?rss=1 Yu, Z. Vromman, A. Nguyen, N. Q. H. Vellarikkal, S. K. Uddin, M. M. Niroula, A. Griffin, G. Honigberg, M. C. Lin, A. E. Gibson, C. J. Katz, D. H. Tahir, U. Haidermota, S. Ganesh, S. Antoine, T. Weinstock, J. Austin, T. R. Vasan, R. S. peloso, G. M. Hornsby, W. Ganz, P. Manson, J. E. Haring, B. Kooperberg, C. L. Reiner, A. P. Bis, J. C. Psaty, B. M. Min, Y.-I. Correa, A. Lange, L. A. Post, W. Rotter, J. I. Rich, S. S. Wilson, J. G. Ebert, B. L. Yu, B. Ballantyne, C. M. Coresh, J. Sankaran, V. G. Bick, A. G. Jaiswal, S. Libby, P. Gerszten, R. E. NHLBI T 2023-07-27 doi:10.1101/2023.07.25.550557 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Decoding working memory information from persistent and activity-silent neurons in the primate prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2023.07.25.550371v1?rss=1 Thrower, L. Dang, W. Jaffe, R. Sun, J. Constantinidis, C. 2023-07-28 doi:10.1101/2023.07.25.550371 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Drug screening in human physiologic medium identifies uric acid as an inhibitor of rigosertib efficacy ]]> https://biorxiv.org/content/10.1101/2023.07.26.550731v1?rss=1 Rawat, V. DeLear, P. Prashanth, P. Ozgurses, M. E. Tebeje, A. Burns, P. A. Conger, K. O. Solis, C. Hasnain, Y. Novikova, A. Endress, J. E. Gonzalez-Sanchez, P. Dong, W. Stephanopoulos, G. DeNicola, G. M. Harris, I. S. Sept, D. S. Mason, F. M. Coloff, J. L. 2023-07-28 doi:10.1101/2023.07.26.550731 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Ribosome subunit attrition and activation of the p53-MDM4 axis dominate the response of MLL-rearranged cancer cells to WDR5 WIN site inhibition ]]> https://biorxiv.org/content/10.1101/2023.07.26.550648v1?rss=1 Howard, G. C. Wang, J. Rose, K. L. Patel, P. Tsui, T. Florian, A. C. Lorey, S. L. Grieb, B. C. Smith, B. N. Slota, M. J. Reynolds, E. M. Goswami, S. Savona, M. R. Lee, T. Fesik, S. W. Liu, Q. Tansey, W. P. 2023-07-29 doi:10.1101/2023.07.26.550648 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ Laminar pattern of adolescent development changes in working memory neuronal activity ]]> https://biorxiv.org/content/10.1101/2023.07.28.550982v1?rss=1 Zhu, J. Hammond, B. M. Zhou, X. M. Constantinidis, C. 2023-07-29 doi:10.1101/2023.07.28.550982 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ Topoisomerase IIα C-terminal Domain Mutations and Catalytic Function ]]> https://biorxiv.org/content/10.1101/2023.07.29.551120v1?rss=1 Musselman, J. R. England, D. C. Fielding, L. A. Durham, C. T. Baxter, E. Jiang, X. Lisic, E. C. Deweese, J. E. 2023-07-29 doi:10.1101/2023.07.29.551120 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ A test of time-resolved functional MRI with subsecond event durations ]]> https://biorxiv.org/content/10.1101/2023.07.30.550770v1?rss=1 Wong, A. P. H. Wu, E. X. W. Rogers, B. P. Asplund, C. L. 2023-07-30 doi:10.1101/2023.07.30.550770 Cold Spring Harbor Laboratory Press 2023-07-30 <![CDATA[ Mitochondrial Genome Diversity across the Subphylum Saccharomycotina ]]> https://biorxiv.org/content/10.1101/2023.07.28.551029v1?rss=1 Wolters, J. F. LaBella, A. Opulente, D. Rokas, A. Hittinger, C. T. 2023-07-31 doi:10.1101/2023.07.28.551029 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ Improved modeling of human vision by incorporating robustness to blur in convolutional neural networks ]]> https://biorxiv.org/content/10.1101/2023.07.29.551089v1?rss=1 Jang, H. Tong, F. 2023-07-31 doi:10.1101/2023.07.29.551089 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ Flavinated SDHA Underlies the Change in Intrinsic Optical Properties of Oral Cancers ]]> https://biorxiv.org/content/10.1101/2023.07.30.551184v1?rss=1 Marumo, T. Maduka, C. V. Ural, E. Apu, E. H. Chung, S.-J. van den Berg, N. S. Zhou, Q. Martin, B. A. Rosenthal, E. L. Shibahara, T. Contag, C. H. 2023-07-31 doi:10.1101/2023.07.30.551184 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ Flexibility and distributive synthesis regulate RNA priming and handoff in human DNA polymerase α-primase ]]> https://biorxiv.org/content/10.1101/2023.08.01.551538v1?rss=1 Cordoba, J. J. Mullins, E. A. Salay, L. E. Eichman, B. F. Chazin, W. J. 2023-08-01 doi:10.1101/2023.08.01.551538 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ EZH2 inhibition sensitizes IDH1R132H mutant gliomas to histone deacetylase inhibitor. ]]> https://biorxiv.org/content/10.1101/2023.07.31.551045v1?rss=1 Sprinzen, L. Garcia, F. G. Mela, A. Lei, L. Upadhyayula, P. Mahajan, A. Humala, N. Manier, L. Caprioli, R. M. Quinones-Hinojosa, A. Casaccia, P. Canoll, P. 2023-08-02 doi:10.1101/2023.07.31.551045 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Molecular Basis of Cell Membrane Adaptation in Daptomycin-Resistant Enterococcus faecalis ]]> https://biorxiv.org/content/10.1101/2023.08.02.551704v1?rss=1 Nguyen, A. Tran, T. Panesso, D. Hood, K. Polamraju, V. Zhang, R. Khan, A. Miller, W. R. Mileykovskaya, E. Shamoo, Y. Xu, L. Vitrac, H. Arias, C. A. 2023-08-02 doi:10.1101/2023.08.02.551704 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ A molecular atlas of adult C. elegans motor neurons reveals ancient diversity delineated by conserved transcription factor codes ]]> https://biorxiv.org/content/10.1101/2023.08.04.552048v1?rss=1 Smith, J. J. Taylor, S. R. Blum, J. A. Gitler, A. Miller, D. M. Kratsios, P. 2023-08-06 doi:10.1101/2023.08.04.552048 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ Ultrasound Imaging Enables Longitudinal Tracking of Vascular Changes that Correlate with Immune Cell Infiltration After Radiotherapy ]]> https://biorxiv.org/content/10.1101/2023.08.04.552076v1?rss=1 Martello, S. E. Xia, J. Kusunose, J. Hacker, B. C. Mayeaux, M. A. Lin, E. J. Hawkes, A. Singh, A. Caskey, C. F. Rafat, M. 2023-08-06 doi:10.1101/2023.08.04.552076 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ Approximating conformational Boltzmann distributions with AlphaFold2 predictions ]]> https://biorxiv.org/content/10.1101/2023.08.06.552168v1?rss=1 Brown, B. P. Stein, R. A. Meiler, J. Mchaourab, H. 2023-08-07 doi:10.1101/2023.08.06.552168 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Enhancing Fairness in Disease Prediction with Optimizing Multiple Domain Adversarial Networks ]]> https://biorxiv.org/content/10.1101/2023.08.04.551906v1?rss=1 Li, B. Shi, X. Gao, H. Jinag, X. Zhang, K. Harmanci, A. O. Malin, B. 2023-08-09 doi:10.1101/2023.08.04.551906 Cold Spring Harbor Laboratory Press 2023-08-09 <![CDATA[ A convolutional neural network estimation of brain age is sensitive to cognitive impairment and decline ]]> https://biorxiv.org/content/10.1101/2023.08.10.552494v1?rss=1 Yang, Y. Sathe, A. Schilling, K. Shashikumar, N. Moore, E. Dumitrescu, L. Pechman, K. R. Landman, B. A. Gifford, K. A. Hohman, T. J. Jefferson, A. L. Archer, D. B. 2023-08-14 doi:10.1101/2023.08.10.552494 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Pancreatic islet α cell function and proliferation requires the arginine transporter SLC7A2 ]]> https://biorxiv.org/content/10.1101/2023.08.10.552656v1?rss=1 Spears, E. Stanley, J. E. Shou, M. Dai, C. Bradley, A. Yin, L. Li, X. Sellick, K. Poffenberger, G. Coate, K. C. Shrestha, S. D. Jenkins, R. Sloop, K. Wilson, K. T. Attie, A. D. Keller, M. P. Chen, W. Powers, A. C. Dean, E. D. 2023-08-14 doi:10.1101/2023.08.10.552656 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Mapping the functional form of the trade-off between infection resistance and reproductive fitness under dysregulated immune signaling ]]> https://biorxiv.org/content/10.1101/2023.08.10.552815v1?rss=1 Critchlow, J. T. Prakash, A. Zhong, K. Y. Tate, A. T. 2023-08-14 doi:10.1101/2023.08.10.552815 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ MidRISH: Unbiased harmonization of rotationally invariant harmonics of the diffusion signal ]]> https://biorxiv.org/content/10.1101/2023.08.12.553099v1?rss=1 Newlin, N. R. Kim, M. E. Kanakaraj, P. Yao, T. Hohman, T. Pechman, K. R. Beason-Held, L. Resnick, S. M. Archer, D. B. Jefferson, A. Landman, B. A. Moyer, D. 2023-08-15 doi:10.1101/2023.08.12.553099 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Structural basis of allosteric modulation ofmetabotropic glutamate receptor activation and desensitization ]]> https://biorxiv.org/content/10.1101/2023.08.13.552748v1?rss=1 Strauss, A. Gonzalez-Hernandez, A. J. Lee, J. Abreu, N. Selvakumar, P. Salas-Estrada, L. Kristt, M. Marx, D. Gilliland, K. Melancon, B. Filizola, M. Meyerson, J. Levitz, J. 2023-08-15 doi:10.1101/2023.08.13.552748 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ LiaX is a surrogate marker for cell-envelope stress and daptomycin non-susceptibility in Enterococcus faecium ]]> https://biorxiv.org/content/10.1101/2023.08.18.553907v1?rss=1 Axell-House, D. B. Simar, S. R. Panesso, D. Rincon, S. Miller, W. R. Khan, A. Pemberton, O. A. Valdez, L. Nguyen, A. H. Hood, K. S. Rydell, K. DeTranaltes, A. M. Jones, M. N. Atterstrom, R. L. Reyes, J. Sahasrabhojanec, P. Suleyman, G. Zervos, M. J. Shelburne, S. A. Singh, K. V. Shamoo, Y. Hanson, B. M. Tran, T. T. Arias, C. A. 2023-08-18 doi:10.1101/2023.08.18.553907 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ Caloric restriction promotes beta cell longevity and delays aging and senescence by enhancing cell identity and homeostasis mechanisms. ]]> https://biorxiv.org/content/10.1101/2023.08.23.554369v1?rss=1 Santos, C. d. Shrestha, S. Cottam, M. A. Perkins, G. Lev-Ram, V. Roy, B. Acree, C. Kim, K.-Y. Deerinck, T. Cutler, M. Dean, D. Cartailler, J. P. MacDonald, P. E. Hetzer, M. W. Ellisman, M. H. Arrojo e Drigo, R. 2023-08-24 doi:10.1101/2023.08.23.554369 Cold Spring Harbor Laboratory Press 2023-08-24 <![CDATA[ A phylogenetic approach to explore the Aspergillus fumigatus conidial surface-associated proteome and its role in pathogenesis ]]> https://biorxiv.org/content/10.1101/2023.08.22.553365v1?rss=1 Valero, C. Pinzan, C. F. de Castro, P. A. van Rhijn, N. Earle, K. Liu, H. Horta, M. A. C. Kniemeyer, O. Krüger, T. Pschibul, A. Coemert, D. N. Heinekamp, T. Brakhage, A. A. Steenwyk, J. L. Mead, M. E. Rokas, A. Filler, S. G. da Rosa-Garzon, N. G. Cabral, H. Deljabe, E. Bromley, M. J. Angeli, C. B. Palmisano, G. Ibrahim, A. S. Gago, S. dos Reis, T. F. Goldman, G. H. 2023-08-26 doi:10.1101/2023.08.22.553365 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ Divergent Pairwise Epistasis in the Context of Unstable Membrane Protein Variants ]]> https://biorxiv.org/content/10.1101/2023.08.25.554866v1?rss=1 Chamness, L. M. Kuntz, C. P. McKee, A. G. Penn, W. D. Hemmerich, C. M. Rusch, D. B. Woods, H. Dyotima, Meiler, J. Schlebach, J. P. 2023-08-27 doi:10.1101/2023.08.25.554866 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Utilizing Mentorship Education to Promote a Culturally Responsive Research Training Environment in the Biomedical Sciences ]]> https://biorxiv.org/content/10.1101/2023.08.25.554846v1?rss=1 Suiter, S. Byars-Winston, A. Sancheznieto, F. Pfund, C. Sealy, L. 2023-08-28 doi:10.1101/2023.08.25.554846 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Convolutional neural network models of neuronal responses in macaque V1 reveal limited non-linear processing ]]> https://biorxiv.org/content/10.1101/2023.08.26.554952v1?rss=1 Miao, H.-Y. Tong, F. 2023-08-28 doi:10.1101/2023.08.26.554952 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Local organization of spatial and shape information during working memory in the primate prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2023.08.26.554962v1?rss=1 Sun, Y. Dang, W. Jaffe, R. G. Constantinidis, C. 2023-08-28 doi:10.1101/2023.08.26.554962 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Mammalian orthoreovirus can exit cells in extracellular vesicles ]]> https://biorxiv.org/content/10.1101/2023.08.29.555250v1?rss=1 Smith, S. C. Krystofiak, E. Ogden, K. 2023-08-29 doi:10.1101/2023.08.29.555250 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ HIV-1 binds dynein directly to hijack microtubule transport machinery ]]> https://biorxiv.org/content/10.1101/2023.08.29.555335v1?rss=1 Badieyan, S. Lichon, D. Andreas, M. P. Gillies, J. P. Peng, W. Shi, J. DeSantis, M. E. Aiken, C. R. Böcking, T. Giessen, T. W. Campbell, E. M. Cianfrocco, M. A. 2023-08-29 doi:10.1101/2023.08.29.555335 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Saccharomycotina yeasts defy longstanding macroecological patterns ]]> https://biorxiv.org/content/10.1101/2023.08.29.555417v1?rss=1 David, K. T. Harrison, M.-C. Opulente, D. A. LaBella, A. L. Wolters, J. F. Zhou, X. Shen, X.-X. Groenewald, M. Pennell, M. Hittinger, C. T. Rokas, A. 2023-08-31 doi:10.1101/2023.08.29.555417 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Early life adversity has sex-dependent effects on survival across the lifespan in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2023.08.30.555589v1?rss=1 Patterson, S. K. Andonov, E. Arre, A. M. Martinez, M. I. Negron-Del Valle, J. E. Petersen, R. M. Phillips, D. Rahman, A. Ruiz-Lambides, A. Villanueva, I. Lea, A. J. Snyder-Mackler, N. Brent, L. J. N. Higham, J. P. 2023-09-01 doi:10.1101/2023.08.30.555589 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Myostatin is a major endocrine driver of follicle-stimulating hormone synthesis ]]> https://biorxiv.org/content/10.1101/2023.08.30.555595v1?rss=1 Ongaro, L. Zhou, X. Wang, Y. Zhou, Z. Schultz, H. Buddle, E. R. S. Brule, E. Lin, Y.-F. Schang, G. Castonguay, R. Liu, Y. Su, G. H. Seidah, N. Ray, K. C. Karp, S. J. Boehm, U. Lee, S.-J. Bernard, D. J. 2023-09-01 doi:10.1101/2023.08.30.555595 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Translocation of gut commensal bacteria to the brain ]]> https://biorxiv.org/content/10.1101/2023.08.30.555630v1?rss=1 Thapa, M. Kumari, A. Chin, C.-Y. Choby, J. Jin, F. Bogati, B. Chopyk, D. Koduri, N. Pahnke, A. Elrod, E. Burd, E. M. Weiss, D. S. Grakoui, A. 2023-09-01 doi:10.1101/2023.08.30.555630 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Training-dependent gradients of timescales of neural dynamics in the primate prefrontal cortex and their contributions to working memory ]]> https://biorxiv.org/content/10.1101/2023.09.01.555857v1?rss=1 Trepka, E. Spitmaan, M. Qi, X.-L. Constantinidis, C. Soltani, A. 2023-09-02 doi:10.1101/2023.09.01.555857 Cold Spring Harbor Laboratory Press 2023-09-02 <![CDATA[ Environmental factors and cultural drift influence song evolution in New World Sparrows ]]> https://biorxiv.org/content/10.1101/2023.09.01.555954v1?rss=1 Provost, K. L. Yang, J. Carstens, B. C. 2023-09-04 doi:10.1101/2023.09.01.555954 Cold Spring Harbor Laboratory Press 2023-09-04 <![CDATA[ Exercise training adaptations in liver glycogen and glycerolipids require hepatic AMP-activated protein kinase in mice ]]> https://biorxiv.org/content/10.1101/2023.09.01.555935v1?rss=1 Hughey, C. C. Bracy, D. P. Rome, F. I. Goelzer, M. Donahue, E. P. Viollet, B. Foretz, M. Wasserman, D. H. 2023-09-05 doi:10.1101/2023.09.01.555935 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Bone Morphogenetic Protein (BMP) signaling upregulates expression of the E protein repressors, ID1 and ID3, in pancreatitis and pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2023.09.01.555987v1?rss=1 Raghunathan, M. K. Scully, K. M. Wehrmaker, A. Lowy, A. M. DelGiorno, K. E. Itkin-Ansari, P. 2023-09-05 doi:10.1101/2023.09.01.555987 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Propofol-mediated loss of consciousness disrupts predictive routing and local field phase modulation of neural activity ]]> https://biorxiv.org/content/10.1101/2023.09.02.555990v1?rss=1 200 ms from stimulus onset) period spiking, and superficial layer sinks in sensory cortex. Therefore, auditory cortex was in a disinhibited state during propofol-mediated LOC. However, despite these enhanced feedforward responses in auditory cortex, there was a loss of differential spiking to oddballs in higher order cortex. This may be a consequence of a loss of within-area and inter-area spike-field coupling in the alpha/beta and gamma frequency bands. These results provide strong constraints for current theories of consciousness. Significance statementNeurophysiology studies have found alpha/beta oscillations (8-30Hz), gamma oscillations (40-100Hz), and spiking activity during cognition. Alpha/beta power has an inverse relationship with gamma power/spiking. This inverse relationship suggests that gamma/spiking are under the inhibitory control of alpha/beta. The predictive routing model hypothesizes that alpha/beta oscillations selectively inhibit (and thereby control) cortical activity that is predictable. We tested whether this inhibitory control is a signature of consciousness. We used multi-area neurophysiology recordings in monkeys presented with tone sequences that varied in predictability. We recorded brain activity as the anesthetic propofol was administered to manipulate consciousness. Compared to conscious processing, propofol-mediated unconsciousness disrupted alpha/beta inhibitory control during predictive processing. This led to a disinhibition of gamma/spiking, consistent with the predictive routing model. ]]> Xiong, Y. Donoghue, J. A. Lundqvist, M. Mahnke, M. Major, A. J. Brown, E. N. Miller, E. K. Bastos, A. M. 2023-09-05 doi:10.1101/2023.09.02.555990 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Rosetta Energy Analysis of AlphaFold2 models: Point Mutations and Conformational Ensembles ]]> https://biorxiv.org/content/10.1101/2023.09.05.556364v1?rss=1 Stein, R. A. Mchaourab, H. S. 2023-09-05 doi:10.1101/2023.09.05.556364 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Convergent Sequence Features of Antiviral B Cells ]]> https://biorxiv.org/content/10.1101/2023.09.06.556442v1?rss=1 Abu-Shmais, A. A. Vukovich, M. J. Wasdin, P. T. Suresh, Y. P. Rush, S. A. Gillespie, R. A. Sankhala, R. S. Choe, M. Joyce, M. G. Kanekiyo, M. McLellan, J. S. Georgiev, I. S. 2023-09-07 doi:10.1101/2023.09.06.556442 Cold Spring Harbor Laboratory Press 2023-09-07 <![CDATA[ Brain-wide human oscillatory LFP activity during visual working memory ]]> https://biorxiv.org/content/10.1101/2023.09.06.556554v1?rss=1 Singh, B. Wang, Z. Madiah, L. M. Gatti, S. E. Fulton, J. N. Johnson, G. W. Rui, L. Dawant, B. M. Englot, D. J. Bick, S. k. Roberson, S. W. Constantinidis, C. 2023-09-07 doi:10.1101/2023.09.06.556554 Cold Spring Harbor Laboratory Press 2023-09-07 <![CDATA[ Learning site-invariant features of connectomes to harmonize complex network measures ]]> https://biorxiv.org/content/10.1101/2023.09.07.556721v1?rss=1 Newlin, N. R. Kanakaraj, P. Li, T. Z. Pechman, K. Archer, D. B. Jefferson, A. Landman, B. A. Moyer, D. 2023-09-09 doi:10.1101/2023.09.07.556721 Cold Spring Harbor Laboratory Press 2023-09-09 <![CDATA[ Identification of functional white matter networks in BOLD fMRI ]]> https://biorxiv.org/content/10.1101/2023.09.08.556881v1?rss=1 Eby, A. L. Remedios, L. W. Kim, M. E. Li, M. Gao, Y. Gore, J. Schilling, K. Landman, B. A. 2023-09-09 doi:10.1101/2023.09.08.556881 Cold Spring Harbor Laboratory Press 2023-09-09 <![CDATA[ Encoding the Space of Protein-protein Binding Interfaces by Artificial Intelligence ]]> https://biorxiv.org/content/10.1101/2023.09.08.556812v1?rss=1 Su, Z. Dhusia, K. Wu, Y. 2023-09-10 doi:10.1101/2023.09.08.556812 Cold Spring Harbor Laboratory Press 2023-09-10 <![CDATA[ Spatiospectral image processing workflow considerations for advanced MR spectroscopy of the brain ]]> https://biorxiv.org/content/10.1101/2023.09.07.556701v1?rss=1 Cai, L. Y. Del Tufo, S. N. Barquero, L. D'Archangel, M. Sachs, L. Cutting, L. Glaser, N. Ghetti, S. Jaser, S. S. Anderson, A. W. Jordan, L. C. Landman, B. A. 2023-09-12 doi:10.1101/2023.09.07.556701 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Predicting fungal secondary metabolite activity from biosynthetic gene cluster data using machine learning ]]> https://biorxiv.org/content/10.1101/2023.09.12.557468v1?rss=1 Riedling, O. Walker, A. S. Rokas, A. 2023-09-12 doi:10.1101/2023.09.12.557468 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Asymmetric framework motion of TCR alpha beta controls load-dependent peptide discrimination ]]> https://biorxiv.org/content/10.1101/2023.09.10.557064v1?rss=1 Chang-Gonzalez, A. C. Mallis, R. J. Lang, M. J. Reinherz, E. Hwang, W. 2023-09-13 doi:10.1101/2023.09.10.557064 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Tissue-Specific Dependence of Th1 Cells on the Amino Acid Transporter SLC38A1 in Inflammation ]]> https://biorxiv.org/content/10.1101/2023.09.13.557496v1?rss=1 Sugiura, A. Beier, K. Chi, C. Heintzman, D. Ye, X. Wolf, M. M. Cephus, J.-Y. C. Hong, H. Lyssiotis, C. A. Newcomb, D. C. Rathmell, J. 2023-09-13 doi:10.1101/2023.09.13.557496 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ IMPROVING ANTIBODY AFFINITY USING LABORATORYDATA WITH LANGUAGE MODEL GUIDED DESIGN ]]> https://biorxiv.org/content/10.1101/2023.09.13.557505v1?rss=1 Krause, B. Subramanian, S. Yuan, T. Yang, M. Sato, A. Naik, N. 2023-09-13 doi:10.1101/2023.09.13.557505 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Tissue-specific transfer-learning enables retasking of a general comprehensive model to a specific domain ]]> https://biorxiv.org/content/10.1101/2023.09.11.557208v1?rss=1 Li, Q. Perera, D. Chen, Z. Wen, W. Wang, D. Yan, J. Shu, X.-o. Zheng, W. Guo, X. Long, Q. 2023-09-15 doi:10.1101/2023.09.11.557208 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Development and implementation of an integrated preclinical atherosclerosis database ]]> https://biorxiv.org/content/10.1101/2023.09.12.557423v1?rss=1 Xiang, R. R. Wang, Y. Shuey, M. M. Carvajal, B. Wells, Q. S. Beckman, J. A. Jaffe, I. Z. 2023-09-15 doi:10.1101/2023.09.12.557423 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Song distinguishability predicts reproductive isolation between subspecies of the dark-eyed junco ]]> https://biorxiv.org/content/10.1101/2023.09.14.557432v1?rss=1 Hourihan, S. K. Hudson, E. J. Du'Mottuchi, X. L. Beach, E. Smith, S. Creanza, N. 2023-09-15 doi:10.1101/2023.09.14.557432 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Plasma cell differentiation, antibody quality, and initial germinal center B cell population depend on glucose influx rate ]]> https://biorxiv.org/content/10.1101/2023.09.13.557599v1?rss=1 Brookens, S. K. Cho, S. H. Paik, Y. Meyer, K. Raybuck, A. L. Park, C. Greenwood, D. L. Rathmell, J. C. Boothby, M. 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Shen, X.-X. Rokas, A. Li, Y. 2023-09-21 doi:10.1101/2023.09.20.556338 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ GammaGateR: semi-automated marker gating for single-cell multiplexed imaging ]]> https://biorxiv.org/content/10.1101/2023.09.20.558645v1?rss=1 Xiong, J. Kaur, H. Heiser, C. N. McKinley, E. T. Roland, J. T. Coffey, R. J. Shrubsole, M. J. Wrobel, J. Ma, S. Lau, K. S. Vandekar, S. 2023-09-23 doi:10.1101/2023.09.20.558645 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ Characterizing Low-cost Registration for Photographic Images to Computed Tomography ]]> https://biorxiv.org/content/10.1101/2023.09.22.558989v1?rss=1 Kim, M. E. Lee, H. H. Ramadass, K. Gao, C. Van Schaik, K. Tkaczyk, E. Spraggins, J. M. Moyer, D. C. Landman, B. 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A. 2023-09-24 doi:10.1101/2023.09.23.559125 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ Quantitative Assessment of Morphological Changes in Lipid Droplets and Lipid-Mito Interactions with Aging in Brown Adipose ]]> https://biorxiv.org/content/10.1101/2023.09.23.559135v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@e5b7org.highwire.dtl.DTLVardef@e965e5org.highwire.dtl.DTLVardef@120c7e9org.highwire.dtl.DTLVardef@124bfb5_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract Workflow highlighting the process of murine interscapular BAT extraction, processing and imaging serial block facing-scanning electron microscopy and using Amira software for 3D reconstruction of LDs and mitochondrial lipid contact sites to elucidate their structure across aging. C_FIG ]]> Crabtree, A. Neikirk, K. Whiteside, A. McKenzie, J. Vue, Z. Vang, L. Owens, T. C. Oliver, A. Zeleke, F. Beasley, H. K. Garza-Lopez, E. Scudese, E. Koh, A. Navarro, S. Lam, J. Kirk, B. Mungai, M. Sweetwyne, M. T. 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Wu, Z. Wetsel, W. C. Roth, B. L. 2023-09-26 doi:10.1101/2023.09.25.559347 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Influence of preprocessing, distortion correction and cardiac triggering on the quality of diffusion MR images of spinal cord ]]> https://biorxiv.org/content/10.1101/2023.09.26.559530v1?rss=1 Schilling, K. Combes, A. Ramadass, K. Rheault, F. Sweeney, G. Prock, L. Sriram, S. Cohen-Adad, J. Gore, J. C. Landman, B. A. Smith, S. O'Grady, K. P. 2023-09-27 doi:10.1101/2023.09.26.559530 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Development of LIBRA-seq for the Guinea Pig Model System as a Tool for the Evaluation of Antibody Responses to Multivalent HIV-1 Vaccines ]]> https://biorxiv.org/content/10.1101/2023.09.25.559382v1?rss=1 80% CDR3 identity, thus establishing the existence of public clonotypes in guinea pigs elicited through vaccination. ]]> Vukovich, M. J. Raju, N. Kgagudi, P. Manamela, N. P. Abu-Shmais, A. A. Gripenstraw, K. R. Wasdin, P. T. 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Grayfer, L. 2023-10-01 doi:10.1101/2023.09.29.560127 Cold Spring Harbor Laboratory Press 2023-10-01 <![CDATA[ Admix-kit: An Integrated Toolkit and Pipeline for Genetic Analyses of Admixed Populations ]]> https://biorxiv.org/content/10.1101/2023.09.30.560263v1?rss=1 Hou, K. Gogarten, S. Kim, J. Hua, X. Dias, J.-A. Sun, Q. Wang, Y. Tan, T. Polygenic Risk Methods in Diverse Populations (PRIMED) Consortium Methods Working Group, Atkinson, E. G. Martin, A. Shortt, J. Hirbo, J. Li, Y. Pasaniuc, B. Zhang, H. 2023-10-02 doi:10.1101/2023.09.30.560263 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ A Specialized Epithelial Cell Type Regulating Mucosal Immunity and Driving Human Crohn's Disease ]]> https://biorxiv.org/content/10.1101/2023.09.30.560293v1?rss=1 Li, J. Simmons, A. J. Chiron, S. Ramirez-Solano, M. A. Tasneem, N. Kaur, H. Xu, Y. Revetta, F. Vega, P. N. Bao, S. Cui, C. Tyree, R. N. Raber, L. W. Conner, A. N. Beaulieu, D. B. Dalal, R. L. Horst, S. N. Pabla, B. S. Huo, Y. 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Carroll, R. K. Stemmler, T. L. 2023-10-04 doi:10.1101/2023.10.03.560778 Cold Spring Harbor Laboratory Press 2023-10-04 <![CDATA[ Laminar architecture of visual responses in supplementary eye field of macaques ]]> https://biorxiv.org/content/10.1101/2023.10.03.560770v1?rss=1 Thirunavukkarasu, P. Errington, S. Sajad, A. Schall, J. D. 2023-10-05 doi:10.1101/2023.10.03.560770 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Trade-offs, trade-ups, and high mutational parallelism underlie microbial adaptation to extreme feast/famine ]]> https://biorxiv.org/content/10.1101/2023.10.04.560893v1?rss=1 Behringer, M. G. Ho, W.-C. Miller, S. F. Worthan, S. B. Cen, Z. Stikeleather, R. Lynch, M. 2023-10-06 doi:10.1101/2023.10.04.560893 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Differential Requirement for Dimerization of the Membrane-Binding PH-TH Module of BTK in B cells and T cells ]]> https://biorxiv.org/content/10.1101/2023.10.05.561114v1?rss=1 Eisen, T. J. Ghaffari-Kashani, S. Weiss, A. Kuriyan, J. 2023-10-06 doi:10.1101/2023.10.05.561114 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ The Essential Role of Latrophilin-1 Adhesion GPCR Nanoclusters in Inhibitory Synapses ]]> https://biorxiv.org/content/10.1101/2023.10.08.561368v1?rss=1 Matus, D. Lopez, J. M. Sando, R. C. Südhof, T. C. 2023-10-08 doi:10.1101/2023.10.08.561368 Cold Spring Harbor Laboratory Press 2023-10-08 <![CDATA[ Benchmarking AlphaMissense Pathogenicity Predictions Against Cystic Fibrosis Variants ]]> https://biorxiv.org/content/10.1101/2023.10.05.561147v1?rss=1 McDonald, E. F. Oliver, K. E. Schlebach, J. P. Meiler, J. Plate, L. 2023-10-09 doi:10.1101/2023.10.05.561147 Cold Spring Harbor Laboratory Press 2023-10-09 <![CDATA[ Pleiotropy alleviates the fitness costs associated with resource allocation trade-offs in immune signaling networks ]]> https://biorxiv.org/content/10.1101/2023.10.06.561276v1?rss=1 Martin, R. Tate, A. 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C. 2023-10-11 doi:10.1101/2023.10.11.561953 Cold Spring Harbor Laboratory Press 2023-10-11 <![CDATA[ Restriction of Arginine Induces Antibiotic Tolerance in Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/2023.10.12.561972v1?rss=1 Freiberg, J. A. Ruiz, V. M. R. Green, E. R. Skaar, E. P. 2023-10-12 doi:10.1101/2023.10.12.561972 Cold Spring Harbor Laboratory Press 2023-10-12 <![CDATA[ Negative Binomial Mixture Model for Identification of Noise in Antigen-Specificity Predictions by LIBRA-seq ]]> https://biorxiv.org/content/10.1101/2023.10.13.562258v1?rss=1 Wasdin, P. T. Abu-Shmais, A. A. Irvin, M. W. Vukovich, M. J. Georgiev, I. S. 2023-10-17 doi:10.1101/2023.10.13.562258 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ A purine salvage bottleneck leads to bacterial adenine cross-feeding ]]> https://biorxiv.org/content/10.1101/2023.10.17.562681v1?rss=1 Chuang, Y.-C. Haas, N. W. Pepin, R. Behringer, M. Oda, Y. LaSarre, B. Harwood, C. S. McKinlay, J. B. 2023-10-17 doi:10.1101/2023.10.17.562681 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ A Tumour-Specific Molecular Network Promotes Tumour Growth in Drosophila by Enforcing a JNK-YKI Feedforward Loop ]]> https://biorxiv.org/content/10.1101/2023.10.18.561369v1?rss=1 Waghmare, I. Gangwani, K. Rai, A. Singh, A. Kango-Singh, M. 2023-10-18 doi:10.1101/2023.10.18.561369 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ Detection of EGFR and its Activity State in Plasma CD63-EVs from Glioblastoma Patients: Rapid Profiling using an Anion Exchange Membrane Sensor ]]> https://biorxiv.org/content/10.1101/2023.10.16.562628v1?rss=1 Maniya, N. Kumar, S. Franklin, J. L. Higginbotham, J. N. Scott, A. M. Gan, H. K. Coffey, R. J. Senapati, S. Chang, H.-C. 2023-10-19 doi:10.1101/2023.10.16.562628 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Adaptive capacity of a DNA polymerase clamp-loader ATPase complex ]]> https://biorxiv.org/content/10.1101/2023.10.18.562948v1?rss=1 Subramanian, S. Zhang, W. Nimkar, S. Kamel, M. O'Donnell, M. E. Kuriyan, J. 2023-10-19 doi:10.1101/2023.10.18.562948 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Collagen IV of basement membranes: I. Origin and diversification of COL4 genes enabling animal evolution ]]> https://biorxiv.org/content/10.1101/2023.10.18.563013v1?rss=1 Page-McCaw, P. S. Pokidysheva, E. N. Darris, C. E. Chetyrkin, S. Murawala, P. Gallup, J. Aspirnauts, Hudson, J. K. Hudson, B. G. 2023-10-21 doi:10.1101/2023.10.18.563013 Cold Spring Harbor Laboratory Press 2023-10-21 <![CDATA[ A High-Fat and Fructose Diet in Dogs Mirrors Insulin Resistance and β-cell Dysfunction Characteristic of Impaired Glucose Tolerance in Humans ]]> https://biorxiv.org/content/10.1101/2023.10.19.563103v1?rss=1 Gregory, J. M. Kraft, G. Man, C. D. Slaughter, J. C. Scott, M. F. Hastings, J. R. Edgerton, D. Moore, M. C. Cherrington, A. D. 2023-10-23 doi:10.1101/2023.10.19.563103 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ The evolution of gestation length in eutherian mammals ]]> https://biorxiv.org/content/10.1101/2023.10.22.563491v1?rss=1 Danis, T. Rokas, A. 2023-10-24 doi:10.1101/2023.10.22.563491 Cold Spring Harbor Laboratory Press 2023-10-24 <![CDATA[ Acoustomechanically activatable liposomes for ultrasonic drug uncaging ]]> https://biorxiv.org/content/10.1101/2023.10.23.563690v1?rss=1 Purohit, M. P. Sinha Roy, K. Xiang, Y. Yu, B. J. Azadian, M. M. Muwanga, G. Hart, A. R. Taoube, A. K. Gomez Lopez, D. Airan, R. D. 2023-10-25 doi:10.1101/2023.10.23.563690 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ Noradrenergic alpha-2a Receptor Stimulation Enhances Prediction Error Signaling in Anterior Cingulate Cortex and Striatum ]]> https://biorxiv.org/content/10.1101/2023.10.25.564052v1?rss=1 Hassani, S. A. Womelsdorf, T. 2023-10-25 doi:10.1101/2023.10.25.564052 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ Integrating population-level and cell-based signatures for drug repositioning ]]> https://biorxiv.org/content/10.1101/2023.10.25.564079v1?rss=1 He, C. Xu, Y. Zhou, Y. Fan, J. Cheng, C. Meng, R. Gamazon, E. R. Zhou, D. 2023-10-26 doi:10.1101/2023.10.25.564079 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees ]]> https://biorxiv.org/content/10.1101/2023.10.26.564272v1?rss=1 Brand, C. M. Kuang, S. Gilbertson, E. N. McArthur, E. Pollard, K. S. Webster, T. H. Capra, J. A. 2023-10-26 doi:10.1101/2023.10.26.564272 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ HLTF Prevents G4 Accumulation and Promotes G4-induced Fork Slowing to Maintain Genome Stability ]]> https://biorxiv.org/content/10.1101/2023.10.27.563641v1?rss=1 Bai, G. Endres, T. Kühbacher, U. Greer, B. H. Peacock, E. M. Crossley, M. P. Sathirachinda, A. Cortez, D. Eichman, B. F. Cimprich, K. A. 2023-10-27 doi:10.1101/2023.10.27.563641 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Adolescent social anxiety is associated with diminished discrimination of anticipated threat and safety ]]> https://biorxiv.org/content/10.1101/2023.10.30.564701v1?rss=1 Hur, J. Tillman, R. M. Kim, H. C. Didier, P. Anderson, A. S. Islam, S. Stockbridge, M. D. De Los Reyes, A. DeYoung, K. A. Smith, J. F. Shackman, A. J. 2023-11-02 doi:10.1101/2023.10.30.564701 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Cultivation, chemistry, and genome of Psilocybe zapotecorum ]]> https://biorxiv.org/content/10.1101/2023.11.01.564784v1?rss=1 Miller, D. R. Jacobs, J. T. Rockefeller, A. Singer, H. Bollinger, I. M. Conway, J. Slot, J. R. Cliffel, D. E. 2023-11-02 doi:10.1101/2023.11.01.564784 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ The shared genetic architecture and evolution of human language and musical rhythm ]]> https://biorxiv.org/content/10.1101/2023.11.01.564908v1?rss=1 Alagoez, G. Eising, E. Mekki, Y. Bignardi, G. Fontanillas, P. 23andMe Research Team, Nivard, M. G. Luciano, M. Cox, N. J. Fisher, S. E. Gordon, R. L. 2023-11-02 doi:10.1101/2023.11.01.564908 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Nitrate-mediated luminal expansion of Salmonella Typhimurium is dependent on the ER stress protein CHOP ]]> https://biorxiv.org/content/10.1101/2023.11.03.565559v1?rss=1 Sweet, L. A. Kuss-Duerkop, S. K. Byndloss, M. X. Keestra-Gounder, A. M. 2023-11-03 doi:10.1101/2023.11.03.565559 Cold Spring Harbor Laboratory Press 2023-11-03 <![CDATA[ Machine learning-based exploration, expansion and definition of the atropopeptide family of ribosomally synthesized and posttranslationally modified peptides ]]> https://biorxiv.org/content/10.1101/2023.11.03.565440v1?rss=1 Biermann, F. Tan, B. Breitenbach, M. Nanudorn, P. Dimitrova, Y. Kakumu, Y. Walker, A. S. Ueoka, R. Helfrich, E. J. N. 2023-11-05 doi:10.1101/2023.11.03.565440 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Purinergic calcium signaling drives drug tolerance through ERK reactivation in BRAF-mutant melanoma ]]> https://biorxiv.org/content/10.1101/2023.11.03.565532v1?rss=1 Stauffer, P. E. Brinkley, J. Jacobson, D. A. Quaranta, V. Tyson, D. R. 2023-11-05 doi:10.1101/2023.11.03.565532 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Transcriptomic Profiling Reveals Claudin 18.2 as a Diagnostic Biomarker of Menetrier Disease and the Role of Hedgehog Signaling in Pathogenesis ]]> https://biorxiv.org/content/10.1101/2023.11.03.565570v1?rss=1 Shin, M. Gabriel, T. Coffey, R. J. Huh, W. J. 2023-11-06 doi:10.1101/2023.11.03.565570 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Generation of human induced pluripotent stem cell (hiPSC) lines from patients with extreme high and low polygenic scores for QT interval ]]> https://biorxiv.org/content/10.1101/2023.11.03.565486v1?rss=1 Mitchell, D. Ullah, R. Vanags, L. Shen, A. Jones, L. ONeill, M. Davogustto, G. Shaffer, C. Roden, D. Shoemaker, B. Williams, H. Strickland, T. Agee, T. Johnson, C. Kroncke, B. 2023-11-08 doi:10.1101/2023.11.03.565486 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ The HIV-1 capsid serves as a nanoscale reaction vessel for reverse transcription ]]> https://biorxiv.org/content/10.1101/2023.11.08.566350v1?rss=1 Aiken, C. Jennings, J. Bracey, H. Nguyen, D. T. Dasgupta, R. Rivera, A. V. Sluis-Cremer, N. Shi, J. 2023-11-09 doi:10.1101/2023.11.08.566350 Cold Spring Harbor Laboratory Press 2023-11-09 <![CDATA[ A Multi-task Platform for Profiling Cognitive and Motivational Constructs in Humans and Nonhuman Primates ]]> https://biorxiv.org/content/10.1101/2023.11.09.566422v1?rss=1 Watson, M. R. Traczewski, N. Dhungana, S. Boroujeni, K. B. Neumann, A. Wen, X. Womelsdorf, T. 2023-11-13 doi:10.1101/2023.11.09.566422 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Spatiotemporal EP4-fibulin-1 expression is associated with vascular intimal hyperplasia ]]> https://biorxiv.org/content/10.1101/2023.11.09.566500v1?rss=1 Okumura, S. Yokoyama, U. Oka, S. Sasaki, T. Cooley, M. A. Hidaka, Y. Tanifuji, S. Kaneko, M. Abe, T. Breyer, R. M. Homma, H. Kato, Y. 2023-11-13 doi:10.1101/2023.11.09.566500 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Network Enrichment Significance Testing in Brain-Phenotype Association Studies ]]> https://biorxiv.org/content/10.1101/2023.11.10.566593v1?rss=1 Weinstein, S. M. Vandekar, S. N. Alexander-Bloch, A. F. Raznahan, A. Li, M. Gur, R. E. Gur, R. C. Roalf, D. R. Park, M. T. M. Chakravarty, M. Baller, E. B. Linn, K. A. Satterthwaite, T. D. Shinohara, R. T. 2023-11-13 doi:10.1101/2023.11.10.566593 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Single cell RNA-sequencing suggests a novel lipid associated mast cell population following weight cycling ]]> https://biorxiv.org/content/10.1101/2023.11.12.566786v1?rss=1 Caslin, H. L. Cottam, M. A. Betjemann, A. M. Mashayekhi, M. Silver, H. J. Hasty, A. 2023-11-15 doi:10.1101/2023.11.12.566786 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ 3D Mitochondrial Structure in Aging Human Skeletal Muscle: Insights into MFN-2 Mediated Changes ]]> https://biorxiv.org/content/10.1101/2023.11.13.566502v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@1d2be0eorg.highwire.dtl.DTLVardef@bba6caorg.highwire.dtl.DTLVardef@1c335e5org.highwire.dtl.DTLVardef@10789c9_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO Age-related skeletal muscle atrophy shows morphological alterations in mitochondrial structure associated with declining function. Our findings propose that exercise intervention may counteract these structural declines by reinstating levels of mitofusin 2, thus highlighting a potential mechanism by which exercise attenuates age-induced mitochondrial dysfunction. C_FIG ]]> Scudese, E. Vue, Z. Katti, P. Marshall, A. Vang, L. Garza Lopez, E. Neikirk, K. Stephens, D. Hall, D. D. Rostami, R. Shao, J.-q. Mungai, M. AshShareef, S. Hicsasmaz, I. Manus, S. Whiteside, A. Williams, C. Damo, S. Gaddy, J. Kirabo, A. Glancy, B. Henrique Martin Dantas, E. Kinder, A. Scartoni, F. Baffi, M. McReynolds, M. Wanjalla, C. N. Phillips, M. A. Exil, V. Mobley, B. Hinton, A. 2023-11-15 doi:10.1101/2023.11.13.566502 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Potent antibody-dependent cellular cytotoxicity of a V2-specific antibody is not sufficient for protection of macaques against SIV challenge ]]> https://biorxiv.org/content/10.1101/2023.11.14.567003v1?rss=1 Grunst, M. W. Gil, H. M. Grandea, A. G. Snow, B. J. Andrabi, R. Nedellec, R. Burton, I. Clark, N. M. Janaka, S. K. Keles, N. K. Moriarty, R. V. Weiler, A. M. Capuano, S. Fennessey, C. M. Friedrich, T. C. O'Connor, S. L. O'Connor, D. H. Broman, A. T. Keele, B. F. Lifson, J. D. Hangartner, L. Burton, D. R. Evans, D. T. 2023-11-15 doi:10.1101/2023.11.14.567003 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Extracellular Matrix Abnormalities Contribute to Cardiac Insulin Resistance and Associated Dysfunction in Diet-induced Obese Mice ]]> https://biorxiv.org/content/10.1101/2023.11.14.567128v1?rss=1 Musale, V. Murdoch, C. Banah, A. K. Hasib, A. Hennayake, C. K. Dong, B. Lang, C. C. Wasserman, D. H. Kang, L. 2023-11-16 doi:10.1101/2023.11.14.567128 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ VTA dopamine neurons are hyperexcitable in 3xTg-AD mice due to casein kinase 2-dependent SK channel dysfunction ]]> https://biorxiv.org/content/10.1101/2023.11.16.567486v1?rss=1 Blankenship, H. E. Carter, K. A. Cassidy, N. T. Markiewicz, A. N. Thellmann, M. I. Sharpe, A. L. Freeman, W. M. Beckstead, M. J. 2023-11-17 doi:10.1101/2023.11.16.567486 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Insulin at the Intersection of Thermoregulation and Glucose Homeostasis ]]> https://biorxiv.org/content/10.1101/2023.11.17.566254v1?rss=1 Winn, N. C. Schleh, M. W. Garcia, J. N. Lantier, L. McGuinness, O. P. Blair, J. A. Hasty, A. H. Wasserman, D. H. 2023-11-17 doi:10.1101/2023.11.17.566254 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Protein-lipid interactions drive presynaptic assembly upstream of cell adhesion molecules ]]> https://biorxiv.org/content/10.1101/2023.11.17.567618v1?rss=1 Frankel, E. B. Tiroumalechetty, A. R. Henry, P. S. Su, Z. Wu, Y. Kurshan, P. T. 2023-11-17 doi:10.1101/2023.11.17.567618 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Whole genome association testing in 333,100 individuals across three biobanks identifies rare non-coding single variant and genomic aggregate associations with height ]]> https://biorxiv.org/content/10.1101/2023.11.19.566520v1?rss=1 Hawkes, G. Beaumont, R. N. Li, Z. Mandla, R. Li, X. Albert, C. M. Arnett, D. K. Ashley-Koch, A. E. Ashrani, A. A. Barnes, K. C. Boerwinkle, E. Brody, J. A. Carson, A. P. Chami, N. Chen, Y.-D. I. Chung, M. K. Curran, J. E. Darbar, D. Ellinor, P. T. Fornage, M. Gordeuk, V. R. Guo, X. He, J. Hwu, C.