bioRxiv Channel: Oregon Health & Science University https://biorxiv.org This feed contains articles for bioRxiv Channel "Oregon Health & Science University" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ The classic psychedelic DOI induces a persistent desynchronized state in medial prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2023.02.26.529963v1?rss=1 Olson, R. Bartlett, L. Sonneborn, A. Bretton-Granatoor, Z. Firdous, A. Harris, A. Abbas, A. 2023-02-27 doi:10.1101/2023.02.26.529963 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Spontaneous allelic variant in Ush1g resulting in an expanded phenotype ]]> https://biorxiv.org/content/10.1101/2023.02.28.529432v1?rss=1 Vartanian, V. Krey, J. F. Chatterjee, P. Jones, S. M. Curtis, A. Ryals, R. Lloyd, R. S. Barr-Gillespie, P. G. 2023-03-01 doi:10.1101/2023.02.28.529432 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ GIPC3 couples to MYO6 and PDZ domain proteins and shapes the hair cell apical region ]]> https://biorxiv.org/content/10.1101/2023.02.28.530466v1?rss=1 Chatterjee, P. Morgan, C. P. Krey, J. F. Benson, C. Goldsmith, J. Bateschell, M. Ricci, A. Barr-Gillespie, P. G. 2023-03-01 doi:10.1101/2023.02.28.530466 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Structurally divergent and recurrently mutated regions of primate genomes ]]> https://biorxiv.org/content/10.1101/2023.03.07.531415v1?rss=1 Mao, Y. Harvey, W. T. Porubsky, D. Munson, K. M. Hoekzema, K. Lewis, A. P. Audano, P. A. Rozanski, A. Yang, X. Zhang, S. Gordon, D. S. Wei, X. Logsdon, G. A. Haukness, M. Dishuck, P. C. Jeong, H. del Rosario, R. Bauer, V. L. Fattor, W. T. Wilkerson, G. K. Lu, Q. Paten, B. Feng, G. Sawyer, S. L. Warren, W. C. Carbone, L. Eichler, E. E. 2023-03-07 doi:10.1101/2023.03.07.531415 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function ]]> https://biorxiv.org/content/10.1101/2023.03.07.531534v1?rss=1 Okhovat, M. VanCampen, J. Lima, A. C. Nevonen, K. Layman, C. E. Ward, S. Herrera, J. Stendahl, A. M. Yang, R. Harshman, L. Li, W. Sheng, R. R. Mao, Y. Fedorov, L. Ndjamen, B. Vigh-Conrad, K. A. Matthews, I. R. Easow, S. A. Chan, D. K. Jan, T. A. Eichler, E. E. Rugonyi, S. Conrad, D. F. Ahituv, N. Carbone, L. 2023-03-07 doi:10.1101/2023.03.07.531534 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ CEP76 is a critical regulator of male germ cell transition zone function and tail composition ]]> https://biorxiv.org/content/10.1101/2023.03.08.531794v1?rss=1 Houston, B. J. Merriner, D. J. Stathatos, G. G. O'Connor, A. E. Lopes, A. M. Conrad, D. F. Baker, M. Dunleavy, J. E. O'Bryan, M. K. 2023-03-09 doi:10.1101/2023.03.08.531794 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Characterization of extracellular matrix deposited by segmental trabecular meshwork cells ]]> https://biorxiv.org/content/10.1101/2023.03.11.532242v1?rss=1 Raghunathan, V. Nartey, A. Dhamodaran, K. Baidouri, H. Staverosky, J. A. Keller, K. Zientek, K. Reddu, A. Acott, T. Vranka, J. A. 2023-03-12 doi:10.1101/2023.03.11.532242 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ The landscape of cancer rewired GPCR signaling axes ]]> https://biorxiv.org/content/10.1101/2023.03.13.532291v1?rss=1 Raimondi, F. Arora, C. Matic, M. Rosa, N. D. O. Nemati, L. Clubb, L. Kargas, G. Vukotic, R. Licata, L. Wu, G. Gutkind, J. S. 2023-03-14 doi:10.1101/2023.03.13.532291 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Vertical transmission of African-lineage Zika virus through the fetal membranes in a rhesus Macaque (Macaca mulatta) model ]]> https://biorxiv.org/content/10.1101/2023.03.13.532348v1?rss=1 Koenig, M. R. Mitzey, A. M. Zeng, X. Reyes, L. Simmons, H. A. Morgan, T. K. Bohm, E. K. Pritchard, J. C. Schmidt, J. A. Ren, E. Jaimes, F. L. Winston, E. Basu, P. Weiler, A. M. Friedrich, T. C. Aliota, M. T. Mohr, E. L. Golos, T. G. 2023-03-14 doi:10.1101/2023.03.13.532348 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Thermogenetic control of Ca2+ levels in cells and tissues ]]> https://biorxiv.org/content/10.1101/2023.03.22.533774v1?rss=1 Ermakova, Y. G. Waadt, R. Ozturk, M. S. Roshchin, M. Lanin, A. A. Chebotarev, A. Pochechuev, M. Pak, V. Kelmanson, I. Smolyarovasmol, D. Keutler, K. Matyushenko, A. M. Tischer, C. V. Balaban, P. M. Nikitin, E. S. Schumacher, K. Zheltikov, A. Prevedel, R. Schultz, C. Belousov, V. V. 2023-03-22 doi:10.1101/2023.03.22.533774 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ Supervised learning of high-confidence phenotypic subpopulations from single-cell data ]]> https://biorxiv.org/content/10.1101/2023.03.23.533712v1?rss=1 Ren, T. Chen, C. Danilov, A. V. Liu, S. Guan, X. Du, S. Wu, X. Sherman, M. H. Spellman, P. T. Coussens, L. M. Adey, A. C. Mills, G. B. Wu, L.-Y. Xia, Z. 2023-03-25 doi:10.1101/2023.03.23.533712 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ A naturally occurring variant of MBD4 causes maternal germline hypermutation in primates ]]> https://biorxiv.org/content/10.1101/2023.03.27.534460v1?rss=1 T deamination mutations at CpG locations and has been linked to somatic hypermutation and cancer predisposition in humans. We show here that MBD4-associated hypermutation also affects the germline: the 6 offspring of the MBD4-null dam have a 4-6 fold increase in de novo mutation burden. This excess burden was predominantly C>T mutations at CpG locations consistent with MBD4 loss-of-function in the dam. There was also a significant excess of C>T at CpA sites, indicating an important, underappreciated role for MBD4 to repair deamination in CpA contexts. The MBD4-null dam developed sustained eosinophilia later in life, but we saw no other signs of neoplastic processes associated with MBD4 loss-of-function in humans, nor any obvious disease in the hypermutated offspring. This work provides what is likely the first evidence for a genetic factor causing hypermutation in the maternal germline of a mammal, and adds to the very small list of naturally occurring variants known to modulate germline mutation rates in mammals. ]]> Stendahl, A. Sanghvi, R. Peterson, S. Ray, K. Lima, A. C. Rahbari, R. Conrad, D. 2023-03-29 doi:10.1101/2023.03.27.534460 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Glycosylation differentially affects immune cell-specific tetraspanins CD37 and CD53 ]]> https://biorxiv.org/content/10.1101/2023.03.29.534715v1?rss=1 van Deventer, S. J. Hoogvliet, I. A. van de Voort, M. Arnold, F. van Spriel, A. 2023-03-29 doi:10.1101/2023.03.29.534715 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Integrated single cell analysis shows chronic alcohol drinking disrupts monocyte differentiation in the bone marrow niche ]]> https://biorxiv.org/content/10.1101/2023.03.29.534727v1?rss=1 Lewis, S. A. Doratt, B. M. Qiao, Q. Blanton, M. B. Grant, K. A. Messaoudi, I. 2023-03-30 doi:10.1101/2023.03.29.534727 Cold Spring Harbor Laboratory Press 2023-03-30 <![CDATA[ Dopamine D1 and NMDA receptor co-regulation of protein translation in cultured nucleus accumbens neurons ]]> https://biorxiv.org/content/10.1101/2023.04.02.535293v1?rss=1 Zimbelman, A. R. Wong, B. Murray, C. H. Wolf, M. E. Stefanik, M. T. 2023-04-02 doi:10.1101/2023.04.02.535293 Cold Spring Harbor Laboratory Press 2023-04-02 <![CDATA[ Protective effect of pre-existing natural immunity in a nonhuman primate reinfection model of congenital cytomegalovirus infection ]]> https://biorxiv.org/content/10.1101/2023.04.10.536057v1?rss=1 Mostrom, M. J. Yu, S. Tran, D. Saccoccio, F. Versoza, C. J. Malouli, D. J. Mirza, A. Valencia, S. Gilbert, M. Blair, R. V. Hansen, S. G. Barry, P. A. Fruh, K. Jensen, J. D. Pfeifer, S. P. Kowalik, T. F. Permar, S. R. Kaur, A. 2023-04-10 doi:10.1101/2023.04.10.536057 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ Sequential chromogenic immunohistochemistry: spatial analysis of lymph nodes identifies contact interactions between plasmacytoid dendritic cells and plasmablasts ]]> https://biorxiv.org/content/10.1101/2023.04.13.536793v1?rss=1 Claudio, N. M. Nguyen, M.-T. Wanner, A. Pucci, F. 2023-04-14 doi:10.1101/2023.04.13.536793 Cold Spring Harbor Laboratory Press 2023-04-14 <![CDATA[ Structure-function Analyses Reveal Key Molecular Determinants of HIV-1 CRF01_AE Resistance to the Entry Inhibitor Temsavir ]]> https://biorxiv.org/content/10.1101/2023.04.17.537181v1?rss=1 Pazgier, M. Prevost, J. Chen, Y. Zhou, F. Tolbert, W. D. Gasser, R. Medjahed, H. Gottumukkala, S. Hessell, A. Rao, V. B. Pozharski, E. Huang, R. Motthies, D. Finzi, A. 2023-04-17 doi:10.1101/2023.04.17.537181 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Gemcitabine plus nab-paclitaxel preserves skeletal and cardiac mass and function in a murine model of pancreatic cancer cachexia ]]> https://biorxiv.org/content/10.1101/2023.04.15.536434v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@1d394f7org.highwire.dtl.DTLVardef@1d8fdaforg.highwire.dtl.DTLVardef@f709d4org.highwire.dtl.DTLVardef@a668e0_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG ]]> Narasimhan, A. Jengelley, D. Huot, J. Umberger, T. Doud, E. Mosley, A. L. Wang, M. Zhong, X. Counts, B. Rupert, J. Young, A. Bonetto, A. Horan, D. Robling, A. G. Fishel, M. Kelley, M. Koniaris, L. Zimmers, T. 2023-04-18 doi:10.1101/2023.04.15.536434 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ RhoA GEF Mcf2lb regulates rosette integrity during collective cell migration ]]> https://biorxiv.org/content/10.1101/2023.04.19.537573v1?rss=1 Olson, H. M. Maxfield, A. Calistri, N. L. Heiser, L. M. Nechiporuk, A. V. 2023-04-20 doi:10.1101/2023.04.19.537573 Cold Spring Harbor Laboratory Press 2023-04-20 <![CDATA[ Relationship of maternal cytomegalovirus-specific antibody responses and viral load to vertical transmission risk following primary maternal infection in a rhesus macaque model ]]> https://biorxiv.org/content/10.1101/2023.04.21.537769v1?rss=1 Otero, C. E. Barfield, R. Scheef, E. Nelson, C. S. Rodgers, N. Wang, H.-Y. Moström, M. Manuel, T. D. Sass, J. Schmidt, K. Taher, H. Papen, C. Sprehe, L. Kendall, S. Davalos, A. Barry, P. A. Früh, K. Pollara, J. Malouli, D. Chan, C. Kaur, A. Permar, S. R. 2023-04-21 doi:10.1101/2023.04.21.537769 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Layer 5a Corticostriatal Projection Neurons are Selectively Vulnerable in Huntington's Disease ]]> https://biorxiv.org/content/10.1101/2023.04.24.538096v1?rss=1 Pressl, C. Mätlik, K. Kus, L. Darnell, P. Luo, J.-D. Weiss, A. R. Liguore, W. Carroll, T. Davis, D. A. McBride, J. Heintz, N. 2023-04-24 doi:10.1101/2023.04.24.538096 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ Dopamine D2 receptors in mossy cells reduce excitatory transmission and are essential for hippocampal function ]]> https://biorxiv.org/content/10.1101/2023.05.05.539468v1?rss=1 Gulfo, M. C. Lebowitz, J. J. Ramos, C. Hwang, D.-W. Nasrallah, K. Castillo, P. E. 2023-05-05 doi:10.1101/2023.05.05.539468 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ Mild/Asymptomatic Maternal SARS-CoV-2 Infection Leads to Immune Paralysis in Fetal Circulation and Immune Dysregulation in Fetal-Placental Tissues ]]> https://biorxiv.org/content/10.1101/2023.05.10.540233v1?rss=1 Doratt, B. M. Sureshchandra, S. True, H. Rincon, M. Marshall, N. E. Messaoudi, I. 2023-05-11 doi:10.1101/2023.05.10.540233 Cold Spring Harbor Laboratory Press 2023-05-11 <![CDATA[ Mcam stabilizes a luminal progenitor-like breast cancer cell state via Ck2 control and Src/Akt/Stat3 attenuation ]]> https://biorxiv.org/content/10.1101/2023.05.10.540211v1?rss=1 Balcioglu, O. Gates, B. L. Freeman, D. W. Hagos, B. M. Mehrabad, E. M. Ayala-Talavera, D. Spike, B. T. 2023-05-12 doi:10.1101/2023.05.10.540211 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ A Masked Image Modeling Approach to Cyclic Immunofluorescence (CyCIF) Panel Reduction and Marker Imputation ]]> https://biorxiv.org/content/10.1101/2023.05.10.540265v1?rss=1 Sims, Z. Chang, Y. H. 2023-05-13 doi:10.1101/2023.05.10.540265 Cold Spring Harbor Laboratory Press 2023-05-13 <![CDATA[ Molecular Basis for Maternal Inheritance of Human Mitochondrial DNA ]]> https://biorxiv.org/content/10.1101/2023.05.12.540615v1?rss=1 Lee, W. Zamudio-Ochoa, A. Buchel, G. Podlesniy, P. Marti Gutierrez, N. Puigros, M. Calderon, A. Koski, A. Tang, H.-Y. Li, L. Trullas, R. Mitalipov, S. Temiakov, D. 2023-05-13 doi:10.1101/2023.05.12.540615 Cold Spring Harbor Laboratory Press 2023-05-13 <![CDATA[ txci-ATAC-seq, a massive-scale single-cell technique to profile chromatin accessibility ]]> https://biorxiv.org/content/10.1101/2023.05.11.540245v1?rss=1 Zhang, H. Mulqueen, R. M. Iannuzo, N. Farrera, D. O. Polverino, F. Galligan, J. J. Ledford, J. G. Adey, A. C. Cusanovich, D. A. 2023-05-14 doi:10.1101/2023.05.11.540245 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ NAIP-NLRC4 Inflammasome Activation in Tuft Cells Activates a PGD2-ILC3 Signaling Circuit that Protects Against Enteric Infection. ]]> https://biorxiv.org/content/10.1101/2023.05.11.540443v1?rss=1 Churchill, M. J. Bauer, R. Honodel, R. Christopher, T. Smita, S. Warner, L. Mooney, B. M. Wojno, E. D. T. Rauch, I. 2023-05-14 doi:10.1101/2023.05.11.540443 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ 3D organoid modeling identified that targeting IGF1R signaling may overcome drug resistance in breast cancer ]]> https://biorxiv.org/content/10.1101/2023.05.14.540701v1?rss=1 Mittal, E. Qian, D. 2023-05-14 doi:10.1101/2023.05.14.540701 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Exact Reconstruction of Gene Regulatory Networks using Compressive Sensing ]]> https://biorxiv.org/content/10.1101/004242v1?rss=1 Young Hwan Chang Joe W. Gray Claire J. Tomlin 2014-04-20 doi:10.1101/004242 Cold Spring Harbor Laboratory Press 2014-04-20 <![CDATA[ Disentangling Multidimensional Spatio-Temporal Data into their Common and Aberrant Responses ]]> https://biorxiv.org/content/10.1101/004259v1?rss=1 Young Hwan Chang Jim Korkola Dhara N. Amin Mark M. Moasser Jose M. Carmena Joe W. Gray Claire J. Tomlin 2014-04-23 doi:10.1101/004259 Cold Spring Harbor Laboratory Press 2014-04-23 <![CDATA[ An Approximate Bayesian Computation Approach to Examining the Phylogenetic Relationships among the Four Gibbon Genera using Whole Genome Sequence Data ]]> https://biorxiv.org/content/10.1101/009498v1?rss=1 Krishna Veeramah August E Woerner Laurel Johnstone Ivo Gut Marta Gut Tomas Marques-Bonet Lucia Carbone Jeff D Wall Michael F Hammer 2014-09-22 doi:10.1101/009498 Cold Spring Harbor Laboratory Press 2014-09-22 <![CDATA[ A Comprehensive Assessment of Somatic Mutation Calling in Cancer Genomes ]]> https://biorxiv.org/content/10.1101/012997v1?rss=1 Tyler S Alioto Sophia Derdak Timothy A Beck Paul C Boutros Lawrence Bower Ivo Buchhalter Matthew D Eldridge Nicholas J Harding Lawrence Edward Heisler Eivind Hovig David T W Jones Andrew G Lynch Sigve Nakken Paolo Ribeca Anne-Sophie Sertier Jared T Simpson Paul Spellman Patrick Tarpey Laurie Tonon Daniel Vodák Takafumi N Yamaguchi Sergi Beltran Agullo Marc Dabad Robert E Denroche Philip Ginsbach Simon C Heath Emanuele Raineri Charlotte L Anderson Benedikt Brors Ruben Drews Roland Eils Akihiro Fujimoto Francesc Castro Giner Minghui He Pablo Hennings-Yeomans Barbara Hutter Natalie Jäger Rolf Kab 2014-12-24 doi:10.1101/012997 Cold Spring Harbor Laboratory Press 2014-12-24 <![CDATA[ Context-specificity in causal signaling networks revealed by phosphoprotein profiling ]]> https://biorxiv.org/content/10.1101/039636v1?rss=1 Steven M. Hill Nicole K. Nesser Katie Johnson-Camacho Mara Jeffress Aimee Johnson Chris Boniface Simon E.F. Spencer Yiling Lu Laura M. Heiser Yancey Lawrence Nupur T. Pande James E. Korkola Joe W. Gray Gordon B. Mills Sach Mukherjee Paul T. Spellman 2016-02-15 doi:10.1101/039636 Cold Spring Harbor Laboratory Press 2016-02-15 <![CDATA[ Whole-genome characterization in pedigreed non-human primates using Genotyping-By-Sequencing and imputation. ]]> https://biorxiv.org/content/10.1101/043240v1?rss=1 4 individuals with WGS for imputation. We used this ratio of 4 WGS to 12 GBS individuals to impute an expanded set of ~14.4 million variants across all 20 macaque autosomes, achieving ~85-88% accuracy per chromosome.nnConclusionsWe conclude that an optimal tradeoff exists at the ratio of 1 individual selected for WGS using the GIGI-Pick algorithm, per 3-5 relatives selected for GBS, a cost savings of ~67-83% over WGS of all individuals. This approach makes feasible the collection of accurate, dense genome-wide sequence data in large pedigreed macaque cohorts without the need for expensive WGS data on all individuals. ]]> Ben N Bimber Michael J Raboin John Letaw Kimberly Nevonen Jennifer E Spindel Susan McCouch Rita Cervera-Juanes Eliot Spindel Lucia Carbone Betsy Ferguson Amanda Vinson 2016-03-12 doi:10.1101/043240 Cold Spring Harbor Laboratory Press 2016-03-12 <![CDATA[ k-BOOM: A Bayesian approach to ontology structure inference, with applications in disease ontology construction ]]> https://biorxiv.org/content/10.1101/048843v1?rss=1 Christopher J Mungall Sebastian Koehler Peter Robinson Ian Holmes Melissa Haendel 2016-04-15 doi:10.1101/048843 Cold Spring Harbor Laboratory Press 2016-04-15 <![CDATA[ Architecture of fully occupied GluA2 AMPA receptor - TARP complex elucidated by single particle cryo-electron microscopy ]]> https://biorxiv.org/content/10.1101/060046v1?rss=1 Yan Zhao Shanshuang Chen Craig Yoshioka Isabelle Baconguis Eric Gouaux 2016-06-21 doi:10.1101/060046 Cold Spring Harbor Laboratory Press 2016-06-21 <![CDATA[ Construction of thousands of single cell genome sequencing libraries using combinatorial indexing ]]> https://biorxiv.org/content/10.1101/065482v1?rss=1 Sarah A Vitak Kristof A Torkenczy Jimi L Rosenkrantz Andrew J Fields Lena Christiansen Melissa H Wong Lucia Carbone Frank J Steemers Andrew Adey 2016-07-23 doi:10.1101/065482 Cold Spring Harbor Laboratory Press 2016-07-23 <![CDATA[ Network Identification Methods ]]> https://biorxiv.org/content/10.1101/071217v1?rss=1 Young Hwan Chang Claire Tomlin 2016-08-23 doi:10.1101/071217 Cold Spring Harbor Laboratory Press 2016-08-23 <![CDATA[ Reproducibility and replicability of rodent phenotyping in preclinical studies ]]> https://biorxiv.org/content/10.1101/079350v1?rss=1 Neri Kafkafi Joseph Agassi Elissa J Chesler John C Crabbe Wim E Crusio David Eilam Robert Gerlai Ilan Golani Alex Gomez-Marin Ruth Heller Fuad Iraqi Iman Jaljuli Natasha A Karp Hugh Morgan George Nicholson Donald W Pfaff Helene S Richter Philip B Stark Oliver Stiedl Victoria Stodden Lisa M Tarantino Valter Tucci William Valdar Robert W Williams Hanno Wurbel Yoav Benjamini 2016-10-05 doi:10.1101/079350 Cold Spring Harbor Laboratory Press 2016-10-05 <![CDATA[ Analysis of copy number variants on chromosome 21 in Down syndrome-associated congenital heart defects ]]> https://biorxiv.org/content/10.1101/093583v1?rss=1 Rambo-Martin, B. L. Mulle, J. G. Cutler, D. J. Bean, L. J. H. Rosser, T. C. Dooley, K. J. Cua, C. Capone, G. Maslen, C. L. Reeves, R. H. Sherman, S. L. Zwick, M. E. 2016-12-28 doi:10.1101/093583 Cold Spring Harbor Laboratory Press 2016-12-28 <![CDATA[ Cryo-EM structure of the ATP-sensitive potassium channel illuminates mechanisms of assembly and gating ]]> https://biorxiv.org/content/10.1101/094649v1?rss=1 Martin, G. M. Yoshioka, C. Rex, E. A. Fay, J. F. Xie, Q. Whorton, M. R. Chen, J. Z. Shyng, S.-L. 2016-12-16 doi:10.1101/094649 Cold Spring Harbor Laboratory Press 2016-12-16 <![CDATA[ Interactive analysis of Long-read RNA isoforms with Iso-Seq Browser ]]> https://biorxiv.org/content/10.1101/102905v1?rss=1 Hu, J. Uapinyoying, P. Goecks, J. 2017-01-25 doi:10.1101/102905 Cold Spring Harbor Laboratory Press 2017-01-25 <![CDATA[ Poly(A)-ClickSeq: click-chemistry for next-generation 3´-end sequencing without RNA enrichment or fragmentation ]]> https://biorxiv.org/content/10.1101/109272v1?rss=1 Routh, A. Ji, P. Jaworski, E. Xia, Z. Li, W. Wagner, E. J. 2017-02-24 doi:10.1101/109272 Cold Spring Harbor Laboratory Press 2017-02-24 <![CDATA[ Identifiers for the 21st century:How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data ]]> https://biorxiv.org/content/10.1101/117812v1?rss=1 McMurry, J. Juty, N. Blomberg, N. Burdett, A. Conlin, T. Conte, N. Courtot, M. Deck, J. Dumontier, M. Fellows, D. Gonzalez-Beltran, A. Gormanns, P. Grethe, J. Hastings, J. Hermjakob, H. Heriche, J.-K. Ison, J. Jimenez, R. Jupp, S. Kunze, J. Laibe, C. Le Novere, N. Malone, J. R. Martin, M.-J. McEntyre, J. Morris, C. Muilu, J. Mueller, W. Rocca-Serra, P. Sansone, S.-A. Sariyar, M. Snoep, J. Stanford, N. J. Soiland-Reyes, S. Swainston, N. Washington, N. Williams, A. Wimalaratne, S. Winfree, L. Wolstencroft, K. Goble, C. Mungall, C. Haendel, M. Parkinson, 2017-03-20 doi:10.1101/117812 Cold Spring Harbor Laboratory Press 2017-03-20 <![CDATA[ Dystroglycan Maintains Inner Limiting Membrane Integrity To Coordinate Retinal Development ]]> https://biorxiv.org/content/10.1101/121756v1?rss=1 Clements, R. Turk, R. Campbell, K. Wright, K. M. 2017-03-29 doi:10.1101/121756 Cold Spring Harbor Laboratory Press 2017-03-29 <![CDATA[ Burst Activation Of Dopamine Neurons Produces Prolonged Post-Burst Availability Of Actively Released Dopamine ]]> https://biorxiv.org/content/10.1101/125062v1?rss=1 20 min) of extracellular dopamine in nucleus accumbens and prefrontal cortex. This elevation is not due to spillover from the stimulation surge but depends on impulse flow-mediated dopamine release. We identified Rho-mediated internalization of dopamine transporter as a mechanism responsible for prolonged availability of actively released dopamine. These results demonstrate that phasic and tonic dopamine neurotransmission can be a continuum and may explain why both modes of signaling are critical for motivational and cognitive functions associated with dopamine. ]]> Lohani, S. Martig, A. Underhill, S. DeFrancesco, A. Roberts, M. Rinaman, L. Amara, S. Moghaddam, B. 2017-04-06 doi:10.1101/125062 Cold Spring Harbor Laboratory Press 2017-04-06 <![CDATA[ MicroRNA perturbation of the MRN complex buffers DNA damage response from VEGF signaling ]]> https://biorxiv.org/content/10.1101/132258v1?rss=1 Espinosa-Diez, C. Wilson, R. Chatterjee, N. Hudson, C. Ruhl, R. Hipfinger, C. Helms, E. Khan, O. F. Anderson, D. G. Anand, S. 2017-04-28 doi:10.1101/132258 Cold Spring Harbor Laboratory Press 2017-04-28 <![CDATA[ Distinct Temporal Filters In Mitral Cells And External Tufted Cells Of The Olfactory Bulb ]]> https://biorxiv.org/content/10.1101/135541v1?rss=1 Vaaga, C. E. Westbrook, G. L. 2017-05-08 doi:10.1101/135541 Cold Spring Harbor Laboratory Press 2017-05-08 <![CDATA[ MicroRNA-451a regulates colorectal cancer radiosensitivity ]]> https://biorxiv.org/content/10.1101/136234v1?rss=1 Ruhl, R. Rana, S. Kelley, K. Espinosa-Diez, C. Hudson, C. Lanciault, C. Thomas, C. Tsikitis, L. V. Anand, S. 2017-05-09 doi:10.1101/136234 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ Preferential targeting of lateral entorhinal inputs onto newly integrated granule cells ]]> https://biorxiv.org/content/10.1101/153767v1?rss=1 Woods, N. I. Vaaga, C. E. Chatzi, C. Adelson, J. D. Collie, M. F. Perederiy, J. V. Tovar, K. R. Westbrook, G. L. 2017-06-21 doi:10.1101/153767 Cold Spring Harbor Laboratory Press 2017-06-21 <![CDATA[ Discrete and coordinated encoding of punishment contingent on rewarded actions by prefrontal cortex and VTA ]]> https://biorxiv.org/content/10.1101/157032v1?rss=1 Park, J. Moghaddam, B. 2017-06-28 doi:10.1101/157032 Cold Spring Harbor Laboratory Press 2017-06-28 <![CDATA[ Scalable and efficient single-cell DNA methylation sequencing by combinatorial indexing. ]]> https://biorxiv.org/content/10.1101/157230v1?rss=1 Mulqueen, R. M. Pokholok, D. Norberg, S. Fields, A. J. Sun, D. Torkenczy, K. A. Shendure, J. Trapnell, C. O'Roak, B. J. Xia, Z. Steemers, F. J. Adey, A. C. 2017-06-28 doi:10.1101/157230 Cold Spring Harbor Laboratory Press 2017-06-28 <![CDATA[ Neutral tumor evolution? ]]> https://biorxiv.org/content/10.1101/158006v1?rss=1 Tarabichi, M. Martincorena, I. Gerstung, M. Markowetz, F. Spellman, P. T. Morris, Q. D. Lingjaerde, O. C. Wedge, D. C. Van Loo, P. - PCAWG Evolution and Heterogeneity Working Group, 2017-06-30 doi:10.1101/158006 Cold Spring Harbor Laboratory Press 2017-06-30 <![CDATA[ Activation and desensitization mechanism of AMPA receptor-TARP complex by cryo-EM ]]> https://biorxiv.org/content/10.1101/158402v1?rss=1 Gouaux, E. Chen, S. Zhao, Y. Wang, Y. S. Shekhar, M. Tajkhorshid, E. 2017-07-01 doi:10.1101/158402 Cold Spring Harbor Laboratory Press 2017-07-01 <![CDATA[ Sexually divergent DNA methylation programs with hippocampal aging ]]> https://biorxiv.org/content/10.1101/161752v1?rss=1 Masser, D. Hadad, N. Porter, H. Mangold, C. Unnikrishnan, A. Ford, M. Giles, C. Georgescu, C. Dozmorov, M. Wren, J. Richardson, A. Stanford, D. Freeman, W. 2017-07-10 doi:10.1101/161752 Cold Spring Harbor Laboratory Press 2017-07-10 <![CDATA[ Correlated gene expression and anatomical communication support synchronized brain activity in the mouse functional connectome ]]> https://biorxiv.org/content/10.1101/167304v1?rss=1 Mills, B. D. Grayson, D. Shunmugavel, A. Miranda-Dominguez, O. Feczko, E. Earl, E. Neve, K. Fair, D. 2017-07-22 doi:10.1101/167304 Cold Spring Harbor Laboratory Press 2017-07-22 <![CDATA[ Image velocimetry and spectral analysis enable quantitative characterization of larval zebrafish gut motility ]]> https://biorxiv.org/content/10.1101/169979v1?rss=1 Ganz, J. Baker, R. P. Hamilton, M. K. Melancon, E. Diba, P. Eisen, J. S. Parthasarathy, R. 2017-07-28 doi:10.1101/169979 Cold Spring Harbor Laboratory Press 2017-07-28 <![CDATA[ Anti-diabetic drug binding site in KATP channels revealed by Cryo-EM ]]> https://biorxiv.org/content/10.1101/172908v1?rss=1 Martin, G. M. Yoshioka, C. Kandasamy, B. DiMaio, F. Shyng, S.-L. 2017-08-05 doi:10.1101/172908 Cold Spring Harbor Laboratory Press 2017-08-05 <![CDATA[ Ectopic Expression of DNA Repair Enzymes Modulates Survival following Ultraviolet Irradiation Challenge ]]> https://biorxiv.org/content/10.1101/185058v1?rss=1 Garg, S. P. Minko, I. G. Coskun, E. Erdem, O. Jaruga, P. Dizdaroglu, M. Lloyd, R. S. 2017-09-06 doi:10.1101/185058 Cold Spring Harbor Laboratory Press 2017-09-06 <![CDATA[ ELMOD1 stimulates ARF6-GTP hydrolysis to stabilize apical structures in developing vestibular hair cells ]]> https://biorxiv.org/content/10.1101/189621v1?rss=1 Krey, J. F. Dumont, R. A. Wilmarth, P. A. David, L. L. Johnson, K. R. Barr-Gillespie, P. G. 2017-09-15 doi:10.1101/189621 Cold Spring Harbor Laboratory Press 2017-09-15 <![CDATA[ Enabling Precision Medicine via standard communication of NGS provenance, analysis, and results ]]> https://biorxiv.org/content/10.1101/191783v1?rss=1 Alterovitz, G. Dean, D. A. Goble, C. Crusoe, M. R. Soiland-Reyes, S. Bell, A. Hayes, A. King, C. H. H. Johanson, E. Thompson, E. E. Donaldson, E. Tsang, H. S. Goecks, J. Almeida, J. S. Guo, L. Walderhaug, M. Walsh, P. Kahsay, R. Bloom, T. Lai, Y. Simonyan, V. Mazumder, R. 2017-09-21 doi:10.1101/191783 Cold Spring Harbor Laboratory Press 2017-09-21 <![CDATA[ Population-level distribution and putative immunogenicity of cancer neoepitopes ]]> https://biorxiv.org/content/10.1101/192716v1?rss=1 Wood, M. A. Paralkar, M. Paralkar, M. P. Nguyen, A. Struck, A. J. Ellrott, K. Margolin, A. Nellore, A. Thompson, R. F. 2017-09-22 doi:10.1101/192716 Cold Spring Harbor Laboratory Press 2017-09-22 <![CDATA[ Re-evaluation of lysyl hydroxylation in the collagen triple helix: lysyl hydroxylase 1 and prolyl 3-hydroxylase 3 have site-differential and collagen type-dependent roles in lysine hydroxylation. ]]> https://biorxiv.org/content/10.1101/2019.12.16.877852v1?rss=1 Ishikawa, Y. Taga, Y. Zientek, K. Mizuno, N. Salo, A. M. Semenova, O. Tufa, S. Keene, D. R. Holden, P. Mizuno, K. Myllyharju, J. Bächinger, H. P. 2019-12-16 doi:10.1101/2019.12.16.877852 Cold Spring Harbor Laboratory Press 2019-12-16 <![CDATA[ Analysis of model organism viability through an interspecies pathway comparison pipeline using the dynamic impact approach ]]> https://biorxiv.org/content/10.1101/2019.12.18.448985v1?rss=1 Nguyen, A. D. Bionaz, M. 2019-12-19 doi:10.1101/2019.12.18.448985 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Investigating β-lactam drug targets in Mycobacterium tuberculosis using chemical probes ]]> https://biorxiv.org/content/10.1101/2019.12.19.881631v1?rss=1 Beatty, K. E. Levine, S. R. 2019-12-19 doi:10.1101/2019.12.19.881631 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Short-term Effects of Vagus Nerve Stimulationon Learning and Evoked Activity in AuditoryCortex ]]> https://biorxiv.org/content/10.1101/2019.12.19.883165v1?rss=1 Lai, J. David, S. V. 2019-12-20 doi:10.1101/2019.12.19.883165 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Postnatal expansion, maturation and functionality of MR1 T cells in humans ]]> https://biorxiv.org/content/10.1101/2019.12.20.882746v1?rss=1 Swarbrick, G. M. Gela, A. Cansler, M. E. Null, M. D. Duncan, R. B. Nemes, E. Shey, M. Nsereko, M. Mayanja-Kizza, H. Kiguli, S. Koh, J. Hanekom, W. Hatherill, M. Lancioni, C. Lewinsohn, D. M. Scriba, T. Lewinsohn, D. A. 2019-12-21 doi:10.1101/2019.12.20.882746 Cold Spring Harbor Laboratory Press 2019-12-21 <![CDATA[ KCNQ channels enable reliable presynaptic spiking and synaptic transmission at high-frequency ]]> https://biorxiv.org/content/10.1101/2019.12.26.888875v1?rss=1 Zhang, Y. Li, D. Darwish, Y. Trussell, L. O. Huang, H. 2019-12-27 doi:10.1101/2019.12.26.888875 Cold Spring Harbor Laboratory Press 2019-12-27 <![CDATA[ A sample preparation protocol for high throughput immunofluorescence of suspension cells ]]> https://biorxiv.org/content/10.1101/2020.01.05.895201v1?rss=1 Backstrom, A. Kugel, L. Gnann, C. Xu, H. Aslan, J. E. Lundberg, E. Stadler, C. 2020-01-06 doi:10.1101/2020.01.05.895201 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ Cerebellar Purkinje cell activity modulates aggressive behavior ]]> https://biorxiv.org/content/10.1101/2020.01.06.891127v1?rss=1 Jackman, S. L. Chen, C. H. Offermann, H. L. Drew, I. R. Harrison, B. M. Bowman, A. M. Flick, K. M. Flaquer, I. Regehr, W. G. 2020-01-06 doi:10.1101/2020.01.06.891127 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ Individual variability in functional organization of the human and monkey auditory cortex ]]> https://biorxiv.org/content/10.1101/2020.01.06.895474v1?rss=1 Ren, J. Liu, H. Xu, T. Schoeppe, F. Wang, D. Li, M. Lin, Y. Ramirez, J. Lu, J. Li, L. Ahveninen, J. 2020-01-07 doi:10.1101/2020.01.06.895474 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ Regulation of HDAC2-PDX1 by RNF125 defines pancreatic cancer development ]]> https://biorxiv.org/content/10.1101/2020.01.06.896555v1?rss=1 Hasnis, E. Kim, H. Verma, S. Feng, Y. Almog, R. Matsliah, S. Vavinskaya, V. Alelbaum, R. Ben-Ishay, O. Tuveson, D. Sears, R. Ronai, Z. A. 2020-01-07 doi:10.1101/2020.01.06.896555 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ Human cytomegalovirus evades ZAP detection by suppressing CpG dinucleotides in the major immediate early genes. ]]> https://biorxiv.org/content/10.1101/2020.01.07.897132v1?rss=1 Lee, C.-H. Chiweshe, S. McCormick, D. Raper, A. R. wickenhagen, A. DeFilippis, V. R. GAUNT, E. Simmonds, P. Wilson, S. J. Grey, F. 2020-01-08 doi:10.1101/2020.01.07.897132 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Local retinoic acid directs emergence of the extraocular muscle functional unit ]]> https://biorxiv.org/content/10.1101/2020.01.07.897694v1?rss=1 Comai, G. E. Tesarova, M. Dupe, V. Rhinn, M. Vallecillo Garcia, P. da Silva, F. Feret, B. Exelby, K. Dolle, P. Carlsson, L. Pryce, B. Spitz, F. Stricker, S. Zikmund, T. Kaiser, J. Briscoe, J. Schedl, A. Ghyselinck, N. B. Schweitzer, R. Tajbakhsh, S. 2020-01-07 doi:10.1101/2020.01.07.897694 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ A new long-read RNA-seq analysis approach identifies and quantifies novel transcripts of very large genes ]]> https://biorxiv.org/content/10.1101/2020.01.08.898627v1?rss=1 Uapinyoying, P. B. Goecks, J. Knoblach, S. Panchapakesan, K. Bonnemann, C. Partridge, T. Jaiswal, J. Hoffman, E. 2020-01-09 doi:10.1101/2020.01.08.898627 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Portable Automated Rapid Testing ( PART ) for auditory research: Validation in a normal hearing population ]]> https://biorxiv.org/content/10.1101/2020.01.08.899088v1?rss=1 Lelo de Larrea-Mancera, E. S. Stavropoulos, T. Hoover, E. C. Eddins, D. A. Gallun, F. J. Seitz, A. R. 2020-01-09 doi:10.1101/2020.01.08.899088 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Discovery of a novel inhibitory neuron class, the L-Stellate cells of the cochlear nucleus ]]> https://biorxiv.org/content/10.1101/2020.01.09.900092v1?rss=1 Ngodup, T. Romero, G. E. Trussell, L. 2020-01-09 doi:10.1101/2020.01.09.900092 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ MATERNAL ZIKA VIRUS (ZIKV) INFECTION FOLLOWING VAGINAL INOCULATION WITH ZIKV-INFECTED SEMEN IN THE TIMED-PREGNANT OLIVE BABOON ]]> https://biorxiv.org/content/10.1101/2020.01.10.902692v1?rss=1 Gurung, S. Nadeau, H. Maxted, M. Peregrine, J. Reuter, D. N. Norris, A. Edwards, R. K. Hyatt, K. Singleton, K. Papin, J. F. Myers, D. A. 2020-01-11 doi:10.1101/2020.01.10.902692 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Dietary Amino Acids Impact LRRK2-induced Neurodegeneration in Parkinson's Disease Models ]]> https://biorxiv.org/content/10.1101/2020.01.13.905471v1?rss=1 Chittoor-Vinod, V. G. Villalobos-Cantor, S. Roshak, H. Shea, K. Martin, I. 2020-01-16 doi:10.1101/2020.01.13.905471 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ Complementary effects of adaptation and gain control on sound encoding in primary auditory cortex ]]> https://biorxiv.org/content/10.1101/2020.01.14.905000v1?rss=1 Pennington, J. R. David, S. V. 2020-01-15 doi:10.1101/2020.01.14.905000 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Genetic ablation of the mitochondrial ribosome in Plasmodium falciparum sensitizes the human malaria parasite to antimalarial drugs targeting mitochondrial functions ]]> https://biorxiv.org/content/10.1101/2020.01.14.906198v1?rss=1 Ling, L. Mulaka, M. Munro, J. Dass, S. Mather, M. W. Riscoe, M. K. Llinas, M. Zhou, J. Ke, H. 2020-01-14 doi:10.1101/2020.01.14.906198 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Transient Commensal Clonal Interactions Can Drive Tumor Metastasis ]]> https://biorxiv.org/content/10.1101/2020.01.16.907071v1?rss=1 Naffar-Abu Amara, S. Kuiken, H. J. Selfors, L. M. Butler, T. Leung, M. L. Leung, C. T. Kuhn, E. P. Kolarova, T. R. Hage, C. Ganesh, K. Foster, R. Rueda, B. R. Aktipis, A. Spellman, P. T. Ince, T. Navin, N. Mills, G. B. Bronson, R. T. Brugge, J. S. S. 2020-01-16 doi:10.1101/2020.01.16.907071 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ Intra-striatal AAV2.retro administration leads to extensive retrograde transport in the rhesus macaque brain: implications for disease modeling and therapeutic development ]]> https://biorxiv.org/content/10.1101/2020.01.17.910893v1?rss=1 Weiss, A. R. Liguore, W. A. Domire, J. S. Button, D. McBride, J. L. 2020-01-18 doi:10.1101/2020.01.17.910893 Cold Spring Harbor Laboratory Press 2020-01-18 <![CDATA[ Purine-responsive expression of the Leishmania donovani NT3 purine nucleobase transporter is mediated by a conserved RNA stem-loop ]]> https://biorxiv.org/content/10.1101/2020.01.26.920504v1?rss=1 Licon, M. H. Yates, P. A. 2020-01-27 doi:10.1101/2020.01.26.920504 Cold Spring Harbor Laboratory Press 2020-01-27 <![CDATA[ A global lipid map defines a network essential for Zika virus replication ]]> https://biorxiv.org/content/10.1101/2020.01.27.910919v1?rss=1 Leier, H. C. Weinstein, J. B. Kyle, J. E. Lee, J.-Y. Bramer, L. M. Stratton, K. G. Kempthorne, D. Navratil, A. R. Tafesse, E. G. Hornemann, T. Messer, W. B. Dennis, E. A. Metz, T. O. Barklis, E. Tafesse, F. G. 2020-01-27 doi:10.1101/2020.01.27.910919 Cold Spring Harbor Laboratory Press 2020-01-27 <![CDATA[ Gut carriage of antimicrobial resistance genes in women exposed to small-scale poultry farms in rural Uganda: a feasibility study ]]> https://biorxiv.org/content/10.1101/2020.02.13.947226v1?rss=1 Weil, A. A. Debela, M. D. Muyanja, D. Kakuhikire, B. Baguma, C. Bangsberg, D. Tsai, A. C. Lai, P. S. 2020-02-13 doi:10.1101/2020.02.13.947226 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Composition of the Lipid Droplets of the Bovine Corpus Luteum ]]> https://biorxiv.org/content/10.1101/2020.02.13.948117v1?rss=1 Talbott, H. A. Plewes, M. R. Krause, C. Hou, X. Zhang, P. Rizzo, W. B. Wood, J. R. Cupp, A. S. Davis, J. S. 2020-02-13 doi:10.1101/2020.02.13.948117 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Inflammation promotes tumor aggression by stimulating stromal cell-dependent collagen crosslinking and stromal stiffening ]]> https://biorxiv.org/content/10.1101/2020.02.13.948141v1?rss=1 Maller, O. Drain, A. P. Barrett, A. S. Borgquist, S. Ruffell, B. Thanh, P. T. Gruosso, T. Kuasne, H. Lakins, J. N. Acerbi, I. Barnes, J. M. Nemkov, T. Chauhan, A. Gruenberg, J. Nasir, A. Bjarnadottir, O. Werb, Z. Kabos, P. Hwang, E. S. Park, M. Coussens, L. M. Nelson, A. C. Hansen, K. C. Weaver, V. M. 2020-02-13 doi:10.1101/2020.02.13.948141 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Mucin 4 Protects Female Mice from Coronavirus Pathogenesis ]]> https://biorxiv.org/content/10.1101/2020.02.19.957118v1?rss=1 Plante, J. A. Plante, K. Gralinski, L. Beall, A. Ferris, M. T. Bottomly, D. Green, R. R. McWeeney, S. Heise, M. T. Baric, R. S. Menachery, V. D. 2020-02-20 doi:10.1101/2020.02.19.957118 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Accumulative deamidation of human lens protein γS-crystallin leads to partially unfolded intermediates with enhanced aggregation propensity ]]> https://biorxiv.org/content/10.1101/2020.02.21.960237v1?rss=1 Vetter, C. J. Thorn, D. Wheeler, S. G. Mundorff, C. Halverson-Kolkind, K. Carver, J. A. David, L. L. Lampi, K. J. 2020-02-22 doi:10.1101/2020.02.21.960237 Cold Spring Harbor Laboratory Press 2020-02-22 <![CDATA[ Mesoscopic-scale functional networks in the primate amygdala ]]> https://biorxiv.org/content/10.1101/2020.02.24.963587v1?rss=1 Morrow, J. K. Cohen, M. X. Gothard, K. M. 2020-02-26 doi:10.1101/2020.02.24.963587 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ Gut Microbiome Pattern Reflects Healthy Aging and Predicts Extended Survival in Humans ]]> https://biorxiv.org/content/10.1101/2020.02.26.966747v1?rss=1 Wilmanski, T. Diener, C. Rappaport, N. Patwardhan, S. Wiedrick, J. Lapidus, J. Earls, J. C. Zimmer, A. Glusman, G. Robinson, M. Yurkovich, J. T. Kado, D. M. Cauley, J. A. Zmuda, J. Lane, N. E. Magis, A. T. Lovejoy, J. C. Gibbons, S. M. Hood, L. Orwoll, E. S. Price, N. D. 2020-02-28 doi:10.1101/2020.02.26.966747 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ Crosstalk between invadopodia and the extracellular matrix ]]> https://biorxiv.org/content/10.1101/2020.02.26.966762v1?rss=1 Iizuka, S. Leon, R. P. Gribbin, K. P. Zhang, Y. Navarro, J. Smith, R. Devlin, K. Wang, L. G. Gibbs, S. L. Korkola, J. Nan, X. Courtneidge, S. A. 2020-02-27 doi:10.1101/2020.02.26.966762 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ In vivo repair of a protein underlying a neurological disorder by programmable RNA editing ]]> https://biorxiv.org/content/10.1101/2020.02.26.966820v1?rss=1 Sinnamon, J. Kim, S. Y. Fisk, J. R. Song, Z. Nakai, H. Jeng, S. McWeeney, S. K. Mandel, G. 2020-02-27 doi:10.1101/2020.02.26.966820 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ Chemical and structural investigation of the paroxetine-human serotonin transporter complex ]]> https://biorxiv.org/content/10.1101/2020.02.26.966895v1?rss=1 Coleman, J. A. Navratna, V. Antermite, D. Yang, D. Bull, J. A. Gouaux, E. 2020-02-27 doi:10.1101/2020.02.26.966895 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ Subphase Material Stabilizes Films of Pulmonary Surfactant ]]> https://biorxiv.org/content/10.1101/2020.02.27.968099v1?rss=1 Andreev, K. Martynowycz, M. Kuzmenko, I. Bu, W. Hall, S. B. Gidalevitz, D. 2020-02-28 doi:10.1101/2020.02.27.968099 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ The serine-threonine kinase TAO3 promotes cancer invasion and tumor growth by facilitating trafficking of endosomes containing the invadopodia scaffold TKS5α ]]> https://biorxiv.org/content/10.1101/2020.02.27.968305v1?rss=1 Iizuka, S. Quintavalle, M. Ceja Navarro, J. Gribbin, K. P. Ardecky, R. J. Abelman, M. Ma, C.-T. Sergienko, E. Zeng, F.-Y. Pass, I. Thomas, G. McWeeney, S. Hassig, C. A. Pinkerton, A. B. Courtneidge, S. A. 2020-02-28 doi:10.1101/2020.02.27.968305 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ BoneMA - Synthesis and Characterization of a Methacrylated Bone-derived Hydrogel for Bioprinting of Vascularized Tissues ]]> https://biorxiv.org/content/10.1101/2020.03.02.974063v1?rss=1 S., P. P. Athirasala, A. Tahayeri, A. Abdelmoniem, R. George, A. Bertassoni, L. E. 2020-03-04 doi:10.1101/2020.03.02.974063 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ Conserved His-Gly motif of acid-sensing ion channels resides in a reentrant loop implicated in gating and ion selectivity ]]> https://biorxiv.org/content/10.1101/2020.03.02.974154v1?rss=1 Yoder, N. Gouaux, E. 2020-03-03 doi:10.1101/2020.03.02.974154 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ 3D printing of Microgel-loaded Modular LEGO-like Cages as Instructive Scaffolds for Tissue Engineering ]]> https://biorxiv.org/content/10.1101/2020.03.02.974204v1?rss=1 View larger version (88K): org.highwire.dtl.DTLVardef@1a97a72org.highwire.dtl.DTLVardef@1a60fbeorg.highwire.dtl.DTLVardef@1538f13org.highwire.dtl.DTLVardef@d6345b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hipfinger, C. Subbiah, R. Tahayeri, A. Athirasala, A. Horsophonphong, S. Thrivikraman, G. Franca, C. M. Cunha, D. A. Mansoorifar, A. Zahariev, A. Jones, J. M. Coelho, P. G. Witek, L. Xie, H. Guldberg, R. E. Bertassoni, L. E. 2020-03-04 doi:10.1101/2020.03.02.974204 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ The physical form of microbial ligands bypasses the need for dendritic cell migration to stimulate adaptive immunity ]]> https://biorxiv.org/content/10.1101/2020.03.03.973727v1?rss=1 Borriello, F. Spreafico, R. Poli, V. Chou, J. Barrett, N. Lacanfora, L. Franco, M. Marongiu, L. Iwakura, Y. Pucci, F. Kruppa, M. Ma, Z. Williams, D. Zanoni, I. 2020-03-05 doi:10.1101/2020.03.03.973727 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Functional Identification of Specialized Basal Ganglia Circuits that Regulate Vocal Motor Sequences ]]> https://biorxiv.org/content/10.1101/2020.03.14.991042v1?rss=1 Xiao, L. Merullo, D. P. Cao, M. Co, M. Kulkarni, A. Konopka, G. Roberts, T. F. 2020-03-16 doi:10.1101/2020.03.14.991042 Cold Spring Harbor Laboratory Press 2020-03-16 <![CDATA[ Autism-linked gene FoxP1 selectively regulates the cultural transmission of learned vocalizations ]]> https://biorxiv.org/content/10.1101/2020.03.14.992016v1?rss=1 Garcia-Oscos, F. Koch, T. Pancholi, H. Trusel, M. Daliparthi, V. Ayhan, F. Co, M. Alam, D. H. Holdway, J. E. Konopka, G. Roberts, T. F. 2020-03-16 doi:10.1101/2020.03.14.992016 Cold Spring Harbor Laboratory Press 2020-03-16 <![CDATA[ Orally Bioavailable Endochin-like Quinolone Carbonate Ester Prodrug Reduces Toxoplasma gondii Brain Cysts ]]> https://biorxiv.org/content/10.1101/2020.03.19.999664v1?rss=1 Doggett, J. S. Schultz, T. L. Miller, A. Bruzual, I. Pou, S. Winter, R. W. Dodean, R. Zakharov, L. N. Nilsen, A. Riscoe, M. K. Carruthers, V. B. 2020-03-20 doi:10.1101/2020.03.19.999664 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Efficacy of Guanabenz Combination Therapy Against Chronic Toxoplasmosis Across Multiple Mouse Strains ]]> https://biorxiv.org/content/10.1101/2020.03.19.999672v1?rss=1 Martynowicz, J. Doggett, J. S. Sullivan, W. J. 2020-03-20 doi:10.1101/2020.03.19.999672 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Selective interferon responses of intestinal epithelial cells minimize TNFα cytotoxicity ]]> https://biorxiv.org/content/10.1101/2020.03.20.000604v1?rss=1 Van Winkle, J. A. Constant, D. A. Li, L. Nice, T. J. 2020-03-22 doi:10.1101/2020.03.20.000604 Cold Spring Harbor Laboratory Press 2020-03-22 <![CDATA[ Sulfopin, a selective covalent inhibitor of Pin1, blocks Myc-driven tumor initiation and growth in vivo ]]> https://biorxiv.org/content/10.1101/2020.03.20.998443v1?rss=1 Dubiella, C. Pinch, B. J. Zaidman, D. Manz, T. D. Poon, E. He, S. Resnick, E. Langer, E. M. Daniel, C. J. Seo, H.-S. Chen, Y. Ficarro, S. B. Jamin, Y. Lian, X. Kibe, S. Kozono, S. Koikawa, K. Doctor, Z. M. Nabet, B. Browne, C. M. Yang, A. Stoler-Barak, L. Shah, R. B. Vangos, N. E. Geffken, E. A. Oren, R. Sidi, S. Shulman, Z. Wang, C. Marto, J. A. Dhe-Paganon, S. Look, T. Zhou, X. Z. Lu, K. P. Sears, R. C. Chesler, L. Gray, N. S. London, N. 2020-03-21 doi:10.1101/2020.03.20.998443 Cold Spring Harbor Laboratory Press 2020-03-21 <![CDATA[ Effects of Controlled Dual Growth Factor Delivery on Bone Regeneration Following Composite Bone-Muscle Injury ]]> https://biorxiv.org/content/10.1101/2020.03.25.008813v1?rss=1 90%, revealing a strong affinity of VEGF and BMP-2 to heparin and alginate. The system could achieve simultaneous or sequential release of VEGF and BMP-2 by varying the loading strategy. Single growth factor delivery (VEGF or BMP-2 alone) significantly enhanced vascular growth in vitro. However, no synergistic effect was observed for dual growth factor (BMP-2 + VEGF) delivery. Effective bone healing was achieved in all treatment groups (BMP-2, simultaneous or sequential delivery of BMP-2 and VEGF) in the composite injury model. The mechanics of the regenerated bone reached a maximum strength of [~]52% of intact bone with sequential delivery of VEGF and BMP-2. Overall, simultaneous or sequential co-delivery of low-dose BMP-2 and VEGF failed to fully restore the mechanics of bone in this injury model. Given the severity of the composite injury, VEGF alone may not be sufficient to establish mature and stable blood vessels when compared with previous studies co-delivering BMP-2+VEGF enhanced bone tissue regeneration. Hence, future studies are warranted to develop an alternative treatment strategy focusing on better control over growth factor dose, spatiotemporal delivery, and additional growth factors to regenerate fully functional bone tissue. HighlightsO_LIWe developed a smart growth factor delivery system using heparin microparticles and alginate that facilitates tunable delivery of VEGF and BMP-2 in a simultaneous or sequential manner by merely varying the loading strategy. C_LIO_LIIn vitro, both VEGF and BMP-2 alone promoted vascular growth; however, VEGF was significantly more potent, and there was no detectable benefit of co-delivery. C_LIO_LIIn vivo, both BMP-2 alone and co-delivery of VEGF and BMP-2 promoted bone formation in the challenging bone/muscle polytrauma model; however, none of the treatment groups restored biomechanical properties to that of uninjured bone. C_LI ]]> Subbiah, R. Cheng, A. Ruehle, M. A. Hettiaratchi, M. H. Bertassoni, L. E. Guldberg, R. E. 2020-03-26 doi:10.1101/2020.03.25.008813 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ In vivo photopharmacology enabled by multifunctional fibers ]]> https://biorxiv.org/content/10.1101/2020.03.28.012567v1?rss=1 Frank, J. A. Antonini, M.-J. Chiang, P.-H. Canales, A. Konrad, D. Garwood, I. Rajic, G. Koehler, F. Fink, Y. Anikeeva, P. 2020-03-30 doi:10.1101/2020.03.28.012567 Cold Spring Harbor Laboratory Press 2020-03-30 <![CDATA[ Identification and characterization of diverse OTU deubiquitinases in bacteria ]]> https://biorxiv.org/content/10.1101/2020.03.28.013474v1?rss=1 Schubert, A. F. Nguyen, J. V. Franklin, T. G. Geurink, P. P. Roberts, C. G. Sanderson, D. J. Miller, L. N. Ovaa, H. Hofmann, K. Pruneda, J. N. Komander, D. 2020-03-29 doi:10.1101/2020.03.28.013474 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ VISTA: Virtual ImmunoSTAining for pancreatic disease quantification in murine cohorts ]]> https://biorxiv.org/content/10.1101/2020.04.01.020842v1?rss=1 Ternes, L. Huang, G. Lanciault, C. Thibault, G. Riggers, R. Gray, J. W. Muschler, J. Chang, Y. H. 2020-04-02 doi:10.1101/2020.04.01.020842 Cold Spring Harbor Laboratory Press 2020-04-02 <![CDATA[ Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 A ]]> https://biorxiv.org/content/10.1101/2020.04.14.036384v1?rss=1 Flores, J. A. Haddad, B. G. Dolan, K. A. Myers, J. B. Yoshioka, C. C. Copperman, J. Zuckerman, D. M. Reichow, S. L. 2020-04-15 doi:10.1101/2020.04.14.036384 Cold Spring Harbor Laboratory Press 2020-04-15 <![CDATA[ PD-1 Specific 'Blocking' Antibodies That Deplete PD-1+ T Cells Present An Inconvenient Variable In Pre-clinical Immunotherapy Experiments ]]> https://biorxiv.org/content/10.1101/2020.04.14.041608v1?rss=1 Polesso, F. Munks, M. W. Rott, K. H. Smart, S. Hill, A. B. Moran, A. E. 2020-04-16 doi:10.1101/2020.04.14.041608 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Invasion of homogeneous and polyploid populations in nutrient-limiting environments ]]> https://biorxiv.org/content/10.1101/2020.04.15.041566v1?rss=1 Kimmel, G. J. Dane, M. Heiser, L. Altrock, P. M. Andor, N. 2020-04-17 doi:10.1101/2020.04.15.041566 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ Analysis of SARS-CoV-2 Antibodies in COVID-19 Convalescent Plasma using a Coronavirus Antigen Microarray ]]> https://biorxiv.org/content/10.1101/2020.04.15.043364v1?rss=1 de Assis, R. R. Jain, A. Nakajima, R. Jasinskas, A. Felgner, J. Obiero, J. M. Adenaiye, O. O. Tai, S. Hong, F. H. Norris, P. Stone, M. Simmons, G. Bagri, A. Schreiber, M. Buser, A. Holbro, A. Battegay, M. Milton, D. K. Prometheus Study Group, Davies, H. Corash, L. M. Busch, M. P. Felgner, P. L. Khan, S. 2020-04-17 doi:10.1101/2020.04.15.043364 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ Coronavirus Infection and PARP Expression Dysregulate the NAD Metabolome: A Potentially Actionable Component of Innate Immunity ]]> https://biorxiv.org/content/10.1101/2020.04.17.047480v1?rss=1 Heer, C. D. Sanderson, D. J. Alhammad, Y. M. O. Schmidt, M. S. Trammell, S. A. J. Perlman, S. Cohen, M. S. Fehr, A. R. Brenner, C. 2020-04-18 doi:10.1101/2020.04.17.047480 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Multiscale cardiac imaging to capture the whole heart and its internal cellular architecture, with applications to congenital heart disease ]]> https://biorxiv.org/content/10.1101/2020.04.22.055418v1?rss=1 Rykiel, G. Lopez, C. S. Riesterer, J. L. Fries, I. Deosthali, S. Courchaine, K. Maloyan, A. Thornburg, K. Rugonyi, S. 2020-04-23 doi:10.1101/2020.04.22.055418 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ A Cytoskeletal Protein Complex is Essential for Division of Intracellular Amastigotes of Leishmania mexicana ]]> https://biorxiv.org/content/10.1101/2020.04.29.068445v1?rss=1 Kelly, F. D. Tran, K. D. Hatfield, J. Schmidt, K. Sanchez, M. A. Landfear, S. M. 2020-04-30 doi:10.1101/2020.04.29.068445 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Structural and molecular determinants of CCS-mediated copper activation of MEK1/2 ]]> https://biorxiv.org/content/10.1101/2020.05.01.072124v1?rss=1 Grasso, M. Bond, G. J. Kim, Y.-J. Alwan, K. B. Boyd, S. Dzebo, M. M. Valenzuela, S. Tsang, T. Schibrowsky, N. A. Matthews, M. L. Burslem, G. M. Wittung-Stafshede, P. Winkler, D. D. Blackburn, N. J. Marmorstein, R. Brady, D. C. 2020-05-02 doi:10.1101/2020.05.01.072124 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ A miR-494 dependent feedback loop regulates ER stress ]]> https://biorxiv.org/content/10.1101/2020.05.12.088856v1?rss=1 Anand, S. Chatterjee, N. Espinosa-Diez, C. 2020-05-13 doi:10.1101/2020.05.12.088856 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ Exploiting KRAS-driven Ferroaddiction in Cancer Through Ferrous Iron-Activatable Drug Conjugates (FeADC) ]]> https://biorxiv.org/content/10.1101/2020.05.12.088971v1?rss=1 Jiang, H. Muir, R. K. Gonciarz, R. L. Olshen, A. B. Yeh, I. Hann, B. C. Zhao, N. Wang, Y.-h. Korkola, J. Behr, S. C. Evans, M. J. collisson, e. Renslo, A. 2020-05-14 doi:10.1101/2020.05.12.088971 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Astrocytes close a critical period of motor circuit plasticity ]]> https://biorxiv.org/content/10.1101/2020.05.15.098608v1?rss=1 Ackerman, S. D. Perez-Catalan, N. A. Freeman, M. R. Doe, C. Q. 2020-05-16 doi:10.1101/2020.05.15.098608 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia ]]> https://biorxiv.org/content/10.1101/2020.05.16.099366v1?rss=1 Namasivayam, S. Baptista, R. d. P. Xiao, W. Hall, E. M. Doggett, J. S. Troell, K. Kissinger, J. C. 2020-05-18 doi:10.1101/2020.05.16.099366 Cold Spring Harbor Laboratory Press 2020-05-18 <![CDATA[ NAIP-NLRC4-deficient mice are susceptible to shigellosis ]]> https://biorxiv.org/content/10.1101/2020.05.16.099929v1?rss=1 Mitchell, P. S. Roncaioli, J. L. Turcotte, E. A. Goers, L. Chavez, R. A. Lee, A. Y. Lesser, C. F. Rauch, I. Vance, R. E. 2020-05-17 doi:10.1101/2020.05.16.099929 Cold Spring Harbor Laboratory Press 2020-05-17 <![CDATA[ Gbx2 identifies two amacrine cell subtypes with distinct molecular, morphological, and physiological properties ]]> https://biorxiv.org/content/10.1101/2020.05.19.104307v1?rss=1 Kerstein, P. C. Leffler, J. Sivyer, B. Taylor, W. R. Wright, K. M. 2020-05-20 doi:10.1101/2020.05.19.104307 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ S-nitrosylated and non-nitrosylated COX2 has differential expression and distinct subcellular localization in normal and breast cancer tissue ]]> https://biorxiv.org/content/10.1101/2020.05.20.104612v1?rss=1 Jindal, S. Pennock, N. D. Klug, A. Narasimhan, J. Calhoun, A. Roberts, M. R. Tamimi, R. M. Eliassen, A. H. Weinmann, S. Borges, V. F. Schedin, P. J. 2020-05-21 doi:10.1101/2020.05.20.104612 Cold Spring Harbor Laboratory Press 2020-05-21 <![CDATA[ Towards complete and error-free genome assemblies of all vertebrate species ]]> https://biorxiv.org/content/10.1101/2020.05.22.110833v1?rss=1 Rhie, A. McCarthy, S. A. Fedrigo, O. Damas, J. Formenti, G. Koren, S. Uliano-Silva, M. Chow, W. Fungtammasan, A. Gedman, G. L. Cantin, L. J. Thibaud-Nissen, F. Haggerty, L. Lee, C. Ko, B. J. Kim, J. Bista, I. Smith, M. Haase, B. Mountcastle, J. Winkler, S. Paez, S. Howard, J. Vernes, S. C. Lama, T. M. Grutzner, F. C. Warren, W. C. Balakrishnan, C. Burt, D. George, J. M. Biegler, M. Iorns, D. Digby, A. Eason, D. Edwards, T. Wilkinson, M. Turner, G. F. Meyer, A. Kautt, A. F. Franchini, P. Detrich, H. W. Svardal, H. Wagner, M. Naylor, G. J. P. Pippel, M 2020-05-23 doi:10.1101/2020.05.22.110833 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ Ventral tegmental area GABA neurons mediate stress-induced anhedonia. ]]> https://biorxiv.org/content/10.1101/2020.05.28.121905v1?rss=1 Lowes, D. C. Chamberlin, L. A. Kretsge, L. N. Holt, E. S. Abbas, A. I. Park, A. J. Yusufova, L. Bretton, Z. H. Firdous, A. Gordon, J. A. Harris, A. Z. 2020-05-31 doi:10.1101/2020.05.28.121905 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ A deep intronic variant activates a pseudoexon in the MTM1 gene in a family with X-linked myotubular myopathy ]]> https://biorxiv.org/content/10.1101/2020.05.28.122333v1?rss=1 G variant in deep intronic space activates a cryptic 5 donor splice site resulting in the inclusion of a 48bp pseudoexon into the mature MTM1 mRNA. The variant is present in all affected males, absent in unaffected males and heterozygous in the mother of the affected males. The included intronic sequence contains a premature stop codon and experiments using a translational inhibitor indicate that the mutant mRNAs undergo nonsense-mediate decay. We conclude that affected males produce no, or low, levels of myotubularin-1 protein leading to a severe neonatal myopathy. The study highlights the need to consider non-coding variants in genomic screening in families with X-linked myotubular myopathy. ]]> Fitzgerald, J. Feist, C. Dietz, P. Moore, S. Basel, D. 2020-05-30 doi:10.1101/2020.05.28.122333 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ CRISPR Knockdown of Kcnq3 Attenuates the M-current in NPY/AgRP Neurons ]]> https://biorxiv.org/content/10.1101/2020.05.28.122341v1?rss=1 Stincic, T. L. Bosch, M. A. Hunker, A. C. Juarez, B. Connors, A. M. Zweifel, L. Rønnekleiv, O. K. Kelly, M. J. 2020-05-29 doi:10.1101/2020.05.28.122341 Cold Spring Harbor Laboratory Press 2020-05-29 <![CDATA[ Competition and Caries on Enamel of a Dual-species Biofilm Model of Streptococcus mutans and Streptococcus sanguinis. ]]> https://biorxiv.org/content/10.1101/2020.05.28.122697v1?rss=1 Diaz-Garrido, N. Lozano, C. Kreth, J. Giacaman, R. A. 2020-05-31 doi:10.1101/2020.05.28.122697 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Lmo7a Coordinates Neural Crest Migration and Lineage Specification by Regulating Cell Adhesion Dynamics ]]> https://biorxiv.org/content/10.1101/2020.05.30.125468v1?rss=1 Tatarakis, D. M. Tuttle, A. Schilling, T. F. 2020-05-31 doi:10.1101/2020.05.30.125468 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes ]]> https://biorxiv.org/content/10.1101/2020.06.02.128850v1?rss=1 Grzadkowski, M. R. Manning, H. Somers, J. Demir, E. 2020-06-03 doi:10.1101/2020.06.02.128850 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ In vitro and in vivo characterization of a recombinant rhesus cytomegalovirus containing a complete genome ]]> https://biorxiv.org/content/10.1101/2020.06.02.129486v1?rss=1 Taher, H. Mahyari, E. Kreklywich, C. Uebelhoer, L. S. McArdle, M. R. Moström, M. J. Bhusari, A. Nekorchuk, M. Whitmer, T. Scheef, E. A. Sprehe, L. M. Roberts, D. Hughes, C. M. Jackson, K. A. Selseth, A. N. Ventura, A. B. Yue, Y. Schmidt, K. A. Shao, J. Edlefsen, P. T. Smedley, J. Stanton, R. J. Axthelm, M. K. Estes, J. D. Hansen, S. G. Kaur, A. Barry, P. A. Bimber, B. N. Picker, L. J. Streblow, D. N. Früh, K. Malouli, D. 2020-06-02 doi:10.1101/2020.06.02.129486 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ Phenotype-guided subpopulation identification from single-cell sequencing data ]]> https://biorxiv.org/content/10.1101/2020.06.05.137240v1?rss=1 Sun, D. Guan, X. Moran, A. E. Qian, D. Z. Schedin, P. J. Adey, A. Spellman, P. T. Xia, Z. 2020-06-07 doi:10.1101/2020.06.05.137240 Cold Spring Harbor Laboratory Press 2020-06-07 <![CDATA[ Kinome Profiling of Gastrointestinal Stromal Tumors Using Multiplexed Inhibitor Beads and Mass Spectrometry Identifies Wee1 as Candidate Therapeutic Target ]]> https://biorxiv.org/content/10.1101/2020.06.07.138693v1?rss=1 Ye, S. Sharipova, D. Kozinova, M. Klug, L. D'Souza, J. Belinsky, M. G. Johnson, K. J. Einarson, M. B. Cai, K. Devarajan, K. Zhou, Y. Litwin, S. Heinrich, M. C. DeMatteo, R. von Mehren, M. Duncan, J. Rink, L. 2020-06-08 doi:10.1101/2020.06.07.138693 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ Dissociation of task engagement and arousal effects in auditory cortex and midbrain ]]> https://biorxiv.org/content/10.1101/2020.06.16.155432v1?rss=1 Saderi, D. Schwartz, Z. P. Heller, C. R. Pennington, J. R. David, S. V. 2020-06-17 doi:10.1101/2020.06.16.155432 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Modeling heterogeneity of Triple-Negative Breast Cancer highlights potency of WEE1 and BCL-XL targeting ]]> https://biorxiv.org/content/10.1101/2020.06.22.164418v1?rss=1 Lamballe, F. Ahmad, F. Vinik, Y. Castellanet, O. Daian, F. Mueller, A. Koehler, U. Bailly, A.-L. Josselin, E. Castellano, R. Cayrou, C. Charafe-Jauffret, E. Mills, G. B. Geli, V. Borg, J.-P. Lev, S. Maina, F. 2020-06-22 doi:10.1101/2020.06.22.164418 Cold Spring Harbor Laboratory Press 2020-06-22 <![CDATA[ Accessible, Reproducible, and Scalable Machine Learning for Biomedicine ]]> https://biorxiv.org/content/10.1101/2020.06.25.172445v1?rss=1 Gu, Q. Kumar, A. Bray, S. A. Creason, A. Khanteymoori, A. Jalili, V. Gruning, B. Goecks, J. 2020-06-28 doi:10.1101/2020.06.25.172445 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ Myristoylation alone is sufficient for PKA catalytic subunits to fractionally associate with the plasma membrane to regulate neuronal functions ]]> https://biorxiv.org/content/10.1101/2020.06.25.172676v1?rss=1 Xiong, W.-H. Qin, M. Zhong, H. 2020-06-27 doi:10.1101/2020.06.25.172676 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Multi- and transgenerational disruption of maternal behavior and female puberty by Endocrine Disrupting Chemical (EDC) mixture exposure ]]> https://biorxiv.org/content/10.1101/2020.06.26.172965v1?rss=1 Lopez Rodriguez, D. Aylwin, C. F. Delli, V. Sevrin, E. Campanile, M. Martin, M. Franssen, D. Gerard, A. Blacher, S. Tirelli, E. Noel, A. Lomniczi, A. Parent, A.-S. 2020-06-29 doi:10.1101/2020.06.26.172965 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Inhibition of CMP-sialic acid transport by endogenous 5-methyl CMP ]]> https://biorxiv.org/content/10.1101/2020.06.30.180356v1?rss=1 Ahjua, S. Cahill, J. Hartfield, K. A. Whorton, M. R. 2020-07-01 doi:10.1101/2020.06.30.180356 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Connexin 46 and connexin 50 gap junction channel open stability and unitary conductance are shaped by structural and dynamic features of their N-terminal domains ]]> https://biorxiv.org/content/10.1101/2020.07.01.182584v1?rss=1 Yue, B. Haddad, B. G. Khan, U. Chen, H. Atalla, M. Zhang, Z. Zuckerman, D. M. Reichow, S. L. Bai, D. 2020-07-01 doi:10.1101/2020.07.01.182584 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into the complex genetic architecture ]]> https://biorxiv.org/content/10.1101/2020.07.06.185066v1?rss=1 Chia, R. Sabir, M. S. Bandres-Ciga, S. Saez-Atienzar, S. Reynolds, R. H. Gustavsson, E. Walton, R. L. Ahmed, S. Viollet, C. Ding, J. Makarious, M. B. Diez-Fairen, M. Portley, M. K. Shah, Z. Abramzon, Y. Hernandez, D. G. Blauwendraat, C. Stone, D. J. Eicher, J. Parkkinen, L. Ansorge, O. Clark, L. Honig, L. S. Marder, K. Lemstra, A. St. George-Hyslop, P. Londos, E. Morgan, K. Lashley, T. Warner, T. T. Jaunmuktane, Z. Galasko, D. Santana, I. Tienari, P. Myllykangas, L. Oinas, M. Cairns, N. J. Morris, J. C. Halliday, G. M. Van Deerlin, V. M. Trojanowski, J. 2020-07-06 doi:10.1101/2020.07.06.185066 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Genome-wide assessment of REST binding profiles reveals distinctions between human and mouse hippocampus ]]> https://biorxiv.org/content/10.1101/2020.07.07.192229v1?rss=1 McGann, J. C. Spinner, M. A. Garg, S. K. Mullendorf, K. Woltjer, R. L. Mandel, G. 2020-07-07 doi:10.1101/2020.07.07.192229 Cold Spring Harbor Laboratory Press 2020-07-07 <![CDATA[ A targeted computational screen of the SWEETLEAD database reveals FDA-approved compounds with anti-dengue viral activity ]]> https://biorxiv.org/content/10.1101/2020.07.09.194993v1?rss=1 Jasmine Moshiri David A. Constant Bowen Liu Roberto Mateo Steven Kearnes Paul Novick Ritika Prasad Claude Nagamine Vijay Pande Karla Kirkegaard 2020-07-09 doi:10.1101/2020.07.09.194993 Cold Spring Harbor Laboratory Press 2020-07-09 <![CDATA[ Primary and secondary motoneurons use different calcium channel types to control escape and swimming behaviors in zebrafish ]]> https://biorxiv.org/content/10.1101/2020.07.14.202853v1?rss=1 Wen, H. Eckenstein, K. Weihrauch, V. Stigloher, C. Brehm, P. 2020-07-14 doi:10.1101/2020.07.14.202853 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ The S1 protein of SARS-CoV-2 crosses the blood-brain barrier: Kinetics, distribution, mechanisms, and influence of ApoE genotype, sex, and inflammation ]]> https://biorxiv.org/content/10.1101/2020.07.15.205229v1?rss=1 Rhea, E. M. Logsdon, A. F. Hansen, K. M. Williams, L. Reed, M. Baumann, K. Holden, S. Raber, J. Banks, W. A. Erickson, M. A. 2020-07-15 doi:10.1101/2020.07.15.205229 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ BMP signalling directs a fibroblast-to-myoblast conversion at the connective tissue/muscle interface to pattern limb muscles ]]> https://biorxiv.org/content/10.1101/2020.07.20.211342v1?rss=1 Esteves de Lima, J. Blavet, C. Bonnin, M.