bioRxiv Channel: University of Kansas https://biorxiv.org This feed contains articles for bioRxiv Channel "University of Kansas" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ When genomes collide: multiple modes of germline misregulation in a dysgenic syndrome of Drosophila virilis ]]> https://biorxiv.org/content/10.1101/005124v1?rss=1 Mauricio A. Galdos Alexandra A. Erwin Michelle L. Wickersheim Chris C. Harrison Kendra D. Marr Justin Blumenstiel 2014-05-13 doi:10.1101/005124 Cold Spring Harbor Laboratory Press 2014-05-13 <![CDATA[ Pollen feeding proteomics: salivary proteins of the passion flower butterfly, Heliconius melpomene ]]> https://biorxiv.org/content/10.1101/013128v1?rss=1 Desiree Harpel Darron A Cullen Swidbert Ott Chris D Jiggins James R Walters 2014-12-22 doi:10.1101/013128 Cold Spring Harbor Laboratory Press 2014-12-22 <![CDATA[ Phylesystem: a git-based data store for community curated phylogenetic estimates ]]> https://biorxiv.org/content/10.1101/013862v1?rss=1 Emily Jane B. McTavish Cody E. Hinchliff James F. Allman Joseph W. Brown Karen A. Cranston Mark T. Holder Jonathan A. Rees Stephen A. Smith 2015-01-16 doi:10.1101/013862 Cold Spring Harbor Laboratory Press 2015-01-16 <![CDATA[ Sex chromosome dosage compensation in Heliconius butterflies: global yet still incomplete? ]]> https://biorxiv.org/content/10.1101/016675v1?rss=1 James R Walters Thomas J Hardcastle Chris Jiggins 2015-03-17 doi:10.1101/016675 Cold Spring Harbor Laboratory Press 2015-03-17 <![CDATA[ Phylogenomic analyses support traditional relationships within Cnidaria ]]> https://biorxiv.org/content/10.1101/017632v1?rss=1 Felipe Zapata Freya E Goetz Stephen A Smith Mark Howison Stefan Siebert Samuel Church Steven M Sanders Cheryl Lewis Ames Catherine S McFadden Scott C France Marymegan Daly Allen G Collins Steven HD Haddock Casey Dunn Paulyn Cartwright 2015-04-06 doi:10.1101/017632 Cold Spring Harbor Laboratory Press 2015-04-06 <![CDATA[ Identification of Slco1a6 as a candidate gene that broadly affects gene expression in mouse pancreatic islets ]]> https://biorxiv.org/content/10.1101/020974v1?rss=1 Jianan Tian Mark P. Keller Angie T. Oler Mary E. Rabaglia Kathryn L. Schueler Donald S. Stapleton Aimee Teo Broman Wen Zhao Christina Kendziorski Brian S. Yandell Bruno Hagenbuch Karl W Broman Alan D. Attie 2015-06-15 doi:10.1101/020974 Cold Spring Harbor Laboratory Press 2015-06-15 <![CDATA[ The C. elegans ephrin EFN-4 functions non-cell autonomously with heparan sulfate proteoglycans to promote axon outgrowth and branching ]]> https://biorxiv.org/content/10.1101/022756v1?rss=1 Alicia A Schwieterman Alyse N Steves Vivian Yee Cory J Donelson Aaron Pital Taylor Voyles Austin M Howard Danielle E Ereddia Kelsie S Effrein Jonathan L McMurry Brian D Ackley Andrew D Chisholm Martin L Hudson 2015-07-17 doi:10.1101/022756 Cold Spring Harbor Laboratory Press 2015-07-17 <![CDATA[ Phylogenetic relationships of the Helmeted Woodpecker (Dryocopus galeatus): A case of interspecific mimicry? ]]> https://biorxiv.org/content/10.1101/023663v1?rss=1 Brett W. Benz Mark B. Robbins Kevin J. Zimmer 2015-07-31 doi:10.1101/023663 Cold Spring Harbor Laboratory Press 2015-07-31 <![CDATA[ A segregating inversion generates fitness variation in a yellow monkeyflower (Mimulus guttatus) population ]]> https://biorxiv.org/content/10.1101/028670v1?rss=1 John Kelly John Willis Young Wha Lee Lila Fishman 2015-10-08 doi:10.1101/028670 Cold Spring Harbor Laboratory Press 2015-10-08 <![CDATA[ Comprehensive cross-population analysis of high-grade serous ovarian cancer supports no more than three subtypes ]]> https://biorxiv.org/content/10.1101/030239v1?rss=1 130 tumors using k-means and non-negative matrix factorization. Within each population, we summarized differential expression patterns for each cluster as moderated t statistic vectors using Significance Analysis of Microarrays. We calculated Pearsons correlations of these vectors to determine similarities and differences in expression patterns between clusters. We defined syn-clusters (SC) as sets of clusters that were strongly correlated across populations, and associated their expression patterns with biological pathways using geneset overrepresentation analyses.nnResultsAcross populations, for k = 3, moderated t score correlations for clusters 1, 2 and 3, respectively, ranged between 0.77-0.85, 0.80-0.90, and 0.65-0.77. For k = 4, correlations for clusters 1-4, respectively, ranged between 0.77-0.85, 0.83-0.89, 0.51-0.76, and 0.61-0.75. Within populations, comparing analogous clusters (k = 3 versus k = 4), correlations were high for clusters 1 and 2 (0.91-1.00), but were lower for cluster 3 (0.22-0.80). Results are similar using non-negative matrix factorization. SC1 corresponds to previously-reported mesenchymal-like, SC2 to proliferative-like, SC3 to immunoreactive-like, and SC4 to differentiated-like subtypes.nnConclusionsThe mesenchymal-like and proliferative-like subtypes are remarkably consistent across populations and could be uniquely targeted for treatment. The other two previously described subtypes are considerably less robust, and since cross-population comparison reveals that k = 3 and k = 4 are both consistent with our results, they may not represent clear subtypes. ]]> Gregory P Way James Rudd Chen Wang Habib Hamidi Brooke L Fridley Gottfried Konecny Ellen L Goode Casey S Greene Jennifer A Doherty 2015-10-30 doi:10.1101/030239 Cold Spring Harbor Laboratory Press 2015-10-30 <![CDATA[ Convergent patterns of sex chromosome dosage compensation between lepidopteran species (WZ/ZZ) and eutherian mammals (XX/XY): insights from a moth neo-Z chromosome ]]> https://biorxiv.org/content/10.1101/030767v1?rss=1 Liuqi Gu James Walters Douglas Knipple 2015-11-06 doi:10.1101/030767 Cold Spring Harbor Laboratory Press 2015-11-06 <![CDATA[ Whole genome sequencing of 56 Mimulus individuals illustrates population structure and local selection ]]> https://biorxiv.org/content/10.1101/031575v1?rss=1 Joshua Robert Puzey John H Willis John K Kelly 2015-11-13 doi:10.1101/031575 Cold Spring Harbor Laboratory Press 2015-11-13 <![CDATA[ A neo-sex chromosome in the Monarch butterfly, Danaus plexippus ]]> https://biorxiv.org/content/10.1101/036483v1?rss=1 90% of D. plexippus genes lays the foundation for novel insights concerning sex chromosome evolution in this female-heterogametic model species for functional and evolutionary genomics. ]]> James Walters Andrew J Mongue 2016-01-12 doi:10.1101/036483 Cold Spring Harbor Laboratory Press 2016-01-12 <![CDATA[ TreeToReads - a pipeline for simulating raw reads from phylogenies ]]> https://biorxiv.org/content/10.1101/037655v1?rss=1 Emily Jane McTavish James Pettengill Steven Davis Hugh Rand Errol Strain Marc Allard Ruth E Timme 2016-01-22 doi:10.1101/037655 Cold Spring Harbor Laboratory Press 2016-01-22 <![CDATA[ Zika Virus: Endemic Versus Epidemic Dynamics and Implications for Disease Spread in the Americas ]]> https://biorxiv.org/content/10.1101/041897v1?rss=1 Sharon Bewick William F Fagan Justin M Calabrese Folashade Agusto 2016-02-29 doi:10.1101/041897 Cold Spring Harbor Laboratory Press 2016-02-29 <![CDATA[ Positive selection on a regulatory insertion-deletion polymorphism in FADS2 influences apparent endogenous synthesis of arachidonic acid ]]> https://biorxiv.org/content/10.1101/042549v1?rss=1 Kumar S.D. Kothapalli Kaixiong Ye Maithili S. Gadgil Susan E. Carlson Kimberly O. O'Brien Ji Yao Zhang Hui Gyu Park Kinsley Ojukwu James Zou Stephanie S. Hyon Kalpana S. Joshi Alon Keinan J. Thomas Brenna 2016-03-06 doi:10.1101/042549 Cold Spring Harbor Laboratory Press 2016-03-06 <![CDATA[ Syndecan functions to regulate Wnt-dependent axon guidance in C. elegans ]]> https://biorxiv.org/content/10.1101/046094v1?rss=1 Samantha N Hartin Brian D Ackley 2016-03-28 doi:10.1101/046094 Cold Spring Harbor Laboratory Press 2016-03-28 <![CDATA[ The C. elegans NF2/Merlin Molecule NFM-1 Non-Autonomously Regulates Neuroblast Migration and Interacts Genetically with the Guidance Cue SLT-1/Slit ]]> https://biorxiv.org/content/10.1101/055079v1?rss=1 Matthew P Josephson Rana Aliani Erik Lundquist 2016-05-24 doi:10.1101/055079 Cold Spring Harbor Laboratory Press 2016-05-24 <![CDATA[ Defining the risk of Zika and chikungunya virus transmission in human population centers of the eastern United States ]]> https://biorxiv.org/content/10.1101/061382v1?rss=1 10% of the introductions could generate a disease outbreak of at least 100 people. Despite Ae. albopictus propensity for biting non-human vertebrates, we also demonstrate that local virus transmission and human outbreaks may occur when vectors feed from humans even just 40% of the time. This work demonstrates how a conditional series of non-average events can result in local arbovirus transmission and outbreaks of disease in humans, even in temperate cities.nnAuthor SummaryZika and chikungunya viruses are transmitted by Aedes mosquitoes, including Ae. albopictus, which is abundant in many temperate cities. While disease risk is lower in temperate regions where viral amplification cannot build across years, there is significant potential for localized disease outbreaks in urban populations. We use a model informed by field data to assess the conditions likely to facilitate local transmission of virus from an infected traveler to Ae. albopictus and then to other humans in USA cities with variable human densities and seasonality. The model predicts that one of every two infectious travelers arriving at peak mosquito season could initiate local transmission and > 10% of the introductions could generate a disease outbreak of >100 people.nnClassification: Ecology ]]> Carrie Manore Richard Ostfeld Folashade Agusto Holly Gaff Shannon LaDeau 2016-07-24 doi:10.1101/061382 Cold Spring Harbor Laboratory Press 2016-07-24 <![CDATA[ Distal axotomy enhances retrograde presynaptic excitability onto injured pyramidal neurons via trans-synaptic signaling ]]> https://biorxiv.org/content/10.1101/065391v1?rss=1 Tharkika Nagendran Rebecca Bigler Rylan Larsen Benjamin Philpot Anne Marion Taylor 2016-07-25 doi:10.1101/065391 Cold Spring Harbor Laboratory Press 2016-07-25 <![CDATA[ A defensive body plan was pre-adaptive for termitophily in the rove beetle tribe Termitohospitini (Staphylinidae: Aleocharinae) ]]> https://biorxiv.org/content/10.1101/083881v1?rss=1 Kanao, T. Eldredge, K. Maruyama, M. 2016-10-27 doi:10.1101/083881 Cold Spring Harbor Laboratory Press 2016-10-27 <![CDATA[ Shifting microbial communities sustain multi-year iron reduction and methanogenesis in ferruginous sediment incubations ]]> https://biorxiv.org/content/10.1101/087783v1?rss=1 Bray, M. S. Wu, J. Reed, B. C. Kretz, C. B. Simister, R. L. Henny, C. Stewart, F. J. DiChristina, T. J. Brandes, J. A. Fowle, D. A. Crowe, S. A. Glass, J. B. 2016-11-15 doi:10.1101/087783 Cold Spring Harbor Laboratory Press 2016-11-15 <![CDATA[ A community-based collaboration to build prediction models for short-term discontinuation of docetaxel in metastatic castration-resistant prostate cancer patients ]]> https://biorxiv.org/content/10.1101/087809v1?rss=1 Seyednasrollah, F. Koestler, D. C. Wang, T. Piccolo, S. R. Vega, R. Greiner, R. Fuchs, C. Gofer, E. Kumar, L. Wolfinger, R. D. Kanigel Winner, K. Bare, C. Neto, E. C. Yu, T. Shen, L. Abdallah, K. Norman, T. Stolovitzky, G. PCC-DREAM Community, Soule, H. Sweeney, C. J. Ryan, C. J. Scher, H. I. Sartor, O. Elo, L. L. Zhou, F. L. Guinney, J. Costello, J. C. 2016-11-15 doi:10.1101/087809 Cold Spring Harbor Laboratory Press 2016-11-15 <![CDATA[ Flagellar synchronization is a simple alternative to cell cycle synchronization for ciliary and flagellar studies ]]> https://biorxiv.org/content/10.1101/089185v1?rss=1 Dutta, S. Avasthi, P. 2016-11-22 doi:10.1101/089185 Cold Spring Harbor Laboratory Press 2016-11-22 <![CDATA[ Chlamydomonas reinhardtii formin and profilin are optimized for acute rapid actin filament assembly ]]> https://biorxiv.org/content/10.1101/096008v1?rss=1 Christensen, J. R. Glista, M. J. Mueller, D. M. Li, Y. Sees, J. A. Skau, C. T. Mets, L. J. Avasthi, P. Kovar, D. R. 2016-12-21 doi:10.1101/096008 Cold Spring Harbor Laboratory Press 2016-12-21 <![CDATA[ A SUPERNOVA AT 50 PC: EFFECTS ON THE EARTHS ATMOSPHERE AND BIOTA ]]> https://biorxiv.org/content/10.1101/108936v1?rss=1 Melott, A. Thomas, B. Kachelriess, M. Semikoz, D. Overholt, A. 2017-02-15 doi:10.1101/108936 Cold Spring Harbor Laboratory Press 2017-02-15 <![CDATA[ The genomic architecture of flowering time varies across space and time in Mimulus guttatus ]]> https://biorxiv.org/content/10.1101/111203v1?rss=1 Monnahan, P. Kelly, J. K. 2017-02-23 doi:10.1101/111203 Cold Spring Harbor Laboratory Press 2017-02-23 <![CDATA[ Evolutionary dynamics of male reproductive genes in the Drosophila virilis subgroup ]]> https://biorxiv.org/content/10.1101/111377v1?rss=1 Ahmed-Braimah, Y. H. Unckless, R. L. Clark, A. G. 2017-02-24 doi:10.1101/111377 Cold Spring Harbor Laboratory Press 2017-02-24 <![CDATA[ Correcting For Cell-Type Heterogeneity In Epigenome-Wide Association Studies: Premature Analyses And Conclusions ]]> https://biorxiv.org/content/10.1101/121533v1?rss=1 Zheng, S. Beck, S. Jaffe, A. Koestler, D. Hansen, K. Houseman, A. Widschwendter, M. Irizarry, R. Teschendorff, A. 2017-03-28 doi:10.1101/121533 Cold Spring Harbor Laboratory Press 2017-03-28 <![CDATA[ C. elegans Flavin Monooxygenases Regulate C. elegans Axon Guidance and Growth Cone Protrusion with UNC-6/Netrin signaling and Rac GTPases ]]> https://biorxiv.org/content/10.1101/131755v1?rss=1 Gujar, M. R. Stricker, A. M. Lundquist, E. A. 2017-04-28 doi:10.1101/131755 Cold Spring Harbor Laboratory Press 2017-04-28 <![CDATA[ Global analysis of plasma lipids identifies liver-derived acyl-carnitines as a fuel source for brown fat thermogenesis ]]> https://biorxiv.org/content/10.1101/132241v1?rss=1 nView larger version (80K):norg.highwire.dtl.DTLVardef@1282891org.highwire.dtl.DTLVardef@17f7c7forg.highwire.dtl.DTLVardef@c6b637org.highwire.dtl.DTLVardef@1e4f40d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Simcox, J. Geoghegan, G. Maschek, J. A. Pasquali, M. Miao, R. Lee, S. Jiang, L. Huck, I. Donato, A. Apte, U. Longo, N. Rutter, J. Cox, J. Villanueva, C. J. 2017-04-28 doi:10.1101/132241 Cold Spring Harbor Laboratory Press 2017-04-28 <![CDATA[ Naturally-segregating Variation at Ugt86Dd Contributes to Nicotine Resistance in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/134429v1?rss=1 Highfill, C. Tran, J. Nguyen, S. Moldenhauer, T. Wang, X. Macdonald, S. J. 2017-05-05 doi:10.1101/134429 Cold Spring Harbor Laboratory Press 2017-05-05 <![CDATA[ Contrasting Patterns Of Evolutionary Constraint And Novelty Revealed By Comparative Sperm Proteomic Analysis ]]> https://biorxiv.org/content/10.1101/144089v1?rss=1 Whittington, E. Forsythe, D. Karr, T. L. Walters, J. Dorus, S. 2017-05-30 doi:10.1101/144089 Cold Spring Harbor Laboratory Press 2017-05-30 <![CDATA[ Dynamical predictors of an imminent phenotypic switch in bacteria ]]> https://biorxiv.org/content/10.1101/145821v1?rss=1 Wang, H. Ray, J. C. J. 2017-06-03 doi:10.1101/145821 Cold Spring Harbor Laboratory Press 2017-06-03 <![CDATA[ De novo discovery of structural motifs in RNA 3D structures through clustering ]]> https://biorxiv.org/content/10.1101/155580v1?rss=1 Ge, P. Islam, S. Zhong, C. Zhang, S. 2017-06-27 doi:10.1101/155580 Cold Spring Harbor Laboratory Press 2017-06-27 <![CDATA[ Understanding the dynamics of scaffold-mediated signaling ]]> https://biorxiv.org/content/10.1101/167205v1?rss=1 Suderman, R. Schauer, A. Deeds, E. 2017-07-21 doi:10.1101/167205 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ The Microbiomes of Pancreatic Tissue in Pancreatic Cancer and Non-Cancer Subjects ]]> https://biorxiv.org/content/10.1101/189043v1?rss=1 del Castillo, E. Meier, R. Koestler, D. C. Chen, T. Paster, B. J. Charpentier, K. P. Kelsey, K. T. Izard, J. Michaud, D. S. 2017-09-15 doi:10.1101/189043 Cold Spring Harbor Laboratory Press 2017-09-15 <![CDATA[ The dynamic evolution of Drosophila innubila Nudivirus ]]> https://biorxiv.org/content/10.1101/197293v1?rss=1 Hill, T. Unckless, R. 2017-10-02 doi:10.1101/197293 Cold Spring Harbor Laboratory Press 2017-10-02 <![CDATA[ Hox-logic of preadaptations for social insect symbiosis in rove beetles ]]> https://biorxiv.org/content/10.1101/198945v1?rss=1 Parker, J. Eldredge, K. T. Thomas, I. Coleman, R. Davis, S. 2017-10-05 doi:10.1101/198945 Cold Spring Harbor Laboratory Press 2017-10-05 <![CDATA[ Protein-protein interactions with fructose-1-kinase alter function of the central Escherichia coli transcription regulator, Cra ]]> https://biorxiv.org/content/10.1101/201277v1?rss=1 100 genes in central metabolism by binding upstream DNA operator sequences. Genes encoding glycolytic enzymes are repressed, whereas those for gluconeogenesis and the citric acid cycle are activated. Cra-DNA binding is allosterically diminished by binding to either fructose-1-phosphate (F-1-P, generated upon fructose import) or fructose-1,6-bisphosphate (F-1,6-BP). F-1,6-BP is generated from F-1-P by the enzyme fructose-1-kinase (FruK) or from other sugars and is a key intermediate in glycolysis. Here, we report that Cra directly interacts with FruK to form a tight protein-protein complex. Further, growth assays with a fruK knockout strain show that FruK has a broader role in metabolism than its known role in fructose catabolism. Biochemical experiments show that F-1,6-BP binding enhances either the Cra/FruK interaction and/or CRA binding to DNA and that FruK can catalyze the reverse reaction of F-1,6-BP to F-1-P. Results were used to propose a model in which the Cra-FruK complex enhances activation of gluconeogenic genes. Finally, since FruK itself is repressed by Cra, these newly-reported events add layers to the dynamic regulation of E. coli central metabolism that occur in response to changing nutrients. ]]> Singh, D. Fairlamb, M. S. Harrison, K. S. Weeramange, C. Meinhardt, S. Tungtur, S. Rau, B. F. Hefty, P. S. Fenton, A. W. Swint-Kruse, L. 2017-10-11 doi:10.1101/201277 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ broad controls leg imaginal disc morphogenesis in Drosophila via regulation of cell shape changes and remodeling of extracellular matrix ]]> https://biorxiv.org/content/10.1101/2019.12.21.885848v1?rss=1 Rice, C. Wang, X. Macdonald, S. Ward, R. 2019-12-22 doi:10.1101/2019.12.21.885848 Cold Spring Harbor Laboratory Press 2019-12-22 <![CDATA[ Expression and function of voltage gated proton channels (H V 1) in MDA-MB-231 cells ]]> https://biorxiv.org/content/10.1101/2019.12.23.886945v1?rss=1 Bare, D. Cherny, V. Abukhdeir, A. DeCoursey, T. morgan, d. 2019-12-23 doi:10.1101/2019.12.23.886945 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ Contrasting model mechanisms of alanine aminotransferase (ALT) release from damaged and necrotic hepatocytes as an example of general biomarker mechanisms ]]> https://biorxiv.org/content/10.1101/2019.12.24.887869v1?rss=1 Smith, A. K. Ropella, G. E. P. McGill, M. R. Krishnan, P. Dutta, L. Kennedy, R. C. Jaeschke, H. Hunt, C. A. 2019-12-24 doi:10.1101/2019.12.24.887869 Cold Spring Harbor Laboratory Press 2019-12-24 <![CDATA[ Teratogenic Drug Topiramate Upregulates TGFβ1 and SOX9 Expression in Primary Palatal Mesenchyme Cells ]]> https://biorxiv.org/content/10.1101/2019.12.31.892042v1?rss=1 Rafi, S. K. Goering, J. P. Olm-Shipman, A. J. Hipp, L. A. Ernst, N. J. Wilson, N. R. Hall, E. G. Gunewardena, S. Saadi, I. 2020-01-02 doi:10.1101/2019.12.31.892042 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ Multi-scalar Approaches to the stable isotope ecology of late Quaternary Proboscideans in the Midcontinent ]]> https://biorxiv.org/content/10.1101/2020.01.08.896647v1?rss=1 Widga, C. Hodgins, G. Kolis, K. Lengyel, S. N. Saunders, J. J. Walker, J. D. Wanamaker, A. D. 2020-01-09 doi:10.1101/2020.01.08.896647 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Retrospective Ensemble Docking of Allosteric Modulators in an Adenosine G-Protein-Coupled Receptor ]]> https://biorxiv.org/content/10.1101/2020.01.11.902809v1?rss=1 Bhattarai, A. Wang, J. Miao, Y. 2020-01-13 doi:10.1101/2020.01.11.902809 Cold Spring Harbor Laboratory Press 2020-01-13 <![CDATA[ Microbiome composition differs in hybrid and inbred maize ]]> https://biorxiv.org/content/10.1101/2020.01.13.904979v1?rss=1 Wagner, M. R. Roberts, J. H. Balint-Kurti, P. J. Holland, J. B. 2020-01-14 doi:10.1101/2020.01.13.904979 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Dispersal limitation and fire feedbacks maintain mesic savannas in Madagascar ]]> https://biorxiv.org/content/10.1101/2020.01.14.905208v1?rss=1 Goel, N. Vleck, E. V. Aleman, J. C. Staver, A. C. 2020-01-15 doi:10.1101/2020.01.14.905208 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ WNT and inflammatory signaling distinguish human Fallopian tube epithelial cell populations ]]> https://biorxiv.org/content/10.1101/2020.01.15.908293v1?rss=1 Rose, I. M. Bidarimath, M. Webster, A. Godwin, A. K. Flesken-Nikitin, A. Nikitin, A. Y. 2020-01-16 doi:10.1101/2020.01.15.908293 Cold Spring Harbor Laboratory Press 2020-01-16 <![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[ Molecular evolution of luciferase diversified bioluminescent signals in sea fireflies (Crustacea:Ostracoda:Cypridinidae) ]]> https://biorxiv.org/content/10.1101/2020.01.23.917187v1?rss=1 Hensley, N. M. Ellis, E. A. Leung, N. Y. Coupart, J. Mikhailovsky, A. Taketa, D. A. Tessler, M. Gruber, D. F. De Tomaso, A. W. Rivers, T. J. Gerrish, G. A. Torres, E. Oakley, T. H. 2020-01-24 doi:10.1101/2020.01.23.917187 Cold Spring Harbor Laboratory Press 2020-01-24 <![CDATA[ Early life stress reduces voluntary exercise and its prevention of diet-induced obesity and metabolic dysfunction in mice ]]> https://biorxiv.org/content/10.1101/2020.01.24.918805v1?rss=1 Eller-Smith, O. C. Morris, E. M. M. Thyfault, J. P. Christianson, J. A. 2020-01-25 doi:10.1101/2020.01.24.918805 Cold Spring Harbor Laboratory Press 2020-01-25 <![CDATA[ Thm2 interacts with paralog, Thm1, and sensitizes to Hedgehog signaling in postnatal skeletogenesis ]]> https://biorxiv.org/content/10.1101/2020.01.26.920165v1?rss=1 Allard, B. A. Wang, W. Pottorf, T. S. Mumtaz, H. Silva, L. M. Jacobs, D. T. Wang, J. Bumann, E. E. Tran, P. V. 2020-01-27 doi:10.1101/2020.01.26.920165 Cold Spring Harbor Laboratory Press 2020-01-27 <![CDATA[ Chromatin features define adaptive genomic regions in a fungal plant pathogen ]]> https://biorxiv.org/content/10.1101/2020.01.27.921486v1?rss=1 Cook, D. E. Kramer, M. H. Seidl, M. F. Thomma, B. P. 2020-01-28 doi:10.1101/2020.01.27.921486 Cold Spring Harbor Laboratory Press 2020-01-28 <![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[ Multiscale modelling of motility wave propagation in cell migration ]]> https://biorxiv.org/content/10.1101/2020.01.28.924191v1?rss=1 Khataee, H. Neufeld, Z. Czirok, A. 2020-01-29 doi:10.1101/2020.01.28.924191 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ Phylogenomics of monitor lizards and the role of competition in dictating body size disparity ]]> https://biorxiv.org/content/10.1101/2020.02.02.931188v1?rss=1 Brennan, I. G. Lemmon, A. R. Moriarty Lemmon, E. Portik, D. M. Weijola, V. Welton, L. Donnellan, S. C. Keogh, J. S. 2020-02-03 doi:10.1101/2020.02.02.931188 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ PICH translocase activity is required for proper distribution of SUMOylated proteins on mitotic chromosomes ]]> https://biorxiv.org/content/10.1101/2020.02.06.937243v1?rss=1 Hassebroek, V. A. Park, H. Pandey, N. Lerbakken, B. Aksenova, V. Arnaoutov, A. Dasso, M. Azuma, Y. 2020-02-07 doi:10.1101/2020.02.06.937243 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ A gatekeeping role of ESR2 to maintain the primordial follicle reserve ]]> https://biorxiv.org/content/10.1101/2020.02.06.937953v1?rss=1 Rumi, M. A. Chakravarthi, V. P. Ghosh, S. Roby, K. F. Wolfe, M. W. 2020-02-07 doi:10.1101/2020.02.06.937953 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Trait-based aerial dispersal of arbuscular mycorrhizal fungi ]]> https://biorxiv.org/content/10.1101/2020.02.12.943878v1?rss=1 Chaudhary, B. Nolimal, S. Sosa Hernandez, M. A. Egan, C. Kastens, J. 2020-02-12 doi:10.1101/2020.02.12.943878 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ The predicted RNA-binding protein ETR-1/CELF1 acts in muscles to regulate neuroblast migration in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2020.02.25.965277v1?rss=1 Ochs, M. E. Josephson, M. P. Lundquist, E. A. 2020-02-25 doi:10.1101/2020.02.25.965277 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Theoretical analysis of neural crest cell migration ]]> https://biorxiv.org/content/10.1101/2020.03.04.976209v1?rss=1 Khataee, H. Neufeld, Z. Czirok, A. 2020-03-04 doi:10.1101/2020.03.04.976209 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ A comparative analysis of Caenorhabditis and Drosophila transcriptional changes in response to pathogen infection ]]> https://biorxiv.org/content/10.1101/2020.03.04.977595v1?rss=1 Unckless, R. L. Lansdon, P. A. Ackley, B. D. 2020-03-05 doi:10.1101/2020.03.04.977595 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Mechanisms of γ-Secretase Activation and Substrate Processing ]]> https://biorxiv.org/content/10.1101/2020.03.09.984534v1?rss=1 Bhattarai, A. Devkota, S. Bhattarai, S. Wolfe, M. S. Miao, Y. 2020-03-11 doi:10.1101/2020.03.09.984534 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Controlling the Growth of the Skin Commensal Staphylococcus epidermidis Using D-Alanine Auxotrophy ]]> https://biorxiv.org/content/10.1101/2020.03.10.985911v1?rss=1 Whitfill, T. M. Dodds, D. Bose, J. L. Dong, M.-D. Dube, G. Grossman, T. Kaiser, A. Kulkarni, K. Leger, R. Mootien-Boyd, S. Munivar, A. Oh, J. Pestrak, M. Rajpura, K. Tikhonov, A. Turecek, T. 2020-03-11 doi:10.1101/2020.03.10.985911 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Feeding-dependent tentacle development in the sea anemone Nematostella vectensis ]]> https://biorxiv.org/content/10.1101/2020.03.12.985168v1?rss=1 Ikmi, A. Steenbergen, P. J. Anzo, M. McMullen, M. R. Stokkermans, A. Ellington, L. R. Gibson, M. C. 2020-03-12 doi:10.1101/2020.03.12.985168 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ Mutant p53 suppresses innate immune signaling to promote tumorigenesis ]]> https://biorxiv.org/content/10.1101/2020.03.12.989384v1?rss=1 Ghosh, M. Saha, S. Bettke, J. A. Nagar, R. Parrales, A. Iwakuma, T. van der Velden, A. W. M. Martinez, L. A. 2020-03-13 doi:10.1101/2020.03.12.989384 Cold Spring Harbor Laboratory Press 2020-03-13 <![CDATA[ Testing the Effect of the Toba Volcanic Eruption on Population Sizes in Worldwide Mammal Species ]]> https://biorxiv.org/content/10.1101/2020.04.06.028050v1?rss=1 Torosin, N. S. Raff, J. S. Hayes, M. G. 2020-04-07 doi:10.1101/2020.04.06.028050 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Visualizing Rev1 Catalyze Protein-template DNA Synthesis ]]> https://biorxiv.org/content/10.1101/2020.04.10.036236v1?rss=1 Weaver, T. M. Cortez, L. M. Khoang, T. H. Washington, M. T. Agarwal, P. Freudenthal, B. D. 2020-04-12 doi:10.1101/2020.04.10.036236 Cold Spring Harbor Laboratory Press 2020-04-12 <![CDATA[ Evolutionary divergence of potential drought adaptations between two subspecies of an annual plant: Do some constraints need to be broken? ]]> https://biorxiv.org/content/10.1101/2020.04.16.042572v1?rss=1 Burnette, T. E. Eckhart, V. M. 2020-04-18 doi:10.1101/2020.04.16.042572 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Coronavirus Infection and PARP Expression Dysregulate the NAD Metabolome: A Potentially Actionable Component of Innate Immunity ]]> https://biorxiv.org/content/10.1101/2020.04.17.047480v1?rss=1 Heer, C. D. Sanderson, D. J. Alhammad, Y. M. O. Schmidt, M. S. Trammell, S. A. J. Perlman, S. Cohen, M. S. Fehr, A. R. Brenner, C. 2020-04-18 doi:10.1101/2020.04.17.047480 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Caught in the Act: Anthrax Toxin Translocation Complex Reveals insight into the Lethal Factor Unfolding and Refolding mechanism ]]> https://biorxiv.org/content/10.1101/2020.04.20.049601v1?rss=1 Machen, A. J. Fisher, M. T. Freudenthal, B. D. 2020-04-20 doi:10.1101/2020.04.20.049601 Cold Spring Harbor Laboratory Press 2020-04-20 <![CDATA[ Ligand Gaussian accelerated molecular dynamics (LiGaMD): Characterization of ligand binding thermodynamics and kinetics ]]> https://biorxiv.org/content/10.1101/2020.04.20.051979v1?rss=1 Miao, Y. Bhattarai, A. Wang, J. 2020-04-21 doi:10.1101/2020.04.20.051979 Cold Spring Harbor Laboratory Press 2020-04-21 <![CDATA[ Tumor-infiltrating nerves create an electro-physiologically active microenvironment and contribute to treatment resistance ]]> https://biorxiv.org/content/10.1101/2020.04.24.058594v1?rss=1 Kovacs, A. Vermeer, D. W. Madeo, M. Vermeer, S. J. Williamson, C. S. Rickel, A. Stamp, J. Lucido, C. T. Cain, J. Bell, M. Morgan, M. Yoon, J.-Y. Mitchell, M. A. Tulina, N. Stuckelberger, S. Budina, A. Orman, D. Jung, E. Schwartz, L. E. Eichwald, T. Hong, Z. Weimer, J. Hooper, J. E. Godwin, A. K. Talbot, S. Drapkin, R. Vermeer, P. D. 2020-04-25 doi:10.1101/2020.04.24.058594 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Establishment of a Replicon System for Bourbon Virus and Identification of Small Molecules that Efficiently Inhibit Virus Replication ]]> https://biorxiv.org/content/10.1101/2020.04.24.058693v1?rss=1 Hao, S. Ning, K. Wang, X. Wang, J. Cheng, F. Ganaie, S. S. Tavis, J. E. Qiu, J. 2020-04-25 doi:10.1101/2020.04.24.058693 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Intraflagellar transport-A deficiency ameliorates ADPKD renal cystogenesis in a renal tubular- and maturation-dependent manner ]]> https://biorxiv.org/content/10.1101/2020.04.26.061796v1?rss=1 Wang, W. Silva, L. Allard, B. Pottorf, T. Wang, H. Jacobs, D. Cornelius, J. Chaturvedi, A. Pritchard, M. Sharma, M. Wallace, D. Calvet, J. Tran, P. 2020-04-28 doi:10.1101/2020.04.26.061796 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Transcriptome Sequencing Reveals Sex Differences in Human Meniscal Cell Response to Estrogen Based on Dosing Kinetics ]]> https://biorxiv.org/content/10.1101/2020.04.27.064451v1?rss=1 Knewtson, K. E. Gonzalez Flores, J. G. Pacicca, D. M. Robinson, J. L. 2020-04-29 doi:10.1101/2020.04.27.064451 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Atypical meiosis can be adaptive in outcrossed S. pombe due to wtf meiotic drivers ]]> https://biorxiv.org/content/10.1101/2020.04.28.066035v1?rss=1 Bravo Nunez, M. A. Sabbarini, I. M. Eide, L. E. Unckless, R. L. Zanders, S. E. 2020-05-01 doi:10.1101/2020.04.28.066035 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ Placental microRNA Expression Associates with Birthweight through Control of Adipokines: Results from Two Independent Cohorts ]]> https://biorxiv.org/content/10.1101/2020.04.28.067025v1?rss=1 Kennedy, E. M. Hermetz, K. Burt, A. Everson, T. M. Deyssenroth, M. Hao, K. Chen, J. Karagas, M. R. Pei, D. Koestler, D. C. Marsit, C. J. 2020-04-29 doi:10.1101/2020.04.28.067025 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Microbe-dependent heterosis in maize ]]> https://biorxiv.org/content/10.1101/2020.05.05.078766v1?rss=1 Wagner, M. R. Tang, C. Salvato, F. Clouse, K. M. Bartlett, A. Sermons, S. Hoffmann, M. Balint-Kurti, P. J. Kleiner, M. 2020-05-07 doi:10.1101/2020.05.05.078766 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Recognition memory via repetition suppression in mouse hippocampal dorsal CA2 pyramidal neurons expressing the vasopressin 1b receptor ]]> https://biorxiv.org/content/10.1101/2020.05.11.078915v1?rss=1 Cymerblit-Sabba, A. Stackmann, M. Williams Avram, S. Granovetter, M. C. Cliz, N. I. Pereira, F. Smith, A. S. Song, J. Lee, H.-J. Young, W. S. 2020-05-12 doi:10.1101/2020.05.11.078915 Cold Spring Harbor Laboratory Press 2020-05-12 <![CDATA[ The SARS-CoV-2 conserved macrodomain is a highly efficient ADP-ribosylhydrolase enzyme ]]> https://biorxiv.org/content/10.1101/2020.05.11.089375v1?rss=1 Alhammad, Y. M. O. Kashipathy, M. M. Roy, A. Johnson, D. K. McDonald, P. Battaile, K. P. Gao, P. Lovell, S. W. Fehr, A. R. 2020-05-12 doi:10.1101/2020.05.11.089375 Cold Spring Harbor Laboratory Press 2020-05-12 <![CDATA[ Characterizing the genetic basis of copper toxicity in Drosophila reveals a complex pattern of allelic, regulatory, and behavioral variation ]]> https://biorxiv.org/content/10.1101/2020.05.13.094524v1?rss=1 Everman, E. R. Cloud-Richardson, K. M. Macdonald, S. J. 2020-05-15 doi:10.1101/2020.05.13.094524 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Superior Colliculus-Projected GABAergic Retinal Ganglion Cells Mediate Looming-Evoked Flight Response ]]> https://biorxiv.org/content/10.1101/2020.05.14.090167v1?rss=1 Luo, X. Cai, D. Shen, K. Deng, Q. Lei, X. Jin, S. Zeng, W.-B. Li, H. Xu, F. Huang, L. Ren, C. Luo, M.-H. Xie, T. Shen, Y. 2020-05-16 doi:10.1101/2020.05.14.090167 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Selection and demography shape genomic variation in a Sky Island species ]]> https://biorxiv.org/content/10.1101/2020.05.14.096008v1?rss=1 Hill, T. Unckless, R. 2020-05-16 doi:10.1101/2020.05.14.096008 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Recurrent evolution of two competing haplotypes in an insect DNA virus ]]> https://biorxiv.org/content/10.1101/2020.05.14.096024v1?rss=1 Hill, T. Unckless, R. 2020-05-16 doi:10.1101/2020.05.14.096024 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Nutrient restriction, inducer of yeast meiosis, induces mammalian meiosis ]]> https://biorxiv.org/content/10.1101/2020.05.15.074542v1?rss=1 Zhang, X. Gunewardena, S. Wang, N. 2020-05-16 doi:10.1101/2020.05.15.074542 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Rapid divergence of the copulation proteins in the Drosophila dunni group is associated with hybrid post-mating-prezygotic incompatibilities ]]> https://biorxiv.org/content/10.1101/2020.05.20.106724v1?rss=1 Hill, T. Rosales-Stephens, H.-L. Unckless, R. 2020-05-22 doi:10.1101/2020.05.20.106724 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Burkholderia thailandensis methylated hydroxy-alkylquinolines: biosynthesis and antimicrobial activity in co-culture experiments ]]> https://biorxiv.org/content/10.1101/2020.05.27.120295v1?rss=1 Klaus, J. R. Majerczyk, C. Eppler, N. A. Ball, P. Groleau, M.-C. Asfahl, K. L. Smalley, N. E. Hayden, H. Piochon, M. Dandekar, A. A. Gauthier, C. Deziel, E. Chandler, J. R. 2020-05-28 doi:10.1101/2020.05.27.120295 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ The long non-coding RNA lnc-HLX-2-7 is oncogenic in group 3 medulloblastomas ]]> https://biorxiv.org/content/10.1101/2020.06.08.140251v1?rss=1 KATSUSHIMA, K. Lee, B. Kunhiraman, H. Zhong, C. Murath, R. Ying, J. Liu, B. Garancher, A. Gonzalez-Gomez, I. Stapleton, S. Vibhakar, R. Bettegowda, C. Wechsler-Reya, R. J. Jallo, G. Raabe, E. Eberhart, C. G. Perera, R. J. 2020-06-09 doi:10.1101/2020.06.08.140251 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Structural characterization of the essential cell division protein FtsE and its interaction with FtsX in Streptococcus pneumoniae ]]> https://biorxiv.org/content/10.1101/2020.06.08.141481v1?rss=1 Alcorlo, M. Straume, D. Lutkenhaus, J. Havarstein, L. S. Hermoso, J. A. 2020-06-12 doi:10.1101/2020.06.08.141481 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Corticocortical Connections of the Rostral Forelimb Area in Rats: A Quantitative Tract-Tracing Study ]]> https://biorxiv.org/content/10.1101/2020.06.10.144923v1?rss=1 Urban, E. T. Nudo, R. J. Nishibe, M. Barbay, S. Guggenmos, D. J. 2020-06-10 doi:10.1101/2020.06.10.144923 Cold Spring Harbor Laboratory Press 2020-06-10 <![CDATA[ Task Related Neural Activity Following Primary Motor Cortical Ischemic Injury in Rats ]]> https://biorxiv.org/content/10.1101/2020.06.11.146266v1?rss=1 Pack, A. Murphy, M. D. Nudo, R. J. Barbay, S. Guggenmos, D. J. 2020-06-12 doi:10.1101/2020.06.11.146266 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Effects Of A Contusive Spinal Cord Injury On Spinal Motor Neuron Activity And Conduction Time In Rats ]]> https://biorxiv.org/content/10.1101/2020.06.11.146837v1?rss=1 Borrell, J. A. Krizsan-Agbas, D. Nudo, R. J. Frost, S. B. 2020-06-12 doi:10.1101/2020.06.11.146837 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Activity Dependent Stimulation Increases Synaptic Efficacy In Spared Pathways In An Anesthetized Rat Model Of Spinal Cord Contusion Injury ]]> https://biorxiv.org/content/10.1101/2020.06.11.146910v1?rss=1 Borrell, J. A. Krizsan-Agbas, D. Nudo, R. J. Frost, S. B. 2020-06-12 doi:10.1101/2020.06.11.146910 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Functional Suppression of Premotor Activity in a Transient Model of Motor Cortex Injury ]]> https://biorxiv.org/content/10.1101/2020.06.12.148403v1?rss=1 Elliott, K. C. Borrell, J. A. Barbay, S. Nudo, R. J. 2020-06-13 doi:10.1101/2020.06.12.148403 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ Anatomical Plasticity of the Distal Forelimb Projection of the Ventral Premotor Cortex Four weeks After Primary Motor Cortex Injury ]]> https://biorxiv.org/content/10.1101/2020.06.12.148494v1?rss=1 McNeal, D. W. Barbay, S. Frost, S. B. Taylor, M. Guggenmos, D. J. Nudo, R. J. 2020-06-13 doi:10.1101/2020.06.12.148494 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ ZZ Top: faster and more adaptive Z chromosome evolution in two Lepidoptera ]]> https://biorxiv.org/content/10.1101/2020.06.13.142711v1?rss=1 Mongue, A. J. Hansen, M. E. Walters, J. R. 2020-06-15 doi:10.1101/2020.06.13.142711 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Transcriptomic analysis of four cerianthid (Cnidaria, Ceriantharia) venoms ]]> https://biorxiv.org/content/10.1101/2020.06.18.159541v1?rss=1 Klompen, A. M. L. Macrander, J. Reitzel, A. M. Stampar, S. N. 2020-06-20 doi:10.1101/2020.06.18.159541 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Structure-Based Design with Tag-Based Purification and In-Process Biotinylation Enable Streamlined Development of SARS-CoV-2 Spike Molecular Probes ]]> https://biorxiv.org/content/10.1101/2020.06.22.166033v1?rss=1 5 mg/L for several subregions. Probes were characterized for antigenicity and ACE2 recognition, and the structure of the spike ectodomain probe was determined by cryo-electron microscopy. We also characterized antibody-binding specificities and cell-sorting capabilities of the biotinylated probes. Altogether, structure-based design coupled to efficient purification and biotinylation processes can thus enable streamlined development of SARS-CoV-2 spike-ectodomain probes. ]]> Zhou, T. Teng, I.-T. Olia, A. S. Cerutti, G. Gorman, J. Nazzari, A. Shi, W. Tsybovsky, Y. Wang, L. Wang, S. Zhang, B. Zhang, Y. Katsamba, P. S. Petrova, Y. Banach, B. B. Fahad, A. S. Liu, L. Lopez Acevedo, S. N. Madan, B. Oliveira de Souza, M. Pan, X. Wang, P. Wolfe, J. R. Yin, M. Ho, D. D. Phung, E. DiPiazza, A. Chang, L. Abiona, O. Corbett, K. S. DeKosky, B. J. Graham, B. S. Mascola, J. R. Misasi, J. Ruckwardt, T. Sullivan, N. J. Shapiro, L. Kwong, P. D. 2020-06-23 doi:10.1101/2020.06.22.166033 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ Predicting evolutionary change at the DNA level in a natural Mimulus population ]]> https://biorxiv.org/content/10.1101/2020.06.23.166736v1?rss=1 Monnahan, P. Colicchio, J. Fishman, L. Macdonald, S. Kelly, J. K. 2020-06-23 doi:10.1101/2020.06.23.166736 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ Germline gene de-silencing by a transposon insertion is triggered by an altered landscape of local piRNA biogenesis ]]> https://biorxiv.org/content/10.1101/2020.06.26.173187v1?rss=1 Miller, D. Van Vaerenberghe, K. Li, A. Grantham, E. K. Cummings, C. Barragan, M. Egidy, R. Scott, A. R. Hall, K. Perera, A. Gilliland, W. D. Blumenstiel, J. P. 2020-06-26 doi:10.1101/2020.06.26.173187 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ A clinically-relevant polymorphism in the Na+/taurocholate cotransporting polypeptide (NTCP) occurs at a rheostat position ]]> https://biorxiv.org/content/10.1101/2020.07.02.184424v1?rss=1 Ruggiero, M. J. Malhotra, S. Fenton, A. W. Swint-Kruse, L. Karanicolas, J. Hagenbuch, B. 2020-07-03 doi:10.1101/2020.07.02.184424 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ Substitutions at Non-Conserved Rheostat Positions Modulate Function by Re-Wiring Long-Range, Dynamic Interactions ]]> https://biorxiv.org/content/10.1101/2020.07.02.185207v1?rss=1 Campitelli, P. Swint-Kruse, L. Ozkan, S. B. 2020-07-03 doi:10.1101/2020.07.02.185207 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ Entrainment of network activity by closed-loop microstimulation in healthy ambulatory rats ]]> https://biorxiv.org/content/10.1101/2020.07.10.196725v1?rss=1 Alberto Averna Page Hayley Maxwell D. Murphy Jimmy Nguyen Stefano Buccelli Federico Barban Randolph J. Nudo Michela Chiappalone David J. Guggenmos 2020-07-11 doi:10.1101/2020.07.10.196725 Cold Spring Harbor Laboratory Press 2020-07-11 <![CDATA[ Geography is more important than life history in the recent diversification of the tiger salamander complex ]]> https://biorxiv.org/content/10.1101/2020.07.10.197624v1?rss=1 Kathryn Michelle Everson Levi N Gray Angela G Jones Nicolette M Lawrence Mary E Foley Kelly L Sovacool Justin D Kratovil Scott Hotaling Paul M Hime Andrew Storfer Gabriela Parra-Olea X Aguilar-Miguel Eric M O'Neill Luis Zambrano H Bradley Shaffer David W Weisrock 2020-07-12 doi:10.1101/2020.07.10.197624 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy calculations of peptide binding ]]> https://biorxiv.org/content/10.1101/2020.07.13.200774v1?rss=1 Wang, J. Miao, Y. 2020-07-14 doi:10.1101/2020.07.13.200774 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ A gene-level methylome-wide association analysis identifies novel Alzheimer's disease genes ]]> https://biorxiv.org/content/10.1101/2020.07.13.201376v1?rss=1 Wu, C. Bradley, J. Li, Y. Wu, L. deng, H.-W. 2020-07-14 doi:10.1101/2020.07.13.201376 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ Voluntary wheel running improves outcomes in an early life stress-induced model of urologic chronic pelvic pain syndrome in male mice ]]> https://biorxiv.org/content/10.1101/2020.07.20.212480v1?rss=1 Fuentes, I. M. Jones, B. M. Brake, A. D. Pierce, A. N. Eller, O. C. Supple, R. M. Wright, D. E. Christianson, J. A. 2020-07-22 doi:10.1101/2020.07.20.212480 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ ERβ regulated ovarian kisspeptin plays an important role in oocyte maturation ]]> https://biorxiv.org/content/10.1101/2020.07.27.223693v1?rss=1 Chakravarthi, V. P. Ghosh, S. Roby, K. F. Wolfe, M. W. Rumi, M. A. K. 2020-07-29 doi:10.1101/2020.07.27.223693 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Geographic potential of the world largest hornet, Vespa mandarinia Smith (Hymenoptera: Vespidae), worldwide and particularly in North America ]]> https://biorxiv.org/content/10.1101/2020.08.11.246991v1?rss=1 Nunez-Penichet, C. Osorio-Olvera, L. Gonzalez, V. H. Cobos, M. E. Jimenez, L. DeRaad, D. A. Alkishe, A. Contreras-Diaz, R. Nava-Bolanos, A. Utzumi, K. Ashraf, U. Adeboje, A. Peterson, A. T. Soberon, J. 2020-08-12 doi:10.1101/2020.08.11.246991 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Breast cancer endocrine therapy exhausts adipocyte progenitors promoting weight gain and glucose intolerance ]]> https://biorxiv.org/content/10.1101/2020.08.21.259440v1?rss=1 30 kg/m2. To understand the mechanisms behind these clinical findings, we investigated the impact of estrogen deprivation and tamoxifen in a relevant pre-clinical model of obesity. Specifically, mature female mice were housed at thermoneutrality and fed either a low-fat/low-sucrose (LFLS) or a high-fat/high-sucrose (HFHS) diet. Consistent with the high expression of Esr1 observed in single-cell RNA sequencing of mesenchymal stem cells from adipose tissue, endocrine therapies induced adipose accumulation and preadipocyte expansion, but resulted in adipocyte progenitor depletion only in the context of HFHS. Consequently, 7-week endocrine therapy supported adipocyte hypertrophy and was associated with hepatic steatosis, hyperinsulinemia, insulin resistance, and glucose intolerance, particularly in HFHS fed females. Metformin or pioglitazone, glucose lowering drugs used to treat diabetes, prevented the effects of tamoxifen but not estrogen deprivation on adipocyte size and insulin resistance in HFHS-fed mice. This translational study suggests that endocrine therapies act via ER to directly disrupt adipocyte progenitors and support adipocyte hypertrophy, leading to ectopic lipid deposition that may promote hyperinsulinemia, insulin resistance and type 2 diabetes. Interventions that target insulin action should be considered for some women receiving life-saving endocrine therapies for breast cancer. ]]> Scalzo, R. L. Foright, R. M. Hull, S. E. Knaub, L. A. Johnson-Murguia, S. Kinanee, F. Kaplan, J. Freije, B. Verzosa, G. Houck, J. A. Johnson, G. Zhang, A. M. Y. Johnson, J. D. MacLean, P. S. Reusch, J. E. B. Wright-Hobart, S. Wellberg, E. A. 2020-08-23 doi:10.1101/2020.08.21.259440 Cold Spring Harbor Laboratory Press 2020-08-23 <![CDATA[ Long Period Modeling SARS-CoV-2 Infection of in Vitro Cultured Polarized Human Airway Epithelium ]]> https://biorxiv.org/content/10.1101/2020.08.27.271130v1?rss=1 Hao, S. Ning, K. Kuz, C. A. Vorhies, K. Yan, Z. Qiu, J. 2020-08-28 doi:10.1101/2020.08.27.271130 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ Essential role for FtsL in activation of septal PG synthesis ]]> https://biorxiv.org/content/10.1101/2020.09.01.275982v1?rss=1 Park, K.-T. Du, S. Lutkenhaus, J. 2020-09-01 doi:10.1101/2020.09.01.275982 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Experimental evolution confirms signatures of sexual selection in genomic divergence. ]]> https://biorxiv.org/content/10.1101/2020.09.07.285650v1?rss=1 Wiberg, R. A. W. Veltsos, P. Snook, R. R. Ritchie, M. G. 2020-09-07 doi:10.1101/2020.09.07.285650 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ The Lonidamine Derivative H2-Gamendazole Reduces Cyst Formation in Polycystic Kidney Disease ]]> https://biorxiv.org/content/10.1101/2020.09.09.258160v1?rss=1 Sundar, S. V. Zhou, X. Magenheimer, B. S. Reif, G. A. Wallace, D. P. Georg, G. I. Jakkaraj, S. R. Tash, J. S. Yu, A. Li, X. Calvet, J. P. 2020-09-09 doi:10.1101/2020.09.09.258160 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Radiation induced toxicity in rectal epithelial stem cell contributes to acute radiation injury in rectum ]]> https://biorxiv.org/content/10.1101/2020.09.10.288696v1?rss=1 Tirado, F. R. Bhanja, P. Castro-Nallar, E. Olea, X. D. Salamanca, C. Saha, S. 2020-09-11 doi:10.1101/2020.09.10.288696 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ IFT-A deficiency in juvenile mice impairs biliary development and exacerbates ADPKD liver disease ]]> https://biorxiv.org/content/10.1101/2020.09.10.289645v1?rss=1 Wang, W. Pottorf, T. S. Wang, H. H. Dong, R. Kavanaugh, M. Cornelius, J. T. Apte, U. Pritchard, M. Sharma, M. Tran, P. 2020-09-10 doi:10.1101/2020.09.10.289645 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[ Differential expression of transposable elements in stem cell lineages of the preimplantation embryo ]]> https://biorxiv.org/content/10.1101/2020.09.13.295501v1?rss=1 Dai, E. Alvarez, N. S. Rumi, M. A. K. 2020-09-13 doi:10.1101/2020.09.13.295501 Cold Spring Harbor Laboratory Press 2020-09-13 <![CDATA[ SATB homeobox 1 regulated genes in the mouse ectoplacental cone are important for placental development ]]> https://biorxiv.org/content/10.1101/2020.09.13.295584v1?rss=1 Chakravarthi, V. P. Borosha, S. Ratri, A. Ghosh, S. Wolfe, M. W. Rumi, M. A. K. 2020-09-14 doi:10.1101/2020.09.13.295584 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ High yield preparation of outer-membrane protein efflux pumps by in vitro refolding is concentration dependent ]]> https://biorxiv.org/content/10.1101/2020.09.14.296756v1?rss=1 Budiardjo, S. J. Ikujuni, A. P. Firlar, E. Cordova, A. Kaelber, J. Slusky, J. S. G. 2020-09-14 doi:10.1101/2020.09.14.296756 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ The Structures of SctK and SctD from Pseudomonas aeruginosa Reveal the Interface of the Type III Secretion System Basal Body and Sorting Platform ]]> https://biorxiv.org/content/10.1101/2020.09.22.308627v1?rss=1 View larger version (59K): org.highwire.dtl.DTLVardef@1efcf14org.highwire.dtl.DTLVardef@1043d81org.highwire.dtl.DTLVardef@161f21corg.highwire.dtl.DTLVardef@15e4357_HPS_FORMAT_FIGEXP M_FIG Graphical abstract. The first reported structure for a T3SS SctK protein family member was solved for PscK from Pseudomonas aeruginosa and this allowed for modeling of the interface between this sorting platform protein and the cytoplasmic domain of PscD (a SctD protein family member). This allowed for identification of amino acid residues that may play a role in the interaction between these proteins. The interface appears to be dominated by electrostatic interactions and mutagenesis confirmed the importance of key residues in driving their interaction based on two-hybrid analysis. C_FIG ]]> Muthuramalingam, M. Whittier, S. Lovell, S. Battaile, K. P. Tachiyama, S. Johnson, D. K. Picking, W. L. Picking, W. D. 2020-09-22 doi:10.1101/2020.09.22.308627 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Harnessing Ionic Selectivity In Acetyltransferase Chemoproteomic Probes ]]> https://biorxiv.org/content/10.1101/2020.09.24.311530v1?rss=1 Jing, Y. Montano, J. L. Levy, M. J. Lopez, J. Kung, P.-P. Richardson, P. Krajewski, K. Florens, L. Washburn, M. Meier, J. L. 2020-09-25 doi:10.1101/2020.09.24.311530 Cold Spring Harbor Laboratory Press 2020-09-25 <![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[ Metagenomic Noncoding RNA Profiling and Biomarker Discovery ]]> https://biorxiv.org/content/10.1101/2020.09.27.315507v1?rss=1 Liu, B. Thippabhotla, S. Zhang, J. Zhong, C. 2020-09-28 doi:10.1101/2020.09.27.315507 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ A high fat anti-inflammatory diet improves widespread allodynia despite worsening metabolic outcomes in adult mice exposed to neonatal maternal separation ]]> https://biorxiv.org/content/10.1101/2020.09.29.317297v1?rss=1 Eller, O. C. Foright, R. M. Brake, A. D. Winter, M. K. Bantis, L. E. Morris, E. M. M. Thyfault, J. P. Christianson, J. A. 2020-10-01 doi:10.1101/2020.09.29.317297 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ The Role of DOT1L Methyltransferase Activity in Fetal Hematopoiesis ]]> https://biorxiv.org/content/10.1101/2020.09.30.319889v1?rss=1 Malcom, C. A. Piaseka-Srader, J. Chakravarthi, V. P. Borosha, S. Ratri, A. Alvarez, N. Vivian, J. L. Fields, T. A. Rumi, M. A. Fields, P. E. 2020-10-01 doi:10.1101/2020.09.30.319889 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ DOT1L methyltransferase regulates the calcium influx in erythroid progenitor cells in response to erythropoietin ]]> https://biorxiv.org/content/10.1101/2020.10.04.325746v1?rss=1 Feng, Y. Borosha, S. Ratri, A. Housami, S. M. Chakravarthi, V. P. Wang, H. Vivian, J. L. Fields, T. A. Kinsey, W. H. Rumi, M. A. Fields, P. E. 2020-10-05 doi:10.1101/2020.10.04.325746 Cold Spring Harbor Laboratory Press 2020-10-05 <![CDATA[ Acute exposure to sublethal doses of neonicotinoid insecticides increases heat tolerance in honey bees ]]> https://biorxiv.org/content/10.1101/2020.10.07.329482v1?rss=1 GONZALEZ, V. H. Hranitz, J. M. McGonigle, M. B. Manweiler, R. E. Smith, D. R. Barthell, J. F. 2020-10-08 doi:10.1101/2020.10.07.329482 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Redesigning OmpA Loops Using Canonical Outer Membrane Protein Loop Structures ]]> https://biorxiv.org/content/10.1101/2020.10.08.331546v1?rss=1 Franklin, M. W. Krise, J. Stevens, J. J. Slusky, J. S. G. 2020-10-08 doi:10.1101/2020.10.08.331546 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ DOT1L primarily acts as a transcriptional repressor in hematopoietic progenitor cells ]]> https://biorxiv.org/content/10.1101/2020.10.15.341255v1?rss=1 Borosha, S. Rtari, A. Housami, S. M. Rai, S. Ghosh, S. Malcom, C. A. Chakravarthi, V. P. Vivian, J. L. Fields, T. A. Rumi, M. A. Fields, P. E. 2020-10-16 doi:10.1101/2020.10.15.341255 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Quinomycin A reduces cyst progression in Polycystic Kidney Disease ]]> https://biorxiv.org/content/10.1101/2020.10.18.344689v1?rss=1 Radadiya, P. S. Thornton, M. M. Magenheimer, B. Subramaniam, D. Tran, P. V. Calvet, J. P. Wallace, D. P. Sharma, M. 2020-10-19 doi:10.1101/2020.10.18.344689 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ Septate junction proteins are required for egg elongation and border cell migration during oogenesis in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.10.19.346064v1?rss=1 Alhadyian, H. Shoaib, D. Ward, R. E. 2020-10-19 doi:10.1101/2020.10.19.346064 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ HPF1-dependent PARP activation promotes LIG3-XRCC1-mediated backup pathway of Okazaki fragment ligation ]]> https://biorxiv.org/content/10.1101/2020.10.21.348292v1?rss=1 Kumamoto, S. Nishiyama, A. Chiba, Y. Miyashita, R. Konishi, C. Azuma, Y. Nakanishi, M. 2020-10-21 doi:10.1101/2020.10.21.348292 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Mutation-specific pathophysiological mechanisms define different neurodevelopmental disorders associated with SATB1 dysfunction ]]> https://biorxiv.org/content/10.1101/2020.10.23.352278v1?rss=1 den Hoed, J. Boer, E. d. Voisin, N. Dingemans, A. Guex, N. Wiel, L. Nellaker, C. Amudhavalli, S. Banka, S. Bena, F. Ben-Zeev, B. Bonagura, V. Bruel, A.-L. Brunet, T. Brunner, H. Chew, H. Chrast, J. Cimbalistien, L. Coon, H. Study, T. D. Delot, E. Demurger, F. Denomme-Pichon, A.-S. Depienne, C. Donnai, D. Dyment, D. Elpeleg, O. Faivre, L. Gilissen, C. Granger, L. Haber, B. Hachiya, Y. Hamzavi Abedi, Y. Hanebeck, J. Hehir-Kwa, J. Horist, B. Itai, T. Jackson, A. Jewell, R. Jones, K. Joss, S. Kashii, H. Kato, M. Kattentidt-Mouravieva, A. Kok, F. Kotzaer 2020-10-24 doi:10.1101/2020.10.23.352278 Cold Spring Harbor Laboratory Press 2020-10-24 <![CDATA[ Untargeted Metabolomics of the Cavefish Astyanax mexicanus Reveals the Basis of Metabolic Strategies in Adaptation to Extreme Conditions ]]> https://biorxiv.org/content/10.1101/2020.10.27.358077v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@bcaff5org.highwire.dtl.DTLVardef@1c40b89org.highwire.dtl.DTLVardef@1d17d69org.highwire.dtl.DTLVardef@80a483_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1.C_FLOATNO Metabolic resilience survivability under a variety of extreme conditions. Certain populations of cavefish have adaptations that cause increased appetite (1) and increased fat accumulation (2) (in cases where nutrients are plentiful, such as in lab-raised populations). These same populations also exhibit robust health and longevity (2, 3) and do not suffer ill-effects due to high levels of visceral fat and hyper-glycemia, both of which are features of most cave populations. However, visceral fat accumulation in cave populations is highly dependent on nutrient availability and is not displayed in wild-caught specimens (4). Thus, cavefish paradoxically appear to tolerate both extremely low and extremely high levels of triglycerides, glucose, and other energy storage metabolites. We argue that these differences can be reconciled under a hypothesis whereby the cave environment selects not for resistance to nutrient deprivation per se, but rather resilience to a variety of nutrient availability states (such as seasonal floods). Survival under such challenging conditions ostensibly favors the ability to tolerate extreme metabolic states, including not only starvation but also high levels of potentially deleterious metabolites such as triglycerides and reactive oxygen species (ROS). We find evidence for elevated antioxidant levels and altered cholesterol / cholesteryl ester homeostasis in cavefish, suggesting that cavefish may use these mechanisms to offset potentially harmful metabolites and tolerate a broad range of metabolic conditions. C_FIG ]]> Medley, J. K. Persons, J. Peuss, R. Olsen, L. Xiong, S. Rohner, N. 2020-10-28 doi:10.1101/2020.10.27.358077 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Mechanism of ligand recognition by human ACE2 receptor ]]> https://biorxiv.org/content/10.1101/2020.10.30.362749v1?rss=1 Bhattarai, A. Pawnikar, S. Miao, Y. 2020-11-01 doi:10.1101/2020.10.30.362749 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ Mechanism of RNA recognition by a Musashi RNA-binding protein ]]> https://biorxiv.org/content/10.1101/2020.10.30.362756v1?rss=1 Wang, J. Lan, L. Wu, X. Xu, L. Miao, Y. 2020-10-31 doi:10.1101/2020.10.30.362756 Cold Spring Harbor Laboratory Press 2020-10-31 <![CDATA[ Population differentiation and structural variation in the genome of Manduca sexta across the United States ]]> https://biorxiv.org/content/10.1101/2020.11.01.364000v1?rss=1 Mongue, A. J. Kawahara, A. Y. 2020-11-02 doi:10.1101/2020.11.01.364000 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ Loss of Cnot6l impairs inosine RNA modifications in mouse oocytes ]]> https://biorxiv.org/content/10.1101/2020.11.04.358010v1?rss=1 Brachova, P. Alvarez, N. S. Christenson, L. K. 2020-11-05 doi:10.1101/2020.11.04.358010 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ A single QTL with large effect is associated with female functional virginity in an asexual parasitoid wasp ]]> https://biorxiv.org/content/10.1101/2020.11.05.370544v1?rss=1 Ma, W.-J. Pannebakker, B. A. Li, X. Geuverink, E. Anvar, S. Y. Veltsos, P. Schwander, T. van de Zande, L. Beukeboom, L. W. 2020-11-06 doi:10.1101/2020.11.05.370544 Cold Spring Harbor Laboratory Press 2020-11-06 <![CDATA[ Tobramycin adaptation enhances policing of social cheaters in Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2020.11.15.383836v1?rss=1 Abisado, R. Kimbrough, J. H. McKee, B. M. Craddock, V. Smalley, N. Dandekar, A. A. Chandler, J. R. 2020-11-15 doi:10.1101/2020.11.15.383836 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ Rapid evolution and horizontal gene transfer in the genome of a male-killing Wolbachia ]]> https://biorxiv.org/content/10.1101/2020.11.16.385294v1?rss=1 Hill, T. Unckless, R. L. Perlmutter, J. I. 2020-11-17 doi:10.1101/2020.11.16.385294 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ "Multiplex" rheostat positions cluster around allosterically critical regions of the lactose repressor protein ]]> https://biorxiv.org/content/10.1101/2020.11.17.386979v1?rss=1 40% of LacI positions, more than either toggle or neutral positions. Single rheostat positions were broadly distributed over the structure. Multiplex rheostat positions structurally overlapped with positions involved in allosteric regulation. When their phenotypic outcomes were interpreted within a thermodynamic framework, functional changes at multiplex positions were uncorrelated. This suggests that substitutions lead to complex changes in the underlying molecular biophysics. Bivariable and multivariable analyses of evolutionary signals within multiple sequence alignments could not differentiate single and multiplex rheostat positions. Phylogenetic analyses - such as ConSurf - could distinguish rheostats from toggle and neutral positions. Multivariable analyses could also identify a subset of neutral positions with high probability. Taken together, these results suggest that detailed understanding of the underlying molecular biophysics, likely including protein dynamics, will be required to discriminate single and multiplex rheostat positions from each other and to predict substitution outcomes at these sites. ]]> Bantis, L. E. Parente, D. J. Fenton, A. W. Swint-Kruse, L. 2020-11-17 doi:10.1101/2020.11.17.386979 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ Redistribution of centrosomal proteins by centromeres and Polo kinase controls nuclear envelope breakdown ]]> https://biorxiv.org/content/10.1101/2020.12.01.406553v1?rss=1 Bestul, A. J. Yu, Z. Unruh, J. R. Jaspersen, S. L. 2020-12-01 doi:10.1101/2020.12.01.406553 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Reduced Liver-Specific PGC1a Increases Susceptibility for Short-Term Diet-induced Weight Gain in Male Mice ]]> https://biorxiv.org/content/10.1101/2020.12.04.412460v1?rss=1 Morris, E. M. Noland, R. D. Ponte, M. E. Montonye, M. L. Christianson, J. A. Stanford, J. A. Miles, J. M. Hayes, M. R. Thyfault, J. P. 2020-12-06 doi:10.1101/2020.12.04.412460 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Testing impacts of goal-oriented outreach with the Girl Scouts: Can a single activity change attitudes towards insects? ]]> https://biorxiv.org/content/10.1101/2020.12.10.413583v1?rss=1 Mongue, A. J. Colyott, K. L. 2020-12-11 doi:10.1101/2020.12.10.413583 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ OpenTree: A Python package for Accessing andAnalyzing data from the Open Tree of Life ]]> https://biorxiv.org/content/10.1101/2020.12.14.422759v1?rss=1 McTavish, E. J. Sanchez Reyes, L. L. Holder, M. T. 2020-12-15 doi:10.1101/2020.12.14.422759 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Paired heavy and light chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses ]]> https://biorxiv.org/content/10.1101/2020.12.31.424987v1?rss=1 Banach, B. B. Cerutti, G. Fahad, A. S. Shen, C.-H. Oliveira de Souza, M. Katsamba, P. S. Tsybovsky, Y. Wang, P. Nair, M. S. Huang, Y. Francino Urdaniz, I. M. Steiner, P. J. Gutierrez-Gonzalez, M. Liu, L. Lopez Acevedo, S. N. Nazzari, A. Wolfe, J. R. Luo, Y. Olia, A. S. Teng, I.-T. Yu, J. Zhou, T. Reddem, E. R. Bimela, J. Pan, X. Madan, B. Laflin, A. D. Nimrania, R. Yuen, K.-T. Whitehead, T. A. Ho, D. D. Kwong, P. D. Shapiro, L. DeKosky, B. J. 2021-01-03 doi:10.1101/2020.12.31.424987 Cold Spring Harbor Laboratory Press 2021-01-03 <![CDATA[ Codon composition in human oocytes reveals age-associated defects in mRNA decay ]]> https://biorxiv.org/content/10.1101/2021.01.05.425501v1?rss=1 Alvarez, N. Brachova, P. Christenson, L. 2021-01-06 doi:10.1101/2021.01.05.425501 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Colistin resistance in Acinetobacter baumannii is driven by multiple genomic traits: Evaluating the role of ISAba1-driven eptA overexpression among Indian isolates ]]> https://biorxiv.org/content/10.1101/2021.01.07.425695v1?rss=1 Vijayakumar, S. Jacob, J. J. Vasudevan, K. Shankar, B. A. Francis, M. L. Kirubananthan, A. Anandan, S. Gunasekaran, K. Walia, K. Biswas, I. Kaye, K. S. Veeraraghavan, B. 2021-01-07 doi:10.1101/2021.01.07.425695 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Simple and Rapid High-Throughput Assay to Identify HSV-1 ICP0 Transactivation Inhibitors ]]> https://biorxiv.org/content/10.1101/2021.01.13.426532v1?rss=1 Ly, C. Y. Yu, C. McDonald, P. R. Roy, A. Johnson, D. K. Davido, D. J. 2021-01-13 doi:10.1101/2021.01.13.426532 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ Reconstructing tumor trajectories during therapy through integration of multiple measurement modalities. ]]> https://biorxiv.org/content/10.1101/2021.01.14.426737v1?rss=1 Griffiths, J. I. Chen, J. O'Dea, A. Sharma, P. Winblad, O. Trivedi, M. Kalinsky, K. Wisinski, K. O'Regan, R. Makhoul, I. Spring, L. Bardia, A. Yuan, Y. Jahanzeb, M. Adler, F. Cohen, A. Bild, A. Khan, Q. 2021-01-17 doi:10.1101/2021.01.14.426737 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Human antibody immune responses are personalized by selective removal of MHC-II peptide epitopes ]]> https://biorxiv.org/content/10.1101/2021.01.15.426750v1?rss=1 Gutierrez-Gonzalez, M. Fahad, A. S. Ardito, M. Nanaware, P. Lu, L. Normandin, E. Madan, B. Tivin, J. Coates, E. Henry, A. R. Laboune, F. Graham, B. S. Douek, D. C. Ledgerwood, J. E. Mascola, J. R. Martin, W. D. Stern, L. De Groot, A. S. DeKosky, B. J. 2021-01-17 doi:10.1101/2021.01.15.426750 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Convergent evolution of resistance pathways during early stage breast cancer treatment with combination cell cycle (CDK) and endocrine inhibitors ]]> https://biorxiv.org/content/10.1101/2021.01.19.427299v1?rss=1 Griffiths, J. I. Chen, J. Cosgrove, P. A. O'Dea, A. Sharma, P. Ma, C. Trivedi, M. Kalinsky, K. Wisinski, K. B. O'Regan, R. Makhoul, , I. Spring, L. M. Bardia, A. Adler, F. R. Cohen, A. L. Chang, J. T. Khan, Q. J. Bild, A. 2021-01-20 doi:10.1101/2021.01.19.427299 Cold Spring Harbor Laboratory Press 2021-01-20 <![CDATA[ Ocular elongation and retraction in foveated reptiles ]]> https://biorxiv.org/content/10.1101/2021.01.20.427408v1?rss=1 Rasys, A. M. Pau, S. H. Irwin, K. E. Luo, S. Trainor, P. A. Menke, D. B. Lauderdale, J. D. 2021-01-21 doi:10.1101/2021.01.20.427408 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Genetic analysis of the septal peptidoglycan synthase FtsWI complex supports a conserved activation mechanism for SEDS-bPBP complexes ]]> https://biorxiv.org/content/10.1101/2021.01.21.427617v1?rss=1 Du, S. Li, Y. Gong, H. Zhan, R. Ouyang, S. Park, K.-T. Lutkenhaus, J. 2021-01-21 doi:10.1101/2021.01.21.427617 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Estimating the fundamental niche: accounting for the uneven1availability of existing climates ]]> https://biorxiv.org/content/10.1101/2021.01.25.428165v1?rss=1 Jimenez, L. M. Soberon, J. 2021-01-27 doi:10.1101/2021.01.25.428165 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ In-frame deletion of SPECC1L microtubule binding domain results in embryonic tissue movement and fusion defects ]]> https://biorxiv.org/content/10.1101/2021.01.28.428634v1?rss=1 Goering, J. P. Wenger, L. W. Stetsiv, M. Moedritzer, M. Hall, E. G. Isai, D. G. Jack, B. Umar, Z. Rickabaugh, M. K. Czirok, A. Saadi, I. 2021-01-28 doi:10.1101/2021.01.28.428634 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Experimental sexual selection reveals rapid divergence in male and female reproductive transcriptomes and their interactions ]]> https://biorxiv.org/content/10.1101/2021.01.29.428831v1?rss=1 Veltsos, P. Porcelli, D. Fang, Y. Cossins, A. R. Ritchie, M. G. Snook, R. R. 2021-01-31 doi:10.1101/2021.01.29.428831 Cold Spring Harbor Laboratory Press 2021-01-31 <![CDATA[ Membrane barrels are taller, fatter, inside-out soluble barrels ]]> https://biorxiv.org/content/10.1101/2021.01.30.428970v1?rss=1 Dhar, R. Feehan, R. Slusky, J. S. G. 2021-02-01 doi:10.1101/2021.01.30.428970 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Variation in Placental microRNA Expression Associates with Familial Cardiovascular Disease ]]> https://biorxiv.org/content/10.1101/2021.02.01.429202v1?rss=1 Tehrani, J. M. Kennedy, E. M. Tian, F.-Y. Everson, T. M. Deyssenroth, M. Burt, A. Hermetz, K. Hao, K. Chen, J. Koestler, D. C. Marsit, C. J. 2021-02-02 doi:10.1101/2021.02.01.429202 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ The Collagens DPY-17 and SQT-3 Direct Anterior-Posterior Migration of the Q Neuroblasts in C. elegans. ]]> https://biorxiv.org/content/10.1101/2021.02.01.429218v1?rss=1 Lang, A. E. Lundquist, E. A. 2021-02-02 doi:10.1101/2021.02.01.429218 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Machine Learning Differentiates Enzymatic and Non-Enzymatic Metals in Proteins ]]> https://biorxiv.org/content/10.1101/2021.02.01.429261v1?rss=1 Feehan, R. Franklin, M. W. Slusky, J. S. G. 2021-02-02 doi:10.1101/2021.02.01.429261 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ The SARS-CoV-2 transcriptome and the dynamics of the S gene furin cleavage site in primary human airway epithelia ]]> https://biorxiv.org/content/10.1101/2021.02.03.429670v1?rss=1 Zou, W. Xiong, M. Hao, S. Zhang-Chen, E. Y. Baumlin, N. Kim, M. D. Salathe, M. Yan, Z. Qiu, J. 2021-02-04 doi:10.1101/2021.02.03.429670 Cold Spring Harbor Laboratory Press 2021-02-04 <![CDATA[ Perturbation of BRMS1 interactome reveals pathways that impact cell migration ]]> https://biorxiv.org/content/10.1101/2021.02.04.429764v1?rss=1 Zimmermann, R. C. Sardiu, M. E. Manton, C. A. Miah, M. S. Banks, C. A. Adams, M. K. Koestler, D. C. Washburn, M. P. Welch, D. R. 2021-02-04 doi:10.1101/2021.02.04.429764 Cold Spring Harbor Laboratory Press 2021-02-04 <![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[ Direct activation of endothelial cells by SARS-CoV-2 nucleocapsid protein is blocked by Simvastatin ]]> https://biorxiv.org/content/10.1101/2021.02.14.431174v1?rss=1 Qian, Y. Lei, T. Patel, P. Lee, C. Monaghan-Nichols, P. Xin, H.-B. Qiu, J. Fu, M. 2021-02-15 doi:10.1101/2021.02.14.431174 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ REPROGRAMMING CBX8-PRC1 FUNCTION WITH A POSITIVE ALLOSTERIC MODULATOR ]]> https://biorxiv.org/content/10.1101/2021.02.23.432388v1?rss=1 Suh, J. L. Bsteh, D. Si, Y. Hart, B. Weaver, T. M. Pribitzer, C. Lau, R. Soni, S. Ogana, H. Rectenwald, J. M. Norris, J. L. Cholensky, S. H. Sagum, C. Umana, J. D. Li, D. Hardy, B. Bedford, M. T. Mumenthaler, S. M. Lenz, H.-J. Kim, Y.-m. Wang, G. G. Pearce, K. H. James, L. Kireev, D. B. Musselman, C. A. Frye, S. V. Bell, O. 2021-02-23 doi:10.1101/2021.02.23.432388 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Spontaneous Facet Joint Osteoarthritis in NFAT1-Mutant Mice ]]> https://biorxiv.org/content/10.1101/2021.02.23.432595v1?rss=1 Wang, J. Lu, Q. Mackay, M. J. Liu, X. Burton, D. C. Asher, M. A. 2021-02-24 doi:10.1101/2021.02.23.432595 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ Periodic synchronization of dengue epidemics in Thailand: the roles played by temperature and immunity ]]> https://biorxiv.org/content/10.1101/2021.03.01.433325v1?rss=1 Garcia-Carreras, B. Yang, B. Grabowski, M. K. Sheppard, L. W. Huang, A. T. Salje, H. Clapham, H. E. Iamsirithaworn, S. Doung-Ngern, P. Lessler, J. Cummings, D. A. T. 2021-03-01 doi:10.1101/2021.03.01.433325 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Engineered SARS-CoV-2 receptor binding domain improves immunogenicity in mice and elicits protective immunity in hamsters ]]> https://biorxiv.org/content/10.1101/2021.03.03.433558v1?rss=1 Dalvie, N. C. Rodriguez-Aponte, S. A. Hartwell, B. L. Tostanoski, L. H. Biedermann, A. M. Crowell, L. E. Kaur, K. Kumru, O. Carter, L. Yu, J. Chang, A. McMahan, K. Courant, T. Lebas, C. Lemnios, A. A. Rodrigues, K. A. Silva, M. Johnston, R. S. Naranjo, C. A. Tracey, M. K. Brady, J. R. Whittaker, C. A. Yun, D. Kar, S. Porto, M. Lok, M. Andersen, H. Lewis, M. G. Love, K. R. Camp, D. L. Silverman, J. M. Kleanthous, H. Joshi, S. B. Volkin, D. B. Dubois, P. M. Collin, N. King, N. P. Barouch, D. H. Irvine, D. J. Love, J. C. 2021-03-04 doi:10.1101/2021.03.03.433558 Cold Spring Harbor Laboratory Press 2021-03-04 <![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[ Ecological correlates of gene family size: the draft genome of the redheaded pine sawfly Neodiprion lecontei ]]> https://biorxiv.org/content/10.1101/2021.03.14.435331v1?rss=1 Vertacnik, K. Herrig, D. Godfrey, R. K. Hill, T. Geib, S. Unckless, R. Nelson, D. Linnen, C. R. 2021-03-16 doi:10.1101/2021.03.14.435331 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Thermal stress triggers productive viral infection of a key coral reef symbiont ]]> https://biorxiv.org/content/10.1101/2021.03.17.435810v1?rss=1 Grupstra, C. Howe-Kerr, L. I. Veglia, A. J. Bryant, R. L. Coy, S. R. Blackwelder, P. L. Correa, A. M. 2021-03-19 doi:10.1101/2021.03.17.435810 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Proteasome autophagy is specifically regulated and requires factors dispensible for general autophagy ]]> https://biorxiv.org/content/10.1101/2021.03.26.437055v1?rss=1 Waite, K. A. Burrris, A. Vontz, G. Lang, A. Roelofs, J. 2021-03-29 doi:10.1101/2021.03.26.437055 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ Asymmetric structures and conformational plasticity of the uncleaved full-length human immunodeficiency virus (HIV-1) envelope glycoprotein trimer ]]> https://biorxiv.org/content/10.1101/2021.03.28.437443v1?rss=1 Zhang, S. Wang, K. Wei Li, W. Nguyen, H. T. Chen, S. Lu, M. Go, E. P. Ding, H. Steinbock, R. T. Desaire, H. Kappes, J. C. Sodroski, J. G. Mao, Y. 2021-03-29 doi:10.1101/2021.03.28.437443 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ An MHV macrodomain mutant predicted to lack ADP-ribose binding activity is severely attenuated, indicating multiple roles for the macrodomain in coronavirus replication ]]> https://biorxiv.org/content/10.1101/2021.03.30.437796v1?rss=1 Voth, L. S. O'Connor, J. J. Kerr, C. M. Doerger, E. Schwarting, N. Sperstad, P. Johnson, D. K. Fehr, A. R. 2021-03-31 doi:10.1101/2021.03.30.437796 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein ]]> https://biorxiv.org/content/10.1101/2021.04.01.438120v1?rss=1 Zhang, S. Go, E. P. Ding, H. Anang, S. Kappes, J. C. Desaire, H. Sodroski, J. G. 2021-04-01 doi:10.1101/2021.04.01.438120 Cold Spring Harbor Laboratory Press 2021-04-01 <![CDATA[ New distributional opportunities with niche innovation in Eurasian snowfinches ]]> https://biorxiv.org/content/10.1101/2021.04.06.438738v1?rss=1 Cobos, M. E. Cheng, Y. Song, G. Lei, F. Peterson, A. T. 2021-04-08 doi:10.1101/2021.04.06.438738 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ In-depth phylogenomic analysis of arbuscular mycorrhizal fungi based on a comprehensive set of de novo genome assemblies ]]> https://biorxiv.org/content/10.1101/2021.04.09.439159v1?rss=1 Montoliu-Nerin, M. Sanchez-Garcia, M. Bergin, C. Kutschera, V. E. Johannesson, H. Bever, J. D. Rosling, A. 2021-04-11 doi:10.1101/2021.04.09.439159 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Isolation of sensory hair cell specific exosomes in human perilymph ]]> https://biorxiv.org/content/10.1101/2021.04.11.439339v1?rss=1 Pei, Z. Suiching, P. Warnecke, A. Arambula, A. St. Peter, M. He, M. Staecker, H. 2021-04-12 doi:10.1101/2021.04.11.439339 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Enhanced cell deconvolution of peripheral blood using DNA methylation for high-resolution immune profiling ]]> https://biorxiv.org/content/10.1101/2021.04.11.439377v1?rss=1 Salas, L. A. Zhang, Z. Koestler, D. C. Butler, R. A. Hansen, H. M. Molinaro, A. M. Wiencke, J. K. Kelsey, K. T. Christensen, B. C. 2021-04-12 doi:10.1101/2021.04.11.439377 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ DEPDC1/ EEF1A1 complex promotes the progression of human osteosarcoma via downregulation of FOXO3a ]]> https://biorxiv.org/content/10.1101/2021.04.14.439766v1?rss=1 Shen, L. Li, H. Zhang, A. Liu, R. Zhou, C. Zhang, Y. Zhao, K. Bretches, M. Lu, L. Yang, S.-Y. Ning, B. 2021-04-14 doi:10.1101/2021.04.14.439766 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Enhanced lipogenesis through Pparγ helps cavefish adapt to food scarcity. ]]> https://biorxiv.org/content/10.1101/2021.04.27.441667v1?rss=1 Xiong, S. Wang, W. Kenzior, A. Olsen, L. Krishnan, J. Persons, J. Medley, K. Peuss, R. Wang, Y. Chen, S. Zhang, N. Thomas, N. Miles, J. Sanchez Alvarado, A. Rohner, N. 2021-04-28 doi:10.1101/2021.04.27.441667 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ A Modified Comprehensive Grading System for Murine Knee Osteoarthritis: Scoring the Whole Joint as an Organ ]]> https://biorxiv.org/content/10.1101/2021.05.05.442864v1?rss=1 0.9) for both experienced and novice scorers. Sensitivity and reliability analyses confirmed the ability of the new system to detect minimal OA progression between two timepoints with a two-week interval and to accurately identify tissue-specific OA severity within the knee joint. ConclusionsThe comprehensive histologic grading system presented here covers all-stage osteoarthritic changes in all major knee joint tissues of mice, which enable us to score OA severity for the whole joint reproducibly and accurately without software-assisted time-consuming measurements. ]]> Grote, C. Mackay, M. Liu, X. Lu, Q. Wang, J. 2021-05-06 doi:10.1101/2021.05.05.442864 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Construction of a 3-color prism-based TIRF microscope to study the interactions and dynamics of macromolecules ]]> https://biorxiv.org/content/10.1101/2021.05.10.443430v1?rss=1 Fairlamb, M. S. Whitaker, A. M. Bain, F. E. Spies, M. Freudenthal, B. D. 2021-05-11 doi:10.1101/2021.05.10.443430 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ Composition and Biophysical Properties of the Sorting Platform Pods in the Shigella Type III Secretion System ]]> https://biorxiv.org/content/10.1101/2021.05.13.444006v1?rss=1 Tachiyama, S. Skaar, R. Chang, Y. Carroll, B. Muthuramalingam, M. Whittier, S. K. Barta, M. L. Picking, W. L. Liu, J. Picking, W. D. 2021-05-13 doi:10.1101/2021.05.13.444006 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ Rational Drug Design of Targeted and Enzyme Cleavable Vitamin E Analogs as Neoadjuvant to Chemotherapy: In Vitro and In Vivo Evaluation on Reduction of Cardiotoxicity of Doxorubicin. ]]> https://biorxiv.org/content/10.1101/2021.05.20.445072v1?rss=1 Pandurangi, R. S. Cseh, O. Luchman, A. Xu, s. Ma, C. Senedheera, S. Forrest, l. 2021-05-21 doi:10.1101/2021.05.20.445072 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ Structural basis of the interaction between SETD2 methyltransferase and hnRNP L paralogs for governing co-transcriptional splicing ]]> https://biorxiv.org/content/10.1101/2021.05.22.445248v1?rss=1 Bhattacharya, S. Wang, S. Reddy, D. Shen, S. Zhang, Y. Zhang, N. Li, H. Washburn, M. Florens, L. Shi, Y. Li, F. Workman, J. 2021-05-23 doi:10.1101/2021.05.22.445248 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ Diverse mating phenotypes impact the spread of wtf meiotic drivers in S. pombe ]]> https://biorxiv.org/content/10.1101/2021.05.28.446231v1?rss=1 Zanders, S. E. Lopez Hernandez, J. F. Helston, R. M. Lange, J. J. Billmyre, R. B. Schaffner, S. H. Eickbush, M. T. McCroskey, S. 2021-05-29 doi:10.1101/2021.05.28.446231 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ Genome-wide association mapping of transcriptome variation in Mimulus guttatus indicates differing patterns of selection on cis- versus trans-acting mutations ]]> https://biorxiv.org/content/10.1101/2021.06.02.446804v1?rss=1 Brown, K. Kelly, J. K. 2021-06-02 doi:10.1101/2021.06.02.446804 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Unique Features of Different Classes of G-Protein-Coupled Receptors Revealed from Sequence Coevolutionary and Structural Analysis ]]> https://biorxiv.org/content/10.1101/2021.06.03.446974v1?rss=1 Do, H. Haldane, A. Levy, R. Miao, Y. 2021-06-03 doi:10.1101/2021.06.03.446974 Cold Spring Harbor Laboratory Press 2021-06-03 <![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[ A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq ]]> https://biorxiv.org/content/10.1101/2021.06.10.447896v1?rss=1 Mudge, J. M. Ruiz-Orera, J. Prensner, J. R. Brunet, M. A. Gonzalez, J. M. Magrane, M. Martinez, T. Schulz, J. F. Yang, Y. T. Alba, M. M. Baranov, P. V. Bazzini, A. Bruford, E. Martin, M. J. Carvunis, A.-R. Chen, J. Couso, J. P. Flicek, P. Frankish, A. Gerstein, M. Hubner, N. Ingolia, N. T. Menschaert, G. Ohler, U. Roucou, X. Saghatelian, A. Weissman, J. van Heesch, S. 2021-06-10 doi:10.1101/2021.06.10.447896 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Comprehensive Phenotyping of Cutaneous Afferents Reveals Rapid-Onset Alterations in Nociceptor Response Properties Following Spinal Cord Injury ]]> https://biorxiv.org/content/10.1101/2021.06.15.448577v1?rss=1 Eller, O. C. Stair, R. N. Nelson-Brantley, J. Young, E. E. Baumbauer, K. M. 2021-06-16 doi:10.1101/2021.06.15.448577 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ SPIKE-TRIGGERED INTRASPINAL MICROSTIMULATION IMPROVES MOTOR PERFORANCE IN AN AMBULATORY RAT MODEL OF SPINAL CORD INJURY ]]> https://biorxiv.org/content/10.1101/2021.06.21.449323v1?rss=1 Borrell, J. A. Gattozzi, D. Krizsan-Agbas, D. Nudo, R. J. FROST, S. B. 2021-06-22 doi:10.1101/2021.06.21.449323 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Regulatory approved monoclonal antibodies contain framework mutations predicted from human antibody repertoires ]]> https://biorxiv.org/content/10.1101/2021.06.22.449488v1?rss=1 Petersen, B. M. Ulmer, S. A. Rhodes, E. R. Gutierrez Gonzalez, M. F. Dekosky, B. J. Sprenger, K. G. Whitehead, T. A. 2021-06-22 doi:10.1101/2021.06.22.449488 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Sex Differences in Cerebral Edema after Experimental Traumatic Brain Injury ]]> https://biorxiv.org/content/10.1101/2021.06.25.449932v1?rss=1 Minchew, H. M. Christian, S. K. Keselman, P. Hu, J. Andrews, B. T. Harris, J. L. 2021-06-25 doi:10.1101/2021.06.25.449932 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Photoredox-catalyzed decarboxylative C-terminal differentiation for bulk and single molecule proteomics ]]> https://biorxiv.org/content/10.1101/2021.07.08.451692v1?rss=1 Zhang, L. Floyd, B. M. Chilamari, M. Mapes, J. Swaminathan, J. Bloom, S. Marcotte, E. M. Anslyn, E. V. 2021-07-09 doi:10.1101/2021.07.08.451692 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ A modular protein subunit vaccine candidate produced in yeast confers protection against SARS-CoV-2 in non-human primates ]]> https://biorxiv.org/content/10.1101/2021.07.13.452251v1?rss=1 104) above the range of protection for other licensed vaccines in non-human primates. Interestingly, addition of a second adjuvant (CpG1018) appeared to improve the cellular response while reducing the humoral response. We challenged animals with SARS-CoV-2, and observed a ~3.4 and ~2.9 log10 reduction in median viral loads in bronchoalveolar lavage and nasal mucosa, respectively, compared to sham controls. These results inform the design and formulation of current clinical COVID-19 vaccine candidates like the one described here, and future designs of RBD-based vaccines against variants of SARS-CoV-2 or other betacoronaviruses. ]]> Dalvie, N. C. Tostanoski, L. H. Rodriguez-Aponte, S. A. Kaur, K. Bajoria, S. Kumru, O. Martinot, A. J. Chandrashekar, A. McMahan, K. Mercado, N. B. Yu, J. Chang, A. Giffin, V. M. Nampanya, F. Patel, S. Bowman, L. Naranjo, C. A. Yun, D. Flinchbaugh, Z. Pessaint, L. Brown, R. Velasco, J. Teow, E. Cook, A. Andersen, H. Lewis, M. G. Camp, D. L. Silverman, J. M. Kleanthous, H. Joshi, S. B. Volkin, D. B. Biswas, S. Love, J. C. Barouch, D. H. 2021-07-14 doi:10.1101/2021.07.13.452251 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ Generalizing Bayesian phylogenetics to infer shared evolutionary events ]]> https://biorxiv.org/content/10.1101/2021.07.23.453597v1?rss=1 Oaks, J. R. Wood, P. L. 2021-07-26 doi:10.1101/2021.07.23.453597 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ A machine-learning approach for detection of local brain networks and marginally weak signals identifies novel AD/MCI differentiating connectomic neuroimaging biomarkers ]]> https://biorxiv.org/content/10.1101/2021.07.29.454368v1?rss=1 Li, Y. Kang, J. Wu, C. Dinov, I. Hu, j. Chalise, P. Mahnken, J. 2021-07-30 doi:10.1101/2021.07.29.454368 Cold Spring Harbor Laboratory Press 2021-07-30 <![CDATA[ A distinct inner nuclear membrane proteome in Saccharomyces cerevisiae gametes ]]> https://biorxiv.org/content/10.1101/2021.08.02.454801v1?rss=1 Shelton, S. N. Smith, S. E. Unruh, J. R. Jaspersen, S. L. 2021-08-02 doi:10.1101/2021.08.02.454801 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ Mechanism of Tripeptide Trimming by γ-Secretase ]]> https://biorxiv.org/content/10.1101/2021.08.05.455243v1?rss=1 Bhattarai, A. Devkota, S. Do, H. N. Wang, J. Bhattarai, S. Wolfe, M. S. Miao, Y. 2021-08-05 doi:10.1101/2021.08.05.455243 Cold Spring Harbor Laboratory Press 2021-08-05 <![CDATA[ Mechanism of Tethered Agonist-Mediated Signaling by Polycystin-1 ]]> https://biorxiv.org/content/10.1101/2021.08.05.455255v1?rss=1 Pawnikar, S. Magenheimer, B. S. Nevarez-Munoz, E. Maser, R. L. Miao, Y. 2021-08-05 doi:10.1101/2021.08.05.455255 Cold Spring Harbor Laboratory Press 2021-08-05 <![CDATA[ Design of Transmembrane Mimetic Structural Probes to Trap Different Stages of γ-Secretase-Substrate Interaction ]]> https://biorxiv.org/content/10.1101/2021.08.05.455313v1?rss=1 Bhattarai, S. Devkota, S. Wolfe, M. S. 2021-08-05 doi:10.1101/2021.08.05.455313 Cold Spring Harbor Laboratory Press 2021-08-05 <![CDATA[ In vitro tau aggregation inducer molecules influence the effects of MAPT mutations on aggregation dynamics ]]> https://biorxiv.org/content/10.1101/2021.08.06.455436v1?rss=1 Ingham, D. J. Hillyer, K. M. McGuire, M. J. Gamblin, T. C. 2021-08-06 doi:10.1101/2021.08.06.455436 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Discovery of aryl aminothiazole γ-secretase modulators with novel effects on amyloid β-peptide production ]]> https://biorxiv.org/content/10.1101/2021.08.09.455471v1?rss=1 Bhattarai, S. Liu, L. Wolfe, M. S. 2021-08-09 doi:10.1101/2021.08.09.455471 Cold Spring Harbor Laboratory Press 2021-08-09 <![CDATA[ Constitutive signaling by the C-terminal fragment of polycystin-1 is mediated by a tethered peptide agonist ]]> https://biorxiv.org/content/10.1101/2021.08.20.457171v1?rss=1 Magenheimer, B. S. Nevarez Munoz, E. Ravichandran, J. Maser, R. L. 2021-08-21 doi:10.1101/2021.08.20.457171 Cold Spring Harbor Laboratory Press 2021-08-21 <![CDATA[ TWIST1 interacts with adherens junction proteins during neural tube formation and regulates fate transition in cranial neural crest cells ]]> https://biorxiv.org/content/10.1101/2021.08.22.457283v1?rss=1 Bertol, J. W. Johnston, S. Ahmed, R. Xie, V. K. Cruz, L. Nitschke, L. Stetsiv, M. Goering, J. P. Nistor, P. Lowell, S. Hoskens, H. Claes, P. Weinberg, S. M. Saadi, I. Farach-Carson, M. C. Fakhouri, W. D. 2021-08-22 doi:10.1101/2021.08.22.457283 Cold Spring Harbor Laboratory Press 2021-08-22 <![CDATA[ The PH/MyTH4/FERMmolecule MAX-1 inhibits UNC-5 activity in regulation of VD growth cone protrusion in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2021.08.25.457713v1?rss=1 Mahadik, S. S. Lundquist, E. A. 2021-08-26 doi:10.1101/2021.08.25.457713 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ DOCKGROUND scoring benchmarks for protein docking ]]> https://biorxiv.org/content/10.1101/2021.09.02.458795v1?rss=1 Kotthoff, I. Kundrotas, P. J. Vakser, I. A. 2021-09-04 doi:10.1101/2021.09.02.458795 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ Powerful, efficient QTL mapping in Drosophila melanogaster using bulked phenotyping and pooled sequencing ]]> https://biorxiv.org/content/10.1101/2021.09.02.458801v1?rss=1 =4 replicates, >=5000 individuals/replicate, and a selection intensity of 5-10%) yield at least the same power as traditional RIL-based QTL mapping, and can localize variants with sub-centimorgan resolution. We empirically demonstrate the effectiveness of the approach using a 4-fold replicated X-QTL experiment that identifies 7 QTL for caffeine resistance. Two mapped X-QTL factors replicate loci previously identified in RILs, 6/7 are associated with excellent candidate genes, and RNAi knock-downs support the involvement of 4 genes in the genetic control of trait variation. For many traits of interest to drosophilists a bulked phenotyping/genotyping X-QTL design has considerable advantages. ]]> Macdonald, S. J. Cloud-Richardson, K. M. Sims-West, D. J. Long, A. D. 2021-09-04 doi:10.1101/2021.09.02.458801 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ Relationship Between Inter-individual Variation in Circadian Rhythm and Sociality: A case Study Using Halictid Bees ]]> https://biorxiv.org/content/10.1101/2021.09.03.458748v1?rss=1 Melendez Cartagena, S. Ortiz-Alvarado, C. A. Ordonez, P. Cordero-Martinez, C. S. Ambrose, A. F. Roman Lizasoain, L. A. Santos Vega, M. A. Velez Velez, A. V. Acevedo-Gonzalez, J. P. Gibbs, J. Petanidou, T. Tscheulin, T. Barthell, J. T. Gonzalez, V. H. Giray, T. Agosto-Rivera, J. L. 2021-09-06 doi:10.1101/2021.09.03.458748 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Transcriptome phylogenies support ancient evolutionary transitions in bioluminescence traits of cypridinid ostracods ]]> https://biorxiv.org/content/10.1101/2021.09.03.458903v1?rss=1 Ellis, E. A. Goodheart, J. A. Hensley, N. M. Gonzalez, V. L. Reda, N. J. Rivers, T. J. Morin, J. G. Torres, E. Gerrish, G. A. Oakley, T. H. 2021-09-05 doi:10.1101/2021.09.03.458903 Cold Spring Harbor Laboratory Press 2021-09-05 <![CDATA[ BCN057, a Modulator of GSK3b Induces KRAS G12D Mutant Pancreatic Cancer Cell Death ]]> https://biorxiv.org/content/10.1101/2021.09.03.458938v1?rss=1 Singer, E. M. Chugh, R. M. Bhanja, P. Gomez, A. Gao, L. Whitelegge, J. P. McBride, W. H. Saha, S. Norris, A. J. 2021-09-04 doi:10.1101/2021.09.03.458938 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ Integrated de novo Gene Prediction and Peptide Assembly of Metagenomic Sequencing Data ]]> https://biorxiv.org/content/10.1101/2021.09.20.461079v1?rss=1 90%). iMPP further allowed for more sensitive and accurate peptide assembly, recovering more reference proteins and delivering more hypothetical protein sequences. The high performance of iMPP can provide a more comprehensive and unbiased view of the microbial communities under investigation. iMPP is freely available from https://github.com/Sirisha-t/iMPP. ]]> Thippabhotla, S. Liu, B. Yooseph, S. Yang, Y. Zhang, J. Zhong, C. 2021-09-23 doi:10.1101/2021.09.20.461079 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Integrated phylogenomics and fossil data illuminate the evolution of beetles ]]> https://biorxiv.org/content/10.1101/2021.09.22.461358v1?rss=1 Cai, C. Tihelka, E. Giacomelli, M. Lawrence, J. F. Slipinski, A. Kundrata, R. Yamamoto, S. Thayer, M. K. Newton, A. F. Leschen, R. A. B. Gimmel, M. L. Lu, L. Engel, M. S. Huang, D. Pisani, D. Donoghue, P. C. J. 2021-09-24 doi:10.1101/2021.09.22.461358 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Dynamic regulation and requirement for ribosomal RNA transcription duringmammalian development ]]> https://biorxiv.org/content/10.1101/2021.09.22.461379v1?rss=1 Terrazas Falcon, K. Watt, K. Dash, S. Achilleos, A. Moore, E. Zhao, R. Fitriasari, S. Sakai, D. Childers, M. Sardiu, M. Swanson, S. Tsuchiya, D. Unruh, J. Bugarinovic, G. Li, L. Shiang, R. Dixon, J. Dixon, M. Trainor, P. 2021-09-22 doi:10.1101/2021.09.22.461379 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ Lipoproteome screening of the Lyme disease agent identifies novel inhibitors of antibody-mediated complement killing ]]> https://biorxiv.org/content/10.1101/2021.09.23.461563v1?rss=1 Pereira, M. J. Wager, B. Garrigues, R. J. Gerlach, E. Quinn, J. D. Dowdell, A. Osburne, M. S. Zuckert, W. R. Kraiczy, P. Garcia, B. L. Leong, J. M. 2021-09-23 doi:10.1101/2021.09.23.461563 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Transoceanic voyages of drywood termites (Isoptera: Kalotermitidae) inferred from extant and extinct species ]]> https://biorxiv.org/content/10.1101/2021.09.24.461667v1?rss=1 Bucek, A. Wang, M. Sobotnik, J. Sillam-Dusses, D. Mizumoto, N. Stiblik, P. Clitheroe, C. Lu, T. Gonzalez Plaza, J. J. Mohagan, A. Rafanomezantsoa, J. J. Fisher, B. Engel, M. Roisin, Y. Evans, T. Scheffrahn, R. Bourguignon, T. 2021-09-24 doi:10.1101/2021.09.24.461667 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Protein-protein interaction-Gaussian accelerated molecular dynamics (PPI-GaMD): Characterization of protein binding thermodynamics and kinetics ]]> https://biorxiv.org/content/10.1101/2021.09.27.461974v1?rss=1 Wang, J. Miao, Y. 2021-09-28 doi:10.1101/2021.09.27.461974 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ Chromosome-scale genome assembly of the brown anole (Anolis sagrei), a model species for evolution and ecology ]]> https://biorxiv.org/content/10.1101/2021.09.28.462146v1?rss=1 Geneva, A. J. Park, S. Bock, D. de Mello, P. Sarigol, F. Tollis, M. Donihue, C. Reynolds, R. G. Feiner, N. Rasys, A. Lauderdale, J. Minchey, S. G. Alcala, A. J. Infante, C. Kolbe, J. J. Schluter, D. Menke, D. B. Losos, J. B. 2021-09-30 doi:10.1101/2021.09.28.462146 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Role of the Topoisomerase IIα Chromatin Tether domain in Nucleosome Binding & Chromosome Segregation ]]> https://biorxiv.org/content/10.1101/2021.10.03.462934v1?rss=1 Sundararajan, S. Park, H. Kawano, S. Johansson, M. Saito-Fujita, T. Saitoh, N. Arnaoutov, A. Dasso, M. Clarke, D. Azuma, Y. 2021-10-03 doi:10.1101/2021.10.03.462934 Cold Spring Harbor Laboratory Press 2021-10-03 <![CDATA[ Regulation of Liver Regeneration by hepatocyte O-GlcNAcylation in mice ]]> https://biorxiv.org/content/10.1101/2021.10.14.464401v1?rss=1 Robarts, D. R. McGreal, S. R. Umbaugh, D. S. Parkes, W. S. Kotulkar, M. Abernathy, S. Lee, N. Jaeschke, H. Gunewardena, S. Whelan, S. A. Hanover, J. A. Zachara, N. E. Slawson, C. Apte, U. 2021-10-14 doi:10.1101/2021.10.14.464401 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Source-sink connectivity: a novel resting-state EEG marker of the epileptogenic zone ]]> https://biorxiv.org/content/10.1101/2021.10.15.464594v1?rss=1 Gunnarsdottir, K. M. Li, A. Smith, R. J. Kang, J.-Y. Crone, N. Korzeniewska, A. Rouse, A. G. Cameron, N. Cajigas, I. Inati, S. Zaghloul, K. A. Boerwinkle, V. Wyckoff, S. Barot, N. Elarjani, T. Bicchi, M. M. Gonzalez-Martinez, J. Sarma, S. V. 2021-10-18 doi:10.1101/2021.10.15.464594 Cold Spring Harbor Laboratory Press 2021-10-18 <![CDATA[ Wild-type Caenorhabditis elegans Isolates Exhibit Distinct Gene Expression Profiles in Response to Microbial Infection ]]> https://biorxiv.org/content/10.1101/2021.10.16.464663v1?rss=1 Lansdon, P. Carlson, M. Ackley, B. D. 2021-10-17 doi:10.1101/2021.10.16.464663 Cold Spring Harbor Laboratory Press 2021-10-17 <![CDATA[ Immortalization and Functional Screening of Natively Paired Human T Cell Receptor Repertoires ]]> https://biorxiv.org/content/10.1101/2021.10.19.465057v1?rss=1 Fahad, A. S. Yu Chung, C. Lopez Acevedo, S. N. Boyle, N. Madan, B. Gutierrez-Gonzalez, M. F. Matus-Nicodemos, R. Laflin, A. D. Ladi, R. R. Zhou, J. Wolfe, J. Llewellyn-Lacey, S. Doueck, D. Balfour, H. H. Price, D. A. DeKosky, B. J. 2021-10-21 doi:10.1101/2021.10.19.465057 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ Application of sequence semantic and integrated cellular geography approach to study biogenesis of exonic circular RNA ]]> https://biorxiv.org/content/10.1101/2021.10.26.465935v1?rss=1 Kumar, R. Lahiri, T. Pal, M. K. 2021-10-26 doi:10.1101/2021.10.26.465935 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex ]]> https://biorxiv.org/content/10.1101/2021.10.29.466335v1?rss=1 Akey, C. Singh, D. Ouch, C. Echeverria, I. Nudelman, I. Varberg, J. M. Yu, Z. Fang, F. Shi, Y. Wang, J. Saltzberg, D. Song, K. Xu, C. Gumbart, J. Suslov, S. Unruh, J. Jaspersen, S. L. Chait, B. Sali, A. Menendez-Martinez, J. Ludke, S. J. Villa, E. Rout, M. 2021-10-29 doi:10.1101/2021.10.29.466335 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ DOCKGROUND Membrane Protein-Protein Set ]]> https://biorxiv.org/content/10.1101/2021.11.04.467360v1?rss=1 Kotthoff, I. Kundrotas, P. Vakser, I. 2021-11-08 doi:10.1101/2021.11.04.467360 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ Towards a structurally resolved human protein interaction network ]]> https://biorxiv.org/content/10.1101/2021.11.08.467664v1?rss=1 Burke, D. F. Bryant, P. Barrio-Hernandez, I. Memon, D. Pozzati, G. Shenoy, A. Zhu, W. Dunham, A. S. Albanese, P. Keller, A. Scheltema, R. A. Bruce, J. B. Leitner, A. Kundrotas, P. Beltrao, P. Elofsson, A. 2021-11-09 doi:10.1101/2021.11.08.467664 Cold Spring Harbor Laboratory Press 2021-11-09 <![CDATA[ Investigating Increased CO2 concentration on the pH of various plant species ]]> https://biorxiv.org/content/10.1101/2021.11.13.468474v1?rss=1 Schafer, J. Puga, T. Harris, P. Strasser, N. Branum, G. Agbedanu, P. N. 2021-11-14 doi:10.1101/2021.11.13.468474 Cold Spring Harbor Laboratory Press 2021-11-14 <![CDATA[ Interleukin-6 Drives Key Pathologic Outcomes in Experimental Acetaminophen-induced Liver Failure ]]> https://biorxiv.org/content/10.1101/2021.11.15.468664v1?rss=1 Roth, K. Strickland, J. Gonzalez-Pons, R. Pant, A. Yen, T.-C. Freeborn, R. Kennedy, R. Bhushan, B. Boss, A. Rockwell, C. E. Dorrance, A. M. Apte, U. Luyendyk, J. P. Copple, B. L. 2021-11-16 doi:10.1101/2021.11.15.468664 Cold Spring Harbor Laboratory Press 2021-11-16 <![CDATA[ Distinct roles for two Caenorhabditis elegans acid-sensing ion channels in an ultradian clock ]]> https://biorxiv.org/content/10.1101/2021.11.15.468673v1?rss=1 Kaulich, E. Ackley, B. D. Tang, Y. Q. Hardege, I. Schafer, W. Walker, D. 2021-11-17 doi:10.1101/2021.11.15.468673 Cold Spring Harbor Laboratory Press 2021-11-17 <![CDATA[ Induction and inhibition of Drosophila X chromosome gene expression are both impeded by the dosage compensation complex ]]> https://biorxiv.org/content/10.1101/2021.11.22.469548v1?rss=1 Meisel, R. P. Asgari, D. Schlamp, F. Unckless, R. L. 2021-11-22 doi:10.1101/2021.11.22.469548 Cold Spring Harbor Laboratory Press 2021-11-22 <![CDATA[ Cerebrovascular response to exercise interacts with individual genotype and amyloid-beta deposition to influence response inhibition with aging ]]> https://biorxiv.org/content/10.1101/2021.11.22.469615v1?rss=1 Palmer, J. Kaufman, C. S. Vidoni, E. D. Honea, R. A. Burns, J. M. Billinger, S. 2021-11-25 doi:10.1101/2021.11.22.469615 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ START domain mediates Arabidopsis GLABRA2 transcription factor dimerization and turnover independently of homeodomain DNA binding ]]> https://biorxiv.org/content/10.1101/2021.11.23.469727v1?rss=1 Mukherjee, T. Subedi, B. Khosla, A. Warner, A. L. Lerma-Reyes, R. Thompson, K. A. Gunewardena, S. Schrick, K. 2021-11-23 doi:10.1101/2021.11.23.469727 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ Processing of oxidatively damaged DNA dirty ends by APE1 ]]> https://biorxiv.org/content/10.1101/2021.11.28.470279v1?rss=1 Whitaker, A. M. Stark, W. J. Freudenthal, B. D. 2021-11-29 doi:10.1101/2021.11.28.470279 Cold Spring Harbor Laboratory Press 2021-11-29 <![CDATA[ ESR2 regulates indian hedgehog signaling in neonatal rat ovary ]]> https://biorxiv.org/content/10.1101/2021.12.01.470808v1?rss=1 Dilower, I. Chakravarthi, V. R. P. Lee, E. B. Ghosh, S. Borosha, S. Roy, R. Masumi, S. Paul, A. Ghosh, H. Wolfe, M. W. Rumi, M. K. 2021-12-01 doi:10.1101/2021.12.01.470808 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1 ]]> https://biorxiv.org/content/10.1101/2021.12.01.470840v1?rss=1 Weaver, T. M. Click, T. H. Khoang, T. H. Washington, T. M. Agarwal, P. Freudenthal, B. D. 2021-12-01 doi:10.1101/2021.12.01.470840 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Historical biogeography of early diverging termite lineages (Isoptera: Teletisoptera) ]]> https://biorxiv.org/content/10.1101/2021.12.02.471008v1?rss=1 Wang, M. Hellemans, S. Sobotnik, J. Arora, J. Bucek, A. Sillam-Dusses, D. Clitheroe, C. Lu, T. Lo, N. Engel, M. Roisin, Y. Evans, T. A. bourguignon, t. 2021-12-03 doi:10.1101/2021.12.02.471008 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ Intraspecific variation in migration timing of green sturgeon in the Sacramento River system ]]> https://biorxiv.org/content/10.1101/2021.12.03.471146v1?rss=1 Colborne, S. F. Sheppard, L. W. O'Donnell, D. R. Reuman, D. C. Walter, J. A. Singer, G. P. Kelly, J. T. Thomas, M. J. Rypel, A. L. 2021-12-05 doi:10.1101/2021.12.03.471146 Cold Spring Harbor Laboratory Press 2021-12-05 <![CDATA[ Cell cycle-dependent recruitment of FtsN to the divisome in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2021.12.09.472041v1?rss=1 Mannik, J. Pichoff, S. Lutkenhaus, J. Mannik, J. 2021-12-10 doi:10.1101/2021.12.09.472041 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ RNA binding protein RBM3 augments kissing loop formation with lncRNAs to enhance translational control ]]> https://biorxiv.org/content/10.1101/2021.12.14.472669v1?rss=1 Sayed, A. A. A. Choudhury, S. Subramaniam, D. Gunewardena, S. Ponnurangam, S. Dandawate, P. Tawfik, O. Standing, D. Padhye, S. Iwakuma, T. Umar, S. Weir, S. J. Jensen, R. A. Thomas, S. M. Anant, S. 2021-12-14 doi:10.1101/2021.12.14.472669 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ Human Mitochondrial AAA+ ATPase SKD3/CLPB forms Nucleotide-Stabilized Dodecamers ]]> https://biorxiv.org/content/10.1101/2021.12.16.472980v1?rss=1 Spaulding, Z. Thevarajan, I. Schrag, L. G. Zubcevic, L. Zolkiewska, A. Zolkiewski, M. 2021-12-16 doi:10.1101/2021.12.16.472980 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Overlapping stimulons arising in response to divergent stresses in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2021.12.17.473201v1?rss=1 Wang, H. McElfresh, G. Wijesuriya, N. Podgorny, A. Hecht, A. D. Ray, J. C. J. 2021-12-18 doi:10.1101/2021.12.17.473201 Cold Spring Harbor Laboratory Press 2021-12-18 <![CDATA[ Variant-to-gene-mapping followed by cross-species genetic screening identifies GPI-anchor biosynthesis as novel regulator of sleep ]]> https://biorxiv.org/content/10.1101/2021.12.19.472248v1?rss=1 Palermo, J. Chesi, A. Zimmerman, A. Sonti, S. Lasconi, C. Brown, E. B. Pippin, J. A. Wells, A. D. Doldur-Balli, F. Mazzotti, D. Pack, A. I. Gehrman, P. R. Grant, S. F. Keene, A. C. 2021-12-21 doi:10.1101/2021.12.19.472248 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ MERS-CoV endoribonuclease and accessory proteins jointly evade host innate immunity during infection of lung and nasal epithelial cells ]]> https://biorxiv.org/content/10.1101/2021.12.20.473564v1?rss=1 Comar, C. Otter, C. Pfannenstiel, J. Doerger, E. Renner, D. Tan, L. H. Perlman, S. Cohen, N. Fehr, A. Weiss, S. R. 2021-12-21 doi:10.1101/2021.12.20.473564 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Molecular probes of spike ectodomain and its subdomains for SARS-CoV-2 variants, Alpha through Omicron ]]> https://biorxiv.org/content/10.1101/2021.12.29.474491v1?rss=1 Teng, I.-T. Nazzari, A. F. Choe, M. Liu, T. Oliveira de Souza, M. Petrova, Y. Tsybovsky, Y. Wang, S. Zhang, B. Artamonov, M. Madan, B. Huang, A. Lopez Acevedo, S. N. Pan, X. Ruckwardt, T. J. DeKosky, B. J. Mascola, J. R. Misasi, J. Sullivan, N. Zhou, T. Kwong, P. D. 2021-12-30 doi:10.1101/2021.12.29.474491 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ Potent protease inhibitors of deadly lagoviruses: rabbit hemorrhagic disease virus and European brown hare syndrome virus ]]> https://biorxiv.org/content/10.1101/2022.01.10.474982v1?rss=1 Perera, K. D. Johnson, D. K. Lovell, S. Groutas, W. Chang, K.-O. Kim, Y. 2022-01-10 doi:10.1101/2022.01.10.474982 Cold Spring Harbor Laboratory Press 2022-01-10 <![CDATA[ 40 new specimens of Ichthyornis provide unprecedented insight into the postcranial morphology of crownward stem group birds. ]]> https://biorxiv.org/content/10.1101/2022.01.11.475364v1?rss=1 Benito, J. Chen, A. Wilson, L. E. Bhullar, B.-A. S. Burnham, D. Field, D. J. 2022-01-12 doi:10.1101/2022.01.11.475364 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Proteasome granular localization is regulated through mitochondrial respiration and kinase signaling ]]> https://biorxiv.org/content/10.1101/2022.01.13.476202v1?rss=1 Waite, K. A. Roelofs, J. 2022-01-13 doi:10.1101/2022.01.13.476202 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ HuR-dependent expression of Wisp1 is necessary for TGF????-induced cardiac myofibroblast activity ]]> https://biorxiv.org/content/10.1101/2022.01.19.476976v1?rss=1 Green, L. C. Slone, S. Anthony, S. R. Aube, J. Wu, X. Xu, L. Kanisicak, O. Tranter, M. 2022-01-20 doi:10.1101/2022.01.19.476976 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Broad-Spectrum Antimicrobial Potential of Crassula ovata ]]> https://biorxiv.org/content/10.1101/2022.01.20.477177v1?rss=1 Agbedanu, P. N. Puga, T. B. Schafer, J. Buffalo, A. 2022-01-25 doi:10.1101/2022.01.20.477177 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Genomic rearrangements of mobile genetic elements associated with carbapenem resistance of Acinetobacter baumannii ]]> https://biorxiv.org/content/10.1101/2022.02.03.478955v1?rss=1 Vijayakumar, S. Jacob, J. J. Vasudevan, K. Mathur, P. Ray, P. Neeravi, A. R. Baskaran, A. Kirubananthan, A. Anandan, S. Biswas, I. Walia, K. Veeraraghavan, B. 2022-02-03 doi:10.1101/2022.02.03.478955 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Understanding the Separation of Timescales in Rhodococcus erythropolis Proteasome Core Particle Assembly ]]> https://biorxiv.org/content/10.1101/2022.02.04.479176v1?rss=1 Itagi, P. Kante, A. Lagunes, L. Deeds, E. J. 2022-02-05 doi:10.1101/2022.02.04.479176 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ Hoisted with his own petard: how sex-ratio meiotic drive in Drosophila affinis creates resistance alleles that limit its spread ]]> https://biorxiv.org/content/10.1101/2022.02.14.480432v1?rss=1 Ma, W.-J. Patch, K. B. Knoles, E. M. Shoaib, M. M. Unckless, R. L. 2022-02-16 doi:10.1101/2022.02.14.480432 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ Integrated epigenome and transcriptome analysis of normal and arrested meiotic initiation during mouse spermatogenesis ]]> https://biorxiv.org/content/10.1101/2022.02.18.481086v1?rss=1 Zhang, X. Gunewardena, S. Wang, N. 2022-02-19 doi:10.1101/2022.02.18.481086 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ PKD1 and PKD2 mRNA cis-inhibition drives polycystic kidney disease progression ]]> https://biorxiv.org/content/10.1101/2022.02.23.479396v1?rss=1 Lakhia, R. Ramalingam, H. Chang, C.-M. Cobo-Stark, P. Biggers, L. Flaten, A. Alvarez, J. Valencia, T. Wallace, D. P. Lee, E. Patel, V. 2022-02-24 doi:10.1101/2022.02.23.479396 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Design, Synthesis and Evaluation of Inhibitors of the SARS-CoV-2 nsp3 Macrodomain ]]> https://biorxiv.org/content/10.1101/2022.02.27.482176v1?rss=1 View larger version (16K): org.highwire.dtl.DTLVardef@167aceorg.highwire.dtl.DTLVardef@1d88c47org.highwire.dtl.DTLVardef@1e1b34borg.highwire.dtl.DTLVardef@c2321a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sherrill, L. M. Joya, E. E. Walker, A. Roy, A. Alhammad, Y. M. Atobatele, M. Wazir, S. Abbas, G. Keane, P. Zhuo, J. Leung, A. Johnson, D. K. Lehtio, L. Fehr, A. Ferraris, D. V. 2022-02-28 doi:10.1101/2022.02.27.482176 Cold Spring Harbor Laboratory Press 2022-02-28 <![CDATA[ Maturation of cortical endoplasmic reticulum clusters in the mouse oocyte: changes at fertilization. ]]> https://biorxiv.org/content/10.1101/2022.02.28.482320v1?rss=1 Wang, H. Christenson, L. K. Kinsey, W. H. 2022-02-28 doi:10.1101/2022.02.28.482320 Cold Spring Harbor Laboratory Press 2022-02-28 <![CDATA[ HIF1A modulate glycolysis function to governs mouse ovarian microenvironment metabolic plasticity in aging single cell resolution ]]> https://biorxiv.org/content/10.1101/2022.03.01.481557v1?rss=1 Zhang, X. Gunewardena, S. Liu, Y. Wang, N. 2022-03-01 doi:10.1101/2022.03.01.481557 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Discovery of compounds that inhibit SARS-CoV-2 Mac1-ADP-ribose binding by high-throughput screening ]]> https://biorxiv.org/content/10.1101/2022.03.01.482536v1?rss=1 Roy, A. Alhammad, Y. M. McDonald, P. Johnson, D. K. Zhuo, J. Wazir, S. Ferraris, D. V. Lehtiö, L. Leung, A. Fehr, A. R. 2022-03-02 doi:10.1101/2022.03.01.482536 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ A new method to estimate the ecological niche through n-dimensional hypervolumes that combines convex hulls and elliptical envelopes ]]> https://biorxiv.org/content/10.1101/2022.03.03.482921v1?rss=1 Carrasco, J. A. Lison, F. Jimenez, L. Weintraub, A. 2022-03-04 doi:10.1101/2022.03.03.482921 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Mesoscale corticocortical connectivity corresponds with intracortical microstimulation-evoked neural activity ]]> https://biorxiv.org/content/10.1101/2022.03.03.482925v1?rss=1 Bundy, D. T. Barbay, S. Hudson, H. M. Frost, S. B. Nudo, R. J. Guggenmos, D. J. 2022-03-04 doi:10.1101/2022.03.03.482925 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Discovery of small molecule inhibitors of Plasmodium falciparum apicoplast DNA polymerase ]]> https://biorxiv.org/content/10.1101/2022.03.04.482688v1?rss=1 Kaur, S. Nieto, N. McDonald, P. Beck, J. R. Honzatko, R. B. Roy, A. Nelson, S. W. 2022-03-04 doi:10.1101/2022.03.04.482688 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Hippo Signaling Cofactor, WWTR1, at the Crossroads of Human Trophoblast Progenitor Self-Renewal and Differentiation. ]]> https://biorxiv.org/content/10.1101/2022.03.06.483207v1?rss=1 Ray, S. Saha, A. Ghosh, A. Roy, N. Kumar, R. P. Meinhardt, G. Mukerjee, A. Gunewardena, S. Kumar, R. Knofler, M. Paul, S. 2022-03-07 doi:10.1101/2022.03.06.483207 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Coevolution of the Tlx homeobox gene with medusa development (Cnidaria: Medusozoa) ]]> https://biorxiv.org/content/10.1101/2022.03.08.483504v1?rss=1 Travert, M. K. Boohar, R. Sanders, S. M. Nicotra, M. L. Leclere, L. Steele, R. E. Cartwright, P. 2022-03-10 doi:10.1101/2022.03.08.483504 Cold Spring Harbor Laboratory Press 2022-03-10 <![CDATA[ Structural basis for APE1 processing DNA damage in the nucleosome ]]> https://biorxiv.org/content/10.1101/2022.03.09.483662v1?rss=1 Weaver, T. M. Hoitsma, N. M. Spencer, J. J. Freudenthal, B. D. Gakhar, L. Schnicker, N. J. 2022-03-10 doi:10.1101/2022.03.09.483662 Cold Spring Harbor Laboratory Press 2022-03-10 <![CDATA[ Predicting the structure of large protein complexes using AlphaFold and sequential assembly ]]> https://biorxiv.org/content/10.1101/2022.03.12.484089v1?rss=1 Bryant, P. Pozzati, G. Zhu, W. Shenoy, A. Kundrotas, P. Elofsson, A. 2022-03-12 doi:10.1101/2022.03.12.484089 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ Gram-negative Antimicrobial spectrum of Ulmus pumila ]]> https://biorxiv.org/content/10.1101/2022.03.12.484112v1?rss=1 Schafer, J. Puga, T. B. Miller, S. R. T. Agbedanu, P. N. 2022-03-14 doi:10.1101/2022.03.12.484112 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ The Envelope Protein of SARS-CoV-2 Inhibits Viral Protein Synthesis and Infectivity of Human Immunodeficiency Virus type 1 (HIV-1) ]]> https://biorxiv.org/content/10.1101/2022.03.23.485576v1?rss=1 Stephens, E. B. Henke, W. Polpitiya Arachchige, S. Waisner, H. Kalamvoki, M. 2022-03-27 doi:10.1101/2022.03.23.485576 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ SARS-CoV-2 harnesses host translational shutoff and autophagy to optimize virus yields: The role of the envelope (E) protein ]]> https://biorxiv.org/content/10.1101/2022.03.24.485734v1?rss=1 Waisner, H. Grieshaber, B. Saud, R. Henke, W. Stephens, E. B. Kalamvoki, M. 2022-03-25 doi:10.1101/2022.03.24.485734 Cold Spring Harbor Laboratory Press 2022-03-25 <![CDATA[ Loss of the repressor REST affects progesterone receptor function and promotes uterine leiomyoma pathogenesis ]]> https://biorxiv.org/content/10.1101/2022.04.11.487902v1?rss=1 Cloud, A. S. McWilliams, M. M. Koohestani, F. Ganeshkumar, S. Gunewardena, S. Graham, A. Nothnick, W. B. Chennathukuzhi, V. M. 2022-04-11 doi:10.1101/2022.04.11.487902 Cold Spring Harbor Laboratory Press 2022-04-11 <![CDATA[ Is It A Barrel? General Features of Transmembrane Beta Barrels from a Large Database ]]> https://biorxiv.org/content/10.1101/2022.04.13.488089v1?rss=1 240,000 unrelated to previously structurally-resolved OMPs. We identify ten types of OMPs in our database. The largest types signal sequence--used for targeting the membrane-insertion machinery--varies by phylogenetic class. All other types of OMPs do not have a related signal sequence, raising new questions of how these proteins fold. Our web-accessible database will allow for further exploration of the varieties of outer membrane proteins to uncover new targets for controlling antibiotic resistance. ]]> Montezano, D. Bernstein, R. Copeland, M. Slusky, J. S. 2022-04-13 doi:10.1101/2022.04.13.488089 Cold Spring Harbor Laboratory Press 2022-04-13 <![CDATA[ High total water loss driven by low-fat diet in desert-adapted mice ]]> https://biorxiv.org/content/10.1101/2022.04.15.488461v1?rss=1 Blumstein, D. M. Colella, J. P. Linder, E. MacManes, M. D. 2022-04-15 doi:10.1101/2022.04.15.488461 Cold Spring Harbor Laboratory Press 2022-04-15 <![CDATA[ Detergent headgroups control TolC folding in vitro ]]> https://biorxiv.org/content/10.1101/2022.04.28.489915v1?rss=1 Ikujuni, A. P. Budiardjo, S. J. Slusky, J. S. G. 2022-04-29 doi:10.1101/2022.04.28.489915 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ Visualizing the Coordination of APE1 and DNA Polymerase β During Base Excision Repair ]]> https://biorxiv.org/content/10.1101/2022.05.02.490312v1?rss=1 Fairlamb, M. Washington, T. Freudenthal, B. D. 2022-05-02 doi:10.1101/2022.05.02.490312 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ A data-driven approach to quantifying meal characteristics influencing energy intake ]]> https://biorxiv.org/content/10.1101/2022.05.08.491083v1?rss=1 Fazzino, T. L. Guo, J. Courville, A. B. Hall, K. D. 2022-05-08 doi:10.1101/2022.05.08.491083 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ USP11 promotes endothelial apoptosis-resistance in pulmonary hypertension by deubiquitinating HINT3 ]]> https://biorxiv.org/content/10.1101/2022.05.17.492159v1?rss=1 Jang, A. J. Tseng, V. Kim, J. S. Stearman, R. S. Zhao, Y. Zhao, J. Choi, J. Lister, J. Passineau, M. J. Lam, W. A. Park, C. Benza, R. L. Kang, B.-Y. 2022-05-19 doi:10.1101/2022.05.17.492159 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Short tandem repeats bind transcription factors to tune eukaryotic gene expression ]]> https://biorxiv.org/content/10.1101/2022.05.24.493321v1?rss=1 Horton, C. A. Alexandari, A. M. Hayes, M. G. B. Marklund, E. Schaepe, J. M. Aditham, A. K. Shah, N. Shrikumar, A. A. Afek, A. Greenleaf, W. J. Gordan, R. Zeitlinger, J. Kundaje, A. Fordyce, P. M. 2022-05-25 doi:10.1101/2022.05.24.493321 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Doublecortin like kinase 1 is a target in squamous cell carcinoma ]]> https://biorxiv.org/content/10.1101/2022.05.26.493670v1?rss=1 Standing, D. Arnold, L. Dandawate, P. Ottemann, B. Snyder, V. Ponnurangam, S. Subramaniam, D. Srinivasan, P. Choudhury, S. New, J. Kwatra, D. Ramamoorthy, P. Roy, B. C. Shadoin, M. Al-Rajabi, R. O'Neil, M. Gunewardena, S. Ashcraft, J. Umar, S. Weir, S. J. Tawfik, O. Padhye, S. Anant, S. Thomas, S. M. 2022-05-28 doi:10.1101/2022.05.26.493670 Cold Spring Harbor Laboratory Press 2022-05-28 <![CDATA[ Novel insights into the fundamentals of palatal shelf elevation dynamics in normal mouse embryos ]]> https://biorxiv.org/content/10.1101/2022.06.02.494562v1?rss=1 Goering, J. P. Moedritzer, M. Stetsiv, M. Isai, D. G. Hufft-Martinez, B. M. Umar, Z. Rickabaugh, M. K. Keselman, P. Chauhan, M. Brooks, W. M. Fischer, K. J. Czirok, A. Saadi, I. 2022-06-04 doi:10.1101/2022.06.02.494562 Cold Spring Harbor Laboratory Press 2022-06-04 <![CDATA[ Docking-based long timescale simulation of cell-size protein systems at atomic resolution ]]> https://biorxiv.org/content/10.1101/2022.06.07.495183v1?rss=1 Vakser, I. A. Grudinin, S. Jenkins, N. W. Kundrotas, P. J. Deeds, E. J. 2022-06-09 doi:10.1101/2022.06.07.495183 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Conservation at the uterine-placental interface ]]> https://biorxiv.org/content/10.1101/2022.06.14.496152v1?rss=1 Scott, R. L. Vu, H. T. H. Jain, A. Iqbal, K. Tuteja, G. Soares, M. J. 2022-06-17 doi:10.1101/2022.06.14.496152 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ AKT1-FOXO4 AXIS REGULATES HEMOCHORIAL PLACENTATION ]]> https://biorxiv.org/content/10.1101/2022.06.15.496110v1?rss=1 Kozai, K. Moreno Irusta, A. Iqbal, K. Winchester, M.-L. Scott, R. L. Simon, M. E. Muto, M. Parrish, M. R. Soares, M. J. 2022-06-17 doi:10.1101/2022.06.15.496110 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ CITED2 Is A Conserved Regulator Of Deep Hemochorial Placentation ]]> https://biorxiv.org/content/10.1101/2022.06.15.496287v1?rss=1 Kuna, M. Dhakal, P. Iqbal, K. Dominguez, E. M. Kent, L. N. Muto, M. Moreno-Irusta, A. Kozai, K. Varberg, K. M. Okae, H. Arima, T. Sucov, H. M. Soares, M. J. 2022-06-17 doi:10.1101/2022.06.15.496287 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ TOM-1/Tomosyn acts with the UNC-6/Netrin receptor UNC-5 to inhibit growth cone protrusion in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2022.06.16.496459v1?rss=1 Mahadik, S. S. Lundquist, E. A. 2022-06-17 doi:10.1101/2022.06.16.496459 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ EWSR1 prevents the induction of aneuploidy by regulating the localization of Aurora B at inner centromere ]]> https://biorxiv.org/content/10.1101/2022.06.17.496636v1?rss=1 Kim, H. Park, H. Schulz, E. T. Azuma, Y. Azuma, M. 2022-06-18 doi:10.1101/2022.06.17.496636 Cold Spring Harbor Laboratory Press 2022-06-18 <![CDATA[ The wtf meiotic driver gene family has unexpectedly persisted for over 100 million years ]]> https://biorxiv.org/content/10.1101/2022.06.24.497463v1?rss=1 De Carvalho, M. Jia, G.-S. Nidamangala Srinivasa, A. Billmyre, R. B. Xu, Y.-H. Lange, J. J. Sabbarini, I. M. Du, L.-L. Zanders, S. E. 2022-06-26 doi:10.1101/2022.06.24.497463 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Development of allosteric, selective cyclin-dependent kinase 2 (CDK2) inhibitors that are negatively cooperative with cyclin binding and show potential as contraceptive agents ]]> https://biorxiv.org/content/10.1101/2022.06.30.497818v1?rss=1 Faber, E. B. Tang, J. Roberts, E. Ganeshkumar, S. Sun, L. Wang, N. Rasmussen, D. Majumbar, A. John, K. Yang, A. Khalid, H. Hawkinson, J. E. Levinson, N. M. Schonbrunn, E. Chennathukuzhi, V. Harki, D. A. Georg, G. I. 2022-07-02 doi:10.1101/2022.06.30.497818 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Obesity Disrupts Pituitary UPR Leading to NAFLD ]]> https://biorxiv.org/content/10.1101/2022.07.06.498610v1?rss=1 Qian, Q. Li, M. Zhang, Z. Davis, S. Rahmouni, K. Norris, A. W. Cao, H. Ding, W.-X. Yang, L. 2022-07-06 doi:10.1101/2022.07.06.498610 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ Early life stress exposure increases susceptibility to high fat/high sucrose diet in female mice ]]> https://biorxiv.org/content/10.1101/2022.07.14.500119v1?rss=1 Frick, J. M. Eller, O. C. Foright, R. M. Levasseur, B. M. Yang, X. Wang, R. Winter, M. K. O'Neil, M. Morris, E. M. Thyfault, J. P. Christianson, J. A. 2022-07-14 doi:10.1101/2022.07.14.500119 Cold Spring Harbor Laboratory Press 2022-07-14 <![CDATA[ Hippocampal blood flow rapidly and preferentially increases after a bout of moderate-intensity exercise in older adults with poor cerebrovascular health ]]> https://biorxiv.org/content/10.1101/2022.07.15.500132v1?rss=1 Palmer, J. A. Morris, J. K. Billinger, S. A. Lepping, R. J. Martin, L. Green, Z. Vidoni, E. 2022-07-16 doi:10.1101/2022.07.15.500132 Cold Spring Harbor Laboratory Press 2022-07-16 <![CDATA[ Discovery of malathion resistance QTL in Drosophila melanogaster using a bulked phenotyping approach ]]> https://biorxiv.org/content/10.1101/2022.07.19.500708v1?rss=1 Macdonald, S. J. Long, A. D. 2022-07-20 doi:10.1101/2022.07.19.500708 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Data-Independent Acquisition and Quantification of Extracellular Matrix from Human Lung in Chronic Inflammation-Associated Carcinomas ]]> https://biorxiv.org/content/10.1101/2022.08.05.503012v1?rss=1 Bons, J. Pan, D. Shah, S. Bai, R. Chen-Tanyolac, C. Wang, X. Fels Elliott, D. R. Urisman, A. O'Broin, A. Basisty, N. Rose, J. Sangwan, V. Camilleri-Broet, S. Tankel, J. Gascard, P. Ferri, L. Tlsty, T. D. Schilling, B. 2022-08-06 doi:10.1101/2022.08.05.503012 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ Soil variation among natural habitats alters glucosinolate content in a wild perennial mustard ]]> https://biorxiv.org/content/10.1101/2022.08.16.504215v1?rss=1 Wagner, M. R. Mitchell-Olds, T. 2022-08-18 doi:10.1101/2022.08.16.504215 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ Mechanistic Insight into AP-Endonuclease 1 Cleavage of Abasic Sites at Stalled Replication Forks ]]> https://biorxiv.org/content/10.1101/2022.08.22.504733v1?rss=1 Hoitsma, N. M. Norris, J. Khoang, T. Kaushik, V. Antony, E. Hedglin, M. Freudenthal, B. 2022-08-22 doi:10.1101/2022.08.22.504733 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Identifying climatic drivers of hybridization in Heuchereae (Saxifragaceae) ]]> https://biorxiv.org/content/10.1101/2022.08.24.505154v1?rss=1 Folk, R. A. Gaynor, M. L. Engle-Wrye, N. J. O'Meara, B. C. Soltis, P. S. Soltis, D. E. Guralnick, R. P. Smith, S. A. Grady, C. J. Okuyama, Y. 2022-08-26 doi:10.1101/2022.08.24.505154 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Characterization of a novel estrogen- and progesterone-responsive endometrial cancer cell line: HCI-EC-23 ]]> https://biorxiv.org/content/10.1101/2022.08.25.505203v1?rss=1 Rush, C. M. Blanchard, Z. Polaski, J. T. Osborne, K. S. Osby, K. Vahrenkamp, J. M. Yang, C.-H. Lum, D. H. Hagan, C. R. Leslie, K. K. Pufall, M. A. Thiel, K. W. Gertz, J. 2022-08-25 doi:10.1101/2022.08.25.505203 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Habitat use differences mediate anthropogenic threat exposure in white sturgeon ]]> https://biorxiv.org/content/10.1101/2022.08.31.505999v1?rss=1 50% of reproductive-age fish may have been residing in areas affected by the red tide. Future monitoring and management of white sturgeon might benefit from examining multiple phases of white sturgeon life history. For example, additional tracking studies could improve understanding of juvenile habitat use, adult survival rates, patterns of anadromy, and cross-basin habitat utilization. ]]> Walter, J. A. Singer, G. P. Reuman, D. C. Colborne, S. F. Sheppard, L. W. O'Donnell, D. R. Coombs, N. Johnston, M. Miller, E. A. Steel, A. E. Kelly, J. T. Fangue, N. A. Rypel, A. L. 2022-09-02 doi:10.1101/2022.08.31.505999 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Metadata preservation and stewardship for genomic data is possible, but must happen now ]]> https://biorxiv.org/content/10.1101/2022.09.12.507034v1?rss=1 Crandall, E. D. Toczydlowski, R. H. Liggins, L. Holmes, A. E. Ghoojaei, M. Gaither, M. R. Wham, B. E. Pritt, A. L. Noble, C. Anderson, T. J. Barton, R. L. Berg, J. T. Beskid, S. G. Delgado, A. Farrell, E. Himmelsbach, N. Queeno, S. R. Trinh, T. Weyand, C. A. Bentley, A. Deck, J. Riginos, C. Bradburd, G. S. Toonen, R. J. 2022-09-15 doi:10.1101/2022.09.12.507034 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Molecular engineering of a cryptic epitope in Spike RBD improves manufacturability and neutralizing breadth against SARS-CoV-2 variants ]]> https://biorxiv.org/content/10.1101/2022.09.14.507842v1?rss=1 Rodriguez-Aponte, S. A. Dalvie, N. C. Wong, T. Y. Johnston, R. S. Naranjo, C. A. Bajoria, S. Kumru, O. S. Kaur, K. Russ, B. P. Lee, K. S. Cyphert, H. A. Barbier, M. Rao, H. D. Rajurkar, M. P. Lothe, R. R. Shaligram, U. Batwal, S. Chandrasekaran, R. Nagar, G. Kleanthous, H. Biswas, S. Bevere, J. R. Joshi, S. B. Volkin, D. B. Damron, F. H. Love, J. C. 2022-09-14 doi:10.1101/2022.09.14.507842 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ Cancer cells communicate with macrophages to prevent T cell activation during development of cell cycle therapy resistance ]]> https://biorxiv.org/content/10.1101/2022.09.14.507931v1?rss=1 Griffiths, J. I. Cosgrove, P. A. Medina Castaneda, E. Nath, A. Chen, J. Adler, F. R. Chang, J. T. Khan, Q. J. Bild, A. H. 2022-09-17 doi:10.1101/2022.09.14.507931 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Temporal dynamics of the multi-omic response to endurance exercise training across tissues ]]> https://biorxiv.org/content/10.1101/2022.09.21.508770v1?rss=1 MoTrPAC Study Group, Amar, D. Gay, N. R. Jean Beltran, P. M. Adkins, J. N. Almagro Armenteros, J. J. Ashley, E. Avila-Pacheco, J. Bae, D. Bararpour, N. Burant, C. Clish, C. Cutter, G. Dasari, S. Dennis, C. Evans, C. R. Fernandez, F. M. Gaul, D. Ge, Y. Gerszten, R. Goodyear, L. J. Hou, Z. Ilkayeva, O. Ivanova, A. A. Jimenez-Morales, D. Kachman, M. T. Keshishian, H. Kraus, W. E. Lanza, I. R. Li, J. Lindholm, M. E. Lira, A. C. Many, G. M. Marwaha, S. Miller, M. E. Muehlbauer, M. J. Nair, K. S. Nair, V. D. Natarajan Raja, A. Newgard, C. Ortlund, E. A. Pie 2022-09-23 doi:10.1101/2022.09.21.508770 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Genetic Variation in Chromatin State Across Multiple Tissues in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2022.09.26.509449v1?rss=1 Huynh, K. Smith, B. Macdonald, S. Long, A. 2022-09-27 doi:10.1101/2022.09.26.509449 Cold Spring Harbor Laboratory Press 2022-09-27 <![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[ Acclimating to degraded environments: The social rationale for swift action on restoration ]]> https://biorxiv.org/content/10.1101/2022.09.27.509807v1?rss=1 Karatayev, V. A. Wilson, R. S. Webster, D. G. Axelrod, M. Bauch, C. T. Anand, M. 2022-09-28 doi:10.1101/2022.09.27.509807 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ A cnidarian phylogenomic tree fitted with hundreds of 18S leaves ]]> https://biorxiv.org/content/10.1101/2022.10.03.510641v1?rss=1 DeBiasse, M. Buckenmeyer, A. Macrander, J. Babonis, L. Bentlage, B. S. Cartwright, P. Prada, C. Reitzel, A. M. Stampar, S. Collins, A. Daly, M. Ryan, J. F. 2022-10-05 doi:10.1101/2022.10.03.510641 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Zebrafish screen of high-confidence targets at insomnia GWAS loci implicates MEIS1, SKIV2L, and ARFGAP2 as conserved regulators of sleep-wake behaviors ]]> https://biorxiv.org/content/10.1101/2022.10.05.511011v1?rss=1 Zimmerman, A. J. Doldur-Balli, F. Keenan, B. T. Shetty, Z. Y. Palermo, J. Chesi, A. Sonti, S. Pahl, M. C. Brown, E. B. Pippin, J. A. Wells, A. D. Mazzotti, D. R. Veatch, O. J. Krishnan, A. Gehrman, P. R. Keene, A. C. Grant, S. F. A. Pack, A. I. 2022-10-07 doi:10.1101/2022.10.05.511011 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Broad-scale factors shaping the ecological niche and geographic distribution of Spirodela polyrhiza ]]> https://biorxiv.org/content/10.1101/2022.10.18.512760v1?rss=1 Cobos, M. E. Peterson, A. T. 2022-10-21 doi:10.1101/2022.10.18.512760 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ The genetic basis of variation immune defense against Lysinibacillus fusiformis infection in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2022.10.19.512815v1?rss=1 Smith, B. R. Patch, K. B. Unckless, R. L. 2022-10-21 doi:10.1101/2022.10.19.512815 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Convergence and divergence of the adaptive landscape in two ecologically similar and sympatric damselfly species ]]> https://biorxiv.org/content/10.1101/2022.10.19.512907v1?rss=1 Gupta, A. Svensson, E. I. Frietsch, H. Tsuboi, M. 2022-10-21 doi:10.1101/2022.10.19.512907 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Repurposing the CRISPR-Cas9 System for Targeted Chromatin O-linked β-N- acetylglucosamine Editing ]]> https://biorxiv.org/content/10.1101/2022.10.27.514044v1?rss=1 Parker, M. P. Dias, W. B. Brautman, W. Lowe, N. Fedosyuk, H. Peterson, K. R. Slawson, C. 2022-10-27 doi:10.1101/2022.10.27.514044 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Cross-species activation of hydrogen cyanide production by a promiscuous quorum-sensing receptor promotes Chromobacterium subtsugae competition in a dual-species model ]]> https://biorxiv.org/content/10.1101/2022.11.01.514797v1?rss=1 Chandler, J. R. Loo, C. Koirala, P. Smith, N. C. Oller, A. Evans, K. C. Benomar, S. Parisi, I. R. 2022-11-02 doi:10.1101/2022.11.01.514797 Cold Spring Harbor Laboratory Press 2022-11-02 <![CDATA[ Structural Elucidation of a Protective B cell Epitope on Outer Surface Protein C (OspC) of the Lyme disease spirochete, Borreliella burgdorferi ]]> https://biorxiv.org/content/10.1101/2022.11.28.518297v1?rss=1 Rudolph, M. J. Davis, S. Haque, H. M. E. Weis, D. D. Vance, D. J. Piazza, C. L. Ejemel, M. Cavacini, L. A. Wang, Y. Mbow, L. Gilmore, R. D. Mantis, N. J. 2022-11-29 doi:10.1101/2022.11.28.518297 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ The complete sequence of a human Y chromosome ]]> https://biorxiv.org/content/10.1101/2022.12.01.518724v1?rss=1 Rhie, A. Nurk, S. Cechova, M. Hoyt, S. J. Taylor, D. J. Altemose, N. Hook, P. W. Koren, S. Rautiainen, M. Alexandrov, I. A. Allen, J. Asri, M. Bzikadze, A. V. Chen, N.