-M. Kalyani, R. R. Kaplan, R. Kardia, S. L. R. Kooperberg, C. Loos, R. J. F. Lubitz, S. A. Minster, R. L. Mitchell, B. D. Murabito, J. M. Palmer, N. D. Psaty, B. M. Redline, S. Shoemaker, M. B. Silverman, E. K. Telen, M. J. Weiss, S. T. Yanek, L. R. Zhou, H. NH 2023-11-20 doi:10.1101/2023.11.19.566520 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ Muscle cofilin alters neuromuscular junction postsynaptic development to strengthen functional neurotransmission ]]> https://biorxiv.org/content/10.1101/2023.11.21.568166v1?rss=1 Christophers, B. Leahy, S. N. Soffar, D. von Saucken, V. Broadie, K. Baylies, M. 2023-11-22 doi:10.1101/2023.11.21.568166 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Preoptic area controls sleep-related seizure onset in a genetic epilepsy mouse model ]]> https://biorxiv.org/content/10.1101/2023.11.24.568593v1?rss=1 Potesta, C. V. Cargile, M. S. Yan, A. Macdonald, R. L. Gallagher, M. J. Zhou, C. 2023-11-24 doi:10.1101/2023.11.24.568593 Cold Spring Harbor Laboratory Press 2023-11-24 <![CDATA[ Propofol anesthesia destabilizes neural dynamics across cortex ]]> https://biorxiv.org/content/10.1101/2023.11.24.568595v1?rss=1 Eisen, A. J. Kozachkov, L. Bastos, A. M. Donoghue, J. A. Mahnke, M. K. Brincat, S. L. Chandra, S. Brown, E. N. Fiete, I. Miller, E. K. 2023-11-25 doi:10.1101/2023.11.24.568595 Cold Spring Harbor Laboratory Press 2023-11-25 <![CDATA[ Multiomic single-cell sequencing defines tissue-specific responses in Stevens-Johnson Syndrome and Toxic epidermal necrolysis. ]]> https://biorxiv.org/content/10.1101/2023.11.26.568771v1?rss=1 Gibson, A. Ram, R. Gangula, R. Li, Y. Mukherjee, E. Palubinsky, A. M. Campbell, C. N. Thorne, M. Konvinse, K. C. Choshi, P. Deshpande, P. Pedretti, S. O'Neil, R. T. Wanjalla, C. N. Kalams, S. A. Gaudieri, S. Lehloenya, R. J. Bailin, S. S. Chopra, A. Trubiano, J. A. Peter, J. G. Mallal, S. A. Phillips, E. J. 2023-11-27 doi:10.1101/2023.11.26.568771 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ Human Heart Failure Alters Mitochondria and Fiber 3D Structure Triggering Metabolic Shifts ]]> https://biorxiv.org/content/10.1101/2023.11.28.569095v1?rss=1 Vue, Z. Ajayi, P. T. Neikirk, K. Murphy, A. Prasad, P. Jenkins, B. C. Vang, L. Garza-Lopez, E. Mungai, M. Marshall, A. G. Beasley, H. K. Killion, M. Parker, R. Anukodem, J. Lavine, K. Ajijola, O. Mobley, B. Dai, D.-F. Exil, V. Kirabo, A. Ru Su, Y. Tomasek, K. Zhang, X. Wanjalla, C. N. Hubert, D. L. Phillips, M. A. McReynolds, M. Glancy, B. Hinton, A. 2023-11-30 doi:10.1101/2023.11.28.569095 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ Parsing digital or analogue TCR performance through piconewton forces ]]> https://biorxiv.org/content/10.1101/2023.11.29.568292v1?rss=1 Akitsu, A. Kobayashi, E. Feng, Y. Stephens, H. M. Brazin, K. N. Masi, D. J. Kirpatrick, E. H. Mallis, R. J. Duke-Cohan, J. S. Booker, M. A. Cinella, V. Feng, W. W. Holliday, E. L. Lee, J. J. Zienkiewicz, K. J. Tolstorukov, M. Y. Hwang, W. S. Lang, M. J. Reinherz, E. 2023-11-30 doi:10.1101/2023.11.29.568292 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ Haems relevance genuine? Re-visiting the roles of TANGO2 homologues including HRG-9 and HRG-10 in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.11.29.569072v1?rss=1 Sandkuhler, S. E. Youngs, K. Owlett, L. Bandora, M. Naaz, A. Kim, E. S. Wang, L. Wojtovich, A. P. Gupta, V. A. Sacher, M. Mackenzie, S. J. 2023-11-30 doi:10.1101/2023.11.29.569072 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ Leptomeningeal Neural Organoid (LMNO) Fusions as Models to Study Meninges-Brain Signaling ]]> https://biorxiv.org/content/10.1101/2023.12.01.569648v1?rss=1 Jones, H. E. Robertson, G. L. Romero-Morales, A. I. O'Rourke, R. Siegenthaler, J. A. Gama, V. 2023-12-02 doi:10.1101/2023.12.01.569648 Cold Spring Harbor Laboratory Press 2023-12-02 <![CDATA[ Intracellular Ebola Virus nucleocapsid assembly revealed by in situ cryo-electron tomography. ]]> https://biorxiv.org/content/10.1101/2023.12.01.569666v1?rss=1 Watanabe, R. Zyla, D. Parekh, D. Hong, C. Jones, Y. Schendel, S. L. Wan, W. Castillon, G. Saphire, E. O. 2023-12-02 doi:10.1101/2023.12.01.569666 Cold Spring Harbor Laboratory Press 2023-12-02 <![CDATA[ In situ lipidomics of Staphylococcus aureus osteomyelitis using imaging mass spectrometry ]]> https://biorxiv.org/content/10.1101/2023.12.01.569690v1?rss=1 Good, C. J. Butrico, C. E. Colley, M. E. Gibson-Corley, K. N. Cassat, J. E. Spraggins, J. M. Caprioli, R. M. 2023-12-02 doi:10.1101/2023.12.01.569690 Cold Spring Harbor Laboratory Press 2023-12-02 <![CDATA[ A foundational atlas of autism protein interactions reveals molecular convergence ]]> https://biorxiv.org/content/10.1101/2023.12.03.569805v1?rss=1 Wang, B. Vartak, R. Zaltsman, Y. Naing, Z. Z. C. Hennick, K. M. Polacco, B. J. Bashir, A. Eckhardt, M. Bouhaddou, M. Xu, J. Sun, N. Lasser, M. Zhou, Y. Guiley, K. Z. Chan, U. Kaye, J. A. Khare, P. Drake, S. Drury, V. Burke, D. F. Gonzalez, S. Alkhairy, S. Morris, M. Baum, T. Krasnoff, R. Wang, S. Pham, P. Arbalaez, J. Pratt, D. Chag, S. Rolland, T. Bourgeron, T. Finkbeiner, S. Bandyopadhay, S. Ideker, T. Beltrao, P. Willsey, H. R. Obernier, K. Nowakowski, T. J. Huttenhain, R. State, M. W. Willsey, A. J. Krogan, N. J. 2023-12-03 doi:10.1101/2023.12.03.569805 Cold Spring Harbor Laboratory Press 2023-12-03 <![CDATA[ Identification and Characterization of a Novel Nematode Pan Allergen (NPA) from Wuchereria bancrofti and their Potential Role in Human Filarial Tropical Pulmonary Eosinophilia (TPE) ]]> https://biorxiv.org/content/10.1101/2023.12.04.569914v1?rss=1 Katru, S. C. Munirathinam, G. Hadadianpour, A. Balakrishnan, A. S. Smith, S. A. Kalyanasundaram, R. 2023-12-04 doi:10.1101/2023.12.04.569914 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ Queuosine Salvage in Bartonella henselae Houston 1: A Unique Evolutionary Path ]]> https://biorxiv.org/content/10.1101/2023.12.05.570228v1?rss=1 Quaiyum, S. Yuan, Y. Sun, G. Ratnayake, M. Hutinet, G. Dedon, P. C. Minnick, M. F. de Crecy-Lagard, V. 2023-12-06 doi:10.1101/2023.12.05.570228 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ State-dependent circuit dynamics of superficial and deep CA1 pyramidal cells in macaques ]]> https://biorxiv.org/content/10.1101/2023.12.06.570369v1?rss=1 Abbaspoor, S. Hoffman, K. L. 2023-12-06 doi:10.1101/2023.12.06.570369 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ Machine-learning-based Structural Analysis of Interactions between Antibodies and Antigens ]]> https://biorxiv.org/content/10.1101/2023.12.06.570397v1?rss=1 Zhang, G. Su, Z. Zhang, T. Wu, Y. 2023-12-08 doi:10.1101/2023.12.06.570397 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ A Fluorescence-Based Sensor for Calibrated Measurement of Protein Kinase Stability in Live Cells ]]> https://biorxiv.org/content/10.1101/2023.12.07.570636v1?rss=1 Paul, J. W. Muratcioglu, S. Kuriyan, J. 2023-12-08 doi:10.1101/2023.12.07.570636 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Byproducts of inflammatory radical metabolism provide transient nutrient niches for microbes in the inflamed gut ]]> https://biorxiv.org/content/10.1101/2023.12.08.570695v1?rss=1 Spiga, L. Winter, M. G. Muramatsu, M. Rojas, V. Chanin, R. Zhu, W. Hughes, E. R. Taylor, S. Faber, F. Porwollik, S. Carvalho, T. Qin, T. Santos, R. Andrews-Polymenis, H. L. McClelland, M. Winter, S. E. 2023-12-08 doi:10.1101/2023.12.08.570695 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Exploring the embodied mind: functional connectome fingerprinting of meditation expertise ]]> https://biorxiv.org/content/10.1101/2023.12.06.570128v1?rss=1 Czajko, S. Zorn, J. Perry, R. Daumail, L. Chetelat, G. Margulies, D. Lutz, A. 2023-12-11 doi:10.1101/2023.12.06.570128 Cold Spring Harbor Laboratory Press 2023-12-11 <![CDATA[ Rescue of Impaired Blood-Brain Barrier in Tuberous Sclerosis Complex Patient Derived Neurovascular Unit ]]> https://biorxiv.org/content/10.1101/2023.12.15.571738v1?rss=1 Brown, J. Faley, S. Judge, M. Ward, P. Ihrie, R. A. Carson, R. Armstrong, L. Sahin, M. Wikswo, J. Ess, K. Neely, D. 2023-12-16 doi:10.1101/2023.12.15.571738 Cold Spring Harbor Laboratory Press 2023-12-16 <![CDATA[ Image-based spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/2023.12.15.571954v1?rss=1 Vannan, A. Lyu, R. Williams, A. L. Negretti, N. M. Mee, E. D. Hirsh, J. Hirsh, S. Nichols, D. S. Calvi, C. L. Talor, C. J. Polosukhin, V. V. Serezani, A. P. McCall, A. S. Gokey, J. J. Shim, H. Ware, L. B. Bacchetta, M. J. Shaver, C. M. Blackwell, T. S. Kropski, J. A. Walia, R. Sucre, J. M. McCarthy, D. J. Banovich, N. E. 2023-12-16 doi:10.1101/2023.12.15.571954 Cold Spring Harbor Laboratory Press 2023-12-16 <![CDATA[ A choroid plexus apocrine secretion mechanism shapes CSF proteome and embryonic brain development ]]> https://biorxiv.org/content/10.1101/2024.01.08.574486v1?rss=1 Courtney, Y. Head, J. P. Yimer, E. D. Dani, N. Shipley, F. B. Libermann, T. A. Lehtinen, M. K. 2024-01-08 doi:10.1101/2024.01.08.574486 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ Identifying Patient-Specific Root Causal Genes with High Throughput Perturbations ]]> https://biorxiv.org/content/10.1101/2024.01.13.574491v1?rss=1 Strobl, E. V. Gamazon, E. R. 2024-01-14 doi:10.1101/2024.01.13.574491 Cold Spring Harbor Laboratory Press 2024-01-14 <![CDATA[ Structure of the extracellular region of the adhesion GPCR CELSR1 reveals a compact module which regulates G protein-coupling ]]> https://biorxiv.org/content/10.1101/2024.01.26.577439v1?rss=1 Bandekar, S. J. Garbett, K. Kordon, S. P. Dintzner, E. Shearer, T. Sando, R. Arac, D. 2024-01-27 doi:10.1101/2024.01.26.577439 Cold Spring Harbor Laboratory Press 2024-01-27 <![CDATA[ Sex differences in immune function and disease risk are not easily explained by an evolutionary mismatch ]]> https://biorxiv.org/content/10.1101/2024.02.13.580011v1?rss=1 Arner, A. M. Muhoya, B. Rozado, M. S. Gurven, M. R. Kahumbu, J. Kamau, J. Kinyua, P. Lotukoi, F. Martins, D. J. Miano, C. Montague, M. J. Njeru, S. Peng, J. Straub, P. Watowich, M. M. Davis, L. K. Snyder-Mackler, N. Ayroles, J. F. Lea, A. J. 2024-02-16 doi:10.1101/2024.02.13.580011 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ Multifocal Ectopic Purkinje Premature Contractions due to neutralization of an SCN5A negative charge: structural insights into the gating pore hypothesis ]]> https://biorxiv.org/content/10.1101/2024.02.13.580021v1?rss=1 Roden, D. M. Glazer, A. M. Yang, T. Page, D. Fouda, M. Wada, Y. Lancaster, M. C. O'Neill, M. J. Muhammad, A. Gao, X. Ackerman, M. J. Sanatani, S. Ruben, P. Li, B. 2024-02-16 doi:10.1101/2024.02.13.580021 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ CNVeil enables accurate and robust tumor subclone identification and copy number estimation from single-cell DNA sequencing data ]]> https://biorxiv.org/content/10.1101/2024.02.21.581409v1?rss=1 Yuan, W. Luo, C. Hu, Y. Zhang, L. Wen, Z. Liu, Y. H. Mallory, X. Zhou, X. M. 2024-02-23 doi:10.1101/2024.02.21.581409 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Revealing In Situ Molecular Profiles of Glomerular Cell Types and Substructures with Integrated Imaging Mass Spectrometry and Multiplexed Immunofluorescence Microscopy ]]> https://biorxiv.org/content/10.1101/2024.02.21.581450v1?rss=1 Esselman, A. B. Moser, F. A. Tideman, L. Migas, L. G. Djambazova, K. V. Colley, M. E. Pingry, E. L. Patterson, N. H. Farrow, M. A. Yang, H. Fogo, A. B. de Caestecker, M. Van de Plas, R. Spraggins, J. M. 2024-02-23 doi:10.1101/2024.02.21.581450 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Evolution of pH-sensitive transcription termination during adaptation to repeated long-term starvation. ]]> https://biorxiv.org/content/10.1101/2024.03.01.582989v1?rss=1 Worthan, S. B. McCarthy, R. D. P. Delaleau, M. Stikeleather, R. Bratton, B. P. Boudvillain, M. Behringer, M. G. 2024-03-02 doi:10.1101/2024.03.01.582989 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ Intermittent stimulation of the basal forebrain improves working memory in aged nonhuman primates. ]]> https://biorxiv.org/content/10.1101/2024.03.01.582925v1?rss=1 Wang, Z. Pennington, K. R. Debs, L. Chung, S. Bava, J. M. Garin, C. Vale, F. L. Bick, S. K. Englot, D. J. Terry, A. V. Constantinidis, C. Blake, D. T. 2024-03-06 doi:10.1101/2024.03.01.582925 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Medial prefrontal dopamine dynamics reflect allocation of selective attention ]]> https://biorxiv.org/content/10.1101/2024.03.04.583245v1?rss=1 Melugin, P. R. Nolan, S. O. Kandov, E. Ferrara, C. F. Farahbakhsh, Z. Z. Siciliano, C. A. 2024-03-06 doi:10.1101/2024.03.04.583245 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Arteriolar degeneration and stiffness in cerebral amyloid angiopathy are linked to β-amyloid deposition and lysyl oxidase. ]]> https://biorxiv.org/content/10.1101/2024.03.08.583563v1?rss=1 Ventura-Antunes, L. Nackenoff, A. Romero-Fernandez, W. Bosworth, A. M. Prusky, A. Wang, E. Carvajal-Tapia, C. Shostak, A. Harmsen, H. Mobley, B. Maldonado, J. Solopova, E. Snider, J. C. Merryman, W. D. D. Lippmann, E. Schrag, M. 2024-03-13 doi:10.1101/2024.03.08.583563 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Strain heterogeneity in a non-pathogenic fungus highlights factors contributing to virulence ]]> https://biorxiv.org/content/10.1101/2024.03.08.583994v1?rss=1 Rinker, D. C. Sauters, T. J. C. Steffen, K. Gumilang, A. Raja, H. A. Rangel-Grimaldo, M. Pinzan, C. F. de Castro, P. A. dos Reis, T. F. Delbaje, E. Houbraken, J. Goldman, G. H. Oberlies, N. H. Rokas, A. 2024-03-10 doi:10.1101/2024.03.08.583994 Cold Spring Harbor Laboratory Press 2024-03-10 <![CDATA[ Neurobiological Changes Across Pregnancy: A Longitudinal Investigation ]]> https://biorxiv.org/content/10.1101/2024.03.08.584178v1?rss=1 Niu, Y. Conrad, B. N. Camacho, M. C. Ravi, S. Piersiak, H. A. Bailes, L. G. Barnett, W. Manhard, M. K. Cole, D. A. Clayton, E. W. Osmundson, S. S. Smith, S. A. Kujawa, A. Humphreys, K. L. 2024-03-08 doi:10.1101/2024.03.08.584178 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ Cytokine and Chemokine Receptor Profiles in Adipose Tissue Vasculature Unravel Endothelial Cell Responses in HIV ]]> https://biorxiv.org/content/10.1101/2024.03.10.584280v1?rss=1 Obare, L. M. Priest, S. Ismael, A. Mashayekhi, M. Zhang, X. Stolze, L. Sheng, Q. Vue, Z. Neikirk, K. Beasley, H. Gabriel, C. Temu, T. Gianella, S. Mallal, S. Koethe, J. Hinton, A. Bailin, S. Wanjalla, C. N. 2024-03-12 doi:10.1101/2024.03.10.584280 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Benchmarking clustering, alignment, and integration methods for spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2024.03.12.584114v1?rss=1 Hu, Y. Li, Y. Xie, M. Rao, M. Shen, W. Luo, C. Qin, H. Baek, J. Zhou, X. M. 2024-03-13 doi:10.1101/2024.03.12.584114 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Development of a series of genetically engineered NTRK fusion-driven pediatric-type high-grade glioma mouse models ]]> https://biorxiv.org/content/10.1101/2024.03.13.584849v1?rss=1 Schmid, S. Russell, Z. R. Yamashita, A. S. West, M. E. Parrish, A. G. Walker, J. Rudoy, D. Yan, J. Z. Quist, D. C. Gessesse, B. N. Alvinez, N. Cimino, P. J. Kumasaka, D. K. Parchment, R. E. Holland, E. C. Szulzewsky, F. 2024-03-13 doi:10.1101/2024.03.13.584849 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Enhanced mucosal mitochondrial function corrects dysbiosis and OXPHOS metabolism in IBD ]]> https://biorxiv.org/content/10.1101/2024.03.14.584471v1?rss=1 View larger version (46K): org.highwire.dtl.DTLVardef@41e437org.highwire.dtl.DTLVardef@1eddf37org.highwire.dtl.DTLVardef@1d9bff3org.highwire.dtl.DTLVardef@c925f0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kapur, N. Alam, A. Hassan, S. A. Patel, P. H. Wempe, L. Bhogoju, S. Goretsky, T. Kim, J. H. Herzog, J. Ge, Y. Awuah, S. Byndloss, M. Baumler, A. J. Zadeh, M. Sator, R. B. Barrett, T. A. 2024-03-14 doi:10.1101/2024.03.14.584471 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Synchrony between midbrain gene transcription and dopamine terminal regulation is modulated by chronic alcohol drinking ]]> https://biorxiv.org/content/10.1101/2024.03.15.584711v1?rss=1 Farahbakhsh, Z. Z. Holleran, K. M. Sens, J. P. Fordahl, S. C. Mauterer, M. I. Lopez, A. J. Cuzon Carlson, V. C. Kiraly, D. D. Grant, K. A. Jones, S. R. Siciliano, C. A. 2024-03-17 doi:10.1101/2024.03.15.584711 Cold Spring Harbor Laboratory Press 2024-03-17 <![CDATA[ Loss of intermicrovillar adhesion impairs basolateral junctional complexes in transporting epithelia ]]> https://biorxiv.org/content/10.1101/2024.03.19.585733v1?rss=1 Cencer, C. S. Robinson, K. L. Tyska, M. J. 2024-03-19 doi:10.1101/2024.03.19.585733 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Intestinal tuft cells assemble a cytoskeletal superstructure composed of co-aligned actin bundles and microtubules ]]> https://biorxiv.org/content/10.1101/2024.03.19.585757v1?rss=1 Silverman, J. B. Krystofiak, E. Caplan, L. R. Lau, K. S. Tyska, M. J. 2024-03-19 doi:10.1101/2024.03.19.585757 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Design of Antigen-Specific Antibody CDRH3 Sequences Using AI and Germline-Based Templates ]]> https://biorxiv.org/content/10.1101/2024.03.22.586241v1?rss=1 Marinov, T. M. Abu-Shmais, A. Janke, A. K. Georgiev, I. 2024-03-22 doi:10.1101/2024.03.22.586241 Cold Spring Harbor Laboratory Press 2024-03-22 <![CDATA[ STING-Activating Polymer-Drug Conjugates for Cancer Immunotherapy ]]> https://biorxiv.org/content/10.1101/2024.03.23.585817v1?rss=1 Sheehy, T. L. Kwiatkowski, A. J. Arora, K. Kimmel, B. R. Schulman, J. A. Gibson-Corley, K. Wilson, J. T. 2024-03-27 doi:10.1101/2024.03.23.585817 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Characterization of a cytokinin-binding protein locus in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2024.03.25.586654v1?rss=1 Darwin, K. H. Yoo, J. H. Santarossa, C. Thomas, A. K. Ekiert, D. 2024-03-26 doi:10.1101/2024.03.25.586654 Cold Spring Harbor Laboratory Press 2024-03-26 <![CDATA[ Ligand-induced CaMKIIα hub Trp403 flip, hub domain stacking and kinase inhibition ]]> https://biorxiv.org/content/10.1101/2024.03.26.586665v1?rss=1 Narayanan, D. Larsen, A. S. G. Gauger, S. J. Adafia, R. Hammershoi, R. B. Hamborg, L. Bruus-Jensen, J. Griem-Krey, N. Gee, C. L. Frolund, B. Stratton, M. M. Kuriyan, J. Kastrup, J. S. Langkilde, A. E. Wellendorph, P. Solbak, S. M. O. 2024-03-27 doi:10.1101/2024.03.26.586665 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ CYRI-B loss promotes enlarged mature focal adhesions and restricts microtubule and ERC1 access to the cell leading edge ]]> https://biorxiv.org/content/10.1101/2024.03.26.586838v1?rss=1 Whitelaw, J. A. Lilla, S. Nikolaou, S. Tweedy, L. Fort, L. Paul, N. R. Zanivan, S. Gadegaard, N. Insall, R. H. Machesky, L. M. 2024-03-27 doi:10.1101/2024.03.26.586838 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Development and Organization of the Retinal Orientation Selectivity Map ]]> https://biorxiv.org/content/10.1101/2024.03.27.585774v1?rss=1 Vita, D. J. Orsi, F. S. Stanko, N. G. Clark, N. A. Tiriac, A. 2024-03-28 doi:10.1101/2024.03.27.585774 Cold Spring Harbor Laboratory Press 2024-03-28 <![CDATA[ Macromolecular interactions and geometrical confinement determine the 3D diffusion of ribosome-sized particles in live Escherichia coli cells ]]> https://biorxiv.org/content/10.1101/2024.03.27.587083v1?rss=1 Valverde-Mendez, D. Sunol, A. M. Bratton, B. P. Delarue, M. Hofmann, J. L. Sheehan, J. P. Gitai, Z. Holt, L. J. Shaevitz, J. W. Zia, R. N. 2024-03-28 doi:10.1101/2024.03.27.587083 Cold Spring Harbor Laboratory Press 2024-03-28 <![CDATA[ The laminar organization of cell types in macaque cortex and its relationship to neuronal oscillations ]]> https://biorxiv.org/content/10.1101/2024.03.27.587084v1?rss=1 Lichtenfeld, M. J. Mulvey, A. G. Nejat, H. Xiong, Y. S. Carlson, B. M. Mitchell, B. A. Mendoza-Halliday, D. Westerberg, J. A. Desimone, R. Maier, A. Kaas, J. H. Bastos, A. M. 2024-03-30 doi:10.1101/2024.03.27.587084 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Mitochondrial genome variation affects humoral and cell-mediated innate immune responses and infection outcomes ]]> https://biorxiv.org/content/10.1101/2024.03.28.587162v1?rss=1 Salminen, T. S. Vesala, L. Basikhina, Y. Kutzer, M. Tuomela, T. Lucas, R. Monteith, K. Prakash, A. Tietz, T. Vale, P. F. 2024-03-28 doi:10.1101/2024.03.28.587162 Cold Spring Harbor Laboratory Press 2024-03-28 <![CDATA[ IL-8 Instructs Macrophage Identity in Lateral Ventricle Contacting Glioblastoma ]]> https://biorxiv.org/content/10.1101/2024.03.29.587030v1?rss=1 Medina, S. Brockman, A. A. Cross, C. E. Hayes, M. J. Mobley, B. C. Mistry, A. M. Chotai, S. Weaver, K. D. Thompson, R. Chambless, L. B. Ihrie, R. A. Irish, J. M. 2024-03-30 doi:10.1101/2024.03.29.587030 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Intrapartum antibiotic prophylaxis selects for mutators in group B streptococci among persistently colonized patients ]]> https://biorxiv.org/content/10.1101/2024.04.01.587590v1?rss=1 Pell, M. E. Blankenship, H. M. Gaddy, J. A. Davies, H. D. Manning, S. D. 2024-04-02 doi:10.1101/2024.04.01.587590 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Group Heteroscedasticity - A Silent Saboteur of Power and False Discovery in RNA-Seq Differential Expression ]]> https://biorxiv.org/content/10.1101/2024.04.01.587633v1?rss=1 Chatterjee, S. Fadikar, A. Hanumesh, V. Meshram, S. S. Zoh, R. S. Ma, S. Arunkumar, G. Mallick, H. 2024-04-02 doi:10.1101/2024.04.01.587633 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Regulation of fatty acid delivery to metastases by tumor endothelium ]]> https://biorxiv.org/content/10.1101/2024.04.02.587724v1?rss=1 Edwards, D. N. Wang, S. Song, W. Kim, L. C. Ngwa, V. M. Hwang, Y. Ess, K. C. Boothby, M. R. Chen, J. 2024-04-03 doi:10.1101/2024.04.02.587724 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Distinct Type 1 Immune Networks Underlie the Severity of Restrictive Lung Disease after COVID-19 ]]> https://biorxiv.org/content/10.1101/2024.04.03.587929v1?rss=1 Canderan, G. Muehling, L. Kadl, A. Ladd, S. Bonham, C. Cross, C. Lima, S. Yin, X. Sturek, J. Wilson, J. Keshavarz, B. Bryant, N. Murphy, D. Cheon, I. S. McNamara, C. Sun, J. Utz, P. J. Dolatshahi, S. Irish, J. Woodfolk, J. 2024-04-04 doi:10.1101/2024.04.03.587929 Cold Spring Harbor Laboratory Press 2024-04-04 <![CDATA[ Leveraging cross-source heterogeneity to improve the performance of bulk gene expression deconvolution ]]> https://biorxiv.org/content/10.1101/2024.04.07.588458v1?rss=1 Shen, W. Liu, C. Hu, Y. Lei, Y. Wong, H.-S. Wu, S. Zhou, X. M. 2024-04-09 doi:10.1101/2024.04.07.588458 Cold Spring Harbor Laboratory Press 2024-04-09 <![CDATA[ Alternating Access of a Neurotransmitter:Sodium Symporter Bacterial Homolog Determined from AlphaFold2 Ensembles and DEER Spectroscopy ]]> https://biorxiv.org/content/10.1101/2024.04.08.587957v1?rss=1 Schwartz, A. C. Stein, R. A. Gil-Itrube, E. Quick, M. Mchaourab, H. S. 2024-04-11 doi:10.1101/2024.04.08.587957 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ Hierarchical determinants of the oxidation-induced mutational landscape in human cells. ]]> https://biorxiv.org/content/10.1101/2024.04.08.588428v1?rss=1 T substitutions that compose COSMIC single base substitution signature 18 (SBS18) in human cancers. Determinants of local and regional differences in 8-oxoG-induced mutability are currently unknown. To uncover factors influencing the topology of 8-oxoG-induced mutations, we assessed spontaneous and KBrO3-induced 8-oxoG mutagenesis in human cell lines. KBrO3 exposure produced a SBS18-like substitution spectrum and a distinct never-before reported INDEL signature that we also observed in human cancers. KBrO3-induced 8-oxoG lesions occurred with similar sequence preference as KBrO3-induced substitutions, indicating that the reactivity of specific reactive oxygen species (ROS) dictates the trinucleotide motif specificity for 8-oxoG-induced mutagenesis. While 8-oxoG lesions occurred relatively uniformly across chromatin states and nucleosomes, 8-oxoG-induced mutations occurred more frequently in more compact regions of the genome, within nucleosomal DNA, and at inward facing guanines within strongly positioned nucleosomes. Cryo-EM structures of OGG1 bound to nucleosomes indicate that these effects originate from OGG1s ability to flip outward positioned 8-oxoG lesions into the catalytic pocket with only minor alterations to nucleosome structure, while inward facing lesions occluded by the histone octamer are unrecognized. Mutation spectra from cells with DNA repair deficiencies revealed a hierarchical DNA repair network limiting 8-oxoG mutagenesis in human cells, where OGG1- and MUTY-mediated BER is supplemented by replication-associated factors participating in tolerance of 8-oxoG or derived repair intermediates (i.e. Pol {eta} and HMCES). Surprisingly, analysis of transcriptional asymmetry of KBrO3-induced mutations demonstrated transcription-coupled repair of 8-oxoG in Pol {eta}-deficient cells. Thus, radical chemistry, chromatin structures, and DNA repair processes combine to dictate the oxidative mutational landscape in human genomes. ]]> Cordero, C. Mehta, K. P. M. Weaver, T. M. Ling, J. A. Freudenthal, B. D. Cortez, D. Roberts, S. A. 2024-04-11 doi:10.1101/2024.04.08.588428 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ Multi-Niche Human Bone Marrow On-A-Chip for Studying the Interactions of Adoptive CAR-T Cell Therapies with Multiple Myeloma ]]> https://biorxiv.org/content/10.1101/2024.04.08.588601v1?rss=1 Ghoshal, D. Petersen, I. Ringquist, R. Kramer, L. Bhatia, E. Hu, T. Richard, A. Park, R. Corbin, J. Agarwal, S. Thomas, A. Ramirez, S. Tharayil, J. Downey, E. Ketchum, F. Ochal, A. Sonthi, N. Lonial, S. Kochenderfer, J. N. Tran, R. Zhu, M. Lam, W. A. Coskun, A. F. Roy, K. 2024-04-12 doi:10.1101/2024.04.08.588601 Cold Spring Harbor Laboratory Press 2024-04-12 <![CDATA[ A tale of two tumors: differential, but detrimental, effects of glioblastoma extracellular vesicles (EVs) on normal human brain cells ]]> https://biorxiv.org/content/10.1101/2024.04.08.588622v1?rss=1 Wang, M. Graner, A. Knowles, B. McRae, C. Fringuello, A. Paucek, P. Gavrilovic, M. Redwine, M. Coughlan, C. Hanson, C. Metzger, B. Bolus, V. Kopper, T. Smith, M. Zhou, W. Lenz, M. Abosch, A. Ojemann, S. Lillehei, K. Yu, X. Graner, M. W. 2024-04-12 doi:10.1101/2024.04.08.588622 Cold Spring Harbor Laboratory Press 2024-04-12 <![CDATA[ Inhibiting CRF Projections from the Central Amygdala to Lateral Hypothalamus and Amygdala Deletion of CRF Alters Binge-Like Ethanol Drinking in a Sex-Dependent Manner ]]> https://biorxiv.org/content/10.1101/2024.04.09.588750v1?rss=1 Bendrath, S. Mendez, H. Dankert, A. Lerma-Cebrera, J. M. Carvajal, F. Dornellas-Loper, A. P. Lee, S. Neira, S. Haun, H. Delpire, E. Navarro, M. N. Kash, T. Thiele, T. E. 2024-04-13 doi:10.1101/2024.04.09.588750 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ Glia-derived secretory fatty acid binding protein Obp44a regulates lipid storage and efflux in the developing Drosophila brain ]]> https://biorxiv.org/content/10.1101/2024.04.10.588417v1?rss=1 Yin, J. Chen, H.-l. Grigsby-Brown, A. He, Y. Cotten, M. L. Short, J. Dermady, A. Lei, J. Gibbs, M. Cheng, E. S. Zhang, D. Long, C. Xu, L. Zhong, T. Abzalimov, R. Haider, M. Sun, R. Zhou, Q. Tjandra, N. Yuan, Q. 2024-04-11 doi:10.1101/2024.04.10.588417 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ Reward Circuit Local Field Potential Modulations Precede Risk Taking ]]> https://biorxiv.org/content/10.1101/2024.04.10.588629v1?rss=1 Hughes, N. C. Qian, H. Zargari, M. Zhao, Z. Singh, B. Wang, Z. Fulton, J. N. Johnson, G. W. Li, R. Dawant, B. M. Englot, D. J. Constantinidis, C. Roberson, S. T. W. Bick, S. K. 2024-04-11 doi:10.1101/2024.04.10.588629 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ A registration strategy to characterize DTI-observed changes in skeletal muscle architecture due to passive shortening ]]> https://biorxiv.org/content/10.1101/2024.04.11.589123v1?rss=1 Hooijmans, M. T. Lockard, C. A. Zhou, X. Coolbaugh, C. Guzman, R. P. Kersh, M. E. Damon, B. M. 2024-04-14 doi:10.1101/2024.04.11.589123 Cold Spring Harbor Laboratory Press 2024-04-14 <![CDATA[ Association of 10 VEGF Family Genes with Alzheimer's Disease Pathology at Single Cell Resolution ]]> https://biorxiv.org/content/10.1101/2024.04.12.589221v1?rss=1 Wu, Y. Libby, J. B. Dumitrescu, L. De Jager, P. L. Menon, V. Schneider, J. A. Bennett, D. A. Hohman, T. J. 2024-04-15 doi:10.1101/2024.04.12.589221 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ UK BioCoin: Swift Trait-Specific Summary Statistics Regression for UK Biobank ]]> https://biorxiv.org/content/10.1101/2024.04.12.589273v1?rss=1 He, J.-C. Qi, G.-A. Ying, J. Qian, Y. Han, L. Mao, Y. Zheng, H.-F. Jiang, H. Chen, G.-B. 2024-04-15 doi:10.1101/2024.04.12.589273 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ Repair of leukemia-associated single nucleotide variants via interallelic gene conversion ]]> https://biorxiv.org/content/10.1101/2024.04.16.587991v1?rss=1 Silver, A. J. Brown, D. J. Olmstead, S. D. Watke, J. M. Gorska, A. E. Tanner, L. Ramsey, H. E. Savona, M. R. 2024-04-20 doi:10.1101/2024.04.16.587991 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Rostral Pedunculopontine Nucleus Infusion of M4 Positive Allosteric Modulator VU0467154 Augments L-DOPA Effects in Hemiparkinsonian Rats ]]> https://biorxiv.org/content/10.1101/2024.04.16.589785v1?rss=1 Chambers, N. E. MClune, A. Coyle, M. Centner, A. Sergio, J. Del Priore, I. Lanza, K. Lindsley, C. W. Conn, P. J. Bishop, C. 2024-04-20 doi:10.1101/2024.04.16.589785 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Functional and antigenic landscape of the Nipah virus receptor binding protein ]]> https://biorxiv.org/content/10.1101/2024.04.17.589977v1?rss=1 Larsen, B. B. McMahon, T. Brown, J. T. Wang, Z. Radford, C. E. Crowe, J. E. Veesler, D. Bloom, J. D. 2024-04-19 doi:10.1101/2024.04.17.589977 Cold Spring Harbor Laboratory Press 2024-04-19 <![CDATA[ BNST GluN2D-containing NMDARs contribute to ethanol intake but not negative affective behaviors in female mice ]]> https://biorxiv.org/content/10.1101/2024.04.19.590258v1?rss=1 Doyle, M. A. Salimando, G. J. Altemus, M. E. Badt, J. K. Bedenbaugh, M. N. Vardy, A. S. Adank, D. N. Park, A. S. Winder, D. G. 2024-04-21 doi:10.1101/2024.04.19.590258 Cold Spring Harbor Laboratory Press 2024-04-21 <![CDATA[ Unified somatic calling and machine learning-based classification enhance the discovery of clonal hematopoiesis of indeterminate potential ]]> https://biorxiv.org/content/10.1101/2024.04.22.590586v1?rss=1 Tian, S. Ferrer, A. Yan, H. Morales-Rosado, J. Lasho, T. L. Wang, K. Baheti, S. Olson, J. E. Baughn, L. B. Slager, S. L. Patnaik, M. M. Lazaridis, K. N. Klee, E. W. 2024-04-27 doi:10.1101/2024.04.22.590586 Cold Spring Harbor Laboratory Press 2024-04-27 <![CDATA[ Testing frameworks for early life effects: the developmental constraints and adaptive responsehypotheses do not explain key fertility outcomes in wild female baboons ]]> https://biorxiv.org/content/10.1101/2024.04.23.590627v1?rss=1 Rosenbaum, S. Malani, A. Lea, A. J. Tung, J. Alberts, S. C. Archie, E. A. 2024-04-28 doi:10.1101/2024.04.23.590627 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Ligand efficacy shifts a nuclear receptor conformational ensemble between transcriptionally active and repressive states ]]> https://biorxiv.org/content/10.1101/2024.04.23.590805v1?rss=1 MacTavish, B. Zhu, D. Shang, J. Shao, Q. Yang, Z. Kamenecka, T. Kojetin, D. 2024-04-24 doi:10.1101/2024.04.23.590805 Cold Spring Harbor Laboratory Press 2024-04-24 <![CDATA[ Epithelial IL-2 is critical for NK cell-mediated cancer immunosurveillance in mammary glands ]]> https://biorxiv.org/content/10.1101/2024.04.25.591178v1?rss=1 Wang, L. Maharjan, C. Borcherding, N. Master, R. P. Mo, j. Tithi, T. I. Carelock, M. Master, A. Gibson-Corley, K. Kolb, R. H. Smith, K. A. Zhang, W. 2024-04-28 doi:10.1101/2024.04.25.591178 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ The transcription factor ZNF469 regulates collagen production in liver fibrosis ]]> https://biorxiv.org/content/10.1101/2024.04.25.591188v1?rss=1 Steinhauser, S. Estoppey, D. Buehler, D. P. Xiong, Y. Pizzato, N. Rietsch, A. Wu, F. Leroy, N. Wunderlin, T. Claerr, I. Tropberger, P. Mueller, M. Davison, L. M. Sheng, Q. Bergling, S. Wild, S. Moulin, P. Liang, J. English, W. J. Williams, B. Knehr, J. Altorfer, M. Reyes, A. Mickanin, C. Hoepfner, D. Nigsch, F. Frederiksen, M. Flynn, C. R. Fodor, B. D. Brown, J. D. Kolter, C. 2024-04-25 doi:10.1101/2024.04.25.591188 Cold Spring Harbor Laboratory Press 2024-04-25 <![CDATA[ Body size interacts with the structure of the central nervous system: A multi-center in vivo neuroimaging study ]]> https://biorxiv.org/content/10.1101/2024.04.29.591421v1?rss=1 Labounek, R. Bondy, M. T. Paulson, A. L. Bedard, S. Abramovic, M. Alonso-Ortiz, E. Atcheson, N. T. Barlow, L. R. Barry, R. L. Barth, M. Battiston, M. Buchel, C. Budde, M. D. Callot, V. Combes, A. De Leener, B. Descoteaux, M. Loureiro de Sousa, P. Dostal, M. Doyon, J. Dvorak, A. V. Eippert, F. Epperson, K. R. Epperson, K. S. Freund, P. Finsterbusch, J. Foias, A. Fratini, M. Fukunaga, I. Gandini Wheeler-Kingshott, C. A. M. Germani, G. Gilbert, G. Giove, F. Grussu, F. Hagiwara, A. Henry, P.-G. Horak, T. Hori, M. Joers, J. M. Kamiya, K. Karbasforoushan, H. 2024-05-01 doi:10.1101/2024.04.29.591421 Cold Spring Harbor Laboratory Press 2024-05-01 <![CDATA[ IPMK regulates HDAC3 activity and histone H4 acetylation in human cells. ]]> https://biorxiv.org/content/10.1101/2024.04.29.591660v1?rss=1 Sowd, G. A. Stivision, E. A. Chapagain, P. Hale, A. T. Poland, J. C. Rameh, L. E. Blind, R. D. 2024-04-29 doi:10.1101/2024.04.29.591660 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Mechano-metabolism of adherent cells in 2D and 3D microenvironments ]]> https://biorxiv.org/content/10.1101/2024.04.30.591879v1?rss=1 Jaganathan, A. Toth, J. M. Chen, X. Pieuchot, L. Shen, Y. Reinhart-King, C. A. Shenoy, V. B. 2024-05-03 doi:10.1101/2024.04.30.591879 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Single Cell Profiling Distinguishes Leukemia-Selective Chemotypes ]]> https://biorxiv.org/content/10.1101/2024.05.01.591362v1?rss=1 Thirman, H. L. Hayes, M. J. Brown, L. E. Porco, J. A. Irish, J. M. 2024-05-03 doi:10.1101/2024.05.01.591362 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Velociraptor: Cross-Platform Quantitative Search Using Hallmark Cell Features ]]> https://biorxiv.org/content/10.1101/2024.05.01.591375v1?rss=1 Cross, C. E. Mayeda, C. Medina, S. Hayes, M. J. Kaviany, S. Connelly, J. A. Rathmell, J. C. Weaver, K. D. Thompson, R. C. Chambless, L. B. Ihrie, R. A. Irish, J. M. 2024-05-04 doi:10.1101/2024.05.01.591375 Cold Spring Harbor Laboratory Press 2024-05-04 <![CDATA[ Multiple inositol phosphate species enhance stability of active mTOR ]]> https://biorxiv.org/content/10.1101/2024.05.01.592113v1?rss=1 Rameh Plant, L. York, J. D. Blind, R. 2024-05-02 doi:10.1101/2024.05.01.592113 Cold Spring Harbor Laboratory Press 2024-05-02 <![CDATA[ TOMOMAN: a software package for large scale cryo-electron tomography data preprocessing, community data sharing, and collaborative computing ]]> https://biorxiv.org/content/10.1101/2024.05.02.589639v1?rss=1 Khavnekar, S. Wan, W. 2024-05-03 doi:10.1101/2024.05.02.589639 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Bilirubin is a new ligand for nuclear receptor Liver Receptor Homolog-1. ]]> https://biorxiv.org/content/10.1101/2024.05.05.592606v1?rss=1 Chapagain, P. Haratipour, Z. Malabanan, M. M. Choi, W. J. Blind, R. 2024-05-06 doi:10.1101/2024.05.05.592606 Cold Spring Harbor Laboratory Press 2024-05-06 <![CDATA[ A novel heuristic of rigid docking scores positively correlates with full-length nuclear receptor LRH-1 regulation. ]]> https://biorxiv.org/content/10.1101/2024.05.05.592617v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@1e3a780org.highwire.dtl.DTLVardef@109fcdcorg.highwire.dtl.DTLVardef@b80fa6org.highwire.dtl.DTLVardef@b68fe_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO C_FIG ]]> Haratipour, Z. Foutch, D. Blind, R. 2024-05-07 doi:10.1101/2024.05.05.592617 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ Protection against Clostridioides difficile disease by a naturally avirulent C. difficile strain ]]> https://biorxiv.org/content/10.1101/2024.05.06.592814v1?rss=1 Dong, Q. Harper, S. McSpadden, E. Son, S. S. Allen, M.-M. Lin, H. Smith, R. C. Metcalfe, C. Burgo, V. Woodson, C. Sundararajan, A. Rose, A. McMillin, M. Moran, D. Little, J. Mullowney, M. W. Sidebottom, A. M. Shen, A. Fortier, L.-C. Pamer, E. G. 2024-05-07 doi:10.1101/2024.05.06.592814 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ Improving Drug Sensitivity Prediction and Inference by Multitask Learning ]]> https://biorxiv.org/content/10.1101/2024.05.09.593186v1?rss=1 Strauch, J. Asiaee, A. 2024-05-13 doi:10.1101/2024.05.09.593186 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ Design, synthesis and cellular characterization of a new class of IPMK kinase inhibitors ]]> https://biorxiv.org/content/10.1101/2024.05.09.593371v1?rss=1 Zhou, Y. Chapagain, P. Desmarini, D. Uredi, D. Rameh Plant, L. E. Djordjevic, J. T. Blind, R. D. Wang, X. 2024-05-14 doi:10.1101/2024.05.09.593371 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Quantifying Differential Rhythmicity based on Effect Sizes with LimoRhyde2 ]]> https://biorxiv.org/content/10.1101/2024.05.09.593377v1?rss=1 Obodo, D. Asiaee, A. 2024-05-20 doi:10.1101/2024.05.09.593377 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ A TRANSLAMINAR SPACETIME CODE SUPPORTS TOUCH-EVOKED TRAVELING WAVES ]]> https://biorxiv.org/content/10.1101/2024.05.09.593381v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@c98840org.highwire.dtl.DTLVardef@1105364org.highwire.dtl.DTLVardef@d2f2c9org.highwire.dtl.DTLVardef@1418744_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIWhisker touch evokes both early- and late-traveling waves in the barrel cortex over 100s of milliseconds C_LIO_LIReward reinforcement modulates wave dynamics C_LIO_LILate wave emergence coincides with network sparsity in L23 and time-locked L5 dendritic Ca2+ spikes C_LIO_LIExperimental and computational results link motor feedback to distinct translaminar spacetime patterns C_LI ]]> Gonzales, D. L. Khan, H. F. Keri, H. V. S. Yadav, S. Steward, C. Muller, L. Pluta, S. Jayant, K. 2024-05-09 doi:10.1101/2024.05.09.593381 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ X-ray crystallographic analyses of 14 IPMK inhibitor complexes ]]> https://biorxiv.org/content/10.1101/2024.05.09.593385v1?rss=1 Wang, H. Blind, R. D. Shears, S. B. 2024-05-09 doi:10.1101/2024.05.09.593385 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ Neuronal protein phosphatase 1β regulates glutamate release, cortical myelination, node of Ranvier formation, and action potential propagation in the optic nerve ]]> https://biorxiv.org/content/10.1101/2024.05.10.593531v1?rss=1 McKee, C. Foley, K. Andersh, K. Marola, O. Wadzinski, B. LIbby, R. T. Shrager, P. Xia, H. 2024-05-10 doi:10.1101/2024.05.10.593531 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Duration of Morning Hyperinsulinemia is Key to the Enhancement of Hepatic Glucose Uptake and Glycogen Storage Later in the Day ]]> https://biorxiv.org/content/10.1101/2024.05.10.593551v1?rss=1 Waterman, H. L. Moore, M. C. Smith, M. Farmer, B. Scott, M. Edgerton, D. S. Cherrington, A. D. 2024-05-14 doi:10.1101/2024.05.10.593551 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Machine Learning Approaches for Skin Neoplasm Diagnosis ]]> https://biorxiv.org/content/10.1101/2024.05.12.593773v1?rss=1 Asaduzzaman, A. Thompson, C. C. Uddin, M. J. 2024-05-14 doi:10.1101/2024.05.12.593773 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Revealing the principles of inter- and intra-domain regulation in a signaling enzyme via scanning mutagenesis ]]> https://biorxiv.org/content/10.1101/2024.05.13.593907v1?rss=1 Jiang, Z. van Vlimmeren, A. E. Karandur, D. Semmelman, A. Shah, N. H. 2024-05-13 doi:10.1101/2024.05.13.593907 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ Bacteria can anticipate the seasons: photoperiodism in cyanobacteria ]]> https://biorxiv.org/content/10.1101/2024.05.13.593996v1?rss=1 Jabbur, M. L. Johnson, C. H. 2024-05-13 doi:10.1101/2024.05.13.593996 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ Inhibition of EGFR/ErbB does not protect against C. difficile toxin B ]]> https://biorxiv.org/content/10.1101/2024.05.13.594035v1?rss=1 Siddiqi, U. Lunnemann, H. M. Childress, K. O. Shupe, J. A. Rutherford, S. A. Farrow, M. A. Washington, M. K. Coffey, R. J. Lacy, D. B. Markham, N. O. 2024-05-14 doi:10.1101/2024.05.13.594035 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Molecular counting of myosin force generators in growing filopodia ]]> https://biorxiv.org/content/10.1101/2024.05.14.593924v1?rss=1 Tyska, M. J. Fitz, G. N. 2024-05-17 doi:10.1101/2024.05.14.593924 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ Unanticipated mechanisms of covalent inhibitor and synthetic ligand cobinding to PPARgamma ]]> https://biorxiv.org/content/10.1101/2024.05.15.594037v1?rss=1 Shang, J. Kojetin, D. 2024-05-15 doi:10.1101/2024.05.15.594037 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Alternative splicing across the C. elegans nervous system ]]> https://biorxiv.org/content/10.1101/2024.05.16.594567v1?rss=1 Weinreb, A. Varol, E. Barrett, A. McWhirter, R. M. Taylor, S. R. Courtney, I. Basavaraju, M. Poff, A. Tipps, J. A. Collings, B. The CeNGEN Consortium, Krishnaswamy, S. Miller, D. M. Hammarlund, M. 2024-05-16 doi:10.1101/2024.05.16.594567 Cold Spring Harbor Laboratory Press 2024-05-16 <![CDATA[ Maternal Western-style diet programs skeletal muscle gene expression in lean adolescent Japanese macaque offspring ]]> https://biorxiv.org/content/10.1101/2024.05.17.594191v1?rss=1 Beck, E. A. Hetrick, B. Nassar, L. Turnball, D. W. Dean, T. A. Gannon, M. Aagaard, K. M. Wesolowski, S. R. Friedman, J. E. Kievit, P. McCurdy, C. E. 2024-05-21 doi:10.1101/2024.05.17.594191 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Cardioprotection by Poloxamer 188 is Mediated through Increased Endothelial Nitric Oxide Production ]]> https://biorxiv.org/content/10.1101/2024.05.18.593838v1?rss=1 Chen, G. Douglas, H. F. Li, Z. Cleveland, W. J. Balzer, C. Yannopolous, D. Chen, I. Y.