-A. Hirsinger, E. Comai, G. Yvernogeau, L. Bellenger, l. Mella, S. Nassari, S. Robin, C. Schweitzer, R. Fournier-Thibault, C. Tajbakhsh, S. Relaix, F. DUPREZ, D. 2020-07-21 doi:10.1101/2020.07.20.211342 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Rapid generation of circulating and mucosal decoy ACE2 using mRNA nanotherapeutics for the potential treatment of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.07.24.205583v1?rss=1 Kim, J. Mukherjee, A. Nelson, D. Jozic, A. Sahay, G. 2020-07-25 doi:10.1101/2020.07.24.205583 Cold Spring Harbor Laboratory Press 2020-07-25 <![CDATA[ Single cell tracing reveals heterogeneous drug-, dose-, and time-dependent effects on cancer cell fates ]]> https://biorxiv.org/content/10.1101/2020.07.24.219907v1?rss=1 Gross, S. M. Sanchez-Aguila, C. Zhan, P. J. Heiser, L. M. 2020-07-25 doi:10.1101/2020.07.24.219907 Cold Spring Harbor Laboratory Press 2020-07-25 <![CDATA[ Genotypic Complexity in Initial Cleavage Divisions of Mammalian Embryos is Contributed by Defective BUB1B/BUBR1 Signaling ]]> https://biorxiv.org/content/10.1101/2020.07.24.220475v1?rss=1 Brooks, K. E. Daughtry, B. L. Davis, B. Yan, M. Y. Fei, S. S. Carbone, L. Chavez, S. L. 2020-07-24 doi:10.1101/2020.07.24.220475 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Cross-Tissue Transcriptomic Analysis Leveraging Machine Learning Approaches Identifies New Biomarkers for Rheumatoid Arthritis ]]> https://biorxiv.org/content/10.1101/2020.07.24.220483v1?rss=1 Rychkov, D. Neely, J. Oskotsky, T. Sirota, M. 2020-07-26 doi:10.1101/2020.07.24.220483 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ Identification of clinical combination therapies to induce durable responses in kidney cancers ]]> https://biorxiv.org/content/10.1101/2020.07.25.221507v1?rss=1 Thomas, G. V. 2020-07-26 doi:10.1101/2020.07.25.221507 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ Natural food intake patterns do not synchronize peripheral clocks ]]> https://biorxiv.org/content/10.1101/2020.07.28.220509v1?rss=1 Xie, X. Kukino, A. Calcagno, H. E. Berman, A. Garner, J. P. Butler, M. P. 2020-07-29 doi:10.1101/2020.07.28.220509 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Cross-reactivity of SARS-CoV structural protein antibodies against SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.07.30.229377v1?rss=1 Bates, T. A. Weinstein, J. B. Farley, S. E. Leier, H. C. Messer, W. B. Tafesse, F. G. 2020-07-30 doi:10.1101/2020.07.30.229377 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ The identity of human tissue-emigrant CD8+ T cells ]]> https://biorxiv.org/content/10.1101/2020.08.11.236372v1?rss=1 Buggert, M. Vella, L. A. Nguyen, S. Wu, V. Sekine, T. Perez-Potti, A. Maldini, C. R. Manne, S. Darko, S. Ransier, A. Kuri-Cervantes, L. Sada Japp, A. Bukh Brody, I. Ivarsson, M. A. Hertwig, L. Antel, J. P. Johnson, M. E. Okoye, A. Picker, L. J. Vahedi, G. Sparrelid, E. Llewellyn-Lacey, S. Gostick, E. Bjorkstrom, N. K. Bar-Or, A. Dori, Y. Naji, A. Canaday, D. Laufer, T. M. Wells, A. D. Price, D. Frank, I. Douek, D. Wherry, E. J. Itkin, M. G. Betts, M. R. 2020-08-11 doi:10.1101/2020.08.11.236372 Cold Spring Harbor Laboratory Press 2020-08-11 <![CDATA[ Postembryonic screen for mutations affecting spine development in zebrafish ]]> https://biorxiv.org/content/10.1101/2020.08.12.248716v1?rss=1 GRAY, R. Gonzalez, R. Ackerman, S. D. Minowa, R. C. Griest, J. F. Bayrak, M. N. Troutwine, B. R. Canter, S. Monk, K. R. Sepich, D. S. Solnica-Krezel, L. 2020-08-12 doi:10.1101/2020.08.12.248716 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ CD300lf conditional knockout mouse reveals strain-specific cellular tropism for murine norovirus ]]> https://biorxiv.org/content/10.1101/2020.08.19.258467v1?rss=1 Graziano, V. R. Alfajaro, M. M. Schmitz, C. Filler, R. B. Strine, M. S. Wei, J. Hsieh, L. L. Baldridge, M. T. Nice, T. J. Lee, S. Orchard, R. C. Wilen, C. B. 2020-08-21 doi:10.1101/2020.08.19.258467 Cold Spring Harbor Laboratory Press 2020-08-21 <![CDATA[ Single cell tracking based on Voronoi partition via stable matching ]]> https://biorxiv.org/content/10.1101/2020.08.20.259408v1?rss=1 Chang, Y. H. Linsley, J. W. Lamstein, J. Kalra, J. Epstein, I. Barch, M. Daily, K. Snyder, P. Omberg, L. Heiser, L. Finkbeiner, S. 2020-08-20 doi:10.1101/2020.08.20.259408 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ Towards Reproducible Brain-Wide Association Studies ]]> https://biorxiv.org/content/10.1101/2020.08.21.257758v1?rss=1 Marek, S. Tervo-Clemmens, B. Calabro, F. J. Montez, D. F. Kay, B. P. Hatoum, A. S. Donohue, M. R. Foran, W. Miller, R. L. Feczko, E. Miranda Dominguez, O. Graham, A. Earl, E. A. Perrone, A. Cordova, M. Doyle, O. Moore, L. A. Conan, G. Uriarte, J. Snider, K. Tam, A. Chen, J. Newbold, D. J. Zheng, A. Seider, N. A. Van, A. N. Laumann, T. O. Thompson, W. K. Greene, D. J. Petersen, S. E. Nichols, T. Yeo, B. T. T. Barch, D. M. Garavan, H. Luna, B. Fair, D. A. Dosenbach, N. U. F. 2020-08-22 doi:10.1101/2020.08.21.257758 Cold Spring Harbor Laboratory Press 2020-08-22 <![CDATA[ A sort-seq approach to the development of single fluorescent protein biosensors ]]> https://biorxiv.org/content/10.1101/2020.08.21.261578v1?rss=1 Koberstein, J. N. Stewart, M. L. Mighell, T. L. Smith, C. B. Cohen, M. S. 2020-08-22 doi:10.1101/2020.08.21.261578 Cold Spring Harbor Laboratory Press 2020-08-22 <![CDATA[ Transcriptomic analysis of primate placentas and novel rhesus trophoblast cell lines informs investigations of human placentation ]]> https://biorxiv.org/content/10.1101/2020.08.21.262030v1?rss=1 Rosenkrantz, J. L. Gaffney, J. E. Roberts, V. H. Carbone, L. Chavez, S. L. 2020-08-22 doi:10.1101/2020.08.21.262030 Cold Spring Harbor Laboratory Press 2020-08-22 <![CDATA[ BAX is necessary for neuronal death following exposure to isoflurane during the neonatal period ]]> https://biorxiv.org/content/10.1101/2020.08.25.267120v1?rss=1 Slupe, A. M. Villasana, L. Wright, K. M. 2020-08-26 doi:10.1101/2020.08.25.267120 Cold Spring Harbor Laboratory Press 2020-08-26 <![CDATA[ Base Pairing and Functional Insights into N3-methylcytidine (m3C) in RNA ]]> https://biorxiv.org/content/10.1101/2020.08.27.270322v1?rss=1 Mao, S. Haruehanroengra, P. Ranganathan, S. V. Shen, F. Begley, T. Sheng, J. 2020-08-28 doi:10.1101/2020.08.27.270322 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ Targeting uncoupling of copy number and gene expression in cancers ]]> https://biorxiv.org/content/10.1101/2020.08.28.272641v1?rss=1 Mohanty, V. Wang, F. Mills, G. B. Chen, K. 2020-08-30 doi:10.1101/2020.08.28.272641 Cold Spring Harbor Laboratory Press 2020-08-30 <![CDATA[ Selective effects of arousal on population coding of natural sounds in primary auditory cortex ]]> https://biorxiv.org/content/10.1101/2020.08.31.276584v1?rss=1 Heller, C. R. Schwartz, Z. P. Saderi, D. David, S. V. 2020-09-01 doi:10.1101/2020.08.31.276584 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ QSIPrep: An integrative platform for preprocessing and reconstructing diffusion MRI ]]> https://biorxiv.org/content/10.1101/2020.09.04.282269v1?rss=1 Cieslak, M. Cook, P. A. He, X. Yeh, F.-C. Dhollander, T. Adebimpe, A. Aguirre, G. K. Bassett, D. S. Betzel, R. F. Bourque, J. Cabral, L. Davatzikos, C. Detre, J. Earl, E. Elliott, M. A. Fadnavis, S. Fair, D. A. Foran, W. Fotiadis, P. Garyfallidis, E. Giesbrecht, B. Gur, R. C. Gur, R. E. Kelz, M. Keshavan, A. Larsen, B. S. Luna, B. Mackey, A. P. Milham, M. Oathes, D. J. Perrone, A. Pines, A. R. Roalf, D. R. Richie-Halford, A. Rokem, A. Sydnor, V. Tapera, T. M. Tooley, U. A. Vettel, J. M. Yeatman, J. Grafton, S. T. Satterthwaite, T. D. 2020-09-04 doi:10.1101/2020.09.04.282269 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ DISSECT: DISentangle SharablE ConTent for Multimodal Integration and Crosswise-mapping ]]> https://biorxiv.org/content/10.1101/2020.09.04.283234v1?rss=1 Schau, G. Burlingame, E. A. Chang, Y. H. 2020-09-06 doi:10.1101/2020.09.04.283234 Cold Spring Harbor Laboratory Press 2020-09-06 <![CDATA[ Insulin potentiates the synchronous firing of arcuate nucleus Kiss1 neurons that protects against diet-induced obesity ]]> https://biorxiv.org/content/10.1101/2020.09.09.289017v1?rss=1 Qiu, J. Stincic, T. L. Bosch, M. A. Connors, A. M. Petrie, S. K. Ronnekleiv, O. K. Kelly, M. J. 2020-09-11 doi:10.1101/2020.09.09.289017 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Supraphysiological testosterone induces ferroptosis and activates NF-kappaB mediated immune pathways in prostate cancer through nucleophagy ]]> https://biorxiv.org/content/10.1101/2020.09.10.286252v1?rss=1 Mendonca, J. Kumar, R. Owoyemi, O. Boyapati, K. Thomas, N. Kanacharoen, S. Coffey, M. Topiwala, D. Gomes, C. Ozbek, B. Jones, T. Rosen, M. Dong, L. Wiens, S. Brennen, W. N. Isaacs, J. De Marzo, A. M. Markowski, M. Antonarakis, E. S. Qian, D. Pienta, K. Pardoll, D. Carducci, M. Denmeade, S. Kachhap, S. 2020-09-10 doi:10.1101/2020.09.10.286252 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Microbial colonization induces histone acetylation critical for inherited gut-germline-neural signaling ]]> https://biorxiv.org/content/10.1101/2020.09.10.291823v1?rss=1 Aballay, A. Hong, C. 2020-09-11 doi:10.1101/2020.09.10.291823 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ ASXL1 Directs Neutrophilic Differentiation via Modulation of MYC and RNA Polymerase II. ]]> https://biorxiv.org/content/10.1101/2020.09.14.295295v1?rss=1 Braun, T. P. Estabrook, J. Coleman, D. J. Schonrock, Z. Smith, B. M. Enright, T. Coblentz, C. Callahan, R. Mohammed, H. Druker, B. J. Lusardi, T. Maxson, J. E. 2020-09-14 doi:10.1101/2020.09.14.295295 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ Polycomb represses a gene network controlling puberty via modulation of histone demethylase Kdm6b expression ]]> https://biorxiv.org/content/10.1101/2020.09.14.297135v1?rss=1 Wright, H. Aylwin, C. F. Toro, C. A. Ojeda, S. R. Lomniczi, A. 2020-09-14 doi:10.1101/2020.09.14.297135 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ Baricitinib treatment resolves lower airway inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques ]]> https://biorxiv.org/content/10.1101/2020.09.16.300277v1?rss=1 Hoang, T. N. Pino, M. Boddapati, A. K. Viox, E. G. Starke, C. E. Upadhyay, A. A. Gumber, S. Busman-Sahay, K. Strongin, Z. Harper, J. L. Tharp, G. K. Pellegrini, K. L. Kirejczyk, S. Zandi, K. Tao, S. Horton, T. R. Beagle, E. N. Mahar, E. A. Lee, M. Y. Cohen, J. Jean, S. Wood, J. S. Connor-Stroud, F. Stammen, R. L. Delmas, O. M. Wang, S. Cooney, K. A. Sayegh, M. N. Wang, L. Weiskopf, D. Filev, P. D. Waggoner, J. Piantadosi, A. Kasturi, S. P. Al-Shakhshir, H. Ribeiro, S. P. Sekaly, R. P. Levit, R. D. Estes, J. D. Vanderford, T. H. Schinazi, R. F. Bosinger, 2020-09-16 doi:10.1101/2020.09.16.300277 Cold Spring Harbor Laboratory Press 2020-09-16 <![CDATA[ Chronic Psychosocial Stress and Experimental Pubertal Delay Affect Socioemotional Behavior and Amygdala Functional Connectivity in Adolescent Female Rhesus Macaques ]]> https://biorxiv.org/content/10.1101/2020.09.18.304048v1?rss=1 Pincus, M. Godfrey, J. S. Feczko, E. Earl, E. Miranda Dominguez, O. Fair, D. Wilson, M. E. Sanchez, M. M. Kelly, C. 2020-09-19 doi:10.1101/2020.09.18.304048 Cold Spring Harbor Laboratory Press 2020-09-19 <![CDATA[ Baseline T cell immune phenotypes predict virologic and disease control upon SARS-CoV infection ]]> https://biorxiv.org/content/10.1101/2020.09.21.306837v1?rss=1 Graham, J. Swarts, J. Leist, S. R. Schafer, A. Menachery, V. D. Gralinski, L. Jeng, S. Miller, D. R. Mooney, M. McWeeney, S. Ferris, M. T. Pardo-Manuel de Villena, F. Heise, M. T. Baric, R. S. Lund, J. M. 2020-09-21 doi:10.1101/2020.09.21.306837 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ Increased oxidative stress tolerance of a spontaneously-occurring perR gene mutation in Streptococcus mutans UA159 ]]> https://biorxiv.org/content/10.1101/2020.09.24.312702v1?rss=1 Kajfasz, J. K. Zuber, P. Ganguly, T. Abranches, J. Lemos, J. A. 2020-09-25 doi:10.1101/2020.09.24.312702 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Human cytomegalovirus UL7, miR-US5-1 and miR-UL112-3p inactivation of FOXO3a protects CD34+ hematopoietic progenitor cells from apoptosis ]]> https://biorxiv.org/content/10.1101/2020.09.28.317859v1?rss=1 Hancock, M. H. Crawford, L. B. Perez, W. Struthers, H. M. Mitchell, J. Caposio, P. 2020-09-29 doi:10.1101/2020.09.28.317859 Cold Spring Harbor Laboratory Press 2020-09-29 <![CDATA[ Modulation of MHC-E transport by viral decoy ligands is required for RhCMV/SIV vaccine efficacy ]]> https://biorxiv.org/content/10.1101/2020.09.30.321158v1?rss=1 Verweij, M. Hansen, S. G. Iyer, R. John, N. Malouli, D. Morrow, D. Scholz, I. Womack, J. Abdulhaqq, S. Gilbride, R. M. Hughes, C. M. Ventura, A. B. Ford, J. C. Selseth, A. N. Oswald, K. Shoemaker, R. Berkemeier, B. Borsche, W. J. Hull, M. Shao, J. Sacha, J. Axthelm, M. K. Edlefsen, P. Lifson, J. D. Picker, L. J. Früh, K. 2020-10-02 doi:10.1101/2020.09.30.321158 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Cytomegaloviral determinants of CD8+ T cell programming and RhCMV/SIV vaccine efficacy ]]> https://biorxiv.org/content/10.1101/2020.09.30.321349v1?rss=1 Malouli, D. Hansen, S. G. Hancock, M. H. Hughes, C. M. Ford, J. C. Gilbride, R. M. Ventura, A. B. Morrow, D. Taher, H. Uebelhoer, L. S. McArdle, M. R. Papen, C. R. Espinosa Trethewy, R. Oswald, K. Shoemaker, R. Berkemeier, B. Bosche, W. Hull, M. Green, J. Axthelm, M. K. Shao, J. Edlefsen, P. Grey, F. Nelson, J. A. Lifson, J. D. Streblow, D. N. Sacha, J. Früh, K. Picker, L. J. 2020-10-01 doi:10.1101/2020.09.30.321349 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ The macaque brain ONPRC18 template with combined gray and white matter labelmap for multimodal neuroimaging studies of nonhuman primates ]]> https://biorxiv.org/content/10.1101/2020.10.06.323063v1?rss=1 Weiss, A. R. Liu, Z. Wang, X. Liguore, W. A. Kroenke, C. McBride, J. 2020-10-08 doi:10.1101/2020.10.06.323063 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ The Trypanosoma brucei Cytoskeletal Protein KHARON Associates with Partner Proteins to Mediate Both Cytokinesis and Trafficking of Flagellar Membrane Proteins ]]> https://biorxiv.org/content/10.1101/2020.10.07.330316v1?rss=1 Landfear, S. M. Sanchez, M. A. 2020-10-07 doi:10.1101/2020.10.07.330316 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ Atypical molecular basis for drug resistance to mitochondrial function inhibitors in Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2020.10.08.330241v1?rss=1 Painter, H. J. Morrisey, J. M. Mather, M. W. Orchard, L. M. Luck, C. Smilkstein, M. J. Riscoe, M. K. Vaidya, A. B. Llinas, M. 2020-10-08 doi:10.1101/2020.10.08.330241 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Distinct cis-acting elements govern purine-responsive regulation of the Leishmania donovani nucleoside transporters, LdNT1 and LdNT2 ]]> https://biorxiv.org/content/10.1101/2020.10.15.336420v1?rss=1 Licon, M. H. Goodstein, F. Ortiz, D. Landfear, S. M. Yates, P. A. 2020-10-15 doi:10.1101/2020.10.15.336420 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Large, stable spikes exhibit differential broadening in excitatory and inhibitory neocortical boutons ]]> https://biorxiv.org/content/10.1101/2020.10.19.346346v1?rss=1 Ritzau-Jost, A. Tsintsadze, T. Krueger, M. Ader, J. Bechmann, I. Eilers, J. Barbour, B. Smith, S. M. Hallermann, S. 2020-10-20 doi:10.1101/2020.10.19.346346 Cold Spring Harbor Laboratory Press 2020-10-20 <![CDATA[ Antisense oligonucleotides targeting alpha-synuclein reduce pre-formed fibril-induced Lewy pathology and improve some domains of cognitive and motor performance ]]> https://biorxiv.org/content/10.1101/2020.10.21.349191v1?rss=1 Boutros, S. J. Raber, J. Unni, V. K. 2020-10-21 doi:10.1101/2020.10.21.349191 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Incomplete removal of extracellular glutamate controls synaptic transmission and integration at a cerebellar synapse ]]> https://biorxiv.org/content/10.1101/2020.10.23.352120v1?rss=1 Balmer, T. S. Borges-Merjane, C. Trussell, L. O. 2020-10-23 doi:10.1101/2020.10.23.352120 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ Diurnal changes in perineuronal nets and parvalbumin neurons in the rat medial prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2020.10.25.354134v1?rss=1 Harkness, J. H. Gonzalez, A. E. Bushana, P. N. Jorgensen, E. T. Hegarty, D. M. Di Nardo, A. A. Prochiantz, A. Wisor, J. P. Aicher, S. A. Brown, T. E. Sorg, B. A. 2020-10-25 doi:10.1101/2020.10.25.354134 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ Species level resolution of female bladder microbiota from marker gene surveys ]]> https://biorxiv.org/content/10.1101/2020.10.27.358408v1?rss=1 Hoffman, C. Siddiqui, N. Y. Fields, I. Gregory, W. T. SImon, H. Mooney, M. A. Wolfe, A. J. Karstens, L. 2020-10-28 doi:10.1101/2020.10.27.358408 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Enhancer of Zeste Homolog 2 (Ezh2) is essential for patterning of multiple musculoskeletal tissues but dispensable for tendon differentiation ]]> https://biorxiv.org/content/10.1101/2020.10.30.361949v1?rss=1 Pal, D. Riester, S. M. Hasan, B. Tufa, S. F. Dudakovic, A. Keene, D. R. van Wijnen, A. Schweitzer, R. 2020-10-30 doi:10.1101/2020.10.30.361949 Cold Spring Harbor Laboratory Press 2020-10-30 <![CDATA[ Regulatory diversity contributes to a divergent transcriptional response to dietary changes in mammals ]]> https://biorxiv.org/content/10.1101/2020.11.01.364232v1?rss=1 Costello, K. R. Shin, H. Trac, C. Varlamov, O. Schones, D. E. 2020-11-02 doi:10.1101/2020.11.01.364232 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ A Simple and Efficient Pipeline for Construction, Merging, Expansion, and Simulation of Large-Scale, Single-Cell Mechanistic Models ]]> https://biorxiv.org/content/10.1101/2020.11.09.373407v1?rss=1 Erdem, C. Bensman, E. M. Mutsuddy, A. Saint-Antoine, M. M. Bouhaddou, M. Blake, R. C. Dodd, W. Gross, S. M. Heiser, L. M. Feltus, F. A. Birtwistle, M. R. 2020-11-10 doi:10.1101/2020.11.09.373407 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ What Markov state models can and cannot do: Correlation versus path-based observables in protein folding models ]]> https://biorxiv.org/content/10.1101/2020.11.09.374496v1?rss=1 Suarez, E. Wiewiora, R. P. Wehmeyer, C. Noe, F. Chodera, J. D. Zuckerman, D. M. 2020-11-09 doi:10.1101/2020.11.09.374496 Cold Spring Harbor Laboratory Press 2020-11-09 <![CDATA[ Cell autonomous TGF-beta signaling is essential for cell recruitment into degenerating tendons ]]> https://biorxiv.org/content/10.1101/2020.11.11.378505v1?rss=1 Tan, G.-K. Pryce, B. A. Stabio, A. Keene, D. R. Tufa, S. F. Schweitzer, R. 2020-11-11 doi:10.1101/2020.11.11.378505 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ Adding software to package management systems can increase their citation by 280% ]]> https://biorxiv.org/content/10.1101/2020.11.16.385211v1?rss=1 Jalili, V. Clements, D. Gruning, B. Blankenberg, D. Goecks, J. 2020-11-17 doi:10.1101/2020.11.16.385211 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ Human methylome variation across Infinium 450K data on the Gene Expression Omnibus ]]> https://biorxiv.org/content/10.1101/2020.11.17.387548v1?rss=1 Maden, S. K. Thompson, R. F. Hansen, K. D. Nellore, A. 2020-11-19 doi:10.1101/2020.11.17.387548 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ Cancer cells are sensitive to wild-type IDH1 inhibition under nutrient limitation ]]> https://biorxiv.org/content/10.1101/2020.11.19.390633v1?rss=1 Vaziri-Gohar, A. Hue, J. J. Graor, H. J. Prendergast, E. Chen, V. Cassel, J. Mohammed, F. S. Abbas, A. Dukleska, K. Khokhar, I. Hajhassani, O. Zarei, M. Wang, R. Rothermel, L. D. Bederman, I. Browers, J. Getts, R. Brunengraber, H. Salvino, J. M. Brody, J. R. Winter, J. M. 2020-11-20 doi:10.1101/2020.11.19.390633 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ AKAP79/150 coordinates leptin-induced PKA activation to regulate KATP channel trafficking in pancreatic β-cells ]]> https://biorxiv.org/content/10.1101/2020.11.25.397059v1?rss=1 Cochrane, V. Yang, Z. Dell'Acqua, M. Shyng, S.-L. 2020-11-26 doi:10.1101/2020.11.25.397059 Cold Spring Harbor Laboratory Press 2020-11-26 <![CDATA[ Eosinophil peroxidase induces inflammation in an animal model of dermatitis ]]> https://biorxiv.org/content/10.1101/2020.11.25.399006v1?rss=1 Roth-Carter, Q. Luo, H. Ochkur, S. I. Jacobsen, E. Datena, M. Fryer, A. D. Lee, J. J. Jacoby, D. B. 2020-11-27 doi:10.1101/2020.11.25.399006 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ African-lineage Zika virus replication dynamics and maternal-fetal interface infection in pregnant rhesus macaques ]]> https://biorxiv.org/content/10.1101/2020.11.30.405670v1?rss=1 Crooks, C. M. Weiler, A. M. Rybarczyk, S. L. Bliss, M. I. Jaeger, A. S. Murphy, M. E. Simmons, H. A. Mejia, A. Fritsch, M. K. Hayes, J. M. Eickhoff, J. C. Mitzey, A. M. Razo, E. Braun, K. Brown, E. A. Yamamoto, K. Shepard, P. M. Possell, A. Weaver, K. Antony, K. M. Morgan, T. K. Dudley, D. Peterson, E. Schultz-Darken, N. O'Connor, D. H. Mohr, E. L. Golos, T. G. Aliota, M. Friedrich, T. C. 2020-12-01 doi:10.1101/2020.11.30.405670 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ HLA-E restricted, HIV-1 suppressing, Gag specific CD8+ T cells offer universal vaccine opportunities ]]> https://biorxiv.org/content/10.1101/2020.12.01.406066v1?rss=1 50% of animals. However, human immunodeficiency virus type 1 (HIV-1) specific HLA-E restricted T cells have not been observed in HIV-1-infected individuals. Here we primed HLA-E restricted HIV-1 specific CD8+ T cells in vitro. These T cell clones, and allogeneic CD8+ T cells transduced with their T cell receptors, suppressed HIV-1 replication in CD4+ T cells in vitro. Vaccine induction of efficacious HLA-E restricted HIV-1 specific T cells should therefore be possible. One Sentence SummaryCD8+ T cells that recognize a Gag peptide presented by HLA-E suppress HIV-1 replication in vitro. ]]> Yang, H. Rei, M. Brackenridge, S. Brenna, E. Sun, H. abdulhaqq, s. Liu, M. K. Ma, W. Kurupati, P. Xu, x. Cerundolo, V. Jenkins, E. Davis, S. J. Sacha, J. B. Frueh, K. Picker, L. J. Borrow, P. Gillespie, G. McMichael, A. J. 2020-12-02 doi:10.1101/2020.12.01.406066 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Illuminating endosomal escape of polymorphic lipid nanoparticles that boost mRNA delivery ]]> https://biorxiv.org/content/10.1101/2020.12.02.407601v1?rss=1 Herrera, M. Kim, J. Eygeris, Y. Jozic, A. Sahay, G. 2020-12-03 doi:10.1101/2020.12.02.407601 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Functional and genomic adaptations of blood monocytes to pregravid obesity during pregnancy ]]> https://biorxiv.org/content/10.1101/2020.12.02.409185v1?rss=1 Messaoudi, I. Sureshchandra, S. Marshall, N. E. Mendoza, N. Jankeel, A. Zulu, M. Z. 2020-12-03 doi:10.1101/2020.12.02.409185 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Multiple viral microRNAs regulate interferon release and signaling early during infection with Epstein-Barr virus ]]> https://biorxiv.org/content/10.1101/2020.12.03.393306v1?rss=1 Bouvet, M. Voigt, S. Tagawa, T. Albanese, M. Chen, Y.-F. A. Chen, Y. Fachko, D. N. Pich, D. Goebel, C. Skalsky, R. Hammerschmidt, W. 2020-12-03 doi:10.1101/2020.12.03.393306 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ An Integrated Clinical, Omic, and Image Atlas of an Evolving Metastatic Breast Cancer ]]> https://biorxiv.org/content/10.1101/2020.12.03.408500v1?rss=1 Johnson, B. E. Creason, A. L. Stommel, J. M. Keck, J. Parmar, S. Betts, C. B. Blucher, A. Boniface, C. Bucher, E. Burlingame, E. A. Chin, K. Eng, J. Feiler, H. S. Kolodzie, A. Kong, B. Labrie, M. Leyshock, P. Mitri, S. Patterson, J. Riesterer, J. L. Sivagnanam, S. Sudar, D. Thibault, G. Zheng, C. Nan, X. Heiser, L. M. Spellman, P. T. Thomas, G. V. Demir, E. Chang, Y. H. Coussens, L. M. Guimaraes, A. R. Corless, C. Goecks, J. Bergan, R. Mitri, Z. Mills, G. B. Gray, J. W. 2020-12-03 doi:10.1101/2020.12.03.408500 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ High-fidelity, efficient, and reversible labeling of endogenous proteins using CRISPR-based designer exon insertion ]]> https://biorxiv.org/content/10.1101/2020.12.03.409417v1?rss=1 Zhong, H. Massengill, C. I. Muniak, M. A. Ma, L. Qin, M. Petrie, S. K. Mao, T. 2020-12-03 doi:10.1101/2020.12.03.409417 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Ribavirin shows antiviral activity against SARS-CoV-2 and downregulates the activity of TMPRSS2 and the expression of ACE2 in vitro ]]> https://biorxiv.org/content/10.1101/2020.12.04.410092v1?rss=1 Unal, M. A. Bitirim, C. V. Summak, G. Y. Bereketoglu, S. Cevher Zeytin, I. Besbinar, O. Gurcan, C. Aydos, D. Goksoy, E. Kocakaya, E. Eran, Z. Murat, M. Demir, N. Somers, J. Demir, E. Nazir, H. Ozkan, S. A. Ozkul, A. Azap, A. Yilmazer, A. Akcali, K. C. 2020-12-05 doi:10.1101/2020.12.04.410092 Cold Spring Harbor Laboratory Press 2020-12-05 <![CDATA[ A pragmatic reevaluation of the efficacy of nonhuman primate optogenetics ]]> https://biorxiv.org/content/10.1101/2020.12.10.420331v1?rss=1 Bliss-Moreau, E. Costa, V. D. Baxter, M. G. 2020-12-11 doi:10.1101/2020.12.10.420331 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Toward reproducible, scalable, and robust data analysis across multiplex tissue imaging platforms ]]> https://biorxiv.org/content/10.1101/2020.12.11.422048v1?rss=1 Burlingame, E. A. Eng, J. Thibault, G. Chin, K. Gray, J. W. Chang, Y. H. 2020-12-11 doi:10.1101/2020.12.11.422048 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Longitudinal profiling of the macaque vaginal microbiome reveals similarities to diverse human vaginal communities: implications for use as a pre-clinical model for bacterial vaginosis ]]> https://biorxiv.org/content/10.1101/2020.12.14.422805v1?rss=1 Rhoades, N. S. Hendrickson, S. M. Gerken, D. R. Martinez, K. Slayden, O. D. Slifka, M. K. Messaoudi, I. 2020-12-15 doi:10.1101/2020.12.14.422805 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Stretch-activated ion channels identified in the touch-sensitive structures of carnivorous Droseraceae plants ]]> https://biorxiv.org/content/10.1101/2020.12.15.422915v1?rss=1 Procko, C. Murthy, S. Keenan, W. T. Mousavi, S. A. R. Dabi, T. Coombs, A. Procko, E. Baird, L. Patapoutian, A. Chory, J. 2020-12-15 doi:10.1101/2020.12.15.422915 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ A neural crest stem cell-like state drives nongenetic resistance to targeted therapy in melanoma ]]> https://biorxiv.org/content/10.1101/2020.12.15.422929v1?rss=1 Marin-Bejar, O. Rogiers, A. Dewaele, M. Femel, J. Karras, P. Pozniak, J. Bervoets, G. Van Raemdonck, N. Pedri, D. Swings, T. Demeulemeester, J. Vander Borght, S. Bosisio, F. van den Oord, J. J. Vanden Bempt, I. Lambrechts, D. Voet, T. Bechter, O. Rizos, H. Levesque, M. Leucci, E. Lund, A. W. Rambow, F. Marine, J.-C. 2020-12-16 doi:10.1101/2020.12.15.422929 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ TRPM channels mediate learned pathogen avoidance following intestinal distention ]]> https://biorxiv.org/content/10.1101/2020.12.18.423492v1?rss=1 Filipowicz, A. Aballay, A. 2020-12-19 doi:10.1101/2020.12.18.423492 Cold Spring Harbor Laboratory Press 2020-12-19 <![CDATA[ THE URINARY MICROBIOME IN POSTMENOPAUSAL WOMEN WITH RECURRENT URINARY TRACT INFECTIONS ]]> https://biorxiv.org/content/10.1101/2020.12.21.423901v1?rss=1 4 weeks after last treatment for UTI. Samples were evaluated using expanded quantitative urine culture (EQUC) and 16S rRNA gene sequencing. With EQUC techniques, there were no significant differences in the median numbers of microbial species isolated among groups (p=0.96), even when considering Lactobacilli (p=0.72). However, there were trends towards different Lactobacillus species between groups. With sequencing the overwhelming majority of urinary samples contained Lactobacilli, with non-significant trends in relative abundance of Lactobacilli among groups. Using a Bayesian regression analysis for compositional data, we identified significant differences in anaerobic taxa that were associated with phenotypic groups. Most of these differences centered on Bacteroidales and the family Prevotellaceae, though differences were also noted in Actinobacteria and certain genera of Clostridiales. Associations between anaerobes within the urinary microbiome and recurrent UTI warrants further investigation. IMPORTANCEIn menopausal women with recurrent urinary tract infections (UTIs) compared to those without, the abundance of Lactobacillus within the urinary microbiome is not significantly different when vaginal estrogen is regularly used. In this population, Lactobacillaceae were identified in 97% of urine samples using culture-independent techniques. However, with expanded urine cultures, women with recurrent UTIs taking daily antibiotics had a disproportionately low amount of L. gasseri/L. acidophilus compared to the other phenotypic groups. These findings support the theory that certain Lactobacillus species may be more important than others in the pathophysiology of postmenopausal recurrent UTIs. Furthermore, when using culture-independent techniques to explore urinary microbiota across phenotypic groups, we identified differences in multiple anaerobic taxa. Taken together, these results suggest that altered ratios of anaerobes and certain Lactobacillus species within the urinary microbiome may be implicated in postmenopausal recurrent UTI. ]]> Vaughan, M. H. Mao, J. Karstens, L. Ma, L. Amundsen, C. L. Schmader, K. E. Siddiqui, N. Y. 2020-12-22 doi:10.1101/2020.12.21.423901 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ A cancer cell-intrinsic GOT2-PPARδ axis suppresses antitumor immunity ]]> https://biorxiv.org/content/10.1101/2020.12.25.424393v1?rss=1 Sanford-Crane, H. Abrego, J. Oon, C. Xiao, X. Nagarajan, S. Bhattacharyya, S. Tontonoz, P. Sherman, M. H. 2020-12-26 doi:10.1101/2020.12.25.424393 Cold Spring Harbor Laboratory Press 2020-12-26 <![CDATA[ Activity-Dependent Modulation of Synapse-Regulating Genes in Astrocytes ]]> https://biorxiv.org/content/10.1101/2020.12.30.424365v1?rss=1 Farhy-Tselnicker, I. Boisvert, M. M. Liu, H. Dowling, C. Erikson, G. A. Blanco-Suarez, E. Farhy, C. Shokhirev, M. Ecker, J. R. Allen, N. J. 2020-12-30 doi:10.1101/2020.12.30.424365 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ Extracellular Matrix Dysfunction in Sorsby Patient-Derived Retinal Pigment Epithelium ]]> https://biorxiv.org/content/10.1101/2021.01.06.425613v1?rss=1 Engel, A. L. Wang, Y. Khuu, T. Worrall, E. Manson, M. A. Knight, K. Yanagida, A. Qi, J. H. Ramakrishnan, A. Weleber, R. G. Klein, M. Wilson, D. J. Anand-Apte, B. Hurley, J. B. Du, J. L. Chao, J. R. 2021-01-07 doi:10.1101/2021.01.06.425613 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ High-content single-cell combinatorial indexing ]]> https://biorxiv.org/content/10.1101/2021.01.11.425995v1?rss=1 Mulqueen, R. M. Pokholok, D. O'Connell, B. L. Thornton, C. A. Zhang, F. O'Roak, B. J. Link, J. Yardimci, G. G. Sears, R. C. Steemers, F. J. Adey, A. C. 2021-01-12 doi:10.1101/2021.01.11.425995 Cold Spring Harbor Laboratory Press 2021-01-12 <![CDATA[ Sustained IL-15 response signature predicts RhCMV/SIV vaccine efficacy ]]> https://biorxiv.org/content/10.1101/2021.01.11.426199v1?rss=1 Barrenäs, F. Hansen, S. G. Law, L. Driscoll, C. Green, R. R. Smith, E. Chang, J. Golez, I. Urion, T. Peng, X. Whitmore, L. Newhouse, D. Hughes, C. M. Morrow, D. Randall, K. T. Selseth, A. Ford, J. C. Gilbride, R. M. Randall, B. Ainslie, E. Oswald, K. Shoemaker, R. Fast, R. Bosche, W. J. Axthelm, M. K. Fukazawa, Y. Pavlakis, G. N. Felber, B. K. Fourati, S. Sekaly, R.-P. Lifson, J. D. Komorowski, J. Kosmider, E. Shao, J. Song, W. Edlefsen, P. T. Picker, L. J. Gale, M. 2021-01-11 doi:10.1101/2021.01.11.426199 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Gene expression profiling of lymph node sub-capsular sinus macrophages in cancer ]]> https://biorxiv.org/content/10.1101/2021.01.14.425337v1?rss=1 Pucci, F. Claudio, N. Danilo, P. 2021-01-15 doi:10.1101/2021.01.14.425337 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation ]]> https://biorxiv.org/content/10.1101/2021.01.15.426843v1?rss=1 Wagner, A. H. Babb, L. Alterovitz, G. Baudis, M. Brush, M. Cameron, D. L. Cline, M. Griffith, M. Griffith, O. Hunt, S. Kreda, D. Lee, J. Lopez, J. Moyer, E. Nelson, T. Patel, R. Y. Riehle, K. Robinson, P. N. Rynearson, S. Schuilenburg, H. Tsukanov, K. Walsh, B. Konopko, M. Rehm, H. Yates, A. D. Freimuth, R. R. Hart, R. K. 2021-01-17 doi:10.1101/2021.01.15.426843 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Human Neural Stem Cells Differentiate and Integrate, Innervating Implanted zQ175 Huntington's Disease Mouse Striatum ]]> https://biorxiv.org/content/10.1101/2021.01.18.427078v1?rss=1 Thompson, L. M. Holley, S. M. Reidling, J. C. Cepeda, C. Lau, A. Moore, C. Orellana, I. Fury, B. Kopan, L. Yeung, S. Neel, M. Coleal-Bergum, D. Monuki, E. K. Meshul, C. Bauer, G. Levine, M. S. 2021-01-19 doi:10.1101/2021.01.18.427078 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ TREM2 is thyroid hormone regulated making the TREM2 pathway druggable with ligands for thyroid hormone receptor ]]> https://biorxiv.org/content/10.1101/2021.01.25.428149v1?rss=1 Ferrara, S. J. Chaudhary, P. DeBell, M. J. Marracci, G. Miller, H. Calkins, E. Pocius, E. Napier, B. A. Emery, B. Bourdette, D. Scanlan, T. S. 2021-01-27 doi:10.1101/2021.01.25.428149 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Prior dengue immunity enhances Zika virus infection of the maternal-fetal interface in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2021.01.25.428184v1?rss=1 Crooks, C. M. Weiler, A. M. Rybarczyk, S. L. Bliss, M. I. Jaeger, A. S. Murphy, M. E. Simmons, H. A. Mejia, A. Fritsch, M. K. Hayes, J. M. Eickhoff, J. C. Mitzey, A. M. Razo, E. Braun, K. M. Brown, E. A. Yamamoto, K. Shepherd, P. M. Possell, A. Weaver, K. Antony, K. M. Morgan, T. K. Newman, C. M. Dudley, D. M. Schultz-Darken, N. Peterson, E. Katzelnick, L. C. Balmaseda, A. Harris, E. OConnor, D. H. Mohr, E. L. Golos, T. G. Friedrich, T. C. Aliota, M. T. 2021-01-26 doi:10.1101/2021.01.25.428184 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ A noncanonical FLT3 gatekeeper mutation disrupts gilteritinib binding and confers resistance ]]> https://biorxiv.org/content/10.1101/2021.01.27.428336v1?rss=1 Joshi, S. K. Sharzehi, S. Pittsenbarger, J. Bottomly, D. Tognon, C. E. McWeeney, S. Druker, B. Traer, E. 2021-01-28 doi:10.1101/2021.01.27.428336 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Natural loss of function of ephrin-B3 shapes spinal flight circuitry in birds ]]> https://biorxiv.org/content/10.1101/2021.01.29.428748v1?rss=1 Haimson, B. Meir, O. Sudakevitz-Merzbach, R. Elberg, G. Friedrich, S. Lovell, p. Paixao, s. Klen, R. Mello, C. V. Klar, A. 2021-01-29 doi:10.1101/2021.01.29.428748 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ Mutant SETBP1 enhances NRAS-driven MAPK pathway activation to promote aggressive leukemia ]]> https://biorxiv.org/content/10.1101/2021.02.01.429244v1?rss=1 Carratt, S. A. Braun, T. P. Coblentz, C. Schonrock, Z. Callahan, R. Smith, B. M. Maloney, L. Foley, A. Maxson, J. E. 2021-02-02 doi:10.1101/2021.02.01.429244 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ The impact of genetic background and sex on the phenotype of IL-23 induced murine arthritis ]]> https://biorxiv.org/content/10.1101/2021.02.03.429523v1?rss=1 Haley, E. Matmusaev, M. Hossain, I. N. Davin, S. Martin, T. M. Ermann, J. 2021-02-03 doi:10.1101/2021.02.03.429523 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Single-cell Visualization and Quantification of Trace Metals in Chlamydomonas Lysosome-Related Organelles ]]> https://biorxiv.org/content/10.1101/2021.02.12.431000v1?rss=1 Schmollinger, S. Chen, S. Strenkert, D. Hui, C. Ralle, M. Merchant, S. S. 2021-02-13 doi:10.1101/2021.02.12.431000 Cold Spring Harbor Laboratory Press 2021-02-13 <![CDATA[ Human cytomegalovirus blocks canonical TGFβ signaling during lytic infection to limit induction of type I interferons ]]> https://biorxiv.org/content/10.1101/2021.02.16.431411v1?rss=1 Pham, A. H. Mitchell, J. Botto, S. Pryke, K. M. Defilippis, V. R. Hancock, M. 2021-02-16 doi:10.1101/2021.02.16.431411 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Pregnancy and weaning regulate human maternal liver size and function ]]> https://biorxiv.org/content/10.1101/2021.02.18.431862v1?rss=1 Bartlett, A. Q. Francisco, M. Goddard, E. DeBarber, A. Leo, M. C. Baetscher, E. Rooney, W. Naugler, W. Catalano, P. Guimaraes, A. Purnell, J. Q. Vesco, K. K. Schedin, P. J. 2021-02-18 doi:10.1101/2021.02.18.431862 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Widespread ripples synchronize human cortical activity ]]> https://biorxiv.org/content/10.1101/2021.02.23.432582v1?rss=1 Dickey, C. W. Verzhbinsky, I. A. Jiang, X. Rosen, B. Q. Kajfez, S. Stedelin, B. Shih, J. J. Ben-Haim, S. Raslan, A. M. Madsen, J. R. Eskandar, E. N. Gonzalez-Martinez, J. Cash, S. S. Halgren, E. 2021-02-24 doi:10.1101/2021.02.23.432582 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ Immunity-longevity tradeoff neurally controlled by GABAergic transcription factor PITX1/UNC-30 ]]> https://biorxiv.org/content/10.1101/2021.02.25.432801v1?rss=1 Otarigho, B. Aballay, A. 2021-02-26 doi:10.1101/2021.02.25.432801 Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ IL-10 driven memory T cell survival and Tfh differentiation promote HIV persistence ]]> https://biorxiv.org/content/10.1101/2021.02.26.432955v1?rss=1 Pereira Ribeiro, S. Aid, M. Dupuy, F. P. Ngai Chan, C. Hultquist, J. Deleage, C. Moysi, E. Kulpa, D. A. Li, L. Xu, X. Tamilselvan, B. Tomalka, J. A. Nekorchuk, M. Busman-Sahay, K. Bordi, R. Simoneau, C. Goulet, J. P. Marconi, V. Routy, J. P. Balderas, R. Micci, L. J Howell, B. H Barouch, D. Krogan, N. J. Petrovas, C. Paiardini, M. Deeks, S. Estes, J. D. Gorman, D. J Hazuda, D. Sekaly, R.-P. 2021-02-26 doi:10.1101/2021.02.26.432955 Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ A de novo paradigm for male infertility ]]> https://biorxiv.org/content/10.1101/2021.02.27.433155v1?rss=1 Oud, M. S. Smits, R. M. Smith, H. E. Mastrorosa, F. K. Holt, G. S. Houston, B. J. de Vries, P. F. Alobaidi, B. K. Batty, L. E. Ismail, H. Greenwood, J. Sheth, H. Mikulasova, A. Astuti, G. Gilissen, C. S. McEleny, K. Turner, H. Coxhead, J. Cockell, S. J. Braat, D. Fleischer, K. D'Hauwers, K. Schaafsma, E. GEMINI Consortium, Nagirnaja, L. Conrad, D. Friedrich, C. Kliesch, S. Aston, K. I. Riera-Escamilla, A. Krausz, C. G. Gonzaga-Jauregui, C. Santibanez-Koref, M. Elliott, D. Vissers, L. Tüttelmann, F. O'Bryan, M. Ramos, L. Xavier, M. J. van der Heijden, G 2021-02-27 doi:10.1101/2021.02.27.433155 Cold Spring Harbor Laboratory Press 2021-02-27 <![CDATA[ Distinct forms of synaptic plasticity during ascending vs. descending control of medial olivocochlear efferent neurons ]]> https://biorxiv.org/content/10.1101/2021.03.02.433557v1?rss=1 Romero, G. E. Trussell, L. O. 2021-03-02 doi:10.1101/2021.03.02.433557 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ CaSR modulates sodium channel-mediated Ca 2+ -dependent excitability ]]> https://biorxiv.org/content/10.1101/2021.03.03.433701v1?rss=1 Martiszus, B. J. Tsintsadze, T. Smith, S. M. Chang, W. 2021-03-04 doi:10.1101/2021.03.03.433701 Cold Spring Harbor Laboratory Press 2021-03-04 <![CDATA[ Capturing scientific knowledge in computable form ]]> https://biorxiv.org/content/10.1101/2021.03.10.382333v1?rss=1 Wong, J. V. Franz, M. Siper, M. C. Fong, D. Durupinar, F. Dallago, C. Luna, A. Giorgi, J. M. Rodchenkov, I. Babur, O. Gyori, B. M. Bachman, J. A. Demir, E. Bader, G. D. Sander, C. 2021-03-11 doi:10.1101/2021.03.10.382333 Cold Spring Harbor Laboratory Press 2021-03-11 <![CDATA[ Single-Cell Spatial Proteomics Analyses of Head and Neck Squamous Cell Carcinoma Reveal Tumor Heterogeneity and Immune Architectures Associated with Clinical Outcome ]]> https://biorxiv.org/content/10.1101/2021.03.10.434649v1?rss=1 Blise, K. E. Sivagnanam, S. Banik, G. L. Coussens, L. M. Goecks, J. 2021-03-11 doi:10.1101/2021.03.10.434649 Cold Spring Harbor Laboratory Press 2021-03-11 <![CDATA[ Relevance of Circulating Hybrid Cells as a Non-Invasive Biomarker for Myriad Solid Tumors ]]> https://biorxiv.org/content/10.1101/2021.03.11.434896v1?rss=1 Dietz, M. S. Sutton, T. L. Walker, B. S. Gast, C. E. Zarour, L. Sengupta, S. K. Swain, J. R. Eng, J. Parappilly, M. Limbach, K. Sattler, A. Burlingame, E. Chin, Y. Gower, A. Montoya Mira, J. L. Sapre, A. Chiu, Y.-J. Clayburgh, D. R. Pommier, S. J. Cetnar, J. P. Fischer, J. M. Jaboin, J. J. Pommier, R. F. Sheppard, B. C. Tsikitis, V. L. Skalet, A. H. Mayo, S. C. Lopez, C. D. Gray, J. W. Mills, G. B. Mitri, Z. Chang, Y. H. Chin, K. Wong, M. H. 2021-03-12 doi:10.1101/2021.03.11.434896 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Using synthetic MR images for field map-less distortion correction ]]> https://biorxiv.org/content/10.1101/2021.03.13.435270v1?rss=1 Montez, D. F. Van, A. N. Miller, R. L. Seider, N. A. Marek, S. Zheng, A. Newbold, D. J. Scheidter, K. Feczko, E. Perrone, A. J. Miranda Dominguez, O. Earl, E. A. Kay, B. P. Jha, A. K. Sotiras, A. Laumann, T. O. Greene, D. J. Gordon, E. M. Tisdall, M. D. van der Kouwe, A. Fair, D. A. Dosenbach, N. U. F. 2021-03-15 doi:10.1101/2021.03.13.435270 Cold Spring Harbor Laboratory Press 2021-03-15 <![CDATA[ 3D genomic capture of regulatory immuno-genetic profiles in COVID-19 patients for prognosis of severe COVID disease outcome ]]> https://biorxiv.org/content/10.1101/2021.03.14.435295v1?rss=1 Hunter, E. Koutsothanasi, C. Wilson, A. Santos, F. C. Salter, M. Powell, R. Dring, A. Brajer, P. Egan, B. Westra, J. Ramadass, A. Messner, W. Brunton, A. Lyski, Z. Vancheeswaran, R. Barlow, A. Pchejetski, D. Robbins, P. Mellor, J. Akoulitchev, A. 2021-03-16 doi:10.1101/2021.03.14.435295 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging ]]> https://biorxiv.org/content/10.1101/2021.03.15.435473v1?rss=1 Schapiro, D. Sokolov, A. Yapp, C. Muhlich, J. L. Hess, J. Lin, J.-R. Chen, Y.-A. Nariya, M. K. Baker, G. J. Ruokonen, J. Maliga, Z. Jacobson, C. A. Farhi, S. L. Abbondanza, D. McKinley, E. T. Betts, C. Regev, A. Coffey, R. J. Coussens, L. M. Santagata, S. Sorger, P. K. 2021-03-16 doi:10.1101/2021.03.15.435473 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ BCL-XL blockage in TNBC models confers vulnerability to inhibition of specific cell cycle regulators ]]> https://biorxiv.org/content/10.1101/2021.03.16.435600v1?rss=1 Castellanet, O. Ahmad, F. Vinik, Y. Mills, G. B. Habermann, B. H. Borg, J.-P. H. Lev, S. Lamballe, F. Maina, F. 2021-03-17 doi:10.1101/2021.03.16.435600 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Generation of functional ciliates cholangiocytes from human pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2021.03.23.436530v1?rss=1 Ogawa, M. Jiang, J.-X. Xia, S. Yang, D. Ding, A. Laselva, O. Chin, S. Hernandez, M. Cui, C. Higuchi, Y. Suemizu, H. Dorrell, C. Grompe, M. Bear, C. Keller, G. Ogawa, S. 2021-03-23 doi:10.1101/2021.03.23.436530 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ α2δ-2 is Required for Functional Postsynaptic Calcium Channel Nanodomain Signaling ]]> https://biorxiv.org/content/10.1101/2021.03.25.437080v1?rss=1 Beeson, K. Westbrook, G. Schnell, E. 2021-03-26 doi:10.1101/2021.03.25.437080 Cold Spring Harbor Laboratory Press 2021-03-26 <![CDATA[ Novel insights in the pathophysiology of α-synuclein dysregulation on D2 receptor activity contributing to the vulnerability of dopamine neurons ]]> https://biorxiv.org/content/10.1101/2021.03.30.437775v1?rss=1 Dagra, A. Miller, D. R. Shaerzadeh, F. Lin, M. Gopinath, A. Harris, S. Sorrentino, Z. A. Velasco, S. Alonge, A. R. Azar, J. Lebowitz, J. J. Ulm, B. Bu, A.-M. Hansen, C. A. Urs, N. M. Giasson, B. I. Khoshbouei, H. 2021-03-30 doi:10.1101/2021.03.30.437775 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ Effective Therapy Targeting Cytochrome bc1 Prevents Babesia Erythrocytic Development and Protects from Lethal Infection ]]> https://biorxiv.org/content/10.1101/2021.03.31.438003v1?rss=1 Chiu, J. E. Renard, I. Chattopadhyay Pal, A. Singh, P. Vydyam, P. Thekkiniath, J. Kumar, M. Gihaz, S. Pou, S. Winter, R. W. Dodean, R. Nilsen, A. Riscoe, M. K. Doggett, J. S. Ben Mamoun, C. 2021-04-01 doi:10.1101/2021.03.31.438003 Cold Spring Harbor Laboratory Press 2021-04-01 <![CDATA[ Acetylated α-tubulin residue K394 regulates microtubule stability to shape the growth of axon terminals ]]> https://biorxiv.org/content/10.1101/2021.04.01.438108v1?rss=1 Saunders, H. A. J. Johnson-Schlitz, D. M. Jenkins, B. V. Volkert, P. J. Yang, S. Z. Wildonger, J. 2021-04-02 doi:10.1101/2021.04.01.438108 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ Early embryonic loss following intravaginal Zika virus challenge in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2021.04.03.437254v1?rss=1 Newman, C. M. Tarantal, A. F. Martinez, M. L. Simmons, H. A. Morgan, T. K. Zeng, X. Rosinski, J. R. Bliss, M. I. Bohm, E. K. Dudley, D. M. Aliota, M. Friedrich, T. Miller, C. J. O'Connor, D. 2021-04-03 doi:10.1101/2021.04.03.437254 Cold Spring Harbor Laboratory Press 2021-04-03 <![CDATA[ An aging clock using metabolomic CSF ]]> https://biorxiv.org/content/10.1101/2021.04.04.438397v1?rss=1 Hwangbo, N. Zhang, X. Raftery, D. Gu, H. Hu, S.-C. Montine, T. J. Quinn, J. F. Chung, K. A. Hiller, A. L. Wang, D. Fei, Q. Bettcher, L. Zabetian, C. P. Peskind, E. Li, G. Promislow, D. E. L. Franks, A. 2021-04-05 doi:10.1101/2021.04.04.438397 Cold Spring Harbor Laboratory Press 2021-04-05 <![CDATA[ Distinct in vivo dynamics of excitatory synapses onto cortical pyramidal neurons and inhibitory interneurons ]]> https://biorxiv.org/content/10.1101/2021.04.04.438418v1?rss=1 Melander, J. B. Nayebi, A. Jongbloets, B. C. Fortin, D. A. Qin, M. Ganguli, S. Mao, T. Zhong, H. 2021-04-05 doi:10.1101/2021.04.04.438418 Cold Spring Harbor Laboratory Press 2021-04-05 <![CDATA[ False gene and chromosome losses affected by assembly and sequence errors ]]> https://biorxiv.org/content/10.1101/2021.04.09.438906v1?rss=1 Kim, J. Lee, C. Ko, B. J. Yoo, D. Won, S. Phillippy, A. Fedrigo, O. Zhang, G. Howe, K. Wood, J. Durbin, R. Formenti, G. Brown, S. Cantin, L. Mello, C. V. Cho, S. Rhie, A. Kim, H. Jarvis, E. D. 2021-04-09 doi:10.1101/2021.04.09.438906 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ High-speed widefield handheld swept-source OCT angiography with a VCSEL light source ]]> https://biorxiv.org/content/10.1101/2021.04.10.439295v1?rss=1 Ni, S. Wei, X. Ng, R. Ostmo, S. Chiang, M. Huang, D. Jia, Y. Campbell, P. Jian, Y. 2021-04-11 doi:10.1101/2021.04.10.439295 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ A complex feature-based representation of vocalizations emerges in the superficial layers of primary auditory cortex ]]> https://biorxiv.org/content/10.1101/2021.04.11.439331v1?rss=1 Montes-Lourido, P. Kar, M. David, S. V. Sadagopan, S. 2021-04-11 doi:10.1101/2021.04.11.439331 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Adaptive mossy cell circuit plasticity after status epilepticus ]]> https://biorxiv.org/content/10.1101/2021.04.12.439511v1?rss=1 Butler, C. R. Westbrook, G. L. Schnell, E. 2021-04-14 doi:10.1101/2021.04.12.439511 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Targeting Adaptation to Cancer Treatment by Drug Combinations ]]> https://biorxiv.org/content/10.1101/2021.04.14.439861v1?rss=1 Wang, H. Luna, A. Yan, G. Li, X. Babur, O. Mills, G. B. Sander, C. Korkut, A. 2021-04-14 doi:10.1101/2021.04.14.439861 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Speech-related auditory salience detection in the posterior superior temporal region ]]> https://biorxiv.org/content/10.1101/2021.04.14.439910v1?rss=1 Brown, E. C. Stedelin, B. Raslan, A. M. Selden, N. R. 2021-04-14 doi:10.1101/2021.04.14.439910 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Cross-Species Analysis Defines the Conservation of Anatomically-Segregated VMH Neuron Populations ]]> https://biorxiv.org/content/10.1101/2021.04.16.439833v1?rss=1 Affinati, A. H. Sabatini, P. V. True, C. Tomlinson, A. J. Kirigiti, M. Lindsley, S. R. Li, C. Olson, D. P. Kievit, P. Myers, M. G. Rupp, A. C. 2021-04-18 doi:10.1101/2021.04.16.439833 Cold Spring Harbor Laboratory Press 2021-04-18 <![CDATA[ Single-cell analysis of localized low- and high-grade prostate cancers ]]> https://biorxiv.org/content/10.1101/2021.04.16.440238v1?rss=1 Eksi, S. E. Chitsazan, A. Sayar, Z. Fields, A. Kopp, R. Thomas, G. V. Spellman, P. T. Adey, A. 2021-04-17 doi:10.1101/2021.04.16.440238 Cold Spring Harbor Laboratory Press 2021-04-17 <![CDATA[ Dimensionality reduction for neural population decoding ]]> https://biorxiv.org/content/10.1101/2021.04.18.440336v1?rss=1 Heller, C. R. David, S. V. 2021-04-20 doi:10.1101/2021.04.18.440336 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ An ELISA-based method for rapid genetic screens in Drosophila ]]> https://biorxiv.org/content/10.1101/2021.04.21.440847v1?rss=1 Jay, T. R. Kang, Y. Jefferson, A. Freeman, M. 2021-04-22 doi:10.1101/2021.04.21.440847 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Transfer Learning for Inference of Metastatic Origin from Whole Slide Histology ]]> https://biorxiv.org/content/10.1101/2021.04.21.440864v1?rss=1 Schau, G. Ghani, H. Burlingame, E. A. Thibault, G. Gray, J. W. Corless, C. Chang, Y. H. 2021-04-22 doi:10.1101/2021.04.21.440864 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) ]]> https://biorxiv.org/content/10.1101/2021.04.22.436044v1?rss=1 Schatz, M. C. Philippakis, A. A. Afgan, E. Banks, E. Carey, V. J. Carroll, R. J. Culotti, A. Ellrott, K. Goecks, J. Grossman, R. L. Hall, I. Hansen, K. D. Lawson, J. Leek, J. T. O'Donnell Luria, A. Mosher, S. Morgan, M. Nekrutenko, A. O'Connor, B. D. Osborn, K. Paten, B. Patterson, C. Tan, F. J. Overby Taylor, C. Vessio, J. Waldron, L. D. Wang, T. Wuichet, K. AnVIL Team, 2021-04-23 doi:10.1101/2021.04.22.436044 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ ME-VAE: Multi-Encoder Variational AutoEncoder for Controlling Multiple Transformational Features in Single Cell Image Analysis ]]> https://biorxiv.org/content/10.1101/2021.04.22.441005v1?rss=1 Ternes, L. Dane, M. Labrie, M. Mills, G. B. Gray, J. W. Heiser, L. Chang, Y. H. 2021-04-23 doi:10.1101/2021.04.22.441005 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Functional independence of endogenous mu- and delta-opioid receptors co-expressed in cholinergic interneurons ]]> https://biorxiv.org/content/10.1101/2021.04.23.441175v1?rss=1 Arttamangkul, S. Platt, E. J. Carroll, J. Farrens, D. L. 2021-04-24 doi:10.1101/2021.04.23.441175 Cold Spring Harbor Laboratory Press 2021-04-24 <![CDATA[ Neuronal Dystroglycan regulates postnatal development of CCK/cannabinoid receptor-1 interneurons ]]> https://biorxiv.org/content/10.1101/2021.04.26.441492v1?rss=1 Miller, D. S. Wright, K. M. 2021-04-26 doi:10.1101/2021.04.26.441492 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Maternal Obesity Dysregulates Fetal Hematopoietic Stem and Progenitor Cell Development in Rhesus Macaques ]]> https://biorxiv.org/content/10.1101/2021.04.26.441556v1?rss=1 Sureshchandra, S. Robino, J. J. Goldman, D. Takahashi, D. Shen, W. Hennebold, J. D. Roberts, C. T. Burwitz, B. J. Messaoudi, I. Varlamov, O. 2021-04-27 doi:10.1101/2021.04.26.441556 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Astrocytic GABA Transporter controls sleep by modulating GABAergic signaling in Drosophila circadian neurons ]]> https://biorxiv.org/content/10.1101/2021.04.27.441638v1?rss=1 Chaturvedi, R. Stork, T. Yuan, C. Freeman, M. R. Emery, P. 2021-04-27 doi:10.1101/2021.04.27.441638 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Effects of BCG vaccination on donor unrestricted T cells in humans ]]> https://biorxiv.org/content/10.1101/2021.04.29.441927v1?rss=1 Gela, A. Murphy, M. Hadley, K. Hanekom, W. Boom, H. Johnson, J. Hoft, D. Joosten, S. Ottenhoff, T. Suliman, S. Moody, B. Lewinsohn, D. Hatherill, M. Seshadri, C. Nemes, E. Scriba, T. 2021-04-29 doi:10.1101/2021.04.29.441927 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Mesenchymal Lineage Heterogeneity Underlies Non-Redundant Functions of Pancreatic Cancer-Associated Fibroblasts ]]> https://biorxiv.org/content/10.1101/2021.05.01.442252v1?rss=1 Helms, E. J. Berry, M. W. Chaw, R. C. DuFort, C. C. Sun, D. Onate, M. K. Oon, C. Bhattacharyya, S. Sanford-Crane, H. Horton, W. Finan, J. M. Sattler, A. Makar, R. Dawson, D. W. Xia, Z. Hingorani, S. R. Sherman, M. H. 2021-05-02 doi:10.1101/2021.05.01.442252 Cold Spring Harbor Laboratory Press 2021-05-02 <![CDATA[ Transcriptional, epigenetic, and functional reprogramming of blood monocytes in non-human primates following chronic alcohol drinking ]]> https://biorxiv.org/content/10.1101/2021.05.12.443856v1?rss=1 Lewis, S. A. Sureshchandra, S. Doratt, B. Jimenez, V. Stull, C. Grant, K. A. Messaoudi, I. 2021-05-13 doi:10.1101/2021.05.12.443856 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ The FDA-approved drug apremilast suppresses alcohol intake: clinical and pre-clinical validation ]]> https://biorxiv.org/content/10.1101/2021.05.13.444033v1?rss=1 Grigsby, K. B. Mangieri, R. A. Roberts, A. J. Lopez, M. J. Tran, A. Firsick, E. J. Townsley, K. G. Beneze, A. Bess, J. Eisenstein, T. K. Meissler, J. J. Light, J. M. Miller, J. Quello, S. Shadan, F. Skinner, M. Aziz, H. C. Metten, P. Morissett, R. A. Crabbe, J. C. Roberto, M. Becker, H. C. Mason, B. J. Ozburn, A. R. 2021-05-15 doi:10.1101/2021.05.13.444033 Cold Spring Harbor Laboratory Press 2021-05-15 <![CDATA[ Pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification ]]> https://biorxiv.org/content/10.1101/2021.05.14.444244v1?rss=1 Weeder, B. Wood, M. Li, E. Nellore, A. Thompson, R. F. 2021-05-17 doi:10.1101/2021.05.14.444244 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Vascular KATP channel structural dynamics reveal regulatory mechanism by Mg-nucleotides ]]> https://biorxiv.org/content/10.1101/2021.05.15.444267v1?rss=1 Sung, M. W. Yang, Z. Patton, B. L. Mostofian, B. Russo, J. Zuckerman, D. M. Shyng, S.-L. 2021-05-16 doi:10.1101/2021.05.15.444267 Cold Spring Harbor Laboratory Press 2021-05-16 <![CDATA[ Virus-Dependent Immune Conditioning of Tissue Microenvironments ]]> https://biorxiv.org/content/10.1101/2021.05.21.444548v1?rss=1 Jiang, S. Chan, C. N. Rovira-Clave, X. Chen, H. Bai, Y. Zhu, B. McCaffrey, E. Greenwald, N. F. Liu, C. Barlow, G. L. Weirather, J. L. Busman-Sahay, K. Nekorchuk, M. Terry, M. Younger, S. Oliveria, J. P. Bosse, M. Demeter, J. Philips, D. Mukherjee, N. Golstev, Y. McIlwain, D. R. Angelo, M. Estes, J. D. Nolan, G. P. 2021-05-23 doi:10.1101/2021.05.21.444548 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ Non-neutralizing antibodies targeting the immunogenic regions of HIV-1 envelope reduce mucosal infection and virus burden in humanized mice ]]> https://biorxiv.org/content/10.1101/2021.05.24.445493v1?rss=1 Hioe, C. E. Li, G. Liu, X. Tsahouridis, O. He, X. Funaki, M. Klingler, J. Tang, A. F. Feyznezhad, R. Heindel, D. W. Wang, X.-H. Spencer, D. A. Hu, G. Satija, N. Prevost, J. Finzi, A. Hessell, A. Wang, S. Lu, S. Chen, B. K. Zolla-Pazner, S. Upadhyay, C. Alvarez, R. A. Su, L. 2021-05-24 doi:10.1101/2021.05.24.445493 Cold Spring Harbor Laboratory Press 2021-05-24 <![CDATA[ Mu opioid receptors acutely regulate adenosine signaling in a thalamo-striatal circuit. ]]> https://biorxiv.org/content/10.1101/2021.05.25.445648v1?rss=1 Adhikary, S. Birdsong, W. T. 2021-05-25 doi:10.1101/2021.05.25.445648 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Sex Differences in Functional Topography of Association Networks ]]> https://biorxiv.org/content/10.1101/2021.05.25.445671v1?rss=1 Shanmugan, S. Seidlitz, J. Cui, Z. Adebimpe, A. Bassett, D. S. Bertolero, M. A. Davatzikos, C. Fair, D. A. Gur, R. E. Gur, R. C. Larsen, B. Li, H. Pines, A. R. Raznahan, A. Roalf, D. R. Shinohara, R. T. Vogel, J. Wolf, D. H. Fan, Y. Alexander-Bloch, A. Satterthwaite, T. D. 2021-05-26 doi:10.1101/2021.05.25.445671 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ The P5-ATPase ATP13A1 modulates MR1-mediated antigen presentation ]]> https://biorxiv.org/content/10.1101/2021.05.26.445708v1?rss=1 Kulicke, C. A. De Zan, E. Hein, Z. Gonzalez-Lopez, C. Ghanwat, S. Veerapen, N. Besra, G. Klenerman, P. Christianson, J. C. Springer, S. Nijman, S. Cerundolo, V. Salio, M. 2021-05-27 doi:10.1101/2021.05.26.445708 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Novel aspects of iron homeostasis in pathogenic bloodstream form Trypanosoma brucei ]]> https://biorxiv.org/content/10.1101/2021.05.27.445749v1?rss=1 Carbajo, C. G. Cornell, L. J. Madbouly, Y. Lai, Z. Yates, P. A. Tinti, M. Tiengwe, C. 2021-05-27 doi:10.1101/2021.05.27.445749 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Robust Segmentation of Cellular Ultrastructure on Sparsely Labeled 3D Electron Microscopy Images using Deep Learning ]]> https://biorxiv.org/content/10.1101/2021.05.27.446019v1?rss=1 Machireddy, A. Thibault, G. Loftis, K. G. Stoltz, K. Bueno, C. E. Smith, H. R. Riesterer, J. L. Gray, J. W. Song, X. 2021-05-28 doi:10.1101/2021.05.27.446019 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Noise Reconstruction & Removal Network: A New Architecture to Denoise FIB-SEM Images ]]> https://biorxiv.org/content/10.1101/2021.05.27.446051v1?rss=1 Giannios, K. Chaurasia, A. Thibault, G. Riesterer, J. L. Stempinski, E. Lo, T. DeLaRosa, B. Gray, J. W. 2021-05-28 doi:10.1101/2021.05.27.446051 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ A homeostatic interferon-lambda response to bacterial microbiota stimulates preemptive antiviral defense within discrete pockets of intestinal epithelium ]]> https://biorxiv.org/content/10.1101/2021.06.02.446828v1?rss=1 Van Winkle, J. A. Peterson, S. T. Kennedy, E. A. Wheadon, M. J. Ingle, H. Desai, C. Constant, D. A. Wright, A. P. Li, L. Artyomov, M. Lee, S. Baldridge, M. T. Nice, T. J. 2021-06-02 doi:10.1101/2021.06.02.446828 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Incorporation of unnatural amino acid for the tagging of cannabinoid receptors 1 and 2 reveals receptor roles in regulating cAMP levels ]]> https://biorxiv.org/content/10.1101/2021.06.09.447758v1?rss=1 Thomas, A. Schultz, C. Laguerre, A. 2021-06-09 doi:10.1101/2021.06.09.447758 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ Encapsulated allografts preclude host sensitization and promote ovarian endocrine function in ovariectomized young rhesus monkeys and sensitized mice ]]> https://biorxiv.org/content/10.1101/2021.06.10.447598v1?rss=1 Day, J. R. Flanagan, C. L. David, A. Hartigan-O'Connor, D. J. de Mattos Barbosa, M. G. Martinez, M. L. Lee, C. Barnes, J. Farkash, E. Zelinski, M. Tarantal, A. Cascalho, M. Shikanov, A. 2021-06-13 doi:10.1101/2021.06.10.447598 Cold Spring Harbor Laboratory Press 2021-06-13 <![CDATA[ Mechanical stress in pancreatic cancer: Signaling pathway adaptation activates cytoskeletal remodeling and enhances cell migration ]]> https://biorxiv.org/content/10.1101/2021.06.11.448065v1?rss=1 Kalli, M. Li, R. Mills, G. B. Stylianopoulos, T. Zervantonakis, I. K. 2021-06-11 doi:10.1101/2021.06.11.448065 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Dietary palmitic acid induces trained immunity that controls inflammation and infection ]]> https://biorxiv.org/content/10.1101/2021.06.15.448579v1?rss=1 Seufert, A. L. Hickman, J. W. Traxler, S. K. Peterson, R. M. Lashley, S. J. Shulzhenko, N. Napier, R. J. Napier, B. A. 2021-06-16 doi:10.1101/2021.06.15.448579 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ Physiologically distinct neurons within the ventrolateral periaqueductal gray are not defined by mu-opioid receptor expression but are differentially activated by persistent inflammation ]]> https://biorxiv.org/content/10.1101/2021.06.16.448597v1?rss=1 McPherson, K. B. Bouchet, C. A. Ingram, S. L. 2021-06-17 doi:10.1101/2021.06.16.448597 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ The neurocomputational architecture of explore-exploit decision making ]]> https://biorxiv.org/content/10.1101/2021.06.21.449128v1?rss=1 Hogeveen, J. Mullins, T. S. Romero, J. Eversole, E. Rogge-Obando, K. Mayer, A. R. Costa, V. D. 2021-06-21 doi:10.1101/2021.06.21.449128 Cold Spring Harbor Laboratory Press 2021-06-21 <![CDATA[ Persistence of SARS CoV-2 S1 Protein in CD16+ Monocytes in Post-Acute Sequelae of COVID-19 (PASC) Up to 15 Months Post-Infection ]]> https://biorxiv.org/content/10.1101/2021.06.25.449905v1?rss=1 Patterson, B. Francisco, E. B. Yogendra, R. Long, E. Pise, A. Rodrigues, H. Hall, E. Herrera, o. Parikh, P. Guevara-Coto, J. Chang, X. Sacha, J. B. Rodriguez, R. Mora, J. 2021-06-25 doi:10.1101/2021.06.25.449905 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Structural Insights into the Venus flytrap Mechanosensitive Ion Channel Flycatcher1 ]]> https://biorxiv.org/content/10.1101/2021.06.30.449980v1?rss=1 Jojoa-Cruz, S. Saotome, K. Tsui, C. C. Lee, W.-H. Sansom, M. S. P. Murthy, S. E. Patapoutian, A. Ward, A. B. 2021-06-30 doi:10.1101/2021.06.30.449980 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ Adolescent dopamine neurons represent reward differently during action and state guided learning ]]> https://biorxiv.org/content/10.1101/2021.07.05.451195v1?rss=1 McCane, A. Wegener, M. Faraji, M. Garcia, M. R. Wallin-Miller, K. Costa, V. Moghaddam, B. 2021-07-06 doi:10.1101/2021.07.05.451195 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Holistic Characterization of Tumor Monocyte-to-Macrophage Differentiation Integrates Distinct Immune Phenotypes in Kidney Cancer ]]> https://biorxiv.org/content/10.1101/2021.07.07.451502v1?rss=1 Mujal, A. M. Combes, A. J. Rao, A. A. Binnewies, M. Samad, B. Tsui, J. Boissonnas, A. Pollack, J. L. Arguello, R. J. Ruhland, M. K. Barry, K. C. Chan, V. Krummel, M. F. 2021-07-08 doi:10.1101/2021.07.07.451502 Cold Spring Harbor Laboratory Press 2021-07-08 <![CDATA[ Pyroptosis-dependent and -independent cross-priming of CD8+ T cells by intestinal epithelial cell-derived antigen ]]> https://biorxiv.org/content/10.1101/2021.07.08.451636v1?rss=1 Deets, K. A. Nichols, R. D. Rauch, I. Vance, R. E. 2021-07-08 doi:10.1101/2021.07.08.451636 Cold Spring Harbor Laboratory Press 2021-07-08 <![CDATA[ Prolonged partner separation erodes nucleus accumbens transcriptional signatures of pair bonding in male prairie voles ]]> https://biorxiv.org/content/10.1101/2021.07.14.452355v1?rss=1 Sadino, J. M. Bradeen, X. G. Kelly, C. J. Walker, D. M. Donaldson, Z. R. 2021-07-14 doi:10.1101/2021.07.14.452355 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ GPR39 Localization in Aging Human Brain and Correlation of Expression and Polymorphism with Vascular Cognitive Impairment ]]> https://biorxiv.org/content/10.1101/2021.07.15.452525v1?rss=1 Davis, C. Bah, T. Zhang, W. Nelson, J. Golgotiu, K. Nie, X. Alkayed, F. Young, J. Woltjer, R. Silbert, L. Grafe, M. Alkayed, N. J. 2021-07-15 doi:10.1101/2021.07.15.452525 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ Axial spondyloarthritis patients have altered mucosal IgA response to oral and fecal microbiota ]]> https://biorxiv.org/content/10.1101/2021.07.15.452558v1?rss=1 Gill, T. Stauffer, P. Asquith, M. Laderas, T. Martin, T. M. Davin, S. Schleisman, M. Ramirez, C. Ogle, K. Lindquist, I. Nguyen, J. Planck, S. R. Shaut, C. Diamond, S. Rosenbaum, J. T. Karstens, L. 2021-07-19 doi:10.1101/2021.07.15.452558 Cold Spring Harbor Laboratory Press 2021-07-19 <![CDATA[ Lateral habenula M2 muscarinic receptor control of neuronal activity and cocaine seeking behavior ]]> https://biorxiv.org/content/10.1101/2021.07.24.453572v1?rss=1 Wolfe, C. I. C. Hwang, E.-K. Zapata, A. Hoffman, A. F. Lupica, C. R. 2021-07-25 doi:10.1101/2021.07.24.453572 Cold Spring Harbor Laboratory Press 2021-07-25 <![CDATA[ EXPRESSION OF A SECRETABLE, CELL-PENETRATING CDKL5 PROTEIN ENHANCES THE EFFICACY OF AAV VECTOR-MEDIATED GENE THERAPY FOR CDKL5 DEFICIENCY DISORDER. ]]> https://biorxiv.org/content/10.1101/2021.07.26.453746v1?rss=1 Medici, G. Tassinari, M. Galvani, G. Bastianini, S. Gennaccaro, L. Loi, M. Fuchs, C. Mottolese, N. Alvente, S. Berteotti, C. Bagget, H. R. Zoccoli, G. Giustetto, M. Muotri, A. R. Nakai, H. Trazzi, S. Ciani, E. 2021-07-26 doi:10.1101/2021.07.26.453746 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ Exploratory extracellular vesicle-bound miRNA profiling to identify candidate biomarkers of chronic alcohol drinking in non-human primates ]]> https://biorxiv.org/content/10.1101/2021.07.28.454223v1?rss=1 Lewis, S. A. Doratt, B. Sureshchandra, S. Pan, T. Gonzalez, S. W. Shen, W. Grant, K. A. Messaoudi, I. 2021-07-29 doi:10.1101/2021.07.28.454223 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Chronic ethanol drinking in non-human primates induces inflammatory cathepsin gene expression in alveolar macrophages accompanied by functional defects ]]> https://biorxiv.org/content/10.1101/2021.07.30.454528v1?rss=1 Lewis, S. A. Doratt, B. Sureshchandra, S. Jankeel, A. Newman, N. Grant, K. A. Messaoudi, I. 2021-07-31 doi:10.1101/2021.07.30.454528 Cold Spring Harbor Laboratory Press 2021-07-31 <![CDATA[ Sex-dependent development of Kras-induced anal squamous cell carcinoma in mice ]]> https://biorxiv.org/content/10.1101/2021.08.04.455138v1?rss=1 Walcheck, M. Matkowskyj, K. Turco, A. E. Blaine-Sauer, S. Nukaya, M. Noel, J. L. Ronnekleiv, O. K. Ronnekleiv-Kelly, S. 2021-08-06 doi:10.1101/2021.08.04.455138 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ BET inhibitors synergize with anti-PD1 by rescuing TCF1+ progenitor exhausted CD8+ T cells in Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/2021.08.04.455147v1?rss=1 Romine, K. A. Cho, H. J. Kosaka, Y. Byrd, K. Coy, J. L. Flynn, P. A. Newman, M. T. Loo, C. Scott, J. Lind, E. F. 2021-08-04 doi:10.1101/2021.08.04.455147 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ A LINCS microenvironment perturbation resource for integrative assessment of ligand-mediated molecular and phenotypic responses ]]> https://biorxiv.org/content/10.1101/2021.08.06.455429v1?rss=1 Gross, S. M. Dane, M. A. Smith, R. L. Devlin, K. Mclean, I. Derrick, D. Mills, C. Subramanian, K. London, A. Torre, D. Erdem, C. Lyons, N. Natoli, T. Pessa, S. Lu, X. Mullahoo, J. Li, J. Adam, M. Wassie, B. Liu, M. Kilburn, D. F. Liby, T. Bucher, E. Sanchez-Aguila, C. Daily, K. Omberg, L. Wang, Y. Jacobson, C. Yapp, C. Chung, M. Vidovic, D. Lu, Y. Schurer, S. Lee, A. Pillai, A. Subramanian, A. Papanastasiou, M. Fraenkel, E. Feiler, H. Mills, G. B. Jaffe, J. Ma'ayan, A. Birtwistle, M. R. Sorger, P. K. Korkola, J. E. Gray, J. W. Heiser, L. M. 2021-08-09 doi:10.1101/2021.08.06.455429 Cold Spring Harbor Laboratory Press 2021-08-09 <![CDATA[ Immediate Impact of Yogic Breathing on Pulsatile Cerebrospinal Fluid Dynamics ]]> https://biorxiv.org/content/10.1101/2021.08.09.455068v1?rss=1 Yildiz, S. Grinstead, J. Hildebrand, A. Oshinski, J. Rooney, W. D. Lim, M. M. Oken, B. 2021-08-10 doi:10.1101/2021.08.09.455068 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ FLARIM v2.0, an improved method to quantify transcript-ribosome interactions in vivo in the adult Drosophila brain ]]> https://biorxiv.org/content/10.1101/2021.08.13.456301v1?rss=1 Richer, P. Speese, S. D. Logan, M. A. 2021-08-14 doi:10.1101/2021.08.13.456301 Cold Spring Harbor Laboratory Press 2021-08-14 <![CDATA[ Fanconi Anemia Pathway Deficiency Drives Copy Number Variation in Squamous Cell Carcinomas ]]> https://biorxiv.org/content/10.1101/2021.08.14.456365v1?rss=1 Webster, A. L. H. Sanders, M. A. Patel, K. Dietrich, R. Noonan, R. J. Lach, F. P. White, R. R. Goldfarb, A. Hadi, K. Edwards, M. M. Donovan, F. X. Jung, M. Sridhar, S. Fedrigo, O. Tian, H. Rosiene, J. Heineman, T. Kennedy, J. A. Bean, L. Rosti, O. Tryon, R. Gonzalez, A.-M. Rosenberg, A. Luo, J.