bioRxiv Channel: University of California, San Francisco https://biorxiv.org This feed contains articles for bioRxiv Channel "University of California, San Francisco" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Experimental Zika Virus Infection in a New World Monkey Model Reproduces Key Features of the Human Disease ]]> https://biorxiv.org/content/10.1101/102145v1?rss=1 Chiu, C. Y. Bouquet, J. Li, T. Yagi, S. Sanchez San Martin, C. Tamhankar, M. Hodara, V. L. Parodi, L. L. Somasekar, S. Yu, G. Giavedoni, L. D. Tardif, S. Patterson, J. 2017-01-21 doi:10.1101/102145 Cold Spring Harbor Laboratory Press 2017-01-21 <![CDATA[ Autoantibody and hormone activation of the thyrotropin G protein-coupled receptor ]]> https://biorxiv.org/content/10.1101/2022.01.06.475289v1?rss=1 Faust, B. Singh, I. Zhang, K. Hoppe, N. Pinto, A. F. M. Muftuoglu, Y. Billesboelle, C. B. Saghatelian, A. Cheng, Y. Manglik, A. 2022-01-07 doi:10.1101/2022.01.06.475289 Cold Spring Harbor Laboratory Press 2022-01-07 <![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[ Conservation and structural analysis of the Xenopus laevis phospho-proteome ]]> https://biorxiv.org/content/10.1101/009100v1?rss=1 Jeffrey R Johnson Silvia D Santos Tasha Johnson Ursula Pieper Andrej Sali Nevan J Krogan Pedro Beltrao 2014-09-14 doi:10.1101/009100 Cold Spring Harbor Laboratory Press 2014-09-14 <![CDATA[ Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes ]]> https://biorxiv.org/content/10.1101/011569v1?rss=1 Daniel S Himmelstein Sergio E Baranzini 2014-12-11 doi:10.1101/011569 Cold Spring Harbor Laboratory Press 2014-12-11 <![CDATA[ From deep TLS validation to ensembles of atomic models built from elemental motions ]]> https://biorxiv.org/content/10.1101/012930v1?rss=1 Alexandre Urzhumtsev Pavel Afonine Andrew H Van Benschoten James Fraser Paul D Adams 2015-01-02 doi:10.1101/012930 Cold Spring Harbor Laboratory Press 2015-01-02 <![CDATA[ Predicting X-ray Diffuse Scattering from Translation Libration Screw Structural Ensembles ]]> https://biorxiv.org/content/10.1101/012955v1?rss=1 Andrew Van Benschoten Pavel Afonine Thomas Terwilliger Michael Wall Colin Jackson Nicholas Sauter Paul Adams Alexandre Urzhumtsev James Fraser 2015-01-02 doi:10.1101/012955 Cold Spring Harbor Laboratory Press 2015-01-02 <![CDATA[ Side-chain-directed model and map validation for 3D Electron Cryomicroscopy ]]> https://biorxiv.org/content/10.1101/014738v1?rss=1 Benjamin A Barad Nathaniel Echols Ray Yu-Ruei Wang Yifan Cheng Frank DiMaio Paul D Adams James S Fraser 2015-02-03 doi:10.1101/014738 Cold Spring Harbor Laboratory Press 2015-02-03 <![CDATA[ Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species ]]> https://biorxiv.org/content/10.1101/014902v1?rss=1 Aram Avila-Herrera Katherine Pollard 2015-02-06 doi:10.1101/014902 Cold Spring Harbor Laboratory Press 2015-02-06 <![CDATA[ Selection and explosive growth may hamper the performance of rare variant association tests ]]> https://biorxiv.org/content/10.1101/015917v1?rss=1 Lawrence H. Uricchio John S. Witte Ryan D. Hernandez 2015-03-02 doi:10.1101/015917 Cold Spring Harbor Laboratory Press 2015-03-02 <![CDATA[ Mapping the Conformational Landscape of a Dynamic Enzyme by XFEL and Multitemperature Crystallography ]]> https://biorxiv.org/content/10.1101/016733v1?rss=1 Daniel A Keedy Lillian R Kenner Matthew Warkentin Rahel Woldeyes Michael C Thompson Aaron S Brewster Andrew H Van Benschoten Elizabeth L Baxter Jesse B Hopkins Monarin Uervirojnangkoorn Scott E McPhillps Jinhu Song Roberto Alonso-Mori James M Holton William I Weis Axel T Brunger S. Michael Soltis Henrik Lemke Ana Gonzalez Nicholas K Sauter Aina E Cohen Henry van den Bedem Robert E Thorne James Fraser 2015-03-19 doi:10.1101/016733 Cold Spring Harbor Laboratory Press 2015-03-19 <![CDATA[ Exposing hidden alternative backbone conformations in X-ray crystallography using qFit ]]> https://biorxiv.org/content/10.1101/018879v1?rss=1 Daniel A Keedy James Fraser Henry van den Bedem 2015-05-04 doi:10.1101/018879 Cold Spring Harbor Laboratory Press 2015-05-04 <![CDATA[ Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis ]]> https://biorxiv.org/content/10.1101/020420v1?rss=1 98% accuracy. Using nanopore sequencing, metagenomic detection of viral pathogens directly from clinical samples was performed within an unprecedented <6 hours sample-to-answer turnaround time and in a timeframe amenable for actionable clinical and public health diagnostics. ]]> Alex L Greninger Samia N Naccache Scot Federman Guixia Yu Placide Mbala Vanessa Bres Jerome Bouquet Doug Stryke Sneha Somasekar Jeffrey Linnen Roger Dodd Prime Mulembakani Bradley Schneider Jean-Jacques Muyembe Susan Stramer Charles Y Chiu 2015-06-03 doi:10.1101/020420 Cold Spring Harbor Laboratory Press 2015-06-03 <![CDATA[ BRAINformat: A Data Standardization Framework for Neuroscience Data ]]> https://biorxiv.org/content/10.1101/024521v1?rss=1 Oliver Rübel Mr. Prabhat Peter Denes David Conant Edward Chang Kristofer Bouchard 2015-08-13 doi:10.1101/024521 Cold Spring Harbor Laboratory Press 2015-08-13 <![CDATA[ SFS_CODE: More Efficient and Flexible Forward Simulations ]]> https://biorxiv.org/content/10.1101/025064v1?rss=1 Ryan D. Hernandez Lawrence H. Uricchio 2015-08-20 doi:10.1101/025064 Cold Spring Harbor Laboratory Press 2015-08-20 <![CDATA[ Statistical Inference of a Convergent Antibody Repertoire Response to Influenza Vaccine ]]> https://biorxiv.org/content/10.1101/025098v1?rss=1 Nicolas Strauli Ryan Hernandez 2015-08-20 doi:10.1101/025098 Cold Spring Harbor Laboratory Press 2015-08-20 <![CDATA[ Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting ]]> https://biorxiv.org/content/10.1101/025452v1?rss=1 David Mavor Participants in UCSF PUBS Class James Fraser 2015-08-25 doi:10.1101/025452 Cold Spring Harbor Laboratory Press 2015-08-25 <![CDATA[ Tyrosination of α-Tubulin Controls The Initiation of Processive Dynein-Dynactin Motility ]]> https://biorxiv.org/content/10.1101/027631v1?rss=1 Richard J McKenney Walter Huynh Ronald D. Vale Minhaj Sirajuddin 2015-09-25 doi:10.1101/027631 Cold Spring Harbor Laboratory Press 2015-09-25 <![CDATA[ Measuring and modeling diffuse scattering in protein X-ray crystallography ]]> https://biorxiv.org/content/10.1101/033746v1?rss=1 Andrew H Van Benschoten Lin Liu Ana Gonzalez Aaron S Brewster Nicholas K Sauter James S Fraser Michael Wall 2015-12-06 doi:10.1101/033746 Cold Spring Harbor Laboratory Press 2015-12-06 <![CDATA[ Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus ]]> https://biorxiv.org/content/10.1101/034017v1?rss=1 Betty M Booker Tara Friedrich Mandy K Mason Julia E VanderMeer Jingjing Zhao Walter L Eckalbar Malcolm Logan Nicola