-L. Obal, D. Riess, M. L. 2024-05-20 doi:10.1101/2024.05.18.593838 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ Germline status and micronutrient availability regulate a somatic mitochondrial quality control pathway via short-chain fatty acid metabolism ]]> https://biorxiv.org/content/10.1101/2024.05.20.594820v1?rss=1 Held, J. P. Dbouk, N. H. Strozak, A. M. Grub, L. K. Ryou, H. Schaffner, S. H. Patel, M. R. 2024-05-21 doi:10.1101/2024.05.20.594820 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[ The variability of multidimensional diffusion-relaxation MRI estimates in the human brain ]]> https://biorxiv.org/content/10.1101/2024.05.20.594998v1?rss=1 Manninen, E. Bao, S. Landman, B. A. Yang, Y. Topgaard, D. Benjamini, D. 2024-05-20 doi:10.1101/2024.05.20.594998 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ A novel splicing graph allows a direct comparison between exon-based and splice junction-based approaches to alternative splicing detection ]]> https://biorxiv.org/content/10.1101/2024.05.20.595048v1?rss=1 Aquino, J. Witoslawski, D. Park, S. Holder, J. Amei, A. Han, M. 2024-05-21 doi:10.1101/2024.05.20.595048 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ A novel mouse home cage lickometer system reveals sex- and housing-based influences on alcohol drinking ]]> https://biorxiv.org/content/10.1101/2024.05.22.595186v1?rss=1 Petersen, N. Adank, D. N. Quan, Y. Edwards, C. M. Taylor, A. Winder, D. Doyle, M. A. 2024-05-23 doi:10.1101/2024.05.22.595186 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Molecular Specializations Underlying Phenotypic Differences in Inner Ear Hair Cells of Zebrafish and Mice ]]> https://biorxiv.org/content/10.1101/2024.05.24.595729v1?rss=1 Giffen, K. Liu, H. Yamane, K. L. Li, Y. Chen, L. Kramer, K. L. Zallocchi, M. He, D. Z. Z. 2024-05-26 doi:10.1101/2024.05.24.595729 Cold Spring Harbor Laboratory Press 2024-05-26 <![CDATA[ Bispecific GD2 x B7-H3 Antibody Improves Tumor Targeting and Reduces Toxicity while Maintaining Efficacy for Neuroblastoma ]]> https://biorxiv.org/content/10.1101/2024.05.23.595588v1?rss=1 Erbe, A. K. Feils, A. S. Hampton, A. Rosenkrans, Z. T. Felder, M. Wiwczar, J. Gerhardt, D. J. Bercher, M. Wenke, B. Haertle, C. Heck, M. VandenHeuvel, S. N. Frankel, E. Nielsen, M. Spiegelman, D. Tsarovsky, N. Zaborek, J. Rakhmilevich, A. L. Hank, J. A. Aluicio-Sarduy, E. Engle, J. Davis, J. H. Glaser, B. Subbotin, V. Green, R. Hernandez, R. T. Hammer, B. Sondel, P. M. 2024-05-28 doi:10.1101/2024.05.23.595588 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ Association between mosaic loss of chromosome Y and pulmonary fibrosis susceptibility and severity ]]> https://biorxiv.org/content/10.1101/2024.05.25.595885v1?rss=1 Wang, D. Hadad, N. Moss, S. Lopez-Jimenez, E. Johnson, S. R. Maher, T. M. Molyneaux, P. L. Zhao, Y. Perry, J. R. B. Wolters, P. J. Kropski, J. A. Jenkins, R. G. Banovich, N. E. Stewart, I. 2024-05-30 doi:10.1101/2024.05.25.595885 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Brain-state modeling using electroencephalography: Application to adaptive closed-loop neuromodulation for epilepsy ]]> https://biorxiv.org/content/10.1101/2024.06.01.596884v1?rss=1 Johnson, G. W. Doss, D. J. Makhoul, G. S. Cai, L. Y. Bibro, C. E. Paulo, D. L. Reddy, S. B. Naftel, R. P. Haas, K. F. Wallace, M. T. Dawant, B. M. Crudele, A. N. Morgan, V. L. Constantinidis, C. Williams Roberson, S. Bick, S. K. Englot, D. J. 2024-06-01 doi:10.1101/2024.06.01.596884 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Deficiency of the hemoglobin-haptoglobin receptor, CD163, worsens insulin sensitivity in obese male mice ]]> https://biorxiv.org/content/10.1101/2024.05.31.596887v1?rss=1 Schleh, M. Ameka, M. Rodriguez, A. Hasty, A. 2024-06-03 doi:10.1101/2024.05.31.596887 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ AgRP neurons mediate activity-dependent development of oxytocin connectivity and autonomic regulation ]]> https://biorxiv.org/content/10.1101/2024.06.02.592838v1?rss=1 Biddinger, J. E. Elson, A. E. T. Fathi, P. Sweet, S. R. Nishimori, K. Ayala, J. E. Simerly, R. B. 2024-06-03 doi:10.1101/2024.06.02.592838 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Compositional Differential Abundance Testing: Defining and Finding a New Type of Health-Microbiome Associations ]]> https://biorxiv.org/content/10.1101/2024.06.04.596112v1?rss=1 Ma, S. Huttenhower, C. Janson, L. 2024-06-06 doi:10.1101/2024.06.04.596112 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Human TSC2 Mutant Cells Exhibit Aberrations in Early Neurodevelopment Accompanied by Changes in the DNA Methylome ]]> https://biorxiv.org/content/10.1101/2024.06.04.597443v1?rss=1 Chalkley, M.-B. L. Guerin, L. N. Iyer, T. Mallahan, S. Nelson, S. N. Sahin, M. Hodges, E. Ess, K. C. Ihrie, R. A. 2024-06-06 doi:10.1101/2024.06.04.597443 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage ]]> https://biorxiv.org/content/10.1101/2024.06.05.597512v1?rss=1 Feng, B. Li, Y. Liu, H. Steenwyk, J. L. David, K. T. Tian, X. Xu, B. Goncalves, C. Opulente, D. A. LaBella, A. L. Harrison, M.-C. Wolters, J. F. Shao, S. Chen, Z. Fisher, K. J. Groenewald, M. Hittinger, C. T. Shen, X.-X. Rokas, A. Zhou, X. Li, Y. 2024-06-06 doi:10.1101/2024.06.05.597512 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Structure of the Ion Channel Kir7.1 and Implications for its Function in Normal and Pathophysiologic States ]]> https://biorxiv.org/content/10.1101/2024.06.07.597981v1?rss=1 Peisley, A. Hernandez, C. Q. Dahir, N. Koepping, L. Raczkowski, A. Su, M. Ghamari-Langroudi, M. Ji, X. Gimenez, L. Cone, R. D. 2024-06-08 doi:10.1101/2024.06.07.597981 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Ribosome-Associated Vesicles promote activity-dependent local translation ]]> https://biorxiv.org/content/10.1101/2024.06.07.598007v1?rss=1 Martin-Solana, E. Carter, S. D. Donahue, E. K. Ning, J. Glausier, J. R. Preisegger, M. A. Eisenman, L. Joseph, P. N. Bouchet-Marquis, C. Wu, K. Mobini, C. L. Frantz, A. N. Puig, S. Hampton, C. M. Kabbani, N. Jensen, G. J. Watkins, S. C. Deisseroth, K. Fenno, L. E. Gold, M. S. Wills, Z. P. Burkewitz, K. Das, S. Freyberg, Z. 2024-06-08 doi:10.1101/2024.06.07.598007 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Microphthalmia and disrupted retinal development due to a LacZ knock-in/knock-out allele at the Vsx2 locus ]]> https://biorxiv.org/content/10.1101/2024.06.08.597937v1?rss=1 Napoli, F. R. Li, X. Hurtado, A. A. Levine, E. M. 2024-06-08 doi:10.1101/2024.06.08.597937 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ The Association between the JAK-STAT Pathway and Hypertension among Kenyan Women Diagnosed with Breast Cancer ]]> https://biorxiv.org/content/10.1101/2024.06.07.597892v1?rss=1 GITAU, J. Wagutu, G. Sayed, S. Mohammad, S. Makokha, F. Kirabo, A. 2024-06-09 doi:10.1101/2024.06.07.597892 Cold Spring Harbor Laboratory Press 2024-06-09 <![CDATA[ Polymeric Micellar Nanoparticles Enable Image-guided Drug Delivery in Solid Tumors ]]> https://biorxiv.org/content/10.1101/2024.06.07.598019v1?rss=1 Uddin, M. J. Oltman, C. G. Lo, J. H. Gupta, M. K. Werfel, T. A. mohyuddin, m. T. nazmin, f. Rahman, M. S. Crews, B. C. kingsley, p. J. Marnett, L. J. Duvall, C. L. Cook, R. S. 2024-06-10 doi:10.1101/2024.06.07.598019 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Lipid-siRNA conjugate accesses a perivascular transport mechanism and achieves widespread and durable knockdown in the central nervous system ]]> https://biorxiv.org/content/10.1101/2024.06.09.598079v1?rss=1 Sorets, A. Schwensen, K. Francini, N. Kjar, A. Abdulrahman, A. Shostak, A. Katdare, K. Schoch, K. Cowell, R. Park, J. Ligocki, A. Ford, W. Ventura-Antunes, L. Hoogenboezem, E. Prusky, A. Castleberry, M. Michell, D. L. Miller, T. Vickers, K. Schrag, M. Duvall, C. Lippmann, E. 2024-06-10 doi:10.1101/2024.06.09.598079 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Sex, racial, and APOE-ϵ4 allele differences in longitudinal white matter microstructure in multiple cohorts of aging and Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2024.06.10.598357v1?rss=1 Peterson, A. Sathe, A. Zaras, D. Yang, Y. Durant, A. Deters, K. D. Shashikumar, N. Pechman, K. R. Kim, M. E. Gao, C. Mohd Khairi, N. Li, Z. Yao, T. Huo, Y. Dumitrescu, L. Gifford, K. Wilson, J. E. Cambronero, F. Risacher, S. L. Beason-Held, L. L. An, Y. Arfanakis, K. Erus, G. Davatzikos, C. Tosun, D. Toga, A. W. Thompson, P. M. Mormino, E. C. Zhang, P. Schilling, K. Alzheimer's Disease Neuroimaging Initiative, The BIOCARD Study Team, The Alzheimer's Disease Sequencing Project, Albert, M. Kukull, W. Biber, S. A. Landman, B. A. Johnson, S. C. Schneider 2024-06-12 doi:10.1101/2024.06.10.598357 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ Myeloid Cell Glucocorticoid, Not Mineralocorticoid Receptor Signaling, Contributes to Salt-Sensitive Hypertension in Humans via Cortisol ]]> https://biorxiv.org/content/10.1101/2024.06.10.598374v1?rss=1 Albritton, C. Demirci, M. Neikirk, K. Ishimwe, J. Mutchler, A. Sheng, Q. Laffer, C. L. Wanjalla, C. N. Ahmad, T. Haynes, A. P. Saleem, M. Beasley, H. K. Marshall, A. G. Vue, Z. Ikizler, A. T. Kleyman, T. R. Kon, V. Hinton, A. Kirabo, A. 2024-06-12 doi:10.1101/2024.06.10.598374 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ MYC and HSF1 Cooperate to Drive PLK1 inhibitor Sensitivity in High Grade Serous Ovarian Cancer ]]> https://biorxiv.org/content/10.1101/2024.06.11.598486v1?rss=1 Williams, I. DeHart, H. O'Malley, M. Walker, B. Ulhaskumar, V. Ray, H. Delaney, J. R. Nephew, K. P. Carpenter, R. L. 2024-06-13 doi:10.1101/2024.06.11.598486 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Anterior Cingulate Cortex Causally Supports Meta-Learning ]]> https://biorxiv.org/content/10.1101/2024.06.12.598723v1?rss=1 Treuting, R. L. Boroujeni, K. B. Gerrity, C. G. Tiesinga, P. Womelsdorf, T. 2024-06-13 doi:10.1101/2024.06.12.598723 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Cyclophilin A Facilitates HIV-1 DNA Integration ]]> https://biorxiv.org/content/10.1101/2024.06.15.599180v1?rss=1 Padron, A. Dwivedi, R. Chakraborty, R. Prakash, P. Kim, K. Shi, J. Ahn, J. Pandhare, J. Luban, J. Aiken, C. Balasubramaniam, M. Dash, C. 2024-06-17 doi:10.1101/2024.06.15.599180 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ A widespread electrical brain network encodes anxiety in health and depressive states ]]> https://biorxiv.org/content/10.1101/2024.06.26.600900v1?rss=1 Hughes, D. N. Klein, M. H. Walder-Christensen, K. K. Thomas, G. E. Grossman, Y. Waters, D. Matthews, A. E. Carson, W. E. Filali, Y. Tsyglakova, M. Fink, A. Gallagher, N. M. Perez-Balaguer, M. McClung, C. A. Zarate, J. M. Hultman, R. C. Mague, S. D. Carlson, D. Dzirasa, K. 2024-06-30 doi:10.1101/2024.06.26.600900 Cold Spring Harbor Laboratory Press 2024-06-30 <![CDATA[ Selection for early reproduction leads to accelerated aging and extensive metabolic remodeling in Drosophila melanogaster populations ]]> https://biorxiv.org/content/10.1101/2024.06.28.601037v1?rss=1 Hubert, D. L. Arnold, K. R. Greenspan, Z. G. Pupo, A. Robinson, R. D. Chavarin, V. V. Barter, T. T. Djukovic, D. Raftery, D. Vue, Z. Hinton, A. McReynolds, M. R. Harrison, B. R. Phillips, M. A. 2024-07-02 doi:10.1101/2024.06.28.601037 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Atf4 protects islet beta-cell identity and function under acute glucose-induced stress but promotes beta-cell failure in the presence of free fatty acid ]]> https://biorxiv.org/content/10.1101/2024.06.28.601249v1?rss=1 Yagan, M. Najam, S. Hu, R. Wang, Y. DAdi, P. Xu, Y. Simmons, A. J. Stein, R. Adams, C. M. Jacobson, D. J. Lau, K. Liu, Q. Gu, G. 2024-07-02 doi:10.1101/2024.06.28.601249 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Convergent reductive evolution in bee-associated lactic acid bacteria ]]> https://biorxiv.org/content/10.1101/2024.06.28.601270v1?rss=1 Pontes, A. Harrison, M.-C. Rokas, A. Goncalves, C. 2024-07-03 doi:10.1101/2024.06.28.601270 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ Cryo-EM of AKAP350 reveals fibrillar clusters and a potential association with DNA ]]> https://biorxiv.org/content/10.1101/2024.07.02.601773v1?rss=1 Dai, D. L. Keszei, A. F. A. kolobova, e. St-Germain, J. Hasan, S. M. N. Liu, A. C. H. Zhang, X. Raught, B. Goldenring, J. R. Mazhab-Jafari, M. T. 2024-07-04 doi:10.1101/2024.07.02.601773 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ FapR regulates HssRS-mediated heme homeostasis in Bacillus anthracis ]]> https://biorxiv.org/content/10.1101/2024.07.08.602573v1?rss=1 Skaar, E. P. Pi, H. Carlin, S. M. Beavers, W. N. Hillebrand, G. H. Krystofiak, E. S. Stauff, D. L. 2024-07-08 doi:10.1101/2024.07.08.602573 Cold Spring Harbor Laboratory Press 2024-07-08 <![CDATA[ Pathogenicity is associated with population structure in a fungal pathogen of humans ]]> https://biorxiv.org/content/10.1101/2024.07.05.602241v1?rss=1 75% of clinical isolates were from population D. Accessory genes, including genes within biosynthetic gene clusters, were significantly more common in some populations but rare in others. Population D was enriched for genes associated with zinc ion binding, lipid metabolism, and certain types of hydrolase activity. In contrast to the major human pathogen Aspergillus fumigatus, A. flavus pathogenicity in humans is strongly associated with population structure, making it a great system for investigating how population-specific genes contribute to pathogenicity. ]]> Hatmaker, E. A. Barber, A. E. Drott, M. T. Sauters, T. J. C. Alastruey-Izquierdo, A. Garcia-Hermoso, D. Kurzai, O. Rokas, A. 2024-07-10 doi:10.1101/2024.07.05.602241 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Newly discovered base barrier cells provide compartmentalization of choroid plexus, brain and CSF ]]> https://biorxiv.org/content/10.1101/2024.07.08.601696v1?rss=1 View larger version (47K): org.highwire.dtl.DTLVardef@181e787org.highwire.dtl.DTLVardef@1875f33org.highwire.dtl.DTLVardef@7b2bcdorg.highwire.dtl.DTLVardef@78baa6_HPS_FORMAT_FIGEXP M_FIG Newly discovered base barrier cells provide compartmentalization of choroid plexus, brain and CSF The choroid plexus (ChP) hangs in the brain ventricles and is composed of an epithelial cell layer which produces the cerebrospinal fluid (CSF) and forms the blood-CSF barrier. The ChP epithelial cells are continuous with the ependymal cells lining the ventricle wall. At this base region, we identified and characterized a novel subtype of fibroblasts coined the ChP base barrier cells (BBCs). ChP BBCs express tight junctions (TJs), cluster together and seal the ChP stroma from CSF and brain parenchyma. The subarachnoid space (SAS) CSF penetrates deep into choroid plexus invaginations where it is halted by ChP BBCs. Abbreviations: E9-16.5 (embryonic day 9-16.5); P1-4 (postnatal day 1-4). C_FIG ]]> Verhaege, D. De Nolf, C. Castelein, J. Claeys, W. Van Wonterghem, E. Van Imschoot, G. Dujardin, P. De Spiegelaere, W. Hoste, E. Boone, F. Lidov, H. G. Dani, N. Derk, J. Kremer, A. Van Hamme, E. Borghgraef, P. Lippens, S. Lehtinen, M. K. Siegenthaler, J. Van Hoecke, L. Vandenbroucke, R. E. 2024-07-11 doi:10.1101/2024.07.08.601696 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Structural Mapping of Polyclonal IgG Responses to HA After Influenza Virus Vaccination or Infection ]]> https://biorxiv.org/content/10.1101/2024.07.08.601940v1?rss=1 Leon, A. N. Rodriguez, A. J. Richey, S. T. Torrents de la Pena, A. Wolters, R. M. Jackson, A. M. Webb, K. Creech, C. B. Yoder, S. Mudd, P. A. Crowe, J. E. Han, J. Ward, A. B. 2024-07-11 doi:10.1101/2024.07.08.601940 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Single cell profiling to determine influence of wheeze and early-life viral infection on developmental programming of airway epithelium ]]> https://biorxiv.org/content/10.1101/2024.07.08.602506v1?rss=1 Berdnikovs, S. Newcomb, D. C. McKernan, K. E. Kuehnle, S. N. Haruna, N.-F. Gebretsadik, T. McKennan, C. G. Ma, S. Cephus, J.-Y. Rosas-Salazar, C. Anderson, L. J. Gern, J. E. Hartert, T. 2024-07-11 doi:10.1101/2024.07.08.602506 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Mitochondrial Fatty Acid Synthesis and Mecr Regulate CD4+ T Cell Function and Oxidative Metabolism ]]> https://biorxiv.org/content/10.1101/2024.07.08.602554v1?rss=1 Steiner, K. K. Young, A. C. Patterson, A. R. Jennings, E. Q. Chi, C. Hatem, Z. Heintzman, D. Sugiura, A. Arner, E. N. Sewell, A. E. Madden, M. Z. Okparaugo, R. Fallman, E. V. Gibson-Corley, K. Voss, K. Mogilenko, D. Rathmell, J. 2024-07-11 doi:10.1101/2024.07.08.602554 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ VARP binds SNX27 to promote endosomal supercomplex formation on membranes ]]> https://biorxiv.org/content/10.1101/2024.07.11.603126v1?rss=1 Chandra, M. Kendall, A. Ford, M. Jackson, L. P. 2024-07-11 doi:10.1101/2024.07.11.603126 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ CACHE Challenge #1: targeting the WDR domain of LRRK2, a Parkinson's Disease associated protein. ]]> https://biorxiv.org/content/10.1101/2024.07.18.603797v1?rss=1 Ackloo, S. Arrowsmith, C. H. Ban, F. Barden, C. J. Beck, H. Beranek, J. Berenger, F. Bolotokova, A. Bret, G. Breznik, M. Carosati, E. Chau, I. Chen, Y. Cherkasov, A. Della Corte, D. Denzinger, K. Dong, A. Draga, S. Dunn, I. Edfeldt, K. Edwards, A. Eguida, M. Eisenhuth, P. Friedrich, L. Fuerll, A. Gardiner, S. Gentile, F. Ghiabi, P. Gibson, E. Glavatskikh, M. Gorgulla, C. Guenther, J. Gunnarsson, A. Guseve, F. Gutkin, E. Hillisch, A. Hoffer, L. Hogner, A. Irwin, J. J. Isayev, O. Ivanova, A. Jacquemard, C. Jarrett, A. J. Jensen, J. H. Kireev, D. Klebe 2024-07-18 doi:10.1101/2024.07.18.603797 Cold Spring Harbor Laboratory Press 2024-07-18 <![CDATA[ Secreted exosomes induce filopodia formation ]]> https://biorxiv.org/content/10.1101/2024.07.20.604139v1?rss=1 McAtee, C. Patel, M. R. Hoshino, D. Sung, B. H. von Lersner, A. K. Shi, M. Hong, N. H. Young, A. Krystofiak, E. Zijlstra, A. Weaver, A. M. 2024-07-22 doi:10.1101/2024.07.20.604139 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ A tethering mechanism underlies Pin1-catalyzed proline cis-trans isomerization at a noncanonical site ]]> https://biorxiv.org/content/10.1101/2024.07.19.604348v1?rss=1 Williams, C. C. Chuck, J. Munoz-Tello, P. Kojetin, D. 2024-07-23 doi:10.1101/2024.07.19.604348 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Convergent expansions of keystone gene families drive metabolic innovation in a major eukaryotic clade ]]> https://biorxiv.org/content/10.1101/2024.07.22.604484v1?rss=1 David, K. T. Schraiber, J. G. Crandall, J. G. LaBella, A. L. Opulente, D. A. Harrison, M.-C. Wolters, J. F. Zhou, X. Shen, X.-X. Groenewald, M. Hittinger, C. T. Pennell, M. Rokas, A. 2024-07-23 doi:10.1101/2024.07.22.604484 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Specialization restricts the evolutionary paths available to yeast sugar transporters ]]> https://biorxiv.org/content/10.1101/2024.07.22.604696v1?rss=1 Crandall, J. G. Zhou, X. Rokas, A. Hittinger, C. T. 2024-07-23 doi:10.1101/2024.07.22.604696 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Th2 cell extracellular vesicles promote eosinophil survival through the cytokine cargo IL-3 and prolong airway eosinophilia. ]]> https://biorxiv.org/content/10.1101/2024.07.23.600647v1?rss=1 Bunn, K. E. Giese-Byrne, B. G. Pua, H. H. 2024-07-24 doi:10.1101/2024.07.23.600647 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Multi-omic ADNI CSF and plasma data integration identifies distinct metabolic transitions in disease progression in Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2024.07.23.604835v1?rss=1 Paterson, T. Rohrs, J. Hohman, T. J. Mapstone, M. Levey, A. I. Hood, L. Funk, C. C. 2024-07-24 doi:10.1101/2024.07.23.604835 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ SGLT2 inhibitors activate pantothenate kinase in the human heart ]]> https://biorxiv.org/content/10.1101/2024.07.26.605401v1?rss=1 Forelli, N. Eaton, D. Patel, J. Bowman, C. Kawakami, R. Kuzetsnov, I. Li, K. Brady, C. Bedi, K. Yang, Y. Koya, K. Megill, E. Kantner, D. Smith, L. Bowman, G. Snyder, N. Edwards, J. Margulies, K. Arany, Z. 2024-07-27 doi:10.1101/2024.07.26.605401 Cold Spring Harbor Laboratory Press 2024-07-27 <![CDATA[ Abnormal multisensory facilitation patterns relate to disorganized thinking severity and cognitive decline in schizophrenia ]]> https://biorxiv.org/content/10.1101/2024.07.26.605377v1?rss=1 Rogge-Obando, K. Coffman, B. Stephen, J. 2024-07-29 doi:10.1101/2024.07.26.605377 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ DNA damage response signatures are associated with frontline chemotherapy response and routes of tumor evolution in extensive stage small cell lung cancer ]]> https://biorxiv.org/content/10.1101/2024.07.29.605595v1?rss=1 Morris, B. B. Heeke, S. Xi, Y. Diao, L. Wang, Q. Rocha, P. Arriola, E. Lee, M. C. Tyson, D. R. Concannon, K. Ramkumar, K. Stewart, C. A. Cardnell, R. J. Wang, R. Quaranta, V. Wang, J. Heymach, J. V. Nabet, B. Y. Shames, D. S. Gay, C. M. Byers, L. A. 2024-07-30 doi:10.1101/2024.07.29.605595 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Passive infusion of an S2-Stem broadly neutralizing antibody protects against SARS-CoV-2 infection and lower airway inflammation in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2024.07.30.605768v1?rss=1 Bosinger, S. E. Edwards, C. T. Karunakaran, K. A. Garcia, E. Beutler, N. Gagne, M. Golden, N. Aoued, H. Pellegrini, K. Burnett, M. R. Honeycutt, C. C. Lapp, S. A. Ton, T. Lin, M. C. Metz, A. Bombin, A. Goff, K. Scheuermann, S. E. Wilkes, A. Wood, J. S. Ehnert, S. Weissman, S. Curran, E. H. Moore, I. N. Roy, M. Dessasau, E. Paiardini, M. Upadhyay, A. A. Maness, N. J. Douek, D. C. Piantadosi, A. Andrabi, R. Rogers, T. R. Burton, D. R. 2024-07-30 doi:10.1101/2024.07.30.605768 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Assessing the ability of ChatGPT to extract natural product bioactivity and biosynthesis data from publications ]]> https://biorxiv.org/content/10.1101/2024.08.01.606186v1?rss=1 Kalmer, T. L. Ancajas, C. M. F. Cheng, Z. Oyedele, A. S. Davis, H. L. Walker, A. 2024-08-02 doi:10.1101/2024.08.01.606186 Cold Spring Harbor Laboratory Press 2024-08-02 <![CDATA[ Microglia are Required for Developmental Specification of AgRP Innervation in the Hypothalamus of Offspring Exposed to Maternal High Fat Diet During Lactation ]]> https://biorxiv.org/content/10.1101/2024.08.12.607566v1?rss=1 Mendoza-Romero, H. N. Biddinger, J. E. Bedenbaugh, M. N. Simerly, R. 2024-08-12 doi:10.1101/2024.08.12.607566 Cold Spring Harbor Laboratory Press 2024-08-12 <![CDATA[ The ubiquitin-proteasome system regulates the formation of specialized ribosomes during high salt stress in yeast ]]> https://biorxiv.org/content/10.1101/2024.08.15.608112v1?rss=1 Karbstein, K. Yang, Y.-M. 2024-08-15 doi:10.1101/2024.08.15.608112 Cold Spring Harbor Laboratory Press 2024-08-15 <![CDATA[ Extracellular Vesicles heterogeneity through the lens of multiomics ]]> https://biorxiv.org/content/10.1101/2024.08.14.607999v1?rss=1 Silva, T. F. Hutchins, E. Zhao, W. Ciani, Y. Kim, M. Mariscal, J. Qiu, Z. Kittel, A. Zhou, B. Wang, Y. Hall, M. Galasso, F. Reiman, R. Freeman, M. R. Parker, S. Van Eyk, J. Yang, W. Posadas, E. Guarnerio, J. Nolan, J. Thery, C. Zijlstra, A. Stott, S. You, S. Demichelis, F. Boutros, P. Van Keuren-Jensen, K. Di Vizio, D. 2024-08-19 doi:10.1101/2024.08.14.607999 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Influenza A virus within-host evolution and positive selection in a densely sampled household cohort over three seasons ]]> https://biorxiv.org/content/10.1101/2024.08.15.608152v1?rss=1 75% mutations present at <2% frequency. Children (0-5 years) had marginally higher within-host evolutionary rates than adolescents (6-18 years) and adults (>18 years, 4.4x10-6 vs. 9.42x10-7 and 3.45x10-6, p <0.001). Forty-five iSNV had evidence of parallel evolution, but were not overrepresented in HA and NA. Several increased from minority to consensus level, with strong linkage among iSNV across segments. A Wright Fisher Approximate Bayesian Computational model identified positive selection at 23/256 loci (9%) in A(H3N2) specimens and 19/176 loci (11%) in A(H1N1)pdm09 specimens, and these were infrequently found in circulation. Overall, we found that within-host IAV populations were subject to purifying selection and genetic drift, with only subtle differences across seasons, subtypes, and age strata. Positive selection was rare and inconsistently detected. ]]> Bendall, E. E. Zhu, Y. Fitzsimmons, W. J. Rolfes, M. Mellis, A. Halasa, N. Martin, E. T. Grijalva, C. G. Talbot, H. K. Lauring, A. S. 2024-08-19 doi:10.1101/2024.08.15.608152 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Endothelial β1 Integrins are Necessary for Microvascular Function and Glucose Uptake ]]> https://biorxiv.org/content/10.1101/2024.08.18.607045v1?rss=1 Winn, N. C. Roby, D. A. McClatchey, P. M. Williams, I. M. Bracy, D. P. Bedenbaugh, M. N. Lantier, L. Plosa, E. J. Pozzi, A. Zent, R. Wasserman, D. H. 2024-08-19 doi:10.1101/2024.08.18.607045 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Early Natural History of Cardiomyopathy and Cardiac Stress Response in Young Dogs with Golden Retriever Muscular Dystrophy ]]> https://biorxiv.org/content/10.1101/2024.08.19.608721v1?rss=1 Guo, L.-J. Nghiem, P. P. Bettis, A. K. Soslow, J. H. Spurney, C. Kornegay, J. N. 2024-08-20 doi:10.1101/2024.08.19.608721 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ Human melanoma cell lines that possess wild-type BRAF alleles but are dependent on ERBB4 and ERBB2 ]]> https://biorxiv.org/content/10.1101/2024.08.22.609260v1?rss=1 Dwivedi, V. Lucas, L. M. Cooke, R. Davis, J. Wilson, E. Scott, M. O'Daniel, K. Dion, C. Kerley, J. Zelan, M. DeFeo, N. Huffman, V. Ingrao, M. N. Riese, D. J. 2024-08-23 doi:10.1101/2024.08.22.609260 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ The oncometabolite D-2-hydroxyglutarate promotes DNA hypermethylation at lineage-specific enhancers controlling microglial activation in IDHmut gliomas ]]> https://biorxiv.org/content/10.1101/2024.08.23.608811v1?rss=1 Laurenge, A. Pugliese, P. Richard, Q. Mathon, B. Jouannet, S. Hayat, Y. Scuderi, S. Marijon, P. Labreche, K. Alentorn, A. Verreault, M. Idbaih, A. Birzu, C. Huillard, E. Pottier, N. Aurore Desmons, A. D. Fayache, I. Kaas, G. A. Kingsley, P. J. Marnett, L. J. Duplus, E. El-Habr, E. Salas, L. A. Mokhtari, K. Tran, S. Touat, M. Bielle, F. Suva, M. L. Iavarone, A. Ceccarelli, M. Mallat, M. Sanson, M. Castro-Vega, L. J. 2024-08-23 doi:10.1101/2024.08.23.608811 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ Patient mutations in DRP1 perturb synaptic maturation of cortical neurons ]]> https://biorxiv.org/content/10.1101/2024.08.23.609462v1?rss=1 Baum, T. B. Bodnya, C. Costanzo, J. Gama, V. 2024-08-25 doi:10.1101/2024.08.23.609462 Cold Spring Harbor Laboratory Press 2024-08-25 <![CDATA[ msiFlow: Automated Workflows for Reproducible and Scalable Multimodal Mass Spectrometry Imaging and Immunofluorescence Microscopy Data Processing and Analysis ]]> https://biorxiv.org/content/10.1101/2024.08.24.609403v1?rss=1 Spangenberg, P. Bessler, S. Widera, L. Bottek, J. Richter, M. Thiebes, S. Siemes, D. Krauss, S. Migas, L. G. Kasarla, S. S. Phapale, P. Kleesiek, J. Fuehrer, D. Moeller, L. C. Heuer, H. Van de Plas, R. Gunzer, M. Soehnlein, O. Soltwisch, J. Shevchuk, O. Dreisewerd, K. Engel, D. R. 2024-08-26 doi:10.1101/2024.08.24.609403 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Flanker task parameters are related to the strength of association between the ERN and anxiety: a meta-analysis ]]> https://biorxiv.org/content/10.1101/2024.08.27.609944v1?rss=1 Buzzell, G. A. Niu, Y. Machado, E. Dickinson, R. Moser, J. S. Morales, S. Troller-Renfree, S. V. 2024-08-28 doi:10.1101/2024.08.27.609944 Cold Spring Harbor Laboratory Press 2024-08-28 <![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[ Brain Charts for the Rhesus Macaque Lifespan ]]> https://biorxiv.org/content/10.1101/2024.08.28.610193v1?rss=1 Alldritt, S. Ramirez, J. S. B. Vos de Wael, R. Bethlehem, R. Seidlitz, J. Wang, Z. Nenning, K.-H. Esper, N. B. Smallwood, J. Franco, A. R. Byeon, K. Alexander-Bloch, A. Messinger, A. Chen, A. Thiele, A. Weiss, A. R. Shmuel, A. Fox, A. Tusche, A. Brambrink, A. M. Falchier, A. Hiba, B. Jarraya, B. Jung, B. Butler, B. Russ, B. E. Howell, B. R. Drzewiecki, C. M. Guedj, C. Schwiedrzik, C. M. Amiez, C. Wilson, C. R. E. Klink, C. Kroenke, C. Constantinidis, C. Garin, C. M. Poirier, C. Gale, D. J. Leopold, D. A. Rudko, D. A. Amaral, D. G. Tsao, D. Cook, D. J. 2024-08-30 doi:10.1101/2024.08.28.610193 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Do fungi look like macroparasites? Quantifying the patterns and mechanisms of aggregation for host-fungal parasite relationships ]]> https://biorxiv.org/content/10.1101/2024.08.29.609018v1?rss=1 Schrock, S. A. Walsman, J. C. DeMarchi, J. LeSage, E. H. Ohmer, M. E. B. Rollins-Smith, L. A. Briggs, C. J. Richards-Zawacki, C. L. Woodhams, D. C. Knapp, R. A. R. Smith, T. C. Haddad, C. F. B. Becker, C. G. Johnson, P. T. J. Wilber, M. Q. 2024-08-30 doi:10.1101/2024.08.29.609018 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ A Comparison of Skeletal Muscle Diffusion Tensor Imaging Tractography Seeding Methods ]]> https://biorxiv.org/content/10.1101/2024.08.29.610343v1?rss=1 Damon, B. M. Guzman, R. P. Lockard, C. Zhou, X. 2024-08-30 doi:10.1101/2024.08.29.610343 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Determining the off-target activity of antibiotics and novel translation initiation sites in mitochondria ]]> https://biorxiv.org/content/10.1101/2024.08.29.610400v1?rss=1 Marks, J. Young, E. Hafner, M. 2024-08-30 doi:10.1101/2024.08.29.610400 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Use of equine H3N8 hemagglutinin as a broadly protective influenza vaccine immunogen ]]> https://biorxiv.org/content/10.1101/2024.08.30.610504v1?rss=1 Verhoeven, D. Sponseller, B. Crowe, J. E. Bangaru, S. Webby, R. J. Lee, B. M. 2024-09-02 doi:10.1101/2024.08.30.610504 Cold Spring Harbor Laboratory Press 2024-09-02 <![CDATA[ Phosphorylation of CRYAB Induces a Condensatopathy to Worsen Post-Myocardial Infarction Left Ventricular Remodeling. ]]> https://biorxiv.org/content/10.1101/2024.08.30.610556v1?rss=1 Islam, M. Rawnsley, D. R. Ma, X. Navid, W. Zhao, C. Foroughi, L. Murphy, J. T. Navid, H. Weinheimer, C. J. Kovacs, A. Nigro, J. Diwan, A. Chang, R. Kumari, M. Young, M. Razani, B. Margulies, K. Abdellatif, M. Sedej, S. Javaheri, A. Covey, D. F. Mani, K. Diwan, A. 2024-09-03 doi:10.1101/2024.08.30.610556 Cold Spring Harbor Laboratory Press 2024-09-03 <![CDATA[ Early brain neuroinflammatory and metabolic changes identified by dual tracer microPET imaging in mice with acute liver injury ]]> https://biorxiv.org/content/10.1101/2024.09.02.610840v1?rss=1 Palandira, S. Falvey, A. Carrion, J. Zeng, Q. Chaudhry, S. Grossman, K. Turecki, L. Nguyen, N. Brines, M. Chavan, S. S. Metz, C. N. Al-Abed, Y. Chang, E. H. Ma, Y. Eidelberg, D. Vo, A. Tracey, K. J. Pavlov, V. A. 2024-09-03 doi:10.1101/2024.09.02.610840 Cold Spring Harbor Laboratory Press 2024-09-03 <![CDATA[ Genetic ancestry in Puerto Rican Afro-descendants illustrates diverse histories of African diasporic populations ]]> https://biorxiv.org/content/10.1101/2024.09.02.610898v1?rss=1 Nieves-Colon, M. A. Ulrich, E. C. Chen, L. Torres Colon, G. A. Rivera Clemente, M. La Corporacion Pinones Se Integra (COPI), Benn Torres, J. 2024-09-04 doi:10.1101/2024.09.02.610898 Cold Spring Harbor Laboratory Press 2024-09-04 <![CDATA[ Altered cellular metabolic pathway and epithelial cell maturation induced by MYO5B defects are partially reversible by LPAR5 activation ]]> https://biorxiv.org/content/10.1101/2024.09.03.610579v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@54b5borg.highwire.dtl.DTLVardef@1966a5aorg.highwire.dtl.DTLVardef@2073f1org.highwire.dtl.DTLVardef@9c12e1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Momoh, M. Rathan-Kumar, S. Burman, A. Brown, M. E. Adeniran, F. Ramos, C. Goldenring, J. R. Roland, J. T. Kaji, I. 2024-09-08 doi:10.1101/2024.09.03.610579 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Identifying deleterious noncoding variation through gain and loss of CTCF binding activity ]]> https://biorxiv.org/content/10.1101/2024.09.04.609712v1?rss=1 Tubbs, C. Benton, M. L. McArthur, E. Capra, J. A. Ruderfer, D. M. 2024-09-08 doi:10.1101/2024.09.04.609712 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Cost-effective solutions for high-throughput enzymatic DNA methylation sequencing ]]> https://biorxiv.org/content/10.1101/2024.09.09.612068v1?rss=1 Longtin, A. Watowich, M. M. Sadoughi, B. Petersen, R. Brosnan, S. F. Buetow, K. Cai, Q. Gurven, M. D. Highland, H. M. Huang, Y.-T. Kaplan, H. Kraft, T. S. Lim, Y. A. L. Long, J. Melin, A. D. Roberson, J. Ng, K.-S. Stieglitz, J. Trumble, B. C. Venkataraman, V. V. Wallace, I. J. Wu, J. Snyder-Mackler, N. Jones, A. Bick, A. G. Lea, A. 2024-09-09 doi:10.1101/2024.09.09.612068 Cold Spring Harbor Laboratory Press 2024-09-09 <![CDATA[ Direct measurement of PIP2 densities in biological membranes using a peptide-based sensor ]]> https://biorxiv.org/content/10.1101/2024.09.11.612554v1?rss=1 Menon, V. K. Wu, J. Alonzo, A. Rogers, K. Scrudders, K. L. Selvarajan, S. Walke, A. Kundu, R. Datta, A. Low-Nam, S. T. 2024-09-13 doi:10.1101/2024.09.11.612554 Cold Spring Harbor Laboratory Press 2024-09-13 <![CDATA[ Partial repair causes permanent defects in papillary structure and function after reversal of urinary obstruction ]]> https://biorxiv.org/content/10.1101/2024.09.11.612436v1?rss=1 View larger version (57K): org.highwire.dtl.DTLVardef@1438af5org.highwire.dtl.DTLVardef@157ff60org.highwire.dtl.DTLVardef@3f09c0org.highwire.dtl.DTLVardef@9950b1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Vanichapol, T. Gonzalez, A. Delgado, R. Brewer, M. Clouthier, K. Menshikh, A. Snyder, W. Raman, T. Sander, V. Davidson, A. J. de Caestecker, M. 2024-09-15 doi:10.1101/2024.09.11.612436 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Validation of a refined protocol for mouse oral glucose tolerance testing without gavage ]]> https://biorxiv.org/content/10.1101/2024.09.13.612859v1?rss=1 Pye, K. R. Lantier, L. Ayala, J. E. Beall, C. Ellacott, K. L. 2024-09-19 doi:10.1101/2024.09.13.612859 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Yatakemycin biosynthesis requires two deoxyribonucleases for toxin self-resistance ]]> https://biorxiv.org/content/10.1101/2024.09.16.613364v1?rss=1 Dorival, J. Yuan, H. Walker, A. S. Tang, G.-L. Eichman, B. F. 2024-09-19 doi:10.1101/2024.09.16.613364 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Strand dependent bypass of DNA lesions during fork reversal by ATP-dependent translocases SMARCAL1, ZRANB3, and HLTF ]]> https://biorxiv.org/content/10.1101/2024.09.17.613558v1?rss=1 Adolph, M. B. Warren, G. M. Couch, F. B. Greer, B. H. Eichman, B. F. Cortez, D. 2024-09-19 doi:10.1101/2024.09.17.613558 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Single Cell Profiling in the Sox10Dom/+ Hirschsprung Mouse Implicates Hoxa6 in Enteric Neuron Lineage Allocation ]]> https://biorxiv.org/content/10.1101/2024.09.18.613729v1?rss=1 Avila, J. A. Benthal, J. T. Schafer, J. C. Southard-Smith, E. M. 2024-09-19 doi:10.1101/2024.09.18.613729 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Increased cGMP improves microvascular exercise training adaptations independent of endothelial nitric oxide synthase ]]> https://biorxiv.org/content/10.1101/2024.09.18.612717v1?rss=1 Winn, N. C. Cappel, D. A. Pollock, E. D. Lantier, L. Riveros, J. K. Debrow, P. Bracy, D. P. Beckman, J. A. Wasserman, D. H. 2024-09-22 doi:10.1101/2024.09.18.612717 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Acute tuft cell ablation induces malabsorption and alterations in secretory and immune cell lineages in small intestine ]]> https://biorxiv.org/content/10.1101/2024.09.18.613746v1?rss=1 Momoh, M. Adeniran, F. Ramoth, C. DelGiorno, K. E. Seno, H. Roland, J. T. Kaji, I. 2024-09-22 doi:10.1101/2024.09.18.613746 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Gli2 Overexpression Alters the Differentiation Status of Dedifferentiated Liposarcoma Cells and Results in an Immunosuppressive Myeloid Phenotype in Orthotopic Tumors ]]> https://biorxiv.org/content/10.1101/2024.09.18.613793v1?rss=1 Bennett, N. E. Beadle, E. P. Parker, D. V. Coe, E. J. Cottam, M. A. Baum, J. E. Miller, J. S. Serrenho, J. A. Rhoades, J. A. 2024-09-22 doi:10.1101/2024.09.18.613793 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Widespread brain activity increases in frontal lobe seizures with impaired consciousness ]]> https://biorxiv.org/content/10.1101/2024.09.20.614207v1?rss=1 Salardini, E. Vaddiparti, A. Kumar, A. Martin, R. A. Gebere, R. Z. Arencibia, C. A. Dhakar, M. B. Grover, E. H. Quraishi, I. H. Sternberg, E. J. George, I. C. Sivaraju, A. Bonito, J. Zaveri, H. P. Gober, L. M. Ahmed, S. Ghoshal, S. Wu, K. Farooque, P. Hirsch, L. J. Damisah, E. Gerrard, J. L. Spencer, D. D. Yoo, J. Y. Young, J. J. Friedman, D. Shum, J. Blumenfeld, H. 2024-09-23 doi:10.1101/2024.09.20.614207 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ Lysosomal LRRC8 complex regulates lysosomal pH, morphology and systemic glucose metabolism ]]> https://biorxiv.org/content/10.1101/2024.09.22.614256v1?rss=1 Kumar, A. Zhao, Y. Xie, L. Chadda, R. Abraham, N. Hong, J. Feng, E. Tranter, J. D. Rawnsley, D. Liu, H. Henry, K. M. Meyer, G. Hu, M. Xu, H. Hinton, A. Grueter, C. E. Abel, E. D. Norris, A. W. Diwan, A. Sah, R. 2024-09-23 doi:10.1101/2024.09.22.614256 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ Building a literature knowledge base towards transparent biomedical AI ]]> https://biorxiv.org/content/10.1101/2024.09.22.614323v1?rss=1 Huang, Y. Han, Z. Luo, X. Luo, X. Gao, Y. Zhao, M. Tang, F. Wang, Y. Chen, J. Li, C. Lu, X. Qiu, J. Deng, F. Jiao, T. Xue, D. Feng, F. Vu, T. H. H. Guan, L. Cartailler, J.-P. Stitzel, M. Chen, S. Brissova, M. Parker, S. Liu, J. 2024-09-24 doi:10.1101/2024.09.22.614323 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Analysis of genetic requirements and nutrient availability for Staphylococcus aureus growth in cystic fibrosis sputum ]]> https://biorxiv.org/content/10.1101/2024.09.24.614743v1?rss=1 Shull, L. M. Wolter, D. J. Kunkle, D. E. Legg, K. A. Giedroc, D. P. Skaar, E. P. Hoffman, L. R. Reniere, M. L. 2024-09-25 doi:10.1101/2024.09.24.614743 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ The Proteostasis Network is a Therapeutic Target in Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/2024.09.24.614781v1?rss=1 Lam, K. Kim, Y. J. Ong, C. M. Liu, A. Z. Zhou, F. J. Sunshine, M. J. Chua, B. A. Vicenzi, S. Ford, P. Zhou, J.-H. Hong, Y. Bennett, E. J. Crews, L. A. Ball, E. D. Signer, R. A. J. 2024-09-26 doi:10.1101/2024.09.24.614781 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Trem2 deficiency attenuates breast cancer tumor growth in lean, but not obese or weight loss, mice and is associated with alterations of clonal T cell populations ]]> https://biorxiv.org/content/10.1101/2024.09.25.614811v1?rss=1 Pierro, E. W. Cottam, M. A. An, H. Lehmann, B. D. Pietenpol, J. A. Wellen, K. E. Makowski, L. Rathmell, J. C. Fingleton, B. Hasty, A. H. 2024-09-27 doi:10.1101/2024.09.25.614811 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Morning Engagement of Hepatic Insulin Receptors Improves Afternoon Hepatic Glucose Disposal and Storage ]]> https://biorxiv.org/content/10.1101/2024.09.25.614969v1?rss=1 Waterman, H. L. Moore, M. C. Smith, M. Farmer, B. Yankey, K. Scott, M. Edgerton, D. S. Cherrington, A. D. 2024-09-27 doi:10.1101/2024.09.25.614969 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Rationalize the Functional Roles of Protein-Protein Interactions in Targeted Protein Degradation by Kinetic Monte-Carlo Simulations ]]> https://biorxiv.org/content/10.1101/2024.09.26.615190v1?rss=1 Su, Z. Yin, S. Wu, Y. 2024-09-28 doi:10.1101/2024.09.26.615190 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ HEXIM1 is correlated with Alzheimer's disease pathology and regulates immediate early gene dynamics in neurons ]]> https://biorxiv.org/content/10.1101/2024.09.27.615234v1?rss=1 Htet, M. Estay-Olmos, C. Hu, L. Wu, Y. Powers, B. E. Campbell, C. Ahmed, M. R. Hohman, T. J. Schneider, J. A. Bennett, D. A. Menon, V. De Jager, P. Kaas, G. A. Colbran, R. J. Greer, C. B. 2024-09-28 doi:10.1101/2024.09.27.615234 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ Evolution of tRNA pool shapes variation in selection on codon usage across the Saccharomycotina subphylu ]]> https://biorxiv.org/content/10.1101/2024.09.27.615277v1?rss=1 Cope, A. L. Shah, P. 2024-09-28 doi:10.1101/2024.09.27.615277 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ Anatomically and Physiologically Accurate Engineered Neurovascular Unit and Blood-Brain Barrier Model Using Microvessels Isolated from Postmortem Human Brain Tissue ]]> https://biorxiv.org/content/10.1101/2024.09.26.615283v1?rss=1 O'Grady, B. McCall, A. S. Cullison, S. Chavarria, D. Kjar, A. Schrag, M. Lippmann, E. 2024-09-29 doi:10.1101/2024.09.26.615283 Cold Spring Harbor Laboratory Press 2024-09-29 <![CDATA[ Early hominin arrival in Southeast Asia triggered the evolution of major human malaria vectors ]]> https://biorxiv.org/content/10.1101/2024.09.28.615606v1?rss=1 Singh, U. S. Harbach, R. E. Hii, J. Chang, M. S. Somboon, P. Prakash, A. Sarma, D. Broomfield, B. Morgan, K. Albert, S. Das, A. Linton, Y.