-D. Carrol, T. Velleuer, E. Rastatter, J. C. Wells, S. I. Surralles, J. Bagby, G. MacMillan, M. L. Wagner, J. E. Cancio, M. Boulad, F. Scognamiglio, T. Vaughan, R. Koren, A. Imielinski, M. Chandrasekharappa, S. Auerbach, A. D. Singh, B. Kutler, D. I. Campbell, P. 2021-08-16 doi:10.1101/2021.08.14.456365 Cold Spring Harbor Laboratory Press 2021-08-16 <![CDATA[ Deep immune profiling of the maternal-fetal interface with mild SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2021.08.23.457408v1?rss=1 Sureshchandra, S. Zulu, M. Z. Doratt, B. Jankeel, A. Tifrea, D. Edwards, R. A. Rincon, M. Marshall, N. E. Messaoudi, I. 2021-08-23 doi:10.1101/2021.08.23.457408 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ PU.1 and MYC transcriptional network defines synergistic drug responses to KIT and LSD1 inhibition in acute myeloid leukemia ]]> https://biorxiv.org/content/10.1101/2021.08.24.456354v1?rss=1 Smith, B. M. VanCampen, J. Kong, G. L. Yashar, W. Horton, W. Coleman, D. J. Estabrook, J. Lusardi, T. A. Druker, B. J. Maxson, J. E. Braun, T. P. 2021-08-24 doi:10.1101/2021.08.24.456354 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ Increased 20-HETE signaling suppresses neurovascular coupling after ischemic stroke in regions beyond the infarct ]]> https://biorxiv.org/content/10.1101/2021.08.25.457547v1?rss=1 Li, Z. McConnell, H. L. Stackhouse, T. L. Pike, M. M. Zhang, W. Mishra, A. 2021-08-27 doi:10.1101/2021.08.25.457547 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Infection-induced dermal lymphatic zippering restricts viral dissemination from skin and promotes anti-viral CD8+ T cell expansion. ]]> https://biorxiv.org/content/10.1101/2021.08.26.457551v1?rss=1 Churchill, M. J. du Bois, H. Heim, T. A. Mudianto, T. Steele, M. M. Nolz, J. C. Lund, A. W. 2021-08-27 doi:10.1101/2021.08.26.457551 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ MRI-Visible Perivascular Space (PVS) Changes with Long-Duration Spaceflight ]]> https://biorxiv.org/content/10.1101/2021.08.26.457870v1?rss=1 Hupfeld, K. Richmond, S. McGregor, H. Schwartz, D. Luther, M. Beltran, N. Kofman, I. De Dios, Y. Riascos, R. Wood, S. Bloomberg, J. Mulavara, A. Silbert, L. Iliff, J. Seidler, R. Piantino, J. 2021-08-28 doi:10.1101/2021.08.26.457870 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Highly sensitive genetically-encoded sensors for population and subcellular imaging of cAMP in vivo ]]> https://biorxiv.org/content/10.1101/2021.08.27.457999v1?rss=1 Massengill, C. I. Bayless-Edwards, L. Ceballos, C. C. Cebul, E. R. Qin, M. Whorton, M. R. Ye, B. Mao, T. Zhong, H. 2021-08-28 doi:10.1101/2021.08.27.457999 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Multiplex spatial systems analysis of local nanodose drug responses predicts effective treatment combinations of immunotherapies and targeted agents in mammary carcinoma ]]> https://biorxiv.org/content/10.1101/2021.09.01.458631v1?rss=1 Tatarova, Z. Blumberg, D. C. Korkola, J. E. Heiser, L. M. Muschler, J. L. Schedin, P. J. Ahn, S. W. Mills, G. B. Coussens, L. M. Jonas, O. Gray, J. W. 2021-09-02 doi:10.1101/2021.09.01.458631 Cold Spring Harbor Laboratory Press 2021-09-02 <![CDATA[ Glial TGFβ activity promotes axon survival in peripheral nerves ]]> https://biorxiv.org/content/10.1101/2021.09.02.458753v1?rss=1 Lassetter, A. Corty, M. Barria, R. Sheehan, A. Aicher, S. Fox, A. N. Hill, J. Freeman, M. 2021-09-03 doi:10.1101/2021.09.02.458753 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Analysis of Rod/Cone Gap Junctions from the Reconstruction of Mouse Photoreceptor Terminals ]]> https://biorxiv.org/content/10.1101/2021.09.06.459091v1?rss=1 Massey, S. Ishibashi, M. Keung, J. Morgans, C. W. Aicher, S. Carroll, J. Singer, J. H. Jia, L. Li, W. Fahrenfort, I. Ribelayga, C. 2021-09-06 doi:10.1101/2021.09.06.459091 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Ascertaining cells' synaptic connections and RNA expression simultaneously with massively barcoded rabies virus libraries ]]> https://biorxiv.org/content/10.1101/2021.09.06.459177v1?rss=1 Saunders, A. Huang, K. W. Vondrak, C. Hughes, C. Smolyar, K. Sen, H. Philson, A. C. Nemesh, J. Wysoker, A. Kashin, S. Sabatini, B. L. McCarroll, S. A. 2021-09-06 doi:10.1101/2021.09.06.459177 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Resurgent Na+ currents promote ultrafast spiking in projection neurons that drive fine motor control ]]> https://biorxiv.org/content/10.1101/2021.09.09.459677v1?rss=1 Zemel, B. Nevue, A. A. Dagostin, A. Lovell, P. V. Mello, C. V. von Gersdorff, H. 2021-09-10 doi:10.1101/2021.09.09.459677 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ c-Kit mediates cutaneous sensory axon innervation and multi-kinase inhibitor-induced neurotoxicity ]]> https://biorxiv.org/content/10.1101/2021.09.13.460106v1?rss=1 Tuttle, A. M. Pomaville, M. B. Delgado, K. C. Wright, K. M. Nechiporuk, A. V. 2021-09-15 doi:10.1101/2021.09.13.460106 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Discoidin domain receptor regulates ensheathment, survival, and caliber of peripheral axons ]]> https://biorxiv.org/content/10.1101/2021.09.21.461270v1?rss=1 Corty, M. M. Lassetter, A. P. Hill, J. Q. Sheehan, A. E. Bernardo-Garcia, F. J. Davis, G. W. Aicher, S. A. Freeman, M. R. 2021-09-23 doi:10.1101/2021.09.21.461270 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Aldh2 dependent formaldehyde metabolism fuels purine demands in melanocyte stem cells ]]> https://biorxiv.org/content/10.1101/2021.09.23.461061v1?rss=1 Brunsdon, H. Brombin, A. Peterson, S. Postlethwait, J. H. Patton, E. E. 2021-09-23 doi:10.1101/2021.09.23.461061 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Vertex-wise characterization of Non-Human Primate cortical development with prenatal insights. ]]> https://biorxiv.org/content/10.1101/2021.09.23.461551v1?rss=1 Ramirez, J. S. B. Hermosillo, R. Thomas, E. Zhu, J. Y. Sturgeon, D. Schifsky, E. Galassi, A. Thompson, J. R. Bagley, J. L. Milham, M. P. Miranda-Dominguez, O. Papadakis, S. Bah, M. Mitchell, A. Xu, T. Graham, A. M. Feczko, E. Sullivan, E. L. Fair, D. A. 2021-09-24 doi:10.1101/2021.09.23.461551 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Fast resupply of synaptic vesicles requires Synaptotagmin-3 ]]> https://biorxiv.org/content/10.1101/2021.09.27.462028v1?rss=1 Weingarten, D. J. Shrestha, A. Kissiwaa, S. A. Spruston, E. Jackman, S. L. 2021-09-27 doi:10.1101/2021.09.27.462028 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ A cell-based screen identifies HDAC inhibitors and PLK inhibitor as activators of RIG-I signaling ]]> https://biorxiv.org/content/10.1101/2021.09.28.462211v1?rss=1 Fraile-Bethencourt, E. Foss, M. H. Nelson, D. Malhotra, S. V. Anand, S. 2021-09-30 doi:10.1101/2021.09.28.462211 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Ad26.COV2.S Prevents SARS-CoV-2 Induced Pathways of Inflammation and Thrombosis in Hamsters ]]> https://biorxiv.org/content/10.1101/2021.09.30.462514v1?rss=1 Aid, M. Vidal, S. Piedra-Mora, C. Ducat, S. Chan, C. Bondoc, S. Colarusse, A. Starke, C. Nekorchuk, M. Busman-Sahay, K. Estes, J. Martinot, A. Barouch, D. H. 2021-09-30 doi:10.1101/2021.09.30.462514 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Structural basis for C-type inactivation in a Shaker family voltage gated K+ channel ]]> https://biorxiv.org/content/10.1101/2021.10.01.462615v1?rss=1 Reddi, R. Matulef, K. Riederer, E. Whorton, M. Valiyaveetil, F. 2021-10-01 doi:10.1101/2021.10.01.462615 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Molecular structure and conformation of stereocilia tip-links elucidated by cryo-electron tomography ]]> https://biorxiv.org/content/10.1101/2021.10.01.462800v1?rss=1 Elferich, J. Clark, S. Ge, J. Goehring, A. Matsui, A. Gouaux, E. 2021-10-01 doi:10.1101/2021.10.01.462800 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Systematic discovery of mutation-directed neo-protein-protein interactions in cancer ]]> https://biorxiv.org/content/10.1101/2021.10.03.462422v1?rss=1 Mo, X. Niu, Q. Ivanov, A. A. Tsang, Y. H. Tang, C. Shu, C. Wahafu, A. Doyle, S. Cicka, D. Yang, X. Fan, D. Reyna, M. A. Cooper, L. A. D. Moreno, C. S. Zhou, W. Owonikoko, T. Lonial, S. Khuri, F. R. Du, Y. Ramalingam, S. S. Mill, G. B. Fu, H. 2021-10-03 doi:10.1101/2021.10.03.462422 Cold Spring Harbor Laboratory Press 2021-10-03 <![CDATA[ Cell Stiffening Contributes to Complement-mediated Injury of Choroidal Endothelial Cells in Early AMD ]]> https://biorxiv.org/content/10.1101/2021.10.06.463274v1?rss=1 Cabrera, A. P. Stoddard, J. Tierno, I. S. Matisioudis, N. Agarwal, M. Renner, L. Palegar, N. Neuringer, M. McGill, T. J. Ghosh, K. 2021-10-08 doi:10.1101/2021.10.06.463274 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ Morphodynamical cell-state description via live-cell imaging trajectory embedding ]]> https://biorxiv.org/content/10.1101/2021.10.07.463498v1?rss=1 Copperman, J. Gross, S. M. Chang, Y. H. Heiser, L. M. Zuckerman, D. M. 2021-10-09 doi:10.1101/2021.10.07.463498 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ Quantitative multiplex immunohistochemistry reveals inter- and intra-patient lymphovascular and immune heterogeneity in primary cutaneous melanoma ]]> https://biorxiv.org/content/10.1101/2021.10.08.463675v1?rss=1 Femel, J. Booth, J. L. Asnaashari, T. G. Leachman, S. A. Tsujikawa, T. White, K. Chang, Y. H. W. Lund, A. W. 2021-10-09 doi:10.1101/2021.10.08.463675 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ Structural Diversity of Photoswitchable Sphingolipids for Optodynamic Control of Lipid Raft Microdomains ]]> https://biorxiv.org/content/10.1101/2021.10.11.463883v1?rss=1 Hartrampf, N. Leitao, S. M. Winter, N. Toombs-Ruane, H. Frank, J. A. Schwille, P. Trauner, D. Franquelim, H. G. 2021-10-12 doi:10.1101/2021.10.11.463883 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ In vivo versus in silico assessment of potentially pathogenic missense variants in human reproductive genes ]]> https://biorxiv.org/content/10.1101/2021.10.12.464112v1?rss=1 Ding, X. Singh, P. Tran, T. N. Fragoza, R. Yu, H. Schimenti, J. C. 2021-10-12 doi:10.1101/2021.10.12.464112 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ Synaptotagmin-7 enhances phasic dopamine release ]]> https://biorxiv.org/content/10.1101/2021.10.17.464710v1?rss=1 Jackman, S. L. Kissiwaa, S. A. Lebowitz, J. J. Engeln, K. A. Bowman, A. M. Williams, J. T. 2021-10-17 doi:10.1101/2021.10.17.464710 Cold Spring Harbor Laboratory Press 2021-10-17 <![CDATA[ A peroxide-responding sRNA evolved from a peroxidase mRNA ]]> https://biorxiv.org/content/10.1101/2021.10.18.464853v1?rss=1 Krieger, M. C. Dutcher, H. A. Ashford, A. J. Raghavan, R. 2021-10-18 doi:10.1101/2021.10.18.464853 Cold Spring Harbor Laboratory Press 2021-10-18 <![CDATA[ Preventing ovariectomy-induced weight gain decreases tumor burden in rodent models of obesity and postmenopausal breast cancer. ]]> https://biorxiv.org/content/10.1101/2021.10.18.464856v1?rss=1 Wellberg, E. A. Corleto, K. A. Checkley, L. A. Jindal, S. Johnson, G. Higgins, J. A. Obeid, S. Anderson, S. M. Thor, A. D. Schedin, P. J. MacLean, P. S. Giles, E. D. 2021-10-19 doi:10.1101/2021.10.18.464856 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Transcriptional integration of distinct microbial and nutritional signals by the small intestinal epithelium ]]> https://biorxiv.org/content/10.1101/2021.11.01.465976v1?rss=1 Lickwar, C. R. Davison, J. M. Kelly, C. Padilla Mercado, G. Wen, J. Davis, B. R. Tillman, M. C. Semova, I. Andres, S. F. Vale, G. McDonald, J. G. Rawls, J. F. 2021-11-03 doi:10.1101/2021.11.01.465976 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Btbd11 is an inhibitory interneuron specific synaptic scaffolding protein that supports excitatory synapse structure and function ]]> https://biorxiv.org/content/10.1101/2021.11.01.466782v1?rss=1 Bygrave, A. M. Sengupta, A. Jackert, E. P. Ahmed, M. Adenuga, B. Nelson, E. Goldschmidt, H. L. Johnson, R. C. Zhong, H. Yeh, F. L. Sheng, M. Huganir, R. L. 2021-11-02 doi:10.1101/2021.11.01.466782 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Transcription factor control of dendrite targeting via combinatorial cell-surface codes ]]> https://biorxiv.org/content/10.1101/2021.11.03.467130v1?rss=1 Xie, Q. Li, J. Li, H. Udeshi, N. D. Svinkina, T. Kohani, S. Guajardo, R. Mani, D. R. Xu, C. Li, T. Han, S. Wei, W. Shuster, S. A. Luginbuhl, D. J. Ting, A. Y. Carr, S. A. Luo, L. 2021-11-04 doi:10.1101/2021.11.03.467130 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Mutant-SETBP1 activates transcription of Myc programs to accelerate CSF3R-driven myeloproliferative neoplasms ]]> https://biorxiv.org/content/10.1101/2021.11.04.467367v1?rss=1 Carratt, S. A. Kong, G. L. Smith, B. M. Schonrock, Z. Maloney, L. Baris, A. Druker, B. J. Braun, T. P. Maxson, J. E. 2021-11-05 doi:10.1101/2021.11.04.467367 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ Genome-wide identification of novel sRNAs in Streptococcus mutans ]]> https://biorxiv.org/content/10.1101/2021.11.16.468913v1?rss=1 Krieger, M. Merritt, J. Raghavan, R. 2021-11-17 doi:10.1101/2021.11.16.468913 Cold Spring Harbor Laboratory Press 2021-11-17 <![CDATA[ Investigation of Human Endogenous Retrovirus-K (ERVK) Expression and Function in Normal Placentation and Preterm Pregnancy ]]> https://biorxiv.org/content/10.1101/2021.11.22.469425v1?rss=1 Rosenkrantz, J. L. Martinez, M. Mahankali, A. Carbone, L. Chavez, S. L. 2021-11-22 doi:10.1101/2021.11.22.469425 Cold Spring Harbor Laboratory Press 2021-11-22 <![CDATA[ A framework for multiplex imaging optimization and reproducible analysis ]]> https://biorxiv.org/content/10.1101/2021.11.29.470281v1?rss=1 Eng, J. R. Bucher, E. Hu, Z. Zheng, T. Gibbs, S. Chin, K. Gray, J. W. 2021-11-30 doi:10.1101/2021.11.29.470281 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Distinct roles of the Na+ binding sites in the allosteric coupling mechanism of the glutamate transporter homolog, GltPh. ]]> https://biorxiv.org/content/10.1101/2021.11.29.470416v1?rss=1 Valiyaveetil, F. Riederer, E. Moenne-Loccoz, P. 2021-11-30 doi:10.1101/2021.11.29.470416 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Potassium effects on NCC are attenuated during inhibition of Cullin E3-ubiquitin ligases ]]> https://biorxiv.org/content/10.1101/2021.11.30.470531v1?rss=1 Murali, S. K. Little, R. Poulsen, S. B. Ferdaus, M. Ellison, D. H. McCormick, J. A. Fenton, R. A. 2021-12-01 doi:10.1101/2021.11.30.470531 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ The Long Noncoding RNA FEDORA is a Cell-Type- and Sex-Specific Regulator of Depression ]]> https://biorxiv.org/content/10.1101/2021.11.30.470628v1?rss=1 Issler, O. van der Zee, Y. Y. Ramakrishnan, A. Xia, S. Zinsmaier, A. K. Tan, C. Li, W. Browne, C. J. Walker, D. M. Salery, M. Torres-Berrio, A. Futamura, R. Duffy, J. E. Labonte, B. Tamminga, C. A. Dupree, J. L. Dong, Y. Murrough, J. W. Shen, L. Nestler, E. J. 2021-12-01 doi:10.1101/2021.11.30.470628 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Babesia duncani as a model organism to study the development, virulence and drug susceptibility of intraerythrocytic parasites in vitro and in vivo ]]> https://biorxiv.org/content/10.1101/2021.12.01.470698v1?rss=1 Mamoun, C. Pal, A. C. Renard, I. Singh, P. Vydyam, P. Chiu, J. E. Pou, S. W. Winter, R. Dodean, R. Frueh, L. Nilsen, A. C. Riscoe, M. K. Doggett, J. S. 2021-12-01 doi:10.1101/2021.12.01.470698 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Sleep Dependent Changes of Lactate Concentration in Human Brain ]]> https://biorxiv.org/content/10.1101/2021.12.05.471196v1?rss=1 Yildiz, S. Lim, M. M. Sammi, M. K. Powers, K. Murchison, C. F. Iliff, J. J. Rooney, W. D. 2021-12-07 doi:10.1101/2021.12.05.471196 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ WESTPA 2.0: High-performance upgrades for weighted ensemble simulations and analysis of longer-timescale applications ]]> https://biorxiv.org/content/10.1101/2021.12.05.471280v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@575710org.highwire.dtl.DTLVardef@151c3dorg.highwire.dtl.DTLVardef@1f0f525org.highwire.dtl.DTLVardef@6e5956_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Russo, J. Zhang, S. Leung, J. Bogetti, A. Thompson, J. DeGrave, A. Torrillo, P. Pratt, A. J. Wong, K. Xia, J. Copperman, J. T. Adelman, J. Zwier, M. LeBard, D. Zuckerman, D. M. Chong, L. 2021-12-06 doi:10.1101/2021.12.05.471280 Cold Spring Harbor Laboratory Press 2021-12-06 <![CDATA[ Neurexins in serotonergic neurons regulate serotonin transmission and complex mouse behaviors ]]> https://biorxiv.org/content/10.1101/2021.12.09.471904v1?rss=1 Cheung, A. Matsui, A. Abe, M. Sakimura, K. Sasaoka, T. Uemura, T. Imamura Kawasawa, Y. Futai, K. 2021-12-09 doi:10.1101/2021.12.09.471904 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Salmonella Typhimurium induces NAIP/NLRC4- and NLRP3/ASC-independent, caspase-1/4-dependent inflammasome activation in human intestinal epithelial cells ]]> https://biorxiv.org/content/10.1101/2021.12.09.472040v1?rss=1 Naseer, N. Bauer, R. Zhang, J. Brodsky, I. E. Rauch, I. Shin, S. 2021-12-10 doi:10.1101/2021.12.09.472040 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ Transcriptional and Cytotoxic Responses of Human Intestinal Organoids to Interferon Types I, II, and III ]]> https://biorxiv.org/content/10.1101/2021.12.11.472223v1?rss=1 Constant, D. A. Van Winkle, J. A. VanderHoek, E. Dekker, S. E. Sofia, M. A. Regner, E. Tsikitis, V. L. Modiano, N. Nice, T. J. 2021-12-13 doi:10.1101/2021.12.11.472223 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Plexins Promote Hedgehog Signaling Through Their Cytoplasmic GAP Activity ]]> https://biorxiv.org/content/10.1101/2021.12.15.472757v1?rss=1 Pinskey, J. M. Hoard, T. M. Zhao, X.-F. Franks, N. E. Frank, Z. C. McMellen, A. N. Giger, R. J. Allen, B. L. 2021-12-16 doi:10.1101/2021.12.15.472757 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ The origins and functional effects of postzygotic mutations throughout the human lifespan ]]> https://biorxiv.org/content/10.1101/2021.12.20.473199v1?rss=1 Rockweiler, N. B. Ramu, A. Nagirnaja, L. Wong, W. H. Noordam, M. J. Drubin, C. W. Huang, N. Miller, B. Todres, E. Z. Vigh-Conrad, K. A. Zito, A. Small, K. S. Ardlie, K. G. Cohen, B. A. Conrad, D. F. 2021-12-21 doi:10.1101/2021.12.20.473199 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Effects of α-crystallin gene knockout on zebrafish lens development ]]> https://biorxiv.org/content/10.1101/2021.12.22.473921v1?rss=1 Posner, M. Murray, K. L. Andrew, B. Brdicka, S. Butterbaugh-Roberts, A. Franklin, K. Hussen, A. Kaye, T. Kepp, E. McDonald, M. Snodgrass, T. Zientek, K. David, L. 2021-12-23 doi:10.1101/2021.12.22.473921 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Mistimed feeding disrupts circadian rhythms of male mating behavior and female preovulatory LH surges in mice ]]> https://biorxiv.org/content/10.1101/2021.12.27.474267v1?rss=1 Kukino, A. Walbeek, T. J. Sun, L. J. Watt, A. T. Park, J. H. Kauffman, A. S. Butler, M. P. 2021-12-28 doi:10.1101/2021.12.27.474267 Cold Spring Harbor Laboratory Press 2021-12-28 <![CDATA[ Diversity of microglial transcriptional responses during opioid exposure and neuropathic pain ]]> https://biorxiv.org/content/10.1101/2021.12.29.473853v1?rss=1 Sypek, E. I. Collins, H. Y. McCallum, W. M. Bourdillon, A. T. Bohlen, C. J. Scherrer, G. 2021-12-29 doi:10.1101/2021.12.29.473853 Cold Spring Harbor Laboratory Press 2021-12-29 <![CDATA[ PD1+ T-cells correlate with Nerve Fiber Density as a prognostic biomarker in patients with resected perihilar cholangiocarcinoma. ]]> https://biorxiv.org/content/10.1101/2022.01.07.475344v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@e30fadorg.highwire.dtl.DTLVardef@11a4e4aorg.highwire.dtl.DTLVardef@a04d8org.highwire.dtl.DTLVardef@1c425db_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Tan, X. Rosin, M. Appinger, S. Bednarsch, J. Liu, D. Wiltberger, G. Garcia Vallejo, J. Jang, S. Czigany, Z. Boroojerdi, S. Gaisa, N. Boor, P. Buelow, R. de Vos-Geelen, J. Valkenburg-van Iersel, L. Clahsen-van Groningen, M. de Jong, E. Groot Koerkamp, B. Doukas, M. Rocha, F. Luedde, T. Klinge, U. Sivakumar, S. Neumann, U. Heij, L. 2022-01-11 doi:10.1101/2022.01.07.475344 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ GoPeaks: Histone Modification Peak Calling for CUT&Tag ]]> https://biorxiv.org/content/10.1101/2022.01.10.475735v1?rss=1 Yashar, W. M. Kong, G. VanCampen, J. Smith, B. M. Coleman, D. J. Carbone, L. Yardimci, G. G. Maxson, J. E. Braun, T. P. 2022-01-12 doi:10.1101/2022.01.10.475735 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Responses to song playback differ in sleeping versus anesthetized songbirds ]]> https://biorxiv.org/content/10.1101/2022.01.11.475714v1?rss=1 Bottjer, S. W. Le Moing, C. L. Li, E. J. Yuan, R. C. 2022-01-12 doi:10.1101/2022.01.11.475714 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ A Precision Functional Atlas of Network Probabilities and Individual-Specific Network Topography ]]> https://biorxiv.org/content/10.1101/2022.01.12.475422v1?rss=1 0.999) and between methods (r=0.96), revealing both regions of high invariance and high variability. Compared to using parcellations based on groups averages, the MIDB Precision Brain Atlas allowed us to derive a set of brain regions that are largely invariant in network topography across populations, which provides more reproducible statistical maps of executive function in brain-wide associations. We also explore an example use case for probabilistic maps, highlighting their potential for use in targeted neuromodulation. The MIDB Precision Brain Atlas is expandable to alternative datasets and methods and is provided open-source with an online web interface to encourage the scientific community to experiment with probabilistic atlases and individual-specific topographies to more precisely relate network phenomenon to functional organization of the human brain. ]]> Hermosillo, R. J. Moore, L. A. Feczko, E. J. Pines, A. R. Dworetsky, A. Conan, G. Mooney, M. A. Randolph, A. Adeyemo, B. Earl, E. Perrone, A. Carrasco, C. M. Uriarte-Lopez, J. Snider, K. Doyle, O. Cordova, M. Nagel, B. J. Ewing, S. W. F. Satterthwaite, T. D. Dosenbach, N. Gratton, C. Petersen, S. Dominguez, O. M. Fair, D. A. 2022-01-13 doi:10.1101/2022.01.12.475422 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ Cryo-EM Structure of Adeno-associated virus-4 at 2.2 A resolution ]]> https://biorxiv.org/content/10.1101/2022.01.12.476110v1?rss=1 Zane, G. M. Silveria, M. A. Meyer, N. L. White, T. A. Chapman, M. S. 2022-01-13 doi:10.1101/2022.01.12.476110 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ Dual Targeting of FLT3 and LSD1 Disrupts the MYC Super-Enhancer Complex in Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/2022.01.17.476469v1?rss=1 Yashar, W. M. Smith, B. M. Coleman, D. J. VanCampen, J. Kong, G. Macaraeg, J. Estabrook, J. Demir, E. Long, N. Bottomly, D. McWeeney, S. K. Tyner, J. W. Druker, B. J. Maxson, J. E. Braun, T. P. 2022-01-18 doi:10.1101/2022.01.17.476469 Cold Spring Harbor Laboratory Press 2022-01-18 <![CDATA[ A potent alpaca-derived nanobody that neutralizes SARS-CoV-2 variants ]]> https://biorxiv.org/content/10.1101/2022.01.18.476801v1?rss=1 Weinstein, J. B. Bates, T. A. Leier, H. C. McBride, S. K. Barklis, E. Tafesse, F. G. 2022-01-20 doi:10.1101/2022.01.18.476801 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Identification of differential hypothalamic DNA methylation and gene expression associated with sexual partner preferences in rams ]]> https://biorxiv.org/content/10.1101/2022.01.18.476818v1?rss=1 Bhattacharya, S. Amodei, R. Vilain, E. Roselli, C. E. 2022-01-18 doi:10.1101/2022.01.18.476818 Cold Spring Harbor Laboratory Press 2022-01-18 <![CDATA[ A human DNA methylation atlas reveals principles of cell type-specific methylation and identifies thousands of cell type-specific regulatory elements ]]> https://biorxiv.org/content/10.1101/2022.01.24.477547v1?rss=1 99.5% identical, demonstrating robustness of cell identity programs to genetic variation and environmental perturbation. Unsupervised clustering of the atlas recapitulates key elements of tissue ontogeny, and identifies methylation patterns retained since gastrulation. Loci uniquely unmethylated in an individual cell type often reside in transcriptional enhancers and contain DNA binding sites for tissue-specific transcriptional regulators. Uniquely hyper-methylated loci are rare and are enriched for CpG islands, polycomb targets, and CTCF binding sites, suggesting a novel role in shaping cell type-specific chromatin looping. The atlas provides an essential resource for interpretation of disease-associated genetic variants, and a wealth of potential tissue-specific biomarkers for use in liquid biopsies. Summary paragraphDNA methylation, a fundamental epigenetic mark, governs chromatin organization and gene expression1, thus defining the molecular identity of cells and providing a window into developmental processes with wide-ranging physiologic and clinical ramifications. Current DNA methylation datasets have limitations, typically including only a fraction of methylation sites, many from cell lines that underwent massive changes in culture or from tissues containing unspecified mixtures of cells2-6. We present a human methylome atlas based on deep whole-genome bisulfite sequencing of 39 sorted, primary cell types and use this dataset to address fundamental questions in developmental biology, physiology and pathology. Biological replicates are >99.5% identical, demonstrating unappreciated robustness to genetic variation and environmental perturbations. Clustering recapitulates key elements of tissue ontogeny, identifying methylation patterns retained since gastrulation. Loci uniquely unmethylated in individual cell types identify novel transcriptional enhancers and are enriched for tissue-specific transcription factors binding motifs. In contrast, loci uniquely hyper-methylated in specific cell types are rare, enriched for CpG islands and polycomb targets, and overlap CTCF binding sites, suggesting a novel role in shaping cell-type-specific chromatin looping. Finally, the atlas facilitates fragment-level deconvolution of tissue and plasma methylomes across thousands of cell-type specific regions to quantify their individual components at unprecedented resolution. The human cell-type-specific methylation atlas provides an essential resource for studying gene regulation by defining cell-type-specific distal enhancers and regulators of 3D organization, for identifying pathological changes in DNA methylation, and for the interpretation of methylation-based liquid biopsies. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY O_LIA deep methylation atlas of 39 human cell types, sorted from healthy samples C_LIO_LIMethylomes record developmental history of cells C_LIO_LIThousands of novel cell type-specific methylation markers C_LIO_LIHypo-methylation uncovers cell type-specific regulatory map of distal enhancers C_LIO_LIHyper-methylation across CTCF sites C_LIO_LICell type-specific biomarkers facilitate fragment-level deconvolution of tissues and cfDNA C_LI ]]> Loyfer, N. Magenheim, J. Peretz, A. Cann, G. Bredno, J. Klochendler, A. Fox-Fisher, I. Shabi-Porat, S. Hecht, M. Pelet, T. Moss, J. Drawshy, Z. Amini, H. Moradi, P. Nagaraju, S. Bauman, D. Shveiky, D. Porat, S. Rivkin, G. Or, O. Hirshoren, N. Carmon, E. Pikarsky, A. Khalaileh, A. Zamir, G. Grinboim, R. Abu Gazala, M. Mizrahi, I. Shussman, N. Korach, A. Wald, O. Izhar, U. Erez, E. Yutkin, V. Samet, Y. Rotnemer Golinkin, D. Spalding, K. L. Druid, H. Arner, P. Shapiro, A. M. J. Grompe, M. Aravanis, A. Venn, O. Jamshidi, A. Shemer, R. Dor, Y. Glaser, B 2022-01-25 doi:10.1101/2022.01.24.477547 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Resveratrol increases tear production and spontaneous ocular pain after corneal abrasion in male, but not female, rats using a preclinical model of photorefractive keratectomy (PRK) ]]> https://biorxiv.org/content/10.1101/2022.01.25.477730v1?rss=1 Hegarty, D. M. Carroll, J. R. Nguyen, D. Halls, V. S. Robbins, D. I. Price, T. J. Dussor, G. Aicher, S. A. 2022-01-28 doi:10.1101/2022.01.25.477730 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Grandmaternal allergen exposure causes distinct epigenetic trajectories in offspring associated with airway hyperreactivity and inflammation. ]]> https://biorxiv.org/content/10.1101/2022.01.25.477760v1?rss=1 Lebold, K. M. Cook, M. Pincus, A. B. Nevonen, K. A. Davis, B. A. Carbone, L. Calco, G. N. Fryer, A. D. Jacoby, D. B. Drake, M. G. 2022-01-27 doi:10.1101/2022.01.25.477760 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ Abnormal CCK/CB1R axon targeting in mouse models of dystroglycanopathy ]]> https://biorxiv.org/content/10.1101/2022.01.26.477791v1?rss=1 Miller, D. S. Jahncke, J. N. Schnell, E. Wright, K. M. 2022-01-26 doi:10.1101/2022.01.26.477791 Cold Spring Harbor Laboratory Press 2022-01-26 <![CDATA[ Development of the First Tractable Genetic System for Parvimonas micra, a Ubiquitous Pathobiont in Human Dysbiotic Disease ]]> https://biorxiv.org/content/10.1101/2022.01.27.477930v1?rss=1 Higashi, D. L. McGuire, S. Abdelrahman, Y. Zou, Z. Qin, H. Anderson, D. Palmer, E. A. Kreth, J. Merritt, J. 2022-01-28 doi:10.1101/2022.01.27.477930 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Shared and distinct functional effects of patient-specific Tbr1 mutations on cortical development ]]> https://biorxiv.org/content/10.1101/2022.01.27.478064v1?rss=1 Co, M. Barnard, R. A. Jahncke, J. N. Grindstaff, S. Fedorov, L. M. Adey, A. C. Wright, K. M. O'Roak, B. J. 2022-01-28 doi:10.1101/2022.01.27.478064 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ A novel rhesus macaque model of Huntington's disease recapitulates key neuropathological changes along with progressive motor and cognitive decline ]]> https://biorxiv.org/content/10.1101/2022.02.02.478920v1?rss=1 Weiss, A. R. Liguore, W. A. Brandon, K. Wang, X. Liu, Z. Domire, J. S. Button, D. Kroenke, C. D. McBride, J. L. 2022-02-04 doi:10.1101/2022.02.02.478920 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ CD8 T Cell Memory Inflation is Driven by Latent CMV Infection of Lymphatic Endothelial Cells ]]> https://biorxiv.org/content/10.1101/2022.02.10.479848v1?rss=1 Hill, A. B. Munks, M. Rott, K. Nesterenko, P. Smart, S. Smith, T. Xu, G. Williams, V. Murray, S. Tatum, A. 2022-02-10 doi:10.1101/2022.02.10.479848 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ A global lipid map reveals host dependency factors conserved across SARS-CoV-2 variants ]]> https://biorxiv.org/content/10.1101/2022.02.14.480430v1?rss=1 Farley, S. E. Kyle, J. Leier, H. Bramer, L. M. Weinstein, J. Bates, T. A. Lee, J.-Y. Metz, T. O. Schultz, C. Tafesse, F. 2022-02-15 doi:10.1101/2022.02.14.480430 Cold Spring Harbor Laboratory Press 2022-02-15 <![CDATA[ Contribution of individual excitatory synapses on dendritic spines to electrical signaling ]]> https://biorxiv.org/content/10.1101/2022.02.15.480607v1?rss=1 Weng, J.-Y. Ceballos, C. Zecevic, D. 2022-02-17 doi:10.1101/2022.02.15.480607 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ Oligodendrocytes form paranodal bridges that generate chains of myelin sheaths vulnerable to degeneration with age ]]> https://biorxiv.org/content/10.1101/2022.02.16.480718v1?rss=1 Call, C. L. Neely, S. A. Early, J. J. James, O. G. Zoupi, L. Williams, A. C. Chandran, S. Lyons, D. A. Bergles, D. E. 2022-02-17 doi:10.1101/2022.02.16.480718 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ Temporal continuity shapes visual responses of macaque face patch neurons ]]> https://biorxiv.org/content/10.1101/2022.02.22.481478v1?rss=1 Russ, B. E. Koyano, K. W. Day-Cooney, J. Perwez, N. Leopold, D. A. 2022-02-24 doi:10.1101/2022.02.22.481478 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ NEDD8 activity is important for direct antigen MHC class I antigen presentation ]]> https://biorxiv.org/content/10.1101/2022.02.25.482016v1?rss=1 Vijayasimha, K. Leestemaker-Palmer, A. L. Gibbs, J. S. Yewdell, J. W. Dolan, B. P. 2022-02-27 doi:10.1101/2022.02.25.482016 Cold Spring Harbor Laboratory Press 2022-02-27 <![CDATA[ Chronic obstructive pulmonary disease and cigarette smoke exposure lead to dysregulated MAIT cell activation by bronchial epithelial cells ]]> https://biorxiv.org/content/10.1101/2022.02.28.482383v1?rss=1 Huber, M. E. Larson, E. Lust, T. N. Heisler, C. M. Harriff, M. J. 2022-03-02 doi:10.1101/2022.02.28.482383 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Taxonomic and functional shifts in the perinatal gut microbiome of rhesus macaques ]]> https://biorxiv.org/content/10.1101/2022.03.02.482686v1?rss=1 Rhoades, N. S. Cinco, I. R. Hendrickson, S. M. Slifka, M. K. Messaoudi, I. 2022-03-03 doi:10.1101/2022.03.02.482686 Cold Spring Harbor Laboratory Press 2022-03-03 <![CDATA[ Ligand-mediated structural dynamics of a mammalian pancreatic KATP channel ]]> https://biorxiv.org/content/10.1101/2022.03.02.482692v1?rss=1 Sung, M. W. Driggers, C. M. Mostofian, B. Russo, J. D. Patton, B. L. Zuckerman, D. M. Shyng, S.-L. 2022-03-02 doi:10.1101/2022.03.02.482692 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Kv7 channel antagonists block glycine receptors ]]> https://biorxiv.org/content/10.1101/2022.03.02.482705v1?rss=1 Lu, H.-W. Romero, G. E. Apostolides, P. F. Huang, H. Trussell, L. O. 2022-03-02 doi:10.1101/2022.03.02.482705 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Rapid in vivo multiplexed editing (RIME) of the adult mouse liver ]]> https://biorxiv.org/content/10.1101/2022.03.04.483011v1?rss=1 95% of target cells. To highlight its utility, we used this system to inactivate, alone or in combination, genes with functions spanning metabolism, mitosis, mitochondrial maintenance, and cell proliferation. ConclusionRIME enables the rapid, efficient, and inexpensive analysis of multiple genes in the mouse liver in vivo. ]]> Katsuda, T. Cure, H. Simeonov, K. P. Arany, Z. Grompe, M. Stanger, B. 2022-03-05 doi:10.1101/2022.03.04.483011 Cold Spring Harbor Laboratory Press 2022-03-05 <![CDATA[ In silico screening and testing of FDA approved small molecules to block SARS-CoV-2 entry to the host cell by inhibiting Spike protein cleavage ]]> https://biorxiv.org/content/10.1101/2022.03.07.483324v1?rss=1 Ozdemir, E. S. Le, H. H. Yildirim, A. Ranganathan, S. V. 2022-03-07 doi:10.1101/2022.03.07.483324 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Chondroitin Sulfate Proteoglycan 4,6 sulfation regulates sympathetic nerve regeneration after myocardial infarction ]]> https://biorxiv.org/content/10.1101/2022.03.10.483746v1?rss=1 Blake, M. R. Parrish, D. C. Staffenson, M. A. Sueda, S. Woodward, W. R. Beth Habecker, B. A. 2022-03-13 doi:10.1101/2022.03.10.483746 Cold Spring Harbor Laboratory Press 2022-03-13 <![CDATA[ Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads ]]> https://biorxiv.org/content/10.1101/2022.03.11.484016v1?rss=1 David, J. K. Maden, S. K. Wood, M. A. Thompson, R. F. Nellore, A. 2022-03-12 doi:10.1101/2022.03.11.484016 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ Synapses in oligodendrocyte precursor cells are dynamic and contribute to Ca2+ activity ]]> https://biorxiv.org/content/10.1101/2022.03.18.484955v1?rss=1 Li, J. Miramontes, T. Czopka, T. Monk, K. R. 2022-03-19 doi:10.1101/2022.03.18.484955 Cold Spring Harbor Laboratory Press 2022-03-19 <![CDATA[ Three-dimensional structure of the single domain cupredoxin AcoP ]]> https://biorxiv.org/content/10.1101/2022.03.21.484586v1?rss=1 Roger, M. Leone, P. Blackburn, N. Horrel, S. Chicano, T. M. Giudici-Orticoni, M.-T. Abriata, L. A. Hura, G. L. Hough, M. A. Sciara, G. Ilbert, M. 2022-03-21 doi:10.1101/2022.03.21.484586 Cold Spring Harbor Laboratory Press 2022-03-21 <![CDATA[ Fetal loss in pregnant rhesus macaques infected with high-dose African-lineage Zika virus ]]> https://biorxiv.org/content/10.1101/2022.03.21.485088v1?rss=1 Raasch, L. Yamamoto, K. Newman, C. M. Rosinski, J. R. Shepherd, P. M. Razo, E. Crooks, C. M. Bliss, M. I. Breitbach, M. E. Sneed, E. L. Weiler, A. M. Zeng, X. Noguchi, K. K. Morgan, T. K. Fuhler, N. A. Bohm, E. K. Alberts, A. J. Havlicek, S. J. Kabakov, S. Mitzey, A. M. Antony, K. M. Ausderau, K. K. Mejia, A. Basu, P. Simmons, H. A. Eickhoff, J. C. Aliota, M. T. Mohr, E. L. Friedrich, T. C. Golos, T. G. O'Connor, D. H. Dudley, D. M. 2022-03-22 doi:10.1101/2022.03.21.485088 Cold Spring Harbor Laboratory Press 2022-03-22 <![CDATA[ PRMT5 as a Novel Druggable Vulnerability for EWSR1-ATF1-driven Clear Cell Sarcoma ]]> https://biorxiv.org/content/10.1101/2022.03.23.485409v1?rss=1 Li, B. X. Xiao, X. David, L. L. Davis, L. E. 2022-03-23 doi:10.1101/2022.03.23.485409 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Classification of Movement-Related Oscillations in sEEG Recordings with Machine Learning ]]> https://biorxiv.org/content/10.1101/2022.03.28.486094v1?rss=1 Rockhill, A. P. Mantovani, A. Stedelin, B. Raslan, A. M. Swann, N. C. 2022-03-29 doi:10.1101/2022.03.28.486094 Cold Spring Harbor Laboratory Press 2022-03-29 <![CDATA[ Profiling the diversity of agonist-selective effects on the proximal proteome environment of G protein-coupled receptors ]]> https://biorxiv.org/content/10.1101/2022.03.28.486115v1?rss=1 Polacco, B. J. Lobingier, B. T. Blythe, E. E. Abreu, N. Xu, J. Li, Q. Naing, Z. Z. C. Shoichet, B. K. Levitz, J. Krogan, N. J. Von Zastrow, M. Huttenhain, R. 2022-03-29 doi:10.1101/2022.03.28.486115 Cold Spring Harbor Laboratory Press 2022-03-29 <![CDATA[ A Distinct Chromatin State Drives Therapeutic Resistance in Invasive Lobular Breast Cancer ]]> https://biorxiv.org/content/10.1101/2022.03.29.486217v1?rss=1 Nardone, A. Qui, X. Feiglin, A. Fu, X. Spisak, S. Feit, A. Cohen Feit, G. Xie, Y. Font-Tello, A. Guarducci, C. Hermida Prado, F. Syamala, S. Lim, K. Pun, M. Cornwell, M. Liu, W. Ors, A. Mohammed, H. Brock, J. E. Freedman, M. L. Schiff, R. Winer, E. Long, H. W. Metzger Filho, O. Jeselsohn, R. 2022-03-30 doi:10.1101/2022.03.29.486217 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ Learning of probabilistic punishment as a model of anxiety produces changes in action but not punishment encoding in the dmPFC and VTA ]]> https://biorxiv.org/content/10.1101/2022.03.29.486234v1?rss=1 Jacobs, D. S. Allen, M. C. Park, J. Moghaddam, B. 2022-03-29 doi:10.1101/2022.03.29.486234 Cold Spring Harbor Laboratory Press 2022-03-29 <![CDATA[ An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences ]]> https://biorxiv.org/content/10.1101/2022.03.30.486449v1?rss=1 Gurun, B. Horton, W. Murugan, D. Zhu, B. Leyshock, P. Kumar, S. Byrne, K. T. Vonderheide, R. H. Margolin, A. A. Mori, M. Spellman, P. T. Coussens, L. M. Speed, T. P. 2022-04-01 doi:10.1101/2022.03.30.486449 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Appia: a web interface for chromatography ]]> https://biorxiv.org/content/10.1101/2022.04.01.486784v1?rss=1 Posert, R. Hartfield, K. Baconguis, I. 2022-04-02 doi:10.1101/2022.04.01.486784 Cold Spring Harbor Laboratory Press 2022-04-02 <![CDATA[ Vascular inflammation exposes perivascular cells to SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2022.04.05.487240v1?rss=1 Franca, C. M. Mansoorifar, A. Athirasala, A. Subbiah, R. Tahayeri, A. Bertassoni, L. E. 2022-04-06 doi:10.1101/2022.04.05.487240 Cold Spring Harbor Laboratory Press 2022-04-06 <![CDATA[ A subtype of melanopsin ganglion cells encodes ground luminance ]]> https://biorxiv.org/content/10.1101/2022.04.06.485949v1?rss=1 Berry, M. H. Moldavan, M. Garrett, T. Meadows, M. Cravetchi, O. White, E. von Gersdorff, H. Wright, K. M. Allen, C. Sivyer, B. M. 2022-04-10 doi:10.1101/2022.04.06.485949 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Reduced affinity of calcium sensing-receptor heterodimers and reduced mutant homodimer trafficking combine to impair function in a mouse model of Familial Hypocalciuric Hypercalcemia Type 1 ]]> https://biorxiv.org/content/10.1101/2022.04.11.487493v1?rss=1 Wang, X. Lundblad, J. Smith, S. M. 2022-04-11 doi:10.1101/2022.04.11.487493 Cold Spring Harbor Laboratory Press 2022-04-11 <![CDATA[ Effect of Positive Allosteric Modulation and Orthosteric Agonism of Dopamine D2 Receptors on Respiration in Mouse Models of Rett Syndrome ]]> https://biorxiv.org/content/10.1101/2022.04.13.488220v1?rss=1 Maletz, S. N. Reid, B. T. Baekey, D. M. Whitaker-Fornek, J. R. Bateman, J. T. Bissonnette, J. M. Levitt, E. S. 2022-04-14 doi:10.1101/2022.04.13.488220 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ SATINN: An automated neural network-based classification of testicular sections allows for high-throughput histopathology of mouse mutants ]]> https://biorxiv.org/content/10.1101/2022.04.16.488549v1?rss=1 Yang, R. Stendahl, A. Vigh-Conrad, K. Held, M. Lima, A. Conrad, D. 2022-04-16 doi:10.1101/2022.04.16.488549 Cold Spring Harbor Laboratory Press 2022-04-16 <![CDATA[ Dissection of a sensorimotor circuit that regulates aversion to odors and pathogenic bacteria in C. elegans by whole-brain simulation ]]> https://biorxiv.org/content/10.1101/2022.04.21.489073v1?rss=1 Filipowicz, A. Lalsiamthara, J. Aballay, A. 2022-04-22 doi:10.1101/2022.04.21.489073 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Epigenetic Control of Hundreds of Chromosome-Associated lncRNA Genes Essential for Replication and Stability ]]> https://biorxiv.org/content/10.1101/2022.04.25.489405v1?rss=1 Heskett, M. B. Vouzas, A. E. Smith, L. G. Yates, P. A. Boniface, C. Bouhassira, E. E. Spellman, P. T. Gilbert, D. M. Thayer, M. J. 2022-04-25 doi:10.1101/2022.04.25.489405 Cold Spring Harbor Laboratory Press 2022-04-25 <![CDATA[ Chemotherapy Signatures Map Evolution of Therapy-Related Myeloid Neoplasms ]]> https://biorxiv.org/content/10.1101/2022.04.26.489507v1?rss=1 Diamond, B. T. Ziccheddu, B. Maclachlan, K. H. Taylor, J. Boyle, E. Arrango Ossa, J. Jahn, J. T. Affer, M. Totiger, T. M. Coffey, D. G. Watts, J. Lu, S. X. Bolli, N. Bolton, K. Park, J. H. Landau, H. Ganesh, K. McPherson, A. Sekeres, M. Lesokhin, A. Chung, D. Zhang, Y. Ho, C. Roshal, M. Tyner, J. Nimer, S. Papaemmanuil, E. Usmani, S. Morgan, G. Landgren, O. Maura, F. 2022-04-27 doi:10.1101/2022.04.26.489507 Cold Spring Harbor Laboratory Press 2022-04-27 <![CDATA[ Cancer stem cell-derived extracellular vesicles preferentially target MHCII- macrophages and PD1+ T cells in the tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2022.04.26.489579v1?rss=1 Gonzalez-Callejo, P. Guo, Z. Ziglari, T. Claudio, N. M. Oshimori, N. Seras-Franzoso, J. Pucci, F. 2022-04-26 doi:10.1101/2022.04.26.489579 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ Systematic Replication Enables Normalization of High-throughput Imaging Assays ]]> https://biorxiv.org/content/10.1101/2022.04.26.489617v1?rss=1 Hunt, G. J. Dane, M. A. Korkola, J. E. Heiser, L. M. Gagnon-Bartsch, J. A. 2022-04-28 doi:10.1101/2022.04.26.489617 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Human Lung-resident Mucosal-Associated Invariant T cells are Abundant, Express Antimicrobial Proteins, and are Cytokine Responsive ]]> https://biorxiv.org/content/10.1101/2022.04.28.489781v1?rss=1 Meermeier, E. Zheng, C. Soma, S. Worley, A. Weiss, D. Modlin, R. Swarbrick, G. Karamooz, E. Khuzwayo, S. Wong, E. Gold, M. Lewinsohn, D. 2022-05-02 doi:10.1101/2022.04.28.489781 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Increased glucose availability sensitizes pancreatic cancer to chemotherapy ]]> https://biorxiv.org/content/10.1101/2022.04.29.490090v1?rss=1 Vaziri-Gohar, A. Hue, J. J. Graor, H. J. Abbas, A. Zarei, M. Hajihassani, O. Titomihelakis, G. Feczko, J. Rathore, M. Wang, R. Zarei, M. Goudarzi, M. Zhang, R. Willard, B. Zhang, L. Wang, G.-M. Tatsuoka, C. Salvino, J. M. Bederman, I. Brunengraber, H. Lyssiotis, C. A. Brody, J. R. Winter, J. M. 2022-05-01 doi:10.1101/2022.04.29.490090 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ An in situ quantitative map of initial human colorectal HIV transmission ]]> https://biorxiv.org/content/10.1101/2022.04.30.490175v1?rss=1 View larger version (67K): org.highwire.dtl.DTLVardef@ef8000org.highwire.dtl.DTLVardef@1bc8ed7org.highwire.dtl.DTLVardef@45ddbdorg.highwire.dtl.DTLVardef@e0a57c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Baharlou, H. Canete, N. P. Vine, E. E. hu, k. Yuan, D. Sandgren, K. J. Bertram, K. M. Nasr, `Najla Rhodes, J. W. Gosselink, M. Di Re, A. Reza, F. Ctercteko, G. Pathma-Nathan, N. ` Collins, G. Toh, J. Patrick, E. Haniffa, M. A. Estes, J. D. Byrne, S. N. Cunningham, T. L. Harman, A. N. 2022-05-01 doi:10.1101/2022.04.30.490175 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Aminomethanesulfonic acid illuminates the boundary between full and partial agonists of the pentameric glycine receptor ]]> https://biorxiv.org/content/10.1101/2022.05.03.490487v1?rss=1 Sivilotti, L. Ivica, J. Zhu, H. Lape, R. Gouaux, E. 2022-05-04 doi:10.1101/2022.05.03.490487 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Ongoing Replication Stress Response and New Clonal T Cell Development Discriminate Between Liver and Lung Recurrence Sites and Patient Outcomes in Pancreatic Ductal Adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2022.05.04.490552v1?rss=1 Link, J. M. Pelz, C. Worth, P. J. Owen, S. Keith, D. Langer, E. M. Grossblatt-Wait, A. Creason, A. L. Egger, J. Holly, H. English, I. MacPherson, K. Tsuda, M. Goecks, J. Demir, E. Kardosh, A. Lopez, C. D. Sheppard, B. C. Guimaraes, A. Brinkerhoff, B. Morgan, T. K. C. Mills, G. B. Brody, J. Sears, R. C. 2022-05-06 doi:10.1101/2022.05.04.490552 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Structure of C. elegans TMC-1 complex illuminates auditory mechanosensory transduction ]]> https://biorxiv.org/content/10.1101/2022.05.06.490478v1?rss=1 Jeong, H. Clark, S. Goehring, A. Dehghani-Ghahnaviyeh, S. Rasouli, A. Tajkhorshid, E. Gouaux, E. 2022-05-06 doi:10.1101/2022.05.06.490478 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Evolution avoids a pathological stabilizing interaction in the immune protein S100A9 ]]> https://biorxiv.org/content/10.1101/2022.05.09.490804v1?rss=1 Harman, J. L. Reardon, P. N. Costello, S. M. Warren, G. D. Phillips, S. R. Connor, P. J. Marqusee, S. Harms, M. J. 2022-05-09 doi:10.1101/2022.05.09.490804 Cold Spring Harbor Laboratory Press 2022-05-09 <![CDATA[ Deaza-modification of MR1 ligands modulates recognition by MR1-restricted T cells ]]> https://biorxiv.org/content/10.1101/2022.05.11.491531v1?rss=1 Jin, H. Ladd, N. A. Peev, A. M. Swarbrick, G. M. Cansler, M. Null, M. Boughter, C. T. McMurtrey, C. Nilsen, A. Dobos, K. M. Hildebrand, W. H. Lewinsohn, D. A. Adams, E. J. Lewinsohn, D. M. Harriff, M. 2022-05-11 doi:10.1101/2022.05.11.491531 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Mechanism of Lys6 poly-ubiquitin specificity by the L. pneumophila deubiquitinase LotA ]]> https://biorxiv.org/content/10.1101/2022.05.11.491541v1?rss=1 Warren, G. D. Kitao, T. Franklin, T. G. Nguyen, J. V. Geurink, P. P. Kubori, T. Nagai, H. Pruneda, J. N. 2022-05-11 doi:10.1101/2022.05.11.491541 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ CITE-Viz: Replicating the Interactive Flow Cytometry Workflow in CITE-Seq ]]> https://biorxiv.org/content/10.1101/2022.05.15.491411v1?rss=1 Kong, G. L. Nguyen, T. T. Rosales, W. K. Panikar, A. D. Cheney, J. H. W. Curtiss, B. M. Carratt, S. A. Braun, T. P. Maxson, J. E. 2022-05-16 doi:10.1101/2022.05.15.491411 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ Therapeutic neutralizing monoclonal antibody administration protects against lethal viscerotropic Yellow Fever infection ]]> https://biorxiv.org/content/10.1101/2022.05.16.491863v1?rss=1 Ricciardi, M. J. Rust, L. N. Pedreno-Lopez, N. Yusova, S. Biswas, S. Webb, G. M. Fischer, M. Gonsales-Nieto, L. Voigt, T. B. Louw, J. J. Laurino, F. D. DiBello, J. R. Raue, H.-P. Raphael, L. M. S. Yrizarry-Medina, A. Rosen, B. C. Agnor, R. Gao, L. Labriola, C. Axthelm, M. Smedley, J. Julander, J. G. Bonaldo, M. C. Walker, L. M. Slifka, M. K. Messaoudi, I. Burton, D. R. Kallas, E. G. Sacha, J. B. Watkins, D. I. Burwitz, B. J. 2022-05-18 doi:10.1101/2022.05.16.491863 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Infection of the maternal-fetal interface and vertical transmission following low-dose inoculation of pregnant rhesus macaques (Macaca mulatta) with an African-lineage Zika virus ]]> https://biorxiv.org/content/10.1101/2022.05.16.492053v1?rss=1 Koenig, M. R. Mitzey, A. M. Morgan, T. K. Zeng, X. Simmons, H. A. Mejia, A. Leyva Jaimes, F. Keding, L. T. Crooks, C. M. Weiler, A. M. Bohm, E. K. Aliota, M. T. Friedrich, T. C. Mohr, E. L. Golos, T. G. 2022-05-16 doi:10.1101/2022.05.16.492053 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ Timed Notch Inhibition drives Photoreceptor fate specification in Human Retinal Organoids ]]> https://biorxiv.org/content/10.1101/2022.05.19.492679v1?rss=1 Chew, S. Martinez, C. Chirco, K. Kandoi, S. Lamba, D. A. 2022-05-20 doi:10.1101/2022.05.19.492679 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ recountmethylation enables flexible analysis ofpublic blood DNA methylation array data ]]> https://biorxiv.org/content/10.1101/2022.05.19.492680v1?rss=1 Maden, S. K. Walsh, B. Ellrott, K. Hansen, K. D. Thompson, R. Nellore, A. 2022-05-20 doi:10.1101/2022.05.19.492680 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Single-Cell RNA Sequencing Reveals the Effects of Chemotherapy on Human Pancreatic Adenocarcinoma and its Tumor Microenvironment ]]> https://biorxiv.org/content/10.1101/2022.05.24.493132v1?rss=1 Werba, G. Weissinger, D. Kawaler, E. A. Zhao, E. Kalfakakou, D. Dhara, S. Oh, G. Jing, X. Beri, N. Khanna, L. Gonda, T. Oberstein, P. Hajdu, C. Loomis, C. A. Heguy, A. Sherman, M. H. Lund, A. W. Welling, T. H. Dolgalev, I. Tsirigos, A. Simeone, D. M. 2022-05-25 doi:10.1101/2022.05.24.493132 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Hemin shows antiviral activity in vitro, possibly through suppression of viral entry mediators. ]]> https://biorxiv.org/content/10.1101/2022.05.24.493187v1?rss=1 UNAL, M. A. BITIRIM, C. V. SOMERS, J. SUMMAK, G. Y. BUL BESBINAR, O. KOCAKAYA, E. GURCAN, C. NAZIR, H. Aksoy Ozer, Z. B. OZKAN, S. A. BEREKETOGLU, S. OZKUL, A. DEMIR, E. AKCALI, K. C. YILMAZER, A. 2022-05-25 doi:10.1101/2022.05.24.493187 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Leucine-Rich Repeat Kinase 2 limits dopamine D1 receptor signaling in the striatum and biases against heavy persistent alcohol drinking ]]> https://biorxiv.org/content/10.1101/2022.05.26.493614v1?rss=1 da Silva e Silva, D. Matsui, A. Murray, E. M. Mamais, A. Shaw, M. Ron, D. Cookson, M. R. Alvarez, V. A. 2022-05-29 doi:10.1101/2022.05.26.493614 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ T cell Egress via Lymphatic Vessels Limits the Intratumoral T cell Repertoire in Melanoma ]]> https://biorxiv.org/content/10.1101/2022.05.30.494080v1?rss=1 Steele, M. M. Dryg, I. D. Murugan, D. Femel, J. du Bois, H. Hill, C. Leachman, S. A. Chang, Y. H. Coussens, L. M. Lund, A. W. 2022-05-30 doi:10.1101/2022.05.30.494080 Cold Spring Harbor Laboratory Press 2022-05-30 <![CDATA[ Recording large-scale, cellular-resolution neuronal activity from freely-moving mice ]]> https://biorxiv.org/content/10.1101/2022.06.01.494442v1?rss=1 Das, A. Holden, S. Borovicka, J. Icardi, J. Patel, D. Patel, R. Raber, J. Dana, H. 2022-06-03 doi:10.1101/2022.06.01.494442 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Community assessment of methods to deconvolve cellular composition from bulk gene expression ]]> https://biorxiv.org/content/10.1101/2022.06.03.494221v1?rss=1 White, B. S. de Reynies, A. Newman, A. M. Waterfall, J. J. Lamb, A. Petitprez, F. Yu, T. Guo, X. Valdeolivas, A. Lin, Y. Li, H. Xiao, X. Wang, S. Zheng, F. Yang, W. Yu, R. Guerrero-Gimenez, M. E. Catania, C. A. Lang, B. J. Domanskyi, S. Bertus, T. J. Piermarocchi, C. Monaco, G. Caruso, F. P. Ceccarelli, M. Coller, J. Maecker, H. Duault, C. Sokoohi, V. Patel, S. Liliental, J. E. Simon, S. Tumor Deconvolution DREAM Challenge consortium, Saez-Rodriguez, J. Heiser, L. M. Guinney, J. Gentles, A. J. 2022-06-05 doi:10.1101/2022.06.03.494221 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ Gait Abnormalities and Aberrant D2 Receptor Expression and Signaling in a Mouse Model of the Human Pathogenic Mutation DRD2I212F ]]> https://biorxiv.org/content/10.1101/2022.06.09.495548v1?rss=1 Rodriguez-Contreras, D. Gong, S. Lebowitz, J. J. Fedorov, L. M. Asad, N. Dore, T. M. Ford, C. P. Williams, J. T. Neve, K. A. 2022-06-11 doi:10.1101/2022.06.09.495548 Cold Spring Harbor Laboratory Press 2022-06-11 <![CDATA[ Can Deep Learning Provide a Generalizable Model for Dynamic Sound Encoding in Auditory Cortex? ]]> https://biorxiv.org/content/10.1101/2022.06.10.495698v1?rss=1 Pennington, J. R. David, S. V. 2022-06-13 doi:10.1101/2022.06.10.495698 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ Crowd-sourced benchmarking of single-sample tumour subclonal reconstruction ]]> https://biorxiv.org/content/10.1101/2022.06.14.495937v1?rss=1 Salcedo, A. Tarabichi, M. Buchanan, A. Espiritu, S. M. G. Zhang, H. Zhu, K. Yang, T.-H. O. Leshchiner, I. Anastassiou, D. Guan, Y. Jang, G. H. Haase, K. Deshwar, A. G. Zou, W. Umar, I. Dentro, S. Wintersinger, J. A. Chiotti, K. Demeulemeester, J. Jolly, C. Scyza, L. Ko, M. PCAWG-11 Working Group, SMC-Het Participants, Wedge, D. C. Morris, Q. D. Ellrot, K. Van Loo, P. Boutros, P. C. 2022-06-15 doi:10.1101/2022.06.14.495937 Cold Spring Harbor Laboratory Press 2022-06-15 <![CDATA[ Daily administration of low-dose daunorubicin or doxorubicin inhibits hypoxia-inducible factor 1 and tumor vascularization ]]> https://biorxiv.org/content/10.1101/2022.06.15.492526v1?rss=1 Yang, Y. Chen, D. Z. Rey, S. Liu, J. O. Semenza, G. L. 2022-06-17 doi:10.1101/2022.06.15.492526 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Persistent inflammation promotes endocannabinoid release and presynaptic cannabinoid 1 receptor desensitization ]]> https://biorxiv.org/content/10.1101/2022.06.20.496891v1?rss=1 Bouchet, C. A. Janowsky, A. Ingram, S. L. 2022-06-22 doi:10.1101/2022.06.20.496891 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ Liver Endothelium Microenvironment Promotes HER3-mediated Cell Growth in Pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2022.06.24.497507v1?rss=1 Zhang, W. Wright, M. Rathore, M. Zarei, M. Vaziri-Gohar, A. Winter, J. Brody, J. Wang, R. 2022-06-28 doi:10.1101/2022.06.24.497507 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ Electrical Signaling in Cochlear Efferents is Driven by an Intrinsic Neuronal Oscillator ]]> https://biorxiv.org/content/10.1101/2022.06.27.497817v1?rss=1 Hong, H. Trussell, L. O. 2022-06-30 doi:10.1101/2022.06.27.497817 Cold Spring Harbor Laboratory Press 2022-06-30 <![CDATA[ Quantifying cooperative multisite binding through Bayesian inference ]]> https://biorxiv.org/content/10.1101/2022.06.29.498022v1?rss=1 Estelle, A. B. George, A. Barbar, E. Zuckerman, D. M. 2022-07-01 doi:10.1101/2022.06.29.498022 Cold Spring Harbor Laboratory Press 2022-07-01 <![CDATA[ Senescent cell-derived extracellular vesicles recruit antigen presenting cells and limit squamous carcinoma recurrence ]]> https://biorxiv.org/content/10.1101/2022.06.30.498366v1?rss=1 Ziglari, T. Claudio, N. M. Kyle, J. E. Nakayasu, E. S. Guo, Z. Pucci, F. 2022-07-02 doi:10.1101/2022.06.30.498366 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Epigenetic biomarkers of autoimmune risk and protective antioxidant signaling in methylmercury-exposed adults ]]> https://biorxiv.org/content/10.1101/2022.07.05.498896v1?rss=1 10 g/g) vs. N=16 individuals with low (<1 g/g) total hair mercury (a proxy for methylmercury exposure), matched on age and sex. ResultsWe identified nine differentially methylated CpG sites (FDR<0.05), including several with known links to MeHg toxicity. The most significantly different CpG site was in an intronic enhancer of the SLC5A7 gene, which encodes the L-type amino acid transporter 1 (LAT1) that facilitates MeHg transport into protein-rich tissue, including muscle and brain. Our Gene Ontology and transcription factor motif enrichment analyses identified differential methylation of genes involved in several outcomes with established links to MeHg, including immune response, neurotoxicity, and type 2 diabetes (T2D) risk. Last, we identified candidate epigenetic biomarkers of PUFA-mediated protection against MeHg toxicity. DiscussionHere, we show that a small EWAS on samples with high MeHg exposure variance can detect candidate differentially methylated CpGs and pathways of interest relevant to MeHg biology. Similar EWAS in global populations with known high exposure variance can be leveraged to develop targeted, custom sequencing panels and microarrays limited to replicated, validated biomarkers of a given exposure. ]]> Weinhouse, C. Perez, L. Ryde, I. Goodrich, J. M. Miranda, J. J. Hsu-Kim, H. Murphy, S. K. Meyer, J. N. Pan, W. K. 2022-07-06 doi:10.1101/2022.07.05.498896 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ Delivery of loaded MR1 Monomer Results in Efficient Ligand Exchange to Host MR1 and Subsequent MR1T cell activation ]]> https://biorxiv.org/content/10.1101/2022.07.11.499573v1?rss=1 Kulicke, C. A. Swarbrick, G. M. Ladd, N. A. Cansler, M. Null, M. Worley, A. Lemon, C. Ahmed, T. Bennett, J. Lewinsohn, D. A. Adams, E. J. Lewinsohn, D. M. Harriff, M. J. 2022-07-12 doi:10.1101/2022.07.11.499573 Cold Spring Harbor Laboratory Press 2022-07-12 <![CDATA[ REM sleep has minute-scale rhythms in mice and humans: A non-binary continuum between phasic and tonic microstates ]]> https://biorxiv.org/content/10.1101/2022.07.11.499612v1?rss=1 Bueno-Junior, L. S. Ruckstuhl, M. S. Lim, M. M. Watson, B. O. 2022-07-13 doi:10.1101/2022.07.11.499612 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ NudC regulated Lis1 stability is essential for maintenance of dynamic microtubule ends in the axon terminal ]]> https://biorxiv.org/content/10.1101/2022.07.12.499810v1?rss=1 Kawano, D. Pinter, K. Chlebowski, M. Petralia, R. S. Wang, Y.-X. Nechiporuk, A. Drerup, C. 2022-07-13 doi:10.1101/2022.07.12.499810 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Cas9+ conditionally immortalized neutrophil progenitors as a tool for genome wide CRISPR screening for neutrophil differentiation and function ]]> https://biorxiv.org/content/10.1101/2022.07.19.500665v1?rss=1 Jong, R. M. Ching, K. Garelis, N. E. Zilinskas, A. Nguyenla, X. Rawal, S. Hill, B. Luckie, B. Shallow, L. Cox, J. S. Barton, G. Stanley, S. 2022-07-20 doi:10.1101/2022.07.19.500665 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Gabapentin Disrupts Binding of Perlecan to the α2δ1 Voltage Sensitive Calcium Channel Subunit and Impairs Skeletal Mechanosensation ]]> https://biorxiv.org/content/10.1101/2022.07.20.500827v1?rss=1 Fernandez, P. C. R. Wright, C. S. Masterson, A. N. Yi, X. Tellman, T. V. Bonteanu, A. Rust, K. Noonan, M. L. White, K. E. Lewis, K. J. Sankar, U. Hum, J. M. Bix, G. Wu, D. Robling, A. G. Sardar, R. Farach-Carson, M. C. Thompson, W. R. 2022-07-21 doi:10.1101/2022.07.20.500827 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Multi-Omics Binary Integration via Lasso Ensembles (MOBILE) for identification of context-specific networks and new regulatory mechanisms ]]> https://biorxiv.org/content/10.1101/2022.07.24.501297v1?rss=1 View larger version (76K): org.highwire.dtl.DTLVardef@12fa3a5org.highwire.dtl.DTLVardef@a0b6a8org.highwire.dtl.DTLVardef@137efb7org.highwire.dtl.DTLVardef@15aec85_HPS_FORMAT_FIGEXP M_FIG C_FIG Multi-Omics Binary Integration via Lasso Ensembles (MOBILE) pipeline yields statistically robust, context-specific association networksThe MOBILE pipeline integrates omics datasets in a data-driven, biologically-structured manner. The pipeline outputs are gene-level, contextspecific association networks. These association networks nominate differentially enriched pathways, subnetworks, and new connections. Broadly applicable to find condition specific networks using multi-omics datasets. ]]> Erdem, C. Gross, S. M. Heiser, L. Birtwistle, M. R. 2022-07-24 doi:10.1101/2022.07.24.501297 Cold Spring Harbor Laboratory Press 2022-07-24 <![CDATA[ Trophoblast glycoprotein is required for efficient synaptic vesicle exocytosis from retinal rod bipolar cells. ]]> https://biorxiv.org/content/10.1101/2022.07.25.501380v1?rss=1 View larger version (18K): org.highwire.dtl.DTLVardef@13d5916org.highwire.dtl.DTLVardef@a3c259org.highwire.dtl.DTLVardef@12c74e0org.highwire.dtl.DTLVardef@1ad43a8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wakeham, C. M. Shi, Q. Ren, G. Haley, T. L. Duvoisin, R. von Gersdorff, H. Morgans, C. W. 2022-07-26 doi:10.1101/2022.07.25.501380 Cold Spring Harbor Laboratory Press 2022-07-26 <![CDATA[ JBrowse 2: A modular genome browser with views of synteny and structural variation ]]> https://biorxiv.org/content/10.1101/2022.07.28.501447v1?rss=1 Diesh, C. Stevens, G. J. Xie, P. Martinez, T. D. J. Hershberg, E. A. Leung, A. Guo, E. Dider, S. Zhang, J. Bridge, C. Hogue, G. Duncan, A. Morgan, M. Flores, T. Bimber, B. N. Haw, R. Cain, S. Buels, R. M. Stein, L. D. Holmes, I. 2022-07-31 doi:10.1101/2022.07.28.501447 Cold Spring Harbor Laboratory Press 2022-07-31 <![CDATA[ Optimal drug treatment for reducing long-term drug resistance ]]> https://biorxiv.org/content/10.1101/2022.07.29.502041v1?rss=1 Ghodsi Asnaashari, T. Chang, Y. H. 2022-08-02 doi:10.1101/2022.07.29.502041 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ De novo assembly and annotation of the singing mouse genome ]]> https://biorxiv.org/content/10.1101/2022.07.29.502048v1?rss=1 Smith, S. K. Frazel, P. W. Khodadadi-Jamayran, A. Zappile, P. Marier, C. Okhovat, M. Brown, S. M. Long, M. A. Heguy, A. Phelps, S. M. 2022-07-29 doi:10.1101/2022.07.29.502048 Cold Spring Harbor Laboratory Press 2022-07-29 <![CDATA[ A tumour-promoting senescent secretome triggered by platinum chemotherapy exploits a targetable TGFβR1/Akt-mTOR axis in lung cancer ]]> https://biorxiv.org/content/10.1101/2022.08.01.502019v1?rss=1 Gonzalez-Gualda, E. Macias, D. Morsli, S. Martin, E. Ou, H.-L. Denholm, M. Olan, I. Hoffmann, R. Dane, M. Veroutis, D. Medrano, G. Mulero, F. Martins, C. Barbacid, M. Gorgoulis, V. Korkola, J. Rassl, D. M. Doherty, G. J. Rintoul, R. C. Narita, M. Munoz-Espin, D. 2022-08-03 doi:10.1101/2022.08.01.502019 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Mutational screens highlight glycosylation as a modulator of CSF3R activity ]]> https://biorxiv.org/content/10.1101/2022.08.01.502088v1?rss=1 Hollander, M. J. Malaker, S. A. Perez, I. Maxson, J. E. Cochran, J. R. Bertozzi, C. R. 2022-08-01 doi:10.1101/2022.08.01.502088 Cold Spring Harbor Laboratory Press 2022-08-01 <![CDATA[ Persistent effects of acute trauma on Pavlovian-to-instrumental transfer ]]> https://biorxiv.org/content/10.1101/2022.08.05.502959v1?rss=1 Derman, R. C. Lattal, M. 2022-08-06 doi:10.1101/2022.08.05.502959 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ Multiplexed and millimeter-scale superresolution imaging of cells and tissue sections via prism-illumination and microfluidics-enhanced DNA-PAINT ]]> https://biorxiv.org/content/10.1101/2022.08.07.503091v1?rss=1 Rames, M. J. Kenison, J. Heineck, D. Civitci, F. Szczepaniak, M. Tao, K. Zheng, T. Shangguan, J. Esener, S. Nan, X. 2022-08-07 doi:10.1101/2022.08.07.503091 Cold Spring Harbor Laboratory Press 2022-08-07 <![CDATA[ Follicle-innervating Aδ-low threshold mechanoreceptors organize through a population-dependent mechanism ]]> https://biorxiv.org/content/10.1101/2022.08.09.503379v1?rss=1 Pomaville, M. B. Wright, K. M. 2022-08-10 doi:10.1101/2022.08.09.503379 Cold Spring Harbor Laboratory Press 2022-08-10 <![CDATA[ Anandamide reduces excitability by preferentially targeting somatic VGSCs via CB1 ]]> https://biorxiv.org/content/10.1101/2022.08.12.503665v1?rss=1 Steiger, L. J. Tsintsadze, T. Mattheisen, G. B. Smith, S. M. 2022-08-14 doi:10.1101/2022.08.12.503665 Cold Spring Harbor Laboratory Press 2022-08-14 <![CDATA[ Inactivated voltage-gated sodium channels are preferentially targeted in cinacalcet block of mouse neocortical action potentials ]]> https://biorxiv.org/content/10.1101/2022.08.15.504002v1?rss=1 slow-inactivated > resting. The state dependence of block contributes to the non-linearity of action potential block by cinacalcet. This dynamic and abundant signaling pathway by which G-proteins regulate VGSC currents provides an important voltage-dependent mechanism for modulating central neuronal excitability. Key points summaryVoltage-gated sodium channels are essential for the action potential generation and propagation that is central to physiological function in excitable cells. VGSC inhibitors are useful therapies to treat epilepsy, pain, and cardiac arrhythmias. Cinacalcet inhibits VGSC currents strongly and the underlying G-protein dependent signaling pathway occurs in the vast majority of neocortical and hippocampal neurons. Here we demonstrate that cinacalcet inhibits the VGSC current by activating a downstream blocking molecule that preferentially binds to the fast-inactivated state, that the blocking molecule stabilizes the inactivated states, and that cinacalcet impacts neuronal excitability in a non-linear manner. Characterization of the mechanism by which cinacalcet operates will facilitate the determination of its role in regulating neocortical excitability and the identification of new therapeutic targets for epilepsy, pain, and arrythmias. ]]> Lindner, J. S. Rajayer, S. R. Smith, S. M. 2022-08-15 doi:10.1101/2022.08.15.504002 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ The pharmacokinetics and pharmacodynamics of 4-methylumbelliferone and its glucuronide metabolite in mice ]]> https://biorxiv.org/content/10.1101/2022.08.18.504417v1?rss=1 Nagy, N. Kaber, G. Haddock, N. Hargil, A. Rajadas, J. Malhotra, S. Unger, M. Frymoyer, A. Bollyky, P. 2022-08-18 doi:10.1101/2022.08.18.504417 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ A Web-based Software Resource for Interactive Analysis of Multiplex Tissue Imaging Datasets ]]> https://biorxiv.org/content/10.1101/2022.08.18.504436v1?rss=1 Creason, A. L. Watson, C. Gu, Q. Persson, D. Sargent, L. L. Chen, Y.-A. Lin, J.-R. Sivagnanam, S. Wünnemann, F. Nirmal, A. J. Chin, K. Feiler, H. S. Coussens, L. M. Schapiro, D. Grüning, B. A. Sorger, P. K. Sokolov, A. Goecks, J. 2022-08-19 doi:10.1101/2022.08.18.504436 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ Cortical Betz cells analogue in songbirds utilizes Kv3.1 to generate ultranarrow spikes ]]> https://biorxiv.org/content/10.1101/2022.08.22.504741v1?rss=1 Zemel, B. Nevue, A. Tavares, L. E. S. Dadostin, A. Lovell, P. Jin, D. Z. Mello, C. von Gersdorff, H. 2022-08-22 doi:10.1101/2022.08.22.504741 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Computational Multiplex Panel Reduction to Maximize Information Retention in Breast Cancer Tissue Microarrays ]]> https://biorxiv.org/content/10.1101/2022.08.24.505142v1?rss=1 Ternes, L. Gray, J. W. Chang, Y. H. 2022-08-26 doi:10.1101/2022.08.24.505142 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Alcohol dependence modifies brain networks activated during abstinence and reaccess: a c-fos-based analysis in mice ]]> https://biorxiv.org/content/10.1101/2022.08.26.505400v1?rss=1 Roland, A. Coelho, C. Haun, H. Gianessi, C. Lopez, M. D'Ambrosio, S. Machinski, S. Kroenke, C. Frankland, P. Becker, H. Kash, T. 2022-08-26 doi:10.1101/2022.08.26.505400 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Alignment, Segmentation and Neighborhood Analysis in Cyclic Immunohistochemistry Data Using CASSATT ]]> https://biorxiv.org/content/10.1101/2022.08.29.504975v1?rss=1 Brockman, A. Khurana, R. Bartkowiak, T. Thomas, P. L. Sivagnanam, S. Betts, C. B. Coussens, L. M. Lovly, C. Irish, J. M. Ihrie, R. A. 2022-08-29 doi:10.1101/2022.08.29.504975 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Nuclear-enriched protein phosphatase 4 ensures outer kinetochore assemblyprior to nuclear dissolution ]]> https://biorxiv.org/content/10.1101/2022.09.01.505886v1?rss=1 Rocha, H. Simoes, P. A. Budrewicz, J. Lara-Gonzalez, P. Xavier de Carvalho, A. Dumont, J. Desai, A. Gassmann, R. 2022-09-02 doi:10.1101/2022.09.01.505886 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants ]]> https://biorxiv.org/content/10.1101/2022.09.03.506477v1?rss=1 Yang, D. Zhao, Z. Tajkhorshid, E. Gouaux, E. 2022-09-05 doi:10.1101/2022.09.03.506477 Cold Spring Harbor Laboratory Press 2022-09-05 <![CDATA[ Rad51-mediated interhomolog recombination during budding yeast meiosis is promoted by the meiotic recombination checkpoint and the conserved Pif1 helicase ]]> https://biorxiv.org/content/10.1101/2022.09.05.506590v1?rss=1 Ziesel, A. Weng, Q. Ahuja, J. S. Bhattacharya, A. Dutta, R. Cheng, E. Börner, G. V. Lichten, M. Hollingsworth, N. M. 2022-09-06 doi:10.1101/2022.09.05.506590 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ Low HER2 enables dedifferentiation and transformation of normal breast epithelial cells via chromatin opening ]]> https://biorxiv.org/content/10.1101/2022.09.06.506760v1?rss=1 Hayat, A. Carter, E. King, H. W. Ors, A. Doe, A. Teijeiro, S. A. Charrot, S. Godinho, S. Cutillas, P. R. Mohammed, H. Grose, R. P. Ficz, G. 2022-09-06 doi:10.1101/2022.09.06.506760 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ High Resolution Imaging of the Osteogenic and Angiogenic Interface at the Site of Cranial Bone Defect Repair via Multiphoton Microscopy ]]> https://biorxiv.org/content/10.1101/2022.09.11.507477v1?rss=1 Schilling, K. Zhai, Y. Zhou, Z. Zhou, B. Brown, E. Zhang, X. 2022-09-13 doi:10.1101/2022.09.11.507477 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Fanconi anemia-isogenic head and neck cancer cell line pairs - a basic and translational science resource ]]> https://biorxiv.org/content/10.1101/2022.09.11.507488v1?rss=1 Nguyen, H. T. Tang, W. Webster, A. L. H. Whiteaker, J. R. Chandler, C. M. Errazquin, R. Sullivan, L. B. Jonlin, E. Hoskins, E. E. Chen, E. Y. Fritzke, M. Paulovich, A. G. Wells, S. I. Roohollahi, K. Dorsman, J. Brakenhoff, R. Garcia-Escudero, R. Smogorzewska, A. Wakefield, L. Grompe, M. Monnat, R. J. 2022-09-13 doi:10.1101/2022.09.11.507488 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Capillary electrophoresis mass spectrometry identifies new isomers of inositol pyrophosphates in mammalian tissues ]]> https://biorxiv.org/content/10.1101/2022.09.14.507917v1?rss=1 Qiu, D. Gu, C. Liu, G. Ritter, K. Eisenbeis, V. B. Bittner, T. Gruzdev, A. Seidel, L. Bengsch, B. Shears, S. B. Jessen, H. 2022-09-14 doi:10.1101/2022.09.14.507917 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ The transcriptional and epigenetic reprogramming mediated by chronic IL1β exposure drives self-renewal ability and myeloid priming in TET2 deficient stem and progenitor cells. ]]> https://biorxiv.org/content/10.1101/2022.09.15.507688v1?rss=1 McClatchy, J. Strogantsev, R. Wolfe, E. Estabrook, J. Lin, H.