bioRxiv Channel: Washington University in St. Louis https://biorxiv.org This feed contains articles for bioRxiv Channel "Washington University in St. Louis" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Psychiatric Genomics: An Update and an Agenda ]]> https://biorxiv.org/content/10.1101/115600v1?rss=1 Sullivan, P. F. Agrawal, A. Bulik, C. Andreassen, O. A. Borglum, A. Breen, G. Cichon, S. Edenberg, H. Faraone, S. V. Gelernter, J. Mathews, C. A. Nievergelt, C. M. Smoller, J. O'Donovan, M. Psychiatric Genomics Consortium, 2017-03-10 doi:10.1101/115600 Cold Spring Harbor Laboratory Press 2017-03-10 <![CDATA[ Kif9 is an active kinesin motor required for ciliary beating and proximodistal patterning of motile axonemes ]]> https://biorxiv.org/content/10.1101/2021.08.26.457815v1?rss=1 konjikusic, M. wallingford, j. gray, r. verhey, k. yang, y. prakash, v. horani, a. brody, s. nguimtsop, m. lee, c. Shrestha, B. 2021-08-27 doi:10.1101/2021.08.26.457815 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Multimerization and tubulin binding are required for the SPIRAL2 protein to localize to and stabilize microtubule minus ends ]]> https://biorxiv.org/content/10.1101/2021.10.05.463238v1?rss=1 FAN, Y. Bilkey, N. Dixit, R. 2021-10-05 doi:10.1101/2021.10.05.463238 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ Lipid associated polygenic enrichment in Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/383844v1?rss=1 500,000 cases and controls) and validated tools to quantify genetic pleiotropy, we systematically identified single nucleotide polymorphisms (SNPs) jointly associated with AD and one or more CV RFs, namely body mass index (BMI), type 2 diabetes (T2D), coronary artery disease (CAD), waist hip ratio (WHR), total cholesterol (TC), low-density (LDL) and high-density lipoprotein (HDL). In fold enrichment plots, we observed robust genetic enrichment in AD as a function of plasma lipids (TC, LDL, and HDL); we found minimal AD genetic enrichment conditional on BMI, T2D, CAD, and WHR. Beyond APOE, at conjunction FDR < 0.05 we identified 57 SNPs on 19 different chromosomes that were jointly associated with AD and CV outcomes including APOA4, ABCA1, ABCG5, LIPG, and MTCH2/SPI1. We found that common genetic variants influencing AD are associated with multiple CV RFs, at times with a different directionality of effect. Expression of these AD/CV pleiotropic genes was enriched for lipid metabolism processes, over-represented within astrocytes and vascular structures, highly co-expressed, and differentially altered within AD brains. Beyond APOE, we show that the polygenic component of AD is enriched for lipid associated RFs. Rather than a single causal link between genetic loci, RF and the outcome, we found that common genetic variants influencing AD are associated with multiple CV RFs. Our collective findings suggest that a network of genes involved in lipid biology also influence Alzheimers risk. ]]> Broce, I. Tan, C. H. Fan, C. C. Witoelar, A. Wen, N. Jansen, I. Hess, C. Dillon, W. Glastonbury, C. Glymour, M. Yokoyama, J. Elahi, F. Rabinovici, G. Miller, B. Mormino, E. Sperling, R. Bennett, D. McEvoy, L. Brewer, J. Feldman, H. Posthuma, D. Hyman, B. Schellenberg, G. Yaffe, K. Andreassen, O. Dale, A. Sugrue, L. Karch, C. Desikan, R. 2018-08-03 doi:10.1101/383844 Cold Spring Harbor Laboratory Press 2018-08-03 <![CDATA[ FRA1 modulates cortical microtubule localization of CMU proteins ]]> https://biorxiv.org/content/10.1101/760389v1?rss=1 Ganguly, A. Zhu, C. Chen, W. Dixit, R. 2019-09-06 doi:10.1101/760389 Cold Spring Harbor Laboratory Press 2019-09-06 <![CDATA[ Intrinsic cortical dynamics dominate population responses to natural images across human visual cortex ]]> https://biorxiv.org/content/10.1101/008961v1?rss=1 Linda Henriksson Seyed-Mahdi Khaligh-Razavi Kendrick Kay Nikolaus Kriegeskorte 2014-09-12 doi:10.1101/008961 Cold Spring Harbor Laboratory Press 2014-09-12 <![CDATA[ Fixed versus mixed RSA: Explaining visual representations by fixed and mixed feature sets from shallow and deep computational models ]]> https://biorxiv.org/content/10.1101/009936v1?rss=1 Seyed-Mahdi Khaligh-Razavi Linda Henriksson Kendrick Kay Nikolaus Kriegeskorte 2014-10-03 doi:10.1101/009936 Cold Spring Harbor Laboratory Press 2014-10-03 <![CDATA[ SpeedSeq: Ultra-fast personal genome analysis and interpretation ]]> https://biorxiv.org/content/10.1101/012179v1?rss=1 Colby Chiang Ryan M Layer Gregory G Faust Michael R Lindberg David B Rose Erik P Garrison Gabor T Marth Aaron R Quinlan Ira M Hall 2014-12-04 doi:10.1101/012179 Cold Spring Harbor Laboratory Press 2014-12-04 <![CDATA[ Model based normalization improves differential expression calling in low-depth RNA-seq ]]> https://biorxiv.org/content/10.1101/013854v1?rss=1 Pavel Zakharov Alexey Sergushichev Alexander Predeus Maxim Artyomov 2015-01-15 doi:10.1101/013854 Cold Spring Harbor Laboratory Press 2015-01-15 <![CDATA[ Rapid quantitative pharmacodynamic imaging with Bayesian estimation ]]> https://biorxiv.org/content/10.1101/017921v1?rss=1 Jonathan M Koller M. Jonathan Vachon G. Larry Bretthorst Kevin J Black 2015-04-13 doi:10.1101/017921 Cold Spring Harbor Laboratory Press 2015-04-13 <![CDATA[ The anatomical distribution of genetic associations ]]> https://biorxiv.org/content/10.1101/021824v1?rss=1 Alan B Wells Nathan Kopp Xiaoxiao Xu David R O'Brien Wei Yang Arye Nehorai Tracy L. Adair-Kirk Raphael Kopan Joseph D Dougherty 2015-07-01 doi:10.1101/021824 Cold Spring Harbor Laboratory Press 2015-07-01 <![CDATA[ Sulfur Isotope Effects of Dissimilatory Sulfite Reductase ]]> https://biorxiv.org/content/10.1101/023002v1?rss=1 William D. Leavitt Alexander S. Bradley André A. Santos Inês A.C. Pereira David T. Johnston 2015-07-22 doi:10.1101/023002 Cold Spring Harbor Laboratory Press 2015-07-22 <![CDATA[ Divergent MLS1 promoters lie on a fitness plateau for gene expression ]]> https://biorxiv.org/content/10.1101/026427v1?rss=1 Andrew C Bergen Gerilyn M Olsen Justin C Fay 2015-09-09 doi:10.1101/026427 Cold Spring Harbor Laboratory Press 2015-09-09 <![CDATA[ Climate and developmental plasticity: interannual variability in grapevine leaf morphology ]]> https://biorxiv.org/content/10.1101/030957v1?rss=1 5,500 leaves representing 270 grapevines of multiple Vitis species between two growing seasons. Leaves are paired one-to-one, vine-to-vine accounting for developmental context, between growing seasons. Linear Discriminant Analysis reveals shape features that specifically define growing season, regardless of species or developmental context. The shape feature, a more pronounced distal sinus, is associated with the colder, drier growing season, consistent with patterns observed in the paleorecord. We discuss the implications of such plasticity in a long-lived woody perennial, such as grapevine, with respect to the evolution and functionality of plant morphology and changes in climate. ]]> Daniel H Chitwood Susan M Rundell Darren Y Li Quaneisha L Woodford Tommy T Yu Jose R Lopez Danny Greenblatt Julie Kang Jason P Londo 2015-11-08 doi:10.1101/030957 Cold Spring Harbor Laboratory Press 2015-11-08 <![CDATA[ Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions ]]> https://biorxiv.org/content/10.1101/031724v1?rss=1 Steven H Wu Rachel S Schwartz David J Winter Don Conrad Reed A Cartwright 2015-11-14 doi:10.1101/031724 Cold Spring Harbor Laboratory Press 2015-11-14 <![CDATA[ Changes in the relative abundance of two Saccharomyces species from oak forests to wine fermentations ]]> https://biorxiv.org/content/10.1101/034157v1?rss=1 Sofia Dashko Ping Liu Helena Volk Lorena Butinar Jure Piskur Justin C. Fay 2015-12-10 doi:10.1101/034157 Cold Spring Harbor Laboratory Press 2015-12-10 <![CDATA[ Transhydrogenase and growth substrate influence lipid hydrogen isotope ratios in Desulfovibrio alaskensis G20 ]]> https://biorxiv.org/content/10.1101/039792v1?rss=1 William D. Leavitt Theodore M Flynn Melanie K Suess Alexander S Bradley 2016-02-17 doi:10.1101/039792 Cold Spring Harbor Laboratory Press 2016-02-17 <![CDATA[ Computational Pan-Genomics: Status, Promises and Challenges ]]> https://biorxiv.org/content/10.1101/043430v1?rss=1 Tobias Marschall Manja Marz Thomas Abeel Louis Dijkstra Bas E Dutilh Ali Ghaffaari Paul Kersey Wigard Kloosterman Veli Makinen Adam Novak Benedict Paten David Porubsky Eric RIVALS Can Alkan Jasmijn Baaijens Paul I. W. de Bakker Valentina Boeva Raoul J.P. Bonnal Francesca Chiaromonte Rayan Chikhi Francesca D. Ciccarelli Robin Cijvat Erwin Datema Cornelia M. Van Duijn Evan E. Eichler Corinna Ernst Eleazar Eskin Erik Garrison Mohammed El-Kebir Gunnar W. Klau Jan O Korbel Eric-Wubbo Lameijer Ben Langmead Marcel Martin Paul Medvedev John C. Mu Pieter Neerincx Klaasjan Ouwens Pierre Peterlongo Pisan 2016-03-12 doi:10.1101/043430 Cold Spring Harbor Laboratory Press 2016-03-12 <![CDATA[ The Interaction of Genotype and Environment Determines Variation in the Maize Kernel Ionome ]]> https://biorxiv.org/content/10.1101/048173v1?rss=1 Alexandra B Asaro Gregory R Ziegler Cathrine Ziyomo Owen A Hoekenga Brian P Dilkes Ivan Baxter 2016-04-13 doi:10.1101/048173 Cold Spring Harbor Laboratory Press 2016-04-13 <![CDATA[ Best Practices in Data Analysis and Sharing in Neuroimaging using MRI ]]> https://biorxiv.org/content/10.1101/054262v1?rss=1 Thomas E. Nichols Samir Das Simon B. Eickhoff Alan C. Evans Tristan Glatard Michael Hanke Nikolaus Kriegeskorte Michael P. Milham Russell A. Poldrack Jean-Baptiste Poline Erika Proal Bertrand Thirion David C. Van Essen Tonya White B. T. Thomas Yeo 2016-05-20 doi:10.1101/054262 Cold Spring Harbor Laboratory Press 2016-05-20 <![CDATA[ Brain structure in pediatric Tourette syndrome ]]> https://biorxiv.org/content/10.1101/054437v1?rss=1 Alton C. Williams Deanna J. Greene Jonathan M. Koller Bradley L. Schlaggar Kevin J. Black The Tourette Association of America Neuroimaging C 2016-05-20 doi:10.1101/054437 Cold Spring Harbor Laboratory Press 2016-05-20 <![CDATA[ MIGS: Methylation Interpolated Gene Signatures Determine Associations Between Differential Methylation and Gene Expression ]]> https://biorxiv.org/content/10.1101/063941v1?rss=1 Christopher E Schlosberg Nathan D VanderKraats John R Edwards 2016-07-15 doi:10.1101/063941 Cold Spring Harbor Laboratory Press 2016-07-15 <![CDATA[ SVScore: An Impact Prediction Tool For Structural Variation ]]> https://biorxiv.org/content/10.1101/073833v1?rss=1 Liron Ganel Haley J Abel Ira M Hall 2016-09-06 doi:10.1101/073833 Cold Spring Harbor Laboratory Press 2016-09-06 <![CDATA[ A Hypothesis to Explain Cancers in Confined Colonies of Naked Mole Rats ]]> https://biorxiv.org/content/10.1101/079012v1?rss=1 Michael E Hochberg Robert J Noble Stanton Braude 2016-10-03 doi:10.1101/079012 Cold Spring Harbor Laboratory Press 2016-10-03 <![CDATA[ The E. coli molecular phenotype under different growth conditions ]]> https://biorxiv.org/content/10.1101/082032v1?rss=1 CAGLAR, M. U. U. HOUSER, J. R. Barnhart, C. S. Boutz, D. R. Carroll, S. M. Dasgupta, A. Lenoir, W. F. Smith, B. L. Sridhara, V. Sydykova, D. K. Wood, D. V. Marx, C. J. Marcotte, E. M. Barrick, J. E. Wilke, C. O. 2016-10-20 doi:10.1101/082032 Cold Spring Harbor Laboratory Press 2016-10-20 <![CDATA[ Directional evolution in temperature-responsive gene expression in yeast ]]> https://biorxiv.org/content/10.1101/086785v1?rss=1 Li, X. C. Fay, J. C. 2016-11-09 doi:10.1101/086785 Cold Spring Harbor Laboratory Press 2016-11-09 <![CDATA[ Response variability and population coupling of cortical synaptic inputs are strongly influenced by network properties ]]> https://biorxiv.org/content/10.1101/087031v1?rss=1 Wright, N. C. Hoseini, M. S. Yasar, T. B. Wessel, R. 2016-11-10 doi:10.1101/087031 Cold Spring Harbor Laboratory Press 2016-11-10 <![CDATA[ Adaptation modulates correlated response variability in visual cortex ]]> https://biorxiv.org/content/10.1101/087049v1?rss=1 Wright, N. C. Hoseini, M. S. Wessel, R. 2016-11-10 doi:10.1101/087049 Cold Spring Harbor Laboratory Press 2016-11-10 <![CDATA[ Network activity influences the subthreshold and spiking visual responses of pyramidal neurons in a three-layer cortex ]]> https://biorxiv.org/content/10.1101/087288v1?rss=1 Wright, N. C. Wessel, R. 2016-11-11 doi:10.1101/087288 Cold Spring Harbor Laboratory Press 2016-11-11 <![CDATA[ High levels of antibiotic tolerance and persistence are induced by the commercial anti-microbial triclosan ]]> https://biorxiv.org/content/10.1101/090829v1?rss=1 10%) having urine concentrations equal to or greater than the minimal inhibitory concentration for Escherichia coli and methicillin-resistant Staphylococcus aureus (MRSA). Previous work has identified connections between defects in fatty acid synthesis and accumulation of the alarmone guanosine tetraphosphate (ppGpp), which has been repeatedly associated with antibiotic tolerance and persistence. Based on these data, we hypothesized that triclosan exposure may inadvertently drive bacteria into a state in which they are able to tolerate normally lethal concentrations of antibiotics. Here we report that clinically relevant concentrations of triclosan increased E. coli and MRSA tolerance to bactericidal antibiotics as much as 10,000 fold in vitro and reduced antibiotic efficacy up to 100-fold in a mouse urinary tract infection model. Genetic analysis indicated that triclosan-mediated antibiotic tolerance requires ppGpp synthesis, but is independent of growth. These data highlight an unexpected and certainly unintended consequence of adding high concentrations of antimicrobials in consumer products, supporting an urgent need to reevaluate the costs and benefits of the prophylactic use of triclosan and other bacteriostatic compounds.nnImportanceAdded as a prophylactic to a wide range of consumer products, the fatty acid synthesis inhibitor triclosan accumulates to high levels in humans and the environment. Based on links between defects in fatty acid synthesis and accumulation of the alarmone ppGpp, we hypothesized that triclosan would render cells tolerant to bactericidal compounds due to ppGpp-mediated inhibition of biosynthetic capacity. Our data indicate that clinically relevant concentrations of triclosan induces higher tolerance of E. coli and methicillin resistant S. aureus (MRSA) to a panel of bactericidal antibiotics up to 10,000-fold. In a urinary tract infection model, mice exposed to triclosan exhibited bacterial loads ~100-fold higher in the bladder than control animals following ciprofloxacin challenge. These findings highlight an unexpected consequence of antimicrobials in consumer products and support an urgent need to reevaluate the costs and benefits of the prophylactic use of triclosan and other bacteriostatic compounds. ]]> Westfall, C. S. Levin, P. A. 2016-12-01 doi:10.1101/090829 Cold Spring Harbor Laboratory Press 2016-12-01 <![CDATA[ Understanding genetic changes underlying the molybdate resistance and the glutathione production in Saccharomyces cerevisiae wine strains using an evolution-based strategy ]]> https://biorxiv.org/content/10.1101/092007v1?rss=1 Mezzetti, F. Fay, J. C. Giudici, P. De Vero, L. 2016-12-06 doi:10.1101/092007 Cold Spring Harbor Laboratory Press 2016-12-06 <![CDATA[ Flux through lipid synthesis dictates bacterial cell size. ]]> https://biorxiv.org/content/10.1101/092684v1?rss=1 Vadia, S. Tse, J. L. Wang, J. D. Levin, P. A. 2016-12-08 doi:10.1101/092684 Cold Spring Harbor Laboratory Press 2016-12-08 <![CDATA[ Function of the Arabidopsis kinesin-4, FRA1, requires abundant processive motility ]]> https://biorxiv.org/content/10.1101/107870v1?rss=1 Ganguly, A. DeMott, L. Dixit, R. 2017-02-13 doi:10.1101/107870 Cold Spring Harbor Laboratory Press 2017-02-13 <![CDATA[ Heritability of the structures and 13C fractionation in tomato leaf wax alkanes: a genetic model system to inform paleoenvironmental reconstructions ]]> https://biorxiv.org/content/10.1101/110718v1?rss=1 Bender, A. L. D. Chitwood, D. H. Bradley, A. S. 2017-02-21 doi:10.1101/110718 Cold Spring Harbor Laboratory Press 2017-02-21 <![CDATA[ A common haplotype lowers SPI1 (PU.1) expression in myeloid cells and delays age at onset for Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/110957v1?rss=1 Huang, K.-l. Marcora, E. Pimenova, A. Di Narzo, A. Kapoor, M. Jin, S. C. Harari, O. Bertelsen, S. Fairfax, B. Czajkowski, J. Chouraki, V. Grenier-Boley, B. Bellenguez, C. Deming, Y. McKenzie, A. Raj, T. Renton, A. Budde, J. Smith, A. Fitzpatrick, A. Bis, J. DeStefano, A. Adams, H. Ikram, M. A. van der Lee, S. Del-Aguila, J. Fernandez, M. Ibanez, L. The International Genomics of Alzheimer's Project, The Alzheimer's Disease Neuroimaging Initiative, Sims, R. Escott-Price, V. Mayeux, R. Haines, J. Farrer, L. Pericak-Vance, M. Lambert, J. C. van Duijn, C. L 2017-02-26 doi:10.1101/110957 Cold Spring Harbor Laboratory Press 2017-02-26 <![CDATA[ Subdomains of the Pol V largest subunit CTD mediate locus-specific RNA-directed DNA methylation ]]> https://biorxiv.org/content/10.1101/111831v1?rss=1 5' exoribonuclease, RRP6L1 was identified as an interactor with the DeCL subdomain and DeCL and glutamine-serine-rich (QS) subdomains, located downstream from an Argonaute-binding repeat subdomain. Experimental evidence indicates that RRP6L1 trims the 3 ends of Pol V transcripts sliced by ARGONAUTE 4 (AGO4), suggesting a model whereby the CTD enables the spatial and temporal coordination of AGO4 and RRP6L1 RNA processing activities. ]]> Wendte, J. Haag, J. Singh, J. McKinlay, A. Pontes, O. Pikaard, C. 2017-02-25 doi:10.1101/111831 Cold Spring Harbor Laboratory Press 2017-02-25 <![CDATA[ Multimodal Neural Correlates Of Cognitive Control In The Human Connectome Project ]]> https://biorxiv.org/content/10.1101/124123v1?rss=1 Lerman-Sinkoff, D. B. Sui, J. Rachakonda, S. Kandala, S. Calhoun, V. D. Barch, D. M. 2017-04-04 doi:10.1101/124123 Cold Spring Harbor Laboratory Press 2017-04-04 <![CDATA[ Association Between Substance Use Disorder And Polygenic Liability To Schizophrenia ]]> https://biorxiv.org/content/10.1101/129288v1?rss=1 Hartz, S. Horton, A. C. Oehlert, M. Carey, C. E. Agrawal, A. Bogdan, R. Chen, L.-S. Hancock, D. B. Johnson, E. O. Pato, C. Pato, M. Rice, J. P. Bierut, L. J. 2017-04-21 doi:10.1101/129288 Cold Spring Harbor Laboratory Press 2017-04-21 <![CDATA[ Dynamic Current Clamp Experiments Define The Functional Roles Of IK1 And Ito,f In Human Induced Pluripotent Stem Cell Derived Cardiomyocytes ]]> https://biorxiv.org/content/10.1101/135400v1?rss=1 Marrus, S. Springer, S. Johnson, E. Martinez, R. Dranoff, E. Mellor, R. Yamada, K. 2017-05-08 doi:10.1101/135400 Cold Spring Harbor Laboratory Press 2017-05-08 <![CDATA[ Local-Global Parcellation of the Human Cerebral Cortex From Intrinsic Functional Connectivity MRI ]]> https://biorxiv.org/content/10.1101/135632v1?rss=1 Schaefer, A. Kong, R. Gordon, E. M. Laumann, T. O. Zuo, X.-N. Holmes, A. Eickhoff, S. B. Yeo, B. T. T. 2017-06-06 doi:10.1101/135632 Cold Spring Harbor Laboratory Press 2017-06-06 <![CDATA[ Hydrogen Isotope Composition Of Thermoanaerobacterium saccharolyticum Lipids: Comparing Wild Type To A nfn- Transhydrogenase Mutant ]]> https://biorxiv.org/content/10.1101/138651v1?rss=1 Leavitt, W. D. Murphy, S. J.-L. Lynd, L. R. Bradley, A. S. 2017-05-17 doi:10.1101/138651 Cold Spring Harbor Laboratory Press 2017-05-17 <![CDATA[ Early warning signals regarding environmental suitability in the Drosophila antenna ]]> https://biorxiv.org/content/10.1101/146522v1?rss=1 Rong, H. Das, P. Lube, A. Yang, D. Saha, D. Ben-Shahar, Y. Raman, B. 2017-06-07 doi:10.1101/146522 Cold Spring Harbor Laboratory Press 2017-06-07 <![CDATA[ Neuronal adaptation and optimal coding in economic decisions ]]> https://biorxiv.org/content/10.1101/147900v1?rss=1 Rustichini, A. Conen, K. E. Cai, X. Padoa-Schioppa, C. 2017-06-08 doi:10.1101/147900 Cold Spring Harbor Laboratory Press 2017-06-08 <![CDATA[ rTMS with individualized resting-state network mapping for neuropsychiatric sequelae of repetitive traumatic brain injury in a retired NFL player ]]> https://biorxiv.org/content/10.1101/151696v1?rss=1 Siddiqi, S. H. Trapp, N. T. Hacker, C. D. Laumann, T. O. Kandala, S. Shahim, P. Carter, A. R. Brody, D. L. 2017-11-21 doi:10.1101/151696 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ Microevolutionary processes underlying macroevolutionary patterns of electric signal diversity in mormyrid fish ]]> https://biorxiv.org/content/10.1101/154047v1?rss=1 Gallant, J. R. Sperling, J. Cheng, C. Arnegard, M. E. Carlson, B. Hopkins, C. 2017-06-22 doi:10.1101/154047 Cold Spring Harbor Laboratory Press 2017-06-22 <![CDATA[ Polygenic hazard scores in preclinical Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/156331v1?rss=1 Tan, C. H. Sugrue, L. P. Broce, I. J. Tong, E. Tan, J. Hess, C. P. Dillon, W. P. Bonham, L. W. Yokoyama, J. S. Rabinovici, G. D. Rosen, H. J. Miller, B. L. Hyman, B. T. Schellenberg, G. D. Besser, L. M. Kukull, W. A. Karch, C. M. Brewer, J. B. Kauppi, K. McEvoy, L. K. Andreassen, O. A. Dale, A. M. Fan, C. C. Desikan, R. S. 2017-06-27 doi:10.1101/156331 Cold Spring Harbor Laboratory Press 2017-06-27 <![CDATA[ Inert and seed-competent tau monomers elucidate the structural origins of aggregation ]]> https://biorxiv.org/content/10.1101/163394v1?rss=1 Mirbaha, H. Morozova, O. A. Ruff, K. M. Sharma, A. Pappu, R. V. Colby, D. W. Mirzaei, H. Joachimiak, L. A. Diamond, M. I. 2017-07-14 doi:10.1101/163394 Cold Spring Harbor Laboratory Press 2017-07-14 <![CDATA[ Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins ]]> https://biorxiv.org/content/10.1101/164301v1?rss=1 Harmon, T. S. Holehouse, A. S. Rosen, M. K. Pappu, R. V. 2017-07-16 doi:10.1101/164301 Cold Spring Harbor Laboratory Press 2017-07-16 <![CDATA[ Polygenic hazard score: an enrichment marker for Alzheimer’s associated amyloid and tau deposition ]]> https://biorxiv.org/content/10.1101/165373v1?rss=1 Tan, C. H. Fan, C. C. Mormino, E. C. Sugrue, L. P. Broce, I. J. Hess, C. P. Dillion, W. P. Bonham, L. W. Yokoyama, J. S. Karch, C. M. Brewer, J. B. Rabinovici, G. D. Miller, B. L. Schellenberg, G. D. Kauppi, K. Feldman, H. A. Holland, D. McEvoy, L. K. Hyman, B. T. Andreassen, O. A. Dale, A. M. Desikan, R. S. 2017-07-18 doi:10.1101/165373 Cold Spring Harbor Laboratory Press 2017-07-18 <![CDATA[ Optogenetic silencing of primary afferents reduces evoked and ongoing bladder pain ]]> https://biorxiv.org/content/10.1101/167841v1?rss=1 Samineni, V. K. Mickle, A. D. Yoon, J. Grajales-Reyes, J. G. Pullen, M. Crawford, K. Noh, K. N. Gereau, G. Vogt, S. Lai, H. Rogers, J. Gereau, R. 2017-08-02 doi:10.1101/167841 Cold Spring Harbor Laboratory Press 2017-08-02 <![CDATA[ Mapping Movement, Mood, Motivation, and Mentation in the Subthalamic Nucleus ]]> https://biorxiv.org/content/10.1101/168302v1?rss=1 Gourisankar, A. Eisenstein, S. A. Trapp, N. T. Koller, J. M. Campbell, M. C. Ushe, M. Perlmutter, J. S. Hershey, T. Black, K. J. 2017-07-27 doi:10.1101/168302 Cold Spring Harbor Laboratory Press 2017-07-27 <![CDATA[ Bioinformatics Core Competencies for Undergraduate Life Sciences Education ]]> https://biorxiv.org/content/10.1101/170993v1?rss=1 Wilson Sayres, M. A. Hauser, C. Sierk, M. Robic, S. Rosenwald, A. G. Smith, T. M. Triplett, E. W. Williams, J. J. Dinsdale, E. Morgan, W. Burnette, J. M. Donovan, S. S. Drew, J. C. Elgin, S. C. R. Fowlks, E. R. Galindo-Gonzalez, S. Goodman, A. L. Grandgenett, N. F. Goller, C. C. Jungck, J. Newman, J. D. Pearson, W. R. Ryder, E. Tosado-Acevedo, R. Tapprich, W. Tobin, T. C. Toro-Martinez, A. Welch, L. R. Wright, R. Ebenbach, D. Olney, K. C. McWilliams, M. Pauley, M. A. 2017-08-03 doi:10.1101/170993 Cold Spring Harbor Laboratory Press 2017-08-03 <![CDATA[ Indole-3-Acetaldehyde Dehydrogenase-dependent Auxin Synthesis Contributes to Virulence of Pseudomonas syringae Strain DC3000 ]]> https://biorxiv.org/content/10.1101/173302v1?rss=1 McClerklin, S. A. Lee, S. G. Nwumeh, R. Jez, J. M. Kunkel, B. N. 2017-08-08 doi:10.1101/173302 Cold Spring Harbor Laboratory Press 2017-08-08 <![CDATA[ A nutrient-dependent division antagonist is regulated post-translationally by the Clp proteases in Bacillus subtilis ]]> https://biorxiv.org/content/10.1101/176222v1?rss=1 Hill, N. S. Zuke, J. D. Buske, P. J. Chien, A.-C. Levin, P. A. 2017-08-14 doi:10.1101/176222 Cold Spring Harbor Laboratory Press 2017-08-14 <![CDATA[ Tadpole-like conformations of huntingtin exon 1 with expanded polyglutamine engenders novel interactions in cells ]]> https://biorxiv.org/content/10.1101/179663v1?rss=1 Newcombe, E. A. Ruff, K. M. Sethi, A. Ormsby, A. Ramdzan, Y. M. Fox, A. Purcell, A. W. Gooley, P. R. Pappu, R. V. Hatters, D. M. 2017-08-22 doi:10.1101/179663 Cold Spring Harbor Laboratory Press 2017-08-22 <![CDATA[ CXCR4 involvement in neurodegenerative diseases ]]> https://biorxiv.org/content/10.1101/181693v1?rss=1 Bonham, L Karch, C Fan, C Tan, C Geier, E Wang, Y Wen, N Broce, I Li, Y Barkovich, M Ferrari, R Hardy, J Momeni, P Höeglinger, G Müller, U Hess, C Sugrue, L Dillon, W Schellenberg, G Miller, B Andreassen, O Dale, A Barkovich, A Yokoyama, J Desikan, R 2017-08-29 doi:10.1101/181693 Cold Spring Harbor Laboratory Press 2017-08-29 <![CDATA[ Raspberry Pi Powered Imaging for Plant Phenotyping ]]> https://biorxiv.org/content/10.1101/183822v1?rss=1 Tovar, J. Hoyer, J. S. Lin, A. Tielking, A. Callen, S. Castillo, E. Miller, M. Tessman, M. Fahlgren, N. Carrington, J. Nusinow, D. Gehan, M. A. 2017-09-01 doi:10.1101/183822 Cold Spring Harbor Laboratory Press 2017-09-01 <![CDATA[ Dynamic patterns of cortical expansion during folding of the preterm human brain ]]> https://biorxiv.org/content/10.1101/185389v1?rss=1 Garcia, K. E. Robinson, E. C. Alexopoulos, D. Dierker, D. L. Glasser, M. F. Coalson, T. S. Ortinau, C. M. Rueckert, D. Taber, L. A. Van Essen, D. C. Rogers, C. E. Smyser, C. D. Bayly, P. V. 2017-09-07 doi:10.1101/185389 Cold Spring Harbor Laboratory Press 2017-09-07 <![CDATA[ Precision genome-editing with CRISPR/Cas9 in human induced pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/187377v1?rss=1 Budde, J. P. Martinez, R. Hsu, S. Wen, N. Chen, J. A. Coppola, G. Goate, A. M. Cruchaga, C. Karch, C. 2017-09-12 doi:10.1101/187377 Cold Spring Harbor Laboratory Press 2017-09-12 <![CDATA[ Dynamic contrast enhancement and flexible odor codes ]]> https://biorxiv.org/content/10.1101/188011v1?rss=1 Nizampatnam, S. Saha, D. Chandak, R. Raman, B. 2017-09-12 doi:10.1101/188011 Cold Spring Harbor Laboratory Press 2017-09-12 <![CDATA[ Comprehensive analysis of central carbon metabolism reveals multiple connections between nutrients, biosynthetic capacity, and cell morphology in Escherichia coli ]]> https://biorxiv.org/content/10.1101/191585v1?rss=1 Westfall, C. S. Levin, P. 2017-09-20 doi:10.1101/191585 Cold Spring Harbor Laboratory Press 2017-09-20 <![CDATA[ Neural coding of fine-grained object knowledge in perirhinal cortex ]]> https://biorxiv.org/content/10.1101/194829v1?rss=1 Price, A. R. Bonner, M. F. Peelle, J. E. Grossman, M. 2017-09-27 doi:10.1101/194829 Cold Spring Harbor Laboratory Press 2017-09-27 <![CDATA[ Native and engineered clifednamide biosynthesis in multiple Streptomyces spp. ]]> https://biorxiv.org/content/10.1101/197616v1?rss=1 Qi, Y. Ding, E. Blodgett, J. 2017-10-03 doi:10.1101/197616 Cold Spring Harbor Laboratory Press 2017-10-03 <![CDATA[ Sleep-drive reprograms clock neuronal identity through CREB-binding protein induced PDFR expression ]]> https://biorxiv.org/content/10.1101/2019.12.12.874628v1?rss=1 Klose, M. K. Shaw, P. 2019-12-13 doi:10.1101/2019.12.12.874628 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ Systems analysis of blood transcriptomes in dementia patients reveals an innate immune response shared across disorders ]]> https://biorxiv.org/content/10.1101/2019.12.13.875112v1?rss=1 Nachun, D. Ramos, E. M. Karydas, A. Dokuru, D. Gao, F. Yang, Z. Van Berlo, V. Sears, R. L. Kramer, J. Boxer, A. L. Rosen, H. H. Miller, B. L. Coppola, G. 2019-12-13 doi:10.1101/2019.12.13.875112 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ Structural dynamics of isolated myosin motor domains encode differences in their mechanochemical cycles ]]> https://biorxiv.org/content/10.1101/2019.12.16.878264v1?rss=1 Porter, J. R. Meller, A. Zimmerman, M. I. Greenberg, M. J. Bowman, G. R. 2019-12-17 doi:10.1101/2019.12.16.878264 Cold Spring Harbor Laboratory Press 2019-12-17 <![CDATA[ Population Responses Represent Vocalization Identity, Intensity, and Signal-to-Noise Ratio in Primary Auditory Cortex ]]> https://biorxiv.org/content/10.1101/2019.12.21.886101v1?rss=1 Ni, R. Bender, D. A. Barbour, D. L. 2019-12-23 doi:10.1101/2019.12.21.886101 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ Dual role of auxin in regulating plant defense and bacterial virulence gene expression during Pseudomonas syringae PtoDC3000 pathogenesis. ]]> https://biorxiv.org/content/10.1101/2019.12.29.881581v1?rss=1 Djami-Tchatchou, A. T. Harrison, G. A. Harper, C. P. Wang, R. Prigge, M. J. Estelle, M. Kunkel, B. N. 2019-12-30 doi:10.1101/2019.12.29.881581 Cold Spring Harbor Laboratory Press 2019-12-30 <![CDATA[ Geometric Classification of Brain Network Dynamics via Donic Derivative Discriminants ]]> https://biorxiv.org/content/10.1101/201905v1?rss=1 Singh, M. F. Braver, T. Ching, S. 2017-10-11 doi:10.1101/201905 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ Memory Guides the Comprehension of Event Changes for Older and Younger Adults ]]> https://biorxiv.org/content/10.1101/201939v1?rss=1 Wahlheim, C. Zacks, J. 2017-10-12 doi:10.1101/201939 Cold Spring Harbor Laboratory Press 2017-10-12 <![CDATA[ New analysis pipeline for high-throughput domain-peptide affinity experiments improves SH2 interactiondata ]]> https://biorxiv.org/content/10.1101/2020.01.02.892901v1?rss=1 Ronan, T. Garnett, R. Naegle, K. M. 2020-01-02 doi:10.1101/2020.01.02.892901 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism. ]]> https://biorxiv.org/content/10.1101/2020.01.06.896258v1?rss=1 Buckley, R. M. Davis, B. W. Brashear, W. A. Farias, F. H. G. Kuroki, K. Graves, T. Hillier, L. W. Kremitzki, M. Li, G. Middleton, R. Minx, P. M. Tomlinson, C. Lyons, L. A. Murphy, W. J. Warren, W. C. 2020-01-07 doi:10.1101/2020.01.06.896258 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ Adult mice lacking VIP SCN neurons retain circadian locomotor behavior but exhibit dampened daily glucocorticoid rhythms ]]> https://biorxiv.org/content/10.1101/2020.01.07.897140v1?rss=1 Mazuski, C. Chen, S. P. Herzog, E. D. 2020-01-07 doi:10.1101/2020.01.07.897140 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ Dose-Dependent Induction Of CPP Or CPA By Intra-pVTA Ethanol: Role Of Mu Opioid Receptors And Effects On NMDA Receptors ]]> https://biorxiv.org/content/10.1101/2020.01.07.897702v1?rss=1 Campos-Jurado, Y. Marti-Prats, L. Moron, J. A. Polache, A. Granero, L. Hipolito, L. 2020-01-07 doi:10.1101/2020.01.07.897702 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ The Gossypium longicalyx genome as a resource for cotton breeding and evolution ]]> https://biorxiv.org/content/10.1101/2020.01.08.898908v1?rss=1 Grover, C. E. Pan, M. Yuan, D. Arick, M. A. Hu, G. Brase, L. Stelly, D. M. Lu, Z. Schmitz, R. J. Peterson, D. G. Wendel, J. F. Udall, J. A. 2020-01-09 doi:10.1101/2020.01.08.898908 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Population sequencing data reveal a compendium of mutational processes in human germline ]]> https://biorxiv.org/content/10.1101/2020.01.10.893024v1?rss=1 Seplyarskiy, V. B. Soldatov, R. McGinty, R. J. Goldmann, J. M. Hernandez, R. Barnes, K. Correa, A. Burchard, E. Ellinor, P. McGarvey, S. Mitchell, B. Ramachandran, V. Redline, S. Silverman, E. Weiss, S. Arnett, D. Blangero, J. Boerwinkle, E. He, J. Montgomery, C. Rao, D. C. Rotter, J. Brody, J. Chen, Y.-D. I. Fuentes, L. Hwu, C.-M. Rich, S. Manichaikul, A. Mychaleckyj, J. Palmer, N. Smith, J. Kardia, S. Peyser, P. Bielak, L. O'Connor, T. Emery, L. NHLBI Trans-Omics for Precision Medicine (TOPMed), TOPMed Population Genetics Working Group, Gilissen, C. 2020-01-11 doi:10.1101/2020.01.10.893024 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Systems level profiling of arginine starvation reveals MYC and ERK adaptive metabolic reprogramming ]]> https://biorxiv.org/content/10.1101/2020.01.13.904011v1?rss=1 Brashears, C. B. Rathore, R. Schultze, M. Ehrhardt, W. R. Tzeng, S.-C. Van Tine, B. A. Held, J. M. 2020-01-13 doi:10.1101/2020.01.13.904011 Cold Spring Harbor Laboratory Press 2020-01-13 <![CDATA[ 25-Hydroxycholesterol amplifies microglial IL-1β production in an apoE isoform-dependent manner ]]> https://biorxiv.org/content/10.1101/2020.01.14.906966v1?rss=1 >E2/E3) and thus may be an important mediator of neuroinflammation in AD. ]]> Wong, M. Y. Lewis, M. Doherty, J. J. Shi, Y. Sullivan, P. Qian, M. Covey, D. F. Petsko, G. A. Holtzman, D. M. Paul, S. M. Luo, W. 2020-01-15 doi:10.1101/2020.01.14.906966 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ High-resolution transcriptional and morphogenetic profiling of cells from micropatterned human embryonic stem cell gastruloid cultures ]]> https://biorxiv.org/content/10.1101/2020.01.22.915777v1?rss=1 Minn, K. T. Fu, Y. C. He, S. George, S. C. Anastasio, M. A. Morris, S. A. Solnica-Krezel, L. 2020-01-23 doi:10.1101/2020.01.22.915777 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Single-molecule orientation localization microscopy for resolving structural heterogeneities within amyloid fibrils ]]> https://biorxiv.org/content/10.1101/2020.01.22.916122v1?rss=1 Ding, T. Wu, T. Mazidi, H. Zhang, O. Lew, M. D. 2020-01-23 doi:10.1101/2020.01.22.916122 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ A new Spirodela polyrhiza genome and proteome reveal a conserved chromosomal structure with high abundances of proteins favoring energy production ]]> https://biorxiv.org/content/10.1101/2020.01.23.909457v1?rss=1 Harkess, A. E. McLoughlin, F. Bilkey, N. Elliott, K. Emenecker, R. Mattoon, E. Miller, K. Czymmek, K. Vierstra, R. Meyers, B. C. Michael, T. 2020-01-24 doi:10.1101/2020.01.23.909457 Cold Spring Harbor Laboratory Press 2020-01-24 <![CDATA[ TMEM184B controls pruriceptor specification and function ]]> https://biorxiv.org/content/10.1101/2020.01.25.919902v1?rss=1 Larsen, E. G. Cho, T. S. McBride, M. L. Feng, J. Manivannan, B. Madura, C. Klein, N. E. Wright, E. B. Garcia-Verdugo, H. D. Jarvis, C. Khanna, R. Hu, H. Largent-Milnes, T. M. Bhattacharya, M. R. C. 2020-01-26 doi:10.1101/2020.01.25.919902 Cold Spring Harbor Laboratory Press 2020-01-26 <![CDATA[ Non-invasive red-light optogenetic control of Drosophila cardiac function ]]> https://biorxiv.org/content/10.1101/2020.01.26.920132v1?rss=1 Men, J. Li, A. Jerwick, J. Li, Z. Tanzi, R. Zhou, C. 2020-01-26 doi:10.1101/2020.01.26.920132 Cold Spring Harbor Laboratory Press 2020-01-26 <![CDATA[ Sonogenetics for noninvasive and cellular-level neuromodulation in rodent brain ]]> https://biorxiv.org/content/10.1101/2020.01.28.919910v1?rss=1 Yang, Y. Pacia, C. P. Ye, D. Zhu, L. Baek, H. Yue, Y. Yuan, J. Miller, M. J. Cui, J. Culver, J. P. Bruchas, M. R. Chen, H. 2020-01-28 doi:10.1101/2020.01.28.919910 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ Alterations in neuronal physiology, development, and function associated with a common duplication of chromosome 15 involving CHRNA7 ]]> https://biorxiv.org/content/10.1101/2020.01.28.922187v1?rss=1 Meganathan, K. Prakasam, R. Baldridge, D. Gontarz, P. Zhang, B. Urano, F. Bonni, A. Constantino, J. N. Kroll, K. L. 2020-01-28 doi:10.1101/2020.01.28.922187 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ Synchronized genetic activities in Alzheimer's brains revealed by heterogeneity-capturing network analysis ]]> https://biorxiv.org/content/10.1101/2020.01.28.923730v1?rss=1 Climer, S. Templeton, A. R. Garvin, M. Jacobson, D. Lane, M. Hulver, S. Scheid, B. Chen, Z. Cruchaga, C. Zhang, W. 2020-01-29 doi:10.1101/2020.01.28.923730 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ Neural Circuit Dynamics for Sensory Detection ]]> https://biorxiv.org/content/10.1101/2020.01.28.923839v1?rss=1 Mallik, S. Nizampatnam, S. Nandi, A. Saha, D. Raman, B. Ching, S. 2020-01-29 doi:10.1101/2020.01.28.923839 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ ADAR1 editing dependency in triple-negative breast cancer ]]> https://biorxiv.org/content/10.1101/2020.01.31.928911v1?rss=1 Kung, C.-P. Cottrell, K. A. Ryu, S. Bramel, E. R. Kladney, R. D. Bross, E. A. Maggi, L. Weber, J. D. 2020-02-02 doi:10.1101/2020.01.31.928911 Cold Spring Harbor Laboratory Press 2020-02-02 <![CDATA[ The Oft-Overlooked Massively Parallel Reporter Assay: Where, When, and Which Psychiatric Genetic Variants are Functional? ]]> https://biorxiv.org/content/10.1101/2020.02.02.931337v1?rss=1 Mulvey, B. Lagunas, T. Dougherty, J. D. 2020-02-03 doi:10.1101/2020.02.02.931337 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ Exploring the coronavirus epidemic using the new WashU Virus Genome Browser ]]> https://biorxiv.org/content/10.1101/2020.02.07.939124v1?rss=1 Flynn, J. Purushotham, D. Choudhary, M. N. Zhuo, X. Fan, C. Matt, G. Li, D. Wang, T. 2020-02-11 doi:10.1101/2020.02.07.939124 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ ARF suppresses 5'-terminal oligopyrimidine mRNA translation ]]> https://biorxiv.org/content/10.1101/2020.02.07.939165v1?rss=1 Cottrell, K. A. Chiou, R. C. Weber, J. D. 2020-02-09 doi:10.1101/2020.02.07.939165 Cold Spring Harbor Laboratory Press 2020-02-09 <![CDATA[ Discovery of a cryptic allosteric site in Ebola's 'undruggable' VP35 protein using simulations and experiments ]]> https://biorxiv.org/content/10.1101/2020.02.09.940510v1?rss=1 Cruz, M. A. Frederick, T. E. Singh, S. Vithani, N. Zimmerman, M. I. Porter, J. R. Moeder, K. E. Amarasinghe, G. K. Bowman, G. R. 2020-02-10 doi:10.1101/2020.02.09.940510 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ Recent ultra-rare inherited mutations identify novel autism candidate risk genes ]]> https://biorxiv.org/content/10.1101/2020.02.10.932327v1?rss=1 Wilfert, A. B. Turner, T. N. Murali, S. C. Hsieh, P. Sulovari, A. Wang, T. Coe, B. P. Guo, H. Hoekzema, K. Bakken, T. E. Winterkorn, L. H. Evani, U. S. Byrska-Bishop, M. Earl, R. K. Bernier, R. A. The SPARK Consortium, Zody, M. C. Eichler, E. E. 2020-02-11 doi:10.1101/2020.02.10.932327 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ Explosive sensing with insect-based biorobots ]]> https://biorxiv.org/content/10.1101/2020.02.10.940866v1?rss=1 Saha, D. Mehta, D. Altan, E. Chandak, R. Traner, M. Lo, R. Gupta, P. Singamaneni, S. Chakrabartty, S. Raman, B. 2020-02-11 doi:10.1101/2020.02.10.940866 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ Remote-controlled insect navigation using plasmonic nanotattoos ]]> https://biorxiv.org/content/10.1101/2020.02.10.942540v1?rss=1 Tadepalli, S. Cao, S. Saha, D. Liu, K.-K. Chen, A. Bae, S. H. Raman, B. Singamaneni, S. 2020-02-11 doi:10.1101/2020.02.10.942540 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ Increased mTOR activity and metabolic efficiency in mouse and human cells containing the African-centric tumor-predisposing p53 variant Pro47Ser ]]> https://biorxiv.org/content/10.1101/2020.02.14.946269v1?rss=1 Gnanapradeepan, K. Basu, S. Barnoud, T. Leu, J. I.-J. Good, M. Lee, J. V. Quinn, W. J. Kung, C.-P. Ahima, R. S. Baur, J. A. Wellen, K. E. Liu, Q. Schug, Z. T. George, D. L. Murphy, M. E. 2020-02-15 doi:10.1101/2020.02.14.946269 Cold Spring Harbor Laboratory Press 2020-02-15 <![CDATA[ Central vestibular tuning arises from patterned convergence of otolith afferents ]]> https://biorxiv.org/content/10.1101/2020.02.14.948356v1?rss=1 Liu, Z. Kimura, Y. Higashijima, S.-i. Hildebrand, D. Morgan, J. Holy, T. Bagnall, M. W. 2020-02-15 doi:10.1101/2020.02.14.948356 Cold Spring Harbor Laboratory Press 2020-02-15 <![CDATA[ Vitamin D receptor protects against dysbiosis and tumorigenesis via the JAK/STAT pathway in intestine ]]> https://biorxiv.org/content/10.1101/2020.02.18.946335v1?rss=1 Zhang, Y.-g. Lu, R. Wu, S. Chatterjee, I. Zhou, D. Xia, Y. Sun, J. 2020-02-19 doi:10.1101/2020.02.18.946335 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Latent Plasticity of Effector-like Exhausted CD8 T cells contributes to memory responses ]]> https://biorxiv.org/content/10.1101/2020.02.22.960278v1?rss=1 Raju, S. Xia, Y. Daniel, B. Yost, K. E. Bradshaw, E. Tonc, E. Verbaro, D. J. Satpathy, A. T. Egawa, T. 2020-02-25 doi:10.1101/2020.02.22.960278 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Global Motion Detection and Censoring in High-Density Diffuse Optical Tomography ]]> https://biorxiv.org/content/10.1101/2020.02.22.961219v1?rss=1 Sherafati, A. Snyder, A. Z. Eggebrecht, A. T. Bergonzi, K. M. Burns-Yocum, T. M. Lugar, H. M. Ferradal, S. L. Robichaux-Viehoever, A. Smyser, C. D. Palanca, B. J. Hershey, T. Culver, J. P. 2020-02-25 doi:10.1101/2020.02.22.961219 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ 3D Epigenomic Characterization Reveals Insights Into Gene Regulation and Lineage Specification During Corticogenesis ]]> https://biorxiv.org/content/10.1101/2020.02.24.963652v1?rss=1 Song, M. Pebworth, M.-P. Yang, X. Abnousi, A. Fan, C. Wen, J. Rosen, J. Choudhary, M. Cui, X. Jones, I. Bergenholtz, S. Eze, U. Juric, I. Li, B. Maliskova, L. Liu, W. Pollen, A. Li, Y. Wang, T. Hu, M. Kriegstein, A. Shen, Y. 2020-02-25 doi:10.1101/2020.02.24.963652 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ ConsHMM Atlas: conservation state annotations for major genomes and human genetic variation ]]> https://biorxiv.org/content/10.1101/2020.03.01.955443v1?rss=1 Arneson, A. Felsheim, B. Chien, J. Ernst, J. 2020-03-02 doi:10.1101/2020.03.01.955443 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Extended amygdala-parabrachial circuits alter threat assessment to regulate feeding ]]> https://biorxiv.org/content/10.1101/2020.03.03.975193v1?rss=1 Bhatti, D. L. Luskin, A. T. Pedersen, C. E. Mulvey, B. Oden-Brunson, H. Kimbell, K. Sawyer, A. Gereau, R. W. Dougherty, J. D. Bruchas, M. R. 2020-03-05 doi:10.1101/2020.03.03.975193 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Chemokine receptor 2-targeted molecular imaging in pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/2020.03.04.960179v1?rss=1 Brody, S. L. Gunsten, S. P. Luehmann, H. P. Sultan, D. H. Hoelscher, M. Heo, G. S. Pan, J. Koenitzer, J. R. Lee, E. C. Huang, T. Mpoy, C. Guo, S. Laforest, R. Salter, A. Russell, T. D. Shifren, A. Combadiere, C. Lavine, K. J. Kreisel, D. Humphreys, B. D. Rogers, B. E. Grierada, D. S. Byers, D. E. Gropler, R. J. Chen, D. L. Atkinson, J. J. Liu, Y. 2020-03-05 doi:10.1101/2020.03.04.960179 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Computing and Optimizing Over All Fixed-Points of Discrete Systems on Large Networks ]]> https://biorxiv.org/content/10.1101/2020.03.04.960724v1?rss=1 Riehl, J. R. Zimmerman, M. I. Singh, M. F. Bowman, G. R. Ching, S. 2020-03-05 doi:10.1101/2020.03.04.960724 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Single nucleus RNASeq profiling of mouse lung: reduced dissociation bias and improved detection of rare cell types compared with single cell RNASeq ]]> https://biorxiv.org/content/10.1101/2020.03.06.981407v1?rss=1 Koenitzer, J. R. Wu, H. Atkinson, J. J. Brody, S. L. Humphreys, B. D. 2020-03-07 doi:10.1101/2020.03.06.981407 Cold Spring Harbor Laboratory Press 2020-03-07 <![CDATA[ Harnessing Expressed Single Nucleotide Variation and Single Cell RNA Sequencing to Define Immune Cell Chimerism in the Rejecting Kidney Transplant ]]> https://biorxiv.org/content/10.1101/2020.03.10.986075v1?rss=1 Malone, A. F. Wu, H. Fronick, C. Fulton, R. Gaut, J. P. Humphreys, B. D. 2020-03-11 doi:10.1101/2020.03.10.986075 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ IRF8 Governs Tumor-Associated Macrophage Control of T Cell Exhaustion ]]> https://biorxiv.org/content/10.1101/2020.03.12.989731v1?rss=1 Nixon, B. Kuo, F. Liu, M. Capistrano, K. Do, M. Franklin, R. Wu, X. Kansler, E. Srivastava, R. Purohit, T. Sanchez, A. Vuong, L. Krishna, C. Morse, H. Hsieh, J. Chan, T. Murphy, K. Moon, J. Hakimi, A. Li, M. 2020-03-14 doi:10.1101/2020.03.12.989731 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ CRISPR-TRAPSeq identifies the QKI RNA binding protein as important for astrocytic maturation and control of thalamocortical synapses. ]]> https://biorxiv.org/content/10.1101/2020.03.13.991224v1?rss=1 Sakers, K. Liu, Y. Llaci, L. Vasek, M. J. Rieger, M. A. Brophy, S. a. Tycksen, E. Lewis, R. Maloney, S. E. Dougherty, J. 2020-03-14 doi:10.1101/2020.03.13.991224 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ Scalable Surrogate Deconvolution for Identification of Partially-Observable Systems and Brain Modeling ]]> https://biorxiv.org/content/10.1101/2020.03.20.000661v1?rss=1 Singh, M. F. Wang, A. Braver, T. S. Ching, S. 2020-03-23 doi:10.1101/2020.03.20.000661 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury ]]> https://biorxiv.org/content/10.1101/2020.03.22.002261v1?rss=1 Kirita, Y. Wu, H. Uchimura, K. Wilson, P. Humphreys, B. 2020-03-23 doi:10.1101/2020.03.22.002261 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ A reversibly induced CRISPRi system targeting Photosystem II in the cyanobacterium Synechocystis sp. PCC 6803 ]]> https://biorxiv.org/content/10.1101/2020.03.24.005744v1?rss=1 Liu, D. Johnson, V. M. Pakrasi, H. B. 2020-03-25 doi:10.1101/2020.03.24.005744 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Human microglia upregulate cytokine signatures and accelerate maturation of neural networks ]]> https://biorxiv.org/content/10.1101/2020.03.24.006874v1?rss=1 Schmunk, G. Chang, K. N. Soliman, S. S. Keefe, M. G. Bogdanoff, D. Tejera, D. Ziffra, R. S. Shin, D. Allen, D. E. Chhun, B. B. McGinnis, C. S. Winkler, E. A. Abla, A. A. Chang, E. F. Gartner, Z. J. Mehta, S. B. Piao, X. Hengen, K. B. Nowakowski, T. J. 2020-03-25 doi:10.1101/2020.03.24.006874 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Mechanisms of Action of Autophagy Modulators Dissected by Quantitative Systems Pharmacology Analysis ]]> https://biorxiv.org/content/10.1101/2020.03.25.007344v1?rss=1 Shi, Q. Pei, F. Perlmutter, D. H. Liu, B. Bahar, I. 2020-03-25 doi:10.1101/2020.03.25.007344 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Therapeutic genetic variation revealed in diverse Hsp104 homologs ]]> https://biorxiv.org/content/10.1101/2020.03.25.008748v1?rss=1 March, Z. Sweeney, K. Kim, H. Yan, X. Castellano, L. Jackrel, M. Chuang, E. Gomes, E. Michalska, K. Jedrzejczak, R. Joachimiak, A. Caldwell, K. Caldwell, G. Shalem, O. Shorter, J. 2020-03-26 doi:10.1101/2020.03.25.008748 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ Facilitative priority effects drive parasite assembly under coinfection ]]> https://biorxiv.org/content/10.1101/2020.03.30.015495v1?rss=1 Halliday, F. W. Penczykowski, R. M. Barres, B. Eck, J. L. Numminen, E. Laine, A.-L. 2020-03-31 doi:10.1101/2020.03.30.015495 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ Ventral arkypallidal neurons modulate accumbal firing to promote reward consumption. ]]> https://biorxiv.org/content/10.1101/2020.04.01.020099v1?rss=1 Vachez, Y. M. Tooley, J. R. Casey, E. Earnest, T. Abiraman, K. Silberberg, H. Godynyuk, E. Uddin, O. Marconi, L. J. Le Pichon, C. Creed, M. C. 2020-04-02 doi:10.1101/2020.04.01.020099 Cold Spring Harbor Laboratory Press 2020-04-02 <![CDATA[ Diffusion Basis Spectrum Imaging with Deep Neural Network Differentiates Distinct Histology in Pediatric Brain Tumors ]]> https://biorxiv.org/content/10.1101/2020.04.02.020875v1?rss=1 Ye, Z. Srinivasa, K. Lin, J. Viox, J. Song, C. Wu, A. Sun, P. Song, S.-K. Dahiya, S. Rubin, J. B. 2020-04-03 doi:10.1101/2020.04.02.020875 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ The Mechanosensitive Ion Channel MSL10 Potentiates Responses to Cell Swelling in Arabidopsis Seedlings ]]> https://biorxiv.org/content/10.1101/2020.04.02.021683v1?rss=1 Basu, D. Haswell, E. 2020-04-03 doi:10.1101/2020.04.02.021683 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ One-step RNA extraction for RT-qPCR detection of 2019-nCoV ]]> https://biorxiv.org/content/10.1101/2020.04.02.022384v1?rss=1 Sentmanat, M. Kouranova, E. Cui, X. 2020-04-05 doi:10.1101/2020.04.02.022384 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression program ]]> https://biorxiv.org/content/10.1101/2020.04.07.029751v1?rss=1 Mondal, B. Jin, H. Kallappagoudar, S. Sedkov, Y. Martinez, T. Sentmanat, M. F. Poet, G. J. Li, C. Fan, Y. Pruett-Miller, S. M. Herz, H.-M. 2020-04-07 doi:10.1101/2020.04.07.029751 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Geographic mosaic of selection by avian predators on hindwing warning colour in a polymorphic aposematic moth ]]> https://biorxiv.org/content/10.1101/2020.04.08.032078v1?rss=1 Ronka, K. Valkonen, J. Nokelainen, O. Rojas, B. Gordon, S. Burdfield-Steel, E. Mappes, J. 2020-04-09 doi:10.1101/2020.04.08.032078 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Activity-dependent translation in astrocytes ]]> https://biorxiv.org/content/10.1101/2020.04.08.033027v1?rss=1 Sapkota, D. Sakers, K. Liu, Y. Lake, A. M. Khazanchi, R. Khankan, R. R. Zhang, Y. Dougherty, J. D. 2020-04-09 doi:10.1101/2020.04.08.033027 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ In silico APC/C substrate discovery reveals cell cycle degradation of chromatin regulators including UHRF1 ]]> https://biorxiv.org/content/10.1101/2020.04.09.033621v1?rss=1 Kernan, J. Martinez-Chacin, R. C. Wang, X. Tiedemann, R. L. Bonacci, T. Choudhury, R. Bolhuis, D. Damrauer, J. S. Yan, F. Harrison, J. S. Major, M. B. Hoadley, K. Suzuki, A. Rothbart, S. B. Brown, N. G. Emanuele, M. J. 2020-04-10 doi:10.1101/2020.04.09.033621 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ Sphingolipid Biosynthesis Inhibition As A Host Strategy Against Diverse Pathogens ]]> https://biorxiv.org/content/10.1101/2020.04.10.035683v1?rss=1 Kumar, S. Li, J. Park, J. Hart, S. K. Bean, N. L. Song, N. J. Coler-Reilly, A. Jacobs, N. C. Burrow, D. T. Onyshchenko Pendergrass, A. Pierre, T. H. Bradley, I. C. Varadarajan, M. Carette, J. E. Brummelkamp, T. R. Dolle, R. E. Peterson, T. R. 2020-04-14 doi:10.1101/2020.04.10.035683 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Predicting Tumor Cell Response to Synergistic Drug Combinations Using a Novel Simplified Deep Learning Model ]]> https://biorxiv.org/content/10.1101/2020.04.10.036491v1?rss=1 Zhang, H. Feng, J. Zeng, A. Payne, P. R. Li, F. 2020-04-13 doi:10.1101/2020.04.10.036491 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ Investigate the relevance of major signaling pathways in cancer survival using a biologically meaningful deep learning model ]]> https://biorxiv.org/content/10.1101/2020.04.13.039487v1?rss=1 Feng, J. Zhang, H. Li, F. 2020-04-14 doi:10.1101/2020.04.13.039487 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Ancestry-Specific Predisposing Germline Variants in Cancer ]]> https://biorxiv.org/content/10.1101/2020.04.14.032557v1?rss=1 Oak, N. Cherniak, A. D. Mashl, R. J. TCGA Analysis Network, Hirsch, F. R. Ding, L. Beroukhim, R. Gumus, Z. Plon, S. E. Huang, K.-l. 2020-04-14 doi:10.1101/2020.04.14.032557 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Signal diversification is associated with corollary discharge evolution in weakly electric fish ]]> https://biorxiv.org/content/10.1101/2020.04.16.044842v1?rss=1 Fukutomi, M. Carlson, B. A. 2020-04-18 doi:10.1101/2020.04.16.044842 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Organ-on-a-chip model of vascularized human bone marrow niches ]]> https://biorxiv.org/content/10.1101/2020.04.17.039339v1?rss=1 Glaser, D. E. Curtis, M. B. Sariano, P. A. Rollins, Z. A. Shergill, B. S. Anand, A. Deely, A. M. Shirure, V. S. Anderson, L. Lowen, J. M. Ng, N. R. Weilbaecher, K. Link, D. C. George, S. C. 2020-04-18 doi:10.1101/2020.04.17.039339 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ TMPRSS2 and TMPRSS4 mediate SARS-CoV-2 infection of human small intestinal enterocytes ]]> https://biorxiv.org/content/10.1101/2020.04.21.054015v1?rss=1 Zang, R. Castro, M. F. G. McCune, B. T. Zeng, Q. Rothlauf, P. W. Sonnek, N. M. Liu, Z. Brulois, K. F. Wang, X. Greenberg, H. B. Diamond, M. S. Ciorba, M. A. Whelan, S. P. J. Ding, S. 2020-04-23 doi:10.1101/2020.04.21.054015 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Cognitive Deficits and Altered Functional Brain Network Organization in Pediatric Brain Tumor Patients ]]> https://biorxiv.org/content/10.1101/2020.04.22.055459v1?rss=1 Anandarajah, H. Seitzman, B. A. McMichael, A. Dworetsky, A. Coalson, R. S. Jiang, C. Gu, H. Barbour, D. L. Schlaggar, B. L. Limbrick, D. D. Rubin, J. B. Shimony, J. S. Perkins, S. M. 2020-04-24 doi:10.1101/2020.04.22.055459 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Peptidoglycan editing provides immunity to Acinetobacter baumannii during bacterial warfare ]]> https://biorxiv.org/content/10.1101/2020.04.23.058008v1?rss=1 Le, N.-H. Peters, K. Espaillat, A. Sheldon, J. R. Gray, J. Di Venanzio, G. Lopez, J. Djahanschiri, B. Mueller, E. A. Hennon, S. W. Levin, P. A. Ebersberger, I. Skaar, E. P. Cava, F. Vollmer, W. Feldman, M. F. 2020-04-25 doi:10.1101/2020.04.23.058008 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ The qBED track: a novel genome browser visualization for point processes ]]> https://biorxiv.org/content/10.1101/2020.04.27.060061v1?rss=1 Moudgil, A. Li, D. Hsu, S. Purushotham, D. Wang, T. Mitra, R. D. 2020-04-29 doi:10.1101/2020.04.27.060061 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Site-specific effects of neurosteroids on GABAA receptor activation and desensitization ]]> https://biorxiv.org/content/10.1101/2020.04.27.063404v1?rss=1 Sugasawa, Y. Cheng, W. W. Bracamontes, J. Chen, Z.-W. Wang, L. Germann, A. L. Pierce, S. R. Senneff, T. C. Krishnan, K. Reichert, D. E. Covey, D. F. Akk, G. Evers, A. 2020-04-28 doi:10.1101/2020.04.27.063404 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Proteomic and functional mapping of cardiac NaV1.5 channel phosphorylation reveals multisite regulation of surface expression and gating ]]> https://biorxiv.org/content/10.1101/2020.04.29.067835v1?rss=1 Lorenzini, M. Burel, S. Lesage, A. Wagner, E. Charriere, C. Chevillard, P.-M. Evrard, B. Maloney, D. Ruff, K. M. Pappu, R. V. Wagner, S. Nerbonne, J. M. Silva, J. R. Townsend, R. R. Maier, L. S. Marionneau, C. 2020-04-30 doi:10.1101/2020.04.29.067835 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ A synthetic mechanogenetic gene circuit for autonomous drug delivery in engineered tissues ]]> https://biorxiv.org/content/10.1101/2020.04.29.069294v1?rss=1 Nims, R. Pferdehirt, L. Ho, N. Savadipour, A. Lorentz, J. Sohi, S. Kassab, J. Ross, A. O'Conor, C. Liedtke, W. Zhang, B. McNulty, A. Guilak, F. 2020-05-01 doi:10.1101/2020.04.29.069294 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ Earlier springs enable High-Arctic wolf spiders to produce a second clutch ]]> https://biorxiv.org/content/10.1101/2020.04.30.070029v1?rss=1 Hoye, T. T. Kresse, J.-C. Koltz, A. M. Bowden, J. J. 2020-05-02 doi:10.1101/2020.04.30.070029 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ Mechanical dysfunction induced by a hypertrophic cardiomyopathy mutation is the primary driver of cellular adaptation ]]> https://biorxiv.org/content/10.1101/2020.05.04.067181v1?rss=1 Clippinger, S. R. Cloonan, P. E. Wang, W. Greenberg, L. Stump, W. T. Angsutararux, P. Nerbonne, J. M. Greenberg, M. J. 2020-05-05 doi:10.1101/2020.05.04.067181 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Brain/MINDS Beyond Human Brain MRI Study: Multi-Site Harmonization for Brain Disorders Throughout the Lifespan ]]> https://biorxiv.org/content/10.1101/2020.05.05.076273v1?rss=1 Koike, S. Tanaka, S. Okada, T. Aso, T. Asano, M. Maikusa, N. Morita, K. Okada, N. Fukunaga, M. Uematsu, A. Togo, H. Miyazaki, A. Murata, K. Urushibata, Y. Autio, J. A. Ose, T. Yoshiomoto, J. Araki, T. Glasser, M. F. Van Essen, D. C. Murayama, M. Sadato, N. Kawato, M. Kasai, K. Okamoto, Y. Hanakawa, T. Hayashi, T. Brain/MINDS Beyond Human Brain MRI Group, 2020-05-05 doi:10.1101/2020.05.05.076273 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Genetic redundancy in iron and manganese transport in the metabolically versatile bacterium Rhodopseudomonas palustris TIE-1 ]]> https://biorxiv.org/content/10.1101/2020.05.08.085498v1?rss=1 Singh, R. Ranaivoarisoa, T. O. Gupta, D. Bai, W. Bose, A. 2020-05-10 doi:10.1101/2020.05.08.085498 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Conspecific negative density dependence and why its study should not be abandoned ]]> https://biorxiv.org/content/10.1101/2020.05.11.089334v1?rss=1 LaManna, J. A. Mangan, S. A. Myers, J. A. 2020-05-13 doi:10.1101/2020.05.11.089334 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ Single-molecule 3D orientation imaging reveals nanoscale compositional heterogeneity in lipid membranes ]]> https://biorxiv.org/content/10.1101/2020.05.12.091421v1?rss=1 3000 molecules/m2) of single molecules with nanoscale resolution remains elusive. We present SMOLM, single-molecule orientation localization microscopy, to directly measure the orientation spectra (3D orientation plus "wobble") of lipophilic probes transiently bound to lipid membranes, revealing that Nile reds (NR) orientation spectra are extremely sensitive to membrane chemical composition. SMOLM images resolve nanodomains and enzyme-induced compositional heterogeneity within membranes, where NR within liquid-ordered vs. liquid-disordered domains shows a ~4{degrees} difference in polar angle and a ~0.3{pi} sr difference in wobble angle. As a new type of imaging spectroscopy, SMOLM exposes the organizational and functional dynamics of lipid-lipid, lipid-protein, and lipid-dye interactions with single-molecule, nanoscale resolution. ]]> Lu, J. Mazidi, H. Ding, T. Zhang, O. Lew, M. D. 2020-05-13 doi:10.1101/2020.05.12.091421 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ Gait asymmetry, and bilateral coordination of gait during a six-minute walk test in persons with multiple sclerosis ]]> https://biorxiv.org/content/10.1101/2020.05.13.093161v1?rss=1 Plotnik, M. Wagner, J. M. Adusumilli, G. Gottlieb, A. Naismith, R. T. 2020-05-17 doi:10.1101/2020.05.13.093161 Cold Spring Harbor Laboratory Press 2020-05-17 <![CDATA[ Connecting coil-to-globule transitions to full phase diagrams for intrinsically disordered proteins ]]> https://biorxiv.org/content/10.1101/2020.05.13.093351v1?rss=1 Zeng, X. Holehouse, A. S. Chilkoti, A. Mittag, T. Pappu, R. V. 2020-05-17 doi:10.1101/2020.05.13.093351 Cold Spring Harbor Laboratory Press 2020-05-17 <![CDATA[ Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2. ]]> https://biorxiv.org/content/10.1101/2020.05.18.102038v1?rss=1 Case, J. B. Rothlauf, P. W. Chen, R. E. Liu, Z. Zhao, H. Kim, A. S. Bloyet, L.-M. Zeng, Q. Tahan, S. Droit, L. Ilagan, M. X. G. Tartell, M. A. Amarasinghe, G. K. Henderson, J. P. Miersch, S. Ustav, M. Sidhu, S. Virgin, H. W. Wang, D. Ding, S. Corti, D. Theel, E. S. Fremont, D. H. Diamond, M. S. Whelan, S. P. J. 2020-05-18 doi:10.1101/2020.05.18.102038 Cold Spring Harbor Laboratory Press 2020-05-18 <![CDATA[ Integrated hiPSC-based liver and heart microphysiological systems predict unsafe drug-drug interaction ]]> https://biorxiv.org/content/10.1101/2020.05.24.112771v1?rss=1 Lee-Montiel, F. T. Laemmle, A. Dumont, L. Lee, C. S. Huebsch, N. Charwat, V. Okochi, H. Hancock, M. J. Siemons, B. Bogess, S. Goswami, I. Miller, E. Willenbring, H. Healy, K. 2020-05-27 doi:10.1101/2020.05.24.112771 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data ]]> https://biorxiv.org/content/10.1101/2020.05.25.108654v1?rss=1 Ma, C. Z. Brent, M. 2020-05-26 doi:10.1101/2020.05.25.108654 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Tumor-on-a-chip platform to interrogate the role of macrophages in tumor progression ]]> https://biorxiv.org/content/10.1101/2020.05.27.119636v1?rss=1 Bi, Y. Shirure, V. S. Liu, R. Cunningham, C. Ding, L. Meacham, M. Goedegebuure, P. George, S. C. Fields, R. C. 2020-05-28 doi:10.1101/2020.05.27.119636 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ SARS-CoV-2 infection leads to acute infection with dynamic cellular and inflammatory flux in the lung that varies across nonhuman primate species ]]> https://biorxiv.org/content/10.1101/2020.06.05.136481v1?rss=1 Singh, D. K. Ganatra, S. R. Singh, B. Cole, J. Alfson, K. J. Clemmons, E. Gazi, M. Gonzalez, O. Escabedo, R. Lee, T.-H. Chatterjee, A. Goez-Gazi, Y. Sharan, R. Thippeshappa, R. Gough, M. Alvarez, C. Blakely, A. Ferdin, J. Bartley, C. Staples, H. Parodi, L. Callery, J. Mannino, A. Klaffke, B. Escareno, P. Platt, R. N. Hodara, V. Scordo, J. Oyejide, A. Ajithdoss, D. K. Copin, R. Baum, A. Kyratsous, C. Alvarez, X. Rosa, B. Ahmed, M. Goodroe, A. Dutton, J. Hall-Ursone, S. Frost, P. Voges, A. K. Ross, C. N. Sayers, K. Chen, C. Hallam, C. Khader, S. A. M 2020-06-05 doi:10.1101/2020.06.05.136481 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Artificial scaffolds that mimic the plant extracellular environment for the culture and attachment of plant cells ]]> https://biorxiv.org/content/10.1101/2020.06.05.136614v1?rss=1 Calcutt, R. Vincent, R. Dean, D. Arinzeh, T. L. Dixit, R. 2020-06-05 doi:10.1101/2020.06.05.136614 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Cholesterol 25-hydroxylase suppresses SARS-CoV-2 replication by blocking membrane fusion ]]> https://biorxiv.org/content/10.1101/2020.06.08.141077v1?rss=1 Ding, S. Zang, R. Case, J. B. Gomez Castro, M. F. Liu, Z. Zeng, Q. Zhao, H. Son, J. Rothlauf, P. W. Hou, G. Bose, S. Wang, X. Vahey, M. D. Kirchhausen, T. Fremont, D. H. Diamond, M. S. Whelan, S. P. J. 2020-06-09 doi:10.1101/2020.06.08.141077 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney ]]> https://biorxiv.org/content/10.1101/2020.06.14.151167v1?rss=1 Muto, Y. Wilson, P. C. Wu, H. Waikar, S. S. Humphreys, B. 2020-06-15 doi:10.1101/2020.06.14.151167 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ PKIS Deep Dive Yields a Chemical Starting Point for Dark Kinases and a Cell Active BRSK2 Inhibitor ]]> https://biorxiv.org/content/10.1101/2020.06.15.153072v1?rss=1 Tamir, T. Y. Drewry, D. H. Wells, C. Major, M. Axtman, A. D. 2020-06-16 doi:10.1101/2020.06.15.153072 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ Habitat patchiness drives spatial structure in morphological trait variation and co-variation in spotted salamanders (Ambystoma maculatum) ]]> https://biorxiv.org/content/10.1101/2020.06.15.153312v1?rss=1 Green, E. T. Dell, A. I. Crawford, J. A. Biro, E. G. Daversa, D. R. 2020-06-16 doi:10.1101/2020.06.15.153312 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ Shared and unique brain network features predict cognition, personality and mental health in childhood ]]> https://biorxiv.org/content/10.1101/2020.06.24.168724v1?rss=1 Chen, J. Tam, A. Kebets, V. Orban, C. Ooi, L. Q. R. Marek, S. Dosenbach, N. Eickhoff, S. Bzdok, D. Holmes, A. J. Yeo, B. T. T. 2020-06-24 doi:10.1101/2020.06.24.168724 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ GENERATION OF HEART ORGANOIDS MODELING EARLY HUMAN CARDIAC DEVELOPMENT UNDER DEFINED CONDITIONS ]]> https://biorxiv.org/content/10.1101/2020.06.25.171611v1?rss=1 Israeli, Y. Gabalski, M. Ball, K. Wasserman, A. Zou, J. Ni, G. Zhou, C. Aguirre, A. 2020-06-26 doi:10.1101/2020.06.25.171611 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ N-terminal modification of actin by acetylation and arginylation determines the architecture and assembly rate of linear and branched actin networks ]]> https://biorxiv.org/content/10.1101/2020.06.25.172320v1?rss=1 Chin, S. M. Hatano, T. Sivashanmugam, L. Suchenko, A. Kashina, A. S. BALASUBRAMANIAN, M. K. Jansen, S. 2020-06-27 doi:10.1101/2020.06.25.172320 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ The structure and diversity of strain level variation in vaginal bacteria ]]> https://biorxiv.org/content/10.1101/2020.06.26.173922v1?rss=1 Tortelli, B. A. Fay, J. C. Lewis, A. L. 2020-06-26 doi:10.1101/2020.06.26.173922 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ LINE-1 expression in cancer correlates with DNA damage response, copy number variation, and cell cycle progression ]]> https://biorxiv.org/content/10.1101/2020.06.26.174052v1?rss=1 McKerrow, W. H. Wang, X. Mita, P. Cao, S. Grivainis, M. Ding, L. LaCava, J. Boeke, J. Fenyö, D. H. 2020-06-27 doi:10.1101/2020.06.26.174052 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Citizen Scientists Create an Exascale Computer to Combat COVID-19 ]]> https://biorxiv.org/content/10.1101/2020.06.27.175430v1?rss=1 Zimmerman, M. I. Porter, J. R. Ward, M. D. Singh, S. Vithani, N. Meller, A. Mallimadugula, U. L. Kuhn, C. E. Borowsky, J. H. Wiewiora, R. P. Hurley, M. F. D. Harbison, A. M. Fogarty, C. A. Coffland, J. E. Fadda, E. Voelz, V. A. Chodera, J. D. Bowman, G. R. 2020-06-30 doi:10.1101/2020.06.27.175430 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ A Parallel Ratchet-Stroke Mechanism Leads to an Optimum Force for Molecular Motor Function. ]]> https://biorxiv.org/content/10.1101/2020.06.29.177964v1?rss=1 Mallimadugula, U. L. Galburt, E. 2020-06-29 doi:10.1101/2020.06.29.177964 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ The transcription factor Pdr802 regulates Cryptococcus neoformans Titan cell production and pathogenicity ]]> https://biorxiv.org/content/10.1101/2020.06.29.179242v1?rss=1 Reuwsaat, J. C. V. Motta, H. Agustinho, D. P. Brown, H. Chang, A. L. Kmetzsch, L. Doering, T. L. 2020-06-30 doi:10.1101/2020.06.29.179242 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ Smoothened Transduces Hedgehog Signals via Activity-Dependent Sequestration of PKA Catalytic Subunits ]]> https://biorxiv.org/content/10.1101/2020.07.01.183079v1?rss=1 Arveseth, C. D. Happ, J. T. Hedeen, D. S. Zhu, J.-F. Capener, J. L. Shaw, D. K. Deshpande, I. Liang, J. Xu, J. Stubben, S. L. Nelson, I. B. Walker, M. F. Krogan, N. J. Grunwald, D. J. Hüttenhain, R. Manglik, A. Myers, B. R. 2020-07-02 doi:10.1101/2020.07.01.183079 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Calmodulin acts as a state-dependent switch to control a cardiac potassium channel opening ]]> https://biorxiv.org/content/10.1101/2020.07.04.187161v1?rss=1 Kang, P. W. Westerlund, A. M. Shi, J. McFarland White, K. Dou, A. K. Cui, A. H. Silva, J. R. Delemotte, L. Cui, J. 2020-07-04 doi:10.1101/2020.07.04.187161 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Virulent disease epidemics can increase host density by depressing foraging of hosts ]]> https://biorxiv.org/content/10.1101/2020.07.06.189878v1?rss=1 Penczykowski, R. M. Hall, S. R. Shocket, M. S. Housley Ochs, J. Lemanski, B. C. P. Sundar, H. Duffy, M. A. 2020-07-06 doi:10.1101/2020.07.06.189878 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Replication-competent vesicular stomatitis virus vaccine vector protects against SARS-CoV-2-mediated pathogenesis ]]> https://biorxiv.org/content/10.1101/2020.07.09.196386v1?rss=1 James Brett Case Paul Rothlauf Rita E. Chen Natasha Kafai Julie M. Fox Swathi Shrihari Broc T. McCune Ian B. Harvey Brittany Smith Shamus Keeler Louis-Marie Bloyet Emma S Winkler Michael J. Holtzman Daved H. Fremont Sean P. J. Whelan Michael S. Diamond 2020-07-10 doi:10.1101/2020.07.09.196386 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ DNMT3A haploinsufficiency results in behavioral deficits and global epigenomic dysregulation shared across neurodevelopment disorders ]]> https://biorxiv.org/content/10.1101/2020.07.10.195859v1?rss=1 Christian, D. L. Wu, D. Y. Martin, J. R. Moore, J. R. Liu, Y. R. Clemens, A. W. Nettles, S. A. Kirkland, N. M. Hill, C. A. Wozniak, D. F. Dougherty, J. D. Gabel, H. W. 2020-07-13 doi:10.1101/2020.07.10.195859 Cold Spring Harbor Laboratory Press 2020-07-13 <![CDATA[ Small molecule resensitizes Salmonella to itaconate and decreases bacterial proliferation in macrophages ]]> https://biorxiv.org/content/10.1101/2020.07.15.204305v1?rss=1 Duncan, D. Chang, J. H. Artyomov, M. N. Auclair, K. 2020-07-15 doi:10.1101/2020.07.15.204305 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ Liver inflammation before spinal cord injury worsens neuropathology, hepatic injury, metabolic syndrome and locomotor deficits ]]> https://biorxiv.org/content/10.1101/2020.07.15.204578v1?rss=1 Goodus, M. T. Carson, K. E. Sauerbeck, A. D. Dey, P. Alfredo, A. N. Popovich, P. G. Bruno, R. S. McTigue, D. M. 2020-07-16 doi:10.1101/2020.07.15.204578 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ cDC1 Coordinate Innate and Adaptive Responses in the Omentum required for T cell Priming and Memory ]]> https://biorxiv.org/content/10.1101/2020.07.21.214809v1?rss=1 Christian, D. A. Adams, T. A. Smith, T. E. Shallberg, L. A. Theisen, D. J. Phan, A. T. Abraha, M. Perry, J. Ruthel, G. Clark, J. T. Murphy, K. M. Kedl, R. M. Hunter, C. A. 2020-07-22 doi:10.1101/2020.07.21.214809 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ The glycoprotease CpaA secreted by medically relevant Acinetobacter species targets multiple O-linked host glycoproteins ]]> https://biorxiv.org/content/10.1101/2020.07.22.216978v1?rss=1 Haurat, M. F. Scott, N. E. Di Venanzio, G. Lopez, J. Pluvinage, B. Boraston, A. Ferracane, M. J. Feldman, M. F. 2020-07-23 doi:10.1101/2020.07.22.216978 Cold Spring Harbor Laboratory Press 2020-07-23 <![CDATA[ Modelling white matter in gyral blades as a continuous vector field ]]> https://biorxiv.org/content/10.1101/2020.07.27.222778v1?rss=1 Cottaar, M. Bastiani, M. Boddu, N. Glasser, M. F. Haber, S. Van Essen, D. C. Sotiropoulos, S. N. Jbabdi, S. 2020-07-28 doi:10.1101/2020.07.27.222778 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Charged Pore-lining Residues are Required for Normal Channel Kinetics in the Eukaryotic Mechanosensitive Ion Channel MSL1 ]]> https://biorxiv.org/content/10.1101/2020.07.27.222992v1?rss=1 Schlegel, A. M. Haswell, E. 2020-07-28 doi:10.1101/2020.07.27.222992 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Lesion Quantification Toolkit: A MATLAB software tool for estimating grey matter damage and white matter disconnections in patients with focal brain lesions ]]> https://biorxiv.org/content/10.1101/2020.07.28.225771v1?rss=1 Griffis, J. C. Metcalf, N. V. Corbetta, M. Shulman, G. L. 2020-07-29 doi:10.1101/2020.07.28.225771 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Network variants are similar between task and rest states ]]> https://biorxiv.org/content/10.1101/2020.07.30.229492v1?rss=1 Kraus, B. Perez, D. Ladwig, Z. Seitzman, B. A. Dworetsky, A. Petersen, S. Gratton, C. 2020-07-31 doi:10.1101/2020.07.30.229492 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ Increasing temperature threatens an already endangered coastal dune plant ]]> https://biorxiv.org/content/10.1101/2020.08.02.233288v1?rss=1 Compagnoni, A. Pardini, E. Knight, T. M. 2020-08-03 doi:10.1101/2020.08.02.233288 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Brain Network Mechanisms of Visual Shape Completion ]]> https://biorxiv.org/content/10.1101/2020.08.03.233403v1?rss=1 Keane, B. P. Barch, D. M. Mill, R. Silverstein, S. M. Krekelberg, B. Cole, M. W. 2020-08-04 doi:10.1101/2020.08.03.233403 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ The SWELL1-LRRC8 complex regulates endothelial AKT-eNOS-mTOR signaling and vascular function ]]> https://biorxiv.org/content/10.1101/2020.08.04.236182v1?rss=1 Alghanem, A. F. Ta, C. Maurer, J. M. Gunasekar, S. K. Kumar, A. Fatima, U. Kang, C. Xie, L. Adeola, O. Abello, J. Riker, M. Elliot-Hudson, M. Minerath, R. A. Stratman, A. Grueter, C. E. Mullins, R. F. Sah, R. 2020-08-04 doi:10.1101/2020.08.04.236182 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Ligand Effects on Phase Separation of Multivalent Macromolecules ]]> https://biorxiv.org/content/10.1101/2020.08.15.252346v1?rss=1 Ruff, K. M. Dar, F. Pappu, R. V. 2020-08-15 doi:10.1101/2020.08.15.252346 Cold Spring Harbor Laboratory Press 2020-08-15 <![CDATA[ Regulation of Vacuole Morphology by PIEZO Channels in Spreading Earth Moss ]]> https://biorxiv.org/content/10.1101/2020.08.27.269282v1?rss=1 Radin, I. Richardson, R. A. Weiner, E. R. Bascom, C. S. Bezanilla, M. Haswell, E. 2020-08-27 doi:10.1101/2020.08.27.269282 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ De Novo Mutation in an Enhancer of EBF3 in simplex autism ]]> https://biorxiv.org/content/10.1101/2020.08.28.270751v1?rss=1 Padhi, E. M. Hayeck, T. J. Mannion, B. Chatterjee, S. Byrska-Bishop, M. Musunuri, R. Narzisi, G. Abhyankar, A. Cheng, Z. Hunter, R. D. Akiyama, J. Fries, L. E. Ng, J. Stong, N. Allen, A. S. Dickel, D. E. Bernier, R. A. Gorkin, D. U. Pennacchio, L. A. Zody, M. C. Turner, T. N. 2020-08-28 doi:10.1101/2020.08.28.270751 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ Aberrant RNA methylation triggers recruitment of an alkylation repair complex ]]> https://biorxiv.org/content/10.1101/2020.08.28.271874v1?rss=1 Brickner, J. R. Tsao, N. Rodell, R. Oyeniran, C. Lukinovic, V. Bacolla, A. Zhang, L. Soll, J. M. Casanova, A. Ganguly, A. He, C. Tainer, J. Reynoird, N. Mosammaparast, N. 2020-08-31 doi:10.1101/2020.08.28.271874 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Cingulo-Opercular Control Network Supports Disused Motor Circuits in Standby Mode ]]> https://biorxiv.org/content/10.1101/2020.09.03.275479v1?rss=1 Newbold, D. J. Gordon, E. M. Laumann, T. O. Montez, D. F. Seider, N. A. Gross, S. J. Zheng, A. Nielsen, A. N. Hoyt, C. R. Hampton, J. M. Ortega, M. Adeyemo, B. Miller, D. B. Van, A. N. Marek, S. Schlaggar, B. L. Carter, A. R. Kay, B. P. Greene, D. J. Raichle, M. E. Petersen, S. E. Snyder, A. Z. Dosenbach, N. U. F. 2020-09-04 doi:10.1101/2020.09.03.275479 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ Dysregulation of adipose ILC2 underlies thermogenic failure in aging ]]> https://biorxiv.org/content/10.1101/2020.09.08.288431v1?rss=1 Goldberg, E. L. Shchukina, I. Youm, Y.-H. Camell, C. D. Dlugos, T. Artyomov, M. Dixit, V. D. 2020-09-08 doi:10.1101/2020.09.08.288431 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ Ketogenesis restrains aging-induced exacerbation of COVID in a mouse model ]]> https://biorxiv.org/content/10.1101/2020.09.11.294363v1?rss=1 Ryu, S. Shchukina, I. Youm, Y.-H. Qing, H. Hilliard, B. K. Dlugos, T. Zhang, X. Yasumoto, Y. Booth, C. J. Fernandez-Hernando, C. Suarez, Y. Khanna, K. M. Horvath, T. Dietrich, M. O. Artyomov, M. Wang, A. Dixit, V. D. 2020-09-12 doi:10.1101/2020.09.11.294363 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ Gut metabolites influence susceptibility of neonatal mice to cryptosporidiosis. ]]> https://biorxiv.org/content/10.1101/2020.09.11.294462v1?rss=1 VanDussen, K. L. Funkhouser-Jones, L. Akey, M. E. Schaefer, D. A. Ackerman, K. Riggs, M. W. Stappenbeck, T. S. Sibley, L. D. 2020-09-12 doi:10.1101/2020.09.11.294462 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ The Dual Mechanisms of Cognitive Control (DMCC) Project ]]> https://biorxiv.org/content/10.1101/2020.09.18.304402v1?rss=1 Braver, T. S. Kizhner, A. Tang, R. Freund, M. C. Etzel, J. A. 2020-09-20 doi:10.1101/2020.09.18.304402 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ Dorsal Anterior Cingulate Cortex Encodes the Subjective Motivational Value of Cognitive Task Performance ]]> https://biorxiv.org/content/10.1101/2020.09.20.305482v1?rss=1 Yee, D. M. Crawford, J. L. Braver, T. S. 2020-09-20 doi:10.1101/2020.09.20.305482 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ A deep learning algorithm to translate and classify cardiac electrophysiology: From iPSC-CMs to adult cardiac cells ]]> https://biorxiv.org/content/10.1101/2020.09.28.317461v1?rss=1 Aghasafari, P. Yang, P.-C. Kernik, D. C. Sakamoto, K. Kanda, Y. Kurokawa, J. Vorobyov, I. Clancy, C. E. 2020-09-29 doi:10.1101/2020.09.28.317461 Cold Spring Harbor Laboratory Press 2020-09-29 <![CDATA[ Brazilin Removes Toxic alpha-Synuclein and Seeding Competent Assemblies from Parkinson Brain by Altering Conformational Equilibrium ]]> https://biorxiv.org/content/10.1101/2020.09.29.318220v1?rss=1 View larger version (18K): org.highwire.dtl.DTLVardef@447629org.highwire.dtl.DTLVardef@a9871dorg.highwire.dtl.DTLVardef@1e5a83dorg.highwire.dtl.DTLVardef@8843eb_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Nahass, G. R. Sun, Y. Xu, Y. Batchelor, M. Reilly, M. Benilova, I. Kedia, N. Spehar, K. Sobott, F. Sessions, R. B. Caughey, B. Radford, S. E. Jat, P. Collinge, J. Bieschke, J. 2020-10-01 doi:10.1101/2020.09.29.318220 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Novel Chlamydiae and Amoebophilus endosymbionts are prevalent in wild isolates of the model social amoebae Dictyostelium discoideum ]]> https://biorxiv.org/content/10.1101/2020.09.30.320895v1?rss=1 Haselkorn, T. S. Jimenez, D. Bashir, U. Sallinger, E. Queller, D. C. Strassmann, J. E. DiSalvo, S. 2020-09-30 doi:10.1101/2020.09.30.320895 Cold Spring Harbor Laboratory Press 2020-09-30 <![CDATA[ Ontogenetic Oxycodone Exposure Affects Early-Life Communicative Behaviors, Sensorimotor Reflexes, and Weight Trajectory in Mice ]]> https://biorxiv.org/content/10.1101/2020.09.30.321372v1?rss=1 Minakova, E. Sarafinovska, S. Mikati, M. O. Barclay, K. M. McCullough, K. B. Dougherty, J. D. Al-Hasani, R. Maloney, S. E. 2020-10-02 doi:10.1101/2020.09.30.321372 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Peripheral kappa opioid receptor activation drives cold hypersensitivity in mice ]]> https://biorxiv.org/content/10.1101/2020.10.04.325118v1?rss=1 Madasu, M. K. Thang, L. V. Chilukuri, P. Palanisamy, S. Arackal, J. S. Sheahan, T. D. Foshage, A. M. Houghten, R. A. McLaughlin, J. P. McCall, J. G. Al-Hasani, R. 2020-10-04 doi:10.1101/2020.10.04.325118 Cold Spring Harbor Laboratory Press 2020-10-04 <![CDATA[ Ablation of Proliferating Osteoblast Lineage Cells After Fracture Leads to Atrophic Nonunion in a Mouse Model ]]> https://biorxiv.org/content/10.1101/2020.10.06.327288v1?rss=1 Hixon, K. R. Sykes, D. A. Yoneda, S. Hensley, A. Buettmann, E. G. Skouteris, D. McKenzie, J. A. Miller, A. N. Silva, M. J. 2020-10-08 doi:10.1101/2020.10.06.327288 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Sustainable Production of the Biofuel n-Butanol by Rhodopseudomonas palustris TIE-1 ]]> https://biorxiv.org/content/10.1101/2020.10.13.336636v1?rss=1 Bai, W. Ranaivoarisoa, T. O. Singh, R. Rengasamy, K. Bose, A. 2020-10-14 doi:10.1101/2020.10.13.336636 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ The active repertoire of Escherichia coli peptidoglycan amidases varies with physiochemical environment ]]> https://biorxiv.org/content/10.1101/2020.10.19.344754v1?rss=1 Mueller, E. A. Iken, A. G. Oeztuerk, M. A. Schmitz, M. Di Ventura, B. Levin, P. A. 2020-10-19 doi:10.1101/2020.10.19.344754 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ Contribution of noncanonical antigens to virulence and adaptive immunity in human infection with enterotoxigenic E. coli ]]> https://biorxiv.org/content/10.1101/2020.10.20.348110v1?rss=1 Kuhlmann, F. M. Laine, R. O. Afrin, S. Nakajima, R. Akhtar, M. Vickers, T. J. Parker, K. Nizam, N. Grigura, V. Goss, C. W. Felgner, P. L. Rasko, D. Qadri, F. Fleckenstein, J. M. 2020-10-21 doi:10.1101/2020.10.20.348110 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Spatial and Temporal Organization of Odor-evoked Responses in a Fly Olfactory Circuit: Inputs, Outputs and Idiosyncrasies ]]> https://biorxiv.org/content/10.1101/2020.10.21.349688v1?rss=1 Rong, H. Zhang, L. Greer, C. Ben-Shahar, Y. Holy, T. E. Raman, B. 2020-10-22 doi:10.1101/2020.10.21.349688 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ Goblet cell LRRC26 regulates BK channel activation and protects against colitis in mice ]]> https://biorxiv.org/content/10.1101/2020.10.23.341396v1?rss=1 Gonzalez-Perez, V. M. Martinez-Espinosa, P. L. Sala-Rabanal, M. Bharadwaj, N. Xia, X. Chen, A. C. Alvarado, D. Gustafsson, J. K. Hu, H. Ciorba, M. A. Lingle, C. J. 2020-10-23 doi:10.1101/2020.10.23.341396 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ Spontaneous emergence of behaviorally relevant motifs in human motor cortex ]]> https://biorxiv.org/content/10.1101/2020.10.25.353326v1?rss=1 Livne, T. Kim, D. Metcalf, N. V. Shulman, G. L. Corbetta, M. 2020-10-26 doi:10.1101/2020.10.25.353326 Cold Spring Harbor Laboratory Press 2020-10-26 <![CDATA[ Modulating Intra-Nuclear LC3 with Small Molecules Rescues Cells from a Docetaxel-Induced Phenotype ]]> https://biorxiv.org/content/10.1101/2020.10.28.355826v1?rss=1 Rosenberg, D. P. Kolla, L. Heo, D. Cassio, E. Veenstra, M. J. Vakaki, M. Zhang, J. Anyetei-Anum, C. Allison, L. A. Buchser, W. J. 2020-10-28 doi:10.1101/2020.10.28.355826 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Human transcriptional activation domains require hydrophobic and acidic residues ]]> https://biorxiv.org/content/10.1101/2020.10.28.359026v1?rss=1 Staller, M. V. Ramirez, E. Holehouse, A. S. Pappu, R. V. Cohen, B. A. 2020-10-28 doi:10.1101/2020.10.28.359026 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Label-free cell viability assay using phase imaging with computational specificity ]]> https://biorxiv.org/content/10.1101/2020.10.28.359554v1?rss=1 Hu, C. He, S. Lee, Y. J. He, Y. Kong, E. M. Li, H. Anastasio, M. A. Popescu, G. 2020-10-28 doi:10.1101/2020.10.28.359554 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Fast inactivation of Na+ current in rat adrenal chromaffin cells involves two independent inactivation pathways ]]> https://biorxiv.org/content/10.1101/2020.10.31.363341v1?rss=1 Martinez-Espinosa, P. L. Neely, A. Ding, J. Lingle, C. J. 2020-11-01 doi:10.1101/2020.10.31.363341 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ Nav1.3 and fibroblast growth factor homologous factor 14 are primary determinants of the TTX-sensitive sodium current in mouse adrenal chromaffin cells ]]> https://biorxiv.org/content/10.1101/2020.10.31.363416v1?rss=1 Martinez-Espinosa, P. L. Yang, C. Xia, X. Lingle, C. J. 2020-10-31 doi:10.1101/2020.10.31.363416 Cold Spring Harbor Laboratory Press 2020-10-31 <![CDATA[ The genetic architecture of larval aggregation behavior in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.11.01.363994v1?rss=1 McKinney, R. Ben-Shahar, Y. 2020-11-01 doi:10.1101/2020.11.01.363994 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ Transient K+ current explains cross-species differences in the effects of myofibroblasts on myocytes ]]> https://biorxiv.org/content/10.1101/2020.11.02.365650v1?rss=1 Liu, F. Wu, H. Yang, X. Dong, Y. Huang, G. Genin, G. M. Lu, T. J. Xu, F. 2020-11-02 doi:10.1101/2020.11.02.365650 Cold Spring Harbor Laboratory Press 2020-11-02 <![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[ Mechanistic inferences from analysis of measurements of protein phase transitions in live cells ]]> https://biorxiv.org/content/10.1101/2020.11.04.369017v1?rss=1 Posey, A. E. Ruff, K. M. Lalmansingh, J. M. Kandola, T. S. Lange, J. J. Halfmann, R. Pappu, R. V. 2020-11-05 doi:10.1101/2020.11.04.369017 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Cryo-EM structure of a proton-activated chloride channel TMEM206 ]]> https://biorxiv.org/content/10.1101/2020.11.05.369835v1?rss=1 Deng, Z. Zhao, Y. Feng, J. Zhang, J. Zhao, H. Rau, M. J. Fitzpatrick, J. Hu, H. Yuan, P. 2020-11-05 doi:10.1101/2020.11.05.369835 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Landscape analysis of escape variants identifies SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization ]]> https://biorxiv.org/content/10.1101/2020.11.06.372037v1?rss=1 Liu, Z. VanBlargan, L. A. Rothlauf, P. W. Bloyet, L.-M. Chen, R. E. Stumpf, S. Zhao, H. Errico, J. M. Theel, E. S. Ellebedy, A. H. Fremont, D. H. Diamond, M. S. Whelan, S. P. J. 2020-11-08 doi:10.1101/2020.11.06.372037 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ Invariant Odor Recognition with ON-OFF Neural Ensembles ]]> https://biorxiv.org/content/10.1101/2020.11.07.372870v1?rss=1 Nizampatnam, S. Zhang, L. Chandak, R. Katta, N. Raman, B. 2020-11-08 doi:10.1101/2020.11.07.372870 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ Design of intrinsically disordered proteins that undergo phase transitions with lower critical solution temperatures ]]> https://biorxiv.org/content/10.1101/2020.11.13.381897v1?rss=1 Zeng, X. Liu, C. Fossat, M. J. Ren, P. Chilkoti, A. Pappu, R. V. 2020-11-15 doi:10.1101/2020.11.13.381897 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ Ancestral class-promiscuity as a driver of functional diversity in the BAHD acyltransferase family in plants ]]> https://biorxiv.org/content/10.1101/2020.11.18.385815v1?rss=1 160 published activities revealed the wide prevalence of promiscuity among BAHDs. Using phylogenetic analysis, we predicted the substrate classes that the ancestral enzymes were likely capable of using prior to land plant origins. While the anthocyanin acylation activity was fixed in BAHDs later near the origin of angiosperms, in vitro testing of BAHDs from non-seed plant lineages suggested that the ability to acylate anthocyanins likely existed promiscuously millions of years prior to its fixation. Motif enrichment analysis in anthocyanin-acylating BAHDs identified two motifs fixed in the largest anthocyanin acylating clade. Molecular dynamic simulations and enzyme kinetics revealed the important role of an active site tryptophan, whose bulkiness, hydrophobicity and aromaticity are critical for anthocyanin acylation. Our results thus describe the molecular processes in robust, evolvable enzymes that drive emergence of functional diversity in enzyme families. One sentence summaryUsing a combination of phylogenetics, biochemistry and protein structure analysis, we investigated how the BAHD acyltransferase family evolved to use a structurally diverse array of substrates. ]]> Kruse, L. H. Weigle, A. T. Martinez-Gomez, J. Chobirko, J. D. Schaffer, J. E. Bennett, A. A. Specht, C. D. Jez, J. M. Shukla, D. Moghe, G. D. 2020-11-20 doi:10.1101/2020.11.18.385815 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Frontoparietal pattern similarity analyses of cognitive control in monozygotic twins ]]> https://biorxiv.org/content/10.1101/2020.11.19.390492v1?rss=1 Tang, R. Etzel, J. A. Kizhner, A. Braver, T. S. 2020-11-20 doi:10.1101/2020.11.19.390492 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ A representational similarity analysis of cognitive control during color-word Stroop ]]> https://biorxiv.org/content/10.1101/2020.11.22.392704v1?rss=1 Freund, M. C. Bugg, J. M. Braver, T. S. 2020-11-23 doi:10.1101/2020.11.22.392704 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ Neuroskeletal effects of chronic bioelectric nerve stimulation in health and diabetes ]]> https://biorxiv.org/content/10.1101/2020.11.24.396143v1?rss=1 Beeve, A. T. Shen, I. Zhang, X. Magee, K. Yan, Y. MacEwan, M. Scheller, E. L. 2020-11-25 doi:10.1101/2020.11.24.396143 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ The kinase specificity of protein kinase inhibitor peptide (PKI) ]]> https://biorxiv.org/content/10.1101/2020.11.25.399204v1?rss=1 Chen, Y. Sabatini, B. L. 2020-11-27 doi:10.1101/2020.11.25.399204 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Microfluidic Device Facilitates Novel In Vitro Modeling of Human Neonatal Necrotizing Enterocolitis-on-a-Chip ]]> https://biorxiv.org/content/10.1101/2020.11.29.402735v1?rss=1 Lanik, W. E. Luke, C. J. Nolan, L. S. Gong, Q. Rimer, J. M. Gale, S. E. Luc, R. Bidani, S. S. Sibald, C. A. Lewis, A. N. Mihi, B. Agrawal, P. Goree, M. Maestas, M. Hu, E. Peters, D. G. Good, M. 2020-11-29 doi:10.1101/2020.11.29.402735 Cold Spring Harbor Laboratory Press 2020-11-29 <![CDATA[ Characterization of SARS-CoV-2 N protein reveals multiple functional consequences of the C-terminal domain ]]> https://biorxiv.org/content/10.1101/2020.11.30.404905v1?rss=1 Wu, C. Qavi, A. J. Hachim, A. Kavian, N. Cole, A. R. Moyle, A. B. Wagner, N. D. Sweeney-Gibbons, J. Rohrs, H. W. Gross, M. L. Peiris, J. S. M. Basler, C. F. Farnsworth, C. W. Valkenburg, S. A. Amarasinghe, G. K. Leung, D. W. 2020-11-30 doi:10.1101/2020.11.30.404905 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ Parallel Hippocampal-Parietal Circuits for Self- and Goal-oriented Processing ]]> https://biorxiv.org/content/10.1101/2020.12.01.395210v1?rss=1 Zheng, A. Montez, D. F. Marek, S. Gilmore, A. Newbold, D. J. Laumann, T. O. Kay, B. P. Seider, N. A. Van, A. N. Hampton, J. M. Alexopolous, D. Schlaggar, B. L. Sylvester, C. M. Greene, D. J. Shimony, J. S. Nelson, S. M. Wig, G. S. Gratton, C. McDermott, K. B. Raichle, M. E. Gordon, E. M. Dosenbach, N. U. 2020-12-02 doi:10.1101/2020.12.01.395210 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ A single intranasal or intramuscular immunization with chimpanzee adenovirus vectored SARS-CoV-2 vaccine protects against pneumonia in hamsters. ]]> https://biorxiv.org/content/10.1101/2020.12.02.408823v1?rss=1 Bricker, T. Darling, T. Hassan, A. Harastani, H. Soung, A. Jiang, X. Dai, Y.-N. Zhao, H. Adams, L. Holtzman, M. Bailey, A. Case, J. B. Fremont, D. Klein, R. S. Diamond, M. Boon, A. 2020-12-03 doi:10.1101/2020.12.02.408823 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Insulinase like protease 1 contributes to macrogamont formation in Cryptosporidium parvum ]]> https://biorxiv.org/content/10.1101/2020.12.03.411165v1?rss=1 Xu, R. Feng, Y. Xiao, L. Sibley, L. D. 2020-12-04 doi:10.1101/2020.12.03.411165 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ Probing E. coli SSB Protein-DNA topology by reversing DNA backbone polarity ]]> https://biorxiv.org/content/10.1101/2020.12.05.412478v1?rss=1 200 mM) and displays "limited" low cooperativity. Crystal structures of E. coli SSB and P. falciparum SSB show ssDNA bound to the SSB subunits (OB-folds) with opposite polarities of the sugar phosphate backbones. To investigate whether SSB subunits show a polarity preference for binding ssDNA, we examined EcSSB and PfSSB binding to a series of (dT)70 constructs in which the backbone polarity was switched in the middle of the DNA by incorporating a reverse polarity (RP) phosphodiester linkage, either 3-3 or 5-5. We find only minor effects on the DNA binding properties for these RP constructs, although (dT)70 with a 3-3 polarity switch shows decreased affinity for EcSSB in the (SSB)65 mode and lower cooperativity in the (SSB)35 mode. However, (dT)70 in which every phosphodiester linkage is reversed, does not form a completely wrapped (SSB)65 mode, but rather binds EcSSB in the (SSB)35 mode, with little cooperativity. In contrast, PfSSB, which binds ssDNA only in an (SSB)65 mode and with opposite backbone polarity and different topology, shows little effect of backbone polarity on its DNA binding properties. We present structural models suggesting that strict backbone polarity can be maintained for ssDNA binding to the individual OB-folds if there is a change in ssDNA wrapping topology of the RP ssDNA. Statement of SignificanceSingle stranded (ss) DNA binding (SSB) proteins are essential for genome maintenance. Usually homo-tetrameric, bacterial SSBs bind ssDNA in multiple modes, one of which involves wrapping 65 nucleotides of ssDNA around all four subunits. Crystal structures of E. coli and P. falciparum SSB-ssDNA complexes show ssDNA bound with different backbone polarity orientations raising the question of whether these SSBs maintain strict backbone polarity in binding ssDNA. We show that both E. coli and P. falciparum SSBs can still form high affinity fully wrapped complexes with non-natural DNA containing internal reversals of the backbone polarity. These results suggest that both proteins maintain a strict backbone polarity preference, but adopt an alternate ssDNA wrapping topology. ]]> Lohman, T. M. Kozlov, A. G. 2020-12-06 doi:10.1101/2020.12.05.412478 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Starvation induces shrinkage of the bacterial cytoplasm ]]> https://biorxiv.org/content/10.1101/2020.12.06.413849v1?rss=1 Shi, H. Westfall, C. S. Kao, J. Odermatt, P. D. Cesar, S. Sievert, M. Moore, J. Gonzalez, C. G. Zhang, L. Elias, J. E. Chang, F. Huang, K. C. Levin, P. A. 2020-12-07 doi:10.1101/2020.12.06.413849 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ Accurate neoantigen prediction depends on mutation position relative to patient allele-specific MHC anchor location ]]> https://biorxiv.org/content/10.1101/2020.12.08.416271v1?rss=1 Xia, H. McMichael, J. F. Supabphol, S. Richters, M. M. Basu, A. Ramirez, C. A. Puig-Saus, C. Cotto, K. C. Hundal, J. Kiwala, S. Goedegebuure, S. P. Johanns, T. M. Dunn, G. P. Fehniger, T. A. Ribas, A. Miller, C. A. Gillanders, W. E. Griffith, O. L. Griffith, M. 2020-12-08 doi:10.1101/2020.12.08.416271 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential ]]> https://biorxiv.org/content/10.1101/2020.12.10.420109v1?rss=1 Vithani, N. Ward, M. D. Zimmerman, M. I. Novak, B. Borowsky, J. H. Singh, S. Bowman, G. R. 2020-12-10 doi:10.1101/2020.12.10.420109 Cold Spring Harbor Laboratory Press 2020-12-10 <![CDATA[ Enhancing Task fMRI Preprocessing via Individualized Model-Based Filtering of Intrinsic Activity Dynamics ]]> https://biorxiv.org/content/10.1101/2020.12.10.420273v1?rss=1 Singh, M. F. Wang, A. Cole, M. Ching, S. Braver, T. S. 2020-12-11 doi:10.1101/2020.12.10.420273 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Bridges, not walls: the hippocampus builds narrative memories across distant events ]]> https://biorxiv.org/content/10.1101/2020.12.11.422162v1?rss=1 Cohn-Sheehy, B. I. Delarazan, A. I. Reagh, Z. M. Crivelli-Decker, J. E. Zacks, J. M. Ranganath, C. 2020-12-12 doi:10.1101/2020.12.11.422162 Cold Spring Harbor Laboratory Press 2020-12-12 <![CDATA[ Association of Structural Variation with Cardiometabolic Traits in Finns ]]> https://biorxiv.org/content/10.1101/2020.12.13.422502v1?rss=1 Chen, L. Abel, H. J. Das, I. Larson, D. E. Ganel, L. Kanchi, K. L. Regier, A. A. Young, E. P. Kang, C. J. Scott, A. J. Chiang, C. Wang, X. Lu, S. Christ, R. Service, S. Chiang, C. W. K. Havulinna, A. S. Kuusisto, J. Boehnke, M. W. K. Laakso, M. Palotie, A. Ripatti, S. Freimer, N. B. Locke, A. E. Stitziel, N. O. Hall, I. M. 2020-12-13 doi:10.1101/2020.12.13.422502 Cold Spring Harbor Laboratory Press 2020-12-13 <![CDATA[ Total recall: episodic memory retrieval,choice, and memory confidence in the rat ]]> https://biorxiv.org/content/10.1101/2020.12.14.420174v1?rss=1 Joo, H. R. Liang, H. Chung, J. E. Geaghan-Breiner, C. Fan, J. L. Nachman, B. Kepecs, A. Frank, L. M. 2020-12-15 doi:10.1101/2020.12.14.420174 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Microbial Species Abundance Distributions Guide Human Population Size Estimation from Sewage Metagenomes ]]> https://biorxiv.org/content/10.1101/2020.12.15.390716v1?rss=1 Ling, F. Chen, L. Zhang, L. Yu, X. Duvallet, C. Isazadeh, S. Dai, C. Park, S. Frois-Moniz, K. Duarte, F. Ratti, C. Alm, E. J. 2020-12-15 doi:10.1101/2020.12.15.390716 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Structure-guided microbial targeting of antistaphylococcal prodrugs ]]> https://biorxiv.org/content/10.1101/2020.12.15.408237v1?rss=1 Miller, J. Shah, I. T. Hatten, J. Barekatain, Y. Mueller, E. A. Moustafa, A. M. Edwards, R. L. Dowd, C. S. Planet, P. J. Muller, F. L. Jez, J. M. Odom John, A. R. 2020-12-15 doi:10.1101/2020.12.15.408237 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Predicting which genes will respond to perturbations of a TF: TF-independent properties of genes are major determinants of their responsiveness ]]> https://biorxiv.org/content/10.1101/2020.12.15.422864v1?rss=1 Kang, Y. Brent, M. 2020-12-15 doi:10.1101/2020.12.15.422864 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ A MYT1L Syndrome mouse model recapitulates patient phenotypes and reveals altered brain development due to disrupted neuronal maturation ]]> https://biorxiv.org/content/10.1101/2020.12.17.423095v1?rss=1 Chen, J. Lambo, M. E. Xia, G. Dearborn, J. T. Liu, Y. McCullough, K. B. Swift, R. G. Tabachnick, D. R. Tian, L. Noguchi, K. Garbow, J. R. Gabel, H. W. Hengen, K. B. Maloney, S. E. Dougherty, J. D. 2020-12-17 doi:10.1101/2020.12.17.423095 Cold Spring Harbor Laboratory Press 2020-12-17 <![CDATA[ SARS-CoV-2 protein ORF3a is pathogenic in Drosophila and causes phenotypes associated with COVID-19 post-viral syndrome ]]> https://biorxiv.org/content/10.1101/2020.12.20.423533v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@1be5b38org.highwire.dtl.DTLVardef@56e061org.highwire.dtl.DTLVardef@1a52040org.highwire.dtl.DTLVardef@1e86751_HPS_FORMAT_FIGEXP M_FIG C_FIG SummaryInfections and neurodegenerative diseases induce neuroinflammation, but affected individuals often show a number of non-neural symptoms including muscle pain and muscle fatigue. The molecular pathways by which neuroinflammation causes pathologies outside the central nervous system (CNS) are poorly understood, so we developed three models to investigate the impact of neuroinflammation on muscle performance. We found that bacterial infection, COVID-like viral infection, and expression of a neurotoxic protein associated with Alzheimer' s disease promoted the accumulation of reactive oxygen species (ROS) in the brain. Excessive ROS induces the expression of the cytokine Unpaired 3 (Upd3) in insects, or its orthologue IL-6 in mammals, and CNS-derived Upd3/IL-6 activates the JAK/Stat pathway in skeletal muscle. In response to JAK/Stat signaling, mitochondrial function is impaired and muscle performance is reduced. Our work uncovers a brain-muscle signaling axis in which infections and chronic diseases induce cytokine-dependent changes in muscle performance, suggesting IL-6 could be a therapeutic target to treat muscle weakness caused by neuroinflammation. ]]> Yang, S. Tian, M. Johnson, A. N. 2020-12-20 doi:10.1101/2020.12.20.423533 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ The evolutionary assembly of forest communities along environmental gradients: recent diversification or sorting of pre-adapted clades? ]]> https://biorxiv.org/content/10.1101/2020.12.22.424032v1?rss=1 Linan, A. G. Myers, J. A. Edwards, C. E. Zanne, A. E. Smith, S. A. Arellano, G. Cayola, L. Farfan-Rios, W. Fuentes, A. F. Garcia-Cabrera, K. Gonzales-Caro, S. Loza, M. I. Macia, M. J. Malhi, Y. Nieto-Ariza, B. Salinas, N. Silman, M. R. Tello, S. J. 2020-12-22 doi:10.1101/2020.12.22.424032 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Multi-Modal Biomarkers of Cerebral Edema in Low Resolution MRI ]]> https://biorxiv.org/content/10.1101/2020.12.23.424020v1?rss=1 Tu, D. Goyal, M. S. Dworkin, J. D. Kampondeni, S. Vidal, L. Biondo-Savin, E. Juvvadi, S. Raghavan, P. Nicholas, J. Chetcuti, K. Clark, K. Satterthwaite, T. D. Yushkevich, P. Davatzikos, C. Erus, G. Postels, D. G. Taylor, T. E. Small, D. S. Shinohara, R. T. 2020-12-25 doi:10.1101/2020.12.23.424020 Cold Spring Harbor Laboratory Press 2020-12-25 <![CDATA[ Signaling interaction link prediction using deep graph neural networks integrating protein-protein interactions and omics data ]]> https://biorxiv.org/content/10.1101/2020.12.23.424230v1?rss=1 Feng, J. Zeng, A. Chen, Y. Payne, P. R. Li, F. 2020-12-24 doi:10.1101/2020.12.23.424230 Cold Spring Harbor Laboratory Press 2020-12-24 <![CDATA[ Deciphering how naturally occurring sequence features impact the phase behaviors of disordered prion-like domains ]]> https://biorxiv.org/content/10.1101/2021.01.01.425046v1?rss=1 Bremer, A. Farag, M. Borcherds, W. M. Peran, I. Martin, E. W. Pappu, R. V. Mittag, T. 2021-01-04 doi:10.1101/2021.01.01.425046 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Stroke-related alterations in inter-areal communication revealed via Granger causality analysis ]]> https://biorxiv.org/content/10.1101/2021.01.04.425190v1?rss=1 Allegra, M. Favaretto, C. Metcalf, N. Corbetta, M. Brovelli, A. 2021-01-04 doi:10.1101/2021.01.04.425190 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase ]]> https://biorxiv.org/content/10.1101/2021.01.05.425498v1?rss=1 Carney, S. P. Ma, W. Whitley, K. D. Jia, H. Lohman, T. M. Luthey-Schulten, Z. A. Chemla, Y. R. 2021-01-06 doi:10.1101/2021.01.05.425498 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Spatial drivers and pre-cancer populations collaborate with the microenvironment in untreated and chemo-resistant pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2021.01.13.426413v1?rss=1 Cui Zhou, D. Jayasinghe, R. G. Herndon, J. M. Storrs, E. Mo, C.-K. Wu, Y. Fulton, R. S. Wyczalkowski, M. A. Fronick, C. C. Fulton, L. A. Thammavong, L. Sato, K. Zhu, H. Sun, H. Wang, L.-B. Li, Y. Zuo, C. McMichael, J. F. Davies, S. R. Appelbaum, E. L. Robbins, K. J. Chasnoff, S. E. Yang, X. Liu, R. Reeb, A. N. Wendl, M. C. Oh, C. Serasanambati, M. Lal, P. Varghese, R. Mashl, J. R. Ponce, J. Terekhanova, N. V. Naser Al Deen, N. Yao, L. Wang, F. Chen, L. Schnaubelt, M. Puram, S. V. Kim, A. H. Song, S.-K. Shoghi, K. I. Ju, T. Hawkins, W. G. Chen, K. Ch 2021-01-14 doi:10.1101/2021.01.13.426413 Cold Spring Harbor Laboratory Press 2021-01-14 <![CDATA[ Spontaneous neural synchrony links intrinsic spinal sensory and motor networks during unconsciousness ]]> https://biorxiv.org/content/10.1101/2021.01.15.426828v1?rss=1 McPherson, J. G. Bandres, M. F. 2021-01-17 doi:10.1101/2021.01.15.426828 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Neutralizing and protective human monoclonal antibodies recognizing the N-terminaldomain of the SARS-CoV-2 spike protein ]]> https://biorxiv.org/content/10.1101/2021.01.19.427324v1?rss=1 Suryadevara, N. Shrihari, S. Gilchuk, P. VanBlargan, L. Binshtein, E. Zost, S. Nargi, R. Sutton, R. Winkler, E. S. Chen, E. C. Fouch, M. E. Davidson, E. Doranz, B. Carnahan, R. H. Thackray, L. Diamond, M. D. Crowe, J. E. 2021-01-20 doi:10.1101/2021.01.19.427324 Cold Spring Harbor Laboratory Press 2021-01-20 <![CDATA[ Effect of mutations in the SARS-CoV-2 spike protein on protein stability, cleavage, and cell-cell fusion function ]]> https://biorxiv.org/content/10.1101/2021.01.24.428007v1?rss=1 Barrett, C. T. Neal, H. E. Edmonds, K. Moncman, C. L. Thompson, R. Branttie, J. M. Boggs, K. B. Wu, C.-Y. Leung, D. W. Dutch, R. E. 2021-01-25 doi:10.1101/2021.01.24.428007 Cold Spring Harbor Laboratory Press 2021-01-25 <![CDATA[ P. falciparum K13 mutations present varying degrees of artemisinin resistance and reduced fitness in African parasites ]]> https://biorxiv.org/content/10.1101/2021.01.27.428390v1?rss=1 Stokes, B. H. Rubiano, K. Dhingra, S. K. Mok, S. Straimer, J. Gnadig, N. F. Bath, J. R. Deni, I. Ward, K. E. Striepen, J. Yeo, T. Ross, L. S. Legrand, E. Ariey, F. Cunningham, C. H. Souleymane, I. M. Gansane, A. Nzoumbou-Boko, R. Ndayikunda, C. Kabanywanyi, A. M. Uwimana, A. Smith, S. J. Kolley, O. Ndounga, M. Warsame, M. Leang, R. Nosten, F. Anderson, T. Rosenthal, P. J. Menard, D. Fidock, D. A. 2021-01-30 doi:10.1101/2021.01.27.428390 Cold Spring Harbor Laboratory Press 2021-01-30 <![CDATA[ Genetic and structural basis for recognition of SARS-CoV-2 spike protein by a two-antibody cocktail ]]> https://biorxiv.org/content/10.1101/2021.01.27.428529v1?rss=1 Dong, J. Zost, S. Greaney, A. Starr, T. N. Dingens, A. S. Chen, E. C. Chen, R. Case, B. Sutton, R. Gilchuk, P. Rodriguez, J. Armstrong, E. Gainza, C. Nargi, R. Binshtein, E. Xie, X. Zhang, X. Shi, P.-Y. Logue, J. Weston, S. McGrath, M. Frieman, M. Brady, T. Tuffy, K. Bright, H. Loo, Y.-M. McvTamney, P. Esser, M. Carnahan, R. Diamond, M. Bloom, J. Crowe, J. E. 2021-01-28 doi:10.1101/2021.01.27.428529 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ 3D Visualization of the Podocyte Actin Network using Integrated Membrane Extraction, Electron Microscopy, and Deep Learning ]]> https://biorxiv.org/content/10.1101/2021.01.29.428712v1?rss=1 Qu, C. Roth, R. Loitman, C. Hammad, D. Genin, G. M. Miner, J. H. Suleiman, H. Y. 2021-01-29 doi:10.1101/2021.01.29.428712 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ Glutamatergic dysfunction precedes neuron loss in cerebral organoids with MAPT mutation. ]]> https://biorxiv.org/content/10.1101/2021.02.03.429623v1?rss=1 Bowles, K. R. Silva, M. C. Whitney, K. Bertucci, T. Garza, J. Boles, N. C. Strang, K. H. Mahali, S. Marsh, J. A. Chen, C. Pugh, D. A. Liu, Y. Berlind, J. E. Lai, J. D. Goderie, S. K. Chowdhury, R. Lotz, S. Lane, K. Onanuga, K. Karch, C. Ichida, J. Crary, J. F. Haggarty, S. J. Goate, A. M. Temple, S. 2021-02-03 doi:10.1101/2021.02.03.429623 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Evolution of butterfly-plant networks over time, as revealed by Bayesian inference of host repertoire ]]> https://biorxiv.org/content/10.1101/2021.02.04.429735v1?rss=1 Braga, M. P. Janz, N. Nylin, S. Ronquist, F. Landis, M. J. 2021-02-05 doi:10.1101/2021.02.04.429735 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Uncovering Differences in Hydration Free Energies for Model Compound Mimics of Charged Sidechains of Amino Acids ]]> https://biorxiv.org/content/10.1101/2021.02.04.429838v1?rss=1 Fossat, M. J. Zeng, X. Pappu, R. V. 2021-02-05 doi:10.1101/2021.02.04.429838 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Modeling features of addiction with an oral oxycodone self-administration paradigm ]]> https://biorxiv.org/content/10.1101/2021.02.08.430180v1?rss=1 Murphy, C. Chang, Y.-H. Pareta, R. Li, J.-N. Earnest, T. Tooley, J. R. Vachez, Y. M. Gereau, R. Copits, B. A. Kravitz, A. V. Creed, M. C. 2021-02-09 doi:10.1101/2021.02.08.430180 Cold Spring Harbor Laboratory Press 2021-02-09 <![CDATA[ Gene dosage effects of polyA track engineered hypomorphs ]]> https://biorxiv.org/content/10.1101/2021.02.10.430645v1?rss=1 Powell, G. N. Pavlovic-Djuranovic, S. Djuranovic, S. 2021-02-11 doi:10.1101/2021.02.10.430645 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ An endogenous opioid circuit determines state-dependent appetitive behavior ]]> https://biorxiv.org/content/10.1101/2021.02.10.430657v1?rss=1 Castro, D. C. Oswell, C. S. Zhang, E. T. Pedersen, C. E. Piantadosi, S. C. Rossi, M. A. Hunker, A. Guglin, A. Moron, J. A. Zweifel, L. S. Stuber, G. D. Bruchas, M. R. 2021-02-10 doi:10.1101/2021.02.10.430657 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Spatially Interacting Phosphorylation Sites and Mutations in Cancer ]]> https://biorxiv.org/content/10.1101/2021.02.14.431184v1?rss=1 Huang, K.-l. Scott, A. Zhou, D. C. Wang, L.-b. Weerasinghe, A. Elmas, A. Liu, R. Wu, Y. Wendl, M. Wyczalkowski, M. Baral, J. Sengupta, S. Lai, C.-W. Ruggles, K. Payne, S. Raphael, B. Fenyo, D. Chen, K. Mills, G. Ding, L. 2021-02-15 doi:10.1101/2021.02.14.431184 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ Cellular, Circuit and Transcriptional Framework for Modulation of Itch in the Central Amygdala ]]> https://biorxiv.org/content/10.1101/2021.02.18.431884v1?rss=1 Samineni, V. K. Grajales-Reyes, J. Grajales-Reyes, G. E. Tycksen, E. Copits, B. Pedersen, C. Ankudey, E. Sackey, J. N. Sewell, S. B. Bruchas, M. R. Gereau, R. W. 2021-02-18 doi:10.1101/2021.02.18.431884 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ A photoswitchable GPCR-based opsin for presynaptic silencing ]]> https://biorxiv.org/content/10.1101/2021.02.19.432008v1?rss=1 Copits, B. A. O'Neill, P. R. Gowrishankar, R. Yoo, J. J. Meshik, X. Parker, K. E. Spangler, S. M. Vasquez, A. M. Elerding, A. J. Stander, M. C. Kalyanaraman, V. Vogt, S. K. Samineni, V. K. Gautam, N. Sunahara, R. K. Gereau, R. W. Bruchas, M. R. 2021-02-20 doi:10.1101/2021.02.19.432008 Cold Spring Harbor Laboratory Press 2021-02-20 <![CDATA[ Vesicular stomatitis virus chimeras expressing the Oropouche virus glycoproteins elicit protective immune responses in mice. ]]> https://biorxiv.org/content/10.1101/2021.02.19.432025v1?rss=1 Stubbs, S. H. Pontelli, M. C. MISHRA, N. Zhuo, C. Souza, J. d. P. Viana, R. M. M. Lipkin, W. I. H. Knipe, D. Arruda, E. A. Whelan, S. P. J. 2021-02-19 doi:10.1101/2021.02.19.432025 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Precise topology of adjacent domain-general and sensory-biased regions in the human brain ]]> https://biorxiv.org/content/10.1101/2021.02.21.431622v1?rss=1 Assem, M. Shashidhara, S. Glasser, M. F. Duncan, J. 2021-02-22 doi:10.1101/2021.02.21.431622 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ Deletion of Fibroblast growth factor 9 globally and in skeletal muscle results in enlarged tuberosities at sites of deltoid tendon attachments ]]> https://biorxiv.org/content/10.1101/2021.02.23.432498v1?rss=1 Leek, C. C. Soulas, J. M. Bhattacharya, I. Ganji, E. Locke, R. C. Smith, M. C. Bhavsar, J. D. Polson, S. W. Ornitz, D. Killian, M. L. 2021-02-23 doi:10.1101/2021.02.23.432498 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Modulating the voltage sensor of a cardiac potassium channel shows antiarrhythmic effects ]]> https://biorxiv.org/content/10.1101/2021.02.25.432939v1?rss=1 Lin, Y. Grinter, S. Z. Lu, Z. Xu, X. Wang, H. Z. Liang, H. Hou, P. Gao, J. Clausen, C. Shi, J. Zhao, W. Ma, Z. Liu, Y. White, K. M. Zhao, L. Kang, P.-W. Zhang, G. Cohen, I. S. Zou, X. Cui, J. 2021-02-25 doi:10.1101/2021.02.25.432939 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Ultrapotent miniproteins targeting the receptor-binding domain protect against SARS-CoV-2 infection and disease in mice ]]> https://biorxiv.org/content/10.1101/2021.03.01.433110v1?rss=1 Case, J. B. Chen, R. E. Cao, L. Ying, B. Winkler, E. S. Goreshnik, I. Shrihari, S. Kafai, N. M. Bailey, A. L. Xie, X. Shi, P.-Y. Ravichandran, R. Carter, L. Stewart, L. Baker, D. Diamond, M. S. 2021-03-01 doi:10.1101/2021.03.01.433110 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell ]]> https://biorxiv.org/content/10.1101/2021.03.01.433431v1?rss=1 Puray-Chavez, M. Lapak, K. M. Schrank, T. P. Elliott, J. L. Bhatt, D. P. Agajanian, M. J. Jasuja, R. Lawson, D. Q. Davis, K. Rothlauf, P. W. Jo, H. Lee, N. Tenneti, K. Eschbach, J. E. Shema Mugisha, C. Vuong, H. R. Bailey, A. L. Hayes, D. N. Whelan, S. P. J. Horani, A. Brody, S. L. Goldfarb, D. Major, M. B. Kutluay, S. B. 2021-03-01 doi:10.1101/2021.03.01.433431 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Genome-wide analysis of focal DNA hypermethylation in IDH-mutant AML samples ]]> https://biorxiv.org/content/10.1101/2021.03.03.433799v1?rss=1 Wilson, E. R. Helton, N. Heath, S. E. Fulton, R. S. Miller, C. Payton, J. E. Welch, J. S. Walter, M. Westervelt, P. DiPersio, J. F. Link, D. C. Ley, T. J. Spencer, D. H. 2021-03-03 doi:10.1101/2021.03.03.433799 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ Intraspecific variation in elemental accumulation and its association with salt tolerance in Paspalum vaginatum ]]> https://biorxiv.org/content/10.1101/2021.03.04.433795v1?rss=1 Goad, D. M. Kellogg, E. A. Baxter, I. Olsen, K. M. 2021-03-05 doi:10.1101/2021.03.04.433795 Cold Spring Harbor Laboratory Press 2021-03-05 <![CDATA[ Killing of Gram-negative and Gram-positive bacteria by a bifunctional cell wall-targeting T6SS effector ]]> https://biorxiv.org/content/10.1101/2021.03.04.433973v1?rss=1 Le, N.-H. Pinedo, V. Lopez, J. Cava, F. Feldman, M. F. 2021-03-04 doi:10.1101/2021.03.04.433973 Cold Spring Harbor Laboratory Press 2021-03-04 <![CDATA[ A genetic screen for regulators of muscle morphogenesis in Drosophila ]]> https://biorxiv.org/content/10.1101/2021.03.04.434006v1?rss=1 Johnson, A. N. Skeath, J. B. Ou, T. Wilson, B. Gontarz, P. Huang, G. 2021-03-05 doi:10.1101/2021.03.04.434006 Cold Spring Harbor Laboratory Press 2021-03-05 <![CDATA[ Engineered Peptide-Functionalized Hydrogels Modulate the RNA Transcriptome of Human Nucleus Pulposus Cells In Vitro ]]> https://biorxiv.org/content/10.1101/2021.03.05.434094v1?rss=1 Barcellona, M. N. Speer, J. E. Jing, L. Gupta, M. C. Buchowski, J. M. Kelly, M. P. Setton, L. A. 2021-03-06 doi:10.1101/2021.03.05.434094 Cold Spring Harbor Laboratory Press 2021-03-06 <![CDATA[ Transcriptional-Regulatory Convergence Across Functional MDD Risk Variants Identified by Massively Parallel Reporter Assays ]]> https://biorxiv.org/content/10.1101/2021.03.05.434177v1?rss=1 100 SNPs with allelic effects on expression in a retinoid-responsive model system. Further, functional SNPs were enriched for binding sequences of retinoic acid-receptive transcription factors (TFs); with additional allelic differences unmasked by treatment with all-trans retinoic acid (ATRA). Finally, motifs overrepresented across functional SNPs corresponded to TFs highly specific to serotonergic neurons, suggesting an in vivo site of action. Our application of MPRAs to screen MDD-associated SNPs suggests a shared transcriptional regulatory program across loci, a subset of which are unmasked by retinoids. ]]> Mulvey, B. Dougherty, J. D. 2021-03-07 doi:10.1101/2021.03.05.434177 Cold Spring Harbor Laboratory Press 2021-03-07 <![CDATA[ Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes ]]> https://biorxiv.org/content/10.1101/2021.03.06.434233v1?rss=1 Scott, A. J. Chiang, C. Hall, I. M. 2021-03-08 doi:10.1101/2021.03.06.434233 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Multiple nucleotide polymorphism DNA markers for the accurate evaluation of genetic variations ]]> https://biorxiv.org/content/10.1101/2021.03.09.434561v1?rss=1 Fang, Z. Li, L. Zhou, J. You, A. Gao, L. Li, T. Chen, H. Han, R. Cui, Y. Chen, L. Xiao, H. Zhang, J. Xu, N. Fu, X. Zhang, J. Li, X. Ma, A. Zhang, W. Peng, H. 2021-03-10 doi:10.1101/2021.03.09.434561 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Bruton's Tyrosine Kinase Supports Gut Mucosal Immunity and Commensal Microbiome Recognition in Autoimmune Arthritis ]]> https://biorxiv.org/content/10.1101/2021.03.10.434762v1?rss=1 Bonami, R. H. Thurman, C. E. Nyhoff, L. E. Westlake, C. S. Barron, B. B. Kendall, P. L. 2021-03-10 doi:10.1101/2021.03.10.434762 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Mitochondrial Phenotypes Distinguish Pathogenic MFN2 Mutations by Pooled Functional Genomics Screen ]]> https://biorxiv.org/content/10.1101/2021.03.12.434746v1?rss=1 View larger version (46K): org.highwire.dtl.DTLVardef@c774b4org.highwire.dtl.DTLVardef@bee63corg.highwire.dtl.DTLVardef@fd7099org.highwire.dtl.DTLVardef@eb7d87_HPS_FORMAT_FIGEXP M_FIG C_FIG Here, we address the need to evaluate the impact of numerous genetic variants. This manuscript depicts the methods of using machine learning on a biologically relevant phenotype to predict specific point mutations, followed by physically capturing those mutated cells. ]]> Yenkin, A. L. Bramley, J. C. Waligorski, J. E. Kremitzki, C. L. Liebeskind, M. J. Xu, X. E. Vakaki, M. A. Chandrasekaran, V. Mitra, R. D. Milbrandt, J. D. Buchser, W. J. 2021-03-12 doi:10.1101/2021.03.12.434746 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Mental health explains individual deviations from normative range in cognition-associated brain states ]]> https://biorxiv.org/content/10.1101/2021.03.12.435017v1?rss=1 Zhang, W. Vidaurre, D. Bijsterbosch, J. D. 2021-03-12 doi:10.1101/2021.03.12.435017 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Individualized precision targeting of dorsal attention and default mode networks with rTMS in traumatic brain injury-associated depression ]]> https://biorxiv.org/content/10.1101/2021.03.13.435127v1?rss=1 Siddiqi, S. H. Kandala, S. Hacker, C. D. Trapp, N. T. Leuthardt, E. C. Carter, A. R. Brody, D. L. 2021-03-15 doi:10.1101/2021.03.13.435127 Cold Spring Harbor Laboratory Press 2021-03-15 <![CDATA[ RCytoGPS: An R Package for Reading and Visualizing Cytogenetics Data ]]> https://biorxiv.org/content/10.1101/2021.03.16.389791v1?rss=1 Abrams, Z. B. Tally, D. G. Abruzzo, L. V. Coombes, K. R. 2021-03-17 doi:10.1101/2021.03.16.389791 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ The arrested state of processing bodies supports mRNA regulation in early development ]]> https://biorxiv.org/content/10.1101/2021.03.16.435709v1?rss=1 Sankaranarayanan, M. Emenecker, R. J. Jahnel, M. Trussina, I. R. E. A. Wayland, M. T. Alberti, S. Holehouse, A. S. Weil, T. T. 2021-03-16 doi:10.1101/2021.03.16.435709 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ GABAergic neuronal IL-4R mediates T cell effect on memory ]]> https://biorxiv.org/content/10.1101/2021.03.16.435727v1?rss=1 Kipnis, J. Fu, Z. Dykstra, T. Li, H. Salvador, A. Zou, B. Yan, N. Andrews, P. Papadopoulos, Z. Smirnov, I. Xie, X. Herz, J. 2021-03-17 doi:10.1101/2021.03.16.435727 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Continuous Polony Gels for Tissue Mapping with High Resolution and RNA Capture Efficiency ]]> https://biorxiv.org/content/10.1101/2021.03.17.435795v1?rss=1 1,000 unique molecular identifiers/10x10 {micro}m2. In other words, this global, naive platform achieves subcellular spatial transcriptome mapping while maintaining high transcript capture efficiencies. ]]> Fu, X. Sun, L. Chen, J. Dong, R. Lin, Y. Palmiter, R. Lin, S. Gu, L. 2021-03-17 doi:10.1101/2021.03.17.435795 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Nonsense Mediated RNA Decay Is a Unique Vulnerability of Cancer Cells with SF3B1 and U2AF1 Mutations ]]> https://biorxiv.org/content/10.1101/2021.03.19.436079v1?rss=1 You, Z. Cheruiyot, A. Li, S. Srivatsan, S. N. Ahmed, T. Chen, Y. Lemacon, D. S. Li, Y. Yang, Z. Wadugu, B. A. Warner, W. Pruett-Miller, S. M. Obeng, E. A. Link, D. C. He, D. Xiao, F. Wang, X. Bailis, J. M. Walter, M. J. 2021-03-19 doi:10.1101/2021.03.19.436079 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Mining signaling flow to interpret mechanisms of synergy of drug combinations using deep graph neural networks ]]> https://biorxiv.org/content/10.1101/2021.03.25.437003v1?rss=1 Zhang, H. Chen, Y. Payne, P. R. Li, F. 2021-03-26 doi:10.1101/2021.03.25.437003 Cold Spring Harbor Laboratory Press 2021-03-26 <![CDATA[ Oxytocin receptor activation does not mediate associative fear deficits in a Williams Syndrome model ]]> https://biorxiv.org/content/10.1101/2021.03.29.437431v1?rss=1 Nygaard, K. R. Swift, R. G. Glick, R. M. Wagner, R. E. Maloney, S. E. Gould, G. G. Dougherty, J. D. 2021-03-30 doi:10.1101/2021.03.29.437431 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ Functional connectivity of the developing mouse cortex ]]> https://biorxiv.org/content/10.1101/2021.04.04.438377v1?rss=1 Rahn, R. M. Brier, L. M. Bice, A. R. Reisman, M. D. Dougherty, J. D. Culver, J. P. 2021-04-04 doi:10.1101/2021.04.04.438377 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Identification of Structures for Ion Channel Kinetic Models ]]> https://biorxiv.org/content/10.1101/2021.04.06.438566v1?rss=1 Mangold, K. E. Wang, W. Johnson, E. K. Bhagavan, D. Moreno, J. D. Nerbonne, J. M. Silva, J. 2021-04-06 doi:10.1101/2021.04.06.438566 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Sustained Oxygenation Accelerates Diabetic Wound Healing by Simultaneously Promoting Epithelialization and Angiogenesis, and Decreasing Tissue Inflammation ]]> https://biorxiv.org/content/10.1101/2021.04.06.438689v1?rss=1 Guan, Y. Niu, H. Liu, Z. Dang, Y. Shen, J. Zayed, M. Ma, L. Guan, J. 2021-04-08 doi:10.1101/2021.04.06.438689 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ An open source statistical and data processing toolbox for wide-field optical imaging in mice ]]> https://biorxiv.org/content/10.1101/2021.04.07.438885v1?rss=1 Brier, L. M. Culver, J. P. 2021-04-09 doi:10.1101/2021.04.07.438885 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Modern Acinetobacter baumannii clinical isolates replicate inside spacious vacuoles and egress from macrophages ]]> https://biorxiv.org/content/10.1101/2021.04.08.439081v1?rss=1 Sycz, G. Di Venanzio, G. Sartorio, M. G. Le, N.-H. Scott, N. Beatty, W. Feldman, M. F. 2021-04-09 doi:10.1101/2021.04.08.439081 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ The Shu Complex Prevents Mutagenesis and Cytotoxicity of Single-Strand Specific Alkylation Lesions ]]> https://biorxiv.org/content/10.1101/2021.04.09.439200v1?rss=1 Bonilla, B. Brown, A. I. Hengel, S. R. Rapchak, K. S. Mitchell, D. Pressimone, C. A. Fagunloye, A. A. Luong, T. T. Zaher, H. S. Mosammaparast, N. Malc, E. P. Mieczkowski, P. A. Roberts, S. Bernstein, K. A. 2021-04-11 doi:10.1101/2021.04.09.439200 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Human Fronto-Striatal Connectivity is Organized into Discrete Functional Subnetworks ]]> https://biorxiv.org/content/10.1101/2021.04.12.439415v1?rss=1 Gordon, E. M. Laumann, T. O. Marek, S. Newbold, D. J. Hampton, J. M. Seider, N. A. Montez, D. F. Nielsen, A. M. Van, A. N. Zheng, A. Miller, R. Siegel, J. S. Kay, B. P. Snyder, A. Z. Greene, D. J. Schlaggar, B. L. Petersen, S. Nelson, S. M. Dosenbach, N. 2021-04-12 doi:10.1101/2021.04.12.439415 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Opening of a Cryptic Pocket in β-lactamase Increases Penicillinase Activity ]]> https://biorxiv.org/content/10.1101/2021.04.14.439842v1?rss=1 Knoverek, C. R. Mallimadugula, U. L. Singh, S. Rennella, E. Frederick, T. E. Yuwen, T. Raavicharla, S. Kay, L. E. Bowman, G. R. 2021-04-14 doi:10.1101/2021.04.14.439842 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Measuring Transcription Factor Binding and Gene Expression using Barcoded Self-Reporting Transposon Calling Cards and Transcriptomes ]]> https://biorxiv.org/content/10.1101/2021.04.15.439516v1?rss=1 Lalli, M. A. Dong, F. Chen, X. Milbrandt, J. Dougherty, J. D. Mitra, R. D. 2021-04-15 doi:10.1101/2021.04.15.439516 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ A cortico-hippocampal scaffold for representing and recalling lifelike events ]]> https://biorxiv.org/content/10.1101/2021.04.16.439894v1?rss=1 Reagh, Z. M. Ranganath, C. 2021-04-17 doi:10.1101/2021.04.16.439894 Cold Spring Harbor Laboratory Press 2021-04-17 <![CDATA[ Sequence determinants of in cell condensate assembly morphology, dynamics, and oligomerization as measured by number and brightness analysis ]]> https://biorxiv.org/content/10.1101/2021.04.18.440340v1?rss=1 Emenecker, R. J. Holehouse, A. S. Strader, L. 2021-04-19 doi:10.1101/2021.04.18.440340 Cold Spring Harbor Laboratory Press 2021-04-19 <![CDATA[ Negative regulation of a ribonucleoprotein condensate driven by dilute phase oligomerization ]]> https://biorxiv.org/content/10.1101/2021.04.19.440511v1?rss=1 Seim, I. Posey, A. E. Snead, W. T. Stormo, B. M. Klotsa, D. Pappu, R. V. Gladfelter, A. S. 2021-04-20 doi:10.1101/2021.04.19.440511 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ HSP90 inhibitors reduce cholesterol storage in Niemann-Pick type C1 mutant fibroblasts ]]> https://biorxiv.org/content/10.1101/2021.04.22.440982v1?rss=1 Pipalia, N. H. Saad, S. Z. Subramanian, K. Cross, A. Al-Motawa, A. Garg, K. K. Blagg, B. Neckers, L. Helquist, P. Wiest, O. Ory, D. S. Maxfield, F. R. 2021-04-22 doi:10.1101/2021.04.22.440982 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ The F-box protein AFF1 regulates ARF protein accumulation to regulate auxin response ]]> https://biorxiv.org/content/10.1101/2021.04.25.441346v1?rss=1 Jing, H. Korasick, D. Emenecker, R. Morffy, N. Wilkinson, E. Powers, S. Strader, L. 2021-04-26 doi:10.1101/2021.04.25.441346 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Abscisic acid modulates auxin-responsive hypocotyl elongation ]]> https://biorxiv.org/content/10.1101/2021.04.25.441358v1?rss=1 Emenecker, R. Cammarata, J. Yuan, I. Strader, L. 2021-04-26 doi:10.1101/2021.04.25.441358 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ A potently neutralizing anti-SARS-CoV-2 antibody inhibits variants of concern by binding a highly conserved epitope ]]> https://biorxiv.org/content/10.1101/2021.04.26.441501v1?rss=1 VanBlargan, L. Adams, L. Liu, Z. Chen, R. E. Gilchuk, P. Raju, S. Smith, B. Zhao, H. Case, J. B. Winkler, E. S. Whitener, B. Droit, L. Aziati, I. Shi, P.-Y. Creanga, A. Pegu, A. Handley, S. Wang, D. Boon, A. Crowe, J. E. Whelan, S. P. J. Fremont, D. Diamond, M. 2021-04-26 doi:10.1101/2021.04.26.441501 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ TNF drives AKI-to-CKD transition downstream of proximal tubule EGFR ]]> https://biorxiv.org/content/10.1101/2021.04.29.442002v1?rss=1 Abdelmageed, M. M. Kefaloyianni, E. Arthanarisami, A. Khamissi, F. Atkinson, J. J. Herrlich, A. 2021-04-29 doi:10.1101/2021.04.29.442002 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Shelterin components modulate nucleic acids condensation and phase-separation ]]> https://biorxiv.org/content/10.1101/2021.04.30.442189v1?rss=1 Soranno, A. Incicco, J. J. De Bona, P. Tomko, E. J. Galburt, E. Holehouse, A. S. Galletto, R. 2021-04-30 doi:10.1101/2021.04.30.442189 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Convergent antibody responses to the SARS-CoV-2 spike protein in convalescent and vaccinated individuals ]]> https://biorxiv.org/content/10.1101/2021.05.02.442326v1?rss=1 Chen, E. C. Gilchuk, P. Zost, S. J. Suryadevara, N. Winkler, E. S. Cabel, C. R. Binshtein, E. Sutton, R. E. Rodriguez, J. L. Day, S. Myers, L. Trivette, A. Williams, J. K. Davidson, E. Li, S. Doranz, B. J. Campos, S. K. Carnahan, R. H. Thorne, C. A. Diamond, M. S. Crowe, J. E. 2021-05-03 doi:10.1101/2021.05.02.442326 Cold Spring Harbor Laboratory Press 2021-05-03 <![CDATA[ Homotopic contralesional excitation suppresses spontaneous circuit repair and global network reconnections following ischemic stroke ]]> https://biorxiv.org/content/10.1101/2021.05.02.442355v1?rss=1 Bice, A. R. Xiao, Q. Kong, J. Yan, P. Rosenthal, Z. P. Kraft, A. W. Smith, K. P. Wieloch, T. Lee, J.-M. Culver, J. Bauer, A. Q. 2021-05-02 doi:10.1101/2021.05.02.442355 Cold Spring Harbor Laboratory Press 2021-05-02 <![CDATA[ Circadian pacemaker neurons display co-phasic rhythms in basal calcium level and in fast calcium fluctuations ]]> https://biorxiv.org/content/10.1101/2021.05.03.442479v1?rss=1 Liang, X. Holy, T. E. Taghert, P. H. 2021-05-04 doi:10.1101/2021.05.03.442479 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ A morphological transformation in respiratory syncytial virus leads to enhanced complement activation ]]> https://biorxiv.org/content/10.1101/2021.05.06.442421v1?rss=1 Kuppan, J. P. Mitrovich, M. D. Vahey, M. D. 2021-05-06 doi:10.1101/2021.05.06.442421 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Failure to detect mutations U2AF1 due to changes in the GRCh38 reference sequence ]]> https://biorxiv.org/content/10.1101/2021.05.07.442430v1?rss=1 Miller, C. A. Walker, J. R. Jensen, T. L. Hooper, W. F. Fulton, R. S. Painter, J. S. Sekeres, M. A. Ley, T. J. Spencer, D. H. Goll, J. B. Walter, M. J. 2021-05-08 doi:10.1101/2021.05.07.442430 Cold Spring Harbor Laboratory Press 2021-05-08 <![CDATA[ Mathematical Analysis and Topology of SARS-CoV-2, Bonding with Cells and Unbonding ]]> https://biorxiv.org/content/10.1101/2021.05.07.443177v1?rss=1 S.R. Srinivasa Rao, A. Krantz, S. 2021-05-09 doi:10.1101/2021.05.07.443177 Cold Spring Harbor Laboratory Press 2021-05-09 <![CDATA[ An intranasal vaccine durably protects against SARS-CoV-2 variants in mice ]]> https://biorxiv.org/content/10.1101/2021.05.08.443267v1?rss=1 Hassan, A. O. Shrihari, S. Gorman, M. J. Ying, B. Yuan, D. Raju, S. Chen, R. E. Dmitriev, I. P. Kashentseva, E. Adams, L. J. Shi, P.