-M. Carlton, J. M. Walton, C. 2024-09-30 doi:10.1101/2024.09.28.615606 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Preserving Full Spectrum Information in ImagingMass Spectrometry Data Reduction ]]> https://biorxiv.org/content/10.1101/2024.09.30.614425v1?rss=1 Moens, R. A. R. Migas, L. G. Van Ardenne, J. M. Skaar, E. P. Spraggins, J. M. Van de Plas, R. 2024-10-01 doi:10.1101/2024.09.30.614425 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Actomyosin Contractility is a Potent Suppressor of Mesoderm Induction by Human Pluripotent Stem Cells ]]> https://biorxiv.org/content/10.1101/2024.09.30.615859v1?rss=1 Fort, L. Wang, W. Macara, I. G. 2024-10-01 doi:10.1101/2024.09.30.615859 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Autophosphorylation of the oncogenic protein TEL-ABL confers resistance to the allosteric ABL inhibitor asciminib ]]> https://biorxiv.org/content/10.1101/2024.10.02.616342v1?rss=1 2000-fold less potent against TEL-ABL than BCR-ABL in cell-growth assays. This is surprising because the ABL components of the two fusion proteins, including the asciminib binding sites, have identical sequence. We deleted a short helical segment in the ABL kinase domain that closes over asciminib when it is bound. This deletion results in asciminib resistance in BCR-ABL, but has no effect on TEL-ABL, suggesting that the native autoinhibitory mechanism that asciminib engages in BCR-ABL is disrupted in TEL-ABL. We show, using mammalian cell expression and single-molecule microscopy, that BCR-ABL is mainly dimeric while TEL-ABL forms higher-order oligomers. Oligomerization can promote trans-autophosphorylation of ABL, and we find that a regulatory phosphorylation site in the SH3 domain of ABL (Tyr 89) is highly phosphorylated in TEL-ABL. This phosphorylation is expected to disassemble the autoinhibited conformation of ABL, thereby preventing asciminib binding. We show that TEL-ABL is intrinsically susceptible to inhibition by asciminib, but that increased phosphorylation results in resistance. Our results demonstrate that different ABL fusion proteins can have dramatically different responses to allosteric inhibitors due to differential phosphorylation. One Sentence SummaryWhen TEL-ABL is phosphorylated, it is insensitive to asciminib. However, when TEL-ABL is dephosphorylated by a phosphatase, asciminib sensitivity is restored. ]]> Muratcioglu, S. Eide, C. A. Gorday, K. Sumpena, E. Zuo, W. Groves, J. T. Druker, B. J. Kuriyan, J. 2024-10-02 doi:10.1101/2024.10.02.616342 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ MORC-1 is a key component of the C. elegans CSR-1 germline gene licensing mechanism ]]> https://biorxiv.org/content/10.1101/2024.10.02.616347v1?rss=1 Kirshner, J. A. Picard, C. L. Weiser, N. E. Mehta, N. Feng, S. Murphy, V. N. Vakhnovetsky, A. Alessi, A. F. Xiao, C. Inoki, K. El Mouridi, S. Frokjaer-Jensen, C. Jacobsen, S. E. Kim, J. K. 2024-10-02 doi:10.1101/2024.10.02.616347 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Changes in Myofibril Size, Shape, and Network Connectivity in Aging Muscle ]]> https://biorxiv.org/content/10.1101/2024.10.01.615981v1?rss=1 View larger version (54K): org.highwire.dtl.DTLVardef@1b06d92org.highwire.dtl.DTLVardef@1e99c7eorg.highwire.dtl.DTLVardef@2151b3org.highwire.dtl.DTLVardef@17ac3f7_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ajayi, P. T. Vue, Z. Hinton, A. O. Glancy, B. 2024-10-03 doi:10.1101/2024.10.01.615981 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Baby Open Brains: An Open-Source Repository of Infant Brain Segmentations ]]> https://biorxiv.org/content/10.1101/2024.10.02.616147v1?rss=1 Feczko, E. J. Stoyell, S. M. Moore, L. A. Alexopoulos, D. Bagonis, M. Barrett, K. Bower, B. Cavender, A. Chamberlain, T. A. Conan, G. Day, T. K. Goradia, D. Graham, A. Heisler-Roman, L. Hendrickson, T. J. Houghton, A. Kardan, O. Kiffmeyer, E. A. Lee, E. G. Lundquist, J. T. Lucena, C. Martin, T. Mummaneni, A. Myricks, M. Narnur, P. Perrone, A. J. Reiners, P. Rueter, A. R. Saw, H. Styner, M. Sung, S. Tiklasky, B. Wisnowski, J. L. Yacoub, E. Zimmermann, B. Smyser, C. D. Rosenberg, M. D. Fair, D. A. Elison, J. T. 2024-10-03 doi:10.1101/2024.10.02.616147 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Mitochondrial reactive oxygen species cause arrhythmias in hypertrophic cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2024.10.02.616214v1?rss=1 Kohlhaas, M. Sequeira, V. Parikh, S. Dietl, A. Richter, O. Bay, J. Bertero, E. Schwemmlein, J. Tian, Q. Friedrich, F. W. Flenner, F. Nickel, A. G. Alscher, F. Nanadikar, M. S. Venkataraman, R. Baudenbacher, F. J. Kappl, R. Johnson, V. Prates Roma, L. Kasakow, A. Hohl, M. Laufs, U. Hoth, M. Katschinski, D. M. Bohm, M. Lipp, P. Carrier, L. Eschenhagen, T. Knollmann, B. C. Maack, C. 2024-10-03 doi:10.1101/2024.10.02.616214 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Stimulus history, not expectation, drives sensory prediction errors in mammalian cortex ]]> https://biorxiv.org/content/10.1101/2024.10.02.616378v1?rss=1 Westerberg, J. A. Xiong, Y. S. Nejat, H. Sennesh, E. Durand, S. Cabasco, H. Belski, H. Gillis, R. Loeffler, H. Bawany, A. Peene, C. R. Han, W. Nguyen, K. Ha, V. Johnson, T. Grasso, C. Hardcastle, B. Young, A. Swapp, J. Ouellete, B. Caldejon, S. Williford, A. Groblewski, P. A. Olsen, S. R. Kiselycznyk, C. Lecoq, J. A. Maier, A. Bastos, A. M. 2024-10-03 doi:10.1101/2024.10.02.616378 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Conflict neurons in cingulate cortex of macaques ]]> https://biorxiv.org/content/10.1101/2024.10.03.616355v1?rss=1 Corrigan, B. W. Errington, S. P. Sajad, A. Schall, J. D. 2024-10-04 doi:10.1101/2024.10.03.616355 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Aging at scale: Younger dogs and larger breeds from the Dog Aging Project show accelerated epigenetic aging. ]]> https://biorxiv.org/content/10.1101/2024.10.03.616519v1?rss=1 McCoy, B. M. Mariner, B. L. Cheng, C. F. Silkas, E. Adjangba, C. Greenier, A. Brassington, L. Marye, A. Harrison, B. R. Partida-Aguilar, M. Bamberger, T. Algavi, Y. Muller, E. Harris, A. Rout, E. Avery, A. Promislow, D. Borenstein, E. The Dog Aging Project Consortium, Snyder-Mackler, N. 2024-10-04 doi:10.1101/2024.10.03.616519 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Single-cell resolution map of innate-like lymphocyte response to Francisella tularensis infection reveals MAIT cell role in protection from tularemia-like disease ]]> https://biorxiv.org/content/10.1101/2024.10.04.616759v1?rss=1 JOYCE, S. 2024-10-06 doi:10.1101/2024.10.04.616759 Cold Spring Harbor Laboratory Press 2024-10-06 <![CDATA[ Longitudinal multi-omics reveals pathogenic TSC2 variants disrupt developmental trajectories of human cortical organoids derived from Tuberous Sclerosis Complex ]]> https://biorxiv.org/content/10.1101/2024.10.07.617121v1?rss=1 Niu, W. Yu, S. Li, X. Wang, Z. Chen, R. Michalski, C. Jahangiri, A. Zohdy, Y. Chern, J. J. Whitworth, T. J. Wang, J. Xu, J. Zhou, Y. Qin, Z. Li, B. Gambello, M. J. Peng, J. Wen, Z. 2024-10-11 doi:10.1101/2024.10.07.617121 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Torsion-Induced Traumatic Optic Neuropathy (TITON): A Physiologically Relevant Animal Model of Traumatic Optic Neuropathy ]]> https://biorxiv.org/content/10.1101/2024.10.08.617086v1?rss=1 Ryan, A. K. Asemota, B. I. Heisler-Taylor, T. Mello, C. Rodriguez, L. Sponsel, W. E. Racine, J. Rex, T. S. Glickman, R. D. Reilly, M. A. 2024-10-11 doi:10.1101/2024.10.08.617086 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ DNA methylation of transposons pattern aging differences across a diverse cohort of dogs from the Dog Aging Project ]]> https://biorxiv.org/content/10.1101/2024.10.08.617286v1?rss=1 Mariner, B. L. McCoy, B. M. Greenier, A. Brassington, L. Silkas, E. Adjangba, C. Marye, A. Harrison, B. R. Bamberger, T. Algavi, Y. Muller, E. Harris, A. Rout, E. The Dog Aging Project Consortium, Avery, A. Borenstein, E. Promislow, D. Snyder-Mackler, N. 2024-10-11 doi:10.1101/2024.10.08.617286 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Reliable RNA-seq analysis from FFPE specimens as a means to accelerate cancer-related health disparities research ]]> https://biorxiv.org/content/10.1101/2024.10.10.617597v1?rss=1 13,000 protein coding genes which could be used to differentiate HPV-associated from HPV-independent OPSCCs. Co-isolated DNA was used to identify patient ancestry. Utilizing the methods described in this study provides a robust, reliable, and standardized means of DNA & RNA extraction from FFPE as well as a means by which to assure the quality of the data generated. ]]> Sandulache, V. Perez-Bello, D. C. Yadollahi, P. Castro, P. Frederick, A. Frederick, A. Osman, R. Essien, F. Yebra, I. Hamlin, A. Ow, T. Skinner, H. 2024-10-11 doi:10.1101/2024.10.10.617597 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ An approach for coherent periodogram averaging of tilt-series data for improved CTF estimation ]]> https://biorxiv.org/content/10.1101/2024.10.10.617684v1?rss=1 Khavnekar, S. Wan, W. 2024-10-11 doi:10.1101/2024.10.10.617684 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Public RNA-seq data are not representative of global human diversity ]]> https://biorxiv.org/content/10.1101/2024.10.11.617967v1?rss=1 Gallego Romero, I. Rodenberg, G. Arner, A. M. Li, L. Beasley, I. J. A. Rossow, R. Ryan, N. Wang, S. Lea, A. A. 2024-10-12 doi:10.1101/2024.10.11.617967 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ High-dimensional confounding in causal mediation: a comparison study of double machine learning and regularized partial correlation network ]]> https://biorxiv.org/content/10.1101/2024.10.12.617110v1?rss=1 Chen, M. Nguyen, T. T. Liu, J. 2024-10-12 doi:10.1101/2024.10.12.617110 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Toxicokinetics for organ-on-chip devices ]]> https://biorxiv.org/content/10.1101/2024.10.10.617253v1?rss=1 Hermann, N. G. Ficek, R. A. Markov, D. A. McCawley, L. J. Hutson, M. S. 2024-10-14 doi:10.1101/2024.10.10.617253 Cold Spring Harbor Laboratory Press 2024-10-14 <![CDATA[ Synthesis and characterization of chloroquine-modified albumin-binding siRNA-lipid conjugates for improved intracellular delivery and gene silencing in cancer cells ]]> https://biorxiv.org/content/10.1101/2024.10.14.618042v1?rss=1 Lo, J. H. Gbur, E. F. Francini, N. Ma, J. Sorets, A. G. Fletcher, R. B. Yu, F. D'Arcy, R. Oltman, C. G. Uddin, M. J. Duvall, C. L. 2024-10-17 doi:10.1101/2024.10.14.618042 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Load-based divergence in the dynamic allostery of two TCRs recognizing the same pMHC ]]> https://biorxiv.org/content/10.1101/2024.10.16.618634v1?rss=1 Chang-Gonzalez, A. C. Akitsu, A. Mallis, R. J. Lang, M. J. Reinherz, E. L. Hwang, W. 2024-10-18 doi:10.1101/2024.10.16.618634 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ B cell expression of the enzyme PexRAP, an intermediary in ether lipid biosynthesis, promotes antibody responses and germinal center size ]]> https://biorxiv.org/content/10.1101/2024.10.17.618760v1?rss=1 Cho, S. H. Jones, M. A. Meyer, K. Anderson, D. M. Chetyrkin, S. Calcutt, M. W. Caprioli, R. M. Semekovich, C. F. Boothby, M. R. 2024-10-18 doi:10.1101/2024.10.17.618760 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Expression-Driven Genetic Dependency Reveals Targets for Precision Medicine ]]> https://biorxiv.org/content/10.1101/2024.10.17.618926v1?rss=1 Elmas, A. Layden, H. Ellis, J. Barlett, L. Zhao, X. Kawabata-Iwakawa, R. Obinata, H. Hiebert, S. Huang, K.-l. 2024-10-21 doi:10.1101/2024.10.17.618926 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ Integrin alpha1 beta1 promotes interstitial fibrosis in a mouse model of polycystic kidney disease ]]> https://biorxiv.org/content/10.1101/2024.10.18.619080v1?rss=1 Grenier, C. Lin, I.-H. Peters, D. Pozzi, A. Lennon, R. Naylor, R. W. 2024-10-21 doi:10.1101/2024.10.18.619080 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ Apical clathrin-coated endocytic pits control the growth and size of epithelial microvilli ]]> https://biorxiv.org/content/10.1101/2024.10.21.619431v1?rss=1 Perkins, O. L. Mulligan, A. G. Krystofiak, E. S. Peebles, K. E. Meenderink, L. M. Millis, B. A. Tyska, M. J. 2024-10-21 doi:10.1101/2024.10.21.619431 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ Loss of Cdc42 causes abnormal optic cup morphogenesis and microphthalmia in mouse ]]> https://biorxiv.org/content/10.1101/2024.10.20.619331v1?rss=1 Hofstetter, K. S. Haas, P. M. Kuntz, J. P. Zheng, Y. Fuhrmann, S. 2024-10-22 doi:10.1101/2024.10.20.619331 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Executive control can query hidden human memories ]]> https://biorxiv.org/content/10.1101/2024.10.22.619676v1?rss=1 Zhao, C. Fukuda, K. Woodman, G. F. 2024-10-22 doi:10.1101/2024.10.22.619676 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Somatic Mutations in MCOLN3 in Aldosterone-Producing Adenomas cause Primary Aldosteronism. ]]> https://biorxiv.org/content/10.1101/2024.10.20.619295v1?rss=1 van Rooyen, D. Bandulik, S. Coon, G. Laukemper, M. Kumar-Sinha, C. Udager, A. M. Lee, C. Wachtel, H. Cohen, D. L. Luther, J. M. Giordano, T. Turcu, A. Warth, R. Rainey, W. E. Rege, J. 2024-10-23 doi:10.1101/2024.10.20.619295 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Pancreatic islet alpha cells regulate microtubule stability in neighboring beta cells to tune insulin secretion and induce functional heterogeneity in individual mouse and human islets ]]> https://biorxiv.org/content/10.1101/2024.10.21.619544v1?rss=1 Ho, K.-H. Barmaver, S. Ho, R. Yagan, M. Ahmed, H. K. Kaverina, I. Gu, G. 2024-10-23 doi:10.1101/2024.10.21.619544 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ EFP Analyzer: A fast, accurate, and easy-to-teach program for analyzing Extracellular Field Potentials from iPSC-derived cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2024.10.21.619481v1?rss=1 Patel, N. P. Shen, A. Wada, Y. Blair, M. A. Mitchell, D. W. Vanags, L. R. Woo, S. Ku, M. J. Dauda, K. S. Morris, W. A. Yang, M. Knollmann, B. C. Roden, D. M. Salem, J. E. Glazer, A. M. Kroncke, B. M. 2024-10-24 doi:10.1101/2024.10.21.619481 Cold Spring Harbor Laboratory Press 2024-10-24 <![CDATA[ Annexin A6 modulates the secretion of pro-inflammatory cytokines and exosomes via interaction with SNAP23 in triple negative breast cancer cells ]]> https://biorxiv.org/content/10.1101/2024.10.22.619710v1?rss=1 Sakwe, N. I. Vuong, N. B. Black, P. J. Ball, D. D. Thomas, P. Beasley, H. K. Hinton, A. Ochieng, J. Sakwe, A. M. 2024-10-25 doi:10.1101/2024.10.22.619710 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Early perturbations to fluid homeostasis alter development of hypothalamic feeding circuits with context-specific changes in ingestive behavior ]]> https://biorxiv.org/content/10.1101/2024.10.25.620307v1?rss=1 Sweet, S. R. Biddinger, J. E. Zimmermann, J. B. Yu, G. L. Simerly, R. B. 2024-10-26 doi:10.1101/2024.10.25.620307 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ LassoESM: A tailored language model for enhanced lasso peptide property prediction ]]> https://biorxiv.org/content/10.1101/2024.10.25.620295v1?rss=1 Mi, X. Barrett, S. E. Mitchell, D. A. Shukla, D. 2024-10-29 doi:10.1101/2024.10.25.620295 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ 5hmC enhances PARP trapping and restores PARP inhibitor sensitivity in chemoresistant BRCA1/2-deficient cells ]]> https://biorxiv.org/content/10.1101/2024.10.25.620335v1?rss=1 Kharat, S. S. Mishra, A. P. Sengodan, S. K. Dierman, D. Fox, S. D. Sharan, S. K. 2024-10-29 doi:10.1101/2024.10.25.620335 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Mu opioid receptor expression by nucleus accumbens inhibitory interneurons promotes affiliative social behavior ]]> https://biorxiv.org/content/10.1101/2024.10.28.620729v1?rss=1 Toddes, C. Lefevre, E. M. Retzlaff, C. L. Zugschwert, L. Khan, S. Myhre, E. Gauthier, E. A. Fernandez de Velasco, E. M. Kieffer, B. L. Rothwell, P. E. 2024-10-29 doi:10.1101/2024.10.28.620729 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Scientific reasoning driven by influential data: resuscitate dfstat! ]]> https://biorxiv.org/content/10.1101/2024.10.30.621016v1?rss=1 Spiess, A. N. Roediger, S. Schaks, M. Burdukiewicz, M. Tellinghuisen, J. 2024-10-30 doi:10.1101/2024.10.30.621016 Cold Spring Harbor Laboratory Press 2024-10-30 <![CDATA[ Small-molecule modulators of lipid raft stability and protein-raft partitioning ]]> https://biorxiv.org/content/10.1101/2024.10.28.620521v1?rss=1 Stefanski, K. M. Huang, H. Luu, D. D. Hutchison, J. M. Saksena, N. Fisch, A. J. Hasaka, T. P. Bauer, J. A. Kenworthy, A. K. Van Horn, W. D. Sanders, C. 2024-10-31 doi:10.1101/2024.10.28.620521 Cold Spring Harbor Laboratory Press 2024-10-31 <![CDATA[ Systemic inhibition of de novo purine biosynthesis prevents weight gain and improves metabolic health by increasing thermogenesis and decreasing food intake ]]> https://biorxiv.org/content/10.1101/2024.10.28.620705v1?rss=1 Myers, J. W. Park, W. Y. Eddie, A. M. Shinde, A. B. Prasad, P. Murphy, A. C. Leonard, M. Z. Pinette, J. A. Rampy, J. J. Montufar, C. Shaikh, Z. Hickman, T. T. Reynolds, G. N. Winn, N. C. Lantier, L. Peck, S. H. Coate, K. C. Stein, R. W. Carrasco, N. Calipari, E. S. McReynolds, M. R. Zaganjor, E. 2024-11-01 doi:10.1101/2024.10.28.620705 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Modeling Protein Conformations by Guiding AlphaFold2 with Distance Distributions. Application to Double Electron Electron Resonance (DEER) Spectroscopy. ]]> https://biorxiv.org/content/10.1101/2024.10.30.621127v1?rss=1 Wu, T. A. Stein, R. Kao, T.-Y. Brown, B. S. Mchaourab, H. 2024-11-01 doi:10.1101/2024.10.30.621127 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ N-Aldehyde-Modified Phosphatidylethanolamines generated by lipid peroxidation are robust substrates of N-Acyl Phosphatidylethanolamine Phospholipase D ]]> https://biorxiv.org/content/10.1101/2024.10.30.621135v1?rss=1 Fadaei, R. Bernstein, A. C. Jenkins, A. N. Pickens, A. G. Zarrow, J. E. Alli-oluwafuyi, A.-m. O. Tallman, K. A. Davies, S. S. 2024-11-01 doi:10.1101/2024.10.30.621135 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ A potently neutralizing and protective human antibody targeting antigenic site V on RSV and hMPV fusion glycoprotein ]]> https://biorxiv.org/content/10.1101/2024.10.31.621295v1?rss=1 Abu-Shmais, A. A. Guo, L. Khalil, A. M. Miller, R. J. Janke, A. K. Vukovich, M. J. Bass, L. E. Suresh, Y. P. Rush, S. A. Wolters, R. M. Kose, N. Carnahan, R. H. Crowe, J. E. Bonami, R. H. Mousa, J. J. McLellan, J. S. Georgiev, I. S. 2024-11-01 doi:10.1101/2024.10.31.621295 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Directed insulin secretion occurs at precise cortical regions with optimal ELKS content that are devoid of microtubules ]]> https://biorxiv.org/content/10.1101/2024.10.31.621333v1?rss=1 Fye, M. A. Sangowdar, P. Jayathilake, A. Regan, P. Gu, G. Kaverina, I. 2024-11-01 doi:10.1101/2024.10.31.621333 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Platelets are Protective in Early Abdominal Aortic Aneurysm Formation ]]> https://biorxiv.org/content/10.1101/2024.10.29.616205v1?rss=1 Russell, H. M. Spuzzillo, A. Benson, T. W. Jaworski, J. Clement, M. Boulaftali, Y. Saum, K. Conrad, K. A. Howatt, D. A. Luyendyk, J. P. Cameron, S. J. Nieswandt, B. Steinhubl, S. R. Daugherty, A. Bergmeier, W. Tong, W. Damrauer, S. Tsao, P. Mallat, Z. Edwards, T. L. Mackman, N. Owens, A. P. 2024-11-03 doi:10.1101/2024.10.29.616205 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Meta-atlas of Juvenile and Adult Enteric Neuron scRNA-seq for Dataset Comparisons and Consensus on Transcriptomic Definitions of Enteric Neuron Subtypes ]]> https://biorxiv.org/content/10.1101/2024.10.31.621315v1?rss=1 Benthal, J. T. May-Zhang, A. A. Southard-Smith, E. M. 2024-11-04 doi:10.1101/2024.10.31.621315 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ A consensus definition for deep layer 6 excitatory neurons in mouse neocortex ]]> https://biorxiv.org/content/10.1101/2024.11.04.621933v1?rss=1 Kim, S.-J. Babola, T. A. Lee, K. Matney, C. J. Spiegel, A. C. Liew, M. H. Schulteis, E. M. Coye, A. E. Proskurin, M. Kang, H. Kim, J. A. Chevee, M. Lee, K. Kanold, P. O. Goff, L. A. Kim, J. Brown, S. P. 2024-11-05 doi:10.1101/2024.11.04.621933 Cold Spring Harbor Laboratory Press 2024-11-05 <![CDATA[ ENaC contributes to macrophage dysfunction in cystic fibrosis ]]> https://biorxiv.org/content/10.1101/2024.11.06.622340v1?rss=1 Moran, J. Pugh, C. Brown, N. Thomas, A. Zhang, S. McCauley, E. Cephas, A. Shrestha, C. Partida-Sanchez, S. Bai, S. Bruscia, E. M. Kopp, B. 2024-11-08 doi:10.1101/2024.11.06.622340 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Perilipin 5 Phosphorylation is Dispensable for Upregulation of Hepatic Lipid Metabolism Genes upon Fasting but Required for Insulin Receptor Substrate 2 Expression in Male Mice ]]> https://biorxiv.org/content/10.1101/2024.11.09.622792v1?rss=1 Bovee, C. Grandgenett, R. Trevino, M. Dutta, S. Peachee, S. Kopriva, S. Haider, F. Liu, S. Bhardwaj, G. Penniman, C. O'Neill, B. Imai, Y. 2024-11-09 doi:10.1101/2024.11.09.622792 Cold Spring Harbor Laboratory Press 2024-11-09 <![CDATA[ Multimodal state-dependent connectivity analysis of arousal and autonomic centers in the brainstem and basal forebrain ]]> https://biorxiv.org/content/10.1101/2024.11.11.623092v1?rss=1 Pourmotabbed, H. Martin, C. G. Goodale, S. E. Doss, D. J. Wang, S. Bayrak, R. G. Kang, H. Morgan, V. L. Englot, D. J. Chang, C. 2024-11-13 doi:10.1101/2024.11.11.623092 Cold Spring Harbor Laboratory Press 2024-11-13 <![CDATA[ Communication subspaces align with training in ANNs ]]> https://biorxiv.org/content/10.1101/2024.11.11.623065v1?rss=1 Poggi, P. G. Mihalas, S. Mastrovito, D. 2024-11-14 doi:10.1101/2024.11.11.623065 Cold Spring Harbor Laboratory Press 2024-11-14 <![CDATA[ Gestation length drives brain size and litter size variation in eutherian mammals ]]> https://biorxiv.org/content/10.1101/2024.11.13.623395v1?rss=1 Danis, T. Lin, D. Caetano, D. S. Funston, G. F. Rokas, A. 2024-11-15 doi:10.1101/2024.11.13.623395 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Quantitative mapping of cerebrovascular reactivity amplitude and delay with breath-hold BOLD fMRI when end-tidal CO2 quality is low ]]> https://biorxiv.org/content/10.1101/2024.11.18.624159v1?rss=1 Clements, R. G. Zvolanek, K. M. Reddy, N. A. Hemmerling, K. J. Bayrak, R. G. Chang, C. Bright, M. G. 2024-11-19 doi:10.1101/2024.11.18.624159 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ Sensing the shape of a surface by intracellular filaments ]]> https://biorxiv.org/content/10.1101/2024.11.18.624198v1?rss=1 Shi, H. Nguyen, J. Gitai, Z. Shaevitz, J. W. Bratton, B. P. Gopinathan, A. Grason, G. Huang, K. C. 2024-11-20 doi:10.1101/2024.11.18.624198 Cold Spring Harbor Laboratory Press 2024-11-20 <![CDATA[ SuperWater: Predicting Water Molecule Positions on Protein Structures by Generative AI ]]> https://biorxiv.org/content/10.1101/2024.11.18.624208v1?rss=1 Kuang, X. su, z. Liu, Y. Lin, X. Smith, J. S. Derr, T. Wu, Y. Meiler, J. 2024-11-20 doi:10.1101/2024.11.18.624208 Cold Spring Harbor Laboratory Press 2024-11-20 <![CDATA[ Pleiotropy increases with gene age in six model multicellular eukaryotes ]]> https://biorxiv.org/content/10.1101/2024.11.19.624372v1?rss=1 Martin, R. A. Tate, A. T. 2024-11-21 doi:10.1101/2024.11.19.624372 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Machine learning application to predict binding affinity between peptide containing non-canonical amino acids and HLA0201 ]]> https://biorxiv.org/content/10.1101/2024.11.19.624425v1?rss=1 Jiang, S. Su, Z. Bloodworth, N. Liu, Y. Martina, C. Harrison, D. G. Meiler, J. 2024-11-21 doi:10.1101/2024.11.19.624425 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Heterogeneous endocrine cell composition defines human islet functional phenotypes ]]> https://biorxiv.org/content/10.1101/2024.11.20.623809v1?rss=1 Evans-Molina, C. Pettway, Y. D. Saunders, D. C. Sharp, S. A. Bate, T. S. Sun, H. Durai, H. Mei, S. Coldren, A. Davis, C. Reihsmann, C. V. Hopkirk, A. L. Taylor, J. Bradley, A. Aramandla, R. Poffenberger, G. Eskaros, A. Jenkins, R. Shi, D. Kang, H. Rajesh, V. Thaman, S. Feng, F. Cartailler, J.-P. Powers, A. C. Abraham, K. Gloyn, A. L. Niland, J. C. Brissova, M. 2024-11-21 doi:10.1101/2024.11.20.623809 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ FocalSV: target region-based structural variant assembly and refinement using single-molecule long read sequencing data ]]> https://biorxiv.org/content/10.1101/2024.11.21.624735v1?rss=1 Luo, C. Zhou, Z. J. Zhou, X. M. 2024-11-21 doi:10.1101/2024.11.21.624735 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ In depth sequencing of a serially sampled household cohort reveals the within-host dynamics of Omicron SARS-CoV-2 and rare selection of novel spike variants ]]> https://biorxiv.org/content/10.1101/2024.11.21.624722v1?rss=1 0.5% frequency, and the majority of the iSNV were at frequencies <2%. Within-host dynamics were dominated by genetic drift and purifying selection. Positive selection was rare but highly concentrated in spike. Two individuals with BA.1 infections had S:371F, a lineage defining substitution for BA.2. A Wright Fisher Approximate Bayesian Computational model identified positive selection at 14 loci with 7 in spike, including S:448 and S:339. We also detected significant genetic hitchhiking between synonymous changes and nonsynonymous iSNV under selection. The detectable immune-mediated selection may be caused by the relatively narrow antibody repertoire in individuals during the early Omicron phase of the SARS-CoV-2 pandemic. As both the virus and population immunity evolve, understanding the corresponding shifts in SARS-CoV-2 within-host dynamics will be important. ]]> Bendall, E. E. Dimcheff, D. Papalambros, L. Fitzsimmons, W. J. Zhu, Y. Schmitz, J. E. Halasa, N. Chappell, J. D. Martin, E. T. Biddle, J. E. Smith-Jeffcoat, S. E. Rolfes, M. A. Mellis, A. Talbot, H. K. Grijalva, C. G. Lauring, A. S. 2024-11-22 doi:10.1101/2024.11.21.624722 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ A quantitative framework for structural interpretation of DMS reactivity ]]> https://biorxiv.org/content/10.1101/2024.11.21.624766v1?rss=1 Deenalattha, S. Jurich, C. P. Lange, B. Armstrong, D. Nein, K. Yesselman, J. D. 2024-11-22 doi:10.1101/2024.11.21.624766 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ Flexible Learning and Re-ordering of Context-dependent Object Sequences in Nonhuman Primates ]]> https://biorxiv.org/content/10.1101/2024.11.24.625056v1?rss=1 Wen, X. Neumann, A. Dhungana, S. Womelsdorf, T. 2024-11-24 doi:10.1101/2024.11.24.625056 Cold Spring Harbor Laboratory Press 2024-11-24 <![CDATA[ A non-muscle α-actinin is an intrinsic component of the cardiac Z-disc and regulates sarcomere turnover, contractility, and heart remodeling ]]> https://biorxiv.org/content/10.1101/2024.11.26.625523v1?rss=1 Hayes, J. B. Ritter, D. Neininger-Castro, A. C. Willet, A. H. Caplan, L. R. Wang, Y. Liu, X. Taneja, N. Sanchez, Z. C. Smart, K. Reinhart-King, C. A. Liu, Q. Tyska, M. J. Tabdanov, E. D. Wells, Q. S. Knapik, E. W. Burnette, D. T. 2024-11-28 doi:10.1101/2024.11.26.625523 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Global patterns of species diversity and distribution in the biomedically and biotechnologically important fungal genus Aspergillus ]]> https://biorxiv.org/content/10.1101/2024.11.29.626055v1?rss=1 Riedling, O. L. David, K. T. Rokas, A. 2024-12-03 doi:10.1101/2024.11.29.626055 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Spatiochemical Investigation of Potential Biocontrol Agents Against Phytophthora capsici Infection in Tomato ]]> https://biorxiv.org/content/10.1101/2024.12.02.626494v1?rss=1 Robinson, J. Y. Shepard, H. S. Ambachew, D. Eyegheleme, P. J. May, J. C. Mmbaga, M. McLean, J. A. 2024-12-03 doi:10.1101/2024.12.02.626494 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Collapse of Interictal Suppressive Networks Permits Seizure Spread ]]> https://biorxiv.org/content/10.1101/2024.12.04.626580v1?rss=1 Makhoul, G. S. P. Doss, D. J. Johnson, G. W. Withers, C. P. Cavender, A. C. Hidalso Monroy Lerma, B. Reda, A. Bibro, C. E. Liao, E. Kang, H. Dawant, B. M. Reddy, S. B. Crudele, A. N. Constantinidis, C. Roberson, S. W. Bick, S. K. Morgan, V. L. Englot, D. J. 2024-12-07 doi:10.1101/2024.12.04.626580 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ A CRISPRi Library Screen in Group B Streptococcus Identifies Surface Immunogenic Protein (Sip) as a Mediator of Multiple Host Interactions ]]> https://biorxiv.org/content/10.1101/2024.12.06.627252v1?rss=1 Firestone, K. Gopalakrishna, K. P. Rogers, L. M. Peters, A. Gaddy, J. Nichols, C. Hall, M. H. Varela, H. N. Carlin, S. M. Hillebrand, G. H. Giacobe, E. J. Aronoff, D. M. Hooven, T. A. 2024-12-07 doi:10.1101/2024.12.06.627252 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ OrthoHMM: Improved Inference of Ortholog Groups using Hidden Markov Models ]]> https://biorxiv.org/content/10.1101/2024.12.07.627370v1?rss=1 Steenwyk, J. L. Buida, T. J. Rokas, A. King, N. 2024-12-12 doi:10.1101/2024.12.07.627370 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Naturalistic language comprehension engages a cascade of widespread brain networks in the one second following comprehension ]]> https://biorxiv.org/content/10.1101/2024.12.17.629054v1?rss=1 Hong, M. K. Janson, A. P. Koirala, P. Fotidzis, T. S. Polyn, S. M. Aboud, K. S. 2024-12-18 doi:10.1101/2024.12.17.629054 Cold Spring Harbor Laboratory Press 2024-12-18 <![CDATA[ Post-transcriptional modifications on tRNA fragments confer functional changes to high-density lipoproteins in atherosclerosis ]]> https://biorxiv.org/content/10.1101/2024.12.19.628772v1?rss=1 Semler, E. M. Michell, D. L. Kingsley, P. J. Massick, C. Ramirez, M. A. Castleberry, M. A. Doran, A. C. Carr, J. J. Marnett, L. J. Sheng, Q. Linton, M. F. Vickers, K. C. 2024-12-20 doi:10.1101/2024.12.19.628772 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ A Toolbox for Generating Multidimensional 3-D Objects with Fine-Controlled Feature Space: Quaddle 2.0 ]]> https://biorxiv.org/content/10.1101/2024.12.19.629479v1?rss=1 Wen, X. Malchin, L. A. Womelsdorf, T. 2024-12-20 doi:10.1101/2024.12.19.629479 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ MCL-1 regulates cellular transitions during oligodendrocyte development ]]> https://biorxiv.org/content/10.1101/2024.12.20.629796v1?rss=1 Gil, M. Hanna, M. R. Gama, V. 2024-12-21 doi:10.1101/2024.12.20.629796 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ TrimNN: Characterizing cellular community motifs for studying multicellular topological organization in complex tissues ]]> https://biorxiv.org/content/10.1101/2024.12.19.629384v1?rss=1 Yu, Y. Wang, S. Li, J. Yu, M. McCrocklin, K. Kang, J.-Q. Ma, A. Ma, Q. Xu, D. Wang, J. 2024-12-22 doi:10.1101/2024.12.19.629384 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Generation of antigen-specific paired heavy-light chain antibody sequences using large language models ]]> https://biorxiv.org/content/10.1101/2024.12.20.629482v1?rss=1 Wasdin, P. T. Johnson, N. V. Janke, A. K. Held, S. Marinov, T. M. Jordaan, G. Vandenabeele, L. Pantouli, F. Gillespie, R. A. Vukovich, M. J. Holt, C. M. Kim, J. Hansman, G. Logue, J. Chu, H. Y. Andrews, S. F. Kanekiyo, M. Sautto, G. A. Ross, T. M. Sheward, D. J. McLellan, J. S. Abu-Shmais, A. A. Georgiev, I. S. 2024-12-22 doi:10.1101/2024.12.20.629482 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Mapping histological and functional maturation of human endocrine pancreas across early postnatal periods ]]> https://biorxiv.org/content/10.1101/2024.12.20.629754v1?rss=1 Saunders, D. C. Hart, N. Pan, F. C. Reihsmann, C. V. Hopkirk, A. L. Izmaylov, N. Mei, S. Sherrod, B. A. Davis, C. Duryea, J. Haliyur, R. Aramandla, R. Durai, H. Poffenberger, G. Martin, A. Posgai, A. L. Kusmartseva, I. Beery, M. L. Yang, M. Kang, H. Greiner, D. L. Shultz, L. D. Cartailler, J.-P. Aamodt, K. I. Bottino, R. Atkinson, M. A. Wright, C. V. E. Powers, A. C. Brissova, M. 2024-12-22 doi:10.1101/2024.12.20.629754 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Haplotype editing with CRISPR/Cas9 as a therapeutic approach for dominant-negative missense mutations in NEFL ]]> https://biorxiv.org/content/10.1101/2024.12.20.629813v1?rss=1 Dua, P. H. Simon, B. M. Marley, C. B. Feliciano, C. M. Watry, H. L. Steury, D. Abraham, A. Gilbertson, E. N. Ramey, G. D. Capra, J. A. Conklin, B. R. Judge, L. M. 2024-12-22 doi:10.1101/2024.12.20.629813 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Predictive routing emerges from self-supervised stochastic neural plasticity ]]> https://biorxiv.org/content/10.1101/2024.12.31.630823v1?rss=1 Nejat, H. Sherfey, J. Bastos, A. M. 2024-12-31 doi:10.1101/2024.12.31.630823 Cold Spring Harbor Laboratory Press 2024-12-31 <![CDATA[ Sex-specific Associations of Gene Expression with Alzheimer's Disease Neuropathology and Ante-mortem Cognitive Performance ]]> https://biorxiv.org/content/10.1101/2025.01.02.631098v1?rss=1 Seto, M. Clifton, M. Gomez, M. L. Coughlan, G. Gifford, K. A. Jefferson, A. L. De Jager, P. Bennett, D. A. Wang, Y. Barnes, L. L. Schneider, J. A. Hohman, T. J. Buckley, R. F. Dumitrescu, L. 2025-01-02 doi:10.1101/2025.01.02.631098 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ NR6A1 is essential for neural crest cell specification, formation and survival ]]> https://biorxiv.org/content/10.1101/2025.01.02.630962v1?rss=1 Moore, E. L. Munoz, W. Bhatt, S. Sakai, D. Achilleos, A. Zhao, R. Lamb, M. Price, A. Seidel, C. Tiana, M. Barral, A. Clawson, D. Manzanares, M. Trainor, P. 2025-01-03 doi:10.1101/2025.01.02.630962 Cold Spring Harbor Laboratory Press 2025-01-03 <![CDATA[ Transcriptional stochasticity reveals multiple mechanisms of long noncoding RNA regulation at the Xist - Tsix locus ]]> https://biorxiv.org/content/10.1101/2025.01.05.631290v1?rss=1 Kesler, B. K. Adams, J. Neuert, G. 2025-01-05 doi:10.1101/2025.01.05.631290 Cold Spring Harbor Laboratory Press 2025-01-05 <![CDATA[ Activity dependent Clustering of Neuronal L-Type Calcium Channels by CaMKII ]]> https://biorxiv.org/content/10.1101/2025.01.08.631979v1?rss=1 Yang, Q. Hu, L. Lawson-Qureshi, D. Colbran, R. J. 2025-01-09 doi:10.1101/2025.01.08.631979 Cold Spring Harbor Laboratory Press 2025-01-09 <![CDATA[ A Broad Survey and Functional Analysis of Immunoglobulin Loci Variation in Rhesus Macaques ]]> https://biorxiv.org/content/10.1101/2025.01.07.631319v1?rss=1 Peres, A. Upadhyay, A. A. Klein, V. H. Saha, S. Rodriguez, O. L. Vanwinkle, Z. M. Granholm, L. Karunakaran, K. Lauer, W. Lin, M. C. Melton, T. Metz, A. Polak, P. Raju, N. Shields, K. Schultze, S. Ton, T. Ericsen, A. Lapp, S. A. Smith, M. Lees, W. Watson, C. T. Yaari, G. Bosinger, S. E. 2025-01-10 doi:10.1101/2025.01.07.631319 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ Peptidic tryptophan halogenation by a promiscuous flavin-dependent enzyme ]]> https://biorxiv.org/content/10.1101/2025.01.12.632611v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@897b21org.highwire.dtl.DTLVardef@1f2bafborg.highwire.dtl.DTLVardef@d1e800org.highwire.dtl.DTLVardef@d68381_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Rice, A. Gadgil, M. G. Mitchell, D. A. 2025-01-13 doi:10.1101/2025.01.12.632611 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Frontoparietal activity related to neuropsychological assessment of working memory ]]> https://biorxiv.org/content/10.1101/2025.01.13.632797v1?rss=1 Jurva, A. Singh, B. Qian, H. Wang, Z. Jacobs, M. Dhima, K. Englot, D. Williams Roberson, S. Bick, S. Constantinidis, C. 2025-01-13 doi:10.1101/2025.01.13.632797 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Small or absent Visual Word Form Area is a trait of dyslexia ]]> https://biorxiv.org/content/10.1101/2025.01.14.632854v1?rss=1 Mitchell, J. L. Yablonski, M. Stone, H. L. Fuentes-Jimenez, M. Takada, M. Tang, K. A. Tran, J. E. Chou, C. Yeatman, J. D. 2025-01-15 doi:10.1101/2025.01.14.632854 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Glycan-reactive antibodies isolated from human HIV-1 vaccine trial participants show broad pathogen cross-reactivity ]]> https://biorxiv.org/content/10.1101/2025.01.17.633475v1?rss=1 Jamieson, P. J. Shen, X. Abu-Shmais, A. A. Wasdin, P. T. Janowska, K. Edwards, R. J. Scapellato, G. Richardson, S. I. Manamela, N. P. Liu, S. Barr, M. Gillespie, R. A. Mimms, J. Suryadevara, N. Sornberger, T. A. Zost, S. Parks, R. Flaherty, S. Janke, A. K. Howard, B. N. Suresh, Y. P. Ruprecht, R. M. Crowe, J. E. Carnahan, R. H. Bailey, J. R. Masaru, K. Haynes, B. F. Moore, P. L. Acharya, P. Montefiori, D. C. Kalams, S. A. Lu, S. Georgiev, I. S. 2025-01-20 doi:10.1101/2025.01.17.633475 Cold Spring Harbor Laboratory Press 2025-01-20 <![CDATA[ Interrupting T cell memory ameliorates exaggerated metabolic response to weight cycling ]]> https://biorxiv.org/content/10.1101/2025.01.17.633599v1?rss=1 Garcia, J. N. Cottam, M. A. Rodriguez, A. S. Hussein Agha, A. F. Winn, N. C. Hasty, A. H. 2025-01-22 doi:10.1101/2025.01.17.633599 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ CLASP1/2 REGULATE IMMUNE SYNAPSE MATURATION IN NATURAL KILLER CELLS ]]> https://biorxiv.org/content/10.1101/2025.01.20.633904v1?rss=1 Pariani, A. P. Huhn, V. Rivabella-Maknis, T. Alonso, V. L. Almada, E. Vena, R. Favre, C. Goldenring, J. R. Kaverina, I. Larocca, M. C. 2025-01-22 doi:10.1101/2025.01.20.633904 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Macromolecular Diamidobenzimidazole Conjugates Activate STING ]]> https://biorxiv.org/content/10.1101/2025.01.21.634206v1?rss=1 Arora, K. Sheehy, T. L. Schulman, J. A. Kimmel, B. R. McAtee, C. Bharti, V. Weaver, A. Wilson, J. T. 2025-01-24 doi:10.1101/2025.01.21.634206 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Diet gel-based oral drug delivery system for controlled dosing of small molecules for microglia depletion and inducible Cre recombination in mice ]]> https://biorxiv.org/content/10.1101/2025.01.23.634530v1?rss=1 99% after one and two weeks. The Tamoxifen-93M diet confirmed suitability for inducible Cre recombination, with significant treatment-time dependent efficacy and a positive correlation between total Tamoxifen dose and tdTomato expression. This study demonstrates that a diet gel-based drug delivery system offers a controllable and less invasive alternative to current drug application methods for PLX5622 and Tamoxifen. ]]> Jovanovic, J. Stone, M. L. Dooyema, S. R. Tao, Y. K. Fuhrmann, S. Levine, E. M. 2025-01-24 doi:10.1101/2025.01.23.634530 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Inferring single-cell dynamics of a molecular reporter from unlabeled live-cell light microscopy data analyzed with delay embedding ]]> https://biorxiv.org/content/10.1101/2025.01.23.634593v1?rss=1 Singh, J. Copperman, J. Heiser, L. M. Zuckerman, D. M. 2025-01-24 doi:10.1101/2025.01.23.634593 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Integrating bulk and single cell RNA-seq refines transcriptomic profiles of individual C. elegans neurons ]]> https://biorxiv.org/content/10.1101/2025.01.26.634951v1?rss=1 Barrett, A. Varol, E. Weinreb, A. Taylor, S. R. McWhirter, R. M. Cros, C. C. Vidal, B. Basaravaju, M. Poff, A. Tipps, J. A. Majeed, M. Wang, C. Bayer, E. A. Reilly, M. B. Yemini, E. Sun, H. Hobert, O. Miller, D. M. Hammarlund, M. 2025-01-27 doi:10.1101/2025.01.26.634951 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ Metabolic Adaptations Rewire CD4 T Cells in a Subset-Specific Manner in Human Critical Illness with and without Sepsis ]]> https://biorxiv.org/content/10.1101/2025.01.27.635146v1?rss=1 Stier, M. T. Sewell, A. E. Mwizerwa, E. L. Sim, C. Y. Tanner, S. M. Nichols, C. M. Durai, H. H. Jennings, E. Q. Lindau, P. Wilfong, E. M. Newcomb, D. C. Bastarache, J. A. Ware, L. B. Rathmell, J. C. 2025-01-29 doi:10.1101/2025.01.27.635146 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ Biophysical Basis of the in vivo Electroretinogram of the Mouse: 4-Shell Current Source Density Model ]]> https://biorxiv.org/content/10.1101/2025.01.28.635195v1?rss=1 Peinado Allina, G. Meleppat, R. K. Yao, V. Calkins, D. J. FitzGerald, P. Schiesser, W. E. Pugh, E. N. 2025-01-29 doi:10.1101/2025.01.28.635195 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ CPSF6 Promotes HIV-1 Preintegration Complex Function ]]> https://biorxiv.org/content/10.1101/2025.01.28.635394v1?rss=1 Chaudhuri, E. Jang, S. Chakraborty, R. Radhakrishnan, R. Arnarson, B. Prakash, P. Cornish, D. Rohlfes, N. Singh, P. K. Shi, J. Aiken, C. Campbell, E. M. Hultquist, J. F. Engelman, A. Balasubramaniam, M. Dash, C. 2025-01-29 doi:10.1101/2025.01.28.635394 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ 1,2,4-Triazole-based first-in-class non-nucleoside inhibitors of bacterial enzyme MraY ]]> https://biorxiv.org/content/10.1101/2025.01.30.635793v1?rss=1 View larger version (54K): org.highwire.dtl.DTLVardef@14b1f84org.highwire.dtl.DTLVardef@1024f45org.highwire.dtl.DTLVardef@a246d0org.highwire.dtl.DTLVardef@1d70e52_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Roy, S. Berida, T. Huang, T.-Y. Weck, S. C. Lutz, M. McKee, S. R. Kagerah, N. Manning, D. L. Jahan, M. E. Mishra, S. K. Doerksen, R. J. Stallings, C. L. Ducho, C. 2025-01-31 doi:10.1101/2025.01.30.635793 Cold Spring Harbor Laboratory Press 2025-01-31 <![CDATA[ SCGclust: Single Cell Graph clustering using graphautoencoders integrating SNVs and CNAs ]]> https://biorxiv.org/content/10.1101/2025.01.28.635357v1?rss=1 Potu, T. Hu, Y. Khan, R. Dharani, S. Ni, J. Zhang, L. Zhou, X. M. Mallory, X. 2025-02-01 doi:10.1101/2025.01.28.635357 Cold Spring Harbor Laboratory Press 2025-02-01 <![CDATA[ Dicer loss in Muller glia leads to a defined sequence of pathological events beginning with cone dysfunction ]]> https://biorxiv.org/content/10.1101/2025.01.30.635744v1?rss=1 Larbi, D. Rief, A. M. Kang, S. Chen, S. Batsuuri, K. Fuhrmann, S. Viswanathan, S. Wohl, S. G. 2025-02-01 doi:10.1101/2025.01.30.635744 Cold Spring Harbor Laboratory Press 2025-02-01 <![CDATA[ Analysis of The Senescence Secretome During Zebrafish Retina Regeneration ]]> https://biorxiv.org/content/10.1101/2025.01.31.635944v1?rss=1 Konar, G. J. Vallone, K. T. Nguyen, T. D. Patton, J. G. 2025-02-03 doi:10.1101/2025.01.31.635944 Cold Spring Harbor Laboratory Press 2025-02-03 <![CDATA[ Spatial profiling of longitudinal glioblastoma reveals consistent changes in cellular architecture, post-treatment ]]> https://biorxiv.org/content/10.1101/2025.01.31.635832v1?rss=1 Ajaib, S. Pollock, S. Hemmings, G. Gusnanto, A. Chakrabarty, A. Ismail, A. Wilson, E. Hunter, B. Filby, A. McDonald, D. Brockman, A. Ihrie, R. A. Stead, L. F. 2025-02-05 doi:10.1101/2025.01.31.635832 Cold Spring Harbor Laboratory Press 2025-02-05 <![CDATA[ Loss of an uncharacterized mitochondrial methionine tRNA-synthetase induces mitochondrial unfolded protein response in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2025.02.03.636310v1?rss=1 Thapa, B. V. Das, M. Held, J. P. Patel, M. R. 2025-02-05 doi:10.1101/2025.02.03.636310 Cold Spring Harbor Laboratory Press 2025-02-05 <![CDATA[ Developmental Variations in Recurrent Spatiotemporal Brain Propagations from Childhood to Adulthood ]]> https://biorxiv.org/content/10.1101/2025.02.04.635765v1?rss=1 Byeon, K. Park, H. Park, S. Cluce, J. Mehta, K. Cieslak, M. Cui, Z. Hong, S.