-C. Chin, C.-S. Diekhans, M. Flicek, P. Formenti, G. Fungtammasan, A. Garcia Giron, C. Garrison, E. Gershman, A. Gerton, J. Grady, P. G. Guarracino, A. Haggerty, L. Halabian, R. Hansen, N. F. Harris, R. Hartley, G. A. Harvey, W. T. Haukness, M. Heinz, J. Hourlier, T. Hubley, R. M. Hunt, S. E. Hwang, S. Jain, M. Kesharwani, R. K. Lewis, A. P. Li, H. Logsdon, G. A. Lucas, J. K. Makalowski, 2022-12-01 doi:10.1101/2022.12.01.518724 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Inducible CRISPRi-based operon silencing and selective in trans gene complementation in Borrelia burgdorferi ]]> https://biorxiv.org/content/10.1101/2022.12.05.519228v1?rss=1 Murphy, B. T. Wiepen, J. J. He, H. Pramanik, A. S. Peters, J. M. Stevenson, B. Zueckert, W. R. 2022-12-08 doi:10.1101/2022.12.05.519228 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ Is niche divergence more likely in parapatry? A test in Sclerurus mexicanus sensu lato (Aves: Furnariidae) ]]> https://biorxiv.org/content/10.1101/2022.12.06.519370v1?rss=1 Cooper, J. C. Barragan Diaz, D. 2022-12-10 doi:10.1101/2022.12.06.519370 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ Metabolomic Profiling to Identify Early Urinary Biomarkers and Metabolic Pathway Alterations in Autosomal Dominant Polycystic Kidney Disease ]]> https://biorxiv.org/content/10.1101/2022.12.08.519365v1?rss=1 Hahn, A. K. Houske, E. A. Glimm, M. G. Bergstrom, A. R. Slipher, S. K. Welhaven, H. D. Greenwood, M. C. Linse, G. M. June, R. K. Yu, A. S. L. Wallace, D. P. 2022-12-08 doi:10.1101/2022.12.08.519365 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ Identification of a covert evolutionary pathway between two protein folds ]]> https://biorxiv.org/content/10.1101/2022.12.08.519646v1?rss=1 Chakravarty, D. Sreenivasan, S. Swint-Kruse, L. Porter, L. 2022-12-12 doi:10.1101/2022.12.08.519646 Cold Spring Harbor Laboratory Press 2022-12-12 <![CDATA[ Ligand Gaussian accelerated molecular dynamics 2 (LiGaMD2): Improved calculations of ligand binding thermodynamics and kinetics with closed protein pocket ]]> https://biorxiv.org/content/10.1101/2022.12.16.520748v1?rss=1 Wang, J. Miao, Y. 2022-12-16 doi:10.1101/2022.12.16.520748 Cold Spring Harbor Laboratory Press 2022-12-16 <![CDATA[ Chromatin accessibility is a two-tier process regulated by transcription factor pioneering and enhancer activation ]]> https://biorxiv.org/content/10.1101/2022.12.20.520743v1?rss=1 Brennan, K. J. Weilert, M. Krueger, S. Pampari, A. Liu, H.-Y. Yang, A. W. H. Hughes, T. R. Rushlow, C. A. Kundaje, A. Zeitlinger, J. 2022-12-20 doi:10.1101/2022.12.20.520743 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ A Borrelia burgdorferi LptD Homolog Facilitates Flipping of Surface Lipoproteins Through the Spirochetal Outer Membrane ]]> https://biorxiv.org/content/10.1101/2022.12.21.521298v1?rss=1 He, H. Pramanik, A. S. Swanson, S. K. Johnson, D. K. Florens, L. Zueckert, W. R. 2022-12-22 doi:10.1101/2022.12.21.521298 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ A ferritin-based COVID-19 nanoparticle vaccine that elicits robust, durable, broad-spectrum neutralizing antisera in non-human primates ]]> https://biorxiv.org/content/10.1101/2022.12.25.521784v1?rss=1 Weidenbacher, P. A.- B. Sanyal, M. Friedland, N. Tang, S. S Arunachalam, P. Hu, M. Kumru, O. S. Morris, M. K. Fontenot, J. Shirreff, L. Do, J. Cheng, Y.-C. Vasudevan, G. Feinberg, M. B. Villinger, F. J. Hanson, C. Joshi, S. B. Volkin, D. B. Pulendran, B. Kim, P. S. 2022-12-26 doi:10.1101/2022.12.25.521784 Cold Spring Harbor Laboratory Press 2022-12-26 <![CDATA[ Functional connectivity favors hyperactivity leading to synapse loss in amyloidosis ]]> https://biorxiv.org/content/10.1101/2023.01.05.522900v1?rss=1 L'esperance, O. J. McGhee, J. Davidson, G. Smith, A. S. Subramanian, J. 2023-01-05 doi:10.1101/2023.01.05.522900 Cold Spring Harbor Laboratory Press 2023-01-05 <![CDATA[ To design or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design ]]> https://biorxiv.org/content/10.1101/2023.01.06.522983v1?rss=1 Gustafson, G. Glynn, R. Short, A. Tarasov, S. Gunter, N. 2023-01-06 doi:10.1101/2023.01.06.522983 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry ]]> https://biorxiv.org/content/10.1101/2023.01.09.523326v1?rss=1 Bai, N. Adeshina, Y. Bychkov, I. Xia, Y. Gowthaman, R. Miller, S. A. Gupta, A. K. Johnson, D. K. Lan, L. Golemis, E. A. Makhov, P. B. Xu, L. Pillai, M. M. Boumber, Y. Karanicolas, J. 2023-01-10 doi:10.1101/2023.01.09.523326 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Ketolysis is Required for the Proper Development and Function of the Somatosensory Nervous System. ]]> https://biorxiv.org/content/10.1101/2023.01.11.523492v1?rss=1 Enders, J. Jack, J. Thomas, S. Lynch, P. Lasnier, S. Cao, X. Swanson, M. T. Ryals, J. M. Thyfault, J. P. Puchalska, P. Crawford, P. A. Wright, D. E. 2023-01-13 doi:10.1101/2023.01.11.523492 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ The mitochondrial multi-omic response to exercise training across tissues ]]> https://biorxiv.org/content/10.1101/2023.01.13.523698v1?rss=1 Amar, D. Gay, N. R. Jimenez-Morales, D. Jean Beltran, P. M. Ramaker, M. E. Natarajan Raja, A. Zhao, B. Sun, Y. Marwaha, S. Gaul, D. Hershman, S. G. Xia, A. Lanza, I. Fernandez, F. M. Montgomery, S. B. Hevener, A. L. Ashley, E. Walsh, M. J. Sparks, L. M. Burant, C. F. Rector, R. S. Thyfault, J. Wheeler, M. T. Goodpaster, B. H. Coen, P. M. Schenk, S. Bodine, S. C. Lindholm, M. E. MoTrPAC Study Group, 2023-01-13 doi:10.1101/2023.01.13.523698 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Tobramycin adaptation alters the antibiotic susceptibility of Pseudomonas aeruginosa quorum sensing-null mutants ]]> https://biorxiv.org/content/10.1101/2023.01.13.523864v1?rss=1 Abisado-Duquea, R. G. McKee, B. M. Townsend, K. A. Woods, K. Holder, A. J. Craddock, V. D. Cabeen, M. T. Chandler, J. R. 2023-01-14 doi:10.1101/2023.01.13.523864 Cold Spring Harbor Laboratory Press 2023-01-14 <![CDATA[ Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors ]]> https://biorxiv.org/content/10.1101/2023.01.15.524128v1?rss=1 Do, H. N. Wang, J. Miao, Y. 2023-01-18 doi:10.1101/2023.01.15.524128 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[ HuR inhibition reduces post-ischemic cardiac remodeling by dampening acute inflammatory gene expression and the innate immune response ]]> https://biorxiv.org/content/10.1101/2023.01.17.524420v1?rss=1 Slone, S. Anthony, S. R. Green, L. C. Nieman, M. L. Alam, P. Wu, X. Roy, S. Aube, J. Xu, L. Lorenz, J. N. Owens, A. P. Kanisicak, O. Tranter, M. 2023-01-18 doi:10.1101/2023.01.17.524420 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ DYRK1A interacts with Tuberous Sclerosis complex and promotes mTORC1 activity ]]> https://biorxiv.org/content/10.1101/2023.01.18.524493v1?rss=1 Wang, P. Sarkar, S. Zhang, M. Zhang, Z. Datta, S. Jayaram, N. Datta, S. He, R. Wu, P. Chao, P. Zhang, Y. Washburn, M. P. Florens, L. Nagarkar, S. Jaiswal, M. Mohan, M. 2023-01-18 doi:10.1101/2023.01.18.524493 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Post-Ischemic Reorganization of Sensory Responses in Cerebral Cortex ]]> https://biorxiv.org/content/10.1101/2023.01.18.524583v1?rss=1 Hayley, P. Tuchek, C. Dalla, S. Borrell, J. Murphy, M. D. Nudo, R. J. Guggenmos, D. J. 2023-01-20 doi:10.1101/2023.01.18.524583 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Global Transcriptomics of Congenital Hepatic Fibrosis in Autosomal Recessive Polycystic Kidney Disease using PCK rats ]]> https://biorxiv.org/content/10.1101/2023.01.19.524760v1?rss=1 Khare, S. Jiang, L. Paine Cabrera, D. Apte, U. Pritchard, M. T. 2023-01-20 doi:10.1101/2023.01.19.524760 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Lumbar endplate microfracture injury induces Modic-like changes, intervertebral disc degeneration and spinal cord sensitization-An In Vivo Rat Model ]]> https://biorxiv.org/content/10.1101/2023.01.27.525924v1?rss=1 Wang, D. Lai, A. Gansau, J. Seifert, A. Munitz, J. Zaheer, K. Bhadouria, N. Lee, Y. Nasser, P. Laudier, D. Holguin, N. Hecht, A. Iatridis, J. C. 2023-01-30 doi:10.1101/2023.01.27.525924 Cold Spring Harbor Laboratory Press 2023-01-30 <![CDATA[ Borrelia burgdorferi PlzA is a c-di-GMP dependent DNA and RNA binding protein ]]> https://biorxiv.org/content/10.1101/2023.01.30.526351v1?rss=1 Jusufovic, N. Savage, C. Saylor, T. C. Brissette, C. A. Zueckert, W. R. Schlax, P. MOTALEB, M. A. R. Stevenson, B. 2023-01-31 doi:10.1101/2023.01.30.526351 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Serial Capture Affinity Purification and Integrated Structural Modeling of the H3K4me3 Binding and DNA Damage Related WDR76:SPIN1 Complex ]]> https://biorxiv.org/content/10.1101/2023.01.31.526478v1?rss=1 Liu, X. Zhang, Y. Wen, Z. Hao, Y. Banks, C. Lange, J. J. Cesare, J. Bhattacharya, S. Slaughter, B. Unruh, J. Florens, L. Workman, J. Washburn, M. 2023-02-03 doi:10.1101/2023.01.31.526478 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Genome sequence of Ophryocystis elektroscirrha, an apicomplexan parasite of monarch butterflies: cryptic diversity and response to host-sequestered plant chemicals ]]> https://biorxiv.org/content/10.1101/2023.02.01.526615v1?rss=1 Mongue, A. J. Martin, S. H. Manweiler, R. E. Scullion, H. Koehn, J. L. de Roode, J. C. Walters, J. R. 2023-02-02 doi:10.1101/2023.02.01.526615 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ Identifying Human Specific Adverse Outcome Pathways of Per- and Polyfluoroalkyl Substances Using Liver-Chimeric Humanized Mice ]]> https://biorxiv.org/content/10.1101/2023.02.01.526711v1?rss=1 Robarts, D. R. Paine-Cabrera, D. Kotulkar, M. Venneman, K. K. Gunewardena, S. Corton, J. C. Lau, C. Foquet, L. Bial, G. Apte, U. 2023-02-03 doi:10.1101/2023.02.01.526711 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Signatures of antibiotic tolerance and persistence in response to divergent stresses ]]> https://biorxiv.org/content/10.1101/2023.02.05.527212v1?rss=1 Wang, H. McElfresh, G. Wijesuriya, N. Podgorny, A. Hecht, A. D. Ray, C. J. 2023-02-06 doi:10.1101/2023.02.05.527212 Cold Spring Harbor Laboratory Press 2023-02-06 <![CDATA[ Quantitative analyses of interactions between SpoVG and RNA/DNA ]]> https://biorxiv.org/content/10.1101/2023.02.06.527361v1?rss=1 Saylor, T. C. Savage, C. R. Krusensjerna, A. C. Jusufovic, N. Zueckert, W. R. Brissette, C. A. MOTALEB, M. A. Schlax, P. J. Stevenson, B. 2023-02-06 doi:10.1101/2023.02.06.527361 Cold Spring Harbor Laboratory Press 2023-02-06 <![CDATA[ Individual recombinant repeats of MUC16 display variable binding to CA125 antibodies ]]> https://biorxiv.org/content/10.1101/2023.02.08.527749v1?rss=1 Wang, C.-W. Hanson, E. K. Minkoff, L. Whelan, R. J. 2023-02-09 doi:10.1101/2023.02.08.527749 Cold Spring Harbor Laboratory Press 2023-02-09 <![CDATA[ The Essential Role of O-GlcNAcylation in Hepatic Differentiation ]]> https://biorxiv.org/content/10.1101/2023.02.16.528884v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@aed343org.highwire.dtl.DTLVardef@1b00966org.highwire.dtl.DTLVardef@391ef9org.highwire.dtl.DTLVardef@206d8c_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LISingle-Cell RNA-sequencing reveals loss of metabolic liver zonation in O-GlcNAcylation deficient livers. C_LIO_LILoss of O-GlcNAcylation promoted DEN-Induced HCC. C_LIO_LIIncrease of hepatic O-GlcNAcylation prevented HCC progression. C_LI ]]> Robarts, D. R. Kotulkar, M. Paine-Cabrera, D. Venneman, K. K. Hanover, J. A. Zachara, N. E. Slawson, C. Apte, U. 2023-02-17 doi:10.1101/2023.02.16.528884 Cold Spring Harbor Laboratory Press 2023-02-17 <![CDATA[ Land-cover change in Cuba may favor biodiversity: An example using Omphalea (Angiosperma: Euphorbiaceae) and Urania boisduvalii (Lepidoptera: Uraniidae) ]]> https://biorxiv.org/content/10.1101/2023.02.17.529023v1?rss=1 Nunez-Penicet, C. Maita-Chamba, J. Soberon, J. 2023-02-19 doi:10.1101/2023.02.17.529023 Cold Spring Harbor Laboratory Press 2023-02-19 <![CDATA[ Validation of the association between MRI and gene signatures in facioscapulohumeral dystrophy muscle: implications for clinical trial design ]]> https://biorxiv.org/content/10.1101/2023.02.20.529303v1?rss=1 Wong, C.-J. Friedman, S. D. Snider, L. Bennett, S. R. Jones, T. I. Jones, P. L. Shaw, D. W. Blemker, S. S. Riem, L. DuCharme, O. Lemmers, R. J. van der Maarel, S. M. Wang, L. H. Tawil, R. Statland, J. M. Tapscott, S. J. 2023-02-20 doi:10.1101/2023.02.20.529303 Cold Spring Harbor Laboratory Press 2023-02-20 <![CDATA[ Repeated passive visual experience modulates spontaneous and novelty-evoked neural activity. ]]> https://biorxiv.org/content/10.1101/2023.02.21.529278v1?rss=1 Niraula, S. Hauser, W. Rouse, A. G. Subramanian, J. 2023-02-22 doi:10.1101/2023.02.21.529278 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Rescue of Auditory Function by a Single Administration of AAV-TMPRSS3 Gene Therapy in Aged Mice of Human Recessive Deafness DFNB8 ]]> https://biorxiv.org/content/10.1101/2023.02.25.530035v1?rss=1 Du, W. Ergin, V. Loeb, C. Huang, M. Silver, S. Armstrong, A. M. Huang, Z. Gurumurthy, C. Staecker, H. Liu, X. Chen, Z.-Y. 2023-02-26 doi:10.1101/2023.02.25.530035 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ MAHOMES II: A webserver for predicting if a metal binding site is enzymatic ]]> https://biorxiv.org/content/10.1101/2023.03.08.531790v1?rss=1 Feehan, R. Copeland, M. Franklin, M. W. Slusky, J. S. G. 2023-03-12 doi:10.1101/2023.03.08.531790 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Correlating physicochemical and biological properties to define critical quality attributes of a recombinant AAV vaccine candidate ]]> https://biorxiv.org/content/10.1101/2023.03.10.532114v1?rss=1 Kumar, P. Wang, M. Kumru, O. S. Hickey, J. Sanmiguel, J. Zabaleta, N. Vandenberghe, L. H. Joshi, S. B. Volkin, D. B. 2023-03-13 doi:10.1101/2023.03.10.532114 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds ]]> https://biorxiv.org/content/10.1101/2023.03.15.530646v1?rss=1 McLaughlin, J. F. Aguilar, C. Bernstein, J. M. Navia-Gine, W. G. Cueto-Aparicio, L. E. Alarcon, A. C. Alarcon, B. D. Collier, R. Takyar, A. Vong, S. J. Lopez-Chong, O. G. Driver, R. Loaiza, J. R. De Leon, L. F. Saltonstall, K. Lipshutz, S. E. Arcila, D. Brock, K. M. Miller, M. J. 2023-03-16 doi:10.1101/2023.03.15.530646 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal ]]> https://biorxiv.org/content/10.1101/2023.03.20.533418v1?rss=1 Kandola, T. Venkatesan, S. Zhang, J. Lerbakken, B. T. Von Schulze, A. Blanck, J. F. Wu, J. Unruh, J. R. Berry, P. Lange, J. J. Box, A. C. Cook, M. Sagui, C. Halfmann, R. 2023-03-21 doi:10.1101/2023.03.20.533418 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ MetaLLM: Residue-wise Metal ion Prediction UsingDeep Transformer Model ]]> https://biorxiv.org/content/10.1101/2023.03.20.533488v1?rss=1 Shishir, F. S. Sarker, B. Rahman, F. Shomaji, S. 2023-03-23 doi:10.1101/2023.03.20.533488 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Artificial Intelligence Boosted Molecular Dynamics ]]> https://biorxiv.org/content/10.1101/2023.03.25.534210v1?rss=1 Do, H. N. Miao, Y. 2023-03-27 doi:10.1101/2023.03.25.534210 Cold Spring Harbor Laboratory Press 2023-03-27 <![CDATA[ Widespread PRC barrel proteins play critical roles in archaeal cell division ]]> https://biorxiv.org/content/10.1101/2023.03.28.534520v1?rss=1 Zhao, S. Makarova, K. Zheng, W. Liu, Y. Zhan, L. Wan, Q. Gong, H. Krupovic, M. Lutkenhaus, J. Chen, X. Koonin, E. V. Du, S. 2023-03-28 doi:10.1101/2023.03.28.534520 Cold Spring Harbor Laboratory Press 2023-03-28 <![CDATA[ CORE CONSERVED TRANSCRIPTIONAL REGULATORY NETWORKS DEFINE THE INVASIVE TROPHOBLAST CELL LINEAGE ]]> https://biorxiv.org/content/10.1101/2023.03.30.534962v1?rss=1 Vu, H. T. H. Scott, R. L. Iqbal, K. Soares, M. J. Tuteja, G. 2023-04-03 doi:10.1101/2023.03.30.534962 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Predicting climate-driven distribution shifts in Hyalomma marginatum (Ixodidae) ]]> https://biorxiv.org/content/10.1101/2023.04.01.535198v1?rss=1 Hekimoglu, O. Elverici, C. Kuyucu, A. C. 2023-04-03 doi:10.1101/2023.04.01.535198 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Formulation development and comparability studies with an aluminum-salt adjuvanted SARS-CoV-2 Spike ferritin nanoparticle vaccine antigen produced from two different cell lines ]]> https://biorxiv.org/content/10.1101/2023.04.03.535447v1?rss=1 Kumru, O. Sanyal, M. Friedland, N. Hickey, J. Joshi, R. Weidenbacher, P. Do, J. Cheng, Y.-C. Kim, P. S. Joshi, S. B. Volkin, D. B. 2023-04-04 doi:10.1101/2023.04.03.535447 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ Chemical-guided SHAPE sequencing (cgSHAPE-seq) informs the binding site of RNA-degrading chimeras targeting SARS-CoV-2 5' untranslated region ]]> https://biorxiv.org/content/10.1101/2023.04.03.535453v1?rss=1 Tang, Z. Hegde, S. Hao, S. Selvaraju, M. Qiu, J. Wang, J. 2023-04-04 doi:10.1101/2023.04.03.535453 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ SARS-CoV-2 Mac1 is required for IFN antagonism and efficient virus replication in mice ]]> https://biorxiv.org/content/10.1101/2023.04.06.535927v1?rss=1 Alhammad, Y. M. Parthasarathy, S. Ghimire, R. O'Connor, J. J. Kerr, C. M. Pfannenstiel, J. J. Chanda, D. Miller, C. A. Unckless, R. Zuniga, S. Enjuanes, L. More, S. Channappanavar, R. Fehr, A. 2023-04-06 doi:10.1101/2023.04.06.535927 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Legacy effects of precipitation and land use impact maize growth and microbiome assembly under drought stress ]]> https://biorxiv.org/content/10.1101/2023.04.11.536405v1?rss=1 Swift, J. F. Kolp, M. R. Carmichael, A. Ford, N. E. Hansen, P. M. Sikes, B. A. Kleiner, M. Wagner, M. R. 2023-04-12 doi:10.1101/2023.04.11.536405 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Aspergillus SUMOylation mutants have normal dynein function but exhibit chromatin bridges ]]> https://biorxiv.org/content/10.1101/2023.04.16.537086v1?rss=1 Zhang, J. Qiu, R. Bieger, B. D. Oakley, E. Oakley, B. R. Egan, M. J. Xiang, X. 2023-04-18 doi:10.1101/2023.04.16.537086 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Purifying Selection and Persistent Polymorphism among Nuclei in the Multinucleate Arbuscular Mycorrhizal (AM) Fungi ]]> https://biorxiv.org/content/10.1101/2023.04.18.537338v1?rss=1 Manyara, D. Sanchez-Garcia, M. Thoren, M. H. Montoliu-Nerin, M. Cheng, G. Bever, J. D. Johannesson, H. Rosling, A. 2023-04-20 doi:10.1101/2023.04.18.537338 Cold Spring Harbor Laboratory Press 2023-04-20 <![CDATA[ Amyloid pathology impairs homeostatic inhibitory synaptic plasticity ]]> https://biorxiv.org/content/10.1101/2023.05.04.539450v1?rss=1 Niraula, S. Yan, S. S. Subramanian, J. 2023-05-05 doi:10.1101/2023.05.04.539450 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ Soluble antigen arrays improve the efficacy and safety of peptide-based tolerogenic immunotherapy ]]> https://biorxiv.org/content/10.1101/2023.05.05.539161v1?rss=1 Firdessa Fite, R. Johnson, S. N. Leon, M. A. Sestak, J. O. Berkland, C. Creusot, R. J. 2023-05-07 doi:10.1101/2023.05.05.539161 Cold Spring Harbor Laboratory Press 2023-05-07 <![CDATA[ Screening effects of HCN channel blockers on sleep/wake behavior in zebrafish ]]> https://biorxiv.org/content/10.1101/2023.05.05.539631v1?rss=1 Doldur Balli, F. Keenan, B. Zimmerman, A. J. Veatch, O. J. Smieszek, S. P. Pack, A. I. 2023-05-08 doi:10.1101/2023.05.05.539631 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Evaluation of ready-to-use freezer stocks of a synthetic microbial community for maize root colonization ]]> https://biorxiv.org/content/10.1101/2023.05.10.540175v1?rss=1 Parnell, J. J. Vintila, S. Tang, C. Wagner, M. R. Kleiner, M. 2023-05-10 doi:10.1101/2023.05.10.540175 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ The essential domain of FtsN triggers cell division by promoting interaction between FtsL and FtsI ]]> https://biorxiv.org/content/10.1101/2023.05.12.540521v1?rss=1 Park, K.-T. Johnson, D. K. Pichoff, S. Du, S. Lutkenhaus, J. 2023-05-12 doi:10.1101/2023.05.12.540521 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ SRC-1 controls growth cone polarity and protrusion with the UNC-6/Netrin receptor UNC-5 in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2023.05.20.541322v1?rss=1 Mahadik, S. S. Burt, E. K. Lundquist, E. A. 2023-05-20 doi:10.1101/2023.05.20.541322 Cold Spring Harbor Laboratory Press 2023-05-20 <![CDATA[ ATP-Gated Potassium Channels Contribute to Ketogenic Diet-Mediated Analgesia in Mice. ]]> https://biorxiv.org/content/10.1101/2023.05.22.541799v1?rss=1 Enders, J. D. Thomas, S. Lynch, P. Jack, J. Ryals, J. Puchalska, P. Crawford, P. A. Wright, D. E. 2023-05-24 doi:10.1101/2023.05.22.541799 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Exomap1 mouse: a transgenic model for in vivo studies of exosome biology ]]> https://biorxiv.org/content/10.1101/2023.05.29.542707v1?rss=1 5 nm in size. Taken together, these results establish the exomap1 mouse as a useful tool for in vivo studies of exosome biology, and for mapping cell type-specific contributions to biofluid exosome populations. In addition, our data confirm that CD81 is a highly-specific marker for exosomes and is not enriched in the larger microvesicle class of EVs. ]]> Fordjour, F. K. Abuelreich, S. Hong, X. Chatterjee, E. Lallai, V. Ng, M. Saftics, A. Deng, F. Carnel-Amar, N. Wakimoto, H. Shimizu, K. Anh Phu, T. Vu, N. K. Geiger, P. C. Raffai, R. L. Fowler, C. D. Shimizu, K. Das, S. Christenson, L. K. Jovanovic-Talisman, T. Gould, S. 2023-05-29 doi:10.1101/2023.05.29.542707 Cold Spring Harbor Laboratory Press 2023-05-29 <![CDATA[ An abundant future for quagga mussels in deep European lakes ]]> https://biorxiv.org/content/10.1101/2023.05.31.543086v1?rss=1 Kraemer, B. M. Boudet, S. Burlakova, L. E. Haltiner, L. Ibelings, B. W. Karatayev, A. Y. Karatayev, V. A. Rossbacher, S. Stoeckli, R. Straile, D. Piet, S. 2023-06-04 doi:10.1101/2023.05.31.543086 Cold Spring Harbor Laboratory Press 2023-06-04 <![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[ HNF4a regulates acyl chain remodeling and ether lipid accumulation in hepatic steatosis ]]> https://biorxiv.org/content/10.1101/2023.06.08.544272v1?rss=1 Von Bank, H. Geoghegan, G. Jain, R. Kotulkar, M. Hurtado-Thiele, M. Gonzalez, P. Kirsh, C. Chevalier, A. Schueler, K. L. Attie, A. D. Keller, M. P. Apte, U. Simcox, J. 2023-06-09 doi:10.1101/2023.06.08.544272 Cold Spring Harbor Laboratory Press 2023-06-09 <![CDATA[ 3D spheroid culturing of Astyanax mexicanus liver-derived cell lines recapitulates distinct transcriptomic and metabolic states of in vivo tissue environment. ]]> https://biorxiv.org/content/10.1101/2023.06.09.544423v1?rss=1 Biswas, T. Rajendran, N. Hassan, H. Zhao, C. Rohner, N. 2023-06-10 doi:10.1101/2023.06.09.544423 Cold Spring Harbor Laboratory Press 2023-06-10 <![CDATA[ CD22L Conjugation to Insulin Attenuates Insulin-Specific B cell Activation ]]> https://biorxiv.org/content/10.1101/2023.06.13.544802v1?rss=1 Apley, K. D. Griffith, A. S. Downes, G. Ross, P. A. Farrell, M. P. Kendall, P. L. Berkland, C. J. 2023-06-14 doi:10.1101/2023.06.13.544802 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ Evolutionary engineering a larger porin using a loop-to-hairpin mechanism ]]> https://biorxiv.org/content/10.1101/2023.06.14.544993v1?rss=1 Dhar, R. Bowman, A. M. Hatungimana, B. Slusky, J. S. G. 2023-06-14 doi:10.1101/2023.06.14.544993 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ FLOWERING LOCUS C drives delayed flowering in Arabidopsis grown and selected at elevated CO2 ]]> https://biorxiv.org/content/10.1101/2023.06.15.545149v1?rss=1 Henderson-Carter, A. L. Kinmonth-Schultz, H. Hileman, L. Ward, J. K. 2023-06-15 doi:10.1101/2023.06.15.545149 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ Collective synchrony of mating signals modulated by ecological cues and social signals in bioluminescent sea fireflies ]]> https://biorxiv.org/content/10.1101/2023.06.16.545275v1?rss=1 Hensley, N. M. Rivers, T. J. Gerrish, G. A. Oakley, T. H. 2023-06-19 doi:10.1101/2023.06.16.545275 Cold Spring Harbor Laboratory Press 2023-06-19 <![CDATA[ Endometrial cyclin A2 deficiency is associated with human female infertility and is recapitulated in a conditional knockout mouse model ]]> https://biorxiv.org/content/10.1101/2023.06.16.545284v1?rss=1 View larger version (18K): org.highwire.dtl.DTLVardef@150b471org.highwire.dtl.DTLVardef@176a804org.highwire.dtl.DTLVardef@110a47dorg.highwire.dtl.DTLVardef@19f186c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Aljubran, F. Schumacher, K. Graham, A. Gunewardena, S. Marsh, C. Lydic, M. Holoch, K. Nothnick, W. B. 2023-06-19 doi:10.1101/2023.06.16.545284 Cold Spring Harbor Laboratory Press 2023-06-19 <![CDATA[ PARP12 is required to repress the replication of a Mac1 mutant coronavirus in a cell and tissue specific manner ]]> https://biorxiv.org/content/10.1101/2023.06.16.545351v1?rss=1 Kerr, C. M. Parthasarathy, S. Schwarting, N. O'Connor, J. J. Giri, E. More, S. Orozco, R. C. Fehr, A. R. 2023-06-17 doi:10.1101/2023.06.16.545351 Cold Spring Harbor Laboratory Press 2023-06-17 <![CDATA[ GATA-regulated transcriptional program dictate cell fate equilibrium to establish the maternal-fetal exchange interface and fetal development ]]> https://biorxiv.org/content/10.1101/2023.06.19.545618v1?rss=1 Ghosh, A. Kumar, R. Kumar, R. P. Ray, S. Saha, A. Roy, N. Dasgupta, P. Marsh, C. Paul, S. 2023-06-22 doi:10.1101/2023.06.19.545618 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Oligosaccharide production and signaling correlate with delayed flowering in an Arabidopsis genotype grown and selected in high ]]> https://biorxiv.org/content/10.1101/2023.06.19.545630v1?rss=1 Kinmonth-Schultz, H. Walker, S. M. Bingol, K. Hoyt, D. W. Kim, Y.-M. Markillie, L. M. Mitchell, H. D. Nicora, C. D. Taylor, R. Ward, J. K. 2023-06-20 doi:10.1101/2023.06.19.545630 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ The VEGF G-quadruplex forming promoter is repaired via long-patch BER ]]> https://biorxiv.org/content/10.1101/2023.06.25.546439v1?rss=1 Hussen, A. Kravitz, H. L. Freudenthal, B. D. Whitaker, A. M. 2023-06-25 doi:10.1101/2023.06.25.546439 Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ Proteasome condensate formation is driven by multivalent interactions with shuttle factors and K48-linked ubiquitin chains ]]> https://biorxiv.org/content/10.1101/2023.06.25.546446v1?rss=1 Waite, K. A. Vontz, G. Lee, S. Y. Roelofs, J. 2023-06-26 doi:10.1101/2023.06.25.546446 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Electron microscopic and crystallographic studies of bacteriophage Sf6 procapsid-like particles assembled from heterologously expressed capsid protein gp5 ]]> https://biorxiv.org/content/10.1101/2023.06.28.546888v1?rss=1 Tang, L. Zhao, H. 2023-06-28 doi:10.1101/2023.06.28.546888 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ Paleo-Eskimo genetic legacy across North America ]]> https://biorxiv.org/content/10.1101/203018v1?rss=1 Flegontov, P. Altinisik, N. E. Changmai, P. Rohland, N. Mallick, S. Bolnick, D. A. Candilio, F. Flegontova, O. Jeong, C. Harper, T. K. Keating, D. Kennett, D. J. Kim, A. M. Lamnidis, T. C. Olalde, I. Raff, J. Sattler, R. A. Skoglund, P. Vajda, E. J. Vasilyev, S. Veselovskaya, E. Hayes, M. G. O'Rourke, D. H. Pinhasi, R. Krause, J. Reich, D. Schiffels, S. 2017-10-13 doi:10.1101/203018 Cold Spring Harbor Laboratory Press 2017-10-13 <![CDATA[ Impaired Cu-Zn superoxide dismutase (SOD1) and calcineurin (Cn) interaction in ALS: A presumed consequence for TDP-43 and zinc aggregation in Tg SOD1G93A rodent spinal cord tissue. ]]> https://biorxiv.org/content/10.1101/220210v1?rss=1 Kim, J. M. Billington, E. Reyes, A. Notarianni, T. Sage, J. M. Agbas, E. Taylor, M. Monast, I. Stanford, J. A. Agbas, A. 2017-11-15 doi:10.1101/220210 Cold Spring Harbor Laboratory Press 2017-11-15 <![CDATA[ Actin Redundancy in Chlamydomonas is Required for Flagellar Protein Synthesis and Gating ]]> https://biorxiv.org/content/10.1101/227553v1?rss=1 Jack, B. Mueller, D. M. Fee, A. C. Tetlow, A. Avasthi, P. 2017-11-30 doi:10.1101/227553 Cold Spring Harbor Laboratory Press 2017-11-30 <![CDATA[ Terrestrial effects of moderately nearby supernovae ]]> https://biorxiv.org/content/10.1101/230847v1?rss=1 Melott, A. L. Thomas, B. C. 2017-12-08 doi:10.1101/230847 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ CLAN: the CrossLinked reads ANalysis tool ]]> https://biorxiv.org/content/10.1101/233841v1?rss=1 Zhong, C. Zhang, S. 2017-12-14 doi:10.1101/233841 Cold Spring Harbor Laboratory Press 2017-12-14 <![CDATA[ Muon Radiation Dose and Marine Megafaunal Extinction at the end-Pliocene Supernova ]]> https://biorxiv.org/content/10.1101/240093v1?rss=1 Melott, A. Marinho, F. Paulucci, L. 2017-12-28 doi:10.1101/240093 Cold Spring Harbor Laboratory Press 2017-12-28 <![CDATA[ Lineage space and the propensity of bacterial cells to undergo growth transitions ]]> https://biorxiv.org/content/10.1101/256123v1?rss=1 Bandyopadhyay, A. Ray, C. 2018-01-30 doi:10.1101/256123 Cold Spring Harbor Laboratory Press 2018-01-30 <![CDATA[ The Atypical Rho GTPase CHW-1 Works With SAX-3/Robo to Mediate Axon Guidance in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/265066v1?rss=1 Alan, J. Robinson, S. Magsig, K. Demarco, R. Lundquist, E. A. 2018-02-13 doi:10.1101/265066 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ A comment on "Species are not most abundant in the center of their geographic range or climatic niche" ]]> https://biorxiv.org/content/10.1101/266510v1?rss=1 Soberon, J. Peterson, A. T. Osorio-Olvera, L. 2018-02-16 doi:10.1101/266510 Cold Spring Harbor Laboratory Press 2018-02-16 <![CDATA[ High-quality genome assemblies of 15 Drosophila species generated using Nanopore sequencing ]]> https://biorxiv.org/content/10.1101/267393v1?rss=1 Miller, D. E. Staber, C. Zeitlinger, J. Hawley, R. S. 2018-02-18 doi:10.1101/267393 Cold Spring Harbor Laboratory Press 2018-02-18 <![CDATA[ Rapid low-cost assembly of the Drosophila melanogaster reference genome using low-coverage, long-read sequencing ]]> https://biorxiv.org/content/10.1101/267401v1?rss=1 Solares, E. A. Chakraborty, M. Miller, D. E. Kalsow, S. Hall, K. E. Perera, A. G. Emerson, J. J. Hawley, R. S. 2018-02-18 doi:10.1101/267401 Cold Spring Harbor Laboratory Press 2018-02-18 <![CDATA[ Efflux Pumps Represent Possible Evolutionary Convergence onto the Beta Barrel Fold ]]> https://biorxiv.org/content/10.1101/268029v1?rss=1 Franklin, M. W. Nepomnyachiy, S. Feehan, R. Ben-Tal, N. Kolodny, R. Slusky, J. S. G. 2018-02-19 doi:10.1101/268029 Cold Spring Harbor Laboratory Press 2018-02-19 <![CDATA[ ADAR1 A-to-I RNA alters codon usage ]]> https://biorxiv.org/content/10.1101/268813v1?rss=1 Brachova, P. Alvarez, N. S. Hong, X. Vincent, K. A. Latham, K. E. Christenson, L. K. 2018-02-21 doi:10.1101/268813 Cold Spring Harbor Laboratory Press 2018-02-21 <![CDATA[ Species delimitation and biogeography of the gnatcatchers and gnatwrens (Aves: Polioptilidae) ]]> https://biorxiv.org/content/10.1101/271494v1?rss=1 Smith, B. T. Bryson, R. W. Mauck, W. M. Chaves, J. Robbins, M. B. Aleixo, A. Klicka, J. 2018-02-26 doi:10.1101/271494 Cold Spring Harbor Laboratory Press 2018-02-26 <![CDATA[ Intermediate filaments EXC-2 and IFA-4 Maintain Luminal Structure of the Tubular Excretory Canals in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/277111v1?rss=1 Al-Hashimi, H. I. Hall, D. H. Ackley, B. D. Lundquist, E. A. Buechner, M. 2018-03-06 doi:10.1101/277111 Cold Spring Harbor Laboratory Press 2018-03-06 <![CDATA[ Synaptonemal complex architecture facilitates the chromosome-specific regulation of recombination in Drosophila ]]> https://biorxiv.org/content/10.1101/277764v1?rss=1 Cahoon, C. Heenan, G. M. Yu, Z. Unruh, J. R. McKinney, S. Hawley, R. S. 2018-03-06 doi:10.1101/277764 Cold Spring Harbor Laboratory Press 2018-03-06 <![CDATA[ Extensive horizontal exchange of transposable elements in the Drosophila pseudoobscura group ]]> https://biorxiv.org/content/10.1101/284117v1?rss=1 Hill, T. Betancourt, A. 2018-03-18 doi:10.1101/284117 Cold Spring Harbor Laboratory Press 2018-03-18 <![CDATA[ Structural insights into the conformational plasticity of the full-length trimeric HIV-1 envelope glycoprotein precursor ]]> https://biorxiv.org/content/10.1101/288472v1?rss=1 Zhang, S. Wang, W. L. Chen, S. Lu, M. Go, E. P. Steinbock, R. T. Ding, H. Desaire, H. Kappes, J. C. Sodroski, J. G. Mao, Y. 2018-03-25 doi:10.1101/288472 Cold Spring Harbor Laboratory Press 2018-03-25 <![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[ Balancing selection drives maintenance of geneticvariation in Drosophila antimicrobial peptides ]]> https://biorxiv.org/content/10.1101/298893v1?rss=1 Chapman, J. R. Hill, T. Unckless, R. L. 2018-04-11 doi:10.1101/298893 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ Tight Turns of Outer Membrane Proteins: An Analysis of Sequence, Structure, and Hydrogen Bonding ]]> https://biorxiv.org/content/10.1101/304287v1?rss=1 Franklin, M. Slusky, J. 2018-04-19 doi:10.1101/304287 Cold Spring Harbor Laboratory Press 2018-04-19 <![CDATA[ Hepatocyte Nuclear Factor 4 alpha (HNF4α) Activation is Essential for Termination of Liver Regeneration ]]> https://biorxiv.org/content/10.1101/304808v1?rss=1 Huck, I. Gunewardena, S. Espanol-Suner, R. Willenbring, H. Apte, U. 2018-04-20 doi:10.1101/304808 Cold Spring Harbor Laboratory Press 2018-04-20 <![CDATA[ Elevated O-GlcNAcylation Enhances Pro-Inflammatory Th17 Function by Altering the Lipid Microenvironment ]]> https://biorxiv.org/content/10.1101/305722v1?rss=1 Machacek, M. Zhang, Z. Tan, E. P. Li, J. Li, T. Villar, M. T. Artigues, A. Lydic, T. Slawson, C. Fields, P. 2018-04-20 doi:10.1101/305722 Cold Spring Harbor Laboratory Press 2018-04-20 <![CDATA[ Evolution of Environmentally-Enforced, Repeat Protein Topology in the Outer Membrane ]]> https://biorxiv.org/content/10.1101/309393v1?rss=1 Franklin, M. W. Nepomnyaciy, S. Feehan, R. Ben-Tal, N. Kolodny, R. Slusky, J. 2018-04-27 doi:10.1101/309393 Cold Spring Harbor Laboratory Press 2018-04-27 <![CDATA[ A synthesis of mapping experiments reveals extensive genomic structural diversity in the Mimulus guttatus species complex ]]> https://biorxiv.org/content/10.1101/330159v1?rss=1 Flagel, L. Blackman, B. K. Fishman, L. Monnahan, P. J. Sweigart, A. Kelly, J. K. 2018-05-24 doi:10.1101/330159 Cold Spring Harbor Laboratory Press 2018-05-24 <![CDATA[ A novel method for systematic genetic analysis and visualization of phenotypic heterogeneity applied to orofacial clefts ]]> https://biorxiv.org/content/10.1101/332270v1?rss=1 Carlson, J. Anand, D. Buxo, C. Christensen, K. Deleyiannis, F. Hecht, J. Moreno-Uribe, L. Orioli, I. Padilla, C. Shaffer, J. Vieira, A. Wehby, G. Weinberg, S. Murray, J. Beaty, T. Saadi, I. Lachke, S. Marazita, M. Feingold, E. Leslie, E. 2018-05-28 doi:10.1101/332270 Cold Spring Harbor Laboratory Press 2018-05-28 <![CDATA[ The role of gene flow in rapid and repeated evolution of cave related traits in Mexican tetra, Astyanax mexicanus ]]> https://biorxiv.org/content/10.1101/335182v1?rss=1 Herman, A. Brandvain, Y. Weagley, J. Jeffery, W. R. Keene, A. C. Kono, T. J. Y. Bilandzija, H. Borowsky, R. Espinasa, L. O'Quin, K. Ornelas-Garcia, C. P. Yoshizawa, M. Carlson, B. Maldonado, E. Gross, J. B. Cartwright, R. A. Rohner, N. Warren, W. C. McGaugh, S. E. 2018-05-31 doi:10.1101/335182 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ An examination of the evolve-and-resequence method using Drosophila simulans ]]> https://biorxiv.org/content/10.1101/337188v1?rss=1 Kelly, J. K. Hughes, K. 2018-06-03 doi:10.1101/337188 Cold Spring Harbor Laboratory Press 2018-06-03 <![CDATA[ O-GlcNAc Homeostasis Controls Cell Fate Decisions During Hematopoiesis ]]> https://biorxiv.org/content/10.1101/337881v1?rss=1 Zhang, Z. Parker, M. P. Graw, S. Novikova, L. Fedosyuk, H. Fontes, J. Koestler, D. Peterson, K. Slawson, C. 2018-06-04 doi:10.1101/337881 Cold Spring Harbor Laboratory Press 2018-06-04 <![CDATA[ Contrasting effects of aging on the expression of transposons, the piRNA machinery and mitochondrial transcripts in the Drosophila ovary. ]]> https://biorxiv.org/content/10.1101/342105v1?rss=1 Erwin, A. A. Blumenstiel, J. P. 2018-06-08 doi:10.1101/342105 Cold Spring Harbor Laboratory Press 2018-06-08 <![CDATA[ The Recombination Landscape of Drosophila virilis is Robust to Transposon Activation in Hybrid Dysgenesis ]]> https://biorxiv.org/content/10.1101/342824v1?rss=1 Hemmer, L. W. Blumenstiel, J. P. 2018-06-08 doi:10.1101/342824 Cold Spring Harbor Laboratory Press 2018-06-08 <![CDATA[ O-GlcNAc modification of oncogenic transcription factor Sox2 promotes protein stability and regulates self-renewal in pancreatic cancer ]]> https://biorxiv.org/content/10.1101/345223v1?rss=1 Sharma, N. Gupta, V. K. Dauer, P. Kesh, K. Hadad, R. Giri, B. Chandra, A. Dudeja, V. Slawson, C. Banerjee, S. Vickers, S. M. Saluja, A. Banerjee, S. 2018-06-12 doi:10.1101/345223 Cold Spring Harbor Laboratory Press 2018-06-12 <![CDATA[ Fine Specificity Epitope Analysis by HX-MS Identifies Contact Points on Ricin Toxin Recognized by Protective Monoclonal Antibodies ]]> https://biorxiv.org/content/10.1101/345561v1?rss=1 Van Slyke, G. Angalakurthi, S. K. Toth, R. T. Vance, D. J. Rong, Y. Ehrbar, D. Shi, Y. Middaught, C. R. Volkin, D. Weis, D. Mantis, N. 2018-06-14 doi:10.1101/345561 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ Novel exc Genes Involved in Formation of the Tubular Excretory Canals of C. elegans ]]> https://biorxiv.org/content/10.1101/359653v1?rss=1 Al-Hashimi, H. Chiarelli, T. Lundquist, E. A. Buechner, M. 2018-06-30 doi:10.1101/359653 Cold Spring Harbor Laboratory Press 2018-06-30 <![CDATA[ Dissection of complex, fitness-related traits in multiple Drosophila mapping populations offers insight into the genetic control of stress resistance ]]> https://biorxiv.org/content/10.1101/383802v1?rss=1 1600 genotypes of the multiparental Drosophila Synthetic Population Resource (DSPR) we map numerous starvation stress QTL that collectively explain a substantial fraction of trait heritability. QTL effects further allowed us to estimate DSPR founder phenotypes, predictions that were correlated with the actual founder phenotypes. Starvation resistance has been linked to triglyceride level, and while we observe a modest phenotypic correlation between the traits in the DSPR, overlap among the QTL identified for each trait is low. Since we show that DSPR strains with extreme starvation phenotypes also differ in desiccation resistance and activity level, our data imply that multiple physiological mechanisms contribute to starvation variability. We also exploit the Drosophila Genetic Reference Panel (DGRP), identifying a number of sequence variants associated with starvation resistance. Consistent with prior work these sites rarely fall within QTL intervals mapped in the DSPR. Two other groups previously measured starvation resistance in the DGRP, offering a unique opportunity to directly compare mapping results across labs. We found strong phenotypic correlations among studies, but extremely low overlap in the sets of genomewide significant sites. Despite this, our analyses revealed that the most highly-associated variants from each study typically showed the same additive effect sign in independent studies, in contrast to otherwise equivalent sets of random variants. This consistency provides evidence for reproducible trait-associated sites in a widely-used mapping panel, and highlights the polygenic nature of starvation resistance. ]]> Everman, E. McNeil, C. Hackett, J. Bain, C. Macdonald, S. J. 2018-08-02 doi:10.1101/383802 Cold Spring Harbor Laboratory Press 2018-08-02 <![CDATA[ Antiviral genes are not rapidly evolving in Drosophila innubila ]]> https://biorxiv.org/content/10.1101/383877v1?rss=1 Hill, T. Koseva, B. Unckless, R. L. 2018-08-02 doi:10.1101/383877 Cold Spring Harbor Laboratory Press 2018-08-02 <![CDATA[ Evolutionary proteomics reveals distinct patterns of complexity and divergence between lepidopteran sperm morphs ]]> https://biorxiv.org/content/10.1101/384164v1?rss=1 Whittington, E. Karr, T. Mongue, A. J. Dorus, S. Walters, J. 2018-08-03 doi:10.1101/384164 Cold Spring Harbor Laboratory Press 2018-08-03 <![CDATA[ Molecular analysis of Drosophila melanogaster B chromosomes reveals their origin, composition, and structure ]]> https://biorxiv.org/content/10.1101/386995v1?rss=1 Hanlon, S. L. Miller, D. E. Eche, S. Hawley, R. S. 2018-08-07 doi:10.1101/386995 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ Extreme copy number variation at a tRNA ligase affecting phenology and fitness in yellow monkeyflowers ]]> https://biorxiv.org/content/10.1101/392183v1?rss=1 Nelson, T. C. Monnahan, P. McIntosh, M. Finseth, F. Anderson, K. Macarthur-Waltz, E. Kelly, J. K. Fishman, L. 2018-08-17 doi:10.1101/392183 Cold Spring Harbor Laboratory Press 2018-08-17 <![CDATA[ The comparative biogeography of geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago ]]> https://biorxiv.org/content/10.1101/395434v1?rss=1 Oaks, J. R. Siler, C. D. Brown, R. M. 2018-08-20 doi:10.1101/395434 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ Differences in DNA methylation of white blood cell types at birth and in adulthood reflect postnatal immune maturation and influence accuracy of cell type prediction ]]> https://biorxiv.org/content/10.1101/399279v1?rss=1 Jones, M. Dinh, L. Razzaghian, H. R. de Goede, O. MacIsaac, J. L. Morin, A. M. Gervin, K. Ng, R. Duijts, L. van Zelm, M. C. Moll, H. A. Lyle, R. Robinson, W. P. Koestler, D. C. Felix, J. F. Lavoie, P. M. Mostafavi, S. Kobor, M. S. 2018-08-23 doi:10.1101/399279 Cold Spring Harbor Laboratory Press 2018-08-23 <![CDATA[ Hepatocyte-Specific Hepatocyte Nuclear Factor 4 alpha (HNF4α) Deletion Decreases Resting Energy Expenditure By Disrupting Lipid and Carbohydrate Homeostasis ]]> https://biorxiv.org/content/10.1101/401802v1?rss=1 Huck, I. Morris, E. M. Thyfault, J. P. Apte, U. 2018-08-27 doi:10.1101/401802 Cold Spring Harbor Laboratory Press 2018-08-27 <![CDATA[ Adaptive evolution of sperm proteins depends on sperm competition in a pair of Lepidoptera ]]> https://biorxiv.org/content/10.1101/404236v1?rss=1 Mongue, A. J. Hansen, M. E. Gu, L. Sorenson, C. E. Walters, J. R. 2018-08-31 doi:10.1101/404236 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ Structural variants exhibit allelic heterogeneity and shape variation in complex traits ]]> https://biorxiv.org/content/10.1101/419275v1?rss=1 Chakraborty, M. Emerson, J. J. Macdonald, S. J. Long, A. D. 2018-09-18 doi:10.1101/419275 Cold Spring Harbor Laboratory Press 2018-09-18 <![CDATA[ Molecular mechanism of off-target effects in CRISPR-Cas9 ]]> https://biorxiv.org/content/10.1101/421537v1?rss=1 Ricci, C. G. Chen, J. S. Miao, Y. Jinek, M. Doudna, J. A. McCammon, J. A. Palermo, G. 2018-09-19 doi:10.1101/421537 Cold Spring Harbor Laboratory Press 2018-09-19 <![CDATA[ The C. elegans CHP1 homolog, pbo-1, functions in innate immunity by regulating the pH of the intestinal lumen ]]> https://biorxiv.org/content/10.1101/424382v1?rss=1 Benomar, S. Bender, A. M. Peterson, B. R. Ackley, B. D. Chandler, J. R. 2018-09-23 doi:10.1101/424382 Cold Spring Harbor Laboratory Press 2018-09-23 <![CDATA[ Identification of the bacterial biosynthetic gene clusters of the oral microbiome illuminates the unexplored social language of bacteria during health and disease ]]> https://biorxiv.org/content/10.1101/431510v1?rss=1 Aleti, G. Baker, J. L. Tang, X. Alvarez, R. Boltelho, M. Tran, N. C. Melnik, A. V. Zhong, C. Ernst, M. Dorrestein, P. C. Edlund, A. 2018-10-02 doi:10.1101/431510 Cold Spring Harbor Laboratory Press 2018-10-02 <![CDATA[ Host-pathogen coevolution increases genetic variation in susceptibility to infection ]]> https://biorxiv.org/content/10.1101/474924v1?rss=1 Duxbury, E. M. Day, J. P. Maria Vespasiani, D. Thüringer, Y. Tolosana, I. Smith, S. C. Tagliaferri, L. Kamacioglu, A. Lindsley, I. Love, L. Unckless, R. Jiggins, F. M. Longdon, B. 2018-11-26 doi:10.1101/474924 Cold Spring Harbor Laboratory Press 2018-11-26 <![CDATA[ Reconciling in vitro and in vivo activities of engineered, LacI-based repressor proteins: Contributions of DNA looping and operator sequence variation ]]> https://biorxiv.org/content/10.1101/477893v1?rss=1 Tungtur, S. Schwingen, K. M. Riepe, J. J. Weeramange, C. J. Swint-Kruse, L. 2018-11-23 doi:10.1101/477893 Cold Spring Harbor Laboratory Press 2018-11-23 <![CDATA[ Microfluidic On-demand Engineering of Exosomes towards Cancer Immunotherapy ]]> https://biorxiv.org/content/10.1101/478875v1?rss=1 10 h) isolation protocols. Exosome engineering approaches, such as the transfection of parent cells, also suffer from poor yield, low purity, and time-consuming operations. In this paper, we introduce a streamlined microfluidic cell culture platform for integration of harvesting, antigenic modification, and photo-release of surface engineered exosomes in one workflow, which enables the production of intact, MHC peptide surface engineered exosomes for cytolysis activation. The PDMS microfluidic cell culture chip is simply cast from a 3D-printed mold. The proof-of-concept study demonstrated the enhanced ability of harvested exosomes in antigen presentation and T cell activation, by decorating melanoma tumor peptides on the exosome surface (e.g., gp-100, MART-1, MAGE-A3). Such surface engineered antigenic exosomes were harvested in real-time from the on-chip culture of leukocytes isolated from human blood, leading to much faster cellular uptake. The activation of gp100-specific CD8 T cells which were purified from the spleen of 2 Pmel1 transgenic mice was evaluated using surface engineered exosomes prepared from muring antigen presenting cells. Antigen-specific CD8 T cell proliferation was significantly induced by the engineered exosomes compared to native, non-engineered exosomes. This microfluidic platform serves as an automated and highly integrated cell culture device for rapid, and real-time production of therapeutic exosomes that could advance cancer immunotherapy. ]]> Zhao, Z. McGill, J. He, M. 2018-11-27 doi:10.1101/478875 Cold Spring Harbor Laboratory Press 2018-11-27 <![CDATA[ Next-generation sequencing based hospital outbreak investigation yields insight into Klebsiella aerogenes population structure and determinants of carbapenem resistance and virulence ]]> https://biorxiv.org/content/10.1101/497958v1?rss=1 Malek, A. McGlynn, K. Taffner, S. Fine, L. Tesini, B. Wang, J. Mostafa, H. H. Petry, S. Perkins, A. Graman, P. Hardy, D. J. Pecora, N. D. 2018-12-17 doi:10.1101/497958 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ Hepatic JARID1a ablation disrupts the transcription adaptation to feeding and alters systemic metabolism ]]> https://biorxiv.org/content/10.1101/499566v1?rss=1 DiTacchio, K. A. Kalinowska, D. Saran, A. R. Byrne, A. Vollmers, C. DiTacchio, L. 2018-12-19 doi:10.1101/499566 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ A complex copy number variant underlies differences in both colour plumage and cold adaptation in a dimorphic seabird. ]]> https://biorxiv.org/content/10.1101/507384v1?rss=1 Tigano, A. Reiertsen, T. K. Walters, J. R. Friesen, V. L. 2018-12-28 doi:10.1101/507384 Cold Spring Harbor Laboratory Press 2018-12-28 <![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[ 3D-printing Enabled Micro-assembly of Microfluidic Electroporation System for 3D Tissue Engineering ]]> https://biorxiv.org/content/10.1101/519496v1?rss=1 Zhu, Q. Hamilton, M. He, M. 2019-01-12 doi:10.1101/519496 Cold Spring Harbor Laboratory Press 2019-01-12 <![CDATA[ Impaired Regulation of Redox Transcriptome during the Differentiation of iPSCs into Induced Cardiomyocytes (iCMs) ]]> https://biorxiv.org/content/10.1101/519793v1?rss=1 2) were significantly altered in human iCMs compared to the parent iPSCs, in which 4,784 transcripts were substantially upregulated and 4,506 transcripts were down-regulated during differentiation. GO enrichment and IPA analyses revealed the top 10 regulatory networks (i.e. hierarchical order) involved in differentiation of iCMs including cardiomyocyte remodeling, integrin-linked kinase signaling, Rho family of GTPases, etc. Surprisingly, none of the top 10 pathways listed the genes liable for redox signaling networks that are crucial for the basal cellular redox homeostasis, Nrf2-dependent antioxidant defense, mitochondrial functions and cell survival. Our deeper and unbiased analysis of this data revealed that the genes involved in above canonical signaling pathways are found in the middle of the inverted vertical cone. Of note, although these pathways are significantly altered during the differentiation (of iPS into cardiomyocytes), a majority of them are ranked low in the hierarchical list (>150). Validation of the randomly selected genes representing various pathways real-time qPCR confirmed the global transcriptome changes observed in NGS.nnConclusionWe highlight the significance of Nrf2-redox and mitochondrial transcriptome during differentiation of iPSC into iCMs. Thus, targeting the redox signaling mechanisms in iCMs may enhance their efficiency for cell therapy and improved myocardial repair. ]]> Shanmugam, G. Crossman, D. Rajasingh, J. Dalley, B. Zhang, J. Namakkal-Soorappan, R. 2019-01-14 doi:10.1101/519793 Cold Spring Harbor Laboratory Press 2019-01-14 <![CDATA[ RHO-1 and the Rho GEF RHGF-1 interact with UNC-6/Netrin signaling to regulate growth cone protrusion and microtubule organization in C. elegans ]]> https://biorxiv.org/content/10.1101/520262v1?rss=1 Gujar, M. R. Stricker, A. Lundquist, E. A. 2019-01-14 doi:10.1101/520262 Cold Spring Harbor Laboratory Press 2019-01-14 <![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[ Aqueous synthesis of a small-molecule lanthanide chelator amenable to copper-free click chemistry ]]> https://biorxiv.org/content/10.1101/531087v1?rss=1 Bishop, S. C. Winefield, R. Anbanandam, A. Lampe, J. N. 2019-01-26 doi:10.1101/531087 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Differential effects of open- and closed-loop intracortical microstimulation on firing patterns of neurons in distant cortical areas ]]> https://biorxiv.org/content/10.1101/534032v1?rss=1 Averna, A. Pasquale, V. Murphy, M. Rogantin, M. P. Van Acker, G. Nudo, R. Chiappalone, M. Guggenmos, D. 2019-01-29 doi:10.1101/534032 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors Revealed by Accelerated Molecular Simulations ]]> https://biorxiv.org/content/10.1101/541250v1?rss=1 Wang, J. Miao, Y. 2019-02-05 doi:10.1101/541250 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Evolution of leaf-cutter behavior in bees (Hymenoptera: Megachilidae) as inferred from total-evidence tip-dating analyses ]]> https://biorxiv.org/content/10.1101/543082v1?rss=1 Gonzalez Betancourt, V. H. Gustafson, G. T. Engel, M. S. 2019-02-07 doi:10.1101/543082 Cold Spring Harbor Laboratory Press 2019-02-07 <![CDATA[ Epigenetic regulation of DNA repair mediated by the histone methyltransferase DOT1L ]]> https://biorxiv.org/content/10.1101/544981v1?rss=1 Alvarez, N. S. 2019-02-09 doi:10.1101/544981 Cold Spring Harbor Laboratory Press 2019-02-09 <![CDATA[ The elusive actin cytoskeleton of a green alga expressing both conventional and divergent actins ]]> https://biorxiv.org/content/10.1101/554279v1?rss=1 Craig, E. W. Mueller, D. M. Schaffer, M. Engel, B. D. Avasthi, P. 2019-02-18 doi:10.1101/554279 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ 3D cell culture stimulates the secretion of in vivo like exosomes ]]> https://biorxiv.org/content/10.1101/556621v1?rss=1 Thippabhotla, S. Wei, L. Zhong, C. He, M. 2019-02-21 doi:10.1101/556621 Cold Spring Harbor Laboratory Press 2019-02-21 <![CDATA[ Two resistance nodulation division-family efflux pumps in Chromobacterium species and their role in antibiotic resistance and tolerance ]]> https://biorxiv.org/content/10.1101/562140v1?rss=1 Benomar, S. Evans, K. C. Unckless, R. Chandler, J. R. 2019-02-26 doi:10.1101/562140 Cold Spring Harbor Laboratory Press 2019-02-26 <![CDATA[ RanGTP regulates cilium formation and ciliary trafficking of a kinesin-II subunit independent of its nuclear functions ]]> https://biorxiv.org/content/10.1101/562272v1?rss=1 Huang, S. Avasthi, P. 2019-02-27 doi:10.1101/562272 Cold Spring Harbor Laboratory Press 2019-02-27 <![CDATA[ Systematic evaluation and validation of reference and library selection methods for deconvolution of cord blood DNA methylation data ]]> https://biorxiv.org/content/10.1101/570457v1?rss=1 Gervin, K. Salas, L. A. Bakulski, K. M. van Zelm, M. C. Koestler, D. C. Wiencke, J. K. Duijts, L. Moll, H. A. Kelsey, K. T. Kobor, M. S. Lyle, R. Christensen, B. C. Felix, J. Jones, M. J. 2019-03-07 doi:10.1101/570457 Cold Spring Harbor Laboratory Press 2019-03-07 <![CDATA[ Pluripotent Stem Cells Can Be Isolated from Human Peripheral Nerves after in vitro BMP-2 Stimulation ]]> https://biorxiv.org/content/10.1101/598433v1?rss=1 Sun, R.-Y. Heggeness, M. H. Jia, T. Shrestha, S. Dart, B. Yang, S.-Y. 2019-04-03 doi:10.1101/598433 Cold Spring Harbor Laboratory Press 2019-04-03 <![CDATA[ Assessment and representation of variability in ecological niche model predictions ]]> https://biorxiv.org/content/10.1101/603100v1?rss=1 Cobos, M. E. Osorio-Olvera, L. Peterson, A. T. 2019-04-09 doi:10.1101/603100 Cold Spring Harbor Laboratory Press 2019-04-09 <![CDATA[ Transcriptomics of monarch butterflies (Danaus plexippus) reveals strong differential gene expression in response to host plant toxicity, but weak response to parasite infection ]]> https://biorxiv.org/content/10.1101/618546v1?rss=1 Tan, W.-H. Acevedo, T. Harris, E. V. Alcaide, T. Y. Walters, J. R. Hunter, M. D. Gerardo, N. M. de Roode, J. C. 2019-04-25 doi:10.1101/618546 Cold Spring Harbor Laboratory Press 2019-04-25 <![CDATA[ Population genomics reveals complex patterns of immune gene evolution in monarch butterflies (Danaus plexippus) ]]> https://biorxiv.org/content/10.1101/620013v1?rss=1 Tan, W.-H. Mongue, A. J. de Roode, J. C. Gerardo, N. M. Walters, J. R. 2019-04-26 doi:10.1101/620013 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Linking patterns of genetic variation to processes of diversification in Malaysian torrent frogs (Anura: Ranidae: Amolops): a landscape genomics approach ]]> https://biorxiv.org/content/10.1101/628891v1?rss=1 Chan, K. O. Brown, R. 2019-05-06 doi:10.1101/628891 Cold Spring Harbor Laboratory Press 2019-05-06 <![CDATA[ Semaphorin 7a dependent programs of cell surivival, matrix remodeling, and EMT drive postpartum breast tumor progression ]]> https://biorxiv.org/content/10.1101/631044v1?rss=1 Tarullo, S. Hill, R. Hansen, K. Behbod, F. Borges, V. F. Nelson, A. Lyons, T. R. 2019-05-08 doi:10.1101/631044 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Mutational mimics of allosteric effectors: a genome editing design to validate allosteric drug targets ]]> https://biorxiv.org/content/10.1101/632232v1?rss=1 Tang, Q. Villar, M. T. Artigues, A. Thyfault, J. P. Apte, U. Zhu, H. Peterson, K. R. Fenton, A. W. 2019-05-09 doi:10.1101/632232 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Functional tunability from a distance: Rheostat positions influence allosteric coupling between two distant binding sites ]]> https://biorxiv.org/content/10.1101/632422v1?rss=1 Wu, T. Swint-Kruse, L. Fenton, A. W. 2019-05-09 doi:10.1101/632422 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Do neutral protein positions really exist? A case study with allostery in human liver pyruvate kinase ]]> https://biorxiv.org/content/10.1101/632562v1?rss=1 Martin, T. A. Wu, T. Tang, Q. Dougherty, L. L. Parente, D. J. Swint-Kruse, L. Fenton, A. W. 2019-05-09 doi:10.1101/632562 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ An intergenic non-coding RNA promoter required for histone modifications in the human β-globin chromatin domain ]]> https://biorxiv.org/content/10.1101/639807v1?rss=1 Debrand, E. Chakalova, L. Miles, J. Dai, Y.-F. Goyenechea, B. Dye, S. Osborne, C. Harju-Baker, S. Pink, R. Caley, D. Carter, D. Peterson, K. R. Fraser, P. 2019-05-15 doi:10.1101/639807 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ Breeding for broad-spectrum disease resistance alters the maize leaf microbiome ]]> https://biorxiv.org/content/10.1101/647446v1?rss=1 Wagner, M. R. Busby, P. E. Balint-Kurti, P. J. 2019-05-24 doi:10.1101/647446 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Ecological and genomic attributes of novel bacterial taxa that thrive in subsurface soil horizons ]]> https://biorxiv.org/content/10.1101/647651v1?rss=1 Brewer, T. E. Aronson, E. L. Arogyaswamy, K. Billings, S. A. Botthoff, J. K. Campbell, A. N. Dove, N. C. Fairbanks, D. Gallery, R. E. Hart, S. Kaye, J. King, G. M. Logan, G. Lohse, K. A. Maltz, M. R. Mayorga, E. O'Neill, C. Owens, S. Packman, A. I. Pett-Ridge, J. Plante, A. F. Richter, D. D. Silver, W. L. Yang, W. H. Fierer, N. 2019-05-24 doi:10.1101/647651 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Copulas reveal complex and informative dependencies propagating throughout ecology ]]> https://biorxiv.org/content/10.1101/650838v1?rss=1 Ghosh, S. Sheppard, L. W. Holder, M. T. Loecke, T. E. Reid, P. C. Bever, J. D. Reuman, D. C. 2019-05-27 doi:10.1101/650838 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Transposable element dynamics are consistent across the Drosophila phylogeny, despite drastically differing content ]]> https://biorxiv.org/content/10.1101/651059v1?rss=1 Hill, T. 2019-05-27 doi:10.1101/651059 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Mitonuclear interactions influence Alzheimer’s disease risk ]]> https://biorxiv.org/content/10.1101/654400v1?rss=1 Andrews, S. J. Fulton-Howard, B. Patterson, C. McFall, G. P. Gross, A. Michaelis, E. K. Goate, A. M. J. Swerdlow, R. H. Pa, J. the Alzheimers Disease Neuroimaging Initiative, 2019-05-31 doi:10.1101/654400 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ A Simple Deep Learning Approach for Detecting Duplications and Deletions in Next-Generation Sequencing Data ]]> https://biorxiv.org/content/10.1101/657361v1?rss=1 Hill, T. Unckless, R. L. 2019-06-03 doi:10.1101/657361 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Antigen-Specific Immune Decoys Intercept and Exhaust Autoimmunity to Prevent Disease ]]> https://biorxiv.org/content/10.1101/662973v1?rss=1 Griffin, J. D. Song, J. Y. Huang, A. Sedlacek, A. R. Flannagan, K. L. Berkland, C. J. 2019-06-06 doi:10.1101/662973 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ A systems chemoproteomic analysis of acyl-CoA signaling networks ]]> https://biorxiv.org/content/10.1101/665281v1?rss=1 Levy, M. J. Montgomery, D. C. Sardiu, M. E. Thorpe, A. L. Fox, S. D. Lin, Q. Andresson, T. Florens, L. Washburn, M. P. Meier, J. L. 2019-06-10 doi:10.1101/665281 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes ]]> https://biorxiv.org/content/10.1101/668343v1?rss=1 Bray, M. S. Wu, J. Padilla, C. C. Stewart, F. J. Fowle, D. A. Henny, C. Simister, R. L. Thompson, K. J. Crowe, S. A. Glass, J. B. 2019-06-13 doi:10.1101/668343 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ NMDA receptor in vasopressin 1b neurons is not required for short-term social memory, object memory or aggression. ]]> https://biorxiv.org/content/10.1101/670893v1?rss=1 Williams Avram, S. Fastman, J. Cymerblit-Sabba, A. Smith, A. Vincent, M. Song, J. Lee, H.-J. Granovetter, M. Lee, S. H. Cilz, N. Stackmann, M. Chaturvedi, R. Young, W. S. 2019-06-13 doi:10.1101/670893 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ A Bayesian framework for identifying consistent patterns of microbial abundance between body sites ]]> https://biorxiv.org/content/10.1101/673277v1?rss=1 Meier, R. Thompson, J. A. Chung, M. Zhao, N. Kelsey, K. T. Michaud, D. S. Koestler, D. C. 2019-06-18 doi:10.1101/673277 Cold Spring Harbor Laboratory Press 2019-06-18 <![CDATA[ Chronic Stability of Single-Channel Neurophysiological Correlates of Gross and Fine Reaching Movements in the Rat ]]> https://biorxiv.org/content/10.1101/674101v1?rss=1 Bundy, D. Guggenmos, D. J. Murphy, M. D. Nudo, R. J. 2019-06-18 doi:10.1101/674101 Cold Spring Harbor Laboratory Press 2019-06-18 <![CDATA[ A novel metric reveals previously unrecognized distortion in dimensionality reduction of scRNA-Seq data ]]> https://biorxiv.org/content/10.1101/689851v1?rss=1 Cooley, S. M. Hamilton, T. Deeds, E. J. Ray, J. C. J. 2019-07-02 doi:10.1101/689851 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Colicin E1 Fragments Potentiate Antibiotics by Plugging TolC ]]> https://biorxiv.org/content/10.1101/692251v1?rss=1 Budiardjo, S. J. Deay, J. J. Calkins, A. L. Wimalasena, V. K. Montezano, D. Biteen, J. S. Slusky, J. S. G. 2019-07-04 doi:10.1101/692251 Cold Spring Harbor Laboratory Press 2019-07-04 <![CDATA[ Foot shock stress generates persistent widespread hypersensitivity and anhedonic behavior in an anxiety-prone strain of mice ]]> https://biorxiv.org/content/10.1101/700310v1?rss=1 Wu, P. Y. Yang, X. Wright, D. E. Christianson, J. A. 2019-07-14 doi:10.1101/700310 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ Interaction between induced and natural variation at oil yellow1 delays flowering in maize ]]> https://biorxiv.org/content/10.1101/706846v1?rss=1 Khangura, R. S. Venkata, B. Marla, S. Mickelbart, M. Dhungana, S. Braun, D. Dilkes, B. Johal, G. 2019-07-18 doi:10.1101/706846 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ On Some Problems of Estimating Fundamental Niche from Physiological Data ]]> https://biorxiv.org/content/10.1101/716688v1?rss=1 Gutierrez-Ruelas, J. S. Jimenez, L. Quiroz-Reyes, A. P. Sotelo-Pedroza, S. C. Soberon, J. 2019-07-28 doi:10.1101/716688 Cold Spring Harbor Laboratory Press 2019-07-28 <![CDATA[ Parachute geckos free fall into synonymy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements ]]> https://biorxiv.org/content/10.1101/717520v1?rss=1 Wood, P. L. Guo, X. Travers, S. L. Su, Y.-C. Olson, K. V. Bauer, A. M. Grismer, L. L. Siler, C. D. Moyle, R. G. Andersen, M. J. Brown, R. M. 2019-07-28 doi:10.1101/717520 Cold Spring Harbor Laboratory Press 2019-07-28 <![CDATA[ A new variance ratio metric to detect the timescale of compensatory dynamics ]]> https://biorxiv.org/content/10.1101/742510v1?rss=1 Zhao, L. Wang, S. Hallett, L. M. Rypel, A. Sheppard, L. W. Castorani, M. C. N. Shoemaker, L. G. Cottingham, K. L. Suding, K. Reuman, D. C. 2019-08-28 doi:10.1101/742510 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ Labeling proteins within Drosophila embryos by combining FRET reporters, position-specific genomic integration, and GAL4-reponsive expression ]]> https://biorxiv.org/content/10.1101/743492v1?rss=1 Chiba, A. Deng, T.-C. Hsieh, C.-J. De Freitas, M. Boulina, M. Sharifai, N. Samarajeewa, H. Yanaba, T. Baker, J. D. Kim, M. D. Zusman, S. Wan, K. H. Yu, C. Celniker, S. E. 2019-08-22 doi:10.1101/743492 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ G-Protein-Coupled Receptor-Membrane Interactions Depend on the Receptor Activation state ]]> https://biorxiv.org/content/10.1101/743757v1?rss=1 Bhattarai, A. Wang, j. Miao, Y. 2019-08-21 doi:10.1101/743757 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Improved Modeling of Peptide-Protein Binding through Global Docking and Accelerated Molecular Dynamics Simulations ]]> https://biorxiv.org/content/10.1101/743773v1?rss=1 Wang, j. Alekseenko, A. Kozakov, D. Miao, Y. 2019-08-24 doi:10.1101/743773 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Seasonal Effects of Environmental Change on Yellow-Bellied Marmot Population Dynamics ]]> https://biorxiv.org/content/10.1101/745620v1?rss=1 Paniw, M. Childs, D. Armitage, K. B. Blumstein, D. T. Martin, J. Oli, M. Ozgul, A. 2019-08-24 doi:10.1101/745620 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Regulation of defeat-induced social avoidance by medial amygdala DRD1 in male and female prairie voles ]]> https://biorxiv.org/content/10.1101/747923v1?rss=1 Tickerhoof, M. C. Hale, L. H. Smith, A. S. 2019-08-28 doi:10.1101/747923 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ RNA-Binding Proteins MSI-1 (Musashi) and EXC-7 (HuR) Regulate Serotonin-Mediated Behaviors in C. elegans ]]> https://biorxiv.org/content/10.1101/748509v1?rss=1 Yang, Z. Lan, L. Wu, X. Xu, L. Buechner, M. 2019-08-27 doi:10.1101/748509 Cold Spring Harbor Laboratory Press 2019-08-27 <![CDATA[ Exons, Introns, and UCEs Reveal Conflicting Phylogenomic Signals in a Rapid Radiation of Frogs (Ranidae: Hylarana) ]]> https://biorxiv.org/content/10.1101/765610v1?rss=1 Chan, K. O. Hutter, C. Wood, P. L. Grismer, L. Brown, R. 2019-09-11 doi:10.1101/765610 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ Robustness and the evolution of length control strategies in the type III secretion system and flagellar hook ]]> https://biorxiv.org/content/10.1101/766733v1?rss=1 Nariya, M. K. Mallela, A. Shi, J. J. Deeds, E. J. 2019-09-12 doi:10.1101/766733 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ 17α Estradiol promotes plasticity of spared inputs in the adult amblyopic visual cortex ]]> https://biorxiv.org/content/10.1101/773374v1?rss=1 Sengupta, D. C. Lantz, C. L. Rumi, M. A. K. Quinlan, E. M. 2019-09-17 doi:10.1101/773374 Cold Spring Harbor Laboratory Press 2019-09-17 <![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[ PICH promotes SUMOylated TopoisomeraseIIα dissociation from mitotic centromeres for proper chromosome segregation ]]> https://biorxiv.org/content/10.1101/781401v1?rss=1 Hassebroek, V. Park, H. Pandey, N. Lerbakken, B. T. Aksenova, V. Arnaoutov, A. Dasso, M. Azuma, Y. 2019-09-24 doi:10.1101/781401 Cold Spring Harbor Laboratory Press 2019-09-24 <![CDATA[ Further Exploration of the SAR of Imidazoquinolines; Identification of Potent C7 Substituted Imidazoquinolines ]]> https://biorxiv.org/content/10.1101/793232v1?rss=1 Hunt, J. Kleindl, P. A. Moulder, R. Prisinzano, T. E. Forrest, M. L. 2019-10-04 doi:10.1101/793232 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ MetAP2 inhibition reduces food intake and body weight in a ciliopathy mouse model of obesity ]]> https://biorxiv.org/content/10.1101/800151v1?rss=1 Pottorf, T. S. Fagan, M. Burkey, B. Cho, D. J. Vath, J. E. Tran, P. V. 2019-10-13 doi:10.1101/800151 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ Genetic interaction of mammalian IFT-A paralogs regulates cilia disassembly, ciliary protein trafficking, Hedgehog signaling and embryogenesis ]]> https://biorxiv.org/content/10.1101/803544v1?rss=1 Wang, W. Allard, B. A. Pottorf, T. S. Vivian, J. L. Tran, P. V. 2019-10-13 doi:10.1101/803544 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ Evolution in novel environments: do restored prairie populations experience strong selection? ]]> https://biorxiv.org/content/10.1101/824409v1?rss=1 Magnoli, S. M. Lau, J. A. 2019-10-30 doi:10.1101/824409 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ FrogCap: A modular sequence capture probe set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales ]]> https://biorxiv.org/content/10.1101/825307v1?rss=1 Hutter, C. R. Cobb, K. A. Portik, D. Travers, S. L. Wood, P. L. Brown, R. M. 2019-10-31 doi:10.1101/825307 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Species delimitation in the grey zone: introgression obfuscates phylogenetic inference and species boundaries in a cryptic frog complex (Ranidae: Pulchrana picturata) ]]> https://biorxiv.org/content/10.1101/832683v1?rss=1 Chan, K. O. Hutter, C. Wood, P. L. Grismer, L. Brown, R. 2019-11-06 doi:10.1101/832683 Cold Spring Harbor Laboratory Press 2019-11-06 <![CDATA[ Trophoblast paracrine signaling regulates placental hematoendothelial niche ]]> https://biorxiv.org/content/10.1101/840660v1?rss=1 Home, P. Ghosh, A. Parikshan, R. K. Ganguly, A. Bhattacharya, B. Islam, M. R. Ray, S. Gunewardena, S. Paul, S. 2019-11-13 doi:10.1101/840660 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ Divergent Energy Expenditure Impacts Mouse Metabolic Adaptation to Acute High-Fat/High-Sucrose Diet Producing Sexually Dimorphic Weight Gain Patterns ]]> https://biorxiv.org/content/10.1101/840702v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@39eb69org.highwire.dtl.DTLVardef@8e564forg.highwire.dtl.DTLVardef@c46714org.highwire.dtl.DTLVardef@4b5898_HPS_FORMAT_FIGEXP M_FIG Legend: Male and female mice housed at 30{degrees}C had lower energy expenditure (EE) & energy intake (EI), while having greater energy balance (EB), during 7-day high-fat/high-sucrose (HFHS) feeding compared to male and female mice, respectively, housed at 20{degrees}C. However, female mice had lower EB compared to males at both housing temperature. Female mice housed at 30{degrees}C gained less weight than 30{degrees}C males but gained the same relative amount of fat mass during acute HFHS feeding. Interestingly, 20{degrees}C females gained the same amount of weight as 20{degrees}C males but gained primarily fat-free mass, while the males gained the same proportion of fat as 30{degrees}C males and females. C_FIG ]]> Morris, E. M. M. Noland, R. D. Allen, J. A. McCoin, C. S. Xia, Q. Koestler, D. C. Shook, R. P. Lighton, J. R. B. Christianson, J. A. Thyfault, J. P. 2019-11-13 doi:10.1101/840702 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ Atypical Protein Kinase C iota (PKC{lambda}/{iota}) Ensures Mammalian Development by Establishing the Maternal-Fetal Exchange Interface ]]> https://biorxiv.org/content/10.1101/843375v1?rss=1 Bhattacharya, B. Home, P. Ganguly, A. Ray, S. Ghosh, A. Islam, M. R. French, V. Marsh, C. Gunewardena, S. Okae, H. Arima, T. Paul, S. 2019-11-15 doi:10.1101/843375 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ The Legionella pneumophila metaeffector Lpg2505 (SusF) regulates SidI-mediated translation inhibition and GDP-dependent glycosyltransferase activity. ]]> https://biorxiv.org/content/10.1101/845313v1?rss=1 Joseph, A. M. Pohl, A. E. Ball, T. J. Abram, T. G. Johnson, D. K. Geisbrecht, B. V. Shames, S. R. 2019-11-16 doi:10.1101/845313 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ Pharmacological complementation remedies an inborn error of lipid metabolism ]]> https://biorxiv.org/content/10.1101/848119v1?rss=1 Hartley, M. D. Shokat, M. D. DeBell, M. J. Banerji, T. Kirkemo, L. L. Scanlan, T. S. 2019-11-20 doi:10.1101/848119 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Viscoelastic properties of ECM-rich embryonic microenvironments ]]> https://biorxiv.org/content/10.1101/853044v1?rss=1 Akos, Z. Isai, D. G. Rajasingh, S. Kosa, E. Ghazvini, S. Dhar, P. Czirok, A. 2019-11-23 doi:10.1101/853044 Cold Spring Harbor Laboratory Press 2019-11-23 <![CDATA[ SPECC1L-deficient palate mesenchyme cells show speed and directionality defect ]]> https://biorxiv.org/content/10.1101/854273v1?rss=1 Goering, J. P. Isai, D. G. Hall, E. G. Wilson, N. R. Kosa, E. Wenger, L. W. Umar, Z. Yousaf, A. Czirok, A. Saadi, I. 2019-11-25 doi:10.1101/854273 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Matchmaker, Matchmaker, Make Me a Match: Migration of Populations via Marriages in the Past ]]> https://biorxiv.org/content/10.1101/000257v1?rss=1 Sang Hoon Lee Robyn Ffrancon Daniel M. Abrams Beom Jun Kim Mason A. Porter 2013-11-12 doi:10.1101/000257 Cold Spring Harbor Laboratory Press 2013-11-12 <![CDATA[ IVT-seq reveals extreme bias in RNA-sequencing ]]> https://biorxiv.org/content/10.1101/005371v1?rss=1 1000 in vitro transcribed (IVT) RNAs from a full-length human cDNA library and sequenced them with poly-A and total RNA-seq, the most common protocols. Because each cDNA is full length and we show IVT is incredibly processive, each base in each transcript should be equivalently represented. However, with common RNA-seq applications and platforms, we find [~]50% of transcripts have > 2-fold and [~]10% have > 10-fold differences in within-transcript sequence coverage. Strikingly, we also find > 6% of transcripts have regions of high, unpredictable sequencing coverage, where the same transcript varies dramatically in coverage between samples, confounding accurate determination of their expression. To get at causal factors, we used a combination of experimental and computational approaches to show that rRNA depletion is responsible for the most significant variability in coverage and that several sequence determinants also strongly influence representation.nnConclusionsIn sum, these results show the utility of IVT-seq in promoting better understanding of bias introduced by RNA-seq and suggest caution in its interpretation. Furthermore, we find that rRNA-depletion is responsible for substantial, unappreciated biases in coverage. Perhaps most importantly, these coverage biases introduced during library preparation suggest exon level expression analysis may be inadvisable. ]]> Nicholas F Lahens Ibrahim Halil Kavakli Ray Zhang Katharina Hayer Michael B Black Hannah Dueck Angel Pizarro Junhyong Kim Rafael A Irizarry Russell S Thomas Gregory R Grant John B Hogenesch 2014-05-21 doi:10.1101/005371 Cold Spring Harbor Laboratory Press 2014-05-21 <![CDATA[ Synthesis of phylogeny and taxonomy into a comprehensive tree of life ]]> https://biorxiv.org/content/10.1101/012260v1?rss=1 Cody Hinchliff Stephen A Smith James F Allman J Gordon Burleigh Ruchi Chaudhary Lyndon M Cognill Keith A Crandall Jiabin Deng Bryan T Drew Romina Gazis Karl Gude David S Hibbett Laura A Katz H Dail Laughinghouse IV Emily Jane McTavish Peter E. Midford Christopher L Owen Richard Ree Jonathan A Rees Doug E Soltis Tiffani Williams Karen Ann Cranston 2014-12-05 doi:10.1101/012260 Cold Spring Harbor Laboratory Press 2014-12-05 <![CDATA[ Estimating information flow through a memory system: the utility of meta-analytic methods for genetics ]]> https://biorxiv.org/content/10.1101/020586v1?rss=1 Tugce Yildizoglu Jan-Marek Weislogel Farhan Mohammad Edwin S.-Y. Chan Pryseley N. Assam Adam Claridge-Chang 2015-06-08 doi:10.1101/020586 Cold Spring Harbor Laboratory Press 2015-06-08 <![CDATA[ Reduced Glucose Sensation Can Increase the Fitness of Saccharomyces cerevisiae Lacking Mitochondrial DNA ]]> https://biorxiv.org/content/10.1101/024331v1?rss=1 Emel Akdoğan Mehmet Tardu Görkem Garipler Gülkız Baytek İbrahim Halil Kavaklı Cory D. Dunn 2015-08-10 doi:10.1101/024331 Cold Spring Harbor Laboratory Press 2015-08-10 <![CDATA[ Progressive lengthening of 3′ untranslated regions of mRNAs by alternative cleavage and polyadenylation in cellular senescence of mouse embryonic fibroblasts ]]> https://biorxiv.org/content/10.1101/031302v1?rss=1 Miao Han Guo liang Lv Hong bo Nie Ting Shen Yi chi Niu Xue ping Li Meng Chen Xia Zheng Wei Li Chen Ding Gang Wei Jun Gu Xiao Li Tian Yu fang Zheng Xin hua Liu Jin feng Hu Wei Tao Ting Ni 2015-11-11 doi:10.1101/031302 Cold Spring Harbor Laboratory Press 2015-11-11 <![CDATA[ Global lengthening of 3′ untranslated regions of mRNAs by alternative cleavage and polyadenylation in cellular senescence ]]> https://biorxiv.org/content/10.1101/033480v1?rss=1 Miao Han Guoliang Lv Hongbo Nie Ting Shen Yichi Niu Xueping Li Meng Chen Xia Zheng Wei Li Chen Ding Gang Wei Jun Gu Xiao-Li Tian Yufang Zheng Xinhua Liu Jinfeng Hu Tao Wei Ting Ni 2015-12-02 doi:10.1101/033480 Cold Spring Harbor Laboratory Press 2015-12-02 <![CDATA[ AnnoLnc: a web server for systematically annotating novel human lncRNAs ]]> https://biorxiv.org/content/10.1101/042655v1?rss=1 Mei Hou Xing Tang Feng Tian Fangyuan Shi Fenglin Liu Ge Gao 2016-03-07 doi:10.1101/042655 Cold Spring Harbor Laboratory Press 2016-03-07 <![CDATA[ Deep mutational scanning reveals tail anchor characteristics important for mitochondrial targeting ]]> https://biorxiv.org/content/10.1101/045351v1?rss=1 Abdurrahman Keskin Emel Akdogan Cory D. Dunn 2016-03-23 doi:10.1101/045351 Cold Spring Harbor Laboratory Press 2016-03-23 <![CDATA[ Timing appearance and integration of actin-organizing palladin protein in dynamic myofibril assembly ]]> https://biorxiv.org/content/10.1101/047183v1?rss=1 Ngoc-Uyen-Nhi Nguyen Tz-Yu Liu Hao-Ven Wang 2016-04-05 doi:10.1101/047183 Cold Spring Harbor Laboratory Press 2016-04-05 <![CDATA[ Glu-370 in the Large Subunit Influences the Substrate Binding, Allosteric, and Heat Stability Properties of Potato ADP-glucose Pyrophosphorylase ]]> https://biorxiv.org/content/10.1101/054106v1?rss=1 Ayse B Seferoglu Seref Gul Ugur M Dikbas Kaan Koper Ibrahim Baris Mahmut Caliskan Gul Cevahir Ibrahim Kavakli 2016-05-18 doi:10.1101/054106 Cold Spring Harbor Laboratory Press 2016-05-18 <![CDATA[ Characterization of kinase gene expression and splicing profile in prostate cancer with RNA-Seq data ]]> https://biorxiv.org/content/10.1101/061085v1?rss=1 Huijuan Feng Tingting Li Xuegong Zhang 2016-06-29 doi:10.1101/061085 Cold Spring Harbor Laboratory Press 2016-06-29 <![CDATA[ Intrinsic K-Ras dynamics: A novel molecular dynamics data analysis method shows causality between residue pairs ]]> https://biorxiv.org/content/10.1101/067496v1?rss=1 Sezen Vatansever Zeynep Gumus Burak Erman 2016-08-02 doi:10.1101/067496 Cold Spring Harbor Laboratory Press 2016-08-02 <![CDATA[ DNA Methylation Landscape Reflects the Spatial Organization of Chromatin in Different Cells ]]> https://biorxiv.org/content/10.1101/080531v1?rss=1 Zhang, L. Xie, W. J. Liu, S. Meng, L. Gu, C. Gao, Y. Q. 2016-10-13 doi:10.1101/080531 Cold Spring Harbor Laboratory Press 2016-10-13 <![CDATA[ Phosphorylation energy and nonlinear kinetics as key determinants for G2/M transition in fission yeast cell cycle ]]> https://biorxiv.org/content/10.1101/084400v1?rss=1 Wang, T. Zhao, J. Ouyang, Q. Qian, H. Fu, Y. V. Li, F. 2016-10-30 doi:10.1101/084400 Cold Spring Harbor Laboratory Press 2016-10-30 <![CDATA[ Entropy Transfer between Residue Pairs Shows that Allostery is an Intrinsic Propertyof Proteins: Quantifying Allosteric Communication in Ubiquitin ]]> https://biorxiv.org/content/10.1101/084756v1?rss=1 Hacisuleyman, A. Erman, B. 2016-11-01 doi:10.1101/084756 Cold Spring Harbor Laboratory Press 2016-11-01 <![CDATA[ Causality, Transfer Entropy and Allosteric Communication Landscapes inProteins with Harmonic Interactions ]]> https://biorxiv.org/content/10.1101/084764v1?rss=1 Hacisuleyman, A. Erman, B. 2016-11-01 doi:10.1101/084764 Cold Spring Harbor Laboratory Press 2016-11-01 <![CDATA[ Folding Principle of Chromosome Emerges from Mapping of Genome Features onto its 3D Structure ]]> https://biorxiv.org/content/10.1101/085167v1?rss=1 Xie, W. J. Meng, L. Liu, S. Zhang, L. Cai, X. Gao, Y. Q. 2016-11-02 doi:10.1101/085167 Cold Spring Harbor Laboratory Press 2016-11-02 <![CDATA[ Genomic rearrangements near genes leading to upregulation across a diverse subset of human cancers ]]> https://biorxiv.org/content/10.1101/099861v1?rss=1 Creighton, C. Zhang, Y. Chen, F. 2017-01-12 doi:10.1101/099861 Cold Spring Harbor Laboratory Press 2017-01-12 <![CDATA[ Bacterial tail anchors can target to the mitochondrial outer membrane ]]> https://biorxiv.org/content/10.1101/111716v1?rss=1 Bal, G. L. Keskin, A. Seferoglu, A. B. Dunn, C. D. 2017-02-25 doi:10.1101/111716 Cold Spring Harbor Laboratory Press 2017-02-25 <![CDATA[ Optimal Growth Of Microbes On Mixed Carbon Sources ]]> https://biorxiv.org/content/10.1101/120667v1?rss=1 Wang, X. Tang, C. 2017-03-26 doi:10.1101/120667 Cold Spring Harbor Laboratory Press 2017-03-26 <![CDATA[ A Shortened Version Of SecA (SecAN) Functions As The Protein-Conducting Channel For Nascent β-Barrel Outer Membrane Proteins ]]> https://biorxiv.org/content/10.1101/121335v1?rss=1 Jin, F. Chang, Z. 2017-03-28 doi:10.1101/121335 Cold Spring Harbor Laboratory Press 2017-03-28 <![CDATA[ Multiplexed sgRNA Expression Allows Versatile Single Non-repetitive DNA Labeling and Endogenous Gene Regulation ]]> https://biorxiv.org/content/10.1101/121905v1?rss=1 Shao, S. Chang, L. Sun, Y. Hou, Y. Fan, X. Sun, Y. 2017-03-29 doi:10.1101/121905 Cold Spring Harbor Laboratory Press 2017-03-29 <![CDATA[ How Does Mixed Reality Affect Quiet Stance? ]]> https://biorxiv.org/content/10.1101/129239v1?rss=1 Kong, G. Wei, K. Kording, K. P. 2017-04-21 doi:10.1101/129239 Cold Spring Harbor Laboratory Press 2017-04-21 <![CDATA[ Silencing Of Transposable Elements May Not Be A Major Driver Of Regulatory Evolution In Primate Induced Pluripotent Stem Cells ]]> https://biorxiv.org/content/10.1101/142455v1?rss=1 Ward, M. C. Zhao, S. Luo, K. Pavlovic, B. J. Karimi, M. M. Stephens, M. Gilad, Y. 2017-05-28 doi:10.1101/142455 Cold Spring Harbor Laboratory Press 2017-05-28 <![CDATA[ Fluctuations of fMRI activation patterns reveal theta-band dynamics of visual object priming ]]> https://biorxiv.org/content/10.1101/148635v1?rss=1 Guo, B. Lu, Z. Goold, J. E. Luo, H. Meng, M. 2017-06-12 doi:10.1101/148635 Cold Spring Harbor Laboratory Press 2017-06-12 <![CDATA[ Faster carbon accumulation in global forest soils ]]> https://biorxiv.org/content/10.1101/149393v1?rss=1 Zhang, W. Chen, Y. Shi, L. Wang, X. Liu, Y. Rao, X. Lin, Y. Shao, Y. Li, X. Liu, S. Piao, S. Zhu, W. Zou, X. Fu, S. 2017-06-13 doi:10.1101/149393 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ Application of High-Dimensional Statistics and Network based Visualization techniques on Arab Diabetes and Obesity data ]]> https://biorxiv.org/content/10.1101/151621v1?rss=1 Mall, R. Rawi, R. Ullah, E. Kunji, K. Khadir, A. Tiss, A. Abubaker, J. Dehbi, M. Bensmail, H. 2017-06-18 doi:10.1101/151621 Cold Spring Harbor Laboratory Press 2017-06-18 <![CDATA[ Genomic footprints of activated telomere maintenance mechanisms in cancer ]]> https://biorxiv.org/content/10.1101/157560v1?rss=1 Sieverling, L. Hong, C. Koser, S. D. Ginsbach, P. Kleinheinz, K. Hutter, B. Braun, D. M. Cortes-Ciriano, I. Xi, R. Kabbe, R. Park, P. J. Eils, R. Schlesner, M. Rippe, K. Jones, D. T. W. Brors, B. Feuerbach, L. 2017-06-30 doi:10.1101/157560 Cold Spring Harbor Laboratory Press 2017-06-30 <![CDATA[ In vivo Imaging β-cell Function Reveals Two Waves of β-cell Maturation ]]> https://biorxiv.org/content/10.1101/159673v1?rss=1 Zhao, J. Zong, W. Wu, Y. Shen, J. Gou, D. Zhao, Y. Wu, R. Niu, F. Wang, X. Zheng, X. Wang, A. Zhang, Y. Xiong, J.-W. Chen, L. Liu, Y. 2017-07-05 doi:10.1101/159673 Cold Spring Harbor Laboratory Press 2017-07-05 <![CDATA[ An exact transformation of convolutional kernels applied directly to DNA/RNA sequences ]]> https://biorxiv.org/content/10.1101/163220v1?rss=1 Ding, Y. Li, J. Wang, M. Gao, G. 2017-07-13 doi:10.1101/163220 Cold Spring Harbor Laboratory Press 2017-07-13 <![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[ The Effects Of Oncogenic G12D Mutation On K-Ras Structure, Conformation And Dynamics ]]> https://biorxiv.org/content/10.1101/178483v1?rss=1 Vatansever, S. Gumus, Z. Erman, B. 2017-08-19 doi:10.1101/178483 Cold Spring Harbor Laboratory Press 2017-08-19 <![CDATA[ GVC: A superfast and universal genomic variant caller ]]> https://biorxiv.org/content/10.1101/182089v1?rss=1 Zhang, Z. Yin, L. Cao, L. Liu, C. Hao, L. Ling, S. 2017-08-29 doi:10.1101/182089 Cold Spring Harbor Laboratory Press 2017-08-29 <![CDATA[ Ahr and Cyp1a2 genotypes both affect susceptibility to motor deficits following gestational and lactational exposure to polychlorinated biphenyls ]]> https://biorxiv.org/content/10.1101/184010v1?rss=1 Colter, B. T. Garber, H. F. Fleming, S. M. Fowler, J. P. Harding, G. D. Hooven, M. K. Howes, A. A. Infante, S. K. Lang, A. L. MacDougall, M. C. Stegman, M. Taylor, K. Curran, C. P. 2017-09-04 doi:10.1101/184010 Cold Spring Harbor Laboratory Press 2017-09-04 <![CDATA[ Genetic load and mutational meltdown in cancer cell populations ]]> https://biorxiv.org/content/10.1101/193482v1?rss=1 Zhang, Y. Li, Y. Zhu, T. Shen, X. Tao, Y. Li, T. Li, X. Wang, D. Ma, Q. Hu, Z. Liu, J. Zheng, C. Ruan, J. Cai, J. Wu, C.-I. Wang, H.-Y. Lu, X. 2017-10-05 doi:10.1101/193482 Cold Spring Harbor Laboratory Press 2017-10-05 <![CDATA[ Genetic differences in the aryl hydrocarbon receptor and CYP1A2 affect susceptibility to developmental polychlorinated biphenyl exposure in mice: Relevance to studies of human neurological disorders ]]> https://biorxiv.org/content/10.1101/194472v1?rss=1 Klinefelter, K. Hooven, M. K. Bates, C. Colter, B. T. Dailey, A. Infante, S. K. Kania-Korwel, I. Lehmler, H.-J. Lopez-Juarez, A. Ludwig, C. P. Curran, C. P. 2017-09-27 doi:10.1101/194472 Cold Spring Harbor Laboratory Press 2017-09-27 <![CDATA[ Integrative Statistical Inferences for Drug Sensitivity Biomarkers in Cancer ]]> https://biorxiv.org/content/10.1101/194670v1?rss=1 Ullah, E. Shama, S. Al Muftah, N. Thompson, I. R. Rawi, R. Mall, R. Bensmail, H. 2017-09-27 doi:10.1101/194670 Cold Spring Harbor Laboratory Press 2017-09-27 <![CDATA[ Response to Qian et al (2017): Daily and seasonal climate variations are both critical in the evolution of species’ elevational range size ]]> https://biorxiv.org/content/10.1101/195248v1?rss=1 Chan, W.-P. Chen, I.-C. Colwell, R. K. Liu, W.-C. Huang, C.-y. Shen, S.-F. 2017-09-30 doi:10.1101/195248 Cold Spring Harbor Laboratory Press 2017-09-30 <![CDATA[ Identification of Cancer-associated Metabolic Vulnerabilities by Modeling Multi-objective Optimality in Metabolism ]]> https://biorxiv.org/content/10.1101/198333v1?rss=1 Dai, Z. Xu, L. Hu, H. Liao, K. Deng, S. Chen, Q. Yang, S. Wang, Q. Gao, S. Li, B. Lai, L. 2017-10-04 doi:10.1101/198333 Cold Spring Harbor Laboratory Press 2017-10-04 <![CDATA[ Automatic and fast encoding of representational uncertainty underlies probability distortion ]]> https://biorxiv.org/content/10.1101/2019.12.17.879684v1?rss=1 Ren, X. Luo, H. Zhang, H. 2019-12-17 doi:10.1101/2019.12.17.879684 Cold Spring Harbor Laboratory Press 2019-12-17 <![CDATA[ Enhancing generating and collecting efficiency of single particle upconverting luminescence at low-level power excitation ]]> https://biorxiv.org/content/10.1101/2019.12.17.879858v1?rss=1 2.5 MW/cm2). However, such particles are inadequate for in-vitro live-cell imaging and single-particle tracking since high excitation power can cause photodamage. Here, we compared UCNPs luminescence intensities with different dopants concentrations and presented a more efficient ([~]7x) UCNPs at low excitation power by increasing the concentrations of Yb3+ and Tm3+ dopants (NaYF4: 60% Yb3+, 8% Tm3+) and adding a core-shell structure. ]]> Ma, C. Shan, C. Park, K. Mok, A. T. Yang, X. 2019-12-18 doi:10.1101/2019.12.17.879858 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ Developing a DeSipher method for conformational change detection of membrane receptor complex at residue resolution ]]> https://biorxiv.org/content/10.1101/2019.12.18.873729v1?rss=1 Liu, Q. He, Q.-t. Lyu, X.-x. Yang, F. Zhu, Z.-l. Xiao, P. Yang, Z. Zhang, F. Yang, Z.-y. Wang, X.-y. Sun, P. Wang, Q.-w. Qu, C.-x. Gong, Z. Lin, J.-Y. Xu, Z. Song, S.-l. Huang, S.-m. Guo, S.-c. Han, M.-j. Zhu, K.-k. Chen, X. Kahsai, A. W. Xiao, K.-H. Kong, W. Yu, X. Ruan, K. Li, F.-h. Niu, X.-g. Jin, C.-w. Wang, J. Sun, J. 2019-12-19 doi:10.1101/2019.12.18.873729 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Enzyme capacity-based genome scale modelling of CHO cells ]]> https://biorxiv.org/content/10.1101/2019.12.19.883652v1?rss=1 Yeo, H. C. Hong, J. Lakshmanan, M. Lee, D.-Y. 2019-12-20 doi:10.1101/2019.12.19.883652 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ NADPH diaphorase neuronal dystrophy in gracile nucleus, cuneatus nucleus and spinal trigeminal nucleus in aged rat ]]> https://biorxiv.org/content/10.1101/2019.12.21.885988v1?rss=1 Hou, W. Jia, Y. Li, Y. Wei, Z. Wen, X. Rao, C. Xu, X. Li, F. Wu, X. Sun, H. Li, H. Huang, Y. Sun, J. Shu, G. Wang, X. Zhang, T. Shi, G. Guo, A. Xu, S. Du, G. Tan, H. 2019-12-23 doi:10.1101/2019.12.21.885988 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ CNV-BAC: Copy Number Variation Detection in Bacterial Circular Genome ]]> https://biorxiv.org/content/10.1101/2019.12.24.887992v1?rss=1 Wu, L. Wang, H. Xia, Y. Xi, R. 2019-12-27 doi:10.1101/2019.12.24.887992 Cold Spring Harbor Laboratory Press 2019-12-27 <![CDATA[ Multi-Parametric Profiling of Endothelial Cell Networks Reveals Functional Role of Glutamate Receptors in Angiogenesis ]]> https://biorxiv.org/content/10.1101/2019.12.25.888479v1?rss=1 Sailem, H. Z. Al Haj Zen, A. 2019-12-27 doi:10.1101/2019.12.25.888479 Cold Spring Harbor Laboratory Press 2019-12-27 <![CDATA[ Subcellular protein profiling with far-red light mediated proximal labeling ]]> https://biorxiv.org/content/10.1101/2019.12.28.890095v1?rss=1 Li, Z. 2019-12-30 doi:10.1101/2019.12.28.890095 Cold Spring Harbor Laboratory Press 2019-12-30 <![CDATA[ Correlated Gene Modules Uncovered by Single-Cell Transcriptomics with High Detectability and Accuracy ]]> https://biorxiv.org/content/10.1101/2019.12.31.892190v1?rss=1 Chapman, A. R. Lee, D. F. Cai, W. Ma, W. Li, X. Sun, W. Xie, X. S. 2020-01-02 doi:10.1101/2019.12.31.892190 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ Fine Sieving of Collected Atmospheric Particles using Oil Electrophoresis (iSCAPE) ]]> https://biorxiv.org/content/10.1101/2020.01.04.894998v1?rss=1 View larger version (21K): org.highwire.dtl.DTLVardef@8d50f9org.highwire.dtl.DTLVardef@1bf1b1aorg.highwire.dtl.DTLVardef@18c70ddorg.highwire.dtl.DTLVardef@145c317_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Li, X. Xu, S. Yao, M. 2020-01-06 doi:10.1101/2020.01.04.894998 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ Inhibition mechanism of human sterol O-acyltransferase 1 by competitive inhibitor ]]> https://biorxiv.org/content/10.1101/2020.01.07.897124v1?rss=1 Guan, C. Niu, Y. Chen, S.-C. Kang, Y. Wu, J.-X. Nishi, K. Chang, C. C. Y. Chang, T.-Y. Luo, T. Chen, L. 2020-01-08 doi:10.1101/2020.01.07.897124 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ CRY1-CBS binding regulates circadian clock function and metabolism ]]> https://biorxiv.org/content/10.1101/2020.01.09.898866v1?rss=1 Cal-Kayitmazbatir, S. Kulkoyluoglu-Cotul, E. Growe, J. Selby, C. P. Rhoades, S. D. Malik, D. Oner, H. Asimgil, H. Francey, L. J. Sancar, A. Kruger, W. D. Hogenesch, J. B. Weljie, A. Anafi, R. Kavakli, I. H. 2020-01-09 doi:10.1101/2020.01.09.898866 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Circadian Rhythm Is Disrupted by ZNF704 in Breast Carcinogenesis ]]> https://biorxiv.org/content/10.1101/2020.01.09.900548v1?rss=1 Yang, C. Wu, J. Liu, X. Wang, Y. Liu, B. Chen, X. Wu, X. Yan, D. Han, L. Liu, S. Shan, L. Shang, Y. 2020-01-09 doi:10.1101/2020.01.09.900548 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Scalable generation of mesenchymal stem cells and adipocytes from human pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2020.01.11.902833v1?rss=1 Karam, M. Younis, I. Abdelalim, E. M. 2020-01-11 doi:10.1101/2020.01.11.902833 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Toward an understanding of the relation between gene regulation and 3D genome organization ]]> https://biorxiv.org/content/10.1101/2020.01.13.903872v1?rss=1 Tian, H. Yang, Y. Liu, S. Quan, H. Gao, Y. Q. 2020-01-14 doi:10.1101/2020.01.13.903872 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Domain segregated 3D chromatin structure and segmented DNA methylation in carcinogenesis ]]> https://biorxiv.org/content/10.1101/2020.01.13.903963v1?rss=1 Xue, Y. Yang, Y. Tian, H. Quan, H. Liu, S. Zhang, L. Gao, Y. Q. 2020-01-14 doi:10.1101/2020.01.13.903963 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ The Nonequilibrium Mechanism of Noise Enhancer synergizing with Activator in HIV Latency Reactivation ]]> https://biorxiv.org/content/10.1101/2020.01.14.905653v1?rss=1 Guo, X. Tang, T. Duan, M. Zhang, L. Ge, H. 2020-01-15 doi:10.1101/2020.01.14.905653 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ A global map of root biomass across the world's forests ]]> https://biorxiv.org/content/10.1101/2020.01.14.906883v1?rss=1 Huang, Y. Ciais, P. Santoro, M. Makowski, D. Chave, J. Schepaschenko, D. Abramoff, R. Goll, D. S. Yang, H. Chen, Y. Wei, W. Piao, S. 2020-01-15 doi:10.1101/2020.01.14.906883 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Evolutionary forces on A-to-I RNA editing revealed by sequencing individual honeybee drones ]]> https://biorxiv.org/content/10.1101/2020.01.15.907287v1?rss=1 Duan, Y. Dou, S. Huang, J. Eisenberg, E. Lu, J. 2020-01-15 doi:10.1101/2020.01.15.907287 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Genetic interactions shaping evolutionary trajectories in an RNA virus population ]]> https://biorxiv.org/content/10.1101/2020.01.16.908129v1?rss=1 Chang, C. Bianco, S. Acevedo, A. Tang, C. Andino, R. 2020-01-17 doi:10.1101/2020.01.16.908129 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ PE5-PPE4-EspG3 trimer structure from mycobacterial ESX-3 secretion system gives insight into cognate substrate recognition by ESX systems ]]> https://biorxiv.org/content/10.1101/2020.01.16.909523v1?rss=1 Williamson, Z. A. Chaton, C. T. Ciocca, W. A. Korotkova, N. Korotkov, K. V. 2020-01-17 doi:10.1101/2020.01.16.909523 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ Dissecting endothelial to haematopoietic stem cell transition by single-cell transcriptomic and functional analyses ]]> https://biorxiv.org/content/10.1101/2020.01.18.910356v1?rss=1 Hou, S. Li, Z. Zheng, X. Gao, Y. Dong, J. Ni, Y. Wang, X. Li, Y. Ding, X. Chang, Z. Li, S. Hu, Y. Fan, X. Hou, Y. Wen, L. Liu, B. Tang, F. Lan, Y. 2020-01-20 doi:10.1101/2020.01.18.910356 Cold Spring Harbor Laboratory Press 2020-01-20 <![CDATA[ Surveying Brain Tumor Heterogeneity by Single-Cell RNA Sequencing of Multi-sector Biopsies ]]> https://biorxiv.org/content/10.1101/2020.01.19.911701v1?rss=1 Yu, K. Hu, Y. Wu, F. Guo, Q. Qian, Z. Hu, W. Chen, J. Wang, K. Fan, X. Wu, X. Rasko, J. E. Fan, X. Iavarone, A. Jiang, T. Tang, F. Su, X.-D. 2020-01-19 doi:10.1101/2020.01.19.911701 Cold Spring Harbor Laboratory Press 2020-01-19 <![CDATA[ Neutralizing PD-L1 and PD-L2 Enhances the Efficacy of Immune Checkpoint Inhibitors in Ovarian Cancer. ]]> https://biorxiv.org/content/10.1101/2020.01.19.911941v1?rss=1 Miao, Y. R. Thakkar, K. N. Qian, J. Kariolis, M. S. Huang, W. Nandagopal, S. A. Yang, T. Diep, A. N. Cherf, G. M. Xu, Y. Moon, E. J. Xiao, Y. Alemany, H. Li, T. Yu, W. Wei, B. Rankin, E. B. Giaccia, A. J. 2020-01-20 doi:10.1101/2020.01.19.911941 Cold Spring Harbor Laboratory Press 2020-01-20 <![CDATA[ Schisandrin B for treatment of male infertility ]]> https://biorxiv.org/content/10.1101/2020.01.20.912147v1?rss=1 zou, D.-X. Meng, X.-D. Xie, Y. Liu, R. Duan, J.-L. Bao, C.-J. Liu, Y.-X. Du, Y.-F. Xu, J.-R. Luo, Q. Zhang, Z. Ma, S. Yang, W.-P. Lin, R.-C. Lu, W.-L. 2020-01-21 doi:10.1101/2020.01.20.912147 Cold Spring Harbor Laboratory Press 2020-01-21 <![CDATA[ Host and infectivity prediction of Wuhan 2019 novel coronavirus using deep learning algorithm ]]> https://biorxiv.org/content/10.1101/2020.01.21.914044v1?rss=1 Zhu, H. Guo, Q. Li, M. Wang, C. Fang, Z. Wang, P. Tan, J. Wu, S. Xiao, Y. 2020-01-24 doi:10.1101/2020.01.21.914044 Cold Spring Harbor Laboratory Press 2020-01-24 <![CDATA[ Identifying Priority Landscapes for Conservation of Snow Leopards in Pakistan ]]> https://biorxiv.org/content/10.1101/2020.01.27.920975v1?rss=1 Hameed, S. Din, J. u. Ali, H. Kabir, M. Younas, M. Hao, W. Bischof, R. Nawaz, M. A. 2020-01-27 doi:10.1101/2020.01.27.920975 Cold Spring Harbor Laboratory Press 2020-01-27 <![CDATA[ Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II and Pol III ]]> https://biorxiv.org/content/10.1101/2020.01.28.923995v1?rss=1 jiang, y. p. huang, j. lun, k. h. li, b. y. zheng, h. n. li, y. j. zhou, r. duan, w. j. feng, y. q. yao, h. li, c. Ji, X. 2020-01-29 doi:10.1101/2020.01.28.923995 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ Landscape of transcript isoforms in single T cells infiltrating in non-small cell lung cancer ]]> https://biorxiv.org/content/10.1101/2020.01.29.924308v1?rss=1 Li, J. Zhang, Z. Ren, X. 2020-01-30 doi:10.1101/2020.01.29.924308 Cold Spring Harbor Laboratory Press 2020-01-30 <![CDATA[ Transposase assisted tagmentation of RNA/DNA hybrid duplexes ]]> https://biorxiv.org/content/10.1101/2020.01.29.926105v1?rss=1 Yi, C. Lu, B. Dong, L. Yi, D. Zhu, C. Zhang, M. Li, X. 2020-01-31 doi:10.1101/2020.01.29.926105 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Germline genetic contribution to the immune landscape of cancer ]]> https://biorxiv.org/content/10.1101/2020.01.30.926527v1?rss=1 9,000 individuals in The Cancer Genome Atlas, we investigated the association of common and rare variants with 139 well-defined immune traits. Our analysis of common variants identified 10 immune traits with significant heritability estimates, and an additional 23 with suggestive heritability, including estimates of T-cell subset abundance and interferon signaling. We performed genome-wide association on the 33 heritable traits and identified 23 genome-wide significant loci associated with at least one immune trait, including SNPs in the IFIH1 locus previously associated with several autoimmune diseases. We also found significant associations between immune traits and pathogenic or likely-pathogenic rare variants in BRCA1 and in genes functionally linked to telomere stabilization, and Wnt/Beta-catenin signaling. We conclude that germline genetic variants significantly impact the composition and functional orientation of the tumor immune microenvironment. ]]> Sayaman, R. W. Saad, M. Thorsson, V. Hendrickx, W. Roelands, J. Mokrab, Y. Farshidfar, F. Kirchhoff, T. Sweis, R. F. Bathe, O. F. Porta-Pardo, E. Campbell, M. J. Stretch, C. Hu, D. Huntsman, S. Graff, R. E. Syed, N. Radvanyi, L. Shelly, S. Wolf, D. Marincola, F. M. Ceccarelli, M. Galon, J. Ziv, E. Bedognetti, D. 2020-01-31 doi:10.1101/2020.01.30.926527 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Pial surface CSF-contacting texture, subpial and funicular plexus in the thoracic spinal cord in monkey: NADPH diaphorase histological configuration ]]> https://biorxiv.org/content/10.1101/2020.01.30.927509v1?rss=1 Li, Y. Hou, W. Jia, Y. Wen, X. Rao, C. Xu, X. Wei, Z. Bai, L. Tan, H. 2020-01-31 doi:10.1101/2020.01.30.927509 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Clinically applicable histopathological diagnosis system for gastric cancer detection using deep learning ]]> https://biorxiv.org/content/10.1101/2020.01.30.927749v1?rss=1 Song, Z. Zou, S. Zhou, W. Huang, Y. Shao, L. Yuan, J. Gou, X. Jin, W. Wang, Z. Chen, X. Ding, X. Liu, J. Yu, C. Ku, C. Liu, C. Sun, Z. Xu, G. Wang, Y. Zhang, X. Wang, D. Wang, S. Xu, W. Davis, R. C. Shi, H. 2020-01-31 doi:10.1101/2020.01.30.927749 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ The hidden cost of receiving favors: A theory of indebtedness ]]> https://biorxiv.org/content/10.1101/2020.02.03.926295v1?rss=1 Gao, X. Jolly, E. Yu, H. Liu, H. Zhou, X. Chang, L. J. 2020-02-04 doi:10.1101/2020.02.03.926295 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ DPHL: A pan-human protein mass spectrometry library for robust biomarker discovery using Data-Independent Acquisition and Parallel Reaction Monitoring ]]> https://biorxiv.org/content/10.1101/2020.02.03.931329v1?rss=1 Zhu, T. Zhu, Y. J. Xuan, Y. Gao, H. Cai, X. Piersma, S. R. Pham, T. V. Schelfhorst, T. de Haas, R. R. Bijnsdorp, I. V. Sun, R. Yue, L. Ruan, G. Zhang, Q. Hu, M. Zhou, Y. Houdt, W. J. V. Le Large, T. Y. Cloos, J. Wojtuszkiewicz, A. Koppers-Lalic, D. Bottger, F. Scheepbouwer, C. Brakenhoff, R. H. Leenders, G. J. L. H. v. Ijzermans, J. N. M. Martens, J. W. M. Steenbergen, R. D. M. Grieken, N. C. Selvarajan, S. Mantoo, S. Lee, S. S. Yeow, S. J. Y. Alkaff, S. M. F. Nan, X. Sun, Y. Yi, X. Dai, S. Liu, W. Lu, T. Wu, Z. Liang, X. Wang, M. Shao, Y. Zheng, X. 2020-02-03 doi:10.1101/2020.02.03.931329 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ Fluctuation, correlation and perturbation-response behavior of nature-made and artificial nanobodies ]]> https://biorxiv.org/content/10.1101/2020.02.06.936856v1?rss=1 Hacisuleyman, A. Erman, B. Erkip, A. Erman, B. 2020-02-06 doi:10.1101/2020.02.06.936856 Cold Spring Harbor Laboratory Press 2020-02-06 <![CDATA[ Acute inhibition of centriolar satellite function and positioning reveals their functions at the primary cilium ]]> https://biorxiv.org/content/10.1101/2020.02.10.941658v1?rss=1 Aydin, O. Z. Taflan, S. O. Firat-Karalar, E. N. Gurkaslar, C. 2020-02-10 doi:10.1101/2020.02.10.941658 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ Long-read Individual-molecule Sequencing Reveals CRISPR-induced Genetic Heterogeneity in Human ESCs ]]> https://biorxiv.org/content/10.1101/2020.02.10.942151v1?rss=1 Bi, C. Wang, L. Yuan, B. Zhou, X. Li, Y. Wang, S. Pang, Y. Gao, X. Huang, Y. Li, M. 2020-02-11 doi:10.1101/2020.02.10.942151 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ Structural insights into secretory immunoglobulin A and its interaction with a pneumococcal adhesin ]]> https://biorxiv.org/content/10.1101/2020.02.11.943233v1?rss=1 Wang, Y. Wang, G. Li, Y. Shen, H. Chu, H. Gao, N. Xiao, J. 2020-02-11 doi:10.1101/2020.02.11.943233 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ Ancestral duplicated DL/CRC orthologs display function on orchid reproductive organ innovation ]]> https://biorxiv.org/content/10.1101/2020.02.12.945865v1?rss=1 Chen, Y.-Y. Hsiao, Y.-Y. Li, C.-I. Yeh, C.-M. Mitsuda, N. Yang, H. Chiu, C.-C. Chang, S.-B. Liu, Z.-J. Tsai, W.-C. 2020-02-17 doi:10.1101/2020.02.12.945865 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ Development of Small Molecule MEIS Inhibitors that modulate HSC activity ]]> https://biorxiv.org/content/10.1101/2020.02.12.946491v1?rss=1 Turan, R. D. Albayrak, E. Uslu, M. Siyah, P. Alyazici, L. Y. Kalkan, B. M. Aslan, G. S. Yucel, D. Aksoz, M. Tuysuz, E. C. Meric, N. Durdagi, S. Gulbas, Z. Kocabas, F. 2020-02-13 doi:10.1101/2020.02.12.946491 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Reconstruction of cell spatial organization based on ligand-receptor mediated self-assembly ]]> https://biorxiv.org/content/10.1101/2020.02.13.948521v1?rss=1 Ren, X. Zhong, G. Zhang, Q. Zhang, L. sun, y. Zhang, Z. 2020-02-14 doi:10.1101/2020.02.13.948521 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Revealing Atomic-scale Molecular Diffusion of a Plant Transcription Factor WRKY domain protein along DNA ]]> https://biorxiv.org/content/10.1101/2020.02.14.950295v1?rss=1 Dai, L. Xu, Y. Du, Z. Su, X.-d. Yu, J. 2020-02-15 doi:10.1101/2020.02.14.950295 Cold Spring Harbor Laboratory Press 2020-02-15 <![CDATA[ Infrared heater warming system markedly reduces dew formation: An overlooked factor in arid ecosystems ]]> https://biorxiv.org/content/10.1101/2020.02.15.950584v1?rss=1 FENG, T. Zhang, L. Chen, Q. Ma, Z. Wang, H. Shangguan, Z. Wang, L. He, J.-S. 2020-02-15 doi:10.1101/2020.02.15.950584 Cold Spring Harbor Laboratory Press 2020-02-15 <![CDATA[ Basal forebrain-derived acetylcholine encodes valence-free reinforcement prediction error. ]]> https://biorxiv.org/content/10.1101/2020.02.17.953141v1?rss=1 Sturgill, J. F. Hegedüs, P. Li, S. Chevy, Q. Siebels, A. Jing, M. Li, Y. Hangya, B. Kepecs, A. 2020-02-18 doi:10.1101/2020.02.17.953141 Cold Spring Harbor Laboratory Press 2020-02-18 <![CDATA[ Plasmon-Coupled Photocapacitor Neuromodulators ]]> https://biorxiv.org/content/10.1101/2020.02.18.953604v1?rss=1 Melikov, R. Srivastava, S. B. Karatum, O. Dogru, I. B. Bahmani Jalali, H. Sadeghi, S. Dikbas, U. M. Ulgut, B. Kavakli, I. H. Nizamoglu, S. 2020-02-19 doi:10.1101/2020.02.18.953604 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Genome Wide Analysis of Dinucleotide Distribution along the Genomes of Species and its Biological Implication ]]> https://biorxiv.org/content/10.1101/2020.02.20.957142v1?rss=1 Cai, Z. Liu, S. Xue, Y. Quan, H. Zhang, L. Gao, Y. Q. 2020-02-20 doi:10.1101/2020.02.20.957142 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Improved Parameterization of Protein-DNA Interactions for Molecular Dynamics Simulations of PCNA Diffusion on DNA ]]> https://biorxiv.org/content/10.1101/2020.02.23.961573v1?rss=1 You, S. Lee, H. Kim, K. Yoo, J. 2020-02-24 doi:10.1101/2020.02.23.961573 Cold Spring Harbor Laboratory Press 2020-02-24 <![CDATA[ A genetically encoded GRAB sensor for measuring serotonin dynamics in vivo ]]> https://biorxiv.org/content/10.1101/2020.02.24.962282v1?rss=1 Wan, J. Peng, W. Li, X. Qian, T. Song, K. Zeng, J. Deng, F. Hao, S. Feng, J. Zhang, P. Zhang, Y. Zou, J. Pan, S. Zhu, J. J. Jing, M. Xu, M. Li, Y. 2020-02-25 doi:10.1101/2020.02.24.962282 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Key histone chaperones have distinct roles in replisome progression and genomic stability ]]> https://biorxiv.org/content/10.1101/2020.02.25.964221v1?rss=1 Tsirkas, I. Dovrat, D. Lei, Y. Kalyva, A. Lotysh, D. Li, Q. Aharoni, A. 2020-02-25 doi:10.1101/2020.02.25.964221 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Automatic encoding of a view-centered background image in the macaque temporal lobe ]]> https://biorxiv.org/content/10.1101/2020.03.01.971507v1?rss=1 Chen, H. Naya, Y. 2020-03-03 doi:10.1101/2020.03.01.971507 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ Somatic cell-derived BMPs induce male germ cell meiosis initiation during embryonic stage via regulating Dazl expression ]]> https://biorxiv.org/content/10.1101/2020.03.01.971937v1?rss=1 Gao, F. Zhang, L. Li, Y. Hu, Y. Lin, L. Zhou, J. Chen, M. Qin, Y. Zhou, Y. Chen, M. Cui, X. Tang, F. 2020-03-02 doi:10.1101/2020.03.01.971937 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Amorphous nickel titanium alloy film: a new choice for cryo electron microscopy sample preparation ]]> https://biorxiv.org/content/10.1101/2020.03.02.963959v1?rss=1 Huang, X. Zhang, L. Wen, Z. Chen, H. Li, S. Ji, G. Yin, C.-c. Sun, F. 2020-03-02 doi:10.1101/2020.03.02.963959 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Rapid & reversable mutations generate subclonal genetic diversity ]]> https://biorxiv.org/content/10.1101/2020.03.03.972455v1?rss=1 Dan, L. Li, Y. Chen, S. Liu, J. Wang, Y. Li, F. He, X. Carey, L. B. 2020-03-04 doi:10.1101/2020.03.03.972455 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ MosaicBase: A Knowledgebase of Postzygotic Mosaic Variants in Noncancer Diseases and Asymptomatic Human Individuals ]]> https://biorxiv.org/content/10.1101/2020.03.04.976803v1?rss=1 Yang, X. Yang, C. Zheng, X. Xiong, L. Tao, Y. Wang, M. Ye, A. Y. Wu, Q. Dou, Y. Luo, J. Wei, L. Huang, A. Y. 2020-03-05 doi:10.1101/2020.03.04.976803 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Hippocampal cells integrate past memory and present perception for the future ]]> https://biorxiv.org/content/10.1101/2020.03.08.982355v1?rss=1 Yang, C. Naya, Y. 2020-03-09 doi:10.1101/2020.03.08.982355 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ Quantifying temperature compensation of Bicoid gradients with a fast T-tunable microfluidic device ]]> https://biorxiv.org/content/10.1101/2020.03.09.983742v1?rss=1 Zhu, H. Cui, Y. Luo, C. Liu, F. 2020-03-09 doi:10.1101/2020.03.09.983742 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ A quasi-paired cohort strategy reveals the impaired detoxifying function of microbes in the gut of autistic children ]]> https://biorxiv.org/content/10.1101/2020.03.10.984872v1?rss=1 Zhang, M. Chu, Y. Meng, Q. Ding, R. Shi, X. Wang, Z. He, Y. Zhang, J. Liu, J. Zhang, J. Yu, J. Kang, Y. Wang, J. 2020-03-11 doi:10.1101/2020.03.10.984872 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Consensus-seeking and conflict-resolving -an fMRI study on college couples shopping interaction ]]> https://biorxiv.org/content/10.1101/2020.03.11.986786v1?rss=1 Jo, H. Chen, C.-Y. Chen, D.-Y. Weng, M.-H. Kung, C.-C. 2020-03-12 doi:10.1101/2020.03.11.986786 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ Three-dimensional genome structure and chromatin accessibility reorganization during in vivo induction of human T cell tolerance ]]> https://biorxiv.org/content/10.1101/2020.03.11.988253v1?rss=1 Li, R. Guo, H. Hou, Y. Liu, S. Wang, M. Peng, T. Zhao, X. Lu, L. Han, Y. Shao, Y. Chang, Y.-J. Li, C. Huang, X. 2020-03-12 doi:10.1101/2020.03.11.988253 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ 3D Genome Analysis Identifies Enhancer Hijacking Mechanism for High-Risk Factors in Human T-Lineage Acute Lymphoblastic Leukemia ]]> https://biorxiv.org/content/10.1101/2020.03.11.988279v1?rss=1 Yang, L. Chen, F. Zhu, H. Chen, Y. Dong, B. Shi, M. Wang, W. Jiang, Q. Zhang, L. Huang, X. Zhang, M. Q. Wu, H. 2020-03-12 doi:10.1101/2020.03.11.988279 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ Structures of a P4-ATPase lipid flippase in lipid bilayers ]]> https://biorxiv.org/content/10.1101/2020.03.14.992305v1?rss=1 He, Y. Xu, J. Wu, X. Li, L. 2020-03-15 doi:10.1101/2020.03.14.992305 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ Identification and functional analysis of long non-coding RNAs in autism spectrum disorders ]]> https://biorxiv.org/content/10.1101/2020.03.15.986497v1?rss=1 Tong, Z. Zhou, Y. Wang, J. 2020-03-16 doi:10.1101/2020.03.15.986497 Cold Spring Harbor Laboratory Press 2020-03-16 <![CDATA[ DNA methylation is indispensable for leukemia inhibitory factor dependent embryonic stem cells reprogramming ]]> https://biorxiv.org/content/10.1101/2020.03.17.994939v1?rss=1 Bao, S. Wu, B. Li, Y. Li, B. Zhang, B. Wang, Y. Li, L. Peng, G. Fu, Y. Li, S. Tang, F. Li, X. 2020-03-18 doi:10.1101/2020.03.17.994939 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ Click-ExM enables expansion microscopy for all biomolecules ]]> https://biorxiv.org/content/10.1101/2020.03.19.998039v1?rss=1 Sun, D.-e. Fan, X. Zhang, H. Huang, Z. Tang, Q. Li, W. Bai, J. Lei, X. Chen, X. 2020-03-20 doi:10.1101/2020.03.19.998039 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Sulfopin, a selective covalent inhibitor of Pin1, blocks Myc-driven tumor initiation and growth in vivo ]]> https://biorxiv.org/content/10.1101/2020.03.20.998443v1?rss=1 Dubiella, C. Pinch, B. J. Zaidman, D. Manz, T. D. Poon, E. He, S. Resnick, E. Langer, E. M. Daniel, C. J. Seo, H.-S. Chen, Y. Ficarro, S. B. Jamin, Y. Lian, X. Kibe, S. Kozono, S. Koikawa, K. Doctor, Z. M. Nabet, B. Browne, C. M. Yang, A. Stoler-Barak, L. Shah, R. B. Vangos, N. E. Geffken, E. A. Oren, R. Sidi, S. Shulman, Z. Wang, C. Marto, J. A. Dhe-Paganon, S. Look, T. Zhou, X. Z. Lu, K. P. Sears, R. C. Chesler, L. Gray, N. S. London, N. 2020-03-21 doi:10.1101/2020.03.20.998443 Cold Spring Harbor Laboratory Press 2020-03-21 <![CDATA[ Glycoengineering of NK cells with glycan ligands of CD22 and selectins for B-cell lymphoma therapy ]]> https://biorxiv.org/content/10.1101/2020.03.23.004325v1?rss=1 Hong, S. Yu, C. Wang, P. Shi, Y. Cheng, B. CHEN, M. Chapla, D. G. Reigh, N. Narimatsu, Y. Chen, X. Clausen, H. Moremen, K. W. Macauley, M. S. Paulson, J. C. Wu, P. 2020-03-25 doi:10.1101/2020.03.23.004325 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein ]]> https://biorxiv.org/content/10.1101/2020.03.24.005561v1?rss=1 Liu, H. Lupala, C. Li, X. Lei, J. Chen, H. Qi, J. Su, X. 2020-03-27 doi:10.1101/2020.03.24.005561 Cold Spring Harbor Laboratory Press 2020-03-27 <![CDATA[ The Genomic Formation of Human Populations in East Asia ]]> https://biorxiv.org/content/10.1101/2020.03.25.004606v1?rss=1 Wang, C.-C. Yeh, H.-Y. Popov, A. N. Zhang, H.-Q. Matsumura, H. Sirak, K. Cheronet, O. Kovalev, A. Rohland, N. Kim, A. M. Bernardos, R. Tumen, D. Zhao, J. Liu, Y.-C. Liu, J.-Y. Mah, M. Mallick, S. Wang, K. Zhang, Z. Adamski, N. Broomandkhoshbacht, N. Callan, K. Culleton, B. J. Eccles, L. Lawson, A. M. Michel, M. Oppenheimer, J. Stewardson, K. Wen, S. Yan, S. Zalzala, F. Chuang, R. Huang, C.-J. Shiung, C.-C. Nikitin, Y. G. Tabarev, A. V. Tishkin, A. A. Lin, S. Sun, Z.-Y. Wu, X.-M. Yang, T.-L. Hu, X. Chen, L. Du, H. Bayarsaikhan, J. Mijiddorj, E. Erde 2020-03-25 doi:10.1101/2020.03.25.004606 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Comparative effects of oncogenic mutations G12C, G12V, G13D, and Q61H on local conformations and dynamics of K-Ras ]]> https://biorxiv.org/content/10.1101/2020.03.26.010710v1?rss=1 Vatansever, S. Erman, B. Gumus, Z. H. 2020-03-29 doi:10.1101/2020.03.26.010710 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ New and improved GRAB fluorescent sensors for monitoring dopaminergic activity in vivo ]]> https://biorxiv.org/content/10.1101/2020.03.28.013722v1?rss=1 Sun, F. Zhou, J. Dai, B. Qian, T. Zeng, J. Li, X. Zhuo, Y. Zhang, Y. Tan, K. Feng, J. Dong, H. Qian, C. Lin, D. Cui, G. Li, Y. 2020-03-28 doi:10.1101/2020.03.28.013722 Cold Spring Harbor Laboratory Press 2020-03-28 <![CDATA[ Hormone Receptor-status Prediction in Breast Cancer Using Gene Expression Profiles and Their Macroscopic Landscape ]]> https://biorxiv.org/content/10.1101/2020.03.29.014050v1?rss=1 Yoon, S. Won, H. S. Kang, K. Qiu, K. Park, W. J. Ko, Y. H. 2020-03-30 doi:10.1101/2020.03.29.014050 Cold Spring Harbor Laboratory Press 2020-03-30 <![CDATA[ Revealing the functions of supra-temporal and insular auditory responsive areas in humans ]]> https://biorxiv.org/content/10.1101/2020.03.30.015289v1?rss=1 65%), while sparsely on InsP (9.49%). The results of cortico-cortical evoked potentials (CCEPs) showed strong bidirectional connectivity within supra-temporal areas, but weak connectivity between supra-temporal areas and InsP. These findings suggest that even the InsP has similar basic auditory response properties to the primary or non-primary cortex, it may not directly participate in the formation of auditory perception. ]]> Wang, Q. Luo, L. Xu, N. Wang, J. Gao, Y. Li, S. Wang, M. Teng, P. Guan, Y. Zhou, J. Tian, X. Luan, G. 2020-03-31 doi:10.1101/2020.03.30.015289 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ Behavioral and neural decomposition of skull-induced death awareness ]]> https://biorxiv.org/content/10.1101/2020.03.31.018309v1?rss=1 Gao, T. Pu, Y. Zhou, J. Zheng, G. Zhou, Y. Han, S. 2020-04-01 doi:10.1101/2020.03.31.018309 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Polygenic adaptation of rosette growth variation in Arabidopsis thaliana populations ]]> https://biorxiv.org/content/10.1101/2020.03.31.018341v1?rss=1 de Meaux, J. Wieters, B. Steige, K. He, F. Koch, E. Ramos-Onsins, S. Gu, H. Y. Guo, Y. Sunyaev, S. 2020-03-31 doi:10.1101/2020.03.31.018341 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ Transformation of single-cell three-dimensional genome structure during postnatal development of the mammalian brain ]]> https://biorxiv.org/content/10.1101/2020.04.02.022657v1?rss=1 Tan, L. Xing, D. Daley, N. Xie, X. S. 2020-04-03 doi:10.1101/2020.04.02.022657 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ High affinity of Skp to OmpC revealed by single-molecule detection ]]> https://biorxiv.org/content/10.1101/2020.04.03.022855v1?rss=1 Pan, S. Yang, C. Zhao, X. S. 2020-04-03 doi:10.1101/2020.04.03.022855 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ Annulohypoxylon sp. strain MUS1, an Endophyte isolated from Taxus wallichiana Zucc. produces Taxol and Other Bioactive Metabolites ]]> https://biorxiv.org/content/10.1101/2020.04.05.025858v1?rss=1 Gauchan, D. P. Velez, H. Acharya, A. Ostman, J. R. Lunden, K. Elfstrand, M. Garcia Gil, M. R. 2020-04-05 doi:10.1101/2020.04.05.025858 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Trade-Offs between Speed, Accuracy, and Dissipation in tRNAIle Aminoacylation ]]> https://biorxiv.org/content/10.1101/2020.04.06.027615v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@f4f4e1org.highwire.dtl.DTLVardef@1f8e45forg.highwire.dtl.DTLVardef@1591e16org.highwire.dtl.DTLVardef@1c650b0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yu, Q. Mallory, J. D. Kolomeisky, A. Ling, J. Igoshin, O. A. 2020-04-07 doi:10.1101/2020.04.06.027615 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Vulnerabilities of the SARS-CoV-2 virus to proteotoxicity -- opportunity for repurposed chemotherapy of COVID-19 infection ]]> https://biorxiv.org/content/10.1101/2020.04.07.029488v1?rss=1 Al-Motawa, M. Abbas, H. Wijten, P. de la Fuente, A. Xue, M. Rabbani, N. Thornalley, P. 2020-04-09 doi:10.1101/2020.04.07.029488 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ D4: Deep Drug-drug interaction Discovery and Demystification ]]> https://biorxiv.org/content/10.1101/2020.04.08.032011v1?rss=1 Noor, A. Wang, L. Barnawi, A. Noor, R. Assiri, A. A. Bukhari, S. A. C. Hoehndorf, R. 2020-04-09 doi:10.1101/2020.04.08.032011 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ CBRPP: a new RNA-centric method to study RNA-protein interactions ]]> https://biorxiv.org/content/10.1101/2020.04.09.033290v1?rss=1 Li, Y. Liu, S. Cao, L. Luo, Y. Du, H. Li, S. You, F. 2020-04-09 doi:10.1101/2020.04.09.033290 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ sTAM: An Online Tool for the Discovery of miRNA-set Level Disease Biomarkers ]]> https://biorxiv.org/content/10.1101/2020.04.10.035345v1?rss=1 Shi, J. Cui, Q. 2020-04-10 doi:10.1101/2020.04.10.035345 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro ]]> https://biorxiv.org/content/10.1101/2020.04.10.035824v1?rss=1 Liu, H. Ye, F. Sun, Q. Liang, H. Li, C. Lu, R. Huang, B. Tan, W. Lai, L. 2020-04-12 doi:10.1101/2020.04.10.035824 Cold Spring Harbor Laboratory Press 2020-04-12 <![CDATA[ Genomic Architecture of Cells in Tissues (GeACT): Study of Human Mid-gestation Fetus ]]> https://biorxiv.org/content/10.1101/2020.04.12.038000v1?rss=1 Tian, F. Zhou, F. Li, X. Ma, W. Wu, H. Yang, M. Chapman, A. R. Lee, D. F. Tan, L. Xing, D. Yin, G. Semayel, A. Wang, J. Wang, J. Sun, W. He, R. Zhang, S. Cao, Z. Wei, L. Lu, S. Yang, D. Mao, Y. Gao, Y. Chen, K. Zhang, Y. Liu, X. Yong, J. Yan, L. Huang, Y. Qiao, J. Tang, F. Gao, G. Xie, X. S. 2020-04-13 doi:10.1101/2020.04.12.038000 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication ]]> https://biorxiv.org/content/10.1101/2020.04.17.033415v1?rss=1 Yurtman, E. Özer, O. Yüncü, E. Dagtas, N. D. Koptekin, D. Cakan, Y. G. Özkan, M. Akbaba, A. Kaptan, D. Atag, G. Vural, K. B. Gündem, C. Y. Martin, L. Kılınc, G. M. Ghalichi, A. Acan, S. C. Yaka, R. Saglıcan, E. Lagerholm, V. K. Krzewinska, M. Piskin, E. Sevketoglu, M. Bilgin, C. C. Atakuman, C. Erdal, Y. S. Sürer, E. Lenstra, J. A. Yorulmaz, S. Abazari, F. Sadati, J. H. Baird, D. Bıcakcı, E. Cevik, O. Gerritsen, F. Özbal, R. Götherström, A. Somel, M. Togan, I. Özer, F. 2020-04-18 doi:10.1101/2020.04.17.033415 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Pseudomonas aeruginosa biofilms display carbohydrate ligands for CD206 and CD209 that interfere with their receptor function ]]> https://biorxiv.org/content/10.1101/2020.04.20.051292v1?rss=1 132,000Da) with KDs in the nM range. HMW preparations contain 74.9-80.9% mannose, display -mannan segments and alter the morphology of human dendritic cells without causing obvious changes in cytokine responses. Finally, HMW interferes with the endocytic activity of cell-associated MR and DC-SIGN. This work identifies MR and DC-SIGN as receptors for bacterial biofilms and highlights the potential for biofilm-associated carbohydrates as immunomodulators through engagement of C-type lectin receptors. Author SummarySelective engagement of pattern recognition receptors during infection guides the decision-making process during induction of immune responses. This work identifies mannose-rich carbohydrates within bacterial biofilms as novel molecular patterns associated with bacterial infections. P. aeruginosa biofilms and biofilm-derived carbohydrates bind two important lectin receptors, MR (CD206) and DC-SIGN (CD209), involved in recognition of self and immune evasion. Abundance of MR and DC-SIGN ligands in the context of P. aeruginosa biofilms could impact immune responses and promote chronic infection. ]]> Singh, S. Almuhanna, Y. Alshahrani, M. Lowman, D. Rice, P. J. Gell, C. Ma, Z. Graves, B. M. Jackson, D. Lee, K. Kelkar, R. Koranteng, J. Mitchell, D. da Silva, A. Hussain, F. Yilmaz, G. Mastrotto, F. Irie, Y. Williams, P. Williams, D. L. Camara, M. Martinez-Pomares, L. 2020-04-20 doi:10.1101/2020.04.20.051292 Cold Spring Harbor Laboratory Press 2020-04-20 <![CDATA[ Cellbow: a robust customizable cell segmentation program ]]> https://biorxiv.org/content/10.1101/2020.04.21.052597v1?rss=1 Ren, H. Zhao, M. Liu, B. Yao, R. Liu, Q. Ren, Z. Wu, Z. Gao, Z. Yang, X. Tang, C. 2020-04-22 doi:10.1101/2020.04.21.052597 Cold Spring Harbor Laboratory Press 2020-04-22 <![CDATA[ Structural basis for human TRPC5 channel inhibition by two distinct inhibitors ]]> https://biorxiv.org/content/10.1101/2020.04.21.052910v1?rss=1 Song, K. Wei, M. Guo, W. Kang, Y. Wu, J.-X. Chen, L. 2020-04-21 doi:10.1101/2020.04.21.052910 Cold Spring Harbor Laboratory Press 2020-04-21 <![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? The ability of incretins to bypass defects in mitochondrial function might be exploited by the design of new agonists which target this pathway. ]]> Georgiadou, E. Muralidharan, C. Martinez, M. Chabosseau, P. Tomas, A. Wern, F. Y. S. Stylianides, T. Rothery, S. M. Gregorio, A. D. Leclerc, I. Ali, Y. Linnemann, A. K. Rodriguez, T. A. Rutter, G. A. 2020-04-24 doi:10.1101/2020.04.22.055384 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Cytotoxicity evaluation of chloroquine and hydroxychloroquine in multiple cell lines and tissues by dynamic imaging system and PBPK model ]]> https://biorxiv.org/content/10.1101/2020.04.22.056762v1?rss=1 Yang, J. Wu, M. Liu, X. Liu, Q. Guo, Z. Yao, X. Liu, Y. Cui, C. Li, H. Song, C. Liu, D. Xue, L. 2020-04-27 doi:10.1101/2020.04.22.056762 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ TRPM7 kinase-mediated immunomodulation in macrophage plays a central role in magnesium ion-induced bone regeneration ]]> https://biorxiv.org/content/10.1101/2020.04.24.059881v1?rss=1 Qiao, W. Wong, K. H. M. Shen, J. Wang, W. Wu, J. Li, J. Lin, Z. Chen, Z. Matinlinna, J. P. Zheng, Y. Wu, S. Liu, X. Lai, K. P. Chen, Z. Lam, Y. W. Cheung, K. M. C. Yeung, K. W. K. 2020-04-25 doi:10.1101/2020.04.24.059881 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Sessile bacterium unlocks ability of surface motility through mutualistic interspecies interaction ]]> https://biorxiv.org/content/10.1101/2020.04.24.060913v1?rss=1 Wang, M. Geng, S. Hu, B. Nie, Y. Wu, X.-L. 2020-04-25 doi:10.1101/2020.04.24.060913 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ MINERVA: A facile strategy for SARS-CoV-2 whole genome deep sequencing of clinical samples ]]> https://biorxiv.org/content/10.1101/2020.04.25.060947v1?rss=1 Chen, C. Li, J. Di, L. Jing, Q. Du, P. Song, C. Li, J. Li, Q. Cao, Y. Xie, S. Wu, A. R. Zeng, H. Huang, Y. Wang, J. 2020-04-25 doi:10.1101/2020.04.25.060947 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Generation and Validation of Versatile Inducible CRISPRi Embryonic Stem Cell and Mouse Models ]]> https://biorxiv.org/content/10.1101/2020.04.28.065854v1?rss=1 Wu, X. Li, R. Xia, X. Wang, X. Sun, X. Dai, Z. Huo, D. Zheng, H. Xiong, H. He, A. 2020-04-28 doi:10.1101/2020.04.28.065854 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Impairment of the Gβγ-SNAP25 brake on exocytosis enhances insulin action, protects against diet-induced obesity, and promotes adipocyte browning ]]> https://biorxiv.org/content/10.1101/2020.04.29.069138v1?rss=1 View larger version (46K): org.highwire.dtl.DTLVardef@2c1fa0org.highwire.dtl.DTLVardef@d076ceorg.highwire.dtl.DTLVardef@27e351org.highwire.dtl.DTLVardef@bce219_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ceddia, R. P. Zurawski, Z. Thompson Gray, A. Adegboye, F. Shi, F. Liu, D. McGuinness, O. P. Collins, S. Hamm, H. E. 2020-04-30 doi:10.1101/2020.04.29.069138 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ An artificial intelligence system reveals liquiritin inhibits SARS-CoV-2 by mimicking type I interferon ]]> https://biorxiv.org/content/10.1101/2020.05.02.074021v1?rss=1 Zhu, J. Deng, Y.-Q. Wang, X. Li, X.-F. Zhang, N.-N. Liu, Z. Zhang, B. Qin, C. Xie, Z. 2020-05-02 doi:10.1101/2020.05.02.074021 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ A pathway of NADPH diaphorase positivity between central canal and pial surface at anterior fissure in spinal cord: Supra fissure area with hypothesis configuring from dog, rat, monkey and pigeon ]]> https://biorxiv.org/content/10.1101/2020.05.02.074450v1?rss=1 Jia, Y. Li, Y. Hou, W. Li, F. Sun, H. Wu, X. Wen, X. Wei, Z. Rao, C. Xu, X. Masse, S. F. Abulikim, K. Xu, S. Du, G. Tan, H. 2020-05-04 doi:10.1101/2020.05.02.074450 Cold Spring Harbor Laboratory Press 2020-05-04 <![CDATA[ Computational analysis on the ACE2-derived peptides for neutralizing the ACE2 binding to the spike protein of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.05.03.075473v1?rss=1 lupala, c. s. Kumar, V. li, x. su, x. liu, h. 2020-05-04 doi:10.1101/2020.05.03.075473 Cold Spring Harbor Laboratory Press 2020-05-04 <![CDATA[ A GRAB sensor reveals activity-dependent non-vesicular somatodendritic adenosine release ]]> https://biorxiv.org/content/10.1101/2020.05.04.075564v1?rss=1 Wu, Z. Cui, Y. Wang, H. Song, K. Yuan, Z. Dong, A. Wu, H. Wan, Y. Pan, S. Peng, W. Jing, M. Xu, M. Luo, M. Li, Y. 2020-05-05 doi:10.1101/2020.05.04.075564 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ An in silico approach to identification, categorization and prediction of nucleic acid binding proteins ]]> https://biorxiv.org/content/10.1101/2020.05.05.078741v1?rss=1 Xu, L. Jiang, S. Zou, Q. 2020-05-07 doi:10.1101/2020.05.05.078741 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Roles of developmentally regulated KIF2A alternative isoforms in cortical neuron migration and differentiation ]]> https://biorxiv.org/content/10.1101/2020.05.07.081216v1?rss=1 Akkaya, C. Atak, D. Kamacioglu, A. Akarlar, B. A. Guner, G. Bayam, E. Taskin, A. C. Ozlu, N. Ince Dunn, G. 2020-05-07 doi:10.1101/2020.05.07.081216 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum ]]> https://biorxiv.org/content/10.1101/2020.05.10.087585v1?rss=1 800,000 individual nuclei from 45 regions spanning the adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei, and use the resulting data to define 491,818 candidate cis regulatory DNA elements in 160 distinct sub-types. We link a significant fraction of them to putative target genes expressed in diverse cerebral cell types and uncover transcriptional regulators involved in a broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Our results provide a foundation for comprehensive analysis of gene regulatory programs of the mammalian brain and assist in the interpretation of non-coding risk variants associated with various neurological disease and traits in humans. To facilitate the dissemination of information, we have set up a web portal (http://catlas.org/mousebrain). ]]> Li, Y. Preissl, S. Hou, X. Zhang, z. Zhang, K. Fang, R. Qiu, Y. Poirion, O. Li, B. Yan, Y. Liu, H. Wang, X. Han, J. Y. Lucero, J. Kuan, S. Gorkin, D. Nunn, M. Mukamel, E. A. Behrens, M. M. Ecker, J. R. Ren, B. 2020-05-11 doi:10.1101/2020.05.10.087585 Cold Spring Harbor Laboratory Press 2020-05-11 <![CDATA[ Modeling the IL-2-Teff-Treg system in Systemic Lupus Erythematosus patients: possible mechanism and treatment strategies ]]> https://biorxiv.org/content/10.1101/2020.05.14.095513v1?rss=1 Gao, X. Sun, X. He, J. Li, F. 2020-05-15 doi:10.1101/2020.05.14.095513 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Seesaw Conformations of Npl4 in the Human p97 Complex and the Inhibitory Mechanism of a Disulfiram Derivative ]]> https://biorxiv.org/content/10.1101/2020.05.18.103085v1?rss=1 Pan, M. Zheng, Q. Yu, Y. Ai, H. Xie, Y. Zeng, X. Wang, C. Liu, L. Zhao, M. 2020-05-20 doi:10.1101/2020.05.18.103085 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Computational study on ratio-sensing in yeast galactose utilization pathway ]]> https://biorxiv.org/content/10.1101/2020.05.19.103903v1?rss=1 Hong, J. Hua, B. Tang, C. Springer, M. 2020-05-19 doi:10.1101/2020.05.19.103903 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ High burden of Mycoplasma genitalium and other reproductive tract infections among pregnant women in Papua New Guinea ]]> https://biorxiv.org/content/10.1101/2020.05.22.109983v1?rss=1 Scoullar, M. J. L. Boeuf, P. Peach, E. Fidelis, R. Tokmun, K. Melepia, P. Elijah, A. Bradshaw, C. S. Fehler, G. Siba, P. M. Erskine, S. Mokany, E. Kennedy, E. Umbers, A. J. Luchters, S. Robinson, L. J. Wong, N. C. Vallely, A. Badman, S. G. Vallely, L. M. Fowkes, F. J. I. Morgan, C. Pomat, W. Crabb, B. S. Beeson, J. G. 2020-05-23 doi:10.1101/2020.05.22.109983 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ Protocadherin 7 localizes to the plasma membrane during mitosis and promotes cytokinesis by a palmitoylation-dependent mechanism ]]> https://biorxiv.org/content/10.1101/2020.05.24.111831v1?rss=1 Ozkan-Kucuk, N. E. Qureshi, M. H. Yigit, B. N. Kamacioglu, A. Bavili, N. Kiraz, A. Ozlu, N. 2020-05-24 doi:10.1101/2020.05.24.111831 Cold Spring Harbor Laboratory Press 2020-05-24 <![CDATA[ Targeted CRISPR screening identifies PRMT5 as synthetic lethality combinatorial target with gemcitabine in pancreatic cancer cells ]]> https://biorxiv.org/content/10.1101/2020.05.25.112896v1?rss=1 Wei, X. Yang, J. Adair, S. J. Kuscu, C. Lee, K. Y. Kane, W. O'Hara, P. E. Liu, D. Demirlenk, Y. M. Habieb, A. H. Yilmaz, E. Dutta, A. Bauer, T. Adli, M. 2020-05-26 doi:10.1101/2020.05.25.112896 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ NF45/NF90-mediated rDNA transcription provides a novel target for immunosuppressant development ]]> https://biorxiv.org/content/10.1101/2020.05.26.116897v1?rss=1 Hsiang-i, T. Zeng, X. Liu, L. Xin, S. Wu, Y. Xu, Z. Liu, G. Bi, Z. Su, D. Yang, M. Wang, C. Zhao, J. Eriksson, J. E. Deng, W. Cheng, F. Chen, H. 2020-05-28 doi:10.1101/2020.05.26.116897 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Light-Sheet Fluorescence Imaging Charts the Gastrula Origin of Vascular Endothelial Cells in Early Zebrafish Embryos ]]> https://biorxiv.org/content/10.1101/2020.05.27.118661v1?rss=1 Xiong, J.