-Y. Fremont, D. H. Curiel, D. T. Alter, G. Diamond, M. S. 2021-05-09 doi:10.1101/2021.05.08.443267 Cold Spring Harbor Laboratory Press 2021-05-09 <![CDATA[ RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes ]]> https://biorxiv.org/content/10.1101/2021.05.10.443470v1?rss=1 Tribble, C. M. Freyman, W. A. Lim, J. Y. Landis, M. J. Barido-Sottani, J. Kopperud, B. T. Höhna, S. May, M. R. 2021-05-11 doi:10.1101/2021.05.10.443470 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ Autophagy gene-dependent intracellular immunity triggered by interferon-γ ]]> https://biorxiv.org/content/10.1101/2021.05.10.443539v1?rss=1 McAllaster, M. R. Bhushan, J. Balce, D. R. Orvedahl, A. Park, A. Hwang, S. Sullender, M. E. Sibley, D. Virgin, H. W. 2021-05-12 doi:10.1101/2021.05.10.443539 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ 8-azaadenosine and 8-chloroadenosine are not selective inhibitors of ADAR ]]> https://biorxiv.org/content/10.1101/2021.05.12.443853v1?rss=1 Cottrell, K. A. Torres, L. S. Weber, J. D. 2021-05-14 doi:10.1101/2021.05.12.443853 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ A Trio of Ubiquitin Ligases Sequentially Drive Ubiquitylation and Autophagic Degradation of Dysfunctional Yeast Proteasomes ]]> https://biorxiv.org/content/10.1101/2021.05.12.443936v1?rss=1 Marshall, R. S. Vierstra, R. D. 2021-05-13 doi:10.1101/2021.05.12.443936 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ Conformational buffering underlies functional selection in intrinsically disordered protein regions ]]> https://biorxiv.org/content/10.1101/2021.05.14.444182v1?rss=1 Gonzalez-Foutel, N. S. Borcherds, W. M. Glavina, J. Barrera-Vilarmau, S. Sagar, A. Estana, A. Barozet, A. Fernandez-Ballester, G. Blanes-Mira, C. Sanchez, I. E. de Prat Gay, G. Cortes, J. Bernado, P. Pappu, R. V. Holehouse, A. S. Daughdrill, G. W. Chemes, L. B. 2021-05-16 doi:10.1101/2021.05.14.444182 Cold Spring Harbor Laboratory Press 2021-05-16 <![CDATA[ Zika virus infection of pregnant Ifnar1-/- mice triggers strain-specific differences in fetal outcomes ]]> https://biorxiv.org/content/10.1101/2021.05.14.444269v1?rss=1 Bohm, E. K. Vangorder-Braid, J. T. Jaeger, A. S. Moriarty, R. V. Baczenas, J. J. Bennett, N. C. O'Connor, S. L. Fritsch, M. K. Fuhler, N. A. Noguchi, K. K. Aliota, M. 2021-05-15 doi:10.1101/2021.05.14.444269 Cold Spring Harbor Laboratory Press 2021-05-15 <![CDATA[ Differential sphingosine-1-phosphate receptor-1 (S1PR1) protein expressions in the dorsolateral prefrontal cortex between schizophrenia Type 1 and Type 2 ]]> https://biorxiv.org/content/10.1101/2021.05.15.444302v1?rss=1 Chand, G. B. Jiang, H. Brier, M. Rahmani, F. Benzinger, T. L. S. Rhodes, C. H. Tu, Z. Wong, D. F. 2021-05-17 doi:10.1101/2021.05.15.444302 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Dissecting the Cellular Landscape and Transcriptome Network in Viral Myocarditis by Single-Cell RNA Sequencing ]]> https://biorxiv.org/content/10.1101/2021.05.16.444367v1?rss=1 Lasrado, N. Borcherding, N. Arumugam, R. Starr, T. K. Reddy, J. 2021-05-17 doi:10.1101/2021.05.16.444367 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Bexarotene derivatives modify responses in acute myeloid leukemia ]]> https://biorxiv.org/content/10.1101/2021.05.17.444475v1?rss=1 Hadwiger, G. di Martino, O. Ferris, M. A. Vu, A. Frederick, T. E. Bowman, G. R. Ruminski, P. Wagner, C. Welch, J. S. 2021-05-17 doi:10.1101/2021.05.17.444475 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ A Cre-dependent massively parallel reporter assay allows for cell-type specific assessment of the functional effects of genetic variants in vivo ]]> https://biorxiv.org/content/10.1101/2021.05.17.444514v1?rss=1 Lagunas, T. Plassmyer, S. P. Friedman, R. Z. Rieger, M. A. Fischer, A. D. Lucero, A. F. A. An, J.-Y. Sanders, S. J. Cohen, B. A. Dougherty, J. D. 2021-05-18 doi:10.1101/2021.05.17.444514 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Reduced calcium storage blunts calcium signaling in Toxoplasma bradyzoites and impedes motility and egress ]]> https://biorxiv.org/content/10.1101/2021.05.17.444531v1?rss=1 Fu, Y. Brown, K. M. Jones, N. G. Moreno, S. N. J. Sibley, L. 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F. 2021-05-22 doi:10.1101/2021.05.21.445229 Cold Spring Harbor Laboratory Press 2021-05-22 <![CDATA[ A Promising Chemical Series of Positive Allosteric Modulators of the μ-Opioid Receptor that Enhance the Antinociceptive Efficacy of Opioids but not their Adverse Effects ]]> https://biorxiv.org/content/10.1101/2021.05.24.445057v1?rss=1 Pryce, K. D. Kang, H. J. Sakloth, F. Liu, Y. Khan, S. Toth, K. Kapoor, A. Nicolais, A. Che, T. Qin, L. Bertherat, F. Kaniskan, H. U. Jin, J. Cameron, M. Roth, B. L. Zachariou, V. Filizola, M. 2021-05-25 doi:10.1101/2021.05.24.445057 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Variation in upstream open reading frames contributes to allelic diversity in protein abundance ]]> https://biorxiv.org/content/10.1101/2021.05.25.445499v1?rss=1 Gage, J. L. Mali, S. McLoughlin, F. Khaipho-Burch, M. Monier, B. Bailey-Serres, J. Vierstra, R. D. Buckler, E. S. 2021-05-25 doi:10.1101/2021.05.25.445499 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Precise genotyping of circular mobile elements uncovers human associated plasmids with surprisingly recent common ancestors ]]> https://biorxiv.org/content/10.1101/2021.05.25.445656v1?rss=1 Shalon, N. Relman, D. Yaffe, E. 2021-05-26 doi:10.1101/2021.05.25.445656 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ The complete sequence of a human genome ]]> https://biorxiv.org/content/10.1101/2021.05.26.445798v1?rss=1 Nurk, S. Koren, S. Rhie, A. Rautiainen, M. Bzikadze, A. V. Mikheenko, A. Vollger, M. R. Altemose, N. Uralsky, L. Gershman, A. Aganezov, S. Hoyt, S. J. Diekhans, M. Logsdon, G. A. Alonge, M. Antonarakis, S. E. Borchers, M. Bouffard, G. G. Brooks, S. Y. Caldas, G. V. Cheng, H. Chin, C.-S. Chow, W. de Lima, L. G. Dishuck, P. C. Durbin, R. Dvorkina, T. Fiddes, I. T. Formenti, G. Fulton, R. S. Fungtammasan, A. Garrison, E. Grady, P. G. S. Graves-Lindsay, T. A. Hall, I. M. Hansen, N. F. Hartley, G. A. Haukness, M. Howe, K. Hunkapiller, M. W. Jain, C. Jain, M. 2021-05-27 doi:10.1101/2021.05.26.445798 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ The Dual Mechanisms of Cognitive Control dataset: A theoretically-guided within-subject task fMRI battery ]]> https://biorxiv.org/content/10.1101/2021.05.28.446178v1?rss=1 Etzel, J. A. Brough, R. Freund, M. C. Kizhner, A. Lin, Y. Singh, M. F. Tang, R. Tay, A. Wang, A. Braver, T. S. 2021-05-30 doi:10.1101/2021.05.28.446178 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ metapredict: a fast, accurate, and easy-to-use cross-platform predictor of consensus disorder ]]> https://biorxiv.org/content/10.1101/2021.05.30.446349v1?rss=1 Emenecker, R. J. Griffith, D. Holehouse, A. S. 2021-05-30 doi:10.1101/2021.05.30.446349 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ Anatomical Structures, Cell Types, and Biomarkers Tables Plus 3D Reference Organs in Support of a Human Reference Atlas ]]> https://biorxiv.org/content/10.1101/2021.05.31.446440v1?rss=1 Borner, K. Teichmann, S. A. Quardokus, E. M. Gee, J. Browne, K. Osumi-Sutherland, D. Herr, B. W. Bueckle, A. Paul, H. Haniffa, M. A. Jardine, L. Bernard, A. Ding, S.-L. Miller, J. A. Lin, S. Halushka, M. Boppana, A. Longacre, T. A. Hickey, J. Lin, Y. Valerius, M. T. He, Y. Pryhuber, G. Sun, X. Jorgensen, M. Radtke, A. Wasserfall, C. Ginty, F. Ho, J. Sunshine, J. Beuschel, R. T. Brusko, M. Lee, S. Malhotra, R. Jain, S. Weber, G. 2021-06-01 doi:10.1101/2021.05.31.446440 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ Building Back More Equitable STEM Education: Teach Science by Engaging Students in Doing Science ]]> https://biorxiv.org/content/10.1101/2021.06.01.446616v1?rss=1 Elgin, S. C. R. Hays, S. Mingo, V. Shaffer, C. D. Williams, J. 2021-06-01 doi:10.1101/2021.06.01.446616 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ Gonadal sex patterns p21-induced cellular senescence in mouse and human glioblastoma ]]> https://biorxiv.org/content/10.1101/2021.06.02.446756v1?rss=1 Broestl, L. Grandison, L. Shenoy, S. Tallman, M. M. Rhee, G. Yang, W. Sponagel, J. Kfoury-Beaumont, N. Hill, C. M. Mao, D. D. Kim, A. H. Stewart, S. A. Venere, M. Luo, J. Rubin, J. B. 2021-06-02 doi:10.1101/2021.06.02.446756 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ NeTOIF: A Network-based Approach for Time-Series Omics Data Imputation and Forecasting ]]> https://biorxiv.org/content/10.1101/2021.06.05.447209v1?rss=1 Shi, M. Mollah, S. 2021-06-07 doi:10.1101/2021.06.05.447209 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Brain charts for the human lifespan ]]> https://biorxiv.org/content/10.1101/2021.06.08.447489v1?rss=1 Bethlehem, R. A. I. Seidlitz, J. White, S. R. Vogel, J. W. Anderson, K. M. Adamson, C. Adler, S. Alexopoulos, G. S. Anagnostou, E. Areces-Gonzalez, A. Astle, D. E. Auyeung, B. Ayub, M. Ball, G. Baron-Cohen, S. Beare, R. Bedford, S. A. Benegal, V. Beyer, F. Bin Bae, J. Blangero, J. Blesa Cabez, M. Boardman, J. P. Borzage, M. Bosch-Bayard, J. F. Bourke, N. Calhoun, V. D. Chakravarty, M. M. Chen, C. Chertavian, C. Chetelat, G. Chong, Y. S. Cole, J. H. Corvin, A. Courchesne, E. Crivello, F. Cropley, V. L. Crosbie, J. Crossley, N. Delarue, M. Desrivieres, S. 2021-06-10 doi:10.1101/2021.06.08.447489 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Normal Aging in Mice is Associated with a Global Reduction in Cortical Spectral Power and a Network-Specific Decline in Functional Connectivity ]]> https://biorxiv.org/content/10.1101/2021.06.09.447772v1?rss=1 Albertson, A. J. Landsness, E. C. Tang, M. J. Yan, P. Miao, H. Rosenthal, Z. P. Kim, B. Culver, J. C. Bauer, A. Q. Lee, J.-M. 2021-06-10 doi:10.1101/2021.06.09.447772 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ p53 mutations exhibit sex specific gain-of-function activity in gliomagenesis ]]> https://biorxiv.org/content/10.1101/2021.06.11.448124v1?rss=1 Rockwell, N. C. Yang, W. Warrington, N. Griffith, M. Griffith, O. L. Gurnett, C. Cohen, B. Baldridge, D. Rubin, J. B. 2021-06-11 doi:10.1101/2021.06.11.448124 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Evolution of the open-access CIViC knowledgebase is driven by the needsof the cancer variant interpretation community ]]> https://biorxiv.org/content/10.1101/2021.06.13.448171v1?rss=1 2500 variants in >400 genes from >2800 publications. ]]> Krysiak, K. Danos, A. M. Kiwala, S. McMichael, J. F. Coffman, A. C. Barnell, E. K. Sheta, L. Saliba, J. Grisdale, C. J. Kujan, L. Pema, S. Lever, J. Spies, N. C. Chiorean, A. Rieke, D. T. Clark, K. A. Jani, P. Takahashi, H. Horak, P. Ritter, D. I. Zhou, X. Ainscough, B. J. Delong, S. Lamping, M. Marr, A. R. Li, B. V. Lin, W.-H. Terraf, P. Salama, Y. Campbell, K. Farncombe, K. M. Ji, J. Zhao, X. Xu, X. Kanagal-Shamanna, R. Cotto, K. Skidmore, Z. L. Walker, J. R. Zhang, J. Milosavljevic, A. Patel, R. Y. Giles, R. H. Kim, R. H. Schriml, L. M. Mardis, E. 2021-06-14 doi:10.1101/2021.06.13.448171 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ SOD1 Mediates Lysosome-to-Mitochondria Communication and its Dysregulation by Amyloid-β Oligomers ]]> https://biorxiv.org/content/10.1101/2021.06.14.448281v1?rss=1 Norambuena, A. Sun, X. Wallrabe, H. Cao, R. Sun, N. Pardo, E. Shivange, N. Wang, D. B. Post, L. A. Ferris, H. A. Hu, S. Periasamy, A. Bloom, G. S. 2021-06-16 doi:10.1101/2021.06.14.448281 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ Live Imaging Reveals the Cellular Events Downstream of SARM1 Activation ]]> https://biorxiv.org/content/10.1101/2021.06.14.448297v1?rss=1 Ko, K. W. Milbrandt, J. DiAntonio, A. 2021-06-15 doi:10.1101/2021.06.14.448297 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ Skeletal dysplasia-causing TRPV4 mutations suppress the hypertrophic differentiation of human iPSC-derived chondrocytes ]]> https://biorxiv.org/content/10.1101/2021.06.15.448562v1?rss=1 Dicks, A. R. Maksaev, G. I. Harissa, Z. Savadipour, A. Tang, R. Steward, N. Liedtke, W. Wu, C.-L. Guilak, F. 2021-06-15 doi:10.1101/2021.06.15.448562 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ ACES: Analysis of Conservation with Expansive Species ]]> https://biorxiv.org/content/10.1101/2021.06.16.448733v1?rss=1 Padhi, E. M. Mehinovic, E. Sams, E. I. Ng, J. K. Turner, T. N. 2021-06-17 doi:10.1101/2021.06.16.448733 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Rotavirus NSP1 contributes to intestinal viral replication, pathogenesis, and transmission ]]> https://biorxiv.org/content/10.1101/2021.06.17.448915v1?rss=1 Hou, G. Zeng, Q. Matthijnssens, J. Greenberg, H. B. Ding, S. 2021-06-18 doi:10.1101/2021.06.17.448915 Cold Spring Harbor Laboratory Press 2021-06-18 <![CDATA[ Economic Choices under Simultaneous or Sequential Offers Rely on the Same Neural Circuit ]]> https://biorxiv.org/content/10.1101/2021.06.18.449049v1?rss=1 Shi, W. Ballesta, S. Padoa-Schioppa, C. 2021-06-20 doi:10.1101/2021.06.18.449049 Cold Spring Harbor Laboratory Press 2021-06-20 <![CDATA[ The Role of the Human Brain Neuron-Glia-Synaptic Composition in Forming Resting State Functional Connectivity Networks ]]> https://biorxiv.org/content/10.1101/2021.07.01.449170v1?rss=1 Kahali, S. Raichle, M. E. Yablonskiy, D. A. 2021-07-03 doi:10.1101/2021.07.01.449170 Cold Spring Harbor Laboratory Press 2021-07-03 <![CDATA[ Enzymatic and structural characterization of HAD5, an essential phosphomannomutase of malaria parasites ]]> https://biorxiv.org/content/10.1101/2021.07.03.451008v1?rss=1 Frasse, P. M. Miller, J. J. Soleimani, E. Zhu, J.-S. Jakeman, D. L. Jez, J. M. Goldberg, D. E. Odom John, A. R. 2021-07-04 doi:10.1101/2021.07.03.451008 Cold Spring Harbor Laboratory Press 2021-07-04 <![CDATA[ Stable Isotope Tracing In Vivo Reveals A Metabolic Bridge Linking The Microbiota To Host Histone Acetylation ]]> https://biorxiv.org/content/10.1101/2021.07.05.450926v1?rss=1 Lund, P. J. Gates, L. A. Leboeuf, M. Smith, S. A. Chau, L. Friedman, E. S. Lopes, M. Saiman, Y. Kim, M. S. Petucci, C. Allis, C. D. Wu, G. D. Garcia, B. A. 2021-07-05 doi:10.1101/2021.07.05.450926 Cold Spring Harbor Laboratory Press 2021-07-05 <![CDATA[ KSTAR: An algorithm to predict patient-specific kinase activities from phosphoproteomic data ]]> https://biorxiv.org/content/10.1101/2021.07.06.451378v1?rss=1 Crowl, S. Jordan, B. Ma, C. Naegle, K. M. 2021-07-08 doi:10.1101/2021.07.06.451378 Cold Spring Harbor Laboratory Press 2021-07-08 <![CDATA[ High-throughput functional analysis of CFTR and other apically localized channels in iPSC derived intestinal organoids ]]> https://biorxiv.org/content/10.1101/2021.07.07.451180v1?rss=1 Xia, S. Bozoky, Z. Laselva, O. DiPaola, M. Ahmadi, S. Jiang, J. X. Pitstick, A. Jiang, C. Rotin, D. Mayhew, C. Jones, N. L. Bear, C. E. 2021-07-07 doi:10.1101/2021.07.07.451180 Cold Spring Harbor Laboratory Press 2021-07-07 <![CDATA[ Connectome-based Modeling of Mnemonic Discrimination in Younger and Older Adults ]]> https://biorxiv.org/content/10.1101/2021.07.09.451777v1?rss=1 Wahlheim, C. N. Christensen, A. P. Reagh, Z. M. Cassidy, B. S. 2021-07-10 doi:10.1101/2021.07.09.451777 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ Neurotoxins subvert the allosteric activation mechanism of SARM1 to induce neuronal loss ]]> https://biorxiv.org/content/10.1101/2021.07.16.452689v1?rss=1 Wu, T. Zhu, J. Strickland, A. Ko, K. W. Sasaki, Y. Dingwall, C. Yamada, Y. Figley, M. D. Mao, X. Neiner, A. Bloom, J. DiAntonio, A. Milbrandt, J. 2021-07-16 doi:10.1101/2021.07.16.452689 Cold Spring Harbor Laboratory Press 2021-07-16 <![CDATA[ Connectivity and dynamics in the olfactory bulb ]]> https://biorxiv.org/content/10.1101/2021.07.19.452784v1?rss=1 Kersen, D. E. Tavoni, G. Balasubramanian, V. 2021-07-20 doi:10.1101/2021.07.19.452784 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ Drop, Swap, and Generate: A Self-Supervised Approach for Generating Neural Activity ]]> https://biorxiv.org/content/10.1101/2021.07.21.453285v1?rss=1 Liu, R. Azabou, M. Dabagia, M. Lin, C.-H. Azar, M. G. Hengen, K. B. Valko, M. Dyer, E. L. 2021-07-23 doi:10.1101/2021.07.21.453285 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Mesalamine Reduces Intestinal ACE2 Expression Without Modifying SARS-CoV-2 Infection or Disease Severity in Mice. ]]> https://biorxiv.org/content/10.1101/2021.07.23.453393v1?rss=1 Alvarado, D. M. Son, J. Thackray, L. B. Diamond, M. Ding, S. Ciorba, M. A. Washington University IBD Investigators Group, 2021-07-23 doi:10.1101/2021.07.23.453393 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Understanding SARS-CoV-2 budding through molecular dynamics simulations of M and E protein complexes ]]> https://biorxiv.org/content/10.1101/2021.07.26.453874v1?rss=1 Collins, L. T. Elkholy, T. Mubin, S. Williams, R. Ezike, K. Singhal, A. 2021-07-27 doi:10.1101/2021.07.26.453874 Cold Spring Harbor Laboratory Press 2021-07-27 <![CDATA[ Increased risk of thrombocytopenia and death in patients with bacteremia caused by high alpha toxin-producing methicillin-resistant Staphylococcus aureus. ]]> https://biorxiv.org/content/10.1101/2021.07.27.454087v1?rss=1 Alhurayri, F. Porter, E. Douglas-Louis, R. Minejima, E. Bubeck Wardenburg, J. Wong-Beringer, A. 2021-07-28 doi:10.1101/2021.07.27.454087 Cold Spring Harbor Laboratory Press 2021-07-28 <![CDATA[ Internet of Things Architecture for High Throughput Biology ]]> https://biorxiv.org/content/10.1101/2021.07.29.453595v1?rss=1 Parks, D. F. Voitiuk, K. Geng, J. Elliott, M. A. T. Keefe, M. G. Jung, E. A. Robbins, A. Baudin, P. V. Ly, V. T. Hawthorne, N. Yong, D. Sanso, S. E. Rezaee, N. Sevetson, J. L. Seiler, S. T. Currie, R. Hengen, K. B. Nowakowski, T. J. Salama, S. R. Teodorescu, M. Haussler, D. 2021-08-01 doi:10.1101/2021.07.29.453595 Cold Spring Harbor Laboratory Press 2021-08-01 <![CDATA[ Uncertainty quantification in subject-specific estimation of local vessel mechanical properties ]]> https://biorxiv.org/content/10.1101/2021.08.02.454803v1?rss=1 Rego, B. V. Weiss, D. Bersi, M. R. Humphrey, J. D. 2021-08-04 doi:10.1101/2021.08.02.454803 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ Single Cell Atlas of Human Dura Reveals Cellular Meningeal Landscape and Insights into Meningioma Immune Response ]]> https://biorxiv.org/content/10.1101/2021.08.03.454066v1?rss=1 Wang, A. Z. Bowman-Kirigin, J. Desai, R. Patel, P. Patel, B. Khan, S. Bender, D. Marlin, M. C. Liu, J. Osbun, J. Leuthardt, E. Chicoine, M. Dacey, R. Zipfel, G. Kim, A. Petti, A. A. Dunn, G. 2021-08-03 doi:10.1101/2021.08.03.454066 Cold Spring Harbor Laboratory Press 2021-08-03 <![CDATA[ Principles of sensor-effector organization in six-transmembrane ion channels ]]> https://biorxiv.org/content/10.1101/2021.08.03.454958v1?rss=1 Dou, A. K. Kang, P. W. Hou, P. Zaydman, M. A. Zheng, J. Jegla, T. Cui, J. 2021-08-05 doi:10.1101/2021.08.03.454958 Cold Spring Harbor Laboratory Press 2021-08-05 <![CDATA[ Neural manifolds for odor-driven innate and acquired appetitive preferences ]]> https://biorxiv.org/content/10.1101/2021.08.05.455310v1?rss=1 Chandak, R. Raman, B. 2021-08-06 doi:10.1101/2021.08.05.455310 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Recombinant NAGLU-IGF2 prevents physical and neurological disease and improves survival in Sanfilippo B syndrome ]]> https://biorxiv.org/content/10.1101/2021.08.06.455469v1?rss=1 Le, S. Q. Kan, S.-h. Nunez, M. Dearborn, J. Wang, F. LI, S. Snella, L. Jens, J. K. Valentine, B. N. Nelvagal, H. R. Sorensen, A. Cooper, J. D. Chou, T.-F. Ellinwood, N. M. Smith, J. D. Sands, M. S. Dickson, P. 2021-08-08 doi:10.1101/2021.08.06.455469 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ Transmit Field Bias Correction of T1w/T2w Myelin Maps ]]> https://biorxiv.org/content/10.1101/2021.08.08.455570v1?rss=1 Glasser, M. F. Coalson, T. S. Harms, M. P. Baum, G. L. Autio, J. A. Auerbach, E. A. Xu, J. Greve, D. N. Yacoub, E. Van Essen, D. C. Bock, N. A. Hayashi, T. 2021-08-08 doi:10.1101/2021.08.08.455570 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ Intrinsically disordered pathogen effector alters the STAT1 dimer to prevent recruitment of co-transcriptional activators CBP/p300 ]]> https://biorxiv.org/content/10.1101/2021.08.09.455663v1?rss=1 Huang, Z. Liu, H. Nix, J. Knoverek, C. R. Bowman, G. R. Amarasinghe, G. K. Sibley, L. D. 2021-08-09 doi:10.1101/2021.08.09.455663 Cold Spring Harbor Laboratory Press 2021-08-09 <![CDATA[ isotracer: An R package for the analysis of tracer addition experiments ]]> https://biorxiv.org/content/10.1101/2021.08.09.455668v1?rss=1 Bruneaux, M. Lopez-Sepulcre, A. 2021-08-10 doi:10.1101/2021.08.09.455668 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Sulfonylureas target the neurovascular response to decrease Alzheimer's pathology ]]> https://biorxiv.org/content/10.1101/2021.08.11.455969v1?rss=1 Macauley, S. L. Stanley, M. Caesar, E. E. Moritz, W. R. Bice, A. R. Cruz-Diaz, N. Carroll, C. M. Day, S. M. Grizzanti, J. Mahan, T. E. Snipes, J. A. Orr, T. C. Culver, J. Remedi, M. S. Nichols, C. G. Karch, C. Cox, L. A. Diz, D. I. Bauer, A. Q. Holtzman, D. M. 2021-08-12 doi:10.1101/2021.08.11.455969 Cold Spring Harbor Laboratory Press 2021-08-12 <![CDATA[ Structural transitions in the GTP cap visualized by cryo-EM of catalytically inactive microtubules ]]> https://biorxiv.org/content/10.1101/2021.08.13.456308v1?rss=1 LaFrance, B. J. Roostalu, J. Henkin, G. Greber, B. J. Zhang, R. Normanno, D. McCollum, C. Surrey, T. Nogales, E. 2021-08-13 doi:10.1101/2021.08.13.456308 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Molecular Swiss Army Knives: Tardigrade CAHS Proteins Mediate Desiccation Tolerance Through Multiple Mechanisms ]]> https://biorxiv.org/content/10.1101/2021.08.16.456555v1?rss=1 Hesgrove, C. S. Nguyen, K. H. Biswas, S. Childs, C. A. KC, S. Medina, B. X. Alvarado, V. Sukenik, S. Yu, F. Malferrari, M. Francia, F. Venturoli, G. Martin, E. W. Holehouse, A. S. Boothby, T. C. 2021-08-17 doi:10.1101/2021.08.16.456555 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ A Test of the Pioneer Factor Hypothesis ]]> https://biorxiv.org/content/10.1101/2021.08.17.456650v1?rss=1 Hansen, J. L. Cohen, B. A. 2021-08-18 doi:10.1101/2021.08.17.456650 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ Uncovering non-random sequence patterns within intrinsically disordered proteins ]]> https://biorxiv.org/content/10.1101/2021.08.19.456831v1?rss=1 Cohan, M. C. Shinn, M. K. Lalmansingh, J. M. Pappu, R. V. 2021-08-19 doi:10.1101/2021.08.19.456831 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Sequence grammar underlying unfolding and phase separation of globular proteins ]]> https://biorxiv.org/content/10.1101/2021.08.20.457073v1?rss=1 Ruff, K. M. Choi, Y. H. Cox, D. Ormsby, A. R. Myung, Y. Ascher, D. B. Radford, S. E. Pappu, R. V. Hatters, D. M. 2021-08-20 doi:10.1101/2021.08.20.457073 Cold Spring Harbor Laboratory Press 2021-08-20 <![CDATA[ TopoRoot: A method for computing hierarchy and fine-grained traits of maize roots from X-ray CT images ]]> https://biorxiv.org/content/10.1101/2021.08.24.457522v1?rss=1 Zeng, D. Li, M. Jiang, N. Ju, Y. Schreiber, H. Chambers, E. Letscher, D. Ju, T. Topp, C. N. 2021-08-25 doi:10.1101/2021.08.24.457522 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ Interactions between a mechanosensitive channel and cell wall integrity signaling influence pollen germination in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2021.08.24.457556v1?rss=1 Wang, Y. Coomey, J. Miller, K. Jensen, G. S. Haswell, E. S. 2021-08-25 doi:10.1101/2021.08.24.457556 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ Weakly activated core inflammation pathways were identified as a central signaling mechanism contributing to the chronic neurodegeneration in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2021.08.30.458295v1?rss=1 Li, F. Eteleeb, A. Buchser, W. Wang, G. Xiong, C. Payne, P. R. McDade, E. Karch, C. M. Harari, O. Cruchaga, C. 2021-09-01 doi:10.1101/2021.08.30.458295 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Quantifying charge state heterogeneity for proteins with multiple ionizable residues ]]> https://biorxiv.org/content/10.1101/2021.08.31.458420v1?rss=1 Fossat, M. J. Posey, A. E. Pappu, R. V. 2021-09-01 doi:10.1101/2021.08.31.458420 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Immunosuppression and Outcomes in Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/2021.09.03.458879v1?rss=1 5 years) after standard-of-care chemotherapy, unless classified as favorable risk at presentation. Identification of the mechanisms responsible for long vs. more typical, short remissions may help to define prognostic determinants for chemotherapy responses. Using exome sequencing, RNA-sequencing and functional immunologic studies, we characterized 28 Normal Karyotype (NK)-AML patients with >5 year first remissions after chemotherapy (Long First Remissions, LFR) and compared them to a well-matched group of 31 NK-AML patients who relapsed within 2 years (Standard First Remissions, SFR). Our combined analyses indicated that genetic risk profiling at presentation (as defined by ELN 2017 Criteria) was not sufficient to explain the outcomes of many SFR cases. Single cell RNA-sequencing studies of 15 AML samples showed that SFR AML cells differentially expressed many genes associated with immune suppression. The bone marrow of SFR cases had significantly fewer CD4+ Th1 cells; these T-cells expressed an exhaustion signature and were resistant to activation by T-cell receptor stimulation in the presence of autologous AML cells. T-cell activation could be restored by removing the AML cells, or blocking the inhibitory MHC Class II receptor, LAG3. Most LFR cases did not display these features, suggesting that their AML cells were not as immunosuppressive. These findings were confirmed and extended in an independent set of 50 AML cases representing all ELN 2017 risk groups. AML cell-mediated suppression of CD4+ T-cell activation at presentation is strongly associated with unfavorable outcomes in AML patients treated with standard chemotherapy. ]]> Ferraro, F. Miller, C. Christensen, K. Helton, N. M. O'Laughlin, M. Fronick, C. C. Fulton, R. S. Kohlschmidt, J. Eisfeld, A.-K. Bloomfield, C. D. Ramakrishnan, S. M. Day, R. B. Wartman, L. D. Uy, G. L. Welch, J. S. Christopher, M. J. Heath, S. E. Baty, J. D. Schuelke, M. J. Payton, J. E. Spencer, D. H. Rettig, M. P. Link, D. C. Walter, M. J. Peter, W. DiPersio, J. F. Ley, T. J. 2021-09-06 doi:10.1101/2021.09.03.458879 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Single-cell perturbation dissects transcription factor control of progression speed and trajectory choice in early T-cell development ]]> https://biorxiv.org/content/10.1101/2021.09.03.458944v1?rss=1 Zhou, W. Gao, F. Romero-Wolf, M. Jo, S. Rothenberg, E. V. 2021-09-06 doi:10.1101/2021.09.03.458944 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Over-expression Screen of Interferon-Stimulated Genes Identifies RARRES3 as a Restrictor of Toxoplasma gondii Infection ]]> https://biorxiv.org/content/10.1101/2021.09.04.458998v1?rss=1 Rinkenberger, N. Abrams, M. E. Matta, S. K. Schoggins, J. W. Alto, N. M. Sibley, L. D. 2021-09-05 doi:10.1101/2021.09.04.458998 Cold Spring Harbor Laboratory Press 2021-09-05 <![CDATA[ Deep-Learning-Based Accelerated and Noise-Suppressed Estimation (DANSE) of quantitative Gradient Recalled Echo (qGRE) MRI metrics associated with Human Brain Neuronal Structure and Hemodynamic Properties ]]> https://biorxiv.org/content/10.1101/2021.09.10.459810v1?rss=1 Kahali, S. Kothapalli, S. V. V. N. Xu, X. Kamilov, U. S. Yablonskiy, D. A. 2021-09-11 doi:10.1101/2021.09.10.459810 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ The conventional dendritic cell 1 subset primes CD8+ T cells and traffics tumor antigen to drive anti-tumor immunity in the brain ]]> https://biorxiv.org/content/10.1101/2021.09.13.460088v1?rss=1 Bowman-Kirigin, J. A. Saunders, B. T. Desai, R. Wang, A. Z. Schaettler, M. O. Liu, C. J. Livingstone, A. J. Kobayashi, D. K. Durai, V. Kretzer, N. M. Zipfel, G. J. Leuthardt, E. C. Osbun, J. W. Chicoine, M. R. Kim, A. H. Murphy, K. M. Johanns, T. M. Zinselmeyer, B. H. Dunn, G. P. 2021-09-15 doi:10.1101/2021.09.13.460088 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Single-Molecule Localization Microscopy of 3D Orientation and Anisotropic Wobble using a Polarized Vortex Point Spread Function ]]> https://biorxiv.org/content/10.1101/2021.09.13.460135v1?rss=1 Ding, T. Lew, M. D. 2021-09-15 doi:10.1101/2021.09.13.460135 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Donor Macrophages Modulate Rejection after Heart Transplantation ]]> https://biorxiv.org/content/10.1101/2021.09.17.459296v1?rss=1 Kopecky, B. Dun, H. Amrute, J. Lin, C.-Y. Bredemeyer, A. Terada, Y. Bayguinov, P. Koenig, A. Frye, C. Fitzpatrick, J. Kreisel, D. Lavine, K. 2021-09-20 doi:10.1101/2021.09.17.459296 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ Context, competition, and symbiont-induced bet-hedging between Dictyostelium discoideum and Paraburkholderia ]]> https://biorxiv.org/content/10.1101/2021.09.17.459779v1?rss=1 Scott, T. J. Queller, D. C. Strassmann, J. E. 2021-09-19 doi:10.1101/2021.09.17.459779 Cold Spring Harbor Laboratory Press 2021-09-19 <![CDATA[ m6A modifications regulate intestinal immunity and rotavirus infection ]]> https://biorxiv.org/content/10.1101/2021.09.17.460776v1?rss=1 Zhu, S. Wang, A. Wang, J. Tao, W. Ding, S. Flavell, R. A. Tong, J. Hou, G. Gao, J. Zhang, G. Li, R. Ren, X. Wang, D. Zhang, K. Pan, W. Li, H. Qian, C. 2021-09-17 doi:10.1101/2021.09.17.460776 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ Two common and distinct forms of variation in human functional brain networks ]]> https://biorxiv.org/content/10.1101/2021.09.17.460799v1?rss=1 Dworetsky, A. Seitzman, B. A. Adeyemo, B. Smith, D. M. Petersen, S. E. Gratton, C. 2021-09-18 doi:10.1101/2021.09.17.460799 Cold Spring Harbor Laboratory Press 2021-09-18 <![CDATA[ Identification and Functional Annotation of Long Intergenic Non-coding RNAs in the Brassicaceae ]]> https://biorxiv.org/content/10.1101/2021.09.17.460835v1?rss=1 24 Tbp of RNA-seq data from >16,000 experiments to identify ~130,000 lincRNAs in four Brassicaceae: Arabidopsis thaliana, Camelina sativa, Brassica rapa, and Eutrema salsugineum. We used Nanopore RNA-seq, transcriptome-wide structural information, peptide data, and epigenomic data to characterize these lincRNAs and identify functional motifs. We then used comparative genomic and transcriptomic approaches to highlight lincRNAs in our dataset with sequence or transcriptional evolutionary conservation, including lincRNAs transcribed adjacent to orthologous genes that display little sequence similarity and likely function as transcriptional regulators. Finally, we used guilt-by-association techniques to further classify these lincRNAs according to putative function. LincRNAs with Brassicaceae-conserved putative miRNA binding motifs, short ORFs, and whose expression is modulated by abiotic stress are a few of the annotations that will prioritize and guide future functional analyses. ]]> Palos, K. R. Nelson Dittrich, A. C. Yu, L. Brock, J. R. Wu, L. Sokolowska, E. Skirycz, A. Hsu, P. Y. Lyons, E. Beilstein, M. Nelson, A. D. L. 2021-09-20 doi:10.1101/2021.09.17.460835 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ Loss of Fgfr1 and Fgfr2 in Scleraxis-lineage cells leads to enlarged bone eminences and attachment cell death ]]> https://biorxiv.org/content/10.1101/2021.09.20.461087v1?rss=1 Shuff, J. Offutt, C. Killian, M. L. Ornitz, D. M. Leek, C. C. Ganji, E. Tata, Z. Paparella, E. Sonnenfelt, M. A. Sullivan, A. L. Wernle, K. K. 2021-09-20 doi:10.1101/2021.09.20.461087 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ Progenitor-intrinsic Metabolic Sensing Promotes Hematopoietic Homeostasis ]]> https://biorxiv.org/content/10.1101/2021.09.20.461098v1?rss=1 Pizzato, H. A. Wang, Y. Wolfgang, M. Finck, B. Patti, G. J. Bhattacharya, D. 2021-09-20 doi:10.1101/2021.09.20.461098 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ Distinct ground state and activated state modes of spiking in forebrain neurons ]]> https://biorxiv.org/content/10.1101/2021.09.20.461152v1?rss=1 Levenstein, D. Girardeau, G. Gornet, J. Grosmark, A. Huszar, R. Peyrache, A. Senzai, Y. Watson, B. Rinzel, J. Buzsaki, G. 2021-09-21 doi:10.1101/2021.09.20.461152 Cold Spring Harbor Laboratory Press 2021-09-21 <![CDATA[ Association of RACK1 protein with ribosomes in Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2021.09.21.461325v1?rss=1 Djuranovic, S. Erath, J. 2021-09-22 doi:10.1101/2021.09.21.461325 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ Defining hierarchical protein interaction networks from spectral analysis of bacterial proteomes ]]> https://biorxiv.org/content/10.1101/2021.09.28.462107v1?rss=1 Zaydman, M. A. Little, A. Haro, F. Aksianiuk, V. Buchser, W. DiAntonio, A. Gordon, J. I. Milbrandt, J. Raman, A. 2021-09-28 doi:10.1101/2021.09.28.462107 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[ Ex Vivo and In Vivo CD46 Receptor Utilization by Species D Human Adenovirus Serotype 26 (HAdV26) ]]> https://biorxiv.org/content/10.1101/2021.09.28.462271v1?rss=1 Hemsath, J. R. Liaci, M. Rubin, J. Parrett, B. Lu, S.-C. Nguyen, T. Turner, M. Chen, C. Reddy, V. S. Cupelli, K. Stehle, T. Liszewski, K. Atkinson, J. Barry, M. A. 2021-10-01 doi:10.1101/2021.09.28.462271 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Sex Differences in Brain Tumor Glutamine Metabolism Reveal Sex-Specific Vulnerabilities to Treatment ]]> https://biorxiv.org/content/10.1101/2021.09.29.461531v1?rss=1 Sponagel, J. Jones, J. K. Frankfater, C. Zhang, S. Tung, O. Cho, K. Tinkum, K. L. Gass, H. Nunez, E. Spitz, D. R. Chinnaiyan, P. Schaefer, J. Patti, G. J. Graham, M. S. Mauguen, A. Grkovski, M. Dunphy, M. P. Krebs, S. Luo, J. Rubin, J. B. Ippolito, J. E. 2021-10-01 doi:10.1101/2021.09.29.461531 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Convergent mosaic brain evolution is associated with the evolution of novel electrosensory systems in teleost fishes. ]]> https://biorxiv.org/content/10.1101/2021.09.29.462233v1?rss=1 Schumacher, E. L. Carlson, B. A. 2021-10-01 doi:10.1101/2021.09.29.462233 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Polyunsaturated fatty acids inhibit a pentameric ligand-gated ion channel through one of two binding sites ]]> https://biorxiv.org/content/10.1101/2021.10.08.463634v1?rss=1 Dietzen, N. M. Arcario, M. J. Chen, L. J. Petroff, J. T. Krishnan, K. Brannigan, G. Covey, D. F. Cheng, W. W. 2021-10-08 doi:10.1101/2021.10.08.463634 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ Reliability and Stability Challenges in ABCD Task fMRI Data ]]> https://biorxiv.org/content/10.1101/2021.10.08.463750v1?rss=1 Kennedy, J. T. Harms, M. P. Korucuoglu, O. Astafiev, S. V. Barch, D. M. Thompson, W. K. Bjork, J. M. Anokhin, A. P. 2021-10-09 doi:10.1101/2021.10.08.463750 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ Genome-edited zebrafish model of ABCC8 loss-of-function disease ]]> https://biorxiv.org/content/10.1101/2021.10.10.461291v1?rss=1 Ikle, J. M. Tryon, R. C. Singareddy, S. S. York, N. W. Remedi, M. S. Nichols, C. G. 2021-10-11 doi:10.1101/2021.10.10.461291 Cold Spring Harbor Laboratory Press 2021-10-11 <![CDATA[ Chemical inhibition of auxin inactivation pathway uncovers the metabolic turnover of auxin homeostasis ]]> https://biorxiv.org/content/10.1101/2021.10.12.464031v1?rss=1 Fukui, K. Arai, K. Tanaka, Y. Aoi, Y. Kukshal, V. Jez, J. M. Kubes, M. F. Napier, R. Zhao, Y. Kasahara, H. Hayashi, K.-i. 2021-10-13 doi:10.1101/2021.10.12.464031 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Dorsolateral prefrontal cortex supports speech perception in listeners with cochlear implants ]]> https://biorxiv.org/content/10.1101/2021.10.16.464654v1?rss=1 Sherafati, A. Dwyer, N. Bajracharya, A. Hassanpour, M. S. Eggebrecht, A. T. Firszt, J. B. Culver, J. P. Peelle, J. E. 2021-10-16 doi:10.1101/2021.10.16.464654 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ The ASCC2 CUE domain contacts adjacent ubiquitins to recognize K63-linked polyubiquitin ]]> https://biorxiv.org/content/10.1101/2021.10.17.464694v1?rss=1 Lombardi, P. M. Haile, S. Rusanov, T. Rodell, R. Anoh, R. Baer, J. G. Burke, K. A. Gray, L. N. Hacker, A. R. Kebreau, K. R. Ngandu, C. K. Orland, H. A. Osei-Asante, E. Schmelyun, D. P. Shorb, D. E. Syed, S. H. Veilleux, J. M. Majumdar, A. Mosammaparast, N. Wolberger, C. 2021-10-17 doi:10.1101/2021.10.17.464694 Cold Spring Harbor Laboratory Press 2021-10-17 <![CDATA[ Adaptation of peristaltic pumps for laminar flow experiments ]]> https://biorxiv.org/content/10.1101/2021.10.17.464751v1?rss=1 Abello, J. Yien, Y. Y. Stratman, A. N. 2021-10-18 doi:10.1101/2021.10.17.464751 Cold Spring Harbor Laboratory Press 2021-10-18 <![CDATA[ In vitro experiments and kinetic models of pollen hydration show that MSL8 is not a simple tension-gated osmoregulator ]]> https://biorxiv.org/content/10.1101/2021.10.19.464977v1?rss=1 Miller, K. Strychalski, W. Nickaeen, M. Carlsson, A. Haswell, E. 2021-10-19 doi:10.1101/2021.10.19.464977 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Dynamic Brain Network States during Suspenseful Film Viewing ]]> https://biorxiv.org/content/10.1101/2021.10.19.465030v1?rss=1 Bezdek, M. A. Keilholz, S. D. Schumacher, E. H. 2021-10-19 doi:10.1101/2021.10.19.465030 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Resolving the 3D rotational and translational dynamics of single molecules using radially and azimuthally polarized fluorescence ]]> https://biorxiv.org/content/10.1101/2021.10.19.465033v1?rss=1 Zhang, O. Zhou, W. Lu, J. Wu, T. Lew, M. D. 2021-10-19 doi:10.1101/2021.10.19.465033 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Defining cellular complexity in human autosomal dominant polycystic kidney disease by multimodal single cell analysis ]]> https://biorxiv.org/content/10.1101/2021.10.21.465323v1?rss=1 Muto, Y. Dixon, E. E. Yoshimura, Y. Wu, H. Omachi, K. King, A. J. Olson, E. N. Gunawan, M. G. Kuo, J. J. Cox, J. Miner, J. H. Seliger, S. L. Woodward, O. M. Welling, P. A. Watnick, T. J. Humphreys, B. D. 2021-10-22 doi:10.1101/2021.10.21.465323 Cold Spring Harbor Laboratory Press 2021-10-22 <![CDATA[ Enterotoxigenic Escherichia coli degrades the host MUC2 mucin barrier to facilitate critical pathogen-enterocyte interactions in human small intestine. ]]> https://biorxiv.org/content/10.1101/2021.10.22.465536v1?rss=1 Sheikh, A. Wangdi, T. Vickers, T. J. Aaron, B. Palmer, M. P. Miller, M. Kim, S. Herring, C. Simoes, R. Crainic, J. A. Gildersleeve, J. van der Post, S. Hansson, G. C. Fleckenstein, J. M. 2021-10-23 doi:10.1101/2021.10.22.465536 Cold Spring Harbor Laboratory Press 2021-10-23 <![CDATA[ Mecp2 deletion results in profound alterations of developmental and adult functional connectivity ]]> https://biorxiv.org/content/10.1101/2021.10.28.466323v1?rss=1 Rahn, R. M. Yen, A. Chen, S. Gaines, S. H. Bice, A. R. Brier, L. M. Swift, R. G. Lee, L. Maloney, S. E. Culver, J. P. Dougherty, J. D. 2021-10-28 doi:10.1101/2021.10.28.466323 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Development and Validation of Subject-Specific 3D Human Head Models Based on a Nonlinear Visco-Hyperelastic Constitutive Framework ]]> https://biorxiv.org/content/10.1101/2021.10.28.466370v1?rss=1 Upadhyay, K. Alshareef, A. Knutsen, A. K. Johnson, C. L. Carass, A. Bayly, P. V. Ramesh, K. T. 2021-11-01 doi:10.1101/2021.10.28.466370 Cold Spring Harbor Laboratory Press 2021-11-01 <![CDATA[ Coiled Coil Crosslinked Alginate Hydrogels Dampen Macrophage-Driven Inflammation ]]> https://biorxiv.org/content/10.1101/2021.11.01.466776v1?rss=1 Clapacs, Z. O'Neill, C. L. Shrimali, P. Lokhande, G. Files, M. Kim, D. D. Gaharwar, A. Rudra, J. S. 2021-11-04 doi:10.1101/2021.11.01.466776 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Sex significantly impacts the function of major depression-linked variants in vivo ]]> https://biorxiv.org/content/10.1101/2021.11.01.466849v1?rss=1 1,000 variants from >30 MDD loci, identifying extensive sex-by-allele effects in mature hippocampal neurons and suggesting sex-differentiated impacts of genetic risk may underlie sex bias in disease. Unbiased informatics approaches indicated that functional MDD variants recurrently disrupt sex hormone receptor binding sequences. We confirmed this with MPRAs in neonatal brains, comparing brains undergoing the masculinizing hormone surge to hormonally-quiescent juveniles. Our study provides novel insights into the influence of age, biological sex, and cell type on regulatory-variant function, and provides a framework for in vivo parallel assays to functionally define interactions between organismal variables like sex and regulatory variation. One-Sentence SummaryMassively parallel assays in vivo identified extensive functional and sex-interacting common variants in depression risk loci. ]]> Mulvey, B. Selmanovic, D. Dougherty, J. D. 2021-11-04 doi:10.1101/2021.11.01.466849 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Ultrapotent and Broad Neutralization of SARS-CoV-2 Variants by Modular, Tetravalent, Bi-paratopic Antibodies ]]> https://biorxiv.org/content/10.1101/2021.11.02.466984v1?rss=1 Miersch, S. Saberianfar, R. Chen, C. Sharma, N. Amarasinghe, G. K. Caruso, A. Caccuri, F. Zani, A. Novelli, G. Sidhu, S. S. 2021-11-04 doi:10.1101/2021.11.02.466984 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ An ex vivo culture model of kidney podocyte injury reveals mechanosensitive, synaptopodin-templating, sarcomere-like structures. ]]> https://biorxiv.org/content/10.1101/2021.11.03.466963v1?rss=1 Shumeng, J. Alisafaei, F. Yuan, H. Peng, X. Huang, Y.-Y. Miner, J. H. Genin, G. M. Suleiman, H. Y. 2021-11-04 doi:10.1101/2021.11.03.466963 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Measuring G Protein Activation with Spectrally Resolved Fluorescence Fluctuation Spectroscopy ]]> https://biorxiv.org/content/10.1101/2021.11.03.467169v1?rss=1 Foust, D. J. Piston, D. W. 2021-11-04 doi:10.1101/2021.11.03.467169 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Sleep promoting neurons remodel their response properties to calibrate sleep drive with environmental demands. ]]> https://biorxiv.org/content/10.1101/2021.11.05.467459v1?rss=1 Dissel, S. Klose, M. K. van Swinderen, B. Cao, L. Shaw, P. J. 2021-11-07 doi:10.1101/2021.11.05.467459 Cold Spring Harbor Laboratory Press 2021-11-07 <![CDATA[ Cell cycle stage classification using phase imaging with computational specificity ]]> https://biorxiv.org/content/10.1101/2021.11.05.467526v1?rss=1 He, Y. He, S. Kandel, M. E. Lee, Y. J. Hu, C. Sobh, N. Anastasio, M. Popescu, G. 2021-11-07 doi:10.1101/2021.11.05.467526 Cold Spring Harbor Laboratory Press 2021-11-07 <![CDATA[ Neuronal origins of biases in economic choices under sequential offers ]]> https://biorxiv.org/content/10.1101/2021.11.07.467645v1?rss=1 Shi, W. Ballesta, S. Padoa-Schioppa, C. 2021-11-08 doi:10.1101/2021.11.07.467645 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ Macrophage proliferation machinery leads to PDAC progression, but susceptibility to innate immunotherapy. ]]> https://biorxiv.org/content/10.1101/2021.11.08.467770v1?rss=1 DeNardo, D. G. Zuo, C. Baer, J. M. Knolhoff, B. L. Belle, J. I. Liu, X. Hogg, G. D. Fu, C. Kingston, N. L. Brenden, M. A. Alarcon De La Lastra, A. Dodhiawala, P. B. Zhou, C. James, A. Ding, L. Kian-Huat, L. Fields, R. C. Hawkins, W. G. Zhao, G. Weber, J. D. 2021-11-08 doi:10.1101/2021.11.08.467770 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ Effects of tendon viscoelasticity in the distribution of forces over sutures in a model tendon-to-bone repair ]]> https://biorxiv.org/content/10.1101/2021.11.09.467963v1?rss=1 Huang, Y. hoppe, e. Kurtaliaj, I. Birman, V. Thomopoulos, S. Genin, G. M. 2021-11-11 doi:10.1101/2021.11.09.467963 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ A single-cell massively parallel reporter assay detects cell type specific cis-regulatory activity ]]> https://biorxiv.org/content/10.1101/2021.11.11.468308v1?rss=1 Zhao, S. Hong, C. Granas, D. M. Cohen, B. A. 2021-11-12 doi:10.1101/2021.11.11.468308 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ Essential functions of MLL1 and MLL2 in retinal development and cone cell maintenance ]]> https://biorxiv.org/content/10.1101/2021.11.15.468679v1?rss=1 Sun, C. Zhang, X. Ruzycki, P. A. Chen, S. 2021-11-15 doi:10.1101/2021.11.15.468679 Cold Spring Harbor Laboratory Press 2021-11-15 <![CDATA[ Lateral Line Ablation by Toxins Results in Distinct Rheotaxis Profiles in Fish ]]> https://biorxiv.org/content/10.1101/2021.11.15.468723v1?rss=1 Newton, K. Kacev, D. Nilsson, S. R. Golden, S. A. Sheets, L. 2021-11-19 doi:10.1101/2021.11.15.468723 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ SC2MeNetDrug: A computational tool to uncover inter-cell signaling targets and identify relevant drugs based on single cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/2021.11.15.468755v1?rss=1 Feng, J. Goedegebuure, S. P. Zeng, A. Bi, Y. Wang, T. Payne, P. R. Ding, L. DeNardo, D. Hawkins, W. Fields, R. C. Li, F. 2021-11-19 doi:10.1101/2021.11.15.468755 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Antenna modification leads to enhanced nitrogenase activity in a high light tolerant cyanobacterium ]]> https://biorxiv.org/content/10.1101/2021.11.15.468767v1?rss=1 Bandyopadhyay, A. Ye, Z. Benedikty, Z. Trtilek, M. Pakrasi, H. B. 2021-11-16 doi:10.1101/2021.11.15.468767 Cold Spring Harbor Laboratory Press 2021-11-16 <![CDATA[ Hidden structure in disordered proteins is adaptive to intracellular changes ]]> https://biorxiv.org/content/10.1101/2021.11.24.469609v1?rss=1 Moses, D. Guadalupe, K. Yu, F. Flores, E. Perez, A. McAnelly, R. L. Shamoon, N. M. Cuevas-Zepeda, E. Merg, A. Martin, E. W. Holehouse, A. S. Sukenik, S. 2021-11-25 doi:10.1101/2021.11.24.469609 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ Protein proximity networks and functional evaluation of the Casein Kinase 1 γ family reveals unique roles for CK1γ3 in WNT signaling ]]> https://biorxiv.org/content/10.1101/2021.11.30.470617v1?rss=1 Agajanian, M. J. Potjewyd, F. M. Bowman, B. M. Solomon, S. LaPak, K. M. Bhatt, D. P. Smith, J. L. Goldfarb, D. Axtman, A. D. Major, M. B. 2021-11-30 doi:10.1101/2021.11.30.470617 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Disrupted controlling mechanism of salience network on default-mode network and central-executive network in schizophrenia ]]> https://biorxiv.org/content/10.1101/2021.12.03.471183v1?rss=1 Chand, G. B. Thakuri, D. S. Soni, B. 2021-12-07 doi:10.1101/2021.12.03.471183 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Structural insights into distinct signaling profiles of the μOR activated by diverse agonists ]]> https://biorxiv.org/content/10.1101/2021.12.07.471645v1?rss=1 Qu, Q. Huang, W. Aydin, D. Paggi, J. M. Seven, A. B. Wang, H. Chakraborty, S. Che, T. DiBerto, J. F. Robertson, M. J. Inoue, A. Roth, B. L. Majumdar, S. Dror, R. O. Kobilka, B. K. Skiniotis, G. 2021-12-08 doi:10.1101/2021.12.07.471645 Cold Spring Harbor Laboratory Press 2021-12-08 <![CDATA[ Shared mechanisms of auditory and non-auditory vocal learning in the songbird brain ]]> https://biorxiv.org/content/10.1101/2021.12.09.471883v1?rss=1 McGregor, J. Grassler, A. Jaffe, P. I. Jacob, A. L. Brainard, M. Sober, S. J. 2021-12-10 doi:10.1101/2021.12.09.471883 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ Islet primary cilia motility controls insulin secretion ]]> https://biorxiv.org/content/10.1101/2021.12.14.472629v1?rss=1 Cho, J. H. Li, Z. A. Zhu, L. Muegge, B. Roseman, H. Utterback, T. Woodhams, L. Bayly, P. V. HUGHES, J. 2021-12-14 doi:10.1101/2021.12.14.472629 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ Paw placement during walking is altered by analgesic doses of opioids and post-surgical injury in mice ]]> https://biorxiv.org/content/10.1101/2021.12.15.472818v1?rss=1 Brings, V. E. Payne, M. A. Gereau, R. W. 2021-12-16 doi:10.1101/2021.12.15.472818 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Orbitofrontal cortex contributes to the comparison of values underlying economic choices ]]> https://biorxiv.org/content/10.1101/2021.12.16.473020v1?rss=1 Ballesta, S. Shi, W. Padoa-Schioppa, C. 2021-12-19 doi:10.1101/2021.12.16.473020 Cold Spring Harbor Laboratory Press 2021-12-19 <![CDATA[ Global cerebrospinal fluid circulation mapping using gold nanoparticle enhanced X-ray microtomography reveals region-specific brain and spinal cord CSF pathways ]]> https://biorxiv.org/content/10.1101/2021.12.18.473250v1?rss=1 Pan, S. DeFreitas, D. Ramagiri, S. Bayguinov, P. Hacker, C. D. Snyder, A. Z. Wilborn, J. Huang, H. Yang, P. H. Raval, D. K. Sviben, S. Achilefu, S. Tang, R. Haller, G. Quirk, J. D. Fitzpatrick, J. A. Esakky, P. Strahle, J. 2021-12-20 doi:10.1101/2021.12.18.473250 Cold Spring Harbor Laboratory Press 2021-12-20 <![CDATA[ Deep Learning-powered Bessel-beam Multi-parametric Photoacoustic Microscopy ]]> https://biorxiv.org/content/10.1101/2021.12.21.473705v1?rss=1 Zhou, Y. Sun, N. Hu, S. 2021-12-23 doi:10.1101/2021.12.21.473705 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ An ensemble of toxic channel types underlies the severity of the de novo variant G375R of the human BK channel ]]> https://biorxiv.org/content/10.1101/2021.12.22.473917v1?rss=1 Geng, Y. Li, P. Butler, A. Wang, B. Salkoff, L. Magleby, K. L. 2021-12-23 doi:10.1101/2021.12.22.473917 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Conserved angio-immune subtypes of the cancer microenvironment predict response to immune checkpoint blockade therapy ]]> https://biorxiv.org/content/10.1101/2021.12.23.470799v1?rss=1 Subramanian, M. Kabir, A. U. Barisas, D. A. G. Krchma, K. Choi, K. 2021-12-24 doi:10.1101/2021.12.23.470799 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ Ultra-high-speed multi-parametric photoacoustic microscopy ]]> https://biorxiv.org/content/10.1101/2021.12.25.474038v1?rss=1 Hu, S. Zhong, F. 2021-12-25 doi:10.1101/2021.12.25.474038 Cold Spring Harbor Laboratory Press 2021-12-25 <![CDATA[ pixOL: pixel-wise dipole-spread function engineering for simultaneously measuring the 3D orientation and 3D localization of dipole-like emitters ]]> https://biorxiv.org/content/10.1101/2021.12.30.474544v1?rss=1 Wu, T. Lu, J. Lew, M. D. 2021-12-30 doi:10.1101/2021.12.30.474544 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ Structure-function relationships in mitochondrial transcriptional condensates ]]> https://biorxiv.org/content/10.1101/2021.12.30.474545v1?rss=1 Feric, M. Sarfallah, A. Dar, F. Temiakov, D. Pappu, R. V. Misteli, T. 2022-01-01 doi:10.1101/2021.12.30.474545 Cold Spring Harbor Laboratory Press 2022-01-01 <![CDATA[ A pleiotropic chemoreceptor facilitates the functional coupling of pheromone production and perception ]]> https://biorxiv.org/content/10.1101/2022.01.10.475668v1?rss=1 Vernier, C. Zelle, k. Leitner, N. Liang, X. Halloran, S. Millar, J. Ben-Shahar, Y. 2022-01-10 doi:10.1101/2022.01.10.475668 Cold Spring Harbor Laboratory Press 2022-01-10 <![CDATA[ Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically disordered proteins ]]> https://biorxiv.org/content/10.1101/2022.01.11.475920v1?rss=1 Zeng, X. Ruff, K. M. Pappu, R. V. 2022-01-12 doi:10.1101/2022.01.11.475920 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Enhanced food motivation in obese mice is controlled by D1R expressing spiny projection neurons in the nucleus accumbens. ]]> https://biorxiv.org/content/10.1101/2022.01.12.476057v1?rss=1 Matikainen-Ankney, B. A. Legaria, A. A. Vachez, Y. M. Murphy, C. A. Pan, Y. A. Schaefer, R. F. McGrath, Q. J. Wang, J. G. Bluitt, M. N. Norris, A. J. Creed, M. C. Kravitz, A. V. 2022-01-13 doi:10.1101/2022.01.12.476057 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ An antibody targeting the N-terminal domain of SARS-CoV-2 disrupts the spike trimer ]]> https://biorxiv.org/content/10.1101/2022.01.12.476120v1?rss=1 Suryadevara, N. Shiakolas, A. VanBlargan, L. Binshtein, E. Chen, R. Case, J. B. Kramer, K. Armstrong, E. Myers, L. Trivette, A. Gainza, C. Nargi, R. Selverian, C. Davidson, E. Doranz, B. Diaz, S. Handal, L. Carnahan, R. H. Diamond, M. S. Georgiev, I. Crowe, J. E. 2022-01-13 doi:10.1101/2022.01.12.476120 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ Contrast-enhanced microCT evaluation of degeneration following partial and full width injuries to mouse lumbar intervertebral disc ]]> https://biorxiv.org/content/10.1101/2022.01.14.476362v1?rss=1 Walk, R. E. Moon, H. J. Tang, S. Y. Gupta, M. C. 2022-01-16 doi:10.1101/2022.01.14.476362 Cold Spring Harbor Laboratory Press 2022-01-16 <![CDATA[ How Glutamate Promotes Liquid-liquid Phase Separation and DNA Binding Cooperativity of E. coli SSB Protein ]]> https://biorxiv.org/content/10.1101/2022.01.17.476650v1?rss=1 Kozlov, A. G. Cheng, X. Zhang, H. Shinn, M. K. Weiland, E. Nguyen, B. Shkel, I. A. Zytkiewicz, E. Finkelstein, I. J. Record, M. T. Lohman, T. M. 2022-01-18 doi:10.1101/2022.01.17.476650 Cold Spring Harbor Laboratory Press 2022-01-18 <![CDATA[ Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome Browser ]]> https://biorxiv.org/content/10.1101/2022.01.18.476849v1?rss=1 Li, D. Purushotham, D. Harrison, J. K. Wang, T. 2022-01-21 doi:10.1101/2022.01.18.476849 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Longitudinal Morphological and Functional Characterization of Human Heart Organoids Using Optical Coherence Tomography ]]> https://biorxiv.org/content/10.1101/2022.01.19.476972v1?rss=1 Ming, Y. Hao, S. Xu, Z. Goestenkors, A. Lewis-Israeli, Y. R. Volmert, B. D. Aguirre, A. Zhou, C. 2022-01-21 doi:10.1101/2022.01.19.476972 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Nasally-delivered interferon-{lambda} protects mice against upper and lower respiratory tract infection of SARS-CoV-2 variants including Omicron ]]> https://biorxiv.org/content/10.1101/2022.01.21.477296v1?rss=1 Chong, Z. Karl, C. E. Halfmann, P. J. Kawaoka, Y. Winkler, E. S. Yu, J. Diamond, M. S. 2022-01-24 doi:10.1101/2022.01.21.477296 Cold Spring Harbor Laboratory Press 2022-01-24 <![CDATA[ BOLD cofluctuation 'events' are predicted from static functional connectivity ]]> https://biorxiv.org/content/10.1101/2022.01.24.477543v1?rss=1 50% of BOLD timepoints show high modularity and similarity to time- averaged FC C_LIO_LIStationary null models identified events with similar behavior to real data C_LIO_LIEvents may not be a transient driver of static FC, but rather an expected outcome of it. C_LI ]]> Ladwig, Z. Seitzman, B. A. Dworetsky, A. Yu, Y. Adeyemo, B. Smith, D. M. Petersen, S. E. Gratton, C. 2022-01-27 doi:10.1101/2022.01.24.477543 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ Multimodal single cell sequencing of human diabetic kidney disease implicates chromatin accessibility and genetic background in disease progression ]]> https://biorxiv.org/content/10.1101/2022.01.28.478204v1?rss=1 Wilson, P. C. Muto, Y. Wu, H. Karihaloo, A. Waikar, S. S. Humphreys, B. 2022-01-28 doi:10.1101/2022.01.28.478204 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ An allosteric agonist activates BK channels by perturbing coupling between Ca2+ binding and pore opening ]]> https://biorxiv.org/content/10.1101/2022.01.28.478270v1?rss=1 Zhang, G. Xu, X. Jia, Z. Geng, Y. Liang, H. Shi, J. Marras, M. Abella, C. Magleby, K. L. Silva, J. R. Chen, J. Zou, X. Cui, J. 2022-01-29 doi:10.1101/2022.01.28.478270 Cold Spring Harbor Laboratory Press 2022-01-29 <![CDATA[ Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes and gene regulation ]]> https://biorxiv.org/content/10.1101/2022.02.01.475239v1?rss=1 Choudhary, M. N. Quaid, K. Xing, X. Schmidt, H. Wang, T. 2022-02-03 doi:10.1101/2022.02.01.475239 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Apolipoprotein E4 has extensive conformational heterogeneity in lipid free and bound forms ]]> https://biorxiv.org/content/10.1101/2022.02.02.478828v1?rss=1 Stuchell-Brereton, M. D. Zimmerman, M. I. Miller, J. J. Mallimadugula, U. L. Incicco, J. J. Roy, D. Smith, L. G. Baban, B. DeKoster, G. T. Frieden, C. Bowman, G. R. Soranno, A. 2022-02-04 doi:10.1101/2022.02.02.478828 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Lung epithelial cell-derived C3 protects against pneumonia-induced lung injury ]]> https://biorxiv.org/content/10.1101/2022.02.03.478963v1?rss=1 Ozanturk, A. N. Sahu, S. K. Kulkarni, D. H. Ma, L. Barve, R. A. McPhatter, J. Garnica, L. Dannull, L. Wu, X. Brody, S. L. Atkinson, J. P. Kulkarni, H. S. 2022-02-05 doi:10.1101/2022.02.03.478963 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ Phase separating RNA binding proteins form heterogeneous distributions of clusters in subsaturated solutions ]]> https://biorxiv.org/content/10.1101/2022.02.03.478969v1?rss=1 Kar, M. Dar, F. Welsh, T. J. Vogel, L. Kuhnemuth, R. Majumdar, A. Krainer, G. Franzmann, T. M. Alberti, S. Seidel, C. A. M. Hyman, A. A. Pappu, R. V. 2022-02-03 doi:10.1101/2022.02.03.478969 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Pancreas resident macrophage-induced fibrosis has divergent roles in pancreas inflammatory injury and PDAC ]]> https://biorxiv.org/content/10.1101/2022.02.09.479745v1?rss=1 Baer, J. M. Zuo, C. Kang, L.-I. Alarcon de la Lastra, A. Borcherding, N. C. Knolhoff, B. L. Bogner, S. J. Zhu, Y. Lewis, M. A. Zhang, N. Kim, K.-w. Fields, R. C. Mills, J. C. Ding, L. Randolph, G. J. DeNardo, D. G. 2022-02-10 doi:10.1101/2022.02.09.479745 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Targeting fatty acid beta-oxidation impairs monocyte differentiation and prolongs heart allograft survival ]]> https://biorxiv.org/content/10.1101/2022.02.09.479789v1?rss=1 Zhu, Y. Dun, H. Ye, L. Terada, Y. Shriver, L. Patti, G. J. Kreisel, D. Gelman, A. E. Wong, B. W. 2022-02-10 doi:10.1101/2022.02.09.479789 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ OzTracs: Optical Osmolality Reporters Engineered from Mechanosensitive Ion Channels ]]> https://biorxiv.org/content/10.1101/2022.02.10.479916v1?rss=1 Kleist, T. J. Lin, I. W. Xu, S. Maksaev, G. Sadoine, M. Haswell, E. S. Frommer, W. B. Wudick, M. M. 2022-02-10 doi:10.1101/2022.02.10.479916 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Perinatal Oxycodone Exposure Causes Long Term Sex-Dependent Changes in Sensory and Reward Processing in Adult Mice ]]> https://biorxiv.org/content/10.1101/2022.02.15.480568v1?rss=1 Minakova, E. Mikati, M. O. Madasu, M. K. Conway, S. M. Baldwin, J. W. Swift, R. G. McCullough, K. B. Dougherty, J. D. Maloney, S. E. Al-Hasani, R. 2022-02-17 doi:10.1101/2022.02.15.480568 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ Multimodal Thrombectomy Device for Treatment of Acute Deep Venous Thrombosis ]]> https://biorxiv.org/content/10.1101/2022.02.21.481340v1?rss=1 Ismail, U. N. Rowe, R. A. Cashin, J. L. Genin, G. M. Zayed, M. 2022-02-22 doi:10.1101/2022.02.21.481340 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Quality assessment and refinement of chromatin accessibility data using a sequence-based predictive model ]]> https://biorxiv.org/content/10.1101/2022.02.24.481844v1?rss=1 Han, S. K. Muto, Y. Wilson, P. C. Chakravarti, A. Humphreys, B. D. Sampson, M. G. Lee, D. 2022-02-25 doi:10.1101/2022.02.24.481844 Cold Spring Harbor Laboratory Press 2022-02-25 <![CDATA[ Macrophage depletion blocks congenital SARM1-dependent neuropathy ]]> https://biorxiv.org/content/10.1101/2022.02.26.482110v1?rss=1 Dingwall, C. B. Strickland, A. Yum, S. W. Yim, A. K. Y. Zhu, J. Wang, P. L. Yamada, Y. Schmidt, R. E. Sasaki, Y. Bloom, J. DiAntonio, A. Milbrandt, J. 2022-03-01 doi:10.1101/2022.02.26.482110 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Oropouche orthobunyavirus infection is mediated by the cellular host factor Lrp1 ]]> https://biorxiv.org/content/10.1101/2022.02.26.482111v1?rss=1 Schwarz, M. Price, D. A. Ganaie, S. Feng, A. Mishra, N. Hoehl, R. Fatma, F. Stubbs, S. Whelan, S. P. J. Cui, X. Egawa, T. Leung, D. Amarasinghe, G. Hartman, A. L. 2022-02-27 doi:10.1101/2022.02.26.482111 Cold Spring Harbor Laboratory Press 2022-02-27 <![CDATA[ Acentrosomal spindles assemble from branching microtubule nucleation near chromosomes ]]> https://biorxiv.org/content/10.1101/2022.02.28.482415v1?rss=1 Gouveia, B. Setru, S. U. King, M. R. Stone, H. A. Shaevitz, J. W. Petry, S. 2022-03-01 doi:10.1101/2022.02.28.482415 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Isolation of a potently neutralizing and protective human monoclonal antibody targeting yellow fever virus ]]> https://biorxiv.org/content/10.1101/2022.02.28.482437v1?rss=1 Crowe, J. E. Doyle, M. Genualdi, J. R. Bailey, A. Kose, N. Gainza, C. Rodriguez, J. Reeder, K. M. Nelson, C. A. Jethva, P. N. Sutton, R. E. Bombardi, R. G. Gross, M. Julander, J. G. Fremont, D. H. Diamond, M. 2022-03-01 doi:10.1101/2022.02.28.482437 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Effects of chronic cannabidiol in a mouse model of naturally occurring neuroinflammation, neurodegeneration, and spontaneous seizures ]]> https://biorxiv.org/content/10.1101/2022.03.07.483344v1?rss=1 Dearborn, J. T. Nelvagal, H. R. Rensing, N. R. Hughes, S. M. Wishart, T. M. Cooper, J. D. Wong, M. Sands, M. S. 2022-03-08 doi:10.1101/2022.03.07.483344 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Cortical interneuron loss and seizure generation as novel clinically relevant disease phenotypes in Cln2R207X mice ]]> https://biorxiv.org/content/10.1101/2022.03.11.483984v1?rss=1 Takahashi, K. Eultgen, E. M. Wang, S. H. Rensing, N. R. Nelvagal, H. R. Dearborn, J. T. Sands, M. S. Wong, M. Cooper, J. D. 2022-03-13 doi:10.1101/2022.03.11.483984 Cold Spring Harbor Laboratory Press 2022-03-13 <![CDATA[ Tension anisotropy drives phenotypic transitions of cells via two-way cell-ECM feedback ]]> https://biorxiv.org/content/10.1101/2022.03.13.484154v1?rss=1 Alisafaei, F. Shakiba, D. Iannucci, L. Davidson, M. Pryse, K. Chao, P.-h. G. Burdick, J. Lake, S. Elson, E. Shenoy, V. Genin, G. 2022-03-14 doi:10.1101/2022.03.13.484154 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Loss of Stathmin-2, a hallmark of TDP-43-associated ALS, causes motor neuropathy ]]> https://biorxiv.org/content/10.1101/2022.03.13.484188v1?rss=1 Krus, K. L. Strickland, A. Yamada, Y. Devault, L. Schmidt, R. E. Bloom, A. J. Milbrandt, J. DiAntonio, A. 2022-03-14 doi:10.1101/2022.03.13.484188 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Evolution of transposable element-derived enhancer activity ]]> https://biorxiv.org/content/10.1101/2022.03.16.483999v1?rss=1 Du, A. Y. Zhuo, X. Sundaram, V. Jensen, N. O. Chaudhari, H. G. Saccone, N. L. Cohen, B. A. Wang, T. 2022-03-17 doi:10.1101/2022.03.16.483999 Cold Spring Harbor Laboratory Press 2022-03-17 <![CDATA[ Urbanization alters phenology of plant reproduction, foliar infection, and herbivory ]]> https://biorxiv.org/content/10.1101/2022.03.22.485313v1?rss=1 Fox, Q. N. Bugay, M. J. Grant, E. Shaw, O. S. Farah, K. N. Penczykowski, R. M. 2022-03-23 doi:10.1101/2022.03.22.485313 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Small Molecule Modulation of the Archetypal UbiB protein COQ8 ]]> https://biorxiv.org/content/10.1101/2022.03.22.485346v1?rss=1 Murray, N. H. Lewis, A. Asquith, C. R. M. Pabon, J. P. R. Fang, Z. Ptak, N. Smith, R. W. Vasta, J. D. Zimprich, C. A. Corona, C. R. Robers, M. B. Bingman, C. A. Gross, M. L. Henzler-Wildman, K. Pagliarini, D. J. 2022-03-23 doi:10.1101/2022.03.22.485346 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Prevalence of Bourbon and Heartland viruses in field collected ticks at an environmental field station in St. Louis County, Missouri, USA ]]> https://biorxiv.org/content/10.1101/2022.03.23.485543v1?rss=1 Aziati, I. D. McFarland, D. Antia, A. Joshi, A. Aviles Gamboa, A. Lee, P. Harastani, H. H. Wang, D. Adalsteinsson, S. A. Boon, A. 2022-03-24 doi:10.1101/2022.03.23.485543 Cold Spring Harbor Laboratory Press 2022-03-24 <![CDATA[ Neuroimaging within the Dominantly Inherited Alzheimer's Network (DIAN): PET and MRI ]]> https://biorxiv.org/content/10.1101/2022.03.25.485799v1?rss=1 McKay, N. S. Gordon, B. A. Hornbeck, R. C. Jack, C. R. Koeppe, R. Flores, S. Keefe, S. Hobbs, D. A. Joseph-Mathurin, N. Wang, Q. Rahmani, F. Chen, C. D. McCullough, A. Koudelis, D. Chua, J. Ances, B. M. Millar, P. R. Nickels, M. L. Perrin, R. J. Allegri, R. F. Berman, S. B. Brooks, W. S. Cash, D. M. Chhatwal, J. P. Farlow, M. R. Fox, N. C. Fulham, M. Ghetti, B. Graff-Radford, N. Ikeuchi, T. Day, G. S. Klunk, W. Levin, J. Lee, J.-H. Martins, R. Masters, C. L. Mori, H. McConathy, J. Noble, J. M. Rowe, C. Salloway, S. Sanchez-Valle, R. Schofield, P. R. 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A. 2022-04-11 doi:10.1101/2022.04.10.487814 Cold Spring Harbor Laboratory Press 2022-04-11 <![CDATA[ A recombinant murine rotavirus with Nano-Luciferase expression reveals tissue tropism, replication dynamics, and virus transmission ]]> https://biorxiv.org/content/10.1101/2022.04.12.488073v1?rss=1 Zhu, Y. Sanchez-Tacuba, L. Hou, G. Kawagishi, T. Feng, N. Greenberg, H. B. Ding, S. 2022-04-12 doi:10.1101/2022.04.12.488073 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ Multi-omics analyses cannot identify true-positive novel associations from underpowered genome-wide association studies of four brain-related traits ]]> https://biorxiv.org/content/10.1101/2022.04.13.487655v1?rss=1 Baranger, D. A. Hatoum, A. S. Polimanti, R. A. Gelernter, J. Edenberg, H. J. Bogdan, R. Agrawal, A. 2022-04-14 doi:10.1101/2022.04.13.487655 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ SARS-CoV-2 Omicron BA.1 variant infection of human colon epithelial cells ]]> https://biorxiv.org/content/10.1101/2022.04.13.487939v1?rss=1 Antia, A. Alvarado, D. M. Zeng, Q. Davis, D. L. Ciorba, M. A. Ding, S. 2022-04-14 doi:10.1101/2022.04.13.487939 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ Language and the cerebellum: structural connectivity to the eloquent brain ]]> https://biorxiv.org/content/10.1101/2022.04.19.488812v1?rss=1 Jobson, K. R. Hoffman, L. J. Metoki, A. Popal, H. Dick, A. S. Reilly, J. Olson, I. R. 2022-04-20 doi:10.1101/2022.04.19.488812 Cold Spring Harbor Laboratory Press 2022-04-20 <![CDATA[ Retinotopic organization of feedback projections in primate early visual cortex: implications for active vision ]]> https://biorxiv.org/content/10.1101/2022.04.27.489651v1?rss=1 Wang, M. Hou, Y. Magrou, L. Autio, J. A. Misery, P. Coalson, T. Reid, E. Xu, Y. Lamy, C. Falchier, A. Zhang, Q. Poo, M.-M. Dehay, C. Glasser, M. F. Hayashi, T. Knoblauch, K. Van Essen, D. Shen, Z. Kennedy, H. 2022-04-28 doi:10.1101/2022.04.27.489651 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Cortex-wide fast activation of VIP-expressing inhibitory neurons by reward and punishment ]]> https://biorxiv.org/content/10.1101/2022.04.27.489695v1?rss=1 Szadai, Z. Pi, H.-J. Chevy, Q. Ocsai, K. Albeanu, F. Chiovini, B. Szalay, G. Katona, G. Kepecs, A. Rozsa, B. 2022-04-29 doi:10.1101/2022.04.27.489695 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ Dapagliflozin improves endothelial integrity and hemodynamics in endotoxin treated mice through an apolipoprotein M dependent pathway ]]> https://biorxiv.org/content/10.1101/2022.04.27.489709v1?rss=1 Valenzuela Ripoll, C. Guo, Z. Kumari, T. Miyata, K. N. Ozcan, M. Diab, A. Girardi, A. He, L. Kovacs, A. Weinheimer, C. J. Nigro, J. Oscarsson, J. Esterline, R. Schilling, J. Kosiborod, M. Christoffersen, C. Cho, J. Javaheri, A. 2022-04-28 doi:10.1101/2022.04.27.489709 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Multiscale obstruction sensitivity in collective cell migration ]]> https://biorxiv.org/content/10.1101/2022.04.28.489943v1?rss=1 Lee, Y. L. Mathur, J. Walter, C. Zmuda, H. Pathak, A. 2022-04-29 doi:10.1101/2022.04.28.489943 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ Ex vivo to in vivo model of malignant peripheral nerve sheath tumors for precision oncology ]]> https://biorxiv.org/content/10.1101/2022.04.29.490078v1?rss=1 Bhatia^, H. Larsson^, A. T. Calizo^, A. Pollard, K. Zhang, X. Conniff, E. Tibbitts, J. F. Osum, S. H. Williams, K. B. Crampton, A. L. Jubenville, T. Schefer, D. Yang, K. Lyu, Y. Bade, J. Pino, J. C. Gosline, S. J. Pratilas, C. A. Largaespada, D. A. Wood, D. K. Hirbe, A. C. 2022-05-02 doi:10.1101/2022.04.29.490078 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Mechanically primed cells transfer memory to fibrous matrices for persistent invasion ]]> https://biorxiv.org/content/10.1101/2022.05.02.490316v1?rss=1 Almeida, J. Mathur, J. Lee, Y. L. Sarker, B. Pathak, A. 2022-05-02 doi:10.1101/2022.05.02.490316 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ A Self-Healing, Viscoelastic Hydrogel Promotes Healing of Brain Lesions ]]> https://biorxiv.org/content/10.1101/2022.05.05.490746v1?rss=1 Hu, Y. Jia, Y. Wang, S. Ma, Y. Huang, G. Ding, T. Feng, D. Genin, G. M. Wei, Z. Xu, F. 2022-05-05 doi:10.1101/2022.05.05.490746 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Intracellular connections between basal bodies promote the coordinated behavior of motile cilia ]]> https://biorxiv.org/content/10.1101/2022.05.06.490816v1?rss=1 Soh, A. W. J. Woodhams, L. G. Junker, A. D. Enloe, C. M. Noren, B. E. Harned, A. Westlake, C. J. Narayan, K. Oakey, J. S. Bayly, P. V. Pearson, C. G. 2022-05-06 doi:10.1101/2022.05.06.490816 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Chemical structures of cyclic ADP ribose (cADPR) isomers and the molecular basis of their production and signaling ]]> https://biorxiv.org/content/10.1101/2022.05.07.491051v1?rss=1 Manik, M. K. Shi, Y. Li, S. Zaydman, M. A. Damaraju, N. Eastman, S. Smith, T. Gu, W. Masic, V. Mosaiab, T. Weagley, J. S. Hancock, S. J. Vasquez, E. Hartley-Tassell, L. Maruta, N. Lim, B. Y. Burdett, H. Lansdberg, M. J. Schembri, M. A. Prokes, I. Song, L. Grant, M. DiAntonio, A. Nanson, J. D. Guo, M. Milbrandt, J. Ve, T. Kobe, B. 2022-05-08 doi:10.1101/2022.05.07.491051 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ A Cdh3-Lam332 signaling axis in a leader cell subpopulation controls protrusion dynamics and tumor organoid collective migration ]]> https://biorxiv.org/content/10.1101/2022.05.10.491382v1?rss=1 Hwang, P. Y. Mathur, J. Cao, Y. Almeida, J. Cornish, D. Clarke, M. Pathak, A. Longmore, G. D. 2022-05-10 doi:10.1101/2022.05.10.491382 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Mitochondrial Pyruvate Carrier Inhibition Initiates Metabolic Crosstalk to Stimulate Branched Chain Amino Acid Catabolism ]]> https://biorxiv.org/content/10.1101/2022.05.11.491550v1?rss=1 Ferguson, D. Eichler, S. J. Yiew, N. K. H. Colca, J. R. Cho, K. Patti, G. J. McCommis, K. S. Niemi, N. M. Finck, B. 2022-05-11 doi:10.1101/2022.05.11.491550 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Evolution and diversification dynamics of butterflies ]]> https://biorxiv.org/content/10.1101/2022.05.17.491528v1?rss=1 Kawahara, A. Y. Storer, C. Carvalho, A. P. S. Plotkin, D. M. Condamine, F. Braga, M. P. Ellis, E. A. St Laurent, R. A. Li, X. Barve, V. Cai, L. Earl, C. Frandsen, P. B. Owens, H. L. Valencia-Montoya, W. A. Aduse-Poku, K. Toussaint, E. F. A. Dexter, K. M. Doleck, T. Markee, A. Messcher, R. Nguyen, Y.-L. Badon, J. A. T. Benitez, H. A. Braby, M. F. Buenavente, P. A. C. Chan, W.-P. Collins, S. C. Childers, R. A. R. Dankowicz, E. Eastwood, R. Fric, Z. F. Gott, R. Hall, J. P. W. Hallwachs, W. Hardy, N. B. Sipe, R. L. H. Heath, A. Hinolan, J. D. Homziak, N. T. 2022-05-19 doi:10.1101/2022.05.17.491528 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ SARM1 promotes axonal, synaptic, and mitochondrial pathologies in Charcot-Marie-Tooth disease type 2A ]]> https://biorxiv.org/content/10.1101/2022.05.17.492364v1?rss=1 Yamada, Y. Strickland, A. Sasaki, Y. Bloom, J. DiAntonio, A. Milbrandt, J. 2022-05-20 doi:10.1101/2022.05.17.492364 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Interplay between VSD, pore and membrane lipids in electromechanical coupling in HCN channels ]]> https://biorxiv.org/content/10.1101/2022.05.20.492765v1?rss=1 Elbahnsi, A. Cowgill, J. Burtscher, V. Wedemann, L. Zeckey, L. Chanda, B. Delemotte, L. 2022-05-20 doi:10.1101/2022.05.20.492765 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Mutation in the matricellular gene fibulin-4 leads to endothelial dysfunction in resistance arteries ]]> https://biorxiv.org/content/10.1101/2022.05.20.492867v1?rss=1 Lin, M. Jones, K. Brengle, B. M. Mecham, R. P. Halabi, C. M. 2022-05-21 doi:10.1101/2022.05.20.492867 Cold Spring Harbor Laboratory Press 2022-05-21 <![CDATA[ Condensates of disordered proteins have small-world network structures and interfaces defined by expanded conformations ]]> https://biorxiv.org/content/10.1101/2022.05.21.492916v1?rss=1 Farag, M. Cohen, S. R. Borcherds, W. M. Bremer, A. Mittag, T. Pappu, R. V. 2022-05-22 doi:10.1101/2022.05.21.492916 Cold Spring Harbor Laboratory Press 2022-05-22 <![CDATA[ A comprehensive assay of social motivation reveals sex-differential roles of ASC-associated genes and oxytocin ]]> https://biorxiv.org/content/10.1101/2022.05.21.492918v1?rss=1 Maloney, S. E. Sarafinovska, S. Weichselbaum, C. McCullough, K. B. Swift, R. G. Liu, Y. Dougherty, J. D. 2022-05-21 doi:10.1101/2022.05.21.492918 Cold Spring Harbor Laboratory Press 2022-05-21 <![CDATA[ Unbiased proteomic and forward genetic screens reveal that mechanosensitive ion channel MSL10 functions at ER-plasma membrane contact sites in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2022.05.23.493056v1?rss=1 Codjoe, J. M. Richardson, R. A. Haswell, E. 2022-05-23 doi:10.1101/2022.05.23.493056 Cold Spring Harbor Laboratory Press 2022-05-23 <![CDATA[ A quantitative metric of pioneer activity reveals that HNF4A has stronger in vivo pioneer activity than FOXA1 ]]> https://biorxiv.org/content/10.1101/2022.05.24.493302v1?rss=1 Hansen, J. L. Cohen, B. A. 2022-05-25 doi:10.1101/2022.05.24.493302 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Accumulation of copy-back viral genomes during respiratory syncytial virus infection is preceded by diversification of the copy-back viral genome population followed by selection ]]> https://biorxiv.org/content/10.1101/2022.05.25.493350v1?rss=1 Felt, S. A. Achouri, E. Faber, S. R. Lopez, C. B. 2022-05-26 doi:10.1101/2022.05.25.493350 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ The dynseq genome browser track enables visualization of context-specific, dynamic DNA sequence features at single nucleotide resolution ]]> https://biorxiv.org/content/10.1101/2022.05.26.493621v1?rss=1 Nair, S. Barrett, A. Li, D. Raney, B. J. Lee, B. T. Kerpedjiev, P. Ramalingam, V. Pampari, A. Lekschas, F. Wang, T. Haeussler, M. Kundaje, A. 2022-05-28 doi:10.1101/2022.05.26.493621 Cold Spring Harbor Laboratory Press 2022-05-28 <![CDATA[ The salivary and nasopharyngeal microbiomes are associated with SARS-CoV-2 infection and disease severity ]]> https://biorxiv.org/content/10.1101/2022.05.31.494162v1?rss=1 Kim, J. G. Zhang, A. Rauseo, A. M. Goss, C. W. Mudd, P. A. O'Halloran, J. Wang, L. 2022-05-31 doi:10.1101/2022.05.31.494162 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Opto-MASS: a high-throughput engineering platform for genetically encoded fluorescentsensors enabling all optical in vivo detection of monoamines and neuropeptides ]]> https://biorxiv.org/content/10.1101/2022.06.01.494241v1?rss=1 Rappleye, M. Gordon-Fennel, A. Castro, D. C. Matarasso, A. K. Zamorano, C. A. Wait, S. J. Lee, J. D. Siebart, J. D. Suko, A. Smith, N. C. Muster, J. Matreyek, K. A. Fowler, D. M. Stuber, G. D. Bruchas, M. R. Berndt, A. 2022-06-02 doi:10.1101/2022.06.01.494241 Cold Spring Harbor Laboratory Press 2022-06-02 <![CDATA[ Mapping genomic regulation of kidney disease and traits through high-resolution and interpretable eQTLs ]]> https://biorxiv.org/content/10.1101/2022.06.01.494352v1?rss=1 Han, S. K. McNulty, M. T. Benway, C. J. Wen, P. Greenberg, A. Onuchic-Whitford, A. C. NEPTUNE, Wilson, P. C. Humphreys, B. D. Wen, X. Han, Z. Lee, D. Sampson, M. G. 2022-06-01 doi:10.1101/2022.06.01.494352 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ A Unified Dynamic and Computational Mechanism for Persistent and Transient Neural Activity Patterns During Delayed-Response Tasks ]]> https://biorxiv.org/content/10.1101/2022.06.01.494426v1?rss=1 Ye, Z. Tian, L. Zhou, C. 2022-06-03 doi:10.1101/2022.06.01.494426 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ QuNex -- An Integrative Platform forReproducible Neuroimaging Analytics ]]> https://biorxiv.org/content/10.1101/2022.06.03.494750v1?rss=1 Ji, J. L. Demsar, J. Fonteneau, C. Tamayo, Z. Pan, L. Kraljic, A. Matkovic, A. Purg, N. Helmer, M. Warrington, S. Sotiropoulos, S. Harms, M. Murray, J. D. Anticevic, A. Repovs, G. 2022-06-05 doi:10.1101/2022.06.03.494750 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ Metapredict V2: An update to metapredict, a fast, accurate, and easy-to-use predictor of consensus disorder and structure ]]> https://biorxiv.org/content/10.1101/2022.06.06.494887v1?rss=1 Emenecker, R. J. Griffith, D. Holehouse, A. S. 2022-06-09 doi:10.1101/2022.06.06.494887 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Tracking infectious entry routes of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2022.06.09.495472v1?rss=1 Kreutzberger, A. J. B. Sanyal, A. Saminathan, A. Bloyet, L.-M. Stumpf, S. Liu, Z. Ojha, R. Patjas, M. T. Geneid, A. Scanavachi, G. Doyle, C. A. Somerville, E. Cunha Correira, R. Di Caprio, G. Toppila-Salmi, S. Makitie, A. Kiessling, V. Vapalahti, O. Whelan, S. P. J. Balistreri, G. Kirchhausen, T. 2022-06-09 doi:10.1101/2022.06.09.495472 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Non-standard viral genome-derived RNA activates TLR3 and type I IFN signaling to induce cDC1-dependent CD8+ T-cell responses during vaccination in mice ]]> https://biorxiv.org/content/10.1101/2022.06.09.495494v1?rss=1 Fisher, D. Holthausen, D. Lopez, C. B. 2022-06-09 doi:10.1101/2022.06.09.495494 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Nuclear export inhibition jumbles epithelial-mesenchymal states and gives rise to migratory disorder in healthy epithelia ]]> https://biorxiv.org/content/10.1101/2022.06.11.495764v1?rss=1 Krull, C. M. Li, H. Pathak, A. 2022-06-13 doi:10.1101/2022.06.11.495764 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ Comparative genomics support reduced-genome Paraburkholderia symbionts of Dictyostelium discoideum amoebas are ancestrally adapted professional symbionts ]]> https://biorxiv.org/content/10.1101/2022.06.13.495842v1?rss=1 Noh, S. Capodanno, B. J. Xu, S. Hamilton, M. C. Strassmann, J. E. Queller, D. C. 2022-06-16 doi:10.1101/2022.06.13.495842 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Mechanotransductive feedback control of endothelial cell motility and vascular morphogenesis ]]> https://biorxiv.org/content/10.1101/2022.06.15.496293v1?rss=1 Mason, D. E. Goeckel, M. Vega, S. L. Wu, P.-H. Johnson, D. Heo, S.-J. Wirtz, D. Burdick, J. A. Wood, L. Chow, B. Y. Stratman, A. N. Boerckel, J. D. 2022-06-16 doi:10.1101/2022.06.15.496293 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Single cell preparations of Mycobacterium tuberculosis damage the mycobacterial envelope and disrupt macrophage interactions ]]> https://biorxiv.org/content/10.1101/2022.06.16.496372v1?rss=1 Mittal, E. Roth, A. Seth, A. Singamaneni, S. Beatty, W. A. Philips, J. 2022-06-16 doi:10.1101/2022.06.16.496372 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Charting the Spatial Landscape of Cancer Hallmarks ]]> https://biorxiv.org/content/10.1101/2022.06.18.496114v1?rss=1 Sibai, M. Cervilla, S. Grases, D. Musulen, E. Fortian, A. Romeo, M. Bernat, A. Tokheim, C. Esteller, M. Barretina, J. Ding, L. Bailey, M. Porta-Pardo, E. 2022-06-19 doi:10.1101/2022.06.18.496114 Cold Spring Harbor Laboratory Press 2022-06-19 <![CDATA[ The polycomb repressor complex 2 and Enhancer of Zeste 2 regulate glial reactivity and are required for the formation of Muller glia-derived progenitor cells in the retina ]]> https://biorxiv.org/content/10.1101/2022.06.23.497349v1?rss=1 Campbell, W. J. El-Hodiri, H. Torres, D. Hawthorn, E. Kelly, L. Volkov, L. Akanonu, D. Fischer, A. J. 2022-06-26 doi:10.1101/2022.06.23.497349 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Cooperation genes are more pleiotropic than private genes in the bacterium Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2022.06.25.495533v1?rss=1 Scott, T. J. 2022-06-29 doi:10.1101/2022.06.25.495533 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Six-Dimensional Single-Molecule Imaging with Isotropic Resolution using a Multi-View Reflector Microscope ]]> https://biorxiv.org/content/10.1101/2022.06.26.497661v1?rss=1 Zhang, O. Guo, Z. He, Y. Wu, T. Vahey, M. D. Lew, M. D. 2022-06-29 doi:10.1101/2022.06.26.497661 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Predicting the locations of cryptic pockets from single protein structures using the PocketMiner graph neural network ]]> https://biorxiv.org/content/10.1101/2022.06.28.497399v1?rss=1 1,000-fold faster than existing methods. We apply PocketMiner across the human proteome and show that predicted pockets open in simulations, suggesting that over half of proteins thought to lack pockets based on available structures are likely to contain cryptic pockets, vastly expanding the druggable proteome. ]]> Meller, A. Ward, M. Borowsky, J. Lotthammer, J. M. Kshirsagar, M. Oveido, F. Lavista Ferres, J. Bowman, G. R. 2022-06-29 doi:10.1101/2022.06.28.497399 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Disruption of lactate metabolism in the peripheral nervous system leads to motor-selective deficits ]]> https://biorxiv.org/content/10.1101/2022.06.29.497865v1?rss=1 Bloom, J. Hackett, A. Strickland, A. Yamada, Y. Ippolito, J. E. Schmidt, R. E. Sasaki, Y. DiAntonio, A. Milbrandt, J. 2022-06-30 doi:10.1101/2022.06.29.497865 Cold Spring Harbor Laboratory Press 2022-06-30 <![CDATA[ Connecting sequence features within the disordered C-terminal linker of B. subtilis FtsZ to function and bacterial cell division ]]> https://biorxiv.org/content/10.1101/2022.06.29.498098v1?rss=1 Shinn, M. K. Cohan, M. C. Bullock, J. L. Ruff, K. M. Levin, P. A. Pappu, R. V. 2022-06-29 doi:10.1101/2022.06.29.498098 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Genetically corrected iPSC-derived Neural Stem Cell Grafts deliver NAGLU-IGFII fusion protein to affect CNS disease in Sanfilippo B Mice ]]> https://biorxiv.org/content/10.1101/2022.06.30.498131v1?rss=1 Pearse, Y. Clarke, D. Kan, S.-h. Le, S. Q. Sanghez, V. Luzzi, A. Pham, I. Nih, L. R. Cooper, J. D. Dickson, P. Iacovino, M. 2022-07-02 doi:10.1101/2022.06.30.498131 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Functional analysis of recurrent non-coding variants in human melanoma ]]> https://biorxiv.org/content/10.1101/2022.06.30.498319v1?rss=1 Godoy, P. M. Zarov, A. Kaufman, C. K. 2022-07-02 doi:10.1101/2022.06.30.498319 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Gene Regulatory Network Reconfiguration in Direct Lineage Reprogramming ]]> https://biorxiv.org/content/10.1101/2022.07.01.497374v1?rss=1 Kamimoto, K. Adil, M. T. Jindal, K. Hoffmann, C. M. Kong, W. Yang, X. Morris, S. A. 2022-07-03 doi:10.1101/2022.07.01.497374 Cold Spring Harbor Laboratory Press 2022-07-03 <![CDATA[ Single Cell RNA-Sequence Analyses Reveal Uniquely Expressed Genes and Heterogeneous Immune Cell Involvement in the Rat Model of Intervertebral Disc Degeneration ]]> https://biorxiv.org/content/10.1101/2022.07.05.498865v1?rss=1 Rohanifar, M. Clayton, S. W. Easson, G. Patil, D. S. Lee, F. Jing, L. Barcellona, M. N. Speer, J. E. Stivers, J. J. Tang, S. Y. Setton, L. A. 2022-07-05 doi:10.1101/2022.07.05.498865 Cold Spring Harbor Laboratory Press 2022-07-05 <![CDATA[ Jointly Modeling Species Niche and Phylogenetic Model in a Bayesian Hierarchical Framework ]]> https://biorxiv.org/content/10.1101/2022.07.06.499056v1?rss=1 McHugh, S. W. Espindola, A. White, E. Uyeda, J. C. 2022-07-08 doi:10.1101/2022.07.06.499056 Cold Spring Harbor Laboratory Press 2022-07-08 <![CDATA[ Transcriptomic cell type structures in vivo neuronal activity across multiple time scales. ]]> https://biorxiv.org/content/10.1101/2022.07.10.499487v1?rss=1 30 min). We show that transcriptomic cell class information is robustly embedded in the timing of single neuron activity recorded in the intact brain of behaving animals (calcium imaging and extracellular electrophysiology), as well as in a bio-realistic model of visual cortex. In contrast, we were unable to reliably extract cell identity from summary measures of rate, variance, and interevent interval statistics. We applied our analyses to the question of whether transcriptomic subtypes of excitatory neurons represent functionally distinct classes. In the calcium imaging dataset, which contains a diverse set of excitatory Cre lines, we found that a subset of excitatory cell types are computationally distinguishable based upon their Cre lines, and that excitatory types can be classified with higher accuracy when considering their cortical layer and projection class. Here we address the fundamental question of whether a neuron, within a complex cortical network, embeds a fingerprint of its transcriptomic identity into its activity. Our results reveal robust computational fingerprints for transcriptomic types and classes across diverse contexts, defined over multiple timescales. ]]> Schneider, A. Azabou, M. McDougall-Vigier, L. Parks, D. B. Ensley, S. Bhaskaran-Nair, K. Nowakowski, T. J. Dyer, E. L. Hengen, K. B. 2022-07-11 doi:10.1101/2022.07.10.499487 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Staphylococcus aureus Breast Implant Infection Isolates Display Recalcitrance to Antibiotic Pocket Irrigants ]]> https://biorxiv.org/content/10.1101/2022.07.18.500563v1?rss=1 Duran Ramirez, J. M. Gomez, J. Hanson, B. M. Isa, T. Myckatyn, T. M. Walker, J. N. 2022-07-19 doi:10.1101/2022.07.18.500563 Cold Spring Harbor Laboratory Press 2022-07-19 <![CDATA[ Oral oxycodone self-administration leads to features of opioid addiction in male and female mice ]]> https://biorxiv.org/content/10.1101/2022.07.19.500655v1?rss=1 Slivicki, R. Earnest, T. Chang, Y.-H. Pareta, R. Casey, E. Li, J.-N. Tooley, J. Abiraman, K. Vachez, Y. M. Wolf, D. K. Sackey, J. T. Gereau, R. Copits, B. A. Kravitz, A. V. Creed, M. C. 2022-07-20 doi:10.1101/2022.07.19.500655 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ IMC-Denoise: a content aware denoising pipeline to enhance Imaging Mass Cytometry ]]> https://biorxiv.org/content/10.1101/2022.07.21.501021v1?rss=1 Lu, P. Oetjen, K. A. Bender, D. E. Ruzinova, M. B. Fisher, D. A. Shim, K. G. Pachynski, R. K. Brennen, W. N. Oh, S. Link, D. C. Thorek, D. L. 2022-07-22 doi:10.1101/2022.07.21.501021 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Hydrogel Assisted Double Molding of 3D-Print Enables Prestress Regulation of Micro-Heart Muscle Physiology ]]> https://biorxiv.org/content/10.1101/2022.07.23.501265v1?rss=1 Simmons, D. W. Shuftan, D. R. Guo, J. Oguntuyo, K. Ramahdita, G. Munsell, M. K. Kandalaft, B. Pear, M. Huebsch, N. 2022-07-24 doi:10.1101/2022.07.23.501265 Cold Spring Harbor Laboratory Press 2022-07-24 <![CDATA[ Tenotomy-induced muscle atrophy is sex-specific and independent of NFκB ]]> https://biorxiv.org/content/10.1101/2022.07.26.501541v1?rss=1 Meyer, G. A. Thomopoulos, S. Abu-Amer, Y. Shen, K. 2022-07-27 doi:10.1101/2022.07.26.501541 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ Deep-SMOLM: Deep Learning Resolves the 3D Orientations and 2D Positions of Overlapping Single Molecules with Optimal Nanoscale Resolution ]]> https://biorxiv.org/content/10.1101/2022.07.31.502237v1?rss=1 Wu, T. Lu, P. Rahman, M. A. Li, X. Lew, M. D. 2022-08-01 doi:10.1101/2022.07.31.502237 Cold Spring Harbor Laboratory Press 2022-08-01 <![CDATA[ Neuronal Maturation-dependent Nano-Neuro Interaction and Modulation ]]> https://biorxiv.org/content/10.1101/2022.08.03.502650v1?rss=1 Gupta, P. Rathi, P. Gupta, R. Baldi, H. Coquerel, Q. Debnath, A. Gholami Derami, H. Raman, B. Singamaneni, S. 2022-08-05 doi:10.1101/2022.08.03.502650 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Hypoxia Sensing in Resident Cardiac Macrophages Regulates Monocyte-Derived Macrophage Fate Specification following Myocardial Infarction ]]> https://biorxiv.org/content/10.1101/2022.08.04.502542v1?rss=1 Kadyrov, F. F. Koenig, A. L. Amrute, J. M. Li, W. Lai, L. Weinheimer, C. J. Nigro, J. M. Kovacs, A. Bredemeyer, A. L. Kreisel, D. Lavine, K. J. 2022-08-05 doi:10.1101/2022.08.04.502542 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Dorsal Hippocampus To Nucleus Accumbens Projections Drive Reinforcement Via Activation of Accumbal Dynorphin Neurons. ]]> https://biorxiv.org/content/10.1101/2022.08.08.503098v1?rss=1 Massaly, N. Ibrahim, K. M. Yoon, H.-J. Sandoval, R. Williams, S. Frye, H. Post, W. Yu, W. Idowu, O. Zec, A. Pathiranage, S. Kash, T. Moron, J. A. 2022-08-10 doi:10.1101/2022.08.08.503098 Cold Spring Harbor Laboratory Press 2022-08-10 <![CDATA[ LinguaPhylo: a probabilistic model specification language for reproducible phylogenetic analyses ]]> https://biorxiv.org/content/10.1101/2022.08.08.503246v1?rss=1 Drummond, A. J. Chen, K. Mendes, F. K. Xie, D. 2022-08-11 doi:10.1101/2022.08.08.503246 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Circadian rhythms in multiple behaviors depend on sex, neuropeptide signaling, and ambient light ]]> https://biorxiv.org/content/10.1101/2022.08.18.504454v1?rss=1 Wahba, L. R. Perez, B. Nikhil, K. Herzog, E. D. Jones, J. R. 2022-08-19 doi:10.1101/2022.08.18.504454 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ Regulation of iron transport is required for terminal erythroid differentiation even under iron-replete conditions that are sufficient for hemoglobinization ]]> https://biorxiv.org/content/10.1101/2022.08.22.504833v1?rss=1 Chen, M. Danoff, A. West, R. Stratman, A. N. Yien, Y. Y. 2022-08-22 doi:10.1101/2022.08.22.504833 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Site-1 Protease inhibits mitochondrial metabolism by controlling the TGF-β target gene MSS51 ]]> https://biorxiv.org/content/10.1101/2022.08.24.504591v1?rss=1 Mousa, M. G. Vuppaladhadiam, L. Kelly, M. O. Pietka, T. Ek, S. Shen, K. C. Meyer, G. A. Finck, B. N. Brookheart, R. T. 2022-08-24 doi:10.1101/2022.08.24.504591 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ Multimodal brain age estimates relate to Alzheimer disease biomarkers and cognition in early stages: a cross-sectional observational study ]]> https://biorxiv.org/content/10.1101/2022.08.25.505251v1?rss=1 0) participants, we tested relationships between BAG and AD biomarkers of amyloid, tau, and neurodegeneration, as well as a global cognitive composite. ResultsAll models predicted age in the control training set, with the multimodal model outperforming the unimodal models. All three BAG estimates were significantly elevated in CI compared to controls. FC-BAG and Vol+FC-BAG were marginally reduced in preclinical AD participants compared to controls. In CI participants only, elevated Vol-BAG and Vol+FC-BAG were associated with more advanced AD pathology and lower cognitive performance. ConclusionsBoth FC-BAG and Vol-BAG are elevated in CI participants. However, FC and volumetric MRI also capture complementary signals. Specifically, FC-BAG may capture a unique biphasic response to preclinical AD pathology, while Vol-BAG may capture pathological progression and cognitive decline in the symptomatic stage. A multimodal age-prediction model captures these modality-specific patterns, and further, improves sensitivity to healthy age differences. FundingThis work was supported by the National Institutes of Health (P01-AG026276, P01-AG03991, P30-AG066444, 5-R01-AG052550, 5-R01-AG057680, 1-R01-AG067505, 1S10RR022984-01A1, U19-AG032438), the BrightFocus Foundation (A2022014F), and the Alzheimers Association (SG-20-690363-DIAN). ]]> Millar, P. R. the Dominantly Inherited Alzheimer Network, Gordon, B. A. Luckett, P. H. Benzinger, T. Cruchaga, C. Fagan, A. M. Hassenstab, J. Perrin, R. J. Schindler, S. E. Allegri, R. F. Day, G. S. Farlow, M. R. Mori, H. Nübling, G. Bateman, R. Morris, J. Ances, B. 2022-08-27 doi:10.1101/2022.08.25.505251 Cold Spring Harbor Laboratory Press 2022-08-27 <![CDATA[ Targeted Deletion of Fgf9 in Tendon Disrupts Mineralization of the Developing Enthesis ]]> https://biorxiv.org/content/10.1101/2022.08.25.505295v1?rss=1 Ganji, E. Leek, C. Duncan, W. Patra, D. Ornitz, D. M. Killian, M. L. 2022-08-25 doi:10.1101/2022.08.25.505295 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Host network-based discovery of critical regulators of innate immunity, virus growth, and pathogenesis in influenza virus infection ]]> https://biorxiv.org/content/10.1101/2022.08.29.505723v1?rss=1 Eisfeld, A. J. Fan, S. Rao, H. Venkatachalam, B. A. Smith, D. W. Halfmann, P. J. Walters, K. B. Nair, S. Thackray, L. B. Kocher, J. F. Sims, A. C. Mitchell, H. D. Neumann, G. Blank, V. Waters, K. M. Baric, R. S. Diamond, M. S. Kawaoka, Y. 2022-08-30 doi:10.1101/2022.08.29.505723 Cold Spring Harbor Laboratory Press 2022-08-30 <![CDATA[ Molecular regulation of GPCR-G-protein-governed PIP3 generation and its adaptation ]]> https://biorxiv.org/content/10.1101/2022.08.31.506078v1?rss=1 Wijayaratna, D. Ratnayake, K. Ubeysinghe, S. Kankanamge, D. Tennakoon, M. Karunarathne, A. 2022-09-01 doi:10.1101/2022.08.31.506078 Cold Spring Harbor Laboratory Press 2022-09-01 <![CDATA[ Effect of genomic and cellular environments on gene expression noise ]]> https://biorxiv.org/content/10.1101/2022.08.31.506082v1?rss=1 Hong, C. K. Ramu, A. Zhao, S. Cohen, B. A. 2022-09-01 doi:10.1101/2022.08.31.506082 Cold Spring Harbor Laboratory Press 2022-09-01 <![CDATA[ Mucosal and systemic neutralizing antibodies to norovirus and rotavirus by oral immunization with recombinant rotavirus in infant mice ]]> https://biorxiv.org/content/10.1101/2022.09.01.505917v1?rss=1 Kawagishi, T. Sanchez-Tacuba, L. Feng, N. Costantini, V. P. Tan, M. Jiang, X. Green, K. Y. Vinje, J. Ding, S. Greenberg, H. B. 2022-09-02 doi:10.1101/2022.09.01.505917 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domains ]]> https://biorxiv.org/content/10.1101/2022.09.05.506254v1?rss=1 Meller, A. Lotthammer, J. M. Smith, L. G. Novak, B. Lee, L. A. Kuhn, C. C. Greenberg, L. Leinwand, L. A. Greenberg, M. J. Bowman, G. R. 2022-09-05 doi:10.1101/2022.09.05.506254 Cold Spring Harbor Laboratory Press 2022-09-05 <![CDATA[ Barriers to Integration of Bioinformatics into Undergraduate Life Sciences Education ]]> https://biorxiv.org/content/10.1101/204420v1?rss=1 Williams, J. Drew, J. Galindo-Gonzalez, S. Robic, S. Dinsdale, E. Morgan, W. Triplett, E. Burnette, J. Donovan, S. Elgin, S. Fowlks, E. Goodman, A. Grandgenett, N. Goller, C. Hauser, C. Jungck, J. R. Newman, J. Pearson, W. Ryder, E. Wilson Sayres, M. Sierk, M. Smith, T. Tosado-Acevedo, R. Tapprich, W. Tobin, T. Toro-Martinez, A. Welch, L. Wright, R. Ebenbach, D. McWilliams, M. Rosenwald, A. Pauley, M. 2017-10-19 doi:10.1101/204420 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ Maternal SSRI treatment during offspring development results in long-term behavioral, cellular, and neuroimaging disruptions ]]> https://biorxiv.org/content/10.1101/205708v1?rss=1 Maloney, S. E. Rahn, R. Akula, S. Rieger, M. A. McCullough, K. B. Jakes, C. Avdagic, S. Chandler, K. Bauernfeind, A. L. Culver, J. P. Dougherty, J. D. 2017-10-18 doi:10.1101/205708 Cold Spring Harbor Laboratory Press 2017-10-18 <![CDATA[ Use of a scoring strategy to determine clinical risk of progression and risk group-specific treatment adherence in subjects with latent tuberculosis infection ]]> https://biorxiv.org/content/10.1101/207852v1?rss=1 Scolarici, M. Dekitani, K. Chen, L. Sokol-Anderson, M. Hoft, D. F. Chatterjee, S. 2017-10-25 doi:10.1101/207852 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ Germline determinants of the somatic mutation landscape in 2,642 cancer genomes ]]> https://biorxiv.org/content/10.1101/208330v1?rss=1 T mutagenesis at CpG dinucleotides, a ubiquitous mutational process acting across tissues. Analysis of somatic structural variation exposed complex rearrangement patterns, involving cycles of templated insertions and tandem duplications, in BRCA1-deficient tumours. Genome-wide association analysis implicated common genetic variation at the APOBEC3 gene cluster with reduced basal levels of somatic mutagenesis attributable to APOBEC cytidine deaminases across cancer types. We further inferred over a hundred polymorphic L1/LINE elements with somatic retrotransposition activity in cancer. Our study highlights the major impact of rare and common germline variants on mutational landscapes in cancer. ]]> Waszak, S. M. Tiao, G. Zhu, B. Rausch, T. Muyas, F. Rodriguez-Martin, B. Rabionet, R. Yakneen, S. Escaramis, G. Li, Y. Saini, N. Roberts, S. A. Demidov, G. M. Pitkanen, E. Delaneau, O. Heredia-Genestar, J. M. Weischenfeldt, J. Shringarpure, S. S. Chen, J. Nakagawa, H. Alexandrov, L. B. Drechsel, O. Dursi, L. J. Segre, A. V. Garrison, E. Erkek, S. Habermann, N. Urban, L. Khurana, E. Cafferkey, A. Hayashi, S. Imoto, S. Aaltonen, L. A. Alvarez, E. G. Baez-Ortega, A. Bailey, M. Bosio, M. Bruzos, A. L. Buchhalter, I. Bustamante, C. D. Calabrese, C. DiBiase, 2017-11-01 doi:10.1101/208330 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Terminal uridylyltransferases target RNA viruses as part of the innate immune system in animals ]]> https://biorxiv.org/content/10.1101/209114v1?rss=1 Le Pen, J. Jiang, H. Di Domenico, T. Kneuss, E. Kosalka, J. Morgan, M. Much, C. Rudolph, K. L. M. Enright, A. J. O'Carroll, D. Wang, D. Miska, E. A. 2017-10-25 doi:10.1101/209114 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ The relationship between spatial configuration and functional connectivity of brain regions ]]> https://biorxiv.org/content/10.1101/210195v1?rss=1 Bijsterbosch, J. D. Woolrich, M. W. Glasser, M. F. Robinson, E. C. Beckmann, C. F. Van Essen, D. C. Harrison, S. J. Smith, S. M. 2017-10-27 doi:10.1101/210195 Cold Spring Harbor Laboratory Press 2017-10-27 <![CDATA[ Towards sustainable bioplastic production in resource limited environments using the photoferroautotrophic and photoelectroautotrophic bacterium Rhodopseudomonas palustris TIE-1 ]]> https://biorxiv.org/content/10.1101/214551v1?rss=1 Ranaivoarisoa, T. O. Rengasamy, K. Guzman, M. S. Singh, R. Bose, A. 2017-11-06 doi:10.1101/214551 Cold Spring Harbor Laboratory Press 2017-11-06 <![CDATA[ Improving microbial electrosynthesis of polyhydroxybutyrate (PHB) from CO2 by Rhodopseudomonas palustris TIE-1 using an immobilized iron complex modified cathode ]]> https://biorxiv.org/content/10.1101/214577v1?rss=1 Rengasamy, K. Ranaivoarisoa, T. O. Singh, R. Bose, A. 2017-11-07 doi:10.1101/214577 Cold Spring Harbor Laboratory Press 2017-11-07 <![CDATA[ Species abundance plays a dominant role in local and regional extinctions in freshwater communities and allows the identification of selective extinctions ]]> https://biorxiv.org/content/10.1101/219469v1?rss=1 Almeida, R. J. Biro, E. G. Woods, L. M. Smith, K. G. 2017-11-14 doi:10.1101/219469 Cold Spring Harbor Laboratory Press 2017-11-14 <![CDATA[ Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal ]]> https://biorxiv.org/content/10.1101/223081v1?rss=1 Jeong, C. Witonsky, D. B. Basnyat, B. Neupane, M. Beall, C. M. Childs, G. Craig, S. R. Novembre, J. Di Rienzo, A. 2017-11-23 doi:10.1101/223081 Cold Spring Harbor Laboratory Press 2017-11-23 <![CDATA[ Neuronal tracing and analysis by multispectral tracing in densely labeled mouse brain ]]> https://biorxiv.org/content/10.1101/230458v1?rss=1 Roossien, D. H. Webb, J. M. Sadis, B. V. Yan, Y. Min, L. Y. Dizaji, A. S. Bogart, L. J. Mazuski, C. Huth, R. S. Stecher, J. S. Lichtman, J. W. Hensch, T. K. Herzog, E. D. Cai, D. 2017-12-07 doi:10.1101/230458 Cold Spring Harbor Laboratory Press 2017-12-07 <![CDATA[ A deep mutational scan of an acidic activation domain ]]> https://biorxiv.org/content/10.1101/230987v1?rss=1 Staller, M. V. Holehouse, A. S. Swain-Lenz, D. Das, R. K. Pappu, R. V. Cohen, B. A. 2017-12-08 doi:10.1101/230987 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ Comparative analysis of kidney organoid and adult human kidney single cell and single nucleus transcriptomes ]]> https://biorxiv.org/content/10.1101/232561v1?rss=1 Wu, H. Uchimura, K. Donnelly, E. Kirita, Y. Morris, S. A. Humphreys, B. D. 2017-12-11 doi:10.1101/232561 Cold Spring Harbor Laboratory Press 2017-12-11 <![CDATA[ A Quantitative Assessment of Prefrontal Cortex in Humans Relative to Nonhuman Primates ]]> https://biorxiv.org/content/10.1101/233346v1?rss=1 Donahue, C. J. Glasser, M. F. Preuss, T. M. Rilling, J. K. Van Essen, D. C. 2017-12-13 doi:10.1101/233346 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ Chromatin interaction data visualization in the WashU Epigenome Browser ]]> https://biorxiv.org/content/10.1101/239368v1?rss=1 Li, D. Hsu, S. Purushotham, D. Wang, T. 2017-12-24 doi:10.1101/239368 Cold Spring Harbor Laboratory Press 2017-12-24 <![CDATA[ The influence of everyday events on prospective timing "in the moment" ]]> https://biorxiv.org/content/10.1101/246975v1?rss=1 Bangert, A. S. Kurby, C. A. Zacks, J. M. 2018-01-12 doi:10.1101/246975 Cold Spring Harbor Laboratory Press 2018-01-12 <![CDATA[ Atomic force microscopy of phase separation on ruptured, giant unilamellar vesicles ]]> https://biorxiv.org/content/10.1101/250944v1?rss=1 Jiang, Y. Genin, G. M. Pryse, K. M. Elson, E. L. 2018-01-20 doi:10.1101/250944 Cold Spring Harbor Laboratory Press 2018-01-20 <![CDATA[ A constraint-based model reveals hysteresis in island biogeography ]]> https://biorxiv.org/content/10.1101/251926v1?rss=1 Burger, J. R. Anderson, R. P. Balk, M. A. Fristoe, T. S. 2018-01-22 doi:10.1101/251926 Cold Spring Harbor Laboratory Press 2018-01-22 <![CDATA[ Lost in Space: The Impact of Traditional Neuroimaging Methods on the Spatial Localization of Cortical Areas ]]> https://biorxiv.org/content/10.1101/255620v1?rss=1 Coalson, T. S. Van Essen, D. C. Glasser, M. 2018-01-29 doi:10.1101/255620 Cold Spring Harbor Laboratory Press 2018-01-29 <![CDATA[ Trans-ancestral GWAS of alcohol dependence reveals common genetic underpinnings with psychiatric disorders ]]> https://biorxiv.org/content/10.1101/257311v1?rss=1 Walters, R. K. Adams, M. J. Adkins, A. E. Aliev, F. Bacanu, S.-A. Batzler, A. Bertelsen, S. Biernacka, J. Bigdeli, T. B. Chen, L.-S. Clarke, T.-K. Chou, Y.-L. Degenhardt, F. Docherty, A. R. Fontanillas, P. Foo, J. Fox, L. Frank, J. Giegling, I. Gordon, S. Hack, L. -, Hartz, S. M. Heilmann-Heimbach, S. Herms, S. Hodgkinson, C. Hoffmann, P. Hottenga, J.-J. Kennedy, M. A. Alanne-Kinnunen, M. Konte, B. Lahti, J. Lahti-Pulkkinen, M. Ligthart, L. Loukola, A.-M. Maher, B. S. Mbarek, H. McIntosh, A. M. McQueen, M. B. Milaneschi, Y. Palviainen, T. Pearson, J. 2018-03-10 doi:10.1101/257311 Cold Spring Harbor Laboratory Press 2018-03-10 <![CDATA[ Motif Scraper: A cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files ]]> https://biorxiv.org/content/10.1101/265108v1?rss=1 Roberson, E. D. O. 2018-02-13 doi:10.1101/265108 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ Hedgehog signaling controls progenitor differentiation timing during heart development ]]> https://biorxiv.org/content/10.1101/270751v1?rss=1 Rowton, M. Hoffmann, A. D. Steimle, J. D. Yang, X. H. Guzzetta, A. Lazarevic, S. Kim, C. Deng, N. Lu, E. Jacobs-Li, J. Yu, S. Hanson, E. Perez-Cervantes, C. Chan, S. S.-K. Ikegami, K. Garry, D. J. Kyba, M. Moskowitz, I. P. 2018-02-23 doi:10.1101/270751 Cold Spring Harbor Laboratory Press 2018-02-23 <![CDATA[ The Structural Basis of IKs Ion-Channel Activation: Mechanistic Insights from Molecular Simulations ]]> https://biorxiv.org/content/10.1101/275180v1?rss=1 Ramasubramanian, S. Rudy, Y. 2018-03-30 doi:10.1101/275180 Cold Spring Harbor Laboratory Press 2018-03-30 <![CDATA[ Measuring NDC80 binding reveals the molecular basis of tension-dependent kinetochore-microtubule attachments ]]> https://biorxiv.org/content/10.1101/276212v1?rss=1 Yoo, T. Y. Choi, J.-M. Yu, C.-H. Pappu, R. V. Needleman, D. J. 2018-03-07 doi:10.1101/276212 Cold Spring Harbor Laboratory Press 2018-03-07 <![CDATA[ Encoding the expectation of a sensory stimulus ]]> https://biorxiv.org/content/10.1101/281071v1?rss=1 Zhang, L. Chen, A. B. Saha, D. Li, C. Raman, B. 2018-03-13 doi:10.1101/281071 Cold Spring Harbor Laboratory Press 2018-03-13 <![CDATA[ Transdiagnostic multimodal neuroimaging in psychosis: structural, resting-state, and task MRI correlates of cognitive control ]]> https://biorxiv.org/content/10.1101/284273v1?rss=1 Lerman-Sinkoff, D. B. Kandala, S. Calhoun, V. D. Barch, D. M. Mamah, D. T. 2018-03-18 doi:10.1101/284273 Cold Spring Harbor Laboratory Press 2018-03-18 <![CDATA[ Modeling semantic encoding in a common neural representational space ]]> https://biorxiv.org/content/10.1101/288605v1?rss=1 Van Uden, C. E. Nastase, S. A. Connolly, A. C. Feilong, M. Hansen, I. Gobbini, M. I. Haxby, J. V. 2018-03-25 doi:10.1101/288605 Cold Spring Harbor Laboratory Press 2018-03-25 <![CDATA[ Circadian clock neurons mediate time-of-day dependent responses to light ]]> https://biorxiv.org/content/10.1101/291955v1?rss=1 Jones, J. R. Simon, T. Lones, L. Herzog, E. D. 2018-04-04 doi:10.1101/291955 Cold Spring Harbor Laboratory Press 2018-04-04 <![CDATA[ The Genomic Formation of South and Central Asia ]]> https://biorxiv.org/content/10.1101/292581v1?rss=1 Narasimhan, V. M. Patterson, N. J. Moorjani, P. Lazaridis, I. Mark, L. Mallick, S. Rohland, N. Bernardos, R. Kim, A. M. Nakatsuka, N. Olalde, I. Coppa, A. Mallory, J. Moiseyev, V. Monge, J. Olivieri, L. M. Adamski, N. Broomandkhoshbacht, N. Candilio, F. Cheronet, O. Culleton, B. J. Ferry, M. Fernandes, D. Gamarra, B. Gaudio, D. Hajdinjak, M. Harney, E. Harper, T. K. Keating, D. Lawson, A.-M. Michel, M. Novak, M. Oppenheimer, J. Rai, N. Sirak, K. Slon, V. Stewardson, K. Zhang, Z. Akhatov, G. Bagashev, A. N. Baitanayev, B. Bonora, G. L. Chikisheva, T. D 2018-03-31 doi:10.1101/292581 Cold Spring Harbor Laboratory Press 2018-03-31 <![CDATA[ Natural selection on gene-specific codon usage bias is common across eukaryotes ]]> https://biorxiv.org/content/10.1101/292938v1?rss=1 Peng, Z. Zaher, H. Ben-Shahar, Y. 2018-03-31 doi:10.1101/292938 Cold Spring Harbor Laboratory Press 2018-03-31 <![CDATA[ Minimizing Structural Bias in Single-Molecule Super-Resolution Microscopy ]]> https://biorxiv.org/content/10.1101/293670v1?rss=1 Mazidi, H. Lu, J. Nehorai, A. Lew, M. D. 2018-04-03 doi:10.1101/293670 Cold Spring Harbor Laboratory Press 2018-04-03 <![CDATA[ Molecular determinants of enterotoxigenic Escherichia coli heat-stable toxin secretion and delivery ]]> https://biorxiv.org/content/10.1101/299313v1?rss=1 Zhu, Y. Luo, Q. Davis, S. Westra, C. Vickers, T. J. Fleckenstein, J. M. 2018-04-11 doi:10.1101/299313 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ Evolved sequence features within the intrinsically disordered tail influence FtsZ assembly and bacterial cell division ]]> https://biorxiv.org/content/10.1101/301622v1?rss=1 Cohan, M. C. Posey, A. E. Grigsby, S. J. Mittal, A. Holehouse, A. S. Buske, P. J. Levin, P. A. Pappu, R. V. 2018-04-14 doi:10.1101/301622 Cold Spring Harbor Laboratory Press 2018-04-14 <![CDATA[ Genetics of brain age suggest an overlap with common brain disorders ]]> https://biorxiv.org/content/10.1101/303164v1?rss=1 Kaufmann, T. van der Meer, D. Doan, N. T. Schwarz, E. Lund, M. J. Agartz, I. Alnaes, D. Barch, D. M. Baur-Streubel, R. Bertolino, A. Bettella, F. Beyer, M. K. Boen, E. Borgwardt, S. Brandt, C. L. Buitelaar, J. Celius, E. G. Cervenka, S. Conzelmann, A. Cordova-Palomera, A. Dale, A. M. de Quervain, D. J.- F. Di Carlo, P. Djurovic, S. Dorum, E. S. Eisenacher, S. Elvsashagen, T. Espeseth, T. Fatouros-Bergman, H. Flyckt, L. Franke, B. Frei, O. Haatveit, B. Haberg, A. K. Harbo, H. F. Hartman, C. A. Heslenfeld, D. Hoekstra, P. J. Hogestol, E. A. Jernigan, T. Jo 2018-04-17 doi:10.1101/303164 Cold Spring Harbor Laboratory Press 2018-04-17 <![CDATA[ A Coupled Network of Growth Transform Neurons for Spike-Encoded Auditory Feature Extraction ]]> https://biorxiv.org/content/10.1101/303453v1?rss=1 Gangopadhyay, A. Aono, K. Mehta, D. Chakrabartty, S. 2018-04-18 doi:10.1101/303453 Cold Spring Harbor Laboratory Press 2018-04-18 <![CDATA[ Endosymbiotic adaptations in three new bacterial species associated with Dictyostelium discoideum: Burkholderia agricolaris sp. nov., Burkholderia hayleyella sp. nov., and Burkholderia bonniea sp. nov. ]]> https://biorxiv.org/content/10.1101/304352v1?rss=1 Brock, D. A. Hubert, A. M. Noh, S. DiSalvo, S. Geist, K. S. Haselkorn, T. S. Queller, D. Strassmann, J. E. 2018-04-19 doi:10.1101/304352 Cold Spring Harbor Laboratory Press 2018-04-19 <![CDATA[ Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding ]]> https://biorxiv.org/content/10.1101/306647v1?rss=1 Sun, X. Singh, S. Blumer, K. J. Bowman, G. R. 2018-04-23 doi:10.1101/306647 Cold Spring Harbor Laboratory Press 2018-04-23 <![CDATA[ The HCP 7T Retinotopy Dataset ]]> https://biorxiv.org/content/10.1101/308247v1?rss=1 Benson, N. Jamison, K. W. Arcaro, M. J. Vu, A. Glasser, M. F. Coalson, T. S. Van Essen, D. Yacoub, E. Ugurbil, K. Winawer, J. Kay, K. 2018-04-25 doi:10.1101/308247 Cold Spring Harbor Laboratory Press 2018-04-25 <![CDATA[ Genetic basis of variation in heat and ethanol tolerance in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/318212v1?rss=1 Riles, L. Fay, J. C. 2018-05-09 doi:10.1101/318212 Cold Spring Harbor Laboratory Press 2018-05-09 <![CDATA[ Integrative analysis of 5-methyl- and 5-hydroxymethylcytosine indicates a role for 5-hydroxymethylcytosine as a repressive epigenetic mark ]]> https://biorxiv.org/content/10.1101/318808v1?rss=1 Schlosberg, C. E. Edwards, J. R. 2018-05-10 doi:10.1101/318808 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Entrainment of circadian rhythms depends on firing rates and neuropeptide release of VIP SCN neurons ]]> https://biorxiv.org/content/10.1101/322339v1?rss=1 Mazuski, C. Abel, J. H. Chen, S. P. Hermanstyne, T. O. Jones, J. R. Simon, T. Doyle, F. J. Herzog, E. D. 2018-05-16 doi:10.1101/322339 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Exposons exploit cooperative changes in solvent exposure to detect cryptic allosteric sites and other functionally-relevant conformational transitions ]]> https://biorxiv.org/content/10.1101/323568v1?rss=1 Porter, J. R. Moeder, K. E. Sibbald, C. A. Zimmerman, M. I. Hart, K. M. Greenberg, M. J. Bowman, G. R. 2018-05-16 doi:10.1101/323568 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Tau monomer encodes strains ]]> https://biorxiv.org/content/10.1101/325043v1?rss=1 Sharma, A. M. Thomas, T. L. Woodard, D. R. Kashmer, O. M. Diamond, M. I. 2018-05-17 doi:10.1101/325043 Cold Spring Harbor Laboratory Press 2018-05-17 <![CDATA[ Low fidelity assembly of influenza A virus promotes escape from host cells ]]> https://biorxiv.org/content/10.1101/332650v1?rss=1 Vahey, M. D. Fletcher, D. A. 2018-05-28 doi:10.1101/332650 Cold Spring Harbor Laboratory Press 2018-05-28 <![CDATA[ Hierarchical heterogeneity across human cortex shapes large-scale neural dynamics ]]> https://biorxiv.org/content/10.1101/341966v1?rss=1 Demirtas, M. Burt, J. B. Helmer, M. Ji, J. L. Adkinson, B. D. Glasser, M. F. Van Essen, D. C. Sotiropoulos, S. N. Anticevic, A. Murray, J. D. 2018-06-08 doi:10.1101/341966 Cold Spring Harbor Laboratory Press 2018-06-08 <![CDATA[ Dynamic Prediction During Perception of Everyday Events ]]> https://biorxiv.org/content/10.1101/348946v1?rss=1 Eisenberg, M. L. Zacks, J. M. Flores, S. 2018-06-22 doi:10.1101/348946 Cold Spring Harbor Laboratory Press 2018-06-22 <![CDATA[ Nicastrin haploinsufficiency alters expression of type-I interferon-stimulated genes in two immortalized human cell lines ]]> https://biorxiv.org/content/10.1101/353482v1?rss=1 Cao, L. Morales-Heil, D. Roberson, E. D. O. 2018-06-22 doi:10.1101/353482 Cold Spring Harbor Laboratory Press 2018-06-22 <![CDATA[ Career Choice, Gender, and Mentor Impact: Results of the U.S. National Postdoc Survey ]]> https://biorxiv.org/content/10.1101/355511v1?rss=1 McConnell, S. C. Westerman, E. L. Pierre, J. F. Heckler, E. J. Schwartz, N. B. 2018-06-26 doi:10.1101/355511 Cold Spring Harbor Laboratory Press 2018-06-26 <![CDATA[ Functional grading of pericellular matrix surrounding chondrocytes: potential roles in signaling and fluid transport ]]> https://biorxiv.org/content/10.1101/365569v1?rss=1 Saadat, F. Lagieski, M. J. Birman, V. Thomopoulos, S. Genin, G. M. 2018-07-09 doi:10.1101/365569 Cold Spring Harbor Laboratory Press 2018-07-09 <![CDATA[ In Vitro Assay for the Detection of Network Connectivity in Embryonic Stem Cell-Derived Cultures ]]> https://biorxiv.org/content/10.1101/377689v1?rss=1 Gamble, J. R. Zhang, E. T. Iyer, N. Sakiyama-Elbert, S. Barbour, D. L. 2018-07-26 doi:10.1101/377689 Cold Spring Harbor Laboratory Press 2018-07-26 <![CDATA[ A dual motif mediates outer-membrane translocation and packing of glycosidases into Bacteroides Outer Membrane Vesicles. ]]> https://biorxiv.org/content/10.1101/377861v1?rss=1 Valguarnera, E. Scott, N. E. Feldman, M. 2018-07-26 doi:10.1101/377861 Cold Spring Harbor Laboratory Press 2018-07-26 <![CDATA[ Plasticity in Escherichia coli cell wall metabolism promotes fitness and mediates intrinsic antibiotic resistance across environmental conditions ]]> https://biorxiv.org/content/10.1101/379271v1?rss=1 Mueller, E. A. Levin, P. A. 2018-07-29 doi:10.1101/379271 Cold Spring Harbor Laboratory Press 2018-07-29 <![CDATA[ Mitochondria-encoded genes contribute to the evolution of heat and cold tolerance among Saccharomyces species ]]> https://biorxiv.org/content/10.1101/390500v1?rss=1 Li, X. C. Peris, D. Hittinger, C. T. Sia, E. A. Fay, J. C. 2018-08-14 doi:10.1101/390500 Cold Spring Harbor Laboratory Press 2018-08-14 <![CDATA[ In vivo detection of optically-evoked opioid peptide release ]]> https://biorxiv.org/content/10.1101/393603v1?rss=1 Al-Hasani, R. Wong, J.-M. T. Mabrouk, O. S. McCall, J. G. Schmitz, G. P. Porter-Stransky, K. A. Aragona, B. J. Kennedy, R. T. Bruchas, M. R. 2018-08-16 doi:10.1101/393603 Cold Spring Harbor Laboratory Press 2018-08-16 <![CDATA[ Whole brain imaging reveals distinct spatial patterns of amyloid beta deposition in three mouse models of Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/395236v1?rss=1 Whitesell, J. D. Buckley, A. R. Knox, J. E. Kuan, L. Graddis, N. Pelos, A. Mukora, A. Wakeman, W. Bohn, P. Ho, A. Hirokawa, K. E. Harris, J. A. 2018-08-18 doi:10.1101/395236 Cold Spring Harbor Laboratory Press 2018-08-18 <![CDATA[ Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome ]]> https://biorxiv.org/content/10.1101/396671v1?rss=1 Rajshekar, S. Yao, J. Arnold, P. K. Payne, S. G. Zhang, Y. Bowman, T. V. Schmitz, R. J. Edwards, J. R. Goll, M. G. 2018-08-23 doi:10.1101/396671 Cold Spring Harbor Laboratory Press 2018-08-23 <![CDATA[ Subclinical infection of macaques and baboons with a baboon simartevirus ]]> https://biorxiv.org/content/10.1101/397430v1?rss=1 Buechler, C. Semler, M. Baker, D. A. Newman, C. Cornish, J. P. Chavez, D. Guerra, B. Lanford, R. Brasky, K. Kuhn, J. H. Johnson, R. F. O'Connor, D. H. Bailey, A. 2018-08-22 doi:10.1101/397430 Cold Spring Harbor Laboratory Press 2018-08-22 <![CDATA[ Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in Mouse Embryonic Stem Cells ]]> https://biorxiv.org/content/10.1101/398107v1?rss=1 King, D. M. Maricque, B. B. Cohen, B. A. 2018-08-22 doi:10.1101/398107 Cold Spring Harbor Laboratory Press 2018-08-22 <![CDATA[ CLIP-Seq and massively parallel functional analysis of the CELF6 RNA binding protein reveals a role in destabilizing synaptic gene mRNAs through interaction with 3’UTR elements in vivo ]]> https://biorxiv.org/content/10.1101/401604v1?rss=1 Rieger, M. A. King, D. M. Cohen, B. A. Dougherty, J. D. 2018-08-27 doi:10.1101/401604 Cold Spring Harbor Laboratory Press 2018-08-27 <![CDATA[ The dark side of the mean: brain structural heterogeneity in schizophrenia and its polygenic risk. ]]> https://biorxiv.org/content/10.1101/407890v1?rss=1 Alnaes, D. Kaufmann, T. van der Meer, D. Cordova-Palomera, A. Rokicki, J. Moberget, T. Bettella, F. Agartz, I. Barch, D. M. Bertolino, A. Brandt, C. L. Cervenka, S. Djurovic, S. Doan, N. T. Eisenacher, S. Fatouros-Bergman, H. Flyckt, L. Di Giorgio, A. Haatveit, B. Jonsson, E. G. KaSP Consortium, Kirsch, P. Lund, M. J. Meyer-Lindenberg, A. Pergola, G. Schwarz, E. Smeland, O. B. Quarto, T. Zink, M. Andreassen, O. A. Westlye, L. T. 2018-09-04 doi:10.1101/407890 Cold Spring Harbor Laboratory Press 2018-09-04 <![CDATA[ Chemical signatures of honey bee group membership develop via a socially-modulated innate process ]]> https://biorxiv.org/content/10.1101/412353v1?rss=1 Vernier, C. Krupp, J. Marcus, K. Hefetz, A. Levine, J. Ben-Shahar, Y. 2018-09-09 doi:10.1101/412353 Cold Spring Harbor Laboratory Press 2018-09-09 <![CDATA[ The community structure of functional brain networks exhibits scale-specific patterns of variability across individuals and time ]]> https://biorxiv.org/content/10.1101/413278v1?rss=1 Betzel, R. F. Bertolero, M. A. Gordon, E. M. Gratton, C. Dosenbach, N. U. Bassett, D. S. 2018-09-11 doi:10.1101/413278 Cold Spring Harbor Laboratory Press 2018-09-11 <![CDATA[ PolyA tracks and poly-lysine repeats are the Achilles heel of Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/420109v1?rss=1 Pavlovic Djuranovic, S. Erath, J. Andrews, R. J. Bayguinov, P. O. Chung, J. J. Chalker, D. L. Fitzpatrick, J. A. Moss, W. N. Szczesny, P. Djuranovic, S. 2018-09-18 doi:10.1101/420109 Cold Spring Harbor Laboratory Press 2018-09-18 <![CDATA[ Trans-ethnic genome-wide association study provides insight into effector genes and molecular mechanisms for kidney function and highlights a causal effect on kidney-specific disease aetiologies ]]> https://biorxiv.org/content/10.1101/420273v1?rss=1 Morris, A. P. Le, T. H. Wu, H. Akbarov, A. van der Most, P. P. Mahajan, A. Hemani, G. Gaulton, K. J. Nadkarni, G. Valladares-Salgado, A. Wacher-Rodarte, N. Mychaleckyj, J. C. Dueker, N. D. Guo, X. Hai, Y. Haessler, J. Kamatani, Y. Stilp, A. Zhu, G. Cook, J. P. Arnlov, J. Blanton, S. H. de Borst, M. Bottinger, E. P. Buchanan, T. A. Charchar, F. J. Damman, J. Eales, J. M. Gharavi, A. G. Giedraitis, V. Heath, A. C. Ipp, E. Kiryluk, K. Kubo, M. Larsson, A. Lindgren, C. Lu, Y. Madden, P. A. Kramer, H. J. Montgomery, G. W. Papanicolaou, G. J. Raffel, L. J. S 2018-09-18 doi:10.1101/420273 Cold Spring Harbor Laboratory Press 2018-09-18 <![CDATA[ Morning and Evening Circadian Pacemakers Independently Drive Premotor Centers via a Specific Dopamine Relay ]]> https://biorxiv.org/content/10.1101/424499v1?rss=1 Liang, X. Ho, M. C. W. Wu, M. N. Holy, T. E. Taghert, P. H. 2018-09-21 doi:10.1101/424499 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ Assessment of biological role and insight into druggability of the Plasmodium falciparum protease plasmepsin V ]]> https://biorxiv.org/content/10.1101/426486v1?rss=1 Goldberg, D. E. Niles, J. Polino, A. J. Nasamu, A. S. 2018-09-26 doi:10.1101/426486 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ Enspara: Modeling molecular ensembles with scalable data structures and parallel computing ]]> https://biorxiv.org/content/10.1101/431072v1?rss=1 Porter, J. Zimmerman, M. I. Bowman, G. R. 2018-09-29 doi:10.1101/431072 Cold Spring Harbor Laboratory Press 2018-09-29 <![CDATA[ A complex symbiosis involving within species variation in the response of Dictyostelium amoebae to Burkholderia bacteria ]]> https://biorxiv.org/content/10.1101/436386v1?rss=1 Shu, L. Brock, D. A. Geist, K. S. Miller, J. W. Queller, D. C. Strassmann, J. E. DiSalvo, S. 2018-10-05 doi:10.1101/436386 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ FoxM1 drives proximal tubule proliferation during repair from acute kidney injury ]]> https://biorxiv.org/content/10.1101/436576v1?rss=1 Chang-Panesso, M. Kadyrov, F. F. Lalli, M. Wu, H. Ikeda, S. Kobayashi, A. Humphreys, B. D. 2018-10-05 doi:10.1101/436576 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ A set of functionally-defined brain regions with improved representation of the subcortex and cerebellum ]]> https://biorxiv.org/content/10.1101/450452v1?rss=1 Seitzman, B. A. Gratton, C. Marek, S. Raut, R. V. Dosenbach, N. U. Schlaggar, B. L. Petersen, S. E. Greene, D. J. 2018-10-24 doi:10.1101/450452 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ The Heterotaxy Gene, CCDC11, is Essential for Cytokinesis and Cell-Cell Adhesion Via RhoA Regulation ]]> https://biorxiv.org/content/10.1101/452631v1?rss=1 Kulkarni, S. S. Stephenson, R. Amalraj, S. Betleja, E. Moresco, J. J. Yates, J. R. Mahjoub, M. R. Miller, A. Khokha, M. 2018-10-24 doi:10.1101/452631 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ Genome-wide association and functional studies identify 46 novel loci for alcohol consumption and suggest common genetic mechanisms with neuropsychiatric disorders ]]> https://biorxiv.org/content/10.1101/453332v1?rss=1 Evangelou, E. Gao, H. Chu, C. Ntritsos, G. Blakeley, P. Butts, A. R. Pazoki, R. Suzuki, H. Koskeridis, F. Yiorkas, A. M. Karaman, I. Elliott, J. Aeschbacher, S. Bartz, T. M. Baumeister, S. E. Braund, P. S. Brown, M. R. Brody, J. A. Clarke, T.-K. Dimou, N. Faul, J. D. Homuth, G. Jackson, A. U. Kentistou, K. A. Joshi, P. K. Lemaitre, R. N. Lind, P. A. Lyytikainen, L.-P. Mangino, M. Milaneschi, Y. Nelson, C. P. Nolte, I. M. Perala, M.-M. Polasek, O. Porteous, D. Ratliff, S. M. Smith, J. A. Stancakova, A. Teumer, A. Tuominen, S. Theriault, S. Vangipurapu, J 2018-10-30 doi:10.1101/453332 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ Hypermorphic SERK1 mutations function via a SOBIR1 pathway to activate floral abscission signaling ]]> https://biorxiv.org/content/10.1101/453944v1?rss=1 Taylor, I. Baer, J. Calcutt, R. Walker, J. C. 2018-10-26 doi:10.1101/453944 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ Glycan cross-feeding drives mutualism between Fusobacterium and the vaginal microbiota ]]> https://biorxiv.org/content/10.1101/463349v1?rss=1 Agarwal, K. Robinson, L. Perry, J. Foster, L. Lin, H. Tortelli, B. O Brien, V. P. Reno, H. Gilbert, N. Lewis, W. Lewis, A. 2018-11-06 doi:10.1101/463349 Cold Spring Harbor Laboratory Press 2018-11-06 <![CDATA[ A polyploid admixed origin of beer yeasts derived from European and Asian wine populations ]]> https://biorxiv.org/content/10.1101/466276v1?rss=1 Fay, J. Liu, P. Ong, G. Dunham, M. Cromie, G. Jeffrey, E. Ludlow, C. Dudley, A. 2018-11-08 doi:10.1101/466276 Cold Spring Harbor Laboratory Press 2018-11-08 <![CDATA[ Dual cryo-radiofrequency ablation enhances lesion depth in beating human left ventricular preparations ]]> https://biorxiv.org/content/10.1101/469882v1?rss=1 Sulkin, M. Laughner, J. Rogge, M. Philpott, J. Efimov, I. R. 2018-11-14 doi:10.1101/469882 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ A platform for case-control matching enables association studies without genotype sharing ]]> https://biorxiv.org/content/10.1101/470450v1?rss=1 Artomov, M. Loboda, A. A. Artyomov, M. N. Daly, M. 2018-11-14 doi:10.1101/470450 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ How does cilium length affect beating? ]]> https://biorxiv.org/content/10.1101/474346v1?rss=1 Bottier, M. Thomas, K. A. Dutcher, S. K. Bayly, P. V. 2018-11-19 doi:10.1101/474346 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ The urge to blink in Tourette syndrome ]]> https://biorxiv.org/content/10.1101/477372v1?rss=1 Botteron, H. E. Richards, C. A. Bihun, E. C. Nishino, T. Acevedo, H. K. Koller, J. M. Black, K. J. 2018-12-12 doi:10.1101/477372 Cold Spring Harbor Laboratory Press 2018-12-12 <![CDATA[ Mechanistic origin of cell-size control and homeostasis in bacteria ]]> https://biorxiv.org/content/10.1101/478818v1?rss=1 Si, F. Le Treut, G. Sauls, J. T. Vadia, S. Levin, P. A. Jun, S. 2018-11-26 doi:10.1101/478818 Cold Spring Harbor Laboratory Press 2018-11-26 <![CDATA[ Co-opted transposons help perpetuate conserved higher-order chromosomal structures ]]> https://biorxiv.org/content/10.1101/485342v1?rss=1 Choudhary, M. N. Friedman, R. Z. Wang, J. T. Jang, H. S. Zhuo, X. Wang, T. 2018-12-05 doi:10.1101/485342 Cold Spring Harbor Laboratory Press 2018-12-05 <![CDATA[ Cell type-specific modulation of sensory and affective components of itch in the periaqueductal gray ]]> https://biorxiv.org/content/10.1101/486332v1?rss=1 Samineni, V. K. Grajales-Reyes, J. G. Sundaram, S. S. Gereau, R. W. 2018-12-03 doi:10.1101/486332 Cold Spring Harbor Laboratory Press 2018-12-03 <![CDATA[ Cell growth is an omniphenotype ]]> https://biorxiv.org/content/10.1101/487157v1?rss=1 Peterson, T. 2018-12-05 doi:10.1101/487157 Cold Spring Harbor Laboratory Press 2018-12-05 <![CDATA[ Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties ]]> https://biorxiv.org/content/10.1101/492793v1?rss=1 Boeynaems, S. Holehouse, A. S. Weinhardt, V. Kovacs, D. Van Lindt, J. Larabell, C. Van Den Bosch, L. Das, R. Tompa, P. Pappu, R. V. Gitler, A. 2018-12-11 doi:10.1101/492793 Cold Spring Harbor Laboratory Press 2018-12-11 <![CDATA[ Single-cell membrane potential fluctuations evince network scale-freeness and quasicriticality ]]> https://biorxiv.org/content/10.1101/498477v1?rss=1 Johnson, J. K. Wright, N. C. Xia, J. Wessel, R. 2018-12-17 doi:10.1101/498477 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ G-OnRamp: A Galaxy-based platform for creating genome browsers for collaborative genome annotation ]]> https://biorxiv.org/content/10.1101/499558v1?rss=1 Liu, Y. Sargent, L. Leung, W. Elgin, S. C. R. Goecks, J. 2018-12-18 doi:10.1101/499558 Cold Spring Harbor Laboratory Press 2018-12-18 <![CDATA[ Fast Objective Coupled Planar Illumination Microscopy ]]> https://biorxiv.org/content/10.1101/501890v1?rss=1 Greer, C. J. Holy, T. E. 2018-12-19 doi:10.1101/501890 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Influenza A virus surface proteins are organized to help penetrate host mucus ]]> https://biorxiv.org/content/10.1101/512467v1?rss=1 Vahey, M. D. Fletcher, D. A. 2019-01-04 doi:10.1101/512467 Cold Spring Harbor Laboratory Press 2019-01-04 <![CDATA[ A Domain-general Cognitive Core defined in Multimodally Parcellated Human Cortex ]]> https://biorxiv.org/content/10.1101/517599v1?rss=1 Assem, M. Glasser, M. F. Van Essen, D. C. Duncan, J. 2019-01-10 doi:10.1101/517599 Cold Spring Harbor Laboratory Press 2019-01-10 <![CDATA[ Resting multivoxel activity patterns in human visual cortex are linked to patterns evoked by preferred visual stimuli ]]> https://biorxiv.org/content/10.1101/518712v1?rss=1 Kim, D. Livne, T. Metcalf, N. Corbetta, M. Shulman, G. L. 2019-01-14 doi:10.1101/518712 Cold Spring Harbor Laboratory Press 2019-01-14 <![CDATA[ Microtubule bundling by MAP65-1 protects against severing by inhibiting the binding of katanin ]]> https://biorxiv.org/content/10.1101/520445v1?rss=1 Burkart, G. Dixit, R. 2019-01-14 doi:10.1101/520445 Cold Spring Harbor Laboratory Press 2019-01-14 <![CDATA[ The Drosophila ERG channel seizure plays a role in the neuronal homeostatic stress response ]]> https://biorxiv.org/content/10.1101/521005v1?rss=1 Hill, A. Jain, P. Ben-Shahar, Y. 2019-01-15 doi:10.1101/521005 Cold Spring Harbor Laboratory Press 2019-01-15 <![CDATA[ Mechanism of microtubule plus-end tracking by the plant-specific SPR1 protein and its development as a versatile plus-end marker ]]> https://biorxiv.org/content/10.1101/521047v1?rss=1 Balkunde, R. S. Foroughi, L. Ewan, E. Emenecker, R. Cavalli, V. Dixit, R. 2019-01-15 doi:10.1101/521047 Cold Spring Harbor Laboratory Press 2019-01-15 <![CDATA[ Effects of Standing on Spinal Alignment and Lumbar Intervertebral Discs in Young, Healthy Individuals Determined by Positional Magnetic Resonance Imaging ]]> https://biorxiv.org/content/10.1101/522565v1?rss=1 Weber, C. I. Hwang, C.