-J. Chang, C. Smallwood, J. Satterthwaite, T. D. Milham, M. P. Xu, T. 2025-02-05 doi:10.1101/2025.02.04.635765 Cold Spring Harbor Laboratory Press 2025-02-05 <![CDATA[ Epigenomic insights into extreme longevity in the world's oldest terrestrial animal, Jonathan ]]> https://biorxiv.org/content/10.1101/2025.02.05.636284v1?rss=1 Vaisvil, B. Schmitt, D. W. Jones, A. Kapatral, V. Ford, J. M. Taylor, M. L. Colwell, M. Hollins, J. Pascucci, S. Weissenow, K. Rost, B. Notin, P. Gerlach, J. Terwilliger, T. C. Hung, L.-W. Jensen, L. J. Horvath, S. Faulk, C. Ma, Y. Clark, S. W. 2025-02-06 doi:10.1101/2025.02.05.636284 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ stDyer-image improves clustering analysis of spatially resolved transcriptomics and proteomics with morphological images ]]> https://biorxiv.org/content/10.1101/2025.02.07.634992v1?rss=1 XU, K. Zhou, X. M. Zhang, L. 2025-02-07 doi:10.1101/2025.02.07.634992 Cold Spring Harbor Laboratory Press 2025-02-07 <![CDATA[ Cryo-EM reveals a new allosteric binding site at the M5 mAChR ]]> https://biorxiv.org/content/10.1101/2025.02.05.636602v1?rss=1 Burger, W. A. C. Mobbs, J. I. Rana, B. Wang, J. Joshi, K. Gentry, P. R. Yeasmin, M. Venugopal, H. Bender, A. Lindsley, C. W. Miao, Y. Christopoulos, A. Valant, C. Thal, D. M. 2025-02-08 doi:10.1101/2025.02.05.636602 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Ketamine Alters Tuning of Neural and Behavioral Spatial Working Memory Precision ]]> https://biorxiv.org/content/10.1101/2025.02.10.637233v1?rss=1 Rahmati, M. Moujaes, F. Suljic, N. P. Ji, J. L. Berkovitch, L. Lee, K. Fonteneau, C. Schleifer, C. H. Adkinson, B. D. Savic, A. Santamauro, N. Tamayo, Z. Diehl, C. Kolobaric, A. Flynn, M. Camarro, T. Curtis, C. E. Repovs, G. Fineberg, S. K. Morgan, P. T. Preller, K. H. Krystal, J. H. Murray, J. D. Cho, Y. T. Anticevic, A. 2025-02-12 doi:10.1101/2025.02.10.637233 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Semiparametric Confidence Sets for Arbitrary Effect Sizes in Longitudinal Neuroimaging ]]> https://biorxiv.org/content/10.1101/2025.02.10.637497v1?rss=1 Zhang, X. Liao, K. Seidlitz, J. McHugo, M. Avery, S. N. Huang, A. Alexander-Bloch, A. Woodward, N. Heckers, S. Vandekar, S. 2025-02-12 doi:10.1101/2025.02.10.637497 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Discovering new amyloid-like peptides using all-atom simulations and artificial intelligence. ]]> https://biorxiv.org/content/10.1101/2025.02.12.637911v1?rss=1 Kuang, X. Jalali, S. Rahman, T. Michalowski, J. Sheng-Wong, C. Wong-Ekkabut, J. Su, Z. Dias, C. L. 2025-02-14 doi:10.1101/2025.02.12.637911 Cold Spring Harbor Laboratory Press 2025-02-14 <![CDATA[ In vitro cellular phenotypes of cortical neurons from R255X MECP2 knock-in mice are improved by either expression of wildtype MeCP2 or read-through with G418 ]]> https://biorxiv.org/content/10.1101/2025.02.17.638700v1?rss=1 Xu, X. Merritt, J. K. Gray, S. J. Neul, J. Pozzo-Miller, L. 2025-02-21 doi:10.1101/2025.02.17.638700 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ The forkhead transcription factor FKH-7/FOXP acts in chemosensory neurons to regulate developmental decision-making ]]> https://biorxiv.org/content/10.1101/2025.02.17.638733v1?rss=1 Chai, C. M. Taylor, S. R. Tischbirek, C. H. Wong, W.-R. Cai, L. Miller, D. M. Sternberg, P. W. 2025-02-21 doi:10.1101/2025.02.17.638733 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ Characterization of neurite and soma organization in the brain and spinal cord with diffusion MRI ]]> https://biorxiv.org/content/10.1101/2025.02.19.638936v1?rss=1 Schilling, K. Palombo, M. Witt, A. A. O'Grady, K. P. Pizzolato, M. P. Landman, B. A. Smith, S. A. 2025-02-21 doi:10.1101/2025.02.19.638936 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ Linking molecular pathways and islet cell dysfunction in human type 1 diabetes ]]> https://biorxiv.org/content/10.1101/2025.02.20.639325v1?rss=1 dos Santos, T. Dai, X. Q. Jones, R. C. Spigelman, A. F. Mummey, H. M. Ewald, J. D. Ellis, C. E. Lyon, J. G. Smith, N. Bautista, A. Manning Fox, J. E. Neff, N. F. Detweiler, A. Tan, M. Arrojo e Drigo, R. Xia, J. Camunas-Soler, J. Gaulton, K. J. Quake, S. R. MacDonald, P. E. 2025-02-21 doi:10.1101/2025.02.20.639325 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ Using The Cancer Genome Atlas from cBioPortal to Develop Genomic Datasets for Machine Learning Assisted Cancer Treatment ]]> https://biorxiv.org/content/10.1101/2025.02.17.638660v1?rss=1 Asaduzzaman, A. Thompson, C. Sibai, F. Uddin, M. J. 2025-02-22 doi:10.1101/2025.02.17.638660 Cold Spring Harbor Laboratory Press 2025-02-22 <![CDATA[ Artificial intelligence-enabled automated analysis of transmission electron micrographs to evaluate chemotherapy impact on mitochondrial morphology in triple negative breast cancer ]]> https://biorxiv.org/content/10.1101/2025.02.19.635300v1?rss=1 Arriojas, A. baek, M. L. Berner, M. J. Zhurkevich, A. Hinton, A. O. Meyer, M. D. Dobrolecki, L. E. Lewis, M. T. Zarringhalam, K. Echeverria, G. V. 2025-02-23 doi:10.1101/2025.02.19.635300 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ A conserved mechanism of LRRC8 channel inhibition by distinct drugs ]]> https://biorxiv.org/content/10.1101/2025.02.24.639894v1?rss=1 Yamada, T. Bisignano, P. Karakas, E. Denton, J. S. 2025-02-28 doi:10.1101/2025.02.24.639894 Cold Spring Harbor Laboratory Press 2025-02-28 <![CDATA[ Lipid-mediated mechanism of drug extrusion by a heterodimeric ABC exporter ]]> https://biorxiv.org/content/10.1101/2025.02.26.640354v1?rss=1 Tang, Q. Sinclair, M. Bisignano, P. Zhang, Y. Tajkhorshid, E. Mchaourab, H. 2025-02-28 doi:10.1101/2025.02.26.640354 Cold Spring Harbor Laboratory Press 2025-02-28 <![CDATA[ Genomic factors limiting the diversity of Saccharomycotina plant pathogens ]]> https://biorxiv.org/content/10.1101/2025.02.27.640420v1?rss=1 Lee, S. K. West, C. Opulente, D. A. Harrison, M.-C. Wolters, J. F. Shen, X.-x. Zhou, X. Groenewald, M. Hittinger, C. T. Rokas, A. LaBella, A. L. 2025-02-28 doi:10.1101/2025.02.27.640420 Cold Spring Harbor Laboratory Press 2025-02-28 <![CDATA[ Elevated rates and biased spectra of mutations in anaerobically cultured lactic acid bacteria ]]> https://biorxiv.org/content/10.1101/2025.02.28.639667v1?rss=1 Hale, O. F. Yin, M. Behringer, M. G. 2025-02-28 doi:10.1101/2025.02.28.639667 Cold Spring Harbor Laboratory Press 2025-02-28 <![CDATA[ Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE ]]> https://biorxiv.org/content/10.1101/2025.02.25.640190v1?rss=1 Schroeder, A. Loth, M. Yao, S. Luo, C. Yan, H. Zhang, D. Piya, S. Plowey, E. Hu, W. Clemenceau, J. R. Jang, I. Kim, M. Barnfather, I. Chan, S. J. Reynolds, T. Carlile, T. Cullen, P. Sung, J.-Y. Tsai, H.-H. Park, J. H. Hwang, T. H. Zhang, B. Li, M. 2025-03-01 doi:10.1101/2025.02.25.640190 Cold Spring Harbor Laboratory Press 2025-03-01 <![CDATA[ Higher-Order Biomarkers Through Network Motif Mining: A COVID-19 Case Study ]]> https://biorxiv.org/content/10.1101/2025.02.27.638877v1?rss=1 Chahley, N. Murira, A. Nakhla, N. Oliver, C. 2025-03-02 doi:10.1101/2025.02.27.638877 Cold Spring Harbor Laboratory Press 2025-03-02 <![CDATA[ Contrastive Learning Enables Epitope Overlap Predictions for Targeted Antibody Discovery ]]> https://biorxiv.org/content/10.1101/2025.02.25.640114v1?rss=1 70% CDRH3 sequence identity among antibodies sharing both heavy and light chain V-genes reliably predicts overlapping-epitope antibody pairs. Next, we develop a supervised contrastive fine-tuning framework for antibody large language models which results in embeddings that better correlate with epitope information than those from pre-trained models. Applying this contrastive learning approach to SARS-CoV-2 receptor binding domain antibodies, we achieve 82.7% balanced accuracy in distinguishing same-epitope versus different-epitope antibody pairs and demonstrate the ability to predict relative levels of structural overlap from learning on functional epitope bins (Spearman{rho} = 0.25). Finally, we create AbLang-PDB, a generalized model for predicting overlapping-epitope antibodies for a broad range of protein families. AbLang-PDB achieves five-fold improvement in average precision for predicting overlapping-epitope antibody pairs compared to sequence-based methods, and effectively predicts the amount of epitope overlap among overlapping-epitope pairs ({rho} = 0.81). In an antibody discovery campaign searching for overlapping-epitope antibodies to the HIV-1 broadly neutralizing antibody 8ANC195, 70% of computationally selected candidates demonstrated HIV-1 specificity, with 50% showing competitive binding with 8ANC195. Together, the computational models presented here provide powerful tools for epitope-targeted antibody discovery, while demonstrating the efficacy of contrastive learning for improving epitope-representation. ]]> Holt, C. M. Janke, A. K. Amlashi, P. B. Marinov, T. M. Georgiev, I. S. 2025-03-03 doi:10.1101/2025.02.25.640114 Cold Spring Harbor Laboratory Press 2025-03-03 <![CDATA[ FakeRotLib: expedient non-canonical amino acid parameterization in Rosetta ]]> https://biorxiv.org/content/10.1101/2025.02.27.640629v1?rss=1 Bell, E. W. Brown, B. P. Meiler, J. 2025-03-03 doi:10.1101/2025.02.27.640629 Cold Spring Harbor Laboratory Press 2025-03-03 <![CDATA[ Correlative In Situ Cryo-ET Reveals Cellular and Viral Remodeling Associated with Selective HIV-1 Core Nuclear Import ]]> https://biorxiv.org/content/10.1101/2025.03.04.641496v1?rss=1 Hou, Z. Shen, Y. Fronik, S. Shen, J. Shi, J. Xu, J. Chen, L. Hardenbrook, N. Thompson, C. Neumann, S. Engelman, A. N. Aiken, C. zhang, p. 2025-03-04 doi:10.1101/2025.03.04.641496 Cold Spring Harbor Laboratory Press 2025-03-04 <![CDATA[ Dynamic responses to rejection in the transplanted human heart revealed through spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.02.28.640852v1?rss=1 Amancherla, K. Taravella Oill, A. M. Bledsoe, X. Williams, A. L. Chow, N. Zhao, S. Sheng, Q. Bearl, D. W. Hoffman, R. D. Menachem, J. N. Siddiqi, H. K. Brinkley, D. M. Mee, E. D. Hadad, N. Agrawal, V. Schmeckpepper, J. Rali, A. S. Tsai, S. Farber-Eger, E. H. Wells, Q. S. Freedman, J. E. Tucker, N. R. Schlendorf, K. H. Gamazon, E. R. Shah, R. V. Banovich, N. 2025-03-06 doi:10.1101/2025.02.28.640852 Cold Spring Harbor Laboratory Press 2025-03-06 <![CDATA[ An Integrative Multi-Omics Random Forest Framework for Robust Biomarker Discovery ]]> https://biorxiv.org/content/10.1101/2025.03.05.641533v1?rss=1 Zhang, W. Huang, H. Wang, L. Brian, L. D. Chen, S. X. 2025-03-06 doi:10.1101/2025.03.05.641533 Cold Spring Harbor Laboratory Press 2025-03-06 <![CDATA[ Salt-inducible kinase inhibition promotes weight loss and improves the diastolic function of obesity-related heart failure with preserved ejection fraction in mice ]]> https://biorxiv.org/content/10.1101/2025.03.02.640935v1?rss=1 Shi, F. Agrawal, V. Munkhjargal, U. Kobeck, E. Patel, H. U. Zhang, W. Collins, S. 2025-03-10 doi:10.1101/2025.03.02.640935 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Resolution of collapsed forks is separate from completion of DNA synthesis ]]> https://biorxiv.org/content/10.1101/2025.03.03.641087v1?rss=1 Conwell, S. C. Dahmen, S. N. Cranford, M. T. Mulvaney, R. J. Long, D. T. Cortez, D. Dewar, J. M. 2025-03-10 doi:10.1101/2025.03.03.641087 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Assigning Targetable Molecular Pathways to Transdiagnostic Subgroups Across Autism and Related Neurodevelopmental Disorders ]]> https://biorxiv.org/content/10.1101/2025.03.04.641443v1?rss=1 Ellegood, J. Beauchamp, A. Yee, Y. Devenyi, G. Ziolkowski, J. Qiu, L. Askalan, R. Ayub, M. Suetterlin, P. Donovan, A. Basson, M. A. Quesnel, K. M. Berube, N. G. Woo, T. Beversdorf, D. Bjornsson, H. Blakely, R. Crawley, J. Crosbie, J. Orr, B. O. Davis, G. W. Genestine, M. DiCicco-Bloom, E. Egan, S. Fink, K. D. Asbury, S. Lai, J. Rilett, K. Foster, J. A. Vincent, J. B. Frankland, P. Georgiades, S. Penagarikano, O. Geschwind, D. Giger, R. J. Markx, S. Gogos, J. Golzio, C. Pagani, M. Gozzi, A. Pacey, L. K. Hampson, D. Huang, T.-N. Yen, T.-L. Hsueh, Y.-P. 2025-03-10 doi:10.1101/2025.03.04.641443 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Adolescent onset of volitional ethanol intake normalizes sex differences observed with adult-onset ethanol intake and negative affective behaviors during protracted forced abstinence ]]> https://biorxiv.org/content/10.1101/2025.03.06.641859v1?rss=1 PND49). MethodsMale and female C57BL/6J mice underwent the Chronic Drinking Forced Abstinence (CDFA) paradigm, with the "Ethanol" group given two-bottle choice access to ethanol and water, and the "Water" group given two water bottles. Ethanol intake and preference were measured over six weeks. Two weeks following ethanol removal, mice underwent behavioral testing for negative affective-like behavior. ResultsAdult-onset female mice consumed significantly more ethanol and displayed higher ethanol preference compared to adult-onset male mice. In contrast, adolescent-onset male and female mice consumed similar ethanol levels and displayed similar preference. We observed increased immobility during the forced swim test in adult-onset ethanol females, but not males, during protracted abstinence. However, both sexes of adolescent-onset ethanol mice displayed increased immobility during forced abstinence. ConclusionsThese findings highlight adolescence as a critical period during which both sexes voluntarily consume ethanol and are equally vulnerable to the behavioral disturbances associated with ethanol abstinence. ]]> Edwards, C. M. Xu, Z. Winder, D. 2025-03-10 doi:10.1101/2025.03.06.641859 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Coordinated changes in thymic stromal and hematopoietic cells that define the perinatal to juvenile transition ]]> https://biorxiv.org/content/10.1101/2025.03.04.641047v1?rss=1 Vasudev, A. Moore, C. R. Calindi, A. Kang, S. W. Helm, B. R. Srinivasan, J. Shah, S. Zong, R. Singarapu, N. Casey, S. Macintyre, A. N. Lau, K. S. Hale, L. P. Liu, Q. Manley, N. R. Ehrlich, L. I. R. Richie, E. R. 2025-03-11 doi:10.1101/2025.03.04.641047 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ AUC-PR is a More Informative Metric for Assessing the Biological Relevance of In Silico Cellular Perturbation Prediction Models ]]> https://biorxiv.org/content/10.1101/2025.03.06.641935v1?rss=1 Zhu, H. Asiaee, A. Azinfar, L. Li, J. Liang, H. Irajizad, E. Do, K.-A. Long, J. P. 2025-03-11 doi:10.1101/2025.03.06.641935 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Solid-State NMR Analysis of Schizosaccharomyces pombe Reveals Role of α-Amylase Family Enzymes in Cell Wall Structure and Function ]]> https://biorxiv.org/content/10.1101/2025.03.10.642465v1?rss=1 Jacob, A. Willet, A. H. Igarashi, M. G. El Nokab, M. E. H. Turner, L. A. Alsanad, A. K. A. Wang, T. Gould, K. L. 2025-03-11 doi:10.1101/2025.03.10.642465 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Data-independent acquisition parallel accumulation-serial fragmentation (diaPASEF) analysis of the separated zebrafish lens improves identifications ]]> https://biorxiv.org/content/10.1101/2025.03.13.642445v1?rss=1 Zelle, S. R. McDonald, W. H. Rose, K. L. Mchourab, H. S. Schey, K. L. 2025-03-15 doi:10.1101/2025.03.13.642445 Cold Spring Harbor Laboratory Press 2025-03-15 <![CDATA[ Proteomic Analysis of PTEN-Deficient Cells Reveals Src-Mediated Upregulation of EphA2 and Therapeutic Potential of Dual Inhibition ]]> https://biorxiv.org/content/10.1101/2025.03.13.643053v1?rss=1 Wang, Q. Kong, X. Song, H. Wang, L. Li, L. Hou, X. Renuse, S. Cheng, R. Khan, M. K. H. Fang, L. Lotan, T. L. Park, B. H. Weroha, S. J. Zhou, H. Pandey, A. Wu, X. 2025-03-15 doi:10.1101/2025.03.13.643053 Cold Spring Harbor Laboratory Press 2025-03-15 <![CDATA[ Amyloid-β-regulated gene circuits for programmable Alzheimer's disease therapy ]]> https://biorxiv.org/content/10.1101/2025.03.12.642808v1?rss=1 Spetz, M. R. Kim, H. Chavarria, D. Conger, D. J. Shattuck-Brandt, R. Shekharan, S. R. Shostak, A. Ligocki, A. P. Brien, H. J. Embalabala, R. J. Mobley, B. C. Schrag, M. S. Lippmann, E. S. Brunger, J. M. 2025-03-17 doi:10.1101/2025.03.12.642808 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ Intravenous lipid-siRNA conjugate mediates gene silencing at the blood-brain barrier and blood-CSF barrier ]]> https://biorxiv.org/content/10.1101/2025.03.14.642142v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@b00a52org.highwire.dtl.DTLVardef@175a363org.highwire.dtl.DTLVardef@39be75org.highwire.dtl.DTLVardef@1072093_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sorets, A. Schwensen, K. Francini, N. Kjar, A. Lyons, S. Park, J. Palmer, D. Abdulrahman, A. Cowell, R. Katdare, K. Hoogenboezem, E. Wang, A. Dani, N. Duvall, C. Lippmann, E. 2025-03-17 doi:10.1101/2025.03.14.642142 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ Stable hypermutators revealed by the genomic landscape of DNA repair genes among yeast species ]]> https://biorxiv.org/content/10.1101/2025.03.15.643480v1?rss=1 Goncalves, C. Steenwyk, J. L. Rinker, D. Opulente, D. A. LaBella, A. L. Harrison, M.-C. Wolters, J. F. Zhou, X. Shen, X.-X. Covo, S. Groenewald, M. Hittinger, C. T. Rokas, A. 2025-03-17 doi:10.1101/2025.03.15.643480 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ Maternal α-cypermethrin and permethrin exert differential effects on fetal growth, placental morphology, and fetal neurodevelopment in mice ]]> https://biorxiv.org/content/10.1101/2025.03.16.643434v1?rss=1 Elser, B. A. Hing, B. Eliasen, S. Afrifa, M. A. Meurice, N. Rimi, F. Chimenti, M. Schulz, L. C. Dailey, M. E. Gibson-Corley, K. N. Stevens, H. E. 2025-03-17 doi:10.1101/2025.03.16.643434 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ Aging-associated Increase of GATA4 levels in Articular Cartilage is Linked to Impaired Regenerative Capacity of Chondrocytes and Osteoarthritis ]]> https://biorxiv.org/content/10.1101/2025.03.18.643933v1?rss=1 Makarczyk, M. Zhang, Y. Aguglia, A. Bartholomew, O. Hines, S. Sinkar, S. Liu, S. Duvall, C. Lin, H. 2025-03-19 doi:10.1101/2025.03.18.643933 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ The Stmn1-lineage contributes to acinar regeneration but not to neoplasia upon oncogenic Kras expression ]]> https://biorxiv.org/content/10.1101/2025.03.18.643944v1?rss=1 Dahiya, S. Reyes Arbujas, J. Hajihassani, A. Amini, S. Wageley, M. Gurbuz, K. Ma, Z. Copeland, C. Saleh, M. Gittes, G. K. Koo, B.-K. DelGiorno, K. E. Esni, F. 2025-03-19 doi:10.1101/2025.03.18.643944 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ Towards a unified molecular mechanism for ligand-dependent activation of NR4A-RXR heterodimers ]]> https://biorxiv.org/content/10.1101/2025.03.19.642122v1?rss=1 Yu, X. He, Y. Kamenecka, T. M. Kojetin, D. J. 2025-03-19 doi:10.1101/2025.03.19.642122 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ Pcdh20 is a POU2F3 target gene required for proper tuft cell microvillus formation ]]> https://biorxiv.org/content/10.1101/2025.03.18.644042v1?rss=1 Ankenbauer, K. E. Yang, Y. Chung, C.-Y. Andrade, L. R. Weiser Novak, S. Jarvis, B. Ali Hanel, W. H. Liu, J. Sarkisian, V. Dani, N. Krystofiak, E. Hu, G. Ebrahim, S. Kachar, B. Gong, Q. Wahl, G. Manor, U. Lau, K. DelGiorno, K. E. 2025-03-20 doi:10.1101/2025.03.18.644042 Cold Spring Harbor Laboratory Press 2025-03-20 <![CDATA[ AI-assisted isolation of bioactive Dipyrimicins from Amycolatopsis azurea and identification of its corresponding dip biosynthetic gene cluster ]]> https://biorxiv.org/content/10.1101/2025.03.21.644653v1?rss=1 Ancajas, C. M. F. Shuster, I. E. Walker, A. 2025-03-21 doi:10.1101/2025.03.21.644653 Cold Spring Harbor Laboratory Press 2025-03-21 <![CDATA[ SpatialRNA: a Python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomicsdataset ]]> https://biorxiv.org/content/10.1101/2025.03.20.644258v1?rss=1 Lyu, R. Vannan, A. Kropski, J. A. Banovich, N. E. McCarthy, D. J. 2025-03-23 doi:10.1101/2025.03.20.644258 Cold Spring Harbor Laboratory Press 2025-03-23 <![CDATA[ Dissecting Branch-Specific Unfolded Protein Response Activation in Drug-Tolerant BRAF-Mutant Melanoma using Data-Independent Acquisition Mass Spectrometry ]]> https://biorxiv.org/content/10.1101/2025.03.20.644425v1?rss=1 Barny, L. A. Hermanson, J. N. Garcia, S. K. Stauffer, P. E. Plate, L. 2025-03-24 doi:10.1101/2025.03.20.644425 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation ]]> https://biorxiv.org/content/10.1101/2025.03.23.644697v1?rss=1 Zhou, J. Wu, Y. Liu, H. Tian, W. Castanon, R. G. Bartlett, A. Zhang, Z. Yao, G. Shi, D. Clock, B. Marcotte, S. Nery, J. R. Liem, M. Claffey, N. Boggeman, L. Barragan, C. eDrigo, R. A. Weimer, A. K. Shi, M. Cooper-Knock, J. Zhang, S. Snyder, M. P. Preissl, S. Ren, B. O'Connor, C. Chen, S. Luo, C. Dixon, J. R. Ecker, J. R. 2025-03-24 doi:10.1101/2025.03.23.644697 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ SuperMetal: A Generative AI Framework for Rapid and Precise Metal Ion Location Prediction in Proteins ]]> https://biorxiv.org/content/10.1101/2025.03.21.644685v1?rss=1 Lin, X. Su, Z. Liu, Y. Liu, J. Kuang, X. Cummings, P. T. Spencer-Smith, J. Meiler, J. 2025-03-25 doi:10.1101/2025.03.21.644685 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Microbiota promote enhanced CD39 expression in γδ intraepithelial lymphocytes through the activation of TCR and IL-15 signaling ]]> https://biorxiv.org/content/10.1101/2025.03.22.644616v1?rss=1 Alonso, S. Kaur, H. Jia, L. Nguyen, M.-U. Fong, A. Skariah, N. Argüello, R. J. Verzi, M. P. Swamy, M. Lau, K. S. Edelblum, K. L. 2025-03-25 doi:10.1101/2025.03.22.644616 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Depletion of Polypyrimidine tract binding protein 1 (ptbp1) activates Muller glia-derived proliferation during zebrafish retina regeneration via modulation of the senescence secretome ]]> https://biorxiv.org/content/10.1101/2025.03.24.645057v1?rss=1 Konar, G. J. Lingan, A. L. Vallone, K. T. Nguyen, T. D. Flickinger, Z. R. Patton, J. G. 2025-03-25 doi:10.1101/2025.03.24.645057 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Short-term alterations in dietary amino acids override host genetic susceptibility and reveal mechanisms of Salmonella Typhimurium small intestine colonization ]]> https://biorxiv.org/content/10.1101/2025.03.25.645332v1?rss=1 Shealy, N. Baltagulov, M. de Brito, C. McGovern, A. Castro, P. Schrimpe-Rutledge, A. C. Malekshahi, C. Condreanu, S. G. Sherrod, S. D. Jana, S. Jones, K. Machado Ribeiro, T. R. McLean, J. Beiting, D. P. Byndloss, M. X. 2025-03-25 doi:10.1101/2025.03.25.645332 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Inherited resilience to clonal hematopoiesis by modifying stem cell RNA regulation ]]> https://biorxiv.org/content/10.1101/2025.03.24.645017v1?rss=1 Agarwal, G. Antoszewski, M. Xie, X. Pershad, Y. Arora, U. P. Poon, C.-L. Lyu, P. Lee, A. J. Guo, C.-J. Ye, T. Norford, L. B. Neehus, A.-L. della Volpe, L. Wahlster, L. Ranasinghe, D. Ho, T.-C. Barlowe, T. S. Chow, A. Schurer, A. Taggart, J. Durham, B. H. Abdel-Wahab, O. McGraw, K. L. Allan, J. M. Soldatov, R. Bick, A. G. Kharas, M. G. Sankaran, V. G. 2025-03-26 doi:10.1101/2025.03.24.645017 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Salient objects in a scene trigger enhanced perceptual selection and memory encoding ]]> https://biorxiv.org/content/10.1101/2025.03.25.645146v1?rss=1 Xi, P. Lin, R. Woodman, G. F. Wang, B. 2025-03-26 doi:10.1101/2025.03.25.645146 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Alpha-actinin-1 stabilizes focal adhesions to facilitate sarcomere assembly in cardiac myocytes ]]> https://biorxiv.org/content/10.1101/2025.03.28.645933v1?rss=1 Hayes, J. B. Bainbridge, A. M. Burnette, D. T. 2025-03-29 doi:10.1101/2025.03.28.645933 Cold Spring Harbor Laboratory Press 2025-03-29 <![CDATA[ Whole-brain, all-optical interrogation of neuronal dynamics underlying gut interoception in zebrafish ]]> https://biorxiv.org/content/10.1101/2025.03.26.645305v1?rss=1 Chen, W. James, B. Ruetten, V. M. S. Banala, S. Wei, Z. Fleishman, G. Rubinov, M. Fishman, M. C. Engert, F. Lavis, L. D. Fitzgerald, J. E. Ahrens, M. B. 2025-03-30 doi:10.1101/2025.03.26.645305 Cold Spring Harbor Laboratory Press 2025-03-30 <![CDATA[ Polygenic Associations between Motor Behaviour, Neuromotor Traits, and Active Music Engagement in Four Cohorts ]]> https://biorxiv.org/content/10.1101/2025.03.27.645667v1?rss=1 Henechowicz, T. L. Coleman, P. L. Gustavson, D. E. Mekki, Y. N. Nayak, S. Nitin, R. Scartozzi, A. C. Tio, E. S. van Klei, R. Felsky, D. Thaut, M. H. Gordon, R. L. 2025-03-30 doi:10.1101/2025.03.27.645667 Cold Spring Harbor Laboratory Press 2025-03-30 <![CDATA[ Functional profiling of KCNE1 variants informs population carrier frequency of Jervell and Lange-Nielsen syndrome type 2 ]]> https://biorxiv.org/content/10.1101/2025.03.28.646046v1?rss=1 Vanoye, C. G. Desai, R. R. John, J. Hoffman, S. Fink, N. Zhang, Y. Venkatesh, O. Roe, J. Adusumilli, S. Jairam, N. Sanders, C. Gordon, A. George, A. L. 2025-04-01 doi:10.1101/2025.03.28.646046 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Photoperiodic Regulation of SK Channels in Dorsal Raphe Serotonin Neurons ]]> https://biorxiv.org/content/10.1101/2025.03.29.646123v1?rss=1 Giannoni Guzman, M. A. Zepeda, J. C. Kamitakahara, A. Magalong, V. Levitt, P. Grueter, B. McMahon, D. G. 2025-04-01 doi:10.1101/2025.03.29.646123 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Overnutrition directly impairs thyroid hormone biosynthesis and utilization, causing hypothyroidism, despite remarkable thyroidal adaptations ]]> https://biorxiv.org/content/10.1101/2025.03.31.645596v1?rss=1 Rampy, J. Torres-Manzo, A. P. Hoffsmith, K. Loberg, M. A. Sheng, Q. Salas-Lucia, F. Bianco, A. C. Arrojo e Drigo, R. Wang, H. Weiss, V. L. Carrasco, N. 2025-04-02 doi:10.1101/2025.03.31.645596 Cold Spring Harbor Laboratory Press 2025-04-02 <![CDATA[ Substrate stiffness and shear stress collectively regulate the inflammatory phenotype in cultured human brain microvascular endothelial cells ]]> https://biorxiv.org/content/10.1101/2025.03.31.646228v1?rss=1 Yates, A. Murray, H. Kjar, A. Chavarria, D. Masters, H. Kim, H. Ligocki, A. Jefferson, A. Lippmann, E. 2025-04-02 doi:10.1101/2025.03.31.646228 Cold Spring Harbor Laboratory Press 2025-04-02 <![CDATA[ Transmembrane Serine Protease TMPRSS11B promotes an acidified tumor microenvironment and immune suppression in lung squamous cell carcinoma ]]> https://biorxiv.org/content/10.1101/2025.04.01.646727v1?rss=1 Sunil, H. S. Clemenceau, J. Barnfather, I. Nakkireddy, S. R. Grichuk, A. Izzo, L. T. Evers, B. M. Thomas, L. Subramaniyan, I. Li, L. Putnam, W. T. Zhu, J. Updegraff, B. Minna, J. D. DeBerardinis, R. J. Gao, J. Hwang, T. H. Oliver, T. G. O'Donnell, K. A. 2025-04-03 doi:10.1101/2025.04.01.646727 Cold Spring Harbor Laboratory Press 2025-04-03 <![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[ The Physiological Component of the BOLD Signal: Impact of Age and Heart Rate Variability Biofeedback Training ]]> https://biorxiv.org/content/10.1101/2025.04.04.647252v1?rss=1 Song, R. W. Min, J. Wang, S. Goodale, S. E. Rogge-Obando, K. Yang, R. Yoo, H. J. Nashiro, K. Chen, J. E. Mather, M. Chang, C. 2025-04-08 doi:10.1101/2025.04.04.647252 Cold Spring Harbor Laboratory Press 2025-04-08 <![CDATA[ Functional MRI Signatures of Autonomic Physiology in Aging ]]> https://biorxiv.org/content/10.1101/2025.04.05.647057v1?rss=1 Fan, J. Juttukonda, M. R. Goodale, S. E. Wang, S. Orban, C. Varadarajan, D. Polimeni, J. R. Chang, C. Salat, D. H. Chen, J. E. 2025-04-10 doi:10.1101/2025.04.05.647057 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ A Multimodal Imaging Pipeline for the Discovery of Molecular Markers of Cellular Neighborhoods ]]> https://biorxiv.org/content/10.1101/2025.04.07.647675v1?rss=1 Pham, T. Farrow, M. A. Migas, L. G. Dufresne, M. Colley, M. E. Allen, J. L. de Caestecker, M. Van de Plas, R. Spraggins, J. M. 2025-04-10 doi:10.1101/2025.04.07.647675 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ White matter geometry confounds Diffusion Tensor Imaging Along Perivascular Space (DTI-ALPS) measures ]]> https://biorxiv.org/content/10.1101/2025.04.14.648733v1?rss=1 Schilling, K. Newton, A. T. Tax, C. M. Nilsson, M. Chamberland, M. Anderson, A. W. Landman, B. A. Descoteaux, M. 2025-04-19 doi:10.1101/2025.04.14.648733 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ Newly trained navigation and verbal memory skills elicit changes in task-related networks but not brain structure ]]> https://biorxiv.org/content/10.1101/2025.04.14.648747v1?rss=1 Zheng, L. Boogaart, Z. McAvan, A. Garren, J. Doner, S. Wilkes, B. J. Groves, W. Yuksel, E. Cherep, L. Ekstrom, A. Weisberg, S. M. 2025-04-19 doi:10.1101/2025.04.14.648747 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ Correspondence between sleep patterns and anhedonia in adult male mice exposed to early-life stress ]]> https://biorxiv.org/content/10.1101/2025.04.18.649529v1?rss=1 Hall, A. G. Burek, D. J. Hisey, E. E. Seabrook, L. T. Fritsch, E. L. Beatty, Z. G. Ressler, K. J. Kangas, B. D. Carlezon, W. A. 2025-04-19 doi:10.1101/2025.04.18.649529 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ Widespread gray and white matter microstructural alterations in dual cognitive-motor impairment ]]> https://biorxiv.org/content/10.1101/2025.04.18.649603v1?rss=1 Singh, K. An, Y. Schilling, K. Benjamini, D. 2025-04-21 doi:10.1101/2025.04.18.649603 Cold Spring Harbor Laboratory Press 2025-04-21 <![CDATA[ Neuropathological hallmarks during the chronic phase of ischemic stroke in mice and humans ]]> https://biorxiv.org/content/10.1101/2025.04.16.649173v1?rss=1 Khan, R. Guzman, G. U. Do, T. H. Devlin, P. Ahn, J. J. Tan, C. Venna, V. R. Marrelli, S. P. Koochak, H. P. DiGesu, C. Flores, A. McCullough, L. D. Ritzel, R. M. 2025-04-22 doi:10.1101/2025.04.16.649173 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ Single Cell Landscape of Sex-specific Drivers of Alzheimers Disease ]]> https://biorxiv.org/content/10.1101/2025.04.18.647076v1?rss=1 Wu, Y. Travaglini, K. J. Gabitto, M. Keene, D. Dunn, A. Kaczorowski, C. Harari, O. De Jager, P. Menon, V. Schneider, J. A. Bennett, D. A. Dumitrescu, L. Hohman, T. J. 2025-04-22 doi:10.1101/2025.04.18.647076 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ Starvation drives co-existence in cross-feeding bacterial populations ]]> https://biorxiv.org/content/10.1101/2025.04.22.650053v1?rss=1 McLaughlin, W. F. Behringer, M. G. 2025-04-23 doi:10.1101/2025.04.22.650053 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Neural trajectories reveal orchestration of cortical coding underlying natural language composition ]]> https://biorxiv.org/content/10.1101/2025.04.24.650382v1?rss=1 Tang, X. Booth, J. R. Zhang, Y. Wang, S. Ding, G. 2025-04-25 doi:10.1101/2025.04.24.650382 Cold Spring Harbor Laboratory Press 2025-04-25 <![CDATA[ Ancient co-option of LTR retrotransposons as yeast centromeres ]]> https://biorxiv.org/content/10.1101/2025.04.25.647736v1?rss=1 Haase, M. A. B. Lazar-Stefanita, L. Baudry, L. Wudzinska, A. Zhou, X. Rokas, A. Hittinger, C. T. Musacchio, A. Boeke, J. D. 2025-04-25 doi:10.1101/2025.04.25.647736 Cold Spring Harbor Laboratory Press 2025-04-25 <![CDATA[ Design of an orally bioavailable small molecule that modulates the microtubule-associated protein tau's pre-mRNA splicing ]]> https://biorxiv.org/content/10.1101/2025.04.30.651234v1?rss=1 Zhang, P. Taghavi, A. Abe, M. Aikawa, H. Akahori, Y. Chen, J. L. Tong, Y. Baisden, J. T. Cameron, M. D. childs-disney, J. L. Disney, M. D. 2025-04-30 doi:10.1101/2025.04.30.651234 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Spatial and longitudinal tracking of enhancer-AAV vectors that target transgene expression to injured mouse myocardium ]]> https://biorxiv.org/content/10.1101/2025.04.28.651096v1?rss=1 Wolfson, D. Hull, J. Li, Y. Gonzalez, T. Jayaram, M. Devlin, G. Cigliola, V. Oonk, K. Rosales, A. Bursac, N. Asokan, A. Poss, K. D. 2025-05-01 doi:10.1101/2025.04.28.651096 Cold Spring Harbor Laboratory Press 2025-05-01 <![CDATA[ Inflammasome Activation in Cutaneous Squamous Cell Carcinoma ]]> https://biorxiv.org/content/10.1101/2025.04.29.650608v1?rss=1 Patel, K. R. Shu, R. R. Wang, R. Tekale, K. Hamersky, M. Perez, A. B. Solano, D. Syed, N. Stewart, C. E. Lee, J. Hanlon, A. M. Blalock, T. W. Li, C. Seldin, L. 2025-05-02 doi:10.1101/2025.04.29.650608 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ Antiviral CD4+ T and myeloid cell responses to influenza vaccines are attenuated in older adults ]]> https://biorxiv.org/content/10.1101/2025.04.30.651528v1?rss=1 Oakes, J. M. Simmons, J. D. Hager-Nochowicz, C. Kirk, L. Eason, J. Halasa, N. B. Talbot, H. K. Bailin, S. S. Castilho, J. L. Kalams, S. A. 2025-05-06 doi:10.1101/2025.04.30.651528 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ Structural basis of PPARγ-mediated transcriptional repression by the covalent inverse agonist FX-909 ]]> https://biorxiv.org/content/10.1101/2025.05.04.651770v1?rss=1 Laughlin, Z. T. Arifova, L. Munoz-Tello, P. Yu, X. Dong, J. Harp, J. M. Zu, D. Kamenecka, T. M. Kojetin, D. J. 2025-05-06 doi:10.1101/2025.05.04.651770 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ Sialylated CD43 is a glyco-immune checkpoint for macrophage phagocytosis ]]> https://biorxiv.org/content/10.1101/2025.05.05.652090v1?rss=1 Chung, J. Vallurupalli, M. Noel, S. Schor, G. Liu, Y. Nobrega, C. Perera, J. Wrona, E. Hu, M. Lin, Y. Wu, D. w. Saberi, M. Scapozza, I. Cruickshank, A. Woods, E. C. Chuong, C. L. Birocchi, F. Kammula, A. Avila, O. I. Kocak, M. Doench, J. G. Procter, D. Thornton, L. Brunner, A. M. Winer, E. DeAngelo, D. J. Garcia, J. S. Stone, R. M. Jenkins, R. W. Maus, M. V. Graubert, T. A. Yates, K. B. Golub, T. R. Manguso, R. T. 2025-05-06 doi:10.1101/2025.05.05.652090 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ A ubiquitous spectrolaminar motif across independent studies, including in the Mackey et al. dataset ]]> https://biorxiv.org/content/10.1101/2025.05.07.652644v1?rss=1 Major, A. J. Abdaltawab, A. Phillips, J. M. Wang, T. Lee, E. K. Lichtenfeld, M. J. Chandrasekaran, C. Saalmann, Y. B. Maier, A. Desimone, R. Miller, E. K. Bastos, A. M. Mendoza-Halliday, D. 2025-05-08 doi:10.1101/2025.05.07.652644 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ An integrative genomic and chemical similarity approach linking fungal secondary metabolites and biosynthetic gene clusters ]]> https://biorxiv.org/content/10.1101/2025.05.08.652894v1?rss=1 Steffen, K. Rangel-Grimaldo, M. Sauters, T. J. C. Rinker, D. Raja, H. A. Graf, T. N. Gumilang, A. Riedling, O. L. Goldman, G. Oberlies, N. H. Rokas, A. 2025-05-08 doi:10.1101/2025.05.08.652894 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Profiling metabotropic glutamate receptor 7 expression in Rett syndrome: consequences for pharmacotherapy ]]> https://biorxiv.org/content/10.1101/2025.05.08.652716v1?rss=1 Vermudez, S. A. D. Freitas, G. A. Smith, M. Gogliotti, R. Niswender, C. M. 2025-05-12 doi:10.1101/2025.05.08.652716 Cold Spring Harbor Laboratory Press 2025-05-12 <![CDATA[ BrainVAE: Exploring the role of white matter BOLD in preclinical Alzheimer disease classification ]]> https://biorxiv.org/content/10.1101/2025.05.07.652697v1?rss=1 Li, Y. Xu, L. Zuo, L. Chang, Y. Ding, Z. Anderson, A. W. Schilling, K. Gore, J. C. Gao, Y. 2025-05-13 doi:10.1101/2025.05.07.652697 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Smooth muscle LRRC8A knockout preserves vascular function in AngII hypertension ]]> https://biorxiv.org/content/10.1101/2025.05.08.652978v1?rss=1 Choi, H. Panja, S. Nguyen, H.-N. Stark, R. J. Lamb, F. S. 2025-05-14 doi:10.1101/2025.05.08.652978 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Methionine-triggered growth arrest reveals activation of Gcn2 by methionine transporter endocytosis ]]> https://biorxiv.org/content/10.1101/2025.05.12.653625v1?rss=1 Hepowit, N. L. Singkhek, H. L. Johnson, D. J. MacGurn, J. A. 2025-05-14 doi:10.1101/2025.05.12.653625 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Deregulated Myt3 translation predisposes islet β-cells to dysfunction under obesity-induced metabolic stress ]]> https://biorxiv.org/content/10.1101/2025.05.11.653323v1?rss=1 Hu, R. Wang, Y. Yagan, M. Xu, Y. Simmons, A. Lau, K. Liu, Q. Gu, G. 2025-05-15 doi:10.1101/2025.05.11.653323 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ RNA polymerase III transcription-associated polyadenylation promotes the accumulation of noncoding retrotransposons during infection ]]> https://biorxiv.org/content/10.1101/2025.05.14.654096v1?rss=1 Lari, A. Shah, S. B. Mao, X. Sanghrajka, P. Karijolich, J. Lareau, L. F. Glaunsinger, B. A. 2025-05-16 doi:10.1101/2025.05.14.654096 Cold Spring Harbor Laboratory Press 2025-05-16 <![CDATA[ Non-canonical EGFR signaling is essential for MAPK-mediated apical extrusion of epithelial cells ]]> https://biorxiv.org/content/10.1101/2025.05.16.654585v1?rss=1 Molina, P. Daniel, M. Wang, J. MACARA, I. G. 2025-05-17 doi:10.1101/2025.05.16.654585 Cold Spring Harbor Laboratory Press 2025-05-17 <![CDATA[ Modeling Immunosenescence on-a-chip: a platform for cancer vaccine efficacy assessment ]]> https://biorxiv.org/content/10.1101/2025.05.14.654059v1?rss=1 Maity, S. Hassani Najafabadi, A. Kawakita, S. Khorsandi, D. Yilgor, C. Jewell, C. Mohaghegh, N. Dokmeci, M. R. Khademhosseini, A. Jucaud, V. 2025-05-18 doi:10.1101/2025.05.14.654059 Cold Spring Harbor Laboratory Press 2025-05-18 <![CDATA[ In vivo CRISPR screening identifies NF1/RASA1/TP53 co-mutations and downstream MEK signaling as a common key mechanism of sinonasal tumorigenesis ]]> https://biorxiv.org/content/10.1101/2025.05.19.654661v1?rss=1 Vu, K. P. Gunti, S. Viswanathan, R. Nandal, A. Larkin, R. Cho, S. Zou, J. Ramolia, S. Hoke, A. T. K. Barbosa, S. M. Gallia, G. L. Rooper, L. M. Floudas, C. S. Cheng, H. Miller, C. N. Guest, M. R. Notaro, M. Raziuddin, A. Sun, Z. Wu, X. Faraji, F. Lechner, M. Comoglio, F. Edmondson, E. F. Chari, R. London, N. R. 2025-05-23 doi:10.1101/2025.05.19.654661 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ ALPHA/BETA HYDROLASE DOMAIN CONTAINING 5 SUPPORTS GLUCOSE-STIMULATED-LIPOLYSIS AND INSULIN SECRETION IN PANCREATIC BETA CELLS ]]> https://biorxiv.org/content/10.1101/2025.05.21.655350v1?rss=1 Kim, L. Liu, S. Peachee, S. Richtsmeier, S. Jun, C. Gianna, S. Vikram, A. Freshly, A. Imai, Y. 2025-05-24 doi:10.1101/2025.05.21.655350 Cold Spring Harbor Laboratory Press 2025-05-24 <![CDATA[ Genetic background influences the heterogeneous phenotypes driven by the MAFAS64F MODY variant in male mice ]]> https://biorxiv.org/content/10.1101/2025.05.20.653758v1?rss=1 Loyd, Z. Lee, D. Maurer, M. Liu, J.-H. Guo, M. Reynolds, G. Magnuson, M. A. Cartailler, J.-P. Stein, R. Cha, J. 2025-05-25 doi:10.1101/2025.05.20.653758 Cold Spring Harbor Laboratory Press 2025-05-25 <![CDATA[ Cell Density and mRNA Expression of Inhibitory Interneurons in Schizophrenia: A Meta-Analysis ]]> https://biorxiv.org/content/10.1101/2025.05.23.655812v1?rss=1 Mulvey, A. G. Gabhart, K. M. Grent-T-Jong, T. Herculano-Houzel, S. Uhlhaas, P. J. Bastos, A. M. 2025-05-27 doi:10.1101/2025.05.23.655812 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Scaled multidimensional assays of variant effect identify sequence-function relationships in hypertrophic cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2025.05.23.655878v1?rss=1 Yamamoto, Y. Chua, K. Ferrasse, A. Kirillova, A. De Jong, H. Floyd, B. Cadisch, C. Wiel, L. Wang, Q. O'Neill, M. Tabet, D. R. Staudt, D. W. Gorzynski, J. E. Huang, Y. Wilson, R. H. Sharma, A. Tapales, A. Agrawal, R. Wheeler, M. T. MacRae, C. A. Roden, D. M. Roth, F. Glazer, A. M. Ashley, E. A. Parikh, V. N. 2025-05-27 doi:10.1101/2025.05.23.655878 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Comparing Brain-Behavior Relationships Across Dimensional, Tail-Sampled, and Propensity-Matched Models ]]> https://biorxiv.org/content/10.1101/2025.05.23.655740v1?rss=1 Murtha, K. Dorfschmidt, L. Bethlehem, R. A. I. Kang, K. Vandekar, S. Alexander-Bloch, A. F. Waller, R. Seidlitz, J. 2025-05-28 doi:10.1101/2025.05.23.655740 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Adaptive-like NK cell responses to influenza correlate with humoral immunity and are influenced by age and sex ]]> https://biorxiv.org/content/10.1101/2025.05.24.655902v1?rss=1 Alves, E. Oakes, J. M. Simmons, J. D. Currenti, J. Coudert, J. D. Foley, B. Eason, J. Halasa, N. B. Talbot, H. K. Castilho, J. L. Mallal, S. Gaudieri, S. Kalams, S. A. 2025-05-28 doi:10.1101/2025.05.24.655902 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Robust Serum Proteomic Signatures of APOE2 ]]> https://biorxiv.org/content/10.1101/2025.05.24.655950v1?rss=1 Sebastiani, P. Reed, E. Chandler, K. B. Lopez, P. Lords, H. Bae, H. Costello, C. E. Au, M. Denn, L. Li, M. Xiang, Q. Noh, H. Pflieger, L. Funk, C. Rappaport, N. Nygaard, M. Short, M. Brent, M. Monti, S. Andersen-Toomey, S. L. Perls, T. 2025-05-29 doi:10.1101/2025.05.24.655950 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ Kidney cystogenesis in embryonic- and adult-onset ADPKD is suppressed from lack of adenylyl cyclase targeting to cilia ]]> https://biorxiv.org/content/10.1101/2025.05.27.656198v1?rss=1 Hwang, S.