-W. Pang, M. Bai, L. Zong, W. Wang, X. Bu, Y. Xiong, C. Zheng, J. Li, J. Gao, W. Feng, Z. Chen, L. Zhang, J. Cheng, H. Zhu, X. 2020-05-28 doi:10.1101/2020.05.27.118661 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Deep learning approach for automated cancer detection and tumor proportion score estimation of PD-L1 expression in lung adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2020.05.31.126797v1?rss=1 Wu, J. Liu, C. Liu, X. Sun, W. Li, L. Zhang, Y. Zhang, J. Wang, H. Liu, X. Yang, X. Huang, X. Lin, D. Ling, S. 2020-06-01 doi:10.1101/2020.05.31.126797 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ Epigenetic Consequences of Hormonal Interactions between Opposite-sex Twin Fetuses ]]> https://biorxiv.org/content/10.1101/2020.06.09.141242v1?rss=1 Kong, S. Peng, Y. Wei, C. Ma, X. Wei, Y. Zhao, Y. Li, R. Yan, L. Qiao, J. 2020-06-09 doi:10.1101/2020.06.09.141242 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Thiamine pyrophosphokinase deficiency induces Alzheimer's pathology ]]> https://biorxiv.org/content/10.1101/2020.06.09.141358v1?rss=1 Sang, S. Qian, T. Cai, F. Qiu, H. Xu, Y. Zhang, Y. Zhang, Q. Huang, S. Jiang, D. Wu, Y. Tong, H. Pan, X. Wang, C. Cheng, X. Zhong, K. Guan, Y. Zhu, M. X. Yu, X. Song, W. Zhong, C. 2020-06-11 doi:10.1101/2020.06.09.141358 Cold Spring Harbor Laboratory Press 2020-06-11 <![CDATA[ Structural and Functional Analyses of Hub MicroRNAs in an Integrated Gene Regulatory Network of Arabidopsis ]]> https://biorxiv.org/content/10.1101/2020.06.10.145185v1?rss=1 Gao, Z. Li, J. Li, L. Yang, Y. Li, J. Fu, C. Zhu, D. He, H. Cai, H. Li, L. 2020-06-12 doi:10.1101/2020.06.10.145185 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ RPRH: a web-based tool for the inference of potential roles of plant microRNAs in human body ]]> https://biorxiv.org/content/10.1101/2020.06.11.145367v1?rss=1 Gao, Y. Jia, K. Cui, C. Zhou, Y. Cui, Q. 2020-06-12 doi:10.1101/2020.06.11.145367 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ A hybrid Embden-Meyerhof-Parnas pathway provides a synthetic link between sugar and phosphate metabolism ]]> https://biorxiv.org/content/10.1101/2020.06.11.147082v1?rss=1 Lee, Y. Cho, H. J. Woo, H. M. 2020-06-12 doi:10.1101/2020.06.11.147082 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Structure of a dominant negative mutant reveals a stalled intermediate in anthrax protective antigen pore maturation ]]> https://biorxiv.org/content/10.1101/2020.06.15.152231v1?rss=1 Scott, H. Huang, W. Ganti, S. Zhang, K. Mehzabeen, N. Day, A. Battaile, K. P. Lovell, S. G. Bann, J. Taylor, D. J. 2020-06-15 doi:10.1101/2020.06.15.152231 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Sequence structure organizes items in varied latent states of working memory neural network ]]> https://biorxiv.org/content/10.1101/2020.06.20.162438v1?rss=1 Huang, Q. Zhang, H. Luo, H. 2020-06-20 doi:10.1101/2020.06.20.162438 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Characterization of a gene-trap knockout mouse model of Scn2a encoding voltage-gated sodium channel Nav1.2 ]]> https://biorxiv.org/content/10.1101/2020.06.23.150367v1?rss=1 Eaton, M. Zhang, J. Ma, Z. Park, A. C. Lietzke, E. E. Romero, C. M. Liu, Y. Coleman, E. R. Chen, X. Xiao, T. Huang, Z. Skarnes, W. C. Koss, W. A. Yang, Y. 2020-06-23 doi:10.1101/2020.06.23.150367 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ Mutant glucocorticoid receptor binding elements on Interleukin-6 promoter regulate dexamethasone effects ]]> https://biorxiv.org/content/10.1101/2020.06.24.168666v1?rss=1 Chang, W.-T. Hong, M.-Y. Chen, C.-L. Tsai, C.-C. Hwang, C.-Y. Chuang, C.-C. 2020-06-24 doi:10.1101/2020.06.24.168666 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Preferred endocytosis of amyloid precursor protein from cholesterol-enriched lipid raft microdomains ]]> https://biorxiv.org/content/10.1101/2020.06.26.172874v1?rss=1 Cho, Y. Y. Kwon, O.-H. Chung, S. 2020-06-26 doi:10.1101/2020.06.26.172874 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Berberine reverses multidrug resistance in Candida albicans by hijacking the drug efflux pump Mdr1p ]]> https://biorxiv.org/content/10.1101/2020.06.26.173484v1?rss=1 Tong, Y. Sun, N. Wang, X. Wei, Q. Zhang, Y. Huang, R. Pu, Y. Dai, H. Ren, B. Pei, G. Song, F. Zhu, G. Wang, X. Xia, X. Chen, X. Jiang, L. Zhang, J. Ouyang, L. Zhang, B. Jiang, Y. Liu, X. Calderone, R. Bai, F. Zhang, L. Alterovitz, G. 2020-06-26 doi:10.1101/2020.06.26.173484 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Genetics of human gut microbiome composition ]]> https://biorxiv.org/content/10.1101/2020.06.26.173724v1?rss=1 Kurilshikov, A. Medina-Gomez, C. Bacigalupe, R. Radjabzadeh, D. Wang, J. Demirkan, A. Le Roy, C. I. Raygoza Garay, J. A. Finnicum, C. Liu, X. Zhernakova, D. Bonder, M. J. Hansen, T. H. Frost, F. Ruhlemann, M. C. Turpin, W. Moon, J.-Y. Kim, H.-N. Lull, K. Barkan, E. Shah, S. A. Fornage, M. Szopinska-Tokov, J. Wallen, Z. Borisevich, D. Agreus, L. Andreasson, A. Bang, C. Bedrani, L. Bell, J. T. Bisgaard, H. Boehnke, M. Boomsma, D. I. Burk, R. D. Claringbould, A. Croitoru, K. Davies, G. Van Duijn, C. Duijts, L. Falony, G. Fu, J. van der Graaf, A. Hansen, T 2020-06-28 doi:10.1101/2020.06.26.173724 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ Ultra-Fast Homomorphic Encryption Models enable Secure Outsourcing of Genotype Imputation ]]> https://biorxiv.org/content/10.1101/2020.07.02.183459v1?rss=1 Kim, M. Harmanci, A. O. Bossuat, J.-P. Carpov, S. Cheon, J. H. Chilotti, I. Cho, W. Froelicher, D. Gama, N. Georgieva, M. Hong, S. Hubaux, J.-P. Kim, D. Lauter, K. Ma, Y. Ohno-Machado, L. Sofia, H. J. Son, Y. Song, Y. Troncoso-Pastoriza, J. R. Jiang, X. 2020-07-04 doi:10.1101/2020.07.02.183459 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Structures of potent and convergent neutralizing antibodies bound to the SARS-CoV-2 spike unveil a unique epitope responsible for exceptional potency ]]> https://biorxiv.org/content/10.1101/2020.07.09.195263v1?rss=1 Shuo Du Yunlong Cao Qinyu Zhu Guopeng Wang Xiaoxia Du Runsheng He Hua Xu Yinghui Zheng Bo Wang Yali Bai Chenggong Ji Ayijiang Yisimayi Qisheng Wang Ning Gao X. Sunney Xie Xiao-dong Su Junyu Xiao 2020-07-09 doi:10.1101/2020.07.09.195263 Cold Spring Harbor Laboratory Press 2020-07-09 <![CDATA[ Cognitive and Neural State Dynamics of Story Comprehension ]]> https://biorxiv.org/content/10.1101/2020.07.10.194647v1?rss=1 Hayoung Song Bo-yong Park Hyunjin Park Won Mok Shim 2020-07-10 doi:10.1101/2020.07.10.194647 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Induction of a SALL4-dependency for targeted cancer therapy ]]> https://biorxiv.org/content/10.1101/2020.07.10.197434v1?rss=1 Junyu Yang Chong Gao Miao Liu Zhiyuan Chen Yao-Chung Liu Junsu Kwon Jun Qi Xi Tian Alicia Stein Yanjing Liu Nikki R. Kong Yue Wu Shenyi Yin Jianzhong Xi Hongbo Luo Leslie E. Silberstein Julie A.I. Thoms Ashwin Unnikrishnan John E. Pimanda Daniel Geoffrey Tenen LI Chai 2020-07-11 doi:10.1101/2020.07.10.197434 Cold Spring Harbor Laboratory Press 2020-07-11 <![CDATA[ A simple and efficient metric quantifying druggable property of chemical small molecules ]]> https://biorxiv.org/content/10.1101/2020.07.13.199752v1?rss=1 Huang, C. Yang, J. Cui, Q. 2020-07-13 doi:10.1101/2020.07.13.199752 Cold Spring Harbor Laboratory Press 2020-07-13 <![CDATA[ Fibroblast growth factor 9 stimulates neurite outgrowth through NF-kB signaling in striatal cell Huntington's disease models ]]> https://biorxiv.org/content/10.1101/2020.07.17.207837v1?rss=1 Yusuf, I. O. Chen, H.-M. Cheng, P.-H. Chang, C.-Y. Tsai, S.-J. Chuang, J.-I. Wu, C.-C. Huang, B.-M. Sun, H. S. Chen, C.-M. Yang, S.-H. 2020-07-17 doi:10.1101/2020.07.17.207837 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Structural basis for the inhibition of the papain-like protease of SARS-CoV-2 by small molecules ]]> https://biorxiv.org/content/10.1101/2020.07.17.208959v1?rss=1 Fu, Z. Huang, B. Tang, J. Liu, S. Liu, M. Ye, Y. Liu, Z. Xiong, Y. Cao, D. Li, J. Niu, X. Zhou, H. Zhao, Y. J. Zhang, G. Huang, H. 2020-07-18 doi:10.1101/2020.07.17.208959 Cold Spring Harbor Laboratory Press 2020-07-18 <![CDATA[ Gaze dynamics of feature-based distractor inhibition under the prior-knowledge and expectation ]]> https://biorxiv.org/content/10.1101/2020.07.19.210781v1?rss=1 Wen, W. Zhang, Y. Li, S. 2020-07-19 doi:10.1101/2020.07.19.210781 Cold Spring Harbor Laboratory Press 2020-07-19 <![CDATA[ Distributed Sampling-based Bayesian Inference in Coupled Neural Circuits ]]> https://biorxiv.org/content/10.1101/2020.07.20.212126v1?rss=1 Zhang, W. Lee, T. S. Doiron, B. Wu, S. 2020-07-22 doi:10.1101/2020.07.20.212126 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ The PIF1-MIR408-Plantacyanin Repression Cascade Regulates Light Dependent Seed Germination ]]> https://biorxiv.org/content/10.1101/2020.07.20.212340v1?rss=1 Jiang, A. Guo, Z. Pan, J. Zhuang, Y. Zuo, D. Hao, C. Gao, Z. Xin, P. Chu, J. Zhong, S. Li, L. 2020-07-21 doi:10.1101/2020.07.20.212340 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Distinct brain networks coupled with the parietal cortex represent target location inside and outside the visual field ]]> https://biorxiv.org/content/10.1101/2020.07.22.215517v1?rss=1 Zhang, B. Wang, F. Naya, Y. 2020-07-23 doi:10.1101/2020.07.22.215517 Cold Spring Harbor Laboratory Press 2020-07-23 <![CDATA[ Single-cell landscape of immunological responses in COVID-19 patients ]]> https://biorxiv.org/content/10.1101/2020.07.23.217703v1?rss=1 Wang, F.-S. Zhang, J.-Y. Wang, X. Xing, X. Xu, Z. Zhang, C. Song, J.-W. Fan, X. Xia, P. Fu, J.-L. Wang, S.-Y. Xu, R.-N. Dai, X.-P. Shi, L. Huang, L. Jiang, T.-J. Shi, M. Zhang, Y. Zumla, A. Maeurer, M. Bai, F. 2020-07-24 doi:10.1101/2020.07.23.217703 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ β-Coronaviruses use lysosomal organelles for cellular egress. ]]> https://biorxiv.org/content/10.1101/2020.07.25.192310v1?rss=1 Altan-Bonnet, N. Altan-Bonnet, G. Y. Ghosh, S. Dellibovi-Ragheb, T. Pak, E. Qiu, Q. Fisher, M. Takvorian, P. Bleck, C. Hsu, V. Fehr, A. Perlman, S. Straus, M. Whittaker, G. de Haan, C. A. 2020-07-25 doi:10.1101/2020.07.25.192310 Cold Spring Harbor Laboratory Press 2020-07-25 <![CDATA[ NanoReviser: An Error-correction Tool for Nanopore Sequencing Based on a Deep Learning Algorithm ]]> https://biorxiv.org/content/10.1101/2020.07.25.220855v1?rss=1 Wang, L. Qu, L. Yang, L. Wang, Y. Zhu, H. 2020-07-26 doi:10.1101/2020.07.25.220855 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ Structure of voltage-modulated sodium-selective NALCN-FAM155A channel complex ]]> https://biorxiv.org/content/10.1101/2020.07.26.221747v1?rss=1 Kang, Y. Wu, J.-X. Chen, L. 2020-07-26 doi:10.1101/2020.07.26.221747 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ The landscape of micro-inversions provides clues for population genetic analysis of humans ]]> https://biorxiv.org/content/10.1101/2020.07.27.218867v1?rss=1 Qu, L. Wang, L. He, F. Han, Y. Yang, L. Wang, M. D. Zhu, H. 2020-07-27 doi:10.1101/2020.07.27.218867 Cold Spring Harbor Laboratory Press 2020-07-27 <![CDATA[ Human Cytomegalovirus Drives WDR5 to the Virion Assembly Compartment to Facilitate Virion Assembly ]]> https://biorxiv.org/content/10.1101/2020.08.03.235630v1?rss=1 Luo, M.-H. Yang, B. Yao, Y. Wu, H. Yang, H. Ma, X.-H. Li, D. Wang, X.-Z. Huang, S.-N. Jiang, X. Cheng, S. Sun, J.-Y. Huang, Z.-L. Zhao, C. McVoy, M. A. Ahn, J.-H. Zeng, W.-B. Britt, W. J. Gong, S. 2020-08-04 doi:10.1101/2020.08.03.235630 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ SARS-CoV-2 genome analysis of strains in Pakistan reveals GH, S and L clade strains at the start of the pandemic ]]> https://biorxiv.org/content/10.1101/2020.08.04.234153v1?rss=1 Ghanchi, N. K. Masood, K. I. Nasir, A. Khan, W. Abidi, S. H. Shahid, S. Mahmood, S. F. Kanji, A. R. Razzak, S. A. Ansar, Z. Islam, N. Dharejo, M. B. Hasan, Z. Hasan, R. 2020-08-04 doi:10.1101/2020.08.04.234153 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Worldwide tracing of mutations and the evolutionary dynamics of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.08.07.242263v1?rss=1 Zhou, Z.-Y. Liu, H. Zhang, Y.-D. Wu, Y.-Q. Peng, M.-S. Li, A. Irwin, D. M. Li, H. Lu, J. Bao, Y. Lu, X. Liu, D. Zhang, Y.-P. 2020-08-12 doi:10.1101/2020.08.07.242263 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Protein kinase D1 phosphorylates CBX8 to facilitate the disassociation of PRC1 complex from p16 promoter and promotes cell senescence ]]> https://biorxiv.org/content/10.1101/2020.08.09.242891v1?rss=1 Su, Y. Liang, Y. Xu, C. Zhang, N. Liu, D. Li, G. Tong, T. Chen, J. 2020-08-10 doi:10.1101/2020.08.09.242891 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Antagonistic crosstalk fine-tunes sensitivities of IRE1 and PERK signaling during unfolded protein response ]]> https://biorxiv.org/content/10.1101/2020.08.09.243527v1?rss=1 Jiang, J. Qu, Y. Liu, X. Tang, C. Wei, P. 2020-08-10 doi:10.1101/2020.08.09.243527 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Bioinformatic Analysis Reveals That Some Mutations May Affect On Both Spike Structure Damage and Ligand Binding Site ]]> https://biorxiv.org/content/10.1101/2020.08.10.244632v1?rss=1 Aktas, E. 2020-08-10 doi:10.1101/2020.08.10.244632 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ ATF3 drives senescence by reconstructing accessible chromatin profiles ]]> https://biorxiv.org/content/10.1101/2020.08.13.249458v1?rss=1 Zhang, C. Zhang, X. Guan, Y. Huang, X. Zhang, L. Tian, X.-L. Tao, W. 2020-08-13 doi:10.1101/2020.08.13.249458 Cold Spring Harbor Laboratory Press 2020-08-13 <![CDATA[ Non-epigenetic mechanisms enable short memories of the environment for cell cycle commitment ]]> https://biorxiv.org/content/10.1101/2020.08.14.250704v1?rss=1 Qu, Y. Jiang, J. Liu, X. Yang, X. Tang, C. 2020-08-14 doi:10.1101/2020.08.14.250704 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Pancreatic α and β cells are globally phase-locked ]]> https://biorxiv.org/content/10.1101/2020.08.16.252304v1?rss=1 Ren, H. Li, Y. Yu, Y. Shi, B. Peng, X. Wu, S. Zhu, W. Yang, G. Yang, X. sneppen, k. Chen, L. Tang, C. 2020-08-17 doi:10.1101/2020.08.16.252304 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency ]]> https://biorxiv.org/content/10.1101/2020.08.16.252668v1?rss=1 Li, Y. Xue, B. Zhang, L. Su, Q. P. Zhang, M. Long, H. Wang, Y. Jin, Y. Hou, Y. Cao, Y. Li, G. sun, y. 2020-08-17 doi:10.1101/2020.08.16.252668 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Characteristics of fMRI responses to visual stimulation in anesthetized vs. awake mice ]]> https://biorxiv.org/content/10.1101/2020.08.17.253500v1?rss=1 DINH, T. N. A. Jung, W. B. Shim, H. Kim, S.-G. 2020-08-17 doi:10.1101/2020.08.17.253500 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ A Transferable Deep Learning Approach to Fast Screen Potent Antiviral Drugs against SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.08.28.271569v1?rss=1 Wang, S. Sun, Q. Xu, Y. Pei, J. Lai, L. 2020-08-28 doi:10.1101/2020.08.28.271569 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ Protein Phosphatase 1 in association with Bud14 inhibits mitotic exit in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2020.08.30.273946v1?rss=1 Kocakaplan, D. Karaburk, H. Kirdok, I. Erkan, S. N. Dilege, C. Caydasi, A. K. 2020-08-30 doi:10.1101/2020.08.30.273946 Cold Spring Harbor Laboratory Press 2020-08-30 <![CDATA[ Homeotic Regulation of Olfactory Receptor Choice via NFI-dependent Heterochromatic Silencing and Genomic Compartmentalization ]]> https://biorxiv.org/content/10.1101/2020.08.30.274035v1?rss=1 1000 olfactory receptor (OR) genes is stochastic but, yet, spatially organized in stereotypic anatomical segments, or "zones", along the dorsoventral axis of the mouse olfactory epithelium. We discovered that zonal OR expression is specified by OR chromatin structure and genome architecture during olfactory neuron differentiation. Specifically, across every zone dorsally expressed ORs have higher levels of heterochromatic marks and long-range contacts than ORs expressed ventrally. However, OR heterochromatin levels and frequency of genomic contacts between ORs gradually increase towards ventral zones. Consequently, ORs from dorsal indexes accumulate high H3K9me3/H3K79me3 enrichment and become silenced in ventral zones, while ORs from ventral indexes lack activating long-range genomic interactions and, thus, cannot be chosen in dorsal segments. This process is regulated by NFIA, B, and X gradients along the dorsoventral axis, triple deletion of which causes homeotic transformations on zonal OR expression, heterochromatin formation, and genomic compartmentalization. ]]> Bashkirova, E. Monahan, K. Campbell, C. E. Osinski, J. M. Tan, L. Schieren, I. Barnea, G. Xie, S. Gronostajski, R. M. Lomvardas, S. 2020-08-30 doi:10.1101/2020.08.30.274035 Cold Spring Harbor Laboratory Press 2020-08-30 <![CDATA[ Ecological specialization promotes diversity and diversification in the East Mediterranean genus Ricotia (Brassicaceae) ]]> https://biorxiv.org/content/10.1101/2020.08.30.274670v1?rss=1 ozudogru, b. karacaoglu, c. akaydin, g. erik, s. mummenhoff, k. SAGLAM, I. K. 2020-08-31 doi:10.1101/2020.08.30.274670 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Dynamic fluctuations of the locus coeruleus-norepinephrine system underlie sleep state transitions ]]> https://biorxiv.org/content/10.1101/2020.09.01.274977v1?rss=1 Kjaerby, C. Andersen, M. Hauglund, N. L. Ding, F. Wang, W. Xu, Q. Deng, S. Kang, N. Peng, S. Sun, Q. Dall, C. Joergensen, P. K. Feng, J. Li, Y. Weikop, P. Hirase, H. Nedergaard, M. 2020-09-02 doi:10.1101/2020.09.01.274977 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ Single-cell RNA-seq reveals early heterogeneity during ageing in yeast ]]> https://biorxiv.org/content/10.1101/2020.09.04.282525v1?rss=1 Zhang, Y. Wang, J. Sang, Y. Jin, S. Wang, X. Azad, G. K. McCormick, M. A. Kennedy, B. K. Li, Q. Wang, J. Zhang, X. Huang, Y. 2020-09-04 doi:10.1101/2020.09.04.282525 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ Loss of Kallmann syndrome-associated gene WDR11 disrupts primordial germ cell development by affecting canonical and non-canonical Hedgehog signalling ]]> https://biorxiv.org/content/10.1101/2020.09.06.284927v1?rss=1 Lee, J. Kim, Y. Ataliotis, P. Kim, H.-G. Kim, D.-W. Bennett, D. C. Brown, N. A. Layman, L. C. Kim, S.-H. 2020-09-06 doi:10.1101/2020.09.06.284927 Cold Spring Harbor Laboratory Press 2020-09-06 <![CDATA[ The structural basis of the oncogenic mutant K-Ras4B homodimers ]]> https://biorxiv.org/content/10.1101/2020.09.07.285783v1?rss=1 Kosoglu, K. Omur, M. E. Jang, H. Nussinov, R. Keskin, O. Gursoy, A. 2020-09-07 doi:10.1101/2020.09.07.285783 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing ]]> https://biorxiv.org/content/10.1101/2020.09.09.287987v1?rss=1 Durdagi, S. Dag, C. Dogan, B. Yigin, M. Avsar, T. Buyukdag, C. Erol, I. Ertem, F. B. Calis, S. Yildirim, G. Orhan, M. Guven, O. Aksoydan, B. Destan, E. Sahin, K. Besler, S. O. Oktay, L. Shafiei, A. Tolu, I. Ayan, E. Yuksel, B. Peksen, A. B. Gocenler, O. Yucel, A. D. Can, O. Ozabrahamyan, S. Olkan, A. Erdemoglu, E. Aksit, F. Tanisali, G. H. Yefanov, O. M. Barty, A. Tolstikova, A. Ketawala, G. K. Botha, S. Dao, E. H. Hayes, B. Liang, M. Seaberg, M. H. Hunter, M. S. Batyuk, A. Mariani, V. Su, Z. Poitevin, F. Yoon, C. H. Kupitz, C. J. Sierra, R. G. Sn 2020-09-09 doi:10.1101/2020.09.09.287987 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Small molecules inhibit SARS-COV-2 induced aberrant inflammation and viral replication in mice by targeting S100A8/A9-TLR4 axis ]]> https://biorxiv.org/content/10.1101/2020.09.09.288704v1?rss=1 Guo, Q. Zhao, Y. Li, J. Liu, J. Qin, C. Wang, X. You, F. Guo, X. Zhang, Z. Cao, L. Luo, Y. Wang, X. Wei, X. Chen, L. Bao, L. Deng, W. Zhu, H. Gao, R. 2020-09-09 doi:10.1101/2020.09.09.288704 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Coordination of two enhancers drives expression of olfactory trace amine-associated receptors ]]> https://biorxiv.org/content/10.1101/2020.09.10.288951v1?rss=1 Fei, A. Wu, W. Tan, L. Tang, C. Xu, Z. Huo, X. Bao, H. Johnson, M. Hartmann, G. Talay, M. Yang, C. Riegler, C. Joseph, K. Engert, F. Xie, S. Barnea, G. Liberles, S. Yang, H. Li, Q. 2020-09-11 doi:10.1101/2020.09.10.288951 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Tumor Edge-to-Core Transition Promotes Malignancy in Primary-to-Recurrent Glioblastoma Progression in a PLAGL1/CD109-mediated mechanism ]]> https://biorxiv.org/content/10.1101/2020.09.14.293753v1?rss=1 Li, C. Cho, H. J. Yamashita, D. Abdelrashid, M. Chen, Q. Bastola, S. Chagoya, G. A. Elsayed, G. Komarova, S. Ozaki, S. Ohtsuka, Y. Kunieda, T. I Kornblum, H. Kondo, T. Nam, D.-H. Nakano, I. 2020-09-15 doi:10.1101/2020.09.14.293753 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ Synchronous and Asynchronous Response in Dynamically Perturbed Proteins ]]> https://biorxiv.org/content/10.1101/2020.09.14.296111v1?rss=1 Erkip, A. Hacisuleyman, A. Erman, B. Erman, B. 2020-09-14 doi:10.1101/2020.09.14.296111 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ MicroRNA775 Promotes Intrinsic Leaf Size and Reduces Cell Wall Pectin Level via a Target Galactosyltransferase in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2020.09.17.301705v1?rss=1 Li, L. Zhang, H. Zhuang, Y. Guo, Z. Suo, Y. Du, J. Gao, Z. Pan, J. Li, L. Wang, T. Xiao, L. Qin, G. Jiao, Y. Cai, H. 2020-09-18 doi:10.1101/2020.09.17.301705 Cold Spring Harbor Laboratory Press 2020-09-18 <![CDATA[ On the Mathematics of RNA Velocity I: Theoretical Analysis ]]> https://biorxiv.org/content/10.1101/2020.09.19.304584v1?rss=1 Li, T. Shi, J. Wu, Y. Zhou, P. 2020-09-20 doi:10.1101/2020.09.19.304584 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ Proteasome Regulation by Reversible Tyrosine Phosphorylation at the Membrane ]]> https://biorxiv.org/content/10.1101/2020.09.20.305532v1?rss=1 Chen, L. Shu, X. Chen, Q. Wei, T. Wang, X. Wu, Q. Wang, H. Zhang, X. Liu, X. Zhang, Y. Zheng, S. Huang, L. Xiao, J. Jiang, C. Wang, Z. Yang, B. Guo, X. 2020-09-20 doi:10.1101/2020.09.20.305532 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ Structure and mechanism of human dual oxidase 1 complex ]]> https://biorxiv.org/content/10.1101/2020.09.23.309245v1?rss=1 Wu, J.-X. Liu, R. Song, K. Chen, L. 2020-09-23 doi:10.1101/2020.09.23.309245 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ SARS-CoV-2 and Malayan pangolin coronavirus infect human endoderm, ectoderm and induced lung progenitor cells ]]> https://biorxiv.org/content/10.1101/2020.09.25.313270v1?rss=1 Xiang, K. Hong, B. Lai, X. Chen, Y. Luo, T. An, X. Song, L. Zhuang, H. Fan, H. Li, T. Tong, Y.-G. 2020-09-25 doi:10.1101/2020.09.25.313270 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Mitochondria fragment and reassemble to initiate the formation and development of the nucleus ]]> https://biorxiv.org/content/10.1101/2020.09.29.319723v1?rss=1 Hou, B. Xu, Y. Li, E. Cao, P. Liu, S. Xi, Z. Yang, H. Huo, Y. Che, Y. Jiang, X. 2020-10-01 doi:10.1101/2020.09.29.319723 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ HiCORE: Hi-C analysis for identification of core chromatin loops with higher resolution and reliability ]]> https://biorxiv.org/content/10.1101/2020.10.01.322024v1?rss=1 Lee, H. Seo, P. J. 2020-10-01 doi:10.1101/2020.10.01.322024 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Gait-symmetry-based human-in-the-loop optimization for unilateral transtibial amputees with robotic prostheses ]]> https://biorxiv.org/content/10.1101/2020.10.04.325720v1?rss=1 Feng, Y. Wang, Q. Mao, C. 2020-10-05 doi:10.1101/2020.10.04.325720 Cold Spring Harbor Laboratory Press 2020-10-05 <![CDATA[ A fluorescent sensor for spatiotemporally resolved endocannabinoid dynamics in vitro and in vivo ]]> https://biorxiv.org/content/10.1101/2020.10.08.329169v1?rss=1 Dong, A. He, K. Dudok, B. Farrell, J. S. Guan, W. Liput, D. J. Puhl, H. L. Cai, R. Duan, J. Albarran, E. Ding, J. Lovinger, D. M. Li, B. Soltesz, I. Li, Y. 2020-10-08 doi:10.1101/2020.10.08.329169 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Attractive internuclear force drives the collective behavior of nuclear arrays in Drosophila embryos ]]> https://biorxiv.org/content/10.1101/2020.10.08.330845v1?rss=1 Wu, X. Kong, K. Xiao, W. Feng, L. 2020-10-08 doi:10.1101/2020.10.08.330845 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ A novel density-based neural mass model for simulating neuronal network dynamics with conductance-based synapses and membrane current adaptation ]]> https://biorxiv.org/content/10.1101/2020.10.09.334144v1?rss=1 Huang, C.-H. Lin, C.-C. K. 2020-10-10 doi:10.1101/2020.10.09.334144 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ Auxin guides germ cell specification in Arabidopsis anthers ]]> https://biorxiv.org/content/10.1101/2020.10.13.337634v1?rss=1 Zheng, Y. Wang, D. Ye, S. Chen, W. Li, G. Xu, Z. Bai, S. Zhao, F. 2020-10-14 doi:10.1101/2020.10.13.337634 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ DEBKS: A Tool to Detect Differentially Expressed Circular RNA ]]> https://biorxiv.org/content/10.1101/2020.10.14.336982v1?rss=1 Liu, Z. Ding, H. She, J. Chen, C. Zhang, W.-G. Yang, E. 2020-10-14 doi:10.1101/2020.10.14.336982 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ A connectome-wide functional signature of trait anger ]]> https://biorxiv.org/content/10.1101/2020.10.14.338863v1?rss=1 Kim, M. J. Elliott, M. L. Knodt, A. R. Hariri, A. R. 2020-10-15 doi:10.1101/2020.10.14.338863 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions ]]> https://biorxiv.org/content/10.1101/2020.10.15.339226v1?rss=1 Xiong, H. Luo, Y. Wang, Q. Yu, X. He, A. 2020-10-16 doi:10.1101/2020.10.15.339226 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs ]]> https://biorxiv.org/content/10.1101/2020.10.15.340794v1?rss=1 Lu, B. Yan, Y. Dong, L. Han, L. Liu, Y. Yu, J. Chen, J. Yi, D. Zhang, M. Wang, C. Wang, R. Wang, D. Wei, H. Liu, D. Yi, C. 2020-10-15 doi:10.1101/2020.10.15.340794 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Resolving transcriptional states and predicting lineages in the annelid Capitella teleta using single-cell RNAseq ]]> https://biorxiv.org/content/10.1101/2020.10.16.342709v1?rss=1 Sur, A. Meyer, N. 2020-10-16 doi:10.1101/2020.10.16.342709 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Overcoming resistance to immune checkpoint therapy in PTEN-null prostate cancer by sequential intermittent anti-PI3Ka/b/δ and anti-PD-1 treatment ]]> https://biorxiv.org/content/10.1101/2020.10.17.343608v1?rss=1 Qi, Z. Hong, W. Xu, Z. zhang, l. Zou, Y. Yan, W. Li, C. Liu, N. 2020-10-17 doi:10.1101/2020.10.17.343608 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ A novel design of transcriptional factor-mediated dynamic control of DNA recombination. ]]> https://biorxiv.org/content/10.1101/2020.10.20.346668v1?rss=1 Zhang, Y. Li, J. Zong, Y. 2020-10-20 doi:10.1101/2020.10.20.346668 Cold Spring Harbor Laboratory Press 2020-10-20 <![CDATA[ Partial epithelial-to-mesenchymal transition is prognostic and associates with Slug in head and neck cancer ]]> https://biorxiv.org/content/10.1101/2020.10.20.346692v1?rss=1 Schinke, H. Pan, M. Akyol, M. Kranz, G. Libl, D. Simon, F. Canis, M. Baumeister, P. Gires, O. 2020-10-21 doi:10.1101/2020.10.20.346692 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Experience-dependent alteration of mnemonic representation in early visual cortex and intraparietal sulcus ]]> https://biorxiv.org/content/10.1101/2020.10.20.347179v1?rss=1 Jia, K. Li, Y. Gong, M. Huang, H. Wang, Y. Li, S. 2020-10-21 doi:10.1101/2020.10.20.347179 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ The Genetics and Evolution of Eye Color in Domestic Pigeons (Columba livia) ]]> https://biorxiv.org/content/10.1101/2020.10.25.340760v1?rss=1 Si, S. Xu, X. Zhuang, Y. Luo, S.-J. 2020-10-26 doi:10.1101/2020.10.25.340760 Cold Spring Harbor Laboratory Press 2020-10-26 <![CDATA[ Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients ]]> https://biorxiv.org/content/10.1101/2020.10.29.360479v1?rss=1 Ren, X. Wen, W. Fan, X. Hou, W. Su, B. Cai, P. Li, J. Liu, Y. Tang, F. Zhang, F. Yang, Y. He, J. Ma, W. He, J. Wang, P. Cao, Q. Chen, F. Chen, Y. Cheng, X. Deng, G. Deng, X. Ding, W. Feng, Y. Gan, R. Guo, C. Guo, W. He, S. Jiang, C. Liang, J. Li, Y.-M. Lin, J. Ling, Y. Liu, H. Liu, J. Liu, N. Liu, Y. Luo, M. Ma, Q. Song, Q. Sun, W. Wang, G. Wang, F. Wang, Y. Wen, X. Wu, Q. Xu, G. Xie, X. Xiong, X. Xing, X. Xu, H. Yin, C. Yu, D. Yu, K. Yuan, J. Zhang, B. Zhang, T. Zhao, J. Zhao, P. Zhou, J. Zhou, W. Zhong, S. Zhong, X. Zhang, S. Zhu 2020-10-29 doi:10.1101/2020.10.29.360479 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ Ontology-Aware Deep Learning Enables Ultrafast, Accurate and Interpretable Source Tracking among Sub-Million Microbial Community Samples from Hundreds of Niches ]]> https://biorxiv.org/content/10.1101/2020.11.01.364208v1?rss=1 Ning, K. Zha, Y. Chong, H. Qiu, H. Kang, K. Dun, Y. Chen, Z. Cui, X. 2020-11-02 doi:10.1101/2020.11.01.364208 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ Scaling up biodiversity ecosystem functioning relationships: the role of environmental variability in space and time ]]> https://biorxiv.org/content/10.1101/2020.11.04.367250v1?rss=1 Thompson, P. L. Kefi, S. Zelnik, Y. R. Dee, L. E. Wang, S. de Mazancourt, C. Loreau, M. Gonzalez, A. 2020-11-05 doi:10.1101/2020.11.04.367250 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ MarkovHC: Markov hierarchical clustering for the topological structure of high-dimensional single-cell omics data ]]> https://biorxiv.org/content/10.1101/2020.11.04.368043v1?rss=1 Wang, Z. Zhong, Y. Ye, Z. Zeng, L. Chen, Y. Shi, M. Qian, M. Zhang, M. Q. 2020-11-05 doi:10.1101/2020.11.04.368043 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ A Fast Lysine Cross-linker DOPA Enables Mass Spectrometry Analyses of Protein Unfolding and Weak Protein-protein Interactions ]]> https://biorxiv.org/content/10.1101/2020.11.05.369280v1?rss=1 Wang, J.-H. Tang, Y.-L. Jain, R. Xiao, F. Gong, Z. Zhou, Y. Tan, D. Li, Q. Dong, X. Liu, S.-Q. Tang, C. Huang, N. Ye, K. Dong, M.-Q. Lei, X. 2020-11-05 doi:10.1101/2020.11.05.369280 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Dimerization of the Mineralocorticoid Receptor LigandBinding Domain by helix 9, 10 and the F-domain ]]> https://biorxiv.org/content/10.1101/2020.11.05.369587v1?rss=1 BIANCHETTI, L. Sinar, D. Depenveiller, C. Dejaegere, A. 2020-11-06 doi:10.1101/2020.11.05.369587 Cold Spring Harbor Laboratory Press 2020-11-06 <![CDATA[ Aurora Kinase A proximity interactome reveals centriolar satellites as regulators of its function during primary cilium biogenesis ]]> https://biorxiv.org/content/10.1101/2020.11.05.370320v1?rss=1 Arslanhan, M. D. Rauniyar, N. Yates, J. R. Firat-Karalar, E. N. 2020-11-06 doi:10.1101/2020.11.05.370320 Cold Spring Harbor Laboratory Press 2020-11-06 <![CDATA[ Target-driven design of a coumarinyl chalcone scaffold based novel EF2 Kinase inhibitor suppresses breast cancer growth in vivo ]]> https://biorxiv.org/content/10.1101/2020.11.06.371062v1?rss=1 Comert Onder, F. Kahraman, N. Bellur Atici, E. Cagir, A. Kandemir, H. Tatar, G. Taskin Tok, T. Karliga, B. Durdagi, S. Ay, M. Ozpolat, B. 2020-11-08 doi:10.1101/2020.11.06.371062 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ Knockdown of LC3 increases mitochondria-to-micronucleus transition ]]> https://biorxiv.org/content/10.1101/2020.11.06.372144v1?rss=1 Jiang, X. Hou, B. Li, E. Huang, H. Yang, H. Xi, Z. 2020-11-08 doi:10.1101/2020.11.06.372144 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ Simultaneous, cell-intrinsic downregulation of PD-1 and TIGIT enhances the effector function of CD19-targeting CAR T cells and promotes an early-memory phenotype ]]> https://biorxiv.org/content/10.1101/2020.11.07.372334v1?rss=1 Lee, Y. Lee, H. J. Kim, H. C. Lee, Y. Nam, S. K. Hupperetz, C. Ma, J. S. Wang, X. Singer, O. Kim, W. S. Kim, S. J. Koh, Y. Jung, I. Kim, C. H. 2020-11-08 doi:10.1101/2020.11.07.372334 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ SlSWEET15 exports sucrose from phloem and seed coat in tomato to supply carbon for fruit and seed development ]]> https://biorxiv.org/content/10.1101/2020.11.09.374827v1?rss=1 Ko, H.-Y. Ho, L.-H. Neuhaus, H. E. Guo, W.-J. 2020-11-10 doi:10.1101/2020.11.09.374827 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ CD127 imprints functional heterogeneity to diversify monocyte responses in human inflammatory diseases ]]> https://biorxiv.org/content/10.1101/2020.11.10.376277v1?rss=1 Zhang, B. Zhang, Y. Xiong, L. Li, Y. Zhang, Y. Zhao, J. Jiang, H. Li, C. Liu, Y. Liu, X. Liu, H. Ping, Y.-F. Zhang, Q. C. Zhang, Z. Bian, X.-W. Zhao, Y. Hu, X. 2020-11-10 doi:10.1101/2020.11.10.376277 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ Comparative genomic analyses provide clues to capsule switch in Streptococcus suis ]]> https://biorxiv.org/content/10.1101/2020.11.11.377622v1?rss=1 Zhu, Y. Dong, W. Ma, J. Zhang, Y. Zhong, X. Pan, Z. Liu, G. Wu, Z. Yao, H. 2020-11-11 doi:10.1101/2020.11.11.377622 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ Label-free bone marrow white blood cell classification using refractive index tomograms and deep learning ]]> https://biorxiv.org/content/10.1101/2020.11.13.381244v1?rss=1 99 % accuracy for the binary classification of myeloids and lymphoids and >96 % accuracy for the four-type classification of B, T lymphocytes, monocytes, and myelocytes. Furthermore, the feature learning of our approach was visualized via an unsupervised dimension reduction technique. We envision that this framework can be integrated into existing workflows for blood cell investigation, thereby providing cost-effective and rapid diagnosis of hematologic malignancy. ]]> Ryu, D. Kim, J. Lim, D. Min, H.-S. You, I. Cho, D. Park, Y. 2020-11-15 doi:10.1101/2020.11.13.381244 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ DeepMosaic: Control-independent mosaic single nucleotide variant detection using deep convolutional neural networks ]]> https://biorxiv.org/content/10.1101/2020.11.14.382473v1?rss=1 Yang, X. Xu, X. Breuss, M. W. Antaki, D. Ball, L. L. Chung, C. Li, C. George, R. D. Wang, Y. Bae, T. Abyzov, A. Sebat, J. Gleeson, J. G. 2020-11-16 doi:10.1101/2020.11.14.382473 Cold Spring Harbor Laboratory Press 2020-11-16 <![CDATA[ Role of BMP signaling during early development of the annelid Capitella teleta ]]> https://biorxiv.org/content/10.1101/2020.11.15.383695v1?rss=1 Webster, N. B. Sur, A. Corbet, M. Meyer, N. P. 2020-11-17 doi:10.1101/2020.11.15.383695 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ scPretrain: Multi-task self-supervised learning for cell type classification ]]> https://biorxiv.org/content/10.1101/2020.11.18.386102v1?rss=1 Zhang, R. Luo, Y. Ma, J. Zhang, M. Wang, S. 2020-11-20 doi:10.1101/2020.11.18.386102 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Substrate traits govern the assembly and spatial organization of microbial community engaged in metabolic division of labor ]]> https://biorxiv.org/content/10.1101/2020.11.18.387787v1?rss=1 Wang, M. Chen, X. Nie, Y. Wu, X.-L. 2020-11-18 doi:10.1101/2020.11.18.387787 Cold Spring Harbor Laboratory Press 2020-11-18 <![CDATA[ Recurrent circuit based neural population codes for stimulus representation and inference ]]> https://biorxiv.org/content/10.1101/2020.11.18.389197v1?rss=1 Zhang, W. Wu, S. Josic, K. Doiron, B. 2020-11-20 doi:10.1101/2020.11.18.389197 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ The structural mechanism underlying the antithetic effect of homologous RND1 and RhoD GTPases in plexin regulation ]]> https://biorxiv.org/content/10.1101/2020.11.19.389494v1?rss=1 Shan, Y. Zhang, X. Song, C. Liu, Y. Ke, P. Kuo, Y.-C. Wang, Y. 2020-11-19 doi:10.1101/2020.11.19.389494 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ Molecular engineering improves antigen quality and enables integrated manufacturing of a trivalent subunit vaccine candidate for rotavirus ]]> https://biorxiv.org/content/10.1101/2020.11.20.391532v1?rss=1 Dalvie, N. C. Brady, J. R. Crowell, L. E. Tracey, M. K. Biedermann, A. M. Kaur, K. Hickey, J. M. Kristensen, D. L. Bonnyman, A. Rodriguez-Aponte, S. A. Whittaker, C. A. Bok, M. Vega, C. Mukhopadhyay, T. Joshi, S. B. Volkin, D. B. Parreno, V. Love, K. R. Love, J. C. 2020-11-20 doi:10.1101/2020.11.20.391532 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ The SC-SNc pathway boosts appetitive locomotion in predatory hunting ]]> https://biorxiv.org/content/10.1101/2020.11.23.395004v1?rss=1 Huang, M. Li, D. Pei, Q. Xie, z. Gu, H. Liu, A. Chen, Z. Wang, Y. Sun, F. Li, Y. Zhang, J. He, M. Xie, Y. Zhang, F. Qi, X. Shang, C. Cao, P. 2020-11-24 doi:10.1101/2020.11.23.395004 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ Response of methanogen community to elevation of cathode potentials in the presence of magnetite ]]> https://biorxiv.org/content/10.1101/2020.11.24.397190v1?rss=1 Gao, K. Wang, X. Huang, J. Xia, X. Lu, Y. 2020-11-25 doi:10.1101/2020.11.24.397190 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ 3D8, a nucleic acid-hydrolyzing scFv, confers antiviral activity against SARS-CoV-2 and multiple coronaviruses in vitro ]]> https://biorxiv.org/content/10.1101/2020.11.25.398909v1?rss=1 Lee, G. Budhathoki, S. Choi, H. S. Oh, K.-j. Lee, G.-Y. Ham, Y. K. Kim, Y. J. Lim, Y. R. Hoang, P. T. Lee, Y. Lim, S.-W. Kim, J.-M. Cho, S. Song, J.-W. Lee, S. Kim, W.-K. 2020-11-25 doi:10.1101/2020.11.25.398909 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ Combined inhibition of KDM6A/B and HDACs exacerbates integrated stress response and mediates therapeutic effects in IDH1-mutant glioma ]]> https://biorxiv.org/content/10.1101/2020.11.26.400234v1?rss=1 Kayabolen, A. Sahin, G. N. Seker-Polat, F. Cingoz, A. Isik, B. Acar, S. Wakimoto, H. Cahill, D. P. Solaroglu, I. Cribbs, A. Oppermann, U. Bagci-Onder, T. 2020-11-26 doi:10.1101/2020.11.26.400234 Cold Spring Harbor Laboratory Press 2020-11-26 <![CDATA[ A Large-Scale Structural and Functional Connectome of Social Mentalizing ]]> https://biorxiv.org/content/10.1101/2020.11.27.400929v1?rss=1 Wang, Y. Metoki, A. Xia, Y. Zang, Y. He, Y. Olson, I. R. 2020-11-27 doi:10.1101/2020.11.27.400929 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ A spiking neural circuit model for learning multi-sensory integration ]]> https://biorxiv.org/content/10.1101/2020.11.27.401216v1?rss=1 Song, D. Niu, X. Zhang, W.-H. Lee, T. S. 2020-11-27 doi:10.1101/2020.11.27.401216 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ A body map of somatic mutagenesis in morphologically normal human tissues ]]> https://biorxiv.org/content/10.1101/2020.11.30.403436v1?rss=1 Li, R. Di, L. Li, J. Fan, W. Liu, Y. Guo, W. Liu, W. Liu, L. Li, Q. Chen, L. Chen, Y. Miao, C. Liu, H. Wang, Y. Ma, Y. Xu, D. Lin, D. Huang, Y. Wang, J. Bai, F. Wu, C. 2020-12-01 doi:10.1101/2020.11.30.403436 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Localization, proteomics and metabolite profiling reveal a putative vesicular transporter for UDP-glucose ]]> https://biorxiv.org/content/10.1101/2020.12.01.405605v1?rss=1 Qian, C. Wu, Z. Sun, R. Yu, H. Zeng, J. Rao, Y. Li, Y. 2020-12-02 doi:10.1101/2020.12.01.405605 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Modeling of Internal and External Factors affecting a Complex Dengue Network ]]> https://biorxiv.org/content/10.1101/2020.12.01.406033v1?rss=1 Malik, H. A. M. Abid, F. Wahiddin, M. R. Waqas, A. 2020-12-01 doi:10.1101/2020.12.01.406033 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Cognitive and neural bases of collateral damage during intergroup conflict ]]> https://biorxiv.org/content/10.1101/2020.12.04.411280v1?rss=1 Han, X. Zhou, S. Fahoum, N. Wu, T. Gao, T. Shamay-Tsoory, S. Gelfand, M. J. Wu, X. Han, S. 2020-12-07 doi:10.1101/2020.12.04.411280 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ Dissociated neural representations of content and ordinal structure in auditory sequence memory ]]> https://biorxiv.org/content/10.1101/2020.12.05.412791v1?rss=1 Fan, Y. Han, Q. Guo, S. Luo, H. 2020-12-06 doi:10.1101/2020.12.05.412791 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Quantifying liquid-liquid phase separation property of chromatin under physiological conditions using Hi-MS and Hi-C ]]> https://biorxiv.org/content/10.1101/2020.12.07.415489v1?rss=1 Shi, M. You, K. Hou, C. Chen, T. Liang, Z. Liu, M. Wang, J. Wei, T. Qin, J. Chen, Y. Li, T. Zhang, M. Q. 2020-12-08 doi:10.1101/2020.12.07.415489 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ In-House Forecasting of Crop Latitude Adaptation through a Daylength-sensing-based Environment Adaptation Simulator (DEAS) ]]> https://biorxiv.org/content/10.1101/2020.12.09.418558v1?rss=1 Qiu, L. Wu, Q. Wang, X. Zhuang, G. Han, J. Wang, H. Shang, Z. Tian, W. Chen, Z. Lin, Z. He, H. Hu, J. Lv, Q. Ren, J. Xu, J. Li, C. Wang, X. Li, Y. Li, S. Huang, R. Chen, X. Zhang, C. Lu, M. Liang, C. Qin, P. Huang, X. Li, S. Ouyang, X. 2020-12-10 doi:10.1101/2020.12.09.418558 Cold Spring Harbor Laboratory Press 2020-12-10 <![CDATA[ Non-coding loci without epigenomic signals can be essential for maintaining global chromatin organization and cell viability ]]> https://biorxiv.org/content/10.1101/2020.12.13.422541v1?rss=1 Ding, B. Liu, Y. Liu, Z. Zheng, L. Xu, P. Chen, Z. Wu, P. Zhao, Y. Pan, Q. Guo, Y. Wei, W. Wang, W. 2020-12-14 doi:10.1101/2020.12.13.422541 Cold Spring Harbor Laboratory Press 2020-12-14 <![CDATA[ Regulatory elements can be essential for maintaining broad chromatin organization and cell viability ]]> https://biorxiv.org/content/10.1101/2020.12.13.422554v1?rss=1 Liu, Y. Ding, B. Zheng, L. Xu, P. Liu, Z. Chen, Z. Wu, P. Zhao, Y. Pan, Q. Guo, Y. Wang, W. Wei, W. 2020-12-13 doi:10.1101/2020.12.13.422554 Cold Spring Harbor Laboratory Press 2020-12-13 <![CDATA[ Computable Early C. elegans Embryo with a Data-driven Phase Field Model ]]> https://biorxiv.org/content/10.1101/2020.12.13.422560v1?rss=1 Kuang, X. Guan, G. Wong, M.-K. Chan, L.-Y. Zhao, Z. Tang, C. Zhang, L. 2020-12-13 doi:10.1101/2020.12.13.422560 Cold Spring Harbor Laboratory Press 2020-12-13 <![CDATA[ Phase separation of Mer2 organizes the meiotic loop-axis structure of chromatin during meiosis I ]]> https://biorxiv.org/content/10.1101/2020.12.15.422856v1?rss=1 Tsai, B. Liu, W. Dong, D. Shi, K. Chen, L. Gao, N. 2020-12-15 doi:10.1101/2020.12.15.422856 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Human Surfactant Protein D Binds S1 and Receptor Binding Domain of Spike protein and acts as an entry inhibitor of SARS-CoV-2 Pseudotyped viral particles in vitro ]]> https://biorxiv.org/content/10.1101/2020.12.18.423418v1?rss=1 Hsieh, M.-H. Beirag, N. Murugaiah, V. Chou, Y.-C. Kuo, W.-S. Kao, H.-F. Madan, T. Kishore, U. Wang, J.-Y. 2020-12-18 doi:10.1101/2020.12.18.423418 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ SARS-CoV-2 spike protein interacts with and activates TLR4 ]]> https://biorxiv.org/content/10.1101/2020.12.18.423427v1?rss=1 Zhao, Y. Kuang, M. Wang, X. You, F. 2020-12-18 doi:10.1101/2020.12.18.423427 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ Transcriptional analysis of immune modulatory genes in melanoma treated with PD-1 blockade ]]> https://biorxiv.org/content/10.1101/2020.12.20.397000v1?rss=1 Song, H. Lee, S. Lee, S.-H. Kim, M. Lee, S. Y. Yoon, S.-S. Yun, H. Koh, Y. 2020-12-21 doi:10.1101/2020.12.20.397000 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ AF10 (MLLT10) prevents somatic cell reprogramming through regulation of H3K79 methylation ]]> https://biorxiv.org/content/10.1101/2020.12.22.423908v1?rss=1 Ugurlu-Cimen, D. Odluyurt, D. Sevinc, K. Ozkan-Kucuk, N. E. Ozcimen, B. Demirtas, D. Philpott, M. Oppermann, U. Ozlu, N. Onder, T. T. 2020-12-22 doi:10.1101/2020.12.22.423908 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Deep manifold learning reveals hidden dynamics of proteasome autoregulation ]]> https://biorxiv.org/content/10.1101/2020.12.22.423932v1?rss=1 Wu, Z. Zhang, S. Wang, W. L. Ma, Y. Dong, Y. Mao, Y. 2020-12-22 doi:10.1101/2020.12.22.423932 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Distinguish virulent and temperate phage-derived sequences in metavirome data with a deep learning approach ]]> https://biorxiv.org/content/10.1101/2020.12.25.424404v1?rss=1 Wu, S. Fang, Z. Tan, J. Li, M. Wang, C. Guo, Q. Xu, C. Jiang, X. Zhu, H. 2020-12-26 doi:10.1101/2020.12.25.424404 Cold Spring Harbor Laboratory Press 2020-12-26 <![CDATA[ The neutralization effect of Montelukast on SARS-CoV-2 is shown by multiscale in silico simulations and combined in vitro studies ]]> https://biorxiv.org/content/10.1101/2020.12.26.424423v1?rss=1 Durdagi, S. Avsar, T. Orhan, M. D. Serhatli, M. Balcioglu, B. K. Ozturk, H. U. Kayabolen, A. Cetin, Y. Aydinlik, S. Bagci-Onder, T. Tekin, S. Demirci, H. Guzel, M. Akdemir, A. Calis, S. Oktay, L. Tolu, I. Butun, Y. E. Erdemoglu, E. Olkan, A. Tokay, N. Isik, S. Ozcan, A. Acar, E. Buyukkilic, S. Yumak, Y. 2020-12-27 doi:10.1101/2020.12.26.424423 Cold Spring Harbor Laboratory Press 2020-12-27 <![CDATA[ Single cell gene fusion detection by scFusion ]]> https://biorxiv.org/content/10.1101/2020.12.27.424506v1?rss=1 Jin, Z. Huang, W. Shen, N. Li, J. Wang, X. Park, P. J. Xi, R. 2020-12-28 doi:10.1101/2020.12.27.424506 Cold Spring Harbor Laboratory Press 2020-12-28 <![CDATA[ Single-cell Individual Complete mtDNA Sequencing Uncovers Hidden Mitochondrial Heterogeneity in Human and Mouse Oocytes ]]> https://biorxiv.org/content/10.1101/2020.12.28.424537v1?rss=1 Bi, C. Wang, L. Fan, Y. Ramos-Mandujano, G. Yuan, B. Zhou, X. Wang, J. Shao, Y. Zhang, P.-Y. Huang, Y. Yu, Y. Izpisua Belmonte, J. C. Li, M. 2020-12-28 doi:10.1101/2020.12.28.424537 Cold Spring Harbor Laboratory Press 2020-12-28 <![CDATA[ Host Specific SARS-CoV-2 Mutations: Insertion of the Phenylalanine in the NSP6 Linked to the United Kingdome and Premature Termination of the ORF-8 Associated with the European and the United States of America Derived Samples. ]]> https://biorxiv.org/content/10.1101/2020.12.29.424530v1?rss=1 Khalid, M. Al-ebini, Y. Murphy, D. Shoai, M. 2020-12-29 doi:10.1101/2020.12.29.424530 Cold Spring Harbor Laboratory Press 2020-12-29 <![CDATA[ Structured illumination microscopy artifacts caused by illumination scattering ]]> https://biorxiv.org/content/10.1101/2021.01.01.425033v1?rss=1 Mo, Y. Feng, F. Mao, H. Fan, J. Chen, L. 2021-01-04 doi:10.1101/2021.01.01.425033 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Protein scaffold-based multimerization of soluble ACE2 efficiently blocks SARS-CoV-2 infection in vitro ]]> https://biorxiv.org/content/10.1101/2021.01.04.425128v1?rss=1 Kayabolen, A. Akcan, U. Ozturan, D. Sarayloo, E. Nurtop, E. Ozer, B. Sahin, G. N. Dogan, O. Lack, N. Kaya, M. Albayrak, C. Can, F. Solaroglu, I. Bagci-Onder, T. 2021-01-06 doi:10.1101/2021.01.04.425128 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Epigenetic analysis of Paget's disease of bone identifies differentially methylated loci that predict disease status ]]> https://biorxiv.org/content/10.1101/2021.01.04.425216v1?rss=1 Diboun, I. Wani, S. Ralston, S. H. Albagha, O. M. E. 2021-01-05 doi:10.1101/2021.01.04.425216 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Stable Interaction Of The UK B.1.1.7 lineage SARS-CoV-2 S1 Spike N501Y Mutant With ACE2 Revealed By Molecular Dynamics Simulation ]]> https://biorxiv.org/content/10.1101/2021.01.07.425307v1?rss=1 Ahmed, W. Phillip, A. M. Biswas, K. H. 2021-01-07 doi:10.1101/2021.01.07.425307 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Monitoring the promoter activity of long noncoding RNAs and stem cell differentiation through knock-in of sgRNA flanked by tRNA in an intron ]]> https://biorxiv.org/content/10.1101/2021.01.08.425823v1?rss=1 Zhao, Y.-T. Wang, Y. 2021-01-08 doi:10.1101/2021.01.08.425823 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Nuclear m6A reader Ythdc1 regulates the scaffold function of LINE1 in mouse ESCs ]]> https://biorxiv.org/content/10.1101/2021.01.10.426065v1?rss=1 Chen, C. Liu, W. Guo, J. Liu, Y. Liu, X. Liu, J. Dou, X. Le, R. Huang, Y. Li, C. Yang, L. Kou, X. Zhao, Y. Wu, Y. Chen, J. Wang, H. Shen, B. Gao, Y. Gao, S. 2021-01-11 doi:10.1101/2021.01.10.426065 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ The PELOTA-HBS1 Complex Orchestrates mRNA Translation Surveillance and PDK1-mediated Plant Growth and Development ]]> https://biorxiv.org/content/10.1101/2021.01.11.426208v1?rss=1 Kong, W. Tan, S. Zhao, Q. Lin, D.-L. Xu, Z.-H. Friml, J. Xue, H.-W. 2021-01-11 doi:10.1101/2021.01.11.426208 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Human leukocyte antigen class II gene diversity tunes antibody repertoires to common pathogens ]]> https://biorxiv.org/content/10.1101/2021.01.11.426296v1?rss=1 Khan, T. Rahman, M. Ahmed, I. Al Ali, F. Jithesh, P. V. Marr, N. 2021-01-12 doi:10.1101/2021.01.11.426296 Cold Spring Harbor Laboratory Press 2021-01-12 <![CDATA[ Antifungal activities of artesunate, chloramphenicol, and cotrimoxazole against Basidiobolus species, the causal agents of gastrointestinal basidiobolomycosis ]]> https://biorxiv.org/content/10.1101/2021.01.11.426312v1?rss=1 Al-Qahtani, S. Joseph, M. R. P. AL-HAKAMI, A. M. Asseri, A. A. Mathew, A. Al Bshabshe, A. Alhumayed, S. Hamid, M. E. 2021-01-12 doi:10.1101/2021.01.11.426312 Cold Spring Harbor Laboratory Press 2021-01-12 <![CDATA[ Identification of the Molecular Targets of Disulfide Bond Disrupting Agents ]]> https://biorxiv.org/content/10.1101/2021.01.13.426390v1?rss=1 Law, M. E. Yaaghubi, E. Ghilardi, A. Davis, B. J. Ferreira, R. B. Koh, J. Chen, S. DePeter, S. F. Schilson, C. M. Chiang, C.-W. Heldermon, C. D. Norgaard, P. Castellano, R. K. Law, B. K. 2021-01-15 doi:10.1101/2021.01.13.426390 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ Learning interpretable cellular and gene signature embeddings from single-cell transcriptomic data ]]> https://biorxiv.org/content/10.1101/2021.01.13.426593v1?rss=1 Zhao, Y. Cai, H. Zhang, Z. Tang, J. Li, Y. 2021-01-15 doi:10.1101/2021.01.13.426593 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ Discovering hidden brain network responses to naturalistic stimuli via tensor component analysis of multi-subject fMRI data ]]> https://biorxiv.org/content/10.1101/2021.01.14.426756v1?rss=1 Hu, G. Li, H. Zhao, W. Hao, Y. Bai, Z. Nickerson, L. D. Cong, F. 2021-01-17 doi:10.1101/2021.01.14.426756 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Correlation of Computerized Tomography (CT) Severity Score for COVID-19 pneumonia with Clinical Outcomes ]]> https://biorxiv.org/content/10.1101/2021.01.15.426787v1?rss=1 50% involvement was scored 2. Maximum score for one lobe was 2 and hence total maximum overall score for all lobes was 10. Continuous data was represented using mean and standard deviation, and compared using independent sample t-tests. Categorical data was represented using frequencies and percentages, and compared using Chi-squared tests. Inter-observer reliability between radiologist and COVID intensivist for the 10 point CT-SS rated on 0-10 was assessed using the Kappa statistic. A p-value < 0.05 was considered significant for all analyses. ResultsA total of 73 patients were included, the majority male (58.9%) with mean age 55.8 {+/-} 13.93 years. The CT-SS rated on 0-10 showed substantial inter-observer reliability between radiologist and intensivist with a Kappa statistic of 0.78. Patients with CT-SS 8-10 had a significantly higher ICU admission & intubation rate (53.8% vs. 23.5%) and mortality rate (35.9% vs. 11.8%; p = 0.017), as compared to those with CT-SS 0-7. ConclusionWe conclude that the described CT severity score (CT-SS) is a quick, effective and easily reproducible tool for prediction of adverse clinical outcome in patients with COVID 19 pneumonia. The tool shows good inter-observer agreement when calculated by radiologist and physician independently. ]]> Hilal, K. Shahid, J. Aameen, A. Seth Martins, R. Nankani, A. Arshad, A. Tu, H. 2021-01-15 doi:10.1101/2021.01.15.426787 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ Lipid contact probability: an essential and predictive character for the structural and functional studies of membrane proteins ]]> https://biorxiv.org/content/10.1101/2021.01.17.426988v1?rss=1 Wang, L. Zhang, J. Wang, D. Song, C. 2021-01-18 doi:10.1101/2021.01.17.426988 Cold Spring Harbor Laboratory Press 2021-01-18 <![CDATA[ Neural mechanisms underlying regulation of empathy and altruism by beliefs of others' pain ]]> https://biorxiv.org/content/10.1101/2021.01.18.427136v1?rss=1 Yu, T. Han, S. 2021-01-21 doi:10.1101/2021.01.18.427136 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Inspiratory muscle training for enhancing repeated-sprint ability: A pilot study ]]> https://biorxiv.org/content/10.1101/2021.01.22.427755v1?rss=1 Rodriguez, R. F. Aughey, R. J. Billaut, F. Townsend, N. E. 2021-01-22 doi:10.1101/2021.01.22.427755 Cold Spring Harbor Laboratory Press 2021-01-22 <![CDATA[ Effects of carbon, nitrogen, phosphorus, and potassium on flowering and Fruiting of Glycyrrhiza uralensis ]]> https://biorxiv.org/content/10.1101/2021.01.23.427937v1?rss=1 yan, b. zhang, y. Zhang, X. Wang, S. Cui, J. Sun, K. Wang, T. Kang, C. Sun, J. Ge, Y. guo, l. Wang, W. 2021-01-25 doi:10.1101/2021.01.23.427937 Cold Spring Harbor Laboratory Press 2021-01-25 <![CDATA[ Deconstruction of the retrosplenial granular cortex for social behavior in the mouse model of fragile X syndrome ]]> https://biorxiv.org/content/10.1101/2021.01.24.428008v1?rss=1 Shang, H.-F. Cai, R. Sun, H. Sheng, T. Lian, Y.-N. Liu, L. Chen, W. Gao, L. Xu, H. Zhang, C. Luo, J.-H. Li, X. Li, X.-Y. 2021-01-26 doi:10.1101/2021.01.24.428008 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Surface-based Single-subject Morphological Brain Networks: Effects of Morphological Index, Brain Parcellation and Similarity Measure, Sample Size-varying Stability and Test-retest Reliability ]]> https://biorxiv.org/content/10.1101/2021.01.25.428021v1?rss=1 Li, Y. Wang, N. Wang, H. Lv, Y. Zou, Q. Wang, J. 2021-01-26 doi:10.1101/2021.01.25.428021 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Heterogeneous recruitment abilities to RNA polymerases generate superlinear and sublinear scaling of gene expression level with cell volume ]]> https://biorxiv.org/content/10.1101/2021.01.26.428201v1?rss=1 Lin, J. 2021-01-27 doi:10.1101/2021.01.26.428201 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Macaque V1 responses to 2nd-order contrast-modulated stimuli and the possible subcortical and cortical contributions ]]> https://biorxiv.org/content/10.1101/2021.01.28.428627v1?rss=1 Ju, N.-S. Guan, S.-C. Tang, S. Yu, C. 2021-01-29 doi:10.1101/2021.01.28.428627 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ Progressive domain segregation in early embryonic development and underlying correlation to genetic and epigenetic changes ]]> https://biorxiv.org/content/10.1101/2021.02.02.429282v1?rss=1 Quan, H. Tian, H. Liu, S. Xue, Y. Zhang, Y. Xie, W. Gao, Y. Q. 2021-02-02 doi:10.1101/2021.02.02.429282 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Computational insights into differential interaction of mamalian ACE2 with the SARS-CoV-2 spike receptor binding domain ]]> https://biorxiv.org/content/10.1101/2021.02.02.429327v1?rss=1 Lupala, C. S. Kumar, V. Su, X.-d. Wu, C. Liu, H. 2021-02-02 doi:10.1101/2021.02.02.429327 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Modeling of histone modifications reveals formation mechanism and function of bivalent chromatin ]]> https://biorxiv.org/content/10.1101/2021.02.03.429504v1?rss=1 Zhao, W. Qiao, L. Yan, S. Nie, Q. Zhang, L. 2021-02-03 doi:10.1101/2021.02.03.429504 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Post-infection treatment with a protease inhibitor increases survival of mice with a fatal SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2021.02.05.429937v1?rss=1 Dampalla, C. Zheng, J. Perera, K. Wong, L. Y. R. Meyerholz, D. Nguyen, H. Kashipathy, M. Battaile, K. Lovell, S. Kim, Y. Perlman, S. Groutas, W. Chang, K.-O. 2021-02-05 doi:10.1101/2021.02.05.429937 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Emergence of Probabilistic Representation in the Neural Network of Primary Visual Cortex ]]> https://biorxiv.org/content/10.1101/2021.02.06.429971v1?rss=1 Li, A. A. Wang, F. Zhang, X. Wu, S. 2021-02-08 doi:10.1101/2021.02.06.429971 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ A data-driven method to learn a jump diffusion process from aggregate biological gene expression data ]]> https://biorxiv.org/content/10.1101/2021.02.06.430082v1?rss=1 Gao, J.-X. Wang, Z.-Y. Zhang, M. Q. Qian, M.-P. Jiang, D.-Q. 2021-02-08 doi:10.1101/2021.02.06.430082 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Physiological underpinning of default-mode network emergence in the human infant brain ]]> https://biorxiv.org/content/10.1101/2021.02.08.430158v1?rss=1 Yu, Q. Ouyang, M. Detre, J. A. Kang, H. Hu, D. Hong, B. Fang, F. Peng, Y. Huang, H. 2021-02-08 doi:10.1101/2021.02.08.430158 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Mitochondriomics reveals the underlying neuoprotective mechanism of TrkB receptor agonist R13 in the 5xFAD mice ]]> https://biorxiv.org/content/10.1101/2021.02.08.430227v1?rss=1 Li, X. Li, T. Xie, Y. Zhang, Z. Liu, J. Yu, H. Li, S. Song, X. Yang, X. Liu, G. 2021-02-08 doi:10.1101/2021.02.08.430227 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Quantitative proteomics identifies secreted diagnostic biomarkers as well as tumor-dependent prognostic targets for clear cell Renal Cell Carcinoma ]]> https://biorxiv.org/content/10.1101/2021.02.08.430238v1?rss=1 Senturk, A. Sahin, A. T. Armutlu, A. Kiremit, M. C. Acar, O. Erdem, S. Bagbudar, S. Esen, T. Tuncbag, N. Ozlu, N. 2021-02-09 doi:10.1101/2021.02.08.430238 Cold Spring Harbor Laboratory Press 2021-02-09 <![CDATA[ Selective inhibition reveals the regulatory function of DYRK2 in protein synthesis and calcium entry ]]> https://biorxiv.org/content/10.1101/2021.02.12.430909v1?rss=1 Lei, X. Wei, T. Wang, J. Liang, R. Chen, W. He, A. Du, Y. Zhou, W. Zhang, Z. Ma, M. Lu, J. Guo, X. Chen, X. Tian, R. Xiao, J. 2021-02-12 doi:10.1101/2021.02.12.430909 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ An allosteric ligand stabilizes distinct conformations in the M2 muscarinic acetylcholine receptor ]]> https://biorxiv.org/content/10.1101/2021.02.14.431178v1?rss=1 Xu, J. Hubner, H. Hu, Y. Niu, X. Gmeiner, P. Jin, C. Kobilka, B. 2021-02-15 doi:10.1101/2021.02.14.431178 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ Global detection of DNA repair outcomes induced by CRISPR-Cas9 ]]> https://biorxiv.org/content/10.1101/2021.02.15.431335v1?rss=1 Liu, M. Zhang, W. Xin, C. Yin, J. Shang, Y. Ai, C. Li, J. Meng, F.-l. Hu, J. 2021-02-16 doi:10.1101/2021.02.15.431335 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Gene loss during the transition to multicellularity ]]> https://biorxiv.org/content/10.1101/2021.02.16.431445v1?rss=1 Jimenez-Marin, B. Rakijas, J. B. Tyagi, A. Pandey, A. Hanschen, E. R. Anderson, J. Heffel, M. G. Platt, T. G. Olson, B. J. S. C. 2021-02-17 doi:10.1101/2021.02.16.431445 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Probe the effect of clustering on EphA2 receptor signaling efficiency by subcellular control of ligand-receptor mobility ]]> https://biorxiv.org/content/10.1101/2021.02.16.431455v1?rss=1 Chen, Z. Oh, D. Biswas, K. H. Zaidel-Bar, R. Groves, J. T. 2021-02-17 doi:10.1101/2021.02.16.431455 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Impaired pattern separation in Tg2576 mice is associated with hyperexcitable dentate gyrus caused by Kv4.1 downregulation ]]> https://biorxiv.org/content/10.1101/2021.02.17.431569v1?rss=1 Kim, K.-R. Kim, Y. Jeong, H.-j. Kang, J.-S. Lee, S. H. Kim, Y. Lee, S.-H. Ho, W.-K. 2021-02-18 doi:10.1101/2021.02.17.431569 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-Path Neolithic expansion to Western Europe ]]> https://biorxiv.org/content/10.1101/2021.02.19.431761v1?rss=1 Rohrlach, A. B. Papac, L. Childebayeva, A. Rivollat, M. Villalba-Mouco, V. Neumann, G. U. Penske, S. Skourtanioti, E. B. van de Loosdrecht, M. Akar, M. Boyadzhiev, K. Boyadzhiev, Y. Deguilloux, M.-F. Dobes, M. Erdal, Y. S. Ernee, M. Frangipane, M. Furmanek, M. Friederich, S. Ghesquiere, E. Haluszko, A. Hansen, S. Kuessner, M. Mannino, M. Oezbal, R. Reinhold, S. Rottier, S. Salazar-Garcia, D. C. Diaz, J. S. Stockhammer, P. W. de Togores Munoz, C. R. Yener, K. A. Posth, C. Krause, J. Herbig, A. Haak, W. 2021-02-19 doi:10.1101/2021.02.19.431761 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Antiviral effect of a nucleic acid hydrolyzing scFv against oseltamivir resistant influenza A virus ]]> https://biorxiv.org/content/10.1101/2021.02.19.432068v1?rss=1 Lee, Y. Kim, D. Kim, T. Oh, Y. Kim, w.-k. Lee, S. 2021-02-22 doi:10.1101/2021.02.19.432068 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ Structural insight into host plasma membrane association and assembly of HIV-1 Matrix protein ]]> https://biorxiv.org/content/10.1101/2021.02.21.432153v1?rss=1 Ciftci, H. Tateishi, H. Koiwai, K. Koga, R. Anraku, K. Monde, K. Dag, C. Destan, E. Yuksel, B. Ayan, E. Yildirim, G. Yigin, M. Ertem, F. B. Shafiei, A. Guven, O. Besler, S. O. Sierra, R. G. Yoon, C. H. Su, Z. Liang, M. Acar, B. Haliloglu, T. Otsuka, M. Yumoto, F. Fujita, M. Senda, T. DeMirci, H. 2021-02-21 doi:10.1101/2021.02.21.432153 Cold Spring Harbor Laboratory Press 2021-02-21 <![CDATA[ The role of interspecies recombinations in the evolution of antibiotic resistant pneumococci ]]> https://biorxiv.org/content/10.1101/2021.02.22.432219v1?rss=1 D'Aeth, J. C. van der Linden, M. P. G. McGee, L. De Lencastre, H. C. Turner, P. Song, J.-H. Lo, S. W. Gladstone, R. A. Sá-Leão, R. Ko, K. S. Hanage, W. P. Beall, B. Bentley, S. D. Croucher, N. J. The GPS Consortium, 2021-02-22 doi:10.1101/2021.02.22.432219 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ Resurrection of human endogenous retroviruses during aging reinforces senescence ]]> https://biorxiv.org/content/10.1101/2021.02.22.432260v1?rss=1 View larger version (64K): org.highwire.dtl.DTLVardef@31d384org.highwire.dtl.DTLVardef@13594c0org.highwire.dtl.DTLVardef@b8e070org.highwire.dtl.DTLVardef@196e5be_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Liu, X. Liu, Z. Sun, L. Ren, J. Wu, Z. Jiang, X. Ji, Q. Wang, Q. Fan, Y. Cai, Y. Wang, S. Li, W. Cao, G. Song, M. Lu, F. Zhang, W. Qu, J. liu, g. 2021-02-22 doi:10.1101/2021.02.22.432260 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ Evolutionary priming and transition to the ectomycorrhizal habit in an iconic lineage of mushroom-forming fungi: is preadaptation a requirement? ]]> https://biorxiv.org/content/10.1101/2021.02.23.432530v1?rss=1 Looney, B. P. Miyauchi, S. Morin, E. Drula, E. Courty, P.-E. Kohler, A. P. Lindquist, E. Kuo, A. LaButti, K. Pangilinan, J. Lipzen, A. Riley, R. Andreopoulos, W. He, G. Johnson, J. Barry, K. W. Grigoriev, I. V. Nagy, L. G. Hibbett, D. Henrissat, B. Matheny, P. B. Labbe, J. Martin, F. M. 2021-02-24 doi:10.1101/2021.02.23.432530 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ REVA as a Well-curated Database for Human Expression-modulating Variants ]]> https://biorxiv.org/content/10.1101/2021.02.24.432622v1?rss=1 Wang, Y. Shi, F.-Y. Liang, Y. Gao, G. 2021-02-25 doi:10.1101/2021.02.24.432622 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ An ultrasensitive GRAB sensor for detecting extracellular ATP in vitro and in vivo ]]> https://biorxiv.org/content/10.1101/2021.02.24.432680v1?rss=1 Wu, Z. He, K. Chen, Y. Li, H. Pan, S. Li, B. Liu, T. Wang, H. Du, J. Jing, M. Li, Y. 2021-02-24 doi:10.1101/2021.02.24.432680 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ Permeant Fluorescent Probes Visualize the Activation of SARM1 and Uncover an Anti-neurodegenerative Drug Candidate ]]> https://biorxiv.org/content/10.1101/2021.02.24.432704v1?rss=1 Li, W. H. Huang, K. Cai, Y. Wang, Q. W. Zhu, W. J. Hou, Y. N. Wang, S. Cao, S. Zhao, Z. Y. Xie, X. J. Du, Y. Lee, C. Lee, H. C. Zhang, H. Zhao, Y. J. 2021-02-25 doi:10.1101/2021.02.24.432704 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Natural selections on both amino acid sequences and expression levels are determinants of ohnolog retention ]]> https://biorxiv.org/content/10.1101/2021.02.24.432806v1?rss=1 Miao, L. Li, M. 2021-02-25 doi:10.1101/2021.02.24.432806 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Withaferin A promotes white adipose browning and prevents obesity through sympathetic nerve-activated Prdm16-FATP1 axis ]]> https://biorxiv.org/content/10.1101/2021.02.25.432705v1?rss=1 Zheng, R. Guo, B. Liu, J. Wang, B. Zhang, C. Su, Z. Zhao, M. 2021-02-26 doi:10.1101/2021.02.25.432705 Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ AIM-CICs: automatic identification method for Cell-in-cell structures based on convolutional neural network ]]> https://biorxiv.org/content/10.1101/2021.02.26.432996v1?rss=1 0.99), but also accurately categorize CICs into five subclasses based on CICs stages and cell number involved (AUC > 0.97 for all subclasses). The application of AIM-CICs would systemically fuel researches on CICs-mediated cell death such as high-throughput screening. ]]> Tang, M. Su, Y. Zhao, W. Niu, Z. Ruan, B. Li, Q. Zheng, Y. Wang, C. Zhou, Y. Zhang, B. Zhou, F. Huang, H. Shi, H. Sun, Q. 2021-02-26 doi:10.1101/2021.02.26.432996 Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ Allostery in Proteins as Point-to-Point Telecommunication in a Network: Frequency Decomposed Signal-to-Noise Ratio and Channel Capacity Analysis ]]> https://biorxiv.org/content/10.1101/2021.02.26.433010v1?rss=1 Bozkurt Varolgunes, Y. Rudzinski, J. F. Demir, A. 2021-02-26 doi:10.1101/2021.02.26.433010 Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ Calbindin regulates Kv4.1 trafficking and excitability of dentate granule cells via CaMKII-dependent phosphorylation ]]> https://biorxiv.org/content/10.1101/2021.02.26.433035v1?rss=1 Kim, K.-R. Jeong, H.-J. Kim, Y. Lee, S. Y. Kim, Y. Kim, H.-J. Lee, S.-H. Cho, H. Kim, J.-S. Ho, W.-K. 2021-02-26 doi:10.1101/2021.02.26.433035 Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ A role for the immune system-released activating agent (ISRAA) in the ontogenetic development of brain astrocytes ]]> https://biorxiv.org/content/10.1101/2021.03.01.433338v1?rss=1 Al-Awadi, A. M. I. AlJawder, A. I. Mousa, A. Taha, S. Bakhiet, M. 2021-03-01 doi:10.1101/2021.03.01.433338 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Identify phage hosts from metaviromic short reads based on deep learning and Markov chain model ]]> https://biorxiv.org/content/10.1101/2021.03.01.433351v1?rss=1 Tan, J. Fang, Z. Wu, S. Guo, Q. Jiang, X. Zhu, H. 2021-03-01 doi:10.1101/2021.03.01.433351 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Cooperative regulation of coupled oncoprotein translation and stability in triple-negative breast cancer by EGFR and CDK12 ]]> https://biorxiv.org/content/10.1101/2021.03.03.433762v1?rss=1 Ang, H. X. Sutiman, N. Deng, X. L. Bartelt, L. 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Tang, C. 2021-03-05 doi:10.1101/2021.03.04.433820 Cold Spring Harbor Laboratory Press 2021-03-05 <![CDATA[ Efficient Inhibition of SARS-CoV-2 Using Chimeric Antisense Oligonucleotides through RNase L Activation ]]> https://biorxiv.org/content/10.1101/2021.03.04.433849v1?rss=1 Su, X. Ma, W. Cheng, B. Wang, Q. Guo, Z. Zhou, D. Tang, X. 2021-03-04 doi:10.1101/2021.03.04.433849 Cold Spring Harbor Laboratory Press 2021-03-04 <![CDATA[ Recovery of high-qualitied Genomes from a deep-inland Salt Lake Using BASALT ]]> https://biorxiv.org/content/10.1101/2021.03.05.434042v1?rss=1 Yu, K. Qiu, Z. Mu, R. Qiao, X. Zhang, L. Lian, C.-A. Deng, C. Wu, Y. Xu, Z. Li, B. Pan, B. Zhang, Y. Fan, L. Liu, Y. Cao, H. Jin, T. Chen, B. Wang, F. Yan, Y. Xie, L. Zhou, L. Yi, S. Chi, S. Zhang, T. Zhuang, W. 2021-03-05 doi:10.1101/2021.03.05.434042 Cold Spring Harbor Laboratory Press 2021-03-05 <![CDATA[ A chloride efflux transporter OsBIRG1 regulates grain size and salt tolerance in rice ]]> https://biorxiv.org/content/10.1101/2021.03.07.434240v1?rss=1 Ren, Z. Bai, F. Xu, J. Wang, L. Wang, X. Zhang, Q. Feng, C. Niu, Q. Zhang, L. Li, M. Song, J. Bao, F. Liu, L. He, Y. Ma, L. Qiu, J. Tian, W. Hou, C. Li, L. 2021-03-08 doi:10.1101/2021.03.07.434240 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Dissecting Transition Cells from Single-Cell Transcriptome Data through Multiscale Stochastic Dynamics ]]> https://biorxiv.org/content/10.1101/2021.03.07.434281v1?rss=1 Zhou, P. Wang, S. Li, T. Nie, Q. 2021-03-08 doi:10.1101/2021.03.07.434281 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ A General LSTM-based Deep Learning Method for Estimating Neuronal Models and Inferring Neural Circuitry ]]> https://biorxiv.org/content/10.1101/2021.03.14.434027v1?rss=1 Sheng, K. Qu, P. Yang, L. Liu, X. He, L. Ma, L. Du, K. 2021-03-15 doi:10.1101/2021.03.14.434027 Cold Spring Harbor Laboratory Press 2021-03-15 <![CDATA[ Gel-like inclusions of C-terminal fragments of TDP-43 sequester and inhibit proteasomes in neurons ]]> https://biorxiv.org/content/10.1101/2021.03.15.435268v1?rss=1 Riemenschneider, H. Guo, Q. Bader, J. Frottin, F. Farny, D. Kleinberger, G. Haass, C. Mann, M. Hartl, F. U. Baumeister, W. Hipp, M. S. Meissner, F. Fernandez-Busnadiego, R. Edbauer, D. 2021-03-16 doi:10.1101/2021.03.15.435268 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Circular RNA Vaccines against SARS-CoV-2 and Emerging Variants ]]> https://biorxiv.org/content/10.1101/2021.03.16.435594v1?rss=1 Qu, L. Yi, Z. Shen, Y. Xu, Y. Wu, Z. Tang, H. Xiao, X. Dong, X. Guo, L. Yisimayi, A. Cao, Y. Zhou, Z. Wang, J. Xie, X. S. Wei, W. 2021-03-16 doi:10.1101/2021.03.16.435594 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Amelioration of hemophilia B through CRISPR/Cas9 induced homology-independent targeted integration ]]> https://biorxiv.org/content/10.1101/2021.03.18.435908v1?rss=1 Chen, X. Niu, X. Liu, Y. Zheng, R. Wang, L. Yang, L. Lu, J. Yin, S. Shao, Y. Wei, Y. Pan, J. Sayed, A. Ma, X. Liu, M. Jing, F. Liu, M. Hu, J. Zhang, X. Li, D. 2021-03-19 doi:10.1101/2021.03.18.435908 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Predicting hosts based on early SARS-CoV-2 samples and analyzing later world-wide pandemic in 2020 ]]> https://biorxiv.org/content/10.1101/2021.03.21.436312v1?rss=1 Guo, Q. Li, M. Wang, C. Guo, J. Jiang, X. Tan, J. Wu, S. Wang, P. Xiao, T. Zhou, M. Fang, Z. Xiao, Y. Zhu, H. 2021-03-22 doi:10.1101/2021.03.21.436312 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Overexpression-based detection of translatable circular RNAs is vulnerable to coexistent linear byproducts ]]> https://biorxiv.org/content/10.1101/2021.03.23.433163v1?rss=1 Jiang, Y. Chen, X. Zhang, W. 2021-03-23 doi:10.1101/2021.03.23.433163 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ A short ERK5 isoform modulates nucleocytoplasmic shuttling of active ERK5 and associates with poor survival in breast cancer ]]> https://biorxiv.org/content/10.1101/2021.03.23.436061v1?rss=1 View larger version (58K): org.highwire.dtl.DTLVardef@1491ed5org.highwire.dtl.DTLVardef@1875fbeorg.highwire.dtl.DTLVardef@9edbbcorg.highwire.dtl.DTLVardef@16c34c8_HPS_FORMAT_FIGEXP M_FIG C_FIG ERK5 isoform-3 expression deploys active ERK5 (pERK5) outside the nucleus to facilitate EMT and cell migration. 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Zhang, D. Wei, W. Baek, M. Gao, J. Nielsen, A. L. Bolding, J. E. Yang, L. Jameson, S. T. Wong, J. Olsen, C. A. Zhao, Y. 2021-03-24 doi:10.1101/2021.03.24.436780 Cold Spring Harbor Laboratory Press 2021-03-24 <![CDATA[ Disrupting hierarchical control of nitrogen fixation enables carbon-dependent regulation of ammonia excretion in soil diazotrophs ]]> https://biorxiv.org/content/10.1101/2021.03.25.436926v1?rss=1 Bueno Batista, M. Brett, P. Appia-Ayme, C. Wang, Y.-P. Dixon, R. 2021-03-25 doi:10.1101/2021.03.25.436926 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Structural insights into GlcNAc-1-phosphotransferase that directs lysosomal protein transport ]]> https://biorxiv.org/content/10.1101/2021.03.25.436948v1?rss=1 Du, S. Wang, G. Zhang, Z. Ma, C. Gao, N. Xiao, J. 2021-03-25 doi:10.1101/2021.03.25.436948 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Epithelial Regeneration Ability of Crohn's Disease Assessed Using Patient-Derived Intestinal Organoids ]]> https://biorxiv.org/content/10.1101/2021.03.25.437111v1?rss=1 Lee, C. Hong, S. N. Kim, E. R. Chang, D. K. Kim, Y.-H. 2021-03-27 doi:10.1101/2021.03.25.437111 Cold Spring Harbor Laboratory Press 2021-03-27 <![CDATA[ A spatial and cellular distribution of neurotropic virus infection in the mouse brain revealed by fMOST and single cell RNA-seq ]]> https://biorxiv.org/content/10.1101/2021.03.26.436691v1?rss=1 Zhang, Y. Xing, X. Long, B. Cao, Y. Hu, S. Li, X. Yu, Y. Tian, D. Luo, Z. Sui, B. Liu, W. Lv, L. Wu, Q. Dai, J. Zhou, M. Han, H. Fu, Z. F. Gong, H. Bai, F. Zhao, L. 2021-03-26 doi:10.1101/2021.03.26.436691 Cold Spring Harbor Laboratory Press 2021-03-26 <![CDATA[ Epigenome erosion drives neural crest-like phenotypic mimicry in triple-negative breast cancer and other SOX10+ malignancies ]]> https://biorxiv.org/content/10.1101/2021.03.30.437624v1?rss=1 Saunus, J. M. De Luca, X. M. Northwood, K. Raghavendra, A. Hasson, A. McCart Reed, A. E. Lim, M. Lal, S. Vargas, A. C. Kutasovic, J. R. Dalley, A. J. Miranda, M. Kalaw, E. Kalita-de Croft, P. Gresshoff, I. Al-Ejeh, F. Gee, J. M. Ormandy, C. J. Khanna, K. K. Beesley, J. Chenevix-Trench, G. Green, A. R. Rakha, E. A. Ellis, I. O. Nicolau, D. V. Simpson, P. T. Lakhani, S. R. 2021-03-30 doi:10.1101/2021.03.30.437624 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ Discovery of Latent Drivers from Double Mutations in Pan-Cancer Data Reveal their Clinical Impact ]]> https://biorxiv.org/content/10.1101/2021.04.02.438239v1?rss=1 Yavuz, B. R. Tsai, C.-J. Nussinov, R. Tuncbag, N. 2021-04-04 doi:10.1101/2021.04.02.438239 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Construction of continuously expandable single-cell atlases through integration of heterogeneous datasets in a generalized cell-embedding space ]]> https://biorxiv.org/content/10.1101/2021.04.06.438536v1?rss=1 Xiong, L. Tian, K. Li, Y. Zhang, Q. C. 2021-04-08 doi:10.1101/2021.04.06.438536 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ The causal role of transcranial alternating current stimulation at alpha frequency in boosting visual perceptual learning ]]> https://biorxiv.org/content/10.1101/2021.04.08.438912v1?rss=1 He, Q. Gong, B. Bi, K. Fang, F. 2021-04-09 doi:10.1101/2021.04.08.438912 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Genome-wide CRISPR activation screen identifies novel receptors for SARS-CoV-2 entry ]]> https://biorxiv.org/content/10.1101/2021.04.08.438924v1?rss=1 Zhu, S. Liu, Y. Zhou, Z. Zhang, Z. Xiao, X. Liu, Z. Chen, A. Dong, X. Tian, F. Chen, S. Xu, Y. Wang, C. Li, Q. Niu, X. Pan, Q. Du, S. Xiao, J. Wang, J. Wei, W. 2021-04-09 doi:10.1101/2021.04.08.438924 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ The dual nature of metacommunity variability ]]> https://biorxiv.org/content/10.1101/2021.04.09.439168v1?rss=1 Lamy, T. Wisnoski, N. I. Andrade, R. M. Castorani, M. C. Compagnoni, A. Lany, N. K. Marazzi, L. Record, S. Swan, C. Tonkin, J. D. Wang, S. Voelker, N. Zarnetske, P. L. Sokol, E. R. 2021-04-11 doi:10.1101/2021.04.09.439168 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Selective Chemical Labeling and Sequencing of 5-Hydroxymethylcytosine in DNA at Single-Base Resolution ]]> https://biorxiv.org/content/10.1101/2021.04.13.439733v1?rss=1 Li, X. Shi, X. Guo, W. Liu, Y. Peng, C. Xu, Y. 2021-04-14 doi:10.1101/2021.04.13.439733 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Reduced graphene oxide membrane as supporting film for high-resolution cryo-EM ]]> https://biorxiv.org/content/10.1101/2021.04.15.439953v1?rss=1 Liu, N. Zheng, L. Xu, J. Wang, J. Hu, C. Lan, J. Zhang, X. Zhang, J. Xu, K. Cheng, H. Yang, Z. Gao, X. Wang, X. Peng, H. Chen, Y. Wang, H.-W. 2021-04-15 doi:10.1101/2021.04.15.439953 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ Imaging the ultrastructures and dynamics of live erythrocyte membranes at the single-molecule level with a far-red probe on a microfluidic platform ]]> https://biorxiv.org/content/10.1101/2021.04.22.441044v1?rss=1 Ye, Z. Yang, W. Wang, S. Zheng, Y. Zhang, X. Yu, H. Luo, C. Peng, X. Xiao, Y. 2021-04-23 doi:10.1101/2021.04.22.441044 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Binding mechanism of neutralizing Nanobodies targeting SARS-CoV-2 Spike Glycoprotein ]]> https://biorxiv.org/content/10.1101/2021.04.23.441186v1?rss=1 Golcuk, M. Hacisuleyman, A. Erman, B. Yildiz, A. Gur, M. 2021-04-26 doi:10.1101/2021.04.23.441186 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Toward comprehensive functional analysis of gene lists weighted by gene essentiality scores ]]> https://biorxiv.org/content/10.1101/2021.04.26.441450v1?rss=1 Fan, R. Cui, Q. 2021-04-27 doi:10.1101/2021.04.26.441450 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ The Taxus genome provides insights into paclitaxel biosynthesis ]]> https://biorxiv.org/content/10.1101/2021.04.29.441981v1?rss=1 Xiong, X. Gou, J. Liao, Q. Li, Y. Zhou, Q. Bi, G. Li, C. Du, R. Wang, X. Sun, T. Guo, L. Liang, H. Lu, P. Wu, Y. Zhang, Z. Ro, D.-K. Shang, Y. Huang, S. Yan, J. 2021-04-29 doi:10.1101/2021.04.29.441981 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ A tissue-level phenome-wide network map of colocalized genes and phenotypes in the UK Biobank ]]> https://biorxiv.org/content/10.1101/2021.04.30.441974v1?rss=1 Rocheleau, G. Forrest, I. S. Duffy, A. Bafna, S. Dobbyn, A. Verbanck, M. Won, H.-H. Jordan, D. M. Do, R. 2021-05-01 doi:10.1101/2021.04.30.441974 Cold Spring Harbor Laboratory Press 2021-05-01 <![CDATA[ Effects of short-term plasticity in early olfactory information processing in Drosophila ]]> https://biorxiv.org/content/10.1101/2021.05.02.442289v1?rss=1 Liu, Y. Li, Q. Tang, C. Qin, S. Tu, Y. 2021-05-02 doi:10.1101/2021.05.02.442289 Cold Spring Harbor Laboratory Press 2021-05-02 <![CDATA[ The Immune landscape of solid pediatric tumors. ]]> https://biorxiv.org/content/10.1101/2021.05.04.442503v1?rss=1 Sherif, S. Roelands, J. Mifsud, W. Ahmed, E. Mifsud, B. Bedognetti, D. Hendrickx, W. 2021-05-04 doi:10.1101/2021.05.04.442503 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ SCON - A Short Conditional intrON for conditional knockout with one-step zygote injection ]]> https://biorxiv.org/content/10.1101/2021.05.09.443220v1?rss=1 Wu, S.-H. S. Szep-Bakonyi, R. Lee, H. Colozza, G. Boese, A. Gert, K. R. Hallay, N. Kim, J. Zhu, Y. Pilat-Carotta, S. Theussl, H.-C. Pauli, A. Koo, B.-K. 2021-05-10 doi:10.1101/2021.05.09.443220 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ High-dose drug heat map based on organoid array chip for drug selection with high safety and efficacy ]]> https://biorxiv.org/content/10.1101/2021.05.11.443550v1?rss=1 Lee, S.-Y. Teng, Y. Son, M. Ku, B. Moon, H. S. Tergaonkar, V. Chow, P. K.-H. Lee, D. W. Nam, D.-H. 2021-05-11 doi:10.1101/2021.05.11.443550 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ Single-cell epigenomic tracing of lifelong endothelial cell plasticity across mouse organs ]]> https://biorxiv.org/content/10.1101/2021.05.12.443777v1?rss=1 Yu, X. Liu, Y. Liu, X. Xiong, H. He, A. 2021-05-13 doi:10.1101/2021.05.12.443777 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ Direct Reconstruction of Gene Regulatory Networks underlying Cellular state Transitions without Pseudo-time Inference ]]> https://biorxiv.org/content/10.1101/2021.05.12.443928v1?rss=1 Wan, R. Zhang, Y. Peng, Y. Tian, F. Gao, G. Tang, F. Xie, S. Jia, J. Ge, H. 2021-05-14 doi:10.1101/2021.05.12.443928 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ Lung Epithelial Cells Can Produce Antibodies Participating In Adaptive Humoral Immune Responses ]]> https://biorxiv.org/content/10.1101/2021.05.13.443498v1?rss=1 Gao, E. Shao, W. Zhang, C. Yu, M. Dai, H. Fan, T. Zhu, Z. Xu, W. Huang, J. Zhang, Y. Qin, Z. Qiu, X. 2021-05-15 doi:10.1101/2021.05.13.443498 Cold Spring Harbor Laboratory Press 2021-05-15 <![CDATA[ EPIKOL, a chromatin-focused CRISPR/Cas9-based screening platform, to identify cancer-specific epigenetic vulnerabilities ]]> https://biorxiv.org/content/10.1101/2021.05.14.444239v1?rss=1 Yedier-Bayram, O. Gokbayrak, B. Aksu, A. C. Cavga, A. D. Kayabolen, A. Kala, E. Y. Karabiyik, G. Gunsay, R. Morova, T. Uyulur, F. Lack, N. A. Onder, T. T. Bagci-Onder, T. 2021-05-17 doi:10.1101/2021.05.14.444239 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ A new type of ERGIC-ERES membrane contact mediated by TMED9 and SEC12 is required for autophagosome biogenesis ]]> https://biorxiv.org/content/10.1101/2021.05.19.444771v1?rss=1 Li, S. Yan, R. Xu, J. Zhao, S. Ma, X. Sun, Q. Zhang, M. Li, Y. Liu, J.-J. G. Chen, L. Li, S. Xu, K. Ge, L. 2021-05-19 doi:10.1101/2021.05.19.444771 Cold Spring Harbor Laboratory Press 2021-05-19 <![CDATA[ In vivo direct imaging of neuronal activity at high temporo-spatial resolution ]]> https://biorxiv.org/content/10.1101/2021.05.21.444581v1?rss=1 Toi, P. T. Jang, H. J. Min, K. Kim, S.-P. Lee, S.-K. Lee, J. Kwag, J. Park, J.-Y. 2021-05-23 doi:10.1101/2021.05.21.444581 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ Modelling, Analysis, and Optimization of Three-Dimensional Restricted Visual Field Metric-Free Swarms ]]> https://biorxiv.org/content/10.1101/2021.05.24.445404v1?rss=1 Li, Q. Zhang, L. Jia, Y. Lu, T. 2021-05-24 doi:10.1101/2021.05.24.445404 Cold Spring Harbor Laboratory Press 2021-05-24 <![CDATA[ Tapping into non-English-language science for the conservation of global biodiversity ]]> https://biorxiv.org/content/10.1101/2021.05.24.445520v1?rss=1 Amano, T. Berdejo Espinola, V. Christie, A. P. Willott, K. Akasaka, M. Baldi, A. Berthinussen, A. Bertolino, S. Bladon, A. J. Chen, M. Choi, C.-Y. Bou Dagher Kharrat, M. de Oliveira, L. G. Farhat, P. Golivets, M. Hidalgo Aranzamendi, N. Jantke, K. Kajzer-Bonk, J. Kemahli Aytekin, M. C. Khorozyan, I. Kito, K. Konno, K. Lin, D.-L. Littlewood, N. Liu, Y. Liu, Y. Loretto, M.-C. Marconi, V. Martin, P. Morgan, W. H. Narvaez-Gomez, J. P. Negret, P. Nourani, E. Ochoa Quintero, J. M. Ockendon, N. Oh, R. Petrovan, S. Piovezan-Borges, A. C. Pollet, I. L. Ramos, D. L 2021-05-26 doi:10.1101/2021.05.24.445520 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ BRD9-containing non-canonical BAF complexes safeguard cell identity and prevent reprogramming ]]> https://biorxiv.org/content/10.1101/2021.05.27.445940v1?rss=1 Sevinc, K. Gürhan Sevinc, G. Cavga, A. D. Philpott, M. Kelekci, S. Can, H. Cribbs, A. P. Ayar, E. S. Arabacı, D. H. Dunford, J. P. Demir, A. B. Sigua, L. Qi, J. Oppermann, U. Önder, T. T. 2021-05-29 doi:10.1101/2021.05.27.445940 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ A homing suppression gene drive with multiplexed gRNAs maintains high drive conversion efficiency and avoids functional resistance alleles ]]> https://biorxiv.org/content/10.1101/2021.05.27.446071v1?rss=1 Yang, E. Metzloff, M. Langmüller, A. M. Clark, A. G. Messer, P. W. Champer, J. 2021-05-28 doi:10.1101/2021.05.27.446071 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Implicit adaptation to mirror-reversal is in the correct coordinate system but the wrong direction ]]> https://biorxiv.org/content/10.1101/2021.05.28.446174v1?rss=1 Wang, T. Taylor, J. 2021-05-28 doi:10.1101/2021.05.28.446174 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ U-RISC: An Ultra-high Resolution EM Dataset Challenging Existing Deep Learning Algorithms ]]> https://biorxiv.org/content/10.1101/2021.05.30.446334v1?rss=1 Shi, R. Wang, W. Li, Z. He, L. Sheng, K. Ma, L. Du, K. Jiang, T. Huang, T. 2021-05-31 doi:10.1101/2021.05.30.446334 Cold Spring Harbor Laboratory Press 2021-05-31 <![CDATA[ Serial Dependence in Temporal Perception Reveals the Dynamics of Constructing an Internal Reference Frame ]]> https://biorxiv.org/content/10.1101/2021.05.31.446431v1?rss=1 Wang, T. Luo, Y. Poeppel, E. Bao, Y. 2021-05-31 doi:10.1101/2021.05.31.446431 Cold Spring Harbor Laboratory Press 2021-05-31 <![CDATA[ Chronic opioid treatment arrests neurodevelopment and alters synaptic activity in human midbrain organoids ]]> https://biorxiv.org/content/10.1101/2021.06.02.446827v1?rss=1 Kim, H. S. Xiao, Y. Chen, X. He, S. Im, J. Willner, M. J. Finlayson, M. O. Xu, C. Zhu, H. Choi, S. J. Mosharov, E. V. Kim, H.-W. Xu, B. Leong, K. W. 2021-06-02 doi:10.1101/2021.06.02.446827 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ The Copper Responsive Transcription Factor SPL7 Represses Key Abscisic Acid Biosynthetic Genes to Balance Growth and Drought Tolerance ]]> https://biorxiv.org/content/10.1101/2021.06.03.446925v1?rss=1 Li, L. Yang, Y. Du, J. Tao, Y. Hao, C. Kuang, Z. Li, Z. 2021-06-03 doi:10.1101/2021.06.03.446925 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ Identification of a motif in Trm732 required for 2'-O-methylation of the tRNA anticodon loop by Trm7 ]]> https://biorxiv.org/content/10.1101/2021.06.03.446962v1?rss=1 Funk, H. M. DiVita, D. J. Sizemore, H. E. Wehrle, K. Weiner, C. L. Guy, A. R. Phizicky, E. M. Guy, M. P. 2021-06-03 doi:10.1101/2021.06.03.446962 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ TRPC3 and NALCN channels drive pacemaking in substantia nigra dopaminergic neurons ]]> https://biorxiv.org/content/10.1101/2021.06.03.447013v1?rss=1 Um, K. B. Hahn, S. Kim, S. W. Lee, Y. J. Birnbaumer, L. Kim, H. J. Park, M. K. 2021-06-04 doi:10.1101/2021.06.03.447013 Cold Spring Harbor Laboratory Press 2021-06-04 <![CDATA[ Limits and potential of combined folding and docking using PconsDock. ]]> https://biorxiv.org/content/10.1101/2021.06.04.446442v1?rss=1 Pozzati, G. Zhu, W. Lamb, J. Bassot, C. Kundrotas, P. Elofsson, A. 2021-06-07 doi:10.1101/2021.06.04.446442 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Cell-to-cell variability in inducible Caspase9-mediated cell death ]]> https://biorxiv.org/content/10.1101/2021.06.08.447627v1?rss=1 Yuan, Y. Ren, H. Li, Y. Qin, S. Yang, X. Tang, C. 2021-06-08 doi:10.1101/2021.06.08.447627 Cold Spring Harbor Laboratory Press 2021-06-08 <![CDATA[ Ghrelin proteolysis by insulin-degrading enzyme ]]> https://biorxiv.org/content/10.1101/2021.06.10.447714v1?rss=1 Bocach, D. D. Jones, K. L. Bell, J. M. Zheng, Q. Lazo, N. D. Smith-Carpenter, J. E. Alper, B. J. 2021-06-10 doi:10.1101/2021.06.10.447714 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ A novel and accurate full-length HTT mouse model for Huntington's disease ]]> https://biorxiv.org/content/10.1101/2021.06.14.448318v1?rss=1 Li, C. Zheng, S. Shenoy, S. A. Liu, W. Dai, Y. Liu, Y. Hou, Z. Mori, S. Duan, W. 2021-06-14 doi:10.1101/2021.06.14.448318 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ Dopamine enhanced auditory perceptual learning in humans via long-term memory consolidation ]]> https://biorxiv.org/content/10.1101/2021.06.16.448678v1?rss=1 Tang, D.-l. Zhang, J.-Y. Li, X. Zhang, Y.-X. 2021-06-17 doi:10.1101/2021.06.16.448678 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Systematic evaluation of genome-wide metabolic landscapes in lactic acid bacteria reveals diet-induced and strain-specific probiotic idiosyncrasies ]]> https://biorxiv.org/content/10.1101/2021.06.20.449192v1?rss=1 Koduru, L. Lakshmanan, M. Lim, P.-Y. Ho, P.-L. Banu, M. Park, D.-S. Ow, D. S.-W. Lee, D.-Y. 2021-06-21 doi:10.1101/2021.06.20.449192 Cold Spring Harbor Laboratory Press 2021-06-21 <![CDATA[ Protective role of the Atg8 1 homologue Gabarapl1 in regulating cardiomyocyte glycophagy in diabetic heart disease ]]> https://biorxiv.org/content/10.1101/2021.06.21.449174v1?rss=1 Mellor, K. M. Varma, U. Koutsifeli, P. Curl, C. L. Janssens, J. V. Daniels, L. J. Bernasochi, G. B. Raaijmakers, A. J. A. Benson, V. L. Chan, E. J. Annandale, M. Li, X. Nursalim, Y. Ip, W. T. K. Taylor, D. J. Raedschelders, K. Stotland, A. Robinson, A. E. Mills, R. J. Lamberts, R. R. Powell, K. L. O'Brien, T. J. Katare, R. Chandramouli, C. Ritchie, R. H. Lim, S. Y. Parton, R. G. Hu, X. Bell, J. R. Porrello, E. R. Hudson, J. E. Xiao, R.-P. Van Eyk, J. E. Gottlieb, R. A. Delbridge, L. M. D. 2021-06-22 doi:10.1101/2021.06.21.449174 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ The impact of mutation L138F/L210F on the Orai channel: a molecular dynamics simulation study ]]> https://biorxiv.org/content/10.1101/2021.06.23.449681v1?rss=1 Zhang, X. Yu, H. Liu, X. Song, C. 2021-06-24 doi:10.1101/2021.06.23.449681 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ The endoplasmic reticulum-plasma membrane tethering protein TMEM24 is a regulator of cellular Ca2+ homeostasis ]]> https://biorxiv.org/content/10.1101/2021.06.23.449694v1?rss=1 Xie, B. Panagiotou, S. Cen, J. Gilon, P. Bergsten, P. Idevall-Hagren, O. 2021-06-24 doi:10.1101/2021.06.23.449694 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Yeast cells under glucose-limitation environment need increased response cost for osmostress defense ]]> https://biorxiv.org/content/10.1101/2021.06.24.449709v1?rss=1 Luo, C. Shen, W. Gao, Z. Chen, K. Ouyang, Q. 2021-06-25 doi:10.1101/2021.06.24.449709 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Membraneless organelles formed by liquid-liquid phase separation increase bacterial fitness ]]> https://biorxiv.org/content/10.1101/2021.06.24.449778v1?rss=1 Jin, X. Lee, J.-E. Schaefer, C. Luo, X. Wollman, A. J. Payne-Dwyer, A. L. Tian, T. Zhang, X. Chen, X. Li, Y. Leake, M. C. Bai, F. C. 2021-06-25 doi:10.1101/2021.06.24.449778 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Modeling adsorption, conformation, and orientation of the Fis1 tail anchor at the mitochondrial outer membrane ]]> https://biorxiv.org/content/10.1101/2021.06.29.450436v1?rss=1 Ozgur, B. Dunn, C. D. Sayar, M. 2021-06-30 doi:10.1101/2021.06.29.450436 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ Discovery of UPSTREAM OF FLOWERING LOCUS C (UFC) and FLOWERING LOCUS C EXPRESSOR (FLX) in Gladiolus xhybridus, G. dalenii ]]> https://biorxiv.org/content/10.1101/2021.07.02.450944v1?rss=1 Aljaser, J. Anderson, N. O. Noyszewski, A. 2021-07-03 doi:10.1101/2021.07.02.450944 Cold Spring Harbor Laboratory Press 2021-07-03 <![CDATA[ circFL-seq reveals full-length circular RNAs with rolling circular reverse transcription and nanopore sequencing ]]> https://biorxiv.org/content/10.1101/2021.07.05.451107v1?rss=1 Liu, Z. Tao, C. Li, S. Du, M. Bai, Y. Hu, X. Li, Y. Chen, J. Yang, E. 2021-07-05 doi:10.1101/2021.07.05.451107 Cold Spring Harbor Laboratory Press 2021-07-05 <![CDATA[ Phosphorylation of STIM1 at ERK/CDK sites is dispensable for cell migration and ER partitioning in mitosis ]]> https://biorxiv.org/content/10.1101/2021.07.06.451280v1?rss=1 Hammad, A. S. Yu, F. Botheju, W. Elmi, A. A. Alcantara-Adap, E. Machaca, K. 2021-07-06 doi:10.1101/2021.07.06.451280 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ SAFA facilitates chromatin opening of immune genes through interacting with nascent antiviral RNAs ]]> https://biorxiv.org/content/10.1101/2021.07.06.451336v1?rss=1 Cao, L. Li, Y. Luo, Y. Guo, X. Li, S. Zhang, Z. Gao, F. Zhang, Q. Ji, X. Gao, X. Wang, Y. Zhao, Y. You, F. Liu, S. Li, J. 2021-07-07 doi:10.1101/2021.07.06.451336 Cold Spring Harbor Laboratory Press 2021-07-07 <![CDATA[ Micronutrient supplements with iron promote disruptive protozoan and fungal communities in the developing infant gut ]]> https://biorxiv.org/content/10.1101/2021.07.06.451346v1?rss=1 Popovic, A. Bourdon, C. Wang, P. W. Guttman, D. S. Soofi, S. Bhutta, Z. A. Bandsma, R. H. J. Parkinson, J. Pell, L. G. 2021-07-06 doi:10.1101/2021.07.06.451346 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ EpicPCR-Directed Cultivation of a Candidatus Saccharibacteria Symbiont Reveals a Type IV Pili-dependent Epibiotic Lifestyle ]]> https://biorxiv.org/content/10.1101/2021.07.08.451036v1?rss=1 Xie, B. Wang, J. Nie, Y. Chen, D. Hu, B. Wu, X. Du, W. 2021-07-08 doi:10.1101/2021.07.08.451036 Cold Spring Harbor Laboratory Press 2021-07-08 <![CDATA[ Gating mechanism of human N-type voltage-gated calcium channel ]]> https://biorxiv.org/content/10.1101/2021.07.08.451561v1?rss=1 Dong, Y. Gao, Y. Xu, S. Wang, Y. Yu, Z. Li, Y. Li, B. Yang, B. Zhang, X. C. Jiang, D. Huang, Z. Zhao, Y. 2021-07-08 doi:10.1101/2021.07.08.451561 Cold Spring Harbor Laboratory Press 2021-07-08 <![CDATA[ Single-cell transcriptomics for the 99.9% of species without reference genomes ]]> https://biorxiv.org/content/10.1101/2021.07.09.450799v1?rss=1 99.9% do not have any submitted genome assembly. To enable scRNA-seq for the vast majority of animals on the planet, here we introduce the concept of "k-mer homology," combining biochemical synonyms in degenerate protein alphabets with uniform data subsampling via MinHash into a pipeline called Kmermaid. Implementing this pipeline enables direct detection of similar cell types across species from transcriptomic data without the need for a reference genome. Underpinning Kmermaid is the tool Orpheum, a memory-efficient method for extracting high-confidence protein-coding sequences from RNA-seq data. After validating Kmermaid using datasets from human and mouse lung, we applied Kmermaid to the Chinese horseshoe bat (Rhinolophus sinicus), where we propagated cellular compartment labels at high fidelity. Our pipeline provides a high-throughput tool that enables analyses of transcriptomic data across divergent species transcriptomes in a genome- and gene annotation-agnostic manner. Thus, the combination of Kmermaid and Orpheum identifies cell type-specific sequences that may be missing from genome annotations and empowers molecular cellular phenotyping for novel model organisms and species. ]]> Botvinnik, O. B. Vemuri, P. Pierce Ward, N. T. Logan, P. A. Nafees, S. Karanam, L. Travaglini, K. J. Ezran, C. S. Ren, L. Wang, J. Huang, Y. Wang, J. Brown, C. T. 2021-07-10 doi:10.1101/2021.07.09.450799 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ Successful microbial colonization of space using an anti-aggregation strategy ]]> https://biorxiv.org/content/10.1101/2021.07.09.451734v1?rss=1 Liu, X. Wang, M. Nie, Y. Wu, X.-L. 2021-07-10 doi:10.1101/2021.07.09.451734 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ Tracking neural markers of template formation and implementation in attentional inhibition under different distractor consistency ]]> https://biorxiv.org/content/10.1101/2021.07.09.451861v1?rss=1 Wen, W. Huang, Z. Hou, Y. Li, S. 2021-07-11 doi:10.1101/2021.07.09.451861 Cold Spring Harbor Laboratory Press 2021-07-11 <![CDATA[ Dynamics of glioma-associated microglia and macrophages reveals their divergent roles in the immune response of brain ]]> https://biorxiv.org/content/10.1101/2021.07.11.451874v1?rss=1 Qian, J. Wang, C. Wang, B. Li, C. Fu, K. Wang, Y. Gao, Y. Niu, C. Zhao, C. Liu, J. Wang, L. Liu, R. Luo, F. Lu, M. Liu, Y. Chu, Y. 2021-07-12 doi:10.1101/2021.07.11.451874 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Collaborations and deceptions in strategic interactions revealed by hyperscanning fMRI ]]> https://biorxiv.org/content/10.1101/2021.07.11.451985v1?rss=1 Shen, S.-S. Cheng, J.-T. Hsu, Y.-R. Chen, D.-Y. Weng, M.-H. Kung, C.-C. 2021-07-12 doi:10.1101/2021.07.11.451985 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Sex differences in tissue gene regulation -- contributions of three classes of sex-biasing factors ]]> https://biorxiv.org/content/10.1101/2021.07.18.451543v1?rss=1 Blencowe, M. Itoh, Y. Chen, X. Zhao, Y. Han, Y. Shou, B. McClusky, R. Reue, K. Arnold, A. P. Yang, X. 2021-07-20 doi:10.1101/2021.07.18.451543 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ ENKD1 is a centrosomal and ciliary microtubule-associated protein important for primary cilium assembly and Hedgehog signaling ]]> https://biorxiv.org/content/10.1101/2021.07.20.453048v1?rss=1 Tiryaki, F. Deretic, J. Firat-Karalar, E. N. 2021-07-20 doi:10.1101/2021.07.20.453048 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ Cerebral coherence in task-based fMRI hyperscanning: a new trick to an old dog ]]> https://biorxiv.org/content/10.1101/2021.07.21.452832v1?rss=1 Wang, L.-S. Cheng, J.-T. Hsu, I.-J. Liou, S. Kung, C.-C. Chen, D.-Y. Weng, M.-H. 2021-07-23 doi:10.1101/2021.07.21.452832 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Discovery of a small molecule that selectively destabilizes Cryptochrome 1 and enhances life span in p53 knockout mice ]]> https://biorxiv.org/content/10.1101/2021.07.21.453206v1?rss=1 Gul, S. Akyel, Y. K. Gul, Z. M. Isin, S. Korkmaz, T. Selvi, S. Danis, I. Ipek, O. S. Aygenli, F. Taskin, A. C. Ozturk, N. Ozturk, N. Ozer Unal, D. Guzel, M. Turkay, M. Okyar, A. Kavakli, I. H. 2021-07-21 doi:10.1101/2021.07.21.453206 Cold Spring Harbor Laboratory Press 2021-07-21 <![CDATA[ Dissection of brain-wide spontaneous and functional somatosensory circuits by fMRI with optogenetic silencing ]]> https://biorxiv.org/content/10.1101/2021.07.22.453311v1?rss=1 Jung, W. B. Jiang, H. Lee, S. Kim, S.-G. 2021-07-23 doi:10.1101/2021.07.22.453311 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Identification of a distal RXFP1 gene enhancer with differential activity in fibrotic lung fibroblasts involving AP-1 ]]> https://biorxiv.org/content/10.1101/2021.07.23.453556v1?rss=1 Chen, T.-Y. Li, X. Goobie, G. C. Hung, C.-H. hamilton, H. Bahudhanapati, H. Tan, J. Kass, D. J. Zhang, Y. 2021-07-23 doi:10.1101/2021.07.23.453556 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Miniature inverted-repeat transposable elements drive rapid microRNA diversification in angiosperms ]]> https://biorxiv.org/content/10.1101/2021.07.25.453727v1?rss=1 Guo, Z. Kuang, Z. Tao, Y. Wang, H. Wan, M. Hao, C. Shen, F. Yang, X. Li, L. 2021-07-26 doi:10.1101/2021.07.25.453727 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ Structures of SARS-CoV-2 B.1.351 neutralizing antibodies provide insights into cocktail design against concerning variants ]]> https://biorxiv.org/content/10.1101/2021.07.30.454402v1?rss=1 Du, S. Liu, P. Zhang, Z. Xiao, T. Yasimayi, A. Huang, W. Wang, Y. Cao, Y. R. Xie, X. S. Xiao, J. 2021-08-01 doi:10.1101/2021.07.30.454402 Cold Spring Harbor Laboratory Press 2021-08-01 <![CDATA[ Regional Variant Analysis of Spike Glycoprotein Mutations of SARS-CoV-2 and Its Implications in COVID-19 Pandemic Control ]]> https://biorxiv.org/content/10.1101/2021.08.02.454771v1?rss=1 Punnoth Poonkuzhi, N. Elayadeth-Meethal, M. Ollakkot, S. UK, I. Saheer Kuruniyan, M. 2021-08-02 doi:10.1101/2021.08.02.454771 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ Preferential interactions of a crowder protein with the specific binding site of a native protein complex ]]> https://biorxiv.org/content/10.1101/2021.08.06.455410v1?rss=1 Dong, X. Qin, L.-Y. Gong, Z. Qin, S. Zhou, H.-X. Tang, C. 2021-08-09 doi:10.1101/2021.08.06.455410 Cold Spring Harbor Laboratory Press 2021-08-09 <![CDATA[ Development of Functional Connectome Gradients during Childhood and Adolescence ]]> https://biorxiv.org/content/10.1101/2021.08.08.455594v1?rss=1 Xia, Y. Xia, M. Liu, J. Liao, X. Lei, T. Liang, X. Zhao, T. Shi, Z. Sun, L. Chen, X. Men, W. Wang, Y. Pan, Z. Luo, J. Peng, S. Chen, M. Lei, H. Tan, S. Gao, J. Qin, S. Gong, G. Tao, S. Dong, Q. He, Y. 2021-08-09 doi:10.1101/2021.08.08.455594 Cold Spring Harbor Laboratory Press 2021-08-09 <![CDATA[ Visualizing conformational space of functional biomolecular complexes by deep manifold learning ]]> https://biorxiv.org/content/10.1101/2021.08.09.455739v1?rss=1 Wu, Z. Chen, E. Zhang, S. Ma, Y. Liu, C. Yin, C.-C. Mao, Y. 2021-08-10 doi:10.1101/2021.08.09.455739 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Stable Flow-induced Expression of KLK10 Inhibits Endothelial Inflammation and Atherosclerosis ]]> https://biorxiv.org/content/10.1101/2021.08.10.455857v1?rss=1 Williams, D. Mahmoud, M. Liu, R. Andueza, A. Kumar, S. Kang, D.-W. Zhang, J. Tamargo, I. Villa-Roel, N. Baek, K.-I. Lee, H. An, Y. Zhang, L. Tate, E. W. Bagchi, P. Pohl, J. Mosnier, L. Diamandis, E. P. Mihara, K. Hollenberg, M. Dai, Z. Jo, H. 2021-08-10 doi:10.1101/2021.08.10.455857 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Multiomics reveals the genomic, proteomic and metabolic influences of histidyl dipeptides on heart ]]> https://biorxiv.org/content/10.1101/2021.08.10.455864v1?rss=1 Baba, S. Yan, K. Mei, Z. Zhao, J. Prodhan, M. A. Obal, D. Katragadda, K. Doelling, B. Hoetker, D. Posa, D. K. He, L. Yin, X. Shah, J. Pan, J. Rai, S. Lorkiewicz, P. K. Zhang, X. Li, S. Bhatnagar, A. 2021-08-10 doi:10.1101/2021.08.10.455864 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Heterochromatin rewiring and domain disruption-mediated chromatin compaction during erythropoiesis ]]> https://biorxiv.org/content/10.1101/2021.08.12.456090v1?rss=1 Li, D. Wu, F. Zhou, S. Huang, X. Lee, H.-Y. S. 2021-08-12 doi:10.1101/2021.08.12.456090 Cold Spring Harbor Laboratory Press 2021-08-12 <![CDATA[ Humanoid robots are perceived as an evolutionary threat ]]> https://biorxiv.org/content/10.1101/2021.08.13.456053v1?rss=1 Wei, Z. Chen, Y. Ren, J. Piao, Y. Zhang, P. Zha, R. Qiu, B. Zhang, D. Bi, Y. Han, S. Li, C. Zhang, X. 2021-08-13 doi:10.1101/2021.08.13.456053 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Clock genes Period1 and Period2 in the hippocampal CA1 mediate depression-like behaviors and rapid antidepressant response ]]> https://biorxiv.org/content/10.1101/2021.08.14.456364v1?rss=1 Wang, X.-L. Liu, X. Yuan, K. Han, Y. Xue, Y.-X. Meng, S.-Q. Li, S.-X. 2021-08-15 doi:10.1101/2021.08.14.456364 Cold Spring Harbor Laboratory Press 2021-08-15 <![CDATA[ Musicians and non-musicians consonant/dissonant perception investigated by EEG and fMRI ]]> https://biorxiv.org/content/10.1101/2021.08.15.456377v1?rss=1 Jo, H. Hsieh, T.-H. Chhien, W.-C. Shaw, F.-Z. Liang, S.-F. Kung, C.-C. 2021-08-15 doi:10.1101/2021.08.15.456377 Cold Spring Harbor Laboratory Press 2021-08-15 <![CDATA[ Trade-driven trapping dampens the biodiversity benefits of forest restoration in Southeast Asia ]]> https://biorxiv.org/content/10.1101/2021.08.20.457106v1?rss=1 Sagar, H. S. S. C. Gilroy, J. J. Swinfield, T. Yong, D. L. Gemita, E. Novriyanti, N. Lee, D. C. Janra, M. N. Balmford, A. Hua, F. 2021-08-20 doi:10.1101/2021.08.20.457106 Cold Spring Harbor Laboratory Press 2021-08-20 <![CDATA[ Plasma Contains Ultra-short Single-stranded DNA in Addition to Nucleosomal cfDNA ]]> https://biorxiv.org/content/10.1101/2021.08.22.457243v1?rss=1 Cheng, J. C. Morselli, M. Huang, W.-L. Heo, Y. J. Pinheiro-Ferreira, T. Li, F. Wei, F. Chia, D. He, H.-J. Cole, K. Su, W.-C. Pellegrini, M. Wong, D. T. 2021-08-24 doi:10.1101/2021.08.22.457243 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ Multi-omics integration and regulatory inference for unpaired single-cell data with a graph-linked unified embedding framework ]]> https://biorxiv.org/content/10.1101/2021.08.22.457275v1?rss=1 Cao, Z.-J. Gao, G. 2021-08-24 doi:10.1101/2021.08.22.457275 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ Reorganizations of latency structure within white matter from wakefulness to sleep ]]> https://biorxiv.org/content/10.1101/2021.08.25.457605v1?rss=1 Guo, B. Zhou, F. Zou, G. Jiang, J. Zou, Q. Gao, J. 2021-08-27 doi:10.1101/2021.08.25.457605 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Improved protein docking by predicted interface residues ]]> https://biorxiv.org/content/10.1101/2021.08.25.457642v1?rss=1 300.000 low-resolution rigid-body template free docking decoys. Overall we find that BIPSPI is the best method to identify interface amino acids and score docking solutions. Further, using BIPSPI provides better docking results than state of the art scoring functions, with >12% of first ranked docking models being acceptable. Additional experiments indicated precision as a high-importance metric when estimating interface prediction quality, focusing on docking constraints production. We also discussed several limitations for the adoption of interface predictions as constraints in a docking protocol. ]]> Pozatti, G. Kundrotas, P. Elofsson, A. 2021-08-26 doi:10.1101/2021.08.25.457642 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ C. elegans enteric motor neurons fire synchronized action potentials underlying the defecation motor program ]]> https://biorxiv.org/content/10.1101/2021.08.25.457687v1?rss=1 Jiang, J. Su, Y. Zhang, R. Li, H. Tao, L. Liu, Q. 2021-08-26 doi:10.1101/2021.08.25.457687 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ Role of sleep quality in the acceleration of biological aging and its potential for preventive interaction on air pollution insults: findings from the UK Biobank cohort ]]> https://biorxiv.org/content/10.1101/2021.08.27.457922v1?rss=1 Gao, X. Huang, N. Huang, T. 2021-09-15 doi:10.1101/2021.08.27.457922 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Hexose translocation mediated by SlSWEET5b is required for pollen maturation in Solanum lycopersicum ]]> https://biorxiv.org/content/10.1101/2021.08.30.458256v1?rss=1 Ko, H.-Y. Tseng, H.-W. Ho, L.-H. Wang, L. Chang, T.-F. Lin, A. Ruan, Y.-L. Neuhaus, H. E. Guo, W.-J. 2021-08-31 doi:10.1101/2021.08.30.458256 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Clustering single cell CITE-seq data with a canonical correlation based deep learning method ]]> https://biorxiv.org/content/10.1101/2021.09.07.459236v1?rss=1 Musu, Y. Liang, C. Deng, M. 2021-09-08 doi:10.1101/2021.09.07.459236 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ The chromatin-remodeling enzyme Smarca5 regulates erythrocyte aggregation via Keap1-Nrf2 signaling ]]> https://biorxiv.org/content/10.1101/2021.09.08.459391v1?rss=1 Liu, F. Ding, Y. Li, Y. Cliff Zhang, Q. 2021-09-09 doi:10.1101/2021.09.08.459391 Cold Spring Harbor Laboratory Press 2021-09-09 <![CDATA[ α-/γ-Taxilin are required for centriolar subdistal appendage assembly and microtubule organization ]]> https://biorxiv.org/content/10.1101/2021.09.08.459392v1?rss=1 Ma, D. Wang, R. Wang, F. Chen, Z. Huang, N. Xia, Y. Teng, J. Chen, J. 2021-09-08 doi:10.1101/2021.09.08.459392 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ Even allocation of benefits stabilizes microbial community engaged in metabolic division of labor ]]> https://biorxiv.org/content/10.1101/2021.09.10.459869v1?rss=1 Wang, M. Chen, X. Liu, x. Fang, Y. Zheng, X. Huang, T. Tang, Y.-Q. Nie, Y. Wu, X.-L. 2021-09-11 doi:10.1101/2021.09.10.459869 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ ProtAnno, an Automated Cell Type Annotation Tool for Single Cell Proteomics Data that Integrates Information from Multiple Reference Sources ]]> https://biorxiv.org/content/10.1101/2021.09.13.460162v1?rss=1 Deng, W. Zhu, B. Park, S. Sumida, T. S. Unterman, A. Hafler, D. A. Cruz, C. S. D. Kaminski, N. Lucas, C. L. Zhao, H.-y. 2021-09-13 doi:10.1101/2021.09.13.460162 Cold Spring Harbor Laboratory Press 2021-09-13 <![CDATA[ Secretin channel-interactors prevent antibiotic influx during type IV pili assembly in P. aeruginosa ]]> https://biorxiv.org/content/10.1101/2021.09.13.460190v1?rss=1 Cho, H. Kwon, O. H. Sher, J. W. Kim, B.-o. Cho, Y.-H. 2021-09-14 doi:10.1101/2021.09.13.460190 Cold Spring Harbor Laboratory Press 2021-09-14 <![CDATA[ Principles governing the topological organization of object selectivities in ventral temporal cortex ]]> https://biorxiv.org/content/10.1101/2021.09.15.460220v1?rss=1 Zhang, Y. Zhou, K. Bao, P. Liu, J. 2021-09-17 doi:10.1101/2021.09.15.460220 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ Mechanistic insights into dynamic mutual regulation of USP14 and proteasome ]]> https://biorxiv.org/content/10.1101/2021.09.15.460436v1?rss=1 Zhang, S. Zou, S. Yin, D. Finley, D. Wu, Z. Mao, Y. 2021-09-15 doi:10.1101/2021.09.15.460436 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ ppGpp Is Present in, and Regulates Sleep of, Drosophila ]]> https://biorxiv.org/content/10.1101/2021.09.16.460595v1?rss=1 Rao, Y. Young, W. Zhang, X. Dai, H. X. Zhou, E. Zhang, W. 2021-09-17 doi:10.1101/2021.09.16.460595 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ Increased Activation in the Fusiform Face Area to Greebles is a Result of Expertise Training, Not by its Face-likeness ]]> https://biorxiv.org/content/10.1101/2021.09.16.460714v1?rss=1 Liu, K. Chun, C.-Y. Wang, L.-S. Kung, C.-C. 2021-09-20 doi:10.1101/2021.09.16.460714 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ Functional network topography of the medial entorhinal cortex ]]> https://biorxiv.org/content/10.1101/2021.09.20.461016v1?rss=1 Obenhaus, H. A. Zong, W. Jacobsen, R. I. Rose, T. Donato, F. Chen, L. Cheng, H. Bonhoeffer, T. Moser, M.-B. Moser, E. I. 2021-09-21 doi:10.1101/2021.09.20.461016 Cold Spring Harbor Laboratory Press 2021-09-21 <![CDATA[ PCDH7 Promotes Cell Migration by Regulating Myosin Activity ]]> https://biorxiv.org/content/10.1101/2021.09.21.460794v1?rss=1 Qureshi, M. H. Cinko, M. T. Bayraktar, H. Akkaya, C. Kamacioglu, A. Uretmen, Z. C. Bozluolcay, E. Ozlu, N. 2021-09-21 doi:10.1101/2021.09.21.460794 Cold Spring Harbor Laboratory Press 2021-09-21 <![CDATA[ Ratiometric RNA labeling allows dynamic multiplexed analysis of gene circuits in single cells ]]> https://biorxiv.org/content/10.1101/2021.09.23.461487v1?rss=1 Xu, S. Li, K. Ma, L. Zhang, J. Yoon, S. Elowitz, M. B. Lin, Y. 2021-09-23 doi:10.1101/2021.09.23.461487 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ A structural biology community assessment of AlphaFold 2 applications ]]> https://biorxiv.org/content/10.1101/2021.09.26.461876v1?rss=1 Akdel, M. Pires, D. E. Porta-Pardo, E. Janes, J. Zalevsky, A. O. Meszaros, B. Bryant, P. Good, L. L. Laskowski, R. A. Pozzati, G. Shenoy, A. Zhu, W. Kundrotas, P. Ruiz-Serra, V. Rodrigues, C. H. Dunham, A. S. Burke, D. Borkakoti, N. Velankar, S. Frost, A. Lindorff-Larsen, K. Valencia, A. Ovchinnikov, S. Durairaj, J. Ascher, D. B. Thornton, J. M. Davey, N. E. Stein, A. Elofsson, A. Croll, T. I. Beltrao, P. 2021-09-26 doi:10.1101/2021.09.26.461876 Cold Spring Harbor Laboratory Press 2021-09-26 <![CDATA[ Gaussian Network Model Revisited: Effects of Mutation and Ligand Binding on Protein Behavior ]]> https://biorxiv.org/content/10.1101/2021.09.29.462446v1?rss=1 Erman, B. 2021-10-01 doi:10.1101/2021.09.29.462446 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Postsynaptic synucleins mediate vesicular exocytosis of endocannabinoids ]]> https://biorxiv.org/content/10.1101/2021.10.04.462870v1?rss=1 Albarran, E. Sun, Y. Liu, Y. Raju, K. Dong, A. Li, Y. Wang, S. Sudhof, T. C. Ding, J. B. 2021-10-05 doi:10.1101/2021.10.04.462870 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ Vernalization-triggered expression of the antisense transcript COOLAIR is mediated by CBF genes ]]> https://biorxiv.org/content/10.1101/2021.10.07.463455v1?rss=1 Jeon, M. Jeong, G. Hyun, Y. Lee, I. 2021-10-09 doi:10.1101/2021.10.07.463455 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ Nanchangmycin regulates FYN, FAK and ERK to control the fibrotic activity of hepatic stellate cells ]]> https://biorxiv.org/content/10.1101/2021.10.08.463221v1?rss=1 Li, W. Chen, J. Y. Sun, C. Sparks, R. P. Pantano, L. Rahman, R.-U. Moran, S. P. Pondick, J. V. Kirchner, R. Wrobel, D. Bieler, M. Ho Sui, S. J. Doerner, J. F. Rippmann, J. F. Mullen, A. C. 2021-10-09 doi:10.1101/2021.10.08.463221 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ Progressive chromatin silencing of ABA biosynthesis gene permits seed germination in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2021.10.08.463712v1?rss=1 Yang, D. Zhao, F. Zhu, D. Chen, X. Kong, X. Wu, Y. Chen, M. Du, J. Qu, L.-J. Wu, Z. 2021-10-09 doi:10.1101/2021.10.08.463712 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ In vivo emergence of high-level resistance during treatment reveals the first identified mechanism of amphotericin B resistance in Candida auris ]]> https://biorxiv.org/content/10.1101/2021.10.08.463721v1?rss=1 32-fold increase in amphotericin B resistance, and comprehensive sterol profiling revealed an abrogation of ergosterol biosynthesis and a corresponding accumulation of cholesta-type sterols in isolates and strains harboring the clinically derived ERG6 mutation. Together these findings represent the first significant step forward in the understanding of clinical amphotericin B resistance in C. auris. ]]> Rybak, J. M. Barker, K. S. Munoz, J. F. Parker, J. E. Ahmad, S. Mokaddas, E. Abdullah, A. Elhagracy, R. S. Kelly, S. L. Cuomo, C. A. Rogers, P. D. 2021-10-09 doi:10.1101/2021.10.08.463721 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ Methylome inheritance and enhancer dememorization reset an epigenetic gate safeguarding embryonic programs ]]> https://biorxiv.org/content/10.1101/2021.10.10.463758v1?rss=1 Wu, X. Zhang, H. Zhang, B. Zhang, Y. Wang, Q. Shen, W. Wu, X. Li, L. Xia, W. Nakamura, R. Liu, B. Liu, F. Takeda, H. Meng, A. Xie, W. 2021-10-11 doi:10.1101/2021.10.10.463758 Cold Spring Harbor Laboratory Press 2021-10-11 <![CDATA[ A Multi-proxy assessment of the impact of climate change on Late Holocene (ca 4500-3800 BP) Native American villages of the Georgia coast ]]> https://biorxiv.org/content/10.1101/2021.10.11.463980v1?rss=1 Garland, C. J. Thompson, V. D. Sanger, M. C. Smith, K. Y. Andrus, F. T. Lawres, N. R. Napora, K. G. Calaninno, C. E. Compton, J. M. Jones, S. Hadden, C. S. Cherkinsky, A. Maddox, T. Deng, Y.-t. Lulewicz, I. H. Parsons, L. 2021-10-11 doi:10.1101/2021.10.11.463980 Cold Spring Harbor Laboratory Press 2021-10-11 <![CDATA[ Prion-like α-synuclein pathology in the brains of infants: Krabbe disease as a novel seed-competent α-synucleinopathy ]]> https://biorxiv.org/content/10.1101/2021.10.12.463948v1?rss=1 Hatton, C. Ghanem, S. S. Koss, D. Abdi, I. Y. Gibbons, E. Guerreiro, R. Bras, J. International DLB Genetics Consortium, Walker, L. Gelpi, E. Heywood, W. Outeiro, T. F. Attems, J. McFarland, B. Forsyth, R. El-Agnaf, O. M. Erskine, D. 2021-10-14 doi:10.1101/2021.10.12.463948 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Modeling homing suppression gene drive in haplodiploid organisms ]]> https://biorxiv.org/content/10.1101/2021.10.12.464047v1?rss=1 Liu, Y. Champer, J. 2021-10-13 doi:10.1101/2021.10.12.464047 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Calcium-independent but voltage-dependent secretion (CiVDS) mediates synaptic transmission in a mammalian central synapse ]]> https://biorxiv.org/content/10.1101/2021.10.13.464194v1?rss=1 100 times faster than CDS in vesicle recycling with much less short-term depression; (4) the fusion machinery of CiVDS includes Cav2.2 (voltage sensor) and SNARE (fusion pore). Together, an essential component of activity-induced EPSCs is mediated by CiVDS in a central synapse. ]]> Wang, Y. Huang, R. Chai, Z. Wang, C. Du, X. Hang, Y. Xu, Y. Li, J. Jiang, X. Wu, X. Qiao, Z. Li, Y. Liu, B. Zhang, X. Cao, P. Zhu, F. Zhou, Z. 2021-10-14 doi:10.1101/2021.10.13.464194 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Inhibiting ACSL1 related ferroptosis restrains MHV-A59 infection ]]> https://biorxiv.org/content/10.1101/2021.10.14.464337v1?rss=1 Xia, H. Zhang, Z. You, F. 2021-10-14 doi:10.1101/2021.10.14.464337 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Dynamic Functional Brain Reconfiguration During Sustained Pain ]]> https://biorxiv.org/content/10.1101/2021.10.16.464642v1?rss=1 Lee, J.-J. Lee, S. Lee, D. H. Woo, C.-W. 2021-10-16 doi:10.1101/2021.10.16.464642 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ Type IV pilus shapes a "bubble-jet" pattern opposing spatial intermixing of two interacting bacterial populations ]]> https://biorxiv.org/content/10.1101/2021.10.17.464652v1?rss=1 Wang, M. Chen, X. Ma, Y. Johnson, D. Nie, Y. Wu, X.-L. 2021-10-17 doi:10.1101/2021.10.17.464652 Cold Spring Harbor Laboratory Press 2021-10-17 <![CDATA[ Extrasynaptic NMDA receptors bidirectionally modulate intrinsic excitability of inhibitory neurons ]]> https://biorxiv.org/content/10.1101/2021.10.17.464733v1?rss=1 zhou, q. Yao, L. Rong, Y. Ma, X. Li, H. Deng, D. Chen, Y. Yang, S. Peng, T. Ye, T. Liang, F. Xu, N. 2021-10-18 doi:10.1101/2021.10.17.464733 Cold Spring Harbor Laboratory Press 2021-10-18 <![CDATA[ An improved vector for baculovirus-mediated protein production in mammalian cells ]]> https://biorxiv.org/content/10.1101/2021.10.18.464913v1?rss=1 Guo, W. Wang, M. Chen, L. 2021-10-19 doi:10.1101/2021.10.18.464913 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ The hallucinogenic serotonin2A receptor agonist, DOI, promotes CREB-dependent gene expression of specific plasticity-associated genes in the rodent neocortex ]]> https://biorxiv.org/content/10.1101/2021.10.19.464691v1?rss=1 Desouza, L. A. Benekareddy, M. Fanibunda, S. E. Mohammad, F. Gur, T. Blendy, J. A. Vaidya, V. A. 2021-10-19 doi:10.1101/2021.10.19.464691 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Global distribution of mammal herbivore biomass reveals megafauna extinction patterns ]]> https://biorxiv.org/content/10.1101/2021.10.19.464976v1?rss=1 5 kg) and 138 Mt by small species. Anthropogenic activity reduced large herbivores biomass by 57%, estimated now at 82 Mt; consequently, small herbivores now dominate global herbivore biomass with 98 Mt (-29%). Losses vary greatly across climatic zones and functional groups, suggesting that size is not the only discriminant feature of biomass decline. Actual evapotranspiration is the most important driver of total, large, and small herbivore biomass and explains 64%, 59%, and 49% of its variation, respectively. Energy and water dependency is high for large herbivores, whose biomass is greater in hot and wet areas, challenging the notion that large herbivore biomass peaks in savannas only. Outside Africa and the Tropics, potential-biomass hotspots occur in areas today dominated by humans; this could undermine the recovery of larger species in certain areas. These herbivore biomass estimates provide a quantitative benchmark for setting conservation and rewilding goals at large spatial scales. The herbivore model and functional classification create new opportunities to integrate mammals into Earth System science and models. ]]> Berzaghi, F. Zhu, D. Alroy, J. Ciais, P. 2021-10-20 doi:10.1101/2021.10.19.464976 Cold Spring Harbor Laboratory Press 2021-10-20 <![CDATA[ OsMADS58 stabilizes gene regulatory circuits during rice stamen development ]]> https://biorxiv.org/content/10.1101/2021.10.20.465065v1?rss=1 Bai, S.-N. Shen, L. Tian, F. Cheng, Z. Zhao, Q. Feng, Q. Zhao, Y. Han, B. Fang, Y. Lin, Y. Chen, R. Wang, D. Sun, W. Sun, J. Zeng, H. Yao, N. Gao, G. Luo, J. Xu, Z. 2021-10-20 doi:10.1101/2021.10.20.465065 Cold Spring Harbor Laboratory Press 2021-10-20 <![CDATA[ The behavioral effects of gestational and lactational benzopyrene exposure vary by sex and genotype in mice with differences at the Ahr and Cyp1a2 loci ]]> https://biorxiv.org/content/10.1101/2021.10.22.465510v1?rss=1 Honaker, A. Kyntchev, A. Foster, E. Clough, K. Asiedu, E. Feltner, M. Ferguson, V. Forrest, P. T. Sene, Y. Mullaguru, J. Niang, M. D. Perry, C. Curran, C. P. 2021-10-24 doi:10.1101/2021.10.22.465510 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ Double-check the zebrafish 18s rRNA qPCR primers: they may be wrong ]]> https://biorxiv.org/content/10.1101/2021.10.23.464780v1?rss=1 Wang, J. Yang, Z. Xiao, A. 2021-10-25 doi:10.1101/2021.10.23.464780 Cold Spring Harbor Laboratory Press 2021-10-25 <![CDATA[ Inhibition of SAR S-CoV-2 infection and replication by lactoferrin, MUC1 and α-lactalbumin identified in human breastmilk ]]> https://biorxiv.org/content/10.1101/2021.10.29.466402v1?rss=1 Xiang, K. Lai, X. Yu, Y. Xian, W. Ye, F. Ju, X. Luo, Y. Dong, H. Zhou, Y. Tan, W. Zhuang, H. Li, T. Liu, X. Ding, Q. 2021-11-02 doi:10.1101/2021.10.29.466402 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Quantitative model suggests both intrinsic and contextual features contribute to the transcript coding ability determination in cells ]]> https://biorxiv.org/content/10.1101/2021.10.30.466534v1?rss=1 Kang, Y.-j. Li, J.-Y. Ke, L. Jiang, S. Yang, D.-c. Hou, M. Gao, G. 2021-11-02 doi:10.1101/2021.10.30.466534 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Emergence of an adaptive epigenetic cell state in human bladder urothelial carcinoma evolution ]]> https://biorxiv.org/content/10.1101/2021.10.30.466556v1?rss=1 Xiao, Y. Jin, W. Qian, K. Wu, K. Wang, G. Jiang, W. Cao, R. Ju, L. Zhao, Y. Zheng, H. Liu, T. Chang, L. Xu, Z. Wang, T. Luo, J. Shan, L. Yu, F. Chen, X. Liu, D. Cao, H. Yang, Z. Li, S. Shi, H. Guo, Z. Gong, Y. Liu, N. Li, S. Wang, Y. Cao, X. Ding, W. Zhou, W. Cui, D. Tian, Y. Ji, C. Luo, Y. Hong, X. Ma, H. Chen, F. Peng, M. Zhang, Y. Wang, X. 2021-11-02 doi:10.1101/2021.10.30.466556 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Understanding gene regulatory mechanisms based on gene classification ]]> https://biorxiv.org/content/10.1101/2021.10.31.466641v1?rss=1 Tian, H. He, Y. Xue, Y. Gao, Y. Q. 2021-11-02 doi:10.1101/2021.10.31.466641 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Dominant species determine ecosystem stability across scales in Inner Mongolian grassland ]]> https://biorxiv.org/content/10.1101/2021.10.31.466650v1?rss=1 Wang, Y. Wang, S.-P. Zhao, L. Liang, C. Miao, B. Zhang, Q. Niu, X. Ma, W. Schmid, B. 2021-11-03 doi:10.1101/2021.10.31.466650 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Sleep Need, the Key Regulator of Sleep Homeostasis, Is Indicated and Controlled by Phosphorylation of Threonine 221 in Salt Inducible Kinase 3 ]]> https://biorxiv.org/content/10.1101/2021.11.06.467421v1?rss=1 Li, Y. Zhou, E. Liu, Y. Yu, J. Yang, J. Li, C. Cui, Y. Wang, T. Li, C. Liu, Z. Rao, Y. 2021-11-07 doi:10.1101/2021.11.06.467421 Cold Spring Harbor Laboratory Press 2021-11-07 <![CDATA[ Nucleobase clustering contributes to the formation and hollowing of repeat-expansion RNA condensate ]]> https://biorxiv.org/content/10.1101/2021.11.08.467691v1?rss=1 Ma, Y. Li, H. Gong, Z. Yang, S. Wang, P. Tang, C. 2021-11-08 doi:10.1101/2021.11.08.467691 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ Determining the architecture of nuclear ring of Xenopus laevis nuclear pore complex using integrated approaches ]]> https://biorxiv.org/content/10.1101/2021.11.10.468004v1?rss=1 Ren, H. Tai, L. Zhu, Y. Chan, C. Zhao, Q. Xu, J. Wang, X. Ma, X. Zhao, L. Huang, X. Yin, G. Jia, M. Zhu, X. An, Y. Zhao, G. Huang, C. Zhang, L. Fan, J. Sun, F. Zhang, C. 2021-11-11 doi:10.1101/2021.11.10.468004 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ 8 A structure of the nuclear ring of the Xenopus laevis nuclear pore complex solved by cryo-EM and AI ]]> https://biorxiv.org/content/10.1101/2021.11.10.468008v1?rss=1 Ren, H. Tai, L. Zhu, Y. Huang, X. Sun, F. Zhang, C. 2021-11-11 doi:10.1101/2021.11.10.468008 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ 8 A structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex solved by cryo-EM and AI ]]> https://biorxiv.org/content/10.1101/2021.11.10.468011v1?rss=1 Tai, L. Zhu, Y. Ren, H. Huang, X. Zhang, C. Sun, F. 2021-11-11 doi:10.1101/2021.11.10.468011 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Low frequency somatic copy number alterations in normal human lymphocytes revealed by large scale single-cell whole genome profiling ]]> https://biorxiv.org/content/10.1101/2021.11.10.468149v1?rss=1 Liu, L. Chen, H. Sun, C. Zhang, J. Wang, J. Du, M. Li, J. Di, L. Shen, J. Geng, S. Pang, Y. Luo, Y. Wu, C. Fu, Y. Zheng, Z. Wang, J. Huang, Y. 2021-11-13 doi:10.1101/2021.11.10.468149 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ EBV LMP1-activated mTORC1 and mTORC2 Coordinately Promote Nasopharyngeal Cancer Stem Cell Properties ]]> https://biorxiv.org/content/10.1101/2021.11.10.468172v1?rss=1 Zhu, N. Wang, Q. Wu, Z. Wang, Y. Zeng, M.