-T. Van Dillen, L. R. Tang, S. Y. 2019-01-18 doi:10.1101/522565 Cold Spring Harbor Laboratory Press 2019-01-18 <![CDATA[ A Spiking Neuron and Population Model based on the Growth Transform Dynamical System ]]> https://biorxiv.org/content/10.1101/523944v1?rss=1 Gangopadhyay, A. Mehta, D. Chakrabartty, S. 2019-01-18 doi:10.1101/523944 Cold Spring Harbor Laboratory Press 2019-01-18 <![CDATA[ Vocal Transmission of Breeding Status May Facilitate Dispersal in a Cooperative Breeding Primate ]]> https://biorxiv.org/content/10.1101/525121v1?rss=1 Robakis, E. Erkenswick, G. Watsa, M. 2019-01-20 doi:10.1101/525121 Cold Spring Harbor Laboratory Press 2019-01-20 <![CDATA[ Erroneous inference based on a lack of preference within one group: autism, mice, and the Social Approach Task. ]]> https://biorxiv.org/content/10.1101/530279v1?rss=1 Nygaard, K. R. R. Maloney, S. E. E. Dougherty, J. D. 2019-01-25 doi:10.1101/530279 Cold Spring Harbor Laboratory Press 2019-01-25 <![CDATA[ Codon clusters with biased synonymous codon usage represent hidden functional domains in protein-coding DNA sequences ]]> https://biorxiv.org/content/10.1101/530345v1?rss=1 Peng, Z. Ben-Shahar, Y. 2019-01-25 doi:10.1101/530345 Cold Spring Harbor Laboratory Press 2019-01-25 <![CDATA[ Stool-derived eukaryotic RNA biomarkers for detection of high-risk adenomas ]]> https://biorxiv.org/content/10.1101/534412v1?rss=1 Barnell, E. K. Kang, Y. Barnell, A. R. Campbell, K. M. Kruse, K. R. Wurtzler, E. M. Griffith, M. Chaudhuri, A. A. Griffith, O. L. 2019-01-29 doi:10.1101/534412 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Transposon-mediated, cell type-specific transcription factor recording in the mouse brain ]]> https://biorxiv.org/content/10.1101/538504v1?rss=1 Cammack, A. J. Moudgil, A. Lagunas, T. Vasek, M. J. Shabsovich, M. He, J. Chen, X. Wilkinson, M. N. Miller, T. M. Mitra, R. D. Dougherty, J. D. 2019-02-01 doi:10.1101/538504 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ Self-reporting transposons enable simultaneous readout of gene expression and transcription factor binding in single cells ]]> https://biorxiv.org/content/10.1101/538553v1?rss=1 Moudgil, A. Wilkinson, M. N. Chen, X. He, J. Cammack, A. J. Vasek, M. J. Lagunas, T. Qi, Z. Morris, S. A. Dougherty, J. D. Mitra, R. D. 2019-02-01 doi:10.1101/538553 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ Hippocampal Activity Dynamics During Contextual Reward Association in Virtual Reality Place Conditioning ]]> https://biorxiv.org/content/10.1101/545608v1?rss=1 Williams, S. B. Arriaga, M. Post, W. W. Korgaonkar, A. A. Moron, J. A. Han, E. B. 2019-02-10 doi:10.1101/545608 Cold Spring Harbor Laboratory Press 2019-02-10 <![CDATA[ Computational tool to study perturbations in muscle regulation and its application to heart disease ]]> https://biorxiv.org/content/10.1101/548404v1?rss=1 Barrick, S. K. Clippinger, S. R. Greenberg, L. Greenberg, M. J. 2019-02-19 doi:10.1101/548404 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ Disrupted mechanobiology links the molecular and cellular phenotypes in familial dilated cardiomyopathy ]]> https://biorxiv.org/content/10.1101/555391v1?rss=1 Clippinger, S. R. Cloonan, P. E. Greenberg, L. Ernst, M. Stump, W. T. Greenberg, M. J. 2019-02-21 doi:10.1101/555391 Cold Spring Harbor Laboratory Press 2019-02-21 <![CDATA[ A Signaling Network based Computational Model to Uncover Loop as the Novel Molecular Mechanisms for Medulloblastoma ]]> https://biorxiv.org/content/10.1101/561076v1?rss=1 Xu, J. Li, F. 2019-02-26 doi:10.1101/561076 Cold Spring Harbor Laboratory Press 2019-02-26 <![CDATA[ Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program ]]> https://biorxiv.org/content/10.1101/563866v1?rss=1 400 million single-nucleotide and insertion/deletion variants were detected by alignment with the reference genome. Additional novel variants are detectable through assembly of unmapped reads and customized analysis in highly variable loci. Among the >400 million variants detected, 97% have frequency <1% and 46% are singletons. These rare variants provide insights into mutational processes and recent human evolutionary history. The nearly complete catalog of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and non-coding sequence variants to phenotypic variation. Furthermore, combining TOPMed haplotypes with modern imputation methods improves the power and extends the reach of nearly all genome-wide association studies to include variants down to ~0.01% in frequency. ]]> Taliun, D. Harris, D. N. Kessler, M. D. Carlson, J. Szpiech, Z. A. Torres, R. Gagliano Taliun, S. A. Corvelo, A. Gogarten, S. M. Min Kang, H. Pitsillides, A. N. LeFaive, J. Lee, S.-b. Tian, X. Browning, B. L. Das, S. Emde, A.-K. Clarke, W. E. Loesch, D. P. Shetty, A. C. Blackwell, T. W. Wong, Q. Aguet, F. Albert, C. Alonso, A. Ardlie, K. G. Aslibekyan, S. Auer, P. L. Barnard, J. Barr, R. G. Becker, L. C. Beer, R. L. Benjamin, E. J. Bielak, L. F. Blangero, J. Boehnke, M. Bowden, D. W. Brody, J. A. Burchard, E. G. Cade, B. E. Casella, J. F. Chalazan, B. L 2019-03-06 doi:10.1101/563866 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ PCH1 regulates light, temperature, and circadian signaling as a structural component of phytochrome B-photobodies in Arabidopsis ]]> https://biorxiv.org/content/10.1101/566687v1?rss=1 Huang, H. McLoughlin, K. Sorkin, M. Burgie, E. S. Bindbeutel, R. Vierstra, R. Nusinow, D. 2019-03-04 doi:10.1101/566687 Cold Spring Harbor Laboratory Press 2019-03-04 <![CDATA[ Short translational ramp determines efficiency of protein synthesis ]]> https://biorxiv.org/content/10.1101/571059v1?rss=1 Verma, M. Choi, J. Cottrell, K. A. Lavagnino, Z. Thomas, E. N. Pavlovic Djuranovic, S. Szczesny, P. Piston, D. W. Zaher, H. Puglisi, J. D. Djuranovic, S. 2019-03-09 doi:10.1101/571059 Cold Spring Harbor Laboratory Press 2019-03-09 <![CDATA[ The genetic architecture of sporadic and recurrent miscarriage ]]> https://biorxiv.org/content/10.1101/575167v1?rss=1 Laisk, T. Soares, A. L. G. Ferreira, T. Painter, J. N. Laber, S. Bacelis, J. Chen, C.-Y. Lepamets, M. Lin, K. Liu, S. Millwood, I. Y. Ramu, A. Southcombe, J. Andersen, M. S. Yang, L. Becker, C. M. Gordon, S. D. Byberg-Grauholm, J. Helgeland, O. Hougaard, D. M. Jin, X. Johansson, S. Juodakis, J. Kartsonaki, C. Kukushkina, V. Lind, P. A. Metspalu, A. Montgomery, G. W. Morris, A. P. Mortensen, P. B. Njolstad, P. R. Nyholt, D. R. Lippincott, M. Seminara, S. Salumets, A. Snieder, H. Zondervan, K. Chen, Z. Conrad, D. F. Jacobsson, B. Li, L. Martin, N. G. Nea 2019-03-12 doi:10.1101/575167 Cold Spring Harbor Laboratory Press 2019-03-12 <![CDATA[ CytoGPS: A Web-Enabled Karyotype Analysis Tool for Cytogenetics ]]> https://biorxiv.org/content/10.1101/575423v1?rss=1 Abrams, Z. B. Zhang, L. Abruzzo, L. V. Heerema, N. A. Li, S. Dillon, T. Rodriguez, R. Coombes, K. Payne, P. R. O. 2019-03-13 doi:10.1101/575423 Cold Spring Harbor Laboratory Press 2019-03-13 <![CDATA[ Visual recognition of the female body axis drives spatial elements of male courtship in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/576322v1?rss=1 McKinney, R. Ben-Shahar, Y. 2019-03-12 doi:10.1101/576322 Cold Spring Harbor Laboratory Press 2019-03-12 <![CDATA[ Ten-year retrospective analysis of Acinetobacter baumannii clinical isolates reveals a proportionately large, non-nosocomial, multidrug-resistant endemic reservoir ]]> https://biorxiv.org/content/10.1101/576868v1?rss=1 Calix, J. J. Burnham, J. P. Feldman, M. F. 2019-03-14 doi:10.1101/576868 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ A catalog of CasX genome editing sites in common model organisms ]]> https://biorxiv.org/content/10.1101/585521v1?rss=1 27,000 CasX sites per megabase on average. More than 90% of genes in each genome had at least one unique site overlapping an exon, with median unique sites per gene of 6 - 45. I also annotated sites in the GRCm38 reference and 15 additional mouse strain genomes. The presence of specific guide sequences varied amongst the strains, with CAST/EiJ and PWK/PhJ showing the greatest divergence from the reference strain. The high density of CasX sites and number of exon overlapping sites suggests that CasX has the potential to be used as a common genome editor. ]]> Roberson, E. D. O. 2019-03-21 doi:10.1101/585521 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Noda-like RNA viruses infecting Caenorhabditis nematodes: sympatry, diversity and reassortment ]]> https://biorxiv.org/content/10.1101/605840v1?rss=1 Frezal, L. Jung, H. Tahan, S. Wang, D. Felix, M.-A. 2019-04-12 doi:10.1101/605840 Cold Spring Harbor Laboratory Press 2019-04-12 <![CDATA[ LASSI: A lattice model for simulating phase transitions of multivalent proteins ]]> https://biorxiv.org/content/10.1101/611095v1?rss=1 Choi, J.-M. Dar, F. Pappu, R. V. 2019-04-16 doi:10.1101/611095 Cold Spring Harbor Laboratory Press 2019-04-16 <![CDATA[ Two-Color Spatial Cumulant Analysis Detects Heteromeric Interactions between Membrane Proteins ]]> https://biorxiv.org/content/10.1101/613927v1?rss=1 Foust, D. J. Godin, A. G. Ustione, A. Wiseman, P. W. Piston, D. W. 2019-04-19 doi:10.1101/613927 Cold Spring Harbor Laboratory Press 2019-04-19 <![CDATA[ Neurostructural Heterogeneity in Youth with Internalizing Symptoms ]]> https://biorxiv.org/content/10.1101/614438v1?rss=1 Kaczkurkin, A. N. Sotiras, A. Baller, E. B. Calkins, M. E. Chand, G. B. Cui, Z. Erus, G. Fan, Y. Gur, R. E. Gur, R. C. Moore, T. M. Roalf, D. R. Rosen, A. F. G. Ruparel, K. Shinohara, R. T. Varol, E. Wolf, D. H. Davatzikos, C. Satterthwaite, T. D. 2019-04-23 doi:10.1101/614438 Cold Spring Harbor Laboratory Press 2019-04-23 <![CDATA[ Telomere dysfunction represses HNF4α leading to impaired hepatocyte development and function ]]> https://biorxiv.org/content/10.1101/619601v1?rss=1 Niero, E. L. Fok, W. C. Vessoni, A. T. Brenner, K. A. Batista, L. F. Z. 2019-04-25 doi:10.1101/619601 Cold Spring Harbor Laboratory Press 2019-04-25 <![CDATA[ Spatial and temporal alterations in protein structure by EGF regulate cryptic cysteine oxidation ]]> https://biorxiv.org/content/10.1101/624304v1?rss=1 Behring, J. B. van der Post, S. Mooradian, A. D. Egan, M. J. Zimmerman, M. I. Clements, J. L. Bowman, G. R. Held, J. M. 2019-04-30 doi:10.1101/624304 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ Dissemination and Stakeholder Engagement Practices Among Dissemination & Implementation Scientists: Results from an Online Survey ]]> https://biorxiv.org/content/10.1101/627042v1?rss=1 Knoepke, C. Ingle, M. P. Matlock, D. D. Brownson, R. C. Glasgow, R. E. 2019-05-03 doi:10.1101/627042 Cold Spring Harbor Laboratory Press 2019-05-03 <![CDATA[ Why Do Long Zinc Finger Proteins have Short Motifs? A case study of ZFY and CTCF reveals non-independent recognition of tandem zinc finger proteins. ]]> https://biorxiv.org/content/10.1101/637298v1?rss=1 Zuo, Z. Billings, T. Walker, M. Petkov, P. Fordyce, P. Stormo, G. 2019-05-15 doi:10.1101/637298 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ Pattern similarity analyses of frontoparietal task coding: Individual variation and genetic influences ]]> https://biorxiv.org/content/10.1101/642397v1?rss=1 Etzel, J. Courtney, Y. Carey, C. E. Agrawal, A. Braver, T. S. 2019-05-20 doi:10.1101/642397 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Transcriptomic analysis of bone and fibrous tissue morphogenesis during digit tip regeneration in the adult mouse ]]> https://biorxiv.org/content/10.1101/643361v1?rss=1 Qu, F. Palte, I. C. Gontarz, P. M. Zhang, B. Guilak, F. 2019-05-20 doi:10.1101/643361 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ The Single Cell Transcriptomic Landscape of Early Human Diabetic Nephropathy ]]> https://biorxiv.org/content/10.1101/645424v1?rss=1 Wilson, P. C. Wu, H. Kirita, Y. Uchimura, K. Rennke, H. G. Welling, P. A. Waikar, S. S. Humphreys, B. D. 2019-05-24 doi:10.1101/645424 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Comparison of miRNA profiling methods using synthetic miRNA pools and standardized exRNA samples reveals substantial performance differences ]]> https://biorxiv.org/content/10.1101/645762v1?rss=1 Godoy, P. M. Barczak, A. J. DeHoff, P. Srinivasan, S. Das, S. Erle, D. J. Laurent, L. C. 2019-05-24 doi:10.1101/645762 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Predicting failures of Molteno and Baerveldt glaucoma drainage devices using machine learning models ]]> https://biorxiv.org/content/10.1101/646885v1?rss=1 Rahmani, B. Morrison, P. Dixon, M. Sheybani, A. 2019-05-22 doi:10.1101/646885 Cold Spring Harbor Laboratory Press 2019-05-22 <![CDATA[ MCH4 is a multicopy suppressor of glycine toxicity in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/653444v1?rss=1 Melnykov, A. V. Elson, E. L. 2019-05-29 doi:10.1101/653444 Cold Spring Harbor Laboratory Press 2019-05-29 <![CDATA[ Behavioral and neural signatures of working memory in childhood ]]> https://biorxiv.org/content/10.1101/659409v1?rss=1 Rosenberg, M. D. Martinez, S. A. Rapuano, K. M. Conley, M. I. Cohen, A. O. Cornejo, M. D. Hagler, D. J. Anderson, K. M. Wager, T. D. Feczko, E. Earl, E. Fair, D. A. Barch, D. M. Watts, R. Casey, B. 2019-06-06 doi:10.1101/659409 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Single cell RNA-sequencing reveals cellular heterogeneity and trajectories of lineage specification during murine embryonic limb development ]]> https://biorxiv.org/content/10.1101/659656v1?rss=1 Kelly, N. H. Huynh, N. P. Guilak, F. 2019-06-04 doi:10.1101/659656 Cold Spring Harbor Laboratory Press 2019-06-04 <![CDATA[ A Novel Antenna Protein Complex in the Life Cycle of Cyanobacterial Photosystem II ]]> https://biorxiv.org/content/10.1101/660712v1?rss=1 Weisz, D. A. Johnson, V. M. Niedzwiedzki, D. M. Shinn, M. K. Liu, H. Klitzke, C. F. Gross, M. L. Blankenship, R. E. Lohman, T. M. Pakrasi, H. B. 2019-06-05 doi:10.1101/660712 Cold Spring Harbor Laboratory Press 2019-06-05 <![CDATA[ Spectral Hallmark of Auditory-Tactile Interactions in Somatosensory Cortex ]]> https://biorxiv.org/content/10.1101/668319v1?rss=1 Zhang, M. Kwon, S. E. Ben-Johny, M. O'Connor, D. H. Issa, J. B. 2019-06-13 doi:10.1101/668319 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Individualized Dynamic Brain Models: Estimation and Validation with Resting-State fMRI ]]> https://biorxiv.org/content/10.1101/678243v1?rss=1 Singh, M. Braver, T. Cole, M. Ching, S. 2019-06-21 doi:10.1101/678243 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ An individual interneuron participates in many kinds of inhibition and spans much of the mouse visual thalamus ]]> https://biorxiv.org/content/10.1101/683276v1?rss=1 Morgan, J. L. Lichtman, J. W. 2019-06-27 doi:10.1101/683276 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Improving ATAC-seq Data Analysis with AIAP, a Quality Control and Integrative Analysis Package ]]> https://biorxiv.org/content/10.1101/686808v1?rss=1 Liu, S. Li, D. Lyu, C. Gontarz, P. Miao, B. Madden, P. Wang, T. Zhang, B. 2019-06-28 doi:10.1101/686808 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ A molecular logic of sensory coding revealed by optical tagging of physiologically-defined neuronal types ]]> https://biorxiv.org/content/10.1101/692079v1?rss=1 Lee, D. Kume, M. Holy, T. E. 2019-07-05 doi:10.1101/692079 Cold Spring Harbor Laboratory Press 2019-07-05 <![CDATA[ Immune Landscapes Predict Chemotherapy Resistance And Immunotherapy Response In Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/702001v1?rss=1 Vadakekolathu, J. Minden, M. D. Hood, T. Church, S. E. Reeder, S. Altmann, H. Sullivan, A. H. Viboch, E. J. Patel, T. Ibrahimova, N. Warren, S. E. Arruda, A. Liang, Y. Muth, J. Schmitz, M. Cesano, A. Pockley, A. G. Valk, P. J. Lowenberg, B. Bornhauser, M. Tasian, S. K. Rettig, M. P. Davidson-Moncada, J. K. DiPersio, J. F. Rutella, S. 2019-07-26 doi:10.1101/702001 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ The C. elegans RIG-I homolog drh-1 mediates the Intracellular Pathogen Response upon viral infection ]]> https://biorxiv.org/content/10.1101/707141v1?rss=1 Sowa, J. N. Jiang, H. Somasundaram, L. Xu, G. Wang, D. Troemel, E. 2019-07-18 doi:10.1101/707141 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ TANGLED1 mediates interactions between microtubules that may promote spindle organization and phragmoplast guidance to the division site in maize ]]> https://biorxiv.org/content/10.1101/711796v1?rss=1 Martinez, P. Dixit, R. Balkunde, R. O'Leary, S. E. Brakke, K. Rasmussen, C. G. 2019-07-24 doi:10.1101/711796 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Measuring localization confidence for quantifying accuracy and heterogeneity in single-molecule super-resolution microscopy ]]> https://biorxiv.org/content/10.1101/721837v1?rss=1 Mazidi, H. Ding, T. Nehorai, A. Lew, M. D. 2019-08-01 doi:10.1101/721837 Cold Spring Harbor Laboratory Press 2019-08-01 <![CDATA[ Functional characterization of Ralstonia insidiosa, a bona fide resident at the maternal-fetal interface ]]> https://biorxiv.org/content/10.1101/721977v1?rss=1 Parnell, L. A. Willsey, G. G. Joshi, C. S. Yin, Y. Wargo, M. J. Mysorekar, I. U. 2019-08-01 doi:10.1101/721977 Cold Spring Harbor Laboratory Press 2019-08-01 <![CDATA[ Interactions between the N- and C- termini of mechanosensitive ion channel AtMSL10 support a three-step mechanism for activating its signaling function ]]> https://biorxiv.org/content/10.1101/726521v1?rss=1 Basu, D. Shoots, J. Harkess, A. Veley, K. Haswell, E. 2019-08-07 doi:10.1101/726521 Cold Spring Harbor Laboratory Press 2019-08-07 <![CDATA[ Statins Stimulate Hepatic Glucose Production via the miR-183/96/182 Cluster ]]> https://biorxiv.org/content/10.1101/726695v1?rss=1 Marquart, T. J. Allen, R. M. Chen, M. R. Dorn, G. W. Matkovich, S. J. Baldan, A. 2019-08-07 doi:10.1101/726695 Cold Spring Harbor Laboratory Press 2019-08-07 <![CDATA[ Brain microRNA expression associated with social evolution in bees ]]> https://biorxiv.org/content/10.1101/730317v1?rss=1 Kapheim, K. M. Jones, B. M. Sovik, E. Stolle, E. Waterhouse, R. M. Bloch, G. Ben-Shahar, Y. 2019-08-08 doi:10.1101/730317 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ High-throughput experimental evolution using barcoded strains of Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/731349v1?rss=1 Fasanello, V. J. Botero, C. A. Liu, P. Fay, J. C. 2019-08-10 doi:10.1101/731349 Cold Spring Harbor Laboratory Press 2019-08-10 <![CDATA[ Related enteric viruses have different requirements for host microbiota in mice ]]> https://biorxiv.org/content/10.1101/733766v1?rss=1 Robinson, C. M. Woods Acevedo, M. McCune, B. T. Pfeiffer, J. K. 2019-08-13 doi:10.1101/733766 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Entry by multiple picornaviruses is dependent on a pathway that includes TNK2, WASL and NCK1 ]]> https://biorxiv.org/content/10.1101/737635v1?rss=1 Jiang, H. Leung, C. Tahan, S. Wang, D. 2019-08-16 doi:10.1101/737635 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ Evolution of resistance in vitro reveals a novel mechanism of artemisinin activity in Toxoplasma gondii. ]]> https://biorxiv.org/content/10.1101/746065v1?rss=1 Rozenberg, A. Luth, M. R. Behnke, M. Winzeler, E. Sibley, L. D. 2019-08-24 doi:10.1101/746065 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Environmental pH impacts division assembly and cell size in Escherichia coli ]]> https://biorxiv.org/content/10.1101/747808v1?rss=1 Mueller, E. A. Westfall, C. S. Levin, P. A. 2019-08-28 doi:10.1101/747808 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ The aminoalkylindole, BML-190, negatively regulates chitosan synthesis via the cAMP/PKA1 pathway in Cryptococcus neoformans ]]> https://biorxiv.org/content/10.1101/751172v1?rss=1 Maybruck, B. T. Lam, W. C. Specht, C. Ilagan, M. X. G. Donlin, M. J. Lodge, J. K. 2019-08-29 doi:10.1101/751172 Cold Spring Harbor Laboratory Press 2019-08-29 <![CDATA[ Controlling Structural Bias in Intrinsically Disordered Proteins Using Solution Space Scanning ]]> https://biorxiv.org/content/10.1101/752378v1?rss=1 Holehouse, A. S. Sukenik, S. 2019-08-30 doi:10.1101/752378 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ Chitosan biosynthesis and virulence in the human fungal pathogen Cryptococcus gattii ]]> https://biorxiv.org/content/10.1101/759050v1?rss=1 Lam, W. C. Upadhya, R. Specht, C. Ragsdale, A. E. Hole, C. R. Levitz, S. M. Lodge, J. K. 2019-09-05 doi:10.1101/759050 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Hippocampal subfields integrate information about past temporal and cognitive contexts ]]> https://biorxiv.org/content/10.1101/766311v1?rss=1 Dimsdale-Zucker, H. R. Montchal, M. E. Reagh, Z. M. Wang, S.-F. Libby, L. A. Ranganath, C. R. 2019-09-12 doi:10.1101/766311 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Rapid dissemination and monopolization of viral populations in mice revealed using a panel of barcoded viruses ]]> https://biorxiv.org/content/10.1101/769976v1?rss=1 McCune, B. T. Lanahan, M. R. tenOever, B. R. Pfeiffer, J. K. 2019-09-16 doi:10.1101/769976 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ Arginine-enriched mixed-charge domains provide cohesion for nuclear speckle condensation ]]> https://biorxiv.org/content/10.1101/771592v1?rss=1 Greig, J. A. Nguyen, T. A. Lee, M. Holehouse, A. S. Posey, A. E. Pappu, R. V. Jedd, G. J. 2019-09-16 doi:10.1101/771592 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ Mutation of CFAP57 causes primary ciliary dyskinesia by disrupting theasymmetric targeting of a subset of ciliary inner dynein arms ]]> https://biorxiv.org/content/10.1101/773028v1?rss=1 T) p.(Arg588*) exon 11] in the uncharacterized CFAP57 gene. In normal human nasal epithelial cells, CFAP57 localizes throughout the ciliary axoneme. Analysis of cells from the PCD patient shows a loss of CFAP57, reduced beat frequency, and an alteration in the ciliary waveform. Knockdown of CFAP57 in human tracheobronchial epithelial cells (hTECs) recapitulates these findings. Phylogenetic analysis showed that CFAP57 is conserved in organisms that assemble motile cilia, and CFAP57 is allelic with the BOP2 gene identified previously in Chlamydomonas. Two independent, insertional fap57 Chlamydomonas mutant strains show reduced swimming velocity and altered waveforms. Tandem mass spectroscopy showed that CFAP57 is missing, and the "g" inner dyneins (DHC7 and DHC3) and the "d" inner dynein (DHC2) are reduced. Our data demonstrate that the FAP57 protein is required for the asymmetric assembly of inner dyneins on only a subset of the microtubule doublets, and this asymmetry is essential for the generation of an effective axonemal waveform. Together, our data identifies mutations in CFAP57 as a cause of PCD with a specific defect in the inner dynein arm assembly process.nnSignificanceMotile cilia are found throughout eukaryotic organisms and performs essential functions. Primary ciliary dyskinesia (PCD) is a rare disease that affects the function of motile cilia. By applying a novel population sampling probability algorithm (PSAP) that uses large population sequencing databases and pathogenicity prediction algorithms, we identified a variant in an uncharacterized gene, CFAP57. This is the first reported example of PCD caused by a mutation that affects only a subset of the inner dynein arms, which are needed to generate the waveform. CFAP57 identifies an address for specific dynein arms. These findings demonstrate the effectiveness of the PSAP algorithm, expand our understanding of the positioning of dynein arms, and identify mutations in CFAP57 as a cause of PCD. ]]> Bustamante Marin, X. Horani, A. Stoyanova, M. Charng, W.-L. Bottier, M. Sears, P. Daniels, L. A. Bowen, H. Conrad, D. Knowles, M. Ostrowski, L. E. Zariwala, M. A. Dutcher, S. K. 2019-09-24 doi:10.1101/773028 Cold Spring Harbor Laboratory Press 2019-09-24 <![CDATA[ G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation ]]> https://biorxiv.org/content/10.1101/781658v1?rss=1 Sargent, L. Liu, Y. Leung, W. Mortimer, N. T. Lopatto, D. Goecks, J. Elgin, S. C. R. 2019-10-02 doi:10.1101/781658 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Chemerin increases T-cell mediated cytotoxicity of human tumors via modulation of a novel CMKLR1/PTEN/PD-L1 axis ]]> https://biorxiv.org/content/10.1101/787697v1?rss=1 Rennier, K. Krug, E. Virdi, G. Shin, W. J. Pachynski, R. 2019-09-30 doi:10.1101/787697 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ Robust organelle size control via bursty growth ]]> https://biorxiv.org/content/10.1101/789453v1?rss=1 Amiri, K. P. Kalish, A. Mukherji, S. 2019-10-01 doi:10.1101/789453 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Homeostatic mechanisms regulate distinct aspects of cortical circuit dynamics ]]> https://biorxiv.org/content/10.1101/790410v1?rss=1 Wu, Y. Hengen, K. B. Turrigiano, G. G. Gjorgjieva, J. 2019-10-02 doi:10.1101/790410 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ ProteoClade: a taxonomic toolkit for multi-species and metaproteomic analysis ]]> https://biorxiv.org/content/10.1101/793455v1?rss=1 Mooradian, A. D. van der Post, S. Naegle, K. M. Held, J. M. 2019-10-07 doi:10.1101/793455 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Structural basis of cowpox evasion of NKG2D immunosurveillance ]]> https://biorxiv.org/content/10.1101/796862v1?rss=1 Lazear, E. Sun, M. M. Wang, X. Geurs, T. L. Nelson, C. A. Campbell, J. A. Lippold, D. Krupnick, A. S. Davis, R. S. Carayannolpoulos, L. N. French, A. R. Fremont, D. H. 2019-10-07 doi:10.1101/796862 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Fatty acid oxidation impairs macrophage effector functions that control Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/799619v1?rss=1 Chandra, P. He, L. Zimmerman, M. Yang, G. Koster, S. Ouimet, M. Wang, H. Moore, K. J. Dartois, V. Schilling, J. D. Philips, J. A. 2019-10-10 doi:10.1101/799619 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Encephalitic alphaviruses exploit caveolae-mediated transcytosis at the blood-brain barrier for CNS entry ]]> https://biorxiv.org/content/10.1101/805945v1?rss=1 Klein, R. S. Salimi, H. Cain, M. D. Jiang, X. Roth, R. Beatty, W. Sun, C. Klimstra, W. B. Hou, J. S. 2019-10-16 doi:10.1101/805945 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ The tip of the VgrG spike is essential to functional type VI secretion assembly in Acinetobacter baumannii ]]> https://biorxiv.org/content/10.1101/808725v1?rss=1 Lopez, J. Ly, P. M. Feldman, M. F. 2019-10-17 doi:10.1101/808725 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Joint phylogenetic estimation of geographic movements and biome shifts during the global diversification of Viburnum ]]> https://biorxiv.org/content/10.1101/811067v1?rss=1 Landis, M. J. Eaton, D. A. R. Clement, W. L. Park, B. Spriggs, E. L. Sweeney, P. W. Edwards, E. J. Donoghue, M. J. 2019-10-21 doi:10.1101/811067 Cold Spring Harbor Laboratory Press 2019-10-21 <![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[ The genetic architecture of human brainstem structures and their involvement in common brain disorders ]]> https://biorxiv.org/content/10.1101/811711v1?rss=1 Elvsashagen, T. Bahrami, S. van der Meer, D. Agartz, I. Alnaes, D. Barch, D. M. Baur-Streubel, R. Bertolino, A. Beyer, M. K. Blasi, G. Borgwardt, S. Boye, B. Buitelaar, J. Boen, E. Celius, E. G. Cervenka, S. Conzelmann, A. Coynel, D. Di Carlo, P. Djurovic, S. Eisenacher, S. Espeseth, T. Fatouros-Bergman, H. Flyckt, L. Franke, B. Frei, O. Gelao, B. Harbo, H. F. Hartman, C. A. Haberg, A. Heslenfeld, D. Hoekstra, P. Hogestol, E. A. Jonassen, R. Jonsson, E. G. Kirsch, P. Kloszewska, I. Lagerberg, T. V. Landro, N. I. Le Hellard, S. Lesch, K.-P. Maglanoc, L. 2019-10-21 doi:10.1101/811711 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Dopamine buffering capacity imaging: A pharmacodynamic fMRI method for staging Parkinson disease ]]> https://biorxiv.org/content/10.1101/817106v1?rss=1 Black, K. J. Acevedo, H. K. Koller, J. M. 2019-10-24 doi:10.1101/817106 Cold Spring Harbor Laboratory Press 2019-10-24 <![CDATA[ NADPH and glutathione redox link TCA cycle activity to endoplasmic reticulum stress ]]> https://biorxiv.org/content/10.1101/822775v1?rss=1 Gansemer, E. R. McCommis, K. S. Martino, M. King-McAlpin, A. Q. Potthoff, M. J. Finck, B. N. Taylor, E. B. Rutkowski, D. T. 2019-10-29 doi:10.1101/822775 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ Gain-of-function genetic screen of the kinome reveals BRSK2 as an inhibitor of the NRF2 transcription factor ]]> https://biorxiv.org/content/10.1101/832279v1?rss=1 Tamir, T. Y. Bowman, B. M. Agajanian, M. J. Goldfarb, D. Schrank, T. P. Stohrer, T. Hale, A. E. Siesser, P. F. Weir, S. J. Murphy, R. M. LaPak, K. M. Weissman, B. E. Moorman, N. J. Major, M. B. 2019-11-05 doi:10.1101/832279 Cold Spring Harbor Laboratory Press 2019-11-05 <![CDATA[ Modeling phylogenetic biome shifts on a planet with a past ]]> https://biorxiv.org/content/10.1101/832527v1?rss=1 Landis, M. J. Edwards, E. J. Donoghue, M. J. 2019-11-07 doi:10.1101/832527 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Removal of high frequency contamination from motion estimates in single-band fMRI saves data without biasing functional connectivity ]]> https://biorxiv.org/content/10.1101/837161v1?rss=1 0.1 Hz, here referred to as HF-motion), primarily in the phase-encoding direction. This periodicity can sometimes be obscured in standard single-band fMRI (TR 2.0 - 2.5 s.) due to aliasing. Here we examined (1) how prevalent HF-motion effects are in seven single-band datasets with TR from 2.0 - 2.5 s and (2) how HF-motion affects functional connectivity. We demonstrate that HF-motion is relatively trait-like and more common in older adults, those with higher body mass index, and those with lower cardiorespiratory fitness. We propose a low-pass filtering approach to remove the contamination of high frequency effects from motion summary measures, such as framewise displacement (FD). We demonstrate that in most datasets this filtering approach saves a substantial amount of data from FD-based frame censoring, while at the same time reducing motion biases in functional connectivity measures. These findings suggest that filtering motion parameters is an effective way to improve the fidelity of head motion estimates, even in single band datasets. Particularly large data savings may accrue in datasets acquired in older and less fit participants. Highlights- Single-band fMRI motion traces show factitious high-frequency content (HF-motion) - The magnitude of HF-motion relates to age and other demographic factors - HF-motion elevates framewise displacement (FD) and causes data loss - Substantial fMRI data can be recovered from censoring by filtering motion traces - Filtering motion traces reduces motion artifacts in functional connectivity ]]> Gratton, C. Coalson, R. S. Dworetsky, A. Adeyemo, B. Laumann, T. O. Wig, G. S. Kong, T. S. Gratton, G. Fabiani, M. Barch, D. M. Tranel, D. Miranda-Dominguez, O. Fair, D. A. Dosenbach, N. U. F. Snyder, A. Z. Perlmutter, J. S. Petersen, S. E. Campbell, M. C. 2019-11-09 doi:10.1101/837161 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Protein prenylation and Hsp40 in thermotolerance of Plasmodium falciparum malaria parasites ]]> https://biorxiv.org/content/10.1101/842468v1?rss=1 Mathews, E. S. Jezewski, A. J. Odom John, A. R. 2019-11-14 doi:10.1101/842468 Cold Spring Harbor Laboratory Press 2019-11-14 <![CDATA[ Diffusion Histology Imaging Detects and Classifies Glioblastoma Pathology Missed by Conventional Magnetic Resonance Imaging ]]> https://biorxiv.org/content/10.1101/843367v1?rss=1 Ye, Z. Price, R. L. Liu, X. Lin, J. Yang, Q. Sun, P. Wu, A. T. Wang, L. Han, R. Song, C. Yang, R. Gary, S. E. Mao, D. D. Wallendorf, M. Campian, J. L. Li, J.-S. Dahiya, S. Kim, A. H. Song, S.-K. 2019-11-16 doi:10.1101/843367 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ Fluorescence correlation spectroscopy and photon count histograms in small domains. Part I: General theory ]]> https://biorxiv.org/content/10.1101/847129v1?rss=1 Elson, E. L. Jiang, Y. Xu, B. Melnykov, A. Genin, G. M. 2019-11-20 doi:10.1101/847129 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Wnt Regulation: Exploring Axin-Disheveled interactions and defining mechanisms by which the SCF E3 ubiquitin ligase is recruited to the destruction complex ]]> https://biorxiv.org/content/10.1101/847384v1?rss=1 Schaefer, K. Pronobis, M. Williams, C. Zhang, S. Bauer, L. Goldfarb, D. Yan, F. Major, M. Peifer, M. 2019-11-20 doi:10.1101/847384 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Light dependent activation of the GCN2 kinase under cold and salt stress is mediated by the photosynthetic status of the chloroplast ]]> https://biorxiv.org/content/10.1101/849257v1?rss=1 Lokdarshi, A. Morgan, P. W. Franks, M. Emert, Z. Emanuel, C. von Arnim, A. G. 2019-11-21 doi:10.1101/849257 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Single Cell RNA Sequencing Reveals Heterogeneity of Human MSC Chondrogenesis: Lasso Regularized Logistic Regression to Identify Gene and Regulatory Signatures ]]> https://biorxiv.org/content/10.1101/854406v1?rss=1 Huynh, N. P. Kelly, N. H. Katz, D. B. Pham, M. Guilak, F. 2019-11-25 doi:10.1101/854406 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Functions of Gtf2i and Gtf2ird1 in the developing brain: transcription, DNA-binding, and long term behavioral consequences. ]]> https://biorxiv.org/content/10.1101/854851v1?rss=1 Kopp, N. D. Nygaard, K. R. McCullough, K. B. Maloney, S. E. Gabel, H. W. Dougherty, J. 2019-11-25 doi:10.1101/854851 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Multiplexed single-cell autism modeling reveals convergent mechanisms altering neuronal differentiation ]]> https://biorxiv.org/content/10.1101/862680v1?rss=1 Lalli, M. A. Avey, D. Dougherty, J. D. Milbrandt, J. Mitra, R. D. 2019-12-03 doi:10.1101/862680 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ Contacting domains that segregate lipid from solute transporters in malaria parasites ]]> https://biorxiv.org/content/10.1101/863993v1?rss=1 Garten, M. Beck, J. R. Roth, R. Tenkova-Heuser, T. Heuser, J. Bleck, C. K. Goldberg, D. E. Zimmerberg, J. 2019-12-06 doi:10.1101/863993 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Genome-wide association study of 40,000 individuals identifies two novel loci associated with bipolar disorder ]]> https://biorxiv.org/content/10.1101/044412v1?rss=1 9 million genetic variants in 9,784 bipolar disorder patients and 30,471 controls, the largest GWAS of BD to date. In this study, to increase power we used ~2,000 lithium-treated cases with a long-term diagnosis of BD from the Consortium on Lithium Genetics, excess controls, and analytic methods optimized for markers on the X-chromosome. In addition to four known loci, results revealed genome-wide significant associations at two novel loci: an intergenic region on 9p21.3 (rs12553324, p = 5.87x10-9; odds ratio = 1.12) and markers within ERBB2 (rs2517959, p = 4.53x10-9; odds ratio = 1.13). No significant X-chromosome associations were detected and X-linked markers explained very little BD heritability. The results add to a growing list of common autosomal variants involved in BD and illustrate the power of comparing well-characterized cases to an excess of controls in GWAS. ]]> Liping Hou Sarah E Bergen Nirmala Akula Jie Song Christina M Hultman Mikael Landen Mazda Adli Martin Alda Raffaella Ardau Barbara Arias Jean-Michel Aubry Lena Backlund Judith A Badner Thomas B Barrett Michael Bauer Bernhard T Baune Frank Bellivier Antonio Benabarre Susanne Bengesser Wade H Berrettini Abesh Kumar Bhattacharjee Joanna M Biernacka Armin Birner Cinnamon S Bloss Clara Brichant-Petitjean Elise T Bui William Byerley Pablo Cervantes Caterina Chillotti Sven Cichon Francesc Colom William Coryell David W Craig Cristiana Cruceanu Piotr M Czerski Tony Davis Alexandre Dayer Franziska Degenh 2016-03-22 doi:10.1101/044412 Cold Spring Harbor Laboratory Press 2016-03-22 <![CDATA[ Components Of Alcohol Use And All-Cause Mortality ]]> https://biorxiv.org/content/10.1101/129270v1?rss=1 Hartz, S. Oehlert, M. Horton, A. C. Grucza, R. Fisher, S. L. Nelson, K. G. Sumerall, S. W. Neal, C. Regnier, P. Chen, G. Williams, A. Bhattarai, J. Evanoff, B. Bierut, L. J. 2017-04-21 doi:10.1101/129270 Cold Spring Harbor Laboratory Press 2017-04-21 <![CDATA[ Macrophage-to-sensory neuron crosstalk mediated by Angiotensin II type-2 receptor elicits neuropathic pain ]]> https://biorxiv.org/content/10.1101/166546v1?rss=1 Shepherd, A. J. Mickle, A. D. Copits, B. A. Karlsson, P. Kadunganattil, S. Golden, J. P. Tadinada, S. M. Mack, M. R. Haroutounian, S. de Kloet, A. D. Samineni, V. K. Valtcheva, M. V. McIlvried, L. A. Sheahan, T. D. Jain, S. Ray, P. R. Usachev, Y. M. Dussor, G. Kim, B. S. Krause, E. G. Price, T. J. Gereau, R. W. Mohapatra, D. P. 2017-08-25 doi:10.1101/166546 Cold Spring Harbor Laboratory Press 2017-08-25 <![CDATA[ Genome-wide analysis of risk-taking behaviour and cross-disorder genetic correlations in 116,255 individuals from the UK Biobank cohort ]]> https://biorxiv.org/content/10.1101/177014v1?rss=1 Strawbridge, R. J. Ward, J. Cullen, B. Tunbridge, E. M. Hartz, S. Bierut, L. Horton, A. Bailey, M. E. S. Graham, N. Ferguson, A. Lyall, D. M. Mackay, D. Pidgeon, L. M. Cavanagh, J. Pell, J. P. O'Donovan, M. Escott-Price, V. Harrison, P. J. Smith, D. J. 2017-08-16 doi:10.1101/177014 Cold Spring Harbor Laboratory Press 2017-08-16 <![CDATA[ Hippocampal volume in Provisional Tic Disorder predicts tic severity at 12-month follow-up ]]> https://biorxiv.org/content/10.1101/2020.02.05.935908v1?rss=1 Kim, S. Greene, D. J. Badke D'Andrea, C. Bihun, E. C. Koller, J. M. O'Reilly, B. Schlaggar, B. L. Black, K. J. 2020-02-07 doi:10.1101/2020.02.05.935908 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Functional Ensemble Survival Tree: Dynamic Prediction of Alzheimer's Disease Progression Accommodating Multiple Time-Varying Covariates ]]> https://biorxiv.org/content/10.1101/2020.02.17.952994v1?rss=1 Jiang, S. Xie, Y. Colditz, G. A. 2020-02-19 doi:10.1101/2020.02.17.952994 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Ascending dorsal column sensory neurons respond to spinal cord injury anddownregulate genes related to lipid metabolism ]]> https://biorxiv.org/content/10.1101/2020.05.07.083584v1?rss=1 Ewan, E. E. Carlin, D. Goncalves, T. M. Zhao, G. Cavalli, V. 2020-05-09 doi:10.1101/2020.05.07.083584 Cold Spring Harbor Laboratory Press 2020-05-09 <![CDATA[ REV-ERBalpha mediates complement expression and circadian regulation of microglial synaptic phagocytosis ]]> https://biorxiv.org/content/10.1101/2020.05.11.088443v1?rss=1 Griffin, P. Sheehan, P. W. Dimitry, J. M. Guo, C. Kanan, M. F. Lee, J. Zhang, J. Musiek, E. S. 2020-05-13 doi:10.1101/2020.05.11.088443 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ SARS-CoV-2 infection in the lungs of human ACE2 transgenic mice causes severe inflammation, immune cell infiltration, and compromised respiratory function ]]> https://biorxiv.org/content/10.1101/2020.07.09.196188v1?rss=1 Emma S Winkler Adam L Bailey Natasha M Kafai Sharmila Nair Broc T McCune Jinsheng Yu Julie M Fox Rita E Chen James T Earnest Shamus P Keeler Jon H Ritter Liang-I Kang Sarah Dort Annette Robichaud Richard Head Michael J Holtzman Michael S Diamond 2020-07-10 doi:10.1101/2020.07.09.196188 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Mechanical overstimulation causes acute injury followed by fast recovery in lateral-line neuromasts of larval zebrafish ]]> https://biorxiv.org/content/10.1101/2020.07.15.205492v1?rss=1 Holmgren, M. Ravicz, M. E. Hancock, K. E. Strelkova, O. Indzhykulian, A. A. Warchol, M. E. Sheets, L. 2020-07-17 doi:10.1101/2020.07.15.205492 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Digital spatial profiling of coronary plaques from persons living with HIV reveals high levels of STING and CD163 in macrophage enriched regions ]]> https://biorxiv.org/content/10.1101/2020.07.28.221325v1?rss=1 View larger version (51K): org.highwire.dtl.DTLVardef@1a4757forg.highwire.dtl.DTLVardef@1e2236org.highwire.dtl.DTLVardef@582f4borg.highwire.dtl.DTLVardef@188f376_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Characterization of coronary plaques. Representative coronary plaques from three HIV-positive and three HIV-negative individuals were stained with H&E and Movat stain (A). Plaque area (m2) and % plaque stenosis were measured and calculated in 6 individuals per group (B). Statistical analysis, Mann-Whitney; ns not significant C_FIG ConclusionsIncreased inflammation within the coronary plaques of PLWH is characterized by more innate and adaptive immune cells. Higher STING expression in PLWH suggests that immune response to viral antigens within the plaque might be a driver above other stimulants. STING inhibitors are available and could be investigated as a future therapeutic target in PWH if these results are replicated with a larger number of plaques. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/221325v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@27fa00org.highwire.dtl.DTLVardef@8e4a65org.highwire.dtl.DTLVardef@1b65320org.highwire.dtl.DTLVardef@10b7c9a_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIImmunohistochemical and fluorescent stains combined with GeoMx(R) digital spatial profiling allowed for deep characterization of immune cells within intact coronary plaques and perivascular adipose tissue C_LIO_LICoronary plaques from HIV-positive persons had higher proportion of CD163+ immune cells compared to HIV-negative persons C_LIO_LIDifferential protein expression of immune-rich regions of interest within intact 5m sections of coronary plaques revealed higher levels of stimulator of interferon gamma (STING) in HIV-positive persons C_LI ]]> Wanjalla, C. N. Guo, L. Fuller, D. T. Mashayekhi, M. Bailin, S. Gabriel, C. L. Temu, T. Gong, J. Liang, Y. Virmani, R. Finn, A. V. Kalams, S. A. Mallal, S. A. Miner, J. Beckman, J. A. Koethe, J. R. 2020-07-29 doi:10.1101/2020.07.28.221325 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ SLO2.1 and NALCN form a functional complex to modulate myometrial cell excitability ]]> https://biorxiv.org/content/10.1101/2020.07.31.229138v1?rss=1 Ferreira, J. J. Amazu, C. Puga-Molina, L. C. England, S. K. Santi, C. M. 2020-08-03 doi:10.1101/2020.07.31.229138 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Sequence- and structure-specific cytosine-5 mRNA methylation by NSUN6 ]]> https://biorxiv.org/content/10.1101/2020.10.01.320036v1?rss=1 Selmi, T. Hussain, S. Dietmann, S. Heiss, M. Carter, J.-M. Dennison, R. Flad, S. Huang, Y.-L. Kellner, S. Borneloev, S. Frye, M. 2020-10-01 doi:10.1101/2020.10.01.320036 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Oncometabolism Drives Autophagy Activation in Skeletal Muscle ]]> https://biorxiv.org/content/10.1101/2020.10.13.338202v1?rss=1 Karlstaedt, A. Vitrac, H. Salazar, R. L. Gould, B. D. Soedkamp, D. Spivia, W. Raedschelders, K. Dinh, A. Q. Guzman, A. Tan, L. Azinas, S. Taylor, D. J. R. Schiffer, W. McNavish, D. Burks, H. B. Gottlieb, R. A. Lorenzi, P. L. Hanson, B. Van Eyk, J. E. Taegtmeyer, H. 2020-10-14 doi:10.1101/2020.10.13.338202 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Biofilm Formation and Virulence of Shigella flexneri is Modulated by pH of Gastrointestinal Tract ]]> https://biorxiv.org/content/10.1101/2020.10.16.336651v1?rss=1 Chiang, I.-L. Wang, Y. Fujii, S. Muegge, B. Lu, Q. Stappenbeck, T. 2020-10-16 doi:10.1101/2020.10.16.336651 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Non-lesioned subcortical brain volumes are associated with post-stroke sensorimotor behavior across 28 cohorts worldwide: An ENIGMA Stroke Recovery study ]]> https://biorxiv.org/content/10.1101/2020.11.04.366856v1?rss=1 Liew, S.-L. Zavaliangos-Petropulu, A. Schweighofer, N. Jahanshad, N. Lang, C. E. Lohse, K. R. Banaj, N. Barisano, G. Baugh, L. A. Bhattacharya, A. K. Bigjahan, B. Borich, M. R. Boyd, L. A. Brodtmann, A. Buetefisch, C. M. Byblow, W. D. Cassidy, J. M. Ciullo, V. Conforto, A. B. Craddock, R. C. Dula, A. N. Egorova, N. Feng, W. Fercho, K. A. Gregory, C. M. Hanlon, C. A. Hayward, K. S. Holguin, J. A. Hordacre, B. Hwang, D. H. Kautz, S. A. Khlif, M. S. Kim, B. Kuceyeski, A. Liu, J. Lin, D. Lotze, M. Kim, H. MacIntosh, B. J. Margetis, J. L. Mohamed, F. B. Nord 2020-11-05 doi:10.1101/2020.11.04.366856 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ A Non-Negative Tensor Factorization Approach to Deconvolute Microenvironment in Breast Cancer ]]> https://biorxiv.org/content/10.1101/2020.12.01.406249v1?rss=1 Shi, M. Klindziuk, L. Mollah, S. 2020-12-02 doi:10.1101/2020.12.01.406249 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Revealing the Physiological Origin of Event-Related Potentials using Electrocorticography in Humans ]]> https://biorxiv.org/content/10.1101/2021.02.12.430921v1?rss=1 Cho, H. Schalk, G. Adamek, M. Moheimanian, L. Coon, W. G. Jun, S. C. Wolpaw, J. R. Brunner, P. 2021-02-16 doi:10.1101/2021.02.12.430921 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Small molecule SWELL1-LRRC8 complex induction improves glycemic control and nonalcoholic fatty liver disease in murine Type 2 diabetes ]]> https://biorxiv.org/content/10.1101/2021.02.28.432901v1?rss=1 Gunasekar, S. K. Xie, L. Chheda, P. R. Kang, C. Kern, D. M. My-Ta, C. Kumar, A. Maurer, J. M. Gerber, E. E. Grzesik, W. J. Elliot-Hudson, M. Zhang, Y. Kulkarni, C. A. Samuel, I. Smith, J. K. Nau, P. Imai, Y. Sheldon, R. D. Taylor, E. B. Lerner, D. J. Norris, A. W. Brohawn, S. G. Kerns, R. Sah, R. 2021-03-02 doi:10.1101/2021.02.28.432901 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Neuronal mechanisms of novelty seeking ]]> https://biorxiv.org/content/10.1101/2021.03.12.435019v1?rss=1 Ogasawara, T. Sogukpinar, F. Zhang, K. Feng, Y.-Y. Pai, J. Jezzini, A. Monosov, I. E. 2021-03-13 doi:10.1101/2021.03.12.435019 Cold Spring Harbor Laboratory Press 2021-03-13 <![CDATA[ A public vaccine-induced human antibody protects against SARS-CoV-2 and emerging variants ]]> https://biorxiv.org/content/10.1101/2021.03.24.436864v1?rss=1 Schmitz, A. J. Turner, J. S. Liu, Z. Aziati, I. D. Chen, R. E. Joshi, A. Bricker, T. L. Darling, T. L. Adelsberg, D. C. Al Soussi, W. B. Case, J. B. Lei, T. Thapa, M. Amanat, F. O'Halloran, J. A. Shi, P.-Y. Presti, R. M. Krammer, F. Bajic, G. Whelan, S. P. J. Diamond, M. S. Boon, A. C. M. Ellebedy, A. H. 2021-03-25 doi:10.1101/2021.03.24.436864 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Temporal specificity of abnormal neural oscillations during phonatory events in Laryngeal Dystonia ]]> https://biorxiv.org/content/10.1101/2021.04.08.438908v1?rss=1 Kothare, H. Schneider, S. Mizuiri, D. Hinkley, L. Bhutada, A. Ranasinghe, K. Honma, S. Garrett, C. Klein, D. Naunheim, M. Yung, K. Cheung, S. Rosen, C. Courey, M. Nagarajan, S. Houde, J. 2021-04-08 doi:10.1101/2021.04.08.438908 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Influence of Mpv17 on hair-cell mitochondrial homeostasis, synapse integrity, and vulnerability to damage in the zebrafish lateral line ]]> https://biorxiv.org/content/10.1101/2021.04.12.439521v1?rss=1 Holmgren, M. Sheets, L. 2021-04-14 doi:10.1101/2021.04.12.439521 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Increased mitochondrial activity upon CatSper channel activation is required for sperm capacitation. ]]> https://biorxiv.org/content/10.1101/2021.05.04.442630v1?rss=1 Ferreira, J. J. Cassina, A. Irigoyen, P. Ford, M. Pietroroia, S. Radi, R. Santi, C. M. Sapiro, R. 2021-05-04 doi:10.1101/2021.05.04.442630 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Brain structure and function predict adherence to an exercise intervention in older adults ]]> https://biorxiv.org/content/10.1101/2021.07.30.454451v1?rss=1 Morris, T. P. Burzynska, A. Voss, M. Fanning, J. Salerno, E. A. Prakash, R. Gothe, N. P. Whitfield-Gabrieli, S. Hillman, C. H. McAuley, E. Kramer, A. F. 2021-08-01 doi:10.1101/2021.07.30.454451 Cold Spring Harbor Laboratory Press 2021-08-01 <![CDATA[ Human KIR+CD8+ T cells target pathogenic T cells in Celiac disease and are active in autoimmune diseases and COVID-19 ]]> https://biorxiv.org/content/10.1101/2021.12.23.473930v1?rss=1 Li, J. Zaslavsky, M. E. Su, Y. Sikora, M. van Unen, V. Christophersen, A. Chiou, S.-H. Chen, L. Li, J. Ji, X. Wilhelmy, J. McSween, A. Palanski, B. A. Mallajosyula, V. Dhondalay, G. Bhamidipati, K. Pai, J. Kipp, L. Dunn, J. Hauser, S. Oksenberg, J. Satpathy, A. Robinson, W. Steinmetz, L. Khosla, C. Utz, P. Sollid, L. M. Heath, J. Fernandez-Becker, N. Nadeau, K. Saligrama, N. Davis, M. 2021-12-25 doi:10.1101/2021.12.23.473930 Cold Spring Harbor Laboratory Press 2021-12-25 <![CDATA[ Permethylation of ribonucleosides provides enhanced mass spectrometry quantification of post-transcriptional modifications ]]> https://biorxiv.org/content/10.1101/2022.01.26.477959v1?rss=1 View larger version (16K): org.highwire.dtl.DTLVardef@a16649org.highwire.dtl.DTLVardef@424b26org.highwire.dtl.DTLVardef@53d701org.highwire.dtl.DTLVardef@48a9cd_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Xie, Y. Janssen, K. A. Scacchetti, A. Bonasio, R. Garcia, B. A. 2022-01-27 doi:10.1101/2022.01.26.477959 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ Encoding and decoding analysis of music perception using intracranial EEG ]]> https://biorxiv.org/content/10.1101/2022.01.27.478085v1?rss=1 Bellier, L. Llorens, A. Marciano, D. Schalk, G. Brunner, P. Knight, R. T. Pasley, B. N. 2022-01-28 doi:10.1101/2022.01.27.478085 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Context-dependent triggering of STING-interferon signaling by CD11b agonists supports anti-tumor immunity in mouse models and human cancer patients ]]> https://biorxiv.org/content/10.1101/2022.03.22.485233v1?rss=1 Liu, X. Hogg, G. D. zuo, c. Baer, J. M. Lander, V. E. Kang, L. Borcherding, N. C. Knolhoff, B. L. Osterhout, R. E. Galkin, A. V. Bruey, J. M. Carter, L. L. Mpoy, C. Schwarz, J. K. Park, H. Gupta, V. DeNardo, D. 2022-03-23 doi:10.1101/2022.03.22.485233 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ MFGE8 links absorption of dietary fatty acids with catabolism of enterocyte lipid stores through HNF4 γ- dependent transcription of CES enzymes ]]> https://biorxiv.org/content/10.1101/2022.05.16.492147v1?rss=1 Datta, R. Gholampour, M. A. Yang, C. D. Volk, R. Lin, S. Podolsky, M. J. Arnold, T. Rieder, F. Zaro, B. W. Verzi, M. Lehner, R. Abumrad, N. Lizama, C. O. Atabai, K. 2022-05-18 doi:10.1101/2022.05.16.492147 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ CREWdb: Optimizing Chromatin Readers, Erasers, and Writers Database using Machine Learning-Based Approach ]]> https://biorxiv.org/content/10.1101/2022.06.02.494594v1?rss=1 Natesan, M. Kong, M. Shi, M. Ghag, R. Mollah, S. A. 2022-06-04 doi:10.1101/2022.06.02.494594 Cold Spring Harbor Laboratory Press 2022-06-04 <![CDATA[ Swapped genetic code blocks viral infections and gene transfer ]]> https://biorxiv.org/content/10.1101/2022.07.08.499367v1?rss=1 Nyerges, A. Vinke, S. Flynn, R. Owen, S. V. Rand, E. A. Budnik, B. Keen, E. Narasimhan, K. Marchand, J. A. Baas-Thomas, M. Liu, M. Chen, K. Chiappino-Pepe, A. Hu, F. Baym, M. Church, G. M. 2022-07-10 doi:10.1101/2022.07.08.499367 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ A neural mechanism for conserved value computations integrating information and rewards ]]> https://biorxiv.org/content/10.1101/2022.08.14.503903v1?rss=1 Bromberg-Martin, E. S. Feng, Y.-Y. Ogasawara, T. White, J. K. Zhang, K. Monosov, I. E. 2022-08-15 doi:10.1101/2022.08.14.503903 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Concentration of 2’C-methyladenosine triphosphate by Leishmania guyanensis enables specific inhibition of Leishmania RNA virus 1 via its RNA polymerase ]]> https://biorxiv.org/content/10.1101/261172v1?rss=1 Robinson, J. I. Beverley, S. M. 2018-02-07 doi:10.1101/261172 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ Deep Learning Global Glomerulosclerosis in Transplant Kidney Frozen Sections ]]> https://biorxiv.org/content/10.1101/292789v1?rss=1 Marsh, J. N. Matlock, M. K. Kudose, S. Liu, T.-C. Stappenbeck, T. S. Gaut, J. P. Swamidass, S. J. 2018-04-02 doi:10.1101/292789 Cold Spring Harbor Laboratory Press 2018-04-02 <![CDATA[ Cell type specific profiling of alternative translation identifies novel protein isoforms in the mouse brain ]]> https://biorxiv.org/content/10.1101/324236v1?rss=1 Sapkota, D. Lake, A. M. Yang, W. Yang, C. Wesseling, H. Guise, A. Uncu, C. Dalal, J. S. Kraft, A. Lee, J.-M. Sands, M. S. Steen, J. A. Dougherty, J. D. 2018-05-16 doi:10.1101/324236 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Cell-autonomous regulation of astrocyte activation by the circadian clock protein BMAL1 ]]> https://biorxiv.org/content/10.1101/362814v1?rss=1 Lananna, B. V. Nadarajah, C. J. Izumo, M. Cedeno, M. R. Xiong, D. D. Dimitry, J. Tso, C. F. McKee, C. A. Griffin, P. Sheehan, P. W. Haspel, J. A. Barres, B. A. Liddelow, S. A. Takahashi, J. S. Karatsoreos, I. N. Musiek, E. S. 2018-07-05 doi:10.1101/362814 Cold Spring Harbor Laboratory Press 2018-07-05 <![CDATA[ A smartphone-based tool for rapid, portable, and automated wide-field retinal imaging ]]> https://biorxiv.org/content/10.1101/364265v1?rss=1 Kim, T. Myers, F. Reber, C. Loury, P. Loumou, P. Webster, D. Echanique, C. Li, P. Davila, J. Maamari, R. Switz, N. Keenan, J. Woodward, M. Paulus, Y. Margolis, T. Fletcher, D. 2018-07-07 doi:10.1101/364265 Cold Spring Harbor Laboratory Press 2018-07-07 <![CDATA[ Somatically Mutated Genes Under Positive and Negative Selection Found by Transcriptome Sequence Analysis Include Oncogene and Tumor Suppressor Candidates ]]> https://biorxiv.org/content/10.1101/396739v1?rss=1 1, padj <0.05). Our GWAS identified 2 sites associated with post-transcriptional modification (1 approaching significance with p=5.99x10-8, 1 with p<5x10-8) and [~]20 sites associated with somatic mutation burden (p<5x10- 8).nnConclusionsTo our knowledge these are the first genome-wide association studies on normal somatic mutation burden. These studies were an attempt to increase understanding of the somatic mutation process. Our work identified somatic mutations at the global organismal level that may promote cell proliferation in a tissue-specific manner. By identifying tissue-specific mutations in actively expressed genes that appear before cancer phenotype is detected, this work also identifies gene candidates that might initiate tumorigenesis. ]]> Drubin, C. W. Ramu, A. Rockweiler, N. B. Conrad, D. F. 2018-08-21 doi:10.1101/396739 Cold Spring Harbor Laboratory Press 2018-08-21 <![CDATA[ Analysis of whole genome-transcriptomic organization in brain to identify genes associated with alcoholism ]]> https://biorxiv.org/content/10.1101/500439v1?rss=1 Kapoor, M. Wang, J.-C. Farris, S. P. Liu, Y. McClintick, J. Gupta, I. Meyers, J. L. Bertelsen, S. Chao, M. Nurnberger, J. Tischfield, J. Harari, O. Zeran, L. Hesselbroc, V. Bauer, L. Raj, T. Porjesz, B. Agrawal, A. Foroud, T. Edenberg, H. Mayfield, R. D. Goate, A. 2018-12-19 doi:10.1101/500439 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Farnesyl Transferase Inhibition for the Treatment of Tauopathies ]]> https://biorxiv.org/content/10.1101/500801v1?rss=1 Hernandez, I. Luna, G. Rauch, J. N. Giroux, M. Karch, C. M. Boctor, D. Storm, N. J. Diaz, A. Zekanowski, C. Kang, A. A. Hinman, C. Cerovac, V. Guzman, E. Zhou, H. Goate, A. Fisher, S. K. Cuervo, A. M. Kosik, K. S. 2018-12-18 doi:10.1101/500801 Cold Spring Harbor Laboratory Press 2018-12-18 <![CDATA[ SEQUIN multiscale imaging of mammalian central synapses reveals loss of synaptic microconnectivity resulting from diffuse traumatic brain injury ]]> https://biorxiv.org/content/10.1101/704916v1?rss=1 Sauerbeck, A. D. Gangolli, M. Reitz, S. J. Salyards, M. H. Kim, S. H. Hemingway, C. Makkapati, T. Kerschensteiner, M. Brody, D. L. Kummer, T. T. 2019-07-16 doi:10.1101/704916 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ Shared Genetic Risk between Eating Disorder- and Substance-Use-Related Phenotypes: Evidence from Genome-Wide Association Studies ]]> https://biorxiv.org/content/10.1101/741512v1?rss=1 Munn-Chernoff, M. Johnson, E. C. Chou, Y.-L. Coleman, J. R. Thornton, L. M. Walters, R. K. Yilmaz, Z. Baker, J. Hubel, C. Gordon, S. Medland, S. Watson, H. Gaspar, H. A. Bryois, J. Hinney, A. Leppa, V. Mattheisen, M. Ripke, S. Yao, S. Giusti-Rodriguez, P. Hanscombe, K. B. Adan, R. Alredsson, L. Ando, T. Andreassen, O. A. Berrettini, W. Boehm, I. Boni, C. Boraska Perica, V. Buehren, K. Burghardt, R. Cassina, M. Cichon, S. Clementi, M. Cone, R. Courtet, P. Crow, S. Crowley, J. J. Danner, U. Davis, O. de Zwaan, M. Dedoussis, G. Degortes, D. DeSocio, J. 2019-08-23 doi:10.1101/741512 Cold Spring Harbor Laboratory Press 2019-08-23 <![CDATA[ The Angiosarcoma Project: enabling genomic and clinical discoveries in a rare cancer through patient-partnered research ]]> https://biorxiv.org/content/10.1101/741744v1?rss=1 Painter, C. A. Jain, E. Tomson, B. N. Dunphy, M. Stoddard, R. E. Thomas, B. S. Damon, A. L. Shah, S. Kim, D. Gomez Tejeda Zanudo, J. Hornick, J. L. Chen, Y.-L. Merriam, P. Raut, C. P. Demetri, G. D. Van Tine, B. A. Lander, E. S. Golub, T. Wagle, N. 2019-08-26 doi:10.1101/741744 Cold Spring Harbor Laboratory Press 2019-08-26 <![CDATA[ Novel genetic determinants of telomere length from a multi-ethnic analysis of 75,000 whole genome sequences in TOPMed ]]> https://biorxiv.org/content/10.1101/749010v1?rss=1 1 independent signal. Fine-mapping at OBFC1 indicated the independent signals colocalized with cell-type specific eQTLs for OBFC1 (STN1). We further identified two novel genes, DCLRE1B (SNM1B) and PARN, using a multi-variant gene-based approach. ]]> Taub, M. A. Weinstock, J. S. Iyer, K. R. Yanek, L. R. Conomos, M. P. NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Reiner, A. P. Mathias, R. A. 2019-09-04 doi:10.1101/749010 Cold Spring Harbor Laboratory Press 2019-09-04 <![CDATA[ Dissecting the chitinolytic activity of mammalian chitinases ]]> https://biorxiv.org/content/10.1101/762336v1?rss=1 Barad, B. A. Liu, L. Diaz, R. E. Basilio, R. Van Dyken, S. J. Locksley, R. M. Fraser, J. S. 2019-09-08 doi:10.1101/762336 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ An enhancer:involucrin regulatory module impacts human skin barrier adaptation out-of-Africa and modifies atopic dermatitis risk ]]> https://biorxiv.org/content/10.1101/816520v1?rss=1 Mathyer, M. E. Brettmann, E. A. Schmidt, A. D. Goodwin, Z. A. Quiggle, A. M. Oh, I. Y. Tycksen, E. Zhou, L. Estrada, Y. D. Wong, X. F. C. C. Denil, S. L. Matkovich, S. A. Shemer, A. Common, J. E. Guttman-Yassky, E. de Guzman Strong, C. 2019-11-05 doi:10.1101/816520 Cold Spring Harbor Laboratory Press 2019-11-05 <![CDATA[ Oncologic Therapy Shapes the Fitness Landscape of ClonalHematopoiesis ]]> https://biorxiv.org/content/10.1101/848739v1?rss=1 Bolton, K. L. Ptashkin, R. N. Gao, T. Braunstein, L. Devlin, S. M. Kelly, D. Patel, M. Berthon, A. Syed, A. Yabe, M. Coombs, C. Caltabellotta, N. M. Walsh, M. Offit, K. Stadler, Z. Mandelker, D. Schulman, J. W. Patel, A. Philip, J. Bernard, E. Gundem, G. Arango, J. E. Levine, M. Medina, J. S. Farnhoud, N. Glodzik, D. Li, S. Robson, M. E. Lee, C. Pharoah, P. Stopsack, K. Spitzer, B. Mantha, S. Fagin, J. Boucai, L. Gibson, C. J. Ebert, B. L. Young, A. L. Druley, T. Takahashi, K. Gillis, N. Ball, M. Padron, E. Hyman, D. M. Baselga, J. Norton, L. Gardo 2019-11-20 doi:10.1101/848739 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts ]]> https://biorxiv.org/content/10.1101/861393v1?rss=1 Woo, X. Y. Giordano, J. Srivastava, A. Zhao, Z.-M. Lloyd, M. W. de Bruijn, R. Suh, Y.-S. Patidar, R. Chen, L. Scherer, S. Bailey, M. Yang, C.-H. Cortes-Sanchez, E. Xi, Y. Wang, J. Wickramasinghe, J. Kossenkov, A. V. Rebecca, V. Sun, H. Mashl, R. J. Davies, S. Jeon, R. Frech, C. Randjelovic, J. Rosains, J. Galimi, F. Bertotti, A. Lafferty, A. O'Farrell, A. C. Modave, E. Lambrechts, D. ter Brugge, P. Serra, V. Marangoni, E. El Botty, R. Kim, H. Kim, J.-I. Yang, H.-K. Lee, C. Dean, D. A. Davis-Dusenbery, B. Evrard, Y. Doroshow, J. Welm, A. L. Welm, B. E 2019-12-03 doi:10.1101/861393 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ Embryonic Vitamin D Deficiency Programs Hematopoietic Stem Cells to Induce Type 2 Diabetes ]]> https://biorxiv.org/content/10.1101/2022.09.08.507174v1?rss=1 Bernal-Mizrachi, C. Oh, J. Riek, A. E. Bauerle, K. T. Dusso, A. McNerney, K. Barve, R. Darwech, I. Sprague, J. Moynihan, C. Zhang, R. M. Wang, T. Xing, X. Li, D. Head, R. D. Bambouskova, M. Mrad, M. Collins, A. Sands, M. S. 2022-09-12 doi:10.1101/2022.09.08.507174 Cold Spring Harbor Laboratory Press 2022-09-12 <![CDATA[ Defining Cardiac Recovery at Single Cell Resolution ]]> https://biorxiv.org/content/10.1101/2022.09.11.507463v1?rss=1 Amrute, J. M. Lai, L. Ma, P. Koenig, A. L. Kamimoto, K. Bredemeyer, A. Shankar, T. S. Kuppe, C. Kadyrov, F. F. Schulte, L. J. Stoutenburg, D. Kopecky, B. Navankasattusas, S. Visker, J. Morris, S. A. Kramann, R. Leuschner, F. Mann, D. L. Drakos, S. G. Lavine, K. J. 2022-09-13 doi:10.1101/2022.09.11.507463 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Quantifying coexistence concentrations in multi-component phase-separating systems using analytical HPLC ]]> https://biorxiv.org/content/10.1101/2022.09.11.507495v1?rss=1 Bremer, A. Posey, A. E. Borgia, M. B. Borcherds, W. M. Farag, M. Pappu, R. V. Mittag, T. 2022-09-13 doi:10.1101/2022.09.11.507495 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Bivalent SARS-CoV-2 mRNA vaccines increase breadth of neutralization and protect against the BA.5 Omicron variant ]]> https://biorxiv.org/content/10.1101/2022.09.12.507614v1?rss=1 Scheaffer, S. M. Lee, D. Whitener, B. Ying, B. Wu, K. Jani, H. Martin, P. Amato, N. J. Avena, L. E. Berrueta, D. M. Schmidt, S. D. O'Dell, S. Nasir, A. Chuang, G.-Y. Stewart-Jones, G. Koup, R. A. Doria-Rose, N. A. Carfi, A. Elbashir, S. M. Thackray, L. B. Edwards, D. K. Diamond, M. S. 2022-09-13 doi:10.1101/2022.09.12.507614 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Evolutionary crowdsourcing: alignment of fitness landscapes allows cross-species adaptation of a horizontally transferred gene ]]> https://biorxiv.org/content/10.1101/2022.09.13.507827v1?rss=1 Kosterlitz, O. Grassi, N. Werner, B. McGee, R. S. Top, E. M. Kerr, B. 2022-09-15 doi:10.1101/2022.09.13.507827 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Dentate gyrus morphogenesis is regulated by β-CATENIN function in hem-derived fimbrial glia. ]]> https://biorxiv.org/content/10.1101/2022.09.15.508086v1?rss=1 Parichha, A. Datta, D. Suresh, V. Chatterjee, M. Holtzman, M. J. Tole, S. 2022-09-15 doi:10.1101/2022.09.15.508086 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Acute hyper- and hypoglycemia uncouples the metabolic cooperation between glucose and lactate to disrupt sleep ]]> https://biorxiv.org/content/10.1101/2022.09.15.507967v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@9102eborg.highwire.dtl.DTLVardef@5699c5org.highwire.dtl.DTLVardef@1897ebeorg.highwire.dtl.DTLVardef@1e00661_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Carroll, C. M. Stanley, M. Raut, R. V. Constantino, N. J. Irmen, R. E. Mitra, A. Snipes, J. A. Raichle, M. E. Holtzman, D. M. Gould, R. W. Kishida, K. T. Macauley, S. L. 2022-09-17 doi:10.1101/2022.09.15.507967 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Multi-omics data integration via novel interpretable k-hop graph attention network for signaling network inference ]]> https://biorxiv.org/content/10.1101/2022.09.16.508281v1?rss=1 Yuan, R. Feng, J. Zhang, H. Chen, Y. Payne, P. R. Li, F. 2022-09-17 doi:10.1101/2022.09.16.508281 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ The cingulo-opercular network is composed of two distinct sub-systems ]]> https://biorxiv.org/content/10.1101/2022.09.16.508254v1?rss=1 Gratton, C. Dworetsky, A. Adeyemo, B. Seitzman, B. A. Smith, D. M. Petersen, S. E. Neta, M. 2022-09-18 doi:10.1101/2022.09.16.508254 Cold Spring Harbor Laboratory Press 2022-09-18 <![CDATA[ Genetic, clinical underpinnings of subtle early brain change along Alzheimer's dimensions ]]> https://biorxiv.org/content/10.1101/2022.09.16.508329v1?rss=1 WEN, J. Yang, Z. Nasrallah, I. Cui, Y. Erus, G. Srinivasan, D. Abdulkadir, A. Mamourian, E. Hwang, G. Singh, A. Bergman, M. Bao, J. Varol, E. Zhou, Z. Boquet-Pujadas, A. Chen, J. Toga, A. W. Saykin, A. J. Hohman, T. Thompson, P. Villeneuve, S. Gollub, R. Sotiras, A. Wittfeld, K. Grabe, H. Tosun, D. Bilgel, M. An, Y. Marcus, D. LaMontagne, P. J. Heckbert, S. Austin, T. Launer, L. Espeland, M. Masters, C. Maruff, P. Fripp, J. Johnson, S. C. Morris, j. Albert, M. Nick, R. Resnick, S. M. Ferrucci, L. Fan, Y. Mohamad, H. Wolk, D. Shen, L. Shou, H. Dav 2022-09-19 doi:10.1101/2022.09.16.508329 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ SHEPHARD: a modular and extensible software architecture for analyzing and annotating large protein datasets ]]> https://biorxiv.org/content/10.1101/2022.09.18.508433v1?rss=1 Ginell, G. M. Flynn, A. J. Holehouse, A. S. 2022-09-19 doi:10.1101/2022.09.18.508433 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ The incidence of candidate binding sites for β-arrestin in Drosophila neuropeptide GPCRs ]]> https://biorxiv.org/content/10.1101/2022.09.19.508524v1?rss=1 Taghert, P. H. 2022-09-20 doi:10.1101/2022.09.19.508524 Cold Spring Harbor Laboratory Press 2022-09-20 <![CDATA[ Loss of estrogen unleashing neuro-inflammation increases the risk of Alzheimer's disease in women ]]> https://biorxiv.org/content/10.1101/2022.09.19.508592v1?rss=1 Li, F. Oh, I. Kumar, S. Eteleeb, A. Gupta, A. Buchser, W. Xiong, C. Cole, S. F. McDade, E. Karch, C. Harari, O. Payne, P. R. Cruchaga, C. 2022-09-20 doi:10.1101/2022.09.19.508592 Cold Spring Harbor Laboratory Press 2022-09-20 <![CDATA[ Neuraminidase activity modulates cellular co-infection during influenza A virus multicycle growth ]]> https://biorxiv.org/content/10.1101/2022.09.20.508375v1?rss=1 Guo, Z. He, Y. Benegal, A. N. Vahey, M. D. 2022-09-20 doi:10.1101/2022.09.20.508375 Cold Spring Harbor Laboratory Press 2022-09-20 <![CDATA[ ETV6 Deficiency and Microsatellite Enhancers Drive Transcriptional Dysregulation in B-Lymphoblastic Leukemia ]]> https://biorxiv.org/content/10.1101/2022.09.20.508499v1?rss=1 Kodgule, R. Goldman, J. W. Monovich, A. C. Saari, T. Hall, C. N. Rajesh, N. Gupta, J. Aguilar, A. R. Brown, N. A. Chiang, M. Y. Cieslik, M. P. Ryan, R. J. H. 2022-09-21 doi:10.1101/2022.09.20.508499 Cold Spring Harbor Laboratory Press 2022-09-21 <![CDATA[ SARS-CoV-2 Omicron boosting induces de novo B cell response in humans ]]> https://biorxiv.org/content/10.1101/2022.09.22.509040v1?rss=1 Alsoussi, W. B. Malladi, S. K. Zhou, J. Q. Liu, Z. Ying, B. Kim, W. Schmitz, A. J. Lei, T. Horvath, S. C. Sturtz, A. J. McIntire, K. M. Evavold, B. Han, F. Scheaffer, S. M. Fox, I. F. Parra-Rodriguez, L. Nachbagauer, R. Nestorova, B. Chalkias, S. Farnsworth, C. W. Klebert, M. K. Pusic, I. Strnad, B. S. Middleton, W. D. Teefey, S. A. Whelan, S. P. J. Diamond, M. S. Paris, R. O'Halloran, J. A. Presti, R. M. Turner, J. S. Ellebedy, A. H. 2022-09-22 doi:10.1101/2022.09.22.509040 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Glutamatergic Supramammillary Nucleus Neurons Promote Active Coping to Stress ]]> https://biorxiv.org/content/10.1101/2022.09.22.507167v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@717f84org.highwire.dtl.DTLVardef@16ad323org.highwire.dtl.DTLVardef@4ba5b6org.highwire.dtl.DTLVardef@6c811e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 6.C_FLOATNO SuMVGLUT2+::POA neurons can drive instrumental action-outcome operant behavior (A) Schematic of injection and implant in VGLUT2+ Cre mice and paradigm of testing in 10-minute trials with four days before a progressive ratio (PR) trial on day five. (B) Illustration of the testing paradigm and set up. 10 Hz photostimulation was applied during the trials. Activation of the active port triggered the house light and paused stimulation for 10 seconds. Also shown is the progressive ratio used with number of required port activations per reward on vertical axis and reward number on the horizontal. (C) Cre+ mice (n=11) activated the active port triggering significantly (****p<0.0001) more pauses in stimulation than Cre- mice (n=11) mice on all four days of testing. (D) Cre+ mice activated the port significantly (****p<0.0001, ***p<0.001) more than the Cre- mice on all four trials. (E) The time to first activation of the active port was significantly (*p=0.046) different during the first trial, and Cre+ mice activated the active port significantly (**p<0.01, **p<0.01, **p=0.034) faster on subsequent trials. (F) On the fifth day after four 10-minute trials, mice were tested for 30 minutes using a progressive ratio. Cre+ performed significantly (****p<0.001) more active port activations than Cre- mice and activated the inactive port significantly more (**p=0.001) times. Cre+ mice also triggered significantly (****p<0.001) more pauses in photostimulation than Cre- mice. (G) Individual data for a representative (n=7) cohort of Cre+ mice showing cumulative active port activations as a function of time during the progressive ratio test show on-going engagement of the active port throughout the 30-minute trial. (H) The cumulative pauses in photostimulation (rewards) earned as a function of time during the progressive ratio trial are shown for individual Cre+ mice. Mice earned between 7 and 11 pause rewards during the trial. All data plotted as means {+/-}SEM. C_FIG ]]> Holloway, S.-A. Votoupal, M. Escobedo, A. Legaria, A. Ndiokho, I. Floyd, T. Kravitz, A. V. Bruchas, M. R. Norris, A. J. 2022-09-23 doi:10.1101/2022.09.22.507167 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Dopaminergic innervation at the central nucleus of the amygdala reveals distinct topographically and functionally segregated regions ]]> https://biorxiv.org/content/10.1101/2022.09.22.508929v1?rss=1 Casey, E. Avale, M. E. Kravitz, A. V. Rubinstein, M. 2022-09-23 doi:10.1101/2022.09.22.508929 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Comparison Between Gradients and Parcellations for Functional Connectivity Prediction of Behavior ]]> https://biorxiv.org/content/10.1101/2022.09.22.509045v1?rss=1 Kong, R. Tan, Y. R. Wulan, N. Ooi, L. Q. R. Farahibozorg, S.-R. Harrison, S. Bijsterbosch, J. D. Bernhardt, B. C. Eickhoff, S. Yeo, B. T. T. 2022-09-23 doi:10.1101/2022.09.22.509045 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Aging and Obesity Prime the Methylome and Transcriptome of Adipose Stem Cells for Disease and Dysfunction ]]> https://biorxiv.org/content/10.1101/2022.09.26.509507v1?rss=1 Xie, S. Choudhari, S. Wu, C.-L. Abramson, K. Corcoran, D. Gregory, S. G. Thimmapuram, J. M. Guilak, F. Little, D. 2022-09-26 doi:10.1101/2022.09.26.509507 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Amyloid-beta biomarkers in Braak stages and their predictive relationships with cognitive impairment: Support vector machine and deep learning approaches ]]> https://biorxiv.org/content/10.1101/2022.09.25.509432v1?rss=1 Taha, A. Soni, B. Thakuri, D. S. Ritter, E. Bhattarai, P. Chand, G. 2022-09-27 doi:10.1101/2022.09.25.509432 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Clonally related, Notch-differentiated spinal neurons integrate into distinct circuits ]]> https://biorxiv.org/content/10.1101/2022.09.26.509532v1?rss=1 Bello-Rojas, S. Bagnall, M. W. 2022-09-27 doi:10.1101/2022.09.26.509532 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Integrated Model of the Vertebrate Augmin Complex ]]> https://biorxiv.org/content/10.1101/2022.09.26.509603v1?rss=1 Travis, S. M. Mahon, B. P. Huang, W. Ma, M. Rale, M. J. Kraus, J. S. Taylor, D. Zhang, R. Petry, S. 2022-09-27 doi:10.1101/2022.09.26.509603 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Age-associated sleep-wake patterns are altered with Prdm13 signaling in the dorsomedial hypothalamus and dietary restriction in mice ]]> https://biorxiv.org/content/10.1101/2022.09.26.509442v1?rss=1 Tsuji, S. Brace, C. S. Yao, R. Tanie, Y. Tada, H. Rensing, N. Mizuno, S. Almunia, J. Kong, Y. Nakamura, K. Ogiso, N. Toyokuni, S. Takahashi, S. Wong, M. Imai, S.-i. Satoh, A. 2022-09-28 doi:10.1101/2022.09.26.509442 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Control of lipolysis by a population of oxytocinergic sympathetic neurons ]]> https://biorxiv.org/content/10.1101/2022.09.27.509745v1?rss=1 Li, E. Wang, L. Wang, D. Chi, J. Smith, G. Klein, S. Cohen, P. Rosen, E. 2022-09-28 doi:10.1101/2022.09.27.509745 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ A Multivariate Approach to Understanding the Genetic Overlap between Externalizing Phenotypes and Substance Use Disorders ]]> https://biorxiv.org/content/10.1101/2022.09.27.509777v1?rss=1 .87) and similarly genetically correlated with external criteria, suggesting they did not represent meaningfully distinct dimensions. Results from this study can be used to inform future efforts to characterize genetic liability for broad externalizing as well as specific externalizing phenotypes. ]]> Poore, H. E. Hatoum, A. Mallard, T. T. Sanchez-Roige, S. Waldman, I. D. Palmer, A. A. Harden, K. P. Barr, P. B. Dick, D. M. 2022-09-28 doi:10.1101/2022.09.27.509777 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ The Neurotoxin DSP-4 Dysregulates the Locus Coeruleus-Norepinephrine System and Recapitulates Molecular and Behavioral Aspects of Prodromal Neurodegenerative Disease ]]> https://biorxiv.org/content/10.1101/2022.09.27.509797v1?rss=1 Iannitelli, A. F. Kelberman, M. A. Lustberg, D. J. Korukonda, A. McCann, K. E. Mulvey, B. Segal, A. Liles, L. C. Sloan, S. A. Dougherty, J. Weinshenker, D. 2022-09-28 doi:10.1101/2022.09.27.509797 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Uncovering the contributions of charge regulation to the stability of single alpha helices ]]> https://biorxiv.org/content/10.1101/2022.09.28.509894v1?rss=1 Fossat, M. J. Posey, A. E. Pappu, R. V. 2022-09-28 doi:10.1101/2022.09.28.509894 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Fluorescence lifetime enables high-resolution analysis of neuromodulator dynamics across time and animals ]]> https://biorxiv.org/content/10.1101/2022.09.28.510014v1?rss=1 Ma, P. Chen, P. Tilden, E. Aggarwal, S. Oldenborg, A. Chen, Y. 2022-09-30 doi:10.1101/2022.09.28.510014 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Microbiota-dependent histone butyrylation in the mammalian intestine ]]> https://biorxiv.org/content/10.1101/2022.09.29.510184v1?rss=1 Gates, L. A. Reis, B. S. Lund, P. J. Paul, M. R. Leboeuf, M. Nadeem, Z. Carroll, T. S. Garcia, B. Mucida, D. Allis, C. D. 2022-09-30 doi:10.1101/2022.09.29.510184 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Maturation of SARS-CoV-2 Spike-specific memory B cells drives resilience to viral escape ]]> https://biorxiv.org/content/10.1101/2022.09.30.509852v1?rss=1 Marzi, R. Bassi, J. Silacci-Fregni, C. Bartha, I. Muoio, F. Culap, K. Sprugasci, N. Lombardo, G. Saliba, C. Cameroni, E. Cassotta, A. Low, J. S. Walls, A. C. McCallum, M. Tortorici, M. A. Bowen, J. E. Dellota, E. A. Dillen, J. R. Czudnochowski, N. Pertusini, L. Terrot, T. Lepori, V. Tarkowski, M. Riva, A. Biggiogero, M. Franzetti Pellanda, A. Garzoni, C. Ferrari, P. Ceschi, A. Giannini, O. Havenar-Daughton, C. Telenti, A. Arvin, A. Virgin, H. W. Sallusto, F. Veesler, D. Lanzavecchia, A. Corti, D. Piccoli, L. 2022-09-30 doi:10.1101/2022.09.30.509852 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Helicase Activity Promoted Through Dynamic Interactions Between a ssDNA Translocase and a Diffusing SSB Protein ]]> https://biorxiv.org/content/10.1101/2022.09.30.510372v1?rss=1 Mersch, K. Sokoloski, J. E. Nguyen, B. Galletto, R. Lohman, T. M. 2022-10-01 doi:10.1101/2022.09.30.510372 Cold Spring Harbor Laboratory Press 2022-10-01 <![CDATA[ We the Hunted ]]> https://biorxiv.org/content/10.1101/2022.09.29.510060v1?rss=1 Martin, J. Leece, A. Herries, A. I. Baker, S. Strait, D. 2022-10-03 doi:10.1101/2022.09.29.510060 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ RefDeduR: A text-normalization and decision-tree aided R package enabling accurate and high-throughput reference deduplication for large datasets ]]> https://biorxiv.org/content/10.1101/2022.09.29.510210v1?rss=1 Shen, J. Ling, F. Hartmann, E. M. 2022-10-03 doi:10.1101/2022.09.29.510210 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ Memory CD4 T cell subset organization in the female reproductive tract is regulated via the menstrual cycle through CCR5 signaling ]]> https://biorxiv.org/content/10.1101/2022.10.01.510445v1?rss=1 Swaims-Kohlmeier, A. Wein, A. N. Hardnett, F. P. Sheth, A. N. Li, Z.-R. T. Williams, M. E. Radzio-Basu, J. Zheng, H. Dinh, C. Haddad, L. B. Collins, E. M. Lobby, J. L. Kost, K. Hayward, S. L. Ofotokun, I. Antia, R. Scharer, C. D. Lowen, A. C. Garcia-Lerma, J. G. Kohlmeier, J. 2022-10-03 doi:10.1101/2022.10.01.510445 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ Insulin receptor substrate 4 deficiency mediates the insulin effect on the epithelial magnesium channel TRPM6 and causes hypomagnesemia ]]> https://biorxiv.org/content/10.1101/2022.10.01.510479v1?rss=1 Zhang, J. An, S. W. Neelam, S. Bhatta, A. Nie, M. Duran, C. Bal, M. Latta, F. Hou, J. S. Otto, J. J. Kozlitina, J. Lemoff, A. Hoenderop, J. Baum, M. Wolf, M. T. 2022-10-04 doi:10.1101/2022.10.01.510479 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ Genomic Analysis of Two Phlebotomine Sand Fly Vectors of Leishmania from the New and Old World ]]> https://biorxiv.org/content/10.1101/2022.10.05.510924v1?rss=1 McDowell, M. A. Labbe, F. Abdeladhim, M. Abrudan, J. Araki, A. S. Araujo, R. N. Arensburger, P. Beniot, J. B. Brazil, R. P. Bruno, R. V. Bueno da Silva Rivas, G. Carvalho de Abreu, V. Charamis, J. Coutinho-Abreu, I. da Costa-Latge, S. G. Darby, A. Dillon, V. Emrich, S. J. Fernandez-Medina, D. Figueiredo Gontijo, N. Flannley, C. M. Gatherer, D. Genta, F. A. Gesing, S. Giraldo-Calderon, G. I. Gomes, B. Aguiar, E. R. G. R. Hamarsheh, O. Hawksworth, M. Hendershot, J. M. Hickner, P. V. Imler, J.-L. Ioannidis, P. Jennings, E. C. Kamhawi, S. Karageorgiou, C. Kenned 2022-10-05 doi:10.1101/2022.10.05.510924 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ A Synthetic ERRα Agonist Induces an Acute AerobicExercise Response and Enhances Exercise Capacity ]]> https://biorxiv.org/content/10.1101/2022.10.05.510974v1?rss=1 Billon, C. Banerjee, S. Situala, S. Welch, R. Hegazy, L. Elgendy, B. Oh, T. G. Kazantzis, M. Chatterjee, A. Chrivia, J. Hayes, M. Xu, W. Hamilton, A. Huss, J. Zhang, L. Walker, J. K. Downes, M. Evans, R. Burris, T. 2022-10-07 doi:10.1101/2022.10.05.510974 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Development of SARS-CoV-2 mRNA vaccines encoding spike N-terminal and receptor binding domains ]]> https://biorxiv.org/content/10.1101/2022.10.07.511319v1?rss=1 Stewart-Jones, G. Elbashir, S. M. Wu, K. Lee, D. Renzi, I. Ying, B. Koch, M. Sein, C. E. Choi, A. Whitener, B. Garcia-Dominguez, D. Henry, C. Woods, A. Ma, L. Montes Berrueta, D. Avena, L. E. Quinones, J. Falcone, S. Hsiao, C. J. Scheaffer, S. M. Thackray, L. B. White, P. Diamond, M. S. Edwards, D. K. Carfi, A. 2022-10-07 doi:10.1101/2022.10.07.511319 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Genome-Wide Epigenomic Profiling of Primary Non-Small Cell Lung Cancer Reveals Specific and Recurrent DNA Methylation Alterations in Smoker Versus Never-Smoker Patients ]]> https://biorxiv.org/content/10.1101/2022.10.06.511208v1?rss=1 Karlow, J. A. Pehrsson, E. C. Xing, X. Watson, M. Devarakonda, S. Govindan, R. Wang, T. 2022-10-08 doi:10.1101/2022.10.06.511208 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ An alternative mechanism for skeletal muscle dysfunction in long-term post-viral lung disease ]]> https://biorxiv.org/content/10.1101/2022.10.07.511313v1?rss=1 Martin, R. A. Keeler, S. P. Wu, K. Shearon, W. J. Patel, D. Hoang, M. Hoffmann, C. M. Hughes, M. E. Holtzman, M. J. 2022-10-08 doi:10.1101/2022.10.07.511313 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ Distinct roles for canonical and variant histone H3 lysine 36 in Polycomb silencing ]]> https://biorxiv.org/content/10.1101/2022.10.11.511749v1?rss=1 Salzler, H. R. Vandadi, V. McMichael, B. D. Brown, J. C. Boerma, S. A. Leatham-Jensen, M. P. Adams, K. M. Meers, M. P. Simon, J. M. Duronio, R. J. McKay, D. J. Matera, A. G. 2022-10-11 doi:10.1101/2022.10.11.511749 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Data Descriptor: Human whole exome genotype data for Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2022.10.11.511653v1?rss=1 30. Our new strategy for processing these diversely generated WES samples has shown to generate high-quality data. The improved ability to combine data sequenced in different batches benefits the whole genomics research community. The WES data are accessible to the scientific community via https://dss.niagads.org/. ]]> Leung, Y. Y. Naj, A. C. Chou, Y.-F. Valladares, O. Wheeler, N. Lin, H. Gangadharan, P. Qu, L. Clark, K. Cantwell, L. Nicaretta, H. the Alzheimer's Disease Sequencing Project, Seshadri, S. Brkanac, Z. Cruchaga, C. Pericak-Vance, M. A. Mayeux, R. Kuzma, A. B. Lee, W.-P. Bush, W. S. DeStefano, A. L. Martin, E. Schellenberg, G. D. Wang, L.-S. 2022-10-13 doi:10.1101/2022.10.11.511653 Cold Spring Harbor Laboratory Press 2022-10-13 <![CDATA[ Polyphasic circadian neural circuits drive differential activities in multiple downstream rhythmic centers ]]> https://biorxiv.org/content/10.1101/2022.10.11.511837v1?rss=1 Liang, X. Holy, T. E. Taghert, P. 2022-10-13 doi:10.1101/2022.10.11.511837 Cold Spring Harbor Laboratory Press 2022-10-13 <![CDATA[ Smaller total and subregional cerebellar volumes in posttraumatic stress disorder: a mega-analysis by the ENIGMA-PGC PTSD workgroup ]]> https://biorxiv.org/content/10.1101/2022.10.13.512111v1?rss=1 Huggins, A. A. Baird, C. L. Briggs, M. Laskowitz, S. Fouda, S. Haswell, C. C. Sun, D. Salminen, L. E. Jahanshad, N. Thomopoulos, S. I. Veltman, D. J. Frijling, J. L. Olff, M. van Zuiden, M. Koch, S. B. J. Nawijn, L. Wang, L. Zhu, Y. Li, G. Stein, D. J. Ipser, J. Seedat, S. du Plessis, S. van den Heuvel, L. L. Suarez-Jimenez, B. Zhu, X. Kim, Y. He, X. Zilcha-Mano, S. Lazarov, A. Neria, Y. Stevens, J. S. Ressler, K. J. Jovanovic, T. van Rooij, S. J. H. Fani, N. Hudson, A. R. Mueller, S. C. Sierk, A. Manthey, A. Walter, H. Daniels, J. K. Schmahl, C. Herz 2022-10-17 doi:10.1101/2022.10.13.512111 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Declining autozygosity over time: an exploration in over 1 million individuals from three diverse cohorts ]]> https://biorxiv.org/content/10.1101/2022.10.13.512166v1?rss=1 Colbert, S. M. Wendt, F. R. Pathak, G. Helmer, D. A. Hauser, E. Keller, M. C. Polimanti, R. Johnson, E. C. 2022-10-17 doi:10.1101/2022.10.13.512166 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ MYT1L is required for suppressing earlier neuronal development programs in the adult mouse brain ]]> https://biorxiv.org/content/10.1101/2022.10.17.512591v1?rss=1 Chen, J. Fuhler, N. A. Noguchi, K. Dougherty, J. D. 2022-10-18 doi:10.1101/2022.10.17.512591 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ RNAs undergo phase transitions with lower critical solution temperatures ]]> https://biorxiv.org/content/10.1101/2022.10.17.512593v1?rss=1 Wadsworth, G. M. Zahurancik, W. J. Zeng, X. Pullara, P. Lai, L. B. Sidharthan, V. Pappu, R. V. Gopalan, V. Banerjee, P. R. 2022-10-18 doi:10.1101/2022.10.17.512593 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Two forms of asynchronous release with distinctive spatiotemporal dynamics in central synapses ]]> https://biorxiv.org/content/10.1101/2022.10.19.512860v1?rss=1 Malagon, G. Myeong, J. Klyachko, V. 2022-10-19 doi:10.1101/2022.10.19.512860 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ Targeting the Immune-Fibrosis Axis in Myocardial Infarction and Heart Failure ]]> https://biorxiv.org/content/10.1101/2022.10.17.512579v1?rss=1 Amrute, J. M. Luo, X. Penna, V. Bredemeyer, A. Yamawaki, T. Heo, G. S. Shi, S. Koenig, A. L. Yang, S. Kadyrov, F. F. Jones, C. Kuppe, C. Kopecky, B. Hayat, S. Ma, P. Feng, G. Terada, Y. Fu, A. Furtado, M. Kreisel, D. Stitziel, N. O. Li, C.-M. K. Kramann, R. Liu, Y. Ason, B. Lavine, K. 2022-10-21 doi:10.1101/2022.10.17.512579 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Genetic mapping reveals Pou2af2-dependent tuning of tuft cell differentiation and intestinal type 2 immunity ]]> https://biorxiv.org/content/10.1101/2022.10.19.512785v1?rss=1 Nadjsombati, M. S. Niepoth, N. Webeck, L. M. Kennedy, E. A. Jones, D. L. Baldridge, M. T. Bendesky, A. von Moltke, J. 2022-10-21 doi:10.1101/2022.10.19.512785 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Striatal dopamine synthesis and cognitive flexibility differ between hormonal contraceptive users and non-users ]]> https://biorxiv.org/content/10.1101/2022.10.20.513082v1?rss=1 Taylor, C. Furman, D. Berry, A. White, R. L. Jagust, W. J. D'Esposito, M. Jacobs, E. G. 2022-10-21 doi:10.1101/2022.10.20.513082 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Molecular Basis for Interferon-mediated Pathogen Restriction in Human Cells ]]> https://biorxiv.org/content/10.1101/2022.10.21.513197v1?rss=1 Matta, S. K. Kohio, H. P. Chandra, P. Brown, A. Doench, J. G. A. Philips, J. Ding, S. Sibley, L. D. 2022-10-21 doi:10.1101/2022.10.21.513197 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Molecular early burst associated with the diversification of birds at the K-Pg boundary ]]> https://biorxiv.org/content/10.1101/2022.10.21.513146v1?rss=1 Berv, J. S. Singhal, S. Field, D. J. Walker-Hale, N. McHugh, S. W. Shipley, J. R. Miller, E. T. Kimball, R. T. Braun, E. L. Dornburg, A. Parins-Fukuchi, C. T. Prum, R. O. Friedman, M. Smith, S. A. 2022-10-22 doi:10.1101/2022.10.21.513146 Cold Spring Harbor Laboratory Press 2022-10-22 <![CDATA[ Loss of altruism in the social amoeba Dictyostelium discoideum is associated with the G protein-coupled receptor, grlG ]]> https://biorxiv.org/content/10.1101/2022.10.21.513250v1?rss=1 Walker, L. M. Sherpa, R. N. Ivaturi, S. Brock, D. A. Walker, J. R. Strassmann, J. E. Queller, D. C. 2022-10-22 doi:10.1101/2022.10.21.513250 Cold Spring Harbor Laboratory Press 2022-10-22 <![CDATA[ Computationally restoring the potency of a clinical antibody against SARS-CoV-2 Omicron subvariants ]]> https://biorxiv.org/content/10.1101/2022.10.21.513237v1?rss=1 Desautels, T. A. Arrildt, K. T. Zemla, A. T. Lau, E. Y. Zhu, F. Ricci, D. Cronin, S. Zost, S. Binshtein, E. Scheaffer, S. M. Engdahl, T. B. Chen, E. Goforth, J. W. Vashchenko, D. Nguyen, S. Weilhammer, D. R. Lo, J. K.-Y. Rubinfeld, B. Saada, E. A. Weisenberger, T. Lee, T.-H. Whitener, B. Case, J. B. Ladd, A. Silva, M. S. Haluska, R. M. Grzesiak, E. A. Bates, T. W. Petersen, B. K. Thackray, L. B. Segelke, B. W. Lillo, A. M. Sundaram, S. Diamond, M. S. Crowe, J. E. Carnahan, R. H. Faissol, D. M. 2022-10-24 doi:10.1101/2022.10.21.513237 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ A fast yet force-effective mode of collective cell migration on aligned fibers due to rapid stabilization of contractile forces ]]> https://biorxiv.org/content/10.1101/2022.10.22.513348v1?rss=1 Bagchi, A. Sarker, B. Zhang, J. Foston, M. Pathak, A. 2022-10-24 doi:10.1101/2022.10.22.513348 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Multiomic single-cell lineage tracing to dissect fate-specific gene regulatory programs ]]> https://biorxiv.org/content/10.1101/2022.10.23.512790v1?rss=1 Jindal, K. Adil, M. T. Yamaguchi, N. Wang, H. C. Yang, X. Kamimoto, K. Rivera-Gonzalez, G. C. Morris, S. A. 2022-10-24 doi:10.1101/2022.10.23.512790 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Epigenetic Priming Enhances Chondrogenic Potential of Expanded Chondrocytes for Cartilage Repair ]]> https://biorxiv.org/content/10.1101/2022.10.23.513439v1?rss=1 Scott, A. K. Gallagher, K. M. Schneider, S. E. Kurse, A. Neu, C. P. 2022-10-24 doi:10.1101/2022.10.23.513439 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Extraction Optimization, Characterization, and Antioxidant Capacity of Phenolics from Cowpeas (Vigna Unguiculata) ]]> https://biorxiv.org/content/10.1101/2022.10.24.513571v1?rss=1 Webber, D. M. Horax, R. Hettiarachchy, N. S. 2022-10-25 doi:10.1101/2022.10.24.513571 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Multi-Mode Fiber-Based Speckle Contrast Optical Spectroscopy: Analysis of Speckle Statistics ]]> https://biorxiv.org/content/10.1101/2022.10.25.513089v1?rss=1 >10), SCOS/T has increased signal-to-noise ratio relative to diffuse correlation spectroscopy, which measures one or a few speckles. However, the current free-space SCOS/T designs are not ideal for large field-of-view imaging in humans because the curved head contour cannot be readily imaged with a single flat sensor and hair obstructs optical access. Herein we evaluate the feasibility of using cost-efficient multi-mode fiber (MMF) bundles for use in SCOS/T systems. One challenge with speckle contrast measurements is the potential for confounding noise sources (e.g., shot noise, readout noise) to contribute to the standard deviation measure and corrupt the speckle contrast measure that is central to the SCOS/T systems. However, for true speckle measurements, the histogram of pixel intensities from light interference follows a non-Gaussian distribution, specifically a gamma distribution with non-zero skew, whereas most noise sources have pixel intensity distributions that are Gaussian. By evaluating speckle data from static and dynamic targets imaged through MMF, we use histograms and statistical analysis of pixel histograms to evaluate whether the statistical properties of the speckles are retained. We show that flow-based speckle can be distinguished from static speckle and from sources of system noise through measures of skew in the pixel intensity histograms. Finally, we illustrate in humans that MMF bundles relay blood flow information. (C) 2022 Optica Publishing Group ]]> Lin, C.-H. P. Orukari, I. Tracy, C. Frisk, L. K. Verma, M. Chetia, S. Durduran, T. Trobaugh, J. W. Culver, J. P. 2022-10-27 doi:10.1101/2022.10.25.513089 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Gradual cerebral hypoperfusion in a knock-in mouse model of Alzheimer's disease triggers cortical network dysfunctions ]]> https://biorxiv.org/content/10.1101/2022.10.25.513783v1?rss=1 Singh, S. Lacoursiere, S. G. Mehla, J. Nazari, M. Sutherland, R. J. McDonald, R. J. Mohajerani, M. H. 2022-10-27 doi:10.1101/2022.10.25.513783 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ A pan-cancer PDX histology image repository with genomic and pathological annotations for deep learning analysis ]]> https://biorxiv.org/content/10.1101/2022.10.26.512745v1?rss=1 White, B. S. Woo, X. Koc, S. Sheridan, T. Neuhauser, S. B. Wang, S. Evrard, Y. A. Landua, J. D. Mashl, R. J. Davies, S. R. Fang, B. Raso, M. G. Evans, K. W. Bailey, M. H. Chen, Y. Xiao, M. Rubinstein, J. Foroughi pour, A. Dobrolecki, L. E. Fujita, M. Fujimoto, J. Xiao, G. Fields, R. C. Mudd, J. L. Xu, X. Hollingshead, M. G. Jiwani, S. PDXNet Consortium, Davis-Dusenbery, B. Wallace, T. A. Moscow, J. A. Doroshow, J. H. Mitsiades, N. Kaochar, S. Pan, C.-x. Chen, M. S. Carvajal-Carmona, L. G. Welm, A. L. Welm, B. E. Govindan, R. Li, S. Davies, M. A. Roth 2022-10-27 doi:10.1101/2022.10.26.512745 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Spike-phase coupling patterns reveal laminar identity in primate cortex ]]> https://biorxiv.org/content/10.1101/2022.10.26.513932v1?rss=1 Davis, Z. W. Dotson, N. M. Franken, T. Muller, L. Reynolds, J. 2022-10-27 doi:10.1101/2022.10.26.513932 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ A mind-body interface alternates with effector-specific regions in motor cortex ]]> https://biorxiv.org/content/10.1101/2022.10.26.513940v1?rss=1 Gordon, E. M. Chauvin, R. J. Van, A. N. Rajesh, A. Nielsen, A. Newbold, D. J. Lynch, C. J. Seider, N. A. Krimmel, S. R. Scheidter, K. M. Monk, J. Miller, R. L. Metoki, A. Montez, D. F. Zheng, A. Elbau, I. Madison, T. Nishino, T. Myers, M. J. Kaplan, S. D'Andrea, C. B. Demeter, D. V. Feigelis, M. Barch, D. M. Smyser, C. D. Rogers, C. E. Zimmerman, J. Botteron, K. N. Pruett, J. R. Willie, J. T. Brunner, P. Shimony, J. S. Kay, B. P. Marek, S. Norris, S. A. Gratton, C. Sylvester, C. M. Power, J. D. Liston, C. Greene, D. J. Roland, J. L. Petersen, S. E. Rai 2022-10-28 doi:10.1101/2022.10.26.513940 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Integrated PET and confocal imaging informs a functional timeline for the dynamic process of vascular reconnection during grafting. ]]> https://biorxiv.org/content/10.1101/2022.10.27.513862v1?rss=1 Frank, M. Komarov, S. Wang, Q. Li, K. Hecking, M. Fowler, H. Ravenburg, C. Widmier, A. Johnson, A. Thomas, H. Coneva, V. Chitwood, D. H. Tai, Y.-C. 2022-10-28 doi:10.1101/2022.10.27.513862 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Expanding the epitranscriptomic RNA sequencing and modification mapping mass spectrometry toolbox with field asymmetric waveform ion mobility and electrochemical elution liquid chromatography ]]> https://biorxiv.org/content/10.1101/2022.10.28.514273v1?rss=1 Lauman, R. Kim, H. J. Pino, L. Scacchetti, A. Bonasio, R. Garcia, B. A. 2022-10-30 doi:10.1101/2022.10.28.514273 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ Defining the roles of pyruvate oxidation, TCA cycle, and mannitol metabolism in methicillin resistance Staphylococcus aureus urinary tract infection ]]> https://biorxiv.org/content/10.1101/2022.10.28.514332v1?rss=1 Kulkarni, R. Paudel, S. Guedry, S. Walker, J. N. Obernuefemann, C. L. Hultgren, S. 2022-10-30 doi:10.1101/2022.10.28.514332 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ An expanded proteomic survey of the human parasite Leishmania major focusing on changes in null mutants of the Golgi GDP-Mannose/Fucose/Arabinopyranose transporter LPG2 or the mitochondrial fucosyltransferase FUT1 ]]> https://biorxiv.org/content/10.1101/2022.10.29.514353v1?rss=1 Polanco, G. Scott, N. E. Lye, L. F. Beverley, S. M. 2022-10-30 doi:10.1101/2022.10.29.514353 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ TRPV1-mediated sonogenetic neuromodulation of motor cortex in freely moving mice ]]> https://biorxiv.org/content/10.1101/2022.10.28.514307v1?rss=1 Xu, K. Yang, Y. Hu, Z. Yue, Y. Cui, J. Culver, J. P. Bruchas, M. R. Chen, H. 2022-10-31 doi:10.1101/2022.10.28.514307 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ Mechanically manipulate glymphatic transportation by ultrasound combined with microbubbles ]]> https://biorxiv.org/content/10.1101/2022.10.28.514316v1?rss=1 Ye, D. Chen, S. Liu, Y. Weixel, C. Hu, Z. Chen, H. 2022-10-31 doi:10.1101/2022.10.28.514316 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ Photonic-Plasmonic Coupling Enhanced Fluorescence Enabling Digital-Resolution Ultrasensitive Protein Detection ]]> https://biorxiv.org/content/10.1101/2022.10.29.514360v1?rss=1 Barya, P. Xiong, Y. Shepherd, S. Gupta, R. Akin, L. D. Tibbs, J. Lee, H. K. Singamaneni, S. Cunningham, B. T. 2022-10-31 doi:10.1101/2022.10.29.514360 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ Punishment Risk Task: Monitoring anxiogenic states during goal directed actions in mice ]]> https://biorxiv.org/content/10.1101/2022.10.30.514458v1?rss=1 Parker, K. E. Arackal, J. S. Hunter, S. C. McCall, J. G. 2022-11-01 doi:10.1101/2022.10.30.514458 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Capsular polysaccharide inhibits vaccine-induced O-antigen antibody binding and function across both classical and hypervirulent K2:O1 strains of Klebsiella pneumoniae ]]> https://biorxiv.org/content/10.1101/2022.11.01.514596v1?rss=1 Wantuch, P. L. Knoot, C. J. Robinson, L. S. Vinogradov, E. Scott, N. E. Harding, C. M. Rosen, D. A. 2022-11-01 doi:10.1101/2022.11.01.514596 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Uncovering the principles coordinating systems-level organelle biogenesis with cellular growth ]]> https://biorxiv.org/content/10.1101/2022.11.01.514705v1?rss=1 Wang, S. Mukherji, S. 2022-11-02 doi:10.1101/2022.11.01.514705 Cold Spring Harbor Laboratory Press 2022-11-02 <![CDATA[ Decipher macrophage-fibroblast-cardiomyocyte signaling interactions associated with heart failure using deep graph neural network models and single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/2022.11.02.514928v1?rss=1 Li, W. Feng, J. Payne, P. R. Chen, Y. Li, F. 2022-11-04 doi:10.1101/2022.11.02.514928 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Inhibition of extracellular vesicle-encapsulated miRNA produced by estrogen-mediated upregulation of cellular processing suppresses target organ inflammation in a humanized model of systemic lupus erythematosus ]]> https://biorxiv.org/content/10.1101/2022.11.03.514940v1?rss=1 Young, N. A. Schwarz, E. Mesa, R. A. Jablonski, K. Wu, L.-C. Roberson, E. D. O. Jarjour, W. 2022-11-04 doi:10.1101/2022.11.03.514940 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ A condensate forming tether for lariat debranching enzyme is defective in non-photosensitive trichiothiodystrophy ]]> https://biorxiv.org/content/10.1101/2022.11.03.515106v1?rss=1 Townley, B. A. Buerer, L. Bacolla, A. Rusanov, T. Schmidt, N. Srivatsan, S. N. Clark, N. E. Mansoori, F. Sample, R. A. Brickner, J. R. McDonald, D. Tsai, M.-S. Walter, M. Wozniak, D. F. Holehouse, A. S. Tainer, J. Fairbrother, W. Mosammaparast, N. 2022-11-04 doi:10.1101/2022.11.03.515106 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Autophagy protects against high-dose Mycobacterium tuberculosis infection ]]> https://biorxiv.org/content/10.1101/2022.11.04.515158v1?rss=1 Feng, S. Nehls, E. M. Kinsella, R. L. Chavez, S. M. Naik, S. K. McKee, S. R. Dubey, N. Samuels, A. Swain, A. Cui, X. Hendrix, S. V. Woodson, R. Kreamalmeyer, D. Smirnov, A. Artyomov, M. N. Virgin, H. W. Wang, Y.-T. Stallings, C. L. 2022-11-04 doi:10.1101/2022.11.04.515158 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ A Peptide-Centric Quantitative Proteomics Dataset for the Phenotypic Assessment of Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2022.11.04.515203v1?rss=1 Merrihew, G. E. Park, J. Plubell, D. Searle, B. C. Keene, C. D. Larsen, E. B. Bateman, R. Perrin, R. J. Chhatwal, J. P. Farlow, M. R. McLean, C. A. Ghetti, B. Newell, K. L. Frosh, M. P. Montine, T. MacCoss, M. J. 2022-11-04 doi:10.1101/2022.11.04.515203 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Autophagy is required in macrophages and dendritic cells to prevent early recruitment of neutrophils during Mycobacterium tuberculosis infection ]]> https://biorxiv.org/content/10.1101/2022.11.04.515221v1?rss=1 Kinsella, R. L. Kimmey, J. M. Smirnov, A. Woodson, R. Gaggioli, M. R. Chavez, S. M. Kreamalmeyer, D. Stallings, C. L. 2022-11-04 doi:10.1101/2022.11.04.515221 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Uncovering molecular grammars of intrinsically disordered regions that organize nucleolar fibrillar centers ]]> https://biorxiv.org/content/10.1101/2022.11.05.515292v1?rss=1 King, M. R. Lin, A. Z. Ruff, K. M. Farag, M. Ouyang, W. Vahey, M. D. Lundberg, E. Pappu, R. V. 2022-11-05 doi:10.1101/2022.11.05.515292 Cold Spring Harbor Laboratory Press 2022-11-05 <![CDATA[ Third-party effects in the Dictyostelium-Paraburkholderia symbiosis: food bacteria that are eaten, carried, or left behind ]]> https://biorxiv.org/content/10.1101/2022.11.06.513053v1?rss=1 Scott, T. J. Queller, D. C. Strassmann, J. E. 2022-11-06 doi:10.1101/2022.11.06.513053 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ Deep unfolded convolutional dictionary learning for motif discovery ]]> https://biorxiv.org/content/10.1101/2022.11.06.515322v1?rss=1 Chu, S. K.-H. Stormo, G. D. 2022-11-06 doi:10.1101/2022.11.06.515322 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ Charge-voltage curves of Shaker potassium channel are not hysteretic at steady state ]]> https://biorxiv.org/content/10.1101/2022.11.07.515208v1?rss=1 Cowgill, J. Chanda, B. 2022-11-07 doi:10.1101/2022.11.07.515208 Cold Spring Harbor Laboratory Press 2022-11-07 <![CDATA[ Ibex: Variational autoencoder for single-cell BCR sequencing. ]]> https://biorxiv.org/content/10.1101/2022.11.09.515787v1?rss=1 Borcherding, N. Sun, B. DeNardo, D. Brestoff, J. 2022-11-10 doi:10.1101/2022.11.09.515787 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ Breast cancer mutations HER2 V777L and PIK3CA H1047R activate the p21/CDK4/6/Cyclin D1 axis driving tumorigenesis and drug resistance. ]]> https://biorxiv.org/content/10.1101/2022.11.09.515796v1?rss=1 Cheng, X. Sun, Y. Highkin, M. Vemalapally, N. Jin, X. Zhou, B. Prior, J. L. Tipton, A. R. Li, S. Iliuk, A. Achilefu, S. Hagemann, I. S. Edwards, J. R. Bose, R. 2022-11-10 doi:10.1101/2022.11.09.515796 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ Neuropathic injury drives a generalized negative affective state in mice ]]> https://biorxiv.org/content/10.1101/2022.11.10.515959v1?rss=1 Norris, M. R. Bilbily, J. Becker, L. J. Borges, G. Chang, Y.-H. Dunn, S. S. Madasu, M. K. Al-Hasani, R. Creed, M. C. McCall, J. G. 2022-11-13 doi:10.1101/2022.11.10.515959 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Circuit-specific selective vulnerability in the DMN persists in the face of widespread amyloid burden. ]]> https://biorxiv.org/content/10.1101/2022.11.14.516510v1?rss=1 Brunwasser, S. J. Farris, C. Elmore, H. Dyer, E. L. Nair, K. B. Whitesell, J. D. Harris, J. A. Hengen, K. B. 2022-11-14 doi:10.1101/2022.11.14.516510 Cold Spring Harbor Laboratory Press 2022-11-14 <![CDATA[ Discovery, Synthesis, and Optimization of 1,2,4-Triazolyl Pyridines Targeting Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2022.11.14.516356v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@1fd7a78org.highwire.dtl.DTLVardef@738c7dorg.highwire.dtl.DTLVardef@c7957org.highwire.dtl.DTLVardef@f26ae3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Roy, S. Berida, T. McKee, S. R. Chatterjee, S. Li, W. Pandey, P. Tripathi, S. K. Doerksen, R. J. Jackson, M. Ducho, C. Stallings, C. L. 2022-11-15 doi:10.1101/2022.11.14.516356 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ An RNA interference (RNAi) toolkit and its utility for functional genetic analysis of Leishmania ( Viannia ) ]]> https://biorxiv.org/content/10.1101/2022.11.14.516516v1?rss=1 Lye, L.-F. Owens, K. L. Jang, S. Marcus, J. E. Brettmann, E. A. Beverley, S. M. 2022-11-15 doi:10.1101/2022.11.14.516516 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Aim18p and Aim46p are CHI-domain-containing mitochondrial hemoproteins in Saccharomyces cerevisiae. ]]> https://biorxiv.org/content/10.1101/2022.11.15.516536v1?rss=1 Schmitz, J. M. Wolters, J. F. Murray, N. H. Guerra, R. M. Bingman, C. A. Hittinger, C. T. Pagliarini, D. J. 2022-11-15 doi:10.1101/2022.11.15.516536 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Identification and Characterization of ML321: a Novel and Highly Selective D2 Dopamine Receptor Antagonist with Efficacy in Animal Models that Predict Atypical Antipsychotic Activity ]]> https://biorxiv.org/content/10.1101/2022.11.14.516475v1?rss=1 Free, R. B. Nilson, A. N. Boldizsar, N. M. Doyle, T. Rodriguiz, R. M. Pogorelov, V. M. Machino, M. Lee, K. H. Bertz, J. W. Xu, J. Lim, H. D. Dulcey, A. E. Mach, R. H. Woods, J. H. Lane, J. R. Shi, L. Marugan, J. J. Wetsel, W. C. Sibley, D. R. 2022-11-16 doi:10.1101/2022.11.14.516475 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Inhibition of Centrosome Clustering Reduces Cystogenesis and Improves Kidney Function in Autosomal Dominant Polycystic Kidney Disease ]]> https://biorxiv.org/content/10.1101/2022.11.16.516801v1?rss=1 Cheng, T. Mariappan, A. Langner, E. Shim, K. Gopalakrishnan, J. Mahjoub, M. R. 2022-11-17 doi:10.1101/2022.11.16.516801 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ DNAJB6 Isoform Specific Knockdown: Therapeutic Potential for LGMDD1 ]]> https://biorxiv.org/content/10.1101/2022.11.17.516920v1?rss=1 Findlay, A. R. Paing, M. M. Daw, J. A. Bengoechea, R. Pittman, S. K. Li, S. Wang, F. Miller, T. M. True, H. L. Weihl, C. C. 2022-11-17 doi:10.1101/2022.11.17.516920 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Modulation of TRPV4 Protects against Degeneration Induced by Sustained Loading and Promotes Matrix Synthesis in the Intervertebral Disc ]]> https://biorxiv.org/content/10.1101/2022.11.18.516994v1?rss=1 Easson, G. W. D. Savadipour, A. Anandarajah, A. Iannucci, L. E. Lake, S. P. Guilak, F. Tang, S. Y. 2022-11-18 doi:10.1101/2022.11.18.516994 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state ]]> https://biorxiv.org/content/10.1101/2022.11.18.517051v1?rss=1 Barrett, T. F. Patel, B. Khan, S. M. Yim, A. K. Y. Pugazenthi, S. Mahlokozera, T. Mullins, R. D. Z. Zipfel, G. J. Herzog, J. A. Chicoine, M. R. Wick, C. C. Durakovic, N. Osbun, J. W. Shew, M. Sweeney, A. D. Patel, A. J. Buchman, C. A. Petti, A. A. Puram, S. V. Kim, A. H. 2022-11-19 doi:10.1101/2022.11.18.517051 Cold Spring Harbor Laboratory Press 2022-11-19 <![CDATA[ Lipid nanodisc scaffold and size alters the structure of a pentameric ligand-gated ion channel ]]> https://biorxiv.org/content/10.1101/2022.11.20.517256v1?rss=1 Dalal, V. Arcario, M. J. Petroff, J. T. Dietzen, N. M. Rau, M. J. Fitzpatrick, J. A. J. Brannigan, G. Cheng, W. W. L. 2022-11-20 doi:10.1101/2022.11.20.517256 Cold Spring Harbor Laboratory Press 2022-11-20 <![CDATA[ Homunculus Interruptus: A motor association area in the depth of the central sulcus ]]> https://biorxiv.org/content/10.1101/2022.11.20.517292v1?rss=1 Jensen, M. A. Huang, H. Ojeda Valencia, G. Klassen, B. van den Boom, M. Kaufmann, T. Schalk, G. Brunner, P. Hermes, D. Worrell, G. Miller, K. J. 2022-11-21 doi:10.1101/2022.11.20.517292 Cold Spring Harbor Laboratory Press 2022-11-21 <![CDATA[ A human mitofusin 2 mutation causes mitophagic cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2022.11.22.517462v1?rss=1 Franco, A. Li, J. Kelly, D. P. Hershberger, R. E. Marian, A. J. Lewis, R. M. Song, M. Dang, X. Schmidt, A. D. Mathyer, M. E. Strong, C. d. G. Dorn, G. W. 2022-11-23 doi:10.1101/2022.11.22.517462 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ Engineered reporter phages for rapid detection of Escherichia coli, Klebsiella spp., and Enterococcus spp. in urine ]]> https://biorxiv.org/content/10.1101/2022.11.23.517494v1?rss=1 Meile, S. Du, J. Staubli, S. Grossmann, S. Koliwer-Brandl, H. Piffaretti, P. Leitner, L. Matter, C. I. Baggenstos, J. Hunold, L. Milek, S. Guebeli, C. Kozomara-Hocke, M. Neumeier, V. Botteon, A. Klumpp, J. Marschall, J. McCallin, S. Zbinden, R. Kessler, T. M. Loessner, M. J. Dunne, M. Kilcher, S. 2022-11-23 doi:10.1101/2022.11.23.517494 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ Starfysh reveals heterogeneous spatial dynamics in the breast tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2022.11.21.517420v1?rss=1 He, S. Jin, Y. Nazaret, A. Shi, L. Chen, X. Rampersaud, S. Dhillon, B. S. Valdez, I. Friend, L. E. Fan, J. L. Park, C. Y. Mintz, R. Lao, Y.-H. Carrera, D. Fang, K. W. Mehdi, K. Rohde, M. McFaline-Figueroa, J. L. Blei, D. Leong, K. W. Rudensky, A. Y. Plitas, G. Azizi, E. 2022-11-24 doi:10.1101/2022.11.21.517420 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Accelerating cryptic pocket discovery using AlphaFold ]]> https://biorxiv.org/content/10.1101/2022.11.23.517577v1?rss=1 Meller, A. Bhakat, S. Solieva, S. Bowman, G. R. 2022-11-25 doi:10.1101/2022.11.23.517577 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ Fc-gamma receptor-dependent antibody effector functions are required for vaccine protection against infection by antigenic variants of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2022.11.27.518117v1?rss=1 Mackin, S. R. Desai, P. Whitener, B. M. Karl, C. E. Liu, M. Baric, R. S. Edwards, D. K. Chicz, T. M. McNamara, R. P. Alter, G. Diamond, M. S. 2022-11-29 doi:10.1101/2022.11.27.518117 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ Type I IFN signaling mediates NET release to promote Mycobacterium tuberculosis replication and granuloma caseation ]]> https://biorxiv.org/content/10.1101/2022.11.29.518376v1?rss=1 Sur Chowdhury, C. Kinsella, R. L. Nehls, E. M. Naik, S. K. Lane, D. S. Talukdar, P. Chavez, S. M. Smirnov, A. Beatty, W. Kreamalmeyer, D. Mattila, J. T. Stallings, C. L. 2022-11-29 doi:10.1101/2022.11.29.518376 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ Calpain-2 mediates SARS-CoV-2 entry and represents a therapeutic target ]]> https://biorxiv.org/content/10.1101/2022.11.29.518418v1?rss=1 Zeng, Q. Antia, A. Chavez, M. P. Kutluay, S. B. Ding, S. 2022-11-29 doi:10.1101/2022.11.29.518418 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ Comparing Genomic and Epigenomic Features across Species Using the WashU Comparative Epigenome Browser ]]> https://biorxiv.org/content/10.1101/2022.11.29.518374v1?rss=1 Zhuo, X. Hsu, S. Purushotham, D. Chen, S. Li, D. Wang, T. 2022-12-02 doi:10.1101/2022.11.29.518374 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Rho enhancers play unexpectedly minor roles in Rhodopsin transcription and rod cell integrity ]]> https://biorxiv.org/content/10.1101/2022.12.02.518920v1?rss=1 Sun, C. Ruzycki, P. A. Chen, S. 2022-12-02 doi:10.1101/2022.12.02.518920 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ A cortical circuit for orchestrating oromanual food manipulation ]]> https://biorxiv.org/content/10.1101/2022.12.03.518964v1?rss=1 An, X. Matho, K. S. Li, Y. Mohan, H. Xu, X. H. Whishaw, I. Kepecs, A. Huang, Z. J. 2022-12-03 doi:10.1101/2022.12.03.518964 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ GEMC1 and MCIDAS interactions with SWI/SNF complexes regulate the multiciliated cell-specific transcriptional program ]]> https://biorxiv.org/content/10.1101/2022.12.02.518887v1?rss=1 Lewis, M. Terre, B. Knobel, P. A. Cheng, T. Lu, H. Attolini, C. S. Smak, J. Coyaud, E. Garcia-Cao, I. Querol, J. Gil-Gomez, G. Piergiovanni, G. Costanzo, V. Peiro, S. Raught, B. Zhao, H. Salvatella, X. Roy, S. Mahjoub, M. Stracker, T. H. 2022-12-05 doi:10.1101/2022.12.02.518887 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[ 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[ Moderate High Temperature is Beneficial or Detrimental Depending on Carbon Availability in the Green Alga Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2022.12.04.519034v1?rss=1 Zhang, N. Xia, M. Bailey, C. E. Mattoon, E. M. Zhang, R. 2022-12-07 doi:10.1101/2022.12.04.519034 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Pleiotropy of autism-associated chromatin regulators ]]> https://biorxiv.org/content/10.1101/2022.12.07.519375v1?rss=1 Lasser, M. Sun, N. Xu, Y. Law, K. Gonzalez, S. Wang, B. Drury, V. Drake, S. Zaltsman, Y. Dea, J. Bader, E. McCluskey, K. E. State, M. W. Willsey, A. J. Willsey, H. R. 2022-12-07 doi:10.1101/2022.12.07.519375 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Sleep restores an optimal computational regime in cortical networks ]]> https://biorxiv.org/content/10.1101/2022.12.07.519478v1?rss=1 Xu, Y. Schneider, A. Wessel, R. Hengen, K. B. 2022-12-07 doi:10.1101/2022.12.07.519478 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Small Molecule Screen Identifies Pyrimethamine as an Inhibitor of NRF2-driven Esophageal Hyperplasia ]]> https://biorxiv.org/content/10.1101/2022.12.05.519147v1?rss=1 35,000 small molecules identified eleven potential NRF2 inhibitors. Pyrimethamine and mitoxantrone were validated to inhibit the expression of NRF2 and NQO1 in human ESCC cells in both dose- and time-dependent manners. C_LIO_LIPyrimethamine enhanced NRF2 protein ubiquitination and degradation, resulting a decreased half-life. C_LIO_LIA genetically modified mouse model was established to express the Nrf2E79Q mutant allele in the mouse esophageal epithelium upon tamoxifen induction. Pyrimethamine suppressed the NRF2high esophageal phenotype induced by the mutant allele. C_LI How this study might affect research, practice or policy - summarise the implications of this studyO_LIAs an FDA-approved drug, Pyrimethamine has the potential for immediate translation to a clinical trial on NRF2high ESCC in humans. C_LIO_LIFurther exploration of its mechanisms of action may lead to more potent NRF2 inhibitors for future use. C_LI ]]> Paiboonrungruang, C. Xiong, Z. Lamson, D. Li, Y. Bowman, B. Chembo, J. Huang, C. Li, J. Livingston, E. W. Frank, J. E. Chen, V. Li, Y. Weissman, B. Yuan, H. Williams, K. P. Major, M. Chen, X. 2022-12-08 doi:10.1101/2022.12.05.519147 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ The build-up of the present-day tropical diversity of tetrapods ]]> https://biorxiv.org/content/10.1101/2022.12.05.519156v1?rss=1 Quintero, I. Landis, M. J. Jetz, W. MORLON, H. 2022-12-08 doi:10.1101/2022.12.05.519156 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ ERK1/2 Activation in Macrophages Promotes Leishmania Internalization and Pathogenesis ]]> https://biorxiv.org/content/10.1101/2022.12.08.517760v1?rss=1 Barrie, U. Floyd, K. Datta, A. Wetzel, D. M. 2022-12-09 doi:10.1101/2022.12.08.517760 Cold Spring Harbor Laboratory Press 2022-12-09 <![CDATA[ Neisseria gonorrhoeae co-opts C4b-binding protein to enhance complement-independent survival from neutrophils ]]> https://biorxiv.org/content/10.1101/2022.12.08.519701v1?rss=1 Werner, L. M. Alcott, A. Mohlin, F. Ray, J. C. Belcher Dufrisne, M. Smirnov, A. Columbus, L. Blom, A. M. Criss, A. K. 2022-12-09 doi:10.1101/2022.12.08.519701 Cold Spring Harbor Laboratory Press 2022-12-09 <![CDATA[ Frequent first-trimester pregnancy loss in rhesus macaques infected with African-lineage Zika virus ]]> https://biorxiv.org/content/10.1101/2022.12.09.519791v1?rss=1 Rosinski, J. R. Raasch, L. E. Barros Tiburcio, P. Breitbach, M. E. Shepherd, P. M. Yamamoto, K. Razo, E. Krabbe, N. P. Bliss, M. I. Richardson, A. D. Einwalter, M. A. Weiler, A. M. Sneed, E. L. Fuchs, K. B. Zeng, X. Noguchi, K. K. Morgan, T. K. Alberts, A. J. Antony, K. M. Spanton, R. V. Kabakov, S. Ausderau, K. K. Bohm, E. K. Pritchard, J. C. Ver Hoeve, J. Spanton, R. V. Kim, C. Nork, T. M. Katz, A. W. Rasmussen, C. A. Hartman, A. Mejia, A. Basu, P. Simmons, H. A. Eickhoff, J. C. Friedrich, T. C. Aliota, M. T. Mohr, E. L. Dudley, D. M. O'Connor, D. H. N 2022-12-09 doi:10.1101/2022.12.09.519791 Cold Spring Harbor Laboratory Press 2022-12-09 <![CDATA[ Multiomic Profiling Reveals Metabolic Alterations Mediating Aberrant Platelet Activity and Inflammation in Myeloproliferative Neoplasms ]]> https://biorxiv.org/content/10.1101/2022.12.08.519689v1?rss=1 He, F. Laranjeira, A. B. A. kong, t. Liu, A. Bark, K. Lasky, N. M. Fisher, D. A. C. Cox, M. J. Fulbright, M. Yu, L. Sykes, S. M. DAlessandro, A. Di Paola, J. Oh, S. 2022-12-11 doi:10.1101/2022.12.08.519689 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Ecological drivers and evolutionary consequences of torpor in Andean hummingbirds ]]> https://biorxiv.org/content/10.1101/2022.12.08.519654v1?rss=1 Hernandez, D. C. R. Baldwin, J. Londono, G. A. 2022-12-12 doi:10.1101/2022.12.08.519654 Cold Spring Harbor Laboratory Press 2022-12-12 <![CDATA[ Phantasus: web-application for visual and interactive gene expression analysis ]]> https://biorxiv.org/content/10.1101/2022.12.10.519861v1?rss=1 Kleverov, M. Zenkova, D. Kamenev, V. Sablina, M. Artyomov, M. Sergushichev, A. 2022-12-12 doi:10.1101/2022.12.10.519861 Cold Spring Harbor Laboratory Press 2022-12-12 <![CDATA[ Awake Hippocampal-Cortical Co-reactivation Is Associated with Forgetting ]]> https://biorxiv.org/content/10.1101/2022.12.10.519896v1?rss=1 Tanriverdi, B. Cowan, E. T. Metoki, A. Jobson, K. R. Murty, V. P. Chein, J. Olson, I. R. 2022-12-13 doi:10.1101/2022.12.10.519896 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Multimodal Imaging-Based Classification of PTSD Using Data-Driven Computational Approaches: A Multisite Big Data Study from the ENIGMA-PGC PTSD Consortium ]]> https://biorxiv.org/content/10.1101/2022.12.12.519838v1?rss=1 Zhu, X. Kim, Y. Ravid, O. He, X. Suarez-Jimenez, B. Zilcha-Mano, S. Lazarov, A. Lee, S. Abdallah, C. G. Angstadt, M. Averill, C. L. Baird, C. L. Baugh, L. A. Blackford, J. U. Bomyea, J. Bruce, S. E. Bryant, R. A. Cao, Z. Choi, K. Cisler, J. Cotton, A. S. Daniels, J. K. Davenport, N. D. Davidson, R. J. DeBellis, M. D. Dennis, E. L. Densmore, M. deRoon-Cassini, T. Disner, S. G. El Hage, W. Etkin, A. Fani, N. Fercho, K. A. Fitzgerald, J. Forster, G. L. Frijling, J. L. Geuze, E. Gonenc, A. Gordon, E. M. Gruber, S. Grupe, D. W. Guenette, J. P. Haswell, C. C 2022-12-13 doi:10.1101/2022.12.12.519838 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Conditional deletion of LRRC8A in the brain protects against stroke damage independently of effect on swelling-activated glutamate release ]]> https://biorxiv.org/content/10.1101/2022.12.13.520314v1?rss=1 Balkaya, M. Dohare, P. Chen, S. Schober, A. L. Fidaleo, A. M. Nalwalk, J. W. Sah, R. Mongin, A. A. 2022-12-13 doi:10.1101/2022.12.13.520314 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Enhanced survival and low proliferation marks multifunctional virus specific memory CD4 T cells ]]> https://biorxiv.org/content/10.1101/2022.12.13.520219v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@93e62forg.highwire.dtl.DTLVardef@1ed2444org.highwire.dtl.DTLVardef@1e7f79borg.highwire.dtl.DTLVardef@30e31d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG ]]> Westerhof, L. M. Noonan, J. Hargrave, K. E. Chimbayo, E. T. Cheng, Z. Purnell, T. Jackson, M. R. Borcherding, N. MacLeod, M. K. 2022-12-15 doi:10.1101/2022.12.13.520219 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Motion Impact Score for Detecting Spurious Brain-Behavior Associations ]]> https://biorxiv.org/content/10.1101/2022.12.16.520797v1?rss=1 95% specific at sample sizes of n = 100 and above. SHAMAN was powered to detect motion overestimation scores 80% of the time at sample sizes of n = 5,000 but could detect motion underestimation scores only 50% of the time at n = 5000, making it most useful for researchers seeking to avoid overestimating trait-FC effects in large BWAS. We computed motion impact scores for trait-FC effect with 45 demographic, biophysical, cognitive, and personality traits from n = 7,270 participants in the Adolescent Brain Cognitive Development (ABCD) Study. After standard denoising with ABCD-BIDS and without motion censoring, 42% (19/45) of traits had significant (p < 0.05) motion overestimation scores and 38% (17/45) of traits had significant motion underestimation scores. Censoring at framewise displacement (FD) < 0.2 mm reduced the proportion of traits with significant motion overestimation scores from 42% to 2% (1/45) but did not decrease the number of traits with significant motion underestimation scores. ]]> Kay, B. P. Montez, D. F. Marek, S. Tervo-Clemmens, B. Siegel, J. S. Adeyemo, B. Laumann, T. O. Metoki, A. Chauvin, R. J. Van, A. N. Krimmel, S. R. Miller, R. Newbold, D. J. Zheng, A. Seider, N. A. Scheidter, K. M. Monk, J. Feczko, E. J. Randolph, A. Miranda Dominguez, O. Moore, L. A. Perrone, A. J. Conan, G. M. Earl, E. A. Malone, S. M. Cordova, M. Doyle, O. Lynch, B. J. Wilgenbusch, J. C. Pengo, T. Graham, A. M. Roland, J. L. Gordon, E. M. Snyder, A. Z. Barch, D. Fair, D. A. Dosenbach, N. U. 2022-12-17 doi:10.1101/2022.12.16.520797 Cold Spring Harbor Laboratory Press 2022-12-17 <![CDATA[ A patterned human heart tube organoid model generated by pluripotent stem cell self-assembly ]]> https://biorxiv.org/content/10.1101/2022.12.16.519611v1?rss=1 Volmert, B. Aguirre, A. Riggs, A. Wang, F. Juhong, A. Kiselev, A. Kostina, A. O'Hern, C. Muniyandi, P. Wasserman, A. Huang, A. Lewis-Israeli, Y. Park, S. Qiu, Z. Zhou, C. 2022-12-19 doi:10.1101/2022.12.16.519611 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ A high-impact COL6A3 mutation alters the response of chondrocytes in neo-cartilage organoids to hyper-physiologic mechanical loading ]]> https://biorxiv.org/content/10.1101/2022.12.19.520461v1?rss=1 Bloks, N. G. C. Harissa, Z. Adkar, S. S. Dicks, A. Hajmousa, G. Steward, N. Koning, R. I. Mulder, A. de Koning, B. B. R. Kloppenburg, M. Coutinho de Almeida, R. Ramos, Y. F. M. Guilak, F. Meulenbelt, I. 2022-12-19 doi:10.1101/2022.12.19.520461 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ NEK7 activates the NLRP1 Inflammasome ]]> https://biorxiv.org/content/10.1101/2022.12.21.521400v1?rss=1 Muela-Zarzuela, I. Gallardo-Orihuela, A. Pino-Angeles, A. Suarez-Rivero, J. M. Boy-Ruiz, D. de Gregorio-Procopio, M. Oroz, J. Mbalaviele, G. Cordero, M. D. 2022-12-22 doi:10.1101/2022.12.21.521400 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Deep Generative Design of Epitope-Specific Binding Proteins by Latent Conformation Optimization ]]> https://biorxiv.org/content/10.1101/2022.12.22.521698v1?rss=1 Eguchi, R. R. Choe, C. A. Parekh, U. Khalek, I. S. Ward, M. D. Vithani, N. Bowman, G. R. Jardine, J. G. Huang, P. 2022-12-23 doi:10.1101/2022.12.22.521698 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ RanGTP regulates the augmin complex ]]> https://biorxiv.org/content/10.1101/2022.12.23.521824v1?rss=1 Kraus, J. Travis, S. M. King, M. R. Petry, S. 2022-12-23 doi:10.1101/2022.12.23.521824 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ Crystal structure of the Arabidopsis SPIRAL2 C-terminal domain reveals a p80-Katanin-like domain ]]> https://biorxiv.org/content/10.1101/2022.12.28.522140v1?rss=1 Bolhuis, D. L. Dixit, R. Slep, K. C. 2022-12-29 doi:10.1101/2022.12.28.522140 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Deficiency in Galectin-3, -8, and -9 impairs immunity to chronic Mycobacterium tuberculosis infection but not acute infection with multiple intracellular pathogens ]]> https://biorxiv.org/content/10.1101/2022.12.29.522180v1?rss=1 Morrison, H. M. Craft, J. Rivera-Lugo, R. Johnson, J. R. Golovkine, G. R. Dodd, C. E. Van Dis, E. Beatty, W. L. Margolis, S. R. Repasy, T. Shaker, I. Lee, A. Y. Vance, R. E. Stanley, S. A. Krogan, N. J. Portnoy, D. A. Penn, B. H. Cox, J. S. 2022-12-29 doi:10.1101/2022.12.29.522180 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Evaluating the efficacy of commercially available antisense oligonucleotides to reduce mouse and human tau in vivo ]]> https://biorxiv.org/content/10.1101/2022.12.29.522258v1?rss=1 Vemula, P. Schoch, K. M. Miller, T. M. 2022-12-29 doi:10.1101/2022.12.29.522258 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Starvation sensing by mycobacterial RelA/SpoT homologue through constitutive surveillance of translation ]]> https://biorxiv.org/content/10.1101/2022.12.29.522164v1?rss=1 Li, Y. Majumdar, S. Treen, R. Sharma, M. R. Corro, J. Gamper, H. Manjari, S. R. Prusa, J. Banavali, N. K. Stallings, C. L. Hou, Y.-M. Agrawal, R. L. Ojha, A. K. 2022-12-30 doi:10.1101/2022.12.29.522164 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ Predicting regulators of epithelial cell state through regularized regression analysis of single cell multiomic sequencing ]]> https://biorxiv.org/content/10.1101/2022.12.29.522232v1?rss=1 Ledru, N. Wilson, P. C. Muto, Y. Yoshimura, Y. Wu, H. Asthana, A. Tullius, S. G. Waikar, S. S. Orlando, G. Humphreys, B. 2022-12-30 doi:10.1101/2022.12.29.522232 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ Intracranial recordings reveal three distinct neural response patterns in the language network ]]> https://biorxiv.org/content/10.1101/2022.12.30.522216v1?rss=1 Regev, T. I. Casto, C. Hosseini, E. A. Adamek, M. Brunner, P. Fedorenko, E. 2022-12-30 doi:10.1101/2022.12.30.522216 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ Simple Models For Neuroscience Research Discoveries: How Often Are These Models Used In Africa ]]> https://biorxiv.org/content/10.1101/2022.12.30.522314v1?rss=1 Hamidu, S. k. Ahmad, U. Abdulazeez, R. Zaid, M. Alkhamis, A. I. Umar, M. Ladan, A. A. Nasr, F. E. Ahmad, A. Musa, S. Ya'u, J. Hamman, W. O. Yoshimatsu, T. Issa, S. R. Maina, M. B. 2022-12-31 doi:10.1101/2022.12.30.522314 Cold Spring Harbor Laboratory Press 2022-12-31 <![CDATA[ Predicting alcohol-related memory problems in older adults: A machine learning study with multi-domain features ]]> https://biorxiv.org/content/10.1101/2022.12.30.522330v1?rss=1 Kamarajan, C. Pandey, A. K. Chorlian, D. B. Meyers, J. L. Kinreich, S. Pandey, G. Subbie Saenz de Viteri, S. Zhang, J. Kuang, W. Barr, P. B. Aliev, F. Anokhin, A. P. Plawecki, M. H. Kuperman, S. Almasy, L. Merikangas, A. Brislin, S. J. Bauer, L. Hesselbrock, V. Chan, G. Kramer, J. Lai, D. Hartz, S. Bierut, L. J. McCutcheon, V. V. Bucholz, K. K. Dick, D. M. Schuckit, M. A. Edenberg, H. J. Porjesz, B. 2023-01-02 doi:10.1101/2022.12.30.522330 Cold Spring Harbor Laboratory Press 2023-01-02 <![CDATA[ Apolipoprotein E O-glycosylation is associated with amyloid plaques and APOE genotype. ]]> https://biorxiv.org/content/10.1101/2023.01.03.522616v1?rss=1 Lawler, P. E. Bollinger, J. G. Schindler, S. E. Hodge, C. R. Iglesias, N. J. Krishnan, V. Coulton, J. B. Li, Y. Holtzman, D. M. Bateman, R. J. 2023-01-03 doi:10.1101/2023.01.03.522616 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Human CCR6+ Th cells show both an extended stable gradient of Th17 activity and imprinted plasticity ]]> https://biorxiv.org/content/10.1101/2023.01.05.522630v1?rss=1 Singh, S. P. Parween, F. Edara, N. Zhang, H. H. Chen, J. Otaizo-Carrasquero, F. Cheng, D. Oppenheim, N. A. Ransier, A. Zhu, W. Shamsaddini, A. Gardina, P. J. Darko, S. W. Singh, T. P. Douek, D. C. Myers, T. G. Farber, J. M. 2023-01-06 doi:10.1101/2023.01.05.522630 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Single Molecule Mechanics and Kinetics of Cardiac Myosin Interacting with Regulated Thin Filaments ]]> https://biorxiv.org/content/10.1101/2023.01.09.522880v1?rss=1 Clippinger Schulte, S. R. Scott, B. Barrick, S. K. Stump, W. T. Greenberg, M. J. 2023-01-10 doi:10.1101/2023.01.09.522880 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue ]]> https://biorxiv.org/content/10.1101/2023.01.09.523303v1?rss=1 Dhavale, D. D. Barclay, A. M. Borcik, C. G. Basore, K. Gordon, I. R. Liu, J. Milchberg, M. H. O'Shea, J. Y. Rau, M. J. Smith, Z. Sen, S. Summers, B. Smith, J. W. Warmuth, O. A. Chen, Q. Fitzpatrick, J. A. J. Schwieters, C. D. Tajkhorshid, E. Rienstra, C. M. Kotzbauer, P. T. 2023-01-10 doi:10.1101/2023.01.09.523303 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ 13C and 15N Resonance Assignments of Alpha Synuclein Fibrils Amplified from Lewy Body Dementia Tissue ]]> https://biorxiv.org/content/10.1101/2023.01.09.523339v1?rss=1 Barclay, A. M. Dhavale, D. D. Borcik, C. G. Milchberg, M. H. Kotzbauer, P. T. Rienstra, C. M. 2023-01-10 doi:10.1101/2023.01.09.523339 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Spatial transcriptomics reveals a conserved segment polarity program that governs muscle patterning in Nematostella vectensis ]]> https://biorxiv.org/content/10.1101/2023.01.09.523347v1?rss=1 He, S. Shao, W. Chen, S. Wang, T. Gibson, M. 2023-01-10 doi:10.1101/2023.01.09.523347 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Ethanolaminephosphate cytidyltransferase is essential for survival, lipid homeostasis and stress tolerance in Leishmania major ]]> https://biorxiv.org/content/10.1101/2023.01.10.523530v1?rss=1 Basu, S. Pawlowic, M. Hsu, F.