-Y. Mohammadhosseini, M. Davis, B. Eden, C. Goldman, D. Fleming, W. Cimmino, L. Mohammed, H. Agarwal, A. 2022-09-16 doi:10.1101/2022.09.15.507688 Cold Spring Harbor Laboratory Press 2022-09-16 <![CDATA[ The Tre1/S1pr1 phospholipid-binding G protein-coupled receptor signaling pathway is required for astrocyte morphogenesis ]]> https://biorxiv.org/content/10.1101/2022.09.15.508188v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@1e86db5org.highwire.dtl.DTLVardef@7abd6borg.highwire.dtl.DTLVardef@29f163org.highwire.dtl.DTLVardef@1a6c4b9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chen, J. Stork, T. Kang, Y. Sheehan, A. Paton, C. Monk, K. Freeman, M. 2022-09-17 doi:10.1101/2022.09.15.508188 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Purification and biochemical analysis of native AMPA receptors from three different mammalian species ]]> https://biorxiv.org/content/10.1101/2022.09.16.508249v1?rss=1 Rao, P. Gouaux, E. 2022-09-16 doi:10.1101/2022.09.16.508249 Cold Spring Harbor Laboratory Press 2022-09-16 <![CDATA[ Comparing acute IOP-induced lamina cribrosa deformations pre-mortem and post-mortem ]]> https://biorxiv.org/content/10.1101/2022.09.18.508448v1?rss=1 Wei, J. Hua, Y. Yang, B. Wang, B. Schmitt, S. E. Wang, B. Lucy, K. A. Ishikawa, H. Schuman, J. S. Smith, M. A. Wollstein, G. Sigal, I. A. 2022-09-19 doi:10.1101/2022.09.18.508448 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ A small molecule RIG-I agonist serves to adjuvant broad multifaceted influenza virus vaccine immunity ]]> https://biorxiv.org/content/10.1101/2022.09.20.508779v1?rss=1 Hemann, E. A. Knoll, M. L. Wilkins, C. R. Subra, C. Green, R. Garcia-Sastre, A. Thomas, P. Trautmann, L. Ireton, R. Loo, Y.-M. Gale, M. 2022-09-20 doi:10.1101/2022.09.20.508779 Cold Spring Harbor Laboratory Press 2022-09-20 <![CDATA[ A Genome Scale Transcriptional Regulatory Model of the Human Placenta ]]> https://biorxiv.org/content/10.1101/2022.09.27.509541v1?rss=1 0.7 for 3 of the 4 TFs. Our final model contained 113,158 interactions across 391 TFs and 7,712 target genes and is publicly available. We identified six TFs which were significantly enriched as regulators for genes previously associated with preterm birth. ]]> Paquette, A. G. Ahuna, K. Hwang, Y. M. Pearl, J. Liao, H. Shannon, P. Kadam, L. Lapehn, S. Bucher, M. Roper, R. Funk, C. C. MacDonald, J. Bammler, T. Baloni, P. Brockway, H. Mason, W. A. Bush, N. LeWinn, K. Z. Carr, C. J. Stamatoyannopoulos, J. Muglia, L. J. Jones, H. M. Sadovsky, Y. Myatt, L. Sathyanarayana, S. Price, N. Environmental influences on Child Health Outcomes, 2022-09-28 doi:10.1101/2022.09.27.509541 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ MHC class I and MHC class II reporter mice enable analysis of immune oligodendroglia in mouse models of multiple sclerosis ]]> https://biorxiv.org/content/10.1101/2022.09.27.509669v1?rss=1 Harrington, E. P. Catenacci, R. B. Smith, M. D. Heo, D. Miller, C. E. Meyers, K. R. Glatzer, J. Bergles, D. E. Calabresi, P. A. 2022-09-28 doi:10.1101/2022.09.27.509669 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Pericytes control vascular stability and auditory spiral ganglion neuron survival ]]> https://biorxiv.org/content/10.1101/2022.09.27.509698v1?rss=1 Zhang, Y. Neng, L. Sharma, K. Hou, Z. Johnson, A. Song, J. Dabdoub, A. Shi, X. 2022-09-28 doi:10.1101/2022.09.27.509698 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Dual states of Bmi1-expressing intestinal stem cells drive epithelial development and tissue regeneration ]]> https://biorxiv.org/content/10.1101/2022.09.30.509798v1?rss=1 Smith, N. R. Sengupta, S. K. Conley, P. Giske, N. R. Klocke, C. Walker, B. S. McPhail, N. Swain, J. R. Yoo, Y. J. Anderson, A. N. Davies, P. S. Sanati, N. Nguyen, T. N. Torkenczy, K. Adey, A. C. Fischer, J. M. Wu, G. Wong, M. H. 2022-10-01 doi:10.1101/2022.09.30.509798 Cold Spring Harbor Laboratory Press 2022-10-01 <![CDATA[ Three-dimensional structure of inner ear hair cell mitochondrial networks and ribbon synapses in a zebrafish model of Usher syndrome type 1B ]]> https://biorxiv.org/content/10.1101/2022.10.01.510403v1?rss=1 Riley, K. C. Koleilat, A. Dugdale, J. A. Cooper, S. A. Christensen, T. A. Schimmenti, L. A. 2022-10-02 doi:10.1101/2022.10.01.510403 Cold Spring Harbor Laboratory Press 2022-10-02 <![CDATA[ Rapid Cell Type-Specific Nascent Proteome Labeling in Drosophila ]]> https://biorxiv.org/content/10.1101/2022.10.03.510650v1?rss=1 Villalobos-Cantor, S. Barrett, R. M. Condon, A. F. Arreola-Bustos, A. Rodriguez, K. M. Cohen, M. S. Martin, I. 2022-10-05 doi:10.1101/2022.10.03.510650 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ A Suite of Advanced Tutorials for the WESTPA 2.0 Rare-Events Sampling Software ]]> https://biorxiv.org/content/10.1101/2022.10.04.510803v1?rss=1 Bogetti, A. Leung, J. Russo, J. Zhang, S. Thompson, J. Saglam, A. Ray, D. Abraham, R. Faeder, J. Andricioaei, I. Adelman, J. Zwier, M. LeBard, D. Zuckerman, D. M. Chong, L. 2022-10-07 doi:10.1101/2022.10.04.510803 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ A Novel Mouse Model that Recapitulates the Heterogeneity of Human Triple Negative Breast Cancer ]]> https://biorxiv.org/content/10.1101/2022.10.07.511231v1?rss=1 Doha, Z. O. Wang, X. Calistri, N. Eng, J. Daniel, C. J. Ternes, L. Kim, E. N. Pelz, C. Munks, M. Betts, C. Kirchberger, N. Kwon, S. Bucher, E. Li, X. Waugh, T. Pietenpol, J. A. Sanders, M. E. Mills, G. B. Chin, K. Chang, Y. H. Coussens, L. M. Gray, J. W. Heiser, L. Sears, R. C. 2022-10-07 doi:10.1101/2022.10.07.511231 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ A genome-wide CRISPR interference screen using an engineered trafficking biosensor reveals a role for RME-8 in opioid receptor regulation ]]> https://biorxiv.org/content/10.1101/2022.10.11.511646v1?rss=1 Novy, B. Adoff, H. De Maria, M. Kampmann, M. Tsvetanova, N. Von Zastrow, M. Lobingier, B. 2022-10-11 doi:10.1101/2022.10.11.511646 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Early-life sleep disruption impairs subtle social behaviors during pair bond formation in prairie voles: A computer vision study ]]> https://biorxiv.org/content/10.1101/2022.10.12.511931v1?rss=1 Bueno-Junior, L. S. Jones-Tinsley, C. E. Wickham, P. T. Watson, B. O. Lim, M. M. 2022-10-17 doi:10.1101/2022.10.12.511931 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Agonistic anti-CD40 converts Tregs into Type 1 effectors within the tumor micro-environment ]]> https://biorxiv.org/content/10.1101/2022.10.17.512537v1?rss=1 Maltez, V. Arora, C. Sor, R. Lian, Q. Vonderheide, R. H. Germain, R. N. Byrne, K. T. 2022-10-20 doi:10.1101/2022.10.17.512537 Cold Spring Harbor Laboratory Press 2022-10-20 <![CDATA[ Early life sleep disruption has long lasting, sex specific effects on later development of sleep in prairie voles ]]> https://biorxiv.org/content/10.1101/2022.10.18.512732v1?rss=1 Jones-Tinsley, C. E. Olson, R. J. Mader, M. Wickham, P. T. Gutowsky, K. Wong, C. Chu, S. S. Milman, N. E. P. Cao, H. Lim, M. M. 2022-10-21 doi:10.1101/2022.10.18.512732 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ IL-6/STAT3 signaling drives early-stage pancreatic cancer cachexia via suppressed ketogenesis ]]> https://biorxiv.org/content/10.1101/2022.10.18.512778v1?rss=1 Arneson-Wissink, P. C. Mendez, H. Pelz, K. Dickie, J. Bartlett, A. Q. Worley, B. L. Krasnow, S. M. Eil, R. Grossberg, A. J. 2022-10-21 doi:10.1101/2022.10.18.512778 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Modulation of type I interferon responses potently inhibits SARS-CoV-2 replication and inflammation in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2022.10.21.512606v1?rss=1 Hoang, T. N. Viox, E. G. Upadhyay, A. A. Strongin, Z. Tharp, G. K. Pino, M. Nchioua, R. Hirschenberger, M. Gagne, M. Nguyen, K. Harper, J. L. Marciano, S. Boddapati, A. K. Pellegrini, K. L. Tisoncik-Go, J. Whitmore, L. S. Karunakaran, K. A. Roy, M. Kirejczyk, S. Curran, E. H. Wallace, C. Wood, J. S. Connor-Stroud, F. Kasturi, S. P. Levit, R. D. Gale, M. Vanderford, T. H. Silvestri, G. Busman-Sahay, K. Estes, J. D. Vaccari, M. Douek, D. C. Sparrer, K. M. J. Kirchhoff, F. Johnson, R. P. Schreiber, G. Bosinger, S. E. Paiardini, M. 2022-10-24 doi:10.1101/2022.10.21.512606 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Metformin use history and genome-wide DNA methylation profile: potential molecular mechanism for aging and longevity ]]> https://biorxiv.org/content/10.1101/2022.10.22.513357v1?rss=1 Marra, P. S. Yamanashi, T. Crutchley, K. J. Wahba, N. E. Anderson, Z.-E. M. Modukuri, M. Chang, G. Tran, T. Iwata, M. Cho, H. R. Shinozaki, G. 2022-10-24 doi:10.1101/2022.10.22.513357 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Reversing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome ]]> https://biorxiv.org/content/10.1101/2022.10.28.514267v1?rss=1 Newman, N. K. Zhang, Y. Padiadpu, J. Miranda, C. Magana, A. A. Hioki, K. Pederson, J. W. Li, Z. Gurung, M. Bruce, A. M. Brown, K. Bobe, G. Sharpton, T. J. Shulzhenko, N. Maier, C. Stevens, J. F. Gombart, A. F. Morgun, A. 2022-10-31 doi:10.1101/2022.10.28.514267 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ Multimodal profiling of term human decidua reveals tissue-specific immune adaptations with maternal obesity ]]> https://biorxiv.org/content/10.1101/2022.11.01.514598v1?rss=1 Sureshchandra, S. Doratt, B. M. Mendoza, N. Rincon, M. Marshall, N. E. Messaoudi, I. 2022-11-02 doi:10.1101/2022.11.01.514598 Cold Spring Harbor Laboratory Press 2022-11-02 <![CDATA[ A generalizable epigenetic clock captures aging in two nonhuman primates. ]]> https://biorxiv.org/content/10.1101/2022.11.01.514719v1?rss=1 Goldman, E. A. Watowich, M. M. Chiou, K. L. Mercer, A. Sams, S. N. Horvath, J. E. Anderson, J. Cayo Biobank Research Unit, Tung, J. Higham, J. P. Brent, L. J. Martinez, M. I. Montague, M. J. Platt, M. L. Sterner, K. N. Snyder-Mackler, N. 2022-11-02 doi:10.1101/2022.11.01.514719 Cold Spring Harbor Laboratory Press 2022-11-02 <![CDATA[ Magnetic Levitation and Sorting of Neoplastic Circulating Cell Hybrids ]]> https://biorxiv.org/content/10.1101/2022.11.03.515127v1?rss=1 Liang, K. Yaman, S. Patel, R. K. Parappilly, M. S. Walker, B. S. Wong, M. H. Durmus, N. G. 2022-11-04 doi:10.1101/2022.11.03.515127 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ PathExpSurv: Pathway Expansion for Explainable Survival Analysis and Disease Gene Discovery ]]> https://biorxiv.org/content/10.1101/2022.11.08.515625v1?rss=1 Hou, Z. Leng, J. Yu, J. Xia, Z. Wu, L.-Y. 2022-11-09 doi:10.1101/2022.11.08.515625 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ Flexible, Scalable, High Channel Count Stereo-Electrode for Recording in the Human Brain ]]> https://biorxiv.org/content/10.1101/2022.11.08.515705v1?rss=1 Lee, K. Paulk, A. C. Ro, Y. G. Cleary, D. R. Tonsfeldt, K. J. Kfir, Y. Pezaris, J. Tchoe, Y. Lee, J. Bourhis, A. M. Vatsyayan, R. Russman, S. M. Yang, J. C. Baohan, A. Richardson, M. Williams, Z. M. Fried, S. Raslan, A. Halgren, E. Cash, S. S. Dayeh, S. A. 2022-11-09 doi:10.1101/2022.11.08.515705 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ Septins and K63 chains form separate bacterial microdomains during autophagy of entrapped Shigella ]]> https://biorxiv.org/content/10.1101/2022.11.14.516380v1?rss=1 Lobato-Marquez, D. Conesa, J. J. Lopez-Jimenez, A. T. Divine, M. E. Pruneda, J. N. Mostowy, S. 2022-11-15 doi:10.1101/2022.11.14.516380 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Computational Pipeline to Identify Gene signatures that Define Cancer Subtypes ]]> https://biorxiv.org/content/10.1101/2022.11.20.517258v1?rss=1 Mittal, E. Parikh, V. Kirchgaessner, R. 2022-11-22 doi:10.1101/2022.11.20.517258 Cold Spring Harbor Laboratory Press 2022-11-22 <![CDATA[ Adaptive nanopore sequencing for single cell characterization of cancer mutations and gene rearrangements ]]> https://biorxiv.org/content/10.1101/2022.11.22.517284v1?rss=1 Grimes, S. M. Kim, H. S. Roy, S. Sathe, A. Ayala, C. I. Almeida-Notestine, A. F. Haebe, S. Shree, T. Levy, R. Lau, B. T. Ji, H. P. 2022-11-24 doi:10.1101/2022.11.22.517284 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Consensus Label Propagation with Graph Convolutional Networks for Single-Cell RNA Sequencing Cell Type Annotation ]]> https://biorxiv.org/content/10.1101/2022.11.23.517739v1?rss=1 Lewinsohn, D. P. Vigh-Conrad, K. A. Conrad, D. Scott, C. B. 2022-11-25 doi:10.1101/2022.11.23.517739 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ SARS-CoV-2 Vaccine Booster Elicits Robust Prolonged Maternal Antibody Responses and Passive Transfer Via The Placenta And Breastmilk ]]> https://biorxiv.org/content/10.1101/2022.11.29.518385v1?rss=1 Marshall, N. E. Blanton, M. B. Doratt, B. M. Malherbe, D. C. Rincon, M. True, H. McDonald, T. Beauregard, C. Adatorwovor, R. Messaoudi, I. 2022-11-29 doi:10.1101/2022.11.29.518385 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ Intermittent treatment with elamipretide preserves exercise tolerance in aged female mice ]]> https://biorxiv.org/content/10.1101/2022.11.29.518431v1?rss=1 Campbell, M. D. Samuelson, A. T. Chiao, Y. A. Sweetwyne, M. T. Ladiges, W. C. Rabinovitch, P. S. Marcinek, D. 2022-12-02 doi:10.1101/2022.11.29.518431 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Data mining and experimental approaches to identify combination of natural herbs against bacterial infections ]]> https://biorxiv.org/content/10.1101/2022.11.29.518436v1?rss=1 turmeric > neem > fenugreek > asafoetida as compared to vehicle (ethanol) treated control. Among all the tested combinations the turmeric and fenugreek combination had the best efficacy in inhibiting the bacterial growth. Next to understand the mechanism of action and to predict the effective combinations among available herbs, we used a data mining and computational analysis approach. Using NPASS, BindingDB, and pathway analysis tools, we identified the bioactive compounds for each herb, then identified the targets for each bioactive compound, and then identified associated pathways for these targets. Then we measured the target/pathway overlap for each herb and identified that the most effective combinations were those which have non-overlapping targets/pathways. For example, we showed as a proof-of-concept that turmeric and fenugreek have the least overlapping targets/pathways and thus is most effective in inhibiting bacteria growth. Our approach is applicable to treat bacterial infections and other human diseases such as cancer. Overall, the computational prediction along with experimental validation can help identify novel combinations that have significant antibacterial activity and may help prevent drug-resistant microbial diseases in human and plants. ]]> Mittal, E. Duncan, S. Chamberlin, S. 2022-11-29 doi:10.1101/2022.11.29.518436 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ Discordant results among MHC binding affinity prediction tools ]]> https://biorxiv.org/content/10.1101/2022.12.04.518984v1?rss=1 Nguyen, A. Nellore, A. Thompson, R. F. 2022-12-07 doi:10.1101/2022.12.04.518984 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ DNA damage-induced lncRNA MEG9 impacts angiogenesis ]]> https://biorxiv.org/content/10.1101/2022.12.07.519382v1?rss=1 Fraile-Bethencourt, E. Khou, S. Wilson, R. Baris, A. Ruhl, R. Espinosa-Diez, C. Anand, S. 2022-12-10 doi:10.1101/2022.12.07.519382 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ SARM1 detection in oligodendrocytes but not Schwann cells though sarm1/Sarm1 deletion does not perturb CNS nor PNS myelination in zebrafish and mice. ]]> https://biorxiv.org/content/10.1101/2022.12.08.519209v1?rss=1 Fazal, S. V. Mutschler, C. Chen, C. Turmaine, M. Chen, C.-Y. Hsueh, Y.-P. Loreto, A. Casillas-Bajo, A. Cabedo, H. Franklin, R. J. Barker, R. A. Monk, K. Steventon, B. Coleman, M. Gomez-Sanchez, J. A. Arthur-Farraj, P. 2022-12-09 doi:10.1101/2022.12.08.519209 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[ 3D multiplexed tissue imaging reconstruction and optimized region-of-interest (ROI) selection through deep learning model of channels embedding ]]> https://biorxiv.org/content/10.1101/2022.12.09.519807v1?rss=1 Burlingame, E. Ternes, L. Lin, J.-R. Chen, Y.-A. Kim, E. N. Gray, J. W. Santagata, S. Sorger, P. K. Chang, Y. H. 2022-12-12 doi:10.1101/2022.12.09.519807 Cold Spring Harbor Laboratory Press 2022-12-12 <![CDATA[ A set of orthogonal versatile interacting peptide tags for imaging cellular proteins ]]> https://biorxiv.org/content/10.1101/2022.12.14.520515v1?rss=1 Suyama, A. Devlin, K. L. Macias Contreras, M. Doh, J. K. Shinde, U. Beatty, K. E. 2022-12-15 doi:10.1101/2022.12.14.520515 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Predicting transcription factor activity using prior biological information ]]> https://biorxiv.org/content/10.1101/2022.12.16.520295v1?rss=1 Estabrook, J. Yashar, W. M. Holly, H. D. Somers, J. Nikolova, O. Barbur, O. Braun, T. P. Demir, E. 2022-12-19 doi:10.1101/2022.12.16.520295 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Identification of novel PGRP3 protein -protein interactions using yeast two hybrid system ]]> https://biorxiv.org/content/10.1101/2022.12.16.520769v1?rss=1 Lin, L.-j. Lee, C. Merritt, J. Kreth, J. Ranganathan, S. Prakasam, S. 2022-12-18 doi:10.1101/2022.12.16.520769 Cold Spring Harbor Laboratory Press 2022-12-18 <![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 versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms ]]> https://biorxiv.org/content/10.1101/2022.12.17.520865v1?rss=1 Niarakis, A. Ostaszewski, M. Mazein, A. Kuperstein, I. Gillespie, M. E. Kutmon, M. Funahashi, A. Acencio, M. L. Hemedan, A. Aichem, M. Klein, K. Czauderna, T. Burtscher, F. Yamada, T. G. Hiki, Y. Hiroi, N. F. Hu, F. Pham, N. Ehrhart, F. Willighagen, E. L. Valdeolivas, A. Dugourd, A. Messina, F. Esteban-Medina, M. Pena-Chilet, M. Rian, K. Soliman, S. Aghamiri, S. S. Puniya, B. L. Naldi, A. Helikar, T. Singh, V. Farinas Fernandez, M. Bermudez, V. Tsirvouli, E. Montagud, A. Noel, V. Ponce de Leon, M. Maier, D. Bauch, A. Gyori, B. M. Bachman, J. A. Luna, A 2022-12-19 doi:10.1101/2022.12.17.520865 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Control of stereocilia length during development of hair bundles ]]> https://biorxiv.org/content/10.1101/2022.12.18.520962v1?rss=1 Krey, J. F. Chatterjee, P. Halford, J. Cunningham, C. L. Perrin, B. J. Barr-Gillespie, P. G. 2022-12-19 doi:10.1101/2022.12.18.520962 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Silencing neuroinflammatory reactive astrocyte activating factors ameliorates disease outcomes in perinatal white matter injury ]]> https://biorxiv.org/content/10.1101/2022.12.19.521083v1?rss=1 Renz, P. V. Surbek, D. Haesler, V. Tscherrig, V. Huang, E. J. Chavali, M. Liddelow, S. A. Rowitch, D. Schoeberlein, A. Brosius Lutz, A. R. 2022-12-20 doi:10.1101/2022.12.19.521083 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Multi-center integrated analysis of non-coding CRISPR screens ]]> https://biorxiv.org/content/10.1101/2022.12.21.520137v1?rss=1 Yao, D. Tycko, J. Oh, W. Bounds, L. R. Gosai, S. J. Lataniotis, L. Mackay-Smith, A. Doughty, B. R. Gabdank, I. Schmidt, H. Youngworth, I. Andreeva, K. Ren, X. Barrera, A. Luo, Y. Siklenka, K. Yardimci, G. G. The ENCODE4 Consortium, Tewhey, R. Kundaje, A. Greenleaf, W. J. Sabeti, P. C. Leslie, C. Pritykin, Y. Moore, J. E. Beer, M. A. Gersbach, C. Reddy, T. E. Shen, Y. Engreitz, J. M. Bassik, M. C. Reilly, S. K. 2022-12-22 doi:10.1101/2022.12.21.520137 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Tumor cell intrinsic RIG-I activation is sufficient to drive immune mediated tumor rejection ]]> https://biorxiv.org/content/10.1101/2022.12.21.521495v1?rss=1 Fraile-Bethencourt, E. Khou, S. Baris, A. Ruhl, R. Anand, S. 2022-12-22 doi:10.1101/2022.12.21.521495 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Discovery of oncogenic ROS1 missense mutations with sensitivity to tyrosine kinase inhibitors ]]> https://biorxiv.org/content/10.1101/2022.12.27.521482v1?rss=1 Iyer, S. R. Nusser, K. Jones, K. Shinde, P. Beach, C. Z. Keddy, C. Aguero, E. Force, J. Shinde, U. Davare, M. A. 2022-12-27 doi:10.1101/2022.12.27.521482 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Adaptation of prokaryotic toxins for negative selection and cloning-independent markerless mutagenesis (CIMM) in Streptococcus species ]]> https://biorxiv.org/content/10.1101/2023.01.03.522674v1?rss=1 Li, L. Qin, H. Zou, Z. Kreth, J. Merritt, J. 2023-01-07 doi:10.1101/2023.01.03.522674 Cold Spring Harbor Laboratory Press 2023-01-07 <![CDATA[ Acute psilocybin enhances cognitive flexibility in rats ]]> https://biorxiv.org/content/10.1101/2023.01.09.523291v1?rss=1 Torrado Pacheco, A. Olson, R. J. Garza, G. Moghaddam, B. 2023-01-09 doi:10.1101/2023.01.09.523291 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ Neuronal activity-driven O-GlcNAcylation promotes mitochondrial plasticity ]]> https://biorxiv.org/content/10.1101/2023.01.11.523512v1?rss=1 Yu, S. B. Sanchez, R. G. Papich, Z. D. Whisenant, T. C. Ghassemian, M. Koberstein, J. N. Stewart, M. L. Pekkurnaz, G. 2023-01-11 doi:10.1101/2023.01.11.523512 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ The absence of a neurogenic response to a repeated concussive-like injury in mice ]]> https://biorxiv.org/content/10.1101/2023.01.16.524157v1?rss=1 Weingarten, A. Bah, T. M. Yeturu, S. Samudrala, N. Villasana, L. E. 2023-01-19 doi:10.1101/2023.01.16.524157 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ UL135 and UL136 Epistasis Controls Reactivation of Human Cytomegalovirus ]]> https://biorxiv.org/content/10.1101/2023.01.24.525282v1?rss=1 Moy, M. A. Collins-McMillen, D. K. Crawford, L. Parkins, C. Zeltzer, S. Caviness, K. Caposio, P. Goodrum, F. 2023-01-24 doi:10.1101/2023.01.24.525282 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ In vivo Modulation of Intraocular and Intracranial Pressures Causes Nonlinear and Non-monotonic Deformations of the Lamina Cribrosa and Scleral Canal ]]> https://biorxiv.org/content/10.1101/2023.01.29.526113v1?rss=1 Zhu, Z. Waxman, S. Wang, B. Wallace, J. Schmitt, S. E. Tyler-Kabara, E. Ishikawa, H. Schuman, J. S. Smith, M. A. Wollstein, G. Sigal, I. A. 2023-01-31 doi:10.1101/2023.01.29.526113 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Rewiring of the host cell metabolome and lipidome during lytic gammaherpesvirus infection is essential for infectious virus production ]]> https://biorxiv.org/content/10.1101/2023.01.30.526357v1?rss=1 Clark, S. A. Vazquez, A. Furiya, K. Splattstoesser, M. K. Bashmail, A. K. Schwartz, H. Russell, M. Bhark, S.-J. Moreno, O. K. McGovern, M. Owsley, E. R. Nelson, T. A. Sanchez, E. Delgado, T. 2023-01-31 doi:10.1101/2023.01.30.526357 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Robust biomarker discovery through multiplatform multiplex image analysis of breast cancer clinical cohorts ]]> https://biorxiv.org/content/10.1101/2023.01.31.525753v1?rss=1 Eng, J. R. Bucher, E. Hu, Z. Sanders, M. Chakravarthy, B. Pietenpol, J. A. Gibbs, S. L. Chin, K. 2023-02-03 doi:10.1101/2023.01.31.525753 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Human Cytomegalovirus UL138 Interaction with USP1 Activates STAT1 in infection ]]> https://biorxiv.org/content/10.1101/2023.02.07.527452v1?rss=1 Zarrella, K. Longmire, P. Zeltzer, S. Collins-McMillen, D. Hancock, M. Buehler, J. Reitsma, J. M. Terhune, S. S. Nelson, J. A. Goodrum, F. 2023-02-07 doi:10.1101/2023.02.07.527452 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ Impact of aging on the immunological and microbial landscape of the lung during non-tuberculous mycobacterial infection ]]> https://biorxiv.org/content/10.1101/2023.02.11.528140v1?rss=1 Cinco, I. R. Rhoades, N. S. Napier, E. G. Davies, M. Allison, D. B. Kohama, S. G. Bermudez, L. E. Winthrop, K. Fuss, C. Spindel, E. R. Messaoudi, I. 2023-02-13 doi:10.1101/2023.02.11.528140 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ Tertiary Lymphoid Structures Sustain Cutaneous B cell Activity in Hidradenitis Suppurativa ]]> https://biorxiv.org/content/10.1101/2023.02.14.528504v1?rss=1 Lowe, M. M. Cohen, J. N. Moss, M. I. Clancy, S. Adler, J. Yates, A. Naik, H. B. Pauli, M. Taylor, I. McKay, A. Harris, H. Kim, E. Hansen, S. L. Rosenblum, M. D. Moreau, J. M. 2023-02-15 doi:10.1101/2023.02.14.528504 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Regulated assembly and neurosteroid modulation constrain GABAA receptor pharmacology in vivo ]]> https://biorxiv.org/content/10.1101/2023.02.16.528867v1?rss=1 Sun, C. Zhu, H. Clark, S. A. Gouaux, E. 2023-02-16 doi:10.1101/2023.02.16.528867 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Dual-modality imaging of immunofluorescence and imaging mass cytometry for whole slide imaging with accurate single-cell segmentation ]]> https://biorxiv.org/content/10.1101/2023.02.23.529718v1?rss=1 Kim, E. N. Chen, P. Z. Bressan, D. Tripathi, M. Miremadi, A. di Pietro, M. Coussens, L. M. Hannon, G. J. Fitzgerald, R. C. Zhuang, L. Chang, Y. H. 2023-02-23 doi:10.1101/2023.02.23.529718 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ SEG: Segmentation Evaluation in absence of Ground truth labels ]]> https://biorxiv.org/content/10.1101/2023.02.23.529809v1?rss=1 Sims, Z. Strgar, L. Thirumalaisamy, D. Heussner, R. Thibault, G. Chang, Y. H. 2023-02-24 doi:10.1101/2023.02.23.529809 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ The acetylase activity of Cdu1 protects Chlamydia effectors from degradation to regulate bacterial exit from infected cells ]]> https://biorxiv.org/content/10.1101/2023.02.28.530337v1?rss=1 Bastidas, R. J. Kedzior, M. Dolat, L. Sixt, B. S. Pruneda, J. N. Valdivia, R. H. 2023-02-28 doi:10.1101/2023.02.28.530337 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ MEMO1 is a Metal Containing Regulator of Iron Homeostasis in Cancer Cells ]]> https://biorxiv.org/content/10.1101/2023.02.28.530460v1?rss=1 Dolgova, N. Uhlemann, E.-M. E. Boniecki, M. T. Vizeacoumar, F. S. Ralle, M. Tonelli, M. Abbas, S. A. Patry, J. Elhasasna, H. Freywald, A. Vizeacoumar, F. Dmitriev, O. Y. 2023-02-28 doi:10.1101/2023.02.28.530460 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ Monomethylation of Lysine 27 at Histone 3 Confers Lifelong Susceptibility to Stress ]]> https://biorxiv.org/content/10.1101/2023.05.08.539829v1?rss=1 Torres-Berrio, A. Estill, M. Ramakrishnan, A. Kronman, H. Patel, V. Minier-Toribio, A. Issler, O. Browne, C. J. Parise, E. van der Zee, Y. Walker, D. Martinez-Rivera, F. J. Lardner, C. K. Durand, R. Russo, S. Shen, L. Sidoli, S. Nestler, E. J. 2023-05-08 doi:10.1101/2023.05.08.539829 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ TRPV5, TRPV6, TRPM6, and TRPM7 do not contribute to hair-cell mechanotransduction ]]> https://biorxiv.org/content/10.1101/204172v1?rss=1 Morgan, C. P. Zhao, H. LeMasurier, M. Xiong, W. Pan, B. Avenarius, M. R. Bateschell, M. Larisch, R. Ricci, A. J. Mueller, U. Barr-Gillespie, P. G. 2017-10-16 doi:10.1101/204172 Cold Spring Harbor Laboratory Press 2017-10-16 <![CDATA[ Germline Contamination and Leakage in Whole Genome Somatic Single Nucleotide Variant Detection ]]> https://biorxiv.org/content/10.1101/204370v1?rss=1 Sendorek, D. H. Caloian, C. Ellrott, K. Bare, J. C. Yamaguchi, T. N. Ewing, A. D. Houlahan, K. E. Norman, T. C. Margolin, A. A. Stuart, J. M. Boutros, P. C. 2017-10-17 doi:10.1101/204370 Cold Spring Harbor Laboratory Press 2017-10-17 <![CDATA[ Structural basis for recognition of diverse antidepressants by the human serotonin transporter ]]> https://biorxiv.org/content/10.1101/204859v1?rss=1 Coleman, J. Gouaux, E. 2017-10-17 doi:10.1101/204859 Cold Spring Harbor Laboratory Press 2017-10-17 <![CDATA[ Genetic analysis of de novo variants reveals sex differences in complex and isolated congenital diaphragmatic hernia and indicates MYRF as a candidate gene ]]> https://biorxiv.org/content/10.1101/206037v1?rss=1 Qi, H. Yu, L. Zhou, X. Kitaygorodsky, A. Wynn, J. Zhu, N. Aspelund, G. Lim, F. Y. Crombleholme, T. Cusick, R. Azarow, K. Danko, M. E. Chung, D. Warner, B. W. Mychaliska, G. B. Potoka, D. Wagner, A. J. ElFiky, M. Wilson, J. M. High, F. A. Longoni, M. Donahoe, P. Chung, W. K. Shen, Y. 2017-10-19 doi:10.1101/206037 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ A multi-center study on factors influencing the reproducibility of in vitro drug-response studies ]]> https://biorxiv.org/content/10.1101/213553v1?rss=1 Niepel, M. Hafner, M. Williams, E. H. Chung, M. Barrette, A. M. Stern, A. D. Hu, B. LINCS Consortium, Gray, J. W. Birtwistle, M. R. Heiser, L. M. Sorger, P. K. 2017-11-03 doi:10.1101/213553 Cold Spring Harbor Laboratory Press 2017-11-03 <![CDATA[ Metagenomics for chronic meningitis: clarifying interpretation and diagnosis ]]> https://biorxiv.org/content/10.1101/213561v1?rss=1 Wilson, M. R. O'Donovan, B. D. Gelfand, J. M. Sample, H. A. Chow, F. C. Betjemann, J. P. Shah, M. P. Richie, M. B. Gorman, M. P. Hajj-Ali, R. A. Calabrese, L. H. Zorn, K. C. Greenlee, J. E. Blum, J. H. Green, G. Khan, L. M. Banerji, D. Langelier, C. Bryson-Cahn, C. Harrington, W. Lingappa, J. R. Shanbhag, N. M. Green, A. J. Brew, B. J. Soldatos, A. Strnad, L. Doernberg, S. B. Jay, C. A. Douglas, V. Josephson, S. A. DeRisi, J. L. 2017-11-07 doi:10.1101/213561 Cold Spring Harbor Laboratory Press 2017-11-07 <![CDATA[ Aquaporin-4 dependent glymphatic solute transport in rodent brain ]]> https://biorxiv.org/content/10.1101/216499v1?rss=1 Mestre, H. Kress, B. T. Zou, W. Pu, T. Murlidharan, G. Castellanos Rivera, R. M. Simon, M. J. Pike, M. M. Plog, B. A. Xavier, A. L. R. Thrane, A. S. Lundgaard, I. Thomas, J. H. Xiao, M. Asokan, A. Iliff, J. J. Nedergaard, M. 2017-11-09 doi:10.1101/216499 Cold Spring Harbor Laboratory Press 2017-11-09 <![CDATA[ An adaptable chromosome preparation methodology for use in invertebrate research organisms ]]> https://biorxiv.org/content/10.1101/226084v1?rss=1 Guo, L. Accorsi, A. He, S. Guerrero-Hernandez, C. Sivagnanam, S. McKinney, S. Gibson, M. Sanchez Alvarado, A. 2017-11-29 doi:10.1101/226084 Cold Spring Harbor Laboratory Press 2017-11-29 <![CDATA[ Transcription activation domains of the yeast factors Met4 and Ino2: tandem activation domains with properties similar to the yeast Gcn4 activator ]]> https://biorxiv.org/content/10.1101/228536v1?rss=1 Pacheco, D. warfield, l. brajcich, m. robbins, h. luo, j. ranish, j. Hahn, S. 2017-12-04 doi:10.1101/228536 Cold Spring Harbor Laboratory Press 2017-12-04 <![CDATA[ TRIF is a key inflammatory mediator of acute sickness behavior and cancer cachexia ]]> https://biorxiv.org/content/10.1101/232280v1?rss=1 Burfeind, K. G. Zhu, X. Levasseur, P. R. Michaelis, K. A. Norgard, M. A. Marks, D. L. 2017-12-11 doi:10.1101/232280 Cold Spring Harbor Laboratory Press 2017-12-11 <![CDATA[ The genomic false shuffle: epigenetic maintenance of topological domains in the rearranged gibbon genome ]]> https://biorxiv.org/content/10.1101/238360v1?rss=1 Lazar, N. H. Nevonen, K. A. O'Connell, B. Green, R. E. Meyer, T. J. Okhovat, M. Carbone, L. 2017-12-22 doi:10.1101/238360 Cold Spring Harbor Laboratory Press 2017-12-22 <![CDATA[ Task Engagement Enhances Population Encoding of Stimulus Meaning in Primary Auditory Cortex ]]> https://biorxiv.org/content/10.1101/240556v1?rss=1 Bagur, S. Averseng, M. Elgueda, D. David, S. Fritz, J. Yin, P. Shamma, S. Boubenec, Y. Ostojic, S. 2017-12-28 doi:10.1101/240556 Cold Spring Harbor Laboratory Press 2017-12-28 <![CDATA[ Chromosome Removal Via Cellular Fragmentation and Aneuploid Blastomere Exclusion in Primate Embryos ]]> https://biorxiv.org/content/10.1101/241851v1?rss=1 Daughtry, B. L. Rosenkrantz, J. L. Lazar, N. H. Fei, S. S. Redmayne, N. Torkenczy, K. A. Adey, A. Gao, L. Park, B. Nevonen, K. A. Carbone, L. Chavez, S. L. 2018-01-02 doi:10.1101/241851 Cold Spring Harbor Laboratory Press 2018-01-02 <![CDATA[ Acute Hyperalgesia and Delayed Dry Eye After Corneal Abrasion Injury ]]> https://biorxiv.org/content/10.1101/242685v1?rss=1 Hegarty, D. M. Hermes, S. M. Morgan, M. M. Aicher, S. A. 2018-01-04 doi:10.1101/242685 Cold Spring Harbor Laboratory Press 2018-01-04 <![CDATA[ Differential regulation of microRNA-15a by radiation affects angiogenesis and tumor growth via modulation of acid sphingomyelinase ]]> https://biorxiv.org/content/10.1101/242933v1?rss=1 Rana, S. Espinosa-Diez, C. Ruhl, R. Thomas, C. R. Anand, S. 2018-01-04 doi:10.1101/242933 Cold Spring Harbor Laboratory Press 2018-01-04 <![CDATA[ Cellular tolerance at the μ-opioid receptor is phosphorylation dependent ]]> https://biorxiv.org/content/10.1101/252387v1?rss=1 Williams, J. T. Arttamangkul, S. Heinze, D. A. Bunzow, J. R. Song, X. 2018-01-23 doi:10.1101/252387 Cold Spring Harbor Laboratory Press 2018-01-23 <![CDATA[ A saturation mutagenesis approach to understanding PTEN lipid phosphatase activity and genotype-phenotypes relationships ]]> https://biorxiv.org/content/10.1101/255265v1?rss=1 Mighell, T. L. Evans-Dutson, S. O'Roak, B. 2018-01-29 doi:10.1101/255265 Cold Spring Harbor Laboratory Press 2018-01-29 <![CDATA[ RNAi screening of the tyrosine kinome in primary patient samples of acute myeloid leukemia ]]> https://biorxiv.org/content/10.1101/256040v1?rss=1 Edwards, D. Eryildiz, F. Tyner, J. W. 2018-01-30 doi:10.1101/256040 Cold Spring Harbor Laboratory Press 2018-01-30 <![CDATA[ Causal interactions from proteomic profiles: molecular data meets pathway knowledge ]]> https://biorxiv.org/content/10.1101/258855v1?rss=1 Babur, O. Luna, A. Korkut, A. Durupinar, F. Siper, M. C. Dogrusoz, U. Aslan, J. E. Sander, C. Demir, E. 2018-02-02 doi:10.1101/258855 Cold Spring Harbor Laboratory Press 2018-02-02 <![CDATA[ Cryo-EM visualization of an active high open probability CFTR ion channel ]]> https://biorxiv.org/content/10.1101/274316v1?rss=1 Fay, J. F. Aleksandrov, L. A. Jensen, T. J. Cui, L. L. Kousouros, J. N. He, L. Aleksandrov, A. A. Gingerich, D. S. Riordan, J. Chen, J. Z. 2018-03-02 doi:10.1101/274316 Cold Spring Harbor Laboratory Press 2018-03-02 <![CDATA[ A Measure of Open Data: A Metric and Analysis of Reusable Data Practices in Biomedical Data Resources ]]> https://biorxiv.org/content/10.1101/282830v1?rss=1 Carbon, S. Champieux, R. McMurry, J. Winfree, L. Wyatt, L. R. Haendel, M. 2018-03-16 doi:10.1101/282830 Cold Spring Harbor Laboratory Press 2018-03-16 <![CDATA[ Retinal Ganglion Cell Axon Sorting at the Optic Chiasm Requires Dystroglycan ]]> https://biorxiv.org/content/10.1101/286005v1?rss=1 Clements, R. Wright, K. M. 2018-03-21 doi:10.1101/286005 Cold Spring Harbor Laboratory Press 2018-03-21 <![CDATA[ Thrombospondins 1 and 2 affect lysyl oxidase protein and collagen matrix maturation in cortical bone of growing male and female mice via non-redundant pathways ]]> https://biorxiv.org/content/10.1101/287763v1?rss=1 Shearer, D. Mervis, M. O. Manley, E. Reddy, A. B. Alford, A. I. 2018-03-23 doi:10.1101/287763 Cold Spring Harbor Laboratory Press 2018-03-23 <![CDATA[ Autoregulation of the S. mutans SloR metalloregulator is constitutive and driven by an independent promoter ]]> https://biorxiv.org/content/10.1101/301416v1?rss=1 Monette, P. Brach, R. Cowan, A. Winters, R. Weisman, J. Seybert, F. Goguen, K. Chen, J. Glasfeld, A. Spatafora, G. A. 2018-04-14 doi:10.1101/301416 Cold Spring Harbor Laboratory Press 2018-04-14 <![CDATA[ Efficient sorting of single-unit activity from midbrain cells using KiloSort is as accurate as manual sorting. ]]> https://biorxiv.org/content/10.1101/303479v1?rss=1 Allen, M. Chowdhury, T. Wegener, M. Moghaddam, B. 2018-04-18 doi:10.1101/303479 Cold Spring Harbor Laboratory Press 2018-04-18 <![CDATA[ Creating Standards for Evaluating Tumour Subclonal Reconstruction ]]> https://biorxiv.org/content/10.1101/310425v1?rss=1 Boutros, P. C. Salcedo, A. Tarabichi, M. Espiritu, S. M. G. Deshwar, A. G. David, M. Wilson, N. M. Dentro, S. Wintersinger, J. A. Liu, L. Y. Ko, M. Sivanandan, S. Zhang, H. Zhu, K. Yang, T.-H. Chilton, J. M. Buchanan, A. Lalansingh, C. M. P'ng, C. Anghel, C. V. Umar, I. Lo, B. Simpson, J. T. Stuart, J. M. Anastassiou, D. Guan, Y. Ewing, A. Ellrott, K. Wedge, D. C. Morris, Q. D. Van Loo, P. DREAM SMC-Het Participants, 2018-04-28 doi:10.1101/310425 Cold Spring Harbor Laboratory Press 2018-04-28 <![CDATA[ An RNAi screen in human cell lines reveals conserved DNA damage repair pathways that mitigate formaldehyde sensitivity ]]> https://biorxiv.org/content/10.1101/310730v1?rss=1 Juarez, E. Chambwe, N. Tang, W. Mitchell, A. D. Owen, N. Kumari, A. Monnat, R. J. McCullough, A. 2018-04-30 doi:10.1101/310730 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection ]]> https://biorxiv.org/content/10.1101/311696v1?rss=1 Fourati, S. Talla, A. Mahmoudian, M. Burkhart, J. G. Klen, R. Henao, R. Aydin, Z. Yeung, K. Y. Ahsen, M. E. Almugbel, R. Jahandideh, S. Liang, X. Nordling, T. E. M. Shiga, M. Stanescu, A. Vogel, R. The Respiratory Viral DREAM Challenge Consortium, Pandey, G. Chiu, C. McClain, M. T. Woods, C. W. Ginsburg, G. S. Elo, L. L. Tsalik, E. L. Mangravite, L. M. Sieberts, S. K. 2018-04-30 doi:10.1101/311696 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Expression and purification of a functional heteromeric GABAA receptor for structural studies ]]> https://biorxiv.org/content/10.1101/318832v1?rss=1 Claxton, D. P. Gouaux, E. 2018-05-09 doi:10.1101/318832 Cold Spring Harbor Laboratory Press 2018-05-09 <![CDATA[ Controlling for contaminants in low biomass 16S rRNA gene sequencing experiments ]]> https://biorxiv.org/content/10.1101/329854v1?rss=1 Karstens, L. Asquith, M. Davin, S. Fair, D. Gregory, W. T. Wolfe, A. J. Braun, J. McWeeney, S. 2018-05-25 doi:10.1101/329854 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Clarification and confocal imaging of the non-human primate placental micro-anatomy ]]> https://biorxiv.org/content/10.1101/330647v1?rss=1 Sargent, J. Roberts, V. Gaffney, J. Frias, A. 2018-05-24 doi:10.1101/330647 Cold Spring Harbor Laboratory Press 2018-05-24 <![CDATA[ Genetic Modifiers of Pathogenic LRRK2 G2019S Neurodegeneration in Drosophila ]]> https://biorxiv.org/content/10.1101/331991v1?rss=1 Lavoy, S. Chittoor-Vinod, V. Chow, C. Martin, I. 2018-05-30 doi:10.1101/331991 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ Thermostabilization and purification of the human dopamine transporter (hDAT) in an inhibitor and allosteric ligand bound conformation ]]> https://biorxiv.org/content/10.1101/335968v1?rss=1 Navratna, V. Tosh, D. K. Jacobson, K. A. Gouaux, E. 2018-05-31 doi:10.1101/335968 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ Correction of respiratory artifacts in MRI head motion estimates ]]> https://biorxiv.org/content/10.1101/337360v1?rss=1 Fair, D. A. Miranda-Dominguez, O. Snyder, A. Z. Perrone, A. A. Earl, E. A. Van, A. N. Koller, J. M. Feczko, E. Klein, R. L. Mirro, A. E. Hampton, J. M. Adeyemo, B. Laumann, T. O. Gratton, C. Greene, D. J. Schlaggar, B. Hagler, D. Watts, R. Garavan, H. Barch, D. M. Nigg, J. T. Petersen, S. E. Dale, A. Feldstein-Ewing, S. W. Nagel, B. J. Dosenbach, N. U. F. 2018-06-07 doi:10.1101/337360 Cold Spring Harbor Laboratory Press 2018-06-07 <![CDATA[ Cryo-EM structure of the benzodiazepine-sensitive α1β1γ2 heterotrimeric GABAA receptor in complex with GABA illuminates mechanism of receptor assembly and agonist binding ]]> https://biorxiv.org/content/10.1101/337659v1?rss=1 Phulera, S. Zhu, H. Yu, J. Claxton, D. Yoder, N. Yoshioka, C. Gouaux, E. 2018-06-03 doi:10.1101/337659 Cold Spring Harbor Laboratory Press 2018-06-03 <![CDATA[ High-throughput mapping of meiotic crossover and chromosome mis-segregation events in interspecific hybrid mice ]]> https://biorxiv.org/content/10.1101/338053v1?rss=1 Yin, Y. Jiang, Y. Berletch, J. B. Disteche, C. M. Noble, W. S. Steemers, F. J. Adey, A. C. Shendure, J. A. 2018-06-04 doi:10.1101/338053 Cold Spring Harbor Laboratory Press 2018-06-04 <![CDATA[ Fbxw7 is a critical regulator of Schwann cell myelinating potential ]]> https://biorxiv.org/content/10.1101/342931v1?rss=1 Harty, B. L. Coelho, F. Ackerman, S. D. Herbert, A. L. Lyons, D. A. Monk, K. R. 2018-06-08 doi:10.1101/342931 Cold Spring Harbor Laboratory Press 2018-06-08 <![CDATA[ Evolution of Endothelin signaling and diversification of adult pigment pattern in Danio fishes ]]> https://biorxiv.org/content/10.1101/363879v1?rss=1 Spiewak, J. Bain, E. Liu, J. Kou, K. Sturiale, S. Patterson, L. Diba, P. Eisen, J. Braasch, I. Ganz, J. Parichy, D. M. 2018-07-06 doi:10.1101/363879 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ Caspase-mediated cleavage of Murine Norovirus NS1/2 potentiates apoptosis and is required for persistent infection ]]> https://biorxiv.org/content/10.1101/372615v1?rss=1 Robinson, B. A. McCune, B. T. Peters, A. M. Nice, T. 2018-07-19 doi:10.1101/372615 Cold Spring Harbor Laboratory Press 2018-07-19 <![CDATA[ Accurate transmission of IGF-I into AKT signaling activity in individual cells ]]> https://biorxiv.org/content/10.1101/373993v1?rss=1 Gross, S. M. Dane, M. A. Bucher, E. Heiser, L. M. 2018-07-21 doi:10.1101/373993 Cold Spring Harbor Laboratory Press 2018-07-21 <![CDATA[ Opposing effects of impulsivity and mindset on sources of science self-efficacy and STEM interest in adolescents ]]> https://biorxiv.org/content/10.1101/377994v1?rss=1 Marriott, L. K. Coppola, L. K. Mitchell, S. H. Bouwma-Gearhart, J. Chen, Z. Shifrer, D. Shannon, J. K. 2018-07-26 doi:10.1101/377994 Cold Spring Harbor Laboratory Press 2018-07-26 <![CDATA[ Mechanisms for zinc and proton inhibition of the GluN1/GluN2A NMDA receptor ]]> https://biorxiv.org/content/10.1101/378422v1?rss=1 Jalali-Yazdi, F. Chowdhury, S. Yoshioka, C. Gouaux, E. 2018-07-26 doi:10.1101/378422 Cold Spring Harbor Laboratory Press 2018-07-26 <![CDATA[ Divalent cation and chloride ion sites of chicken acid sensing ion channel 1a elucidated by x-ray crystallography ]]> https://biorxiv.org/content/10.1101/379685v1?rss=1 Yoder, N. Gouaux, E. 2018-07-30 doi:10.1101/379685 Cold Spring Harbor Laboratory Press 2018-07-30 <![CDATA[ Effects of cochlear synaptopathy on spontaneous and sound-evoked activity in the mouse inferior colliculus ]]> https://biorxiv.org/content/10.1101/381087v1?rss=1 Shaheen, L. Liberman, M. C. 2018-08-06 doi:10.1101/381087 Cold Spring Harbor Laboratory Press 2018-08-06 <![CDATA[ Isolation and Characterization of a Myoviridae phage that lyses two Escherichia coli pathotypes ]]> https://biorxiv.org/content/10.1101/385104v1?rss=1 Cepko, L. Garling, E. Dinsdale, M. Bandy, L. Mellies, J. 2018-08-04 doi:10.1101/385104 Cold Spring Harbor Laboratory Press 2018-08-04 <![CDATA[ Putative pore-forming subunits of the mechano-electrical transduction channel, Tmc1/2b, require Tmie to localize to the site of mechanotransduction in zebrafish sensory hair cells ]]> https://biorxiv.org/content/10.1101/393330v1?rss=1 Pacentine, I. Nicolson, T. 2018-08-16 doi:10.1101/393330 Cold Spring Harbor Laboratory Press 2018-08-16 <![CDATA[ Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma ]]> https://biorxiv.org/content/10.1101/396358v1?rss=1 Berlow, N. E. Rikhi, R. Geltzeiler, M. N. Abraham, J. Svalina, M. N. Davis, L. E. Wise, E. Mancini, M. Noujaim, J. Mansoor, A. Quist, M. J. Matlock, K. L. Goros, M. W. Hernandez, B. S. Duong, Y. C. Thway, K. Tsukahara, T. Nishio, J. Huang, E. C. Airhart, S. Bult, C. J. Gandour-Edwards, R. Maki, R. G. Jones, R. L. Michalek, J. E. Milovancev, M. Ghosh, S. Pal, R. Keller, C. 2018-08-21 doi:10.1101/396358 Cold Spring Harbor Laboratory Press 2018-08-21 <![CDATA[ Epigenetic factors coordinate intestinal development ]]> https://biorxiv.org/content/10.1101/399410v1?rss=1 Ganz, J. Melancon, E. Wilson, C. Amores, A. Batzel, P. Strader, M. Braasch, I. Diba, P. Kuhlman, J. A. Postlethwait, J. H. Eisen, J. S. 2018-08-23 doi:10.1101/399410 Cold Spring Harbor Laboratory Press 2018-08-23 <![CDATA[ Genetic control of the HDL proteome ]]> https://biorxiv.org/content/10.1101/405811v1?rss=1 80 associated proteins, phospholipids, cholesterol and cholesteryl esters. A comprehensive genetic analysis of the regulation of proteome of HDL isolated from a panel of 100 diverse inbred strains of mice, Hybrid Mouse Diversity Panel (HMDP), revealed widely varied HDL protein levels across the strains. Some of this variation was explained by local, cis-acting regulation, termed cis-protein quantitative trait loci. Variations in apolipoprotein A-II and apolipoprotein C-3 affected the abundance of multiple HDL proteins indicating a coordinated regulation. We identified modules of co-varying proteins and define a protein-protein interaction network describing the protein composition of the naturally occurring subspecies of HDL in mice. Sterol efflux capacity varied up to 3-fold across the strains and HDL proteins displayed distinct correlation patterns with macrophage and ABCA1 specific cholesterol efflux capacity and cholesterol exchange, suggesting that subspecies of HDL participate in discrete functions. The baseline and stimulated sterol efflux capacity phenotypes associated with distinct QTLs with smaller effect size suggesting a multi genetic regulation. Our results highlight the complexity of HDL particles by revealing high degree of heterogeneity and intercorrelation, some of which is associated with functional variation, supporting the concept that HDL-cholesterol alone is not an accurate measure of HDLs properties such as protection against CAD. ]]> Pamir, N. Pan, C. Plubell, D. L. Hutchins, P. M. Tang, C. Wimberger, J. Irwin, A. Vallim, T. Q. d. A. Heinecke, J. W. Lusis, A. J. 2018-08-31 doi:10.1101/405811 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ Aperture Phase Modulation with Adaptive Optics: A Novel Approach for Speckle Reduction and Structure Extraction in Optical Coherence Tomography ]]> https://biorxiv.org/content/10.1101/406108v1?rss=1 Zhang, P. Manna, S. K. Miller, E. B. Jian, Y. Meleppat, R. K. Sarunic, M. V. Pugh, E. N. Zawadzki, R. J. 2018-08-31 doi:10.1101/406108 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ The accessible chromatin landscape of the hippocampus at single-cell resolution ]]> https://biorxiv.org/content/10.1101/407668v1?rss=1 Sinnamon, J. R. Torkenczy, K. A. Linhoff, M. W. Vitak, S. A. Pliner, H. A. Trapnell, C. Steemers, F. J. Mandel, G. Adey, A. C. 2018-09-04 doi:10.1101/407668 Cold Spring Harbor Laboratory Press 2018-09-04 <![CDATA[ Specific detection of cell-free DNA derived from intestinal epithelial cells using methylation patterns ]]> https://biorxiv.org/content/10.1101/409219v1?rss=1 Lehmann-Werman, R. Zick, A. Paweletz, C. Welch, M. Hubert, A. Maoz, M. Davidy, T. Magenheim, J. Piyanzin, S. Neiman, D. Moss, J. Golan, H. Israeli, E. Fischer, M. Segal, E. Grompe, M. Pikarsky, A. Golan, T. Glaser, B. Shemer, R. Wolpin, B. Dor, Y. 2018-09-05 doi:10.1101/409219 Cold Spring Harbor Laboratory Press 2018-09-05 <![CDATA[ Maternal Circulating MicroRNAs Control the Placental Response to Alcohol ]]> https://biorxiv.org/content/10.1101/409854v1?rss=1 Tseng, A. M. Mahnke, A. H. Wells, A. B. Salem, N. A. Allan, A. M. Roberts, V. H. J. Newman, N. Walter, N. A. R. Kroenke, C. D. Grant, K. A. Akison, L. K. Moritz, K. M. Chambers, C. D. Miranda, R. C. 2018-09-06 doi:10.1101/409854 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ Dystroglycan is a scaffold for extracellular axon guidance decisions ]]> https://biorxiv.org/content/10.1101/410944v1?rss=1 Lindenmaier, L. B. Parmentier, N. Guo, C. Tissir, F. Wright, K. 2018-09-06 doi:10.1101/410944 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ neoepiscope Improves Neoepitope Prediction with Multi-variant Phasing ]]> https://biorxiv.org/content/10.1101/418129v1?rss=1 Wood, M. A. Nguyen, A. Struck, A. J. Ellrott, K. Nellore, A. Thompson, R. F. 2018-09-14 doi:10.1101/418129 Cold Spring Harbor Laboratory Press 2018-09-14 <![CDATA[ Mutual transcriptional repression between Gli3 and Hox13 genes determines the anterior-posterior asymmetry of the autopod ]]> https://biorxiv.org/content/10.1101/419606v1?rss=1 Bastida, M. F. Perez-Gomez, R. Trofka, A. Sheth, R. Stadler, H. S. Mackem, S. Ros, M. A. 2018-09-17 doi:10.1101/419606 Cold Spring Harbor Laboratory Press 2018-09-17 <![CDATA[ Bidirectional Control of Coronary Vascular Resistance by Eicosanoids via a Novel GPCR ]]> https://biorxiv.org/content/10.1101/420406v1?rss=1 Alkayed, N. J. Cao, Z. Qian, Z. Y. Nagarajan, S. Liu, X. Nelson, J. Xie, F. Li, B. Fan, W. Liu, L. Grafe, M. R. Xiao, X. Barnes, A. P. Kaul, S. 2018-09-19 doi:10.1101/420406 Cold Spring Harbor Laboratory Press 2018-09-19 <![CDATA[ A specific Ret receptor isoform is required for pioneer axon outgrowth and growth cone dynamics ]]> https://biorxiv.org/content/10.1101/424432v1?rss=1 Tuttle, A. M. Drerup, C. M. Marra, M. H. Nechiporuk, A. V. 2018-09-21 doi:10.1101/424432 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α ]]> https://biorxiv.org/content/10.1101/424952v1?rss=1 Spiriti, J. Subramanian, S. R. Palli, R. Wu, M. Zuckerman, D. M. 2018-09-24 doi:10.1101/424952 Cold Spring Harbor Laboratory Press 2018-09-24 <![CDATA[ Computational estimation of ms-sec atomistic folding times ]]> https://biorxiv.org/content/10.1101/427393v1?rss=1 Adhikari, U. Mostofian, B. Petersen, A. Zuckerman, D. M. 2018-09-29 doi:10.1101/427393 Cold Spring Harbor Laboratory Press 2018-09-29 <![CDATA[ Network stress test reveals novel drug potentiators in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/429373v1?rss=1 Ma, S. Morrison, R. Hobbs, S. J. Farrow-Johnson, J. Rustad, T. R. Sherman, D. R. 2018-09-27 doi:10.1101/429373 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ Targeting mitochondria in cancer therapy could provide a basis for the selective anti-cancer activity ]]> https://biorxiv.org/content/10.1101/432252v1?rss=1 Rozanov, D. Cheltsov, A. Nilsen, A. Boniface, C. Korkola, J. Gray, J. Tyner, J. Tognon, C. E. Mills, G. B. Spellman, P. 2018-10-01 doi:10.1101/432252 Cold Spring Harbor Laboratory Press 2018-10-01 <![CDATA[ TrkB activation during a critical period mimics the protective effects of early visual experience on the stability of receptive fields in adult superior colliculus ]]> https://biorxiv.org/content/10.1101/435784v1?rss=1 Mudd, D. B. Balmer, T. S. Kim, S. Y. Machhour, N. Pallas, S. L. 2018-10-04 doi:10.1101/435784 Cold Spring Harbor Laboratory Press 2018-10-04 <![CDATA[ DNA damage dependent hypomethylation regulates the pro-angiogenic LncRNA MEG9 ]]> https://biorxiv.org/content/10.1101/442699v1?rss=1 Espinosa-Diez, C. Wilson, R. Mukherjee, R. Feltham, M. Hudson, C. Ruhl, R. Anand, S. 2018-10-14 doi:10.1101/442699 Cold Spring Harbor Laboratory Press 2018-10-14 <![CDATA[ Dopamine modulation of prefrontal cortex activity is manifold and operates at multiple temporal and spatial scales ]]> https://biorxiv.org/content/10.1101/452862v1?rss=1 Lohani, S. Martig, A. K. Deisseroth, K. Witten, I. Moghaddam, B. 2018-10-25 doi:10.1101/452862 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Cyclic, condition-independent activity in primary motor cortex predicts corrective movement behavior ]]> https://biorxiv.org/content/10.1101/453746v1?rss=1 Rouse, A. G. 2018-10-25 doi:10.1101/453746 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Image processing and analysis methods for the Adolescent Brain Cognitive Development Study ]]> https://biorxiv.org/content/10.1101/457739v1?rss=1 Hagler, D. J. Hatton, S. N. Makowski, C. Cornejo, M. D. Fair, D. A. Dick, A. S. Sutherland, M. T. Casey, B. J. Barch, D. M. Harms, M. P. Watts, R. Bjork, J. M. Garavan, H. P. Hilmer, L. Pung, C. J. Sicat, C. S. Kuperman, J. Bartsch, H. Xue, F. Heitzeg, M. M. Laird, A. R. Trinh, T. T. Gonzalez, R. Tapert, S. F. Riedel, M. C. Squeglia, L. M. Hyde, L. W. Rosenberg, M. D. Earl, E. A. Howlett, K. D. Baker, F. C. Soules, M. Diaz, J. Ruiz de Leon, O. Thompson, W. K. Neale, M. C. Herting, M. Sowell, E. R. Alvarez, R. P. Hawes, S. W. Sanchez, M. Bodurka, J. Bre 2018-11-04 doi:10.1101/457739 Cold Spring Harbor Laboratory Press 2018-11-04 <![CDATA[ Early detonation by sprouted mossy fibers enables aberrant dentate network activity ]]> https://biorxiv.org/content/10.1101/466300v1?rss=1 Hendricks, W. D. Westbrook, G. L. Schnell, E. 2018-11-08 doi:10.1101/466300 Cold Spring Harbor Laboratory Press 2018-11-08 <![CDATA[ Anti-NMDA receptor encephalitis in mice induced by active immunization with conformationally-stabilized holoreceptors ]]> https://biorxiv.org/content/10.1101/467902v1?rss=1 Jones, B. E. Tovar, K. R. Goehring, A. Okada, N. J. Gouaux, E. Westbrook, G. L. 2018-11-10 doi:10.1101/467902 Cold Spring Harbor Laboratory Press 2018-11-10 <![CDATA[ Identification of A Disintegrin and Metalloproteinase 9 domain (ADAM9) required in the early stages of encephalomyocarditis virus infection ]]> https://biorxiv.org/content/10.1101/491068v1?rss=1 Bazzone, L. E. King, M. MacKay, C. R. Kyawe, P. P. Meraner, P. Lindstrom, D. Rojas-Quintero, J. Owen, C. A. Wang, J. P. Brass, A. L. Kurt-Jones, E. A. Finberg, R. W. 2018-12-09 doi:10.1101/491068 Cold Spring Harbor Laboratory Press 2018-12-09 <![CDATA[ Convergent Allostery in Ribonucleotide Reductase ]]> https://biorxiv.org/content/10.1101/504290v1?rss=1 Thomas, W. C. Brooks, F. P. Burnim, A. A. Bacik, J.-P. Stubbe, J. Kaelber, J. T. Chen, J. Z. Ando, N. 2018-12-21 doi:10.1101/504290 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ Prevention of heart failure in hypertension: disentangling the role of evolving left ventricular hypertrophy and blood pressure lowering: the ALLHAT study ]]> https://biorxiv.org/content/10.1101/514323v1?rss=1 Johnson, K. Oparil, S. Davis, B. R. Tereshchenko, L. G. 2019-01-12 doi:10.1101/514323 Cold Spring Harbor Laboratory Press 2019-01-12 <![CDATA[ Dynamic Predictive Accuracy of Electrocardiographic Biomarkers of Sudden Cardiac Death within a Survival Framework: The Atherosclerosis Risk in Communities (ARIC) study ]]> https://biorxiv.org/content/10.1101/514380v1?rss=1 Perez-Alday, E. Bender, A. Li-Pershing, Y. German, D. Mai, T. Mukundan, S. Thomas, J. Hamilton, C. Tereshchenko, L. 2019-01-08 doi:10.1101/514380 Cold Spring Harbor Laboratory Press 2019-01-08 <![CDATA[ Selective targeting of unipolar brush cell subtypes by cerebellar mossy fibers ]]> https://biorxiv.org/content/10.1101/523266v1?rss=1 Balmer, T. S. Trussell, L. 2019-01-17 doi:10.1101/523266 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ Synapse-specific Opioid Modulation of Thalamo-cortico-striatal Circuits ]]> https://biorxiv.org/content/10.1101/525782v1?rss=1 Birdsong, W. T. Jongbloets, B. C. Engeln, K. A. Wang, D. Scherrer, G. Mao, T. 2019-01-21 doi:10.1101/525782 Cold Spring Harbor Laboratory Press 2019-01-21 <![CDATA[ Inter-individual Variability of Functional Connectivity in Awake and Anesthetized Rhesus Monkeys ]]> https://biorxiv.org/content/10.1101/531293v1?rss=1 Xu, T. Sturgeon, D. Ramirez, J. S. B. Froudist-Walsh, S. Margulies, D. S. Schroeder, C. E. Fair, D. A. Milham, M. 2019-01-26 doi:10.1101/531293 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Spectral tuning of adaptation supports coding of sensory context in auditory cortex ]]> https://biorxiv.org/content/10.1101/534537v1?rss=1 Lopez Espejo, M. Schwartz, Z. P. David, S. V. 2019-01-29 doi:10.1101/534537 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Exercise-induced enhancement of synaptic functiontriggered by the inverse BAR protein, Mtss1L. ]]> https://biorxiv.org/content/10.1101/545582v1?rss=1 Chatzi, C. Zhang, Y. Hendricks, W. D. Chen, Y. Schnell, E. Goodman, R. H. Westbrook, G. L. 2019-02-09 doi:10.1101/545582 Cold Spring Harbor Laboratory Press 2019-02-09 <![CDATA[ Variable Retention of Differentiation-specific DNA Replication Timing in Human Pediatric Leukemia ]]> https://biorxiv.org/content/10.1101/549196v1?rss=1 100 pediatric leukemic samples and normally differentiating human B-lineage cells isolated from xenografted immunodeficient mice were generated. Comparison of these identified potentially clinically relevant features that both match and deviate from the normal profiles. ]]> Rivera-Mulia, J. C. Sasaki, T. Trevilla-Garcia, C. Nakamichi, N. Knapp, D. J. H. F. Hammond, C. Chang, B. Tyner, J. W. Devidas, M. Zimmerman, J. Klein, K. Somasundaram, V. Druker, B. Gruber, T. Koren, A. Eaves, C. J. Gilbert, D. M. 2019-02-13 doi:10.1101/549196 Cold Spring Harbor Laboratory Press 2019-02-13 <![CDATA[ High-throughput single-particle tracking reveals nested membrane nanodomain organization that dictates Ras diffusion and trafficking ]]> https://biorxiv.org/content/10.1101/552075v1?rss=1 Lee, Y. Phelps, C. Huang, T. Mostofian, B. Wu, L. Zhang, Y. Chang, Y. H. Stork, P. J. S. Gray, J. W. Zuckerman, D. M. Nan, X. 2019-02-15 doi:10.1101/552075 Cold Spring Harbor Laboratory Press 2019-02-15 <![CDATA[ Sphingomyelin is critical in organizing phosphoinositide dynamics during phagocytic uptake of Mycobacterium tuberculosis. ]]> https://biorxiv.org/content/10.1101/565226v1?rss=1 Niekamp, P. Guzman, G. Leier, H. Rashidfarrokhi, A. Richina, V. Holthuis, J. Tafesse, F. G. 2019-03-01 doi:10.1101/565226 Cold Spring Harbor Laboratory Press 2019-03-01 <![CDATA[ Mechanism of pharmacochaperoning in KATP channels revealed by cryo-EM ]]> https://biorxiv.org/content/10.1101/572297v1?rss=1 Martin, G. M. Sung, M. W. Yang, Z. Innes, L. M. Kandasamy, B. David, L. Yoshioka, C. Shyng, S.-L. 2019-03-08 doi:10.1101/572297 Cold Spring Harbor Laboratory Press 2019-03-08 <![CDATA[ Sex differences in reward- and punishment-guided actions ]]> https://biorxiv.org/content/10.1101/581546v1?rss=1 Tara, C. G. Wallin-Miller, K. G. Rear, A. A. Park, J. Diaz, V. Simon, N. W. Moghaddam, B. 2019-03-18 doi:10.1101/581546 Cold Spring Harbor Laboratory Press 2019-03-18 <![CDATA[ Identification of PKC -dependent phosphoproteins in mouse retina ]]> https://biorxiv.org/content/10.1101/589184v1?rss=1 Wakeham, C. M. Wilmarth, P. A. Cunliffe, J. M. Klimek, J. E. Ren, G. David, L. L. Morgans, C. W. 2019-03-27 doi:10.1101/589184 Cold Spring Harbor Laboratory Press 2019-03-27 <![CDATA[ Expression and distribution of Trophoblast Glycoprotein in the mouse retina ]]> https://biorxiv.org/content/10.1101/590216v1?rss=1 Wakeham, C. M. Ren, G. Morgans, C. W. 2019-03-27 doi:10.1101/590216 Cold Spring Harbor Laboratory Press 2019-03-27 <![CDATA[ The Dialysis Procedure Triggers Autonomic Imbalance and Cardiac Arrhythmias: Insights from Continuous 14-day ECG Monitoring ]]> https://biorxiv.org/content/10.1101/601542v1?rss=1 Rogovoy, N. M. Howell, S. J. Lee, T. L. Hamilton, C. Perez-Alday, E. A. Kabir, M. M. Li-Pershing, Y. Zhang, Y. Kim, E. D. Fitzpatrick, J. Monroy-Trujillo, J. M. Estrella, M. M. Sozio, S. M. Jaar, B. G. Parekh, R. S. Tereshchenko, L. G. 2019-04-12 doi:10.1101/601542 Cold Spring Harbor Laboratory Press 2019-04-12 <![CDATA[ Post-ictal neuronal network remodeling and Wnt pathway dysregulation in the intra-hippocampal kainate mouse model of temporal lobe epilepsy ]]> https://biorxiv.org/content/10.1101/604975v1?rss=1 Gupta, K. Schnell, E. 2019-04-10 doi:10.1101/604975 Cold Spring Harbor Laboratory Press 2019-04-10 <![CDATA[ Pupil-associated states modulate excitability but not stimulus selectivity in primary auditory cortex ]]> https://biorxiv.org/content/10.1101/619619v1?rss=1 Schwartz, Z. P. Buran, B. N. David, S. V. 2019-04-26 doi:10.1101/619619 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Transformation and Integration of Microenvironment Microarray Data Improves Discovery of Latent Effects ]]> https://biorxiv.org/content/10.1101/627802v1?rss=1 Hunt, G. J. Dane, M. A. Korkola, J. E. Heiser, L. M. Gagnon-Bartsch, J. A. 2019-05-05 doi:10.1101/627802 Cold Spring Harbor Laboratory Press 2019-05-05 <![CDATA[ Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis ]]> https://biorxiv.org/content/10.1101/637256v1?rss=1 Mulqueen, R. M. DeRosa, B. A. Thornton, C. A. Sayar, Z. Torkenczy, K. A. Fields, A. J. Wright, K. M. Nan, X. Ramji, R. Steemers, F. J. O'Roak, B. J. Adey, A. C. 2019-05-15 doi:10.1101/637256 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ Myeloid Lineage Enhancers Drive Oncogene Synergy in CEBPA/CSF3R Mutant Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/639617v1?rss=1 Braun, T. P. Okhovat, M. Coblentz, C. Carratt, S. A. Foley, A. Schonrock, Z. Nevonen, K. Davis, B. Garcia, B. LaTocha, D. Weeder, B. R. Grzadkowski, M. R. Estabrook, J. C. Manning, H. G. Watanabe-Smith, K. Smith, J. L. Leonti, A. R. Ries, R. E. Jeng, S. McWeeney, S. Di Genua, C. Drissen, R. Nerlov, C. Meshinchi, S. Carbone, L. Druker, B. J. Maxson, J. E. 2019-05-15 doi:10.1101/639617 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ HCMV miR-US22 down-regulation of EGR-1 regulates CD34+ hematopoietic progenitor cell proliferation and viral reactivation ]]> https://biorxiv.org/content/10.1101/645374v1?rss=1 Mikell, I. A. Crawford, L. B. Hancock, M. H. Mitchell, J. Buehler, J. Goodrum, F. Nelson, J. A. 2019-05-21 doi:10.1101/645374 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ Cataract-associated deamidations on the surface of γS-crystallin increase protein unfolding and flexibility at distant regions ]]> https://biorxiv.org/content/10.1101/646083v1?rss=1 Forsythe, H. M. Vetter, C. J. Jara, K. J. Reardon, P. N. David, L. L. Barbar, E. J. Lampi, K. 2019-05-22 doi:10.1101/646083 Cold Spring Harbor Laboratory Press 2019-05-22 <![CDATA[ EGR1 transcriptional control of human cytomegalovirus latency ]]> https://biorxiv.org/content/10.1101/648543v1?rss=1 Buehler, J. C. Carpenter, E. Zeltzer, S. Igarashi, S. Rak, M. Mikell, I. Nelson, J. A. Goodrum, F. 2019-05-24 doi:10.1101/648543 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Mutually exclusive autism mutations point to the circadian clock and PI3K signaling pathways ]]> https://biorxiv.org/content/10.1101/653527v1?rss=1 Manning, H. O'Roak, B. J. Babur, O. 2019-05-30 doi:10.1101/653527 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ HER2 Cancer Protrusion Growth Signaling Regulated by Unhindered, Localized Filopodial Dynamics ]]> https://biorxiv.org/content/10.1101/654988v1?rss=1 Lam, W. Y. Wang, Y. Mostofian, B. Jorgens, D. Kwon, S. Chin, K. Carpenter, M. Jacob, T. Heiser, K. Agrawal, A. Wang, J. Nan, X. Chang, Y. H. Zuckerman, D. M. Gray, J. Bruchez, M. Lidke, K. Vu, T. Q. 2019-06-02 doi:10.1101/654988 Cold Spring Harbor Laboratory Press 2019-06-02 <![CDATA[ Affective Pavlovian motivation is enhanced in obesity susceptible populations; implications for incentive motivation in obesity ]]> https://biorxiv.org/content/10.1101/657833v1?rss=1 Derman, R. C. Ferrario, C. 2019-06-02 doi:10.1101/657833 Cold Spring Harbor Laboratory Press 2019-06-02 <![CDATA[ A distinct neutrophil population invades the central nervous system during pancreatic cancer ]]> https://biorxiv.org/content/10.1101/659060v1?rss=1 Burfeind, K. G. Zhu, X. Norgard, M. A. Levasseur, P. R. Olson, B. Michaelis, K. A. Torres, E. R. S. Jeng, S. McWeeney, S. Raber, J. Marks, D. L. 2019-06-03 doi:10.1101/659060 Cold Spring Harbor Laboratory Press 2019-06-03 <![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[ Burden of tumor mutations, neoepitopes, and other variants are cautionary predictors of cancer immunotherapy response and overall survival ]]> https://biorxiv.org/content/10.1101/665026v1?rss=1 Wood, M. A. Weeder, B. R. David, J. K. Nellore, A. Thompson, R. F. 2019-06-08 doi:10.1101/665026 Cold Spring Harbor Laboratory Press 2019-06-08 <![CDATA[ The Eya1 phosphatase mediates Shh-driven symmetric cell division of cerebellar granule cell precursors ]]> https://biorxiv.org/content/10.1101/668277v1?rss=1 Merk, D. J. Zhou, P. Cohen, S. M. Pazyra-Murphy, M. F. Hwang, G. H. Rehm, K. J. Alfaro, J. Zhao, X. Park, E. Xu, P.-X. Chan, J. A. Eck, M. J. Nazemi, K. J. Segal, R. A. 2019-06-11 doi:10.1101/668277 Cold Spring Harbor Laboratory Press 2019-06-11 <![CDATA[ Extensive Evaluation of Weighted Ensemble Strategies for Calculating Rate Constants and Binding Affinities of Molecular Association/Dissociation Processes ]]> https://biorxiv.org/content/10.1101/671172v1?rss=1 Pratt, A. Suarez, E. Zuckerman, D. Chong, L. 2019-06-14 doi:10.1101/671172 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ How to build a fast and highly sensitive sound detector that remains robust to temperature shifts ]]> https://biorxiv.org/content/10.1101/673186v1?rss=1 Chen, M. von Gersdorff, H. 2019-06-16 doi:10.1101/673186 Cold Spring Harbor Laboratory Press 2019-06-16 <![CDATA[ Does Sex Modify an Association of Electrophysiological Substrate with Sudden Cardiac Death? The Atherosclerosis Risk in Communities (ARIC) Study ]]> https://biorxiv.org/content/10.1101/674689v1?rss=1 Howell, S. German, D. Bender, A. Phan, F. Mukundan, S. Perez-Alday, E. Rogovoy, N. Haq, K. Yang, K. Wirth, A. Jensen, K. Tereshchenko, L. G. 2019-06-21 doi:10.1101/674689 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ A workflow for visualizing human cancer biopsies using large-format electron microscopy ]]> https://biorxiv.org/content/10.1101/675371v1?rss=1 Riesterer, J. L. Lopez, C. S. Stempinski, E. S. Williams, M. Loftis, K. Stoltz, K. Thibault, G. Lanicault, C. Williams, T. Gray, J. W. 2019-06-19 doi:10.1101/675371 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Host mucin is subverted by Pseudomonas aeruginosa during infection to provide free glycans required for successful colonization ]]> https://biorxiv.org/content/10.1101/675538v1?rss=1 Hoffman, C. L. Aballay, A. 2019-06-20 doi:10.1101/675538 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ Using a bar-coded AAV capsid library to select for novel clinically relevant gene therapy vectors ]]> https://biorxiv.org/content/10.1101/683672v1?rss=1 Pekrun, K. De Alencastro, G. Luo, Q.