-S. Yuan, Y. 2021-11-12 doi:10.1101/2021.11.10.468172 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ Scaling between DNA and cell size governs bacterial growth homeostasis and resource allocation ]]> https://biorxiv.org/content/10.1101/2021.11.12.468234v1?rss=1 Li, B. Zhang, S. Zhang, L. Qiao, X. Shi, Y. Li, C. Ouyang, Q. Wei, P. Qian, L. 2021-11-12 doi:10.1101/2021.11.12.468234 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ RIF1-ASF1-mediated high-order chromatin structure safeguards genome integrity ]]> https://biorxiv.org/content/10.1101/2021.11.19.469338v1?rss=1 Xu, D. Feng, S. Ma, S. Li, K. Gao, S. Ning, S. Shang, J. Guo, R. Li, Q. Guo, R. Blumenfeld, B. Simon, I. 2021-11-19 doi:10.1101/2021.11.19.469338 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ A fast variational algorithm to detect the clonal copy number substructure of tumors from single-cell data ]]> https://biorxiv.org/content/10.1101/2021.11.20.469390v1?rss=1 De Falco, A. Caruso, F. P. Su, X. D. Iavarone, A. Ceccarelli, M. 2021-11-22 doi:10.1101/2021.11.20.469390 Cold Spring Harbor Laboratory Press 2021-11-22 <![CDATA[ The Flowering Repressor SVP recruits the TOPLESS co-repressor to control flowering in chrysanthemum and Arabidopsis ]]> https://biorxiv.org/content/10.1101/2021.11.23.469726v1?rss=1 Jiang, J. Zhang, Z. Hu, Q. Zhu, Y. Gao, Z. Shang, E. Liu, G. Liu, W. Hu, R. Chong, X. Guan, Z. Fang, W. Chen, S. Sun, B. He, Y. Chen, F. 2021-11-24 doi:10.1101/2021.11.23.469726 Cold Spring Harbor Laboratory Press 2021-11-24 <![CDATA[ Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography ]]> https://biorxiv.org/content/10.1101/2021.11.28.468932v1?rss=1 Guven, O. Gul, M. Ayan, E. Johnson, J. A. Cakilkaya, B. Usta, G. Ertem, F. B. Tokay, N. Yuksel, B. Gocenler, O. Buyukdag, C. Botha, S. Ketawala, G. Su, Z. Hayes, B. Poitevin, F. Batyuk, A. Yoon, C. H. Kupitz, C. Durdagi, S. Sierra, R. G. DeMirci, H. 2021-11-30 doi:10.1101/2021.11.28.468932 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Structural insights into the mechanism of nucleotide regulation of pancreatic KATP channel ]]> https://biorxiv.org/content/10.1101/2021.11.29.470334v1?rss=1 Wang, M. Wu, J.-X. Ding, D. Duan, X. Ma, S. Lai, L. Chen, L. 2021-11-29 doi:10.1101/2021.11.29.470334 Cold Spring Harbor Laboratory Press 2021-11-29 <![CDATA[ GraphPrompt: Biomedical Entity Normalization Using Graph-based Prompt Templates ]]> https://biorxiv.org/content/10.1101/2021.11.29.470486v1?rss=1 Zhang, J. Wang, Z. Zhang, S. Bhalerao, M. M. Liu, Y. Zhu, D. Wang, S. 2021-12-01 doi:10.1101/2021.11.29.470486 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Effect of spatiotemporally changing environment on serial dependence in ensemble representations ]]> https://biorxiv.org/content/10.1101/2021.11.30.470662v1?rss=1 Son, S. Lee, J. Kwon, O.-S. Kim, Y. J. 2021-12-02 doi:10.1101/2021.11.30.470662 Cold Spring Harbor Laboratory Press 2021-12-02 <![CDATA[ A nuclear import pathway exploited by viroid RNAs ]]> https://biorxiv.org/content/10.1101/2021.12.02.470923v1?rss=1 Ma, J. Mudiyanselage, S. D. D. Park, W. J. Wang, M. Takeda, R. Liu, B. Wang, Y. 2021-12-03 doi:10.1101/2021.12.02.470923 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ Universality and non-universality of the growth law ]]> https://biorxiv.org/content/10.1101/2021.12.02.471021v1?rss=1 Wang, Q. Lin, J. 2021-12-03 doi:10.1101/2021.12.02.471021 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ Engineering RNA viruses with unnatural amino acid to evoke adjustable immune response in mice ]]> https://biorxiv.org/content/10.1101/2021.12.04.471206v1?rss=1 Zheng, Z. Wang, Y. Wu, X. Zhang, H. Chen, H. Lin, H. Shen, Y. Xia, Q. 2021-12-07 doi:10.1101/2021.12.04.471206 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Sterilization of drug-resistant influenza virus through genetic interference: use of unnatural amino acid-engineered virions ]]> https://biorxiv.org/content/10.1101/2021.12.04.471209v1?rss=1 Wu, X. Zheng, Z. Chen, H. Lin, H. Yang, Y. Bai, Y. Xia, Q. 2021-12-05 doi:10.1101/2021.12.04.471209 Cold Spring Harbor Laboratory Press 2021-12-05 <![CDATA[ A deep learning-based multisite neuroimage harmonization framework established with traveling-subject dataset ]]> https://biorxiv.org/content/10.1101/2021.12.05.471192v1?rss=1 Tian, d. Zeng, Z. Sun, X. Tong, Q. Li, H. He, H. Gao, J. He, Y. Xia, M. 2021-12-07 doi:10.1101/2021.12.05.471192 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Cohesin modulates DNA replication to preserve genome integrity ]]> https://biorxiv.org/content/10.1101/2021.12.06.471507v1?rss=1 Wu, J. Liu, Y. Zhangding, Z. Liu, X. Ai, C. Gan, T. Liu, Y. Yin, J. Zhang, W. Hu, J. 2021-12-07 doi:10.1101/2021.12.06.471507 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ B.1.1.529 escapes the majority of SARS-CoV-2 neutralizing antibodies of diverse epitopes ]]> https://biorxiv.org/content/10.1101/2021.12.07.470392v1?rss=1 Cao, Y. R. Wang, J. Jian, F. Xiao, T. Song, W. Yisimayi, A. Huang, W. Li, Q. Wang, P. An, R. Wang, J. Wang, Y. Niu, X. Yang, S. Liang, H. Sun, H. Li, T. Yu, Y. Cui, Q. Liu, S. Yang, X. Du, S. Zhang, Z. Hao, X. Shao, F. Jin, R. Wang, X. Xiao, J. Wang, Y. Xie, X. S. 2021-12-09 doi:10.1101/2021.12.07.470392 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Escape Steering by Cholecystokinin Peptidergic Signaling ]]> https://biorxiv.org/content/10.1101/2021.12.08.471862v1?rss=1 Chen, L. Liu, Y. Su, P. Hung, W. Li, H. Wang, Y. Yue, Z. Ge, M. Wu, Z. Zhang, Y. Fei, P. Chen, L.-M. Tao, L. Mao, H. Zhen, M. Gao, S. 2021-12-09 doi:10.1101/2021.12.08.471862 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Deficiency in endocannabinoid synthase DAGLB contributes to Parkinson's disease and dopaminergic neuron dysfunction ]]> https://biorxiv.org/content/10.1101/2021.12.09.471983v1?rss=1 Liu, Z. Yang, N. Dong, J. Tian, W. Chang, L. Ma, J. Guo, J. Tan, J. Dong, A. He, K. Zhou, J. Cinar, R. Wu, J. Salinas, A. Sun, L. Kung, J. Xie, C. Oldham, B. Kumar, M. Hawes, S. Ding, J. Wang, L. Wang, T. Chan, P. Zhang, Z. Le, W. Chen, S. Lovinger, D. M. Cui, G. Li, Y. Cai, H. Tang, B. 2021-12-09 doi:10.1101/2021.12.09.471983 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Mutations in RBD of SARS-CoV-2 Omicron variant result stronger binding to human ACE2 protein ]]> https://biorxiv.org/content/10.1101/2021.12.10.472102v1?rss=1 Lupala, C. S. Ye, Y. Chen, H. Su, X. Liu, H. 2021-12-13 doi:10.1101/2021.12.10.472102 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Two Stages of Speech Envelope Tracking in Human Auditory Cortex Modulated by Speech Intelligibility ]]> https://biorxiv.org/content/10.1101/2021.12.11.472249v1?rss=1 Xu, N. Zhao, B. Luo, L. Zhang, K. Shao, X. Luan, G. Wang, Q. Hu, W. Wang, Q. 2021-12-13 doi:10.1101/2021.12.11.472249 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ High temporal resolution transcriptomic profiling delineates distinct patterns of interferon response following Covid-19 mRNA vaccination and SARS-CoV2 infection ]]> https://biorxiv.org/content/10.1101/2021.12.12.472257v1?rss=1 Rinchai, D. Deola, S. Zoppoli, G. Kabeer, B. S. A. Taleb, S. A. Pavlovski, I. Maacha, S. Gentilcore, G. Toufiq, M. Matthew, L. Liu, L. Vempalli, F. R. Mubarak, G. Lorenz, S. Sivieri, I. Cirmena, G. Dentone, C. Cuccarolo, P. Giacobbe, D. Baldi, F. Garbarino, A. Cigolini, B. Cremonesi, P. Bedognetti, M. Ballestrero, A. Bassetti, M. Hejblum, B. P. Augustine, T. Panhuys, N. V. Thiebaut, R. Branco, R. Chew, T. Shojaei, M. Short, K. Feng, C. Zughaier, S. M. Maria, A. D. Tang, B. Hssain, A. A. Bedognetti, D. Grivel, J.-C. Chaussabel, D. 2021-12-14 doi:10.1101/2021.12.12.472257 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ Contrastive Cycle Adversarial Autoencoders for Single-cell Multi-omics Alignment and Integration ]]> https://biorxiv.org/content/10.1101/2021.12.12.472268v1?rss=1 Wang, X. Hu, Z. Yu, T. Wang, R. Wei, Y. Shu, J. Zhu, M. Li, Y. 2021-12-13 doi:10.1101/2021.12.12.472268 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift ]]> https://biorxiv.org/content/10.1101/2021.12.12.472269v1?rss=1 Cameroni, E. Saliba, C. Bowen, J. E. Rosen, L. E. Culap, K. Pinto, D. De Marco, A. Zepeda, S. K. di Iulio, J. Zatta, F. Kaiser, H. Noack, J. Farhat, N. Czudnochowski, N. Havenar-Daughton, C. Sprouse, K. R. Dillen, J. R. Powell, A. E. Chen, A. Maher, C. Yin, L. Sun, D. Soriaga, L. Gustafsson, C. Chu, H. Franko, N. M. Logue, J. Iqbal, N. T. Mazzitelli, I. Geffner, J. Grifantini, R. Gori, A. Riva, A. Giannini, O. Ceschi, A. Ferrari, P. Franzetti-Pellanda, A. Garzoni, C. Hebner, C. Purcell, L. Piccoli, L. Pizzuto, M. S. Walls, A. C. Telenti, A. Virgin, H 2021-12-14 doi:10.1101/2021.12.12.472269 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ Antimicrobial resistance determinants in silage ]]> https://biorxiv.org/content/10.1101/2021.12.12.472282v1?rss=1 Nagy, S. A. Toth, A. G. Papp, M. Kaplan, S. Solymosi, N. 2021-12-13 doi:10.1101/2021.12.12.472282 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ LKB1 Is Physiologically Required for Sleep from Drosophila to the Mouse ]]> https://biorxiv.org/content/10.1101/2021.12.13.472078v1?rss=1 Liu, Z. Jiang, L. Li, C. Li, C. Yang, J. Wang, D. Mao, R. Rao, Y. 2021-12-14 doi:10.1101/2021.12.13.472078 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ Modeling of microRNA-derived disease network repurposes methotrexate for the prevention and therapy of abdominal aortic aneurysm in mice ]]> https://biorxiv.org/content/10.1101/2021.12.13.472366v1?rss=1 Shen, Y. Gao, Y. Shi, J. Huang, Z. Dai, R. Fu, Y. Zhou, Y. Kong, W. Cui, Q. 2021-12-13 doi:10.1101/2021.12.13.472366 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ The dual role of N6-methyladenosine on mouse maternal RNAs and 2-cell specific RNAs revealed by ULI-MeRIP sequencing ]]> https://biorxiv.org/content/10.1101/2021.12.13.472368v1?rss=1 Wu, Y. Xu, X. Qi, M. Chen, C. Zhang, M. Yan, R. Kou, X. Zhao, Y. Liu, W. Zhang, M. Yi, C. Li, Y. Wang, H. Shen, B. Gao, Y. Gao, S. 2021-12-16 doi:10.1101/2021.12.13.472368 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Opposing regulation of short-term memory by basal ganglia direct and indirect pathways that are coactive during behavior ]]> https://biorxiv.org/content/10.1101/2021.12.15.472735v1?rss=1 Tang, Y. Yang, H. Chen, X. Zhang, Z. Yao, X. Yin, X. Guo, Z. V. 2021-12-16 doi:10.1101/2021.12.15.472735 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Simple contextual cueing prevents retroactive interference in short-term perceptual training of orientation detection tasks ]]> https://biorxiv.org/content/10.1101/2021.12.15.472760v1?rss=1 Huang, H. Zhang, Y. Li, S. 2021-12-16 doi:10.1101/2021.12.15.472760 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ A dual reporter system identifies an intermediate state and sequential regulators of 2-cell-like-to-pluripotent state transition ]]> https://biorxiv.org/content/10.1101/2021.12.17.473100v1?rss=1 Zhang, C. Hao, J. Shi, M. Li, Y.-X. Yao, W. Wang, Y. 2021-12-17 doi:10.1101/2021.12.17.473100 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ When self comes to a wandering mind: Brain representations and dynamics of self-generated concepts in spontaneous thought ]]> https://biorxiv.org/content/10.1101/2021.12.18.473276v1?rss=1 Kim, B. Andrews-Hanna, J. R. Han, J. Lee, E. Woo, C.-W. 2021-12-21 doi:10.1101/2021.12.18.473276 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ rareSurvival: rare variant association analysis for time-to-event outcomes. ]]> https://biorxiv.org/content/10.1101/2021.12.19.473338v1?rss=1 Syed, H. Jorgensen, A. Morris, A. 2021-12-21 doi:10.1101/2021.12.19.473338 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ MOPower: an R-shiny application for the simulation and power calculation of multi-omics studies. ]]> https://biorxiv.org/content/10.1101/2021.12.19.473339v1?rss=1 Syed, H. Otto, G. W. Kelberman, D. Bacchelli, C. Beales, P. L. 2021-12-21 doi:10.1101/2021.12.19.473339 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Structure and mechanism of NALCN-FAM155A-UNC79-UNC80 channel complex ]]> https://biorxiv.org/content/10.1101/2021.12.20.473568v1?rss=1 Kang, Y. Chen, L. 2021-12-21 doi:10.1101/2021.12.20.473568 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Network design principle for robust oscillatory behaviors with respect to biological noise ]]> https://biorxiv.org/content/10.1101/2021.12.22.473835v1?rss=1 Qiao, L. Zhang, Z.-B. Zhao, W. Wei, P. Zhang, L. 2021-12-23 doi:10.1101/2021.12.22.473835 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Biological regulatory networks are less nonlinear than expected by chance ]]> https://biorxiv.org/content/10.1101/2021.12.22.473903v1?rss=1 Manicka, S. Johnson, K. Murrugarra, D. Levin, M. 2021-12-23 doi:10.1101/2021.12.22.473903 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ A novel high-throughput assay using mixed genomic DNA for fast screening germline pathogenic variants in breast cancer susceptibility genes ]]> https://biorxiv.org/content/10.1101/2021.12.23.474057v1?rss=1 Wan, Q. Hu, L. Yao, L. Chen, J. Sun, J. Zhang, J. Xu, Y. Yun, Y. 2021-12-24 doi:10.1101/2021.12.23.474057 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ SHERRY2: A method for rapid and sensitive single cell RNA-seq ]]> https://biorxiv.org/content/10.1101/2021.12.25.474161v1?rss=1 Di, L. Liu, B. Lyu, Y. Zhao, S. Pang, Y. Zhang, C. Wang, J. Qi, H. Shen, J. Huang, Y. 2021-12-25 doi:10.1101/2021.12.25.474161 Cold Spring Harbor Laboratory Press 2021-12-25 <![CDATA[ Structural and functional characterizations of altered infectivity and immune evasion of SARS-CoV-2 Omicron variant ]]> https://biorxiv.org/content/10.1101/2021.12.29.474402v1?rss=1 Cui, Z. Liu, P. Wang, N. Wang, L. Fan, K. Zhu, Q. Wang, K. Chen, R. Feng, R. Jia, Z. Yang, M. Zhu, B. Fu, W. Chu, T. Feng, L. Wang, Y. Pei, X. Yang, P. Xie, X. S. Cao, L. Cao, Y. R. Wang, X. 2021-12-30 doi:10.1101/2021.12.29.474402 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ Visual search training benefits from the integrative effect of enhanced covert attention and optimized overt eye movements ]]> https://biorxiv.org/content/10.1101/2022.01.03.474790v1?rss=1 Zhang, Q. Huang, Z. Li, L. Li, S. 2022-01-04 doi:10.1101/2022.01.03.474790 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ Analytical time-dependent distributions for gene expression models with complex promoter switching mechanisms ]]> https://biorxiv.org/content/10.1101/2022.01.05.475050v1?rss=1 Jia, C. Li, Y. 2022-01-06 doi:10.1101/2022.01.05.475050 Cold Spring Harbor Laboratory Press 2022-01-06 <![CDATA[ CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-related Genes and Clinical Manifestations ]]> https://biorxiv.org/content/10.1101/2022.01.06.475217v1?rss=1 Zhou, W.-Z. Li, W. Shen, H. Wang, R. W. Chen, W. Zhang, Y. Zeng, Q. Wang, H. Yuan, M. Zeng, Z. Cui, J. Li, C.-Y. Ye, F. Y. Zhou, Z. 2022-01-07 doi:10.1101/2022.01.06.475217 Cold Spring Harbor Laboratory Press 2022-01-07 <![CDATA[ Patterns of Saliency and Semantic Features Distinguish Gaze of Expert and Novice Viewers of Surveillance Footage ]]> https://biorxiv.org/content/10.1101/2022.01.09.475588v1?rss=1 Peng, Y. Burling, J. M. Todorova, G. K. Neary, C. Pollick, F. E. Lu, H. 2022-01-11 doi:10.1101/2022.01.09.475588 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ How many bits of information can be transferred between residues in a protein and how fast? ]]> https://biorxiv.org/content/10.1101/2022.01.10.475716v1?rss=1 Hacisuleyman, A. Erman, B. 2022-01-12 doi:10.1101/2022.01.10.475716 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Tuftsin: a natural molecule against SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2022.01.10.475746v1?rss=1 Huang, J. Wang, J. Wang, Z. Chu, M. Wang, Y. 2022-01-17 doi:10.1101/2022.01.10.475746 Cold Spring Harbor Laboratory Press 2022-01-17 <![CDATA[ Comparison of neural population dynamics in the regression subspace between continuous and categorical task parameters ]]> https://biorxiv.org/content/10.1101/2022.01.13.476265v1?rss=1 Chen, H. Kunimatsu, J. Oya, T. Imaizumi, Y. Hori, Y. Matsumoto, M. Minamimoto, T. Naya, Y. Yamada, H. 2022-01-17 doi:10.1101/2022.01.13.476265 Cold Spring Harbor Laboratory Press 2022-01-17 <![CDATA[ Comparative Phenotyping of Two Commonly Used Chlamydomonas reinhardtii Background Strains: CC-1690 (21gr) and CC-5325 (the CLiP Mutant Library Background) ]]> https://biorxiv.org/content/10.1101/2022.01.15.476454v1?rss=1 Zhang, N. Pazouki, L. Nguyen, H. Jacobshagen, S. Xia, M. Klebanovych, A. Czymmek, K. J. Zhang, R. 2022-01-17 doi:10.1101/2022.01.15.476454 Cold Spring Harbor Laboratory Press 2022-01-17 <![CDATA[ A whole-brain 3D myeloarchitectonic atlas: mapping the Vogt-Vogt legacy to the cortical surface ]]> https://biorxiv.org/content/10.1101/2022.01.17.476369v1?rss=1 Foit, N. A. Yung, S. Lee, H. M. Bernasconi, A. Bernasconi, N. Hong, S.-J. 2022-01-20 doi:10.1101/2022.01.17.476369 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Palatal morphology predicts the paleobiology of early salamanders ]]> https://biorxiv.org/content/10.1101/2022.01.17.476642v1?rss=1 Jia, J. Li, G. Gao, K.-Q. 2022-01-17 doi:10.1101/2022.01.17.476642 Cold Spring Harbor Laboratory Press 2022-01-17 <![CDATA[ Collateral cleavage of 28s rRNA by RfxCas13d causes death of mice ]]> https://biorxiv.org/content/10.1101/2022.01.17.476700v1?rss=1 Li, Y. Xu, J. Guo, X. Li, Z. Cao, L. Liu, S. Guo, Y. Wang, G. Luo, Y. Zhang, Z. Wei, X. Zhao, Y. Liu, T. Wang, X. Xia, H. Kuang, M. Guo, Q. Li, J. Chen, L. Wang, Y. Li, Q. Wang, F. Liu, Q. You, F. 2022-01-18 doi:10.1101/2022.01.17.476700 Cold Spring Harbor Laboratory Press 2022-01-18 <![CDATA[ Spatially resolved profiling of protein conformation and interactions by biocompatible chemical cross-linking in living cells ]]> https://biorxiv.org/content/10.1101/2022.01.20.476705v1?rss=1 Zhao, L. Zhao, Q. An, Y. Gao, H. Zhang, W. Gong, Z. Liu, X. Zhao, B. Liang, Z. Tang, C. Zhang, L. Zhang, Y. 2022-01-20 doi:10.1101/2022.01.20.476705 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Dopamine and ALK4 signaling synergize to induce PCBP1-mediated alternative splicing of FosB and sustained behavioral sensitization to cocaine ]]> https://biorxiv.org/content/10.1101/2022.01.20.477040v1?rss=1 Krapacher, F. A. Fernandez-Suarez, D. Andersson, A. Carrier-Ruiz, A. Ibanez, C. F. 2022-01-22 doi:10.1101/2022.01.20.477040 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ Tissue-Specific Control of Ribosomal RNA Synthesis Revealed by Transcription Factor Profiling ]]> https://biorxiv.org/content/10.1101/2022.01.21.476118v1?rss=1 Antony, C. George, S. S. Blum, J. Somers, P. Thorsheim, C. L. Wu-Corts, D. J. Ai, Y. Gao, L. Lv, K. Tremblay, M. G. Moss, T. Tan, K. Wilusz, J. E. Ganley, A. R. D. Pimkin, M. Paralkar, V. R. 2022-01-22 doi:10.1101/2022.01.21.476118 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ CavitySpace: A database of potential ligand binding sites in the human proteome ]]> https://biorxiv.org/content/10.1101/2022.01.25.477691v1?rss=1 Wang, S. Lin, H. Huang, Z. He, Y. Deng, X. Xu, Y. Pei, J. Lai, L. 2022-01-27 doi:10.1101/2022.01.25.477691 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ Existence of blood circulating immune-cell clusters (CICs) comprising antigen-presenting cells and B cells ]]> https://biorxiv.org/content/10.1101/2022.01.26.477834v1?rss=1 Bae, S. Lee, Y. Kang, M. Noh, J. Seo, D. Seo, H. Lee, S. Kwon, S. 2022-01-28 doi:10.1101/2022.01.26.477834 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Sampling-based Bayesian inference in recurrent circuits of stochastic spiking neurons ]]> https://biorxiv.org/content/10.1101/2022.01.26.477877v1?rss=1 Zhang, W. Wu, S. Josic, K. Doiron, B. 2022-01-28 doi:10.1101/2022.01.26.477877 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Molecular insights into the MCM8/9 helicase complex in DNA unwinding and translocation ]]> https://biorxiv.org/content/10.1101/2022.01.26.477944v1?rss=1 Weng, Z. Li, J. Zheng, J. Li, H. Lu, Z. Zhou, Y. Xu, D. Liang, H. Liu, Y. 2022-01-27 doi:10.1101/2022.01.26.477944 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ Origin of hexagonal metric of grid cells in navigating spaces ]]> https://biorxiv.org/content/10.1101/2022.01.29.478346v1?rss=1 Zhang, B. Zhang, Y. Liu, J. 2022-01-31 doi:10.1101/2022.01.29.478346 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ Toward an atomistic model of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2022.01.31.478415v1?rss=1 Wang, D. Li, J. Wang, L. Cao, Y. Li, S. Song, C. 2022-02-02 doi:10.1101/2022.01.31.478415 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ A Genetically Encoded BRET-based SARS-CoV-2 Mpro Protease Activity Sensor ]]> https://biorxiv.org/content/10.1101/2022.01.31.478460v1?rss=1 Geethakumari, A. M. Ahmed, W. S. Rasool, S. H. Fatima, A. H. Uddin, S. M. N. Aouida, M. H. Biswas, K. H. 2022-02-01 doi:10.1101/2022.01.31.478460 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Requirement of cholesterol for calcium-dependent vesicle fusion by stabilizing synaptotagmin-1-induced membrane bending ]]> https://biorxiv.org/content/10.1101/2022.02.03.478933v1?rss=1 Moussa, H. Y. A. Shin, K. C. Tong, Y. Kim, S. J. Ryu, J.-K. Mansour, S. Park, Y. 2022-02-03 doi:10.1101/2022.02.03.478933 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Comprehensive Epitope Mapping of Broad Sarbecovirus Neutralizing Antibodies ]]> https://biorxiv.org/content/10.1101/2022.02.07.479349v1?rss=1 Cao, Y. Yisimayi, A. Jian, F. Xiao, T. Song, W. Wang, J. Du, S. Zhang, Z. Liu, P. Hao, X. Li, Q. Wang, P. An, R. Wang, Y. Wang, J. Sun, H. Zhao, L. Zhang, W. Zhao, D. Zheng, J. Yu, L. Li, C. Zhang, N. Wang, R. Niu, X. Yang, S. Song, X. Zheng, L. Li, Z. Gu, Q. Shao, F. Huang, W. Wang, Y. Jin, R. Xiao, J. Xie, X. S. 2022-02-07 doi:10.1101/2022.02.07.479349 Cold Spring Harbor Laboratory Press 2022-02-07 <![CDATA[ Auto-Immunoproteomics Analysis of COVID-19 ICU Patients Revealed Increased Levels of Autoantibodies Related to Male Reproductive System ]]> https://biorxiv.org/content/10.1101/2022.02.09.479669v1?rss=1 Schmidt, F. Abdesselem, H. B. Suhre, K. Sohail, m. u. Al-Nesf, M. Bensmail, I. Mashod, F. Sarwath, H. Bernhardt, J. Tan, T.-M. Morris, P. E. Schenck, E. J. Price, D. Vaikath, N. Mohamed-Ali, V. Al-Maadheedh, M. Arredouani, A. Decock, J. V. Blackburn, J. Choi, A. M. K. El-Agnaf, O. M. A. 2022-02-09 doi:10.1101/2022.02.09.479669 Cold Spring Harbor Laboratory Press 2022-02-09 <![CDATA[ Elasticity generates indissoluble biomolecular condensates ]]> https://biorxiv.org/content/10.1101/2022.02.09.479808v1?rss=1 Meng, L. Lin, J. 2022-02-10 doi:10.1101/2022.02.09.479808 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Compartmental Neuropeptide Release Measured Using a New Oxytocin Sensor ]]> https://biorxiv.org/content/10.1101/2022.02.10.480016v1?rss=1 Qian, T. Wang, H. Wang, P. Geng, L. Mei, L. Osakada, T. Tang, Y. Kania, A. Grinevich, V. Stoop, R. Lin, D. Luo, M. Li, Y. 2022-02-11 doi:10.1101/2022.02.10.480016 Cold Spring Harbor Laboratory Press 2022-02-11 <![CDATA[ Assessing base-resolution DNA mechanics on the genome scale ]]> https://biorxiv.org/content/10.1101/2022.02.16.480786v1?rss=1 Jiang, W.-j. Hu, C. Yi, X. Xu, Q. Lou, T. Wang, H. Zhou, J. Zhu, H. Li, Y. Wen, Y. Fan, R. Shen, J. Wong, C. C. Zheng, X. Wu, H.-J. 2022-02-19 doi:10.1101/2022.02.16.480786 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ A Neuropsin-based Optogenetic Tool for Precise Control of Gq signaling ]]> https://biorxiv.org/content/10.1101/2022.02.22.481462v1?rss=1 Luo, M. Dai, R. Yu, T. Weng, D. Li, H. Cui, Y. Wu, Z. Guo, Q. Zou, H. Wu, W. Gao, X. Qi, Z. Ren, Y. Shu, W. Li, Y. 2022-02-23 doi:10.1101/2022.02.22.481462 Cold Spring Harbor Laboratory Press 2022-02-23 <![CDATA[ Frequency dependent growth of bacteria in living materials ]]> https://biorxiv.org/content/10.1101/2022.02.22.481564v1?rss=1 Lewis, D. Gong, T. Xu, Y. Tan, C. 2022-02-24 doi:10.1101/2022.02.22.481564 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Proteomic analysis of human milk reveals nutritional and immune benefits in the colostrum from mothers with COVID-19 ]]> https://biorxiv.org/content/10.1101/2022.02.25.481966v1?rss=1 Guo, J. Tan, M. Zhu, J. Tian, Y. Liu, H. Luo, F. Wang, J. Huang, Y. Zhang, Y. Yang, Y. Wang, G. 2022-02-26 doi:10.1101/2022.02.25.481966 Cold Spring Harbor Laboratory Press 2022-02-26 <![CDATA[ A cooperative switch within the KaiC hexamer revealed by cryo-EM ]]> https://biorxiv.org/content/10.1101/2022.02.27.481910v1?rss=1 Han, X. Zhang, D. Hong, L. Yu, D. Wu, Z. Yang, T. Rust, M. Tu, Y. Ouyang, Q. 2022-02-28 doi:10.1101/2022.02.27.481910 Cold Spring Harbor Laboratory Press 2022-02-28 <![CDATA[ Deciphering of Somatic Mutational Signatures of Cancer ]]> https://biorxiv.org/content/10.1101/2022.03.01.482591v1?rss=1 Ji, X. Wang, E. Cui, Q. 2022-03-04 doi:10.1101/2022.03.01.482591 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Antiviral and Neuroprotective Abilities of Influenza Virus Infection in Tractable Brain Organoids ]]> https://biorxiv.org/content/10.1101/2022.03.02.482634v1?rss=1 Zhang, X. Lin, H. Dong, L. Xia, Q. 2022-03-02 doi:10.1101/2022.03.02.482634 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Rapid quantification of polyhydroxyalkanoates accumulated in living cells based on green fluorescence protein labeled phasin: The qPHA method ]]> https://biorxiv.org/content/10.1101/2022.03.02.482659v1?rss=1 Liu, X. Li, D. Yan, X. Zhang, Z. Zheng, S. Zhang, J. Wu, F. Li, F. Chen, G.-Q. 2022-03-04 doi:10.1101/2022.03.02.482659 Cold Spring Harbor Laboratory Press 2022-03-04 <![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[ Subgroups of eating behavior traits independent of obesity defined using functional connectivity and feature representation learning ]]> https://biorxiv.org/content/10.1101/2022.03.03.482759v1?rss=1 Choi, H. Byeon, K. Lee, J.-e. Hong, S.-J. Park, B.-y. Park, H. 2022-03-04 doi:10.1101/2022.03.03.482759 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Canine saliva is a source of interspecies antimicrobial resistance gene transfer ]]> https://biorxiv.org/content/10.1101/2022.03.07.483304v1?rss=1 Toth, A. G. Toth, I. Rozsa, B. Kovacs, E. G. Dubecz, A. Patai, A. V. Nemeth, T. Kaplan, S. Makrai, L. Solymosi, N. 2022-03-07 doi:10.1101/2022.03.07.483304 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Niche-based deterministic assembly processes strengthen the effects of β-diversity on metacommunity functioning of marine bacterioplankton ]]> https://biorxiv.org/content/10.1101/2022.03.09.483723v1?rss=1 Chang, F.-H. Yang, J. W. Liu, A. C.-H. Lu, H.-P. Gong, G.-C. Shiah, F.-K. Hsieh, C.-h. 2022-03-11 doi:10.1101/2022.03.09.483723 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ Structure and mechanism of a mitochondrial AAA+ disaggregase CLBP ]]> https://biorxiv.org/content/10.1101/2022.03.10.483744v1?rss=1 Wu, D. Liu, Y. Dai, Y. Wang, G. Lu, G. Chen, Y. Li, N. Lin, J. Gao, N. 2022-03-10 doi:10.1101/2022.03.10.483744 Cold Spring Harbor Laboratory Press 2022-03-10 <![CDATA[ A Spatiotemporal Reconstruction of the C. elegans Pharyngeal Cuticle Reveals a Structure Rich in Phase-Separating Proteins ]]> https://biorxiv.org/content/10.1101/2022.03.11.483951v1?rss=1 Kamal, M. Tokmakjian, L. Knox, J. Mastrangelo, P. Ji, J. Cai, H. Wojciechowski, J. Hughes, M. P. Takacs, K. Chu, X. Pei, J. Grolmusz, V. Kotulska, M. Forman-Kay, J. D. Roy, P. J. 2022-03-14 doi:10.1101/2022.03.11.483951 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ PP2A forestalls mitophagy by dephosphorylating Parkin and ubiquitin ]]> https://biorxiv.org/content/10.1101/2022.03.12.484070v1?rss=1 Ye, S.-X. Liu, X.-Y. Nie, Z.-F. Meng, L.-S. Dong, X. Li, F.-F. Gong, Z. Yang, W. Zhang, W.-P. Tang, C. 2022-03-13 doi:10.1101/2022.03.12.484070 Cold Spring Harbor Laboratory Press 2022-03-13 <![CDATA[ Real-time denoising of fluorescence time-lapse imaging enables high-sensitivity observations of biological dynamics beyond the shot-noise limit ]]> https://biorxiv.org/content/10.1101/2022.03.14.484230v1?rss=1 Li, X. Li, Y. Zhou, Y. Wu, J. Zhao, Z. Fan, J. Deng, F. Wu, Z. Xiao, G. He, J. Zhang, Y. Zhang, G. Hu, X. Zhang, Y. Qiao, H. Xie, H. Li, Y. Wang, H. Fang, L. Dai, Q. 2022-03-14 doi:10.1101/2022.03.14.484230 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Non-ribosomal peptide synthetase domain boundary identification and new motifs discovery based on motif-intermotifs standardized architecture ]]> https://biorxiv.org/content/10.1101/2022.03.14.484258v1?rss=1 He, R. Zhang, J. Gu, S. Yin, W.-B. Li, Z. 2022-03-17 doi:10.1101/2022.03.14.484258 Cold Spring Harbor Laboratory Press 2022-03-17 <![CDATA[ Structure and influence in an interconnected world: neurocomputational mechanism of real-time distributed learning on social networks ]]> https://biorxiv.org/content/10.1101/2022.03.22.485414v1?rss=1 Jiang, Y. Mi, Q. Zhu, L. 2022-03-25 doi:10.1101/2022.03.22.485414 Cold Spring Harbor Laboratory Press 2022-03-25 <![CDATA[ Sub-cellular dynamic investigation of the multi-component drug on the gastric cancer cell BGC823 using Raman spectroscopy ]]> https://biorxiv.org/content/10.1101/2022.03.24.485691v1?rss=1 shang, w. ye, a. fang, t. 2022-03-26 doi:10.1101/2022.03.24.485691 Cold Spring Harbor Laboratory Press 2022-03-26 <![CDATA[ A toolkit of highly selective and sensitive genetically encoded neuropeptide sensors ]]> https://biorxiv.org/content/10.1101/2022.03.26.485911v1?rss=1 Wang, H. Qian, T. Zhao, Y. Zhuo, Y. Wu, C. Osakada, T. Chen, P. Ren, H. Yan, Y. Geng, L. Fu, S. Mei, L. Li, G. Wu, L. Jiang, Y. Qian, W. Peng, W. Xu, M. Hu, J. Chen, L. Tang, C. Lin, D. Zhou, J.-N. Li, Y. 2022-03-28 doi:10.1101/2022.03.26.485911 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Local 5-HT signal bi-directionally regulates the coincidence time window of associative learning ]]> https://biorxiv.org/content/10.1101/2022.03.27.485970v1?rss=1 Zeng, J. Li, X. Zhangren, Z. Lv, M. Wang, Y. Tan, K. Xia, X. Wan, J. Jing, M. Yang, Y. Li, Y. Li, Y. 2022-03-27 doi:10.1101/2022.03.27.485970 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Finding the strongest gene drive: Simulations reveal unexpected performance differences between Anopheles homing suppression drive candidates ]]> https://biorxiv.org/content/10.1101/2022.03.28.486009v1?rss=1 Champer, S. E. Kim, I. K. Clark, A. G. Messer, P. W. Champer, J. 2022-03-28 doi:10.1101/2022.03.28.486009 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ An in situ cut-and-paste genome editing platform mediated by CRISPR/Cas9 or Cas12a ]]> https://biorxiv.org/content/10.1101/2022.03.30.486486v1?rss=1 Jiang, P. Kemper, K. M. Chang, K.-T. Qian, C. Li, Y. Guan, L. van Hasselt, P. Caradonna, S. Strich, R. 2022-03-31 doi:10.1101/2022.03.30.486486 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ Monitoring promoter activity by RNA editing based reporter ]]> https://biorxiv.org/content/10.1101/2022.03.30.486490v1?rss=1 Wang, J. Zhao, Y.-T. Hu, L.-F. Wang, Y. 2022-03-31 doi:10.1101/2022.03.30.486490 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ Single-cell profiling of lncRNAs in human germ cells and molecular analysis reveals transcriptional regulation of LNC1845 on LHX8 ]]> https://biorxiv.org/content/10.1101/2022.04.01.486705v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@31290forg.highwire.dtl.DTLVardef@17ec505org.highwire.dtl.DTLVardef@1b8cd0dorg.highwire.dtl.DTLVardef@19e4de3_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIlncRNAs are expressed at significantly higher levels in both male and female germ cells than in somatic cells during human gonadal development. C_LIO_LIDivergent lncRNAs are enriched in the female meiotically and male mitotically arrested germ cells. C_LIO_LILNC1845 regulates the transcriptional expression of LHX8 by modulating H3K4me3 and H3K27Ac levels. C_LI ]]> Wang, N. He, J. Feng, X. Liao, S. Zhao, Y. Tang, F. Kee, K. 2022-04-03 doi:10.1101/2022.04.01.486705 Cold Spring Harbor Laboratory Press 2022-04-03 <![CDATA[ Frequency of change determines effectiveness of microbial response strategies in sulfidic stream microbiomes ]]> https://biorxiv.org/content/10.1101/2022.04.01.486770v1?rss=1 Li, S. Mosier, D. Dong, X. Kouris, A. Ji, G. Strous, M. Diao, M. 2022-04-01 doi:10.1101/2022.04.01.486770 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Reactivating ordinal position information from auditory sequence memory in human brains ]]> https://biorxiv.org/content/10.1101/2022.04.04.487064v1?rss=1 Fan, Y. Luo, H. 2022-04-07 doi:10.1101/2022.04.04.487064 Cold Spring Harbor Laboratory Press 2022-04-07 <![CDATA[ Phylogenetic and Ecological Trends in Specialization: Disentangling the Drivers of Ectoparasite Host Specificity ]]> https://biorxiv.org/content/10.1101/2022.04.06.487338v1?rss=1 Brown, A. M. Speer, K. Tiexeira, T. Clare, E. Simmons, N. B. Balbuena, J. A. Dick, C. Dittmar, K. Perkins, S. 2022-04-07 doi:10.1101/2022.04.06.487338 Cold Spring Harbor Laboratory Press 2022-04-07 <![CDATA[ CCDC66 regulates primary cilium length and signaling competence via multi-site interactions with transition zone and axonemal proteins ]]> https://biorxiv.org/content/10.1101/2022.04.10.487777v1?rss=1 Conkar, D. Odabasi, E. Deretic, J. Batman, U. Frikstad, K.-A. M. Patzke, S. Firat-Karalar, E. N. 2022-04-10 doi:10.1101/2022.04.10.487777 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Multimodal single cell data integration challenge: results and lessons learned ]]> https://biorxiv.org/content/10.1101/2022.04.11.487796v1?rss=1 Lance, C. Luecken, M. D. Burkhardt, D. B. Cannoodt, R. Rautenstrauch, P. Laddach, A. C. Ubingazhibov, A. Cao, Z.-J. Deng, K. Khan, S. Liu, Q. Russkikh, N. Ryazantsev, G. Ohler, U. NeurIPS 2021 Multimodal data integration competition participants, Pisco, A. O. Bloom, J. M. Krishnaswamy, S. Theis, F. J. 2022-04-12 doi:10.1101/2022.04.11.487796 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ Proximal Exploration for Model-guided Protein Sequence Design ]]> https://biorxiv.org/content/10.1101/2022.04.12.487986v1?rss=1 Ren, Z. Li, J. Ding, F. Zhou, Y. Ma, J. Peng, J. 2022-04-13 doi:10.1101/2022.04.12.487986 Cold Spring Harbor Laboratory Press 2022-04-13 <![CDATA[ A genetic model for in vivo proximity labeling of the mammalian secretome ]]> https://biorxiv.org/content/10.1101/2022.04.13.488228v1?rss=1 Yang, R. Meyer, A. S. Droujinine, I. A. Udeshi, N. D. Hu, Y. Guo, J. McMahon, J. A. Carey, D. K. Xu, C. Fang, Q. Sha, J. Qin, S. Rocco, D. Wohlschlegel, J. Ting, A. Y. Carr, S. A. Perrimon, N. McMahon, A. P. 2022-04-15 doi:10.1101/2022.04.13.488228 Cold Spring Harbor Laboratory Press 2022-04-15 <![CDATA[ Chronically radiation-exposed survivor glioblastoma cells display poor response to Chk1 inhibition ]]> https://biorxiv.org/content/10.1101/2022.04.16.488495v1?rss=1 Pinarbasi Degirmenci, N. Sur-Erdem, I. Akcay, V. Bolukbasi, Y. Selek, U. Solaroglu, I. Bagci-Onder, T. 2022-04-16 doi:10.1101/2022.04.16.488495 Cold Spring Harbor Laboratory Press 2022-04-16 <![CDATA[ Plant-on-Chip: core morphogenesis processes in the tiny plant Wolffia australiana ]]> https://biorxiv.org/content/10.1101/2022.04.16.488569v1?rss=1 Li, F. Yang, J.-J. Sun, Z.-Y. Wang, L. Qi, L.-Y. A, S. Liu, Y.-Q. Zhang, H.-M. Dang, L.-F. Wang, S.-J. Luo, C.-X. Nian, W.-F. O'Conner, S. Ju, L.-Z. Quan, W.-P. Li, X.-K. Wang, C. Wang, D.-P. You, H.-L. Cheng, Z.-K. Yan, J. Tang, F.-C. Yang, D.-C. Xia, C.-W. Gao, G. Wang, Y. Zhang, B.-C. Zhou, Y.-H. Guo, X. Xiang, S.-H. Liu, H. Peng, T.-B. Su, X.-D. Chen, Y. Ouyang, Q. Wang, D.-H. Zhang, D.-M. Xu, Z.-H. Hou, H.-W. Bai, S.-N. Li, L. 2022-04-17 doi:10.1101/2022.04.16.488569 Cold Spring Harbor Laboratory Press 2022-04-17 <![CDATA[ SOAR: a spatial transcriptomics analysis resource to model spatial variability and cell type interactions ]]> https://biorxiv.org/content/10.1101/2022.04.17.488596v1?rss=1 Li, Y. Dennis, S. Hutch, M. Li, Y. Broad, M. Zeng, Z. Luo, Y. 2022-04-17 doi:10.1101/2022.04.17.488596 Cold Spring Harbor Laboratory Press 2022-04-17 <![CDATA[ Benchmarking the Widely Used Structure-based Binding Affinity Predictors on the Spike-ACE2 Deep Mutational Interaction Set ]]> https://biorxiv.org/content/10.1101/2022.04.18.488633v1?rss=1 Samiloglu, E. Kosaca, M. Oktayoglu, M. Yukruk, C. Erguven, M. Arslan, N. Karakulah, G. Barlas, A. B. Savas, B. Ozden, B. Karaca, E. 2022-04-18 doi:10.1101/2022.04.18.488633 Cold Spring Harbor Laboratory Press 2022-04-18 <![CDATA[ Global and gene-specific translational regulation in Escherichia coli across different conditions ]]> https://biorxiv.org/content/10.1101/2022.04.19.488838v1?rss=1 Zhang, D. Li, S. H.-J. King, C. G. Wingreen, N. S. Gitai, Z. Li, Z. 2022-04-21 doi:10.1101/2022.04.19.488838 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ The ciliopathy protein CCDC66 controls mitotic progression and cytokinesis by promoting microtubule nucleation and organization ]]> https://biorxiv.org/content/10.1101/2022.04.22.489036v1?rss=1 Batman, U. Deretic, J. Firat-Karalar, E. N. 2022-04-22 doi:10.1101/2022.04.22.489036 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Structural insights into the high selectivity of the anti-diabetic drug mitiglinide ]]> https://biorxiv.org/content/10.1101/2022.04.26.489624v1?rss=1 Wang, M. Wu, J.-X. Chen, L. 2022-04-28 doi:10.1101/2022.04.26.489624 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ A bacteriophage-based, highly efficacious, needle and adjuvant-free, mucosal COVID-19 vaccine ]]> https://biorxiv.org/content/10.1101/2022.04.28.489809v1?rss=1 Zhu, J. Jain, S. Sha, J. Batra, H. Ananthaswamy, N. Kilgore, P. B. Hendrix, E. Hosakote, Y. M. Wu, X. Olano, J. P. Kayode, A. Galindo, C. L. Banga, S. Drelich, A. Tat, V. Tseng, C.-T. K. Chopra, A. K. Rao, V. B. 2022-04-29 doi:10.1101/2022.04.28.489809 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ Aggression and multimodal signaling in noise in the European robin ]]> https://biorxiv.org/content/10.1101/2022.04.29.490020v1?rss=1 Onsal, C. Yelimlies, A. Akcay, C. 2022-05-01 doi:10.1101/2022.04.29.490020 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection ]]> https://biorxiv.org/content/10.1101/2022.04.30.489997v1?rss=1 Cao, Y. R. Yisimayi, A. Jian, F. Song, W. Xiao, T. Wang, L. Du, S. Wang, J. Li, Q. Chen, X. Wang, P. Zhang, Z. Liu, P. An, R. Hao, X. Wang, Y. Wang, J. Feng, R. Sun, H. Zhao, L. Zhang, W. Zhao, D. Zheng, J. Yu, L. Li, C. Zhang, N. Wang, R. Niu, X. Yang, S. Song, X. Zheng, L. Li, Z. Gu, Q. Shao, F. Huang, W. Jin, R. Shen, Z. Wang, Y. Wang, X. Xiao, J. Xie, X. S. 2022-05-02 doi:10.1101/2022.04.30.489997 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Rebound Excitation of Epileptiform Activities by Transcranial Focused Ultrasound Stimulation ]]> https://biorxiv.org/content/10.1101/2022.04.30.490021v1?rss=1 Choi, T. Koo, M. Joo, J. Kim, T. Shon, Y.-M. Park, J. 2022-05-01 doi:10.1101/2022.04.30.490021 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Neurocomputational evidence that conflicting prosocial motives guide distributive justice ]]> https://biorxiv.org/content/10.1101/2022.05.02.490266v1?rss=1 Li, Y. Hu, J. Ruff, C. Zhou, X. 2022-05-02 doi:10.1101/2022.05.02.490266 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Spatiotemporal landscape of SARS-CoV-2 pulmonary infection reveals Slamf9+Spp1+ macrophages promoting viral clearance and inflammation resolution ]]> https://biorxiv.org/content/10.1101/2022.05.03.490381v1?rss=1 Cong, B. Dong, X. Yang, Z. Yu, P. Chai, Y. Liu, J. Zhang, M. Zang, Y. Kang, J. Feng, Y. Liu, Y. Feng, W. Deng, W. Li, F. Yu, Q. Gu, Y. Li, Z. Liu, S. Xu, X. Zhong, N. Ren, X. Qin, C. Liu, L. Wang, J. Cao, X. 2022-05-03 doi:10.1101/2022.05.03.490381 Cold Spring Harbor Laboratory Press 2022-05-03 <![CDATA[ Dynamic emergence of relational structure network in human brains ]]> https://biorxiv.org/content/10.1101/2022.05.07.491053v1?rss=1 Ren, X. Zhang, H. Luo, H. 2022-05-08 doi:10.1101/2022.05.07.491053 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ Adversarial interspecies relationships facilitate population suppression by gene drive in spatially explicit models ]]> https://biorxiv.org/content/10.1101/2022.05.08.491087v1?rss=1 Liu, Y. Teo, W. Yang, H. Champer, J. 2022-05-08 doi:10.1101/2022.05.08.491087 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ Multi-color live-cell STED nanoscopy of mitochondria with a gentle inner membrane stain ]]> https://biorxiv.org/content/10.1101/2022.05.09.491019v1?rss=1 Liu, T. Stephan, T. Chen, P. Chen, J. Riedel, D. Yang, Z. Jakobs, S. Chen, Z. 2022-05-09 doi:10.1101/2022.05.09.491019 Cold Spring Harbor Laboratory Press 2022-05-09 <![CDATA[ Tracking single cell evolution via clock-like chromatin accessibility ]]> https://biorxiv.org/content/10.1101/2022.05.12.491736v1?rss=1 Wang, X. Jin, W. Wang, G. Ju, L. Chen, F. Qian, K. Xiao, Y. Zhang, Y. 2022-05-13 doi:10.1101/2022.05.12.491736 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ DNA binding domain undergoes dynamic and selective protein-protein interactions to facilitate CTCF insulation ]]> https://biorxiv.org/content/10.1101/2022.05.15.491938v1?rss=1 Rong, Z. Kai, T. Jie, H. Wenjia, D. Hongye, F. Ying, F. Hui, W. Yongpeng, J. Yuanjun, L. Rui, W. Jiazhi, H. Hanhui, M. Zhi, Q. Xiong, J. 2022-05-15 doi:10.1101/2022.05.15.491938 Cold Spring Harbor Laboratory Press 2022-05-15 <![CDATA[ Retina Gap Junction Networks Facilitate Blind Denoising in Visual Hierarchy ]]> https://biorxiv.org/content/10.1101/2022.05.16.491952v1?rss=1 Yue, Y. Lun, K. He, L. He, G. Zhang, S. Ma, L. Liu, J. K. Tian, Y. Du, K. Huang, T. 2022-05-17 doi:10.1101/2022.05.16.491952 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ SARS-CoV-2 accessory proteins ORF7a and ORF3a use distinct mechanisms to downregulate MHC-I surface expression ]]> https://biorxiv.org/content/10.1101/2022.05.17.492198v1?rss=1 Arshad, N. Laurent-Rolle, M. Ahmed, W. S. Hsu, J. C.-C. Mitchell, S. M. Pawlak, J. Sengupta, D. Biswas, K. H. Cresswell, P. 2022-05-17 doi:10.1101/2022.05.17.492198 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ Endothelial Brg1 fine-tunes Notch signaling during zebrafish heart regeneration ]]> https://biorxiv.org/content/10.1101/2022.05.18.492445v1?rss=1 Xiao, C. Hou, J. Wang, F. Song, Y. Zheng, J. Luo, L. Wang, J. Ding, W. Zhu, X. Xiong, J.-W. 2022-05-25 doi:10.1101/2022.05.18.492445 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ ABHD6 selectively controls Gq-dependent increases in 2-AG production ]]> https://biorxiv.org/content/10.1101/2022.05.18.492553v1?rss=1 Singh, S. Sarroza, D. English, A. Whittington, D. Dong, A. van der Stelt, M. Li, Y. Zweifel, L. Bruchas, M. R. Land, B. B. Stella, N. 2022-05-19 doi:10.1101/2022.05.18.492553 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Biomolecular solution X-ray scattering at n2STAR Beamline ]]> https://biorxiv.org/content/10.1101/2022.05.20.492803v1?rss=1 Gocenler, O. Yenici, C. M. Kahraman, K. Buyukdag, C. Dag, C. 2022-05-22 doi:10.1101/2022.05.20.492803 Cold Spring Harbor Laboratory Press 2022-05-22 <![CDATA[ A common mechanism of temperature-sensing in thermoTRP channels ]]> https://biorxiv.org/content/10.1101/2022.05.23.493163v1?rss=1 Xu, L. Liang, X. Zhen, W. Xue, Z. Zhang, F. Yi, X. Chen, X. Hu, L. Li, B. Zhang, B. Wang, Y. Deng, Z. Yang, W. Wen, H. Guo, T. Zhu, Y. Fan, Y. 2022-05-24 doi:10.1101/2022.05.23.493163 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ Specific Pupylation as IDEntity Reporter (SPIDER) for the identification of Protein-Biomolecule interactions ]]> https://biorxiv.org/content/10.1101/2022.05.26.493537v1?rss=1 Jiang, H.-W. Chen, H. Zheng, Y.-X. Wang, X.-N. Meng, Q. Xie, J. Zhang, J. Zhang, C.-S. Xu, Z.-W. Chen, Z.-Q. Wang, L. Kong, W.-S. Zhou, K. Ma, M.-L. Zhang, H.-N. Guo, S.-J. Xue, J.-B. Hou, J.-L. Liu, Z.-Y. Niu, W.-X. Wang, F.-J. Wang, T. Li, W. Wang, R.-N. Dang, Y.-J. Czajkowsky, D. M. Qiao, Y. Dong, J.-J. Pei, J. Tao, S.-C. 2022-05-26 doi:10.1101/2022.05.26.493537 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ Representing linguistic communicative goals in the premotor cortex ]]> https://biorxiv.org/content/10.1101/2022.05.26.493580v1?rss=1 Chang, W. Wang, L. Yang, R. Wang, X. Gao, Z. Zhou, X. 2022-05-26 doi:10.1101/2022.05.26.493580 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ Herd immunity on chip: recapitulating virus transmission in human society ]]> https://biorxiv.org/content/10.1101/2022.05.27.493795v1?rss=1 LIm, W. Jung, N. Zhang, J. Chen, Z. Weon, B. M. Park, S. 2022-05-30 doi:10.1101/2022.05.27.493795 Cold Spring Harbor Laboratory Press 2022-05-30 <![CDATA[ Genome similarities between human-derived and mink-derived SARS-CoV-2 make mink a potential reservoir of the virus ]]> https://biorxiv.org/content/10.1101/2022.05.29.493871v1?rss=1 Khalid, M. Al-ebini, Y. 2022-05-30 doi:10.1101/2022.05.29.493871 Cold Spring Harbor Laboratory Press 2022-05-30 <![CDATA[ The Effect of Perturbation Variability on Sensorimotor Adaptation Does Not Require an Implicit Memory of Errors ]]> https://biorxiv.org/content/10.1101/2022.05.30.493844v1?rss=1 Wang, T. Avraham, G. Tsay, J. Ivry, R. 2022-05-31 doi:10.1101/2022.05.30.493844 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Sensitive bacterial Vm sensors revealed the excitability of bacterial Vm and its role in antibiotic tolerance ]]> https://biorxiv.org/content/10.1101/2022.06.02.494477v1?rss=1 Jin, X. Zhang, X. Ding, X. Tian, T. Tseng, C.-K. Luo, X. Chen, X. Lo, C.-J. Leake, M. C. Bai, F. 2022-06-02 doi:10.1101/2022.06.02.494477 Cold Spring Harbor Laboratory Press 2022-06-02 <![CDATA[ Biosynthetic diversification of peptaibol mediates fungus-mycohost interactions ]]> https://biorxiv.org/content/10.1101/2022.06.05.494846v1?rss=1 Fan, J. Ren, J. He, R. Wei, P. Li, Y. Li, W. Chen, D. Druzhinina, I. Li, Z. Yin, W. 2022-06-05 doi:10.1101/2022.06.05.494846 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ Preferential cross-linking of the stereospecific complex over the encounter complexes by DOPA2, a faster cross-linker than DSS ]]> https://biorxiv.org/content/10.1101/2022.06.06.494913v1?rss=1 Wang, J.-H. Gong, Z. Dong, X. Liu, S.-Q. Tang, Y.-L. Lei, X. Tang, C. Dong, M.-Q. 2022-06-06 doi:10.1101/2022.06.06.494913 Cold Spring Harbor Laboratory Press 2022-06-06 <![CDATA[ Identification of ASPDH as a novel NAADP-binding protein ]]> https://biorxiv.org/content/10.1101/2022.06.06.494947v1?rss=1 He, X. Kang, Y. Chen, L. 2022-06-06 doi:10.1101/2022.06.06.494947 Cold Spring Harbor Laboratory Press 2022-06-06 <![CDATA[ Exploring the alternative conformation of a known protein structure based on contact map prediction ]]> https://biorxiv.org/content/10.1101/2022.06.07.495232v1?rss=1 Li, J. Wang, L. Zhu, Z. Song, C. 2022-06-09 doi:10.1101/2022.06.07.495232 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Co-occurrence of past and present shifts current neural representations and mediates serial biases ]]> https://biorxiv.org/content/10.1101/2022.06.08.495281v1?rss=1 Zhang, H. Luo, H. 2022-06-10 doi:10.1101/2022.06.08.495281 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Transcriptome-wide analysis suggests piRNAs preferentially recognize the coding region of mRNAs in C. elegans ]]> https://biorxiv.org/content/10.1101/2022.06.08.495319v1?rss=1 Wu, W.-S. Brown, J. S. Shiue, S.-C. Lee, D.-E. Zhang, D. Lee, H.-C. 2022-06-10 doi:10.1101/2022.06.08.495319 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Markonv: a novel convolutional layer with inter-positional correlations modeled ]]> https://biorxiv.org/content/10.1101/2022.06.09.495500v1?rss=1 Li, J.-Y. Tan, Y. Wen, Z.-Y. Kang, Y.-J. Ding, Y. Gao, G. 2022-06-13 doi:10.1101/2022.06.09.495500 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ Learning better by learning together: dyadic visual perceptual learning on orientation discrimination ]]> https://biorxiv.org/content/10.1101/2022.06.10.495635v1?rss=1 Zhang, Y. Li, J. Wang, Y. Fang, F. 2022-06-13 doi:10.1101/2022.06.10.495635 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ A GPU-based computational framework that bridges Neuron simulation and Artificial Intelligence ]]> https://biorxiv.org/content/10.1101/2022.06.12.495784v1?rss=1 Zhang, Y. He, G. Liu, X. Hjorth, J. Kozlov, A. He, Y. Zhang, S. Ma, L. Kotaleski, J. Tian, Y. Grillner, S. Du, K. Huang, T. 2022-06-15 doi:10.1101/2022.06.12.495784 Cold Spring Harbor Laboratory Press 2022-06-15 <![CDATA[ Structural and mechanistic insights into the DNA glycosylase AAG-mediated base excision in nucleosome ]]> https://biorxiv.org/content/10.1101/2022.06.16.496441v1?rss=1 Zheng, L. Tsai, B. Gao, N. 2022-06-17 doi:10.1101/2022.06.16.496441 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Cable-free brain imaging with miniature wireless microscopes ]]> https://biorxiv.org/content/10.1101/2022.06.20.496795v1?rss=1 Wang, Y. Ma, Z. Li, W. Su, F. Wang, C. Xiong, W. Li, C. Zhang, C. 2022-06-21 doi:10.1101/2022.06.20.496795 Cold Spring Harbor Laboratory Press 2022-06-21 <![CDATA[ Pancreatic tumors activate arginine biosynthesis to adapt to myeloid-driven amino acid stress ]]> https://biorxiv.org/content/10.1101/2022.06.21.497008v1?rss=1 Saab, J. J. A. Dzierozynski, L. N. Jonker, P. B. Zhu, Z. Chen, R. N. Oh, M. Sheehan, C. Macleod, K. F. Weber, C. R. Muir, A. 2022-06-25 doi:10.1101/2022.06.21.497008 Cold Spring Harbor Laboratory Press 2022-06-25 <![CDATA[ A Novel Selective ERK1/2 Inhibitor, Laxiflorin B, Targets EGFR Mutation Subtypes in Non-small-cell Lung Cancer ]]> https://biorxiv.org/content/10.1101/2022.06.27.497627v1?rss=1 Chiang, C. Zhang, M. Huang, J. Zeng, J. Chen, C. Pan, D. Yang, H. Yang, M. Han, Q. Zou, W. Xiao, T. Zou, Y. Yin, F. Li, Z. Zhu, L. Zheng, D. 2022-06-29 doi:10.1101/2022.06.27.497627 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Terminal flourishes but not trills differ between urban and rural chaffinch song ]]> https://biorxiv.org/content/10.1101/2022.06.29.498165v1?rss=1 Yelimlies, A. Atalas, B. Onsal, C. Akcay, C. 2022-07-03 doi:10.1101/2022.06.29.498165 Cold Spring Harbor Laboratory Press 2022-07-03 <![CDATA[ The specificity of different-distance connections in human structural connectomes ]]> https://biorxiv.org/content/10.1101/2022.07.09.499310v1?rss=1 Yang, Y. Zheng, Y. Zhen, Y. Tang, S. Zheng, H. Zheng, Z. 2022-07-11 doi:10.1101/2022.07.09.499310 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Growth mindset promotes children's working memory performance through cortico-striatal interaction and fronto-parietal activation ]]> https://biorxiv.org/content/10.1101/2022.07.11.499525v1?rss=1 Zhao, Y. Xu, J. Chen, M. Hao, L. He, Y. Wang, H. Wang, Y. Wang, D. Han, Z. R. Tan, S. Men, W. Gao, J. He, Y. Tao, S. Dong, Q. Qin, S. 2022-07-12 doi:10.1101/2022.07.11.499525 Cold Spring Harbor Laboratory Press 2022-07-12 <![CDATA[ Computational Enhanced Hi-C data reveals the function of structural geometry in genomic regulation ]]> https://biorxiv.org/content/10.1101/2022.07.12.499232v1?rss=1 He, Y. Xue, Y. Wang, J. Huang, Y. Liu, L. Huang, Y. Gao, Y. Q. 2022-07-13 doi:10.1101/2022.07.12.499232 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Whole-brain mapping of effective connectivity by fMRI with cortex-wide patterned optogenetics ]]> https://biorxiv.org/content/10.1101/2022.07.12.499420v1?rss=1 Kim, S. Moon, H. S. Vo, T. T. Kim, C.-H. Im, G. H. Choi, M. Kim, S.-G. 2022-07-13 doi:10.1101/2022.07.12.499420 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Noncovalent antibody catenation on a target surface drastically increases the antigen-binding avidity ]]> https://biorxiv.org/content/10.1101/2022.07.12.499671v1?rss=1 Song, J. Jeong, B.-S. Kim, S.-W. Im, S.-B. Cho, W. Ahn, M.-J. Oh, B.-H. 2022-07-13 doi:10.1101/2022.07.12.499671 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Crossmodal reorganization in deaf auditory cortices compensates for the impaired body-centered visuomotor transformation after early deafness ]]> https://biorxiv.org/content/10.1101/2022.07.14.500143v1?rss=1 Song, L. Wang, P. Li, H. Weiss, P. H. Fink, G. R. Zhou, X. Chen, Q. 2022-07-16 doi:10.1101/2022.07.14.500143 Cold Spring Harbor Laboratory Press 2022-07-16 <![CDATA[ Proximal dendritic localization of NALCN channels underlies tonic and burst firing in nigral dopaminergic neurons ]]> https://biorxiv.org/content/10.1101/2022.07.17.500361v1?rss=1 Park, M. K. Hahn, S. Kim, H. J. Um, K. B. 2022-07-18 doi:10.1101/2022.07.17.500361 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Neutralizing antibody evasion and receptor binding features of SARS-CoV-2 Omicron BA.2.75 ]]> https://biorxiv.org/content/10.1101/2022.07.18.500332v1?rss=1 Cao, Y. Yu, Y. Song, W. Jian, F. Yisimayi, A. Yue, C. Feng, R. Wang, P. Yu, L. Zhang, N. Wang, J. Xiao, T. An, R. Wang, Y. Wang, J. Liu, L. Yang, S. Niu, X. Gu, Q. Shao, F. Hao, X. Jin, R. Wang, X. Wang, Y. Xie, X. S. 2022-07-19 doi:10.1101/2022.07.18.500332 Cold Spring Harbor Laboratory Press 2022-07-19 <![CDATA[ Dopamine Activates Astrocytes in Prefrontal Cortex via α1-Adrenergic Receptors ]]> https://biorxiv.org/content/10.1101/2022.07.19.500710v1?rss=1 View larger version (55K): org.highwire.dtl.DTLVardef@e71858org.highwire.dtl.DTLVardef@1ef506forg.highwire.dtl.DTLVardef@89e4edorg.highwire.dtl.DTLVardef@11483e1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pittolo, S. Yokoyama, S. Willoughby, D. Taylor, C. Reitman, M. Tse, V. Wu, Z. Etchenique, R. Li, Y. Poskanzer, K. E. 2022-07-20 doi:10.1101/2022.07.19.500710 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Establishment of Transgenic Fluorescent Mice for Screening Synaptogenic Adhesion Molecules ]]> https://biorxiv.org/content/10.1101/2022.07.20.500799v1?rss=1 Yang, L. Zhang, J. Zhang, Y. Wang, L. Wang, X. Wang, S. Li, K. Wei, M. Zhang, C. 2022-07-21 doi:10.1101/2022.07.20.500799 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Mechanistic basis for targeting homologous recombination defective liver cancer via synthetic lethality ]]> https://biorxiv.org/content/10.1101/2022.07.21.500952v1?rss=1 Zeng, M. Tang, Z. Ren, L. Wang, H. Wang, X. Zhu, W. Mao, X. Li, Z. Mo, X. Chen, J. Han, J. Kong, D. Ji, J. Carr, A. Liu, C. 2022-07-22 doi:10.1101/2022.07.21.500952 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Genetic architecture of creativity and extensive genetic overlap with psychiatric disorders revealed from genome-wide association analyses of 241,736 individuals ]]> https://biorxiv.org/content/10.1101/2022.07.25.501322v1?rss=1 Kim, H. Ahn, Y. Yoon, J. Jung, K. Kim, S. Shim, I. Park, T. H. Ko, H. Jung, S.-H. Kim, J. Park, S. Lee, D. J. Choi, S. Cha, S. Kim, B. Cho, M. Y. Cho, H. Kim, D. S. Ihm, H. K. Park, W.-Y. Bakhshi, H. O'Connell, K. Andreassen, O. Flint, J. Kendler, K. S. Myung, W. Won, H.-H. 2022-07-25 doi:10.1101/2022.07.25.501322 Cold Spring Harbor Laboratory Press 2022-07-25 <![CDATA[ Coevolution-based prediction of key allosteric residues for protein function regulation ]]> https://biorxiv.org/content/10.1101/2022.07.25.501401v1?rss=1 Xie, J. Zhang, W. Zhu, X. Deng, M. Lai, L. 2022-07-26 doi:10.1101/2022.07.25.501401 Cold Spring Harbor Laboratory Press 2022-07-26 <![CDATA[ Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience ]]> https://biorxiv.org/content/10.1101/2022.07.27.501675v1?rss=1 Abdellah, M. Garcia Cantero, J. J. Roman Guerrero, N. Foni, A. Coggan, J. S. Cali, C. Agus, M. Zisis, E. Keller, D. Hadwiger, M. Magistretti, P. Markram, H. Schürmann, F. 2022-07-29 doi:10.1101/2022.07.27.501675 Cold Spring Harbor Laboratory Press 2022-07-29 <![CDATA[ Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing ]]> https://biorxiv.org/content/10.1101/2022.07.27.501701v1?rss=1 Lee, J. Kim, M. Kang, K. Yang, C.-S. Yoon, S. 2022-07-29 doi:10.1101/2022.07.27.501701 Cold Spring Harbor Laboratory Press 2022-07-29 <![CDATA[ Genetically encoded photocatalytic protein labeling enables spatially-resolved profiling of intracellular proteome ]]> https://biorxiv.org/content/10.1101/2022.08.01.502286v1?rss=1 Zheng, F. Yu, C. Zhou, X. Zou, P. 2022-08-02 doi:10.1101/2022.08.01.502286 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Rational identification of potent and broad sarbecovirus-neutralizing antibody cocktails from SARS convalescents ]]> https://biorxiv.org/content/10.1101/2022.08.03.499114v1?rss=1 Cao, Y. R. Jian, F. Zhang, Z. Yisimayi, A. Hao, X. Bao, L. Yuan, F. Yu, Y. Du, S. Wang, J. Xiao, T. Song, W. Zhang, Y. Liu, P. An, R. Wang, P. Wang, Y. Yang, S. Niu, X. Zhang, Y. Gu, Q. Shao, F. Hu, Y. Yin, W. Zheng, A. Wang, Y. Qin, C. Jin, R. Xiao, J. Xie, X. S. 2022-08-04 doi:10.1101/2022.08.03.499114 Cold Spring Harbor Laboratory Press 2022-08-04 <![CDATA[ Plasmodium falciparum has evolved multiple mechanisms to hijack human immunoglobulin M ]]> https://biorxiv.org/content/10.1101/2022.08.03.502706v1?rss=1 Ji, C. Shen, H. Su, C. Li, Y. Chen, S. Sharp, T. H. Xiao, J. 2022-08-04 doi:10.1101/2022.08.03.502706 Cold Spring Harbor Laboratory Press 2022-08-04 <![CDATA[ Characterization of network hierarchy reflects cell-state specificity in genome organization ]]> https://biorxiv.org/content/10.1101/2022.08.03.502724v1?rss=1 Wang, J. Xue, Y. He, Y. Quan, H. Zhang, J. Gao, Y. Q. 2022-08-05 doi:10.1101/2022.08.03.502724 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Uni-Fold: An Open-Source Platform for Developing Protein Folding Models beyond AlphaFold ]]> https://biorxiv.org/content/10.1101/2022.08.04.502811v1?rss=1 Li, Z. Liu, X. Chen, W. Shen, F. Bi, H. Ke, G. Zhang, L. 2022-08-06 doi:10.1101/2022.08.04.502811 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ MetaTiME: Meta-components of the Tumor Immune Microenvironment ]]> https://biorxiv.org/content/10.1101/2022.08.05.502989v1?rss=1 Zhang, Y. Xiang, G. Jiang, A. Y. Lynch, A. Zeng, Z. Wang, C. Zhang, W. Fan, J. Kang, J. Gu, S. Wan, C. Zhang, B. Liu, X. S. Brown, M. Meyer, C. A. 2022-08-06 doi:10.1101/2022.08.05.502989 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ Recovery of structural integrity of epithelial monolayer in response to massive apoptosis-induced defects ]]> https://biorxiv.org/content/10.1101/2022.08.08.503238v1?rss=1 Yuan, Y. Han, Y. L. Xia, J. Li, H. Tang, C. Ye, F. Weitz, D. Guo, M. 2022-08-08 doi:10.1101/2022.08.08.503238 Cold Spring Harbor Laboratory Press 2022-08-08 <![CDATA[ Harnessing Wolbachia cytoplasmic incompatibility alleles for confined gene drive: a modeling study ]]> https://biorxiv.org/content/10.1101/2022.08.09.503337v1?rss=1 Li, J. Champer, J. 2022-08-11 doi:10.1101/2022.08.09.503337 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Further humoral immunity evasion of emerging SARS-CoV-2 BA.4 and BA.5 subvariants ]]> https://biorxiv.org/content/10.1101/2022.08.09.503384v1?rss=1 Jian, F. Yu, Y. Song, W. Yisimayi, A. Yu, L. Gao, Y. Zhang, N. Wang, Y. Shao, F. Hao, X. Xu, Y. Jin, R. Wang, Y. Xie, X. S. Cao, Y. 2022-08-10 doi:10.1101/2022.08.09.503384 Cold Spring Harbor Laboratory Press 2022-08-10 <![CDATA[ Macrophage migrates on alternate non-adhesive surfaces ]]> https://biorxiv.org/content/10.1101/2022.08.10.503454v1?rss=1 Xing, F. Dong, H. Yang, J. Fan, C. Hou, M. Zhang, P. Hu, F. Zhou, J. Chen, L. Pan, L. Xu, J. 2022-08-11 doi:10.1101/2022.08.10.503454 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Engineering precise adenine base editor with infinitesimal rates of bystander mutations and off-target editing ]]> https://biorxiv.org/content/10.1101/2022.08.12.503700v1?rss=1 Chen, L. Zhang, S. Xue, N. Hong, M. Zhang, X. Zhang, D. Yang, J. Bai, S. Huang, Y. Meng, H. Wu, H. Luan, C. Zhu, B. Ru, G. Liu, M. Liu, M. Cheng, Y. Yi, C. Song, G. Wang, L. Li, D. 2022-08-13 doi:10.1101/2022.08.12.503700 Cold Spring Harbor Laboratory Press 2022-08-13 <![CDATA[ Sequential involvements of macaque perirhinal cortex and hippocampus in semantic-like memory including spatial component ]]> https://biorxiv.org/content/10.1101/2022.08.15.504057v1?rss=1 Yang, C. Naya, Y. 2022-08-16 doi:10.1101/2022.08.15.504057 Cold Spring Harbor Laboratory Press 2022-08-16 <![CDATA[ Epigenetic-focused CRISPR/Cas9 screen identifies ASH2L as a regulator of glioblastoma cell survival ]]> https://biorxiv.org/content/10.1101/2022.08.17.504245v1?rss=1 Ozyerli-Goknar, E. Kala, E. Y. Aksu, A. C. Bulut, I. Cingoz, A. Nizamuddin, S. Biniossek, M. Seker-Polat, F. Morova, T. Aztekin, C. Kung, S. H. A. Syed, H. Tuncbag, N. Gonen, M. Philpott, M. Cribbs, A. P. Acilan, C. Lack, N. A. Onder, T. T. Timmers, H. T. M. Bagci-Onder, T. 2022-08-17 doi:10.1101/2022.08.17.504245 Cold Spring Harbor Laboratory Press 2022-08-17 <![CDATA[ Genetically encoded sensors for measuring histamine release both in vitro and in vivo ]]> https://biorxiv.org/content/10.1101/2022.08.19.504485v1?rss=1 Dong, H. Li, M. Yan, Y. Qian, T. Lin, Y. Ma, X. Vischer, H. F. Liu, C. Li, G. Wang, H. Leurs, R. Li, Y. 2022-08-19 doi:10.1101/2022.08.19.504485 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ Engineering of NEMO as calcium indicators with ultra-high dynamics and sensitivity ]]> https://biorxiv.org/content/10.1101/2022.08.23.504677v1?rss=1 100-fold). NEMO indicators report Ca2+ transients with peak SBRs ~20-fold larger than the top-of-the-range GCaMP series. NEMO sensors further enable the quantification of absolution calcium concentration with ratiometric or photochromic imaging. Compared to GCaMPs, NEMOs could detect single action potentials in neurons with a peak SBR two times higher and a median peak SBR four times larger in vivo, thereby outperforming most existing state-of-the-art GECIs. Given their high sensitivity and resolution to report intracellular Ca2+ signals, NEMO sensors may find broad applications in monitoring neuronal activities and other Ca2+-modulated physiological processes in both mammals and plants. ]]> Li, J. Shang, Z. Chen, J.-H. Gu, W. Yao, L. Yang, X. Sun, X. Wang, L. Hou, T. Wang, S.-Q. Xing, D. Gill, D. L. Hou, L. Zhou, Y. Tang, A.-H. Zhang, X. Wang, Y. 2022-08-23 doi:10.1101/2022.08.23.504677 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ Downregulated NPAS4 in multiple brain regions is associated with Major Depressive Disorder ]]> https://biorxiv.org/content/10.1101/2022.08.23.505036v1?rss=1 Selcuk, B. Aksu, T. Dereli, O. Adebali, O. 2022-08-24 doi:10.1101/2022.08.23.505036 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ Kinetics-based Inference of Environment-Dependent Microbial Interactions and Their Dynamic Variation ]]> https://biorxiv.org/content/10.1101/2022.08.27.505268v1?rss=1 Song, H.-S. Lee, N.-R. Kessell, A. K. Park, S.-Y. Zhou, K. Lee, D.-Y. 2022-08-29 doi:10.1101/2022.08.27.505268 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ A computational framework linking synaptic adaptation to circuit behaviors in the early visual system ]]> https://biorxiv.org/content/10.1101/2022.08.27.505287v1?rss=1 He, L. He, Y. Lun, K. Ma, L. Du, K. Huang, T. 2022-08-29 doi:10.1101/2022.08.27.505287 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Local Field Potentials, Spiking Activity, and Receptive Fields in Human Visual Cortex ]]> https://biorxiv.org/content/10.1101/2022.08.28.505627v1?rss=1 Luo, L. Wang, X. Lu, J. Chen, G. Luan, G. Li, W. Wang, Q. Fang, F. 2022-08-29 doi:10.1101/2022.08.28.505627 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Uni-Fold Symmetry: Harnessing Symmetry in Folding Large Protein Complexes ]]> https://biorxiv.org/content/10.1101/2022.08.30.505833v1?rss=1 Li, Z. Yang, S. Liu, X. Chen, W. Wen, H. Shen, F. Ke, G. Zhang, L. 2022-08-30 doi:10.1101/2022.08.30.505833 Cold Spring Harbor Laboratory Press 2022-08-30 <![CDATA[ Biologic that disrupts PDE11A4 homodimerization in hippocampus CA1 reverses age-related proteinopathies in PDE11A4 and cognitive decline of social memories ]]> https://biorxiv.org/content/10.1101/2022.08.31.506102v1?rss=1 Pilarzyk, K. Capell, W. Rips-Goodwin, A. Porcher, L. Kelly, M. 2022-09-03 doi:10.1101/2022.08.31.506102 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Dissociated amplitude and phase effects of alpha oscillation in a nested structure of rhythm- and sequence-based temporal expectation ]]> https://biorxiv.org/content/10.1101/2022.09.01.506156v1?rss=1 Su, Z. Zhou, X. Wang, L. 2022-09-03 doi:10.1101/2022.09.01.506156 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Reactivation-induced memory integration prevents proactive interference in perceptual learning ]]> https://biorxiv.org/content/10.1101/2022.09.01.506161v1?rss=1 Huang, Z. Niu, Z. Li, S. 2022-09-05 doi:10.1101/2022.09.01.506161 Cold Spring Harbor Laboratory Press 2022-09-05 <![CDATA[ Optimization and deoptimization of codons in SARS-CoV-2 and the implications for vaccine development ]]> https://biorxiv.org/content/10.1101/2022.09.03.506470v1?rss=1 Wu, X. Shan, K. Zan, F. Tang, X. Qian, Z. Lu, J. 2022-09-05 doi:10.1101/2022.09.03.506470 Cold Spring Harbor Laboratory Press 2022-09-05 <![CDATA[ Initial niche condition determines the aging speed and regenerative activity of quiescent cells ]]> https://biorxiv.org/content/10.1101/2022.09.06.506737v1?rss=1 Liu, Q. Sheng, N. Zhang, Z. He, C. Zhao, Y. Sun, H. Chen, J. Yang, X. Tang, C. 2022-09-07 doi:10.1101/2022.09.06.506737 Cold Spring Harbor Laboratory Press 2022-09-07 <![CDATA[ Calcium binding and permeation in TRPV channels: insights from molecular dynamics simulations ]]> https://biorxiv.org/content/10.1101/2022.09.07.506889v1?rss=1 Liu, C. Song, C. 2022-09-07 doi:10.1101/2022.09.07.506889 Cold Spring Harbor Laboratory Press 2022-09-07 <![CDATA[ High-throughput TCRB enrichment sequencing of human cord blood exhibited a distinct fetal T cell repertoire in the third trimester of pregnancy ]]> https://biorxiv.org/content/10.1101/2022.09.08.506871v1?rss=1 Dong, Y. Wei, C. Wang, J. Wu, X. Zhao, Y. Cai, Y. Han, Y. Wang, Y. Li, H. Qiao, J. Yuan, W. 2022-09-12 doi:10.1101/2022.09.08.506871 Cold Spring Harbor Laboratory Press 2022-09-12 <![CDATA[ Identification of the Metaphyseal Skeletal Stem Cell ]]> https://biorxiv.org/content/10.1101/2022.09.08.506930v1?rss=1 Yang, G. He, Q. Guo, X. Li, R.-Y. Lin, J. Tao, W. Liu, W. Lin, H. Tang, M. Xing, S. Qi, Y. Peng, Y. Dong, L. Han, J.-D. J. Zhou, B. Teng, Y. Yang, X. 2022-09-09 doi:10.1101/2022.09.08.506930 Cold Spring Harbor Laboratory Press 2022-09-09 <![CDATA[ Predicting microbial community compositions in wastewater treatment plants using artificial neural networks ]]> https://biorxiv.org/content/10.1101/2022.09.08.507071v1?rss=1 10%) and core taxa were 35.09% and 42.99%, respectively. We also found that the predictability of ASVs>10% was significantly positively correlated with their relative abundance and occurrence frequency, but significantly negatively correlated with potential migration rate. The typical functional groups such as nitrifiers, denitrifiers, polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs), and filamentous organisms in AS systems could also be well recovered using an ANN model, with the R21:1 ranging from 32.62% to 56.81%. Furthermore, we found that industry wastewater source (IndConInf) had good predictive abilities, although its correlation with ASVs>10% in the Mantel test analysis was weak, which suggested important factors that cannot be identified using traditional methods may be highlight by the ANN model. Our results provide a better understanding of the factors affecting AS communities through the prediction of the microbial community of AS systems, which could lead to insights for improved operating parameters and control of community structure. ]]> Liu, X. Nie, Y. Wu, X.-L. 2022-09-11 doi:10.1101/2022.09.08.507071 Cold Spring Harbor Laboratory Press 2022-09-11 <![CDATA[ Extraction and characterization of cellulose from invasive weeds from central Nepal: A potential prospect of environmental management. ]]> https://biorxiv.org/content/10.1101/2022.09.08.507090v1?rss=1 Dhakal, S. Tiwari, A. Adhikari, A. Shrestha, S. K. Adhikari, B. 2022-09-08 doi:10.1101/2022.09.08.507090 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Molecular mechanism of substrate recognition by folate transporter SLC19A1 ]]> https://biorxiv.org/content/10.1101/2022.09.09.507238v1?rss=1 Dang, Y. Zhou, D. Du, X. Zhao, H. Lee, C.-H. Yang, J. Qin, C. Guo, Z. Zhang, Z. 2022-09-10 doi:10.1101/2022.09.09.507238 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Crystal structure of Vibrio cholerae (6-4) photolyase with DNA binding region ]]> https://biorxiv.org/content/10.1101/2022.09.10.507404v1?rss=1 Cakilkaya, B. Kavakli, I. H. DeMirci, H. 2022-09-11 doi:10.1101/2022.09.10.507404 Cold Spring Harbor Laboratory Press 2022-09-11 <![CDATA[ Siderophore-mediated iron partition promotes dynamical coexistence between cooperators and cheaters ]]> https://biorxiv.org/content/10.1101/2022.09.13.507871v1?rss=1 Shao, J. Rong, N. Wu, Z. Liu, B. Shen, N. Li, Z. 2022-09-15 doi:10.1101/2022.09.13.507871 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Ancient DNA Reveals China as a Historical Genetic Melting Pot in Tiger Evolution ]]> https://biorxiv.org/content/10.1101/2022.09.14.507899v1?rss=1 Sun, X. Liu, Y.-C. Tiunov, M. P. Gimranov, D. O. Zhuang, Y. Han, Y. Driscoll, C. A. Pang, Y.-H. Li, C. Pan, Y. Velasco, M. S. Gopalakrishnan, S. Yang, R.-Z. Li, B.-G. Jin, K. Xu, X. Uphyrkina, O. Huang, Y.-Y. Wu, X.-H. Gilbert, M. T. P. O'Brien, S. J. Yamaguchi, N. Luo, S.-J. 2022-09-17 doi:10.1101/2022.09.14.507899 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Advanced Feedback Enhances Sensorimotor Adaptation ]]> https://biorxiv.org/content/10.1101/2022.09.14.508027v1?rss=1 Wang, T. Avraham, G. Tsay, J. Thummala, T. Ivry, R. B. 2022-09-16 doi:10.1101/2022.09.14.508027 Cold Spring Harbor Laboratory Press 2022-09-16 <![CDATA[ An R-R-type MYB transcription factor promotes nonclimacteric pepper fruit ripening pigmentation ]]> https://biorxiv.org/content/10.1101/2022.09.15.507774v1?rss=1 Ning, Z. Song, J. Chen, C. Sun, B. Zhang, S. Cai, Y. Zheng, X. Cao, B. Chen, G. Jin, D. Li, B. Bian, J. Lei, J. He, H. Zhu, Z. 2022-09-17 doi:10.1101/2022.09.15.507774 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Imprinted SARS-CoV-2 humoral immunity induces converging Omicron RBD evolution ]]> https://biorxiv.org/content/10.1101/2022.09.15.507787v1?rss=1 Cao, Y. Jian, F. Wang, J. Yu, Y. Song, W. Yisimayi, A. Wang, J. An, R. Zhang, N. Wang, Y. Wang, P. Zhao, L. Sun, H. Yu, L. Yang, S. Niu, X. Xiao, T. Gu, Q. Shao, F. Hao, X. Xu, Y. Jin, R. Wang, Y. Xie, X. S. 2022-09-16 doi:10.1101/2022.09.15.507787 Cold Spring Harbor Laboratory Press 2022-09-16 <![CDATA[ Nutrient addition increases grassland resistance during dry and wet climate extremes despite functional diversity loss ]]> https://biorxiv.org/content/10.1101/2022.09.16.508233v1?rss=1 Chen, Q. Wang, S.-P. Seabloom, E. W. Isbell, F. Borer, E. T. Bakker, J. D. Bharath, s. Roscher, C. Peri, P. L. Power, S. A. Donohue, I. Stevens, C. Ebeling, A. Nogueira, C. Caldeira, M. C. MacDougall, A. Moore, J. Bagchi, S. Jentsch, A. Tedder, M. Kirkman, K. Alberti, J. Hautier, Y. 2022-09-19 doi:10.1101/2022.09.16.508233 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Under the shadow: Old-biased genes are subject to weak purifying selection at both the tissue and cell type-specific levels ]]> https://biorxiv.org/content/10.1101/2022.09.21.508695v1?rss=1 Yıldız, M. Izgi, H. Rahimova, F. Altıntas, U. B. Turan, Z. G. Somel, M. 2022-09-21 doi:10.1101/2022.09.21.508695 Cold Spring Harbor Laboratory Press 2022-09-21 <![CDATA[ Neural correlates of an illusive sense of agency caused by virtual reality ]]> https://biorxiv.org/content/10.1101/2022.09.21.508963v1?rss=1 Cai, Y. Yang, H. Xiong, Z. Kühn, S. Bi, Y. Wei, K. 2022-09-25 doi:10.1101/2022.09.21.508963 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[ Identification of potential human pancreatic α-amylase inhibitors from natural products by molecular docking, MM/GBSA calculations, MD simulations, and ADMET analysis ]]> https://biorxiv.org/content/10.1101/2022.09.26.509544v1?rss=1 Basnet, S. Ghimire, M. P. Lamichhane, T. R. Adhikari, R. Adhikari, A. 2022-09-27 doi:10.1101/2022.09.26.509544 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Domain Adaptive Neural Inference for Neurons, Microcircuits and Networks ]]> https://biorxiv.org/content/10.1101/2022.10.03.510694v1?rss=1 Sheng, K. Zhang, S. Beau, M. Qu, P. Yang, L. Liu, X. He, L. Zhang, Y. Ma, L. Du, K. 2022-10-07 doi:10.1101/2022.10.03.510694 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Structure of human phagocyte NADPH oxidase in the resting state ]]> https://biorxiv.org/content/10.1101/2022.10.04.510768v1?rss=1 Liu, R. Song, K. Wu, J.-X. Geng, X.-P. Zheng, L. Gao, X. Peng, H. Chen, L. 2022-10-04 doi:10.1101/2022.10.04.510768 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ Nuclear autophagy interactome unveils WSTF as a constitutive nuclear inhibitor of inflammation ]]> https://biorxiv.org/content/10.1101/2022.10.04.510822v1?rss=1 Wang, Y. Eapen, V. V. Kournoutis, A. Onorati, A. Li, X. Zhou, X. Cetinbas, M. Wang, L. Liu, J. Bretz, C. Zhou, Z. Ho Sui, S. J. Saladi, S. V. Sadreyev, R. Adams, P. D. Kingston, R. E. Yue, Z. Johansen, T. Dou, Z. 2022-10-05 doi:10.1101/2022.10.04.510822 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ A hybrid reconstruction of the physical model with the deep-learning that improves structured illumination microscopy ]]> https://biorxiv.org/content/10.1101/2022.10.04.510914v1?rss=1 Wang, J. Fan, J. Zhou, B. Huang, X. Chen, L. 2022-10-07 doi:10.1101/2022.10.04.510914 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Triangulation reduces the polygon of error for the history of Transeurasian ]]> https://biorxiv.org/content/10.1101/2022.10.05.510045v1?rss=1 Robbeets, M. Hudson, M. Ning, C. Bouckaert, R. Savelyev, A. Kim, G. Li, T. Oskolskaya, S. Gruntov, I. Mazo, O. Rhee, S. Ahn, K.-D. Fernandes, R. Shinoda, K.-i. Kanzawa-Kiriyama, H. Bjorn, R. Deng, B. An, D.-i. Bentley, J. Kawashima, T. Dolinska, J. 2022-10-07 doi:10.1101/2022.10.05.510045 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ GESIAP: A Versatile Genetically Encoded Sensor-based Image Analysis Program ]]> https://biorxiv.org/content/10.1101/2022.10.05.511006v1?rss=1 Zheng, W. S. Zhang, Y. Zhu, R. E. Zhang, P. Gupta, S. Huang, L. Sahoo, D. Guo, K. Glover, M. E. Vadodaria, K. C. Li, M. Qian, T. Jing, M. Feng, J. Wan, J. Borden, P. M. Podgorski, K. Ali, F. Kwan, A. C. Gan, L. Lin, L. Gage, F. H. Venton, B. J. Marvin, J. S. Clinton, S. M. Zhang, M. Looger, L. Li, Y. Zhu, J. J. 2022-10-07 doi:10.1101/2022.10.05.511006 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Discovery and biosynthesis of imidazolium antibiotics from a probiotic Bacillus licheniformis ]]> https://biorxiv.org/content/10.1101/2022.10.05.511033v1?rss=1 View larger version (8K): org.highwire.dtl.DTLVardef@184f545org.highwire.dtl.DTLVardef@2a69eorg.highwire.dtl.DTLVardef@8cf13org.highwire.dtl.DTLVardef@530001_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ham, S. L. Lee, T. H. Kim, K. J. Kim, J. H. Hwang, S. J. Lee, S. H. Lee, W. Kim, C. S. 2022-10-05 doi:10.1101/2022.10.05.511033 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ The conserved upstream ORF of the Arabidopsis ANAC082 gene mediates translational upregulation in response to nucleolar stress ]]> https://biorxiv.org/content/10.1101/2022.10.07.511279v1?rss=1 Sasaki, S. Murakami, T. Yasumuro, M. Makita, A. Oi, Y. Hiragori, Y. Watanabe, S. Kudo, R. Hayashi, N. Ohbayash, I. Sugiyama, M. Yamashita, Y. Naito, S. Onouchi, H. 2022-10-07 doi:10.1101/2022.10.07.511279 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Gαs slow conformational transition upon GTP binding and a novel Gαs regulator ]]> https://biorxiv.org/content/10.1101/2022.10.10.511514v1?rss=1 Ahn, D. Provasi, D. Duc, N. M. Xu, J. Salas-Estrada, L. Spasic, A. Yun, M. W. Kang, J. Gim, D. Lee, J. Filizola, M. Chung, K. Y. 2022-10-10 doi:10.1101/2022.10.10.511514 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ Allee effects mediate the impact of land-use change on the thermal niche of social species ]]> https://biorxiv.org/content/10.1101/2022.10.11.511768v1?rss=1 Chan, S.-F. Rubenstein, D. R. Wang, T.-W. Chen, Y.-Y. Chen, I.-C. Ni, D.-Z. Shih, W.-K. Shen, S.-F. 2022-10-14 doi:10.1101/2022.10.11.511768 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ Rapid and High Resolution Ambient Temperature Structure Determination at Turkish Light Source ]]> https://biorxiv.org/content/10.1101/2022.10.12.511637v1?rss=1 Gul, M. Ayan, E. Destan, E. Johnson, J. A. Shafiei, A. Kepceoglu, A. Yilmaz, M. Ertem, F. B. Yapici, I. Tosun, B. Baldir, N. Tokay, N. Nergiz, Z. Karakadioglu, G. Paydos, S. S. Kulakman, C. Ferah, C. K. Guven, O. Atalay, N. Akcan, E. K. Cetinok, H. Arslan, N. E. Sabanoglu, K. Asci, B. Tavli, S. Altuntas, S. Otsuka, M. Fujita, M. Tekin, S. Ciftci, H. Durdagi, S. Karaca, E. Kaplan Turkoz, B. Kabasakal, B. V. Kati, A. DeMirci, H. 2022-10-17 doi:10.1101/2022.10.12.511637 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Prefrontal norepinephrine represents a threat prediction error under uncertainty ]]> https://biorxiv.org/content/10.1101/2022.10.13.511463v1?rss=1 Basu, A. Yang, J.-h. Yu, A. L. Glaeser-Khan, S. Feng, J. Krystal, J. H. Li, Y. Kaye, A. P. 2022-10-17 doi:10.1101/2022.10.13.511463 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Baculovirus Surface Display of Hemagglutinin and Neuraminidase for Monoclonal Antibody Production ]]> https://biorxiv.org/content/10.1101/2022.10.16.512416v1?rss=1 Lo, H.-R. Wu, C.-P. Jan, J.-T. Chao, Y.-C. Tsai, C.-H. 2022-10-18 doi:10.1101/2022.10.16.512416 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Predicting individualized tissue gene expression profiles with multi-task learning ]]> https://biorxiv.org/content/10.1101/2022.10.19.512838v1?rss=1 He, G. Chen, M. Bian, Y. Yang, E. 2022-10-21 doi:10.1101/2022.10.19.512838 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Novel Master Regulators of Microglial Phagocytosis and Repurposed FDA-approved Drug for Treatment of Alzheimer Disease ]]> https://biorxiv.org/content/10.1101/2022.10.19.512953v1?rss=1 Zhu, K. He, Q. Tsai, S.-F. Mudalige, D. M. Tang, A. Henrion, M. Y. R. Liu, Y. Vijayan, R. Zaidi, S. S. A. Branden, L. Cadiz, M. P. Hodos-Nkhereanye, R. Moein, S. Alamprese, M. L. Bennett, D. A. De Jager, P. Kuo, Y.-M. Ronaldson, P. T. Chang, R. 2022-10-21 doi:10.1101/2022.10.19.512953 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Chinese fir genome and the evolution of gymnosperms ]]> https://biorxiv.org/content/10.1101/2022.10.25.513437v1?rss=1 Lin, S.-Z. Chen, Y. Wu, C. Sun, W.-H. Li, Z. Chen, H. Wang, J. Ji, C. Li, S.-B. Wang, Z.-W. Tsai, W.-C. Ma, X.-Q. Lan, S.-R. Zhang, F.-P. Xie, Y.-C. Yao, L. Zhang, Y. Lv, M.-M. Zhang, J.-J. Zhang, D.-Y. Ye, Y.-Q. Yu, X. Xu, S.-S. Ma, Z.-H. Ding, G.-C. Cao, G.-Q. He, Z.-M. Wu, P.-F. Lin, K.-M. Liu, A.-Q. Lin, Y.-Q. Ruan, S.-N. Liu, B. Cao, S.-J. Zhou, L.-L. Li, M. Shuai, P. Hou, X.-L. Wu, Y.-H. Li, N. Xiong, S. Hao, Y. Zhou, Z. Liu, X.-D. Zuo, D.-D. Li, J. Wang, P. Zhang, J. Liu, D.-K. Chen, G.-Z. Huang, J. Huang, M.-Z. Li, Y. Zheng, Q. Zhao 2022-10-26 doi:10.1101/2022.10.25.513437 Cold Spring Harbor Laboratory Press 2022-10-26 <![CDATA[ Quantitative profiling of pseudouridylation landscape in the human transcriptome ]]> https://biorxiv.org/content/10.1101/2022.10.25.513650v1?rss=1 Zhang, M. Jiang, Z. Ma, Y. Liu, W. Zhuang, Y. Lu, B. Li, K. Yi, C. 2022-10-25 doi:10.1101/2022.10.25.513650 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Importance of Glutamine in Synaptic Vesicles Revealed by Functional Studies of SLC6A17 and Its Mutations Pathogenic for Intellectual Disability ]]> https://biorxiv.org/content/10.1101/2022.10.25.513688v1?rss=1 Jia, X. Bian, X. Zhu, J. Liu, S. Liang, W. Yu, S. Jiang, L. Mao, R. Rao, Y. 2022-10-27 doi:10.1101/2022.10.25.513688 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ BrainPy: a flexible, integrative, efficient, and extensible framework towards general-purpose brain dynamics programming ]]> https://biorxiv.org/content/10.1101/2022.10.28.514024v1?rss=1 Wang, C. Chen, X. Zhang, T. Wu, S. 2022-10-28 doi:10.1101/2022.10.28.514024 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Structural and Functional Insights into the Action Mode of A Mitochondrial AAA+ Disaggregase CLPB ]]> https://biorxiv.org/content/10.1101/2022.10.28.514188v1?rss=1 Wu, D. Liu, Y. Dai, Y. Wang, G. Lu, G. Chen, Y. Li, N. Lin, J. Gao, N. 2022-10-28 doi:10.1101/2022.10.28.514188 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Simulations reveal high efficiency and confinement of a population suppression CRISPR toxin-antidote gene drive ]]> https://biorxiv.org/content/10.1101/2022.10.30.514459v1?rss=1 Zhu, Y. Champer, J. 2022-11-01 doi:10.1101/2022.10.30.514459 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Making waves: Comparative analysis of gene drive spread characteristics in a continuous space model ]]> https://biorxiv.org/content/10.1101/2022.11.01.514650v1?rss=1 Pan, M. Champer, J. 2022-11-02 doi:10.1101/2022.11.01.514650 Cold Spring Harbor Laboratory Press 2022-11-02 <![CDATA[ Global terrestrial nitrogen uptake and nitrogen use efficiency ]]> https://biorxiv.org/content/10.1101/2022.11.01.514661v1?rss=1 Peng, Y. Prentice, I. C. Bloomfield, K. J. Campioli, M. Guo, Z. Sun, Y. Tian, D. Wang, X. Vicca, S. Stocker, B. D. 2022-11-02 doi:10.1101/2022.11.01.514661 Cold Spring Harbor Laboratory Press 2022-11-02 <![CDATA[ Oocytes can repair DNA damage during meiosis via a microtubule-dependent recruitment of CIP2A-MDC1-TOPBP1 complex from spindle pole to chromosomes ]]> https://biorxiv.org/content/10.1101/2022.11.04.514992v1?rss=1 Leem, J. Kim, J.-S. Oh, J. S. 2022-11-04 doi:10.1101/2022.11.04.514992 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Large-scale neural dynamics in a shared low-dimensional state space reflect cognitive and attentional dynamics ]]> https://biorxiv.org/content/10.1101/2022.11.05.515307v1?rss=1 Song, H. Shim, W. M. Rosenberg, M. D. 2022-11-05 doi:10.1101/2022.11.05.515307 Cold Spring Harbor Laboratory Press 2022-11-05 <![CDATA[ Transcription-independent hold of the G1/S transition is exploited to cope with DNA replication stress ]]> https://biorxiv.org/content/10.1101/2022.11.10.515958v1?rss=1 Jin, Y. lan, G. Zhang, J. Sun, H. Li, X. Cao, Q. Tang, C. Yang, X. Lou, H. Hou, W. 2022-11-11 doi:10.1101/2022.11.10.515958 Cold Spring Harbor Laboratory Press 2022-11-11 <![CDATA[ Serial dependence in timing at the perceptual level being modulated by working memory ]]> https://biorxiv.org/content/10.1101/2022.11.11.516083v1?rss=1 Chen, S. Wang, T. Bao, Y. 2022-11-13 doi:10.1101/2022.11.11.516083 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Exploration of mechanisms of drug resistance by polyaneuploid cancer cells in a microfluidic device and patient tissues ]]> https://biorxiv.org/content/10.1101/2022.11.14.515727v1?rss=1 Lim, W. Hwang, I. Zhang, J. Chen, Z. Jeonghun, J. Koo, B.-K. Kim, S. Lee, J. E. Pienta, K. j. Amend, S. R. Austin, R. H. Ahn, J.-Y. Park, S. 2022-11-16 doi:10.1101/2022.11.14.515727 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Formation process of the twinning β-form anhydrous guanine platelets in the scallop eyes ]]> https://biorxiv.org/content/10.1101/2022.11.14.516375v1?rss=1 Guo, D. Liu, Y. Hou, X. Wang, X. Fan, C. Bao, L. He, X. Zhang, H. Ma, Y. 2022-11-15 doi:10.1101/2022.11.14.516375 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Firing rate adaptation in continuous attractor neural networks accounts for theta phase shift of hippocampal place cells ]]> https://biorxiv.org/content/10.1101/2022.11.14.516400v1?rss=1 Chu, T. Ji, Z. Zuo, J. Mi, Y. Zhang, W.-H. Huang, T. Bush, D. Burgess, N. Wu, S. 2022-11-14 doi:10.1101/2022.11.14.516400 Cold Spring Harbor Laboratory Press 2022-11-14 <![CDATA[ Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-design ]]> https://biorxiv.org/content/10.1101/2022.11.14.516404v1?rss=1 Gao, K. Wu, L. Zhu, J. Peng, T. Xia, Y. He, L. Xie, S. Qin, T. Liu, H. He, K. Liu, T.-Y. 2022-11-15 doi:10.1101/2022.11.14.516404 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Deletion of TRPC6, an autism risk gene, induces hyperexcitability in cortical neurons derived from human pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2022.11.14.516407v1?rss=1 Shin, K. C. Ali, G. Ali Moussa, H. Y. Gupta, V. de la Fuente, A. Kim, H.-G. Stanton, L. Park, Y. 2022-11-14 doi:10.1101/2022.11.14.516407 Cold Spring Harbor Laboratory Press 2022-11-14 <![CDATA[ Modulation of the microhomology-mediated end joining pathway suppresses large deletions and enhances homology-directed repair following CRISPR-Cas9-induced DNA breaks ]]> https://biorxiv.org/content/10.1101/2022.11.16.516713v1?rss=1 Yuan, B. Bi, C. Wang, J. Jin, Y. Alsayegh, K. Tehseen, M. Yi, G. Hamdan, S. Huang, Y. Li, M. 2022-11-16 doi:10.1101/2022.11.16.516713 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Rapid and Signal Crowdedness-Robust In-Situ Sequencing through Hybrid Block Coding ]]> https://biorxiv.org/content/10.1101/2022.11.16.516714v1?rss=1 Chang, T. Han, W. Jiang, M. Li, J. Shen, J. Chen, Z. Fei, P. Ren, X. Pang, Y. Wang, G. Wang, J. Huang, Y. 2022-11-17 doi:10.1101/2022.11.16.516714 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ ppGpp is Present in and Functions to Regulate Sleep in Drosophila ]]> https://biorxiv.org/content/10.1101/2022.11.17.516975v1?rss=1 Dai, X. Yang, W. Zhang, X. Zhou, E. Liu, Y. Wang, T. V. Zhang, W. Zhang, X. Rao, Y. 2022-11-18 doi:10.1101/2022.11.17.516975 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ Mapping single-cell responses to population-level dynamics during antibiotic treatment ]]> https://biorxiv.org/content/10.1101/2022.11.18.517151v1?rss=1 Kim, K. Wang, T. Ma, H. R. Simsek, E. Li, B. Andreani, V. You, L. 2022-11-19 doi:10.1101/2022.11.18.517151 Cold Spring Harbor Laboratory Press 2022-11-19 <![CDATA[ Instantaneous antidepressant effect of lateral habenula deep brain stimulation in rats studied with functional magnetic resonance imaging ]]> https://biorxiv.org/content/10.1101/2022.11.20.517264v1?rss=1 Li, G. Bo, B. Wang, P. Qian, P. Li, M. Li, Y. Tong, C. Zhang, K. Zhang, B. Jiang, T. Liang, Z. Duan, X. 2022-11-22 doi:10.1101/2022.11.20.517264 Cold Spring Harbor Laboratory Press 2022-11-22 <![CDATA[ Pisces: A combo-wise contrastive learning approach to synergistic drug combination prediction ]]> https://biorxiv.org/content/10.1101/2022.11.21.517439v1?rss=1 Lin, J. Xu, H. Woicik, A. Ma, J. Wang, S. 2022-11-22 doi:10.1101/2022.11.21.517439 Cold Spring Harbor Laboratory Press 2022-11-22 <![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[ The shadowing effect of initial expectation on learning asymmetry ]]> https://biorxiv.org/content/10.1101/2022.11.22.517473v1?rss=1 Sun, J. Ni, Y. Li, J. 2022-11-22 doi:10.1101/2022.11.22.517473 Cold Spring Harbor Laboratory Press 2022-11-22 <![CDATA[ Predicting Lung Cancer in Korean Never-Smokers with Polygenic Risk Scores ]]> https://biorxiv.org/content/10.1101/2022.11.23.515119v1?rss=1 Kim, J. Park, Y. S. Kim, J. H. Hong, Y.-C. Kim, Y.-C. Oh, I.-J. Jee, S. H. Ahn, M.-J. Kim, J.-W. Yim, J.-J. Won, S. 2022-11-25 doi:10.1101/2022.11.23.515119 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ Monitoring the intestinal magnetic field with optically pumped atomic magnetometers ]]> https://biorxiv.org/content/10.1101/2022.11.23.517508v1?rss=1 Sun, C. Zhao, B. Wu, T. Zhang, J. Leng, Y. Guo, H. CREAM Bioelectromagnetism Group, 2022-11-25 doi:10.1101/2022.11.23.517508 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ ExposomeX: Integrative Exposomic Platform Expediates Discovery of "Exposure-Biology-Disease" Nexus ]]> https://biorxiv.org/content/10.1101/2022.11.23.517586v1?rss=1 Wang, B. Lan, C. Zhang, G. Ren, M. Feng, Y. Gao, N. Lin, W. Jiangtulu, B. Liu, Z. Shao, X. Su, S. Wang, Y. Wang, H. Zhao, F. Peng, B. Ji, X. Chen, X. Nian, M. Fang, M. 2022-11-25 doi:10.1101/2022.11.23.517586 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ Cryo-EM Structure of the 50S-HflX Complex Reveals a Novel Mechanism of Antibiotic Resistance in E. coli ]]> https://biorxiv.org/content/10.1101/2022.11.25.517942v1?rss=1 Wu, D. Dai, Y. Gao, N. 2022-11-25 doi:10.1101/2022.11.25.517942 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ Modeling cell size control using differential scaling of cell-cycle regulators with cell size ]]> https://biorxiv.org/content/10.1101/2022.11.30.518453v1?rss=1 Ji, X. Lin, J. 2022-12-01 doi:10.1101/2022.11.30.518453 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ BBIBP-CorV (Sinopharm) vaccination- induced immunity is affected by age, gender and prior COVID-19 and activates responses to spike and other antigens ]]> https://biorxiv.org/content/10.1101/2022.11.30.518633v1?rss=1 Hasan, Z. Masood, K. I. Qaiser, S. Khan, E. Hussain, A. Ghous, Z. Khan, U. Yameen, M. Hassan, I. Nisar, M. I. Qazi, M. F. Memon, H. A. Ali, S. Baloch, S. Bhutta, Z. A. Veldhoen, M. Simas, J. P. Mahmood, S. F. Hussain, R. Ghias, K. 2022-12-02 doi:10.1101/2022.11.30.518633 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Bright and sensitive red voltage indicators for imaging action potentials in brain slices and pancreatic islets ]]> https://biorxiv.org/content/10.1101/2022.12.01.518652v1?rss=1 Han, Y. Yang, J. Li, Y. Cen, Y. Ren, H. Ding, R. Qian, W. Ren, K. Xie, B. Deng, M. Xiao, Y. Chu, J. Zou, P. 2022-12-01 doi:10.1101/2022.12.01.518652 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Candida khanbhai sp. nov., a new clinically relevant yeast within the Candida haemulonii species complex ]]> https://biorxiv.org/content/10.1101/2022.12.01.518802v1?rss=1 de Jong, A. Al-Obaid, K. Mohd Tap, R. Gerrits van den Ende, B. Groenewald, M. Joseph, L. Ahmad, S. Hagen, F. 2022-12-02 doi:10.1101/2022.12.01.518802 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Effect of rectified gap junctional electrical coupling and spatial distribution of biologically engineered pacemaking cells on ventricular excitation ]]> https://biorxiv.org/content/10.1101/2022.12.02.518808v1?rss=1 Li, Y. Li, Q. Liu, J. Ma, L. Wang, K. Zhang, H. 2022-12-03 doi:10.1101/2022.12.02.518808 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ A Unitary Mechanism Underlies Adaptation to Both Local and Global Environmental Statistics in Time Perception ]]> https://biorxiv.org/content/10.1101/2022.12.03.519001v1?rss=1 Wang, T. Luo, Y. Ivry, R. B. Tsay, J. Poeppel, E. Bao, Y. 2022-12-05 doi:10.1101/2022.12.03.519001 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ Prior expectation enhances sensorimotor behavior by modulating population tuning and subspace activity in the sensory cortex ]]> https://biorxiv.org/content/10.1101/2022.12.04.516847v1?rss=1 Park, J. Kim, S. Kim, H. R. Lee, J. 2022-12-05 doi:10.1101/2022.12.04.516847 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ A Community Challenge to Predict Clinical Outcomes After Immune Checkpoint Blockade in Non-Small Cell Lung Cancer ]]> https://biorxiv.org/content/10.1101/2022.12.05.518667v1?rss=1 Mason, M. Lapuente-Santana, O. Halkola, A. S. Wang, W. Mall, R. Xiao, X. Kaufman, J. Fu, J. Pfeil, J. Banerjee, J. Chung, V. Chang, H. Chasalow, S. D. Lin, H. Y. Chai, R. Yu, T. Finotello, F. Mirtti, T. Mayranpaa, M. I. Bao, J. Verschuren, E. W. Ahmed, E. I. Ceccarelli, M. Miller, L. D. Monaco, G. Hendrickx, W. R. L. Sherif, S. Yang, L. Tang, M. Gu, S. S. Zhang, W. Zhang, Y. Zeng, Z. Sahu, A. D. Liu, Y. Yang, W. Bedognetti, D. Tang, J. Eduati, F. Laajala, T. D. Geese, W. J. Guinney, J. Szustakowski, J. D. Carbone, D. P. Vincent, B. G. 2022-12-08 doi:10.1101/2022.12.05.518667 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ Boosting wheat functional genomics via indexed EMS mutant library of KN9204 ]]> https://biorxiv.org/content/10.1101/2022.12.05.519108v1?rss=1 Wang, D. Li, Y. Wang, H. Xu, Y. Yang, Y. Zhou, Y. Chen, Z. Zhou, Y. Gui, L. Guo, Y. Zhou, C. Tang, W. Zheng, S. Wang, L. Guo, X. Zhang, Y. Cui, F. Lin, X. Jiao, Y. He, Y. Li, J. He, F. Liu, X. Xiao, J. 2022-12-08 doi:10.1101/2022.12.05.519108 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ Molecular dynamics analysis of Superoxide Dismutase 1 mutations suggests decoupling between mechanisms underlying ALS onset and progression ]]> https://biorxiv.org/content/10.1101/2022.12.05.519128v1?rss=1 Kalia, M. Miotto, M. Ness, D. Opie-Martin, S. Spargo, T. P. Di Rienzo, L. Biagini, T. Petrizzelli, F. Al-Khleifat, A. Kabiljo, R. Topp, S. Mayl, K. Fogh, I. Mehta, P. R. Williams, K. L. Jockel-Balsarotti, J. Bali, T. Self, W. Henden, L. Nicholson, G. A. Ticozzi, N. McKenna-Yasek, D. Tang, L. Shaw, P. Chio, A. Ludolph, A. Weishaupt, J. H. Landers, J. E. Glass, J. D. Mora, J. S. Robberecht, W. Van Damme, P. McLaughlin, R. Hardiman, O. van den Berg, L. H. Veldink, J. H. Corcia, P. Stevic, Z. Siddique, N. Ratti, A. Silani, V. Blair, I. P. Fan, D.-s. Essel 2022-12-05 doi:10.1101/2022.12.05.519128 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ A Host-Harbored Metabolic Susceptibility of Coronavirus Enables Broad-Spectrum Targeting ]]> https://biorxiv.org/content/10.1101/2022.12.07.519404v1?rss=1 Fang, H. Wang, Y. Liu, L. Cheng, K. Li, P. Tan, Y. Hao, X. Mei, M. Xu, X. Yao, Y. Zan, F. Wu, L. Zhu, Y. Xu, B. Huang, D. Wang, C. Tan, X. Qian, Z. Chen, X.-W. 2022-12-10 doi:10.1101/2022.12.07.519404 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ Multiple sites on glycoprotein H (gH) functionally interact with the gB fusion protein to promote fusion during herpes simplex virus (HSV) entry ]]> https://biorxiv.org/content/10.1101/2022.12.07.519554v1?rss=1 Fan, Q. Hippler, D. P. Yang, Y. Longnecker, R. Connolly, S. A. 2022-12-08 doi:10.1101/2022.12.07.519554 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ Expanding the diversity of Accumulibacter with a novel type and deciphering the transcriptional and morphological features among co-occurring strains ]]> https://biorxiv.org/content/10.1101/2022.12.09.519852v1?rss=1 Wang, Z.-j. Song, W. Zhang, X. Zheng, M. Li, H. Yu, K. Guo, F. 2022-12-11 doi:10.1101/2022.12.09.519852 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Structural basis for BIRC6 to balance apoptosis and autophagy ]]> https://biorxiv.org/content/10.1101/2022.12.10.519866v1?rss=1 Liu, S. Jiang, T. Bu, F. Zhao, J. Wang, G. Yang, G. Kong, J. Qie, Y. Wen, P. Fan, L. Li, N. Gao, N. Qiu, X. 2022-12-11 doi:10.1101/2022.12.10.519866 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Absence of the bile acid enzyme CYP8B1 increases brain chenodeoxycholic acid and reduces neuronal excitotoxicity in mice ]]> https://biorxiv.org/content/10.1101/2022.12.11.520005v1?rss=1 Monteiro-Cardoso, V. F. Yeo, X. Y. Bae, H.-G. Castano Mayan, D. Wehbe, M. Lee, S. Krishna-K, K. Baek, S. H. Palomera, L. F. Shanmugam, S. Sem, K. P. Parsons, M. P. Hayden, M. R. Liehn, E. A. Sajikumar, S. Davanger, S. Jo, D.-G. Jung, S. Singaraja, R. R. 2022-12-14 doi:10.1101/2022.12.11.520005 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ Switching the left and the right hearts: A novel bi-ventricle mechanical support strategy with spared native single-ventricle ]]> https://biorxiv.org/content/10.1101/2022.12.12.519951v1?rss=1 Sisli, E. Pekkan, K. Yildirim, C. Aka, I. B. Tuncer, O. N. Atay, Y. Ozbaran, M. 2022-12-14 doi:10.1101/2022.12.12.519951 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ The compact CasPi (Cas12l) bracelet "provides" a unique structural platform for DNA manipulation ]]> https://biorxiv.org/content/10.1101/2022.12.16.519550v1?rss=1 Sun, A. Li, C. Chen, Z. Zhang, S. Li, D. Yang, Y. Li, L.-Q. Zhao, Y. Wang, K. Li, Z. Liu, J. Liu, S. Wang, J. Liu, J.-J. G. 2022-12-16 doi:10.1101/2022.12.16.519550 Cold Spring Harbor Laboratory Press 2022-12-16 <![CDATA[ Open-3DSIM: an Open-source three-dimensional structured illumination microscopy reconstruction platform ]]> https://biorxiv.org/content/10.1101/2022.12.16.520543v1?rss=1 Cao, R. Li, Y. Chen, X. Ge, X. Li, M. Guan, M. Hou, Y. Fu, Y. Jiang, S. Gao, B. Xi, P. 2022-12-19 doi:10.1101/2022.12.16.520543 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Perinuclear force regulates SUN2 dynamics and distribution on the nuclear envelope for proper nuclear mechanotransduction ]]> https://biorxiv.org/content/10.1101/2022.12.16.520837v1?rss=1 Niu, J. Wang, X. Zhao, W. Wang, Y. Qin, Y. Huang, X. Xue, B. Li, C. Sun, Y. 2022-12-19 doi:10.1101/2022.12.16.520837 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Correlated protein modules reflecting functional coordination of interacting proteins are uncovered by single-cell proteomics ]]> https://biorxiv.org/content/10.1101/2022.12.18.520903v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@10e27corg.highwire.dtl.DTLVardef@857044org.highwire.dtl.DTLVardef@8d9731org.highwire.dtl.DTLVardef@1c149a4_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hu, M. Zhang, Y. Yuan, Y. Ma, W. Zheng, Y. Gu, Q. Xie, X. S. 2022-12-19 doi:10.1101/2022.12.18.520903 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Molecular insights into the gating mechanisms of voltage-gated calcium channel CaV2.3 ]]> https://biorxiv.org/content/10.1101/2022.12.19.521133v1?rss=1 Gao, Y. Xu, S. Cui, X. Xu, H. Qiu, Y. Wei, Y. Dong, Y. Zhu, B. Peng, C. Liu, S. Zhang, X. C. Sun, J. Huang, Z. Zhao, Y. 2022-12-20 doi:10.1101/2022.12.19.521133 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Spatial transcriptomics deconvolution at single-cell resolution by Redeconve ]]> https://biorxiv.org/content/10.1101/2022.12.22.521551v1?rss=1 Zhou, Z. Zhong, Y. Zhang, Z. Ren, X. 2022-12-22 doi:10.1101/2022.12.22.521551 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Evidence suggesting creatine as a new central neurotransmitter: presence in synaptic vesicles, release upon stimulation, effects on cortical neurons and uptake into synaptosomes and synaptic vesicles ]]> https://biorxiv.org/content/10.1101/2022.12.22.521565v1?rss=1 Bian, X. Zhu, J. Jia, X. Liang, W. Li, Z. Yu, S. Rao, Y. 2022-12-23 doi:10.1101/2022.12.22.521565 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ Molecular evolution of protein sequences and codon usage in monkeypox viruses ]]> https://biorxiv.org/content/10.1101/2022.12.23.521708v1?rss=1 IIa and IIb-A > IIb-B. Although the decrease in fatality rate in the three groups matched the CAI pattern, it is unclear whether this is a coincidence or if the deoptimization of codon usage in MPXV induced a decrease in fatality. This study sheds new light on the processes influencing the evolution of MPXV in human populations. ]]> Shan, K.-j. Wu, C. Tang, X. Lu, R. Tan, W. Lu, J. 2022-12-26 doi:10.1101/2022.12.23.521708 Cold Spring Harbor Laboratory Press 2022-12-26 <![CDATA[ Structural and Dynamic Characterization of Candida boidinii Formate Dehydrogenase by High-Resolution X-ray Crystallography ]]> https://biorxiv.org/content/10.1101/2022.12.25.521900v1?rss=1 Gul, M. Yuksel, B. Bulut, H. DeMirci, H. 2022-12-25 doi:10.1101/2022.12.25.521900 Cold Spring Harbor Laboratory Press 2022-12-25 <![CDATA[ Instar determination by constrained gaussian mixture models according to Dyar's rule ]]> https://biorxiv.org/content/10.1101/2022.12.26.521363v1?rss=1 Ji, S. 2022-12-27 doi:10.1101/2022.12.26.521363 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Visualization of mitochondrial cristae and mtDNA evolvement and interactions with super-resolution microscopy ]]> https://biorxiv.org/content/10.1101/2022.12.26.521907v1?rss=1 Ren, W. Ge, X. Li, M. Li, S. Shan, C. Gao, B. Xi, P. 2022-12-26 doi:10.1101/2022.12.26.521907 Cold Spring Harbor Laboratory Press 2022-12-26 <![CDATA[ VHL Mutation Drives Human Clear Cell Renal Cell Carcinoma Progression Through PI3K/AKT-Dependent Cholesteryl Ester Accumulation ]]> https://biorxiv.org/content/10.1101/2023.01.02.522447v1?rss=1 Zhang, S. He, Y. Feng, W. Zheng, Y. Hu, S. Fang, T. Liu, Z. Liu, J. Yu, J. He, A. Gong, Y. He, Z. Yang, K. Xi, Z. Yu, W. Zhou, L. Yao, L. Yue, S. 2023-01-07 doi:10.1101/2023.01.02.522447 Cold Spring Harbor Laboratory Press 2023-01-07 <![CDATA[ Enhanced transmissibility of XBB.1.5 is contributed by both strong ACE2 binding and antibody evasion ]]> https://biorxiv.org/content/10.1101/2023.01.03.522427v1?rss=1 Yue, C. Song, W. Wang, L. Jian, F. Chen, X. Gao, F. Shen, Z. Wang, Y. Wang, X. Cao, Y. R. 2023-01-03 doi:10.1101/2023.01.03.522427 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Evaluating Evasion Strategies in Zebrafish Larvae ]]> https://biorxiv.org/content/10.1101/2023.01.05.522537v1?rss=1 Jiao, Y. Colvert, B. Man, Y. McHenry, M. J. Kanso, E. 2023-01-05 doi:10.1101/2023.01.05.522537 Cold Spring Harbor Laboratory Press 2023-01-05 <![CDATA[ Accurate and Rapid Detection of Peritoneal Metastasis from Gastric Cancer by AI-assisted Stimulated Raman Cytology ]]> https://biorxiv.org/content/10.1101/2023.01.05.522829v1?rss=1 Chen, X. Wu, Z. He, Y. Hao, Z. Wang, Q. Zhou, K. Zhou, W. Wang, P. Shan, F. Li, Z. Ji, J. Fan, Y. Li, Z. Yue, S. 2023-01-06 doi:10.1101/2023.01.05.522829 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ The Use of Class Imbalanced Learning Methods on ULSAM Data to Predict the Case-Control Status in Genome-Wide Association Studies ]]> https://biorxiv.org/content/10.1101/2023.01.05.522884v1?rss=1 Oztornaci, R. O. Syed, H. Morris, A. Tasdelen, B. 2023-01-06 doi:10.1101/2023.01.05.522884 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Assessment of distant-site rescue elements for CRISPR toxin-antidote gene drives ]]> https://biorxiv.org/content/10.1101/2023.01.06.522951v1?rss=1 Chen, J. Xu, X. Champer, J. 2023-01-06 doi:10.1101/2023.01.06.522951 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ An axon - T cell feedback loop enhances inflammation and axon degeneration ]]> https://biorxiv.org/content/10.1101/2023.01.06.523014v1?rss=1 Liu, T. Wang, H. Kutsovsky, D. Y. Ohn, C. Y. Patel, N. Yang, J. Simon, D. J. 2023-01-07 doi:10.1101/2023.01.06.523014 Cold Spring Harbor Laboratory Press 2023-01-07 <![CDATA[ Smooth Muscle Cell Death Drives an Osteochondrogenic Phenotype and Severe Proximal Vascular Disease in Progeria ]]> https://biorxiv.org/content/10.1101/2023.01.10.523266v1?rss=1 Murtada, S.-I. Kawamura, Y. Cavinato, C. Wang, M. Ramachandra, A. B. Spronck, B. Tellides, G. Humphrey, J. 2023-01-11 doi:10.1101/2023.01.10.523266 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ Noise improves the association between effects of local stimulation and structural degree of brain networks ]]> https://biorxiv.org/content/10.1101/2023.01.10.523529v1?rss=1 Zheng, Y. Tang, S. Zheng, H. Wang, X. Liu, L. Yang, Y. Zhen, Y. Zheng, Z. 2023-01-12 doi:10.1101/2023.01.10.523529 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ iTie controls intestinal tolerance through suppressing the NLRP6 inflammasome ]]> https://biorxiv.org/content/10.1101/2023.01.12.523719v1?rss=1 Qin, X. Zhu, F. Li, W. Wang, S. Xia, P. 2023-01-12 doi:10.1101/2023.01.12.523719 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ Knowledge "installed" diffusion model predicts the geometry of actin cytoskeleton from cell morphology ]]> https://biorxiv.org/content/10.1101/2023.01.12.523863v1?rss=1 Li, H. Liu, S. Deguchi, S. Matsunaga, D. 2023-01-16 doi:10.1101/2023.01.12.523863 Cold Spring Harbor Laboratory Press 2023-01-16 <![CDATA[ Astrocytic control of extra-cellular GABA drives circadian time-keeping in the suprachiasmatic nucleus ]]> https://biorxiv.org/content/10.1101/2023.01.16.523253v1?rss=1 Patton, A. P. Morris, E. L. McManus, D. Wang, H. Li, Y. Chin, J. W. Hastings, M. H. 2023-01-18 doi:10.1101/2023.01.16.523253 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Does the territorial behaviour of the Amur tiger affect the accuracy of occupancy estimation? ]]> https://biorxiv.org/content/10.1101/2023.01.16.524338v1?rss=1 Xie, B. Gong, Y. Fu, Y. Feng, L. Yang, H. 2023-01-19 doi:10.1101/2023.01.16.524338 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Aurora B Kinase Dependent Phosphorylation of Keratin 8 is required for Cytokinesis in Mammalian Cells of Epithelial Origin ]]> https://biorxiv.org/content/10.1101/2023.01.22.525045v1?rss=1 Harmanda, B. Kaya, O. Waide, X. Qureshi, M. H. Nesvizhskii, A. Mitchison, T. Ozlu, N. 2023-01-22 doi:10.1101/2023.01.22.525045 Cold Spring Harbor Laboratory Press 2023-01-22 <![CDATA[ EDA2R/NIK signaling promotes skeletal muscle atrophy linked to cancer cachexia ]]> https://biorxiv.org/content/10.1101/2023.01.23.525138v1?rss=1 Bilgic, S. N. Domaniku, A. Toledo, B. Agca, S. Weber, B. Z. C. Arabaci, D. H. Ozornek, Z. Lause, P. Thissen, J.-P. Loumaye, A. Kir, S. 2023-01-23 doi:10.1101/2023.01.23.525138 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Investigating the effect of changes in model parameters on optimal control policies, time to absorption, and mixing times ]]> https://biorxiv.org/content/10.1101/2023.01.23.525286v1?rss=1 Johnson, K. Plaugher, D. R. Murrugarra, D. 2023-01-24 doi:10.1101/2023.01.23.525286 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize ]]> https://biorxiv.org/content/10.1101/2023.01.24.525389v1?rss=1 Zhou, L.-Z. Wang, L. Ge, Z. Mergner, J. Li, X. Kuster, B. Längst, G. Qu, L.-J. Dresselhaus, T. 2023-01-26 doi:10.1101/2023.01.24.525389 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ Structure of human NaV1.6 channel reveals Na+ selectivity and pore blockade by 4,9-anhydro-tetrodotoxin ]]> https://biorxiv.org/content/10.1101/2023.01.26.525614v1?rss=1 Li, Y. Yuan, T. Huang, B. Zhou, F. Peng, C. Li, X. Qiu, Y. Yang, B. Zhao, Y. Huang, Z. Jiang, D. 2023-01-27 doi:10.1101/2023.01.26.525614 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Activated Oncostatin M signaling drives cancer-associated skeletal muscle wasting ]]> https://biorxiv.org/content/10.1101/2023.01.26.525658v1?rss=1 Domaniku, A. Agca, S. Toledo, B. Bilgic, S. N. Kashgari, A. E. Kir, S. 2023-01-27 doi:10.1101/2023.01.26.525658 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Perturbation Variability Does Not Influence Implicit Sensorimotor Adaptation ]]> https://biorxiv.org/content/10.1101/2023.01.27.525949v1?rss=1 Wang, T. Avraham, G. Tsay, J. S. Abram, S. J. Ivry, R. B. 2023-01-29 doi:10.1101/2023.01.27.525949 Cold Spring Harbor Laboratory Press 2023-01-29 <![CDATA[ Depletion-assisted multiplexing cell-free RNA sequencing reveals distinct human and microbial signatures in plasma versus extracellular vesicle ]]> https://biorxiv.org/content/10.1101/2023.01.31.526408v1?rss=1 Wang, H. Zhan, Q. Guo, H. Zhao, J. Xing, S. Chen, S. Zuo, S. Li, M. Wang, P. Lu, Z. J. 2023-02-03 doi:10.1101/2023.01.31.526408 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Cell-free multi-omics analysis reveals tumor status-informative signatures in gastrointestinal cancer patients' plasma ]]> https://biorxiv.org/content/10.1101/2023.01.31.526431v1?rss=1 Tao, Y. Xing, S. Zuo, S. Bao, P. Jin, Y. Li, Y. Wu, Y. Chen, S. Wang, X. Zhu, Y. Feng, Y. Zhang, X. Wang, X. Xi, Q. Lu, Q. Wang, P. Lu, Z. J. 2023-02-03 doi:10.1101/2023.01.31.526431 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Imaging Microglia Surveillance during Sleep-wake Cycles in Freely Behaving Mice ]]> https://biorxiv.org/content/10.1101/2023.02.03.527083v1?rss=1 Gu, X. Zhang, L. Zhao, Z. Fang, H. Zhao, T. Ju, S. Chen, X. Gao, W. Qian, X. Wang, X. Zhang, J. Cheng, H. 2023-02-04 doi:10.1101/2023.02.03.527083 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Underlying driving forces of the SARS-CoV-2 evolution: immune evasion and ACE2 binding affinity ]]> https://biorxiv.org/content/10.1101/2023.02.06.527236v1?rss=1 Ma, W. Fu, H. Jian, F. Cao, Y. Li, M. 2023-02-07 doi:10.1101/2023.02.06.527236 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ A small molecule cocktail for robust induction of blood-brain barrier properties ]]> https://biorxiv.org/content/10.1101/2023.02.09.527899v1?rss=1 Porkolab, G. Meszaros, M. Szecsko, A. Vigh, J. P. Walter, F. R. Figueiredo, R. Kalomista, I. Vizsnyiczai, G. Jan, J.-S. Gosselet, F. Vastag, M. Veszelka, S. Deli, M. A. 2023-02-10 doi:10.1101/2023.02.09.527899 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Protective effect of plasma neutralization from prior SARS-CoV-2 Omicron infection against BA.5 subvariant symptomatic reinfection ]]> https://biorxiv.org/content/10.1101/2023.02.14.527605v1?rss=1 Chen, X. Xu, Y. Xie, Y. Song, W. Hu, Y. Yisimayi, A. Shao, F. Geng, L. Wang, Y. Gao, H. Shi, Y. Zhang, S. Jin, R. Shen, Z. Cao, Y. R. 2023-02-19 doi:10.1101/2023.02.14.527605 Cold Spring Harbor Laboratory Press 2023-02-19 <![CDATA[ Comprehensive Multi-omics Analysis Reveals the Core Role of Glycerophospholipid Metabolism in Rheumatoid Arthritis Development ]]> https://biorxiv.org/content/10.1101/2023.02.15.528612v1?rss=1 Jian, C. Wei, L. Wu, T. Li, S. Wang, T. Chen, J. Chang, S. Zhang, J. He, B. Wu, J. Su, J. Zhu, J. Wu, M. Zhang, Y. Zeng, F. 2023-02-15 doi:10.1101/2023.02.15.528612 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Pangolin genomes offer key insights and resources for the world's most trafficked wild mammals ]]> https://biorxiv.org/content/10.1101/2023.02.16.528682v1?rss=1 Heighton, S. P. Allio, R. Murienne, J. Salmona, J. Meng, H. Scornavacca, C. Bastos, A. D. S. Njiokou, F. Pietersen, D. W. Tilak, M.-K. Luo, S.-J. Delsuc, F. Gaubert, P. 2023-02-17 doi:10.1101/2023.02.16.528682 Cold Spring Harbor Laboratory Press 2023-02-17 <![CDATA[ CCDC15 localizes to the centriole inner scaffold and regulates centriole integrity and ciliogenesis ]]> https://biorxiv.org/content/10.1101/2023.02.16.528810v1?rss=1 Arslanhan, M. D. Steib, E. Hamel, V. Guichard, P. Firat-Karalar, E. N. 2023-02-18 doi:10.1101/2023.02.16.528810 Cold Spring Harbor Laboratory Press 2023-02-18 <![CDATA[ Extruding transcription elongation loops observed in high-resolution single-cell 3D genomes ]]> https://biorxiv.org/content/10.1101/2023.02.18.529096v1?rss=1 Wu, H. Zhang, J. Tan, L. Xie, X. S. 2023-02-19 doi:10.1101/2023.02.18.529096 Cold Spring Harbor Laboratory Press 2023-02-19 <![CDATA[ Hippocampal replay facilitates the formation of entorhinal grid cells ]]> https://biorxiv.org/content/10.1101/2023.02.19.529130v1?rss=1 Zhang, B. Liu, J. 2023-02-19 doi:10.1101/2023.02.19.529130 Cold Spring Harbor Laboratory Press 2023-02-19 <![CDATA[ Similarity in Functional Connectome Architecture Predicts Teenage Grit ]]> https://biorxiv.org/content/10.1101/2023.02.23.529637v1?rss=1 Park, S. Park, D. Kim, M. J. 2023-02-24 doi:10.1101/2023.02.23.529637 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ High immigration rates critical for establishing emigration-driven diversity in microbial communities ]]> https://biorxiv.org/content/10.1101/2023.02.24.529875v1?rss=1 Chen, X. Wang, M. Luo, L. An, L. Liu, X. Fang, Y. Huang, T. Nie, Y. Wu, X. 2023-02-24 doi:10.1101/2023.02.24.529875 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Structural Characterization of TRAF6 N-terminal for Therapeutic Uses ]]> https://biorxiv.org/content/10.1101/2023.02.25.529911v1?rss=1 Guven, O. Ciftci, H. Tateishi, H. Koga, R. Radwan, M. O. Sever, B. Inoue, J.-i. Otsuka, M. Fujita, M. DeMirci, H. 2023-02-25 doi:10.1101/2023.02.25.529911 Cold Spring Harbor Laboratory Press 2023-02-25 <![CDATA[ NuSAP participates in metaphase spindle length control in mammalians ]]> https://biorxiv.org/content/10.1101/2023.02.26.530101v1?rss=1 Zhang, C. Wang, Y. Sun, M. Xin, G. Yang, B. Jiang, Q. 2023-02-27 doi:10.1101/2023.02.26.530101 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Keystone taxa responsible for the microbial community stability and performance of activated sludges ]]> https://biorxiv.org/content/10.1101/2023.02.26.530128v1?rss=1 Liu, X. Wang, M. Liu, B. Chen, X. An, L. Nie, Y. Wu, X.-L. 2023-02-27 doi:10.1101/2023.02.26.530128 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Noise-robust, physical microscopic deconvolution algorithm enabled by multi-resolution analysis regularization ]]> https://biorxiv.org/content/10.1101/2023.03.02.530744v1?rss=1 Hou, Y. Wang, W. Fu, Y. Ge, X. Li, M. Xi, P. 2023-03-02 doi:10.1101/2023.03.02.530744 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Integrated single-cell analysis defines the epigenetic basis of castration-resistant prostate luminal cells ]]> https://biorxiv.org/content/10.1101/2023.03.03.530998v1?rss=1 View larger version (62K): org.highwire.dtl.DTLVardef@8bd384org.highwire.dtl.DTLVardef@1ebc004org.highwire.dtl.DTLVardef@8b4dbforg.highwire.dtl.DTLVardef@19d7052_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kirk, J. S. Wang, J. Tracz, A. Long, M. Rosario, S. R. Ji, Y. Kumar, R. Liu, X. Singh, P. K. Puzanov, I. Chatta, G. Cheng, Q. Huang, J. Wrana, J. L. Lovell, J. Yu, H. Liu, S. Shen, M. M. Liu, T. Tang, D. G. 2023-03-06 doi:10.1101/2023.03.03.530998 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Pharmacological characterization of the endocannabinoid sensor GRABeCB2.0 ]]> https://biorxiv.org/content/10.1101/2023.03.03.531053v1?rss=1 Singh, S. Sarroza, D. English, A. McGrory, M. Dong, A. Zweifel, L. Land, B. B. Li, Y. Bruchas, M. Stella, N. 2023-03-06 doi:10.1101/2023.03.03.531053 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ A Slow but Steady NanoLuc: R162A mutation results in a decreased, but stable, NanoLuc activity ]]> https://biorxiv.org/content/10.1101/2023.03.05.531182v1?rss=1 Ahmed, W. S. Geethakumari, A. M. Sultana, A. Fatima, A. Philip, A. M. Nasiruddin, S. M. Biswas, K. H. 2023-03-06 doi:10.1101/2023.03.05.531182 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Spatially Resolved Proteomic Profiling Uncovers Structural and Functional Regulators of the Axon Initial Segment ]]> https://biorxiv.org/content/10.1101/2023.03.06.531334v1?rss=1 Zhang, W. Fu, Y. Peng, L. Ogawa, Y. Zhou, X. Rasband, M. N. Zou, P. 2023-03-08 doi:10.1101/2023.03.06.531334 Cold Spring Harbor Laboratory Press 2023-03-08 <![CDATA[ Distinct activation mechanisms of β-arrestin 1 revealed by 19F NMR spectroscopy ]]> https://biorxiv.org/content/10.1101/2023.03.06.531433v1?rss=1 Zhai, R. Wang, Z. Chai, Z. Li, C. Jin, C. Hu, Y. 2023-03-07 doi:10.1101/2023.03.06.531433 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Coordinated transformation of object representations across human visual cortex ]]> https://biorxiv.org/content/10.1101/2023.03.07.531635v1?rss=1 Xu, R. Xu, X. Ling, Z. Zhou, W. Liu, H. HONG, B. 2023-03-10 doi:10.1101/2023.03.07.531635 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Ambient temperature crystal structure of Escherichia coli CyaY protein displays alternate conformation ]]> https://biorxiv.org/content/10.1101/2023.03.08.531761v1?rss=1 Shafiei, A. Baldir, N. Na, J. Kim, J. H. DeMirci, H. 2023-03-08 doi:10.1101/2023.03.08.531761 Cold Spring Harbor Laboratory Press 2023-03-08 <![CDATA[ Topographical similarity of cortical thickness represents generalized anxiety symptoms in adolescence ]]> https://biorxiv.org/content/10.1101/2023.03.09.531836v1?rss=1 Yoo, C. Kim, M. J. 2023-03-10 doi:10.1101/2023.03.09.531836 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Debottlenecking and reformulating feed media for improved CHO cell growth and titer by data-driven and model-guided analyses ]]> https://biorxiv.org/content/10.1101/2023.03.09.531884v1?rss=1 Park, S.-Y. Lee, D.-Y. Choi, D.-H. Song, J. Park, U. Cho, H. Hong, B. H. Silberberg, Y. R. 2023-03-10 doi:10.1101/2023.03.09.531884 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Loss-of-SIRT7 sensitizes hepatocellular carcinoma to sorafenib through the regulation of ERK Phosphorylation ]]> https://biorxiv.org/content/10.1101/2023.03.13.531998v1?rss=1 Kim, Y. Jung, K.-Y. Kim, Y. H. Xu, P. Jo, Y. Kang, B. E. Pandit, N. Kwon, J. Gariani, K. Gariani, J. Lee, J. Verbeek, J. Nam, S. Bae, S.-J. Ha, K.-T. Yi, H.-S. Shong, M. Kim, K.-H. Kim, D. Lee, C.-W. Jung, H. J. Kim, K. R. Schoonjans, K. Ryu, D. Auwerx, J. 2023-03-15 doi:10.1101/2023.03.13.531998 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice ]]> https://biorxiv.org/content/10.1101/2023.03.15.532726v1?rss=1 Bashkirova, E. Klimpert, N. Pourmorady, A. Monahan, K. Campbell, C. Osinski, J. Tan, L. Schieren, I. Stecky, R. Barnea, G. Xie, X. S. Abdus-Saboor, I. Shykind, B. Marlin, B. J. Gronostajski, R. Fleischmann, A. Lomvardas, S. 2023-03-15 doi:10.1101/2023.03.15.532726 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Multiple sequence-alignment-based RNA language model and its application to structural inference ]]> https://biorxiv.org/content/10.1101/2023.03.15.532863v1?rss=1 Zhang, Y. Lang, M. Jiang, J. Gao, Z. Xu, F. Litfin, T. Chen, K. Singh, J. Huang, X. Song, G. Tian, Y. Zhan, J. Chen, J. Zhou, Y. 2023-03-16 doi:10.1101/2023.03.15.532863 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ 6mA-Sniper: Quantifying 6mA Sites in Eukaryotes at Single-Nucleotide Resolution ]]> https://biorxiv.org/content/10.1101/2023.03.16.530559v1?rss=1 Zhang, J. Peng, Q. Ma, C. Wang, J. Xiao, C. Li, T. Liu, X. Zhou, L. Zhou, W.-Z. Ding, W. An, N. A. Zhang, L. Liu, Y. Li, C.-Y. 2023-03-17 doi:10.1101/2023.03.16.530559 Cold Spring Harbor Laboratory Press 2023-03-17 <![CDATA[ Coupling of Slack and NaV1.6 sensitizes Slack to quinidine blockade and guides anti-seizure strategy development ]]> https://biorxiv.org/content/10.1101/2023.03.16.532982v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@1127858org.highwire.dtl.DTLVardef@19ad9f4org.highwire.dtl.DTLVardef@15b5542org.highwire.dtl.DTLVardef@13a86b4_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yuan, T. Wang, Y. Jin, Y. Xu, S. Zhang, H. Chen, Q. Li, N. Ma, X. Song, H. Peng, C. Yang, H. Geng, Z. Dong, J. Duan, G. Sun, Q. Yang, Y. Yang, F. Huang, Z. 2023-03-18 doi:10.1101/2023.03.16.532982 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ Structure of a fungal 1,3-β-glucan synthase ]]> https://biorxiv.org/content/10.1101/2023.03.19.532754v1?rss=1 Zhao, C.-R. You, Z.-L. Chen, D.-d. Hang, J. Wang, Z.-B. Wang, L.-X. Zhao, P. Qiao, J. Yun, C.-H. Bai, L. 2023-03-20 doi:10.1101/2023.03.19.532754 Cold Spring Harbor Laboratory Press 2023-03-20 <![CDATA[ Mammalian Esophageal Stratified Tissue Homeostasis is Maintained Distinctively by the Epithelial Pluripotent p63+Sox2+ and p63-Sox2+ Cell Populations ]]> https://biorxiv.org/content/10.1101/2023.03.22.533592v1?rss=1 Yu, X. Yuan, H. Yang, Y. Zheng, W. Zheng, X. Lu, S.-H. Jiang, W. Yu, X. 2023-03-24 doi:10.1101/2023.03.22.533592 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Mind of a dauer: Comparative connectomics reveals developmental plasticity ]]> https://biorxiv.org/content/10.1101/2023.03.23.533915v1?rss=1 Yim, H. Choe, D. T. Bae, J. A. Kang, H.-M. Nguyen, K. C. Q. Choi, M.-k. Ahn, S. Bahn, S.-k. Yang, H. Hall, D. H. Kim, J. S. Lee, J. 2023-03-23 doi:10.1101/2023.03.23.533915 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ ScRNA-seq of Diverse Pheochromocytoma Patients Reveals Distinct Microenvironment Characteristics and Supports an Informative Molecular Classification System ]]> https://biorxiv.org/content/10.1101/2023.03.26.534245v1?rss=1 Qin, S. Xu, Y. Yu, S. Han, W. Fan, S. Ai, W. Zhang, K. Wang, Y. Zhou, X. Shen, Q. Gong, K. Sun, L. Zhang, Z. 2023-03-27 doi:10.1101/2023.03.26.534245 Cold Spring Harbor Laboratory Press 2023-03-27 <![CDATA[ Activity-dependent constraints on catecholamine signaling ]]> https://biorxiv.org/content/10.1101/2023.03.30.534970v1?rss=1 Li, L. Rana, A. N. Li, E. M. Feng, J. Li, Y. Bruchas, M. 2023-03-31 doi:10.1101/2023.03.30.534970 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ CilioGenics: an integrated method and database for predicting novel ciliary genes ]]> https://biorxiv.org/content/10.1101/2023.03.31.535034v1?rss=1 Pir, M. S. Yenisert, F. Karaman, A. Begar, E. Tsiropoulou, S. Firat-Karalar, E. N. Blacque, O. E. Oner, S. S. Doluca, O. Cevik, S. Kaplan, O. I. 2023-04-02 doi:10.1101/2023.03.31.535034 Cold Spring Harbor Laboratory Press 2023-04-02 <![CDATA[ Modulation of SLFN11 induces changes in DNA Damage response ]]> https://biorxiv.org/content/10.1101/2023.04.02.535254v1?rss=1 Raynaud, C. M. Ahmed, E. I. Jabeen, A. Sanchez, A. Sherif, S. Carneiro-Lobo, T. C. Awad, A. Awartani, D. Naik, A. Thomas, R. Decock, J. Zoppoli, G. Bedognetti, D. Hendrickx, W. 2023-04-03 doi:10.1101/2023.04.02.535254 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Astrocytic Slc4a4 regulates blood-brain barrier integrity in healthy and stroke brains via a NO-CCL2-CCR2 pathway ]]> https://biorxiv.org/content/10.1101/2023.04.03.535167v1?rss=1 Ye, Q. Jo, J. Wang, C.-Y. Oh, H. Choy, T. Kim, K. D'Alessandro, A. Reshetnyak, Y. K. Jung, S. Y. Chen, Z. Marrelli, S. P. Lee, H. K. 2023-04-03 doi:10.1101/2023.04.03.535167 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ The DEAD-box helicase RCF1 plays roles in miRNA biogenesis and RNA splicing in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2023.04.03.535409v1?rss=1 Xu, C. Zhang, Z. He, J. Bai, Y. Liu, L. Tang, J. Tang, G. Chen, X. Mo, B. 2023-04-04 doi:10.1101/2023.04.03.535409 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ Massively parallel single-cell profiling of transcriptome and multiple epigenetic proteins in cell fate regulation ]]> https://biorxiv.org/content/10.1101/2023.04.04.535478v1?rss=1 Xiong, H. Wang, Q. Li, C. C. He, A. 2023-04-06 doi:10.1101/2023.04.04.535478 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Spatial-linked alignment tool (SLAT) for aligning heterogenous slices properly ]]> https://biorxiv.org/content/10.1101/2023.04.07.535976v1?rss=1 Xia, C.-R. Cao, Z.-J. Tu, X.-M. Gao, G. 2023-04-08 doi:10.1101/2023.04.07.535976 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Bioorthogonal photocatalytic quinone methide decaging for cell-cell interaction labeling ]]> https://biorxiv.org/content/10.1101/2023.04.08.536099v1?rss=1 Zhang, Y. Liu, S. Guo, F. Qin, S. Zhou, N. Fan, X. Chen, P. 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Yu, F. Fu, H. Wang, S. Tian, C. Wang, Z. Gao, Y. Q. 2023-04-17 doi:10.1101/2023.04.14.536890 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Neurodevelopmental disorders and cancer networks share pathways; but differ in mechanisms, signaling strength, and outcome ]]> https://biorxiv.org/content/10.1101/2023.04.16.536718v1?rss=1 Yavuz, B. R. Arici, M. K. Demirel, H. C. Nussinov, R. Tsai, C.-J. Jang, H. Tuncbag, N. 2023-04-16 doi:10.1101/2023.04.16.536718 Cold Spring Harbor Laboratory Press 2023-04-16 <![CDATA[ Multidimensional responses of ecological stability to eutrophication in grasslands ]]> https://biorxiv.org/content/10.1101/2023.04.16.537045v1?rss=1 Chen, Q. Wang, S.-P. Borer, E. T. Bakker, J. D. Seabloom, E. W. Harpole, W. S. Eisenhauer, N. Lekberg, Y. Buckley, Y. M. Catford, J. A. Roscher, C. Donohue, I. Power, S. A. Daleo, P. Ebeling, A. Knops, J. M. H. Martina, J. P. Eskelinen, A. Morgan, J. W. Risch, A. C. Caldeira, M. C. Bugalho, M. N. Virtanen, R. Barrio, I. C. Niu, Y. Jentsch, A. Stevens, C. J. Alberti, J. Hautier, Y. 2023-04-17 doi:10.1101/2023.04.16.537045 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Amyloplast sedimentation repolarizes LAZYs to achieve gravity sensing in plants ]]> https://biorxiv.org/content/10.1101/2023.04.17.537121v1?rss=1 Chen, J. Yu, R. Li, N. Deng, Z. Zhang, X. Zhao, Y. Qu, C. Yuan, Y. Pan, Z. Zhou, Y. Li, K. Wang, J. Chen, Z. Wang, X. Wang, X. Dong, J. Deng, X. W. Chen, H. 2023-04-18 doi:10.1101/2023.04.17.537121 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Fine Tuning Rigid Body Docking Results Using the Dreiding Force Field: A Computational Study of 36 Known Nanobody-Protein Complexes ]]> https://biorxiv.org/content/10.1101/2023.04.18.537388v1?rss=1 Hacisuleyman, A. Erman, B. 2023-04-19 doi:10.1101/2023.04.18.537388 Cold Spring Harbor Laboratory Press 2023-04-19 <![CDATA[ GAN-MAT: Generative Adversarial Network-based Microstructural Profile Covariance Analysis Toolbox ]]> https://biorxiv.org/content/10.1101/2023.04.20.537642v1?rss=1 Park, Y. J. Lee, M. J. Yoo, S. Kim, C. Y. Namgung, J. Y. Park, Y. Park, H. Lee, E.-C. Yun, Y. D. Paquola, C. Bernhardt, B. Park, B.-y. 2023-04-24 doi:10.1101/2023.04.20.537642 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ A Logic-incorporated Gene Regulatory Network Deciphers Principles in Cell Fate Decisions ]]> https://biorxiv.org/content/10.1101/2023.04.21.537440v1?rss=1 Xue, G. Zhang, X. Li, W. Zhang, L. Zhang, Z. Zhou, X. Zhang, D. Zhang, L. Li, Z. 2023-04-21 doi:10.1101/2023.04.21.537440 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ daf-42 is an evolutionarily young gene essential for dauer development in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2023.04.24.538107v1?rss=1 Lim, D. S. Kim, J. Kim, W. Kim, N. Lee, S.-h. Lee, D. Lee, J. 2023-04-24 doi:10.1101/2023.04.24.538107 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ The potential of Senicapoc, a KCNN4 inhibitor, for the prevention and treatment of breast cancer ]]> https://biorxiv.org/content/10.1101/2023.04.25.538345v1?rss=1 Chenevix-Trench, G. Britt, K. Xiao, C. Miranda, M. Shi, W. Beesley, J. Saunus, J. Civitarese, A. Black, D. Ruppert, M. Perreira, M. Jackson, S. Teale, Z. Carter-Cusack, D. Kalinowski, L. McCart Reed, A. Handoko, H. Chen, X. Bessette, D. MacDonald, K. Lakhani, S. Al-Ejeh, F. 2023-04-28 doi:10.1101/2023.04.25.538345 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Designer DNA NanoGripper ]]> https://biorxiv.org/content/10.1101/2023.04.26.538490v1?rss=1 Zhou, L. Xiong, Y. Cooper, L. Shepherd, S. Song, T. Dwivedy, A. Rong, L. Wang, T. Cunningham, B. Wang, X. 2023-04-27 doi:10.1101/2023.04.26.538490 Cold Spring Harbor Laboratory Press 2023-04-27 <![CDATA[ The trade-off between individual metabolic specialization and versatility determines the metabolic efficiency of microbial communities ]]> https://biorxiv.org/content/10.1101/2023.04.28.538737v1?rss=1 Wang, M. Chen, X. Fang, Y. Zheng, X. Huang, T. Nie, Y. Wu, X.-L. 2023-04-28 doi:10.1101/2023.04.28.538737 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Repeated Omicron infection alleviates SARS-CoV-2 immune imprinting ]]> https://biorxiv.org/content/10.1101/2023.05.01.538516v1?rss=1 Yisimayi, A. Song, W. Wang, J. Jian, F. Yu, Y. Chen, X. Xu, Y. Yang, S. Niu, X. Xiao, T. Wang, J. An, R. Zhang, N. Wang, Y. Wang, P. Zhao, L. Sun, H. Yu, L. Gu, Q. Shao, F. Jin, R. Shen, Z. Xie, X. S. Wang, Y. Cao, Y. 2023-05-02 doi:10.1101/2023.05.01.538516 Cold Spring Harbor Laboratory Press 2023-05-02 <![CDATA[ An Excitatory Projection from the Basal Forebrain to the Ventral Tegmental Area Underlying Anorexia-like Phenotypes ]]> https://biorxiv.org/content/10.1101/2023.05.05.539422v1?rss=1 Cai, J. Xu, Y. Jiang, Z. Jiang, Y. Young, C. Li, H. Otiz-Guzman, J. Zhuo, Y. Li, Y. Xu, Y. Arenkiel, B. R. Tong, Q. 2023-05-07 doi:10.1101/2023.05.05.539422 Cold Spring Harbor Laboratory Press 2023-05-07 <![CDATA[ Neural representation strength of predicted category features biases decision behavior ]]> https://biorxiv.org/content/10.1101/2023.05.05.539587v1?rss=1 Yan, Y. Zhan, J. Garrod, O. Cui, X. Ince, R. A. A. Schyns, P. G. 2023-05-08 doi:10.1101/2023.05.05.539587 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Neural response properties predict perceived contents and locations elicited by intracranial electrical stimulation of human auditory cortex ]]> https://biorxiv.org/content/10.1101/2023.05.06.539680v1?rss=1 Wang, Q. Luo, L. Na, X. Wang, J. Yang, R. Chen, G. Ren, J. Luan, G. Fang, F. 2023-05-08 doi:10.1101/2023.05.06.539680 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ SeMOE allows for quantitative glycan perception and exhibits anti-cancer potentiality ]]> https://biorxiv.org/content/10.1101/2023.05.08.539922v1?rss=1 Tian, X. Zheng, L. Wang, C. Han, Y. Li, Y. Cui, T. Liu, J. Liu, C. Jia, G. Yang, L. Zeng, C. Ding, L. Wang, C. Cheng, B. Wang, M. Xie, R. 2023-05-09 doi:10.1101/2023.05.08.539922 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Molecular mechanisms for activation of the 26S proteasome ]]> https://biorxiv.org/content/10.1101/2023.05.09.540094v1?rss=1 Lu, Y. Goldberg, A. Colson, L. Lee, D. Zhu, Y. Wang, X. Huang, L. Chen, S. Ouyang, Q. Tkacik, E. 2023-05-10 doi:10.1101/2023.05.09.540094 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ Diazo-carboxyl click chemistry enables rapid and sensitive quantification of carboxylic acid metabolites ]]> https://biorxiv.org/content/10.1101/2023.05.11.540288v1?rss=1 Chen, Z. Quan, L. Li, C. Cheng, K. Zhao, Q. Jin, L. Wang, X. Liufu, T. Zhao, X. Li, X. Wang, X. Lyu, J. Huang, D. Li, P. Wang, Z. Chen, X.