-F. Thomas, G. Zhang, K. 2023-01-11 doi:10.1101/2023.01.10.523530 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ MANF stimulates autophagy and restores mitochondrial homeostasis to treat toxic proteinopathy ]]> https://biorxiv.org/content/10.1101/2023.01.10.523171v1?rss=1 Kim, Y. Li, C. Gu, C. Tycksen, E. Puri, A. Pietka, T. A. Sivapackiam, J. Fang, Y. Kidd, K. Park, S.-J. Johnson, B. G. Kmoch, S. Duffield, J. S. Bleyer, A. J. Jackrel, M. E. Urano, F. Vijay, s. Lindahl, M. Chen, Y. M. 2023-01-12 doi:10.1101/2023.01.10.523171 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ Poison exon annotations improve the yield of clinically relevant variants in genomic diagnostic testing ]]> https://biorxiv.org/content/10.1101/2023.01.12.523654v1?rss=1 Felker, S. A. Lawlor, J. M. J. Hiatt, S. M. Thompson, M. L. Latner, D. R. Finnila, C. R. Bowling, K. M. Bonnstetter, Z. T. Bonini, K. E. Kelly, N. R. Kelley, W. V. Hurst, A. C. E. Kelly, M. A. Nakouzi, G. Hendon, L. G. Bebin, E. M. Kenny, E. Cooper, G. M. 2023-01-13 doi:10.1101/2023.01.12.523654 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Real-time feedback reduces participant motion during task-based fMRI ]]> https://biorxiv.org/content/10.1101/2023.01.12.523791v1?rss=1 Rogers, C. S. Jones, M. S. McConkey, S. McLaughlin, D. J. Peelle, J. E. 2023-01-13 doi:10.1101/2023.01.12.523791 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Adsorption of RNA to interfaces of biomolecular condensates enables wetting transitions ]]> https://biorxiv.org/content/10.1101/2023.01.12.523837v1?rss=1 Erkamp, N. A. Farag, M. Qian, D. Sneideris, T. Welsh, T. J. Ausserwoger, H. Weitz, D. Pappu, R. V. Knowles, T. 2023-01-13 doi:10.1101/2023.01.12.523837 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Perinatal folate levels do not influence tumor latency or multiplicity in a model of NF1 associated plexiform-like neurofibromas ]]> https://biorxiv.org/content/10.1101/2023.01.13.523962v1?rss=1 Marley, A. R. Williams, K. B. Tibbitts, J. Moertel, C. L. Johnson, K. Linden, M. A. Largaespada, D. A. Marcotte, E. L. 2023-01-13 doi:10.1101/2023.01.13.523962 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ The effect of Dnaaf5 gene dosage on primary ciliary dyskinesia phenotypes ]]> https://biorxiv.org/content/10.1101/2023.01.13.523966v1?rss=1 Horani, A. Gupta, D. K. Xu, J. Xu, H. Puga-Molina, L. D. C. Santi, C. Ramagiri, S. Brennen, S. K. Pan, J. Huang, T. Hyland, R. M. Gunsten, S. Tzeng, S.-C. Strahle, J. M. Mill, P. Mahjoub, M. R. Dutcher, S. K. Brody, S. L. 2023-01-14 doi:10.1101/2023.01.13.523966 Cold Spring Harbor Laboratory Press 2023-01-14 <![CDATA[ Activation of the Plasmodium egress effector subtilisin-like protease 1 is achieved by plasmepsin X destruction of the propiece. ]]> https://biorxiv.org/content/10.1101/2023.01.13.524002v1?rss=1 Mukherjee, S. Nasamu, A. S. Rubiano, K. Goldberg, D. 2023-01-14 doi:10.1101/2023.01.13.524002 Cold Spring Harbor Laboratory Press 2023-01-14 <![CDATA[ Automated quantitative trait locus analysis (AutoQTL) ]]> https://biorxiv.org/content/10.1101/2023.01.12.523835v1?rss=1 Freda, P. J. Ghosh, A. Zhang, E. Luo, T. Chitre, A. Polesskaya, O. St. Pierre, C. L. Gao, J. Martin, C. D. Chen, H. Garcia-Martinez, A. G. Wang, T. Han, W. Ishiwari, K. Meyer, P. Lamparelli, A. King, C. P. Palmer, A. A. Li, R. Moore, J. H. 2023-01-15 doi:10.1101/2023.01.12.523835 Cold Spring Harbor Laboratory Press 2023-01-15 <![CDATA[ Therapeutic and vaccine-induced cross-reactive antibodies with effector function against emerging Omicron variants ]]> https://biorxiv.org/content/10.1101/2023.01.17.523798v1?rss=1 Addetia, A. Piccoli, L. Case, J. B. Park, Y.-J. Beltramello, M. Guarino, B. Dang, H. Pinto, D. Scheaffer, S. Sprouse, K. Bassi, J. Silacci-Fregni, C. Muoio, F. Dini, M. Vincenzetti, L. Acosta, R. Johnson, D. Subramanian, S. Saliba, C. Giurdanella, M. Lombardo, G. Leoni, G. Culap, K. McAlister, C. Rajesh, A. Dellota, E. Cameroni, E. Whitener, B. Giannini, O. Ceschi, A. Ferrari, P. Franzetti-Pellanda, A. Biggiogero, M. Garzoni, C. Zappi, S. Bernasconi, L. Kim, M. J. Schnell, G. Czudnochowski, N. Franko, N. Logue, J. K. Yoshiyama, C. Stewart, C. Chu, H. 2023-01-17 doi:10.1101/2023.01.17.523798 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ Extensive characterization of a Williams Syndrome murine model shows Gtf2ird1-mediated rescue of select sensorimotor tasks, but no effect on enhanced social behavior ]]> https://biorxiv.org/content/10.1101/2023.01.18.523029v1?rss=1 Dougherty, J. D. Nygaard, K. R. Maloney, S. E. Swift, R. G. McCullough, K. B. Wagner, R. E. Fass, S. B. Garbett, K. Mirnics, K. Veenstra-VanderWeele, J. 2023-01-18 doi:10.1101/2023.01.18.523029 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ A dual MTOR/NAD+ acting gerotherapy ]]> https://biorxiv.org/content/10.1101/2023.01.16.523975v1?rss=1 Li, J. Kumar, S. Miachin, K. Bean, N. L. Halawi, O. Lee, S. Niehoff, M. Pierre, T. H. Colca, J. Kletzien, R. F. Tanis, S. P. Chen, Y. Griffett, K. Niehoff, M. Miller, T. M. Hor, J.-H. Ng, S.-Y. Wallace, K. Rindtorff, N. Farr, S. A. McCommis, K. S. Finck, B. N. Peterson, T. R. 2023-01-19 doi:10.1101/2023.01.16.523975 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ ProteoM enables deep and precise identification of peptides in data-dependent acquisition proteomics ]]> https://biorxiv.org/content/10.1101/2023.01.17.524387v1?rss=1 Zhang, Q. 2023-01-19 doi:10.1101/2023.01.17.524387 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Tipifarnib potentiates the antitumor effects of PI3Kα inhibition in PIK3CA- and HRAS-dysregulated HNSCC via convergent inhibition of mTOR activity ]]> https://biorxiv.org/content/10.1101/2023.01.17.523964v1?rss=1 45% of R/M HNSCC patients. By blocking feedback reactivation of mTORC1, tipifarnib may prevent adaptive resistance to additional targeted therapies, thereby enhancing their clinical utility. ]]> Smith, A. E. Chan, S. Wang, Z. McCloskey, A. Reilly, Q. Wang, J. Z. Patel, H. V. Koshizuka, K. Soifer, H. S. Kessler, L. Dayoub, A. Villaflor, V. Adkins, D. Bruce, J. Y. Ho, A. Perez, C. A. Hanna, G. J. Gasco Hernandez, A. Saunders, A. Dale, S. Gutkind, J. S. Burrows, F. Malik, S. 2023-01-20 doi:10.1101/2023.01.17.523964 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Limits to the spread of an obligate social cheater in the social amoeba Dictyostelium discoideum ]]> https://biorxiv.org/content/10.1101/2023.01.17.524501v1?rss=1 Medina, J. M. Queller, D. Strassmann, J. E. 2023-01-20 doi:10.1101/2023.01.17.524501 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Aging reduces motivation through decreased Bdnf expression in the ventral tegmental area ]]> https://biorxiv.org/content/10.1101/2023.01.19.524624v1?rss=1 Lei, H. C. Parker, K. E. Yuede, C. M. McCall, J. G. Imai, S.-i. 2023-01-20 doi:10.1101/2023.01.19.524624 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Gut-associated lymphoid tissue attrition associates with response to anti-α4β7 therapy in ulcerative colitis ]]> https://biorxiv.org/content/10.1101/2023.01.19.524731v1?rss=1 Canales-Herrerias, P. Uzzan, M. Seki, A. Czepielewski, R. S. Verstockt, B. Livanos, A. Raso, F. Dunn, A. Dai, D. Wang, A. Al-taie, Z. Martin, J. Ko, H. M. Tokuyama, M. Tankelevich, M. Meringer, H. Cossarini, F. Jha, D. Krek, A. Paulsen, J. D. Zuber Nakadar, M. Wong, J. Erlich, E. C. Onufer, E. J. Helmink, B. A. Sharma, K. Rosenstein, A. Chung, G. Dawson, T. Juarez, J. Yajnik, V. Cerutti, A. Faith, J. Suarez-Farinas, M. Argmann, C. Petralia, F. Randolph, G. J. Polydorides, A. D. Reboldi, A. Colombel, J. F. Mehandru, S. 2023-01-20 doi:10.1101/2023.01.19.524731 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ A cathepsin C-like protease post-translationally modifies Toxoplasma gondii secretory proteins for optimal invasion and egress. ]]> https://biorxiv.org/content/10.1101/2023.01.21.525043v1?rss=1 Thornton, L. B. Key, M. Micchelli, C. Stasic, A. J. Kwain, S. Floyd, K. Moreno, S. N. J. Dominy, B. N. Whitehead, D. C. Dou, Z. 2023-01-22 doi:10.1101/2023.01.21.525043 Cold Spring Harbor Laboratory Press 2023-01-22 <![CDATA[ Cognitive and neural bases of salience-driven incidental learning ]]> https://biorxiv.org/content/10.1101/2023.01.23.525123v1?rss=1 Sun, S. Yu, H. Wang, S. Yu, R. 2023-01-23 doi:10.1101/2023.01.23.525123 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Three-dimensional imaging and quantification of mouse ovarian follicles via optical coherence tomography ]]> https://biorxiv.org/content/10.1101/2023.01.23.525192v1?rss=1 Amaral, M. M. Sun, A. Li, Y. Ren, C. Truong, A. B. Nigam, S. Jiao, Z. Wang, P. Zhou, C. 2023-01-23 doi:10.1101/2023.01.23.525192 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Functional connectivity between the amygdala and prefrontal cortex underlies processing of emotion ambiguity ]]> https://biorxiv.org/content/10.1101/2023.01.24.525116v1?rss=1 Sun, S. Yu, H. Yu, R. Wang, S. 2023-01-25 doi:10.1101/2023.01.24.525116 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Structural variation across 138,134 samples in the TOPMed consortium ]]> https://biorxiv.org/content/10.1101/2023.01.25.525428v1?rss=1 90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hemotologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression. ]]> Jun, G. English, A. C. Metcalf, G. A. Yang, J. Chaisson, M. J. Pankratz, N. Menon, V. K. Salerno, W. J. Krasheninina, O. Smith, A. V. Lane, J. A. Blackwell, T. Kang, H. M. Salvi, S. Meng, Q. Shen, H. Pasham, D. Bhamidipati, S. Kottapalli, K. Arnett, D. K. Ashley-Koch, A. Auer, P. L. Beutel, K. M. Bis, J. C. Blangero, J. Bowden, D. W. Brody, J. A. Cade, B. E. Chen, Y.-D. I. Cho, M. H. Curran, J. E. Fornage, M. Freedman, B. I. Fingerlin, T. Gelb, B. D. Hou, L. Hung, Y.-J. Kane, J. P. Kaplan, R. Kim, W. Loos, R. J. F. Marcus,, G. M. Mathias, R. A. McGarv 2023-01-26 doi:10.1101/2023.01.25.525428 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ Strain Tracking with Uncertainty Quantification ]]> https://biorxiv.org/content/10.1101/2023.01.25.525531v1?rss=1 Kim, Y. Worby, C. J. Acharya, S. van Dijk, L. R. Alfonsetti, D. Gromko, Z. J. Azimzadeh, P. N. Dodson, K. W. Gerber, G. K. Hultgren, S. J. Earl, A. M. Berger, B. Gibson, T. E. 2023-01-26 doi:10.1101/2023.01.25.525531 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ Costimulatory domains direct distinct fates of CAR-driven T cell dysfunction ]]> https://biorxiv.org/content/10.1101/2023.01.26.525725v1?rss=1 Selli, M. E. Landmann, J. H. Terekhova, M. Lattin, J. Heard, A. Hsu, Y.-S. Chang, T.-C. Warrington, J. M. Ha, H. Kingston, N. Hogg, G. Slade, M. Berrien-Elliot, M. M. Foster, M. Kersting-Schadek, S. Gruszczynska, A. DeNardo, D. Fehniger, T. A. Artyomov, M. Singh, N. 2023-01-27 doi:10.1101/2023.01.26.525725 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Single fluorogen imaging reveals spatial inhomogeneities within biomolecular condensates ]]> https://biorxiv.org/content/10.1101/2023.01.26.525727v1?rss=1 Wu, T. King, M. R. Farag, M. Pappu, R. V. Lew, M. D. 2023-01-27 doi:10.1101/2023.01.26.525727 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ The Autophagy Receptor NBR1 Directs the Clearance of Photodamaged Chloroplasts ]]> https://biorxiv.org/content/10.1101/2023.01.27.525901v1?rss=1 Lee, H.-N. V Chacko, J. Gonzalez Solis, A. Chen, K.-E. Barros, J. A. S. Signorelli, S. Havey Millar, A. Vierstra, R. D. Eliceiri, K. W. Otegui, M. S. 2023-01-28 doi:10.1101/2023.01.27.525901 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ HAT: de novo variant calling for highly accurate short-read and long-read sequencing data ]]> https://biorxiv.org/content/10.1101/2023.01.27.525940v1?rss=1 Ng, J. K. Turner, T. N. 2023-01-28 doi:10.1101/2023.01.27.525940 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ Dimerization mechanism of an inverted-topology ion channel in membranes ]]> https://biorxiv.org/content/10.1101/2023.01.27.525942v1?rss=1 Ernst, M. Orabi, E. A. Stockbridge, R. B. Faraldo-Gomez, J. D. Robertson, J. L. 2023-01-28 doi:10.1101/2023.01.27.525942 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ Exponential increase in QTL detection with increased sample size. ]]> https://biorxiv.org/content/10.1101/2023.01.27.525982v1?rss=1 Chitre, A. S. Polesskaya, O. Munro, D. Cheng, R. Mohammadi, P. Holl, K. Gao, J. Bimschleger, H. V. Garcia Martinez, A. George, A. Gileta, A. F. Han, W. Horvath, A. Hughson, A. Ishiwari, K. King, C. P. Lamparelli, A. Versaggi, C. L. Martin, C. St. Pierre, C. L. Tripi, J. A. Richards, J. B. Wang, T. Chen, H. Flagel, S. B. Meyer, P. Robinson, T. E. Solberg Woods, L. C. Palmer, A. A. 2023-01-29 doi:10.1101/2023.01.27.525982 Cold Spring Harbor Laboratory Press 2023-01-29 <![CDATA[ Arrhythmia-associated Calmodulin Variants Interact with KCNQ1 to Confer Aberrant Membrane Trafficking and Function ]]> https://biorxiv.org/content/10.1101/2023.01.28.526031v1?rss=1 10 arrhythmia-associated CaM variants effect on KCNQ1. We identify one variant (G114W) that exhibits severely weakened binding to KCNQ1 but find that most other CaM variants interact with similar binding affinity to KCNQ1 when compared to CaM wild-type over physiological Ca2+ ranges. We further identify several CaM variants that affect KCNQ1 and IKs membrane trafficking and/or baseline current activation kinetics, thereby contextualizing KCNQ1 dysfunction in calmodulinopathy. Lastly, we delineate CaM variants with no effect on KCNQ1 function. ConclusionsThis study provides comprehensive functional data that reveal how CaM variants contribute to creating a pro-arrhythmic substrate by causing abnormal KCNQ1 membrane trafficking and current conduction. We find that CaM variant regulation of KCNQ1 is not uniform with effects varying from benign to significant loss of function. This study provides a new approach to collecting details of CaM binding that are key for understanding how CaM variants predispose patients to arrhythmia via the dysregulation of multiple cardiac ion channels. ]]> Kang, P. w. Woodbury, L. Angsutararux, P. Sambare, N. Shi, J. Marras, M. Abella, C. Bedi, A. Zinn, D. Cui, J. Silva, J. R. 2023-01-29 doi:10.1101/2023.01.28.526031 Cold Spring Harbor Laboratory Press 2023-01-29 <![CDATA[ Improved Ethanol Tolerance and Production in Pyruvate Dehydrogenase Mutant of Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2023.01.29.526136v1?rss=1 Yang, A. Ranaivoarisoa, T. O. Bose, A. 2023-01-30 doi:10.1101/2023.01.29.526136 Cold Spring Harbor Laboratory Press 2023-01-30 <![CDATA[ Functional Trajectories after Zebrafish Spinal Cord Transection ]]> https://biorxiv.org/content/10.1101/2023.01.31.526502v1?rss=1 Jensen, N. O. Burris, B. Zhou, L. Yamada, H. Reyes, C. Mokalled, M. H. 2023-01-31 doi:10.1101/2023.01.31.526502 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Kv12-Encoded K+ Channels Drive the Day-Night Switch in the Repetitive Firing Rates of SCN Neurons ]]> https://biorxiv.org/content/10.1101/2023.01.30.526323v1?rss=1 Hermanstyne, T. O. Yang, N.-D. Granados-Fuentes, D. Li, X. Mellor, R. Jegla, T. Herzog, E. Nerbonne, J. M. 2023-02-02 doi:10.1101/2023.01.30.526323 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ Metabolomics reveals nucleoside analogs for regulating mucosal-associated invariant T cell responses ]]> https://biorxiv.org/content/10.1101/2023.01.30.526332v1?rss=1 Huang, S. Sharma, M. Sallans, L. Li, C. Kh, Z. Choubey, D. Newburg, D. Huaman, M. Hansen, T. Cao, S. 2023-02-02 doi:10.1101/2023.01.30.526332 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ Replicative Acinetobacter baumannii strains interfere with phagosomal maturation by modulating the vacuolar pH ]]> https://biorxiv.org/content/10.1101/2023.02.02.526753v1?rss=1 Distel, J. S. Di Venanzio, G. Mackel, J. J. Rosen, D. Feldman, M. F. 2023-02-02 doi:10.1101/2023.02.02.526753 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ FHF2 phosphorylation and regulation of native myocardial NaV1.5 channels ]]> https://biorxiv.org/content/10.1101/2023.01.31.526475v1?rss=1 Lesage, A. Lorenzini, M. Burel, S. Sarlandie, M. Bibault, F. Maloney, D. Silva, J. Townsend, R. R. Nerbonne, J. M. Marionneau, C. 2023-02-03 doi:10.1101/2023.01.31.526475 Cold Spring Harbor Laboratory Press 2023-02-03 <![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[ Extracellular Vesicles from Inflammation-Primed Adipose-Derived Stem Cells Enhance Achilles Tendon Repair by Reducing Inflammation and Promoting Intrinsic Healing ]]> https://biorxiv.org/content/10.1101/2023.01.31.526532v1?rss=1 Shen, H. Lane, R. A. 2023-02-03 doi:10.1101/2023.01.31.526532 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ SCCA1/SERPINB3 promotes suppressive immune environment via STAT-dependent chemokine production, blunting the therapy-induced T cell responses ]]> https://biorxiv.org/content/10.1101/2023.02.01.526675v1?rss=1 Markovina, S. Chen, L.-Y. Shi, V. Wang, S. Freeman, R. Ruiz, F. Jayachandran, K. Zhang, J. Cosper, P. Sun, L. Luke, C. Spina, C. Grigsby, P. Schwarz, J. 2023-02-03 doi:10.1101/2023.02.01.526675 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Adipocyte lipin 1 is positively associated with metabolic health in humans and regulates systemic metabolism in mice. ]]> https://biorxiv.org/content/10.1101/2023.02.01.526676v1?rss=1 LaPoint, A. Singer, J. M. Ferguson, D. Shew, T. M. RenKemeyer, K. Palacios, H. Field, R. Shankaran, M. Smith, G. I. Yoshino, J. He, M. Patti, G. J. Hellerstein, M. Klein, S. Brestoff, J. R. Finck, B. Lutkewitte, A. J. 2023-02-03 doi:10.1101/2023.02.01.526676 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ An electrochemical approach for rapid, sensitive, and selective detection of dynorphin ]]> https://biorxiv.org/content/10.1101/2023.02.01.526701v1?rss=1 Conway, S. M. Kuo, C.-C. Gardiner, W. Wu, R.-N. Thang, L. Gereau, G. Yuede, C. Cirrito, J. McCall, J. G. Al-Hasani, R. 2023-02-03 doi:10.1101/2023.02.01.526701 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ CDK4/6 inhibition enhances SHP2 inhibitor efficacy and is dependent upon restoration of RB function in malignant peripheral nerve sheath tumors ]]> https://biorxiv.org/content/10.1101/2023.02.02.526674v1?rss=1 Wang, J. Calizo, A. Zhang, L. Pino, J. C. Lyu, Y. Pollard, K. Zhang, X. Larsson, A. T. Conniff, E. Llosa, N. Wood, D. K. Largaespada, D. A. Moody, S. E. Gosline, S. J. Hirbe, A. C. Pratilas, C. A. 2023-02-03 doi:10.1101/2023.02.02.526674 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Phenelzine-based probes reveal Secernin-3 is involved in thermal nociception ]]> https://biorxiv.org/content/10.1101/2023.02.02.526866v1?rss=1 Bustin, K. A. Shishikura, K. Chen, I. Lin, Z. McNight, N. Chang, Y. Wang, X. Pei, L. Lin, J. J. Arellano, E. Morton, P. D. Gregus, A. M. Buczynski, M. W. Matthews, M. L. 2023-02-03 doi:10.1101/2023.02.02.526866 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms ]]> https://biorxiv.org/content/10.1101/2023.02.01.526652v1?rss=1 Zheng, Y. Sun, C. Zhang, X. Ruzycki, P. Chen, S. 2023-02-04 doi:10.1101/2023.02.01.526652 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ C-terminus induced asymmetry within a Rad52 homodecamer dictates single-position Rad51 nucleation in homologous recombination ]]> https://biorxiv.org/content/10.1101/2023.02.05.527205v1?rss=1 Deveryshetty, J. Chadda, R. Mattice, J. Karunakaran, S. Rau, M. Basore, K. Pokhrel, N. Englander, N. Fitzpatrick, J. Bothner, B. Antony, E. 2023-02-05 doi:10.1101/2023.02.05.527205 Cold Spring Harbor Laboratory Press 2023-02-05 <![CDATA[ Physiological adaptation in flagellar architecture improves Vibrio alginolyticus chemotaxis in complex environments ]]> https://biorxiv.org/content/10.1101/2023.02.06.526967v1?rss=1 Grognot, M. Nam, J. W. Elson, L. E. Taute, K. M. 2023-02-06 doi:10.1101/2023.02.06.526967 Cold Spring Harbor Laboratory Press 2023-02-06 <![CDATA[ NLRP1 inflammasome modulates senescence and senescence-associated secretory phenotype ]]> https://biorxiv.org/content/10.1101/2023.02.06.527254v1?rss=1 Muela-Zarzuela, I. Suarez-Rivero, J. M. Gallardo-Orihuela, A. Wang, C. Izawa, K. de Gregorio-Procopio, M. Couillin, I. Ryffel, B. Kitaura, J. Sanz, A. von Zglinicki, T. Mbalaviele, G. Cordero, M. D. 2023-02-06 doi:10.1101/2023.02.06.527254 Cold Spring Harbor Laboratory Press 2023-02-06 <![CDATA[ TFEB-vacuolar ATPase signaling regulates lysosomal function and microglial activation in tauopathy ]]> https://biorxiv.org/content/10.1101/2023.02.06.527293v1?rss=1 Wang, B. Martini-Stoica, H. Qi, C. Lu, T.-C. Wang, S. Xiong, W. Qi, Y. Xu, Y. Sardiello, M. Li, H. Zheng, H. 2023-02-06 doi:10.1101/2023.02.06.527293 Cold Spring Harbor Laboratory Press 2023-02-06 <![CDATA[ C3 in the 10-20 system may not be the best target for the motor hand area ]]> https://biorxiv.org/content/10.1101/2023.02.06.527390v1?rss=1 Kim, H. Wright, D. L. Rhee, J. Kim, T. 2023-02-06 doi:10.1101/2023.02.06.527390 Cold Spring Harbor Laboratory Press 2023-02-06 <![CDATA[ Horizontal gene transfer and CRISPR targeting drive phage-bacterial host interactions and co-evolution in pink berry marine microbial aggregates ]]> https://biorxiv.org/content/10.1101/2023.02.06.527410v1?rss=1 Kosmopolous, J. C. Campbell, D. E. Whitaker, R. Wilbanks, E. 2023-02-07 doi:10.1101/2023.02.06.527410 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ Inducing vulnerability to InhA inhibition restores isoniazid susceptibility in drug resistant Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2023.02.06.527416v1?rss=1 Harrison, G. A. Cho, K. Wang, E. R. Sarkar, S. Almqvist, F. Patti, G. Stallings, C. L. 2023-02-08 doi:10.1101/2023.02.06.527416 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ POLCAM: Instant molecular orientation microscopy for the life sciences ]]> https://biorxiv.org/content/10.1101/2023.02.07.527479v1?rss=1 Bruggeman, E. Zhang, O. Needham, L.-M. Koerbel, M. Daly, S. Cheetham, M. Peters, R. Wu, T. Klymchenko, A. S. Davis, S. J. Paluch, E. K. Klenerman, D. Lew, M. D. O'Holleran, K. Lee, S. F. 2023-02-08 doi:10.1101/2023.02.07.527479 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ Deep learning approaches to viral phylogeography are fast and as robust as likelihood methods to model misspecification ]]> https://biorxiv.org/content/10.1101/2023.02.08.527714v1?rss=1 Thompson, A. Liebeskind, B. Scully, E. J. Landis, M. 2023-02-10 doi:10.1101/2023.02.08.527714 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Development of White Matter Fiber Covariance Networks Supports Executive Function in Youth ]]> https://biorxiv.org/content/10.1101/2023.02.09.527696v1?rss=1 Bagautdinova, J. Bourque, J. Sydnor, V. J. Cieslak, M. Alexander-Bloch, A. F. Bertolero, M. A. Cook, P. A. Gur, R. C. Gur, R. E. Larsen, B. Moore, T. M. Radhakrishnan, H. Roalf, D. R. Shinohara, R. T. Tapera, T. M. Zhao, C. Sotiras, A. Davatzikos, C. Satterthwaite, T. D. 2023-02-10 doi:10.1101/2023.02.09.527696 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Evaluating the Performance of Widely Used Phylogenetic Models for Gene Expression Evolution ]]> https://biorxiv.org/content/10.1101/2023.02.09.527893v1?rss=1 Dimayacyac, J. R. Wu, S. Pennell, M. 2023-02-10 doi:10.1101/2023.02.09.527893 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Yersiniabactin is a quorum sensing autoinducer and siderophore in uropathogenic Escherichia coli ]]> https://biorxiv.org/content/10.1101/2023.02.09.527953v1?rss=1 Heffernan, J. R. Katumba, G. L. McCoy, W. H. Henderson, J. P. 2023-02-10 doi:10.1101/2023.02.09.527953 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Neonatal Subarachnoid Hemorrhage Disrupts Multiple Aspects of Cerebellar Development ]]> https://biorxiv.org/content/10.1101/2023.02.10.528048v1?rss=1 Butler, D. F. Skibo, J. Traudt, C. M. Millen, K. J. 2023-02-10 doi:10.1101/2023.02.10.528048 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ The disordered N-terminal tail of SARS CoV-2 Nucleocapsid protein forms a dynamic complex with RNA ]]> https://biorxiv.org/content/10.1101/2023.02.10.527914v1?rss=1 Cubuk, J. Alston, J. J. Incicco, J. J. Holehouse, A. S. Hall, K. B. Stuchell-Brereton, M. D. Soranno, A. 2023-02-13 doi:10.1101/2023.02.10.527914 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ Aerobic exercise reverses aging-induced depth-dependent decline in cerebral microcirculation ]]> https://biorxiv.org/content/10.1101/2023.02.12.528244v1?rss=1 Shin, P. Pian, Q. Ishikawa, H. Hamanaka, G. Mandeville, E. T. Shuzhen, G. Buyin, F. Alfadhel, M. Allu, S. R. Sencan-Egilmez, I. Li, B. Ran, C. Vinogradov, S. A. Ayata, C. Lo, E. Arai, K. Devor, A. Sakadzic, S. 2023-02-14 doi:10.1101/2023.02.12.528244 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ Mitochondrial Pyruvate Carrier Inhibition in Hepatic Stellate Cells Attenuates Fibrosis in Nonalcoholic Steatohepatitis in Mice ]]> https://biorxiv.org/content/10.1101/2023.02.13.528384v1?rss=1 Ferguson, D. Habibi, M. Eichler, S. J. LaPoint, A. Shew, T. M. He, M. Lutkewitte, A. J. Finck, B. N. 2023-02-14 doi:10.1101/2023.02.13.528384 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ Low Gut Microbial Diversity Augments Estrogen-driven Pulmonary Fibrosis in Female-Predominant Interstitial Lung Disease ]]> https://biorxiv.org/content/10.1101/2023.02.15.528630v1?rss=1 Chioma, O. S. Mallott, E. Bandhi, B. S. Wiggins, Z. Langford, M. Lancaster, A. W. Gelbard, A. Wu, H. Johnson, J. Lancaster, L. Wilfong, E. Crofford, L. J. Montgomery, C. Van Kaer, L. Bordenstein, S. Newcomb, D. Drake, W. 2023-02-15 doi:10.1101/2023.02.15.528630 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Scanning electron microscopy of human islet cilia ]]> https://biorxiv.org/content/10.1101/2023.02.15.528685v1?rss=1 Polino, A. J. Sviben, S. Melena, I. Piston, D. W. HUGHES, J. 2023-02-15 doi:10.1101/2023.02.15.528685 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Mapping Sleep's Oscillatory Events as a Biomarker of Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2023.02.15.528725v1?rss=1 Pulver, R. L. Kronberg, E. Medenblik, L. M. Kheyfets, V. O. Ramos, A. R. Holtzman, D. M. Morris, J. C. Toedebusch, C. D. Sillau, S. H. Bettcher, B. M. Lucey, B. P. McConnell, B. V. 2023-02-16 doi:10.1101/2023.02.15.528725 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Highly sensitive in vivo detection of dynamic changes in enkephalins following acute stress ]]> https://biorxiv.org/content/10.1101/2023.02.15.528745v1?rss=1 Mikati, M. O. Erdmann-Gilmore, P. Connors, R. Conway, S. M. Malone, J. Woods, J. Sprung, R. W. Townsend, R. R. Al-Hasani, R. 2023-02-16 doi:10.1101/2023.02.15.528745 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ SOURSOP: A Python package for the analysis of simulations of intrinsically disordered proteins ]]> https://biorxiv.org/content/10.1101/2023.02.16.528879v1?rss=1 Lalmansingh, J. M. Keeley, A. T. Ruff, K. M. Pappu, R. V. Holehouse, A. S. 2023-02-17 doi:10.1101/2023.02.16.528879 Cold Spring Harbor Laboratory Press 2023-02-17 <![CDATA[ NSD1 deposits histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons ]]> https://biorxiv.org/content/10.1101/2023.02.17.528965v1?rss=1 Hamagami, N. Wu, D. Y. Clemens, A. W. Nettles, S. A. Gabel, H. W. 2023-02-17 doi:10.1101/2023.02.17.528965 Cold Spring Harbor Laboratory Press 2023-02-17 <![CDATA[ Ergosterol distribution controls surface structure formation and fungal pathogenicity ]]> https://biorxiv.org/content/10.1101/2023.02.17.528979v1?rss=1 Choy, H. L. Gaylord, E. A. Doering, T. L. 2023-02-17 doi:10.1101/2023.02.17.528979 Cold Spring Harbor Laboratory Press 2023-02-17 <![CDATA[ Effects of hepatic mitochondrial pyruvate carrier deficiency on de novo lipogenesis and glycerol-mediated gluconeogenesis in mice ]]> https://biorxiv.org/content/10.1101/2023.02.17.528992v1?rss=1 Yiew, N. K. H. Ferguson, D. Cho, K. Deja, S. Jarasvaraparn, C. Lutkewitte, A. J. Mukherjee, S. Fu, X. Singer, J. M. Patti, G. J. Burgess, S. C. Finck, B. N. 2023-02-18 doi:10.1101/2023.02.17.528992 Cold Spring Harbor Laboratory Press 2023-02-18 <![CDATA[ Pulmonary osteoclast-like cells in silica induced pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/2023.02.17.528996v1?rss=1 Hasegawa, Y. Franks, J. M. Tanaka, Y. Uehara, Y. Read, D. F. Williams, C. Srivatsan, S. Pitstick, L. B. Nikolaidis, N. M. Shaver, C. M. Wu, H. Gardner, J. C. Osterburg, A. R. Yu, J. J. Kopras, E. J. Teitelbaum, S. L. Wikenheiser-Brokamp, K. A. Trapnell, C. McCormack, F. X. 2023-02-18 doi:10.1101/2023.02.17.528996 Cold Spring Harbor Laboratory Press 2023-02-18 <![CDATA[ Cortical activity emerges in region-specific patterns during early brain development ]]> https://biorxiv.org/content/10.1101/2023.02.18.529078v1?rss=1 Suarez, R. Bluett, T. McCullough, M. Avitan, L. Black, D. Paolino, A. Fenlon, L. Goodhill, G. Richards, L. J. 2023-02-19 doi:10.1101/2023.02.18.529078 Cold Spring Harbor Laboratory Press 2023-02-19 <![CDATA[ Development and evaluation of a wearable peripheral vascular compensation sensor in a swine model of hemorrhage ]]> https://biorxiv.org/content/10.1101/2023.02.20.529156v1?rss=1 Bonetta-Misteli, F. Collins, T. Pavek, T. Carlgren, M. Frolova, A. Shmuylovich, L. O'Brien, C. M. 2023-02-21 doi:10.1101/2023.02.20.529156 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Epithelial multicellular clustering enabled by polarized macrophages on soft matrices ]]> https://biorxiv.org/content/10.1101/2023.02.20.529258v1?rss=1 Zmuda, H. Pathak, A. 2023-02-21 doi:10.1101/2023.02.20.529258 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Ketosis Prevents Abdominal Aortic Aneurysm Rupture Through CCR2 Downregulation and Enhanced MMP Balance ]]> https://biorxiv.org/content/10.1101/2023.02.21.529460v1?rss=1 Sastriques-Dunlop, S. Elizondo-Benedetto, S. Arif, B. Meade, R. Zaghloul, M. S. Luehmann, H. Heo, G. S. English, S. J. Liu, Y. Zayed, M. A. 2023-02-22 doi:10.1101/2023.02.21.529460 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Life stage and vaccination shape the gut microbiome of hatchery-reared Atlantic salmon (Salmo salar) ]]> https://biorxiv.org/content/10.1101/2023.02.21.529474v1?rss=1 Andres, K. J. Liu, B. Johnson, L. E. Kapuscinski, K. L. Moerke, A. H. Ling, F. Knouft, J. H. 2023-02-22 doi:10.1101/2023.02.21.529474 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Single neurons in the human medial temporal lobe flexibly shift representations across spatial and memory tasks ]]> https://biorxiv.org/content/10.1101/2023.02.22.529437v1?rss=1 Donoghue, T. Cao, R. Han, C. Z. Holman, C. M. Brandmeir, N. J. Wang, S. Jacobs, J. 2023-02-22 doi:10.1101/2023.02.22.529437 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ The ATM-E6AP-MASTL axis mediates DNA damage checkpoint recovery ]]> https://biorxiv.org/content/10.1101/2023.02.22.529521v1?rss=1 Li, Y. Wang, F. Li, X. Wang, L. Yang, Z. You, Z. Peng, A. 2023-02-22 doi:10.1101/2023.02.22.529521 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Dynamic walking behavior during odor trail-following in locusts ]]> https://biorxiv.org/content/10.1101/2023.02.22.529569v1?rss=1 Traner, M. Raman, B. 2023-02-22 doi:10.1101/2023.02.22.529569 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ MAP9/MAPH-9 supports axonemal microtubule doublets and modulates motor movement ]]> https://biorxiv.org/content/10.1101/2023.02.23.529616v1?rss=1 Tran, M. V. Ferguson, J. W. Cote, L. E. Khuntsariya, D. Fetter, R. D. Wang, J. T. Wellard, S. R. Sallee, M. D. Eskinazi, S. Genova, M. Magiera, M. M. Janke, C. Stearns, T. Lansky, Z. Shen, K. Magescas, J. Feldman, J. L. 2023-02-23 doi:10.1101/2023.02.23.529616 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ MeCP2 Represses the Activity of Topoisomerase IIβ in Long Neuronal Genes ]]> https://biorxiv.org/content/10.1101/2023.02.24.529960v1?rss=1 100 kilobases). These genes encode proteins with essential functions in neuronal physiology, and disruption of long gene expression has been implicated in neurological disorders. DNA topoisomerases resolve topological constraints that arise on DNA and facilitate the expression of long genes in neurons. Conversely, methyl-CpG binding protein 2 (MeCP2), which is disrupted in Rett syndrome, can act as a transcriptional repressor to downregulate the expression of long genes. The molecular mechanisms underlying the regulation of long genes by these factors are not fully understood, however, and whether or not they directly influence each other is not known. Here, we identify a functional interaction between MeCP2 and Topoisomerase II-beta (TOP2{beta}) in neurons. We show that MeCP2 and TOP2{beta} physically interact in vivo and map protein sequences sufficient for their physical interaction in vitro. We profile TOP2{beta} activity genome-wide in neurons and detect enrichment at regulatory regions and gene bodies of long neuronal genes, including long genes regulated by MeCP2. Further, we find that knockdown and overexpression of MeCP2 leads to altered TOP2{beta} activity at MeCP2-regulated genes. Our findings uncover a mechanism by which MeCP2 inhibits the activity of TOP2{beta} at long genes in neurons and suggest that this mechanism is disrupted in neurodevelopment disorders caused by mutation of MeCP2. ]]> Nettles, S. A. Ikeuchi, Y. Agwu, C. Bonni, A. Gabel, H. W. 2023-02-26 doi:10.1101/2023.02.24.529960 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ Short Tandem Repeat Profiling via Next Generation Sequencing for Cell Line Authentication ]]> https://biorxiv.org/content/10.1101/2023.02.25.530013v1?rss=1 Chen, Y.-H. Connelly, J. P. Florian, C. Cui, X. Pruett-Miller, S. M. 2023-02-26 doi:10.1101/2023.02.25.530013 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ Specialized cingulo-opercular network activation in judging ambiguity of facial expressions in a slow reveal fMRI paradigm ]]> https://biorxiv.org/content/10.1101/2023.02.25.529948v1?rss=1 Pierce, J. E. Petro, N. M. Clancy, E. Gratton, C. Petersen, S. Neta, M. 2023-02-27 doi:10.1101/2023.02.25.529948 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Induction of viral mimicry upon loss of DHX9 and ADAR1 in breast cancer cells ]]> https://biorxiv.org/content/10.1101/2023.02.27.530307v1?rss=1 Cottrell, K. A. Ryu, S. Torres, L. S. Schab, A. M. Weber, J. D. 2023-02-27 doi:10.1101/2023.02.27.530307 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Systematic Identification of Post-Transcriptional Regulatory Modules ]]> https://biorxiv.org/content/10.1101/2023.02.27.530345v1?rss=1 Khoroshkin, M. S. Buyan, A. Dodel, M. Navickas, A. Yu, J. Trejo, F. Doty, A. Baratam, R. Zhou, S. Joshi, T. Miglani, S. Choi, B. Subramanyam, V. Modi, H. Corces, R. Markett, D. Kulakovskiy, I. V. Mardakheh, F. K. Goodarzi, H. 2023-03-01 doi:10.1101/2023.02.27.530345 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Pptc7 maintains mitochondrial protein content by suppressing receptor-mediated mitophagy ]]> https://biorxiv.org/content/10.1101/2023.02.28.530351v1?rss=1 Niemi, N. M. Serrano, L. R. Muehlbauer, L. K. Balnis, C. Kozul, K.-L. Rashan, E. H. Shishkova, E. Schueler, K. L. Keller, M. P. Attie, A. D. Pagan, J. Coon, J. J. Pagliarini, D. J. 2023-03-01 doi:10.1101/2023.02.28.530351 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Uncovering and mitigating bias in large, automated MRI analyses of brain development ]]> https://biorxiv.org/content/10.1101/2023.02.28.530498v1?rss=1 Elyounssi, S. Kunitoki, K. Clauss, J. A. Laurent, E. Kane, K. Hughes, D. E. Hopkinson, C. E. Bazer, O. Sussman, R. F. Doyle, A. E. Lee, H. Tervo-Clemmens, B. Eryilmaz, H. Gollub, R. L. Barch, D. M. Satterthwaite, T. D. Dowling, K. F. Roffman, J. L. 2023-03-01 doi:10.1101/2023.02.28.530498 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Brain-wide neural activity underlying memory-guided movement ]]> https://biorxiv.org/content/10.1101/2023.03.01.530520v1?rss=1 Chen, S. Liu, Y. Wang, Z. Colonell, J. Liu, L. D. Hou, H. Tien, N.-W. Wang, T. Harris, T. Druckmann, S. Li, N. Svoboda, K. 2023-03-02 doi:10.1101/2023.03.01.530520 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Cat LCA-CRX model, homozygous for an antimorphic mutation has a unique phenotype ]]> https://biorxiv.org/content/10.1101/2023.03.01.530650v1?rss=1 Occelli, L. M. Tran, N. M. Chen, S. Petersen-Jones, S. M. 2023-03-02 doi:10.1101/2023.03.01.530650 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Distinct cellular expression and subcellular localization of Kv2 voltage-gated K+ channel subtypes in dorsal root ganglion neurons conserved between mice and humans ]]> https://biorxiv.org/content/10.1101/2023.03.01.530679v1?rss=1 Stewart, R. G. Camacena, M. Copits, B. A. Sack, J. T. 2023-03-02 doi:10.1101/2023.03.01.530679 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Sleep Deprivation, Sleep Fragmentation and Social Jet Lag increase temperature preference in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.03.02.530812v1?rss=1 Roach, T. S. Ford, M. C. Simhambhatla, V. Loutrianakis, V. Farah, H. Li, Z. Periandri, E. Abdalla, D. Huang, I. Kalra, A. Shaw, P. J. 2023-03-02 doi:10.1101/2023.03.02.530812 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Zbtb46 coordinates angiogenesis and immunity to control tumor outcome ]]> https://biorxiv.org/content/10.1101/2023.03.02.530835v1?rss=1 KABIR, A. U. SUBRAMANIAN, M. KIM, M. WU, J. KRCHMA, K. WANG, X. HALABI, C. M. PAN, H. WICKLINE, S. A. FREMONT, D. H. CHOI, K. 2023-03-02 doi:10.1101/2023.03.02.530835 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ The Estrogen Receptor-Related Orphan Receptors (ERRs) Regulate Autophagy through TFEB ]]> https://biorxiv.org/content/10.1101/2023.03.02.530836v1?rss=1 Losby, M. Hayes, M. Valfort, A. Walker, J. Xu, W. L. Zhang, L. Billon, C. Burris, T. 2023-03-02 doi:10.1101/2023.03.02.530836 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Transcription factor interactions explain the context-dependent activity of CRX binding sites ]]> https://biorxiv.org/content/10.1101/2023.03.05.531194v1?rss=1 Loell, K. J. Friedman, R. Z. Myers, C. A. Corbo, J. C. Cohen, B. A. White, M. A. 2023-03-05 doi:10.1101/2023.03.05.531194 Cold Spring Harbor Laboratory Press 2023-03-05 <![CDATA[ Rapid generation of C. elegans single copy transgenes combining RMCE and drug selection ]]> https://biorxiv.org/content/10.1101/2023.03.05.531207v1?rss=1 1 insertion per 2 injected P0 animals). Landing sites for this approach are available on four chromosomes in several configurations which yield lines marked in distinct cell types. An array of vectors permit creating transgenes using a variety of selection methods (HygR, NeoR, PuroR, unc-119(+)) that yield lines expressing different colored FP tagged lines (BFP, GFP, mNG, and Scarlet). Although these transgenes retain a plasmid backbone and a selection marker, the inclusion of these sequences typically does not alter the expression of several cell specific promoters tested. However, in certain orientations promoters exhibits crosstalk with adjacent transcription units. In cases where crosstalk is problematic, the loxP-flanked fluorescent marker, plasmid backbone and hygR gene can be excised by crossing through germline Cre expressing lines also created using this technique. Finally, genetic and molecular reagents designed to facilitate customization of both targeting vectors and landing sites are also described. Together, the rRMCE toolbox provides a platform for developing further innovative uses of RMCE to create complex genetically engineered tools. ]]> Nonet, M. L. 2023-03-05 doi:10.1101/2023.03.05.531207 Cold Spring Harbor Laboratory Press 2023-03-05 <![CDATA[ Novel crAssphage isolates exhibit conserved gene order and purifying selection of the host specificity protein ]]> https://biorxiv.org/content/10.1101/2023.03.05.531146v1?rss=1 Papudeshi, B. Vega, A. A. Souza, C. Giles, S. K. Mallawaarachchi, V. Roach, M. J. An, M. Jacobson, N. McNair, K. Mora, M. F. Pastrana, K. Leigh, C. Cram, C. Plewa, W. S. Grigson, S. R. Bouras, G. Decewicz, P. Luque, A. Droit, L. Handley, S. A. Segall, A. Dinsdale, E. A. Edwards, R. A. 2023-03-06 doi:10.1101/2023.03.05.531146 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Tmem178 negatively regulates IL-1β production through inhibition of the NLRP3 inflammasome ]]> https://biorxiv.org/content/10.1101/2023.03.07.531385v1?rss=1 Khanna, K. Yan, H. Mehra, M. Rohatgi, N. Mbalaviele, G. Faccio, R. 2023-03-07 doi:10.1101/2023.03.07.531385 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Spatial and Amplitude Dynamics of Neurostimulation: Insights from the Acute Intrahippocampal Kainate Seizure Mouse Model ]]> https://biorxiv.org/content/10.1101/2023.03.07.531440v1?rss=1 Foutz, T. J. Rensing, N. Han, L. Durand, D. M. Wong, M. 2023-03-09 doi:10.1101/2023.03.07.531440 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Inferring functional organization of posterior parietal cortex circuitry based on information flow ]]> https://biorxiv.org/content/10.1101/2023.03.08.531516v1?rss=1 Kang, J. U. Mooshagian, E. Snyder, L. H. 2023-03-09 doi:10.1101/2023.03.08.531516 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Aberrant phase separation is a common killing strategy of positively charged peptides in biology and human disease ]]> https://biorxiv.org/content/10.1101/2023.03.09.531820v1?rss=1 Boeynaems, S. Ma, X. R. Yeong, V. Ginell, G. M. Chen, J.-H. Blum, J. A. Nakayama, L. Sanyal, A. Briner, A. Van Haver, D. Pauwels, J. Ekman, A. Schmidt, H. B. Sundararajan, K. Porta, L. Lasker, K. Larabell, C. Hayashi, M. A. F. Kundaje, A. Impens, F. Obermeyer, A. Holehouse, A. S. Gitler, A. D. 2023-03-09 doi:10.1101/2023.03.09.531820 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Tyrosinase-induced neuromelanin accumulation triggers rapid dysregulation and degeneration of the mouse locus coeruleus ]]> https://biorxiv.org/content/10.1101/2023.03.07.530845v1?rss=1 Iannitelli, A. F. Segal, A. Pare, J.-F. Mulvey, B. Liles, L. C. Sloan, S. A. McCann, K. E. Dougherty, J. D. Smith, Y. Weinshenker, D. 2023-03-10 doi:10.1101/2023.03.07.530845 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Sirtuin3 ensures the metabolic plasticity of neurotransmission during glucose deprivation ]]> https://biorxiv.org/content/10.1101/2023.03.08.531724v1?rss=1 Tiwari, A. Hashemiaghdam, A. Laramie, M. Maschi, D. Haddad, T. Stunault, M. Bergom, C. Javaheri, A. Klyachko, V. Ashrafi, G. 2023-03-10 doi:10.1101/2023.03.08.531724 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ LRRC8A anion channels modulate vasodilation via association with Myosin Phosphatase Rho Interacting Protein (MPRIP) ]]> https://biorxiv.org/content/10.1101/2023.03.08.531807v1?rss=1 Choi, H. Miller, M. R. Nguyen, H.-N. Rohrbough, J. C. Koch, S. R. Boatwright, N. Yarboro, M. T. Sah, R. McDonald, H. Reese, J. J. Stark, R. J. Lamb, F. S. 2023-03-11 doi:10.1101/2023.03.08.531807 Cold Spring Harbor Laboratory Press 2023-03-11 <![CDATA[ Genome-scale enzymatic reaction prediction by variational graph autoencoders ]]> https://biorxiv.org/content/10.1101/2023.03.08.531729v1?rss=1 Wang, C. Yuan, C. Wang, Y. Chen, R. Shi, Y. Patti, G. Hou, Q. 2023-03-12 doi:10.1101/2023.03.08.531729 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Optical coherence tomography of human fetal membrane sub-layers during dynamic loading ]]> https://biorxiv.org/content/10.1101/2023.03.09.531932v1?rss=1 0.8). Intact amniochorion bilayer and separated amnion and chorion were individually loaded, and the amnion layer was identified as the load-bearing layer within intact fetal membranes for both labored and C-section samples, consistent with prior work. Additionally, the rupture pressure and thickness of the amniochorion bilayer from the near-placental region were greater than those of the near-cervical region for labored samples. This location-dependent change in fetal membrane thickness was not attributable to the load-bearing amnion layer. Finally, the initial phase of the loading curve indicates that amniochorion bilayer from the near-cervical region is strain-hardened compared to the near-placental region in labored samples. Overall, these studies fill a gap in our understanding of the structural and mechanical properties of human fetal membranes at high resolution under dynamic loading events. ]]> Samimi, K. Contreras Guzman, E. Wu, M. Carlson, L. Feltovich, H. Hall, T. J. Myers, K. M. Oyen, M. L. Skala, M. C. 2023-03-12 doi:10.1101/2023.03.09.531932 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ The analytical Flory random coil is a simple-to-use reference model for unfolded and disordered proteins ]]> https://biorxiv.org/content/10.1101/2023.03.12.531990v1?rss=1 Alston, J. J. Ginell, G. T. Soranno, A. S. Holehouse, A. S. 2023-03-13 doi:10.1101/2023.03.12.531990 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ High-throughput, fluorescent-aptamer-based measurements of steady-state transcription rates for Mycobacterium tuberculosis RNA polymerase ]]> https://biorxiv.org/content/10.1101/2023.03.13.532464v1?rss=1 Jensen, D. Manzano, A. R. Tomko, E. J. Rector, M. Record, M. T. Galburt, E. A. 2023-03-13 doi:10.1101/2023.03.13.532464 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ Geneneralising the HCP multimodal cortical parcellation to UK Biobank ]]> https://biorxiv.org/content/10.1101/2023.03.14.532531v1?rss=1 Williams, L. Z. J. Glasser, M. F. Alfaro-Almagro, F. Dahan, S. Fawaz, A. Coalson, T. S. Fitzgibbon, S. P. Suliman, M. Van Essen, D. C. Smith, S. M. Edwards, A. D. Robinson, E. C. 2023-03-14 doi:10.1101/2023.03.14.532531 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Hem25p is a mitochondrial IPP transporter ]]> https://biorxiv.org/content/10.1101/2023.03.14.532620v1?rss=1 Tai, J. Guerra, R. M. Rogers, S. W. Fang, Z. Muehlbauer, L. K. Shishkova, E. Overmyer, K. A. Coon, J. J. Pagliarini, D. J. 2023-03-14 doi:10.1101/2023.03.14.532620 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Molecular mechanisms of functional impairment for active site mutations in glucose-6-phosphatase catalytic subunit 1 linked to glycogen storage disease type 1a. ]]> https://biorxiv.org/content/10.1101/2023.03.13.532485v1?rss=1 Sinclair, M. Stein, R. A. Sheehan, J. Hawes, E. M. O'Brien, R. M. Tajkhorshid, E. Claxton, D. P. 2023-03-15 doi:10.1101/2023.03.13.532485 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ A thermodynamic analysis of CLC transporter dimerization in lipid bilayers ]]> https://biorxiv.org/content/10.1101/2023.03.14.532678v1?rss=1 Chadda, R. Lee, T. Sandal, P. Mahoney-Kruszka, R. Robertson, J. L. 2023-03-15 doi:10.1101/2023.03.14.532678 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Phase Separation in Mixtures of Prion-Like Low Complexity Domains is Driven by the Interplay of Homotypic and Heterotypic Interactions ]]> https://biorxiv.org/content/10.1101/2023.03.15.532828v1?rss=1 Farag, M. Borcherds, W. M. Bremer, A. Mittag, T. Pappu, R. V. 2023-03-16 doi:10.1101/2023.03.15.532828 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ The highly conserved stem-loop II motif is dispensable for SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2023.03.15.532878v1?rss=1 Jiang, H. Joshi, A. Gan, T. Janowski, A. B. Fujii, C. Bricker, T. L. Darling, T. Harastani, H. H. Seehra, K. Chen, H. Tahan, S. Jung, A. Febles, B. Blatter, J. A. Handley, S. Parikh, B. A. Wang, D. Boon, A. C. 2023-03-16 doi:10.1101/2023.03.15.532878 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Transcription regulation by CarD in mycobacteria is guided by basal promoter kinetics ]]> https://biorxiv.org/content/10.1101/2023.03.16.533025v1?rss=1 Zhu, D. X. Stallings, C. L. 2023-03-16 doi:10.1101/2023.03.16.533025 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Targeted proteomic quantitation of NRF2 signaling and predictive biomarkers in HNSCC ]]> https://biorxiv.org/content/10.1101/2023.03.13.532474v1?rss=1 Wamsley, N. Wilkerson, E. Guan, L. LaPak, K. Schrank, T. Holmes, B. Sprung, R. Gilmore, P. E. Gerndt, S. Jackson, R. Paniello, R. Pipkorn, P. Puram, S. V. Rich, J. Townsend, R. R. Zevallos, J. Zolkind, P. Le, Q.-T. Goldfarb, D. Major, M. B. 2023-03-17 doi:10.1101/2023.03.13.532474 Cold Spring Harbor Laboratory Press 2023-03-17 <![CDATA[ Dual impact of PTEN mutation on CSF dynamics and cortical networks via the dysregulation of neural precursors and their interneuron descendants ]]> https://biorxiv.org/content/10.1101/2023.03.18.533275v1?rss=1 DeSpenza, T. Kiziltug, E. Allington, G. Barson, D. O'Connor, D. Robert, S. M. Mekbib, K. Y. Nanda, P. Greenberg, A. Singh, A. Duy, P. Q. Mandino, F. Zhao, S. Lynn, A. Reeves, B. C. Marlier, A. Getz, S. A. Nelson-Williams, C. Shimelis, H. Zhang, J. Walsh, L. K. Wang, W. Smith, H. OuYang, A. Deniz, E. Lake, E. Jin, S. C. Luikart, B. W. Kahle, K. T. 2023-03-19 doi:10.1101/2023.03.18.533275 Cold Spring Harbor Laboratory Press 2023-03-19 <![CDATA[ The CARD8 inflammasome drives CD4+ T-cell depletion in HIV-1 infection ]]> https://biorxiv.org/content/10.1101/2023.03.18.533283v1?rss=1 Wang, Q. Shan, L. 2023-03-19 doi:10.1101/2023.03.18.533283 Cold Spring Harbor Laboratory Press 2023-03-19 <![CDATA[ Mitigation of membrane morphology defects explain stability and orientational specificity of CLC dimers ]]> https://biorxiv.org/content/10.1101/2023.03.16.533024v1?rss=1 Ozturk, T. N. Bernhardt, N. Schwartz, N. Chadda, R. Robertson, J. L. Faraldo-Gomez, J. 2023-03-20 doi:10.1101/2023.03.16.533024 Cold Spring Harbor Laboratory Press 2023-03-20 <![CDATA[ Genetic dysregulation of an endothelial Ras signaling network in vein of Galen malformations ]]> https://biorxiv.org/content/10.1101/2023.03.18.532837v1?rss=1 Zhao, S. Mekbib, K. Y. van der Ent, M. A. Allington, G. Prendergast, A. Chau, J. E. Smith, H. Shohfi, J. Ocken, J. Duran, D. Furey, C. G. Le, H. T. Duy, P. Q. Reeves, B. C. Zhang, J. Nelson-Williams, C. Chen, D. Li, B. Nottoli, T. Bai, S. Rolle, M. Zeng, X. Dong, W. Fu, P.-Y. Wang, Y.-C. Mane, S. Piwowarczyk, P. Fehnel, K. P. See, A. P. Iskandar, B. J. Aagaard-Kienitz, B. Kundishora, A. J. DeSpenza, T. Greenberg, A. B. W. Kidanemariam, S. M. Prendergast, A. Johnston, J. M. Jackson, E. Storm, P. B. Lang, S.-S. Butler, W. E. Carter, B. S. Chapman, P. St 2023-03-22 doi:10.1101/2023.03.18.532837 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ FIREBALL: A tool to fit protein phase diagrams based on mean-field theories for polymer solutions ]]> https://biorxiv.org/content/10.1101/2023.03.19.533322v1?rss=1 Farag, M. Holehouse, A. S. Zeng, X. Pappu, R. V. 2023-03-22 doi:10.1101/2023.03.19.533322 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ Structure and Function of the Dot/Icm T4SS ]]> https://biorxiv.org/content/10.1101/2023.03.22.533729v1?rss=1 Dutka, P. Liu, Y. Maggi, S. Ghosal, D. Wang, J. Carter, S. D. Zhao, W. Vijayrajratnam, S. Vogel, J. P. Jensen, G. J. 2023-03-22 doi:10.1101/2023.03.22.533729 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency of its allosteric inhibitors ]]> https://biorxiv.org/content/10.1101/2023.03.22.533829v1?rss=1 Meller, A. de Oliviera, S. H. Abramyan, T. Davtyan, A. Bowman, G. R. van den Bedem, H. 2023-03-24 doi:10.1101/2023.03.22.533829 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Parasite hybridization promotes spreading of endosymbiotic viruses ]]> https://biorxiv.org/content/10.1101/2023.03.24.534103v1?rss=1 Heeren, S. Maes, I. Sanders, M. Lye, L.-F. Arevalo, J. Llanos Cuentas, A. Garcia, L. Lemey, P. Beverley, S. M. Cotton, J. Dujardin, J.-C. Van den Broeck, F. 2023-03-25 doi:10.1101/2023.03.24.534103 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Learning the functional landscape of microbial communities ]]> https://biorxiv.org/content/10.1101/2023.03.24.534159v1?rss=1 Skwara, A. Gowda, K. Yousef, M. Diaz-Colunga, J. Raman, A. S. Sanchez, A. Tikhonov, M. Kuehn, S. 2023-03-25 doi:10.1101/2023.03.24.534159 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Evolution of a Functionally Intact but Antigenically Distinct DENV Fusion Loop ]]> https://biorxiv.org/content/10.1101/2023.03.22.533803v1?rss=1 Meganck, R. M. Zhu, D. Dong, S. Snoderly-Foster, L. J. Dalben, Y. R. Thiono, D. J. White, L. J. DeSilva, A. M. Baric, R. Tse, L. V. 2023-03-27 doi:10.1101/2023.03.22.533803 Cold Spring Harbor Laboratory Press 2023-03-27 <![CDATA[ Interpretable spatial cell learning enhances the characterization of patient tissue microenvironments with highly multiplexed imaging data ]]> https://biorxiv.org/content/10.1101/2023.03.26.534306v1?rss=1 Lu, P. Oetjen, K. Oh, S. Thorek, D. L. 2023-03-28 doi:10.1101/2023.03.26.534306 Cold Spring Harbor Laboratory Press 2023-03-28 <![CDATA[ Endothelial cells are a key target of IFN-g during response to combined PD-1/CTLA-4 ICB treatment in a mouse model of bladder cancer ]]> https://biorxiv.org/content/10.1101/2023.03.28.534561v1?rss=1 Freshour, S. L. Chen, T. H.-P. Fisk, B. Shen, H. Mosior, M. Skidmore, Z. L. Fronick, C. Bolzenius, J. K. Griffith, O. L. Arora, V. K. Griffith, M. 2023-03-29 doi:10.1101/2023.03.28.534561 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Enhanced selectivity of transcutaneous spinal cord stimulation by multielectrode configuration ]]> https://biorxiv.org/content/10.1101/2023.03.30.534835v1?rss=1 Bryson, N. K. Lombardi, L. Hawthorn, R. Fei, J. Keesey, R. Peiffer, J. D. Seanez, I. 2023-03-31 doi:10.1101/2023.03.30.534835 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ Bradykinin receptor expression and bradykinin-mediated sensitization of human sensory neurons ]]> https://biorxiv.org/content/10.1101/2023.03.31.534820v1?rss=1 Yi, J. Bertels, Z. Del Rosario, J. S. Widman, A. J. Slivicki, R. A. Payne, M. Susser, H. M. Copits, B. A. Gereau, R. W. 2023-04-01 doi:10.1101/2023.03.31.534820 Cold Spring Harbor Laboratory Press 2023-04-01 <![CDATA[ Experimentally induced active and quiet sleep engage non-overlapping transcriptomes in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.04.03.535331v1?rss=1 Anthoney, N. Tainton-Heap, L. Luong, H. Notaras, E. Zhao, Q. Perry, T. Batterham, P. Shaw, P. van Swinderen, B. 2023-04-03 doi:10.1101/2023.04.03.535331 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Targeting the TCA cycle can ameliorate widespread axonal energy deficiency in neuroinflammatory lesions ]]> https://biorxiv.org/content/10.1101/2023.04.03.535354v1?rss=1 Tai, Y.-H. Engels, D. Locatelli, G. Fecher, C. Theodorou, D. Mueller, S. A. Licht-Mayer, S. Kreutzfeldt, M. Wagner, I. Emmanouilidis, I. Gkotzamani, S.-N. Trovo, L. Kendirli, A. Aljovic, A. Breckwoldt, M. O. Naumann, R. Bareyre, F. M. Mahad, D. Merkler, D. Lichtenthaler, S. F. Kerschensteiner, M. Misgeld, T. 2023-04-03 doi:10.1101/2023.04.03.535354 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Human gut bacteria tailor extracellular vesicle cargo for the breakdown of diet- and host-derived glycans ]]> https://biorxiv.org/content/10.1101/2023.04.03.535451v1?rss=1 Sartorio, M. G. Pardue, E. J. Scott, N. E. Feldman, M. F. 2023-04-03 doi:10.1101/2023.04.03.535451 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Acute kidney injury-induced circulating TNFR1/2 elevations correlate with persistent kidney injury and progression to fibrosis ]]> https://biorxiv.org/content/10.1101/2023.04.03.534558v1?rss=1 Arthanarisami, A. Komaru, Y. Katsouridi, C. Schumacher, J. Verges, D. K. Ning, L. Abdelmageed, M. M. Herrlich, A. Kefaloyianni, E. 2023-04-04 doi:10.1101/2023.04.03.534558 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ Identification of overlapping and distinct mural cell populations during early embryonic development ]]> https://biorxiv.org/content/10.1101/2023.04.03.535476v1?rss=1 Colijn, S. Nambara, M. Stratman, A. N. 2023-04-04 doi:10.1101/2023.04.03.535476 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ Aberrant centrosome biogenesis disrupts nephron progenitor cell renewal and fate resulting in fibrocystic kidney disease ]]> https://biorxiv.org/content/10.1101/2023.04.04.535568v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@198c93forg.highwire.dtl.DTLVardef@1c4750dorg.highwire.dtl.DTLVardef@e0c829org.highwire.dtl.DTLVardef@17512c3_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsDefective centrosome biogenesis in nephron progenitors causes: O_LIReduced abundance of metanephric mesenchyme and premature differentiation into tubular structures C_LIO_LIAbnormal branching morphogenesis leading to reduced nephron endowment and smaller kidneys C_LIO_LIChanges in cell-autonomous and paracrine signaling that drive cystogenesis and fibrosis C_LIO_LIUnique cellular and developmental defects when compared to Pkd1 knockout models C_LI ]]> Cheng, T. Agwu, C. Shim, K. Wang, B. Jain, S. Mahjoub, M. R. 2023-04-05 doi:10.1101/2023.04.04.535568 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ Untangling the mechanisms of pulmonary hypertension-induced right ventricular stiffening in a large animal model ]]> https://biorxiv.org/content/10.1101/2023.04.03.535491v1?rss=1 Kakaletsis, S. Malinowski, M. Mathur, M. Sugerman, G. P. Luci, J. J. Snider, C. Jazwiec, T. Bersi, M. R. Timek, T. A. Rausch, M. K. 2023-04-06 doi:10.1101/2023.04.03.535491 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Impaired centrosome biogenesis in kidney stromal progenitors reduces abundance of interstitial lineages and accelerates injury-induced fibrosis ]]> https://biorxiv.org/content/10.1101/2023.04.04.535583v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@a3b059org.highwire.dtl.DTLVardef@8ed18corg.highwire.dtl.DTLVardef@5f573borg.highwire.dtl.DTLVardef@1581c20_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDefective centrosome biogenesis in kidney stroma causes: C_LIO_LIReduced abundance of stromal progenitors, interstitial and mesangial cell populations C_LIO_LIDefects in cell-autonomous and paracrine signaling C_LIO_LIAbnormal/delayed nephrogenesis and tubular dilations C_LIO_LIAccelerates injury-induced fibrosis via defective TGF-{beta}/Smad3-Gli2 signaling axis C_LI ]]> Langner, E. Cheng, T. Kefaloyianni, E. Gluck, C. Wang, B. Mahjoub, M. R. 2023-04-06 doi:10.1101/2023.04.04.535583 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Sequence-encoded grammars determine material properties and physical aging of protein condensates ]]> https://biorxiv.org/content/10.1101/2023.04.06.535902v1?rss=1 Alshareedah, I. Borcherds, W. M. Cohen, S. R. Farag, M. Singh, A. Bremer, A. Pappu, R. V. Mittag, T. Banerjee, P. R. 2023-04-06 doi:10.1101/2023.04.06.535902 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Hormonal coordination of peripheral motor output and corollary discharge in a communication system ]]> https://biorxiv.org/content/10.1101/2023.04.10.536282v1?rss=1 Fukutomi, M. Carlson, B. A. 2023-04-10 doi:10.1101/2023.04.10.536282 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ Transitions in density, pressure, and effective temperature drive collective cell migration into confining environments ]]> https://biorxiv.org/content/10.1101/2023.04.10.536258v1?rss=1 Lin, W.-J. Pathak, A. 2023-04-11 doi:10.1101/2023.04.10.536258 Cold Spring Harbor Laboratory Press 2023-04-11 <![CDATA[ An in vitro model for vitamin A transport across the human blood-brain barrier ]]> https://biorxiv.org/content/10.1101/2023.04.11.536348v1?rss=1 Est, C. B. Murphy, R. M. 2023-04-12 doi:10.1101/2023.04.11.536348 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ acorn: an R package for de novo variant analysis ]]> https://biorxiv.org/content/10.1101/2023.04.11.536422v1?rss=1 Turner, T. N. 2023-04-12 doi:10.1101/2023.04.11.536422 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Motor-targeted spinal stimulation promotes concurrent rebalancing of pathologic nociceptive transmission in chronic spinal cord injury ]]> https://biorxiv.org/content/10.1101/2023.04.12.536477v1?rss=1 Bandres, M. F. Gomes, J. L. McPherson, J. G. 2023-04-12 doi:10.1101/2023.04.12.536477 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Severe Central Nervous System Demyelination in Sanfilippo Disease ]]> https://biorxiv.org/content/10.1101/2023.04.12.536631v1?rss=1 Taherzadeh, M. Zhang, E. Londono, I. Song, S.-K. Wang, S. Cooper, J. D. Kennedy, T. E. Morales, C. R. Chen, Z. Lodygensky, G. A. Pshezhetsky, A. V. 2023-04-12 doi:10.1101/2023.04.12.536631 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Kir7.1 is the physiological target for hormones and steroids that regulate uteroplacental function ]]> https://biorxiv.org/content/10.1101/2023.04.11.536476v1?rss=1 Haoui, M. Vergara, C. Lishko, P. V. 2023-04-13 doi:10.1101/2023.04.11.536476 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Volatile profiling distinguishes Streptococcus pyogenes from other respiratory streptococcal species ]]> https://biorxiv.org/content/10.1101/2023.04.13.536753v1?rss=1 Berna, A. Z. Merriman, J. A. Mellet, L. Parchment, D. K. Caparon, M. G. Odom John, A. 2023-04-13 doi:10.1101/2023.04.13.536753 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ NEURAL BASIS OF SOUND-SYMBOLIC PSEUDOWORD-SHAPE CORRESPONDENCES ]]> https://biorxiv.org/content/10.1101/2023.04.14.536865v1?rss=1 Barany, D. A. Lacey, S. Matthews, K. L. Nygaard, L. C. Sathian, K. 2023-04-14 doi:10.1101/2023.04.14.536865 Cold Spring Harbor Laboratory Press 2023-04-14 <![CDATA[ Gardnerella vaginolysin potentiates glycan molecular mimicry by Neisseria gonorrhoeae ]]> https://biorxiv.org/content/10.1101/2023.04.15.537036v1?rss=1 Morrill, S. R. Saha, S. Varki, A. P. Lewis, W. G. Ram, S. Lewis, A. L. 2023-04-15 doi:10.1101/2023.04.15.537036 Cold Spring Harbor Laboratory Press 2023-04-15 <![CDATA[ All-in-one AAV-delivered epigenome-editing platform: proof-of-concept and therapeutic implications for neurodegenerative disorders ]]> https://biorxiv.org/content/10.1101/2023.04.14.536951v1?rss=1 Kantor, B. Odonovan, B. Rittiner, J. Lindner, N. Dong, W. Zhang, A. Nicholls, P. Chiba-Falek, O. 2023-04-16 doi:10.1101/2023.04.14.536951 Cold Spring Harbor Laboratory Press 2023-04-16 <![CDATA[ Resistance to abemaciclib is associated with increased metastatic potential and lysosomal protein deregulation in breast cancer cells ]]> https://biorxiv.org/content/10.1101/2023.04.17.537215v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@1bd5e3aorg.highwire.dtl.DTLVardef@175559borg.highwire.dtl.DTLVardef@473d17org.highwire.dtl.DTLVardef@fbf0bf_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sheidemann, E. R. Demas, D. M. Hou, C. Ma, J. He, W. Weilbaecher, K. N. Shajahan-Haq, A. N. 2023-04-18 doi:10.1101/2023.04.17.537215 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Transcriptome Complexity Disentangled: A Regulatory Elements Approach ]]> https://biorxiv.org/content/10.1101/2023.04.17.537241v1?rss=1 Asiaee, A. Abrams, Z. B. Coombes, K. R. 2023-04-18 doi:10.1101/2023.04.17.537241 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ How host-like signals drive gene expression and gene expression drives capsule expansion in Cryptococcus neoformans ]]> https://biorxiv.org/content/10.1101/2023.04.19.537239v1?rss=1 Jung, J. Kang, Y. S. Brown, H. Mateusiak, C. Doering, T. L. Brent, M. 2023-04-20 doi:10.1101/2023.04.19.537239 Cold Spring Harbor Laboratory Press 2023-04-20 <![CDATA[ BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale ]]> https://biorxiv.org/content/10.1101/2023.04.19.537435v1?rss=1 Backman, T. W. H. Schenk, C. Radivojevic, T. Ando, D. Singh, J. Czajka, J. J. Costello, Z. Keasling, J. D. Tang, Y. Akhmatskaya, E. Garcia Martin, H. 2023-04-20 doi:10.1101/2023.04.19.537435 Cold Spring Harbor Laboratory Press 2023-04-20 <![CDATA[ Unbiased discovery of natural sequence variants that influence fungal virulence ]]> https://biorxiv.org/content/10.1101/2023.04.23.537984v1?rss=1 Agustinho, D. P. Brown, H. L. Chen, G. Brent, M. Doering, T. L. 2023-04-23 doi:10.1101/2023.04.23.537984 Cold Spring Harbor Laboratory Press 2023-04-23 <![CDATA[ Conserved neural dynamics and computations across species in olfaction ]]> https://biorxiv.org/content/10.1101/2023.04.24.538157v1?rss=1 Ling, D. Hanson Moss, E. Smith, C. L. Kroeger, R. Reimer, J. L. Raman, B. Arenkiel, B. R. 2023-04-24 doi:10.1101/2023.04.24.538157 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ IL-15 priming alters IFN-γ regulation in murine NK cells ]]> https://biorxiv.org/content/10.1101/2023.04.23.537947v1?rss=1 Cimpean, M. Keppel, M. P. Gainullina, A. Fan, C. Schedler, N. C. Swain, A. Kolicheski, A. Shapiro, H. Young, H. A. Wang, T. Artyomov, M. Cooper, M. A. 2023-04-25 doi:10.1101/2023.04.23.537947 Cold Spring Harbor Laboratory Press 2023-04-25 <![CDATA[ VODKA2: An accurate method to detect copy-back and deletion viral genomes from next-generation sequencing data ]]> https://biorxiv.org/content/10.1101/2023.04.25.537842v1?rss=1 Achouri, E. Felt, S. A. Hackbart, M. Lopez, C. B. 2023-04-25 doi:10.1101/2023.04.25.537842 Cold Spring Harbor Laboratory Press 2023-04-25 <![CDATA[ Annelid adult cell type diversity and their pluripotent cellular origins ]]> https://biorxiv.org/content/10.1101/2023.04.25.537979v1?rss=1 Alvarez-Campos, P. Garcia-Castro, H. Emili, E. Perez-Posada, A. Salamanca-Diaz, D. A. Mason, V. Metzger, B. Bely, A. E. Kenny, N. Özpolat, B. D. Solana, J. 2023-04-26 doi:10.1101/2023.04.25.537979 Cold Spring Harbor Laboratory Press 2023-04-26 <![CDATA[ A bivalent ChAd nasal vaccine protects against SARS-CoV-2 BQ.1.1 and XBB.1.5 infection and disease in mice and hamsters ]]> https://biorxiv.org/content/10.1101/2023.05.04.539332v1?rss=1 Ying, B. Darling, T. L. Desai, P. Liang, C.-Y. Dmitriev, I. P. Soudani, N. Bricker, T. L. Kashentseva, E. A. Harastani, H. H. Schmidt, A. G. Curiel, D. T. Boon, A. C. M. Diamond, M. S. 2023-05-04 doi:10.1101/2023.05.04.539332 Cold Spring Harbor Laboratory Press 2023-05-04 <![CDATA[ Effects of TP63 Mutations on Keratinocyte Adhesion and Migration ]]> https://biorxiv.org/content/10.1101/2023.05.04.539104v1?rss=1 Salois, M. N. Gugger, J. A. Webb, S. Sheldon, C. E. Parraga, S. P. Lewitt, G. M. Grange, D. K. Koch, P. J. Koster, M. I. 2023-05-05 doi:10.1101/2023.05.04.539104 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ Direct prediction of intrinsically disordered protein conformational properties from sequence ]]> https://biorxiv.org/content/10.1101/2023.05.08.539824v1?rss=1 Lotthammer, J. M. Ginell, G. M. Griffith, D. Emenecker, R. J. Holehouse, A. S. 2023-05-08 doi:10.1101/2023.05.08.539824 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Histone H3.3 lysine 9 and 27 control repressive chromatin states at cryptic cis-regulatory elements and bivalent promoters in mouse embryonic stem cells ]]> https://biorxiv.org/content/10.1101/2023.05.08.539859v1?rss=1 Trovato, M. Bunina, D. Yildiz, U. Marx, N. F.-N. Uckelmann, M. Levina, V. Kori, Y. Janeva, A. Garcia, B. Davidovich, C. Zaugg, J. B. Noh, K.-M. 2023-05-10 doi:10.1101/2023.05.08.539859 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ TGFβ controls alveolar type 1 epithelial cell plasticity and alveolar matrisome gene transcription ]]> https://biorxiv.org/content/10.1101/2023.05.09.540035v1?rss=1 Callaway, D. A. Penkala, I. J. Zhou, S. Cardenas-Diaz, F. Babu, A. Morley, M. P. Lopes, M. Garcia, B. Morrisey, E. 2023-05-10 doi:10.1101/2023.05.09.540035 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ Foxj1 controls olfactory ciliogenesis and differentiation program of the olfactory sensory neurons ]]> https://biorxiv.org/content/10.1101/2023.05.10.540158v1?rss=1 Rayamajhi, D. Ege, M. Ukhanov, K. Ringers, C. Zhang, Y. Jeong, I. D'Gama, P. P. Li, S. S. Cosacak, M. I. Kizil, C. Park, H.-C. Yaksi, E. Martens, J. R. Brody, S. L. Jurisch-Yaksi, N. Roy, S. 2023-05-10 doi:10.1101/2023.05.10.540158 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ Adaptation invariant concentration discrimination in an insect olfactory system ]]> https://biorxiv.org/content/10.1101/2023.05.10.540073v1?rss=1 Ling, D. Zhang, L. Saha, D. Chen, A. B. Raman, B. 2023-05-11 doi:10.1101/2023.05.10.540073 Cold Spring Harbor Laboratory Press 2023-05-11 <![CDATA[ Carotenoid assembly regulates quinone diffusion and the Roseiflexus castenholzii reaction center-light harvesting complex architecture ]]> https://biorxiv.org/content/10.1101/2023.05.14.540707v1?rss=1 Xin, J. Shi, Y. Zhang, X. Yuan, X. Xin, Y. He, H. Shen, J. Blankenship, R. Xu, X. 2023-05-15 doi:10.1101/2023.05.14.540707 Cold Spring Harbor Laboratory Press 2023-05-15 <![CDATA[ TREM2 limits necrotic core formation during atherogenesis by controlling macrophage survival and efferocytosis ]]> https://biorxiv.org/content/10.1101/2023.05.15.539977v1?rss=1 Piollet, M. Porsch, F. Rizzo, G. Kapser, F. Schulz, D. J. Kiss, M. G. Schlepckow, K. Morenas-Rodriguez, E. Sen, M. O. Gropper, J. Roesch, M. Goederle, L. Hladik, A. Knapp, S. Colonna, M. Martini, R. Haass, C. Zernecke, A. Binder, C. J. Cochain, C. 2023-05-15 doi:10.1101/2023.05.15.539977 Cold Spring Harbor Laboratory Press 2023-05-15 <![CDATA[ The transcription factor DksA exerts opposing effects on cell division depending on the presence of ppGpp ]]> https://biorxiv.org/content/10.1101/2023.05.15.540843v1?rss=1 Anderson, S. E. Vadia, S. E. McKelvy, J. Levin, P. A. 2023-05-15 doi:10.1101/2023.05.15.540843 Cold Spring Harbor Laboratory Press 2023-05-15 <![CDATA[ Defining distinct RNA-protein interactomes of SARS-CoV-2 genomic and subgenomic RNAs ]]> https://biorxiv.org/content/10.1101/2023.05.15.540806v1?rss=1 Whitworth, I. T. Knoener, R. Puray Chavez, M. Halfmann, P. Romero, S. Baddouh, M. Scalf, M. Kawaoka, Y. Kutluay, S. B. Smith, L. M. Sherer, N. M. 2023-05-16 doi:10.1101/2023.05.15.540806 Cold Spring Harbor Laboratory Press 2023-05-16 <![CDATA[ Automated model building and protein identification in cryo-EM maps ]]> https://biorxiv.org/content/10.1101/2023.05.16.541002v1?rss=1 Jamali, K. Kall, L. Zhang, R. Brown, A. Kimanius, D. Scheres, S. 2023-05-16 doi:10.1101/2023.05.16.541002 Cold Spring Harbor Laboratory Press 2023-05-16 <![CDATA[ SRF-deficient astrocytes provide neuroprotection in mouse models of excitotoxicity and neurodegeneration ]]> https://biorxiv.org/content/10.1101/2023.05.17.541074v1?rss=1 Thumu, S. C. R. Jain, M. Soman, S. Das, S. Verma, V. Nandi, A. Gutmann, D. H. Jayaprakash, B. Nair, D. Clement, J. P. Marathe, S. Ramanan, N. 2023-05-17 doi:10.1101/2023.05.17.541074 Cold Spring Harbor Laboratory Press 2023-05-17 <![CDATA[ The mature N termini of Plasmodium effector proteins confer specificity of export ]]> https://biorxiv.org/content/10.1101/2023.05.17.541120v1?rss=1 Hasan, M. M. Polino, A. J. Mukherjee, S. Vaupel, B. Goldberg, D. E. 2023-05-17 doi:10.1101/2023.05.17.541120 Cold Spring Harbor Laboratory Press 2023-05-17 <![CDATA[ Copyback viral genomes trigger stress granule formation independent of the antiviral response to interfere with viral translation in acute and persistent infections ]]> https://biorxiv.org/content/10.1101/2023.05.17.541157v1?rss=1 Lopez, C. B. Gonzalez Aparicio, L. J. Yang, Y. Hackbart, M. S. Manzoni, T. B. 2023-05-17 doi:10.1101/2023.05.17.541157 Cold Spring Harbor Laboratory Press 2023-05-17 <![CDATA[ Improving bioplastic production by Rhodopseudomonas palustris TIE-1 using synthetic biology and metabolic engineering ]]> https://biorxiv.org/content/10.1101/2023.05.17.541174v1?rss=1 Ranaivoarisoa, T. O. Bai, W. Rengasamy, K. Steele, H. Silberman, M. Olabode, J. Bose, A. 2023-05-17 doi:10.1101/2023.05.17.541174 Cold Spring Harbor Laboratory Press 2023-05-17 <![CDATA[ The phototrophic bacteria Rhodomicrobium spp. are novel chassis for bioplastic production ]]> https://biorxiv.org/content/10.1101/2023.05.17.541187v1?rss=1 Conners, E. M. Rengasamy, K. Bose, A. 2023-05-17 doi:10.1101/2023.05.17.541187 Cold Spring Harbor Laboratory Press 2023-05-17 <![CDATA[ The structure of NAD+ consuming protein Acinetobacter baumannii TIR domain shows unique kinetics and conformations. ]]> https://biorxiv.org/content/10.1101/2023.05.19.541320v1?rss=1 Klontz, E. Obi, J. O. Wang, Y. Glendening, G. Carr, J. Tsibouris, C. Buddula, S. Nallar, S. Soares, A. Beckett, D. Redzic, J. S. Eisenmesser, E. Palm, C. Schmidt, K. Scudder, A. Obiorah, T. Essuman, K. Milbrandt, J. Diantonio, A. Ray, K. Snyder, M. L. Deredge, D. Snyder, G. A. 2023-05-20 doi:10.1101/2023.05.19.541320 Cold Spring Harbor Laboratory Press 2023-05-20 <![CDATA[ In utero pulse injection of isotopic amino acids quantifies protein turnover rates during murine fetal development ]]> https://biorxiv.org/content/10.1101/2023.05.18.541242v1?rss=1 Baeza, J. Coons, B. E. Lin, Z. Riley, J. Mendoza, M. Peranteau, W. H. Garcia, B. A. 2023-05-21 doi:10.1101/2023.05.18.541242 Cold Spring Harbor Laboratory Press 2023-05-21 <![CDATA[ Latitudinal scaling of aggregation with abundance and its consequences for coexistence in species rich forests ]]> https://biorxiv.org/content/10.1101/2023.05.18.541254v1?rss=1 Wiegand, T. Wang, X. Fischer, S. Kraft, N. J. B. Bourg, N. A. Brockelman, W. Y. Cao, M. Chanthorn, W. Chu, C. Davies, S. Ediriweera, S. Gunatilleke, C. V. S. Gunatilleke, I. A. U. N. Hao, Z. Howe, R. Jiang, M. Jin, G. Kress, W. J. Li, B. Lian, J. Lin, L. Liu, F. Ma, K. McShea, W. Mi, X. Myers, J. A. Nathalang, A. Orwig, D. A. Shen, G. Su, S.-H. Sun, I.-F. Wang, X. Wolf, A. Yan, E. Ye, W. Zhu, Y. Huth, A. 2023-05-21 doi:10.1101/2023.05.18.541254 Cold Spring Harbor Laboratory Press 2023-05-21 <![CDATA[ Single-cell analysis of innate spinal cord regeneration identifies intersecting modes of neuronal repair. ]]> https://biorxiv.org/content/10.1101/2023.05.19.541505v1?rss=1 Muraleedharan Saraswathy, V. Zhou, L. Mokalled, M. H. 2023-05-22 doi:10.1101/2023.05.19.541505 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Novel mechanism of MYC deregulation in Multiple Myeloma ]]> https://biorxiv.org/content/10.1101/2023.05.19.541506v1?rss=1 Rahmat, M. Clement, K. Alberge, J.-B. Sklavenitis-Pistofidis, R. Kodgule, R. Fulco, C. Heilpern-Mallory, D. Nilsson, K. Dorfman, D. Engreitz, J. Getz, G. Pinello, L. Ryan, R. Ghobrial, I. M. 2023-05-22 doi:10.1101/2023.05.19.541506 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ C-terminal cysteines of HRas control Erk signaling and 15-deoxy-Δ12,14-prostaglandin J2 (15d-PGJ2) mediated inhibition of myoblast differentiation. ]]> https://biorxiv.org/content/10.1101/2023.05.20.541575v1?rss=1 Pundlik, S. S. Sahoo, S. S. Barik, A. Jaysingh, M. A. Venkateshvaran, A. Math, R. G. H. Ramanathan, A. 2023-05-22 doi:10.1101/2023.05.20.541575 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ HOIL1 regulates group 3 innate lymphoid cell numbers in the colon and protects against systemic dissemination, colonic ulceration, and lethality from Citrobacter rodentium infection ]]> https://biorxiv.org/content/10.1101/2023.05.22.541746v1?rss=1 Hartley, V. L. Qaqish, A. M. Wood, M. J. Studnicka, B. T. Iwai, K. Liu, T.-C. MacDuff, D. A. 2023-05-24 doi:10.1101/2023.05.22.541746 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Long-read genome assemblies for the study of chromosome expansion: Drosophila kikkawai Drosophila takahashii, Drosophila bipectinata, and Drosophila ananassae ]]> https://biorxiv.org/content/10.1101/2023.05.22.541758v1?rss=1 18 Mb. Here, we present chromosome-level long read genome assemblies for four Drosophila species with expanded F Elements ranging in size from 2.3 Mb to 20.5 Mb. Each Muller Element is present as a single scaffold in each assembly. These assemblies will enable new insights into the evolutionary causes and consequences of chromosome size expansion. ]]> Leung, W. Torosin, N. Cao, W. Reed, L. K. Arrigo, C. Elgin, S. C. R. Ellison, C. E. 2023-05-24 doi:10.1101/2023.05.22.541758 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway ]]> https://biorxiv.org/content/10.1101/2023.05.23.540554v1?rss=1 Hoppe, N. Harrison, S. Hwang, S.-H. Chen, Z. Karelina, M. Deshpande, I. Suomivuori, C.-M. Palicharla, V. R. Berry, S. P. Tschaikner, P. Regele, D. Covey, D. F. Stefan, E. Marks, D. S. Reiter, J. Dror, R. O. Evers, A. S. Mukhopadhyay, S. Manglik, A. 2023-05-24 doi:10.1101/2023.05.23.540554 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Harmonization of CSF and imaging biomarkers for Alzheimer's disease biomarkers: need and practical applications for genetics studies and preclinicalclassification ]]> https://biorxiv.org/content/10.1101/2023.05.24.542118v1?rss=1 Cruchaga, C. Timsina, J. Ali, M. Do, A. Wang, L. Sung, Y. J. 2023-05-24 doi:10.1101/2023.05.24.542118 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Endogenous recapitulation of Alzheimers disease neuropathology through human 3D direct neuronal reprogramming ]]> https://biorxiv.org/content/10.1101/2023.05.24.542155v1?rss=1 Sun, Z. Kwon, J.-S. Ren, Y. Chen, S. Cates, K. Lu, X. Walker, C. K. Karahan, H. Sviben, S. Fitzpatrick, J. A. Valdez, C. Houlden, H. Karch, C. M. Bateman, R. J. Sato, C. Mennerick, S. J. Diamond, M. I. Kim, J. Tanzi, R. E. Holtzman, D. M. Yoo, A. S. 2023-05-25 doi:10.1101/2023.05.24.542155 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Oxaliplatin-induced cardiotoxicity in mice is connected to the changes in energy metabolism in the heart tissue ]]> https://biorxiv.org/content/10.1101/2023.05.24.542198v1?rss=1 Du, J. Sudlow, L. C. Shahverdi, K. Zhou, H. Michie, M. Schindler, T. H. Mitchell, J. D. Berezin, M. Y. 2023-05-25 doi:10.1101/2023.05.24.542198 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Microbiota produced indole metabolites disrupt host cell mitochondrial energy production and inhibit Cryptosporidium parvum growth ]]> https://biorxiv.org/content/10.1101/2023.05.25.542157v1?rss=1 Funkhouser-Jones, L. Xu, R. Wilke, G. Fu, Y. Shriefer, L. A. Makimaa, H. Rodgers, R. Kennedy, E. A. VanDussen, K. Stappenbeck, T. Baldridge, M. T. Sibley, L. D. 2023-05-25 doi:10.1101/2023.05.25.542157 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Association of an estrogen-sensitive Pax1-Col11a1-Mmp3 signaling axis with adolescent idiopathic scoliosis ]]> https://biorxiv.org/content/10.1101/2023.05.26.542293v1?rss=1 T; p.(Pro1335Leu); P=7.07e-11, OR=1.118). Using CRISPR mutagenesis we generated Pax1 knockout mice (Pax1-/-). In postnatal spines we found that PAX1 and collagen (1) XI protein both localize within the intervertebral disc (IVD)-vertebral junction region encompassing the growth plate, with less collagen (1) XI detected in Pax1-/- spines compared to wildtype. By genetic targeting we found that wildtype Col11a1 expression in costal chondrocytes suppresses expression of Pax1 and of Mmp3, encoding the matrix metalloproteinase 3 enzyme implicated in matrix remodeling. However, this suppression was abrogated in the presence of the AIS-associated COL11A1P1335L mutant. Further, we found that either knockdown of the estrogen receptor gene Esr2, or tamoxifen treatment, significantly altered Col11a1 and Mmp3 expression in chondrocytes. We propose a new molecular model of AIS pathogenesis wherein genetic variation and estrogen signaling increase disease susceptibility by altering a Pax1-Col11a1-Mmp3 signaling axis in spinal chondrocytes. ]]> Wise, C. Yu, H. Khanshour, A. M. Ushiki, A. Otomo, N. Koike, Y. Einarsdottir, E. Fan, Y. Antunes, L. Kidane, Y. H. Sheng, R. Zhang, Y. Pei, J. Grishin, N. V. Evers, B. M. V. Cheung, J. P. Y. Herring, J. A. Terao, C. Song, Y.-Q. Gurnett, C. Gerdhem, P. Ikegawa, S. Rios, J. J. Ahituv, N. 2023-05-27 doi:10.1101/2023.05.26.542293 Cold Spring Harbor Laboratory Press 2023-05-27 <![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[ Symbiotic bacteria, immune-like sentinel cells, and the response to pathogens in a social amoeba ]]> https://biorxiv.org/content/10.1101/2023.05.27.542568v1?rss=1 Scott, T. J. Larsen, T. J. Brock, D. A. Uhm, S. Y. S. Queller, D. C. Strassmann, J. E. 2023-05-27 doi:10.1101/2023.05.27.542568 Cold Spring Harbor Laboratory Press 2023-05-27 <![CDATA[ Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors ]]> https://biorxiv.org/content/10.1101/2023.05.27.542576v1?rss=1 Shepherdson, J. L. Friedman, R. Z. Zheng, Y. Sun, C. Oh, I. Y. Granas, D. M. Cohen, B. A. Chen, S. White, M. A. 2023-05-27 doi:10.1101/2023.05.27.542576 Cold Spring Harbor Laboratory Press 2023-05-27 <![CDATA[ Bowel dysmotility and enteric neuron degeneration in lysosomal storage disease mice is prevented by gene therapy ]]> https://biorxiv.org/content/10.1101/2023.05.26.542524v1?rss=1 Jansen, M. J. Williams, L. L. Wang, S. Eultgen, E. M. Takahashi, K. Nelvagal, H. R. Sharma, J. Sardiello, M. DeBosch, B. J. Anderson, J. B. Sax, S. E. Wright, C. M. Makita, T. Grider, J. R. Sands, M. S. Heuckeroth, R. Cooper, J. D. 2023-05-29 doi:10.1101/2023.05.26.542524 Cold Spring Harbor Laboratory Press 2023-05-29 <![CDATA[ Complexes of vertebrate TMC1/2 and CIB2/3 proteins form hair-cell mechanotransduction cation channels ]]> https://biorxiv.org/content/10.1101/2023.05.26.542533v1?rss=1 Giese, A. P. J. Weng, W.-H. Kindt, K. S. Chang, V. H. H. Montgomery, J. S. Ratzan, E. M. Beirl, A. J. Aponte Rivera, R. Lotthammer, J. M. Walujkar, S. Foster, M. P. Zobeiri, O. A. Holt, J. R. Riazuddin, S. Cullen, K. E. Sotomayor, M. Ahmed, Z. M. 2023-05-30 doi:10.1101/2023.05.26.542533 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ Genetically engineering endothelial niche in human kidney organoids enables multilineage maturation, vascularization, and de novo cell types ]]> https://biorxiv.org/content/10.1101/2023.05.30.542848v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@1b129d4org.highwire.dtl.DTLVardef@313ae3org.highwire.dtl.DTLVardef@111c91org.highwire.dtl.DTLVardef@16a8d45_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Maggiore, J. C. LeGraw, R. Przepiorski, A. Velazquez, J. Chaney, C. Streeter, E. Silva-Barbosa, A. Franks, J. Hislop, J. Hill, A. Wu, H. Pfister, K. Howden, S. E. Watkins, S. C. Little, M. Humphreys, B. Watson, A. Stolz, D. B. Kiani, S. Davidson, A. J. Carroll, T. J. Cleaver, O. J. Sims-Lucas, S. Ebrahimkhani, M. R. Hukriede, N. A. 2023-05-30 doi:10.1101/2023.05.30.542848 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ Visual deprivation during mouse critical period reorganizes network-level functional connectivity ]]> https://biorxiv.org/content/10.1101/2023.05.30.542957v1?rss=1 Chen, S. Rahn, R. M. Bice, A. R. Gaines, S. H. Hengen, K. B. Dougherty, J. D. Culver, J. P. 2023-05-31 doi:10.1101/2023.05.30.542957 Cold Spring Harbor Laboratory Press 2023-05-31 <![CDATA[ In vivo evolution of a Klebsiella pneumoniae capsule defect promotes complement-mediated opsono-phagocytosis and persistence during recurrent infection ]]> https://biorxiv.org/content/10.1101/2023.05.31.542722v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@155736eorg.highwire.dtl.DTLVardef@10d47c0org.highwire.dtl.DTLVardef@e1ab83org.highwire.dtl.DTLVardef@1c33131_HPS_FORMAT_FIGEXP M_FIG Graphical abstract Created with BioRender.com C_FIG ]]> Bain, W. Ahn, B. Penaloza, H. McElheny, C. Tolman, N. van der Geest, R. Gonzalez-Ferrer, S. Chen, N. An, X. Hosuru, R. Tabary, M. Papke, E. Kohli, N. Farooq, N. Bachman, W. Olonisakin, T. Xiong, Z. Griffith, M. P. Sullivan, M. Franks, J. Mustapha, M. Iovleva, A. Suber, T. Shanks, R. M. Ferreira, V. Stolz, D. B. Van Tyne, D. Doi, Y. Lee, J. 2023-06-01 doi:10.1101/2023.05.31.542722 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Ribosomal protein control of hematopoietic stem cell transformation through direct, non-canonical regulation of metabolism ]]> https://biorxiv.org/content/10.1101/2023.05.31.543132v1?rss=1 Harris, B. Singh, D. K. Verma, M. Fahl, S. P. Rhodes, M. Sprinkle, S. R. Wang, M. Zhang, Y. Perrigoue, J. Kessel, R. Peri, S. West, J. Giricz, O. Boultwood, J. Pellagatti, A. Ramesh, K. Montangna, C. Pradhan, K. Tyner, J. Kennedy, B. K. Holinstat, M. Steidl, U. Sykes, S. Verma, A. Wiest, D. L. 2023-06-01 doi:10.1101/2023.05.31.543132 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ The lipid phosphatase activity of PTEN dampens FRA1 expression via AKT/mTOR signaling to suppress melanoma ]]> https://biorxiv.org/content/10.1101/2023.06.01.543131v1?rss=1 Xu, X. Bok, I. Jasani, N. Wang, K. Chadourne, M. Deng, O. Welsh, E. A. Kinose, F. Rix, U. Karreth, F. A. 2023-06-01 doi:10.1101/2023.06.01.543131 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Condensate partitioning governs the mechanism of action of FUS phase separation modulators ]]> https://biorxiv.org/content/10.1101/2023.05.31.543137v1?rss=1 Ausserwoeger, H. Qian, D. Krainer, G. Welsh, T. J. Sneideris, T. Franzmann, T. M. Qamar, S. S. Nixon-Abell, J. Kar, M. St George-Hyslop, P. Hyman, A. A. Alberti, S. Pappu, R. V. Knowles, T. P. J. 2023-06-03 doi:10.1101/2023.05.31.543137 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase ]]> https://biorxiv.org/content/10.1101/2023.06.03.542675v1?rss=1 Diaz, R. E. Ecker, A. K. Correy, G. J. Asthana, P. Young, I. D. Faust, B. Thompson, M. C. Seiple, I. B. Van Dyken, S. J. Locksley, R. M. Fraser, J. S. 2023-06-03 doi:10.1101/2023.06.03.542675 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ Single-cell lineage tracing reveals hierarchy and mechanism of adipocyte precursor maturation ]]> https://biorxiv.org/content/10.1101/2023.06.01.543318v1?rss=1 Gonzalez, G. C. R. Butka, E. G. Gonzalez, C. E. Kong, W. Jindal, K. Morris, S. A. 2023-06-04 doi:10.1101/2023.06.01.543318 Cold Spring Harbor Laboratory Press 2023-06-04 <![CDATA[ Stability of navigation in catheter-based endovascular procedures ]]> https://biorxiv.org/content/10.1101/2023.06.02.543219v1?rss=1 Hartquist, C. M. Lee, J. V. Qiu, M. Y. Suskin, C. Chandrasekaran, V. Lowe, H. R. Zayed, M. A. Osbun, J. W. Genin, G. M. 2023-06-05 doi:10.1101/2023.06.02.543219 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Multi-Scale Cortical Bone Traits Vary in Two Mouse Models of Genetic Diversity ]]> https://biorxiv.org/content/10.1101/2023.06.02.543484v1?rss=1 View larger version (47K): org.highwire.dtl.DTLVardef@1e61c1org.highwire.dtl.DTLVardef@a3f941org.highwire.dtl.DTLVardef@1411dceorg.highwire.dtl.DTLVardef@bfc8c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Migotsky, N. Kumar, S. Shuster, J. T. Coulombe, J. C. Senwar, B. Gestos, A. A. Farber, C. R. Ferguson, V. L. Silva, M. J. 2023-06-06 doi:10.1101/2023.06.02.543484 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ Unpredictable soil conditions affect the prevalence of a microbial symbiosis ]]> https://biorxiv.org/content/10.1101/2023.06.07.543465v1?rss=1 Scott, T. J. Stephenson, C. J. Rao, S. Queller, D. Strassmann, J. E. 2023-06-07 doi:10.1101/2023.06.07.543465 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Haplotype-resolved, chromosome-level assembly of white clover (Trifolium repens L., Fabaceae) ]]> https://biorxiv.org/content/10.1101/2023.06.06.543960v1?rss=1 Santangelo, J. Battlay, P. Hendrickson, B. Kuo, W.-H. Olsen, K. M. Kooyers, N. J. Johnson, M. Hodgins, K. Ness, R. 2023-06-08 doi:10.1101/2023.06.06.543960 Cold Spring Harbor Laboratory Press 2023-06-08 <![CDATA[ Calling Cards: a customizable platform to longitudinally record protein-DNA interactions over time in cells and tissues ]]> https://biorxiv.org/content/10.1101/2023.06.07.544098v1?rss=1 Yen, A. Mateusiak, C. Sarafinovska, S. Gachechiladze, M. A. Guo, J. Chen, X. Moudgil, A. Cammack, A. J. Hoisington-Lopez, J. Crosby, M. Brent, M. Mitra, R. D. Dougherty, J. D. 2023-06-09 doi:10.1101/2023.06.07.544098 Cold Spring Harbor Laboratory Press 2023-06-09 <![CDATA[ A non-oscillatory, millisecond-scale embedding of brain state provides insight into behavior. ]]> https://biorxiv.org/content/10.1101/2023.06.09.544399v1?rss=1 Parks, D. F. Schneider, A. M. Xu, Y. Brunwasser, S. J. Funderburk, S. Thurber, D. Blanche, T. Dyer, E. L. Haussler, D. Hengen, K. B. 2023-06-09 doi:10.1101/2023.06.09.544399 Cold Spring Harbor Laboratory Press 2023-06-09 <![CDATA[ The chromatin landscape of healthy and injured cell types in the human kidney ]]> https://biorxiv.org/content/10.1101/2023.06.07.543965v1?rss=1 Gisch, D. L. Brennan, M. Lake, B. B. Basta, J. Keller, M. Melo Ferreira, R. Akilesh, S. Ghag, R. Lu, C. Cheng, Y.-H. Collins, K. S. Parikh, S. V. Rovin, B. H. Robbins, L. Conklin, K. Y. Diep, D. Zhang, B. Knoten, A. Barwinska, D. Asghari, M. Sabo, A. R. Ferkowicz, M. J. Sutton, T. A. Kelly, K. J. De Boer, I. H. Rosas, S. E. Kiryluk, K. Hodgin, J. B. Alakwaa, F. Jefferson, N. Gaut, J. P. Gehlenborg, N. Phillips, C. L. El-Achkar, T. M. Dagher, P. C. Hato, T. Zhang, K. Himmelfarb, J. Kretzler, M. Mollah, S. Kidney Precision Medicine Project, Jain, S. Ra 2023-06-10 doi:10.1101/2023.06.07.543965 Cold Spring Harbor Laboratory Press 2023-06-10 <![CDATA[ Ketamine rescues anhedonia by cell-type and input specific adaptations in the Nucleus Accumbens ]]> https://biorxiv.org/content/10.1101/2023.06.08.544088v1?rss=1 Lucantonio, F. Li, S. Lu, J. Roeglin, J. Bontempi, L. Shields, B. C. Zarate, C. A. Tadross, M. R. Pignatelli, M. 2023-06-13 doi:10.1101/2023.06.08.544088 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ Dominance metric in multi-component binary phase equilibria ]]> https://biorxiv.org/content/10.1101/2023.06.12.544666v1?rss=1 Qian, D. Ausserwoger, H. Sneideris, T. Pappu, R. V. Knowles, T. 2023-06-13 doi:10.1101/2023.06.12.544666 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[ 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[ Intrinsic Homeostatic Plasticity in Mouse and Human Sensory Neurons ]]> https://biorxiv.org/content/10.1101/2023.06.13.544829v1?rss=1 Mcllvried, L. A. Del Rosario, J. S. Pullen, M. Y. Wangzhou, A. Sheahan, T. D. Shepherd, A. J. Slivicki, R. A. Lemen, J. A. Price, T. J. Copits, B. A. Gereau, R. W. 2023-06-14 doi:10.1101/2023.06.13.544829 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ Generative artificial intelligence GPT-4 accelerates knowledge mining and machine learning for synthetic biology ]]> https://biorxiv.org/content/10.1101/2023.06.14.544984v1?rss=1 Xiao, Z. Li, W. Moon, H. Roell, G. W. Chen, Y. Tang, Y. J. 2023-06-14 doi:10.1101/2023.06.14.544984 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ Inhibition of Retinoic Acid Signaling in Proximal Tubular Epithelial cells Protects against Acute Kidney Injury by Enhancing Kim-1-dependent Efferocytosis ]]> https://biorxiv.org/content/10.1101/2023.06.15.545113v1?rss=1 View larger version (18K): org.highwire.dtl.DTLVardef@140ba6borg.highwire.dtl.DTLVardef@8f02f0org.highwire.dtl.DTLVardef@10a123eorg.highwire.dtl.DTLVardef@33b564_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yang, M. Lopez, L. N. Brewer, M. Delgado, R. D. Menshikh, A. A. Clouthier, K. A. Zhu, Y. Vanichapol, T. Yang, H. Harris, R. Gewin, L. Brooks, C. R. Davidson, A. de Caestecker, M. 2023-06-15 doi:10.1101/2023.06.15.545113 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ M3NetFlow: a novel multi-scale multi-hop modular graph AI model for multi-omics data integration and signaling network inference ]]> https://biorxiv.org/content/10.1101/2023.06.15.545130v1?rss=1 Zhang, H. Goedegebuure, P. Ding, L. Hawkins, W. DeNardo, D. Fields, R. Chen, Y. Li, F. 2023-06-16 doi:10.1101/2023.06.15.545130 Cold Spring Harbor Laboratory Press 2023-06-16 <![CDATA[ Fluctuating selection facilitates the discovery of broadly effective but difficult to reach adaptive outcomes in yeast ]]> https://biorxiv.org/content/10.1101/2023.06.17.545402v1?rss=1 Fasanello, V. J. Liu, P. Fay, J. C. Botero, C. A. 2023-06-18 doi:10.1101/2023.06.17.545402 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Androgen exposure impairs neutrophil maturation and function within the infected kidney ]]> https://biorxiv.org/content/10.1101/2023.06.19.545598v1?rss=1 Hreha, T. N. Collins, C. A. Hunstad, D. A. 2023-06-22 doi:10.1101/2023.06.19.545598 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Testing relationships between multiple regional features and biogeographic processes of speciation, extinction, and dispersal ]]> https://biorxiv.org/content/10.1101/2023.06.19.545613v1?rss=1 Swiston, S. K. Landis, M. J. 2023-06-22 doi:10.1101/2023.06.19.545613 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ ALS-related p97 R155H mutation disrupts lysophagy in iPSC-derived motor neurons ]]> https://biorxiv.org/content/10.1101/2023.06.21.545956v1?rss=1 Klickstein, J. A. Johnson, M. A. Antonoudiou, P. Maguire, J. Paulo, J. Gygi, S. Weihl, C. C. Raman, M. 2023-06-24 doi:10.1101/2023.06.21.545956 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ Cellular endosomal potassium ion flux regulates arenavirus uncoating during virus entry ]]> https://biorxiv.org/content/10.1101/2023.06.23.546275v1?rss=1 Shaw, A. B. Tse, H. N. Byford, O. plahe, g. Moon-Walker, A. Saphire, E. O. Whelan, S. P. J. Mankouri, J. Fontana, J. Barr, J. N. 2023-06-26 doi:10.1101/2023.06.23.546275 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Incorporating physics to overcome data scarcity in predictive modeling of protein function: a case study of BK channels ]]> https://biorxiv.org/content/10.1101/2023.06.24.546384v1?rss=1 Nordquist, E. Zhang, G. Barethiya, S. Ji, N. White, K. W. Han, L. Jia, Z. Shi, J. Cui, J. Chen, J. 2023-06-26 doi:10.1101/2023.06.24.546384 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ TOMM40 and TOMM22 of the Translocase Outer Mitochondrial Membrane Complex rescue statin-impaired mitochondrial dynamics, morphology, and mitophagy in skeletal myotubes ]]> https://biorxiv.org/content/10.1101/2023.06.24.546411v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@1845842org.highwire.dtl.DTLVardef@1be8a26org.highwire.dtl.DTLVardef@5fd618org.highwire.dtl.DTLVardef@1e0f523_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yang, N. V. Rogers, S. Guerra, R. Pagliarini, D. J. Theusch, E. Krauss, R. M. 2023-06-26 doi:10.1101/2023.06.24.546411 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Multiple pathways for glucose phosphate transport and utilization support growth of Cryptosporidium parvum ]]> https://biorxiv.org/content/10.1101/2023.06.27.546703v1?rss=1 Xu, R. Beatty, W. Greigert, V. Witola, W. H. Sibley, L. D. 2023-06-27 doi:10.1101/2023.06.27.546703 Cold Spring Harbor Laboratory Press 2023-06-27 <![CDATA[ Lymphocytic choriomeningitis arenavirus utilises tunnelling nanotube-like intercellular connections for cell-to-cell spread ]]> https://biorxiv.org/content/10.1101/2023.06.28.546878v1?rss=1 Byford, O. Shaw, A. B. Tse, H. N. Moon-Walker, A. Saphire, E. O. Whelan, S. P. J. Stacey, M. Hewson, R. Fontana, J. Barr, J. N. 2023-06-28 doi:10.1101/2023.06.28.546878 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ Engineering Human Pluripotent Stem Cell Lines to Evade Xenogeneic Transplantation Barriers ]]> https://biorxiv.org/content/10.1101/2023.06.27.546594v1?rss=1 Pizzato, H. A. Alonso-Guallart, P. Woods, J. Johannesson, B. Connelly, J. P. Fehniger, T. A. Atkinson, J. Pruett-Miller, S. M. Monsma, F. J. Bhattacharya, D. 2023-06-29 doi:10.1101/2023.06.27.546594 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ Cortical Origin of Theta Error Signals ]]> https://biorxiv.org/content/10.1101/2023.06.27.546752v1?rss=1 Herrera, B. Sajad, A. Errington, S. P. Schall, J. D. Diaz, J. R. 2023-06-30 doi:10.1101/2023.06.27.546752 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Discovery of New Broad-Spectrum Anti-Infectives for Eukaryotic Pathogens Using Bioorganometallic Chemistry ]]> https://biorxiv.org/content/10.1101/2023.06.28.546819v1?rss=1 Lin, Y. Jung, H. Bulman, C. A. Ng, J. Vinck, R. O'Beirne, C. Moser, M. S. Tricoche, N. Peguero, R. Li, R. W. Urban, J. F. Le Pape, P. Pagniez, F. Moretto, M. Weil, T. Lustigman, S. Cariou, K. Mitreva, M. Sakanari, J. Gasser, G. 2023-06-30 doi:10.1101/2023.06.28.546819 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Post-exposure intranasal IFNα suppresses replication and neuroinvasion of Venezualen Equine Encephalitis virus within olfactory sensory neurons ]]> https://biorxiv.org/content/10.1101/2023.06.30.547169v1?rss=1 Klein, R. S. Cain, M. D. Klein, N. R. Jiang, X. 2023-06-30 doi:10.1101/2023.06.30.547169 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Electrophysiology of human iPSC-derived vascular smooth muscle cells and cell autonomous consequences of Cantu Syndrome mutations ]]> https://biorxiv.org/content/10.1101/2023.06.29.547088v1?rss=1 Hanson, A. McClenaghan, C. Weng, K.-C. Colijn, S. Stratman, A. N. Halabi, C. M. Grange, D. K. Silva, J. R. Nichols, C. G. 2023-07-01 doi:10.1101/2023.06.29.547088 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ Fetal daily rhythms develop during pregnancy and entrain to the maternal circadian system ]]> https://biorxiv.org/content/10.1101/2023.06.30.547166v1?rss=1 Bates, K. Sapiro, E. Amme, J. L. McCarthy, R. Nikhil, K. L. Speck, S. Vasireddy, V. Roberts, E. Martin-Fairey, C. Dominguez-Romero, M.-E. Garcia Cardenas, S. P. England, S. K. Herzog, E. D. 2023-07-01 doi:10.1101/2023.06.30.547166 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ Labile assembly of a tardigrade protein induces biostasis ]]> https://biorxiv.org/content/10.1101/2023.06.30.547219v1?rss=1 Sanchez-Martinez, S. Nguyen, K. Biswas, S. Nicholson, V. Romanyuk, A. V. Ramirez, J. F. KC, S. Akter, A. Childs, C. Usher, E. T. Ginell, G. M. Yu, F. Gollub, E. Malferrari, M. Francia, F. Venturoli, G. Martin, E. W. Caporaletti, F. Giubertoni, G. Woutersen, S. Sukenik, S. Woolfson, D. Holehouse, A. S. Boothby, T. C. 2023-07-02 doi:10.1101/2023.06.30.547219 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ A bistable inhibitory OptoGPCR for multiplexed optogenetic control of neural circuits ]]> https://biorxiv.org/content/10.1101/2023.07.01.547328v1?rss=1 Wietek, J. Nozownik, A. Pulin, M. Saraf-Sinik, I. Matosevich, N. Malan, D. Brown, B. J. Dine, J. Levy, R. Litvin, A. Regev, N. Subramaniam, S. Bitton, E. Benjamin, A. Copits, B. A. Sasse, P. Rost, B. R. Schmitz, D. Soba, P. Nir, Y. Wiegert, J. S. Yizhar, O. 2023-07-02 doi:10.1101/2023.07.01.547328 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Homologous mutations in β, embryonic, and perinatal muscle myosins have divergent effects on molecular power generation ]]> https://biorxiv.org/content/10.1101/2023.07.02.547385v1?rss=1 Liu, C. Karabina, A. Meller, A. Bhattacharjee, A. Agostino, C. J. Bowman, G. Ruppel, K. M. Spudich, J. A. Leinwand, L. A. 2023-07-02 doi:10.1101/2023.07.02.547385 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Crowder titrations enable the quantification of driving forces for macromolecular phase separation ]]> https://biorxiv.org/content/10.1101/2023.07.03.547544v1?rss=1 Chauhan, G. Bremer, A. Dar, F. Mittag, T. Pappu, R. V. 2023-07-03 doi:10.1101/2023.07.03.547544 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Subcellular pathways through VG3 amacrine cells provide regionally tuned object-motion-selective signals in mouse retina. ]]> https://biorxiv.org/content/10.1101/2023.07.03.547571v1?rss=1 Friedrichsen, K. Hsiang, J.-C. McCoy, L. Valkova, K. Kerschensteiner, D. Morgan, J. L. 2023-07-03 doi:10.1101/2023.07.03.547571 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Divergent Molecular Phenotypes in Point Mutations at the Same Residue in Beta-Myosin Heavy Chain Lead to Distinct Cardiomyopathies ]]> https://biorxiv.org/content/10.1101/2023.07.03.547580v1?rss=1 Lehman, S. J. Meller, A. Solieva, S. O. Lotthammer, J. M. Greenberg, L. Langer, S. J. Greenberg, M. J. Tardiff, J. C. Bowman, G. R. Leinwand, L. A. 2023-07-03 doi:10.1101/2023.07.03.547580 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Functional variations in gamma-secretase activity are critical determinants of the clinical, biomarker, and cognitive progression of autosomal dominant Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2023.07.04.547688v1?rss=1 Schultz, S. Liu, L. Schultz, A. Fitzpatrick, C. Levin, R. Bellier, J.-P. Shirzadi, Z. Mathurin, N. Chen, C. Benzinger, T. Day, G. Farlow, M. Gordon, B. Hassenstab, J. Jack, C. Jucker, M. Karch, C. Lee, J. Levin, J. Perrin, R. Schofield, P. Xiong, C. Johnson, K. McDade, E. Bateman, R. Sperling, R. Selkoe, D. Chhatwal, J. the Dominantly Inherited Alzheimer's Network Investigators, 2023-07-05 doi:10.1101/2023.07.04.547688 Cold Spring Harbor Laboratory Press 2023-07-05 <![CDATA[ Harmonized cross-species cell atlases of trigeminal and dorsal root ganglia ]]> https://biorxiv.org/content/10.1101/2023.07.04.547740v1?rss=1 Bhuiyan, S. Xu, M. Yang, L. Semizoglou, E. Bhatia, P. Pantaleo, K. I. Tochitsky, I. Jain, A. A. Erdogan, B. Blair, S. Cat, V. Mwirigi, J. M. Sankaranarayanan, I. Tavares-Ferreira, D. Green, U. McIlvried, L. A. Copits, B. A. Bertels, Z. Del Rosario, J. S. Widman, A. Slivicki, R. A. Yi, J. Woolf, C. J. Lennerz, J. K. Whited, J. Price, T. J. Gereau, R. Renthal, W. 2023-07-05 doi:10.1101/2023.07.04.547740 Cold Spring Harbor Laboratory Press 2023-07-05 <![CDATA[ Myeloid cell activation during Zika virus encephalitis predicts recovery of functional cortical connectivity ]]> https://biorxiv.org/content/10.1101/2023.07.06.547991v1?rss=1 Agner, S. C. Brier, L. M. Hill, J. D. Liu, E. Y. Bice, A. Rahn, R. M. Culver, J. P. Klein, R. S. 2023-07-06 doi:10.1101/2023.07.06.547991 Cold Spring Harbor Laboratory Press 2023-07-06 <![CDATA[ Helicity of a tardigrade disordered protein promotes desiccation tolerance ]]> https://biorxiv.org/content/10.1101/2023.07.06.548010v1?rss=1 Biswas, S. Gollub, E. Yu, F. Ginell, G. Holehouse, A. S. Sukenik, S. Boothby, T. C. 2023-07-06 doi:10.1101/2023.07.06.548010 Cold Spring Harbor Laboratory Press 2023-07-06 <![CDATA[ Spared nerve injury causes motor phenotypes unrelated to pain in mice ]]> https://biorxiv.org/content/10.1101/2023.07.07.548155v1?rss=1 Norris, M. R. Dunn, S. S. Aravamuthan, B. R. McCall, J. G. 2023-07-09 doi:10.1101/2023.07.07.548155 Cold Spring Harbor Laboratory Press 2023-07-09 <![CDATA[ Patterns of recombination in snakes reveal a tug of war between PRDM9 and promoter-like features ]]> https://biorxiv.org/content/10.1101/2023.07.11.548536v1?rss=1 Hoge, C. R. de Manuel, M. Mahgoub, M. Okami, N. Fuller, Z. L. Banerjee, S. Baker, Z. Mcnulty, M. Andolfatto, P. Macfarlan, T. S. Schumer, M. Tzika, A. C. Przeworski, M. 2023-07-11 doi:10.1101/2023.07.11.548536 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Improved Protocol for Reproducible Human Cortical Organoids Reveals Early Alterations in Metabolism with MAPT Mutations ]]> https://biorxiv.org/content/10.1101/2023.07.11.548571v1?rss=1 Bertucci, T. Bowles, K. R. Lotz, S. Qi, L. Stevens, K. Goderie, S. K. Borden, S. Oja, L. Lane, K. Lotz, R. Lotz, H. Chowdhury, R. Joy, S. Arduini, B. L. Butler, D. C. Miller, M. Baron, H. Sandhof, C. A. Silva, M. C. Haggarty, S. J. Karch, C. M. Geschwind, D. H. Goate, A. M. Temple, S. 2023-07-11 doi:10.1101/2023.07.11.548571 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Mechanisms of Innate Immune Injury in Arrhythmogenic Cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2023.07.12.548682v1?rss=1 Chelko, S. P. Penna, V. Engel, M. Landim-Vieira, M. Cannon, E. N. Lavine, K. Saffitz, J. E. 2023-07-13 doi:10.1101/2023.07.12.548682 Cold Spring Harbor Laboratory Press 2023-07-13 <![CDATA[ Dual Membrane-Sspanning Anti-Sigma Factors Regulate Vesiculation in Gut Bacteroidota ]]> https://biorxiv.org/content/10.1101/2023.07.13.548920v1?rss=1 Pardue, E. J. Sartorio, M. Jana, B. Scott, N. Beatty, W. Ortiz-Marquez, J. van Opijnen, T. Hsu, F.-F. Potter, R. F. Feldman, M. 2023-07-13 doi:10.1101/2023.07.13.548920 Cold Spring Harbor Laboratory Press 2023-07-13 <![CDATA[ In vivo single-cell CRISPR uncovers distinct TNF-alphaprograms in clonal expansion and tumorigenesis ]]> https://biorxiv.org/content/10.1101/2023.07.13.548697v1?rss=1 Renz, P. F. Ghoshdastider, U. Baghai Sain, S. Valdivia-Francia, F. Khandekar, A. Ormiston, M. Bernasconi, M. Kretz, J. A. Lee, M. Hyams, K. Forny, M. Pohly, M. Ficht, X. Ellis, S. J. Moor, A. E. Sendoel, A. 2023-07-14 doi:10.1101/2023.07.13.548697 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ Disrupting actin filaments enhances glucose-stimulated insulin secretion independent of the cortical actin cytoskeleton ]]> https://biorxiv.org/content/10.1101/2023.07.15.549141v1?rss=1 Polino, A. J. Ng, X. W. Rooks, R. Piston, D. W. 2023-07-16 doi:10.1101/2023.07.15.549141 Cold Spring Harbor Laboratory Press 2023-07-16 <![CDATA[ POPSHIFT: A THERMODYNAMICALLY SOUND APPROACH TO ESTIMATE BINDING FREE ENERGIES BY ACCOUNTING FOR LIGAND-INDUCED POPULATION SHIFTS FROM A LIGAND-FREE MSM ]]> https://biorxiv.org/content/10.1101/2023.07.14.549110v1?rss=1 Smith, L. G. Novak, B. Osato, M. Mobley, D. L. Bowman, G. R. 2023-07-18 doi:10.1101/2023.07.14.549110 Cold Spring Harbor Laboratory Press 2023-07-18 <![CDATA[ The ACE-inhibitor drug captopril inhibits ACN-1 to control dauer formation and aging ]]> https://biorxiv.org/content/10.1101/2023.07.17.549402v1?rss=1 Egan, B. M. Pohl, F. Anderson, X. Williams, S. C. Adodo, I. G. Hunt, P. Wang, Z. Chiu, C.-H. Scharf, A. Mosley, M. Kumar, S. Schneider, D. L. Fujiwara, H. Hsu, F.-F. Kornfeld, K. 2023-07-19 doi:10.1101/2023.07.17.549402 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ A modular chemigenetic calcium indicator enables in vivo functional imaging with near-infrared light ]]> https://biorxiv.org/content/10.1101/2023.07.18.549527v1?rss=1 Farrants, H. Shuai, Y. Lemon, W. C. Hernandez, C. M. Yang, S. Patel, R. Qiao, G. Frei, M. S. Grimm, J. B. Hanson, T. L. Tomaska, F. Turner, G. C. Stringer, C. Keller, P. J. Beyene, A. G. Chen, Y. Liang, Y. Lavis, L. D. Schreiter, E. R. 2023-07-19 doi:10.1101/2023.07.18.549527 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ The HCM-Linked Mutation Arg92Leu in TNNT2 Allosterically Alters the cTnC-cTnI Interface and Disrupts the PKA-mediated Regulation of Myofilament Relaxation ]]> https://biorxiv.org/content/10.1101/2023.07.18.549569v1?rss=1 Lynn, M. L. Jimenez, J. Castillo, R. L. Klass, M. M. Vasquez, C. Baldo, A. P. Gibson, C. Murphy, A. M. Tardiff, J. C. 2023-07-19 doi:10.1101/2023.07.18.549569 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Microglia at Sites of Atrophy Restrict the Progression of Retinal Degeneration via Galectin-3 and Trem2 Interactions ]]> https://biorxiv.org/content/10.1101/2023.07.19.549403v1?rss=1 Yu, C. Lad, E. M. Mathew, R. Littleton, S. Chen, Y. Schlepckow, K. Degan, S. Chew, L. Amason, J. Kalnitsky, J. Bowes Rickman, C. Proia, A. D. Colonna, M. Haass, C. Saban, D. 2023-07-19 doi:10.1101/2023.07.19.549403 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ On-Demand Expansion Fluorescence and Photoacoustic Microscopy (ExFLPAM) ]]> https://biorxiv.org/content/10.1101/2023.07.19.549787v1?rss=1 Mu, X. Ma, C. Mei, X. Liao, J. Bojar, R. Kuang, S. Rong, Q. Yao, J. Zhang, Y. S. 2023-07-20 doi:10.1101/2023.07.19.549787 Cold Spring Harbor Laboratory Press 2023-07-20 <![CDATA[ No evidence for the association between COVID-19 and neuroinflammation: A diffusion basis spectrum imaging study. ]]> https://biorxiv.org/content/10.1101/2023.07.20.549891v1?rss=1 0.05), but with greater DBSI-HF in left pre- and post-central gyri and right middle frontal gyrus ({beta}s>0.3, all pFDR=0.03). Intriguingly, the brain areas exhibiting increased putative vasogenic edema had previously been linked to COVID-19-related functional and structural alterations, whereas brain regions displaying subtle differences in cellularity between COVID-19 cases and controls included regions within or functionally connected to the olfactory network, which has been implicated in COVID-19 psychopathology. Nevertheless, our study might not have captured acute and transitory neuroinflammatory effects linked to SARS-CoV-2 infection, possibly due to symptom resolution before the imaging scan. Future research is warranted to explore the potential time- and symptom-dependent neuroinflammatory relationship with COVID-19. ]]> Zhang, W. Gorelik, A. J. Wang, Q. Norton, S. A. Hershey, T. Bijsterbosch, J. D. Bogdan, R. 2023-07-20 doi:10.1101/2023.07.20.549891 Cold Spring Harbor Laboratory Press 2023-07-20 <![CDATA[ Coenyzme Q4 is a functional substitute for coenyzme Q10 and can be targeted to the mitochondria ]]> https://biorxiv.org/content/10.1101/2023.07.20.549963v1?rss=1 Steenberge, L. H. Sung, A. Y. Fan, J. Pagliarini, D. J. 2023-07-20 doi:10.1101/2023.07.20.549963 Cold Spring Harbor Laboratory Press 2023-07-20 <![CDATA[ Chronic striatal cholinergic interneuron excitation induces clinically-relevant dystonic behavior in mice ]]> https://biorxiv.org/content/10.1101/2023.07.19.549778v1?rss=1 Gemperli, K. Lu, X. Chintalapati, K. Rust, A. Bajpai, R. Suh, N. Blackburn, J. Gelineau-Morel, R. Kruer, M. C. Mingbunjerdsuk, D. O'Malley, J. Tochen, L. Waugh, J. Wu, S. Feyma, T. Perlmutter, J. Mennerick, S. McCall, J. G. Aravamuthan, B. R. 2023-07-21 doi:10.1101/2023.07.19.549778 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ Generation of an induced pluripotent stem cell line from a healthy adult indigenous Nigerian participant ]]> https://biorxiv.org/content/10.1101/2023.07.21.550059v1?rss=1 Muhammad, Z. Brown, P. W. Babazau, L. Alkhamis, A. I. Goni, B. W. Nggada, H. A. Mbaya, K. M. Wray, S. Marte, I. H. Karch, C. Serpell, L. Maina, M. B. 2023-07-21 doi:10.1101/2023.07.21.550059 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ Contrasting roles of different mismatch repair proteins in basal-like breast cancer ]]> https://biorxiv.org/content/10.1101/2023.07.20.549745v1?rss=1 Mo, J. Borcherding, N. Jo, S. Tithi, T. I. Cho, E. Cash, C. E. Honda, M. Ahmed, K. K. kolb, R. Weigel, R. Spies, M. Zhang, W. 2023-07-22 doi:10.1101/2023.07.20.549745 Cold Spring Harbor Laboratory Press 2023-07-22 <![CDATA[ Metabolomic rearrangement controls the intrinsic microbial response to temperature changes ]]> https://biorxiv.org/content/10.1101/2023.07.22.550177v1?rss=1 Knapp, B. Willis, L. Gonzalez, C. Vashistha, H. Touma, J. J. Tikhonov, M. Ram, J. Salman, H. Elias, J. E. Huang, K. C. 2023-07-24 doi:10.1101/2023.07.22.550177 Cold Spring Harbor Laboratory Press 2023-07-24 <![CDATA[ Evaluation of gliovascular functions of Aqp4 readthrough isoforms ]]> https://biorxiv.org/content/10.1101/2023.07.21.549379v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@18f8f32org.highwire.dtl.DTLVardef@25afeorg.highwire.dtl.DTLVardef@a3e0e1org.highwire.dtl.DTLVardef@100f2e1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mueller, S. M. White, K. M. Fass, S. B. Chen, S. Shi, Z. Ge, X. Engelbach, J. A. Gaines, S. H. Bice, A. R. Vasek, M. J. Garbow, J. R. Culver, J. P. Martinez-Lozada, Z. Cohen-Salmon, M. Dougherty, J. D. Sapkota, D. 2023-07-25 doi:10.1101/2023.07.21.549379 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Ultra-high density imaging arrays for diffuse optical tomography of human brain improve resolution, signal-to-noise, and information decoding ]]> https://biorxiv.org/content/10.1101/2023.07.21.549920v1?rss=1 Markow, Z. E. Trobaugh, J. W. Richter, E. J. Tripathy, K. Rafferty, S. M. Svoboda, A. M. Schroeder, M. L. Burns-Yocum, T. M. Bergonzi, K. M. Chevillet, M. A. Mugler, E. M. Eggebrecht, A. T. Culver, J. P. 2023-07-25 doi:10.1101/2023.07.21.549920 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ M1 recruitment during interleaved practice is important for encoding, not just consolidation, of novel skill memory ]]> https://biorxiv.org/content/10.1101/2023.07.21.550118v1?rss=1 Kim, T. Kim, H. Philip, B. A. Wright, D. L. 2023-07-25 doi:10.1101/2023.07.21.550118 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ High dimensional analyses reveal activation of lymphocyte subsets and reversal of immunoresistance by cytokine enhancement of adoptive cellular vaccine therapy in prostate cancer. ]]> https://biorxiv.org/content/10.1101/2023.07.23.550213v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@130adb0org.highwire.dtl.DTLVardef@db2567org.highwire.dtl.DTLVardef@174a953org.highwire.dtl.DTLVardef@18c049_HPS_FORMAT_FIGEXP M_FIG C_FIG One sentence summaryIL-15 treatment can enhance the efficacy/anti-tumor immunity of sipuleucel-T by modulating CD8+ T-cell and CD56+ NKT subsets. ]]> Saeed, M. Peng, B. Kim, K. Borkowski, A. Van Tine, B. Sheikh, N. Vu, T. Thorek, D. Fehniger, T. Pachynski, R. 2023-07-25 doi:10.1101/2023.07.23.550213 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Evolution and spread of a persistent P. aeruginosa outbreak clone over decades in a single US hospital. ]]> https://biorxiv.org/content/10.1101/2023.07.24.550326v1?rss=1 Stribling, W. Hall, L. R. Powell, A. Harless, C. Martin, M. J. Corey, B. W. Snesrud, E. Ong, A. Maybank, R. Stam, J. Bartlett, K. Jones, B. T. Preston, L. N. Lane, K. F. Thompson, B. Young, L. M. Kwak, Y. I. Barsoumian, A. E. Markelz, A.-E. Kiley, J. L. Cybulski, R. J. Bennett, J. W. Mc Gann, P. T. Lebreton, F. 2023-07-25 doi:10.1101/2023.07.24.550326 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Uropathogenic Escherichia coli wield enterobactin-derived catabolites as siderophores ]]> https://biorxiv.org/content/10.1101/2023.07.25.550588v1?rss=1 Zou, Z. Robinson, J. I. Steinberg, L. K. Henderson, J. P. 2023-07-25 doi:10.1101/2023.07.25.550588 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Same same but different; The global response of Escherichia coli to five different LpxC inhibitors ]]> https://biorxiv.org/content/10.1101/2023.07.25.550486v1?rss=1 Moller, A. M. Vazquez Hernandez, M. Kutscher, B. Brysch, R. Bruckner, S. Marino, E. C. Kleetz, J. Senges, C. H. R. Schakermann, S. Bandow, J. E. Narberhaus, F. 2023-07-26 doi:10.1101/2023.07.25.550486 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ The components of an electrical synapse as revealed by expansion microscopy of a single synaptic contact ]]> https://biorxiv.org/content/10.1101/2023.07.25.550347v1?rss=1 Cardenas- Garcia, S. P. Ijaz, S. Pereda, A. E. 2023-07-28 doi:10.1101/2023.07.25.550347 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Mechanosensitive ion channel MSL8 is required for pulsatile growth and cell wall dynamics in Arabidopsis pollen tubes ]]> https://biorxiv.org/content/10.1101/2023.07.27.550874v1?rss=1 Coomey, J. H. Haswell, E. S. 2023-07-28 doi:10.1101/2023.07.27.550874 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Neural population dynamics reveal that motor-targeted intraspinal microstimulation preferentially depresses nociceptive transmission in spinal cord injury-related neuropathic pain. ]]> https://biorxiv.org/content/10.1101/2023.07.27.550880v1?rss=1 McPherson, J. G. Bandres, M. F. 2023-07-28 doi:10.1101/2023.07.27.550880 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Quantitative description of the phase separation behavior of the multivalent SLP65-CIN85 complex ]]> https://biorxiv.org/content/10.1101/2023.07.31.551239v1?rss=1 Maier, J. Sieme, D. Wong, L. E. Dar, F. Wienands, J. Becker, S. Griesinger, C. 2023-08-02 doi:10.1101/2023.07.31.551239 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ IST1 regulates select endosomal recycling pathways ]]> https://biorxiv.org/content/10.1101/2023.07.31.551359v1?rss=1 View larger version (16K): org.highwire.dtl.DTLVardef@14c2658org.highwire.dtl.DTLVardef@699063org.highwire.dtl.DTLVardef@867084org.highwire.dtl.DTLVardef@44f7b6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Clippinger, A. K. Naismith, T. V. Yoo, W. Jansen, S. Kast, D. Hanson, P. I. 2023-08-02 doi:10.1101/2023.07.31.551359 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Epigenetic regulation of Leukocyte associated immunoglobulin-like receptors 1 and 2 by interferon signaling in macrophages and T cells ]]> https://biorxiv.org/content/10.1101/2023.07.31.551385v1?rss=1 Dorando, H. K. Mutic, E. C. Li, J. Y. Perrin, E. P. Wurtz, M. Quinn, C. C. Payton, J. E. 2023-08-02 doi:10.1101/2023.07.31.551385 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Molecular Basis of Cell Membrane Adaptation in Daptomycin-Resistant Enterococcus faecalis ]]> https://biorxiv.org/content/10.1101/2023.08.02.551704v1?rss=1 Nguyen, A. Tran, T. Panesso, D. Hood, K. Polamraju, V. Zhang, R. Khan, A. Miller, W. R. Mileykovskaya, E. Shamoo, Y. Xu, L. Vitrac, H. Arias, C. A. 2023-08-02 doi:10.1101/2023.08.02.551704 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ A comprehensive workflow and its validation for simulating diffuse speckle statistics for optical blood flow measurements ]]> https://biorxiv.org/content/10.1101/2023.08.03.551830v1?rss=1 Kobayashi Frisk, L. C. Verma, M. Beslija, F. Lin, C.-H. P. Patil, N. Chetia, S. Trobaugh, J. Culver, J. P. Durduran, T. 2023-08-04 doi:10.1101/2023.08.03.551830 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ Resident memory T cell precursors in tumor draining lymph nodes require type-1 IFN for optimal differentiation ]]> https://biorxiv.org/content/10.1101/2023.08.02.551658v1?rss=1 Khatwani, N. Searles, T. Han, J. Messier, C. Mittal, N. Molodtsov, A. Ramirez, D. Hawkes, A. Williams, O. M. Huang, Y. H. Kolling, F. W. Rosato, P. Turk, M. J. 2023-08-05 doi:10.1101/2023.08.02.551658 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ KAT6A mutations in Arboleda-Tham syndrome drive epigenetic regulation of posterior HOXC cluster ]]> https://biorxiv.org/content/10.1101/2023.08.03.550595v1?rss=1 Singh, M. Spendlove, S. Wei, A. Nava, A. A. Bondhus, l. A. N. de L. Vitorino, F. Gomez, D. Lee, J. Echeverria, G. Amano, S. Garcia, B. Arboleda, V. A. 2023-08-05 doi:10.1101/2023.08.03.550595 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ Costs of being a diet generalist in the super-generalist protist predator Dictyostelium discoideum ]]> https://biorxiv.org/content/10.1101/2023.08.05.552129v1?rss=1 Shreenidhi, P. M. Brock, D. A. McCabe, R. I. Strassmann, J. E. Queller, D. C. 2023-08-07 doi:10.1101/2023.08.05.552129 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Conserved molecular recognition by an intrinsically disordered region in the absence of sequence conservation ]]> https://biorxiv.org/content/10.1101/2023.08.06.552128v1?rss=1 Alston, J. Soranno, A. Holehouse, A. S. 2023-08-07 doi:10.1101/2023.08.06.552128 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Material Properties of Nonpregnant and Pregnant Human Uterine Layers ]]> https://biorxiv.org/content/10.1101/2023.08.07.551726v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@2d347eorg.highwire.dtl.DTLVardef@1d14584org.highwire.dtl.DTLVardef@2b0920org.highwire.dtl.DTLVardef@1642359_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Fodera, D. M. Russell, S. R. Lund-Jackson, J. L. Fang, S. Vink, J.-S. Y. Oyen, M. L. Myers, K. M. 2023-08-08 doi:10.1101/2023.08.07.551726 Cold Spring Harbor Laboratory Press 2023-08-08 <![CDATA[ NVX-CoV2373 ancestral and NVX-CoV2540 BA.5 protein nanoparticle vaccines protect against Omicron BA.5 variant in Syrian hamsters ]]> https://biorxiv.org/content/10.1101/2023.08.07.552330v1?rss=1 Bricker, T. L. Joshi, A. Soudani, N. Scheaffer, S. Patel, N. Xabier, M. G. Smith, G. Diamond, M. Boon, A. C. 2023-08-08 doi:10.1101/2023.08.07.552330 Cold Spring Harbor Laboratory Press 2023-08-08 <![CDATA[ Assessment of bovine cortical bone fracture behavior using impact microindentation as a surrogate of fracture toughness ]]> https://biorxiv.org/content/10.1101/2023.08.07.552351v1?rss=1 Vaidya, R. Jahani, B. Jin, J. Broz, K. Aboytes, D. Pujari, B. Krothapalli, S. Tang, S. Y. 2023-08-08 doi:10.1101/2023.08.07.552351 Cold Spring Harbor Laboratory Press 2023-08-08 <![CDATA[ Antibody inhibition of influenza A virus assembly and release ]]> https://biorxiv.org/content/10.1101/2023.08.08.552198v1?rss=1 He, Y. Guo, Z. Subiaur, S. Benegal, A. Vahey, M. D. 2023-08-09 doi:10.1101/2023.08.08.552198 Cold Spring Harbor Laboratory Press 2023-08-09 <![CDATA[ GenomeMUSter mouse genetic variation service enables multi-trait, multi-population data integration and analyses ]]> https://biorxiv.org/content/10.1101/2023.08.08.552506v1?rss=1 Ball, R. L. Bogue, M. A. Liang, H. Srivastava, A. Ashbrook, D. G. Lamoureux, A. Gerring, M. W. Hatoum, A. S. Kim, M. J. He, H. Emerson, J. Berger, A. K. Walton, D. O. Sheppard, K. El Kassaby, B. Castellanos, F. Ramamoorthy, G. Lu, L. Bluis, J. Desai, S. Sundberg, B. A. Peltz, G. Fang, Z. Churchill, G. A. Williams, R. W. Agrawal, A. Bult, C. J. Philip, V. M. Chesler, E. J. 2023-08-10 doi:10.1101/2023.08.08.552506 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ Utilization of 5-deoxy-nucleosides as Growth Substrates by Extraintestinal Pathogenic E. coli via the Dihydroxyacetone Phosphate Shunt ]]> https://biorxiv.org/content/10.1101/2023.08.10.552779v1?rss=1 Huening, K. A. Groves, J. T. Wildenthal, J. A. Tabita, F. R. North, J. A. 2023-08-10 doi:10.1101/2023.08.10.552779 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ Generalization of procedural motor sequence learning after a single practice trial ]]> https://biorxiv.org/content/10.1101/2023.08.08.552542v1?rss=1 Johnson, B. P. Iturrate, I. Fakhreddine, R. Y. Bonstrup, M. Buch, E. R. Robertson, E. M. Cohen, L. G. 2023-08-11 doi:10.1101/2023.08.08.552542 Cold Spring Harbor Laboratory Press 2023-08-11 <![CDATA[ Serotonergic amplification of odor-evoked neural responses maps flexibly onto behavioral outcomes ]]> https://biorxiv.org/content/10.1101/2023.08.08.552516v1?rss=1 Bessonova, Y. Raman, B. 2023-08-12 doi:10.1101/2023.08.08.552516 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ Spatiotemporal optical control of Gαq-PLCβ interactions ]]> https://biorxiv.org/content/10.1101/2023.08.10.552801v1?rss=1 Ubeysinghe, S. Kankanamge, D. Thotamune, W. Wijayaratna, D. Mohan, T. M. Karunarathne, A. 2023-08-12 doi:10.1101/2023.08.10.552801 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ Glutamate helps unmask the differences in driving forces for phase separation versus clustering of FET family proteins in sub-saturated solutions ]]> https://biorxiv.org/content/10.1101/2023.08.11.552963v1?rss=1 Kar, M. Vogel, L. T. Chauhan, G. Ausserwoger, H. Welsh, T. J. Kamath, A. R. Knowles, T. P. J. Hyman, A. A. Seidel, C. A. M. Pappu, R. V. 2023-08-13 doi:10.1101/2023.08.11.552963 Cold Spring Harbor Laboratory Press 2023-08-13 <![CDATA[ Studies on the International Space Station to assess the effects of microgravity on iPSC-derived neural organoids ]]> https://biorxiv.org/content/10.1101/2023.08.10.552814v1?rss=1 Marotta, D. Ijaz, L. Barbar, L. Nijsure, M. Stein, J. Clements, T. Stoudemire, J. Grisanti, P. Noggle, S. A. Loring, J. F. Fossati, V. 2023-08-14 doi:10.1101/2023.08.10.552814 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Meningeal CSF transport is primarily mediated by the arachnoid and pia maters during development ]]> https://biorxiv.org/content/10.1101/2023.08.10.552826v1?rss=1 Pan, S. Koleske, J. Koller, G. M. Halupnik, G. L. Alli, A.-H. O. Koneru, S. DeFreitas, D. Ramagiri, S. Strahle, J. M. 2023-08-14 doi:10.1101/2023.08.10.552826 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ MICROGLIAL CELL EXPRESSION OF THE TYPE 2 CANNABINOID RECEPTOR REGULATES IMMUNE-MEDIATED NEUROINFLAMMATION ]]> https://biorxiv.org/content/10.1101/2023.08.10.552854v1?rss=1 Moe, A. Rayasam, A. Sauber, G. Shah, R. Yuan, C. Y. Szabo, A. Moore, B. Colonna, M. Cui, W. Romero, J. Zamora, A. Hillard, C. Drobyski, W. 2023-08-14 doi:10.1101/2023.08.10.552854 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Does urbanization lead to parallel demographic shifts across the world in a cosmopolitan plant? ]]> https://biorxiv.org/content/10.1101/2023.08.14.552623v1?rss=1 Caizergues, A. E. Santangelo, J. S. Ness, R. W. Angeoletto, F. Anstett, D. N. Anstett, J. Baena-Diaz, F. Carlen, E. J. Chaves, J. A. Comerford, M. S. Dyson, K. Falahati-Anbaran, M. Fellowes, M. D. E. Hodgins, K. A. Hood, G. R. Iniguez-Armijos, C. Kooyers, N. J. Lazaro-Lobo, A. Moles, A. T. Munshi-South, J. Paule, J. Porth, I. M. Santiago-Rosario, L. Y. Stack Whitney, K. Tack, A. J. M. Johnson, M. T. J. 2023-08-14 doi:10.1101/2023.08.14.552623 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Prevotella copri-linked effects of a therapeutic food for malnutrition ]]> https://biorxiv.org/content/10.1101/2023.08.11.553030v1?rss=1 Gordon, J. Wang, Y. Chang, H.-W. Lee, E. M. Zhou, C. Pruss, K. M. Henrissat, S. Chen, R. Y. Kao, C. Hibberd, M. C. Lynn, H. M. Webber, D. M. Crane, M. Cheng, J. Rodionov, D. A. Arzamasov, A. A. Castillo, J. J. Couture, G. Chen, Y. Balcazo, N. P. Lebrilla, C. B. Terrapon, N. Henrissat, B. Ilkayeva, O. Muehlbauer, M. J. Newgard, C. Mostafa, I. Das, S. Mahfuz, M. Osterman, A. Barratt, M. J. Ahmed, T. 2023-08-15 doi:10.1101/2023.08.11.553030 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Structure and function of the human mitochondrial MRS2 channel ]]> https://biorxiv.org/content/10.1101/2023.08.12.553106v1?rss=1 He, Z. Tu, Y.-C. Tsai, C.-W. Mount, J. Zhang, J. Tsai, M.-F. Yuan, P. 2023-08-15 doi:10.1101/2023.08.12.553106 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ F-box protein FBXB-65 regulates anterograde transport of UNC-104 through modification near the PH domain ]]> https://biorxiv.org/content/10.1101/2023.08.13.553108v1?rss=1 Sabharwal, V. Boyanapalli, S. P. P. Shee, A. Nonet, M. L. Nandi, A. Chaudhuri, D. Koushika, S. P. 2023-08-15 doi:10.1101/2023.08.13.553108 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ The Spatial Patterns and Determinants of Cerebrospinal Fluid Circulation in the Human Brain ]]> https://biorxiv.org/content/10.1101/2023.08.13.553149v1?rss=1 Nazeri, A. Dehkharghanian, T. Lindsay, K. E. LaMontagne, P. J. Shimony, J. S. Benzinger, T. L. S. Sotiras, A. 2023-08-15 doi:10.1101/2023.08.13.553149 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Early life high fructose exposure disrupts microglia function and impedes neurodevelopment ]]> https://biorxiv.org/content/10.1101/2023.08.14.553242v1?rss=1 Perry, J. Wang, Z. Lipschutz, A. Liu, Z.