-J. Kim, Y. Nygaard, S. Galivo, F. Zhang, F. Song, R. Tiffany, M. Xu, J. Hebron, M. Grompe, M. Kay, M. A. 2019-06-27 doi:10.1101/683672 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Should virus capsids assemble perfectly? A simple equilibrium model for defects ]]> https://biorxiv.org/content/10.1101/684563v1?rss=1 Spiriti, J. Conway, J. Zuckerman, D. M. 2019-06-27 doi:10.1101/684563 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ α2δ-2 protein controls structure and function at the cerebellar climbing fiber synapse ]]> https://biorxiv.org/content/10.1101/685818v1?rss=1 Beeson, K. A. Beeson, R. Westbrook, G. L. Schnell, E. 2019-06-28 doi:10.1101/685818 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ What is that molecular machine really doing? Automated exploration of alternative transporter mechanisms ]]> https://biorxiv.org/content/10.1101/685933v1?rss=1 George, A. Bisignano, P. Rosenberg, J. Grabe, M. Zuckerman, D. M. 2019-06-28 doi:10.1101/685933 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ ELQ-331 as a prototype for extremely durable chemoprotection against malaria ]]> https://biorxiv.org/content/10.1101/687756v1?rss=1 Smilkstein, M. J. Pou, S. Krollenbrock, A. Bleyle, L. A. Dodean, R. A. Frueh, L. Hinrichs, D. J. Li, Y. Martinson, T. Munar, M. Y. Winter, R. W. Bruzual, I. Whiteside, S. Nilsen, A. Koop, D. R. Kelly, J. X. Kappe, S. H. I. Wilder, B. K. Riscoe, M. K. 2019-07-02 doi:10.1101/687756 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Dendritic speeding of synaptic potentials in an auditory brainstem principal neuron ]]> https://biorxiv.org/content/10.1101/688309v1?rss=1 Srinivasan, G. Dagostin, A. Leao, R. N. Balakrishnan, V. Holcomb, P. Jackson, D. Spirou, G. von Gersdorff, H. 2019-07-02 doi:10.1101/688309 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Predicting Primary Site of Secondary Liver Cancer with a Neural Estimator of Metastatic Origin (NEMO) ]]> https://biorxiv.org/content/10.1101/689828v1?rss=1 Schau, G. F. Burlingame, E. A. Thibault, G. Anekpuritanang, T. Wang, Y. Gray, J. W. Corless, C. Chang, Y. H. 2019-07-02 doi:10.1101/689828 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Restructuring of amygdala subregion apportion across adolescence ]]> https://biorxiv.org/content/10.1101/690875v1?rss=1 Campbell, C. E. Mezher, A. F. Eckel, S. P. Tyszka, J. M. Pauli, W. M. Nagel, B. J. Herting, M. M. 2019-07-09 doi:10.1101/690875 Cold Spring Harbor Laboratory Press 2019-07-09 <![CDATA[ Individual Variation in Control Network Topography Supports Executive Function in Youth ]]> https://biorxiv.org/content/10.1101/694489v1?rss=1 Cui, Z. Li, H. Xia, C. H. Larsen, B. Adebimpe, A. Baum, G. L. Cieslak, M. Gur, R. E. Gur, R. C. Moore, T. M. Oathes, D. J. Alexander-Bloch, A. F. Raznahan, A. Roalf, D. R. Shinohara, R. T. Wolf, D. H. Davatzikos, C. Bassett, D. S. Fair, D. A. Fan, Y. Satterthwaite, T. D. 2019-07-08 doi:10.1101/694489 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Alternative Splicing of MR1 regulates antigen presentation to MAIT cells ]]> https://biorxiv.org/content/10.1101/695296v1?rss=1 Narayanan, G. A. Nellore, A. Tran, J. Worley, A. H. Meermeier, E. W. Karamooz, E. Huber, M. Kurapova, R. Tafesse, F. Harriff, M. J. Lewinsohn, D. M. 2019-07-11 doi:10.1101/695296 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Effects of hM4Di activation in CamKII basolateral amygdala neurons and CNO treatment on Sensory-Specific vs. General-PIT; refining PIT circuits and considerations for using CNO. ]]> https://biorxiv.org/content/10.1101/700120v1?rss=1 Derman, R. C. Bass, C. E. Ferrario, C. 2019-07-14 doi:10.1101/700120 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ Trace amine-associated receptor gene polymorphism increases drug craving ]]> https://biorxiv.org/content/10.1101/703256v1?rss=1 Loftis, J. M. Lasarev, M. Shi, X. Lapidus, J. Janowsky, A. Hoffman, W. Huckans, M. 2019-07-15 doi:10.1101/703256 Cold Spring Harbor Laboratory Press 2019-07-15 <![CDATA[ Acidic fibroblast growth factor underlies microenvironmental regulation of MYC in pancreatic cancer ]]> https://biorxiv.org/content/10.1101/709261v1?rss=1 Bhattacharyya, S. Oon, C. Kothari, A. Horton, W. Link, J. Sears, R. C. Sherman, M. H. 2019-07-22 doi:10.1101/709261 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ BET inhibition induces an anti-apoptotic adaptive response and therapeutic vulnerability to MCL1 inhibitors in breast cancer ]]> https://biorxiv.org/content/10.1101/711895v1?rss=1 30%) and gains (>50%) in basal-like breast cancers suggests that BET and MCL1 co-inhibition may have therapeutic utility in this aggressive subtype. ]]> Yan, G. Wang, H. Luna, A. Bozorgui, B. Li, X. Dereli, Z. Chen, X. Lu, Y. Babur, O. Sander, C. Mills, G. Korkut, A. 2019-07-23 doi:10.1101/711895 Cold Spring Harbor Laboratory Press 2019-07-23 <![CDATA[ Myelin and nodal plasticity modulate action potential conduction in the adult mouse brain ]]> https://biorxiv.org/content/10.1101/726760v1?rss=1 Cullen, C. L. Pepper, R. E. Clutterbuck, M. T. Pitman, K. A. Oorschot, V. Auderset, L. Tang, A. D. Ramm, G. Emery, B. Rodger, J. Jolivet, R. B. Young, K. M. 2019-08-06 doi:10.1101/726760 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ Single-cell proteomics reveals downregulation of TMSB4X to drive actin release for stereocilia assembly ]]> https://biorxiv.org/content/10.1101/727412v1?rss=1 Zhu, Y. Scheibinger, M. Ellwanger, D. C. Krey, J. F. Choi, D. Kelly, R. T. Heller, S. Barr-Gillespie, P. G. 2019-08-06 doi:10.1101/727412 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ Structured Reviews for Data and Knowledge Driven Research ]]> https://biorxiv.org/content/10.1101/729475v1?rss=1 Queralt-Rosinach, N. Stupp, G. S. Li, T. S. Mayers, M. Hoatlin, M. E. Might, M. Good, B. M. Su, A. I. 2019-08-12 doi:10.1101/729475 Cold Spring Harbor Laboratory Press 2019-08-12 <![CDATA[ SHIFT: speedy histological-to-immunofluorescent translation of whole slide images enabled by deep learning ]]> https://biorxiv.org/content/10.1101/730309v1?rss=1 Burlingame, E. A. McDonnell, M. Schau, G. F. Thibault, G. Lanciault, C. Morgan, T. Johnson, B. E. Corless, C. Gray, J. W. Chang, Y. H. 2019-08-15 doi:10.1101/730309 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Mechanotransduction-dependent control of stereocilia dimensions and row identity in inner hair cells ]]> https://biorxiv.org/content/10.1101/731455v1?rss=1 Krey, J. F. Chatterjee, P. Dumont, R. A. Choi, D. Bird, J. E. Barr-Gillespie, P. G. 2019-08-13 doi:10.1101/731455 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6. ]]> https://biorxiv.org/content/10.1101/732784v1?rss=1 200 kb), lacking splicing of the transcripts, lacking polyadenylation, and being retained in the nucleus on the chromosomes where they are made. ASAR6 and ASAR15 also have the unusual property of being expressed from only one copy of the two genes located on homologous chromosome pairs. Using these unusual characteristics shared between ASAR6 and ASAR15, we have identified a second ASAR lncRNA gene located on human chromosome 6, which we have named ASAR6-141. ASAR6-141 is expressed from the opposite chromosome 6 homolog as ASAR6, and disruption of the expressed allele results in delayed replication of chromosome 6. ASAR6-141 RNA had previously been annotated as vlinc273. The very long intergenic non-coding (vlinc)RNAs represent a recently annotated class of RNAs that are long (>50 kb), non-spliced, and non-polyadenlyated nuclear RNAs. There are currently >2,700 vlincRNAs expressed from every chromosome, are encoded by >15% of the human genome, and with a few exceptions have no known function. Our results suggest the intriguing possibility that the vlinc class of RNAs may be functioning to control the replication timing program of all human chromosomes. ]]> Heskett, M. B. Smith, L. Spellman, P. Thayer, M. J. 2019-08-12 doi:10.1101/732784 Cold Spring Harbor Laboratory Press 2019-08-12 <![CDATA[ Streaming of repeated noise in primary and secondary fields of auditory cortex ]]> https://biorxiv.org/content/10.1101/738583v1?rss=1 Saderi, D. Buran, B. N. David, S. V. 2019-08-19 doi:10.1101/738583 Cold Spring Harbor Laboratory Press 2019-08-19 <![CDATA[ The tooth on-a-chip: a microphysiologic model system mimicking the pulp-dentin interface and its interaction with biomaterials ]]> https://biorxiv.org/content/10.1101/748053v1?rss=1 SB>PA (p<0.05), and cells presented consistently higher metabolic activity on-chip than off-chip (p<0.05). Furthermore, the tooth-on-a-chip enabled real-time tracking of odontoblast monolayer formation, remodeling, and death in response to biomaterial treatments, and gelatinolytic activity in a model hybrid layer (HL) formed in the microdevice. In conclusion, the tooth-on-a-chip is a novel platform that replicates near-physiologic conditions of the pulp-dentin interface, and enables live-cell imaging to study dental pulp cell response to biomaterials. ]]> Miranda Franca, C. Tahayeri, A. Sousa Rodrigues, N. Fedorsian, S. Puppin-Rontani, R. Ferracane, J. Bertassoni, L. E. 2019-08-28 doi:10.1101/748053 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ Defective cell death of distinct microglial subsets contributes to ADHD-like behavior in mice ]]> https://biorxiv.org/content/10.1101/749390v1?rss=1 Chuang, H.-C. Nichols, E. K. Rauch, I. Chang, W.-C. Misra, R. Lin, P. M. Kitaoka, M. Vance, R. E. Saijo, K. 2019-08-30 doi:10.1101/749390 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ Putatively cancer-specific alternative splicing is shared across patients and present in developmental and other non-cancer cells ]]> https://biorxiv.org/content/10.1101/754044v1?rss=1 David, J. K. Maden, S. K. Weeder, B. R. Thompson, R. F. Nellore, A. 2019-09-05 doi:10.1101/754044 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Co-option of the gibbon-specific LAVA retrotransposon in DNA repair pathways ]]> https://biorxiv.org/content/10.1101/765230v1?rss=1 Okhovat, M. Nevonen, K. A. Davis, B. Michener, P. Ward, S. Milhaven, M. Harshman, L. Sohota, A. O'Neill, R. J. Ahituv, N. Veeramah, K. R. Carbone, L. 2019-09-11 doi:10.1101/765230 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ New mutant mouse models clarify the role of NAIPs, phosphorylation, NLRP3, and tumors in NLRC4 inflammasome activation ]]> https://biorxiv.org/content/10.1101/765313v1?rss=1 Tenthorey, J. Chavez, R. A. Thompson, T. W. Deets, K. A. Vance, R. E. Rauch, I. 2019-09-18 doi:10.1101/765313 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Estimating The Lateral Margin Of Stability During Walking And Turning Using Inertial Sensors ]]> https://biorxiv.org/content/10.1101/768192v1?rss=1 Fino, P. C. Horak, F. B. Curtze, C. 2019-09-23 doi:10.1101/768192 Cold Spring Harbor Laboratory Press 2019-09-23 <![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[ Exploring Integrative Analysis using the BioMedical Evidence Graph ]]> https://biorxiv.org/content/10.1101/773911v1?rss=1 Struck, A. Walsh, B. Buchanan, A. Lee, J. A. Spangler, R. Stuart, J. Ellrott, K. 2019-09-25 doi:10.1101/773911 Cold Spring Harbor Laboratory Press 2019-09-25 <![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[ Optimizing auditory brainstem response acquisition using interleaved frequencies ]]> https://biorxiv.org/content/10.1101/781831v1?rss=1 Buran, B. N. Elkins, S. Kempton, J. B. Porsov, E. V. Brigande, J. V. David, S. V. 2019-09-25 doi:10.1101/781831 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Systematic profiling of full-length immunoglobulin and T-cell receptor repertoire diversity in rhesus macaque through long read transcriptome sequencing ]]> https://biorxiv.org/content/10.1101/782938v1?rss=1 Brochu, H. Tseng, E. Smith, E. Thomas, M. J. Jones, A. Diveley, K. Law, L. Hansen, S. G. Picker, L. Gale, M. Peng, X. 2019-09-26 doi:10.1101/782938 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Mechanism of gating and partial agonist action in the glycine receptor ]]> https://biorxiv.org/content/10.1101/786632v1?rss=1 Gouaux, E. Yu, J. Zhu, H. Du, J. Lu, W. Tajkhorshid, E. Shahoei, R. Wang, Y. Sivilotti, L. Lape, R. Greiner, T. 2019-09-30 doi:10.1101/786632 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ Pathway Commons: 2019 Update ]]> https://biorxiv.org/content/10.1101/788521v1?rss=1 Rodchenkov, I. Babur, O. Luna, A. Aksoy, B. A. Wong, J. V. Fong, D. Franz, M. Siper, M. C. Cheung, M. Wrana, M. Mistry, H. Mosier, L. Dlin, J. Wen, Q. O'Callaghan, C. Li, W. Elder, G. Smith, P. T. Dallago, C. Cerami, E. Gross, B. E. Dogrusoz, U. Demir, E. Bader, G. Sander, C. 2019-10-01 doi:10.1101/788521 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Long-term alterations in brain and behavior after postnatal Zika virus infections in infant macaques ]]> https://biorxiv.org/content/10.1101/788794v1?rss=1 Raper, J. Kovacs-Balint, Z. Mavinger, M. Gumber, S. Burke, M. W. Habib, J. Mattingly, C. Fair, D. Earl, E. Feczko, E. Styner, M. Jean, S. Cohen, J. Suthar, M. Sanchez, M. M. Alvarado, M. C. Chahroudi, A. 2019-10-01 doi:10.1101/788794 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ RESTORE: Robust intEnSiTy nORmalization mEthod for Multiplexed Imaging ]]> https://biorxiv.org/content/10.1101/792770v1?rss=1 Chang, Y. H. Chin, K. Thibault, G. Eng, J. Grace, L. Gray, J. W. 2019-10-03 doi:10.1101/792770 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ The lhfpl5 ohnologs lhfpl5a and lhfpl5b are required for mechanotransduction in distinct populations of sensory hair cells in zebrafish. ]]> https://biorxiv.org/content/10.1101/793042v1?rss=1 Erickson, T. Pacentine, I. V. Venuto, A. Clemens, R. Nicolson, T. 2019-10-07 doi:10.1101/793042 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Herpes Simplex Virus type 1 Inflammasome Activation in Human Macrophages is Dependent on NLRP3, ASC, and Caspase-1 ]]> https://biorxiv.org/content/10.1101/796235v1?rss=1 Karaba, A. H. Figueroa, A. Massaccesi, G. Botto, S. DeFilippis, V. R. Cox, A. 2019-10-07 doi:10.1101/796235 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Biallelic mutations in M1AP are a frequent cause of meiotic arrest leading to male infertility ]]> https://biorxiv.org/content/10.1101/803346v1?rss=1 Wyrwoll, M. J. Temel, S. G. Nagirnaja, L. Oud, M. S. Lopes, A. M. van der Heijden, G. W. Rotte, N. Wistuba, J. Wöste, M. Ledig, S. Krenz, H. Smits, R. M. Carvalho, F. Goncalves, J. Fietz, D. Türkgenc, B. Ergören, M. C. Cetinkaya, M. Basar, M. Kahraman, S. Pilatz, A. Röpke, A. Dugas, M. Kliesch, S. Neuhaus, N. Aston, K. I. Conrad, D. F. Veltman, J. A. Friedrich, C. Tüttelmann, F. 2019-10-15 doi:10.1101/803346 Cold Spring Harbor Laboratory Press 2019-10-15 <![CDATA[ Broad binaural fusion impairs segregation of speech based on voice pitch differences in a cocktail party environment ]]> https://biorxiv.org/content/10.1101/805309v1?rss=1 Oh, Y. Hartling, C. L. Srinivasan, N. K. Eddolls, M. Diedesch, A. C. Gallun, F. J. Reiss, L. A. J. 2019-10-16 doi:10.1101/805309 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Structural basis for adhesion G protein-coupled receptor Gpr126 function ]]> https://biorxiv.org/content/10.1101/805515v1?rss=1 Leon, K. Cunningham, R. Riback, J. Feldman, E. Li, J. Sosnick, T. Zhao, M. Monk, K. Arac, D. 2019-10-17 doi:10.1101/805515 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Spatially-mapped single-cell chromatin accessibility ]]> https://biorxiv.org/content/10.1101/815720v1?rss=1 Thornton, C. A. Mulqueen, R. M. Torkenczy, K. A. Lowenstein, E. G. Fields, A. J. Steemers, F. J. Wright, K. M. Adey, A. C. 2019-10-22 doi:10.1101/815720 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Multi-region exome sequencing of ovarian teratomas reveals 2N near-diploid genomes, paucity of somatic mutations, and extensive allelic imbalances shared across mature, immature, and disseminated components ]]> https://biorxiv.org/content/10.1101/818534v1?rss=1 Heskett, M. B. Sanborn, J. Z. Boniface, C. Goode, B. Chapman, J. Garg, K. Rabban, J. T. Zaloudek, C. Benz, S. C. Spellman, P. T. Solomon, D. A. Cho, R. J. 2019-10-28 doi:10.1101/818534 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ TGF-β signaling is critical for maintenance of the tendon cell fate ]]> https://biorxiv.org/content/10.1101/823021v1?rss=1 Tan, G.-K. Pryce, B. A. Stabio, A. Brigande, J. V. Wang, C. Xia, Z. Tufa, S. F. Keene, D. R. Schweitzer, R. 2019-10-29 doi:10.1101/823021 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ A cryo-tomography-based volumetric model of the actin core of mouse vestibular hair cell stereocilia lacking plastin 1 ]]> https://biorxiv.org/content/10.1101/825737v1?rss=1 Song, J. Patterson, R. Krey, J. F. Hao, S. Wang, L. Ng, B. Sazzed, S. Kovacs, J. Wriggers, W. He, J. Barr-Gillespie, P. G. Auer, M. G. 2019-10-31 doi:10.1101/825737 Cold Spring Harbor Laboratory Press 2019-10-31 <![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[ B Cell Receptor-Responsive miR-141 and viral miR-BART9 promote Epstein-Barr Virus Reactivation Through FOXO3 Inhibition ]]> https://biorxiv.org/content/10.1101/837294v1?rss=1 Chen, Y. Fachko, D. L. Ivanov, N. S. Skalsky, R. L. 2019-11-10 doi:10.1101/837294 Cold Spring Harbor Laboratory Press 2019-11-10 <![CDATA[ Distinct roles for the Charcot-Marie-Tooth disease-causing endosomal regulators Mtmr5 and Mtmr13 in axon radial sorting and Schwann cell myelination ]]> https://biorxiv.org/content/10.1101/843219v1?rss=1 Mammel, A. E. Delgado, K. C. Chin, A. L. Condon, A. F. Hill, J. Q. Aicher, S. A. Wang, Y. Fedorov, L. M. Robinson, F. L. 2019-11-15 doi:10.1101/843219 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Pharmacological complementation remedies an inborn error of lipid metabolism ]]> https://biorxiv.org/content/10.1101/848119v1?rss=1 Hartley, M. D. Shokat, M. D. DeBell, M. J. Banerji, T. Kirkemo, L. L. Scanlan, T. S. 2019-11-20 doi:10.1101/848119 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Semaphorin 3A induces cytoskeletal paralysis in tumor-specific CD8+ T cells ]]> https://biorxiv.org/content/10.1101/849083v1?rss=1 Barnkob, M. B. Michaels, Y. S. Andre, V. Macklin, P. S. Gileadi, U. Valvo, S. Rei, M. Kulicke, C. Chen, J.-L. Jain, V. Woodcock, V. Colin-York, H. Hadjinicolaou, A. V. Kong, Y. Mayya, V. Bull, J. A. Rijal, P. Pugh, C. W. Townsend, A. Olsen, L. R. Fritzsche, M. Fulga, T. A. Dustin, M. L. Jones, E. Y. Cerundolo, V. 2019-11-20 doi:10.1101/849083 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Head Stabilization During Standing in People with Persisting Symptoms after Mild Traumatic Brain Injury ]]> https://biorxiv.org/content/10.1101/850081v1?rss=1 Fino, P. C. Raffegeau, T. E. Parrington, L. Peterka, R. J. King, L. A. 2019-11-21 doi:10.1101/850081 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Divergent strategies for learning in males and females ]]> https://biorxiv.org/content/10.1101/852830v1?rss=1 Chen, C. S. Ebitz, R. B. Bindas, S. Redish, A. D. Hayden, B. Grissom, N. M. 2019-11-25 doi:10.1101/852830 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Maternal Obesity and Western-style Diet Impair Fetal and Juvenile Offspring Skeletal Muscle Insulin-Stimulated Glucose Transport in Nonhuman Primates ]]> https://biorxiv.org/content/10.1101/864082v1?rss=1 Campodonico-Burnett, W. Hetrick, B. Wesolowski, S. R. Schenk, S. Takahashi, D. L. Dean, T. A. Sullivan, E. L. Kievit, P. Gannon, M. Aagaard-Tillery, K. Friedman, J. E. McCurdy, C. E. 2019-12-03 doi:10.1101/864082 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ Evolution of multifunctionality through a pleiotropic substitution in the innate immune protein S100A9 ]]> https://biorxiv.org/content/10.1101/865493v1?rss=1 Harman, J. L. Loes, A. N. Warren, G. D. Heaphy, M. C. Lampi, K. J. Harms, M. J. 2019-12-05 doi:10.1101/865493 Cold Spring Harbor Laboratory Press 2019-12-05 <![CDATA[ TrpML-mediated astrocyte microdomain Ca2+ transients regulate astrocyte-tracheal interactions in CNS ]]> https://biorxiv.org/content/10.1101/865659v1?rss=1 Ma, Z. Freeman, M. R. 2019-12-08 doi:10.1101/865659 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ Cocaine memory reactivation induces functional adaptations of fast-spiking interneurons in the rat medial prefrontal cortex ]]> https://biorxiv.org/content/10.1101/868299v1?rss=1 Jorgensen, E. T. Gonzalez, A. E. Harkness, J. H. Hegarty, D. M. Burchi, D. J. Aadland, J. A. Aicher, S. A. Sorg, B. A. Brown, T. E. 2019-12-06 doi:10.1101/868299 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Navigating the phenotype frontier: The Monarch Initiative ]]> https://biorxiv.org/content/10.1101/059204v1?rss=1 Julie McMurry Sebastian Kohler James Balhoff Charles Borromeo Matthew Brush Seth Carbon Tom Conlin Nathan Dunn Mark Engelstad Erin Foster Jean-Philippe Gourdine Julius Jacobsen Daniel Keith Bryan Laraway Suzanna Lewis Jeremy Nguyen Xuan Kent Shefchek Nicole Vasilevsky Zhou Yuan Nicole Washington Harry Hochheiser Christopher Mungall Tudor Groza Damian Smedley Peter Robinson Melissa Haendel 2016-06-15 doi:10.1101/059204 Cold Spring Harbor Laboratory Press 2016-06-15 <![CDATA[ Exonic somatic mutations contribute risk for autism spectrum disorder ]]> https://biorxiv.org/content/10.1101/083428v1?rss=1 Krupp, D. R. Barnard, R. A. Duffourd, Y. Evans, S. Bernier, R. Riviere, J.-B. Fombonne, E. O'Roak, B. J. 2016-10-26 doi:10.1101/083428 Cold Spring Harbor Laboratory Press 2016-10-26 <![CDATA[ In vivo imaging of coral tissue and skeleton with optical coherence tomography ]]> https://biorxiv.org/content/10.1101/088682v1?rss=1 Wangpraseurt, D. Wentzel, C. Jacques, S. L. Wagner, M. Kuhl, M. 2016-11-22 doi:10.1101/088682 Cold Spring Harbor Laboratory Press 2016-11-22 <![CDATA[ Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing ]]> https://biorxiv.org/content/10.1101/104844v1?rss=1 Cao, J. Packer, J. S. Ramani, V. Cusanovich, D. A. Huynh, C. Daza, R. Qiu, X. Lee, C. Furlan, S. N. Steemers, F. J. Adey, A. Waterston, R. H. Trapnell, C. Shendure, J. 2017-02-02 doi:10.1101/104844 Cold Spring Harbor Laboratory Press 2017-02-02 <![CDATA[ Delineating the macroscale areal organization of the macaque cortex in vivo ]]> https://biorxiv.org/content/10.1101/155952v1?rss=1 Xu, T. Falchier, A. Sullivan, E. Linn, G. Ramirez, J. Ross, D. Feczko, E. Opitz, A. Bagley, J. Sturgeon, D. Earl, E. Miranda-Domingue, O. Perrone, A. Craddock, C. Schroeder, C. Colcombe, S. Fair, D. Milham, M. 2017-06-26 doi:10.1101/155952 Cold Spring Harbor Laboratory Press 2017-06-26 <![CDATA[ Common Garlic (Allium sativum) has Potent Anti-Bacillus anthracis Activity among Various Commonly Used Spices and Herbs ]]> https://biorxiv.org/content/10.1101/162214v1?rss=1 80% anti-B. anthracis activity retained on incubation at 50{degrees}C for 12 h) and stability in gastric pH range (2-8). It did not antagonize the activity of FDA-approved antibiotics used for anthrax control. GC-MS analysis of the TLC separated bioactive fractions of AGE indicated the presence of previously unreported constituents such as phthalic acid derivatives, acid esters, phenyl group-containing compounds, steroids etc. ConclusionThe Aqueous Garlic Extract (AGE) displayed potent anti-B. anthracis activity. It was better than that displayed by Azadirachta indica A. Juss. (Neem) and Mangifera indica L. while Curcuma longa L. (Turmeric) did not show any activity under the assay conditions used. Further work should be undertaken to explore the possible application of AGE in preventing anthrax incidences in endemic areas. O_FIG O_LINKSMALLFIG WIDTH=161 HEIGHT=200 SRC="FIGDIR/small/162214v3_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@682faaorg.highwire.dtl.DTLVardef@114d64org.highwire.dtl.DTLVardef@1efe980org.highwire.dtl.DTLVardef@1caea0f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kaur, R. Tiwari, A. Manish, M. Maurya, I. K. Bhatnagar, R. Singh, S. 2017-07-11 doi:10.1101/162214 Cold Spring Harbor Laboratory Press 2017-07-11 <![CDATA[ Ocular and uteroplacental pathology in macaque congenital Zika virus infection ]]> https://biorxiv.org/content/10.1101/195701v1?rss=1 Mohr, E. L. Block, L. N. Newman, C. M. Stewart, L. M. Koenig, M. Semler, M. Breitbach, M. E. Teixeira, L. B. C. Zeng, X. Weiler, A. M. Barry, G. L. Thoong, T. H. Wiepz, G. J. Dudley, D. M. Simmons, H. A. Mejia, A. Morgan, T. K. Salamat, M. S. Kohn, S. Antony, K. M. Aliota, M. T. Mohns, M. S. Hayes, J. M. Schultz-Darken, N. Schotzko, M. L. Peterson, E. Capuano, S. Osorio, J. E. O'Connor, S. L. Friedrich, T. C. O'Connor, D. H. Golos, T. G. 2017-09-30 doi:10.1101/195701 Cold Spring Harbor Laboratory Press 2017-09-30 <![CDATA[ Mapping Cortical Brain Asymmetry in 17,141 Healthy Individuals Worldwide via the ENIGMA Consortium ]]> https://biorxiv.org/content/10.1101/196634v1?rss=1 Kong, X.-Z. Mathias, S. Guadalupe, T. Abe, C. Agartz, I. Akudjedu, T. N. Aleman, A. Alhusaini, S. Allen, N. B. Ames, D. Andreassen, O. A. Armstrong, N. J. Bergo, F. Bastin, M. E. Batalla, A. Bauer, J. Baune, B. Baur, R. Biederman, J. Blaine, S. K. Boedhoe, P. Boen, E. Bose, A. Bralten, J. Brandeis, D. Brem, S. Brodaty, H. Bröhl, H. Buitelaar, J. Bürger, C. Bülow, R. Calhoun, V. Calvo, A. Canales-Rodriguez, E. J. Canive, J. M. Cannon, D. M. Caparelli, E. C. Castellanos, F. X. Cavalleri, G. L. Cendes, F. Chaim-Avancini, T. M. Chant 2017-10-01 doi:10.1101/196634 Cold Spring Harbor Laboratory Press 2017-10-01 <![CDATA[ Shotgun Proteomics of non-depleted and depleted hemolymph of human Schistosomiasis snail vector; Biomphalaria glabrata, revealed vital immune related proteins ]]> https://biorxiv.org/content/10.1101/2020.01.12.903708v1?rss=1 Otarigho, B. 2020-01-13 doi:10.1101/2020.01.12.903708 Cold Spring Harbor Laboratory Press 2020-01-13 <![CDATA[ Specificity of Gβ and γ subunits to SNARE complex both at rest and after α2aadrenergic receptor stimulation ]]> https://biorxiv.org/content/10.1101/2020.04.29.065136v1?rss=1 Yim, Y. Y. McDonald, W. H. Betke, K. M. Kaya, A. Hyde, K. Gilsbach, R. Hein, L. Hamm, H. E. 2020-05-01 doi:10.1101/2020.04.29.065136 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ Autoantibody landscape of advanced prostate cancer ]]> https://biorxiv.org/content/10.1101/2020.05.02.074575v1?rss=1 Chen, W. S. Haynes, W. A. Waitz, R. Kamath, K. Vega-Crespo, A. Shrestha, R. Foye, A. Baselga Carretero, I. Zhang, M. Zhao, S. G. Sjostrom, M. Quigley, D. A. Chou, J. Beer, T. Rettig, M. Gleave, M. Evans, C. Lara, P. Chi, K. N. Reiter, R. E. Alumkal, J. J. Aggarwal, R. Small, E. J. Daugherty, P. S. Ribas, A. Oh, D. Y. Shon, J. C. Feng, F. Y. 2020-05-03 doi:10.1101/2020.05.02.074575 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ Rod signals are routed through specific Off cone bipolar cells in primate retina ]]> https://biorxiv.org/content/10.1101/2020.05.17.100982v1?rss=1 McLaughlin, A. J. Percival, K. A. Gayet-Primo, J. Puthussery, T. 2020-05-19 doi:10.1101/2020.05.17.100982 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ FREQUENT GENE CONVERSION IN HUMAN EMBRYOS INDUCED BY DOUBLE STRAND BREAKS ]]> https://biorxiv.org/content/10.1101/2020.06.19.162214v1?rss=1 Mitalipov, S. 2020-06-20 doi:10.1101/2020.06.19.162214 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ The ITS region provides a reliable DNA barcode for identifying reishi/lingzhi (Ganoderma) from herbal supplements ]]> https://biorxiv.org/content/10.1101/2020.07.15.204073v1?rss=1 Whittall, J. B. McFerrin, J. Creswell, M. Gunnels, T. 2020-07-15 doi:10.1101/2020.07.15.204073 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ Rcn3 is Involved in Postnatal Tendon Development by Regulating Collagen Modification and Fibrillogenesis ]]> https://biorxiv.org/content/10.1101/2020.09.25.313098v1?rss=1 Park, N. R. Shetye, S. Keene, D. R. Tufa, S. Hudson, D. M. Archer, M. Soslowsky, L. J. Dyment, N. A. Joeng, K. S. 2020-09-25 doi:10.1101/2020.09.25.313098 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms ]]> https://biorxiv.org/content/10.1101/2020.10.26.356014v1?rss=1 Ostaszewski, M. Niarakis, A. Mazein, A. Kuperstein, I. Phair, R. Orta-Resendiz, A. Singh, V. Aghamiri, S. S. Acencio, M. L. Glaab, E. Ruepp, A. Fobo, G. Montrone, C. Brauner, B. Frishman, G. Monraz Gomez, L. C. Somers, J. Hoch, M. Gupta, S. K. Scheel, J. Borlinghaus, H. Czauderna, T. Schreiber, F. Montagud, A. Ponce de Leon, M. Funahashi, A. Hiki, Y. Hiroi, N. Yamada, T. G. Drager, A. Renz, A. Naveez, M. Bocskei, Z. Messina, F. Bornigen, D. Fergusson, L. Conti, M. Rameil, M. Nakonecnij, V. Vanhoefer, J. Schmiester, L. Wang, M. Ackerman, E. E. Shoemake 2020-10-28 doi:10.1101/2020.10.26.356014 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Benchmarking DNA isolation kits used in analyses of the urinary microbiome ]]> https://biorxiv.org/content/10.1101/2020.11.10.375279v1?rss=1 Karstens, L. Siddiqui, N. Y. Zaza, T. Barstad, A. Amundsen, C. L. Sysoeva, T. A. 2020-11-10 doi:10.1101/2020.11.10.375279 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ Cas12a-Capture: a novel, low-cost, and scalable method for targeted sequencing ]]> https://biorxiv.org/content/10.1101/2020.11.18.388876v1?rss=1 Mighell, T. L. Nishida, A. O'Connell, B. L. Miller, C. V. Grindstaff, S. Thornton, C. A. Adey, A. C. Doherty, D. O'Roak, B. J. 2020-11-20 doi:10.1101/2020.11.18.388876 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Thyroid hormone and thyromimetics inhibit myelin and axonal degeneration and oligodendrocyte loss in EAE ]]> https://biorxiv.org/content/10.1101/2020.12.20.423638v1?rss=1 Chaudhary, P. Marracci, G. H. Calkins, E. Pocius, E. Bensen, A. L. Scanlan, T. S. Emery, B. Bourdette, D. N. 2020-12-21 doi:10.1101/2020.12.20.423638 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ Common Mechanism of SARS-CoV and SARS-CoV-2 Pathogenesis across Species ]]> https://biorxiv.org/content/10.1101/2021.05.14.444205v1?rss=1 Schafer, A. Gralinski, L. E. Leist, S. R. Winkler, E. S. Hampton, B. K. Mooney, M. A. Jensen, K. L. Graham, R. L. Agnihothram, S. Jeng, S. Chamberlin, S. Bell, T. A. Scobey, D. T. VanBlargan, L. A. Thackray, L. B. Hock, P. Miller, D. R. Shaw, G. D. Pardo Manuel de Villena, F. McWeeney, S. K. Montgomery, S. A. Diamond, M. S. Heise, M. T. Menachery, V. D. Ferris, M. T. Baric, R. S. 2021-05-14 doi:10.1101/2021.05.14.444205 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ Alcohol Use Disrupts Age-Appropriate Cortical Thinning in Adolescence: A Data Driven Approach ]]> https://biorxiv.org/content/10.1101/2021.05.17.444458v1?rss=1 Sun, D. Adduru, V. R. Phillips, R. D. Bouchard, H. C. Sotiras, A. Michael, A. M. Baker, F. C. Tapert, S. F. Brown, S. A. Clark, D. B. Goldston, D. Nooner, K. B. Nagel, B. J. Thompson, W. K. De Bellis, M. Morey, R. A. 2021-05-17 doi:10.1101/2021.05.17.444458 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ recount3: summaries and queries for large-scale RNA-seq expression and splicing ]]> https://biorxiv.org/content/10.1101/2021.05.21.445138v1?rss=1 Wilks, C. Zheng, S. C. Chen, F. Y. Charles, R. Solomon, B. Ling, J. P. Imada, E. L. Zhang, D. Joseph, L. Leek, J. T. Jaffe, A. E. Nellore, A. Collado-Torres, L. Hansen, K. D. Langmead, B. 2021-05-23 doi:10.1101/2021.05.21.445138 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies ]]> https://biorxiv.org/content/10.1101/2021.06.01.446587v1?rss=1 Jackson, R. C. Matentzoglu, N. Overton, J. A. Vita, R. Balhoff, J. P. Buttigieg, P. L. Carbon, S. Courtot, M. Diehl, A. D. Dooley, D. Duncan, W. Harris, N. L. Haendel, M. A. Lewis, S. E. Natale, D. A. Osumi-Sutherland, D. Ruttenberg, A. Schriml, L. M. Smith, B. Stoeckert, C. J. Vasilevsky, N. A. Walls, R. L. Zheng, J. Mungall, C. J. Peters, B. 2021-06-02 doi:10.1101/2021.06.01.446587 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Utilizing proteomics and phosphoproteomics to predict ex vivo drug sensitivity across genetically diverse AML patients ]]> https://biorxiv.org/content/10.1101/2021.06.04.447154v1?rss=1 Gosline, S. J. Tognon, C. Nestor, M. Joshi, S. Modak, R. Damnernsawad, A. Moon, J. Hansen, J. R. Hutchinson-Bunch, C. Gritsenko, M. A. Weitz, K. K. Traer, E. Drucker, B. Agarwal, A. Piehowski, P. McDermott, J. E. Rodland, K. 2021-06-06 doi:10.1101/2021.06.04.447154 Cold Spring Harbor Laboratory Press 2021-06-06 <![CDATA[ Pulsation changes link to impaired glymphatic function in a mouse model of vascular cognitive impairment ]]> https://biorxiv.org/content/10.1101/2021.06.08.447375v1?rss=1 Li, M. Kitamura, A. Beverley, J. Koudelka, J. Duncombe, J. Platt, B. Wiegand, U. K. Carare, R. O. Kalaria, R. N. Iliff, J. J. Horsburgh, K. 2021-06-09 doi:10.1101/2021.06.08.447375 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ Predictors of cognitive impairment in primary age-related tauopathy: an autopsy study ]]> https://biorxiv.org/content/10.1101/2021.06.08.447553v1?rss=1 Iida, M. A. Farrell, K. Walker, J. M. Richardson, T. E. Marx, G. Bryce, C. H. Purohit, D. Ayalon, G. Beach, T. G. Bigio, E. H. Cortes, E. Gearing, M. Haroutunian, V. McMillan, C. T. Lee, E. B. Dickson, D. McKee, A. C. Stein, T. D. Trojanowski, J. Q. Woltjer, R. L. Kovacs, G. G. Kofler, J. K. Kaye, J. White, C. L. Crary, J. F. 2021-06-09 doi:10.1101/2021.06.08.447553 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ A community-based approach to image analysis of cells, tissues and tumors ]]> https://biorxiv.org/content/10.1101/2021.07.22.451363v1?rss=1 CSBC/PS-ON Image Analysis Working Group, Vizcarra, J. C. Burlingame, E. A. Hug, C. B. Goltsev, Y. White, B. S. Tyson, D. R. Sokolov, A. 2021-07-25 doi:10.1101/2021.07.22.451363 Cold Spring Harbor Laboratory Press 2021-07-25 <![CDATA[ Metformin in nucleus accumbens core reduces cue-induced cocaine seeking in male and female rats ]]> https://biorxiv.org/content/10.1101/2021.09.05.458975v1?rss=1 Chan, A. Willard, A. Mulloy, S. Ibrahim, N. Sciaccotta, A. Schonfeld, M. Spencer, S. 2021-09-06 doi:10.1101/2021.09.05.458975 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ OpenMonkeyChallenge: Dataset and Benchmark Challenges for Pose Tracking of Non-human Primates ]]> https://biorxiv.org/content/10.1101/2021.09.08.459549v1?rss=1 Yao, Y. Abhiraj Mohan, A. Bliss-Moreau, E. Coleman, K. Freeman, S. M. Machado, C. J. Raper, J. Zimmermann, J. Hayden, B. Y. Park, H. S. 2021-09-10 doi:10.1101/2021.09.08.459549 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol ]]> https://biorxiv.org/content/10.1101/2021.11.12.468428v1?rss=1 Dommer, A. Casalino, L. Kearns, F. Rosenfeld, M. Wauer, N. Ahn, S.-H. Russo, J. Oliveira, S. Morris, C. Bogetti, A. Trifan, A. Brace, A. Sztain, T. Clyde, A. Ma, H. Chennubhotla, C. Lee, H. Turilli, M. Khalid, S. Tamayo-Mendoza, T. Welborn, M. Christiansen, A. Smith, D. G. A. Qiao, Z. Sirumalla, S. K. O'Connor, M. Manby, F. Anandkumar, A. Hardy, D. Phillips, J. Stern, A. Romero, J. Clark, D. Dorrell, M. Maiden, T. Huang, L. McCalpin, J. Woods, C. Gray, A. Williams, M. Barker, B. Rajapaksha, H. Pitts, R. Gibbs, T. Stone, J. Zuckerman, D. Muholland, 2021-11-15 doi:10.1101/2021.11.12.468428 Cold Spring Harbor Laboratory Press 2021-11-15 <![CDATA[ Overlapping stimulons arising in response to divergent stresses in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2021.12.17.473201v1?rss=1 Wang, H. McElfresh, G. Wijesuriya, N. Podgorny, A. Hecht, A. D. Ray, J. C. J. 2021-12-18 doi:10.1101/2021.12.17.473201 Cold Spring Harbor Laboratory Press 2021-12-18 <![CDATA[ Functional, transcriptional, and microbial shifts associated with healthy pulmonary aging: insights from rhesus macaques ]]> https://biorxiv.org/content/10.1101/2022.02.08.479578v1?rss=1 Rhoades, N. S. Davies, M. Lewis, S. A. Cinco, I. R. Kohama, S. G. Bermudez, L. E. Winthorp, K. L. Fuss, C. Mattison, J. A. Spindel, E. R. Messaoudi, I. 2022-02-10 doi:10.1101/2022.02.08.479578 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ HIV rapidly targets a diverse pool of CD4+ T cells to establish productive and latent infections ]]> https://biorxiv.org/content/10.1101/2022.05.10.491275v1?rss=1 Gantner, P. Buranapraditkun, S. Pagliuzza, A. Dufour, C. Pardons, M. Mitchell, J. L. Kroon, E. Sacdalan, C. Tulmethakaan, N. Pinyakorn, S. Robb, M. L. Phanuphak, N. Ananworanich, J. Hsu, D. Vasan, S. Trautmann, L. Fromentin, R. Chomont, N. 2022-05-10 doi:10.1101/2022.05.10.491275 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Adenosine Reduces Sinoatrial Node Cell AP Firing Rate by uncoupling its Membrane and Calcium Clocks ]]> https://biorxiv.org/content/10.1101/2022.06.20.496874v1?rss=1 100 {micro}M): small stochastic LCRs of the Ca2+ clock failed to self-organize and synchronize to the membrane clock, thus creating a failed attempt to generate an AP resulting in arrhythmia and cessation of AP firing. Thus, the effects of ado to activate G{beta}{gamma} and IKACh, Ado and to activate Gi, suppressing adenylyl cyclase activity, both contribute to the ado-induced increase in the mean APCL and APCL variability by reducing the fidelity of clock coupling and AP firing rate. ]]> Wirth, A. N. Tsutsui, K. Maltsev, V. A. Lakatta, E. G. 2022-06-20 doi:10.1101/2022.06.20.496874 Cold Spring Harbor Laboratory Press 2022-06-20 <![CDATA[ Meta-analysis of metagenomes via machine learning and assembly graphs reveals strain switches in Crohn's disease ]]> https://biorxiv.org/content/10.1101/2022.06.30.498290v1?rss=1 Reiter, T. E. Irber, L. C. Gingrich, A. A. Haynes, D. Pierce-Ward, N. T. Brooks, P. T. Mizutani, Y. Moritz, D. Reidl, F. Willis, A. D. Sullivan, B. D. Brown, C. T. 2022-07-05 doi:10.1101/2022.06.30.498290 Cold Spring Harbor Laboratory Press 2022-07-05 <![CDATA[ An adhesive signaling axis regulates the establishment of the cortical glial scaffold. ]]> https://biorxiv.org/content/10.1101/2022.08.02.502565v1?rss=1 Wong, W. Estep, J. A. Ubina, T. Jahncke, J. N. Wright, K. M. Riccomagno, M. M. 2022-08-05 doi:10.1101/2022.08.02.502565 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Physics-based Deep Learning for Imaging Neuronal Activity via Two-photon and Light Field Microscopy ]]> https://biorxiv.org/content/10.1101/2022.10.11.511633v1?rss=1 Verinaz-Jadan, H. Howe, C. L. Song, P. Lesept, F. Kittler, J. Foust, A. J. Dragotti, P. L. 2022-10-13 doi:10.1101/2022.10.11.511633 Cold Spring Harbor Laboratory Press 2022-10-13 <![CDATA[ A Machine-learning-based Method to Detect Degradation of Motor Control Stability with Applications to Diagnosis of Presymptomatic Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2022.10.17.512460v1?rss=1 Shah, V. V. Jadav, S. Goyal, S. Palanthandalam-Madapusi, H. J. 2022-10-20 doi:10.1101/2022.10.17.512460 Cold Spring Harbor Laboratory Press 2022-10-20 <![CDATA[ Systematic assessment of the contribution of structural variants to inherited retinal diseases ]]> https://biorxiv.org/content/10.1101/2023.01.02.522522v1?rss=1 Wen, S. Wang, M. Qian, X. Li, Y. Wang, K. Choi, J. Pennesi, M. E. Yang, P. Marra, M. Koenekoop, R. K. Lopez, I. Matynia, A. Gorin, M. Sui, R. Yao, F. Goetz, K. Porto, F. B. O. Chen, R. 2023-01-03 doi:10.1101/2023.01.02.522522 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ CXCR6 promotes dermal CD8+ T cell survival and transition to long-term tissue residence ]]> https://biorxiv.org/content/10.1101/2023.02.14.528487v1?rss=1 Heim, T. A. Lin, Z. Steele, M. M. Mudianto, T. Lund, A. W. 2023-02-15 doi:10.1101/2023.02.14.528487 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ The dual role of TonB genes in turnerbactin uptake and carbohydrate utilization in the shipworm symbiont Teredinibacter turnerae ]]> https://biorxiv.org/content/10.1101/2023.02.23.529781v1?rss=1 Naka, H. Haygood, M. G. 2023-02-24 doi:10.1101/2023.02.23.529781 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ BIBSNet: A Deep Learning Baby Image Brain Segmentation Network for MRI Scans ]]> https://biorxiv.org/content/10.1101/2023.03.22.533696v1?rss=1 Hendrickson, T. J. Reiners, P. Moore, L. A. Perrone, A. J. Alexopoulos, D. Lee, E. G. Styner, M. Kardan, O. Chamberlain, T. A. Mummaneni, A. Caldas, H. A. Bower, B. Stoyell, S. Martin, T. Sung, S. Fair, E. Uriarte-Lopez, J. Rueter, A. R. Rosenberg, M. D. Smyser, C. D. Elison, J. T. Graham, A. Fair, D. A. Feczko, E. 2023-03-24 doi:10.1101/2023.03.22.533696 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ An automated statistical technique for counting distinct multiple sclerosis lesions can recover aspects of lesion history and provide relevant disease information ]]> https://biorxiv.org/content/10.1101/212860v1?rss=1 .40). Reliability was determined using 14 scans of a clinically stable subject acquired at 7 sites, and variability of lesion count was equivalent to that of lesion load. Accounting for lesion load and age, lesion count was negatively associated (t58 = -2.73, p < .01) with the Expanded Disability Status Scale (EDSS). Average lesion size had a higher association with EDSS (r =.35, p < .01) than lesion load (r = .10, p > .40) or lesion count (r = -.12, p > .30) alone.nnConclusionThese findings demonstrate that it is possible to recover important aspects of the natural history of lesion formation without longitudinal data, and suggest that lesion size provides complementary information about disease.nnGrant SupportThe project described was supported in part by the NIH grants R01 NS085211, R21 NS093349, and R01 NS094456 from the National Institute of Neurological Disorders and Stroke (NINDS). The study was also supported by the Intramural Research Program of NINDS and the Race to Erase MS Foundation. The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies. ]]> Dworkin, J. D. Linn, K. A. Oguz, I. Fleishman, G. M. Bakshi, R. Nair, G. Calabresi, P. A. Henry, R. G. Oh, J. Papinutto, N. Pelletier, D. Rooney, W. Stern, W. Sicotte, N. L. Reich, D. S. Shinohara, R. T. 2017-11-01 doi:10.1101/212860 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Combining accurate tumour genome simulation with crowd sourcing to benchmark somatic structural variant detection ]]> https://biorxiv.org/content/10.1101/224733v1?rss=1 Lee, A. Y.-W. Ewing, A. D. Ellrott, K. Hu, Y. Houlahan, K. E. Bare, J. C. Espiritu, S. M. G. Huang, V. Dang, K. Chong, Z. Caloian, C. Yamaguchi, T. N. ICGC-TCGA DREAM Somatic Mutation Calling Challenge, Kellen, M. R. Chen, K. Norman, T. C. Friend, S. H. Guinney, J. Stolovitzky, G. Haussler, D. Margolin, A. A. Stuart, J. M. Boutros, P. C. 2017-11-25 doi:10.1101/224733 Cold Spring Harbor Laboratory Press 2017-11-25 <![CDATA[ Teaching data science fundamentals through realistic synthetic clinical cardiovascular data ]]> https://biorxiv.org/content/10.1101/232611v1?rss=1 Laderas, T. Vasilevsky, N. Pederson, B. Haendel, M. McWeeney, S. Dorr, D. 2017-12-12 doi:10.1101/232611 Cold Spring Harbor Laboratory Press 2017-12-12 <![CDATA[ Valection: Design Optimization for Validation and Verification Studies ]]> https://biorxiv.org/content/10.1101/254839v1?rss=1 Cooper, C. I. Yao, D. Sendorek, D. H. Yamaguchi, T. N. P'ng, C. Houlahan, K. E. Caloian, C. Fraser, M. SMC-DNA Challenge Participants, Ellrott, K. Margolin, A. A. Bristow, R. G. Stuart, J. M. Boutros, P. C. 2018-01-28 doi:10.1101/254839 Cold Spring Harbor Laboratory Press 2018-01-28 <![CDATA[ Individual differences in functional brain connectivity predict temporal discounting preference in the transition to adolescence ]]> https://biorxiv.org/content/10.1101/255679v1?rss=1 Anandakumar, J. Mills, K. Earl, E. Irwin, L. Miranda-Dominguez, O. Demeter, D. V. Walton-Weston, A. Karalunas, S. Nigg, J. Fair, D. A. 2018-01-29 doi:10.1101/255679 Cold Spring Harbor Laboratory Press 2018-01-29 <![CDATA[ Small effect size leads to reproducibility failure in resting-state fMRI studies ]]> https://biorxiv.org/content/10.1101/285171v1?rss=1 Jia, X.-Z. Zhao, N. Barton, B. Burciu, R. Carriere, N. Cerasa, A. Chen, B.-Y. Chen, J. Coombes, S. Defebvre, L. Delmaire, C. Dujardin, K. Esposito, F. Fan, G.-G. Federica, D. N. Feng, Y.-X. Fling, B. W. Garg, S. Gilat, M. Gorges, M. Ho, S.-L. Horak, F. B. Hu, X. Hu, X.-F. Huang, B. Huang, P.-Y. Jia, Z.-J. Jones, C. Kassubek, J. Krajcovicova, L. Kurani, A. Li, J. Li, Q. Liu, A.-P. Liu, B. Liu, H. Liu, W.-G. Lopes, R. Lou, Y.-T. Luo, W. Madhyastha, T. Mao, N.-N. McAlonan, G. McKeown, M. J. Pang, S. Y. Quattrone, A. Rektorova, I. Sarica, A. Shang, H 2018-03-20 doi:10.1101/285171 Cold Spring Harbor Laboratory Press 2018-03-20 <![CDATA[ Divergent gene expression among phytoplankton taxa in response to upwelling ]]> https://biorxiv.org/content/10.1101/286138v1?rss=1 Lampe, R. H. Cohen, N. R. Ellis, K. A. Bruland, K. W. Maldonado, M. T. Peterson, T. D. Till, C. P. Brzezinski, M. A. Bargu, S. Thamatrakoln, K. Kuzminov, F. I. Twining, B. S. Marchetti, A. 2018-03-23 doi:10.1101/286138 Cold Spring Harbor Laboratory Press 2018-03-23 <![CDATA[ Sorting Nexin 27 (SNX27): A Novel Regulator of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Trafficking ]]> https://biorxiv.org/content/10.1101/304717v1?rss=1 McDermott, M. I. Thelin, W. R. Chen, Y. Lyons, P. T. Reilly, G. Gentzsch, M. Lei, C. Hong, W. Stutts, M. J. Playford, M. P. Bankaitis, V. A. 2018-04-19 doi:10.1101/304717 Cold Spring Harbor Laboratory Press 2018-04-19 <![CDATA[ Transmembrane Protein 135 (TMEM135) is a Liver X Receptor Target Gene that Mediates an Auxiliary Peroxisome Matrix Protein Import Pathway ]]> https://biorxiv.org/content/10.1101/334979v1?rss=1 Renquist, B. J. Madanayake, T. W. Ghimire, S. Geisler, C. E. Xu, Y. Bogan, R. L. 2018-05-30 doi:10.1101/334979 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ Amyloid β oligomers constrict human capillaries in Alzheimer’s disease via signalling to pericytes ]]> https://biorxiv.org/content/10.1101/357095v1?rss=1 Nortley, R. Mishra, A. Jaunmuktane, Z. Kyrargyri, V. Madry, C. Gong, H. Richard-Loendt, A. Brandner, S. Sethi, H. Attwell, D. 2018-06-27 doi:10.1101/357095 Cold Spring Harbor Laboratory Press 2018-06-27 <![CDATA[ Stochastic Simulation to Visualize Gene Expression and Error Correction in Living Cells ]]> https://biorxiv.org/content/10.1101/418772v1?rss=1 Chen, K. Y. Zuckerman, D. M. Nelson, P. C. 2018-09-15 doi:10.1101/418772 Cold Spring Harbor Laboratory Press 2018-09-15 <![CDATA[ Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease ]]> https://biorxiv.org/content/10.1101/448142v1?rss=1 Moss, J. Magenheim, J. Neiman, D. Zemmour, H. Loyfer, N. Korach, A. Samet, Y. Maoz, M. Druid, H. Arner, P. Fu, K.-Y. Kiss, E. Spalding, K. L. Landesberg, G. Zick, A. Grinshpun, A. Shapiro, A. J. Grompe, M. Dreazan Wittenberg, A. Glaser, B. Shemer, R. Kaplan, T. Dor, Y. 2018-10-20 doi:10.1101/448142 Cold Spring Harbor Laboratory Press 2018-10-20 <![CDATA[ Electron cryo-tomography of vestibular hair-cell stereocilia ]]> https://biorxiv.org/content/10.1101/496513v1?rss=1 Metlagel, Z. Krey, J. F. Song, J. Swift, M. F. Tivol, W. J. Dumont, R. A. Thai, J. Chang, A. Seifikar, H. Volkmann, N. Hanein, D. Barr-Gillespie, P. G. Auer, M. 2018-12-13 doi:10.1101/496513 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ HLA alleles associated with risk of ankylosing spondylitis and rheumatoid arthritis influence the gut microbiome ]]> https://biorxiv.org/content/10.1101/517813v1?rss=1 Asquith, M. Sternes, P. R. Costello, M.-E. Karstens, L. Diamond, S. Martin, T. M. Spector, T. D. le Cao, K.-A. Rosenbaum, J. T. Brown, M. A. 2019-01-11 doi:10.1101/517813 Cold Spring Harbor Laboratory Press 2019-01-11 <![CDATA[ Semantic Integration of Clinical Laboratory Tests from Electronic Health Records for Deep Phenotyping and Biomarker Discovery ]]> https://biorxiv.org/content/10.1101/519231v1?rss=1 Zhang, X. A. Yates, A. Vasilevsky, N. Gourdine, J. Carmody, L. C. Danis, D. Joachimiak, M. P. Ravanmehr, V. Pfaff, E. R. Champion, J. Robasky, K. Xu, H. Fecho, K. Walton, N. A. Zhu, R. Ramsdill, J. Mungall, C. Kohler, S. Haendel, M. A. McDonald, C. Vreeman, D. J. Peden, D. B. Chute, C. G. Robinson, P. N. 2019-01-13 doi:10.1101/519231 Cold Spring Harbor Laboratory Press 2019-01-13 <![CDATA[ Feeling left out or just surprised? Neural correlates of social exclusion and expectancy violations in adolescence ]]> https://biorxiv.org/content/10.1101/524934v1?rss=1 Cheng, T. Vijayakumar, N. Flournoy, J. C. Op de Macks, Z. Peake, S. J. Flannery, J. E. Mobasser, A. Alberti, S. L. Fisher, P. A. Pfeifer, J. H. 2019-01-20 doi:10.1101/524934 Cold Spring Harbor Laboratory Press 2019-01-20 <![CDATA[ Altered structural brain asymmetry in autism spectrum disorder: large-scale analysis via the ENIGMA Consortium ]]> https://biorxiv.org/content/10.1101/570655v1?rss=1 Postema, M. C. van Rooij, D. Anagnostou, E. Arango, C. Auzias, G. Behrmann, M. Filho, G. B. Calderoni, S. Calvo, R. Daly, E. Deruelle, C. Di Martino, A. Dinstein, I. Duran, F. L. S. Durston, S. Ecker, C. Ehrlich, S. Fair, D. Fedor, J. Feng, X. Fitzgerald, J. Floris, D. L. Freitag, C. M. Gallagher, L. Glahn, D. C. Gori, I. Haar, S. Hoekstra, L. Jahansad, N. Jalbrzikowski, M. Janssen, J. King, J. A. Zaro, L. L. Lerch, J. P. Luna, B. Martinho, M. M. McGrath, J. Medland, S. E. Muratori, F. Murphy, C. M. Murphy, D. G. M. O'Hearn, K. Oranje, B. Parellada, 2019-03-09 doi:10.1101/570655 Cold Spring Harbor Laboratory Press 2019-03-09 <![CDATA[ Consensus Machine Learning for Gene Target Selection in Pediatric AML Risk ]]> https://biorxiv.org/content/10.1101/632166v1?rss=1 Smith, J. Maden, S. Lee, D. Buie, R. Peddu, V. Shean, R. Busby, B. 2019-05-10 doi:10.1101/632166 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Somatodendritic HCN channels in hippocampal OLM cells revealed by a convergence of computational models and experiments ]]> https://biorxiv.org/content/10.1101/633941v1?rss=1 Sekulic, V. Lawrence, J. Guet-McCreight, A. Yi, F. Garrett, T. Wang, R. Liu, X. Lopez, Y. Solis-Wheeler, M. Skinner, F. K. 2019-05-13 doi:10.1101/633941 Cold Spring Harbor Laboratory Press 2019-05-13 <![CDATA[ Pseudomonas isolates degrade and form biofilms on polyethylene terephthalate (PET) plastic ]]> https://biorxiv.org/content/10.1101/647321v1?rss=1 Vague, M. Chan, G. Roberts, C. Swartz, N. Mellies, J. 2019-05-24 doi:10.1101/647321 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Cross-species Functional Alignment Reveals Evolutionary Hierarchy Within the Connectome ]]> https://biorxiv.org/content/10.1101/692616v1?rss=1 Xu, T. Nenning, K.-H. Schwartz, E. Hong, S.-J. Vogelstein, J. T. Fair, D. A. Schroeder, C. E. Margulies, D. S. Smallwood, J. Milham, M. P. Langs, G. 2019-07-04 doi:10.1101/692616 Cold Spring Harbor Laboratory Press 2019-07-04 <![CDATA[ Effective buprenorphine use and tapering strategies: Endorsements and insights by people in recovery from opioid use disorder on a Reddit forum ]]> https://biorxiv.org/content/10.1101/871608v1?rss=1 Graves, R. L. Sarker, A. Al-Garadi, M. A. Yang, Y.-c. Love, J. S. O'Connor, K. Gonzalez-Hernandez, G. Perrone, J. 2019-12-11 doi:10.1101/871608 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ Comprehensively defining cellular specializations for initiating parallel auditory pathways in the mouse cochlear nucleus ]]> https://biorxiv.org/content/10.1101/2023.05.15.539065v1?rss=1 Jing, J. Hu, M. Ngodup, T. Ma, Q. Lau, S. N. N. Ljungberg, C. McGinley, M. J. Trussell, L. O. Jiang, X. 2023-05-15 doi:10.1101/2023.05.15.539065 Cold Spring Harbor Laboratory Press 2023-05-15 <![CDATA[ Recovery of a learned behavior despite partial restoration of neuronal dynamics after chronic inactivation of inhibitory neurons ]]> https://biorxiv.org/content/10.1101/2023.05.17.541057v1?rss=1 Torok, Z. Luebbert, L. Feldman, J. Duffy, A. Nevue, A. Wongso, S. Mello, C. Fairhall, A. Pachter, L. Gonzalez, W. Lois, C. 2023-05-18 doi:10.1101/2023.05.17.541057 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Human Herpesvirus 8 ORF57 protein is able to reduce TDP-43 pathology: Network analysis Identifies Interacting Pathways ]]> https://biorxiv.org/content/10.1101/2023.05.18.540717v1?rss=1 Webber, C. J. Murphy, C. N. Rondon-Ortiz, A. N. van der Spek, S. J. Kelly, E. X. Lampl, N. M. Chiesa, G. Khalil, A. S. Emili, A. Wolozin, B. 2023-05-18 doi:10.1101/2023.05.18.540717 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Transcriptional profiling of mucus production and modification in rhesus macaque endocervical cells under hormonal regulation ]]> https://biorxiv.org/content/10.1101/2023.05.18.541362v1?rss=1 Rapp, K. Wei, S. Roberts, M. Yao, S. Fei, S. Gao, L. Ray, K. Wang, A. Godiah, R. Han, L. 2023-05-18 doi:10.1101/2023.05.18.541362 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Computational modeling of methylation impact of AML drivers reveals new pathways and refines AML risk-stratification ]]> https://biorxiv.org/content/10.1101/2023.05.17.541249v1?rss=1 Gurun, B. Tyner, J. W. Demir, E. Druker, B. J. Spellman, P. T. 2023-05-21 doi:10.1101/2023.05.17.541249 Cold Spring Harbor Laboratory Press 2023-05-21 <![CDATA[ Muscle-specific MEF2D alpha 2 isoform regulates mice exercise capacity, muscle ketolysis, and systemic ketone body availability in mice ]]> https://biorxiv.org/content/10.1101/2023.05.22.540988v1?rss=1 Kumar, S. Xiangnan, G. Mis, B. Iqbal, H. Kumar, S. Besler, J. Xia, Z. Singh, R. K. 2023-05-22 doi:10.1101/2023.05.22.540988 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Accelerated prime-and-trap vaccine regimen in mice using repRNA-based CSP malaria vaccine ]]> https://biorxiv.org/content/10.1101/2023.05.23.541932v1?rss=1 MacMillen, Z. Hatzakis, K. Simpson, A. Shears, M. J. Watson, F. Erasmus, J. Khandhar, A. P. Wilder, B. K. Murphy, S. C. Reed, S. G. Davie, J. W. Avril, M. 2023-05-23 doi:10.1101/2023.05.23.541932 Cold Spring Harbor Laboratory Press 2023-05-23 <![CDATA[ Adaptor protein complex 2 in the orbitofrontal cortexpredicts alcohol use disorder ]]> https://biorxiv.org/content/10.1101/2023.05.28.542637v1?rss=1 Mulholland, P. J. Berto, S. Wilmarth, P. McMahan, C. Ball, L. Woodward, J. 2023-05-30 doi:10.1101/2023.05.28.542637 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ N-glycans show distinct spatial distribution in mouse brain ]]> https://biorxiv.org/content/10.1101/2023.05.30.542954v1?rss=1 Noel, M. Cummings, R. D. Mealer, R. G. 2023-05-31 doi:10.1101/2023.05.30.542954 Cold Spring Harbor Laboratory Press 2023-05-31 <![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[ Small regulatory RNAs are mediators of the Streptococcus mutans SloR regulon ]]> https://biorxiv.org/content/10.1101/2023.06.02.543485v1?rss=1 Drummond, I. Y. DePaolo, A. Krieger, M. Driscoll, H. E. Eckstrom, K. Spatafora, G. A. 2023-06-03 doi:10.1101/2023.06.02.543485 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ Illuminating Dark Proteins using Reactome Pathways ]]> https://biorxiv.org/content/10.1101/2023.06.05.543335v1?rss=1 Brunson, T. Sanati, N. Matthews, L. Haw, R. Beavers, D. Shorser, S. Sevilla, C. Viteri, G. Conley, P. Rothfels, K. Hermjakob, H. Stein, L. D'Eustachio, P. Wu, G. 2023-06-05 doi:10.1101/2023.06.05.543335 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Bacterial mimicry of eukaryotic HECT ubiquitin ligation ]]> https://biorxiv.org/content/10.1101/2023.06.05.543783v1?rss=1 Franklin, T. G. Brzovic, P. S. Pruneda, J. N. 2023-06-05 doi:10.1101/2023.06.05.543783 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Single cell RNA-seq analysis of spinal locomotor circuitry in larval zebrafish ]]> https://biorxiv.org/content/10.1101/2023.06.06.543939v1?rss=1 Kelly, J. J. Wen, H. Brehm, P. 2023-06-07 doi:10.1101/2023.06.06.543939 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Structural basis for flagellin induced NAIP5 activation. ]]> https://biorxiv.org/content/10.1101/2023.06.13.544801v1?rss=1 Zhang, L. Paidimuddala, B. Cao, J. 2023-06-13 doi:10.1101/2023.06.13.544801 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ Sensory context for coding of natural sounds in auditory cortex ]]> https://biorxiv.org/content/10.1101/2023.06.14.544866v1?rss=1 Lopez Espejo, M. David, S. V. 2023-06-14 doi:10.1101/2023.06.14.544866 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ Calcineurin inhibition enhances Caenorhabditis elegans lifespan by defecation defects-mediated calorie restriction and nuclear hormone signaling ]]> https://biorxiv.org/content/10.1101/2023.06.21.545873v1?rss=1 Das, P. Aballay, A. Singh, J. 2023-06-24 doi:10.1101/2023.06.21.545873 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ The Na+ leak channel NALCN controls spontaneous activity and mediates synaptic modulation by α2-adrenergic receptors in auditory neurons ]]> https://biorxiv.org/content/10.1101/2023.06.23.546323v1?rss=1 Ngodup, T. Irie, T. Elkins, S. Trussell, L. O. 2023-06-25 doi:10.1101/2023.06.23.546323 Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ Bats possess the anatomical substrate for a laryngeal motor cortex ]]> https://biorxiv.org/content/10.1101/2023.06.26.546619v1?rss=1 Nevue, A. A. Mello, C. V. Portfors, C. V. 2023-06-26 doi:10.1101/2023.06.26.546619 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Task-specific invariant representation in auditory cortex ]]> https://biorxiv.org/content/10.1101/2023.06.29.547009v1?rss=1 Heller, C. R. Hamersky, G. R. David, S. V. 2023-06-29 doi:10.1101/2023.06.29.547009 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ Tuberculosis susceptibility in genetically diverse mice reveals functional diversity of neutrophils ]]> https://biorxiv.org/content/10.1101/2023.06.29.547125v1?rss=1 Ravesloot-Chavez, M. M. Van Dis, E. Fox, D. Nguyenla, X. H. Rawal, S. L. Ballinger, M. A. Thomas, H. Kotov, D. I. Vance, R. Nachman, M. Stanley, S. 2023-06-30 doi:10.1101/2023.06.29.547125 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample ]]> https://biorxiv.org/content/10.1101/2023.06.30.547175v1?rss=1 Sandoval-Velasco, M. Dudchenko, O. Antonio Rodriguez, J. Perez Estrada, C. Dehasque, M. Fontsere, C. Mak, S. S. T. Plotnikov, V. Khan, R. Weisz, D. Contessoto, V. G. Oliveira Junior, A. B. Kalluchi, A. Omer, A. D. Batra, S. S. Shamim, M. S. Durand, N. C. O'Connell, B. Roca, A. L. Gnirke, A. Garcia-Trevino, I. Coke, R. Flanagan, J. P. Pletch, K. Ruiz-Herrera, A. Lander, E. S. Rowley, M. J. Onuchic, J. N. Dalen, L. Marti-Renom, M. A. Gilbert, M. T. P. Aiden, E. L. 2023-06-30 doi:10.1101/2023.06.30.547175 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Gestational and postnatal age associations for striatal tissue iron deposition in early infancy ]]> https://biorxiv.org/content/10.1101/2023.06.30.547249v1?rss=1 Cabral, L. Calabro, F. Rasmussen, J. Foran, W. Moore, L. A. Graham, A. O'Connor, T. G. Wadhwa, P. D. Entringer, S. Fair, D. Buss, C. Panigrahy, A. Luna, B. 2023-06-30 doi:10.1101/2023.06.30.547249 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Environmental enrichment promotes adaptive responding during tests of behavioral regulation in male heterogeneous stock rats ]]> https://biorxiv.org/content/10.1101/2023.06.30.547228v1?rss=1 Ishiwari, K. King, C. P. Martin, C. D. Tripi, J. A. George, A. M. Lamparelli, A. C. Chitre, A. Polesskaya, O. Richards, J. B. Solberg Woods, L. C. Gancarz, A. Palmer, A. A. Dietz, D. M. Mitchell, S. H. Meyer, P. J. 2023-07-03 doi:10.1101/2023.06.30.547228 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ KRAS-mediated upregulation of CIP2A promotes suppression of PP2A-B56α to initiate pancreatic cancer development ]]> https://biorxiv.org/content/10.1101/2023.07.01.547283v1?rss=1 Tinsley, S. L. Shelley, R. A. Mall, G. K. Chianis, E. R. D. Dhiman, A. Baral, G. Kothandaraman, H. Thoma, M. C. Daniel, C. Lanman, N. A. Pasca di Magliano, M. Narla, G. Solorio, L. Dykhuizen, E. Sears, R. C. Allen-Petersen, B. 2023-07-03 doi:10.1101/2023.07.01.547283 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis ]]> https://biorxiv.org/content/10.1101/2023.07.03.547507v1?rss=1 Inamo, J. Keegan, J. Griffith, A. Ghosh, T. Horisberger, A. Howard, K. Pulford, J. Murzin, E. Hancock, B. Jonsson, A. H. Seifert, J. Feser, M. L. Norris, J. M. Cao, Y. Apruzzese, W. Bridges, S. L. Bykerk, V. Goodman, S. Donlin, L. Firestein, G. S. Perlman, H. Bathon, J. M. Hughes, L. B. Tabechian, D. Filer, A. Pitzalis, C. H. Anolik, J. Moreland, L. Guthridge, J. M. James, J. A. Brenner, M. B. Raychaudhuri, S. Sparks, J. A. The Accelerating Medicines Partnership RA/SLE Network, Holers, V. M. Deane, K. D. Lederer, J. A. Rao, D. A. Zhang, F. 2023-07-04 doi:10.1101/2023.07.03.547507 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ DISCOVERY AND VALIDATION OF GENES DRIVING DRUG-INTAKE AND RELATED BEHAVIORAL TRAITS IN MICE ]]> https://biorxiv.org/content/10.1101/2023.07.09.548280v1?rss=1 Roy, T. Bubier, J. A. Dickson, P. E. Wilcox, T. Ndukum, J. Clark, J. W. Rizzo, S. J. S. Crabbe, J. C. Denegre, J. Svenson, K. L. Braun, R. E. Kumar, V. Murray, S. A. White, J. K. Philip, V. Chesler, E. 2023-07-10 doi:10.1101/2023.07.09.548280 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ sciMET-cap: High-throughput single-cell methylation analysis with a reduced sequencing burden ]]> https://biorxiv.org/content/10.1101/2023.07.12.548718v1?rss=1 Acharya, S. Nichols, R. V. Rylaarsdam, L. E. O'Connell, B. L. Braun, T. P. Adey, A. C. 2023-07-14 doi:10.1101/2023.07.12.548718 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ Cell networks in the mouse liver during partial hepatectomy ]]> https://biorxiv.org/content/10.1101/2023.07.16.549116v1?rss=1 Li, B. Rodrigo-Torres, D. Pelz, C. Innes, B. T. Canaday, P. Chai, S. Zandstra, P. Bader, G. Grompe, M. 2023-07-18 doi:10.1101/2023.07.16.549116 Cold Spring Harbor Laboratory Press 2023-07-18 <![CDATA[ The Brain Electroencephalogram Microdisplay for Precision Neurosurgery ]]> https://biorxiv.org/content/10.1101/2023.07.19.549735v1?rss=1 Tchoe, Y. Wu, T. U, H. S. Roth, D. M. Kim, D. Lee, J. Cleary, D. R. Pizarro, P. Tonsfeldt, K. J. Lee, K. Chen, P. C. Bourhis, A. M. Galton, I. Coughlin, B. Yang, J. C. Paulk, A. C. Halgren, E. Cash, S. S. Dayeh, S. A. 2023-07-21 doi:10.1101/2023.07.19.549735 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ Addressing persistent challenges in digital image analysis of cancerous tissues ]]> https://biorxiv.org/content/10.1101/2023.07.21.548450v1?rss=1 Prabhakaran, S. Yapp, C. Baker, G. J. Beyer, J. Chang, Y. H. Creason, A. L. Krueger, R. Muhlich, J. Patterson, N. H. Sidak, K. Sudar, D. Taylor, A. J. Ternes, L. Troidl, J. Yubin, X. Sokolov, A. Tyson, D. R. Participants of the Cell Imaging Hackathon 2022, 2023-07-24 doi:10.1101/2023.07.21.548450 Cold Spring Harbor Laboratory Press 2023-07-24 <![CDATA[ Systematic analysis of the sphingomyelin synthase family in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.07.25.550547v1?rss=1 Guzman, G. D. Farley, S. E. Kyle, J. E. Bramer, L. Hoeltzl, S. van den Dikkenberg, J. Holthuis, J. C. M. Tafesse, F. 2023-07-25 doi:10.1101/2023.07.25.550547 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Elevated peripheral and nervous system inflammation is associated with decreased short-chain fatty acid levels in Zika-virus infected macaques ]]> https://biorxiv.org/content/10.1101/2023.07.25.550459v1?rss=1 Miller, C. Manuzak, J. Gustin, A. Basting, C. Cheu, R. Schroeder, T. Velez, A. Driscoll, C. Tisoncik-Go, J. Schifanella, L. Hensley-McBain, T. Evandy, C. Smith, E. Bratt, D. Smedley, J. O'Connor, M. Fuller, D. Barouch, D. Gale, M. Klatt, N. R. 2023-07-26 doi:10.1101/2023.07.25.550459 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Calcium-sensitive subthreshold oscillations and electrical coupling in principal cells of mouse dorsal cochlear nucleus ]]> https://biorxiv.org/content/10.1101/2023.07.27.550887v1?rss=1 1.7 mM, due in part to the shunting effect of small-conductance calcium-activated potassium (SK) channels. This effect explains their apparent absence in previous in vitro studies of cochlear nucleus which routinely employed high-Ca2+ extracellular solution. In contrast, oscillations were amplified in reduced Ca2+ solutions, due to relief of suppression by Ca2+ of Na+ channel gating. Our results thus reveal mechanisms for synchronous oscillatory activity in auditory brainstem, suggesting that slow oscillations, and by extension their perceptual effects, may originate at the earliest stages of sensory processing. SIGNIFICANCE STATEMENT (120 words max.)Many studies show that electrical activity in higher brain regions is regulated by brain oscillations. Here we show that such oscillatory activity can arise even in the first levels of auditory processing in the cochlear nucleus of the brainstem (fusiform cells), and is generated not by neural networks but by the biophysical properties of individual neurons. Oscillations are highly sensitive to external Ca2+ due to interplay of multiple ionic conductances. Gap junctions between cells allows for amplification and synchrony of such activity. Oscillations are absent in pre-hearing neurons, suggesting that sound activity might be important for their emergence. We propose that such early-level oscillations may serve to enhance signaling associated with particular environmental stimuli. ]]> Hong, H. Moore, L. A. Apostolides, P. F. Trussell, L. O. 2023-07-28 doi:10.1101/2023.07.27.550887 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Neuronal NPR-15 controls the interplay between molecular and behavioral immune responses through the amphid sensory neuron-intestinal axis in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.07.27.550570v1?rss=1 Otarigho, B. Butts, A. F. Aballay, A. 2023-07-29 doi:10.1101/2023.07.27.550570 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ Enhancing gene transfer to renal tubules and podocytes by context-dependent selection of AAV capsids ]]> https://biorxiv.org/content/10.1101/2023.07.28.548760v1?rss=1 Furusho, T. Adachi, K. Galbraith-Liss, M. Sairavi, A. Das, R. Nakai, H. 2023-07-29 doi:10.1101/2023.07.28.548760 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ Structure of an open KATP channel reveals tandem PIP2 binding sites mediating the Kir6.2 and SUR1 regulatory interface ]]> https://biorxiv.org/content/10.1101/2023.08.01.551546v1?rss=1 Driggers, C. M. Kuo, Y.-Y. Zhu, P. ElSheikh, A. Shyng, S.-L. 2023-08-01 doi:10.1101/2023.08.01.551546 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ Specific configurations of electrical synapses filter sensory information to drive choices in behavior ]]> https://biorxiv.org/content/10.1101/2023.08.01.551556v1?rss=1 Almoril-Porras, A. Calvo, A. Niu, L.-G. Beagan, J. Hawk, J. D. Aljobeh, A. Wisdom, E. Ren, I. Diaz-Garcia, M. Wang, Z.-W. Colon-Ramos, D. 2023-08-03 doi:10.1101/2023.08.01.551556 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ Gbx2 controls amacrine cell dendrite stratification through Robo1/2 receptors ]]> https://biorxiv.org/content/10.1101/2023.08.03.551861v1?rss=1 Kerstein, P. C. Santana Agreda, Y. Curran, B. M. Ma, L. Wright, K. M. 2023-08-04 doi:10.1101/2023.08.03.551861 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ Intrinsic control of DRG sensory neuron diversification by Pten ]]> https://biorxiv.org/content/10.1101/2023.08.04.552039v1?rss=1 Fernandez, A. Sarn, N. Eng, C. Wright, K. M. 2023-08-06 doi:10.1101/2023.08.04.552039 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ A Novel Burn / Synovectomy Mouse Model for Temporomandibular Joint Osteoarthritis ]]> https://biorxiv.org/content/10.1101/2023.08.07.552340v1?rss=1 Hsu, G. C.