-W. Hu, X. 2023-05-13 doi:10.1101/2023.05.11.540288 Cold Spring Harbor Laboratory Press 2023-05-13 <![CDATA[ BiATNovo: A Self-Attention based Bidirectional Peptide Sequencing Method ]]> https://biorxiv.org/content/10.1101/2023.05.11.540352v1?rss=1 Wu, S. Luan, Z. Fu, Z. Wang, Q. Guo, T. 2023-05-14 doi:10.1101/2023.05.11.540352 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Getting personal: brain decoding of spontaneous thought using personal narratives ]]> https://biorxiv.org/content/10.1101/2023.05.12.540141v1?rss=1 Kim, H. Lux, B. K. Finn, E. S. Woo, C.-W. 2023-05-12 doi:10.1101/2023.05.12.540141 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ Monitoring and maturation of cardiomyocyte differentiated from human induced pluripotent stem cells using a multi-functional tissue engineering platform ]]> https://biorxiv.org/content/10.1101/2023.05.15.540892v1?rss=1 Lee, N.-e. Kim, A.-R. Shrivastava, S. Lee, H.-B. 2023-05-18 doi:10.1101/2023.05.15.540892 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Telomere-to-telomere genome of the model plant Physcomitrium patens ]]> https://biorxiv.org/content/10.1101/2023.05.19.541548v1?rss=1 Bi, G. Zhao, S. Yao, J. Wang, H. Zhao, M. Sun, Y. Hou, X. Jiao, Y. Ma, Y. Yan, J. Dai, J. 2023-05-22 doi:10.1101/2023.05.19.541548 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Cancer initiation is influenced by sex-biased tissue environment or imbalanced hormones ]]> https://biorxiv.org/content/10.1101/2023.05.20.541565v1?rss=1 Zhang, F. Deng, M. 2023-05-22 doi:10.1101/2023.05.20.541565 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Spider: a flexible and unified framework for simulating spatial transcriptomics data ]]> https://biorxiv.org/content/10.1101/2023.05.21.541605v1?rss=1 Yang, J. Qu, Y. Wei, N. Hu, C. Wu, H.-J. Zheng, X. 2023-05-22 doi:10.1101/2023.05.21.541605 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Tumor-specific neutrophils originating from meninges promote glioblastoma ]]> https://biorxiv.org/content/10.1101/2023.05.23.542010v1?rss=1 Zhao, J. Wu, D. Liu, J. Zhang, Y. Cao, P. Li, C. Wu, S. Li, M. Cui, Y. Sun, Y. Yang, E. Ji, N. Yang, J. Chen, J. 2023-05-26 doi:10.1101/2023.05.23.542010 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Projectome-defined subtypes and modular intra-hypothalamic subnetworks of peptidergic neurons ]]> https://biorxiv.org/content/10.1101/2023.05.25.542241v1?rss=1 Jiao, Z. Gao, T. Wang, X. Zhang, W. Biglari, N. Boxer, E. E. Steuernagel, L. Ding, X. Yu, Z. Li, M. Hao, M. Zhou, H. Cao, X. Li, S. Jiang, T. Qi, J. Jia, X. Feng, Z. Ren, B. Chen, Y. Shi, X. Wang, D. Wang, X. Han, L. Liang, Y. Wang, C. Li, E. Hu, Y. Tao, Z. Li, H. Xiang, Y. Xu, M. Chang, H.-C. Zhang, Y. Xu, H.-t. Yan, J. Li, A. Luo, Q. Stoop, R. Sternson, S. Bruning, J. C. Poo, M.-m. Anderson, D. J. Gong, H. Sun, Y. Xu, X.-H. 2023-05-25 doi:10.1101/2023.05.25.542241 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Histone lactylation antagonizes senescence and skeletal muscle aging via facilitating gene expression reprogramming ]]> https://biorxiv.org/content/10.1101/2023.05.26.542348v1?rss=1 Zhang, X. Meng, F. Lyu, W. He, J. Wei, R. Du, Z. Zhang, C. Guan, Y. Huang, X. Lyu, G. Tian, X.-L. Zhang, L. Tao, W. 2023-05-26 doi:10.1101/2023.05.26.542348 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ No Replication of Direct Neuronal Activity-related (DIANA) fMRI in Anesthetized Mice ]]> https://biorxiv.org/content/10.1101/2023.05.26.542419v1?rss=1 Choi, S.-H. Im, G. H. Choi, S. Yu, X. Bandettini, P. A. Menon, R. S. Kim, S.-G. 2023-05-29 doi:10.1101/2023.05.26.542419 Cold Spring Harbor Laboratory Press 2023-05-29 <![CDATA[ A new MAPK13-guided inhibitor for respiratory inflammation and mucus production ]]> https://biorxiv.org/content/10.1101/2023.05.26.542451v1?rss=1 Keeler, S. P. Wu, K. Zhang, Y. Mao, D. Li, M. Iberg, C. A. Austin, S. R. Glaser, S. A. Yantis, J. Podgorny, S. Brody, S. L. Chartock, J. R. Han, Z. Byers, D. E. Romero, A. G. Holtzman, M. J. 2023-05-27 doi:10.1101/2023.05.26.542451 Cold Spring Harbor Laboratory Press 2023-05-27 <![CDATA[ CD5L is a canonical component of circulatory IgM ]]> https://biorxiv.org/content/10.1101/2023.05.27.542462v1?rss=1 Oskam, N. den Boer, M. A. Lukassen, M. V. Ooijevaar-de Heer, P. Veth, T. S. van Mierlo, G. Lai, S.-H. Derksen, N. I. Yin, V. C. Streutker, M. Franc, V. Siborova, M. Damen, M. Kos, D. Barendregt, A. Bondt, A. van Goudoever, J. B. Haas, C. J. Aerts, P. C. Muts, R. M. Rooijakkers, S. H. Vidarsson, G. Rispens, T. Heck, A. J. 2023-05-27 doi:10.1101/2023.05.27.542462 Cold Spring Harbor Laboratory Press 2023-05-27 <![CDATA[ Ripening and synchronization of biomolecular condensates in a heterogeneous elastic medium ]]> https://biorxiv.org/content/10.1101/2023.05.27.542561v1?rss=1 Meng, L. Mao, S. Lin, J. 2023-05-28 doi:10.1101/2023.05.27.542561 Cold Spring Harbor Laboratory Press 2023-05-28 <![CDATA[ Dual-color GRAB sensors for monitoring spatiotemporal serotonin release in vivo ]]> https://biorxiv.org/content/10.1101/2023.05.27.542566v1?rss=1 Deng, F. Wan, J. Li, G. Dong, H. Xia, X. Wang, Y. Li, X. Zhuang, C. Zheng, Y. Liu, L. Yan, Y. Feng, J. Zhao, Y. Xie, H. Li, Y. 2023-05-30 doi:10.1101/2023.05.27.542566 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ IPEV: Identification of Prokaryotic and Ekaryotic Vrus-derived sequences in virome using deep learning ]]> https://biorxiv.org/content/10.1101/2023.05.28.541705v1?rss=1 Yin, H. Wu, S. Tan, J. Guo, Q. Li, M. Jiang, X. Zhu, H. 2023-05-30 doi:10.1101/2023.05.28.541705 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ Fingering instability accelerates population growth of an expanding cell collective ]]> https://biorxiv.org/content/10.1101/2023.05.28.542614v1?rss=1 Ye, Y. Lin, J. 2023-05-30 doi:10.1101/2023.05.28.542614 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ PIP2 electrostatically triggers vesicle fusion: arresting full SNARE assembly and vesicle fusion by PIP2-masking ]]> https://biorxiv.org/content/10.1101/2023.05.28.542642v1?rss=1 Moussa, H. Y. A. Shin, K. C. Ponraj, J. Park, S. H. Lee, O.-S. Mansour, S. Park, Y. 2023-05-29 doi:10.1101/2023.05.28.542642 Cold Spring Harbor Laboratory Press 2023-05-29 <![CDATA[ Closed ecosystems extract energy through self-organized nutrient cycles ]]> https://biorxiv.org/content/10.1101/2023.05.30.542875v1?rss=1 Goyal, A. Flamholz, A. I. Petroff, A. P. Murugan, A. 2023-06-01 doi:10.1101/2023.05.30.542875 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ GIMLET: A Unified Graph-Text Model for Instruction-Based Molecule Zero-Shot Learning ]]> https://biorxiv.org/content/10.1101/2023.05.30.542904v1?rss=1 Zhao, H. Liu, S. Ma, C. Xu, H. Fu, J. Deng, Z.-H. Kong, L. Liu, Q. 2023-06-01 doi:10.1101/2023.05.30.542904 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Developmental Alterations in Brain Network Asymmetry in 3- to 9-Month Infants with Congenital Sensorineural Hearing Loss ]]> https://biorxiv.org/content/10.1101/2023.05.31.543147v1?rss=1 Liu, G. Zhou, X. Hu, Z. Liu, Y. Huo, E. Bortfeld, H. Dong, Q. Liu, H. Niu, H. 2023-06-01 doi:10.1101/2023.05.31.543147 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Mendelian randomization analysis with pleiotropy-robust log-linear model for binary outcomes ]]> https://biorxiv.org/content/10.1101/2023.06.03.543587v1?rss=1 Li, M. Huang, T. Jia, J. 2023-06-06 doi:10.1101/2023.06.03.543587 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ A deep learning-based drug repurposing screening and validation for anti-SARS-CoV-2 compounds by targeting the cell entry mechanism ]]> https://biorxiv.org/content/10.1101/2023.06.03.543589v1?rss=1 Yao, Y. Zhang, Y. Li, Z. Chen, Z. Wang, X. Li, Z. Yu, L. Cheng, X. Li, W. Jiang, W.-J. Wu, H.-J. Feng, Z. Sun, J. Fei, T. 2023-06-05 doi:10.1101/2023.06.03.543589 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ A mutation-mediated host shift drives Avian paramyxovirus type 1 evolution ]]> https://biorxiv.org/content/10.1101/2023.06.05.543675v1?rss=1 Chang, H. Feng, S. Tang, X. Wang, Z. Su, W. Han, S. Li, G. Hu, B. Jing, S. Wang, B. Xiang, C. Xing, Y. Wang, Y. Lu, J. He, h. 2023-06-05 doi:10.1101/2023.06.05.543675 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Warming and altered precipitation independently and interactively suppress alpine soil microbial growth in a decadal-long experiment ]]> https://biorxiv.org/content/10.1101/2023.06.08.544195v1?rss=1 Ruan, Y. Ling, N. Jiang, S. Jing, X. He, J.-S. Shen, Q. Nan, Z. 2023-06-08 doi:10.1101/2023.06.08.544195 Cold Spring Harbor Laboratory Press 2023-06-08 <![CDATA[ Multi-scale models reveal hypertrophic cardiomyopathy MYH7 G256E mutation drives hypercontractility and elevated mitochondrial respiration ]]> https://biorxiv.org/content/10.1101/2023.06.08.544276v1?rss=1 Lee, S. Vander Roest, A. S. Blair, C. Kao, K. Bremner, S. B. Childers, M. C. Pathak, D. Heinrich, P. Lee, D. Chirikian, O. Mohran, S. Roberts, B. Smith, J. E. Jahng, J. W. S. Paik, D. T. Wu, J. C. Gunawardane, R. N. Spudich, J. A. Ruppel, K. M. Mack, D. Pruitt, B. L. Regnier, M. Wu, S. M. Bernstein, D. 2023-06-09 doi:10.1101/2023.06.08.544276 Cold Spring Harbor Laboratory Press 2023-06-09 <![CDATA[ On the Mathematics of RNA Velocity II: Algorithmic Aspects ]]> https://biorxiv.org/content/10.1101/2023.06.09.544270v1?rss=1 Li, T. Wang, Y. Guoguo, Y. Zhou, P. 2023-06-11 doi:10.1101/2023.06.09.544270 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ Profiling The Compendium Of Changes In Saccharomyces cerevisiae Due To Mutations That Alter Availability Of The Main Methyl Donor S-Adenosylmethionine ]]> https://biorxiv.org/content/10.1101/2023.06.09.544294v1?rss=1 Remines, M. Schnoover, M. Zoey, K. Kailee, K. Hoffert, K. M. Coric, A. Mead, J. Ampfer, J. Seye, S. Strome, E. 2023-06-10 doi:10.1101/2023.06.09.544294 Cold Spring Harbor Laboratory Press 2023-06-10 <![CDATA[ Genome duplications, genomic conflict, and rapid phenotypic evolution characterize the Cretaceous radiation of Fagales ]]> https://biorxiv.org/content/10.1101/2023.06.11.544004v1?rss=1 Yang, Y.-Y. Stull, G. W. Qu, X. Zhao, L. Hu, Y. Wang, Z. Ma, H. Li, D. Smith, S. A. Yi, T. 2023-06-12 doi:10.1101/2023.06.11.544004 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ Defining the single base importance of human mRNAs and lncRNAs ]]> https://biorxiv.org/content/10.1101/2023.06.12.544536v1?rss=1 Fan, R. Ji, X. Li, J. Cui, Q. Cui, C. 2023-06-15 doi:10.1101/2023.06.12.544536 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ Unraveling the dynamic transcriptomic changes during the dimorphic transition of Talaromyces marneffei through time-course analysis ]]> https://biorxiv.org/content/10.1101/2023.06.12.544618v1?rss=1 Du, M. Tao, C. Hu, X. Zhang, Y. Kan, J. Wang, J. Yang, E. 2023-06-15 doi:10.1101/2023.06.12.544618 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ Microglial P2Y6 calcium signaling promotes phagocytosis and shapes neuroimmune responses in epileptogenesis ]]> https://biorxiv.org/content/10.1101/2023.06.12.544691v1?rss=1 Umpierre, A. D. Li, B. Ayasoufi, K. Zhao, S. Xie, M. Thyen, G. Hur, B. Zheng, J. Liang, Y. Wu, Z. D. Yu, X. Sung, J. Johnson, A. J. Li, Y. Wu, L.-J. 2023-06-13 doi:10.1101/2023.06.12.544691 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ NOP16 is a histone mimetic that regulates Histone H3K27 methylation and gene repression ]]> https://biorxiv.org/content/10.1101/2023.06.13.544862v1?rss=1 Takashima, K. Lee, D.-J. Trovero, M. F. Rothi, M. H. Mistry, M. Zhang, Y. Li, Z. Davis, C. P. Li, Z. Natale, J. Schmid, E. Al Haddad, J. Hoffmann, G. B. Dietmann, S. Sui, S. H. Oshiumi, H. Lieberman, J. Greer, E. L. 2023-06-13 doi:10.1101/2023.06.13.544862 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ Exploring phytoconstituents of Juglans regia to treat cervical cancer using integrative Bioinformatics ]]> https://biorxiv.org/content/10.1101/2023.06.15.545164v1?rss=1 Dua, R. Ahmad, I. Bhardwaj, T. Somvanshi, P. 2023-06-15 doi:10.1101/2023.06.15.545164 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ Overlooked Candida glabrata petites are echinocandin tolerant, induce host inflammatory responses, and display poor in vivo fitness ]]> https://biorxiv.org/content/10.1101/2023.06.15.545195v1?rss=1 Amir Arastehfar, A. Daneshnia, F. Hovhannisyan, H. Fuentes, D. Cabrera, N. Quinteros, C. Ilkit, M. Ünal, N. Hilmioglu-Polat, S. Jabeen, K. Zaka, S. Desai, J. V. Lass-Flörl, C. Shor, E. Gabaldon, T. Perlin, D. S. 2023-06-18 doi:10.1101/2023.06.15.545195 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ KaScape: A sequencing-based method for global characterization of protein-DNA binding affinity ]]> https://biorxiv.org/content/10.1101/2023.06.19.545523v1?rss=1 Chen, H. Xu, Y. Jin, J. Su, X. 2023-06-19 doi:10.1101/2023.06.19.545523 Cold Spring Harbor Laboratory Press 2023-06-19 <![CDATA[ Biochemical and chemical biological approaches to mammalian sleep: roles of calcineurin in site-specific dephosphorylation and sleep regulation ]]> https://biorxiv.org/content/10.1101/2023.06.19.545643v1?rss=1 Yu, J. Wang, T. V. Gao, R. Li, C. Liu, H. Yang, L. Liu, Y. Cui, Y. Chen, P. R. Rao, Y. 2023-06-22 doi:10.1101/2023.06.19.545643 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Spatiotemporal Control of Genomics and Epigenomics by Ultrasound ]]> https://biorxiv.org/content/10.1101/2023.06.21.544125v1?rss=1 Wu, Y. Huang, Z. Liu, Y. Yoon, C.-W. Sun, K. Situ, Y. Ho, P. Yuan, Z. Zhu, L. Eyquem, J. Zhao, Y. Liu, T. Kwong, G. A. Chien, S. Wang, Y. 2023-06-23 doi:10.1101/2023.06.21.544125 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Storm: Incorporating transient dynamics to infer the RNA velocity with metabolic labeling information ]]> https://biorxiv.org/content/10.1101/2023.06.21.545990v1?rss=1 Peng, Q. Qiu, X. Li, T. 2023-06-23 doi:10.1101/2023.06.21.545990 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Molecular pathway of mitochondrial preprotein import through the TOM-TIM23 ]]> https://biorxiv.org/content/10.1101/2023.06.21.546012v1?rss=1 Zhou, X. Yang, Y. Wang, G. Wang, S. Sun, D. Ou, X. Lian, Y. Li, L. 2023-06-22 doi:10.1101/2023.06.21.546012 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Monitoring norepinephrine release in vivo using next-generation GRABNE sensors ]]> https://biorxiv.org/content/10.1101/2023.06.22.546075v1?rss=1 Feng, J. Dong, H. Lischinsky, J. E. Zhou, J. Deng, F. Zhuang, C. Miao, X. Wang, H. Xie, H. Cui, G. Lin, D. Li, Y. 2023-06-25 doi:10.1101/2023.06.22.546075 Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ An adversarial collaboration to critically evaluate theories of consciousness ]]> https://biorxiv.org/content/10.1101/2023.06.23.546249v1?rss=1 Cogitate Consortium, Ferrante, O. Gorska-Klimowska, U. Henin, S. Hirschhorn, R. Khalaf, A. Lepauvre, A. Liu, L. Richter, D. Vidal, Y. Bonacchi, N. Brown, T. Sripad, P. Armendariz, M. Bendtz, K. Ghafari, T. Hetenyi, D. Jeschke, J. Kozma, C. Mazumder, D. R. Montenegro, S. Seedat, A. Sharafeldin, A. Yang, S. Baillet, S. Chalmers, D. J. Cichy, R. M. Fallon, F. Panagiotaropoulos, T. I. Blumenfeld, H. Devore, S. Jensen, O. Kreiman, G. de Lange, F. P. Luo, H. Boly, M. Dehaene, S. Koch, C. Tononi, G. Pitts, M. Mudrik, L. Melloni, L. 2023-06-26 doi:10.1101/2023.06.23.546249 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Genome-wide analysis of promoter contacts identifies novel regulators of late-stage adipogenesis ]]> https://biorxiv.org/content/10.1101/2023.06.27.546683v1?rss=1 Sandovici, I. Mifsud, B. Emery, A. Gulati, P. Kentistou, K. A. Banu, A. Hardwick, B. S. Campbell, N. Crooks, A. T. Fernandez-Twinn, D. S. Mennitti, L. V. Srour, L. Awad, S. Chiarugi, D. Hamilton, R. H. Wingett, S. W. Fraser, P. Ong, K. K. Shoenfelder, S. Mohammad, F. O'Rahilly, S. Perry, J. R. B. Venkitaraman, A. R. E. Ozanne, S. Constancia, M. 2023-06-30 doi:10.1101/2023.06.27.546683 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Unravelling Biosynthesis and Biodegradation Potentials of Microbial Dark Matters in Hypersaline Lakes ]]> https://biorxiv.org/content/10.1101/2023.06.28.546814v1?rss=1 Qiu, Z. Zhu, Y. Zhang, Q. Qiao, X. Mu, R. Xu, Z. Yan, Y. Wang, F. Zhang, T. Yu, K. 2023-06-28 doi:10.1101/2023.06.28.546814 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ Base-resolution mapping reveals distinct m1A methylome in nuclear- and mitochondrial-encoded transcripts ]]> https://biorxiv.org/content/10.1101/202747v1?rss=1 Li, X. Xiong, X. Zhang, M. Wang, K. Chen, Y. Zhou, J. Mao, Y. Lv, J. Yi, D. Chen, X.-W. Wang, C. Qian, S.-B. Yi, C. 2017-10-13 doi:10.1101/202747 Cold Spring Harbor Laboratory Press 2017-10-13 <![CDATA[ TraRECo: A Greedy Approach based de novo Transcriptome Assembler with Read Error Correction using Consensus Matrix ]]> https://biorxiv.org/content/10.1101/216077v1?rss=1 Yoon, S. Kim, D. Kang, K. Park, W. J. 2017-11-08 doi:10.1101/216077 Cold Spring Harbor Laboratory Press 2017-11-08 <![CDATA[ MapZ forms a stable ring structure that acts as a track for FtsZ treadmilling in Streptococcus mutans ]]> https://biorxiv.org/content/10.1101/218677v1?rss=1 Li, Y. Shao, S. Xu, X. Su, X. Sun, Y. Wei, S. 2017-11-13 doi:10.1101/218677 Cold Spring Harbor Laboratory Press 2017-11-13 <![CDATA[ Androgen receptor binding sites are highly mutated in prostate cancer ]]> https://biorxiv.org/content/10.1101/225433v1?rss=1 MOROVA, T. GÖNEN, M. GÜRSOY, A. KESKIN, O. LACK, N. A. 2017-11-27 doi:10.1101/225433 Cold Spring Harbor Laboratory Press 2017-11-27 <![CDATA[ Assessing the Gene Regulatory Landscape in 1,188 Human Tumors ]]> https://biorxiv.org/content/10.1101/225441v1?rss=1 Calabrese, C. Lehmann, K.-V. Urban, L. Liu, F. Erkek, S. Fonseca, N. Kahles, A. Kilpinen-Barrett, L. H. Markowski, J. PCAWG-3, Waszak, S. Korbel, J. Zhang, Z. Brazma, A. Raetsch, G. Schwarz, R. Stegle, O. 2017-11-29 doi:10.1101/225441 Cold Spring Harbor Laboratory Press 2017-11-29 <![CDATA[ Dynamic protein aggregation regulates bacterial dormancy depth critical for antibiotic tolerance ]]> https://biorxiv.org/content/10.1101/233890v1?rss=1 Pu, Y. Li, Y. Ma, Q. Tian, T. Zhao, Z. McVey, A. Bai, F. 2017-12-13 doi:10.1101/233890 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ Real-value and confidence prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning ]]> https://biorxiv.org/content/10.1101/236851v1?rss=1 Gao, Y. Wang, S. Deng, M. Xu, J. 2017-12-20 doi:10.1101/236851 Cold Spring Harbor Laboratory Press 2017-12-20 <![CDATA[ Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes ]]> https://biorxiv.org/content/10.1101/237313v1?rss=1 2,500 whole cancer genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We developed a statistically rigorous strategy for combining significance levels from multiple driver discovery methods and demonstrate that the integrated results overcome limitations of individual methods. We combined this strategy with careful filtering and applied it to protein-coding genes, promoters, untranslated regions (UTRs), distal enhancers and non-coding RNAs. These analyses redefine the landscape of non-coding driver mutations in cancer genomes, confirming a few previously reported elements and raising doubts about others, while identifying novel candidate elements across 27 cancer types. Novel recurrent events were found in the promoters or 5UTRs of TP53, RFTN1, RNF34, and MTG2, in the 3UTRs of NFKBIZ and TOB1, and in the non-coding RNA RMRP. We provide evidence that the previously reported non-coding RNAs NEAT1 and MALAT1 may be subject to a localized mutational process. Perhaps the most striking finding is the relative paucity of point mutations driving cancer in non-coding genes and regulatory elements. Though we have limited power to discover infrequent non-coding drivers in individual cohorts, combined analysis of promoters of known cancer genes show little excess of mutations beyond TERT. ]]> Rheinbay, E. Nielsen, M. M. Abascal, F. Tiao, G. Hornshoj, H. Hess, J. M. Pedersen, R. I. I. Feuerbach, L. Sabarinathan, R. Madsen, H. T. KIM, J. Mularoni, L. Shuai, S. Lanzos Camaioni, A. A. Herrmann, C. Maruvka, Y. E. Shen, C. Amin, S. B. Bertl, J. Dhingra, P. Diamanti, K. Gonzalez-Perez, A. Guo, Q. Haradhvala, N. J. Isaev, K. Juul, M. Komorowski, J. kumar, s. Lee, D. Lochovsky, L. Liu, E. M. M. Pich, O. tamborero, d. Umer, H. M. Uusküla-Reimand, L. Wadelius, C. Wadi, L. Zhang, J. Boroevich, K. A. Carlevaro-Fita, J. Chakravarty, D. Chan, C. W. 2017-12-23 doi:10.1101/237313 Cold Spring Harbor Laboratory Press 2017-12-23 <![CDATA[ Spatial gradient in activity within the insula reflects dissociable neural mechanisms underlying context-dependent advantageous and disadvantageous inequity aversion ]]> https://biorxiv.org/content/10.1101/243428v1?rss=1 Gao, X. Yu, H. Saez, I. Blue, P. R. Zhu, L. Hsu, M. Zhou, X. 2018-01-05 doi:10.1101/243428 Cold Spring Harbor Laboratory Press 2018-01-05 <![CDATA[ Large-scale two-photon imaging revealed super-sparse population codes in V1 superficial layer of awake monkeys ]]> https://biorxiv.org/content/10.1101/252940v1?rss=1 Tang, S. Zhang, Y. Li, Z. Li, M. Liu, F. Jiang, H. Lee, T. S. 2018-01-25 doi:10.1101/252940 Cold Spring Harbor Laboratory Press 2018-01-25 <![CDATA[ From 1D sequence to 3D chromatin dynamics and cellular functions: a phase separation perspective ]]> https://biorxiv.org/content/10.1101/255174v1?rss=1 Liu, S. Zhang, L. Quan, H. Tian, H. Meng, L. Yang, L. Feng, H. Gao, Y. Q. 2018-01-28 doi:10.1101/255174 Cold Spring Harbor Laboratory Press 2018-01-28 <![CDATA[ Inhibition of Hsp70 suppresses neuronal hyperexcitability and attenuates seizures by enhancing A-type potassium currents ]]> https://biorxiv.org/content/10.1101/256602v1?rss=1 Hu, F. Zhou, J. Lu, Y. Guan, L. Wei, N. Huang, Z. Tang, Y. Wang, K. 2018-01-30 doi:10.1101/256602 Cold Spring Harbor Laboratory Press 2018-01-30 <![CDATA[ Quantifying Waddington’s epigenetic landscape: a comparison of single-cell potency measures ]]> https://biorxiv.org/content/10.1101/257220v1?rss=1 Shi, J. Teschendorff, A. Chen, W. Chen, L. Li, T. 2018-01-30 doi:10.1101/257220 Cold Spring Harbor Laboratory Press 2018-01-30 <![CDATA[ Xist Intron 1 Repression by TALE Transcriptional Factor Improves Somatic Cell Reprogamming in Mice ]]> https://biorxiv.org/content/10.1101/259234v1?rss=1 Zhang, J. Gao, X. Yang, J. Fan, X. Wang, W. Liang, Y. Fan, L. Han, H. Xu, X. Tang, F. Bao, S. Liu, P. Li, X. 2018-02-02 doi:10.1101/259234 Cold Spring Harbor Laboratory Press 2018-02-02 <![CDATA[ The critical role of ASD-related gene CNTNAP3 in regulating synaptic development and social behavior in mice ]]> https://biorxiv.org/content/10.1101/260083v1?rss=1 Tong, D. Chen, R. Lu, Y. Li, W. Zhang, Y. Lin, J. He, L. Dang, T. Shan, S. Xu, X. Zhang, Y. Zhang, C. Du, Y. Zhou, W.-H. Wang, X. Qiu, Z. 2018-02-05 doi:10.1101/260083 Cold Spring Harbor Laboratory Press 2018-02-05 <![CDATA[ Structure of the 30S ribosomal decoding complex at ambient temperature ]]> https://biorxiv.org/content/10.1101/262972v1?rss=1 Dao, E. H. Poitevin, F. Sierra, R. G. Gati, C. Rao, Y. Ciftci, H. I. Aksit, F. McGurk, A. Obrinski, T. Mgbam, P. Hayes, B. de Lichtenberg, C. Pardo-Avila, F. Corsepius, N. Zhang, L. Seaberg, M. Hunter, M. S. Liang, M. Koglin, J. E. Wakatsuki, S. Demirci, H. 2018-02-10 doi:10.1101/262972 Cold Spring Harbor Laboratory Press 2018-02-10 <![CDATA[ Mechanistic model of temperature influence on flowering through whole-plant accumulation of FT ]]> https://biorxiv.org/content/10.1101/267104v1?rss=1 Kinmonth-Schultz, H. A. MacEwen, M. J. Seaton, D. D. Millar, A. J. Imaizumi, T. Kim, S.-H. 2018-02-18 doi:10.1101/267104 Cold Spring Harbor Laboratory Press 2018-02-18 <![CDATA[ Long-term all-optical interrogation of cortical neurons in awake-behaving non-human primates ]]> https://biorxiv.org/content/10.1101/274308v1?rss=1 Ju, N. Jiang, R. Macknik, S. L. Martinez-Conde, S. Tang, S. 2018-03-01 doi:10.1101/274308 Cold Spring Harbor Laboratory Press 2018-03-01 <![CDATA[ Trends in female lifespan in South Korea, 1987-2016 ]]> https://biorxiv.org/content/10.1101/278291v1?rss=1 Weon, B. M. 2018-03-07 doi:10.1101/278291 Cold Spring Harbor Laboratory Press 2018-03-07 <![CDATA[ Acidic microenvironment shaped by lactate accumulation promotes pluripotency through multiple mechanisms ]]> https://biorxiv.org/content/10.1101/282475v1?rss=1 Guo, W.-T. Wang, S.-H. Zhang, X.-S. Shi, M. Hao, J. Wang, X.-W. Gu, K.-L. Duan, F.-F. Yan, Y. Yang, X. Zhang, C. Liao, L.-Q. Wang, Y. 2018-03-15 doi:10.1101/282475 Cold Spring Harbor Laboratory Press 2018-03-15 <![CDATA[ Structure of the receptor-activated human TRPC6 ion channel ]]> https://biorxiv.org/content/10.1101/282814v1?rss=1 Tang, Q. Guo, W. Zheng, L. Wu, J.-X. Liu, M. Zhou, X. Zhang, X. Chen, L. 2018-03-15 doi:10.1101/282814 Cold Spring Harbor Laboratory Press 2018-03-15 <![CDATA[ Ligand binding and conformational changes of SUR1 subunit in pancreatic ATP-sensitive potassium channels ]]> https://biorxiv.org/content/10.1101/283440v1?rss=1 Wu, J.-X. Ding, D. Wang, M. Kang, Y. Zeng, X. Chen, L. 2018-03-16 doi:10.1101/283440 Cold Spring Harbor Laboratory Press 2018-03-16 <![CDATA[ Immuno-genomic PanCancer Landscape Reveals Diverse Immune Escape Mechanisms and Immuno-Editing Histories ]]> https://biorxiv.org/content/10.1101/285338v1?rss=1 Mizuno, S. Yamaguchi, R. Hasegawa, T. Hayashi, S. Fujita, M. Zhang, F. Koh, Y. Lee, S.-Y. Yoon, S.-S. Shimizu, E. Komura, M. Fujimoto, A. Nagai, M. Kato, M. Liang, H. Miyano, S. Zhang, Z. Nakagawa, H. Imoto, S. 2018-03-20 doi:10.1101/285338 Cold Spring Harbor Laboratory Press 2018-03-20 <![CDATA[ THE MITOCHONDRIAL DNA CONTROL REGION MIGHT HAVE USEFUL DIAGNOSTIC AND PROGNOSTIC BIOMARKERS FOR THYROID TUMORS ]]> https://biorxiv.org/content/10.1101/291435v1?rss=1 Bircan, R. Iliksu Gozu, H. Ulu, E. Sarikaya, S. Ege Gul, A. Yasar Sirin, D. Ozcelik, S. Aral, C. 2018-03-29 doi:10.1101/291435 Cold Spring Harbor Laboratory Press 2018-03-29 <![CDATA[ Glucocorticoid receptor gene polymorhisms and breast cancer: significant association in cancerous tissue samples from Turkish patients ]]> https://biorxiv.org/content/10.1101/292631v1?rss=1 Akyildiz, G. Akkiprik, M. Ozer, A. Kaya, H. Gulluoglu, B. M. Aral, C. 2018-03-31 doi:10.1101/292631 Cold Spring Harbor Laboratory Press 2018-03-31 <![CDATA[ Co-expression of MDM2 and CDK4 in transformed human mesenchymal stem cells induces dedifferentiated liposarcoma potency ]]> https://biorxiv.org/content/10.1101/293068v1?rss=1 Kim, Y. J. Sung, M. Yu, D. B. Kim, M. Song, J.-Y. Song, K. Jung, K. Choi, Y. 2018-04-01 doi:10.1101/293068 Cold Spring Harbor Laboratory Press 2018-04-01 <![CDATA[ Convolutional neural network models of V1 responses to complex patterns ]]> https://biorxiv.org/content/10.1101/296301v1?rss=1 Zhang, Y. Lee, T. S. Li, M. Liu, F. Tang, S. 2018-04-06 doi:10.1101/296301 Cold Spring Harbor Laboratory Press 2018-04-06 <![CDATA[ Connectivity Patterns in Cognitive Control Networks Predict Naturalistic Multitasking Ability ]]> https://biorxiv.org/content/10.1101/296475v1?rss=1 Wen, T. Liu, D.-C. Hsieh, S. 2018-04-06 doi:10.1101/296475 Cold Spring Harbor Laboratory Press 2018-04-06 <![CDATA[ Molecular mechanisms controlling the multistage post-translational processing of endogenous Nrf1α/TCF11 proteins to yield distinct proteoforms within the coupled positive and negative feedback circuits ]]> https://biorxiv.org/content/10.1101/300327v1?rss=1 Xiang, Y. Wang, M. Hu, S. Qiu, L. Yang, F. Zhang, Z. Yu, S. Pi, J. Zhang, Y. 2018-04-12 doi:10.1101/300327 Cold Spring Harbor Laboratory Press 2018-04-12 <![CDATA[ Mono-homologous linear DNA recombination by the non-homologous end-joining pathway as a novel and simple gene inactivation method: a proof of concept study in Dietzia sp. DQ12-45-1b ]]> https://biorxiv.org/content/10.1101/300723v1?rss=1 Lu, S. Nie, Y. Wang, M. Xu, H. Ma, D. Liang, J.-L. Wu, X.-L. 2018-04-13 doi:10.1101/300723 Cold Spring Harbor Laboratory Press 2018-04-13 <![CDATA[ Cross-sectional white matter microstructure differences in aging and mindfulness ]]> https://biorxiv.org/content/10.1101/301739v1?rss=1 Boekel, W. Hsieh, S. 2018-04-16 doi:10.1101/301739 Cold Spring Harbor Laboratory Press 2018-04-16 <![CDATA[ NDUFAB1 Protects Heart by Coordinating Mitochondrial Respiratory Complex and Supercomplex Assembly ]]> https://biorxiv.org/content/10.1101/302281v1?rss=1 Hou, T. Zhang, R. Jian, C. Ding, W. Wang, Y. Ma, Q. Hu, X. Cheng, H. Wang, X. 2018-04-16 doi:10.1101/302281 Cold Spring Harbor Laboratory Press 2018-04-16 <![CDATA[ In vivo Chemical Reprogramming of Astrocytes into Functional Neurons ]]> https://biorxiv.org/content/10.1101/305185v1?rss=1 Ma, Y. Xie, H. Du, X. Wang, L. Jin, X. Sun, S. Han, Y. Han, Y. Xu, J. Huang, Z. Chai, Z. Deng, H. 2018-04-20 doi:10.1101/305185 Cold Spring Harbor Laboratory Press 2018-04-20 <![CDATA[ Distinctive types of postzygotic single-nucleotide mosaicisms in healthy individuals revealed by genome-wide profiling of multiple organs ]]> https://biorxiv.org/content/10.1101/309005v1?rss=1 T mutations with elevated mutation rate at CpG sites. We observed differences in replication timing between these two types of pSNMs, with embryonic and clonal expansion pSNMs enriched in early- and late-replicating regions, respectively. An increased number of embryonic pSNMs were located in open chromatin states and topologically associating domains that transcribed embryonically. Our findings provide new insights into the origin and spatial distribution of postzygotic mosaicism during normal human development.nnAuthor SummaryGenomic mosaicism led by postzygotic mutation is the major cause of cancers and many non-cancer developmental disorders. Theoretically, postzygotic mutations should be accumulated during the developmental process of healthy individuals, but the genome-wide characterization of postzygotic mosaicisms across many organ types of the same individual remained limited. In this study, we identified and validated two types of postzygotic mosaicism from the whole-genomes of 27 organs obtained from five healthy donors. We further found that the postzygotic mosaicisms arising during early embryogenesis and later clonal expansion events show distinct genomic patterns in mutation spectrum, replication timing, and chromatin status. ]]> Huang, Y. Yang, X. Wang, S. Zheng, X. Wu, Q. Ye, Y. Wei, L. 2018-04-26 doi:10.1101/309005 Cold Spring Harbor Laboratory Press 2018-04-26 <![CDATA[ Oscillatory cortical forces promote three dimensional cell intercalations that shape the mandibular arch ]]> https://biorxiv.org/content/10.1101/309120v1?rss=1 Tao, H. Zhu, M. Lau, K. Whitley, O. Samani, M. Xiao, X. Chen, X. X. Hahn, N. A. Liu, W. Valencia, M. Wu, M. Wang, X. Fenelon, K. D. Pasiliao, C. C. Hu, D. Wu, J. Spring, S. Ferguson, J. Karuana, E. P. Henkelman, R. M. Dunn, A. Huang, H. Ho, H.-Y. H. Atit, R. Goyal, S. Sun, Y. Hopyan, S. 2018-04-26 doi:10.1101/309120 Cold Spring Harbor Laboratory Press 2018-04-26 <![CDATA[ Comparative analysis of droplet-based ultra-high-throughput single-cell RNA-seq systems ]]> https://biorxiv.org/content/10.1101/313130v1?rss=1 Zhang, X. Li, T. Liu, F. Chen, Y. Li, Z. Huang, Y. Wang, J. 2018-05-02 doi:10.1101/313130 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Histone deacetylase HDA19 affects cortical cell fate by interacting with SCARECROW in the Arabidopsis root ]]> https://biorxiv.org/content/10.1101/313791v1?rss=1 Chen, W. Drapek, C. Li, D. Xu, Z. Benfey, P. Bai, S. 2018-05-03 doi:10.1101/313791 Cold Spring Harbor Laboratory Press 2018-05-03 <![CDATA[ Response to \"No evidence of functional co-adaptation between clustered microRNAs\" ]]> https://biorxiv.org/content/10.1101/313817v1?rss=1 Wang, Y. Zhang, H. Lu, J. 2018-05-03 doi:10.1101/313817 Cold Spring Harbor Laboratory Press 2018-05-03 <![CDATA[ Structure for Energy Cycle: A unique status of Second Law of Thermodynamics for living systems ]]> https://biorxiv.org/content/10.1101/314567v1?rss=1 Bai, S.-N. Ge, H. Qian, H. 2018-05-07 doi:10.1101/314567 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ Quality Control and Integration of Genotypes from Two Calling Pipelines for Whole Genome Sequence Data in the Alzheimer’s Disease Sequencing Project ]]> https://biorxiv.org/content/10.1101/318857v1?rss=1 Naj, A. C. Lin, H. Vardarajan, B. N. White, S. Lancour, D. Ma, Y. Schmidt, M. Sun, F. Butkiewicz, M. Bush, W. S. Kunkle, B. W. Malamon, J. Amin, N. Choi, S. H. Hamilton-Nelson, K. L. van der Lee, S. J. Gupta, N. Koboldt, D. C. Saad, M. Wang, B. Nato, A. Q. Sohi, H. K. Kuzma, A. Alzheimer's Disease Sequencing Project (ADSP), Wang, L.-S. Cupples, L. A. van Duijn, C. Seshadri, S. Schellenberg, G. D. Boerwinkle, E. Bis, J. C. Dupuis, J. Salerno, W. J. Wijsman, E. M. Martin, E. DeStefano, A. L. 2018-05-11 doi:10.1101/318857 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Post-reactivation new learning impairs and updates human episodic memory through dissociable processes ]]> https://biorxiv.org/content/10.1101/320101v1?rss=1 Zhu, Z. Wang, Y. Jia, J. Huang, L. Rao, Y. Wu, Y. 2018-05-11 doi:10.1101/320101 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Ancestral resurrection reveals mechanisms of kinase regulatory evolution ]]> https://biorxiv.org/content/10.1101/331637v1?rss=1 Sang, D. Pinglay, S. Vatansever, S. Lou, H. J. Turk, B. E. Gumus, Z. H. Holt, L. J. 2018-05-25 doi:10.1101/331637 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Identifying individual risk rare variants using protein structure-guided local tests (POINT) ]]> https://biorxiv.org/content/10.1101/333245v1?rss=1 Marceau West, R. Lu, W. Rotroff, D. M. Kuenemann, M. Chang, S.-M. Wagner, M. J. Buse, J. B. Motsinger-Reif, A. Fourches, D. Tzeng, J.-Y. 2018-05-29 doi:10.1101/333245 Cold Spring Harbor Laboratory Press 2018-05-29 <![CDATA[ Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing ]]> https://biorxiv.org/content/10.1101/333617v1?rss=1 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy number states, a considerable fraction of the events involves multiple chromosomes as well as additional structural alterations. In addition to non-homologous end-joining, we detect signatures of replicative processes and templated insertions. Chromothripsis contributes to oncogene amplification as well as to inactivation of genes such as mismatch-repair related genes. These findings show that chromothripsis is a major process driving genome evolution in human cancer. ]]> Cortes-Ciriano, I. Lee, J.-K. Xi, R. Jain, D. Jung, Y. L. Yang, L. Gordenin, D. Klimczak, L. J. Zhang, C.-Z. Pellman, D. S. Park, P. J. PCAWG Structural Variation Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network, 2018-05-30 doi:10.1101/333617 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ Does a history of sexual and physical childhood abuse contribute to HIV infection risk in adulthood? A study among post-natal women in Harare, Zimbabwe ]]> https://biorxiv.org/content/10.1101/333872v1?rss=1 Shamu, S. Shamu, P. Zarowsky, C. Temmerman, M. Shefer, T. Abrahams, N. 2018-05-29 doi:10.1101/333872 Cold Spring Harbor Laboratory Press 2018-05-29 <![CDATA[ Pellino 1 Communicates Intercellular Signaling in Chronic Skin Inflammatory Microenvironment ]]> https://biorxiv.org/content/10.1101/334433v1?rss=1 Lee, C.-W. Kim, S. Bae, S. Park, J. Ha, G.-H. Hwang, K. Kim, H.-S. Ji, J.-H. Go, H. 2018-05-30 doi:10.1101/334433 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ The cargo receptor SURF4 promotes the efficient cellular secretion of PCSK9 ]]> https://biorxiv.org/content/10.1101/336016v1?rss=1 Emmer, B. T. Hesketh, G. G. Kotnik, E. Tang, V. T. Lascuna, P. J. Xiang, J. Gingras, A.-C. Chen, X.-W. Ginsburg, D. 2018-05-31 doi:10.1101/336016 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ Associations between Afrotropical bats, parasites, and microbial symbionts ]]> https://biorxiv.org/content/10.1101/340109v1?rss=1 Lutz, H. L. Jackson, E. W. Webala, P. W. Babyesiza, W. S. Kerbis Peterhans, J. C. Demos, T. C. Patterson, B. D. Gilbert, J. A. 2018-06-07 doi:10.1101/340109 Cold Spring Harbor Laboratory Press 2018-06-07 <![CDATA[ SSCC: a computational framework for rapid and accurate clustering of large-scale single cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/344242v1?rss=1 Ren, X. Zheng, L. Zhang, Z. 2018-06-11 doi:10.1101/344242 Cold Spring Harbor Laboratory Press 2018-06-11 <![CDATA[ A Mechanism for Synaptic Copy between Neural Circuits ]]> https://biorxiv.org/content/10.1101/351114v1?rss=1 Shao, Y. Wang, B. Sornborger, A. Tao, L. 2018-06-20 doi:10.1101/351114 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ A computational protocol to characterize elusive Candidate Phyla Radiation bacteria in oral environments using metagenomic data ]]> https://biorxiv.org/content/10.1101/358812v1?rss=1 Meng, P. Lu, C. Lou, X. Zhang, Q. Jia, P. Yan, Z. Lin, J. Chen, F. 2018-06-29 doi:10.1101/358812 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ What you see depends on what you hear: temporal averaging and crossmodal integration ]]> https://biorxiv.org/content/10.1101/362665v1?rss=1 Chen, L. Zhou, X. Müller, H. J. Shi, Z. 2018-07-04 doi:10.1101/362665 Cold Spring Harbor Laboratory Press 2018-07-04 <![CDATA[ Accurate Prediction of Antibody Resistance in Clinical HIV-1 Isolates ]]> https://biorxiv.org/content/10.1101/364828v1?rss=1 Rawi, R. Mall, R. Shen, C.-H. Doria-Rose, N. A. Farney, S. K. Shiakolas, A. Zhou, J. Chun, T.-W. Lynch, R. M. Mascola, J. R. Kwong, P. D. Chuang, G.-Y. 2018-07-08 doi:10.1101/364828 Cold Spring Harbor Laboratory Press 2018-07-08 <![CDATA[ Saccharomyces cerevisiae adapted to grow in the presence of low-dose rapamycin exhibit altered amino acid metabolism ]]> https://biorxiv.org/content/10.1101/368266v1?rss=1 Dikicioglu, D. Dereli Eke, E. Eraslan, S. Oliver, S. G. Kirdar, B. 2018-07-13 doi:10.1101/368266 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ Toward deciphering developmental patterning with deep neural network ]]> https://biorxiv.org/content/10.1101/374439v1?rss=1 Shen, J. Liu, F. Tang, C. 2018-07-22 doi:10.1101/374439 Cold Spring Harbor Laboratory Press 2018-07-22 <![CDATA[ Fast-backward replay of sequentially memorized items in humans ]]> https://biorxiv.org/content/10.1101/376202v1?rss=1 Huang, Q. Jia, J. Han, Q. Luo, H. 2018-07-25 doi:10.1101/376202 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ A comprehensive ensemble model for comparing the allosteric effect of ordered and disordered proteins ]]> https://biorxiv.org/content/10.1101/377135v1?rss=1 Zhang, L. Li, M. Liu, Z. 2018-07-25 doi:10.1101/377135 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ Structural basis and mechanism of the unfolding-induced activation of an acid response chaperone HdeA ]]> https://biorxiv.org/content/10.1101/390104v1?rss=1 Yu, X.-C. Hu, Y. Ding, J. Li, H. Jin, C. 2018-08-12 doi:10.1101/390104 Cold Spring Harbor Laboratory Press 2018-08-12 <![CDATA[ Sequencing of the MHC region defines HLA-DQA1 as the major independent risk for anti-citrullinated protein antibodies (ACPA)-positive rheumatoid arthritis in Han population ]]> https://biorxiv.org/content/10.1101/400937v1?rss=1 Guo, J. Zhang, T. Cao, H. Li, X. Liang, H. Liu, M. Zou, Y. Zhang, Y. Sun, X. Hu, F. Du, Y. Mo, X. Liu, X. Yang, Y. Yang, H. Wu, X. Zhang, X. Jia, H. Jiang, H. Hou, Y. Liu, X. Su, Y. Zhang, M. Yang, H. Wang, J. Sun, L. Liu, L. Padyukov, L. Lai, L. Yamamoto, K. Zhang, X. Klareskog, L. Xu, X. Li, Z. 2018-08-27 doi:10.1101/400937 Cold Spring Harbor Laboratory Press 2018-08-27 <![CDATA[ Hydroxymethylated-P16 Allele Is Transcription-Inactive ]]> https://biorxiv.org/content/10.1101/405522v1?rss=1 Gan, Y. Li, P. Han, X. Qin, S. Cui, C. Liu, Z. Zhou, J. Gu, L. Lu, Z. Zhang, B. Deng, D. 2018-08-31 doi:10.1101/405522 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ Diagnostic Whole Exome Sequencing in Patients with Short Stature ]]> https://biorxiv.org/content/10.1101/414987v1?rss=1 Zhu, H. Yang, Z. Sun, J. Li, W. Yang, H. Wang, L. Gong, F. Chen, S. Lu, L. Miao, H. Yuan, X. Liang, H. Li, R. Huang, H. Peng, Z. Asan, A. Pan, H. 2018-09-12 doi:10.1101/414987 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ HBx enhances CPAP expression via interacting with CREB to promote hepatocarcinogenesis in HBV-associated HCC ]]> https://biorxiv.org/content/10.1101/423194v1?rss=1 Yen, C.-J. Yang, S.-T. Chen, R.-Y. Huang, W. Chayama, K. Lee, M.-H. Yang, S.-J. Hsiao, Y.-W. Wang, J.-M. Lin, Y.-J. Hung, L.-Y. 2018-09-20 doi:10.1101/423194 Cold Spring Harbor Laboratory Press 2018-09-20 <![CDATA[ Estimating Residue-Specific Accuracies of Protein Structure Models Using Molecular Dynamics Simulations ]]> https://biorxiv.org/content/10.1101/439760v1?rss=1 Hu, J.-H. Xun, S.-N. Wu, H.-N. Wu, Y.-D. Jiang, F. 2018-10-11 doi:10.1101/439760 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Metatranscriptome profiling of the dynamic transcription of mRNA and sRNA of a probiotic Lactobacillus strain in human gut ]]> https://biorxiv.org/content/10.1101/442673v1?rss=1 He, Q. sun, z. Qiao, J. Chen, D. Huang, J. Luo, X. Ding, J. Zhang, J. Hou, Q. Zhang, Y. Zhang, H. 2018-10-14 doi:10.1101/442673 Cold Spring Harbor Laboratory Press 2018-10-14 <![CDATA[ Regrowth-delay Body as a Bacterial Subcellular Structure marking multidrug tolerant Persisters ]]> https://biorxiv.org/content/10.1101/448092v1?rss=1 Chang, Z. Yu, J. Liu, Y. Yin, H. 2018-10-20 doi:10.1101/448092 Cold Spring Harbor Laboratory Press 2018-10-20 <![CDATA[ A genetically encoded fluorescent sensor for rapid and specific in vivo detection ofnorepinephrine ]]> https://biorxiv.org/content/10.1101/449546v1?rss=1 Feng, J. Zhang, C. Lischinsky, J. Jing, M. Zhou, J. Wang, H. Zhang, Y. Dong, A. Wu, Z. Wu, H. Chen, W. Zhang, P. Zou, J. Hires, A. Zhu, J. Cui, G. Lin, D. Du, J. Li, Y. 2018-10-23 doi:10.1101/449546 Cold Spring Harbor Laboratory Press 2018-10-23 <![CDATA[ scRMD: Imputation for single cell RNA-seq data via robust matrix decomposition ]]> https://biorxiv.org/content/10.1101/459404v1?rss=1 Chen, C. Wu, C. Wu, L. Wang, Y. Deng, M. Xi, R. 2018-11-04 doi:10.1101/459404 Cold Spring Harbor Laboratory Press 2018-11-04 <![CDATA[ Role of the Fourth Transmembrane Segment in TRAAK Channel Mechanosensitivity ]]> https://biorxiv.org/content/10.1101/463034v1?rss=1 Zhang, M. Yao, F. Pan, C. Yan, Z. 2018-11-05 doi:10.1101/463034 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ Anterior insular cortex plays a critical role in interoceptive attention ]]> https://biorxiv.org/content/10.1101/464867v1?rss=1 Wang, X. Wu, Q. Egan, L. Gu, X. Liu, P. Yang, Y. Gu, H. Luo, J. Wu, Y. Gao, Z. Fan, J. 2018-11-07 doi:10.1101/464867 Cold Spring Harbor Laboratory Press 2018-11-07 <![CDATA[ Statistical properties of the optimal sensitivity matrix for compressed sensing with nonlinear sensors ]]> https://biorxiv.org/content/10.1101/464875v1?rss=1 Qin, S. Li, Q. Tang, C. Tu, Y. 2018-11-07 doi:10.1101/464875 Cold Spring Harbor Laboratory Press 2018-11-07 <![CDATA[ A Framework to Incorporate D-trace Loss into Compositional Data Analysis ]]> https://biorxiv.org/content/10.1101/464982v1?rss=1 He, S. Deng, M. 2018-11-07 doi:10.1101/464982 Cold Spring Harbor Laboratory Press 2018-11-07 <![CDATA[ PARIS, an optogenetic method for functionally mapping gap junctions ]]> https://biorxiv.org/content/10.1101/465781v1?rss=1 Wu, L. Dong, A. Dong, L. Wang, S.-Q. Li, Y. 2018-11-08 doi:10.1101/465781 Cold Spring Harbor Laboratory Press 2018-11-08 <![CDATA[ Differential requirement for centriolar satellites in cilium formation among different vertebrate cells ]]> https://biorxiv.org/content/10.1101/478974v1?rss=1 Odabasi, E. Ohlsen, S. K. Gul, S. Kavakli, H. I. Andersen, J. S. Firat-Karalar, E. N. 2018-11-26 doi:10.1101/478974 Cold Spring Harbor Laboratory Press 2018-11-26 <![CDATA[ De novo aging-related meganeurites: alteration of NADPH diaphorase positivity in the sacral spinal cord of the aged dog ]]> https://biorxiv.org/content/10.1101/483990v1?rss=1 Li, Y. Jia, Y. Huo, W. Wei, Z. Wen, X. Tian, Y. Zhang, W. Lu, B. Guo, A. Du, G. Tan, H. 2018-12-08 doi:10.1101/483990 Cold Spring Harbor Laboratory Press 2018-12-08 <![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[ Decoding functional regulatory maps via genomic evolutionary footprints in 63 green plants ]]> https://biorxiv.org/content/10.1101/484493v1?rss=1 Tian, F. Yang, D.-C. Meng, Y.-Q. Jin, J. Gao, G. 2018-12-03 doi:10.1101/484493 Cold Spring Harbor Laboratory Press 2018-12-03 <![CDATA[ Adaptation of Acinetobacter baumannii to colistin exposure: Laboratory mimicking of a clinical case ]]> https://biorxiv.org/content/10.1101/493221v1?rss=1 Oralkan, E. Keske, S. Ergonul, O. Can, F. 2018-12-19 doi:10.1101/493221 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Somatic LINE-1 retrotransposition in cortical neurons of Rett patients and healthy individuals ]]> https://biorxiv.org/content/10.1101/506758v1?rss=1 Zhao, B. Wu, Q. Ye, Y. Guo, J. Zheng, X. Yang, X. Yan, L. Liu, Q.-R. Hyde, T. M. Wei, L. Huang, Y. 2018-12-31 doi:10.1101/506758 Cold Spring Harbor Laboratory Press 2018-12-31 <![CDATA[ Identification of TTN as a novel candidate gene for atrioventricular block in a Chinese pedigree by whole-exome sequencing ]]> https://biorxiv.org/content/10.1101/506824v1?rss=1 A (p.N16429K), in the titin (TTN, NM_001267550.2) gene in all 5 affected family members, but not in the unaffected family members. The point mutation is predicted to be functionally deleterious by in-silico software tools. Our finding was further supported by the conservative analysis across species.nnConclusionBased on this study, TTN was identified as a potential novel candidate gene for autosomal dominant AVB; this study expands the mutational spectrum of TTN gene and is the first to implicate TTN mutations as AVB disease causing in a Chinese pedigree. ]]> Li, W. Liu, G. Yang, Z. Chen, W. Yang, P. Xu, J. Miao, L. Yu, Q. Guo, J. Xu, H. Liu, F. Sun, Y. Huang, H. Peng, Z. Sun, J. 2018-12-27 doi:10.1101/506824 Cold Spring Harbor Laboratory Press 2018-12-27 <![CDATA[ Causes of death among hospitalized adults with dengue fever in Tainan, 2015: emphasis on cardiac events and bacterial infections ]]> https://biorxiv.org/content/10.1101/507137v1?rss=1 Lee, J.-C. Cia, C.-T. Lee, N.-Y. Ko, N.-Y. Chen, P.-L. Ko, W.-C. 2018-12-27 doi:10.1101/507137 Cold Spring Harbor Laboratory Press 2018-12-27 <![CDATA[ A new convolution model for effective bio-motif detection via rationally design the \"black box\" ]]> https://biorxiv.org/content/10.1101/508242v1?rss=1 Jin, S. Li, J. Ding, Y. Gao, G. 2018-12-31 doi:10.1101/508242 Cold Spring Harbor Laboratory Press 2018-12-31 <![CDATA[ Bi-clustering based biological and clinical characterization of colorectal cancer in complementary to CMS classification ]]> https://biorxiv.org/content/10.1101/508275v1?rss=1 Cao, S. Chang, W. Wan, C. Zhang, Y. Zhao, J. Li, B. Ma, Q. Zhang, C. 2018-12-31 doi:10.1101/508275 Cold Spring Harbor Laboratory Press 2018-12-31 <![CDATA[ Time- and size-resolved bacterial aerosol dynamics in highly polluted air: new clues for haze formation mechanism ]]> https://biorxiv.org/content/10.1101/513093v1?rss=1 96% abundance at a corresponding PM2.5 level of 208 ng/m3. The bacterial aerosol changes corresponded to the observed PM2.5 mass peak shift from 3.2-5.6 m to the high viability size range of 0.56-1m. Additionally, it is interesting that elevated levels of soluble Na, Ca, Mg, K, Al, Fe and P elements that are required for bacterial growth were observed to co-occur with those significant bacterial aerosol structure shifts in the air. For particular time-resolved PM2.5 pollution episodes, Acinetobacter and Massilia were shown to alternate in dominating the time-resolved aerosol community structures. The results from a HYSPLIT trajectory model simulation suggested that the role by air mass transport in affecting the observed bacterial aerosol dynamics could be minor. As an evidence, we found that Acinetobacter, Psychrobacter, Exiguobacterium, and Bacillus genera were emitted into the air with a level of > 3000 CFU/m3 from a pharmaceutical plant. In addition, high level of VOCs up to 15,030 ppbv, mainly Acetone (61%) and Acetaldehyde (11%), were also detected in the air inside the plant. All the data including size-resolved viability and time-resolved bacterial aerosol dynamics together with their growth conditions detected in the air suggested that airborne bacteria in the size range of 0.56- 1m could have played important roles for haze formation in Beijing. The results about time- and size-resolved bacterial aerosol dynamics from this work provide a fresh understanding of aerosol chemistry especially in highly polluted air. It is hoped that these findings could lend a support in future cost-effective air pollution control practices. ]]> Zhang, T. Li, X. Wang, M. Chen, H. Yao, M. 2019-01-07 doi:10.1101/513093 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ Cyclin A2/Cdk1 is Essential for the in vivo S Phase Entry by Phosphorylating Top2a. ]]> https://biorxiv.org/content/10.1101/513861v1?rss=1 Jin, M. Hu, R. Xu, B. Huang, W. Wang, H. Chen, B. He, J. Cao, Y. 2019-01-07 doi:10.1101/513861 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ Immune gene expression profiling reveals heterogeneity in luminal breast tumors ]]> https://biorxiv.org/content/10.1101/515486v1?rss=1 Zhu, B. Tse, S. L. A. Wang, D. Koka, H. Zhang, T. Abubakar, M. Lee, P. Wang, F. Wu, C. Tsang, K. H. Chan, W.-c. Law, S. H. Li, M. Li, W. Wu, S. Liu, Z. Huang, B. Zhang, H. Tang, E. Kan, Z. Lee, S. Park, Y. H. Nam, S. J. Wang, M. Sun, X. Jones, K. Zhu, B. Hutchinson, A. Hicks, B. Prokunina-Olsson, L. Shi, J. Garcia-Closas, M. Chanock, S. Yang, X. R. 2019-01-09 doi:10.1101/515486 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ Osmoregulation of glutamine synthetase from Giant freshwater prawn (Macrobrachium rosenbergii) under osmotic stress ]]> https://biorxiv.org/content/10.1101/517409v1?rss=1 gills > heart > stomach > brain > haemolymph. Mr-GS expression and the glutamine concentrations were analyzed in the gills and muscle tissues of prawn under hyper/hypo-osmotic stress conditions. Under hyper-osmotic stress, the mRNA expression of Mr-GS was significantly increased in both gills and muscle at 3, 6 and 12 h post-treatment with 2.54, 4.21 and 10.83 folds, and 11.66, 17.97 and 45.92 folds, respectively. Protein analysis by western blot (WB) and Immunohistochemistry (IHC) further confirmed the Mr-GS expression was increased at 12 h post treatment. On the other hand, under hypo-osmotic stress, the mRNA expression of Mr-GS was also significantly increased in both gills and muscle at 3, 6 and 12 h post treatment with 1.63, 3.30 and 3.52 folds, and 4.06, 42.99 and 26.69 folds, respectively. Furthermore, under hyperosmotic stress, Gln concentration was increased in both gills and muscle at 6 and 12 h post treatment with 1.83, 2.02 folds, and 1.41, 1.29 folds, respectively. While, under hypo-osmotic stress, Gln concentration was increased in both gills and muscle at 3, 6 and 12 h post treatment with 3.99, 3.40, 2.59 folds, and 1.72, 1.83, 1.80 folds, respectively. Taken together, these results suggest that Mr-GS might play a key role in osmoregulation in M. rosenbergii. ]]> Zhijie, L. Zhendong, Q. Vijayaraman, S. B. Chengkai, Y. Guomao, S. Jiabo, L. Guang, Y. Haiyang, S. Gan, P. Li, L. Zhijie Lu, Zhendong Qin, Sarath Babu V, Chengkai Ye, Guomao Su, Jiabo Li, Guang Yang, Haiyang Shen,, 2019-01-10 doi:10.1101/517409 Cold Spring Harbor Laboratory Press 2019-01-10 <![CDATA[ Motion direction representation in multivariate electroencephalography activity for smooth pursuit eye movements ]]> https://biorxiv.org/content/10.1101/519074v1?rss=1 Lee, J. Jeong, W. Kim, S. Kim, Y.-J. 2019-01-13 doi:10.1101/519074 Cold Spring Harbor Laboratory Press 2019-01-13 <![CDATA[ How many bits of information can be transferred within a protein and how fast? ]]> https://biorxiv.org/content/10.1101/519827v1?rss=1 Hacisuleyman, A. Erman, B. 2019-01-14 doi:10.1101/519827 Cold Spring Harbor Laboratory Press 2019-01-14 <![CDATA[ JuLI: accurate detection of DNA fusions in clinical sequencing for precision oncology ]]> https://biorxiv.org/content/10.1101/521039v1?rss=1 Shin, H.-T. Kim, N. K. D. Yun, J. W. Lee, B. Kyung, S. Lee, K.-W. Ryu, D. Kim, J. Bae, J. S. Park, D. Choi, Y.-L. Lee, S.-H. Ahn, M.-J. Park, K. Park, W.-Y. 2019-01-16 doi:10.1101/521039 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ Phase separation during mouse early embryonic development and underlying genetic and epigenetic correlations ]]> https://biorxiv.org/content/10.1101/521401v1?rss=1 Quan, H. Liu, S. Zhang, Y. Xie, W. Gao, Y. Q. 2019-01-17 doi:10.1101/521401 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ Age-dependent characterization of the carotid and cerebral artery morphologies in a transgenic mouse model of sickle cell anemia using ultrasound and microcomputed tomography ]]> https://biorxiv.org/content/10.1101/522748v1?rss=1 Rivera, C. P. Li, L. Cai, S. Pei, N. McAlear, G. Bollavaram, K. Ariyo, O. V. Omojola, V. O. Song, H. Tan, W. Huo, Y. Platt, M. O. 2019-01-16 doi:10.1101/522748 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ 3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients ]]> https://biorxiv.org/content/10.1101/523563v1?rss=1 Dincer, C. Kaya, T. Keskin, O. Gursoy, A. Tuncbag, N. 2019-01-17 doi:10.1101/523563 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ CTCF-mediated Chromatin Structures Dictate the Spatio-temporal Propagation of Replication Foci ]]> https://biorxiv.org/content/10.1101/525915v1?rss=1 Su, Q. P. Zhao, Z. W. Meng, L. Ding, M. Zhang, W. Li, Y. Liu, M. Li, R. Gao, Y.-Q. Xie, X. S. Sun, Y. 2019-01-21 doi:10.1101/525915 Cold Spring Harbor Laboratory Press 2019-01-21 <![CDATA[ Dual forms of aging-related NADPH diaphorase neurodegeneration in the sacral spinal cord of aged non-human primates ]]> https://biorxiv.org/content/10.1101/527358v1?rss=1 Li, Y. Wei, Z. Jia, Y. Hou, W. Wang, Y. Yu, S. Shi, G. Du, G. Tan, H. 2019-01-30 doi:10.1101/527358 Cold Spring Harbor Laboratory Press 2019-01-30 <![CDATA[ Multi-omics profiling of CHO parental hosts reveals cell line-specific variations in bioprocessing traits ]]> https://biorxiv.org/content/10.1101/532150v1?rss=1 Lakshmanan, M. Kok, Y. J. Lee, A. P. Kyriakopoulos, S. Lim, H. L. Teo, G. Poh, S. L. Tang, W. Q. Hong, J. Tan, A. H.-M. Bi, X. Ho, Y. S. Zhang, P. Ng, S. K. Lee, D.-Y. 2019-01-31 doi:10.1101/532150 Cold Spring Harbor Laboratory Press 2019-01-31 <![CDATA[ GIGI2: A Fast Approach for Parallel Genotype Imputation in Large Pedigrees ]]> https://biorxiv.org/content/10.1101/533687v1?rss=1 Ullah, E. Kunji, K. Wijsman, E. M. Saad, M. 2019-01-29 doi:10.1101/533687 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Conditional activation of immune-related signatures and prognostic significance: a pan-cancer analysis ]]> https://biorxiv.org/content/10.1101/546069v1?rss=1 Roelands, J. Hendrickx, W. Mall, R. Saad, M. Halliwill, K. Zoppoli, G. Curigliano, G. Rinchai, D. Decock, J. Delogu, L. Chouchane, L. Wang, E. Kuppen, P. Finetti, P. Bertucci, F. Miller, L. Galon, J. Marincola, F. Ceccarelli, M. Bedognetti, D. 2019-02-12 doi:10.1101/546069 Cold Spring Harbor Laboratory Press 2019-02-12 <![CDATA[ Spatiotemporal functional organization of excitatory synaptic inputs onto macaque V1 neurons ]]> https://biorxiv.org/content/10.1101/558163v1?rss=1 Ju, N. Li, Y. Liu, F. Jiang, H. Macknik, S. L. Martinez-Conde, S. Tang, S. 2019-02-22 doi:10.1101/558163 Cold Spring Harbor Laboratory Press 2019-02-22 <![CDATA[ Pressure overload leads to coronary plaque formation, progression and myocardial events in ApoE-/- mice ]]> https://biorxiv.org/content/10.1101/562181v1?rss=1 Marino, A. Zhang, Y. Rubinelli, L. Ip, J. E. Di Lorenzo, A. 2019-02-26 doi:10.1101/562181 Cold Spring Harbor Laboratory Press 2019-02-26 <![CDATA[ Autistic traits lower the flexibility of information sampling: insights from a two-stage decision model ]]> https://biorxiv.org/content/10.1101/582783v1?rss=1 Lu, H. Yi, L. Zhang, H. 2019-03-20 doi:10.1101/582783 Cold Spring Harbor Laboratory Press 2019-03-20 <![CDATA[ Cell cycle inhibitor Whi5 records environmental information to coordinate growth and division in yeast ]]> https://biorxiv.org/content/10.1101/583666v1?rss=1 Qu, Y. Jiang, J. Liu, X. Wei, P. Yang, X. Tang, C. 2019-03-20 doi:10.1101/583666 Cold Spring Harbor Laboratory Press 2019-03-20 <![CDATA[ Deliver on Your Own: Disrespectful Maternity Care in rural Kenya ]]> https://biorxiv.org/content/10.1101/586693v1?rss=1 Lusambili, A. M. Naanyu, V. N. Wade, T. J. Mossman, L. Pell, R. Mulama, K. Nyaga, L. Obure, J. Mantel, M. Ngetich, A. Temmerman, M. 2019-03-22 doi:10.1101/586693 Cold Spring Harbor Laboratory Press 2019-03-22 <![CDATA[ Cell BLAST: Searching large-scale scRNA-seq database via unbiased cell embedding ]]> https://biorxiv.org/content/10.1101/587360v1?rss=1 Cao, Z.-J. Wei, L. Lu, S. Yang, D.-C. Gao, G. 2019-03-24 doi:10.1101/587360 Cold Spring Harbor Laboratory Press 2019-03-24 <![CDATA[ TDP-43 proteinopathy impairs neuronal mRNP granule mediated postsynaptic local translation and mRNA metabolism ]]> https://biorxiv.org/content/10.1101/589416v1?rss=1 Wong, C.-E. Tsai, K.-J. 2019-03-30 doi:10.1101/589416 Cold Spring Harbor Laboratory Press 2019-03-30 <![CDATA[ CoBATCH for high-throughput single-cell epigenomic profiling ]]> https://biorxiv.org/content/10.1101/590661v1?rss=1 Wang, Q. Xioong, H. Ai, S. Yu, X. Liu, Y. Zhang, J. He, A. 2019-03-28 doi:10.1101/590661 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ Chromatin-lamin B1 interaction promotes genomic compartmentalization and constrains chromatin dynamics ]]> https://biorxiv.org/content/10.1101/601849v1?rss=1 Chang, L. Li, M. Shao, S. Xue, B. Hou, Y. Zhang, Y. Li, R. Li, C. Sun, Y. 2019-04-07 doi:10.1101/601849 Cold Spring Harbor Laboratory Press 2019-04-07 <![CDATA[ Prevalence of Hepatitis C Virus Genotypes in the Southern Region, Saudi Arabia ]]> https://biorxiv.org/content/10.1101/603902v1?rss=1 Alkahtani, A. M. Alsultan, M. N. Hakami, A. R. Alamri, M. 2019-04-10 doi:10.1101/603902 Cold Spring Harbor Laboratory Press 2019-04-10 <![CDATA[ Sustained visual priming effects can emerge from attentional oscillation and temporal expectation ]]> https://biorxiv.org/content/10.1101/604702v1?rss=1 Wang, M. Huang, Y. Luo, H. Zhang, H. 2019-04-10 doi:10.1101/604702 Cold Spring Harbor Laboratory Press 2019-04-10 <![CDATA[ Leveraging Endogenous ADAR for Programmable Editing on RNA ]]> https://biorxiv.org/content/10.1101/605972v1?rss=1 Qu, L. Yi, Z. Zhu, S. Wang, C. Cao, Z. Zhou, Z. Yuan, P. Yu, Y. Tian, F. Liu, Z. Bao, Y. Zhao, Y. Wei, W. 2019-04-19 doi:10.1101/605972 Cold Spring Harbor Laboratory Press 2019-04-19 <![CDATA[ Escherichia coli’s physiology can turn membrane voltage dyes into actuators ]]> https://biorxiv.org/content/10.1101/607838v1?rss=1 Mancini, L. Terradot, G. Tian, T. Pu, Y. Li, Y. Lo, C.-J. Bai, F. Pilizota, T. 2019-04-12 doi:10.1101/607838 Cold Spring Harbor Laboratory Press 2019-04-12 <![CDATA[ Phylo-comparative analyses reveal the dual role of drift and selection in reproductive character displacement. ]]> https://biorxiv.org/content/10.1101/610857v1?rss=1 Saglam, I. K. Miller, M. O'Rourke, S. Caglar, S. S. 2019-04-16 doi:10.1101/610857 Cold Spring Harbor Laboratory Press 2019-04-16 <![CDATA[ A Genetically Encoded Fluorescent Sensor Enables Real-time Detection of the Intracellular GTP:GDP Ratio ]]> https://biorxiv.org/content/10.1101/614412v1?rss=1 Zhang, J. Song, Y. Liu, S. Wang, W. Zhang, M. Yang, G. Zou, P. Wang, J. 2019-04-21 doi:10.1101/614412 Cold Spring Harbor Laboratory Press 2019-04-21 <![CDATA[ Direct Comparative Analysis of 10X Genomics Chromium and Smart-seq2 ]]> https://biorxiv.org/content/10.1101/615013v1?rss=1 Wang, X. Yao, H. Zhang, Q. Ren, X. Zhang, Z. 2019-04-22 doi:10.1101/615013 Cold Spring Harbor Laboratory Press 2019-04-22 <![CDATA[ DeepInterface: Protein-protein interface validation using 3D Convolutional Neural Networks ]]> https://biorxiv.org/content/10.1101/617506v1?rss=1 Balci, A. T. Gumeli, C. Hakouz, A. Yuret, D. Keskin, O. Gursoy, A. 2019-04-24 doi:10.1101/617506 Cold Spring Harbor Laboratory Press 2019-04-24 <![CDATA[ The neural basis for response latency in a sensory-motor behavior ]]> https://biorxiv.org/content/10.1101/623256v1?rss=1 Lee, J. Darlington, T. R. Lisberger, S. G. 2019-04-30 doi:10.1101/623256 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ Contrasting biogeographic patterns of bacterial and archaeal diversity in the top- and subsoils of temperate grasslands ]]> https://biorxiv.org/content/10.1101/623264v1?rss=1 Liu, N. Hu, H. Ma, W. Deng, Y. Liu, Y. Hao, B. Zhang, X. Dimitrov, D. Feng, X. Wang, Z. 2019-04-30 doi:10.1101/623264 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ Cellular precision of orientation and spatial frequency maps in macaque V1 ]]> https://biorxiv.org/content/10.1101/631416v1?rss=1 Yu, C. Ju, N.-S. Guan, S.-C. Tang, S. 2019-05-08 doi:10.1101/631416 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Manipulating serial replay during memory retention rapidly alters human sequence memory ]]> https://biorxiv.org/content/10.1101/631531v1?rss=1 Li, J. Huang, Q. Han, Q. Luo, H. 2019-05-08 doi:10.1101/631531 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Landscape and regulation of m6A and m6Am methylome across human and mouse tissues ]]> https://biorxiv.org/content/10.1101/632000v1?rss=1 Liu, J. Li, K. Cai, J. Zhang, M. Zhang, X. Xiong, X. Meng, H. Xu, X. Huang, Z. Fan, J. Yi, C. 2019-05-08 doi:10.1101/632000 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ MRGPRX4 is a novel bile acid receptor in cholestatic itch ]]> https://biorxiv.org/content/10.1101/633446v1?rss=1 Yu, H. Zhao, T. Liu, S. Wu, Q. Johnson, O. Wu, Z. Zhuang, Z. Shi, Y. He, R. Yang, Y. Sun, J. Wang, X. Xu, H. Zeng, Z. Lei, X. Luo, W. Li, Y. 2019-05-09 doi:10.1101/633446 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Girdin: an essential component of pre-replicative complex in human cells ]]> https://biorxiv.org/content/10.1101/634626v1?rss=1 Wu, L. Hua, Y. Chang, F. Kong, D. 2019-05-13 doi:10.1101/634626 Cold Spring Harbor Laboratory Press 2019-05-13 <![CDATA[ Deep-learning enables proteome-scale identification of phase-separated protein candidates from immunofluorescence images ]]> https://biorxiv.org/content/10.1101/636738v1?rss=1 Yu, C. Shen, B. Huang, Q. Shi, M. You, K. Wu, C. Chen, Y. Li, T. 2019-05-14 doi:10.1101/636738 Cold Spring Harbor Laboratory Press 2019-05-14 <![CDATA[ Fast, Accurate Polarization and Polarity Imaging withPolarized Structured Illumination ]]> https://biorxiv.org/content/10.1101/640268v1?rss=1 Zhanghao, K. Liu, W. Li, M. Chen, X. Shan, C. Wang, H. Xi, P. Dai, Q. 2019-05-15 doi:10.1101/640268 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ SciBet: An ultra-fast classifier for cell type identification using single cell RNA sequencing data ]]> https://biorxiv.org/content/10.1101/645358v1?rss=1 Li, C. Liu, B. Kang, B. Liu, Z. Liu, Y. Ren, X. Zhang, Z. 2019-05-23 doi:10.1101/645358 Cold Spring Harbor Laboratory Press 2019-05-23 <![CDATA[ Mitochondrial dynamics quantitatively revealed by STED nanoscopy with an enhanced squaraine variant probe ]]> https://biorxiv.org/content/10.1101/646117v1?rss=1 Yang, X. Yang, Z. He, Y. Shan, C. Yan, W. Wu, Z. Chai, P. Teng, J. Qu, J. Xi, P. 2019-05-22 doi:10.1101/646117 Cold Spring Harbor Laboratory Press 2019-05-22 <![CDATA[ Comparison of Escherichia coli surface attachment methods for single-cell, in vivo microscopy ]]> https://biorxiv.org/content/10.1101/648840v1?rss=1 Wang, Y. K. Krasnopeeva, E. Lin, S.-Y. Bai, F. Pilizota, T. Lo, C.-J. 2019-05-24 doi:10.1101/648840 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ A comparative assessment of aging-related NADPH diaphorase positivity in the spinal cord and medullary oblongata between pigeon and murine ]]> https://biorxiv.org/content/10.1101/650457v1?rss=1 Jia, Y. Hou, W. Li, Y. Wen, X. Rao, C. Wei, Z. Zhang, T. Wang, X. Li, X. Bai, L. Wang, P. Zhang, W. Bi, J. Guo, A. Wang, J. Tan, H. 2019-05-26 doi:10.1101/650457 Cold Spring Harbor Laboratory Press 2019-05-26 <![CDATA[ NEUROD2 represses Reelin expression and controls dendrite orientation during cortical radial migration ]]> https://biorxiv.org/content/10.1101/651273v1?rss=1 Guzelsoy, G. Akkaya, C. Atak, D. Dunn, C. D. Kabakcioglu, A. Ozlu, N. Ince-Dunn, G. 2019-05-27 doi:10.1101/651273 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ On the impact of biomass composition in constraint-based flux analysis ]]> https://biorxiv.org/content/10.1101/652040v1?rss=1 Lakshmanan, M. Long, S. Ang, K. S. Lewis, N. E. Lee, D.-Y. 2019-05-28 doi:10.1101/652040 Cold Spring Harbor Laboratory Press 2019-05-28 <![CDATA[ Nuclear actin regulates inducible transcription by enhancing RNA polymerase II clustering ]]> https://biorxiv.org/content/10.1101/655043v1?rss=1 Wei, M. Fan, X. Ding, M. Li, R. Shao, S. Hou, Y. Meng, S. Tang, F. Li, C. Sun, Y. 2019-05-30 doi:10.1101/655043 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ Microstructural plasticity in the bilingual brain ]]> https://biorxiv.org/content/10.1101/657932v1?rss=1 Luo, D. Kwok, V. P. Y. Li, P. Liu, Q. Li, W. Yang, Y. Zhou, K. Xu, M. Gao, J. H. Tan, L. H. 2019-06-02 doi:10.1101/657932 Cold Spring Harbor Laboratory Press 2019-06-02 <![CDATA[ Caenorhabditis elegans Exhibits Positive Gravitaxis ]]> https://biorxiv.org/content/10.1101/658229v1?rss=1 Chen, W.-L. Ko, H. Chuang, H.-S. Bau, H. H. Raizen, D. 2019-06-03 doi:10.1101/658229 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Expectation pooling: An effective and interpretable pooling method for predicting DNA-protein binding ]]> https://biorxiv.org/content/10.1101/658427v1?rss=1 Luo, X. Tu, X. Ding, Y. Gao, G. Deng, M. 2019-06-03 doi:10.1101/658427 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Biomarker discovery in inflammatory bowel diseases using network-based feature selection ]]> https://biorxiv.org/content/10.1101/662197v1?rss=1 Abbas, M. Matta, J. Le, T. Bensmail, H. Obafemi-Ajayi, T. Honavar, V. EL-Manzalawy, Y. 2019-06-06 doi:10.1101/662197 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ The bounded rationality of probability distortion: the bounded log-odds model ]]> https://biorxiv.org/content/10.1101/662429v1?rss=1 Zhang, H. Ren, X. Maloney, L. T. 2019-06-06 doi:10.1101/662429 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Specialized NADPH diaphorase membrane-related localizations in the brainstem of the pigeons (Columba livia) ]]> https://biorxiv.org/content/10.1101/663310v1?rss=1 Jia, Y. Hou, W. Li, Y. Zhang, T. Wang, X. Wen, X. Xu, X. Sun, H. Rao, C. Wu, X. Wei, Z. Zhai, Z. Tan, H. 2019-06-06 doi:10.1101/663310 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Modeling microbial diversity with metabolic trade-offs ]]> https://biorxiv.org/content/10.1101/664698v1?rss=1 Li, Z. Liu, B. Li, S. H.-J. King, C. G. Gitai, Z. Wingreen, N. S. 2019-06-09 doi:10.1101/664698 Cold Spring Harbor Laboratory Press 2019-06-09 <![CDATA[ 3D observation of large-scale subcellular dynamics in vivo at the millisecond scale ]]> https://biorxiv.org/content/10.1101/672584v1?rss=1 Wu, J. Lu, Z. Qiao, H. Zhang, X. Zhanghao, K. Xie, H. Yan, T. Zhang, G. Li, X. Jiang, Z. Lin, X. Fang, L. Zhou, B. Fan, J. Xi, P. Dai, Q. 2019-06-18 doi:10.1101/672584 Cold Spring Harbor Laboratory Press 2019-06-18 <![CDATA[ The role of iron uptake systems in the pathogenesis of colistin-resistant hypervirulent K. pneumoniae infections ]]> https://biorxiv.org/content/10.1101/677492v1?rss=1 Dogan, O. Vatansever, C. Atac, N. Albayrak, O. Karahuseyinoglu, S. Sahin, O. E. Kilicoglu, B. K. Demiray, A. Ergonul, O. Gönen, M. Can, F. 2019-06-21 doi:10.1101/677492 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Intramolecular Communication and Allosteric Sites in Enzymes Unraveled by Time-Dependent Linear Response Theory ]]> https://biorxiv.org/content/10.1101/677617v1?rss=1 Huang, B.-C. Chang-Chein, C.-H. Yang, L.-W. 2019-06-21 doi:10.1101/677617 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Object-Based Cognitive Map in the Human Hippocampus and Medial Prefrontal Cortex ]]> https://biorxiv.org/content/10.1101/680199v1?rss=1 Zhang, B. Naya, Y. 2019-06-23 doi:10.1101/680199 Cold Spring Harbor Laboratory Press 2019-06-23 <![CDATA[ The Ca2+ Permeation Mechanism of the Ryanodine Receptor Revealed by a Multi-Site Ion Model ]]> https://biorxiv.org/content/10.1101/682328v1?rss=1 Zhang, A. Yu, H. Liu, C. Song, C. 2019-06-25 doi:10.1101/682328 Cold Spring Harbor Laboratory Press 2019-06-25 <![CDATA[ Evaluation of deep-learning-based lncRNA identification tools ]]> https://biorxiv.org/content/10.1101/683425v1?rss=1 Yang, C. Zhou, M. Xie, H. Zhu, H. 2019-06-28 doi:10.1101/683425 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Guilty by association: How group-based (collective) guilt arises in the brain ]]> https://biorxiv.org/content/10.1101/683730v1?rss=1 Li, Z. Yu, H. Zhou, Y. Kalenscher, T. Zhou, X. 2019-06-27 doi:10.1101/683730 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions ]]> https://biorxiv.org/content/10.1101/684712v1?rss=1 Cai, Y. Zhang, Y. Loh, Y. P. Tng, J. Q. Lim, M. C. Cao, Z. Raju, A. Li, S. Manikandan, L. Tergaonkar, V. Tucker-Kellogg, G. Fullwood, M. J. 2019-06-28 doi:10.1101/684712 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Predicting long-term Type 2 Diabetes with Support Vector Machine using Oral Glucose Tolerance Test ]]> https://biorxiv.org/content/10.1101/688804v1?rss=1 Abbas, H. T. Alic, L. Erraguntla, M. Abdul-Ghani, M. Abbasi, Q. Qaraqe, M. 2019-07-01 doi:10.1101/688804 Cold Spring Harbor Laboratory Press 2019-07-01 <![CDATA[ Two Forms of Knowledge Representations in the Human Brain ]]> https://biorxiv.org/content/10.1101/691931v1?rss=1 Wang, X. Men, W. Gao, J. Caramazza, A. Bi, Y. 2019-07-04 doi:10.1101/691931 Cold Spring Harbor Laboratory Press 2019-07-04 <![CDATA[ Burkholderia cepacia complex bacteremia outbreaks among non-cystic fibrosis patients in the pediatric unit of the university hospital ]]> https://biorxiv.org/content/10.1101/695247v1?rss=1 Tüfekci, S. Safak, B. Kizilca, O. Nalbantoglu, A. Nalbantoglu, B. Samanci, N. Kiraz, N. 2019-07-10 doi:10.1101/695247 Cold Spring Harbor Laboratory Press 2019-07-10 <![CDATA[ Construction of High-Resolution RAD-Seq Based Linkage Map, Anchoring Reference Genome, and QTL Mapping of the Sex Chromosome in the Marine Medaka Oryzias melastigma ]]> https://biorxiv.org/content/10.1101/695304v1?rss=1 Lee, B.-Y. Kim, M.-S. Choi, B.-S. Nagano, A. Au, D. W. T. Wu, R. Takehana, Y. Lee, J.-S. 2019-07-08 doi:10.1101/695304 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Enhancing single-cell cellular state inference by incorporating molecular network features ]]> https://biorxiv.org/content/10.1101/699959v1?rss=1 Dong, J. Zhou, P. Wu, Y. Wang, W. Chen, Y. Zhou, X. Xie, H. Lu, J. Zhang, X. Wen, L. Fu, W. Li, T. Tang, F. 2019-07-14 doi:10.1101/699959 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ Self-assembled primary tumor clusters for precision cancer therapy ]]> https://biorxiv.org/content/10.1101/700724v1?rss=1 Yin, S. Xi, R. Wu, A. Ji, J.-F. Xi, J. 2019-07-14 doi:10.1101/700724 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ Giotto, a pipeline for integrative analysis and visualization of single-cell spatial transcriptomic data ]]> https://biorxiv.org/content/10.1101/701680v1?rss=1 Dries, R. Zhu, Q. Eng, C.-H. L. Sarkar, A. Bao, F. George, R. E. Pierson, N. Cai, L. Yuan, G.-C. 2019-07-13 doi:10.1101/701680 Cold Spring Harbor Laboratory Press 2019-07-13 <![CDATA[ Dimensional Reduction of Emergent Spatiotemporal Cortical Dynamics via a Maximum Entropy Moment Closure ]]> https://biorxiv.org/content/10.1101/703207v1?rss=1 Shao, Y. Zhang, J. Tao, L. 2019-07-15 doi:10.1101/703207 Cold Spring Harbor Laboratory Press 2019-07-15 <![CDATA[ Target Capture Sequencing Unravels Rubus Evolution ]]> https://biorxiv.org/content/10.1101/703926v1?rss=1 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation of Rubus challenging. Our objectives were to: estimate the phylogeny of 94 geographically diverse species and 3 cultivars using chloroplast DNA sequences and target capture of approximately 1,000 low copy nuclear genes; estimate divergence times between major Rubus clades; and examine the historical biogeography of species diversification.nnResultsTarget capture sequencing identified eight major groups within Rubus. Subgenus Orobatus and Subg. Anoplobatus were monophyletic, while other recognized subgenera were para- or polyphyletic. Multiple hybridization events likely occurred across the phylogeny at subgeneric levels, e.g., Subg. Rubus (blackberries) x Subg. Idaeobatus (raspberries) and Subg. Idaeobatus x Subg. Cylactis (Arctic berries) hybrids. The raspberry heritage within known cultivated blackberry hybrids was confirmed. The most recent common ancestor of the genus was most likely distributed in North America. Multiple distribution events occurred during the Miocene (about 20 Ma) from North America into Asia and Europe across the Bering land bridge and southward crossing the Panamanian Isthmus. Rubus species diversified greatly in Asia during the Miocene.nnConclusionsRubus taxonomy does not reflect phylogenetic relationships and subgeneric revision is warranted. Target capture sequencing confirmed that most subgenera are para- or polyphyletic. The most recent common ancestor migrated from North America towards Asia, Europe, and Central and South America early in the Miocene then diversified. Ancestors of the genus Rubus may have migrated to Oceania by long distance bird dispersal. This phylogeny presents a roadmap for further Rubus taxonomic and phylogenetic research. ]]> Hummer, K. E. Carter, K. A. Liston, A. Bassil, N. V. Bryant, D. Alice, L. Bushakra, J. Sutherland, B. Mockler, T. 2019-07-16 doi:10.1101/703926 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ TSG-6 in extracellular vesicles from canine mesenchymal stem/stromal is a major factor in relieving DSS-induced colitis ]]> https://biorxiv.org/content/10.1101/714931v1?rss=1 AN, J.-H. SONG, W.-J. LI, Q. RYU, M.-O. NAM, A.-R. BHANG, D.-H. JUNG, Y.-C. Youn, H.-Y. 2019-07-25 doi:10.1101/714931 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ SMAD3 Determines Conventional versus Plasmacytoid Dendritic Cell Fates ]]> https://biorxiv.org/content/10.1101/715060v1?rss=1 Yoon, J.-H. Bae, E. Sudo, K. Han, J. S. Park, S. H. Nakae, S. Yamashita, T. Lee, I.-K. Ju, J. H. Matsumoto, I. Sumida, T. Kuroda, M. Miyazawa, K. Kato, M. Mamura, M. 2019-07-25 doi:10.1101/715060 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ DeepHiC: A Generative Adversarial Network for Enhancing Hi-C Data Resolution ]]> https://biorxiv.org/content/10.1101/718148v1?rss=1 Hong, H. Jiang, S. Li, H. Quan, C. Zhao, C. Li, R. Li, W. Du, G. Yin, X. Huang, Y. Li, C. Chen, H. Bo, X. 2019-07-29 doi:10.1101/718148 Cold Spring Harbor Laboratory Press 2019-07-29 <![CDATA[ Mining the human tonsillar microbiota as autoimmune modulator ]]> https://biorxiv.org/content/10.1101/719807v1?rss=1 Li, J. Li, S. Jin, J. Guo, R. Sun, X. Guo, J. Hu, F. Liu, Y. Jin, Y. Zhou, Y. Xiao, W. Zhong, Y. Huang, F. Pan, H. Yang, R. Zhou, Y. Deng, K. Wu, L. Liu, L. Qin, J. Wang, J. He, J. Li, Z. 2019-08-07 doi:10.1101/719807 Cold Spring Harbor Laboratory Press 2019-08-07 <![CDATA[ Causal relationship of cerebrospinal fluid biomarkers with the risk of Alzheimer’s disease: A two-sample Mendelian randomization study ]]> https://biorxiv.org/content/10.1101/719898v1?rss=1 Kim, S. Kim, K. Nho, K. Myung, W. Won, H.-H. 2019-07-31 doi:10.1101/719898 Cold Spring Harbor Laboratory Press 2019-07-31 <![CDATA[ Deficiency in the endocytic adaptor protein PHETA1/2 impairs renal and craniofacial development ]]> https://biorxiv.org/content/10.1101/727578v1?rss=1 Ates, K. M. Wang, T. Moreland, T. Veeranan-Karmegam, R. Anand, P. Wenzel, W. Kim, H.-G. Wolfe, L. A. Stephen, J. A. Adams, D. R. Markello, T. Tifft, C. J. Gahl, W. A. Gonsalvez, G. B. Malicdan, M. C. Flanagan-Steet, H. Pan, Y. 2019-08-06 doi:10.1101/727578 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ Deepprune: Learning efficient and interpretable convolutional networks through weight pruning for predicting DNA-protein binding ]]> https://biorxiv.org/content/10.1101/729566v1?rss=1 Luo, X. Chi, W. Deng, M. 2019-08-27 doi:10.1101/729566 Cold Spring Harbor Laboratory Press 2019-08-27 <![CDATA[ Synchrony and complexity in state-related EEG networks: an application of spectral graph theory ]]> https://biorxiv.org/content/10.1101/729806v1?rss=1 Ghaderi, A. H. Baltaretu, B. R. Andevari, M. N. Bharmauria, V. Balci, F. 2019-08-08 doi:10.1101/729806 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ Structural insights into the mechanism of the human soluble guanylate cyclase ]]> https://biorxiv.org/content/10.1101/731679v1?rss=1 Kang, Y. Liu, R. Wu, J.-X. Chen, L. 2019-08-10 doi:10.1101/731679 Cold Spring Harbor Laboratory Press 2019-08-10 <![CDATA[ Chemistry of cation hydration and conduction in a skeletal muscle ryanodine receptor ]]> https://biorxiv.org/content/10.1101/732172v1?rss=1 Wu, Z. Liu, C. Yu, H. Kang, D. Li, X. Zhang, L. Fan, C. Li, X.-Z. Song, C. Yin, C.-C. Mao, Y. 2019-08-11 doi:10.1101/732172 Cold Spring Harbor Laboratory Press 2019-08-11 <![CDATA[ Rats Sniff Off Toxic Air ]]> https://biorxiv.org/content/10.1101/739003v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@f419cdorg.highwire.dtl.DTLVardef@1ca1582org.highwire.dtl.DTLVardef@4a35ceorg.highwire.dtl.DTLVardef@128b6f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chen, H. Li, X. Yao, M. 2019-09-01 doi:10.1101/739003 Cold Spring Harbor Laboratory Press 2019-09-01 <![CDATA[ Lossless and Contamination-Free Digital PCR ]]> https://biorxiv.org/content/10.1101/739243v1?rss=1 Liao, P. Jiang, M. Chen, Z. Zhang, F. Sun, Y. Nie, J. Du, M. Wang, J. Fei, P. Huang, Y. 2019-08-19 doi:10.1101/739243 Cold Spring Harbor Laboratory Press 2019-08-19 <![CDATA[ The Clinical Significance and Biological Function of DPEP1 in B-cell Acute Lymphoblastic Leukemia ]]> https://biorxiv.org/content/10.1101/742551v1?rss=1 Zhang, J.-M. Xu, Y. Gale, R. P. Wu, L.-X. Zhang, J. Feng, Y.-H. Qin, Y.-Z. Jiang, H. Jiang, Q. Jiang, B. Liu, Y.-R. Chen, Y.-H. Wang, Y. Zhang, X.-H. Xu, L.-P. HUANG, X. Liu, K.-Y. Ruan, G.-R. 2019-08-21 doi:10.1101/742551 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Disome-seq reveals sequence-mediated coupling of translational pauses and protein structures ]]> https://biorxiv.org/content/10.1101/746875v1?rss=1 Zhao, T. Chen, Y. Wang, J. Chen, S. Qian, W. 2019-08-28 doi:10.1101/746875 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ Impact of ultrasonography on identifying noninvasive prenatal screening false-negative aneuploidy ]]> https://biorxiv.org/content/10.1101/748269v1?rss=1 Li, W. Zeng, F. Fan, B. Yu, N. Wu, J. Yang, Y. Huang, H. Li, S.-l. Peng, Z. 2019-08-28 doi:10.1101/748269 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ SWR1 Chromatin Remodeling Complex Prevents Mitotic Slippage during Spindle Position Checkpoint Arrest ]]> https://biorxiv.org/content/10.1101/749440v1?rss=1 Caydasi, A. K. Khmelinskii, A. Darieva, Z. Kurtulmus, B. Knop, M. Pereira, G. 2019-08-28 doi:10.1101/749440 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ High-throughput living-cell protein crosslinking analysis uncovers the physiological relevance of forming the \"inserted\" state of the ATP synthase ϵ-subunit ]]> https://biorxiv.org/content/10.1101/749747v1?rss=1 Liu, Y. Yu, J. Wang, M. Zeng, Q. Fu, X. Chang, Z. 2019-08-28 doi:10.1101/749747 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ The Meta-Position of Phe4 in Leu-enkephalin Regulates Potency, Selectivity, Functional Activity, and Signaling Bias at the Delta and Mu Opioid Receptors ]]> https://biorxiv.org/content/10.1101/750794v1?rss=1 View larger version (9K): org.highwire.dtl.DTLVardef@143ee98org.highwire.dtl.DTLVardef@e55c94org.highwire.dtl.DTLVardef@2114b4org.highwire.dtl.DTLVardef@1d63ba4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOTOC FIGUREC_FLOATNO C_FIG ]]> Cassell, R. J. Sharma, K. K. Su, H. Cummins, B. R. Cui, H. Mores, K. L. Altman, R. A. van Rijn, R. M. 2019-09-01 doi:10.1101/750794 Cold Spring Harbor Laboratory Press 2019-09-01 <![CDATA[ TRIM21 and PHLDA3 Negatively Regulate the Cross-Talk between the PI3K/AKT Pathway and PPP Metabolism ]]> https://biorxiv.org/content/10.1101/750976v1?rss=1 Wu, H. Cheng, J. Huang, Y. Zhang, X. Yu, Y. Zhang, W. Wang, M. Zhang, L. Wang, M. Yan, W. Wu, Y. Wu, S. Jiao, J. Tran, L. Chi, F. Jiang, P. Zhang, X. 2019-08-30 doi:10.1101/750976 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ On the delay in propagation of action potentials ]]> https://biorxiv.org/content/10.1101/763698v1?rss=1 Xu, J. Xu, S. Wang, F. Xu, S. 2019-09-09 doi:10.1101/763698 Cold Spring Harbor Laboratory Press 2019-09-09 <![CDATA[ Dynamic production and loss of flagellar filaments during the bacterial life cycle ]]> https://biorxiv.org/content/10.1101/767319v1?rss=1 Zhuang, X.-Y. Guo, S. Li, Z. Zhao, Z. Kojima, S. Homma, M. Wang, P. Lo, C.-J. Bai, F. 2019-09-12 doi:10.1101/767319 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Verbal thinking in rhythm: motor-to-sensory transformation network mediates imagined singing ]]> https://biorxiv.org/content/10.1101/771196v1?rss=1 Li, Y. Luo, H. Tian, X. 2019-09-16 doi:10.1101/771196 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ P16 methylation increases the sensitivity of cancer cells to the CDK4/6 inhibitor palbociclib ]]> https://biorxiv.org/content/10.1101/771337v1?rss=1 Deng, D. Li, P. Zhang, X. Gu, L. Zhou, J. 2019-09-16 doi:10.1101/771337 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ System-Level Quantification and Phenotyping of Early Embryonic Morphogenesis of Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/776062v1?rss=1 nView larger version (37K):norg.highwire.dtl.DTLVardef@2ec730org.highwire.dtl.DTLVardef@11732deorg.highwire.dtl.DTLVardef@ccbf4org.highwire.dtl.DTLVardef@2218d1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Guan, G. Wong, M.-K. Ho, V. W. S. An, X. Chan, L.-Y. Tian, B. Li, Z. Tang, L. Zhao, Z. Tang, C. 2019-09-19 doi:10.1101/776062 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Universal and distinct features of intra-population heterogeneity between differentiated cells and pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/782037v1?rss=1 Jiang, Z. Francesca Generoso, S. Badia, M. Payer, B. Carey, L. B. 2019-09-25 doi:10.1101/782037 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ The Manganese Salt (MnJ) Functions as A Potent Universal Adjuvant ]]> https://biorxiv.org/content/10.1101/783910v1?rss=1 Zhang, R. Wang, C. Guan, Y. Wei, X. Sha, M. Jing, M. Lv, M. Xu, J. Wan, Y. Jiang, Z. 2019-09-27 doi:10.1101/783910 Cold Spring Harbor Laboratory Press 2019-09-27 <![CDATA[ Crystal structure of β-arrestin 2 in complex with an atypical chemokine receptor phosphopeptide reveals an alternative active conformation ]]> https://biorxiv.org/content/10.1101/785527v1?rss=1 Min, K. Yoon, H.-J. Park, J. Y. Baidya, M. Dwivedi, H. Maharana, J. Chung, K. Y. Shukla, A. K. Lee, H. H. 2019-09-29 doi:10.1101/785527 Cold Spring Harbor Laboratory Press 2019-09-29 <![CDATA[ Antibody-free enzyme-assisted chemical labeling for detection of transcriptome-wide N6-methyladenosine ]]> https://biorxiv.org/content/10.1101/790683v1?rss=1 Wang, Y. Xiao, Y. Dong, S. Yu, Q. Jia, G. 2019-10-02 doi:10.1101/790683 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Single-cell transcriptome profiling reveals neutrophil heterogeneity and orchestrated maturation during homeostasis and bacterial infection ]]> https://biorxiv.org/content/10.1101/792200v1?rss=1 25,000 differentiating and mature mouse neutrophils using single-cell RNA sequencing to provide a comprehensive transcriptional landscape of neutrophil maturation, function, and fate decision in their steady state and during bacterial infection. Eight neutrophil populations were defined by distinct molecular signatures. The three mature peripheral blood neutrophil subsets arise from distinct maturing bone marrow neutrophil subsets. Driven by both known and uncharacterized transcription factors, neutrophils gradually acquire microbicidal capability as they traverse the transcriptional landscape, representing an evolved mechanism for fine-tuned regulation of an effective but balanced neutrophil response. Bacterial infection reprograms the genetic architecture of neutrophil populations, alters dynamic transition between each subpopulation, and primes neutrophils for augmented functionality without affecting overall heterogeneity. In summary, these data establish a reference model and general framework for studying neutrophil-related disease mechanisms, biomarkers, and therapeutic targets at single-cell resolution.nnGraphical AbstractnnO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/792200v1_ufig1.gif" ALT="Figure 1">nView larger version (28K):norg.highwire.dtl.DTLVardef@18fed35org.highwire.dtl.DTLVardef@1e68b7org.highwire.dtl.DTLVardef@6cfbc8org.highwire.dtl.DTLVardef@1061a26_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIA comprehensive single-cell resolution transcriptional landscape of mouse neutrophil maturation and fate decision under steady-state and bacterial infection conditions.nC_LIO_LIThe pathogen clearance machinery in neutrophils is continuously and gradually built during neutrophil differentiation, maturation, and aging, driven by both known and uncharacterized transcription factors.nC_LIO_LIThe three mature neutrophil subsets in peripheral blood, including a novel ISG-expressing subset, are derived from distinct bone marrow neutrophil precursors.nC_LIO_LIBacterial infection reprograms the genetic architecture of neutrophil populations, alters dynamic transition between each subpopulation, and primes neutrophils for augmented functionality without affecting overall neutrophil heterogeneity.nC_LIO_LIBacterial infection-induced emergency granulopoiesis is mediated by augmented proliferation of early stage neutrophil progenitors and accelerated post-mitotic maturation.nC_LI ]]> Xie, X. Shi, Q. Wu, P. Zhang, X. Kambara, H. Su, J. Yu, H. Park, S.-Y. Guo, R. Ren, Q. Zhang, S. Xu, Y. Silberstein, L. E. Cheng, T. Ma, F. Li, C. Luo, H. R. 2019-10-04 doi:10.1101/792200 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ SCRIBE: a new approach to dropout imputation and batch effects correction for single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/793463v1?rss=1 Zhang, Y. Liang, K. Liu, M. Li, Y. Ge, H. Zhao, H. 2019-10-04 doi:10.1101/793463 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ Perceptual learning evidence for an interval- and modality invariant representation of subsecond time ]]> https://biorxiv.org/content/10.1101/794032v1?rss=1 Yu, C. Xiong, Y.-Z. Guan, S.-C. 2019-10-07 doi:10.1101/794032 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Paulinella micropora KR01 holobiont genome assembly for studying primary plastid evolution ]]> https://biorxiv.org/content/10.1101/794941v1?rss=1 1 billion years ago, therefore relatively little can be learned about plastid integration during the initial stages of primary endosymbiosis by studying these highly derived species. Here we focused on a unique model for endosymbiosis research, the photosynthetic amoeba Paulinella micropora KR01 (Rhizaria) that underwent a more recent independent primary endosymbiosis about 124 Mya. A total of 149 Gbp of PacBio and 19 Gbp of Illumina data were used to generate the draft assembly that comprises 7,048 contigs with N50=143,028 bp and a total length of 707 Mbp. Genome GC-content was 44% with 76% repetitive sequences. We predicted 32,358 genes that contain 73% of the complete, conserved genes in the BUSCO database. The mean intron length was 882 bp, which is significantly greater than in other Rhizaria (86[~]184 bp). Symbiotic bacteria from the culture were isolated and completed genomes were generated from three species (Mesorhizobium amorphae Pch-S, Methylibium petroeiphilum Pch-M, Polaromonas sp. Pch-P) with one draft genome (Pimelobacter simplex Pch-N). Our holobiont data establish P. micropora KR01 as a model for studying plastid integration and the role of bacterial symbionts in Paulinella biology. ]]> Lhee, D. Lee, J. Cho, C. H. Ha, J.-S. Jeong, S. E. Jeon, C. O. Zelzion, U. Price, D. C. Chan, Y.-F. Gabr, A. Bhattacharya, D. Yoon, H. S. 2019-10-07 doi:10.1101/794941 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ MYPT1 O-GlcNAcylation Dictates Timely Disjunction of Centrosomes ]]> https://biorxiv.org/content/10.1101/795674v1?rss=1 Liu, C. Shi, Y. Liu, X. Xiahou, Z. Li, J. Tan, Z. Chen, X. Li, J. 2019-10-07 doi:10.1101/795674 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Integration of locomotion and auditory signals in the mouse inferior colliculus ]]> https://biorxiv.org/content/10.1101/795872v1?rss=1 Yang, Y. Lee, J. Kim, G. 2019-10-07 doi:10.1101/795872 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Establishment of morphological atlas of Caenorhabditis elegans embryo with cellular resolution using deep-learning-based 4D segmentation ]]> https://biorxiv.org/content/10.1101/797688v1?rss=1 Cao, J. Guan, G. Wong, M.-K. Chan, L.-Y. Tang, C. Zhao, Z. Yan, H. 2019-10-08 doi:10.1101/797688 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Listener’s vmPFC simulates speaker choices when reading between the lines ]]> https://biorxiv.org/content/10.1101/800359v1?rss=1 Mi, Q. Wang, C. Camerer, C. F. Zhu, L. 2019-10-10 doi:10.1101/800359 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ L1 and B1 repeats blueprint the spatial organization of chromatin ]]> https://biorxiv.org/content/10.1101/802173v1?rss=1 Lu, J. Y. Chang, L. Li, T. Sun, Y. Shen, X. 2019-10-13 doi:10.1101/802173 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ Single-cell multiomics sequencing reveals the functional regulatory landscape of early embryos ]]> https://biorxiv.org/content/10.1101/803890v1?rss=1 Wang, Y. Yuan, P. Yan, Z. Yang, M. Huo, Y. Nie, Y. Zhu, X. Yan, L. Qiao, J. 2019-10-14 doi:10.1101/803890 Cold Spring Harbor Laboratory Press 2019-10-14 <![CDATA[ Song overlapping, ambient noise and territorial aggression in great tits ]]> https://biorxiv.org/content/10.1101/808733v1?rss=1 Akcay, C. Porsuk, Y. K. Avsar, A. Cabuk, D. Bilgin, C. C. 2019-10-17 doi:10.1101/808733 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Neural clusters encoding curvature and corners emerged inmacaque V4 ]]> https://biorxiv.org/content/10.1101/808907v1?rss=1 jiang, R. Li, M. Tang, S. 2019-10-17 doi:10.1101/808907 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Amygdalostriatal coupling underpins positive but not negative coloring of ambiguous affect ]]> https://biorxiv.org/content/10.1101/811505v1?rss=1 Kim, M. J. Mattek, A. M. Shin, J. 2019-10-21 doi:10.1101/811505 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ PhyB induces intron retention and uORF-mediated translational inhibition of PIF3 ]]> https://biorxiv.org/content/10.1101/813840v1?rss=1 Dong, J. Chen, H. Deng, X. W. Irish, V. F. Wei, N. 2019-10-21 doi:10.1101/813840 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Epigenetic Effects of Assisted Reproductive Technology in Human Offspring ]]> https://biorxiv.org/content/10.1101/816157v1?rss=1 Wei, C. Peng, Y. Ma, X. y. Kong, S. M. Tang, S. y. Wei, Y. Zhao, Y. y. Zhang, W. Wang, Y. Yan, L. y. Qiao, J. 2019-10-24 doi:10.1101/816157 Cold Spring Harbor Laboratory Press 2019-10-24 <![CDATA[ Computational Assessment of the Regulation-Modulating Potential for Noncoding Variants ]]> https://biorxiv.org/content/10.1101/819409v1?rss=1 Shi, F.-Y. Wang, Y. Huang, D. Liang, Y. Liang, N. Chen, X.-W. Gao, G. 2019-10-28 doi:10.1101/819409 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ ROGUE: an entropy-based universal metric for assessing the purity of single cell population ]]> https://biorxiv.org/content/10.1101/819581v1?rss=1 Liu, B. Li, C. Li, Z. Ren, X. Zhang, Z. 2019-10-27 doi:10.1101/819581 Cold Spring Harbor Laboratory Press 2019-10-27 <![CDATA[ Atomic structures determined from digitally defined nanocrystalline regions ]]> https://biorxiv.org/content/10.1101/820274v1?rss=1 Gallagher-Jones, M. J. Bustillo, K. C. Ophus, C. Richards, L. S. Ciston, J. Lee, S. Minor, A. M. Rodriguez, J. A. 2019-10-29 doi:10.1101/820274 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ ModiBodies: A computational method for modifying nanobodies to improve their antigen binding affinity and specificity ]]> https://biorxiv.org/content/10.1101/820373v1?rss=1 Hacisuleyman, A. Erman, B. 2019-10-28 doi:10.1101/820373 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ Structural basis for the binding selectivity of human CDY chromodomains ]]> https://biorxiv.org/content/10.1101/820647v1?rss=1 Dong, C. Liu, Y. Lyu, T. Beldar, S. Lamb, K. Tempel, W. Li, Y. Li, Z. James, L. Qin, S. Wang, Y. Min, J. 2019-11-07 doi:10.1101/820647 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Screening of Tau Protein Kinase Inhibitors in a Tauopathy-relevant cell-based model of Tau Hyperphosphorylation and Oligomerization ]]> https://biorxiv.org/content/10.1101/821389v1?rss=1 Yadikar, H. Torres, I. Aiello, G. Kurup, M. Yang, Z. Lin, F. Kobeissy, F. Yost, R. Wang, K. K. 2019-10-28 doi:10.1101/821389 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ 6-O-galloylsalidroside, an active ingredient from Acer tegmentosum, ameliorates alcoholic steatosis and liver injury in a mouse model of chronic ethanol consumption ]]> https://biorxiv.org/content/10.1101/821397v1?rss=1 Kim, Y. H. Woo, D.-C. Ra, M. Jung, S. Ham, S. J. Kim, K. H. LEE, Y. 2019-10-28 doi:10.1101/821397 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ Identification of distinct pathological signatures induced by patient-derived α-synuclein structures in non-human primates ]]> https://biorxiv.org/content/10.1101/825216v1?rss=1 Bourdenx, M. Nioche, A. Dovero, S. Arotcarena, M.-L. Camus, S. Porras, G. Thiolat, M.-L. Rougier, N. P. Prigent, A. Aubert, P. Bohic, S. Sandt, C. Laferriere, F. Doudnikoff, E. Kruse, N. Mollenhauer, B. Novello, S. Morari, M. Leste-Lasserre, T. Trigo Damas, I. Goillandeau, M. Perier, C. Estrada, C. Garcia Carrillo, N. Recasens, A. Vaikath, N. N. El-Agnaf, O. M. A. Herrero Ezquerro, M. T. Derkinderen, P. Vila Bover, M. Obeso, J. A. Dehay, B. Bezard, E. 2019-10-31 doi:10.1101/825216 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ LIMD1 phase separation contributes to cellular mechanics and durotaxis by regulating focal adhesion dynamics in response to force ]]> https://biorxiv.org/content/10.1101/828806v1?rss=1 Wang, Y. Zhang, C. Shao, S. Liang, L. Sun, Y. Wu, C. 2019-11-05 doi:10.1101/828806 Cold Spring Harbor Laboratory Press 2019-11-05 <![CDATA[ Mul1 suppresses Nlrp3 inflammasome activation through ubiquitination and degradation of Asc ]]> https://biorxiv.org/content/10.1101/830380v1?rss=1 Kim, J.-H. Lee, Y. Suh, G. Y. Lee, Y.-S. 2019-11-04 doi:10.1101/830380 Cold Spring Harbor Laboratory Press 2019-11-04 <![CDATA[ Metastatic function of METTL18 in breast cancer via actin methylation and Src ]]> https://biorxiv.org/content/10.1101/831701v1?rss=1 Kim, H. G. Kim, J. H. Yang, W. S. Park, J. G. Lee, Y. G. Kim, E. Hong, Y. H. Jo, M. Lee, C. Y. Kim, S. H. Sung, N. Y. Yi, Y.-S. Ratan, Z. A. Kim, S. Yoo, B. C. Kang, S.-U. Kim, Y. B. Kim, S. Paik, H.-J. Lee, J. E. Nam, S. J. Parameswaran, N. Han, J.-W. Cho, J. Y. 2019-11-05 doi:10.1101/831701 Cold Spring Harbor Laboratory Press 2019-11-05 <![CDATA[ Shared anomalies in cortical reading networks in Chinese and French dyslexic children ]]> https://biorxiv.org/content/10.1101/834945v1?rss=1 Feng, X. Altarelli, I. Monzalvo, K. Ding, G. Ramus, F. Shu, H. Dehaene, S. Meng, X. Dehaene-Lambertz, G. 2019-11-08 doi:10.1101/834945 Cold Spring Harbor Laboratory Press 2019-11-08 <![CDATA[ A generalizable multivariate brain pattern for interpersonal guilt ]]> https://biorxiv.org/content/10.1101/835520v1?rss=1 Yu, H. Koban, L. Chang, L. J. Wagner, U. Krishnan, A. Vuilleumier, P. Zhou, X. Wager, T. 2019-11-09 doi:10.1101/835520 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Prediction of liquid-liquid phase separation proteins using machine learning ]]> https://biorxiv.org/content/10.1101/842336v1?rss=1 Sun, T. Li, Q. Xu, Y. Zhang, Z. Lai, L. Pei, J. 2019-11-15 doi:10.1101/842336 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ RNA Sequencing by Direct Tagmentation of RNA/DNA Hybrids ]]> https://biorxiv.org/content/10.1101/843474v1?rss=1 Di, L. Fu, Y. Sun, Y. Li, J. Liu, L. Yao, J. Wang, G. Wu, Y. Lao, K. Lee, R. W. Zheng, G. Xu, J. Oh, J. Wang, D. Xie, X. S. Huang, Y. Wang, J. 2019-11-15 doi:10.1101/843474 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ MyD88-Syk axis is a critical determinant for inflammatory response in macrophages ]]> https://biorxiv.org/content/10.1101/844076v1?rss=1 Yi, Y.-S. Kim, J. H. Yang, W. S. Kim, E. Jeong, D. Park, J. G. Aziz, N. Kim, S. Parameswaran, N. Cho, J. Y. 2019-11-15 doi:10.1101/844076 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Structure based analysis of protein cluster size for super-resolution microscopy in the nervous system ]]> https://biorxiv.org/content/10.1101/845107v1?rss=1 Wong, C.-E. Lee, C.-C. Tsai, K.-J. 2019-11-16 doi:10.1101/845107 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ A genetic map of the response to DNA damage in human cells ]]> https://biorxiv.org/content/10.1101/845446v1?rss=1 Olivieri, M. Cho, T. Alvarez-Quilon, A. Li, K. Schellenberg, M. J. Zimmermann, M. Hustedt, N. Rossi, S. E. Adam, S. Melo, H. Heijink, A. M. Sastre-Moreno, G. Moatti, N. Szilard, R. McEwan, A. Ling, A. K. Serrano-Benitez, A. Ubhi, T. Delgado-Sainz, I. Ferguson, M. W. Brown, G. W. Cortes-Ledesma, F. Williams, R. S. Martin, A. Xu, D. Durocher, D. 2019-11-18 doi:10.1101/845446 Cold Spring Harbor Laboratory Press 2019-11-18 <![CDATA[ Tuning cell motility via cell tension with a mechanochemical cell migration model ]]> https://biorxiv.org/content/10.1101/847046v1?rss=1 Tao, K. Wang, J. Kuang, X. Wang, W. Liu, F. Zhang, L. 2019-11-19 doi:10.1101/847046 Cold Spring Harbor Laboratory Press 2019-11-19 <![CDATA[ NLRP7 Plays A Functional Role in Regulating BMP4 Signaling During Differentiation of Patient-Derived Trophoblasts ]]> https://biorxiv.org/content/10.1101/850420v1?rss=1 Garipcan, A. Ozcimen, B. Suder, I. Ulker, V. Onder, T. T. Ozoren, N. 2019-11-24 doi:10.1101/850420 Cold Spring Harbor Laboratory Press 2019-11-24 <![CDATA[ Proprioception is subject-specific and improved without performance feedback ]]> https://biorxiv.org/content/10.1101/850727v1?rss=1 Wang, T. Zhu, Z. Inoue, K. Yu, Y. He, H. Wei, K. 2019-11-21 doi:10.1101/850727 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Push-to-open: The Gating Mechanism of the Tethered Mechanosensitive Ion Channel NompC ]]> https://biorxiv.org/content/10.1101/853721v1?rss=1 Wang, Y. Guo, Y. Liu, C. Wang, L. Zhang, A. Yan, Z. Song, C. 2019-11-24 doi:10.1101/853721 Cold Spring Harbor Laboratory Press 2019-11-24 <![CDATA[ Pathogenicity of urinary tract infection Escherichia coli in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/858910v1?rss=1 Hashimoto, M. Ma, Y.-F. Wang, S.-T. Chen, C.-S. Teng, C.-H. 2019-11-28 doi:10.1101/858910 Cold Spring Harbor Laboratory Press 2019-11-28 <![CDATA[ An optimized acetylcholine sensor for monitoring in vivo cholinergic activity ]]> https://biorxiv.org/content/10.1101/861690v1?rss=1 jing, m. Li, Y. Zeng, J. Huang, P. Skirzewski, M. Peng, W. Qian, T. Tan, K. Wu, R. Zhang, S. Pan, S. Xu, M. Li, H. Saksida, L. M. Prado, V. F. Bussey, T. Prado, M. A. M. Chen, L. Cheng, H. Li, Y. 2019-12-02 doi:10.1101/861690 Cold Spring Harbor Laboratory Press 2019-12-02 <![CDATA[ Elucidation of the determinant for orchestration of solo unisexual cycle in an important human fungal pathogen ]]> https://biorxiv.org/content/10.1101/867408v1?rss=1 Hu, P. Liu, H. Chen, L. He, G.-J. Tian, X. Yao, X. Zhao, T. Li, C. Tao, C. Yang, E. Wang, L. 2019-12-08 doi:10.1101/867408 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ The dynamic transmission of positional information in stau- mutants during Drosophila embryogenesis ]]> https://biorxiv.org/content/10.1101/868711v1?rss=1 Yang, Z. Zhu, H. Kong, K. Chen, J. Wu, X. Li, P. Jiang, J. Zhao, J. Liu, F. 2019-12-08 doi:10.1101/868711 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ Quantitative assessment of bovine serum albumin proteins for blocking applications ]]> https://biorxiv.org/content/10.1101/869677v1?rss=1 Ma, G. J. Ferhan, A. R. Jackman, J. A. Cho, N.-J. 2019-12-09 doi:10.1101/869677 Cold Spring Harbor Laboratory Press 2019-12-09 <![CDATA[ Parkinson's disease associated mutation E46K of α-synuclein triggers the formation of a novel fibril structure ]]> https://biorxiv.org/content/10.1101/870758v1?rss=1 Liu, C. Li, X. Zhao, K. Li, Y. Liu, Z. Long, H. Zhao, C. Luo, F. Sun, Y. Tao, Y. Su, X.-d. Li, D. 2019-12-10 doi:10.1101/870758 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Astrocytic mechanism of glutamate modulation underlying synchronous bursting in cortical cultures ]]> https://biorxiv.org/content/10.1101/870915v1?rss=1 Kumar, R. Huang, Y.-T. Chen, C.-C. Tzeng, S.-F. Chan, C.-K. 2019-12-11 doi:10.1101/870915 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ Autoimmunity associated allele of tyrosine phosphatase gene PTPN22 enhances anti-viral immunity ]]> https://biorxiv.org/content/10.1101/2023.06.28.546768v1?rss=1 T allele of the tyrosine phosphatase PTPN22 is present in 5-10% of the North American population and is strongly associated with numerous autoimmune diseases. Although research has been done to define how this allele potentiates autoimmunity, the influence PTPN22 and its pro-autoimmune allele has in anti-viral immunity remains poorly defined. Here, we use single cell RNA- sequencing and functional studies to interrogate the impact of this pro- autoimmune allele on anti-viral immunity during Lymphocytic Choriomeningitis Virus clone 13 (LCMV-cl13) infection. Mice homozygous for this allele (PEP- 619WW) clear the LCMV-cl13 virus whereas wildtype (PEP-WT) mice cannot. This is associated with enhanced anti-viral CD4 T cell responses and a more immunostimulatory CD8- cDC phenotype. Adoptive transfer studies demonstrated that PEP-619WW enhanced anti-viral CD4 T cell function through virus-specific CD4 T cell intrinsic and extrinsic mechanisms. Taken together, our data show that the pro-autoimmune allele of Ptpn22 drives a beneficial anti-viral immune response thereby preventing what is normally a chronic virus infection. Author SummaryPTPN22 and its alternative allele, 1858C>T, has largely been studied in the context of autoimmunity. Through these studies, researchers defined roles for PTPN22 in regulating T lymphocyte activation, myeloid cell cytokine production, and macrophage polarization. Despite these immune pathways being critical for anti-viral immunity, little work has studied how this allele impacts virus infection. In this study, we examine gene expression and function of immune cell subsets to demonstrate how a common allelic variant of PTPN22, which strongly increases the risk of autoimmune disease, promotes successful clearance of an otherwise chronic viral infection. ]]> Orozco, R. C. Marquardt, K. Pratumchai, I. Mowen, K. Domissy, A. Teijaro, J. R. Sherman, L. A. 2023-06-30 doi:10.1101/2023.06.28.546768 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication ]]> https://biorxiv.org/content/10.1101/2023.06.29.546885v1?rss=1 Yang, Z. Johnson, B. A. Meliopoulos, V. A. Ju, X. Zhang, P. Hughes, M. P. Wu, J. Koreski, K. P. Chang, T.-C. Wu, G. Hixon, J. Duffner, J. Wong, K. Lemieux, R. Lokugamage, K. G. Alvardo, R. E. Crocquet-Valdes, P. A. Walker, D. H. Plante, K. S. Plante, J. A. Weaver, S. C. Kim, H. J. Meyers, R. Schultz-Cherry, S. Ding, Q. Menachery, V. D. Taylor, J. P. 2023-06-30 doi:10.1101/2023.06.29.546885 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ MicroRNA-122-mediated liver detargeting enhances the tissue specificity of cardiac genome editing ]]> https://biorxiv.org/content/10.1101/2023.06.29.546982v1?rss=1 Yang, L. Guo, C. Liu, Z. Chen, Z. Sun, Y. Hu, X. Zheng, Y. Li, Y. Gao, F. Zhou, P. Pu, W. T. Guo, Y. 2023-06-30 doi:10.1101/2023.06.29.546982 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Shape-changing electrode array for minimally invasive large-scale intracranial brain activity mapping ]]> https://biorxiv.org/content/10.1101/2023.06.29.547140v1?rss=1 Wei, S. Jiang, A. Sun, H. Zhu, J. Liu, X. Xu, Z. Zhang, J. Jia, S. Shang, Y. Fu, X. Li, G. Wang, P. Xia, Z. Jiang, T. Cao, A. Duan, X. 2023-07-02 doi:10.1101/2023.06.29.547140 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Identifying distinct neural features between the initial and corrective phases of precise reaching using AutoLFADS ]]> https://biorxiv.org/content/10.1101/2023.06.30.547252v1?rss=1 Lee, W.-H. Karpowicz, B. M. Pandarinath, C. Rouse, A. G. 2023-07-02 doi:10.1101/2023.06.30.547252 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Grapevine bacterial communities across the Central Valley of California ]]> https://biorxiv.org/content/10.1101/2023.07.01.547327v1?rss=1 Swift, J. F. Migicovsky, Z. Trello, G. E. Miller, A. J. 2023-07-02 doi:10.1101/2023.07.01.547327 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Structural and Biological Evaluations of a Non-Nucleoside STING Agonist Specific for Human STING-A230 Variants ]]> https://biorxiv.org/content/10.1101/2023.07.02.547363v1?rss=1 Tang, Z. Zhao, J. Li, Y. Tomer, S. Selvaraju, M. Tien, N. Sun, D. Johnson, D. K. Zhen, A. Li, P. Wang, J. 2023-07-02 doi:10.1101/2023.07.02.547363 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Initial and corrective submovement encoding differences within primary motor cortex during precision reaching ]]> https://biorxiv.org/content/10.1101/2023.07.01.547340v1?rss=1 Schwartze, K. Lee, W.-H. Rouse, A. G. 2023-07-03 doi:10.1101/2023.07.01.547340 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ A simplified femtosecond laser repetition frequency divider for two-photon imaging ]]> https://biorxiv.org/content/10.1101/2023.07.02.547378v1?rss=1 2-fold increase in fluorescence intensity and a [~]3 dB improvement in signal-to-noise ratio (SNR) for both green (GCaMP5G) and red (mScarlet) indicators. This enhancement proved particularly pronounced in deep-tissue imaging. Furthermore, the system demonstrated excellent long-term stability and induced no detectable phototoxicity. This simple and robust device represents a powerful upgrade for conventional two-photon microscopes, significantly enhancing imaging quality for the investigation of neural circuits within scattering brain tissue. ]]> Tang, S. 2023-07-03 doi:10.1101/2023.07.02.547378 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ ColabDock: inverting AlphaFold structure prediction model for protein-protein docking with experimental restraints ]]> https://biorxiv.org/content/10.1101/2023.07.04.547599v1?rss=1 Feng, S. Chen, Z. Zhang, C. Xie, Y. Ovchinnikov, S. Gao, Y. Q. Liu, S. 2023-07-04 doi:10.1101/2023.07.04.547599 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ A Cerebellar Population Coding Model for Sensorimotor Learning ]]> https://biorxiv.org/content/10.1101/2023.07.04.547720v1?rss=1 Wang, T. Ivry, R. B. 2023-07-04 doi:10.1101/2023.07.04.547720 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ Robust prediction of patient outcomes with immune checkpoint blockade therapy for cancer using common clinical, pathologic, and genomic features ]]> https://biorxiv.org/content/10.1101/2023.07.04.547697v1?rss=1 Chang, T.-G. Cao, Y. Sfreddo, H. Dhruba, S. R. Lee, S.-H. Valero, C. Yoo, S.-K. Chowell, D. Morris, L. G. T. Ruppin, E. 2023-07-05 doi:10.1101/2023.07.04.547697 Cold Spring Harbor Laboratory Press 2023-07-05 <![CDATA[ DeepCristae, a CNN for the restoration of mitochondria cristae in live microscopy images ]]> https://biorxiv.org/content/10.1101/2023.07.05.547594v1?rss=1 Papereux, S. Leconte, L. Valades-Cruz, C. A. Liu, T. Dumont, J. Chen, Z. Salamero, J. Kervrann, C. Badoual, A. 2023-07-05 doi:10.1101/2023.07.05.547594 Cold Spring Harbor Laboratory Press 2023-07-05 <![CDATA[ In vitro reconstitution of the M.tb proteasome core particle reveals conserved aspects of bacterial proteasome assembly ]]> https://biorxiv.org/content/10.1101/2023.07.05.547829v1?rss=1 Kante, A. Roelofs, J. Deeds, E. J. 2023-07-05 doi:10.1101/2023.07.05.547829 Cold Spring Harbor Laboratory Press 2023-07-05 <![CDATA[ Interindividual differences in pain can be explained by fMRI, sociodemographic, and psychological factors ]]> https://biorxiv.org/content/10.1101/2023.07.06.547919v1?rss=1 Gim, S. Lee, D. H. Lee, S. Woo, C.-W. 2023-07-10 doi:10.1101/2023.07.06.547919 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ Effects of aluminum-salt, CpG and emulsion adjuvants on the stability and immunogenicity of a virus-like particle displaying the SARS-CoV-2 receptor binding domain (RBD) ]]> https://biorxiv.org/content/10.1101/2023.07.10.548406v1?rss=1 Kumru, O. S. Bajoria, S. Kaur, K. Hickey, J. M. Van Slyke, G. Doering, J. Berman, K. Richardson, C. Lien, H. Kleanthous, H. Mantis, N. J. Joshi, S. B. Volkin, D. B. 2023-07-11 doi:10.1101/2023.07.10.548406 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Gene expression variation underlying tissue-specific response to copper stress in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2023.07.12.548746v1?rss=1 Everman, E. R. Macdonald, S. J. 2023-07-12 doi:10.1101/2023.07.12.548746 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ TW68, Cryptochromes stabilizer, regulates fasting blood glucose level in ob/ob and fat-induced diabetic mice ]]> https://biorxiv.org/content/10.1101/2023.07.13.548861v1?rss=1 Surme, S. Ergun, C. Gul, S. Akyel, Y. K. Gul, Z. M. Ozcan, O. Savglug Ipek, O. Akarlar, B. A. Ozlu, N. Taskin, A. C. Turkay, M. Goren, A. C. Baris, I. Ozturk, N. Guzel, M. Aydin, C. Okyar, A. Kavakli, I. H. 2023-07-13 doi:10.1101/2023.07.13.548861 Cold Spring Harbor Laboratory Press 2023-07-13 <![CDATA[ Unveiling Hidden Connections in Omics Data via pyPARAGON: an Integrative Hybrid Approach for Disease Network Construction ]]> https://biorxiv.org/content/10.1101/2023.07.13.547583v1?rss=1 Arici, K. M. Tuncbag, N. 2023-07-15 doi:10.1101/2023.07.13.547583 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ A Recurrent Neural Circuit Mechanism of Temporal-scaling Equivariant Representation ]]> https://biorxiv.org/content/10.1101/2023.07.13.548946v1?rss=1 Zuo, J. Liu, X. Wu, Y. WU, S. Zhang, W.-H. 2023-07-15 doi:10.1101/2023.07.13.548946 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ Crystal Structure of 4-Hydroxybutyryl-CoA Synthetase (ADP-forming): A Key Enzyme in the Thaumarchaeal Hydroxypropionate/Hydroxybutyrate cycle ]]> https://biorxiv.org/content/10.1101/2023.07.14.549078v1?rss=1 Johnson, J. A. Tolar, B. B. Tosun, B. Yoshikuni, Y. Francis, C. A. Wakatsuki, S. Demirci, H. 2023-07-15 doi:10.1101/2023.07.14.549078 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ New germline Cas9 promoters show improved performance for homing gene drive ]]> https://biorxiv.org/content/10.1101/2023.07.16.549205v1?rss=1 Du, J. Chen, W. Jia, X. Xu, X. Yang, E. Zhou, R. Zhang, Y. Metzloff, M. Messer, P. W. Champer, J. 2023-07-16 doi:10.1101/2023.07.16.549205 Cold Spring Harbor Laboratory Press 2023-07-16 <![CDATA[ Population suppression by release of insects carrying a dominant sterile homing gene drive targeting doublesex in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.07.17.549342v1?rss=1 Chen, W. Guo, J. Liu, Y. Champer, J. 2023-07-17 doi:10.1101/2023.07.17.549342 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ Selectivity-specialized feedback connections mediate the interaction of distinct neural processes during flexible decision-making ]]> https://biorxiv.org/content/10.1101/2023.07.15.549136v1?rss=1 Zhou, Y. Wu, X. 2023-07-18 doi:10.1101/2023.07.15.549136 Cold Spring Harbor Laboratory Press 2023-07-18 <![CDATA[ Non-cell autonomous cardiomyocyte regulation complicates gene supplementation therapy for LMNA cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2023.07.18.549413v1?rss=1 View larger version (42K): org.highwire.dtl.DTLVardef@37cfdaorg.highwire.dtl.DTLVardef@2f2cd1org.highwire.dtl.DTLVardef@1278d08org.highwire.dtl.DTLVardef@19c4869_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sun, Y. Guo, C. Chen, Z. Lin, J. Yang, L. Zhang, Y. Wu, C. Zhao, D. Jardin, B. Pu, W. Zhao, M. Dong, E. Hu, X. Zhang, S. Guo, Y. 2023-07-18 doi:10.1101/2023.07.18.549413 Cold Spring Harbor Laboratory Press 2023-07-18 <![CDATA[ T2T-YAO: a Telomere-to-telomere Assembled Diploid Reference Genome for Han Chinese ]]> https://biorxiv.org/content/10.1101/2023.07.17.549286v1?rss=1 He, Y. Chu, Y. Guo, S. Hu, J. Li, R. Zheng, Y. Ma, X. Du, Z. Zhao, L. Yu, W. Xue, J. Bian, W. Yang, F. Chen, X. Zhang, P. Wu, R. Ma, Y. Shao, C. Chen, J. Wang, J. Li, J. Wu, J. Hu, X. Long, Q. Jiang, M. Ye, H. Song, S. Li, G. Wei, Y. Xu, Y. Ma, Y. Chen, Y. Wang, K. Bao, J. Xi, W. Wang, F. Ni, W. Zhang, M. Yu, Y. Li, S. Kang, Y. Gao, Z. 2023-07-19 doi:10.1101/2023.07.17.549286 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Use of Large Language Models to Aid Analysis of Textual Data ]]> https://biorxiv.org/content/10.1101/2023.07.17.549361v1?rss=1 Tai, R. H. Bentley, L. R. Xia, X. Sitt, J. M. Fankhauser, S. C. Chicas-Mosier, A. M. Monteith, B. G. 2023-07-19 doi:10.1101/2023.07.17.549361 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Epigenetic Age Acceleration in Surviving versus Deceased COVID-19 Patients with Acute Respiratory Distress Syndrome following Hospitalization ]]> https://biorxiv.org/content/10.1101/2023.07.18.549478v1?rss=1 Bejaoui, Y. Humaira Amanullah, F. Saad, M. Taleb, S. Bradic, M. Megarbane, A. Ait Hssain, A. Abi Khalil, C. El Hajj, N. 2023-07-19 doi:10.1101/2023.07.18.549478 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Shared structure facilitates working memory of multiple sequences via neural replay ]]> https://biorxiv.org/content/10.1101/2023.07.18.549616v1?rss=1 Huang, Q. Luo, H. 2023-07-19 doi:10.1101/2023.07.18.549616 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Response Surface Methodology-Based High-Throughput BioLector Fermentation Screening of Rosetta-2 for Enhanced Production of Insulin Variant: Towards Improved Production Efficiency ]]> https://biorxiv.org/content/10.1101/2023.07.19.549622v1?rss=1 Ayan, E. Aytekin, A. O. Kati, A. Demirci, H. 2023-07-19 doi:10.1101/2023.07.19.549622 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Genome editing induces the transfer of mitochondrial DNA into the nuclear genome ]]> https://biorxiv.org/content/10.1101/2023.07.19.549443v1?rss=1 Wu, J. Liu, Y. Ou, L. Gan, T. Zhangding, Z. Yuan, S. Liu, M. Liu, X. Li, J. Yin, J. Xin, C. Tian, Y. Hu, J. 2023-07-20 doi:10.1101/2023.07.19.549443 Cold Spring Harbor Laboratory Press 2023-07-20 <![CDATA[ Exposure to early life stress impairs weight loss maintenance success in mice. ]]> https://biorxiv.org/content/10.1101/2023.07.19.549724v1?rss=1 Foright, R. M. McQuillan, T. E. Frick, J. M. Minchella, P. M. Levasseur, B. M. Tinoco, O. Birmingham, L. Lewis, A. E. Thyfault, J. P. Christianson, J. A. 2023-07-20 doi:10.1101/2023.07.19.549724 Cold Spring Harbor Laboratory Press 2023-07-20 <![CDATA[ Replication stress inducing ELF3 upregulation promotes BRCA1-deficient breast tumorigenesis in luminal progenitors ]]> https://biorxiv.org/content/10.1101/2023.07.20.549893v1?rss=1 Zhou, J. Zhou, X. A. Hu, L. Ma, Y. Zhan, J. Xu, Z. Zhou, M. Shen, Q. Xie, Y. Wang, J. 2023-07-20 doi:10.1101/2023.07.20.549893 Cold Spring Harbor Laboratory Press 2023-07-20 <![CDATA[ Genetic characterization and dissemination of Staphylococcus aureus and Staphylococci genus: food and health perspective ]]> https://biorxiv.org/content/10.1101/2023.07.24.550257v1?rss=1 M Alkuraythi, D. M. Alkhulaifi, M. Z. Binjomah, A. Alarawi, M. M Aldakhil, H. I. Mujallad, M. Ali Alharbi, S. Alshomrani, M. Mastour Alshahrani, S. Gojobori, T. Alajel, S. M. 2023-07-24 doi:10.1101/2023.07.24.550257 Cold Spring Harbor Laboratory Press 2023-07-24 <![CDATA[ The Role of the Tyrosine-Based Sorting Signals of the ORF3a Protein of SARS-CoV-2 on Intracellular Trafficking, Autophagy, and Apoptosis ]]> https://biorxiv.org/content/10.1101/2023.07.24.550379v1?rss=1 Stephens, E. B. Henke, W. Kalamvoki, M. 2023-07-24 doi:10.1101/2023.07.24.550379 Cold Spring Harbor Laboratory Press 2023-07-24 <![CDATA[ Prominent contributions of selective neuronal subtypes to pediatric drug-resistant focal dysplasia ]]> https://biorxiv.org/content/10.1101/2023.07.21.549980v1?rss=1 Zhang, Y. Li, L. Zhu, F. Zhang, X. Xia, D. Zhong, C. Liang, S. Cao, D. Zou, H. Duan, J. Shu, Y. Yao, Y. Song, J. Hu, S. Liao, J. Zhou, Q. 2023-07-25 doi:10.1101/2023.07.21.549980 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Label-free differentiation of functional zones in mature mouse placenta using micro-Raman imaging ]]> https://biorxiv.org/content/10.1101/2023.07.21.550049v1?rss=1 Inanc, A. Bektas, N. I. Kecoglu, I. Parlatan, U. Durkut, B. Ucak, M. Unlu, M. B. Celik-Ozenci, C. 2023-07-25 doi:10.1101/2023.07.21.550049 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ O-GlcNAcylation of Keratin 18 coordinates TCA cycle to promote cholangiocarcinoma progression ]]> https://biorxiv.org/content/10.1101/2023.07.23.550247v1?rss=1 Xie, R. Liu, J. Wang, L. Meng, X. Zhou, Y. Xu, L. Wang, C. Tian, X. Zhang, X. Hao, Y. Cheng, B. 2023-07-25 doi:10.1101/2023.07.23.550247 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ A Versatile Tool for Precise Variant Calling in Mycobacterium tuberculosis Genetic Polymorphisms ]]> https://biorxiv.org/content/10.1101/2023.07.24.550283v1?rss=1 Abdul Razzak, S. Hasan, Z. Azim, M. K. Kanji, A. Hasan, R. Shakoor, S. 2023-07-26 doi:10.1101/2023.07.24.550283 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Structural Coverage of the Human Interactome ]]> https://biorxiv.org/content/10.1101/2023.07.24.550328v1?rss=1 Kosoglu, K. Aydin, Z. Keskin, O. Tuncbag, N. Gursoy, A. 2023-07-26 doi:10.1101/2023.07.24.550328 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Lipidomic analysis reveals differences in the extent of remyelination in the brain and spinal cord ]]> https://biorxiv.org/content/10.1101/2023.07.24.550351v1?rss=1 Mohotti, N. D. S. Kobayashi, H. Williams, J. M. Binjawadagi, R. Evertsen, M. P. Christ, E. G. Hartley, M. D. 2023-07-26 doi:10.1101/2023.07.24.550351 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Kremen1 regulates the regenerative capacity of support cells and mechanosensory hair cells in the zebrafish lateral line ]]> https://biorxiv.org/content/10.1101/2023.07.27.550825v1?rss=1 Megerson, E. Kuehn, M. Leifer, B. Bell, J. McGraw, H. F. 2023-07-28 doi:10.1101/2023.07.27.550825 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Directly selecting differentially expressed genes for single-cell clustering analyses ]]> https://biorxiv.org/content/10.1101/2023.07.26.550670v1?rss=1 Chen, Z. Wang, C. Huang, S. Shi, Y. Xi, R. 2023-07-29 doi:10.1101/2023.07.26.550670 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ Conserved long noncoding RNA TILAM promotes liver fibrosis through interaction with PML in hepatic stellate cells ]]> https://biorxiv.org/content/10.1101/2023.07.29.551032v1?rss=1 Sun, C. Zhou, C. Daneshvar, K. Kratkiewicz, A. J. Ben Saad, A. Hess, A. Chen, J. Y. Pondick, J. V. York, S. R. Li, W. Moran, S. P. Gentile, S. Ur Rahman, R. Li, Z. Sparks, R. Habboub, T. Kim, B.-M. Choi, M. Affo, S. Schwabe, R. F. Popov, Y. V. Mullen, A. C. 2023-07-30 doi:10.1101/2023.07.29.551032 Cold Spring Harbor Laboratory Press 2023-07-30 <![CDATA[ CONDITIONALLY MUTANT ANIMAL MODEL FOR INVESTIGATING THE INVASIVE TROPHOBLAST CELL LINEAGE ]]> https://biorxiv.org/content/10.1101/2023.08.02.551740v1?rss=1 Iqbal, K. Nixon, B. Crnkovich, B. Dominguez, E. M. Moreno Irusta, A. Scott, R. L. vu, h. Tuteja, G. Vivian, J. L. Soares, M. 2023-08-05 doi:10.1101/2023.08.02.551740 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ Conformational diversity and protein-protein interfaces in drug repurposing in Ras signaling pathway ]]> https://biorxiv.org/content/10.1101/2023.08.03.551801v1?rss=1 Keskin, O. Gursoy, A. Sayin, A. Z. 2023-08-06 doi:10.1101/2023.08.03.551801 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ Functional dissection of KATP channel structures reveals the importance of a conserved interface ]]> https://biorxiv.org/content/10.1101/2023.08.03.551891v1?rss=1 Yang, Y. Chen, L. 2023-08-06 doi:10.1101/2023.08.03.551891 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ Revealing Shared Proteins and Pathways in Cardiovascular and Cognitive Diseases Using Protein Interaction Network Analysis ]]> https://biorxiv.org/content/10.1101/2023.08.03.551914v1?rss=1 Zeylan, M. E. Senyuz, S. Picon-Pages, P. Garcia-Elias, A. Tajes, M. Munoz, F. Oliva, B. Garcia-Ojalvo, J. Barbu, E. Vicente, R. Nattel, S. Ois-Santiago, A. Puig-Pijoan, A. Keskin, O. Gursoy, A. 2023-08-06 doi:10.1101/2023.08.03.551914 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ CD4+ T cell senescence is associated with reduced reactogenicity in severe/critical COVID-19 ]]> https://biorxiv.org/content/10.1101/2023.08.04.551565v1?rss=1 19.78%) showed a decreased survival rate as compared to those with a lower level (<19.78%), especially in the breakthrough infection. The percentage of CD4+ Tsens was negatively correlated with spike-specific antibody titers, neutralization ability and COVID-19 reactive IL-2+ CD4+ T cells. Additionally, IL-2 producing T cells and plasma levels of IL-2 were positively correlated with antibody levels. ConclusionOur data illustrated that the percentage of CD4+ Tsens in the peripheral blood could act as an efficient biomarker for the capacity of spike-specific antibody production and the prognosis of severe COVID-19, especially in the breakthrough infection. Therefore, restoration of the immune response of CD4+ Tsens is one of the key factors to prevent severe illness and improve vaccine efficacy in older adults. ]]> Zhang, J. Chang, C. Liang, Z. Hu, T. Yin, Z. Liang, Y. Zhang, T. Ding, Y. Li, X. Gai, X. Yang, X. Li, X. Dong, X. Ren, J. Rao, Y. Wang, J. Yang, J. Sun, Y. Xue, L. 2023-08-07 doi:10.1101/2023.08.04.551565 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Characterization of m6A modifiers and RNA modifications in uterine fibroids ]]> https://biorxiv.org/content/10.1101/2023.08.07.552278v1?rss=1 George, J. W. Cancino, R. Miller, J. L. G. Qiu, F. Lin, Q. Rowley, J. Chennathukuzhi, V. Davis, J. S. 2023-08-07 doi:10.1101/2023.08.07.552278 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Unilateral ephaptic program underlying sweetness dominance ]]> https://biorxiv.org/content/10.1101/2023.08.04.551918v1?rss=1 Lee, M. Kim, S. Y. Park, T. Joo, K. M. Kwon, J. Y. Kim, K. Kang, K. 2023-08-08 doi:10.1101/2023.08.04.551918 Cold Spring Harbor Laboratory Press 2023-08-08 <![CDATA[ Climatic and biogeographic processes underlying the diversification of the pantropical and early divergent angiosperm family Annonaceae ]]> https://biorxiv.org/content/10.1101/2023.08.08.549183v1?rss=1 Li, W. Wang, R. Liu, M.-F. Folk, R. A. Xue, B. Saunders, R. M. K. 2023-08-09 doi:10.1101/2023.08.08.549183 Cold Spring Harbor Laboratory Press 2023-08-09 <![CDATA[ Ubiquitin phosphorylation accelerates protein aggregation and promotes neurodegeneration in the aging brain ]]> https://biorxiv.org/content/10.1101/2023.08.10.552882v1?rss=1 Chen, C. Yi, H.-W. Zhang, Y. Wang, T. Gao, T.-Y. Lou, Z.-L. Wei, T.-F. Lu, Y.-B. Li, T.-T. Zhang, W.-P. Tang, C. 2023-08-12 doi:10.1101/2023.08.10.552882 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ DiPPI: A curated dataset for drug-like molecules in protein-protein interfaces ]]> https://biorxiv.org/content/10.1101/2023.08.09.552637v1?rss=1 Cankara, F. Senyuz, S. Sayin, A. Z. Gursoy, A. Keskin, O. 2023-08-14 doi:10.1101/2023.08.09.552637 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Exploiting Epigenetic Targets to Overcome Taxane Resistance in Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2023.08.10.552560v1?rss=1 Cevatemre, B. Bulut, I. Dedeoglu, B. Isiklar, A. Syed, H. Yedier Bayram, O. Bagci-Onder, T. Acilan Ayhan, C. 2023-08-14 doi:10.1101/2023.08.10.552560 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ weIMPUTE: A User-Friendly Web-Based Genotype Imputation Platform ]]> https://biorxiv.org/content/10.1101/2023.08.10.552759v1?rss=1 Tang, Y. Li, M. L. Li, Z. Li, Q. Hu, X. D. Yu, J. Lin, J. Bi, C. G. Yu, H. L. Huang, M. 2023-08-14 doi:10.1101/2023.08.10.552759 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Adipose contributes to CXCL5 regulated immune evasion in pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2023.08.15.553432v1?rss=1 Walsh, R. M. Ambrose, J. Messaggio, F. Bye, B. Eades, A. Jack, J. Ruckert, M. Olou, A. Chalise, P. Pei, D. VanSaun, M. 2023-08-16 doi:10.1101/2023.08.15.553432 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ Combined PI3K and MAPK inhibition synergizes to suppress PDAC ]]> https://biorxiv.org/content/10.1101/2023.08.15.553438v1?rss=1 Bye, B. Jack, J. Pierce, A. Walsh, R. M. Eades, A. Olou, A. Chalise, P. VanSaun, M. 2023-08-17 doi:10.1101/2023.08.15.553438 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Glucose intolerance induces anxiety-like behaviors independent of obesity and insulin resistance in a novel model of nutritional metabolic stress ]]> https://biorxiv.org/content/10.1101/2023.08.17.553760v1?rss=1 Al-Onaizi, M. Braysh, K. Alkefeef, S. Altarrah, D. Dannoon, S. Alasousi, D. Adel, H. Al-Ajmi, M. Kandari, A. Najem, R. Nizam, R. Williams, M. R. John, S. Thanaraj, T. A. Ahmad, R. Al-Hussaini, H. Al-Mulla, F. Alzaid, F. 2023-08-20 doi:10.1101/2023.08.17.553760 Cold Spring Harbor Laboratory Press 2023-08-20 <![CDATA[ A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide ]]> https://biorxiv.org/content/10.1101/2023.08.18.553899v1?rss=1 Mullinax, S. R. Darby, A. M. Gupta, A. Chan, P. Smith, B. Unckless, R. 2023-08-21 doi:10.1101/2023.08.18.553899 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ The "motive cocktail" in altruistic behaviors ]]> https://biorxiv.org/content/10.1101/2023.08.20.554026v1?rss=1 Wu, X. Ren, X. Liu, C. Zhang, H. 2023-08-21 doi:10.1101/2023.08.20.554026 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Switching Go-Martini for Investigating Protein Conformational Transitions and Associated Protein-Lipid Interactions ]]> https://biorxiv.org/content/10.1101/2023.08.21.554122v1?rss=1 Yang, S. Song, C. 2023-08-22 doi:10.1101/2023.08.21.554122 Cold Spring Harbor Laboratory Press 2023-08-22 <![CDATA[ Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria ]]> https://biorxiv.org/content/10.1101/2023.08.23.554450v1?rss=1 Vargas-Gastelum, L. B. Romer, A. S. Alexander, N. R. Ghotbi, M. Moe, K. C. McPhail, K. L. Neuhaus, G. F. Shadmani, L. Spatafora, J. W. Stajich, J. E. Tabima, J. F. Walker, D. 2023-08-25 doi:10.1101/2023.08.23.554450 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ Improved dual-color GRAB sensors for monitoring dopaminergic activity in vivo ]]> https://biorxiv.org/content/10.1101/2023.08.24.554559v1?rss=1 Zhuo, Y. Luo, B. Yi, X. Dong, H. Wan, J. Cai, R. Williams, J. T. Qian, T. Campbell, M. G. Miao, X. Li, B. Wei, Y. Li, G. Wang, H. Zheng, Y. Watabe-Uchida, M. Li, Y. 2023-08-25 doi:10.1101/2023.08.24.554559 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ Phage transcriptional regulator X (PtrX)-mediated augmentation of toxin production and virulence in Clostridioides difficile strain R20291 ]]> https://biorxiv.org/content/10.1101/2023.08.24.554564v1?rss=1 Gong, J.