Illing Katherine S Pollard Nadav Ahituv 2015-12-09 doi:10.1101/034017 Cold Spring Harbor Laboratory Press 2015-12-09 <![CDATA[ High-accuracy HLA type inference from whole-genome sequencing data ]]> https://biorxiv.org/content/10.1101/035253v1?rss=1 Alexander Dilthey Pierre-Antoine Gourraud Zamin Iqbal Gil McVean 2015-12-24 doi:10.1101/035253 Cold Spring Harbor Laboratory Press 2015-12-24 <![CDATA[ Differential methylation between ethnic sub-groups reflects the effect of genetic ancestry and environmental exposures ]]> https://biorxiv.org/content/10.1101/036822v1?rss=1 Joshua M Galanter Christopher R Gignoux Sam S Oh Dara Torgerson Maria Pino-Yanes Neeta Thakur Celeste Eng Donglei Hu Scott Huntsmann Harold J Farber Pedro Avila Emerita Brigino-Buenaventura Michael LeNoir Kelly Meade Denise Serebrisky William Rodriguez-Cintron Rajessh Kumar Jose R Rodriguez-Santana Max Seibold Luisa Borrell Esteban G Burchard Noah Zaitlen 2016-01-15 doi:10.1101/036822 Cold Spring Harbor Laboratory Press 2016-01-15 <![CDATA[ Micro-Magellan: A flexible, open source acquisition software for high throughput biological light microscopy ]]> https://biorxiv.org/content/10.1101/038117v1?rss=1 Henry Pinkard Nico Stuurman Kaitlin Corbin Ronald Vale Matthew F Krummel 2016-01-28 doi:10.1101/038117 Cold Spring Harbor Laboratory Press 2016-01-28 <![CDATA[ Local joint testing improves power and identifies missing heritability in association studies ]]> https://biorxiv.org/content/10.1101/040089v1?rss=1 Brielin C Brown Alkes Price Nikolaos Patsopoulos Noah Zaitlen 2016-02-18 doi:10.1101/040089 Cold Spring Harbor Laboratory Press 2016-02-18 <![CDATA[ Subtle stratification confounds estimates of heritability from rare variants ]]> https://biorxiv.org/content/10.1101/048181v1?rss=1 Gaurav Bhatia Alexander Gusev Po-Ru Loh Hilary Kiyo Finucane Bjarni J Vilhjalmsson Stephan Ripke SCZ Working Group of the Psychiatric Genomics Cons Shaun Purcell Eli Stahl Mark Daly Teresa R de Candia Sang Hong Lee Benjamin M Neale Matthew C Keller Noah A Zaitlen Bogdan Pasaniuc Nick Patterson Jian Yang Alkes L Price 2016-04-13 doi:10.1101/048181 Cold Spring Harbor Laboratory Press 2016-04-13 <![CDATA[ Cytokine and Leukocyte Profiling Reveal Pro-Inflammatory and Autoimmune Features in Frontotemporal Dementia Patients ]]> https://biorxiv.org/content/10.1101/049791v1?rss=1 Philipp A. Jaeger Trisha M. Stan Eva Czirr Markus Britschgi Daniela Berdnik Ruo-Pan Huang Bradley F. Boeve Adam L. Boxer NiCole Finch Gabriela K. Fragiadakis Neill R. Graff-Radford Ruochun Huang Hudson Johns Anna Karydas David S. Knopman Michael Leipold Holde T. Maecker Zachary Miller Ronald Petersen Rosa Rademakers Chung-Huan Sun Steve Younkin Bruce L. Miller Tony Wyss-Coray 2016-04-22 doi:10.1101/049791 Cold Spring Harbor Laboratory Press 2016-04-22 <![CDATA[ Chytrid fungi construct actin-rich pseudopods, implicating actin regulators WASP and SCAR in an ancient mode of cell motility ]]> https://biorxiv.org/content/10.1101/051821v1?rss=1 30 m/min with actin-filled pseudopods. By focusing on one migration mode in many eukaryotes, we identify a genetic marker of pseudopod formation, the morphological feature of -motility, providing evidence for a widely distributed mode of cell crawling with a single evolutionary origin. ]]> Lillian K. Fritz-Laylin Samuel J. Lord R. Dyche Mullins 2016-05-04 doi:10.1101/051821 Cold Spring Harbor Laboratory Press 2016-05-04 <![CDATA[ Dumpster diving in RNA-sequencing to find the source of every last read ]]> https://biorxiv.org/content/10.1101/053041v1?rss=1 Serghei Mangul Harry Taegyun Yang Nicolas Strauli Franziska Gruhl Timothy Daley Stephanie Christenson Agata Wesolowska Andersen Roberto Spreafico Cydney Rios Celeste Eng Andrew D. Smith Ryan D. Hernandez Roel A. Ophoff Jose Rodriguez Santana Prescott G. Woodruff Esteban Burchard Max A. Seibold Sagiv Shifman Eleazar Eskin Noah Zaitlen 2016-05-13 doi:10.1101/053041 Cold Spring Harbor Laboratory Press 2016-05-13 <![CDATA[ A scalable strategy for high-throughput GFP tagging of endogenous human proteins ]]> https://biorxiv.org/content/10.1101/055285v1?rss=1 Manuel Leonetti Sayaka Sekine Daichi Kamiyama Jonathan S Weissman Bo Huang 2016-05-24 doi:10.1101/055285 Cold Spring Harbor Laboratory Press 2016-05-24 <![CDATA[ The Effects of Migration and Assortative Mating on Admixture Linkage Disequilibrium ]]> https://biorxiv.org/content/10.1101/056168v1?rss=1 Noah Zaitlen Scott Huntsman Donglei Hu Melissa Spear Celeste Eng Sam S Oh Marquitta J White Angel Mak Adam Davis Kelly Meade Emerita Brigino-Buenaventura Michael A LeNoir Kirsten Bibbins-Domingo Esteban G Burchard Eran Halperin 2016-05-31 doi:10.1101/056168 Cold Spring Harbor Laboratory Press 2016-05-31 <![CDATA[ Proteobacteria drive significant functional variability in the human gut microbiome ]]> https://biorxiv.org/content/10.1101/056614v1?rss=1 Patrick H Bradley Katherine S Pollard 2016-06-02 doi:10.1101/056614 Cold Spring Harbor Laboratory Press 2016-06-02 <![CDATA[ Age-related differences in self-reported sleep quality predict healthy ageing across multiple domains: a multi-modal cohort of 2406 adults ]]> https://biorxiv.org/content/10.1101/060145v1?rss=1 Andrew Gadie Meredith Shafto Yue Leng Cam-CAN Rogier A. Kievit 2016-06-22 doi:10.1101/060145 Cold Spring Harbor Laboratory Press 2016-06-22 <![CDATA[ Interactive online brain shape visualization ]]> https://biorxiv.org/content/10.1101/067678v1?rss=1 Anisha Keshavan Arno Klein Benjamin Cipollini 2016-08-05 doi:10.1101/067678 Cold Spring Harbor Laboratory Press 2016-08-05 <![CDATA[ Lost dollars threaten research in public academic health centers ]]> https://biorxiv.org/content/10.1101/071860v1?rss=1 Henry R. Bourne Eric Vermillion 2016-08-27 doi:10.1101/071860 Cold Spring Harbor Laboratory Press 2016-08-27 <![CDATA[ Personalized genetic assessment of age associated Alzheimers disease risk ]]> https://biorxiv.org/content/10.1101/074864v1?rss=1 Rahul S. Desikan Chun Chieh Fan Yunpeng Wang Andrew J. Schork Howard J. Cabral Adrienne Cupples Wesley K. Thompson Lilah Besser Walter A. Kukull Dominic Holland Chi-Hua Chen James B. Brewer David S. Karow Karolina Kauppi Aree Witoelar Celeste M. Karch Luke W. Bonham Jennifer S. Yokoyama Howard J. Rosen Bruce L. Miller William P. Dillon David M. Wilson Christopher P. Hess Margaret Pericak-Vance Jonathan L. Haines Lindsay A. Farrer Richard Mayeux John Hardy Alison M. Goate Bradley T. Hyman Gerard D. Schellenberg Linda K. McEvoy Ole A. Andreassen Anders N. Dale 2016-09-13 doi:10.1101/074864 Cold Spring Harbor Laboratory Press 2016-09-13 <![CDATA[ Adipocyte JAK2 mediates hepatic insulin sensitivity and the diabetogenic action of Growth