-Y. 2023-08-08 doi:10.1101/2023.08.07.552340 Cold Spring Harbor Laboratory Press 2023-08-08 <![CDATA[ Thyroid hormone rewires cortical circuits to coordinate body-wide metabolism and exploratory drive ]]> https://biorxiv.org/content/10.1101/2023.08.10.552874v1?rss=1 Hochbaum, D. R. Dubinsky, A. C. Farnsworth, H. C. Hulshof, L. Kleinberg, G. Urke, A. Wang, W. Hakim, R. Robertson, K. Park, C. Solberg, A. Yang, Y. Baynard, C. Nadaf, N. M. Beron, C. Girasole, A. Chantranupong, L. Cortopassi, M. Prouty, S. Geistlinger, L. Banks, A. Scanlan, T. Greenberg, M. Boulting, G. L. Macosko, E. Sabatini, B. L. 2023-08-10 doi:10.1101/2023.08.10.552874 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ Cyclin B3 is a dominant fast-acting cyclin that drives rapid early embryonic mitoses ]]> https://biorxiv.org/content/10.1101/2023.08.11.553011v1?rss=1 Lara-Gonzalez, P. Variyar, S. Budrewicz, J. Schlientz, A. Varshney, N. Bellaart, A. Moghareh, S. Nguyen, A. C. N. Oegema, K. Desai, A. 2023-08-12 doi:10.1101/2023.08.11.553011 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ Cryopreservation of cerebrospinal fluid cells preserves transcriptomics integrity for single-cell analysis ]]> https://biorxiv.org/content/10.1101/2023.08.10.552735v1?rss=1 Kodali, M. C. Antone, J. Alsop, E. Jayakuymar, R. Parikh, K. Sanchez-Molina, P. Ajami, B. Arnold, S. E. Van Keuren-Jensen, K. Das, S. Weinberg, M. S. 2023-08-14 doi:10.1101/2023.08.10.552735 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ TIGIT drives the immunosuppressive environment by downregulation of metalloproteinases MMP2 and MMP14 in perihilar cholangiocarcinoma. ]]> https://biorxiv.org/content/10.1101/2023.08.14.553195v1?rss=1 Heij, L. Reichel, K. de Koning, W. Bednarsch, J. Tan, X. Campello Deierl, J. Clahsen-van Groningen, M. Al-Masri, T. van Dam, R. Garcia Vallejo, J. Ulmer, F. Lang, S. Luedde, T. Rocha, F. Dahl, E. Jonigk, D. Kuehnel, M. Sivakumar, S. Neumann, U. 2023-08-15 doi:10.1101/2023.08.14.553195 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Long-term combination therapy with Metformin and Oxymetholone in a Fanconi Anemia mouse model ]]> https://biorxiv.org/content/10.1101/2023.08.16.553572v1?rss=1 Grompe, M. Dorrell, C. S. Peters, A. M. Zhang, Q. Balaji, N. Mochizuki-Kashio, M. Major, A. Finegold, M. J. Liu, C. Lu, K. 2023-08-16 doi:10.1101/2023.08.16.553572 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ The α-crystallin chaperones undergo a quasi-ordered co-aggregation process in response to saturating client interaction ]]> https://biorxiv.org/content/10.1101/2023.08.15.553435v1?rss=1 Miller, A. P. O'Neill, S. E. Lampi, K. J. Reichow, S. L. 2023-08-17 doi:10.1101/2023.08.15.553435 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Structure of C. elegans TMC-2 complex suggests roles of lipid-mediated subunit contacts in mechanosensory transduction ]]> https://biorxiv.org/content/10.1101/2023.08.16.553618v1?rss=1 Clark, S. Jeong, H. Posert, R. Goehring, A. Gouaux, E. 2023-08-17 doi:10.1101/2023.08.16.553618 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ ESAT-6 undergoes self-association at phagosomal pH and an ESAT-6 specific nanobody restricts M. tuberculosis growth in macrophages ]]> https://biorxiv.org/content/10.1101/2023.08.16.553641v1?rss=1 Bates, T. A. Trank-Greene, M. Nguyenla, X. Anastas, A. Merutka, I. R. Dixon, S. D. Shumate, A. Groncki, A. R. Parson, M. A. Barklis, E. Burke, J. E. Shinde, U. Ploegh, H. L. Tafesse, F. G. 2023-08-17 doi:10.1101/2023.08.16.553641 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Complementary roles of orbitofrontal and prelimbic cortices in adaption of reward motivated actions to learned anxiety. ]]> https://biorxiv.org/content/10.1101/2023.08.17.553761v1?rss=1 Jacobs, D. S. Bogachuk, A. P. Moghaddam, B. 2023-08-17 doi:10.1101/2023.08.17.553761 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Enlarged Perivascular Spaces are Associated with White Matter Injury, Brain Atrophy, Cognitive Decline and Markers of Inflammation in an Autosomal Dominant Vascular Neurodegenerative Disease (CADASIL) ]]> https://biorxiv.org/content/10.1101/2023.08.17.553732v1?rss=1 Karvelas, N. Oh, B. Wang, E. Cobigo, Y. Tsuei, T. Fitzsimons, S. Ehrenberg, A. Geschwind, M. Schwartz, D. Kramer, J. Ferguson, A. R. Miller, B. L. Silbert, L. Rosen, H. Elahi, F. M. 2023-08-19 doi:10.1101/2023.08.17.553732 Cold Spring Harbor Laboratory Press 2023-08-19 <![CDATA[ Multiplex imaging of localized prostate tumors reveals changes in mast cell type composition and spatial organization of AR-positive cells in the tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2023.08.18.553854v1?rss=1 Eksi, S. E. Ak, C. Sayar, Z. Thibault, G. Burlingame, E. Eng, J. Chitsazan, A. Adey, A. Boniface, C. Spellman, P. T. Thomas, G. V. Kopp, R. Demir, E. Chang, Y. H. Stavrinides, V. 2023-08-21 doi:10.1101/2023.08.18.553854 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Improved dual-color GRAB sensors for monitoring dopaminergic activity in vivo ]]> https://biorxiv.org/content/10.1101/2023.08.24.554559v1?rss=1 Zhuo, Y. Luo, B. Yi, X. Dong, H. Wan, J. Cai, R. Williams, J. T. Qian, T. Campbell, M. G. Miao, X. Li, B. Wei, Y. Li, G. Wang, H. Zheng, Y. Watabe-Uchida, M. Li, Y. 2023-08-25 doi:10.1101/2023.08.24.554559 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ Quantitative image analysis pipeline for detecting circulating hybrid cells in immunofluorescence images with human-level accuracy ]]> https://biorxiv.org/content/10.1101/2023.08.24.554733v1?rss=1 50,000) when using conventional enumeration methods. On the other hand, our proposed approach is unbiased to ROI size. The SVM classifier trained on the {beta}-VAE encodings achieved an F1 score of 0.80, matching the average performance of annotators. Our pipeline enables researchers to explore the role of CHCs in cancer progression and assess their potential as a clinical biomarker for metastasis. Further, we demonstrate that the pipeline can identify discrete cellular phenotypes among PBMCs, highlighting its utility beyond CHCs. ]]> Anderson, A. Theison, H. Baik, J. Gibbs, S. Wong, M. H. Chang, Y. H. 2023-08-26 doi:10.1101/2023.08.24.554733 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ Local and dynamic regulation of neuronal glycolysis in vivo ]]> https://biorxiv.org/content/10.1101/2023.08.25.554774v1?rss=1 Wolfe, A. D. Koberstein, J. N. Smith, C. B. Stewart, M. L. Hammarlund, M. Hyman, A. A. Stork, P. J. S. Goodman, R. H. Colon-Ramos, D. A. 2023-08-26 doi:10.1101/2023.08.25.554774 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ Functional subtypes of rodent melanopsin ganglion cells switch roles between night and day illumination. ]]> https://biorxiv.org/content/10.1101/2023.08.26.554902v1?rss=1 Berry, M. H. Leffler, J. Allen, C. N. Sivyer, B. 2023-08-27 doi:10.1101/2023.08.26.554902 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Single-cell analysis of Rohon-Beard neurons implicates Fgf signaling in axon maintenance and cell survival ]]> https://biorxiv.org/content/10.1101/2023.08.26.554953v1?rss=1 nechiporuk, a. Tuttle, A. M. Royer, L. J. Kelly, J. J. Wen, H. Calistri, N. Heiser, L. M. 2023-08-28 doi:10.1101/2023.08.26.554953 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Complete correction of murine phenylketonuria by selection-enhanced hepatocyte transplantation ]]> https://biorxiv.org/content/10.1101/2023.08.27.554228v1?rss=1 Vonada, A. Wakefield, L. Martinez, M. Harding, C. O. Grompe, M. Tiyaboonchai, A. 2023-08-28 doi:10.1101/2023.08.27.554228 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Modulation of riboflavin biosynthesis and utilization in mycobacteria ]]> https://biorxiv.org/content/10.1101/2023.08.30.555301v1?rss=1 Chengalroyen, M. D. Mehaffy, C. Lucas, M. Raphela, M. L. Warner, D. F. Lewinsohn, D. Lewinsohn, D. Dobos, K. Mizrahi, V. 2023-08-30 doi:10.1101/2023.08.30.555301 Cold Spring Harbor Laboratory Press 2023-08-30 <![CDATA[ Lymphatic vessel transit seeds precursors to cytotoxic resident memory T cells in skin draining lymph nodes ]]> https://biorxiv.org/content/10.1101/2023.08.29.555369v1?rss=1 Heim, T. Schultz, A. C. Delclaux, I. Cristaldi, V. Churchill, M. J. Lund, A. W. 2023-08-31 doi:10.1101/2023.08.29.555369 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ A Linkable, Polycarbonate Gut Microbiome-Distal Tumor Chip Platform for Interrogating Cancer Promoting Mechanisms ]]> https://biorxiv.org/content/10.1101/2023.08.31.555803v1?rss=1 Brasino, D. S. Speese, S. D. Schilling, K. Schutt, C. E. Barton, M. C. 2023-09-03 doi:10.1101/2023.08.31.555803 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Human milk extracellular vesicles survive neonatal digestion in vivo to be absorbed by neonatal enteroids ]]> https://biorxiv.org/content/10.1101/2023.09.03.556067v1?rss=1 Zhang, Y. Kuhn, M. Yung, C. Armstrong, R. J. Olyaei, A. Aloia, M. Scottoline, B. Andres, S. F. 2023-09-03 doi:10.1101/2023.09.03.556067 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Normative Birth Weight Variation is Associated with White Matter Connectivity in Full-Term Neonates ]]> https://biorxiv.org/content/10.1101/2023.09.05.556390v1?rss=1 2.5 kg and <4.5 kg) and white matter connectivity in full-term neonates. Further, the main objective includes testing associations between normative birth weight variation and cognitive and language developmental scores at 18 months, and if white matter connectivity that is related to birth weight variation is further associated with cognitive language development. We hypothesized, greater normative birth weight would be associated with higher white matter connectivity controlling for gestational age, particularly in thalamic, inferior frontal, and middle temporal connectivity. Further, we predicted greater connectivity for these tracts would be associated with higher scores for cognitive (thalamic) and language development (inferior and middle temporal) at 18 months of age. DesignThe study was an observational longitudinal design of data from the Developing Human Connectome Project (dHCP). Birth weight was measured at the birth of the child, white matter connectivity was measured as neonates (mean=40.07 weeks, SD=1.14), and cognitive/language outcomes were measured at 18 months of age. SettingThe dHCP data was collected at the Evelina Newborn Imaging Centre, Evalina London Childrens Hospital between 2015 and 2019. ParticipantsA sub-sample of the full dHCP was tested. These participants were full-term neonates with birth weight variation in the normative range (> 2.5 kg and < 4.5 kg). Participants also had to have usable diffusion-weighted imaging data as neonates and cognitive/language developmental assessments collected at 18 months (n=323). Exposure(s)The study participants were all born at full-term and in the normative birth weight range. Main Outcome(s) and Measure(s)The study had two main outcomes: white matter connectivity at the neonatal timepoint and cognitive/language developmental scores at 18 months. White matter connectivity was calculated from diffusion-weighted data for the whole-brain. Cognitive/language developmental scores were measured using the Bayley Scales of Infant and Toddler Development, Third Edition (Bayley-III) at 18 months. ResultsUsing a Network-Based Statistic (NBS) approach, we found widespread associations between normative birth weight variation and white matter connectivity in full-term neonates, primarily in the positive direction for the right middle occipital gyrus and left supplementary motor area. Conclusions and RelevanceWhile investigations have been focused on the extreme ends of the birth weight spectrum, we find evidence that there is a robust association between birth weight and white matter connectivity even within the normative birth weight range. As normative birth weight variation and regions of white matter associated with birth weight were further associated with language development scores at 18 months, our results suggest the birth weight to white matter pathway may be an underlying pathway between birth weights association with language development. Key PointsO_ST_ABSQuestionC_ST_ABSAre variations in normative birth weight associated with white matter connectivity and cognitive/language outcomes in infancy? FindingsGreater normative birth weight is associated with greater white matter organization across a widespread network of connections in the neonatal brain. Greater white matter organization in this network for neonates has a positive prospective with expressive language development at 18 months of age. MeaningEven variations within the normative birth weight range have robust associations with early white matter development and can be prospectively linked to language development. ]]> Dufford, A. J. Dai, W. Scheinost, D. 2023-09-05 doi:10.1101/2023.09.05.556390 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Enriched Single-Nucleus RNA-Sequencing reveals unique attributes of distal convoluted tubule cells ]]> https://biorxiv.org/content/10.1101/2023.09.05.555810v1?rss=1 Su, X.-T. Reyes, J. V. Lackey, A. E. Maeoka, Y. Cornelius, R. J. McCormick, J. A. Yang, C.-L. Jung, H. J. Welling, P. A. Nelson, J. W. Ellison, D. H. 2023-09-06 doi:10.1101/2023.09.05.555810 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ PKA catalytic subunits dissociate from regulatory subunits to regulate neuronal functions ]]> https://biorxiv.org/content/10.1101/2023.09.05.556437v1?rss=1 Xiong, W. Qin, M. Zhong, H. 2023-09-07 doi:10.1101/2023.09.05.556437 Cold Spring Harbor Laboratory Press 2023-09-07 <![CDATA[ Mass spectrometry and split luciferase complementation assays reveal the MecA protein interactome of Streptococcus mutans ]]> https://biorxiv.org/content/10.1101/2023.09.08.556943v1?rss=1 100 distinct protein substrates, most of which function in highly conserved metabolic pathways. The interactome results were independently verified using a newly developed prokaryotic split luciferase complementation assay (SLCA) to detect MecA protein-protein interactions in vivo. In addition, we further develop a new application of SLCA to support in vivo measurements of MecA relative protein binding affinities. SLCA results were independently verified using targeted coimmunoprecipitation assays, suggesting the general utility of this approach for prokaryotic protein-protein interaction studies. Our results indicate that MecA indeed regulates its interactome through both Clp-dependent proteolysis as well as through an as yet undefined proteolysis-independent mechanism that may affect more than half of its protein interactome. This suggests a significant aspect of MecA regulatory function still has yet to be discovered. ]]> Qin, H. Anderson, D. Zou, Z. Higashi, D. Borland, C. Kreth, J. L. Merritt, J. 2023-09-09 doi:10.1101/2023.09.08.556943 Cold Spring Harbor Laboratory Press 2023-09-09 <![CDATA[ Cardiac glycosides restore autophagy flux in an iPSC-derived neuronal model of WDR45 deficiency ]]> https://biorxiv.org/content/10.1101/2023.09.13.556416v1?rss=1 Papandreou, A. Singh, N. Gianfrancesco, L. Budinger, D. Barwick, K. Agrotis, A. Luft, C. Shao, Y. Lenaerts, A.-S. Gregory, A. Jeong, S. Y. Hogarth, P. Hayflick, S. Barral, S. Kriston-Vizi, J. Gissen, P. Kurian, M. A. A. Ketteler, R. 2023-09-13 doi:10.1101/2023.09.13.556416 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Extracellular matrix scaffold-assisted tumor vaccines induce tumor regression and long-term immune memory ]]> https://biorxiv.org/content/10.1101/2023.09.12.557449v1?rss=1 Pal, S. Chaudhari, R. Baurceanu, I. Hill, B. J. Nagy, B. A. Wolf, M. 2023-09-15 doi:10.1101/2023.09.12.557449 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Intracellular K+ limits T cell exhaustion and preserves antitumor function ]]> https://biorxiv.org/content/10.1101/2023.09.13.556997v1?rss=1 Collier, C. Wucherer, K. Mcwhorter, M. Jenkins, C. Bartlett, A. Roychoudhuri, R. Eil, R. 2023-09-15 doi:10.1101/2023.09.13.556997 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Androgen blockade primes NLRP3 in macrophages to induce tumor phagocytosis ]]> https://biorxiv.org/content/10.1101/2023.09.15.557996v1?rss=1 Chaudagar, K. K. Srikrishnan, R. Mei, S. Hirz, T. Hu, Y.-M. Argulian, A. Labadie, B. Desai, K. Grimaldo, S. Kahramangil, D. Nair, R. D Souza, S. Zhou, D. Li, M. Doughan, F. Chen, R. Shafran, J. Loyd, M. Xia, Z. Sykes, D. B. Moran, A. E. Patnaik, A. 2023-09-17 doi:10.1101/2023.09.15.557996 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Fetal Membrane Inflammasome Activation by Choriodecidual Ureaplasma parvum Infection without Intra-Amniotic Infection in an NHP Model ]]> https://biorxiv.org/content/10.1101/2023.09.18.557989v1?rss=1 Tripathy, S. Burd, I. Kelleher, M. A. 2023-09-22 doi:10.1101/2023.09.18.557989 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Leukemic mutation FLT3-ITD is retained in dendritic cells and disrupts their homeostasis leading to expanded Th17 frequency ]]> https://biorxiv.org/content/10.1101/2023.09.19.558512v1?rss=1 Flynn, P. A. Long, M. D. Kosaka, Y. Mulkey, J. S. Coy, J. L. Agarwal, A. Lind, E. F. 2023-09-22 doi:10.1101/2023.09.19.558512 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ The Human Infertility Single-cell Testis Atlas (HISTA): An interactive molecular scRNA-Seq reference of the human testis. ]]> https://biorxiv.org/content/10.1101/2023.09.23.558896v1?rss=1 Mahyari, E. Vigh-Conrad, K. A. Daube, C. Lima, A. C. Guo, J. Carell, D. Hotaling, J. M. Aston, K. I. Conrad, D. 2023-09-24 doi:10.1101/2023.09.23.558896 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ Recurrent activity within microcircuits of macaque dorsolateral prefrontal cortex tracks cognitive flexibility ]]> https://biorxiv.org/content/10.1101/2023.09.23.559125v1?rss=1 Nolan, S. O. Melugin, P. R. Erickson, K. R. Adams, W. R. Farahbakhsh, Z. Z. Mcgonigle, C. E. Kwon, M. H. Costa, V. D. Lapish, C. C. Hackett, T. A. Cuzon Carlson, V. C. Constantinidis, C. Grant, K. A. Siciliano, C. A. 2023-09-24 doi:10.1101/2023.09.23.559125 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ Immune Correlates of Hyperglycemia and Vaccination in a Non-human Primate Model of Long-COVID ]]> https://biorxiv.org/content/10.1101/2023.09.22.559019v1?rss=1 Palmer, C. S. Perdios, C. Abdel-Mohsen, M. Mudd, J. Datta, P. Maness, N. Lehmicke, G. Golden, N. Hellmer, L. Coyne, C. Moore Green, K. Midkiff, C. Williams, K. Tiburcio, R. Fahlberg, M. Boykin, K. Kenway, C. Russell-Lodrigue, K. Bohm, R. Blair, R. V. Dufour, J. Fischer, T. Saied, A. Rappaport, J. 2023-09-25 doi:10.1101/2023.09.22.559019 Cold Spring Harbor Laboratory Press 2023-09-25 <![CDATA[ An enhancer RNA recruits MLL1 to regulate transcription of Myb ]]> https://biorxiv.org/content/10.1101/2023.09.26.559528v1?rss=1 Kim, J. Diaz, L. F. Miller, M. J. Leadem, B. Krivega, I. Dean, A. 2023-09-26 doi:10.1101/2023.09.26.559528 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Dysregulation of astrocyte-secreted pleiotrophin contributes to neuronal structural and functional phenotypes in Down Syndrome ]]> https://biorxiv.org/content/10.1101/2023.09.26.559633v1?rss=1 Brandebura, A. N. Asbell, Q. N. Micael, M. K. B. Allen, N. J. 2023-09-27 doi:10.1101/2023.09.26.559633 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Engineered Lactiplantibacillus plantarum as a Biosensor Probe for the Lungs ]]> https://biorxiv.org/content/10.1101/2023.09.27.559779v1?rss=1 Brasino, M. Wagnell, E. Manalo, E. C. Drennan, S. Fischer, J. M. Merritt, J. 2023-09-27 doi:10.1101/2023.09.27.559779 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Longitudinal and multimodal auditing of tumor adaptation to CDK4/6 inhibitors in HR+ metastatic breast cancers ]]> https://biorxiv.org/content/10.1101/2023.09.27.557464v1?rss=1 Creason, A. L. Egger, J. Watson, C. Sivagnanam, S. Chin, K. MacPherson, K. Lin, J.-R. Chen, Y.-A. Johnson, B. E. Feiler, H. S. Galipeau, D. Navin, N. E. Demir, E. Chang, Y. H. Corless, C. L. Mitri, Z. I. Thomas, G. Sorger, P. K. Adey, A. C. Coussens, L. M. Gray, J. W. Mills, G. B. Goecks, J. 2023-09-29 doi:10.1101/2023.09.27.557464 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ MultipleXed Population Selection and Enrichment single nucleus RNA sequencing (XPoSE-seq) enables sample identity retention during transcriptional profiling of rare populations ]]> https://biorxiv.org/content/10.1101/2023.09.27.559834v1?rss=1 Savell, K. E. Madangopal, R. Saravanan, P. Palaganas, R. G. Woods, K. D. Thompson, D. J. Drake, O. R. Brenner, M. B. Weber, S. J. Van Leer, E. Choi, J. H. Martin, T. L. Martin, J. C. Steinberg, M. K. Austin, J. W. Charendoff, C. I. Hope, B. T. 2023-09-29 doi:10.1101/2023.09.27.559834 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Commensal myeloid crosstalk in neonatal skin regulates long-term cutaneous type 17 inflammation ]]> https://biorxiv.org/content/10.1101/2023.09.29.560039v1?rss=1 Dhariwala, M. O. DeRogatis, A. M. Okoro, J. N. Weckel, A. A. Tran, V. M. Habrylo, I. Ojewumi, O. T. Tammen, A. E. Leech, J. M. Merana, G. R. Carale, R. O. Barrere-Cain, R. Hiam-Galvez, K. J. Spitzer, M. H. Scharschmidt, T. C. 2023-10-02 doi:10.1101/2023.09.29.560039 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Remyelination protects neurons from DLK-mediated neurodegeneration ]]> https://biorxiv.org/content/10.1101/2023.09.30.560267v1?rss=1 Duncan, G. J. Ingram, S. D. Emberley, K. Hill, J. Cordano, C. Abdelhak, A. McCane, M. Jabassini, N. Ananth, K. Ferrara, S. J. Stedelin, B. Aicher, S. A. Watkins, T. A. Mishra, A. Nelson, J. Green, A. J. Emery, B. 2023-10-02 doi:10.1101/2023.09.30.560267 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Microbiome imaging goes à la carte: Incorporating click chemistry into the fluorescence-activating and absorption-shifting tag (FAST) imaging platform ]]> https://biorxiv.org/content/10.1101/2023.10.02.560575v1?rss=1 Anderson, D. M. Logan, M. G. Patty, S. S. Kendall, A. J. Borland, C. Z. Pfeifer, C. S. Kreth, J. Merritt, J. L. 2023-10-02 doi:10.1101/2023.10.02.560575 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Targeting the Hippo pathway in cancers via ubiquitination dependent TEAD degradation ]]> https://biorxiv.org/content/10.1101/2023.10.03.560675v1?rss=1 Pham, T. H. Pahuja, K. B. Hagenbeek, T. J. Zbieg, J. Noland, C. L. Pham, V. C. Yao, X. Rose, C. M. Browder, K. C. Lee, H.-J. Yu, M. Liang-Chu, M. Martin, S. E. Verschueren, E. Li, J. Kubala, M. H. Fong, R. Lorenzo, M. Beroza, P. Hsu, P. Paul, S. Villemure, E. Lee, W. Cheung, T. Clausen, S. Lacap, J. Liang, Y. Cheng, J. Schmidt, S. Modrusan, Z. Cohen, M. S. Crawford, J. Jasper, H. Ashworth, A. Lill, J. R. Malek, S. Rudolph, J. Wertz, I. E. Chang, M. Ye, X. Dey, A. 2023-10-04 doi:10.1101/2023.10.03.560675 Cold Spring Harbor Laboratory Press 2023-10-04 <![CDATA[ Analysis of the Diverse Antigenic Landscape of the Malaria Invasion Protein RH5 Identifies a Potent Vaccine-Induced Human Public Antibody Clonotype ]]> https://biorxiv.org/content/10.1101/2023.10.04.560576v1?rss=1 Barrett, J. R. Pipini, D. Wright, N. D. Cooper, A. J. R. Gorini, G. Quinkert, D. Lias, A. M. Davies, H. Rigby, C. Aleshnick, M. Williams, B. G. Bradshaw, W. J. Paterson, N. G. Martinson, T. Kirtley, P. Picard, L. Wiggins, C. D. Donnellan, F. R. King, L. D. W. Wang, L. T. Popplewell, J. F. Silk, S. E. Swain, J. d. R. Skinner, K. Kotraiah, V. Noe, A. R. MacGill, R. S. King, C. R. Birkett, A. J. Soisson, L. A. Minassian, A. M. Lauffenburger, D. A. Miura, K. Long, C. A. Wilder, B. K. Koekemoer, L. Tan, J. Nielsen, C. M. McHugh, K. Draper, S. J. 2023-10-04 doi:10.1101/2023.10.04.560576 Cold Spring Harbor Laboratory Press 2023-10-04 <![CDATA[ Robust CNV detection using single-cell ATAC-seq ]]> https://biorxiv.org/content/10.1101/2023.10.04.560975v1?rss=1 Moore, T. W. Yardimci, G. G. 2023-10-06 doi:10.1101/2023.10.04.560975 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Deciphering Cell-types and Gene Signatures Associated with Disease Activity in Rheumatoid Arthritis using Single Cell RNA-sequencing ]]> https://biorxiv.org/content/10.1101/2023.10.05.560352v1?rss=1 Binvignat, M. Miao, B. Wibrand, C. Yang, M. Rychkov, D. Flynn, E. Nititham, J. Tamaki, W. Khan, U. Carvidi, A. Krueger, M. Niemi, E. Sun, Y. Fragiadakis, G. K. Sellam, J. Mariotti-Ferrandiz, E. Klatzmann, D. Gross, A. Ye, C. J. Butte, A. J. Criswell, L. Nakamura, M. Sirota, M. 2023-10-06 doi:10.1101/2023.10.05.560352 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Thymically imprinted differential responsivity of naive CD4 T cells to IL2 results in a heterogeneity of both Treg induction and subsequent effector functioning ]]> https://biorxiv.org/content/10.1101/2023.10.08.561378v1?rss=1 Pennock, N. D. Qian, Y. Ishihara, K. Nakamura, Y. Cross, E. W. Sakaguchi, S. White, J. T. 2023-10-10 doi:10.1101/2023.10.08.561378 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ In vitro development and optimization of cell-laden injectable bioprinted gelatin methacryloyl (GelMA) microgels mineralized on the nanoscale ]]> https://biorxiv.org/content/10.1101/2023.10.10.560919v1?rss=1 Sousa, M. G. C. Balbinot, G. d. S. Subbiah, R. Visalakshan, R. Tahayeri, A. Verde, M. E. Q. L. Athirasala, A. Romanowicz, G. Guldberg, R. E. Bertassoni, L. E. 2023-10-12 doi:10.1101/2023.10.10.560919 Cold Spring Harbor Laboratory Press 2023-10-12 <![CDATA[ Trifunctional sphinganine: a new tool to dissect sphingolipid function ]]> https://biorxiv.org/content/10.1101/2023.10.16.562528v1?rss=1 Farley, S. E. Stein, F. Haberkant, P. Tafesse, F. G. Schultz, C. 2023-10-16 doi:10.1101/2023.10.16.562528 Cold Spring Harbor Laboratory Press 2023-10-16 <![CDATA[ Membrane Lipids Augment Cell Envelope Stress Signaling and Resistance to Antibiotics and Antimicrobial Peptides in Enterococcus faecalis ]]> https://biorxiv.org/content/10.1101/2023.10.17.562839v1?rss=1 Miller, W. R. Nguyen, A. Singh, K. V. Rizvi, S. Khan, A. Erickson, S. G. Egge, S. L. Cruz, M. Dinh, A. Q. Diaz, L. Zhang, R. Xu, L. Garsin, D. A. Shamoo, Y. Arias, C. A. 2023-10-19 doi:10.1101/2023.10.17.562839 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ A syngeneic spontaneous zebrafish model of tp53-deficient, EGFRviii, and PI3KCA H1047R-driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapse in vivo ]]> https://biorxiv.org/content/10.1101/2023.10.17.562653v1?rss=1 Weiss, A. D'Amata, C. Pearson, B. J. Hayes, M. N. 2023-10-20 doi:10.1101/2023.10.17.562653 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes ]]> https://biorxiv.org/content/10.1101/2023.10.18.562964v1?rss=1 Orlic-Milacic, M. Rothfels, K. Matthews, L. Wright, A. Jassal, B. Shamovsky, V. Trinh, Q. Gillespie, M. Sevilla, C. Tiwari, K. Ragueneau, E. Gong, C. Stephan, R. May, B. Haw, R. Weiser, J. Beavers, D. Conley, P. Hermjakob, H. Stein, L. D. D'Eustachio, P. Wu, G. 2023-10-22 doi:10.1101/2023.10.18.562964 Cold Spring Harbor Laboratory Press 2023-10-22 <![CDATA[ Machine learning links T cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2023.10.20.563335v1?rss=1 Blise, K. E. Sivagnanam, S. Betts, C. B. Betre, K. Kirchberger, N. Tate, B. Furth, E. E. Dias Costa, A. Nowak, J. A. Wolpin, B. M. Vonderheide, R. H. Goecks, J. Coussens, L. M. Byrne, K. 2023-10-23 doi:10.1101/2023.10.20.563335 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Fine-tuning TrailMap: The utility of transfer learning to improve the performance of deep learning in axon segmentation of light-sheet microscopy images ]]> https://biorxiv.org/content/10.1101/2023.10.23.563546v1?rss=1 Oostrom, M. Muniak, M. Eichler West, R. M. Akers, S. Pande, P. Obiri, M. Wang, W. Bowyer, K. Wu, Z. Bramer, L. M. Mao, T. Webb-Robertson, B.-J. M. 2023-10-23 doi:10.1101/2023.10.23.563546 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Sex and species associated differences in Complement-mediated immunity in Humans and Rhesus macaques ]]> https://biorxiv.org/content/10.1101/2023.10.23.563614v1?rss=1 Kelkar, N. S. Goldberg, B. S. Dufloo, J. Bruel, T. Schwartz, O. Hessell, A. J. Ackerman, M. E. 2023-10-25 doi:10.1101/2023.10.23.563614 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ The prevalence of Fusobacterium nucleatum subspecies in the oral cavity stratifies by local health status ]]> https://biorxiv.org/content/10.1101/2023.10.25.563997v1?rss=1 Krieger, M. AbdelRahman, Y. M. Choi, D. Palmer, E. A. Yoo, A. McGuire, S. Kreth, J. Merritt, J. 2023-10-26 doi:10.1101/2023.10.25.563997 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ Analysis of uveal melanoma scRNA sequencing data identifies neoplastic-immune hybrid cells that exhibit metastatic potential ]]> https://biorxiv.org/content/10.1101/2023.10.24.563815v1?rss=1 Anderson, A. N. Conley, P. Klocke, C. D. Sengupta, S. K. Giske, N. R. Robinson, T. L. Fan, Y. Jones, J. A. Gibbs, S. L. Skalet, A. H. Wu, G. Wong, M. H. 2023-10-27 doi:10.1101/2023.10.24.563815 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Dock1 acts cell-autonomously in Schwann cells to regulate the development, maintenance, and repair of peripheral myelin ]]> https://biorxiv.org/content/10.1101/2023.10.26.564271v1?rss=1 Doan, R. A. Monk, K. R. 2023-10-27 doi:10.1101/2023.10.26.564271 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Gardenin A improves cognitive and motor function in A53T-α-syn mice ]]> https://biorxiv.org/content/10.1101/2023.10.27.564401v1?rss=1 Hack, W. Gladen-Kolarsky, N. Chatterjee, S. Lang, Q. Maitra, U. Ciesla, L. Gray, N. E. 2023-11-01 doi:10.1101/2023.10.27.564401 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Efficient semi-supervised semantic segmentation of electron microscopy cancer images with sparse annotations ]]> https://biorxiv.org/content/10.1101/2023.10.30.563998v1?rss=1 Pagano, L. Thibault, G. Bousselham, W. Riesterer, J. L. Song, X. Gray, J. W. 2023-11-01 doi:10.1101/2023.10.30.563998 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ From average transient transporter currents to microscopic mechanism -- A Bayesian analysis ]]> https://biorxiv.org/content/10.1101/2023.10.31.565026v1?rss=1 10 rate constants. We use a Bayesian framework applied to synthetic data for three tasks: to quantify and check (i) the precision of parameter estimates under different assumptions, (ii) the ability of computation to guide selection of experimental conditions, and (iii) the ability of SSME data to distinguish among mechanisms. When the general mechanism - event order - is known in advance, we show that a subset of kinetic parameters can be "practically identified" within[~] 1 order of magnitude, based on SSME current traces that visually appear to exhibit simple exponential behavior. This remains true even when accounting for systematic measurement bias and realistic uncertainties in experimental inputs (concentrations) are incorporated into the analysis. When experimental conditions are optimized or different experiments are combined, the number of practically identifiable parameters can be increased substantially. Some parameters remain intrinsically difficult to estimate through SSME data alone, suggesting additional experiments are required to fully characterize parameters. We additionally demonstrate the ability to perform model selection and determine the order of events when that is not known in advance, comparing Bayesian and maximum-likelihood approaches. Finally, our studies elucidate good practices for the increasingly popular, but subtly challenging, Bayesian calculations for structural and systems biology. ]]> George, A. Zuckerman, D. M. 2023-11-02 doi:10.1101/2023.10.31.565026 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ CG-SLENP: A chemical genetics strategy to selectively label existing proteins and newly synthesized proteins ]]> https://biorxiv.org/content/10.1101/2023.11.02.565346v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@d18268org.highwire.dtl.DTLVardef@c8b9ddorg.highwire.dtl.DTLVardef@226bf5org.highwire.dtl.DTLVardef@1dda80c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wang, J. Chao, B. Piesner, J. Kelly, F. Petrie, S. K. Xiao, X. Li, B. X. 2023-11-02 doi:10.1101/2023.11.02.565346 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ AXDND1 is required to balance spermatogonial commitment and for sperm tail formation in mice and humans ]]> https://biorxiv.org/content/10.1101/2023.11.02.565050v1?rss=1 Houston, B. J. Nguyen, J. Merriner, D. J. O'Connor, A. E. Lopes, A. M. Nagirnaja, L. Friedrich, C. Kliesch, S. Tuettelmann, F. Aston, K. I. Conrad, D. Hobbs, R. M. Dunleavy, J. E. O'Bryan, M. K. 2023-11-04 doi:10.1101/2023.11.02.565050 Cold Spring Harbor Laboratory Press 2023-11-04 <![CDATA[ Rapid nongenomic estrogen signaling controls alcohol drinking behavior ]]> https://biorxiv.org/content/10.1101/2023.11.02.565358v1?rss=1 Zallar, L. J. Rivera-Irizarry, J. K. Hamor, P. U. Pigulevskiy, I. Liu, D. Welday, J. P. Rico Rozo, A.-S. Bender, R. Asfouri, J. Skelly, M. J. Fecteau, K. M. Hadley, C. K. Levine, O. B. Mehanna, H. Nelson, S. Miller, J. Ghazal, P. Bellotti, P. Erikson, D. W. Geri, J. Pleil, K. E. 2023-11-05 doi:10.1101/2023.11.02.565358 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Tweek-dependent formation of ER-PM contact sites enables astrocyte phagocytic function and remodeling of neurons ]]> https://biorxiv.org/content/10.1101/2023.11.06.565932v1?rss=1 Kang, Y. Jefferson, A. Sheehan, A. De La Torre, R. Jay, T. Chiao, L. Hulegaard, A. Corty, M. M. Baconguis, I. Zhou, Z. Freeman, M. 2023-11-07 doi:10.1101/2023.11.06.565932 Cold Spring Harbor Laboratory Press 2023-11-07 <![CDATA[ ChatGPT usage in the Reactome curation process ]]> https://biorxiv.org/content/10.1101/2023.11.08.566195v1?rss=1 Tiwari, K. K. Matthews, L. May, B. Shamovsky, V. Orlic-Milacic, M. Rothfels, K. Ragueneau, E. Gong, C. Stephan, R. Li, N. Wu, G. Stein, L. D. D'eustachio, P. Hermjakob, H. 2023-11-08 doi:10.1101/2023.11.08.566195 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Altered hippocampal activation in seizure-prone CACNA2D2 knockout mice ]]> https://biorxiv.org/content/10.1101/2023.11.08.565511v1?rss=1 Danis, A. Gallagher, A. A. Anderson, A. N. Isakharov, A. Beeson, K. A. Schnell, E. 2023-11-10 doi:10.1101/2023.11.08.565511 Cold Spring Harbor Laboratory Press 2023-11-10 <![CDATA[ Identification of Cellular Interactions in the Tumor Immune Microenvironment Underlying CD8 T Cell Exhaustion ]]> https://biorxiv.org/content/10.1101/2023.11.09.566384v1?rss=1 Klocke, C. D. Moran, A. Adey, A. McWeeney, S. Wu, G. 2023-11-13 doi:10.1101/2023.11.09.566384 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Prior Fc Receptor activation primes macrophage for increased sensitivity to IgG via long term and short term mechanisms ]]> https://biorxiv.org/content/10.1101/2023.11.14.567059v1?rss=1 Bond, A. Fiaz, S. Rollins, K. R. Nario, J. E. Q. Rosen, S. J. Granados, A. Wilson, M. Z. Morrissey, M. A. 2023-11-14 doi:10.1101/2023.11.14.567059 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ The Impact of SIV-Induced Immunodeficiency on Clinical Manifestation, Immune Response, and Viral Dynamics in SARS-CoV-2 Coinfection ]]> https://biorxiv.org/content/10.1101/2023.11.15.567132v1?rss=1 Melton, A. Rowe, L. A. Penney, T. Krzykwa, C. Goff, K. Scheuermann, S. E. Melton, H. J. Williams, K. Golden, N. Moore Green, K. Smith, B. Russell-Lodrigue, K. Dufour, J. P. Doyle-Meyers, L. A. Schiro, F. Aye, P. P. Lifson, J. D. Beddingfield, B. J. Blair, R. V. Bohm, R. P. Kolls, J. K. Rappaport, J. Hoxie, J. A. Maness, N. J. 2023-11-16 doi:10.1101/2023.11.15.567132 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Water inside the selectivity filter of a K+ ion channel: structural heterogeneity, picosecond dynamics, and hydrogen-bonding ]]> https://biorxiv.org/content/10.1101/2023.11.16.567415v1?rss=1 Ryan, M. J. Gao, L. Valiyaveetil, F. I. Kananenka, A. A. Zanni, M. T. 2023-11-17 doi:10.1101/2023.11.16.567415 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Towards Generalizability and Robustness in Biological Object Detection in Electron Microscopy Images ]]> https://biorxiv.org/content/10.1101/2023.11.27.568889v1?rss=1 GIANNIOS, K. Chaurasia, A. Bueno, C. Riesterer, J. L. Pagano, L. Lo, T. P. Thibault, G. Gray, J. W. Song, X. DeLaRosa, B. 2023-11-27 doi:10.1101/2023.11.27.568889 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ Natural and age-related variation in circulating human hematopoietic stem cells ]]> https://biorxiv.org/content/10.1101/2023.11.30.569167v1?rss=1 Furer, N. Rappoport, N. Lifshitz, A. bercovich, A. Ben-Kiki, O. Danin, A. Kedmi, M. Shipony, Z. Lipson, D. Meiri, E. Yanai, G. Shapira, S. Arber, N. Berdichevsky, S. Tavor, S. Tyner, J. Joshi, S. K. Landau, D. Ganesan, S. Dusaj, N. Chamely, P. Kaushansky, N. Chapal Ilani, N. Shamir, R. Tanay, A. Shlush, L. 2023-11-30 doi:10.1101/2023.11.30.569167 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ Metabolic abnormalities in the bone marrow cells of young offspring born to obese mothers ]]> https://biorxiv.org/content/10.1101/2023.11.29.569274v1?rss=1 Phillips, E. A. Alharithi, Y. J. Kadam, L. Coussens, L. M. Kumar, S. Maloyan, A. 2023-12-01 doi:10.1101/2023.11.29.569274 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes ]]> https://biorxiv.org/content/10.1101/2023.11.30.569198v1?rss=1 100 great ape individuals. These reference assemblies are expected to inform human evolution and conservation genetics of nonhuman apes, all of which are endangered species. ]]> Makova, K. D. Pickett, B. D. Harris, R. S. Hartley, G. A. Cechova, M. Pal, K. Nurk, S. Yoo, D. Li, Q. Hebbar, P. McGrath, B. C. Antonacci, F. Aubel, M. Biddanda, A. Borchers, M. Bornberg, E. Bouffard, G. G. Brooks, S. Y. Carbone, L. Carrel, L. Carroll, A. Chang, P.-C. Chin, C.-S. Cook, D. E. Craig, S. J. C. de Gennaro, L. Diekhans, M. Dutra, A. Garcia, G. H. Grady, P. G. S. Green, R. E. Haddad, D. Hallast, P. Harvey, W. T. Hickey, G. Hillis, D. A. Hoyt, S. J. Jeong, H. Kamali, K. Pond, S. L. K. LaPolice, T. M. Lee, C. Lewis, A. P. Loh, Y.-H. E. Maste 2023-12-01 doi:10.1101/2023.11.30.569198 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ The Parkinson's Disease related mutant VPS35 (D620N) amplifies the LRRK2 response to endolysosomal stress ]]> https://biorxiv.org/content/10.1101/2023.12.02.569621v1?rss=1 McCarron, K. R. Elcocks, H. Mortiboys, H. J. Urbe, S. Clague, M. J. 2023-12-03 doi:10.1101/2023.12.02.569621 Cold Spring Harbor Laboratory Press 2023-12-03 <![CDATA[ A non-conducting role of the Cav1.4 Ca2+ channel drives homeostatic plasticity at the cone photoreceptor synapse ]]> https://biorxiv.org/content/10.1101/2023.12.05.570129v1?rss=1 Maddox, W. Ordemann, G. J. de la Rosa Vazquez, J. Huang, A. Gault, C. Wisner, S. R. Randall, K. Futagi, D. DeVries, S. Hoon, M. Lee, A. 2023-12-06 doi:10.1101/2023.12.05.570129 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ Astrocyte-dependent local neurite pruning and Hox gene-mediated cell death in Beat-Va neurons ]]> https://biorxiv.org/content/10.1101/2023.12.05.570324v1?rss=1 Lehmann, K. S. Hupp, M. T. Jefferson, A. Cheng, Y.-C. Sheehan, A. E. Kang, Y. Freeman, M. 2023-12-06 doi:10.1101/2023.12.05.570324 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ Three-dimensional reconstruction of fetal rhesus macaque kidneys at single-cell resolution reveals complex inter-relation of structures ]]> https://biorxiv.org/content/10.1101/2023.12.07.570622v1?rss=1 Dequiedt, L. Forjaz, A. Lo, J. O. McCarty, O. J. Wu, P.-H. Rosenberg, A. Wirtz, D. Kiemen, A. L. 2023-12-08 doi:10.1101/2023.12.07.570622 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ BMI and BPH correlate with urinary microbiome diversity and lower urinary tract symptoms in men ]]> https://biorxiv.org/content/10.1101/2023.12.14.571758v1?rss=1 Bowie, K. Garzotto, M. Orwoll, E. Karstens, L. 2023-12-15 doi:10.1101/2023.12.14.571758 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Rapid turnover of CTLA4 is associated with a complex architecture of reversible ubiquitylation. ]]> https://biorxiv.org/content/10.1101/2023.12.31.573735v1?rss=1 Tey, P. Y. Dufner, A. Knobeloch, K.-P. Pruneda, J. N. Clague, M. J. Urbe, S. 2024-01-01 doi:10.1101/2023.12.31.573735 Cold Spring Harbor Laboratory Press 2024-01-01 <![CDATA[ Alpha-synuclein regulates nucleolar DNA double-strand break repair in melanoma ]]> https://biorxiv.org/content/10.1101/2024.01.13.575526v1?rss=1 Arnold, M. R. Cohn, G. M. Oxe, K. C. Elliott, S. N. Moore, C. Laraia, P. V. Shekoohi, S. Brownell, D. Meshul, C. K. Witt, S. N. Larsen, D. H. Unni, V. K. 2024-01-14 doi:10.1101/2024.01.13.575526 Cold Spring Harbor Laboratory Press 2024-01-14 <![CDATA[ Mutation of the peptide-regulated transcription factor ComR for amidated peptide specificity and heterologous function in Lactiplantibacillus plantarum WCFS1 ]]> https://biorxiv.org/content/10.1101/2024.01.25.577207v1?rss=1 Brasino, M. Wagnell, E. Ozdemir, S. Ranganathan, S. Merritt, J. 2024-01-26 doi:10.1101/2024.01.25.577207 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ Estradiol elicits distinct firing patterns in arcuate nucleus kisspeptin neurons of females through altering ion channel conductances ]]> https://biorxiv.org/content/10.1101/2024.02.20.581121v1?rss=1 Qiu, J. Voliotis, M. Bosch, M. A. Li, X. F. Zweifel, L. S. Tsaneva-Atanasova, K. O'Byrne, K. Ronnekleiv, O. K. Kelly, M. J. 2024-02-23 doi:10.1101/2024.02.20.581121 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Peptide Amphiphiles Hitchhike on Endogenous Biomolecules for Enhanced Cancer Imaging and Therapy ]]> https://biorxiv.org/content/10.1101/2024.02.21.580762v1?rss=1 Fischer, J. M. Stewart, M. Dai, M. Drennan, S. Holland, S. Quentel, A. Sabuncu, S. Kingston, B. R. Dengos, I. Xiang, L. Bonic, K. Goncalves, F. Yi, X. Ranganathan, S. Branchaud, B. P. Muldoon, L. L. Barajas, R. F. Yildirim, A. 2024-02-23 doi:10.1101/2024.02.21.580762 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Development of novel tools for dissection of central versus peripheral dopamine D2-like receptor signaling in dysglycemia ]]> https://biorxiv.org/content/10.1101/2024.02.21.581451v1?rss=1 Bonifazi, A. Ellenberger, M. Farino, Z. J. Aslanoglou, D. Rais, R. Pereira, S. Mantilla-Rivas, J. O. Boateng, C. A. Eshleman, A. J. Janowsky, A. Hahn, M. K. Schwartz, G. J. Slusher, B. S. Freyberg, Z. 2024-02-23 doi:10.1101/2024.02.21.581451 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Maternal cannabis use alters excitatory inputs to corticostriatal efferent neurons in rat offspring ]]> https://biorxiv.org/content/10.1101/2024.03.03.583210v1?rss=1 Ginder, D. E. Weimar, H. V. Lindberg, J. E. M. Fisher, Z. D. G. Lim, M. M. Peters, J. H. McLaughlin, R. J. 2024-03-06 doi:10.1101/2024.03.03.583210 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Deletion of Robo4 worsens neuroinflammation and motor coordination in a mouse model of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2024.03.07.583582v1?rss=1 Cullen, A. E. Winder, N. Lee, B. Krishna Kumaran, S. Arora, N. Wolf, J. Woltjer, R. Walker, A. 2024-03-12 doi:10.1101/2024.03.07.583582 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Fatiguing Exercise Reduces Cellular Passive Young's Modulus in Human Vastus Lateralis Muscle ]]> https://biorxiv.org/content/10.1101/2024.03.07.583989v1?rss=1 Privett, G. E. Ricci, A. W. David, L. Needham, K. W. Tan, Y. H. Nakayama, K. H. Callahan, D. M. 2024-03-12 doi:10.1101/2024.03.07.583989 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Structure-based probe reveals the presence of large transthyretin aggregates in plasma of ATTR amyloidosis patients ]]> https://biorxiv.org/content/10.1101/2024.03.09.584228v1?rss=1 Pedretti, R. Wang, L. Yakubovska, A. Zhang, Q. S. Nguyen, B. Grodin, J. L. Masri, A. Saelices, L. 2024-03-10 doi:10.1101/2024.03.09.584228 Cold Spring Harbor Laboratory Press 2024-03-10 <![CDATA[ Multi-modal comparison of molecular programs driving nurse cell death and clearance in Drosophila melanogaster oogenesis ]]> https://biorxiv.org/content/10.1101/2024.03.12.584558v1?rss=1 Bandyadka, S. Lebo, D. P. Mondragon, A. Serizier, S. B. Kwan, J. Peterson, J. S. Chasse, A. Y. Jenkins, V. Calikyan, A. Ortega, A. Campbell, J. D. Emili, A. McCall, K. 2024-03-14 doi:10.1101/2024.03.12.584558 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Synchrony between midbrain gene transcription and dopamine terminal regulation is modulated by chronic alcohol drinking ]]> https://biorxiv.org/content/10.1101/2024.03.15.584711v1?rss=1 Farahbakhsh, Z. Z. Holleran, K. M. Sens, J. P. Fordahl, S. C. Mauterer, M. I. Lopez, A. J. Cuzon Carlson, V. C. Kiraly, D. D. Grant, K. A. Jones, S. R. Siciliano, C. A. 2024-03-17 doi:10.1101/2024.03.15.584711 Cold Spring Harbor Laboratory Press 2024-03-17 <![CDATA[ Structural diversity and clustering of bacterial flagellar outer domains ]]> https://biorxiv.org/content/10.1101/2024.03.18.585621v1?rss=1 Fields, J. L. Zhang, H. Bellis, N. F. Petersen, H. A. Halder, S. K. Rich-New, S. T. Wu, H. Wang, F. 2024-03-18 doi:10.1101/2024.03.18.585621 Cold Spring Harbor Laboratory Press 2024-03-18 <![CDATA[ Trace Amines are Essential Metabolites for the Autocrine Regulation of β-Cell Signaling and Insulin Secretion ]]> https://biorxiv.org/content/10.1101/2024.03.21.585773v1?rss=1 Keutler, K. Hauke, S. Laguerre, A. Andreu-Carbo, M. Rada, J. Grandy, D. Yushchenko, D. A. Schultz, C. 2024-03-23 doi:10.1101/2024.03.21.585773 Cold Spring Harbor Laboratory Press 2024-03-23 <![CDATA[ Cannabinoid Receptor Signaling is Dependent on Sub-Cellular Location ]]> https://biorxiv.org/content/10.1101/2024.03.21.586146v1?rss=1 Thomas, A. Lobingier, B. Schultz, C. Laguerre, A. 2024-03-22 doi:10.1101/2024.03.21.586146 Cold Spring Harbor Laboratory Press 2024-03-22 <![CDATA[ Discovery of a cell-active chikungunya virus nsP2 protease inhibitor using a covalent fragment-based screening approach ]]> https://biorxiv.org/content/10.1101/2024.03.22.586341v1?rss=1 Merten, E. M. Sears, J. D. Leisner, T. M. Hardy, P. B. Ghoshal, A. Hossain, M. A. Asressu, K. H. Brown, P. J. Stashko, M. A. Herring, L. E. Mordant, A. L. Webb, T. S. Mills, C. A. Barker, N. K. Arnold, J. J. Cameron, C. E. Streblow, D. N. Moorman, N. J. Heise, M. Willson, T. M. Popov, K. I. Pearce, K. H. 2024-03-22 doi:10.1101/2024.03.22.586341 Cold Spring Harbor Laboratory Press 2024-03-22 <![CDATA[ Dynamic fibrillar assembly of αB-crystallin induced by perturbation of the conserved NT-IXI motif resolved by cryo-EM. ]]> https://biorxiv.org/content/10.1101/2024.03.22.586355v1?rss=1 Reichow, S. L. McFarland, R. 2024-03-27 doi:10.1101/2024.03.22.586355 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Prevalent co-release of glutamate and GABA throughout the mouse brain ]]> https://biorxiv.org/content/10.1101/2024.03.27.587069v1?rss=1 Ceballos, C. C. Ma, L. Qin, M. Zhong, H. 2024-03-29 doi:10.1101/2024.03.27.587069 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Tools for Cre-mediated conditional deletion of floxed alleles from developing cerebellar Purkinje cells ]]> https://biorxiv.org/content/10.1101/2024.03.28.587263v1?rss=1 Jahncke, J. N. Wright, K. M. 2024-03-30 doi:10.1101/2024.03.28.587263 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Cryo-electron tomographic investigation of native hippocampal glutamatergic synapses ]]> https://biorxiv.org/content/10.1101/2024.04.01.587595v1?rss=1 Matsui, A. Spangler, C. Elferich, J. Shiozaki, M. Jean, N. Zhao, X. Qin, M. Zhong, H. Yu, Z. Gouaux, E. 2024-04-01 doi:10.1101/2024.04.01.587595 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ Biologically informed machine learning modeling of immune cells to reveal physiological and pathological aging process ]]> https://biorxiv.org/content/10.1101/2024.04.01.587649v1?rss=1 Xia, Z. Zhang, B. Sun, L. Zhang, C. Ren, T. Zhao, X. Su, Y. Wang, Q. Zhang, T. He, B. Wu, L.-Y. 2024-04-02 doi:10.1101/2024.04.01.587649 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Development of BODIPY-based fluorescent probes for highly selective amino acid identification ]]> https://biorxiv.org/content/10.1101/2024.04.02.587799v1?rss=1 Hendrick, N. Martin, A. Chan, A. Lenihan, J. Reiter, H. Clough, M. Jiang, L. Whaley, E. Jeong Huh, Y. McNeely, J. Chen, A. Emili, A. Beeler, A. B. 2024-04-02 doi:10.1101/2024.04.02.587799 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Detailed phenotyping of Tbr1-2A-CreER knock-in mice demonstrates significant impacts on TBR1 protein levels and axon development ]]> https://biorxiv.org/content/10.1101/2024.04.04.588147v1?rss=1 50%) are required for normal suppression of layer 5 identity. In total, these results strongly support the conclusion that Tbr1-2A-CreER is a hypomorphic allele. We advise caution when interpreting experiments using this allele, such as transcriptomic studies, considering the sensitivity of various corticogenic processes to TBR1 dosage and the association of heterozygous TBR1 mutations with complex neurodevelopmental disorders. ]]> Co, M. O'Brien, G. K. Wright, K. M. O'Roak, B. J. 2024-04-04 doi:10.1101/2024.04.04.588147 Cold Spring Harbor Laboratory Press 2024-04-04 <![CDATA[ Chronic alcohol consumption alters sex-dependent BNST neuron function in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2024.04.11.589120v1?rss=1 Pleil, K. E. Grant, K. A. Carlson, V. C. C. Kash, T. L. 2024-04-15 doi:10.1101/2024.04.11.589120 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ Relaxin Modulates the Genomic Actions and Biological Effects of Estrogen in the Myometrium by Reducing Estrogen Receptor Alpha Phosphorylation ]]> https://biorxiv.org/content/10.1101/2024.04.15.589654v1?rss=1 Sudeshna Tripathy, S. Nagari, A. Chiu, S.-P. Nandu, T. Camacho, C. V. Mahendroo, M. Kraus, W. L. 2024-04-16 doi:10.1101/2024.04.15.589654 Cold Spring Harbor Laboratory Press 2024-04-16 <![CDATA[ Massively parallel jumping assay decodes Alu retrotransposition activity ]]> https://biorxiv.org/content/10.1101/2024.04.16.589814v1?rss=1 Ahituv, N. Matharu, N. Zhao, J. Sohota, A. Deng, L. Hung, Y. Li, Z. Sims, J. Rattanasopha, S. Meyer, J. Carbone, L. Kircher, M. 2024-04-19 doi:10.1101/2024.04.16.589814 Cold Spring Harbor Laboratory Press 2024-04-19 <![CDATA[ A Futile Cycle? Tissue Homeostatic Trans-Membrane Water Co-Transport: Kinetics, Thermodynamics, Metabolic Consequences ]]> https://biorxiv.org/content/10.1101/2024.04.17.589812v1?rss=1 Springer, C. S. Pike, M. M. Barbara, T. M. 2024-04-19 doi:10.1101/2024.04.17.589812 Cold Spring Harbor Laboratory Press 2024-04-19 <![CDATA[ Proteomic Discovery of RNA-Protein Molecular Clamps Using a Thermal Shift Assay with ATP and RNA (TSAR) ]]> https://biorxiv.org/content/10.1101/2024.04.19.590252v1?rss=1 Goldstein, S. I. Fan, A. C. Wang, Z. Naineni, S. K. Lengqvist, J. Chernobrovkin, A. Garcia-Gutierrez, S. B. Cencic, R. Patel, K. Huang, S. Brown, L. E. Emili, A. Porco, J. A. 2024-04-19 doi:10.1101/2024.04.19.590252 Cold Spring Harbor Laboratory Press 2024-04-19 <![CDATA[ Divergent Subregional Information Processing in Mouse Prefrontal Cortex During Working Memory ]]> https://biorxiv.org/content/10.1101/2024.04.25.591167v1?rss=1 Sonneborn, A. Bartlett, L. Olson, R. J. Milton, R. Abbas, A. I. 2024-04-28 doi:10.1101/2024.04.25.591167 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ PARP14 is pro- and anti-viral host factor that promotes IFN production and affects the replication of multiple viruses ]]> https://biorxiv.org/content/10.1101/2024.04.26.591186v1?rss=1 Parthasarathy, S. Saenjamsai, P. Hao, H. Ferkul, A. Pfannenstiel, J. J. Suder, E. L. Bejan, D. S. Chen, Y. Schwarting, N. Aikawa, M. Muhlberger, E. Orozco, R. C. Sullivan, C. S. Cohen, M. S. Davido, D. Hume, A. J. Fehr, A. 2024-04-26 doi:10.1101/2024.04.26.591186 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ IL-12/IL23 blockade reveals patterns of asynchronous inflammation in pyoderma gangrenosum ]]> https://biorxiv.org/content/10.1101/2024.04.26.591387v1?rss=1 Yadav, R. Vague, M. Rettig, M. Loo, C. P. Brown, K. Samiea, A. Moreau, J. M. Ortega-Loayza, A. G. 2024-04-29 doi:10.1101/2024.04.26.591387 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Investigating the Triple Code Model in Numerical Cognition Using Stereotactic Electroencephalography ]]> https://biorxiv.org/content/10.1101/2024.04.27.591485v1?rss=1 Tan, H. Rockhill, A. P. Lopez Ramos, C. G. Nerison, C. Shafie, B. Shahin, M. N. Fecker, A. L. Ismail, M. Cleary, D. R. Collins, K. L. Raslan, A. M. 2024-04-29 doi:10.1101/2024.04.27.591485 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Elucidating the Impact of Hypericum alpestre Extract and L-NAME on the PI3K/Akt Signaling Pathway in A549 Lung Adenocarcinoma Cells ]]> https://biorxiv.org/content/10.1101/2024.05.02.592167v1?rss=1 Javrushyan, H. Ginovyan, M. Petrosyan, G. Qocharyan, M. Harutyunyan, T. Gevorgyan, S. Karabekian, Z. Maloyan, A. Avtandilyan, N. 2024-05-04 doi:10.1101/2024.05.02.592167 Cold Spring Harbor Laboratory Press 2024-05-04 <![CDATA[ A novel genetic mouse model of fatal aortic dissection reveals massive inflammatory cell infiltration in the thoracic aorta ]]> https://biorxiv.org/content/10.1101/2024.05.02.592287v1?rss=1 Kimura, K. Motoyama, E. Kanki, S. Asano, K. Sheikh, M. A. A. Clarin, M. T. R. D. C. Raja, E. Takeda, M. Ishii, R. Murata, K. Deleeuw, V. Sips, P. Muino-Mosquera, L. De Backer, J. Mizuno, S. Sakai, L. Y. Nakamura, T. Yanagisawa, H. 2024-05-07 doi:10.1101/2024.05.02.592287 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ COEXIST: Coordinated single-cell integration of serial multiplexed tissue images ]]> https://biorxiv.org/content/10.1101/2024.05.05.592573v1?rss=1 Heussner, R. T. Watson, C. F. Eddy, C. Z. Wang, K. Cramer, E. M. Creason, A. L. Mills, G. B. Chang, Y. H. 2024-05-07 doi:10.1101/2024.05.05.592573 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ Androgen receptor activity inversely correlates with immune cell infiltration and immunotherapy response across multiple cancer lineages ]]> https://biorxiv.org/content/10.1101/2024.05.08.593181v1?rss=1 Hu, Y.-M. Zhao, F. Graff, J. Chen, C. Zhao, X. Thomas, G. V. Wu, H. Kardosh, A. Mills, G. Alumkal, J. Moran, A. E. Xia, Z. 2024-05-14 doi:10.1101/2024.05.08.593181 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ O-GalNAc glycans enrich in white matter tracts and regulate nodes of Ranvier ]]> https://biorxiv.org/content/10.1101/2024.05.09.593410v1?rss=1 Noel, M. Suttapitugsakul, S. Cummings, R. D. Mealer, R. G. 2024-05-09 doi:10.1101/2024.05.09.593410 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ A phosphorylation code coordinating transcription condensate dynamics with DNA replication ]]> https://biorxiv.org/content/10.1101/2024.05.10.593572v1?rss=1 Marmolejo, C. O. Sanchez, C. Lee, J. Werner, M. Roberts, P. Hamperl, S. Saldivar, J. C. 2024-05-11 doi:10.1101/2024.05.10.593572 Cold Spring Harbor Laboratory Press 2024-05-11 <![CDATA[ Structural basis of autoantibody binding in Neuromyelitis Optica ]]> https://biorxiv.org/content/10.1101/2024.05.12.592631v1?rss=1 Gupta, M. Khandelwal, N. K. Nelson, A. Hwang, P. Pourmal, S. Bennett, J. L. Stroud, R. M. 2024-05-14 doi:10.1101/2024.05.12.592631 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Coumarin as a general switching auxiliary to prepare photochromic and spontaneously blinking fluorophores ]]> https://biorxiv.org/content/10.1101/2024.05.12.593749v1?rss=1 Jradi, F. English, B. P. Brown, T. A. Arron, J. Khuon, S. Galbraith, J. A. Galbraith, C. G. Lavis, L. D. 2024-05-12 doi:10.1101/2024.05.12.593749 Cold Spring Harbor Laboratory Press 2024-05-12 <![CDATA[ Detection of ATTR aggregates in plasma of polyneuropathic ATTR-V30M amyloidosis patients ]]> https://biorxiv.org/content/10.1101/2024.05.13.593968v1?rss=1 Pedretti, R. Wang, L. Grodin, J. L. Masri, A. Kelly, J. Saelices, L. 2024-05-13 doi:10.1101/2024.05.13.593968 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ Trifunctional fatty acid derivatives demonstrate the impact of diazirine placement ]]> https://biorxiv.org/content/10.1101/2024.05.15.594383v1?rss=1 Farley, S. E. Hashimoto, R. Evangelista, J. Stein, F. Haberkant, P. Kikuchi, K. Tafesse, F. Schultz, C. 2024-05-15 doi:10.1101/2024.05.15.594383 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Genomic loss of GPR108 disrupts AAV transduction in birds ]]> https://biorxiv.org/content/10.1101/2024.05.16.589954v1?rss=1 Nevue, A. A. Sairavi, A. Huang, S. J. Nakai, H. Mello, C. V. 2024-05-17 doi:10.1101/2024.05.16.589954 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ Protein CoAlation on TXNRD2 regulates mitochondrial thioredoxin system to protect against ferroptosis ]]> https://biorxiv.org/content/10.1101/2024.05.16.594391v1?rss=1 Lin, C.-C. Lin, Y.-T. Chen, S.-Y. Setayeshpour, Y. Chen, Y. Dunn, D. E. Soderblom, E. J. Zhang, G. Filonenko, V. Jeong, S. Y. Floyd, S. R. Hayflick, S. Gout, I. Chi, J.-T. A. 2024-05-18 doi:10.1101/2024.05.16.594391 Cold Spring Harbor Laboratory Press 2024-05-18 <![CDATA[ In vivo Targeting MEK and TNK2/SRC pathways in PTPN11 driven leukemia ]]> https://biorxiv.org/content/10.1101/2024.05.16.594555v1?rss=1 Chang, B. H. Thiel-Klare, K. Tyner, J. 2024-05-18 doi:10.1101/2024.05.16.594555 Cold Spring Harbor Laboratory Press 2024-05-18 <![CDATA[ Maternal Western-style diet programs skeletal muscle gene expression in lean adolescent Japanese macaque offspring ]]> https://biorxiv.org/content/10.1101/2024.05.17.594191v1?rss=1 Beck, E. A. Hetrick, B. Nassar, L. Turnball, D. W. Dean, T. A. Gannon, M. Aagaard, K. M. Wesolowski, S. R. Friedman, J. E. Kievit, P. McCurdy, C. E. 2024-05-21 doi:10.1101/2024.05.17.594191 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Viral and host network analysis of the human cytomegalovirus transcriptome in latency. ]]> https://biorxiv.org/content/10.1101/2024.05.21.594597v1?rss=1 Collins-McMillen, D. K. De Oliveira Pessoa, D. Zarrella, K. Parkins, C. J. Daily, M. Moorman, N. K. Kamil, J. P. Caposio, P. Padi, M. Goodrum, F. 2024-05-21 doi:10.1101/2024.05.21.594597 Cold Spring Harbor Laboratory Press 2024-05-21 <![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[ Clonal spheroids capture functional and genetic heterogeneity of head and neck cancer ]]> https://biorxiv.org/content/10.1101/2024.05.24.595655v1?rss=1 Pandey, J. Malik, M. Z. Shyanti, R. k. Parashar, P. kujur, P. K. Mishra, D. Tailor, D. Lee, J. M. Kataria, T. Gupta, D. Verma, H. Malhotra, S. V. Kateriya, S. Tandon, V. Chaturvedi, R. Singh, R. P. 2024-05-28 doi:10.1101/2024.05.24.595655 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ Comprehensive multi-site profiling of the malignant pleural mesothelioma micro-environment identifies candidate molecular determinants of histopathologic type ]]> https://biorxiv.org/content/10.1101/2024.05.24.595690v1?rss=1 Severson, D. T. Freyaldenhoven, S. Wadowski, B. Hughes, T. Hung, Y. P. Chirieac, L. Jensen, R. V. Richards, W. G. Sedak, A. A. Gustafson, C. E. Vermilya, K. Innocenti, S. Korle, S. Barlow, J. S. Couger, M. B. Anderson, J. Meyervitz, J. Wang, V. Dao, M. N. Shalek, A. K. De Rienzo, A. Bueno, R. 2024-05-28 doi:10.1101/2024.05.24.595690 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ Altered liver metabolism post-wean abolishes efficacy of vitamin D for breast cancer prevention in a mouse model ]]> https://biorxiv.org/content/10.1101/2024.05.28.596304v1?rss=1 Bernhardt, S. M. Ozaki, M. K. Betts, C. Bleyle, L. A. DeBarber, A. E. Fornetti, J. Liberty, A. L. De Wilde, E. Zhang, Y. Xia, Z. Schedin, P. 2024-06-02 doi:10.1101/2024.05.28.596304 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ TNBC response to paclitaxel phenocopies interferon response which reveals cell cycle-associated resistance mechanisms ]]> https://biorxiv.org/content/10.1101/2024.06.04.596911v1?rss=1 Calistri, N. L. Liby, T. A. Hu, Z. Zhang, H. Dane, M. A. Gross, S. M. Heiser, L. M. 2024-06-06 doi:10.1101/2024.06.04.596911 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ A Nanobody Interaction with SARS-CoV-2 Spike Allows the Versatile Targeting of Lentivirus Vectors ]]> https://biorxiv.org/content/10.1101/2024.06.06.597774v1?rss=1 Alfadhli, A. Bates, T. A. Barklis, R. L. Romanaggi, C. Tafesse, F. Barklis, E. 2024-06-07 doi:10.1101/2024.06.06.597774 Cold Spring Harbor Laboratory Press 2024-06-07 <![CDATA[ Synthesis of ionizable lipopolymers using split-Ugi reaction for pulmonary delivery of various size RNAs and gene editing ]]> https://biorxiv.org/content/10.1101/2024.06.11.598497v1?rss=1 Vlasova, K. Y. Kerr, A. Pennock, N. D. Jozic, A. Sahel, D. Gautam, M. Murthy, N. Roberts, A. Ali, M. W. MacDonald, K. D. Walker, J. Luxenhofer, R. Sahay, G. 2024-06-13 doi:10.1101/2024.06.11.598497 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ A genetically encoded sensor for real-time monitoring of poly-ADP-ribosylation dynamics in-vitro and in cells ]]> https://biorxiv.org/content/10.1101/2024.06.11.598597v1?rss=1 Thomas, A. Upadhyaya, K. Bejan, D. Adoff, H. Cohen, M. S. Schultz, C. 2024-06-13 doi:10.1101/2024.06.11.598597 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Transcriptomic comparison of in vitro models of the human placenta ]]> https://biorxiv.org/content/10.1101/2024.06.14.598695v1?rss=1 Lapehn, S. Nair, S. Firsick, E. J. MacDonald, J. Thoreson, C. Litch, J. A. Bush, N. R. Kadam, L. Girard, S. Myatt, L. Prasad, B. Sathyanarayana, S. Paquette, A. G. 2024-06-16 doi:10.1101/2024.06.14.598695 Cold Spring Harbor Laboratory Press 2024-06-16 <![CDATA[ Discovery of ester-linked ubiquitylation of PARP10 mono-ADP-ribosylation in cells: a dual post-translational modification on Glu/Asp side chains ]]> https://biorxiv.org/content/10.1101/2024.06.27.600929v1?rss=1 Bejan, D. S. Lacoursiere, R. E. Pruneda, J. N. Cohen, M. S. 2024-06-27 doi:10.1101/2024.06.27.600929 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Dopamine transmission at D1 and D2 receptors in the nucleus accumbens contributes to the expression of incubation of cocaine craving ]]> https://biorxiv.org/content/10.1101/2024.06.26.600812v1?rss=1 Weber, S. J. Kawa, A. B. Moutier, A. L. Beutler, M. M. Koyshman, L. M. Moreno, C. D. Westlake, J. G. Wunsch, A. M. Wolf, M. E. 2024-06-30 doi:10.1101/2024.06.26.600812 Cold Spring Harbor Laboratory Press 2024-06-30 <![CDATA[ Quantifying social roles in multi-animal videos using subject-aware deep-learning ]]> https://biorxiv.org/content/10.1101/2024.07.07.602350v1?rss=1 Goss, K. Bueno-Junior, L. S. Stangis, K. Ardoin, T. Carmon, H. Zhou, J. Satapathy, R. Baker, I. Jones-Tinsley, C. E. Lim, M. M. Watson, B. O. Sueur, C. Ferrario, C. R. Murphy, G. G. Ye, B. Hu, Y. 2024-07-10 doi:10.1101/2024.07.07.602350 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Goal-directed action preparation in humans entails a mixture of corticospinal neural computations ]]> https://biorxiv.org/content/10.1101/2024.07.08.602530v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@9f2444org.highwire.dtl.DTLVardef@5f6eforg.highwire.dtl.DTLVardef@196f41corg.highwire.dtl.DTLVardef@1746035_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOC_FLOATNO Goal-directed action preparation shapes corticospinal output across selected, nonselected, and task-irrelevant motor representations. This study examined whether additive and multiplicative neural computations, common in sensory systems, occur within the corticospinal pathway during action preparation. We probed corticospinal input-output during the performance of various instructed-delay response tasks by applying a range of transcranial magnetic stimulation (TMS) intensities (input) over the primary motor cortex and measuring the resultant motor-evoked potentials (output) from the hand. We found that goal-directed action preparation increases corticospinal gain multiplicatively in task-relevant motor representations while additively suppressing nonselected and irrelevant representations. Greater gain modulation predicted faster responses, highlighting how these computations can enhance signal-to-noise (SNR) to enable efficient action selection and execution in the human motor system. C_FIG Key pointsO_LINeural computations determine what information is transmitted through brain circuits. C_LIO_LIWe investigated whether the motor system uses computations similar to those observed in sensory systems by noninvasively stimulating the corticospinal pathway in humans during goal-directed action preparation. C_LIO_LIWe discovered physiological evidence that corticospinal projections to behaviorally relevant muscles exhibit nonlinear gain computations, while projections to behaviorally irrelevant muscles exhibit linear suppression. C_LIO_LIOur findings suggest that certain computational principles generalize to the human motor system and serve to enhance the contrast between relevant and background neural activity. C_LIO_LIThese results indicate that neural computations during goal-directed action preparation may support motor control by increasing signal-to-noise within the corticospinal pathway. C_LI ]]> Wadsley, C. G. Nguyen, T. Horton, C. Greenhouse, I. 2024-07-11 doi:10.1101/2024.07.08.602530 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Mild neonatal hypoxia disrupts adult hippocampal learning and memory and is associated with CK2-mediated dysregulation of synaptic calcium-activated potassium channel KCNN2 ]]> https://biorxiv.org/content/10.1101/2024.07.10.602558v1?rss=1 Riddle, A. Srivastava, T. Wang, K. Tellez, E. O'neill, H. Gong, X. O'Neil, A. Bell, J. A. Raber, J. Lattal, M. Maylie, J. Back, S. A. 2024-07-16 doi:10.1101/2024.07.10.602558 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import ]]> https://biorxiv.org/content/10.1101/2024.07.17.604013v1?rss=1 Chang, Y.-T. Barad, B. A. Rahmani, H. Zid, B. M. Grotjahn, D. A. 2024-07-19 doi:10.1101/2024.07.17.604013 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Quantifiable Blood TCR Repertoire Components Associated with Immune Aging ]]> https://biorxiv.org/content/10.1101/2024.07.19.604275v1?rss=1 Li, B. Hu, J. Pan, M. Reid, B. Tworoger, S. 2024-07-19 doi:10.1101/2024.07.19.604275 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Spike inference from mouse spinal cord calcium imaging data ]]> https://biorxiv.org/content/10.1101/2024.07.17.603957v1?rss=1 Rupprecht, P. Fan, W. Sullivan, S. J. Helmchen, F. Sdrulla, A. 2024-07-22 doi:10.1101/2024.07.17.603957 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ Smooth Muscle Cells-Expressed Bmal1 Regulates Vascular Calcification Independent of the Canonical Circadian Pathway ]]> https://biorxiv.org/content/10.1101/2024.07.22.604443v1?rss=1 He, M. Sun, Y. Huang, F. Zhu, Z. Velazquez-Miranda, E. Chong, Z. Chen, Y. 2024-07-22 doi:10.1101/2024.07.22.604443 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ A high-performance genetically encoded sensor for cellular imaging of PKC activity in vivo ]]> https://biorxiv.org/content/10.1101/2024.07.19.604387v1?rss=1 Yahiro, T. Bayless-Edwards, L. Jones, J. A. Ma, L. Qin, M. Mao, T. Zhong, H. 2024-07-23 doi:10.1101/2024.07.19.604387 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Changes in maternal blood and placental lipidomic profile in obesity and gestational diabetes: Evidence for sexual dimorphism ]]> https://biorxiv.org/content/10.1101/2024.07.24.605016v1?rss=1 30) and type A2 GDM (matched to obese BMI) with male or female fetus (n=4 each group). Lipids were extracted and fatty acid composition of different lipid classes were analyzed by LC-MS/MS analysis. Significant changes in GDM vs obese, GDM vs lean, and obese vs lean were determined using t-test with a Tukey correction set at p<0.05. ResultsIn placental samples 436 lipids were identified, among which 85 showed significant changes. Of note only in male placentas significant decreases in C22:6 - docosahexaenoic acid (DHA) in phosphatidylcholine (PC) and triglyceride lipid species were seen when comparing tissue from GDM women to lean. In maternal plasma we observed no effect of obesity. GDM or fetal sex. ConclusionThis is the first study assessing fatty acid composition of lipids in matched maternal plasma and placental tissue from lean, obese, and GDM women stratified by fetal sex. It highlights how GDM affects distribution of fatty acids in lipid classes changes in a sexually dimorphic manner in the placenta. ]]> Kadam, L. Velickovic, M. Straton, K. Nicora, C. D. Kyle, J. Wang, E. Monroe, M. Bramer, L. Myatt, L. Burnum-Johnson, K. 2024-07-25 doi:10.1101/2024.07.24.605016 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ Human P2X4 receptor gating is modulated by a stable cytoplasmic cap and a unique allosteric pocket ]]> https://biorxiv.org/content/10.1101/2024.07.25.605151v1?rss=1 Shi, H. Ditter, I. A. Oken, A. C. Mansoor, S. E. 2024-07-25 doi:10.1101/2024.07.25.605151 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ Stromal KITL/SCF promotes pancreas tissue homeostasis and restrains tumor progression ]]> https://biorxiv.org/content/10.1101/2024.07.29.605485v1?rss=1 Onate, M. K. Oon, C. Bhattacharyya, S. Low, V. Chen, C. Zhao, X. Yan, Z. Hang, Y. Kim, S. K. Xia, Z. Sherman, M. H. 2024-07-30 doi:10.1101/2024.07.29.605485 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Complete sequencing of ape genomes ]]> https://biorxiv.org/content/10.1101/2024.07.31.605654v1?rss=1 Yoo, D. Rhie, A. Hebbar, P. Antonacci, F. Logsdon, G. A. Solar, S. J. Antipov, D. Pickett, B. D. Safonova, Y. Montinaro, F. Luo, Y. Malukiewicz, J. Storer, J. M. Lin, J. Sequeira, A. N. Mangan, R. J. Hickey, G. Anez, G. M. Balachandran, P. Bankevich, A. Beck, C. R. Biddanda, A. Borchers, M. Bouffard, G. G. Brannan, E. Brooks, S. Y. Carbone, L. Carrel, L. Chan, A. P. Crawford, J. Diekhans, M. Engelbrecht, E. Feschotte, C. Formenti, G. Garcia, G. H. Gennaro, L. d. Gilbert, D. Green, R. E. Guarracino, A. Gupta, I. Haddad, D. Han, J. Harris, R. S. Hartley 2024-07-31 doi:10.1101/2024.07.31.605654 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Comparative lifespan and healthspan of nonhuman primate species common to biomedical research ]]> https://biorxiv.org/content/10.1101/2024.07.31.606010v1?rss=1 Huber, H. F. Ainsworth, H. C. Quillen, E. E. Salmon, A. Ross, C. Azhar, A. D. Bales, K. Basso, M. A. Coleman, K. Colman, R. Darusman, H. S. Hopkins, B. Hotchkiss, C. E. Jorgensen, M. J. Kavanagh, K. Li, C. Mattison, J. A. Nathanielsz, P. W. Saputro, S. Scorpio, D. G. Sosa, P.