-H. Choi, K. Badgandi, H. White, K. Xun, Y. Qian, F. Mukhopadhyay, S. 2025-05-29 doi:10.1101/2025.05.27.656198 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ Functional Implications of the Conformational Landscape of a Multidrug Transporter Revealed by Structures of Zebrafish Abcb4 ]]> https://biorxiv.org/content/10.1101/2025.05.30.656806v1?rss=1 Zhan, J. Hsieh, C.-M. Esser, L. Lang, Z. C. Morton, A. J. Robey, R. W. Zhou, F. Ambudkar, S. V. Huang, R. K. Gottesman, M. M. Xia, D. 2025-05-30 doi:10.1101/2025.05.30.656806 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Molecular dynamics driving phenotypic divergence among KRAS mutants in pancreatic tumorigenesis ]]> https://biorxiv.org/content/10.1101/2025.05.28.656689v1?rss=1 Grimont, A. Falvo, D. J. Sisso, W. J. Zumbo, P. Chan, C. W. Santos, F. Pan, G. Cleveland, M. Yaron, T. Osterhoudt, A. S. Meng, Y. Zafra, M. P. Fall, W. B. Rendeiro, A. F. Hissong, E. Yantiss, R. K. Betel, D. Magnuson, M. A. Leach, S. D. Rustgi, A. K. Dow, L. E. Chandwani, R. 2025-06-01 doi:10.1101/2025.05.28.656689 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Biocompatible Multi-functional Polymeric Material for Mineralized Tissue Adhesion ]]> https://biorxiv.org/content/10.1101/2025.05.30.656989v1?rss=1 Luo, Y. Zhang, C. Fulco, S. Liu, J. Chen, K. Hu, Y. Jiang, Y. Xu, R. Rakesh, L. Ozer, F. Tertuliano, O. Turner, K. Vining, K. H. 2025-06-02 doi:10.1101/2025.05.30.656989 Cold Spring Harbor Laboratory Press 2025-06-02 <![CDATA[ VGLL3-centered network connects placental, vascular, and immune defects in preeclampsia ]]> https://biorxiv.org/content/10.1101/2025.05.30.657097v1?rss=1 Plazyo, O. Chopp, L. B. Peela, R. Young, K. Zhang, H. Bogle, R. Hesson, A. Langen, E. Bergin, I. L. Syu, L.-J. Erba, J. Kirma, J. Dey, P. Zhang, L. Sarkar, M. K. Swindell, W. R. Gallagher, K. A. Ward, N. L. Singer, K. Kahlenberg, J. M. Billi, A. C. Dlugosz, A. A. Ganesh, S. K. Tsoi, L. C. Gudjonsson, J. E. 2025-06-03 doi:10.1101/2025.05.30.657097 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ The interferon response signature links to increased expression of transposable elements in neutrophils of systemic lupus erythematosus patients ]]> https://biorxiv.org/content/10.1101/2025.05.30.657099v1?rss=1 Arteaga-Vazquez, L. J. Sepulveda, H. Villalobos, B. Suzuki, K. Kalunian, K. Ay, F. Boothby, M. R. Rao, A. 2025-06-03 doi:10.1101/2025.05.30.657099 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Assessing Attentiveness and Cognitive Engagement across Tasks using Video-based Action Understanding in Non-Human Primates ]]> https://biorxiv.org/content/10.1101/2025.05.31.657183v1?rss=1 90% decoding accuracy with [≤]3min time segments. The analysis procedure allows setting subject-specific thresholds for segmenting subject specific movements for a time-resolved scoring of attentiveness and screen engagement. Comparison with existing methodsCurrent methods also extract poses and segment action units; however, they havent been combined into a framework that enables subject-adjusted thresholding for specific task contexts. This integration is needed for inferring cognitive state variables and differentiating performance across various tasks. ConclusionThe proposed method integrates video segmentation, scoring of attentiveness and screen engagement, and classification of task performance at high temporal resolution. This integrated framework provides a tool for assessing attention functions from video. ]]> Cheung, S.-M. Neumann, A. Womelsdorf, T. 2025-06-03 doi:10.1101/2025.05.31.657183 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Coordinated dynamics of excitatory and inhibitory synapse assembly ]]> https://biorxiv.org/content/10.1101/2025.06.02.657384v1?rss=1 Garbett, K. Allen, J. Sando, R. 2025-06-03 doi:10.1101/2025.06.02.657384 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ A spatial transcriptomic atlas of acute neonatal lung injury across development and disease severity ]]> https://biorxiv.org/content/10.1101/2025.06.02.656433v1?rss=1 Mallapragada, S. Lyu, R. Williams-Katek, A. L. Fischer, B. K. Vannan, A. Hadad, N. Mee, E. D. Shirazi, S. P. Jetter, C. S. Negretti, N. M. Hilgendorff, A. Eldredge, L. C. Deutsch, G. H. McCarthy, D. J. Kropski, J. A. Sucre, J. M. S. Banovich, N. E. 2025-06-05 doi:10.1101/2025.06.02.656433 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ Mechanical force-mediated cellular crosstalk maintains the integrity of the lung gas exchange niche ]]> https://biorxiv.org/content/10.1101/2025.06.04.657878v1?rss=1 Shen, C. Morley, M. P. Zhao, G. Jones, D. L. Schaefer, S. E. Planer, J. D. Chembazhi, U. V. Kim, M. Ying, Y. Zhou, S. Li, S. Hallquist, H. Lange, A. Basil, M. C. Morrisey, E. E. 2025-06-05 doi:10.1101/2025.06.04.657878 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ Calorie restriction suppresses aging alpha cell pro-inflammatory signaling ]]> https://biorxiv.org/content/10.1101/2025.06.04.657914v1?rss=1 Schleh, M. Cambraia, A. Cutler, M. Ferguson, G. Arrojo e Drigo, R. 2025-06-09 doi:10.1101/2025.06.04.657914 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Early life environments shape adult cardiometabolic health during rapid lifestyle change ]]> https://biorxiv.org/content/10.1101/2025.06.06.658350v1?rss=1 Petersen, R. M. Tennyson, R. A/P Tan Boon Huat, T. B. T. Tam, K. L. Watowich, M. M. Solhaimi bin Fadzil, K. Nicholas, C. bin Mohd Sayed, I. Seong Ng, K. A L Lim, Y. Venkataraman, V. V. Wallace, I. J. Kraft, T. S. Lea, A. J. 2025-06-10 doi:10.1101/2025.06.06.658350 Cold Spring Harbor Laboratory Press 2025-06-10 <![CDATA[ Layer 6 is a hub for cholinergic modulation in the mouse auditory cortex ]]> https://biorxiv.org/content/10.1101/2025.06.09.658740v1?rss=1 Vattino, L. G. Clayton, K. K. Hackett, T. A. Takesian, A. E. Polley, D. B. 2025-06-10 doi:10.1101/2025.06.09.658740 Cold Spring Harbor Laboratory Press 2025-06-10 <![CDATA[ A reversible feedback mechanism regulating mitochondrial heme synthesis ]]> https://biorxiv.org/content/10.1101/2025.06.09.658730v1?rss=1 Chitrakar, I. Roberson, A. B. Ayres-Galhardo, P. H. Brown, B. L. 2025-06-11 doi:10.1101/2025.06.09.658730 Cold Spring Harbor Laboratory Press 2025-06-11 <![CDATA[ Advancing Fair and Explainable Machine Learning for Neuroimaging Dementia Pattern Classification in Multi-Ethnic Populations ]]> https://biorxiv.org/content/10.1101/2025.06.09.658375v1?rss=1 Ho, N.-H. Charisis, S. Honnorat, N. Brandigampala, S. R. Wang, D. Heckbert, S. R. Fox, P. T. Martinez, D. Wang, D. H. Hughes, T. M. Archer, D. B. Hohman, T. J. Seshadri, S. Davatzikos, C. Habes, M. 2025-06-12 doi:10.1101/2025.06.09.658375 Cold Spring Harbor Laboratory Press 2025-06-12 <![CDATA[ Unbiased recording of clonal potency reveals species-specific regulation of mammalian intestine ]]> https://biorxiv.org/content/10.1101/2025.06.10.658707v1?rss=1 Islam, M. Bechard, M. E. Yang, Y. Simmons, A. J. Xu, Y. Higginbotham, J. N. Zhao, P. Cao, Z. Tasneem, N. Glass, S. E. Markham, N. O. Revetta, F. Ramirez-Solano, M. A. Liu, Q. Franklin, J. L. Lau, K. Coffey, R. J. 2025-06-12 doi:10.1101/2025.06.10.658707 Cold Spring Harbor Laboratory Press 2025-06-12 <![CDATA[ Integration of Audiovisual Motion in Dorsolateral Prefrontal Cortical Neurons ]]> https://biorxiv.org/content/10.1101/2025.06.11.656227v1?rss=1 Karimi, A. Mozumder, R. Schoenhaut, A. Rausis, O. Wallace, M. Ramachandran, R. Constantinidis, C. 2025-06-12 doi:10.1101/2025.06.11.656227 Cold Spring Harbor Laboratory Press 2025-06-12 <![CDATA[ Reversible Antagonism of Dopamine D1 Receptor using a Photoswitchable Remotely Tethered Ligand ]]> https://biorxiv.org/content/10.1101/2025.06.10.658926v1?rss=1 Hetzler, B. E. Donthamsetti, P. C. Wolesensky, R. M. Stanley, C. Isacoff, E. Trauner, D. 2025-06-15 doi:10.1101/2025.06.10.658926 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Precision targeting of C3+ reactive astrocyte subpopulations with endogenous ADAR in an iPSC-derived model ]]> https://biorxiv.org/content/10.1101/2025.06.11.659213v1?rss=1 Kim, H. Kjar, A. Embalabala, R. Brunger, J. Lippmann, E. 2025-06-15 doi:10.1101/2025.06.11.659213 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Image-Based Meta- and Mega-Analysis (IBMMA): A Unified Framework for Large-Scale, Multi-Site, Neuroimaging Data Analysis ]]> https://biorxiv.org/content/10.1101/2025.06.16.657725v1?rss=1 Steele, N. Morey, R. Hussain, A. Russell, C. Suarez-Jimenez, B. Pozzi, E. Jameei, H. Schmaal, L. Veer, I. Waller, L. Jahanshad, N. Thomopoulos, S. Salminen, L. Olff, M. Frijling, J. Veltman, D. Koch, S. Nawijn, L. van Zuiden, M. Wang, L. Zhu, Y. Li, G. Stein, D. Ipser, J. Neria, Y. Zhu, X. Ravid, O. Zilcha-Mano, S. Lazarov, A. Huggins, A. Stevens, J. Ressler, K. Jovanovic, T. van Rooij, S. Fani, N. Mueller, S. Hudson, A. Daniels, J. Sierk, A. Manthey, A. Walter, H. van der Wee, N. van der Werff, S. Vermeiren, R. Schmahl, C. Herzog, J. Rektor, I. i 2025-06-17 doi:10.1101/2025.06.16.657725 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Multisensory integration for active mechanosensation in Drosophila flight ]]> https://biorxiv.org/content/10.1101/2025.06.20.660728v1?rss=1 Mills, K. M. Cowan, N. J. Suver, M. P. 2025-06-24 doi:10.1101/2025.06.20.660728 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ Exosomes are specialized vehicles to induce fibronectin assembly ]]> https://biorxiv.org/content/10.1101/2025.06.23.661091v1?rss=1 Sung, B. H. Emmanuel, M. Gari, M. Guerrero, J. Virumbrales-Munoz, M. Inman, D. Krystofiak, E. Rapraeger, A. C. Ponik, S. M. Weaver, A. 2025-06-24 doi:10.1101/2025.06.23.661091 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ CellSpliceNet: Interpretable Multimodal Modeling ofAlternative Splicing Across Neurons in C. elegans ]]> https://biorxiv.org/content/10.1101/2025.06.22.660966v1?rss=1 Afrasiyabi, A. Kovalic, J. Liu, C. Castro, E. Weinreb, A. Varol, E. Miller, D. Hammarlund, M. Krishnaswamy, S. 2025-06-26 doi:10.1101/2025.06.22.660966 Cold Spring Harbor Laboratory Press 2025-06-26 <![CDATA[ Nutrient-Responsive Formation of Mitochondrial-Derived Structures in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2025.06.24.661357v1?rss=1 Valera-Alberni, M. Lanjuin, A. Romero-Sanz, S. Burkewitz, K. Hughes, A. Mair, W. B. 2025-06-26 doi:10.1101/2025.06.24.661357 Cold Spring Harbor Laboratory Press 2025-06-26 <![CDATA[ Temporal and cell-specific changes to cellular iron sequestration and lipid peroxidation in a murine model of neonatal hypoxic-ischemic brain injury. ]]> https://biorxiv.org/content/10.1101/2025.07.02.662653v1?rss=1 Vithayathil, J. Shankar, A. Milne, G. L. Jensen, F. E. Talos, D. M. Dunaief, J. L. 2025-07-03 doi:10.1101/2025.07.02.662653 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Detection of Region-specific Fiber Damage within Injured Spinal Cord Using Advanced Diffusion MRI ]]> https://biorxiv.org/content/10.1101/2025.07.02.662840v1?rss=1 ventral > lateral WM tracts) and along the dorsal column tract across segments (in an order of lesion center > rostral > caudal). Among the diffusion parameters, fractional anisotropy (FA), axonal volume fraction (Vax), radial diffusivity (RD), and extra axonal transverse diffusivity (Dex) showed most significant changes at and around the lesion site where severe tissue damage occurred. FA, Vax, and axial diffusivity (AD) exhibited marked changes in dorsal column proximal to the lesion center, where moderate axonal damage occurred. Additionally, AD and FA showed the greatest sensitivity (true positive rate) and specificity (true negative rate) to mild fiber disruption and demyelination in regions distal to the lesion. Overall, FA provided the highest sensitivity and specificity for detecting fiber degeneration and demyelination, while Vax demonstrated the strongest spatial correlation with histologic markers of regional fiber damage. The combination of DTI and SMT thus offers reliable biomarkers for assessing SCI. ]]> Wang, F. Xu, J. Wu, T.-L. Yang, P.-F. Chen, L. M. Gore, J. C. 2025-07-03 doi:10.1101/2025.07.02.662840 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Early Detection of Neuroinflammation and White Matter Damage Following Dorsal Spinal Nerve Root Sectioning in a Nonhuman Primate Model ]]> https://biorxiv.org/content/10.1101/2025.07.02.662878v1?rss=1 Wang, F. Gore, J. C. Chen, L. M. 2025-07-03 doi:10.1101/2025.07.02.662878 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ MarkerMatch: A Proximity-Based Probe-Matching Algorithm for Joint Analysis of Copy-Number Variants from Different Genotyping Arrays ]]> https://biorxiv.org/content/10.1101/2025.06.30.662249v1?rss=1 Ivankovic, F. Yu, D. Shen, J. Zhan, L. Niarchou, M. Kaylor, A. Domenech, L. Miller-Fleming, T. W. Porras, L. M. Giusti-Rodriguez, P. Ophoff, R. A. Scharf, J. M. Mathews, C. A. 2025-07-04 doi:10.1101/2025.06.30.662249 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Morning Elevation in Insulin Enhances Afternoon Postprandial Insulin Action and Glucose Effectiveness ]]> https://biorxiv.org/content/10.1101/2025.07.01.662587v1?rss=1 Waterman, H. L. Smith, M. Farmer, B. Yankey, K. Howard, T. Kraft, G. Cherrington, A. Edgerton, D. 2025-07-05 doi:10.1101/2025.07.01.662587 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ Endogenous glucocorticoids moderate the gastric inflammatory response to Helicobacter infection and protect from autoimmunity. ]]> https://biorxiv.org/content/10.1101/2025.07.03.662976v1?rss=1 Druffner, S. R. Duncan, B. C. Morris, M. T. Pascoe, J. L. Abner, T. M. Hussain, S. Piazuelo, M. B. Peek, R. M. Zhang, M. DiPaolo, R. J. Busada, J. T. 2025-07-06 doi:10.1101/2025.07.03.662976 Cold Spring Harbor Laboratory Press 2025-07-06 <![CDATA[ Cytoplasmic tail composition modulates the G protein and arrestin-3 signaling bias of the adhesion GPCR LPHN2 ]]> https://biorxiv.org/content/10.1101/2025.07.04.663222v1?rss=1 Garbett, K. Zheng, C. Drube, J. Hoffmann, C. Gurevich, V. Sando, R. 2025-07-06 doi:10.1101/2025.07.04.663222 Cold Spring Harbor Laboratory Press 2025-07-06 <![CDATA[ Decoding Lymphangioleiomyomatosis (LAM) Niche Environment via Integrative Analysis of Single Cell Multiomics and Spatial Transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.07.07.663390v1?rss=1 Chen, K. Zhao, S. Guo, M. Reza, H. Wagner, A. Cakar, A. C. Jiang, C. Zhang, E. Green, J. Martin, E. Wikenheiser-Brokamp, K. Perl, A.-K. T. Sinner, D. I. Yu, J. J. Xu, Y. 2025-07-10 doi:10.1101/2025.07.07.663390 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ Evaluation of natural killer cell tumor homing and effector function in response to CDK4/6 and AURKA inhibition in a melanoma tumor-on-a-chip platform ]]> https://biorxiv.org/content/10.1101/2025.07.09.662476v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@17bf445org.highwire.dtl.DTLVardef@e1e1d9org.highwire.dtl.DTLVardef@1b29c2corg.highwire.dtl.DTLVardef@12b1f03_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chakraborty, S. Durham, C. Bharti, V. Capece, M. Davies, A. Vilgelm, A. Skardal, A. 2025-07-11 doi:10.1101/2025.07.09.662476 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ KIASORT: Knowledge-Integrated Automated Spike Sorting for Geometry-Free Neuron Tracking ]]> https://biorxiv.org/content/10.1101/2025.07.10.664175v1?rss=1 Boroujeni, K. B. Womelsdorf, T. Kastner, S. 2025-07-16 doi:10.1101/2025.07.10.664175 Cold Spring Harbor Laboratory Press 2025-07-16 <![CDATA[ A versatile enzymatic pathway for modification of peptide C-termini ]]> https://biorxiv.org/content/10.1101/2025.07.11.664356v1?rss=1 Dommaraju, S. R. Kandy, S. K. Ren, H. Luciano, D. P. Fujiki, S. Sarlah, D. Zhao, H. Chekan, J. R. Mitchell, D. A. 2025-07-16 doi:10.1101/2025.07.11.664356 Cold Spring Harbor Laboratory Press 2025-07-16 <![CDATA[ Mouse Adapted Omicron BA.5 Induces A Fibrotic Lung Disease Phenotype in BALB/c Mice ]]> https://biorxiv.org/content/10.1101/2025.07.16.665104v1?rss=1 Powers, J. M. Leist, S. R. Suryadevara, N. Zost, S. Binshtein, E. Abdelgadir, A. Mallory, M. L. Edwards, C. E. Gully, K. L. Hubbard, M. L. Zweigart, M. R. Bailey, A. B. Sheahan, T. P. Crowe, J. E. Montgomery, S. A. Harkema, J. R. Baric, R. S. 2025-07-16 doi:10.1101/2025.07.16.665104 Cold Spring Harbor Laboratory Press 2025-07-16 <![CDATA[ Inflammaging in aged tissues drives remodeling of the CD8+ T cell compartment ]]> https://biorxiv.org/content/10.1101/2025.07.11.664388v1?rss=1 Shchukina, I. Rodriguez-Hernandez, C. Ruiz, H. S. Kleverov, M. Mintz, R. L. Mineura, K. Gunawardana, S. C. Hsiung, S. Vachova, V. Kossl, J. Vander Wielen, B. Mogilenko, D. A. Huckstep, C. G. Piston, D. W. Egawa, T. Kreisel, D. Randolph, G. J. Artyomov, M. N. 2025-07-17 doi:10.1101/2025.07.11.664388 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Spef1 is a microvillar component that limits apical actomyosin contractility and preserves intestinal barrier function ]]> https://biorxiv.org/content/10.1101/2025.07.17.665359v1?rss=1 Tapia Pastrana, R. Morales Obregon, E. A. Hecht, G. Tyska, M. J. 2025-07-17 doi:10.1101/2025.07.17.665359 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Age and early life adversity shape heterogeneity of the epigenome across tissues in macaques ]]> https://biorxiv.org/content/10.1101/2025.07.13.664445v1?rss=1 Sadoughi, B. Petersen, R. Patterson, S. K. Slikas, E. Adjandba, C. Ryan, N. Costa, C. E. Newman, L. E. Watowich, M. M. Kelsey, C. R. Greenier, A. Goldman, E. A. Negron-Del Valle, J. E. Phillips, D. Thompson, I. Surratt, S. E. B. Gonzalez, O. Compo, N. R. Burgos-Rodriguez, A. G. Cayo Biobank Research Unit, DeCasien, A. R. Chiou, K. L. Walker, C. S. Lambides, A. V. R. Martinez, M. I. Sterner, K. N. Brent, L. J. N. Higham, J. P. Montague, M. J. Platt, M. L. Snyder-Mackler, N. Lea, A. J. 2025-07-18 doi:10.1101/2025.07.13.664445 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Sustained Yap/Taz activation promotes aberrant alveolar epithelial cell differentiation and drives persistent fibrotic remodeling ]]> https://biorxiv.org/content/10.1101/2025.07.16.665213v1?rss=1 Gaona, I. P. McCall, A. S. Geis, N. M. Colvard, A. C. DiGiovanni, G. T. Sherrill, T. P. Singha, U. K. Nichols, D. S. Serezani, A. P. David, H. E. Cartailler, J.-P. Shrestha, S. Gutor, S. S. Blackwell, T. S. Kropski, J. A. Gokey, J. J. 2025-07-18 doi:10.1101/2025.07.16.665213 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Oncogenic H-Ras Reprograms Madin-Darby Canine Kidney (MDCK) Cell-derived Midbody Remnant Proteins Following Epithelial-Mesenchymal Transition ]]> https://biorxiv.org/content/10.1101/2025.07.17.665448v1?rss=1 Shafiq, A. Rai, A. Xu, R. Chen, M. Suwakulsiri, W. Greening, D. Simpson, R. 2025-07-21 doi:10.1101/2025.07.17.665448 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Sphingomyelinase Licensing of Mesenchymal Stromal Cells Alters Lipid and Protein Metabolites for Immunomodulation ]]> https://biorxiv.org/content/10.1101/2025.07.17.665406v1?rss=1 DeVeaux, S. A. Shah, D. C. Rui, K. Chiappa, N. F. Zhang, H. Lal, N. ONeill, R. Jang, Y. C. Mortensen, L. J. Roy, K. Botchwey, E. 2025-07-22 doi:10.1101/2025.07.17.665406 Cold Spring Harbor Laboratory Press 2025-07-22 <![CDATA[ Hippocampal input-driven plasticity of prefrontal interneurons reveals a circuit basis for impaired spatial working memory. ]]> https://biorxiv.org/content/10.1101/2025.07.21.665987v1?rss=1 View larger version (61K): org.highwire.dtl.DTLVardef@29a326org.highwire.dtl.DTLVardef@1964208org.highwire.dtl.DTLVardef@1c94e4corg.highwire.dtl.DTLVardef@1336edb_HPS_FORMAT_FIGEXP M_FIG C_FIG IN BRIEFSilverstein et al. investigated how ventral hippocampus (vHPC) inputs to medial prefrontal cortex (mPFC) interact with mPFC interneuron populations to support spatial working memory (SWM) in mice. They show that repeated vHPC input stimulation that reduces vHPC drive onto vasoactive intestinal peptide (VIP) interneurons also elevates delay-related VIP interneuron activity in early SWM task training, and this enhanced activity correlates with poorer training performance. Mice modelling the 22q11.2 deletion syndrome--known to have SWM learning deficits--recapitulate this altered VIP interneuron activity and show reduced vHPC input targeting of VIP interneurons. HIGHLIGHTSO_LIRepeated stimulation of vHPC inputs to mPFC persistently depresses VIP interneuron activity and enhances SST interneuron activity in mice C_LIO_LIBlunted monosynaptic drive onto mPFC VIP interneurons by repeated vHPC input stimulation plausibly reproduces in vivo activity changes C_LIO_LIStimulated mice show heightened VIP interneuron activity during the delay epoch in early SWM task training that correlates with poorer training performance C_LIO_LIMice modeling the 22q11.2 deletion syndrome with known SWM task learning deficits mirror this aberrant VIP interneuron activity profile and show reduced vHPC input targeting of VIP interneurons C_LI ]]> Silverstein, S. E. Clarity, T. T. Deshpande, M. S. Vaughan, E. Novik, S. Yarur, H. E. Zhang, S. Tsai, V. S. Ye, R. Mikofsky, R. M. Hsiang, M. Bauman, A. Loewinger, G. Pereira, F. Morales, M. Sohal, V. S. Tejeda, H. Gordon, J. A. Kupferschmidt, D. A. 2025-07-24 doi:10.1101/2025.07.21.665987 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ RAD52 and RPA act in a concert promoting inverse RNA strand exchange ]]> https://biorxiv.org/content/10.1101/2025.07.22.666130v1?rss=1 DiDomenico, S. F. Dinh, H. H. Rossi, M. J. Baudin, A. Sekhon, S. S. Chazin, W. J. Libich, D. S. Mazin, A. V. 2025-07-25 doi:10.1101/2025.07.22.666130 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ Volumetric Differences of Thalamic Nuclei are Associated with Post-Trauma Psychopathology ]]> https://biorxiv.org/content/10.1101/2025.07.24.666644v1?rss=1 Steele, N. Hussain, A. Baird, C. L. Haswell, C. C. Sun, D. Rangel-Jimenez, L. Abdallah, C. G. Angstadt, M. August, G. Berg, H. Blackford, J. U. Cisler, J. Daniels, J. K. Davenport, N. D. Davidson, R. J. Densmore, M. Disner, S. G. El-Hage, W. Etkin, A. Fani, N. Frijling, J. L. Gordon, E. M. Grupe, D. W. Herringa, R. J. Hudson, A. R. Jahanshad, N. Jovanovic, T. King, A. Koch, S. B. J. Lanius, R. Lazarov, A. Li, G. Liberzon, I. Lissek, S. Lu, G. M. Manthey, A. Maron-Katz, A. Nawijn, L. Nelson, S. M. Neria, Y. Neufeld, R. W. J. Nitschke, J. B. Olatunji, B. 2025-07-25 doi:10.1101/2025.07.24.666644 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ Bidirectional Crosstalk Between Sleep and Pulmonary Arterial Hypertension ]]> https://biorxiv.org/content/10.1101/2025.07.23.666314v1?rss=1 Imani, S. Halouani, A. Dahlka, J. Burgess, N. Antar, S. Zhao, Y. Chan, S. Y. West, J. D. Weston, M. Sassi, Y. 2025-07-27 doi:10.1101/2025.07.23.666314 Cold Spring Harbor Laboratory Press 2025-07-27 <![CDATA[ What is memorable across the Pacific Ocean shows evidence of prior learning on the memorability of new visual inputs ]]> https://biorxiv.org/content/10.1101/2025.07.23.666320v1?rss=1 Chen, H. Wang, B. Woodman, G. F. 2025-07-28 doi:10.1101/2025.07.23.666320 Cold Spring Harbor Laboratory Press 2025-07-28 <![CDATA[ Bacterial type II topoisomerases cleave DNA in a species-specific manner ]]> https://biorxiv.org/content/10.1101/2025.07.28.667256v1?rss=1 Morgan, I. L. Jian, J. Y. Osheroff, N. neuman, k. C. 2025-07-28 doi:10.1101/2025.07.28.667256 Cold Spring Harbor Laboratory Press 2025-07-28 <![CDATA[ Chronic semaglutide treatment reveals stage-dependent changes to feeding behavior and metabolic adaptations in male mice ]]> https://biorxiv.org/content/10.1101/2025.07.24.666640v1?rss=1 Shah, H. Ayala, J. E. 2025-07-30 doi:10.1101/2025.07.24.666640 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ ADCY3 Ser107Pro links difficulty awakening in the morning to adiposity through circadian regulation of adipose thermogenesis ]]> https://biorxiv.org/content/10.1101/2025.07.28.667339v1?rss=1 Tchio, C. Maher, M. Moth, C. Meiler, J. Lane, J. Taylor, H. Williams, J. Saxena, R. 2025-07-30 doi:10.1101/2025.07.28.667339 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ Recent lifestyle change impacts sleep and circadian rhythms among the Indigenous peoples of Peninsular Malaysia ]]> https://biorxiv.org/content/10.1101/2025.07.26.666903v1?rss=1 Reinhardt, K. D. Kraft, T. S. Lea, A. J. Wallace, I. J. Lim, Y. A. L. Nicholas, C. Huat, T. b. T. A. T. B. Tam, K. L. Chow, S. K. W. Sayed, I. b. M. Fadzil, K. S. Antle, M. C. Venkataraman, V. V. 2025-07-31 doi:10.1101/2025.07.26.666903 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Historical Contingency Limits Adaptive Diversification in a Spatially Structured Environment ]]> https://biorxiv.org/content/10.1101/2025.07.27.667043v1?rss=1 Patton, G. Meraz, J. C. Yin, M. Worthan, S. B. Williams, S. Behringer, M. G. 2025-07-31 doi:10.1101/2025.07.27.667043 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Distributed control circuits across a brain-and-cord connectome ]]> https://biorxiv.org/content/10.1101/2025.07.31.667571v1?rss=1 Bates, A. S. Phelps, J. S. Kim, M. Yang, H. H. Matsliah, A. Ajabi, Z. Perlman, E. Delgado, K. M. Osman, M. A. M. Salmon, C. K. Gager, J. Silverman, B. Renauld, S. Collie, M. F. Fan, J. Pacheco, D. A. Zhao, Y. Patel, J. Zhang, W. Serratosa Capdevilla, L. Roberts, R. J. Munnelly, E. J. Griggs, N. Langley, H. Moya-Llamas, B. Maloney, R. T. Yu, S.-c. Sterling, A. R. Sorek, M. Kruk, K. Serafetinidis, N. Dhawan, S. Stuerner, T. Klemm, F. Brooks, P. Lesser, E. Jones, J. M. Pierce-Lundgren, S. E. Lee, S.-Y. Luo, Y. Cook, A. P. McKim, T. H. Kophs, E. C. Falt, 2025-08-01 doi:10.1101/2025.07.31.667571 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Ubiquitous predictive processing in the spectral domain of sensory cortex ]]> https://biorxiv.org/content/10.1101/2025.07.31.667946v1?rss=1 Sennesh, E. Z. Westerberg, J. A. Spencer-Smith, J. Bastos, A. M. 2025-08-01 doi:10.1101/2025.07.31.667946 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Clostridioides difficile toxin A and toxin B inhibit toxin-specific adaptive immune responses through glucosyltransferase-dependent activity ]]> https://biorxiv.org/content/10.1101/2025.07.30.667646v1?rss=1 Maslanka, J. R. Londregan, J. Denny, J. E. Hulit, E. N. Mdluli, N. V. Peritore-Galve, F. C. Alam, M. Z. Alameh, M.-G. Lacy, B. Zackular, J. P. Abt, M. C. 2025-08-02 doi:10.1101/2025.07.30.667646 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Patient-derived Cellular Models of Polygenic Scores: Application to Long QT Syndrome ]]> https://biorxiv.org/content/10.1101/2025.08.05.667271v1?rss=1 Mitchell, D. O'Neill, M. Vanags, L. Patel, N. Strickland, T. Davogustto, G. Shoemaker, M. B. Salem, J.-E. Kroncke, B. M. 2025-08-07 doi:10.1101/2025.08.05.667271 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Conditional deletion of human STN1 leads to telomere dysfunction and telomerase-dependent genome instability and proliferation defects ]]> https://biorxiv.org/content/10.1101/2025.08.06.669015v1?rss=1 Holbrooks, J. S. Loveless, C. A. Reed, S. D. Duvall, G. H. Romney, C. V. Kircher, M. B. Stewart, J. A. 2025-08-07 doi:10.1101/2025.08.06.669015 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Dehydration promotes intracellular lipid synthesis and accumulation ]]> https://biorxiv.org/content/10.1101/2025.08.07.669190v1?rss=1 Carty, J. S. Selvasingh, J. Zuchowski, Y. Nam, H.-J. Penalva, C. Nanayakkara, G. Jennings, E. Q. Voss, K. Adame, E. T. Tossberg, J. Yap, W. S. Melzer, M. Viquez, O. McCall, A. S. Piotrowski, E. R. Bessho, R. Cao, S. Leaptrot, K. Schrimpe-Rutledge, A. C. Codreanu, S. G. Sherrod, S. D. McLean, J. A. Trapani, J. B. Cottam, M. A. Wan, M. Shrivastava, D. Delker, D. A. Wilson, M. H. Hassenour, C. M. Lantier, L. Chernova, I. Young, J. D. Haase, V. H. Medina, J.-P. V. Kosma, D. K. Kim, P. Cartailler, J. P. Zhang, M. Zent, R. Harris,, R. C. Watts, J. A. Terker, 2025-08-11 doi:10.1101/2025.08.07.669190 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ Generalized brain-state modeling with KenazLBM ]]> https://biorxiv.org/content/10.1101/2025.08.10.669538v1?rss=1 Johnson, G. W. Makhoul, G. Doss, D. Hidalgo, B. Cai, L. Liao, E. Paulo, D. Reda, A. Withers, C. P. Cavender, A. Qian, H. Obiri-Yeboah, D. Mensah-Brown, K. Kerezoudis, P. Baker, M. Jensen, M. Reddy, S. Roberson, S. W. Crudele, A. Naftel, R. Hermes, D. Hawkes, M. Kremen, V. Bydon, M. Ali, R. Lee, K. Lanzino, G. Bick, S. Van Gompel, J. Constantinidis, C. Morgan, V. Marsh, R. Zadeh, G. Worrell, G. Miller, K. Englot, D. 2025-08-12 doi:10.1101/2025.08.10.669538 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Proteostasis and Unfolded Protein Response Dynamics in Human Neuron and Mouse Glia Co-culture Reveal Cell-Specific Aging Responses ]]> https://biorxiv.org/content/10.1101/2025.08.11.669714v1?rss=1 Barny, L. A. Garcia, S. K. Houcek, A. J. Uzay, B. Kim, M. Kavalali, E. T. Plate, L. 2025-08-13 doi:10.1101/2025.08.11.669714 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ Unmasking Pathogen Traits for Chronic Colonization in Neurogenic Bladder Patients ]]> https://biorxiv.org/content/10.1101/2025.08.14.669717v1?rss=1 Reasoner, S. A. Frainey, B. T. Hale, O. F. Borden, A. Graham, M. K. Turner, E. Brenes, L. R. Soderstrom, C. B. Green, H. Schmitz, J. E. Laub, M. T. Kelly, M. S. Clayton, D. B. Hadjifrangiskou, M. 2025-08-14 doi:10.1101/2025.08.14.669717 Cold Spring Harbor Laboratory Press 2025-08-14 <![CDATA[ Cross-ancestry information transfer framework improves protein abundance prediction and protein-trait association identification ]]> https://biorxiv.org/content/10.1101/2025.08.13.670235v1?rss=1 Zhai, W. Sun, L. Fang, W. Dong, Y. Cheng, C. Liu, Y. Zhou, Y. Ji, J. Wu, L. Pan, A. Gamazon, E. R. Pan, X.-F. Zhou, D. 2025-08-16 doi:10.1101/2025.08.13.670235 Cold Spring Harbor Laboratory Press 2025-08-16 <![CDATA[ Structural rationalization of IPMK inhibitor potency. ]]> https://biorxiv.org/content/10.1101/2025.08.16.670669v1?rss=1 Wang, H. Shears, S. B. Blind, R. D. 2025-08-16 doi:10.1101/2025.08.16.670669 Cold Spring Harbor Laboratory Press 2025-08-16 <![CDATA[ Distinct Electrophysiological Signatures Define Neuronal Subtypes in the Fasciola Cinereum ]]> https://biorxiv.org/content/10.1101/2025.08.13.670170v1?rss=1 Incontro, S. Sandoval-Burnside, J. Guo, L. Clark, C. Dryden, M. Kazimuddin, S. Nguyen, Q.-A. 2025-08-18 doi:10.1101/2025.08.13.670170 Cold Spring Harbor Laboratory Press 2025-08-18 <![CDATA[ MDS-associated SF3B1 mutations promote aberrant fate choice of hematopoietic stem cell via mis-splicing of mediator kinase module component CDK8 ]]> https://biorxiv.org/content/10.1101/2025.08.14.670174v1?rss=1 Bonner, E. A. Hsueh, T.-Y. Song, A. Arriaga-Gomez, E. A. Venkataraman, R. Sinha, S. Nguyen, E. Ferrell, P. B. Welner, R. S. Lu, R. Stirewalt, D. L. Doulatov, S. Lee, S. C. 2025-08-19 doi:10.1101/2025.08.14.670174 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ TrueProbes: Quantitative Single-Molecule RNA-FISH Probe Design Improves RNA Detection ]]> https://biorxiv.org/content/10.1101/2025.08.14.670355v1?rss=1 Hughes, J. J. Kesler, B. K. Adams, J. E. Hospelhorn, B. G. Neuert, G. 2025-08-19 doi:10.1101/2025.08.14.670355 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ Imaging cellular activity simultaneously across all organs of a vertebrate reveals body-wide circuits ]]> https://biorxiv.org/content/10.1101/2025.08.20.670374v1?rss=1 Ruetten, V. M. Zheng, W. Siwanowicz, I. R. Mensh, B. D. Eddison, M. Hu, A. Chi, Y. Lemire, A. L. Guo, C. Kadobianskyi, M. Renz, M. Lelek-Greskovic, S. He, Y. Close, K. Ihrke, G. Dev, A. Petruncio, A. Wan, Y. Engert, F. Fishman, M. C. Judkewitz, B. Rubinov, M. Keller, P. J. Satou, C. Yu, G. Tillberg, P. W. Sahani, M. Ahrens, M. B. 2025-08-21 doi:10.1101/2025.08.20.670374 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Novel Roles of Sonic Hedgehog Signaling in Retinal Patterning and Neurogenesis During Mammalian Eye Development ]]> https://biorxiv.org/content/10.1101/2025.08.19.671114v1?rss=1 Krueger, M. R. Cheema, S. K. Simo, S. Levine, E. Brown, N. L. La Torre, A. 2025-08-22 doi:10.1101/2025.08.19.671114 Cold Spring Harbor Laboratory Press 2025-08-22 <![CDATA[ Co-evolved Partners of Immunity: A Trait-Based Map of Human Keystone Organisms ]]> https://biorxiv.org/content/10.1101/2025.08.19.671142v1?rss=1 Asiaee, A. Mallal, N. Phillips, E. Mallal, S. 2025-08-23 doi:10.1101/2025.08.19.671142 Cold Spring Harbor Laboratory Press 2025-08-23 <![CDATA[ Neuronal Decoding of Decisions in Multidimensional Feature Space Using a Gated Recurrent Variational Autoencoder ]]> https://biorxiv.org/content/10.1101/2025.08.20.671126v1?rss=1 Gerrity, C. G. Treuting, R. L. Peters, R. A. Womelsdorf, T. 2025-08-25 doi:10.1101/2025.08.20.671126 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ Exogenous Delivery of Sphingomyelinase Mediates Mesenchymal Stromal Cell-Extracellular Vesicle Biogenesis, Alters Cargo Sorting, and Therapeutic Potency in vitro ]]> https://biorxiv.org/content/10.1101/2025.08.21.671536v1?rss=1 Shah, D. C. DeVeaux, S. A. Zhang, H. Liu, A. Y. Adedipe, T. A. Chiappa, N. F. Patel, K. A. Jang, Y. C. Goudy, S. L. Sulchek, T. Roy, K. Botchwey, E. A. 2025-08-26 doi:10.1101/2025.08.21.671536 Cold Spring Harbor Laboratory Press 2025-08-26 <![CDATA[ Characterization of Distinct Monocyte Subtypes and Immune Features Associated with HIV, Tuberculosis, and Coronary Artery Disease in a Ugandan Cohort Using Mass Cytometry ]]> https://biorxiv.org/content/10.1101/2025.08.25.672210v1?rss=1 2), showed reduced surface expression of the anti-inflammatory scavenger receptor CD163 on non-classical monocytes. Notably, unsupervised clustering further revealed two distinct non-classical monocyte subsets associated with disease states: A CD86dim CX3CR1dim CD45RA+ GPR56+ CXCR3+ subset significantly depleted in individuals with CAD, and a CD86+ CX3CR1++ CD45RA++ GPR56- CD38- CXCR3- subset enriched in individuals with TB. These findings underscore the complexity of the monocyte landscape in CAD progression, particularly within settings of HIV and TB co-endemicity. We hope this work motivates further research and offers insights for the development of new precision biomarkers and immune-targeted therapies to prevent or treat CAD, TB, and HIV in populations. ]]> Reyes, J. C. Wanjalla, C. N. Feria, M. G. Simmons, J. Temu, T. Nochowicz, C. Arafat, S. Y. Kityo, C. Erem, G. Longenecker, C. T. Andorf, S. Huaman, M. A. 2025-08-27 doi:10.1101/2025.08.25.672210 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ An Efficient Lasso Framework for Admixture-Aware Polygenic Scores ]]> https://biorxiv.org/content/10.1101/2025.08.26.671106v1?rss=1 Ockerman, F. P. Chen, B. D. Sun, Q. Kharitonova, E. V. Chen, C. Zhou, L. Y. Loos, R. J. Kooperberg, C. Peters, U. Haessler, J. Reiner, A. P. Jung, S. Y. Manson, J. E. Nassir, R. North, K. E. Buyske, S. Haiman, C. A. Conti, D. V. Wilkens, L. R. Lange, E. M. Cox, N. J. Cao, H. Raffield, L. M. Li, Y. Tao, R. 2025-08-27 doi:10.1101/2025.08.26.671106 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Subtyping psychotic disorders using a data-driven approach reveals divergent cortical and cellular signatures ]]> https://biorxiv.org/content/10.1101/2025.08.26.672411v1?rss=1 Hill, L. D. Zhang, X.-H. Rogers, B. P. Huang, A. S. Fox, V. Feola, B. Heckers, S. Holmes, A. J. Woodward, N. D. 2025-08-27 doi:10.1101/2025.08.26.672411 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ BCL6 in T cells promotes type 1 diabetes by redirecting fates of insulin-autoreactive B lymphocytes ]]> https://biorxiv.org/content/10.1101/2025.08.25.671997v1?rss=1 View larger version (49K): org.highwire.dtl.DTLVardef@bf0daforg.highwire.dtl.DTLVardef@11b95fdorg.highwire.dtl.DTLVardef@141ccaorg.highwire.dtl.DTLVardef@6e4100_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Clark, L. M. McAninch, J. C. McNitt, D. H. Padgett, M. L. Jenkins, T. W. Bass, L. E. Nichols, C. M. Rathmell, J. C. Bonami, R. H. 2025-08-28 doi:10.1101/2025.08.25.671997 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ Modified tau leads to neuronal and global ribosome dysfunction in C. elegans model of tauopathy ]]> https://biorxiv.org/content/10.1101/2025.08.29.670302v1?rss=1 Ata, A. Somers, H. M. Lind, N. A. Fuqua, J. H. Rollins, J. A. 2025-08-30 doi:10.1101/2025.08.29.670302 Cold Spring Harbor Laboratory Press 2025-08-30 <![CDATA[ Evaluation of Deep Learning Algorithms to Predict Multiple Dementia-Related Neuropathologies from Brain MRI, Clinical and Genetic Data ]]> https://biorxiv.org/content/10.1101/2025.08.27.672683v1?rss=1 Chattopadhyay, T. Kush, R. Senthilkumar, P. Patterson, C. Owens-Walton, C. Gleave, E. J. Thomopoulos, S. I. Johnson, S. C. Mormino, E. C. Hohman, T. J. Thompson, P. M. 2025-09-01 doi:10.1101/2025.08.27.672683 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ Parallel Belief States account for Learning and Updating of Attentional Priorities in Multidimensional Environments ]]> https://biorxiv.org/content/10.1101/2025.09.03.674042v1?rss=1 Tiesinga, P. Womelsdorf, T. 2025-09-03 doi:10.1101/2025.09.03.674042 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Genetically-based sperm discrimination in the vaginal tract of a primate species ]]> https://biorxiv.org/content/10.1101/2025.08.29.672970v1?rss=1 Petersen, R. M. Nonnamaker, L. M. Anderson, J. A. Bergey, C. M. Roos, C. Melin, A. D. Higham, J. P. 2025-09-04 doi:10.1101/2025.08.29.672970 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Natural killer cell TGF- signaling regulates senolytic activity and vascular patterning in the postnatal lung ]]> https://biorxiv.org/content/10.1101/2025.08.29.673190v1?rss=1 Gainer, D. J. Coyle, K. M. Rätsep, M. T. Quilty, D. Tran, B. Skebo, S. I. VandenBroek, M. M. Laverty, K. J. Deng, Y. Shirazi, S. P. Brady, H. J. M. Sucre, J. M. S. Vivier, E. Shrestha, N. Wong, H. C. Stewart, D. J. Domnik, N. J. Ormiston, M. L. 2025-09-04 doi:10.1101/2025.08.29.673190 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ InsP3R signaling mediates mitochondrial stress-induced longevity through actomyosin-dependent mitochondrial dynamics ]]> https://biorxiv.org/content/10.1101/2025.08.30.673265v1?rss=1 Feng, G. Ruark, E. M. Mulligan, A. G. Donahue, E. K. F. Hoang, A. Jacquet-Cribe, B. Peng, L. Burkewitz, K. 2025-09-04 doi:10.1101/2025.08.30.673265 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Calorie Restriction modulates beta cell IP3R activity to regulate Ca2+ homeostasis and cell network connectivity ]]> https://biorxiv.org/content/10.1101/2025.09.01.673520v1?rss=1 Pfabe, J. dos Santos, C. Cutler, M. Acree, C. Habashy, A. Cambraia, A. Perkins, G. Ellisman, M. Slak Rupnik, M. Arrojo e Drigo, R. 2025-09-04 doi:10.1101/2025.09.01.673520 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Effects of combined prenatal exposure to air pollution and maternal stress on social behavior and oxytocin and vasopressin systems in male and female mice ]]> https://biorxiv.org/content/10.1101/2025.09.04.672354v1?rss=1 Stoehr, M. C. Martin, E. M. Babalola, J. T. Xue, J. Kern, M. J. Li, N. Y. Winters, M. F. Bhagwagar, S. Smith, C. J. 2025-09-04 doi:10.1101/2025.09.04.672354 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ NASP functions in the cytoplasm to prevent histone H3 aggregation during early embryogenesis ]]> https://biorxiv.org/content/10.1101/2025.09.03.673952v1?rss=1 Das, M. Coronado-Chavez, E. Bhatt, A. D. Tirgar, R. Amodeo, A. A. Nordman, J. 2025-09-06 doi:10.1101/2025.09.03.673952 Cold Spring Harbor Laboratory Press 2025-09-06 <![CDATA[ NERV: A Comprehensive Framework for Rapid, Reproducible, and Hardware-Synchronized Neuroscience Experiment Design and Execution ]]> https://biorxiv.org/content/10.1101/2025.09.04.674131v1?rss=1 Coutray, K. Constantinidis, C. 2025-09-08 doi:10.1101/2025.09.04.674131 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ peakScout - a user-friendly and reversible peak-to-gene translator for genomic peak calling results ]]> https://biorxiv.org/content/10.1101/2025.09.07.671934v1?rss=1 Lin, A. L. Cartailler, L. A. Cartailler, J.