Hormone ]]> https://biorxiv.org/content/10.1101/076265v1?rss=1 Kevin Corbit Joao Paulo G. Camporez Jennifer L Tran Camella G Wilson Rachel J Perry Gerald Schulman Michael J Jurczak Ethan Weiss 2016-09-20 doi:10.1101/076265 Cold Spring Harbor Laboratory Press 2016-09-20 <![CDATA[ AN INTERNATIONAL INTER-LABORATORY DIGITAL PCR STUDY DEMONSTRATES HIGH REPRODUCIBILITY FOR THE MEASUREMENT OF A RARE SEQUENCE VARIANT ]]> https://biorxiv.org/content/10.1101/077917v1?rss=1 Alexandra S Whale Alison S Devonshire George Karlin-Neumann Jack Regan Leanne Javier Simon Cowen Ana Fernandez-Gonzalez Gerwyn M Jones Nicholas Redshaw Julia Beck Andreas W Berger Valerie Combaret Nina Dahl Kjersgaard Lisa Davis Frederic Fina Tim Forshew Rikke Fredslund Andersen Silvia Galbiati Alvaro Gonzalez Hernandez Charles Haynes Filip Janku Roger Lacave Justin Lee Vilas Mistry Alexandra Pender Anne Pradines Charlotte Proudhon Lao Saal Elliot Stieglitz Bryan Ulrich Carole A Foy Helen Parkes Svilen Tzonev Jim Huggett 2016-09-28 doi:10.1101/077917 Cold Spring Harbor Laboratory Press 2016-09-28 <![CDATA[ BIDS Apps: Improving ease of use, accessibility and reproducibility of neuroimaging data analysis methods ]]> https://biorxiv.org/content/10.1101/079145v1?rss=1 Krzysztof J. Gorgolewski Fidel Alfaro-Almagro Tibor Auer Pierre Bellec Mihai Capota Mallar Chakravarty Nathan W. Churchill R. Cameron Craddock Gabriel Devenyi Anders Eklund Oscar Esteban Guillaume Flandin Satrajit Ghosh J. Swaroop Guntupalli Mark Jenkinson Anisha Keshavan Gregory Kiar Pradeep Reddy Raamana David Raffelt Christopher J. Steele Pierre-Olivier Quirion Robert E. Smith Stephen Strother Gael Varoquaux Tal Yarkoni Yida Wang Russell Poldrack 2016-10-04 doi:10.1101/079145 Cold Spring Harbor Laboratory Press 2016-10-04 <![CDATA[ Disruption of Hepatocyte Jak2 leads to Spontaneous NASH in Aged Mice and Uncouples Metabolic Liver Disease from Insulin Resistance ]]> https://biorxiv.org/content/10.1101/079236v1?rss=1 Camella G. Wilson Jennifer L. Tran Aras N. Mattis Kevin Corbit Ethan J. Weiss 2016-10-04 doi:10.1101/079236 Cold Spring Harbor Laboratory Press 2016-10-04 <![CDATA[ Flexibility and design: conformational heterogeneity along the evolutionary trajectory of a redesigned ubiquitin ]]> https://biorxiv.org/content/10.1101/081646v1?rss=1 Biel, J. T. Thompson, M. C. Cunningham, C. N. Corn, J. E. Fraser, J. S. 2016-10-17 doi:10.1101/081646 Cold Spring Harbor Laboratory Press 2016-10-17 <![CDATA[ 16S rRNA Gene Sequencing as a Clinical Diagnostic Aid for Gastrointestinal-related Conditions ]]> https://biorxiv.org/content/10.1101/084657v1?rss=1 Almonacid, D. E. Kraal, L. Ossandon, F. J. Budovskaya, Y. V. Cardenas, J. P. Richman, J. Apte, Z. S. 2016-10-31 doi:10.1101/084657 Cold Spring Harbor Laboratory Press 2016-10-31 <![CDATA[ Engineering Genetically-Encoded Mineralization and Magnetism via Directed Evolution ]]> https://biorxiv.org/content/10.1101/085233v1?rss=1 Liu, X. L. Lopez, P. A. Giessen, T. W. Giles, M. Way, J. C. Silver, P. A. 2016-11-02 doi:10.1101/085233 Cold Spring Harbor Laboratory Press 2016-11-02 <![CDATA[ Novel computational method for predicting polytherapy switching strategies to overcome tumor heterogeneity and evolution ]]> https://biorxiv.org/content/10.1101/086553v1?rss=1 Jonsson, V. D. Blakely, C. M. Lin, L. Asthana, S. Olivas, V. Gubens, M. A. Matni, N. Bastian, B. C. Taylor, B. S. Doyle, J. C. Bivona, T. G. 2016-11-08 doi:10.1101/086553 Cold Spring Harbor Laboratory Press 2016-11-08 <![CDATA[ DNA-polymerase guided elimination of paternal mitochondrial genomes:An escape-proof obstacle to their transmission ]]> https://biorxiv.org/content/10.1101/086702v1?rss=1 Yu, Z. O'Farrell, P. H. Yakubovich, N. DeLuca, S. Z. 2016-11-09 doi:10.1101/086702 Cold Spring Harbor Laboratory Press 2016-11-09 <![CDATA[ Profiling adaptive immune repertoires across multiple human tissues by RNA Sequencing ]]> https://biorxiv.org/content/10.1101/089235v1?rss=1 Mangul, S. Mandric, I. Yang, H. T. Strauli, N. Montoya, D. Rotman, J. Der Wey, W. V. Ronas, J. R. Statz, B. Zelikovsky, A. Spreafico, R. Shifman, S. Zaitlen, N. Rossetti, M. Ansel, K. M. Eskin, E. 2016-11-22 doi:10.1101/089235 Cold Spring Harbor Laboratory Press 2016-11-22 <![CDATA[ Genetic determinants of chromatin accessibility and gene regulation in T cell activation across human individuals ]]> https://biorxiv.org/content/10.1101/090241v1?rss=1 Cheng, C. S. Gate, R. E. Aiden, A. P. Siba, A. Tabaka, M. Lituiev, D. Machol, I. Subramaniam, M. Shammim, M. Hougen, K. L. Wortman, I. Huang, S.-C. Durand, N. C. Feng, T. De Jager, P. L. Chang, H. Y. Lieberman Aiden, E. Benoist, C. Beer, M. A. Ye, C. J. Regev, A. 2016-12-02 doi:10.1101/090241 Cold Spring Harbor Laboratory Press 2016-12-02 <![CDATA[ Mindcontrol: A Web Application for Brain Segmentation Quality Control ]]> https://biorxiv.org/content/10.1101/090431v1?rss=1 Keshavan, A. Datta, E. McDonough, I. Madan, C. R. Jordan, K. Henry, R. 2016-11-29 doi:10.1101/090431 Cold Spring Harbor Laboratory Press 2016-11-29 <![CDATA[ Genomic characterization of serial-passaged Ebola virus in a boa constrictor cell line ]]> https://biorxiv.org/content/10.1101/091603v1?rss=1 10,000x) demonstrated the existence of only a single non-synonymous variant (EBOV glycoprotein precursor preGP T544I) of unknown significance within the viral population that exhibited a shift in frequency of at least 10% over six passages. Our data suggest that boid snake derived cells are competent for filovirus infection without appreciable genomic adaptation; that cellular filovirus infection without CPE may be more common than currently appreciated; and that there may be significant differences between the natural host spectra of ebolaviruses and marburgviruses.nnIMPORTANCEEbola virus (EBOV) causes a high case-fatality form of viral hemorrhagic fever. The natural reservoir of EBOV remains unknown. EBOV is distantly related to Marburg virus (MARV), which has been found in bats in the wild. The glycoprotein of a reptarenavirus known to infect boid snakes (pythons and boas) shows similarity in sequence and structure to these viruses, suggesting that EBOV and MARV may be able to infect and replicate in snake cells. We demonstrate that JK, a boa constrictor cell line, does not support MARV infection, but does support EBOV infection without causing overt cytopathic effect or the need for appreciable adaptation. These findings suggest different filoviruses may have a more diverse natural host spectra than previously thought. ]]> Fedewa, G. Radoshitzky, S. R. Chī, X. Dŏng, L. Spear, M. Strauli, N. Stenglein, M. D. Hernandez, R. Jahrling, P. B. Kuhn, J. H. DeRisi, J. 2016-12-07 