-L. Trzeciak, A. Miranda, I. Martinez de la Torre, C. Schild, T. Lazarov, T. Rojas, W. S. Saavedra, P. Romero-Pichardo, J. Baako, A. Geissmann, F. Faraco, G. Gan, L. Etchegaray, J. I. Lucas, C. Parkhurst, C. Zeng, M. Keshari, K. 2023-08-15 doi:10.1101/2023.08.14.553242 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ APOE2 gene therapy reduces amyloid deposition, and improves markers of neuroinflammation and neurodegeneration in a mouse model of Alzheimer disease ]]> https://biorxiv.org/content/10.1101/2023.08.14.552850v1?rss=1 Jackson, R. J. Keiser, M. S. Meltzer, J. C. Fykstra, D. P. Dierksmeier, S. E. Melloni, A. Nakajima, T. Tecedor, L. Ranum, P. T. Carrell, E. Chen, Y. Holtzman, D. M. Davidson, B. L. Hyman, B. T. 2023-08-16 doi:10.1101/2023.08.14.552850 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ Population coding of time-varying sounds in the non-lemniscal Inferior Colliculus ]]> https://biorxiv.org/content/10.1101/2023.08.14.553263v1?rss=1 Shi, K. Quass, G. L. Rogalla, M. M. Ford, A. N. Czarny, J. E. Apostolides, P. F. 2023-08-16 doi:10.1101/2023.08.14.553263 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ Normative Modeling Using Multimodal Variational Autoencoders to Identify Individual Heterogeneity in Alzheimer Disease ]]> https://biorxiv.org/content/10.1101/2023.08.15.553412v1?rss=1 Kumar, S. Earnest, T. Payne, P. Sotiras, A. 2023-08-17 doi:10.1101/2023.08.15.553412 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Biophysical Mechanism of Allosteric Regulation of Actin Capping Protein ]]> https://biorxiv.org/content/10.1101/2023.08.16.553570v1?rss=1 Mooren, O. L. Stuchell-Brereton, M. D. McConnell, P. Yan, C. Wilkerson, E. M. Goldfarb, D. Cooper, J. A. Sept, D. Soranno, A. 2023-08-17 doi:10.1101/2023.08.16.553570 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Structural Basis for Hyperpolarization-dependent Opening of the Human HCN1 Channel ]]> https://biorxiv.org/content/10.1101/2023.08.17.553623v1?rss=1 Burtscher, V. Mount, J. Cowgill, J. Chang, Y. Bickel, K. Yuan, P. Chanda, B. 2023-08-17 doi:10.1101/2023.08.17.553623 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Thermodynamic Coupling of the tandem RRM domains of hnRNP A1 underlie its Pleiotropic RNA Binding Functions ]]> https://biorxiv.org/content/10.1101/2023.08.17.553700v1?rss=1 Levengood, J. D. Potoyan, D. Penumutchu, S. Kumar, A. Wang, Y. Hansen, A. L. Kutluay, S. Roche, J. Tolbert, B. S. 2023-08-17 doi:10.1101/2023.08.17.553700 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization ]]> https://biorxiv.org/content/10.1101/2023.08.16.553610v1?rss=1 20 healthy and pathological cell states, and identified diseased niches enriched in transcriptionally altered epithelial cells and myofibroblasts. ]]> Kalhor, K. Chen, C.-j. Lee, H. S. Cai, M. Nafisi, M. Que, R. Yuan, Y. Song, J. Lake, B. Zhang, K. Kharchenko, P. Zhang, Y. Palmer, C. Chun, J. Jain, S. Knoten, A. Gaut, J. Keene, D. Lein, E. Fan, J.-B. 2023-08-18 doi:10.1101/2023.08.16.553610 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ Dorsal raphe neurons signal integrated value during multi-attribute decision-making ]]> https://biorxiv.org/content/10.1101/2023.08.17.553745v1?rss=1 Feng, Y.-Y. Bromberg-Martin, E. S. Monosov, I. E. 2023-08-21 doi:10.1101/2023.08.17.553745 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Prenatal environment is associated with the pace of cortical network development over the first three years of life ]]> https://biorxiv.org/content/10.1101/2023.08.18.552639v1?rss=1 Tooley, U. Latham, A. Kenley, J. K. Alexopoulos, D. Smyser, T. Warner, B. B. Shimony, J. S. Neil, J. J. Luby, J. L. Barch, D. M. Rogers, C. E. Smyser, C. D. 2023-08-21 doi:10.1101/2023.08.18.552639 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Active learning of enhancer and silencer regulatory grammar in photoreceptors ]]> https://biorxiv.org/content/10.1101/2023.08.21.554146v1?rss=1 Friedman, R. Z. Ramu, A. Lichtarge, S. Myers, C. A. Granas, D. M. Gause, M. Corbo, J. C. Cohen, B. A. White, M. A. 2023-08-22 doi:10.1101/2023.08.21.554146 Cold Spring Harbor Laboratory Press 2023-08-22 <![CDATA[ Cell-extrinsic effects of Irf2 on cDC2 development ]]> https://biorxiv.org/content/10.1101/2023.08.24.554658v1?rss=1 O'Connor, K. W. Liu, T. Kim, S. Murphy, T. Murphy, K. M. 2023-08-25 doi:10.1101/2023.08.24.554658 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ TRPM7-dependent electrical signals drive phagocytic clearance for effective anti-fungal defense ]]> https://biorxiv.org/content/10.1101/2023.08.26.554944v1?rss=1 Stremska, M. E. Stipes, E. J. Jang, J. J. Busey, G. W. Iobst, W. H. Seegren, P. V. Kennedy, J. Desai, B. N. 2023-08-26 doi:10.1101/2023.08.26.554944 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ Glioblastoma-infiltrating CD8+ T cells are predominantly a clonally expanded GZMK+ effector population ]]> https://biorxiv.org/content/10.1101/2023.08.25.554678v1?rss=1 Wang, A. Z. Mashimo, B. L. Schaettler, M. O. Sherpa, N. D. Leavitt, L. A. Livingstone, A. J. Khan, S. M. Li, M. Anzaldua-Campos, M. Bradley, J. D. Leuthardt, E. C. Kim, A. H. Dowling, J. L. Chicoine, M. R. Jones, P. S. Choi, B. D. Cahill, D. P. Carter, B. S. Petti, A. A. Johanns, T. M. Dunn, G. P. 2023-08-27 doi:10.1101/2023.08.25.554678 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Energy flux couples sulfur isotope fractionation to proteomic and metabolite profiles in Desulfovibrio vulgaris ]]> https://biorxiv.org/content/10.1101/2023.08.27.555018v1?rss=1 Leavitt, W. D. Waldbauer, J. Venceslau, S. S. Sim, M. S. Zhang, L. Boidi, F. J. Plummer, S. Diaz, J. M. Pereira, I. A. C. Bradley, A. S. 2023-08-27 doi:10.1101/2023.08.27.555018 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Brain mechanisms underlying the emotion processing bias in treatment-resistant depression ]]> https://biorxiv.org/content/10.1101/2023.08.26.554837v1?rss=1 Fan, X. Mocchi, M. Pascuzzi, B. Xiao, J. Metzger, B. A. Mathura, R. K. Hacker, C. Adkinson, J. A. Bartoli, E. Elhassa, S. Watrous, A. J. Zhang, Y. Goodman, W. Pouratian, N. Bijanki, K. R. 2023-08-28 doi:10.1101/2023.08.26.554837 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Brain-Derived CCN3 Is An Osteoanabolic Hormone That Sustains Bone in Lactating Females ]]> https://biorxiv.org/content/10.1101/2023.08.28.554707v1?rss=1 Babey, M. E. Krause, W. C. Herber, C. B. Chen, K. Nikkannen, J. Rodriquez, R. Zhang, X. Castro-Navarro, F. Wang, Y. Villeda, S. Lance, N. E. Scheller, E. L. Chan, C. K. F. Ambrosi, T. H. Ingraham, H. A. 2023-08-28 doi:10.1101/2023.08.28.554707 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Cryptosporidium infection of human small intestinal epithelial cells induces type III interferon and impairs infectivity of Rotavirus. ]]> https://biorxiv.org/content/10.1101/2023.08.30.555581v1?rss=1 Greigert, V. Saraav, I. Son, J. Dayao, D. Antia, A. Tzipori, S. Witola, W. Stappenbeck, T. S. Ding, S. Sibley, L. D. 2023-08-30 doi:10.1101/2023.08.30.555581 Cold Spring Harbor Laboratory Press 2023-08-30 <![CDATA[ Spatiotemporal development of the human T follicular helper cell response to Influenza vaccination ]]> https://biorxiv.org/content/10.1101/2023.08.29.555186v1?rss=1 Schattgen, S. Turner, J. S. Ghonim, M. A. Crawford, J. C. Schmitz, A. J. Kim, H. Zhou, J. Q. Awad, W. Kim, W. McIntire, K. M. Haile, A. Klebert, M. K. Suessen, T. Middleton, W. D. Teefey, S. A. Presti, R. M. Ellebedy, A. Thomas, P. 2023-08-31 doi:10.1101/2023.08.29.555186 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Substrate-Specific Function of PNPLA3 Facilitates Hepatic VLDL-Triglyceride Secretion During Stimulated Lipogenesis ]]> https://biorxiv.org/content/10.1101/2023.08.30.553213v1?rss=1 Johnson, S. M. Bao, H. McMahon, C. Chen, Y. Burr, S. Anderson, A. Madeyski-Bengtson, K. Linden, D. Han, X. Liu, J. 2023-08-31 doi:10.1101/2023.08.30.553213 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Large-scale annotated dataset for cochlear hair cell detection and classification ]]> https://biorxiv.org/content/10.1101/2023.08.30.553559v1?rss=1 Buswinka, C. J. Rosenberg, D. B. Simikyan, R. G. Osgood, R. T. Fernandez, K. Nitta, H. Hayashi, Y. Liberman, L. W. Nguyen, E. Yildiz, E. Kim, J. Jarysta, A. Renauld, J. Wesson, E. Thapa, P. Bordiga, P. McMurtry, N. Llamas, J. Kitcher, S. R. Lopez-Porras, A. I. Cui, R. Behnammanesh, G. Bird, J. E. Ballesteros, A. Velez-Ortega, A. C. Edge, A. S. Deans, M. Gnedeva, K. Shrestha, B. R. Manor, U. Zhao, B. Ricci, A. J. Tarchini, B. Basch, M. Stepanyan, R. S. Landegger, L. D. Rutherford, M. Liberman, M. C. Walters, B. J. Kros, C. Richardson, G. P. Cunningham, L 2023-09-01 doi:10.1101/2023.08.30.553559 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Chromatin Profiling of CBFA2T3-GLIS2 AMLs Identifies Key Transcription Factor Dependencies and BRG1 Inhibition as a Novel Therapeutic Strategy ]]> https://biorxiv.org/content/10.1101/2023.08.30.555598v1?rss=1 Kaonis, S. Smith, J. L. Katiyar, N. Merrill, M. Hylkema, T. Namciu, S. Le, Q. Babaeva, E. Ikeda, T. Morris, S. M. Girard, E. Furuyama, S. Ries, R. Bernstein, I. Meshinchi, S. Henikoff, S. Meers, M. P. Hadland, B. K. Sarthy, J. F. 2023-09-01 doi:10.1101/2023.08.30.555598 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Outer mitochondrial membrane E3 Ub ligase MARCH5 controls mitochondrial steps in peroxisome biogenesis. ]]> https://biorxiv.org/content/10.1101/2023.08.31.555756v1?rss=1 Karbowski, M. Verhoeven, N. Oshima, Y. Cartier-Zamorano, E. Neutzner, A. Boyman, L. 2023-09-01 doi:10.1101/2023.08.31.555756 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Sequential early-life viral infections modulate the microbiota and adaptive immune responses to systemic and mucosal vaccination ]]> https://biorxiv.org/content/10.1101/2023.08.31.555772v1?rss=1 Li, Y. Molleston, J. M. Kim, A. H. Ingle, H. Aggarwal, S. Nolan, L. Hassan, A. Foster, L. Diamond, M. Baldridge, M. T. 2023-09-01 doi:10.1101/2023.08.31.555772 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Tauopathy severely disrupts homeostatic set-points in emergent neural dynamics but not the activity of individual neurons. ]]> https://biorxiv.org/content/10.1101/2023.09.01.555947v1?rss=1 McGregor, J. N. Farris, C. A. Ensley, S. Schneider, A. Wang, C. Liu, Y. Tu, J. Elmore, H. Ronayne, K. D. Wessel, R. Dyer, E. L. Bhaskaran-Nair, K. Holtzman, D. M. Hengen, K. B. 2023-09-05 doi:10.1101/2023.09.01.555947 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ KAT2 paralogs prevent dsRNA accumulation and interferon signaling to maintain intestinal stem cells ]]> https://biorxiv.org/content/10.1101/2023.09.04.556156v1?rss=1 Nguyen, M.-U. T. Potgieter, S. Huang, W. Pfeffer, J. Woo, S. Zhao, C. Lawlor, M. Yang, R. Halstead, A. Dent, S. Saenz, J. Zheng, H. Yuan, Z.-F. Sidoli, S. Ellison, C. E. Verzi, M. 2023-09-05 doi:10.1101/2023.09.04.556156 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Distractor-specific control adaptation in multidimensional environments ]]> https://biorxiv.org/content/10.1101/2023.09.04.556248v1?rss=1 Gheza, D. Kool, W. 2023-09-05 doi:10.1101/2023.09.04.556248 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Reduced social function in experimentally evolved Dictyostelium discoideum implies selection for social conflict in nature ]]> https://biorxiv.org/content/10.1101/2023.09.02.556041v1?rss=1 Larsen, T. Jahan, I. Brock, D. A. Strassmann, J. Queller, D. 2023-09-06 doi:10.1101/2023.09.02.556041 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Atrial arrhythmogenesis in ex vivo aged mouse hearts with hypokalemia and right atrial stretch ]]> https://biorxiv.org/content/10.1101/2023.09.05.555978v1?rss=1 Cayton, J. Nourian, Z. Lambert, M. Liu, Z. Domeier, T. L. 2023-09-06 doi:10.1101/2023.09.05.555978 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Regulatory Transposable Elements in the Encyclopedia of DNA Elements ]]> https://biorxiv.org/content/10.1101/2023.09.05.556380v1?rss=1 Du, A. Y. Chobirko, J. D. Zhuo, X. Feschotte, C. Wang, T. 2023-09-06 doi:10.1101/2023.09.05.556380 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Anatomical Modeling and Optimization of Speckle Contrast Optical Tomography ]]> https://biorxiv.org/content/10.1101/2023.09.06.556565v1?rss=1 Lin, C.-H. P. Orukari, I. Frisk, L. C. Verma, M. Chetia, S. Beslija, F. Eggebrecht, A. T. Durduran, T. Culver, J. P. Trobaugh, J. W. 2023-09-06 doi:10.1101/2023.09.06.556565 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ In the social amoeba D. discoideum, shortened stalks limit obligate cheater success even when exploitable partners are available. ]]> https://biorxiv.org/content/10.1101/2023.09.06.556587v1?rss=1 Medina, J. Larsen, T. Queller, D. Strassmann, J. 2023-09-06 doi:10.1101/2023.09.06.556587 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ In Vivo Biorthogonal Antibody Click for Dual Targeting and Augmented Efficacy in Cancer Treatment ]]> https://biorxiv.org/content/10.1101/2023.09.05.556426v1?rss=1 Pereira, P. R. Panikar, S. Berry, N.-K. Shmuel, S. Keltee, L. 2023-09-07 doi:10.1101/2023.09.05.556426 Cold Spring Harbor Laboratory Press 2023-09-07 <![CDATA[ Colonization of larval zebrafish (Danio rerio) with adherent-invasive Escherichia coli prevents recovery of the intestinal mucosa from drug-induced colitis ]]> https://biorxiv.org/content/10.1101/2023.09.07.556695v1?rss=1 Flores, E. Dutta, S. Bosserman, R. Van Hoof, A. Krachler, A. M. 2023-09-07 doi:10.1101/2023.09.07.556695 Cold Spring Harbor Laboratory Press 2023-09-07 <![CDATA[ Dual Role of Neuroplastin in Pancreatic Beta Cells: Regulating Insulin Secretion and Promoting Islet Inflammation ]]> https://biorxiv.org/content/10.1101/2023.09.08.556759v1?rss=1 Kitamura, R. A. Hummel, D. Urano, F. 2023-09-08 doi:10.1101/2023.09.08.556759 Cold Spring Harbor Laboratory Press 2023-09-08 <![CDATA[ Microglial 25-hydroxycholesterol mediates neuroinflammation and neurodegeneration ina tauopathy mouse model ]]> https://biorxiv.org/content/10.1101/2023.09.08.556884v1?rss=1 Toral-Rios, D. Long, J. M. Ulrich, J. D. Yu, J. Strickland, M. R. Han, X. Holtzman, D. M. CASHIKAR, A. G. Paul, S. M. 2023-09-09 doi:10.1101/2023.09.08.556884 Cold Spring Harbor Laboratory Press 2023-09-09 <![CDATA[ No model to rule them all: a systematic comparison of 83 thermal performance curve models across traits and taxonomic groups ]]> https://biorxiv.org/content/10.1101/2023.09.08.556856v1?rss=1 Kontopoulos, D. - G. Sentis, A. Daufresne, M. Dell, A. I. Pawar, S. 2023-09-10 doi:10.1101/2023.09.08.556856 Cold Spring Harbor Laboratory Press 2023-09-10 <![CDATA[ Negative allosteric modulation of the μ-opioid receptor ]]> https://biorxiv.org/content/10.1101/2023.09.08.556921v1?rss=1 O'Brien, E. S. Rangari, V. A. El Daibani, A. Eans, S. O. White, B. Wang, H. Shiimura, Y. Krishna Kumar, K. Appourchaux, K. Huang, W. Zhang, C. Mathiesen, J. M. Che, T. McLaughlin, J. P. Majumdar, S. Kobilka, B. K. 2023-09-10 doi:10.1101/2023.09.08.556921 Cold Spring Harbor Laboratory Press 2023-09-10 <![CDATA[ NF2 Loss-of-Function and Hypoxia Drive Radiation Resistance in Grade 2 Meningiomas ]]> https://biorxiv.org/content/10.1101/2023.09.08.556892v1?rss=1 Patel, B. Pugazenthi, S. English, C. W. Mahlokozera, T. Leidig, W. A. Lu, H.-C. Yang, A. Roberts, K. DeSouza, P. Mao, D. D. Sinha, N. Ippolito, J. E. Dahiya, S. Petti, A. A. Yano, H. Klisch, T. J. Harmanci, A. S. Patel, A. J. Kim, A. H. 2023-09-11 doi:10.1101/2023.09.08.556892 Cold Spring Harbor Laboratory Press 2023-09-11 <![CDATA[ Multi-OMIC analysis of Huntington disease reveals a neuroprotective astrocyte state ]]> https://biorxiv.org/content/10.1101/2023.09.08.556867v1?rss=1 Paryani, F. Kwon, J.-S. Ng, C. W. Madden, N. Ofori, K. Tang, A. Lu, H. Li, J. Mahajan, A. Davidson, S. M. Basile, A. McHugh, C. Vonsattel, J. P. Hickman, R. Zody, M. Houseman, D. E. Goldman, J. E. Yoo, A. E. Menon, V. Al-Dalahmah, O. 2023-09-12 doi:10.1101/2023.09.08.556867 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Exogenous 4-1BB co-stimulation enhances memory B cell response during malaria. ]]> https://biorxiv.org/content/10.1101/2023.09.12.557411v1?rss=1 Caloba, C. Sturtz, A. Ramachandran, A. John, L. Malkina, K. Minns, A. M. Lindner, S. E. Vijay, R. 2023-09-13 doi:10.1101/2023.09.12.557411 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Resolving the nanoscale structure of β-sheet assemblies using single-molecule orientation-localization microscopy ]]> https://biorxiv.org/content/10.1101/2023.09.13.557571v1?rss=1 Zhou, W. O'Neill, C. L. Ding, T. Zhang, O. Rudra, J. S. Lew, M. D. 2023-09-14 doi:10.1101/2023.09.13.557571 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Poly-basic peptides and polymers as new drug candidate against Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2023.09.16.558069v1?rss=1 Sivakumar, R. Floyd, K. Jessey, E. Kim Kim, J. Bayguinov, P. Fitzpatrick, J. A. J. Goldfarb, D. Jovanovic, M. Tripathi, A. Djuranovic, S. Pavlovic Djuranovic, S. 2023-09-16 doi:10.1101/2023.09.16.558069 Cold Spring Harbor Laboratory Press 2023-09-16 <![CDATA[ Circadian regulation of MGMT expression and promoter methylation underlies daily rhythms in TMZ sensitivity in glioblastoma ]]> https://biorxiv.org/content/10.1101/2023.09.13.557630v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@2e9058org.highwire.dtl.DTLVardef@1069917org.highwire.dtl.DTLVardef@2cf000org.highwire.dtl.DTLVardef@40abc9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gonzalez-Aponte, M. F. Damato, A. R. Trebucq, L. L. Simon, T. Cardenas-Garcia, S. P. Cho, K. Patti, G. J. Golombek, D. A. Chiesa, J. J. Herzog, E. D. 2023-09-17 doi:10.1101/2023.09.13.557630 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ CXCR3-CXCL11 signaling restricts angiogenesis and promotes pericyte recruitment ]]> https://biorxiv.org/content/10.1101/2023.09.16.557842v1?rss=1 Goeckel, M. E. Lee, J. Levitas, A. Colijn, S. Mun, G. Burton, Z. Chintalapati, B. Yin, Y. Abello, J. Stratman, A. N. 2023-09-17 doi:10.1101/2023.09.16.557842 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Attenuating midline thalamus bursting to mitigate absence epilepsy ]]> https://biorxiv.org/content/10.1101/2023.09.18.558258v1?rss=1 Dong, P. Bakhurin, K. Li, Y. Mikati, M. A. Cui, J. Grill, W. M. Yin, H. Yang, H. 2023-09-18 doi:10.1101/2023.09.18.558258 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ Connectome Operations For FSL ExEcution (COFFEE): a turnkey pipeline for preprocessing of fMRI data ]]> https://biorxiv.org/content/10.1101/2023.09.19.558290v1?rss=1 McAvoy, M. M. Liu, L. Zhou, R. Philip, B. A. 2023-09-22 doi:10.1101/2023.09.19.558290 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Evaluating functional brain organization in individuals and identifying contributions to network overlap ]]> https://biorxiv.org/content/10.1101/2023.09.21.558809v1?rss=1 Bijsterbosch, J. D. Farahibozorg, S.-R. Glasser, M. F. Van Essen, D. C. Snyder, L. Woolrich, M. W. Smith, S. M. 2023-09-22 doi:10.1101/2023.09.21.558809 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Periodic and aperiodic changes to cortical EEG in response to pharmacological manipulation ]]> https://biorxiv.org/content/10.1101/2023.09.21.558828v1?rss=1 Salvatore, S. V. Lambert, P. M. Benz, A. Rensing, N. R. Wong, M. Zorumski, C. F. Mennerick, S. 2023-09-22 doi:10.1101/2023.09.21.558828 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Psychedelic 5-HT2A receptor agonism: neuronal signatures and altered neurovascular coupling. ]]> https://biorxiv.org/content/10.1101/2023.09.23.559145v1?rss=1 Padawer-Curry, J. A. Snyder, A. Z. Bice, A. R. Wang, X. Nicol, G. E. McCall, J. G. Siegel, J. S. Bauer, A. Q. 2023-09-24 doi:10.1101/2023.09.23.559145 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ Species- and strain-effects in interferon, innate immunity, and barrier transcriptional response of microbiome interactions of 3D respiratory epithelial cultures ]]> https://biorxiv.org/content/10.1101/2023.09.25.559418v1?rss=1 Horvath, M. Yang, R. Castaneda, D. C. Callender, M. Fleming, E. Voigt, A. Caldwell, R. Fachi, J. Di Luccia, B. Scholar, Z. Yu, P. Salner, A. Colonna, M. Palucka, K. Oh, J. 2023-09-25 doi:10.1101/2023.09.25.559418 Cold Spring Harbor Laboratory Press 2023-09-25 <![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[ FAM210B is dispensable for erythroid differentiation in adult mice ]]> https://biorxiv.org/content/10.1101/2023.09.26.559581v1?rss=1 Perfetto, M. Rondelli, C. M. Gillis, S. Stratman, A. N. Yien, Y. Y. 2023-09-27 doi:10.1101/2023.09.26.559581 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ The most prominent electrophysiological effect of ketamine is not sufficient to cause anesthesia ]]> https://biorxiv.org/content/10.1101/2023.09.26.559594v1?rss=1 Acland, B. T. Palanca, B. J. A. Bijsterbosch, J. D. Snyder, L. H. 2023-09-27 doi:10.1101/2023.09.26.559594 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Systematic perturbations of SETD2, NSD1, NSD2, NSD3 and ASH1L reveals their distinct contributions to H3K36 methylation ]]> https://biorxiv.org/content/10.1101/2023.09.27.559313v1?rss=1 NSD2>NSD3>ASH1L. While NSD1 and NSD2 are responsible for most genome-wide propagation of H3K36me2, the activities of NSD3 and ASH1L are confined to active regulatory elements. ]]> Shipman, G. Padilla, R. Horth, C. Hu, B. Bareke, E. Vitorino, F. Gongora, J. Garcia, B. Lu, C. Majewski, J. 2023-09-27 doi:10.1101/2023.09.27.559313 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Comparative Analysis of SARS-CoV-2 Antigenicity across Assays and in Human and Animal Model Sera ]]> https://biorxiv.org/content/10.1101/2023.09.27.559689v1?rss=1 Mühlemann, B. Wilks, S. H. Baracco, L. Bekliz, M. Carreno, J. M. Corman, V. M. Davis-Gardner, M. E. Dejnirattisai, W. Diamond, M. Doueck, D. Drosten, C. Eckerle, I. Edara, V. V. Ellis, M. Fouchier, R. A. Frieman, M. Godbole, S. Haagmans, B. Halfmann, P. Henry, A. R. Jones, T. C. Katzelnick, L. Kawaoka, Y. Kimpel, J. Krammer, F. Lai, L. Liu, C. Lusvarghi, S. Meyer, B. Mongkolsapaya, J. Montefiori, D. Mykytyn, A. Z. Netzl, A. Pollett, S. Rössler, A. Screaton, G. Shen, X. Sigal, A. Simon, V. Subramanian, R. Supasa, P. Suthar, M. Tureli, S. Wang, W. We 2023-09-27 doi:10.1101/2023.09.27.559689 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Circuit-based intervention corrects excessive dentate gyrus output in the Fragile X mouse model ]]> https://biorxiv.org/content/10.1101/2023.09.27.559792v1?rss=1 Deng, P. Kumar, A. Cavalli, V. Klyachko, V. 2023-09-27 doi:10.1101/2023.09.27.559792 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Leveraging GPT-4 for Identifying Clinical Phenotypes in Electronic Health Records: A Performance Comparison between GPT-4, GPT-3.5-turbo and spaCy's Rule-based & Machine Learning-based methods ]]> https://biorxiv.org/content/10.1101/2023.09.27.559788v1?rss=1 BHATTARAI, K. Oh, I. Y. Sierra, J. M. Payne, P. R. Abrams, Z. B. Lai, A. M. 2023-09-29 doi:10.1101/2023.09.27.559788 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Altered chromatin occupancy of patient-associated H4 mutants misregulate neuronal differentiation ]]> https://biorxiv.org/content/10.1101/2023.09.29.560141v1?rss=1 Feng, L. Barrows, D. Zhong, L. Matlik, K. Porter, E. G. Djomo, A. M. Yau, I. Soshnev, A. A. Carroll, T. S. Wen, D. Hatten, M. E. Garcia, B. A. Allis, C. D. 2023-09-29 doi:10.1101/2023.09.29.560141 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[ Mycobacterium tuberculosis Ku stimulates multi-round DNA unwinding by UvrD1 monomers ]]> https://biorxiv.org/content/10.1101/2023.09.29.560180v1?rss=1 Chadda, A. Kozlov, A. G. Nguyen, B. Lohman, T. M. Galburt, E. 2023-09-30 doi:10.1101/2023.09.29.560180 Cold Spring Harbor Laboratory Press 2023-09-30 <![CDATA[ Analysis of ductal carcinoma in situ by self-reported race reveals molecular differences related to outcome. ]]> https://biorxiv.org/content/10.1101/2023.09.28.560000v1?rss=1 Strand, S. H. Houlahan, K. E. Branch, V. Lynch, T. Harmon, B. Couch, F. Gallagher, K. Kilgore, M. Wei, S. DeMichele, A. King, T. McAuliffe, P. Curtis, C. Owzar, K. Marks, J. R. Colditz, G. A. Hwang, E. S. West, R. B. 2023-10-02 doi:10.1101/2023.09.28.560000 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Identification of a convergent spinal neuron population that encodes itch ]]> https://biorxiv.org/content/10.1101/2023.09.29.560205v1?rss=1 Sheahan, T. D. Warwick, C. A. Cui, A. Y. Baranger, D. A. Perry, V. J. Smith, K. M. Manalo, A. P. Nguyen, E. K. Koerber, H. R. Ross, S. E. 2023-10-02 doi:10.1101/2023.09.29.560205 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Pathogenic Morphological Signatures of Perturbations in Mitochondrial-Related Genes Revealed by Pooled Imaging Assay ]]> https://biorxiv.org/content/10.1101/2023.09.30.560021v1?rss=1 Kremitzki, C. L. Waligorski, J. E. Bachman, G. W. Mohammed Ali, L. K. Bramley, J. C. Vakaki, M. A. Chandrasekaren, V. D. Patel, P. Mathur, D. P. Hime, P. M. Mitra, R. D. Milbrandt, J. D. Buchser, W. J. 2023-10-02 doi:10.1101/2023.09.30.560021 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Postglacial genomes from foragers across Northern Eurasia reveal prehistoric mobility associated with the spread of the Uralic and Yeniseian languages ]]> https://biorxiv.org/content/10.1101/2023.10.01.560332v1?rss=1 Zeng, T. C. Vyazov, L. M. Kim, A. Flegontov, P. N. Sirak, K. Maier, R. Lazaridis, I. Akbari, A. Frachetti, M. Tishkin, A. A. Ryabogina, N. E. Agapov, S. A. Agapov, D. S. Alekseev, A. N. Boeskorov, G. G. Chizhevsky, A. A. Derevianko, A. P. Dyakonov, V. M. Enshin, D. N. Fribus, A. V. Frolov, Y. V. Grushin, S. P. Khokhlov, A. A. Kitov, E. P. Kosintsev, P. Kovtun, I. V. Kiryushin, K. Y. Kiryushin, Y. F. Makarov, N. P. Morozov, V. V. Nikolaev, E. N. Rykun, M. P. Savenkova, T. M. Shchelchkova, M. V. Skochina, S. N. Shirokov, V. Sherstobitova, O. S. Slepchenko, S. 2023-10-02 doi:10.1101/2023.10.01.560332 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Experimental evolution of symbiotic microbes without their partners can imply the presence of cooperative or antagonistic adaptations ]]> https://biorxiv.org/content/10.1101/2023.10.01.560375v1?rss=1 Larsen, T. Jefferson, C. Bartley, A. Strassmann, J. Queller, D. 2023-10-02 doi:10.1101/2023.10.01.560375 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Predation-resistant Pseudomonas bacteria engage in symbiont-like behavior with the social amoeba Dictyostelium discoideum ]]> https://biorxiv.org/content/10.1101/2023.10.02.560472v1?rss=1 Steele, M. I. Peiser, J. M. Shreenidhi, P. M. Strassmann, J. E. Queller, D. C. 2023-10-02 doi:10.1101/2023.10.02.560472 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ MFSD7c functions as a transporter of choline at the blood-brain barrier ]]> https://biorxiv.org/content/10.1101/2023.10.03.560597v1?rss=1 Nguyen, X. T. A. Le, U. T. N. Ha, H. T. T. Nguyen, T. Q. Artati, A. Leong, N. C. P. Nguyen, D. T. Lim, P. Y. Susanto, A. V. Huang, Q. Fam, L. Leong, N. L. Bonne, I. Lee, A. Gooch, C. Granadillo De Luque, J. L. Yu, D. Hua, H. Soong, T. W. Chang, M. W. Wenk, M. R. Jerzy, A. Cazenave-Gassiot, A. Nguyen, L. N. 2023-10-03 doi:10.1101/2023.10.03.560597 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Type I IFN signaling in the absence of IRGM1 promotes M. tuberculosis replication in immune cells by suppressing T cell responses ]]> https://biorxiv.org/content/10.1101/2023.10.03.560720v1?rss=1 Naik, S. K. McNehlan, M. E. Mreyoud, Y. Kinsella, R. L. Smirnov, A. Chowdhury, C. S. McKee, S. R. Dubey, N. Woodson, R. Kreamalmeyer, D. Stallings, C. L. 2023-10-05 doi:10.1101/2023.10.03.560720 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Laminar architecture of visual responses in supplementary eye field of macaques ]]> https://biorxiv.org/content/10.1101/2023.10.03.560770v1?rss=1 Thirunavukkarasu, P. Errington, S. Sajad, A. Schall, J. D. 2023-10-05 doi:10.1101/2023.10.03.560770 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Structure-Function Coupling in Highly Sampled Individual Brains ]]> https://biorxiv.org/content/10.1101/2023.10.04.560909v1?rss=1 Rajesh, A. Seider, N. A. Newbold, D. J. Adeyemo, B. Marek, S. Greene, D. J. Snyder, A. Z. Shimony, J. S. Laumann, T. O. Dosenbach, N. U. F. Gordon, E. M. 2023-10-05 doi:10.1101/2023.10.04.560909 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Novel Cyclic Homogeneous Oscillation Detection Method for High Accuracy and Specific Characterization of Neural Dynamics ]]> https://biorxiv.org/content/10.1101/2023.10.04.560843v1?rss=1 Cho, H. Adamek, M. Willie, J. T. Brunner, P. 2023-10-06 doi:10.1101/2023.10.04.560843 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Beta-catenin inhibition disrupts the homeostasis of osteogenic/adipogenic differentiation leading to the development of glucocorticoid-induced osteonecrosis of femoral head ]]> https://biorxiv.org/content/10.1101/2023.10.04.560853v1?rss=1 Xia, C. Xu, H. Fang, L. Chen, J. Yuan, W. Fu, D. Wang, X. He, B. Xiao, L. Wu, C. Tong, P. Chen, D. Wang, P. Jin, H. 2023-10-06 doi:10.1101/2023.10.04.560853 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Ecological metabolomics of tropical tree communities across an elevational gradient: Implications for chemically-mediated biotic interactions and species diversity ]]> https://biorxiv.org/content/10.1101/2023.10.04.560880v1?rss=1 Henderson, D. Sedio, B. E. Tello, J. S. Cayola, L. Fuentes, A. F. Alvestegui, B. Muchhala, N. Myers, J. A. 2023-10-06 doi:10.1101/2023.10.04.560880 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ DRG Explant Model: Elucidating Mechanisms of Oxaliplatin-Induced Peripheral Neuropathy and Identifying Potential Therapeutic Targets ]]> https://biorxiv.org/content/10.1101/2023.10.05.560580v1?rss=1 Du, J. Sudlow, L. Luzhansky, I. Berezin, M. Y. 2023-10-08 doi:10.1101/2023.10.05.560580 Cold Spring Harbor Laboratory Press 2023-10-08 <![CDATA[ Chemotherapy activates inflammasomes to cause inflammation-associated bone loss ]]> https://biorxiv.org/content/10.1101/2023.10.06.561196v1?rss=1 Wang, C. Kaur, K. Xu, C. Abu-Amer, Y. Mbalaviele, G. 2023-10-09 doi:10.1101/2023.10.06.561196 Cold Spring Harbor Laboratory Press 2023-10-09 <![CDATA[ Biomolecular condensates form spatially inhomogeneous network fluids ]]> https://biorxiv.org/content/10.1101/2023.10.07.561338v1?rss=1 Dar, F. Cohen, S. R. Mitrea, D. M. Phillips, A. H. Nagy, G. Leite, W. C. Stanley, C. B. Choi, J.-M. Kriwacki, R. W. Pappu, R. V. 2023-10-09 doi:10.1101/2023.10.07.561338 Cold Spring Harbor Laboratory Press 2023-10-09 <![CDATA[ LETHAL COVID-19 ASSOCIATES WITH RAAS-INDUCED INFLAMMATION FOR MULTIPLE ORGAN DAMAGE INCLUDING MEDIASTINAL LYMPH NODES ]]> https://biorxiv.org/content/10.1101/2023.10.08.561395v1?rss=1 Guarnieri, J. W. Topper, M. Beigel, K. Haltoom, J. A. Chadburn, A. Frere, J. An, J. Cope, H. Borczuk, A. Sinha, S. Lim, C. Kim, J. Park, J. Meydan, C. Foox, J. Mozsary, C. Bram, Y. Richard, S. Epsi, N. Agan, B. Chenoweth, J. Simons, M. Tribble, D. Burgess, T. Dalgard, C. L. Heise, M. T. Moorman, N. Baxter, V. Madden, E. A. Taft-Benz, S. Anderson, E. Sanders, W. A. Dickmander, R. J. Widjaja, G. A. Janssen, K. Lie, T. Murdock, D. G. Angelin, A. Albrecht, Y. E. S. Olali, A. Dybas, J. M. Priebe, W. Emmett, M. R. Best, S. Johnson, M. K. Trovao, N. S. Cl 2023-10-09 doi:10.1101/2023.10.08.561395 Cold Spring Harbor Laboratory Press 2023-10-09 <![CDATA[ The Cytoskeletal Stress Response Pathway: a homeostatic system driven by Dual Leucine Zipper Kinase (DLK) ]]> https://biorxiv.org/content/10.1101/2023.10.06.561227v1?rss=1 DeVault, L. Mateusiak, C. Palucki, J. Brent, M. Milbrandt, J. DiAntonio, A. 2023-10-10 doi:10.1101/2023.10.06.561227 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Genetic and pharmacologic alterations of claudin9 levels suffice to induce functional and mature inner hair cells ]]> https://biorxiv.org/content/10.1101/2023.10.08.561387v1?rss=1 50% of the mouses life cycle. In vivo, Cldn9 knockdown using shRNA on postnatal days (P) P2-7 yielded analogous functional ectopic IHCs that were equally durably conserved. The findings suggest that Cldn9 levels coordinate embryonic and postnatal HC differentiation, making it a viable target for altering IHC development pre- and post-terminal differentiation. ]]> Chen, Y. Lee, J. H. H. Li, J. Park, S. Perez-Flores, M. C. Peguero, B. Kersigo, J. Kang, M. Choi, J. Levine, L. Gratton, M. A. Friztsch, B. Yamoah, E. N. 2023-10-10 doi:10.1101/2023.10.08.561387 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Cell specific single viral vector CRISPR/Cas9 editing and genetically encoded tool delivery in the central and peripheral nervous systems ]]> https://biorxiv.org/content/10.1101/2023.10.10.561249v1?rss=1 Moffa, J. C. Bland, I. N. Tooley, J. R. Kalyanaraman, V. Heitmeier, M. Creed, M. C. Copits, B. A. 2023-10-10 doi:10.1101/2023.10.10.561249 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Substructure of the brain's Cingulo-Opercular network ]]> https://biorxiv.org/content/10.1101/2023.10.10.561772v1?rss=1 5 hours of resting state functional connectivity (RSFC) and task data, we identified three anatomically and functionally distinct CON subnetworks within each individual. These three distinct subnetworks were linked to Decisions, Actions, and Feedback (including pain processing), respectively, in convergence with a meta-analytic task database. These Decision, Action and Feedback subnetworks represent pathways by which the brain establishes top-down goals, transforms those goals into actions, implemented as movements, and processes critical action feedback such as pain. ]]> D'Andrea, C. B. Laumann, T. O. Newbold, D. J. Nelson, S. M. Nielsen, A. N. Chauvin, R. Marek, S. Greene, D. J. Dosenbach, N. U. F. Gordon, E. M. 2023-10-10 doi:10.1101/2023.10.10.561772 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Single Cell Expression Analysis of Ductal Carcinoma in Situ Identifies Alterations in Epithelial Integrity ]]> https://biorxiv.org/content/10.1101/2023.10.10.561724v1?rss=1 Qin, X. Strand, S. H. Lee, M. R. van Ijzendoorn, D. G. P. Zhu, C. Vennam, S. Varma, S. Hall, A. King, L. Simpson, L. Luo, X. Colditz, G. A. Jiang, S. Hwang, E. S. Marks, J. R. Owzar, K. West, R. B. 2023-10-12 doi:10.1101/2023.10.10.561724 Cold Spring Harbor Laboratory Press 2023-10-12 <![CDATA[ 25-hydroxycholesterol mediates brain cytokine production and neutrophil infiltration in a mouse model of lipopolysaccharide-induced neuroinflammation ]]> https://biorxiv.org/content/10.1101/2023.10.09.561598v1?rss=1 Romero, J. Toral-Rios, D. Yu, J. Paul, S. M. CASHIKAR, A. G. 2023-10-13 doi:10.1101/2023.10.09.561598 Cold Spring Harbor Laboratory Press 2023-10-13 <![CDATA[ Secretory Leukocyte Protease Inhibitor Protects Against Severe Urinary Tract Infection in Mice ]]> https://biorxiv.org/content/10.1101/2023.10.10.561753v1?rss=1 Rosen, A. Lint, M. Voelker, D. Gilbert, N. Tomera, C. Santiago Borges, J. Wallace, M. A. Hannan, T. Burnham, C.-A. D. Hultgren, S. Kau, A. 2023-10-15 doi:10.1101/2023.10.10.561753 Cold Spring Harbor Laboratory Press 2023-10-15 <![CDATA[ Healthy adults favor stable left/right hand choices over performance at an unconstrained reach-to-grasp task ]]> https://biorxiv.org/content/10.1101/2023.10.11.561912v1?rss=1 Kim, T. Zhou, R. Gassass, S. Liu, L. Philip, B. A. 2023-10-16 doi:10.1101/2023.10.11.561912 Cold Spring Harbor Laboratory Press 2023-10-16 <![CDATA[ E. coli RecBCD Nuclease Domain Regulates Helicase Activity but not Single Stranded DNA Translocase Activity ]]> https://biorxiv.org/content/10.1101/2023.10.13.561901v1?rss=1 Fazio, N. Mersch, K. N. Hao, L. Lohman, T. M. 2023-10-17 doi:10.1101/2023.10.13.561901 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Network level enrichment provides a framework for biological interpretation of machine learning results ]]> https://biorxiv.org/content/10.1101/2023.10.14.562358v1?rss=1 Li, J. Segel, A. Feng, X. Tu, J. C. Eck, A. King, K. Adeyemo, B. Karcher, N. R. Chen, L. Eggebrecht, A. T. Wheelock, M. D. 2023-10-17 doi:10.1101/2023.10.14.562358 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ TFEB degradation is regulated by an IKK/β-TrCP2 phosphorylation-ubiquitination cascade ]]> https://biorxiv.org/content/10.1101/2023.10.16.562572v1?rss=1 Xiong, Y. Sharma, J. Young, M. N. Xiong, W. Jazayeri, A. Poncha, K. F. Ilagan, M. X. Wang, Q. Zheng, H. Young, N. L. Sardiello, M. 2023-10-19 doi:10.1101/2023.10.16.562572 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Glucocorticoid intermittence coordinates rescue of energy and mass in aging-related sarcopenia through the myocyte-autonomous PGC1alpha-Lipin1 transactivation ]]> https://biorxiv.org/content/10.1101/2023.10.16.562573v1?rss=1 Prabakaran, A. D. McFarland, K. Miz, K. Durumutla, H. B. Soussi, F. E. A. Piczer, K. Latimer, H. Werbrich, C. Blair, N. S. Millay, D. P. Prideaux, B. Finck, B. N. Quattrocelli, M. 2023-10-19 doi:10.1101/2023.10.16.562573 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Distinct function of Chlamydomonas CTRA-CTR transporters in Cu assimilation and intracellular mobilization ]]> https://biorxiv.org/content/10.1101/2023.10.19.563170v1?rss=1 Strenkert, D. Schmollinger, S. Paruthiyil, S. Brown, B. C. Green, S. Shafer, C. M. Salome, P. A. Nelson, H. Blaby-Haas, C. E. Moseley, J. L. Merchant, S. S. 2023-10-19 doi:10.1101/2023.10.19.563170 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Ataxia-telangiectasia mutated (Atm) disruption sensitizes spatially-directed H3.3K27M/TP53 diffuse midline gliomas to radiation therapy ]]> https://biorxiv.org/content/10.1101/2023.10.18.562892v1?rss=1 Mangoli, A. Wu, S. Liu, H. Q. Aksu, M. Jain, V. J. Foreman, B. E. Regal, J. A. Weidenhammer, L. B. Stewart, C. E. Guerra Garcia, M. E. Hocke, E. Abramson, K. Williams, N. T. Luo, L. Deland, K. Attardi, L. Abe, K. Hashizume, R. Ashley, D. M. Becher, O. J. Kirsch, D. G. Gregory, S. G. Reitman, Z. J. 2023-10-20 doi:10.1101/2023.10.18.562892 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Deletion of NuRD component Mta2 in nephron progenitor cells causes developmentally programmed FSGS ]]> https://biorxiv.org/content/10.1101/2023.10.18.562984v1?rss=1 Basta, J. Robbins, L. Stout, L. Brennan, M. Shapiro, J. Chen, M. Denner, D. Baldan, A. Messias, N. Madhavan, S. M. Parikh, S. V. Rauchman, M. 2023-10-20 doi:10.1101/2023.10.18.562984 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Global control of cellular physiology by biomolecular condensates through modulation of electrochemical equilibria ]]> https://biorxiv.org/content/10.1101/2023.10.19.563018v1?rss=1 Dai, Y. Zhou, Z. Kim, K. Rivera, N. Mohammed, J. Hsu-Kim, H. Chilkoti, A. You, L. 2023-10-20 doi:10.1101/2023.10.19.563018 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Patient-derived tumor organoids from resected non-small cell lung cancers for high-throughput response testing with approved and repurposed drugs ]]> https://biorxiv.org/content/10.1101/2023.10.18.562944v1?rss=1 Suvilesh, K. N. Manjunath, Y. Nussbaum, Y. I. Gadelkarim, M. Srivastava, A. Li, G. Warren, W. C. Shyu, C.-R. Gao, F. Ciorba, M. Mitchem, J. B. Rachagani, S. Kaifi, J. T. 2023-10-21 doi:10.1101/2023.10.18.562944 Cold Spring Harbor Laboratory Press 2023-10-21 <![CDATA[ Endogenous opioids gate the locus coeruleus pain generator ]]> https://biorxiv.org/content/10.1101/2023.10.20.562785v1?rss=1 Norris, M. R. Kuo, C.-C. Kim, J. R. Dunn, S. S. Borges, G. Thang, L. V. McCall, J. G. 2023-10-23 doi:10.1101/2023.10.20.562785 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Cell Chirality of Micropatterned Endometrial Microvascular Endothelial Cells ]]> https://biorxiv.org/content/10.1101/2023.10.20.563368v1?rss=1 Zambuto, S. G. Jain, I. Theriault, H. S. Underhill, G. H. Harley, B. 2023-10-23 doi:10.1101/2023.10.20.563368 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Missense mutations in Myc Box I influence MYC cellular localization, mRNA partitioning and turnover to promote leukemogenesis ]]> https://biorxiv.org/content/10.1101/2023.10.22.563493v1?rss=1 Arthur, N. Christensen, K. A. Mannino, K. Ruzinova, M. Kumar, A. Gruszczynska, A. Day, R. B. Erdmann-Gilmore, P. Mi, Y. Sprung, R. York, C. R. Spencer, D. H. Townsend, R. Sykes, S. M. Ferraro, F. 2023-10-24 doi:10.1101/2023.10.22.563493 Cold Spring Harbor Laboratory Press 2023-10-24 <![CDATA[ A novel glycosyltransferase organizes fungal glycogen and cell wall glucans ]]> https://biorxiv.org/content/10.1101/2023.10.24.563850v1?rss=1 Loza, L. Doering, T. L. 2023-10-24 doi:10.1101/2023.10.24.563850 Cold Spring Harbor Laboratory Press 2023-10-24 <![CDATA[ Lipin-1 restrains macrophage lipid synthesis to promote inflammation resolution. ]]> https://biorxiv.org/content/10.1101/2023.10.23.563587v1?rss=1 Bamgbose, T. T. Schilke, R. M. Igiehon, O. O. Nkadi, E. H. Custis, D. Bharrhan, S. Schwarz, B. Bohrnsen, E. Bosio, C. Scott, R. S. Yurdagul, A. Finck, B. Woolard, M. 2023-10-25 doi:10.1101/2023.10.23.563587 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ Multilayer network associations between the exposome and childhood brain development ]]> https://biorxiv.org/content/10.1101/2023.10.23.563611v1?rss=1 Simpson-Kent, I. L. Gatavins, M. M. Tooley, U. A. Boroshok, A. L. McDermott, C. L. Park, A. T. Reyes, L. D. Bathelt, J. Tisdall, D. Mackey, A. P. 2023-10-25 doi:10.1101/2023.10.23.563611 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ Energy metabolism modulates the regulatory impact of activators on gene expression ]]> https://biorxiv.org/content/10.1101/2023.10.24.563842v1?rss=1 Qiao, S. Bernasek, S. Gallagher, K. D. Yamada, S. Bagheri, N. Amaral, L. A. N. Carthew, R. W. 2023-10-26 doi:10.1101/2023.10.24.563842 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ Designer Fat Cells: Adipogenic Differentiation of CRISPR-Cas9 Genome-Engineered Induced Pluripotent Stem Cells ]]> https://biorxiv.org/content/10.1101/2023.10.26.564206v1?rss=1 Ely, E. V. Kapinski, A. T. Paradi, S. G. Tang, R. Guilak, F. Collins, K. H.-M. 2023-10-26 doi:10.1101/2023.10.26.564206 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ The Hao-Fountain syndrome protein USP7 regulates neuronal connectivity in the brain via a novel p53-independent ubiquitin signaling pathway ]]> https://biorxiv.org/content/10.1101/2023.10.24.563880v1?rss=1 Chen, H. Ferguson, C. J. Mitchell, D. C. Titus, A. Paulo, J. A. Hwang, A. Lin, T.-H. Yano, H. Gu, W. Song, S.-K. Yuede, C. M. Gygi, S. P. Bonni, A. Kim, A. H. 2023-10-27 doi:10.1101/2023.10.24.563880 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ A reinterpretation of the relationship between persistent and resurgent sodium currents ]]> https://biorxiv.org/content/10.1101/2023.10.25.564042v1?rss=1 Brown, S. P. Lawson, R. J. Moreno, J. D. Ransdell, J. L. 2023-10-29 doi:10.1101/2023.10.25.564042 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ Mechanical Resistance to Micro-Heart Tissue Contractility unveils early Structural and Functional Pathology in iPSC Models of Hypertrophic Cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2023.10.30.564856v1?rss=1 GUO, J. Jiang, H. Schuftan, D. Moreno, J. D. Ramahdita, G. Aryan, L. Bhagavan, D. Silva, J. Huebsch, N. 2023-10-31 doi:10.1101/2023.10.30.564856 Cold Spring Harbor Laboratory Press 2023-10-31 <![CDATA[ Multi-echo Acquisition and Thermal Denoising Advances Infant Precision Functional Imaging ]]> https://biorxiv.org/content/10.1101/2023.10.27.564416v1?rss=1 Moser, J. Koirala, S. Madison, T. Labonte, A. K. Morales Carrasco, C. Feczko, E. Moore, L. A. Ahmed, W. Myers, M. J. Yacoub, E. Trevo-Clemmens, B. Larsen, B. Laumann, T. O. Nelson, S. M. Vizioli, L. Sylvester, C. M. Fair, D. A. 2023-11-01 doi:10.1101/2023.10.27.564416 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Sequence-ensemble-function relationships for disordered proteins in live cells ]]> https://biorxiv.org/content/10.1101/2023.10.29.564547v1?rss=1 Emenecker, R. J. Guadalupe, K. Shamoon, N. M. Sukenik, S. Holehouse, A. S. 2023-11-01 doi:10.1101/2023.10.29.564547 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Increasing hub disruption parallels dementia severity in autosomal dominant Alzheimer disease ]]> https://biorxiv.org/content/10.1101/2023.10.29.564633v1?rss=1 Tu, J. C. Millar, P. R. Strain, J. F. Eck, A. Adeyemo, B. Daniels, A. Karch, C. Huey, E. D. McDade, E. Day, G. S. Yakushev, I. Hassenstab, J. Morris, J. Llibre-Guerra, J. J. Ibanez, L. Jucker, M. Mendez, P. C. Bateman, R. J. Perrin, R. J. Benzinger, T. Jack, C. R. Betzel, R. Ances, B. M. Eggebrecht, A. T. Gordon, B. A. Wheelock, M. D. Dominantly Inherited Alzheimer Network, 2023-11-01 doi:10.1101/2023.10.29.564633 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ S RNA Intergenic Deletions Drive Viral Interference during Arenavirus Infections ]]> https://biorxiv.org/content/10.1101/2023.10.31.564889v1?rss=1 Hackbart, M. Lopez, C. B. 2023-11-01 doi:10.1101/2023.10.31.564889 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ NEUTROPHILS ARE INDISPENSABLE FOR ADVERSE CARDIAC REMODELING IN HEART FAILURE ]]> https://biorxiv.org/content/10.1101/2023.10.31.565035v1?rss=1 Rokosh, G. Prabhu, S. S. Antipenko, S. V. Hamid, T. Ismahil, M. A. Mayfield, N. Gunzer, M. Jinno, M. 2023-11-01 doi:10.1101/2023.10.31.565035 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Reduced dosage of multiple dynein arm preassembly factors limits cilia regeneration in Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2023.10.31.564885v1?rss=1 800 structural proteins. Variants in 58 of these genes cause primary ciliary dyskinesia (PCD) in humans. We used a second-site non-complementation approach in diploid Chlamydomonas reinhardtii strains to investigate whether reduced dosage of different combinations of motile cilia proteins affects cilia growth / regeneration. Temperature-sensitive mutants in intraflagellar transport genes fail to complement in heterozygous diploids at the restrictive temperature, which may be due to poisonous interactions or a reduction in protein levels. Diploid strains heterozygous for 211 double mutant combinations in 21 genes are phenotypically recessive when unperturbed and do not show SSNC. Consequently, we developed a sensitized screen. When protein synthesis is inhibited, cells utilize the existing cytoplasmic pool of proteins, which is insufficient to build full-length cilia. Six double heterozygous strains in dynein arm preassembly factors (DNAAFs) pf13, pf23, wdr92, and oda8 regrow cilia that are shorter than wild-type diploids, which suggests that double heterozygosity limits the pool of assembled dynein arms further. We isolated a new null allele (pf23-4) that shows a more severe loss of ODAs and IDAs in cilia than the previously studied pf23-1 hypomorphic allele. We also identified a new role for PF23 in cytoplasmic modification of IC138, protein of the I1/f inner dynein arm. In our SSNC assay, the pf23-4 allele also exhibits a more severe phenotype than pf23-1. Whole cell extract immunoblots show a reduction of PF23 protein to one-half of wild-type levels in both single and double heterozygous genotypes. The pf13 mutant shows SSNC with mutants in two outer dynein arm structural proteins, ODA6, and ODA9. We suggest that reduction of multiple dynein preassembly factors limits the pool of assembled dynein arms needed for cilia assembly and regeneration. Our data support PF23 as a scaffolding hub protein involved in dynein arm assembly. Author SummaryMotile cilia are essential for movement of cells and fluids. In humans, motile cilia defects cause primary ciliary dyskinesia (PCD), a rare disease characterized by recurring respiratory infections, left-right asymmetry defects, ear infections, and infertility. Many genes are involved in motile cilia function and assembly. We use Chlamydomonas reinhardtii to study the effects of changes in protein levels in different combinations of proteins needed for motile cilia. Our results show that the proteins that help fold and assemble the dynein motors in the cytoplasm are sensitive to changes in the dosage of these preassembly factors. Reductions in proteins involved in multiple steps of the pathway prevents efficient dynein preassembly and cilia regeneration under stressful cellular conditions. ]]> Dutcher, S. K. Penny, G. M. 2023-11-02 doi:10.1101/2023.10.31.564885 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ A Cre-dependent reporter mouse for quantitative real-time imaging of Protein Kinase A activity dynamics ]]> https://biorxiv.org/content/10.1101/2023.10.31.565028v1?rss=1 Tilden, E. I. Maduskar, A. Oldenborg, A. Sabatini, B. L. Chen, Y. 2023-11-02 doi:10.1101/2023.10.31.565028 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages ]]> https://biorxiv.org/content/10.1101/2023.10.31.565031v1?rss=1 Iglesia, M. D. Jayasinghe, R. G. Chen, S. Terekhanova, N. V. Herndon, J. M. Storrs, E. Karpova, A. Zhou, D. C. Naser Al Deen, N. Shinkle, A. T. Lu, R. J.-H. Caravan, W. Houston, A. Zhao, Y. Sato, K. Lal, P. Street, C. Rodrigues, F. M. Southard-Smith, A. N. Targino da Costa, A. L. N. Zhu, H. Mo, C.-K. Crowson, L. Fulton, R. S. Wyczalkowski, M. A. Fronick, C. C. Fulton, L. A. Sun, H. Davies, S. R. Appelbaum, E. L. Chasnoff, S. E. Carmody, M. Brooks, C. Liu, R. Wendl, M. C. Oh, C. Bender, D. Cruchaga, C. Harari, O. Bredemeyer, A. Lavine, K. Bose, R. Marge 2023-11-02 doi:10.1101/2023.10.31.565031 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Improving the accuracy of bulk fitness assays by correcting barcode processing biases ]]> https://biorxiv.org/content/10.1101/2023.10.31.565047v1?rss=1 McGee, R. S. Kinsler, G. Petrov, D. Tikhonov, M. 2023-11-02 doi:10.1101/2023.10.31.565047 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Senescent cells impair fracture repair through elevating ubiquitin-proteasome system activity in aged mice. ]]> https://biorxiv.org/content/10.1101/2023.11.01.565138v1?rss=1 Zhang, J. Xu, J. Liu, J. Lipe, B. Wu, T. Boyce, B. Shen, J. Xing, L. ZHANG, H. 2023-11-04 doi:10.1101/2023.11.01.565138 Cold Spring Harbor Laboratory Press 2023-11-04 <![CDATA[ An in vivo platform to identify clinically relevant pathogenic loci using Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2023.11.01.565153v1?rss=1 Yamada, S. Ou, T. N. Nachadalingam, S. Yang, S. Johnson, A. N. 2023-11-04 doi:10.1101/2023.11.01.565153 Cold Spring Harbor Laboratory Press 2023-11-04 <![CDATA[ Linking modulation of bio-molecular phase behaviour with collective interactions ]]> https://biorxiv.org/content/10.1101/2023.11.02.565376v1?rss=1 Qian, D. Ausserwoger, H. Arter, W. E. Scrutton, R. Welsh, T. J. Kartanas, T. Ermann, N. Qamar, S. Fischer, C. Sneideris, T. St George-Hyslop, P. Pappu, R. V. Knowles, T. 2023-11-05 doi:10.1101/2023.11.02.565376 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Biomechanical Modeling of Cesarean Section Scars and Scar Defects ]]> https://biorxiv.org/content/10.1101/2023.11.03.565565v1?rss=1 Scott, A. K. Louwagie, E. M. Myers, K. M. Oyen, M. L. 2023-11-05 doi:10.1101/2023.11.03.565565 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Renal mechanotransduction is an essential regulator of renin ]]> https://biorxiv.org/content/10.1101/2023.11.04.565646v1?rss=1 Hill, R. Z. Shirvan, S. Burquez, S. Dubin, A. E. Servin Vences, M. R. Miner, J. H. Patapoutian, A. 2023-11-05 doi:10.1101/2023.11.04.565646 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ The modified RNA base acp3U is an attachment site for N-glycans in glycoRNA ]]> https://biorxiv.org/content/10.1101/2023.11.06.565735v1?rss=1 Xie, Y. Hemberger, H. Till, N. A. Chai, P. Watkins, C. Lebedenko, C. G. Caldwell, R. M. George, B. Bertozzi, C. R. Garcia, B. A. Flynn, R. A. 2023-11-06 doi:10.1101/2023.11.06.565735 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Coordinated differentiation of human intestinal organoids with functional enteric neurons and vasculature ]]> https://biorxiv.org/content/10.1101/2023.11.06.565830v1?rss=1 Childs, C. J. Poling, H. M. Chen, K. Tsai, Y.-H. Wu, A. Sweet, C. W. Vallie, A. Eiken, M. K. Huang, S. Schreiner, R. Xiao, Z. Conchola, A. S. Anderman, M. F. Holloway, E. M. Singh, A. Giger, R. Mahe, M. M. Walton, K. D. Loebel, C. Helmrath, M. A. Rafii, S. Spence, J. R. 2023-11-06 doi:10.1101/2023.11.06.565830 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Mucosal Adenoviral-vectored Vaccine Boosting Durably Prevents XBB.1.16 Infection in Nonhuman Primates ]]> https://biorxiv.org/content/10.1101/2023.11.06.565765v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@d49b9dorg.highwire.dtl.DTLVardef@347455org.highwire.dtl.DTLVardef@1c1a196org.highwire.dtl.DTLVardef@1579130_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gagne, M. Flynn, B. J. Andrew, S. F. Flebbe, D. R. Mychalowych, A. Lamb, E. Davis-Gardner, M. E. Burnett, M. R. Serebryannyy, L. A. Lin, B. C. Pessaint, L. Todd, J.-P. M. Ziff, Z. E. Maule, E. Carroll, R. Naisan, M. Jethmalani, Y. Case, J. B. Dmitriev, I. P. Kashentseva, E. A. Ying, B. Dodson, A. Kouneski, K. Doria-Rose, N. A. O'Dell, S. Godbole, S. Laboune, F. Henry, A. R. Marquez, J. Teng, I.-T. Wang, L. Zhou, Q. Wali, B. Ellis, M. Zouantchangadou, S. Van Ry, A. Lewis, M. G. Andersen, H. Kwong, P. D. Curiel, D. T. Foulds, K. E. Nason, M. C. Suthar, M 2023-11-08 doi:10.1101/2023.11.06.565765 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Arousal as a universal embedding for spatiotemporal brain dynamics ]]> https://biorxiv.org/content/10.1101/2023.11.06.565918v1?rss=1 Raut, R. V. Rosenthal, Z. P. Wang, X. Miao, H. Zhang, Z. Lee, J.-M. Raichle, M. E. Bauer, A. Q. Brunton, S. L. Brunton, B. W. Kutz, J. N. 2023-11-08 doi:10.1101/2023.11.06.565918 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Disuse-driven plasticity in the human thalamus and putamen ]]> https://biorxiv.org/content/10.1101/2023.11.07.566031v1?rss=1 Chauvin, R. J. Newbold, D. J. Nielsen, A. N. Miller, R. L. Krimmel, S. R. Metoki, A. Wang, A. Van, A. N. Montez, D. F. Suljic, V. Baden, N. J. Ramirez-Perez, N. Scheidter, K. M. Monk, J. S. Whiting, F. I. Adeyemo, B. Kay, B. P. Laumann, T. O. Gordon, E. M. Dosenbach, N. U. F. 2023-11-08 doi:10.1101/2023.11.07.566031 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Murine Parainfluenza Virus Persists in Lung Innate Immune Cells Sustaining Chronic Lung Pathology ]]> https://biorxiv.org/content/10.1101/2023.11.07.566103v1?rss=1 Castro, I. A. Yang, Y. Gnazzo, V. Kim, D.-H. Van Dyken, S. J. Lopez, C. B. 2023-11-08 doi:10.1101/2023.11.07.566103 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Integrated multi-omics single cell atlas of the human retina ]]> https://biorxiv.org/content/10.1101/2023.11.07.566105v1?rss=1 Li, J. Wang, J. Ibarra, I. L. Cheng, X. Luecken, M. D. Lu, J. Monavarfeshani, A. Yan, W. Zheng, Y. Zuo, Z. Colborn, S. L. Z. Cortez, B. S. Owen, L. A. Tran, N. M. Shekhar, K. Sanes, J. R. Stout, J. T. Chen, S. Li, Y. DeAngelis, M. M. Theis, F. J. Chen, R. 2023-11-08 doi:10.1101/2023.11.07.566105 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ DLG1 functions upstream of SDCCAG3 and IFT20 to control targeting of polycystin-2 to the primary cilium ]]> https://biorxiv.org/content/10.1101/2023.11.10.566524v1?rss=1 Rezi, C. K. Aslanyan, M. Diwan, G. D. Cheng, T. Chamlali, M. Junger, K. Anvarian, Z. Lorentzen, E. Pauly, K. B. Bahadori, Y. Fernandes, E. F. Qian, F. Tosi, S. Christensen, S. T. Pedersen, S. F. Stromgaard, K. Russell, R. B. Miner, J. H. Mahjoub, M. R. Boldt, K. Roepman, R. Pedersen, L. B. 2023-11-10 doi:10.1101/2023.11.10.566524 Cold Spring Harbor Laboratory Press 2023-11-10 <![CDATA[ A high-density diffuse optical tomography dataset of naturalistic viewing ]]> https://biorxiv.org/content/10.1101/2023.11.07.565473v1?rss=1 Sherafati, A. Bajracharya, A. Jones, M. Speh, E. Munsi, M. Lin, C.-H. P. Fishell, A. K. Hershey, T. Eggebrecht, A. T. Culver, J. P. Peelle, J. E. 2023-11-11 doi:10.1101/2023.11.07.565473 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ SillyPutty: Improved clustering by optimizing the silhouette width ]]> https://biorxiv.org/content/10.1101/2023.11.07.566055v1?rss=1 Bombina, P. Tally, D. G. Abrams, Z. B. Coombes, K. R. 2023-11-11 doi:10.1101/2023.11.07.566055 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ Functional parcellation of the neonatal brain ]]> https://biorxiv.org/content/10.1101/2023.11.10.566629v1?rss=1 Myers, M. J. Labonte, A. K. Gordon, E. M. Laumann, T. O. Tu, J. C. Wheelock, M. D. Nielsen, A. N. Schwarzlose, R. Camacho, M. C. Warner, B. B. Raghuraman, N. Luby, J. L. Barch, D. M. Fair, D. A. Petersen, S. E. Rogers, C. E. Smyser, C. D. Sylvester, C. M. 2023-11-11 doi:10.1101/2023.11.10.566629 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ Metabolic Regulation of Single Synaptic Vesicle Exo- and Endocytosis in Hippocampal Synapses ]]> https://biorxiv.org/content/10.1101/2023.11.08.566236v1?rss=1 Myeong, J. Stunault, M. I. Klyachko, V. Ashrafi, G. 2023-11-12 doi:10.1101/2023.11.08.566236 Cold Spring Harbor Laboratory Press 2023-11-12 <![CDATA[ Single Nucleus RNA Sequencing of Remnant Kidney Biopsies and Urine Cell RNA Sequencing Reveal Cell Specific Markers of Covid-19 Acute Kidney Injury ]]> https://biorxiv.org/content/10.1101/2023.11.10.566497v1?rss=1 Ghag, R. Kaushal, M. Nwanne, G. Knoten, A. Kiryluk, K. Rosenberg, A. Menez, S. Bagnasco, S. M. Sperati, C. J. Atta, M. G. Gaut, J. P. Williams, J. C. El-Achkar, T. M. Arend, L. J. Parikh, C. R. Jain, S. 2023-11-12 doi:10.1101/2023.11.10.566497 Cold Spring Harbor Laboratory Press 2023-11-12 <![CDATA[ Behavioral adaptation to changing energy constraints via altered frequency of movement selection ]]> https://biorxiv.org/content/10.1101/2023.11.08.566262v1?rss=1 100,000 experimentally-recorded movement bouts from larval zebrafish across different ages and fluid conditions as they hunted Paramecia. We find that these fish adapt to their changing relationship with the fluid environment as they grow by adjusting the frequency with which they select different types of movements, so that more expensive movements are chosen less often. This strategy was preserved when fish were raised in an unnaturally viscous environment. This work suggests a general principle by which animals could minimize energy consumption in the face of changing energy costs over development. ]]> Darveniza, T. Zhu, S. I. Pujic, Z. Sun, B. Levendosky, M. Wong, R. Agarwal, R. McCullough, M. H. Goodhill, G. J. 2023-11-13 doi:10.1101/2023.11.08.566262 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Restoration of Cone Circuit Functionality in the Regenerating Adult Zebrafish Retina ]]> https://biorxiv.org/content/10.1101/2023.11.11.566441v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@c9f038org.highwire.dtl.DTLVardef@1ba255borg.highwire.dtl.DTLVardef@1ea7f60org.highwire.dtl.DTLVardef@50adf3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Abraham, E. Hartmann, H. Yoshimatsu, T. Baden, T. Brand, M. 2023-11-15 doi:10.1101/2023.11.11.566441 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Structural and functional basis of VLDLR receptor usage by Eastern equine encephalitis virus ]]> https://biorxiv.org/content/10.1101/2023.11.15.567188v1?rss=1 Adams, L. J. Raju, S. Ma, H. Gilliland, T. Reed, D. S. Klimstra, W. B. Fremont, D. H. Diamond, M. S. 2023-11-15 doi:10.1101/2023.11.15.567188 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Evaluation of gelatin bloom strength on gelatin methacryloyl hydrogel properties ]]> https://biorxiv.org/content/10.1101/2023.11.13.566924v1?rss=1 Zambuto, S. G. Kolluru, S. S. Ferchichi, E. Rudewick, H. Fodera, D. G. Myers, K. M. Zustiak, S. P. Oyen, M. L. 2023-11-16 doi:10.1101/2023.11.13.566924 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Perigestational Opioid Exposure Alters Alcohol-Driven Reward Behaviors in Adolescent Rats ]]> https://biorxiv.org/content/10.1101/2023.11.14.567041v1?rss=1 Searles, C. T. Harder, H. J. Vogt, M. E. Murphy, A. Z. 2023-11-16 doi:10.1101/2023.11.14.567041 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Precision data-driven modeling of cortical dynamics reveals idiosyncratic mechanisms of canonical oscillations ]]> https://biorxiv.org/content/10.1101/2023.11.14.567088v1?rss=1 Singh, M. F. Braver, T. S. Cole, M. Ching, S. 2023-11-16 doi:10.1101/2023.11.14.567088 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Toxoplasma gondii harbors a hypoxia-responsive coproporphyrinogen dehydrogenase-like protein. ]]> https://biorxiv.org/content/10.1101/2023.11.16.567449v1?rss=1 Key, M. Baptista, C. G. Bergmann, A. Floyd, K. Blader, I. J. Dou, Z. 2023-11-16 doi:10.1101/2023.11.16.567449 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Comparative and Integrative Single Cell Analysis Reveals New Insights into the Transcriptional Immaturity of Stem Cell-Derived β Cells ]]> https://biorxiv.org/content/10.1101/2023.11.15.567281v1?rss=1 Schmidt, M. D. Ishahak, M. Augsornworawat, P. Millman, J. R. 2023-11-17 doi:10.1101/2023.11.15.567281 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Macrophage Depletion Protects Against Cisplatin-Induced Ototoxicity and Nephrotoxicity ]]> https://biorxiv.org/content/10.1101/2023.11.16.567274v1?rss=1 Sung, C. Y. W. Hayase, N. Yuen, P. S. T. Lee, J. Fernandez, K. Hu, X. Cheng, H. Star, R. A. Warchol, M. E. Cunningham, L. L. 2023-11-17 doi:10.1101/2023.11.16.567274 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Genome of the North American wild apple species Malus angustifolia ]]> https://biorxiv.org/content/10.1101/2023.11.16.567428v1?rss=1 Mansfeld, B. N. Ou, S. Burchard, E. Yocca, A. Harkess, A. Gutierrez, B. van Nocker, S. Tang, L. Gottschalk, C. 2023-11-17 doi:10.1101/2023.11.16.567428 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ One-Hour Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer ]]> https://biorxiv.org/content/10.1101/2023.11.21.568149v1?rss=1 Lancaster, N. M. Sinitcyn, P. Forny, P. Peters-Clarke, T. M. Fecher, C. Smith, A. J. Shishkova, E. Arrey, T. N. Pashkova, A. Robinson, M. L. Arp, N. Fan, J. Hansen, J. Galmozzi, A. Serrano, L. R. Westphall, M. S. Stewart, H. Hock, C. Damoc, E. Pagliarini, D. J. Zabrouskov, V. Coon, J. J. 2023-11-21 doi:10.1101/2023.11.21.568149 Cold Spring Harbor Laboratory Press 2023-11-21 <![CDATA[ Giant genes are rare but implicated in cell wall degradation by predatory bacteria ]]> https://biorxiv.org/content/10.1101/2023.11.21.568195v1?rss=1 30,000 aa occur in bacterial phyla such as Firmicutes and Actinobacteria, they are most common in ca. Omnitrophota, ultra small bacteria that adopt predatory lifestyles. All full length giant genes encode numerous transmembrane regions and most encode divergent secA DEAD helicase domains. In silico structural prediction of protein subregions was required to identify domains in unannotated protein segments, and revealed putative domains implicated in attachment and carbohydrate degradation. Many giant genes in new complete and near-complete Omnitrophota genomes occur in close proximity to genes homologous to type II secretion systems as well as carbohydrate import systems. This, in combination with the domain content, suggests that many bacterial giant proteins enable prey adhesion and cell wall digestion during bacterial predation. ]]> West-Roberts, J. A. Valentin Alvarado, L. E. Mullen, S. Sachdeva, R. Smith, J. Hug, L. A. Gregoire, D. Liu, W. Lin, T.-Y. Husain, G. Amano, Y. Ly, L. Banfield, J. 2023-11-22 doi:10.1101/2023.11.21.568195 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Durable immunity to SARS-CoV-2 in both lower and upper airways achieved with a gorilla adenovirus (GRAd) S-2P vaccine in non-human primates ]]> https://biorxiv.org/content/10.1101/2023.11.22.567930v1?rss=1 Moliva, J. I. Andrew, S. F. Flynn, B. J. Wagner, D. A. Foulds, K. E. Gagne, M. Flebbe, D. R. Lamb, E. Provost, S. Marquez, J. Mychalowych, A. Lorag, C. Honeycutt, C. C. Burnett, M. R. McCormick, L. Henry, A. R. Godbole, S. Davis-Gardner, M. E. Minai, M. Bok, K. W. Nagata, B. M. Todd, J.-P. M. McCarthy, E. Dodson, A. Kouneski, K. Cook, A. Pessaint, L. Van Ry, A. Valentin, D. Young, S. Littman, Y. Boon, A. C. M. Suthar, M. S. Lewis, M. G. Andersen, H. Alves, D. A. Woodward, R. Leuzzi, A. Vitelli, A. Colloca, S. Folgori, A. Raggiolli, A. Capone, S. Nason 2023-11-22 doi:10.1101/2023.11.22.567930 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ GDF15 mediates inflammation-associated bone loss through a brain-bone axis ]]> https://biorxiv.org/content/10.1101/2023.11.22.568290v1?rss=1 Van der Cruyssen, R. Devan, J. Heggli, I. Burri, D. Gaublomme, D. Josipovic, I. Dumas, E. Vlieghe, C. Raimondo, M. G. Zakharov, P. Jacques, P. De Mits, S. Lukasik, Z. Vuylsteke, M. Renson, T. Schots, L. Planckaert, G. Stappers, F. Decruy, T. Coudenys, J. Manuello, T. Vereecke, L. Dmitriev, R. I. Lambrecht, S. Van Hoorebeke, L. Lambert, J. Ravichandran, K. Ramming, A. Dudli, S. Schett, G. Gracey, E. Elewaut, D. 2023-11-23 doi:10.1101/2023.11.22.568290 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ Identifying Naturalistic Movies from Human Brain Activity with High-Density Diffuse Optical Tomography ]]> https://biorxiv.org/content/10.1101/2023.11.27.566650v1?rss=1 Markow, Z. E. Tripathy, K. Svoboda, A. M. Schroeder, M. L. Rafferty, S. M. Richter, E. J. Eggebrecht, A. T. Anastasio, M. A. Chevillet, M. A. Mugler, E. M. Naufel, S. N. Yin, A. Trobaugh, J. W. Culver, J. P. 2023-11-28 doi:10.1101/2023.11.27.566650 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs ]]> https://biorxiv.org/content/10.1101/2023.11.28.567931v1?rss=1 Krug, B. Hu, B. Chen, H. Ptack, A. Chen, X. Gretarsson, K. H. Deshmukh, S. Kabir, N. Faria Andrade, A. Jabbour, E. Harutyunyan, A. S. Lee, J. J. Y. Hulswit, M. Faury, D. Russo, C. Xu, X. Johnston, M. J. Baguette, A. Dahl, N. A. Weil, A. G. Ellezam, B. Dali, R. Blanchette, M. Wilson, K. Garcia, B. A. Soni, R. K. Gallo, M. Taylor, M. D. Kleinman, C. L. Majewski, J. Jabado, N. Lu, C. 2023-11-28 doi:10.1101/2023.11.28.567931 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ A biodegradable "one-for-all" nanoparticle for multimodality imaging and enhanced photothermal treatment of breast cancer ]]> https://biorxiv.org/content/10.1101/2023.11.28.568885v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@e6be5dorg.highwire.dtl.DTLVardef@dbce2eorg.highwire.dtl.DTLVardef@bd5360org.highwire.dtl.DTLVardef@1acf01d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hsu, J. C. Barragan, D. Tward, A. E. Hajfathalian, M. Amirshaghaghi, A. Mossburg, K. J. Rosario-Berrios, D. N. Bouche, M. Andrianov, A. K. Delikatny, E. J. Cormode, D. P. 2023-11-28 doi:10.1101/2023.11.28.568885 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ The SMC5/6 complex is required for maintenance of genome integrity upon APOBEC3A-mediated replication stress ]]> https://biorxiv.org/content/10.1101/2023.11.28.568952v1?rss=1 O'Leary, D. R. Hansen, A. R. Fingerman, D. F. Tran, T. A. Harris, B. R. Hayer, K. E. DeWeerd, R. A. Tennekoon, M. Meroni, A. Szeto, J. Weitzman, M. D. Bednarski, J. J. Shalem, O. Vindigni, A. Green, A. M. 2023-11-28 doi:10.1101/2023.11.28.568952 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ Framewise multi-echo distortion correction for superior functional MRI ]]> https://biorxiv.org/content/10.1101/2023.11.28.568744v1?rss=1 Van, A. N. Montez, D. F. Laumann, T. O. Suljic, V. Madison, T. Baden, N. J. Ramirez-Perez, N. Scheidter, K. M. Monk, J. S. Whiting, F. I. Adeyemo, B. Chauvin, R. J. Krimmel, S. R. Metoki, A. Rajesh, A. Roland, J. L. Salo, T. Wang, A. Weldon, K. B. Sotiras, A. Shimony, J. S. Kay, B. P. Nelson, S. M. Tervo-Clemmens, B. Marek, S. A. Vizioli, L. Yacoub, E. Satterthwaite, T. D. Gordon, E. M. Fair, D. A. Tisdall, D. Dosenbach, N. U. F. 2023-11-29 doi:10.1101/2023.11.28.568744 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ (R,S)-ketamine's rapid-acting antidepressant effects are modulated by NR2B- containing NMDA receptors on adult-born hippocampal neurons ]]> https://biorxiv.org/content/10.1101/2023.11.28.569043v1?rss=1 Bulthuis, N. E. McGowan, J. C. Ladner, L. R. LaGamma, C. T. Lim, S. C. Shubeck, C. X. Brachman, R. A. Sydnor, E. Pavlova, I. P. Seo, D.-o. Drew, M. R. Denny, C. A. 2023-11-29 doi:10.1101/2023.11.28.569043 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Morphometrics and phylogenomics of coca (Erythroxylum spp.) illuminate its reticulate evolution, with implications for taxonomy ]]> https://biorxiv.org/content/10.1101/2023.11.28.569066v1?rss=1 Przelomska, N. Diaz, R. Avila, F. A. Ballen, G. A. Cortes-B, R. Kistler, L. Chitwood, D. H. Charitonidou, M. Renner, S. S. Perez-Escobar, O. A. Antonelli, A. 2023-11-29 doi:10.1101/2023.11.28.569066 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Encapsulation of AAV into protein vault nanoparticles as a novel solution to gene therapy's neutralizing antibody problem ]]> https://biorxiv.org/content/10.1101/2023.11.29.569229v1?rss=1 Collins, L. T. Beatty, W. Moyo, B. Alves-Bezerra, M. Hurley, A. Lagor, W. Bao, G. Ponnazhagan, S. McNally, R. Rome, L. Curiel, D. 2023-11-29 doi:10.1101/2023.11.29.569229 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Human Heart Failure Alters Mitochondria and Fiber 3D Structure Triggering Metabolic Shifts ]]> https://biorxiv.org/content/10.1101/2023.11.28.569095v1?rss=1 Vue, Z. Ajayi, P. T. Neikirk, K. Murphy, A. Prasad, P. Jenkins, B. C. Vang, L. Garza-Lopez, E. Mungai, M. Marshall, A. G. Beasley, H. K. Killion, M. Parker, R. Anukodem, J. Lavine, K. Ajijola, O. Mobley, B. Dai, D.-F. Exil, V. Kirabo, A. Ru Su, Y. Tomasek, K. Zhang, X. Wanjalla, C. N. Hubert, D. L. Phillips, M. A. McReynolds, M. Glancy, B. Hinton, A. 2023-11-30 doi:10.1101/2023.11.28.569095 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ Loss of Slc35a2 alters development of the mouse cerebral cortex ]]> https://biorxiv.org/content/10.1101/2023.11.29.569243v1?rss=1 Elziny, S. Sran, S. Yoon, H. Corrigan, R. R. Page, J. Ringland, A. Lanier, A. Lapidus, S. Foreman, J. Heinzen, E. L. Iffland, P. Crino, P. Bedrosian, T. A. 2023-11-30 doi:10.1101/2023.11.29.569243 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ The evolution of diverse antimicrobial responses in vancomycin-intermediate Staphylococcus aureus and its therapeutic implications ]]> https://biorxiv.org/content/10.1101/2023.11.30.569373v1?rss=1 Crozier, D. Gray, J. M. Maltas, J. A. Bonomo, R. A. Card, K. J. Scott, J. G. 2023-12-01 doi:10.1101/2023.11.30.569373 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Hemodynamics regulate spatiotemporal artery muscularization in the developing circle of Willis ]]> https://biorxiv.org/content/10.1101/2023.12.01.569622v1?rss=1 Cheng, S. Xia, I. F. Wanner, R. Abello, J. Stratman, A. N. Nicoli, S. 2023-12-02 doi:10.1101/2023.12.01.569622 Cold Spring Harbor Laboratory Press 2023-12-02 <![CDATA[ An inducible genetic tool for tracking and manipulating specific microglial states in development and disease ]]> https://biorxiv.org/content/10.1101/2023.12.01.569597v1?rss=1 Barclay, K. M. Abduljawad, N. Cheng, Z. Kim, M. W. Zhou, L. Yang, J. Rustenhoven, J. Mazzitelli Perez, J. Smyth, L. Beatty, W. Hou, J. Saligrama, N. Colonna, M. Yu, G. Kipnis, J. Li, Q. 2023-12-04 doi:10.1101/2023.12.01.569597 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[ Impact of delta9-tetrahydrocannabinol and oxycodone co-administration on measures of antinociception, dependence, circadian activity, and reward in mice ]]> https://biorxiv.org/content/10.1101/2023.12.04.569809v1?rss=1 Slivicki, R. A. Wang, J. G. Nhat, V. T. T. Kravitz, A. V. Creed, M. C. Gereau, R. 2023-12-05 doi:10.1101/2023.12.04.569809 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Decreased voluntary alcohol intake and ventral striatal epigenetic and transcriptional remodeling in male Acss2 KO mice ]]> https://biorxiv.org/content/10.1101/2023.12.04.569964v1?rss=1 Egervari, G. Donahue, G. Quijano-Carde, N. Hogan, C. Periandri, E. M. Fleites, V. Alexander, D. C. De Biasi, M. Berger, S. L. 2023-12-06 doi:10.1101/2023.12.04.569964 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ Chimeric systems composed of swapped Tra subunits between distantly-related F plasmids reveal striking plasticity among type IV secretion machines ]]> https://biorxiv.org/content/10.1101/2023.12.05.570194v1?rss=1 Christie, P. Kishida, K. Li, Y. G. Ogawa-Kishida, N. Khara, P. Al Mamun, A. A. M. Bosserman, R. E. 2023-12-06 doi:10.1101/2023.12.05.570194 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ Ergosterol mediates aggregation of natamycin in the yeast plasma membrane ]]> https://biorxiv.org/content/10.1101/2023.12.05.570146v1?rss=1 Szomek, M. Akkerman, V. Lauritsen, L. Walther, H.-L. Juhl, A. D. Thaysen, K. Egebjerg, J. M. Covey, D. F. Lehmann, M. Wessig, P. Foster, A. J. Poolman, B. Werner, S. Schneider, G. Müller, P. Wüstner, D. 2023-12-08 doi:10.1101/2023.12.05.570146 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma ]]> https://biorxiv.org/content/10.1101/2023.12.06.570390v1?rss=1 Weiner, A. K. Radaoui, A. B. Tsang, M. Martinez, D. Sidoli, S. Conkrite, K. L. Delaidelli, A. Modi, A. Rokita, J. L. Patel, K. Lane, M. V. Zhang, B. Zhong, C. Ennis, B. Miller, D. P. Brown, M. A. Rathi, K. S. Raman, P. Pogoriler, J. Bhatti, T. Pawel, B. Glisovic-Aplenc, T. Teicher, B. Erickson, S. W. Earley, E. J. Bosse, K. R. Sorensen, P. H. Krytska, K. Mosse, Y. P. Havenith, K. E. Zammarchi, F. van Berkel, P. H. Smith, M. A. Garcia, B. A. Maris, J. M. Diskin, S. J. 2023-12-08 doi:10.1101/2023.12.06.570390 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Electrostatic encoding of genome organization principles within single native nucleosomes ]]> https://biorxiv.org/content/10.1101/2023.12.08.570828v1?rss=1 Park, S. Athreya, A. Carrizo, G. Benning, N. Mitchener, M. Bhanu, N. Garcia, B. Zhang, B. Muir, T. W. Pearce, E. Ha, T. 2023-12-09 doi:10.1101/2023.12.08.570828 Cold Spring Harbor Laboratory Press 2023-12-09 <![CDATA[ A heptavalent O-antigen bioconjugate vaccine exhibits differential functional antibody responses against diverse Klebsiella pneumoniae isolates ]]> https://biorxiv.org/content/10.1101/2023.12.12.571344v1?rss=1 Wantuch, P. L. Knoot, C. J. Robinson, L. S. Vinogradov, E. Scott, N. Harding, C. M. Rosen, D. A. 2023-12-12 doi:10.1101/2023.12.12.571344 Cold Spring Harbor Laboratory Press 2023-12-12 <![CDATA[ PhyloJunction: a computational framework for simulating, developing, and teaching evolutionary models ]]> https://biorxiv.org/content/10.1101/2023.12.15.571907v1?rss=1 Mendes, F. K. Landis, M. J. 2023-12-16 doi:10.1101/2023.12.15.571907 Cold Spring Harbor Laboratory Press 2023-12-16 <![CDATA[ Identification of a myofibroblast differentiation program during neonatal lung development ]]> https://biorxiv.org/content/10.1101/2023.12.28.573370v1?rss=1 Yin, Y. Koenitzer, J. R. Patra, D. Dietmann, S. Bayguinov, P. Hagan, A. S. Ornitz, D. M. 2023-12-28 doi:10.1101/2023.12.28.573370 Cold Spring Harbor Laboratory Press 2023-12-28 <![CDATA[ Competition for resources during development drives allometric patterns in the grass Setaria ]]> https://biorxiv.org/content/10.1101/2023.12.28.573563v1?rss=1 Dale, R. Banan, D. Millman, B. Leakey, A. Mukherji, S. Baxter, I. 2023-12-28 doi:10.1101/2023.12.28.573563 Cold Spring Harbor Laboratory Press 2023-12-28 <![CDATA[ Calcyphosine is a microtubule-associated protein required for spindle formation and function ]]> https://biorxiv.org/content/10.1101/2023.12.29.573632v1?rss=1 Setu, B. Nie, Q. Echele, G. Spencer, S. A. 2023-12-30 doi:10.1101/2023.12.29.573632 Cold Spring Harbor Laboratory Press 2023-12-30 <![CDATA[ Protosequences in human cortical organoids model intrinsic states in the developing cortex ]]> https://biorxiv.org/content/10.1101/2023.12.29.573646v1?rss=1 Tjitse van der Molen, T. Spaeth, A. Chini, M. Bartram, J. Dendukuri, A. Zhang, Z. Bhaskaran-Nair, K. Blauvelt, L. J. Petzold, L. R. Hansma, P. K. Teodorescu, M. Hierlemann, A. Hengen, K. B. Hanganu-Opatz, I. L. Kosik, K. S. Sharf, T. 2023-12-30 doi:10.1101/2023.12.29.573646 Cold Spring Harbor Laboratory Press 2023-12-30 <![CDATA[ The brainstem's red nucleus was evolutionarily upgraded to support goal-directed action ]]> https://biorxiv.org/content/10.1101/2023.12.30.573730v1?rss=1 Krimmel, S. R. Laumann, T. O. Chauvin, R. Hershey, T. Roland, J. L. Shimony, J. S. Willie, J. T. Norris, S. A. Marek, S. Van, A. N. Monk, J. Scheidter, K. M. Whiting, F. Ramirez-Perez, N. Metoki, A. Wang, A. Kay, B. P. Nahman-Averbuch, H. Fair, D. A. Lynch, C. J. Raichle, M. E. Gordon, E. M. Dosenbach, N. U. F. 2024-01-01 doi:10.1101/2023.12.30.573730 Cold Spring Harbor Laboratory Press 2024-01-01 <![CDATA[ A basally active cGAS-STING pathway limits SARS-CoV-2 replication in a subset of ACE2 positive airway cell models ]]> https://biorxiv.org/content/10.1101/2024.01.07.574522v1?rss=1 Puray-Chavez, M. LaPak, K. Jasuja, R. Pan, J. Xu, J. Eschbach, J. E. Mohammed, S. Lawson, D. Wang, Q. Brody, S. L. Major, M. B. Goldfarb, D. Kutluay, S. B. 2024-01-08 doi:10.1101/2024.01.07.574522 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ Automating the Human Connectome Project's Temporal ICA Pipeline ]]> https://biorxiv.org/content/10.1101/2024.01.15.574667v1?rss=1 Yang, C. Coalson, T. S. Smith, S. M. Elam, J. S. Van Essen, D. C. Glasser, M. F. 2024-01-16 doi:10.1101/2024.01.15.574667 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ Dynamical models reveal anatomically reliable attractor landscapes embedded in resting state brain networks ]]> https://biorxiv.org/content/10.1101/2024.01.15.575745v1?rss=1 Chen, R. Singh, M. F. Braver, T. S. Ching, S. 2024-01-16 doi:10.1101/2024.01.15.575745 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ A Wireless Wearable Ecosystem for Social Network Analysis in Free-living Animals ]]> https://biorxiv.org/content/10.1101/2024.01.15.575769v1?rss=1 Gaidica, M. Zhang, M. Dantzer, B. 2024-01-16 doi:10.1101/2024.01.15.575769 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ Genome streamlining to improve performance of a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 ]]> https://biorxiv.org/content/10.1101/2024.01.16.575707v1?rss=1 Sengupta, A. Bandyopadhyay, A. Sarkar, D. Hendry, J. I. Schubert, M. G. Liu, D. Church, G. Maranas, C. D. Pakrasi, H. B. 2024-01-16 doi:10.1101/2024.01.16.575707 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ Mouse Auditory Cortex Undergoes Asynchronous Maturation in the Right and Left Hemispheres ]]> https://biorxiv.org/content/10.1101/2024.01.16.575905v1?rss=1 Oviedo, H. V. Reid, A. Neophytou, D. Levy, R. 2024-01-16 doi:10.1101/2024.01.16.575905 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ The cost and payout of age on germline regeneration and sexual maturation in Platynereis dumerilii ]]> https://biorxiv.org/content/10.1101/2024.01.22.576726v1?rss=1 Metzger, B. M. Ozpolat, B. D. 2024-01-22 doi:10.1101/2024.01.22.576726 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Drivers of Bird Communities in an Urban Neighborhood Vary by Scale ]]> https://biorxiv.org/content/10.1101/2024.01.21.576560v1?rss=1 Darracq, A. K. Bliznick, C. Yeager, R. Turner, J. Pease, J. Whiteman, H. Smith, T. Bhatnagar, A. 2024-01-24 doi:10.1101/2024.01.21.576560 Cold Spring Harbor Laboratory Press 2024-01-24 <![CDATA[ CD4+ and CD8+ T cells are required to prevent SARS-CoV-2 persistence in the nasal compartment ]]> https://biorxiv.org/content/10.1101/2024.01.23.576505v1?rss=1 Kar, M. Johnson, K. E. E. Vanderheiden, A. Elrod, E. J. Floyd, K. Geerling, E. Stone, E. T. Salinas, E. Banakis, S. Wang, W. Sathish, S. Shrihari, S. Davis-Gardner, M. E. Kohlmeier, J. Pinto, A. Klein, R. Grakoui, A. Ghedin, E. Suthar, M. S. 2024-01-24 doi:10.1101/2024.01.23.576505 Cold Spring Harbor Laboratory Press 2024-01-24 <![CDATA[ Sertraline modulates hippocampal plasticity and learning via sigma 1 receptors, cellular stress and neurosteroids ]]> https://biorxiv.org/content/10.1101/2024.01.23.576911v1?rss=1 Izumi, Y. Reiersen, A. M. Lenze, E. J. Mennerick, S. Zorumski, C. F. 2024-01-24 doi:10.1101/2024.01.23.576911 Cold Spring Harbor Laboratory Press 2024-01-24 <![CDATA[ Genomic features of NF1-associated peripheral nerve sheath tumors: a cohort analysis from the Johns Hopkins NF1 biospecimen repository ]]> https://biorxiv.org/content/10.1101/2024.01.23.576977v1?rss=1 Banerjee, J. Lyu, Y. Makri, S. C. Scott, A. J. Zhang, L. Calizo, A. Pollard, K. Yang, K. Gross, J. M. Wang, J. Romo, C. G. Allaway, R. J. Blakeley, J. O. Hirbe, A. C. Pratilas, C. A. 2024-01-26 doi:10.1101/2024.01.23.576977 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ Breaking free from the clocks tyranny restores memory to brain damaged flies ]]> https://biorxiv.org/content/10.1101/2024.01.25.577231v1?rss=1 Dissel, S. Morgan, E. Cao, L. Wakefield, Z. P. Shetty, S. Chan, D. Duong, V. Donlea, J. M. Farah, H. Loutrianakis, V. Ford, M. Streett, L. Periandri, E. Li, Z. Huang, I. Abdalla, D. Kalra, A. Sousani, L. Holder, B. McAdams, C. van Swinderen, B. Shaw, P. J. 2024-01-26 doi:10.1101/2024.01.25.577231 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ Development of a LRRC15-Targeted Radio-Immunotheranostic Approach to Deplete Pro-tumorigenic Mechanisms and Immunotherapy Resistance ]]> https://biorxiv.org/content/10.1101/2024.01.30.577289v1?rss=1 Storey, C. M. Altai, M. Lueckerath, K. M. Zedan, W. Zhu, H. Trajkovic-Arsic, M. Park, J. E. Peekhaus, N. Siveke, J. Lilljebjorn, H. Abou, D. Marks, H. L. Ulmert, E. Lilja, H. Ridley, A. Safi, M. Yuen, C. Geres, S. Mao, L. Cheng, M. Czernin, J. Herrmann, K. Bentolila, L. Yang, X. Fioretos, T. Graeber, T. Sjostrom, K. Damoiseaux, R. Thorek, D. L. Ulmert, D. 2024-02-02 doi:10.1101/2024.01.30.577289 Cold Spring Harbor Laboratory Press 2024-02-02 <![CDATA[ MXRA8 promotes adipose tissue whitening to drive obesity ]]> https://biorxiv.org/content/10.1101/2024.01.31.578211v1?rss=1 Jia, W. Giwa, R. Moley, J. R. Smith, G. I. Petersen, M. C. Field, R. L. Abousaway, O. Kim, A. S. Coffey, S. R. Varnum, S. Wright, J. M. Zhang, X. Krysa, S. Lodhi, I. J. Abumrad, N. A. Klein, S. Diamond, M. S. Brestoff, J. R. 2024-02-02 doi:10.1101/2024.01.31.578211 Cold Spring Harbor Laboratory Press 2024-02-02 <![CDATA[ Mice born preterm develop gait dystonia and reduced cortical parvalbumin immunoreactivity ]]> https://biorxiv.org/content/10.1101/2024.02.01.578353v1?rss=1 Gemperli, K. Folorunso, F. Norin, B. Joshua, R. Hill, C. Rykowski, R. Galindo, R. Aravamuthan, B. R. 2024-02-02 doi:10.1101/2024.02.01.578353 Cold Spring Harbor Laboratory Press 2024-02-02 <![CDATA[ Mendelian segregation and high recombination rates facilitate genetic analyses in Cryptosporidium parvum ]]> https://biorxiv.org/content/10.1101/2024.02.02.578536v1?rss=1 Kimball, A. Funkhouser-Jones, L. Huang, W. Xu, R. Witola, W. H. Sibley, L. D. 2024-02-02 doi:10.1101/2024.02.02.578536 Cold Spring Harbor Laboratory Press 2024-02-02 <![CDATA[ A Data-Driven Latent Variable Approach to Validating the Research Domain Criteria (RDoC) Framework ]]> https://biorxiv.org/content/10.1101/2024.01.31.577486v1?rss=1 Quah, S. K. L. Jo, B. Geniesse, C. Uddin, L. Q. Mumford, J. A. Barch, D. M. Fair, D. A. Gotlib, I. H. Poldrack, R. A. Saggar, M. 2024-02-03 doi:10.1101/2024.01.31.577486 Cold Spring Harbor Laboratory Press 2024-02-03 <![CDATA[ BRD4-mediated epigenetic regulation of endoplasmic reticulum-mitochondria contact sites is governed by the mitochondrial complex III ]]> https://biorxiv.org/content/10.1101/2024.02.02.578646v1?rss=1 Chen, B. Lynn-Nguyen, T. M. Jadhav, P. Halligan, B. S. Rossiter, N. J. Guerra, R. M. Koshkin, S. Koo, I. Morlacchi, P. Hanna, D. A. Lin, J. Banerjee, R. Pagliarini, D. Patterson, A. D. Mosalaganti, S. Sexton, J. Cali, T. Lyssiotis, C. A. Shah, Y. M. 2024-02-04 doi:10.1101/2024.02.02.578646 Cold Spring Harbor Laboratory Press 2024-02-04 <![CDATA[ Disrupted mitochondrial response to nutrients is a presymptomatic event in the cortex of the APPSAA knock-in mouse model of Alzheimer disease ]]> https://biorxiv.org/content/10.1101/2024.02.02.578668v1?rss=1 Norambuena, A. Sagar, V. K. Wang, Z. Raut, P. Feng, Z. Wallrabe, H. Pardo, E. Kim, T. Alam, S. R. Hu, S. Periasamy, A. Bloom, G. S. 2024-02-04 doi:10.1101/2024.02.02.578668 Cold Spring Harbor Laboratory Press 2024-02-04 <![CDATA[ Variant Surface Protein GP60 Contributes to Host Infectivity of Cryptosporidium parvum ]]> https://biorxiv.org/content/10.1101/2024.02.04.578776v1?rss=1 Li, M. Yang, F. Hou, T. Gong, X. Li, N. Sibley, L. D. Feng, Y. Xiao, L. Guo, Y. 2024-02-04 doi:10.1101/2024.02.04.578776 Cold Spring Harbor Laboratory Press 2024-02-04 <![CDATA[ Mapping changes in uterine contractility during the ovulatory cycle with wide-area calcium imaging in live mice. ]]> https://biorxiv.org/content/10.1101/2024.02.02.578395v1?rss=1 Combs, D. J. Moult, E. M. England, S. K. Cohen, A. E. 2024-02-05 doi:10.1101/2024.02.02.578395 Cold Spring Harbor Laboratory Press 2024-02-05 <![CDATA[ The Vps13-like protein BLTP2 is pro-survival and regulates phosphatidylethanolamine levels in the plasma membrane to maintain its fluidity and function ]]> https://biorxiv.org/content/10.1101/2024.02.04.578804v1?rss=1 Banerjee, S. Daetwyler, S. Bai, X. Michaud, M. Jouhet, J. Madhugiri, S. Johnson, E. Wang, C.-W. Fiolka, R. Toulmay, A. Prinz, W. A. 2024-02-05 doi:10.1101/2024.02.04.578804 Cold Spring Harbor Laboratory Press 2024-02-05 <![CDATA[ ABCC10 roles in plant development and the transport of indole-3-butyric acid ]]> https://biorxiv.org/content/10.1101/2024.02.07.579300v1?rss=1 Homayouni, A. Damodaran, S. Schreiber, K. Michniewicz, M. Gunther, L. Strader, L. C. 2024-02-09 doi:10.1101/2024.02.07.579300 Cold Spring Harbor Laboratory Press 2024-02-09 <![CDATA[ Label free, capillary-scale blood flow mapping in vivo reveals that low intensity focused ultrasound evokes persistent dilation in cortical microvasculature ]]> https://biorxiv.org/content/10.1101/2024.02.08.579513v1?rss=1 Shen, Y. Jethe, J. V. Hehir, J. Amaral, M. M. Ren, C. Hao, S. Zhou, C. Fisher, J. A. N. 2024-02-09 doi:10.1101/2024.02.08.579513 Cold Spring Harbor Laboratory Press 2024-02-09 <![CDATA[ Efficacy of Host Cell Serine Protease Inhibitor MM3122 against SARS-CoV-2 for Treatment and Prevention of COVID-19 ]]> https://biorxiv.org/content/10.1101/2024.02.09.579701v1?rss=1 Boon, A. C. Bricker, T. L. Fritch, E. J. Leist, S. R. Gully, K. L. Baric, R. S. Graham, R. Troan, B. V. Mahoney, M. Janetka, J. W. 2024-02-12 doi:10.1101/2024.02.09.579701 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ Identification Drug Targets for Oxaliplatin-Induced Cardiotoxicity without affecting cancer treatment through Inter Variability Cross-Correlation Analysis (IVCCA) ]]> https://biorxiv.org/content/10.1101/2024.02.11.579390v1?rss=1 Du, J. Sudlow, L. C. Biswas, H. Mitchell, J. D. Mollah, S. Berezin, M. Y. 2024-02-12 doi:10.1101/2024.02.11.579390 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ How to validate a Bayesian evolutionary model ]]> https://biorxiv.org/content/10.1101/2024.02.11.579856v1?rss=1 Mendes, F. K. Bouckaert, R. Carvalho, L. M. Drummond, A. J. 2024-02-12 doi:10.1101/2024.02.11.579856 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ Immuno-Scanning Electron Microscopy of Islet Primary Cilia ]]> https://biorxiv.org/content/10.1101/2024.02.16.580695v1?rss=1 Sviben, S. Polino, A. J. Melena, I. Hughes, J. W. 2024-02-16 doi:10.1101/2024.02.16.580695 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ Ultrastructure expansion microscopy (U-ExM) of mouse and human kidneys for analysis of subcellular structures ]]> https://biorxiv.org/content/10.1101/2024.02.16.580708v1?rss=1 Langner, E. Puapatanakul, P. Pudlowski, R. Alsabbagh, D. Y. Miner, J. Horani, A. Dutcher, S. K. Brody, S. L. Wang, J. Suleiman, H. Y. Mahjoub, M. R. 2024-02-17 doi:10.1101/2024.02.16.580708 Cold Spring Harbor Laboratory Press 2024-02-17 <![CDATA[ MRI economics: Balancing sample size and scan duration in brain wide association studies ]]> https://biorxiv.org/content/10.1101/2024.02.16.580448v1?rss=1 Ooi, L. Q. R. Orban, C. Nichols, T. Zhang, S. Tan, T. W. K. Kong, R. Marek, S. Dosenbach, N. U. F. Laumann, T. O. Gordon, E. M. Zhou, J. H. Bzdok, D. Eickhoff, S. B. Holmes, A. J. Yeo, B. T. T. 2024-02-18 doi:10.1101/2024.02.16.580448 Cold Spring Harbor Laboratory Press 2024-02-18 <![CDATA[ Mice lacking Astn2 have ASD-like behaviors and altered cerebellar circuit properties ]]> https://biorxiv.org/content/10.1101/2024.02.18.580354v1?rss=1 Hanzel, M. Fernando, K. Maloney, S. E. Gong, S. Mätlik, K. Zhao, J. Pasolli, H. A. Heissel, S. Dougherty, J. D. Hull, C. Hatten, M. E. 2024-02-18 doi:10.1101/2024.02.18.580354 Cold Spring Harbor Laboratory Press 2024-02-18 <![CDATA[ Inhibition of Soluble Epoxide Hydrolase Reduces Inflammation and Myocardial Injury in Arrhythmogenic Cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2024.02.17.580812v1?rss=1 Panigrahy, D. Kelly, A. Wang, W. Yang, J. Hwang, S. H. Gillespie, M. Howard, I. Bueno-Beti, C. Asimaki, A. Penna, V. Lavine, K. Edin, M. Zeldin, D. Hammock, B. Saffitz, J. 2024-02-19 doi:10.1101/2024.02.17.580812 Cold Spring Harbor Laboratory Press 2024-02-19 <![CDATA[ Female mice lacking GluA3 show early onset of hearing loss, synaptopathy, and afferent swellings in ambient sound levels ]]> https://biorxiv.org/content/10.1101/2024.02.21.581467v1?rss=1 Pal, I. Bhattacharyya, A. V-Ghaffari, B. Williams, E. D. Xiao, M. Rutherford, M. A. Rubio, M. E. 2024-02-22 doi:10.1101/2024.02.21.581467 Cold Spring Harbor Laboratory Press 2024-02-22 <![CDATA[ Superoxide enters neurons via LRRC8A-containing volume-regulated anion channels ]]> https://biorxiv.org/content/10.1101/2024.02.20.580732v1?rss=1 Harris, K. Uruk, G. Won, S. J. Mai, N. Baxter, P. Everaerts, K. Sah, R. Swanson, R. A. 2024-02-23 doi:10.1101/2024.02.20.580732 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Age-related dysregulation of the retinal transcriptome in African turquoise killifish ]]> https://biorxiv.org/content/10.1101/2024.02.21.581372v1?rss=1 Bergmans, S. Noel, N. C. Masin, L. Harding, E. G. Krzywanska, A. M. De Schutter, J. D. Ayana, R. Hu, C.-K. Arckens, L. Ruzycki, P. A. Clark, B. S. MacDonald, R. B. Moons, L. 2024-02-23 doi:10.1101/2024.02.21.581372 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Rational protein engineering to enhance MHC-independent T cell receptors ]]> https://biorxiv.org/content/10.1101/2024.02.22.581571v1?rss=1 Chang, J. Landmann, J. H. Chang, T.-C. Tenzin, Y. Warrington, J. M. Selli, M. E. Ritchey, J. Hsu, Y.-S. Slade, M. Gupta, D. K. DiPersio, J. F. Singh, N. 2024-02-23 doi:10.1101/2024.02.22.581571 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Interferons and tuft cell numbers are bottlenecks for persistent murine norovirus infection ]]> https://biorxiv.org/content/10.1101/2024.02.22.581634v1?rss=1 Aggarwal, S. Walker, F. C. Weagley, J. S. McCune, B. T. Wu, X. Schreifer, L. Makimaa, H. Lawrence, D. Sridhar, P. Baldridge, M. T. 2024-02-23 doi:10.1101/2024.02.22.581634 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Sterile kidney tissue injury induces neutrophil swarming in lung alveolar capillaries ]]> https://biorxiv.org/content/10.1101/2024.02.27.582396v1?rss=1 Komaru, Y. Ning, L. Lama, C. Suresh, A. Kefaloyianni, E. Miller, M. J. Herrlich, A. 2024-03-02 doi:10.1101/2024.02.27.582396 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ Disordered proteins interact with the chemical environment to tune their protective function during drying ]]> https://biorxiv.org/content/10.1101/2024.02.28.582506v1?rss=1 KC, S. Nguyen, K. H. Nicholson, V. Walgren, A. Trent, T. Gollub, E. Ramero, S. Holehouse, A. S. Sukenik, S. Boothby, T. C. 2024-03-02 doi:10.1101/2024.02.28.582506 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ Analysis of Infiltrating Immune Cells Following Intervertebral Disc Injury Reveals Recruitment of Gamma-Delta (????) T cells in Female Mice ]]> https://biorxiv.org/content/10.1101/2024.03.01.582950v1?rss=1 View larger version (17K): org.highwire.dtl.DTLVardef@90ba37org.highwire.dtl.DTLVardef@1b17f87org.highwire.dtl.DTLVardef@2baa2corg.highwire.dtl.DTLVardef@b155c5_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO Schematic of the workflow to obtain longitudinal analyses of the acute IVD injury response Injured caudal IVDs, CC5/6-CC9/10, were bilaterally punctured with a 30G needle to induce a traumatic injury. Injured IVDs and neighboring uninjured internal Control IVDs, CC12/13-CC16/17, were isolated during the acute injury response every 2-3 days until 21 days post injury (dpi) and a chronic injury time point at 42 dpi in female mice. Male mice samples were only collected at key injury response time points (red numbers): 3, 7, 12, 19, and 42 dpi. Longitudinal analyses of the temporal regulation of immune cell gene expression and cell infiltration were measured with qPCR, flow cytometry, immune fluorescence, and histology analyses to identify a sex-divergent immune response. C_FIG ]]> Clayton, S. W. Walk, R. E. Mpofu, L. Easson, G. W. Tang, S. Y. 2024-03-02 doi:10.1101/2024.03.01.582950 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ A unique subset of pericystic endothelium associates with aberrant microvascular remodelling and impaired blood perfusion early in polycystic kidney disease ]]> https://biorxiv.org/content/10.1101/2024.03.03.583132v1?rss=1 Jafree, D. J. Perera, C. Ball, M. Tolomeo, D. Pomeranz, G. Wilson, L. Davis, B. Mason, W. J. Funk, E. M. Kolatsi-Joannou, M. Polschi, R. Malik, S. Stewart, B. J. Price, K. L. Mitchell, H. Motallebzadeh, R. Muto, Y. Lees, R. Needham, S. R. Moulding, D. Chandler, J. C. Walsh, C. L. Woolf, A. S. Winyard, P. J. Scambler, P. J. Hagerling, R. Clatworthy, M. R. Humphreys, B. Lythgoe, M. F. Walker-Samuel, S. Long, D. A. 2024-03-06 doi:10.1101/2024.03.03.583132 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ The sodium-proton exchangers sNHE and NHE1 control plasma membrane hyperpolarization in mouse sperm. ]]> https://biorxiv.org/content/10.1101/2024.03.04.583310v1?rss=1 Novero, A. G. Rodriguez, P. T. de la Vega Beltran, J. L. Schiavi-Ehrenhaus, L. J. Luque, G. M. Carruba, M. Stival, C. Gentile, I. Ritagliati, C. Santi, C. M. Nishigaki, T. Krapf, D. Buffone, M. G. Darszon, A. Trevino, C. L. Krapf, D. 2024-03-06 doi:10.1101/2024.03.04.583310 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Local adaptation of a fungal pathogen to temperature along a latitudinal gradient ]]> https://biorxiv.org/content/10.1101/2024.03.04.583296v1?rss=1 Fox, Q. N. Goodson, C. Penczykowski, R. M. 2024-03-08 doi:10.1101/2024.03.04.583296 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ DeST-OT: Alignment of Spatiotemporal Transcriptomics Data ]]> https://biorxiv.org/content/10.1101/2024.03.05.583575v1?rss=1 Halmos, P. Liu, X. Gold, J. Chen, F. Ding, L. Raphael, B. 2024-03-10 doi:10.1101/2024.03.05.583575 Cold Spring Harbor Laboratory Press 2024-03-10 <![CDATA[ TREM1 disrupts myeloid bioenergetics and cognitive function in aging and Alzheimer disease models ]]> https://biorxiv.org/content/10.1101/2024.03.05.583562v1?rss=1 Andreasson, K. I. Wilson, E. N. Wang, C. Xin, M. Panchal, M. Rabinowitz, J. D. Minhas, P. S. Swarovski, M. S. Benitez, J. A. R. Durairaj, A. S. Chaney, A. Iweka, C. A. Buckwalter, M. S. Ennerfelt, H. E. Umans, J. Huang, J. Zera, K. A. McReynolds, M. R. Greicius, M. D. James, M. L. Mehta, S. S. Le Guen, Y. Tan, Y. J. Zuckerman, A. J. Blacher, E. Gauba, E. Serrano, G. E. Cropper, H. Jain, P. Liu, Q. 2024-03-11 doi:10.1101/2024.03.05.583562 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics ]]> https://biorxiv.org/content/10.1101/2024.03.09.584244v1?rss=1 Ma, C. Balaban, M. Liu, J. Chen, S. Ding, L. Raphael, B. 2024-03-13 doi:10.1101/2024.03.09.584244 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models ]]> https://biorxiv.org/content/10.1101/2024.03.12.584677v1?rss=1 Zheng, Y. Stormo, G. D. Chen, S. 2024-03-14 doi:10.1101/2024.03.12.584677 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Early-life stress alters chromatin modifications in VTA to prime stress sensitivity ]]> https://biorxiv.org/content/10.1101/2024.03.14.584631v1?rss=1 Geiger, L. T. Balouek, J.-A. R. Farrelly, L. A. Chen, A. S. Tang, M. Bennett, S. N. Nestler, E. J. Garcia, B. A. Maze, I. Pena, C. J. 2024-03-14 doi:10.1101/2024.03.14.584631 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ YTHDC1 cooperates with the THO complex to prevent RNA damage-induced DNA breaks ]]> https://biorxiv.org/content/10.1101/2024.03.14.585107v1?rss=1 90%) formed due to these chemicals, such as alkylating agents, occur in RNA1. However, compared to the well-studied mechanisms for DNA alkylation repair, the biological consequences of RNA damage are largely unexplored. Here, we demonstrate that RNA damage can directly result in loss of genome integrity. Specifically, we show that a human YTH domain-containing protein, YTHDC1, regulates alkylation damage responses in association with the THO complex (THOC)2. In addition to its established binding to N6-methyladenosine (m6A)-containing RNAs, YTHDC1 binds to N1-methyladenosine (m1A)-containing RNAs upon alkylation. In the absence of YTHDC1, alkylation damage results in increased alkylation damage sensitivity and DNA breaks. Such phenotypes are fully attributable to RNA damage, since an RNA-specific dealkylase can rescue these phenotypes. These RNA damage-induced DNA breaks (RDIBs) depend on R-loop formation, which in turn are processed by factors involved in transcription-coupled nucleotide excision repair. Strikingly, in the absence of YTHDC1 or THOC, an RNA m1A methyltransferase targeted to the nucleus is sufficient to induce DNA breaks. Our results uncover a unique role for YTHDC1-THOC in base damage responses by preventing RDIBs, providing definitive evidence for how damaged RNAs can impact genomic integrity. ]]> Tsao, N. Olabode, J. Rodell, R. Sun, H. Brickner, J. R. Tsai, M.-S. Pollina, E. A. Chen, C.-K. Mosammaparast, N. 2024-03-14 doi:10.1101/2024.03.14.585107 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ CD40 is an immune checkpoint regulator that potentiates myocardial inflammation through activation and expansion of CCR2+ macrophages and CD8 T-cells ]]> https://biorxiv.org/content/10.1101/2024.03.14.584418v1?rss=1 Jimenez, J. Amrute, J. Ma, P. Wang, X. Dai, R. Lavine, K. 2024-03-16 doi:10.1101/2024.03.14.584418 Cold Spring Harbor Laboratory Press 2024-03-16 <![CDATA[ Sexual dimorphism and allometry in human scapular morphology ]]> https://biorxiv.org/content/10.1101/2024.03.18.585525v1?rss=1 Lee, E. C. Lawrence, R. L. Rainbow, M. J. 2024-03-20 doi:10.1101/2024.03.18.585525 Cold Spring Harbor Laboratory Press 2024-03-20 <![CDATA[ Reduced STMN2 and pathogenic TDP-43, two hallmarks of ALS, synergize to accelerate motor decline in mice ]]> https://biorxiv.org/content/10.1101/2024.03.19.585052v1?rss=1 Krus, K. Morales Benitez, A. Strickland, A. Milbrandt, J. Bloom, J. DiAntonio, A. 2024-03-20 doi:10.1101/2024.03.19.585052 Cold Spring Harbor Laboratory Press 2024-03-20 <![CDATA[ Mitochondrial pyruvate transport regulates presynaptic metabolism and neurotransmission ]]> https://biorxiv.org/content/10.1101/2024.03.20.586011v1?rss=1 Tiwari, A. Myeong, J. Hashemiaghdam, A. Zhang, H. Niu, X. Laramie, M. Stunault, M. I. sponagel, J. Patti, G. Shriver, L. Klyachko, V. Ashrafi, G. 2024-03-20 doi:10.1101/2024.03.20.586011 Cold Spring Harbor Laboratory Press 2024-03-20 <![CDATA[ Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain ]]> https://biorxiv.org/content/10.1101/2024.03.21.585809v1?rss=1 Shepherdson, J. L. Granas, D. M. Li, J. Shariff, Z. Plassmeyer, S. P. Holehouse, A. S. White, M. A. Cohen, B. A. 2024-03-27 doi:10.1101/2024.03.21.585809 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Single cell resolution analysis of multi-tissue derived human iNKT cells reveals novel transcriptional paradigms ]]> https://biorxiv.org/content/10.1101/2024.03.22.583992v1?rss=1 Jayasinghe, R. G. Hollingsworth, D. Boonchalermvichian, C. Gupta, B. Yan, H. Baker, J. Dejene, B. Weinberg, K. I. Negrin, R. S. Mavers, M. 2024-03-27 doi:10.1101/2024.03.22.583992 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Does Vibrotactile Stimulation of the Auricular Vagus Nerve Enhance Working Memory? A Behavioral and Physiological Investigation ]]> https://biorxiv.org/content/10.1101/2024.03.24.586365v1?rss=1 Tan, G. Adams, J. Donovan, K. Demarest, P. Willie, J. T. Brunner, P. Leuthardt, E. 2024-03-27 doi:10.1101/2024.03.24.586365 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Single-Molecule Orientation Imaging Reveals the Nano-Architecture of Amyloid Fibrils Undergoing Growth and Decay ]]> https://biorxiv.org/content/10.1101/2024.03.24.586510v1?rss=1 Sun, B. Ding, T. Zhou, W. Porter, T. S. Lew, M. D. 2024-03-27 doi:10.1101/2024.03.24.586510 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Higher amplitudes of visual networks are associated with trait but not state- depression. ]]> https://biorxiv.org/content/10.1101/2024.03.25.584801v1?rss=1 Zhang, W. Dutt, R. Lew, D. Barch, D. M. Bijsterbosch, J. D. 2024-03-27 doi:10.1101/2024.03.25.584801 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ A role for δ subunit-containing GABA-A receptors on parvalbumin positive neurons in maintaining electrocortical signatures of sleep states ]]> https://biorxiv.org/content/10.1101/2024.03.25.586604v1?rss=1 Lambert, P. M. Salvatore, S. V. Lu, X. Shu, H.-J. Benz, A. Rensing, N. Yuede, C. Wong, M. Zorumski, C. F. Mennerick, S. 2024-03-29 doi:10.1101/2024.03.25.586604 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Associations between parenting and cognitive and language abilities at age 2 depend on prenatal exposure to disadvantage ]]> https://biorxiv.org/content/10.1101/2024.03.25.586610v1?rss=1 Leverett, S. D. Brady, R. G. Tooley, U. A. Lean, R. E. Tillman, R. Wilson, J. Ruscitti, M. Triplett, R. L. alexopoulos, D. Gerstein, E. D. Smyser, T. A. Warner, B. Luby, J. D. Smyser, C. D. Rogers, C. E. Barch, D. M. 2024-03-29 doi:10.1101/2024.03.25.586610 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Emergent predictability in microbial ecosystems ]]> https://biorxiv.org/content/10.1101/2024.03.26.586882v1?rss=1 Moran, J. Tikhonov, M. 2024-03-29 doi:10.1101/2024.03.26.586882 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Wrapping of single-stranded DNA by Replication Protein A and modulation through phosphorylation ]]> https://biorxiv.org/content/10.1101/2024.03.28.587234v1?rss=1 Chadda, R. Kaushik, V. Ahmad, I. M. Deveryshetty, J. Holehouse, A. S. Sigurdsson, S. T. d. Bothner, B. Dastvan, R. Origanti, S. S. Antony, E. 2024-03-29 doi:10.1101/2024.03.28.587234 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Energy-ordered resource stratification as an agnostic signature of life ]]> https://biorxiv.org/content/10.1101/2024.03.27.586986v1?rss=1 Goyal, A. Tikhonov, M. 2024-03-30 doi:10.1101/2024.03.27.586986 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Human chorionic gonadotropin decreases cerebral cystic encephalomalacia and parvalbumin interneuron degeneration in a pro-inflammatory model of mouse neonatal hypoxia-ischemia. ]]> https://biorxiv.org/content/10.1101/2024.03.27.587006v1?rss=1 Galindo, R. Aravamuthan, B. R. Miller, B. Crider, A. 2024-03-30 doi:10.1101/2024.03.27.587006 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ GABAergic interneurons contribute to the fatal seizure phenotype of CLN2 disease mice ]]> https://biorxiv.org/content/10.1101/2024.03.29.587276v1?rss=1 Takahashi, K. Rensing, N. R. Eultgen, E. M. Wang, S. H. Nelvagal, H. R. Le, S. Q. Roberts, M. S. Doray, B. Han, E. Dickson, P. Wong, M. Sands, M. S. Cooper, J. D. 2024-03-30 doi:10.1101/2024.03.29.587276 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function ]]> https://biorxiv.org/content/10.1101/2024.03.29.587306v1?rss=1 Zhan, J. Belanger, S. Lewis, S. Teng, C. McGregor, M. Beric, A. Schon, M. A. Nodine, M. D. Meyers, B. C. 2024-04-01 doi:10.1101/2024.03.29.587306 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ Regulation of angiogenesis by endocytic trafficking mediated by cytoplasmic dynein 1 light intermediate chain 1 ]]> https://biorxiv.org/content/10.1101/2024.04.01.587559v1?rss=1 Johnson, D. Colijn, S. Richee, J. Yano, J. Burns, M. Davis, A. E. Pham, V. N. Saric, A. Jain, A. Yin, Y. Castranova, D. Melani, M. Fujita, M. Grainger, S. Bonifacino, J. S. Weinstein, B. M. Stratman, A. N. 2024-04-01 doi:10.1101/2024.04.01.587559 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ Genetic editing of primary human dorsal root ganglion neurons using CRISPR-Cas9 with functional confirmation ]]> https://biorxiv.org/content/10.1101/2024.04.02.587857v1?rss=1 Palomino, S. M. Gabriel, K. Mwirigi, J. Cervantes, A. Horton, P. Funk, G. Moutal, A. Martin, L. Khanna, R. Price, T. J. Patwardhan, A. 2024-04-03 doi:10.1101/2024.04.02.587857 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Ipsilateral or contralateral boosting of mice with mRNA vaccines confers equivalent immunity and protection against a SARS-CoV-2 Omicron strain ]]> https://biorxiv.org/content/10.1101/2024.04.05.588051v1?rss=1 Ying, B. Liang, C.-Y. Desai, P. Scheaffer, S. Elbashir, S. Edwards, D. K. Thackray, L. B. Diamond, M. S. 2024-04-07 doi:10.1101/2024.04.05.588051 Cold Spring Harbor Laboratory Press 2024-04-07 <![CDATA[ Single-cell image-based genetic screens systematically identify regulators of Ebola virus subcellular infection dynamics ]]> https://biorxiv.org/content/10.1101/2024.04.06.588168v1?rss=1 Carlson, R. J. Patten, J. J. Stefanakis, G. Soong, B. Y. Radhakrishnan, A. Singh, A. Thakur, N. Amarasinghe, G. K. Hacohen, N. Basler, C. F. Leung, D. Uhler, C. Davey, R. A. Blainey, P. C. 2024-04-07 doi:10.1101/2024.04.06.588168 Cold Spring Harbor Laboratory Press 2024-04-07 <![CDATA[ Microglia drive diurnal variation in susceptibility to inflammatory blood-brain barrier breakdown ]]> https://biorxiv.org/content/10.1101/2024.04.10.588924v1?rss=1 Lawrence, J. H. Patel, A. King, M. W. Nadarajah, C. J. Daneman, R. Musiek, E. S. 2024-04-14 doi:10.1101/2024.04.10.588924 Cold Spring Harbor Laboratory Press 2024-04-14 <![CDATA[ A single-nucleus RNA sequencing atlas of the postnatal retina of the shark Scyliorhinus canicula ]]> https://biorxiv.org/content/10.1101/2024.04.12.589211v1?rss=1 Vidal-Vazquez, N. Hernandez-Nunez, I. Carballo-Pacoret, P. Salisbury, S. Villamayor, P. R. Hervas-Sotomayor, F. Yuan, X. Lamanna, F. Schneider, C. Mazan, S. Kaessmann, H. Adrio, F. Robledo, D. Barreiro-Iglesias, A. Candal, E. 2024-04-15 doi:10.1101/2024.04.12.589211 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ Opaque Ontology: Neuroimaging Classification of ICD-10 Diagnostic Groups in the UK Biobank ]]> https://biorxiv.org/content/10.1101/2024.04.15.589555v1?rss=1 Easley, T. Luo, X. Hannon, K. Lenzini, P. Bijsterbosch, J. D. 2024-04-19 doi:10.1101/2024.04.15.589555 Cold Spring Harbor Laboratory Press 2024-04-19 <![CDATA[ A delta-tubulin/epsilon-tubulin/Ted protein complex is required for centriole architecture ]]> https://biorxiv.org/content/10.1101/2024.04.19.590208v1?rss=1 Pudlowski, R. Xu, L. Milenkovic, L. Hemsworth, K. Stearns, T. Wang, J. T. 2024-04-20 doi:10.1101/2024.04.19.590208 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Transcriptional Variabilities in Human hiPSC-derived Cardiomyocytes: All Genes Are Not Equal and Their Robustness May Foretell Donor's Disease Susceptibility ]]> https://biorxiv.org/content/10.1101/2024.04.18.584138v1?rss=1 Gu, C. C. Matter, A. Turner, A. Aggarwal, P. Yang, W. Sun, X. Hunt, S. C. Lewis, C. E. Arnett, D. K. Anson, B. Kattman, S. Broeckel, U. 2024-04-21 doi:10.1101/2024.04.18.584138 Cold Spring Harbor Laboratory Press 2024-04-21 <![CDATA[ RAG suppresses group 2 innate lymphoid cells ]]> https://biorxiv.org/content/10.1101/2024.04.23.590767v1?rss=1 Ver Heul, A. Mack, M. Zamidar, L. Tamari, M. Yang, T.-L. Trier, A. Kim, D.-H. Janzen-Meza, H. Van Dyken, S. Hsieh, C.-S. Karo, J. M. Sun, J. Kim, B. S. 2024-04-28 doi:10.1101/2024.04.23.590767 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Pervasive but lagged responses in the composition of small mammal communities to a century of climate change ]]> https://biorxiv.org/content/10.1101/2024.04.24.590797v1?rss=1 Abercrombie, E. R. Myers, J. A. Smith, A. B. 2024-04-28 doi:10.1101/2024.04.24.590797 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons ]]> https://biorxiv.org/content/10.1101/2024.04.24.590975v1?rss=1 Yang, L. Liu, F. Hahm, H. Okuda, T. Li, X. Zhang, Y. Kalyanaraman, V. Heitmeier, M. R. Samineni, V. K. 2024-04-28 doi:10.1101/2024.04.24.590975 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Complementary benefits of multivariate and hierarchical models for identifying individual differences in cognitive control ]]> https://biorxiv.org/content/10.1101/2024.04.24.591032v1?rss=1 Freund, M. C. Chen, R. Chen, G. Braver, T. S. 2024-04-28 doi:10.1101/2024.04.24.591032 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Perturbation-Specific Transcriptional Mapping facilitates unbiased target elucidation of antibiotics ]]> https://biorxiv.org/content/10.1101/2024.04.25.590978v1?rss=1 Romano, K. P. Bagnall, J. Warrier, T. Sullivan, J. Ferrara, K. Orzechowski, M. Nguyen, P. Raines, K. Livny, J. Shoresh, N. Hung, D. 2024-04-28 doi:10.1101/2024.04.25.590978 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Measuring single-cell density with high throughput enables dynamic profiling of immune cell and drug response from patient samples ]]> https://biorxiv.org/content/10.1101/2024.04.25.591092v1?rss=1 Wu, W. Ishamuddin, S. H. Quinn, T. W. Yerrum, S. Zhang, Y. Debaize, L. L. Kao, P.-L. Duquette, S. M. Murakami, M. A. Mohseni, M. Chow, K.-H. Miettinen, T. P. Ligon, K. L. Manalis, S. R. 2024-04-28 doi:10.1101/2024.04.25.591092 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Epithelial IL-2 is critical for NK cell-mediated cancer immunosurveillance in mammary glands ]]> https://biorxiv.org/content/10.1101/2024.04.25.591178v1?rss=1 Wang, L. Maharjan, C. Borcherding, N. Master, R. P. Mo, j. Tithi, T. I. Carelock, M. Master, A. Gibson-Corley, K. Kolb, R. H. Smith, K. A. Zhang, W. 2024-04-28 doi:10.1101/2024.04.25.591178 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Rapid adaptive evolution of microbial thermal performance curves ]]> https://biorxiv.org/content/10.1101/2024.04.30.590804v1?rss=1 Liu, M. H. Han, Z.-Y. Yuan, Y. DeWitt, K. Wieczynski, D. J. Yammine, K. M. Yammine, A. Zufall, R. Siepielski, A. Chalker, D. Onishi, M. Machado, F. A. Gibert, J. P. 2024-05-03 doi:10.1101/2024.04.30.590804 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Single-Cell Transcriptomic Analysis of Kaposi Sarcoma ]]> https://biorxiv.org/content/10.1101/2024.05.01.592010v1?rss=1 Rauch, D. A. Valino Ramos, P. Khanfar, M. Harding, J. Joseph, A. Griffith, O. Griffith, M. Ratner, L. 2024-05-03 doi:10.1101/2024.05.01.592010 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Differential effects of PDE4A5 on cAMP-dependent forms of long-term potentiation ]]> https://biorxiv.org/content/10.1101/2024.05.04.592525v1?rss=1 View larger version (53K): org.highwire.dtl.DTLVardef@1ee4ccdorg.highwire.dtl.DTLVardef@1f43c3corg.highwire.dtl.DTLVardef@19eb64dorg.highwire.dtl.DTLVardef@d2bab0_HPS_FORMAT_FIGEXP M_FIG GRAPHICAL ABSTRACT Spaced tetanic stimulation and TBS induce cAMP synthesis and activation of PKA to promote signaling cascades that facilitate expression of long-lasting LTP at the CA3-CA1 synapses. PDE4A5 overexpression in the hippocampus selectively impairs cAMP and PKA dependent TBS-LTP at the CA3-CA1 synapses, while sparing LTP induced by spaced tetanization. C_FIG ]]> Tadinada, S. M. Mukherjee, U. Walsh, E. N. Abel, T. 2024-05-07 doi:10.1101/2024.05.04.592525 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ Mechanism, and treatment of anti-CV2/CRMP5 autoimmune pain ]]> https://biorxiv.org/content/10.1101/2024.05.04.592533v1?rss=1 Martin, L. Stratton, H. J. Gomez, K. Do, L. Loya-lopez, S. Tang, C. Calderon-rivera, A. Ran, D. Nunn, V. Bellampalli, S. S. Francois-Moutal, L. Dumaire, N. L. A. Salih, L. Luo, S. Porreca, F. Ibrahim, M. Rogemond, V. Honnorat, J. Khanna, R. Moutal, A. 2024-05-07 doi:10.1101/2024.05.04.592533 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ Oncogenic KRAS Mutations Confer a Unique Mechanotransduction Response to Peristalsis in Colorectal Cancer Cells ]]> https://biorxiv.org/content/10.1101/2024.05.07.593070v1?rss=1 Clevenger, A. J. Collier, C. A. Gorley, J. P. M. McFarlin, M. K. Solberg, S. C. Kopetz, S. Stratman, A. N. Raghavan, S. 2024-05-08 doi:10.1101/2024.05.07.593070 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Repeat modules and N-linked glycans define structure and antigenicity of a critical enterotoxigenic E. coli adhesin ]]> https://biorxiv.org/content/10.1101/2024.05.08.593125v1?rss=1 Berndsen, Z. T. Akhtar, M. Thapa, M. Vickers, T. J. Schmitz, A. Torres, J. Kumar, P. Khatoon, N. Sheikh, A. Hamrick, M. Diedrich, J. Martinez-Bartolome, S. Garrett, P. Yates, J. Turner, J. Laird, R. M. Porter, C. K. Poly, F. Copps, J. Ellebedy, A. Ward, A. Fleckenstein, J. M. 2024-05-08 doi:10.1101/2024.05.08.593125 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Mechanical Properties of White Matter Tracts in Aging Assessed via Anisotropic MR Elastography ]]> https://biorxiv.org/content/10.1101/2024.05.08.593260v1?rss=1 Caban-Rivera, D. A. Williams, L. T. McGarry, M. D. J. Smith, D. R. Van Houten, E. E. W. Paulsen, K. D. Bayly, P. V. Johnson, C. L. 2024-05-09 doi:10.1101/2024.05.08.593260 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ Cross-species analyses reveal RORγt-expressing dendritic cells are a lineage of antigen presenting cells conserved across tissues ]]> https://biorxiv.org/content/10.1101/2024.05.06.592772v1?rss=1 Narasimhan, H. Richter, M. L. Shakiba, R. Papaioannou, N. E. Stehle, C. Ravi Rengarajan, K. Ulmert, I. Küntzel, V. Stange, E.-L. Antonova, A. U. Klein, L. Dudziak, D. Colonna, M. Torow, N. Hornef, M. W. Lahl, K. Romagnani, C. Colome-Tatche, M. Schraml, B. U. 2024-05-10 doi:10.1101/2024.05.06.592772 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Genetically recoding respiratory syncytial virus to visualize nucleoprotein dynamics and virion assembly ]]> https://biorxiv.org/content/10.1101/2024.05.12.593692v1?rss=1 Mitrovich, M. D. Vahey, M. D. 2024-05-12 doi:10.1101/2024.05.12.593692 Cold Spring Harbor Laboratory Press 2024-05-12 <![CDATA[ Non-selected incompatibilities and their effects on aggregative multicellularity in the social amoeba Dictyostelium discoideum ]]> https://biorxiv.org/content/10.1101/2024.05.12.593719v1?rss=1 Jahan, I. Scott, T. J. Strassmann, J. E. Queller, D. C. 2024-05-14 doi:10.1101/2024.05.12.593719 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Spatial histomorphometry reveals that local peripheral nerves modulate but are not required for skeletal adaptation to applied load in mice ]]> https://biorxiv.org/content/10.1101/2024.05.12.593761v1?rss=1 Beeve, A. T. Hassan, M. G. Li, A. Migotsky, N. Silva, M. J. Scheller, E. L. 2024-05-14 doi:10.1101/2024.05.12.593761 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Reconstitution of Arp2/3-Nucleated Actin Assembly with CP, V-1 and CARMIL ]]> https://biorxiv.org/content/10.1101/2024.05.13.593916v1?rss=1 Mooren, O. L. McConnell, P. DeBrecht, J. D. Jaysingh, A. Cooper, J. A. 2024-05-14 doi:10.1101/2024.05.13.593916 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ PDGF-BB overexpression in p53 null oligodendrocyte progenitors increases H3K27me3 and induces transcriptional changes which favor proliferation ]]> https://biorxiv.org/content/10.1101/2024.05.14.594214v1?rss=1 Huang, D. Mela, A. Natarajan, B. V. Garcia, B. Canoll, P. Casaccia, P. 2024-05-14 doi:10.1101/2024.05.14.594214 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ mosGraphGen: a novel tool to generate multi-omic signaling graphs to facilitate integrative and interpretable graph AI model development ]]> https://biorxiv.org/content/10.1101/2024.05.15.594360v1?rss=1 Zhang, H. Cao, D. Chen, Z. Zhang, Z. Chen, Y. Sessions, C. Cruchaga, C. Payne, P. R. Li, G. Province, M. Li, F. 2024-05-18 doi:10.1101/2024.05.15.594360 Cold Spring Harbor Laboratory Press 2024-05-18 <![CDATA[ Diclofenac sensitizes multi-drug resistant Acinetobacter baumannii to colistin ]]> https://biorxiv.org/content/10.1101/2024.05.17.594771v1?rss=1 Bisaro, F. Jackson-Litteken, C. D. McGuffey, J. C. Hooppaw, A. J. Bodrog, S. Jebeli, L. Ortiz-Marquez, J. C. van Opijnen, T. Scott, N. Di Venanzio, G. Feldman, M. 2024-05-18 doi:10.1101/2024.05.17.594771 Cold Spring Harbor Laboratory Press 2024-05-18 <![CDATA[ Kif1a and intact microtubules maintain synaptic-vesicle populations at ribbon synapses in zebrafish hair cells ]]> https://biorxiv.org/content/10.1101/2024.05.20.595037v1?rss=1 David, S. Pinter, K. Nguyen, K.-K. Lee, D. S. Lei, Z. Sokolova, Y. Sheets, L. Kindt, K. S. 2024-05-20 doi:10.1101/2024.05.20.595037 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ A Novel Gene ARHGAP44 for Longitudinal Changes in Glycated Hemoglobin (HbA1c) in Subjects without Type 2 Diabetes: Evidence from the Long Life Family Study (LLFS) and the Framingham Offspring Study (FOS) ]]> https://biorxiv.org/content/10.1101/2024.05.16.594575v1?rss=1 Wang, S. Lenzini, P. Thygarajan, B. Lee, J. H. Vardarajan, B. N. Yashin, A. Miljkovic, I. Daw, E. W. Lin, S. J. Patti, G. Brent, M. Zmuda, J. M. Perls, T. T. Christensen, K. Province, M. A. An, P. 2024-05-21 doi:10.1101/2024.05.16.594575 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Spatial omics of acute myocardial infarction reveals a novel mode of immune cell infiltration ]]> https://biorxiv.org/content/10.1101/2024.05.20.594955v1?rss=1 Wuennemann, F. Sicklinger, F. Bestak, K. Nimo, J. Thiemann, T. Amrute, J. M. Nordbeck, M. Hartmann, N. Ibarra-Arellano, M. A. Tanevski, J. Heine, C. Frey, N. Lavine, K. Coscia, F. Saez-Rodriguez, J. Leuschner, F. Schapiro, D. 2024-05-21 doi:10.1101/2024.05.20.594955 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Norepinephrine Signals Through Astrocytes To Modulate Synapses ]]> https://biorxiv.org/content/10.1101/2024.05.21.595135v1?rss=1 Lefton, K. B. Wu, Y. Yen, A. Okuda, T. Zhang, Y. Dai, Y. Walsh, S. Manno, R. Dougherty, J. Samineni, V. K. Simpson, P. C. Papouin, T. 2024-05-22 doi:10.1101/2024.05.21.595135 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ Tau pathology leads to lonely non-traveling slow waves that mediate human memory impairment ]]> https://biorxiv.org/content/10.1101/2024.05.22.595043v1?rss=1 Sharon, O. Chen, X. Dude, J. Shah, V. D. Ju, Y.-E. S. Jagust, W. J. Walker, M. P. 2024-05-22 doi:10.1101/2024.05.22.595043 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ TRPV4-Expressing Tissue-Resident Macrophages Regulate the Function of Collecting Lymphatic Vessels via Thromboxane A2 Receptors in Lymphatic Muscle Cells ]]> https://biorxiv.org/content/10.1101/2024.05.21.595189v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@1ce67fforg.highwire.dtl.DTLVardef@dd1beorg.highwire.dtl.DTLVardef@1454c78org.highwire.dtl.DTLVardef@9f76a1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Schulz, M. E. Akerstrom, V. L. Song, K. Broyhill, S. E. Li, M. Lambert, M. D. Goldberg, T. B. Kataru, R. P. Shin, J. Braun, S. E. Norton, C. E. Czepielewski, R. S. Mehrara, B. J. Domeier, T. L. Zawieja, S. D. Castorena-Gonzalez, J. A. 2024-05-23 doi:10.1101/2024.05.21.595189 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Transcriptomic landscape of mammalian ventral pallidum at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2024.05.24.595793v1?rss=1 Fang, L. Z. Yang, L. Lynch, M. R. Xu, C. S. Hahm, H. Zhang, Y. Heitmeier, M. R. Costa, V. Samineni, V. K. Creed, M. C. 2024-05-26 doi:10.1101/2024.05.24.595793 Cold Spring Harbor Laboratory Press 2024-05-26 <![CDATA[ Complimentary vertebrate Wac models exhibit phenotypes relevant to DeSanto-Shinawi Syndrome ]]> https://biorxiv.org/content/10.1101/2024.05.26.595966v1?rss=1 Lee, K.-H. Stafford, A. M. Pacheco-Vergara, M. Cichewicz, K. Canales, C. P. Seban, N. Corea, M. Rahbarian, D. Bonekamp, K. E. Gillie, G. R. Pacheco-Cruz, D. Gill, A. M. Hwang, H.-E. Uhl, K. Shinawi, M. Li, X. Obenaus, A. Crandall, S. R. Jeong, J. Nord, A. S. Kim, C.-H. Vogt, D. 2024-05-26 doi:10.1101/2024.05.26.595966 Cold Spring Harbor Laboratory Press 2024-05-26 <![CDATA[ Lineage-specific proteome remodeling of diverse lung cancer cells by targeted epigenetic inhibitors ]]> https://biorxiv.org/content/10.1101/2024.05.23.592075v1?rss=1 Lin, C. Sniezek, C. M. Giglio, R. M. Karki, R. McGann, C. D. Garcia, B. A. McFaline-Figueroa, J. L. Schweppe, D. K. 2024-05-28 doi:10.1101/2024.05.23.592075 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ Bispecific GD2 x B7-H3 Antibody Improves Tumor Targeting and Reduces Toxicity while Maintaining Efficacy for Neuroblastoma ]]> https://biorxiv.org/content/10.1101/2024.05.23.595588v1?rss=1 Erbe, A. K. Feils, A. S. Hampton, A. Rosenkrans, Z. T. Felder, M. Wiwczar, J. Gerhardt, D. J. Bercher, M. Wenke, B. Haertle, C. Heck, M. VandenHeuvel, S. N. Frankel, E. Nielsen, M. Spiegelman, D. Tsarovsky, N. Zaborek, J. Rakhmilevich, A. L. Hank, J. A. Aluicio-Sarduy, E. Engle, J. Davis, J. H. Glaser, B. Subbotin, V. Green, R. Hernandez, R. T. Hammer, B. Sondel, P. M. 2024-05-28 doi:10.1101/2024.05.23.595588 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ Role of the CTCF Binding Site in Human T-Cell Leukemia Virus-1 Pathogenesis ]]> https://biorxiv.org/content/10.1101/2024.05.28.596170v1?rss=1 Joseph, A. Cheng, X. Harding, J. Al-Saleem, J. Green, P. Veis, D. Rauch, D. A. Ratner, L. 2024-05-28 doi:10.1101/2024.05.28.596170 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ Chromatin profiling identifies putative dual roles for H3K27me3 in regulating transposons and cell type specific genes in choanoflagellates ]]> https://biorxiv.org/content/10.1101/2024.05.28.596151v1?rss=1 Gahan, J. M. Helfrich, L. W. Wetzel, L. A. Bhanu, N. V. Yuan, Z.-F. Garcia, B. A. Klose, R. Booth, D. S. 2024-05-30 doi:10.1101/2024.05.28.596151 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Multi-omics profiling of mouse polycystic kidney disease progression at a single cell resolution ]]> https://biorxiv.org/content/10.1101/2024.05.27.595830v1?rss=1 Muto, Y. Yoshimura, Y. Wu, H. Chang-Panesso, M. Ledru, N. Woodward, O. M. Outeda, P. Cheng, T. Mahjoub, M. R. Watnick, T. J. Humphreys, B. D. 2024-06-01 doi:10.1101/2024.05.27.595830 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Machine Learning Models for Cardiovascular Disease Prediction: A Comparative Study ]]> https://biorxiv.org/content/10.1101/2024.05.27.596092v1?rss=1 Yan, C. Xing, Y. Liu, S. Gao, E. Wang, J. 2024-06-01 doi:10.1101/2024.05.27.596092 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Fully Human Bifunctional Intrabodies Achieve Graded Reduction of Intracellular Tau and Rescue Survival of MAPT Mutation iPSC-derived Neurons ]]> https://biorxiv.org/content/10.1101/2024.05.28.596248v1?rss=1 D'Brant, L. Rugenstein, N. Na, S. K. Miller, M. J. Czajka, T. F. Trudeau, N. Fitz, E. M. Tomaszek, L. Fisher, E. S. Mash, E. S. Joy, S. Lotz, S. Borden, S. Stevens, K. Goderie, S. Wang, Y. Bertucci, T. Karch, C. M. Temple, S. Butler, D. 2024-06-01 doi:10.1101/2024.05.28.596248 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ A glial circadian gene expression atlas reveals cell type and disease-specific reprogramming in response to amyloid pathology or aging. ]]> https://biorxiv.org/content/10.1101/2024.05.28.596297v1?rss=1 Sheehan, P. W. Fass, S. B. Sapkota, D. Kang, S. Hollis, H. C. Lawrence, J. H. Anafi, R. C. Dougherty, J. D. Fryer, J. D. Musiek, E. S. 2024-06-01 doi:10.1101/2024.05.28.596297 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Targeting complement C3a receptor resolves mitochondrial hyperfusion and subretinal microglial activation in progranulin-deficient frontotemporal dementia ]]> https://biorxiv.org/content/10.1101/2024.05.29.595206v1?rss=1 Tan, L. X. Oertel, F. C. Cheng, A. Cobigo, Y. Keihani, A. Bennett, D. Abdelhak, A. Montes, S. C. Chapman, M. Chen, R. Cordano, C. Ward, M. Casaletto, K. Kramer, J. Rosen, H. H. Boxer, A. L. Miller, B. L. Green, A. Elahi, F. Lakkaraju, A. 2024-06-01 doi:10.1101/2024.05.29.595206 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Identification and Characterization of the Lipoprotein N-acyltransferase in Bacteroides ]]> https://biorxiv.org/content/10.1101/2024.05.31.596883v1?rss=1 Koropatkin, N. M. Armbruster, K. M. Jiang, J. Sartorio, M. G. Scott, N. Peterson, J. M. Sexton, J. Z. Feldman, M. 2024-06-01 doi:10.1101/2024.05.31.596883 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ SLO2.1/NALCN Functional Complex Activity in Mouse Myometrial Smooth Muscle Cells During Pregnancy. ]]> https://biorxiv.org/content/10.1101/2024.05.29.596465v1?rss=1 Ferreira, J. J. Kent, L. N. McCarthy, R. Butler, A. Ma, X. Paramsetty, N. Amazu, C. Zhang, A. Whitter, G. C. England, S. K. Santi, C. M. 2024-06-02 doi:10.1101/2024.05.29.596465 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ An Unbiased Proteomic Platform for Activity-based Arginylation Profiling ]]> https://biorxiv.org/content/10.1101/2024.06.01.596974v1?rss=1 Lin, Z. Xie, Y. Gongora, J. Liu, X. Zahn, E. Palai, B. B. Ramirez, D. Searfoss, R. Vitorino, F. N. Dann, G. P. Zhao, C. Han, X. Mactaggart, B. Lan, X. Fu, D. Greenberg, L. Zhang, Y. Lavine, K. J. Greenberg, M. J. Lyu, D. Kashina, A. S. Garcia, B. A. 2024-06-02 doi:10.1101/2024.06.01.596974 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ MAPK13 controls structural remodeling and disease after epithelial injury ]]> https://biorxiv.org/content/10.1101/2024.05.31.596863v1?rss=1 Wu, K. Zhang, Y. Mao, D. Iberg, C. A. Yin-Declue, H. Sun, K. Keeler, S. P. Wikfors, H. A. Young, D. Yantis, J. Austin, S. R. Byers, D. E. Brody, S. L. Crouch, E. C. Holtzman, M. J. 2024-06-03 doi:10.1101/2024.05.31.596863 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Two non-coding variants associated with isolated orofacial cleft promote binding of transcriptional repressors FOXE1 or ETS2 and reduce expression of IRF6 ]]> https://biorxiv.org/content/10.1101/2024.06.01.596914v1?rss=1 Kumari, P. Friedman, R. Z. Pi, L. Curtis, S. Paraiso, K. Visel, A. Rhea, L. Dunnwald, M. Patni, A. P. Mar, D. Bomsztyk, K. Mathieu, J. Ruohola-Baker, H. Leslie, E. White, M. A. Cohen, B. A. Cornell, R. A. 2024-06-03 doi:10.1101/2024.06.01.596914 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Dengue Virus Surveillance in Nepal Yields the First On-Site Whole Genome Sequences of Isolates from the 2022 Outbreak ]]> https://biorxiv.org/content/10.1101/2024.06.02.597008v1?rss=1 Napit, R. Ngono, A. E. Mihindukulasuriya, K. A. Pradhan, A. Khadka, B. Shrestha, S. Droit, L. Paredes, A. Karki, L. Khatiwada, R. Tamang, M. Chalise, B. S. Rawal, M. Jha, B. Wang, D. Handley, S. A. Shresta, S. Manandhar, K. D. 2024-06-03 doi:10.1101/2024.06.02.597008 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Direct prediction of intermolecular interactions driven by disordered regions ]]> https://biorxiv.org/content/10.1101/2024.06.03.597104v1?rss=1 Ginell, G. M. Emenecker, R. J. Lotthammer, J. M. Usher, E. T. Holehouse, A. S. 2024-06-03 doi:10.1101/2024.06.03.597104 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Mechanism of how the universal module XMAP215 γ-TuRC nucleates microtubules ]]> https://biorxiv.org/content/10.1101/2024.06.03.597159v1?rss=1 McManus, C. T. Travis, S. M. Jeffrey, P. D. Zhang, R. Petry, S. 2024-06-03 doi:10.1101/2024.06.03.597159 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ At the onset of active whisking, the input layer of barrel cortex exhibits a 24 h window of increased excitability that depends on prior experience. ]]> https://biorxiv.org/content/10.1101/2024.06.04.597353v1?rss=1 Shallow, M. C. Tian, L. Lin, H. Lefton, K. B. Chen, S. Dougherty, J. Culver, J. P. Lambo, M. E. Hengen, K. B. 2024-06-05 doi:10.1101/2024.06.04.597353 Cold Spring Harbor Laboratory Press 2024-06-05 <![CDATA[ AGS3-based optogenetic GDI induces GPCR-independent Gβγ signaling and macrophage migration ]]> https://biorxiv.org/content/10.1101/2024.06.04.597473v1?rss=1 Thotamune, W. Ubeysinghe, S. Rajarathna, C. Kankanamge, D. Olupothage, K. Chandu, A. Copits, B. A. Karunarathne, A. 2024-06-05 doi:10.1101/2024.06.04.597473 Cold Spring Harbor Laboratory Press 2024-06-05 <![CDATA[ Expression of a single inhibitory Ly49 receptor is sufficient to license NK cells for effector functions ]]> https://biorxiv.org/content/10.1101/2024.06.04.597367v1?rss=1 Piersma, S. J. Li, S. Wong, P. Bern, M. D. Poursine-Laurent, J. Yang, L. Beckman, D. L. Parikh, B. A. Yokoyama, W. M. 2024-06-06 doi:10.1101/2024.06.04.597367 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Neural circuit-selective, multiplexed pharmacological targeting of prefrontal cortex-projecting locus coeruleus neurons drives antinociception ]]> https://biorxiv.org/content/10.1101/2024.06.08.598059v1?rss=1 Kuo, C.