-P. 2025-09-08 doi:10.1101/2025.09.07.671934 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ An RNA regulates iron homeostasis and host mucus colonization in Bacteroides thetaiotaomicron ]]> https://biorxiv.org/content/10.1101/2025.09.08.672848v1?rss=1 Prezza, G. Fansler, R. T. Guest, T. Maedler, G. Schlauch, H. Zhu, W. Westermann, A. J. 2025-09-08 doi:10.1101/2025.09.08.672848 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ Loss of Regulator of telomere elongation helicase (Rtel1) impairs alveolar epithelial cell progenitor function but does not exacerbate experimental fibrosis ]]> https://biorxiv.org/content/10.1101/2025.09.04.674361v1?rss=1 Calvi, C. L. Winters, N. I. McCall, A. S. Fernandez, R. J. Kamga Gninzeko, F. J. Ding, H. Nichols, D. Polosukhin, V. V. Sucre, J. M. Gokey, J. J. Blackwell, T. S. Kropski, J. A. 2025-09-09 doi:10.1101/2025.09.04.674361 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ Identification of a broad and potent V3 glycan site bNAb targeting anN332gp120 glycan-independent epitope ]]> https://biorxiv.org/content/10.1101/2025.09.05.674437v1?rss=1 Gieselmann, L. DeLaitsch, A. T. Rohde, M. Radford, C. Worczinski, J. Momot, A. Ahmadov, E. Burger, J. A. Havenar-Daughton, C. Deshpande, S. Giovannoni, F. Corti, D. Kreer, C. Ercanoglu, M. S. Schommers, P. Georgiev, I. West, A. P. Knuefer, J. Stumpf, R. Kroidl, A. Geldmacher, C. Maganga, L. William, W. Ntinginya, N. E. Hoelscher, M. Yang, Z. Wei, Q. Renfrow, M. Green, T. J. Novak, J. van Gils, M. Gristick, H. B. Gruell, H. Bloom, J. D. Seaman, M. S. Bjorkman, P. Klein, F. 2025-09-10 doi:10.1101/2025.09.05.674437 Cold Spring Harbor Laboratory Press 2025-09-10 <![CDATA[ Intravital Two-Photon Imaging of Touch Sensory Axon Morphology in Mouse Skin ]]> https://biorxiv.org/content/10.1101/2025.09.08.674093v1?rss=1 Kong, S. Barnes, E. Chelliah, G. Meltzer, S. 2025-09-11 doi:10.1101/2025.09.08.674093 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Early life adversity shapes life history trade-offs between growth and reproduction in free-ranging rhesus macaques ]]> https://biorxiv.org/content/10.1101/2025.09.11.675677v1?rss=1 Petersen, R. M. Patterson, S. K. Widdig, A. Turcotte, C. M. Anton, S. C. Williams, S. A. Romero, A. N. Bauman Surratt, S. E. Ruiz Lambides, A. V. The Cayo Biobank Research Unit, Snyder-Mackler, N. Brent, L. J. N. Higham, J. P. Lea, A. J. 2025-09-12 doi:10.1101/2025.09.11.675677 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ Trsp is required by regulatory T cells to prevent lethal autoimmunity in mice ]]> https://biorxiv.org/content/10.1101/2025.09.09.675163v1?rss=1 Jacobse, J. Pilat, J. M. Harris, A. B. Kwag, A. Aziz, Z. Chi, C. Schaefer, S. Neely, M. D. Buendia, M. A. Pahnke, A. Williams, C. S. Deng, W. Washington, M. K. Rathmell, J. Flynn, C. R. Rings, E. H. Short, S. P. Prabhu, K. S. Samsom, J. N. Goettel, J. A. Choksi, Y. A. 2025-09-15 doi:10.1101/2025.09.09.675163 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ Exploring metalloproteome remodeling in calprotectin-stressed Acinetobacter baumannii using chemoproteomics ]]> https://biorxiv.org/content/10.1101/2025.09.16.676631v1?rss=1 Osterberg, M. Bak, D. W. Andreini, C. Critchlow, J. M. Trinidad, J. C. Cornish, P. Akizuki, T. Chazin, W. J. Skaar, E. P. Weerapana, E. Giedroc, D. P. 2025-09-16 doi:10.1101/2025.09.16.676631 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Integrative Spatial Omics for Systems-Level Mapping of Pathological Niches ]]> https://biorxiv.org/content/10.1101/2025.09.12.675904v1?rss=1 Kruse, A. R. S. Lardenoije, R. Migas, L. G. Scott, C. F. Marshall, C. Malek, M. C. Eskaros, A. Pham, T. Aamodt, K. Colley, M. Ventura-Antunes, L. Farrow, M. A. Van de Plas, R. Goncalves, J. Schrag, M. Powers, A. C. Spraggins, J. M. 2025-09-17 doi:10.1101/2025.09.12.675904 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ A role of extracellular vesicle-mediated inter-organ communication in obesity-related arrhythmia ]]> https://biorxiv.org/content/10.1101/2025.09.13.676027v1?rss=1 View larger version (74K): org.highwire.dtl.DTLVardef@114b230org.highwire.dtl.DTLVardef@1be7926org.highwire.dtl.DTLVardef@3d6b0org.highwire.dtl.DTLVardef@3ef15_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Limpitikul, W. B. Garcia-Contreras, M. Betti, M. J. Spangler, P. Sheng, Q. B. Pabel, S. Sossalla, S. Xiao, L. Chatterjee, E. Ellinor, P. T. Gamazon, E. R. Shah, R. Das, S. 2025-09-17 doi:10.1101/2025.09.13.676027 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Microwear variability in a spatially and temporally constrained elephant population: Implications for interpreting the diets of extant and extinct proboscideans ]]> https://biorxiv.org/content/10.1101/2025.09.14.676112v1?rss=1 Barrett, C. A. Pardi, M. DeSantis, L. R. G. 2025-09-17 doi:10.1101/2025.09.14.676112 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Social observation influences the trajectory of performance monitoring across trials: evidence from single-trial estimates of the ERN and CRN ]]> https://biorxiv.org/content/10.1101/2025.09.16.676498v1?rss=1 Niu, Y. Hosseini, K. Pena, A. Rodriguez, C. Buzzell, G. A. 2025-09-17 doi:10.1101/2025.09.16.676498 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Role of Speed Regulation and Speed Modulation in Velocity-Field Based Control ]]> https://biorxiv.org/content/10.1101/2025.09.15.676406v1?rss=1 Nasiri, R. Tang, L. Goldfarb, M. Arami, A. 2025-09-18 doi:10.1101/2025.09.15.676406 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Infants who develop BPD have an airway endotype defined by vimentin expression and ciliary loss ]]> https://biorxiv.org/content/10.1101/2025.09.16.676660v1?rss=1 Eldredge, L. C. Han, Y. Deutsch, G. H. Sucre, J. M. S. Shirazi, S. P. Stefani, C. Pribitzer, S. Reeves, S. R. Rich, L. M. Vanderwall, E. R. Ziegler, S. F. Debley, J. S. 2025-09-18 doi:10.1101/2025.09.16.676660 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Two Distinct Attentional Priorities Guide Exploratory and Exploitative Gaze in Parallel ]]> https://biorxiv.org/content/10.1101/2025.09.20.677503v1?rss=1 Wen, X. Hassani, A. S. Neumann, A. Tiesinga, P. Womelsdorf, T. 2025-09-20 doi:10.1101/2025.09.20.677503 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Kidney kallikrein-1 contributes to cleavage of gamma-ENaC in vivo ]]> https://biorxiv.org/content/10.1101/2025.09.19.677394v1?rss=1 Curry, J. N. Su, X.-T. Wu, Q. Maeoka, Y. Yang, C.-L. Delpire, E. Fenton, R. F. Welling, P. A. Ellison, D. H. 2025-09-21 doi:10.1101/2025.09.19.677394 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Designing smart spatial omics experiments with S2Omics ]]> https://biorxiv.org/content/10.1101/2025.09.21.677634v1?rss=1 Yuan, M. Jin, K. Yan, H. Schroeder, A. Luo, C. Yao, S. Dumoulin, B. Levinsohn, J. Luo, T. Clemenceau, J. Jang, I. Kim, M. Liu, Y. Deng, M. Furth, E. E. Wilson, P. Nayak, A. Lubo, I. Soto, L. M. S. Wang, L. Park, J. H. Susztak, K. Hwang, T. H. Li, M. 2025-09-21 doi:10.1101/2025.09.21.677634 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Alpha Parvin Promotes Glucose Uptake and Metabolism in Skeletal Muscle with Minimal Influence on Hepatic Insulin Sensitivity ]]> https://biorxiv.org/content/10.1101/2025.09.22.676818v1?rss=1 Bock, F. Cappel, D. A. Dong, X. Deaver, J. W. Lark, D. Cozzani, L. Bracy, D. Lantier, L. Ghoshal, K. Do, A. Printz, R. McGuinness, O. P. Wasserman, D. H. Pozzi, A. Zent, R. Winn, N. C. 2025-09-23 doi:10.1101/2025.09.22.676818 Cold Spring Harbor Laboratory Press 2025-09-23 <![CDATA[ Multi-omic screening identifies RBMXL3 as a primate-specific RNA-binding protein and candidate regulator of RNA metabolism in human spermatogenesis ]]> https://biorxiv.org/content/10.1101/2025.09.23.677621v1?rss=1 Barszcz, A. Tutak, K. Zyprych-Walczak, J. Dassi, E. Ilaslan, E. Dabrowska, M. Malcher, A. Olszewska, M. Cysewski, D. Nadel, A. Kolanowski, T. Madeja, Z. E. Hrab, M. Yatsenko, A. Kurpisz, M. Warkocki, Z. Rozwadowska, N. 2025-09-23 doi:10.1101/2025.09.23.677621 Cold Spring Harbor Laboratory Press 2025-09-23 <![CDATA[ Inferring Dynamic Information from Protein Structures by Gaussian Integrals and Deep Learning ]]> https://biorxiv.org/content/10.1101/2025.09.22.677755v1?rss=1 Vilicich, F. Yin, S. Su, Z. Wu, Y. 2025-09-24 doi:10.1101/2025.09.22.677755 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ Staphylococcus aureus inhibits the NLRP3 inflammasome in macrophages during the early phases of intracellular infection, but not the late phases ]]> https://biorxiv.org/content/10.1101/2025.09.24.678325v1?rss=1 Bhagat, S. Kaur, K. O'Connor, L. Wang, C. Li, Y. Swarnkar, G. Khanna, K. Cassat, J. E. Veis, D. Mbalaviele, G. 2025-09-26 doi:10.1101/2025.09.24.678325 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ Nanopore-based sequencing of active DNA replication reveals key principles of metazoan replication fork progression, origin and termination sites ]]> https://biorxiv.org/content/10.1101/2025.09.26.678856v1?rss=1 Han, D. Shepherd, C. Benton, M. L. Nordman, J. T. 2025-09-27 doi:10.1101/2025.09.26.678856 Cold Spring Harbor Laboratory Press 2025-09-27 <![CDATA[ Beta bursts mediate amygdala gating of hippocampal emotional encoding ]]> https://biorxiv.org/content/10.1101/2025.09.26.678792v1?rss=1 Zhou, Y. Huang, Y. Pittaro, G. Zareian, B. Aljishi, A. Toro, A. Zibly, Z. Obaid, S. Sivaraju, A. Harpaz-Rotem, I. Kaye, A. P. Krystal, J. Sheth, K. Gu, X. Pittenger, C. Damisah, E. 2025-09-28 doi:10.1101/2025.09.26.678792 Cold Spring Harbor Laboratory Press 2025-09-28 <![CDATA[ Multi-omics integration at cell type resolution uncovers gene-metabolite mechanisms underlying osteoarthritis heterogeneity ]]> https://biorxiv.org/content/10.1101/2025.09.26.678886v1?rss=1 Ojha, A. Chatterjee, P. Kippner, L. E. Stevens, H. Y. Yeago, C. Drissi, H. Mautner, K. Boden, S. Roy, K. Sinha, S. 2025-09-29 doi:10.1101/2025.09.26.678886 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ MDR1 promotes CD8 T cell persistence in tumors and protects against cytotoxic chemotherapy ]]> https://biorxiv.org/content/10.1101/2025.09.28.679049v1?rss=1 Brown, L. A. Erwin, M. M. Favret, N. R. McDavid, C. N. Roetman, J. J. Ewell, Z. D. Wolf, M. M. Murray, K. A. Smithwick, J. E. Goemann, M. A. Philip, M. 2025-09-30 doi:10.1101/2025.09.28.679049 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ Lifespan Trajectories of Asymmetry in White Matter Tracts ]]> https://biorxiv.org/content/10.1101/2025.09.29.678806v1?rss=1 Kanakaraj, P. Bogdanov, S. Kim, M. E. Samir, J. Gao, C. Ramadass, K. E. Rudravaram, G. Newlin, N. R. Archer, D. B. Hohman, T. J. Jefferson, A. L. Morgan, V. L. Roche, A. Englot, D. J. Resnick, S. M. Held, L. L. B. Cutting, L. Barquero, L. A. D'Archangel, M. A. Nguyen, T. Q. Humphreys, K. L. Niu, Y. Vinci-Booher, S. Cascio, C. J. The HABS-HD Study Team, Alzheimer's Disease Neuroimaging Initiative, The BIOCARD Study Team, Li, Z. Vandekar, S. Zhang, P. Gore, J. C. Forkel, S. J. Landman, B. A. Schilling, K. 2025-09-30 doi:10.1101/2025.09.29.678806 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ Effects of combined prenatal exposure to air pollution and maternal stress on immune and dopaminergic gene expression in the gut-brain axis ]]> https://biorxiv.org/content/10.1101/2025.09.30.678116v1?rss=1 Martin, E. M. Morales, M. J. Li, N. Y. Stoehr, M. C. Kern, M. J. Winters, M. F. Smith, C. J. 2025-10-01 doi:10.1101/2025.09.30.678116 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Structural basis for fork reversal and RAD51 regulation by the SCF ubiquitin ligase complex of F-box helicase 1 ]]> https://biorxiv.org/content/10.1101/2025.09.30.679681v1?rss=1 Greer, B. H. Mendia-Garcia, J. Mullins, E. A. Peacock, E. M. Haigh, S. K. Aicart-Ramos, C. Schiltz, C. Tsai, M.-S. Cortez, D. Moreno Herrero, F. Eichman, B. 2025-10-01 doi:10.1101/2025.09.30.679681 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Gut microbiota as a modulator of circadian neural development in the honey bee model. ]]> https://biorxiv.org/content/10.1101/2025.09.30.678393v1?rss=1 KORU, Y. B. Beer, K. Ruggieri, A. A. Rodriguez-Cordero, J. A. Aviles-Rios, E. Anderson, M. Citron-Rodriguez, E. A. Montes-Mercado, A. De Jesus-Cortes, H. Giannoni-Guzman, M. A. Perez Claudio, E. Courtney, E. C. Andujar-Sierra, C. L. Strubbe-Nieves, A. Ortiz-Alvarado, Y. Doke, M. A. Ortiz-Zuazaga, H. Moore, D. Giordano, R. Ghezzi, A. Scheiner, R. Giray, T. Agosto-Rivera, J. L. 2025-10-02 doi:10.1101/2025.09.30.678393 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ AlveolEye: Rapid and precise lung morphometry guided by computer vision ]]> https://biorxiv.org/content/10.1101/2025.09.30.679300v1?rss=1 Hirsh, J. Hirsh, S. Shirazi, S. P. Hirsh, J. Douglas, I. Garg, S. Son, Y. Pierre-Louis, A. Bunn, C. Jetter, C. S. James, T. J. Sharkey, A. L. Benjamin, J. T. Kropski, J. A. Sucre, J. M. S. Negretti, N. M. 2025-10-02 doi:10.1101/2025.09.30.679300 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Machine-Learning-Guided Video Analysis Identifies Sound-Evoked Pain Behaviors from Facial Grimace and Body Cues in Mice ]]> https://biorxiv.org/content/10.1101/2025.09.30.679579v1?rss=1 Seicol, B. J. Valles, A. Kohler, A. Glowatzki, E. Wood, M. B. 2025-10-02 doi:10.1101/2025.09.30.679579 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Convergent evolution of aerobic fermentation through divergent mechanisms acting on key shared glycolytic genes ]]> https://biorxiv.org/content/10.1101/2025.10.02.679963v1?rss=1 Horianopoulos, L. Rokas, A. Hittinger, C. 2025-10-02 doi:10.1101/2025.10.02.679963 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ A regulatory region that controls Wnt gene expression following tissue injury is required for proper muscle regeneration ]]> https://biorxiv.org/content/10.1101/2025.10.01.679323v1?rss=1 Logan, C. Y. Lim, X. Fish, M. Mizutani, M. Swain, B. Nusse, R. 2025-10-03 doi:10.1101/2025.10.01.679323 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Cell cycle-regulated tug-of-war between microtubule motors positions major trafficking organelles ]]> https://biorxiv.org/content/10.1101/2025.10.01.679872v1?rss=1 Sawant, A. V. Kaverina, I. 2025-10-03 doi:10.1101/2025.10.01.679872 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Catch and release of sialoglycoRNAs enables sequencing-based profiling across cellular and extracellular material ]]> https://biorxiv.org/content/10.1101/2025.10.04.680438v1?rss=1 Flynn, R. A. Ge, R. Rai, S. K. Coffey, R. J. A. Jeppesen, D. K. Zhang, Q. Higginbotham, J. N. 2025-10-05 doi:10.1101/2025.10.04.680438 Cold Spring Harbor Laboratory Press 2025-10-05 <![CDATA[ Archetype analysis of lung adenocarcinoma premalignancy links heterogeneity in premalignant lesions to diverging features of invasive disease ]]> https://biorxiv.org/content/10.1101/2025.10.04.680402v1?rss=1 Anderson, K. E. Tran, L. M. Krysan, K. Kefella, Y. Yu, L. Fishbein, G. A. Rodriguez, E. M. Shabihkhani, M. Stefanko, D. P. Green, E. Liu, G. Liu, H. Zhang, S. Kane, E. E. Mehrad, M. Spira, A. E. Dubinett, S. M. Burks, E. J. Mazzilli, S. A. Lenburg, M. E. Beane, J. E. 2025-10-06 doi:10.1101/2025.10.04.680402 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ V1 interlaminar coherence decreases with interocular conflict ]]> https://biorxiv.org/content/10.1101/2025.10.04.680461v1?rss=1 Carlson, B. M. Mitchell, B. A. Westerberg, J. A. Poggi, P. G. Woodman, G. Maier, A. 2025-10-06 doi:10.1101/2025.10.04.680461 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Pre-division TCF1 drop determines long-term CD8 T cell fates ]]> https://biorxiv.org/content/10.1101/2025.10.06.680655v1?rss=1 Favret, N. R. Astorkia, M. Wolf, M. M. Rudloff, M. W. McDavid, C. N. Erwin, M. M. Murray, K. A. Roetman, J. J. Detres-Roman, C. R. Ewell, Z. D. Brown, L. A. Murray, W. T. Zumbo, P. Betel, D. Philip, M. 2025-10-06 doi:10.1101/2025.10.06.680655 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Isolation and genomic analysis of secondary metabolism in cave Actinomycetota ]]> https://biorxiv.org/content/10.1101/2025.10.06.680698v1?rss=1 Bachmann, I. O. Bachmann, B. O. 2025-10-07 doi:10.1101/2025.10.06.680698 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ A TLR7/9-IFNα-LDHB axis drives vital NET release and compromises antibacterial defense. ]]> https://biorxiv.org/content/10.1101/2025.10.07.680928v1?rss=1 TenBarge, E. G. Wise, A. D. Hetzel, M. L. Hoover, H. A. Esfandiari, H. Holder, B. E. Belevska, E. Mennen, E. C. McDaniel, S. R. Vaccaro, N. M. Lucca, C. C. Williams, J. M. Ferris, J. Sparer, T. E. Crofford, L. J. Bieber, J. D. Monteith, A. J. 2025-10-07 doi:10.1101/2025.10.07.680928 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Engineering substrate selectivity in the human sodium/iodide symporter (NIS) ]]> https://biorxiv.org/content/10.1101/2025.10.07.681042v1?rss=1 Llorente-Esteban, A. Sabbineni, H. Hoffsmith, K. Manville, R. W. Lopez-Gonzalez, D. Reyna-Neyra, A. Leyva, A. Abbott, G. W. Bianchet, M. A. Carrasco, N. 2025-10-08 doi:10.1101/2025.10.07.681042 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Home range is not constrained by number of hippocampal neurons across mammals ]]> https://biorxiv.org/content/10.1101/2025.10.08.681184v1?rss=1 Elbon, M. Casalino, G. Herculano-Houzel, S. 2025-10-09 doi:10.1101/2025.10.08.681184 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ Asynchronous firing and off-states in working memory maintenance ]]> https://biorxiv.org/content/10.1101/2025.10.12.681904v1?rss=1 Mozumder, R. Wang, Z. Dang, W. Zhu, J. Hammond, B. Machado, A. Constantinidis, C. 2025-10-13 doi:10.1101/2025.10.12.681904 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ High Throughput Screening Identifies a Small Molecule Trafficking Corrector for Long-QT Syndrome Associated KCNQ1 Variants ]]> https://biorxiv.org/content/10.1101/2025.10.13.682066v1?rss=1 Clowes Moster, K. R. Vanoye, C. G. Chang-Gonzalez, A. C. Romaine, I. M. Stefanski, K. M. Wilkinson, M. C. Bauer, J. A. Hasaka, T. P. Days, E. L. Desai, R. Butcher, K. R. Sulikowksi, G. A. Waterson, A. G. Meiler, J. Ledwitch, K. George, A. L. Sanders, C. R. 2025-10-14 doi:10.1101/2025.10.13.682066 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Computer Vision Methods for Spatial Transcriptomics: A Survey ]]> https://biorxiv.org/content/10.1101/2025.10.13.682148v1?rss=1 Zhu, J. Deng, R. Guo, J. Yao, T. Lu, S. Qu, C. Xiong, J. Zhu, Y. Lu, Z. Yang, Y. Lionts, M. Tang, Y. Xu, D. Wang, Y. Zhao, S. Yang, H. Huo, Y. 2025-10-14 doi:10.1101/2025.10.13.682148 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Ampyrone (4-Aminoantipyrine) is a Direct Agonist of Human Tyrosinase and Potential Therapeutic for Oculocutaneous Albinism and Disorders of Hypopigmentation. ]]> https://biorxiv.org/content/10.1101/2025.10.13.682036v1?rss=1 Dolinska, M. Wang, Y. Coussens, N. Kalaskar, V. Eraslan, Z. Grondin, S. Bonica, J. Toay, S. Hall, M. Shen, M. Boxer, M. Chen, Q. Gross, S. Attarwala, N. Jittayasothorn, Y. Alur, R. Shukla, D. Kee, R. Deyoung, C. Sha, C. Adams, D. Loftus, S. K. Cogliati, T. Sergeev, Y. V. Zippin, J. H. Brooks, B. 2025-10-15 doi:10.1101/2025.10.13.682036 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ A Yeast-Based High-Throughput Screening Platform for the Discovery of Novel pre-mRNA Splicing Modulators ]]> https://biorxiv.org/content/10.1101/2025.10.20.683303v1?rss=1 Love, S. L. Vollmer, H. Chang, Y.-C. Carrocci, T. J. Paulson, J. Jurica, M. S. Nguyen, H. D. Hoskins, A. 2025-10-20 doi:10.1101/2025.10.20.683303 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Sensory Neural Noise as a Limiting Factor in Visual Working Memory Precision in Neurotypicals and Schizophrenia ]]> https://biorxiv.org/content/10.1101/2025.10.20.683426v1?rss=1 Park, W. J. Ichinose, M. Hu, G. Woodman, G. F. Tadin, D. Park, S. 2025-10-20 doi:10.1101/2025.10.20.683426 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Interactomics of SARS-CoV-2 Macrodomain 1 Reveals Putative Clients of ADP-ribosyl Hydrolase Activity ]]> https://biorxiv.org/content/10.1101/2025.10.21.683784v1?rss=1 Cameron, C. D. Heilmann, G. Plate, L. 2025-10-21 doi:10.1101/2025.10.21.683784 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Bridging Histology and Tractography: First Visualization of the Short-Range Prefrontal Connections in the Human Brain ]]> https://biorxiv.org/content/10.1101/2025.10.22.683760v1?rss=1 80%) and accuracy (>70%) relative to histological findings. The resulting tracts not only captured broad organizational principles but also replicated fine-grained patterns previously only seen in invasive studies. Furthermore, these connections showed high test-retest reliability within individuals alongside significant variability between them, highlighting a stable yet unique anatomical fingerprint. Ultimately, this study shows how linking histology to tractography provides a powerful framework to advance our understanding of the human connectome and opens avenues to investigate local circuitry that underpins cognition and disease. ]]> Amandola, M. Kim, M. E. Rheault, F. Landman, B. A. Schilling, K. 2025-10-23 doi:10.1101/2025.10.22.683760 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Reovirus recombination is highly selective, and its profiles are primarily dictated by viral gene segment identity ]]> https://biorxiv.org/content/10.1101/2025.10.23.684199v1?rss=1 Flores, A. Routh, A. Xavier, R. Ogden, K. M. 2025-10-23 doi:10.1101/2025.10.23.684199 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ A toolbox for navigating and analyzing the spatiotemporal properties of retinal waves ]]> https://biorxiv.org/content/10.1101/2025.10.23.684204v1?rss=1 Yeager, K. M. Gupta, R. K. Gauthier, E. A. Fisch, A. J. Clark, N. A. Orsi, F. S. Tiriac, A. 2025-10-24 doi:10.1101/2025.10.23.684204 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ Encoded cell-material interactions to reroute cytokine signaling for regenerative medicine ]]> https://biorxiv.org/content/10.1101/2025.10.24.684449v1?rss=1 Eidman, Z. M. Sharma, J. Lee, J. C. Schulze, N. F. Brien, H. J. Corn, K. C. Rafat, M. Brunger, J. M. 2025-10-25 doi:10.1101/2025.10.24.684449 Cold Spring Harbor Laboratory Press 2025-10-25 <![CDATA[ Warmer temperature accelerates senescence by modifying the aging-dependent changes in the mosquito transcriptome, altering immunity, metabolism, and DNA repair ]]> https://biorxiv.org/content/10.1101/2025.10.27.684792v1?rss=1 Martin, L. E. Barr, J. S. Cartailler, J.-P. Shrestha, S. Estevez-Lao, T. Y. Hillyer, J. F. 2025-10-27 doi:10.1101/2025.10.27.684792 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ CRISPR-engineered deletion of POGZ alters transcription factor binding at promoters of genes involved in synaptic signaling ]]> https://biorxiv.org/content/10.1101/2025.10.27.684870v1?rss=1 Oliveira, M. M. Liu, Y. Erdin, S. Gao, D. Bhavsar, R. Mohajeri, K. O'Keefe, K. Boone, P. M. Xavier, G. Liao, C. Li, A. Yadav, R. Salani, M. Lucente, D. Currall, B. de Esch, C. E. F. Tai, D. J. C. Ruderfer, D. Brennand, K. J. Gusella, J. F. Talkowski, M. E. 2025-10-27 doi:10.1101/2025.10.27.684870 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Spatial Dependence and Heterogeneity in Molecular Imaging: Moran Quadrant Maps Enable Advanced Spatial-Statistical Analysis ]]> https://biorxiv.org/content/10.1101/2025.10.27.684518v1?rss=1 Tideman, L. E. M. Moser, F. A. Migas, L. G. Spathies, J. Djambazova, K. V. Marshall, C. R. Schrag, M. S. Skaar, E. P. Spraggins, J. M. Van de Plas, R. 2025-10-28 doi:10.1101/2025.10.27.684518 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ Inflammatory Biomarkers of Asymptomatic and Symptomatic Tuberculosis ]]> https://biorxiv.org/content/10.1101/2025.10.26.684319v1?rss=1 Awany, D. Ariefdien, D. Mendelsohn, S. Rozot, V. Mulenga, H. Nyangu, S. Tameris, M. Moloantoa, T. Katona, A. Maruri, F. Noor, F. Panchiar, R. Hlongwane, K. Stanley, K. Van der Heijden, Y. Hadley, K. Fiore-Gartland, A. Innes, C. Brumskine, W. Dheda, K. Jaumdally, S. Perumal, T. Martinson, N. Leslie, A. Fourie, B. Hiemstra, A. Malherbe, S. Walzl, G. Naidoo, K. Churchyard, G. Chegou, N. Sterling, T. Hatherill, M. Scriba, T. J. 2025-10-29 doi:10.1101/2025.10.26.684319 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ A trait syndrome ties cell morphology to glycolysis across the yeast subphylum ]]> https://biorxiv.org/content/10.1101/2025.10.27.684252v1?rss=1 Horianopoulos, L. C. Chavez, C. M. Rokas, A. Hittinger, C. T. 2025-10-30 doi:10.1101/2025.10.27.684252 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Unmixing of Imaging Mass Spectrometry Measurements Using Microscopy-Informed Constraints ]]> https://biorxiv.org/content/10.1101/2025.10.29.685281v1?rss=1 Moens, R. A. R. Patterson, N. H. Migas, L. G. Esselman, A. B. Moser, F. Spraggins, J. M. Van de Plas, R. 2025-10-30 doi:10.1101/2025.10.29.685281 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Structure-based Predictions of Conformational B Cell Epitopes by Protein Language Model and Deep Learning ]]> https://biorxiv.org/content/10.1101/2025.10.29.685313v1?rss=1 Zhang, Y. Vilicich, F. Kuang, X. Liu, Y. Zhang, G. Su, Z. Wu, Y. 2025-10-30 doi:10.1101/2025.10.29.685313 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Wnt5a-mediated Adipo-Cardiac Interorgan Communication in HFpEF ]]> https://biorxiv.org/content/10.1101/2025.10.29.685456v1?rss=1 Fatima, A. Abusharkh, F. Zanetta, Z. Gardner, S. L. Shi, F. Kobeck, E. Fortune, N. Subati, T. Bachmann, K. N. Brown, J. D. Gupta, D. K. Armstrong, D. Wassenaar, J. W. West, J. Brittain, E. Collins, S. Hemnes, A. R. Agrawal, V. 2025-10-30 doi:10.1101/2025.10.29.685456 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ A spatiotemporal analysis of the effect of urbanization on birdsong ]]> https://biorxiv.org/content/10.1101/2025.10.30.685579v1?rss=1 Creanza, N. Hourihan, S. 2025-10-31 doi:10.1101/2025.10.30.685579 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Reciprocal regulation of the H3 histamine receptor in Rett syndrome and MECP2 Duplication 1 syndrome: implications for therapeutic development ]]> https://biorxiv.org/content/10.1101/2025.10.30.685636v1?rss=1 Weiss, K. Vermudez, S. A. D. Freitas, G. A. Dogra, S. Meadows, M. J. Gogliotti, R. G. Niswender, C. M. 2025-10-31 doi:10.1101/2025.10.30.685636 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Combinatorial multiomic analysis from a pedigree of Sox10Dom Hirschsprung mice implicates Dach1 as a modifier of Enteric Nervous System development ]]> https://biorxiv.org/content/10.1101/2025.11.02.686123v1?rss=1 Benthal, J. T. Avila, J. A. Smith, J. R. Southard-Smith, E. M. 2025-11-04 doi:10.1101/2025.11.02.686123 Cold Spring Harbor Laboratory Press 2025-11-04 <![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[ Distinct patterns of de novo coding variants contribute to Tourette Syndrome etiology ]]> https://biorxiv.org/content/10.1101/2025.11.04.686570v1?rss=1 Zhan, L. Yu, D. Ivankovic, F. Niarchou, M. Domenech-Salgado, L. Barr, C. L. Benarroch, F. Budman, C. L. Cath, D. C. Freimer, N. B. Garrido, H. Grados, M. A. Gross-Tsur, V. Herrera-Amighetti, L. King, R. A. Kurlan, R. Leckman, J. F. Lyon, G. J. McMahon, W. M. Pauls, D. L. Pollak, Y. Robertson, M. M. Romero, R. Rouleau, G. A. Sandor, P. Singer, H. S. Giusti-Rodriguez, P. Davis, L. K. Mathews, C. A. Scharf, J. M. Ophoff, R. A. 2025-11-05 doi:10.1101/2025.11.04.686570 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ BASSL-MI: Batch-Agnostic Self-Supervised Learning Uncovers Clinically Relevant Tumor Niches in Multiplexed Imaging ]]> https://biorxiv.org/content/10.1101/2025.11.04.686632v1?rss=1 Lin, A. L. Bao, S. Lau, K. Vandekar, S. Moyer, D. Liu, Q. Ma, S. 2025-11-05 doi:10.1101/2025.11.04.686632 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Immature olfactory sensory neurons provide complementary input in the healthy olfactory system ]]> https://biorxiv.org/content/10.1101/2025.11.05.686656v1?rss=1 Gregory, J. D. Herzog, R. S. Curtis, K. A. Marar, M. I. Cheetham, C. E. J. 2025-11-06 doi:10.1101/2025.11.05.686656 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Atomistic TCR-ligand interactions instruct memory T-cell differentiation ]]> https://biorxiv.org/content/10.1101/2025.11.05.686789v1?rss=1 Akitsu, A. Tan, K. Mallis, R. J. Booker, M. A. Duke-Cohan, J. S. Brazin, K. N. Kirkpatrick, E. H. Parkins, A. N. Aryal, S. Cinella, V. Lee, J. J. Uberoy, K. I. Koenig, J. K. Biddle, M. Messier, C. M. Lizotte, P. H. Tolstorukov, M. Y. Hwang, W. Lang, M. J. Reinherz, E. L. 2025-11-06 doi:10.1101/2025.11.05.686789 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Human coronavirus HKU1 neutralization by glycan receptor mimicry ]]> https://biorxiv.org/content/10.1101/2025.11.05.686863v1?rss=1 Feng, Z. Kose, N. Moreira, F. R. Kimpel, A. L. M. Copps, J. Suryadevara, N. Jackson, D. J. Gern, J. E. Wilson, I. A. Li, S. de Vries, R. P. Baric, R. S. Bangaru, S. Crowe, J. E. Ward, A. B. 2025-11-07 doi:10.1101/2025.11.05.686863 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ Increased levels of HAPLN2, which anchors dense extracellular matrix, in the hippocampus of APOE4 targeted replacement mice ]]> https://biorxiv.org/content/10.1101/2025.11.09.687435v1?rss=1 Deasy, S. Amontree, M. Colon, Z. A. Thorland, E. Modi, K. Hummel, K. A. Blanco, I. Greco, G. A. Maguire-Zeiss, K. Conant, K. 2025-11-10 doi:10.1101/2025.11.09.687435 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Diffusion MRI Processing in the HEALthy Brain and Child Development Study: Innovations and Applications ]]> https://biorxiv.org/content/10.1101/2025.11.10.687672v1?rss=1 Cieslak, M. Irfanoglu, M. O. Meisler, S. L. Salo, T. Raikes, A. C. Cook, P. A. Chung, A. W. Lee, E. G. Li, R. Li, X. Pecheva, D. Fair, D. A. Smyser, C. D. Harms, M. P. Landman, B. A. Wisnowski, J. L. Huang, H. Alexander, A. L. Satterthwaite, T. D. 2025-11-11 doi:10.1101/2025.11.10.687672 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ SLC11A2 affects nutritional immunity in the gastrointestinal epithelium ]]> https://biorxiv.org/content/10.1101/2025.11.12.688034v1?rss=1 Norberg, E. S. Westerman, T. L. Cruz, E. Bushman, S. D. Skaar, E. P. Elfenbein, J. R. Knodler, L. A. 2025-11-12 doi:10.1101/2025.11.12.688034 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Denoising image-based spatial transcriptomics data with DenoIST ]]> https://biorxiv.org/content/10.1101/2025.11.13.688387v1?rss=1 Kwok, A. W. C. Vannan, A. Banovich, N. E. Kropski, J. A. Shim, H. McCarthy, D. J. 2025-11-14 doi:10.1101/2025.11.13.688387 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Cochlear histopathology in macaques after noise-induced temporary threshold shifts ]]> https://biorxiv.org/content/10.1101/2025.11.14.688497v1?rss=1 Mondul, J. Mackey, C. A. Conner, A. N. Alek, C. A. Pitchford, D. Rausis, O. Liberman, L. Liberman, C. Ramachandran, R. Hackett, T. A. 2025-11-16 doi:10.1101/2025.11.14.688497 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ A zebrafish seizure model of cblX syndrome reveals a dose-dependent refractory response to mTor inhibition. ]]> https://biorxiv.org/content/10.1101/2025.11.14.688058v1?rss=1 Gil, C. B. Paz, D. Pinales, B. E. Castro, V. L. Perucho, C. E. Gonzales, A. Francia, G. Masenga, S. K. Hinton, A. Quintana, A. M. 2025-11-17 doi:10.1101/2025.11.14.688058 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Insights into the Datasets, Tools, and Training Needs of the AnVIL Community: 2024 ]]> https://biorxiv.org/content/10.1101/2025.11.14.688517v1?rss=1 Isaac, K. J. Cox, K. E. L. Ho, K. Y. Humphries, E. M. Kucher, N. Leek, J. T. Mosher, S. Schatz, M. C. Tan, F. J. Hoffman, A. M. 2025-11-17 doi:10.1101/2025.11.14.688517 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Biosynthesis of peptidic thiooxazole metallophores installed by multinuclear nonheme iron enzymes. ]]> https://biorxiv.org/content/10.1101/2025.11.18.689057v1?rss=1 Gadgil, M. G. Dommaraju, S. R. Liu, X. Battiste, A. J. Bregman, M. H. Mitchell, D. A. 2025-11-18 doi:10.1101/2025.11.18.689057 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ T-cell Multiomic Analysis Identifies Subsets and Mechanisms of Interaction with Epithelial Cells in Idiopathic Pulmonary Fibrosis ]]> https://biorxiv.org/content/10.1101/2025.11.19.689037v1?rss=1 Serezani, A. Bazzano, J. M. Pascoalino, B. D. da Silva, L. Dietrich, A. J. Taylor, C. J. Sherrill, T. Calvi, C. L. Gonzalez-Ericsson, P. I. Wilfong, E. M. Bacchetta, M. Shaver, C. M. Ware, L. B. Salisbury, M. Van Kaer, L. Banovich, N. Kropski, J. A. Blackwell, T. S. 2025-11-19 doi:10.1101/2025.11.19.689037 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ A gene expression atlas of a juvenile nervous system ]]> https://biorxiv.org/content/10.1101/2025.11.21.689793v1?rss=1 Taylor, S. R. Olson, C. Ripoll-Sanchez, L. Valperga, G. McWhirter, R. Barney, S. T. Atkinson, A. Goel, S. Weinreb, A. Hardin, A. Rolfson, A. Pattee, J. Aguilar, G. R. Merritt, D. M. Eroglu, M. Majeed, M. Grundvig, E. Child, E. Vertes, P. E. Schafer, W. Varol, E. Hammarlund, M. Hobert, O. Miller, D. M. 2025-11-22 doi:10.1101/2025.11.21.689793 Cold Spring Harbor Laboratory Press 2025-11-22 <![CDATA[ Early Host-Virus RNA Interactions Reveal SPEN-Driven m6A Regulation as a Major Determinant of Henipavirus Infection ]]> https://biorxiv.org/content/10.1101/2025.11.21.689838v1?rss=1 Ascura, A. Clarke, S. Livingston, A. F. Trotman, J. B. Haigh, S. Malek, M. C. Calabrese, J. M. Ascano, M. 2025-11-23 doi:10.1101/2025.11.21.689838 Cold Spring Harbor Laboratory Press 2025-11-23 <![CDATA[ Public Cohort Analysis Identifies Thyroglobulin Variants as Hypothyroidism Risk Factors ]]> https://biorxiv.org/content/10.1101/2025.11.21.689591v1?rss=1 Hermanson, J. N. Hudson, A. D. Plate, L. 2025-11-24 doi:10.1101/2025.11.21.689591 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Blood-based Transcriptomics Reveal Sex- and Amyloid-Modulated Biology of Plasma pTau217 in Preclinical Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2025.11.21.689770v1?rss=1 Seto, M. Klinger, H. M. Clifton, M. Janve, V. A. Brown, J. A. Birkenbihl, C. Coughlan, G. T. Townsend, D. L. Wang, T.-C. Properzi, M. Hanseeuw, B. Chhatwal, J. Yang, H.-S. Rissman, R. Aisen, P. Cuppels, M. Donohue, M. C. Raman, R. Johnson, K. A. Sperling, R. A. Dumitrescu, L. Hohman, T. J. Buckley, R. F. 2025-11-24 doi:10.1101/2025.11.21.689770 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Biophysical constraints on mRNA decay rates shape macroevolutionary divergence in steady-state abundances ]]> https://biorxiv.org/content/10.1101/2025.11.24.690267v1?rss=1 Felce, C. Cope, A. L. Schraiber, J. G. Krishnaswamy, M. Pachter, L. Pennell, M. 2025-11-24 doi:10.1101/2025.11.24.690267 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Calibration of MRI-based reference intervals to new samples ]]> https://biorxiv.org/content/10.1101/2025.11.25.690453v1?rss=1 Chen, A. A. Seidlitz, J. Gardner, M. Bethlehem, R. A. I. Dorfschmidt, L. Kafadar, E. Lifespan Brain Chart Consortium, Benitez, A. Jensen, J. H. Vandekar, S. Satterthwaite, T. D. Alexander-Bloch, A. F. 2025-11-26 doi:10.1101/2025.11.25.690453 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ Crystallographic Ensembles Reveal the Structural Basis of Binding Entropy in SARS-CoV2 Macrodomain ]]> https://biorxiv.org/content/10.1101/2025.11.25.690589v1?rss=1 Seo, L. Farran, I. Aslam, A. Li, X. Jaishankar, P. Fraser, J. S. Renslo, A. Wankowicz, S. A. 2025-11-26 doi:10.1101/2025.11.25.690589 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ The Macroevolution of Filamentation Morphology Across the Saccharomycotina Yeast Subphylum ]]> https://biorxiv.org/content/10.1101/2025.11.26.690719v1?rss=1 Chavez, C. M. Harrison, M.-C. Danis, T. Groenewald, M. Hittinger, C. T. Rokas, A. 2025-11-27 doi:10.1101/2025.11.26.690719 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ Brush border intermicrovillar adhesion limits bacterial attachment to the small intestine brush border ]]> https://biorxiv.org/content/10.1101/2025.11.25.690363v1?rss=1 Cowell, R. P. Bickart, A. C. Shashi, S. R. Vasquez, A. Brackman, L. C. Abdel-Dayem, M. A. Chen, W. Bowman, D. M. Krystofiak, E. S. Essalki, Y. Gross, I. Harrison, D. G. Wanjalla, C. N. Algood, H. M. Tyska, M. J. Meenderink, L. M. 2025-11-28 doi:10.1101/2025.11.25.690363 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Mammary Fibroblasts Secrete Damage Associated Molecular Patterns through Extracellular Vesicles in Response to Ionizing Radiation ]]> https://biorxiv.org/content/10.1101/2025.11.25.690532v1?rss=1 Sanchez, G. B. Patel, P. Gomez-Crase, P. Kim, C. Rose, K. L. Rafat, M. 2025-11-28 doi:10.1101/2025.11.25.690532 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ BeadBuddy: user-friendly, nanometer-scale registration of single-molecule imaging data ]]> https://biorxiv.org/content/10.1101/2025.11.25.690467v1?rss=1 Lionnet, T. Clark, F. T. Whitney, P. H. Saiz, N. Ziarno, A. 2025-11-29 doi:10.1101/2025.11.25.690467 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Cancers modulate p53 truncal neoantigen display to evade T cell detection ]]> https://biorxiv.org/content/10.1101/2025.11.26.690562v1?rss=1 Haratani, K. Reinhold, B. Duke-Cohan, J. S. Fahey, C. G. Tan, K. Mallis, R. J. Gusev, A. Kehl, K. L. Luo, J. Holliday, E. L. Masi, D. J. Karmazyn, A. Zienkiewicz, K. J. Hennessey, C. J. Blasco, R. B. Thai, T. C. Gibbons, G. M. Kivlehan, S. Lizotte, P. Paweletz, C. P. Aguirre, A. J. Ligon, K. L. Chiarle, R. Lang, M. J. Barbie, D. A. Reinherz, E. L. 2025-11-30 doi:10.1101/2025.11.26.690562 Cold Spring Harbor Laboratory Press 2025-11-30 <![CDATA[ Improved Estimation of Correlation Accuracy for Machine Learning Brain-Phenotype Associations ]]> https://biorxiv.org/content/10.1101/2025.11.26.690778v1?rss=1 Jones, M. T. Gadiyar, I. Zhang, X. Kang, K. Liu, J. Chen, A. Seidlitz, J. Alexander-Bloch, A. Kennedy, E. Vandekar, S. 2025-12-01 doi:10.1101/2025.11.26.690778 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Capturing Multi-Scale Dynamics of Aortic Valve Calcification With a Coupled Fluid Structure and Systems Biology Model ]]> https://biorxiv.org/content/10.64898/2025.11.28.691136v1?rss=1 Quan, M. Xie, T. Harris, L. A. A. Luo, H. 2025-12-02 doi:10.64898/2025.11.28.691136 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ IsoSpace: Chemistry-Informed Dimensionality Reduction and Automated Isotope Candidate Detection in Imaging Mass Spectrometry ]]> https://biorxiv.org/content/10.64898/2025.11.30.691393v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@5e8977org.highwire.dtl.DTLVardef@93150eorg.highwire.dtl.DTLVardef@4b7aa4org.highwire.dtl.DTLVardef@160aa43_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 0:C_FLOATNO Graphical abstract for IsoSpace, chemistry-informed dimensionality reduction and au-tomated isotope candidate detection in imaging mass spectrometry. C_FIG ]]> Meenakshi, M. Migas, L. G. Djambazova, K. V. Dufresne, M. Spraggins, J. M. Van de Plas, R. 2025-12-02 doi:10.64898/2025.11.30.691393 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ BioLACE: unifying spatial geometry and marker priors for cohesive cell-type clustering in spatial transcriptomics ]]> https://biorxiv.org/content/10.64898/2025.12.01.691603v1?rss=1 Qin, H. Hu, Y. Zhu, Y. Baek, J. Yuan, W. Meltzer, S. Zhou, X. M. 2025-12-02 doi:10.64898/2025.12.01.691603 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ FET proteins and PARylation-dependent condensates promote replication fork reversal and genome stability ]]> https://biorxiv.org/content/10.64898/2025.12.01.691651v1?rss=1 Giansanti, C. Schultz, J. C. Jackson, J. Vindigni, A. Cortez, D. 2025-12-02 doi:10.64898/2025.12.01.691651 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Advancing High-Resolution 7T Diffusion MRI: Evaluating Phase-Encoding Correction Strategies for Distortion Correction from Basic to Four-Way Acquisitions ]]> https://biorxiv.org/content/10.64898/2025.12.01.687254v1?rss=1 Schilling, K. G. Beckett, A. J. S. Amandola, M. Walker, E. B. Feinberg, D. A. Bunge, S. A. Vu, A. T. 2025-12-03 doi:10.64898/2025.12.01.687254 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Smooth muscle LRRC8A knockout reduces superoxide influx, inflammation, senescence and atherosclerosis ]]> https://biorxiv.org/content/10.64898/2025.12.01.691680v1?rss=1 Panja, S. Choi, H. Nguyen, H.-N. Russolillo, J. Dikalov, S. Stark, R. J. Lamb, F. S. 2025-12-03 doi:10.64898/2025.12.01.691680 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Loss of ABC transporters, White, Brown, and Scarlet, prevents increase in mitotic divisions of germline stem cells in response to mating in Drosophila melanogaster ]]> https://biorxiv.org/content/10.64898/2025.12.02.691910v1?rss=1 Wright, M. P. Vladimirova, A. Aston, H. M. Malpe, M. S. Schulz, C. 2025-12-03 doi:10.64898/2025.12.02.691910 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Ovarian Hormones and Obesity Drive Th17-mediated Airway Inflammation through Estrogen Receptor Signaling ]]> https://biorxiv.org/content/10.64898/2025.12.02.691857v1?rss=1 Henriquez-Pilier, E. Cephus, J.