doi:10.1101/091603 Cold Spring Harbor Laboratory Press 2016-12-07 <![CDATA[ MinorityReport, software for generalized analysis of causal genetic variants ]]> https://biorxiv.org/content/10.1101/098731v1?rss=1 Horst, J. Wu, W. DeRisi, J. L. 2017-01-06 doi:10.1101/098731 Cold Spring Harbor Laboratory Press 2017-01-06 <![CDATA[ Local Control of Intracellular Microtubule Dynamics by End Binding Protein 1 (EB1) Photo-Dissociation ]]> https://biorxiv.org/content/10.1101/099598v1?rss=1 van Haren, J. Ettinger, A. Wang, H. Hahn, K. Wittmann, T. 2017-01-10 doi:10.1101/099598 Cold Spring Harbor Laboratory Press 2017-01-10 <![CDATA[ The design principles of biochemical timers: circuits that discriminate between transient and sustained stimulation ]]> https://biorxiv.org/content/10.1101/100651v1?rss=1 Gerardin, J. Lim, W. A. 2017-01-15 doi:10.1101/100651 Cold Spring Harbor Laboratory Press 2017-01-15 <![CDATA[ Tracking multiple genomic elements using correlative CRISPR imaging and sequential DNA FISH ]]> https://biorxiv.org/content/10.1101/101444v1?rss=1 Guan, J. Liu, H. Shi, X. Feng, S. Huang, B. 2017-01-18 doi:10.1101/101444 Cold Spring Harbor Laboratory Press 2017-01-18 <![CDATA[ Locomotion enhances neural encoding of visual stimuli in mouse V1 ]]> https://biorxiv.org/content/10.1101/102673v1?rss=1 Dadarlat, M. C. Stryker, M. P. 2017-01-24 doi:10.1101/102673 Cold Spring Harbor Laboratory Press 2017-01-24 <![CDATA[ Mapping load-bearing in the mammalian spindle reveals local kinetochore-fiber anchorage that provides mechanical isolation and redundancy ]]> https://biorxiv.org/content/10.1101/103572v1?rss=1 Elting, M. W. Prakash, M. Udy, D. B. Dumont, S. 2017-01-26 doi:10.1101/103572 Cold Spring Harbor Laboratory Press 2017-01-26 <![CDATA[ Symmetry broken and rebroken during the ATP hydrolysis cycle of the mitochondrial Hsp90 TRAP1 ]]> https://biorxiv.org/content/10.1101/107094v1?rss=1 Elnatan, D. Betegon, M. Liu, Y. Ramelot, T. Kennedy, M. A. Agard, D. 2017-02-09 doi:10.1101/107094 Cold Spring Harbor Laboratory Press 2017-02-09 <![CDATA[ Distinct neural systems for the production of communicative vocal behaviors ]]> https://biorxiv.org/content/10.1101/107441v1?rss=1 Agnew, Z. K. Ward, L. McGettigan, C. Josephs, O. Scott, S. K. 2017-02-17 doi:10.1101/107441 Cold Spring Harbor Laboratory Press 2017-02-17 <![CDATA[ Duplication events downstream of IRX1 cause North Carolina macular dystrophy at the MCDR3 locus ]]> https://biorxiv.org/content/10.1101/107573v1?rss=1 Cipriani, V. Silva, R. S. Arno, G. Pontikos, N. Kalhoro, A. Valeina, S. Inashkina, I. Audere, M. Rutka, K. Puech, B. Michaelides, M. van Heyningen, V. Lace, B. Webster, A. R. R. Moore, A. T. 2017-02-12 doi:10.1101/107573 Cold Spring Harbor Laboratory Press 2017-02-12 <![CDATA[ Evolution and clinical impact of genetic epistasis within EGFR-mutant lung cancers ]]> https://biorxiv.org/content/10.1101/117291v1?rss=1 Blakely, C. M. Watkins, T. B. K. Wu, W. Gini, B. Chabon, J. J. McCoach, C. E. McGranahan, N. Wilson, G. A. Birkbak, N. J. Olivas, V. Rotow, J. Maynard, A. Wang, V. Gubens, M. Banks, K. Lanman, R. Caulin, A. St. John, J. Cordero, A. Giannikopoulos, P. Mack, P. Gandara, D. Husain, H. Doebele, R. Riess, J. Diehn, M. Swanton, C. Bivona, T. G. 2017-03-16 doi:10.1101/117291 Cold Spring Harbor Laboratory Press 2017-03-16 <![CDATA[ Multiplexing droplet-based single cell RNA-sequencing using natural genetic barcodes ]]> https://biorxiv.org/content/10.1101/118778v1?rss=1 99% of singlets, and identified doublets at rates consistent with previous estimates. In PBMCs, we demonstrate the utility of multiplexed dscRNA-seq in two applications: characterizing cell type specificity and inter-individual variability of cytokine response from 8 lupus patients and mapping genetic variants associated with cell type specific gene expression from 23 donors. Demuxlet is fast, accurate, scalable and could be extended to other single cell datasets that incorporate natural or synthetic DNA barcodes. ]]> Kang, H. M. Subramaniam, M. Targ, S. Nguyen, M. Maliskova, L. Wan, E. Wong, S. Byrnes, L. Lanata, C. Gate, R. Mostafavi, S. Marson, A. Zaitlen, N. Criswell, L. A. Ye, J. 2017-03-20 doi:10.1101/118778 Cold Spring Harbor Laboratory Press 2017-03-20 <![CDATA[ Towards Human Super EEG ]]> https://biorxiv.org/content/10.1101/121020v1?rss=1 Owen, L. L. W. Manning, J. R. 2017-03-27 doi:10.1101/121020 Cold Spring Harbor Laboratory Press 2017-03-27 <![CDATA[ The Human Cell Atlas ]]> https://biorxiv.org/content/10.1101/121202v1?rss=1 Regev, A. Teichmann, S. Lander, E. S. Amit, I. Benoist, C. Birney, E. Bodenmiller, B. Campbell, P. Carninci, P. Clatworthy, M. Clevers, H. Deplancke, B. Dunham, I. Eberwine, J. Eils, R. Enard, W. Farmer, A. Fugger, L. Gottgens, B. Hacohen, N. Haniffa, M. Hemberg, M. Kim, S. K. Klenerman, P. Kriegstein, A. Lein, E. Linnarsson, S. Lundeberg, J. Majumder, P. Marioni, J. Merad, M. Mhlanga, M. Nawijn, M. Netea, M. Nolan, G. Pe'er, D. Philipakis, A. Ponting, C. P. Quake, S. R. Reik, W. Rozenblatt-Rosen, O. Sanes, J. R. Satija, R. Shumacher, T. Shalek, A. K 2017-05-08 doi:10.1101/121202 Cold Spring Harbor Laboratory Press 2017-05-08 <![CDATA[ OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development ]]> https://biorxiv.org/content/10.1101/125419v1?rss=1 Hrit, J. Li, C. Martin, E. A. Goll, M. Panning, B. 2017-04-07 doi:10.1101/125419 Cold Spring Harbor Laboratory Press 2017-04-07 <![CDATA[ Limited contribution of rare, noncoding variation to autism spectrum disorder from sequencing of 2,076 genomes in quartet families ]]> https://biorxiv.org/content/10.1101/127043v1?rss=1 Werling, D. M. Brand, H. An, J.-Y. Stone, M. R. Glessner, J. T. Zhu, L. Collins, R. L. Dong, S. Layer, R. M. Markenscoff-Papadimitriou, E.-C. Farrell, A. Schwartz, G. B. Currall, B. B. Dea, J. Duhn, C. Erdman, C. Gilson, M. Handsaker, R. E. Kashin, S. Klei, L. Mandell, J. D. Nowakowski, T. J. Liu, Y. Pochareddy, S. Smith, L. Walker, M. F. Wang, H. Z. Waterman, M. J. He, X. Kriegstein, A. R. Rubenstein, J. L. Sestan, N. McCarroll, S. A. Neale, B. M. Coon, H. Willsey, A. J. Buxbaum, J. D. Daly, M. J. State, M. W. Quinlan, A. Marth, G. T. Roeder, K. Devli 2017-04-13 doi:10.1101/127043 Cold Spring Harbor Laboratory Press 2017-04-13 <![CDATA[ Nanopore detection of bacterial DNA base modifications ]]> https://biorxiv.org/content/10.1101/127100v1?rss=1 McIntyre, A. B. R. Alexander, N. Burton, A. S. Castro-Wallace, S. Chiu, C. Y. John, K. K. Stahl, S. E. Li, S. Mason, C. E. 2017-04-13 doi:10.1101/127100 Cold Spring Harbor Laboratory Press 2017-04-13 <![CDATA[ Use antibiotics in cell culture with caution: genome-wide identification ofantibiotic-induced changes in gene expression and regulation ]]> https://biorxiv.org/content/10.1101/130484v1?rss=1 Ryu, A. H. Eckalbar, W. L. Kreimer, A. Yosef, N. Ahituv, N. 2017-04-25 doi:10.1101/130484 Cold Spring Harbor Laboratory Press 2017-04-25 <![CDATA[ Topical Silver Diamine Fluoride For Dental Caries Arrest In Preschool Children: A Randomized Controlled Trial ]]> https://biorxiv.org/content/10.1101/131870v1?rss=1 Milgrom, P. Horst, J. A. Ludwig, S. Rothen, M. Chaffee, B. W. Lyalina, S. Pollard, K. DeRisi, J. L. Mancl, L. 2017-04-29 doi:10.1101/131870 Cold Spring Harbor Laboratory Press 2017-04-29 <![CDATA[ Estimating Degree Of Polygenicity, Causal Effect Size Variance, And Confounding Bias In GWAS Summary Statistics ]]> https://biorxiv.org/content/10.1101/133132v1?rss=1 Holland, D. Fan, C.