-C. McCall, J. G. 2024-06-08 doi:10.1101/2024.06.08.598059 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Loss of mitochondrial pyruvate transport initiates cardiac glycogen accumulation and heart failure ]]> https://biorxiv.org/content/10.1101/2024.06.06.597841v1?rss=1 Weiss, R. C. Pyles, K. D. Cho, K. Brennan, M. Fisher, J. S. Patti, G. J. McCommis, K. S. 2024-06-09 doi:10.1101/2024.06.06.597841 Cold Spring Harbor Laboratory Press 2024-06-09 <![CDATA[ Endothelin B receptor inhibition rescues aging-dependent neuronal regenerative decline ]]> https://biorxiv.org/content/10.1101/2024.06.08.597928v1?rss=1 Feng, R. Rosen, S. Ansari, I. Sebastian, J. Thomson, M. B. Geoffroy, C. G. Cavalli, V. 2024-06-10 doi:10.1101/2024.06.08.597928 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Lipid-siRNA conjugate accesses a perivascular transport mechanism and achieves widespread and durable knockdown in the central nervous system ]]> https://biorxiv.org/content/10.1101/2024.06.09.598079v1?rss=1 Sorets, A. Schwensen, K. Francini, N. Kjar, A. Abdulrahman, A. Shostak, A. Katdare, K. Schoch, K. Cowell, R. Park, J. Ligocki, A. Ford, W. Ventura-Antunes, L. Hoogenboezem, E. Prusky, A. Castleberry, M. Michell, D. L. Miller, T. Vickers, K. Schrag, M. Duvall, C. Lippmann, E. 2024-06-10 doi:10.1101/2024.06.09.598079 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Quantifying the genomic determinants of fitness in E. coli ST131 using phylodynamics ]]> https://biorxiv.org/content/10.1101/2024.06.10.598183v1?rss=1 Kepler, L. M. Jara, M. Mahmud, B. Dantas, G. Dubberke, E. Lanzas, C. Rasmussen, D. A. 2024-06-10 doi:10.1101/2024.06.10.598183 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Bred for affection: The canine anterior ectosylvian gyrus responds selectively to social reinforcement ]]> https://biorxiv.org/content/10.1101/2024.06.10.598283v1?rss=1 Miller, K. J. Lampert, F. Mivalt, F. Kim, I. Ince, N. Kim, J. Kremen, V. Baker, M. R. Van den Boom, M. A. Hermes, D. Coenen, V. Schalk, G. Brunner, P. Worrell, G. A. 2024-06-10 doi:10.1101/2024.06.10.598283 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Barcoded SARS-CoV-2 viruses define the impact of time and route of transmission on the transmission bottleneck in a Syrian hamster model. ]]> https://biorxiv.org/content/10.1101/2024.06.08.597602v1?rss=1 200 isogenic SARS-CoV-2 viruses harboring specific 6-nucleotide barcodes inserted in ORF10, a non-translated ORF. We directly inoculated donor Syrian hamsters intranasally with this barcoded virus pool and exposed a paired naive contact hamster to each donor. Following exposure, the nasal turbinates, trachea, and lungs were collected, viral titers were measured, and the number of barcodes in each tissue were enumerated to quantify the transmission bottleneck. The duration and route (airborne, direct contact, and fomite) of exposure were varied to assess their impact on the transmission bottleneck. In airborne-exposed hamsters, the transmission bottleneck increased with longer exposure durations. We found that direct contact exposure produced the largest transmission bottleneck (average 27 BCs), followed by airborne exposure (average 16 BCs) then fomite exposure (average 8 BCs). Interestingly, we detected unique BCs in both the upper and lower respiratory tract of contact animals from all routes of exposure, suggesting that SARS-CoV-2 can directly infect hamster lungs. Altogether, these findings highlight the utility of barcoded viruses as tools to rigorously study virus transmission. In the future, barcoded SARS-CoV-2 will strengthen studies of immune factors that influence virus transmission. ]]> Trende, R. F. Darling, T. L. Gan, T. Wang, D. Boon, A. 2024-06-11 doi:10.1101/2024.06.08.597602 Cold Spring Harbor Laboratory Press 2024-06-11 <![CDATA[ Evaluation of Machine Learning Models for Aqueous Solubility Prediction in Drug Discovery ]]> https://biorxiv.org/content/10.1101/2024.06.10.598383v1?rss=1 Liu, S. Zhang, Y. Xue, N. 2024-06-11 doi:10.1101/2024.06.10.598383 Cold Spring Harbor Laboratory Press 2024-06-11 <![CDATA[ Stat3-mediated Atg7 expression enhances anti-tumor immunity in melanoma ]]> https://biorxiv.org/content/10.1101/2024.06.10.598284v1?rss=1 Zimmerman, S. M. Suh, E. Smith, S. R. Souroullas, G. P. 2024-06-12 doi:10.1101/2024.06.10.598284 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ Phosphorylation of disordered proteins tunes local and global intramolecular interactions ]]> https://biorxiv.org/content/10.1101/2024.06.10.598315v1?rss=1 80 residues) phospho-IDRs that, collectively, survey both local and global phosphorylation-induced changes to the ensemble. Our simulations of four well-studied phospho-IDRs show near-quantitative agreement with published findings for these systems via metrics including changes to radius of gyration, transient helicity, and persistence length. We also leveraged the inherent advantage of sequence control in molecular simulations to explore the conformational effects of diverse combinations of phospho-sites in two multi-phosphorylated IDRs. Our results support and expand on prior observations that connect phosphorylation to changes in the IDR conformational ensemble. Herein, we describe phosphorylation as a means to alter sequence chemistry, net charge and charge patterning, and intramolecular interactions, which can collectively modulate the local and global IDR ensemble features. SIGNIFICANCESpatially and temporally controlled phosphorylation in disordered protein regions is critical to many facets of protein function and broader cellular health. Intrinsically disordered protein regions (IDRs) are overrepresented as targets of phosphorylation, but the structural and functional consequences of such modifications remain elusive for many systems. Toward rigorous modeling of phosphorylated IDRs using all-atom simulations, we present new parameters for phosphoserine and phosphothreonine for the ABSINTH implicit solvent paradigm. Through the study of four example phospho-IDRs, we demonstrate excellent agreement between our phospho-IDR simulations and published datasets. ]]> Usher, E. T. Fossat, M. J. Holehouse, A. S. 2024-06-12 doi:10.1101/2024.06.10.598315 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ Endothelial cell Piezo1 promotes vascular smooth muscle cell differentiation on large arteries ]]> https://biorxiv.org/content/10.1101/2024.06.11.598539v1?rss=1 Abello, J. Yin, Y. Zhao, Y. Maurer, J. M. Lee, J. Bodell, C. Clevenger, A. J. Burton, Z. Goeckel, M. Lin, M. Grainger, S. Halabi, C. M. Raghavan, S. A. Sah, R. Stratman, A. N. 2024-06-12 doi:10.1101/2024.06.11.598539 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ Feasibility of Stereo EEG Based Brain Computer Interfacing in An Adult and Pediatric Cohort ]]> https://biorxiv.org/content/10.1101/2024.06.12.598257v1?rss=1 Jensen, M. A. Schalk, G. Ince, N. Hermes, D. Brunner, P. Miller, K. J. 2024-06-12 doi:10.1101/2024.06.12.598257 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ An optimized and robust workflow for quantifying the canonical histone ubiquitination marks H2AK119ub and H2BK120ub by LC-MS/MS ]]> https://biorxiv.org/content/10.1101/2024.06.11.596744v1?rss=1 Lopes, M. Lund, P. Garcia, B. 2024-06-13 doi:10.1101/2024.06.11.596744 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Cathartocytosis: How Cells Jettison Unwanted Material as They Reprogram ]]> https://biorxiv.org/content/10.1101/2024.06.11.598489v1?rss=1 Brown, J. W. Lin, X. Nicolazzi, G. A. Nguyen, T. Radyk, M. D. Burclaff, J. Mills, J. C. 2024-06-13 doi:10.1101/2024.06.11.598489 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Elevated phagocytic capacity directs innate spinal cord repair ]]> https://biorxiv.org/content/10.1101/2024.06.11.598515v1?rss=1 Shaw, D. K. Saraswathy, V. M. McAdow, A. R. Zhou, L. Park, D. Mote, R. Johnson, A. N. Mokalled, M. H. 2024-06-13 doi:10.1101/2024.06.11.598515 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Direct computations of viscoelastic moduli of biomolecular condensates ]]> https://biorxiv.org/content/10.1101/2024.06.11.598543v1?rss=1 Cohen, S. R. Banerjee, P. R. Pappu, R. V. 2024-06-13 doi:10.1101/2024.06.11.598543 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Sex-biased gene expression precedes sexual dimorphism in the agonadal annelid Platynereis dumerilii ]]> https://biorxiv.org/content/10.1101/2024.06.12.598746v1?rss=1 Ribeiro, R. P. Null, R. W. Ozpolat, B. D. 2024-06-13 doi:10.1101/2024.06.12.598746 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Revealing heterogeneity in dementia using data-driven unsupervised clustering of cognitive profiles ]]> https://biorxiv.org/content/10.1101/2024.06.13.598874v1?rss=1 Kumar, S. Oh, I. Schindler, S. E. Ghoshal, N. Abrams, Z. Payne, P. R. 2024-06-13 doi:10.1101/2024.06.13.598874 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Immunological correlates of protection mediated by a whole organism Cryptococcus neoformans vaccine deficient in chitosan ]]> https://biorxiv.org/content/10.1101/2024.06.12.598760v1?rss=1 100,000 deaths annually, mostly in persons with impaired CD4+ T cell function such as AIDS. There are no approved human vaccines. We previously created a genetically engineered avirulent strain of C. neoformans, designated cda1{Delta}2{Delta}3{Delta}. When used as a vaccine, cda1{Delta}2{Delta}3{Delta} protects mice against a subsequent challenge with a virulent C. neoformans strain. Here, we defined components of the immune system responsible for vaccine-mediated protection. We found that while B cells and CD8+ T cells were dispensible, protection was lost in mice genetically deficient in CD4+ T cells, and the cytokines IFN{gamma}, TNF, or IL-23. A robust influx of cytokine-producing CD4+ T cells was seen in the lungs of vaccinated mice following infection. Importantly, protection was retained in mice depleted of CD4+ T cells following vaccination, suggesting a strategy to protect persons who are at risk for future CD4+ T cell dysfunction. ]]> Specht, C. Wang, R. Oliveira, L. V. N. Hester, M. M. Gomez, C. L. Mou, Z. Carlson, D. Lee, C. K. Hole, C. R. Lam, W. C. Upadhya, R. Lodge, J. Levitz, S. M. 2024-06-14 doi:10.1101/2024.06.12.598760 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ A sensorimotor-association axis of thalamocortical connection development ]]> https://biorxiv.org/content/10.1101/2024.06.13.598749v1?rss=1 Sydnor, V. J. Bagautdinova, J. Larsen, B. Arcaro, M. J. Barch, D. M. Bassett, D. S. Alexander-Bloch, A. F. Cook, P. A. Covitz, S. Franco, A. R. Gur, R. E. Gur, R. C. Mackey, A. P. Mehta, K. Meisler, S. L. Milham, M. P. Moore, T. M. Muller, E. J. Roalf, D. R. Salo, T. Schubiner, G. Seidlitz, J. Shinohara, R. T. Shine, J. M. Yeh, F.-C. Cieslak, M. Satterthwaite, T. D. 2024-06-14 doi:10.1101/2024.06.13.598749 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ The C-terminal activating domain promotes Panx1 channel opening ]]> https://biorxiv.org/content/10.1101/2024.06.13.598903v1?rss=1 Henze, E. Ehrlich, J. Robertson, J. L. Kawate, T. 2024-06-14 doi:10.1101/2024.06.13.598903 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ δ-containing GABAA receptors on parvalbumin interneurons modulate neuronal excitability and network dynamics in the mouse medial prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2024.06.14.599033v1?rss=1 Lu, X. Shu, H.-j. Lambert, P. Benz, A. Zorumski, C. Mennerick, S. 2024-06-14 doi:10.1101/2024.06.14.599033 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Deciphering the molecular landscape of human peripheral nerves: implications for diabetic peripheral neuropathy ]]> https://biorxiv.org/content/10.1101/2024.06.15.599167v1?rss=1 Tavares-Ferreira, D. Shen, B. Q. Mwirigi, J. M. Shiers, S. Sankaranarayanan, I. Kotamarti, M. Inturi, N. N. Mazhar, K. Ubogu, E. E. Thomas, G. Lalli, T. Wukich, D. Price, T. J. 2024-06-16 doi:10.1101/2024.06.15.599167 Cold Spring Harbor Laboratory Press 2024-06-16 <![CDATA[ Mechanosensitive FHL2 tunes endothelial function ]]> https://biorxiv.org/content/10.1101/2024.06.16.599227v1?rss=1 Seetharaman, S. Devany, J. Kim, H. R. van Bodegraven, E. J. Chmiel, T. Tzu-Pin, S. Chou, W.-h. Fang, Y. Gardel, M. 2024-06-17 doi:10.1101/2024.06.16.599227 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Manipulation of Photosensory and Circadian Signalling Restricts Developmental Plasticity in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2024.06.17.598603v1?rss=1 Battle, M. W. Ewing, S. F. Dickson, C. Obaje, J. Edgeworth, K. Bindbeutel, R. Antoniou Kourounioti, R. L. Nusinow, D. A. Jones, M. A. 2024-06-19 doi:10.1101/2024.06.17.598603 Cold Spring Harbor Laboratory Press 2024-06-19 <![CDATA[ Cortical synaptic vulnerabilities revealed in a α-synuclein aggregation model of Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2024.06.20.599774v1?rss=1 Sah, S. Sauerbeck, A. D. Gupta, J. Perez-Acuna, D. Reiber, J. E. Russell, D. Goralski, T. Henderson, M. Volpicelli-Daley, L. A. Higley, M. J. Kummer, T. T. Biederer, T. 2024-06-21 doi:10.1101/2024.06.20.599774 Cold Spring Harbor Laboratory Press 2024-06-21 <![CDATA[ ATP-dependent citrate lyase Drives Left Ventricular Dysfunction by Metabolic Remodeling of the Heart ]]> https://biorxiv.org/content/10.1101/2024.06.21.600099v1?rss=1 Liu, S. Gammon, S. T. Tan, L. Gao, Y. Kim, K. Williamson, I. K. Pham, J. Davidian, A. Khanna, R. Gould, B. D. Salazar, R. Vitrac, H. Dinh, A. Lien, E. C. de L. Vitorino, F. N. Gongora, J. M. Martinez, S. A. Lawrence, C. S. C. Kransdorf, E. P. Leffer, D. Hanson, B. Garcia, B. C. Vander Heiden, M. Lorenzi, P. L. Taegtmeyer, H. Piwnica-Worms, D. Martin, J. F. Karlstaedt, A. 2024-06-21 doi:10.1101/2024.06.21.600099 Cold Spring Harbor Laboratory Press 2024-06-21 <![CDATA[ A genome resource for the marine annelid Platynereis dumerilii ]]> https://biorxiv.org/content/10.1101/2024.06.21.600153v1?rss=1 Mutemi, K. N. Simakov, O. Pan, L. Santangeli, L. Null, R. W. Handberg-Thorsager, M. Vellutini, B. C. Larsson, T. Savage, E. L. Lopez, M. O. Hercog, R. Provaznik, J. Ordonez-Rueda, D. Azevedo, N. Gazave, E. Vervoort, M. Tomancak, P. Tan, W. Winkler, S. Benes, V. Hui, J. Helm, C. Ozpolat, B. D. Arendt, D. 2024-06-23 doi:10.1101/2024.06.21.600153 Cold Spring Harbor Laboratory Press 2024-06-23 <![CDATA[ LINC01432 binds to CELF2 in newly diagnosed multiple myeloma promoting short progression-free survival to standard therapy ]]> https://biorxiv.org/content/10.1101/2024.06.27.600975v1?rss=1 24 months). We identified 157 differentially upregulated lncRNAs with short PFS and focused our efforts on characterizing the most upregulated lncRNA, LINC01432. We investigated LINC01432 overexpression and CRISPR/Cas9 knockdown in MM cell lines to show that LINC01432 overexpression significantly increases cell viability and reduces apoptosis, while knockdown significantly reduces viability and increases apoptosis, supporting the clinical relevance of this lncRNA. Next, we used individual-nucleotide resolution cross-linking immunoprecipitation with RT-qPCR to show that LINC01432 directly interacts with the RNA binding protein, CELF2. Lastly, we showed that LINC01432-targeted locked nucleic acid antisense oligonucleotides reduce viability and increases apoptosis. In summary, this fundamental study identified lncRNAs associated with short PFS to standard NDMM treatment and further characterized LINC01432, which inhibits apoptosis. Key points: lncRNA expression was found to be dysregulated in patients with short PFS to standard multiple myeloma therapy. LINC01432-bound CELF2 inhibits apoptosis. ]]> Mishra, R. Thunuguntla, P. Perkin, A. Duraiyan, D. Bagwill, K. Gonzales, S. Brizuela, V. Daly, S. Chang, Y. J. Abebe, M. Rajana, Y. Wichmann, K. Bolick, C. King, J. Fiala, M. Fortier, J. Jayasinghe, R. Ding, L. Vij, R. Silva-Fisher, J. 2024-06-30 doi:10.1101/2024.06.27.600975 Cold Spring Harbor Laboratory Press 2024-06-30 <![CDATA[ Network for Knowledge Organization (NEKO): an AI knowledge mining workflow for synthetic biology research ]]> https://biorxiv.org/content/10.1101/2024.06.27.601082v1?rss=1 Xiao, Z. Pakrasi, H. Chen, Y. Tang, Y. 2024-06-30 doi:10.1101/2024.06.27.601082 Cold Spring Harbor Laboratory Press 2024-06-30 <![CDATA[ High Throughput Repurposing Screen Reveals Compounds with Activity Against Toxoplasma gondii Bradyzoites ]]> https://biorxiv.org/content/10.1101/2024.07.01.601569v1?rss=1 50% inhibitory effects against bradyzoites, including new highly potent compounds, several of which have precedent for antimicrobial activity. Subsequent characterization of the compound Sanguinarine sulfate revealed potent and rapid killing against in vitro produced bradyzoites and bradyzoites harvested from chronically infected mice. These findings provide a platform for expanded screening and identify promising compounds for further preclinical development against T. gondii bradyzoites responsible for chronic infection. ]]> Uddin, T. Xia, J. Fu, Y. McNamara, C. W. Chatterjee, A. K. Sibley, L. D. 2024-07-01 doi:10.1101/2024.07.01.601569 Cold Spring Harbor Laboratory Press 2024-07-01 <![CDATA[ IGF-1 Peptide Mimetic-functionalized Hydrogels Enhance MSC Survival and Immunomodulatory Activity ]]> https://biorxiv.org/content/10.1101/2024.06.27.600680v1?rss=1 Tan, X. Jing, L. Neal, S. M. Gupta, M. C. Buchowski, J. M. Setton, L. A. Huebsch, N. 2024-07-02 doi:10.1101/2024.06.27.600680 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ An Autonomous Implantable Device for the Prevention of Death from Opioid Overdose ]]> https://biorxiv.org/content/10.1101/2024.06.27.600919v1?rss=1 Ciatti, J. L. Vazquez-Guardado, A. Brings, V. E. Park, J. Ruyle, B. Ober, R. A. McLuckie, A. J. Talcott, M. R. Carter, E. A. Burrell, A. R. Sponenburg, R. A. Trueb, J. Gupta, P. Kim, J. Avila, R. Seong, M. Slivicki, R. A. Kaplan, M. A. Villalpando, B. Massaly, N. Montana, M. C. Pet, M. Huang, Y. Moron, J. A. Gereau, R. W. Rogers, J. A. 2024-07-02 doi:10.1101/2024.06.27.600919 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ PIEZO1-Mediated Mechanotransduction Regulates Collagen Synthesis on Nanostructured 2D and 3D Models of Fibrosis ]]> https://biorxiv.org/content/10.1101/2024.06.30.601386v1?rss=1 Rashidi, N. Harasymowicz, N. Savadipour, A. Steward, N. Tang, R. Oswald, S. Guilak, F. 2024-07-02 doi:10.1101/2024.06.30.601386 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ The fully activated open state of KCNQ1 controls the cardiac 'fight-or-flight' response ]]> https://biorxiv.org/content/10.1101/2024.07.02.601749v1?rss=1 HOU, P. ZHAO, L. ZHONG, L. Shi, J. WANG, H. GAO, J. LIU, H. Zuckerman, J. COHEN, I. S. Cui, J. 2024-07-03 doi:10.1101/2024.07.02.601749 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ Biomolecular condensates are characterized by interphase electric potentials ]]> https://biorxiv.org/content/10.1101/2024.07.02.601783v1?rss=1 Posey, A. E. Bremer, A. Erkamp, N. A. Pant, A. Knowles, T. Dai, Y. Mittag, T. Pappu, R. V. 2024-07-04 doi:10.1101/2024.07.02.601783 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ Backbone-mediated weakening of pairwise interactions enables percolation in mimics of protein condensates ]]> https://biorxiv.org/content/10.1101/2024.07.08.602299v1?rss=1 Zeng, X. Pappu, R. V. 2024-07-08 doi:10.1101/2024.07.08.602299 Cold Spring Harbor Laboratory Press 2024-07-08 <![CDATA[ Biomolecular condensates can function as inherent catalysts ]]> https://biorxiv.org/content/10.1101/2024.07.06.602359v1?rss=1 Guo, X. Farag, M. Qian, N. Yu, X. Ni, A. Ma, Y. Yu, W. King, M. Liu, V. Lee, J. Min, W. Zare, R. N. Pappu, R. V. Dai, Y. 2024-07-10 doi:10.1101/2024.07.06.602359 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Newly discovered base barrier cells provide compartmentalization of choroid plexus, brain and CSF ]]> https://biorxiv.org/content/10.1101/2024.07.08.601696v1?rss=1 View larger version (47K): org.highwire.dtl.DTLVardef@181e787org.highwire.dtl.DTLVardef@1875f33org.highwire.dtl.DTLVardef@7b2bcdorg.highwire.dtl.DTLVardef@78baa6_HPS_FORMAT_FIGEXP M_FIG Newly discovered base barrier cells provide compartmentalization of choroid plexus, brain and CSF The choroid plexus (ChP) hangs in the brain ventricles and is composed of an epithelial cell layer which produces the cerebrospinal fluid (CSF) and forms the blood-CSF barrier. The ChP epithelial cells are continuous with the ependymal cells lining the ventricle wall. At this base region, we identified and characterized a novel subtype of fibroblasts coined the ChP base barrier cells (BBCs). ChP BBCs express tight junctions (TJs), cluster together and seal the ChP stroma from CSF and brain parenchyma. The subarachnoid space (SAS) CSF penetrates deep into choroid plexus invaginations where it is halted by ChP BBCs. Abbreviations: E9-16.5 (embryonic day 9-16.5); P1-4 (postnatal day 1-4). C_FIG ]]> Verhaege, D. De Nolf, C. Castelein, J. Claeys, W. Van Wonterghem, E. Van Imschoot, G. Dujardin, P. De Spiegelaere, W. Hoste, E. Boone, F. Lidov, H. G. Dani, N. Derk, J. Kremer, A. Van Hamme, E. Borghgraef, P. Lippens, S. Lehtinen, M. K. Siegenthaler, J. Van Hoecke, L. Vandenbroucke, R. E. 2024-07-11 doi:10.1101/2024.07.08.601696 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Structural Mapping of Polyclonal IgG Responses to HA After Influenza Virus Vaccination or Infection ]]> https://biorxiv.org/content/10.1101/2024.07.08.601940v1?rss=1 Leon, A. N. Rodriguez, A. J. Richey, S. T. Torrents de la Pena, A. Wolters, R. M. Jackson, A. M. Webb, K. Creech, C. B. Yoder, S. Mudd, P. A. Crowe, J. E. Han, J. Ward, A. B. 2024-07-11 doi:10.1101/2024.07.08.601940 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Local genetic adaptation to habitat in wild chimpanzees ]]> https://biorxiv.org/content/10.1101/2024.07.09.601734v1?rss=1 Ostridge, H. J. Fontsere, C. Lizano, E. Soto, D. C. Schmidt, J. M. Saxena, V. Alvarez-Estape, M. Barratt, C. D. Gratton, P. Bocksberger, G. Lester, J. D. Dieguez, P. Agbor, A. Angedakin, S. Assumang, A. K. Bailey, E. Barubiyo, D. Bessone, M. Brazzola, G. Chancellor, R. Cohen, H. Coupland, C. Danquah, E. Deschner, T. Dotras, L. Dupain, J. Egbe, V. E. Granjon, A.-C. Head, J. Hedwig, D. Hermans, V. Hernandez-Aguilar, R. A. Jeffery, K. J. Jones, S. Junker, J. Kadam, P. Kaiser, M. Kalan, A. K. Kambere, M. Kienast, I. Kujirakwinja, D. Langergraber, K. E. Lap 2024-07-11 doi:10.1101/2024.07.09.601734 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ FUSION: A web-based application for in-depth exploration of multi-omics data with brightfield histology ]]> https://biorxiv.org/content/10.1101/2024.07.09.602778v1?rss=1 Border, S. Melo Ferreira, R. Lucarelli, N. Kumar, S. Paul, A. Manthey, D. Barisoni, L. Strekalova, Y. Ray, J. Cheng, Y.-H. Rosenberg, A. Z. Tomaszewski, J. E. Mimar, S. Hodgin, J. B. HuBMAP consortium, El-Achkar, T. M. Jain, S. Eadon, M. T. Sarder, P. 2024-07-14 doi:10.1101/2024.07.09.602778 Cold Spring Harbor Laboratory Press 2024-07-14 <![CDATA[ A new pathway in central metabolism mediates nutrient control of development and antibiotic production by Streptomyces ]]> https://biorxiv.org/content/10.1101/2024.07.14.603434v1?rss=1 Li, C. Urem, M. Kotsogianni, I. Lau, j. Elsayed, S. S. Martin, N. I. McNae, I. Voskamp, P. Mayer, C. Rigali, S. Pannu, N. Abrahams, J.-P. Schada von Borzyskowski, L. van Wezel, G. P. 2024-07-14 doi:10.1101/2024.07.14.603434 Cold Spring Harbor Laboratory Press 2024-07-14 <![CDATA[ Determining potential immunomodulatory drug efficacy in sepsis using ELISpot ]]> https://biorxiv.org/content/10.1101/2024.07.10.602970v1?rss=1 Walton, A. H. Mazer, M. B. Remy, K. E. Davitt, E. B. Griffith, T. S. Gould, R. W. Badovinac, V. P. Brakenridge, S. C. Drewry, A. M. Loftus, T. J. Efron, P. A. Moldawer, L. L. Caldwell, C. C. Hotchkiss, R. S. 2024-07-16 doi:10.1101/2024.07.10.602970 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases ]]> https://biorxiv.org/content/10.1101/2024.07.11.603080v1?rss=1 Jiang, J. Gwee, J. Fang, J. Leichter, S. M. Sanders, D. Ji, X. Song, J. Zhong, X. 2024-07-16 doi:10.1101/2024.07.11.603080 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ The progression of infiltrating neurovascular features and chemokine production of the caudal intervertebral disc following injury ]]> https://biorxiv.org/content/10.1101/2024.07.12.603182v1?rss=1 Walk, R. Broz, K. Jing, L. Potter, R. Beeve, A. Scheller, E. Gupta, M. Setton, L. Tang, S. Y. 2024-07-16 doi:10.1101/2024.07.12.603182 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ ExPOSE: A comprehensive toolkit to perform expansion microscopy in plant protoplast systems ]]> https://biorxiv.org/content/10.1101/2024.07.12.603300v1?rss=1 Cox, K. L. Pardi, S. A. O'Connor, L. Klebanovych, A. Huss, D. J. Nusinow, D. A. Meyers, B. C. Czymmek, K. J. 2024-07-16 doi:10.1101/2024.07.12.603300 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[ Endogenous and fluorescent sterols reveal the molecular basis for ligand selectivity of human sterol transporters ]]> https://biorxiv.org/content/10.1101/2024.07.22.604041v1?rss=1 Depta, L. Bryce-Rogers, H. P. Dekker, N. J. Bonke, A. W. Camporese, N. Qian, M. Xu, Y. Covey, D. F. Laraia, L. 2024-07-22 doi:10.1101/2024.07.22.604041 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ 3D printed bioelectronic scaffolds with soft tissue-like stiffness ]]> https://biorxiv.org/content/10.1101/2024.07.19.604334v1?rss=1 Okafor, S. S. Park, J. Liu, T. Goestenkors, A. P. Alvarez, R. M. Semar, B. A. Yu, J. S. O'Hare, C. P. Montgomery, S. K. Friedman, L. C. Rutz, A. L. 2024-07-23 doi:10.1101/2024.07.19.604334 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Synapse protein signatures in cerebrospinal fluid and plasma predict cognitive maintenance versus decline in Alzheimers disease ]]> https://biorxiv.org/content/10.1101/2024.07.22.604680v1?rss=1 Oh, H. S.-H. Urey, D. Y. Karlsson, L. Zhu, Z. Shen, Y. Farinas, A. Timsina, J. Guldner, I. H. Morshed, N. Yang, C. Western, D. Ali, M. Le Guen, Y. Trelle, A. Herukka, S.-K. Rauramaa, T. Hiltunen, M. Lipponen, A. Luikku, A. J. Poston, K. L. Mormino, E. Wagner, A. D. Wilson, E. N. Channappa, D. Leinonen, V. Stevens, B. Ehrenberg, A. J. Zetterberg, H. Bennett, D. A. Franzmeier, N. Hansson, O. Cruchaga, C. Wyss-Coray, T. 2024-07-23 doi:10.1101/2024.07.22.604680 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ A disinhibitory basal forebrain to cortex projection supports sustained attention ]]> https://biorxiv.org/content/10.1101/2024.07.22.604711v1?rss=1 Li, S.-J. Hangya, B. Gupta, U. Fischer, K. B. Sturgill, J. F. Callaway, E. M. Kepecs, A. 2024-07-23 doi:10.1101/2024.07.22.604711 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[ Expanding the substrate selectivity of the fimsbactin biosynthetic adenylation domain, FbsH ]]> https://biorxiv.org/content/10.1101/2024.07.26.605314v1?rss=1 Ahmed, S. F. Balutowski, A. Yang, J. Wencewicz, T. A. Gulick, A. M. 2024-07-26 doi:10.1101/2024.07.26.605314 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ The intersection of endocrine signaling and neuroimmune communication regulates neonatal nociception ]]> https://biorxiv.org/content/10.1101/2024.07.26.605393v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@18b0bdorg.highwire.dtl.DTLVardef@fb5ee9org.highwire.dtl.DTLVardef@114179aorg.highwire.dtl.DTLVardef@19979b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Fadaka, A. O. Dourson, A. J. Hofmann, M. C. Gupta, P. Raut, N. G. R. Jankowski, M. P. 2024-07-27 doi:10.1101/2024.07.26.605393 Cold Spring Harbor Laboratory Press 2024-07-27 <![CDATA[ Fundamental limitations of kilohertz-frequency carriers in afferent fiber recruitment with transcutaneous spinal cord stimulation ]]> https://biorxiv.org/content/10.1101/2024.07.26.603982v1?rss=1 Keesey, R. Hofstoetter, U. Hu, Z. Lombardi, L. Hawthorn, R. Bryson, N. K. Rowald, A. Minassian, K. Seanez, I. 2024-07-29 doi:10.1101/2024.07.26.603982 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Protein surface chemistry encodes an adaptive resistance to desiccation ]]> https://biorxiv.org/content/10.1101/2024.07.28.604841v1?rss=1 Romero-Perez, P. S. Moran, H. M. Horani, A. Truong, A. Manriquez-Sandoval, E. Ramirez, J. F. Martinez, A. Golub, E. Hunter, K. Lotthammer, J. M. Emenecker, R. J. Boothby, T. C. Holehouse, A. S. Fried, S. D. Sukenik, S. 2024-07-29 doi:10.1101/2024.07.28.604841 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Three Dimensional Multiscalar Neurovascular Nephron Connectivity Map of the Human Kidney Across the Lifespan ]]> https://biorxiv.org/content/10.1101/2024.07.29.605633v1?rss=1 McLaughlin, L. Zhang, B. Sharma, S. Knoten, A. L. Kaushal, M. Purkerson, J. M. Huyck, H. Pryhuber, G. S. Gaut, J. P. Jain, S. 2024-07-30 doi:10.1101/2024.07.29.605633 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Central activation of catecholamine-independent lipolysis drives the end-stage catabolism of all adipose tissues ]]> https://biorxiv.org/content/10.1101/2024.07.30.605812v1?rss=1 Zhang, X. Majumdar, A. Kim, C. Kleiboeker, B. Magee, K. L. Learman, B. S. Thomas, S. A. Lodhi, I. J. MacDougald, O. A. Scheller, E. L. 2024-07-31 doi:10.1101/2024.07.30.605812 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Receptor Binding Specificity of a Bovine A(H5N1) Influenza Virus ]]> https://biorxiv.org/content/10.1101/2024.07.30.605893v1?rss=1 Chopra, P. Page, C. K. Shepard, J. D. Ray, S. D. Kandeil, A. Jeevan, T. Bowman, A. S. Ellebedy, A. H. Webby, R. J. de Vries, R. P. Tompkins, S. M. Boons, G.-J. 2024-07-31 doi:10.1101/2024.07.30.605893 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Introducing identification probability for automated and transferable assessment of metabolite identification confidence in metabolomics and related studies ]]> https://biorxiv.org/content/10.1101/2024.07.30.605945v1?rss=1 Metz, T. O. Chang, C. H. Gautam, V. Anjum, A. Tian, S. Wang, F. Colby, S. M. Nunez, J. R. Blumer, M. R. Edison, A. S. Fiehn, O. Jones, D. P. Li, S. Morgan, E. T. Patti, G. J. Ross, D. H. Shapiro, M. R. Williams, A. J. Wishart, D. S. 2024-07-31 doi:10.1101/2024.07.30.605945 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Lack of pathogenic involvement of CCL4 and its receptor CCR5 in arthritogenic alphavirus disease ]]> https://biorxiv.org/content/10.1101/2024.07.31.606106v1?rss=1 Hameed, M. A. Solomon, N. Weger-Lucarelli, J. 2024-08-03 doi:10.1101/2024.07.31.606106 Cold Spring Harbor Laboratory Press 2024-08-03 <![CDATA[ Modeling glioblastoma tumor progression via CRISPR-engineered brain organoids ]]> https://biorxiv.org/content/10.1101/2024.08.02.606387v1?rss=1 Ishahak, M. Han, R. H. Annamalai, D. Woodiwiss, T. McCornack, C. Cleary, R. T. DeSouza, P. A. Qu, X. Dahiya, S. Kim, A. H. Millman, J. R. 2024-08-03 doi:10.1101/2024.08.02.606387 Cold Spring Harbor Laboratory Press 2024-08-03 <![CDATA[ Driving forces for condensation of synapsin are governed by sequence-encoded molecular grammars ]]> https://biorxiv.org/content/10.1101/2024.08.03.606464v1?rss=1 Hoffmann, C. Ruff, K. M. Edu, I. Kyung Shinn, M. Tromm, J. King, M. Pant, A. Ausserwoeger, H. Morgan, J. Knowles, T. Pappu, R. V. Milovanovic, D. 2024-08-04 doi:10.1101/2024.08.03.606464 Cold Spring Harbor Laboratory Press 2024-08-04 <![CDATA[ Brain-like border ownership signals support prediction of natural videos ]]> https://biorxiv.org/content/10.1101/2024.08.11.607040v1?rss=1 Ye, Z. Wessel, R. Franken, T. P. 2024-08-12 doi:10.1101/2024.08.11.607040 Cold Spring Harbor Laboratory Press 2024-08-12 <![CDATA[ A conserved regulation of cell expansion underlies notochord mechanics, spine morphogenesis, and endochondral bone lengthening ]]> https://biorxiv.org/content/10.1101/2024.08.12.607640v1?rss=1 Voigt, B. Frazier, K. E. Yazdi, D. Gontarz, P. Zhang, B. Sepich, D. S. Solnica-Krezel, L. GRAY, R. S. 2024-08-13 doi:10.1101/2024.08.12.607640 Cold Spring Harbor Laboratory Press 2024-08-13 <![CDATA[ The Clonal Hematopoiesis-associated Gene Srcap Plays an Essential Role in Hematopoiesis ]]> https://biorxiv.org/content/10.1101/2024.08.16.607812v1?rss=1 Wong, T. N. Mychalowych, A. Feldpausch, E. R. Carson, A. Karpova, D. Link, D. C. 2024-08-19 doi:10.1101/2024.08.16.607812 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Tissue determinants of the human T cell receptor repertoire. ]]> https://biorxiv.org/content/10.1101/2024.08.17.608295v1?rss=1 Sureshchandra, S. Henderson, J. Levendosky, E. Bhattacharyya, S. Kastenschmidt, J. M. Sorn, A. M. Mitul, M. T. Benchorin, A. Batucal, K. Daugherty, A. Murphy, S. J. Thakur, C. Trask, D. Ahuja, G. Moisan, A. Tiffeau-Mayer, A. Saligrama, N. Wagar, L. E. 2024-08-19 doi:10.1101/2024.08.17.608295 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Differential interactions determine anisotropies at interfaces of RNA-based biomolecular condensates ]]> https://biorxiv.org/content/10.1101/2024.08.19.608662v1?rss=1 Erkamp, N. A. Farag, M. Qiu, Y. Qian, D. Sneideris, T. Wu, T. Welsh, T. J. Ausserwoger, H. Krug, T. J. Weitz, D. Lew, M. D. Knowles, T. Pappu, R. V. 2024-08-19 doi:10.1101/2024.08.19.608662 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ High-throughput affinity measurements of direct interactions between activation domains and co-activators ]]> https://biorxiv.org/content/10.1101/2024.08.19.608698v1?rss=1 1,500 Kds), we provide the first quantitative map of these interactions and reveal 334 novel binding pairs. We find that the metazoan-specific co-activator P300 directly binds >100 activation domains, potentially explaining its widespread recruitment across the genome to influence transcriptional activation. Despite sharing similar molecular properties (e.g. enrichment of negative and hydrophobic residues), activation domains utilize distinct biophysical properties to recruit certain co-activator domains. Co-activator domain affinity and occupancy are well-predicted by analytical models that account for multivalency, and in vitro affinities quantitatively predict activation in cells with an ultrasensitive response. Not only do our results demonstrate the ability to measure affinities between even weak protein-protein interactions in high throughput, but they also provide a necessary resource of over 1,500 activation domain/co-activator affinities which lays the foundation for understanding the molecular basis of transcriptional activation. ]]> DelRosso, N. Suzuki, P. Griffith, D. Lotthammer, J. Novak, B. Kocalar, S. Sheth, M. Holehouse, A. Bintu, L. Fordyce, P. 2024-08-20 doi:10.1101/2024.08.19.608698 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ An autonomous robotic system for high-throughput phenotyping and behavioral studies of individual fruit flies ]]> https://biorxiv.org/content/10.1101/2024.08.21.607451v1?rss=1 1,000 flies per day for high-throughput inspection and characterization assays. Robotic handling had no detectable adverse effects on fly longevity or our assessments of fly health. Moreover, the behavioral performance of flies, especially of males, was better and less variable than of flies handled manually. Our system employs deep learning-based machine vision for real-time assessments of picking quality and fly phenotypes. This enables fully pipelined, autonomous experimentation for behavioral assays with individual flies in controlled environments, which was previously infeasible. Overall, FlyMAX constitutes a promising technology to enhance the efficiency and reproducibility of research with flies and other insects in fields such as genetics, neuroscience, and drug screening. ]]> Woo, S. J. Huang, C. Savall, J. Conrad, B. L. Luo, J. Schnitzer, M. J. 2024-08-22 doi:10.1101/2024.08.21.607451 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ A first-in-kind MAPK13 inhibitor that can correct stem cell reprogramming and post-injury disease ]]> https://biorxiv.org/content/10.1101/2024.08.21.608990v1?rss=1 Zhang, Y. Wu, K. Mao, D. Iberg, C. A. Yin-Declue, H. Sun, K. Wikfors, H. A. Keeler, S. P. Li, M. Young, D. Yantis, J. Crouch, E. C. Chartock, J. R. Han, Z. Byers, D. E. Brody, S. L. Romero, A. G. Holtzman, M. J. 2024-08-22 doi:10.1101/2024.08.21.608990 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Quantitative Interpretation of Transverse Spin Relaxation by Translational Diffusion in Liquids Under Arbitrary Potentials ]]> https://biorxiv.org/content/10.1101/2024.08.21.609078v1?rss=1 norm. In this study, we present a rigorous theoretical interpretation of {Gamma} 2 that it is instead proportional to norm and provide explicit formula for calculating norm without any adjustable parameters. This interpretation is independent of the type or strength of interactions and can be broadly applied, including to the precise interpretation of ENS. ]]> Okuno, Y. 2024-08-22 doi:10.1101/2024.08.21.609078 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ The probability of cryptic pocket opening controls functional tradeoffs in filovirus immune evasion. ]]> https://biorxiv.org/content/10.1101/2024.08.22.609218v1?rss=1 Mallimadugula, U. L. Cruz, M. A. Vithani, N. Zimmerman, M. I. Bowman, G. R. 2024-08-23 doi:10.1101/2024.08.22.609218 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ Non-canonical Wnt signaling triggered by WNT2B drives adrenal aldosterone production ]]> https://biorxiv.org/content/10.1101/2024.08.23.609423v1?rss=1 Borges, K. S. Little, D. de Almeida Magalhaes, T. Ribeiro, C. Dumontet, T. Lapensee, C. Basham, K. J. Seth, A. Azova, S. Guagliardo, N. A. Barret, P. Q. Berber, M. O'Connell, A. E. Turcu, A. F. Lerario, A. M. Mohan, D. Rainey, W. Carlone, D. L. Hirschhorn, J. Salic, A. Breault, D. Hammer, G. D. 2024-08-26 doi:10.1101/2024.08.23.609423 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ SCRATCH: A programmable, open-hardware, benchtop robot that automatically scratches cultured tissues to investigate cell migration, healing, and tissue sculpting. ]]> https://biorxiv.org/content/10.1101/2024.08.27.609782v1?rss=1 Lin, Y. Silverman-Dutz, A. Bailey, M. Cohen, D. J. 2024-08-28 doi:10.1101/2024.08.27.609782 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ O-glycosylation contributes to mammalian glycoRNA biogenesis ]]> https://biorxiv.org/content/10.1101/2024.08.28.610074v1?rss=1 Porat, J. Watkins, C. Jin, C. Xie, Y. Tan, X. Lebedenko, C. Hemberger, H. Shin, W. Chai, P. Collins, J. J. Garcia, B. A. Bojar, D. Flynn, R. A. 2024-08-29 doi:10.1101/2024.08.28.610074 Cold Spring Harbor Laboratory Press 2024-08-29 <![CDATA[ Inflammatory pain in mice induces light cycle-dependent effects on sleep architecture ]]> https://biorxiv.org/content/10.1101/2024.08.28.610124v1?rss=1 Burek, D. J. Mohamad Ibrahim, K. Hall, A. G. Sharma, A. Musiek, E. S. Moron, J. A. Carlezon, W. A. 2024-08-29 doi:10.1101/2024.08.28.610124 Cold Spring Harbor Laboratory Press 2024-08-29 <![CDATA[ DAMP-inducing Peptide Nanofibers and PAMP Combination Adjuvants Boost Functional Lung Tissue-resident Memory CD4+ T Cell Responses ]]> https://biorxiv.org/content/10.1101/2024.08.28.610131v1?rss=1 Files, M. A. Das, A. Kim, D. Buck, J. R. Endsley, J. J. Rudra, J. S. 2024-08-29 doi:10.1101/2024.08.28.610131 Cold Spring Harbor Laboratory Press 2024-08-29 <![CDATA[ SLC35A2 modulates paramyxovirus fusion events during infection ]]> https://biorxiv.org/content/10.1101/2024.08.27.609835v1?rss=1 Yang, Y. Wang, Y. Campbell, D. Lee, H.-W. Wang, L. Baldridge, M. Lopez, C. B. 2024-08-30 doi:10.1101/2024.08.27.609835 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Ketone Body Metabolism is Not Required for Improvement of Heart Failure by Ketogenic Diet in Mice ]]> https://biorxiv.org/content/10.1101/2024.08.30.610511v1?rss=1 Foulks, Z. Weinheimer, C. J. Kovacs, A. Michael, J. Pyles, K. D. Menezes, T. N. Cho, K. Patti, G. J. McCommis, K. S. 2024-09-02 doi:10.1101/2024.08.30.610511 Cold Spring Harbor Laboratory Press 2024-09-02 <![CDATA[ A Phylogenetic Model of Established and Enabled Biome Shifts ]]> https://biorxiv.org/content/10.1101/2024.08.30.610561v1?rss=1 McHugh, S. W. Donoghue, M. Landis, M. J. 2024-09-02 doi:10.1101/2024.08.30.610561 Cold Spring Harbor Laboratory Press 2024-09-02 <![CDATA[ Design of linked-domain protein inhibitors of UBE2D as tools to study cellular ubiquitination ]]> https://biorxiv.org/content/10.1101/2024.09.02.610852v1?rss=1 1000 proteins that regulate the ubiquitination of proteins. The E2 Ub-conjugating enzymes are the midpoint, yet their cellular roles remain under-characterized, partly due to a lack of inhibitors. For example, the cellular roles of the promiscuous E2 UBE2D/UBCH5 are not well described. Here, we develop a highly selective, multivalent, engineered protein inhibitor for the UBE2D family that simultaneously targets the RING- and backside-binding sites. In HeLa cells, these inhibitors phenocopy knockdown of UBE2D by reducing the IC50 to cisplatin and whole-cell proteomics reveal an increased abundance of [~]20% of the identified proteins, consistent with reduced Ub degradation and proteotoxic stress. These precision tools will enable new studies probing UBE2Ds central role in proteome management. ]]> Bukhari, Z. Gu, L. Nederstigt, A. E. Cope, L. J. Bolhuis, D. L. Harvey, K. Allen, T. Hill, S. Yang, Y. Lawson, G. Lu, C. Tran, T. Leah, P. Low, L. Chiang, A. Song, J. Fong, M. V. Rangel, V. M. Chan, W. K. Kleiger, G. Goldfarb, D. Vierra, C. A. Brown, N. G. Harrison, J. S. 2024-09-02 doi:10.1101/2024.09.02.610852 Cold Spring Harbor Laboratory Press 2024-09-02 <![CDATA[ Phosphorylation of CRYAB Induces a Condensatopathy to Worsen Post-Myocardial Infarction Left Ventricular Remodeling. ]]> https://biorxiv.org/content/10.1101/2024.08.30.610556v1?rss=1 Islam, M. Rawnsley, D. R. Ma, X. Navid, W. Zhao, C. Foroughi, L. Murphy, J. T. Navid, H. Weinheimer, C. J. Kovacs, A. Nigro, J. Diwan, A. Chang, R. Kumari, M. Young, M. Razani, B. Margulies, K. Abdellatif, M. Sedej, S. Javaheri, A. Covey, D. F. Mani, K. Diwan, A. 2024-09-03 doi:10.1101/2024.08.30.610556 Cold Spring Harbor Laboratory Press 2024-09-03 <![CDATA[ Is criticality a unified set-point of brain function? ]]> https://biorxiv.org/content/10.1101/2024.09.02.610815v1?rss=1 Hengen, K. B. Shew, W. L. 2024-09-03 doi:10.1101/2024.09.02.610815 Cold Spring Harbor Laboratory Press 2024-09-03 <![CDATA[ LEA_4 motifs function alone and in conjunction with synergistic cosolutes to protect a labile enzyme during desiccation ]]> https://biorxiv.org/content/10.1101/2024.09.04.611296v1?rss=1 Nicholson, V. Nguyen, K. H. Gollub, E. McCoy, M. Yu, F. Holehouse, A. S. Sukenik, S. Boothby, T. C. 2024-09-04 doi:10.1101/2024.09.04.611296 Cold Spring Harbor Laboratory Press 2024-09-04 <![CDATA[ DIFFERENTIAL CONTRIBUTIONS OF THE SPECTRO-TEMPORAL AND VOCAL CHARACTERISTICS OF AUDITORY PSEUDOWORDS TO MULTIPLE SOUND-SYMBOLIC MAPPINGS ]]> https://biorxiv.org/content/10.1101/2024.09.03.610973v1?rss=1 Lacey, S. Matthews, K. L. Hoffmann, A. M. Sathian, K. Nygaard, L. C. 2024-09-05 doi:10.1101/2024.09.03.610973 Cold Spring Harbor Laboratory Press 2024-09-05 <![CDATA[ The small MAF transcription factor MAFG co-opts MITF to promote melanoma progression ]]> https://biorxiv.org/content/10.1101/2024.09.03.611024v1?rss=1 Vera, O. Martinez, M. Soto-Vargas, Z. Wang, K. Xu, X. Ruiz-Buceta, S. Mecozzi, N. Chadourne, M. Posorske, B. Angarita, A. Bok, I. Liu, Q. Murikipudi, H. Kim, Y. Messina, J. L. Tsai, K. Y. Major, M. Lau, E. K. Yu, X. Ibanez-de-Caceres, I. Karreth, F. A. 2024-09-06 doi:10.1101/2024.09.03.611024 Cold Spring Harbor Laboratory Press 2024-09-06 <![CDATA[ Structural Basis for Dimerization and Activation of UvrD-family Helicases ]]> https://biorxiv.org/content/10.1101/2024.09.05.611425v1?rss=1 Chadda, A. Nguyen, B. Lohman, T. M. Galburt, E. A. 2024-09-06 doi:10.1101/2024.09.05.611425 Cold Spring Harbor Laboratory Press 2024-09-06 <![CDATA[ Expansion microscopy of axonemal dyneins in islet primary cilia ]]> https://biorxiv.org/content/10.1101/2024.09.06.611752v1?rss=1 Dong, X. Cho, J. H. Hughes, J. W. 2024-09-07 doi:10.1101/2024.09.06.611752 Cold Spring Harbor Laboratory Press 2024-09-07 <![CDATA[ SIRT6 loss causes intervertebral disc degeneration in mice by promoting senescence and SASP status ]]> https://biorxiv.org/content/10.1101/2024.09.09.612072v1?rss=1 Ramteke, P. Watson, B. Toci, M. Tran, V. Johnston, S. Tsingas, M. Barve, R. Mitra, R. Loeser, R. Collins, J. Risbud, M. 2024-09-09 doi:10.1101/2024.09.09.612072 Cold Spring Harbor Laboratory Press 2024-09-09 <![CDATA[ Mast cells promote pathology and susceptibility in tuberculosis ]]> https://biorxiv.org/content/10.1101/2024.09.04.611333v1?rss=1 Gupta, A. Taneja, V. Rangel-Moreno, J. Abhimanyu, A. Ahmed, M. Naqvi, N. Chauhan, K. S. de Leon, D. T.-P. Ramirez-Martinez, G. Jimenez-Alvarez, L. Luna-Rivero, C. Zuniga, J. Kaushal, D. Khader, S. 2024-09-10 doi:10.1101/2024.09.04.611333 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ Hyperglycemia selectively increases cerebral non-oxidative glucose consumption without affecting blood flow ]]> https://biorxiv.org/content/10.1101/2024.09.05.611035v1?rss=1 Blazey, T. Lee, J. J. Snyder, A. Z. Goyal, M. S. Hershey, T. Arbelaez, A. M. Raichle, M. E. 2024-09-10 doi:10.1101/2024.09.05.611035 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ A circular engineered sortase for interrogating histone H3 in chromatin ]]> https://biorxiv.org/content/10.1101/2024.09.10.612318v1?rss=1 Whedon, S. D. Lee, K. Wang, Z. A. Zahn, E. Lu, C. Abeywardana, M. Y. Fairall, L. Nam, E. Dubois-Coyne, S. De Ioannes, P. Sheng, X. Andrei, A. Lundberg, E. Jiang, J. Armache, K.-J. D. Zhao, Y. Schwabe, J. W. R. Wu, M. Garcia, B. Cole, P. A. 2024-09-10 doi:10.1101/2024.09.10.612318 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ Early Life Neuroimaging: The Generalizability of Cortical Area Parcellations Across Development ]]> https://biorxiv.org/content/10.1101/2024.09.09.612056v1?rss=1 Tu, J. Myers, M. Li, W. Li, J. Wang, X. Dierker, D. Day, T. Snyder, A. Z. Latham, A. Kenley, J. K. Sobolewski, C. M. Wang, Y. Labonte, A. K. Feczko, E. Kardan, O. Moore, L. A. Sylvester, C. M. Fair, D. A. Elison, J. T. Warner, B. B. Barch, D. M. Rogers, C. E. Luby, J. L. Smyser, C. D. Gordon, E. M. Laumann, T. O. Eggebrecht, A. T. Wheelock, M. D. 2024-09-11 doi:10.1101/2024.09.09.612056 Cold Spring Harbor Laboratory Press 2024-09-11 <![CDATA[ Autism and Intellectual Disability-Associated MYT1L Mutation Alters Human Cortical Interneuron Differentiation, Maturation, and Physiology ]]> https://biorxiv.org/content/10.1101/2024.09.11.612541v1?rss=1 Prakasam, R. Determan, J. Narasimhan, M. Shen, R. Saleh, M. Chapman, G. Kaushik, K. Gontarz, P. Meganathan, K. Hakim, B. Zhang, B. Huettner, J. E. Kroll, K. L. 2024-09-12 doi:10.1101/2024.09.11.612541 Cold Spring Harbor Laboratory Press 2024-09-12 <![CDATA[ Predictive Prioritization of Enhancers Associated with Pancreas Disease Risk ]]> https://biorxiv.org/content/10.1101/2024.09.07.611794v1?rss=1 Wang, L. Baek, S. Prasad, G. Wildenthal, J. Guo, K. Sturgill, D. Truongvo, T. Char, E. Pegoraro, G. McKinnon, K. The Pancreatic Cancer Cohort Consortium, The Pancreatic Cancer Case-Control Consortium, Hoskins, J. W. Amundadottir, L. T. Arda, E. 2024-09-13 doi:10.1101/2024.09.07.611794 Cold Spring Harbor Laboratory Press 2024-09-13 <![CDATA[ Predicting Task Activation Maps from Resting-State Functional Connectivity using Deep Learning ]]> https://biorxiv.org/content/10.1101/2024.09.10.612309v1?rss=1 Madsen, S. J. Uddin, L. Q. Mumford, J. A. Barch, D. M. Fair, D. A. Gotlib, I. H. Poldrack, R. A. Kuceyeski, A. Saggar, M. 2024-09-14 doi:10.1101/2024.09.10.612309 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Enantiomeric histidine-rich peptide coacervates enhance antigen delivery to T cells ]]> https://biorxiv.org/content/10.1101/2024.09.10.612317v1?rss=1 Pramanik, U. Das, A. Brown, E. M. Struckman, H. L. Wang, H. Stealey, S. Sprunger, M. L. Abdul, W. Fascetti, J. Mondal, J. Silva, J. R. Zustiak, S. P. Jackrel, M. E. Rudra, J. S. 2024-09-14 doi:10.1101/2024.09.10.612317 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ The L1CAM SAX-7 is an antagonistic modulator of Erk signaling ]]> https://biorxiv.org/content/10.1101/2024.09.14.613091v1?rss=1 Moseley-Alldredge, M. Aragon, C. Vargus, M. Alley, D. Somia, N. Chen, L. 2024-09-16 doi:10.1101/2024.09.14.613091 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ A single ancestral ANP32 locus in ticks creates multiple protein variants that all support the Thogoto virus polymerase ]]> https://biorxiv.org/content/10.1101/2024.09.16.613268v1?rss=1 Zhang, Z. Nipper, T. Aziati, I. D. Boon, A. Mehle, A. 2024-09-17 doi:10.1101/2024.09.16.613268 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ A chronic murine model of pulmonary Acinetobacter baumannii infection enabling the investigation of late virulence factors, long-term antibiotic treatments, and polymicrobial infections ]]> https://biorxiv.org/content/10.1101/2024.09.17.613469v1?rss=1 Jackson-Litteken, C. D. D. Di Venanzio, G. Janet-Maitre, M. de Araujo Castro, I. Mackel, J. J. Rosen, D. Lopez, C. B. Feldman, M. 2024-09-17 doi:10.1101/2024.09.17.613469 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ A dopaminergic basis of behavioral control ]]> https://biorxiv.org/content/10.1101/2024.09.17.613524v1?rss=1 Ballard, I. C. Furman, D. J. Berry, A. S. White, R. L. Jagust, W. J. Kayser, A. S. D'Esposito, M. 2024-09-17 doi:10.1101/2024.09.17.613524 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ Cutibacterium adaptation to life on humans provides a novel biomarker of C. acnes infections. ]]> https://biorxiv.org/content/10.1101/2024.09.18.613542v1?rss=1 Shafiuddin, M. Prather, G. W. Huang, W. C. Anton, J. R. Martin, A. L. Sillart, S. B. Tang, J. Z. Vittori, M. R. Prinsen, M. J. Ninneman, J. J. Manithody, C. Henderson, J. P. Aleem, A. W. Ilagan, M. X. G. McCoy, W. H. 2024-09-18 doi:10.1101/2024.09.18.613542 Cold Spring Harbor Laboratory Press 2024-09-18 <![CDATA[ Development and evaluation of a non-invasive brain-spine interface using transcutaneous spinal cord stimulation ]]> https://biorxiv.org/content/10.1101/2024.09.16.612897v1?rss=1 Atkinson, C. J. Lombardi, L. Lang, M. Keesey, R. E. Hawthorn, R. Seitz, Z. Leuthardt, E. C. Brunner, P. Seanez, I. 2024-09-19 doi:10.1101/2024.09.16.612897 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Peripheral opioid receptor antagonism alleviates fentanyl-induced cardiorespiratory depression and is devoid of aversive effects ]]> https://biorxiv.org/content/10.1101/2024.09.16.613257v1?rss=1 Ruyle, B. Masud, S. Kesaraju, R. Tahirkheli, M. Modh, J. Lopera, S. A. Lintz, T. Higginbotham, J. A. Massaly, N. Moron-Concepcion, J. 2024-09-19 doi:10.1101/2024.09.16.613257 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ An integrated view of the structure and function of the human 4D nucleome ]]> https://biorxiv.org/content/10.1101/2024.09.17.613111v1?rss=1 The 4D Nucleome Consortium, Dekker, J. Oksuz, B. A. Zhang, Y. Wang, Y. Minsk, M. K. Kuang, S. Yang, L. Gibcus, J. H. Krietenstein, N. Rando, O. Xu, J. Janssens, D. H. Henikoff, S. Kukalev, A. Willemin, A. Winick-Ng, W. Kempfer, R. Pombo, A. Yu, M. Kumar, P. Zhang, L. Belmont, A. S. Sasaki, T. van Schaik, T. Brueckner, L. Peric-Hupkes, D. van Steensel, B. Wang, P. Chai, H. Kim, M. Ruan, Y. Zhang, R. Quinodoz, S. A. Bhat, P. Guttman, M. Zhao, W. Chien, S. Liu, Y. Venev, S. V. Plewczynski, D. Irastorza Azcarate, I. Szabo, D. Thieme, C. J. Szczepinska, 2024-09-19 doi:10.1101/2024.09.17.613111 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Speed modulations in grid cell information geometry ]]> https://biorxiv.org/content/10.1101/2024.09.18.613797v1?rss=1 Ye, Z. Wessel, R. 2024-09-19 doi:10.1101/2024.09.18.613797 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription ]]> https://biorxiv.org/content/10.1101/2024.09.17.613488v1?rss=1 Taghbalout, A. Tung, C.-H. Clow, P. A. Wang, P. Tjong, H. Wong, C. H. Mao, D. D. Maurya, R. Huang, M.-F. Ngan, C. Y. Kim, A. H. Wei, C.-L. 2024-09-20 doi:10.1101/2024.09.17.613488 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Arterial spin labelling perfusion MRI analysis for the Human Connectome Project Lifespan Ageing and Development studies ]]> https://biorxiv.org/content/10.1101/2024.09.19.613907v1?rss=1 Kirk, T. F. McConnell, F. A. K. Toner, J. Craig, M. S. Carone, D. Li, X. Suzuki, Y. Coalson, T. S. Harms, M. P. Glasser, M. F. Chappell, M. A. 2024-09-20 doi:10.1101/2024.09.19.613907 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ CCR2 limits inflammatory functions of CD8 TRM cells that impair recognition memory during recovery from WNV encephalitis ]]> https://biorxiv.org/content/10.1101/2024.09.17.613307v1?rss=1 Ai, S. Liu, J. Hill, J. D. Jiang, X. Klein, R. S. 2024-09-21 doi:10.1101/2024.09.17.613307 Cold Spring Harbor Laboratory Press 2024-09-21 <![CDATA[ Examination of INPP5A in uveal melanoma uncovers novel calcium transients ]]> https://biorxiv.org/content/10.1101/2024.09.18.613756v1?rss=1 Onken, M. D. Kaltenbronn, K. M. Makepeace, C. M. Piggott, K. D. Blumer, K. J. 2024-09-22 doi:10.1101/2024.09.18.613756 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Temperature-dependent predation predicts a more reptilian future ]]> https://biorxiv.org/content/10.1101/2024.09.19.613816v1?rss=1 Grady, J. M. Amme, J. L. Bhaskaran-Nair, K. Sinha, V. Brunwasser, S. J. Record, S. Dell, A. I. Hengen, K. B. 2024-09-22 doi:10.1101/2024.09.19.613816 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Lysosomal LRRC8 complex regulates lysosomal pH, morphology and systemic glucose metabolism ]]> https://biorxiv.org/content/10.1101/2024.09.22.614256v1?rss=1 Kumar, A. Zhao, Y. Xie, L. Chadda, R. Abraham, N. Hong, J. Feng, E. Tranter, J. D. Rawnsley, D. Liu, H. Henry, K. M. Meyer, G. Hu, M. Xu, H. Hinton, A. Grueter, C. E. Abel, E. D. Norris, A. W. Diwan, A. Sah, R. 2024-09-23 doi:10.1101/2024.09.22.614256 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ Transient Notch Activation Converts Pluripotent Stem Cell-Derived Cardiomyocytes towards a Purkinje Fiber Fate ]]> https://biorxiv.org/content/10.1101/2024.09.22.614353v1?rss=1 Gonzalez, D. M. Dariolli, R. Moyett, J. Song, S. Shewale, B. Bliley, J. M. Ma'ayan, A. Rentschler, S. Feinberg, A. W. Sobie, E. Dubois, N. 2024-09-23 doi:10.1101/2024.09.22.614353 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ Heterogeneous Kinetics of Nanobubble Ultrasound Contrast Agent and Angiogenic Signaling in Head and Neck Cancer ]]> https://biorxiv.org/content/10.1101/2024.09.22.614362v1?rss=1 Van Court, B. Ciccaglione, M. Neupert, B. Knitz, M. W. Maroney, S. P. Nguyen, D. Abdelazeem, K. N. M. Exner, A. A. Saviola, A. J. Benninger, R. K. P. Karam, S. D. 2024-09-24 doi:10.1101/2024.09.22.614362 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ The dimerization domain of SARS CoV 2 Nucleocapsid protein is partially disordered as a monomer and forms a high affinity dynamic complex. ]]> https://biorxiv.org/content/10.1101/2024.09.25.614883v1?rss=1 Cubuk, J. Incicco, J. J. Hall, K. B. Holehouse, A. S. Stuchell-Brereton, M. D. Soranno, A. 2024-09-25 doi:10.1101/2024.09.25.614883 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ SARS-CoV-2 ORF3a Protein Impairs Syncytiotrophoblast Maturation, Alters ZO-1 Localization, and Shifts Autophagic Pathways in Trophoblast Cells and 3D Organoids ]]> https://biorxiv.org/content/10.1101/2024.09.25.614931v1?rss=1 Kumar, D. Karvas, R. M. Jones, B. McColl, E. Diveley, E. Jash, S. Sharma, S. Kelly, J. Theunissen, T. Mysorekar, I. U. 2024-09-25 doi:10.1101/2024.09.25.614931 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Lipopolysaccharide Induces Trained Innate Immune Tolerance in the Heart Through Interferon Signaling in a Model of Stress-Induced Cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2024.09.24.614798v1?rss=1 Lim, K. R. Q. Amrute, J. M. Kovacs, A. Diwan, A. Williams, D. L. Mann, D. L. 2024-09-26 doi:10.1101/2024.09.24.614798 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ The effects of P2Y12 loss on microglial gene expression, dynamics, and injury response in the cerebellum and cerebral cortex. ]]> https://biorxiv.org/content/10.1101/2024.09.25.614526v1?rss=1 Stoessel, M. B. Stowell, R. D. Lowery, R. L. Le, L. H. Vu, A. N. Whitelaw, B. S. Majewska, A. K. 2024-09-26 doi:10.1101/2024.09.25.614526 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Inhibition of Ribosome Biogenesis in vivo Causes p53-Dependent Death and p53-Independent Dysfunction ]]> https://biorxiv.org/content/10.1101/2024.09.25.614959v1?rss=1 Cho, C. J. Nguyen, T. Rougeau, A. K. Huang, Y.-Z. To, S. Lin, X. Gamage, S. T. Meier, J. L. Mills, J. C. 2024-09-26 doi:10.1101/2024.09.25.614959 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Maximizing memory capacity in heterogeneous networks ]]> https://biorxiv.org/content/10.1101/2024.09.25.615056v1?rss=1 Zhang, K. Tavoni, G. 2024-09-27 doi:10.1101/2024.09.25.615056 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Charting Cortical-Layer Specific Area Boundaries Using Gibbs Ringing Attenuated T1w/T2w-FLAIR Myelin MRI ]]> https://biorxiv.org/content/10.1101/2024.09.27.615294v1?rss=1 Autio, J. A. Uematsu, A. Ikeda, T. Ose, T. Hou, Y. Magrou, L. Kimura, I. Ohno, M. Murata, K. Coalson, T. Kennedy, H. Glasser, M. F. Van Essen, D. C. Hayashi, T. 2024-09-28 doi:10.1101/2024.09.27.615294 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ Lysophospholipid headgroup size, and acyl chain length and saturation differentially affect vacuole acidification, Ca2+ transport, and fusion ]]> https://biorxiv.org/content/10.1101/2024.09.27.615487v1?rss=1 Zhang, C. Feng, Y. Calderin, J. D. Balutowski, A. Ahmed, R. Knapp, C. Fratti, R. A. 2024-09-28 doi:10.1101/2024.09.27.615487 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ Non-invasive brain stimulation over the Frontopolar Cortex promotes willingness to exert cognitive effort in a foraging-like sequential choice task ]]> https://biorxiv.org/content/10.1101/2024.09.27.615545v1?rss=1 Bogdanov, M. Bustamante, L. A. Devine, S. Sheldon, S. Otto, A. R. 2024-09-30 doi:10.1101/2024.09.27.615545 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Functional classification of tauopathy strains reveals the role of protofilament core residues. ]]> https://biorxiv.org/content/10.1101/2024.09.30.615521v1?rss=1 Vaquer-Alicea, J. Manon, V. Bommareddy, V. Kunach, P. Gupta, A. Monistrol, J. Perez, V. A. Tran, H. T. Saez-Calveras, N. Du, S. Batra, S. White, C. L. Joachimiak, L. A. Shahmoradian, S. H. Diamond, M. I. 2024-10-01 doi:10.1101/2024.09.30.615521 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ S1PR1 Regulates Lymphatic Valve Development And Prevents Ileitis-Independent Tertiary Lymphoid Organ Formation ]]> https://biorxiv.org/content/10.1101/2024.09.30.615915v1?rss=1 Geng, X. Chen, L. Ahmed, Z. Formigari, G. P. Ho, Y. Gaudio, I. D. Datilo, M. N. Azartash-Namin, Z. J. Shan, X. Keshari, R. S. Chen, H. Lupu, F. Xia, L. Randolph, G. J. Zawieja, S. D. Camerer, E. Davis, M. J. Srinivasan, R. S. 2024-10-01 doi:10.1101/2024.09.30.615915 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Function of the alternative electron transport chain in the Cryptosporidium parvum mitosome ]]> https://biorxiv.org/content/10.1101/2024.10.01.616074v1?rss=1 Deng, S. Sibley, L. D. 2024-10-01 doi:10.1101/2024.10.01.616074 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Circulatory proteins shape microglia state and boost phagocytosis ]]> https://biorxiv.org/content/10.1101/2024.09.30.615861v1?rss=1 Lu, N. Moran-Losada, P. Hahn, O. Saksena, A. Tapp, E. Chadarevian, J. P. Dong, W. Shi, S. M. Shuken, S. R. Guldner, I. Zeng, W. To, N.-S. Wong, P. S. Hasselmann, J. Davtyan, H. Sun, J. Li, L. Luo, J. Yang, A. C. Li, Q. Cheung, T. H. Abu-Remaileh, M. Blurton-Jones, M. Wyss-Coray, T. 2024-10-02 doi:10.1101/2024.09.30.615861 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Autophagic enhancer rescues Tau accumulation in a stem cell model of frontotemporal dementia ]]> https://biorxiv.org/content/10.1101/2024.09.30.615921v1?rss=1 Mirfakhar, F. Marsh, J. Minaya, M. Pak, S. Silverman, G. Perlmutter, D. Macauley, S. Karch, C. 2024-10-02 doi:10.1101/2024.09.30.615921 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Loss of SARM1 protects against retinal ganglion cell degeneration in Autosomal Dominant Optic Atrophy ]]> https://biorxiv.org/content/10.1101/2024.09.30.615936v1?rss=1 Ding, C. Ndiaye, P. S. Campbell, S. R. Fry, M. Y. Gong, J. Wienbar, S. R. Gibbs, W. S. Morquette, P. Chao, L. H. Do, M. T. H. Schwarz, T. L. 2024-10-02 doi:10.1101/2024.09.30.615936 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Single-cell RNA-seq Reveals Early Transcriptional Programs of the Maternal to Zygote Transition in Mice and Rats ]]> https://biorxiv.org/content/10.1101/2024.09.30.615942v1?rss=1 Su, Y. Kouranova, E. Shea, J. Cui, X. Su, Z. 2024-10-02 doi:10.1101/2024.09.30.615942 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Sex differences in the clinical manifestation of autosomal dominant frontotemporal dementia ]]> https://biorxiv.org/content/10.1101/2024.10.01.614851v1?rss=1 Memel, M. Staffaroni, A. Ilan-Gala, I. Garcia Castro, J. Kornak, J. Tartaglia, C. Saloner, R. VandeBunte, A. Paolillo, E. Cadwallader, C. Chen, C. Gorno-Tempini, M. L. Mandelli, M. Apostolova, L. Graff-Radford, N. Litvan, I. Bayram, E. Pressman, P. Miyagawa, T. Mackenzie, I. Goldman, J. Darby, R. Appleby, B. Petrucelli, L. Gendron, T. Heuer, H. Forseberg, L. Rojas, J. Boeve, B. Brushaber, N. Domoto-Reilly, K. Ghoshal, N. Lapid, M. Pascual, B. Lee, S. Ramos, E. Ramanan, V. Rademakers, R. Rascovsky, K. Pantelyat, A. Masdeu, J. Snyder, A. Boxer, A. Rosen 2024-10-03 doi:10.1101/2024.10.01.614851 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ A simple action reduces food intake and obesity in mice ]]> https://biorxiv.org/content/10.1101/2024.10.01.615599v1?rss=1 Barrett, M. R. Pan, Y. Murrell, C. Karolczak, E. O. Wang, J. Fang, L. Thompson, J. M. Chang, S. Casey, E. Czarny, J. So, W. L. Reichenbach, A. Stark, R. Taghipourbibalan, H. Penna, S. R. McCullough, K. B. Westbrook, S. Matikainen-Ankeny, B. Cazares, V. A. Delevich, K. Fobbs, W. Maloney, S. Sutton Hickey, A. McCutcheon, J. E. Andrews, Z. Creed, M. Kravitz, A. V. 2024-10-03 doi:10.1101/2024.10.01.615599 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Baby Open Brains: An Open-Source Repository of Infant Brain Segmentations ]]> https://biorxiv.org/content/10.1101/2024.10.02.616147v1?rss=1 Feczko, E. J. Stoyell, S. M. Moore, L. A. Alexopoulos, D. Bagonis, M. Barrett, K. Bower, B. Cavender, A. Chamberlain, T. A. Conan, G. Day, T. K. Goradia, D. Graham, A. Heisler-Roman, L. Hendrickson, T. J. Houghton, A. Kardan, O. Kiffmeyer, E. A. Lee, E. G. Lundquist, J. T. Lucena, C. Martin, T. Mummaneni, A. Myricks, M. Narnur, P. Perrone, A. J. Reiners, P. Rueter, A. R. Saw, H. Styner, M. Sung, S. Tiklasky, B. Wisnowski, J. L. Yacoub, E. Zimmermann, B. Smyser, C. D. Rosenberg, M. D. Fair, D. A. Elison, J. T. 2024-10-03 doi:10.1101/2024.10.02.616147 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Novel murine model of human astrovirus infection reveals a cardiovascular tropism ]]> https://biorxiv.org/content/10.1101/2024.10.03.616429v1?rss=1 10-fold in heart tissue or serum samples from Rag1 or Stat1 knockout mice, demonstrating the role of both adaptive and innate immunity in the response to VA1 infection. Based on the in vivo tropisms, we also tested cardiac-derived primary cells and determined that VA1 can replicate in human cardiac microvascular and coronary artery endothelial cells, suggesting a novel cardiovascular tropism in human cells. This novel in vivo model of a human-infecting astrovirus enables further characterization of viral pathogenesis and reveals a new cardiovascular tropism of astroviruses. Author SummaryAstroviruses typically cause viral diarrhea in humans but can also cause serious infections of the brain. Previously, the methods available to study how these viruses lead to invasive infections were limited. Here, we describe the first system to study human-infecting astroviruses using mice. We demonstrate that mice are susceptible to astrovirus VA1, a strain that commonly infects humans and has been linked to fatal brain infections. The virus infected heart tissue and was associated with inflammation. When mice with impaired immune systems were infected with VA1, they were found to have higher amounts of virus in their hearts and blood. Linking back to human health, we also found that VA1 can infect cells derived from human blood vessels of the heart. This model will enable us to better understand how astroviruses cause disease and how the immune system responds to infection. Our findings also suggest that astroviruses could be linked to cardiovascular diseases, including in humans. In the future, we can develop interventions that will prevent and treat astrovirus infections in humans. ]]> Owen, M. C. Zhou, Y. Dudley, H. Feehley, T. Hahn, A. Yokoyama, C. C. Axelrod, M. L. Lin, C.-Y. Wang, D. Janowski, A. B. 2024-10-03 doi:10.1101/2024.10.03.616429 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Quantitative proteomic mass spectrometry of protein kinases to determine dynamic heterogeneity of the human kinome ]]> https://biorxiv.org/content/10.1101/2024.10.04.614143v1?rss=1 300 kinases in a single LC-MS experiment using ten micrograms protein from human tissues including biopsies. This enables absolute quantitation of kinase protein abundance at attomole-femtomole expression levels, requiring no kinase enrichment and less than ten micrograms of starting protein from flash-frozen and formalin fixed paraffin embedded tissues. Breast cancer biopsies, organoids, and cell lines were analyzed using the SureQuant method, demonstrating the heterogeneity of kinase protein expression across and within breast cancer clinical subtypes. Kinome quantitation was coupled with nanoscale phosphoproteomics, providing a feasible method for novel clinical diagnosis and understanding of patient kinome responses to treatment. ]]> East, M. P. Sprung, R. W. Okumu, D. O. Olivares-Quintero, J. F. Joisa, C. U. Chen, X. Zhang, Q. Erdmann-Gilmore, P. Mi, Y. Sciaky, N. Malone, J. P. Bhatia, S. McCabe, I. C. Xu, Y. Sutcliffe, M. D. Luo, J. Spears, P. A. Perou, C. M. Earp, H. S. Carey, L. A. Yeh, J. J. Spector, D. L. Gomez, S. M. Spanheimer, P. M. Townsend, R. R. Johnson, G. L. 2024-10-04 doi:10.1101/2024.10.04.614143 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ SATB2 and circ3915 RNA chromatin dysregulation drive KRAS-like oncogenic transformation ]]> https://biorxiv.org/content/10.1101/2024.10.04.616681v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@1314b69org.highwire.dtl.DTLVardef@14df9e1org.highwire.dtl.DTLVardef@505bddorg.highwire.dtl.DTLVardef@1bf3fab_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Eleazer, R. George, S. Shoemaker, L. Saintilnord, W. Lau, K. Chandler, D. Fondufe-Mittendorf, Y. 2024-10-04 doi:10.1101/2024.10.04.616681 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Monosynaptic ventral tegmental area glutamate projections to the locus coeruleus enhance aversive processing ]]> https://biorxiv.org/content/10.1101/2024.10.04.615025v1?rss=1 Parker, K. E. Kuo, C.-C. Buckley, A. R. Patterson, A. P. Duong, V. Hunter, S. C. McCall, J. G. 2024-10-05 doi:10.1101/2024.10.04.615025 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ Suppression of NRF2-dependent cancer growth by a covalent allosteric molecular glue ]]> https://biorxiv.org/content/10.1101/2024.10.04.616592v1?rss=1 Roy, N. Wyseure, T. Lo, I.-C. Metzger, J. Eissler, C. L. Bernard, S. M. Bok, I. Snead, A. N. Parker, A. Green, J. C. Inloes, J. Jacinto, S. R. Kuenzi, B. Horning, B. D. Ibrahim, N. Grabow, S. Panda, H. Bhatt, D. P. Saeidi, S. Zolkind, P. Rush, Z. Negri, K. Williams, H. N. Walton, E. Pastuszka, M. K. Sigler, J. J. Tran, E. Hee, K. McLaughlin, J. Ambrus-Aikelin, G. Pollock, J. Abraham, R. T. Kinsella, T. M. Simon, G. M. Major, M. B. Weinstein, D. S. Patricelli, M. P. 2024-10-05 doi:10.1101/2024.10.04.616592 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ The brain's "dark energy" puzzle upgraded: FDG uptake, delivery and phosphorylation, and their coupling with resting-state brain activity ]]> https://biorxiv.org/content/10.1101/2024.10.05.615717v1?rss=1 Volpi, T. Lee, J. J. Vlassenko, A. G. Goyal, M. S. Corbetta, M. Bertoldo, A. 2024-10-07 doi:10.1101/2024.10.05.615717 Cold Spring Harbor Laboratory Press 2024-10-07 <![CDATA[ Cardiolipin deficiency disrupts CoQ redox state and induces steatohepatitis ]]> https://biorxiv.org/content/10.1101/2024.10.10.617517v1?rss=1 Brothwell, M. J. Cao, G. Maschek, J. A. Poss, A. M. Peterlin, A. D. Wang, L. Baker, T. B. Shahtout, J. L. Siripoksup, P. Pearce, Q. J. Johnson, J. M. Finger, F. M. Prola, A. Pellizzari, S. A. Hale, G. L. Manuel, A. M. Watanabe, S. Miranda, E. R. Affolter, K. E. Tippetts, T. S. Nikolova, L. S. Choi, R. H. Decker, S. T. Patil, M. Catrow, J. L. Holland, W. L. Nowinski, S. M. Lark, D. S. Fisher-Wellman, K. H. Mimche, P. N. Evason, K. J. Cox, J. E. Summers, S. A. Gerhart-Hines, Z. Funai, K. 2024-10-10 doi:10.1101/2024.10.10.617517 Cold Spring Harbor Laboratory Press 2024-10-10 <![CDATA[ Danicamtiv reduces myosin's working stroke but enhances contraction by activating the thin filament ]]> https://biorxiv.org/content/10.1101/2024.10.09.617269v1?rss=1 Scott, B. Greenberg, L. Squarci, C. Campbell, K. S. Greenberg, M. J. 2024-10-11 doi:10.1101/2024.10.09.617269 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Targetable Treatment Resistance in Thyroid Cancer with Clonal Hematopoiesis ]]> https://biorxiv.org/content/10.1101/2024.10.10.617685v1?rss=1 Tiedje, V. Vela, P. S. Yang, J. L. Untch, B. R. Boucai, L. Stonestrom, A. J. Costa, A. B. Exposito, S. F. Srivastava, A. Kerpelev, M. Greenberg, J. Wereski, M. Kulick, A. Chen, K. Qin, T. Im, S.-Y. Krishnan, A. Benitez, A. R. M. Pluvinet, R. Sahin, M. Menghrajani, K. Krishnamoorthy, G. P. De Stanchina, E. Zehir, A. Satija, R. Knauf, J. Bowman, R. Esteller, M. Devlin, S. M. Berger, M. Koche, R. Fagin, J. A. Levine, R. 2024-10-11 doi:10.1101/2024.10.10.617685 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ The Curated Cancer Cell Atlas: comprehensive characterisation of tumours at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2024.10.11.617836v1?rss=1 Tyler, M. Gavish, A. Barbolin, C. Tschernichovsky, R. Hoefflin, R. Mints, M. Puram, S. V. Tirosh, I. 2024-10-12 doi:10.1101/2024.10.11.617836 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Characterization of neural infection by Oropouche orthobunyavirus ]]> https://biorxiv.org/content/10.1101/2024.10.11.617875v1?rss=1 Connors, K. A. Pedlow, M. R. Frey, Z. D. McGaughey, J. J. Amarasinghe, G. K. Duprex, W. P. D'Aiuto, L. Wills, Z. P. Hartman, A. L. 2024-10-12 doi:10.1101/2024.10.11.617875 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Dissecting Regulatory Non-Coding Heart Disease GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Pathophysiological Relevance to Heart Failure ]]> https://biorxiv.org/content/10.1101/2024.10.08.617295v1?rss=1 Gill, R. Lu, D. Eres, I. Lu, J. Cui, J. Yu, Z. J. Yamawaki, T. Zhou, H. Pei, B. Amrute, J. Ang, Y.-s. Wang, S. Lavine, K. Ason, B. Li, C.-M. K. Hsu, Y.-H. 2024-10-13 doi:10.1101/2024.10.08.617295 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ Granulocyte colony-stimulating factor protects against arthritogenic alphavirus pathogenesis in a type I IFN-dependent manner ]]> https://biorxiv.org/content/10.1101/2024.10.09.617470v1?rss=1 Hameed, M. Hossain, M. S. Daamen, A. Lipsky, P. Weger-Lucarelli, J. 2024-10-13 doi:10.1101/2024.10.09.617470 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ mRNA-based influenza vaccine expands breadth of B cell response in humans ]]> https://biorxiv.org/content/10.1101/2024.10.10.617255v1?rss=1 Matz, H. C. Yu, T.-G. Zhou, J. Q. Peyton, L. Madsen, A. Han, F. Schmitz, A. J. Horvath, S. C. Dixit, K. Keplinger, H. K. Strnad, B. S. Hoegger, M. J. Middleton, W. D. Klebert, M. K. Lin, N. H. Nachbagauer, R. Paris, R. Turner, J. S. Presti, R. M. Lee, J. Ellebedy, A. 2024-10-13 doi:10.1101/2024.10.10.617255 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ Obesity-Associated Changes in Immune Cell Dynamics During Alphavirus Infection Revealed by Single Cell Transcriptomic Analysis ]]> https://biorxiv.org/content/10.1101/2024.10.10.617696v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@11e9cbdorg.highwire.dtl.DTLVardef@c44512org.highwire.dtl.DTLVardef@192da94org.highwire.dtl.DTLVardef@4c5ea5_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIObesity worsens disease outcomes following arthritogenic alphavirus infection. C_LIO_LIArthritogenic alphavirus infection causes significant shifts in immune cell populations in the blood and footpad. C_LIO_LIBlood monocytes from lean mice had higher expression of interferon response genes at the later stage of infection. C_LIO_LIFootpads in lean mice have an expanded population of F4/80lo macrophages with an intense interferon response gene signature before and after alphavirus infection that is not found in obese mice. C_LIO_LIMacrophages in obese mice express lower levels of interferon response genes, have a unique necroptosis signature, and higher F4/80 expression. C_LI ]]> Hameed, M. Daamen, A. Hossain, M. S. Coutermarsh-Ott, S. Lipsky, P. E. Weger-Lucarelli, J. 2024-10-13 doi:10.1101/2024.10.10.617696 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ Diversity of ancestral brainstem noradrenergic neurons across species and multiple biological factors ]]> https://biorxiv.org/content/10.1101/2024.10.14.618224v1?rss=1 Kelberman, M. A. Rodberg, E. Arabzadeh, E. Bair-Marshall, C. J. Berridge, C. W. Berrocoso, E. Breton-Provencher, V. Chandler, D. J. Che, A. Davy, O. Devilbiss, D. M. Downs, A. M. Drummond, G. Dvorkin, R. Fazlali, Z. Froemke, R. C. Glennon, E. Gold, J. I. Ito, H. Jiang, X. Johansen, J. P. Kaye, A. P. Kim, J. R. Kuo, C.-c. Liu, R.-j. Liu, Y. Llorca-Torralba, M. McCall, J. G. McElligott, Z. A. McKinney, A. M. Miguelez, C. Min, M.-Y. Nowlan, A. C. Omrani, M. Pickering, A. E. Poe, G. R. Ranjbar-Slamloo, Y. Razquin, J. Rodenkirch, C. Sales, A. C. Satyasambit, 2024-10-16 doi:10.1101/2024.10.14.618224 Cold Spring Harbor Laboratory Press 2024-10-16 <![CDATA[ Epigenetic and 3D genome reprogramming during the aging of human hippocampus ]]> https://biorxiv.org/content/10.1101/2024.10.14.618338v1?rss=1 Zemke, N. Lee, S. Mamde, S. Yang, B. Berchtold, N. Garduno, M. Indralingam, H. Bartosik, W. Lau, P. Dong, K. Yang, A. Tani, Y. Chen, C. Zeng, Q. Ajith, V. Tong, L. Seng, C. Li, D. Wang, T. Xu, X. Ren, B. 2024-10-17 doi:10.1101/2024.10.14.618338 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ A Cortical Microcircuit for Region-Specific Credit Assignment in Reinforcement Learning ]]> https://biorxiv.org/content/10.1101/2024.10.15.618337v1?rss=1 Chevy, Q. Szadai, Z. Hertäg, L. Moll, M. Gibson, E. T. Costa, R. P. Kepecs, A. 2024-10-17 doi:10.1101/2024.10.15.618337 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Spatial proteomics of Onchocerca volvulus with pleomorphic neoplasms shows local and systemic dysregulation of protein expression ]]> https://biorxiv.org/content/10.1101/2024.10.15.618383v1?rss=1 Di Maggio, L. S. Fischer, K. Rosa, B. A. Yates, D. Cho, B.-K. Lukowski, J. Zamacona Calderon, A. Son, M. Goo, Y. A. Opoku, N. O. Weil, G. J. Mitreva, M. Fischer, P. U. 2024-10-17 doi:10.1101/2024.10.15.618383 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Human TRPV4 engineering yields an ultrasound-sensitive actuator for sonogenetics ]]> https://biorxiv.org/content/10.1101/2024.10.16.618766v1?rss=1 Zhao, L. Xu, K. Talyzina, I. Shi, J. Li, S. Yang, Y. Zhang, S. Zheng, j. Sobolevsky, A. Chen, H. Cui, J. 2024-10-18 doi:10.1101/2024.10.16.618766 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ B cell expression of the enzyme PexRAP, an intermediary in ether lipid biosynthesis, promotes antibody responses and germinal center size ]]> https://biorxiv.org/content/10.1101/2024.10.17.618760v1?rss=1 Cho, S. H. Jones, M. A. Meyer, K. Anderson, D. M. Chetyrkin, S. Calcutt, M. W. Caprioli, R. M. Semekovich, C. F. Boothby, M. R. 2024-10-18 doi:10.1101/2024.10.17.618760 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Phosphorylation Toggles the SARS-CoV-2 Nucleocapsid Protein Between Two Membrane-Associated Condensate States ]]> https://biorxiv.org/content/10.1101/2024.10.17.618867v1?rss=1 Favetta, B. Wang, H. Cubuk, J. Barai, M. Ramirez, C. Gormley, A. J. Murthy, S. Soranno, A. Shi, Z. Schuster, B. S. 2024-10-18 doi:10.1101/2024.10.17.618867 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Prey attraction in a generalist microbial predator, Dictyostelium discoideum ]]> https://biorxiv.org/content/10.1101/2024.10.17.618972v1?rss=1 Shreenidhi, P. M. McCabe, R. I. Queller, D. C. Strassmann, J. E. 2024-10-21 doi:10.1101/2024.10.17.618972 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ Shc1 cooperates with Frs2 and Shp2 to recruit Grb2 in FGF-induced lens development ]]> https://biorxiv.org/content/10.1101/2024.10.20.619055v1?rss=1 Wang, Q. Li, H. Mao, Y. Garg, A. Park, E. S. Wu, Y. Chow, A. Peregrin, J. Zhang, X. 2024-10-22 doi:10.1101/2024.10.20.619055 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ A rapid, facile, and economical method for the isolation of ribosomes and translational machinery for structural and functional studies ]]> https://biorxiv.org/content/10.1101/2024.10.21.619433v1?rss=1 Erath, J. Kemper, D. Mugo, E. Jacoby, A. Valenzuela, E. Jungers, C. F. Beatty, W. L. Hashem, Y. Jovanovic, M. Djuranovic, S. Djuranovic, S. P. 2024-10-22 doi:10.1101/2024.10.21.619433 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Reduction in ETFDH expression optimizes cancer cell bioenergetics ]]> https://biorxiv.org/content/10.1101/2024.10.25.620155v1?rss=1 Papadopoli, D. Palia, R. Jovanovic, P. Tabaries, S. Ciccolini, E. Sabourin, V. Igelmann, S. McLaughlan, S. Zhan, L. Kim, H. Chekkal, N. Szkop, K. J. Bertomeu, T. Zeng, J. Vassalakis, J. Afzali, F. Mzoughi, S. Guccione, E. Tyers, M. Avizonis, D. Larsson, O. Postovit, L.-M. Djuranovic, S. Ursini-Siegel, J. Siegel, P. M. Pollak, M. Topisirovic, I. 2024-10-25 doi:10.1101/2024.10.25.620155 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Abl kinases regulate FGF signaling independent of Crk phosphorylation to prevent Peters anomaly ]]> https://biorxiv.org/content/10.1101/2024.10.24.619064v1?rss=1 Wu, H. Mao, Y. Wang, Q. Yu, H. Bouaziz, M. Makrides, N. Koleske, A. J. Radice, G. Zhang, X. 2024-10-26 doi:10.1101/2024.10.24.619064 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ APOBEC3A drives metastasis of ovarian cancer by altering epithelial-to-mesenchymal transition ]]> https://biorxiv.org/content/10.1101/2024.10.25.620297v1?rss=1 Devenport, J. M. Tran, T. Harris, B. R. Fingerman, D. F. DeWeerd, R. A. Elkhidir, L. LaVigne, D. A. Fuh, K. Sun, L. Bednarski, J. J. Drapkin, R. Mullen, M. Green, A. M. 2024-10-28 doi:10.1101/2024.10.25.620297 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Label-Free Optical Biopsy Reveals Biomolecular and Morphological Features of Diabetic Kidney Tissue in 2D and 3D ]]> https://biorxiv.org/content/10.1101/2024.10.27.620507v1?rss=1 View larger version (76K): org.highwire.dtl.DTLVardef@116edb1org.highwire.dtl.DTLVardef@4f010corg.highwire.dtl.DTLVardef@cde718org.highwire.dtl.DTLVardef@1ff0841_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO Label-free indicators of diabetic nephropathies. C_FIG ]]> Fung, A. A. Li, Z. Boote, C. Markov, P. P. Jain, S. A. Shi, L. 2024-10-29 doi:10.1101/2024.10.27.620507 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ DDO-adjuvanted influenza A virus nucleoprotein mRNA vaccine induces robust humoral and cellular type 1 immune responses and protects mice from challenge ]]> https://biorxiv.org/content/10.1101/2024.10.27.620508v1?rss=1 Gnazzo, V. Saleh, H. Castro, I. Boon, A. Pinto, A. Brien, J. Lopez, C. B. 2024-10-29 doi:10.1101/2024.10.27.620508 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Chromosomal and gonadal sex have differing effects on social motivation in mice ]]> https://biorxiv.org/content/10.1101/2024.10.28.620727v1?rss=1 Chaturvedi, S. M. Sarafinovska, S. Selmanovic, D. McCullough, K. B. Swift, R. G. Maloney, S. E. Dougherty, J. D. 2024-10-29 doi:10.1101/2024.10.28.620727 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles ]]> https://biorxiv.org/content/10.1101/2024.10.31.621310v1?rss=1 Song, Y. J. Shinn, M. K. Bangru, S. Wang, Y. Sun, Q. Hao, Q. Chaturvedi, P. Freier, S. M. Perez-Pinera, P. Nelson, E. R. Belmont, A. S. Guttman, M. Prasantth, S. G. Kalsotra, A. Pappu, R. V. Kannanganattu, P. V. 2024-10-31 doi:10.1101/2024.10.31.621310 Cold Spring Harbor Laboratory Press 2024-10-31 <![CDATA[ Metabolic Control of Glycosylation Forms for Establishing Glycan-Dependent Protein Interaction Networks ]]> https://biorxiv.org/content/10.1101/2024.10.30.621210v1?rss=1 Liu, X. Yi, L. Lin, Z. Chen, S. Wang, S. Sheng, Y. Lebrilla, C. B. Garcia, B. A. Xie, Y. 2024-11-01 doi:10.1101/2024.10.30.621210 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Brain functional connectivity, but not neuroanatomy, captures the interrelationship between sex and gender in preadolescents ]]> https://biorxiv.org/content/10.1101/2024.10.31.621379v1?rss=1 Metoki, A. Chauvin, R. J. Gordon, E. M. Laumann, T. O. Kay, B. P. Krimmel, S. R. Marek, S. Wang, A. Van, A. N. Baden, N. J. Suljic, V. Scheidter, K. M. Monk, J. Whiting, F. I. Ramirez-Perez, N. J. Barch, D. M. Sotiras, A. Dosenbach, N. U. F. 2024-11-01 doi:10.1101/2024.10.31.621379 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Novel symbionts reveal amoebae as significant hosts for environmental chlamydiae ]]> https://biorxiv.org/content/10.1101/2024.11.01.621453v1?rss=1 Liu, F. Walker, L. M. Wolf, J. Thompson, C. Haselkorn, T. S. Shi, Y. Ding, J. Strassmann, J. E. Queller, D. Shu, L. 2024-11-01 doi:10.1101/2024.11.01.621453 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Intestinal stem cells enhance local mucosal immunity through apoptotic body phagocytosis ]]> https://biorxiv.org/content/10.1101/2024.10.29.620856v1?rss=1 Zhou, J. Y. Lu, Q. Hu, Y. Fujji, S. Espenschied, S. T. Engelhart, M. J. Lewis, K. J. Karell, P. E. Han, Y. T. Shin, H. Schmidt, R. E. Silver, D. J. Ivanov, A. Yilmaz, O. H. Stappenbeck, T. 2024-11-03 doi:10.1101/2024.10.29.620856 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Cilia dysfunction in the lateral ventricles after neonatal intraventricular hemorrhage does not lead to functional changes in cilia-based CSF flow networks ]]> https://biorxiv.org/content/10.1101/2024.11.03.621724v1?rss=1 Pan, S. Ramagiri, S. Yang, L. Giles, D. A. Xu, I. Garcia Bonilla, M. DeFreitas, D. Siderowf, L. W. Koneru, S. Halupnik, G. L. Koller, G. M. Polavarapu, S. Gupta, D. K. Miller, M. J. Esakky, P. Limbrick, D. D. Bayly, P. V. Horani, A. Brody, S. L. Mahjoub, M. R. Strahle, J. 2024-11-03 doi:10.1101/2024.11.03.621724 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Three positively charged binding sites on the eastern equine encephalitis virus E2 glycoprotein coordinate heparan sulfate- and protein receptor-dependent infection ]]> https://biorxiv.org/content/10.1101/2024.11.04.621500v1?rss=1 Alcorn, M. D. H. Sun, C. Gilliland, T. C. Lukash, T. Crasto, C. M. Raju, S. Diamond, M. Weaver, S. Klimstra, W. B. 2024-11-04 doi:10.1101/2024.11.04.621500 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ Metapredict enables accurate disorder prediction across the Tree of Life ]]> https://biorxiv.org/content/10.1101/2024.11.05.622168v1?rss=1 Lotthammer, J. M. Hernandez-Garcia, J. Griffith, D. Weijers, D. Holehouse, A. S. Emenecker, R. J. 2024-11-07 doi:10.1101/2024.11.05.622168 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ Critical Spacing in Cell-Matrix Mechanical Feedback Controls Tissue Condensation ]]> https://biorxiv.org/content/10.1101/2024.11.05.622090v1?rss=1 Peng, X. Huang, Y. Elson, E. L. Genin, G. M. Feng, X.-Q. 2024-11-08 doi:10.1101/2024.11.05.622090 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Disentangling folding from energetic traps in simulations of disordered proteins ]]> https://biorxiv.org/content/10.1101/2024.11.06.622270v1?rss=1 Lotthammer, J. M. Holehouse, A. S. 2024-11-08 doi:10.1101/2024.11.06.622270 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ DeFrND: detergent-free reconstitution into native nanodiscs with designer membrane scaffold peptides ]]> https://biorxiv.org/content/10.1101/2024.11.07.622281v1?rss=1 Ren, Q. Wang, J. Idikuda, V. Zhang, S. Shin, J. Ludlam, W. G. Real Hernandez, L. M. Levental, I. Martemyanov, K. Chanda, B. Bao, H. 2024-11-08 doi:10.1101/2024.11.07.622281 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Neuropeptides specify and reprogram division of labor in the leafcutter ant Atta cephalotes ]]> https://biorxiv.org/content/10.1101/2024.11.07.622473v1?rss=1 Gilbert, M. B. Glastad, K. M. Fioriti, M. T. Sorek, M. Gannon, T. Xu, D. Pino, L. K. Korotkov, A. Biashad, A. Baeza, J. Lauman, R. Filippova, A. Kacsoh, B. Bonasio, R. Mathis, M. W. Garcia, B. Seluanov, A. Gorbunova, V. Berger, S. L. 2024-11-08 doi:10.1101/2024.11.07.622473 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Proximity proteomics provides a new resource for exploring the function of Afadin and the complexity of cell-cell adherens junctions ]]> https://biorxiv.org/content/10.1101/2024.11.07.622507v1?rss=1 Choi, W. Goldfarb, D. Yan, F. Major, M. Fanning, A. Peifer, M. 2024-11-08 doi:10.1101/2024.11.07.622507 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ The development of aperiodic neural activity in the human brain ]]> https://biorxiv.org/content/10.1101/2024.11.08.622714v1?rss=1 Cross, Z. R. Gray, S. M. Dede, A. J. O. Rivera, Y. M. Yin, Q. Vahidi, P. Rau, E. M. B. Cyr, C. Holubecki, A. M. Asano, E. Lin, J. J. McManus, O. K. Sattar, S. Saez, I. Girgis, F. King-Stephens, D. Weber, P. B. Laxer, K. D. Schuele, S. U. Rosenow, J. M. Wu, J. Y. Kam, S. K. Raskin, J. S. Chang, E. F. Shaikhouni, A. Brunner, P. Roland, J. L. Braga, R. M. Knight, R. T. Ofen, N. Johnson, E. L. 2024-11-09 doi:10.1101/2024.11.08.622714 Cold Spring Harbor Laboratory Press 2024-11-09 <![CDATA[ A global view of the RNA-binding and regulatory protein landscape in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2024.11.07.622524v1?rss=1 Laver, J. D. Duncan, M. Calarco, J. A. 2024-11-11 doi:10.1101/2024.11.07.622524 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ A post-translational cysteine-to-serine conversion in human and mouse insulin generates a diabetogenic neoepitope ]]> https://biorxiv.org/content/10.1101/2024.11.07.622538v1?rss=1 Srivastava, N. Vomund, A. Peterson, O. Abousaway, O. Li, T. Kain, L. Stone, P. Clement, C. Sharma, S. Zhang, B. Joglekar, A. Campisi, L. Hsieh, C.-S. Santambrogio, L. Teyton, L. Arbelaez, A. M. Lichti, C. Wan, X. 2024-11-11 doi:10.1101/2024.11.07.622538 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Elevated type I interferon signaling defines the proliferative advantage of ARF and p53 mutant tumor cells ]]> https://biorxiv.org/content/10.1101/2024.11.11.623046v1?rss=1 Mabry, A. Kuzmicki, C. E. O'Brien, A. Maggi, L. B. Weber, J. D. 2024-11-11 doi:10.1101/2024.11.11.623046 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Human single-neuron activity is modulated by intracranial theta burst stimulation of the basolateral amygdala ]]> https://biorxiv.org/content/10.1101/2024.11.11.622161v1?rss=1 Campbell, J. M. Cowan, R. L. Wahlstrom, K. L. Hollearn, M. K. Jensen, D. Davis, T. Rahimpour, S. Shofty, B. Arain, A. Rolston, J. D. Hamann, S. Wang, S. Eisenman, L. N. Swift, J. Xie, T. Brunner, P. Manns, J. R. Inman, C. S. Smith, E. H. Willie, J. T. 2024-11-12 doi:10.1101/2024.11.11.622161 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ gen3DNet: An R Package for Generating 3D Network Models ]]> https://biorxiv.org/content/10.1101/2024.11.11.623060v1?rss=1 Mollah, S. Morrison, P. Tang, T. Lu, C. 2024-11-12 doi:10.1101/2024.11.11.623060 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Deciphering epigenetic influence of curcumin on histone signatures in breast cancer using 3D network ]]> https://biorxiv.org/content/10.1101/2024.11.13.623008v1?rss=1 Tang, T. Berezin, M. Y. Mollah, S. 2024-11-15 doi:10.1101/2024.11.13.623008 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Human heart assembloids with autologous tissue-resident macrophages recreate physiological immuno-cardiac interactions ]]> https://biorxiv.org/content/10.1101/2024.11.13.623051v1?rss=1 O'Hern, C. Caywood, S. Aminova, S. Kiselev, A. Volmert, B. Wang, F. Sewavi, M.-L. Cao, W. Dionise, M. Muniyandi, P. Popa, M. Basrai, H. Skoric, M. Boulos, G. Huang, A. Nunez-Regueiro, I. Chalfoun, N. Park, S. Zhou, C. Contag, C. H. Aguirre, A. 2024-11-15 doi:10.1101/2024.11.13.623051 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Structural insights into SSNA1 self-assembly and its microtubule binding for centriole maintenance ]]> https://biorxiv.org/content/10.1101/2024.11.13.623454v1?rss=1 Agostini, L. Pfister, J. Basnet, N. Ding, J. Zhang, R. Biertumpfel, C. O'Connell, K. Mizuno, N. 2024-11-15 doi:10.1101/2024.11.13.623454 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Basal cell of origin resolves neuroendocrine-tuft lineage plasticity in cancer ]]> https://biorxiv.org/content/10.1101/2024.11.13.623500v1?rss=1 Ireland, A. S. Hawgood, S. B. Xie, D. A. Barbier, M. W. Lucas-Randolph, S. Tyson, D. R. Zuo, L. Y. Witt, B. L. Govindan, R. Dowlati, A. Moser, J. C. Puri, S. Rudin, C. M. Chan, J. M. Elliott, A. Oliver, T. G. 2024-11-15 doi:10.1101/2024.11.13.623500 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Developmental Stage and Cellular Context Determine Oncogenic and Molecular Outcomes of Ezh2Y641F Mutation in Hematopoiesis ]]> https://biorxiv.org/content/10.1101/2024.11.14.622807v1?rss=1 Zimmerman, S. M. Procasky, S. J. Smith, S. R. Liu, J.-Y. Torrice, C. Souroullas, G. P. 2024-11-15 doi:10.1101/2024.11.14.622807 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ ATR safeguards replication forks against APOBEC3B-induced toxic PARP1 trapping ]]> https://biorxiv.org/content/10.1101/2024.11.14.623607v1?rss=1 Ortega, P. Bournique, E. B. Li, J. Sanchez, A. Santiago, G. Harris, B. R. Green, A. M. Buisson, R. 2024-11-15 doi:10.1101/2024.11.14.623607 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Modulation of B cell receptor activation by antibody competition ]]> https://biorxiv.org/content/10.1101/2024.11.18.624200v1?rss=1 He, Y. Guo, Z. Vahey, M. D. 2024-11-21 doi:10.1101/2024.11.18.624200 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Aberrant expression of histone H2B variants reshape chromatin and alter oncogenic gene expression programs ]]> https://biorxiv.org/content/10.1101/2024.11.18.624207v1?rss=1 Saintilnord, W. N. Hegazy, Y. A. Chestnutt, K. Eckstein, M. Cassidy, R. N. Dhahri, H. Bennett, R. L. Melters, D. P. Lopes, E. Fu, Z. Lau, K. Chandler, D. P. Poirier, M. G. Dalal, Y. Licht, J. D. Fondufe-Mittendorf, Y. 2024-11-21 doi:10.1101/2024.11.18.624207 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ A single high-zinc activation enhancer can control two genes oriented head-to-head in C. elegans ]]> https://biorxiv.org/content/10.1101/2024.11.19.624376v1?rss=1 Liu, H. Earley, B. Mendoza, A. Hunt, P. Teng, S. Schneider, D. L. Kornfeld, K. 2024-11-21 doi:10.1101/2024.11.19.624376 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Controlling human stem cell-derived islet composition using magnetic sorting ]]> https://biorxiv.org/content/10.1101/2024.11.19.624394v1?rss=1 Kelley, A. B. Shunkarova, M. Maestas, M. M. Gale, S. E. Hogrebe, N. J. Millman, J. R. 2024-11-21 doi:10.1101/2024.11.19.624394 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Phospholipid Scramblase 1 (PLSCR1) Regulates Interferon-Lambda Receptor 1 (IFN-lambdaR1) and IFN-lambda Signaling in Influenza A Virus (IAV) Infection ]]> https://biorxiv.org/content/10.1101/2024.11.20.624469v1?rss=1 Yang, A. X. Ramos-Rodriguez, L. Sorkhdini, P. Yang, D. Norbrun, C. Majid, S. Zhang, Y. Holtzman, M. Boyd, D. F. Zhou, Y. 2024-11-21 doi:10.1101/2024.11.20.624469 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish ]]> https://biorxiv.org/content/10.1101/2024.11.20.624586v1?rss=1 Huang, D. Kapadia, E. Liang, Y. Shriver, L. P. Dai, S. Patti, G. J. Humbel, B. M. Laudet, V. PARICHY, D. M. 2024-11-21 doi:10.1101/2024.11.20.624586 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Antigen flexibility supports the avidity of hemagglutinin-specific antibodies at low antigen densities ]]> https://biorxiv.org/content/10.1101/2024.11.20.624560v1?rss=1 Benegal, A. N. He, Y. D. Ho, K. Groff, G. Guo, Z. Vahey, M. D. 2024-11-22 doi:10.1101/2024.11.20.624560 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ Characterizing cytosine methylation of polymorphic human transposable element insertions using human pangenome resources ]]> https://biorxiv.org/content/10.1101/2024.11.22.623804v1?rss=1 Zhuo, X. Tomlinson, C. Belter, E. A. Kuntala, P. K. Saintilnord, W. N. Lindsay, T. Macias, J. Fulton, R. S. Wang, T. 2024-11-23 doi:10.1101/2024.11.22.623804 Cold Spring Harbor Laboratory Press 2024-11-23 <![CDATA[ Large-scale Signal Propagation Modes in the Human Brain ]]> https://biorxiv.org/content/10.1101/2024.11.22.624801v1?rss=1 Song, Y. Kim, P. S. Philip, B. A. Kim, T. 2024-11-23 doi:10.1101/2024.11.22.624801 Cold Spring Harbor Laboratory Press 2024-11-23 <![CDATA[ Replication stress marker phospho-RPA2 predicts response to platinum and PARP inhibitors in homologous recombination-proficient ovarian cancer ]]> https://biorxiv.org/content/10.1101/2024.11.21.624682v1?rss=1 16% of cells had [≥] 2 pRPA2 foci. ResultsIn the discovery cohort, HR-proficient, pRPA2-High tumors demonstrated significantly higher rates of pathologic complete response to platinum chemotherapy than HR-proficient, pRPA2-Low tumors. In the validation cohort, patients with HR-proficient, pRPA2-High tumors had significantly longer survival after platinum treatment than those with HR-proficient, pRPA2-Low tumors. Additionally, the pRPA2 assay effectively predicted survival outcomes in patients treated with PARP inhibitors and in recurrent tumor samples. ConclusionOur study underscores the importance of considering replication stress markers alongside HR status in therapeutic planning. Our work suggest that this assay could be used throughout a patients treatment course to expand the number of patients receiving effective therapy while reducing unnecessary toxicity. ]]> Schab, A. Compadre, A. Drexler, R. Loeb, M. Rodriguez, K. Brill, J. Harrington, S. Sandoval, C. Sanders, B. Kuroki, L. McCourt, C. Hagemann, A. R. Thaker, P. Mutch, D. Powell, M. Serra, V. Hagemann, I. S. Walts, A. E. Karlan, B. Y. Orsulic, S. Fuh, K. Sun, L. Verma, P. Lomonosova, E. Zhao, P. Khabele, D. Mullen, M. M. 2024-11-25 doi:10.1101/2024.11.21.624682 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Key Regulatory Elements of the TGFbeta-LRRC15 Axis Predict Disease Progression and Immunotherapy Resistance Across Cancer Types ]]> https://biorxiv.org/content/10.1101/2024.11.22.624939v1?rss=1 Storey, C. M. Cheng, M. Altai, M. Park, J. E. Tran, J. Lueong, S. S. Thorek, D. L. Mao, L. Zedan, W. Yuen, C. Ridley, A. Trajkovic-Arsic, M. Herrmann, K. Subudhi, S. K. Siddiqui, B. A. Lueckerath, K. Siveke, J. Damoiseaux, R. Yang, X. Ulmert, D. 2024-11-25 doi:10.1101/2024.11.22.624939 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ A survey of hypothalamic phenotypes identifies molecular and behavioral consequences of MYT1L haploinsufficiency in male and female mice. ]]> https://biorxiv.org/content/10.1101/2024.11.25.625294v1?rss=1 Dougherty, J. D. Maloney, S. E. McCullough, K. B. Chaturvedi, S. M. Selmanovic, D. Chase, R. Chen, J. Wu, D. Granadillo, J. L. Kroll, K. L. 2024-11-25 doi:10.1101/2024.11.25.625294 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Mitophagy Facilitates Cytosolic Proteostasis to Preserve Cardiac Function ]]> https://biorxiv.org/content/10.1101/2024.11.24.624947v1?rss=1 Diwan, A. Rawnsley, D. R. Islam, M. Zhao, C. Kargar Gaz Kooh, Y. Mendoza, A. Navid, H. Kumari, M. Guan, X. Murphy, J. T. Nigro, J. Kovacs, A. Mani, K. Huebsch, N. Ma, X. 2024-11-26 doi:10.1101/2024.11.24.624947 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Coupled aging of cyto- and myeloarchitectonic atlas-informed gray and white matter structural properties ]]> https://biorxiv.org/content/10.1101/2024.11.25.625295v1?rss=1 Hoagey, D. A. Pongpipat, E. E. Rodrigue, K. M. Kennedy, K. M. 2024-11-26 doi:10.1101/2024.11.25.625295 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Efficient creation and characterization of multi-kilobase knockins by CRISPR/Cas9 and multiple rAAVs ]]> https://biorxiv.org/content/10.1101/2024.11.26.625457v1?rss=1 View larger version (16K): org.highwire.dtl.DTLVardef@1619b77org.highwire.dtl.DTLVardef@125b0b2org.highwire.dtl.DTLVardef@173b12dorg.highwire.dtl.DTLVardef@7519b1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sentmanat, M. F. Wang, Z. T. Kouranova, E. Peters, S. Chan, W. C. Lin, J. Miao, Y. Richey, J. O'Neal, J. Dipersio, J. White, M. Wallace, M. Cui, X. 2024-11-28 doi:10.1101/2024.11.26.625457 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Integration of spatial multiplexed protein imaging and transcriptomics in the human kidney tracks the regenerative potential timeline of proximal tubules ]]> https://biorxiv.org/content/10.1101/2024.11.26.625544v1?rss=1 Asghari, M. Sabo, A. R. Barwinska, D. Melo Ferreira, R. Ferkowicz, M. Bowen, W. Cheng, Y. Gisch, D. Gulbronson, C. Phillips, C. L. Kelly, K. J. Sutton, T. A. Williams, J. Vazquez, M. O'Toole, J. Palevsky, P. Rosas, S. Waikar, S. S. Kiryluk, K. Parikh, C. Hodgins, J. Sarder, P. De Boer, I. Himmelfarb, J. Kretzler, M. Kidney Precision Medicine Project, Jain, S. Eadon, M. Winfree, S. El-Achkar, T. M. Dagher, P. C. 2024-12-02 doi:10.1101/2024.11.26.625544 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ Detection and characterization of Langya virus in Crocidura lasiura, Republic of Korea ]]> https://biorxiv.org/content/10.1101/2024.12.02.626520v1?rss=1 Natasha, A. Pye, S. E. Park, K. Rajoriya, S. Yang, I. Park, J. Pangestu, H. S. Kim, J. Oh, Y. Lopez, C. B. Song, J.-W. Kim, W.-K. 2024-12-04 doi:10.1101/2024.12.02.626520 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ Investigating the Functional Role of the DI-DII Linker in Nav1.5 Channel Function ]]> https://biorxiv.org/content/10.1101/2024.12.01.626264v1?rss=1 Wagner, E. Marras, M. Kumar, S. Kelley, J. Ruff, K. M. Silva, J. 2024-12-05 doi:10.1101/2024.12.01.626264 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ MOZ and HBO1 Histone Acetyltransferase Complexes Are Molecular Dependencies and Therapeutic Targets in NUP98-Rearranged Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/2024.12.02.624182v1?rss=1 Mullighan, C. G. Michmerhuizen, N. L. Heikamp, E. B. Iacobucci, I. Umeda, M. Arthur, B. Mishra, V. Di Giacomo, D. Hiltenbrand, R. Gao, Q. Radko-Juettner, S. Lott, J. Martucci, C. Subramanyam, V. Hatton, C. Baviskar, P. Portola, P. Claquin, A. Chandra, B. Baggett, D. W. Khalighifar, A. Huang, H. Zhou, P. Long, L. Shi, H. Sun, Y. Papachristou, E. K. Chilamakuri, C. S. R. Vitorino, F. N. d. L. Gongora, J. M. Janke, L. Kentsis, A. D'Santos, C. S. Garcia, B. A. Kriwacki, R. W. Chi, H. Klco, J. M. Armstrong, S. A. 2024-12-05 doi:10.1101/2024.12.02.624182 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ CD226+ adipose tissue macrophages arise from MDP-derived monocytes and regulate lipid metabolism. ]]> https://biorxiv.org/content/10.1101/2024.12.03.626330v1?rss=1 Gallerand, A. Caillot, Z. Terekhova, M. Castiglione, A. Leporati, L. Giacchero, M. Pilot, T. Chang, M. Dolfi, B. Zair, F. N. Goes, E. Bennetot, A. Mlamla, Z. Mass, E. Ginhoux, F. Voehringer, D. Mack, M. Dombrowicz, D. Williams, J. W. Masson, D. Artyomov, M. N. Bertola, A. IVANOV, S. 2024-12-05 doi:10.1101/2024.12.03.626330 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Molecular Insights into the Regulation of GNPTAB by TMEM251 ]]> https://biorxiv.org/content/10.1101/2024.12.05.627003v1?rss=1 Yang, X. Doray, B. Venkatarangan, V. Jennings, B. Henn, D. Liang, J. Zhao, H. Zhang, W. Zhang, B. Yu, L. Chen, L. Kornfeld, K. Li, M. 2024-12-05 doi:10.1101/2024.12.05.627003 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Cultivation and molecular characterization of Foley catheterized urine, clean catch urine, and vaginal swabs from pregnant women prior to delivery ]]> https://biorxiv.org/content/10.1101/2024.12.05.627013v1?rss=1 Greenberg, J. M. Romero, R. Alhousseini, A. Winters, A. D. Tarca, A. L. Gilbert, N. M. Gomez-Lopez, N. Hassan, S. S. Theis, K. R. 2024-12-06 doi:10.1101/2024.12.05.627013 Cold Spring Harbor Laboratory Press 2024-12-06 <![CDATA[ Aging and the Spectral Properties of Brain Hemodynamics ]]> https://biorxiv.org/content/10.1101/2024.12.05.626723v1?rss=1 Park, K. Y. Snyder, A. Z. Goyal, M. S. Laumann, T. O. Lee, J. J. Adeyemo, B. Metcalf, N. Vlassenko, A. G. Shimony, J. S. Leuthardt, E. C. 2024-12-10 doi:10.1101/2024.12.05.626723 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ The Functional Connectome Mediating Circadian Synchrony in the Suprachiasmatic Nucleus ]]> https://biorxiv.org/content/10.1101/2024.12.06.627294v1?rss=1 Nikhil, K. L. Singhal, B. Granados-Fuentes, D. Li, J.-S. Kiss, I. Z. Herzog, E. D. 2024-12-11 doi:10.1101/2024.12.06.627294 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Monoclonal antibodies targeting the FimH adhesin protect against uropathogenic E. coli UTI ]]> https://biorxiv.org/content/10.1101/2024.12.10.627638v1?rss=1 Lopatto, E. D. B. Santiago-Borges, J. M. Sanick, D. A. Malladi, S. K. Azimzadeh, P. N. Timm, M. W. Fox, I. F. Schmitz, A. J. Turner, J. S. Ahmed, S. S. Ortinau, L. Gualberto, N. C. Pinkner, J. S. Dodson, K. W. Ellebedy, A. H. Kau, A. L. Hultgren, S. J. 2024-12-11 doi:10.1101/2024.12.10.627638 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Resolving the design principles that control postnatal vascular growth and scaling ]]> https://biorxiv.org/content/10.1101/2024.12.10.627758v1?rss=1 Pichardo, D. Braun, J. Dutta, S. Patra, D. Bougaran, P. Mompeon, A. Ma, F. Stock, S. R. Choi, S. Garcia-Ortega, L. Pratama, M. Y. Pichardo, D. Ramkhelawon, B. Benedito, R. Bautch, V. L. Ornitz, D. M. Goyal, Y. Iruela-Arispe, M. L. 2024-12-11 doi:10.1101/2024.12.10.627758 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Variant Set Distillation ]]> https://biorxiv.org/content/10.1101/2024.12.06.627210v1?rss=1 Christ, R. Kang, C. J. Aslett, L. Lam, D. Savitski, M. F. Stitziel, N. O. Steinsaltz, D. Hall, I. 2024-12-12 doi:10.1101/2024.12.06.627210 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ CD4 Co-Receptor Regulates Sex-Specific NK Cell Responses to Acute Toxoplasma gondii Infection. ]]> https://biorxiv.org/content/10.1101/2024.12.06.627254v1?rss=1 Roy, T. Bernstein, L. Keplinger, H. K. Fisk, K. Ng, S. K. Denton, S. L. Gigley, J. P. 2024-12-12 doi:10.1101/2024.12.06.627254 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Patient-Derived Xenografts of Triple-Negative Breast Cancer Enable Deconvolution and Prediction of Chemotherapy Responses ]]> https://biorxiv.org/content/10.1101/2024.12.09.627518v1?rss=1 Lei, J. T. Dobrolecki, L. E. Huang, C. Srinivasan, R. R. Vasaikar, S. V. Lewis, A. N. Sallas, C. Zhao, N. Cao, J. Landua, J. D. Moon, C. I. Liao, Y. Hilsenbeck, S. G. Osborne, C. K. Rimawi, M. F. Ellis, M. J. Petrosyan, V. Wen, B. Li, K. Saltzman, A. B. Jain, A. Malovannaya, A. Wulf, G. M. Marangoni, E. Li, S. Kraushaar, D. C. Wang, T. Damodaran, S. Zheng, X. Meric-Bernstam, F. Echeverria, G. V. Anurag, M. Chen, X. Welm, B. E. Welm, A. L. Zhang, B. Lewis, M. T. 2024-12-12 doi:10.1101/2024.12.09.627518 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Mapping Global Causal Responses to Noninvasive Modulation of Genetically and Spatially Targeted Neural Populations with Sonogenetic-fPET ]]> https://biorxiv.org/content/10.1101/2024.12.10.627860v1?rss=1 Yang, Y. Weixel, C. Hu, Z. Yue, Y. Wang, I. Xu, L. Chen, H. 2024-12-16 doi:10.1101/2024.12.10.627860 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Simulating Alpha Particle Doses at the Micron Scale from Prostate Cancer Patient Derived Bone Metastatic Biopsies Using GATE ]]> https://biorxiv.org/content/10.1101/2024.12.11.627943v1?rss=1 Said, A. Hamdi, M. Salerno, I. Benabdallah, N. Turtle, N. F. Abou, D. Thomas, M. A. Mikell, J. Thorek, D. L. 2024-12-16 doi:10.1101/2024.12.11.627943 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Domain Structure and Interface Control of Mechanical Stiffness in Sustainable Cellulose Bio-nanocomposites ]]> https://biorxiv.org/content/10.1101/2024.12.13.628443v1?rss=1 Jin, H. Goldberg, W. Wang, Z. Li, H. Huang, Y. Foston, M. Genin, G. M. 2024-12-18 doi:10.1101/2024.12.13.628443 Cold Spring Harbor Laboratory Press 2024-12-18 <![CDATA[ A signaling inspired synthetic toolkit for efficient production of tyrosine phosphorylated proteins ]]> https://biorxiv.org/content/10.1101/2024.12.22.629992v1?rss=1 Ryan, M. M. Portelance, R. Newman, G. F. Martinez, G. Shekharan, S. Wu, A. Angel, S. Schaberg, K. E. Gilmore, P. Sprung, R. Townsend, R. Naegle, K. M. 2024-12-23 doi:10.1101/2024.12.22.629992 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ Lipid bilayers determine the allostery but not intrinsic affinity of cAMP binding to pacemaker channels ]]> https://biorxiv.org/content/10.1101/2024.12.23.630133v1?rss=1 Idikuda, V. Roy Chowdhury, S. Chang, Y. Ren, Q. Bao, H. Goldsmith, R. Chanda, B. 2024-12-24 doi:10.1101/2024.12.23.630133 Cold Spring Harbor Laboratory Press 2024-12-24 <![CDATA[ Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure ]]> https://biorxiv.org/content/10.1101/2024.12.27.630454v1?rss=1 Scholl, D. Boyd, T. Latham, A. P. Salazar, A. Khan, A. Boeynaems, S. Holehouse, A. S. Lander, G. C. Sali, A. Park, D. Deniz, A. A. Lasker, K. 2024-12-28 doi:10.1101/2024.12.27.630454 Cold Spring Harbor Laboratory Press 2024-12-28 <![CDATA[ Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina ]]> https://biorxiv.org/content/10.1101/2024.12.28.630634v1?rss=1 Yuan, Y. Biswas, P. Zemke, N. Dang, K. Wu, Y. D Antonio, M. Xie, Y. Yang, Q. Dong, K. Lau, P. K. Li, D. Seng, C. Bartosik, W. Buchanan, J. Lin, L. Lancione, R. Wang, K. Lee, S. Gibbs, Z. Ecker, J. Frazer, K. Wang, T. Preissl, S. Wang, A. Ayyagari, R. Ren, B. 2024-12-29 doi:10.1101/2024.12.28.630634 Cold Spring Harbor Laboratory Press 2024-12-29 <![CDATA[ scRepertoire 2: Enhanced and Efficient Toolkit for Single-Cell Immune Profiling ]]> https://biorxiv.org/content/10.1101/2024.12.31.630854v1?rss=1 Yang, Q. Safina, K. R. Borcherding, N. 2024-12-31 doi:10.1101/2024.12.31.630854 Cold Spring Harbor Laboratory Press 2024-12-31 <![CDATA[ Circuit dynamics of approach-avoidance conflict in humans ]]> https://biorxiv.org/content/10.1101/2024.12.31.630927v1?rss=1 Staveland, B. R. Oberschulte, J. Kim-McManus, O. Willie, J. T. Brunner, P. Dastjerdi, M. Lin, J. J. Hsu, M. Knight, R. T. 2025-01-01 doi:10.1101/2024.12.31.630927 Cold Spring Harbor Laboratory Press 2025-01-01 <![CDATA[ Structure of an LGR dimer - an evolutionary predecessor of glycoprotein hormone receptors ]]> https://biorxiv.org/content/10.1101/2024.12.31.630923v1?rss=1 Gong, Z. Chen, S. Fu, Z. Kloss, B. Wang, C. Clarke, O. B. Fan, Q. R. Hendrickson, W. A. 2025-01-02 doi:10.1101/2024.12.31.630923 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ The sex-specific effects of RAGE signaling and Type 2 Diabetes on mouse cortical bone mechanics, structure, and material properties ]]> https://biorxiv.org/content/10.1101/2025.01.01.631018v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@75acedorg.highwire.dtl.DTLVardef@1ac01fforg.highwire.dtl.DTLVardef@1b70d34org.highwire.dtl.DTLVardef@c3f3a7_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hung, T. Broz, K. S. Walk, R. Tang, S. Y. 2025-01-02 doi:10.1101/2025.01.01.631018 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ GENETIC ANALYSIS OF ARABIDOPSIS AUTOPHAGY-RELATED 8 FAMILY PROTEINS REVEALS THEIR REDUNDANT AND REGULATORY ROLES IN PLANT AUTOPHAGY ]]> https://biorxiv.org/content/10.1101/2025.01.01.631040v1?rss=1 Dong, K. Deng, G. Liu, Y. Wei, H. Chen, K.-E. Huang, X. Huang, W. Zheng, P. Ueda, T. Vierstra, R. D. Huang, X. Li, F. 2025-01-02 doi:10.1101/2025.01.01.631040 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ FGF12A Regulates Nav1.5 via CaM-regulated and CaM-independent Mechanisms ]]> https://biorxiv.org/content/10.1101/2025.01.02.631125v1?rss=1 Woodbury, L. S. Angsutararux, P. Marras, M. Wagner, E. S. Abella, C. Li, A. Silva, J. R. 2025-01-03 doi:10.1101/2025.01.02.631125 Cold Spring Harbor Laboratory Press 2025-01-03 <![CDATA[ Parenteral Vaccination with recombinant EtpA glycoprotein impairs enterotoxigenic E. coli colonization ]]> https://biorxiv.org/content/10.1101/2025.01.03.631264v1?rss=1 Vickers, T. J. Buckley, D. Khatoon, N. Sheikh, A. Setu, B. Berndsen, Z. T. Fleckenstein, J. M. 2025-01-04 doi:10.1101/2025.01.03.631264 Cold Spring Harbor Laboratory Press 2025-01-04 <![CDATA[ ATR and PKMYT1 inhibition re-sensitize a subset of TNBC patient-derived models to carboplatin inducing mitotic catastrophe ]]> https://biorxiv.org/content/10.1101/2025.01.07.629892v1?rss=1 Guay, J. Kuasne, H. Chabot, C. Bozek, K. Buchanan, M. Majedi, Y. Aguilar-Mahecha, A. Bareke, E. Kong, T. Yang, K. Elebute, O. Guo, R. Monast, A. Morin, G. Huang, S. Park, M. Basik, M. 2025-01-10 doi:10.1101/2025.01.07.629892 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ NERINE reveals rare variant associations in gene networks across multiple phenotypes and implicates an SNCA-PRL-LRRK2 subnetwork in Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2025.01.07.631688v1?rss=1 Nazeen, S. Wang, X. Morrow, A. Strom, R. Ethier, E. Ritter, D. Henderson, A. Afroz, J. Stitziel, N. O. Gupta, R. M. Luk, K. Studer, L. Khurana, V. Sunyaev, S. R. 2025-01-10 doi:10.1101/2025.01.07.631688 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ Generation and Characterization of a Knockout Mouse of an Enhancer of EBF3 ]]> https://biorxiv.org/content/10.1101/2025.01.09.631762v1?rss=1 Hurtado, E. C. Wotton, J. M. Gulka, A. Burke, C. Ng, J. K. Bah, I. Manuel, J. Heins, H. Murray, S. A. Gorkin, D. U. White, J. K. Peterson, K. A. Turner, T. N. 2025-01-10 doi:10.1101/2025.01.09.631762 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ Neural plate pre-patterning enables specification of intermediate neural progenitors in the spinal cord ]]> https://biorxiv.org/content/10.1101/2025.01.09.632276v1?rss=1 Nandagopal, S. Cha, A. Jia, B. Z. Liao, H. Comenho, C. Lahav, G. Wagner, D. E. Tsai, T. Y.-C. Megason, S. G. 2025-01-10 doi:10.1101/2025.01.09.632276 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ Genome-wide CRISPR knockout screening with viral replicons for identification of host factors involved in viral replication ]]> https://biorxiv.org/content/10.1101/2025.01.09.632058v1?rss=1 Cheng, K. W. Bhave, M. Markhard, A. Peng, D. L. Bhatt, K. D. Travisano, K. A. Medicielo, J. V. Lembirik, S. Njoya, L. Anantpadma, M. Kuhn, J. H. Puschnik, A. S. Kistler, A. L. 2025-01-11 doi:10.1101/2025.01.09.632058 Cold Spring Harbor Laboratory Press 2025-01-11 <![CDATA[ Markers of mitochondrial function and oxidative metabolism in female skeletal muscle do not display intrinsic circadian regulation ]]> https://biorxiv.org/content/10.1101/2025.01.08.631231v1?rss=1 Fitzgerald, L. S. Spurrier, C. S. R. Lau, N. Melamed, M. Burnett, L. A. Meyer, G. A. Gui, C. Hevener, A. L. Sanford, J. A. Schenk, S. 2025-01-13 doi:10.1101/2025.01.08.631231 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Modification of Non-photochemical Quenching Pathways in the C4 Model Plant Setaria viridis Revealed Shared and Unique Photoprotection Mechanisms as Compared to C3 Plants ]]> https://biorxiv.org/content/10.1101/2025.01.12.632622v1?rss=1 Milburn, G. Morris, C. M. Kosola, E. Patel-Tupper, D. Liu, J. Pham, D. H. Acosta-Gamboa, L. Stone, W. D. Pardi, S. Hillman, K. McHargue, W. E. Becker, E. Kang, X. Sumner, J. Bailey, C. Thielen, P. M. Jander, G. Kane, C. N. McAdam, S. A. M. Lawton, T. J. Nusinow, D. A. Zhang, F. Gore, M. A. Cheng, J. Niyogi, K. K. Zhang, R. 2025-01-15 doi:10.1101/2025.01.12.632622 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Clustering Digestive Tract Tumors Using Transcriptomic and Mutation Data ]]> https://biorxiv.org/content/10.1101/2025.01.13.632722v1?rss=1 Tally, D. G. Bombina, P. Reed, J. Kinne, J. Abruzzo, L. V. Coombes, K. R. Abrams, Z. B. 2025-01-15 doi:10.1101/2025.01.13.632722 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Microbiota assembly of specific pathogen-free neonatal mice ]]> https://biorxiv.org/content/10.1101/2025.01.14.633035v1?rss=1 Kennedy, E. Weagley, J. Kim, A. Antia, A. DeVeaux, A. Baldridge, M. 2025-01-15 doi:10.1101/2025.01.14.633035 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Investigation of the Cyanothece nitrogenase cluster in Synechocystis: a blueprint for engineering nitrogen fixing photoautotrophs ]]> https://biorxiv.org/content/10.1101/2025.01.20.633913v1?rss=1 Liu, D. Bandyopadhyay, A. Liberton, M. Pakrasi, H. B. Bhattacharyya-Pakrasi, M. 2025-01-21 doi:10.1101/2025.01.20.633913 Cold Spring Harbor Laboratory Press 2025-01-21 <![CDATA[ Longitudinal Trajectories of Cognition and Neural Metrics as Predictors of Persistent Distressing Psychotic-Like Experiences Across Middle Childhood and Early Adolescence ]]> https://biorxiv.org/content/10.1101/2025.01.20.633817v1?rss=1 Karcher, N. R. Dong, F. Johnson, E. C. Paul, S. E. Kilciksiz, C. M. Oh, H. Schiffman, J. Agrawal, A. Bogdan, R. Jackson, J. J. Barch, D. 2025-01-22 doi:10.1101/2025.01.20.633817 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Small molecule-mediated targeted protein degradation of voltage-gated sodium channels involved in pain ]]> https://biorxiv.org/content/10.1101/2025.01.21.634079v1?rss=1 Chamessian, A. Payne, M. Gordon, I. Zhou, M. Gereau, R. 2025-01-22 doi:10.1101/2025.01.21.634079 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Mapping brain function underlying naturalistic motor observation and imitation using high-density diffuse optical tomography ]]> https://biorxiv.org/content/10.1101/2025.01.21.634109v1?rss=1 Yang, D. George, T. Sobolewski, C. McMorrow, S. Pacheco, C. King, K. Rochowiak, R. Daniels-Day, E. Park, S. Speh, E. Lidstone, D. Santra, R. Crocetti, D. Nebel, M. B. Tuncgenc, B. Vidal, R. Marrus, N. M. Mostofsky, S. H. Eggebrecht, A. T. 2025-01-22 doi:10.1101/2025.01.21.634109 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Macrophage depletion restores the DRG microenvironment and prevents axon degeneration in bortezomib-induced neuropathy ]]> https://biorxiv.org/content/10.1101/2025.01.22.634362v1?rss=1 Thomsen, M. B. Singh, A. Thebeau, C. N. Gao, V. D. Schulze, N. F. Avraham, O. Yang, S. X. Koneru, S. Geier, S. S. Landon, S. M. Pelea, A. Cavalli, V. Geisler, S. 2025-01-24 doi:10.1101/2025.01.22.634362 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Deep-learning based Embedding of Functional Connectivity Profiles for Precision Functional Mapping ]]> https://biorxiv.org/content/10.1101/2025.01.29.635570v1?rss=1 Tu, J. Kim, J.-H. Luckett, P. H. Adeyemo, B. Shimony, J. S. Elison, J. T. Eggebrecht, A. T. Wheelock, M. D. 2025-01-30 doi:10.1101/2025.01.29.635570 Cold Spring Harbor Laboratory Press 2025-01-30 <![CDATA[ Microglial plasticity governed by state-specific enhancer landscapes ]]> https://biorxiv.org/content/10.1101/2025.01.30.635595v1?rss=1 Hamagami, N. Kapadia, D. Abduljawad, N. Cheng, Z. McLaughlin, L. Singhania, D. Barclay, K. Yang, J. Sun, Z. Bayguinov, P. Yu, G. Gabel, H. Li, Q. 2025-01-31 doi:10.1101/2025.01.30.635595 Cold Spring Harbor Laboratory Press 2025-01-31 <![CDATA[ Digging into the general dynamic model: Island ontogeny predicts shifting micro-evolutionary processes in a Mascarene flowering plant radiation ]]> https://biorxiv.org/content/10.1101/2025.01.30.635705v1?rss=1 Mashburn, B. Linan, A. G. Le Pechon, T. Sevathian, J.-C. Olsen, K. M. Edwards, C. E. 2025-01-31 doi:10.1101/2025.01.30.635705 Cold Spring Harbor Laboratory Press 2025-01-31 <![CDATA[ In vivo targeted gene delivery using Adenovirus-antibody molecular glue conjugates ]]> https://biorxiv.org/content/10.1101/2025.01.31.635969v1?rss=1 Rice-Boucher, P. J. Kashentseva, E. A. Dmitriev, I. P. Guo, H. Tremblay, J. M. Shoemaker, C. B. Curiel, D. T. Lu, Z. H. 2025-02-01 doi:10.1101/2025.01.31.635969 Cold Spring Harbor Laboratory Press 2025-02-01 <![CDATA[ A brainstem-thalamic circuitry for affective-motivational responses to cold pain ]]> https://biorxiv.org/content/10.1101/2025.01.31.636010v1?rss=1 Reddy, P. Okuda, T. Rani, M. Prajapati, J. N. Samineni, V. K. Koul, S. Barik, A. 2025-02-01 doi:10.1101/2025.01.31.636010 Cold Spring Harbor Laboratory Press 2025-02-01 <![CDATA[ FISHNET: A Network-based Tool for Analyzing Gene-level P-values to Identify Significant Genes Missed by Standard Methods ]]> https://biorxiv.org/content/10.1101/2025.01.29.635546v1?rss=1 Acharya, S. Moghaddam, V. A. Jung, W. S. Kang, Y. S. Liao, S. Province, M. Brent, M. 2025-02-02 doi:10.1101/2025.01.29.635546 Cold Spring Harbor Laboratory Press 2025-02-02 <![CDATA[ Early cell cycle genes in cortical organoid progenitors predict interindividual variability in infant brain growth trajectories ]]> https://biorxiv.org/content/10.1101/2025.02.07.637106v1?rss=1 Glass, M. R. Matoba, N. Beltran, A. A. Patel, N. K. Farah, T. M. Eswar, K. Bhargava, S. Huang, K. Curtin, I. Ahmed, S. Srivastava, M. Drake, E. Davis, L. T. Yeturi, M. Sun, K. Love, M. I. Simon, J. M. St. John, T. Marrus, N. Pandey, J. Estes, A. Dager, S. Schultz, R. T. Botteron, K. Evans, A. Kim, S. H. Styner, M. McKinstry, R. C. Collins, D. L. Volk, H. Benke, K. Zwaigenbaum, L. Hazlett, H. Beltran, A. S. Girault, J. B. Shen, M. D. Piven, J. Stein, J. L. the Infant Brain Imaging Study Network, 2025-02-08 doi:10.1101/2025.02.07.637106 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Early-life infection with Cryptosporidium parvum induces inflammatory responses to dietary antigens ]]> https://biorxiv.org/content/10.1101/2025.02.07.637163v1?rss=1 Saraav, I. Huang, W. Jung, J. Xu, R. Fu, Y. McDonald, K. G. Schriefer, L. A. Rogers, R. Baldridge, M. T. Newberry, R. D. Hsieh, C.-S. Sibley, L. D. 2025-02-08 doi:10.1101/2025.02.07.637163 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Dietary manipulation of intestinal microbes prolongs survival in a mouse model of Hirschsprung disease ]]> https://biorxiv.org/content/10.1101/2025.02.10.637436v1?rss=1 View larger version (15K): org.highwire.dtl.DTLVardef@d95251org.highwire.dtl.DTLVardef@1ab58caorg.highwire.dtl.DTLVardef@5260b0org.highwire.dtl.DTLVardef@49ce42_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Tjaden, N. E. B. Liou, M. J. Sax, S. Lassoued, N. Lou, M. Schneider, S. Beigel, K. Eisenberg, J. D. Loeffler, E. Anderson, S. E. Yan, G. Litichevskiy, L. Dohnalova, L. Zhu, Y. Jin, D. M. J. C. Raab, J. Furth, E. E. Thompson, Z. Rubenstein, R. C. Pilon, N. Thaiss, C. A. Heuckeroth, R. 2025-02-11 doi:10.1101/2025.02.10.637436 Cold Spring Harbor Laboratory Press 2025-02-11 <![CDATA[ Resting calcium ion fluxes protect cells from fast mitochondrial fragmentation, cell stress responses, and immediate transcriptional reprogramming ]]> https://biorxiv.org/content/10.1101/2025.02.06.636834v1?rss=1 Fecher, C. Sodmann, A. Schlott, F. Jaepel, J. Schmitt, F. Lengfelder, I. Bischler, T. Nieswandt, B. Winklhofer, K. F. Blum, R. 2025-02-12 doi:10.1101/2025.02.06.636834 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ TDP-43 Aggregate Seeding Impairs Autoregulation and Causes TDP-43 Dysfunction ]]> https://biorxiv.org/content/10.1101/2025.02.11.637743v1?rss=1 Mamede, L. D. Hu, M. Titus, A. R. Vaquer-Alicea, J. French, R. L. Diamond, M. I. Miller, T. M. Ayala, Y. M. 2025-02-12 doi:10.1101/2025.02.11.637743 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ MicroRNA-34a suppresses KLF2 to promote pathological angiogenesis through the CXCR4/CXCL12 pathway in age-related macular degeneration ]]> https://biorxiv.org/content/10.1101/2025.02.12.637499v1?rss=1 Colasanti, J. J. Lin, J. B. Terao, R. Lee, T. J. Santeford, A. Apte, R. S. 2025-02-15 doi:10.1101/2025.02.12.637499 Cold Spring Harbor Laboratory Press 2025-02-15 <![CDATA[ The response of mitochondrial position to glucose stimulation in a model system of the pancreatic beta cell ]]> https://biorxiv.org/content/10.1101/2025.02.13.637960v1?rss=1 Perez, L. Ng, X. W. Piston, D. W. Mukherji, S. 2025-02-16 doi:10.1101/2025.02.13.637960 Cold Spring Harbor Laboratory Press 2025-02-16 <![CDATA[ Pyrimethamine and a potent analogue WCDD115 inhibit NRF2 by suppressing DHFR and one-carbon metabolism ]]> https://biorxiv.org/content/10.1101/2025.02.13.637433v1?rss=1 Chembo, J. Bowman, B. M. Lapak, K. Wilkerson, E. Paiboonrungruang, C. Cho, K. Medcalf, M. R. Patti, G. Dolle, R. E. Chen, X. Zolkind, P. Major, M. B. 2025-02-17 doi:10.1101/2025.02.13.637433 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ Molecular grammars of intrinsically disordered regions that span the human proteome ]]> https://biorxiv.org/content/10.1101/2025.02.27.640591v1?rss=1 Ruff, K. M. King, M. R. Ying, A. W. Liu, V. Pant, A. Lieberman, W. E. Shinn, M. K. su, x. Kadoch, C. Pappu, R. V. 2025-02-28 doi:10.1101/2025.02.27.640591 Cold Spring Harbor Laboratory Press 2025-02-28 <![CDATA[ Phosphoinositide Depletion and Compensatory β-adrenergic Signaling in Angiotensin II-Induced Heart Disease: Protection Through PTEN Inhibition ]]> https://biorxiv.org/content/10.1101/2025.02.23.639781v1?rss=1 View larger version (71K): org.highwire.dtl.DTLVardef@126d18borg.highwire.dtl.DTLVardef@1870dadorg.highwire.dtl.DTLVardef@1931836org.highwire.dtl.DTLVardef@1ab23f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO Graphical summary of chronic angiotensin II (AngII) signaling effects on cardiac calcium handling and fibrosis. Chronic AngII signaling through AT1R activates Gq-coupled signaling, leading to PI(4,5)P2 depletion that destabilizes CaV1.2 in the plasma membrane (PM), triggering their endocytosis and reduced channel numbers at the PM. The remaining CaV1.2 channels and RyR2 undergo compensatory phosphorylation by CaMKII and PKA, triggered by sympathetic activation (-AR signaling), leading to enhanced calcium-induced calcium release (CICR). Meanwhile, AngII promotes fibroblast-to-myofibroblast transition via M1 macrophage phenotype activation, increasing cardiac fibrosis. PTEN inhibition preserves PIP3 levels and promotes anti-inflammatory M2 macrophage activation, resulting in reduced fibrosis. These findings reveal a complex interplay between cardiac phosphoinositide signaling, calcium handling, and fibrotic remodeling with chronic AngII. AC, adenylyl cyclase; -AR, beta-adrenergic receptor; DAG, diacylglycerol; IP3, inositol trisphosphate; PLC, phospholipase C; PKA, protein kinase A; PTEN, phosphatase and tensin homolog. C_FIG ]]> Voelker, T. Westhoff, M. del Villar, S. G. Thai, P. N. Chiamvimonvat, N. Nieves-Cintron, M. Dickson, E. J. Dixon, R. E. 2025-03-01 doi:10.1101/2025.02.23.639781 Cold Spring Harbor Laboratory Press 2025-03-01 <![CDATA[ Targeted and random mutagenesis of cassava brown streak disease susceptibility factors reveal molecular determinants of disease severity ]]> https://biorxiv.org/content/10.1101/2025.02.27.640518v1?rss=1 Lin, Z.-J. D. Stanton, M. K. Hernandez, G. L. De Meyer, E. J. von Behren, Z. Benza, K. Tiley, H. Hood, E. Jensen, G. Gilbert, K. B. Carrington, J. Bart, R. 2025-03-01 doi:10.1101/2025.02.27.640518 Cold Spring Harbor Laboratory Press 2025-03-01 <![CDATA[ Ms4a4a deficiency ameliorates plaque pathology in a mouse model of amyloid accumulation ]]> https://biorxiv.org/content/10.1101/2025.03.06.641917v1?rss=1 Danhash, E. P. Verbeck, A. C. Western, D. Diaz-Pacheco, A. Galasso, G. You, S.-F. Nadarajah, C. J. Tiemann-Powles, S. Huang, G. Musiek, E. S. Herz, J. Iyer, A. K. Cirrito, J. Cruchaga, C. Karch, C. M. 2025-03-10 doi:10.1101/2025.03.06.641917 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Targeting Modulated Vascular Smooth Muscle Cells in Atherosclerosis via FAP-Directed Immunotherapy ]]> https://biorxiv.org/content/10.1101/2025.03.03.641211v1?rss=1 Amrute, J. M. Jung, I.