-M. Vallender, E. J. Wang, Y. Zeiss, C. J. Shively, C. A. Cox, L. A. 2024-08-01 doi:10.1101/2024.07.31.606010 Cold Spring Harbor Laboratory Press 2024-08-01 <![CDATA[ Single-cell DNA methylation analysis tool Amethyst reveals distinct noncanonical methylation patterns in human glial cells ]]> https://biorxiv.org/content/10.1101/2024.08.13.607670v1?rss=1 Rylaarsdam, L. E. Nichols, R. V. O'Connell, B. L. Coleman, S. Yardimci, G. Adey, A. C. 2024-08-16 doi:10.1101/2024.08.13.607670 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ An epigenetic memory at the CYP1A gene in cancer-resistant, pollution-adapted killifish ]]> https://biorxiv.org/content/10.1101/2024.08.14.607951v1?rss=1 Carrothers, S. Trevisan, R. Jayasundara, N. Pelletier, N. Weeks, E. Meyer, J. N. Di Giulio, R. T. Weinhouse, C. 2024-08-16 doi:10.1101/2024.08.14.607951 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ Traffic Jam activates the Flamenco piRNA cluster locus and the Piwi pathway to ensure transposon silencing and Drosophila fertility. ]]> https://biorxiv.org/content/10.1101/2024.08.15.608167v1?rss=1 Rivera, A. Lee, J.-H. R. Gupta, S. Yang, L. Goel, R. K. Zaia, J. Lau, N. C. 2024-08-16 doi:10.1101/2024.08.15.608167 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ Comparative Transcriptomes of Canine and Human Prostate Cancers Identify Mediators of Castration Resistance ]]> https://biorxiv.org/content/10.1101/2024.08.18.608482v1?rss=1 Angel, M. R. Seguin, B. Lohr, C. V. Beer, T. Feliciano, J. Ramsey, S. A. Thomas, G. V. 2024-08-18 doi:10.1101/2024.08.18.608482 Cold Spring Harbor Laboratory Press 2024-08-18 <![CDATA[ Aquaporin-4 mis-localization slows glymphatic clearance of α-synuclein and promotes α-synuclein pathology and aggregate propagation ]]> https://biorxiv.org/content/10.1101/2024.08.14.607971v1?rss=1 Braun, M. Simon, M. J. Jang, J. Sanderson, K. Swierz, J. Sevao, M. Pincus, A. B. Schaser, A. J. Elliott, J. E. Lim, M. M. Unni, V. K. Schindler, A. G. Keene, C. D. Latimer, C. S. Iliff, J. 2024-08-19 doi:10.1101/2024.08.14.607971 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Sex differences in nucleus accumbens core circuitry engaged by binge-like ethanol drinking ]]> https://biorxiv.org/content/10.1101/2024.08.15.608144v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@c47435org.highwire.dtl.DTLVardef@1a97d69org.highwire.dtl.DTLVardef@68b2cborg.highwire.dtl.DTLVardef@1b2453a_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Summary:C_FLOATNO Binge-like ethanol drinking engages more regions and NAcc inputs in female relative to male mice.Left: Comparison of regions with both greater c-Fos expression and c-Fos+GFP colocalization in female relative to male ethanol drinking mice. Right: NAcc inputs engaged by binge-like ethanol drinking compared to water drinking mice, sex collapsed. Thalamic (TH) regions include left parasubthalamic nucleus, left anteromedial nucleus of the thalamus, left central medial nucleus of the thalamus, left medial group of the dorsal thalamus, left subparafascicular nucleus, left peripeduncular nucleus, and right paraventricular nucleus of the thalamus. EW, Edinger-Westphal nucleus; GU, gustatory areas. Bottom Middle: NAcc inputs with greater engagement in male than female ethanol drinking mice (left and right main olfactory bulbs (MOB). Bottom Right: NAcc inputs with greater engagement in female than male ethanol drinking mice. Amygdala (AMY) regions include left anterior amygdalar area and left intercalated amygdalar area. Hippocampal (HPF) regions include right dentate gyrus, right Field CA1, right Field CA2, and right Field CA3. Hypothalamic (HY) regions include left and right lateral hypothalamic area, left and right periventricular hypothalamic nucleus, preoptic part, right dorsomedial nucleus of the hypothalamus, right posterior hypothalamic nucleus, and right ventromedial hypothalamic nucleus. Midbrain (MB) regions include left and right midbrain reticular nucleus, retrorubral area, left and right superior colliculus, motor related, left nucleus of the brachium of the inferior colliculus, left nucleus of the posterior commissure, left olivary pretectal nucleus, left posterior pretectal nucleus, left superior colliculus, sensory related, and right substantia nigra, reticular parts. Pontine (P) regions include left superior central nucleus raphe, left supratrigeminal nucleus, right nucleus raphe pontis, right pontine reticular nucleus, and right superior olivary complex. Thalamic (TH) regions include left and right lateral dorsal nucleus of the thalamus, right dorsal part of the lateral geniculate complex, right lateral posterior nucleus of the thalamus, and right parasubthalamic nucleus. CB, Cerebellum; MA, magnocellular nucleus; SSp-m, primary somatosensory cortex, mouth; Created with BioRender.com. See Table S18 for additional information. C_FIG ]]> Chan, A. E. Anderson, J. Q. Grigsby, K. E. Jensen, B. E. Ryabinin, A. E. Ozburn, A. R. 2024-08-19 doi:10.1101/2024.08.15.608144 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Biological sex and BMI influence the longitudinal evolution of adolescent and young adult MRI-visible perivascular spaces ]]> https://biorxiv.org/content/10.1101/2024.08.17.608337v1?rss=1 Yamamoto, E. A. Koike, S. Wong, C. Dennis, L. Luther, M. N. Scatena, A. Khambadkone, S. Iliff, J. Lim, M. M. Levendovszky, S. R. Elliott, J. Barisano, G. Muller-Oehring, E. Morales, A. M. Baker, F. Nagel, B. Piantino, J. 2024-08-19 doi:10.1101/2024.08.17.608337 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Towards Digital Quantification of Ploidy from Pan-Cancer Digital Pathology Slides using Deep Learning ]]> https://biorxiv.org/content/10.1101/2024.08.19.608555v1?rss=1 Carrillo-Perez, F. Cramer, E. M. Pizurica, M. Andor, N. Gevaert, O. 2024-08-20 doi:10.1101/2024.08.19.608555 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ CD4+ but not CD8+ T cells are required for protection against severe guinea pig cytomegalovirus infections ]]> https://biorxiv.org/content/10.1101/2024.08.21.608907v1?rss=1 Rollman, T. B. Berkebile, Z. W. Hicks, D. M. Hatfield, J. S. Chauhan, P. Pravetoni, M. Schleiss, M. R. Milligan, G. N. Morgan, T. K. Bierle, C. J. 2024-08-21 doi:10.1101/2024.08.21.608907 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Brain Charts for the Rhesus Macaque Lifespan ]]> https://biorxiv.org/content/10.1101/2024.08.28.610193v1?rss=1 Alldritt, S. Ramirez, J. S. B. Vos de Wael, R. Bethlehem, R. Seidlitz, J. Wang, Z. Nenning, K.-H. Esper, N. B. Smallwood, J. Franco, A. R. Byeon, K. Alexander-Bloch, A. Messinger, A. Chen, A. Thiele, A. Weiss, A. R. Shmuel, A. Fox, A. Tusche, A. Brambrink, A. M. Falchier, A. Hiba, B. Jarraya, B. Jung, B. Butler, B. Russ, B. E. Howell, B. R. Drzewiecki, C. M. Guedj, C. Schwiedrzik, C. M. Amiez, C. Wilson, C. R. E. Klink, C. Kroenke, C. Constantinidis, C. Garin, C. M. Poirier, C. Gale, D. J. Leopold, D. A. Rudko, D. A. Amaral, D. G. Tsao, D. Cook, D. J. 2024-08-30 doi:10.1101/2024.08.28.610193 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon ]]> https://biorxiv.org/content/10.1101/2024.08.29.610280v1?rss=1 Hartley, G. A. Okhovat, M. Hoyt, S. J. Fuller, E. Pauloski, N. Alexandre, N. Alexandrov, I. A. Drennan, R. S. Dubocanin, D. Gilbert, D. M. Mao, Y. McCann, C. Neph, S. Ryabov, F. Sasaki, T. Storer, J. M. Svendsen, D. Troy, W. Wells, J. Core, L. Stergachis, A. Carbone, L. O'Neill, R. J. 2024-08-30 doi:10.1101/2024.08.29.610280 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Distinct functional domains of Dystroglycan regulate inhibitory synapse formation and maintenance in cerebellar Purkinje cells ]]> https://biorxiv.org/content/10.1101/2024.08.29.610348v1?rss=1 Jahncke, J. N. Schnell, E. Wright, K. M. 2024-08-30 doi:10.1101/2024.08.29.610348 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Atlas-scale Single-cell DNA Methylation Profiling with sciMETv3 ]]> https://biorxiv.org/content/10.1101/2024.08.29.610369v1?rss=1 140k cell library from human middle frontal gyrus split across four multiplexed individuals using both Illumina and Ultima sequencing instrumentation. This library was prepared over two days by one individual and required no expensive equipment (e.g. a flow sorter, as required by sciMETv2). The same experiment produced an estimated 650k additional cells that were not sequenced, representing the power of sciMETv3 to meet the throughput needs of the most demanding atlas-scale projects. Finally, we demonstrate the compatibility of sciMETv3 with multimodal assays by introducing sciMET+ATAC, which will enable high- throughput exploration of the interplay between two layers of epigenetic regulation within the same cell, as well as the ability to directly integrate single-cell methylation datasets with existing single-cell ATAC-seq. HighlightsO_LIAtlas-scale production of single-cell DNA methylation libraries in a single experiment C_LIO_LIProtocols and evaluation using both Illumina and Ultima Genomics sequencing platforms C_LIO_LICompatibility of sciMETv3 with capture techniques to reduce sequencing burden C_LIO_LICompatibility of sciMETv3 with enzymatic conversion methods C_LIO_LIGeneration of an integrated >140,000 cell dataset from human middle frontal gyrus across four individuals C_LIO_LIAbility to profile both ATAC and genome-wide DNA methylation from the same cells and integration with datasets from each modality C_LIO_LIA novel implementation of the s3-ATAC technology that leverages a nanowell chip for increased throughput C_LI MotivationDNA methylation forms a basal layer of epigenomic regulatory control, shaping the genomic permissiveness of mammalian cells during lineage specification and development. Aberrant DNA methylation has been associated with myriad health conditions ranging from developmental disorders to cancer. The high cell type specificity necessitates analysis at the single-cell level, much like transcription or other epigenomic properties. However, robust and cost-effective techniques to produce atlas-scale datasets have not been realized for DNA methylation. Here, we directly meet this need by introducing sciMETv3, a high-throughput protocol capable of producing hundreds of thousands of single-cell DNA methylation profiles in a single experiment. ]]> Nichols, R. V. Rylaarsdam, L. O'Connell, B. L. Shipony, Z. Iremadze, N. Acharya, S. N. Adey, A. 2024-08-30 doi:10.1101/2024.08.29.610369 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Structure and inhibition mechanisms of Mycobacterium tuberculosis essential transporterefflux protein A ]]> https://biorxiv.org/content/10.1101/2024.09.04.611325v1?rss=1 Khandelwal, N. K. Gupta, M. Gomez, J. E. Barkho, S. Guan, Z. Eng, A. Y. Kawate, T. Balasubramani, S. G. Sali, A. Hung, D. T. Stroud, R. M. 2024-09-05 doi:10.1101/2024.09.04.611325 Cold Spring Harbor Laboratory Press 2024-09-05 <![CDATA[ AI-Based Discovery and CryoEM Structural Elucidation of a KATP Channel Pharmacochaperone ]]> https://biorxiv.org/content/10.1101/2024.09.05.611490v1?rss=1 Elsheikh, A. Driggers, C. M. Truong, H. H. Yang, Z. Allen, J. Henriksen, N. Walczewska-Szewc, K. Shyng, S.-L. 2024-09-05 doi:10.1101/2024.09.05.611490 Cold Spring Harbor Laboratory Press 2024-09-05 <![CDATA[ Brain-wide mapping of oligodendrocyte organization and oligodendrogenesis across the murine lifespan ]]> https://biorxiv.org/content/10.1101/2024.09.06.611254v1?rss=1 Xu, Y. K. T. Bush, A. Musheyev, E. Kim, A. A. Zhang, S. Eugenin von Bernhardi, J. Sulam, J. Bergles, D. E. 2024-09-08 doi:10.1101/2024.09.06.611254 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ A computationally guided approach to improve expression of VHH binders ]]> https://biorxiv.org/content/10.1101/2024.09.07.611840v1?rss=1 OZDEMIR, E. S. Tolley, J. Goncalves, F. Gomes, M. Wagnell, E. Branchaud, B. Ranganathan, S. 2024-09-13 doi:10.1101/2024.09.07.611840 Cold Spring Harbor Laboratory Press 2024-09-13 <![CDATA[ Retinoic acid-mediated homeostatic plasticity drives cell type-specific CP-AMPAR accumulation in nucleus accumbens core and incubation of cocaine craving ]]> https://biorxiv.org/content/10.1101/2024.09.12.611703v1?rss=1 Hwang, E.-K. Wunsch, A. M. Wolf, M. E. 2024-09-14 doi:10.1101/2024.09.12.611703 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ A Comprehensive Proteogenomic and Spatial Analysis of Innate and Acquired Resistance of Metastatic Melanoma to Immune Checkpoint Blockade Therapies ]]> https://biorxiv.org/content/10.1101/2024.09.12.612675v1?rss=1 wei, s. Du, K. Lan, H. Yang, Z. Deng, Y. Wei, Z. Frederick, D. T. Lee, J. Labrie, M. Tian, T. Moll, T. Chen, Y. Sullivan, R. J. Mills, G. B. Boland, G. M. Flaherty, K. liu, l. Herlyn, M. Zhang, G. 2024-09-15 doi:10.1101/2024.09.12.612675 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Contribution of amygdala to dynamic model arbitration under uncertainty ]]> https://biorxiv.org/content/10.1101/2024.09.13.612869v1?rss=1 Woo, J. H. Costa, V. D. Taswell, C. A. Rothenhoefer, K. M. Averbeck, B. Soltani, A. 2024-09-15 doi:10.1101/2024.09.13.612869 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Changes in nucleus accumbens core translatome accompanying incubation of cocaine craving ]]> https://biorxiv.org/content/10.1101/2024.09.15.613147v1?rss=1 Kawa, A. B. Hashimoto, J. G. Beutler, M. M. Guizzetti, M. Wolf, M. E. 2024-09-16 doi:10.1101/2024.09.15.613147 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ A functional screen for ubiquitin regulation identifies an E3 ligase secreted by Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2024.09.18.613774v1?rss=1 Roberts, C. G. Kaur, S. Ogden, A. J. Divine, M. E. Warren, G. D. Kang, D. Kirienko, N. V. Geurink, P. P. Mulder, M. P. Nakayasu, E. S. McDermott, J. E. Adkins, J. N. Aballay, A. Pruneda, J. N. 2024-09-18 doi:10.1101/2024.09.18.613774 Cold Spring Harbor Laboratory Press 2024-09-18 <![CDATA[ Melanocortin-4 receptor antagonist TCMCB07 alleviates chemotherapy-induced anorexia and weight loss ]]> https://biorxiv.org/content/10.1101/2024.09.14.613069v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@cbe32borg.highwire.dtl.DTLVardef@1af55e7org.highwire.dtl.DTLVardef@30deb1org.highwire.dtl.DTLVardef@6c39a3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Zhu, X. Potterfield, R. Gruber, K. A. Zhang, E. Newton, S. Norgard, M. A. Levasseur, P. R. Bai, P. Chen, X. Gu, Q. Grossberg, A. Marks, D. L. 2024-09-19 doi:10.1101/2024.09.14.613069 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Heart rate variability impairment during sleep in Veterans with REM sleep behavior disorder, traumatic brain injury, and posttraumatic stress disorder: An early potential window into autonomic dysfunction? ]]> https://biorxiv.org/content/10.1101/2024.09.20.614142v1?rss=1 Cunningham, H. A. Dovek, L. Recoder, N. Bryant-Ekstrand, M. D. Ligman, B. Piantino, J. Lim, M. M. Elliott, J. E. 2024-09-24 doi:10.1101/2024.09.20.614142 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Multi-omics identification of extracellular components of the fetal monkey and human neocortex. ]]> https://biorxiv.org/content/10.1101/2024.09.25.615077v1?rss=1 Vilicich, F. Vettiatil, D. Kattapong Graber, S. Nawsheen, N. Patel, N. Quezada, A. Gurney, E. Smith, E. M. Nelson, H. Pesci, S. Atrio, J. Moreno, N. Jones, A. Murphy, M. Benfield, N. Hennelbold, J. Solansky, N. Lisgo, S. Glass, I. Birth Defects Research Laboratory, Sidoli, S. 2024-09-26 doi:10.1101/2024.09.25.615077 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Pancreatic cancer cells overexpressing interleukin 6 induce T-cell-mediated tumor clearance and durable anti-tumor immune response ]]> https://biorxiv.org/content/10.1101/2024.09.26.615308v1?rss=1 Arneson-Wissink, P. C. Bartlett, A. Q. Mendez, H. Zhu, X. Dickie, J. McWhorter, M. Levasseur, P. R. Diba, P. Byrne, K. Scott, G. D. Eil, R. Grossberg, A. 2024-09-27 doi:10.1101/2024.09.26.615308 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Quantifying Cancer Drug Targetability across Biochemical Pathways ]]> https://biorxiv.org/content/10.1101/2024.09.27.615497v1?rss=1 Hagler, S. 2024-10-01 doi:10.1101/2024.09.27.615497 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Autophosphorylation of the oncogenic protein TEL-ABL confers resistance to the allosteric ABL inhibitor asciminib ]]> https://biorxiv.org/content/10.1101/2024.10.02.616342v1?rss=1 2000-fold less potent against TEL-ABL than BCR-ABL in cell-growth assays. This is surprising because the ABL components of the two fusion proteins, including the asciminib binding sites, have identical sequence. We deleted a short helical segment in the ABL kinase domain that closes over asciminib when it is bound. This deletion results in asciminib resistance in BCR-ABL, but has no effect on TEL-ABL, suggesting that the native autoinhibitory mechanism that asciminib engages in BCR-ABL is disrupted in TEL-ABL. We show, using mammalian cell expression and single-molecule microscopy, that BCR-ABL is mainly dimeric while TEL-ABL forms higher-order oligomers. Oligomerization can promote trans-autophosphorylation of ABL, and we find that a regulatory phosphorylation site in the SH3 domain of ABL (Tyr 89) is highly phosphorylated in TEL-ABL. This phosphorylation is expected to disassemble the autoinhibited conformation of ABL, thereby preventing asciminib binding. We show that TEL-ABL is intrinsically susceptible to inhibition by asciminib, but that increased phosphorylation results in resistance. Our results demonstrate that different ABL fusion proteins can have dramatically different responses to allosteric inhibitors due to differential phosphorylation. One Sentence SummaryWhen TEL-ABL is phosphorylated, it is insensitive to asciminib. However, when TEL-ABL is dephosphorylated by a phosphatase, asciminib sensitivity is restored. ]]> Muratcioglu, S. Eide, C. A. Gorday, K. Sumpena, E. Zuo, W. Groves, J. T. Druker, B. J. Kuriyan, J. 2024-10-02 doi:10.1101/2024.10.02.616342 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ 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[ An effective method of measuring nanobody binding kinetics and competition-based epitope mapping using biolayer interferometry ]]> https://biorxiv.org/content/10.1101/2024.10.03.616354v1?rss=1 Bates, T. A. Gurmessa, S. K. Reyes-Weinstein, J. B. Trank-Greene, M. Wrynla, X. H. Anastas, A. Anley, T. W. Hinchliff, A. Shinde, U. Burke, J. E. Tafesse, F. G. 2024-10-04 doi:10.1101/2024.10.03.616354 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Disruption of riboflavin biosynthesis in mycobacteria establishes 5-amino-6-D-ribitylaminouracil (5-A-RU) as key precursor of MAIT cell agonists ]]> https://biorxiv.org/content/10.1101/2024.10.03.616430v1?rss=1 Chengalroyen, M. D. Oketade, N. Worley, A. Lucas, M. Ramirez, L. N. Raphela, M. L. Swarbrick, G. Warner, D. F. Lewinsohn, D. Mehaffy, C. Adams, E. J. Hildebrand, W. Dobos, K. M. Mizrahi, V. Lewinsohn, D. 2024-10-04 doi:10.1101/2024.10.03.616430 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Cryo-electron tomography reveals coupled flavivirus replication, budding and maturation ]]> https://biorxiv.org/content/10.1101/2024.10.13.618056v1?rss=1 Dahmane, S. Schexnaydre, E. Zhang, J. Rosendal, E. Chotiwan, N. Kumari Singh, B. Yau, W.-L. Lundmark, R. Barad, B. Grotjahn, D. A. Liese, S. Carlson, A. Overby, A. Carlson, L.-A. 2024-10-13 doi:10.1101/2024.10.13.618056 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ In vitro inhibition of the CFTR ion channel in the cervix thickens cervical mucus ]]> https://biorxiv.org/content/10.1101/2024.10.14.618249v1?rss=1 Looney, R. J. Roberts, M. Markovetz, M. Godiah, R. Yao, S. Golgotiu, K. Wei, S. Cellucci, C. Han, L. 2024-10-15 doi:10.1101/2024.10.14.618249 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ FBXW7 regulates MYRF levels to control myelin capacity and homeostasis in the adult CNS ]]> https://biorxiv.org/content/10.1101/2024.10.15.618515v1?rss=1 Collins, H. Y. Doan, R. A. Li, J. Early, J. E. Madden, M. E. Simkins, T. Lyons, D. A. Monk, K. R. Emery, B. 2024-10-18 doi:10.1101/2024.10.15.618515 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Understanding the development of enzalutamide resistance based on a functional single-cell approach ]]> https://biorxiv.org/content/10.1101/2024.10.20.619319v1?rss=1 Xue, C. Ko, H.-K. Shi, K. Pittsenbarger, J. Dao, L. V. Shi, K. Libmann, M. Geng, H. Qian, D. Z. 2024-10-22 doi:10.1101/2024.10.20.619319 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ AI-readiness for Biomedical Data: Bridge2AI Recommendations ]]> https://biorxiv.org/content/10.1101/2024.10.23.619844v1?rss=1 Clark, T. Caufield, H. Mohan, J. A. Al Manir, S. Amorim, E. Eddy, J. Gim, N. Gow, B. Goar, W. Haendel, M. Hansen, J. N. Harris, N. Hermjakob, H. McWeeney, S. K. Nebeker, C. Nikolov, M. Shaffer, J. Sheffield, N. Sheynkman, G. Stevenson, J. Mungall, C. Chen, J. Y. Wagner, A. Kong, S. W. Ghosh, S. S. Patel, B. Williams, A. Munoz-Torres, M. C. 2024-10-25 doi:10.1101/2024.10.23.619844 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Transcriptional profiles of murine oligodendrocyte precursor cells across the lifespan ]]> https://biorxiv.org/content/10.1101/2024.10.27.620502v1?rss=1 Heo, D. Kim, A. A. Neumann, B. Doze, V. N. Xu, Y. K. T. Mironova, Y. A. Slosberg, J. Goff, L. A. Franklin, R. J. M. Bergles, D. E. 2024-10-28 doi:10.1101/2024.10.27.620502 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Reductions of Grin2a in adolescent dopamine neurons confers aberrant salience and related psychosis phenotype ]]> https://biorxiv.org/content/10.1101/2024.10.28.620713v1?rss=1 Kielhold, M. L. Jacobs, D. S. Pacheco, A. T. Lebowitz, J. J. Williams, J. T. Langdon, A. J. Zweifel, L. Moghaddam, B. 2024-10-28 doi:10.1101/2024.10.28.620713 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Drosophila with-no-lysine and frayed Act in Parallel to dSarm to Drive Neurodegeneration Following dNmnat Depletion ]]> https://biorxiv.org/content/10.1101/2024.10.29.620922v1?rss=1 Avetisyan, A. Barria, R. Sheehan, A. Freeman, M. R. 2024-10-31 doi:10.1101/2024.10.29.620922 Cold Spring Harbor Laboratory Press 2024-10-31 <![CDATA[ Thalamic integration of basal ganglia and cerebellar circuits during motor learning ]]> https://biorxiv.org/content/10.1101/2024.10.31.621388v1?rss=1 Roth, R. H. Muniak, M. A. Huang, C. J. Hwang, F.-J. Sun, Y. Min, C. Mao, T. Ding, J. B. 2024-11-01 doi:10.1101/2024.10.31.621388 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Single-cell, spatial, and fate-mapping analyses uncover niche dependent diversity of cochlear myeloid cells. ]]> https://biorxiv.org/content/10.1101/2024.10.30.621184v1?rss=1 Chiot, A. Felgner, M. J. Brownell, D. Rott, K. H. Bogachuk, A. Rosmus, D.-D. Masuda, T. Ching, A. Atkinson, P. J. Prinz, M. Sachs, K. Cheng, A. G. Wieghofer, P. Ajami, B. 2024-11-02 doi:10.1101/2024.10.30.621184 Cold Spring Harbor Laboratory Press 2024-11-02 <![CDATA[ A high-throughput protein tagging toolkit that retains endogenous UTRs for studying gene regulation in Kinetoplastids. ]]> https://biorxiv.org/content/10.1101/2024.11.02.621556v1?rss=1 Carbajo, C. G. Han, X. Savur, B. Upadhyaya, A. Taha, F. Tinti, M. Wheeler, R. J. Yates, P. A. Tiengwe, C. 2024-11-03 doi:10.1101/2024.11.02.621556 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ SloR-SRE binding to the S. mutans mntH promoter is cooperative. ]]> https://biorxiv.org/content/10.1101/2024.11.02.621577v1?rss=1 Ziogas, M. Drummond, I. Y. Todorovic, I. Kraczkowsky, K. N. Zhang, H. Wu, H. Spatafora, G. 2024-11-03 doi:10.1101/2024.11.02.621577 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Multi-omics analysis in mouse primary cortical neurons reveals complex positive and negative biological interactions between constituent compounds in Centella asiatica ]]> https://biorxiv.org/content/10.1101/2024.11.04.621595v1?rss=1 Chamberlin, S. R. Zweig, J. Neff, C. Marney, L. Choi, J. Yang, L. Maier, C. Soumyanath, A. McWeeney, S. Gray, N. E. 2024-11-04 doi:10.1101/2024.11.04.621595 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ Cocaine, via ΔFosB, remodels gene expression and excitability in ventral hippocampus ]]> https://biorxiv.org/content/10.1101/2024.11.06.621895v1?rss=1 Eagle, A. L. Doyle, M. A. Sugimoto, C. Dykstra, M. M. Kuhn, H. M. Murray, B. R. Bastle, R. M. He, J. Maze, I. Mazei-Robison, M. Robison, A. J. 2024-11-07 doi:10.1101/2024.11.06.621895 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ TIA1 Mediates Divergent Inflammatory Responses to Tauopathy in Microglia and Macrophages ]]> https://biorxiv.org/content/10.1101/2024.11.06.622325v1?rss=1 Webber, C. J. Van Der Spek, S. Cruz, A. L. F. Puri, S. Zhang, C. Aw, J. T. M. Papadimitriou, G.-Z. Roberts, R. Jiang, K. Tran, T. N. Zhang, L. Taylor, A. K. Wang, Z. Porter, J. Sotiropoulos, I. Emili, A. Silva, J. M. Li, H. Wolozin, B. 2024-11-07 doi:10.1101/2024.11.06.622325 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ Convolutional neural network models describe the encoding subspace of local circuits in auditory cortex ]]> https://biorxiv.org/content/10.1101/2024.11.07.622384v1?rss=1 Wingert, J. C. Parida, S. Norman-Haignere, S. V. David, S. V. 2024-11-08 doi:10.1101/2024.11.07.622384 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Proteomic characterization of Mycobacterium tuberculosis subjected to carbon starvation ]]> https://biorxiv.org/content/10.1101/2024.11.12.623260v1?rss=1 Devlin, K. L. Leach, D. T. Stratton, K. G. Lamichhane, G. Lin, V. Beatty, K. E. 2024-11-12 doi:10.1101/2024.11.12.623260 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ A genome-wide ATLAS of liver chromatin architecture reveals that sex dictates diet-induced nucleosome dynamics ]]> https://biorxiv.org/content/10.1101/2024.11.13.623052v1?rss=1 ZHANG, Z. Su, V. Wiese, C. B. Cheng, L. Wang, D. Cui, Y. Kim, J. Wu, X. Tran, P. H. Zhou, Z. Casero, D. Li, W. Hevener, A. L. Reue, K. Sallam, T. 2024-11-15 doi:10.1101/2024.11.13.623052 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Ezh2 Delays Activation of Differentiation Genes During Normal Cerebellar Granule Neuron Development and in Medulloblastoma ]]> https://biorxiv.org/content/10.1101/2024.11.21.624171v1?rss=1 Purzner, J. Brown, A. S. Purzner, T. Ellis, L. Broski, S. Litzenburger, U. Andrews, K. Sharma, A. Wang, X. Taylor, M. D. Cho, Y.-J. Fuller, M. T. Scott, M. P. 2024-11-21 doi:10.1101/2024.11.21.624171 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Unraveling SARS-CoV-2 Host-Response Heterogeneity through Longitudinal Molecular Subtyping ]]> https://biorxiv.org/content/10.1101/2024.11.22.624784v1?rss=1 Wang, K. Nie, Y. Maguire, C. Syphurs, C. Sheen, H. Karoly, M. Lapp, L. Gygi, J. P. Jayavelu, N. D. Patel, R. K. Hoch, A. IMPACC Network, Corry, D. Kheradmand, F. McComsey, G. A. Fernandez-Sesma, A. Simon, V. Metcalf, J. P. Agudelo Higuita, N. I. Messer, W. B. David, M. M. Nadeau, K. C. Kraft, M. Bime, C. Schaenman, J. Erle, D. Calfee, C. S. Atkinson, M. A. Brackenridge, S. C. Hafler, D. A. Shaw, A. C. Rahman, A. Hough, C. L. Geng, L. N. Ozonoff, A. Haddad, E. K. Reed, E. F. Bakel, H. v. Kim-Schulze, S. H. Krammer, F. Wilson, M. Eckalbar, W. Bosinger, 2024-11-25 doi:10.1101/2024.11.22.624784 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Targeting the menopause transition with metformin improves breast cancer outcomes, but discontinuation has deleterious effects on metabolic health: Findings from a preclinical model of postmenopausal breast cancer. ]]> https://biorxiv.org/content/10.1101/2024.11.25.625083v1?rss=1 Corleto, K. A. Schedin, P. Kotta, A. S. Strandmo, J. L. Foster, S. M. Lammoglia, N. Karmakar, M. Carroll, R. J. MacLean, P. S. Giles, E. D. 2024-11-26 doi:10.1101/2024.11.25.625083 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Systemic exposure to COVID-19 virus-like particles modulates firing patterns of cortical neurons in the living mouse brain ]]> https://biorxiv.org/content/10.1101/2024.11.26.625543v1?rss=1 Das, A. Icardi, J. Borovicka, J. Holden, S. Harrison, H. F. Hirsch, A. J. Raber, J. Dana, H. 2024-11-27 doi:10.1101/2024.11.26.625543 Cold Spring Harbor Laboratory Press 2024-11-27 <![CDATA[ The TLR7/8 agonist INI-4001 enhances the immunogenicity of a Powassan virus-like-particle vaccine ]]> https://biorxiv.org/content/10.1101/2024.11.28.625832v1?rss=1 Crawford, M. W. Abdelwahab, W. M. Siram, K. Parkins, C. J. Harrison, H. F. Osman, S. R. Schweitzer, D. Evans, J. T. Burkhart, D. J. Pinto, A. K. Brien, J. D. Smith, J. L. Hirsch, A. J. 2024-12-03 doi:10.1101/2024.11.28.625832 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Multinucleated giant cells are hallmarks of ovarian aging with unique immune and degradation-associated molecular signatures ]]> https://biorxiv.org/content/10.1101/2024.12.03.626649v1?rss=1 Converse, A. Perry, M. J. Dipali, S. S. Isola, J. V. Kelley, E. B. Varberg, J. M. Zelinkski, M. B. Gerton, J. L. Stout, M. Pritchard, M. T. Duncan, F. 2024-12-04 doi:10.1101/2024.12.03.626649 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ A negative binomial latent factor model for paired microbiome sequencing data ]]> https://biorxiv.org/content/10.1101/2024.12.01.626246v1?rss=1 Kim, H. Siddiqui, N. Y. Karstens, L. Ma, L. 2024-12-05 doi:10.1101/2024.12.01.626246 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Alpha-synuclein knockout impairs melanoma development and alters DNA damage repair in the TG3 mouse model in a sex-dependent manner ]]> https://biorxiv.org/content/10.1101/2024.12.01.626256v1?rss=1 Arnold, M. R. Chen, S. Unni, V. K. 2024-12-05 doi:10.1101/2024.12.01.626256 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ IFNγ-dependent metabolic reprogramming restrains an immature, pro-metastatic lymphatic state in melanoma ]]> https://biorxiv.org/content/10.1101/2024.12.02.626426v1?rss=1 Karakousi, T. Cristaldi, V. Lopes de Oliveira, M. L. Medeiros Geraldo, L. H. Gonzalez-Robles, T. da Silva, G. Breazeale, A. P. Encarnacion Rosado, J. Pozniak, J. Kimmelman, A. Ruggles, K. Marine, J. C. Chandel, N. S. Lund, A. W. 2024-12-05 doi:10.1101/2024.12.02.626426 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Mechanism of small heat shock protein client sequestration and induced polydispersity ]]> https://biorxiv.org/content/10.1101/2024.12.03.626640v1?rss=1 Miller, A. P. Reichow, S. L. 2024-12-06 doi:10.1101/2024.12.03.626640 Cold Spring Harbor Laboratory Press 2024-12-06 <![CDATA[ UniFORM: Towards Universal Immunofluorescence Normalization for Multiplex Tissue Imaging ]]> https://biorxiv.org/content/10.1101/2024.12.06.626879v1?rss=1 Wang, K. Ait-Ahmad, K. Kupp, S. Sims, Z. Cramer, E. Sayar, Z. Yu, J. Wong, M. H. Mills, G. B. Eksi, S. E. Chang, Y. H. 2024-12-10 doi:10.1101/2024.12.06.626879 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ Recognizing amino acid sidechains in a medium resolution cryo-electron density map ]]> https://biorxiv.org/content/10.1101/2024.12.10.627859v1?rss=1 Mondal, D. Kumar, V. Satler, T. Ramachandran, R. Saltzberg, D. Chemmama, I. Pilla, K. B. Echeverria, I. Webb, B. M. Gupta, M. Verba, K. A. Sali, A. 2024-12-12 doi:10.1101/2024.12.10.627859 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Conformational plasticity of human acid-sensing ion channel 1a ]]> https://biorxiv.org/content/10.1101/2024.12.11.628012v1?rss=1 Cahill, J. Hartfield, K. A. Heusser, S. A. Poulsen, M. H. Yoshioka, C. Pless, S. A. Baconguis, I. 2024-12-12 doi:10.1101/2024.12.11.628012 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Synaptic facilitation enhances the reliability and precision of high frequency neurotransmission ]]> https://biorxiv.org/content/10.1101/2024.12.18.629013v1?rss=1 Bernal-Correa, A. M. Dagostin, A. von Gersdorff, H. Kushmerick, C. 2024-12-18 doi:10.1101/2024.12.18.629013 Cold Spring Harbor Laboratory Press 2024-12-18 <![CDATA[ Statins inhibit onco-dimerization of the 4Ig isoform of B7-H3 ]]> https://biorxiv.org/content/10.1101/2024.12.18.628944v1?rss=1 Sutton, M. N. Glazer, S. E. Al Zaki, A. Napoli, A. Yang, P. Bhosale, P. Liu, J. Gammon, S. T. Piwnica-Worms, D. 2024-12-20 doi:10.1101/2024.12.18.628944 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Deciphering single-cell heterogeneity and cellular ecosystem dynamics during prostate cancer progression ]]> https://biorxiv.org/content/10.1101/2024.12.18.629070v1?rss=1 Zhao, F. Zeng, J. Chen, C. Zhao, X. Zhang, T. Thomas, G. V. Sears, R. C. Alumkal, J. J. Moran, A. E. Mills, G. B. Nelson, P. S. Xia, Z. 2024-12-20 doi:10.1101/2024.12.18.629070 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Host and rabies virus gene expression is shaped by human brain cell type and reveals a preexisting pro-viral transcriptional state in astrocytes ]]> https://biorxiv.org/content/10.1101/2024.12.18.629263v1?rss=1 Feige, L. Young, K. Cerapio, J. P. Kozaki, T. Kergoat, L. Libri, V. Ginhoux, F. Hasan, M. Ben Ameur, L. Chin, G. Goode, Z. Bourhy, H. Saunders, A. 2024-12-20 doi:10.1101/2024.12.18.629263 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ DNAJC13 localization to endosomes is opposed by its J domain and its disordered C-terminal tail ]]> https://biorxiv.org/content/10.1101/2024.12.19.629517v1?rss=1 Adoff, H. Novy, B. Holland, E. Lobingier, B. 2024-12-20 doi:10.1101/2024.12.19.629517 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Anti-Cancer Immune Priming with Beta-Radioligand Therapy and Isoform-Selective Targeting of 4Ig-B7-H3 ]]> https://biorxiv.org/content/10.1101/2024.12.20.629740v1?rss=1 Glazer, S. E. Sutton, M. N. Yang, P. Pisaneschi, F. Sebastian, M. M. Gammon, S. T. Piwnica-Worms, D. 2024-12-22 doi:10.1101/2024.12.20.629740 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Generation of a transgenic P. cynomolgi parasite expressing P. vivax circumsporozoite protein for testing pre-erythrocytic malaria vaccines in non-human primates ]]> https://biorxiv.org/content/10.1101/2024.12.26.630255v1?rss=1 Aleshnick, M. Hegde, S. Jennison, C. Mikolajczak, S. Vaughan, A. M. Haumpy, D. Straimer, J. Wilder, B. 2024-12-26 doi:10.1101/2024.12.26.630255 Cold Spring Harbor Laboratory Press 2024-12-26 <![CDATA[ The RNA-binding protein HuR impairs adipose tissue anabolism in pancreatic cancer cachexia ]]> https://biorxiv.org/content/10.1101/2024.12.27.630549v1?rss=1 Arneson-Wissink, P. C. Pelz, K. Worley, B. Mendez, H. Pham, P. McCarthy, G. Chitsazan, A. Brody, J. R. Grossberg, A. 2024-12-28 doi:10.1101/2024.12.27.630549 Cold Spring Harbor Laboratory Press 2024-12-28 <![CDATA[ Rapid clonal selection within early hematopoietic cell compartments presages outcome to ivosidenib combination therapy ]]> https://biorxiv.org/content/10.1101/2024.12.30.630700v1?rss=1 4 years. To study longitudinal clonal dynamics through hematopoietic differentiation, we performed high-sensitivity single-cell genotyping in index-sorted sequential patient samples. In all patients who relapsed, therapy-resistant clones were selected rapidly, within 1-3 treatment cycles, at times when hematopoiesis was still largely sustained by either normal or pre-leukemic cells. Selection of therapy-resistant clones preceded overt treatment failure by months or even years. Relapse was associated either with clones harboring newly-detected myeloid driver mutations or expansion of minor pre-existing clones that had reduced fitness prior to treatment. In both cases, resistant clones were selected within immature cell populations previously shown to contain leukemic stem cell (LSC) potential, preceding malignant expansion of these compartments by immunophenotyping. In contrast, in both patients remaining in remission, leukemic clones were eradicated and rapidly replaced by clonal and wild-type hematopoiesis. These observations suggest that, in patients treated with non-intensive ivosidenib combination therapy, rapid clonal selection occurs in populations with LSC potential, where failure to eliminate either genetically evolved or persistent leukemic clones ultimately leads to relapse. Key points- Rapid selection of leukemic clones occurs within small populations with LSC potential, months or years prior to relapse. - Rapid eradication of leukemic clones leads to sustained remission in the context of ivosidenib combination therapy. ]]> Turkalj, S. Stoilova, B. Groom, A. J. Radtke, F. A. Mecklenbrauck, R. Jakobsen, N. A. Lachowiez, C. A. Metzner, M. Usukhbayar, B. Salazar, M. A. Zeng, Z. Loghavi, S. Marvin-Peek, J. Koerber, V. Ravandi, F. Issa, G. Kadia, T. Symeonido, V. de Groot, A. P. Kantarjian, H. Takahashi, K. Konopleva, M. DiNardo, C. D. Vyas, P. 2024-12-31 doi:10.1101/2024.12.30.630700 Cold Spring Harbor Laboratory Press 2024-12-31 <![CDATA[ Analysis of mouse lens morphological and proteomic abnormalities following depletion of βB3-crystallin ]]> https://biorxiv.org/content/10.1101/2024.12.30.630781v1?rss=1 Rayee, D. Wilmarth, P. A. VanSlyke, J. K. Zientek, K. Reddy, A. P. Musil, L. S. David, L. L. Cvekl, A. 2024-12-31 doi:10.1101/2024.12.30.630781 Cold Spring Harbor Laboratory Press 2024-12-31 <![CDATA[ Noise-induced hearing loss enhances Ca2+-dependent spontaneous bursting activity in lateralcochlear efferents ]]> https://biorxiv.org/content/10.1101/2025.01.07.631771v1?rss=1 Hong, H. Trussell, L. O. 2025-01-08 doi:10.1101/2025.01.07.631771 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ Developmental axon diameter growth of central nervous system axons does not depend on ensheathment or myelination by oligodendrocytes ]]> https://biorxiv.org/content/10.1101/2025.01.10.632348v1?rss=1 Bin, J. M. Emberley, K. Buscham, T. J. Eichel-Vogel, M. A. Doan, R. A. Steyer, A. M. Nolan, M. F. Möbius, W. Monk, K. R. Werner, H. B. Emery, B. Lyons, D. A. 2025-01-10 doi:10.1101/2025.01.10.632348 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ The bile acid-sensitive ion channel is gated by Ca2+-dependent conformational changes in the transmembrane domain ]]> https://biorxiv.org/content/10.1101/2025.01.10.632481v1?rss=1 Freitas, M. M. Gouaux, E. 2025-01-12 doi:10.1101/2025.01.10.632481 Cold Spring Harbor Laboratory Press 2025-01-12 <![CDATA[ Cholesterol deficiency directs autophagy-dependent secretion of extracellular vesicles ]]> https://biorxiv.org/content/10.1101/2025.01.11.632510v1?rss=1 Yaeger, J. D. Sengupta, S. Walz, A. L. Morita, M. Morgan, T. K. Vermeer, P. D. Francis, K. R. 2025-01-12 doi:10.1101/2025.01.11.632510 Cold Spring Harbor Laboratory Press 2025-01-12 <![CDATA[ A Cross-Species Atlas of the Dorsal Vagal Complex Reveals Neural Mediators of Cagrilintide's Effects on Energy Balance ]]> https://biorxiv.org/content/10.1101/2025.01.13.632726v1?rss=1 Ludwig, M. Q. Coester, B. Gordian, D. Hassan, S. Tomlinson, A. J. Toure, M. H. Christensen, O. P. Moltke-Prehn, A. Brown, J. M. Rausch, D. M. Gowda, A. Wu, I. Kernodle, S. Dong, V. Ayensu-Mensah, M. Sabatini, P. V. Shin, J. H. Kirigiti, M. Egerod, K. L. Le Foll, C. Lundh, S. Gerstenberg, M. K. Lutz, T. A. Kievit, P. Secher, A. Raun, K. Myers, M. G. Pers, T. H. 2025-01-15 doi:10.1101/2025.01.13.632726 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Distinct cell types along thick ascending limb express pathways for monovalent and divalent cation transport ]]> https://biorxiv.org/content/10.1101/2025.01.16.633282v1?rss=1 Bahena-Lopez, J. Demirci, H. Smorodchenko, A. Su, X.-T. Nelson, J. Yang, C.-L. Wang, W.-H. Curry, J. Duan, X.-P. Sharkovska, Y. Liu, R. Yilmaz, D. E. Quintanova, C. Emberly, K. Emery, B. Himmerkus, N. Bleich, M. Bachmann, S. Ellison, D. H. 2025-01-21 doi:10.1101/2025.01.16.633282 Cold Spring Harbor Laboratory Press 2025-01-21 <![CDATA[ A nonhuman primate model mirrors human congenital cytomegalovirus infection and reveals a spectrum of vertical transmission outcomes ]]> https://biorxiv.org/content/10.1101/2025.01.16.633406v1?rss=1 Manuel, T. D. Mostrom, M. J. Crooks, C. Davalos, A. Barfield, R. Scheef, E. A. Kendall, S. Midkiff, C. C. Sprehe, L. M. Trexler, M. Boquet, F. Shroyer, M. Danner, V. Doyle-Meyers, L. Mirza, A. Lammi, S. Otero, C. E. Lee, M. Rogers, L. Kowalik, T. Chan, C. Permar, S. R. Blair, R. V. Frueh, K. Malouli, D. Granek, J. A. Owzar, K. Kaur, A. 2025-01-21 doi:10.1101/2025.01.16.633406 Cold Spring Harbor Laboratory Press 2025-01-21 <![CDATA[ Combinations comprising dual β-lactams and a β-lactamase inhibitor achieve optimal synergistic inhibition of Mycobacterium abscessus growth ]]> https://biorxiv.org/content/10.1101/2025.01.20.633926v1?rss=1 Rimal, B. Xie, Y. Panthi, C. M. Devlin, K. L. Beatty, K. E. Lamichhane, G. 2025-01-21 doi:10.1101/2025.01.20.633926 Cold Spring Harbor Laboratory Press 2025-01-21 <![CDATA[ Neoplastic immune mimicry is a generalizable phenomenon in breast cancer and epithelial CD69 enables early tumor progression ]]> https://biorxiv.org/content/10.1101/2025.01.17.633673v1?rss=1 Berens, E. B. Khou, S. Huang, E. Hoffman, A. Johnson, B. Kirchberger, N. Sivagnanam, S. Calistri, N. L. Derrick, D. Liby, T. A. McLean, I. C. Alanizi, A. A. Ozmen, F. Ozmen, T. Y. Mills, G. B. Hwang, E. S. Schedin, P. J. Gonzalez, H. Werb, Z. Heiser, L. M. Coussens, L. M. 2025-01-22 doi:10.1101/2025.01.17.633673 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Inferring single-cell dynamics of a molecular reporter from unlabeled live-cell light microscopy data analyzed with delay embedding ]]> https://biorxiv.org/content/10.1101/2025.01.23.634593v1?rss=1 Singh, J. Copperman, J. Heiser, L. M. Zuckerman, D. M. 2025-01-24 doi:10.1101/2025.01.23.634593 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ HMG box-containing protein 1 (HBP1) prevents pancreatic injury in experimental pancreatitis but accelerates pancreatic neoplasia progression ]]> https://biorxiv.org/content/10.1101/2025.01.24.634817v1?rss=1 lee, S.-W. Ekstrom, T. Manalo, E. Ye, S. Berry, M. Grygoryev, D. Szczepaniak, M. Marmolejo, C. O. Haverlack, S. Lee, J. Shah, V. M. Keith, D. Muschler, J. L. Chin, K. Sears, R. C. Weisberg, S. P. Morgan, T. K. kim, j. 2025-01-27 doi:10.1101/2025.01.24.634817 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ A spatially resolved single cell proteomic atlas of Small Bowel Adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2025.02.01.634535v1?rss=1 600,000 cells from 136 tumor and matched normal samples from clinically and genomically annotated SBA patients (N=37). The SBA TIME Atlas informs on spatial distribution and interactions of tumor-intrinsic processes, diverse immune cell types, immune checkpoints, and vascularization. Enrichment of proliferating epithelial tissue, stem cells, and likely pro-tumor immune signatures in the tumor niche is contrasted by the representation of naive and early-effector T-cells in the epithelial compartments of adjacent normal tissues. Epithelial-stem-immune cell spatial architectures within tumor and matched-normal niches were strongly associated with patient survival, suggesting malignancy is driven by spatial architecture beyond the tumor microenvironment. The blueprints of therapeutically actionable immune checkpoints at the interface between epithelial and microenvironmental T-cells as well as macrophages have established a guideline for precision immunotherapies tailored to the TIME composition in SBA. We expect that this SBA atlas will contribute to a deeper understanding of the immune contexture in this rare disease as well as other gastrointestinal cancers and help guide future precision immune-oncology strategies. ]]> Dereli, Z. Bozorgui, B. Sanchez, M. Hornstein, N. J. Thibault, G. Wang, H. Mills, G. B. Weinstein, J. N. Overman, M. J. Korkut, A. 2025-02-04 doi:10.1101/2025.02.01.634535 Cold Spring Harbor Laboratory Press 2025-02-04 <![CDATA[ Centella asiatica improves sleep quality and quantity in aged mice ]]> https://biorxiv.org/content/10.1101/2025.02.01.636070v1?rss=1 Dovek, L. Tinsley, C. E. Gutowsky, K. McDaniel, K. Potter, Z. Ruffins, M. Milman, N. Wong, C. Soumyanath, A. Gray, N. E. Lim, M. 2025-02-06 doi:10.1101/2025.02.01.636070 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ mRNA stability factor HuR promotes immune evasion in pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2025.02.07.632847v1?rss=1 Guo, Y. Finan, J. M. Bartlett, A. Q. Sivagnanam, S. Blise, K. E. Kirchberger, N. Betre, K. Hawthorne, K. Chen, C. Grossberg, A. Xia, Z. Coussens, L. M. Sears, R. C. Brody, J. R. Eil, R. 2025-02-07 doi:10.1101/2025.02.07.632847 Cold Spring Harbor Laboratory Press 2025-02-07 <![CDATA[ Cerebellar climbing fibers convey perceptual choice during decision-making ]]> https://biorxiv.org/content/10.1101/2025.02.06.636959v1?rss=1 Yiu, T. L. Wilson, E. A. Yahiro, T. Ma, L. Qin, M. Zhong, H. 2025-02-08 doi:10.1101/2025.02.06.636959 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ IFNγ regulates MR1 transcription and antigen presentation ]]> https://biorxiv.org/content/10.1101/2025.02.09.637183v1?rss=1 Huber, M. E. Larson, E. A. Lust, T. N. Heisler, C. M. Harriff, M. J. 2025-02-10 doi:10.1101/2025.02.09.637183 Cold Spring Harbor Laboratory Press 2025-02-10 <![CDATA[ Astrocyte gap junctions and Kir channels contribute to K+ buffering and regulate neuronal excitability ]]> https://biorxiv.org/content/10.1101/2025.02.10.637549v1?rss=1 Bojovic, D. Dagostin, A. Sullivan, S. von Gersdorff, H. Mishra, A. 2025-02-11 doi:10.1101/2025.02.10.637549 Cold Spring Harbor Laboratory Press 2025-02-11 <![CDATA[ Virus-against-virus dominant-negative interference strategy targeting a viral CC chemokine prevents cytomegalovirus-related neurodevelopmental pathogenesis ]]> https://biorxiv.org/content/10.1101/2025.02.11.637423v1?rss=1 Bauer, S. Tarhini, S. Buhler, E. Saha, S. Stamminger, T. Streblow, D. N. Burnashev, N. Luche, H. Szepetowski, P. 2025-02-12 doi:10.1101/2025.02.11.637423 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Identification of a multi-omics factor predictive of long COVID in the IMPACC study ]]> https://biorxiv.org/content/10.1101/2025.02.12.637926v1?rss=1 500 hospitalized COVID-19 patients in the IMPACC cohort to identify a multi-omics "recovery factor". IMPACC participants who experienced LC had lower recovery factor scores compared to participants without LC. Biologic characterization revealed increased levels of plasma proteins associated with inflammation, elevated transcriptional signatures of heme metabolism, and decreased androgenic steroids in LC patients. The recovery factor was also associated with altered circulating immune cell frequencies. Notably, recovery factor scores were predictive of LC occurrence in patients as early as hospital admission, irrespective of acute disease severity. Thus, the recovery factor identifies patients at risk of LC early after SARS-CoV-2 infection and reveals LC biomarkers and potential treatment targets. ]]> Gabernet, G. Maciuch, J. Gygi, J. P. Moore, J. F. Hoch, A. Syphurs, C. Chu, T. Jayavelu, N. D. Corry, D. B. Kheradmand, F. Baden, L. R. Sekaly, R.-P. McComsey, G. A. Haddad, E. K. Cairns, C. B. Rouphael, N. Fernandez-Sesma, A. Simon, V. Metcalf, J. P. Agudelo Higuita, N. I. Hough, C. L. Messer, W. B. Davis, M. M. Nadeau, K. C. Pulendran, B. Kraft, M. Bime, C. Reed, E. F. Schaenman, J. Erle, D. J. Calfee, C. S. Atkinson, M. A. Brackenridge, S. C. Melamed, E. Shaw, A. C. Hafler, D. A. Ozonoff, A. Bosinger, S. E. Eckalbar, W. Maecker, H. T. Kim-Schulze, S. 2025-02-14 doi:10.1101/2025.02.12.637926 Cold Spring Harbor Laboratory Press 2025-02-14 <![CDATA[ Reversible lipid mediated pH-gating of connexin-46/50 by cryo-EM ]]> https://biorxiv.org/content/10.1101/2025.02.12.637953v1?rss=1 Jarodsky, J. M. Myers, J. B. Reichow, S. L. 2025-02-14 doi:10.1101/2025.02.12.637953 Cold Spring Harbor Laboratory Press 2025-02-14 <![CDATA[ Calcium induced N-terminal gating and pore collapse in connexin-46/50 gap junctions ]]> https://biorxiv.org/content/10.1101/2025.02.12.637955v1?rss=1 Flores, J. A. O'Neill, S. E. Jarodsky, J. M. Reichow, S. L. 2025-02-14 doi:10.1101/2025.02.12.637955 Cold Spring Harbor Laboratory Press 2025-02-14 <![CDATA[ UB-MBX-46 is a potent and selective antagonist of the human P2X7 receptor developed by structure-based drug design ]]> https://biorxiv.org/content/10.1101/2025.02.12.637899v1?rss=1 Oken, A. C. Turcu, A. L. Tzortzini, E. Georgiou, K. Nagel, J. Barniol-Xicota, M. Kim, G.-R. Lee, S.-D. Nicke, A. Kim, Y.-C. Müller, C. E. Kolocouris, A. Vazquez, S. Mansoor, S. E. 2025-02-16 doi:10.1101/2025.02.12.637899 Cold Spring Harbor Laboratory Press 2025-02-16 <![CDATA[ Effect of obesity on the acute response to SARS-CoV-2 infection and development of post-acute sequelae of COVID-19 (PASC) in nonhuman primates ]]> https://biorxiv.org/content/10.1101/2025.02.18.638792v1?rss=1 Sauter, K. A. Webb, G. M. Bader, L. Kreklywich, C. N. Takahashi, D. L. Zaro, C. McGuire, C. M. Lewis, A. D. Colgin, L. M. A. Kirigiti, M. A. Blomenkamp, H. Pessoa, C. Humkey, M. Hulahan, J. Sleeman, M. Zweig, R. C. Thomas, S. Thomas, A. Gao, L. Hirsch, A. J. Levy, M. Cherry, S. R. Kahn, S. E. Slifka, M. K. Sacha, J. B. Kievit, P. Roberts, C. 2025-02-19 doi:10.1101/2025.02.18.638792 Cold Spring Harbor Laboratory Press 2025-02-19 <![CDATA[ Epigenetic and Transcriptomic Alterations Precede Amyloidosis in the Hippocampus of the Alzheimer's Disease AppNL-G-F Knock in Mouse Model ]]> https://biorxiv.org/content/10.1101/2025.02.20.639336v1?rss=1 Okhovat, M. Layman, C. Davis, B. A. Pederson, A. O'Niel, A. Holden, S. Kessler, K. Acharya, S. Wheeler, K. J. Nevonen, K. A. Herrera, J. Ward, S. Vigh-Conrad, K. Adey, A. Raber, J. Carbone, L. 2025-02-21 doi:10.1101/2025.02.20.639336 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ Enhancement of Therapeutic Transgene Insertion for Murine Phenylketonuria ]]> https://biorxiv.org/content/10.1101/2025.02.24.639678v1?rss=1 Martinez, M. Richards, D. Y. Winn, S. R. Baris, A. M. Vonada, A. Dudley, S. Harper, L. Harding, C. O. 2025-02-28 doi:10.1101/2025.02.24.639678 Cold Spring Harbor Laboratory Press 2025-02-28 <![CDATA[ Comprehensive identification of β-lactam antibiotic polypharmacology in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2025.02.25.640225v1?rss=1 Devlin, K. L. Hutchinson, E. Dearing, H. N. Levine, S. R. Reid, D. J. Leach, D. T. Griggs, L. H. Lomas, G. X. Gorham, L. J. Wright, A. T. Lamichhane, G. Lin, V. Beatty, K. E. 2025-02-28 doi:10.1101/2025.02.25.640225 Cold Spring Harbor Laboratory Press 2025-02-28 <![CDATA[ Identification of Direct-acting nsP2 Helicase Inhibitors with Anti-alphaviral Activity ]]> https://biorxiv.org/content/10.1101/2025.03.04.641060v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@856df5org.highwire.dtl.DTLVardef@1f6225borg.highwire.dtl.DTLVardef@4997d5org.highwire.dtl.DTLVardef@18f42f2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Bose, M. R. Sears, J. D. Talbot, K. M. Su, Y.-W. N. Houliston, S. Hossain, M. A. Davis-Gilbert, Z. W. Zhao, C. Oh, H. J. Brown, P. J. Sanders, M. K. Moorman, S. R. Ojha, D. Burdick, J. E. Law, I. Morales, N. L. Martinez, S. A. Loppnau, P. Perez, J. G. Drobish, A. M. Morrison, T. E. Streblow, Z. J. Streblow, D. N. Arrowsmith, C. H. Vargason, A. Counago, R. M. Halabelian, L. Arnold, J. J. Cameron, C. E. Moorman, N. J. Heise, M. T. Willson, T. M. 2025-03-10 doi:10.1101/2025.03.04.641060 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Analysis of factors that regulate HIV-1 fusion in reverse ]]> https://biorxiv.org/content/10.1101/2025.03.10.642481v1?rss=1 Alfadhli, A. Barklis, R. L. Tafesse, F. Barklis, E. 2025-03-13 doi:10.1101/2025.03.10.642481 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Human Neonatal MR1T Cells Have Diverse TCR Usage, are Less Cytotoxic and are Unable to Respond to Many Common Childhood Pathogens. ]]> https://biorxiv.org/content/10.1101/2025.03.17.643805v1?rss=1 Kain, D. Abdelhady, W. McElfresh, G. Cansler, M. Swarbrick, G. Poa, K. McNeice, C. Boggy, G. Rott, K. Null, M. Lewinsohn, D. Rossjohn, J. Bimber, B. N. Lewinsohn, D. 2025-03-20 doi:10.1101/2025.03.17.643805 Cold Spring Harbor Laboratory Press 2025-03-20 <![CDATA[ MYC Serine 62 phosphorylation promotes its binding to DNA double strand breaks to facilitate repair and cell survival under genotoxic stress. ]]> https://biorxiv.org/content/10.1101/2025.03.19.644227v1?rss=1 Cohn, G. M. Daniel, C. Eng, J. Sun, X.-X. Pelz, C. Chin, K. Smith, A. Lopez, C. D. Brody, J. R. DAI, M. Sears, R. C. 2025-03-20 doi:10.1101/2025.03.19.644227 Cold Spring Harbor Laboratory Press 2025-03-20 <![CDATA[ Combining a rhesus cytomegalovirus/SIV vaccine with neutralizing antibody to protect against SIV challenge in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2025.03.20.644395v1?rss=1 Coppola, J. Parren, M. Bastidas, R. Saye-Francisco, K. Malvin, J. Jardine, J. G. Gilbride, R. M. Ojha, S. Feltham, S. Morrow, D. Barber-Axthelm, A. Bochart, R. Fast, R. Oswald, K. Shoemaker, R. Lifson, J. D. Picker, L. J. Burton, D. R. Hansen, S. G. 2025-03-25 doi:10.1101/2025.03.20.644395 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ The Photoswitchable Cannabinoid Azo-HU308 Enables Optical Control of Ca2+ Signaling in Pancreatic β-Cells via a Non CB2 TRPC Channel Mechanism ]]> https://biorxiv.org/content/10.1101/2025.03.21.644674v1?rss=1 Viray, A. E. Frank, J. A. 2025-03-25 doi:10.1101/2025.03.21.644674 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Dissecting the steps in early Simian Immunodeficiency Virus dissemination following mucosal and intravenous infection of rhesus macaques ]]> https://biorxiv.org/content/10.1101/2025.03.24.644849v1?rss=1 Docken, S. S. Macairan, A. Schlub, T. E. Fennessey, C. M. Varco-Merth, B. Picker, L. J. Okoye, A. A. Immonen, T. T. Cromer, D. Keele, B. F. Davenport, M. P. 2025-03-28 doi:10.1101/2025.03.24.644849 Cold Spring Harbor Laboratory Press 2025-03-28 <![CDATA[ Protocol for Extracting Circulating Cell-Free DNA from Murine Saliva: Insights into Oral and Systemic Disease Research ]]> https://biorxiv.org/content/10.1101/2025.03.31.645839v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@19ce903org.highwire.dtl.DTLVardef@85fa20org.highwire.dtl.DTLVardef@1e869eaorg.highwire.dtl.DTLVardef@181c340_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Elamin, I. Rao, M. S. Figliozzi, R. W. Maahs, J. C. Balish, M. Hsia, S. V. Fugolin, A. P. P. Fan, J. 2025-04-02 doi:10.1101/2025.03.31.645839 Cold Spring Harbor Laboratory Press 2025-04-02 <![CDATA[ Complex carbohydrates catabolism capacity of bladder microbiota inhabiting healthy and overactive female bladders ]]> https://biorxiv.org/content/10.1101/2025.04.02.646827v1?rss=1 Gourdine, J.-P. Pacentine, I. V. Barstad, A. Dahl, E. M. Gregory, W. T. Wolfe, A. J. Sysoeva, T. A. Karstens, L. 2025-04-04 doi:10.1101/2025.04.02.646827 Cold Spring Harbor Laboratory Press 2025-04-04 <![CDATA[ Integrative Analysis of EGF, OSM, and TGFB Signaling Pathways Reveals Synergistic Mechanisms Driving Cell Motility Through CXCR2 Chemotactic Signaling and CREB Activation ]]> https://biorxiv.org/content/10.1101/2025.04.03.647095v1?rss=1 McLean, I. C. Gross, S. Copperman, J. Derrick, D. Heiser, L. 2025-04-04 doi:10.1101/2025.04.03.647095 Cold Spring Harbor Laboratory Press 2025-04-04 <![CDATA[ Incubation of oxycodone craving is associated with CP-AMPAR upregulation in D1 and D2 receptor-expressing medium spiny neurons in nucleus accumbens core and shell ]]> https://biorxiv.org/content/10.1101/2025.04.06.647399v1?rss=1 Mount, K. A. Kuhn, H. M. Hwang, E.-K. Beutler, M. M. Wolf, M. E. 2025-04-06 doi:10.1101/2025.04.06.647399 Cold Spring Harbor Laboratory Press 2025-04-06 <![CDATA[ Hepatic Yap1 activates systemic catabolism and muscle loss during organ repair: evidence for a liver-derived common mechanism with cancer cachexia. ]]> https://biorxiv.org/content/10.1101/2025.04.01.646698v1?rss=1 HAMIDI, T. Yang, Y. Robinson, T. P. Kronbergs, A. Au, E. Rupert, J. E. Zhong, X. Lal, S. Liang, T. Robling, A. G. Hoggatt, A. Carvalho, R. Cury, S. S. Wells, C. Zimmers, T. Koniaris, L. G. 2025-04-07 doi:10.1101/2025.04.01.646698 Cold Spring Harbor Laboratory Press 2025-04-07 <![CDATA[ Genome-wide analysis reveals genes mediating resistance to paraquat neurodegeneration in Drosophila ]]> https://biorxiv.org/content/10.1101/2025.04.02.646829v1?rss=1 Villalobos-Cantor, S. Arreola-Bustos, A. Martin, I. 2025-04-08 doi:10.1101/2025.04.02.646829 Cold Spring Harbor Laboratory Press 2025-04-08 <![CDATA[ CODAvision: best practices and a user-friendly interface for rapid, customizable segmentation of medical images ]]> https://biorxiv.org/content/10.1101/2025.04.11.648464v1?rss=1 Matos-Romero, V. Gomez-Becerril, J. Forjaz, A. Dequiedt, L. Newton, T. Joshi, S. Shen, Y. Hanna, E. Nair, P. R. Sivasubramanian, A. Wang, J. Lasse-Opsahl, E. L. Bell, A. T. F. Czum, J. Steenbergen, C. Dai, D.-F. Wood, L. D. Kagohara, L. T. Fertig, E. J. Pasca di Magliano, M. Shatzel, J. McCarty, O. J. Lo, J. O. Rosenberg, A. Hruban, R. H. Munoz-Barrutia, A. Wirtz, D. Kiemen, A. L. 2025-04-14 doi:10.1101/2025.04.11.648464 Cold Spring Harbor Laboratory Press 2025-04-14 <![CDATA[ Submicron-Sampling of Living Cells by Macrophages ]]> https://biorxiv.org/content/10.1101/2025.04.10.648051v1?rss=1 Fan, A. C. Thota, R. Serwas, N. Marchuk, K. Ruhland, M. Edwards, A. Krummel, M. F. 2025-04-16 doi:10.1101/2025.04.10.648051 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ KDM5B expression is suppressed by MYC in a negative feedback loop to promote cell survival. ]]> https://biorxiv.org/content/10.1101/2025.04.12.648490v1?rss=1 Chatterjee, T. Beffert, E. Dewson, G. S. Sullivan, D. K. Anchang, B. Sears, R. C. Liefwalker, D. 2025-04-18 doi:10.1101/2025.04.12.648490 Cold Spring Harbor Laboratory Press 2025-04-18 <![CDATA[ Maternal obesity programs cardiac remodeling in offspring via epigenetic, metabolic, and immune dysregulations. ]]> https://biorxiv.org/content/10.1101/2025.04.15.648971v1?rss=1 Philips, E. A. Alharithi, Y. Wilson, T. D. Broberg, C. Davis, B. A. Koch, S. Carbone, L. Rubinstein, J. Gurley, S. B. Rugonyi, S. Kumar, S. Maloyan, A. 2025-04-19 doi:10.1101/2025.04.15.648971 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ Surface morphometrics reveals local membrane thickness variation in organellar subcompartments ]]> https://biorxiv.org/content/10.1101/2025.04.30.651574v1?rss=1 Medina, M. Chang, Y.-T. Rahmani, H. Fuentes, D. Barad, B. A. Grotjahn, D. 2025-05-01 doi:10.1101/2025.04.30.651574 Cold Spring Harbor Laboratory Press 2025-05-01 <![CDATA[ Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal ]]> https://biorxiv.org/content/10.1101/2025.05.02.651747v1?rss=1 Mitchell, J. T. Stapleton, O. Krishnan, K. Nagaraj, S. Lvovs, D. Cherry, C. Poissonnier, A. Horton, W. Adey, A. Rao, V. Huff, A. Zimmerman, J. W. Kagohara, L. T. Zaidi, N. Coussens, L. M. Jaffee, E. M. Elisseeff, J. H. Fertig, E. J. 2025-05-03 doi:10.1101/2025.05.02.651747 Cold Spring Harbor Laboratory Press 2025-05-03 <![CDATA[ Liver biopsies obtained throughout SIV infection reveal evolving interferon stimulated protein expression within distinct monocyte/macrophage subsets ]]> https://biorxiv.org/content/10.1101/2025.05.01.651668v1?rss=1 Derby, N. Johnson, B. I. Biswas, S. Fischer, M. Fancher, K. A. Luevano-Santos, C. Yusova, S. Meyer, K. A. Abraham, Y. M. Lutz, S. S. Fisher, C. Pacheco, M. C. Smedley, J. V. Burwitz, B. J. Sodora, D. L. 2025-05-07 doi:10.1101/2025.05.01.651668 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Modeling human retinal ganglion cell axonal outgrowth, development, and pathology using pluripotent stem cell-based microfluidic platforms ]]> https://biorxiv.org/content/10.1101/2025.05.02.651934v1?rss=1 Gomes, C. Huang, K.-C. Lavekar, S. S. Harkin, J. Prosser, C. G. Fang, Y. Kallem, C. Oblak, A. Zhang, C. Meyer, J. S. 2025-05-08 doi:10.1101/2025.05.02.651934 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Multiomic profiling of hypoxic glioblastoma stem cells reveals expansion of subpopulations with distinct epigenetic and CNV profiles ]]> https://biorxiv.org/content/10.1101/2025.05.05.652238v1?rss=1 Corseri, A. Moore, T. W. Szczepanski, N. Hwang, H. Zdon, A. Yardimci, G. Tapinos, N. 2025-05-09 doi:10.1101/2025.05.05.652238 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Transfer learning framework via Bayesian group factor analysis incorporating feature-wise dependencies ]]> https://biorxiv.org/content/10.1101/2025.05.07.648613v1?rss=1 Thirumalaisamy, D. Black, N. Gonen, M. Nikolova, O. 2025-05-10 doi:10.1101/2025.05.07.648613 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ Mitochondrial Translation Inhibition Uncovers a Critical Metabolic-Epigenetic Interface in Renal Cell Carcinoma ]]> https://biorxiv.org/content/10.1101/2025.05.07.652786v1?rss=1 Eckenstein, K. Cengiz, B. Chang, M. Cartier, J. M. Flory, M. R. Thomas, G. V. 2025-05-10 doi:10.1101/2025.05.07.652786 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ Exploring the Dynamics of Follicle Development and Hormone Synthesis: The Role of Oxygen Tension in Rhesus Macaque Follicle Culture ]]> https://biorxiv.org/content/10.1101/2025.05.06.652505v1?rss=1 View larger version (17K): org.highwire.dtl.DTLVardef@11fcb62org.highwire.dtl.DTLVardef@61c0beorg.highwire.dtl.DTLVardef@1b5328forg.highwire.dtl.DTLVardef@10a7538_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wang, K. Wolf, S. Zelinski, M. Krieg, A. 2025-05-11 doi:10.1101/2025.05.06.652505 Cold Spring Harbor Laboratory Press 2025-05-11 <![CDATA[ Predicting cochlear synaptopathy in mice with varying degrees of outer hair cell dysfunction using auditory evoked potentials ]]> https://biorxiv.org/content/10.1101/2025.05.09.653157v1?rss=1 Buran, B. N. Elkins, S. He, W. Bramhall, N. F. 2025-05-12 doi:10.1101/2025.05.09.653157 Cold Spring Harbor Laboratory Press 2025-05-12 <![CDATA[ Serine auxotrophy is a targetable vulnerability driven by PSAT1 suppression in AML ]]> https://biorxiv.org/content/10.1101/2025.05.13.651470v1?rss=1 Sinanidis, I. Tsakiroglou, P. Dubner, B. Foertsch, R. Gondek, J. Choi, I. Paun, B. Zhao, L. Ghiaur, G. Dalton, W. B. 2025-05-14 doi:10.1101/2025.05.13.651470 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ PIN1 Drives Cellular Plasticity and Immune Modulation in Chronic Pancreatitis ]]> https://biorxiv.org/content/10.1101/2025.05.13.653850v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@67f9fcorg.highwire.dtl.DTLVardef@4d4c1forg.highwire.dtl.DTLVardef@c099d7org.highwire.dtl.DTLVardef@b41aa5_HPS_FORMAT_FIGEXP M_FIG C_FIG Created in BioRender. Shah, V. (2025) https://BioRender.com/undefined ]]> Shah, V. M. Bartlett, A. Chen, C. Matter, A. Smith, A. Zimny, H. Wang, X. Daniel, C. Eng, J. Youm, I. Tsuda, M. Calistri, N. Reyer, M. Morgan, T. K. Dewson, G. Waugh, T. Keith, D. Haverlack, S. Xia, Z. Chin, K. Sheppard, B. Brody, J. Sears, R. C. 2025-05-14 doi:10.1101/2025.05.13.653850 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Unreliable homeostatic action potential broadening in cultured dissociated neurons ]]> https://biorxiv.org/content/10.1101/2025.05.09.653135v1?rss=1 Ritzau-Jost, A. Rajayer, S. Nerlich, J. Maciag, F. John, A. Russier, M. Gonzalez Sabater, V. Steiger, L. Coq, J.-O. Eilers, J. Engelhardt, M. Burrone, J. Debanne, D. Heine, M. Smith, S. M. Hallermann, S. 2025-05-15 doi:10.1101/2025.05.09.653135 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Isoform-Specific Roles of NTRK2 in Pulmonary Vascular Regeneration ]]> https://biorxiv.org/content/10.1101/2025.05.11.653351v1?rss=1 Tan, C. Liu, Z. Mao, X. Zhang, Y. Li, X. Pek, N. Fu, H. Liu, Y. Kalinichenko, V. V. Pryhuber, G. S. Lu, R. Lai, L. Miao, Y. Guo, M. Gu, M. 2025-05-15 doi:10.1101/2025.05.11.653351 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ A family of E3 ligases extend K11 polyubiquitin on sites of MARUbylation ]]> https://biorxiv.org/content/10.1101/2025.05.11.653360v1?rss=1 Lacoursiere, R. E. Upadhyaya, K. Kaur Sidhu, J. Bejan, D. S. Rodriguez Siordia, I. Cohen, M. S. Pruneda, J. N. 2025-05-15 doi:10.1101/2025.05.11.653360 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Aggregating multimodal cancer data across unaligned embedding spaces maintains tumor of origin signal ]]> https://biorxiv.org/content/10.1101/2025.05.14.653900v1?rss=1 Kirchgaessner, R. Keutler, K. Sivakumar, L. Song, X. Ellrott, K. 2025-05-18 doi:10.1101/2025.05.14.653900 Cold Spring Harbor Laboratory Press 2025-05-18 <![CDATA[ Mutations outside the MR1 antigen binding groove differentially inhibit presentation of exogenous antigens ]]> https://biorxiv.org/content/10.1101/2025.05.14.654109v1?rss=1 Kulicke, C. A. Lemon, C. Krawic, J. R. Ramirez, L. M. N. Kim, S.-J. Narayanan, G. A. Tafesse, F. G. Hildebrand, W. H. Dobos, K. M. Lewinsohn, D. M. 2025-05-19 doi:10.1101/2025.05.14.654109 Cold Spring Harbor Laboratory Press 2025-05-19 <![CDATA[ Identification and Rescue of Congenital Hyperinsulinism-Associated ABCC8 Mutations that Impair KATP Channel Trafficking ]]> https://biorxiv.org/content/10.1101/2025.05.18.654760v1?rss=1 ElSheikh, A. Kuo, Y.-Y. E. Boodhansingh, K. Yang, Z. A. Stanley, C. De Leon, D. D. Shyng, S.-L. 2025-05-19 doi:10.1101/2025.05.18.654760 Cold Spring Harbor Laboratory Press 2025-05-19 <![CDATA[ Distinct age- and pathology-dependent epitranscriptome and translational dysfunction in a tauopathy mouse model ]]> https://biorxiv.org/content/10.1101/2025.05.15.654371v1?rss=1 23,000 protein-coding genes. Analysis of these datasets revealed that aging and tauopathy elicit major adaptation of the tRNA transcriptome and epitranscriptome as well as corresponding evidence of a program of translation of families of codon-biased genes for aging and disease responsive proteins. The mitochondrial tRNA transcriptome showed a strong response to aging and disease with 21 of the 22 mt-tRNAs showing age and disease-linked increases in expression, accompanied by mitochondria-specific modifications such as ms2i6A and f5C. Surprisingly, there were few significant changes in the 203 cytosolic tRNA isodecoders. However, a 10-fold increase tRNA isodecoder tRNA-Arg-TCT-5-1 was accompanied by increased translation of proteins encoded by genes highly enriched in its AGA cognate codon. These changes in tRNA biology are mirrored by strongly biased use of synonymous codons among the most highly upregulated and downregulated proteins in the P301S MAPT mice. Taken together these findings suggest the aging and disease brain produces an integrated response for translational control that is highly integrated with changes in tRNA biology. ]]> Sun, G. Lin, W. Chen, R. Jiang, L. DeMott, M. McShane, A. Chan, M. C. K. Ehrbar, D. Zhang, X. Begley, T. Emili, A. Wolozin, B. Dedon, P. 2025-05-20 doi:10.1101/2025.05.15.654371 Cold Spring Harbor Laboratory Press 2025-05-20 <![CDATA[ Deep-learning-enabled multi-omics analyses for prediction of future metastasis in cancer ]]> https://biorxiv.org/content/10.1101/2025.05.16.654579v1?rss=1 Ma, Q. Wang, X. Duan, M. Su, P.