-C. Frei, O. Shadrin, A. A. Smeland, O. B. Sundar, V. S. ENIGMA, Andreassen, O. A. Dale, A. M. 2017-05-24 doi:10.1101/133132 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ Spike Discharge Prediction Based On Neuro-Fuzzy System ]]> https://biorxiv.org/content/10.1101/133967v1?rss=1 Zarei, M. 2017-05-03 doi:10.1101/133967 Cold Spring Harbor Laboratory Press 2017-05-03 <![CDATA[ Ketogenic diet or BHB improves epileptiform spikes, memory, survival in Alzheimer’s model ]]> https://biorxiv.org/content/10.1101/136226v1?rss=1 Newman, J. C. Kroll, F. Ulrich, S. Palop, J. J. Verdin, E. 2017-05-09 doi:10.1101/136226 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ A Novel Reporter Allele For Monitoring Dll4 Expression Within The Embryonic And Adult Mouse ]]> https://biorxiv.org/content/10.1101/136713v1?rss=1 Herman, A. M. Rhyner, A. M. Devine, W. P. Marrelli, S. P. Bruneau, B. G. Wythe, J. D. 2017-05-11 doi:10.1101/136713 Cold Spring Harbor Laboratory Press 2017-05-11 <![CDATA[ Extending Chemical Perturbations Of The Ubiquitin Fitness Landscape In A Classroom Setting ]]> https://biorxiv.org/content/10.1101/139352v1?rss=1 Mavor, D. Barlow, K. Asarnow, D. Birman, Y. Britain, D. Chen, W. Green, E. M. Kenner, L. R. Mensa, B. Morinishi, L. S. Nelson, C. A. Poss, E. M. Suresh, P. Tian, R. Arhar, T. Ary, B. E. Bauer, D. P. Bergman, I. D. Brunetti, R. M. Chio, C. M. Dai, S. A. Dickinson, M. S. Elledge, S. Hendel, N. L. Helsell, C. V. M. Kang, E. Kern, N. Khoroshkin, M. S. Kirkemo, L. L. Lewis, G. R. Lou, K. Marin, W. M. Maxwell, A. M. McTigue, P. F. Meyers-Turnbull, D. Nagy, T. L. Natale, A. M. Oltion, K. Pourmal, S. Reder, G. K. Rettko, N. J. Rohweder, P. J. Schwarz, D. M. C. 2017-05-17 doi:10.1101/139352 Cold Spring Harbor Laboratory Press 2017-05-17 <![CDATA[ Promoter Or Enhancer Activation By CRISPRa Rescues Haploinsufficiency Caused Obesity ]]> https://biorxiv.org/content/10.1101/140426v1?rss=1 Matharu, N. Rattanasopha, S. Maliskova, L. Wang, Y. Hardin, A. Vaisse, C. Ahituv, N. 2017-05-22 doi:10.1101/140426 Cold Spring Harbor Laboratory Press 2017-05-22 <![CDATA[ Senescence As A Defense Strategy Against Parasites ]]> https://biorxiv.org/content/10.1101/143362v1?rss=1 Chin, R. Y. 2017-05-29 doi:10.1101/143362 Cold Spring Harbor Laboratory Press 2017-05-29 <![CDATA[ Interphase-Arrested Drosophila Embryos Initiate Mid-Blastula Transition At A Low Nuclear-Cytoplasmic Ratio ]]> https://biorxiv.org/content/10.1101/143719v1?rss=1 Strong, I. Yuan, K. O'Farrell, P. H. 2017-06-01 doi:10.1101/143719 Cold Spring Harbor Laboratory Press 2017-06-01 <![CDATA[ Characterization Of Vif Domains That Mediate Feline Immunodeficiency Virus Antagonism Of APOBEC3-H And APOBEC3-CH Restriction ]]> https://biorxiv.org/content/10.1101/144113v1?rss=1 Sims, O. L. Maynard, E. Poeschla, E. M. 2017-05-30 doi:10.1101/144113 Cold Spring Harbor Laboratory Press 2017-05-30 <![CDATA[ An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures ]]> https://biorxiv.org/content/10.1101/146811v1?rss=1 Collord, G. Tarpey, P. Kurbatova, N. Martincorena, I. Moran, S. Castro, M. Nagy, T. Bignell, G. Maura, F. Berna, J. Tubio, J. M. McMurran, C. E. Young, A. M. H. Young, M. D. Noorani, I. Price, S. J. Watts, C. Leipnitz, E. Kirsch, M. Schackert, G. Pearson, D. Devadass, A. Ram, Z. Collins, V. P. Allinson, K. Jenkinson, M. Zakaria, R. Syed, K. Hanemann, C. O. Dunn, J. McDermott, M. Kirollos, R. Vassiliou, G. S. Esteller, M. Behjati, S. Brazma, A. Santarius, T. McDermott, U. 2017-06-06 doi:10.1101/146811 Cold Spring Harbor Laboratory Press 2017-06-06 <![CDATA[ Placental gene expression mediates the interaction between obstetrical history and genetic risk for schizophrenia ]]> https://biorxiv.org/content/10.1101/147207v1?rss=1 Ursini, G. Punzi, G. Chen, Q. Marenco, S. Robinson, J. Porcelli, A. Hamilton, E. Mitjans, M. Maddalena, G. Begemann, M. Seidel, J. Yanamori, H. Jaffe, A. E. Berman, K. F. Egan, M. F. Straub, R. E. Colantuoni, C. Blasi, G. Hashimoto, R. Rujescu, D. Ehrenreich, H. Bertolino, A. Weinberger, D. R. 2017-06-07 doi:10.1101/147207 Cold Spring Harbor Laboratory Press 2017-06-07 <![CDATA[ Epigenetic maintenance of DNA methylation after evolutionary loss of the de novo methyltransferase ]]> https://biorxiv.org/content/10.1101/149385v1?rss=1 50 MY through a process analogous to Darwinian evolution of the genome. ]]> Catania, S. Dumesic, P. A. Stoddard, C. Cooke, S. Burke, J. Cuomo, C. A. Narlikar, G. J. Madhani, H. D. 2017-06-13 doi:10.1101/149385 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ Diffusion as a ruler: modeling kinesin diffusion as a length sensor for intraflagellar transport ]]> https://biorxiv.org/content/10.1101/156760v1?rss=1 Hendel, N. L. Thomson, M. Marshall, W. F. 2017-06-27 doi:10.1101/156760 Cold Spring Harbor Laboratory Press 2017-06-27 <![CDATA[ A Bulky Glycocalyx Fosters Metastasis Formation by Promoting G1 Cell Cycle Progression ]]> https://biorxiv.org/content/10.1101/156893v1?rss=1 Woods, E. C. Barnes, J. M. Pickup, M. W. Pedram, K. Kai, F. Hollander, M. J. Weaver, V. M. Bertozzi, C. R. 2017-06-28 doi:10.1101/156893 Cold Spring Harbor Laboratory Press 2017-06-28 <![CDATA[ A Genome-wide Association and Admixture Mapping Study of Bronchodilator Drug Response in African Americans with Asthma ]]> https://biorxiv.org/content/10.1101/157198v1?rss=1 Spear, M. L. Hu, D. Pino-Yanes, M. Huntsman, S. Eng, C. Levin, A. M. White, M. J. McGarry, M. E. Thakur, N. Galanter, J. M. Mak, A. C. Y. Oh, S. S. Davis, A. Kumar, R. Farber, H. J. Meade, K. Avila, P. C. Serebrisky, D. Lenoir, M. A. Brigino-Buenaventura, E. A. Rodriquez Cintron, W. Thyne, S. M. Rodriguez-Santana, J. R. Ford, J. G. Chapela, R. Moreno Estrada, A. Sandoval, K. Seibold, M. A. Williams, L. K. Winkler, C. A. Torgerson, D. G. Hernandez, R. D. Burchard, E. G. 2017-06-28 doi:10.1101/157198 Cold Spring Harbor Laboratory Press 2017-06-28 <![CDATA[ Toward leveraging big data in human functional connectomics: Generalization of brain graphs across scanners, sessions, and paradigms ]]> https://biorxiv.org/content/10.1101/160440v1?rss=1 Cao, H. McEwen, S. Bearden, C. Addington, J. Goodyear, B. Cadenhead, K. Mirzakhanian, H. Cornblatt, B. Olvet, D. Mathalon, D. McGlashan, T. Perkins, D. Belger, A. Seidman, L. Thermenos, H. Tsuang, M. van Erp, T. Walker, E. Hamann, S. Woods, S. Cannon, T. 2017-07-07 doi:10.1101/160440 Cold Spring Harbor Laboratory Press 2017-07-07 <![CDATA[ Whole Genome Sequencing in Psychiatric Disorders: the WGSPD Consortium ]]> https://biorxiv.org/content/10.1101/160499v1?rss=1 Sanders, S. J. Neale, B. M. Huang, H. Werling, D. M. An, J.