-H. Yamawaki, T. Bredemeyer, A. Diekmann, J. Hayat, S. Lin, W.-L. Zhang, X. Luo, X. Maryam, S. Heo, G. S. Yang, S. Lee, C. J. M. Chou, C. Kuppe, C. Cook, K. D. Kovacs, A. Chintalgattu, V. Pruitt, D. Barreda, J. Stitziel, N. O. Cheng, P. Liu, Y. Kramann, R. Foo, R. S.-Y. Rulifson, I. C. Thomas, M. Cui, J. Quertermous, T. Bengel, F. M. Jackson, S. Li, C.-M. K. Ason, B. Lavine, K. J. 2025-03-11 doi:10.1101/2025.03.03.641211 Cold Spring Harbor Laboratory Press 2025-03-11 <![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[ Inhibitory effects of dopamine agonists on pain-responsive neurons in the central nucleus of the amygdala ]]> https://biorxiv.org/content/10.1101/2025.03.10.642168v1?rss=1 Heuermann, R. J. Gereau, R. W. 2025-03-11 doi:10.1101/2025.03.10.642168 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Single-Cell Resolution of Individual Variation in Hypothalamic Neurons Allows Targeted Manipulation Affecting Social Motivation ]]> https://biorxiv.org/content/10.1101/2025.03.10.642464v1?rss=1 120,000 neurons from tuberal hypothalamus and adjacent thalamus in 36 mice, balanced across sex and autism-associated mutation5, with all mice assessed for social motivation2. First, we show that molecular activation patterns predict behavior across individuals: specifically, activation of paraventricular Agtr1a+ (angiotensin receptor 1a) neurons predicted reduced social behavior. Subsequent inhibition of AGTR1A with telmisartan--an FDA-approved antihypertensive6--improved social orienting. Second, we show natural variation in neuronal proportions--likely arising from stochastic developmental events7--is sufficient to shape adult behavior even among genetically-identical individuals: we identified multiple neuronal populations whose relative abundance predicted social reward-seeking behavior. Chemogenetic inhibition of one such population, Nxph4+ neurons of the postero-lateral hypothalamus8, suppressed multiple aspects of social motivation. This work establishes proof-of-principle for an approach where single-cell genomics precisely maps neural substrates governing behavior. This approach revealed that stochastic variations in neuronal architecture deterministically influence social motivation, and enabled identification of therapeutically-actionable targets with immediate translational potential for disorders with social deficits. ]]> Sarafinovska, S. Koester, S. K. Fang, L. Z. Thorpe, J. W. Chaturvedi, S. M. Ji, J. Jones, E. F. Selmanovic, D. Kornbluth, D. J. Barrett, M. R. Rurak, G. M. Maloney, S. E. Creed, M. C. Mitra, R. D. Dougherty, J. D. 2025-03-12 doi:10.1101/2025.03.10.642464 Cold Spring Harbor Laboratory Press 2025-03-12 <![CDATA[ Disruption of a side portal pathway permits closed-state inactivation by BK β subunit N-termini ]]> https://biorxiv.org/content/10.1101/2025.03.09.642150v1?rss=1 Zhou, Y. Xia, X. Lingle, C. J. 2025-03-13 doi:10.1101/2025.03.09.642150 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Dense Longitudinal Precision Neuroimaging of Recovery from Traumatic Brain Injury ]]> https://biorxiv.org/content/10.1101/2025.03.09.642218v1?rss=1 Rajesh, A. Laumann, T. O. Barch, D. Kay, B. P. Meyer, A. C. Kummer, T. T. Dosenbach, N. U. F. Gordon, E. M. 2025-03-13 doi:10.1101/2025.03.09.642218 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Stathmin 1 regulates mitophagy and cellular function in hematopoietic stem cells ]]> https://biorxiv.org/content/10.1101/2025.03.10.642434v1?rss=1 Chiquetto, L. Schuetz, M. Dong, Q. Warmka, M. Valin, L. Jones, A. Hunt, P. Petermeier, C. Wang, J. Roundy, N. Greenberg, Z. Yang, W. Zhang, C. Challen, G. Luke, C. Signer, R. Beatty, W. Sykes, S. Li, W. Kast, D. Schuettpelz, L. 2025-03-13 doi:10.1101/2025.03.10.642434 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Human pulvinar stimulation engages select cortical pathways in epilepsy ]]> https://biorxiv.org/content/10.1101/2025.03.11.642694v1?rss=1 Bilderbeek, J. A. Gregg, N. M. Yanez-Ramos, M. G. Huang, H. Montoya, M. M. Brunner, P. Willie, J. T. Van Gompel, J. J. Worrell, G. A. Miller, K. J. Hermes, D. 2025-03-13 doi:10.1101/2025.03.11.642694 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Cortical reinstatement of causally related events sparks narrative insights by updating neural representation patterns ]]> https://biorxiv.org/content/10.1101/2025.03.12.642853v1?rss=1 Song, H. Ke, J. Madhogarhia, R. Leong, Y. C. Rosenberg, M. D. 2025-03-13 doi:10.1101/2025.03.12.642853 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ A Neural Circuit Framework for Economic Choice: From Building Blocks of Valuation to Compositionality in Multitasking ]]> https://biorxiv.org/content/10.1101/2025.03.13.643098v1?rss=1 Battista, A. Padoa-Schioppa, C. Wang, X.-J. 2025-03-13 doi:10.1101/2025.03.13.643098 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Endothelial Cept1 Promotes Post-Ischemic Angiogenesis in a Pparα-Dependent Fashion ]]> https://biorxiv.org/content/10.1101/2025.03.11.642511v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@dde6ecorg.highwire.dtl.DTLVardef@63c6c4org.highwire.dtl.DTLVardef@8e753dorg.highwire.dtl.DTLVardef@b314cd_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Khan, T. J. Meade, R. Benedetto, S. E. Belaygorod, L. Saffaf, O. Rusconi, B. Hsu, F.-F. Adak, S. Arif, B. Zaghloul, M. Li, T. Zhang, B. Semenkovich, C. F. Zayed, M. A. 2025-03-14 doi:10.1101/2025.03.11.642511 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Fetal context conveys heritable protection against MLL-rearranged leukemia that depends on MLL3 ]]> https://biorxiv.org/content/10.1101/2025.03.11.642680v1?rss=1 100-fold less common than childhood leukemias overall. This raises the question of whether mechanisms exist to suppress leukemic transformation during fetal life, thereby protecting the developing fetus from malignancy during a period of rapid hematopoietic progenitor expansion. Here, we use mouse models to show that fetal MLL::ENL exposure creates a heritable, leukemia-resistant state. MLL::ENL imposes a negative selective pressure on fetal hematopoietic progenitors. It leads to postnatal loss of self-renewal gene expression and enhanced myeloid differentiation that precludes transformation. These changes do not occur when MLL::ENL is induced shortly after birth, and transformation proceeds efficiently in this context. The fetal barrier to transformation is enforced by the histone methyltransferase MLL3. It can be overcome by cooperating mutations, such as NrasG12D, or through somatic or germline inactivation of MLL3. Heritable fetal protection against leukemic transformation may explain the low incidence of congenital leukemias in humans despite prenatal MLL rearrangement. ]]> Mendoza-Castrejon, J. Yang, W. Denby, E. Wang, H. Casey, E. B. Muthukumar, R. Patel, R. M. Yoon, J. Li, Y. White, J. M. Chen, R. Batista, L. Magee, J. A. 2025-03-14 doi:10.1101/2025.03.11.642680 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Autoregulation of RPL7B by inhibition of a structural splicing enhancer ]]> https://biorxiv.org/content/10.1101/2025.03.14.643126v1?rss=1 Stormo, G. D. Granas, D. Hewa, I. G. White, M. A. 2025-03-15 doi:10.1101/2025.03.14.643126 Cold Spring Harbor Laboratory Press 2025-03-15 <![CDATA[ Programmable chronogenetic gene circuits for self-regulated circadian delivery of biologic drugs ]]> https://biorxiv.org/content/10.1101/2025.03.14.643274v1?rss=1 Cimino, A. Pat, F. Oyebamiji, O. Pferdehirt, L. Pham, C. Herzog, E. Guilak, F. 2025-03-15 doi:10.1101/2025.03.14.643274 Cold Spring Harbor Laboratory Press 2025-03-15 <![CDATA[ Degradation of the intestinal mucus layer by the ETEC protease EatA is species specific determined by the structure of the MUC2 mucin ]]> https://biorxiv.org/content/10.1101/2025.03.16.643548v1?rss=1 Trillo-Muyo, S. Dolan, B. Svensson, F. Vickers, T. J. Arike, L. Garcia-Bonete, M.-J. Gustafsson, J. K. Wandall, H. H. Fleckenstein, J. M. Hansson, G. C. van der Post, S. 2025-03-16 doi:10.1101/2025.03.16.643548 Cold Spring Harbor Laboratory Press 2025-03-16 <![CDATA[ CD34 serves as an intrinsic innate immune guardrail protecting stem cells from replicating retroviruses ]]> https://biorxiv.org/content/10.1101/2025.03.15.643450v1?rss=1 He, S. Haikerwal, A. Tiwari, S. Dabbagh, D. Alam, M. Z. Yoon, J. L. Hetrick, B. Han, Y. Shan, L. Lockhart, C. Wu, Y. 2025-03-17 doi:10.1101/2025.03.15.643450 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ Tracing LYVE1+ peritoneal fluid macrophages unveils two paths to resident macrophage repopulation with differing reliance on monocytes ]]> https://biorxiv.org/content/10.1101/2025.03.19.644175v1?rss=1 Gallerand, A. Han, J. J. Mintz, R. L. Chen, J. Lee, D. D. Chan, M. M. Harmon, M. T. Lin, X. Huckstep, C. G. Du, S. Liu, T. Kipnis, J. Lavine, K. J. Schilling, J. Morley, S. C. Zinselmeyer, B. H. Randolph, G. J. 2025-03-19 doi:10.1101/2025.03.19.644175 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ Two Axes of White Matter Development ]]> https://biorxiv.org/content/10.1101/2025.03.19.644049v1?rss=1 Luo, A. C. Meisler, S. L. Sydnor, V. J. Alexander-Bloch, A. Bagautdinova, J. Barch, D. M. Bassett, D. S. Davatzikos, C. Franco, A. R. Goldsmith, J. Gur, R. E. Gur, R. C. Hu, F. Jaskir, M. Kiar, G. Keller, A. S. Larsen, B. Mackey, A. P. Milham, M. P. Roalf, D. R. Shafiei, G. Shinohara, R. T. Somerville, L. H. Weinstein, S. M. Yeatman, J. D. Cieslak, M. Rokem, A. Satterthwaite, T. D. 2025-03-20 doi:10.1101/2025.03.19.644049 Cold Spring Harbor Laboratory Press 2025-03-20 <![CDATA[ Dual-responsive synthetic gene circuit for dynamic biologic drug delivery via inflammatory and circadian signaling pathways ]]> https://biorxiv.org/content/10.1101/2025.03.20.644403v1?rss=1 Cimino, A. Pat, F. Oyebamiji, O. Pham, C. Herzog, E. Guilak, F. 2025-03-20 doi:10.1101/2025.03.20.644403 Cold Spring Harbor Laboratory Press 2025-03-20 <![CDATA[ Cryo-EM structures of a pentameric ligand-gated ion channel in liposomes ]]> https://biorxiv.org/content/10.1101/2025.03.21.644626v1?rss=1 Dalal, V. Tan, B. K. Xu, H. Cheng, W. W. 2025-03-24 doi:10.1101/2025.03.21.644626 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ Temporal fMRI Dynamics Map Dopamine Physiology ]]> https://biorxiv.org/content/10.1101/2025.03.24.645022v1?rss=1 Ballard, I. Pappas, I. Furman, D. J. Berry, A. S. Frederick, B. d. White, R. L. Kayser, A. S. Jagust, W. J. D'Esposito, M. 2025-03-26 doi:10.1101/2025.03.24.645022 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Human sensory neurons exhibit cell-type-specific, pain-associated differences in intrinsic excitability and expression of SCN9A and SCN10A ]]> https://biorxiv.org/content/10.1101/2025.03.25.645367v1?rss=1 Yi, J. Yang, L. Widman, A. J. Toliver, A. Bertels, Z. Del Rosario, J. S. Slivicki, R. A. Payne, M. Dourson, A. J. Li, J.-N. Kumar, R. Gupta, P. Mwirigi, J. M. Chamessian, A. Lemen, J. Copits, B. A. Gereau, R. W. 2025-03-26 doi:10.1101/2025.03.25.645367 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Phase transition pathways encode distinct physicochemical properties of biomolecular condensates ]]> https://biorxiv.org/content/10.1101/2025.03.26.645448v1?rss=1 Ren, X. Yang, L. Chen, M. W. Dai, Y. 2025-03-29 doi:10.1101/2025.03.26.645448 Cold Spring Harbor Laboratory Press 2025-03-29 <![CDATA[ Establishment of a Reverse Genetics System for the Study of Human Immune Functions in Mice ]]> https://biorxiv.org/content/10.1101/2025.03.26.645295v1?rss=1 Pal, P. Gao, S. Gao, H. Cella, M. Wang, Q. Shan, L. 2025-03-31 doi:10.1101/2025.03.26.645295 Cold Spring Harbor Laboratory Press 2025-03-31 <![CDATA[ Machine Learning-Based Identification of Survival-Associated CpG Biomarkers in Pancreatic Ductal Adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2025.03.29.646090v1?rss=1 Zhang, B. Zhang, Y. Zhao, Y. 2025-04-01 doi:10.1101/2025.03.29.646090 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Expression spectrum of TE-derived transcripts in human adult tissues ]]> https://biorxiv.org/content/10.1101/2025.03.29.646092v1?rss=1 Miao, B. Zhang, B. WU, T. P. Luo, X. Ademovic, A. Yang, Y. 2025-04-03 doi:10.1101/2025.03.29.646092 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Circadian rhythms and the light-dark cycle interact to regulate amyloid plaque accumulation and tau phosphorylation in 5xFAD mice ]]> https://biorxiv.org/content/10.1101/2025.03.31.645805v1?rss=1 95% of SCN cells, and crossed this line to the 5xFAD amyloid mouse model. To examine the role of the light-dark cycle in this process, we aged these mice in either regular 12:12 light-dark (LD) or constant darkness (DD) conditions. Transcriptional, behavioral, and physiological rhythms were examined in VGAT-iCre; Bmal1fl/fl; 5xFAD (VGAT-BMAL1KO;5xFAD) mice under varying light conditions. Amyloid plaque deposition, peri-plaque tau phosphorylation, glial activation, and transcriptomic changes were examined. ResultsVGAT-BMAL1KO;5xFAD mice showed loss of SCN BMAL1 expression and severe disruption of behavioral rhythms in both LD and DD, with loss of day-night rhythms in consolidated sleep and blunting of rhythmic clock gene expression in the brain. Surprisingly, VGAT-BMAL1KO;5xFAD mice kept under LD showed reduced total plaque accumulation and peri-plaque tau phosphorylation, compared to Cre-negative controls. These changes were gated by the light-dark cycle, as they were absent in VGAT-BMAL1KO;5xFAD mice kept in DD conditions. Total plaque accumulation was also reduced in control 5xFAD mice kept in DD as compared to LD, suggesting a general effect of light-dark cycle on amyloid aggregation. Expression of murine presenilin 1 (Psen1), as well as amyloidogenic cleavage of amyloid precursor protein, were suppressed in VGAT-BMAL1KO;5xFAD specifically under LD conditions. ConclusionsIn 5xFAD mice, the central circadian clock and the light-dark cycle interact to regulate amyloid pathology. Disruption of the central clock in the presence of a light-dark cycle may reduce APP cleavage and plaque formation. These results call into question the proposed simple positive feedback loop between circadian rhythm disruption and Alzheimers Disease pathology. ]]> King, M. W. Jacob, S. Sharma, A. Lawrence, J. H. Weaver, D. R. Musiek, E. S. 2025-04-04 doi:10.1101/2025.03.31.645805 Cold Spring Harbor Laboratory Press 2025-04-04 <![CDATA[ A new chromosome-level genome assembly for western painted turtle Chrysemys picta belli, a model for extreme physiological adaptations ]]> https://biorxiv.org/content/10.1101/2025.04.01.646645v1?rss=1 Chen, J. Bermingham, J. R. Minx, P. Kremitzky, M. Lin, Z. Warren, D. E. 2025-04-06 doi:10.1101/2025.04.01.646645 Cold Spring Harbor Laboratory Press 2025-04-06 <![CDATA[ Thermotropic Properties of Large, Circularized Nanodiscs ]]> https://biorxiv.org/content/10.1101/2025.04.07.647641v1?rss=1 Arcario, M. J. Dalal, V. Fan, D. Cheng, W. W.-L. 2025-04-10 doi:10.1101/2025.04.07.647641 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Autophagy-Dependent Regulation of YAP1 by STK38 Governs Recruitment of Differentiated Cells as Progenitor Cells During Regeneration ]]> https://biorxiv.org/content/10.1101/2025.04.14.648819v1?rss=1 Zeng, Y. Huang, Y.-Z. Li, Q. K. Ho, R. Bark, S. J. Willet, S. G. Mills, J. C. 2025-04-16 doi:10.1101/2025.04.14.648819 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ SKIDA1 transiently sustains MLL::ENL-Expressing hematopoietic progenitors during neonatal stages and promotes B-lineage priming ]]> https://biorxiv.org/content/10.1101/2025.04.12.648529v1?rss=1 Mendoza-Castrejon, J. Yang, W. Denby, E. Muthukumar, R. Casey, E. B. Patel, R. M. Tasian, S. K. Magee, J. A. 2025-04-18 doi:10.1101/2025.04.12.648529 Cold Spring Harbor Laboratory Press 2025-04-18 <![CDATA[ Development of a 24-Channel 3T Phased-Array Coil for fMRI in Awake Monkeys - Mitigating Spatiotemporal Artifacts in Ferumoxytol-Weighted Functional Connectivity Estimation ]]> https://biorxiv.org/content/10.1101/2025.04.15.648822v1?rss=1 Autio, J. A. Yoshida, A. Kawabata, Y. Ohno, M. Nishigori, K. Ose, T. Smith, S. M. Van Essen, D. C. Glasser, M. F. Hayashi, T. 2025-04-20 doi:10.1101/2025.04.15.648822 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ Temporal-orbitofrontal pathway regulates choices across physical reward and visual novelty ]]> https://biorxiv.org/content/10.1101/2025.04.15.648986v1?rss=1 Ogasawara, T. Xu, K. Snyder, A. Z. Perlmutter, J. S. Tu, Z. Minamimoto, T. Inoue, K.-i. Takada, M. Monosov, I. E. 2025-04-20 doi:10.1101/2025.04.15.648986 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ Linking neuron-axon-synapse architecture to white matter vasculature using high-resolution multimodal MRI in primate brain ]]> https://biorxiv.org/content/10.1101/2025.04.15.648990v1?rss=1 Kimura, I. Hayashi, T. Autio, J. A. 2025-04-20 doi:10.1101/2025.04.15.648990 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ Long-range massively parallel reporter assay reveals rules of distal enhancer-promoter interactions ]]> https://biorxiv.org/content/10.1101/2025.04.21.649048v1?rss=1 Wu, Y. Li, J. Bartley-Dier, E. L. Pitts, C. Cohen, B. A. 2025-04-22 doi:10.1101/2025.04.21.649048 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ Early-Life Environmental Exposures Reprogram Epigenomic Aging to Alter Gene Expression Trajectories ]]> https://biorxiv.org/content/10.1101/2025.04.21.649824v1?rss=1 Grimm, S. L. Jangid, R. Bartolomei, M. S. Dolinoy, D. C. Aylor, D. L. Mutlu, G. M. Biswal, S. Zhang, B. Wang, T. TaRGET II Consortium, Coarfa, C. Walker, C. L. 2025-04-22 doi:10.1101/2025.04.21.649824 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ Molnupiravir inhibits Bourbon virus infection and disease-associated pathology in mice ]]> https://biorxiv.org/content/10.1101/2025.04.21.649883v1?rss=1 Bamunuarachchi, G. Zhao, F. Bricker, T. L. Seehra, K. Karp, A. Diamond, M. Boon, A. C. 2025-04-22 doi:10.1101/2025.04.21.649883 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ Subtle Cellular Phenotypes Inform Pathological and Benign Genetic Mutants in the Iduronidase-2 Sulfatase Gene ]]> https://biorxiv.org/content/10.1101/2025.04.17.649412v1?rss=1 Viswanathan, A. Elia, S. N. Le, S. Q. Doray, B. Waligorski, J. E. Kelley, K. Buchser, W. J. Dickson, P. I. 2025-04-23 doi:10.1101/2025.04.17.649412 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Genomic and Immunogenomic Profiling of Extramedullary Acute Myeloid Leukemia Reveals Actionable Clonal Branching and Frequent Immune Editing ]]> https://biorxiv.org/content/10.1101/2025.04.18.649610v1?rss=1 Collignon, C. Hansen, T. Hercus, C. Ruzinova, M. B. Guepin, G. R. Bonmati, C. Rubio, M. T. Feugier, P. Gaudfrin, M. Sartelet, H. Divoux, M. Muller, M. Heath, S. Uy, G. Spencer, D. Chen, D. Pagliuca, S. Ferraro, F. 2025-04-24 doi:10.1101/2025.04.18.649610 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Induction of TFEB promotes Kupffer cell survival and reduces lipid accumulation and inflammation in MASLD ]]> https://biorxiv.org/content/10.1101/2025.04.19.649650v1?rss=1 Chan, M. M. Daemen, S. Beatty, W. Byrnes, K. Cho, K. Ferguson, D. Park, A. C. Fu, C. F. Guo, Z. Feldstein, N. Park, C. Florczak, K. L. He, L. Yang, B. Q. Javaheri, A. Patti, G. Finck, B. Razani, B. Schilling, J. D. 2025-04-24 doi:10.1101/2025.04.19.649650 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ 2H MRI-based quantification of leucine uptake in glioblastoma multiforme ]]> https://biorxiv.org/content/10.1101/2025.04.23.648848v1?rss=1 McClendon, S. Ge, X. Song, K.-H. Grief, D. Fortin Ensign, S. P. Kodibagkar, V. D. Hu, L. S. Garbow, J. R. Beeman, S. C. 2025-04-24 doi:10.1101/2025.04.23.648848 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Characterization of betacoronavirus HKU-1 and OC43 internal proteins using a prototypic coronavirus ]]> https://biorxiv.org/content/10.1101/2025.04.23.650176v1?rss=1 Gunawardene, C. D. Pandey, I. Chatterjee, S. Penaflor-Tellez, Y. Odle, A. Messyasz, A. Rajsbaum, R. Sariol, A. Wong, L.-Y. R. 2025-04-24 doi:10.1101/2025.04.23.650176 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ The representational geometry of out-of-distribution generalization in primary visual cortex and artificial neural networks ]]> https://biorxiv.org/content/10.1101/2025.04.23.650305v1?rss=1 Ye, Z. Wessel, R. 2025-04-28 doi:10.1101/2025.04.23.650305 Cold Spring Harbor Laboratory Press 2025-04-28 <![CDATA[ Quantum Magnetization Exchange through Transient Hydrogen Bond Matrix Defines Magnetic Resonance Signal Relaxation and Anisotropy in Central Nervous System ]]> https://biorxiv.org/content/10.1101/2025.04.22.650086v1?rss=1 Yablonskiy, D. A. Sukstanskii, A. L. 2025-04-29 doi:10.1101/2025.04.22.650086 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Basement Membrane Structural Integrity Dictates Trans-Tissue Deposition of Laminin in Mammals ]]> https://biorxiv.org/content/10.1101/2025.04.28.650774v1?rss=1 Miner, J. H. Omachi, K. Yurchenco, P. McKee, K. K. Lin, M.-H. Fujiwara, H. Puapatanakul, P. 2025-04-29 doi:10.1101/2025.04.28.650774 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ LOSS OF ROR2 TYROSINE KINASE RECEPTOR IS ASSOCIATED WITH ENDOTHELIAL DYSFUNCTION IN PAH VIA INAPPROPRIATE INTEGRIN BETA 1 ACTIVATION ]]> https://biorxiv.org/content/10.1101/2025.04.28.651135v1?rss=1 Mitra, A. Chakraborty, A. Zhong, B. Heo, L. Agarwal, S. Pacheco, A. Auer, N. Dunn, A. Chelladurai, P. Jain, A. Matos, J. Bankar, A. Guardado, E. YI, D. Zhao, H. Wai Dede Man, K. Nair, R. V. Guenat, O. T. Dai, Z. de Jesus Perez, V. A. 2025-04-29 doi:10.1101/2025.04.28.651135 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Reduced heparan sulfate levels in cerebrospinal fluid reflect brain neuron correction in Sanfilippo B mice ]]> https://biorxiv.org/content/10.1101/2025.04.30.651515v1?rss=1 Le, S. Q. Sorensen, A. Sukupolvi, S. Jewhurst, G. Austin, G. Doray, B. Cooper, J. D. Dickson, P. 2025-04-30 doi:10.1101/2025.04.30.651515 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Ciliated cells promote high infectious potential of influenza A virus through the efficient intracellular activation of hemagglutinin ]]> https://biorxiv.org/content/10.1101/2025.04.30.651529v1?rss=1 Guo, Z. Banas, V. S. He, Y. Weiland, E. Xu, J. Tan, Y. Xiao, Z. Brody, S. L. Boon, A. C. M. Janetka, J. W. Vahey, M. D. 2025-04-30 doi:10.1101/2025.04.30.651529 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ From Pairwise Distances to Neighborhood Preservation: Benchmarking Dimensionality Reduction Algorithms for CyTOF, scRNA-seq, and CITE-seq ]]> https://biorxiv.org/content/10.1101/2025.04.28.651069v1?rss=1 Bombina, P. Adams, Z. B. McGee, R. L. Coombes, K. R. 2025-05-01 doi:10.1101/2025.04.28.651069 Cold Spring Harbor Laboratory Press 2025-05-01 <![CDATA[ Efficient packaging of HIV-1 genomes via recognition of its adenosine-rich content by a heterologous RNA-binding domain ]]> https://biorxiv.org/content/10.1101/2025.05.01.651415v1?rss=1 Vuong, H. R. Zhou, Q. Lesko, S. Tenneti, K. Davis, K. Scott, S. Boodwa-Ko, D. Eschbach, J. E. Gopal, K. Porter, J. Wang, Y. Mohammed, S. Lee, N. Telesnitsky, A. Sherer, N. M. Kutluay, S. B. 2025-05-01 doi:10.1101/2025.05.01.651415 Cold Spring Harbor Laboratory Press 2025-05-01 <![CDATA[ Alpha-Synuclein Fibril Structures Cluster into Distinct Classes ]]> https://biorxiv.org/content/10.1101/2025.04.30.651534v1?rss=1 Milchberg, M. H. Warmuth, O. A. Borcik, C. G. Dhavale, D. D. Wright, E. R. Kotzbauer, P. T. Rienstra, C. M. 2025-05-02 doi:10.1101/2025.04.30.651534 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ An open, fully-processed data resource for studying mood and sleep variability in the developing brain ]]> https://biorxiv.org/content/10.1101/2025.05.01.651544v1?rss=1 Brook, J. B. H. Salo, T. Luo, A. C. Bagautdinova, J. Rush, S. Alexander-Bloch, A. F. Baller, E. B. Calkins, M. E. Cieslak, M. Cooper, E. C. Detre, J. A. Elliot, M. A. Fair, D. A. Freedman, P. Gehrman, P. R. Gur, R. C. Gur, R. E. Klein, A. Laney, N. Laumann, T. O. Mehta, K. Merikangas, K. Milham, M. P. Mitchell, J. A. Moore, T. M. Nelson, S. M. Ruparel, K. Sevchik, B. L. Shanmugan, S. Shou, H. Taso, M. White, L. K. Wolf, D. H. Tisdall, D. Roalf, D. R. Satterthwaite, T. D. 2025-05-02 doi:10.1101/2025.05.01.651544 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ Fmp30 is a phosphatidylinositol hydrolase that regulates CoQ biosynthesis ]]> https://biorxiv.org/content/10.1101/2025.05.01.651778v1?rss=1 Baker, Z. N. Guerra, R. M. Rogers, S. W. Pagliarini, D. J. 2025-05-02 doi:10.1101/2025.05.01.651778 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ Automatic Individual Cortical Parcellation for the Human Connectome Project ]]> https://biorxiv.org/content/10.1101/2025.04.29.651219v1?rss=1 Yang, C. Coalson, T. S. Farahibozorg, S.-R. Bijsterbosch, J. D. Smith, S. M. Van Essen, D. C. Glasser, M. F. 2025-05-03 doi:10.1101/2025.04.29.651219 Cold Spring Harbor Laboratory Press 2025-05-03 <![CDATA[ Mutations in Hsp40 co-chaperone change the unique canonical inter-domain interactions stimulating LGMDD1 myopathy ]]> https://biorxiv.org/content/10.1101/2025.05.02.651952v1?rss=1 Bhadra, A. K. Aggarwal, G. Jaysingh, M. A. Chen, D. Daw, J. Weihl, C. C. True, H. 2025-05-03 doi:10.1101/2025.05.02.651952 Cold Spring Harbor Laboratory Press 2025-05-03 <![CDATA[ Isomerized Aβ in the brain can distinguish the status of amyloidosis in the Alzheimer's Disease spectrum ]]> https://biorxiv.org/content/10.1101/2025.04.29.650793v1?rss=1 Mukherjee, S. Coyle, R. Dubois, C. Perez, K. Mclean, C. Masters, C. Roberts, B. R. 2025-05-04 doi:10.1101/2025.04.29.650793 Cold Spring Harbor Laboratory Press 2025-05-04 <![CDATA[ Identification of modulated whole-brain dynamical models from nonstationary electrophysiological data ]]> https://biorxiv.org/content/10.1101/2025.05.01.651677v1?rss=1 Schwamb, A. Yu, Z. Ching, S. 2025-05-07 doi:10.1101/2025.05.01.651677 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Preconditioning Matters: Enhancing or Impairing Antitumor Immunity with DC Vaccines ]]> https://biorxiv.org/content/10.1101/2025.05.02.651990v1?rss=1 Kwon, E. Namen, S. Willoughby, C. J. Kang, S. Pandey, G. Kim, A. B. DeSelm, C. J. 2025-05-08 doi:10.1101/2025.05.02.651990 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Structural basis for membrane microdomain formation by a human Stomatin complex ]]> https://biorxiv.org/content/10.1101/2025.05.07.652726v1?rss=1 Fu, Z. Stonger, J. Li, S. 2025-05-09 doi:10.1101/2025.05.07.652726 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Fat cadherin cleavage releases a transcriptionally active nuclear fragment to regulate target gene expression ]]> https://biorxiv.org/content/10.1101/2025.05.08.652952v1?rss=1 Rusch, J. Thanintorn, N. Kuok, C. Tsatskis, Y. Hou, H. Wilson, M. D. Julick, C. McNeill, H. 2025-05-09 doi:10.1101/2025.05.08.652952 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Expression of Arabidopsis Extracellular Vesicle Protein Markers in Nicotiana benthamiana Reveals Distinct Vesicle Subpopulations ]]> https://biorxiv.org/content/10.1101/2025.05.06.652549v1?rss=1 Ghosh, S. Innes, R. W. 2025-05-10 doi:10.1101/2025.05.06.652549 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ Neural Mechanisms Supporting Proactive Control ]]> https://biorxiv.org/content/10.1101/2025.05.09.653198v1?rss=1 100), with task variants that independently assessed proactive and reactive control relative to baseline conditions. Behavioral analyses replicated prior work with the AX-CPT paradigm, in which a measure of target preparation based on contextual cues (the A-cue Bias index) was both reliably increased under task conditions encouraging proactive control and positively associated with WMC. Analyses of fMRI activity indicated that A-cue Bias was selectively linked to increased cue-related neural activity in left motor cortex (lMOT). Additionally, WMC was associated with increased cue-related activation in right dorsolateral prefrontal cortex (rDLPFC), even when statistically controlling for baseline and reactive conditions. The relationship between these two effects was supported by a latent path analysis, which suggested that the rDLPFC-lMOT circuit preferentially mediates the WMC-A-cue Bias relationship present under proactive task conditions. The results suggest this neural circuit may translate strategic task goals into active response preparation as a mechanism of proactive control. Individuals high in WMC may be better able to implement proactive task strategies when instructed via contextual cues. The sensitivity of the rDLPFC-lMOT circuit to individual differences suggest it as a potential target for cognitive enhancement. ]]> Feldman, R. L. Quale, M. Etzel, J. A. Braver, T. S. 2025-05-12 doi:10.1101/2025.05.09.653198 Cold Spring Harbor Laboratory Press 2025-05-12 <![CDATA[ The Functional and Genetic Architecture of Olfaction in Deer Mice ]]> https://biorxiv.org/content/10.1101/2025.05.12.653383v1?rss=1 LASSANCE, J.-M. Kautt, A. F. Gozashti, L. Hoekstra, H. E. 2025-05-13 doi:10.1101/2025.05.12.653383 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Regulation of the Yolk Microtubule and Actin Cytoskeleton by Dachsous Cadherins during Zebrafish Epiboly ]]> https://biorxiv.org/content/10.1101/2025.05.10.653271v1?rss=1 Castelvecchi, G. Li, L. Shin, J. Villarreal, N. L. Roszko, I. Gontarz, P. Li, T. Zhang, B. Sepich, D. Krezel, L. S. 2025-05-14 doi:10.1101/2025.05.10.653271 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Mapping the transcriptional regulatory network of a fungal pathogen by exploiting transcription factor perturbation ]]> https://biorxiv.org/content/10.1101/2025.05.10.653149v1?rss=1 Abid, D. Brown, H. L. Mateusiak, C. Doering, T. L. Brent, M. R. 2025-05-15 doi:10.1101/2025.05.10.653149 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ SARM1 is an essential component of neuronal Parthanatos ]]> https://biorxiv.org/content/10.1101/2025.05.14.654090v1?rss=1 Wu, T. Yuan, L. Sasaki, Y. Buchser, W. Bloom, J. DiAntonio, A. Milbrandt, J. 2025-05-15 doi:10.1101/2025.05.14.654090 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Fungal susceptibility and early flowering in pennycress (Thlaspi arvense) are conferred by naturally occurring mutations in histone demethylase Jumonji 14 ]]> https://biorxiv.org/content/10.1101/2025.05.14.654108v1?rss=1 Codjoe, J. M. Kujur, A. Sirasani, J. P. Shamin, A. Sauer, T. Rai, K. Ulmasov, T. Chopra, R. Shah, D. M. 2025-05-15 doi:10.1101/2025.05.14.654108 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ fMRIPrep Lifespan: Extending A Robust Pipeline for Functional MRI Preprocessing to Developmental Neuroimaging ]]> https://biorxiv.org/content/10.1101/2025.05.14.654069v1?rss=1 Goncalves, M. Moser, J. Madison, T. J. McCollum, r. Lundquist, J. T. Fayzullobekova, B. Hadera, L. Pham, H. H. N. Moore, L. A. Houghton, A. M. Conan, G. Styner, M. A. Alexopoulos, D. Smyser, C. D. Stoyell, S. M. Koirala, S. Nelson, S. M. Weldon, K. B. Lee, E. Hermosillo, R. J. M. Vizioli, L. Yacoub, E. Patel, G. H. Sanchez, J. Wengler, K. Salo, T. Satterthwaite, T. D. Elison, J. T. Markiewicz, C. J. Poldrack, R. A. Feczko, E. Esteban, O. Fair, D. A. 2025-05-18 doi:10.1101/2025.05.14.654069 Cold Spring Harbor Laboratory Press 2025-05-18 <![CDATA[ Signaling and Mechanics influence the number and size of epithelial rosettes in the migrating zebrafish Posterior Lateral Line primordium ]]> https://biorxiv.org/content/10.1101/2025.05.17.650326v1?rss=1 Mukherjee, A. Hilzendeger, M. Rinvelt, A. Fatma, S. Schupp, M. Dalle Nogare, D. Chitnis, A. 2025-05-20 doi:10.1101/2025.05.17.650326 Cold Spring Harbor Laboratory Press 2025-05-20 <![CDATA[ EGR1 drives sex-differences in glioblastoma tumorigenicity ]]> https://biorxiv.org/content/10.1101/2025.05.16.654616v1?rss=1 Abou-Antoun, T. Llaci, L. Wong, J. P. Yang, L. Warrington, N. M. Tripp, L. Luo, J. Muegge, B. Rubin, J. B. Mitra, R. D. 2025-05-21 doi:10.1101/2025.05.16.654616 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Stimulant medications affect arousal and reward, not attention ]]> https://biorxiv.org/content/10.1101/2025.05.19.654915v1?rss=1 Kay, B. P. Wheelock, M. D. Siegel, J. S. Raut, R. Chauvin, R. J. Metoki, A. Rajesh, A. Eck, A. Pollaro, J. Wang, A. Suljic, V. Adeyemo, B. Baden, N. J. Scheidter, K. M. Monk, J. Ramirez-Perez, N. Krimmel, S. R. Shinohara, R. T. Tervo-Clemmens, B. Hermosillo, R. J. M. Nelson, S. M. Hendrickson, T. J. Madison, T. Moore, L. A. Miranda-Domlnguez, O. Randolph, A. Feczko, E. Roland, J. L. Nichol, G. E. Laumann, T. O. Marek, S. A. Gordon, E. M. Raichle, M. E. Barch, D. M. Fair, D. A. Dosenbach, N. U. F. 2025-05-21 doi:10.1101/2025.05.19.654915 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Adaptive Evolution of Gene Regulatory Networks in Mammalian Neocortical Neurons ]]> https://biorxiv.org/content/10.1101/2025.05.20.652233v1?rss=1 Li, Z. Kaur, N. Santpere, G. Muchnik, S. K. Sindhu, S. K. Qi, C. Shibata, M. Clement, O. Klaric, T. S. Martin, X. d. Luria, V. Cho, H. Li, M. Shibata, A. Tebbenkamp, A. T. N. Ma, S. Han, W. Kim, S. K. Pochareddy, S. Phan, D. Q. Xing, X. Bao, Y. Xu, X. Gladwyn-Ng, I. E. Cullen, H. D. Paolino, A. Fenlon, L. R. Kozulin, P. Suarez, R. Risgaard, R. D. Gulden, F. O. Karger, A. Suzuki, I. K. Hirata, T. Gobeske, K. T. Richards, L. J. Sousa, A. M. M. Heng, J. I. Sestan, N. 2025-05-21 doi:10.1101/2025.05.20.652233 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Developmental constraints mediate the summer solstice reversal of climate effects on European beech bud set ]]> https://biorxiv.org/content/10.1101/2025.05.18.654771v1?rss=1 Rebindaine, D. Crowther, T. W. Renner, S. S. Wu, Z. Zou, Y. Mo, L. Ma, H. Bucher, R. Zohner, C. M. 2025-05-23 doi:10.1101/2025.05.18.654771 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Single-Cell Analysis of Meningiomas Reveals Mutation-Associated Tumor and Immune Cell Gene Expression Programs ]]> https://biorxiv.org/content/10.1101/2025.05.21.655421v1?rss=1 Maldonado, J. A. Mashimo, B. L. Wang, A. Z. Desai, R. Khan, S. M. Sherpa, N. D. Anzaldua-Campos, M. I. Zipfel, G. J. Kim, A. H. Dowling, J. L. Leuthardt, E. C. Osbun, J. W. Vellimana, A. K. Chicoine, M. R. Dunn, G. P. Petti, A. A. 2025-05-24 doi:10.1101/2025.05.21.655421 Cold Spring Harbor Laboratory Press 2025-05-24 <![CDATA[ Xist Repeat A coordinates an assembly of SR proteins to recruit SPEN and induce gene silencing ]]> https://biorxiv.org/content/10.1101/2025.05.21.655143v1?rss=1 Trotman, J. B. Porrello, A. Schactler, S. A. DeLeon, L. E. Eberhard, Q. E. Boyson, S. P. Zhang, Z. Lee, D. M. Kirik, S. E. Nguyen, S. N. Beltejar, M.-C. G. Shinn, M. K. Ong, S.-E. Gonzalez-Perez, M. P. Shaffer, S. A. Dominguez, D. Shechner, D. M. Calabrese, M. 2025-05-26 doi:10.1101/2025.05.21.655143 Cold Spring Harbor Laboratory Press 2025-05-26 <![CDATA[ Unveiling functional-metabolic synergy in the healthy brain: multivariate integration of dynamic FDG-PET and resting-state fMRI ]]> https://biorxiv.org/content/10.1101/2025.05.21.655345v1?rss=1 Tarricone, C. Vallini, G. Baron, G. Silvestri, E. Volpi, T. Vlassenko, A. G. Goyal, M. S. Bertoldo, A. 2025-05-27 doi:10.1101/2025.05.21.655345 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Transient effects in corticospinal and reticulospinal tract excitability induced by motor skill and isometric resistance training ]]> https://biorxiv.org/content/10.1101/2025.05.21.655351v1?rss=1 Hawthorn, R. Phelps, N. Atkinson, C. Keesey, R. E. Seitz, Z. Nie, H. Seanez, I. 2025-05-27 doi:10.1101/2025.05.21.655351 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Macrophage-like vascular smooth muscle cells dominate early atherosclerosis and are inhibited by targeting iron regulation ]]> https://biorxiv.org/content/10.1101/2025.05.22.655434v1?rss=1 Gurung, R. Lee, C. J. M. Liehn, E. A. Nurjanah, S. Ren, M. van Kan, J. A. Villanueva, E. Amrute, J. M. Loong, S. Ackers-Johnson, M. Ruberto, F. P. Ng, S. L. Loo, Y. X. Chu, J. Lin, X. Y. Karampinos, K. I. Kofidis, T. Lavine, K. J. Singaraja, R. R. Sorokin, V. Foo, R. S.-Y. 2025-05-27 doi:10.1101/2025.05.22.655434 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Chondrocyte-Specific Knockout of Piezo1 and Piezo2 Protects Against Post-Traumatic Osteoarthritis Structural Damage and Pain in Mice ]]> https://biorxiv.org/content/10.1101/2025.05.22.655585v1?rss=1 Ely, E. Lenz, K. Paradi, S. Ack, S. Behrmann, A. Dunivan, S. Braxton, L. Liedtke, W. Chen, Y. Collins, K. H. Guilak, F. 2025-05-27 doi:10.1101/2025.05.22.655585 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Intervertebral disc impairments in a mouse model of Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2025.05.24.655931v1?rss=1 Gonzalez, C. C. Schurman, C. A. Wilson, K. A. Schilling, B. Ellerby, L. M. Tang, S. Y. 2025-05-28 doi:10.1101/2025.05.24.655931 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ PEDOT:PSS Microparticles for Extrudable and Bioencapsulating Conducting Granular Hydrogel Bioelectronics ]]> https://biorxiv.org/content/10.1101/2025.05.25.655149v1?rss=1 98% viability). Finally, we demonstrate utility as bioencapsulating electrodes for electrophysiological monitoring. These results highlight the functionality of our PEDOT:PSS conducting granular hydrogel, suggesting its potential as 3D printed bioencapsulating electrodes, 3D tissue engineering scaffolds for monitoring encapsulated cells, and injectable therapies for enhanced cell recruitment and tissue regeneration combined with electronic stimulation. ]]> Goestenkors, A. P. Yu, J. S. Park, J. Wu, Y. Espinoza, C. J. V. Friedman, L. C. Okafor, S. S. Liu, T. Chatterjee, S. Debnath, A. Semar, B. A. O'Hare, C. P. Alvarez, R. M. Singamaneni, S. Raman, B. Rutz, A. L. 2025-05-28 doi:10.1101/2025.05.25.655149 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Amino acid sensing by the α-cell mitochondrial phosphoenolpyruvate cycle regulates intracellular Ca2+ levels without impacting glucagon secretion ]]> https://biorxiv.org/content/10.1101/2025.05.26.656009v1?rss=1 View larger version (57K): org.highwire.dtl.DTLVardef@18a29f0org.highwire.dtl.DTLVardef@1c77041org.highwire.dtl.DTLVardef@9adc1dorg.highwire.dtl.DTLVardef@e91407_HPS_FORMAT_FIGEXP M_FIG Graphical abstract-cells as amino acids sensors. Arginine, alanine, and glutamine potentiate glucagon secretion, while leucine has a suppressive effect (left). Independently of glucagon secretion, glutamine and leucine suppress alanine and arginine-stimulated Ca2+ influx via the phosphoenolpyruvate (PEP) cycle, which closes KATP channels and suppresses Vm depolarization (right). C_FIG HighlightsO_LIOur studies identify a role for the -cell PEP cycle in sensing amino acids under hypoglycemic conditions. C_LIO_LIPyruvate kinase and PCK2 are required for glutamine/leucine to close -cell KATP channel and limit membrane depolarization and Ca2+ influx. C_LIO_LIGlutamine/leucine oppose alanine/arginine-stimulated Ca2+ influx and glucagon secretion. C_LIO_LIAll of the amino acids tested regulate glucagon secretion, but none do so by modulating membrane depolarization or intracellular Ca2+ levels. C_LI ]]> Jin, E. Foster, H. R. Potapenko, E. Huang, S. M. Dong, X. Hughes, J. W. Merrins, M. J. 2025-05-28 doi:10.1101/2025.05.26.656009 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Mitochondrial presequences harbor variable strengths to maintain organellar function ]]> https://biorxiv.org/content/10.1101/2025.05.26.655807v1?rss=1 Yan, Y. Erdenepurev, B. Collinson, I. Niemi, N. M. 2025-05-29 doi:10.1101/2025.05.26.655807 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ Microglial SWELL1 Deficiency Drives Male-Specific Seizure Vulnerability but Paradoxical Neuroprotection through Impaired Phagocytosis ]]> https://biorxiv.org/content/10.1101/2025.05.26.656163v1?rss=1 Barath, A. S. Dheer, A. Dale, E. Goche, F. Nguyen, T. T. L. Montier, L. Akter, M. Peshoff, M. Qi, F. Umpierre, A. D. Bosco, D. B. Haruwaka, K. Sah, R. Wu, L.-J. 2025-05-29 doi:10.1101/2025.05.26.656163 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ Application of Spectral Domain Optical Coherence Tomography To Guide Cochlear Implant Electrode Array ]]> https://biorxiv.org/content/10.1101/2025.05.27.656464v1?rss=1 Jiramongkolchai, P. Amaral, M. M. Paul, R. Matt, A. Nie, M. Hao, S. Adkins, A. Liang, H. Holden, T. Buchman, C. Zhou, C. 2025-06-01 doi:10.1101/2025.05.27.656464 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Motor impairment and adaptation in a novel non-human primate model of internal capsule infarct ]]> https://biorxiv.org/content/10.1101/2025.05.27.656471v1?rss=1 Sivakumar, S. S. Anand, S. A. Brawer, L. Mellor, R. L. Burkhalter, A. Burton, H. Brunner, P. Bundy, D. T. Leuthardt, E. C. Moran, D. W. 2025-06-01 doi:10.1101/2025.05.27.656471 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ SMURF Reconstructs Single-Cells from Visium HD Data to Reveal Zonation of Transcriptional Programs in the Intestine ]]> https://biorxiv.org/content/10.1101/2025.05.28.656357v1?rss=1 Guo, J. Sarafinovska, S. Hagenson, R. Valentine, M. Dougherty, J. Mitra, R. D. Muegge, B. D. 2025-06-01 doi:10.1101/2025.05.28.656357 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Cryo-EM structure of DNA-unbound human MCM2-7 complex reveals new disease-relevant regulation ]]> https://biorxiv.org/content/10.1101/2025.05.31.656953v1?rss=1 Liu, Y. Yang, M. Lu, P. Gao, H. He, M. Wang, Y. Qi, A. Cao, T. Zhang, Q. Qi, S. Shi, Y. Yu, H. 2025-06-03 doi:10.1101/2025.05.31.656953 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Adhesive implant interfaces prevent fibrosis by disrupting mechanobiological feedback ]]> https://biorxiv.org/content/10.1101/2025.06.01.657311v1?rss=1 Jafari, M. Aymon, B. Hong, Y. Shakiba, D. Genin, G. M. Zhao, X. Alisafaei, F. 2025-06-03 doi:10.1101/2025.06.01.657311 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ In vitro plasticity between ureteric epithelial and distal nephron identity and maturity is controlled by extracellular signals. ]]> https://biorxiv.org/content/10.1101/2025.06.03.657609v1?rss=1 Kairath, P. Er, P. X. Wilson, S. B. Ghobrial, I. T. Vanslambrouck, J. M. Chen, Y.-H. Pruett-Miller, S. M. Jain, S. Little, M. H. 2025-06-03 doi:10.1101/2025.06.03.657609 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ The Sphingosine-1-phosphate pathway is differentially activated in human gestational tissues. ]]> https://biorxiv.org/content/10.1101/2025.06.02.657487v1?rss=1 Mbadhi, M. N. Fujiwara, H. Gill, R. Mitchum, K. T. Lin, C. Raghuraman, N. Frolova, A. I. 2025-06-05 doi:10.1101/2025.06.02.657487 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ Improved genome assembly of double haploid Prunus persica siblings Lovell 2D and Lovell 5D and the peach NLRome ]]> https://biorxiv.org/content/10.1101/2025.06.03.657495v1?rss=1 Gottschalk, C. Brock, j. R. Mansfeld, B. N. Main, D. Jung, S. Zheng, P. Vann, C. Demuth, M. Bennett, D. Liu, Z. Dardick, C. 2025-06-06 doi:10.1101/2025.06.03.657495 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Ablation of VEGFA following a lumbar intervertebral disc injury attenuates intradiscal neurovascular features and prevents chronic low back pain symptoms ]]> https://biorxiv.org/content/10.1101/2025.06.03.657641v1?rss=1 Potter, R. Clayton, S. W. Walk, R. Liefer, A. L. Jing, L. Stratman, A. N. Setton, L. A. Gupta, M. C. Tang, S. Y. 2025-06-07 doi:10.1101/2025.06.03.657641 Cold Spring Harbor Laboratory Press 2025-06-07 <![CDATA[ Ketogenic diet dampens excitatory neurotransmission by shrinking synaptic vesicle pools ]]> https://biorxiv.org/content/10.1101/2025.06.04.657883v1?rss=1 Stunault, M. I. Deng, P. Periandri, E. M. Vitorino, F. N. Barfield, A. J. Ponce, R. J. Garcia, B. A. Egervari, G. Klyachko, V. A. Ashrafi, G. 2025-06-08 doi:10.1101/2025.06.04.657883 Cold Spring Harbor Laboratory Press 2025-06-08 <![CDATA[ Mechanisms of KCNQ1 gating modulation by KCNE1/3 for cell-specific function ]]> https://biorxiv.org/content/10.1101/2025.06.08.658478v1?rss=1 Cui, C. Zhao, L. Kermani, A. A. Du, S. Pipatpolkai, T. Jiang, M. Chittori, S. Tan, Y. Shi, J. Delemotte, L. Cui, J. Sun, J. 2025-06-08 doi:10.1101/2025.06.08.658478 Cold Spring Harbor Laboratory Press 2025-06-08 <![CDATA[ Hb-EGF directs systemic muscle repair ]]> https://biorxiv.org/content/10.1101/2025.06.04.657846v1?rss=1 Dean, H. C. Saraswathy, V. Saini, A. Ou, T. McAdow, J. Tendolkar, A. Mokalled, M. Johnson, A. N. 2025-06-09 doi:10.1101/2025.06.04.657846 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Ambient Pollution Components and Sources Associated with Hippocampal Architecture and Memory in Pre-Adolescents ]]> https://biorxiv.org/content/10.1101/2025.06.05.658105v1?rss=1 Rosario, M. A. Sukumaran, K. Bottenhorn, K. L. de Jesus, A. Cardenas-Iniguez, C. Ahmadi, H. Habre, R. Abad, S. Pine, J. G. Barch, D. M. Schwartz, J. Hackman, D. A. Chen, J.-C. Herting, M. M. 2025-06-09 doi:10.1101/2025.06.05.658105 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Structural Acrobatics of IAA7: Exercising Fuzzy Regions to Aid Auxin-Mediated Catalysis ]]> https://biorxiv.org/content/10.1101/2025.06.08.657175v1?rss=1 Parra, J. O. F. Ott, M. Bathia, T. Emenecker, R. Wolff, M. Thalhammer, A. Matschi, S. Villalobos, L. I. A. C. 2025-06-09 doi:10.1101/2025.06.08.657175 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Post-translational modifications distinguish amyloid-β isoform patterns extracted from vascular deposits and parenchymal plaques ]]> https://biorxiv.org/content/10.1101/2025.06.11.658821v1?rss=1 0.9) with shorter C-terminal isoforms (A{beta}37, A{beta}38, A{beta}39, A{beta}40). These patterns suggest distinct A{beta} aggregation mechanisms in CAA versus parenchymal plaques. We propose that the intact N-terminus found in CAA with limited Asp isomerization is due to its inclusion within the protofibril structure (less disordered and inaccessible to PTMs), unlike the parenchymal plaques, where the N-terminus is more disordered and accessible to PTMs. These biochemical differences may reflect distinct protofibril architectures with potential implications for biomarker development for early CAA detection and therapeutic targeting of vascular and parenchymal A{beta}. ]]> Koutarapu, S. Roberts, K. F. Coyle, R. A. Mehla, J. Sato, C. Zipfel, G. J. Bateman, R. J. Schwetye, K. E. Mukherjee, S. 2025-06-15 doi:10.1101/2025.06.11.658821 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Induction of Human Pruriceptors from Pluripotent Stem Cells via Transcription Factors ]]> https://biorxiv.org/content/10.1101/2025.06.11.659208v1?rss=1 Iriki, H. Hu, R. Li, X. Baljinnyam, E. Habich, C. Imanishi, I. Miller, L. Chegireddy, K. Malik, L. I. Yassky, D. Heul, A. V. Smith, K. M. Goedken, E. R. Reinhardt, P. Kim, B. S. Marro, S. G. 2025-06-15 doi:10.1101/2025.06.11.659208 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Glutaminolysis Fuels Reactive Astrocytes, Exacerbating Amyloid Pathology in Alzheimer's Disease. ]]> https://biorxiv.org/content/10.1101/2025.06.12.658977v1?rss=1 Devi, S. S. Heese, S. L. Leray, I. Gallardo, G. 2025-06-15 doi:10.1101/2025.06.12.658977 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Logistic regression for estimating functional effects with spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.06.11.659209v1?rss=1 Oviedo, H. V. Barkasi, M. Pham, C. N. Neophytou, D. 2025-06-17 doi:10.1101/2025.06.11.659209 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Image-Based Meta- and Mega-Analysis (IBMMA): A Unified Framework for Large-Scale, Multi-Site, Neuroimaging Data Analysis ]]> https://biorxiv.org/content/10.1101/2025.06.16.657725v1?rss=1 Steele, N. Morey, R. Hussain, A. Russell, C. Suarez-Jimenez, B. Pozzi, E. Jameei, H. Schmaal, L. Veer, I. Waller, L. Jahanshad, N. Thomopoulos, S. Salminen, L. Olff, M. Frijling, J. Veltman, D. Koch, S. Nawijn, L. van Zuiden, M. Wang, L. Zhu, Y. Li, G. Stein, D. Ipser, J. Neria, Y. Zhu, X. Ravid, O. Zilcha-Mano, S. Lazarov, A. Huggins, A. Stevens, J. Ressler, K. Jovanovic, T. van Rooij, S. Fani, N. Mueller, S. Hudson, A. Daniels, J. Sierk, A. Manthey, A. Walter, H. van der Wee, N. van der Werff, S. Vermeiren, R. Schmahl, C. Herzog, J. Rektor, I. i 2025-06-17 doi:10.1101/2025.06.16.657725 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ YAP signaling promotes resistance to MEK and AKT inhibition in NF1-related MPNSTs ]]> https://biorxiv.org/content/10.1101/2025.06.16.659334v1?rss=1 McGee, L. E. Grit, J. L. Essenburg, C. J. Agrusa, S. Turner, L. Becker, K. Dey, A. Klomp, J. E. Klomp, J. A. Adams, M. Beddows, I. Wolfrum, E. Fu, D. Hirbe, A. C. Graveel, C. R. Steensma, M. R. 2025-06-20 doi:10.1101/2025.06.16.659334 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Cerebellum metastasis model of HER2-positive breast cancer unveils key role of IL34-induced Arg1+ macrophages. ]]> https://biorxiv.org/content/10.1101/2025.06.17.660224v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@9f1a50org.highwire.dtl.DTLVardef@178acc5org.highwire.dtl.DTLVardef@196d803org.highwire.dtl.DTLVardef@3fe631_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cheng, X. Patel, K. K. Zhou, B. Fu, Y. Cleary, R. Highkin, M. Hsia, J. Jin, X. Kohn, B. Prior, J. L. Michie, M. S. Sun, R. Van Swearingen, A. E. D. Quirk, J. D. Hagemann, I. S. Li, Q. Jain, V. Gregory, S. G. Kim, A. H. Bose, R. 2025-06-23 doi:10.1101/2025.06.17.660224 Cold Spring Harbor Laboratory Press 2025-06-23 <![CDATA[ daf-16/FOXO promotes the activity of ligand-bound DAF-12/NHR to coordinate dauer recovery and post-dauer seam cell fate ]]> https://biorxiv.org/content/10.1101/2025.06.18.660181v1?rss=1 Wirick, M. J. Smith, I. T. Olson, B. S. Alessi, A. F. Galagali, H. Lalk, K. Schmidt, M. N. Ranke, K. J. Kim, J. K. Karp, X. 2025-06-24 doi:10.1101/2025.06.18.660181 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ Bidirectional regulation of glycoprotein nonmetastatic melanoma protein B by β-glucocerebrosidase deficiency in GBA1 isogenic dopaminergic neurons from a patient with Gaucher disease and parkinsonism ]]> https://biorxiv.org/content/10.1101/2025.06.23.661126v1?rss=1 Chen, C. Ma, C. Sam, R. Lichtenberg, J. Chen, T. Hao, Y. Li, Z. Kowal, I. Andersh, K. Qi, Y. A. Perez, G. Hertz, E. Li, Y. Williams, D. Henderson, M. J. Park, M. Jiang, X. Jerez, P. A. Blauwendraat, C. Sidransky, E. Chen, Y. 2025-06-25 doi:10.1101/2025.06.23.661126 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ TBRS-associated DNMT3A mutations disrupt cortical interneuron differentiation and neuronal networks ]]> https://biorxiv.org/content/10.1101/2025.06.24.661324v1?rss=1 Chapman, G. Determan, J. Edwards, J. R. Huettner, J. E. Crump, S. Jetter, H. Gabel, H. W. Kroll, K. L. 2025-06-25 doi:10.1101/2025.06.24.661324 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Neural correlates of evidence accumulation in social-affective decision-making under perceptual ambiguity ]]> https://biorxiv.org/content/10.1101/2025.06.24.660932v1?rss=1 Sun, S. Xie, T. Chen, Y. Wang, J. Li, X. Yu, R. Brunner, P. Willie, J. Wang, S. Yu, H. 2025-06-26 doi:10.1101/2025.06.24.660932 Cold Spring Harbor Laboratory Press 2025-06-26 <![CDATA[ Identification of Small Molecule Dimethyoxyphenyl Piperazine Inhibitors of Alpha-Synuclein Fibril Growth ]]> https://biorxiv.org/content/10.1101/2025.06.26.661821v1?rss=1 Hwang, H. Dhavale, D. D. Wang, S. J. Beale, J. M. Cairns, N. J. Kotzbauer, P. T. 2025-06-29 doi:10.1101/2025.06.26.661821 Cold Spring Harbor Laboratory Press 2025-06-29 <![CDATA[ A single binge ethanol exposure is apoptotic within hours across neurodevelopment and partially regulated by the Myt1l gene. ]]> https://biorxiv.org/content/10.1101/2025.06.27.662020v1?rss=1 Fuhler, N. Palmer, C. Tunzi, G. Tian, L. Fotedar, M. Chase, R. Prakasam, R. Maloney, S. E. Neblock, C. E. Chen, J. Kroll, K. L. Dougherty, J. D. Noguchi, K. 2025-06-29 doi:10.1101/2025.06.27.662020 Cold Spring Harbor Laboratory Press 2025-06-29 <![CDATA[ SARS-CoV-2 infection disrupts syncytial and endothelial integrity and alters PLGF levels in the placenta ]]> https://biorxiv.org/content/10.1101/2025.06.27.661568v1?rss=1 Jones, B. R. Nobrega, G. M. Kumar, D. Diveley, E. Antolini-Tavares, A. Souza, R. T. Cecatti, J. G. Kelly, J. C. Costa, M. L. Mysorekar, I. U. 2025-06-30 doi:10.1101/2025.06.27.661568 Cold Spring Harbor Laboratory Press 2025-06-30 <![CDATA[ The gut microbiome shapes pharmacology and treatment outcomes for a key anti-inflammatory therapy ]]> https://biorxiv.org/content/10.1101/2025.06.26.661733v1?rss=1 Villa Soto, V. S. Degraeve, A. L. Heath, C. M. Orellana, D. A. Reilly, E. R. Mukherjee, M. Brockert, J. G. Dumlao, D. S. Blank, R. B. Perlmutter, N. Yu, S. Ashouri, J. Scher, J. U. Patterson, A. D. Turnbaugh, P. J. Nayak, R. R. Mukherjee, M. F. 2025-07-01 doi:10.1101/2025.06.26.661733 Cold Spring Harbor Laboratory Press 2025-07-01 <![CDATA[ KAT6A/B inhibition synergizes with retinoic acid and enhances the efficacy of GD2-targeted immunotherapy in neuroblastoma ]]> https://biorxiv.org/content/10.1101/2025.07.01.662644v1?rss=1 Weichert-Leahey, N. Berezovskaya, A. Zimmerman, M. W. Alvarez-Caldero, F. Winschel, M. Salhotra, S. Mabe, N. W. Perez-Atayde, A. Vitorino, F. N. d. L. Garcia, B. Gerdemann, U. Stegmaier, K. Durbin, A. Oldridge, D. Abraham, B. Look, A. T. 2025-07-02 doi:10.1101/2025.07.01.662644 Cold Spring Harbor Laboratory Press 2025-07-02 <![CDATA[ Modular, reconfigurable fiber-based neural probe (MoRF probe) with interchangeable and tunable optical waveguide, microfluidic channel, and microelectrodes ]]> https://biorxiv.org/content/10.1101/2025.06.29.662251v1?rss=1 Huang, H. Liu, Y. Yang, S. Hu, S. English, D. F. Jia, X. 2025-07-03 doi:10.1101/2025.06.29.662251 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Neural Synchrony in Parent-Child Dyads: Profiles Associated with Interparental Conflict and Internalizing Symptoms ]]> https://biorxiv.org/content/10.1101/2025.07.02.662817v1?rss=1 Alvarado, C. Panlilio, C. C. Perez-Edgar, K. Thompsom, K. I. Schaedig, D. Melhem, N. Perlman, S. B. 2025-07-03 doi:10.1101/2025.07.02.662817 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Advancing Inter-brain Synchrony Measurement: A Comparative Hyperscanning Study of High-Density Diffuse Optical Tomography and Functional Near-infrared Spectroscopy ]]> https://biorxiv.org/content/10.1101/2025.07.02.662877v1?rss=1 Guan, S. Li, Y. Geng, Y. Li, D. Xu, Q. Yang, D. Zhang, Y. Li, R. 2025-07-03 doi:10.1101/2025.07.02.662877 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ A causal role for the posterior corpus callosum in bimanual coordination ]]> https://biorxiv.org/content/10.1101/2025.07.02.662886v1?rss=1 Kang, J. U. Snyder, L. H. Mooshagian, E. 2025-07-03 doi:10.1101/2025.07.02.662886 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Characterizing Bacterial and Archaeal Microbiomes of Urban Long-Tailed Macaques in Singapore ]]> https://biorxiv.org/content/10.1101/2025.07.03.662964v1?rss=1 Rivaldi, C.--L. Wilcox, J. J. S. Egan, B. Gombash, B. Hollocher, H. 2025-07-03 doi:10.1101/2025.07.03.662964 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Towards Precision Functional Brain Network Mapping in Parkinsons Disease ]]> https://biorxiv.org/content/10.1101/2025.07.01.662626v1?rss=1 100 minutes of RSFC data from 20 PD and 6 healthy controls participants. We evaluated the level of motion, reliability and stability of RSFC measures in each participant and contrasted these measures between the PD and HC groups, as well as compared to a conventional 5 minutes of RSFC data. In addition, we created individualized brain network measures in PD participants to establish feasibility in this population. ResultsUsing precision methods, the PD group produced reliable and stable RSFC measures of brain networks of similar quality to healthy controls and substantially better than conventional methods. Individualized network maps from individuals with PD demonstrate differences from group averages and from each other, including in key motor systems. ConclusionPrecision RSFC is feasible and reliable in individuals with PD. This approach holds promise for advancing personalized diagnostics and identifying brain-based biomarkers underlying clinical variability in PD. ]]> Chernicky, J. Dworetsky, A. Grossen, S. Carr, E. Eid, A. Campbell, M. C. Gratton, C. 2025-07-07 doi:10.1101/2025.07.01.662626 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ Diet, Climatic Conditions, and Sex Affect the Mycobiome of Wild Common Marmosets (Callithrix jacchus) ]]> https://biorxiv.org/content/10.1101/2025.07.06.663406v1?rss=1 Gombash, B. J. Garber, P. A. Finnegan, P. M. McKenney, A. C. Bicca-Marques, J. C. De la Fuente, M. F. Abreu, F. Souto, A. Schiel, N. Amato, K. R. J. Mallott, E. K. 2025-07-07 doi:10.1101/2025.07.06.663406 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ The neuroimaging correlates of depression established across six large-scale datasets ]]> https://biorxiv.org/content/10.1101/2025.07.02.660888v1?rss=1 Hamilton, K. M. Luo, X. D. Easley, T. O. Ahmad, F. Guo, T. Jarukasemkit, S. Modi, H. Rincon, S. N. Shelton, C. Stahl, L. Wang, Z. Zhu, Y. Lenzini, P. Hannon, K. Bijsterbosch, J. D. 2025-07-08 doi:10.1101/2025.07.02.660888 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ Tendon fibroblast inflammatory responses depend on NF-κβ and JAK/STAT signaling and alter mechanotransduction pathways ]]> https://biorxiv.org/content/10.1101/2025.07.04.663209v1?rss=1 Sup, M. Kim, M. M. Song, L. Genin, G. M. Thomopoulos, S. 2025-07-08 doi:10.1101/2025.07.04.663209 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ Musculoskeletal architecture of the shoulder: A comparative anatomy study in bats and mice informing human rotator cuff function ]]> https://biorxiv.org/content/10.1101/2025.07.04.663211v1?rss=1 Kurtaliaj, I. Kunes, J. Li, S. Rowley, M. Forrester, L. A. Golman, M. Swartz, S. M. Levine, W. N. Genin, G. M. Thomopoulos, S. 2025-07-08 doi:10.1101/2025.07.04.663211 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ Multimodal induction of fulminant HLH by IL-18 includes virus-specific NK immunodeficiency ]]> https://biorxiv.org/content/10.1101/2025.07.04.663237v1?rss=1 Varghese, J. A. Landy, E. Huang, L. Frank-Kamenetskii, A. Klinghoffer, H. Morrissette, J. Dang, V. Carro, S. Eisenlohr, L. C. Canna, S. W. 2025-07-08 doi:10.1101/2025.07.04.663237 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ GAME: Genomic API for Model Evaluation ]]> https://biorxiv.org/content/10.1101/2025.07.04.663250v1?rss=1 Luthra, I. Priyadarshi, S. Guo, R. Mahieu, L. Kempynck, N. Dooley, D. Penzar, D. Vorontsov, I. Sheng, Y. Tu, X. Klie, A. Drusinsky, S. Floren, A. Armand, E. Alasoo, K. Seelig, G. Tewhey, R. Koo, P. Agarwal, V. Gosai, S. Pinello, L. White, M. A. Lal, A. Zeitlinger, J. Pollard, K. S. Libbrecht, M. Carter, H. Mostafavi, S. Kulakovskiy, I. Hsiao, W. Aerts, S. Zhou, J. de Boer, C. G. 2025-07-08 doi:10.1101/2025.07.04.663250 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ HER2; p53 Co-mutated Cancers Show Increased Histone Acetylation and are Sensitive to Neratinib plus Trastuzumab Deruxtecan. ]]> https://biorxiv.org/content/10.1101/2025.07.06.663368v1?rss=1 Cheng, X. Hsia, J. Iraheta, J. Gongora, J. Highkin, M. Jin, X. Guo, Z. Prior, J. L. Edwards, J. R. Li, S. Hagemann, I. S. Ma, C. X. Lin, Z. Garcia, B. A. Bose, R. 2025-07-10 doi:10.1101/2025.07.06.663368 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ Maternal high-fat/high-sugar diet has short-term dental effects and long-term sex-specific skeletal effects on adult offspring mice ]]> https://biorxiv.org/content/10.1101/2025.07.06.663396v1?rss=1 Hassan, M. Koester, K. Harasymowicz, N. Oestreich, A. K. Moley, K. Guilak, F. Scheller, E. L. 2025-07-10 doi:10.1101/2025.07.06.663396 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ Multiple event segmentation mechanisms in the human brain ]]> https://biorxiv.org/content/10.1101/2025.07.07.663487v1?rss=1 Nguyen, T. T. Etzel, J. A. Bezdek, M. A. Zacks, J. 2025-07-10 doi:10.1101/2025.07.07.663487 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ Rapid thermoforming of polycarbonate cell culture accessories from 3D printed molds ]]> https://biorxiv.org/content/10.1101/2025.07.07.663502v1?rss=1 Malayath, G. Huebsch, N. 2025-07-10 doi:10.1101/2025.07.07.663502 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ Precision Functional Mapping of the Individual Human Brain Near Birth ]]> https://biorxiv.org/content/10.1101/2025.07.07.663543v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@b6c63aorg.highwire.dtl.DTLVardef@1903235org.highwire.dtl.DTLVardef@1d05733org.highwire.dtl.DTLVardef@10d0770_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIIt is feasible to obtain precision functional mapping (PFM) in neonates, acquiring 60+ minutes of fMRI data in individual neonates over multiple days. C_LIO_LINeonatal functional connectivity (FC) measures obtained through PFM are moderately reliable with 40 minutes of data. C_LIO_LIPatterns of neonatal FC across the brain are individually specific. C_LIO_LICortical areas, based on patterns of homogenous FC, can be reliably identified across the entire cortical surface in individual neonates. C_LIO_LIThe arrangement of cortical areas at birth is individually specific across the entire brain. C_LI ]]> Labonte, A. K. Moser, J. Camacho, M. C. Tu, J. C. Wheelock, M. Laumann, T. O. Gordon, E. M. Fair, D. A. Sylvester, C. 2025-07-10 doi:10.1101/2025.07.07.663543 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ A LARGE-SCALE EVOLUTIONARY AND STRUCTURAL ANALYSIS OF CLC CHANNELS AND TRANSPORTERS ]]> https://biorxiv.org/content/10.1101/2025.07.07.663545v1?rss=1 Mishra, A. Diaz Vazquez, G. Robertson, J. L. 2025-07-10 doi:10.1101/2025.07.07.663545 Cold Spring Harbor Laboratory Press 2025-07-10 <![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[ Tim-3 Promotes Early Differentiation of Tbet+ Effector T Cells During Acute Viral Infection ]]> https://biorxiv.org/content/10.1101/2025.07.08.663709v1?rss=1 Manandhar, P. Landy, E. Mori, K. Kane, L. P. 2025-07-11 doi:10.1101/2025.07.08.663709 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ Multi-omic mapping of Drosophila protein secretomes reveals tissue-specific origins and inter-organ trafficking ]]> https://biorxiv.org/content/10.1101/2025.07.09.659702v1?rss=1 Bosch, J. A. Beltran, P. M. J. Cavers, C. LaGraff, J. T. Melanson, R. Singh, A. Chen, W. Hu, Y. Tattikota, S. G. Liu, Y. Hashmi, Y. Asara, J. M. Branon, T. Ting, A. Y. Carr, S. A. Perrimon, N. 2025-07-11 doi:10.1101/2025.07.09.659702 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ Identification of novel protective loci for executive function using the trail making test part B in the Long Life Family Study ]]> https://biorxiv.org/content/10.1101/2025.07.08.663708v1?rss=1 3.0). Statistical fine-mapping nominated five variants including three SNPs (NTRK3-rs74031103, protective CEMIP-rs2271159, and protective AGBL1-rs4134376) and two INDELs (protective KLHL25-15:85882445:IND, and protective CEMIP-15:80893381:IND) contributing to the linkage peak. Four out of these five variants are protective for TMT-B. The rs2271159 SNP influences CEMIP expression in cerebellum and hippocampus, while the 15:80893381:IND modulates CEMIP expression in blood. Additionally, the variant rs4134376 is a basal ganglia-specific eQTL for AGBL1. In conclusion, we utilized GWLS, leveraged multi-omics data (whole genome sequence genomic data, transcriptomic data, and lipidomic data), and identified novel protective variants and genes for TMT-B performance. ]]> Wang, L. Tanner, K. Andersen, S. L. Cosentino, S. Moghaddam, V. A. Daw, E. W. Anema, J. A. Lin, S. J. Acharya, S. Province, M. Wojczynski, M. K. 2025-07-12 doi:10.1101/2025.07.08.663708 Cold Spring Harbor Laboratory Press 2025-07-12 <![CDATA[ Loss of FMRP in microglia promotes degeneration of parvalbumin neurons and audiogenic seizures via progranulin insufficiency ]]> https://biorxiv.org/content/10.1101/2025.07.09.663876v1?rss=1 Li, H. Choi, J. J.-Y. Huang, E. J. Xu, B. 2025-07-12 doi:10.1101/2025.07.09.663876 Cold Spring Harbor Laboratory Press 2025-07-12 <![CDATA[ Immune cells regulate circulating adipocyte extracellular vesicle levels in response to metabolic shifts ]]> https://biorxiv.org/content/10.1101/2025.07.11.664236v1?rss=1 Tiash, S. Russo, M. Pai, Y.-L. Jia, W. Field, R. L. Pietka, T. Abumrad, N. A. Smith, G. I. Klein, S. Brestoff, J. R. Crewe, C. 2025-07-14 doi:10.1101/2025.07.11.664236 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ Juxtaposition of human pluripotent stem cells with amnion-like cells is sufficient to trigger primitive streak formation ]]> https://biorxiv.org/content/10.1101/2025.07.11.664380v1?rss=1 Kong, X. Nemashkalo, A. Guerra, M. C. Ortiz-Salazar, M. A. Camacho-Aguilar, E. Warmflash, A. 2025-07-14 doi:10.1101/2025.07.11.664380 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ A comparison of adiponectin-deficient mice reveals the fundamental role of intracellular adiponectin ]]> https://biorxiv.org/content/10.1101/2025.07.12.664095v1?rss=1 Onodera, T. Kim, D.-S. Wang, M.-Y. Virostek, M. Chen, S. Kipp, Z. A. Bates, E. A. Li, Y. Crewe, C. Li, C. Sun, X.-N. Zhang, Q. Shao, M. Shin, J. Kusminski, C. M. Gordillo, R. Gupta, R. K. Hinds, T. D. Shimomura, I. Scherer, P. E. 2025-07-14 doi:10.1101/2025.07.12.664095 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ Tissue transcriptomics of endomyocardial biopsies reveals widespread molecular perturbations independent of leukocyte-rich foci in human myocarditis ]]> https://biorxiv.org/content/10.1101/2025.07.11.664335v1?rss=1 Cohen, C. D. He, J. H. Bermea, K. C. Rousseau, S. T. Luo, A. Ebenebe, O. V. D. Casella, K. Palescandolo, E. Lavine, K. J. Shenderov, E. Halushka, M. Adamo, L. 2025-07-17 doi:10.1101/2025.07.11.664335 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Inflammaging in aged tissues drives remodeling of the CD8+ T cell compartment ]]> https://biorxiv.org/content/10.1101/2025.07.11.664388v1?rss=1 Shchukina, I. Rodriguez-Hernandez, C. Ruiz, H. S. Kleverov, M. Mintz, R. L. Mineura, K. Gunawardana, S. C. Hsiung, S. Vachova, V. Kossl, J. Vander Wielen, B. Mogilenko, D. A. Huckstep, C. G. Piston, D. W. Egawa, T. Kreisel, D. Randolph, G. J. Artyomov, M. N. 2025-07-17 doi:10.1101/2025.07.11.664388 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Cortical neural landscape captures mouse-to-mouse variability in anticipatory vs. inattentive decision making ]]> https://biorxiv.org/content/10.1101/2025.07.11.664420v1?rss=1 Yin, C. Hiratani, N. 2025-07-17 doi:10.1101/2025.07.11.664420 Cold Spring Harbor Laboratory Press 2025-07-17 <![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[ Spatial profiling reveals TREM2+ macrophages as central to Mycobacterium tuberculosis pathogenesis in human pulmonary tuberculosis ]]> https://biorxiv.org/content/10.1101/2025.07.15.664002v1?rss=1 Teles, R. M. B. Benabdessalem, C. Perrie, J. Wei, C. West, J. de Andrade Silva, B. J. Andrade, P. R. Mansky, L. Divakar, P. Fischbacher, L. Lam, K. Ma, F. Rategh, K. Pillai, A. French, S. M. Romdhane, E. Barbouche, M.-R. Klechevsky, E. Colonna, M. Steyn, A. J. C. Bensinger, S. Barber, D. L. Rammeh, S. Dulai, P. S. Bryson, B. D. Pellegrini, M. Belisle, J. T. Bloom, B. R. Modlin, R. L. 2025-07-18 doi:10.1101/2025.07.15.664002 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Biomechanical Phenotyping Reveals Unique Mechanobiological Signatures of Early-Onset Colorectal Cancer ]]> https://biorxiv.org/content/10.1101/2025.07.15.664829v1?rss=1 Huning, N. C. Buhaya, M. H. Nguyen, V. V. Khazi-Syed, A. Ali, H. A. Khan, A. Fan, A. Fisher, R. C. Chi, Z. Raman, I. Chen, G. Zhu, C. Yu, M. Jamieson, A. Roccabianca, S. Varner, V. Lewis, C. M. Huang, E. H. Ferruzzi, J. 2025-07-18 doi:10.1101/2025.07.15.664829 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Whole blood transcriptional signatures of age and survival identified in Long Life Family and Integrative Longevity Omics Studies ]]> https://biorxiv.org/content/10.1101/2025.07.15.664976v1?rss=1 Li, M. Song, Z. Reed, E. Karagiannis, T. T. Andersen, S. Brent, M. Mateusiak, C. Acharya, S. Jung, W. S. Liao, S. Wojczynski, M. K. Feitosa, M. F. O'Connell, J. R. Montasser, M. E. Thorpe, R. J. Arbeev, K. Milman, S. Tai, A. Perls, T. T. Sebastiani, P. Monti, S. 2025-07-18 doi:10.1101/2025.07.15.664976 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ SOX2 utilizes FOXA1 as a heteromeric transcriptional partner to drive proliferation in therapy-resistant prostate cancer ]]> https://biorxiv.org/content/10.1101/2025.07.18.664790v1?rss=1 Phoenix, J. T. Budreika, A. Schmeck, D. A. Kostlan, R. J. Ferrari, M. G. Young, K. S. Rogers, C. S. Deegan, C. D. Bergom, H. E. Boytim, E. Brown, R. M. Bienko, M. W. Walewicz, J. A. Bhagi, S. K. Ellis, L. Antonarakis, E. S. Drake, J. M. Bawa, P. S. Vellky, J. E. Williams, A. Reizine, N. M. Rennhack, J. P. Fanning, S. W. Hwang, J. H. Szmulewitz, R. Z. Vander Griend, D. J. Kregel, S. 2025-07-19 doi:10.1101/2025.07.18.664790 Cold Spring Harbor Laboratory Press 2025-07-19 <![CDATA[ SUZ12-Nucleic Acid Interactions Constrain PRC2 Activity to Maintain Targeted Gene Silencing Essential to Diffuse Midline Glioma ]]> https://biorxiv.org/content/10.1101/2025.07.18.665585v1?rss=1 Reich, T. J. Clark, P. A. Baguette, A. Lempiainen, J. K. Russo, C. Rashoff, A. Q. Do, T. J. Garcia, B. A. Kleinman, C. L. Jabado, N. Morris, Z. S. Lewis, P. W. 2025-07-19 doi:10.1101/2025.07.18.665585 Cold Spring Harbor Laboratory Press 2025-07-19 <![CDATA[ Divergent Cell-Type Specific Hypoxia Responses in Human Stem Cell-Derived and Primary Islets ]]> https://biorxiv.org/content/10.1101/2025.07.16.665006v1?rss=1 Bradley, K. Moore, C. Ishahak, M. Maestas, M. M. Veronese-Paniagua, D. A. Millman, J. R. 2025-07-21 doi:10.1101/2025.07.16.665006 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ CSF1R regulates monocyte subset differentiation and intracellular metabolism. ]]> https://biorxiv.org/content/10.1101/2025.07.17.665275v1?rss=1 Gallerand, A. Merlin, J. Caillot, Z. Delaby, C. Bord, E. Han, J. Dolfi, B. Castiglione, A. Grenet, S. Franceschini, M. Jarretou, G. Zair, F. N. Bore, E. Tuffin, F. Dombrowicz, D. Guinamard, R. R. Randolph, G. J. Bertola, A. Auberger, P. Jacquel, A. Hume, D. A. Williams, J. W. Bajenoff, M. Neels, J. G. Ivanov, S. 2025-07-21 doi:10.1101/2025.07.17.665275 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ MTARC1 Regulates Lipid Droplet Degradation via Phospholipid Remodeling in Metabolic Fatty Liver Disease ]]> https://biorxiv.org/content/10.1101/2025.07.17.665462v1?rss=1 Tie, M. Hu, L. Yang, Y. Song, S. Zhu, Q. Li, J. Wang, W. Xu, P. Yu, J. Wu, M. Zhao, T. Yuan, D. Bao, H. Wang, X. Lodhi, I. J. Chen, Y. Chen, Y. He, A. 2025-07-21 doi:10.1101/2025.07.17.665462 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Precision functional mapping reveals less inter-individual variability in the child vs. adult human brain ]]> https://biorxiv.org/content/10.1101/2025.07.21.665760v1?rss=1 Demeter, D. V. Feigelis, M. DAndrea, C. B. Ali, S. A. Baim, A. R. Koithan, E. Stearns, J. Zreik, S. Ahern, J. Park, S. Chang, S. E. Miller, R. L. Hampton, J. M. Schlaggar, B. L. Marek, S. Gordon, E. M. Dosenbach, N. U. Gratton, C. Greene, D. J. 2025-07-24 doi:10.1101/2025.07.21.665760 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Structural Plasticity of the Membrane-Bound Protein Degradation Assembly Supports Bacterial Adaptation to Stress ]]> https://biorxiv.org/content/10.1101/2025.07.21.662073v1?rss=1 Iqbal, N. Keller, S. Ghanbarpour, A. 2025-07-25 doi:10.1101/2025.07.21.662073 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ Central Amygdala Neuronal Ensembles Coordinate Visceral Pain and Its Affective Behaviors ]]> https://biorxiv.org/content/10.1101/2025.07.21.666026v1?rss=1 Samineni, V. K. Sackey, J. N. Li, J.-N. Yang, L. Chamessian, A. Sewell, S. B. Hahm, H. J. Zhang, Y. Zhang, B. Gereau, R. W. 2025-07-25 doi:10.1101/2025.07.21.666026 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ Volumetric Differences of Thalamic Nuclei are Associated with Post-Trauma Psychopathology ]]> https://biorxiv.org/content/10.1101/2025.07.24.666644v1?rss=1 Steele, N. Hussain, A. Baird, C. L. Haswell, C. C. Sun, D. Rangel-Jimenez, L. Abdallah, C. G. Angstadt, M. August, G. Berg, H. Blackford, J. U. Cisler, J. Daniels, J. K. Davenport, N. D. Davidson, R. J. Densmore, M. Disner, S. G. El-Hage, W. Etkin, A. Fani, N. Frijling, J. L. Gordon, E. M. Grupe, D. W. Herringa, R. J. Hudson, A. R. Jahanshad, N. Jovanovic, T. King, A. Koch, S. B. J. Lanius, R. Lazarov, A. Li, G. Liberzon, I. Lissek, S. Lu, G. M. Manthey, A. Maron-Katz, A. Nawijn, L. Nelson, S. M. Neria, Y. Neufeld, R. W. J. Nitschke, J. B. Olatunji, B. 2025-07-25 doi:10.1101/2025.07.24.666644 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ Targeting RUNX1 in Macrophages Facilitates Cardiac Recovery ]]> https://biorxiv.org/content/10.1101/2025.07.25.665779v1?rss=1 Amrute, J. M. Zhu, A. Pai, Y.-L. Hector-Greene, M. An, Y. Lim, K. R. Sheth, M. Padmanabhan, A. Lee, C. Y. Yamawaki, T. Sicklinger, F. Hartmann, N. Bredemeyer, A. Lee, C. J. M. Xu, V. Bell, L. Harmon, T. Shin, H. Parvathaneni, A. Liu, L. Dutta, A. K. Pruitt, D. Barreda, J. Chen, J. Shroff, U. N. Nadadur, R. Nigro, J. Weinheimer, C. J. Kovacs, A. Cui, J. Wang, C. Li, C.-M. K. Kreisel, D. Liu, Y. Foo, R. S.-Y. Schneider, R. K. Engreitz, J. Mann, D. Rulifson, I. Jackson, S. Ason, B. Kramann, R. Drakos, S. G. Leuschner, F. Alexanian, M. Lavine, K. J. 2025-07-26 doi:10.1101/2025.07.25.665779 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ Adaptive Immunity Governs Regional Aortic Remodeling in Hypertension via Perivascular Adipose Tissue Plasticity ]]> https://biorxiv.org/content/10.1101/2025.07.23.666477v1?rss=1 Xu, Y. Snider, C. Bersi, M. R. 2025-07-27 doi:10.1101/2025.07.23.666477 Cold Spring Harbor Laboratory Press 2025-07-27 <![CDATA[ Ebola virus VP35 NNLNS motif modulates viral RNA synthesis and MIB2-mediated signaling ]]> https://biorxiv.org/content/10.1101/2025.07.27.667045v1?rss=1 Uwase, G. Luthra, P. Vogel, O. A. Batra, J. LaRosa, B. A. Sheehan, K. C. F. Khatavkar, O. Payton, J. Davey, R. A. Krogan, N. J. Basler, C. F. Leung, D. W. Amarasinghe, G. K. 2025-07-27 doi:10.1101/2025.07.27.667045 Cold Spring Harbor Laboratory Press 2025-07-27 <![CDATA[ Distinct Roles of CaMKII in Synaptic Vesicle Dynamics at Zebrafish Retinal Rod Bipolar Ribbon Synapses ]]> https://biorxiv.org/content/10.1101/2025.07.27.667036v1?rss=1 Boff, J. M. Rameshkumar, N. Khamrai, M. Seetharaman, J. Olmos-Carrenno, C. L. Chudasama, N. Yoshimatsu, T. Zenisek, D. Tavalin, S. J. Vaithianathan, T. 2025-07-28 doi:10.1101/2025.07.27.667036 Cold Spring Harbor Laboratory Press 2025-07-28 <![CDATA[ Activation-Free Upgrading of Carboxylic Acids to Aldehydes and Alcohols ]]> https://biorxiv.org/content/10.1101/2025.07.28.667276v1?rss=1 1 g/L, in some cases, after optimization of thermodynamic driving forces. Additionally, we applied this system to upgrade waste-derived carboxylic acid effluent streams from wastewater sludge, food waste, and waste gas (CO2). This activation-free process, termed "reverse aldehyde oxidation" (rAOX), establishes a broadly applicable, energy-efficient platform for carboxylic acid valorization at 100% carbon yield. Analogous to the reverse tricarboxylic acid cycle (rTCA) and reverse {beta}-oxidation (rBOX), rAOX exemplifies that metabolic reactions classically defined as unidirectional may have unexpected plasticity to operate in reverse and open new avenues in biomanufacturing. ]]> Black, W. B. Saleh, S. Perea, S. Luu, E. Cui, Y. Sun, J. Wang, Z. Lambrecht, S. Awachi, S. Hayworth, D. Wang, A. Chuayiuso, C. Hagerty, R. Gilcrease, P. C. Jiao, F. He, Z. Siegel, J. B. Li, H. 2025-07-28 doi:10.1101/2025.07.28.667276 Cold Spring Harbor Laboratory Press 2025-07-28 <![CDATA[ Precision fMRI reveals densely interdigitated network patches with conserved motifs in the lateral prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2025.07.24.666468v1?rss=1 Ladwig, Z. Kermani, K. Z. Dworetsky, A. Labora, N. Hernandez, J. J. Dorn, M. Smith, D. M. Nee, D. E. Braga, R. M. Petersen, S. E. Gratton, C. 2025-07-30 doi:10.1101/2025.07.24.666468 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ Glucose Metabolism echoes Long-Range Temporal Correlations in the Human Brain ]]> https://biorxiv.org/content/10.1101/2025.07.29.667370v1?rss=1 Facca, M. Ridolfo, A. Celli, M. Tarricone, C. Mazzonetto, I. Volpi, T. Vlassenko, A. G. Goyal, M. S. Corbetta, M. Bertoldo, A. 2025-07-30 doi:10.1101/2025.07.29.667370 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ Historical Contingency Limits Adaptive Diversification in a Spatially Structured Environment ]]> https://biorxiv.org/content/10.1101/2025.07.27.667043v1?rss=1 Patton, G. Meraz, J. C. Yin, M. Worthan, S. B. Williams, S. Behringer, M. G. 2025-07-31 doi:10.1101/2025.07.27.667043 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ A stem cell-based platform for functional analysis of genetic variants in lung disease ]]> https://biorxiv.org/content/10.1101/2025.07.28.667211v1?rss=1 Wallman, D. J. Homma, S. T. Finton, M. Beermann, M. Jacob, A. Choksi, S. Pletcher, S. D. Xu, H. Bawa, P. S. Reiter, J. F. Horani, A. Brody, S. L. Berical, A. Hawkins, F. J. 2025-07-31 doi:10.1101/2025.07.28.667211 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ The impact of environmental exposures on the epigenomic and transcriptomic landscape of transposable elements ]]> https://biorxiv.org/content/10.1101/2025.07.28.667212v1?rss=1 Miao, B. Zhang, Y. Shao, W. Fu, S. Bartolomei, M. Walker, C. Coarfa, C. TaRGET II Consortium, Zhang, B. Wang, T. 2025-07-31 doi:10.1101/2025.07.28.667212 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ NLRP3 inflammasome is regulated in osteoclasts through a Tmem178-dependent mechanism that restricts calcium influx ]]> https://biorxiv.org/content/10.1101/2025.07.28.667255v1?rss=1 Kaur, K. Alippe, Y. Wang, C. Semenkovich, N. Bhagat, S. Khanna, K. Li, Y. Pokhrel, N. Peterson, T. Veis, D. Abu-Amer, Y. Faccio, R. Mbalaviele, G. 2025-07-31 doi:10.1101/2025.07.28.667255 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Sleep deprivation selectively reactivates hippocampal CA1 pyramidal neurons. ]]> https://biorxiv.org/content/10.1101/2025.07.30.665413v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@1cfa351org.highwire.dtl.DTLVardef@eb387dorg.highwire.dtl.DTLVardef@c9cf6forg.highwire.dtl.DTLVardef@1518b12_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wang, Y. Walsh, E. N. Resch, J. M. Lyons, L. C. Abel, T. 2025-07-31 doi:10.1101/2025.07.30.665413 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Alanine Catabolism as a Targetable Vulnerability for MYC-Driven Liver Cancer ]]> https://biorxiv.org/content/10.1101/2025.07.29.667471v1?rss=1 Montoya, T. Lee, J. V. Qiu, L. Krall, A. V. Matulionis, N. Seo, Y. Finck, B. Kelley, R. K. Christofk, H. Goga, A. 2025-08-01 doi:10.1101/2025.07.29.667471 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Comprehensive Transcriptomic and Epigenomic Insights into Environmental Toxicant Exposures: The TaRGET II Resource ]]> https://biorxiv.org/content/10.1101/2025.07.28.667191v1?rss=1 Zhang, B. A. Miao, B. Fu, S. Coarfa, C. Kumar, R. Kuntala, P. K. Park, B. Colacino, J. A. Svobada, L. K. Shao, W. Xing, X. Li, D. Liu, S. Hamanaka, R. B. Lalancette, C. Sartor, M. A. Krapp, C. Crawford, G. E. Patisaul, H. B. Wiltshire, T. Aylor, D. L. Biswal, S. Mutlu, G. M. Rajagopalan, S. Tang, W.-Y. Dolinoy, D. C. Wang, T. Bartolomei, M. S. Walker, C. L. Grimm, S. L. Ruiz-Echartea, E. Katz, T. Jangid, R. 2025-08-02 doi:10.1101/2025.07.28.667191 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ ToxiTaRGET: a multi-omics resource for toxicant-responsive molecular targets ]]> https://biorxiv.org/content/10.1101/2025.07.28.667228v1?rss=1 Kumar, R. Fu, T. Kuntala, P. K. Fu, S. Li, D. Bartolomei, M. S. Walker, C. L. Wang, T. Zhang, B. A. 2025-08-02 doi:10.1101/2025.07.28.667228 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Heterochromatin-based silencing of a foreign tandem repeat in Drosophila melanogaster shows unusual biochemistry and temperature sensitivity ]]> https://biorxiv.org/content/10.1101/2025.07.31.667933v1?rss=1 Gu, T. Gracheva, E. Lee, M. Leung, W. M. Bieser, S. Nielsen, A. Smiley, A. T. Vuong, N. N. T. Walther, M. Reuter, G. Elgin, S. C. R. Arsham, A. M. 2025-08-02 doi:10.1101/2025.07.31.667933 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ OmniCellAgent: Towards AI Co-Scientists for Scientific Discovery in Precision Medicine ]]> https://biorxiv.org/content/10.1101/2025.07.31.667797v1?rss=1 Huang, D. Li, H. Li, W. Zhang, H. Dickson, P. Zhan, M. Miller, J. P. Cruchaga, C. Province, M. Chen, Y. Payne, P. Li, F. 2025-08-04 doi:10.1101/2025.07.31.667797 Cold Spring Harbor Laboratory Press 2025-08-04 <![CDATA[ Terminal Loop Sequences in Viral Double-Stranded RNAs Modulate RIG-I Signaling ]]> https://biorxiv.org/content/10.1101/2025.08.02.668285v1?rss=1 Hackbart, M. Wang, P. Gnazzo, V. Lopez, C. B. 2025-08-04 doi:10.1101/2025.08.02.668285 Cold Spring Harbor Laboratory Press 2025-08-04 <![CDATA[ Live-cell imaging and lipidomics of low density lipoprotein containing intrinsically fluorescent cholesteryl esters ]]> https://biorxiv.org/content/10.1101/2025.08.05.668602v1?rss=1 Juhl, A. D. Sprenger, R. R. Modzel, M. Halder, S. Szomek, M. Xu, X. Ejsing, C. S. Covey, D. F. Wüstner, D. 2025-08-05 doi:10.1101/2025.08.05.668602 Cold Spring Harbor Laboratory Press 2025-08-05 <![CDATA[ Targeting the COP9 signalosome overcomes platinum resistance in ovarian cancer through two distinct genome stability mechanisms ]]> https://biorxiv.org/content/10.1101/2025.08.04.668450v1?rss=1 Lomonosova, E. Loeb, M. Rodriguez, K. van Biljon, L. N. Brill, J. Schab, A. Minett, M. Barron, J. Bittner, M. Park, J. Drexler, R. Sandoval, C. Oplt, A. Gallup, E. Thuthika, P. K. Sadeghipour, N. Wu, S. Oberley, M. J. Sanders, B. Kuroki, L. McCourt, C. Hagemann, A. R. Thaker, P. Mutch, D. Powell, M. Hagemann, I. S. Ilagan, M. Fuh, K. Verma, P. Scharer, O. Mosammaparast, N. Khabele, D. Mullen, M. M. 2025-08-06 doi:10.1101/2025.08.04.668450 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ YY1 relieves p300 autoinhibition to promote histone acetylation in advanced prostate cancer, enhancing the oncogenic signaling of Androgen Receptor Splice Variant 7 ]]> https://biorxiv.org/content/10.1101/2025.08.04.668477v1?rss=1 Xu, C. Wu, D. Pan, B. Ren, X. Mackintosh, S. G. Jain, K. Bhanu, N. V. Edmondson, R. D. Liu, X. Garcia, B. Tackett, A. J. Jin, J. Wang, G. G. Cai, L. 2025-08-06 doi:10.1101/2025.08.04.668477 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ Exoproteome of calorie-restricted humans identifies complement deactivation as an immunometabolic checkpoint reducing inflammaging ]]> https://biorxiv.org/content/10.1101/2025.08.04.668533v1?rss=1 Mishra, M. Kim, H.-H. Youm, Y.-H. Gonzalez-Hurtado, E. Zaitsev, K. Dlugos, T. Shchukina, I. Gliniak, C. Ravussin, E. Mohanty, S. Shaw, A. C. Scherer, P. E. Artyomov, M. N. Dixit, V. D. 2025-08-06 doi:10.1101/2025.08.04.668533 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ Defined human tri-lineage brain microtissues ]]> https://biorxiv.org/content/10.1101/2025.08.05.668605v1?rss=1 Uenaka, T. Jung, S. Kumar, I. Vodehnal, K. Rastogi, M. Yoo, Y. Koontz, M. Thome, C. Li, W. Chan, T. Green, E. M. Chesnov, K. Sun, Z. Zhang, S. Wang, J. Venida, A. Mahul Mellier, A.-L. Atkins, M. Jackrel, M. Skotheim, J. M. Wyss-Coray, T. Abu-Remaileh, M. Lashuel, H. A. Bassik, M. C. Sudhof, T. C. del Sol, A. Ullian, E. Wernig, M. 2025-08-07 doi:10.1101/2025.08.05.668605 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[ Platelets drive immune suppression and glioblastoma growth in a sex-dependent manner via PAR4 signaling ]]> https://biorxiv.org/content/10.1101/2025.08.06.668464v1?rss=1 Sloan, A. R. Bukenya, G. Aggarwal, A. Lee, J. Rosoff, D. Alban, T. Juric, I. Silver, D. J. Tacj, L. Navadgi, T. Tannish, G. Yuan, X. Coker, J. Scalise, A. Rajasekar, B. Vincenti, A. Mulkearns-Hubert, E. E. Horbinski, C. Sloan, A. E. Hubert, C. G. Luo, J. Rubin, J. B. Stavrou, E. X. Lohoff, F. W. Nieman, M. T. Sangwan, N. Chan, T. Khorana, A. A. Dhawan, A. Cameron, S. Lathia, J. 2025-08-08 doi:10.1101/2025.08.06.668464 Cold Spring Harbor Laboratory Press 2025-08-08 <![CDATA[ Bottlebrush Polymer Conjugates for Enhanced Antisense Oligonucleotide Therapy in Myotonic Dystrophy Type 1 ]]> https://biorxiv.org/content/10.1101/2025.08.06.668589v1?rss=1 View larger version (21K): org.highwire.dtl.DTLVardef@e3961corg.highwire.dtl.DTLVardef@194225dorg.highwire.dtl.DTLVardef@5c470dorg.highwire.dtl.DTLVardef@3cc46a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Li, Y. Oetheimer, C. Wang, Y. Heo, G. S. Wu, J. Chang, R. Zhang, W. Schneider, E. Chen, J. Fang, Y. Wei, Y. Nian, K. Zhang, H. Sherman, L. Liu, Y. Zhang, K. 2025-08-08 doi:10.1101/2025.08.06.668589 Cold Spring Harbor Laboratory Press 2025-08-08 <![CDATA[ Condensin and topoisomerases cooperate to relieve topological stress at stalled replication forks ]]> https://biorxiv.org/content/10.1101/2025.08.06.668895v1?rss=1 Da Mota, M. Delamarre, A. Barthe, A. Jackson, J. Toran-Vilarrubias, A. Ribeyre, C. Vindigni, A. Lin, Y.-L. Pasero, P. Lengronne, A. 2025-08-09 doi:10.1101/2025.08.06.668895 Cold Spring Harbor Laboratory Press 2025-08-09 <![CDATA[ Anticodon-edited tRNA enables translational readthrough of COL4A5 premature termination codons ]]> https://biorxiv.org/content/10.1101/2025.08.07.669229v1?rss=1 Omachi, K. Porter, J. J. Lueck, J. D. Miner, J. H. 2025-08-09 doi:10.1101/2025.08.07.669229 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[ Molecular response to the non-lytic peptide bac7 (1-35) triggers disruption of Klebsiella pneumoniae biofilm ]]> https://biorxiv.org/content/10.1101/2025.08.08.669280v1?rss=1 Beckman, R. L. Martinez, B. Santiago, F. Z. Echeverria, G. N. Pinheiro, B. D.T. Torres, M. Suits, L. Garcia, S. Wantuch, P. L. de la Fuente-Nunez, C. Eswara, P. Rosen, D. A. Fleeman, R. 2025-08-11 doi:10.1101/2025.08.08.669280 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ Short-term sensory memory mediates adaptation, habituation, and a paradoxical neural-behavioral transformation in C. elegans ]]> https://biorxiv.org/content/10.1101/2025.08.08.669341v1?rss=1 White, H. Mallik, S. Ching, S. Albrecht, D. R. 2025-08-12 doi:10.1101/2025.08.08.669341 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Investigating the impacts of sidechains on de-novo protein design ]]> https://biorxiv.org/content/10.1101/2025.08.08.669410v1?rss=1 Svajda, C. A. Yuan, J. 2025-08-12 doi:10.1101/2025.08.08.669410 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Geometry of neural dynamics along the cortical attractor landscape reflects changes in attention ]]> https://biorxiv.org/content/10.1101/2025.08.08.669432v1?rss=1 Song, H. Chen, R. Botch, T. L. Braver, T. S. Rosenberg, M. D. Zacks, J. M. Ching, S. 2025-08-12 doi:10.1101/2025.08.08.669432 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ GIN-CRC-Pareto: A graph-based Pareto-optimal multi-task learning framework to identify miRNA-target interactions in colorectal cancer ]]> https://biorxiv.org/content/10.1101/2025.08.10.669528v1?rss=1 Li, L. Yang, Q. Li, L. Zhao, H. Xu, J. Xie, M. Yin, R. 2025-08-12 doi:10.1101/2025.08.10.669528 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Unmasking Pathogen Traits for Chronic Colonization in Neurogenic Bladder Patients ]]> https://biorxiv.org/content/10.1101/2025.08.14.669717v1?rss=1 Reasoner, S. A. Frainey, B. T. Hale, O. F. Borden, A. Graham, M. K. Turner, E. Brenes, L. R. Soderstrom, C. B. Green, H. Schmitz, J. E. Laub, M. T. Kelly, M. S. Clayton, D. B. Hadjifrangiskou, M. 2025-08-14 doi:10.1101/2025.08.14.669717 Cold Spring Harbor Laboratory Press 2025-08-14 <![CDATA[ Endothelial LRRC8C associates with LRRC8A and LRRC8B to regulate vascular reactivity and blood pressure ]]> https://biorxiv.org/content/10.1101/2025.08.17.670763v1?rss=1 Yu, Q. Zhao, Y. Mauer, J. Arullampalam, P. John, N. Tranter, J. D. Abd El-Aziz, T. M. Lin, M. Lerner, D. Halabi, C. Sah, R. 2025-08-20 doi:10.1101/2025.08.17.670763 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ Discrete Subfields and Continuous Gradients Coexist: A Multi-Scale View of Hippocampal Organization ]]> https://biorxiv.org/content/10.1101/2025.08.19.671141v1?rss=1 Bouffard, N. R. Moscovitch, M. Barense, M. D. 2025-08-20 doi:10.1101/2025.08.19.671141 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ SnakeAltPromoter Facilitates Differential Alternative Promoter Analysis ]]> https://biorxiv.org/content/10.1101/2025.08.16.669128v1?rss=1 Tan, J. Wu, Y. Barve, R. Li, F. Payne, P. Kong, N. Jin, S. C. Head, R. Sun, Y. 2025-08-21 doi:10.1101/2025.08.16.669128 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Quinolines interfere with heme-mediated activation of artemisinins ]]> https://biorxiv.org/content/10.1101/2025.08.19.670585v1?rss=1 Rosenthal, M. Goldberg, D. 2025-08-23 doi:10.1101/2025.08.19.670585 Cold Spring Harbor Laboratory Press 2025-08-23 <![CDATA[ Computational rheometry of viscoelastic networks: From random graphs to biomolecular condensates ]]> https://biorxiv.org/content/10.1101/2025.08.20.671282v1?rss=1 Zhang, R. Mitra, G. Ghosh, S. Pappu, R. V. 2025-08-23 doi:10.1101/2025.08.20.671282 Cold Spring Harbor Laboratory Press 2025-08-23 <![CDATA[ Age-related cerebello-thalamo-cortical white matter degradation and executive function performance across the lifespan ]]> https://biorxiv.org/content/10.1101/2025.08.22.671779v1?rss=1 Kraft, J. N. Ortega, A. Hoagey, D. A. Rodrigue, K. M. Kennedy, K. M. 2025-08-23 doi:10.1101/2025.08.22.671779 Cold Spring Harbor Laboratory Press 2025-08-23 <![CDATA[ ASAP-ID: Proximity labelling with small tags ]]> https://biorxiv.org/content/10.1101/2025.08.20.671413v1?rss=1 Lyu, R. Ruff, K. M. Palmer, C. S. Ramirez, A. E. Ormsby, A. R. Scott, D. J. Pappu, R. V. Stojanovski, D. Stroud, D. A. Hatters, D. M. 2025-08-24 doi:10.1101/2025.08.20.671413 Cold Spring Harbor Laboratory Press 2025-08-24 <![CDATA[ Serratia marcescens Outer Membrane Vesicles rapidly paralyze Drosophila melanogaster through triggering apoptosis in the nervous system ]]> https://biorxiv.org/content/10.1101/2025.08.18.670980v1?rss=1 Sina Rahme, B. Bruna, R. E. Draheim, M. Cai, C. Molino, M. V. Wu, Y. Yamba, M. Di Venanzio, G. Lestradet, M. Garcia Vescovi, E. Ferrandon, D. 2025-08-25 doi:10.1101/2025.08.18.670980 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ Investigating Neural Correlates of Emotional Regulation as a Function of Age, Race, and Socioeconomic Status ]]> https://biorxiv.org/content/10.1101/2025.08.21.671607v1?rss=1 Shelton, C. Barch, D. Bijsterbosch, J. D. 2025-08-25 doi:10.1101/2025.08.21.671607 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ Cell-cell communication as underlying principle governing color pattern formation in fishes ]]> https://biorxiv.org/content/10.1101/2025.08.21.671633v1?rss=1 Klann, M. Miura, S. Lee, S.-H. Vianello, S. D. Ross, R. Watanabe, M. Gairin, E. Liang, Y. Hutto, H. W. McCluskey, B. M. Herrera, M. Solnica-Krezel, L. Besseau, L. Pigolotti, S. Parichy, D. M. Kinoshita, M. Laudet, V. 2025-08-25 doi:10.1101/2025.08.21.671633 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ A novel homecage operant task reveals circadian dynamics of social motivation in mice ]]> https://biorxiv.org/content/10.1101/2025.08.21.671364v1?rss=1 Chen, Y. Maloney, S. E. Kravitz, A. 2025-08-26 doi:10.1101/2025.08.21.671364 Cold Spring Harbor Laboratory Press 2025-08-26 <![CDATA[ Centromere instability links genome damage to immune activation in systemic sclerosis ]]> https://biorxiv.org/content/10.1101/2025.08.22.671795v1?rss=1 Imtiaz, A. Waseem, M. O'Neill, H. Chen, B.-R. Czaja, W. Contreras-Galindo, R. 2025-08-27 doi:10.1101/2025.08.22.671795 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ The Nox2 NADPH oxidase regulates neutrophilic inflammation in the oral cavity ]]> https://biorxiv.org/content/10.1101/2025.08.26.671820v1?rss=1 Jin, S. Singhal, R. Luo, J. Cooper, K. N. Terekhova, M. Carey, K. A. Artyomov, M. Jala, V. R. Idol, R. A. Dinauer, M. Lamont, R. J. Bagaitkar, J. 2025-08-28 doi:10.1101/2025.08.26.671820 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ Plasmacytoid dendritic cells in the intestine preferentially produce interferon lambda at homeostasis contributing to tonic localized innate immune responses ]]> https://biorxiv.org/content/10.1101/2025.08.25.672167v1?rss=1 Constant, D. A. Van Winkle, J. A. Norwood, P. A. Mishra, G. Meyer, K. A. Laney, M. E. Madden, S. R. Griffith, A. Rodrigues, P. F. Savan, R. Nice, T. J. 2025-08-29 doi:10.1101/2025.08.25.672167 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ Lentiviral-mediated gene complementation rescues pathogenic ABCA3 variants ]]> https://biorxiv.org/content/10.1101/2025.08.29.673150v1?rss=1 Cooney, A. L. Lamer, S. Yang, P. Wenger, D. White, F. V. Cole, F. S. Wohlford-Lenane, C. L. Hennessey, E. Bawa, P. Kotton, D. N. Sinn, P. Wambach, J. A. McCray, P. B. 2025-08-30 doi:10.1101/2025.08.29.673150 Cold Spring Harbor Laboratory Press 2025-08-30 <![CDATA[ A Neural Circuit for Modular Gating of Organ Somatosensation ]]> https://biorxiv.org/content/10.1101/2025.08.27.672386v1?rss=1 Zhang, Y. Liu, F. Yang, L. Hahm, H. Heitmeier, M. R. Okuda, T. Kawatani, M. Harrigan, J. T. Morrison-Rodriguez, E. C. Petukhova, A. Lu, Z. Heitmeier, H. A. Samineni, V. K. 2025-09-01 doi:10.1101/2025.08.27.672386 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ Zebrafish sleep displays distinct sub-states ]]> https://biorxiv.org/content/10.1101/2025.08.28.672887v1?rss=1 Tripathi, R. Oikonomou, G. Prober, D. A. Goodhill, G. 2025-09-02 doi:10.1101/2025.08.28.672887 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ JARID2 Inhibition Reprograms Human Hematopoietic Progenitor Cells To Enhance Bone Marrow Transplantation ]]> https://biorxiv.org/content/10.1101/2025.09.03.672211v1?rss=1 Han, W. Bjeije, H. Celik, H. Rettig, M. Issa, N. Young, A. Li, Y. Xavier Raj, I. Zhang, C. Krishnan, A. Parsons, T. Burkart, S. Arand, J. Yang, W. Magee, J. Challen, G. A. 2025-09-04 doi:10.1101/2025.09.03.672211 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Mapping of the hSOX10 protein interactome in human melanoma ]]> https://biorxiv.org/content/10.1101/2025.09.03.672723v1?rss=1 Newsom-Stewart, C. M. Bhatt, D. P. Major, M. B. Kaufman, C. K. 2025-09-04 doi:10.1101/2025.09.03.672723 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Chemo-mechanotherapy of fibrosis: dynamic control of biological materials through tissue-architecture-dependent crosslink disruption ]]> https://biorxiv.org/content/10.1101/2025.09.01.673308v1?rss=1 Kong, W. Song, M. Peng, X. Bai, L. Zeng, J. Liang, K. Jin, Y. Wang, J. Wang, X. Huang, Y. Niu, Y. Zhou, L. Feng, X.-Q. Wang, C. Genin, G. M. Wang, J. Du, Y. 2025-09-05 doi:10.1101/2025.09.01.673308 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ A neural network with episodic memory learns causal relationships between narrative events ]]> https://biorxiv.org/content/10.1101/2025.09.01.673596v1?rss=1 Song, H. Lu, Q. Nguyen, T. T. Chen, J. Leong, Y. C. Rosenberg, M. D. Ching, S. Zacks, J. M. 2025-09-05 doi:10.1101/2025.09.01.673596 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Neural computations of visual, semantic, and memorability features in the human brain ]]> https://biorxiv.org/content/10.1101/2025.09.06.674646v1?rss=1 Wang, Y. Brunner, P. Willie, J. T. Cao, R. Wang, S. 2025-09-07 doi:10.1101/2025.09.06.674646 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Unfolded protein response signaling promotes myeloid cell production and cooperates with oncogenic mutation ]]> https://biorxiv.org/content/10.1101/2025.09.07.674755v1?rss=1 Choi, H. Jung, S.-E. Paik, H. Cox, M. J. Oh, S. T. Kang, Y.-A. 2025-09-08 doi:10.1101/2025.09.07.674755 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ miR-146a is a Pleiotropic Regulator of Motor Neuron Degeneration ]]> https://biorxiv.org/content/10.1101/2025.09.04.674013v1?rss=1 Galloway, D. A. Patterson, H. L. Hoye, M. L. Shen, T. Shabsovich, M. Schoch, K. M. Ly, C. V. Miller, T. M. 2025-09-09 doi:10.1101/2025.09.04.674013 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ High-resolution single-cell RNA sequencing using canFam4 reveals novel immune subsets and checkpoint programs in healthy dogs ]]> https://biorxiv.org/content/10.1101/2025.09.06.674668v1?rss=1 Kim, M.-C. Gu, T. Seo, H. Borcherding, N. Kolb, R. Yun, Y. Song, W.-J. Lee, C.-Y. Kim, H. J. Zhang, W. 2025-09-11 doi:10.1101/2025.09.06.674668 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Tumor Genotype Dictates Mitochondrial and Immune Vulnerabilities in Liver Cancer ]]> https://biorxiv.org/content/10.1101/2025.09.10.675369v1?rss=1 Unlu, G. Millet, A. Wangdu, K. Donne, R. Erdal, R. DelGaudio, N. L. Uygur, B. Shah, V. Cho, K. Fecke, A. Cansiz, F. Tarcan, Z. C. Isay-Del Viscio, M. Kilic, E. Kurth, I. Molina, H. Sickmann, A. Basturk, O. Patti, G. Beyaz, S. Smith, K. W. Lujambio, A. Tasdogan, A. Tavazoie, S. F. Birsoy, K. 2025-09-11 doi:10.1101/2025.09.10.675369 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Innate detection of Salmonella replication triggers caspase-8-dependent apoptosis via TLR-driven TNF signaling and NLRC4-mediated sensing of the SPI-2 Type III secretion system ]]> https://biorxiv.org/content/10.1101/2025.09.10.675376v1?rss=1 Herrmann, B. I. Zamba-Campero, M. Garcia-Sillas, R. Yost, W. W. Peterson, L. W. Roncaioli, J. L. Rankin, S. C. Schifferli, D. M. Ravichandran, K. Brodsky, I. E. 2025-09-11 doi:10.1101/2025.09.10.675376 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ An Inducible CRISPRi system for phenotypic analysis of essential genes in Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2025.09.11.675340v1?rss=1 Sullivan, J. R. Ferrara, K. Barrick, R. Romano, K. P. Warrier, T. Hung, D. T. 2025-09-11 doi:10.1101/2025.09.11.675340 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ TREM2 macrophages are associated with enhanced response to PD-1 blockade in human hepatocellular carcinoma ]]> https://biorxiv.org/content/10.1101/2025.09.09.675071v1?rss=1 Hamon, P. Park, M. D. Le Berichel, J. Cohen, M. Soong, B. Y. Buckup, M. Hennequin, C. Lindblad, K. E. Mattiuz, R. Figueiredo, I. Tabachnikova, A. Dawson, T. D'souza, D. Troncoso, L. Ioannou, G. Price, C. Fernandez, N. Giladi, A. Barboy, O. Zhao, Z. Ozbey, S. Cappuyns, S. Reid, A. Hamel, S. Kim, J. Donne, R. Chang, C. Marvin, R. Stefanos, H. Chung, G. Merand, R. Halasz, L. Hegde, S. Guerin, L. M. Ni, M. Wei, Y. Atwal, G. Lansky, A. Jamal, H. Yi, N. Chin, T. James, N. Malissen, N. Desland, F. Lavin, Y. Ward, S. C. Fiel, M. I. Brody, R. Dekervel, J. 2025-09-12 doi:10.1101/2025.09.09.675071 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ A framework to detect positive selection using variant effect predictions reveals widespread adaptive evolution of human neurons ]]> https://biorxiv.org/content/10.1101/2025.09.11.675696v1?rss=1 Starr, A. L. Palmer, M. E. Gao, J. Nichols, C. G. Fraser, H. B. 2025-09-12 doi:10.1101/2025.09.11.675696 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ CryoPhold: CryoEM meets AlphaFold and molecular simulation to reveal protein dynamics ]]> https://biorxiv.org/content/10.1101/2025.09.12.675912v1?rss=1 Bhakat, S. Vats, S. Mardt, A. Strauch, E.-M. 2025-09-13 doi:10.1101/2025.09.12.675912 Cold Spring Harbor Laboratory Press 2025-09-13 <![CDATA[ Commonality and Variability in Functional Networks In Young Children Under 5 Years Old ]]> https://biorxiv.org/content/10.1101/2025.09.12.675913v1?rss=1 Tu, J. C. Lu, C. Day, T. K. M. Hermosillo, R. Moore, L. A. Wang, A. Wang, X. Dierker, D. Latham, A. Kenley, J. K. Fair, D. A. Elison, J. T. Sylvester, C. M. Warner, B. B. Luby, J. L. Rogers, C. E. Barch, D. M. Smyser, C. D. Laumann, T. O. Gordon, E. M. Eggebrecht, A. T. Wheelock, M. D. 2025-09-13 doi:10.1101/2025.09.12.675913 Cold Spring Harbor Laboratory Press 2025-09-13 <![CDATA[ Stem-like Prostate Remodeling in Obesity Mediates Resistance to 5α-Reductase Inhibition Therapy in BPH ]]> https://biorxiv.org/content/10.1101/2025.09.08.674969v1?rss=1 Long, X. Sharkey, C. Ge, R. Wang, S. Tang, Y. Fleishman, A. Gu, B. Korets, R. Gershman, B. Rayala, H. Olumi, A. F. wang, z. 2025-09-14 doi:10.1101/2025.09.08.674969 Cold Spring Harbor Laboratory Press 2025-09-14 <![CDATA[ Delineation of a novel assembly intermediate in retroviral integration pathway ]]> https://biorxiv.org/content/10.1101/2025.09.09.675266v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@57a82aorg.highwire.dtl.DTLVardef@e17110org.highwire.dtl.DTLVardef@c5f4c4org.highwire.dtl.DTLVardef@4886d2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chadda, R. Bera, S. Ghoneim, M. De Melo, T. Grandgenett, D. P. Antony, E. Pandey, K. K. 2025-09-14 doi:10.1101/2025.09.09.675266 Cold Spring Harbor Laboratory Press 2025-09-14 <![CDATA[ Evaluating Language Models for Biomedical Fact-Checking: A Benchmark Dataset for Cancer Variant Interpretation Verification ]]> https://biorxiv.org/content/10.1101/2025.09.10.675443v1?rss=1 Reisle, C. Grisdale, C. J. Krysiak, K. Danos, A. M. Khanfar, M. Pleasance, E. Saliba, J. Hanos, M. Patel, N. V. Jain, A. McMichael, J. F. Venigalla, A. C. Griffith, M. Griffith, O. L. Jones, S. J. M. 2025-09-15 doi:10.1101/2025.09.10.675443 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ Systematic evaluation of metatranscriptomic differential gene expression in silico, in vitro, and in vivo enables elucidation of inter-species cross-feeding ]]> https://biorxiv.org/content/10.1101/2025.09.11.675436v1?rss=1 Lee, E. M. McNulty, N. P. Cheng, J. Chang, H.-W. Hibberd, M. C. Cohen, B. A. Gordon, J. 2025-09-16 doi:10.1101/2025.09.11.675436 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ A single-cell immune atlas of primary and secondary lymphoid organs in pigs ]]> https://biorxiv.org/content/10.1101/2025.09.11.675613v1?rss=1 Wiarda, J. E. Kapoor, M. Sivasankaran, S. K. Byrne, K. A. Loving, C. L. Tuggle, C. K. 2025-09-16 doi:10.1101/2025.09.11.675613 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Life in the fast lane: Functional consequences of male-female dynamic differences in the renal autoregulation of flow ]]> https://biorxiv.org/content/10.1101/2025.09.12.675896v1?rss=1 Xiong, L. Garfinkel, A. Bennett, K. M. Baldelomar, E. J. Brown, L. Barrows, K. Edwards, A. McDonough, A. A. Porat-Shliom, N. Deeds, E. J. 2025-09-17 doi:10.1101/2025.09.12.675896 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Membrane potential and feedback dynamics regulate CatSper-mediated progesterone signaling in human sperm ]]> https://biorxiv.org/content/10.1101/2025.09.14.675619v1?rss=1 Kierzek, M. Fridman, D. Biagioni, C. Miller, E. Kaupp, U. B. Brenker, C. Strünker, T. 2025-09-17 doi:10.1101/2025.09.14.675619 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Distribution of big tau isoforms in the human central and peripheral nervous system ]]> https://biorxiv.org/content/10.1101/2025.09.15.676127v1?rss=1 Koppitsetti, R. K. Barthelemy, N. R. Horie, K. Ly, C. V. Roberts, K. R. Koutarapu, S. Melendez, J. Miller, T. M. Sato, C. Ghoshal, N. Karch, C. Bateman, R. J. Mukherjee, S. 2025-09-17 doi:10.1101/2025.09.15.676127 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ ARID1A and ARID1B safeguard B cell identity, prevent myeloid transformation and expose therapeutic vulnerabilities in lymphoma ]]> https://biorxiv.org/content/10.1101/2025.09.16.676393v1?rss=1 Lin, P. N. Park, J. Kang, Y.-A. Souroullas, G. P. 2025-09-18 doi:10.1101/2025.09.16.676393 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ PIEZO channels link mechanical forces to uterine contractions in parturition ]]> https://biorxiv.org/content/10.1101/2025.09.17.676899v1?rss=1 Zhang, Y. Kini, S. A. Mishkanian, S. A. Luo, R. Seradj, S. H. Leung, V. Wang, Y. Rocio, S.-V. M. Keenan, W. T. Sonmez, U. Yarishkin, O. Sanchez-Alavez, M. Liu, Y. Jin, X. Lipomi, D. J. Li, Y. Petrascheck, M. Frolova, A. I. England, S. K. Patapoutian, A. 2025-09-18 doi:10.1101/2025.09.17.676899 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Determination of α-Synuclein Protein Interactions by μMap Photo-proximity Labeling ]]> https://biorxiv.org/content/10.1101/2025.09.18.674129v1?rss=1 Lougee, M. Park, G. Kim, H. Fowler, J. Lin, Z. Fazelinia, H. Spruce, L. Yanagawa, E. Lee, V. M.- Y. Garcia, B. A. Lakadamyali, M. Petersson, E. J. 2025-09-18 doi:10.1101/2025.09.18.674129 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Extracellular matrix chemistry tunes bacterial biofilm metabolism and optimizes fitness ]]> https://biorxiv.org/content/10.1101/2025.09.18.677115v1?rss=1 Li, J. Squyres, G. R. Duong, K. Reichhardt, C. Newman, D. K. Parsek, M. R. 2025-09-18 doi:10.1101/2025.09.18.677115 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Clonal dynamics shaped by diverse drug-tolerant persister states in melanoma resistance ]]> https://biorxiv.org/content/10.1101/2025.09.16.676608v1?rss=1 Li, H. Chen, Y. Kaster, J. Dunne, M. Xiao, M. Li, L. Thomas, M. Promi, N. Fingerman, D. Brown, G. S. Zheng, Q. Zhu, X. Reale, M. Patterson, A. Gao, L. Zhang, X. Jiang, S. Hu, T. Fang, H. Ren, J. Qi, C. Wang, L. Mou, H. Thacker, G. Salazar, E. R. Villanueva, J. Raj, A. Hoon, D. S. Bin, T. Madzo, J. Wei, Z. Auslander, N. Herlyn, M. 2025-09-19 doi:10.1101/2025.09.16.676608 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Local translation of circular RNAs is required for synaptic activity and memory ]]> https://biorxiv.org/content/10.1101/2025.09.18.676988v1?rss=1 Gong, H. Ren, H. Liau, W.-S. Zhao, Q. Walsh, A. D. Musgrove, M. R. B. Davies, J. W. A. Zajackowski, E. L. Madugalle, S. U. Marshall, P. R. Xu, Z. Lan, T. Shi, J. Jiang, J. Wei, W. Li, X. Voineagu, I. U. Wang, J. Sultana, S. Chen, C.-k. Zhang, L. Banerjee, S. Anggono, V. Chang, H. Y. Bredy, T. W. 2025-09-19 doi:10.1101/2025.09.18.676988 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ A multi-omic atlas of human autonomic and sensory ganglia implicates cell types in peripheral neuropathies ]]> https://biorxiv.org/content/10.1101/2025.09.18.677119v1?rss=1 Yang, L. Dourson, A. J. Tao, R. Boyer, K. Meriau, P. Del Rosario, J. Yi, J. Slivicki, R. A. Bertels, Z. Payne, M. Mwirigi, J. M. Gupta, P. Lemen, J. Copits, B. A. Zhao, G. Cavalli, V. Chamessian, A. Gereau, R. W. 2025-09-19 doi:10.1101/2025.09.18.677119 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Strain-level differences in Gardnerella urinary tract persistence and pathogenesis are consistent with comparative phylogenomic analyses. ]]> https://biorxiv.org/content/10.1101/2025.09.19.677092v1?rss=1 Kumar, L. Whang, S. N. Potter, R. F. Gilbert, N. M. 2025-09-19 doi:10.1101/2025.09.19.677092 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Advanced Deep Learning Enables Prediction of Allogeneic Stem Cell Mobilization Success ]]> https://biorxiv.org/content/10.1101/2025.09.17.676674v1?rss=1 Adil, A. Xiang, J. Piccirillo, N. Harris, H. G. Sica, S. DiPersio, J. F. Hurwitz, S. N. 2025-09-20 doi:10.1101/2025.09.17.676674 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Evaluating the Efficacy of Propofol Against Isoniazid-Induced Seizures: A Comparative Study with Diazepam and Pyridoxine in Swiss Albino Mice ]]> https://biorxiv.org/content/10.1101/2025.09.17.676905v1?rss=1 Sohal, P. Gupta, K. Kaushal, S. Mullins, M. E. 2025-09-20 doi:10.1101/2025.09.17.676905 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Intermediately Methylated Regions in Normal Cells Are Epimutation Hotspots in Cancer ]]> https://biorxiv.org/content/10.1101/2025.09.18.677221v1?rss=1 Mahgoub, M. Abel, H. J. Davarapalli, N. Struthers, H. Kotnik, E. Markovic, C. Fronick, C. Fulton, R. S. Meers, M. P. Spencer, D. H. 2025-09-20 doi:10.1101/2025.09.18.677221 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Neuronal Activity in Orbitofrontal Cortex during Trinary Choices under Risk ]]> https://biorxiv.org/content/10.1101/2025.09.19.677423v1?rss=1 Barretto-Garcia, M. Tu, J. C. Padoa-Schioppa, C. 2025-09-20 doi:10.1101/2025.09.19.677423 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ RIPK1 regulates beta-cell fate via actions on gene expression and kinase signaling in a mouse model of beta-cell self-reactivity ]]> https://biorxiv.org/content/10.1101/2025.09.18.676878v1?rss=1 Contreras, C. J. Mukherjee, N. Harris-Kawano, A. Mather, E. G. Amarsaikhan, N. Davis, C. Berryhill, C. A. Peyton, M. Kundu, D. Colglazier, K. A. Miller, A. S. Branco, R. C. S. Johnson, T. S. Angus, S. P. You, S. Cai, E. P. Templin, A. T. 2025-09-21 doi:10.1101/2025.09.18.676878 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Myofibroblastic CAFs arising from bone-resident osteoblast precursors retain an osteolineage signature and support breast cancer progression via Osterix-mediated signaling. ]]> https://biorxiv.org/content/10.1101/2025.09.18.677154v1?rss=1 Furesi, G. Zeng, C. Eul, E. M. Veis, D. Ye, J. Morikis, V. A. Malachowski, T. Khantakova, D. Antonova, A. U. Colonna, M. Longmore, G. D. Stewart, S. Artyomov, M. Faccio, R. 2025-09-21 doi:10.1101/2025.09.18.677154 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ 3D-printing-assisted, microfabricated devices reveal hierarchical and temporal mechanosensing in high-density fibroblast culture ]]> https://biorxiv.org/content/10.1101/2025.09.18.677242v1?rss=1 Ramahdita, G. Peng, X. Jafari, M. Pobee, C. Bhatka, R. Zhang, Z. Pear, M. Wang, F. Schuftan, D. Hong, Y. David, M. Elson, E. L. Zhou, C. Genin, G. M. Alisafaei, F. Huebsch, N. 2025-09-21 doi:10.1101/2025.09.18.677242 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Soybean aphids exploit abscisic acid signaling to suppress jasmonate defense responses ]]> https://biorxiv.org/content/10.1101/2025.09.21.677601v1?rss=1 Hohenstein, J. D. Kanobe, C. Natukunda, M. I. Gallardo, P. Zhang, D. Kovinich, N. Helms, A. M. Tooker, J. F. MacIntosh, G. C. 2025-09-21 doi:10.1101/2025.09.21.677601 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Single nucleus multiomic atlas of human dorsal root ganglia reveals the contribution of non-neuronal cell types to pain ]]> https://biorxiv.org/content/10.1101/2025.09.21.677655v1?rss=1 Zhao, G. Boyer, K. Meriau, P. Yang, L. Naz, H. Rosen, S. Murray, G. Dourson, A. Mwirigi, J. Del Rosario, J. Payne, M. Gupta, P. Yi, J. Slivicki, R. Bertels, Z. Lemen, J. Chen, Y. Wang, T. Chamessian, A. Copits, B. A. Gereau, R. W. Cavalli, V. 2025-09-22 doi:10.1101/2025.09.21.677655 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ Deciphering acquired resistance mechanisms to sustained auxin-inducible protein degradation in cells and mice ]]> https://biorxiv.org/content/10.1101/2025.09.21.677607v1?rss=1 Li, C. Hyle, J. Liu, Z. Wright, S. Yang, J. Chen, X. Qi, W. Zhang, Q. Cho, B.-K. Goo, Y. A. Li, X. Sublett, J. Li, Q. He, L. Klein, J. Xu, P. Pruett-Miller, S. M. Xu, B. 2025-09-23 doi:10.1101/2025.09.21.677607 Cold Spring Harbor Laboratory Press 2025-09-23 <![CDATA[ Neuroanatomical Correlates of Negative Symptoms in Schizophrenia ]]> https://biorxiv.org/content/10.1101/2025.09.22.677864v1?rss=1 Kamalakannan, S. M. V. Male, A. G. Yilanli, M. Lella, A. Lee, J. Quide, Y. Green, M. J. Cairns, M. J. Carr, V. J. Catts, S. Henskens, F. A. Jablensky, A. Loughland, C. Michie, P. Mowry, B. Pantelis, C. Shall, U. Scott, R. J. Belger, A. Bustillo, J. Lim, K. Ford, J. M. Mathalon, D. H. Preda, A. Mueller, B. Potkin, S. G. Satterhwaite, T. D. Gur, R. C. Gur, R. E. Banaj, N. Vecchio, D. Piras, F. Piras, F. Ehrlich, S. Bernardoni, F. Borgwardt, S. Cobia, D. Alpert, K. Wang, L. Agartz, I. Jonsson, E. G. Kaiser, S. Clotet, E. P. Salvador, R. Jaramillo, C. L. 2025-09-23 doi:10.1101/2025.09.22.677864 Cold Spring Harbor Laboratory Press 2025-09-23 <![CDATA[ Colonization of vineyards by non-Saccharomyces yeast species without evolution of copper and sulfite resistance ]]> https://biorxiv.org/content/10.1101/2025.09.22.677406v1?rss=1 Fay, J. C. Miller, J. H. Dashko, S. Hyma, K. E. Liu, P. Volk, H. Cohen, H. Rahman, N. F. Tang, K. Longan, E. R. Li, X. C. Butinar, L. Piskur, J. 2025-09-24 doi:10.1101/2025.09.22.677406 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ Multiple Epigenetic Mechanisms Functionally Cooperate to Silence Expression of Somatostatin Receptor Type 2 in Pancreatic Neuroendocrine Tumors ]]> https://biorxiv.org/content/10.1101/2025.09.23.677935v1?rss=1 Madigan, J. P. Andrews, S. G. Farrell, R. B. Sharma, R. Ceribelli, M. Thomas, C. J. Shamsian, K. N. Lin, S. Cheng, K. C.-C. Sadowski, S. M. 2025-09-25 doi:10.1101/2025.09.23.677935 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ JAK2V617F Myeloproliferative Neoplasms Support Parallel Evolution of Independent Leukemic Clones ]]> https://biorxiv.org/content/10.1101/2025.09.23.678057v1?rss=1 Parsons, T. M. Krishnan, A. Xavier Raj, I. Young, A. L. O'Leary, D. R. Arand, J. Cox, M. Oh, S. T. Challen, G. A. 2025-09-25 doi:10.1101/2025.09.23.678057 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Repurpose of Ritlecitinib Reduces Neointima Formation and Enhances Endothelial Recovery Following Vascular Injury ]]> https://biorxiv.org/content/10.1101/2025.09.23.678172v1?rss=1 Cai, D. Wang, Y.-C. Saint, L. Markley, J. Chen, S.-Y. 2025-09-25 doi:10.1101/2025.09.23.678172 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Staphylococcus aureus inhibits the NLRP3 inflammasome in macrophages during the early phases of intracellular infection, but not the late phases ]]> https://biorxiv.org/content/10.1101/2025.09.24.678325v1?rss=1 Bhagat, S. Kaur, K. O'Connor, L. Wang, C. Li, Y. Swarnkar, G. Khanna, K. Cassat, J. E. Veis, D. Mbalaviele, G. 2025-09-26 doi:10.1101/2025.09.24.678325 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ Targeting RAD52 overcomes PARP inhibitor resistance in preclinical Brca2-deficient ovarian cancer model ]]> https://biorxiv.org/content/10.1101/2025.09.24.678351v1?rss=1 Ota, Y. Gupta, V. Fashemi, B. E. Akande, M. Babu, P. Thuthika, P. Elizagaray, M. L. Sun, L. Sanders, B. Kuroki, L. M. McCourt, C. K. Hagemann, A. R. Hagemann, I. S. Thaker, P. H. Mutch, D. G. Powell, M. A. Hyrc, K. Verma, P. Krais, J. Bitler, B. G. Mullen, M. M. Khabele, D. 2025-09-26 doi:10.1101/2025.09.24.678351 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ Dual Membrane-spanning Anti-Sigma 2 Controls OMV biogenesis and Colonization Fitness in Bacteroides thetaiotaomicron ]]> https://biorxiv.org/content/10.1101/2025.09.27.678952v1?rss=1 Pardue, E. J. Zhong, T. Scott, N. E. Jana, B. Beatty, W. Ortiz-Marquez, J. C. Kaplan, M. Jackson-Litteken, C. Feldman, M. F. 2025-09-27 doi:10.1101/2025.09.27.678952 Cold Spring Harbor Laboratory Press 2025-09-27 <![CDATA[ Mapping CD4+ T Cell Landscapes in Glioblastoma Reveals Effectors and Bystanders ]]> https://biorxiv.org/content/10.1101/2025.09.25.678410v1?rss=1 6% of all CD4+ T cells across both compartments and were shared across different transcriptional subsets, suggesting diverse transcriptional development stemming from a shared progenitor. In contrast, virally annotated clonotypes were broadly dispersed and largely unexpanded, consistent with bystander populations. Collectively, we investigated the cellular and clonal architecture of human CD4+ T cells in GBM and highlight the contrast between PBMC and TIL compartments. ]]> Hill, C. M. Wang, A. Maldonado, J. Johanns, T. M. Petti, A. A. Dunn, G. P. 2025-09-29 doi:10.1101/2025.09.25.678410 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ IBD risk locus rs1077773 is a pharmacogenomic eQTL for aryl hydrocarbon receptor activity and modulates immune cell function. ]]> https://biorxiv.org/content/10.1101/2025.09.26.678301v1?rss=1 200 known genetic susceptibility loci for the development of IBD. The physiological impact of the majority of these loci remain a gap in our knowledge. One such locus is the single nucleotide polymorphism rs1077773, located [~]56kbp downstream from the aryl hydrocarbon receptor (AHR) gene. AHR is a ligand-activated transcription factor that is crucial to maintaining intestinal homeostasis. We hypothesized that rs1077773 enhances AHR activity to regulate mucosal immune response and maintain intestinal homeostasis. MethodsAll study procedures and reagents were approved by the Washington University Institutional Review Board (#202011003). Patient biopsies were collected at Barnes Jewish Hospital and genotyped using the IBD Genetics Consortium custom GSA SNP chip (Broad Institute) followed by imputation using TopMed Imputation Server at University of Michigan. Patient derived organoids (PDOs; N=3 G/G, N=4 G/A, N=5 A/A) were derived and maintained in 3D culture and supplemented with 50% L-WRN conditioned medium with passage every 3-4 days as previously described. PDOs were treated with AHR agonist 6-Formylindolo[3,2-b]carbazole (FICZ) or vehicle for 48h. Expression of AHR and its transcriptional targets Cytochrome P450 1A1 (CYP1A1) and CYP1B1 was assessed by RT-qPCR. Blood was collected from pediatric patients undergoing intestinal resection at St. Louis Childrens Hospital and was genotyped with custom TaqMan SNP assay (N=3 G/G, N=5 G/A). Peripheral blood monocyte-derived macrophages (MDM{Phi}s) were treated with lipopolysaccharide in the presence or absence of AHR ligands FICZ or indole-3-carboxaldehyde for 24h. Cytokine levels in culture supernatant were measured via using the ProcartaPlex human cytokine, chemokine, and growth factor 45-plex (ThermoFisher) on a Luminex FLEXMAP3D instrument. ResultsAHR expression was similar across genotypes and treatments. PDOs homozygous for rs1077773 demonstrate enhanced CYP1A1 expression in response to AHR activation. In PBM{Phi}s, cytokine secretion was stimulated by LPS treatment and was abrogated by FICZ treatment. PBM{Phi}s with rs1077773 alternate allele demonstrated significant reduction in secretion of 17 cytokines and chemokines. ConclusionsThis work demonstrates that rs1077773 is an expression quantitative trait locus (eQTL) for AHR activity and modulates epithelial and immune cell function in vitro. Further mechanistic understanding of this locus and its correlates could improve our understanding of the molecular mechanisms of IBD susceptibility and may lead to novel personalized therapeutic approaches in IBD. SummaryOur work demonstrates rs1077773 alternate allele is associated with enhanced aryl hydrocarbon transcriptional activity in human primary epithelial organoids and reduced lipopolysaccharide-induced inflammatory cytokine production in human peripheral blood monocyte-derived macrophages. Key MessageWe have identified rs1077773 as a pharmacogenomic regulator of inflammatory response in human primary intestinal organoids and peripheral blood monocyte-derived macrophages via AHR activity. Individual genetic variation affecting this pathway may account for differences in response to environmental stimuli and the development and progression of IBD. ]]> King, A. C. Seiler, K. Swanson, K. Ciorba, M. A. Alvarado, D. M. 2025-09-29 doi:10.1101/2025.09.26.678301 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Vaccine Elicitation of HIV-1 Neutralizing Antibodies Against Both V2 Apex and Fusion Peptide in Rhesus Macaques ]]> https://biorxiv.org/content/10.1101/2025.09.29.679292v1?rss=1 1000-fold higher autologous tier 2-neutralization titers than the wildtype Env trimer and enhanced heterologous NAb breadth. Both FP and V2-apex monoclonal antibodies (mAb) were isolated from immunized macaques and showed heterologous neutralization with genetic and structural signatures that were similar to well-characterized FP and V2 apex bNAbs, although the V2 apex mAbs showed incomplete maturation. These results demonstrate proof-of-concept for simultaneous vaccine elicitation of NAbs against multiple sites of Env vulnerability, which will likely be critical for an effective HIV-1 vaccine. HIGHLIGHTSO_LIDesigned a dual-epitope vaccine targeting both fusion peptide (FP) and V2 apex C_LIO_LIV2-SET Env trimer conferred higher binding of V2 apex bNAbs, longer retention in draining lymph nodes, and >1000-fold higher induction of autologous neutralization titers compared with wildtype Env trimer C_LIO_LIDual-epitope vaccine enhanced serum tier 2 neutralization breadth C_LIO_LIDual-epitope vaccine elicited FP- and V2 apex-specific neutralizing mAbs with genetic signatures similar to well-characterized FP and V2 apex bNAbs C_LI ]]> Duan, H. Nkolola, J. P. Wang, S. Chaudhari, J. Teng, I.-T. Lavine, C. Parchment, D. K. Sellers, G. S. McKee, K. O'Dell, S. Choe, M. Du, H. Zhang, B. Perez, A. A. E. Rossler, A. Lasrado, N. Biju, A. Becker, J. E. Carroll, R. Carson, A. S. Henry, A. R. Morano, N. C. Mughal, M. Rawi, R. Roark, R. S. Schramm, C. A. Shen, C.-H. Smith, S. C. Stephens, T. Tsybovsky, Y. Van Wazer, D. J. Wang, H. Yang, Y. Rutten, L. Langedijk, J. P. M. Cheng, C. Wang, L. Douek, D. C. Koup, R. A. Mascola, J. R. Shapiro, L. Zhou, T. Doria-Rose, N. A. Korber, B. Seaman, M. S. P 2025-10-01 doi:10.1101/2025.09.29.679292 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures ]]> https://biorxiv.org/content/10.1101/2025.09.29.679336v1?rss=1 6M single-nucleotide variants, 1.8M small insertions/deletions, 49K structural variations, and 10K mobile element insertions across autosomes, X, and mitochondrial chromosomes. We validated the variants using ultra-deep simulated reads and developed a binomial-based model to estimate coverage requirements for variant detection. Evaluating multiple callers showed CHM13 alignment improves structural variant detection and offers advantages in difficult-to-map regions compared to GRCh38. Systematic characterization showed regions with low detection rate are enriched in centromeres, satellite sequences, tandem repeats, and falsely duplicated genes. This accurate, versatile resource enables systematic evaluation of somatic variant detection technologies. ]]> Kong, N. Tang, Z. Ruttenberg, A. Macias-Velasco, J. F. Li, Z. Zhang, W. Miao, B. Xin, Z. Fu, Q. Park, H. Zhuo, X. Mehinovic, E. Belter, E. Garza, J. E. Dong, S. Casey, E. Johnson, B. K. Majewski, M. F. Palmer, T. Cheng, Y. Lindsay, T. Schedl, T. Li, D. Shen, H. SMaHT Network Assembly/Pangenome Working Group, Fulton, R. Wang, T. Jin, S. C. 2025-10-01 doi:10.1101/2025.09.29.679336 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Illuminating the Role of A-to-I Editing in Gastric Cancer using EndoVIA 2.0 ]]> https://biorxiv.org/content/10.1101/2025.09.29.679362v1?rss=1 Quillin, A. L. Flores, T. F. Purohit, D. Halstead, A. L. Arnould, B. Aastha, Grandi, E. Leffler, M. Saenz, J. Heemstra, J. M. 2025-10-01 doi:10.1101/2025.09.29.679362 Cold Spring Harbor Laboratory Press 2025-10-01 <![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[ Spared nerve injury induces long-term and brain region-specific changes in oligodendrocyte density in mice ]]> https://biorxiv.org/content/10.1101/2025.10.01.679851v1?rss=1 Becker, L. J. O'Shea, R. Borges, G. McCall, J. G. 2025-10-02 doi:10.1101/2025.10.01.679851 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Using gnotobiotic mice to decipher effects of gut microbiome repair in undernourished children on tuft and goblet cell function ]]> https://biorxiv.org/content/10.1101/2025.10.02.680046v1?rss=1 Wang, Y. Chang, H.-W. Cheng, J. Webber, D. M. Lynn, H. M. Hibberd, M. C. Kao, C. Mostafa, I. Ahmed, T. Barratt, M. J. Gordon, J. 2025-10-03 doi:10.1101/2025.10.02.680046 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ ETEC heat-labile toxin promotes β-catenin stabilization and transcriptional reprogramming to disrupt intestinal epithelial differentiation ]]> https://biorxiv.org/content/10.1101/2025.10.02.680135v1?rss=1 Sheikh, A. Setu, B. Joardar, N. Martin, J. C. Rosa, B. A. Mitreva, M. Fleckenstein, J. M. 2025-10-03 doi:10.1101/2025.10.02.680135 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Atg16l1 promotes lung transplant tolerance by regulating glycolysis in macrophages ]]> https://biorxiv.org/content/10.1101/2025.10.02.679826v1?rss=1 Cano, M. Liao, F. Zhou, D. Chen, C. Liu, Z. Zhu, J. H. Bernadt, C. Ebenezer, R. Davis, V. Pugh, K. N. Tao, Y. Tague, L. K. Huang, H. J. Byers, D. Hachem, R. Brody, S. L. Krupnick, A. S. Kreisel, D. Gelman, A. E. 2025-10-04 doi:10.1101/2025.10.02.679826 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ Ragnarok: a flexible and RApid GeNe Annotation (ROcKs) pipeline deployed through Nextflow ]]> https://biorxiv.org/content/10.1101/2025.10.03.680343v1?rss=1 Kuster, R. D. Smith, Z. C. Whitt, L. Staton, M. E. Mansfeld, B. N. Gottschalk, C. 2025-10-04 doi:10.1101/2025.10.03.680343 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ The Liver is an Inflammatory Mediator of Pulmonary Arterial Hypertension ]]> https://biorxiv.org/content/10.1101/2025.10.03.680270v1?rss=1 Singh, N. Lawson, J. Ragavendran, A. Banerjee, S. Hon, A. Hong, J. Mullin, C. J. Pereira, M. Sherman-Roe, A. Jorrin, A. T. Cayton, T. Fishbein, G. Klinger, J. R. Oldham, W. Dai, Z. Fallon, M. Harrington, E. O. Liang, O. D. Umar, S. Ventetuolo, C. E. 2025-10-06 doi:10.1101/2025.10.03.680270 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ DNASE1L3 surveils mitochondrial DNA on the surface of distinct mammalian cells ]]> https://biorxiv.org/content/10.1101/2025.10.05.680464v1?rss=1 Porat, J. Poli, V. Almahayni, K. George, B. M. de Luna Vitorino, F. Yi, L. Bras Costa, C. Zhou, Y. Crompton, A. Wen, H. Zheng, L. Gregersen, P. Agarwal, S. A. Garcia, B. A. Xie, Y. Moeckl, L. Zanoni, I. Simpfendorfer, K. R. Flynn, R. A. 2025-10-06 doi:10.1101/2025.10.05.680464 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Clonal dynamics of monozygotic twinning in early human embryogenesis ]]> https://biorxiv.org/content/10.1101/2025.10.05.680569v1?rss=1 Yoon, C. J. Nam, C. H. N. Lee, S. M. Choi, E. S. Bae, J. H. Kim, H. Lim, J. Kim, R. Derom, C. Meireson, E. Weyers, S. Park, J. W. Lee, J. Sung, J. Griffith, O. L. Griffith, M. Jun, J. K. Ju, Y. S. 2025-10-06 doi:10.1101/2025.10.05.680569 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Sensitivity to ATR-CHK1 pathway inhibition in AML/MDS is enhanced by SRSF2 mutations and reduced by RUNX1 loss ]]> https://biorxiv.org/content/10.1101/2025.10.06.680457v1?rss=1 Eldfors, S. Rai, S. Sharma, V. Hossan, T. Cabrera Pastrana, C. Bertino, A. Gilbert, A. Porkka, K. Walter, M. J. Graubert, T. A. 2025-10-07 doi:10.1101/2025.10.06.680457 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Whole body MondoA deletion protects against diet-induced obesity through uncontrolled multi-organ substrate utilization and futile cycling ]]> https://biorxiv.org/content/10.1101/2025.10.06.680559v1?rss=1 View larger version (47K): org.highwire.dtl.DTLVardef@1ccf42dorg.highwire.dtl.DTLVardef@b2da28org.highwire.dtl.DTLVardef@1081aforg.highwire.dtl.DTLVardef@1b2168d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO 1) Global MondoA deficiency drives 2) tissue glucose uptake which in skeletal muscle is 3) converted and excreted as lactate, while in adipose tissue 4) triglyceride re-esterification requires 5) de novo glycerol synthesis to feed into the futile cycle. C_FIG ]]> Berger, J. H. Lau, A. N. James, L. C. Taing, R. Ahn, B. Yin, X. Sakamoto, T. Batmanov, K. Jordan, O. Patel, J. Zhou, J. Finck, B. N. Titchenell, P. M. Tesz, G. J. Kelly, D. P. 2025-10-07 doi:10.1101/2025.10.06.680559 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Reduced SK channel control of mesolimbic dopamine neuron firing drives reward seeking adaptations in chronic pain ]]> https://biorxiv.org/content/10.1101/2025.10.06.680596v1?rss=1 Thompson, J. M. Graham, R. D. Goff, J. Kalyanaraman, V. Xu, C. S. Wang, H. Barrett, M. R. George, R. Legaria, A. A. Hage, T. Copits, B. A. Kravitz, A. V. Creed, M. C. 2025-10-07 doi:10.1101/2025.10.06.680596 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Risk reshapes amygdala representation of choice ]]> https://biorxiv.org/content/10.1101/2025.10.06.680813v1?rss=1 Piantadosi, P. Coden, K. M. Choi, H. Perry, S. J. Halfeld, M. Schaffer, J. A. Goff, J. P. Spitz, N. A. Schwab, N. R. Sandon, R. Sadiq, S. Devine, M. M. Costa, V. D. da Silva, D. Holmes, A. 2025-10-07 doi:10.1101/2025.10.06.680813 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Structural mechanism of lipid modulation of pentameric ligand-gated ion channel activity ]]> https://biorxiv.org/content/10.1101/2025.10.07.680764v1?rss=1 Tan, B. K. Xu, H. Sandberg, J. W. Brannigan, G. Cheng, W. W. 2025-10-07 doi:10.1101/2025.10.07.680764 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Dissecting Small Noncoding RNA Landscapes in Mouse Preimplantation Embryos and Human Blastoids for Modeling Early Human Embryogenesis ]]> https://biorxiv.org/content/10.1101/2025.10.07.680944v1?rss=1 Biondic, S. Zhao, C. Yin, R. Theunissen, T. W. Petropoulos, S. 2025-10-07 doi:10.1101/2025.10.07.680944 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Targeting Tumor-intrinsic TAK1 triggers anti-tumor immunity and sensitizes pancreatic cancer to checkpoint blockade ]]> https://biorxiv.org/content/10.1101/2025.10.08.681226v1?rss=1 Bansod, S. P. Lim, K.