-L. Li, J. Krull, J. Jin, J. Chen, H. Sun, Y. Wu, W. He, K. Carpenter, R. Zhang, C. Cao, S. Xu, D. Wang, G. Li, L. Xin, G. Carbone, D. P. Li, Z. 2025-05-22 doi:10.1101/2025.05.16.654579 Cold Spring Harbor Laboratory Press 2025-05-22 <![CDATA[ Cervical Mucus Viscoelasticity and Sperm Velocity are Correlated and Concentration-dependent In Vitro ]]> https://biorxiv.org/content/10.1101/2025.05.18.654742v1?rss=1 Markovetz, M. R. Wei, S. Celluci, C. Roberts, M. Han, L. 2025-05-23 doi:10.1101/2025.05.18.654742 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ A New Class of Precision Therapeutics that Inhibit Prostate Cancer Mediated Bone Destruction ]]> https://biorxiv.org/content/10.1101/2025.05.20.654990v1?rss=1 Qiao, F. Gordon, R. Pattanayak, A. Li, W. Knibbe-Hollinger, J. O'Neill, K. Chen, W. Mukthapuram, P. R. Natarajan, A. Bergan, R. 2025-05-24 doi:10.1101/2025.05.20.654990 Cold Spring Harbor Laboratory Press 2025-05-24 <![CDATA[ Molecular mechanism of substrate transport by human peroxisomal ABCD3 ]]> https://biorxiv.org/content/10.1101/2025.05.21.655323v1?rss=1 Gupta, M. Khandelwal, N. K. Seka, D. J. Balasubramani, S. G. Dickinson, M. S. Myasnikov, A. Echeverria, I. Stroud, R. M. 2025-05-27 doi:10.1101/2025.05.21.655323 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Disabling PSGL-1 abrogates immune suppression and resistance to PD-1 blockade in pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2025.05.22.655365v1?rss=1 Hope, J. L. Zhang, Y. Hetrick, H. A. F. Sanchez-Hernandez, E. S. Silvestri, B. Smith, B. J. Nakil, S. H. Roy, S. Lin, M. Palete, A. B. Maganti, S. Ling, L. Otero, D. C. Byrne, K. Romano, G. Wang, Y. X. Commisso, C. Bradley, L. M. 2025-05-27 doi:10.1101/2025.05.22.655365 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ MicroCT enables simultaneous longitudinal tracking of murine pancreatic cancer progression and cachexia ]]> https://biorxiv.org/content/10.1101/2025.05.29.656943v1?rss=1 Pelz, K. R. Jimenez, P. Daniel, C. J. Newton, S. D. Cunningham, M. Sears, R. C. Worth, P. J. Brody, J. R. Zimmers, T. A. 2025-06-01 doi:10.1101/2025.05.29.656943 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Synthetic Serum Markers Enable Noninvasive Monitoring of Gene Expression in Primate Brains ]]> https://biorxiv.org/content/10.1101/2025.06.01.657212v1?rss=1 Lee, S. Romac, M. Romac, M. D. Chernov, M. Li, H. Raisley, E. Szablowski, J. O. Costa, V. D. 2025-06-02 doi:10.1101/2025.06.01.657212 Cold Spring Harbor Laboratory Press 2025-06-02 <![CDATA[ PIVOT: an open-source tool for multi-omic spatial data registration ]]> https://biorxiv.org/content/10.1101/2025.06.08.658506v1?rss=1 Forjaz, A. Romero, V. M. Reucroft, I. Eminizer, M. Kramer, D. Higuera, D. Mojdeganlou, H. Guerrero, P. A. Min, J. Wetzel, M. Lvovs, D. Valentin, A. Shin, S. M. Xuan, Y. Sears, R. C. Chin, K. Maitra, A. Fertig, E. J. Ho, W. J. Kagohara, L. T. Wood, L. D. Wirtz, D. Sidiropoulos, D. N. Kiemen, A. L. 2025-06-09 doi:10.1101/2025.06.08.658506 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Multi-omics profiling reveals atypical sugar utilization and identifies a key membrane composition regulator in Streptococcus pneumoniae ]]> https://biorxiv.org/content/10.1101/2025.06.13.659575v1?rss=1 de Bakker, V. Liu, X. Tang, J. Barbisan, M. Baker, J. L. Veening, J.-W. 2025-06-14 doi:10.1101/2025.06.13.659575 Cold Spring Harbor Laboratory Press 2025-06-14 <![CDATA[ Selective inhibition of MR1-restricted T cell activation by a novel MR1-targeting nanobody ]]> https://biorxiv.org/content/10.1101/2025.06.11.659204v1?rss=1 Bates, T. A. Kulicke, C. A. Gurmessa, S. Kim, S.-J. Suresh, S. Weinstein, J. R. Hinchliff, A. Burke, J. E. Lewinsohn, D. Tafesse, F. G. 2025-06-17 doi:10.1101/2025.06.11.659204 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Specific GPCRs Elicit Unique Extracellular Vesicle MiRNA Array Signatures: An Exploratory Study ]]> https://biorxiv.org/content/10.1101/2025.06.16.659918v1?rss=1 View larger version (53K): org.highwire.dtl.DTLVardef@1a9812org.highwire.dtl.DTLVardef@1f5cbf3org.highwire.dtl.DTLVardef@20d1fdorg.highwire.dtl.DTLVardef@ba4fad_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Shi, X. Palumbo, M. C. Benware, S. Wiedrick, J. Markwardt, S. Janowsky, A. J. 2025-06-20 doi:10.1101/2025.06.16.659918 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Host iron deficiency protects against Plasmodium infection and drives parasite molecular reprofiling. ]]> https://biorxiv.org/content/10.1101/2025.06.24.660981v1?rss=1 Clucas, D. Bennett, C. Harding, R. Pettikiriarachchi, A. Baldi, A. Randall, L. M. Steel, R. Mellin, R. Hobbs, M. Caiazzo, S. Mwangi, M. N. Fielding, K. L. Hickey, P. F. Baldwin, T. M. Amann-Zalcenstein, D. Emery-Corbin, S. J. Mzembe, G. Moya, E. Braat, S. Jex, A. Demir, A. Y. Verhoef, H. Phiri, K. S. Biggs, B.-A. Tham, W.-H. Boddey, J. A. Pasricha, S.-R. Ataide, R. 2025-06-26 doi:10.1101/2025.06.24.660981 Cold Spring Harbor Laboratory Press 2025-06-26 <![CDATA[ Sensitizing Immune-Refractory Ovarian Tumors via p53 Mutation-Tailored Immunotherapy ]]> https://biorxiv.org/content/10.1101/2025.06.23.661120v1?rss=1 Chatterjee, R. Simoni-Nieves, A. Truong, A. Lindzen, M. Ozmen, F. Cherry, C. Zwicky, P. Mukherjee, S. Selvadurai, B.-R. Salame, T. M. Gupta, N. Giri, S. Kramarski, L. Avraham, Y. Weizman, E. Ozmen, T. Noronha, A. Chakrabarti, P. Ramesh-Kumar, D. Downward, J. Dahan, R. Amit, I. Velculescu, V. Brenton, J. Mills, G. Oren, M. Yarden, Y. 2025-06-27 doi:10.1101/2025.06.23.661120 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Methylation dynamics in the decades preceding acute myeloid leukaemia ]]> https://biorxiv.org/content/10.1101/2025.06.26.661643v1?rss=1 Fonseca, A. V. Boniface, C. T. Watson, C. Hackett, S. Gabbutt, C. Ramos-Yamasaki, A. D. Tan, A. B. Montoya, J. M. Strogantsev, R. Hanssen, L. Zhang, Y. Apostolidou, S. Gentry-Maharaj, A. Esener, S. Spellman, P. Graham, T. Menon, U. Mohammed, H. Blundell, J. R. 2025-06-27 doi:10.1101/2025.06.26.661643 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Long Noncoding RNAs Enforce Pancreatic Cancer Identity and Block Reprogramming ]]> https://biorxiv.org/content/10.1101/2025.06.25.661419v1?rss=1 Grygoryev, D. Lee, S.-W. Frankston, C. M. Rakshe, S. Berry, M. Hirano, A. Ekstrom, T. Manalo, E. Tessier, J. Chow-Castro, M. Link, J. Keith, D. Sheppard, B. C. Fei, S. Morgan, T. Remotti, H. E. Yang, W. Furth, E. Thakurela, S. Sears, R. C. Kim, J. 2025-06-28 doi:10.1101/2025.06.25.661419 Cold Spring Harbor Laboratory Press 2025-06-28 <![CDATA[ N-Alkyl Sulfamates as a New Class of nsP2 Cysteine Protease Inhibitors with Broad Spectrum Antialphaviral Activity ]]> https://biorxiv.org/content/10.1101/2025.06.30.662352v1?rss=1 Ghosal, A. Sears, J. D. Hossain, M. A. Tse, E. Howell, S. Burdick, J. E. Morales, N. L. Martinez, S. A. Law, I. Streblow, Z. J. Streblow, D. N. Counago, R. M. Moorman, N. J. Heise, M. T. Willson, T. M. 2025-07-04 doi:10.1101/2025.06.30.662352 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ The IFN I response in tumor cells is shaped by PARP7-p300/CBP interactions through distinct loss- and gain-of-function mechanisms ]]> https://biorxiv.org/content/10.1101/2025.06.30.662483v1?rss=1 Siordia, I. R. Rieth, S. Jeltema, D. Morgan, R. Tullis, J. Orth, J. Yan, N. Marx, A. Cohen, M. S. 2025-07-04 doi:10.1101/2025.06.30.662483 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Human induced pluripotent stem cell-derived microglia with a CX3CR1-V249I genetic variant exhibit dysfunctional phenotypes and modulate neuronal growth and function ]]> https://biorxiv.org/content/10.1101/2025.07.01.662163v1?rss=1 Tutrow, K. D. Harkin, J. Varghese, L. D. Hernandez, M. Huang, K.-C. Fang, Y. Wilcox, P. Bedford, L. M. Lin, T.-Y. Zhang, C. Gomes, C. Puntambekar, S. S. Bissel, S. J. Lamb, B. T. Meyer, J. S. 2025-07-04 doi:10.1101/2025.07.01.662163 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Progressive Remodeling of Global Protein Interaction Networks in a Mouse Model of Tauopathy ]]> https://biorxiv.org/content/10.1101/2025.07.05.663296v1?rss=1 Lin, W. Phanse, S. van der Spek, S. Lampl, N. Stephens, M. C. Rondon Ortiz, A. Taylor, A. Hekman, R. Jiang, L. Havugimana, P. Botas, J. Emili, A. Wolozin, B. 2025-07-06 doi:10.1101/2025.07.05.663296 Cold Spring Harbor Laboratory Press 2025-07-06 <![CDATA[ JAK2 signalling to HNRNPA1 represses retrotransposon activity in haematopoietic stem cells ]]> https://biorxiv.org/content/10.1101/2025.07.07.663405v1?rss=1 Deuel, J. W. Mararovs, A. Goosheh, S. Winder, G. Mohammed, H. Carroll, J. Chapman, M. S. Kapadia, C. D. Campbell, P. Nangalia, J. Schneider, C. Oellerich, T. Green, A. R. Loughran, S. J. 2025-07-09 doi:10.1101/2025.07.07.663405 Cold Spring Harbor Laboratory Press 2025-07-09 <![CDATA[ A Novel FNDC1-NAMPT-NAD axis is Implicated in Small and Large-vessel Arterial Disease and Drives Vascular Calcification ]]> https://biorxiv.org/content/10.1101/2025.07.08.663801v1?rss=1 Lee, S. Guo, Y. Kajuluri, L. P. Roh, K. Singh, K. Jiang, W. Moore, E. Tattersfield, H. Ostrom, K. Birchenough, C. Johnson, A. L. Krinsky, S. Bouchouari, H. Mahamdeh, M. Lee, L. Y. Wyant, G. Rich, S. S. S. Rotter, J. I. I. Taylor, K. D. Malik, S. Gerszten, R. E. Cruz, D. E. Tracy, R. P. Wu, H. Zhang, H. Lu, H. Kavousi, M. Shanahan, C. M. Duer, M. J. Kramann, R. Nazarian, R. M. Eagleton, M. J. Chen, Y. Miller, C. L. Nigwekar, S. U. Malhotra, R. 2025-07-10 doi:10.1101/2025.07.08.663801 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ Evaluation of natural killer cell tumor homing and effector function in response to CDK4/6 and AURKA inhibition in a melanoma tumor-on-a-chip platform ]]> https://biorxiv.org/content/10.1101/2025.07.09.662476v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@17bf445org.highwire.dtl.DTLVardef@e1e1d9org.highwire.dtl.DTLVardef@1b29c2corg.highwire.dtl.DTLVardef@12b1f03_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chakraborty, S. Durham, C. Bharti, V. Capece, M. Davies, A. Vilgelm, A. Skardal, A. 2025-07-11 doi:10.1101/2025.07.09.662476 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ Dynamic extracellular interactions with AMPA receptors ]]> https://biorxiv.org/content/10.1101/2025.07.11.664166v1?rss=1 Merrion, H. G. Barber, C. N. Renuse, S. S. Cutler, J. Kreimer, S. Bygrave, A. M. Meyers, D. J. Hale, W. D. Pandey, A. Huganir, R. L. 2025-07-14 doi:10.1101/2025.07.11.664166 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ Tumor-initiating genetics and therapy drive divergent molecular evolution in IDH-mutant gliomas ]]> https://biorxiv.org/content/10.1101/2025.07.11.664189v1?rss=1 20 years oligodendroglioma survival. We sought to identify genetic changes associated with tumor evolution in response to therapy through multi-timepoint whole-genome/whole-exome sequencing of 206 IDH-mutant glioma patient samples collected through the Glioma Longitudinal Analysis (GLASS) Consortium. We validated known genomic markers of tumor progression, including hypermutation and CDKN2A homozygous deletion, and discovered novel genetic alterations that distinguish the response to treatment in astrocytomas compared to oligodendrogliomas. Point mutations in PIK3CA, PIK3R1, and NOTCH1 were newly acquired in recurrent oligodendrogliomas and associated with increased mutation rates. Focal oncogene amplifications, together with CDKN2A homozygous deletions, were associated with an increase in recurrence-specific chromosomal imbalances in astrocytomas. Mutational signature analysis revealed additional differences and detected enrichment for the SBS11, and SBS119 mutational signatures after temozolomide treatment in both IDH-glioma subtypes, whereas astrocytomas showed increased ID8 signatures after radiotherapy. These signatures suggest that the genomes of oligodendroglioma and astrocytoma adapt to the selective pressures of tumor progression and treatment in different ways. However, in both IDH-mutant glioma subtypes we observed a convergence of acquired driver gene alterations with genome-wide changes and worse patient outcomes, signaling selection of treatment-refractory clones. By identifying new prognostic markers and delineating the genomic divergence of oligodendrogliomas and astrocytomas after diagnosis, our results suggest that different DNA damage response mechanisms are engaged following chemo- and radiation therapy. ]]> Chowdhury, T. Tesileanu, C. M. S. Kocakavuk, E. Johnson, K. C. Lee, J. Erson-Omay, Z. Heo, C. Aldape, K. Amin, S. B. Anderson, K. J. Ashley, D. M. Barnholtz-Sloan, J. S. Brat, D. J. Brodbelt, A. R. Castro, A. V. Claus, E. B. Connelly, J. M. Costello, J. Datta, I. Elliott, C. Finocchiaro, G. French, P. J. Gan, H. K. Garofano, L. Ghospurkar, P. L. Golebiewska, A. Gundla, P. S. Hermes, B. Hong, C. Hoogstrate, Y. Horbinski, C. Huse, J. T. Iavarone, A. Karadag, C. Khasraw, M. Kouwenhoven, M. C. LaViolette, P. S. Li, K. Lowman, A. McCortney, K. Moon, H.-E. Na 2025-07-15 doi:10.1101/2025.07.11.664189 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ MiroSCOPE: An AI-driven digital pathology platform for annotating functional tissue units ]]> https://biorxiv.org/content/10.1101/2025.07.11.664228v1?rss=1 Fenner, M. R. Sevim, S. Wu, G. Beavers, D. Guo, P. Tang, Y. Eddy, C. Z. Ait-Ahmad, K. Rice-Stitt, T. Thomas, G. Kuykendall, M. J. Stavrinides, V. Emberton, M. Xu, D. Song, X. Eksi, S. E. Demir, E. 2025-07-17 doi:10.1101/2025.07.11.664228 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Age and early life adversity shape heterogeneity of the epigenome across tissues in macaques ]]> https://biorxiv.org/content/10.1101/2025.07.13.664445v1?rss=1 Sadoughi, B. Petersen, R. Patterson, S. K. Slikas, E. Adjandba, C. Ryan, N. Costa, C. E. Newman, L. E. Watowich, M. M. Kelsey, C. R. Greenier, A. Goldman, E. A. Negron-Del Valle, J. E. Phillips, D. Thompson, I. Surratt, S. E. B. Gonzalez, O. Compo, N. R. Burgos-Rodriguez, A. G. Cayo Biobank Research Unit, DeCasien, A. R. Chiou, K. L. Walker, C. S. Lambides, A. V. R. Martinez, M. I. Sterner, K. N. Brent, L. J. N. Higham, J. P. Montague, M. J. Platt, M. L. Snyder-Mackler, N. Lea, A. J. 2025-07-18 doi:10.1101/2025.07.13.664445 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Negative Cooperativity in a Polybivalent Complex Allows the Prevalence of a Partial Bound State. ]]> https://biorxiv.org/content/10.1101/2025.07.14.664506v1?rss=1 Walker, D. R. Otten, L. Zuckerman, D. M. Barbar, E. J. 2025-07-18 doi:10.1101/2025.07.14.664506 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Myc and Kras cooperate in adult acinar cells to drive phenotypic heterogeneity, metastasis, and therapeutic resistance in a novel pancreatic cancer mouse model ]]> https://biorxiv.org/content/10.1101/2025.07.14.664767v1?rss=1 English, I. A. Worth, P. J. MacPherson-Hawthorne, K. A. Vergara, M. Pelz, K. Kiemen, A. L. Shah, V. M. Blise, K. E. Pelz, C. Tsuda, M. Heskett, M. B. Farrell, A. S. Allen-Petersen, B. L. Jimenez, P. Joly, M. M. Thoma, M. C. Eng, J. R. Daniel, C. J. Wang, X. Cunningham, M. Salgado-Garza, G. Phipps, J. L. Betts, C. Sivagnanam, S. Morgan, T. K. Wood, L. D. Coussens, L. M. Brody, J. R. Langer, E. M. Sears, R. C. 2025-07-18 doi:10.1101/2025.07.14.664767 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Characterization of a Novel Transmembrane Activating STING Agonist using Genetically Humanized Mice ]]> https://biorxiv.org/content/10.1101/2025.07.14.664814v1?rss=1 Mizuno, N. Abraham, J. Jimenez-Perez, K. Rose, I. Springgay, L. Boehm, D. Ando, T. Streblow, D. N. Haddad, E. Ward, J. Miller, S. Pandey, U. Junaid, A. Joyner, D. Muir, R. Burkhart, D. Rasheed, O. DeFilippis, V. R. 2025-07-18 doi:10.1101/2025.07.14.664814 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ S-Nitrosylated COX-2 is a TME-regulated breast cancer biomarker of mesenchymal phenotypes ]]> https://biorxiv.org/content/10.1101/2025.07.15.664474v1?rss=1 Hoffmann, R. J. Bensen, A. Dane, M. Arterberry, J. Smith, R. Korkola, J. Schedin, P. J. 2025-07-18 doi:10.1101/2025.07.15.664474 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Longitudinal Investigation of Structural and Resting-State Effective Connectivity Alterations in a Non-Human Primate Model of Huntington's Disease ]]> https://biorxiv.org/content/10.1101/2025.07.18.665554v1?rss=1 Petraityte, G. van Rijswijk, J. Liguore, W. McBride, J. L. Verhoye, M. Bertoglio, D. Weiss, A. R. Adhikari, M. H. 2025-07-23 doi:10.1101/2025.07.18.665554 Cold Spring Harbor Laboratory Press 2025-07-23 <![CDATA[ Mild subcortical stroke induces widespread astrogliosis independent of microglia and age ]]> https://biorxiv.org/content/10.1101/2025.07.18.665576v1?rss=1 Stackhouse, T. L. Marxmiller, B. D. Sullivan, S. J. McConnell, H. L. Knittell, L. M. De La Torre, R. Houser, A. M. Zhang, W. Woltjer, R. Mishra, A. 2025-07-23 doi:10.1101/2025.07.18.665576 Cold Spring Harbor Laboratory Press 2025-07-23 <![CDATA[ Distinct antibody-based signatures and functionality distinguish latent and active pediatric tuberculosis ]]> https://biorxiv.org/content/10.1101/2025.07.21.665984v1?rss=1 Nziza, N. Jung, W. Chen, T. Deng, Y. Franken, K. L. Ottenhoff, T. H. M. Kiguli, S. Lewinsohn, D. Boom, W. H. Mayanja-Kizza, H. Nsereko, M. Fortune, S. M. Stein, C. McNamara, R. Alter, G. Lancioni, C. L. 2025-07-24 doi:10.1101/2025.07.21.665984 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Nerve injury promotes glial immune responses through a Draper/Ninjurin A pathway ]]> https://biorxiv.org/content/10.1101/2025.07.21.665563v1?rss=1 Brashaw, C. Griffin, A. Speese, S. D. Logan, M. A. 2025-07-25 doi:10.1101/2025.07.21.665563 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ Developmental time course of social touch, parvalbumin interneurons, perineuronal nets and Mef2c expression reveals a sensitive period of somatosensory cortex development in prairie voles ]]> https://biorxiv.org/content/10.1101/2025.07.25.666627v1?rss=1 Milman, N. E. P. McGuire, N. M. Loeung, J. M. Bueno-Junior, L. S. Tinsley, C. E. Bronstein, H. Kelly, F. D. Wickham, P. T. Ghimire, A. Johnson, Z. Pantazopoulos, H. Watson, B. O. Sorg, B. A. Lim, M. M. 2025-07-26 doi:10.1101/2025.07.25.666627 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ APOE4 genotype negates the benefits of 17β-estradiol on cerebrovascular endothelial and mitochondrial function ]]> https://biorxiv.org/content/10.1101/2025.07.23.666474v1?rss=1 Kehmeier, M. N. Famiano, A. Cullen, A. E. Leonhardt, T. Ferguson, S. Snyder, M. McCurdy, C. E. Tyrrell, D. J. Alkayed, N. J. Walker, A. E. 2025-07-29 doi:10.1101/2025.07.23.666474 Cold Spring Harbor Laboratory Press 2025-07-29 <![CDATA[ Targeting Tmem63b and Piezo2 in C-fiber low threshold mechanoreceptor: limitation of Vglut3-IRES-Cre ]]> https://biorxiv.org/content/10.1101/2025.07.26.666969v1?rss=1 Orlin, D. J. Munoz, A. Berryman, S. Semidey, D. Murthy, S. E. 2025-07-31 doi:10.1101/2025.07.26.666969 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Glucagon and GLP-1 Accelerate Pseudo-Islet Assembly and Unmask Sex-Specific Islet Fragmentation Dynamics ]]> https://biorxiv.org/content/10.1101/2025.08.10.669547v1?rss=1 Keutler, K. Prady, S. B. Canaday, P. Dorrell, C. Schultz, C. 2025-08-12 doi:10.1101/2025.08.10.669547 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Altered molecular signaling pathways in the hippocampus of rhesus monkeys following chronic alcohol use ]]> https://biorxiv.org/content/10.1101/2025.08.12.669930v1?rss=1 Pareek, T. Vergis, J. M. Zhang, X. Platt, D. M. Grant, K. A. McCullumsmith, R. Gisabella, B. O'Donovan, S. M. Pantazopoulos, H. 2025-08-15 doi:10.1101/2025.08.12.669930 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ VO: The Vaccine Ontology ]]> https://biorxiv.org/content/10.1101/2025.08.12.669998v1?rss=1 Zheng, J. Lin, A. Y. Huffman, A. Masci, A. M. Racz, R. Wu, G. Roan, K. Ong, E. Sarntivijai, S. Hu, J. Asfaw, E. Kahn, H. Li, X. Zhang, X. Kosar, N. Li, J. Manuel, W. Abeysinghe, R. Rehana, H. Bansal, B. Pan, Y. Guo, J. He, V. Song, J. Seleznev, A. I. Hur, K. He, A. Davydov, A. Yang, Q. Vita, R. Peters, B. Ruttenberg, A. Diehl, A. D. Hoyt, C. T. Roncaglia, P. Huntley, R. P. Scheuermann, R. H. Courtot, M. Todd, T. Sayers, S. Chen, F. Li, X. Yeh, F.-Y. Xiang, Z. Ozgur, A. Whetzel, P. L. Musen, M. A. Mungall, C. J. Leitner, W. W. Cui, L. Colby, L. 2025-08-15 doi:10.1101/2025.08.12.669998 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Epigenetic Reactivation of CNS Endothelial Developmental Programs Triggers Adult Brain Angiogenesis, Promotes Post-Stroke Revascularization and Neuronal Regeneration. ]]> https://biorxiv.org/content/10.1101/2025.08.15.670554v1?rss=1 Thomas, S. Chandran, C. Ahirwar, L. K. Harmanci, A. O. Chathathayil, S. M. Alkayed, N. J. Dienel, A. C. Blackburn, S. L. McBride, D. W. T, P. K. 2025-08-21 doi:10.1101/2025.08.15.670554 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Cerebral blood flow in elastin haploinsufficient and 3xTg-AD mice ]]> https://biorxiv.org/content/10.1101/2025.08.18.670895v1?rss=1 Cullen, A. E. Reeve, E. H. Winder, N. R. Henson, G. D. Arora, N. Leonhardt, T. Hogan, A. P. Kumaran, S. K. Setthavonsack, N. Krajbich, V. Alkayed, N. J. Pike, M. M. Woltjer, R. L. Walker, A. E. 2025-08-22 doi:10.1101/2025.08.18.670895 Cold Spring Harbor Laboratory Press 2025-08-22 <![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[ Origin and Correlates of Viral Rebound in SIV-Infected Rhesus Macaques Following ART Discontinuation ]]> https://biorxiv.org/content/10.1101/2025.08.30.673277v1?rss=1 King, I. Aid, M. Kose, E. Immonen, T. Goodman, C. Fennessey, C. M. Colarusso, A. Walker-Sperling, V. Borducchi, E. Geleziunas, R. Rinaldi, W. Ferguson, M. Picker, L. J. Lifson, J. D. Keele, B. F. Barouch, D. H. 2025-09-01 doi:10.1101/2025.08.30.673277 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution ]]> https://biorxiv.org/content/10.1101/2025.09.01.673541v1?rss=1 Haller, B. C. Nelson, C. W. Rodrigues, M. F. Messer, P. W. 2025-09-02 doi:10.1101/2025.09.01.673541 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ Biological landscape of acute illness in children in sub-Saharan Africa and South Asia ]]> https://biorxiv.org/content/10.1101/2025.09.01.672585v1?rss=1 Mudibo, E. O. Sande, C. Ngari, M. M. Jenkins, B. Singa, B. O. Lancioni, C. L. Diallo, A. H. Mbale, E. Mupere, E. John, M. Bamouni, R. M. Prendergast, A. J. McGrath, C. J. Koulman, A. Bandsma, R. H. J. Tickell, K. D. Walson, J. L. Berkley, J. A. Gonzales, G. B. Njunge, J. M. 2025-09-03 doi:10.1101/2025.09.01.672585 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Pancreatic Cancer Induces Population-Specific Switching of Myosin Isoforms and Discrete Activation of Cachexia Genes in Skeletal Muscle Myocytes ]]> https://biorxiv.org/content/10.1101/2025.09.01.673500v1?rss=1 Counts, B. R. Jean, S. Gaafer, O. Ota, S. K. Inabathini, I. Guo, T. Guttridge, D. C. Ostrowski, M. C. Koniaris, L. G. Cao, S. Roh, H. C. Zimmers, T. A. 2025-09-05 doi:10.1101/2025.09.01.673500 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Clinical and molecular features of primary gliosarcoma with digital spatial whole-transcriptome analysis of glial and mesenchymal components ]]> https://biorxiv.org/content/10.1101/2025.09.02.673845v1?rss=1 Wood, M. D. Zangirolani, G. Lee, J. Neff, T. Zhang, K. Corless, C. L. 2025-09-07 doi:10.1101/2025.09.02.673845 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ S3R: Spatially Smooth and Sparse Regression Reveals High-Dimensional Regulatory Networks in Spatial Transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.09.06.674629v1?rss=1 zhou, x. dang, p. Tang, H. Peng, L. X. Yeh, J. J. Sears, R. C. Neelon, B. Zimmers, T. Zhang, C. Cao, S. 2025-09-11 doi:10.1101/2025.09.06.674629 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Splicing neoepitope prediction is sensitive to methodological differences ]]> https://biorxiv.org/content/10.1101/2025.09.10.674685v1?rss=1 Prelot, L. David, J. K. Lin, A. Kahles, A. Yurchikova, M. Thompson, R. F. Rätsch, G. 2025-09-16 doi:10.1101/2025.09.10.674685 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Alcohol Dependence-Induced Astrocyte Immune Activation in the Nucleus Accumbens ]]> https://biorxiv.org/content/10.1101/2025.09.12.675849v1?rss=1 Hashimoto, J. G. Mangieri, R. A. Roberts, A. J. Lime, T. Davis, B. A. Carbone, L. Roberto, M. Guizzetti, M. 2025-09-17 doi:10.1101/2025.09.12.675849 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Engineering NIR probes to enhance affinity and clinical workflow compatibility for prostate cancer imaging ]]> https://biorxiv.org/content/10.1101/2025.09.16.676549v1?rss=1 Malankar, G. S. Szafran, D. A. Kumar, G. Pacce, J. Devereux, M. Tao, K. Gomes, M. Greer, W. S. Rounds, C. C. Masillati, A. M. Gergis, S. Ledvina, H. Wong, M. H. Niedre, M. J. Wang, L. G. Gibbs, S. L. 2025-09-18 doi:10.1101/2025.09.16.676549 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Temporal Requirement for Stearoyl-CoA Desaturase 1 in Oligodendrocyte Development but Not Myelin Maintenance ]]> https://biorxiv.org/content/10.1101/2025.09.18.676928v1?rss=1 Farnum, I. Kunkel, T. J. Chavali, M. 2025-09-19 doi:10.1101/2025.09.18.676928 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Kidney kallikrein-1 contributes to cleavage of gamma-ENaC in vivo ]]> https://biorxiv.org/content/10.1101/2025.09.19.677394v1?rss=1 Curry, J. N. Su, X.-T. Wu, Q. Maeoka, Y. Yang, C.-L. Delpire, E. Fenton, R. F. Welling, P. A. Ellison, D. H. 2025-09-21 doi:10.1101/2025.09.19.677394 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Neurotype matching in monogamous rodents is modulated by early-life sleep experience ]]> https://biorxiv.org/content/10.1101/2025.09.24.678442v1?rss=1 Bueno-Junior, L. S. Milman, N. E. P. Jones-Tinsley, C. E. Ghimire, A. Wickham, P. T. Hu, Y. Ye, B. Lim, M. M. Watson, B. O. 2025-09-25 doi:10.1101/2025.09.24.678442 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ A dNmnat-sensitized in vivo platform for unbiased discovery of regulators of neurodegeneration ]]> https://biorxiv.org/content/10.1101/2025.09.25.678663v1?rss=1 Avetisyan, A. Manzo, E. Maturana, R. B. Kocia, M. Hsu, J.-M. Larson, A. Weirnick, R. Balasubramanian, K. Blackwell, N. Freeman, M. Bis, D. M. Fazal, S. Schuchner, S. Neukomm, L. Freeman, M. 2025-09-25 doi:10.1101/2025.09.25.678663 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Oncostatin M orchestrates collective epithelial migration via HIF1A activation ]]> https://biorxiv.org/content/10.1101/2025.09.26.678830v1?rss=1 McLean, I. C. Gross, S. M. Liby, T. A. Dane, M. A. Derrick, D. S. Heiser, L. M. 2025-09-27 doi:10.1101/2025.09.26.678830 Cold Spring Harbor Laboratory Press 2025-09-27 <![CDATA[ Increased sensitivity to myopia and altered retinal ON/OFF balance in a mouse model lacking Dusp4 ]]> https://biorxiv.org/content/10.1101/2025.09.29.678242v1?rss=1 Wilmet, B. Michiels, C. Zhang, J. Louboutin, A. Boranijasevic, S. Frederiksen, H. Callebert, J. Varin, J. Gimenez, M. L. Morgans, C. W. Duvoisin, R. Horan, L. Plevin, R. Picaud, S. Marre, O. Audo, I. Zeitz, C. 2025-10-01 doi:10.1101/2025.09.29.678242 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Endocannabinoid signaling is a critical link between circadian desynchronization and metabolic dysfunction ]]> https://biorxiv.org/content/10.1101/2025.09.29.678590v1?rss=1 Baca, B. A. Denaroso, G. E. Akli, S. Pearson, G. L. Wang, J. Bowles, N. P. Phillips, D. Sorensen, W. Hume, C. Hill, M. Karatsoreos, I. N. 2025-10-01 doi:10.1101/2025.09.29.678590 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Bridging forward-in-time and coalescent simulations using pyslim ]]> https://biorxiv.org/content/10.1101/2025.09.30.679676v1?rss=1 Gopalan, S. Rodrigues, M. F. Ralph, P. L. Haller, B. C. 2025-10-01 doi:10.1101/2025.09.30.679676 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Chronic Ethanol Drinking Alters Medial Prefrontal Cortex and Nucleus Accumbens Astrocyte Translatome and Extracellular Matrix Glycosaminoglycans ]]> https://biorxiv.org/content/10.1101/2025.09.30.679577v1?rss=1 Hashimoto, J. G. Ozburn, A. R. Reed, C. Erk, J. Song, Y. Yang, J. Xia, K. Zhang, F. Yu, Y. Fei, S. S. Gao, L. Linhardt, R. J. Phillips, T. J. Guizzetti, M. 2025-10-02 doi:10.1101/2025.09.30.679577 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Interferon Restores Antigen Presentation and Sensitizes Medulloblastoma to T Cell Killing ]]> https://biorxiv.org/content/10.1101/2025.09.30.679624v1?rss=1 Eisemann, T. Masihi, M. B. Tzaridis, T. Pister, V. Youm, I. Chambers, K. R. Dutta, A. Wenzel, A. T. Chin, K. Pomeroy, S. L. Mesirov, J. P. Fraenkel, E. Bagchi, A. Chavez, L. Wechsler-Reya, R. J. 2025-10-02 doi:10.1101/2025.09.30.679624 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Deveolopment of patient-derived neuroprogenitor cells (hNPCs), neurons, and astrocytes to explore the etiology of Guam Parkinsonism-dementia complex (PDC) ]]> https://biorxiv.org/content/10.1101/2025.10.07.680309v1?rss=1 Chlebowski-Giulietti, A. Yang, Y. Siddique, N. A. Siddique, T. Spencer, P. S. Steele, J. C. KISBY, G. E. 2025-10-07 doi:10.1101/2025.10.07.680309 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ A Rapid Gene Expression Profiler Classifies AML Tumor Responsiveness to Standard Therapies ]]> https://biorxiv.org/content/10.1101/2025.10.08.681215v1?rss=1 Kurtz, S. E. Eide, C. A. Kaempf, A. Long, N. Miller, A. Bottomly, D. McWeeney, S. Anand, S. Ng, S. W. Wang, J. C. Dick, J. E. Tyner, J. W. 2025-10-09 doi:10.1101/2025.10.08.681215 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ Spatial organization of the tumor-immune microenvironment in ER-positive breast cancer: remodeling during treatment and associations with clinical response ]]> https://biorxiv.org/content/10.1101/2025.10.09.681336v1?rss=1 Dahle, M. A. Foerde, J.-L. Egeland, E. V. Creason, A. L. Watson, C. Garred, O. Prasmickaite, L. Maelandsmo, G. M. Mills, G. B. Engebraaten, O. Haugen, M. H. 2025-10-10 doi:10.1101/2025.10.09.681336 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ BCG Vaccination at Birth Shapes the TCR Usage and Functional Profile of MR1T Cells at 9 Weeks of Age ]]> https://biorxiv.org/content/10.1101/2025.10.09.681353v1?rss=1 Kain, D. McElfresh, G. Swarbrick, G. Rott, K. Boggy, G. Walzl, G. Du Plessis, N. Hanekom, W. Nemes, E. Shey, M. Scriba, T. Bimber, B. N. Lewinsohn, D. Lewinsohn, D. 2025-10-10 doi:10.1101/2025.10.09.681353 Cold Spring Harbor Laboratory Press 2025-10-10 <![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[ A Zika Virus-Like Particle Vaccine Mitigates Early Pregnancy Loss In Rhesus Macaques ]]> https://biorxiv.org/content/10.1101/2025.10.16.682761v1?rss=1 Jaeger, H. K. Smith, J. L. Labriola, C. S. Pung, L. J. Hagen, O. L. Denton, M. D'Mello, R. J. Parkins, C. J. Weber, W. C. Medica, S. Kreklywich, C. N. DeFilippis, V. R. Bondoc, S. Busman-Sahay, K. Castro, J. N. Zilverberg, G. White, R. Terry, M. Barber-Axthelm, A. M. Axthelm, M. K. Smedley, J. Aliota, M. T. Weiler, A. M. Friedrich, T. C. Estes, J. Morgan, T. K. Lo, J. O. Roberts, V. H. J. Streblow, D. N. Hirsch, A. J. 2025-10-16 doi:10.1101/2025.10.16.682761 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ Tumor-intrinsic MHC-II activation in pancreatic ductal adenocarcinoma enhances immune response and treatment efficacy ]]> https://biorxiv.org/content/10.1101/2025.10.21.683745v1?rss=1 Chen, C. Gribbin, K. Li, X. Ozmen, T. Ozmen, F. Sivagnanam, S. Kim, J. Blise, K. Yang, X. Zhang, Y. Dai, R. Keith, D. Sherman, M. Dai, M.-s. Coussens, L. Lopez, C. Sears, R. Mills, G. Byrne, K. Xia, Z. 2025-10-22 doi:10.1101/2025.10.21.683745 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Neuronal architecture of the mouse insular cortex underlying its diverse functions ]]> https://biorxiv.org/content/10.1101/2025.10.23.683697v1?rss=1 Jongbloets, B. C. Chen, Y. Gingerich, I. K. Muniak, M. A. Mao, T. 2025-10-24 doi:10.1101/2025.10.23.683697 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ GRASS-NB: Group-structured variable selection for spatial negative binomial data with applications to cancer registry and spatial omics ]]> https://biorxiv.org/content/10.1101/2025.10.24.684446v1?rss=1 Mattila, C. Neelon, B. Sonawane, K. Cao, S. Angel, P. Hill, E. Seal, S. 2025-10-25 doi:10.1101/2025.10.24.684446 Cold Spring Harbor Laboratory Press 2025-10-25 <![CDATA[ Loss of cell cycle gatekeeping by 1 CNOT3 impairs hematopoietic stem and progenitor cell division and repopulating activity ]]> https://biorxiv.org/content/10.1101/2025.10.23.684176v1?rss=1 Vu, L. P. Yuen, K. A. Taibi, T. Hoang, Q. A. Yue, M. Liu, Z. Habibi, E. Spiliotopoulos, E. Ramkumar, N. Nation, N. Edin, G. Ngo, T. T. 2025-10-26 doi:10.1101/2025.10.23.684176 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Brain insulin signaling restores deficits in striatal dopamine release in overweight male mice with preexisting low D2-receptor expression ]]> https://biorxiv.org/content/10.1101/2025.10.28.685173v1?rss=1 Bocarsly, M. E. Mehr, J. B. Swanson, E. S. Sriramoji-Virdi, S. Authement, M. E. Shashikiran, S. Goldbach, H. Matsui, A. Rimondini, R. Bock, R. Alvarez, V. A. 2025-10-30 doi:10.1101/2025.10.28.685173 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Vaginal epithelial estrogen receptor α coordinates glycogen deposition, microbial stability, and pH regulation in mice ]]> https://biorxiv.org/content/10.1101/2025.10.29.685365v1?rss=1 Mahalingam, S. Carulli, E. M. Mao, J. Stephens, K. K. Erickson, J. A. Winuthayanon, W. 2025-10-30 doi:10.1101/2025.10.29.685365 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ The ID93 + GLA-3M-052-LS vaccine candidate elicits mucosal and systemic immunogenicity and protective efficacy against Mycobacterium tuberculosis challenge in BCG-primed Collaborative Cross inbred mice ]]> https://biorxiv.org/content/10.1101/2025.10.31.685426v1?rss=1 Voigt, E. A. Alsharaydeh, A. Kasal, D. N. Jennewein, M. F. Brandt, D. S. Lin, S. Singh, J. Bakken, J. Mohamath, R. Fusco, P. Torrelles, J. B. Beamer, G. Fox, C. B. 2025-11-01 doi:10.1101/2025.10.31.685426 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ Contextual control of CD8+ T cell priming by dendritic cell subsets in tumor and inflammatory microenvironments ]]> https://biorxiv.org/content/10.1101/2025.10.31.685861v1?rss=1 Schuster, V. P. Brown, K. Unsworth, J. R. Berkowitz, N. Ruhland, M. K. 2025-11-03 doi:10.1101/2025.10.31.685861 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ CD38hiCD19dim cells in lymph nodes predict favorable prognosis in patients with stage III melanoma receiving adjuvant PD-1-blockade ]]> https://biorxiv.org/content/10.1101/2025.11.03.685725v1?rss=1 Ailte, I. Chauhan, S. K. Prasmickaite, L. Bassarova, A. V. Poissonnier, A. Feenstra, M. Nyakas, M. Johannessen, B. Ryder, T. Hermann, R. Frich, L. Holth, A. Inderberg, E. M. Jespersen, H. Florenes, V. A. Kyte, J. A. Maelandsmo, G. M. Egeland, E. V. 2025-11-04 doi:10.1101/2025.11.03.685725 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ GNL3 SUMOylation is essential for DNA double-strand break repair by homologous recombination ]]> https://biorxiv.org/content/10.1101/2025.11.04.686352v1?rss=1 Yang, Y. Li, Y. Dai, R. S. Chen, C. Zientek, K. Reddy, A. Xia, Z. Sears, R. C. Sun, X.-X. Dai, M.-S. 2025-11-05 doi:10.1101/2025.11.04.686352 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ The Christchurch point mutation in mouse APOE reduces Aβ-induced tau and α-synuclein pathologies ]]> https://biorxiv.org/content/10.1101/2025.11.05.686857v1?rss=1 View larger version (53K): org.highwire.dtl.DTLVardef@1104377org.highwire.dtl.DTLVardef@bd6c70org.highwire.dtl.DTLVardef@1a4e44org.highwire.dtl.DTLVardef@1087d7f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Soto-Faguas, C. M. O'Niel, A. Mueller, P. A. Sanchez-Molina, P. Woltjer, R. L. Raber, J. Unni, V. K. 2025-11-07 doi:10.1101/2025.11.05.686857 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ Combining the alpha-2 adrenergic agonist clonidine with naloxone rescues fentanyl-induced physiologic dysfunction and increases survival ]]> https://biorxiv.org/content/10.1101/2025.11.07.687263v1?rss=1 Rivera, A. Schutzer, W. E. Sonneborn, A. Shotwell, S. L. Janowsky, A. Abbas, A. Torralva, R. 2025-11-10 doi:10.1101/2025.11.07.687263 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ A Population-Specific PARP1 Gene Variation Modulates PARP Trapping ]]> https://biorxiv.org/content/10.1101/2025.11.11.687916v1?rss=1 Cai, J. Billur, R. Cohen, M. S. Ladurner, A. G. Black, B. E. 2025-11-13 doi:10.1101/2025.11.11.687916 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ CREG1 promotes autophagy and protects the heart against nutritional stress-induced injury and age-associated hypertrophy, fibrosis and diastolic dysfunction ]]> https://biorxiv.org/content/10.1101/2025.11.11.687936v1?rss=1 View larger version (60K): org.highwire.dtl.DTLVardef@1b9fc05org.highwire.dtl.DTLVardef@150e48aorg.highwire.dtl.DTLVardef@1cc47adorg.highwire.dtl.DTLVardef@75ed53_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Qi, Y. Pepe, R. J. Tejeda, G. Joo, Y. Yang, N. K. Hayes, K. B. rahimi, s. Zhou, Z. Li, S. Lee, L. 2025-11-13 doi:10.1101/2025.11.11.687936 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ The retinal light response is modulated by an mGluR5-mediated retrograde signal from ON-bipolar cells to photoreceptors ]]> https://biorxiv.org/content/10.1101/2025.11.13.687902v1?rss=1 Morgans, C. W. Haley, T. L. Ren, G. Taylor, I. A. M. Randall, K. L. Duvoisin, R. M. 2025-11-14 doi:10.1101/2025.11.13.687902 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Degraded neural coding of temporal fine structure with age predicts effortful listening in multi-talker environments ]]> https://biorxiv.org/content/10.1101/2025.11.17.688858v1?rss=1 Zhen, L. Parida, S. McHaney, J. Zink, M. Chandrasekaran, B. Parthasarathy, A. 2025-11-17 doi:10.1101/2025.11.17.688858 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Lipid Tail Length Determines Nano-Bio Interactions of Peptide Amphiphile Nanostructures ]]> https://biorxiv.org/content/10.1101/2025.11.18.689169v1?rss=1 Bonic, K. Stewart, M. R. Xiang, L. Mooney, K. Armstrong, R. Esener, S. Fischer, J. M. Yildirim, A. 2025-11-19 doi:10.1101/2025.11.18.689169 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ RNA switch model for localization and translation of the myelin basic protein mRNA ]]> https://biorxiv.org/content/10.1101/2025.11.19.689361v1?rss=1 Topkar, V. V. Wu, V. Ho, L. T. Ambiel, N. Valenzuela, A. Yoshimura, K. Zuchero, J. B. Fu, M.-m. Das, R. 2025-11-20 doi:10.1101/2025.11.19.689361 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ Sphingosine-1-phosphate receptor modulators resensitize FLT3-ITD acute myeloid leukemia cells with NRAS mutations to FLT3 inhibitors ]]> https://biorxiv.org/content/10.1101/2025.11.21.689510v1?rss=1 Baer, M. R. Chatterjee, A. Ali, M. K. M. Bailey, C. M. Liu, Y. Small, D. Smith, C. C. Traer, E. C. Wang, Y. Silvestri, G. 2025-11-24 doi:10.1101/2025.11.21.689510 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ In vivo assessment of differential toxicity of cancer treatment drugs in Fanconi Anemia ]]> https://biorxiv.org/content/10.1101/2025.11.21.689800v1?rss=1 Grompe, M. Dorrell, C. Burtness, B. Cruz-Gomez, S. MacMillan, A. 2025-11-24 doi:10.1101/2025.11.21.689800 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Infection Of Rhesus Macaques With Onyong-nyong Virus UVIR-O804 Recapitulates Key Aspects of Human Clinical Disease ]]> https://biorxiv.org/content/10.1101/2025.11.20.689439v1?rss=1 Jaeger, H. K. Denton, M. Andoh, T. F. Kreklywich, C. N. Gao, L. Pung, L. J. Streblow, Z. J. McMonigal, A. Ray, K. Graves, B. Streblow, M. M. Barber-Axthelm, A. M. Zilverberg, G. Terry, M. Fei, S. S. Hogan, G. Schultz, D. C. Cherry, S. Axthelm, M. K. Labriola, C. S. Heise, M. T. Streblow, D. N. 2025-11-26 doi:10.1101/2025.11.20.689439 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ Impaired synaptic inhibition and enhanced aversion encoding by lateral habenula neurons during Δ9-tetrahydrocannabinol withdrawal. ]]> https://biorxiv.org/content/10.1101/2025.11.24.690244v1?rss=1 Hwang, E.-K. Daphne, D. Maddox, C. C. Zapata, A. Hoffman, A. F. Lupica, C. R. 2025-11-28 doi:10.1101/2025.11.24.690244 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Gene flow weakens genomic clines while selection maintains adaptive loci: two decades of evolution in Drosophila melanogaster natural populations ]]> https://biorxiv.org/content/10.1101/2025.11.28.691231v1?rss=1 Horvath Miranda, V. da Silva Ribeiro, T. Alves, J. M. Eanes, W. F. Brud, E. Veeramah, K. R. Pool, J. E. Rodrigues, M. F. Cogni, R. 2025-11-29 doi:10.1101/2025.11.28.691231 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Sorting endosomes play key roles in presentation of Mycobacterium tuberculosis-derived ligands to MAIT cells ]]> https://biorxiv.org/content/10.64898/2025.12.03.691670v1?rss=1 Tammen, A. E. Peterson, J. C. Worley, A. Lewinsohn, D. M. Karamooz, E. 2025-12-04 doi:10.64898/2025.12.03.691670 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ Differential targeting of human pyroptotic Caspase-5 and Caspase-4 by Shigella OspC2 and OspC3 ]]> https://biorxiv.org/content/10.64898/2025.12.04.692159v1?rss=1 Kim, K. Valdespino Diaz, M. A. Karr, R. M. muscolo, m. E. Goers, L. Yu, T. Levin, T. Pruneda, J. N. Lesser, C. 2025-12-04 doi:10.64898/2025.12.04.692159 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ The human cytomegalovirus chemokine binding protein UL22A is necessary for efficient reactivation from latency in CD34+ hematopoietic progenitor cells. ]]> https://biorxiv.org/content/10.64898/2025.12.04.692306v1?rss=1 Turner, R. Diggins, N. Slind, L. E. Mitchell, J. Pham, A. Parkins, C. Perez, W. Medica, S. Denton, M. Andoh, T. F. Webb, G. M. Andrade-Vera, D. Streblow, D. N. Caposio, P. Hancock, M. H. 2025-12-04 doi:10.64898/2025.12.04.692306 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ Prodromal pathogenesis of CLN7 Batten Disease revealed by multimodal biomarkers in macaques ]]> https://biorxiv.org/content/10.64898/2025.12.02.691930v1?rss=1 Liguore, W. A. Hilven, W. Lurye, L. Akkermans, J. Decrop, M. Zweig, R. Sherman, L. S. McBride, J. L. Bertoglio, D. Weiss, A. R. 2025-12-05 doi:10.64898/2025.12.02.691930 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Endogenous Osteocyte-Osteoclast Signaling Enables Growth Factor-Free Bone Remodeling, Drug Response, and Cancer Invasion in a Nanoscale Calcified Bone-on-a-Chip Model ]]> https://biorxiv.org/content/10.64898/2025.12.08.693047v1?rss=1 Sousa, M. Athirasala, A. Roth, D. Fraga, M. A. Vignolo, S. Doe, A. Lee, J. Romanowicz, G. Nguyen, J. Lin, A. Franca, C. M. Guldberg, R. Bertassoni, L. E. 2025-12-11 doi:10.64898/2025.12.08.693047 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Activation of cannabinoid receptor CB1 leads to aberrant myelination in development ]]> https://biorxiv.org/content/10.64898/2025.12.10.693544v1?rss=1 Miramontes, T. G. Hamling, K. R. Doan, R. A. Singh, S. Collins, H. Y. Emery, B. Call, C. L. Monk, K. 2025-12-11 doi:10.64898/2025.12.10.693544 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Decoding the interactome for Cyclic-di-AMP-producing enzyme diadenylate cyclase (DacA) ]]> https://biorxiv.org/content/10.64898/2025.12.11.693769v1?rss=1 Mu, R. Xie, B. Momeni, S. Wu, H. 2025-12-12 doi:10.64898/2025.12.11.693769 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ The cyclic nucleotide binding sites of Swiss-Cheese, the Drosophila orthologue of human PNPLA6, are required for its catalytic function ]]> https://biorxiv.org/content/10.64898/2025.12.10.693492v1?rss=1 Law, A. Wentzell, J. da Cruz, A. Marney, L. Kretzschmar, D. 2025-12-13 doi:10.64898/2025.12.10.693492 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ P/Q-type voltage-gated calcium channels regulate calcium signaling and developmental myelination in oligodendrocyte lineage cells ]]> https://biorxiv.org/content/10.64898/2025.12.12.694003v1?rss=1 Piller, M. Doan, R. Call, C. L. Smith, S. Monk, K. 2025-12-13 doi:10.64898/2025.12.12.694003 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ Selective infection and loss of PRDM1+ LN Tfh cells in uncontrolled HIV infection precludes formation of Tfh reservoirs under ART ]]> https://biorxiv.org/content/10.64898/2025.12.11.693731v1?rss=1 Wu, V. H. Nordin, J. M. Pampena, M. B. Rachimi, S. Burgess, W. L. Clark, M. Robinson, J. A. Estrada, P. M. d. R. Schleimann, M. H. Torres-Ruiz, F. Gonzalez-Navarro, M. Salgado, G. Luna-Villalobos, Y. A. Reyes-Teran, G. Bar, K. J. Estes, J. D. Sogaard, O. S. Romberg, N. Avila-Rios, S. Betts, M. R. 2025-12-15 doi:10.64898/2025.12.11.693731 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ A window trial in metastatic pancreatic ductal adenocarcinoma reveals resistance mechanisms to targeting the KRAS-MEK pathway ]]> https://biorxiv.org/content/10.64898/2025.12.12.693851v1?rss=1 Tsuda, M. Keith, D. Daniel, C. J. Pelz, C. Blise, K. E. Ozmen, T. Y. Ozmen, F. Hawthone, K. Eng, J. R. Li, X. Wang, X. Zimny, H. Sivagnanam, S. Betre, K. Kirchberger, N. Chong, B. Lee, J. Matter, _. Smith, A. Agritelley, E. S. Waugh, T. Sannecy, A. Alarcon, K. Youm, I. Protzek, S. Egger, J. English, I. A. Yang, M. Shah, V. M. Link, J. M. Creason, A. L. Worth, P. J. Goodyear, S. M. Chin, K. Muschler, J. L. Suciu, C. G. Corless, C. L. Cao, S. Soucek, L. Kardosh, A. Coussens, L. M. Brody, J. R. Lopez, C. D. Mills, G. B. Sears, R. C. 2025-12-15 doi:10.64898/2025.12.12.693851 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Chemoproteomic elucidation of β-lactam drug targets in Mycobacterium abscessus ]]> https://biorxiv.org/content/10.64898/2025.12.15.694292v1?rss=1 Devlin, K. L. Hutchinson, E. Leach, D. T. Nelson, W. C. Gorham, L. J. Lamichhane, G. Lin, V. S. Beatty, K. E. 2025-12-15 doi:10.64898/2025.12.15.694292 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Multi-timescale Rhythmic Dynamics in Rostral Ventromedial Medulla Neurons ]]> https://biorxiv.org/content/10.64898/2025.12.15.693905v1?rss=1 Ashworth, C. Martenson, M. Shi, Z. De Preter, C. C. Heinricher, M. M. Mancini, F. 2025-12-17 doi:10.64898/2025.12.15.693905 Cold Spring Harbor Laboratory Press 2025-12-17 <![CDATA[ In vitro evidence for bisphenol A as a human liver carcinogen: Environmentally relevant doses inhibit cancer protective ESR1 signaling in a human liver cell line ]]> https://biorxiv.org/content/10.64898/2025.12.18.695265v1?rss=1 Weeks, E. Kennedy, S. R. Searles, R. Carrothers, S. Davis, B. Carbone, L. Turker, M. Lloyd, R. S. Weinhouse, C. 2025-12-22 doi:10.64898/2025.12.18.695265 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Epigenetic plasticity is a driver of heritable pollution tolerance in Atlantic killifish ]]> https://biorxiv.org/content/10.64898/2025.12.18.695277v1?rss=1 Colwell, M. Drown, M. Flack, N. Walls, C. Faulk, C. Carrothers, S. Weeks, E. Weinhouse, C. 2025-12-22 doi:10.64898/2025.12.18.695277 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Dysfunctional memory B cell responses to the protective repeat region of the Plasmodium circumsporozoite protein are associated with waning humoral immunity ]]> https://biorxiv.org/content/10.64898/2025.12.19.695559v1?rss=1 McDougal, C. E. Mkindi, C. G. Rodda, L. B. Lucarelli, C. V. Langowski, M. D. King, N. P. Jongo, S. Daubenberger, C. Pepper, M. 2025-12-22 doi:10.64898/2025.12.19.695559 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Application of Large Language Models for Annotating Genes into Reactome Pathways ]]> https://biorxiv.org/content/10.64898/2025.12.20.695723v1?rss=1 Wu, G. Matthews, L. Boyer, N. Milacic, M. Beavers, D. Li, N. T. May, B. Rothfels, K. Shamovsky, V. Stephan, R. Gillespie, M. Hermjakob, H. DEustachio, P. Stein, L. D. 2025-12-23 doi:10.64898/2025.12.20.695723 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Identification of senescence-associated drivers of tumour growth and progression using a novel microarray platform ]]> https://biorxiv.org/content/10.64898/2025.12.20.695739v1?rss=1 Ou, H.-L. Hoffmann, R. J. Smith, R. Devlin, K. L. Dane, M. Munoz-Espin, D. Korkola, J. 2025-12-23 doi:10.64898/2025.12.20.695739 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ FHIR as a Unifying Format for Genomic Research Data Tracking, Aggregation, and Integration ]]> https://biorxiv.org/content/10.64898/2025.12.22.695544v1?rss=1 Sanati, N. Walsh, B. Gray, P. Hagen, L. Carroll, R. J. Heath, A. P. Charbonneau, A. Ellrott, K. 2025-12-24 doi:10.64898/2025.12.22.695544 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ The synaptic vesicle priming protein Munc13 mediates evoked somatodendritic dopamine release ]]> https://biorxiv.org/content/10.64898/2025.12.23.696181v1?rss=1 Lebowitz, J. J. Banerjee, A. Handy, G. Williams, J. T. Kaeser, P. S. 2025-12-24 doi:10.64898/2025.12.23.696181 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ A New Paradigm of Transcriptional Regulation by the SufR-Like Iron-Sulfur Transcription Factors ]]> https://biorxiv.org/content/10.64898/2025.12.26.696629v1?rss=1 Lu, Z. Ong, C. Zhang, L. Wan, T. Davulcu, O. de Farias, M. Zhang, L.-M. 2025-12-27 doi:10.64898/2025.12.26.696629 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ Evaluating Acridones as Novel Therapeutics for Human Babesiosis ]]> https://biorxiv.org/content/10.64898/2026.01.07.698299v1?rss=1 Vydyam, P. Zhang, E. Chattopadhyay Pal, A. Dodean, R. Kancharla, P. Kelly, J. X. Ben Mamoun, C. 2026-01-08 doi:10.64898/2026.01.07.698299 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ MYST acetyltransferases are a targetable therapeutic vulnerability in SETBP1-mutant leukemia ]]> https://biorxiv.org/content/10.64898/2026.01.08.697228v1?rss=1 Maxson, J. E. Braun, T. P. Carlson, H. Nguyen, T. Tauchmann, S. Carratt, S. A. Kruer, T. L. Dankyi, N. A. Balasis, M. Kim, H. Tsai, C.-F. Liu, T. Shrestha, S. Fischer, J. M. Padron, E. 2026-01-08 doi:10.64898/2026.01.08.697228 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Mutant ASXL1 Drives Transcriptional Activation and Repression in Human Hematopoiesis ]]> https://biorxiv.org/content/10.64898/2026.01.13.699315v1?rss=1 Hall, M. L. Quintal, A. Worme, S. Nguyen, T. Schonrock, Z. Tsuchiya, M. Acharya, S. N. Carlson, H. L. Pacentine, I. V. Shrestha, S. Macaraeg, J. Armstrong, R. McGann, J. Evans-Dutson, S. Lusardi, T. A. O'Connell, B. L. Adey, A. C. Maxson, J. E. Yardımcı, G. G. Braun, T. P. 2026-01-14 doi:10.64898/2026.01.13.699315 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Defects in tissue-resident macrophages lead to smaller eardrums and abnormal neurovascular networks with increased middle-ear infection ]]> https://biorxiv.org/content/10.64898/2026.01.13.699360v1?rss=1 Zhang, Y. Wang, P. Neng, L. Burwood, G. Sharma, K. Kachelmeier, A. Shi, X. 2026-01-14 doi:10.64898/2026.01.13.699360 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Aging macaques bridge the translational gap in perivascular space biology ]]> https://biorxiv.org/content/10.64898/2026.01.14.699534v1?rss=1 Liguore, W. A. Schwartz, D. L. Piantino, J. Rajendran, A. Jensen, G. Karpf, J. A. Chernov, M. M. Woltjer, R. L. Kohama, S. G. Silbert, L. C. Weiss, A. R. 2026-01-15 doi:10.64898/2026.01.14.699534 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ Monounsaturated fatty acid biosynthesis is critical for streptococcal envelope homeostasis and stress tolerance ]]> https://biorxiv.org/content/10.64898/2026.01.14.699484v1?rss=1 Baker, J. L. Tang, J. Guo, M. Farias-da-Silva, F. F. Barbisan, M. Burnside, M. Crofton, K. Williams, S. Rao, S. Lee, M. Drucker, S. G. Higashi, D. L. Merrit, J. Hirose, Y. Jan-Willem, V. Nizet, V. 2026-01-16 doi:10.64898/2026.01.14.699484 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ An Integrated Method for Profiling Lipid-Protein Interactions Using Multifunctional Lipid Probes ]]> https://biorxiv.org/content/10.64898/2026.01.17.700062v1?rss=1 Farley, S. E. Guzman, G. Blume, B. Stein, F. Schultz, C. Tafesse, F. G. 2026-01-17 doi:10.64898/2026.01.17.700062 Cold Spring Harbor Laboratory Press 2026-01-17 <![CDATA[ Selective Pharmacological Blockade of GPR39 Markedly Reduces No Reflow and Infarct Volumes in a Rat Model of Acute Myocardial Infarction ]]> https://biorxiv.org/content/10.64898/2026.01.16.699339v1?rss=1 Methner, C. Le, D. E. Liu, L. Plascencia, M. Kajimoto, M. thompson, a. Cianciulli, A. Pellacani, A. Micheli, F. Kaul, S. 2026-01-20 doi:10.64898/2026.01.16.699339 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ PU.1 inhibition sensitizes stem-monocytic AML to BCL2 blockade ]]> https://biorxiv.org/content/10.64898/2026.01.20.700677v1?rss=1 Yashar, W. M. Pacentine, I. V. Taherinasab, A. Nguyen, T. Worme, S. Tsuchiya, M. Lusardi, T. Hutchinson, C. Fillmore, T. L. Posso, C. Gosline, S. J. Piehowski, P. D. Yardimci, G. G. Adey, A. C. Maxson, J. E. Braun, T. P. 2026-01-23 doi:10.64898/2026.01.20.700677 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ miniMTI: minimal multiplex tissue imaging enhances biomarker expression prediction from histology ]]> https://biorxiv.org/content/10.64898/2026.01.21.700911v1?rss=1 Sims, Z. Govindarajan, S. Ait-Ahmad, K. Ak, C. Kuykendall, M. Mills, G. B. Eksi, E. Chang, Y. H. 2026-01-23 doi:10.64898/2026.01.21.700911 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ A First-In-Class Broad Spectrum Inhibitor of Copper Exporting P1B-type ATPases ]]> https://biorxiv.org/content/10.64898/2026.01.22.700703v1?rss=1 Shanbhag, V. Dinguyella, S. A. Gudekar, N. Conrad, K. Azubuogu, C. Probst, C. Ralle, M. Mediavilla, M. G. Cricco, J. A. Garza, N. M. Gohil, V. M. Peck, S. Kumar, S. Natarajan, A. Horadigala-Gamage, M. Meloni, G. Singh, K. Petris, M. J. 2026-01-24 doi:10.64898/2026.01.22.700703 Cold Spring Harbor Laboratory Press 2026-01-24 <![CDATA[ Differential Assembly of Native ENaC Complexes Across Mouse Epithelial Tissues ]]> https://biorxiv.org/content/10.64898/2026.01.23.701393v1?rss=1 Bharadwaj, A. Curry, J. N. Su, X.-T. Barria Maturana, R. McCormick, J. A. Ellison, D. H. Baconguis, I. 2026-01-25 doi:10.64898/2026.01.23.701393 Cold Spring Harbor Laboratory Press 2026-01-25 <![CDATA[ Transcriptomic profiling reveals neurophysiological gene candidates underlying vocal evolution in African clawed frogs ]]> https://biorxiv.org/content/10.64898/2026.01.24.701475v1?rss=1 Barkan, C. L. Binder, L. Davis, B. A. Carbone, L. Zornik, E. 2026-01-26 doi:10.64898/2026.01.24.701475 Cold Spring Harbor Laboratory Press 2026-01-26 <![CDATA[ Genome-wide CRISPRi screen identifies basigin loss as protective in cardiac hypoxia ]]> https://biorxiv.org/content/10.64898/2026.01.26.701810v1?rss=1 Flanigan, W. R. Midha, A. D. Blume, S. Y. Marti-Mateos, Y. Costa, M. W. Huang, Y. Baik, A. H. Huynh, H. Susarla, G. Bennett, N. K. Nowak, R. A. Srivastava, D. Nakamura, K. Jain, I. H. 2026-01-27 doi:10.64898/2026.01.26.701810 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Mapping SARS-CoV-2 Nucleocapsid Function with Nanobodies ]]> https://biorxiv.org/content/10.64898/2026.01.26.701894v1?rss=1 Weinstein, J. B. Bates, T. A. Anastas, A. Alfahdli, A. Trank-Green, M. McBride, S. K. Garcia, M. Parson, M. A. Jenkins, M. L. Burke, J. E. Barklis, E. Tafesse, F. G. 2026-01-27 doi:10.64898/2026.01.26.701894 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Pre-myelinating oligodendrocyte ADGRG1 is required for axon ensheathment and CNS myelin formation ]]> https://biorxiv.org/content/10.64898/2026.01.26.701898v1?rss=1 Zhu, B. Li, T. Rodrigues, B. V. Piller, M. V. Call, C. L. Mogha, A. Belloso-Iguerategui, A. Chiou, B. Schmidt, R. Wangzhou, A. Thurber, A. Dee, M. Larson, C. Monk, K. Piao, X. 2026-01-27 doi:10.64898/2026.01.26.701898 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Identification of clofibric acid as a SYVN1 ligand for PROTAC development ]]> https://biorxiv.org/content/10.64898/2026.01.26.701774v1?rss=1 View larger version (15K): org.highwire.dtl.DTLVardef@776850org.highwire.dtl.DTLVardef@1616bd0org.highwire.dtl.DTLVardef@ed3e03org.highwire.dtl.DTLVardef@18271e7_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Warren, J. Munakala, A. Zientek, K. Kim, K. Wilmarth, P. Reddy, A. Li, B. X. Xiao, X. 2026-01-28 doi:10.64898/2026.01.26.701774 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ Antigenic stimulation in conjunction with cytokine is required for mediating IL-17A production in human MAIT cells ]]> https://biorxiv.org/content/10.64898/2026.01.27.702041v1?rss=1 Kim, S.-J. Kain, D. Lewinsohn, D. A. Swarbrick, G. M. Cansler, M. E. Bimber, B. N. McElfresh, G. Wong, E. B. Khuzwayo, S. Riffelmacher, T. Lewinsohn, D. M. 2026-01-30 doi:10.64898/2026.01.27.702041 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Small molecule agonists of 8-oxoguanine DNA glycosylase, OGG1 ]]> https://biorxiv.org/content/10.64898/2026.01.30.702659v1?rss=1 Luzadder, M. M. Minko, I. G. Moellmer-Gomez, S. A. Tozaki, N. N. Jaruga, P. Dizdaroglu, M. Jin, H. Devereaux, J. Nilsen, A. Lloyd, R. S. McCullough, A. K. 2026-01-31 doi:10.64898/2026.01.30.702659 Cold Spring Harbor Laboratory Press 2026-01-31 <![CDATA[ Transcriptomics-based modeling of methionine metabolism effectively estimates sample-wise DNA methylation activity and epigenetic aging ]]> https://biorxiv.org/content/10.64898/2026.01.30.702880v1?rss=1 Guo, T. Dang, P. Fang, Y. Zhu, H. Wang, X. Wang, J. Ma, A. Ma, Q. Cao, S. Zhang, C. 2026-02-02 doi:10.64898/2026.01.30.702880 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Maternal Obesity Reprograms Differentiation Trajectories of Fetal Hematopoietic Stem and Progenitor Cells Through Altered Inflammatory Signaling ]]> https://biorxiv.org/content/10.64898/2026.01.29.702548v1?rss=1 Doratt, B. M. Hemati, H. Wagner, S. B. Blanton, M. B. Avila, U. Varlamov, O. Messaoudi, I. 2026-02-03 doi:10.64898/2026.01.29.702548 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ ImmunoPheno: A Computational Framework for Data-Driven Design and Analysis of Immunophenotyping Experiments ]]> https://biorxiv.org/content/10.64898/2026.02.01.703134v1?rss=1 Wu, L. Nguyen, M. A. Yang, Z. Potluri, S. Sivagnanam, S. Kirchberger, N. Joshi, A. Ahn, K. J. Tumulty, J. S. Cruz Cabrera, E. Romberg, N. Tan, K. Coussens, L. M. Camara, P. G. 2026-02-03 doi:10.64898/2026.02.01.703134 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Unwinding of an RNA duplex by the Orthoflavivirus NS3 helicase requires translocation beyond the displaced strand and is stimulated by the NS5 RdRp ]]> https://biorxiv.org/content/10.64898/2026.02.06.704446v1?rss=1 Arnold, J. J. Chib, S. Cameron, C. E. 2026-02-07 doi:10.64898/2026.02.06.704446 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ MetaKnogic-Alpha: A Hyper-Relational Knowledge Base for Grounded Metabolic Reasoning ]]> https://biorxiv.org/content/10.64898/2026.02.05.704050v1?rss=1 Dang, P. Swaminathan, P. Guo, T. Wan, C. Cao, S. Zhang, C. 2026-02-09 doi:10.64898/2026.02.05.704050 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Evaluation and application of chemical decrosslinking in the context of histopathological spatial proteomics ]]> https://biorxiv.org/content/10.64898/2026.02.06.704439v1?rss=1 Nwosu, A. J. Chen, L. Kumar, R. Kwon, Y. Goodyear, S. M. Kardosh, A. Fulcher, J. M. Pasa-Tolic, L. 2026-02-09 doi:10.64898/2026.02.06.704439 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ A Framework for Comparing Mouse Neoantigen Immunogenicity ]]> https://biorxiv.org/content/10.64898/2026.02.10.704454v1?rss=1 Matulich, P. J. Sprague, C. N. Schuster, V. P. Granados, A. M. Chaudhari, R. B. Burger, M. L. 2026-02-12 doi:10.64898/2026.02.10.704454 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ Chronic ethanol self-administration alters dopamine in the caudate nucleus and putamen of rhesus macaques in a sex-dependent manner ]]> https://biorxiv.org/content/10.64898/2026.02.12.705407v1?rss=1 Levy, C. C. Carlson, V. C. Grant, K. A. Salinas, A. G. 2026-02-15 doi:10.64898/2026.02.12.705407 Cold Spring Harbor Laboratory Press 2026-02-15 <![CDATA[ Opposing roles for SNAP23 and SNAP25 in mediating MR1 trafficking and antigen presentation ]]> https://biorxiv.org/content/10.64898/2026.02.18.706493v1?rss=1 Kim, S.-J. Kulicke, C. A. Lewinsohn, D. M. Karamooz, E. 2026-02-19 doi:10.64898/2026.02.18.706493 Cold Spring Harbor Laboratory Press 2026-02-19 <![CDATA[ The archaic CUP pilus SMF-1 uses an antiparallel bundling mechanism to initiate biofilm formation ]]> https://biorxiv.org/content/10.64898/2026.02.19.706768v1?rss=1 Fields, J. L. Sebastian, C. C. Zhang, H. Zia, A. Robertson, A. N. Wu, H. Kiedrowski, M. R. Wang, F. 2026-02-20 doi:10.64898/2026.02.19.706768 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Paired oral clinical specimens reveal the underlying ecology supporting the emergence of inflammophilic microbiome communities ]]> https://biorxiv.org/content/10.64898/2026.02.20.706901v1?rss=1 Krieger, M. Kerns, K. A. Palmer, E. A. McLean, J. S. Kreth, J. Yardimci, G. G. Merritt, J. 2026-02-21 doi:10.64898/2026.02.20.706901 Cold Spring Harbor Laboratory Press 2026-02-21 <![CDATA[ Biased synaptic activation of dentate granule cells by exercise reflects inputs from the lateral entorhinal cortex. ]]> https://biorxiv.org/content/10.64898/2026.02.22.707119v1?rss=1 Chatzi, C. Simmonds, A. Veshagh, A. Ellingson, A. Krush, M. McLean, T. Schnell, E. Westbrook, G. 2026-02-23 doi:10.64898/2026.02.22.707119 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Bradykinin Contributes to Vasogenic Edema in Murine Experimental Cerebral Malaria ]]> https://biorxiv.org/content/10.64898/2026.02.23.704410v1?rss=1 Pinheiro, A. d. S. Teixeira, D. E. Silva-Aguiar, R. P. Shim, Y. J. Merkulova, A. Silbak, S. Skomorovska-Prokvolit, Y. Midem, D. Ogolla, S. Burckhardt, B. B. Gangnus, T. Scharfstein, J. Caruso-Neves, C. McCarty, O. J. Gailani, D. Bader, M. Rosenthal, P. Dent, A. E. Janse, C. J. McCrae, K. Pinheiro, A. A. d. S. Kazura, J. W. Schmaier, A. H. 2026-02-26 doi:10.64898/2026.02.23.704410 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Polycyclic aromatic hydrocarbons, gut microbiome composition, impulsivity, and attention covary in a human cohort ]]> https://biorxiv.org/content/10.64898/2026.03.02.709058v1?rss=1 Hammer, A. J. Kasschau, K. D. Alexiev, A. Davis, E. W. Hoffman, P. Johnson-Camacho, K. Anderson, K. Marriott, L. K. Shannon, J. Sharpton, T. J. 2026-03-02 doi:10.64898/2026.03.02.709058 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ Multi-Omic, Multi-Tissue Responses to Acute Exercise in Sedentary Adults: Findings from the Molecular Transducers of Physical Activity Consortium ]]> https://biorxiv.org/content/10.64898/2026.02.27.702183v1?rss=1 MoTrPAC Study Group, Katz, D. H. Jin, C. A. Many, G. M. Smith, G. R. Keshishian, H. Clark, N. M. Iyer, G. Ahn, C. Lindholm, M. E. Sagendorf, T. J. Amar, D. Barber, J. L. Brandt, A. R. Coen, P. M. Ge, Y. Hart, P. Hsu, F.-C. Jaeger, B. C. Jimenez-Morales, D. Leach, D. T. Mani, D. R. Montalvo, S. Pincas, H. Rao, P. Sanford, J. A. Smith, K. S. Vetr, N. G. Adkins, J. N. Ashley, E. A. Carr, S. A. Miller, M. E. Montgomery, S. B. Nair, V. D. Robbins, J. M. Snyder, M. P. Sparks, L. M. Tracy, R. Walsh, M. J. Wheeler, M. T. Xia, A. Y. Sealfon, S. C. Gerszten, R 2026-03-03 doi:10.64898/2026.02.27.702183 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Combined Menin and XPO1 inhibition drive synergistic antileukemic activity in KMT2Ar and NPM1-m AML ]]> https://biorxiv.org/content/10.64898/2026.03.10.710924v1?rss=1 Uddin, M. H. Dhiman, S. Han, Y. Aboukameel, A. Dhillon, V. Aguillar, J. Buck, S. Deol, A. Boerner, J. L. Polin, L. Kessler, L. Burrows, F. Yang, J. Azmi, A. S. Maciejewski, J. Cutler, J. Du, Y. Balasubramanian, S. K. 2026-03-13 doi:10.64898/2026.03.10.710924 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ SynAPSeg: A novel dataset and image analysis framework for deep learning-based synapse detection and quantification ]]> https://biorxiv.org/content/10.64898/2026.03.12.711395v1?rss=1 Schamber, P. Darbhamulla, S. Boyer, M. Pelletier, M. Hartman, H. Friedman, O. Zhang, S. Blais, A. Oh, S. Zhong, H. Bygrave, A. M. 2026-03-16 doi:10.64898/2026.03.12.711395 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ CROCHET: a versatile pipeline for automated analysis and visual atlas creation from single-cell spatialomic data ]]> https://biorxiv.org/content/10.64898/2026.03.13.711472v1?rss=1 Bozorgui, B. Thibault, G. Yuan, C. Dereli, Z. Wang, H. Overman, M. J. Weinstein, J. N. Korkut, A. 2026-03-17 doi:10.64898/2026.03.13.711472 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ A critical signaling role for diacylglycerol in phagocytosis of M. tuberculosis ]]> https://biorxiv.org/content/10.64898/2026.03.20.713247v1?rss=1 Griffith, A. M. Garcia, M. Guzman, G. Tafesse, F. 2026-03-23 doi:10.64898/2026.03.20.713247 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ Metaplastic sleep regulation in Drosophila determined by microscale circadian neural dynamics ]]> https://biorxiv.org/content/10.64898/2026.03.21.713346v1?rss=1 Hutson, A. N. Zarjetskiy, A. N. Zhang, Y. J. Pokaleva, N. Paul, E. M. Xie, Y. Chong, B. Sanchez Franco, V. M. Zukowski, L. H. Faulk, E. E. Walker, J. A. Brown, A. M. Nguyen, D. L. Ferry, F. S. Snyder, E. M. Tabuchi, M. 2026-03-24 doi:10.64898/2026.03.21.713346 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Cascading periods of language-related brain plasticity across early childhood ]]> https://biorxiv.org/content/10.64898/2026.03.27.714739v1?rss=1 Ellwood-Lowe, M. E. Nishio, M. Dufford, A. E. Arcaro, M. Satterthwaite, T. D. Mackey, A. P. 2026-03-27 doi:10.64898/2026.03.27.714739 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Tumor-immune trajectory context connects static tissue architecture to clinical outcomes ]]> https://biorxiv.org/content/10.64898/2026.03.26.714521v1?rss=1 Cramer, E. M. Heiland, R. Lima da Rocha, H. Bergman, D. R. Gray, J. W. Mills, G. B. Fertig, E. J. Macklin, P. Heiser, L. M. Chang, Y. H. 2026-03-30 doi:10.64898/2026.03.26.714521 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ rAAV prostaglandin-based gene therapy lowers intraocular pressure and preserves optic nerve health in glaucomatous DBA/2J mice ]]> https://biorxiv.org/content/10.64898/2026.03.27.714838v1?rss=1 Chern, K. J. Fehrman, R. L. Marcoe, G. J. Lipinski, D. M. 2026-03-31 doi:10.64898/2026.03.27.714838 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Spontaneous Pregravid Obesity Reshapes Fetal Immune Ontogeny in a Nonhuman Primate Model ]]> https://biorxiv.org/content/10.64898/2026.03.27.714880v1?rss=1 Doratt, B. M. Wagner, S. B. Avila, U. Hodge, T. Martin, L. D. Varlamov, O. Messaoudi, I. 2026-03-31 doi:10.64898/2026.03.27.714880 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Rectifying AI-generated protein structure ensembles for equilibrium using physics-based computations ]]> https://biorxiv.org/content/10.64898/2026.03.24.714034v1?rss=1 Otten, L. Leung, J. M. G. Chong, L. Zuckerman, D. M. 2026-04-03 doi:10.64898/2026.03.24.714034 Cold Spring Harbor Laboratory Press 2026-04-03