-J. Huang, I.-H. Su, S.-W. Xie, S.-X. Liu, W.-Y. Huang, C.-R. Hung, Y. P. Wu, S.-R. Tsai, P. J. Ko, W. C. Chen, J.-W. 2023-08-25 doi:10.1101/2023.08.24.554564 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ The evolution of autonomy from two cooperative specialists in the fluctuating environments ]]> https://biorxiv.org/content/10.1101/2023.08.24.554579v1?rss=1 Chen, X. Wang, M. Luo, L. Liu, X. An, L. Nie, Y. Wu, X. 2023-08-26 doi:10.1101/2023.08.24.554579 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ Enhancing visual perceptual learning using transcranial electrical stimulation: transcranial alternating current stimulation outperforms both transcranial direct current and random noise stimulation ]]> https://biorxiv.org/content/10.1101/2023.08.24.554599v1?rss=1 He, Q. Zhu, X. Fang, F. 2023-08-26 doi:10.1101/2023.08.24.554599 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ Non-Invasive Perfusion Imaging of the Human Brain via Breath-Holding: A DSC MRI Study ]]> https://biorxiv.org/content/10.1101/2023.08.24.554712v1?rss=1 Schulman, J. B. Kashyap, S. Kim, S.-G. Uludag, K. 2023-08-26 doi:10.1101/2023.08.24.554712 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ Heroes and villains: opposing narrative roles engage neural synchronization in the lateral inferior frontal gyrus ]]> https://biorxiv.org/content/10.1101/2023.08.24.554721v1?rss=1 Ryu, H. Kim, M. J. 2023-08-26 doi:10.1101/2023.08.24.554721 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ Long-term breast cancer response to CDK4/6 inhibition defined by TP53-mediated geroconversion ]]> https://biorxiv.org/content/10.1101/2023.08.25.554716v1?rss=1 Kudo, R. Safonov, A. da Silva, E. M. Li, Q. Shao, H. Will, M. Fushimi, A. Nakshatri, H. Reis-Filho, J. S. Goel, S. Koff, A. Weigelt, B. Khan, Q. J. Razavi, P. Chandarlapaty, S. 2023-08-27 doi:10.1101/2023.08.25.554716 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ The genome of the colonial hydroid Hydractinia reveals their stem cells use a toolkit of genes shared with all animals ]]> https://biorxiv.org/content/10.1101/2023.08.25.554815v1?rss=1 Schnitzler, C. E. Chang, E. S. Waletich, J. Wong, W. Y. Nguyen, A.-D. Barreira, S. Doonan, L. Gonzalez, P. Koren, S. Gahan, J. Quiroga-Artigas, G. Sanders, S. Bradshaw, B. DuBuc, T. Febrimarsa, F. de Jong, D. Nawrocki, E. Larson, A. Klasfeld, S. Gornik, S. Moreland, R. T. Wolfsberg, T. Phillippy, A. M. Mullikin, J. Simakov, O. Cartwright, P. Nicotra, M. Frank, U. Baxevanis, A. D. 2023-08-27 doi:10.1101/2023.08.25.554815 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Structural dynamics at cytosolic inter-protomer interfaces control gating of a mammalian TRPM5 channel ]]> https://biorxiv.org/content/10.1101/2023.08.26.554973v1?rss=1 70 % of the total protein. To investigate the mechanism by which the TRPM cytoplasmic domains contribute to gating, we employed electrophysiology and cryo-EM to study TRPM5 - a channel that primarily relies on activation via intracellular Ca2+. Here we show that activation of mammalian TRPM5 channels is strongly altered by desensitization. Structures of rat TRPM5 identify a series of conformational transitions triggered by Ca2+ binding. These transitions involve formation and dissolution of cytoplasmic inter-protomer interfaces, where the MHR1/2 domain and the rib helix play important roles. This study shows the importance of the cytoplasmic assembly in TRPM5 channel function and sets the stage for future investigations of other members of the TRPM family. ]]> Karuppan, S. Schrag, L. G. Jara-Oseguera, A. Zubcevic, L. 2023-08-27 doi:10.1101/2023.08.26.554973 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Discovery of 2-amide-3-methylester thiophenes inhibiting SARS-CoV-2 ADP-ribosyl hydrolysing macrodomain and coronavirus replication ]]> https://biorxiv.org/content/10.1101/2023.08.28.555062v1?rss=1 Wazir, S. Parviainen, T. A. O. Maksimainen, M. M. Duong, M. T. H. Pfannenstiel, J. J. Cluff, D. Sowa, S. T. Galera-Prat, A. Ferraris, D. V. Fehr, A. Heiskanen, J. P. Lehtiö, L. 2023-08-29 doi:10.1101/2023.08.28.555062 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ A trade-off in controlling upstream and downstream noise in signaling networks ]]> https://biorxiv.org/content/10.1101/2023.08.29.555248v1?rss=1 Kong, K. K. Luo, C. Liu, F. 2023-08-31 doi:10.1101/2023.08.29.555248 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Human-brown bear conflicts in Turkey are driven by increased human presence around protected areas ]]> https://biorxiv.org/content/10.1101/2023.08.29.555317v1?rss=1 Sikdokur, E. Naderi, M. Celtik, E. Aytekin, M. C. K. Kusak, J. Saglam, I. K. Sekercioglu, C. H. 2023-08-31 doi:10.1101/2023.08.29.555317 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 enhances antibody evasion and ACE2 binding ]]> https://biorxiv.org/content/10.1101/2023.08.30.555211v1?rss=1 Jian, F. Yang, S. Yu, Y. Song, W. Yisimayi, A. Chen, X. Xu, Y. Wang, P. Yu, L. Wang, J. Liu, L. Niu, X. Wang, J. Xiao, T. Gu, Q. Shao, F. Jin, R. Shen, Z. Wang, Y. Cao, Y. R. 2023-08-31 doi:10.1101/2023.08.30.555211 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Enhancement of Protein Stability by Quenching Millisecond Conformational Dynamics ]]> https://biorxiv.org/content/10.1101/2023.08.30.555640v1?rss=1 Hou, X.-N. Zhao, C. Song, B. Ruan, M.-X. Dong, X. Gong, Z. Weng, X.-X. Zheng, J. Tang, C. 2023-09-01 doi:10.1101/2023.08.30.555640 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ SIDERITE: Unveiling Hidden Siderophore Diversity in the Chemical Space Through Digital Exploration ]]> https://biorxiv.org/content/10.1101/2023.08.31.555687v1?rss=1 He, R. Gu, S. Xu, J. Li, X. Chen, H. Shao, Z. Wang, H. Shao, J. Yin, W.-B. Qian, L. Wei, Z. Li, Z. 2023-09-01 doi:10.1101/2023.08.31.555687 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Timing-dependent modulation of working memory by VTA dopamine release in medial prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2023.09.01.555676v1?rss=1 Ge, C. Chen, Z. Sun, F. Hou, R. Fan, H. Li, Y. Li, C. T. 2023-09-03 doi:10.1101/2023.09.01.555676 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Regulation of an antibiotic resistance efflux pump by quorum sensing and a TetR-family repressor in Chromobacterium subtsugae ]]> https://biorxiv.org/content/10.1101/2023.09.02.556004v1?rss=1 Koirala, P. Doody, C. Blackwell, H. Chandler, J. R. 2023-09-03 doi:10.1101/2023.09.02.556004 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Antigenicity and infectivity characterization of SARS-CoV-2 BA.2.86 ]]> https://biorxiv.org/content/10.1101/2023.09.01.555815v1?rss=1 Yang, S. Yu, Y. Jian, F. Song, W. Yisimayi, A. Chen, X. Xu, Y. Wang, P. Yu, L. Wang, J. Niu, X. Wang, J. Xiao, T. An, R. Wang, Y. Gu, Q. Shao, F. Jin, R. Shen, Z. Wang, Y. Cao, Y. R. 2023-09-04 doi:10.1101/2023.09.01.555815 Cold Spring Harbor Laboratory Press 2023-09-04 <![CDATA[ Dietary road salt and monarch butterflies: minimal effects on larval growth, immunity, wing coloration, and migration to Mexico ]]> https://biorxiv.org/content/10.1101/2023.09.04.554310v1?rss=1 Hund, A. K. Mitchell, T. S. Ramirez, I. Zambre, A. Hagg, L. Stene, A. Porter, K. Carper, A. Agnew, L. Shephard, A. Kobiela, M. Oberhauser, K. Taylor, O. R. Snell-Rood, E. 2023-09-04 doi:10.1101/2023.09.04.554310 Cold Spring Harbor Laboratory Press 2023-09-04 <![CDATA[ HOXB13 alters chromatin accessibility in prostate cancer through interactions with the SWI/SNF complex ]]> https://biorxiv.org/content/10.1101/2023.09.04.556101v1?rss=1 Lingadahalli, S. Fazlioglu, B. E. Altintas, U. B. Cingoz, A. Tekoglu, E. Yu, I. P. L. Andomat, H. Kulac, I. Morova, T. Xiao, K. Dikbas, U. M. Gleave, M. Fazli, L. Cejas, P. Long, H. Cherkasov, A. Zwart, W. Collins, C. Bagci-Onder, T. Lack, N. A. 2023-09-05 doi:10.1101/2023.09.04.556101 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Characterization of Turkish Pine Honey and Differentiation from other floral honey types from Oceania, Aegean, West Coast by NMR spectroscopy and Chemometric Analysis ]]> https://biorxiv.org/content/10.1101/2023.09.05.556430v1?rss=1 Kahraman, K. Gocenler, O. Dag, C. 2023-09-05 doi:10.1101/2023.09.05.556430 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Ghost W chromosomes and unique genome architecture in ghost moths of the family Hepialidae ]]> https://biorxiv.org/content/10.1101/2023.09.03.556148v1?rss=1 Chung Volenikova, A. Sahara, K. Stundlova, J. Dalikova, M. Koutecky, P. Grof-Tisza, P. Simonsen, T. J. Zurovec, M. Provaznikova, I. Walters, J. R. Marec, F. Nguyen, P. 2023-09-06 doi:10.1101/2023.09.03.556148 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ GametesOmics: A Comprehensive Multi-Omics Database for Exploring the Gametogenesis in Humans and Mice ]]> https://biorxiv.org/content/10.1101/2023.09.05.556316v1?rss=1 An, J. Wang, J. Kong, S. Song, S. Chen, W. Yuan, P. He, Q. Chen, Y. Li, Y. Yang, Y. Wang, W. Li, R. Yan, L. Yan, Z. Qiao, J. 2023-09-06 doi:10.1101/2023.09.05.556316 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Exposure-based sequence learning induces backward replay in the human visual cortex ]]> https://biorxiv.org/content/10.1101/2023.09.07.556631v1?rss=1 He, T. Gong, X. Wang, Q. Zhu, X. Liu, Y. Fang, F. 2023-09-09 doi:10.1101/2023.09.07.556631 Cold Spring Harbor Laboratory Press 2023-09-09 <![CDATA[ Alzheimer mutations stabilize synaptotoxic γ-secretase-substrate complexes ]]> https://biorxiv.org/content/10.1101/2023.09.08.556905v1?rss=1 Devkota, S. Zhou, R. Nagarajan, V. Maesako, M. Do, H. Noorani, A. Overmeyer, C. Bhattarai, S. Douglas, J. T. Saraf, A. Miao, Y. Ackley, B. D. Shi, Y. Wolfe, M. S. 2023-09-09 doi:10.1101/2023.09.08.556905 Cold Spring Harbor Laboratory Press 2023-09-09 <![CDATA[ O-GlcNAcylation of YTHDF2 antagonizes ERK-dependent phosphorylation and inhibits lung carcinoma ]]> https://biorxiv.org/content/10.1101/2023.09.09.557012v1?rss=1 Li, J. Zhou, W. Zhang, J. Ma, L. Lv, Z. Geng, Y. Chen, X. Li, J. 2023-09-10 doi:10.1101/2023.09.09.557012 Cold Spring Harbor Laboratory Press 2023-09-10 <![CDATA[ PfMORC protein regulates chromatin accessibility and transcriptional repression in the human malaria parasite, P. falciparum. ]]> https://biorxiv.org/content/10.1101/2023.09.11.557253v1?rss=1 Chahine, Z. M. Gupta, M. Lenz, T. Hollin, T. Abel, S. Banks, C. Saraf, A. Prudhomme, J. Florens, L. Le Roch, K. G. 2023-09-11 doi:10.1101/2023.09.11.557253 Cold Spring Harbor Laboratory Press 2023-09-11 <![CDATA[ A large effect genetic trade-off is caused by a single mutation in CBF2 ]]> https://biorxiv.org/content/10.1101/2023.09.11.557195v1?rss=1 Lee, G. Sanderson, B. J. Dilkes, B. P. Agren, J. Oakley, C. G. 2023-09-12 doi:10.1101/2023.09.11.557195 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Functional connectome through the human life span ]]> https://biorxiv.org/content/10.1101/2023.09.12.557193v1?rss=1 Sun, L. Zhao, T. Liang, X. Xia, M. Li, Q. Liao, X. Gong, G. Wang, Q. Pang, C. Yu, Q. Bi, Y. Chen, P. Chen, R. Chen, Y. Chen, T. Cheng, J. Cheng, Y. Cui, Z. Dai, Z. Deng, Y. Ding, Y. Dong, Q. Duan, D. Gao, J.-H. Gong, Q. Han, Y. Han, Z. Huang, C.-C. Huang, R. Li, L. Lin, C.-P. Lin, Q. Liu, B. Liu, C. Liu, N. Liu, Y. Lu, J. Ma, L. Men, W. Qin, S. Qiu, J. Qiu, S. Si, T. Tan, S. Tang, Y. Tao, S. Wang, D. Wang, F. Wang, J. Wang, P. Wang, X. Wang, Y. Wei, D. Wu, Y. Xie, P. Xu, X. Xu, Y. Xu, Z. Yang, L. Zeng, Z. Zhang, H. Zhang, X. Zhao, G 2023-09-13 doi:10.1101/2023.09.12.557193 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Notch3 deletion regulates HIV-1 gene expression and systemic inflammation to ameliorate chronic kidney disease ]]> https://biorxiv.org/content/10.1101/2023.09.12.557484v1?rss=1 Thornton, M. Sommer, N. McGonigle, M. Ram, A. K. Yerrathota, S. Ehirim, H. Chaturvedi, A. Dinh Phan, J. Gunewardena, S. Talreja, J. Fields, T. A. Ray, P. E. Dhillon, N. K. Sharma, M. 2023-09-13 doi:10.1101/2023.09.12.557484 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ The Effect of Sunlight Intensity on Flower Opening Time and Exposure Duration in Rice (Oryza sativa ssp. indica) Landraces ]]> https://biorxiv.org/content/10.1101/2023.09.10.557080v1?rss=1 Deb, D. Dutta, S. Nauri, M. 2023-09-14 doi:10.1101/2023.09.10.557080 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ CRISPR-Cas9 Extracellular Vesicles for Treating Hearing Loss ]]> https://biorxiv.org/content/10.1101/2023.09.14.557853v1?rss=1 Pan, X. Huang, P. Ali, S. Hutchinson, T. E. Erwin, N. Greenberg, Z. F. Ding, Z. Li, Y. Fernadez, N. E. Staecker, H. He, M. 2023-09-15 doi:10.1101/2023.09.14.557853 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ A cerebellar disinhibitory circuit supports synaptic plasticity ]]> https://biorxiv.org/content/10.1101/2023.09.15.557147v1?rss=1 Park, C. Gim, J. Bahn, S. Kim, G. H. Im, Y. Lee, S.-H. Lee, K. Kim, M.-S. Lee, K. J. Kim, J. S. 2023-09-15 doi:10.1101/2023.09.15.557147 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ SACNet: A Multiscale Diffeomorphic Convolutional Registration Network with Prior Neuroanatomical Constraints for Flexible Susceptibility Artifact Correction in Echo Planar Imaging ]]> https://biorxiv.org/content/10.1101/2023.09.15.557874v1?rss=1 Zeng, Z. Zhang, J. Liang, X. Sun, L. Zhang, Y. Men, W. Wang, Y. Chen, R. Zhang, H. Tan, S. Gao, J.-H. Qin, S. Tong, Q. He, H. Tao, S. Dong, Q. He, Y. Zhao, T. 2023-09-15 doi:10.1101/2023.09.15.557874 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Cryptic splicing mediates genetic and therapeutic perturbation of human gene expression levels ]]> https://biorxiv.org/content/10.1101/2023.09.13.557588v1?rss=1 Fair, B. J. Abad, C. B. Zhao, J. Lozano, S. Reilly, A. K. Staley, J. P. Wang, J. Li, Y. I. 2023-09-16 doi:10.1101/2023.09.13.557588 Cold Spring Harbor Laboratory Press 2023-09-16 <![CDATA[ Recent secondary contact, genome-wide admixture, and limited introgression of neo-sex chromosomes between two Pacific island bird species ]]> https://biorxiv.org/content/10.1101/2023.09.13.557611v1?rss=1 Shogren, E. H. Sardell, J. M. Muirhead, C. A. Marti, E. Moyle, R. G. Presgraves, D. C. Uy, J. A. C. 2023-09-17 doi:10.1101/2023.09.13.557611 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Evaluating the Effectiveness of a Common Approach to Artifact Correction and Rejection in Event-related Potential Research ]]> https://biorxiv.org/content/10.1101/2023.09.16.558075v1?rss=1 Zhang, G. Garrett, D. R. Simmons, A. M. Kiat, J. E. Luck, S. J. 2023-09-17 doi:10.1101/2023.09.16.558075 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Unsaturated intercellular vapor pressure is relevant for leaf water heavy isotope enrichment ]]> https://biorxiv.org/content/10.1101/2023.09.12.557463v1?rss=1 Angove, C. Lehman, M. Saurer, M. Tang, Y. Kilpeläinen, P. Kahmen, A. Schiestl-Aalto, P. P. Tikkasalo, O.-P. Bäck, J. K. Rinne-Garmston, K. T. 2023-09-18 doi:10.1101/2023.09.12.557463 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ Sweetwater: an underrated crude glycerol for sustainable lipid production in non-conventional yeasts ]]> https://biorxiv.org/content/10.1101/2023.09.18.558176v1?rss=1 View larger version (42K): org.highwire.dtl.DTLVardef@1ad5738org.highwire.dtl.DTLVardef@139227eorg.highwire.dtl.DTLVardef@7a8e1org.highwire.dtl.DTLVardef@e072c6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Malika Keita, V. Lee, Y. Q. Lakshmanan, M. Ow, D. S.-W. Staniland, P. Staniland, J. Savill, I. Tee, K. L. Wong, T. S. Lee, D.-Y. 2023-09-18 doi:10.1101/2023.09.18.558176 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ ACE2-Coated Virus-Like Particles Effectively Block SARS-CoV-2 Infection ]]> https://biorxiv.org/content/10.1101/2023.09.19.558424v1?rss=1 View larger version (16K): org.highwire.dtl.DTLVardef@30ac94org.highwire.dtl.DTLVardef@1926217org.highwire.dtl.DTLVardef@165d9f0org.highwire.dtl.DTLVardef@1c737f9_HPS_FORMAT_FIGEXP M_FIG In our study, we demonstrate the prevention of SARS-CoV-2 infection through the use of Ace2-coated VLPs. C_FIG ]]> Bayraktar, C. Kayabolen, A. Odabas, A. Durgun, A. Kok, I. Sevinc, K. Supramaniam, A. Idris, A. Bagci-Onder, T. 2023-09-20 doi:10.1101/2023.09.19.558424 Cold Spring Harbor Laboratory Press 2023-09-20 <![CDATA[ Diversity and distribution of viruses inhabiting the oil reservoirs ]]> https://biorxiv.org/content/10.1101/2023.09.19.558540v1?rss=1 An, L. Liu, X. Wang, J. Xu, J. Chen, X. Liu, X. Hu, B. Nie, Y. Wu, X. 2023-09-20 doi:10.1101/2023.09.19.558540 Cold Spring Harbor Laboratory Press 2023-09-20 <![CDATA[ Comparative single-cell regulome reveals evolutionary innovations in neural progenitor cells during primate corticogenesis ]]> https://biorxiv.org/content/10.1101/2023.09.20.558575v1?rss=1 Liu, Y. Luo, X. Sun, Y. Chen, K. Hu, T. You, B. Xu, J. Zhang, F. Meng, X. Li, X. He, X. Li, C. Su, B. 2023-09-21 doi:10.1101/2023.09.20.558575 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Robust Small Molecule-Aided Cardiac Reprogramming Systems Selective to Cardiac Fibroblasts ]]> https://biorxiv.org/content/10.1101/2023.09.20.558597v1?rss=1 Tao, Y. Yang, Y. Wang, L. Yang, Z. Wang, S.-Q. Zhao, Y. 2023-09-21 doi:10.1101/2023.09.20.558597 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Enhancing Luciferase Activity and Stability through Generative Modeling of Natural Enzyme Sequences ]]> https://biorxiv.org/content/10.1101/2023.09.18.558367v1?rss=1 Xie, W. J. Liu, D. Wang, X. Zhang, A. Wei, Q. Nandi, A. Dong, S. Warshel, A. 2023-09-22 doi:10.1101/2023.09.18.558367 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ High-resolution dissection of human cell type-specific enhancers in cis and trans activities ]]> https://biorxiv.org/content/10.1101/2023.09.23.559140v1?rss=1 Wang, M. Yang, X. Wu, Q. 2023-09-24 doi:10.1101/2023.09.23.559140 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ Adaptive Functions of Structural Variants in Human Brain Development ]]> https://biorxiv.org/content/10.1101/2023.09.25.558917v1?rss=1 Ding, W. Li, X. Zhang, J. Ji, M. Zhang, M. Zhong, X. Cao, Y. Liu, X. Li, C. Xiao, C. Wang, J. Li, T. Yu, Q. Mo, F. Zhang, B. Qi, J. Yang, J.-C. Qi, J. Tian, L. Xu, X. Peng, Q. Zhou, W.-Z. Liu, Z. Fu, A. Zhang, X. Zhang, J.-j. Sun, Y. Hu, B. An, N. A. Zhang, L. Li, C.-Y. 2023-09-26 doi:10.1101/2023.09.25.558917 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Context-aware single-cell multiome approach identified cell-type specific lung cancer susceptibility genes ]]> https://biorxiv.org/content/10.1101/2023.09.25.559336v1?rss=1 Long, E. Yin, J. Shin, J. H. Li, Y. Kane, A. Patel, H. Luong, T. Xia, J. Han, Y. Byun, J. Zhang, T. Zhao, W. Landi, M. T. Rothman, N. Lan, Q. Chang, Y. S. Yu, F. Amos, C. Shi, J. Lee, J. G. Kim, E. Y. Choi, J. 2023-09-26 doi:10.1101/2023.09.25.559336 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ IRAK1 is a critical mediator of low molecular weight hyaluronic acid-induced stemness in high-grade serous ovarian cancer ]]> https://biorxiv.org/content/10.1101/2023.09.25.559366v1?rss=1 Standing, D. Dandawate, P. Gunewardena, S. Covarrubias-Zambrano, O. Roby, K. F. Khabele, D. Jewell, A. Tawfik, O. Bossmann, S. H. Godwin, A. K. Weir, S. J. Jensen, R. A. Anant, S. 2023-09-26 doi:10.1101/2023.09.25.559366 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Quinoclamine inhibits Shiga toxin production in enterohemorrhagic Escherichia coli ]]> https://biorxiv.org/content/10.1101/2023.09.26.559460v1?rss=1 Kar, O. Feng, H.-C. Hirano, H. Teng, C.-H. Osada, H. Hashimoto, M. 2023-09-26 doi:10.1101/2023.09.26.559460 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Conditional Chemoconnectomics: A Set of Libraries Targeting All Chemical Transmission Corresponding Genes Efficiently ]]> https://biorxiv.org/content/10.1101/2023.09.26.559642v1?rss=1 Mao, R. Yu, J. Deng, B. Dai, X. Du, Y. Du, S. Zhang, W. Rao, Y. 2023-09-27 doi:10.1101/2023.09.26.559642 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Identification of Host Restriction Factors Critical for Recombinant AAV Transduction of Polarized Human Airway Epithelium ]]> https://biorxiv.org/content/10.1101/2023.09.27.559795v1?rss=1 Hao, S. Zhang, X. Ning, K. Feng, Z. Park, S. Y. Kuz, C. A. McFarlin, S. Richart, D. Cheng, F. Zhang, E. Y. Zhang-Chen, A. Yan, Z. Qiu, J. 2023-09-27 doi:10.1101/2023.09.27.559795 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Molecular Dynamics Activation of γ-Secretase for Cleavage of Notch1 Substrate ]]> https://biorxiv.org/content/10.1101/2023.09.26.559539v1?rss=1 Do, H. N. Malvankar, S. R. Wolfe, M. S. Miao, Y. 2023-09-28 doi:10.1101/2023.09.26.559539 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ Variable and reversible opacification process on IOLs for cataract simulation ]]> https://biorxiv.org/content/10.1101/2023.09.27.559841v1?rss=1 Akyazı, D. Zolfaghari, P. Sahin, A. Urey, H. 2023-09-29 doi:10.1101/2023.09.27.559841 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Autosomal suppression of meiotic drive can prevent sex chromosome cycling ]]> https://biorxiv.org/content/10.1101/2023.09.28.559847v1?rss=1 Gupta, A. Unckless, R. 2023-09-29 doi:10.1101/2023.09.28.559847 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Genetic diversity of domestic cat hepadnavirus in Taiwan ]]> https://biorxiv.org/content/10.1101/2023.09.29.560097v1?rss=1 Silva, B. B. I. Chen, J.-Y. Villanueva, B. H. A. Lu, Z.-Y. Zhen, H.-H. Montecillo, A. D. Shofa, M. Minh, H. Chuang, J.-P. Huang, H.-Y. Saito, A. Chuang, K.-P. 2023-09-29 doi:10.1101/2023.09.29.560097 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ A shallow-scale phylogenomics approach reveals parallel patterns of diversification among sympatric populations of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae) ]]> https://biorxiv.org/content/10.1101/2023.09.28.559972v1?rss=1 Baca, S. M. Gustafson, G. T. DeRaad, D. A. Alexander, A. Hime, P. M. Short, A. E. 2023-09-30 doi:10.1101/2023.09.28.559972 Cold Spring Harbor Laboratory Press 2023-09-30 <![CDATA[ Wolbachia enhances the survival of Drosophila infected with fungal pathogens ]]> https://biorxiv.org/content/10.1101/2023.09.30.560320v1?rss=1 Perlmutter, J. I. Schedl, M. E. Unckless, R. L. 2023-09-30 doi:10.1101/2023.09.30.560320 Cold Spring Harbor Laboratory Press 2023-09-30 <![CDATA[ Modeling the Evolution of Populations with Multiple Killer Meiotic Drivers ]]> https://biorxiv.org/content/10.1101/2023.09.28.560003v1?rss=1 Hernandez, J. F. L. Rubinstein, B. Y. Unckless, R. L. Zanders, S. E. 2023-10-01 doi:10.1101/2023.09.28.560003 Cold Spring Harbor Laboratory Press 2023-10-01 <![CDATA[ A Retina-inspired Optoelectronic Synapse Using Quantum Dots for Neuromorphic Photostimulation of Neurons ]]> https://biorxiv.org/content/10.1101/2023.09.30.560306v1?rss=1 Balamur, R. Eren, G. O. Kaleli, H. N. Karatum, O. Kaya, L. Hasanreisoglu, M. Nizamoglu, S. 2023-10-02 doi:10.1101/2023.09.30.560306 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Post-ischemic inactivation of HIF prolyl hydroxylases in endothelium promotes maladaptive kidney repair by inducing glycolysis ]]> https://biorxiv.org/content/10.1101/2023.10.03.560700v1?rss=1 Tiwari, R. Sharma, R. Rajendran, G. Borkowski, G. S. An, S. Y. Schonfeld, M. P. O'Sullivan, J. Schipma, M. Zhou, Y. Courbon, G. David, V. Quaggin, S. E. Thorp, E. B. Chandel, N. S. Kapitsinou, P. P. 2023-10-03 doi:10.1101/2023.10.03.560700 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ A Normative Framework Dissociates Need and Motivation in Hypothalamic Neurons ]]> https://biorxiv.org/content/10.1101/2023.10.01.560411v1?rss=1 Kim, K. S. Lee, Y. H. Kim, Y.-B. Yun, J. W. Song, H. Y. Park, J. S. Jung, S.-H. Sohn, J.-W. Kim, K. W. Kim, H. R. Choi, H. J. 2023-10-04 doi:10.1101/2023.10.01.560411 Cold Spring Harbor Laboratory Press 2023-10-04 <![CDATA[ Single-molecule analysis reveals TDG exhibits multiple modes of linear diffusion to process 5-formylcytosine. ]]> https://biorxiv.org/content/10.1101/2023.10.04.560925v1?rss=1 Schnable, B. L. Schaich, M. A. Roginskaya, V. Leary, L. P. Weaver, T. M. Freudenthal, B. D. Drohat, A. C. Van Houten, B. 2023-10-04 doi:10.1101/2023.10.04.560925 Cold Spring Harbor Laboratory Press 2023-10-04 <![CDATA[ Differences in adult survival drive divergent demographic responses to a decade of field warming on the Tibetan Plateau ]]> https://biorxiv.org/content/10.1101/2023.10.03.560467v1?rss=1 Miao, H.-T. Salguero-Gomez, R. Shea, K. Keller, J. A. Zhang, Z. He, J.-S. Li, S.-L. 2023-10-05 doi:10.1101/2023.10.03.560467 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Single-cell bisulfite-free 5mC and 5hmC sequencing with high sensitivity and scalability ]]> https://biorxiv.org/content/10.1101/2023.10.04.560836v1?rss=1 Cao, Y. Bai, Y. Yuan, T. Song, L. Fan, Y. Ren, L. Song, W. Peng, J. An, R. Gu, Q. Zheng, Y. Xie, X. S. 2023-10-05 doi:10.1101/2023.10.04.560836 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Capitella teleta gets left out: Possible evolutionary shift causes loss of left tissues rather than increased neural tissue from dominant-negative BMPR1 ]]> https://biorxiv.org/content/10.1101/2023.10.04.560756v1?rss=1 Webster, N. B. Meyer, N. P. 2023-10-06 doi:10.1101/2023.10.04.560756 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Genome-wide impact of codon usage bias on translation optimization in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2023.10.05.561139v1?rss=1 Wu, X. Yang, J.-R. Lu, J. 2023-10-06 doi:10.1101/2023.10.05.561139 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ A conserved N-terminal motif of CUL3 mediates assembly and licenses E3 ligase activation of CRL3KLHL22 ]]> https://biorxiv.org/content/10.1101/2023.10.07.561329v1?rss=1 Yin, Y. Wang, W. Liang, L. Dai, Z. Zuo, P. Yu, S. Lv, Y. Ding, D. Chen, H. Jin, Y. Mao, Y. 2023-10-08 doi:10.1101/2023.10.07.561329 Cold Spring Harbor Laboratory Press 2023-10-08 <![CDATA[ Functional genomics reveals that a divergent genetic dependency signature is not essential to the synergism of molecular-targeted agent and chemotherapeutic combinations in gastric cancer cells ]]> https://biorxiv.org/content/10.1101/2023.10.07.561351v1?rss=1 Leylek, O. Honeywell, M. E. Lee, M. J. Hemann, M. T. Ozcan, G. 2023-10-10 doi:10.1101/2023.10.07.561351 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Multi-omics analysis reveals novel interplays between intratumoral bacteria and glioma ]]> https://biorxiv.org/content/10.1101/2023.10.08.561332v1?rss=1 Li, T. Zhao, Z. Peng, M. Wang, C. Luo, F. Zeng, M. Sun, K. Fang, Z. Luo, Y. Huang, Q. Xie, Y. Wang, J. Huang, J.-D. Zhou, H. Sun, H. 2023-10-10 doi:10.1101/2023.10.08.561332 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ TAF7L REGULATES EARLY STAGES OF MALE GERM CELL DEVELOPMENT ]]> https://biorxiv.org/content/10.1101/2023.10.08.561408v1?rss=1 Moreno Irusta, A. Dominguez, E. M. Iqbal, K. Zhang, X. Wang, N. Soares, M. J. 2023-10-10 doi:10.1101/2023.10.08.561408 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Efficacy of the first bioactive peptide from the pearl ]]> https://biorxiv.org/content/10.1101/2023.10.10.561660v1?rss=1 Wu, C. Yin, Z. Wang, Y. Chen, X. Li, B. Wang, Q. Yao, L. Zhang, Z. Liu, X. Zhang, R. 2023-10-10 doi:10.1101/2023.10.10.561660 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Prolonged over-expression of PLK4 amplifies centrosomes through formation of inter-connected centrosome rosette clusters ]]> https://biorxiv.org/content/10.1101/2023.10.10.561779v1?rss=1 Ozcan, S. C. Kalkan, B. M. Cicek, E. Canbaz, A. A. Acilan, C. 2023-10-10 doi:10.1101/2023.10.10.561779 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Overriding Mendelian inheritance in Arabidopsis with a CRISPR toxin-antidote gene drive that impairs pollen germination ]]> https://biorxiv.org/content/10.1101/2023.10.10.561637v1?rss=1 Liu, Y. Jiao, B. Champer, J. Qian, W. 2023-10-11 doi:10.1101/2023.10.10.561637 Cold Spring Harbor Laboratory Press 2023-10-11 <![CDATA[ Characterization of the Complete Chloroplast Genome Sequences and Phylogenetic Relationships of Four Oil-Seed Camellia spp. and related taxa ]]> https://biorxiv.org/content/10.1101/2023.10.03.560681v1?rss=1 Luo, H. Liao, B. Li, Y. Huang, R. Zhang, K. Wang, L. Tan, J. Lv, Y. Lai, C. Li, Y. 2023-10-12 doi:10.1101/2023.10.03.560681 Cold Spring Harbor Laboratory Press 2023-10-12 <![CDATA[ A distinct subpopulation of adipocytes in adult perirenal adipose tissue arises through brown-to-white conversion but reverts to a thermogenic phenotype upon cold exposure ]]> https://biorxiv.org/content/10.1101/2023.10.11.561821v1?rss=1 Zhang, H. Li, Y. Ibanez, C. F. Xie, M. 2023-10-14 doi:10.1101/2023.10.11.561821 Cold Spring Harbor Laboratory Press 2023-10-14 <![CDATA[ Alasemenia, the earliest ovule with three wings and without cupule ]]> https://biorxiv.org/content/10.1101/2023.10.11.561822v1?rss=1 Wang, D. Yang, J. Liu, L. Zhou, Y. Xu, P. Qin, M. Huang, P. 2023-10-14 doi:10.1101/2023.10.11.561822 Cold Spring Harbor Laboratory Press 2023-10-14 <![CDATA[ Regulation of Hepatic Xenosensor Function by HNF4alpha ]]> https://biorxiv.org/content/10.1101/2023.10.11.561888v1?rss=1 Kotulkar, M. Paine-Cabrera, D. Robarts, D. Apte, U. 2023-10-14 doi:10.1101/2023.10.11.561888 Cold Spring Harbor Laboratory Press 2023-10-14 <![CDATA[ Exhaustive search for DNA binding sites of Basillus subtilis transcription factor YsiA by KaScape method ]]> https://biorxiv.org/content/10.1101/2023.10.16.562645v1?rss=1 Bing-yao, H. Mia, H. Chen, H. Su, X. 2023-10-17 doi:10.1101/2023.10.16.562645 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Exploring the bounded rationality in human decision anomalies through an assemblable computational framework ]]> https://biorxiv.org/content/10.1101/2023.10.16.562648v1?rss=1 Lu, Y.-L. Lu, Y.-F. Ren, X. Zhang, H. 2023-10-17 doi:10.1101/2023.10.16.562648 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Detecting copy number variations from single-cell chromatin sequencing data by AtaCNV ]]> https://biorxiv.org/content/10.1101/2023.10.15.562383v1?rss=1 Wang, X. Jin, Z. Shi, Y. Xi, R. 2023-10-18 doi:10.1101/2023.10.15.562383 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ Pan-cancer analysis reveals multifaceted roles of retrotransposon-fusion RNAs ]]> https://biorxiv.org/content/10.1101/2023.10.16.562422v1?rss=1 Lee, B. Park, J. Voshall, A. Maury, E. Kang, Y. Kim, Y. J. Lee, J.-Y. Shim, H.-R. Kim, H.-J. Lee, J.-W. Jung, M.-H. Kim, S.-C. Chu, H. B. K. Kim, D.-W. Kim, M. Choi, E.-J. Hwang, O. K. Lee, H. W. Ha, K. Choi, J. K. Kim, Y. Choi, Y. Park, W.-Y. Lee, E. A. 2023-10-19 doi:10.1101/2023.10.16.562422 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ The More Unclear the Hearing, the Faster the Feeling: Speech Comprehension Changes Subjective Speech Rate ]]> https://biorxiv.org/content/10.1101/2023.10.17.562834v1?rss=1 Chen, L. Jin, Y. Ge, Z. Lu, L. Li, L. 2023-10-19 doi:10.1101/2023.10.17.562834 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Local structural flexibility drives oligomorphism in computationally designed protein assemblies ]]> https://biorxiv.org/content/10.1101/2023.10.18.562842v1?rss=1 Khmelinskaia, A. Bethel, N. P. Fatehi, F. Antanasijevic, A. Borst, A. J. Lai, S.-H. Wang, J. Y. Basu Mallik, B. Miranda, M. M. Watkins, A. M. Ogohara, C. Caldwell, S. Wu, M. Heck, A. J. R. Veesler, D. Baker, D. Twarock, R. King, N. P. 2023-10-19 doi:10.1101/2023.10.18.562842 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Extracellular matrix sulfation in the tumor microenvironment stimulates cancer stemness and invasiveness ]]> https://biorxiv.org/content/10.1101/2023.10.17.562578v1?rss=1 Kusoglu, A. Ornek, D. Dansik, A. Uzun, C. Ozkan, S. N. Sarica, S. Yangin, K. Ozdinc, S. Turan Sorhun, D. Solcan, N. Doganalp, E. C. Arlov, O. Cunningham, K. Karaoglu, I. C. Kizilel, S. Solaroglu, I. Bulutay, P. Firat, P. Erus, S. Tanju, S. Dilege, S. Vunjak-Novakovic, G. Tuncbag, N. Ozturk, E. 2023-10-20 doi:10.1101/2023.10.17.562578 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Listeria adhesion protein orchestrates caveolae-mediated apical junctional remodeling of epithelial barrier for L. monocytogenes translocation ]]> https://biorxiv.org/content/10.1101/2023.10.18.563002v1?rss=1 Drolia, R. Tenguria, S. Bryant, D. Thind, J. Amelunke, B. Liu, D. Gallina, N. Mishra, K. Samaddar, M. Sawale, M. Mishra, D. Cox, A. D. Bhunia, A. K. 2023-10-20 doi:10.1101/2023.10.18.563002 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Architecture and activation of human muscle phosphorylase kinase ]]> https://biorxiv.org/content/10.1101/2023.10.22.563451v1?rss=1 Yang, X. Zhu, M. Lu, X. Wang, Y. Xiao, J. 2023-10-23 doi:10.1101/2023.10.22.563451 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ A bioactive peptide from the pearl has dual roles in resisting SARS-CoV-2 infection and its complications ]]> https://biorxiv.org/content/10.1101/2023.10.23.563427v1?rss=1 Liu, X. Wang, Y. Yin, Z. Wang, Q. Chen, X. Li, B. Yao, L. Zhang, Z. Zhang, R. 2023-10-23 doi:10.1101/2023.10.23.563427 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Germline novelty through recurrent copy-number, protein, and regulatory evolution of the synaptonemal complex ]]> https://biorxiv.org/content/10.1101/2023.10.20.563324v1?rss=1 Wei, K. H. Chang, C.-H. Chatla, K. Krishnapura, A. Appiah, S. P. Zhang, J. Unckless, R. L. Blumenstiel, J. Bachtrog, D. 2023-10-24 doi:10.1101/2023.10.20.563324 Cold Spring Harbor Laboratory Press 2023-10-24 <![CDATA[ Tumor-induced alterations in single-nucleus transcriptome of atrophying muscles indicate enhanced protein degradation and reduced oxidative metabolism ]]> https://biorxiv.org/content/10.1101/2023.10.26.564119v1?rss=1 Agca, S. Domaniku Waraich, A. Bilgic, S. N. Sucuoglu, M. Dag, M. Dogan, S. A. Kir, S. 2023-10-26 doi:10.1101/2023.10.26.564119 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ Ambient Temperature Bacterial Large Ribosomal Subunit Structure Enabled by Serial Femtosecond X-ray Crystallography ]]> https://biorxiv.org/content/10.1101/2023.10.24.563633v1?rss=1 Tosun, B. Rao, Y. Destan, E. Dao, E. H. Ertem, F. B. Yilmaz, M. Yapici, I. Gul, M. Ayan, E. Johnson, J. A. Shafiei, A. Kulakman, C. Hayes, B. Liang, M. Yoon, C. H. Su, Z. Hunter, M. S. Kupitz, C. J. Poitevin, F. P. Ciftci, H. I. Sierra, R. G. Gregory, S. Milon, P. Kurkcuoglu, O. DeMirci, H. 2023-10-27 doi:10.1101/2023.10.24.563633 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ A Fuzzy sequencer for rapid DNA fragment counting and genotyping ]]> https://biorxiv.org/content/10.1101/2023.10.24.563729v1?rss=1 Zhou, W. Kang, L. Qiao, S. Duan, H. Yin, C. Liao, Z. Tang, M. Zhang, R. Li, L. Shi, L. Du, M. Wang, Y. Yue, W. Xiao, Y. Di, L. Zhang, X. Pang, Y. Li, M. Ren, L. Wang, J. Chen, Z. Huang, Y. 2023-10-27 doi:10.1101/2023.10.24.563729 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Ocular dominance-dependent binocular combination of monocular neuronal responses in macaque V1 ]]> https://biorxiv.org/content/10.1101/2023.10.27.564359v1?rss=1 Zhang, S.-H. Zhao, X.-N. Tang, S. Yu, C. 2023-10-27 doi:10.1101/2023.10.27.564359 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ 4D Crystallography Captures Transient IF1-Ribosome Dynamics in Translation Initiation ]]> https://biorxiv.org/content/10.1101/2023.10.27.564398v1?rss=1 Yapici, I. Dao, E. H. Yokoi, S. Destan, E. Ayan, E. Shafiei Kamel, A. Ertem, F. B. Kulakman, C. Yilmaz, M. Tosun, B. Ciftci, H. Kepceoglu, A. Johnson, J. A. Guven, O. Ergul, A. Hayes, B. Rao, Y. Kupitz, C. J. Poitevin, F. Liang, M. Hunter, M. S. Milon, P. Mitsutake, A. Sierra, R. G. Wakatsuki, S. DeMirci, H. 2023-10-29 doi:10.1101/2023.10.27.564398 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ PerSEveML: A Web-Based Tool to Identify Persistent Biomarker Structure for Rare Events Using Integrative Machine Learning Approach ]]> https://biorxiv.org/content/10.1101/2023.10.25.564000v1?rss=1 Dutta, S. Mudaranthakam, D. E. Li, Y. Sardiu, M. E. 2023-10-30 doi:10.1101/2023.10.25.564000 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ Social Rank Alters the Synchrony of Attribute Integration in Altruistic Decisions ]]> https://biorxiv.org/content/10.1101/2023.10.26.564311v1?rss=1 Ni, Y. Li, J. 2023-10-31 doi:10.1101/2023.10.26.564311 Cold Spring Harbor Laboratory Press 2023-10-31 <![CDATA[ From sequence to molecules: Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways ]]> https://biorxiv.org/content/10.1101/2023.10.30.564663v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@1dedad4org.highwire.dtl.DTLVardef@1f0a39eorg.highwire.dtl.DTLVardef@185e345org.highwire.dtl.DTLVardef@10beec6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gu, S. Shao, Y. Rehm, K. Bigler, L. Zhang, D. He, R. Shao, J. Jousset, A. Friman, V.-P. Wei, Z. Kummerli, R. Li, Z. 2023-11-01 doi:10.1101/2023.10.30.564663 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Breast cancer risk SNPs converge on estrogen receptor binding sites commonly shared between breast tumors to locally alter estrogen signalling output ]]> https://biorxiv.org/content/10.1101/2023.10.30.564691v1?rss=1 Joosten, S. E. P. Gregoricchio, S. Stelloo, S. Yapici, E. Huang, F. Donaldson Collier, M. Morova, T. Altintas, B. Kim, Y. Canisius, S. Korkmaz, G. Lack, N. Vermeulen, M. Linn, S. Zwart, W. 2023-11-02 doi:10.1101/2023.10.30.564691 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Attenuating amyloid-beta pathology in mice with in situ programmed astrocytes ]]> https://biorxiv.org/content/10.1101/2023.10.30.564697v1?rss=1 Zhang, L. Lu, S. Jia, Y.-b. Hou, S.-j. Zhu, J. Liu, X.-g. Sun, X.-y. Huang, Y.-r. Zhao, Y.-x. Ren, H. Liu, C.-y. Cui, F. Liu, D.-q. Du, X.-y. Niu, X.-y. li, L.-j. Wang, K. Liang, S.-y. Yang, J.-j. Ji, S.-y. Sun, L. Zhou, W.-w. Xie, X.-x. Yu, X.-l. Wang, X. Liu, R.-t. 2023-11-02 doi:10.1101/2023.10.30.564697 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ A foundation model for bioactivity prediction using pairwise meta-learning ]]> https://biorxiv.org/content/10.1101/2023.10.30.564861v1?rss=1 Feng, B. Liu, Z. Huang, N. Xiao, Z. Zhang, H. Mirzoyan, S. Xu, H. Hao, J. Xu, Y. Zhang, M. Wang, S. 2023-11-02 doi:10.1101/2023.10.30.564861 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Single-molecule analysis of purified proteins and nuclear extracts: insights from 8-oxoguanine glycosylase 1 ]]> https://biorxiv.org/content/10.1101/2023.11.01.565178v1?rss=1 Schaich, M. Weaver, T. M. Roginskaya, V. Freudenthal, B. D. Van Houten, B. 2023-11-02 doi:10.1101/2023.11.01.565178 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ The intrinsically disordered transcriptional activation domain of CIITA is functionally tuneable by single substitutions: An exception or a new rule? ]]> https://biorxiv.org/content/10.1101/2023.11.02.565367v1?rss=1 Sreenivasan, S. Heffren, P. Suh, K.-S. Rodnin, M. V. Kosa, E. Fenton, A. W. Ladokhin, A. Smith, P. E. Fontes, J. D. Swint-Kruse, L. 2023-11-02 doi:10.1101/2023.11.02.565367 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Modulation of hepatic transcription factor EB activity during cold exposure uncovers direct regulation of bis(monoacylglycerol)phosphate lipids by Pla2g15 ]]> https://biorxiv.org/content/10.1101/2023.11.03.565498v1?rss=1 Jain, R. Geoghegan, G. Davidson, J. Nesbitt, D. J. Abe, A. Chao, X. James, I. Cavanagh, A. T. Michorowska, S. Verma, R. Schueler, K. L. Hinkoka-Galcheva, V. Shishkova, E. Ding, W.-X. Coon, J. J. Shayman, J. Simcox, J. 2023-11-03 doi:10.1101/2023.11.03.565498 Cold Spring Harbor Laboratory Press 2023-11-03 <![CDATA[ The hidden function of nonspecifically DNA-bound RNA polymerases: a buffer of resource competition in bacteria ]]> https://biorxiv.org/content/10.1101/2023.11.04.565427v1?rss=1 Yan, Y. Li, T. Lin, J. 2023-11-04 doi:10.1101/2023.11.04.565427 Cold Spring Harbor Laboratory Press 2023-11-04 <![CDATA[ Dual long-axis reorganization of hippocampus in youth ]]> https://biorxiv.org/content/10.1101/2023.11.03.565423v1?rss=1 Zeng, D. Li, Q. Li, D. He, Y. Dong, X. Li, S. Bi, S. Liao, X. Zhao, T. Chen, X. Xia, Y. Lei, T. Sun, L. Men, W. Wang, Y. Wang, D. Hu, M. Pan, Z. Tan, S. Gao, J.-H. Qin, S. Tao, S. Dong, Q. He, Y. Zuo, X. Li, S. 2023-11-05 doi:10.1101/2023.11.03.565423 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Acinetobacter guillouiae strain isolated from sludge capable of partially degrade polyethylene terephthalate: genomic and biochemical insights ]]> https://biorxiv.org/content/10.1101/2023.11.05.565377v1?rss=1 Akhtar, N. Najjari, A. Tullberg, C. Awan, M. S. Majeed, Z. Grey, C. Zhang, B. Linares-Pasten, J. A. 2023-11-05 doi:10.1101/2023.11.05.565377 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ From sequence to ecology: siderophore-receptor coevolution algorithm predicts bacterial interactions in complex communities ]]> https://biorxiv.org/content/10.1101/2023.11.05.565711v1?rss=1 90% accuracy based on experimental validation. We derived community-level iron interaction networks to show that selection for siderophore-mediated interactions differs across habitats and lifestyles. Specifically, dense networks of siderophore sharing and competition were observed among environmental (soil/water/plant) strains and non-pathogenic species, while only fragmented networks occurred among human-derived strains and pathogenic species. Altogether, our sequence-to-ecology approach empowers the analyses of social interactions among thousands of bacterial strains and uncovers ways for targeted intervention to microbial communities. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/565711v3_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@60d907org.highwire.dtl.DTLVardef@48756eorg.highwire.dtl.DTLVardef@115aac1org.highwire.dtl.DTLVardef@17d76e5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gu, S. Shao, Z. Shao, Y. Zhu, S. Zhang, D. Allen, R. He, R. Shao, J. Xiong, G. Qu, Z. Jousset, A. Friman, V.-P. Wei, Z. Kuemmerli, R. Li, Z. 2023-11-06 doi:10.1101/2023.11.05.565711 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Poisoning medical knowledge using large language models ]]> https://biorxiv.org/content/10.1101/2023.11.06.565928v1?rss=1 Yang, J. Xu, H. Mirzoyan, S. Chen, T. Liu, Z. Ju, W. Liu, L. Zhang, M. Wang, S. 2023-11-08 doi:10.1101/2023.11.06.565928 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Bni5 tethers myosin-II to septins to enhance retrograde actin flow and the robustness of cytokinesis ]]> https://biorxiv.org/content/10.1101/2023.11.07.566094v1?rss=1 Okada, H. Chen, X. Wang, K. Marquardt, J. Bi, E. 2023-11-08 doi:10.1101/2023.11.07.566094 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ An acidophilic fungus is integral to prey digestion in a carnivorous plant ]]> https://biorxiv.org/content/10.1101/2023.11.07.566145v1?rss=1 Sun, P.-F. Lu, M. R. Liu, Y.-C. Lin, Y.-f. Hoh, D. Z. Ke, H.-M. Wang, I.-F. Lu, M.-Y. J. Kirschner, R. Lin, Y.-C. J. Chen, Y.-L. Tsai, I. J. 2023-11-08 doi:10.1101/2023.11.07.566145 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Elucidating the Synergistic Role of Elm1 and Gin4 Kinases in Regulating Septin Hourglass Assembly ]]> https://biorxiv.org/content/10.1101/2023.11.08.566235v1?rss=1 Marquardt, J. Chen, X. Bi, E. 2023-11-08 doi:10.1101/2023.11.08.566235 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Amalga: Designable Protein Backbone Generation with Folding and Inverse Folding Guidance ]]> https://biorxiv.org/content/10.1101/2023.11.07.565939v1?rss=1 Chen, S. Li, Z. Zeng, X. Ke, G. 2023-11-09 doi:10.1101/2023.11.07.565939 Cold Spring Harbor Laboratory Press 2023-11-09 <![CDATA[ Using Multivariate Pattern Analysis to Increase Effect Sizes for Event-Related Potential Analyses ]]> https://biorxiv.org/content/10.1101/2023.11.07.566051v1?rss=1 Carrasco, C. D. Bahle, B. Simmons, A. M. Luck, S. J. 2023-11-11 doi:10.1101/2023.11.07.566051 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ MAB-5/Hox regulates the Q neuroblast transcriptome, including cwn-1/Wnt, to mediate posterior migration in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2023.11.09.566461v1?rss=1 Paolillo, V. K. Ochs, M. E. Lundquist, E. A. 2023-11-11 doi:10.1101/2023.11.09.566461 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ Ammonia-oxidizing archaea and bacteria differentially contribute to ammonia oxidation in soil under precipitation gradients and land legacy ]]> https://biorxiv.org/content/10.1101/2023.11.08.566028v1?rss=1 Sarkar, S. Kazarina, A. Hansen, P. M. Ward, K. Hargreaves, C. Reese, N. Ran, Q. Kessler, W. de Souza, L. F. T. Loecke, T. D. Sarto, M. V. M. Rice, C. W. Zeglin, L. H. Sikes, B. A. Lee, S. T. M. 2023-11-12 doi:10.1101/2023.11.08.566028 Cold Spring Harbor Laboratory Press 2023-11-12 <![CDATA[ Urine proteomic analysis of patients with schizophrenia ]]> https://biorxiv.org/content/10.1101/2023.11.11.566683v1?rss=1 Zhao, C. Dong, F. Zhou, F. Huan, Y. Gao, Y. Yang, J. 2023-11-12 doi:10.1101/2023.11.11.566683 Cold Spring Harbor Laboratory Press 2023-11-12 <![CDATA[ Mutational scanning reveals oncogenic CTNNB1 mutations have diverse effects on signalling and clinical traits ]]> https://biorxiv.org/content/10.1101/2023.11.09.566307v1?rss=1 Krishna, A. Meynert, A. Kelder, M. Ewing, A. Sheraz, S. Ferrer-Vacquer, A. Grimes, G. Becher, H. Silk, R. Semple, C. A. Kendall, T. Hadjontanakis, A.-K. Bird, T. Marsh, J. A. Hohenstein, P. Wood, A. J. Ozdemir, D. D. 2023-11-13 doi:10.1101/2023.11.09.566307 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Progenitors influence patterning of the sensory epithelium. ]]> https://biorxiv.org/content/10.1101/2023.11.13.566920v1?rss=1 Young, C. A. Burt, E. Munnamalai, V. 2023-11-13 doi:10.1101/2023.11.13.566920 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Meiotic drive, postzygotic isolation, and the Snowball Effect ]]> https://biorxiv.org/content/10.1101/2023.11.14.567107v1?rss=1 Unckless, R. L. 2023-11-14 doi:10.1101/2023.11.14.567107 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ Speeding up iterative applications of the BUILD supertree algorithm ]]> https://biorxiv.org/content/10.1101/2023.11.10.566627v1?rss=1 Redelings, B. D. Holder, M. T. 2023-11-15 doi:10.1101/2023.11.10.566627 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ SARS-CoV-2 nsp15 endoribonuclease antagonizes dsRNA-induced antiviral signaling ]]> https://biorxiv.org/content/10.1101/2023.11.15.566945v1?rss=1 Otter, C. J. Bracci, N. Parenti, N. A. Ye, C. Li Hui, T. Asthana, A. Pfannenstiel, J. J. Jackson, N. Fehr, A. R. Silverman, R. H. Cohen, N. A. Martinez-Sobrido, L. Weiss, S. R. 2023-11-15 doi:10.1101/2023.11.15.566945 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ A shift in the host web occupancy of dew-drop spiders associated with genetic divergence in the Southwest Pacific ]]> https://biorxiv.org/content/10.1101/2023.11.13.566795v1?rss=1 Elias, N. U. Responte, M. A. Wu, C.-Y. Chiu, Y.-F. Peng, P. Liao, H. Brown, R. M. Su, Y.-C. 2023-11-16 doi:10.1101/2023.11.13.566795 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Fast evolution of SARS-CoV-2 BA.2.86 to JN.1 under heavy immune pressure ]]> https://biorxiv.org/content/10.1101/2023.11.13.566860v1?rss=1 Cao, Y. Yang, S. Yu, Y. Xu, Y. Jian, F. Song, W. Yisimayi, A. Wang, P. Wang, J. Liu, J. Yu, L. Niu, X. Wang, J. Wang, Y. Shao, F. Jin, R. Wang, Y. 2023-11-16 doi:10.1101/2023.11.13.566860 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Targeted micro-fiber arrays for measuring and manipulating localized multi-scale neural dynamics over large, deep brain volumes during behavior ]]> https://biorxiv.org/content/10.1101/2023.11.17.567425v1?rss=1 Vu, M.-A. T. Brown, E. H. Wen, M. J. Noggle, C. A. Zhang, Z. Monk, K. J. Bouabid, S. Mroz, L. Graham, B. M. Zhuo, Y. Li, Y. Otchy, T. M. Tian, L. Davison, I. G. Boas, D. A. Howe, M. W. 2023-11-17 doi:10.1101/2023.11.17.567425 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Quantitative cell morphology in C. elegans embryos reveals regulations of cell volume asymmetry ]]> https://biorxiv.org/content/10.1101/2023.11.20.567849v1?rss=1 View larger version (114K): org.highwire.dtl.DTLVardef@1b7d0fforg.highwire.dtl.DTLVardef@fa28b1org.highwire.dtl.DTLVardef@185a0deorg.highwire.dtl.DTLVardef@478a2_HPS_FORMAT_FIGEXP M_FIG C_FIG Potential Cover/Featured Image: Smiling "ghost" face of C. elegans embryo. Center: shown are skins (colored in red, dorsal view with anterior to the bottom) of a 400-celled C. elegans embryo. Cells not covered by the skins are colored in gray, green, blue, and transparent yellow, respectively. Internal and external circles: confocal fluorescence images (GFP for cell nucleus and mCherry for cell membrane) and reconstructed cell morphologies of the C. elegans embryo from the 2- to 550-cell stages respectively, connected with images of a C. elegans adult expressing the same markers. ]]> Guan, G. Li, Z. Ma, Y. Cao, J. Wong, M.-K. Chan, L.-Y. Yan, H. Tang, C. Zhao, Z. 2023-11-20 doi:10.1101/2023.11.20.567849 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ CEP44 is required for maintaining centriole duplication and spindle integrity ]]> https://biorxiv.org/content/10.1101/2023.11.20.567852v1?rss=1 Zhang, D. Wei, W. Zou, X. Meng, H. Li, F. Yao, M. Teng, J. Huang, N. Chen, J. 2023-11-20 doi:10.1101/2023.11.20.567852 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ Aalbo1200: global genetic differentiation and variability of the mosquito Aedes albopictus ]]> https://biorxiv.org/content/10.1101/2023.11.21.568070v1?rss=1 Crawford, J. E. Beebe, N. Bonizzoni, M. Caputo, B. Carter, B. H. Chen, C.-H. Cosme, L. De Marco, C. M. della Torre, A. Estallo, E. L. Guo, X. Liu, W.-L. Maringer, K. Mains, J. Maynard, A. Mogi, M. Livdahl, T. Rose, N. H. Scarafia, P. Y. Severson, D. Stein, M. Surendran, S. N. Tuno, N. Wahid, I. Wang, X. Xu, J. Yan, G. Yee, D. Armbruster, P. A. Caccone, A. White, B. 2023-11-22 doi:10.1101/2023.11.21.568070 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ A Potent Kalihinol Analogue Disrupts Apicoplast Function and Vesicular Trafficking in P. falciparum Malaria. ]]> https://biorxiv.org/content/10.1101/2023.11.21.568162v1?rss=1 Chahine, Z. M. Abel, S. Hollin, T. Chung, J. H. Barnes, G. L. Daub, M. E. Renard, I. Choi, J. Y. Vydyam, P. Chattopadhyay Pal, A. Argomaniz, M. Banks, C. kirkwood, J. Saraf, A. Camino Diaz, I. Castaneda-Casado, P. Cuevas-Martin, M. De Mercado-Arnanz, J. Fernandez Alvaro, E. Garcia-Perez, A. Ibarz-Ferrer, N. Viera-Morilla, S. Prudhomme, J. Joyner, C. J. Bei, A. Florens, L. Ben Mamoun, C. Vanderwal, C. Le Roch, K. G. 2023-11-22 doi:10.1101/2023.11.21.568162 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Siderophore Piracy Promotes Dynamical Coexistence in Microbial Community ]]> https://biorxiv.org/content/10.1101/2023.11.21.568182v1?rss=1 View larger version (42K): org.highwire.dtl.DTLVardef@143f144org.highwire.dtl.DTLVardef@194c2adorg.highwire.dtl.DTLVardef@1792d4aorg.highwire.dtl.DTLVardef@8c96a7_HPS_FORMAT_FIGEXP M_FIG C_FIG How does cheating affect microbial biodiversity? By mapping the strongest benefit flows between species, we discovered a topological rule for survival. While too much cheating creates dead-ends that crash the system, moderate cheating connects species into self-sustaining loops. These "exploitation cycles" act as a scaffold, supporting high diversity and complex population. ]]> Shao, J. Li, Y. Lu, J. Gu, S. Li, Z. 2023-11-22 doi:10.1101/2023.11.21.568182 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Comparative single-cell transcriptomic atlases reveal conserved and divergent features of drosophilid central brains ]]> https://biorxiv.org/content/10.1101/2023.11.22.568274v1?rss=1 Lee, D. Benton, R. 2023-11-23 doi:10.1101/2023.11.22.568274 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ Upstream open reading frames dynamically modulate CLOCK protein translation to regulate circadian rhythm and sleep ]]> https://biorxiv.org/content/10.1101/2023.11.22.568359v1?rss=1 Sun, Y. Shui, K. Li, Q. Jin, W. Liu, C. Lu, J. Zhang, L. 2023-11-23 doi:10.1101/2023.11.22.568359 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ Millimeter-scale magnetic implants paired with a fully integrated wearable device for wireless biophysical and biochemical sensing ]]> https://biorxiv.org/content/10.1101/2023.11.23.568392v1?rss=1 Wan, J. Nie, Z. Xu, J. Zhang, Z. Yao, S. Xiang, Z. Lin, X. Lu, Y. Xu, C. Zhao, P. Wang, Y. Zhang, J. Wang, Y. Zhang, S. Wang, J. Man, W. Zhang, M. Han, M. 2023-11-23 doi:10.1101/2023.11.23.568392 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ Perceptual error based on Bayesian cue combination drives implicit motor adaptation ]]> https://biorxiv.org/content/10.1101/2023.11.23.568442v1?rss=1 Zhang, Z. Wang, H. Zhang, T. Nie, Z. Wei, K. 2023-11-23 doi:10.1101/2023.11.23.568442 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ Host signature as major driver of root and rhizosphere core microbiomes that differently affect plant functional traits ]]> https://biorxiv.org/content/10.1101/2023.11.23.568511v1?rss=1 Luo, J. Wang, Y. Zhang, Y. Gao, W. Liang, Y. Zhao, H.-P. Gu, S. Li, T. 2023-11-24 doi:10.1101/2023.11.23.568511 Cold Spring Harbor Laboratory Press 2023-11-24 <![CDATA[ Nitrite deteriorates bioreactor performance by reducing growth of Ca. Brocadia sapporoensis instead of inhibiting the anammox activity ]]> https://biorxiv.org/content/10.1101/2023.11.24.568540v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@6b199forg.highwire.dtl.DTLVardef@15f2a74org.highwire.dtl.DTLVardef@dc2d8eorg.highwire.dtl.DTLVardef@132deb1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Qiao, X. Zhang, L. Wu, Y. Deng, C. Zhang, Y. Zhang, X. Yan, Y. Zhuang, W. Yu, K. 2023-11-24 doi:10.1101/2023.11.24.568540 Cold Spring Harbor Laboratory Press 2023-11-24 <![CDATA[ ProTokens: A Machine-Learned Language for Compact and Informative Encoding of Protein 3D Structures ]]> https://biorxiv.org/content/10.1101/2023.11.27.568722v1?rss=1 Lin, X. Chen, Z. Li, Y. Lu, X. Fan, C. Cao, Z. Feng, S. Gao, Y. Q. Zhang, J. 2023-11-27 doi:10.1101/2023.11.27.568722 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ Evolution-guided large language model is a predictor of virus mutation trends ]]> https://biorxiv.org/content/10.1101/2023.11.27.568815v1?rss=1 Nie, Z. Liu, X. Chen, J. Wang, Z. Liu, Y. Si, H. Dong, T. Xu, F. Song, G. Wang, Y. Zhou, P. Gao, W. Tian, Y. 2023-11-27 doi:10.1101/2023.11.27.568815 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ Role of HNF4alpha-cMyc Interaction in CDE-diet Induced Liver Injury and Regeneration ]]> https://biorxiv.org/content/10.1101/2023.11.27.568898v1?rss=1 Kotulkar, M. Barbee, J. Robarts, D. Paine-Cabrera, D. Apte, U. 2023-11-27 doi:10.1101/2023.11.27.568898 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ Modeling the effects of Ehrlichia Chaffeensis and movement on dogs ]]> https://biorxiv.org/content/10.1101/2023.11.28.568825v1?rss=1 Agusto, F. Drum, J. 2023-11-29 doi:10.1101/2023.11.28.568825 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ A homing rescue gene drive with multiplexed gRNAs reaches high frequency in cage populations but generates functional resistance ]]> https://biorxiv.org/content/10.1101/2023.11.29.569221v1?rss=1 Chen, J. Hou, S. Feng, R. Xu, X. Liang, N. Champer, J. 2023-11-29 doi:10.1101/2023.11.29.569221 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Mechanistic insights into ligand dissociation from the SARS-CoV-2 spike glycoprotein ]]> https://biorxiv.org/content/10.1101/2023.11.29.569184v1?rss=1 Hasse, T. A. Mantei, E. Shahoei, R. Pawnikar, S. Wang, J. Miao, Y. Huang, Y.-m. M. 2023-11-30 doi:10.1101/2023.11.29.569184 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ Familiarity training enhance straightening of neural trajectory for video prediction ]]> https://biorxiv.org/content/10.1101/2023.11.29.569215v1?rss=1 Qiu, W. Huang, S. Mukundan, M. Lee, T. S. 2023-12-01 doi:10.1101/2023.11.29.569215 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Deciphering the Biosynthetic Potential of Microbial Genomes Using a BGC Language Processing Neural Network Model ]]> https://biorxiv.org/content/10.1101/2023.11.30.569352v1?rss=1 Lai, Q. Yao, S. Zha, Y. Zhang, H. Ye, Y. Zhang, Y. Bai, H. Ning, K. 2023-12-01 doi:10.1101/2023.11.30.569352 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Somatic Mosaicism in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia Reveals Widespread Degeneration from Focal Mutations ]]> https://biorxiv.org/content/10.1101/2023.11.30.569436v1?rss=1 Zhou, Z. Kim, J. Huang, A. Y. Nolan, M. Park, J. Doan, R. Shin, T. Miller, M. B. Chhouk, B. Morillo, K. Yeh, R. C. Kenny, C. Neil, J. E. Lee, C.-Z. Ohkubo, T. Ravits, J. Ansorge, O. Ostrow, L. W. Lagier-Tourenne, C. Lee, E. A. Walsh, C. A. 2023-12-01 doi:10.1101/2023.11.30.569436 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ High-speed Auto-Polarization Synchronization Modulation Three-dimensional Structured Illumination Microscopy ]]> https://biorxiv.org/content/10.1101/2023.12.04.569876v1?rss=1 Li, Y. Cao, R. Ren, W. Fu, Y. Hou, Y. Zhong, S. Zhanghao, K. Li, M. Xi, P. 2023-12-04 doi:10.1101/2023.12.04.569876 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ Whole-genome sequences reveal zygotic composition in chimeric twins ]]> https://biorxiv.org/content/10.1101/2023.12.03.568663v1?rss=1 Yoon, C. J. Nam, C. H. Kim, T. Lee, J. S. Yi, K. Kim, R. Koh, J.-Y. Kim, J. Won, H. Oh, J. Griffith, O. L. Griffith, M. Sung, J. Kim, T. Y. Choi, J. S. Cho, D. Ju, Y. S. 2023-12-05 doi:10.1101/2023.12.03.568663 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Population suppression with dominant female-lethal alleles is boosted by homing gene drive ]]> https://biorxiv.org/content/10.1101/2023.12.05.570109v1?rss=1 Zhu, J. Chen, J. Liu, Y. Xu, X. Champer, J. 2023-12-05 doi:10.1101/2023.12.05.570109 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Improving the suppressive power of homing gene drive by co-targeting a distant-site female fertility gene ]]> https://biorxiv.org/content/10.1101/2023.12.07.570117v1?rss=1 Faber, N. R. Xu, X. Chen, J. Hou, S. Du, J. Pannebakker, B. A. Zwaan, B. J. van den Heuvel, J. Champer, J. 2023-12-08 doi:10.1101/2023.12.07.570117 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Understanding Molecular Links of Vascular Cognitive Impairment: Selective Interaction between Mutant APP, TP53, and MAPKs ]]> https://biorxiv.org/content/10.1101/2023.12.08.570506v1?rss=1 Zeylan, M. E. Senyuz, S. Keskin, O. Gursoy, A. 2023-12-08 doi:10.1101/2023.12.08.570506 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Depletion of tropomyosin 1.6 promotes matrix-degrading phenotype in TGF-β1-induced myofibroblast ]]> https://biorxiv.org/content/10.1101/2023.12.08.570775v1?rss=1 Wu, C. L. Lee, G.-H. Chen, B. Y. Kuo, C.-H. Chan, T. T. Wang, Y.-K. Wong, T. Y. Tang, M.-J. 2023-12-08 doi:10.1101/2023.12.08.570775 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Effective seed sterilization methods require optimization across maize genotypes ]]> https://biorxiv.org/content/10.1101/2023.12.14.571779v1?rss=1 Parnell, J. J. Pal, G. Awan, A. Vintila, S. Houdinet, G. Hawkes, C. V. Balint-Kurti, P. Wagner, M. R. Kleiner, M. 2023-12-15 doi:10.1101/2023.12.14.571779 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Parallel Molecular Data Storage by Printing Epigenetic Bits on DNA ]]> https://biorxiv.org/content/10.1101/2023.12.15.571646v1?rss=1 Zhang, C. Wu, R. Sun, F. Lin, Y. Zhang, Y. Liang, Y. Chen, Y. Teng, J. Song, Z. Liu, N. Ouyang, Q. Qian, L. Yan, H. 2023-12-15 doi:10.1101/2023.12.15.571646 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast ]]> https://biorxiv.org/content/10.1101/2023.12.15.571893v1?rss=1 Chalivendra, S. Shi, S. Li, x. Kuang, Z. Giovinazzo, J. Zhang, L. Rossi, J. Saviola, A. Wang, J. Welty, R. Liu, S. Vaeth, K. Zhou, H. Hansen, K. Taliaferro, M. zhao, R. 2023-12-15 doi:10.1101/2023.12.15.571893 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Effect of mechanical stretching stimulation on maturation of human iPS cell-derived cardiomyocytes co-cultured with human gingival fibroblasts ]]> https://biorxiv.org/content/10.1101/2023.12.15.567696v1?rss=1 Wang, M. Idei, H. Wang, C. Liang, Y. Liu, Y. Matsuda, Y. Takahashi, K. Kamioka, H. Naruse, K. 2023-12-16 doi:10.1101/2023.12.15.567696 Cold Spring Harbor Laboratory Press 2023-12-16 <![CDATA[ Temporal Transcriptome Analysis Uncovers Regulatory Modules Programming Embryo Development from Embryonic Morphogenesis to Post-Germination ]]> https://biorxiv.org/content/10.1101/2023.12.26.573376v1?rss=1 Wang, Y.-C. Hsieh, W.-H. Huang, C.-J. Jhan, Y.-T. Zhan, J. Chang, C.-C. Hsieh, T.-F. Lin, J.-Y. 2023-12-27 doi:10.1101/2023.12.26.573376 Cold Spring Harbor Laboratory Press 2023-12-27 <![CDATA[ ProInterVal: Validation of Protein-Protein Interfaces through Learned Interface Representations ]]> https://biorxiv.org/content/10.1101/2023.12.27.573460v1?rss=1 Ovek, D. Keskin, O. Gursoy, A. 2023-12-27 doi:10.1101/2023.12.27.573460 Cold Spring Harbor Laboratory Press 2023-12-27 <![CDATA[ A Supervised Contrastive Framework for Learning Disentangled Representations of Cell Perturbation Data ]]> https://biorxiv.org/content/10.1101/2024.01.05.574421v1?rss=1 Tu, X. Hutter, J.-C. Wang, Z. J. Kudo, T. Regev, A. Lopez, R. 2024-01-08 doi:10.1101/2024.01.05.574421 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ A new story of four Hexapoda classes: Protura as the sister to all other hexapods ]]> https://biorxiv.org/content/10.1101/2024.01.08.574592v1?rss=1 Du, S. Tihelka, E. Yu, D. Chen, W.-J. Bu, Y. Cai, C. Engel, M. S. Luan, Y.-X. Zhang, F. 2024-01-08 doi:10.1101/2024.01.08.574592 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ Monitoring transcription of miR-15a and miR-124 in mesenchymal stem cells from adipose tissue origin differentiated into pancreatic beta-cells ]]> https://biorxiv.org/content/10.1101/2024.01.18.576237v1?rss=1 Rajabi, H. 2024-01-22 doi:10.1101/2024.01.18.576237 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Multifaceted Roles of Histone Lysine Lactylation in Meiotic Gene Dynamics and Recombination ]]> https://biorxiv.org/content/10.1101/2024.01.25.576681v1?rss=1 Zhang, X. Liu, Y. Wang, N. 2024-01-26 doi:10.1101/2024.01.25.576681 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ Matrix-rigidity cooperates with biochemical cues in M2 macrophage activation through increased nuclear deformation and chromatin accessibility ]]> https://biorxiv.org/content/10.1101/2024.02.13.579995v1?rss=1 Shin, S.-J. Bayarkhangai, B. Tsogtbaataar, K. Yuxuan, M. Kim, S.-H. Kim, Y.-J. Kim, D. Kim, D.-H. Lee, J.-H. Hyun, J. Kim, H.-W. 2024-02-16 doi:10.1101/2024.02.13.579995 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ Thymidine Phosphorylase Mediates SARS-CoV-2 Spike Protein Enhanced Thrombosis in K18-hACE2TG Mice ]]> https://biorxiv.org/content/10.1101/2024.02.23.581661v1?rss=1 Roytenberg, R. Yue, H. DeHart, A. Kim, E. Bai, F. Kim, Y. Denning, K. Kwei, A. Zhang, Q. Liu, J. Zheng, L. Li, W. 2024-02-23 doi:10.1101/2024.02.23.581661 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Single-nucleus Multiomic Analyses Identifies Gene Regulatory Dynamics of Phenotypic Modulation in Human Aneurysmal Aortic Root ]]> https://biorxiv.org/content/10.1101/2024.02.27.582442v1?rss=1 Liu, X. Zeng, Q. Yang, H. Li, W. Chen, Q. Yin, K. Pan, Z. Wang, K. Luo, M. Shu, C. Zhou, Z. 2024-03-02 doi:10.1101/2024.02.27.582442 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ Feature-independent Encoding of Visual Salience inthe Mouse Superior Colliculus ]]> https://biorxiv.org/content/10.1101/2024.03.04.583246v1?rss=1 Wu, R. Xu, J. Li, C. Zhang, Z. Li, L.-y. Li, Y. 2024-03-06 doi:10.1101/2024.03.04.583246 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ DR5 disulfide bonding as a sensor and effector of protein folding stress ]]> https://biorxiv.org/content/10.1101/2024.03.04.583390v1?rss=1 Law, M. E. Dulloo, Z. M. Eggleston, S. R. Takacs, G. P. Alexandrow, G. M. Wang, M. Su, H. Forsyth, B. A. Chiang, C.-W. Sharma, A. Kanumuri, S. R. R. Guryanova, O. A. Harrison, J. K. Tirosh, B. Castellano, R. K. Law, B. K. 2024-03-07 doi:10.1101/2024.03.04.583390 Cold Spring Harbor Laboratory Press 2024-03-07 <![CDATA[ Distinct regions within SAP25 recruit O-linked glycosylation, DNA demethylation, and ubiquitin ligase and hydrolase activities to the Sin3/HDAC complex ]]> https://biorxiv.org/content/10.1101/2024.03.05.583553v1?rss=1 Goswami, P. Banks, C. Thornton, J. Bengs, B. Sardiu, M. E. Florens, L. Washburn, M. 2024-03-08 doi:10.1101/2024.03.05.583553 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ DeepPrep: An accelerated, scalable, and robust pipeline for neuroimaging preprocessing empowered by deep learning ]]> https://biorxiv.org/content/10.1101/2024.03.06.581108v1?rss=1 Ren, J. An, N. Lin, C. Zhang, Y. Sun, Z. Zhang, W. Li, S. Guo, N. Cui, W. Hu, Q. Wang, W. Wu, X. Wang, Y. Jiang, T. Satterthwaite, T. D. Wang, D. Liu, H. 2024-03-07 doi:10.1101/2024.03.06.581108 Cold Spring Harbor Laboratory Press 2024-03-07 <![CDATA[ Deletion of RFX6, a Diabetes-Associated Gene, Impairs iPSC-Derived Islet Organoid Development and Survival, With No Impact on the Generation of PDX1+/NKX6.1+ Progenitors ]]> https://biorxiv.org/content/10.1101/2024.03.06.583663v1?rss=1 Aldous, N. Elsayed, A. K. Memon, B. Ijaz, S. Hayat, S. Abdelalim, E. M. 2024-03-11 doi:10.1101/2024.03.06.583663 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Buzz-world: Global patterns and drivers of buzzing bees and poricidal plants ]]> https://biorxiv.org/content/10.1101/2024.03.06.583730v1?rss=1 Russell, A. L. Buchmann, S. L. Ascher, J. S. Wang, Z. Kriebel, R. Jolles, D. D. Orr, M. C. Hughes, A. C. 2024-03-11 doi:10.1101/2024.03.06.583730 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ High Frequency Terahertz Stimulation Alleviates Neuropathic Pain by Inhibiting the Pyramidal Neuron Activity in the Anterior Cingulate Cortex of mice ]]> https://biorxiv.org/content/10.1101/2024.03.06.583763v1?rss=1 Peng, W. Wang, P. Tan, C. Zhao, H. Chen, K. Si, H. Tian, Y. Lou, A. Zhu, Z. Yuan, Y. Wu, K. Chang, C. Wu, Y. Chen, T. 2024-03-11 doi:10.1101/2024.03.06.583763 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Inference of Transcriptional Regulation From STARR-seq Data ]]> https://biorxiv.org/content/10.1101/2024.03.06.583826v1?rss=1 Safaeesirat, A. Taeb, H. Tekoglu, E. Morova, T. Lack, N. Emberly, E. 2024-03-12 doi:10.1101/2024.03.06.583826 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Antigenicity assessment of SARS-CoV-2 saltation variant BA.2.87.1 ]]> https://biorxiv.org/content/10.1101/2024.03.07.583823v1?rss=1 Yang, S. Yu, Y. Jian, F. Yisimayi, A. Song, W. Liu, J. Wang, P. Xu, Y. Wang, J. Niu, X. Yu, L. Wang, Y. Shao, F. Jin, R. Wang, Y. Cao, Y. 2024-03-08 doi:10.1101/2024.03.07.583823 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ The heritability and structural correlates of brain entropy ]]> https://biorxiv.org/content/10.1101/2024.03.07.583865v1?rss=1 Zhen, Y. Yang, Y. Zheng, Y. Wang, X. Liu, L. Zheng, Z. Zheng, H. Tang, S. 2024-03-12 doi:10.1101/2024.03.07.583865 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Highly Dynamic and Sensitive NEMOer Calcium Indicators for Imaging ER Calcium Signals in Excitable Cells ]]> https://biorxiv.org/content/10.1101/2024.03.08.583332v1?rss=1 Gu, W. Chen, J.-H. Zhang, Y. Wang, Z. Li, J. Wang, S. Zhang, H. Jiang, A. Zhong, Z. Zhang, J. Xi, C. Hou, T. Gill, D. L. Li, D. Mu, Y. Wang, S.-Q. Tang, A.-H. Wang, Y. 2024-03-09 doi:10.1101/2024.03.08.583332 Cold Spring Harbor Laboratory Press 2024-03-09 <![CDATA[ An octopamine-specific GRAB sensor reveals a monoamine relay circuitry that boosts aversive learning ]]> https://biorxiv.org/content/10.1101/2024.03.09.584200v1?rss=1 Lv, M. Cai, R. Zhang, R. Xia, X. Li, X. Wang, Y. Wang, H. Zeng, J. Xue, Y. Mao, L. Li, Y. 2024-03-12 doi:10.1101/2024.03.09.584200 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Interpretable antibody-antigen interaction prediction by bridging structure to sequence ]]> https://biorxiv.org/content/10.1101/2024.03.09.584264v1?rss=1 Liu, Y. Nie, Z. Chen, J. Zheng, X. Fu, J. Liu, Z. Liu, X. Xu, F. Huang, X. Zhang, W.-B. Ma, S. Gao, W. Tian, Y. 2024-03-13 doi:10.1101/2024.03.09.584264 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Deciphering Immune Complexity: Single-Cell Insights into Autoimmune Myocarditis Progression ]]> https://biorxiv.org/content/10.1101/2024.03.12.584698v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@1150607org.highwire.dtl.DTLVardef@13eb725org.highwire.dtl.DTLVardef@6a0be9org.highwire.dtl.DTLVardef@3400ac_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mamdouh, F. Abdulsahib, W. K. Alshaya, D. S. Fayad, E. Eid, R. A. Alsharif, G. Alshehri, M. A. Otifi, H. M. Soltan, M. A. Eldeen, M. A. 2024-03-14 doi:10.1101/2024.03.12.584698 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ The Origin of Movement Biases During Reaching ]]> https://biorxiv.org/content/10.1101/2024.03.15.585272v1?rss=1 Wang, T. Morehead, R. Tsay, J. S. Ivry, R. B. 2024-03-18 doi:10.1101/2024.03.15.585272 Cold Spring Harbor Laboratory Press 2024-03-18 <![CDATA[ N-acetyltransferase 10-mediated mRNA N4-acetylation is Essential for the Translational Regulation During Oocyte Meiotic Maturation in Mice ]]> https://biorxiv.org/content/10.1101/2024.03.15.585321v1?rss=1 Chen, L. Liu, S.-Y. Su, R.-B. Wu, Y.-K. Wang, W.-J. Wu, X. Zhang, S.-Y. Qiao, J. Sha, Q.-Q. Fan, H.-Y. 2024-03-17 doi:10.1101/2024.03.15.585321 Cold Spring Harbor Laboratory Press 2024-03-17 <![CDATA[ Normative growth modeling of brain morphology reveals neuroanatomical heterogeneity and biological subtypes in children with ADHD ]]> https://biorxiv.org/content/10.1101/2024.03.16.582202v1?rss=1 Bu, X. Zhao, Y. Zheng, X. Fu, Z. Zhang, K. Sun, X. Cui, Z. Xia, M. Ma, L. Liu, N. Lu, J. Zhao, G. Ding, Y. Deng, Y. Wang, J. Chen, R. Zhang, H. Men, W. Wang, Y. Gao, J. Tan, S. Sun, L. Qin, S. Tao, S. Wang, Y. Dong, Q. Cao, Q. Yang, L. He, Y. 2024-03-19 doi:10.1101/2024.03.16.582202 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Rapamycin Treatment Reduces Brain Pericyte Constriction in Ischemic Stroke ]]> https://biorxiv.org/content/10.1101/2024.03.18.584333v1?rss=1 Beard, D. Brown, L. S. Morris, G. P. Couch, Y. Adriaanse, B. A. Simoglou Karali, C. Schneider, A. M. Howells, D. W. Redzic, Z. B. Sutherland, B. A. Buchan, A. M. 2024-03-20 doi:10.1101/2024.03.18.584333 Cold Spring Harbor Laboratory Press 2024-03-20 <![CDATA[ A unique and biocompatible approach for corneal collagen crosslinking in vivo ]]> https://biorxiv.org/content/10.1101/2024.03.18.585574v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@c05147org.highwire.dtl.DTLVardef@18244borg.highwire.dtl.DTLVardef@f6e30eorg.highwire.dtl.DTLVardef@b4ec3a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> GULZAR, A. KALELI, H. N. Koseoglu, G. D. Hasanreisoglu, M. Yildiz, A. Sahin, A. KIZILEL, S. 2024-03-20 doi:10.1101/2024.03.18.585574 Cold Spring Harbor Laboratory Press 2024-03-20 <![CDATA[ Mycobacterium dormancy and antibiotic tolerance within the retinal pigment epithelium of ocular tuberculosis ]]> https://biorxiv.org/content/10.1101/2024.03.18.585612v1?rss=1 Liu, R. Dang, J. Rhoeun, L. Lee, J.-J. Ameri, H. Rao, N. Eoh, H. 2024-03-19 doi:10.1101/2024.03.18.585612 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ All-atom protein sequence design based on geometric deep learning ]]> https://biorxiv.org/content/10.1101/2024.03.18.585651v1?rss=1 Liu, J. Guo, Z. Zhang, C. Lai, L. 2024-03-19 doi:10.1101/2024.03.18.585651 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Molecular basis for the activation of the Fatty Acid Kinase complex of Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/2024.03.19.585040v1?rss=1 Myers, M. J. Xu, Z. Ryan, B. J. DeMars, Z. R. Ridder, M. J. Johnson, D. K. Krute, C. N. Flynn, T. S. Kashipathy, M. M. Battaile, K. P. Schnicker, N. J. Lovell, S. Freudenthal, B. D. Bose, J. L. 2024-03-19 doi:10.1101/2024.03.19.585040 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ CADTAD: CAncer Driver Topologically Associated Domains identify oncogenic and tumor suppressive lncRNAs ]]> https://biorxiv.org/content/10.1101/2024.03.19.585685v1?rss=1 Rao, Z. Zhang, M. Huang, S. Wu, C. Zhou, Y. Zhang, W. Lin, X. Zhao, D. 2024-03-21 doi:10.1101/2024.03.19.585685 Cold Spring Harbor Laboratory Press 2024-03-21 <![CDATA[ BRD8 guards the pluripotent state by sensing and maintaining histone acetylation ]]> https://biorxiv.org/content/10.1101/2024.03.20.585857v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@199139forg.highwire.dtl.DTLVardef@d735c6org.highwire.dtl.DTLVardef@10b6e15org.highwire.dtl.DTLVardef@16863cf_HPS_FORMAT_FIGEXP M_FIG C_FIG Key findingsO_LIBRD8 blocks the primed-to-naive transition. C_LIO_LIReduced Brd8 promoted the suppression of somatic and primed genes through reduced chromatin repression. C_LIO_LIReduced Brd8 enabled the accelerated activation of naive-specific genes by opening chromatin. C_LIO_LIBRD8 anchors the histone acetyltransferase KAT5 to acetylated genomic loci. C_LI ]]> Sun, L. Fu, X. Xiao, Z. Ma, G. Zhou, Y. Hu, H. Shi, L. Li, D. Jauch, R. Hutchins, A. 2024-03-20 doi:10.1101/2024.03.20.585857 Cold Spring Harbor Laboratory Press 2024-03-20 <![CDATA[ Single-cell profiling reveals the intratumor heterogeneity and immunosuppressive microenvironment in cervical adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2024.03.20.586024v1?rss=1 Peng, Y. Li, Y. Ao, J. Shen, J. He, X. Tang, D. Chu, C. Liu, C. Weng, L. 2024-03-21 doi:10.1101/2024.03.20.586024 Cold Spring Harbor Laboratory Press 2024-03-21 <![CDATA[ The Sociodemographic and Lifestyle Correlates of Epigenetic Aging in a Nationally Representative U.S. Study of Younger Adults ]]> https://biorxiv.org/content/10.1101/2024.03.21.585983v1?rss=1 Harris, K. M. Levitt, B. E. Gaydosh, L. Martin, C. Meyer, J. M. Mishra, A. A. Kelly, A. L. Aiello, A. E. 2024-03-27 doi:10.1101/2024.03.21.585983 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ The Genomes of Nematode-Trapping Fungi Provide Insights into the Origin and Diversification of Fungal Carnivorism ]]> https://biorxiv.org/content/10.1101/2024.03.21.586190v1?rss=1 Fan, Y. Du, M. Zhang, W. Deng, W. Yang, E. Wang, S. Yan, L. Zhang, L. Kang, S. Steenwyk, J. L. An, Z. Liu, X. Xiang, M. 2024-03-27 doi:10.1101/2024.03.21.586190 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Characterization of novel role for Rab27B in autophagy regulation in colorectal cancer ]]> https://biorxiv.org/content/10.1101/2024.03.22.586334v1?rss=1 Afroz, S. Preet, R. Vishwakarma, V. Evans, A. E. Dixon, D. A. 2024-03-23 doi:10.1101/2024.03.22.586334 Cold Spring Harbor Laboratory Press 2024-03-23 <![CDATA[ State-dependent Online Reactivations for Different Learning Strategies in Foraging ]]> https://biorxiv.org/content/10.1101/2024.03.25.586512v1?rss=1 Son, S. Wang, M. Z. Hayden, B. Y. Yoo, S. B. M. 2024-03-27 doi:10.1101/2024.03.25.586512 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Global variation in prior exposure shapes antibody neutralization profiles of SARS-CoV-2 variants up to BA.2.86 ]]> https://biorxiv.org/content/10.1101/2024.03.27.586820v1?rss=1 Turner, S. Amirthalingam, G. Bailey, D. Barouch, D. H. Bewley, K. R. Brown, K. Cao, Y. R. Chan, Y.-W. Charlton, S. DOVE consortium, Coombes, N. S. Hallis, B. Ho, D. D. Jian, F. Lasrado, N. Lassauniere, R. Lihong, L. Montefiori, D. C. Moss, P. Newman, J. Parry, H. Polacek Strandh, C. Rasmussen, M. Shao, F. Shen, X. Thakur, N. Thomson, E. C. Wang, J. Wang, P. Wang, Q. C. Willett, B. J. Yisimayi, A. Smith, D. J. 2024-03-27 doi:10.1101/2024.03.27.586820 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ The Molecular Architecture of the Nuclear Basket ]]> https://biorxiv.org/content/10.1101/2024.03.27.587068v1?rss=1 Singh, D. Soni, N. Hutchings, J. Echeverria, I. Shaikh, F. Duquette, M. Suslov, S. Li, Z. van Eeuwen, T. Molloy, K. Shi, Y. Wang, J. Guo, Q. Chait, B. T. Fernandez-Martinez, J. Rout, M. P. Sali, A. Villa, E. 2024-03-28 doi:10.1101/2024.03.27.587068 Cold Spring Harbor Laboratory Press 2024-03-28 <![CDATA[ Quantify genetic variants' regulatory potential via a hybrid sequence-oriented model ]]> https://biorxiv.org/content/10.1101/2024.03.28.587115v1?rss=1 Wang, Y. Liang, N. Gao, G. 2024-04-01 doi:10.1101/2024.03.28.587115 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ Mu Suppression During Action Observation Only in the Lower, not in the Higher, Frequency Subband ]]> https://biorxiv.org/content/10.1101/2024.03.28.587150v1?rss=1 Badakul, A. N. Soyman, E. 2024-03-31 doi:10.1101/2024.03.28.587150 Cold Spring Harbor Laboratory Press 2024-03-31 <![CDATA[ triangulaR: an R package for identifying AIMs and building triangle plots using SNP data from hybrid zones ]]> https://biorxiv.org/content/10.1101/2024.03.28.587167v1?rss=1 Wiens, B. J. Colella, J. P. 2024-04-01 doi:10.1101/2024.03.28.587167 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ A next generation of hierarchical Bayesian analyses of hybrid zones enables direct quantification of variation in introgression in R ]]> https://biorxiv.org/content/10.1101/2024.03.29.587395v1?rss=1 Gompert, Z. DeRaad, D. A. Buerkle, C. A. 2024-03-30 doi:10.1101/2024.03.29.587395 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Phylogeography of the Giant Honeybees Based on Mitochondrial Gene Sequences ]]> https://biorxiv.org/content/10.1101/2024.03.30.587434v1?rss=1 Bhatta, C. P. Cluff, S. C. Smith, D. R. 2024-03-31 doi:10.1101/2024.03.30.587434 Cold Spring Harbor Laboratory Press 2024-03-31 <![CDATA[ Detection of changes in membrane potential by magnetic resonance imaging ]]> https://biorxiv.org/content/10.1101/2024.04.02.587661v1?rss=1 Min, K. Chung, S. Lee, S.-K. Lee, J. Toi, P. T. Kim, D. Lee, J. S. Park, J.-Y. 2024-04-03 doi:10.1101/2024.04.02.587661 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Terroir and rootstock effects on leaf shape in California Central Valley vineyards ]]> https://biorxiv.org/content/10.1101/2024.04.02.587833v1?rss=1 Migicovsky, Z. Swift, J. F. Awale, M. Helget, Z. Klein, L. L. Pinkner, L. Woodhouse, K. Cousins, P. Fennell, A. Y. Miller, A. Chitwood, D. H. 2024-04-03 doi:10.1101/2024.04.02.587833 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Comparative Analysis of Structural Alignment Algorithms for Protein-Protein Interfaces in Template-Based Docking Studies ]]> https://biorxiv.org/content/10.1101/2024.04.03.587755v1?rss=1 Cankara, F. Tuncbag, N. Gursoy, A. Keskin, O. 2024-04-05 doi:10.1101/2024.04.03.587755 Cold Spring Harbor Laboratory Press 2024-04-05 <![CDATA[ Prominent involvement of acetylcholine in shaping stable olfactory representation across the Drosophila brain ]]> https://biorxiv.org/content/10.1101/2024.04.03.587915v1?rss=1 Fan, J. Wang, Y. Li, L. He, J. Zhao, Z. Deng, F. Li, G. Li, X. Zhou, Y. Zhao, J. Li, Y. Wu, J. Fang, L. Dai, Q. 2024-04-05 doi:10.1101/2024.04.03.587915 Cold Spring Harbor Laboratory Press 2024-04-05 <![CDATA[ DCLK1-Mediated Regulation of Invadopodia Dynamics and Matrix Metalloproteinase Trafficking Drives Invasive Progression in Head and Neck Squamous Cell Carcinoma ]]> https://biorxiv.org/content/10.1101/2024.04.06.588339v1?rss=1 Arnold, L. Yap, M. K. Jackson, L. K. Ly, T. K. Morrison, A. K. Washburn, M. Standing, D. Gomez, J. Yellap, N. K. Li, L. Umar, S. Anant, S. Thomas, S. M. 2024-04-12 doi:10.1101/2024.04.06.588339 Cold Spring Harbor Laboratory Press 2024-04-12 <![CDATA[ Role of Mutual Information Profile Shifts in Assessing the Pathogenicity of Mutations on Protein Functions: The case of Pyrin Mutations ]]> https://biorxiv.org/content/10.1101/2024.04.07.588500v1?rss=1 Hacisuleyman, A. Gul, A. Erman, B. 2024-04-09 doi:10.1101/2024.04.07.588500 Cold Spring Harbor Laboratory Press 2024-04-09 <![CDATA[ No Reliable Evidence Supports the Presence of Javan Tigers - Data Issues Related to the DNA Analysis of a Recent Hair Sample ]]> https://biorxiv.org/content/10.1101/2024.04.08.588384v1?rss=1 Sui, Z.-Y. Yamaguchi, N. Liu, Y.-C. Xue, H.-R. Sun, X. Nyhus, P. Luo, S.-J. 2024-04-11 doi:10.1101/2024.04.08.588384 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[ FLASH Irradiation Regulates IFN-β induction by mtDNA via Cytochrome c Leakage ]]> https://biorxiv.org/content/10.1101/2024.04.10.588811v1?rss=1 Lv, J. Sun, J. Luo, Y. Liu, J. Wu, D. Fang, Y. Lan, H. Diao, L. Ma, Y. Li, Y. Wang, M. Zhao, Z. Wang, H. Morris, A. Zhang, W. Zhang, Z. Lin, L. Jia, H. Wang, C. Li, T. Mourou, G. Huang, S. Yang, G. Yan, X. 2024-04-13 doi:10.1101/2024.04.10.588811 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ Massively Parallel Polyribosome Profiling Reveals Translation Defects of Human Disease-Relevant UTR Mutations ]]> https://biorxiv.org/content/10.1101/2024.04.11.589132v1?rss=1 0.8) in predicting polysome-shifting mutations in the test dataset. Additionally, several lines of evidence indicate that changes in uORF usage underlie the translation deficiency arising from these mutations. Illustrating this, we demonstrate that a pathogenic mutation in the IRF6 5 UTR suppresses translation of the primary open reading frame by creating a uORF. Remarkably, site- directed ADAR editing of the mutant mRNA rescued this translation deficiency. Overall, our study provides insights into the molecular mechanisms of UTR mutations and their links to clinical impacts through translation defects. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/589132v2_ufig1.gif" ALT="Figure 1000"> View larger version (50K): org.highwire.dtl.DTLVardef@57217corg.highwire.dtl.DTLVardef@575410org.highwire.dtl.DTLVardef@15013bforg.highwire.dtl.DTLVardef@408840_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Li, W.-P. Su, J.-Y. Chang, Y.-C. Wang, Y.-L. Chiang, H.-L. Hsieh, Y.-T. Chiang, Y.-H. Ko, Y.-L. Chiang, B.-J. Yang, C.-H. Huang, Y.-T. Lin, C.-L. 2024-04-13 doi:10.1101/2024.04.11.589132 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ CCDC113 stabilizes sperm axoneme and head-tail coupling apparatus to ensure male fertility ]]> https://biorxiv.org/content/10.1101/2024.04.12.589289v1?rss=1 Wu, B. Long, C. Yang, Y. Zhang, Z. Ma, S. Ma, Y. Wei, H. Li, J. Jiang, H. Li, W. Liu, C. 2024-04-14 doi:10.1101/2024.04.12.589289 Cold Spring Harbor Laboratory Press 2024-04-14 <![CDATA[ MOL-AE: Auto-Encoder Based Molecular Representation Learning With 3D Cloze Test Objective ]]> https://biorxiv.org/content/10.1101/2024.04.13.589331v1?rss=1 Yang, J. Zheng, K. Long, S. Nie, Z. Zhang, M. Dai, X. Ma, W.-Y. Zhou, H. 2024-04-15 doi:10.1101/2024.04.13.589331 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ Machine learning driven image segmentation and shape clustering of algal microscopic images obtained from various water types ]]> https://biorxiv.org/content/10.1101/2024.04.13.589342v1?rss=1 Nelli, F. Ge, Z. Blackall, L. Taheriashtiani, N. Henry, R. Brumley, D. R. Grace, M. Jex, A. Burch, M. Lin, T.-F. Bertelkamp, C. Willis, A. Gao, L. Schmidt, J. Crosbie, N. D. Zamyadi, A. 2024-04-13 doi:10.1101/2024.04.13.589342 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ The transcripts of a gastrula-premarked enhancer prime posterior tissue development through cross-talk with morphogen effector ]]> https://biorxiv.org/content/10.1101/2024.04.14.589453v1?rss=1 Chen, Y. Tan, F. Yang, X. Fang, Q. Zhang, L. Liao, J. Shen, P. Qian, Y. Wen, M. Song, R. Fu, Y. Xu, H. J. Wang, R. Li, C. Shao, Z. Li, J. Jing, N. 2024-04-17 doi:10.1101/2024.04.14.589453 Cold Spring Harbor Laboratory Press 2024-04-17 <![CDATA[ Unveiling the influence of tumor and immune signatures on immune checkpoint therapy in advanced lung cancer ]]> https://biorxiv.org/content/10.1101/2024.04.15.589544v1?rss=1 Kim, N. Park, S. Jo, A. Eum, H. H. Kim, H. K. Lee, K. Cho, J. H. Ku, B. M. Jung, H. A. Sun, J.-M. Lee, S.-H. Ahn, J. S. Lee, J.-I. Choi, J. W. Jeong, D. Na, M. Kang, H. Kim, J. Y. Choi, J. K. Lee, H.-O. Ahn, M.-J. 2024-04-20 doi:10.1101/2024.04.15.589544 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Synthetic G protein-coupled receptors for programmable sensing and control of cell behavior ]]> https://biorxiv.org/content/10.1101/2024.04.15.589622v1?rss=1 Kalogriopoulos, N. A. Tei, R. Yan, Y. Ravalin, M. Li, Y. Ting, A. Y. 2024-04-15 doi:10.1101/2024.04.15.589622 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ That's not a Hybrid: How to Distinguish Patterns of Admixture and Isolation-by-Distance ]]> https://biorxiv.org/content/10.1101/2024.04.15.589658v1?rss=1 Wiens, B. J. Colella, J. P. 2024-04-20 doi:10.1101/2024.04.15.589658 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Chromatin-focused genetic and chemical screens identify BRPF1 as a targetable vulnerability in Taxol-resistant triple-negative breast cancer ]]> https://biorxiv.org/content/10.1101/2024.04.16.587277v1?rss=1 Yedier-Bayram, O. Cingoz, A. Yilmaz, E. Aksu, A. C. Esin, B. Pinarbasi Degirmenci, N. Cavga, A. D. Dedeoglu, B. Cevatemre, B. Syed, H. Philpott, M. Cribbs, A. P. Oppermann, U. Lack, N. ACILAN AYHAN, C. Onder, T. T. Bagci-Onder, T. 2024-04-20 doi:10.1101/2024.04.16.587277 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Multi-Omics after O-GlcNAc Alteration Identifies Cellular Processes Working Synergistically to Promote Aneuploidy ]]> https://biorxiv.org/content/10.1101/2024.04.16.589379v1?rss=1 Boyd, S. Robarts, D. Nguyen, K. Villar, M. Alghusen, I. Kotulkar, M. Denson, A. Fedoosyuk, H. Lee, N. Whelan, S. A. Hanover, J. A. Dias, W. Tan, E. P. McGreal, S. Artigues, A. Swerdlow, R. H. Thompson, J. Apte, U. Slawson, C. 2024-04-16 doi:10.1101/2024.04.16.589379 Cold Spring Harbor Laboratory Press 2024-04-16 <![CDATA[ A generalized framework to identify SARS-CoV-2 broadly neutralizing antibodies ]]> https://biorxiv.org/content/10.1101/2024.04.16.589454v1?rss=1 Jian, F. Wec, A. Z. Feng, L. Yu, Y. Wang, L. Wang, P. Yu, L. Wang, J. Hou, J. Berrueta, D. M. Lee, D. Speidel, T. Ma, L. Kim, T. Yisimayi, A. Song, W. Wang, J. Liu, L. Yang, S. Niu, X. Xiao, T. An, R. Wang, Y. Shao, F. Wang, Y. Pecetta, S. Wang, X. Walker, L. M. Cao, Y. 2024-04-18 doi:10.1101/2024.04.16.589454 Cold Spring Harbor Laboratory Press 2024-04-18 <![CDATA[ X-ray Crystallographic and Hydrogen Deuterium Exchange Studies Confirm Alternate Kinetic Models for Homolog Insulin Monomers ]]> https://biorxiv.org/content/10.1101/2024.04.16.589767v1?rss=1 Ayan, E. Turk, M. Tatli, O. Telek, E. Dingiloglu, B. Dinler Doganay, G. Demirci, H. 2024-04-22 doi:10.1101/2024.04.16.589767 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ Dissociable memory modulation mechanisms facilitate fear amnesia at different timescales ]]> https://biorxiv.org/content/10.1101/2024.04.16.589786v1?rss=1 Wang, Y. Ni, Y. Zhu, Z. Hu, J. Schiller, D. Li, J. 2024-04-20 doi:10.1101/2024.04.16.589786 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ ProLLM: Protein Chain-of-Thoughts Enhanced LLM for Protein-Protein Interaction Prediction ]]> https://biorxiv.org/content/10.1101/2024.04.18.590025v1?rss=1 Jin, M. Haochen, X. Wang, Z. Kang, B. Ye, R. Zhou, K. Du, M. Zhang, Y. 2024-04-21 doi:10.1101/2024.04.18.590025 Cold Spring Harbor Laboratory Press 2024-04-21 <![CDATA[ Nrf2 regulates the activation-driven expansion of CD4+ T-cells by differentially modulating glucose and glutamine metabolism ]]> https://biorxiv.org/content/10.1101/2024.04.18.590146v1?rss=1 Tripathi, A. Dasgupta, D. Pant, A. Bugbee, A. Yellapu, N. K. Choi, B. H. Y. Giri, s. Pyaram, K. 2024-04-22 doi:10.1101/2024.04.18.590146 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ Cerebrospinal fluid proteome profiling using machine learning shows a unique protein signature associated with APOE4 genotype ]]> https://biorxiv.org/content/10.1101/2024.04.18.590160v1?rss=1 Shvetcov, A. Thomson, S. Cho, A.-N. Wilkins, H. M. Reed, J. H. Swerdlow, R. H. Brown, D. A. Alzheimer's Disease Neuroimaging Initiative, Finney, C. A. 2024-04-22 doi:10.1101/2024.04.18.590160 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ Humoral immunogenicity comparison of XBB and JN.1 in human infections ]]> https://biorxiv.org/content/10.1101/2024.04.19.590276v1?rss=1 Jian, F. Yisimayi, A. Song, W. Wang, J. Xu, Y. Chen, X. Yu, Y. Niu, X. Yang, S. Wang, P. Sun, H. Yu, L. Wang, J. Wang, Y. An, R. Wang, W. Xiao, T. Gu, Q. Shao, F. Wang, Y. Shen, Z. Jin, R. Cao, Y. 2024-04-22 doi:10.1101/2024.04.19.590276 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ Directed differentiation of functional corticospinal-like neurons from endogenous SOX6+/NG2+ cortical progenitors ]]> https://biorxiv.org/content/10.1101/2024.04.21.590488v1?rss=1 Ozkan, A. Padmanabhan, H. K. Shipman, S. Azim, E. Kumar, P. Sadegh, C. Basak, N. Macklis, J. D. 2024-04-23 doi:10.1101/2024.04.21.590488 Cold Spring Harbor Laboratory Press 2024-04-23 <![CDATA[ Time-resolved function of cell polarity kinases PRKCZ and PRKCI in CNS myelination ]]> https://biorxiv.org/content/10.1101/2024.04.22.589759v1?rss=1 Mercau, M. E. Hackbarth, R.-M. Liu, X. Wang, H. Zhang, L. Basu, M. K. Rothlin, C. V. Ghosh, S. 2024-04-23 doi:10.1101/2024.04.22.589759 Cold Spring Harbor Laboratory Press 2024-04-23 <![CDATA[ Pharmaco-resistant temporal lobe epilepsy gradually perturbs the cortex-wide excitation-inhibition balance ]]> https://biorxiv.org/content/10.1101/2024.04.22.590555v1?rss=1 Xie, K. Royer, J. Rodriguez-Cruces, R. Horwood, L. Ngo, A. Arafat, T. Auer, H. Sahlas, E. Chen, J. Zhou, Y. Valk, S. L. Hong, S.-J. Frauscher, B. Pana, R. Bernasconi, A. Bernasconi, N. Concha, L. Bernhardt, B. C. 2024-04-27 doi:10.1101/2024.04.22.590555 Cold Spring Harbor Laboratory Press 2024-04-27 <![CDATA[ Towards anchoring evolutionary fitness for protein stability with virtual chemical environment recovery ]]> https://biorxiv.org/content/10.1101/2024.04.22.590665v1?rss=1 Nie, Z. Ma, Y. Chen, J. Liu, Y. Liu, Z. Yang, P. Xu, F. Huang, X. Yin, F. Li, Z. Fu, J. Ren, Z. Zhang, W.-B. Gao, W. Tian, Y. 2024-04-26 doi:10.1101/2024.04.22.590665 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ Short- and long-range roles of UNC-6/Netrin in dorsal-ventral axon guidance in vivo in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2024.04.23.590737v1?rss=1 Hooper, K. M. Lundquist, E. A. 2024-04-23 doi:10.1101/2024.04.23.590737 Cold Spring Harbor Laboratory Press 2024-04-23 <![CDATA[ CRISPR screens reveal convergent targeting strategies against evolutionarily distinct chemoresistance in cancer ]]> https://biorxiv.org/content/10.1101/2024.04.24.591030v1?rss=1 Zhong, C. Jiang, W.-J. Yao, Y. Li, Z. Li, Y. Wang, S. Wang, X. Zhu, W. Wu, S. Wang, J. Fan, S. Ma, S. Liu, Y. Zhang, H. Zhao, W. Zhao, L. Feng, Y. Li, Z. Guo, R. Yu, L. Pei, F. Hu, J. Feng, X. Yang, Z. Yang, Z. Yang, X. Hou, Y. Zhang, D. Xu, D. Sheng, R. Li, Y. Liu, L. Wu, H.-J. Huang, J. Fei, T. 2024-04-27 doi:10.1101/2024.04.24.591030 Cold Spring Harbor Laboratory Press 2024-04-27 <![CDATA[ Massively parallel interrogation of human functional variants modulating cancer immunosurveillance ]]> https://biorxiv.org/content/10.1101/2024.04.25.591036v1?rss=1 Liu, Y. Liu, Y. Niu, X. Chen, A. Li, Y. Yu, Y. Liu, Z. Wei, W. 2024-04-27 doi:10.1101/2024.04.25.591036 Cold Spring Harbor Laboratory Press 2024-04-27 <![CDATA[ An ingestible, battery-free, tissue-adhering robotic interface for non-invasive and chronic electrostimulation of the gut ]]> https://biorxiv.org/content/10.1101/2024.04.25.591220v1?rss=1 Nan, K. Wong, K. Li, D. Ying, B. McRae, J. C. Feig, V. R. Wang, S. Yao, K. Zhou, J. Li, J. Jenkins, J. Ishida, K. Kuosmanen, J. Madani, W. Hayward, A. Ramadi, K. Yu, X. Traverso, G. 2024-04-28 doi:10.1101/2024.04.25.591220 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Effects of Age on Cross-Cultural Differences in the Neural Correlates of Memory Retrieval ]]> https://biorxiv.org/content/10.1101/2024.04.25.591227v1?rss=1 Cho, I. Leger, K. R. Valoumas, I. Mair, R. W. Goh, J. O. S. Gutchess, A. 2024-04-28 doi:10.1101/2024.04.25.591227 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ PARP14 is pro- and anti-viral host factor that promotes IFN production and affects the replication of multiple viruses ]]> https://biorxiv.org/content/10.1101/2024.04.26.591186v1?rss=1 Parthasarathy, S. Saenjamsai, P. Hao, H. Ferkul, A. Pfannenstiel, J. J. Suder, E. L. Bejan, D. S. Chen, Y. Schwarting, N. Aikawa, M. Muhlberger, E. Orozco, R. C. Sullivan, C. S. Cohen, M. S. Davido, D. Hume, A. J. Fehr, A. 2024-04-26 doi:10.1101/2024.04.26.591186 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ Enteropathogenic Providencia alcalifaciens: A subgroup of P. alcalifaciens that causes diarrhea. ]]> https://biorxiv.org/content/10.1101/2024.04.26.591277v1?rss=1 Bulach, D. Carter, G. P. Albert, M. J. 2024-04-26 doi:10.1101/2024.04.26.591277 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ Bacterial stress granule protects mRNA through ribonucleases exclusion ]]> https://biorxiv.org/content/10.1101/2024.04.27.591437v1?rss=1 Pei, L. Xian, Y. Yan, X. Schaefer, C. Syeda, A. H. Howard, J. Liao, H. Bai, F. Leake, M. C. Pu, Y. 2024-04-29 doi:10.1101/2024.04.27.591437 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Comparative investigations of cellular dynamics in the development of medusae (Cnidaria: Medusozoa) ]]> https://biorxiv.org/content/10.1101/2024.04.28.591574v1?rss=1 Travert, M. K. Winata, K. Cartwright, P. 2024-04-30 doi:10.1101/2024.04.28.591574 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ Double training reveals an interval-invariant subsecond temporal structure in the brain ]]> https://biorxiv.org/content/10.1101/2024.04.30.591981v1?rss=1 Guan, S.-C. Xiong, Y.-Z. Yu, C. 2024-05-01 doi:10.1101/2024.04.30.591981 Cold Spring Harbor Laboratory Press 2024-05-01 <![CDATA[ PhaSeDis: A Manually Curated Database of Phase Separation-Disease Associations and Corresponding Small Molecules ]]> https://biorxiv.org/content/10.1101/2024.05.01.591645v1?rss=1 Chen, T. Tang, G. Li, T. Yanghong, Z. Hou, C. Du, Z. Ma, L. Li, T. 2024-05-03 doi:10.1101/2024.05.01.591645 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Co-occurring Mutations in Different Genes Can Fuel Oncogenic Signaling and Serve as Metastatic Tumor Markers ]]> https://biorxiv.org/content/10.1101/2024.05.01.592039v1?rss=1 Yavuz, B. R. Sahin, U. Jang, H. Nussinov, R. Tuncbag, N. 2024-05-03 doi:10.1101/2024.05.01.592039 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Untargeted Plasma Metabolomics Unveils Distinct Metabolite Profiles in Parkinson Disease Subtypes: A Focus on idiopathic REM Sleep Behavior Disorders ]]> https://biorxiv.org/content/10.1101/2024.05.02.592293v1?rss=1 Lee, S. Kim, J. Baek, J. Jung, K.-Y. Lee, Y. Koh, A. Kim, H.-J. 2024-05-05 doi:10.1101/2024.05.02.592293 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Development of the overlapping network modules in the human brain ]]> https://biorxiv.org/content/10.1101/2024.05.03.592316v1?rss=1 He, Y. Lei, T. Liao, X. Liang, X. Sun, L. Xia, M. Xia, Y. Zhao, T. Chen, X. Men, W. Wang, Y. Ma, L. Liu, N. Lu, J. Zhao, G. Ding, Y. Deng, Y. Wang, J. Chen, R. Zhang, H. Tan, S. Gao, J.-H. Qin, S. Tao, S. Dong, Q. 2024-05-05 doi:10.1101/2024.05.03.592316 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Dopamine and acetylcholine correlations in the nucleus accumbens depend on behavioral task states ]]> https://biorxiv.org/content/10.1101/2024.05.03.592439v1?rss=1 Costa, K. M. Zhang, Z. Zhuo, Y. Li, G. Li, Y. Schoenbaum, G. 2024-05-04 doi:10.1101/2024.05.03.592439 Cold Spring Harbor Laboratory Press 2024-05-04 <![CDATA[ A gentle palette of plasma membrane dyes ]]> https://biorxiv.org/content/10.1101/2024.05.04.592408v1?rss=1 Ling, J. Liu, Y. Fu, Y. Liu, S. Ding, L. Huang, L. Xi, P. Chen, Z. 2024-05-04 doi:10.1101/2024.05.04.592408 Cold Spring Harbor Laboratory Press 2024-05-04 <![CDATA[ The Brain Computes Dynamic Facial Movements for Emotion Categorization Using a Third Pathway ]]> https://biorxiv.org/content/10.1101/2024.05.06.592699v1?rss=1 Yan, Y. Zhan, J. Garrod, O. Chen, C. Ince, R. A. A. Jack, R. Schyns, P. G. 2024-05-08 doi:10.1101/2024.05.06.592699 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Characterization of a Biochemical Mouse Model of Primary Aldosteronism for Thermal Therapies ]]> https://biorxiv.org/content/10.1101/2024.05.07.592955v1?rss=1 Keck, S. A. Mullen, N. Taylor, A. E. Gliligan, L. C. Pyle, M. Shrestha, T. B. Sebek, J. Highland, M. A. Challapalli, R. Arlt, W. Bossmann, S. H. Dennedy, M. C. Prakash, P. Basel, M. T. 2024-05-10 doi:10.1101/2024.05.07.592955 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ KF4 anti-CELA1 Antibody and Purified α1-Antitrypsin Have Similar but Not Additive Efficacy in Preventing Emphysema in Murine α1-Antitrypsin Deficiency ]]> https://biorxiv.org/content/10.1101/2024.05.07.592994v1?rss=1 Devine, A. J. Smith, N. J. Joshi, R. Brooks-Patton, B. Dunham, J. Varisco, A. N. Goodman, E. M. Fan, Q. Zingarelli, B. Varisco, B. M. 2024-05-10 doi:10.1101/2024.05.07.592994 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Fuel buildup shapes post-fire fuel decomposition through soil heating effects on plants, fungi, and soil chemistry ]]> https://biorxiv.org/content/10.1101/2024.05.08.592975v1?rss=1 Hopkins, J. R. Semenova-Nelsen, T. A. Huffman, J. M. Jones, N. J. Robertson, K. M. Platt, W. J. Sikes, B. A. 2024-05-10 doi:10.1101/2024.05.08.592975 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Nothing but lies: improving the validity of neural predictors of deception ]]> https://biorxiv.org/content/10.1101/2024.05.08.593230v1?rss=1 Lee, S. Niu, R. Zhu, L. Kayser, A. Hsu, M. 2024-05-09 doi:10.1101/2024.05.08.593230 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ Neuropeptide Y co-opts neuronal ensembles for memory lability and stability ]]> https://biorxiv.org/content/10.1101/2024.05.09.593455v1?rss=1 Wu, Y.-J. Gu, X. Kong, Y. Yang, S. Wang, H. Xu, M. Wang, Q. Yi, X. Lin, Z.-J. Jiao, Z.-H. Cheung, H. Zhao, X.-Y. Bian, X. Jiang, Q. Li, Y. Zhu, M. X. Wang, L.-Y. Li, Y. Huang, J. Li, Q. Li, W.-G. Xu, T.-L. 2024-05-10 doi:10.1101/2024.05.09.593455 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Control of Inflammatory Response by Tissue Microenvironment ]]> https://biorxiv.org/content/10.1101/2024.05.10.592432v1?rss=1 Wu, Z. Pope, S. D. Ahmed, N. S. Leung, D. L. Hajjar, S. Yue, Q. Anand, D. M. Kopp, E. B. Okin, D. Ma, W. Kagan, J. C. Hargreaves, D. C. Medzhitov, R. Zhou, X. 2024-05-14 doi:10.1101/2024.05.10.592432 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Development of a humanized anti-FABP4 monoclonal antibody for treatment of breast cancer ]]> https://biorxiv.org/content/10.1101/2024.05.12.593748v1?rss=1 Hao, J. Jin, R. Yi, Y. Jiang, X. Yu, J. Xu, Z. Schnicker, N. J. Chimenti, M. S. Sugg, S. L. Li, B. 2024-05-14 doi:10.1101/2024.05.12.593748 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Analysis of differential expression of matrix metalloproteins and defensins in the nasopharyngeal milieu of mild and severe COVID-19 cases ]]> https://biorxiv.org/content/10.1101/2024.05.12.593784v1?rss=1 Imtiaz, K. Farooqui, N. Ahmed, K. Zhamalbekova, A. Anwar, M. F. Gul, K. Hussain, A. Sarria-Santamera, A. Abidi, S. H. 2024-05-13 doi:10.1101/2024.05.12.593784 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ Mining the biosynthetic landscape of lactic acid bacteria unearths a new family of RiPPs assembled by a novel type of ThiF-like adenylyltransferases ]]> https://biorxiv.org/content/10.1101/2024.05.13.593846v1?rss=1 View larger version (21K): org.highwire.dtl.DTLVardef@1cd3125org.highwire.dtl.DTLVardef@55a546org.highwire.dtl.DTLVardef@d5a325org.highwire.dtl.DTLVardef@1c9e1f3_HPS_FORMAT_FIGEXP M_FIG C_FIG (For Table of Contents use only) ]]> Wang, M. Wu, M. Han, M. Niu, X. Fan, A. Zhu, S. Tong, Y. 2024-05-13 doi:10.1101/2024.05.13.593846 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ Unveiling Conserved Allosteric Hot Spots in Protein Domains from Sequences ]]> https://biorxiv.org/content/10.1101/2024.05.13.593877v1?rss=1 Hacisuleyman, A. Fasshauer, D. 2024-05-15 doi:10.1101/2024.05.13.593877 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ plantMASST - Community-driven chemotaxonomic digitization of plants ]]> https://biorxiv.org/content/10.1101/2024.05.13.593988v1?rss=1 Gomes, P. W. P. Mannochio-Russo, H. Schmid, R. Zuffa, S. Damiani, T. Quiros-Guerrero, L.-M. Caraballo-Rodriguez, A. M. Zhao, H. N. Yang, H. Xing, S. Charron-Lamoureux, V. Chigumba, D. N. Sedio, B. E. Myers, J. A. Allard, P.-M. Harwood, T. V. Tamayo-Castillo, G. Kang, K. B. Defossez, E. Koolen, H. H. F. da Silva, M. N. e Silva, C. Y. Y. Rasmann, S. Walker, T. W. N. Glauser, G. Chaves-Fallas, J. M. David, B. Kim, H. Lee, K. H. Kim, M. J. Choi, W. J. Keum, Y.-S. de Lima, E. J. S. P. de Medeiros, L. S. Bataglion, G. A. Costa, E. V. da Silva, F. M. A. Carvalho, 2024-05-15 doi:10.1101/2024.05.13.593988 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Omicron-specific naive B cell maturation alleviates immune imprinting induced by SARS-CoV-2 inactivated vaccine ]]> https://biorxiv.org/content/10.1101/2024.05.13.594034v1?rss=1 Yisimayi, A. Song, W. Wang, J. Jian, F. Yu, Y. Chen, X. Xu, Y. An, R. Wang, Y. Wang, J. Sun, H. Wang, P. Yu, L. Shao, F. Jin, R. Shen, Z. Wang, Y. Cao, Y. 2024-05-14 doi:10.1101/2024.05.13.594034 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Amyloid beta glycation leads to neuronal mitochondrial dysfunction and Alzheimers pathogenesis through VDAC1-dependent mtDNA efflux ]]> https://biorxiv.org/content/10.1101/2024.05.14.594173v1?rss=1 Akhter, F. Akhter, A. Schiff, H. Maffei, A. Zhu, X. DOUGLAS, J. Zhao, Z. Zhu, D. 2024-05-14 doi:10.1101/2024.05.14.594173 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Spatiotemporal dynamic models of Amblyomma americanum questing activity in the Central Great Plains ]]> https://biorxiv.org/content/10.1101/2024.05.14.594229v1?rss=1 Cobos, M. E. Winters, T. Martinez, I. Yao, Y. Xiao, X. Ghosh, A. Sundstrom, K. Duncan, K. Brennan, R. E. Little, S. E. Peterson, A. T. 2024-05-17 doi:10.1101/2024.05.14.594229 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ Feeding Rates of Sessile and Motile Ciliates are Hydrodynamically Equivalent ]]> https://biorxiv.org/content/10.1101/2024.05.15.593824v1?rss=1 Liu, J. Man, Y. Costello, J. Kanso, E. 2024-05-18 doi:10.1101/2024.05.15.593824 Cold Spring Harbor Laboratory Press 2024-05-18 <![CDATA[ Efficient DNA base editing via an optimized DYW-like deaminase ]]> https://biorxiv.org/content/10.1101/2024.05.15.594452v1?rss=1 Kweon, J. Park, S. Jeon, M. Y. Lim, K. Jang, G. Jang, A.-H. Lee, M. Seok, C. Lee, C. Park, S. Ahn, J. Jang, J. Sung, Y. Kim, D. Kim, Y. 2024-05-16 doi:10.1101/2024.05.15.594452 Cold Spring Harbor Laboratory Press 2024-05-16 <![CDATA[ Novel phylogenomic inference and 'Out of Asia' biogeography of cobras, coral snakes, and their allies ]]> https://biorxiv.org/content/10.1101/2024.05.17.594737v1?rss=1 Weinell, J. Burbrink, F. Das, S. Brown, R. 2024-05-21 doi:10.1101/2024.05.17.594737 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ A Sap Peptide Conserved across Flowering Plants Positively Regulates Lignin Biosynthesis, Biomass and Immunity ]]> https://biorxiv.org/content/10.1101/2024.05.20.594799v1?rss=1 Chen, C.-H. Liou, P.-C. Hsu, Y.-F. Wang, I.-F. Kuo, C.-Y. Huang, K.-H. Yu, J.-H. Chen, C.-W. Wu, C.-C. Lin, D.-G. Li, C.-B. Tu, Y.-K. Hsu, C.-C. Su, J.-C. Xia, K. Tsai, I. J. Lin, Y.-C. J. Chen, Y.-L. 2024-05-21 doi:10.1101/2024.05.20.594799 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Accurate Conformation Sampling via Protein Structural Diffusion ]]> https://biorxiv.org/content/10.1101/2024.05.20.594916v1?rss=1 Fan, J. Li, Z. Alcaide, E. Ke, G. Huang, H. E, W. 2024-05-21 doi:10.1101/2024.05.20.594916 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ A complete and dynamic tree of birds ]]> https://biorxiv.org/content/10.1101/2024.05.20.595017v1?rss=1 McTavish, E. J. Gerbracht, J. A. Holder, M. T. Iliff, M. J. Lepage, D. Rasmussen, P. C. Redelings, B. Sanchez-Reyes, L. L. Miller, E. T. 2024-05-22 doi:10.1101/2024.05.20.595017 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ Temperature-Dependent Fold-Switching Mechanism of the Circadian Clock Protein KaiB ]]> https://biorxiv.org/content/10.1101/2024.05.21.594594v1?rss=1 Liwang, A. Dinner, A. Sosnick, T. Wang, L.-P. Partch, C. L. Zhang, N. Sood, D. Guo, S. Chen, N. Baxa, M. Chavan, A. Hong, L. Antoszewski, A. Marianchuk, T. Peng, X. Xiao, Y. Dey, S. 2024-05-21 doi:10.1101/2024.05.21.594594 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Different orthology inference algorithms generate similar predicted orthogroups among Brassicaceae species ]]> https://biorxiv.org/content/10.1101/2024.05.21.595184v1?rss=1 Liao, I. T. Sears, K. E. Hileman, L. C. Nikolov, L. A. 2024-05-23 doi:10.1101/2024.05.21.595184 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ A new GRAB sensor reveals differences in the dynamics and molecular regulation between neuropeptide and neurotransmitter release ]]> https://biorxiv.org/content/10.1101/2024.05.22.595424v1?rss=1 Xia, X. Li, Y. 2024-05-23 doi:10.1101/2024.05.22.595424 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Fast evolutionary turnover and overlapping variances of sex-biased gene expression patterns defy a simple binary classification of sexes ]]> https://biorxiv.org/content/10.1101/2024.05.22.595301v1?rss=1 Xie, C. Künzel, S. Tautz, D. 2024-05-26 doi:10.1101/2024.05.22.595301 Cold Spring Harbor Laboratory Press 2024-05-26 <![CDATA[ Multi-omics analysis of longitudinal patient samples reveals the molecular mechanism of AML progression ]]> https://biorxiv.org/content/10.1101/2024.05.28.593678v1?rss=1 Ahmed, N. Cavattoni, I. Villiers, W. Cugno, C. Deola, S. Mifsud, B. 2024-06-02 doi:10.1101/2024.05.28.593678 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Genomic and Genetic Insights into Mendel's Pea Genes ]]> https://biorxiv.org/content/10.1101/2024.05.31.596837v1?rss=1 Feng, C. Chen, B. Hofer, J. Shi, Y. Jiang, M. Song, B. Cheng, H. Lu, L. Wang, L. Howard, A. Bendahmane, A. Fouchal, A. Moreau, C. Sawada, C. LeSignor, C. Barclay, E. Vikeli, E. Tsanakas, G. Zhao, H. Cheema, J. Sayers, L. Wingen, L. Vigouroux, M. Vickers, M. Ambrose, M. Dalmais, M. Higuera-Poveda, P. Spanner, R. Horler, R. Wouters, R. Chundakkad, S. Zhao, X. Li, X. Sun, Y. Huang, Z. Deng, X. Steuernagel, B. Domoney, C. Ellis, N. Chayut, N. Cheng, S. 2024-06-03 doi:10.1101/2024.05.31.596837 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ stVCR: Reconstructing spatio-temporal dynamics of cell development using optimal transport ]]> https://biorxiv.org/content/10.1101/2024.06.02.596937v1?rss=1 Peng, Q. Zhou, P. Li, T. 2024-06-03 doi:10.1101/2024.06.02.596937 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ AARS2 ameliorates myocardial ischemia via fine-tuning PKM2-mediated metabolism ]]> https://biorxiv.org/content/10.1101/2024.06.04.597368v1?rss=1 Zhang, Z. Zheng, L. Chen, Y. Chen, Y. Hou, J. Xiao, C. Zhu, X. Zhao, S. Xiong, J.-W. 2024-06-05 doi:10.1101/2024.06.04.597368 Cold Spring Harbor Laboratory Press 2024-06-05 <![CDATA[ Impact of Parental Time-Restricted Feeding on Offspring Metabolic Phenotypic Traits ]]> https://biorxiv.org/content/10.1101/2024.06.04.597276v1?rss=1 Fan, Y. Peng, X. Tabassum, N. I. Cheng, X. Selvaraji, S. Tran, V. Hughes, T. H. G. Wickramasinghe, B. Jamal, A. Dinh, Q. N. Gelderblom, M. Drummond, G. R. Sobey, C. G. Penman, J. Johns, T. G. Vemuganti, R. Gunaratne, J. Mattson, M. P. Jo, D.-G. Jelinic, M. Arumugam, T. V. 2024-06-06 doi:10.1101/2024.06.04.597276 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ An organoid co-culture model for probing systemic anti-tumor immunity in lung cancer ]]> https://biorxiv.org/content/10.1101/2024.06.04.597327v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@a0829dorg.highwire.dtl.DTLVardef@1df3083org.highwire.dtl.DTLVardef@1ea1065org.highwire.dtl.DTLVardef@1da9464_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Li, K. Liu, C. Li, C. Zhang, T. Zhao, T. Zhang, D. Wu, H. Liu, Y. Wang, S. Yang, Y. Lin, B. Wang, W. Wang, J. Sui, X. Chen, X. Liu, P. 2024-06-06 doi:10.1101/2024.06.04.597327 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Locally released somatostatin triggers cAMP and Ca2+ signaling in primary cilia to modulate pancreatic β-cell function ]]> https://biorxiv.org/content/10.1101/2024.06.05.597562v1?rss=1 Incedal Nilsson, C. Dumral, O. Sanchez, G. Xie, B. Mueller, A. Solimena, M. Ren, H. Idevall-Hagren, O. 2024-06-06 doi:10.1101/2024.06.05.597562 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ CLCC1 Governs Bilayer Equilibration at the Endoplasmic Reticulum to Maintain Cellular and Systemic Lipid Homeostasis ]]> https://biorxiv.org/content/10.1101/2024.06.07.596575v1?rss=1 Wu, L. Wang, J. Wang, Y. Yang, J. Yao, Y. Huang, D. Hu, Y. Xu, X. Wang, R. Du, W. Shi, Y. Li, Q. Liu, L. Zhu, Y. Wang, X. Guo, Q. Xu, L. Li, P. Chen, X.-W. 2024-06-08 doi:10.1101/2024.06.07.596575 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Defining cellular determinants of resistance to PD-1 pathway blockade in non-small-cell lung cancer ]]> https://biorxiv.org/content/10.1101/2024.06.06.597777v1?rss=1 Liu, B. Feng, K. Yu, K. Gao, R. Hu, X. Qin, B. Wang, J. Xue, Z. Han, W. Zhang, Z. 2024-06-09 doi:10.1101/2024.06.06.597777 Cold Spring Harbor Laboratory Press 2024-06-09 <![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[ Myocardial infarction creates a critical time window for AAV gene therapy ]]> https://biorxiv.org/content/10.1101/2024.06.10.597311v1?rss=1 Chen, G. Zhang, Y. Chen, Z. Yang, L. Gao, F. Dong, E. Guo, Y. 2024-06-11 doi:10.1101/2024.06.10.597311 Cold Spring Harbor Laboratory Press 2024-06-11 <![CDATA[ PI(3,5)P2 asymmetry during mitosis is essential for asymmetric vacuolar inheritance ]]> https://biorxiv.org/content/10.1101/2024.06.13.598808v1?rss=1 Huda, M. Koyuncu, M. Dilege, C. Caydasi, A. K. 2024-06-13 doi:10.1101/2024.06.13.598808 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Therapeutic expression of RAS Degrader RRSP in Pancreatic Cancer via Nanocarrier-mediated mRNA delivery ]]> https://biorxiv.org/content/10.1101/2024.06.11.598439v1?rss=1 Escher, T. E. Yuk, S. A. Qian, Y. Stubbs, C. K. Scott, E. A. Satchell, K. J. 2024-06-14 doi:10.1101/2024.06.11.598439 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ The continuous differentiation of multiscale structural gradients from childhood to adolescence correlates with the maturation of cortical morphology and functional specialization ]]> https://biorxiv.org/content/10.1101/2024.06.14.598973v1?rss=1 He, Y. Zeng, D. Li, Q. Chu, L. Dong, X. Liang, X. Sun, L. Liao, X. Zhao, T. Chen, X. Lei, T. Men, W. Wang, Y. Wang, D. Hu, M. Pan, Z. Zhang, H. Liu, N. Tan, S. Gao, J.-H. Qin, S. Tao, S. Dong, Q. He, Y. Li, S. 2024-06-15 doi:10.1101/2024.06.14.598973 Cold Spring Harbor Laboratory Press 2024-06-15 <![CDATA[ Identifying miRNA Signatures Associated with Pancreatic Islet Dysfunction in a FOXA2-Deficient iPSC Model ]]> https://biorxiv.org/content/10.1101/2024.06.15.599142v1?rss=1 Elsayed, A. K. Aldous, N. Alajez, N. Abdelalim, E. M. 2024-06-16 doi:10.1101/2024.06.15.599142 Cold Spring Harbor Laboratory Press 2024-06-16 <![CDATA[ Human transcription factor combinations mapped by genome-wide footprinting with deaminase ]]> https://biorxiv.org/content/10.1101/2024.06.14.599019v1?rss=1 He, R. Dong, W. Ma, W. Wang, Z. Gao, L. Xie, C. Li, D. Shen, K. Jian, F. Zhang, J. Yuan, Y. Wang, X. Pang, Y. Zhang, Z. Zheng, Y. Liu, S. Luo, C. Chai, X. Ren, J. Zhu, Z. Xie, X. S. 2024-06-17 doi:10.1101/2024.06.14.599019 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Bioprinting of aptamer-based programmable bioinks to modulate multiscale microvascular morphogenesis in 4D ]]> https://biorxiv.org/content/10.1101/2024.06.15.599146v1?rss=1 Rana, D. Rangel, V. R. Padmanaban, P. Trikalitis, V. D. Kandar, A. Kim, H.-W. Rouwkema, J. 2024-06-17 doi:10.1101/2024.06.15.599146 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Ccdc66 regulates primary cilium stability, disassembly and signaling important for epithelial organization ]]> https://biorxiv.org/content/10.1101/2024.06.16.599243v1?rss=1 Deretic, J. Cengiz-Emek, S. Seyrek, E. Firat-Karalar, E. N. 2024-06-17 doi:10.1101/2024.06.16.599243 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Prime editor-based high-throughput screening reveals functional synonymous mutations in the human genome ]]> https://biorxiv.org/content/10.1101/2024.06.16.599253v1?rss=1 Niu, X. Tang, W. Liu, Y. Liu, Y. Mo, B. Yu, Y. Wei, W. 2024-06-17 doi:10.1101/2024.06.16.599253 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Nuclear receptor E75/NR1D2 drives tumor malignant transformation by integrating Hippo and Notch pathways ]]> https://biorxiv.org/content/10.1101/2024.06.27.600913v1?rss=1 Wang, X. Guo, Y. Lin, P. Yu, M. Song, S. Xu, W. Kong, D. Wang, Y. Zhang, Y. Lu, F. Xie, Q. Ma, X. 2024-06-27 doi:10.1101/2024.06.27.600913 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Polyommatine blue butterflies reveal unexpected integrity of the W sex chromosome amid extensive chromosome fragmentation ]]> https://biorxiv.org/content/10.1101/2024.06.25.600692v1?rss=1 Hospodarska, M. Chung Volenikova, A. Koutecky, P. Vila, R. Talavera, G. Provaznikova, I. Dalikova, M. Nguyen, P. 2024-06-29 doi:10.1101/2024.06.25.600692 Cold Spring Harbor Laboratory Press 2024-06-29 <![CDATA[ Cellular and Molecular Changes During Aging in MEC: Unveiling the Role of Bglap3 Neurons in Cognitive Aging ]]> https://biorxiv.org/content/10.1101/2024.06.27.600930v1?rss=1 Miao, C. Cao, Q. Uzeen, S. Cheng, S. Liu, Y. Liu, J. Wen, S. Zhong, M. Hao, J. Yao, S. Yang, Y. Yan, X. Guo, W. 2024-07-02 doi:10.1101/2024.06.27.600930 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ PRISM: Multiplexed Profiling of RNA In-Situ through Single-round of Imaging in Three-Dimensional Tissue ]]> https://biorxiv.org/content/10.1101/2024.06.29.601330v1?rss=1 Chang, T. Zhao, S. Deng, K. Liao, Z. Tang, M. Zhu, Y. Han, W. Yu, C. Fan, W. Jiang, M. Wang, G. Liu, D. Peng, J. Pang, Y. Fei, P. Wang, J. Zheng, C. Huang, Y. 2024-07-02 doi:10.1101/2024.06.29.601330 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ GeneLLM: A Large cfRNA Language Model for Cancer Screening from Raw Reads ]]> https://biorxiv.org/content/10.1101/2024.06.29.601341v1?rss=1 Deng, S. Sha, L. Jin, Y. Zhou, T. Wang, C. Liu, Q. Guo, H. Xiong, C. Xue, Y. Li, X. Li, Y. Gao, Y. Hong, M. Xu, J. Chen, S. Wang, P. 2024-07-02 doi:10.1101/2024.06.29.601341 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Devonian stromatoporoid historical collections in the Natural History Museum, London (UK): redescription, taxonomic revision and implications for stromatoporoid global paleobiogeography ]]> https://biorxiv.org/content/10.1101/2024.06.30.601411v1?rss=1 Huang, J. Sendino, C. Kershaw, S. 2024-07-02 doi:10.1101/2024.06.30.601411 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ MetaGXplore: Integrating Multi-Omics Data with Graph Convolutional Networks for Pan-cancer Patient Metastasis Identification ]]> https://biorxiv.org/content/10.1101/2024.06.30.601445v1?rss=1 Jiang, T. Jiang, H. Ma, X. Xu, M. Zhang, W. 2024-07-02 doi:10.1101/2024.06.30.601445 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Progerin Can Induce DNA Damage in the Absence of Global Changes in Replication or Cell Proliferation ]]> https://biorxiv.org/content/10.1101/2024.07.02.601729v1?rss=1 Joudeh, L. A. Schuck, P. L. Van, N. M. DiCintio, A. J. Stewart, J. A. Waldman, A. S. 2024-07-02 doi:10.1101/2024.07.02.601729 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Unsilenced inhibitory cortical ensemble gates remote memory retrieval ]]> https://biorxiv.org/content/10.1101/2024.07.01.601454v1?rss=1 Wang, S. Sheng, T. Su, F. Yang, H. Cao, R. Wang, Q. Zhang, C. Lu, W. 2024-07-03 doi:10.1101/2024.07.01.601454 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ A Drug-Elicitable Alternative-Splicing Module (DreAM) for Tunable AAV Expression and Controlled Myocardial Regeneration ]]> https://biorxiv.org/content/10.1101/2024.07.01.601517v1?rss=1 Chen, Z. Yang, L. Zhang, Y. Li, Y. Chen, G. Wang, Z. Li, J. Yang, Y. Zhao, D. Pu, W. T. Yang, K. Dong, E. Guo, Y. 2024-07-03 doi:10.1101/2024.07.01.601517 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ Floral visitors differentially respond to local and landscape grassland features ]]> https://biorxiv.org/content/10.1101/2024.07.01.601588v1?rss=1 Lichtenberg, E. M. Heiser, J. Baum, K. A. Neff, J. L. Jha, S. 2024-07-04 doi:10.1101/2024.07.01.601588 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ A VgrG2b fragment cleaved by caspase-11/4 promotes Pseudomonas aeruginosa infection through suppressing the NLRP3 inflammasome ]]> https://biorxiv.org/content/10.1101/2024.07.02.601667v1?rss=1 Qian, Y. Liu, Q. Li, W. Wang, C. Kong, C. Li, M. Wang, S. Xia, P. 2024-07-04 doi:10.1101/2024.07.02.601667 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ Physical constraints and biological regulations underlie universal osmoresponses ]]> https://biorxiv.org/content/10.1101/2024.07.02.601668v1?rss=1 Ye, Y. Wang, Q. Lin, J. 2024-07-04 doi:10.1101/2024.07.02.601668 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ Omicron-specific ultra-potent SARS-CoV-2 neutralizing antibodies targeting the N1/N2 loop of Spike N-terminal domain ]]> https://biorxiv.org/content/10.1101/2024.07.10.602843v1?rss=1 Niu, X. Li, Z. Wang, J. Jian, F. Yu, Y. Song, W. Yisimayi, A. Du, S. Zhang, Z. Wang, Q. Wang, J. An, R. Wang, Y. Wang, P. Sun, H. Yu, L. Yang, S. Xiao, T. Gu, Q. Shao, F. Wang, Y. Xiao, J. Cao, Y. 2024-07-10 doi:10.1101/2024.07.10.602843 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ First-male sperm precedence in polyandrous Spodoptera frugiperda allows sterile males induce population suppression ]]> https://biorxiv.org/content/10.1101/2024.07.10.602994v1?rss=1 Sun, H. Bu, L.-A. Zhang, X.-Y. Zhang, Z.-R. Zhu, L.-Y. Su, S. Guo, D. Hu, G. Gao, C.-F. Palli, S. R. Champer, J. Wu, S.-F. 2024-07-16 doi:10.1101/2024.07.10.602994 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Importance of transcript variants in transcriptome analyses ]]> https://biorxiv.org/content/10.1101/2024.07.11.603122v1?rss=1 80%) variants were either down-regulated or showed no significant change in expression analysis. Similarly, the 287 genes reported to be downregulated expressed 856 transcript variants, with only 153 (<20%) downregulated variants and 703 (>82%) variants that were upregulated or showed no significant changes. Additionally, the 682 TF genes that did not show significant changes between ES and TS cells (GE values < 2-fold changes and/or FDR p-values >0.05) expressed 2215 transcript variants, which included 477 (>21%) that were differentially expressed (276 upregulated and 201 downregulated, [≥]2-fold, FDR p-value [≤]0.05). Notably, a particular gene does not express just one protein; rather its transcript variants encode multiple proteins with distinct functional domains, including non-coding regulatory RNAs. Our findings underscore the critical necessity of considering transcript variants in RNA-Seq analyses. Doing so may enable a more precise understanding of the intricate functional and regulatory landscape of genes; ignoring the variants may result in an erroneous interpretation. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/603122v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@1371b9corg.highwire.dtl.DTLVardef@f5c037org.highwire.dtl.DTLVardef@1e5f79org.highwire.dtl.DTLVardef@e20cb_HPS_FORMAT_FIGEXP M_FIG C_FIG Differential expression of transcription factors (TFs) between mouse embryonic stem (ES) cells and trophoblast stem (TS) cells. This graphic presentation clearly demonstrates the importance of including transcript variants during RNA sequencing (RNA-Seq) analyses. Panel A represents the conventional differential gene expression analysis approach after RNA-Seq, where all transcript reads are taken under a single gene name. Panel B takes differential gene expression analysis one step further by examining all the transcript variants that were previously hidden under the main gene name. Our results indicate that exclusive gene expression (GE) analysis inaccurately defines over 80% of the transcript expression (TE). Without analyses of all the transcript variants reads, we fail to uncover the functional importance of the variants and the regulation of their expression. Both GE and TE values are expressed as transcript per million (TPM). Data analyses were performed by using CLC Genomics Workbench. ]]> Vo, K. Mohamadi, R. Sharma, Y. Mohamadi, A. Fields, P. E. Rumi, M. A. K. 2024-07-16 doi:10.1101/2024.07.11.603122 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Mandrel Diameter is a Dominating Parameter for Fiber Alignment Control in Rotating Mandrel Electrospinning Systems ]]> https://biorxiv.org/content/10.1101/2024.07.11.603153v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@a493dorg.highwire.dtl.DTLVardef@14e7d42org.highwire.dtl.DTLVardef@1925eorg.highwire.dtl.DTLVardef@1308da3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Meinhold, K. L. Tankersley, T. Darlington, R. Robinson, J. L. 2024-07-16 doi:10.1101/2024.07.11.603153 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ A Single Trophoblast Layer Acts as the Gatekeeper at the Endothelial-Hematopoietic Crossroad in the Placenta ]]> https://biorxiv.org/content/10.1101/2024.07.12.603303v1?rss=1 Home, P. Ghosh, A. Kumar, R. P. Ray, S. Gunewardena, S. Kumar, R. Dasgupta, P. Roy, N. Saha, A. Ouseph, M. M. Leone, G. W. Paul, S. 2024-07-16 doi:10.1101/2024.07.12.603303 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ The discovery of phages in the Substantia Nigra and its implication for Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2024.07.13.603353v1?rss=1 Zhao, Y. Xiong, C. Wang, B. Li, D. Liu, J. Wei, S. Hou, Y. Zhou, Y. Zheng, R. 2024-07-16 doi:10.1101/2024.07.13.603353 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Beyond Static Models: The Dynamic Interplay of Facial Emotions and Attentional Scope ]]> https://biorxiv.org/content/10.1101/2024.07.15.603432v1?rss=1 Hu, K. He, S. Li, Q. Li, C.-S. 2024-07-16 doi:10.1101/2024.07.15.603432 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Waves of Colonization and Gene Flow in a Great Speciator ]]> https://biorxiv.org/content/10.1101/2024.07.18.603796v1?rss=1 Gyllenhaal, E. F. Brady, S. S. DeCicco, L. H. Naikatini, A. Hime, P. M. Manthey, J. D. Kelly, J. K. Moyle, R. G. Andersen, M. J. 2024-07-22 doi:10.1101/2024.07.18.603796 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ Structural diversity of mitochondria in the neuromuscular system across development ]]> https://biorxiv.org/content/10.1101/2024.07.19.604219v1?rss=1 Bae, J. A. Choi, M.-k. Ahn, S. Ko, G. Choe, D. T. Yim, H. Nguyen, K. C. Q. Hall, D. H. Kim, J. S. Lee, J. 2024-07-23 doi:10.1101/2024.07.19.604219 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ The Orphan G Protein-Coupled Receptor GPR52 is a Novel Regulator of Breast Cancer Multicellular Organization ]]> https://biorxiv.org/content/10.1101/2024.07.22.604482v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@8b0f55org.highwire.dtl.DTLVardef@19bd139org.highwire.dtl.DTLVardef@c52117org.highwire.dtl.DTLVardef@1ffa2bd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG ]]> Hanif, S. Z. Au, C. C. Torregroza, I. Jannath, S. Fabiha, T. Bhinder, B. Washburn, M. Devost, D. Liu, S. Bhardwaj, P. Evans, T. Anand, P. K. Tarran, R. Palikhe, S. Elemento, O. Dow, L. E. Blenis, J. Hebert, T. Brown, K. A. 2024-07-23 doi:10.1101/2024.07.22.604482 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Coxsackievirus B infection invokes unique cell-type specific responses in primary human pancreatic islets ]]> https://biorxiv.org/content/10.1101/2024.07.23.604861v1?rss=1 Veronese-Paniagua, D. A. Hernandez-Rincon, D. C. Taylor, J. P. Tse, H. M. Millman, J. R. 2024-07-24 doi:10.1101/2024.07.23.604861 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Long-Range Enhancer Networks Gradually Emerge as Key Regulators During Human Cortical Neurogenesis ]]> https://biorxiv.org/content/10.1101/2024.07.24.605026v1?rss=1 Li, C. Zhu, L. Su, B. Jia, L. Hou, Y. Cui, Z. Luo, X. Duan, J. Guo, J. Shi, M. Chen, H. Li, T. Zhang, F. 2024-07-25 doi:10.1101/2024.07.24.605026 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ Intracellular lipopolysaccharide regulates ER remodeling upon bacterial infection ]]> https://biorxiv.org/content/10.1101/2024.07.25.605133v1?rss=1 Cheng, Y.-L. Mello-Vieira, J. Covarrubias-Pinto, A. Gonzalez, A. Kuncha, S. K. Kew, C. Zhang, K. Afzal, M. A. Diab, N. Borchert, S. Chen, W. Huang, T. C. Hornef, M. Huebner, C. A. Hensel, M. Dikic, I. 2024-07-25 doi:10.1101/2024.07.25.605133 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ Epileptiform activity and seizure risk follow long-term non-linear attractor dynamics ]]> https://biorxiv.org/content/10.1101/2024.07.26.605279v1?rss=1 Rosch, R. E. Scheid, B. Davis, K. A. Litt, B. Ashourvan, A. 2024-07-26 doi:10.1101/2024.07.26.605279 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ Single field evolution rule governs the dynamics of representational drift in mouse hippocampal dorsal CA1 region. ]]> https://biorxiv.org/content/10.1101/2024.07.27.605419v1?rss=1 Chen, C. Yao, S. Cheng, S. Li, A. A. Yan, Y. Zhang, X. Liu, Y. Wang, Y. Cao, Q. Miao, C. 2024-07-29 doi:10.1101/2024.07.27.605419 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Exploration of Flavonoids to identify Potential Therapeutic Compounds by Targeting the Non-Structural V protein of Nipah Virus ]]> https://biorxiv.org/content/10.1101/2024.07.29.605559v1?rss=1 Ahmad, S. R. Zeyaullah, M. AlShahrani, A. M. Khan, M. S. Ali, H. Muzammil, K. Mohieldin, A. AG Altijani, A. Dawria, A. Mohamed, A. O. A. Kalam, A. 2024-07-29 doi:10.1101/2024.07.29.605559 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Insights into Therapeutic Discovery Through the Kelch Domain Structure of Keap1 at Ambient Temperature ]]> https://biorxiv.org/content/10.1101/2024.07.30.605796v1?rss=1 YILMAZ, M. SEVER, B. KUTLU, Y. GUL, M. OKUDUCU, C. TAVLI, S. OTSUKA, M. FUJITA, M. HALILOGLU, T. CIFTCI, H. Demirci, H. 2024-07-31 doi:10.1101/2024.07.30.605796 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ PRMT7 mediated PTEN activation promotes bone formation in female mice ]]> https://biorxiv.org/content/10.1101/2024.07.31.605998v1?rss=1 Zhang, Y. Qing, J. Li, Y. Gao, X. Lu, D. Wang, Y. Gu, L. Zhang, H. Li, Z. Wang, X. Zhou, Y. Zhang, P. 2024-07-31 doi:10.1101/2024.07.31.605998 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ An updated and expanded characterization of the biological sciences academic job market ]]> https://biorxiv.org/content/10.1101/2024.07.31.606033v1?rss=1 Flynn, B. Kozik, A. J. Cheng, Y. Haagan, A. K. Ng, J. Smith, C. Haage, A. Jadavji, N. M. 2024-08-02 doi:10.1101/2024.07.31.606033 Cold Spring Harbor Laboratory Press 2024-08-02 <![CDATA[ Direct imaging of neural activity reveals neural circuits via spatiotemporal activation mapping ]]> https://biorxiv.org/content/10.1101/2024.07.31.606112v1?rss=1 Keum, J.-Y. Toi, P. T. Park, S. Chun, H. Park, J.