-Y. Dong, S. - Whole Genome Sequencing for Psychiatric Disorders, Abecasis, G. Arguello, P. A. Blangero, J. Boehnke, M. Daly, M. Eggan, K. Geschwind, D. H. Glahn, D. Goldstein, D. B. Gur, R. E. Handsaker, R. E. McCarroll, S. A. Ophoff, R. A. Palotie, A. Pato, C. Sabatti, C. State, M. W. Willsey, A. J. Hyman, S. E. Addington, A. Lehner, T. Freimer, N. B. 2017-07-07 doi:10.1101/160499 Cold Spring Harbor Laboratory Press 2017-07-07 <![CDATA[ GPS2 regulates mitochondria biogenesis via mitochondrial retrograde signaling and chromatin remodeling of nuclear-encoded mitochondrial genes ]]> https://biorxiv.org/content/10.1101/162297v1?rss=1 Cardamone, M. D. Tanasa, B. Cederquist, C. Huang, J. Mahdaviani, K. Li, W. Rosenfeld, M. G. Liesa, M. Perissi, V. 2017-07-11 doi:10.1101/162297 Cold Spring Harbor Laboratory Press 2017-07-11 <![CDATA[ Abnormal Speech Motor Control in Individuals with 16p11.2 Deletions ]]> https://biorxiv.org/content/10.1101/165316v1?rss=1 70%) in individuals with the 600 kb BP4-BP5 16p11.2 deletion; however, the mechanisms that drive these deficits are unclear, limiting our ability to target interventions and advance treatment. This study examined fundamental aspects of speech motor control in participants with the 16p11.2 deletion. To assess capacity for control of voice, we examined how accurately and quickly subjects changed the pitch of their voice within a trial to correct for a transient perturbation of the pitch of their auditory feedback. When compared to sibling controls, 16p11.2 deletion carriers show an over-exaggerated pitch compensation response to unpredictable mid-vocalization pitch perturbations. We also examined sensorimotor adaptation of speech by assessing how subjects learned to adapt their sustained productions of formants (speech spectral peak frequencies important for vowel identity), in response to consistent changes in their auditory feedback during vowel production. Deletion carriers show reduced sensorimotor adaptation to sustained vowel identity changes in auditory feedback. These results together suggest that 16p11.2 deletion carriers have fundamental impairments in the basic mechanisms of speech motor control and these impairments may partially explain the deficits in speech and language in these individuals. ]]> Demopoulos, C. Kothare, H. Mizuiri, D. Henderson-Sabes, J. Fregeau, B. Tjernagel, J. Houde, J. Sherr, E. Nagarajan, S. S. 2017-07-18 doi:10.1101/165316 Cold Spring Harbor Laboratory Press 2017-07-18 <![CDATA[ An Automated Approach to the Quantitation of Vocalizations and Vocal Learning in the Songbird ]]> https://biorxiv.org/content/10.1101/166124v1?rss=1 Mets, D. G. Brainard, M. S. 2017-07-20 doi:10.1101/166124 Cold Spring Harbor Laboratory Press 2017-07-20 <![CDATA[ BRG1/BRM-associated factor complex subunit diversity promotes temporally distinct gene expression programs in cardiogenesis ]]> https://biorxiv.org/content/10.1101/166983v1?rss=1 Hota, S. Johnson, J. Verschueren, E. Zhu, Y. Sun, X. Pennacchio, L. Rossant, J. Krogan, N. Bruneau, B. 2017-07-21 doi:10.1101/166983 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ The transcriptionally permissive chromatin state of ES cells is acutely tuned totranslational output ]]> https://biorxiv.org/content/10.1101/167239v1?rss=1 Bulut-Karslioglu, A. Macrae, T. A. Oses-Prieto, J. A. Covarrubias, S. Percharde, M. Ku, G. Diaz, A. McManus, M. T. Burlingame, A. L. Ramalho-santos, M. 2017-07-22 doi:10.1101/167239 Cold Spring Harbor Laboratory Press 2017-07-22 <![CDATA[ Tau Internalization is Regulated by 6-O Sulfation on Heparan Sulfate Proteoglycans (HSPGs) ]]> https://biorxiv.org/content/10.1101/167874v1?rss=1 Rauch, J. Chen, J. J. Sorum, A. W. Miller, G. M. Sharf, T. See, S. K. Hsieh-Wilson, L. C. Kampmann, M. Kosik, K. S. 2017-07-24 doi:10.1101/167874 Cold Spring Harbor Laboratory Press 2017-07-24 <![CDATA[ A large kinome in a large cell: Stentor coeruleus possesses highly expanded kinase families and novel domain architectures ]]> https://biorxiv.org/content/10.1101/168187v1?rss=1 Reiff, S. B. Marshall, W. F. 2017-07-25 doi:10.1101/168187 Cold Spring Harbor Laboratory Press 2017-07-25 <![CDATA[ Evidence for evolutionary shifts in the fitness landscape of human complex traits ]]> https://biorxiv.org/content/10.1101/173815v1?rss=1 Uricchio, L. H. Kitano, H. C. Gusev, A. Zaitlen, N. A. 2017-08-08 doi:10.1101/173815 Cold Spring Harbor Laboratory Press 2017-08-08 <![CDATA[ Progressive reconfiguration of resting-state brain networks as psychosis develops: Preliminary results from the North American Prodrome Longitudinal Study (NAPLS) consortium ]]> https://biorxiv.org/content/10.1101/179242v1?rss=1 Cao, H. Chung, Y. McEwen, S. Bearden, C. Addington, J. Goodyear, B. Cadenhead, K. Mirzakhanian, H. Cornblatt, B. Olvet, D. Mathalon, D. McGlashan, T. Perkins, D. Belger, A. Seidman, L. Thermenos, H. Tsuang, M. van Erp, T. Walker, E. Hamann, S. Anticevic, A. Woods, S. Cannon, T. 2017-08-21 doi:10.1101/179242 Cold Spring Harbor Laboratory Press 2017-08-21 <![CDATA[ BBSome trains remove activated GPCRs from cilia by enabling passage through the transition zone ]]> https://biorxiv.org/content/10.1101/180620v1?rss=1 Ye, F. Nager, A. R. Nachury, M. V. 2017-08-26 doi:10.1101/180620 Cold Spring Harbor Laboratory Press 2017-08-26 <![CDATA[ Genomic and proteomic analysis of Human herpesvirus 6 reveals distinct clustering of acute versus inherited forms and reannotation of reference strain ]]> https://biorxiv.org/content/10.1101/181248v1?rss=1 90% seroprevalence in the adult population. Unique among human herpesviruses, HHV-6 can integrate into the subtelomeric regions of human chromosomes; when this occurs in germ line cells it causes a condition called inherited chromosomally integrated HHV-6 (iciHHV-6). To date, only two complete genomes are available for HHV-6B. Using a custom capture panel for HHV-6B, we report near-complete genomes from 61 isolates of HHV-6B from active infections (20 from Japan, 35 from New York state, and 6 from Uganda), and 64 strains of iciHHV-6B (mostly from North America). We also report partial genome sequences from 10 strains of iciHHV-6A. Although the overall sequence diversity of HHV-6 is limited relative to other human herpesviruses, our sequencing identified geographical clustering of HHV-6B sequences from active infections, as well as evidence of recombination among HHV-6B strains. One strain of active HHV-6B was more divergent than any other HHV-6B previously sequenced. In contrast to the active infections, sequences from iciHHV-6 cases showed reduced sequence diversity. Strikingly, multiple iciHHV-6B sequences from unrelated individuals were found to be completely identical, consistent with a founder effect. However, several iciHHV-6B strains intermingled with strains from active pediatric infection, consistent with the hypothesis that intermittent de novo integration into host germline cells can occur during active infection Comparative genomic analysis of the newly sequenced strains revealed numerous instances where conflicting annotations between the two existing reference genomes could be resolved. Combining these findings with transcriptome sequencing and shotgun proteomics, we reannotated the HHV-6B genome and found multiple instances of novel splicing and genes that hitherto had gone unannotated. The results presented here constitute a significant genomic resource for future studies on the detection, diversity, and control of HHV-6.nnAuthor SummaryHHV-6 is a ubiquitous large DNA virus that is the most common cause of febrile seizures and reactivates in allogeneic stem cell patients. It also has the unique ability among human herpesviruses to be integrated into the genome of every cell via integration in the germ line, a condition called inherited chromosomally integrated (ici)HHV-6, which affects approximately 1% of the population. To date, very little is known about the comparative genomics of HHV-6. We sequenced 61 isolates of HHV-6B from active infections, 64 strains of iciHHV-6B, and 10 strains of iciHHV-6A. We found geographic clustering of HHV-6B strains from active infections. In contrast, iciHHV-6B had reduced sequence diversity, with many identical sequences of iciHHV-6 found in individuals not known to share recent common ancestry, consistent with a founder effect from a remote common ancestor with iciHHV-6. We also combined our genomic analysis with transcriptome sequencing and shotgun proteomics to correct previous misannotations of the HHV-6 genome. ]]> Greninger, A. Knudsen, G. Roychoudhury, P. Hanson, D. Hall Sedlak, R. A. Xie, H. Guan, J. Nguyen, T. Peddu, V. Boeckh, M. Huang, M.-L. Cook, L. Depledge, D. Zerr, D. Koelle, D. Gantt, S. Yoshikawa, T. Caserta, M. Hill, J. Jerome, K. 2017-08-27 doi:10.1101/181248 Cold Spring Harbor Laboratory Press 2017-08-27 <![CDATA[ Human demographic history has amplified the effects background selection across the genome ]]> https://biorxiv.org/content/10.1101/181859v1?rss=1 Torres, R. Szpiech, Z. A. Hernandez, R. D. 2017-08-29 doi:10.1101/181859 Cold Spring Harbor Laboratory Press 2017-08-29 <![CDATA[ Correction of autoimmune IL2RA mutations in primary human T cells using non-viral genome targeting ]]> https://biorxiv.org/content/10.1101/183418v1?rss=1 1 kilobase) DNA sequences at specific sites in the genomes of primary human T cells while preserving cell viability and function. We successfully tested the potential therapeutic use of this approach in two settings. First, we corrected a pathogenic IL2RA mutation in primary T cells from multiple family members with monogenic autoimmune disease and demonstrated enhanced signalling function. Second, we replaced the endogenous T cell receptor (TCR) locus with a new TCR redirecting T cells to a cancer antigen. The resulting TCR-engineered T cells specifically recognized the tumour antigen, with concomitant cytokine release and tumour cell killing. Taken together, these studies provide preclinical evidence that non-viral genome targeting will enable rapid and flexible experimental manipulation and therapeutic engineering of primary human immune cells. ]]> Roth, T. L. Yu, R. Shifrut, E. Hiatt, J. Li, H. Schumann, K. Tobin, V. Ferris, A. M. Chen, J. Schickel, J.-N. Pellerin, L. Carmody, D. Alkorta-Aranburu, G. Del Gaudio, D. Cho, M. Matsumoto, H. Morell, M. Mao, Y. Nguyen, D. Quadros, R. Gurumurthy, C. Smith, B. Haugwitz, M. Hughes, S. H. Weissman, J. May, A. P. Kupfer, G. Greeley, S. Bacchetta, R. Meffre, E. Roncarolo, M. G. Romberg, N. Herold, K. C. Leonetti, M. D. Marson, A. 2017-08-31 doi:10.1101/183418 Cold Spring Harbor Laboratory Press 2017-08-31 <![CDATA[ Rescue of Conformational Dynamics in Enzyme Catalysis by Directed Evolution ]]> https://biorxiv.org/content/10.1101/185009v1?rss=1 Otten, R. Liu, L. Kenner, L. R. Clarkson, M. W. Mavor, D. Tawfik, D. S. Kern, D. Fraser, J. S. 2017-09-05 doi:10.1101/185009 Cold Spring Harbor Laboratory Press 2017-09-05 <![CDATA[ Phylogeny-corrected identification of microbial gene families relevant to human gut colonization ]]> https://biorxiv.org/content/10.1101/189795v1?rss=1 Bradley, P. H. Nayfach, S. Pollard, K. S. 2017-09-16 doi:10.1101/189795 Cold Spring Harbor Laboratory Press 2017-09-16 <![CDATA[ The geometry of the distance-decay of similarity in ecological communities ]]> https://biorxiv.org/content/10.1101/200212v1?rss=1 Ladau, J. Green, J. L. Pollard, K. S. 2017-10-09 doi:10.1101/200212 Cold Spring Harbor Laboratory Press 2017-10-09 <![CDATA[ Heterogeneity and targeted therapy-induced adaptations in lung cancer revealed by longitudinal single-cell RNA sequencing ]]> https://biorxiv.org/content/10.1101/2019.12.08.868828v1?rss=1 Maynard, A. McCoach, C. E. Rotow, J. K. Harris, L. Haderk, F. Kerr, L. D. Yu, E. A. Schenk, E. L. Tan, W. Zee, A. Tan, M. Gui, P. Lea, T. Wu, W. Urisman, A. Jones, K. Sit, R. Kolli, P. K. Seeley, E. Gesthalter, Y. Le, D. D. Yamauchi, K. A. Naeger, D. M. Thomas, N. J. Gupta, A. Gonzalez, M. Do, H. Tan, L. Gomez-Sjoberg, R. Gubens, M. Jahan, T. Kratz, J. R. Jablons, D. Neff, N. Doebele, R. C. Weissman, J. Blakely, C. M. Darmanis, S. Bivona, T. G. 2019-12-13 doi:10.1101/2019.12.08.868828 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ Systems analysis of blood transcriptomes in dementia patients reveals an innate immune response shared across disorders ]]> https://biorxiv.org/content/10.1101/2019.12.13.875112v1?rss=1 Nachun, D. Ramos, E. M. Karydas, A. Dokuru, D. Gao, F. Yang, Z. Van Berlo, V. Sears, R. L. Kramer, J. Boxer, A. L. Rosen, H. H. Miller, B. L. Coppola, G. 2019-12-13 doi:10.1101/2019.12.13.875112 