-Y. Kuehnle, S. N. Tannous, E. Tomasello, A. McKernan, K. E. Peebles, R. S. Cahill, K. N. Rathmell, J. C. Newcomb, D. C. 2025-12-05 doi:10.64898/2025.12.02.691857 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Cannabidiol Reduces D1 and D2 Medium Spiny Neuron Excitability in the Nucleus Accumbens Core ]]> https://biorxiv.org/content/10.64898/2025.12.02.691956v1?rss=1 Jarrett, Z. E. Grueter, B. A. 2025-12-05 doi:10.64898/2025.12.02.691956 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Brain-AI Alignment in Naturalistic Movies ]]> https://biorxiv.org/content/10.64898/2025.12.03.692164v1?rss=1 Li, M. 2025-12-08 doi:10.64898/2025.12.03.692164 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Targeting CREB remodels the immune microenvironment to enhance immunotherapy responses in pancreatic cancer ]]> https://biorxiv.org/content/10.64898/2025.12.04.691935v1?rss=1 Mehra, S. Srinivasan, S. Jinka, S. Krishnamoorthy, V. Gupta, V. K. Garrido, V. T. Bianchi, A. Adams, A. M. Patel, M. Amirian, H. Nivelo, L. A. Rajkumar, K. Khurana, R. Box, E. W. Ban, Y. McDonald, O. G. Datta, J. DelGiorno, K. E. Merchant, N. B. Goswami, S. Dosch, A. R. Nagathihalli, N. S. 2025-12-08 doi:10.64898/2025.12.04.691935 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ RNY1 partitions into extracellular vesicles and ribonucleoprotein particles during airway inflammation to regulate macrophage programming ]]> https://biorxiv.org/content/10.64898/2025.12.04.691704v1?rss=1 Saffold, C. E. Richardson, A. C. Pua, H. H. 2025-12-09 doi:10.64898/2025.12.04.691704 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ White-Matter BOLD Mediates Time-Varying Cortico-Cortical Functional Connectivity ]]> https://biorxiv.org/content/10.64898/2025.12.04.691728v1?rss=1 Xu, L. Gao, Y. Li, M. Zu, Z. Schilling, K. G. Anderson, A. W. Ding, Z. Gore, J. C. 2025-12-09 doi:10.64898/2025.12.04.691728 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Unraveling the Dual Immunomodulatory and Immunogenic Roles of the Central Conserved Cysteine-Rich Region in Respiratory Syncytial Virus G Protein ]]> https://biorxiv.org/content/10.64898/2025.12.06.692521v1?rss=1 Gutman, J. Paletta, A. Birnberg-Weiss, F. Prato, A. Boudgouste, A. Goldin, C. J. Sastre, S. Byrne, A. Pakciarz, P. Polack, F. P. Dvorkin, J. Zeida, A. Caballero, M. Fernandez, G. Tribulatti, V. Alvarez-Paggi, D. Esperante, S. 2025-12-10 doi:10.64898/2025.12.06.692521 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ The Incoming Influenza Genome Assembles a Host RBP Network that Orchestrates Viral RNA Synthesis ]]> https://biorxiv.org/content/10.64898/2025.12.10.693272v1?rss=1 Clarke, S. Patel, D. B. Ascura, A. Wiser, C. L. Pennise, J. L. Lisy, S. M. Ascano, M. 2025-12-11 doi:10.64898/2025.12.10.693272 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Activation of cannabinoid receptor CB1 leads to aberrant myelination in development ]]> https://biorxiv.org/content/10.64898/2025.12.10.693544v1?rss=1 Miramontes, T. G. Hamling, K. R. Doan, R. A. Singh, S. Collins, H. Y. Emery, B. Call, C. L. Monk, K. 2025-12-11 doi:10.64898/2025.12.10.693544 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ A subject-specific reversible folding model reveals geometry-driven white-matter organization ]]> https://biorxiv.org/content/10.64898/2025.12.10.693407v1?rss=1 Osman, B. Vink, R. Jalba, A. C. Schilling, K. G. Chamberland, M. 2025-12-13 doi:10.64898/2025.12.10.693407 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ Presynaptic GABAB autoreceptors suppress neurotransmitter release during repetitive stimulation via the Gβγ-SNARE pathway. ]]> https://biorxiv.org/content/10.64898/2025.12.10.693514v1?rss=1 Zurawski, Z. Lu, I. Alford, S. Potcoava, M. Delbove, C. Peters, C. J. hamm, h. e. 2025-12-13 doi:10.64898/2025.12.10.693514 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ Tryptophan Chemistry Driven by a Widespread Cytochrome P422 Enzyme Family ]]> https://biorxiv.org/content/10.64898/2025.12.11.692455v1?rss=1 MA, W. WANG, Q. YANG, Q. TENG, Z. HAN, X. SANG, M. LI, Q. WANG, R. FENG, P. ZHONG, J. ZHANG, Y. WEI, Y. JIANG, L. GUENGERICH, F. P. Zhang, W. 2025-12-13 doi:10.64898/2025.12.11.692455 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ DNA binding and lesion recognition by the bacterial interstrand DNA crosslink glycosylase AlkX ]]> https://biorxiv.org/content/10.64898/2025.12.11.693820v1?rss=1 Cai, Y. Kunkle, D. E. Edinbugh, M. D. Skaar, E. P. Eichman, B. F. 2025-12-13 doi:10.64898/2025.12.11.693820 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ Varied monoamine reuptake inhibitors reduce parvalbumin expression; implications for pyramidal cell disinhibition and enhanced neuroplasticity ]]> https://biorxiv.org/content/10.64898/2025.12.12.693967v1?rss=1 Hummel, K. Shautidze, G. Thorland, E. Amontree, M. Wonnenberg, P. Blanco, I. Conant, K. 2025-12-13 doi:10.64898/2025.12.12.693967 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ Pharmacological inhibition of MCL-1 disrupts mitochondrial cristae and depletes the human neural progenitor cell pool ]]> https://biorxiv.org/content/10.64898/2025.12.12.694056v1?rss=1 Hanna, M. R. Yarbrough, M. Gil, M. Costanzo, J. Gama, V. 2025-12-14 doi:10.64898/2025.12.12.694056 Cold Spring Harbor Laboratory Press 2025-12-14 <![CDATA[ scCotag: Diagonal integration of single-cell multi-omics data via prior-informed co-optimal transport and regularized barycentric mapping ]]> https://biorxiv.org/content/10.64898/2025.12.11.693589v1?rss=1 Li, Y. Tan, Y. Chen, R. Zhou, X. M. Chen, Y. Huo, Y. Guo, X. Tiwari, A. Wen, Z. Zhong, X. Malin, B. A. Li, B. Yin, Z. 2025-12-15 doi:10.64898/2025.12.11.693589 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Proteostasis Remodeling Across Development Defines Fetal, Neonatal, and Adult Hematopoietic Stem Cell States ]]> https://biorxiv.org/content/10.64898/2025.12.12.694052v1?rss=1 Yu, H. Kim, Y. J. Chen, K. Liu, A. Z. Sunshine, M. J. Signer, R. A. 2025-12-15 doi:10.64898/2025.12.12.694052 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ The role of MICOS in modulating mitochondrial dynamics and structural changes in vulnerable regions of Alzheimer's Disease ]]> https://biorxiv.org/content/10.64898/2025.12.13.693635v1?rss=1 Shao, B. Kula, B. Le, H. Venkhatesh, P. Katti, P. Marshall, A. G. Chittaranjan, S. Thapilyal, S. Kalpana, N. Nivedya, C. Roszczyk, A. Mobley, H. Killion, M. St. John, E. Martin, P. Rodrigiuez, B. Hamilton, M. Bell, L. Wyckoff, S. Moran, L. A. Philips, M. Hubert, D. Tomeau, B. Afolabi, J. M. Kirabo, A. Blanco, I. Reasonover, S. Drake, L. E. Lippmann, E. S. Evans, C. Santisteban, M. M. Cheairs, T. G. Mesenga, S. Wanjalla, C. Gaddy, J. McMillan, R. Perez, C. P. H. Paing, H. H. Schafer, J. C. Mobley, B. Berry, J. Crabtree, A. Kovtun, O. Goodwin, S. Lopez 2025-12-16 doi:10.64898/2025.12.13.693635 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ HnRNPA2B1 tunes antimycobacterial immune responses in macrophages through alternative splicing of Irgm1 ]]> https://biorxiv.org/content/10.64898/2025.12.16.694586v1?rss=1 Patrick, K. L. Chapman, M. J. Huskey, J. B. Armijo, K. S. Hahn, S. Spellman-Reliford, J. Coleman, A. K. Mabry, C. J. carpenter, s. Watson, R. O. 2025-12-16 doi:10.64898/2025.12.16.694586 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Evaluating the effects of aging on biodistribution and gene silencing activity of lipid-siRNA conjugates delivered into cerebrospinal fluid ]]> https://biorxiv.org/content/10.64898/2025.12.17.693452v1?rss=1 Ligocki, A. Sorets, A. Abdulrahman, A. Francini, N. Park, J. Lee, J. H. Ford, W. Lyons, S. Fritsch, E. Lamantia, Z. Duvall, C. Lippmann, E. 2025-12-19 doi:10.64898/2025.12.17.693452 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ Computational design and experimental characterization of mini-protein binders targeting Nipah, Langya and Measles virus receptor-binding domains ]]> https://biorxiv.org/content/10.64898/2025.12.20.695652v1?rss=1 Rieger, D. Ruediger, C. Peter, A. S. Schlegel, P. Nobis, A. Junker, H. Kiesewetter, L. Beining, M. Beckmann, L. Klier, J. Pipatpadungsin, N. Stass, R. Bowden, T. A. Diederich, S. Meiler, J. Schoeder, C. T. 2025-12-23 doi:10.64898/2025.12.20.695652 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ FHIR as a Unifying Format for Genomic Research Data Tracking, Aggregation, and Integration ]]> https://biorxiv.org/content/10.64898/2025.12.22.695544v1?rss=1 Sanati, N. Walsh, B. Gray, P. Hagen, L. Carroll, R. J. Heath, A. P. Charbonneau, A. Ellrott, K. 2025-12-24 doi:10.64898/2025.12.22.695544 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ Connections of early visual areas with posterior parietal and temporal cortex in galagos, a strepsirrhine primate ]]> https://biorxiv.org/content/10.64898/2025.12.27.696608v1?rss=1 Wang, Q. Kaas, J. H. Stepniewska, I. 2025-12-27 doi:10.64898/2025.12.27.696608 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ Coronavirus membrane protein with a fluorescent protein tag enables tracking of virus particles in live cells ]]> https://biorxiv.org/content/10.64898/2025.12.29.696688v1?rss=1 Stefanos, B. Green, N. R. B. Nadig, I. Lapierre, L. A. Goldenring, J. R. Hogue, I. B. Glenn, H. L. Hogue, B. G. 2025-12-30 doi:10.64898/2025.12.29.696688 Cold Spring Harbor Laboratory Press 2025-12-30 <![CDATA[ Development and application of nbLIBRA-seq for high-throughput discovery of antigen-specific nanobodies ]]> https://biorxiv.org/content/10.64898/2025.12.30.697047v1?rss=1 Leonard, S. E. Wasdin, P. T. Webb, K. E. Amlashi, P. B. Rathmell, J. C. Spiller, B. W. Wadzinski, B. E. Georgiev, I. S. Voss, K. 2025-12-31 doi:10.64898/2025.12.30.697047 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Small Extracellular Vesicle Cargoes Associated with Lymph Node Metastasis in Head and Neck Cancer ]]> https://biorxiv.org/content/10.64898/2025.12.31.697101v1?rss=1 Shafiq, A. Sato, S. Barman, B. Arner, E. N. Brown, B. T. Weaver, A. 2026-01-02 doi:10.64898/2025.12.31.697101 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Biological signatures of history: Examination of composite biomes and Y chromosome analysis from da Vinci-associated cultural artifacts ]]> https://biorxiv.org/content/10.64898/2026.01.06.697880v1?rss=1 Singh, H. Rajagopala, S. V. Hart, R. Hallast, P. Loftus, M. Wiscovitch-Russo, R. Conrad, C. R. K. Thaler, D. S. Pinar, G. Aberg, K. C. Lorenzi, R. Lorente, J. A. Ausubel, J. H. Sakmar, T. P. Roby, R. K. Lee, C. Gonzalez-Juarbe, N. 2026-01-06 doi:10.64898/2026.01.06.697880 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Fishing with Two Lines: A Hybrid Approach to Spatial Transcriptomic Discovery ]]> https://biorxiv.org/content/10.64898/2026.01.07.698201v1?rss=1 Williams-Katek, A. L. Mallapragada, S. Mee, E. D. Fischer, B. K. Eldredge, L. C. Deutsch, G. H. Kropski, J. A. Sucre, J. M. S. Banovich, N. E. 2026-01-08 doi:10.64898/2026.01.07.698201 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ A Hybrid Gag Lattice as a Structural Intermediate in HIV-1 Maturation ]]> https://biorxiv.org/content/10.64898/2026.01.10.698794v1?rss=1 Meuser, M. E. Wu, C. Macke, A. C. Shi, J. Cheng, J. Yang, R. R. Freniere, C. Lin, J. Aiken, C. Perilla, J. R. Xiong, Y. 2026-01-11 doi:10.64898/2026.01.10.698794 Cold Spring Harbor Laboratory Press 2026-01-11 <![CDATA[ Spatial transcriptomics reveals organizational properties of mouse spinal cord and alterations in neuropathic pain ]]> https://biorxiv.org/content/10.64898/2026.01.10.698734v1?rss=1 Wang, Q. Hu, Y. Zhu, Y. Peng, J. Osei-Asante, E. Chelliah, G. Sobanko, M. Sanchez, B. Ginty, D. D. Zhou, X. M. Meltzer, S. 2026-01-12 doi:10.64898/2026.01.10.698734 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ The microtubule GTP-tubulin cap size is modulated during cell division ]]> https://biorxiv.org/content/10.64898/2026.01.13.699367v1?rss=1 Cassidy, A. C. Burnette, D. T. Zanic, M. 2026-01-14 doi:10.64898/2026.01.13.699367 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Signal Strength Aware Latent Spaces Reveal Molecularly Distinct Substructures within Human Kidney Tissue ]]> https://biorxiv.org/content/10.64898/2026.01.15.699686v1?rss=1 Delacour, P.-L. Migas, L. Farrow, M. Yang, H. Fogo, A. B. Spraggins, J. M. Van de Plas, R. 2026-01-16 doi:10.64898/2026.01.15.699686 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ SSNA1 mechanically reinforces the damaged microtubule lattice ]]> https://biorxiv.org/content/10.64898/2026.01.16.699973v1?rss=1 Richardson, L. B. Lawrence, E. J. Pinjakan, A. Zanic, M. 2026-01-18 doi:10.64898/2026.01.16.699973 Cold Spring Harbor Laboratory Press 2026-01-18 <![CDATA[ Persistent impairment of spatial hearing and neural binaural interaction after temporary noise-induced hearing loss ]]> https://biorxiv.org/content/10.64898/2026.01.16.699944v1?rss=1 Mackey, C. Mondul, J. A. Conner, A. N. Peacock, J. Benson, M. A. Hackett, T. A. Tollin, D. J. Ramachandran, R. 2026-01-20 doi:10.64898/2026.01.16.699944 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Fully genetically encoded low-molecular-weight protein tags with defined shapes for direct molecular identification by cryo-electron tomography ]]> https://biorxiv.org/content/10.64898/2026.01.16.700029v1?rss=1 Luo, F. Sun, R. Chalkley, O. R. Li, P. Zhou, Q. 2026-01-20 doi:10.64898/2026.01.16.700029 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Light Microscopy-Based Organelle Quantification: A Comprehensive Protocol ]]> https://biorxiv.org/content/10.64898/2026.01.19.700276v1?rss=1 Thapliyal, S. Kalpana, N. H. Ronald, M. Afolabi, J. Marshall, A. Venkhatesh, P. Pujala, R. K. Hinton, A. O. Parry, H. Glancy, B. Katti, P. 2026-01-20 doi:10.64898/2026.01.19.700276 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ TCF1lo CD8 T cells proliferate and persist autonomously in tumors ]]> https://biorxiv.org/content/10.64898/2026.01.17.700120v1?rss=1 Erwin, M. M. Favret, N. R. McDavid, C. Ewell, Z. D. Wolf, M. Brown, L. A. Roetman, J. J. Rudloff, M. W. Murray, K. A. Detres Roman, C. R. Philip, M. 2026-01-21 doi:10.64898/2026.01.17.700120 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Accumulation of Extracellular GABA, Impaired GABAergic Neurotransmission and 4-Phenylbutyrate Rescue in Mice of SLC6A1 Variant-Mediated Disorders ]]> https://biorxiv.org/content/10.64898/2026.01.20.700615v1?rss=1 Zavalin, K. Randhave, K. Biven, M. Shen, W. Kang, J.-Q. 2026-01-21 doi:10.64898/2026.01.20.700615 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ A Gata4-Loxl2 Axis Controls ECM Remodeling to Enable Scar-Free Spinal Cord Regeneration in Zebrafish ]]> https://biorxiv.org/content/10.64898/2026.01.21.700220v1?rss=1 Noel, N. P. Fernandes, V. F. L. Kjar, A. Pfotenhauer, P. E. Sefogbe, M. P. Akam-Baxter, E. A. Lippmann, E. S. Cigliola, V. 2026-01-22 doi:10.64898/2026.01.21.700220 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Multi-modal and multi-region distance model for neuroimaging: Application to ABCD study ]]> https://biorxiv.org/content/10.64898/2026.01.21.700689v1?rss=1 Zhang, X. Vandekar, S. Chen, A. A. Kang, K. Seidlitz, J. Alexander-Bloch, A. Liu, J. 2026-01-22 doi:10.64898/2026.01.21.700689 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ FrustraMPNN: An ultra-fast deep learning tool for proteome-scale analysis of deep mutational single-residue local energetic frustration in proteins ]]> https://biorxiv.org/content/10.64898/2026.01.22.701012v1?rss=1 Beining, M. Aliaga, F. E. Parra, R. G. Schoeder, C. T. Ramirez-Sarmiento, C. A. Meiler, J. 2026-01-23 doi:10.64898/2026.01.22.701012 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Oxidant-mediated activation and inhibition of LRRC8C and LRRC8D channel currents require N-terminal and Transmembrane 1 pore domains ]]> https://biorxiv.org/content/10.64898/2026.01.22.701128v1?rss=1 Rohrbough, J. Nguyen, H.-N. Lamb, F. S. 2026-01-24 doi:10.64898/2026.01.22.701128 Cold Spring Harbor Laboratory Press 2026-01-24 <![CDATA[ Rapid Assessment of Target-Binding Fractions in Theranostic and Imaging Agents Using Size-Exclusion HPLC ]]> https://biorxiv.org/content/10.64898/2026.01.23.699790v1?rss=1 McAdoo, A. Jouad, K. Rosenthal, E. L. Rosenberg, A. J. 2026-01-25 doi:10.64898/2026.01.23.699790 Cold Spring Harbor Laboratory Press 2026-01-25 <![CDATA[ Tail Flaring as an Agonistic Signal in Hummingbirds ]]> https://biorxiv.org/content/10.64898/2026.01.30.702386v1?rss=1 Elting, R. L. Anwar, M. Z. Powers, D. R. Cheng, B. Luo, H. Tobalske, B. W. 2026-01-30 doi:10.64898/2026.01.30.702386 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ HistoSweep enables cellular-resolution tissue quality control for gigapixel images in digital pathology and spatial omics ]]> https://biorxiv.org/content/10.64898/2026.01.30.702675v1?rss=1 Schroeder, A. Yu, X. Li, W. Mao, L. Yuan, M. Yang, J. Sachs, N. Dumoulin, B. Xu, G. X. Luo, X. Huang, A. Susztak, K. Hwang, T. H. Kadara, H. Maegdefessel, L. Yu, J. Li, M. 2026-02-02 doi:10.64898/2026.01.30.702675 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Transcriptomic Profiling of Diabetic Porcine Wound Healing Model Identifies Key Metabolic, Inflammatory, and Oxidative Stress Pathways ]]> https://biorxiv.org/content/10.64898/2026.01.30.702870v1?rss=1 McCune, J. T. Bezold, M. G. Davidson, J. M. Serezani, C. H. Cook, R. S. Duvall, C. L. 2026-02-02 doi:10.64898/2026.01.30.702870 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Immune checkpoint inhibitors amplify type 2 immune mediated repair bypro-regenerative scaffolds ]]> https://biorxiv.org/content/10.64898/2026.01.31.703034v1?rss=1 Garcia, J. Ruta, A. Yu, F. Mejias, J. Pena, A. Rutkowski, N. Gray-Gaillard, E. Dubois, C. Cherry, C. Browne, M. Stivers, K. Maestas, D. Krishnan, K. Bell, A. Fertig, E. J. Cooney, C. Cooney, D. Byrne, P. Hillel, A. Smith, K. Ji, H. Anders, r. Pardoll, D. Ellisseeff, J. 2026-02-03 doi:10.64898/2026.01.31.703034 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Tissue Injury and Biomaterial Treatment Modulate Tumor Growth and Response to Immunotherapy ]]> https://biorxiv.org/content/10.64898/2026.02.02.703323v1?rss=1 Ruta, A. Gray-Gaillard, E. F. Garcia, J. A. Davenport Huyer, L. Mathkour, Y. Cherry, C. Patatanian, M. Mejias, J. C. Maestas, D. R. Krishnan, K. Abraham, P. Wolf, M. T. Smith, K. N. Pardoll, D. M. Elisseeff, J. H. 2026-02-04 doi:10.64898/2026.02.02.703323 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ ACE-2-like Enzymatic Activity in Anti-SARS-CoV-2 Spike Protein Monoclonal Antibodies ]]> https://biorxiv.org/content/10.64898/2026.02.02.703244v1?rss=1 Song, Y. Mehl, F. No, T. Livingston, L. Quintero Barbosa, J. S. Hayashi, J. Serrero, G. Bortz, P. S. Wilson, J. Crowe, J. E. Ho, D. D. Yin, M. T. Tan, J. Zeichner, S. L. 2026-02-05 doi:10.64898/2026.02.02.703244 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ A Large Animal Model of Heritable Pulmonary Arterial Hypertension UsingGene-edited BMPR2 Sheep ]]> https://biorxiv.org/content/10.64898/2026.02.06.704456v1?rss=1 Datar, S. A. Werry, N. Brown, A. R. Fitzpatrick, D. S. Falade, O. Trott, J. F. Hutchings, R. Amin, E. K. Morgan, J. M. Nawaytou, H. Deutsch, G. H. Johnson, E. G. Gonzales Viera, O. A. Bishop, T. F. Urbino, T. McNabb, B. R. Austin, E. D. Fineman, J. R. Van Eenennaam, A. L. 2026-02-07 doi:10.64898/2026.02.06.704456 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ Widespread data leakage inflates performance estimates in cancer drug response prediction ]]> https://biorxiv.org/content/10.64898/2026.02.05.704016v1?rss=1 Asiaee, A. Strauch, J. Azinfar, L. Pal, S. Pua, H. H. Long, J. P. Coombes, K. R. 2026-02-08 doi:10.64898/2026.02.05.704016 Cold Spring Harbor Laboratory Press 2026-02-08 <![CDATA[ A shape-constrained regression and wild bootstrap framework for reproducible drug synergy testing ]]> https://biorxiv.org/content/10.64898/2026.02.05.704019v1?rss=1 Asiaee, A. Long, J. P. Pal, S. Pua, H. H. Coombes, K. R. 2026-02-09 doi:10.64898/2026.02.05.704019 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Electrical stimulation combined with p27Kip1 inactivation drives proliferative neurogenic reprogramming of Mueller glia in the adult mouse retina ]]> https://biorxiv.org/content/10.64898/2026.02.05.704102v1?rss=1 Stone, M. L. Jovanovic, J. LEVINE, E. 2026-02-09 doi:10.64898/2026.02.05.704102 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Sex-specific control of feeding and defensive behaviors by MC3R neurons in the bed nuclei of the stria terminalis ]]> https://biorxiv.org/content/10.64898/2026.02.08.702109v1?rss=1 Bedenbaugh, M. N. Doyle, M. A. Edwards, C. M. Petersen, N. Srisai, D. Hawkins, S. H. Thomas-Low, N. D. Mendoza-Romero, H. Brown, J. A. Vardy, A. S. Winder, D. G. Simerly, R. B. 2026-02-09 doi:10.64898/2026.02.08.702109 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Intercellular Communication via Mitotic Nanotubes is Influenced by Connexin-43 Trafficking and Actin Remodeling ]]> https://biorxiv.org/content/10.64898/2026.02.08.704470v1?rss=1 Cooper, A. Cetin-Ferra, S. Yonosh, K. A. Hinton, A. Marshall, A. G. Faeder, J. R. Murray, S. A. 2026-02-09 doi:10.64898/2026.02.08.704470 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Longitudinal quantitative streamline tractography: robust estimation of white matter connectivity differences ]]> https://biorxiv.org/content/10.64898/2026.02.09.704742v1?rss=1 Pruckner, P. Mito, R. Vaughan, D. N. Schilling, K. G. Morgan, V. L. Englot, D. J. Smith, R. E. 2026-02-09 doi:10.64898/2026.02.09.704742 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Hyperglycemia promotes maladaptive Dectin-1 signaling and impairs skin antifungal host defense. ]]> https://biorxiv.org/content/10.64898/2026.02.11.705431v1?rss=1 Reyna, D. E. Davis, E. Salina, A. Blackman, A. Martinez Barricarte, R. Doran, A. Serezani, C. 2026-02-14 doi:10.64898/2026.02.11.705431 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Modeling the cell biology of PEX11β deficiency during human neurogenesis ]]> https://biorxiv.org/content/10.64898/2026.02.13.705842v1?rss=1 Bodnya, C. Theart, R. P. Gama, V. 2026-02-16 doi:10.64898/2026.02.13.705842 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ Calorie Restriction Up-regulates Islet PD-L1 Signaling and Decreases the Risk of Auto-immune Diabetes Onset in NOD Mice. ]]> https://biorxiv.org/content/10.64898/2026.02.15.705935v1?rss=1 Cambraia, A. Schleh, M. Cartailler, J.-P. Cutler, M. dos Santos, C. Many, G. Kim, H. Kim, Y.-M. Nakayasu, E. S. Mogilenko, D. Arrojo e Drigo, R. 2026-02-17 doi:10.64898/2026.02.15.705935 Cold Spring Harbor Laboratory Press 2026-02-17 <![CDATA[ Anatolution, an online platform for consensus morphology ]]> https://biorxiv.org/content/10.64898/2026.02.16.706144v1?rss=1 Miller, D. J. Gratton, B. LeBlanc, Z. Kaas, J. H. 2026-02-18 doi:10.64898/2026.02.16.706144 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ A Computational Model of Tumor Interactions with Bone-Resident Cells Predicts Tumor-Type-Specific Responses to Perturbations ]]> https://biorxiv.org/content/10.64898/2026.02.16.706164v1?rss=1 Vega, A. G. Bennett, N. E. Beadle, E. P. Alshafeay, S. Chitturi, R. Nagarimadugu, A. Villur, H. Jaiswal, A. Rhoades, J. A. Harris, L. A. 2026-02-18 doi:10.64898/2026.02.16.706164 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Regulation of tumor proliferation by unlocking silent synapses on metastatic cancer cells ]]> https://biorxiv.org/content/10.64898/2026.02.16.706220v1?rss=1 Houcek, A. J. Uzay, I. A. Monteggia, L. M. Linkous, A. Fingleton, B. Kavalali, E. T. 2026-02-18 doi:10.64898/2026.02.16.706220 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Regulation of spontaneous neurotransmission and homeostatic synaptic plasticity by synaptotagmin-1 disease variants at the SNARE primary interface. ]]> https://biorxiv.org/content/10.64898/2026.02.17.706274v1?rss=1 Bagatelas, E. D. Shin, O.-h. T. Armstrong, R. T. Zhou, Q. T. Kavalali, E. T. 2026-02-18 doi:10.64898/2026.02.17.706274 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ A Glucan Synthase-Remodeler Module Organizes Branched Glucan Assembly in the Fungal Cell Wall ]]> https://biorxiv.org/content/10.64898/2026.02.18.706439v1?rss=1 Willet, A. H. Jacob, A. Turner, L. A. Alsanad, A. K. A. Wang, T. Gould, K. L. 2026-02-19 doi:10.64898/2026.02.18.706439 Cold Spring Harbor Laboratory Press 2026-02-19 <![CDATA[ Differential effects of two common GVHD prophylaxis regimens on the gut microbiome: Results from the BMT CTN 1801 study ]]> https://biorxiv.org/content/10.64898/2026.02.19.706769v1?rss=1 Wirbel, J. Saber, W. Martens, M. J. Peled, J. U. Andermann, T. M. Fei, T. Brooks, E. F. Doyle, B. Pincus, N. B. Jenq, R. R. Bar, M. Bolanos-Meade, J. Bratrude, B. Chhabra, S. Choi, S. W. Clark, W. Das, S. Elmariah, H. Gooptu, M. Holtan, S. G. Jones, R. J. Levine, J. E. Logan, B. R. Al Malki, M. M. Murthy, H. S. Rashidi, A. Rezvani, A. R. Riches, M. L. Runaas, L. Sandhu, K. Spahn, A. Sung, A. D. van den Brink, M. R. M. Horowitz, M. M. Hamadani, M. Kean, L. S. Perales, M.-A. Bhatt, A. S. 2026-02-20 doi:10.64898/2026.02.19.706769 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Prediction of ligand-dependent conformational sampling of ABC transporters by AlphaFold3 and correlation to experimental structures and energetics ]]> https://biorxiv.org/content/10.64898/2026.02.19.706864v1?rss=1 Tang, Q. Mchaourab, H. Wu, T. Soubasis, B. 2026-02-20 doi:10.64898/2026.02.19.706864 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Discovering macroscale functional organization on the structure of brain-like recurrent neural networks ]]> https://biorxiv.org/content/10.64898/2026.02.19.706880v1?rss=1 Chen, P. Cui, Z. Constantinidis, C. 2026-02-20 doi:10.64898/2026.02.19.706880 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Collagen IV of basement membrane: V. Bromide-mediated sulfilimine bonds interlock the quaternary structure of NC1-hexamer of scaffolds enabling metazoan evolution. ]]> https://biorxiv.org/content/10.64898/2026.02.20.707065v1?rss=1 Clarke, B. P. Pedchenko, V. Pedchenko, T. Moran, M. Edwards, J. Vallone, K. Darris, C. Bhave, G. Page-McCaw, P. Hudson, J. K. Boudko, S. P. Hudson, B. G. 2026-02-21 doi:10.64898/2026.02.20.707065 Cold Spring Harbor Laboratory Press 2026-02-21 <![CDATA[ Reconstructing multi-scale tissue spatial architecture from single-cell RNA-seq with REMAP ]]> https://biorxiv.org/content/10.64898/2026.02.21.707167v1?rss=1 Li, M. Jiang, S. Coleman, K. Chen, Z. Jin, K. Liu, Y. Lee, D. H. Hwang, T. H. Xiao, R. Jin, J. Walsh, C. A. Qian, X. Wang, L. 2026-02-22 doi:10.64898/2026.02.21.707167 Cold Spring Harbor Laboratory Press 2026-02-22 <![CDATA[ CellAwareGNN: Single-Cell Enhanced Knowledge Graph Foundation Model for Drug Indication Prediction ]]> https://biorxiv.org/content/10.64898/2026.02.20.707076v1?rss=1 Zhang, X. Jeong, E. Yan, C. Feng, Y. Lyu, L. Guo, X. Chen, Y. 2026-02-23 doi:10.64898/2026.02.20.707076 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Pixel2Gene enables histology-guided reconstruction and prediction of spatial gene expression ]]> https://biorxiv.org/content/10.64898/2026.02.21.707168v1?rss=1 Li, M. Yao, S. Schroeder, A. Jiang, S. Im, S. Park, J. H. Dumoulin, B. Hwang, T. H. Susztak, K. 2026-02-23 doi:10.64898/2026.02.21.707168 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Endocrine-metabolic decoupling drives stress vulnerability in dystrophin deficiency ]]> https://biorxiv.org/content/10.64898/2026.02.22.707291v1?rss=1 Major, G. S. Timpani, C. A. Lalunio, H. Chen, J. Boatner, L. Giourmas, N. Kourakis, S. van den Berg, E. Salimova, E. Eliades, J. Zheng, G. Xu, R. Bhangu, S. K. Mendis, T. V. H. Merry, D. L. Lantier, L. Hagemeyer, C. E. Cavalieri, F. Caeyenberghs, K. Russell, A. P. de Veer, M. Goodman, C. A. Hayes, A. Rybalka, E. Najt, C. P. Lindsay, A. 2026-02-23 doi:10.64898/2026.02.22.707291 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ An Alport variant illuminates the bioactivity of the collagen IV α565- α121 scaffold in Bowman's capsule. ]]> https://biorxiv.org/content/10.64898/2026.02.23.707599v1?rss=1 5,000 reported variants to disease pathology remain poorly understood. To address this gap, we previously examined a distinctive variant, an 8-amino acid "Z-appendage", added to the NC1 domain of the 3 chain. Knock-in mice carrying this variant developed GBM abnormalities and proteinuria, implicating the NC1 hexamer as a critical determinant of GBM function and suggesting that the hexamer surface contains bioactive sites that may mediate signaling and/or organization of macromolecular complexes. Given that approximately 80% of AS cases are associated with COL4A5 variants, including many within the NC1 hexamer, we asked whether relocating the Z-appendage from the 3 NC1 subunit to the 5 subunit produces similar pathology. Strikingly, Col4a5-Z mice did not develop proteinuria and showed only minor changes in GBM morphology. In contrast, the variant induced marked thickening of Bowmans capsule, accompanied by increased deposition of the collagen IV 121 scaffold, increased fibrillar collagen, and cellular deposits. Structural modeling predicts that the collagen IV 565-121 scaffold bearing two Z-appendages adopts an aberrant secondary structure that may stiffen the scaffold and occlude binding sites. Together, these findings reveal a bioactive role for the collagen IV 565-121 scaffold in the Bowmans capsule basement membrane, with potential implications for other 565-121containing tissues such as the aorta and bladder. ]]> Pokidysheva, E. Koirala, R. Clarke, B. Delpire, E. Boudko, S. Hudson, B. G. 2026-02-25 doi:10.64898/2026.02.23.707599 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ Inhibitory Control, Shifting, and Working Memory Updating Domains form Cognitive Phenotypes in Non-human Primates ]]> https://biorxiv.org/content/10.64898/2026.02.24.707708v1?rss=1 Wen, X. Malchin, L. Neumann, A. Womelsdorf, T. 2026-02-25 doi:10.64898/2026.02.24.707708 Cold Spring Harbor Laboratory Press 2026-02-25 <![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. Silva-Aguiar, R. P. Shim, Y. J. Merkulova, A. Silbak, S. Skomorovska-Prokvolit, Y. Midem, D. Ogolla, S. Burckhardt, B. B. Gangnus, T. Scharfstein, J. Caruso-Neves, C. McCarty, O. J. Gailani, D. Bader, M. Rosenthal, P. Dent, A. E. Janse, C. J. McCrae, K. Pinheiro, A. A. d. S. Kazura, J. W. Schmaier, A. H. 2026-02-26 doi:10.64898/2026.02.23.704410 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Epithelial-Mesenchymal Wnt Crosstalk Directs Planar Cell Polarity in the Developing Cochlea ]]> https://biorxiv.org/content/10.64898/2026.02.24.705389v1?rss=1 Kishimoto, I. David, A. P. Rose, K. P. Narasimhan, B. Efron, B. Billings, S. E. Su, E. L. Dong, W. Jan, T. A. Hertzano, R. Cheng, A. 2026-02-26 doi:10.64898/2026.02.24.705389 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Divergent Biological Consequences of APOE Isoforms Across Industrialized and Non-Industrial Environments ]]> https://biorxiv.org/content/10.64898/2026.02.24.706846v1?rss=1 Watowich, M. M. Petersen, R. Brassington, L. Arner, A. Rodenberg, G. Huat, T. B. T. A. T. B. Tam, K. L. Schellenberg, E. Sayed, I. b. M. John, E. Kahumbu, J. Muhoya, B. Gurven, M. Trumble, B. C. Njeru, S. N. Martins, D. Ayroles, J. F. Lim, Y. A. L. Venkataraman, V. v. Wallace, I. Kraft, T. S. Lea, A. J. 2026-02-26 doi:10.64898/2026.02.24.706846 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ A universal regulatory mechanism for prevention of replication restart from RNA:DNA hybrids ]]> https://biorxiv.org/content/10.64898/2026.02.26.708313v1?rss=1 Sensoy, O. Carvajal-Garcia, J. Heyza, J. Wiggins, P. Merrikh, H. 2026-02-27 doi:10.64898/2026.02.26.708313 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ Derlin-mediated ERAD of lipid regulator ORMDL3 safeguards mitochondrial function ]]> https://biorxiv.org/content/10.64898/2026.02.27.708653v1?rss=1 Scott, N. A. Afolabi, J. Marshall, A. G. Schafer, J. C. Baskerville, V. R. Prasad, P. Kadam, A. A. Som de Cerff, C. Whisenant, T. Phillips, M. A. Tomar, D. McReynolds, M. Hinton, A. Neal, S. E. 2026-03-03 doi:10.64898/2026.02.27.708653 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Multiscale confidence quantification for virtual spatial transcriptomics with UTOPIA ]]> https://biorxiv.org/content/10.64898/2026.03.01.708850v1?rss=1 Jin, K. Chen, Z. Yu, X. Yuan, M. Schroeder, A. Dumoulin, B. Liu, Y. Wang, L. Park, J. H. Hwang, T. H. Susztak, K. Ren, Z. Zhang, N. Li, M. 2026-03-03 doi:10.64898/2026.03.01.708850 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Signatures of selection in pleiotropic genes involved in insect neuronal and immune systems ]]> https://biorxiv.org/content/10.64898/2026.03.02.708257v1?rss=1 Senthilkumar, S. Martin, R. A. Tate, A. T. 2026-03-03 doi:10.64898/2026.03.02.708257 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Transient Magnetic Resonance Elastography: a method to measure the mechanics of the active heart ]]> https://biorxiv.org/content/10.64898/2026.03.02.708995v1?rss=1 Barbero-Mota, M. Annio, G. Rucher, G. Martorell, J. 2026-03-04 doi:10.64898/2026.03.02.708995 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Pan-repository analysis reveals a drug-activating function of microbial bile acid conjugation ]]> https://biorxiv.org/content/10.64898/2026.03.03.709330v1?rss=1 75-year-old anti-inflammatory drug 5-aminosalicylic acid (5-ASA) with primary and secondary bile acids, including cholic, deoxycholic and lithocholic acids. These bile acid-drug conjugates were detected specifically in individuals treated with 5-ASA or its prodrugs. Multiple gut bacteria, including members of the Bacteroidota and Bacillota, generated cholyl-5-ASA in vitro, and bile salt hydrolase-associated transaminase activity was required for conjugate formation. In a mouse model of colitis, cholyl-5-ASA was associated with reduced intestinal inflammatory pathology and showed markedly enhanced activation of PPAR-{gamma} in cell-based reporter assays compared with 5-ASA alone. Consistent with this activity, cholyl-5-ASA elicited selective immunophenotypic changes in CD4 T cells in vitro, including increased Foxp3+ regulatory T cells. Together with prior evidence that 5-ASA efficacy depends on the microbiome, these findings support a model in which microbial bile acid conjugation represents a key activation step for 5-ASA therapy. More broadly, this work demonstrates how pan-repository metabolomics can uncover previously unrecognized microbiome-dependent chemical functions with direct therapeutic relevance. ]]> Charron-Lamoureux, V. Kelly, P. Zuffa, S. Patan, A. Sala-Climent, M. Walker, C. Zhao, H. N. Xing, S. Gouda, H. Agongo, J. Reilly, E. R. Sallam, L. Shore, S. F. H. Ghoshal, S. Harpavat, A. K. Murugesan, M. P. Yadav, S. Versalovic, J. Orlovsky, V. El Abiead, Y. Kvitne, K. E. Markle, J. G. Norton, G. J. Walker, G. T. Lee, M. H. Hu, Z. Carrillo Terrazas, M. Zong, D. M. Zarrinpar, A. Raffatellu, M. Martin, A. Chin, L. Devkota, S. Gonzalez, A. Ackermann, G. Patel, L. Weng, Y. Knight, R. Russell, R. K. Hansen, R. Svolos, V. Gkikas, K. Rattray, N. J. Siegel, 2026-03-04 doi:10.64898/2026.03.03.709330 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ The impact of coinfection on population stability and chaos ]]> https://biorxiv.org/content/10.64898/2026.03.06.710155v1?rss=1 Barahona, F. J. M. Simpson, E. Tate, A. T. 2026-03-07 doi:10.64898/2026.03.06.710155 Cold Spring Harbor Laboratory Press 2026-03-07 <![CDATA[ Esophageal epithelial cell-state transitions underlie the severity of pediatric eosinophilic esophagitis ]]> https://biorxiv.org/content/10.64898/2026.03.07.710295v1?rss=1 Wang, Y. Sinha, M. K. Ghattas, P. Pilat, J. M. Choksi, Y. A. Lim, H.-W. Rothenberg, M. E. Sheng, Q. Hiremath, G. Rajagopala, S. V. 2026-03-10 doi:10.64898/2026.03.07.710295 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Arousal state alters brain network switching and moderates cognitive task performance ]]> https://biorxiv.org/content/10.64898/2026.03.09.710652v1?rss=1 Kundert-Obando, K. Pourmotabbed, H. Kaur, K. Wang, S. Gomez Lagandara, J. Goodale, S. E. Martin, C. Morgan, V. L. Englot, D. J. Uddin, L. Q. Rubinov, M. Chang, C. 2026-03-12 doi:10.64898/2026.03.09.710652 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ A novel C57BL/6 mouse model for the study of severe Citrobacter rodentium infection ]]> https://biorxiv.org/content/10.64898/2026.03.12.711355v1?rss=1 McClanahan, K. G. Spiga, L. Piazuelo, M. B. Gaddy, J. Zhu, W. Olivares-Villagomez, D. 2026-03-15 doi:10.64898/2026.03.12.711355 Cold Spring Harbor Laboratory Press 2026-03-15 <![CDATA[ Transcriptomic data and biomedical literature synergize in finding pharmacologic gene regulators ]]> https://biorxiv.org/content/10.64898/2026.03.13.708862v1?rss=1 Deisseroth, C. A. Brazelton, B. Shaik, Z. Liu, Z. Zoghbi, H. Y. 2026-03-15 doi:10.64898/2026.03.13.708862 Cold Spring Harbor Laboratory Press 2026-03-15 <![CDATA[ UniST: A Unified Computational Framework for 3D Spatial Transcriptomics Reconstruction ]]> https://biorxiv.org/content/10.64898/2026.03.12.711362v1?rss=1 Shui, L. Liu, Y. Julio, I. C. L. Clemenceau, J. R. Hoi, X. P. Dai, Y. Lu, W. Min, J. Khan, K. Roemer, B. Jiang, M. Waters, R. E. Colbert, K. Maitra, A. Wintermark, M. Yuan, Y. Chan, K. S. Hwang, T. H. Mansfield, P. F. Davis, J. Solis Soto, L. M. Wang, L. LI, L. Li, Z. 2026-03-16 doi:10.64898/2026.03.12.711362 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ Multimodal Molecular Mapping of the Vasculature in Human Cortex Reveals Lipid Markers of Cerebral Amyloid Angiopathy ]]> https://biorxiv.org/content/10.64898/2026.03.13.711741v1?rss=1 Marshall, C. R. Moser, F. A. Scott, C. F. Ventura-Antunes, L. Romero-Fernandez, W. Migas, L. G. Tideman, L. E. M. Colley, M. E. Dufresne, M. Schrag, M. S. Van de Plas, R. Spraggins, J. M. 2026-03-17 doi:10.64898/2026.03.13.711741 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Microvascular architecture and dynamics of the choroid plexus brain barrier ]]> https://biorxiv.org/content/10.64898/2026.03.16.711715v1?rss=1 Kuszynski, S. Junker, I. Shrestha, S. Brand, A. Pfotenhauer, P. Kovtun, O. Moran, R. Koo, C. Oakes, C. Maldonado, J. Cartailler, J.-P. Tiriac, A. Dani, N. 2026-03-17 doi:10.64898/2026.03.16.711715 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ The osteoclast intracellular environment fosters bacterial growth during Staphylococcus aureus infection ]]> https://biorxiv.org/content/10.64898/2026.03.18.712565v1?rss=1 O'Connor, L. D. Bhagat, S. Rohatgi, N. Mbalaviele, G. Cassat, J. E. Veis, D. J. 2026-03-18 doi:10.64898/2026.03.18.712565 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Development and assessment of tailored illustrations to enhance community understandings of genetics topics ]]> https://biorxiv.org/content/10.64898/2026.03.17.711941v1?rss=1 Arner, A. M. McCabe, T. C. Seyler, A. Zamri, S. N. A/P Tan Boon Huat, T. B. T. Tam, K. L. Kinyua, P. John, E. Ngoci Njeru, S. Lim, Y. A. Gurven, M. Nicholas, C. Ayroles, J. Venkataraman, V. v. Kraft, T. S. Wallace, I. J. Lea, A. J. 2026-03-19 doi:10.64898/2026.03.17.711941 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ Processing of Reversed Replication Forks is Required for the Resolution of Replication-Transcription Conflicts ]]> https://biorxiv.org/content/10.64898/2026.03.20.713164v1?rss=1 Carvajal-Garcia, J. Merrikh, H. 2026-03-23 doi:10.64898/2026.03.20.713164 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ A Novel Eukaryotic Ribosome Factor Enables Translation Restart Following Cellular Dormancy ]]> https://biorxiv.org/content/10.64898/2026.03.21.713407v1?rss=1 Gluc, M. Rosa, H. Bozko, M. Turner, L. A. Prince, C. R. Peskova, Y. Feaga, H. A. Gould, K. L. Mattei, S. Jomaa, A. 2026-03-24 doi:10.64898/2026.03.21.713407 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ The importance of M1 muscarinic receptor phosphorylation in learning and memory ]]> https://biorxiv.org/content/10.64898/2026.03.23.713145v1?rss=1 McFall, A. Gibson, K. Molloy, C. Lindsley, C. W. Tobin, A. B. 2026-03-24 doi:10.64898/2026.03.23.713145 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Strand-independent degradation of uncoupled forks by EXO1 activates ATR and restrains synthesis ]]> https://biorxiv.org/content/10.64898/2026.03.22.666038v1?rss=1 Grogan, E. J. Ozua, O. E. Kavlashvili, T. Conwell, S. C. Dewar, J. M. 2026-03-25 doi:10.64898/2026.03.22.666038 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Physiological, Histological, and Cognitive Characterization of a Macaque Model of Presbycusis ]]> https://biorxiv.org/content/10.64898/2026.03.24.714040v1?rss=1 Kulkarni, S. S. Conner, A. N. Rausis, O. Pitchford, D. Wang, Z. Batchu, A. Liberman, L. Liberman, M. C. Constantinidis, C. Hackett, T. Ramachandran, R. 2026-03-27 doi:10.64898/2026.03.24.714040 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ TRaP: An Open-source, Reproducible Framework for Raman Spectral Preprocessing across Heterogeneous Systems ]]> https://biorxiv.org/content/10.64898/2026.03.26.714582v1?rss=1 Zhu, Y. Lionts, M. M. Haugen, E. Walter, A. B. Voss, T. R. Grow, G. R. Liao, R. McKee, M. E. Locke, A. Hiremath, G. Mahadevan-Jansen, A. Huo, Y. 2026-03-27 doi:10.64898/2026.03.26.714582 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Acute degron-mediated RUNX1 loss reprograms enhancer activity to epigenetically drive epithelial destabilization and initiate cancer hallmarks ]]> https://biorxiv.org/content/10.64898/2026.03.26.711344v1?rss=1 Fritz, A. Greenyer, H. Dillac, L. Chavarkar, P. Ullah, R. Malik, M. Hong, D. Toor, R. Pacht, E. Person, A. Zotkin, G. Korzec, S. Gao, C. Abuarqoub, A. Warren, J. Del Porto, J. Perelman, J. Montecino, M. Lian, J. Van Wijnen, A. Heath, J. Ghule, P. Frietze, S. Stengal, K. Reed, K. S. M. Misteli, T. Gordon, J. Stein, J. Stein, G. 2026-03-28 doi:10.64898/2026.03.26.711344 Cold Spring Harbor Laboratory Press 2026-03-28 <![CDATA[ ATF4 Coordinates Transcriptomic and Structural Adaptations in Aging Muscle ]]> https://biorxiv.org/content/10.64898/2026.03.27.711928v1?rss=1 Crabtree, A. Khan, M. M. Scudese, E. Hernandez Perez, C. P. Venkhatesh, P. Marshall, A. G. Rodriguez, B. Garza Lopez, E. Ochayi, O. M. Dantas, E. H. M. Martin, P. Baffi, M. Scartoni, F. Mungai, M. Neikirk, K. Streeter, J. Pereira, R. O. Dai, D. F. Le, H. Mobley, H. Afolabi, J. Mobley, B. C. Wanjalla, C. N. Hall, D. Berry, J. Kovtun, O. Schafer, J. C. Schaffer, S. Katti, P. Evans, C. Kinder, A. George, J. G. McReynolds, M. Kirabo, A. Masenga, S. K. Hinton, A. 2026-03-30 doi:10.64898/2026.03.27.711928 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Targeting Protease-activated Receptor 4 (PAR4) Protects Against Acute Kidney Injury (AKI) in Ischemia Reperfusion Injury ]]> https://biorxiv.org/content/10.64898/2026.03.27.714572v1?rss=1 Webb, E. M. Cao, S. Pan, Y. Zhang, M.-Z. Harris, R. Boutaud, O. Bouchard, J. L. Jones, C. K. Lindsley, C. W. Hamm, H. E. 2026-03-30 doi:10.64898/2026.03.27.714572 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Treatment of murine autoimmune myocarditis with a novel monoclonal antibody that targets multiple inflammatory pathways ]]> https://biorxiv.org/content/10.64898/2026.03.27.714891v1?rss=1 Toldo, S. Luger, D. Vozenilek, A. Abbate, A. Kelly, J. Mezzaroma, E. Shibao, C. A. Abd-ElDayem, M. A. Klenerman, P. Waksman, R. Virmani, R. Maynard, J. A. Harrison, D. Flugelman, M. Y. Epstein, S. E. 2026-03-31 doi:10.64898/2026.03.27.714891 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Multidimensional MRI reveals cellular-scale microstructural phenotypes in human brain aging ]]> https://biorxiv.org/content/10.64898/2026.03.29.715117v1?rss=1 Park, J. S. Manninen, E. Bao, S. Landman, B. A. Yang, Y. Benjamini, D. 2026-03-31 doi:10.64898/2026.03.29.715117 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ 5-Azacytidine incorporation into mRNAs disrupts translation and induces ribosome collisions ]]> https://biorxiv.org/content/10.64898/2026.03.30.714548v1?rss=1 Roberson, A. B. Marks, J. Pitts, R. Tamilselvam, B. Grieb, B. Tansey, W. P. Meydan, S. 2026-03-31 doi:10.64898/2026.03.30.714548 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Fragile X messenger ribonucleoprotein modulates IL-6 induction and inflammatory cell death in macrophages ]]> https://biorxiv.org/content/10.64898/2026.03.30.712626v1?rss=1 Macha, B. N. Weindel, C. G. Fischer, T. Watson, R. O. Ho, L. A. Vail, K. J. 2026-04-01 doi:10.64898/2026.03.30.712626 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ De novo Folding Mechanisms of Lasso Peptides ]]> https://biorxiv.org/content/10.64898/2026.03.30.715466v1?rss=1 Yin, S. Mi, X. Barrett, S. E. Mitchell, D. A. Shukla, D. 2026-04-01 doi:10.64898/2026.03.30.715466 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ A high-resolution mass spectrometry-based method for quantifying insulin-stimulated glucose uptake in mice following an intraperitoneal injection of tracer ]]> https://biorxiv.org/content/10.64898/2026.03.31.714892v1?rss=1 Zhang, G.-F. Slentz, D. H. Lantier, L. McGuinness, O. P. Muoio, D. M. Williams, A. S. 2026-04-02 doi:10.64898/2026.03.31.714892 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ ER discontinuities are common in C. elegans neurons, revealing a genetically tractable model for ER network maintenance ]]> https://biorxiv.org/content/10.64898/2026.03.31.715740v1?rss=1 Mabry, K. N. 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