-Y. 2024-08-02 doi:10.1101/2024.07.31.606112 Cold Spring Harbor Laboratory Press 2024-08-02 <![CDATA[ Exploration of the Metabolomic Mechanisms of Postmenopausal Hypertension Induced by Low Estrogen State ]]> https://biorxiv.org/content/10.1101/2024.08.01.606107v1?rss=1 Li, Y. Xin, H. Lian, Z. Zhang, W. 2024-08-04 doi:10.1101/2024.08.01.606107 Cold Spring Harbor Laboratory Press 2024-08-04 <![CDATA[ Loss function of tumor suppressor FRMD8 confers resistance to tamoxifen therapy via a dual mechanism ]]> https://biorxiv.org/content/10.1101/2024.08.01.606147v1?rss=1 Wu, W. Yu, M. Li, Q. Zhao, Y. Zhang, L. Sun, Y. Wang, Z. Gong, Y. Wang, W. Liu, C. Zhang, J. Tang, Y. Xu, X. Guo, X. Zhan, J. Zhang, H. 2024-08-04 doi:10.1101/2024.08.01.606147 Cold Spring Harbor Laboratory Press 2024-08-04 <![CDATA[ Borrelia burgdorferi BB0346 is an Essential, Structurally Variant LolA Homolog that is Primarily Required for Homeostatic Localization of Periplasmic Lipoproteins ]]> https://biorxiv.org/content/10.1101/2024.08.06.606844v1?rss=1 Murphy, B. T. Wiepen, J. J. Graham, D. E. Swanson, S. Kashipathy, M. M. Cooper, A. Battaile, K. P. Johnson, D. K. Florens, L. Blevins, J. S. Lovell, S. Zückert, W. R. 2024-08-07 doi:10.1101/2024.08.06.606844 Cold Spring Harbor Laboratory Press 2024-08-07 <![CDATA[ Selecting sites for strategic surveillance of zoonotic pathogens: a case study in Panama ]]> https://biorxiv.org/content/10.1101/2024.08.12.607103v1?rss=1 8,000 georeferenced mammal specimen records, collected as part of a long-term hantavirus surveillance program, to test the completeness of country-wide environmental sampling. Despite 20 years of surveillance, our analyses identified a few key environmental sampling gaps. To refine surveillance strategies, we selected a series of core historically sampled localities, supplemented with additional environmentally distinct sites to more completely represent Panamas environments. Based on lessons learned through decades of surveillance, we propose a series of recommendations to improve strategic sampling for zoonotic pathogen surveillance. ]]> Cobos, M. E. Dunnum, J. L. Armien, B. Gonzalez, P. Juarez, E. Salazar, J. R. Cook, J. A. Colella, J. P. 2024-08-13 doi:10.1101/2024.08.12.607103 Cold Spring Harbor Laboratory Press 2024-08-13 <![CDATA[ Phylogenetic proximity drives temporal succession of marine giant viruses in a five-year metagenomic time-series ]]> https://biorxiv.org/content/10.1101/2024.08.12.607631v1?rss=1 Laperriere, S. M. Minch, B. Weissman, J. Hou, S. Yeh, Y.-C. Ignacio-Espinoza, J. C. L. Ahlgren, N. A. Moniruzzaman, M. Fuhrman, J. A. 2024-08-15 doi:10.1101/2024.08.12.607631 Cold Spring Harbor Laboratory Press 2024-08-15 <![CDATA[ Variable responses of alpine-plant communities to warming and loss of dominant species ]]> https://biorxiv.org/content/10.1101/2024.08.13.604445v1?rss=1 Marraffini, M. L. Classen, A. T. Sanders, N. J. Sundquist, M. k. Deslippe, J. R. He, J. S. McLaren, J. R. Rixen, C. Wipf, S. Chisholm, C. Prager, C. Stouffer, D. B. 2024-08-15 doi:10.1101/2024.08.13.604445 Cold Spring Harbor Laboratory Press 2024-08-15 <![CDATA[ Population dynamics in spatial suppression gene drive models and the effect of resistance, density dependence, and life history ]]> https://biorxiv.org/content/10.1101/2024.08.14.607913v1?rss=1 Zhang, X. Sun, W. Kim, I. K. Messer, P. W. Champer, J. 2024-08-15 doi:10.1101/2024.08.14.607913 Cold Spring Harbor Laboratory Press 2024-08-15 <![CDATA[ MiniXL: An open-source, large field-of-view epifluorescence miniature microscope for mice capable of single-cell resolution and multi-brain region imaging ]]> https://biorxiv.org/content/10.1101/2024.08.16.608328v1?rss=1 Zhao, P. Guo, C. Xie, M. Chen, L. Golshani, P. Aharoni, D. 2024-08-19 doi:10.1101/2024.08.16.608328 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ The molecular mechanism of temperature-dependent phase separation of Heat shock factor 1 ]]> https://biorxiv.org/content/10.1101/2024.08.20.608825v1?rss=1 Ren, Q. Li, L. Li, J. Shi, C. Sun, Y. Yao, X. Hou, Z. Xiang, S. 2024-08-20 doi:10.1101/2024.08.20.608825 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ Inflammatory Signatures of Microglia in the Mouse Model of Corticosterone-Induced Depression ]]> https://biorxiv.org/content/10.1101/2024.08.21.608928v1?rss=1 Zhao, Y. Huang, Y. Cao, Y. Yang, J. 2024-08-22 doi:10.1101/2024.08.21.608928 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ δ-α cell-to-cell interactions modulate pancreatic islet Ca2+ oscillation modes ]]> https://biorxiv.org/content/10.1101/2024.08.21.608986v1?rss=1 Tang, C. Ren, H. Li, Y. Xie, B. Qian, W. Yu, Y. Chang, T. Yang, X. sneppen, k. Chen, L. 2024-08-22 doi:10.1101/2024.08.21.608986 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Epigenetic and transcriptional regulation of ovarian development altered in ErβKO ovaries ]]> https://biorxiv.org/content/10.1101/2024.08.21.608994v1?rss=1 Mohamadi, R. Vo, K. Sharma, Y. Mohamadi, A. Bahadursingh, E. Fields, P. E. Rumi, M. A. 2024-08-22 doi:10.1101/2024.08.21.608994 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ MED26-enriched condensates drive erythropoiesis through modulating transcription pausing ]]> https://biorxiv.org/content/10.1101/2024.08.26.609654v1?rss=1 Zhu, S. Zhang, X. Li, N. Zhao, X. Li, M. Xie, S. Yue, Q. Li, Y. Li, D. Wu, F. Zhang, Z. Feng, Z. Zhang, Y. Choi, W. Jia, X. Deng, Y. Hu, Q. Yao, X. Gao, X. Lee, H.-Y. S. 2024-08-26 doi:10.1101/2024.08.26.609654 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Epidrug Screening Identifies Type I PRMT Inhibitors as Modulators of Lysosomal Exocytosis and Drug Sensitivity in Cancers ]]> https://biorxiv.org/content/10.1101/2024.08.26.609671v1?rss=1 Sergi, B. Yuksel-Catal, N. Ozcan, S. C. Syed, H. Duvvuri, U. Kiselyov, K. Acilan, C. 2024-08-26 doi:10.1101/2024.08.26.609671 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ The Effect of THz Electromagnetic Field on the Conductance of Potassium and Sodium Channels ]]> https://biorxiv.org/content/10.1101/2024.08.27.609902v1?rss=1 Song, Z. Xue, L. Ouyang, Q. Song, C. 2024-08-28 doi:10.1101/2024.08.27.609902 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Is variation in female aggressiveness across Drosophila species associated with reproductive potential? ]]> https://biorxiv.org/content/10.1101/2024.08.27.609931v1?rss=1 Bath, E. Gleason, J. M. 2024-08-28 doi:10.1101/2024.08.27.609931 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ LncRNA-536 and RNA Binding Protein RBM25 Interactions in Pulmonary Arterial Hypertension ]]> https://biorxiv.org/content/10.1101/2024.08.27.610011v1?rss=1 Mahajan, A. Kumar, A. Chen, L. Dhillon, N. K. 2024-08-28 doi:10.1101/2024.08.27.610011 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Genomic insights into the evolution and adaptation of the memorial roses (Rosa lucieae; Rosaceae) in saline environments ]]> https://biorxiv.org/content/10.1101/2024.08.29.610403v1?rss=1 Jeon, J.-H. Shin, Y. Kim, S.-C. 2024-08-30 doi:10.1101/2024.08.29.610403 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ The interaction between abiotic and biotic soil factors drive heterosis expression in maize ]]> https://biorxiv.org/content/10.1101/2024.08.30.610574v1?rss=1 Clouse, K. M. Ellis, M. L. Ford, N. E. Hostetler, R. L. Balint-Kurti, P. Kleiner, M. Wagner, M. R. 2024-09-02 doi:10.1101/2024.08.30.610574 Cold Spring Harbor Laboratory Press 2024-09-02 <![CDATA[ Electrospun Fiber Surface Roughness Modulates Human Monocyte-Derived Macrophage Phenotype ]]> https://biorxiv.org/content/10.1101/2024.08.30.610568v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@1b40283org.highwire.dtl.DTLVardef@1110307org.highwire.dtl.DTLVardef@1ddc63eorg.highwire.dtl.DTLVardef@1021581_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Alemifar, A. Robinson, J. Burnette, K. Jandres, B. Hurt, S. Tse, H. 2024-09-03 doi:10.1101/2024.08.30.610568 Cold Spring Harbor Laboratory Press 2024-09-03 <![CDATA[ Structural and molecular basis of the epistasis effect in enhanced affinity between SARS-CoV-2 KP.3 and ACE2 ]]> https://biorxiv.org/content/10.1101/2024.09.03.610799v1?rss=1 Feng, L. Sun, Z. Zhang, Y. Jian, F. Yang, S. Yu, L. Wang, J. Shao, F. Wang, X. Cao, Y. 2024-09-04 doi:10.1101/2024.09.03.610799 Cold Spring Harbor Laboratory Press 2024-09-04 <![CDATA[ Oxytocin salvages context-specific hyperaltruistic preference through moral framing ]]> https://biorxiv.org/content/10.1101/2024.09.03.611034v1?rss=1 Zhang, H. Ni, Y. Li, J. 2024-09-05 doi:10.1101/2024.09.03.611034 Cold Spring Harbor Laboratory Press 2024-09-05 <![CDATA[ Identification of leptolin as a novel anti-obesity adipokine ]]> https://biorxiv.org/content/10.1101/2024.09.03.610963v1?rss=1 Liu, J. Wang, B. Su, Z. Han, X. He, M. Zhao, Y. Hou, Y. Li, D. Zhang, W. Qin, L. Wang, K. Li, Y. Yan, Y. Yu, S. Huang, X. Yuwen, T. Zheng, R. 2024-09-06 doi:10.1101/2024.09.03.610963 Cold Spring Harbor Laboratory Press 2024-09-06 <![CDATA[ Subtype-specific Patterns of Evolution and Clinically Relevant Genomic Instability in Wilms Tumour ]]> https://biorxiv.org/content/10.1101/2024.09.04.610994v1?rss=1 Cresswell, G. D. Chagtai, T. Al-Saadi, R. Treger, T. D. Madhan, G. Mifsud, B. Vujanic, G. Williams, R. D. Luscombe, N. M. Pritchard-Jones, K. Mifsud, W. 2024-09-07 doi:10.1101/2024.09.04.610994 Cold Spring Harbor Laboratory Press 2024-09-07 <![CDATA[ Methylsulfonylmethane: A Potential Dietary Supplement targeting sphingosine kinase 1 involved in Glioblastomamultiforme ]]> https://biorxiv.org/content/10.1101/2024.09.05.611570v1?rss=1 Ahmad, F. Karan, A. Jayaraj, R. L. 2024-09-09 doi:10.1101/2024.09.05.611570 Cold Spring Harbor Laboratory Press 2024-09-09 <![CDATA[ Photochemical processes drive thermal responses of dissolved organic matter in the dark ocean ]]> https://biorxiv.org/content/10.1101/2024.09.06.611638v1?rss=1 1,000 m). Such increases could elevate recalcitrant deep-ocean carbon sink by approximately 10 Tg C yr-1 which accounts for > 5% of the carbon flux survived to the deep ocean. Our findings highlight the importance of photochemical legacies in driving DOM thermal responses and further help predict the future oceanic carbon sink under global change. ]]> Hu, A. Cui, Y. Bercovici, S. Tanentzap, A. Lennon, J. Lin, X. Yang, Y. Liu, Y. Osterholz, H. Dong, H. Lu, Y. Jiao, N. Wang, J. 2024-09-09 doi:10.1101/2024.09.06.611638 Cold Spring Harbor Laboratory Press 2024-09-09 <![CDATA[ Mechanisms of urate transport and uricosuric drugs inhibition in human URAT1 ]]> https://biorxiv.org/content/10.1101/2024.09.08.611941v1?rss=1 Guo, W. Wei, M. Li, Y. Xu, J. Zang, J. Chen, Y. Chen, L. 2024-09-09 doi:10.1101/2024.09.08.611941 Cold Spring Harbor Laboratory Press 2024-09-09 <![CDATA[ Protocol for Simulating the Effect of THz Electromagnetic Field on Ion Channels ]]> https://biorxiv.org/content/10.1101/2024.09.09.612012v1?rss=1 Xue, L. Song, Z. Ouyang, Q. Song, C. 2024-09-10 doi:10.1101/2024.09.09.612012 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ Learning phenotype associated signature in spatial transcriptomics with PASSAGE ]]> https://biorxiv.org/content/10.1101/2024.09.06.611564v1?rss=1 Guo, C.-K. Xia, C.-R. Peng, G. Cao, Z.-J. Gao, G. 2024-09-11 doi:10.1101/2024.09.06.611564 Cold Spring Harbor Laboratory Press 2024-09-11 <![CDATA[ Molecular recording of cellular protein kinase activity with chemical labeling ]]> https://biorxiv.org/content/10.1101/2024.09.11.611894v1?rss=1 Sun, D.-e. Ng, S. W. Zheng, Y. Xie, S. Schwan, N. Breuer, P. Hoffmann, D. C. Michel, J. Azorin, D. D. Boonekamp, K. E. Winkler, F. Wick, W. Boutros, M. Li, Y. Johnsson, K. 2024-09-11 doi:10.1101/2024.09.11.611894 Cold Spring Harbor Laboratory Press 2024-09-11 <![CDATA[ EmbSAM: Cell boundary localization and Segment Anything Model for fast images of developing embryos ]]> https://biorxiv.org/content/10.1101/2024.09.07.611795v1?rss=1 Zhao, C. Li, Z. Zhang, P. Chen, Y. Ye, P. Wong, M.-K. Chan, L.-Y. Yan, H. Tang, C. Guan, G. Zhao, Z. 2024-09-13 doi:10.1101/2024.09.07.611795 Cold Spring Harbor Laboratory Press 2024-09-13 <![CDATA[ Differential Impact of Multiple Sensory Deprivation on Spatial-coding Cells in Medial Entorhinal Cortex ]]> https://biorxiv.org/content/10.1101/2024.09.09.611946v1?rss=1 Tian, J. Wen, S. Zhou, Y. Yao, S. Zhang, X. Miao, C. 2024-09-13 doi:10.1101/2024.09.09.611946 Cold Spring Harbor Laboratory Press 2024-09-13 <![CDATA[ The Arabidopsis histone H3K4me3-binding ALFIN-like proteins mediate histone H2A ubiquitination and coordinate diverse chromatin modifications ]]> https://biorxiv.org/content/10.1101/2024.09.12.612777v1?rss=1 Su, X.-M. Yuan, D.-Y. Li, L. Yang, M. Chen, S. Zhou, Y. He, X.-J. 2024-09-13 doi:10.1101/2024.09.12.612777 Cold Spring Harbor Laboratory Press 2024-09-13 <![CDATA[ Exploring American Elderberry Compounds for Antioxidant, Antiviral, and Antibacterial Properties Through High-Throughput Screening Assays Combined with Untargeted Metabolomics ]]> https://biorxiv.org/content/10.1101/2024.09.13.611920v1?rss=1 Dwikarina, A. Bayati, M. Efrat, N. Roy, A. Lei, Z. Ho, K.-V. Sumner, L. W. Thomas, A. L. Applequist, W. Michael Greenlief, M. Townesmith, A. Lin, C.-H. 2024-09-14 doi:10.1101/2024.09.13.611920 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Intracortical injection of immune checkpoint inhibitor promotes monocyte/macrophage infiltration and restores microglial function and neuronal activity in an AD mouse model ]]> https://biorxiv.org/content/10.1101/2024.09.13.612389v1?rss=1 Park, T. Chang, L. Chung, S. W. Lee, S. Bae, S. Condello, C. Kim, Y. H. Lee, J. Kim, H.-J. Kwon, H.-K. Suh, M. 2024-09-15 doi:10.1101/2024.09.13.612389 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Structure of small HBV surface antigen reveals mechanism of dimer formation ]]> https://biorxiv.org/content/10.1101/2024.09.13.612767v1?rss=1 He, X. Kang, Y. Tao, W. Xu, J. Liu, X. Chen, L. 2024-09-15 doi:10.1101/2024.09.13.612767 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ A systems model of alternating theta sweeps via firing rate adaptation ]]> https://biorxiv.org/content/10.1101/2024.09.13.612841v1?rss=1 Ji, Z. Chu, T. Wu, S. Burgess, N. 2024-09-15 doi:10.1101/2024.09.13.612841 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Dynamical Modulation of Hippocampal Replay Sequences through Firing Rate Adaptation ]]> https://biorxiv.org/content/10.1101/2024.09.13.612895v1?rss=1 Ji, Z. Chu, T. Dong, X. Yu, C. Bush, D. Burgess, N. Wu, S. 2024-09-15 doi:10.1101/2024.09.13.612895 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Age-related decline of PKA-RIIβ level in SNc dopaminergic neurons underlies PD pathogenesis ]]> https://biorxiv.org/content/10.1101/2024.09.13.612981v1?rss=1 Zhao, Y. Wang, B. Zhao, M. Liu, J. Hou, Y. Wei, S. Xiong, C. Li, D. Zheng, R. 2024-09-15 doi:10.1101/2024.09.13.612981 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Co-transcriptional RNA processing boosts zygotic gene activation ]]> https://biorxiv.org/content/10.1101/2024.09.14.613088v1?rss=1 Xu, J. Li, X. Hao, X. Hu, X. Ma, S. Hong, Y. Zhang, J. Yan, D. Deng, H. Na, J. Ji, X. Chang, Z. Shen, X. 2024-09-15 doi:10.1101/2024.09.14.613088 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Few-shot Algorithms for Consistent Neural Decoding (FALCON) Benchmark ]]> https://biorxiv.org/content/10.1101/2024.09.15.613126v1?rss=1 Karpowicz, B. M. Ye, J. Fan, C. Tostado-Marcos, P. Rizzoglio, F. Washington, C. Scodeler, T. de Lucena, D. Nason-Tomaszewski, S. R. Mender, M. J. Ma, X. Arneodo, E. M. Hochberg, L. R. Chestek, C. A. Henderson, J. M. Gentner, T. Q. Gilja, V. Miller, L. E. Rouse, A. G. Gaunt, R. A. Collinger, J. L. Pandarinath, C. 2024-09-16 doi:10.1101/2024.09.15.613126 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ Interpretable high-resolution dimension reduction of spatial transcriptomics data by DeepFuseNMF ]]> https://biorxiv.org/content/10.1101/2024.09.12.612666v1?rss=1 Tang, J. Chen, Z. Qian, Q. Huang, S. Yin, S. He, Y. He, X. Ye, B. Zhuang, Y. Meng, H. Xi, J. Xi, R. 2024-09-17 doi:10.1101/2024.09.12.612666 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ Loss of PRICKLE1 in the myometrium leads to reduced fertility, abnormal myometrial architecture, and aberrant extracellular matrix deposition in mice. ]]> https://biorxiv.org/content/10.1101/2024.09.12.612708v1?rss=1 Roberts, E. Ganeshkumar, S. Gunewardena, S. Chennathukuzhi, V. M. 2024-09-17 doi:10.1101/2024.09.12.612708 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ The global spectrum of tree crown architecture ]]> https://biorxiv.org/content/10.1101/2024.09.14.613032v1?rss=1 500,000 globally distributed trees, we explored how climate, disturbance, competition, functional traits, and evolutionary history constrain the height, crown size and shape of the worlds tree species. We found that variation in height scaling relationships was primarily controlled by water availability and light competition. Conversely, crown width was predominantly shaped by exposure to wind and fire, while also covarying with other functional traits related to mechanical stability and photosynthesis. Additionally, several plant lineages had crown architectures that defy their environments, such as the exceedingly slender dipterocarps of Southeast Asia, or the extremely wide crowns of legumes in African savannas. Our study charts the global spectrum of tree crown architectural types. It provides a roadmap for integrating crown architecture with vegetation models and remote sensing observations, so that we may better understand the processes that shape the 3D structure of woody ecosystems. ]]> Jucker, T. Fischer, F. Chave, J. Coomes, D. Caspersen, J. Ali, A. Panzou, G. Feldpausch, T. Falster, D. Usoltsev, V. Jackson, T. Adu-Bredu, S. Alves, L. Aminpour, M. Angoboy, I. Anten, N. Antin, C. Askari, Y. Munoz, R. Ayyappan, N. Banin, L. Barbier, N. Battles, J. Beeckman, H. Bocko, Y. Bond-Lamberty, B. Bongers, F. Bowers, S. Breugel, M. Chantrain, A. Chaudhary, R. Dai, J. Dalponte, M. Dimobe, K. Domec, J.-C. Doucet, J.-L. Dupuy-Rada, J. Duursma, R. Enriquez, M. Ewijk, K. Farfan-Rios, W. Fayolle, A. Ferretti, M. Forni, E. Forrester, D. Gilani, H. 2024-09-17 doi:10.1101/2024.09.14.613032 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ Cortical connectivity supports motoric synchronization to both auditory and visual rhythms in a frontal-temporal network ]]> https://biorxiv.org/content/10.1101/2024.09.17.613394v1?rss=1 Lu, Y. Yu, Y. Wang, X. Qin, L. Gao, J.-H. Bi, Y. Tian, X. Ding, N. 2024-09-17 doi:10.1101/2024.09.17.613394 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ RFX3 is essential for the development and maturation of human pancreatic islets derived from pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2024.09.18.613711v1?rss=1 Memon, B. Aldous, N. Elsayed, A. Ijaz, S. Hayat, S. Abdelalim, E. M. 2024-09-19 doi:10.1101/2024.09.18.613711 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ An Inflammation Centered Perspective to the Mechanisms and Interactions Related to Vascular Cognitive Impairment ]]> https://biorxiv.org/content/10.1101/2024.09.19.613013v1?rss=1 Zeylan, M. E. Senyuz, S. Keskin, O. Gursoy, A. 2024-09-20 doi:10.1101/2024.09.19.613013 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Evidence that Dmrta2 acts as a transcriptional repressor of Pax6 in murine cortical progenitors and identification of a mutation crucial for DNA recognition associated with microcephaly in human ]]> https://biorxiv.org/content/10.1101/2024.09.20.614077v1?rss=1 Shen, X. Anirudhan, J. Fatima, A. Szemes, T. Keruzore, M. Plant, E. Sabate San Jose, A. Kricha, S. Delhaye, L. P. Mian, B. A. Khalid, L. B. Ali, F. Zahra, H. Ali, A. Toft, M. Dieu, M. Van Lint, C. Achouri, Y. Renard, P. Iqbal, Z. Bellefroid, E. J. 2024-09-20 doi:10.1101/2024.09.20.614077 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ BrainUnit: Integrating Physical Units into High-Performance AI-Driven Scientific Computing ]]> https://biorxiv.org/content/10.1101/2024.09.20.614111v1?rss=1 Wang, C. He, S. Luo, S. Huan, Y. Wu, S. 2024-09-20 doi:10.1101/2024.09.20.614111 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Tetanizing wakeful consolidation: ten-hertz repetitive visual stimulation enhances the offline gain of visual learning ]]> https://biorxiv.org/content/10.1101/2024.09.20.614122v1?rss=1 Yang, X.-Y. Zhao, C. Zuo, Z. Li, A. Luo, H. He, Q. Fang, F. 2024-09-20 doi:10.1101/2024.09.20.614122 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Integrating various Experimental Information to Assist Protein Complex Structure Prediction by GRASP ]]> https://biorxiv.org/content/10.1101/2024.09.16.613256v1?rss=1 Xie, Y. Zhang, C. Li, S. Du, X. Wang, M. Hu, Y. Liu, S. Gao, Y. Q. 2024-09-21 doi:10.1101/2024.09.16.613256 Cold Spring Harbor Laboratory Press 2024-09-21 <![CDATA[ Fungus-infected Meiogyne flowers offer a brood site for beetle pollinators in a tripartite nursery pollination system ]]> https://biorxiv.org/content/10.1101/2024.09.19.613827v1?rss=1 Liu, M.-F. Chen, J. Xue, B. Wang, R. Saunders, R. M. K. 2024-09-22 doi:10.1101/2024.09.19.613827 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Modulation of β-Catenin is important to promote WNT expression in macrophages and mitigate intestinal injury ]]> https://biorxiv.org/content/10.1101/2024.09.21.614209v1?rss=1 Chugh, R. M. Bhanja, P. Zitter, R. Gunewardena, S. Badkul, R. Saha, S. 2024-09-22 doi:10.1101/2024.09.21.614209 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Trait-dependent biogeography offers insights on the dispersal of Meiogyne (Annonaceae) across the Australasia-Pacific region ]]> https://biorxiv.org/content/10.1101/2024.09.19.614018v1?rss=1 Liu, M.-F. Munzinger, J. Chalermglin, P. Chen, J. Xue, B. Saunders, R. M. K. 2024-09-24 doi:10.1101/2024.09.19.614018 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ A comparative assessment of self-limiting genetic control strategies for population suppression ]]> https://biorxiv.org/content/10.1101/2024.09.23.614516v1?rss=1 Han, Y. Champer, J. 2024-09-24 doi:10.1101/2024.09.23.614516 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Assessment of drive efficiency and resistance allele formation of a homing gene drive in the mosquito Aedes aegypti ]]> https://biorxiv.org/content/10.1101/2024.09.24.614707v1?rss=1 Yang, X. Xu, X. Chen, Y. Wei, J. Huang, W. Wu, S. Champer, J. Wang, J. 2024-09-26 doi:10.1101/2024.09.24.614707 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models ]]> https://biorxiv.org/content/10.1101/2024.09.24.614797v1?rss=1 Raman, K. Kratochvil, M. Olivier, B. G. Konig, M. Sengupta, P. Baskaran, D. K. K. Nguyen, T. V. N. Lobo, D. Wilken, S. E. Tiwari, K. K. Raghu, A. K. Palanikumar, I. Raajaraam, L. Ibrahim, M. Balakrishnan, S. Umale, S. Bergmann, F. Malpani, T. Satagopam, V. P. Schneider, R. Beber, M. E. Keating, S. Anton, M. Renz, A. Lakshmanan, M. Lee, D.-Y. Koduru, L. Mostolizadeh, R. Dias, O. Cunha, E. Oliveira, A. Lee, Y. Q. Zengler, K. Santibanez-Palominos, R. Kumar, M. Barberis, M. Puniya, B. L. Helikar, T. Dinh, H. V. Suthers, P. F. Maranas, C. D. Casini, I. Logh 2024-09-26 doi:10.1101/2024.09.24.614797 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Differential Kinetics of SARS-CoV-2 Proteases Revealed by a Dual-Color, BRET-based Protease Biosensor, DuProSense ]]> https://biorxiv.org/content/10.1101/2024.09.26.615113v1?rss=1 Fatima, A. Geethakumari, A. M. Uddin, S. M. Biswas, K. H. 2024-09-26 doi:10.1101/2024.09.26.615113 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Interpreting Sleep Activity Through Neural Contrastive Learning ]]> https://biorxiv.org/content/10.1101/2024.09.25.615100v1?rss=1 Chen, Z. Zheng, H. Zhou, J. Zheng, L. Lin, P. Wang, H. Dolan, R. J. Behrens, T. E. Liu, Y. 2024-09-27 doi:10.1101/2024.09.25.615100 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Twist is the key to the gating of mechanosensitive ion channel NOMPC ]]> https://biorxiv.org/content/10.1101/2024.09.26.615110v1?rss=1 Duan, J. Song, C. 2024-09-27 doi:10.1101/2024.09.26.615110 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ A Novel Mouse Model Demonstrates In Vivo Replenishment of Central Nervous System Pericytes After Successful Acute Ablation ]]> https://biorxiv.org/content/10.1101/2024.09.27.614665v1?rss=1 Atak, D. Yildiz, E. Ozkan, E. Yousefi, M. Ozkan, A. Gokyuzu, A. B. Kizilirmak, A. B. Alnajjar, I. A. Kanar, C. Caan, Z. L. Zeybek, S. U. Kucukali, C. I. Tuzun, E. Gursoy-Ozdemir, Y. Vural, A. 2024-09-28 doi:10.1101/2024.09.27.614665 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ Single-cell proteomics of pre-implantation mouse embryos uncovers distinct asymmetry of certain proteins among early blastomeres ]]> https://biorxiv.org/content/10.1101/2024.09.28.614398v1?rss=1 Yuan, Y. Hu, M. Zheng, Y. Zhang, Y. Pang, Y. Xie, X. S. 2024-09-30 doi:10.1101/2024.09.28.614398 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ An all-in-one AAV vector for cardiac-specific gene silencing by an adenine base editor ]]> https://biorxiv.org/content/10.1101/2024.09.30.615742v1?rss=1 Liu, Z. Yang, L. Yang, Y. Li, J. Chen, Z. Guo, C. Guo, Q. Li, Q. Sun, Y. Zhao, D. Hu, X. Gao, F. Guo, Y. 2024-09-30 doi:10.1101/2024.09.30.615742 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Phytochemical Analysis and Nematicidal Activity of Medicinal Plants Against Meloidogyne javanica ]]> https://biorxiv.org/content/10.1101/2024.09.29.615697v1?rss=1 Maher, S. Naheed, N. Khan, N. Ishtiaq, H. Solangi, G. S. karim, A. Imran, M. Iqbal, E. Mukhtar, F. Bakhshi, M. Mina, G. Alarfaji, S. S. 2024-10-01 doi:10.1101/2024.09.29.615697 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ An accelerated molecular dynamics study for investigating protein pathways using the bond-boost hyperdynamics method ]]> https://biorxiv.org/content/10.1101/2024.09.30.615751v1?rss=1 Park, S. W. Choi, M.-k. Lee, B. H. Seo, S. Kim, W. K. Kim, M. K. 2024-10-01 doi:10.1101/2024.09.30.615751 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ SC-MAMBA2: Leveraging State-Space Models for Efficient Single-Cell Ultra-Long Transcriptome Modeling ]]> https://biorxiv.org/content/10.1101/2024.09.30.615775v1?rss=1 Zhao, Y. Zhao, B. Zhang, F. He, C. Wu, W. Lai, L. 2024-10-01 doi:10.1101/2024.09.30.615775 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Calcium Homeostasis Modulator 2 Constitutes an ATP-regulation Pore in Mitochondria ]]> https://biorxiv.org/content/10.1101/2024.09.30.615983v1?rss=1 GUO, Q. Hou, T. Xie, W.-J. Zhang, J.-R. Ma, X.-L. Guo, Y. Wang, X.-T. Wang, L.-P. Lu, M.-A. Wu, Z. Wang, H.-G. Chen, Y.-H. Li, Y.-L. Wang, S.-Q. 2024-10-01 doi:10.1101/2024.09.30.615983 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Efficient Coding in Motor Planning ]]> https://biorxiv.org/content/10.1101/2024.09.30.615975v1?rss=1 Wang, T. Fang, Y. Whitney, D. 2024-10-02 doi:10.1101/2024.09.30.615975 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Pathogenicity across variation in microbial virulence and host resistance ]]> https://biorxiv.org/content/10.1101/2024.10.02.616271v1?rss=1 Gupta, A. Unckless, R. 2024-10-03 doi:10.1101/2024.10.02.616271 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Gene-by-environment interactions and adaptive body size variation in mice from the Americas ]]> https://biorxiv.org/content/10.1101/2024.10.03.616282v1?rss=1 Mack, K. L. Landino, N. P. Tertyshnaia, M. Longo, T. C. Vera, S. A. Crew, L. A. McDonald, K. Phifer-Rixey, M. 2024-10-03 doi:10.1101/2024.10.03.616282 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ A genotype-first approach identifies variants for orofacial clefts and other phenotypes in dogs ]]> https://biorxiv.org/content/10.1101/2024.10.04.616687v1?rss=1 Buckley, R. M. Bilgen, N. Harris, A. C. Savolainen, P. Tepeli, C. Erdogan, M. Serres Armero, A. Dreger, D. L. van Steenbeek, F. G. Hytönen, M. K. Hale, J. Lohi, H. Cınar Kul, B. Boyko, A. R. Ostrander, E. A. 2024-10-04 doi:10.1101/2024.10.04.616687 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ C-Reactive Protein Drives Potent Clearance of Blood Bacteria in the Liver by Activating the Complement System ]]> https://biorxiv.org/content/10.1101/2024.10.05.616753v1?rss=1 Chen, D. Hu, J. Zhu, M. Xie, Y. Yao, H. An, H. Meng, Y. Wang, J. Huang, X. Shao, Z. Xiang, Y. Qi, J. Gao, G. F. Zhang, J.-R. 2024-10-05 doi:10.1101/2024.10.05.616753 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ Computational Insights into the Allosteric Behavior of Mini-Insulin in Receptor Binding Driven by C-Peptide Mobility ]]> https://biorxiv.org/content/10.1101/2024.10.05.616825v1?rss=1 AYAN, E. 2024-10-06 doi:10.1101/2024.10.05.616825 Cold Spring Harbor Laboratory Press 2024-10-06 <![CDATA[ Evolutionary conserved sap peptides derived from xylem-specific peptide precursors in woody angiosperms ]]> https://biorxiv.org/content/10.1101/2024.10.08.617308v1?rss=1 Chen, C.-H. Liou, P.-C. Lin, C.-C. Kuo, S.-C. Wu, C.-C. Lin, Y.-C. J. Chen, Y.-L. 2024-10-12 doi:10.1101/2024.10.08.617308 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Estrogen Receptor 1 Signaling in Hepatic Stellate Cells Designates Resistance to Liver Fibrosis ]]> https://biorxiv.org/content/10.1101/2024.10.10.617541v1?rss=1 Li, T. Yang, J. 2024-10-14 doi:10.1101/2024.10.10.617541 Cold Spring Harbor Laboratory Press 2024-10-14 <![CDATA[ Human Brain-Wide Activation of Sleep Rhythms ]]> https://biorxiv.org/content/10.1101/2024.10.14.618165v1?rss=1 Wang, H. Zou, Q. Zhang, J. Gao, J.-H. Liu, Y. 2024-10-16 doi:10.1101/2024.10.14.618165 Cold Spring Harbor Laboratory Press 2024-10-16 <![CDATA[ Mechanistic Studies of Small Molecule Ligands Selective to RNA Single G Bulges ]]> https://biorxiv.org/content/10.1101/2024.10.14.618236v1?rss=1 100-fold reduction in the binding affinity. Our work deepened the understanding of RNA-small molecule interactions and integrated a new generalizable platform for the rational design of selective small-molecule RNA binders. ]]> Hegde, S. Akhter, S. Tang, Z. Qi, C. Yu, C. Lewicka, A. Liu, Y. Koirala, K. Reibarkh, M. Battaile, K. P. Cooper, A. Lovell, S. Holmstrom, E. D. Wang, X. Piccirilli, J. A. Gao, Q. Miao, Y. Wang, J. 2024-10-17 doi:10.1101/2024.10.14.618236 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Spatial frequency channels mediate a visual metric for human spatial perception ]]> https://biorxiv.org/content/10.1101/2024.10.15.615126v1?rss=1 Zhang, S. Mo, C. Mo, L. Fang, F. 2024-10-17 doi:10.1101/2024.10.15.615126 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Identification of SLC35A1 as an essential host factor for the transduction of multi-serotype recombinant adeno-associated virus (AAV) vectors ]]> https://biorxiv.org/content/10.1101/2024.10.16.618764v1?rss=1 Zhang, X. Hao, S. Feng, Z. Ning, K. Kuz, C. A. McFarlin, S. Richart, D. Cheng, F. Zhang-Chen, A. McFarlane, R. Yan, Z. Qiu, J. 2024-10-17 doi:10.1101/2024.10.16.618764 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Du-IN-v2: Unleashing the Power of Vector Quantization for Decoding Cognitive States from Intracranial Neural Signals ]]> https://biorxiv.org/content/10.1101/2024.10.16.618686v1?rss=1 Zheng, H. Wang, H.-T. Jiang, W.-B. Chen, Z.-T. He, L. Lin, P.-Y. Wei, P.-H. Zhao, G.-G. Liu, Y.-Z. 2024-10-18 doi:10.1101/2024.10.16.618686 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ The Circadian Isoform Landscape of Mouse Livers ]]> https://biorxiv.org/content/10.1101/2024.10.16.618716v1?rss=1 Zee, A. Deng, D. Z. Q. DiTacchio, L. Vollmers, C. 2024-10-18 doi:10.1101/2024.10.16.618716 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Mechanical control of germ cell specification in Arabidopsis anthers ]]> https://biorxiv.org/content/10.1101/2024.10.17.618875v1?rss=1 Liu, C. Shi, H. Han, Y. Wang, P. Li, K. Zhang, Z. Liu, J. Zheng, Y. Li, L. Lin, L. Liang, C. Qin, B. Han, H. Bai, S. Liu, X. Chen, W. Zhao, F. 2024-10-19 doi:10.1101/2024.10.17.618875 Cold Spring Harbor Laboratory Press 2024-10-19 <![CDATA[ Elevated Ubiquitin Phosphorylation by PINK1 Contributes to Proteasomal Impairment and Promotes Neurodegeneration ]]> https://biorxiv.org/content/10.1101/2024.10.18.619025v1?rss=1 Chen, C. Gao, T.-Y. Yi, H.-W. Zhang, Y. Wang, T. Lou, Z.-L. Wei, T.-F. Lu, Y.-B. Li, T. Tang, C. Zhang, W.-P. 2024-10-19 doi:10.1101/2024.10.18.619025 Cold Spring Harbor Laboratory Press 2024-10-19 <![CDATA[ Decipher Fundamental Atomic Interactions to Unify Generative Molecular Docking and Design ]]> https://biorxiv.org/content/10.1101/2024.10.17.618827v1?rss=1 Peng, X. Guo, R. Xu, Y. Guan, J. Jia, Y. Huang, Y. Zhang, M. Peng, J. Sun, J. Han, C. Wang, Z. Ma, J. 2024-10-21 doi:10.1101/2024.10.17.618827 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ p-ClustVal: A Novel p-adic Approach for Enhanced Clustering of High-Dimensional scRNASeq Data ]]> https://biorxiv.org/content/10.1101/2024.10.18.619153v1?rss=1 Sharma, P. Mishra, S. Kurban, H. Dalkilic, M. 2024-10-22 doi:10.1101/2024.10.18.619153 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Connectomic Organization of the Suprachiasmatic Nucleus ]]> https://biorxiv.org/content/10.1101/2024.10.20.619252v1?rss=1 Liu, J. Yu, J. Shen, L. Chen, X. Ma, L. Zhai, H. Li, L. Zhang, L. Wang, L. Yuan, J. Chen, B. Hong, B. Liu, J. Lv, Y. Cai, Y. Zhang, Y. Chang, S. Guo, J. Chen, H. Liu, M. Wang, Z. Xin, T. Zhou, F. Zhao, X. Zhang, D. Xie, Q. Ma, H. Xu, Y. Cheng, H. Han, H. 2024-10-22 doi:10.1101/2024.10.20.619252 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Connectome-based Predictive Models of General and Specific Cognitive Control ]]> https://biorxiv.org/content/10.1101/2024.10.21.619468v1?rss=1 Qu, S. Qu, Y. L. Yoo, K. Chun, M. M. 2024-10-22 doi:10.1101/2024.10.21.619468 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ The protease interpain A of Prevotella intermedia promotes human OSCC cells proliferation and migration ]]> https://biorxiv.org/content/10.1101/2024.10.20.619282v1?rss=1 Chang, S.-M. Huang, I.-H. Ciou, Y.-J. Wang, W.-R. Wu, N.-H. Chuu, C.-P. Hsiao, J.-R. Chang, J. S. Chang, J.-Y. Chen, J.-W. 2024-10-23 doi:10.1101/2024.10.20.619282 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Enhanced immune evasion of SARS-CoV-2 KP.3.1.1 and XEC through NTD glycosylation ]]> https://biorxiv.org/content/10.1101/2024.10.23.619754v1?rss=1 Liu, J. Yu, Y. Jian, F. Yang, S. Song, W. Wang, P. Yu, L. Shao, F. Cao, Y. 2024-10-23 doi:10.1101/2024.10.23.619754 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Aerobic capacity and exercise mediate protection against hepatic steatosis via enhanced bile acid metabolism. ]]> https://biorxiv.org/content/10.1101/2024.10.21.619494v1?rss=1 Kugler, B. A. Maurer, A. Fu, X. Franczak, E. Ernst, N. Schwartze, K. Allen, J. Li, T. Crawford, P. A. Koch, L. G. Britton, S. L. Burgess, S. C. Thyfault, J. 2024-10-24 doi:10.1101/2024.10.21.619494 Cold Spring Harbor Laboratory Press 2024-10-24 <![CDATA[ Antibody Profiles Elicited by Potent and Subpotent Whole Cell Pertussis Vaccines in Mice ]]> https://biorxiv.org/content/10.1101/2024.10.22.619719v1?rss=1 10-fold less effective than unstressed vaccine when evaluated in a mouse model of B. pertussis lung clearance following intranasal challenge. We then screened immune sera on a limited B. pertussis Tahoma I proteome array and identified >30 antigens whose antibody reactivity profiles increased, decreased or were unchanged as a function of wP potency. Interestingly, virtually all the "indicator" antigens identified are known virulence factors or reactive with human convalescent sera, thereby establishing a potential link between wP potency and pertussis infection and immunity. These results bode well for the development of a limited B. pertussis antigen array as a stability-indicating surrogate potency assay for the ic-MPT. ]]> Adewunmi, Y. Doering, J. Kumar, P. Pablo, J. V. Teng, A. A. Huynh, V. Secrist, K. Volkin, D. Joshi, S. Campo, J. J. MANTIS, N. J. 2024-10-25 doi:10.1101/2024.10.22.619719 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Exploring the Biochemical Landscape of Bacterial Medium with Pyruvate as the Exclusive Carbon Source for NMR Studies ]]> https://biorxiv.org/content/10.1101/2024.10.26.620443v1?rss=1 Dag, C. Kahraman, K. 2024-10-27 doi:10.1101/2024.10.26.620443 Cold Spring Harbor Laboratory Press 2024-10-27 <![CDATA[ Spatially global effects of feature-based attention in functional subdivisions of human subcortical nuclei ]]> https://biorxiv.org/content/10.1101/2024.10.26.620447v1?rss=1 Lin, W. Zhang, Y.-Y. ZHANG, X. Fang, F. Qian, C. Zhang, P. 2024-10-27 doi:10.1101/2024.10.26.620447 Cold Spring Harbor Laboratory Press 2024-10-27 <![CDATA[ Reduced Liver Mitochondrial Energy Metabolism Impairs Food Intake Regulation Following Gastric Preloads and Fasting ]]> https://biorxiv.org/content/10.1101/2024.10.24.620086v1?rss=1 Ponte, M. E. Prom, J. C. Newcomb, M. A. Jordan, A. B. Comfort, L. L. Hu, J. Geisler, C. E. Hayes, M. R. Morris, E. M. 2024-10-29 doi:10.1101/2024.10.24.620086 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Identification of a series of pyrrolo-pyrimidine based SARS-CoV-2 Mac1 inhibitors that repress coronavirus replication ]]> https://biorxiv.org/content/10.1101/2024.10.28.620664v1?rss=1 Pfannenstiel, J. J. Duong, M. T. H. Cluff, D. Sherrill, L. Colquhoun, I. Cadoux, G. Thorne, D. Paakkonen, J. Schemmel, N. F. O'Connor, J. J. Saenjamsai, P. Feng, M. Hageman, M. Johnson, D. K. Roy, A. Lehtio, L. Ferraris, D. V. Fehr, A. R. 2024-10-29 doi:10.1101/2024.10.28.620664 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ TFAP2C is a key regulator of intrauterine trophoblast cell invasion and deep hemochorial placentation ]]> https://biorxiv.org/content/10.1101/2024.10.31.621324v1?rss=1 Dominguez, E. M. Irusta, A. M. M. Scott, R. L. IQBAL, K. Soares, M. 2024-11-01 doi:10.1101/2024.10.31.621324 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Dentate Gyrus Norepinephrine Ramping Facilitates Aversive Contextual Processing ]]> https://biorxiv.org/content/10.1101/2024.10.31.621389v1?rss=1 Zhang, E. T. Saglimbeni, G. S. Feng, J. Li, Y. Bruchas, M. R. 2024-11-01 doi:10.1101/2024.10.31.621389 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Single-cell atlas of developing mouse palates reveals cellular and molecular transitions in periderm cell fate ]]> https://biorxiv.org/content/10.1101/2024.10.28.620753v1?rss=1 Huang, W. Qian, Z. Zhang, J. Ding, Y. Wang, B. Lin, J. Zhang, X. Zhao, H. Chen, F. 2024-11-03 doi:10.1101/2024.10.28.620753 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Neuron-astrocyte Coupling in Lateral Habenula Mediates Depressive-like Behaviors ]]> https://biorxiv.org/content/10.1101/2024.11.03.621722v1?rss=1 Xin, Q. Wang, J. Zheng, J. Tan, Y. Jia, X. Ni, Z. Feng, J. Wu, Z. Li, Y. Li, X. Ma, H. Hu, H. 2024-11-03 doi:10.1101/2024.11.03.621722 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Structural basis of gap-filling DNA synthesis in the nucleosome by DNA Polymerase β ]]> https://biorxiv.org/content/10.1101/2024.11.04.621902v1?rss=1 Weaver, T. M. Ryan, B. J. Thompson, S. H. Hussen, A. S. Spencer, J. J. Xu, Z. Schnicker, N. J. Freudenthal, B. D. 2024-11-04 doi:10.1101/2024.11.04.621902 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ Structure of Blm10:13S proteasome intermediate reveals parallel assembly pathways for the proteasome core particle ]]> https://biorxiv.org/content/10.1101/2024.11.04.621988v1?rss=1 Kaur, M. Chen, X. Lee, S. Y. Weaver, T. M. Freudenthal, B. D. Walters, K. Roelofs, J. 2024-11-05 doi:10.1101/2024.11.04.621988 Cold Spring Harbor Laboratory Press 2024-11-05 <![CDATA[ Species-specific circular RNA circDS-1 enhances adaptive evolution in Talaromyces marneffei through regulation of dimorphic transition and virulence ]]> https://biorxiv.org/content/10.1101/2024.11.05.622019v1?rss=1 Hu, X. Du, M. Tao, C. Wang, J. Zhang, Y. Jin, Y. Yang, E. 2024-11-05 doi:10.1101/2024.11.05.622019 Cold Spring Harbor Laboratory Press 2024-11-05 <![CDATA[ Salt-dependent non-catalytic allostery of human USP14-regulated 26S proteasome ]]> https://biorxiv.org/content/10.1101/2024.11.07.622408v1?rss=1 Zou, S. Zhang, S. Zhao, L. Mao, Y. 2024-11-07 doi:10.1101/2024.11.07.622408 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ A unified central thalamus mechanism underlying diverse recoveries in disorders of consciousness ]]> https://biorxiv.org/content/10.1101/2024.11.04.621844v1?rss=1 Zhang, H. Ge, Q. Liu, X. Dang, Y. Xu, L. Zhuang, Y. Wu, S. Laureys, S. He, J. Yu, S. 2024-11-08 doi:10.1101/2024.11.04.621844 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Encoding opposing valences through frequency-dependent transmitter switching in single peptidergic neurons ]]> https://biorxiv.org/content/10.1101/2024.11.09.622790v1?rss=1 Kim, D.-I. Kang, S. J. Jhang, J. Jo, Y. S. Park, S. Ye, M. Pyeon, G. H. Im, G.-H. Kim, S.-G. Han, S. 2024-11-09 doi:10.1101/2024.11.09.622790 Cold Spring Harbor Laboratory Press 2024-11-09 <![CDATA[ Living xylem cells encode a large number of conserved gene families responsible for vascular sap peptides ]]> https://biorxiv.org/content/10.1101/2024.11.10.622827v1?rss=1 Lu, M. R. Tung, C.-C. Huang, C.-E. Chen, C.-H. Liou, P.-C. Lin, C.-Y. I. Yu, J.-H. Chen, Y.-L. Lin, Y.-C. J. Tsai, I. J. 2024-11-11 doi:10.1101/2024.11.10.622827 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Sex-dependent effects of CYP2E1 on the kidney and the protective potential of 4MP against cisplatin-induced nephrotoxicity ]]> https://biorxiv.org/content/10.1101/2024.11.10.622845v1?rss=1 Akakpo, J. Y. Abbott, E. Woolbright, B. L. Rick, S. G. Wallace, D. P. Taylor, J. A. 2024-11-11 doi:10.1101/2024.11.10.622845 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Patterns of crossover distribution in Drosophila mauritiana necessitate a re-thinking of the centromere effect on crossing over ]]> https://biorxiv.org/content/10.1101/2024.11.11.623017v1?rss=1 Hawley, R. S. Price, A. Li, H. Jagannathan, M. Staber, C. Hughes, S. E. Williams, S. Perera, A. Egidy, R. R. Lawlor, A. Blumenstiel, J. P. 2024-11-11 doi:10.1101/2024.11.11.623017 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Inhibition of serine and arginine-rich splicing factor 3 induces epidermal differentiation and decreases cutaneous squamous cell carcinoma risk ]]> https://biorxiv.org/content/10.1101/2024.11.07.622551v1?rss=1 Donohue, I. M. He, H. Nguyen, A. Hui, G. Muralidharan, J. Pike, W. C. Jackson, M. L. Ko, C. Srivastava, A. Lee, C. S. 2024-11-12 doi:10.1101/2024.11.07.622551 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Upstream open reading frames buffer translational variability during Drosophila evolution and development ]]> https://biorxiv.org/content/10.1101/2024.11.13.623404v1?rss=1 Sun, Y. Duan, Y. Gao, P. Liu, C. Jin, K. Dou, S. Tang, W. Zhang, H. Lu, J. 2024-11-15 doi:10.1101/2024.11.13.623404 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ A Rapid, Cost-Effective Method for High-Yield DNA Purification from PCR Products and Agarose Gels. ]]> https://biorxiv.org/content/10.1101/2024.11.13.623516v1?rss=1 Fatima, S. Javed, M. Zahra, H. hussain, i. Mian, A. A. 2024-11-15 doi:10.1101/2024.11.13.623516 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ CellPatch: a Highly Efficient Foundation Model for Single-Cell Transcriptomics with Heuristic Patching ]]> https://biorxiv.org/content/10.1101/2024.11.15.623701v1?rss=1 Wu, H.-J. Zheng, X. Ma, Z. Zhu, H. Yuan, Y. Yang, J. Cai, K. Wei, N. Zhang, S. Wang, L. Wenjie, J. Sun, Y. Wang, Y.-J. Liu, A. Lai, F. 2024-11-17 doi:10.1101/2024.11.15.623701 Cold Spring Harbor Laboratory Press 2024-11-17 <![CDATA[ Dual-timescale motor circuit dynamics underlies fast head exploratory behavior and efficient locomotion ]]> https://biorxiv.org/content/10.1101/2024.11.18.624064v1?rss=1 Li, P. Zhang, H. Su, Y. Wang, J. Tao, L. Wen, Q. 2024-11-19 doi:10.1101/2024.11.18.624064 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ Engineered mitochondrial A-to-G editors with enhanced efficiency and targeting scope ]]> https://biorxiv.org/content/10.1101/2024.11.19.623682v1?rss=1 Chen, L. Hong, M. Luan, C. Yuan, M. Wang, Y. Guo, X. Fang, Y. Huang, H. Dong, X. Gao, H. Zhang, D. Chen, X. Meng, D. Huang, M. Yi, Z. Liu, M. Gao, L. Song, G. Zhou, X. Wei, W. Li, D. 2024-11-20 doi:10.1101/2024.11.19.623682 Cold Spring Harbor Laboratory Press 2024-11-20 <![CDATA[ Clinical and Molecular Characterization of Glioma Patients: miR-21 Expression as a Prognostic Biomarker in Tissue and Serum ]]> https://biorxiv.org/content/10.1101/2024.11.20.624501v1?rss=1 Laghari, A. A. Sufiyan, S. Amin, W. Adnan, U. Naeem, S. Abidi, S. H. Ilyas, S. Uddin, S. Bajwa, M. H. Enam, S. A. Mughal, N. 2024-11-21 doi:10.1101/2024.11.20.624501 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Quantification and potential functional relevanceof binding cooperativity of adjacent transcriptionfactors on DNA ]]> https://biorxiv.org/content/10.1101/2024.11.20.624593v1?rss=1 Wang, X. Xie, C. Shen, K. Li, D. Xie, X. S. 2024-11-21 doi:10.1101/2024.11.20.624593 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Opposite-sex pairing alters social interaction-induced GCaMP and dopamine activity in the insular cortex of male prairie voles ]]> https://biorxiv.org/content/10.1101/2024.11.21.624717v1?rss=1 Vitale, E. M. Tbaba, A. H. Tam, K. Gossman, K. R. Smith, A. S. 2024-11-21 doi:10.1101/2024.11.21.624717 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Cardiolipin-mimic lipid nanoparticles without antibody modification delivered senolytic in-vivo CAR-T therapy for inflamm-aging ]]> https://biorxiv.org/content/10.1101/2024.11.21.624667v1?rss=1 Zhang, Z. Ma, B. Li, B. Li, Z. Gao, M. Zhao, H. Peng, R. Hu, J. Wang, Y. You, W. Gui, X. Wang, R. Hu, X. Chen, B. Zhang, Y. Hao, Y. Zhou, D. Yang, Y. Deng, M. Miao, L. 2024-11-22 doi:10.1101/2024.11.21.624667 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ Structural insights into cholesterol sensing by the LYCHOS-mTORC1 pathway ]]> https://biorxiv.org/content/10.1101/2024.11.21.624772v1?rss=1 Yu, S. Ding, J. Wang, W. Wang, J. Zuo, P. Yang, A. Dai, Z. Yin, Y. Sun, J. Liang, L. 2024-11-22 doi:10.1101/2024.11.21.624772 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ ALS driven by mutant NEK1 aggregation is accelerated by Pml loss, but clinically reversed through pharmacologic induction of Pml-mediated degradation ]]> https://biorxiv.org/content/10.1101/2024.11.23.622051v1?rss=1 Georgiadou, P. Erkaya, B. Kawakita, M. Sahin, E. Ozturk, H. Tiryaki, F. Yildiz, K. Ozgenc, I. Pekbilir, E. Dogan, S. A. Lallemand-Breitenbach, V. Vargas, S. Prochiantz, A. L. Firat-Karalar, E. N. de The, H. Sahin, U. 2024-11-23 doi:10.1101/2024.11.23.622051 Cold Spring Harbor Laboratory Press 2024-11-23 <![CDATA[ Versatile Stain Transfer in Histopathology Using a Unified Diffusion Framework ]]> https://biorxiv.org/content/10.1101/2024.11.23.624680v1?rss=1 Yan, X. Yuan, M. Lu, Y. Zhang, Y. Chen, Z. Bao, P. Li, Z. Dong, B. Yang, L. Zhang, L. Zhou, F. 2024-11-23 doi:10.1101/2024.11.23.624680 Cold Spring Harbor Laboratory Press 2024-11-23 <![CDATA[ Innervation density governs crosstalk of GPCR-based norepinephrine and dopamine sensors ]]> https://biorxiv.org/content/10.1101/2024.11.23.624963v1?rss=1 Lopez, R. C. Noble, N. Ozcete, O. D. Cai, X. Handy, G. E. Andersen, J. W. Patriarchi, T. Li, Y. Kaeser, P. S. 2024-11-23 doi:10.1101/2024.11.23.624963 Cold Spring Harbor Laboratory Press 2024-11-23 <![CDATA[ Sex-specific DNA methylation differences in Amyotrophic lateral sclerosis ]]> https://biorxiv.org/content/10.1101/2024.11.22.624866v1?rss=1 Grant, O. Iacoangeli, A. Zwamborn, R. van Rheenen, W. Byrne, R. P. van Eijk, K. R. Kenna, K. Van Vugt, J. Cooper-Knock, J. Kenna, B. Vural, A. Topp, S. Smith, B. Dobson, R. van Es, M. Gotkine, M. Corcia, P. de Carvalho, M. Panades, M. Mora, J. Mill, J. Garton, F. McRae, A. Wray, N. Shaw, P. Landers, J. Glass, J. Shaw, C. Basak, N. Hardiman, O. Van Damme, P. McLaughlin, R. van den Berg, L. Veldink, J. Al Chalabi, A. Al Kheifat, A. 2024-11-25 doi:10.1101/2024.11.22.624866 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Structural and Mechanistic Bases for Resistance of the M66I Capsid Variant to Lenacapavir ]]> https://biorxiv.org/content/10.1101/2024.11.25.625199v1?rss=1 Briganti, L. Annamalai, A. S. Bester, S. M. Wei, G. Andino-Moncada, J. R. Singh, S. P. Kleinpeter, A. Tripathi, M. Nguyen, B. Radhakrishnan, R. Singh, P. K. Greenwood, J. Schope, L. I. Haney, R. Huang, S.-W. Freed, E. O. Engelman, A. N. Francis, A. Kvaratskhelia, M. 2024-11-25 doi:10.1101/2024.11.25.625199 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Adipose-derived Mesenchymal Stem Cells and Retinal Pigment Epithelial Cells Interactions in Stress Environment via Tunneling Nanotubes ]]> https://biorxiv.org/content/10.1101/2024.11.24.624852v1?rss=1 Gozel, M. Senkoylu, K. Kesim, C. Hasanreisoglu, M. 2024-11-26 doi:10.1101/2024.11.24.624852 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Effects of Primed Adipose Mesenchymal Stem Cell-Derived Exosomes on Immunomodulation in Behcet Uveitis ]]> https://biorxiv.org/content/10.1101/2024.11.24.625042v1?rss=1 Gozel, M. Aydemir, D. Kaleli, H. N. Cosar, F. Guleser, U. Y. Kusan Unlu, E. Kesim, C. Sezgin, B. Sahin, A. Ucar, D. Hatemi, G. Hasanreisoglu, M. 2024-11-26 doi:10.1101/2024.11.24.625042 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Enalapril mitigates aging by targeting antioxidative genes via phosphorylated Smad1/5/9 ]]> https://biorxiv.org/content/10.1101/2024.11.27.625711v1?rss=1 Lyu, W. Wang, H. Du, Z. Wei, R. He, J. Meng, F. Bi, J. Zhang, L. Zhang, C. Guan, Y. Tao, W. 2024-11-28 doi:10.1101/2024.11.27.625711 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Deciphering Ca2+ Permeation and Valence Selectivity in Cav1: Molecular Dynamics Simulations Reveal the Three-Ion Knock-on Mechanism ]]> https://biorxiv.org/content/10.1101/2024.11.27.625788v1?rss=1 Xue, L. Yan, N. Song, C. 2024-11-29 doi:10.1101/2024.11.27.625788 Cold Spring Harbor Laboratory Press 2024-11-29 <![CDATA[ Immunomodulatory effects of tumor Lactate Dehydrogenase C (LDHC) in breast cancer ]]> https://biorxiv.org/content/10.1101/2024.11.26.625341v1?rss=1 Naik, A. Thomas, R. Al-Khalifa, A. Qasem, H. Decock, J. 2024-12-01 doi:10.1101/2024.11.26.625341 Cold Spring Harbor Laboratory Press 2024-12-01 <![CDATA[ Thermodynamic Parameter Estimation for Modified Oligonucleotides Using Molecular Dynamics Simulations ]]> https://biorxiv.org/content/10.1101/2024.11.29.626002v1?rss=1 Park, S. W. Lee, J. Park, J. W. Kim, M. K. Seo, S. 2024-12-01 doi:10.1101/2024.11.29.626002 Cold Spring Harbor Laboratory Press 2024-12-01 <![CDATA[ Differential Remodeling of the BRCA1 Interactome by a Unique Minimal Clinical Truncation Mutation ]]> https://biorxiv.org/content/10.1101/2024.11.26.625539v1?rss=1 Chen, J. Sardiu, M. E. Rekowski, M. J. Nde, J. Clark, Z. S. Anant, S. Washburn, M. P. Jensen, R. A. 2024-12-02 doi:10.1101/2024.11.26.625539 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ Polyfunctional IL-21+ IFNg+ T follicular helper cells contribute to checkpoint inhibitor diabetes mellitus and can be targeted by JAK inhibitor therapy ]]> https://biorxiv.org/content/10.1101/2024.11.27.625710v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@ed4acdorg.highwire.dtl.DTLVardef@c9e062org.highwire.dtl.DTLVardef@1aa81eforg.highwire.dtl.DTLVardef@1388747_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Huang, N. Ortega, J. Kimbrell, K. Lee, J. Scott, L. N. Peluso, E. M. Wang, S. J. Kao, E. Kim, K. Olay, J. Quandt, Z. Angell, T. E. Su, M. A. Lechner, M. G. 2024-12-03 doi:10.1101/2024.11.27.625710 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Targeted glycophagy ATG8 therapy for diabetic heart disease ]]> https://biorxiv.org/content/10.1101/2024.11.28.625926v1?rss=1 Mellor, K. M. Varma, U. Koutsifeli, P. Curl, C. L. Janssens, J. V. Daniels, L. J. Bernasochi, G. Raaijmakers, A. J. A. Annandale, M. Li, X. James, S. L. Taylor, D. J. Raedschelders, K. Weeks, K. L. Mills, R. J. Parton, R. G. Hu, X. Bell, J. R. Porrello, E. R. Hudson, J. E. Xiao, R.-P. Van Eyk, J. E. Gottlieb, R. A. Delbridge, L. 2024-12-03 doi:10.1101/2024.11.28.625926 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Constructing a holistic map of cell fate decision by hyper solution landscape ]]> https://biorxiv.org/content/10.1101/2024.11.28.625944v1?rss=1 Zhang, X. Li, Z. Zhang, L. 2024-12-03 doi:10.1101/2024.11.28.625944 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Deep-learning-enabled generative prevalent mutation prediction through host-to-herd in silico virus evolution ]]> https://biorxiv.org/content/10.1101/2024.11.28.625962v1?rss=1 Liu, X. Nie, Z. Si, H. Shen, X. Liu, Y. Huang, X. Dong, T. Xu, F. Chen, J. Zhou, P. Tian, Y. 2024-12-03 doi:10.1101/2024.11.28.625962 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ CGMFinder Identifies Correlated Gene Modules from 3H scRNA-seq Data ]]> https://biorxiv.org/content/10.1101/2024.11.29.624642v1?rss=1 Ma, W. Xie, X. S. 2024-12-03 doi:10.1101/2024.11.29.624642 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Multinucleated giant cells are hallmarks of ovarian aging with unique immune and degradation-associated molecular signatures ]]> https://biorxiv.org/content/10.1101/2024.12.03.626649v1?rss=1 Converse, A. Perry, M. J. Dipali, S. S. Isola, J. V. Kelley, E. B. Varberg, J. M. Zelinkski, M. B. Gerton, J. L. Stout, M. Pritchard, M. T. Duncan, F. 2024-12-04 doi:10.1101/2024.12.03.626649 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ High-fidelity disentangled cellular embeddings for large-scale heterogeneous spatial omics via DECIPHER ]]> https://biorxiv.org/content/10.1101/2024.11.29.626126v1?rss=1 Xia, C.-R. Cao, Z.-J. Gao, G. 2024-12-05 doi:10.1101/2024.11.29.626126 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Structure of the human taurine transporter TauT reveals substrate recognition and mechanisms of inhibition ]]> https://biorxiv.org/content/10.1101/2024.12.04.626611v1?rss=1 lu, Y. Ding, D. Chen, H. Jiang, P. Yin, Y. 2024-12-05 doi:10.1101/2024.12.04.626611 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Discovery of the closest free-living relative of the domesticated "magic mushroom" Psilocybe cubensis in Africa ]]> https://biorxiv.org/content/10.1101/2024.12.03.626483v1?rss=1 Bradshaw, A. J. Sharp, C. Van Der Merwe, B. Tremble, K. S. Dentinger, B. T. M. 2024-12-07 doi:10.1101/2024.12.03.626483 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ ANKRD5: a key component of the axoneme required for spermmotility and male fertility ]]> https://biorxiv.org/content/10.1101/2024.12.03.626701v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@1ca36eforg.highwire.dtl.DTLVardef@dcafe3org.highwire.dtl.DTLVardef@9f6086org.highwire.dtl.DTLVardef@17a0a0b_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance StatementMale infertility affects approximately 8%-12% of men globally, with defects in sperm motility accounting for over 80% of these cases. The axoneme, which functions as the motor apparatus of the sperm, adopts a canonical "9+2" microtubule arrangement, where the nexin-dynein regulatory complex (N-DRC) plays a critical role in providing structural support between adjacent outer microtubule doublets. Elucidating the interplay between the structural organization and protein composition of the N-DRC is essential for advancing the understanding of male reproductive biology. In this study, we identify ANKRD5 as a new component of N-DRC that is essential for maintaining normal sperm motility. These findings contribute to the molecular understanding of sperm motility and highlight ANKRD5 as a potential target for the development of novel male contraceptives. ]]> Yu, S. Yin, G. Jin, P. Zhang, W. Tian, Y. Xu, X. Shao, T. Li, Y. Sun, F. Zhu, Y. Wang, F. 2024-12-07 doi:10.1101/2024.12.03.626701 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ Adrenocortical Cancer Cell uptake of Iron Oxide Nanoparticles ]]> https://biorxiv.org/content/10.1101/2024.12.04.626790v1?rss=1 Challapalli, R. S. Hong, C. Sorushanova, A. Covarrubias-Zambrano, O. Mullen, N. Feely, S. Covarrubias, J. Varghese, S. N. Hantel, C. Owens, P. OHalloran, M. Prakash, P. Bossmann, S. H. Dennedy, M. C. 2024-12-07 doi:10.1101/2024.12.04.626790 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ Longitudinal cellular and humoral immune responses following Covid-19 BNT162b2-mRNA-based booster vaccination of craft and manual workers in Qatar. ]]> https://biorxiv.org/content/10.1101/2024.12.10.627725v1?rss=1 Thomas, R. Zaqout, A. Meqbel, B. Jafar, U. Vaikath, N. Aldushain, A. Naik, A. Shaath, H. Al-Akl, N. S. Adam, A. Ali Moussa, H. Y. Shin, K. C. Taha, R. Z. Abukhattab, M. Almaslamani, M. A. Alajez, N. M. Arredouani, A. Park, Y. Abdulla, S. A. El-Agnaf, O. M. Omrani, A. S. Decock, J. 2024-12-10 doi:10.1101/2024.12.10.627725 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ Effects of transmembrane phenylalanine residues on γ-secretase-mediated Notch-1 proteolysis ]]> https://biorxiv.org/content/10.1101/2024.12.11.628002v1?rss=1 Malvankar, S. Wolfe, M. S. 2024-12-11 doi:10.1101/2024.12.11.628002 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Preferential Release of microRNAs via Extracellular Vesicles is Associated with Ductal Carcinoma In Situ to Invasive Breast Cancer Progression ]]> https://biorxiv.org/content/10.1101/2024.12.09.627283v1?rss=1 Elayapillai, S. P. Dogra, S. Lausen, J. Bruns, M. Behbod, F. Hladik, C. Gin, A. Xu, C. Zhang, R. Ding, W.-Q. Hannafon, B. 2024-12-12 doi:10.1101/2024.12.09.627283 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Multiple-Basin Go-Martini for Investigating Conformational Transitions and Environmental Interactions of Proteins ]]> https://biorxiv.org/content/10.1101/2024.12.11.628061v1?rss=1 Yang, S. Song, C. 2024-12-12 doi:10.1101/2024.12.11.628061 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Dynamic Changes in Gene Expression Through Aging in Drosophila melanogaster Heads ]]> https://biorxiv.org/content/10.1101/2024.12.11.627977v1?rss=1 6,000 significant, age-related genes, nearly all of which have been seen in previous fly aging expression studies, and which include several known to harbor lifespan-altering mutations. We grouped our gene set into 28 clusters via their temporal expression change, observing a diversity of trajectories; some clusters show a linear change over time, while others show more complex, non-linear patterns. Notably, re-analysis of our dataset comparing the earliest and latest timepoints - mimicking a two-timepoint design - revealed fewer differentially-expressed genes (around 4,500). Additionally, those genes exhibiting complex expression trajectories in our multi-timepoint analysis were most impacted in this re-analysis; Their identification, and the inferred change in gene expression with age, was often dependent on the timepoints chosen. Informed by our trajectory-based clusters, we executed a series of gene enrichment analyses, identifying enriched functions/pathways in all clusters, including the commonly seen increase in stress- and immune-related gene expression with age. Finally, we developed a pair of accessible shiny apps to enable exploration of our differential expression and gene enrichment results. ]]> Macdonald, S. J. Hanson, K. M. 2024-12-16 doi:10.1101/2024.12.11.627977 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Functional diversification of the MADS-box gene family in fine-tuning the dimorphic transition of Talaromyces marneffei ]]> https://biorxiv.org/content/10.1101/2024.12.16.628698v1?rss=1 Hu, X. Zhang, Y. Wang, J. Du, M. Yang, Y. Cai, J. J. Yang, E. 2024-12-18 doi:10.1101/2024.12.16.628698 Cold Spring Harbor Laboratory Press 2024-12-18 <![CDATA[ Spatially barcoding biochemical reactions using DNA nanostructures unveil a major contact mechanism in proximity labeling ]]> https://biorxiv.org/content/10.1101/2024.12.17.628942v1?rss=1 Yang, Z. Zhang, Y. Fang, Y. Zhang, Y. Du, J. Shen, X. Zhang, K. Zou, P. Chen, Z. 2024-12-18 doi:10.1101/2024.12.17.628942 Cold Spring Harbor Laboratory Press 2024-12-18 <![CDATA[ GlioME: A Novel Organoid Model Retaining the Glioma Mi-croenvironment for Personalized Drug Screening and Thera-peutic Evaluation ]]> https://biorxiv.org/content/10.1101/2024.12.17.628908v1?rss=1 Zheng, C. Chen, Q. Wang, P. Zhang, D. Fang, Z. Feng, Y. Chen, J. Chen, J. Fu, Y. Yang, B. Zhao, Q. Sun, F. Zhang, Y. Jiang, T. Zheng, L. Bao, Z. 2024-12-20 doi:10.1101/2024.12.17.628908 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ DUSP6 is upregulated in metastasis and influences migration and metabolism in pancreatic cancer cells ]]> https://biorxiv.org/content/10.1101/2024.12.20.629199v1?rss=1 Tannus Ruckert, M. McKinnon Walsh, R. Bye, B. A. Eades, A. E. Yan, W. Bednar, F. Shi, J. Lyssiotis, C. A. VanSaun, M. Silva Silveira, V. 2024-12-22 doi:10.1101/2024.12.20.629199 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ A Palette of Bridged Bicycle-Strengthened Fluorophores ]]> https://biorxiv.org/content/10.1101/2024.12.20.629585v1?rss=1 Zhang, J. Zhang, K. Wang, K. Wang, B. Zhu, S. Qian, H. Ma, Y. Zhang, M. Liu, T. Chen, P. Shen, Y. Fu, Y. Fang, S. Zhang, X. Zou, P. Deng, W. Mu, Y. Chen, Z. 2024-12-22 doi:10.1101/2024.12.20.629585 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Development of a novel peripherally acting alpha2A-adrenergic receptor antagonist for anti-diabetic ]]> https://biorxiv.org/content/10.1101/2024.12.17.628818v1?rss=1 View larger version (49K): org.highwire.dtl.DTLVardef@1d3d7corg.highwire.dtl.DTLVardef@1afbad3org.highwire.dtl.DTLVardef@12a1aborg.highwire.dtl.DTLVardef@1341a02_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hong, F. Wang, J. Chen, D. Wang, Q. Gan, S. Ye, F. Chen, L. Ren, H. Zhang, T. Xie, Y. Jing, X. Wang, R. Xu, Z. Ren, J. Shi, C. Jia, S. Huang, X. Xu, X. Zheng, Y. Lu, J. Lin, W. Dai, J. Wang, L. Chen, L. Tang, C. Liu, H. Xu, T. Xie, X. Liu, X.-a. Du, Y. Nan, F. Chen, Z. 2024-12-23 doi:10.1101/2024.12.17.628818 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ Red-shifted GRAB acetylcholine sensors for multiplex imaging in vivo ]]> https://biorxiv.org/content/10.1101/2024.12.22.627112v1?rss=1 Xie, S. Miao, X. Li, G. Zheng, Y. Li, M. Ji, E. Wang, J. Li, S. Cai, R. Geng, L. Feng, J. Wei, C. Li, Y. 2024-12-23 doi:10.1101/2024.12.22.627112 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ In vivo multiplex imaging of dynamic neurochemical networks with designed far-red dopamine sensors ]]> https://biorxiv.org/content/10.1101/2024.12.22.629999v1?rss=1 Zheng, Y. Cai, R. Wang, K. Zhang, J. Zhuo, Y. Dong, H. Zhang, Y. Wang, Y. Deng, F. Ji, E. Cui, Y. Fang, S. Zhang, X. zhang, k. Wang, J. Li, G. Miao, X. Wang, Z. Yang, Y. Li, S. Grimm, J. Johnsson, K. Schreiter, E. R. Lavis, L. Chen, Z. Mu, Y. Li, Y. 2024-12-23 doi:10.1101/2024.12.22.629999 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ Synergistic activation of the human phosphate exporter XPR1 by KIDINS220 and inositol pyrophosphate ]]> https://biorxiv.org/content/10.1101/2024.12.22.630011v1?rss=1 Zuo, P. Wang, W. Dai, Z. Zheng, J. Yu, S. Wang, G. Yin, Y. Liang, L. Yin, Y. 2024-12-23 doi:10.1101/2024.12.22.630011 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ A self-limiting Sterile Insect Technique alternative for Ceratitis capitata ]]> https://biorxiv.org/content/10.1101/2024.12.23.629662v1?rss=1 Davydova, S. Liu, J. Liu, Y. Prince, K. Mann, J. Kandul, N. P. Braswell, W. E. Champer, J. Akbari, O. S. Meccariello, A. 2024-12-23 doi:10.1101/2024.12.23.629662 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ Atypical Visual Selective Attention in Children with Dyslexia: Evidence from N2pc and PD ]]> https://biorxiv.org/content/10.1101/2024.12.24.630007v1?rss=1 Liu, H. Sun, Y. Wang, Z. Guo, J. Song, Y. Meng, X. 2024-12-24 doi:10.1101/2024.12.24.630007 Cold Spring Harbor Laboratory Press 2024-12-24 <![CDATA[ Genome-wide Mapping Eukaryotic Open Chromatin Regions with Double-Stranded DNA Deaminase ]]> https://biorxiv.org/content/10.1101/2024.12.24.630236v1?rss=1 Dong, W. Zhang, J. Dai, L. Wang, Z. Pang, Y. He, R. Ren, J. Liu, Y. Tian, Y. Xie, X. S. 2024-12-24 doi:10.1101/2024.12.24.630236 Cold Spring Harbor Laboratory Press 2024-12-24 <![CDATA[ Systematic Benchmarking of High-Throughput Subcellular Spatial Transcriptomics Platforms ]]> https://biorxiv.org/content/10.1101/2024.12.23.630033v1?rss=1 Ren, P. Zhang, R. Wang, Y. Zhang, P. Luo, C. Wang, S. Li, X. Zhang, Z. Zhao, Y. He, Y. Zhang, H. Li, Y. Gao, Z. Zhang, X. Zhao, Y. Liu, Z. Meng, Y. Zhang, Z. Zeng, Z. 2024-12-25 doi:10.1101/2024.12.23.630033 Cold Spring Harbor Laboratory Press 2024-12-25 <![CDATA[ Morphological Plasticity and Reproductive Strategies of Kalanchoe Species in Invasive Spread ]]> https://biorxiv.org/content/10.1101/2024.12.25.630291v1?rss=1 Zhang, Z. Sugiura, D. Yamori, W. Tang, Y. 2024-12-25 doi:10.1101/2024.12.25.630291 Cold Spring Harbor Laboratory Press 2024-12-25 <![CDATA[ MethylQUEEN: A Methylation Encoded DNA Foundation Model ]]> https://biorxiv.org/content/10.1101/2024.12.26.630389v1?rss=1 Li, M. Gu, R. Fan, S. Fan, Y. He, B. Yang, J. Chen, Y. Xin, M. Wen, H. Yi, C. 2024-12-26 doi:10.1101/2024.12.26.630389 Cold Spring Harbor Laboratory Press 2024-12-26 <![CDATA[ Fluctuation-Driven Synergy, Redundancy, Signal to Noise Ratio and Error Correction in Protein Allostery ]]> https://biorxiv.org/content/10.1101/2024.12.26.630391v1?rss=1 Erman, B. 2024-12-26 doi:10.1101/2024.12.26.630391 Cold Spring Harbor Laboratory Press 2024-12-26 <![CDATA[ AtKC1 inhibits AtAKT1 activation via its amino-terminal inhibitory domain ]]> https://biorxiv.org/content/10.1101/2024.12.27.630498v1?rss=1 Zheng, Z. Qu, Y. Chen, J. Tang, Y. Liu, D. Huang, Z. Shen, H. 2024-12-27 doi:10.1101/2024.12.27.630498 Cold Spring Harbor Laboratory Press 2024-12-27 <![CDATA[ Keratin 16 spatially inhibits type I interferon responses in stressed skin ]]> https://biorxiv.org/content/10.1101/2024.12.27.630544v1?rss=1 Cohen, E. Xu, Y. Orosco, A. Wang, D. Johnson, C. N. Steen, K. Sarkar, M. K. Ozlu, N. Tsoi, L. C. Gudsonsson, J. E. Parent, C. Coulombe, P. A. 2024-12-28 doi:10.1101/2024.12.27.630544 Cold Spring Harbor Laboratory Press 2024-12-28 <![CDATA[ Dynamic Coupling and Entropy Changes in KRAS G12D Mutation: Insights into Molecular Flexibility, Allostery and Function ]]> https://biorxiv.org/content/10.1101/2024.12.28.630590v1?rss=1 Hacisuleyman, A. Yuret, D. Erman, B. 2024-12-29 doi:10.1101/2024.12.28.630590 Cold Spring Harbor Laboratory Press 2024-12-29 <![CDATA[ RNAGenesis: Foundation Model for Enhanced RNA Sequence Generation and Structural Insights ]]> https://biorxiv.org/content/10.1101/2024.12.30.630826v1?rss=1 Zhang, Z. Chao, L. Jin, R. Zhang, Y. Zhou, G. Yang, Y. Yang, Y. Huang, K. Yang, Q. Xu, Z. Zhang, X. Cong, L. Wang, M. 2024-12-31 doi:10.1101/2024.12.30.630826 Cold Spring Harbor Laboratory Press 2024-12-31 <![CDATA[ ZapA employs a two-pronged mechanism to facilitate Z ring formation in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2024.12.31.629942v1?rss=1 Cui, Y. Gong, H. Yan, D. Li, H. Yang, W. Li, Y. Chen, X. Lutkenhaus, J. Huang, S.-Y. Yang, X. Du, S. 2025-01-01 doi:10.1101/2024.12.31.629942 Cold Spring Harbor Laboratory Press 2025-01-01 <![CDATA[ A kinetic model for USP14 regulated substrate degradation in 26S proteasome ]]> https://biorxiv.org/content/10.1101/2024.12.31.630858v1?rss=1 Wu, D. Ouyang, Q. Wang, H. Mao, Y. 2025-01-01 doi:10.1101/2024.12.31.630858 Cold Spring Harbor Laboratory Press 2025-01-01 <![CDATA[ IFN-γ signaling is required for the efficient replication of murine hepatitis virus (MHV) strain JHM in the brains of infected mice. ]]> https://biorxiv.org/content/10.1101/2025.01.01.631031v1?rss=1 Kerr, C. M. Proctor-Roser, M. A. Parthasarathy, S. OConnor, J. J. Pfannenstiel, J. J. Orozco, R. C. Fehr, A. R. 2025-01-02 doi:10.1101/2025.01.01.631031 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ RNA denaturation underlies circular RNA separation ]]> https://biorxiv.org/content/10.1101/2025.01.04.631262v1?rss=1 View larger version (16K): org.highwire.dtl.DTLVardef@884e54org.highwire.dtl.DTLVardef@ce712corg.highwire.dtl.DTLVardef@16816aforg.highwire.dtl.DTLVardef@a94e58_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jiang, Y. Kjems, J. 2025-01-04 doi:10.1101/2025.01.04.631262 Cold Spring Harbor Laboratory Press 2025-01-04 <![CDATA[ Allosteric Residue Dynamics in Insulin: Temperature Induces Shift from Dihexamer to Hexamer Collective Motion ]]> https://biorxiv.org/content/10.1101/2025.01.04.631292v1?rss=1 Ayan, E. Demirci, H. 2025-01-04 doi:10.1101/2025.01.04.631292 Cold Spring Harbor Laboratory Press 2025-01-04 <![CDATA[ An arginine switch drives the stepwise activation of β-arrestin ]]> https://biorxiv.org/content/10.1101/2025.01.05.631353v1?rss=1 Ji, J. S. Yun, Y. Stepniewski, T. Yoon, H.-J. Min, K. Park, J. Y. Chung, C. Chung, K. Y. Selent, J. Lee, H. H. 2025-01-05 doi:10.1101/2025.01.05.631353 Cold Spring Harbor Laboratory Press 2025-01-05 <![CDATA[ Endocannabinoids facilitate transitory reward engagement through retrograde gain control ]]> https://biorxiv.org/content/10.1101/2025.01.06.630792v1?rss=1 Marcus, D. J. English, A. E. Chun, G. Seth, E. F. Oomen, R. Hwang, S. Wells, B. A. Piantadosi, S. C. Suko, A. Li, Y. Zweifel, L. Land, B. B. Stella, N. Bruchas, M. 2025-01-07 doi:10.1101/2025.01.06.630792 Cold Spring Harbor Laboratory Press 2025-01-07 <![CDATA[ Loss of Elp3 impairs the maturation tempo of brain ependymal cells ]]> https://biorxiv.org/content/10.1101/2025.01.07.631730v1?rss=1 Tielens, S. Boutin, C. Huysseune, S. Thelen, N. Charlet-Briart, M. Reyskens, C. Oskera, L. Boutsen, A. Mateo-Sanchez, S. Delacroix, L. Labedan, P. Thiry, M. Malgrange, B. Chariot, A. Tissir, F. Creppe, C. Seuntjens, E. Laguesse, S. Nguyen, L. 2025-01-07 doi:10.1101/2025.01.07.631730 Cold Spring Harbor Laboratory Press 2025-01-07 <![CDATA[ AR-V7 condensates drive androgen-independent transcription in castration resistant prostate cancer ]]> https://biorxiv.org/content/10.1101/2025.01.08.631986v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@16b50d1org.highwire.dtl.DTLVardef@86e3b6org.highwire.dtl.DTLVardef@1cfe7f3org.highwire.dtl.DTLVardef@8532a2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Massah, S. Pinette, N. Foo, J. Datta, S. Guo, M. Bell, R. Haegert, A. Terrado, M. Volik, S. Le Bihan, S. Tekoglu, E. Bui, J. M. Lack, N. A. Gleave, M. E. Lallous, N. Rhie, S. K. Collins, C. C. Gsponer, J. 2025-01-13 doi:10.1101/2025.01.08.631986 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ CD20+ natural killer cells are polyfunctional, memory-like cells that are enriched in inflammatory disorders ]]> https://biorxiv.org/content/10.1101/2025.01.09.632131v1?rss=1 Albayrak, O. Tiryaki, E. Akkaya, N. Kizilirmak, A. B. Doran, T. Gokmenoglu, G. Yuksel, M. Ulukan, B. Uzulmez, M. Baytekin, I. Soylu, K. Esendagli, G. Meinl, I. Koseoglu, M. Yuksel, B. Erus, S. Arikan, C. Vural, S. Zeybel, M. Soysal, A. Meinl, E. Vural, A. 2025-01-13 doi:10.1101/2025.01.09.632131 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Molecular detection of a cryptic salamander: Development of an eDNA assay for the detection of the mud salamander (Pseudotriton montanus). ]]> https://biorxiv.org/content/10.1101/2025.01.12.632641v1?rss=1 Brammell, B. F. Brewer, S. A. Hoogerheide, E. A. Johnson, M. R. 2025-01-15 doi:10.1101/2025.01.12.632641 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Painting Peptides with Antimicrobial Potency through Deep Reinforcement Learning ]]> https://biorxiv.org/content/10.1101/2025.01.13.632671v1?rss=1 Dong, R. Cao, Q. Song, C. 2025-01-15 doi:10.1101/2025.01.13.632671 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ APE1 active site residue Asn174 stabilizes the AP-site and is essential for catalysis ]]> https://biorxiv.org/content/10.1101/2025.01.14.633034v1?rss=1 DeHart, K. M. Hoitsma, N. M. Thompson, S. H. Borin, V. A. Agarwal, P. K. Freudenthal, B. D. 2025-01-15 doi:10.1101/2025.01.14.633034 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Quorum sensing regulation by the nitrogen phosphotransferase system in Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2025.02.01.636002v1?rss=1 Banerjee, S. Smalley, N. E. Saenjamsai, P. Fehr, A. Dandekar, A. A. Cabeen, M. T. Chandler, J. R. 2025-02-02 doi:10.1101/2025.02.01.636002 Cold Spring Harbor Laboratory Press 2025-02-02 <![CDATA[ High-Throughput Antibody Neutralization Screening in Massively Parallel Droplet Arrays ]]> https://biorxiv.org/content/10.1101/2025.01.31.635965v1?rss=1 Gutierrez-Gonzalez, M. Fahad, A. S. Delley, C. L. Chung, C.-Y. Jin, S. Boyle, N. Oliveira de Souza, M. Pirhanov, A. Galvez, N. M. S. Franca, C. T. Marglous, S. Bhagat, E. Vincent, D. Neumeier, D. Cao, Y. Doria-Rose, N. Reddy, S. T. Schmidt, A. G. Balazs, A. B. Abate, A. R. DeKosky, B. J. 2025-02-04 doi:10.1101/2025.01.31.635965 Cold Spring Harbor Laboratory Press 2025-02-04 <![CDATA[ Antagonistic kinesin-14s within a single chromosomal drive haplotype ]]> https://biorxiv.org/content/10.1101/2025.02.05.636711v1?rss=1 Brady, M. J. Gupta, A. Gent, J. I. Swentowsky, K. W. Unckless, R. L. Dawe, R. K. 2025-02-07 doi:10.1101/2025.02.05.636711 Cold Spring Harbor Laboratory Press 2025-02-07 <![CDATA[ Disruption of Mitochondrial Dynamics and Stasis Leads to Liver Injury and Tumorigenesis ]]> https://biorxiv.org/content/10.1101/2025.02.11.637688v1?rss=1 Ma, X. Wei, X. Niu, m. Zhang, C. Peng, Z. Liu, W. Yan, J. Su, X. Lu, S. Cui, W. Sesaki, H. Zong, W.-X. Ni, H.-M. Ding, W.-X. 2025-02-12 doi:10.1101/2025.02.11.637688 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ A functional map of phosphoprotein phosphatase regulation identifies an evolutionary conserved reductase for the catalytic metal ions ]]> https://biorxiv.org/content/10.1101/2025.02.12.637884v1?rss=1 Meeusen, B. Ambjoern, S. Veis, J. Riley, R. Vit, G. Brauer, B. Moeller, M. Greiner, E. C. Chan, C. Weisser, M. Garvanska, D. Zhu, H. Davey, N. E. Kettenbach, A. Ogris, E. Nilsson, J. 2025-02-16 doi:10.1101/2025.02.12.637884 Cold Spring Harbor Laboratory Press 2025-02-16 <![CDATA[ The sperm specific Na+,K+-ATPase α4 shows a highly structured and dynamic distribution at the sperm flagellum ]]> https://biorxiv.org/content/10.1101/2025.02.14.638303v1?rss=1 Oishee, M. J. McDermott, J. P. Sanchez, G. Blanco, G. 2025-02-16 doi:10.1101/2025.02.14.638303 Cold Spring Harbor Laboratory Press 2025-02-16 <![CDATA[ Efficient Inference of Macrophylogenies: Insights from the Avian Tree of Life ]]> https://biorxiv.org/content/10.1101/2025.02.17.638170v1?rss=1 1,000 taxa) for entire classes across the Tree of Life. However, the inference of large trees remains constrained by logistical, computational, and methodological challenges. The Avian Tree of Life provides an ideal model for evaluating strategies to robustly infer macrophylogenies from intersecting datasets derived from smaller studies. In this study, we leveraged a comprehensive resource of sequence capture datasets to evaluate the phylogenetic accuracy and computational costs of four methodological approaches: (1) supermatrix approaches using concatenation, including the "fast" maximum likelihood (ML) methods, (2) filtering datasets to reduce heterogeneity, (3) supertree estimation based on published phylogenomic trees, and (4) a "divide-and-conquer" strategy, wherein smaller ML trees were estimated and subsequently combined using a supertree approach. Additionally, we examined the impact of these methods on divergence time estimation using a dataset that includes newly vetted fossil calibrations for the Avian Tree of Life. Our findings highlight that recently developed fast tree search approaches offer a reasonable compromise between computational efficiency and phylogenetic accuracy, facilitating inference of macrophylogenies. ]]> Zhao, M. Thom, G. Faircloth, B. C. Andersen, M. J. Barker, F. K. Benz, B. W. Braun, M. J. Bravo, G. A. Brumfield, R. T. Chesser, R. T. Derryberry, E. P. Glenn, T. C. Harvey, M. G. Hosner, P. A. Imfeld, T. S. Joseph, L. Manthey, J. D. McCormack, J. E. McCullough, J. M. Moyle, R. G. Oliveros, C. H. Carreiro, N. D. W. Winker, K. Field, D. J. Ksepka, D. T. Braun, E. L. Kimball, R. T. Smith, B. T. 2025-02-19 doi:10.1101/2025.02.17.638170 Cold Spring Harbor Laboratory Press 2025-02-19 <![CDATA[ Multi-scale machine learning model predicts muscle and functional disease progression in FSHD ]]> https://biorxiv.org/content/10.1101/2025.02.19.639046v1?rss=1 Blemker, S. S. Riem, L. DuCharme, O. Pinette, M. Costanzo, K. E. Weatherley, E. Statland, J. Tapscott, S. J. Wang, L. H. Shaw, D. W. W. The Move+ Investigator Team, Song, X. Leung, D. Friedman, S. 2025-02-20 doi:10.1101/2025.02.19.639046 Cold Spring Harbor Laboratory Press 2025-02-20 <![CDATA[ Neural representation of action symbols in primate frontal cortex ]]> https://biorxiv.org/content/10.1101/2025.03.03.641276v1?rss=1 Tian, L. Y. Garzon, K. U. Rouse, A. G. Eldridge, M. A. Schieber, M. H. Wang, X.-J. Tenenbaum, J. B. Freiwald, W. A. 2025-03-04 doi:10.1101/2025.03.03.641276 Cold Spring Harbor Laboratory Press 2025-03-04 <![CDATA[ Neural Synchrony Links Sensorimotor Cortices in a Network for Facial Motor Control ]]> https://biorxiv.org/content/10.1101/2025.03.04.641458v1?rss=1 Vazquez, Y. Ianni, G. R. Rassi, E. Rouse, A. G. Schieber, M. Yazdani, F. Prut, Y. Freiwald, W. 2025-03-10 doi:10.1101/2025.03.04.641458 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Environmental NaCl affects C. elegans development and aging ]]> https://biorxiv.org/content/10.1101/2025.03.09.641258v1?rss=1 Pohl, F. Egan, B. M. Schneider, D. L. Mosley, M. C. Garcia, M. A. Hou, S. Chiu, C.-H. Kornfeld, K. 2025-03-11 doi:10.1101/2025.03.09.641258 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Comparative Transcriptomic Analysis of Embryonic Stem Cells (ESCs) across Mammalian Species ]]> https://biorxiv.org/content/10.1101/2025.03.11.642582v1?rss=1 Fang, Y. Su, Y. Meisel, R. Walters, J. R. Gamble, T. Randolph, E. C. Yu, X. Shi, M. Li, G. Zhang, J. Tian, X. Tang, Y. Duan, E. 2025-03-12 doi:10.1101/2025.03.11.642582 Cold Spring Harbor Laboratory Press 2025-03-12 <![CDATA[ Intraspecific plant-soil feedbacks alter root traits in a perennial grass ]]> https://biorxiv.org/content/10.1101/2025.03.11.642669v1?rss=1 Kural-Rendon, C. Ford, N. E. Hooser, K. Wagner, M. R. 2025-03-14 doi:10.1101/2025.03.11.642669 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ The critical role of the ZBP1-NINJ1 axis and IRF1/IRF9 in ethanol-induced cell death, PANoptosis, and alcohol-associated liver disease ]]> https://biorxiv.org/content/10.1101/2025.03.12.642836v1?rss=1 Qin, Q. Chen, W. King, C. D. Kumar, S. P. Vogel, P. Tweedell, R. E. Kanneganti, T.-D. 2025-03-14 doi:10.1101/2025.03.12.642836 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ STI1 domain dynamically engages transient helices in disordered regions to drive self-association and phase separation of yeast ubiquilin Dsk2 ]]> https://biorxiv.org/content/10.1101/2025.03.14.643327v1?rss=1 Acharya, N. Daniel, E. Dao, T. P. Mulvey, E. Kraut, D. A. Roelofs, J. Castaneda, C. A. 2025-03-14 doi:10.1101/2025.03.14.643327 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Type I Interferon production in myeloid cells is regulated by factors independent of Ptpn22 ]]> https://biorxiv.org/content/10.1101/2025.03.20.644450v1?rss=1 T, is expressed in 5-15% of the North American population and is strongly associated with the development of autoimmune disease while simultaneously capable of providing protection during virus infection and cancer. In murine models, significant progress has been made in elucidating the molecular mechanisms that PEP and its pro-autoimmune variant (PEP-R619W) modulate T cell function, yet their influence on non-T cell pathways, such as antigen presenting cell cytokine production, remains less defined. Previously, it was reported that PEP promotes type I interferon (IFN-I) production in dendritic cells (DCs) and macrophages following TLR4 stimulus. Here, we show that contrary to previous results, both PEP-WT and the PEP-R619W variant do not promote IFN-I production in DCs and macrophages following exposure to LPS, 3p-hpRNA, or coronavirus MHV A59. We attribute the prior findings to mouse strain-specific differences and conclude that factors independent of PEP may be regulating IFN-I production in these studies. We further show that PEP and its R619W variant distinctly modulate the production of TNF, IL-12 and IL-2 in DCs following LPS stimulus. Taken together, our results challenge the current understanding of the role of PEP during inflammation while providing new insight into how the PEP-R619W variant may alter myeloid cell function during disease. ]]> Barnes, J. R. Shaikh, A. F. Bevis, A. M. Cockerham, T. R. Orozco, R. C. 2025-03-25 doi:10.1101/2025.03.20.644450 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Adaptive Increase of Amylase Gene Copy Number in Peruvians Driven by Potato-rich Diets ]]> https://biorxiv.org/content/10.1101/2025.03.25.644684v1?rss=1 Scheer, K. Landau, L. J. B. Jorgensen, K. Karageorgiou, C. Siao, L. Alkan, C. Morales-Rivera, A. M. Osbourne, C. Garcia, O. Pearson, L. Kiyamu, M. Leon-Velarde, F. Rivera-Chira, M. Lee, F. Brutsaert, T. Bigham, A. Gokcumen, O. 2025-03-29 doi:10.1101/2025.03.25.644684 Cold Spring Harbor Laboratory Press 2025-03-29 <![CDATA[ Distinct yet Overlapping Functions of VMP1 and TMEM41B in Modulating Hepatic Lipoprotein Secretion and Autophagy in MASH ]]> https://biorxiv.org/content/10.1101/2025.04.07.647617v1?rss=1 Chen, A. Nguyen, K. Jiang, X. Yu, X. Xie, Y. Liu, W. Davidson, N. Ding, W.-X. Ni, H.-M. 2025-04-08 doi:10.1101/2025.04.07.647617 Cold Spring Harbor Laboratory Press 2025-04-08 <![CDATA[ Mutations differentially affecting the coronavirus Mac1 ADP-ribose binding and hydrolysis activities indicate that it promotes multiple stages of the viral replication cycle ]]> https://biorxiv.org/content/10.1101/2025.04.08.647734v1?rss=1 O Connor, J. Roy, A. Khattabi, R. Kerr, C. M. Schwarting, N. Alhammad, Y. M. Gao, P. Zhang, X. Deng, X. Fehr, A. R. 2025-04-09 doi:10.1101/2025.04.08.647734 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ Effect of Photoinitiation Process on Photo-Crosslinking of Gelatin Methacryloyl Hydrogel Networks ]]> https://biorxiv.org/content/10.1101/2025.04.10.648118v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@1286f72org.highwire.dtl.DTLVardef@1aca5f6org.highwire.dtl.DTLVardef@1c3bc63org.highwire.dtl.DTLVardef@1850c97_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Duymaz, D. Karaoglu, I. C. KIZILEL, S. 2025-04-16 doi:10.1101/2025.04.10.648118 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ A community-consensus reconstruction of Chinese Hamster metabolism enables structural systems biology analyses to decipher metabolic rewiring in lactate-free CHO cells ]]> https://biorxiv.org/content/10.1101/2025.04.10.647063v1?rss=1 70% of its 7377 metabolites, enabling deeper exploration of the link between molecular structure and cellular metabolism. We used iCHO3K to contextualize transcriptomics and metabolomics data from a CHO cell line in which lactate secretion is abolished. We found the reduced glycolytic flux and enhanced TCA cycle flux were accompanied by an elevated NADH and PEP levels in these cells, consistent with experimental measurements. Leveraging iCHO3Ks structural annotations, we identified candidate binding interactions of NADH and PEP with glycolytic enzymes showing model-predicted differential flux, suggesting novel allosteric regulation associated with the observed decrease in glucose uptake and glycolysis. Overall, iCHO3K offers a valuable framework for systematic integration of omics data, improved flux predictions, and structure-guided insights, thus advancing CHO cell engineering and enhancing biomanufacturing efficiency. ]]> Di Giusto, P. Choi, D.-H. Antonakoudis, A. Duraikannan, V. G. Craveur, P. Cowie, N. L. Ganapathy, T. Ramesh, K. Benavidez-Lopez, S. Orellana, C. A. Jimenez, N. E. Dworkin, L. A. Morrissey, J. Marin de Mas, I. Strain, B. Valdez-Cruz, N. A. Trujillo-Roldan, M. A. Marzluf, J. Martinez, V. S. Zehetner, L. Altamirano, C. Vega-Letter, A. M. Priem, B. Cao, H. C. Hold, M. Ma, J. Hong, Y. Gopalakrishnan, S. Enuh, B. M. Tarzi, C. Pang, K. T. Angione, C. Zanghellini, J. Kontoravdi, C. Hefzi, H. Betenbaugh, M. J. Nielsen, L. K. Lakshmanan, M. Lee, D.-Y. Richelle, A. 2025-04-17 doi:10.1101/2025.04.10.647063 Cold Spring Harbor Laboratory Press 2025-04-17 <![CDATA[ NSUN2 drives intestinal stem cell expansion and colorectal tumour initiation via MAPK/ERK signalling ]]> https://biorxiv.org/content/10.1101/2025.04.11.648351v1?rss=1 Bastem Akan, A. Billard, C. V. Chen, S.-Y. Huang, P.-H. Cammareri, P. Hall, A. E. Preyzner, P. Din, F. V. N. Myant, K. B. 2025-04-17 doi:10.1101/2025.04.11.648351 Cold Spring Harbor Laboratory Press 2025-04-17 <![CDATA[ Discovery of D2469079A, A novel selective Toll-Like Receptor 7/8 Antagonist with Brain Penetrance ]]> https://biorxiv.org/content/10.1101/2025.04.12.648517v1?rss=1 Deng, X. Zhang, X. Tian, W. Xiao, D. Du, Z. Wang, Y. Cao, S. Li, B. Zhao, Y. Chen, H. Su, Y. Zhou, Y. 2025-04-18 doi:10.1101/2025.04.12.648517 Cold Spring Harbor Laboratory Press 2025-04-18 <![CDATA[ Neural Gain Modulation Propagates from Posterior to Anterior Brain Regions to Optimize Orientation Perception in Chronic Astigmatism ]]> https://biorxiv.org/content/10.1101/2025.04.13.648557v1?rss=1 Son, S. Kang, H. Kim, H. R. Shim, W. M. Lee, J. 2025-04-19 doi:10.1101/2025.04.13.648557 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ OmniEM: Unifying the EM Multiverse through a Large-scale Foundation Model ]]> https://biorxiv.org/content/10.1101/2025.04.13.648639v1?rss=1 He, L. Shi, R. Wang, W. Ma, L. 2025-04-19 doi:10.1101/2025.04.13.648639 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ Electrochemical Metabolic Profiling Reveals Mitochondrial Hyperactivation and Enhanced Neural Progenitor Proliferation in MLC1-Mutant Human Cortical Organoids ]]> https://biorxiv.org/content/10.1101/2025.04.16.647364v1?rss=1 Koo, K.-M. Choi, J.-S. Nam, Y.-K. Kim, H.-J. Kim, C.-D. Jeong, S.-H. Jang, H.-J. Lim, K. Lim, B.-C. Kim, T.-H. Cho, K.-O. 2025-04-20 doi:10.1101/2025.04.16.647364 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ Stronger population suppression by gene drive targeting doublesex from dominant female-sterile resistance alleles ]]> https://biorxiv.org/content/10.1101/2025.04.16.649134v1?rss=1 Chen, W. Wang, Z. Champer, J. 2025-04-20 doi:10.1101/2025.04.16.649134 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ Aging alters mRNA processing in the mouse ovary ]]> https://biorxiv.org/content/10.1101/2025.04.16.649248v1?rss=1 Vo, K. Pei, G. J. Thiyagarajan, R. Fields, P. E. Rumi, M. A. K. 2025-04-20 doi:10.1101/2025.04.16.649248 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ Controlled Release of Bone Morphogenetic Protein-2 Improves Motor Function After Traumatic Brain Injury in a Rat Model ]]> https://biorxiv.org/content/10.1101/2025.04.16.649206v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@136d4d4org.highwire.dtl.DTLVardef@cee564org.highwire.dtl.DTLVardef@13612e8org.highwire.dtl.DTLVardef@1134b4c_HPS_FORMAT_FIGEXP M_FIG C_FIG Statement of SignificanceSevere traumatic brain injury (TBI) is a life-threatening condition characterized by internal brain swelling and is commonly treated using a two-stage surgical approach. Complications associated with the two-stage treatment paradigm include secondary neurologic impairment, termed syndrome of the trephined (SOT). SOT is often reversible once the second surgery is performed, whereas a single-stage TBI treatment paradigm may avoid the occurrence of SOT altogether. Utilizing hydrogels comprised of pentenoate-modified hyaluronic acid and thiolated devitalized tendon encapsulating microspheres containing bone morphogenetic protein-2 (BMP-2), the current study demonstrated improvements in motor skill function and reductions in brain atrophy in a rat TBI model. The introduction of hydrogels with controlled release of BMP-2 as a neuroprotective strategy for TBI application offers a promising approach for single-stage TBI treatment. ]]> Townsend, J. M. Deng, J. Z. Barbay, S. Andrews, B. T. Nudo, R. J. Detamore, M. S. 2025-04-22 doi:10.1101/2025.04.16.649206 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ Auto-downregulation of the florigen FT production prevents precocious flowering in plants ]]> https://biorxiv.org/content/10.1101/2025.04.24.650415v1?rss=1 Tian, S. Luo, X. Cui, B. He, Y. 2025-04-24 doi:10.1101/2025.04.24.650415 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Effect of Transcranial Light Stimulation on the Neurovascular Unit in the Human Brain ]]> https://biorxiv.org/content/10.1101/2025.04.23.649937v1?rss=1 Zhao, C. Li, Z. Ding, Z. Zhang, K. Li, Y. Zhang, L. Zou, Q. Gao, Z. Cui, Z. Li, X. 2025-04-29 doi:10.1101/2025.04.23.649937 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ A New Serological Autoantibody Signature Associated with Multiple Sclerosis ]]> https://biorxiv.org/content/10.1101/2025.04.23.650160v1?rss=1 Abdesselem, H. B. Van Benthem, A. D. Bensmail, I. Elbashir, I. E. Tan, T.-M. Abylova, B. Koon, L. Anuar, D. Blackburn, J. M. Malik, R. A. Petropoulos, I. N. 2025-04-29 doi:10.1101/2025.04.23.650160 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ VGLL1 contributes to both the transcriptome and epigenome of the developing trophoblast compartment ]]> https://biorxiv.org/content/10.1101/2025.04.25.650693v1?rss=1 Calderon, R. I. Sah, N. Huang, M. Kittle, R. H. Shaik, W. Chousal, J. N. Kallol, S. Bui, T. Morey, R. Mitre, A. Fogarty, N. M. E. Gerri, C. Zheng, C. DeHoff, P. M. Home, P. Niakan, K. Cook-Andersen, H. Fisch, K. M. Paul, S. Soncin, F. 2025-04-29 doi:10.1101/2025.04.25.650693 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Identification of the Best Filter-based Feature Selection Techniques for Microarray Datasets ]]> https://biorxiv.org/content/10.1101/2025.04.25.650719v1?rss=1 Islam, A. Bhadra, T. Mali, K. Giri, J. Aurangzeb, K. Budhathoki, R. K. Mallik, S. 2025-04-29 doi:10.1101/2025.04.25.650719 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ The structure of phycobilisome with a bicylindrical core from the cyanobacterium Synechococcus elongatus PCC 7942 ]]> https://biorxiv.org/content/10.1101/2025.04.28.650843v1?rss=1 Zhao, J. Gao, N. Zheng, Z. 2025-05-01 doi:10.1101/2025.04.28.650843 Cold Spring Harbor Laboratory Press 2025-05-01 <![CDATA[ Perceptual prediction error supports implicit process in motor learning. ]]> https://biorxiv.org/content/10.1101/2025.04.29.651214v1?rss=1 Zhang, X. Wei, K. 2025-05-01 doi:10.1101/2025.04.29.651214 Cold Spring Harbor Laboratory Press 2025-05-01 <![CDATA[ Antigenic and Virological Characteristics of SARS-CoV-2 Variant BA.3.2, XFG, and NB.1.8.1 ]]> https://biorxiv.org/content/10.1101/2025.04.30.651462v1?rss=1 Guo, C. Yu, Y. Liu, J. Jian, F. Yang, S. Song, W. Shao, F. Yu, L. Cao, Y. 2025-05-01 doi:10.1101/2025.04.30.651462 Cold Spring Harbor Laboratory Press 2025-05-01 <![CDATA[ Tracing Siderophore Precursors to Primary Metabolism for Ecological Applications ]]> https://biorxiv.org/content/10.1101/2025.04.30.651379v1?rss=1 He, R. Xu, J. Shao, J. Wu, Y. Wei, Z. Gu, S. Li, Z. 2025-05-03 doi:10.1101/2025.04.30.651379 Cold Spring Harbor Laboratory Press 2025-05-03 <![CDATA[ SAKPE: A Site Attention Kinetic Parameters Prediction Method for Enzyme Engineering ]]> https://biorxiv.org/content/10.1101/2025.04.30.651216v1?rss=1 Qiu, J.-H. Lin, Z. Chen, K.-W. Sun, T.-Y. Zhang, X. Yuan, L. Tian, Y. Wu, Y.-D. 2025-05-06 doi:10.1101/2025.04.30.651216 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ ZapC crosslinks FtsZ filaments through a dual-binding mechanism modulated by the intrinsically disordered linker of FtsZ ]]> https://biorxiv.org/content/10.1101/2025.05.07.652675v1?rss=1 Du, S. Li, Y. Gong, H. Zhang, R. Cui, Y. Chen, X. Lutkenhaus, J. 2025-05-07 doi:10.1101/2025.05.07.652675 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Specific Pathogen Free Ten Gene-Edited Pig Donor for Xenotransplantation ]]> https://biorxiv.org/content/10.1101/2025.05.06.652168v1?rss=1 Xu, K. Zhao, H. Jia, B. Wang, J. Siddig, N. A. M. A. Jamal, M. A. Mao, A. Liu, K. Cheng, W. Yang, C. Wei, T. Zhu, F. Huo, X. Jiao, D. Guo, J. Zhao, H. Cheng, W. Zhang, Y. Zhang, X. Jiang, L. Zhang, Z. Zhang, W. Liang, T. Zhao, H.-Y. Sun, B.-C. Wei, H.-J. 2025-05-10 doi:10.1101/2025.05.06.652168 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ Transfer learning framework via Bayesian group factor analysis incorporating feature-wise dependencies ]]> https://biorxiv.org/content/10.1101/2025.05.07.648613v1?rss=1 Thirumalaisamy, D. Black, N. Gonen, M. Nikolova, O. 2025-05-10 doi:10.1101/2025.05.07.648613 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ Functional Genomic Screens Reveal RBBP4 as a Key Regulator of Cell Cycle Progression in TMZ-Resistant Glioblastoma ]]> https://biorxiv.org/content/10.1101/2025.05.09.653010v1?rss=1 Kala, E. Y. Senbabaoglu Aksu, F. Ercan, E. Ozbiyik, A. Cingoz, A. Yedier-Bayram, O. Aksu, A. C. Cavga, A. D. Yilmaz, E. Kok, I. Dur Karasayar, A. H. Kulac, I. Syed, H. Philpott, M. Cribbs, A. P. Bagci-Onder, T. 2025-05-10 doi:10.1101/2025.05.09.653010 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ Triple-N Dataset: Non-human Primate Neural Responses to Natural Scenes ]]> https://biorxiv.org/content/10.1101/2025.05.06.652408v1?rss=1 Li, Y. Liu, X. Li, W. Yang, J. Gong, B. Jin, W. Gong, Z. Wang, K. Luo, J. Zhao, Z. Bao, P. 2025-05-11 doi:10.1101/2025.05.06.652408 Cold Spring Harbor Laboratory Press 2025-05-11 <![CDATA[ RNA Helicase A promotes small RNA biogenesis and sorting in germ cells ]]> https://biorxiv.org/content/10.1101/2025.05.11.653140v1?rss=1 Gaylord, O. Brown, J. S. Wu, W.-S. Lee, H.-C. 2025-05-11 doi:10.1101/2025.05.11.653140 Cold Spring Harbor Laboratory Press 2025-05-11 <![CDATA[ Oxidative Base Damage to Telomeres Sensitizes Cancer Cells to ATR Inhibition ]]> https://biorxiv.org/content/10.1101/2025.05.10.653274v1?rss=1 Garbouchian, A. Cestari Moreno, N. Dey, A. Opresko, P. Barnes, R. P. 2025-05-13 doi:10.1101/2025.05.10.653274 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Harmonizing single cell 3D genome data with STARK and scNucleome ]]> https://biorxiv.org/content/10.1101/2025.05.10.653247v1?rss=1 Wen-Jie, J. Kangwen, C. Yuanchen, S. An, L. Hanwen, Z. Ruixiang, G. Chunge, Z. Nana, W. Futing, L. Ten, F. Yu-Juan, W. Xiaoqi, Z. Ming, X. Hua-Jun, W. 2025-05-15 doi:10.1101/2025.05.10.653247 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Coronary Artery Disease Risk Variant rs6903956 Links to Endothelial Dysfunction via PHACTR1 Regulation ]]> https://biorxiv.org/content/10.1101/2025.05.11.653298v1?rss=1 Tay, K. Y. Wee, H. S. Nguyen, N. Autio, M. I. Wazny, V. K. Lee, K. L. Tay, D. Wang, Y. Gao, X. Heng, C. K. Chan, M. Y. Foo, R. S. Lee, J. Loh, M. Cheung, C. 2025-05-15 doi:10.1101/2025.05.11.653298 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Isoform-Specific Roles of NTRK2 in Pulmonary Vascular Regeneration ]]> https://biorxiv.org/content/10.1101/2025.05.11.653351v1?rss=1 Tan, C. Liu, Z. Mao, X. Zhang, Y. Li, X. Pek, N. Fu, H. Liu, Y. Kalinichenko, V. V. Pryhuber, G. S. Lu, R. Lai, L. Miao, Y. Guo, M. Gu, M. 2025-05-15 doi:10.1101/2025.05.11.653351 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Extending the Gaussian Network Model: Integrating Local, Allosteric, and Structural Factors for Improved Residue-Residue Correlation Analysis ]]> https://biorxiv.org/content/10.1101/2025.05.12.653468v1?rss=1 Erman, B. 2025-05-15 doi:10.1101/2025.05.12.653468 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Humans underestimate their body mass in microgravity: evidence from reaching movements during spaceflight ]]> https://biorxiv.org/content/10.1101/2025.05.12.653611v1?rss=1 Zhang, Z. Tian, Y. Wang, C. Jiang, C. Wang, B. Yu, H. Zhao, R. Wei, K. 2025-05-15 doi:10.1101/2025.05.12.653611 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Monte Carlo track-structure simulation of the impact of Ultra-Hight Dose Rate and oxygen concentration on the Fenton reaction. ]]> https://biorxiv.org/content/10.1101/2025.05.13.652705v1?rss=1 Chaoui, M. Tayalati, Y. Bouhali, O. ramos mendez, j. 2025-05-16 doi:10.1101/2025.05.13.652705 Cold Spring Harbor Laboratory Press 2025-05-16 <![CDATA[ Hi-Compass resolves cell-type chromatin interactions by single-cell and spatial ATAC-seq data across biological scales ]]> https://biorxiv.org/content/10.1101/2025.05.14.654019v1?rss=1 Sun, Y.-C. Jiang, W.-J. Cai, K.-W. Wu, H.-J. 2025-05-17 doi:10.1101/2025.05.14.654019 Cold Spring Harbor Laboratory Press 2025-05-17 <![CDATA[ Phosphatase activity is dispensable for PRL-3-mediated oncogenesis and tumor progression ]]> https://biorxiv.org/content/10.1101/2025.05.14.654016v1?rss=1 View larger version (57K): org.highwire.dtl.DTLVardef@41de8dorg.highwire.dtl.DTLVardef@7a3bbdorg.highwire.dtl.DTLVardef@e800d2org.highwire.dtl.DTLVardef@18df51a_HPS_FORMAT_FIGEXP M_FIG C_FIG Statement of significanceThis study demonstrates that PRL-3 drives cancer initiation and progression through a phosphatase-independent mechanism across diverse models, highlighting the need to therapeutically target its non-catalytic protein interactions in future cancer treatment strategies. ]]> Jolly, J. T. Al-Hamaly, M. A. Smith, C. N. Spielmann, H. P. Blackburn, J. S. 2025-05-18 doi:10.1101/2025.05.14.654016 Cold Spring Harbor Laboratory Press 2025-05-18 <![CDATA[ Minimally invasive and in situ capacitive sensing of cardiac biomarker from interstitial fluid ]]> https://biorxiv.org/content/10.1101/2025.05.14.654153v1?rss=1 Mirzajani, H. Zolfaghari, P. Koca, B. Y. Urey, H. 2025-05-18 doi:10.1101/2025.05.14.654153 Cold Spring Harbor Laboratory Press 2025-05-18 <![CDATA[ RBP47 family members are negative regulators of heat stress tolerance in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2025.05.18.654719v1?rss=1 Hernandez-Sanchez, I. E. Tarbiyyah, I. Kearly, A. Martinez-Seidel, F. Maruri-Lopez, I. Chen, Y. S. Rissland, O. Wang, W. Sioud, S. Schwarzenberg, A. Nelson Dittrich, A. C. Nelson, A. Chodasiewicz, M. 2025-05-19 doi:10.1101/2025.05.18.654719 Cold Spring Harbor Laboratory Press 2025-05-19 <![CDATA[ Progressive neuroinflammation and deficits in motor function in a mouse model with an Epg5 pathogenic variant of Vici syndrome ]]> https://biorxiv.org/content/10.1101/2025.05.16.654529v1?rss=1 Thornton, B. T. Hardinger, A. G. Pence, L. Prem Kumar, P. Connolly, N. Weir, S. J. Vivian, J. L. 2025-05-21 doi:10.1101/2025.05.16.654529 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Mechanism-driven screening of membrane-targeting and pore-forming antimicrobial peptides ]]> https://biorxiv.org/content/10.1101/2025.05.17.654650v1?rss=1 Li, J. Yang, C. Dong, R. Bada Juarez, J. F. Wang, L. Wettstein, M. E. Wang, D. Cao, C. Lu, Y. Song, C. 2025-05-21 doi:10.1101/2025.05.17.654650 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Tomosyn-2 Regulates Postnatal β-Cell Expansion and Insulin Secretion to Maintain Glucose Homeostasis. ]]> https://biorxiv.org/content/10.1101/2025.05.19.654959v1?rss=1 Perez, K. C. Alexander, J. Rahman, M. M. Alsharif, H. A. Liu, Y. Kim, J.-A. Hunter, C. S. Nguyen, T. M. Bhatnagar, S. 2025-05-21 doi:10.1101/2025.05.19.654959 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Enhanced anti-nociception by novel dual antagonists for 5HT2aR and mGluR5 in preclinical models of pain ]]> https://biorxiv.org/content/10.1101/2025.05.21.655254v1?rss=1 Choi, D. Heo, H. J. Shin, H. Im, J. Lee, G. Kim, A. H. Hur, K.-H. Nho, Y. Jang, C.-G. Lee, H. 2025-05-22 doi:10.1101/2025.05.21.655254 Cold Spring Harbor Laboratory Press 2025-05-22 <![CDATA[ Maximum Entropy in the Gaussian Network Model: A Thermodynamic Reference State for Protein Dynamics ]]> https://biorxiv.org/content/10.1101/2025.05.18.654696v1?rss=1 Erman, B. 2025-05-23 doi:10.1101/2025.05.18.654696 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Transposable elements drive species-specific and tissue-specific transcriptomes in human development ]]> https://biorxiv.org/content/10.1101/2025.05.19.654775v1?rss=1 Zhang, Y. She, J. Hu, X. Jin, Y. Zhao, J. Hou, S. Tao, C. Du, M. Yang, E. 2025-05-23 doi:10.1101/2025.05.19.654775 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Improved Anisotropic Network Models for Membrane Protein Dynamics and Mechanosensitive Ion Channels ]]> https://biorxiv.org/content/10.1101/2025.05.22.654704v1?rss=1 Han, Z. Wang, L. Song, C. 2025-05-27 doi:10.1101/2025.05.22.654704 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Bridging Scales: Spectral Theory Reveals How Local Connectivity Rules Sculpt Global Neural Dynamics in Spatially Extended Networks ]]> https://biorxiv.org/content/10.1101/2025.05.23.655871v1?rss=1 Huang, Y. Gao, K. Yang, D. Song, S. Chen, G. 2025-05-27 doi:10.1101/2025.05.23.655871 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ ROMO1 loss in cholinergic neurons induces mitochondrial ultrastructural damage and ALS-like neuromuscular degeneration ]]> https://biorxiv.org/content/10.1101/2025.05.24.655877v1?rss=1 Nie, W. Jing, Z. Cheng, L. Li, L. Xu, F. Lin, L. Dong, X. Han, H. Cheng, H. Wang, X. 2025-05-28 doi:10.1101/2025.05.24.655877 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Comparative assessment of co-folding methods for molecular glue ternary structure prediction ]]> https://biorxiv.org/content/10.1101/2025.05.25.655997v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@172b19borg.highwire.dtl.DTLVardef@ea4844org.highwire.dtl.DTLVardef@12ea246org.highwire.dtl.DTLVardef@9fb4bc_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Liao, Y. Zhu, J. Xie, J. Lai, L. Pei, J. 2025-05-28 doi:10.1101/2025.05.25.655997 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Aptamer-Enabled Discovery and Clinical Analysis of Exosomal Surface Biomarkers in Hepatocellular Carcinoma ]]> https://biorxiv.org/content/10.1101/2025.05.28.655095v1?rss=1 Cao, H. Xu, D. Su, Y. Zhang, C. Bian, S. Yan, X. Li, S. Xuan, H. Long, J. Yao, P. Liu, X. Cheng, X. Su, H. Chen, Y. Li, Y. Li, J. Shi, W. Wang, K. Xing, B. Zhang, L. 2025-05-28 doi:10.1101/2025.05.28.655095 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Hierarchical prediction and perturbation of chromatin organization reveal how loop domains mediate higher-order architectures ]]> https://biorxiv.org/content/10.1101/2025.05.25.656045v1?rss=1 Wei, J. Xue, Y. Gao, Y. Q. 2025-05-29 doi:10.1101/2025.05.25.656045 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ VAB-8/KIF26, LIN-17/Frizzled, and EFN-4/Ephrin, control distinct stages of posterior neuroblast migration downstream of the MAB-5/Hox transcription factor in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2025.05.28.656589v1?rss=1 Jain, V. D. Lundquist, E. A. 2025-05-29 doi:10.1101/2025.05.28.656589 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ How Good is AlphaFold3 at Ranking Drug Binding Affinities? ]]> https://biorxiv.org/content/10.1101/2025.05.27.656341v1?rss=1 Hong, X. Gao, B. Jia, Y. Zhu, W. Chen, Q. Tian, X. Zhong, Z. Wang, J. Lan, Y. 2025-05-30 doi:10.1101/2025.05.27.656341 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Structural innovations and neurogenic continuity define avian brain development and evolution ]]> https://biorxiv.org/content/10.1101/2025.05.30.654767v1?rss=1 Shan, H. Mei, Y. Feng, Z. Gu, X. Huang, L. Hui, Y. Li, C. Zhou, Y. He, J. Wu, R. Zhuang, Z. Wang, M. Chen, D. Wu, Y. Zhang, L. Jia, G. 2025-05-30 doi:10.1101/2025.05.30.654767 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Locomotion-induced neural activity independent of auditory feedback in the mouse inferior colliculus ]]> https://biorxiv.org/content/10.1101/2025.05.27.656503v1?rss=1 Han, J. Jiang, H. Ji, Y. R. Kim, G. 2025-06-01 doi:10.1101/2025.05.27.656503 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Controllable Gap Junctions by Vitamin B12 and Light ]]> https://biorxiv.org/content/10.1101/2025.05.28.656405v1?rss=1 Cui, D. Liu, S. Huang, X. Tang, X. A. Zheng, M. He, Z. Xu, R. Sun, C. Xu, Y. Tu, R. Zou, P. Xie, T. Sun, F. 2025-06-01 doi:10.1101/2025.05.28.656405 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Pyruvate kinase activates SARM1 to exacerbate axonal degeneration in diabetic peripheral neuropathy ]]> https://biorxiv.org/content/10.1101/2025.05.28.656718v1?rss=1 Liu, J. Li, W. Li, C. Jiang, Y. Zhu, W. J. Zhang, Z. Zhao, Y. J. Lin, J. YU, W. 2025-06-01 doi:10.1101/2025.05.28.656718 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ A photostable genetically encoded voltage indicator for imaging neural activities in tissue and live animals ]]> https://biorxiv.org/content/10.1101/2025.05.29.656768v1?rss=1 Cao, C. Zhu, R. Zhou, S. Zhao, Z. Lin, C. Liu, S. Peng, L. Subach, F. V. Piatkevich, K. D. Zou, P. 2025-06-01 doi:10.1101/2025.05.29.656768 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Single-cell Characterization of DNA Hydroxymethylation of the Mouse Brain During Aging ]]> https://biorxiv.org/content/10.1101/2025.05.29.656780v1?rss=1 Bai, Y. Yuan, T. Ren, L. Huan, Y. Yang, F. Li, Y. Zhang, A. Liu, Y. Tian, T. Kang, N. Chen, D. Xie, X. Wang, Q. Chen, W. Zheng, Y. Xie, X. S. Cao, Y. 2025-06-01 doi:10.1101/2025.05.29.656780 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Expression, Purification, and Crystallization of Recombinant Human ABL-1 Kinase for Structure-Based Drug Screening Applications ]]> https://biorxiv.org/content/10.1101/2025.06.02.657364v1?rss=1 Irgit, A. Ciftci, H. DeMirci, H. 2025-06-02 doi:10.1101/2025.06.02.657364 Cold Spring Harbor Laboratory Press 2025-06-02 <![CDATA[ Differential metaproteomics of bacteria grown in vitro and in planta reveals functions used during growth on maize roots ]]> https://biorxiv.org/content/10.1101/2025.06.02.657423v1?rss=1 Garrell, A.-K. Cheadle, J. Crook, N. Pal, G. Septer, A. N. Wagner, M. R. Beck, A. E. Kleiner, M. 2025-06-02 doi:10.1101/2025.06.02.657423 Cold Spring Harbor Laboratory Press 2025-06-02 <![CDATA[ A genetically encoded fluorescent sensor for monitoring spatiotemporal prostaglandin E2 dynamics in vivo ]]> https://biorxiv.org/content/10.1101/2025.06.01.657218v1?rss=1 Wang, L. Yang, Y. Deng, F. Yan, Y. Li, Y. 2025-06-03 doi:10.1101/2025.06.01.657218 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Production, Purification, and Crystallization of Recombinant Epidermal Growth Factor Receptor Tyrosine Kinase Domain (EGFR-TKD) for Drug Screening Applications ]]> https://biorxiv.org/content/10.1101/2025.06.02.657332v1?rss=1 TOPALAN, E. Ciftci, H. Demirci, H. 2025-06-03 doi:10.1101/2025.06.02.657332 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Production, Purification, and Crystallization of Recombinant HER2 Tyrosine Kinase Domain (HER2-TKD) as a Platform for Structure-Based Drug Screening ]]> https://biorxiv.org/content/10.1101/2025.06.02.657378v1?rss=1 Topalan, E. Ciftci, H. DeMirci, H. 2025-06-03 doi:10.1101/2025.06.02.657378 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Disentangling the cost of gene expression ]]> https://biorxiv.org/content/10.1101/2025.06.02.656972v1?rss=1 Yan, Y. Lin, J. 2025-06-04 doi:10.1101/2025.06.02.656972 Cold Spring Harbor Laboratory Press 2025-06-04 <![CDATA[ PANDA: A simple and affordable chamber system for measuring the whole-plant net CO2 flux ]]> https://biorxiv.org/content/10.1101/2025.06.02.657330v1?rss=1 Schuler, P. Li, Y. Pittet, P. Favre, P. Li, M.-H. Zhang, Y.-L. Grossiord, C. 2025-06-04 doi:10.1101/2025.06.02.657330 Cold Spring Harbor Laboratory Press 2025-06-04 <![CDATA[ Primary tumor microbiomes predict distant metastasis of colorectal cancer ]]> https://biorxiv.org/content/10.1101/2025.06.02.654060v1?rss=1 Parajuli, B. Midya, V. Kiddle, R. De Jager, N. Eggers, S. Spakowicz, D. Hoyd, R. Salhia, B. Chan, C. H. Churchman, M. Rounbehler, R. J. Yao, S. Rutkowski, M. R. Tarhini, A. A. Mudaranthakam, D. P. Masood, A. Bocklage, T. J. Lentz, R. W. Hatoum, H. Ilozumba, M. N. Hardikar, S. Ulrich, C. M. Round, J. L. Riedlinger, G. Shriver, C. D. Bosch, D. E. 2025-06-05 doi:10.1101/2025.06.02.654060 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ Macrophage-derived reactive oxygen species promote Salmonella aggresome formation contributing to bacterial antibiotic persistence ]]> https://biorxiv.org/content/10.1101/2025.06.03.657582v1?rss=1 View larger version (55K): org.highwire.dtl.DTLVardef@7e5f1forg.highwire.dtl.DTLVardef@970a39org.highwire.dtl.DTLVardef@204449org.highwire.dtl.DTLVardef@632c47_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chen, X. Fang, K. Li, B. Li, Y. Ke, Y. Ke, W. Tian, T. Zhao, Y. Wang, L. Geng, J. Leake, M. C. Bai, F. C. 2025-06-05 doi:10.1101/2025.06.03.657582 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ METTL5 Blockade Enhances Anti-Tumor Immune Response via Inducing Neoantigen Generation ]]> https://biorxiv.org/content/10.1101/2025.06.06.658288v1?rss=1 Zhang, Y. Shi, X. Wang, Y. Wang, R. Cao, Y. Chen, H. 2025-06-07 doi:10.1101/2025.06.06.658288 Cold Spring Harbor Laboratory Press 2025-06-07 <![CDATA[ Investigating multiple types of resistance against a homing gene drive in European populations of Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2025.06.06.658298v1?rss=1 Faber, N. R. Champer, J. Pannebakker, B. A. Zwaan, B. J. van den Heuvel, J. 2025-06-09 doi:10.1101/2025.06.06.658298 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Specificity of Drosophila innubila Nudivirus Infection in Drosophila Cell Culture ]]> https://biorxiv.org/content/10.1101/2025.06.09.658616v1?rss=1 Mulkey, K. M. Adewumi, T. Unckless, R. 2025-06-09 doi:10.1101/2025.06.09.658616 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Semantics across the globe: A universal neurocognitive semantic structure adaptive to climate ]]> https://biorxiv.org/content/10.1101/2025.06.13.659453v1?rss=1 Fu, Z. Chu, Y. Zhang, T. Li, Y. Wang, X. Bi, Y. 2025-06-15 doi:10.1101/2025.06.13.659453 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Environment-dependent selection impacts heritable developmental stability and trait canalization in rice ]]> https://biorxiv.org/content/10.1101/2025.06.13.659410v1?rss=1 Dunivant, T. S. Calic, I. Gilligan, C. Joly-Lopez, Z. Choi, J. Y. Natividad, M. Cabral, C. L. Torres, R. O. Vergara, G. V. Franks, S. J. Henry, A. Purugganan, M. D. Groen, S. C. 2025-06-16 doi:10.1101/2025.06.13.659410 Cold Spring Harbor Laboratory Press 2025-06-16 <![CDATA[ Proteomic and metabolic profiling reveals APOE4-dependent shifts in whole brain, neuronal, and astrocytic mitochondrial function and glycolysis ]]> https://biorxiv.org/content/10.1101/2025.06.15.659811v1?rss=1 Lysaker, C. R. Johnson, C. Csikos, V. Franczak, E. Benson, M. Gilmore, C. Birky, C. Davis, X. McCoin, C. Smith, K. Puchalska, P. Crawford, P. Slawson, C. Thyfault, J. Geiger, P. Morris, J. Wilkins, H. M. 2025-06-16 doi:10.1101/2025.06.15.659811 Cold Spring Harbor Laboratory Press 2025-06-16 <![CDATA[ Gene duplication, translocation and molecular evolution of Dmrt1 and related sex-determining genes in anurans ]]> https://biorxiv.org/content/10.1101/2025.06.11.659201v1?rss=1 200 Ma divergence) and available transcriptomes. We asked how often new master sex-determining genes arise by gene duplication, whether and how often gene translocation associates with sex chromosome turnover, and if new master sex-determining genes evolve under positive selection. We find that chromosome-level synteny is remarkably conserved, with only a few fusions or fissions and no evidence for translocation of four candidate master sex-determining genes (Dmrt1, Foxl2, Bod1l, Sox3). Only Dmrt1 duplicated in 3 out of 50 species (excluding tetraploid Xenopus), and it showed strong testis-biased expression in all 8 species with available gonadal expression data. While Dmrt1 has evolved under purifying selection, Dmrt1 duplicates exhibit elevated nonsynonymous substitution rates and a tendency towards positive selection. Lineage-specific amino acid changes were observed in the conserved DM domain of Dmrt1. These results demonstrate that, in anurans, master sex-determining genes arise rarely via gene duplication, and more likely evolve via allelic diversification. Sex chromosome turnover is not associated with gene translocation, and is more likely driven by mutations on genes involved in sexual developmental pathway. All candidate sex-determining genes were under strong purifying selection, with the exception of duplications which are linked to positive selection. Our results suggest future research on anuran sex determination and sex chromosome evolution should focus on identifying allelic diversification and novel mutations on genes involved in sexual developmental pathway. ]]> Shinde, S. S. Veltsos, P. Ma, W.-J. 2025-06-17 doi:10.1101/2025.06.11.659201 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Deepening imaging-based spatial proteomics at high spatial resolution through controlled tissue resizing and in-situ bottom-up mass spectrometry ]]> https://biorxiv.org/content/10.1101/2025.06.12.659329v1?rss=1 Deng, K. Zhan, L. Yi, L. Zhang, J. Tang, M. Chang, T. Ji, G. Shao, X. Xu, X. Wei, X. Zhang, T. Yao, J. Wang, J. Wang, G. Huang, Y. 2025-06-17 doi:10.1101/2025.06.12.659329 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ High-throughput genetic mapping discovers novel zinc toxicity response loci in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2025.06.12.659401v1?rss=1 Hanson, K. M. Long, A. D. Macdonald, S. J. 2025-06-17 doi:10.1101/2025.06.12.659401 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Super-giga and tiny orchid genomes illuminate evolution of Orchidaceae ]]> https://biorxiv.org/content/10.1101/2025.06.13.659439v1?rss=1 Lan, S. Liu, K.-W. Li, Z. Hsiao, Y.-Y. Liu, Y. Zhang, D. Zhao, X. Sun, W.-H. Liu, D.-K. Huang, M.-Z. Zhou, C.-Y. Zeng, M. Wang, L. Zheng, R. Zhao, Z. Gao, X. Lai, J.-H. Yeh, K.-L. Zhang, L.-S. Chen, J. Ma, X. Li, Y. Chen, D. Li, J. Zhang, M.-M. He, X. Huang, Y. Zhang, C. Wu, X. Chen, C. Ma, L. Zhai, J. Ai, Y. Li, M.-H. Zhou, Y. Zhou, Z. Wu, S. Zhao, K. Guan, Y. Tu, X.-D. Zeng, D. Ji, X. Liu, N. Zou, S. Chen, Y.-Y. Lin, S.-T. Su, W.-Y. Wang, Z.-W. Luo, Y.-B. Zhang, W. Guo, Y.-Y. Tian, Y.-Q. Zou, L.-H. Lv, X. Zhuo, X. Zhu, J. Peng, D.-H. Y 2025-06-17 doi:10.1101/2025.06.13.659439 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Cryo-EM Structure of the Erlin1/2 Complex Reveals a Dynamic Scaffold for Membrane Protein Sequestration and Microdomain Assembly ]]> https://biorxiv.org/content/10.1101/2025.06.14.659634v1?rss=1 Yan, L. Xu, Z. Yao, Y. Wang, X. Wang, Y. Ma, C. Li, N. Chen, X. Gao, N. 2025-06-17 doi:10.1101/2025.06.14.659634 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Single oocyte full-length isoform sequencing unveils the impact of transposable elements on RNA diversity and stability during oocyte maturation ]]> https://biorxiv.org/content/10.1101/2025.06.17.659919v1?rss=1 Wang, Y. Wang, W. Liu, Y. He, Y. Song, H. Yang, M. Wang, N. Wang, X. Ding, L. Kuo, Y. Xiu, Y. Du, Z. Chen, L. Lian, Y. Liu, Q. Yan, L. Qiao, J. Yuan, P. 2025-06-17 doi:10.1101/2025.06.17.659919 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Population-specific brain charts reveal Chinese-Western differences in neurodevelopmental trajectories ]]> https://biorxiv.org/content/10.1101/2025.06.17.659820v1?rss=1 Sun, L. Qin, W. Liang, X. Wang, C. Men, W. Duan, Y. Fan, X.-R. Cai, Q. Qiu, S. Wang, M. Gong, Q. Tian, Y. Liang, P. Liu, Z. Zhang, X. Song, H. Ye, Z. Zhang, P. Dong, Q. Tao, S. Zhu, W. Zhang, J. Xie, F. Feng, J. Zhang, J. Liu, C. Qian, Q. Zhang, B. Meng, M. Hu, L. Gao, J.-H. Jiang, T. Zhu, X. Zhang, Y. Liu, L. Liu, H. Liao, W. Wang, D. Wang, H. Guo, T. Dai, Z. Lui, S. Xu, K. Li, L. Xie, P. Feng, C. Cui, G. Wu, J. Yin, X. Ding, G. Xian, J. Zhao, L. Lu, J. Liu, Z. Han, Y. Yuan, Z. Zhang, X. Si, T. Zhou, F. Bi, Y. Wu, D. Gao, F. Wang, 2025-06-18 doi:10.1101/2025.06.17.659820 Cold Spring Harbor Laboratory Press 2025-06-18 <![CDATA[ UniCure: A Foundation Model for Predicting Personalized Cancer Therapy Response ]]> https://biorxiv.org/content/10.1101/2025.06.14.658531v1?rss=1 Chen, Z. Tian, S. Pei, J. Gu, R. Li, Y. Ding, S. Xu, Y. Zheng, X. Liu, M. Du, X. Zhu, J. Zou, J. Xu, J. Jiang, W. Chen, Y. Dong, B. Zhang, Q. Ren, S. Wang, S. Wen, H. Zhang, W. Chen, L. 2025-06-19 doi:10.1101/2025.06.14.658531 Cold Spring Harbor Laboratory Press 2025-06-19 <![CDATA[ Fluoro-forest: A random forest workflow for cell type annotation in high-dimensional immunofluorescence imaging ]]> https://biorxiv.org/content/10.1101/2025.06.13.659547v1?rss=1 Brand, J. Zhang, W. Carchman, E. Dinh, H. Q. 2025-06-20 doi:10.1101/2025.06.13.659547 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Substrate properties and actin polymerization speed dictate universal modes of cell migration: gripping, slipping, and stick-slip ]]> https://biorxiv.org/content/10.1101/2025.06.20.660727v1?rss=1 Ye, Y. Lin, J. 2025-06-25 doi:10.1101/2025.06.20.660727 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Self-inactivating AAV-CRISPR at different ages enables sustained amelioration of Huntington's disease deficits in BAC226Q mice ]]> https://biorxiv.org/content/10.1101/2025.06.24.661435v1?rss=1 Dai, Y. Abudujielili, Z. Ding, Y. Huang, W. Yin, J. Ou, L. Hu, J. Zheng, S. Li, C. 2025-06-25 doi:10.1101/2025.06.24.661435 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Exploring Cellular Water Dynamics associated with Potassium Ion Changes Using Magnetic Resonance Imaging ]]> https://biorxiv.org/content/10.1101/2025.06.25.661446v1?rss=1 Kim, S.-M. Min, K. Lee, J. S. Park, J.-Y. 2025-06-27 doi:10.1101/2025.06.25.661446 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Hollow condensates emerge from gelation-induced spinodal decomposition ]]> https://biorxiv.org/content/10.1101/2025.06.25.661497v1?rss=1 Li, C. Meng, L. Tong, Y. Lin, J. Qi, Z. 2025-06-27 doi:10.1101/2025.06.25.661497 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Accelerating Virtual Directed Evolution of Proteins via Reinforcement Learning ]]> https://biorxiv.org/content/10.1101/2025.06.25.661516v1?rss=1 Mi, T. Wang, Y. Zhao, J. Wang, W. Shen, Y. Xiao, N. Chen, L. Chen, G.-Q. Zhang, S. Zhang, W.-B. Gong, H. 2025-06-27 doi:10.1101/2025.06.25.661516 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Competing Programs Shape Cortical Sensorimotor-Association Axis Development ]]> https://biorxiv.org/content/10.1101/2025.06.26.660775v1?rss=1 Tsyporin, J. Zhang, M. Qi, C. Segal, A. Finn, T. Kim, H. Choi, S.-H. Li, X. Bandiera, S. Pavlovic, I. Kim, S. K. K. Shibata, A. Onishi, K. Zhang, Z. Hammarlund, E. Su, G. Salla, N. Kachko, J. Hawley, C. Li, S. Doyle, D. Z. Peng, X. Nottoli, T. Ruiz-Reig, N. Tissir, F. Nakagawa, Y. Herzog, E. Ma, S. Gobeske, K. Pattabiraman, K. Shimogori, T. Duque, A. Fornito, A. Huang, H. Shibata, M. Chen, B. Sestan, N. 2025-06-27 doi:10.1101/2025.06.26.660775 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Primary and secondary auditory cortex connectivity with brain regions involved in cognitive and emotional processing: in mouse and human ]]> https://biorxiv.org/content/10.1101/2025.06.26.661219v1?rss=1 Kose-Ozkan, B. Ozkan, M. Gunes, Y. C. Algin, O. Cavdar, S. 2025-06-27 doi:10.1101/2025.06.26.661219 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Spatial Reorganization of Object Representations in High-Level Visual Cortex Distinguishes Working Memory from Perception ]]> https://biorxiv.org/content/10.1101/2025.06.29.662186v1?rss=1 Li, W. Yang, J. Bao, P. 2025-06-29 doi:10.1101/2025.06.29.662186 Cold Spring Harbor Laboratory Press 2025-06-29 <![CDATA[ Human ribomes reveal DNA-embedded ribonucleotides as a new type of epigenetic mark ]]> https://biorxiv.org/content/10.1101/2025.06.27.661996v1?rss=1 Kundnani, D. L. Yang, T. Channagiri, T. Xu, P. Lee, Y. Sun, M. Martinez-Figueroa, F. Randhawa, S. Gogate, A. Jeon, Y. Marsili, S. Newnam, G. Lu, Y. Park, V. Tao, S. Ling, J. Schinazi, R. Pursell, Z. Mohammed, A. Opresko, P. Freudenthal, B. Kim, B. Yi, S. Jonoska, N. Storici, F. 2025-06-30 doi:10.1101/2025.06.27.661996 Cold Spring Harbor Laboratory Press 2025-06-30 <![CDATA[ Single-Cell and Spatial Profiling of Tumor Microenvironment Heterogeneity in Human Osteosarcomas ]]> https://biorxiv.org/content/10.1101/2025.06.27.661729v1?rss=1 zheng, X. Yuan, J. Jin, P. Wang, X. Xu, R. Feng, H. Zhang, X. Xie, Y. Wu, W. 2025-07-02 doi:10.1101/2025.06.27.661729 Cold Spring Harbor Laboratory Press 2025-07-02 <![CDATA[ From Development to Regeneration: Insights into Flight Muscle Adaptations from Bat Muscle Cell Lines ]]> https://biorxiv.org/content/10.1101/2025.07.01.662643v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@490f49org.highwire.dtl.DTLVardef@8ab615org.highwire.dtl.DTLVardef@b840e1org.highwire.dtl.DTLVardef@ab92eb_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Deng, F. Pena, V. Morales-Sosa, P. Bernal-Rivera, A. Yang, B. Ghosh, S. Castellano, L. Katt, M. Huang, S. Maddera, C. Yu, Z. Rohner, N. zhao, c. Camacho, J. 2025-07-03 doi:10.1101/2025.07.01.662643 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Neural trajectories improve motor precision ]]> https://biorxiv.org/content/10.1101/2025.07.01.662682v1?rss=1 Lee, W.-H. Scherschligt, X. Nishimoto, M. Rouse, A. G. 2025-07-03 doi:10.1101/2025.07.01.662682 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ High-Quality PacBio Genome Assembly of Populus alba L. Villafranca ]]> https://biorxiv.org/content/10.1101/2025.06.30.661909v1?rss=1 Sarfraz, I. Zuccolo, A. Celii, M. Francini, A. Wing, R. A. Sebastiani, L. 2025-07-04 doi:10.1101/2025.06.30.661909 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Spatial Proteomics of the Normal Breast Collagen Stroma: Links to BI-RADS Categories and Body Mass Index ]]> https://biorxiv.org/content/10.1101/2025.07.01.660922v1?rss=1 0.7; p-value>0.05). Proteomic alterations were found between overweight to obese categories with strong positive associations to BMI by multivariate analysis. This study provides the first spatial analysis of the collagen proteome in normal breast within contexts of cellular markers and clinical characteristics. ]]> Dunne, J. B. Rujchanarong, D. Park, Y. Macdonald, J. K. Hulahan, T. S. Taylor, H. B. Spruill, L. Jensen-Smith, H. Hollingsworth, M. A. Sandusky, G. E. Mehta, A. S. Drake, R. R. Ford, M. E. Nakshatri, H. Angel, P. M. 2025-07-04 doi:10.1101/2025.07.01.660922 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Age-dependent remodeling of the sciatic proteome in 5xFAD mice can be attenuated by exercise or donepezil treatment to maintain neuromuscular function ]]> https://biorxiv.org/content/10.1101/2025.07.01.662603v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@c41009org.highwire.dtl.DTLVardef@1f8d8e8org.highwire.dtl.DTLVardef@689ba5org.highwire.dtl.DTLVardef@1c28884_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Brisendine, M. H. Nieves-Esparcia, D. Q. Willoughby, O. S. Brown, J. R. Braxton, D. S. Henry, S. N. McCoin, C. Thyfault, J. Morris, J. K. Poelzing, S. Grange, R. W. Najt, C. P. Drake, J. C. 2025-07-04 doi:10.1101/2025.07.01.662603 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ WaveLimit: An optimal spike sorting inclusion boundary ]]> https://biorxiv.org/content/10.1101/2025.07.01.662629v1?rss=1 Scherschligt, X. Lee, W.-H. Dallimore, C. A. Schrader, E. Liu, Z. Rouse, A. G. 2025-07-04 doi:10.1101/2025.07.01.662629 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Citizen science suggests decreased diversity of insects in Mexico, a megadiverse country. ]]> https://biorxiv.org/content/10.1101/2025.07.01.662623v1?rss=1 Soberon, J. L. 2025-07-05 doi:10.1101/2025.07.01.662623 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ Common Signatures of Neutrophils in Diverse Disease Conditions ]]> https://biorxiv.org/content/10.1101/2025.07.02.662891v1?rss=1 Wu, D. Cao, Y. Chen, H. Du, M. Wang, T. Zhao, J. Z. Li, M. Wu, W. Zhang, H. Yang, E. Yang, J. Chen, J. 2025-07-05 doi:10.1101/2025.07.02.662891 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ Neuromodulation of Swarming Behavior in C. elegans: Insights into the Conserved role of Calsyntenins ]]> https://biorxiv.org/content/10.1101/2025.07.06.663344v1?rss=1 Shahi, N. Kumari, N. Khapre, S. Dahiya, D. Saritekin, E. Kocabas, A. Babu, K. 2025-07-06 doi:10.1101/2025.07.06.663344 Cold Spring Harbor Laboratory Press 2025-07-06 <![CDATA[ Alternative splicing contributes to plasticity and regulatory divergence in locally adapted house mice from the Americas ]]> https://biorxiv.org/content/10.1101/2025.07.03.662996v1?rss=1 Phifer-Rixey, M. Ward, J. R. Mack, K. L. 2025-07-07 doi:10.1101/2025.07.03.662996 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ An orally available PfPKG inhibitor blocks sporozoite infection of the liver ]]> https://biorxiv.org/content/10.1101/2025.07.09.663303v1?rss=1 BHANOT, P. Dhiyebi, H. Mbaye, A. Thaniana, A. Gilleran, J. Eck, T. Ashraf, K. Fan, H. Seibold, S. Battaile, K. Siekierka, J. Johnson, E. Roth, A. De Rocher, A. Lovell, S. Miller, E. Roberge, J. Y. 2025-07-09 doi:10.1101/2025.07.09.663303 Cold Spring Harbor Laboratory Press 2025-07-09 <![CDATA[ Metagenomic analysis of antimicrobial resistance, virulence, and mobile genetic elements in the gut microbiota of Caprinae species ]]> https://biorxiv.org/content/10.1101/2025.07.09.663846v1?rss=1 Su, J. Elsheikha, H. M. Guo, L. Liu, R. Shang, K.-M. Yu, H.-L. Ma, H. Ni, H.-B. Chen, B.-N. Zhang, X.-X. Yang, X. 2025-07-09 doi:10.1101/2025.07.09.663846 Cold Spring Harbor Laboratory Press 2025-07-09 <![CDATA[ Deciphering the altered conformational states of bifunctional thaumarchaeal crotonyl-CoA hydratase and 3-hydroxypropionyl-CoA dehydratase from Nitrosopumilus maritimus ]]> https://biorxiv.org/content/10.1101/2025.07.07.663511v1?rss=1 Destan, E. Kang, J. Tosha, T. Yabashi, M. Yapici, I. Tolar, B. B. Kulakman, C. Nergiz, Z. Matsuura, H. Kawano, Y. Deutsch, S. Yoshikuni, Y. Francis, C. A. Wakatsuki, S. DeMirci, H. 2025-07-10 doi:10.1101/2025.07.07.663511 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ f-BGM enables fungi-specific genome mining in high accuracy and interpretability ]]> https://biorxiv.org/content/10.1101/2025.07.08.662937v1?rss=1 Zhou, Y. Liu, D. Huang, Z. Xie, X. Lin, W. Zhang, L. Fan, A. Liu, Z. 2025-07-11 doi:10.1101/2025.07.08.662937 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ NuMA promotes constitutive heterochromatin compaction by stabilizing linker histone H1 on chromatin ]]> https://biorxiv.org/content/10.1101/2025.07.08.663620v1?rss=1 Wang, Y. Zhao, W. Niu, J. Liu, C. Wang, X. Yuan, W. Ai, S. Baumeister, W. Li, G. He, A. Xu, P. Li, C. Sun, Y. 2025-07-11 doi:10.1101/2025.07.08.663620 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ Substituent-based Modulation of Self-Assembly and Immunogenicity of Amphipathic Peptides ]]> https://biorxiv.org/content/10.1101/2025.07.08.663637v1?rss=1 Das, A. Pramanik, U. Brown, E. M. Liu, C.