-H. Chen, H.-P. Somani, V. Li, L. Modekurty, S. Knolhoff, B. Fields, R. C. Ruzinova, M. B. DeNardo, D. G. 2025-10-09 doi:10.1101/2025.10.08.681226 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ Scalable transcription factor mapping uncovers the regulatory dynamics of natural and synthetic transcription factors in human T cell states ]]> https://biorxiv.org/content/10.1101/2025.10.09.681414v1?rss=1 Mullins, R. D. Zaretsky, J. Stoller, E. Moore, M. Takacsi-Nagy, O. Shpynov, O. Sampaleanu, R. Roth, T. L. Satpathy, A. T. Mitra, R. D. Puram, S. V. 2025-10-10 doi:10.1101/2025.10.09.681414 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ A sensorimotor instability drives a locomotor transition during fish development ]]> https://biorxiv.org/content/10.1101/2025.10.10.681567v1?rss=1 Coraggioso, M. Demarchi, L. Wong, R. Dichio, V. Chaumeton, C. Panier, T. Morvan-Dubois, G. Goodhill, G. Bormuth, V. Debregeas, G. 2025-10-11 doi:10.1101/2025.10.10.681567 Cold Spring Harbor Laboratory Press 2025-10-11 <![CDATA[ Bhlhe40 Coordinates T Cell Programs with Distinct CD4 and CD8 T Cell Requirements for Anti-PD-1 Versus Anti-CTLA-4 ]]> https://biorxiv.org/content/10.1101/2025.10.10.681497v1?rss=1 Saha, A. Minowa, T. Shavkunov, A. S. Salmon, A. J. Keshari, S. Jarjour, N. N. Pauken, K. E. Hu, K. H.-H. Edelson, B. T. Chen, K. Gubin, M. M. 2025-10-13 doi:10.1101/2025.10.10.681497 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Combining Motifs, CRE Activity, And Gene Expression Data Using ML Greatly Improves the Accuracy of Tissue-Specific TF Network Maps ]]> https://biorxiv.org/content/10.1101/2025.10.10.681634v1?rss=1 Jung, W. J. Acharya, S. Ruskin, D. P. Liao, S. Akbary Moghaddam, V. Erdenebaatar, Z. Brent, M. R. 2025-10-13 doi:10.1101/2025.10.10.681634 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read data ]]> https://biorxiv.org/content/10.1101/2025.10.13.681545v1?rss=1 2% VAF SNVs, sensitivity and precision approached [~]80% at [≥]300x, with little gain from additional sequencing. This work provides a comprehensive framework for reliable detection of low-VAF mutations in non-cancer tissues and a valuable resource for the community. ]]> Ha, Y.-J. J. Maziec, D. Markowski, J. Georges, S. J. Parmalee, N. L. Berselli, M. Coorens, T. H. Dong, S. Gardiner, S. Kalra, D. Li, D. Miao, B. Musunuri, R. Xue, L. Yu, Z. Walker, K. Anderson, L. Au, N. Y. Cibulskis, C. Doddapaneni, H. Grochowski, C. M. Jensen, D. M. Lindsay, T. Loy, K. Narayan, A. Narzisi, G. Ou, J. Pham, M. M. Runnels, A. M. Stergachis, A. B. Sutherlin, L. M. Wang, T. Jin, H. Feng, W. C. Zhang, Y. Veit, A. D. Kim, C. T. Chun, H.-J. E. Ardlie, K. Fulton, R. S. Germer, S. Gibbs, R. A. Marth, G. T. Bennett, J. T. Park, P. J. 2025-10-14 doi:10.1101/2025.10.13.681545 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Refining RDoC Using Individual-Level Task fMRI Factor Models Reveals Reproducible Brain-wide Motifs ]]> https://biorxiv.org/content/10.1101/2025.10.13.682124v1?rss=1 Quah, S. K. L. Madsen, S. Pirzada, S. Jo, B. Uddin, L. Q. Mumford, J. A. Barch, D. M. Gotlib, I. H. Fair, D. A. Poldrack, R. A. Saggar, M. 2025-10-14 doi:10.1101/2025.10.13.682124 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ ConforFold Recovers Alternative Protein Conformations Beyond MSA Subsampling ]]> https://biorxiv.org/content/10.1101/2025.10.14.682366v1?rss=1 Syrlybaeva, R. Strauch, E.-M. 2025-10-14 doi:10.1101/2025.10.14.682366 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Prognostic and Therapeutic Implications of BRAF Mutations in Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/2025.10.14.682328v1?rss=1 Lee, D. Abu-Shihab, Y. Plas, K. Nicolet, D. Mrozek, K. Routbort, M. J. Patel, K. P. Walker, C. J. Buss, J. Stiff, A. R. Laganson, A. DiNardo, C. D. Daver, N. G. Kadia, T. M. Ravandi, F. Carroll, A. J. Kolitz, J. E. Powell, B. L. Blum, W. G. Baer, M. R. Marcucci, G. Uy, G. L. Stock, W. Stone, R. M. Medeiros, L. J. Byrd, J. C. Blachly, J. S. Bowman, R. L. Tyner, J. Loghavi, S. Eisfeld, A.-K. Miles, L. A. 2025-10-15 doi:10.1101/2025.10.14.682328 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Persistence of vestibular function in the absence of glutamatergic transmission from hair cells ]]> https://biorxiv.org/content/10.1101/2025.10.15.682551v1?rss=1 95%. In vivo recordings of spontaneous activity in the vestibular nerve revealed similar action potential rates and regularity in Vglut3+/+and Vglut3-/- mice, suggesting a divergent underlying mechanism compared to the silent Vglut3-/- auditory nerve. In behavioral studies, Vglut3-/- mice did not exhibit considerable sensorimotor or balance deficits. Collectively, these data support the view that non-quantal transmission is the predominant mode of neurotransmission between type I VHCs and vestibular calyceal afferent neurons. We propose that non-quantal transmission alone underlies the apparently normal vestibular nerve physiology and behavioral function in Vglut3-/- mice. ]]> Mukhopadhyay, M. Modgekar, R. Yang-Hood, A. Ohlemiller, K. K. Militchin, V. Xiao, M. Shen, Z. Rensing, N. Wong, M. Lee, S. J. Seal, R. P. Warchol, M. E. Maloney, S. E. Yuede, C. M. Rutherford, M. A. Pangrsic, T. 2025-10-15 doi:10.1101/2025.10.15.682551 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Asymmetry in hydrophobicity induces electric potential in non-charged protein condensates ]]> https://biorxiv.org/content/10.1101/2025.10.15.682625v1?rss=1 Yang, L. Yu, W. Zeng, X. Dai, Y. 2025-10-15 doi:10.1101/2025.10.15.682625 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ CIViC MCP: Integrating Large Language Models with the Clinical Interpretations of Variants in Cancer ]]> https://biorxiv.org/content/10.1101/2025.10.13.682185v1?rss=1 Schimmelpfennig, L. E. Cody, Q. McMichael, J. Coffman, A. Saliba, J. Danos, A. Kiwala, S. Wagner, A. H. Sanz-Cruzado, J. Lever, J. Griffith, M. Griffith, O. L. 2025-10-16 doi:10.1101/2025.10.13.682185 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ An unconventional HxD motif orchestrates coatomer-dependent coronavirus morphogenesis ]]> https://biorxiv.org/content/10.1101/2025.10.16.682669v1?rss=1 Mohona, S. Shakya, A. K. Singh, S. Kearns, F. L. Jemison, K. Erramilli, S. K. Dey, D. Qing, E. Jennings, B. C. Doray, B. Kossiakoff, A. A. Amaro, R. E. Klose, T. Gallagher, T. Hasan, S. S. 2025-10-17 doi:10.1101/2025.10.16.682669 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[ The effect of two distinct viral-enriched inocula on the immune response and chemical cues in honey bee pupae ]]> https://biorxiv.org/content/10.1101/2025.10.20.683288v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@18e6203org.highwire.dtl.DTLVardef@c4b6d5org.highwire.dtl.DTLVardef@bf6499org.highwire.dtl.DTLVardef@165b9d1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Erez, T. Osabutey, A. F. Bonda, E. Otmy, A. Levin-Nikulin, S. Hesketh-Best, P. J. Ferreira, C. P. Spivak, M. Schroeder, D. C. Chejanovsky, N. Soroker, V. 2025-10-20 doi:10.1101/2025.10.20.683288 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Brain Dynamics of Mental Manipulation ]]> https://biorxiv.org/content/10.1101/2025.10.20.683458v1?rss=1 30 Hz) and slower (< 30 Hz) dynamics in primary and secondary auditory areas, suggesting a decrease in local excitability. Second, there is a distributed increase in oscillatory synchrony (6-10 Hz), which predicts imagery vividness and task performance. This evidence points to a key role of local excitability and inter-areal synchrony in the manipulation of thought. ]]> Quiroga-Martinez, D. R. He, T. Fernandez-Rubio, G. Bonetti, L. Blenkmann, A. O. Endestad, T. Solbakk, A.-K. Meling, T. R. Fabricius, M. E. McManus, O. K. Willie, J. T. Brunner, P. Dastjerdi, M. Lin, J. Knight, R. 2025-10-21 doi:10.1101/2025.10.20.683458 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ N-cadherin in osteolineage cells restrains breast cancer cell growth via inhibition of a PI3K-dependent, Tgf-β1-driven feed-forward loop ]]> https://biorxiv.org/content/10.1101/2025.10.22.683948v1?rss=1 Sugatani, T. Yeo, K. Campioli, M. Fujimoto, H. Civitelli, R. 2025-10-23 doi:10.1101/2025.10.22.683948 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Canonical decision computations underlie behavioral and neural signatures of cooperation in primates ]]> https://biorxiv.org/content/10.1101/2025.10.22.683999v1?rss=1 Shi, W. Meisner, O. C. Jadi, M. P. Chang, S. W. C. Nandy, A. S. 2025-10-23 doi:10.1101/2025.10.22.683999 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Variable and conserved features of copy-back viral genome populations generated de novo during Sendai virus infection ]]> https://biorxiv.org/content/10.1101/2025.10.21.683696v1?rss=1 Yang, Y. Wang, Y. Lopez, C. B. 2025-10-24 doi:10.1101/2025.10.21.683696 Cold Spring Harbor Laboratory Press 2025-10-24 <![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[ Preoptic activation induces a torpor-like hypothermic and hypometabolic state that is cerebroprotective ]]> https://biorxiv.org/content/10.1101/2025.10.24.684192v1?rss=1 Kamal, A. Liu, J. Gonzales, E. R. Mohamad Ibrahim, K. Zhang, F. Skelton, H. E. Kelly Cuenca, J. Yuede, C. Patti, G. J. Shriver, L. P. Lee, J.-M. Norris, A. J. Landsness, E. C. 2025-10-25 doi:10.1101/2025.10.24.684192 Cold Spring Harbor Laboratory Press 2025-10-25 <![CDATA[ VDAC activation inhibits hippocampal plasticity via NLRP3 inflammasome & caspase-1: modulation by allopregnanolone enantiomers ]]> https://biorxiv.org/content/10.1101/2025.10.24.684242v1?rss=1 Izumi, Y. O'Dell, K. A. Covey, D. F. Qian, M. Mennerick, S. Zorumski, C. F. 2025-10-26 doi:10.1101/2025.10.24.684242 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Seventy-five Years of Systematic Biology: Looking Back, Moving Forward ]]> https://biorxiv.org/content/10.1101/2025.10.21.683502v1?rss=1 Landis, M. J. Donoghue, M. J. 2025-10-27 doi:10.1101/2025.10.21.683502 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ The actin assembly regulator toca-1 regulates collateral branching in C. elegans ]]> https://biorxiv.org/content/10.1101/2025.10.27.684948v1?rss=1 Brinck, A. Scott, D. Nonet, M. L. 2025-10-28 doi:10.1101/2025.10.27.684948 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ Adipocytes are dispensable in shaping the ovarian cancer tumor microenvironment in the omentum ]]> https://biorxiv.org/content/10.1101/2025.10.28.685098v1?rss=1 Mintz, R. L. Han, J. Butka, E. G. Gallerand, A. Kim, A. Ning, S. Yiew, N. Wohltmann, M. Zou, W. Zhang, N. Morris, S. Zinselmeyer, B. Randolph, G. J. 2025-10-29 doi:10.1101/2025.10.28.685098 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ Microbiota-derived indole metabolites inhibit rotavirus infection in vitro and in vivo and in human infants ]]> https://biorxiv.org/content/10.1101/2025.10.29.685378v1?rss=1 Wirusanti, N. I. van Schajik, Y. Kim, J. Frempong, J. F. Simkhada, N. Fisher, S. Pucci, N. Piedade, G. J. Luchen, C. C. Chibuye, M. Simuyandi, M. Chisenga, C. Silwamba, S. Chibesa, K. Nzangwa, B. T. Kuntawala, D. H. Ramani, S. Mende, D. Baldridge, M. T. Sovran, B. Harris, V. C. 2025-10-29 doi:10.1101/2025.10.29.685378 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ Pseudouridine selects RNAs for extracellular transport ]]> https://biorxiv.org/content/10.1101/2025.10.28.685156v1?rss=1 Scacchetti, A. Shields, E. J. Reich, L. N. Doherty, J. F. Tasca, J. A. Lee, G. E. Lauman, R. Chanaday, N. L. Garcia, B. A. Conine, C. C. Bonasio, R. 2025-10-30 doi:10.1101/2025.10.28.685156 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Microbial metabolism of mannitol as a tracer for the non-invasive measurement of oral-cecal transit ]]> https://biorxiv.org/content/10.1101/2025.10.28.685202v1?rss=1 Vieira, D. E. Langmeyer, E. M. Cortopassi, M. D. Rubio, W. B. Kotikalapudi, N. Zhou, Y. Flier, S. N. Bry, L. Banks, A. S. 2025-10-30 doi:10.1101/2025.10.28.685202 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Core Activation Program and Selective Regional Responsiveness of Microglia in Aging and Parabiosis ]]> https://biorxiv.org/content/10.1101/2025.10.29.685417v1?rss=1 Naz, H. Palovics, R. Yamada, S. Lu, N. Wyss-Coray, T. Li, Q. Zhao, G. 2025-10-31 doi:10.1101/2025.10.29.685417 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ A Specialized CD107a+ Macrophage Subset Drives Selective Mycobacterial Phagocytosis ]]> https://biorxiv.org/content/10.1101/2025.10.31.685620v1?rss=1 Eto, C. Luiz, G. Silva, H. M. Munari, E. L. Mendes, D. A. G. B. Beck, B. K. Mascarin, L. Z. Starick, M. Canesso, M. C. C. Reis, B. S. Silveira, G. Bordignon, J. de Menezes, Y. K. T. Mansur, D. S. Lummertz da Rocha, E. Bafica, A. L. B. 2025-11-02 doi:10.1101/2025.10.31.685620 Cold Spring Harbor Laboratory Press 2025-11-02 <![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[ Functional Connectivity Localizes a Distributed Supramodal Core for Naturalistic Viewing ]]> https://biorxiv.org/content/10.1101/2025.11.01.685026v1?rss=1 Fokin, V. Sherafati, A. 2025-11-03 doi:10.1101/2025.11.01.685026 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Model-based EEG phenotyping uncovers distinct neurocomputational mechanisms underlying learning impairments across psychopathologies ]]> https://biorxiv.org/content/10.1101/2025.11.01.685815v1?rss=1 Ging-Jehli, N. R. Rac-Lubashevsky, R. Bera, K. Roberts, A. Loder, A. Boudewyn, M. A. Carter, C. S. Erickson, M. A. Gold, J. M. Luck, S. J. Ragland, J. D. Yonelinas, A. P. MacDonald, A. W. Barch, D. M. Frank, M. J. 2025-11-04 doi:10.1101/2025.11.01.685815 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Machine Learning Analysis of Cilia-Driven Particle Transport Distinguishes Primary Ciliary Dyskinesia Cilia from Normal Cilia ]]> https://biorxiv.org/content/10.1101/2025.11.02.686130v1?rss=1 Hadas, N. Xu, H. Neupane, S. Twan, W. K. Elgamal, A. Horani, A. 2025-11-04 doi:10.1101/2025.11.02.686130 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Signal peptidase complex mediates rotavirus VP7 processing and virion assembly ]]> https://biorxiv.org/content/10.1101/2025.11.04.686468v1?rss=1 Zhu, X. Sanchez-Tacuba, L. Beatty, W. Li, B. Ding, S. 2025-11-04 doi:10.1101/2025.11.04.686468 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Himito: a Graph-based Toolkit for Mitochondrial Genome Analysis using Long Reads ]]> https://biorxiv.org/content/10.1101/2025.11.03.686348v1?rss=1 Su, H. Huang, Y. Durham, T. Kong, N. Casey,, E. Benjamin, D. Jin, S. C. Garimella, K. V. 2025-11-05 doi:10.1101/2025.11.03.686348 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Sequestration of clock proteins into repressive nuclear condensates orchestrates circadian gene repression ]]> https://biorxiv.org/content/10.1101/2025.11.03.686412v1?rss=1 Chen, Q. Yuan, Y. Clark, D. Yadlapalli, S. 2025-11-05 doi:10.1101/2025.11.03.686412 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Multimerin1, not Galectin-8, Promotes Gastric Chief Cell Differentiation by Tempering WNT Signaling ]]> https://biorxiv.org/content/10.1101/2025.11.04.685347v1?rss=1 Lin, X. Nicolazzi, G. A. Liu, X. Nwokolo, C. Zick, Y. Saenz, J. Brown, J. W. 2025-11-05 doi:10.1101/2025.11.04.685347 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Inducible Calling Cards: Developing Mouse Reagents for Experimentally Controlled Transposon Insertion in vivo. ]]> https://biorxiv.org/content/10.1101/2025.11.04.685928v1?rss=1 Sarafinovska, S. Venkatesan, A. Akinwe, T. M. Chamessian, A. Chen, X. Payne, M. Creed, M. C. Mitra, R. D. Dougherty, J. D. 2025-11-05 doi:10.1101/2025.11.04.685928 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Direct Optical Quantification of Chain Collapse, Reduced Dielectric, and Water Release Driving Protein Phase Separation ]]> https://biorxiv.org/content/10.1101/2025.11.04.686660v1?rss=1 Perets, E. A. Spies, J. A. Cheong, J. H. Shi, L. Asamoto, D. K. Holehouse, A. S. Kim, J. E. Min, W. Neu, J. Yan, E. C. Y. 2025-11-06 doi:10.1101/2025.11.04.686660 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Modes of action and in planta antifungal activity of Olea europaea defensin OefDef1.1-derived peptide variant ]]> https://biorxiv.org/content/10.1101/2025.11.05.686674v1?rss=1 Tiwari, R. Sekar, H. James, G. Tetorya, M. Usher, E. Shah, D. M. 2025-11-06 doi:10.1101/2025.11.05.686674 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ The Unique Efg1 Fungal Virulence Regulon in the Catheterized Bladder Environment ]]> https://biorxiv.org/content/10.1101/2025.11.06.686417v1?rss=1 La Bella, A. A. Gervais, N. C. Kohler, K. N. Obernuefemann, C. L. P. Jacobsen, I. D. Shapiro, R. S. Caparon, M. Hultgren, S. J. Flores-Mireles, A. L. H. Santiago-Tirado, F. H. 2025-11-07 doi:10.1101/2025.11.06.686417 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ Characterization of an Open-Channel Structure and Lateral Conduction Pathway in the Cation-Selective Pentameric Ligand-Gated Ion Channel, ELIC ]]> https://biorxiv.org/content/10.1101/2025.11.06.686614v1?rss=1 Arcario, M. J. Wu-Chen, E. J. Henin, J. Brannigan, G. Cheng, W. W.-L. 2025-11-08 doi:10.1101/2025.11.06.686614 Cold Spring Harbor Laboratory Press 2025-11-08 <![CDATA[ Structure basis for distinct protective mechanisms of IGHV3-23 antibodies targeting influenza hemagglutinin stem ]]> https://biorxiv.org/content/10.1101/2025.11.06.687086v1?rss=1 Lv, H. Huan, Y. W. Pholcharee, T. Teo, Q. W. Liu, W. Gopal, A. B. Choi, D. Ardagh, M. R. Tan, T. J. C. Sun, Y. Mehta, A. Li, J. Szlembarski, M. Huang, J. J. Ma, E. X. Wittenborn, L. E. Kasture, P. Mok, C. K. P. Wu, N. C. 2025-11-08 doi:10.1101/2025.11.06.687086 Cold Spring Harbor Laboratory Press 2025-11-08 <![CDATA[ Predation limits the abundance of {triangleup}gacA cheaters in Pseudomonas protegens populations ]]> https://biorxiv.org/content/10.1101/2025.11.08.687362v1?rss=1 Steele, M. I. Oxender, E. E. Ge, C. Queller, D. C. Strassmann, J. E. 2025-11-08 doi:10.1101/2025.11.08.687362 Cold Spring Harbor Laboratory Press 2025-11-08 <![CDATA[ Prognosis prediction using autophagy gene expression in osteosarcoma ]]> https://biorxiv.org/content/10.1101/2025.11.05.685081v1?rss=1 Bi, Y. Liu, Q. Zhou, C. xu, k. zhu, Q. Lu, J. zhang, C. Xie, W. Fang, G. chen, X. Tian, D. Jing, J. Li, Y. Wang, H. Duan, W. 2025-11-10 doi:10.1101/2025.11.05.685081 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ QuNex Recipes: Executable, Human-Readable Workflows for Reproducible Neuroimaging Research ]]> https://biorxiv.org/content/10.1101/2025.11.08.687330v1?rss=1 Demsar, J. Kraljic, A. Matkovic, A. Brege, S. Pan, L. Tamayo, Z. Fonteneau, C. Helmer, M. Ji, J. L. Anticevic, A. Korponay, C. Salavrakos, M. Glasser, M. F. Nickerson, L. D. Cho, Y. T. Repovs, G. 2025-11-10 doi:10.1101/2025.11.08.687330 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Precision functional imaging in infants using multi-echo fMRI at 7T ]]> https://biorxiv.org/content/10.1101/2025.11.09.687453v1?rss=1 Moser, J. Sadeghi-Tarakameh, A. Ramirez, J. S. B. Madison, T. J. Hantzsch, L. Weldon, K. B. Pham, H. H. N. Lundquist, J. T. Sung, S. Ukpong, I. Drexler, E. Labonte, A. K. Auerbach, E. J. Adriany, G. Sylvester, C. M. Nelson, S. M. Eryaman, Y. Elison, J. T. Fair, D. A. Yacoub, E. 2025-11-10 doi:10.1101/2025.11.09.687453 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Drosophila melanogaster model of RVCL-S demonstrates age dependent disease progression ]]> https://biorxiv.org/content/10.1101/2025.11.10.687584v1?rss=1 Gracheva, E. Matt, A. Wang, F. Hsin, R. Liang, H. Ouyang, X. Ding, J. Miner, J. J. Zhou, C. 2025-11-10 doi:10.1101/2025.11.10.687584 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Structure-informed evolutionary analysis of the meiotic recombination machinery ]]> https://biorxiv.org/content/10.1101/2025.11.07.687317v1?rss=1 Arter, M. Vedanayagam, J. Lu, M. Diop, M. Liu, K. Lai, E. C. Keeney, S. 2025-11-11 doi:10.1101/2025.11.07.687317 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage ]]> https://biorxiv.org/content/10.1101/2025.11.09.686659v1?rss=1 Angeloni, A. Hammond, J. M. Peters, T. J. Reis, A. L. M. Kemp, L. Amos, T. Gamaarachchi, H. Humphries, S. Wilmott, L. A. Pal, S. Masamsetti, V. P. Weatherstone, M. Ip, K. C. K. Pazaky, K. Steel, A. Lyons, R. Walters, E. D. Liu, N. Tam, P. Polo, J. M. Waters, P. D. Clark, S. J. Richards, L. J. Smith, A. D. Lee, H. Deveson, I. W. Griffith, O. W. Skvortsova, K. 2025-11-11 doi:10.1101/2025.11.09.686659 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ Diffusion MRI Processing in the HEALthy Brain and Child Development Study: Innovations and Applications ]]> https://biorxiv.org/content/10.1101/2025.11.10.687672v1?rss=1 Cieslak, M. Irfanoglu, M. O. Meisler, S. L. Salo, T. Raikes, A. C. Cook, P. A. Chung, A. W. Lee, E. G. Li, R. Li, X. Pecheva, D. Fair, D. A. Smyser, C. D. Harms, M. P. Landman, B. A. Wisnowski, J. L. Huang, H. Alexander, A. L. Satterthwaite, T. D. 2025-11-11 doi:10.1101/2025.11.10.687672 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ Accurate interpretation of within-host dissemination using barcoded bacteria ]]> https://biorxiv.org/content/10.1101/2025.11.11.687827v1?rss=1 Giorgio, R. T. Zhang, T. Holmes, C. L. Hullahalli, K. 2025-11-11 doi:10.1101/2025.11.11.687827 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ Cornichon Homolog-3 (Cnih3) deletion impairs spatial memory, reward-cue association, and fentanyl self-administration behavior. ]]> https://biorxiv.org/content/10.1101/2025.11.12.688051v1?rss=1 Lintz, T. Liu, A. Aal, T. Park, A. Dearman, J. Agrawal, A. Nelson, E. C. Moron, J. 2025-11-13 doi:10.1101/2025.11.12.688051 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Characterization of mechanical tissue properties in post-mortem human brain using magnetic resonance elastography ]]> https://biorxiv.org/content/10.1101/2025.11.12.688069v1?rss=1 Mojumder, J. Lu, Y.-C. Diano, A. M. Alshareef, A. A. McGarry, M. Bayly, P. V. Johnson, C. L. Butman, J. A. Pham, D. L. 2025-11-13 doi:10.1101/2025.11.12.688069 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Comparative Evaluation of Assumption Lean Community Detection Methods for Human Connectome Networks ]]> https://biorxiv.org/content/10.1101/2025.11.13.688333v1?rss=1 Bhattacharya, A. Chakraborty, N. Wang, X. Tu, J. Dierker, D. Eck, A. Lahiri, S. Eggebrecht, A. Wheelock, M. D. 2025-11-14 doi:10.1101/2025.11.13.688333 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Time-resolved phylogenomics analysis reveals patterns in biosphere nutrient limitation through Earth history ]]> https://biorxiv.org/content/10.1101/2025.11.13.688358v1?rss=1 Ni, Z. Osborn, T. Zhong, J. Gonzalez, A. Puzella, W. Klos, A. Le, B. Leonetti, A. Boden, J. S. Stueeken, E. E. Anderson, R. E. 2025-11-14 doi:10.1101/2025.11.13.688358 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Nuclear-import receptors remodel the dilute phase to suppress phase transitions of RNA-binding proteins with prion-like domains. ]]> https://biorxiv.org/content/10.1101/2025.11.14.688546v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@1dd32cforg.highwire.dtl.DTLVardef@132ba1eorg.highwire.dtl.DTLVardef@1593c80org.highwire.dtl.DTLVardef@19311d6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Linsenmeier, M. Shinn, M. K. Mumford, T. R. Liu, V. Bugaj, L. Pappu, R. V. Shorter, J. 2025-11-15 doi:10.1101/2025.11.14.688546 Cold Spring Harbor Laboratory Press 2025-11-15 <![CDATA[ Selective distractor representations resolve multidimensional interference ]]> https://biorxiv.org/content/10.1101/2025.11.16.688701v1?rss=1 Gheza, D. Freund, M. C. Zalabak, T. R. Kool, W. 2025-11-17 doi:10.1101/2025.11.16.688701 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Spatial Multi-Omics Workflow and Analytical Guidelines for Alzheimer's Neuropathology ]]> https://biorxiv.org/content/10.1101/2025.11.16.688710v1?rss=1 Sun, X. Hudson, H. R. Orr, T. C. Koutarapu, S. Rosenbloom, A. Ingalls, M. Braubach, O. Keene, C. D. Beechem, J. M. Orr, M. E. 2025-11-17 doi:10.1101/2025.11.16.688710 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Chronic oral cannabidiol delays or prevents seizures in a mouse model of CLN2 disease ]]> https://biorxiv.org/content/10.1101/2025.11.17.688949v1?rss=1 Dearborn, J. T. Takahashi, K. Rensing, N. R. Wong, M. Cooper, J. D. Sands, M. S. 2025-11-18 doi:10.1101/2025.11.17.688949 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ TGF-β drives the conversion of conventional NK cells into uterine tissue-resident NK cells to support murine pregnancy ]]> https://biorxiv.org/content/10.1101/2025.11.18.688992v1?rss=1 Barahona, J. D. Yang, L. Nelson, D. M. Yokoyama, W. M. 2025-11-18 doi:10.1101/2025.11.18.688992 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ Neural mechanisms of handedness for precision drawing: hand-dependent engagement of cortical networks for bimanual control and tool use ]]> https://biorxiv.org/content/10.1101/2025.11.18.689091v1?rss=1 RH effects on BOLD magnitude and on functional connectivity (FC) modulation via generalized psychophysiological interaction. ResultsDuring LH drawing, contralateral primary motor cortex (M1) had lower magnitude, and greater FC with two networks of equal-or-greater magnitude: left M1-dorsal premotor, and intrahemispheric parieto-temporal network. Contralateral M1 also had reduced interhemispheric FC with inferior parietal lobule, which exhibited lower magnitude. Patient group did not interact with these effects. ConclusionsThree neural mechanisms differentiate LH from RH drawing. First, a left hemisphere bimanual control network engages intrahemispherically (directly) during RH drawing and interhemispherically (indirectly) during LH drawing. Second, LH drawing increases engagement of a contralateral network that may reflect increased task demands. Third, RH drawing increases engagement of an interhemispheric tool use network. The first and third networks may explain the dominant hands performance advantages. PNI patients use the same mechanisms, highlighting their potential as a neuromodulatory target to enhance LH performance after RH impairment. ]]> Kapil, N. Kim, T. Gassass, S. Zhou, R. Carter, A. R. Dobbins, I. G. Liu, L. McAvoy, M. P. Wheelock, M. D. Wang, Y. Brogan, D. M. Dy, C. J. Susan, M. E. Philip, B. A. 2025-11-18 doi:10.1101/2025.11.18.689091 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ Dataset Documentation for Responsible AI: Analysis of Suitability and Usage for Health Datasets ]]> https://biorxiv.org/content/10.1101/2025.11.18.689064v1?rss=1 Heinke, A. Huang, L. Simpkins, K. U. Kalaw, F. G. P. Karsolia, A. Singh, K. Soundarajan, S. Nebeker, C. Baxter, S. L. Lee, C. S. Lee, A. Y. Patel, B. 2025-11-19 doi:10.1101/2025.11.18.689064 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ Single-cell Spatial Transcriptional Profiling Uncovers Heterogeneous Cellular Responses to Pathogenic Tau in a Mouse Model of Neurodegeneration ]]> https://biorxiv.org/content/10.1101/2025.11.19.689127v1?rss=1 Sun, X. Wu, L. Orr, T. C. Heck, A. Young, K. Dunaway, N. Navarro, J. C. Beechem, J. M. Orr, M. E. 2025-11-19 doi:10.1101/2025.11.19.689127 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ Metabolic cross-talk promotes persistence of Enterococcus in a model of polymicrobial catheter-associated urinary tract infection ]]> https://biorxiv.org/content/10.1101/2025.11.19.689321v1?rss=1 Zou, Z. Pinkner, J. S. Obernuefemann, C. L. P. Kleinschmidt, K. R. Sanick, D. A. Hickerson, S. M. Dodson, K. W. Henderson, J. P. Hultgren, S. J. Caparon, M. G. 2025-11-20 doi:10.1101/2025.11.19.689321 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ Diverse infection models demonstrate robust resistance of Mycobacterium tuberculosis to innate immunity ]]> https://biorxiv.org/content/10.1101/2025.11.20.687493v1?rss=1 100,000 CFU) of Lp from the lung within a few days. However, pre-infection with Lp only modestly reduced Mtb CFU compared to mice infected with only Mtb, indicating that Mtb can robustly replicate even in the presence of a strong innate inflammatory response. We performed single-cell RNA-sequencing on myeloid cells from mice either infected with Mtb alone or mice primed with Lp. We found that Lp priming before Mtb infection induced measurable changes in myeloid cells responding to Mtb, but these changes had little effect on innate control of Mtb. Together, these data demonstrate the robust resistance of Mtb to innate immune clearance under diverse experimental conditions. ]]> Fairgrieve, M. R. Brydon, E. C. Chavez, R. A. Kotov, D. I. Vance, R. 2025-11-20 doi:10.1101/2025.11.20.687493 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ Elevated CO2 drives epigenetic reprogramming andchromatin dynamics in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2025.11.20.689512v1?rss=1 Lewis, S. Li, M. Panda, K. Harkess, A. Slotkin, R. K. Meyers, B. C. 2025-11-21 doi:10.1101/2025.11.20.689512 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Sexually dimorphic role of estrogen receptor α in preserving right ventricular endothelial integrity ]]> https://biorxiv.org/content/10.1101/2025.11.20.689545v1?rss=1 Li, J. Karoor, V. Frump, A. L. Zhao, H. Liang, S. Woodcock, C.-S. C. Petrache, I. Dai, Z. Lahm, T. 2025-11-21 doi:10.1101/2025.11.20.689545 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ TDP-43 suppression of ATP8A2 cryptic splicing implicates phosphatidylserine-driven neuroinflammation in ALS/FTD ]]> https://biorxiv.org/content/10.1101/2025.11.21.689833v1?rss=1 O'Connor, J. T. Loo, H. Q. Guo, C. Pickles, S. Sundali, S. Jawahar, V. M. Dickson, D. W. Bloom, A. J. Petrucelli, L. Gitler, A. D. Milbrandt, J. DiAntonio, A. 2025-11-24 doi:10.1101/2025.11.21.689833 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ A cross-species spatial transcriptomic atlas of the human and non-human primate basal ganglia ]]> https://biorxiv.org/content/10.1101/2025.11.22.688128v1?rss=1 Hewitt, M. N. Turner, M. A. Johansen, N. McMillen, D. A. Dan, S. DeBerardine, M. Ruiz, A. Huang, M. Quon, J. Fu, Y. Kapen, I. Barta, S. Martin, N. Cuevas, N. V. Olsen, P. Nagra, J. Campos, J. VanNess, M. M. Ransford, S. Juneau, Z. Hastings, S. Ching, L. Kunst, M. Basu, S. Hollt, T. Li, C. Lelieveldt, B. Yazdani, F. Zhang, Q. Levandowski, K. Feng, G. Rosen, B. Glasser, M. F. Hayashi, T. Garcia, A. D. Kana, O. Maltzer, Z. M. Campagnola, L. Jarsky, T. Kruse, L. Freiwald, W. Keene, C. D. Van Essen, D. C. Ariza, J. Waters, J. Krienen, F. M. Bakken, T. E 2025-11-24 doi:10.1101/2025.11.22.688128 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Injury-Induced Remodeling of Junctional Actin Bands in the Vestibular Maculae of Mice and Chicks: Implications for Sensory Regeneration ]]> https://biorxiv.org/content/10.1101/2025.11.24.682866v1?rss=1 Warchol, M. E. 2025-11-26 doi:10.1101/2025.11.24.682866 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ Two views of the brain are reconciled by a unifying principle of maximal information processing ]]> https://biorxiv.org/content/10.1101/2025.11.25.690580v1?rss=1 Fosque, L. J. Shew, W. Ching, S. Hengen, K. B. 2025-11-26 doi:10.1101/2025.11.25.690580 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ Inorganic pyrophosphate disrupts amorphous hydrated bone mineral interfaces in hypophosphatasia ]]> https://biorxiv.org/content/10.1101/2025.11.24.689921v1?rss=1 Dillon, S. Armiger, A. Murgoci, A. Skingle, L. Tabegna, F. G. A. McDonald, S. Mumm, S. Whyte, M. P. Garton, M. Poole, K. E. S. Duer, M. J. 2025-11-27 doi:10.1101/2025.11.24.689921 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ Learning the mechanism of collective microbial function via random community-media pairing ]]> https://biorxiv.org/content/10.1101/2025.11.25.690499v1?rss=1 Wang, L. Kuehn, S. Tikhonov, M. 2025-11-27 doi:10.1101/2025.11.25.690499 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ Sensorineural regulation of skull healing implicates FGF1 signaling in non-healing bone ]]> https://biorxiv.org/content/10.1101/2025.11.24.690319v1?rss=1 Horenberg, A. L. Villapudua-Gastelum, C. Xu, M. Zeng, E. Dias, S. Sinha, T. Archer, M. Scheller, E. L. Pathak, A. James, A. Grayson, W. 2025-11-28 doi:10.1101/2025.11.24.690319 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ The Vaginal Microbiome in Women Recently Experiencing BV and UTI ]]> https://biorxiv.org/content/10.1101/2025.11.27.690987v1?rss=1 Gilbert, N. Whang, S. N. Wang, X. Thomas-White, K. J. Olmschenk, G. Garza, J. E. Navarro, P. 2025-11-28 doi:10.1101/2025.11.27.690987 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Anatomical 3D Reconstruction of Murine Lymph Nodes for Visualization, Quantitation, and Numerical Simulation ]]> https://biorxiv.org/content/10.1101/2025.11.25.690560v1?rss=1 0.93 for lobules and contour-matching scores up to 77% for vasculature, as validated by quantitative comparison to manual segmentation. Compared to existing methodologies, this pipeline markedly reduces reagent usage ([~]88%), labor time ([~]97%), and technical complexity, offering a broadly accessible and efficient approach to highfidelity 3D anatomical reconstruction of LN architecture. These digital twins can support computational simulations of drug distribution, immune cell trafficking, and spatial pharmacokinetics, providing critical insights into LN-resident disease mechanisms and informing therapeutic design. ]]> Donzanti, M. J. Moghadamnia, Y. Kapinski, A. T. Zurakowski, R. Gleghorn, J. P. 2025-11-29 doi:10.1101/2025.11.25.690560 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ ACSS2 mediates prenatal alcohol exposure-related morphological and behavioral phenotypes ]]> https://biorxiv.org/content/10.1101/2025.11.26.690774v1?rss=1 Dodson, K. M. Periandri, E. M. Yadav, A. Lopes, M. Barfield, A. J. Ola, A. de Luna Vitorino, F. N. Cearlock, C. Garcia, B. A. Hill, C. Maloney, S. E. Egervari, G. 2025-12-01 doi:10.1101/2025.11.26.690774 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ 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[ Proteostasis Stress Drives Stem Cell Aging, Clonal Hematopoiesis and Leukemia ]]> https://biorxiv.org/content/10.1101/2025.11.27.690982v1?rss=1 Zhou, F. J. Le, M. Wang, H. C. Yang, W. Wang, H.-Y. Tiwari, A. Cen, X. Sunshine, M. J. Magee, J. A. Signer, R. A. 2025-12-01 doi:10.1101/2025.11.27.690982 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Lifelong maintenance of locomotion by embryonically active dopamine neurons ]]> https://biorxiv.org/content/10.64898/2025.11.28.691140v1?rss=1 Padmanabhan, A. Rahman, D. Zhu, R. Khorbtli, S. Sathianathan, S. Le Flohic, B. Assanga Bisse, L. Mollereau, B. Huang, C. Konstantinides, N. Issa, A. R. 2025-12-02 doi:10.64898/2025.11.28.691140 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Gut metabolism links precision nutrition, exercise, and healthspan in Drosophila melanogaster ]]> https://biorxiv.org/content/10.64898/2025.11.29.691311v1?rss=1 Wei, F. Liu, S. Sun, Y. Liu, J. 2025-12-02 doi:10.64898/2025.11.29.691311 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ FET proteins and PARylation-dependent condensates promote replication fork reversal and genome stability ]]> https://biorxiv.org/content/10.64898/2025.12.01.691651v1?rss=1 Giansanti, C. Schultz, J. C. Jackson, J. Vindigni, A. Cortez, D. 2025-12-02 doi:10.64898/2025.12.01.691651 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Distinguishing near- versus off-critical phase behaviors of intrinsically disordered proteins ]]> https://biorxiv.org/content/10.64898/2025.12.01.691696v1?rss=1 Mitra, G. Ghosh, S. Ruff, K. M. Zhang, R. Chauhan, G. Pappu, R. V. 2025-12-02 doi:10.64898/2025.12.01.691696 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ The long noncoding RNA Peanut (Gm11454) promotes neurogenesis and rod photoreceptor differentiation during postnatal retinal development. ]]> https://biorxiv.org/content/10.64898/2025.12.02.691925v1?rss=1 Hostetler, J. E. Shiau, F. Zhang, X. Chen, S. Ruzycki, P. A. Blackshaw, S. Clark, B. 2025-12-03 doi:10.64898/2025.12.02.691925 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ The lac operon in uropathogenic Escherichia coli enhances intracellular growth by enabling host glycan utilization ]]> https://biorxiv.org/content/10.64898/2025.12.03.691977v1?rss=1 Puri, D. Villicana, J. B. Nye, T. Hurto, R. L. Hazan, J. Gualberto, N. C. Lopato, E. D. B. Pinkner, J. S. Dodson, K. W. Freddolino, L. Hultgren, S. J. 2025-12-03 doi:10.64898/2025.12.03.691977 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Lemborexant Reduces Infarct Volume and Improves Long-Term Functional Recovery in a Murine Model of Ischemic Stroke ]]> https://biorxiv.org/content/10.64898/2025.12.02.691079v1?rss=1 Jung, H. R. Venkitaraman, S. Blackwood, S. L. Kamal, A. Jiang, Y. Lee, J. Lee, D. Bibi, N. Ibrahim, K. M. Yuede, C. M. Lee, J.-M. Landsness, E. C. 2025-12-05 doi:10.64898/2025.12.02.691079 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Multiscale Spatial Transcriptomic Atlas of Human Basal Ganglia Cell-Type and Cellular Community Organization ]]> https://biorxiv.org/content/10.64898/2025.12.02.691876v1?rss=1 Berackey, B. T. Tan, Z. Wu, G. Das, S. C. Li, R. Esser, B. Ye, Q. Nafisi, M. Park, S. S. Sequeira Mendieta, P. A. Berry, J. Mamdani, F. Zhu, Q. Holmes, T. C. Li, D. Wang, T. Behrens, M. M. Ren, B. Ecker, J. R. Bintu, B. Xu, X. 2025-12-05 doi:10.64898/2025.12.02.691876 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Environmental Enrichment Attenuates Fentanyl-Seeking Behavior and Protects Against Stress-Induced Reinstatement in Both Male and Female Rats ]]> https://biorxiv.org/content/10.64898/2025.12.02.691896v1?rss=1 Higginbotham, J. A. Dearman, J. J. Maqbool, H. Pujol, M. Moron, J. A. 2025-12-05 doi:10.64898/2025.12.02.691896 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Global Evaluation of Congenital Heart Disease-Associated Non-Coding Variants ]]> https://biorxiv.org/content/10.64898/2025.12.02.691900v1?rss=1 3,000 CHD-risk variants for allelic binding for the cardiac TFs NKX2-5, GATA4, and TBX5 in a high-throughput manner. These binding affinity data sets were coupled with a massively parallel reporter assay (MPRA) to screen CHD-risk variant genotype-dependent regulatory activity. We identified 170 variants that exhibit allelic TF binding and 187 that modulate gene expression. Combining both approaches revealed three high-confidence variants with genotype-dependent TF binding, genotype-dependent transcriptional activity, and eQTL behavior in cardiac cells. Collectively, this study provides the first combined high-throughput biochemical and functional genomic evaluation of thousands of CHD-risk variants. HighlightsO_LIAllelic binding affinity measurements of [~]9,600 variants for NKX2-5, GATA4, and TBX5 C_LIO_LIEvaluaFon of >3,000 CHD-risk variants for genotype-dependent regulatory acFvity C_LIO_LIInteracFon networks idenFfy funcFonal variants and genes involving cardiac eQTLs C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/691900v2_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1f2dc96org.highwire.dtl.DTLVardef@1700929org.highwire.dtl.DTLVardef@696ec4org.highwire.dtl.DTLVardef@1e724d8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pena-Martinez, E. G. Sharma, S. Medina-Feliciano, J. G. Root, E. Parks, L. G. Granitto, M. Pomales-Matos, D. A. Messon-Bird, J. L. Barreiro-Rosario, A. C. Sanabria-Alberto, L. Rivera-Madera, A. Rodriguez-Rios, J. M. Velazquez-Roig, R. Figueroa-Rosado, J. A. Noon, M. Donmez, O. A. Forney, C. Hesse, H. K. Dunn, K. A. Chen, X. Hass, M. Lawson, L. Weirauch, M. T. Kottyan, L. Reilly, S. K. Bhimsaria, D. Rodriguez-Martinez, J. A. 2025-12-05 doi:10.64898/2025.12.02.691900 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Noninvasive enrichment of circulating tumor biomarkers in a mouse model of diffuse midline glioma using focused ultrasound ]]> https://biorxiv.org/content/10.64898/2025.12.02.691913v1?rss=1 Zhang, D. Yue, Y. Gong, Y. Yang, L. Xu, K. Yuan, J. Chen, H. 2025-12-05 doi:10.64898/2025.12.02.691913 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Functional Connectivity Graph Theory Analysis of Spoken Word Processing Efficiency in Prefrontal Cortical Activation ]]> https://biorxiv.org/content/10.64898/2025.12.04.690545v1?rss=1 Skolasinska, P. Eggebrecht, A. T. Evans, J. L. 2025-12-05 doi:10.64898/2025.12.04.690545 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Pairing extinction training with vagus nerve stimulation (VNS) reduces drug-seeking by altering activity in afferents to the medial prefrontal cortex ]]> https://biorxiv.org/content/10.64898/2025.12.03.691662v1?rss=1 Driskill, C. Vu, L. Jalilvand, S. Salazar, F. Waydick, L. Suji, N. Tata, S. Khan, A. Hasan, Z. Nuna, R. Kanwal, Z. Molin, N. Kroener, S. 2025-12-06 doi:10.64898/2025.12.03.691662 Cold Spring Harbor Laboratory Press 2025-12-06 <![CDATA[ Visual Semantic Encoding and Identification of Naturalistic Movies via High-Density Diffuse Optical Tomography ]]> https://biorxiv.org/content/10.64898/2025.12.03.692158v1?rss=1 Fehner, W. Fogarty, M. Tang, J. Wilhelm, D. Bajracharya, A. Markow, Z. E. Hines, A. M. Trobaugh, J. W. Huth, A. G. Culver, J. P. 2025-12-08 doi:10.64898/2025.12.03.692158 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Targeting ALC1 can safely expand the therapeutic utility of PARP inhibitors across high-grade serous ovarian cancers ]]> https://biorxiv.org/content/10.64898/2025.12.04.692458v1?rss=1 Verma, P. Aubuchon, L. N. Wong, D. H. Ramakrishnan, N. M. Reddy, R. Compadre, A. Lomonosova, E. Jackson, K. E. Kemper, D. Mehta, V. Zoberi, K. Khabele, D. Christie, E. L. Mullen, M. M. 2025-12-08 doi:10.64898/2025.12.04.692458 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Graded BMP signals modulate yellow and red color in fishes impacting adult pigment pattern and behavior ]]> https://biorxiv.org/content/10.64898/2025.12.04.692427v1?rss=1 Huang, D. de Mello, P. L. H. Liu, T. Liu, Y. Kapadia, E. Liang, Y. Lu, J. Corbo, J. C. Parichy, D. M. 2025-12-09 doi:10.64898/2025.12.04.692427 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Profiles of Aging Based on Cognition, Affect, and Brain Reserve ]]> https://biorxiv.org/content/10.64898/2025.12.04.692428v1?rss=1 Jarukasemkit, S. Stahl, L. Tam, K. M. Feng, B. Rincon, S. N. Luo, X. Modi, H. Hamilton, K. M. Lenzini, P. Ahmad, F. Easley, T. Bijsterbosch, J. D. 2025-12-09 doi:10.64898/2025.12.04.692428 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Harnessing anti-CRISPR to suppress, subtract, and segregate Cas9 activity for precision CRISPR in Drosophila ]]> https://biorxiv.org/content/10.64898/2025.12.07.692848v1?rss=1 Shen, Y. Sheen, M. Yeung, A. T. Chen, X. Wang, B. Huang, Z. Ho, C. A. Lakkis, Z. I. Han, C. 2025-12-09 doi:10.64898/2025.12.07.692848 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Heat-shock pathway activation by TRC051384 protects spiral ganglion neurons from noise-induced hearing loss ]]> https://biorxiv.org/content/10.64898/2025.12.08.693048v1?rss=1 Yu, J. Ramirez, M. A. Wang, Y.-Z. Edassery, S. Shramuk, M. Cheatham, M. A. Rutherford, M. A. Welty, l. Savas, J. 2025-12-11 doi:10.64898/2025.12.08.693048 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Cilia.io: Computer vision and machine learning reveal spatial patterns of cilia beating dynamics in the spinal cord ]]> https://biorxiv.org/content/10.64898/2025.12.10.693099v1?rss=1 Atayeter, E. Ho, J. Blottin, T. G. Joe, I. B. Sistrunk, R. S. Zhang, B. Solnica-Krezel, L. Gerstlauer, A. Wallingford, J. B. Gray, R. S. 2025-12-13 doi:10.64898/2025.12.10.693099 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ Patterns of brain-wide associations reflect socioeconomics ]]> https://biorxiv.org/content/10.64898/2025.12.10.693206v1?rss=1 Marek, S. Donohue, M. R. Karcher, N. Hoyniak, C. Chauvin, R. Meyer, A. Miller, J. Van, A. N. Wang, A. Baden, N. Suljic, V. Scheidter, K. Monk, J. Whiting, F. Ramirez-Perez, N. Krimmel, S. Metoki, A. Paul, S. E. Gorelik, A. Hendrickson, T. J. Malone, S. M. Schwarzlose, R. Cardenas-Iniguez, C. Herting, M. Petersen, S. Luby, J. Randolph, A. Shanahan, M. Turkheimer, E. Kay, B. P. Gordon, E. M. Laumann, T. O. Barch, D. Fair, D. A. Tervo-Clemmens, B. Dosenbach, N. U. 2025-12-13 doi:10.64898/2025.12.10.693206 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ BIOSPONGES EMBEDDED WITH GDNF ENHANCE NEUROMUSCULAR RECOVERY FOLLOWING VOLUMETRIC MUSCLE LOSS ]]> https://biorxiv.org/content/10.64898/2025.12.10.693478v1?rss=1 20% of a muscles mass. VML directly reduces the number of myofibers and causes axonal degeneration of nerves, resulting in reduced muscle function and impaired neuromuscular junctions (NMJs). Biosponge (BSG) scaffolds, composed of gelatin, collagen, and laminin-111, have been shown to improve muscle mass, cross-sectional area, and myofiber number following VML. However, improvements in NMJ quantity were not observed. Glial cell line-derived neurotrophic factor (GDNF) is a growth factor that enhances motor unit survival and neurite outgrowth. In this work, BSG scaffolds were electrostatically coupled with GDNF via gelatin nanoparticles (GNPs) to support myofiber regeneration and preserve NMJs post-VML in a rodent model. In vitro determination of release kinetics revealed an initial burst release of surface bound GDNF with almost an equivalent amount of electrostatically bound GDNF retained within the BSG post 1 week of incubation at 37{degrees}C in phosphate buffered saline (PBS). To create the VML injury in male Lewis rats (10-12 weeks old), [~]20% of the muscle mass was removed from the tibialis anterior (TA) muscle of both hindlimbs. Relative to BSG+GNP alone, treatment with BSG+GNP+GDNF showed a significant increase ([~]25%) in peak isometric torque at 6 weeks post-injury. Qualitative and quantitative histological analysis of NMJs revealed an enhanced overlap between pre- and post-synaptic structures in the BSG+GNP+GDNF group. Additionally, the incorporation of GDNF slowed BSG remodeling and degradation. Overall, these results suggest that the BSG-mediated delivery of GDNF is an effective strategy for mitigating NMJ loss and enhancing muscle recovery following VML. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/693478v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1719d84org.highwire.dtl.DTLVardef@1c6bceorg.highwire.dtl.DTLVardef@1e9a9a5org.highwire.dtl.DTLVardef@180ad57_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical Abstract Tadiwala et al., 2025 Biosponges embedded with GDNF promote neuromuscular recovery following volumetric muscle loss. ]]> Tadiwala, J. Tobo, C. Sekerak, K. Sheetz, R. Ridolfo, A. Gamage, M. E. Ertugral, E. G. Jelliss, P. Wood, M. D. Kothapalli, C. R. Garg, K. 2025-12-13 doi:10.64898/2025.12.10.693478 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ CompBio and MIRaS : A Multi-omic Analysis Platform Built on a Memory-Based Intelligence Engine ]]> https://biorxiv.org/content/10.64898/2025.12.11.693741v1?rss=1 Head, R. D. Barve, R. A. Storer, C. E. Hoxsie, W. D. Marcum, C. McMichael, J. F. Lalmansingh, J. M. Smith, B. K. Johnson, M. R. Kuster, D. J. 2025-12-15 doi:10.64898/2025.12.11.693741 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Personalized biventricular mechanics and sensitivity to model morphology ]]> https://biorxiv.org/content/10.64898/2025.12.11.693778v1?rss=1 Brown, A. Shi, L. Salvador, M. Kong, F. Ennis, D. B. Chen, I. Y. Vedula, V. Marsden, A. L. 2025-12-15 doi:10.64898/2025.12.11.693778 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Immune-mediated Engagement of T Regulatory Cells with Tumor Cells Results in Trogocytosis and Tumor Cell Killing. ]]> https://biorxiv.org/content/10.64898/2025.12.11.693807v1?rss=1 50% of patients with advanced melanoma are unresponsive to current therapies. Using the B78-D14 melanoma model (GD2+/MHC-I-/MHC-II+), we can cure mice with a regimen that includes radiation therapy (RT) in combination with immunocytokine (IC; anti-GD2 monoclonal antibody linked to IL-2) while establishing immunological memory. We interrogated the role of T cells in the antitumor and memory responses following RT+IC. We show a requirement for CD4, but not CD8 T cells, to achieve both the initial and memory responses. Upon IC-induced cell-cell contact, subsets of CD4 T cells, including Foxp3 T regulatory cells, trogocytose GD2 from tumor cells, acquire cytotoxic granules, and kill tumor cells. These results were confirmed using human tumor cell lines. These findings reveal that CD4 T regulatory cells, upon immunologically-induced binding to tumor cells, can trogocytose tumor antigens and directly kill tumor cells, redefining their potential role in antitumor immunity. ]]> Erbe, A. K. Feils, A. S. Gao, A. VandenHeuvel, S. Boyenga, S. Hampton, A. Heck, M. Zaborek, J. Spiegelman, D. Tsarovsky, N. Hoefges, A. Pieper, A. A. Carlson, P. M. Felder, M. Patel, R. B. Gillies, S. D. Heaton, A. Morris, Z. Dinh, H. Q. Rakhmilevich, A. L. Sondel, P. M. 2025-12-15 doi:10.64898/2025.12.11.693807 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Integrative Genomic and Functional Analyses Reveal NINL as a Modulator of Tau Aggregation ]]> https://biorxiv.org/content/10.64898/2025.12.12.694063v1?rss=1 Swift, S. K. Huang, G. Cochran, J. N. Minaya, M. A. Castruita, P. A. Miller, K. J. Starr, E. Galasso, G. Marsh, J. A. Kao, A. Yokoyama, J. S. Karch, C. M. 2025-12-16 doi:10.64898/2025.12.12.694063 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Cross-species consensus atlas of the primate basal ganglia ]]> https://biorxiv.org/content/10.64898/2025.12.15.694496v1?rss=1 Johansen, N. J. Fu, Y. Schmitz, M. Dubuc, A. Kempynck, N. Wirthlin, M. Garcia, A. D. Hewitt, M. Turner, M. A. Seeman, S. C. Long, B. Liu, X.-P. Dan, S. DeBerardine, M. Kapen, I. Yanny, A. M. Avola, A. Barlow, S. T. Bertagnolli, D. Bhandiwad, A. Budzillo, A. Caballero, V. E. N. Caceres, L. Casper, T. Chakka, A. B. Chakrabarty, R. Clark, M. Daniel, S. Eggermont, J. Ferrer, R. French, L. Gloe, J. Goldy, J. Guilford, N. Guzman, J. Hirschstein, D. Ho, W. James, K. Jones, D. L. Jungert, M. Kannan, M. Kedzierska, K. Z. Kroes, T. Leytze, M. Manning, A. McCu 2025-12-16 doi:10.64898/2025.12.15.694496 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Human MutLa activates methylpurine DNA glycosylase to induce alkylation damage cytotoxicity ]]> https://biorxiv.org/content/10.64898/2025.12.15.694403v1?rss=1 Ashour, M. E. Krekeler, E. Bhowmik, M. C. Tsao, N. Herrera-Montavez, C. Tsai, M.-S. Kantar, H. Zaher, M. Galletto, R. Mosammaparast, N. 2025-12-17 doi:10.64898/2025.12.15.694403 Cold Spring Harbor Laboratory Press 2025-12-17 <![CDATA[ The Goldilocks effect drives plant diversification on middle-aged Hawaiian islands ]]> https://biorxiv.org/content/10.64898/2025.12.16.694722v1?rss=1 Lichter-Marck, I. Swiston, S. K. Mendes, F. K. May, M. R. Neupane, S. Baldwin, B. G. Wood, K. Ronsted, N. Wagner, W. L. Zapata, F. Landis, M. J. 2025-12-19 doi:10.64898/2025.12.16.694722 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ Nuclear N-Glycosylation Redefines the Glycoscape and Directs Cell Identity ]]> https://biorxiv.org/content/10.64898/2025.12.17.694357v1?rss=1 Li, F. Wu, X. Xie, Y. Yang, J. Xi, J. Sun, Y. Chen, J. Wu, X. Huang, S. Zhang, C. Zheng, Y. Li, W. Zuo, X. Li, Y. Chen, K. Lai, X. Liu, X. Zhong, W. Zeng, J. Wu, Q. Garcia, B. Lu, H. Xia, H. Zhou, W. Zhang, Y. 2025-12-19 doi:10.64898/2025.12.17.694357 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ Fetoplacental circadian rhythms develop and then synchronize to the mother in utero ]]> https://biorxiv.org/content/10.64898/2025.12.17.695051v1?rss=1 Nikhil, K. L. Bates, K. Sapiro, E. Amme, J. L. McCarthy, R. Speck, S. Vasireddy, V. Roberts, E. Martin-Fairey, C. A. Dominguez-Romero, M.-E. Garcia Cardenas, S. P. England, S. K. Herzog, E. 2025-12-20 doi:10.64898/2025.12.17.695051 Cold Spring Harbor Laboratory Press 2025-12-20 <![CDATA[ Transcriptomic analysis of 40 human and rodent skeletal muscle exerkines ]]> https://biorxiv.org/content/10.64898/2025.12.19.695001v1?rss=1 Taha, H. B. Robbins, N. Zoha, F.-S. Vivek, N. Bogoniewski, A. 2025-12-22 doi:10.64898/2025.12.19.695001 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Stress-induced loss of CTCF reveals an alternative, promoter-based mode of cohesin looping ]]> https://biorxiv.org/content/10.64898/2025.12.19.695003v1?rss=1 Flores, J. P. Perreault, A. Drum, Z. A. Xu, C. Cruz Alonso, D. Petros, G. Wu, Y. Kim, H. Quiroga-Barber, I. Y. Sahasrabudhe, I. Demmerle, J. Wang, G. G. Cai, D. Phanstiel, D. H. 2025-12-22 doi:10.64898/2025.12.19.695003 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Optogenetic Proximity Labeling Maps Spatially Resolved Mitochondrial Surface Proteomes and a Locally Regulated Ribosome Pool ]]> https://biorxiv.org/content/10.64898/2025.12.21.693523v1?rss=1 Kwak, C. S. Du, Z. Creery, J. S. Wilkerson, E. M. Major, M. B. Elias, J. E. Wang, X. 2025-12-23 doi:10.64898/2025.12.21.693523 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Defining bottlenecks and physiological impact of an orthogonal translation initiation system ]]> https://biorxiv.org/content/10.64898/2025.12.21.695813v1?rss=1 Scopelliti, D. Vincent, R. M. Hutvagner, A. Whelan, F. Klare, W. P. Pang, I. Church, G. Jaschke, P. R. 2025-12-23 doi:10.64898/2025.12.21.695813 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Spatial transcriptomic profiling of decalcified murine musculoskeletal samples via Xenium Prime 5K ]]> https://biorxiv.org/content/10.64898/2025.12.22.693132v1?rss=1 View larger version (87K): org.highwire.dtl.DTLVardef@4c4389org.highwire.dtl.DTLVardef@e607bcorg.highwire.dtl.DTLVardef@5f957org.highwire.dtl.DTLVardef@34ce27_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lammlin, L. Tran, H. X. Mohan, A. Newton, M. D. Howser, S. C. Redding, S. J. Capobianco, C. A. Hankenson, K. D. Knights, A. J. Maerz, T. 2025-12-24 doi:10.64898/2025.12.22.693132 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ Associations between amygdala connectivity and experienced discrimination in children ]]> https://biorxiv.org/content/10.64898/2025.12.22.695992v1?rss=1 Goode, N. J. Potter, E. Rasheed, M. Camacho, M. Higashi, R. Nguyen, L. Shah, S. Miranda-Dominguez, O. Hermosillo, R. Juliano, A. Cheaito, A. Thomas, E. 2025-12-24 doi:10.64898/2025.12.22.695992 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ Guiding treatment response by spatiotemporal control of α-particle deposition in solid tumors: the case for 'affinity cocktails' of antibody-radioconjugates ]]> https://biorxiv.org/content/10.64898/2025.12.22.696075v1?rss=1 Nair, R. Sarkar, A. Hariharan, P. Kavousanakis, M. E. Chaudhari, R. Bastiaannet, R. Gabrielson, K. L. Sofou, S. 2025-12-25 doi:10.64898/2025.12.22.696075 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ Activation of the medial entorhinal cortex drives memory-guided navigation behavior ]]> https://biorxiv.org/content/10.64898/2025.12.24.696388v1?rss=1 Ma, Y. Malone, T. J. Tien, N.-W. Tyan, J. Gu, Y. 2025-12-26 doi:10.64898/2025.12.24.696388 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ MLL3 and MLL4 sustain hematopoietic stem cell multipotency by opposing a B-cell default state ]]> https://biorxiv.org/content/10.64898/2025.12.24.696404v1?rss=1 Wang, H. C. Chen, R. Yang, W. Muthukumar, R. Hu, T. Patel, R. M. Casey, E. B. Denby, E. Zhang, R. Xie, G. Ge, K. Challen, G. A. Bednarski, J. J. Magee, J. A. 2025-12-26 doi:10.64898/2025.12.24.696404 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Mast cell extracellular granules are bioactive condensates driven by heparin and polyamine ]]> https://biorxiv.org/content/10.64898/2025.12.25.696514v1?rss=1 Xiong, Y. Tomares, D. T. Guo, J. Sato, K. Zeng, L. Tian, Y. Su, M. Albis, A. Pant, A. Pappu, R. V. Su, X. 2025-12-26 doi:10.64898/2025.12.25.696514 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Cell type diversification and phenotype convergence underlying white fin-ornamentation of cyprinid fishes ]]> https://biorxiv.org/content/10.64898/2025.12.26.696501v1?rss=1 Huang, D. Liu, T. Carr, A. A. de Mello, P. H. Liang, Y. Shriver, L. Chauvigne, F. Johnson, S. L. Cerda, J. Patti, G. J. Parichy, D. M. 2025-12-27 doi:10.64898/2025.12.26.696501 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ Dose-dependent NFI regulation of progenitor lifespan and output underlying human neocortical malformation ]]> https://biorxiv.org/content/10.64898/2025.12.27.696675v1?rss=1 Zhang, Q. Yuan, G. Albizzati, E. Yang, J. Zhao, Z. Yu, X. Chang, X. Lee, C. H. Du, H. Lao, Z. Krishnamurthy, A. Zhang, X. Lv, X. Tang, X. Hu, S. Chi, Y. Ma, J. Gronostajski, R. M. Richards, L. J. Zhang, J. Joyner, A. L. Tchieu, J. Li, Y. Shi, S.-H. 2025-12-27 doi:10.64898/2025.12.27.696675 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ Astrocytic Cholesterol Fine-Tunes the Balance of Different Modes of Synaptic Exo- and Endocytosis ]]> https://biorxiv.org/content/10.64898/2025.12.28.696787v1?rss=1 Myeong, J. Klyachko, V. 2025-12-29 doi:10.64898/2025.12.28.696787 Cold Spring Harbor Laboratory Press 2025-12-29 <![CDATA[ Multi-modal choroid plexus pathology in aging and Alzheimer's disease ]]> https://biorxiv.org/content/10.64898/2025.12.30.697051v1?rss=1 500 postmortem samples age 16 to 105, spatial transcriptomics, and functional studies in 5xFAD mice. We identify fibrosis, calcification, and macrophage abnormalities as hallmarks of ChP aging, with AD pathology conferring additional effects, including expansion of a pro-inflammatory fibroblast-macrophage signaling niche. In 5xFAD mice, macrophage dysfunction is associated with impaired epithelial barrier maintenance and repair. Together, these data provide a foundational resource for understanding ChP dysfunction in aging and AD and propose the macrophage-fibroblast-epithelial barrier axis as a driver of ChP pathology. ]]> Xu, H. Lotfy, P. Englert, B. Oberhauser, J. Byer, L. I. J. Wihlman, J. Colangelo, K. Okar, S. V. Thommana, A. Puttonen, H. Mäyränpää, M. I. Tuimala, J. Pedrosa, R. Kumar, D. Haberberger, J. F. Atkins, M. E. Alimukhamedov, S. Pragana, A. Benson, J. Gabrielle, M. E. Dong, A. DurantLaforet, V. Lin, P. B.-C. Keene, C. D. Latimer, C. S. Prater, K. E. Holtzman, D. M. Isakova, A. E. Wyss-Coray, T. Schafer, D. P. Reich, D. S. Lehtimäki, T. Karhunen, P. J. Kok, E. Jansson, D. Yang, A. C. Myllykangas, L. Ordovas-Montanes, J. Lehtinen, M. K. 2025-12-31 doi:10.64898/2025.12.30.697051 Cold Spring Harbor Laboratory Press 2025-12-31 <![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[ Mucosally sourced complement factor B modulates the host response to colitis ]]> https://biorxiv.org/content/10.64898/2025.12.31.697141v1?rss=1 Thapa, A. Nallapu, A. Muogboh, N. Nedunchezian, S. Talati, K. Yang, B. Hyun, J. Sanchez, J. M. S. Seet, C. S. Koon, H. W. Li, Z. Ciorba, M. A. Michelsen, K. S. Kulkarni, H. S. Kulkarni, D. H. 2026-01-01 doi:10.64898/2025.12.31.697141 Cold Spring Harbor Laboratory Press 2026-01-01 <![CDATA[ Aging, matrix metalloproteinase imaging, and survival prospects in aortic aneurysm ]]> https://biorxiv.org/content/10.64898/2026.01.02.697375v1?rss=1 51-week-old (old) Apoe-/- mice. Aortic MMP activation was quantified by PET/CT using an MMP-targeted tracer, 64Cu-RYM2, at baseline and 1 week after Ang II infusion. MMP activity and expression were quantified by tissue zymography and quantitative reverse transcription polymerase chain reaction, and compared between different segments of the aorta in young and old animals, and before and after Ang II infusion. ResultsOld animals survival to 28 days was significantly lower than that of young Ang-II-infused Apoe-/- mice (P < 0.05). 64Cu-RYM2 PET/CT showed significantly higher aortic MMP activation before and 1 week after Ang-II infusion in old compared to young Apoe-/-mice. The 64Cu-RYM2 signal was significantly higher in animals that did not survive 28 days than those that did (P < 0.01). MMP activity significantly increased by 4 days after Ang-II infusion, when dissection was found in a subset of Apoe-/- mice; and was significantly higher in the dissected, compared to adjacent, apparently normal, segments of the aorta. MMP activity was also significantly higher in the ascending thoracic aorta of untreated young and old mice, as well as of Ang-II-treated Apoe-/-mice (which was associated with significantly higher Mmp2 gene expression), and of old wild-type mice. ConclusionAging is associated with increased MMP activity along the aorta and worse AA survival. MMP-targeted molecular imaging can inform the aneurysm survival prospects. Selective MMP inhibitors and tracers may help prevent and track aneurysm growth, dissection, and rupture. ]]> Ghim, M. Varli, O. Ahmad, A. Neishabouri, A. Kukreja, G. Zhang, Z. Zarnegar, S. Gangemi, N. Toczek, J. Zhang, J. Liu, C. Liu, Y. Gropler, R. Sadeghi, M. M. 2026-01-02 doi:10.64898/2026.01.02.697375 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ KDM7B-mediated demethylation of RNF113A regulates small cell lung cancer sensitivity to alkylation damage ]]> https://biorxiv.org/content/10.64898/2026.01.03.697470v1?rss=1 Ahmad, T. Yang, X. Foucher, A.-E. Ren, L. Tsao, n. Flores, N. Wan, J. Belmudes, L. Dubiez, E. Bhowmik, M. C. Vayr, J. Hausmann, S. Chuffart, F. Lu, X. Blanchet, S. Chasan, T. Boussouar, F. Coute, Y. Mosammaparast, N. Lan, F. Kadlec, J. Mazur, P. K. Reynoird, N. 2026-01-03 doi:10.64898/2026.01.03.697470 Cold Spring Harbor Laboratory Press 2026-01-03 <![CDATA[ Gliomas preferentially develop within the action-mode network ]]> https://biorxiv.org/content/10.64898/2026.01.05.697608v1?rss=1 Cui, W. Zhu, J. Yan, Z. Ren, J. Marek, S. Stoecklein, V. M. Jiang, T. Bao, H. Fang, S. Stoecklein, S. Cai, Z. Fu, X. Gordon, E. M. Wang, D. Wang, Y. Dosenbach, N. U. F. Liu, H. 2026-01-05 doi:10.64898/2026.01.05.697608 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ Biochemical Functions of the Membrane-Binding Domain of CARMIL ]]> https://biorxiv.org/content/10.64898/2026.01.05.697744v1?rss=1 Mooren, O. L. McConnell, P. DeBrecht, J. D. Cooper, J. A. 2026-01-05 doi:10.64898/2026.01.05.697744 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ Detailed single-cell mapping of the transcriptional response to a virus infection driven by copy-back viral genomes ]]> https://biorxiv.org/content/10.64898/2026.01.06.697933v1?rss=1 Yang, Y. Achouri, E. Tambo, M. Lopez, C. B. 2026-01-06 doi:10.64898/2026.01.06.697933 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[ Optimizing Post-Transplantation Detection of Subcutaneously Transplanted Islets Using Dithizone Staining ]]> https://biorxiv.org/content/10.64898/2026.01.06.697969v1?rss=1 Lu, J. Ishahak, M. Maestas, M. M. Millman, J. R. 2026-01-07 doi:10.64898/2026.01.06.697969 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ Latent Regulatory Programs Generate Synthetic T Cell States with Enhanced Therapeutic Potential ]]> https://biorxiv.org/content/10.64898/2026.01.07.698190v1?rss=1 5,000-fold antigen-dependent expansion and antitumor activity, contrasting sharply with its native function in driving terminal differentiation. scGOF-seq further identified TF modules that cooperate with cMyc GOF to promote robust CD8 T cell responses in solid tumors. Together, these findings establish GOF perturbation as a powerful strategy for revealing latent immune regulatory programs and engineering synthetic immune states with therapeutic potential. One-Sentence SummaryIn vivo single-cell gain-of-function screening reveals latent transcriptional programs that can reprogram T cells into highly functional synthetic states. ]]> Pratt, B. M. Mullins, G. N. Brown, N. Green, W. D. Modliszewski, J. Xie, F. van Rooyen, L. Zhabotynsky, V. Jambor, A. N. Cannon, G. Green, J. M. Kennedy, A. Alicea Paunto, C. d. M. Shi, H. Merritt, E. Egawa, T. Somasundaram, A. Wang, W. Thaxton, J. E. Dotti, G. Chung, H. K. Milner, J. J. 2026-01-08 doi:10.64898/2026.01.07.698190 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Molecular Imaging of the TGF-β Activating Integrin αvβ6 Detects Chronic Lung Allograft Dysfunction ]]> https://biorxiv.org/content/10.64898/2026.01.07.698265v1?rss=1 Cano, M. Bathula, C. S. Liao, F. Wieczorek Villas Boas, C. Tao, Y. Liu, Z. Davis, V. Ebenezer, R. Cannady, A. Zhou, D. Liang, S. Byers, D. Krupnick, A. Kreisel, D. Dai, Z. Rogers, B. Gelman, A. E. 2026-01-08 doi:10.64898/2026.01.07.698265 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ High-throughput mapping of 6,888 RAD51D variants identifies distinct biochemical functions needed for homologous recombination and olaparib response ]]> https://biorxiv.org/content/10.64898/2026.01.11.698865v1?rss=1 Darrah, K. E. Hemker, S. L. Rawal, Y. Goff, N. J. Parker, P. Ganesan, G. Stratton, C. M. Oppenheimer, K. Roberts, E. Glick, E. Banks, N. Kumar, A. Casadei, S. Snyder, M. W. Nathanson, K. Domchek, S. M. Starita, L. M. Olsen, S. K. Sung, P. Kitzman, J. O. Bernstein, K. A. 2026-01-11 doi:10.64898/2026.01.11.698865 Cold Spring Harbor Laboratory Press 2026-01-11 <![CDATA[ Evolutionary conservation and innovations of RNA polymerase II transcription elongation factors ]]> https://biorxiv.org/content/10.64898/2026.01.11.698887v1?rss=1 Francette, A. M. Grover, A. Clark, N. Arndt, K. M. 2026-01-11 doi:10.64898/2026.01.11.698887 Cold Spring Harbor Laboratory Press 2026-01-11 <![CDATA[ Functional organization underlying superior performance in a memory champion ]]> https://biorxiv.org/content/10.64898/2026.01.11.698919v1?rss=1 13 hours fMRI). Relative to controls, the Memory Champions network functional connectivity (FC) was strengthened with the retrosplenial, extrastriate visual, and dorsal frontal cortex (area 55b), as well as with the caudate nucleus. The Memory Champion had modules related to scene and semantic processing not seen in controls, alongside stronger connectivity between the caudate and classical memory networks. During rote memorization, the Champions task fMRI patterns were typical, with the hippocampus active during encoding. This pattern was reversed when he used his Method of Loci technique, with greater hippocampal activity during recall than encoding. Hence, intense practice at converting abstract information into more memorable formats can develop a procedural memory skill that utilizes brain regions typically reserved for navigation, language, social cognition, and associative learning. ]]> Chauvin, R. J. Zheng, A. Metoki, A. Krimmel, S. R. Nielsen, A. N. Wang, A. Cho, P. N. Baden, N. J. Bower, D. Scheidter, K. M. Monk, J. S. Whiting, F. I. Adeyemo, B. Marek, S. Kay, B. P. Roediger, H. L. McDermott, K. Nelson, S. M. Gilmore, A. W. Barch, D. M. Laumann, T. O. Gordon, E. M. Dosenbach, N. U. 2026-01-12 doi:10.64898/2026.01.11.698919 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ Simultaneous Real-time Imaging of Neurofluid and Neurovascular Dynamics Using Ultrafast Flow-weighted Echo-Planar Imaging ]]> https://biorxiv.org/content/10.64898/2026.01.15.699612v1?rss=1 Shaker, A. H. Arani, A. H. G. Martin, B. A. Sotiras, A. Eldeniz, C. Shimony, J. S. Limbrick, D. D. Strahle, J. M. Nazeri, A. 2026-01-16 doi:10.64898/2026.01.15.699612 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ dgiLIT: A Method for Prioritization and AI Curation of Drug-Gene Interactions ]]> https://biorxiv.org/content/10.64898/2026.01.16.699733v1?rss=1 Cannon, M. J. Bratulin, A. Stevenson, J. S. Perry, K. Coffman, A. Kiwala, S. Schimmelpfennig, L. Costello, H. McMichael, J. F. Griffith, M. Griffith, O. L. Wagner, A. H. 2026-01-19 doi:10.64898/2026.01.16.699733 Cold Spring Harbor Laboratory Press 2026-01-19 <![CDATA[ Macrophage immunosenescence prolongs intraocular inflammation in aged mice via impaired induction of regulatory T cells ]]> https://biorxiv.org/content/10.64898/2026.01.15.697975v1?rss=1 Yamamoto, T. Hase, K. Lin, J. B. Yamaguchi, S. Misawa, N. Li, J. Kato, K. Terao, R. Sohn, B. S. Du, D. Yoshida, M. Pfeifer, C. W. Lee, T. J. Colasanti, J. Santeford, A. Walsh, J. T. Apte, R. S. 2026-01-20 doi:10.64898/2026.01.15.697975 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Ubiquitous functional synergy partially explains why most transcription factor binding is non-functional ]]> https://biorxiv.org/content/10.64898/2026.01.19.700460v1?rss=1 Mateusiak, C. Jia, E. Plaggenberg, J. N. Erdenebaatar, Z. Wang, Y. Shively, C. Liao, G. Mitra, R. D. Brent, M. R. 2026-01-20 doi:10.64898/2026.01.19.700460 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Searching the Druggable Genome using Large Language Models ]]> https://biorxiv.org/content/10.64898/2026.01.18.700012v1?rss=1 Schimmelpfennig, L. E. Cannon, M. Cody, Q. McMichael, J. Coffman, A. Kiwala, S. Krysiak, K. J. Wagner, A. H. Griffith, M. Griffith, O. L. 2026-01-21 doi:10.64898/2026.01.18.700012 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Calcium interaction with Nav1.5 via FGF12A and CaM binding ]]> https://biorxiv.org/content/10.64898/2026.01.20.700379v1?rss=1 Woodbury, L. S. Li, A. Angsutararux, P. Marras, M. Wagner, E. Silva, J. R. 2026-01-21 doi:10.64898/2026.01.20.700379 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Strong sustained type I IFN signaling acts cell intrinsically to impair IFNγ responses and cause tuberculosis susceptibility ]]> https://biorxiv.org/content/10.64898/2026.01.19.700487v1?rss=1 Fattinger, S. A. Chavez, R. A. Witt, K. C. Parisi, B. Rodriguez, J. J. Turcotte, E. A. Brydon, E. C. Fairgrieve, M. R. Dhaliwal, H. Lee, A. Y. Kotov, D. I. Vance, R. E. 2026-01-22 doi:10.64898/2026.01.19.700487 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Viral Capsid-Membrane Interactions Propel Non-Brownian Movements of Non-enveloped Reoviruses during Entry ]]> https://biorxiv.org/content/10.64898/2026.01.21.700940v1?rss=1 Jiao, M. Cantrall, G. R. Yu, Y. Snyder, A. J. Abel, S. M. Danthi, P. Yu, Y. 2026-01-22 doi:10.64898/2026.01.21.700940 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Microtubules in Arabidopsis pollen tubes are oriented away from the tube apex and are actin-independent at the cortex ]]> https://biorxiv.org/content/10.64898/2026.01.21.700958v1?rss=1 Coomey, J. H. Gallup, E. R. Dixit, R. 2026-01-22 doi:10.64898/2026.01.21.700958 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ N-terminal phosphorylation inhibits Arabidopsis katanin and affects vegetative and reproductive development in opposite ways ]]> https://biorxiv.org/content/10.64898/2026.01.20.700631v1?rss=1 Ambastha, V. Burkart, G. Balkunde, R. Dixit, R. 2026-01-23 doi:10.64898/2026.01.20.700631 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Opposing regulation by Rev1 of DNA polymerase zeta activity on damaged versus undamaged DNA ]]> https://biorxiv.org/content/10.64898/2026.01.21.700666v1?rss=1 View larger version (10K): org.highwire.dtl.DTLVardef@9b40dorg.highwire.dtl.DTLVardef@10bf5d1org.highwire.dtl.DTLVardef@376ff4org.highwire.dtl.DTLVardef@1970db8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Bezalel-Buch, R. Stith, C. M. Makarova, A. V. Binz, S. K. Burgers, P. M. 2026-01-23 doi:10.64898/2026.01.21.700666 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ A cross-species single-cell epigenome kidney atlas identifies epithelial cells as a driver of epigenetic aging ]]> https://biorxiv.org/content/10.64898/2026.01.22.700871v1?rss=1 Jeong, H. Lake, B. B. Diep, D. Li, X. Yan, Q. Gisch, D. L. Reinert, S. Eadon, M. T. Gaut, J. P. Jain, S. Zhang, K. 2026-01-23 doi:10.64898/2026.01.22.700871 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Virtual prototyping of non-invasive spinal cord electrical stimulation targeting upper limb motor function ]]> https://biorxiv.org/content/10.64898/2026.01.22.701010v1?rss=1 Alashqar, A. Brihmat, N. Gemar, V. Hu, Z. Koh, S.-R. Diaz-Pier, S. de Freitas, R. Sasaki, A. Milosevic, M. Keesey, R. Seanez, I. Neufeld, E. Cassoudesalle, H. Hofstötter, U. Minassian, K. Wagner, F. Rowald, A. 2026-01-24 doi:10.64898/2026.01.22.701010 Cold Spring Harbor Laboratory Press 2026-01-24 <![CDATA[ A bireporter recombinant SARS-CoV-2 Omicron BA.5 for in vitro and in vivo studies ]]> https://biorxiv.org/content/10.64898/2026.01.24.700018v1?rss=1 Castro, E. Barre, R. Ye, C. Imbiakha, B. Ezzatpour, S. Cupic, A. Walter, M. R. Kobie, J. Plemper, R. K. Garcia-Sastre, A. Mostafa, A. Aguilar, H. Martinez-Sobrido, L. 2026-01-26 doi:10.64898/2026.01.24.700018 Cold Spring Harbor Laboratory Press 2026-01-26 <![CDATA[ Sonogenetic control of cardiomyocytes and cardiac pacing using exogenous Transient Receptor Potential A1 channels ]]> https://biorxiv.org/content/10.64898/2026.01.24.701376v1?rss=1 Zhang, L. Zhang, J. Wang, T.-M. Walsh, C. Sheikh, F. Chalasani, S. H. Friend, J. 2026-01-26 doi:10.64898/2026.01.24.701376 Cold Spring Harbor Laboratory Press 2026-01-26 <![CDATA[ Trophoblast ferroptosis restricts SARS-CoV-2 spread in the placenta ]]> https://biorxiv.org/content/10.64898/2026.01.26.701742v1?rss=1 McColl, E. Kumar, D. U. Jones, B. Marks, N. Diveley, E. Karvas, R. Theunissen, T. Kelly, J. Mysorekar, I. U. 2026-01-26 doi:10.64898/2026.01.26.701742 Cold Spring Harbor Laboratory Press 2026-01-26 <![CDATA[ Synaptopodin enables directional mechanoadaptation of integrin-based adhesions ]]> https://biorxiv.org/content/10.64898/2026.01.25.701551v1?rss=1 Qu, C. Huang, Y. Jiang, S. Peng, X. Huang, Y.-Y. Puapatanakul, P. Xue, Z. Brathwaite, K. Langner, E. Penn, E. Espinosa, H. D. Halabi, C. M. Elson, E. L. Miner, J. H. Genin, G. M. Suleiman, H. Y. 2026-01-27 doi:10.64898/2026.01.25.701551 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Pleistocene climatic oscillations impact the diversification of deer mice (Peromyscus maniculatus) and the independent evolution of ecotypes ]]> https://biorxiv.org/content/10.64898/2026.01.26.699144v1?rss=1 Boria, R. A. Wooldridge, B. Kautt, A. F. Ashing-Giwa, K. F. McFadden, S. P. Kirby, C. Edwards, S. V. Hoekstra, H. E. 2026-01-27 doi:10.64898/2026.01.26.699144 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Modulation of Avian Iridescence via Malanogenesis ]]> https://biorxiv.org/content/10.64898/2026.01.26.701322v1?rss=1 Barbosa, S. Bittner, C. Arbore, R. Araujo, P. Pereira, P. Andrade, P. Fekete, C. Afonso, R. Afonso, S. Amorim, M. Marques, C. Nicolai, M. Carita, J. Brejcha, J. Lopes, R. Alves, J. Cruz, F. Gomez-Garrido, J. Zamarreno, C. Gut, M. Alyoto, T. Ali, M. Hilpert, A. Hech, A. Spiecker, E. Zubiri, B. A. Ito, S. Wakamatsu, K. Andersson, L. Corbo, J. Vogel, N. Carneiro, M. 2026-01-27 doi:10.64898/2026.01.26.701322 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Preventing Data Leakage in Neural Decoding ]]> https://biorxiv.org/content/10.64898/2026.01.26.701583v1?rss=1 Wong, R. Zhu, S. I. McCullough, M. H. Goodhill, G. J. 2026-01-27 doi:10.64898/2026.01.26.701583 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Multi-omics integration of malignant peripheral nerve sheath tumors identifies potential targets based on chromosome 8q status ]]> https://biorxiv.org/content/10.64898/2026.01.26.701599v1?rss=1 Garana, B. Wang, J. J. Acar, S. Oztosun, G. Makri, S. C. Borcherding, D. C. Zou, Y. Hutchinson-Bunch, C. Gritsenko, M. A. Piehowski, P. Pratilas, C. A. Hirbe, A. Gosline, S. J. 2026-01-27 doi:10.64898/2026.01.26.701599 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ tRF-3021a, a tRNA-Ala-TGC derived 3' fragment, promotes glioblastoma cell invasion, suppresses apoptosis, and is required for normal levels of protein synthesis ]]> https://biorxiv.org/content/10.64898/2026.01.26.701835v1?rss=1 Esmaeili, F. Bannerjee, K. Chatrath, A. Sahu, D. Shibata, Y. Saha, S. Kumar, P. Su, Z. Dutta, A. 2026-01-28 doi:10.64898/2026.01.26.701835 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ Multi-omics Differential Inference for Functional Interpretation (MoDIFI): A Statistical Framework to Prioritize Cell Lines for Neurodevelopmental Variants ]]> https://biorxiv.org/content/10.64898/2026.01.29.702065v1?rss=1 VR, A. Shaw, G. T.-W. Manuel, J. Mosbruger, T. L. Heins, H. Ng, J. K. Kim, H. Hayeck, T. J. Turner, T. N. 2026-01-29 doi:10.64898/2026.01.29.702065 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ Indole-3-acetic acid production is rare among gut bacteria and reflects OFOR-driven amino acid oxidation in acetogens ]]> https://biorxiv.org/content/10.64898/2026.01.29.702580v1?rss=1 DeFeo, M. E. Liu, Y. Zhou, Z. Higginbottom, S. K. Dodd, D. 2026-01-29 doi:10.64898/2026.01.29.702580 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ AADAT-Driven Metabolic Control of Malate and CoQ10 Shapes Immune Evasion in Triple-Negative Breast Cancer ]]> https://biorxiv.org/content/10.64898/2026.01.28.702389v1?rss=1 Chatterjee, M. Gu, F. Samanta, S. Rasaily, U. Thota, S. M. Varghese, D. Qiu, Y. Fordwuo, L. E. E. Villanueva, H. McKenna, M. K. Park, J. H. Zhang, W. Tian, L. Yu, L. Piyarathna, B. Gao, Y. Simons, B. W. Jung, S. Y. Karanam, B. Putluri, V. chandandeep, N. Mohamed, N. Asirvatham, J. R. Jebakumar, D. Rao, A. Gutierrez, C. Omilian, A. R. Morrison, C. Das, G. M. Ambrosone, C. Seeley, E. H. Kaipparettu, B. A. Kurland, I. J. Putluri, N. Elkhanany, A. Davis, A. Zhu, Q. Zhang, X. H. Sreekumar, A. 2026-01-30 doi:10.64898/2026.01.28.702389 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ An Integrated Single-Cell and Epigenomic Resource for Comparative Analysis of the Basal Ganglia ]]> https://biorxiv.org/content/10.64898/2026.01.29.702575v1?rss=1 Zhang, W. Ding, W. Li, K. Chang, L. Klein, A. Baez-Becerra, C. T. Rink, J. A. Bartlett, A. Chen, H. Schenker, N. Johansen, N. Mollenkopf, T. Fu, Y. Yang, X. Liu, S. Seng, C. Miao, B. Liu, T. Zhu, Q. Hodge, R. D. Bakken, T. E. Lein, E. S. Hawrylycz, M. Xu, X. Behrens, M. M. Ren, B. Ecker, J. R. Wang, T. Li, D. 2026-01-30 doi:10.64898/2026.01.29.702575 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Single-cell transcriptomic atlas of glial cells in adult mouse dorsal root ganglia identifies multipotent progenitors ]]> https://biorxiv.org/content/10.64898/2026.01.29.702614v1?rss=1 Meriau, P. Thomsen, M. B. Avraham, O. Trauterman, B. Cavalli, V. 2026-01-30 doi:10.64898/2026.01.29.702614 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Quantifying biomarker ambiguity using metabolic network analysis ]]> https://biorxiv.org/content/10.64898/2026.01.29.702649v1?rss=1 Hinkston, M. A. Bradley, A. S. 2026-02-02 doi:10.64898/2026.01.29.702649 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ cGAS-mediated IFN-I signaling contributes to disease progression in drug-refractory epilepsy ]]> https://biorxiv.org/content/10.64898/2026.01.30.702860v1?rss=1 Huang, Y. Fan, L. Wong, M. Y. Lei, Z. Krishnamachary, B. Zhu, D. Cadiz, M. Nagiri, R. K. Ye, P. Norman, K. Bhagwat, M. Lee, Y. J. Li, H. Zhu, J. Amin, S. Lauderdale, K. Chen, H. Luo, W. Gong, S. Liechty, B. L. Palop, J. J. Sinha, S. C. Wu, J. Zhao, M. Gan, L. 2026-02-02 doi:10.64898/2026.01.30.702860 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Polyploid cardiomyocytes define disease-specific transcriptional states in the mammalian heart ]]> https://biorxiv.org/content/10.64898/2026.01.31.701472v1?rss=1 Kiessling, P. Joodaki, M. Pikulska, D. Scheidereit, E. Cesaro, G. Ruiz, M. Kuehn, D. Peng, K. Goni, O. Foecking, S. Samiei, S. Liao, X. Li, K. Feng, Z. Wang, D. Mavrommatis, L. Vllaho, A.-M. Rombach, M. Cucinella, G. Cheng, M. Lautenschlaeger, T. Morales, D. R. Veltrop, R. J. A. Schurgers, L. J. von Scheidt, M. Klinkhammer, B. M. Kahles, F. Kranz, J. Aguirre, A. Loft, A. Kluemper, N. Eckstein, M. Seidel, T. Forte, G. Westland, R. Zhang, M. Zhao, H. Ren, F. Hayat, S. Amrute, J. M. Kopecky, B. Schneider, R. Medyouf, H. Tharaux, P.-L. Boor, P. Kramann, 2026-02-03 doi:10.64898/2026.01.31.701472 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Crystalline guanine packed within vacuoles serves as nitrogen store in Chromera velia ]]> https://biorxiv.org/content/10.64898/2026.01.31.703024v1?rss=1 Gonepogu, V. G. Pilatova, J. Ennaceur, D. Tomcala, A. Vancova, M. Richtova, J. Roth, R. Goodenough, U. Obornik, M. Mojzes, P. Gruber, A. 2026-02-03 doi:10.64898/2026.01.31.703024 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ SLC33A1 exports oxidized glutathione to maintain endoplasmic reticulum redox homeostasis ]]> https://biorxiv.org/content/10.64898/2026.02.01.703113v1?rss=1 Birsoy, K. Liu, S. Gad, M. Li, C. Cho, K. Liu, Y. Wangdu, k. Belay, V. Millet, A. Kojima, H. Sanford, H. Wolk, M. Urnavicius, L. Fedorova, M. Patti, G. J. J. Vinogradova, E. V. Hite, R. K. 2026-02-03 doi:10.64898/2026.02.01.703113 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Single-Cell Proteomics of Human Peripheral Blood Mononuclear Cells Exceeding 600 Cells per Day ]]> https://biorxiv.org/content/10.64898/2026.02.01.703169v1?rss=1 Fulcher, J. M. Kwon, Y. Dawar, P. Kumar, R. Williams, S. M. Miller, P. Liyu, A. Chen, L. Orton, D. J. Olson, H. M. Yu, F. Nesvizhskii, A. I. Fortier, J. Vij, R. Jayasinghe, R. Ding, L. Zhu, Y. Pasa-Tolic, L. 2026-02-03 doi:10.64898/2026.02.01.703169 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain ]]> https://biorxiv.org/content/10.64898/2026.02.02.703166v1?rss=1 750,000 nuclei spanning 160 cell types and integrate these data with chromatin accessibility, DNA methylation, 3D genome architecture, and spatial transcriptome. This framework annotates >500,000 regulatory elements and resolves cell-type-specific chromatin states. We link enhancers to target genes, infer gene regulatory networks, and classify chromatin interactions, revealing neuron-enriched long-range Polycomb repression of developmental genes. Integrating these maps with GWAS data and sequence-based model prioritizes noncoding variants, effector genes, and vulnerable cell types for neuropsychiatric disorders. Finally, cross-species comparisons show conserved activation but more divergent repression. Together, this study provides a functional reference for interpreting noncoding variants, epigenetic memory, and brain organization. HIGHLIGHTSO_LIJoint single-cell profiling of transcriptomes with active or repressive histone modification in >750,000 nuclei across adult human brain. C_LIO_LIChromatin state annotation of >500,000 candidate cis-regulatory elements distinguishes active enhancers from accessible and Polycomb-repressed regions. C_LIO_LICell-type-resolved regulatory networks and sequence-based deep learning model prioritize functional neuropsychiatric risk variants. C_LIO_LISpatial epigenomic imputation reveals laminar layer-specific Polycomb repression programs. C_LIO_LIIntegration with 3D genome architecture reveals neuron-specific super long-range chromatin loops silencing early developmental genes. C_LIO_LIEvolutionary analysis uncovers conserved active regulatory grammar but divergent repressive landscape. C_LI ]]> Xie, Y. Chang, L. Zhong, G. Rink, J. A. Baez-Becerra, T. Armand, E. Ding, W. Li, K. Boone, E. Lie, A. Indralingam, H. S. Dong, K. Loe, T. Huang, B. Wang, Z. Barcoma, A. S. Willier, J. K. Knutson, K. W. Liu, J. Cho, S. Cao, S. Russo, K. G. Young, C. K. Arzavala, J. Sanchez, Y. Bikkina, A. Schenker-Ahmed, N. Kern, C. Zhao, Z. Klein, A. Flores, J. Tai, C.-Y. Olness, J. Monell, A. Moghadami, S. Barragan, C. Chen, C. Owens, W. OConnor, C. Liem, M. Marrin, M. V. Rose, C. Alt, S. N. Emerson, N. Osteen, J. Lucero, J. Li, D. Hodge, R. D. Wang, T. Keene, 2026-02-03 doi:10.64898/2026.02.02.703166 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ An immune-poised state of human bronchial epithelial cells mediates RSV resistance in adults ]]> https://biorxiv.org/content/10.64898/2026.02.02.703395v1?rss=1 Zhao, C. Bai, Y. Mou, H. Lerou, P. H. Leung, D. W. Narasimhan, H. Wei, X. Sun, J. Xu, J.-F. Fearns, R. Ai, X. 2026-02-03 doi:10.64898/2026.02.02.703395 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Metabolic Flexibility and Energy Substrate Utilization Regulate Contractility in the Human Myometrium ]]> https://biorxiv.org/content/10.64898/2026.02.02.702681v1?rss=1 Prifti, K. K. Dave, R. M. Mitchum, K. T. Rich, J. L. Gill, R. M. Mbadhi, M. N. Frolova, A. I. 2026-02-04 doi:10.64898/2026.02.02.702681 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ The orientation of cholesterol's hydroxyl group affects its membrane dynamics and intracellular transport ]]> https://biorxiv.org/content/10.64898/2026.02.02.703222v1?rss=1 Lauritsen, L. Pauli, A. T. Larsen, M. P. W. Reinholdt, P. Scheidt, H. A. Xu, Y. Covey, D. F. Depta, L. Bryce-Rogers, H. P. Laraia, L. Kongsted, J. Wüstner, D. 2026-02-04 doi:10.64898/2026.02.02.703222 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Molecular and Cellular Determinants of Human Iron Overload Cardiomyopathy ]]> https://biorxiv.org/content/10.64898/2026.02.02.703307v1?rss=1 Modak, S. Greenberg, L. Stump, W. T. Greenberg, A. E. Huebsch, N. Greenberg, M. J. 2026-02-04 doi:10.64898/2026.02.02.703307 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Single-cell Multiome Analysis of Chromatin State and Transcriptome in the Human Basal Ganglia ]]> https://biorxiv.org/content/10.64898/2026.02.03.703645v1?rss=1 Chang, L. Li, K. Xie, Y. Zhong, G. Rink, J. A. Baez-Becerra, C. T. Lie, A. Indralingam, H. S. Dong, K. Loe, T. Wang, Z. Zu, S. Kern, J. C. Zhao, Z. Boone, E. Flores, J. Monell, A. Olness, J. Barragan, C. Osgood, E. Owens, W. Schenker-Ahmed, N. Zhang, W. Liu, D. Barcoma, A. S. Willier, J. K. Knutson, K. W. Russo, K. G. Liu, J. Cho, S. Arzavala, J. Young, C. K. Sundaram, G. V. Manning, A. C. Sanchez, Y. Bikkina, A. Berry, J. Gao, X. OConnor, C. Liem, M. Marrin, M. V. Rose, C. Alt, S. N. Zhu, C. Zemke, N. R. Ding, W. Klein, A. Fu, Y. Johansen, N. B 2026-02-04 doi:10.64898/2026.02.03.703645 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Automated Ventricle Assessment via Three-dimensional Anatomical Reconstruction (AVA-TAR): a computational toolkit for autonomous lateral ventricle assessment in preclinical hydrocephalus models ]]> https://biorxiv.org/content/10.64898/2026.02.02.703412v1?rss=1 Chakladar, S. Pan, S. Limbrick, O. Pandey, M. Halupnik, G. L. Zhao, A. Mahjoub, M. R. Quirk, J. D. Nazeri, A. Strahle, J. M. 2026-02-05 doi:10.64898/2026.02.02.703412 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ Non-invasive genomic sampling uncovers novel connectivities and origins of confiscated gorillas ]]> https://biorxiv.org/content/10.64898/2026.02.03.701083v1?rss=1 Ruiz-Gartzia, I. Pawar, H. Alvarez-Estape, M. Orkin, J. D. Alentorn-Moron, P. Ruibal-Puertas, S. Ostridge, H. J. Fontsere, C. Cuadros-Espinoza, S. Gilardi, K. Nziza, J. Muvunyi, R. Maloueki, U. Caillaud, D. Iyer, N. Ngobobo-As-Ibungu, U. Binyinyi, E. Akomo-Okoue, E. F. Basabose, A. K. Sebulimbwa, K. Ngomanda, A. Yamagiwa, J. Inoue-Murayama, M. Takenoshita, Y. Fujita, S. Pafco, B. Fuh, T. Tagg, N. Mbohli, D. Ayimisin, E. A. Bailey, E. Bessone, M. Deschner, T. Dieguez, P. Dilambaka, E. Dunn, A. Granjon, A.-C. Head, J. Hermans, V. Imong, I. Jeffery, K. J. 2026-02-05 doi:10.64898/2026.02.03.701083 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ SWI/SNF nuclear foci scaffold peripheral gene hubs for circadian chromatin control ]]> https://biorxiv.org/content/10.64898/2026.02.03.703661v1?rss=1 Chen, Q. Yuan, Y. Clark, D. Yadlapalli, S. 2026-02-06 doi:10.64898/2026.02.03.703661 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ Transient activation of potent progenitor cells is required for spinal cord regeneration ]]> https://biorxiv.org/content/10.64898/2026.02.04.703854v1?rss=1 Weinholtz, C. A. Zhou, L. Saraswathy, V. Xu, Y. Shaw, D. K. McAdow, A. R. Park, D. Shin, J. Solnica-Krezel, L. Johnson, A. N. Mokalled, M. 2026-02-07 doi:10.64898/2026.02.04.703854 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ Highly Sensitive Chemigenetic FRET-Based Kinase Biosensors ]]> https://biorxiv.org/content/10.64898/2026.02.06.702961v1?rss=1 He, X. Zhou, D. R. Huan, Y. Berriman-Rozen, Z. Mehta, S. Chen, Y. Frei, M. S. Zhang, J. 2026-02-09 doi:10.64898/2026.02.06.702961 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Divergent phenotypic and functional roles of human T follicular helper cells from infancy to adulthood ]]> https://biorxiv.org/content/10.64898/2026.02.06.704464v1?rss=1 Sureshchandra, S. Kastenschmidt, J. M. Joloya, E. M. Wagoner, Z. W. Nair, A. K. Kim, S. Zane, N. Bhattacharya, G. Monterroso, A. M. Cheng, E. Sorn, A. M. Mitul, M. T. Beares, H. Mendez, G. Yates, T. B. Zhou, F. Daugherty, A. Thakur, C. Brokstad, K. A. Trask, D. Ahuja, G. Zhong, Q. Saligrama, N. Cox, R. J. Wagar, L. E. 2026-02-09 doi:10.64898/2026.02.06.704464 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Mitochondrial genomes of individual microfilariae: Undescribed Dirofilaria-like filariae from Malaysian cats and two filaria species related to Dirofilaria and Mansonella from Indonesian macaques ]]> https://biorxiv.org/content/10.64898/2026.02.09.704775v1?rss=1 Diekmann, I. Choi, Y.-J. Supali, T. Rahmat, A. Destani, Y. Iskandar, E. Sugianto, N. Mutlip, M. H. A. Aziz, N. A. A. Ibrahim, K. Fischer, K. Mitreva, M. Fischer, P. U. 2026-02-09 doi:10.64898/2026.02.09.704775 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ In virio secondary RNA structure analysis of influenza A virus ]]> https://biorxiv.org/content/10.64898/2026.02.09.704913v1?rss=1 Joshi, A. Huang, L.-C. Boon, A. 2026-02-09 doi:10.64898/2026.02.09.704913 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ When attention falters: brain, breathing, and behavioral signals of lapses in interoceptive attention ]]> https://biorxiv.org/content/10.64898/2026.02.07.704566v1?rss=1 0.75). Breathing variability and breathing-behavior coupling showed smaller but generalizable predictive value (AUCs < 0.65). Whole-brain connectivity models also predicted lapses (AUC {approx} 0.65) and incorporated regions within the DMN, dorsal, and ventral attention networks--overlapping with systems implicated in exteroceptive attention-- as well as the somatomotor network. Further, models that included brain connectivity marginally outperformed behavior-only models. Together, these findings suggest that interoceptive lapses reflect both shared mechanisms with exteroceptive attention failures and additional contributions from brain systems involved in bodily representation and sensory pathways. Although generalizability is limited by the clinical sample and absence of an exteroceptive comparison task, these results highlight candidate brain-body markers of interoceptive attention that may inform real-time monitoring during mind-body interventions and improve understanding of interoceptive disturbance in affective disorders. ]]> Treves, I. N. Shaffer, C. Decker, A. Jaffe, N. Tierney, A. O. Auerbach, R. P. Webb, C. A. 2026-02-10 doi:10.64898/2026.02.07.704566 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ thematicGO: A Keyword-Based Framework for Interpreting Gene Ontology Enrichment via Biological Themes ]]> https://biorxiv.org/content/10.64898/2026.02.08.704666v1?rss=1 Wang, Z. Sudlow, L. C. Du, J. Berezin, M. Y. 2026-02-10 doi:10.64898/2026.02.08.704666 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ PEhub resolves the hierarchical regulatory architecture of multi-way enhancer hubs in the human brain ]]> https://biorxiv.org/content/10.64898/2026.02.09.704931v1?rss=1 Tan, J. Sun, Y. 2026-02-10 doi:10.64898/2026.02.09.704931 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ A framework for reparative CAR T engineering in the CNS ]]> https://biorxiv.org/content/10.64898/2026.02.09.703122v1?rss=1 Shalita, R. Ben Yehuda, M. Boskovic, P. Frid, Y. Kuznetsov, Y. Tsoory, M. Kalchenko, V. Brenner, O. David, E. Mazuz, K. Majzner, R. G. Kipnis, J. Amit, I. 2026-02-11 doi:10.64898/2026.02.09.703122 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ Ancient DNA reveals early use of melons in China's Song Dynasty ]]> https://biorxiv.org/content/10.64898/2026.02.10.704887v1?rss=1 Walker-Hale, N. Zheng, Y. Perez-Escobar, O. A. Bendahmane, A. Preick, M. Westbury, M. V. Hofreiter, M. Schaefer, H. Liu, X. Chomicki, G. Renner, S. S. 2026-02-11 doi:10.64898/2026.02.10.704887 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ A cell-nonautonomous heme acquisition pathway enables erythroid hemoglobinization under stress ]]> https://biorxiv.org/content/10.64898/2026.02.10.705195v1?rss=1 Belot, A. Rock, A. Dutt, S. Haemmerle, G. Maros, A. Yuan, X. Otsuru, S. Bodine, D. Hamza, I. 2026-02-11 doi:10.64898/2026.02.10.705195 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ Cellular Aging Signatures in the Plasma Proteome Record Human Health and Disease ]]> https://biorxiv.org/content/10.64898/2026.02.10.704909v1?rss=1 Ding, D. Y. Bot, V. A. Chen, K. L. Groves, J. Palovics, R. Masuda, D. Farinas, A. Oh, H. S.-H. Wagner, V. Lu, N. The Global Neurodegeneration Proteomics Consortium (GNPC), Cruchaga, C. Isakova, A. Schott, J. M. Wyss-Coray, T. 2026-02-12 doi:10.64898/2026.02.10.704909 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ MassID provides near complete annotation of metabolomics data with identification probabilities ]]> https://biorxiv.org/content/10.64898/2026.02.11.704864v1?rss=1 4,000 metabolites (including >1,200 compounds at an FDR <5%) across four complementary LC/MS runs, and enables integrated downstream analyses to understand biochemical dysregulation at both the molecular and pathway level. When compared to the Metabolomics Standards Initiative (MSI) confidence levels, identification probability generally correlated with MSI levels. However, only 356/418 of MSI Level 1 compounds were identified with <5% FDR and the remaining 884 FDR < 5% compounds were identified from MSI L2-L3 compounds, highlighting the enhanced specificity and discovery potential achieved by MassID. ]]> Stancliffe, E. Gandhi, M. Guzior, D. V. Mehta, A. Acharya, S. Richardson, A. D. Cho, K. Cohen, T. Patti, G. J. 2026-02-14 doi:10.64898/2026.02.11.704864 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Intellectual disability risk gene RFX4 regulates cortical neurogenesis by restraining neuronal differentiation ]]> https://biorxiv.org/content/10.64898/2026.02.11.705165v1?rss=1 Kroll, K. L. Determan, J. J. Chapman, G. Crump, S. R. Batool, F. Malik, S. Gujral, T. Buchser, W. Valentine, C. Elia, S. Sentmanat, M. Jetter, H. 2026-02-14 doi:10.64898/2026.02.11.705165 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ A Multimodal Single-Cell Epigenomic and 3D Genome Atlas of the Human Basal Ganglia ]]> https://biorxiv.org/content/10.64898/2026.02.12.705594v1?rss=1 Ding, W. Klein, A. Baez-Becerra, C. T. Rink, J. A. Bartlett, A. Zeng, Q. Wang, R. Castanon, R. G. Nery, J. R. Osgood, E. Owens, W. Petrella, A. Chen, C. Acerbo, A. S. Barcoma, A. S. Liu, J. Russo, K. G. Knutson, K. W. Young, C. K. Willier, J. K. Barragan, C. Arzavala, J. Cho, S. Altshul, J. Chan, D. Soma, E. Luo, J. Jain, M. Velazquez, S. Schenker-Ahmed, N. Sundaram, G. V. Manning, A. C. Sanchez, Y. Bikkina, A. Fu, S. OConnor, C. Liem, M. Marrin, M. V. Rose, C. Alt, S. N. Berry, J. Kern, C. Boone, E. Tian, W. Wu, Y. Hariharan, M. Fu, Y. Xie, Y. L 2026-02-14 doi:10.64898/2026.02.12.705594 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Satellite Glial Cells Control Sensory Neuron Excitability via the Release of Fibulin-2 ]]> https://biorxiv.org/content/10.64898/2026.02.13.705760v1?rss=1 Ansari, I. Deng, P.-Y. Rosen, S. F. Thomsen, M. B. Klyachko, V. A. Cavalli, V. 2026-02-16 doi:10.64898/2026.02.13.705760 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ Fully T2T pedigree assemblies reveal genetic stability and epigenetic plasticity of human centromeres across inheritance and cell-fate transitions ]]> https://biorxiv.org/content/10.64898/2026.02.14.705860v1?rss=1 Dong, S. Xing, X. Cechova, M. Loucks, H. Vijayalingam, S. Neilson, A. Sentmanat, M. Macias-Velasco, J. F. Liu, T. Dong, Z. Miao, B. Zhang, W. Tomlinson, C. Schmidt, H. Belter, E. A. Hu, M. Cui, X. Stitziel, N. O. Miga, K. H. Wang, T. 2026-02-17 doi:10.64898/2026.02.14.705860 Cold Spring Harbor Laboratory Press 2026-02-17 <![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[ Pioneer and Altimeter: Fast Analysis of DIA Proteomics Data Optimized for Narrow Isolation Windows ]]> https://biorxiv.org/content/10.64898/2026.02.16.706201v1?rss=1 Wamsley, N. T. Wilkerson, E. M. Major, M. Goldfarb, D. 2026-02-18 doi:10.64898/2026.02.16.706201 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Mechano-activation of synovial fibroblasts and macrophages during OA progression in the dynamically stiffening synovial microenvironment ]]> https://biorxiv.org/content/10.64898/2026.02.16.706240v1?rss=1 Kim, S. Y. Farrell, E. Burt, K. G. Kwok, B. Liang, Q. Knights, A. J. Sharp, K. Nguyen, V. Murphy, L. A. Hu, B. Kahn, A. Qin, L. Han, L. Maerz, T. Mauck, R. Scanzello, C. R. 2026-02-18 doi:10.64898/2026.02.16.706240 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Phylogenetic estimation of diversity-dependent biogeographic rates using deep learning ]]> https://biorxiv.org/content/10.64898/2026.02.17.706216v1?rss=1 Soewongsono, A. C. Landis, M. J. 2026-02-18 doi:10.64898/2026.02.17.706216 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Kinetics of local C3 production orchestrates neutrophil recruitment in lung injury ]]> https://biorxiv.org/content/10.64898/2026.02.17.706326v1?rss=1 Aponte Alburquerque, R. Hernandez, J. I. Nallapu, A. Starick, M. Etesami, N. Mukherjee, S. K. Ozanturk, A. N. Vazquez, J. Chang, A. Zheng, A. Garnica, L. Lopez, A. Gelman, A. E. Belperio, J. Lee, J. W. Kulkarni, D. H. Hoffmann, A. Kulkarni, H. S. 2026-02-18 doi:10.64898/2026.02.17.706326 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Fusion Loop Modified and Mature Dengue Virus Elicits Protective Serum with Minimal Antibody Dependent Enhancement ]]> https://biorxiv.org/content/10.64898/2026.02.18.706631v1?rss=1 Dalben, Y. R. Adler, J. J. Meganck, R. M. Duenas, K. Snoderly-Foster, L. J. Tse, L. V. 2026-02-19 doi:10.64898/2026.02.18.706631 Cold Spring Harbor Laboratory Press 2026-02-19 <![CDATA[ Hypoxic stress granules trigger immunogenic dormancy in lung cancer ]]> https://biorxiv.org/content/10.64898/2026.02.18.706626v1?rss=1 Smith, M. G. Ramos, A. R. Panchal, H. Cerkezi, N. H. Garcia, C. Spruce, L. Fazelinia, H. Maggi, L. B. Mailloux, A. W. 2026-02-20 doi:10.64898/2026.02.18.706626 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Discovery and dynamic pharmacology of μ-opioid receptor positive allosteric modulators ]]> https://biorxiv.org/content/10.64898/2026.02.20.707058v1?rss=1 O'Brien, E. S. Wang, J. Tanguturi, P. Li, M. White, E. Shiimura, Y. Paul, B. Appourchaux, K. Krishna Kumar, K. Huang, W. Majumdar, S. Traynor, J. R. Streicher, J. M. Chen, C. Kobilka, B. 2026-02-21 doi:10.64898/2026.02.20.707058 Cold Spring Harbor Laboratory Press 2026-02-21 <![CDATA[ Quantitative dissection of the metastatic cascade at single colony resolution ]]> https://biorxiv.org/content/10.64898/2026.02.20.706841v1?rss=1 Roberts, C. D. Xu, A. Fang, X. Visani, A. Peng, C.-W. Qin, X. Chan, I. C. C. Dunterman, M. Giles, D. A. You, Y. Guppy, I. Yang, Z. Kim, A. H. Stegh, A. H. Lu, G. Chen, F. Ding, L. Tang, R. 2026-02-23 doi:10.64898/2026.02.20.706841 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Zinc excess promotes lysosome remodeling by activating HLH-30/TFEB through the action of the high zinc sensor HIZR-1. ]]> https://biorxiv.org/content/10.64898/2026.02.22.707197v1?rss=1 Cubillas, C. Liu, H. Deshmukh, K. Mendoza, A. Schneider, D. L. Herrera, D. Zhao, C. Murphy, J. T. Edwards, J. Diwan, A. Kornfeld, K. 2026-02-24 doi:10.64898/2026.02.22.707197 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ A two-membrane gateway for monocarboxylates couples host glycolysis to Toxoplasma mitochondrial fitness and virulence ]]> https://biorxiv.org/content/10.64898/2026.02.23.707530v1?rss=1 Key, M. Joseph, S. Dou, Z. 2026-02-24 doi:10.64898/2026.02.23.707530 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ Hyperglycemia and hyperfibrinogenemia alter Staphylococcus aureus abscess community morphology, antimicrobial susceptibility, and virulence in vitro. ]]> https://biorxiv.org/content/10.64898/2026.02.25.707959v1?rss=1 Gill, S. R. Britt, E. A. Markle, L. K. Gill, A. L. Ricciardi, B. Bui, T. I. 2026-02-25 doi:10.64898/2026.02.25.707959 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ cGAS inhibition delays TDP-43-driven ALS Pathogenesis ]]> https://biorxiv.org/content/10.64898/2026.02.24.707791v1?rss=1 Liu, Y. Feng, W. Aikedan, A. A. Lee, S.-I. Bhagwat, M. Nagiri, R. K. Wong, M. Y. Amin, S. Qu, W. Zhu, J. Wang, S.-Y. Ye, P. Norman, K. Coronas-Samano, G. B. Olah, M. Tilgner, H. U. Sinha, S. Gan, L. 2026-02-26 doi:10.64898/2026.02.24.707791 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[ CD8+ T cells are primed by cDC1 and exacerbate tau-mediated neurodegeneration ]]> https://biorxiv.org/content/10.64898/2026.02.26.708260v1?rss=1 Hu, H. Lin, P. B.-c. Zeng, C. Sharma, P. Li, Y. Jiang, H. Nulman, J. Ohara, R. A. Wu, T. Li, S. Yokoyama, W. M. Artyomov, M. Murphy, K. M. Ulrich, J. D. Holtzman, D. 2026-03-01 doi:10.64898/2026.02.26.708260 Cold Spring Harbor Laboratory Press 2026-03-01 <![CDATA[ Glia regulate local retinoic acid levels to specify neuronal specialisation for high-acuity vision ]]> https://biorxiv.org/content/10.64898/2026.02.27.708512v1?rss=1 Lahne, M. Lungu, R. Snorton, M. Yoshimatsu, T. MacDonald, R. B. 2026-03-02 doi:10.64898/2026.02.27.708512 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ MANF Clears Mutant Uromodulin in Human Kidney Organoids of Autosomal Dominant Tubulointerstitial Kidney Disease ]]> https://biorxiv.org/content/10.64898/2026.03.02.708095v1?rss=1 Gu, C. Fang, Y. Wang, Y. Tycksen, E. Kondepati, G. Li, C. Kidd, K. Liu, J. Urano, F. Lindahl, M. Bleyer, A. J. Singamaneni, S. Sun, Z. Chen, Y. M. 2026-03-02 doi:10.64898/2026.03.02.708095 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ Minimum inoculum of resistance assay for evaluating for anti-toxoplasmosis compounds that target phenyl alanine tRNA synthetase ]]> https://biorxiv.org/content/10.64898/2026.03.02.709153v1?rss=1 108 parasites) in comparison with an inhibitor of DNA synthesis, and that MIR values vary across inhibitors with closely related chemical structures. Clonal analysis of resistant parasites emerging from MIR assays revealed both new and previously identified resistance conferring mutations in TgPheRS, and structural modeling revealed their potential impact the enzyme active site. The MIR assay provides a functional benchmark to compare new and existing inhibitors, allowing for rational prioritization of lead compounds with a high genetic barrier to resistance. ]]> Uddin, T. Mittal, P. Xie, H. Melillo, B. Sharma, A. Chatterjee, A. Sibley, L. D. 2026-03-03 doi:10.64898/2026.03.02.709153 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Large-scale Perturbation of Systems Biology-Derived Genes Reveals Modifiers of HD-associated Transcriptomic Networks and Pathology ]]> https://biorxiv.org/content/10.64898/2026.03.02.709091v1?rss=1 Langfelder, P. Wang, N. Ramanathan, L. Oh, Y. M. Lee, S. Gao, F. Gu, X. Stricos, M. Plascencia, M. Vaca, R. Richman, J. Vogt, T. F. Horvath, S. Yoo, A. S. Aaronson, J. Rosinski, J. Yang, X. W. 2026-03-04 doi:10.64898/2026.03.02.709091 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Defining the Antigenic Topology and Prospective Binding Breadth of Vaccination-induced SARS-CoV-2 Neutralizing Antibodies ]]> https://biorxiv.org/content/10.64898/2026.03.03.709398v1?rss=1 Jaiswal, D. Altomare, C. G. Adelsberg, D. C. Sapse, I. A. Krammer, F. Simon, V. Ellebedy, A. H. Bajic, G. 2026-03-04 doi:10.64898/2026.03.03.709398 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Force-modulated structural landscape of the catch bonding F-actin crosslinker α-actinin-4 ]]> https://biorxiv.org/content/10.64898/2026.03.04.709699v1?rss=1 Chin, A. C. Mukadum, F. Reynolds, M. J. Hocky, G. M. Alushin, G. M. 2026-03-06 doi:10.64898/2026.03.04.709699 Cold Spring Harbor Laboratory Press 2026-03-06 <![CDATA[ Transitory enhancement of GATA2 chromatin engagement during early erythroid differentiation ]]> https://biorxiv.org/content/10.64898/2026.03.05.709895v1?rss=1 5 s) binding. Surprisingly, early erythroid differentiation was characterized by a transitory strengthening of long-lived GATA2 chromatin engagement. This manifested as increased residence time of GATA2 bound to chromatin in G1E-ER4 cells and an expansion of the long-lived bound population in HPC7 cells and primary mouse progenitors. This transitory phase of enhanced engagement declined upon further differentiation. Genome-wide mapping identified regulatory elements selectively occupied by GATA2 during this early transition state, revealing promoter-proximal sites enriched for GATA/RUNX motifs and distal elements containing composite GATA/E-box signatures. Together, our imaging and chromatin profiling indicate that GATA2 chromatin engagement is kinetically remodeled at the onset of differentiation, with early recruitment targets partitioning into distinct promoter- and enhancer-associated subclasses. These results support a model in which transcription factor kinetics constitute a dynamic chromatin engagement layer that characterizes the GATA2-to-GATA1 transition. ]]> Hobbs, J. W. Taylor, S. J. Kumari, R. Haque, N. Victor, L. Steidl, U. Coleman, R. A. 2026-03-06 doi:10.64898/2026.03.05.709895 Cold Spring Harbor Laboratory Press 2026-03-06 <![CDATA[ Early Binding of Anti-Amyloid Antibodies to CAA Drives Complement Activation, Inflammation and ARIA in Mice ]]> https://biorxiv.org/content/10.64898/2026.03.04.709591v1?rss=1 View larger version (61K): org.highwire.dtl.DTLVardef@14e1950org.highwire.dtl.DTLVardef@5ffad6org.highwire.dtl.DTLVardef@14d19a5org.highwire.dtl.DTLVardef@ceb5d8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Bathini, P. Schilling, S. Rahfeld, J. U. Holtzman, D. M. Sado, T. C. Lemere, C. A. 2026-03-07 doi:10.64898/2026.03.04.709591 Cold Spring Harbor Laboratory Press 2026-03-07 <![CDATA[ Multi-omic profiling of human and mouse dorsal root ganglia enables targeted gene delivery to nociceptors ]]> https://biorxiv.org/content/10.64898/2026.03.05.709931v1?rss=1 He, L. S. Bhatia, P. Bhuiyan, S. A. Semizoglou, E. Wang, J. Li, J. Nam, J. Luo, X. J. Arnhold, C. Zhu, D. Xu, M. Griesemer, D. Yong, H. J. Jayne, L. Gilmer, E. Li, Q. Pantaleo, K. Yang, L. Williams, E. Jayakar, S. Wainger, B. Hrvatin, S. Renthal, W. 2026-03-09 doi:10.64898/2026.03.05.709931 Cold Spring Harbor Laboratory Press 2026-03-09 <![CDATA[ Lysosomal Expansion Compartments Mediate Zinc and Copper Homeostasis in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.64898/2026.03.05.709934v1?rss=1 Armendariz, J. R. Teng, S. Rakow, C. Herrera, R. Herrera, S. Gordon, M. T. Chen, S. Vogt, S. Liu, H. Jarvis, M. Reese, K. Pezacki, A. T. Chang, C. J. Kim, B.-E. Schneider, D. L. Mendoza, A. D. Kornfeld, K. 2026-03-09 doi:10.64898/2026.03.05.709934 Cold Spring Harbor Laboratory Press 2026-03-09 <![CDATA[ Spatial transcriptomics for gene discovery identifies Slc13a5 as a modulator of bone mechanoadaptation ]]> https://biorxiv.org/content/10.64898/2026.03.11.711126v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@14fc0e9org.highwire.dtl.DTLVardef@1023a16org.highwire.dtl.DTLVardef@133aa0eorg.highwire.dtl.DTLVardef@e19c86_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Meslier, Q. A. Beeve, A. T. Gupta, A. Palomo, D. Saleem, S. Eck, S. Lawson, L. Shuster, J. Brennan, M. Dirckx, N. Silva, M. J. Scheller, E. L. 2026-03-13 doi:10.64898/2026.03.11.711126 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Metabolites from plasma-like medium fuel nitrogen metabolism and influence proliferation in Leptospira interrogans ]]> https://biorxiv.org/content/10.64898/2026.03.12.711193v1?rss=1 Ward, M. H. Scherer, N. Shriver, L. P. Patti, G. J. 2026-03-13 doi:10.64898/2026.03.12.711193 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ TMEM106B mediates ACE2-independent replication of the SARS-CoV-2 S-E484D variant in airway-derived cell models ]]> https://biorxiv.org/content/10.64898/2026.03.14.711762v1?rss=1 Xia, M. Wang, Q. Puray-Chavez, M. LaPak, K. Palakurty, S. Liu, Z. Cornejo Pontelli, M. Hui, S. Fremont, D. H. Diamond, M. S. Whelan, S. P. J. Major, M. B. Goldfarb, D. Kutluay, S. B. 2026-03-15 doi:10.64898/2026.03.14.711762 Cold Spring Harbor Laboratory Press 2026-03-15 <![CDATA[ High-channel-count neural recording and stimulation platform with 5,376 simultaneous recording channels ]]> https://biorxiv.org/content/10.64898/2026.03.13.709972v1?rss=1 1.3 Gb/s total data streaming throughput. The ASIC incorporates in-pixel amplification, time-division multiplexed ADCs, and on-chip stimulation capabilities, ensuring precise signal acquisition with minimal power consumption while maintaining a low noise level of 5.5 {micro}Vrms. We further developed an interconnect strategy using gold bump bonding, which allows for high-density integration of the flexible probe and rigid chip. We demonstrate the capacity of this platform through the integration with a flexible ECoG array. The resulting device allows for the high-resolution mapping of in vivo field potentials on the cortical surfaces of rat brains, supported by the precise localization of evoked sensory activities. These results prove an effective approach towards highly integrated neural interfaces with applications in brain-computer interfaces, neuroprosthetics, and large-scale functional brain mapping. ]]> Fan, Y. Ma, Y. Zolotavin, P. Topalli, G. Wang, W. Karlsson, M. Karlsson, M. Luan, L. Xie, C. Chi, T. 2026-03-17 doi:10.64898/2026.03.13.709972 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ C9ORF72-derived polyGR polypeptides disrupt passive nucleocytoplasmic transport by tuning protein affinity for the nuclear pore barrier ]]> https://biorxiv.org/content/10.64898/2026.03.16.711670v1?rss=1 Solomon, D. A. Emenecker, R. J. Salcher-Konrad, M.-T. Konstantinidou, S. M. Houghton, O. H. Wycherley, E. Lee, S. O'Brien, N. L. Alcalde, J. Lourenco Cabaco, I. Ruepp, M.-D. Schmidt, H. B. Holehouse, A. S. Mizielinska, S. 2026-03-17 doi:10.64898/2026.03.16.711670 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[ VICAST: An Integrated Toolkit for Viral Genome Annotation Curation and Low-Frequency Variant Analysis in Passage Studies ]]> https://biorxiv.org/content/10.64898/2026.03.16.712174v1?rss=1 Handley, S. A. Chica Cardenas, L. A. Mihindukulasuriya, K. A. 2026-03-18 doi:10.64898/2026.03.16.712174 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Replicable generation of rhesus macaque iPSCs for in vitro modeling of genetic frontotemporal dementia ]]> https://biorxiv.org/content/10.64898/2026.03.17.712482v1?rss=1 Colwell, J. Maufort, J. P. Williams, K. M. Makulec, A. T. Fiorentino, M. V. Metzger, J. M. Simmons, H. A. Basu, P. Malicki, K. B. Karch, C. Marsh, J. A. Emborg, M. E. Schmidt, J. K. 2026-03-18 doi:10.64898/2026.03.17.712482 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ The osteoclast intracellular environment fosters bacterial growth during Staphylococcus aureus infection ]]> https://biorxiv.org/content/10.64898/2026.03.18.712565v1?rss=1 O'Connor, L. D. Bhagat, S. Rohatgi, N. Mbalaviele, G. Cassat, J. E. Veis, D. J. 2026-03-18 doi:10.64898/2026.03.18.712565 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Circulating miRNA-Protein Signatures Predict Outcomes in Pediatric Dilated Cardiomyopathy ]]> https://biorxiv.org/content/10.64898/2026.03.17.712519v1?rss=1 Vicentino, A. R. Karimpour-Fard, A. Hamza, T. H. Stauffer, B. L. Lavine, K. J. Miyamoto, S. D. Lipschultz, S. Sucharov, C. C. 2026-03-20 doi:10.64898/2026.03.17.712519 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ A history of symbiosis impacts the host evolutionary trajectory in experimentally evolved amoebas ]]> https://biorxiv.org/content/10.64898/2026.03.18.712585v1?rss=1 Jahan, I. Larsen, T. J. Strassmann, J. E. Queller, D. C. 2026-03-20 doi:10.64898/2026.03.18.712585 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Targeting MTHFD2 disrupts mitochondrial redox homeostasis and restores venetoclax sensitivity in acute myeloid leukemia ]]> https://biorxiv.org/content/10.64898/2026.03.18.712743v1?rss=1 Sokei, J. O. di Martino, O. Basse, M. Gabriel, N. Valin, L. York, C. R. Arthur, N. B. J. Zhang, W. Goldman, A. R. Ferraro, F. Sykes, S. M. 2026-03-20 doi:10.64898/2026.03.18.712743 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Cell-specific isotope labeling identifies myo-inositol transfer between neurons and oligodendroglia to support myelin repair ]]> https://biorxiv.org/content/10.64898/2026.03.19.712965v1?rss=1 Adkins-Travis, K. Song, M.-G. Schwaiger-Haber, M. Cho, K. Fowle-Grider, R. Johnson, S. L. Shriver, L. P. Patti, G. 2026-03-22 doi:10.64898/2026.03.19.712965 Cold Spring Harbor Laboratory Press 2026-03-22 <![CDATA[ Aberrant retinal structure and vasculature in mouse models of dominant retinopathies caused by CRX homeodomain mutations ]]> https://biorxiv.org/content/10.64898/2026.03.19.712925v1?rss=1 Sun, C. Pfeifer, C. W. Zheng, Y. Apte, R. S. Chen, S. 2026-03-23 doi:10.64898/2026.03.19.712925 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ Multimodal analysis of cell-free DNA identifies epigenetic biomarkers for amyotrophic lateral sclerosis diagnosis and progression ]]> https://biorxiv.org/content/10.64898/2026.03.20.711195v1?rss=1 La Spada, A. Michels, S. Chen, C. Ruf, W. Garcia Garcia, M. M. Arnold, F. J. Wu, Z. Bennett, C. L. Shams, D. Thompson, L. M. Walker, A. Dickson, D. W. Petrucelli, L. Dorst, J. Prudencio, M. Li, W. 2026-03-23 doi:10.64898/2026.03.20.711195 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ Inter-individual variation of cellular and gene-expression properties of the human striatum ]]> https://biorxiv.org/content/10.64898/2026.03.20.713160v1?rss=1 Burger, S. Yoo, O. Nemesh, J. Muratoglu, E. Vanderburg, C. Yuan, J. Shakir, K. Mello, C. J. Rayan, N. A. Milidantri, J. Kim, K. Drouin, S. Finn, E. Gao, H. Budnik, N. Goldman, M. Fritch, H. Genovese, G. Hogan, M. Catalini, O. Kashin, S. Rockweiler, N. Wysoker, A. Macaisa, L. Reese, L. Flowers, K. Kraft, A. W. Fleming, S. J. Coe, M. Gunaratne, R. Spina, L. Crombie, C. Mohsin, A. Kamitaki, N. Macosko, E. Z. Ichihara, K. McCarroll, S. A. 2026-03-23 doi:10.64898/2026.03.20.713160 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ Metabolic specialization structures gut bacterial niches and drives colorectal cancer progression ]]> https://biorxiv.org/content/10.64898/2026.03.21.712571v1?rss=1 Xu, L.-L. Seelbinder, B. Zhou, Z. Kuo, T.-H. Sae-Ong, T. Treibmann, S. Damerell, V. Brobeil, A. Richter, K. M. Mueller, M. Toriola, A. T. Shibata, D. Li, C. I. Byrd, D. A. Figueiredo, J. C. Hardikar, S. Zielinski, C. E. Bleckmann, A. Ni, Y. Correia-Melo, C. Zimmermann, M. Ulrich, C. M. Gigic, B. Panagiotou, G. 2026-03-23 doi:10.64898/2026.03.21.712571 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ A postnatal human lung developmental atlas reveals windows of genetic vulnerability to chronic lung disease ]]> https://biorxiv.org/content/10.64898/2026.03.20.713166v1?rss=1 Planer, J. D. Morley, M. P. D. Cai, S. Peterson, A. R. Lu, M. Yang, Y. Hallquist, H. Schaefer, S. E. Carl, J. Zhou, S. Lin, S. M. Chandrasekaran, P. Young, L. R. Cantu, E. Peranteau, W. Frank, D. B. Morrisey, E. Basil, M. C. 2026-03-24 doi:10.64898/2026.03.20.713166 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Cross-Species Translation Enhances the Use of Mouse Models for Translatability and Drug Discovery in Late-Onset Alzheimer's Disease ]]> https://biorxiv.org/content/10.64898/2026.03.21.713391v1?rss=1 Park, J. H. Yu, J. Lucey, B. P. Brubaker, D. K. 2026-03-24 doi:10.64898/2026.03.21.713391 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Synaptic Alterations Are Preceding the Axonal Loss in Optic Atrophy of Wolfram Syndrome Mouse Model ]]> https://biorxiv.org/content/10.64898/2026.03.22.713521v1?rss=1 Gurram, V. An, W. Bimal, S. Urano, F. 2026-03-25 doi:10.64898/2026.03.22.713521 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Coronavirus envelope protein drives iron sensing disorder by hijacking the TAp73-FDXR axis ]]> https://biorxiv.org/content/10.64898/2026.03.24.713916v1?rss=1 Zhu, M. Hu, L. Fu, X. Yuan, B. Guan, G. Han, L. Rong, Z. Tian, R. Li, G. Du, M. Ma, Y. Xu, N. Liu, H. Tian, H. Yin, X. Zhong, J. Sun, M. Yang, S. Liu, S. Liu, Q. Li, J. Fan, B. Chen, Y. Zhao, Q. Zhou, T. Chang, L. Zhao, X. Ran, X. Du, Q. Ding, S. Li, B. Huang, Y. Tong, D. 2026-03-25 doi:10.64898/2026.03.24.713916 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Subunit selective modulation of GABAA receptors using pharmacogenetically tethered neurosteroids ]]> https://biorxiv.org/content/10.64898/2026.03.23.713679v1?rss=1 Kumar, A. Shu, H. J. Chisari, M. Qian, M. Xu, Y. Jeong, P. Shields, B. C. Hong, J. TADROSS, M. R. Covey, D. F. Zorumski, C. F. Mennerick, S. 2026-03-26 doi:10.64898/2026.03.23.713679 Cold Spring Harbor Laboratory Press 2026-03-26 <![CDATA[ NetTracer3D Enables User-Friendly Analysis of Diverse Microscopic and Medical 3D Datasets ]]> https://biorxiv.org/content/10.64898/2026.03.25.714104v1?rss=1 McLaughlin, L. Curic, M. Sharma, S. Villazon, J. Salamon, R. J. Yamaguchi, M. Sequeira-Lopez, M. L. S. Kennedy, P. R. Lyons, R. C. Shi, L. Gomez, R. A. Jain, S. 2026-03-27 doi:10.64898/2026.03.25.714104 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Giant viruses encode vitamin K-based redox modules for lipid modification ]]> https://biorxiv.org/content/10.64898/2026.03.26.714578v1?rss=1 Collins, R. Andreani, J. Chavez, D. Rusch, D. B. Boyd, D. Colson, P. LA SCOLA, B. Landeta, C. 2026-03-27 doi:10.64898/2026.03.26.714578 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ STING causes replication stress and nascent DNA degradation via SAMHD1 ]]> https://biorxiv.org/content/10.64898/2026.03.28.714577v1?rss=1 Teodoro-Castro, B. Cancado de Faria, R. Shashkova, E. V. Malique, A. Adolph, M. B. Silva, L. N. D. Gonzalo, S. 2026-03-28 doi:10.64898/2026.03.28.714577 Cold Spring Harbor Laboratory Press 2026-03-28 <![CDATA[ Synthetic circRNAs employ IRES activity for translation in cells and in cell-free translation systems ]]> https://biorxiv.org/content/10.64898/2026.03.28.715045v1?rss=1 Koch, P. Arendrup, F. S. W. Lim, C. Narayanan, S. Adam, A. Clamer, M. Lund, A. H. Chen, C.-K. Leppek, K. 2026-03-29 doi:10.64898/2026.03.28.715045 Cold Spring Harbor Laboratory Press 2026-03-29 <![CDATA[ Charting the landscape of organellar genome evolution in eustigmatophyte algae ]]> https://biorxiv.org/content/10.64898/2026.03.28.715030v1?rss=1 Richtar, M. Klapuchova, E. Yurchenko, T. Fawley, K. P. Fawley, M. W. Barcyte, D. Jaske, K. Wolf, B. M. Li, F.-W. Sevcikova, T. Elias, M. 2026-03-30 doi:10.64898/2026.03.28.715030 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ WayFindR: Investigating Feedback in Biological Pathways ]]> https://biorxiv.org/content/10.64898/2026.03.27.714788v1?rss=1 Bombina, P. McGee, R. L. Reed, J. Abrams, Z. Abruzzo, L. V. Coombes, K. R. 2026-03-31 doi:10.64898/2026.03.27.714788 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Hapln1-HA signaling promotes progenitor cell proliferation and spinal cord regeneration ]]> https://biorxiv.org/content/10.64898/2026.03.28.714985v1?rss=1 Xu, Y. Zhou, L. Saraswathy, V. M. Mcadow, A. R. Mokalled, M. 2026-03-31 doi:10.64898/2026.03.28.714985 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ SnakeHichipTF reveals transcription factor logic underlying enhancer-promoter wiring in the human brain ]]> https://biorxiv.org/content/10.64898/2026.03.30.715320v1?rss=1 Tan, J. Wu, Y. Head, R. Sun, Y. 2026-04-01 doi:10.64898/2026.03.30.715320 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Single-cell, clonal and spatial atlases of cranial placodes illuminate their specification and evolution ]]> https://biorxiv.org/content/10.64898/2026.04.01.715621v1?rss=1 Murtazina, A. Fatieieva, Y. Waern, F. Maunsell, H. R. Thawani, A. Semsch, B. Bostrom, J. Reagor, C. C. Kameneva, P. Araslanova, K. Isaev, S. Schelb, F. Fried, K. Erickson, A. G. Klimovich, A. Streit, A. Kutscher, L. M. Kozmikova, I. Kozmik, Z. Andersson, E. R. Schlosser, G. Groves, A. K. Adameyko, I. 2026-04-03 doi:10.64898/2026.04.01.715621 Cold Spring Harbor Laboratory Press 2026-04-03 <![CDATA[ Targeting the DNA damage repair protein RAD51 alters fibroblast metabolism and enhances apoptosis in pulmonary fibrosis ]]> https://biorxiv.org/content/10.64898/2026.04.01.715935v1?rss=1 Maurya, R. K. Sharma, A. K. Schaefbauer, K. J. Ma, L. Koenitzer, J. R. Limper, A. Choudhury, M. 2026-04-04 doi:10.64898/2026.04.01.715935 Cold Spring Harbor Laboratory Press 2026-04-04 <![CDATA[ Sex differences in exploration-exploitation strategies during home-cage decision making ]]> https://biorxiv.org/content/10.64898/2026.04.02.716124v1?rss=1 30 mice per sex were needed to detect these modest but significant sex differences with 80% power. No consistent sex differences were observed in pellet intake, suggesting that differences in exploitation did not reflect differences in hunger drive or demand for pellets. Exploitation is a more efficient strategy when environmental parameters are fixed, while exploration can be more advantageous when parameters such as reward locations are changing and uncertain. We tested this idea by re-running our mice in a probabilistic foraging task, where actions led to uncertain probabilities of reward. While males continued to show higher levels of win-stay behaviour on this task, this no longer led to increases in accuracy. Behavioural modelling also supported this framework, demonstrating that stronger win-stay behaviour was most advantageous in deterministic models, and less advantageous in probabilistic models. Together, our findings demonstrate that male and female mice have small but significant differences in their exploration-exploitation balance, which leads to more accurate foraging in certain, but not uncertain, environments. ]]> Murrell, C. L. Legaria, A. A. McCullough, K. B. Nwacha, A. Nasiru, M. O. Alves Ferreira Dias, S. Chase, R. Barrett, M. R. Gaidica, M. Hiratani, N. Creed, M. C. Dougherty, J. D. Maloney, S. E. Kravitz, A. V. 2026-04-06 doi:10.64898/2026.04.02.716124 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ Genetic and pharmacologic modulation of RAGE rescues the diabetes-mediated impairments to bone at multiple length scales ]]> https://biorxiv.org/content/10.64898/2026.04.02.716153v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@1c2d4f1org.highwire.dtl.DTLVardef@2a4d62org.highwire.dtl.DTLVardef@13e632borg.highwire.dtl.DTLVardef@e0b341_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Broz, K. S. Hung, T. Walk, R. E. LoTempio, S. Flores, K. M. Tang, S. Y. 2026-04-06 doi:10.64898/2026.04.02.716153 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ Defining the RNA Modification Landscape of Multiple Myeloma Reveals METTL3-Dependent m6A Regulation of NEAT1 ]]> https://biorxiv.org/content/10.64898/2026.04.04.716518v1?rss=1 15,000 m6A sites, including sites on 2,398 lncRNAs. Among these, we validate m6A sites on the paraspeckle-associated lncRNA NEAT1. Functional studies reveal that NEAT1 expression is regulated by the methyltransferase METTL3 and site-specific demethylation of a NEAT1 m6A site reduces MM cell viability. Single-cell RNA sequencing shows consistent NEAT1 enrichment in malignant plasma cells but minimal expression in healthy cells. These findings identify m6A-modified lncRNAs as key regulators of MM biology and establish NEAT1 as an epitranscriptomically controlled driver of MM cell survival. ]]> Thunuguntla, P. Duraiyan, D. Sizemore, C. Sulvaran-Guel, E. Mishra, R. Camacho, J. Gonzales, S. Daly, S. Bagwill, K. Colbert, D. King, J. Samuel, C. David-Pennington, L. Ki, A. Anderson, S. Bras Costa, C. Zhang, J. Vij, R. Garcia, B. A. DiPersio, J. Silva-Fisher, J. 2026-04-07 doi:10.64898/2026.04.04.716518 Cold Spring Harbor Laboratory Press 2026-04-07 <![CDATA[ Thermodynamic rigidity of harmonic brain states relates to general mental ability in juvenile myoclonic epilepsy ]]> https://biorxiv.org/content/10.64898/2026.04.06.715875v1?rss=1 Branco de Paiva, F. Zhao, M. Zhao, M. Philibert-Rosas, S. Brace, C. J. Moe, E. Haworth, S. E. Hermann, B. P. Chung, M. K. Struck, A. F. 2026-04-08 doi:10.64898/2026.04.06.715875 Cold Spring Harbor Laboratory Press 2026-04-08 <![CDATA[ A Non-Classical Neuroactive Steroid Exhibiting Potent, Efficacious GABA A Receptor Agonism and NMDA Receptor Inhibition ]]> https://biorxiv.org/content/10.64898/2026.04.06.716659v1?rss=1 Shu, H.-J. Xu, Y. Qian, M. Benz, A. Yuede, C. M. Covey, D. F. Zorumski, C. F. Mennerick, S. 2026-04-08 doi:10.64898/2026.04.06.716659 Cold Spring Harbor Laboratory Press 2026-04-08