-Y. Gong, H. Fascetti, J. Gibson, M. Stealey, S. Zustiak, S. P. Berkland, C. Jackrel, M. E. White, M. A. Rudra, J. S. 2025-07-11 doi:10.1101/2025.07.08.663637 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ A Fibroblast State Choreographs an Epithelial YAP-dependent Regenerative Program Essential to (Pre)malignancy via ECM-mediated Mechanotransduction ]]> https://biorxiv.org/content/10.1101/2025.07.11.661192v1?rss=1 Pan, D. Gascard, P. Caruso, J. A. Chen-Tanyolac, C. Sangwan, V. Bertos, N. Camilleri-Broet, S. Berube, J. Oikonomopoulos, S. Strasser, M. K. Gibbs, D. L. Bons, J. Burton, J. B. Rose, J. P. Shah, S. Bai, R. Lee, S. Fels-Elliott, D. R. Miyara, S. Alon, U. Urisman, A. Ragoussis, I. Huang, S. Schilling, B. Ferri, L. E. Tlsty, T. D. 2025-07-11 doi:10.1101/2025.07.11.661192 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ CNA detection from spatial transcriptomics using SpaCNA ]]> https://biorxiv.org/content/10.1101/2025.07.08.663688v1?rss=1 Zhang, Z. Wang, X. Xuan, H. Jin, Z. Xi, R. 2025-07-12 doi:10.1101/2025.07.08.663688 Cold Spring Harbor Laboratory Press 2025-07-12 <![CDATA[ Granulin+ macrophages promote lineage plasticity in prostate cancer through paracrine signaling loops ]]> https://biorxiv.org/content/10.1101/2025.07.09.663835v1?rss=1 Zhu, Z. Zhang, M. Song, Y. Jiang, W. Cao, F. Yao, Y. Yu, X. Zhao, H. Baiyin, H. Chang, D. Wu, D. Zhao, X. Wu, G. Li, K. Mao, F. 2025-07-14 doi:10.1101/2025.07.09.663835 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ Plant phylogeny and life history predict AM fungal species and genetic composition, but only life history and genetic composition predict feedback ]]> https://biorxiv.org/content/10.1101/2025.07.10.664051v1?rss=1 Ramos, R. Richards, B. L. Schultz, P. Bever, J. 2025-07-15 doi:10.1101/2025.07.10.664051 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ Topsicle: a method for estimating telomere length from whole genome long-read sequencing data ]]> https://biorxiv.org/content/10.1101/2025.07.10.664126v1?rss=1 Nguyen, L. Choi, J. Y. 2025-07-15 doi:10.1101/2025.07.10.664126 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ Airway Epithelial SARS-CoV-2 Infectious and Repair Responses: Relationships to Age, Sex, and Post-COVID Pulmonary Syndromes ]]> https://biorxiv.org/content/10.1101/2025.07.17.663733v1?rss=1 Dang, H. Edwards, C. E. Kato, T. Reidel, B. Meganck, R. M. Esther, C. R. Ehre, C. Fulcher, M. L. Bailey, A. B. Cooley, M. R. Mikami, Y. Asakura, T. Hawkins, P. E. Saito, M. Meyers, J. L. Konopka, K. Gerayeli, F. V. Park, H. Y. Sin, D. D. Livraghi-Butrico, A. Okuda, K. Pickles, R. J. Klein, S. L. Randell, S. H. O'Neal, W. K. Baric, R. S. Boucher, R. C. 2025-07-17 doi:10.1101/2025.07.17.663733 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ AtlasAgent: Vision language model and Agent-guided Framework for Evaluation of Atlas-scale Single-cell Integration ]]> https://biorxiv.org/content/10.1101/2025.07.15.663271v1?rss=1 Yin, D. Zhang, Z. Liu, X. Ni, K. Su, H. Li, N. L. L. Dong, H. Zhao, Q. Lin, X. Tian, L. Meng, Y. Ho, J. W. K. 2025-07-18 doi:10.1101/2025.07.15.663271 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Spatiotemporal dynamics of questing activity by four tick species in the central Great Plains ]]> https://biorxiv.org/content/10.1101/2025.07.15.664906v1?rss=1 Cobos, M. E. Corimanya, J. L. Ng'eno, E. Nunez-Penicet, C. Perkins, A. C. Ruiz-Utrilla, Z. Alkishe, A. Romero-Alvarez, D. Yao, Y. Ghosh, A. Xiao, X. Peterson, A. T. Duncan, K. T. 2025-07-18 doi:10.1101/2025.07.15.664906 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ A novel interoceptive subfornical organ to infralimbic cortex circuit relays airway inflammation effects on fear extinction ]]> https://biorxiv.org/content/10.1101/2025.07.16.664367v1?rss=1 Allgire, E. McAlees, J. W. Ahlbrand, R. A. Mancz, E. Vollmer, L. L. Winter, A. McMurray, K. Maile, L. Sanders, B. Ryan, W. G. Pool, A.-H. Ifergan, I. Wohleb, E. S. Davidson, S. McCullumsmith, R. E. Lewkowich, I. P. Sah, R. 2025-07-18 doi:10.1101/2025.07.16.664367 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ A 3-genes interferon signature predicts sustained complete remission in pediatric AML patients ]]> https://biorxiv.org/content/10.1101/2025.07.17.664572v1?rss=1 Sherif, S. Ali, A. I. Ibrahim, K. A. Rinchai, D. Elanbari, M. Kizhakayil, D. Toufiq, M. Vempalli, F. R. Mina, T. Comoli, P. Ghias, K. Fadoo, Z. Herrera, S. Lachica, C.-A. Dawoud, E. D. K. Bibawi, H. Sapia, S. Dason, B. Ejaz, A. Anas, M. Y. S. Saleh, A. Gentilcore, G. Bedognetti, D. Cugno, C. Deola, S. 2025-07-18 doi:10.1101/2025.07.17.664572 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ A live tumor fragment platform to assess immunotherapy response in core needle biopsies while addressing challenges of tumor heterogeneity ]]> https://biorxiv.org/content/10.1101/2025.07.18.663728v1?rss=1 Ramasubramanian, T. S. Adstamongkonkul, P. Scribano, C. Johnson, C. Caenepeel, S. Hrycyniak, L. Vedder, L. C. Dana, N. Baltes, C. Browning, T. Chen, Y.-I. Dietz, T. Flietner, E. Kaplewski, N. Kellner, A. Korrer, M. Liu, C. Marhefke, N. McDonnell, P. Nasreen, A. Pope, V. Prasad, A. Richardson, J. Schneider, S. Schultz, M. Sood, C. Sunil, A. von Euw, E. Wait, E. Wargowski, E. Advani, P. Broome, B. Bruckbauer, A. Godwin, A. Kokabi, N. Martin, R. Robaina, M. Toia, G. Routh, J. Friedl, A. Eliceiri, K. Szulczewski, M. Johnson, S. Oliner, J. Galon, J. Capi 2025-07-18 doi:10.1101/2025.07.18.663728 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Self-limiting population suppression gene drive in the West Nile vector mosquito, Culex quinquefasciatus ]]> https://biorxiv.org/content/10.1101/2025.07.16.665070v1?rss=1 Feng, X. Ding, J. Liu, Y. Lopez Del Amo, V. Gantz, V. M. Chen, X.-x. Champer, J. Liu, F. 2025-07-19 doi:10.1101/2025.07.16.665070 Cold Spring Harbor Laboratory Press 2025-07-19 <![CDATA[ A C. elegans model of familial Alzheimer's disease shows age-dependent synaptic degeneration independent of amyloid β-peptide ]]> https://biorxiv.org/content/10.1101/2025.07.16.665161v1?rss=1 Nagarajan, V. Libowitz, C. L. Ackley, B. D. Wolfe, M. S. 2025-07-20 doi:10.1101/2025.07.16.665161 Cold Spring Harbor Laboratory Press 2025-07-20 <![CDATA[ Construction of a genome-wide pooled CRISPRi library as a resource for exploring the acid tolerance mechanism in Streptococcus mutans ]]> https://biorxiv.org/content/10.1101/2025.07.22.666072v1?rss=1 Chi, Y. Chen, Y. Yuan, C. Yang, L. Zhang, M. Chen, X. Zhao, Y. Li, M. Wang, X. Li, Y. 2025-07-22 doi:10.1101/2025.07.22.666072 Cold Spring Harbor Laboratory Press 2025-07-22 <![CDATA[ Complementary role of frontal theta and parietal alpha activity in resolving visual competition ]]> https://biorxiv.org/content/10.1101/2025.07.21.665846v1?rss=1 Wen, W. Wu, Y. Reinhart, R. M. G. Li, S. 2025-07-24 doi:10.1101/2025.07.21.665846 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ The Illusion of Polygenicity in Poolseq studies: Insufficient Power Can Mask Simple Genetic Architectures ]]> https://biorxiv.org/content/10.1101/2025.07.23.666414v1?rss=1 700x sequencing coverage in case and control pools, a directly ascertained SNP-based GWAS failed to reveal clear evidence for major-effect loci. A unique feature of the dataset is that an advanced intercross multiparent population, with known founders, was employed as the base population for the GWAS. We leverage this unique population structure to carry out a second GWAS using imputed haplotype frequency estimates, which in contrast revealed localized regions of major effect. A third reanalysis of the same data using imputed SNP genotypes derived from the founder haplotype frequency estimates uncovered a similar major gene architecture. The key difference between approaches lies in statistical power: directly ascertained SNP counts have errors proportional to sequencing coverage whereas known founder imputation-based approaches can be considerably more accurate. This work highlights that insufficiently powered GWAS studies can mask simple genetic architectures and create the illusion of polygenicity through statistical noise alone. ]]> Long, A. D. Hanson, K. M. Macdonald, S. J. 2025-07-24 doi:10.1101/2025.07.23.666414 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Rag GTPases Suppress Renal Cystic Disease by Inhibiting TFEB Independently of mTORC1 ]]> https://biorxiv.org/content/10.1101/2025.07.24.664930v1?rss=1 de Fatima Silva, F. Boucher, A. R. Li, H. Chen, Q. Gaughan, M. Korobkina, E. Isidor, M. S. Smith, A. O. Shen, K. Allison, D. B. Tran, P. Pazour, G. J. Guertin, D. A. 2025-07-24 doi:10.1101/2025.07.24.664930 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Comprehensive profiling of antibiotic resistance, virulence genes, and mobile genetic elements in the gut microbiome of Tibetan antelopes ]]> https://biorxiv.org/content/10.1101/2025.07.24.666617v1?rss=1 Liu, J. Ni, H.-B. Yu, M.-Y. Qin, S.-Y. Elsheikha, H. M. Peng, P. Guo, L. Xie, L. Liang, H.-R. Lei, C.-C. Xu, Y. Tang, Y. Yu, H.-L. Qin, Y. Liu, J. Sun, H. Zhang, X.-X. Qiu, B. 2025-07-24 doi:10.1101/2025.07.24.666617 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Hybrid peptide DNA nanomaterials enable potent and broad-spectrum virus neutralization ]]> https://biorxiv.org/content/10.1101/2025.07.21.666049v1?rss=1 Umrao, S. Dwivedy, A. Haak, P. L. Gandavadi, D. Rund, L. Chen, C. Zhou, L. Duan, J. Fang, Y. Steelman, A. Wang, X. 2025-07-25 doi:10.1101/2025.07.21.666049 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ GraphTME: a framework for predicting response to immune checkpoint inhibitors by interpreting cell-cell interactions in the tumour microenvironment using spatial transcriptomics of tumour tissue ]]> https://biorxiv.org/content/10.1101/2025.07.24.665835v1?rss=1 Jeong, H. J. Oh, J. Choi, Y.-L. 2025-07-26 doi:10.1101/2025.07.24.665835 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ Centriolar satellites are dynamic membrane-less organelles that assemble via a hierarchical pathway ]]> https://biorxiv.org/content/10.1101/2025.07.27.666075v1?rss=1 Begar, E. Yilmaz, S. Seyrek, E. Arslanhan, M. D. Odabasi, E. Firat-Karalar, E. N. 2025-07-30 doi:10.1101/2025.07.27.666075 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ Selective Observation Under Limited Resources Biases Social Inference Through Hysteresis ]]> https://biorxiv.org/content/10.1101/2025.07.30.667795v1?rss=1 Son, S. Yoo, S. B. M. 2025-08-01 doi:10.1101/2025.07.30.667795 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Surveillance on California dairy farms reveals multiple sources of H5N1 transmission ]]> https://biorxiv.org/content/10.1101/2025.07.31.666798v1?rss=1 Campbell, A. J. Shephard, M. Paulos, A. P. Pauly, M. Vu, M. Stenkamp-Strahm, C. Bushfield, K. Hunter-Binns, B. Sablon, O. Bendall, E. E. Fitzimmons, W. J. Brizuela, K. Quirk, G. Kumar, N. McCluskey, B. Shetty, N. Marr, L. C. Guthmiller, J. Abernathy, K. Lauring, A. S. Melody, B. T. Wolfe, M. Lombard, J. Lakdawala, S. S. 2025-08-01 doi:10.1101/2025.07.31.666798 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Concerted actions of distinct serotonin neurons orchestrate female pup care behavior ]]> https://biorxiv.org/content/10.1101/2025.07.31.667987v1?rss=1 Xiao, S. A. Chen, C. C. Horvath, P. Tsai, V. Cardenas, V. M. Biderman, D. Deng, F. Li, Y. Linderman, S. Dulac, C. Luo, L. 2025-08-01 doi:10.1101/2025.07.31.667987 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ A tale of three types of internal object representations in the human brain ]]> https://biorxiv.org/content/10.1101/2025.08.01.668040v1?rss=1 Tian, S. Mao, X. Feng, R. Wang, X. Wang, D.-H. Bi, Y. 2025-08-01 doi:10.1101/2025.08.01.668040 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Single-gene knockout of RNLS or HIVEP2 are insufficient to protect β-cell spheroids from allo- and xeno-rejection ]]> https://biorxiv.org/content/10.1101/2025.07.30.667633v1?rss=1 Karaoglu, I. C. Odabas, A. Onder, T. T. KIZILEL, S. 2025-08-02 doi:10.1101/2025.07.30.667633 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Tripleknock: predicting lethal effect of three-gene knockout in bacteria by deep learning ]]> https://biorxiv.org/content/10.1101/2025.07.31.667916v1?rss=1 Geng, P. X. Hou, J. Guo, J. Jiang, X. Zhu, H. 2025-08-02 doi:10.1101/2025.07.31.667916 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Neural Correlates of Trial Outcome Monitoring during Long-term Learning in Primate Posterior Parietal Cortex ]]> https://biorxiv.org/content/10.1101/2025.08.05.668637v1?rss=1 liu, Z. Jiang, Z. Shi, L. Fang, F. Tang, S. Zhou, Y. 2025-08-07 doi:10.1101/2025.08.05.668637 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Chromosomal Fusions and Evolutionary Forces: Exploring theNeo-Sex Chromosome System of Anolis distichus ]]> https://biorxiv.org/content/10.1101/2025.08.05.668756v1?rss=1 Falvey, C. de Mello, P. Taft, J. Vanerelli, A. Hime, P. Alexander, A. Glor, R. Geneva, A. J. 2025-08-07 doi:10.1101/2025.08.05.668756 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[ Robust CRISPR Screens Identify TPL1 as a Novel Long Noncoding RNA Driving Triple-Negative Breast Cancer Hallmarks ]]> https://biorxiv.org/content/10.1101/2025.08.06.668327v1?rss=1 Elango, R. Ramnarayanan, S. Ozer, L. Y. Coan, M. Yu, Y. Choi, S. Uroda, T. Pulido-Quetglas, C. Schmidt, F. Ouararhni, K. Al Haj Zen, A. Johnson, R. Alajez, N. M. 2025-08-08 doi:10.1101/2025.08.06.668327 Cold Spring Harbor Laboratory Press 2025-08-08 <![CDATA[ Drive, suppression, and escape from suppression of a selfish chromosome ]]> https://biorxiv.org/content/10.1101/2025.08.07.669186v1?rss=1 Ridges, J. T. Bladen, J. Unckless, R. L. Phadnis, N. 2025-08-09 doi:10.1101/2025.08.07.669186 Cold Spring Harbor Laboratory Press 2025-08-09 <![CDATA[ Integrative Structural Modeling of Intrinsically Disordered Regions in a Human HDAC2 Chromatin Remodeling Complex ]]> https://biorxiv.org/content/10.1101/2025.08.08.669391v1?rss=1 Nde, J. Kempf, C. Zimmermann, R. Cesare, J. Zhang, Y. Workman, J. Florens, L. Washburn, M. 2025-08-09 doi:10.1101/2025.08.08.669391 Cold Spring Harbor Laboratory Press 2025-08-09 <![CDATA[ Complement C3 recognition by C3 convertases ]]> https://biorxiv.org/content/10.1101/2025.08.09.669456v1?rss=1 Changhao, J. Xiaoke, Y. Minghui, Z. Ying, T. Xiao, J. 2025-08-09 doi:10.1101/2025.08.09.669456 Cold Spring Harbor Laboratory Press 2025-08-09 <![CDATA[ RESM: Capturing sequence and structure encoding of RNAs by mapped transfer learning from ESM (evolutionary scale modeling) protein language model ]]> https://biorxiv.org/content/10.1101/2025.08.09.669469v1?rss=1 1000-fold speedup compared to MSA-based approaches. RESM provides a robust foundation for deciphering RNA sequence-structure-function relationships, with broad implications for RNA biology. ]]> Zhang, Y. Zhang, H. Li, G.-W. Wang, H. Zhang, X. Hong, X. Zhang, T. Wen, L. Zhao, Y. Jiang, J. Chen, J. Chen, Y. Liu, L. Zhan, J. Zhou, Y. 2025-08-10 doi:10.1101/2025.08.09.669469 Cold Spring Harbor Laboratory Press 2025-08-10 <![CDATA[ Glycemia Shift Pancreatic Islets Rhythmicity via δ-α Cell in vivo, Impairment in Diabetes ]]> https://biorxiv.org/content/10.1101/2025.08.09.669458v1?rss=1 Deng, Y. Fu, Z. Wang, X. Qiao, Y. Wu, X. Yang, S. Zhou, C. Huang, W. Hui, L. Qian, W. Chen, L. Tang, C. Du, Y. Peng, X. Ren, H. 2025-08-12 doi:10.1101/2025.08.09.669458 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ A unified derivative-like dopaminergic computation across valences ]]> https://biorxiv.org/content/10.1101/2025.08.11.669800v1?rss=1 Park, M. Yun, J. Choi, H. Kim, H. R. 2025-08-15 doi:10.1101/2025.08.11.669800 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Lipid Bilayer Membranes with Asymmetrically Distributed LPC and DAG ]]> https://biorxiv.org/content/10.1101/2025.08.13.670206v1?rss=1 Liu, C. Han, Z. Ma, R. Song, C. 2025-08-16 doi:10.1101/2025.08.13.670206 Cold Spring Harbor Laboratory Press 2025-08-16 <![CDATA[ PXDesign: Fast, Modular, and Accurate De Novo Design of Protein Binders ]]> https://biorxiv.org/content/10.1101/2025.08.15.670450v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@2a414aorg.highwire.dtl.DTLVardef@248f85org.highwire.dtl.DTLVardef@4a6afdorg.highwire.dtl.DTLVardef@1b622dd_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ren, M. Sun, J. Guan, J. Liu, C. Gong, C. Wang, Y. Wang, L. Cai, Q. Chen, X. Xiao, W. 2025-08-16 doi:10.1101/2025.08.15.670450 Cold Spring Harbor Laboratory Press 2025-08-16 <![CDATA[ Developmental benzopyrene exposure alters stress hormones, neurotransmitters and behavioral responses of mice dependent on Cyp1 genotype ]]> https://biorxiv.org/content/10.1101/2025.08.13.670196v1?rss=1 Perry, J. Easybuck, T. Feltner, M. Foster, E. G. Kowalski, M. Honaker, A. Clough, K. M. Easton, A. Berling, K. Pham, D. White, A. Wypasek, K. Curran, C. P. 2025-08-18 doi:10.1101/2025.08.13.670196 Cold Spring Harbor Laboratory Press 2025-08-18 <![CDATA[ Intrinsic Reproductive Isolation among Ecologically Divergent Anolis Lizards ]]> https://biorxiv.org/content/10.1101/2025.08.14.670316v1?rss=1 Geneva, A. J. Glor, R. E. 2025-08-19 doi:10.1101/2025.08.14.670316 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ The growth and pathogenesis of Citrobacter rodentium is compromised by disrupted mucin sugar pathways that accumulate N-acetylglucosamine 6-phosphate ]]> https://biorxiv.org/content/10.1101/2025.08.18.670787v1?rss=1 Huang, Z. C. Mslati, M. A. Ma, C. Yang, H. Liang, Q. Crowley, S. Dyer, R. Ng, I. Yu, H. Vallance, B. A. 2025-08-19 doi:10.1101/2025.08.18.670787 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ Phosphate limitation triggers Fe3+-dependent polymyxin resistance in Enterobacteriaceae ]]> https://biorxiv.org/content/10.1101/2025.08.18.670855v1?rss=1 ZHANG, G. Deng, Z. JIANG, J. WANG, M. Wang, X. Liu, X. Yan, A. 2025-08-19 doi:10.1101/2025.08.18.670855 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ The effects of thermal deterioration on the life history traits of Daphnia magna ]]> https://biorxiv.org/content/10.1101/2025.08.16.670526v1?rss=1 Petkovic, N. Unlu, T. Saglam, I. K. 2025-08-21 doi:10.1101/2025.08.16.670526 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ FAVABEAN and FALAPhyl: Open-Source Pipelines for Scalable 16s rRNA Microbiome Data Processing and Visualization ]]> https://biorxiv.org/content/10.1101/2025.08.19.670115v1?rss=1 Faridoun, A. Carvalho, R. Smith, J. Gibb, A. Jain, L. Zhang, A. Sran, A. Redmond, J. Malik, M. Z. Gibson, M. Haider, A. Rekhi, U. Bhagirath, A. Rock, L. D. Altabtbaei, K. 2025-08-24 doi:10.1101/2025.08.19.670115 Cold Spring Harbor Laboratory Press 2025-08-24 <![CDATA[ Multigram-scale stereoselective synthesis of neurosteroid isomers by gut microbial isolates using plant biomass-derived medium ]]> https://biorxiv.org/content/10.1101/2025.08.20.671209v1?rss=1 95% progesterone conversion into target neurosteroid isomers. The inherent stereoselectivity of these whole-cell biotransformations bypasses downstream chiral chromatographic separation, enabling pharmaceutical-grade product recovery through a simple open-column purification. Compared to using peptone-yeast-glucose media for whole-cell biotransformation, MOM reduced production costs by 90% and carbon footprint by 95% that embodies sustainable bioeconomy principles in pharmaceutical biotechnology. Technology Readiness BoxWe argue that this gut microbiota-derived neurosteroid bioproduction technology has reached a Technology Readiness Level (TRL) of 4, having been validated in laboratory environments with the demonstrated multigram-scale synthesis of high-purity neurosteroids. The platform integrates stereoselective bacterial isolates (Holdemania filiformis, Clostridium innocuum, and Hungatella effluvii) with a sustainable plant-based fermentation medium (molasses-okara medium), achieving >90% progesterone conversion efficiency, >99.9% stereochemical purity, and the successful production of 0.7-0.9 g of neurosteroids per gram of progesterone across multiple 1 L fed-batch fermentations. Compared with conventional chemical synthesis approaches that require expensive chiral catalysts and multi-step purification, this microbial platform offers inherent stereoselectivity while eliminating animal-derived media components. Despite these advantages, several challenges remain for industrial implementation, including scale-up validation beyond laboratory conditions, optimization of anaerobic bioprocess control at pilot scale, and ensuring consistent performance under variable industrial feedstock conditions. Addressing these issues will require pilot-scale demonstration (10-50 L bioreactors), process robustness validation, and supply chain development for plant-based feedstocks. Regulatory pathway development will also be essential for pharmaceutical applications, particularly establishing precedents for gut microbiota-derived therapeutic compounds under existing cGMP frameworks HighlightsO_LIIdentification of gut bacteria for stereoselective synthesis of neurosteroid isomers (isopregnanolone, epipregnanolone, pregnanolone) with >99% chiral purity C_LIO_LISustainable plant biomass-based medium replacing animal-derived components for whole-cell progesterone biotransformation C_LIO_LIMulti-gram scale production of progestogenic neurosteroids and one-step-open-column purification bypassing chiral chromatographic separation C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/671209v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@11147b0org.highwire.dtl.DTLVardef@1799d64org.highwire.dtl.DTLVardef@14c33deorg.highwire.dtl.DTLVardef@1e14e21_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gicana, R. G. Wang, P.-H. Huang, Y.-H. Huang, M.-H. Wu, T.-Y. Lai, Y.-L. Brandon-Mong, G.-J. Wei, Y. Yeo, W. W. Z. Ng, I.-S. Chiang, Y.-R. 2025-08-24 doi:10.1101/2025.08.20.671209 Cold Spring Harbor Laboratory Press 2025-08-24 <![CDATA[ High-throughput 3D super-resolution ultrasound imaging ]]> https://biorxiv.org/content/10.1101/2025.08.20.671215v1?rss=1 Zhao, W. Wang, N. Han, Z. Xu, X. Ma, X. Zhou, T. Gui, J. Liu, Y. Liu, Q. Qu, L. Liu, W. Ding, X. Liu, X. Ta, D. Tan, J. Chen, L. Yao, J. Li, H. 2025-08-24 doi:10.1101/2025.08.20.671215 Cold Spring Harbor Laboratory Press 2025-08-24 <![CDATA[ Capturing trophectoderm-like stem cells enables step-wisely remodeling of placental development ]]> https://biorxiv.org/content/10.1101/2025.08.25.672082v1?rss=1 Jia, X. Peng, B. Zhao, H. Wang, C. Tao, W. Du, P. 2025-08-25 doi:10.1101/2025.08.25.672082 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ A global map of wood density ]]> https://biorxiv.org/content/10.1101/2025.08.25.671920v1?rss=1 Fischer, F. J. Chave, J. Zanne, A. Jucker, T. Fajardo, A. Fayolle, A. de Lima, R. A. F. Vieilledent, G. Beeckman, H. Hubau, W. De Mil, T. Wallenus, D. Aldana, A. M. Alvarez-Davila, E. Alves, L. F. Apgaua, D. M. G. Arcanjo, F. Bastin, J.-F. Bilous, A. Birnbaum, P. Blyshchyk, V. Borah, J. Boukili, V. Camarero, J. J. Casas, L. Cazzolla Gatti, R. Chambers, J. Q. Chimbioputo Fabiano, E. Choat, B. Cifuentes, E. Conti, G. Coomes, D. Cornwell, W. Dar, J. A. Das, A. K. Dobler, M. Dougabka, D. Edwards, D. P. Eggli, U. Evans, R. Falster, D. Fearnside, P. Flores, 2025-08-28 doi:10.1101/2025.08.25.671920 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ Pirfenidone treatment attenuates fibrosis in autosomal dominant polycystic kidney disease ]]> https://biorxiv.org/content/10.1101/2025.08.25.672225v1?rss=1 Remadevi, V. Jamadar, A. Varghese, M. M. Gunewardena, S. Wallace, D. Rao, R. 2025-08-29 doi:10.1101/2025.08.25.672225 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ Neuroprotective Effects of Nigella sativa Extract in a Rat model of Propionic Acid-Induced Autism Spectrum Disorder ]]> https://biorxiv.org/content/10.1101/2025.08.26.672514v1?rss=1 Alshahrani, S. M. Kadasah, S. F. Jan, H. Menaa, F. 2025-08-31 doi:10.1101/2025.08.26.672514 Cold Spring Harbor Laboratory Press 2025-08-31 <![CDATA[ Nucleosome unwrapping and PARP1 allostery drive affinities for chromatin and DNA breaks ]]> https://biorxiv.org/content/10.1101/2025.08.29.673134v1?rss=1 Schaich, M. A. Weaver, T. M. Rakowski, J. A. Roginskaya, V. Leary, L. P. van den Berg, A. A. Iwasa, J. H. Freudenthal, B. D. Van Houten, B. 2025-08-31 doi:10.1101/2025.08.29.673134 Cold Spring Harbor Laboratory Press 2025-08-31 <![CDATA[ Regulatory Role for Tumor Suppressor REST on Estrogen Receptor (ESR1) Expression and Leiomyoma Pathophysiology ]]> https://biorxiv.org/content/10.1101/2025.08.29.673140v1?rss=1 Bird, S. G. Gunewardena, S. Cloud, A. S. Ganeshkumar, S. Chennathukuzhi, V. M. 2025-08-31 doi:10.1101/2025.08.29.673140 Cold Spring Harbor Laboratory Press 2025-08-31 <![CDATA[ Unveiling Eukaryotic Membrane Proteins in High Resolution Using Peptide Solubilization ]]> https://biorxiv.org/content/10.1101/2025.08.27.672771v1?rss=1 Zang, J. Shi, Y. Tao, W. Liu, X. Guo, W. Chen, L. 2025-09-01 doi:10.1101/2025.08.27.672771 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ Extracellular Matrix-Guided Tumor Stratification and Network Models Reveal Clinical Molecular Grades ]]> https://biorxiv.org/content/10.1101/2025.08.29.672994v1?rss=1 Dansik, A. Sarica, S. Ozturk, E. Tuncbag, N. 2025-09-03 doi:10.1101/2025.08.29.672994 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Targeting the TEA DNA binding Domain of TEAD with a Peptide Inhibitor TEAi Suppresses Oncogenic Transcription and Tumor Growth ]]> https://biorxiv.org/content/10.1101/2025.08.31.672803v1?rss=1 Cao, L. Wu, S. Xiong, H. Lin, X. 2025-09-03 doi:10.1101/2025.08.31.672803 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ High-resolution spatial analysis reveals pregnenolone metabolism as a potential target for immuno-suppressive microenvironment of BRAF mutant colorectal cancer ]]> https://biorxiv.org/content/10.1101/2025.09.01.673435v1?rss=1 Wang, X. Zhao, Z. Liu, L. Cheng, J. Ba, Y. 2025-09-03 doi:10.1101/2025.09.01.673435 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Enhanced Neutralization of Japanese Encephalitis Virus Using an Engineered VL Double-Domain ]]> https://biorxiv.org/content/10.1101/2025.09.03.673967v1?rss=1 Marweslie, M. Rini, I. A. Kiba, M. Ayun, R. Q. Lee, T.-K. Lee, S. 2025-09-03 doi:10.1101/2025.09.03.673967 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Structural Role of Stomatin in Organizing Functional Membrane Microdomains ]]> https://biorxiv.org/content/10.1101/2025.08.30.673307v1?rss=1 Yan, L. Zhou, X. Li, M. Wang, C. Xiao, B. Xi, P. Zou, P. Gao, N. 2025-09-04 doi:10.1101/2025.08.30.673307 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Update on the reproduction and interpretation of DIANA fMRI ]]> https://biorxiv.org/content/10.1101/2025.08.31.673005v1?rss=1 Keum, J.-Y. Park, S. Chun, H. Kim, D. Park, J.-Y. 2025-09-04 doi:10.1101/2025.08.31.673005 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ An integrated in silico-in vitro workflow for discovering high-affinity, selective antibodies to the KRAS(G12D)-MHC I complex ]]> https://biorxiv.org/content/10.1101/2025.08.31.673313v1?rss=1 Ahn, S. Oh, T.-S. Suh, S. Jeon, J.-y. Lah, S. Ryu, K. Kim, H. Lee, E. G. Lee, H. Lee, J. Kim, D.-K. Ku, B. M. Jung, W. Ahn, M.-J. Jung, J. U. Kim, Y.-S. Oh, B.-H. Jeong, B.-S. 2025-09-04 doi:10.1101/2025.08.31.673313 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ The Global Canopy Atlas: analysis-ready maps of 3D structure for the world's woody ecosystems ]]> https://biorxiv.org/content/10.1101/2025.08.31.673375v1?rss=1 Fischer, F. J. Morgan, B. Jackson, T. Chave, J. Coomes, D. Cushman, K. Dalagnol, R. Dalponte, M. Duncanson, L. Saatchi, S. Seidl, R. Sterenczak, K. Laurin, G. V. Adu-Bredu, S. Aguirre-Gutierrez, J. Antonielli, B. Armston, J. D. de Assis, M. L. Barbier, N. Burt, A. Cesar, R. G. Cervenka, J. Coops, N. Cullen, L. Dalling, J. W. Davies, A. Demol, M. Ebenbeck, J. Fassnacht, F. Fatoyinbo, L. Garcia, M. Gasparri, N. I. Gobakken, T. Goodbody, T. R. H. Görgens, E. B. Gorum, T. Gosper, C. Guan, H. Heiskanen, J. Heurich, M. Hobi, M. Höfle, B. Hooijer, A. Huth, 2025-09-04 doi:10.1101/2025.08.31.673375 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Structure, dynamics, and processing of 8oxoG:A in the nucleosome ]]> https://biorxiv.org/content/10.1101/2025.09.02.673820v1?rss=1 Vito, A. F. Ling, J. A. Ferrara, J. C. Jacques, C. S. Gillet, N. Gonzalez-Aleman, R. Qiu, Y. Hashemian, M. Trasvina-Arenas, C. H. David, S. S. Delaney, S. Bignon, E. Freudenthal, B. D. 2025-09-05 doi:10.1101/2025.09.02.673820 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Memorability of Images Positively Influences Associative Memory Retention ]]> https://biorxiv.org/content/10.1101/2025.09.03.674110v1?rss=1 Wang, Y. LiMeixuan, M. Yang, L. Tan, L. Li, T. Xiao, H. Deng, Y. Zhang, Y. 2025-09-05 doi:10.1101/2025.09.03.674110 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Sex differences in the developing human cortex intersect with genetic risk of neurodevelopmental disorders ]]> https://biorxiv.org/content/10.1101/2025.09.04.674293v1?rss=1 Hennick, K. Sui, Y. Karunakaran, D. Nicolella, A. Leonard, R. Meyer-Schuman, R. Berk-Rauch, H. Wang, T. Chakravarti, A. Zoghbi, H. Y. Eichler, E. E. Nowakowski, T. J. 2025-09-05 doi:10.1101/2025.09.04.674293 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ The Rapid Anatomics Tool (RAT): A low-cost root anatomical phenotyping pipeline reveals changes in root anatomy along the root axis ]]> https://biorxiv.org/content/10.1101/2025.09.05.674482v1?rss=1 Jones, D. H. Baca Cabrera, J. C. Behrend, D. Wells, D. M. Swift, J. F. Atkinson, J. Lobet, G. Hanlon, M. T. Schneider, H. M. 2025-09-07 doi:10.1101/2025.09.05.674482 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ A neuroendocrine principle: Pancreatic islets actively shape sympathetic innervation ]]> https://biorxiv.org/content/10.1101/2025.09.03.673215v1?rss=1 Li, D.-X. Luo, J.-M. Wang, J.-J. Qian, Y.-Z. Abudujilile, D. Mutailifu, M. Yang, T. Hong, Y.-X. Shi, W.-T. Ma, X.-Y. Ye, Q. Zhu, L. Li, H. Yang, X.-M. Zhang, Y.-L. Jiang, S.-H. Yu, Y.-Q. Wang, K. Li, J. Li, Q. Hu, L.-P. Zhang, X.-L. Zhang, Z.-G. 2025-09-09 doi:10.1101/2025.09.03.673215 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ Framework for analyzing MAE-derived immunopeptidomes from cell lines with shared HLA haplotypes ]]> https://biorxiv.org/content/10.1101/2025.09.05.674575v1?rss=1 Chan, Q. W. T. Luehr, T. Kuan, C.-W. Song, L. Yu, H. Foster, L. J. 2025-09-10 doi:10.1101/2025.09.05.674575 Cold Spring Harbor Laboratory Press 2025-09-10 <![CDATA[ Temporal dynamics of CNS cholesterol esters correlate with demyelination and remyelination ]]> https://biorxiv.org/content/10.1101/2025.09.06.674663v1?rss=1 De Silva Mohotti, N. Williams, J. M. Binjawadagji, R. Kobayashi, H. Dedunupitiya, D. Petersen, J. M. Garcia, A. Hartley, M. D. 2025-09-11 doi:10.1101/2025.09.06.674663 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Single-cell transcriptomic profiling of C. elegans Q neuroblast lineage during migration and differentiation ]]> https://biorxiv.org/content/10.1101/2025.09.09.675151v1?rss=1 Teixeira, F. L. Sanderson, B. Hackett, J. L. Lundquist, E. A. 2025-09-11 doi:10.1101/2025.09.09.675151 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Localized Space Coding and Phase Coding Complement Each Other to Achieve Robust and Efficient Spatial Representation ]]> https://biorxiv.org/content/10.1101/2025.09.07.674775v1?rss=1 Chu, T. Wu, Y. Qiu, W. Jiang, Z. Burgess, N. HONG, B. WU, S. 2025-09-12 doi:10.1101/2025.09.07.674775 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ Distinct Implicit Contributions to Action Selection and Action Execution in Sensorimotor Adaptation ]]> https://biorxiv.org/content/10.1101/2025.09.12.675892v1?rss=1 Wang, T. Lam, T. Taylor, J. A. Ivry, R. B. 2025-09-13 doi:10.1101/2025.09.12.675892 Cold Spring Harbor Laboratory Press 2025-09-13 <![CDATA[ Characterization and engineering of highly efficient Cas12j genome editors ]]> https://biorxiv.org/content/10.1101/2025.09.16.676532v1?rss=1 Gundra, S. R. Jiang, W. Aouida, M. Wang, Q. Kazlak, A. M. Elbehery, A. H. A. Saleh, A. Masood, M. Ghouneimy, A. Mahfouz, M. 2025-09-16 doi:10.1101/2025.09.16.676532 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Kat5 cKO Biological Domain Signatures Align with Human Alzheimer Disease ]]> https://biorxiv.org/content/10.1101/2025.09.13.676046v1?rss=1 Cary, G. A. Young, J. E. Rose, S. E. Frankowski, H. Darvas, M. Bothwell, M. Jayadev, S. Reid, A. N. Greenwood, A. Levey, A. Leal, K. Carter, G. W. Wiley, J. C. 2025-09-17 doi:10.1101/2025.09.13.676046 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Sampling bias obscures biodiversity patterns, reveals data gaps in priority conservation areas: a call for improved documentation ]]> https://biorxiv.org/content/10.1101/2025.09.13.676052v1?rss=1 Pitogo, K. M. E. Meneses, C. G. Decena, S. C. P. Supsup, C. E. Som, H. E. Bernstein, J. M. Chan, K. O. Herr, M. W. Brown, R. M. 2025-09-17 doi:10.1101/2025.09.13.676052 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Hepatic ketogenic insufficiency blunts exercise-induced energy expenditure and alters mitochondrial proteins in skeletal muscle. ]]> https://biorxiv.org/content/10.1101/2025.09.16.676620v1?rss=1 Davis, X. C. McCoin, C. S. Salathe, S. F. Franczak, E. Allen, J. A. Queatham, E. D. Fulghum, K. L. Puchalska, P. Crawford, P. A. Thyfault, J. P. Morris, E. M. M. 2025-09-18 doi:10.1101/2025.09.16.676620 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Convergent utilization of APN receptor by hedgehog merbecoviruses ]]> https://biorxiv.org/content/10.1101/2025.09.16.676546v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@1ea334aorg.highwire.dtl.DTLVardef@cd53bforg.highwire.dtl.DTLVardef@352102org.highwire.dtl.DTLVardef@a1eed_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Liu, P. Zhu, Q. Liu, J. Ma, Z. Yu, Y. Liu, C. Ma, C. Si, J. Yang, X. Huang, M. Sun, Y. Yu, X. Sun, Y. Liu, T. Yu, L. Wang, Q. Li, J. Cao, Y. Wang, X. Yan, H. 2025-09-19 doi:10.1101/2025.09.16.676546 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ A cross model spatial and single-cell atlas reveals the conserved involvement of osteopontin in polycystic kidney disease ]]> https://biorxiv.org/content/10.1101/2025.09.17.676846v1?rss=1 Miller, S. J. Zhong, H. Wu, W. Cordova, A. M. Smith, M. E. Yashchenko, A. Li, Z. Jafree, D. J. Zimmerman, C. N. DeVette, C. I. Do, V. Hignite, M. Darby, I. G. Ahmed, K. Park, Y. Nusrat, F. Maryam, B. Lu, S. Li, X. Gipson, J. R. Li, X. Long, D. A. Weiser-Evans, M. C. Yoder, B. K. Cowley, B. D. Hopp, K. Stubbs, J. Ma, Q. Ma, A. Zimmerman, K. A. 2025-09-20 doi:10.1101/2025.09.17.676846 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Longitudinal analysis of bacterial community dynamics in normal hospital ward following patient occupancy ]]> https://biorxiv.org/content/10.1101/2025.09.18.677220v1?rss=1 An, L. Liu, X. Li, X. Chu, Y. Li, Q. Sun, X. Chu, J. Nie, Y. 2025-09-21 doi:10.1101/2025.09.18.677220 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Candida albicans infiltrates colon and rectal cancers causing therapeutic resistance and decreased survival ]]> https://biorxiv.org/content/10.1101/2025.09.19.677366v1?rss=1 Grencewicz, D. J. Loncar, A. Ferrandon, S. Chatterjee, D. Kreamer, M. Mehra, Y. Carson, A. Hoyd, R. Jahanbakhshi, S. Choueiry, F. Anderson, M. Z. Benej, M. Bosch, D. E. Zhu, J. Wu, J. Pallerla, A. Bocklage, T. McCarter, M. Tarhini, A. Salhia, B. Moskaluk, C. Riedlingeer, G. Yao, S. Masood, A. Hardikar, S. Ilozumba, M. Ulrich, C. M. Chan, C. H. F. Shiver, C. George, S. Mudaranthakam, D. P. Churchman, M. Rounbehler, R. Chambers, L. Carbone, D. Kalady, M. F. Denko, N. Spakowicz, D. 2025-09-21 doi:10.1101/2025.09.19.677366 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Experimental demonstration of daisy chain gene drive and modelling of daisy suppression systems ]]> https://biorxiv.org/content/10.1101/2025.09.20.677490v1?rss=1 Guo, J. Chen, W. Champer, J. 2025-09-21 doi:10.1101/2025.09.20.677490 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Spontaneous mutant in threespine stickleback connects endosome trafficking disorders and inflammatory bowel diseases via changes in the gut microbiome ]]> https://biorxiv.org/content/10.1101/2025.09.20.677535v1?rss=1 Beck, E. A. Smith, C. A. Currey, M. C. Small, C. M. Bohannan, B. J. Cresko, W. A. 2025-09-21 doi:10.1101/2025.09.20.677535 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[ A nuclear pore complex component HOS1 mediates UV-B light-induced UVR8 nuclear localization for activating HY5 cascade in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2025.09.22.677739v1?rss=1 Han, S.-H. Ji, M. G. Kim, W.-Y. Park, C.-M. Jung, J.-H. 2025-09-23 doi:10.1101/2025.09.22.677739 Cold Spring Harbor Laboratory Press 2025-09-23 <![CDATA[ Crystal Structure of 3-Hydroxypropionyl-CoA Synthetase (ADP-forming) from Nitrosopumilus maritimus ]]> https://biorxiv.org/content/10.1101/2025.09.22.677778v1?rss=1 Johnson, J. A. Tosun, B. Yilmaz, M. Tolar, B. Yoshikuni, Y. Francis, C. Doukov, T. Yokoi, S. Wakatsuki, S. DeMirci, H. 2025-09-24 doi:10.1101/2025.09.22.677778 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ A neural circuit for female-specific defensive homeostasis in risk assessment ]]> https://biorxiv.org/content/10.1101/2025.09.23.677968v1?rss=1 Liu, X. Huang, H. Feng, X. Li, X. Ye, J. Yang, H. Liu, J. Liang, Z. Guo, Z. Cai, R. Cai, S. Li, Y. Wu, Z. Wang, L. Wang, F. 2025-09-24 doi:10.1101/2025.09.23.677968 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ Augmented prediction of multi-species protein--RNA interactions using evolutionary conservation of RNA-binding proteins ]]> https://biorxiv.org/content/10.1101/2025.09.27.678913v1?rss=1 He, J. Zhou, T. Hu, L.-F. Jiao, Y. Wang, J. Yan, S. Jia, S. Chen, Q. Wang, Y. Yang, Y. T. Sun, L. 2025-09-28 doi:10.1101/2025.09.27.678913 Cold Spring Harbor Laboratory Press 2025-09-28 <![CDATA[ Macrophage-derived WNT regulates tumor immune microenvironment to reduce colitis-associated colon cancer ]]> https://biorxiv.org/content/10.1101/2025.09.27.679002v1?rss=1 Bhanja, P. Chugh, R. M. Rehman, S. Krepel, S. Mitra, A. Gupta-Saraf, P. Diaz-Olea, X. Pathak, H. Kasi, A. Saha, S. 2025-09-29 doi:10.1101/2025.09.27.679002 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Co-Evolutionary Characterization of PBP2 as the Predominant Siderophore Recognizer in Diverse Gram-Positive Bacteria ]]> https://biorxiv.org/content/10.1101/2025.09.29.679136v1?rss=1 Yu, L. Xiong, G. Li, Z. 2025-09-29 doi:10.1101/2025.09.29.679136 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Proton FLASH Exposure Preserves Gut Commensal Microbiomes and Spares Intestinal Stem Cells ]]> https://biorxiv.org/content/10.1101/2025.09.28.679072v1?rss=1 Chugh, R. M. Setianegara, J. Schueddig, E. Lin, Y. Bhanja, P. Rehman, S. Krepel, S. Koestler, D. Chen, R. C. Cook, K. L. Saha, S. 2025-09-30 doi:10.1101/2025.09.28.679072 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ Enhancing protein structure prediction accuracy by prioritizing important residues using protein language models ]]> https://biorxiv.org/content/10.1101/2025.09.28.679101v1?rss=1 cui, q. Liu, Y. Kang, B. 2025-09-30 doi:10.1101/2025.09.28.679101 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[ Comprehensive benchmarking with guidelines for analyzing transposable element-derived RNA expression ]]> https://biorxiv.org/content/10.1101/2025.09.30.679421v1?rss=1 She, J. Wang, J. Yang, E. 2025-10-01 doi:10.1101/2025.09.30.679421 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ APOE4 carriers resistant to cognitive decline show unique relationships between cerebrovascular response to exercise and dual-task cognitive-balance performance ]]> https://biorxiv.org/content/10.1101/2025.09.30.679544v1?rss=1 0.187). CONCLUSIONSCognitively-normal APOE4 carriers with preserved cognitive-balance dual-task function represent exceptions that may model aging resilience mechanisms. The unique cerebrovascular-behavioral relationships suggest that maintaining cerebrovascular function provides preliminary support for neuromotor and neurocognitive resilience to dual-task challenges in genetically vulnerable populations. ]]> Palmer, J. A. Billinger, S. 2025-10-01 doi:10.1101/2025.09.30.679544 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Neural basis of social-categorization function of language ]]> https://biorxiv.org/content/10.1101/2025.09.30.679494v1?rss=1 Zheng, G. Han, S. 2025-10-02 doi:10.1101/2025.09.30.679494 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Adipose Tissue Overexpression of Nicotinamide Phosphoribosyltransferase Prevents Metabolic Dysfunction in Obese Mice ]]> https://biorxiv.org/content/10.1101/2025.09.30.679563v1?rss=1 Ferguson, D. Gadson, E. I. Markan, K. R. Yoshino, J. Lin, M. Habibi, M. Tiash, S. Cui, X. Kouranova, E. Franczak, E. Guo, Q. Kealing, J. Pietka, T. A. Liss, K. H. H. Thyfault, J. P. Patti, G. J. Finck, B. N. Crewe, C. Mukherjee, S. 2025-10-02 doi:10.1101/2025.09.30.679563 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Arginine methyltransferase PRMT1 equipoises trophoblast development to prevent early pregnancy loss ]]> https://biorxiv.org/content/10.1101/2025.09.30.679604v1?rss=1 Dasgupta, P. Kumar, R. Ray, S. Roy, N. Niloy, A. J. VALLAKATI, M. Marsh, C. Arnold, S. J. Paul, S. 2025-10-02 doi:10.1101/2025.09.30.679604 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Association of cytochrome c oxidase dysfunction with amyloidosis in Alzheimer's disease and patient-derived cerebral organoids ]]> https://biorxiv.org/content/10.1101/2025.10.01.679889v1?rss=1 Chen, Y. Wang, T. Tian, J. Ashraf, K. Guo, L. Ma, T. Du, H. 2025-10-02 doi:10.1101/2025.10.01.679889 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ PM2.5 Exposure Facilitates SARS-CoV-2 Infection through ACE2/TMPRSS2 Regulation and Suppression of Anti-Viral Response ]]> https://biorxiv.org/content/10.1101/2025.10.02.679237v1?rss=1 Rajabi, H. Kayalar, O. Esken, G. Can, F. Bayram, H. 2025-10-03 doi:10.1101/2025.10.02.679237 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ The Critical and Unexpected Role of a Methyl Group in Interleukin-17A Inhibitors ]]> https://biorxiv.org/content/10.1101/2025.10.02.680113v1?rss=1 View larger version (13K): org.highwire.dtl.DTLVardef@3f31adorg.highwire.dtl.DTLVardef@d6873forg.highwire.dtl.DTLVardef@494af7org.highwire.dtl.DTLVardef@1d8b7eb_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Deng, X. Li, B. Chen, H. Zhou, G. Lv, W. Tian, W. Su, Y. Zhou, Y. 2025-10-04 doi:10.1101/2025.10.02.680113 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ A GPCR signaling pathway in insect odor detection ]]> https://biorxiv.org/content/10.1101/2025.10.03.680299v1?rss=1 Takagi, S. Abuin, L. Mermet, J. Lee, D. Benton, R. 2025-10-04 doi:10.1101/2025.10.03.680299 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ TWIST1 Modulates Cilia Length, Endocytic Vesicle Dynamics, and Cell-Cell Junctions during Neural Tube Morphogenesis ]]> https://biorxiv.org/content/10.1101/2025.10.03.680308v1?rss=1 Thomas, D. Martinez, B. M. Lalwani, Z. Pham, V. Elmeniawi, M. N. Tran, A. Xu, J. Saadi, I. Fakhouri, W. D. 2025-10-04 doi:10.1101/2025.10.03.680308 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ E- and N-cadherin drive hepatic polarity and lumen elongation via opposing effects on RhoA activity ]]> https://biorxiv.org/content/10.1101/2025.10.06.680681v1?rss=1 Hayase, J. Yang, L. Zhou, Y.-H. Wang, K. Xu, C.-R. Bi, E. 2025-10-06 doi:10.1101/2025.10.06.680681 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Islet-intrinsic sex differences in inflammatory signaling contribute to autoimmune diabetes susceptibility ]]> https://biorxiv.org/content/10.1101/2025.10.06.680429v1?rss=1 Webster, K. L. Puente, A. A. Enriquez, J. R. Sarkar, S. Nakayasu, E. S. Webb-Robertson, B.-J. M. Bramer, L. M. Figatner, K. Pratuangtham, S. Wu, W. Evans-Molina, C. Tse, H. M. Roy, S. Piganelli, J. D. Hammes, S. R. Tersey, S. A. Mirmira, R. G. 2025-10-07 doi:10.1101/2025.10.06.680429 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Human brains construct individualized global rankings from identical few-shot local learning ]]> https://biorxiv.org/content/10.1101/2025.10.06.680667v1?rss=1 Liu, D. Wang, M. Luo, H. 2025-10-07 doi:10.1101/2025.10.06.680667 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ A Genome-Based Pipeline for Digital Siderophore Typing in Pseudomonas Iron-Interaction Network ]]> https://biorxiv.org/content/10.1101/2025.10.07.680951v1?rss=1 Qu, Z. Shao, Y. Zhang, A. Wang, L. He, R. Ma, L. Z. Gu, S. Li, Z. 2025-10-08 doi:10.1101/2025.10.07.680951 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Finding the perfect promoter: Correlating single-cell transcriptome data with gene drive performance ]]> https://biorxiv.org/content/10.1101/2025.10.08.681126v1?rss=1 Wu, Y. Xia, Y. Yao, Z. Chen, W. Jia, X. Liang, N. Champer, J. 2025-10-08 doi:10.1101/2025.10.08.681126 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ PPARG directs trophoblast cell fate and establishment of the uterine-placental interface ]]> https://biorxiv.org/content/10.1101/2025.10.08.681177v1?rss=1 Dominguez, E. M. Irusta, A. M. IQBAL, K. Chen, K. Finlinson, A. Parrish, M. Okae, H. Arima, T. Tuteja, G. Soares, M. J. 2025-10-08 doi:10.1101/2025.10.08.681177 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ A family of lethal exotoxins defined by cell entry via the Attractin receptor ]]> https://biorxiv.org/content/10.1101/2025.10.08.681221v1?rss=1 Viswanatha, R. Lee, D. Robins, W. P. Mameli, E. Hu, Y. Kim, A.-R. Hashmi, Y. Nishida, H. Prakash, G. Butnaru, M. Churchman, L. S. Mohr, S. Mekalanos, J. Perrimon, N. 2025-10-08 doi:10.1101/2025.10.08.681221 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Amelioration of symptomatic Alzheimer's Disease after selective impairment of p75NTR function in adult forebrainexcitatory neurons ]]> https://biorxiv.org/content/10.1101/2025.10.08.681148v1?rss=1 Li, X. Xie, M. Ibanez, C. F. 2025-10-09 doi:10.1101/2025.10.08.681148 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ The Androgen Receptor and MYC synergise to modulate the synthesis of Siglec-7 ligands in prostate cancer ]]> https://biorxiv.org/content/10.1101/2025.10.15.682547v1?rss=1 Duxfield, A. Garnham, R. Hutton, E. Dowle, A. Wills, J. Luzzi, S. Nelson, R. Lishman-Walker, E. Magee, R. Buskin, A. Hepburn, A. C. Tekoglu, E. Maloney-Friar, K. Frame, F. Maitland, N. Hedley, A. Henderson, H. McCullough, B. Gowardhan, B. Sahadevan, K. McCracken, S. Gaughan, L. Heer, R. Robson, C. N. Coffey, K. Lack, N. A. Signoret, N. Fascione, M. Scott, E. 2025-10-16 doi:10.1101/2025.10.15.682547 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ 3' Nucleotide Asymmetry Directs miRNA Strand Selection ]]> https://biorxiv.org/content/10.1101/2025.10.15.682714v1?rss=1 Medley, J. C. Kurosu Moriya, S. Ouyang, H. Crawshaw, H. Zhang, S. Y. Panzade, G. Sydzyik, W. J. Sydzyik, J. T. Bhandari, M. Hammell, C. M. Zinovyeva, A. 2025-10-16 doi:10.1101/2025.10.15.682714 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ A Novel Unorthodox Dimeric Primary Enoyl-CoA Reductase Structure ]]> https://biorxiv.org/content/10.1101/2025.10.17.683039v1?rss=1 Kulakman, C. Mathews, I. Yoshikun, Y. Wakatsuki, S. DeMirci, H. 2025-10-17 doi:10.1101/2025.10.17.683039 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ A systematic comparison of cooperation and coordination across behavioural, psychological, and neural scales ]]> https://biorxiv.org/content/10.1101/2025.10.17.683048v1?rss=1 Li, Y. Wang, X. Dong, W. Liu, L. Yang, Y. Zheng, Y. Zhen, Y. Zheng, H. tang, s. 2025-10-17 doi:10.1101/2025.10.17.683048 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ The Impact of a Western Diet with High Salt on Metabolic Outcomes in Male C57bl/6J Mice ]]> https://biorxiv.org/content/10.1101/2025.10.17.683134v1?rss=1 Ponte, M. Prom, J. C. Yerrathota, S. Devkota, P. Ha, L. Morris, E. M. M. Lutkewitte, A. J. 2025-10-17 doi:10.1101/2025.10.17.683134 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Protein large language model assisted one-to-one gene homology mapping in cross-species single-cell transcriptome integration ]]> https://biorxiv.org/content/10.1101/2025.10.17.683009v1?rss=1 Kuang, Z.-Y. Sun, Y.-C. Wei, N.-N. Wu, H.-J. 2025-10-18 doi:10.1101/2025.10.17.683009 Cold Spring Harbor Laboratory Press 2025-10-18 <![CDATA[ Divergent roles of DNA methylation, TRIM28, and p53 surveillance in human embryonic and trophoblast stem cells ]]> https://biorxiv.org/content/10.1101/2025.10.19.683051v1?rss=1 Pastor, W. A. Saini, D. Katz, M. S. Beck, S. G. A. Ireland, T. E. Ray, S. Niloy, A. J. Mazloomnejad, R. Fleming, A. Vetrici, S. C. Cinkornpumin, J. K. Sack, T. Duhamel, S. Slim, R. Park, M. Frost, J. M. Paul, S. Martin, R. C. 2025-10-19 doi:10.1101/2025.10.19.683051 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ Predicting SARS-CoV-2 evolution dynamics with spatiotemporal resolution by DMS-empowered protein language model ]]> https://biorxiv.org/content/10.1101/2025.10.17.683094v1?rss=1 Yang, S. Luo, X. Luo, J. Jian, F. Cao, Y. 2025-10-20 doi:10.1101/2025.10.17.683094 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ RNA viruses in water shape the viromes of shrimp and fish in aquaculture systems ]]> https://biorxiv.org/content/10.1101/2025.10.19.683331v1?rss=1 1,000 RPM) across culture stages. Viral abundance in aquatic animals was strongly correlated with that in water, and the temporal trajectories of the 16 most abundant viruses were closely synchronized between water and shrimp. Furthermore, 337 virus species were shared among shrimp and two fish species, of which 309 were present in water. These findings demonstrated that RNA viruses in water shape the composition and dynamics of aquatic animal viromes, underscoring the importance of water virome surveillance and management for disease prevention in shrimp aquaculture. ]]> Zhou, D. Xing, C. Liu, S. Liu, Z. Liu, Y. Wu, Y. Su, H. Xian, D. Guo, G. Cheng, J. Xu, M. Chen, M. Han, P. Wu, C. Zeng, J. He, X. Pang, J. Lu, Q. Zhang, C. Wang, T. Zhang, C. Xu, Y. Tang, X. Zhang, S. Deng, Z. Zeng, S. Weng, S. Shi, M. He, J. 2025-10-20 doi:10.1101/2025.10.19.683331 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ HLA-DQ2/8 genotype imprints strain-level gut microbiome and constrains pantothenate availability in healthy adults ]]> https://biorxiv.org/content/10.1101/2025.10.20.683361v1?rss=1 Kan, C. Hu, M. Wang, N. Zhang, Q. Chaihu, L. Wang, C. Lu, W. Wang, G. Li, M. Zhang, L. 2025-10-20 doi:10.1101/2025.10.20.683361 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ O-GlcNAc clusters attenuate BRD4 phase separation for transcription regulation ]]> https://biorxiv.org/content/10.1101/2025.10.20.683410v1?rss=1 Shao, G. Deng, Q. Wang, T. Li, C. Wang, N. Liu, J. Ge, Y. 2025-10-20 doi:10.1101/2025.10.20.683410 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Loss of ovarian function and estrogen therapy remodel the brain's synaptic and metabolic proteome ]]> https://biorxiv.org/content/10.1101/2025.10.20.683488v1?rss=1 Salathe, S. F. Franczak, E. Busick, Z. Boakye, F. B. Allen, J. Lutkewitte, A. J. Wilkins, H. M. Thyfault, J. Kugler, B. A. 2025-10-21 doi:10.1101/2025.10.20.683488 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Neuroprotective function of astrocyte p75NTR in Alzheimer's Disease through regulation of cholesterol metabolism ]]> https://biorxiv.org/content/10.1101/2025.10.20.683521v1?rss=1 Han, X. Xie, M. Ibanez, C. F. 2025-10-21 doi:10.1101/2025.10.20.683521 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Graph-based tracing of dynamically functioning gene circuits in cell fate decisions with isoform resolution ]]> https://biorxiv.org/content/10.1101/2025.10.21.683820v1?rss=1 Li, W. Dong, H. Zhou, Z. Fan, W. Zhou, Y. Yang, X. Xue, G. Li, Z. 2025-10-23 doi:10.1101/2025.10.21.683820 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Platelet Bioenergetics Profiling Reveals Non-Mitochondrial Dysfunction as a Potential Biomarker of Diabetic Complications ]]> https://biorxiv.org/content/10.1101/2025.10.22.683779v1?rss=1 Agbas, A. Kluding, P. Pasnoor, M. Shae, W. Sage, J. 2025-10-23 doi:10.1101/2025.10.22.683779 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Cell cycle-driven epigenetic resetting maintains stem cell fate for shoot branching ]]> https://biorxiv.org/content/10.1101/2025.10.22.683900v1?rss=1 Guo, Y. Yang, Y. Shi, B. Wang, H. Cao, X. Peng, Z. He, Y. Xiao, J. Tao, L. Wagner, D. Umeda, M. Sablowski, R. Wang, Y. Jiao, Y. 2025-10-23 doi:10.1101/2025.10.22.683900 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Androgens Drive SOX9 Upregulation in Injured Proximal Tubular Cells ]]> https://biorxiv.org/content/10.1101/2025.10.23.684153v1?rss=1 Vermillion Allison, C. Patel, P. Xuanyuan, Q. Stayton, A. Silvaroli, J. A. Karel, I. Z. Thorson, V. A. Sloane, G. Thailammanal, H. J. Scindia, Y. Coss, C. C. Zepeda-Orozco, D. Rao, R. Bolisetty, S. Mallipattu, S. K. Humphreys, B. Bajwa, A. Pabla, N. S. Kim, J. Y. 2025-10-24 doi:10.1101/2025.10.23.684153 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ MemConverter: An Iterative Pipeline for Reprogramming Protein Localization in Membrane or Aqueous Solution ]]> https://biorxiv.org/content/10.1101/2025.10.23.684164v1?rss=1 Li, J. Guo, H. Song, C. 2025-10-24 doi:10.1101/2025.10.23.684164 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ Distinct and compensatory roles of Stag1 and Stag2 in post-mitotic genome refolding ]]> https://biorxiv.org/content/10.1101/2025.10.24.684407v1?rss=1 Wang, M. Shan, F. Shu, L. Xia, S. Liu, F. Jing, D. Zhang, Y. Weng, Y. Li, B. Zhao, H. Lin, Y. Yu, Y. Wang, B. Zhang, H. 2025-10-24 doi:10.1101/2025.10.24.684407 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ Unfolding the Black Box of Recurrent Neural Networks for Path Integration ]]> https://biorxiv.org/content/10.1101/2025.10.25.684492v1?rss=1 Chu, T. Wu, Y. Burgess, N. Ji, Z. Wu, S. 2025-10-26 doi:10.1101/2025.10.25.684492 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Genetic diversity in horseshoe bat ACE2 and sarbecovirus spike proteins mutually shape one another ]]> https://biorxiv.org/content/10.1101/2025.10.26.684670v1?rss=1 Li, W. Sato, S. Takemura, T. Niu, X. Arnold, D. Yo, M. S. Tolentino, J. E. Fujita, S. Kosugi, Y. Thuy, N. T. T. Mai, L. T. Q. Luong, N. T. Oshima, H. S. Matsumoto, K. Sawada, K. Akasaka, H. Shihoya, W. Ito, J. Cao, Y. Hasebe, F. Thong, V. D. Nureki, O. Lytras, S. Sato, K. 2025-10-27 doi:10.1101/2025.10.26.684670 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Inhibition mechanism of pancreatic KATP channels by centipede toxins ]]> https://biorxiv.org/content/10.1101/2025.10.27.684718v1?rss=1 Hou, T. Wang, M. Tan, Y. Fan, C. Chen, L. 2025-10-27 doi:10.1101/2025.10.27.684718 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Palmitoylation of death receptor p75NTR contributes to Alzheimer's Disease progression by regulating APP trafficking and degradation ]]> https://biorxiv.org/content/10.1101/2025.10.28.685019v1?rss=1 Ma, Y. Xie, M. Ibanez, C. F. 2025-10-29 doi:10.1101/2025.10.28.685019 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ Isotope Dilution nanoLC-MS/MS Quantitation of Methylglyoxal DNA-Protein Crosslinks: Formation and Repair in Human Cells ]]> https://biorxiv.org/content/10.1101/2025.10.28.685209v1?rss=1 Omondi, R. O. Barnes, E. M. Gurajala, K. C. Fisette, G. Chaudray, I. Erber, L. 2025-10-30 doi:10.1101/2025.10.28.685209 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ CRISPR-Induced NUT Suppression Promotes Differentiation and Enhances Trop2-Targeted Immunocytokine Response in NUT Carcinoma ]]> https://biorxiv.org/content/10.1101/2025.10.28.685224v1?rss=1 Choi, J. Kim, D. Oh, J. Park, H. G. Yi, H. L. Lee, Y. Jeong, H. Song, J.-Y. Sung, M. Chang, E. S. Jung, K. Lee, S. Shin, Y. K. Lee, S.-H. French, C. Lee, M.-S. Choi, Y.-L. 2025-10-31 doi:10.1101/2025.10.28.685224 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Pollinators in Mexico. Spatial patterns show exceptions to global trends ]]> https://biorxiv.org/content/10.1101/2025.10.30.685361v1?rss=1 Nava-Bolanos, A. Osorio-Olvera, L. Soberon, J. 2025-10-31 doi:10.1101/2025.10.30.685361 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Yippee-like protein Moh1 links gene expression to metabolism and selective stress resistance in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2025.10.30.685511v1?rss=1 Olgun, C. E. Turan Duman, G. Gupur, G. Izgi, H. Huda, M. Cetin, D. Suludere, Z. Kucuk Baloglu, F. Caydasi, A. K. Muyan, M. 2025-10-31 doi:10.1101/2025.10.30.685511 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Molecular mechanism of naturally-encoded signaling-bias at the complement anaphylatoxin receptors ]]> https://biorxiv.org/content/10.1101/2025.11.01.685996v1?rss=1 Tiwari, D. Sawada, K. Dalal, A. Mishra, S. Li, X. X. Dent, J. Kim, K. Yadav, M. K. Roy, N. Ganguly, M. Banerjee, N. Stepniewski, T. M. Ahn, D. Yamaguchi, K. Oshima, H. S. Hashimoto, K. Fung, J. N. Lerskiatiphanich, T. Cui, C. S. Lee, J. Selent, J. Inoue, A. Clark, R. J. Chung, K. Y. Banerjee, R. Sano, F. K. Woodruff, T. Nureki, O. M. SHUKLA, A. K. 2025-11-01 doi:10.1101/2025.11.01.685996 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ A chromosome-level assembly and functional genomic resources for the model annelid Capitella teleta ]]> https://biorxiv.org/content/10.1101/2025.10.31.685816v1?rss=1 Davies, B. E. Gonzalez, P. Sur, A. Wei, J. Frankish, T. Montagne, J. Carrillo-Baltodano, A. M. Guynes, K. Liang, Y. Donnellan, R. D. Moreland, R. T. Singh, S. Zhang, S. Wolfsberg, T. G. Meyer, N. P. Seaver, E. C. Baxevanis, A. D. Martin-Duran, J. M. 2025-11-03 doi:10.1101/2025.10.31.685816 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Absence of cortical reorganization following an internal capsule stroke in rodents ]]> https://biorxiv.org/content/10.1101/2025.10.31.685962v1?rss=1 Cettina, P. E. Guggenmos, D. J. Sivakumar, S. S. Murphy, M. D. Barbay, H. S. Nudo, R. J. Bundy, D. T. 2025-11-03 doi:10.1101/2025.10.31.685962 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Bio-synthesis of 15N-Labeled G-Quadruplexes to Investigate the Structure and Interactions in the Cell Lysate using Nuclear Magnetic Resonance ]]> https://biorxiv.org/content/10.1101/2025.11.03.685478v1?rss=1 Zou, M. Tian, F. Zheng, W. Jiang, M. Zhang, S. Liu, X. Ma, C. Zhao, M. Dai, L. Li, C. Wang, S. 2025-11-04 doi:10.1101/2025.11.03.685478 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ AHA1 regulates Aβ production via modulation of APP expression and γ-secretase assembly ]]> https://biorxiv.org/content/10.1101/2025.11.03.686106v1?rss=1 Noorani, A. A. Islam, S. Catalfano, K. Wilkins, H. M. Blagg, B. S. J. Zou, K. Wolfe, M. S. 2025-11-04 doi:10.1101/2025.11.03.686106 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Circuit-specific gene editing for precision modulation of neuronal activity with CRISPR-rabies virus ]]> https://biorxiv.org/content/10.1101/2025.11.03.686433v1?rss=1 Zhang, Z. Xu, J. Matthews, E. A. Deasy, S. He, L. Arroyo, D. Pan, E. Deshmukh, A. Kaur, K. S. McNamara, J. O. Southwell, D. G. Gersbach, C. A. Ji, R. R. A. Velmeshev, D. 2025-11-04 doi:10.1101/2025.11.03.686433 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Genetic interaction of Specc1l and Thm1 reveals cytoskeletal - ciliary crosstalk ]]> https://biorxiv.org/content/10.1101/2025.11.03.686369v1?rss=1 Hufft-Martinez, B. M. Thalman, D. N. Tran, A. J. Goering, J. P. Stetsiv, M. Moedritzer, M. Wilson, S. C. Wang, H. H. Tran, P. V. Saadi, I. 2025-11-05 doi:10.1101/2025.11.03.686369 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ End-to-end high-throughput single-cell proteomics via SPRINT and dual-spray LC-MS ]]> https://biorxiv.org/content/10.1101/2025.11.03.686420v1?rss=1 1,000 single cells across six organs. These advances establish SCP as a scalable platform ready for broad biological and biomedical applications. ]]> Liu, Z. Dong, W. Gu, L. Ge, R. Zeng, X. Deng, J. Zhang, H. Ye, Z. 2025-11-05 doi:10.1101/2025.11.03.686420 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Variants in Cas9 and nanos regulatory elements modulate activity and reduce resistance allele formation in homing gene drive ]]> https://biorxiv.org/content/10.1101/2025.11.04.686506v1?rss=1 Zhou, R. Du, J. Faber, N. R. Champer, J. 2025-11-05 doi:10.1101/2025.11.04.686506 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Inferring absolute counts from proportions by constraining multivariate normal distributions ]]> https://biorxiv.org/content/10.1101/2025.11.04.686543v1?rss=1 Hage, J. Koestler, D. Christensen, B. 2025-11-05 doi:10.1101/2025.11.04.686543 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Quantifying predictability of gene expression from histology image ]]> https://biorxiv.org/content/10.1101/2025.11.04.686651v1?rss=1 Xia, C.-R. Yao, J.-W. Gao, G. 2025-11-05 doi:10.1101/2025.11.04.686651 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Network-Based Analysis of Human Astrocytes Links Aging to Neurodegenerative and Cardiovascular Diseases ]]> https://biorxiv.org/content/10.1101/2025.11.05.686746v1?rss=1 Bota, P. M. Picon-Pages, P. Fanlo-Ucar, H. Almabhouh, S. Bagudanch, O. Zeylan, M. E. Senyuz, S. Gohl, P. Molina-Fernandez, R. Fernandez-Fuentes, N. Barbu, E. Vicente, R. Nattel, S. Ois, A. Puig-Pijoan, A. Garcia-Ojalvo, J. Keskin, O. Gursoy, A. Munoz, F. J. Oliva, B. 2025-11-06 doi:10.1101/2025.11.05.686746 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Random crosslinks generate anomalous scaling of dynamic modulus of biomolecular condensates ]]> https://biorxiv.org/content/10.1101/2025.11.05.686888v1?rss=1 Lyu, B. Lin, J. 2025-11-07 doi:10.1101/2025.11.05.686888 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ FAM19A4 Enhances Neutrophil Respiratory Burst via p38 MAPK in Lethal Sepsis ]]> https://biorxiv.org/content/10.1101/2025.11.07.687190v1?rss=1 Li, S. Zhu, F. Jiang, L. Xue, H. Li, T. Wang, T. Wang, W. Zhang, K. 2025-11-08 doi:10.1101/2025.11.07.687190 Cold Spring Harbor Laboratory Press 2025-11-08 <![CDATA[ Dissecting mammalian cortical circuit development at single-cell resolution using inducible barcoded rabies virus ]]> https://biorxiv.org/content/10.1101/2025.11.07.687321v1?rss=1 Zhang, Z. D'Arcy, B. He, L. Arroyo, D. Deasy, S. Matthews, E. Yan, Z. Rastogi, N. Mancia Leon, W. Kaur, K. S. Southwell, D. G. Huang, Z. J. Silver, D. Velmeshev, D. 2025-11-10 doi:10.1101/2025.11.07.687321 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Differential controls of forelimb versus whole-body movements by striatum ]]> https://biorxiv.org/content/10.1101/2025.11.10.687756v1?rss=1 Cao, J. Zhao, Y. Yu, J. 2025-11-12 doi:10.1101/2025.11.10.687756 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Scalable spike sorting across thousands of neurons by modeling neural dynamics with NeuroSort ]]> https://biorxiv.org/content/10.1101/2025.11.11.687825v1?rss=1 Liu, L. Hu, Z. Zhang, S. Liu, Y. Jia, H. Sun, H. Jia, S. Sun, X. Liu, J. K. Duan, X. Li, X. 2025-11-12 doi:10.1101/2025.11.11.687825 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ mRNA isoform switching plays a crucial role in mural cumulus differentiation ]]> https://biorxiv.org/content/10.1101/2025.11.11.684658v1?rss=1 Shila, S. Pei, G. J. Peramsetty, N. Bahadursingh, E. Dahiya, V. Marsh, C. A. Thiyagarajan, R. Zhang, M. Fields, P. E. Rumi, M. A. 2025-11-13 doi:10.1101/2025.11.11.684658 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Mesoscopic viscous-to-elastic transition underlies aging of biomolecular condensates ]]> https://biorxiv.org/content/10.1101/2025.11.13.688393v1?rss=1 Li, M. Lin, J. 2025-11-14 doi:10.1101/2025.11.13.688393 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Yuanyang allele pairs enable engineered obligate co-inheritance for population replacement and suppression ]]> https://biorxiv.org/content/10.1101/2025.11.14.688408v1?rss=1 99% hemizygous lethality when crossed with wild type, while maintaining stable transmission and high fitness in transheterozygotes. Cage experiments demonstrate efficient population replacement, positioning YYAP as a confined, resistance-proof alternative to CRISPR homing gene drives. Release of only males represents a self-limiting suppression strategy that was also successful in cage experiments. By imposing a near-complete postzygotic incompatibility, YYAP establishes a programmable framework that not only supports pest management, but also enables modeling of reproductive isolation and allelic co-dependency, thereby creating opportunities to explore speciation and broader synthetic inheritance systems in ecology and evolution. ]]> Li, Y. Qiao, Z. Xian, C. Hu, S. Jia, J. Li, W. Tian, M. Yang, R. Zhang, Q. Hua, H. Champer, J. Ma, W. Zhu, Z. 2025-11-14 doi:10.1101/2025.11.14.688408 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Shared neural geometries for bilingual semantic representations ]]> https://biorxiv.org/content/10.1101/2025.11.16.688726v1?rss=1 Yan, X. Krishna, A. Van Arsdel, K. Gautam, I. Kim, Y. Shrivastava, A. Belanger, J. Chavez, A. G. Chericoni, A. Franch, M. Ismail, T. Katlowitz, K. Mickiewicz, E. Paulo, D. Zhu, H. Goldman, A. M. Krishnan, V. Maheshwari, A. Bartoli, E. Provenza, N. Yoo, S. B. M. Hayden, B. Y. Sheth, S. 2025-11-17 doi:10.1101/2025.11.16.688726 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Global Mapping of circRNA-Target RNA Interactions Reveals P-Body-Mediated Translational Repression ]]> https://biorxiv.org/content/10.1101/2025.11.16.688748v1?rss=1 Li, P. Zhang, H. Cai, Z. Zhang, Y. Yang, R. Ye, R. Li, J. Zhao, H. Liu, B. Yuan, Z. Li, X. Wang, X. Zhu, P. Xue, Y. 2025-11-17 doi:10.1101/2025.11.16.688748 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Vectorial boundary representation of 3D layout in human visual cortex ]]> https://biorxiv.org/content/10.1101/2025.11.17.688791v1?rss=1 Wu, Y. Li, S. 2025-11-17 doi:10.1101/2025.11.17.688791 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Genotype-phenotype correlations in Wilms tumor initiation. ]]> https://biorxiv.org/content/10.1101/2025.11.19.689177v1?rss=1 Pop, N. S. Koot, D. Brouwers, C. M. Linssen, M. M. Claassens, J. W. C. Catrlidge, C. W. J. Ozdemir, D. D. Dolt, K. S. Hohenstein, P. 2025-11-19 doi:10.1101/2025.11.19.689177 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ Causality-oriented regulatory inference and rational transcriptomic reprogramming design with CASCADE ]]> https://biorxiv.org/content/10.1101/2025.11.20.689377v1?rss=1 Cao, Z.-J. Guo, T. Li, C. Zhang, F. Lu, P. Gu, C. Guo, F. Gao, G. 2025-11-21 doi:10.1101/2025.11.20.689377 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ The Human-In-the-Loop Drug Design Framework with Equivariant Rectified Flow ]]> https://biorxiv.org/content/10.1101/2025.11.20.689585v1?rss=1 Zhao, Y. Huang, Y. Peng, X. Lin, H. Xu, Q. Shi, Y. Liu, X. Wang, Y. Liu, Q. Peng, J. Ma, J. 2025-11-21 doi:10.1101/2025.11.20.689585 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Loss of SPECC1L in cranial neural crest cells results in increased hedgehog signaling and frontonasal dysplasia ]]> https://biorxiv.org/content/10.1101/2025.11.21.689834v1?rss=1 Tran, A. J. Hufft-Martinez, B. M. Thalman, D. N. Maili, L. McKinney, S. Goering, J. P. Trainor, P. A. Saadi, I. 2025-11-24 doi:10.1101/2025.11.21.689834 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Injury-induced tau pathology promotes aggressive behavior in Drosophila without neurodegeneration. ]]> https://biorxiv.org/content/10.1101/2025.11.22.689595v1?rss=1 Maxson, R. Smoyer, C. J. Hampton, M. F. Shen, Y. Wiese, K. Yee, C. Singh, A. Funtila, A. McKenney, R. J. Ori-McKenney, K. M. 2025-11-25 doi:10.1101/2025.11.22.689595 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Oncogenic RAS activity is linked to immune priming and adenosine-driven immune evasion in lung adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2025.11.25.690426v1?rss=1 de Carne Trecesson, S. East, P. Pillsbury, C. Silva dos Santos, M. Cha, H. Colliver, E. Gilmore, T. Rana, S. Moore, C. Lighterness, S. Caswell, D. R. Boumelha, J. Tomaschko, M. Baer, R. Eyles, J. Teixeira, B. Saeed, M. Litchfield, K. Molina-Arcas, M. Lee, S.-H. MacRae, J. Hobson, P. Swanton, C. Downward, J. 2025-11-26 doi:10.1101/2025.11.25.690426 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ Slab-PTM: A Coarse-Grained Force Field Parameter Patch for Modeling Post-Translational Modification Effects on Biomolecular Condensates ]]> https://biorxiv.org/content/10.1101/2025.11.24.690320v1?rss=1 Mu, J. Lai, L. 2025-11-27 doi:10.1101/2025.11.24.690320 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ Multi-stem-loop constrained library enables accelerated SELEX for aptamers with superior kinetics and affinity ]]> https://biorxiv.org/content/10.1101/2025.11.27.690911v1?rss=1 Wang, Q. Zhao, Y. Zhao, S. Wu, A. Hao, L. Hong, T. Hong, L. 2025-11-27 doi:10.1101/2025.11.27.690911 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ Integrative spatial multi-omics reveals prognostic tumor niches in female genital tumors ]]> https://biorxiv.org/content/10.1101/2025.11.24.690313v1?rss=1 Xu, T. Lin, S. Wu, Y. He, Y. Zhang, Z. Zhao, Y. Zhang, P. Zhao, L. Yang, W. Ye, M. Zhang, R. Wen, L. Ren, P. Luo, C. Zhang, Z. Zeng, Z. Meng, Y. 2025-11-28 doi:10.1101/2025.11.24.690313 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ PKU tags, novel genetically encoded shape tags for cell labeling in light and electron microscopy ]]> https://biorxiv.org/content/10.1101/2025.11.25.690457v1?rss=1 Sun, R. Yang, P. Wang, L. Hu, Y. Yang, Y. Deng, F. Li, S. Fan, M. Xia, X. Li, Y. 2025-11-29 doi:10.1101/2025.11.25.690457 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Antibody-Protein L Functionalized Microparticles for Detection of Surface Markers in Heterogeneous Colorectal Lesions ]]> https://biorxiv.org/content/10.1101/2025.11.25.690572v1?rss=1 Ramezani, S. Zacharias, N. M. Norton, W. Davis, J. S. Dominic, A. Armijo, R. Wang, M. Wendt, R. E. Carson, D. D. Harrington, D. A. Farach-Carson, M. C. Bhattacharya, P. K. 2025-11-29 doi:10.1101/2025.11.25.690572 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Epitope and functional classification of human neutralizing antibodies against SFTSV Gn ]]> https://biorxiv.org/content/10.1101/2025.11.26.690690v1?rss=1 Wang, Q. Li, H. Jian, F. Han, A. Liu, Y. Liu, J. Yu, Y. Wang, J. Yu, L. Wang, Y. Sun, H. Ma, M. Shao, F. Zhu, L. Liu, W. Cao, Y. 2025-11-30 doi:10.1101/2025.11.26.690690 Cold Spring Harbor Laboratory Press 2025-11-30 <![CDATA[ FuzzAletheia: Mapping dynamic interaction landscapes of intrinsically disordered protein-ligand complexes to accelerate ligand optimization ]]> https://biorxiv.org/content/10.1101/2025.11.26.690418v1?rss=1 Wang, H. Wang, F. Xiong, R. Sun, Q. Lai, L. 2025-12-01 doi:10.1101/2025.11.26.690418 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Mapping the Peptide Interaction Fingerprint of the Behcet's disease associated HLA-B*51 ]]> https://biorxiv.org/content/10.1101/2025.11.26.690622v1?rss=1 Yilmaz, S. Z. Basturk, D. Gul, A. Erman, B. Gur, M. 2025-12-01 doi:10.1101/2025.11.26.690622 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ A Functional Resting-State Network Atlas Based on 420 Older Adults with Hypertension ]]> https://biorxiv.org/content/10.1101/2025.11.26.690831v1?rss=1 Scheel, N. Fernandez, Z. Baker, J. Yanev, P. Keller, J. N. Binder, E. F. Vidoni, E. Burns, J. M. Stowe, A. M. Kerwin, D. R. Cullum, C. M. Hynan, L. S. Vongpatanasin, W. Zhang, R. Zhu, D. C. 2025-12-01 doi:10.1101/2025.11.26.690831 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Rejuvenation capacity of genetic versus human-optimized chemical reprogramming in cellular aging models ]]> https://biorxiv.org/content/10.1101/2025.11.27.690966v1?rss=1 Ergul, O. C. Onder, T. T. 2025-12-01 doi:10.1101/2025.11.27.690966 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Phosphatidylinositol Transfer Protein-1 Integrates Insulin/IGF-1 and TOR Signaling to Negatively Regulate Lifespan and Healthspan in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2025.11.28.691094v1?rss=1 Lin, Y.-H. Liao, Y.-H. Liao, S.-B. Lin, T.-Y. Shanmugam, M. M. Hsu, P.-J. Chen, C.-S. Ching, T.-T. Wagner, O. I. Yuh, C.-H. Wang, H.-D. 2025-12-02 doi:10.1101/2025.11.28.691094 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Disentangling Cephalopod Chromatophores Motor Units with Computer Vision ]]> https://biorxiv.org/content/10.64898/2025.11.30.691401v1?rss=1 Laurent, G. Renard, M. D. M. Ukrow, J. Elmaleh, M. Evans, D. A. Wu, Y. Liang, X. 2025-12-02 doi:10.64898/2025.11.30.691401 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Alphaviral capsid proteins inhibit stress granule assembly via competitive RNA binding with G3BP1 ]]> https://biorxiv.org/content/10.64898/2025.12.01.691496v1?rss=1 Zhang, Y. Liu, Y. Lai, H. Yao, Z. Chen, X. Wang, Z. Bao, Y. Li, T. Zhou, X. Chen, X. YANG, P. 2025-12-02 doi:10.64898/2025.12.01.691496 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Sperm-specific fertility factors SMZ-1/2 promote FB-MO biogenesis and MSP filament assembly in C. elegans ]]> https://biorxiv.org/content/10.64898/2025.12.01.691703v1?rss=1 Peng, H.-F. Liu, C.-L. Jane, W.-N. Chen, C.-S. Wang, C.-W. Wu, J.-c. 2025-12-03 doi:10.64898/2025.12.01.691703 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Surface phase separation in a confined space ]]> https://biorxiv.org/content/10.64898/2025.12.03.692075v1?rss=1 Wu, D. Lin, J. 2025-12-04 doi:10.64898/2025.12.03.692075 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ A panel of near-isogenic lines derived from locally adapted populations of a wild plant: A powerful tool for dissecting additive and non-additive effects on ecologically important traits ]]> https://biorxiv.org/content/10.64898/2025.12.03.692110v1?rss=1 Mantel, S. J. Lee, G. Rojas-Gutierrez, J. D. Sanderson, B. J. Jameel, M. I. Woods, P. Dilkes, B. McKay, J. K. Agren, J. Oakley, C. J. 2025-12-04 doi:10.64898/2025.12.03.692110 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ Exploring multi-level microbial interactions from individual 3D genomes to community networks ]]> https://biorxiv.org/content/10.64898/2025.12.03.692222v1?rss=1 Hua-Jun, W. Jiang, W.-J. Cai, K.-W. Sun, Y.-C. Zheng, Z. Xu, F. Gao, R.-X. Wei, N. Zhu, H. Wang, Y.-J. Xia, Q. Lu, C. Xu, M. 2025-12-04 doi:10.64898/2025.12.03.692222 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ Emergence and spread of outbreak-adapted Candidozyma auris harboring mutations in RBA1 ]]> https://biorxiv.org/content/10.64898/2025.12.04.692421v1?rss=1 Doorley, L. A. La Bella, A. A. Jones, S. J. Zhao, G. Asadzadeh, M. Choudhury, Q. J. Ahmad, S. Mokaddas, E. Al-Obaid, I. Alfouzan, W. Al-Banwan, K. O'Meara, T. Santiago-Tirado, F. H. Flores-Mireles, A. L. Rybak, J. M. 2025-12-04 doi:10.64898/2025.12.04.692421 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ Measuring and modeling ecological rates with neutral theory ]]> https://biorxiv.org/content/10.64898/2025.12.02.691869v1?rss=1 Saulsbury, J. G. Wing, S. L. Hunt, G. 2025-12-05 doi:10.64898/2025.12.02.691869 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Information Network Flux interprets the importance of regulatory circuits in the protein and gene spaces ]]> https://biorxiv.org/content/10.64898/2025.12.03.692218v1?rss=1 Xue, B. Jiang, R. Xue, Y. Zhang, H. Liu, S. Gao, Y. Q. 2025-12-05 doi:10.64898/2025.12.03.692218 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Master clock-thalamic-prefrontal circuit controls circadian social priority ]]> https://biorxiv.org/content/10.64898/2025.12.05.691743v1?rss=1 Kim, J. Yu, J. Kim, B. Kim, M. Park, I. Lee, J. Song, C. Li, Y. Kim, K. Rah, J.-C. Choe, H. K. 2025-12-09 doi:10.64898/2025.12.05.691743 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Evolve and resequence provides a granular view of micro-evolution under different mating systems in Mimulus guttatus ]]> https://biorxiv.org/content/10.64898/2025.12.10.693597v1?rss=1 Tusuubira, S. Madrigal-Roca, L. J. Brown, K. E. Kelly, J. K. 2025-12-11 doi:10.64898/2025.12.10.693597 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Mapping the circulating proteome across neurodegeneration: A harmonized, consortium-scale framework for uncovering molecular pathophysiology ]]> https://biorxiv.org/content/10.64898/2025.12.09.693329v1?rss=1 Finney, C. A. An, L. Winchester, L. M. Vogel, J. Wilkins, H. M. Burns, J. M. Swerdlow, R. H. Slawson, C. Rothstein, J. D. Global Neurodegeneration Proteomics Consortium, Lutz, M. W. Saloner, R. Shvetcov, A. 2025-12-12 doi:10.64898/2025.12.09.693329 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Host species and body site equally impact microbiome structure between sympatric Atlantic sea cucumber species ]]> https://biorxiv.org/content/10.64898/2025.12.12.694001v1?rss=1 Crowley, C. A. Belisle, B. S. Dart, E. Ahlgren, N. A. 2025-12-13 doi:10.64898/2025.12.12.694001 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ Use-dependent learning biases the initial state but not the learning dynamics of implicit adaptation ]]> https://biorxiv.org/content/10.64898/2025.12.12.694069v1?rss=1 Luo, Y. Wei, K. 2025-12-16 doi:10.64898/2025.12.12.694069 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Multiparametric Assessment of TNNI3 Variant Phenotypes in Human iPSC-Cardiomyocytes Correlates with Disease Severity in Patients ]]> https://biorxiv.org/content/10.64898/2025.12.13.691658v1?rss=1 Staudt, D. W. Tran, P. P. Floyd, B. Dunn, K. Han, D. Carhuamaca, X. Serrano, R. Hnatiuk, A. P. Bang, S. Parikh, V. N. Ashley, E. A. Mercola, M. 2025-12-16 doi:10.64898/2025.12.13.691658 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Targeting Ogt in ADPKD mitigates metabolic reprogramming and renal cystogenesis, extending survival ]]> https://biorxiv.org/content/10.64898/2025.12.14.693989v1?rss=1 Kavanaugh, M. A. Ahmad, S. Isai, D. G. Riddle, H. A. L. Assis, A. P. Ranganathan, C. Chaturvedi, A. Lam, V. Muthineni, N. Abid, R. Jurgensmeyer, J. E. Blades, C. Pritchard, M. T. Sharma, M. Wallace, D. P. Parnell, S. C. Slawson, C. Tran, P. V. 2025-12-16 doi:10.64898/2025.12.14.693989 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Torsins Organize CLCC1 Assembly to Safeguard ER Bilayer and Lipid Homeostasis ]]> https://biorxiv.org/content/10.64898/2025.12.14.694184v1?rss=1 Wang, Y. Wang, R. Yao, Y. Hou, R. Lu, Y. Lin, Y. Hu, Y. Li, Y. Wu, L. Zhu, Y. Gao, N. Song, C. Wang, X. Ji, Z. Chen, X.-W. 2025-12-16 doi:10.64898/2025.12.14.694184 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Enterocloster citroniae and related gut microbiome species modulate Vibrio cholerae biofilm formation through the production of bioactive small molecules ]]> https://biorxiv.org/content/10.64898/2025.12.15.694346v1?rss=1 Pauer, H. Nasiri, S. Magalhaes, N. Nguyen, V. Ferreira, N. Ferreira, L. Bradshaw, A. Kirby, K. Sabapathy, T. Udensi, C. G. Feofanova, V. Moreira, D. Parente, T. Wilde, J. Pride, D. T. Allen-Vercoe, E. Antunes, C. 2025-12-16 doi:10.64898/2025.12.15.694346 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Spatial 5mC-seq profiling of embryos and decidua after implantation in mammal ]]> https://biorxiv.org/content/10.64898/2025.12.15.694289v1?rss=1 Liu, J. Gao, L. Shan, X. Tang, Y. Bian, M. 2025-12-17 doi:10.64898/2025.12.15.694289 Cold Spring Harbor Laboratory Press 2025-12-17 <![CDATA[ Conformation-specific Antibody Deciphers K27-linked Ubiquitination in Chaperone-Mediated Proteostasis ]]> https://biorxiv.org/content/10.64898/2025.12.18.695067v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@113b980org.highwire.dtl.DTLVardef@1f7c1a0org.highwire.dtl.DTLVardef@c91656org.highwire.dtl.DTLVardef@1d9a507_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Han, C. Weng, Y. Zheng, Q. Qu, Q. Erramilli, S. K. Su, Z. Duan, Y. Han, Y. Zhai, X. Kossiakoff, A. A. Pan, M. Zhao, M. Liu, L. Yu, Y. 2025-12-18 doi:10.64898/2025.12.18.695067 Cold Spring Harbor Laboratory Press 2025-12-18 <![CDATA[ Microgravity Remodels Longevity Networks in Astronaut PBMCs: Integrated Findings of Telomere Elongation, DNA Repair Responses, and miRNA Suppression ]]> https://biorxiv.org/content/10.64898/2025.12.20.695716v1?rss=1 Cam, E. Demir, O. Tekirdagli, B. Bulut, D. Guzenge, E. Harputoglu Efendi, S. N. Yolver, B. Kolay, K. Kavakli, I. H. Karouia, F. Aydin, B. Tastan, C. 2025-12-22 doi:10.64898/2025.12.20.695716 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Density-based longitudinal neuron tracking in high-density electrophysiological recordings ]]> https://biorxiv.org/content/10.64898/2025.12.19.695632v1?rss=1 Huang, Y. Wang, H. Cao, J. Chen, Y. Wang, X. Zhao, Y. Ren, H. Zheng, Q. Yu, J. 2025-12-23 doi:10.64898/2025.12.19.695632 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ MRMhub: one-stop solution for automated processing of large-scale targeted metabolomics data ]]> https://biorxiv.org/content/10.64898/2025.12.20.695370v1?rss=1 Burla, B. Teo, G. Benke, P. I. Lu, Z. Tan, S. H. Ji, S. Oh, J. Lim, P. Y. Vaitheeswari, Cazenave-Gassiot, A. Venkataraman, K. Tai, E. S. Torta, F. Wenk, M. R. Chan, M. Y. Y. Choi, H. 2025-12-23 doi:10.64898/2025.12.20.695370 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ LAP Drives Monocyte-Mediated and Extracellular Translocation of Listeria monocytogenes Across the Placental Barrier ]]> https://biorxiv.org/content/10.64898/2025.12.22.696054v1?rss=1 Drolia, R. Atique, A. Amelunke, B. Hasan, Z. Bryant, D. Oakley, O. Pierce, M. 2025-12-23 doi:10.64898/2025.12.22.696054 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Longitudinal Resting-State fMRI of Awake Mice During Habituation: Stress, Head Motion, and Functional Connectivity ]]> https://biorxiv.org/content/10.64898/2025.12.22.696087v1?rss=1 Choi, S. Im, G. H. Kim, S.-G. 2025-12-25 doi:10.64898/2025.12.22.696087 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ Intrinsic Error Correction in Protein Allostery: Quantifying Noise Suppression via Spanning Tree Statistics ]]> https://biorxiv.org/content/10.64898/2025.12.22.696126v1?rss=1 Erman, B. 2025-12-25 doi:10.64898/2025.12.22.696126 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ A Foundational Generative Model for Cross-platform Unified Enhancement of Spatial Transcriptomics ]]> https://biorxiv.org/content/10.64898/2025.12.23.696267v1?rss=1 1.7 million H&E-ST pairs and >5.8 million single-cell profiles, demonstrating state-of-the-art performance across ten ST platforms, on both individual and coupled challenges. The real-world utility and generalizability were validated on a rare suprasellar tumor, papillary craniopharyngioma, and an unseen ST platform (Open-ST) for primary and metastatic head and neck squamous cell carcinoma. ]]> Wang, X. Liu, H. Que, N. Tao, C. Jiang, Y. Jiang, Y. Zhu, P. Zhu, J. Li, X. Price, S. Xu, J. Xi, J. Wang, X. Li, C. 2025-12-25 doi:10.64898/2025.12.23.696267 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ To Predict is to Design: Unlocking Generative Capabilities in All-Atom Structure Predictors via Geometric Score Distillation ]]> https://biorxiv.org/content/10.64898/2025.12.23.696242v1?rss=1 Li, Y. Su, Y. Jing, Y. Liu, T. 2025-12-26 doi:10.64898/2025.12.23.696242 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Ensemble-DeepSets: an interpretable deep learning framework for single-cell resolution profiling of immunological aging ]]> https://biorxiv.org/content/10.64898/2025.12.25.696528v1?rss=1 Xu, Y. Luo, Z. He, K. Zhang, F. Wang, J. Wen, H. Li, Y. Han, D. 2025-12-26 doi:10.64898/2025.12.25.696528 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Pan-cancer tumor classification by a holistic tumor microenvironment atlas ]]> https://biorxiv.org/content/10.64898/2025.12.27.696641v1?rss=1 Qin, S. Xiao, D. Li, J. Nan, J. Diao, T. Bo, Y. Gao, Q. Zheng, L. Ling, X. Gao, Q. Li, X. Gao, S. Tang, F. Zhang, W. Li, C. Fang, P. Zhu, L. Wang, D. Zhang, Z. 2025-12-27 doi:10.64898/2025.12.27.696641 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ STEAP4+ neutrophils: a promising circulating biomarker for lung metastasis ]]> https://biorxiv.org/content/10.64898/2025.12.27.696660v1?rss=1 Ai, C. Wu, H. Yang, H. Wang, J. Liu, C. Ng, M. S. F. Zhou, Z. Zhuang, F. Gao, Q. Wang, L. Shi, C. Zhu, L. Bu, Z. Chen, C. Ng, L. G. Zhang, Z. 2025-12-27 doi:10.64898/2025.12.27.696660 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ GenoME: a MoE-based generative model for individualized, multimodal prediction and perturbation of genomic profiles ]]> https://biorxiv.org/content/10.64898/2025.12.28.696482v1?rss=1 Wei, J. Xue, Y. Chai, H. Gao, Y. Q. 2025-12-28 doi:10.64898/2025.12.28.696482 Cold Spring Harbor Laboratory Press 2025-12-28 <![CDATA[ PocketX: Preference Alignment for Protein Pockets Design through Group Relative Policy Optimization ]]> https://biorxiv.org/content/10.64898/2025.12.28.696754v1?rss=1 Fan, Y. He, Z. Li, B. He, B. Zhang, M. Zhang, J. Zhang, H. 2025-12-28 doi:10.64898/2025.12.28.696754 Cold Spring Harbor Laboratory Press 2025-12-28 <![CDATA[ A Comprehensive Treatment-Induced Resistance Atlas of Glioblastoma Reveals a Fibrotic Niche Shielding the Tumor from Immunotherapy ]]> https://biorxiv.org/content/10.64898/2025.12.25.696471v1?rss=1 Wang, F. Huang, R. Ling, H. Bai, Y. Yang, C. Zhao, G. Wu, X. Cao, W. Lu, Y. Zhang, Y. Lu, D. Qiu, Y. Zhang, J. Gao, B. Ma, C. Dang, H. Zhang, Y. Yang, Y. Sun, T. Chen, Z. Wang, Z. 2025-12-29 doi:10.64898/2025.12.25.696471 Cold Spring Harbor Laboratory Press 2025-12-29 <![CDATA[ SARS-CoV-2 and MERS-CoV disrupt host protein synthesis via nsp1 with differential effects on the integrated stress response ]]> https://biorxiv.org/content/10.64898/2025.12.28.696697v1?rss=1 Parenti, N. Cusic, R. Renner, D. Jackson, N. Ye, C. Tan, L. H. Pfannenstiel, J. J. Fehr, A. Cohen, N. Martinez-Sobrido, L. Burke, J. Weiss, S. R. 2025-12-29 doi:10.64898/2025.12.28.696697 Cold Spring Harbor Laboratory Press 2025-12-29 <![CDATA[ APE1 Coordinates Its Disordered Region and Metal Cofactors to Drive Genome Surveillance ]]> https://biorxiv.org/content/10.64898/2025.12.28.696760v1?rss=1 Lee, D. Kim, S. Jo, G. Kim, J. Yoo, J. Yoo, J. Lee, J. Y. Lee, G. 2025-12-29 doi:10.64898/2025.12.28.696760 Cold Spring Harbor Laboratory Press 2025-12-29 <![CDATA[ Protective IFIH1 variant reduces immune-mediated islet stress and dysfunction in a type 1 diabetes genetic background ]]> https://biorxiv.org/content/10.64898/2025.12.30.697107v1?rss=1 Veronese-Paniagua, D. A. Banks, C. Bradley, K. Mukherjee, N. Gale, S. E. Hinshaw, K. E. Meacham, A. M. Iwaloye, O. F. Tse, H. M. Mathews, C. E. Millman, J. R. 2025-12-31 doi:10.64898/2025.12.30.697107 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Fast and slow architectures of cortical dynamics in human brain ]]> https://biorxiv.org/content/10.64898/2025.12.31.696728v1?rss=1 Lu, Y. Li, Z. Mao, H. Lyu, Q. Yao, C. Chen, J. Tao, L. Xiao, Z. Tian, X. 2025-12-31 doi:10.64898/2025.12.31.696728 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Sloppiness and Action Confinement in Cell State Transitions: Are Single Cells Sloppy? ]]> https://biorxiv.org/content/10.64898/2025.12.31.697145v1?rss=1 Ying, J. Wang, Y. Xiao, H. Huang, M. Zhang, L. Wang, W. 2025-12-31 doi:10.64898/2025.12.31.697145 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Proteolytic processing of Argonautes in multiphase condensates promotes transgenerational epigenetic inheritance ]]> https://biorxiv.org/content/10.64898/2026.01.01.697165v1?rss=1 Deng, B. Niu, X. Ma, H. Shi, L. Zhao, C. Chen, W. Li, X. Liang, Y. Hu, S. Chen, K. Liang, Y. Qiu, Y. Jia, H. Wan, G. 2026-01-02 doi:10.64898/2026.01.01.697165 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Microglia stabilize sleep homeostasis via adenosine A3 receptor signaling ]]> https://biorxiv.org/content/10.64898/2026.01.02.697450v1?rss=1 Zhao, Z. Gu, X. Yu, J. Chen, X. Zhang, L. Zhao, T. Ye, W. Cheng, H. 2026-01-03 doi:10.64898/2026.01.02.697450 Cold Spring Harbor Laboratory Press 2026-01-03 <![CDATA[ Taking genomics outdoors: linking local adaptation, trait variation, and gene expression in grass ecotypes across a rainfall gradient ]]> https://biorxiv.org/content/10.64898/2026.01.04.697578v1?rss=1 Sytsma, J. Johnson, L. Galliart, M. Fogarty, K. Howe, K. Olson, B. Baer, S. Gibson, D. Maricle, B. Hartung, E. 2026-01-04 doi:10.64898/2026.01.04.697578 Cold Spring Harbor Laboratory Press 2026-01-04 <![CDATA[ RodZ acts through MreBCD to activate the elongasome in Escherichia coli ]]> https://biorxiv.org/content/10.64898/2026.01.05.697639v1?rss=1 Du, S. Zhan, R. Gong, H. Li, Y. Cui, Y. Chen, X. Lutkenhaus, J. 2026-01-05 doi:10.64898/2026.01.05.697639 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ A Dynamic Search Mechanism Enables APE1 to Identify AP-Sites in DNA ]]> https://biorxiv.org/content/10.64898/2026.01.06.697944v1?rss=1 Dehart, K. Oden, P. Weaver, T. Schaich, M. Van Houten, B. Freudenthal, B. D. 2026-01-06 doi:10.64898/2026.01.06.697944 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Persistent viral infection in the Drosophila fat body is associated with immune activation at the single-cell level ]]> https://biorxiv.org/content/10.64898/2026.01.06.697976v1?rss=1 Roy, N. Unckless, R. L. 2026-01-06 doi:10.64898/2026.01.06.697976 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Evidence of autonomous neural specification for both brain and ventral nerve cord tissue in Annelida ]]> https://biorxiv.org/content/10.64898/2026.01.06.697942v1?rss=1 Webster, N. B. Davila-Sandoval, J. Carrillo-Baltodano, A. Duda, S. Ozpolat, D. Meyer, N. P. 2026-01-07 doi:10.64898/2026.01.06.697942 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ ANKS1B in the Nucleus Accumbens controls escalated cocaine self-administration via regulating CBP-FoxO3 complex ]]> https://biorxiv.org/content/10.64898/2026.01.11.698845v1?rss=1 Yang, L. Wu, X. Chen, X. Peng, C. Li, Z.-H. Gao, S. Lv, L. Han, Y. Xue, Y. Lu, L. Shi, J. Liu, J. Sun, Y. 2026-01-12 doi:10.64898/2026.01.11.698845 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ Conserved Rhizosphere Microbiomes and Metabolic Functions Across Diverse Grapevine Rootstocks: Implications for Plant Elemental Composition ]]> https://biorxiv.org/content/10.64898/2026.01.14.698671v1?rss=1 Swift, J. F. Trello, G. E. Harris, Z. N. Migicovsky, Z. Miller, A. J. 2026-01-15 doi:10.64898/2026.01.14.698671 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ Carbon dioxide sequestration into biomineral armor by ants ]]> https://biorxiv.org/content/10.64898/2026.01.21.700952v1?rss=1 Li, H. Fang, Y. Li, W. Liu, J. Sun, C.-Y. Kang, X. Bruner-Montero, G. Sardina, J. Mo, X. Hao, J.-L. Mo, J. Cheng, L. Liu, Z. Schultz, T. R. Johnston, R. E. Currie, C. R. E. 2026-01-22 doi:10.64898/2026.01.21.700952 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Functional Human Retinohypothalamic Tract Assembloid Model for Circadian Rhythm Research ]]> https://biorxiv.org/content/10.64898/2026.01.21.700761v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@1327027org.highwire.dtl.DTLVardef@61183corg.highwire.dtl.DTLVardef@7e280eorg.highwire.dtl.DTLVardef@77e7ce_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kahveci, B. Cakiroglu, E. Kaleli, H. N. Harputluoglu Efendi, S. N. Derkus, B. Ozelci, O. F. Nizamoglu, S. Kavakli, I. H. Senturk, S. Bolay, H. Yilmaz, B. Guven, S. 2026-01-23 doi:10.64898/2026.01.21.700761 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ A 3D printed mini-gel electrophoresis system for rapid and inexpensive DNA nanoswitch biosensing ]]> https://biorxiv.org/content/10.64898/2026.01.21.700818v1?rss=1 Morya, V. Hayden, A. Zhou, L. Cole, D. Halvorsen, K. 2026-01-23 doi:10.64898/2026.01.21.700818 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ BiHiTo: Biomolecular Hierarchy-inspired Tokenization ]]> https://biorxiv.org/content/10.64898/2026.01.23.701302v1?rss=1 Zheng, R. Liu, Y. Nie, Z. Liu, C. Ma, S. Mao, Y. Chen, J. 2026-01-23 doi:10.64898/2026.01.23.701302 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Dynamic reorganization of Developmental to Adult Genome Topology Controls the Initiation and Stabilization of the Human Muscle Stem Cell State ]]> https://biorxiv.org/content/10.64898/2026.01.23.701436v1?rss=1 Romero, M. A. Chien, P. Nicoletti, C. Liliom, H. L. Cox, G. Skuratovsky, E. Saleh, K. Gibbs, D. Gane, L. Hoang, D.-H. Caputo, L. Massenet, J. Sobreira, D. R. Puri, P. L. Pyle, A. D. 2026-01-25 doi:10.64898/2026.01.23.701436 Cold Spring Harbor Laboratory Press 2026-01-25 <![CDATA[ Stress adaptation pathways and HA-CD44 signaling maintain the survival of pancreatic cancer cells with centrosome amplification ]]> https://biorxiv.org/content/10.64898/2026.01.24.701523v1?rss=1 Ozcan, S. C. Goksel, E. Kalkan, B. M. Cicek, E. Kanevetci, B. Acilan, C. 2026-01-26 doi:10.64898/2026.01.24.701523 Cold Spring Harbor Laboratory Press 2026-01-26 <![CDATA[ Proximity labeling reveals cell cycle-specific NEK2 interactions and a regulatory axis controlling NUSAP1 stability ]]> https://biorxiv.org/content/10.64898/2026.01.25.701545v1?rss=1 Cicek, E. Ozcan, S. C. Kanevetci, B. Kalkan, B. Ozkan, N. E. Ozlu, N. Acilan, C. 2026-01-27 doi:10.64898/2026.01.25.701545 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ A general and extensible algorithmic framework to biological sequence alignment across scales and applications ]]> https://biorxiv.org/content/10.64898/2026.01.28.702355v1?rss=1 Xuan, H. Sun, H. Liu, X. Zhang, H. Zhang, J. Zhong, C. 2026-01-29 doi:10.64898/2026.01.28.702355 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ Keratin 5 marks cancer-propagating cells sustained by an osteopontin-producing niche in high-grade serous ovarian carcinoma ]]> https://biorxiv.org/content/10.64898/2026.01.28.702332v1?rss=1 Bidarimath, M. Ralston, C. Q. Bidarimath, N. Rose, I. M. Colina, D. Schmoeckel, E. Godwin, A. K. Mayr, D. Ellenson, L. H. Flesken-Nikitin, A. Nikitin, A. Y. 2026-01-30 doi:10.64898/2026.01.28.702332 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Isoform-Specific Functions of p73 Drive Survival and Chemoresistance in Diffuse Large B-Cell Lymphoma ]]> https://biorxiv.org/content/10.64898/2026.01.28.702345v1?rss=1 60% of patients; however, approximately one-third ultimately relapse. Although prior studies in normal B cells and lymphoma models implicate p73 in B-cell lymphomagenesis, the functional role of individual p73 isoforms in DLBCL remains poorly defined. TP73, a TP53 family member located on chromosome 1p36, encodes both transcriptionally active (TAp73) and dominant-negative ({Delta}Np73) isoforms that differentially regulate apoptosis and proliferation. In this study, we characterized p73 locus alterations, isoform-specific expression patterns, and their biological relevance in DLBCL. Chromosomal analysis revealed disruption of the 1p36 locus--predominantly via heterozygous deletion--in 35% of patient samples, which significantly correlated with elevated {Delta}Np73 expression. Immunohistochemical profiling demonstrated a positive association between TAp73 and cleaved caspase-3, and between {Delta}Np73 and Ki-67. Conversely, TAp73 expression negatively correlated with the anti-apoptotic proteins Bcl-2 and Bcl-6. Functional studies in DLBCL cell lines further confirmed that TAp73 enhances sensitivity to serum deprivation and doxorubicin, whereas {Delta}Np73 overexpression promotes survival and chemoresistance. Together, these findings identify p73 isoform imbalance as a key contributor to DLBCL pathogenesis and therapeutic response, highlighting {Delta}Np73 as a potential biomarker of aggressive disease and treatment resistance, and TAp73 as a tumor-suppressive axis warranting further investigation. SummaryDiffuse large B-cell lymphoma (DLBCL) is the most common non-Hodgkin lymphoma, yet relapse remains a major challenge. The p73 gene produces two key isoforms with opposing functions: TAp73, which promotes apoptosis, and {Delta}Np73, which inhibits cell death and supports tumor growth. In DLBCL samples, 1p36 chromosomal disruption occurred in 35% of cases and was associated with elevated {Delta}Np73. TAp73 expression correlated with apoptosis markers, whereas {Delta}Np73 correlated with proliferation. Functional studies showed TAp73 sensitizes DLBCL cells to stress and chemotherapy, while {Delta}Np73 enhances resistance. These findings highlight {Delta}Np73 as a potential biomarker and therapeutic target in DLBCL. ]]> Hassan, H. Varney, M. L. Weisenburger, D. D. Singh, R. K. Dave, B. J. 2026-02-02 doi:10.64898/2026.01.28.702345 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ CD8+CD20+ Cytotoxic T Lymphocytes Exhibit Augmented Degranulation and Pro-inflammatory Potential in Multiple Sclerosis ]]> https://biorxiv.org/content/10.64898/2026.01.29.702512v1?rss=1 Albayrak, O. Unlu, S. Akkaya, N. Kizilirmak, A. B. Doran, T. Uzulmez, M. Baytekin, I. Soylu, O. K. Koseoglu, M. Yuksel, B. Soysal, A. Vural, A. 2026-02-02 doi:10.64898/2026.01.29.702512 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Dissociable Effects of Early and Adolescent Adversity on Emotional Contagion ]]> https://biorxiv.org/content/10.64898/2026.01.29.702530v1?rss=1 Maldonado, P. P. Berretta, E. Canicatti, V. Feng, X. Soyman, E. Cuturela, L. I. Rajendran, R. Sadeghi, M. Babiczky, A. Goebel, G. Krugers, H. J. Keysers, C. Gazzola, V. 2026-02-02 doi:10.64898/2026.01.29.702530 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Neural representations of dynamic social interactions ]]> https://biorxiv.org/content/10.64898/2026.02.01.703160v1?rss=1 Kwon, D. Jolly, E. Chang, L. Shim, W. M. 2026-02-02 doi:10.64898/2026.02.01.703160 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ PepMCP: A Graph-Based Membrane Contact Probability Predictor for Membrane-Lytic Antimicrobial Peptides ]]> https://biorxiv.org/content/10.64898/2026.02.01.703163v1?rss=1 Dong, R. Awang, T. Cao, Q. Kang, K. Wang, L. Zhu, Z. Song, C. 2026-02-03 doi:10.64898/2026.02.01.703163 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Methylation-Guided Stratification of Colorectal Cancer Reveals Immune Subtypes with Distinct Clinical Outcomes ]]> https://biorxiv.org/content/10.64898/2026.02.03.703457v1?rss=1 Ahmed, E. I. Mall, R. Raynaud, C. M. Saadeh, H. Sherif, S. Alanany, R. El Hajj, N. Bedognetti, D. Roelands, J. Hendrickx, W. 2026-02-04 doi:10.64898/2026.02.03.703457 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ The kinetics of ribonucleoprotein granules ]]> https://biorxiv.org/content/10.64898/2026.02.04.703460v1?rss=1 Li, Y. Li, X. Xu, M. Qi, Z. 2026-02-07 doi:10.64898/2026.02.04.703460 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ Causal evidence for a shared mechanism linking language and tool use via the putamen ]]> https://biorxiv.org/content/10.64898/2026.02.06.704290v1?rss=1 Fan, Z. Wen, H. Han, Z. Wang, X. Bi, Y. 2026-02-09 doi:10.64898/2026.02.06.704290 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Synergistic integration of inducible RNA switches enhances the manipulation of vector expression ]]> https://biorxiv.org/content/10.64898/2026.02.06.704328v1?rss=1 Zhang, Y. Yang, Y. Liu, Z. Li, Y. Xue, Y. Zhang, Z. Chen, G. Lu, T. Zhang, Y. Zhao, D. Yang, K. Miao, L. Gao, F. Guo, Y. 2026-02-09 doi:10.64898/2026.02.06.704328 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Noncanonical loops regulated by EMF1 and cohesin-associated factors shape the distinct 3D genome architecture in plants ]]> https://biorxiv.org/content/10.64898/2026.02.08.704707v1?rss=1 Wang, D. Xiao, S. Luo, L. Wei, J. Shu, J. Tian, G. Liu, Y. Yang, M. Yang, T. Calonje, M. He, H. Jiao, Y. Zhou, Y. 2026-02-09 doi:10.64898/2026.02.08.704707 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Lmna deficiency promotes EPHX2 nuclear translocation to ameliorate cardiac dysfunction in mice ]]> https://biorxiv.org/content/10.64898/2026.02.09.704693v1?rss=1 Guo, C. Wang, Z. Liu, J. Wu, C. Yang, Y. Lv, Z. Chen, G. Sun, Y. Bai, R. Sun, W. Lu, T. Wang, K. Tian, Z. Zhang, X. Zhao, D. Zhang, S. Guo, Y. 2026-02-10 doi:10.64898/2026.02.09.704693 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ DIA-CLIP: a universal representation learning framework for zero-shot DIA proteomics ]]> https://biorxiv.org/content/10.64898/2026.02.09.704949v1?rss=1 Liao, Y. Wen, H. E, W. Zhang, W. 2026-02-11 doi:10.64898/2026.02.09.704949 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ A novel uN2CpolyG Transgenic Mouse Model Recapitulates Multisystemic polyG Proteinopathy Pathology of Neuronal Intranuclear Inclusion Disease ]]> https://biorxiv.org/content/10.64898/2026.02.10.705201v1?rss=1 Wan, Y. Zheng, Y. Gao, C. Lu, Y. Zheng, F. Yu, Z. Wang, J. Yang, B. Zheng, J. Yuan, Y. Hong, D. Charlet-Berguerand, N. Yu, J. Wang, Z. Deng, J. 2026-02-12 doi:10.64898/2026.02.10.705201 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ Low levels of metabolic auxotrophy among environmental Pseudomonas isolates ]]> https://biorxiv.org/content/10.64898/2026.02.13.705048v1?rss=1 Marechal, S. heiniger, b. Gu, S. Dash, S. Ahrens, C. Kuemmerli, R. 2026-02-14 doi:10.64898/2026.02.13.705048 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Physically Grounded Generative Modeling of All-Atom Biomolecular Dynamics ]]> https://biorxiv.org/content/10.64898/2026.02.15.705956v1?rss=1 Feng, B. Zhang, J. Zhang, X. Zhang, M. Barth, P. Liu, Z. Li, Y. 2026-02-15 doi:10.64898/2026.02.15.705956 Cold Spring Harbor Laboratory Press 2026-02-15 <![CDATA[ Bacterial GTPases act as successive placeholders to mediate ribosome assembly and its coupling to translation initiation ]]> https://biorxiv.org/content/10.64898/2026.02.15.706057v1?rss=1 Cheng, A. Ma, C. Gao, N. 2026-02-16 doi:10.64898/2026.02.15.706057 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ Assessing positive selection in centromere-associated kinetochore proteins across Metazoan groups. ]]> https://biorxiv.org/content/10.64898/2026.02.13.705784v1?rss=1 Healey, H. M. Gomez, L. E. Sheikh, S. I. Camel, B. R. Forbes, A. A. Sterner, K. N. Beck, E. A. 2026-02-18 doi:10.64898/2026.02.13.705784 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Spatial correspondences of Audiovisual Stimuli on Double Flash Illusion Perception and its Cognitive Modeling ]]> https://biorxiv.org/content/10.64898/2026.02.19.706740v1?rss=1 Zheng, Y. Chen, L. 2026-02-19 doi:10.64898/2026.02.19.706740 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[ Chemical activation of mitophagy via the N-degron pathway alleviates mitochondrial neuropathies ]]> https://biorxiv.org/content/10.64898/2026.02.19.706908v1?rss=1 Kwon, S. C. Kim, B.-S. Kim, H. Kang, D. E. Lee, G. E. Jung, E. J. Lee, M. J. Son, Y. S. Park, D.-h. Park, D. Y. Lee, J. Cho, E. H. Kim, S. B. Heo, A. J. Suh, Y. H. Jang, W.-D. Han, D. Ji, C. H. Ahn, J.-Y. Kwon, Y. T. 2026-02-20 doi:10.64898/2026.02.19.706908 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ rRNA Expansion Segments Mediate Ribosome Dimerization as a Conserved Stress Response ]]> https://biorxiv.org/content/10.64898/2026.02.21.707218v1?rss=1 Jiang, W. Chen, C. Wang, X. Huang, W. Taylor, D. Chen, Z. Xie, J. Su, Z. Taylor, D. Hatzoglou, M. Guo, Q. 2026-02-22 doi:10.64898/2026.02.21.707218 Cold Spring Harbor Laboratory Press 2026-02-22 <![CDATA[ Hepatocyte Estrogen Receptor α Mediates Estrogen-induced Augmentation of Hepatic 1 Mitochondrial Respiration Following Ovariectomy. ]]> https://biorxiv.org/content/10.64898/2026.02.22.706993v1?rss=1 Franczak, E. Kugler, B. A. Salathe, S. F. Allen, J. A. McCoin, C. S. Morris, E. M. M. Thyfault, J. P. 2026-02-23 doi:10.64898/2026.02.22.706993 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ UBE3C retrofits the proteasome to enforce degradation of ultra-stable folds ]]> https://biorxiv.org/content/10.64898/2026.02.24.707655v1?rss=1 Zou, S. Yin, D. Shi, M. Chen, E. Luo, X. Zhao, L. Cao, S. Wu, D. Zhang, S. Mao, Y. 2026-02-24 doi:10.64898/2026.02.24.707655 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ HuR inhibition attenuates hypertension and fibrosis in chronic kidney disease ]]> https://biorxiv.org/content/10.64898/2026.02.23.707592v1?rss=1 Zhuang, L. Wang, Z. Fu, Z. Mookherjee, S. Symons, J. D. Aube, J. Wu, X. Xu, L. Huang, Y. 2026-02-25 doi:10.64898/2026.02.23.707592 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ SpaMOAL: A spatial multi-omics graph contrastive learning method for spatial domains identification ]]> https://biorxiv.org/content/10.64898/2026.02.23.707433v1?rss=1 Wang, J. Huo, Y. Zhao, R. Pan, Y. Wang, H. Li, X. 2026-02-26 doi:10.64898/2026.02.23.707433 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Mitotic bookmarking by Prox1 preserves mammalian neuronal lineage identity memory via promoting timely H3K27me3 restoration ]]> https://biorxiv.org/content/10.64898/2026.02.25.707603v1?rss=1 Wong, C. Liu, J. Yang, H. Li, H. Luo, X. Li, T. Chen, Z. Chu, J. Shen, Y. Long, S. Zhang, Y. Song, Y. 2026-02-26 doi:10.64898/2026.02.25.707603 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Molecular Thermodynamics of KRAS Activation ]]> https://biorxiv.org/content/10.64898/2026.02.25.707891v1?rss=1 0) that is offset by a marked gain in conformational entropy ({Delta}S > 0), with a free-energy crossover occurring at kT {approx} 2.41 [A]. Edge marginal inclusion probabilities, obtained via effective-resistance theory, identify Switch I (residues 25-40) as the primary allosteric locus of nucleotide-driven network reorganization. This approach provides a thermodynamically grounded perspective on KRAS allostery, quantitatively demonstrating how network architecture enables functional versatility through entropy-driven conformational flexibility. Entropy-driven KRAS activation revealed by spanning-tree thermodynamicsSpanning-tree partition functions built from weighted residue-contact graphs show that KRAS activation involves entropy-enthalpy compensation. The GDP-bound network (left) is dominated by a small number of low-energy spanning trees, whereas the GTP-bound network (right) accesses a larger ensemble with greater topological diversity. The active state pays an energetic cost ({Delta}[E] > 0) offset by a conformational entropy gain ({Delta}S > 0), with Switch I (residues 25-40, dashed box) emerging as the primary site of nucleotide-driven network reorganisation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/707891v2_ufig1.gif" ALT="Figure 1"> View larger version (12K): org.highwire.dtl.DTLVardef@e4fa0borg.highwire.dtl.DTLVardef@dbf90corg.highwire.dtl.DTLVardef@1bb8f94org.highwire.dtl.DTLVardef@cf46a4_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ciftci, F. S. Erman, B. 2026-02-26 doi:10.64898/2026.02.25.707891 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Neuronal ketone body utilization couples exercise and time-restricted feeding to cognitive enhancement ]]> https://biorxiv.org/content/10.64898/2026.02.25.708044v1?rss=1 Salathe, S. F. Kugler, B. A. Franczak, E. Davis, X. C. Boakye, F. B. Allen, J. Fulghum, K. L. Queathem, E. D. Morris, E. M. Puchalska, P. Crawford, P. A. Thyfault, J. 2026-02-27 doi:10.64898/2026.02.25.708044 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ The not-so-great speciator: Systematics and species limits in a rapid radiation, the Asiatic white-eye complex (Zosterops spp.) ]]> https://biorxiv.org/content/10.64898/2026.02.25.708059v1?rss=1 Mays, H. L. McKay, B. D. Nishiumi, I. Yao, C. Zou, F. Boyd, M. DeRaad, D. Lin, R. Kawakami, K. Kim, C.-H. Kubatko, L. L. Moyle, R. 2026-02-27 doi:10.64898/2026.02.25.708059 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ Multi-Omic, Multi-Tissue Responses to Acute Exercise in Sedentary Adults: Findings from the Molecular Transducers of Physical Activity Consortium ]]> https://biorxiv.org/content/10.64898/2026.02.27.702183v1?rss=1 MoTrPAC Study Group, Katz, D. H. Jin, C. A. Many, G. M. Smith, G. R. Keshishian, H. Clark, N. M. Iyer, G. Ahn, C. Lindholm, M. E. Sagendorf, T. J. Amar, D. Barber, J. L. Brandt, A. R. Coen, P. M. Ge, Y. Hart, P. Hsu, F.-C. Jaeger, B. C. Jimenez-Morales, D. Leach, D. T. Mani, D. R. Montalvo, S. Pincas, H. Rao, P. Sanford, J. A. Smith, K. S. Vetr, N. G. Adkins, J. N. Ashley, E. A. Carr, S. A. Miller, M. E. Montgomery, S. B. Nair, V. D. Robbins, J. M. Snyder, M. P. Sparks, L. M. Tracy, R. Walsh, M. J. Wheeler, M. T. Xia, A. Y. Sealfon, S. C. Gerszten, R 2026-03-03 doi:10.64898/2026.02.27.702183 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ The orbitofrontal cortex constructs allocentric schemas by integrating dynamic mobile agents with static environmental anchors ]]> https://biorxiv.org/content/10.64898/2026.03.01.708836v1?rss=1 Zhu, Z. Zhang, B. Zhang, X. Naya, Y. 2026-03-03 doi:10.64898/2026.03.01.708836 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Behavioral hierarchy without a hierarchical brain ]]> https://biorxiv.org/content/10.64898/2026.03.01.708904v1?rss=1 Han, Y. Liu, Q. Liu, S. Cheng, H. Wei, P. 2026-03-03 doi:10.64898/2026.03.01.708904 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Hierarchical Anchoring Gating Dictates Specific H4K16 Acetylation by the Human MSL Complex ]]> https://biorxiv.org/content/10.64898/2026.03.03.709310v1?rss=1 Shi, Q. Zhao, Y. Deng, Z. Liang, J. Wu, S. Ai, H. Sun, L. Liu, L. 2026-03-04 doi:10.64898/2026.03.03.709310 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Genome-wide maps of transcription factor footprints identify noncoding variants rewiring gene regulatory networks with varTFBridge ]]> https://biorxiv.org/content/10.64898/2026.03.03.708783v1?rss=1 Lin, J. Dong, W. Zhang, J. Xie, C. Jing, X. Zhao, J. Ma, K. Kang, H. Jiang, Y. Xie, X. S. Zhao, Y. 2026-03-05 doi:10.64898/2026.03.03.708783 Cold Spring Harbor Laboratory Press 2026-03-05 <![CDATA[ Optimal spatial release strategies for confined gene drives and Wolbachia ]]> https://biorxiv.org/content/10.64898/2026.03.04.709515v1?rss=1 Wang, Z. Champer, J. 2026-03-06 doi:10.64898/2026.03.04.709515 Cold Spring Harbor Laboratory Press 2026-03-06 <![CDATA[ Modular Scaffold Crystals for Programmable Installation and Structural Observation of DNA-Binding Proteins ]]> https://biorxiv.org/content/10.64898/2026.03.04.709581v1?rss=1 Shields, E. T. Slaughter, C. K. Mekkaoui, F. Magna, E. N. Shepherd, C. LUKEMAN, P. S. Spratt, D. Snow, C. 2026-03-06 doi:10.64898/2026.03.04.709581 Cold Spring Harbor Laboratory Press 2026-03-06 <![CDATA[ A chromosome-level reference genome for the colonial marine hydrozoan Podocoryna americana ]]> https://biorxiv.org/content/10.64898/2026.03.04.709628v1?rss=1 Chang, E. S. Connelly, M. T. Travert, M. Barreira, S. N. Rivera, A. M. Katzer, A. M. Yu, R. Cartwright, P. Baxevanis, A. D. 2026-03-06 doi:10.64898/2026.03.04.709628 Cold Spring Harbor Laboratory Press 2026-03-06 <![CDATA[ PROTOTYPE-BASED CONTINUAL LEARNING FOR SINGLE-CELL ANNOTATION ]]> https://biorxiv.org/content/10.64898/2026.03.05.709973v1?rss=1 Ge, S. He, Q. Ren, Y. Xu, Y. Wang, M. Nie, Z. Xu, H. Cheng, Q. Sun, S. Ren, Z. 2026-03-08 doi:10.64898/2026.03.05.709973 Cold Spring Harbor Laboratory Press 2026-03-08 <![CDATA[ Linear morphometrics fail to support strong sexual dimorphism in Uintatherium anceps ]]> https://biorxiv.org/content/10.64898/2026.03.05.709752v1?rss=1 Mulcahy, K. D. 2026-03-09 doi:10.64898/2026.03.05.709752 Cold Spring Harbor Laboratory Press 2026-03-09 <![CDATA[ Fluorescence anisotropy structured illumination microscopy for quantitative super-resolved mapping of cell microenvironment and cytoskeletal dynamics ]]> https://biorxiv.org/content/10.64898/2026.03.06.710005v1?rss=1 Gao, S. Wang, W. Qiao, L. Wang, H. Liu, M. Hou, Y. Xin, G. Shan, C. Kim, D. Chen, Z. Li, M. Xi, P. 2026-03-09 doi:10.64898/2026.03.06.710005 Cold Spring Harbor Laboratory Press 2026-03-09 <![CDATA[ Counting strands in outer membrane beta-barrels ]]> https://biorxiv.org/content/10.64898/2026.03.07.710327v1?rss=1 Lim, S. Nimmagadda, T. Khamis, A. Montezano, D. Feehan, R. Copeland, M. Slusky, J. 2026-03-10 doi:10.64898/2026.03.07.710327 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Benchmarking zero-shot single-cell foundation model embeddings for cellular dynamics reconstruction ]]> https://biorxiv.org/content/10.64898/2026.03.10.710748v1?rss=1 Zhou, X. Wang, Z. Ling, Y. Tian, Q. Zhang, Z. Li, Y. Zhou, P. Chen, L. 2026-03-12 doi:10.64898/2026.03.10.710748 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ Development of a genetically encoded fluorescent indicator for facilitating deorphanization of GPR52 ]]> https://biorxiv.org/content/10.64898/2026.03.11.711017v1?rss=1 Lan, G. Wang, H. Qian, T. Xie, S. Qian, C. Ursu, D. Bornemann, K. D. Hengerer, B. Li, Y. 2026-03-13 doi:10.64898/2026.03.11.711017 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Cis-regulatory evolution shapes dehydration response in a desert-adapted house mouse ]]> https://biorxiv.org/content/10.64898/2026.03.13.710177v1?rss=1 Whedbee, M. Mack, K. 2026-03-14 doi:10.64898/2026.03.13.710177 Cold Spring Harbor Laboratory Press 2026-03-14 <![CDATA[ Omics-analyses of Fermented Onion pickle in Shaping Gut Microbiota and Immune Response in Women: A Community-Based Trial in Pakistan ]]> https://biorxiv.org/content/10.64898/2026.03.12.711246v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@1a59739org.highwire.dtl.DTLVardef@6b2007org.highwire.dtl.DTLVardef@103bb2borg.highwire.dtl.DTLVardef@1f509b3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hafeez, S. H. Farooq, S. Iqbal, J. Ahmed, K. Ahmed, S. Umrani, F. Jakhro, S. Qureshi, K. Moore, S. Ali, S. A. Iqbal, N. T. 2026-03-15 doi:10.64898/2026.03.12.711246 Cold Spring Harbor Laboratory Press 2026-03-15 <![CDATA[ In vivo-compatible spatial multi-omics via hydrogen peroxide-independent APEX2 labeling ]]> https://biorxiv.org/content/10.64898/2026.03.13.711744v1?rss=1 Chen, B. Guo, H. Yan, Z. Lu, W. Li, C. Xu, S. Zhang, Y. Guo, H. Sun, S. Sun, X. Zhao, S. Shangguan, Q. Chen, Y. Lu, L. Wu, Z. Chen, Y. Qin, W. 2026-03-15 doi:10.64898/2026.03.13.711744 Cold Spring Harbor Laboratory Press 2026-03-15 <![CDATA[ Integrative modeling of read depth and B-allele frequency improves single-cell copy number calling from targeted DNA sequencing panels ]]> https://biorxiv.org/content/10.64898/2026.03.12.711292v1?rss=1 Pei, D. Griffard-Smith, R. Cano Urrego, B. Schueddig, E. 2026-03-16 doi:10.64898/2026.03.12.711292 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ A biosecurity baseline for transboundary management of marine biological invasions in the ROPME Sea Area ]]> https://biorxiv.org/content/10.64898/2026.03.13.711635v1?rss=1 Vilizzi, L. Abbas, A. M. Mubarak, M. A. Alavi, M. H. Shojaei, M. Moghaddas, D. Rahmani, H. Albu Salih, A. A. R. Al-Khayyat, M. F. A. Al-Faisal, A. J. Al-Marhoun, A. F. Abdulhussain, A. H. Alkhamees, J. Karam, Q. E. Behbehani, W. Al Rezaiqi, M. Al Tarshi, M. Salman, S. F. Al Jamaei, A. M. El Mahdi, M. E. A. Mohamed, A. A. Sabbagh, E. I. Mehzoud, N. Al Shamsi, O. A. H. Al-Wazzan, Z. 2026-03-17 doi:10.64898/2026.03.13.711635 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ IgG Propels Atherosclerosis by Noncanonically Activating Macrophages ]]> https://biorxiv.org/content/10.64898/2026.03.13.711718v1?rss=1 Zahr, T. Zhang, K. Huang, S. Xue, C. Yu, L. Yu, Z. Li, B. Liang, D. Wang, Q. Shadrina, M. Wan, Q. Li, X. You, F. Kontorovich, A. R. Reilly, M. Hu, Z. Feng, W. Wang, L. Qiang, L. 2026-03-17 doi:10.64898/2026.03.13.711718 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Deep-learning-assisted simulation of a cortical circuit: integrating anatomy, physiology and function ]]> https://biorxiv.org/content/10.64898/2026.03.13.711751v1?rss=1 Ito, S. Haufler, D. Fraile, J. G. Dai, K. Aman, J. Chen, G. Mirasso, C. R. Maass, W. Arkhipov, A. 2026-03-17 doi:10.64898/2026.03.13.711751 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Exploration of Orally Disintegrating Tablet for Sublingual Vaccination against Mucosal Bacterial Infection ]]> https://biorxiv.org/content/10.64898/2026.03.14.711758v1?rss=1 Liu, Y. Cai, Q. Hu, X. Liu, X. Guo, P. Zhang, Y. Liu, H. Wang, W. Zheng, D. Pan, C. Guo, L. Yu, X. Zhang, Q. Wang, D. Qiu, Y. Wang, D. Li, W. Du, Y. Ma, G. Xu, J. Wang, S. Liu, Y. Wei, W. 2026-03-17 doi:10.64898/2026.03.14.711758 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Multicomplex Integrative Structural Modeling of a Human Histone Deacetylase Interactome ]]> https://biorxiv.org/content/10.64898/2026.03.16.712198v1?rss=1 Nde, J. Majila, K. Zimmermann, R. Kempf, C. Zhang, Y. Cesare, J. Thornton, J. Workman, J. Florens, L. Viswanath, S. Washburn, M. 2026-03-17 doi:10.64898/2026.03.16.712198 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ De Novo Regeneration of Rete Ridges during Cetacean skin wound healing ]]> https://biorxiv.org/content/10.64898/2026.03.16.711258v1?rss=1 Liu, T.-Y. Wang, H.-V. Yang, W.-C. Yang, C.-C. Su, C.-Y. Chiou, Y.-T. Chiou, T.-H. Shieh, S.-J. Tang, M.-J. Chuong, C. M. Hughes, M. W. 2026-03-19 doi:10.64898/2026.03.16.711258 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ evedesign: accessible biosequence design with a unified framework ]]> https://biorxiv.org/content/10.64898/2026.03.17.712115v1?rss=1 Hopf, T. A. Gazizov, A. Garcia Busto, S. Eschbach, E. Lee, S. Mirdita, M. Orenbuch, R. Belahsen, K. Ross, D. Sander, C. Steinegger, M. d'Oelsnitz, S. Marks, D. 2026-03-19 doi:10.64898/2026.03.17.712115 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ Subdiffusive random growth of bacteria ]]> https://biorxiv.org/content/10.64898/2026.03.19.712816v1?rss=1 Wei, J. Lin, J. 2026-03-20 doi:10.64898/2026.03.19.712816 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Social Functioning in Autism: A Systematic Review and Meta-analysis ]]> https://biorxiv.org/content/10.64898/2026.03.20.713084v1?rss=1 Li, S. Wang, H. Wang, Y. Zang, Y. 2026-03-23 doi:10.64898/2026.03.20.713084 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ The Joubert syndrome protein CSPP1 is a conserved regulator of vertebrate multiciliogenesis and motile cilia function ]]> https://biorxiv.org/content/10.64898/2026.03.20.713242v1?rss=1 Dilbaz-Gunden, I. S. Boitel, C. Deretic, J. Touret, M. Aydin, M. S. Yigit, E. Kayalar, O. Bayram, H. Thome, V. Rosnet, O. Brouilly, N. Kodjabachian, L. Boutin, C. Firat-Karalar, E. N. 2026-03-23 doi:10.64898/2026.03.20.713242 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ Polycystin-1 C-Terminus Regulates Protein Synthesis-Related Pathways in Cardiomyocytes ]]> https://biorxiv.org/content/10.64898/2026.03.21.713243v1?rss=1 Fiedler, M. Vasquez Limeta, A. Reyes-Sanchez, E. Reyes-Lozano, M. Perez, W. Carter, L. Ward, C. J. Altamirano, F. 2026-03-24 doi:10.64898/2026.03.21.713243 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ ZeaMiC: a Publicly Available Culture Collection of Maize Root-Associated Bacteria ]]> https://biorxiv.org/content/10.64898/2026.03.23.713778v1?rss=1 Garrell, A.-K. Ginnan, N. Swift, J. F. Pal, G. Zervas, A. Pestalozzi, C. Tang, C. Tso, F. Ford, N. E. Niu, B. Castrillo, G. Schlaeppi, K. Hahnke, R. L. Wagner, M. R. Kleiner, M. 2026-03-24 doi:10.64898/2026.03.23.713778 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ WTR: A Toolkit for Functional Anterograde Transsynaptic Circuit Mapping ]]> https://biorxiv.org/content/10.64898/2026.03.23.713595v1?rss=1 Wang, T. A. Chen, C. Liu, R. Yi-Luo, A. Cao, X. Hu, J. Guan, S. Chang, S.-y. Cui, X. Zhou, W. Zhao, F. Huang, C.-T. Duan, X. Jan, L. Y. 2026-03-25 doi:10.64898/2026.03.23.713595 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Structure-guided discovery and engineering of miniature CRISPR-Cas12m for epigenome editing ]]> https://biorxiv.org/content/10.64898/2026.03.26.714355v1?rss=1 Yu, T. Ji, M. Yu, D. Guan, Z. Zhu, R. Jiang, Y. Yang, Z. Qiu, L. Mu, J. Mao, F. Xiang, K. Bai, L. Li, K. 2026-03-28 doi:10.64898/2026.03.26.714355 Cold Spring Harbor Laboratory Press 2026-03-28 <![CDATA[ Structural analyses of Trichomonas vaginalis pyrophosphate-dependent phosphofructokinase (TvPPi-PFK) ]]> https://biorxiv.org/content/10.64898/2026.03.28.715000v1?rss=1 Chiu, A. Liu, L. Seibold, S. Battaile, K. Craig, J. Harmon, E. Subramanian, S. Chakafana, G. Early, J. Cron, L. Staker, B. Myler, P. J. Lovell, S. J. Van Voorhis, W. Asojo, O. 2026-03-28 doi:10.64898/2026.03.28.715000 Cold Spring Harbor Laboratory Press 2026-03-28 <![CDATA[ AlphaFold Database expands to proteome-scale quaternary structures ]]> https://biorxiv.org/content/10.64898/2026.03.27.714458v1?rss=1 Han, Y. Tsenkov, M. I. Venanzi, N. A. E. Bertoni, D. Cha, S. Chacon, A. Dietrich, N. Fomitchev, B. Goldtzvik, Y. Hsu, D. Austin, J. Ellaway, J. Didi, K. Kovalevskiy, O. Lasecki, D. Laydon, A. Livne, M. Magana, P. Majewski, M. Nair, S. Paramval, U. Patel, N. Patel, R. Pidruchna, I. Santini Lopez, B. Sohani, P. Tanweer, A. Tran, D. Tretina, K. Vollmar, M. Vu, Q. Zidek, A. Velankar, S. Steinegger, M. Fleming, J. Mirdita, M. Dallago, C. 2026-03-29 doi:10.64898/2026.03.27.714458 Cold Spring Harbor Laboratory Press 2026-03-29 <![CDATA[ Apelin inhibits cyst growth and improves kidney function in mice with polycystic kidney disease ]]> https://biorxiv.org/content/10.64898/2026.03.26.714294v1?rss=1 Nyimanu, D. Chakraborty, A. Parnell, S. Wallace, D. Yu, A. 2026-03-30 doi:10.64898/2026.03.26.714294 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Comparative single-cell atlases reveal injury-driven tubal epithelial regeneration as a window for ovarian carcinoma initiation ]]> https://biorxiv.org/content/10.64898/2026.03.26.714557v1?rss=1 Ralston, C. Q. Flesken-Nikitin, A. Fu, D.-J. Ashe, C. S. Harlan, B. A. Hossain, M. M. Wang, D. K. Yemelyanova, A. Schmoeckel, E. Godwin, A. K. Mayr, D. Cosgrove, B. D. Nikitin, A. Y. 2026-03-30 doi:10.64898/2026.03.26.714557 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ EFN-4/Ephrin converges with SAX-3/Robo, UNC-6/Netrin, and Heparan Sulfate Proteoglycan signaling to control MAB-5/Hox-dependent posterior Q neuroblast migration in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.64898/2026.03.27.714887v1?rss=1 Jain, V. D. Johannesen, A. Teixeira, F. L. Lundquist, E. A. 2026-03-31 doi:10.64898/2026.03.27.714887 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ eBiota: Designing microbial communities from large seed pools with desired function using rapid optimization and deep learning ]]> https://biorxiv.org/content/10.64898/2026.03.29.714676v1?rss=1 Jiang, X. Hou, J. Zhang, H. Guo, J. Gu, S. Vandeputte, D. Liao, Y. Guo, Q. Yang, X. Zhou, Y. Geng, P. X. Wang, C. Li, M. Jousset, A. Shen, X. Wei, Z. Zhu, H. 2026-03-31 doi:10.64898/2026.03.29.714676 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ KuafuPrimer: Machine learning empowers the design of 16S amplicon sequencing primers toward minimal bias for bacterial communities ]]> https://biorxiv.org/content/10.64898/2026.03.29.714677v1?rss=1 Zhang, H. Jiang, X. Yu, X. Wang, H. Lu, P. Hou, J. Guo, Q. Xiao, T. Wu, S. Yin, H. Geng, P. X. Guo, J. Jousset, A. Wei, Z. Xiao, Y. Zhu, H. 2026-03-31 doi:10.64898/2026.03.29.714677 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ A lateral linker histone binding mode scaffolds dinucleosome stacking in chromatin fibers ]]> https://biorxiv.org/content/10.64898/2026.03.29.715057v1?rss=1 Dong, A. Wang, Y. Yang, S. Wang, J. Wu, X. Zhou, D. Liu, P. Zha, R. Sun, J. Zhang, J. Lin, J. Zhou, H. Gan, J. 2026-03-31 doi:10.64898/2026.03.29.715057 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Inferring norepinephrine dynamics from partial observations reveals the temporal structure of elevations during arousal ]]> https://biorxiv.org/content/10.64898/2026.03.29.715097v1?rss=1 Neyhart, E. Munn, B. R. Yang, P. Feng, J. Li, Y. Shine, J. Reimer, J. 2026-03-31 doi:10.64898/2026.03.29.715097 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ The Computational and Neural Basis of Zero-Shot Control in Dynamic Pursuit ]]> https://biorxiv.org/content/10.64898/2026.03.30.715455v1?rss=1 Kim, D. Lee, J. J. Hayden, B. Y. Yoo, S. B. M. 2026-04-01 doi:10.64898/2026.03.30.715455 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ The stress-induced transcription factor ATF4 has multiple conserved retrocopies that can alter gene expression ]]> https://biorxiv.org/content/10.64898/2026.03.31.714484v1?rss=1 Dalton, H. M. Brydon, E. M. Chan, T. S. Owings, K. G. Wild, M. M. Young, N. J. Chow, C. Y. 2026-04-02 doi:10.64898/2026.03.31.714484 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ CNS diseases cerebrospinal fluid single-cell atlas reveals immune characteristics of neuropsychiatric systemic lupus erythematosus ]]> https://biorxiv.org/content/10.64898/2026.03.31.715151v1?rss=1 Wang, X.-J. Zhang, S.-Z. Fan, S.-Y. Zhang, W.-J. Ma, T.-Y. Fang, W.-T. Liang, N. Wu, Y. Yang, S.-Q. Xia, C.-R. Zhao, Z.-F. Zhao, J.-L. Xu, D. Zeng, X.-F. Guan, H.-Z. Ding, Y. Gao, G. Li, M.-T. 2026-04-02 doi:10.64898/2026.03.31.715151 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ Generating and navigating single cell dynamics via a geodesic bridge between nonlinear transcriptional and linear latent manifolds ]]> https://biorxiv.org/content/10.64898/2026.03.31.715478v1?rss=1 Zhu, J. Zhang, Z. Sun, Y. Dai, H. Wen, H. Zhou, P. Chen, L. 2026-04-02 doi:10.64898/2026.03.31.715478 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ Integrative Identification and Characterization of PCOS-Associated lncRNAs From the Interface of Genetic Association, Transcriptomics, and Gene Structure Evolution ]]> https://biorxiv.org/content/10.64898/2026.03.31.715548v1?rss=1 He, Z. Li, Y. Shkurat, T. P. Butenko, E. V. Derevyanchuk, E. G. Lomteva, S. V. Chen, L. Lipovich, L. 2026-04-02 doi:10.64898/2026.03.31.715548 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ A confined gene drive for population modification in the malaria vector Anopheles stephensi ]]> https://biorxiv.org/content/10.64898/2026.04.01.715791v1?rss=1 Xu, X. Liu, Y. Jia, X. Yang, J. Xia, Y. Chen, J. Champer, J. 2026-04-03 doi:10.64898/2026.04.01.715791 Cold Spring Harbor Laboratory Press 2026-04-03 <![CDATA[ Identification of Human Transferrin Receptor as an Entry Co-receptor for Parvovirus B19 Infection of Human Erythroid Progenitor Cells ]]> https://biorxiv.org/content/10.64898/2026.04.02.715920v1?rss=1 McFarlin, S. Ning, K. Zhang, X. Kuz, C. A. Zou, W. Cheng, F. Kleiboeker, S. Mietzsch, M. Qiu, J. 2026-04-03 doi:10.64898/2026.04.02.715920 Cold Spring Harbor Laboratory Press 2026-04-03 <![CDATA[ OpenAc4C: A gateway to decode the landscape, regulation and pathogenesis of N4-acetylcytidine (ac4C) epitranscriptome ]]> https://biorxiv.org/content/10.64898/2026.04.01.714364v1?rss=1 Tu, G. Zhang, Y. Wang, X. Zhang, J. Zhu, A. Chen, K. Wu, Z. Wu, Z. Wang, Y. Zhou, J. Wei, Z. Jia, G. Meng, J. Rigden, D. J. Song, B. 2026-04-05 doi:10.64898/2026.04.01.714364 Cold Spring Harbor Laboratory Press 2026-04-05 <![CDATA[ Structural Mechanism of TRPC3 Channel Activation by the Moonwalker Mutation ]]> https://biorxiv.org/content/10.64898/2026.04.03.716262v1?rss=1 Zang, J. Tan, Y. Chen, Y. Guo, W. Zhao, X. Peng, H. Chen, L. 2026-04-06 doi:10.64898/2026.04.03.716262 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ MolClaw: An Autonomous Agent with Hierarchical Skills for Drug Molecule Evaluation, Screening, and Optimization ]]> https://biorxiv.org/content/10.64898/2026.04.03.716272v1?rss=1 Zhang, L. Wang, L. Sun, X. Tang, W. Su, H. Qian, Y. Yang, Q. Li, Q. Tang, Z. Sun, H. Han, Y. Jiang, Y. Lou, W. Zhou, B. Wang, X. Bai, L. Xie, Z. 2026-04-06 doi:10.64898/2026.04.03.716272 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ Reciprocal-space mapping of diffuse scattering by serial femtosecond crystallography reveals analog-specific disorder in insulin analogs ]]> https://biorxiv.org/content/10.64898/2026.04.03.716400v1?rss=1 AYAN, E. Kang, J. Tosha, T. Yabashi, M. Shankar, M. K. 2026-04-07 doi:10.64898/2026.04.03.716400 Cold Spring Harbor Laboratory Press 2026-04-07 <![CDATA[ Low-Intensity Focused Ultrasound Enhances Meningeal Lymphatic Drainage for Preventing Cognitive Decline in Alzheimer's Disease ]]> https://biorxiv.org/content/10.64898/2026.04.06.716653v1?rss=1 Feng, Z. Hou, J. Li, X. Xu, X. Jiang, T. Zhu, C. Tang, Y. Shu, Y. Wang, Q. 2026-04-08 doi:10.64898/2026.04.06.716653 Cold Spring Harbor Laboratory Press 2026-04-08 <![CDATA[ PA-SfM: Tracker-free differentiable acoustic radiation for freehand 3D photoacoustic imaging ]]> https://biorxiv.org/content/10.64898/2026.04.06.716718v1?rss=1 Li, S. Gao, J. Kim, C. Choi, S. Chen, Q. Wang, Y. Wu, S. Zhang, Y. Huang, T. Zhou, Y. Yao, B. Yao, Y. Li, C. 2026-04-08 doi:10.64898/2026.04.06.716718 Cold Spring Harbor Laboratory Press 2026-04-08