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ Differential Correlation of Serum BDNF and microRNA Content in Rats with Rapid or Late Onset of Heavy Alcohol Use ]]> https://biorxiv.org/content/10.1101/2019.12.18.881680v1?rss=1 Ehinger, Y. phamluong, K. Darevesky, D. Welman, M. Moffat, J. Sakhai, S. Whiteley, E. Berger, A. Laguesse, S. Farokhnia, M. Leggio, L. Lordkipanidze, M. Ron, D. 2019-12-19 doi:10.1101/2019.12.18.881680 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Lactoferrin Reverses Methotrexate Driven Epithelial Barrier Defect by Inhibiting TGF-β Mediated Epithelial to Mesenchymal Transition ]]> https://biorxiv.org/content/10.1101/2019.12.23.878207v1?rss=1 Wallach, T. Srivastava, V. Reyes, E. Klein, O. D. Gartner, Z. J. 2019-12-26 doi:10.1101/2019.12.23.878207 Cold Spring Harbor Laboratory Press 2019-12-26 <![CDATA[ LegoBody: facile generation of bispecific and multi-specific antibodies ]]> https://biorxiv.org/content/10.1101/2019.12.25.888586v1?rss=1 Lang, S. Su, Y. Bidlingmaier, S. Lee, N.-K. Liu, B. 2019-12-27 doi:10.1101/2019.12.25.888586 Cold Spring Harbor Laboratory Press 2019-12-27 <![CDATA[ Selective and invariant features of neural response surfaces measured with principal curvature ]]> https://biorxiv.org/content/10.1101/2019.12.26.888933v1?rss=1 Golden, J. R. Vilankar, K. P. Field, D. J. 2019-12-28 doi:10.1101/2019.12.26.888933 Cold Spring Harbor Laboratory Press 2019-12-28 <![CDATA[ Single cell epigenomic atlas of the developing human brain and organoids ]]> https://biorxiv.org/content/10.1101/2019.12.30.891549v1?rss=1 75,000 cells from eight distinct areas of developing human forebrain using single cell ATAC-seq (scATACseq). We identified thousands of loci that undergo extensive cell type-specific changes in accessibility during corticogenesis. Chromatin state profiling also reveals novel distinctions between neural progenitor cells from different cortical areas not seen in transcriptomic profiles and suggests a role for retinoic acid signaling in cortical arealization. Comparison of the cell type-specific chromatin landscape of cerebral organoids to primary developing cortex found that organoids establish broad cell type-specific enhancer accessibility patterns similar to the developing cortex, but lack many putative regulatory elements identified in homologous primary cell types. Together, our results reveal the important contribution of chromatin state to the emerging patterns of cell type diversity and cell fate specification and provide a blueprint for evaluating the fidelity and robustness of cerebral organoids as a model for cortical development. ]]> Ziffra, R. S. Kim, C. N. Wilfert, A. Haeussler, M. Casella, A. M. Przytycki, P. F. Kreimer, A. Pollard, K. S. Ament, S. A. Eichler, E. E. Ahituv, N. Nowakowski, T. J. 2019-12-31 doi:10.1101/2019.12.30.891549 Cold Spring Harbor Laboratory Press 2019-12-31 <![CDATA[ Simultaneous classification of neuroactive compounds in zebrafish ]]> https://biorxiv.org/content/10.1101/2020.01.01.891432v1?rss=1 Myers-Turnbull, D. Taylor, J. C. Helsell, C. Tummino, T. A. Mccarroll, M. N. Alexander, R. Ki, C. S. Gendelev, L. Kokel, D. 2020-01-02 doi:10.1101/2020.01.01.891432 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ Granular Transcriptomic Signatures Derived from Independent Component Analysis of Bulk Nervous Tissue for Studying Labile Brain Physiologies ]]> https://biorxiv.org/content/10.1101/2020.01.01.892281v1?rss=1 Rusan, Z. M. Cary, M. P. Bainton, R. J. 2020-01-02 doi:10.1101/2020.01.01.892281 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ ATP hydrolysis by the SNF2 domain of the ultraspecific maintenance methylase Dnmt5 drives recognition and modification of hemimethylated DNA ]]> https://biorxiv.org/content/10.1101/2020.01.05.895227v1?rss=1 Dumesic, P. A. Stoddard, C. I. Catania, S. Narlikar, G. J. Madhani, H. 2020-01-06 doi:10.1101/2020.01.05.895227 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ cAMP-Fyn signaling in the dorsomedial striatum direct pathway drives excessive alcohol use ]]> https://biorxiv.org/content/10.1101/2020.01.07.898023v1?rss=1 Ehinger, Y. Morisot, N. Sakhai, S. Phamluong, K. Adrover, M. Alvarez, V. Ron, D. 2020-01-08 doi:10.1101/2020.01.07.898023 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ ALPPL2 is a highly specific and targetable tumor cell surface antigen ]]> https://biorxiv.org/content/10.1101/2020.01.07.898122v1?rss=1 Su, Y. Zhang, X. Bidlingmaier, S. Behrens, C. R. Lee, N.-K. Liu, B. 2020-01-08 doi:10.1101/2020.01.07.898122 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Designing and implementing programmable depletion in sequencing libraries with DASHit ]]> https://biorxiv.org/content/10.1101/2020.01.12.891176v1?rss=1 Dynerman, D. Lyden, A. Quan, J. Caldera, S. McGeever, A. Dimitrov, B. King, R. Cirola, G. Tan, M. Sit, R. van den Berge, M. Kerstjens, H. A. M. Faiz, A. Christenson, S. Langelier, C. DeRisi, J. Crawford, E. D. 2020-01-13 doi:10.1101/2020.01.12.891176 Cold Spring Harbor Laboratory Press 2020-01-13 <![CDATA[ Recent fluctuations in Mexican American genomes have altered the genetic architecture of biomedical traits ]]> https://biorxiv.org/content/10.1101/2020.01.13.905141v1?rss=1 Spear, M. L. Diaz-Papkovich, A. Ziv, E. Gravel, S. Torgerson, D. G. Hernandez, R. 2020-01-14 doi:10.1101/2020.01.13.905141 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Clustered γ-Protocadherins Regulate Cortical Interneuron Programmed Cell Death. ]]> https://biorxiv.org/content/10.1101/2020.01.14.906941v1?rss=1 Mancia Leon, W. R. Spatazza, J. Rakela, B. Chatterjee, A. Pande, V. Maniatis, T. Hasenstaub, A. R. Stryker, M. P. Alvarez-Buylla, A. 2020-01-15 doi:10.1101/2020.01.14.906941 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Characterization of Prenylated C-terminal Peptides Using a Novel Capture Technique Coupled with LCMS ]]> https://biorxiv.org/content/10.1101/2020.01.15.908152v1?rss=1 View larger version (21K): org.highwire.dtl.DTLVardef@12579f2org.highwire.dtl.DTLVardef@16934ccorg.highwire.dtl.DTLVardef@94b23org.highwire.dtl.DTLVardef@23f329_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wilkins, J. A. Kaasik, K. Chalkley, R. J. Burlingame, A. 2020-01-15 doi:10.1101/2020.01.15.908152 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Loss of Tet2 affects proliferation and drug sensitivity through altered dynamics of cell-state transitions ]]> https://biorxiv.org/content/10.1101/2020.01.20.911834v1?rss=1 Morinishi, L. S. Kochanowski, K. Levine, R. Wu, L. Altschuler, S. 2020-01-20 doi:10.1101/2020.01.20.911834 Cold Spring Harbor Laboratory Press 2020-01-20 <![CDATA[ Head Movements Control the Activity of Primary Visual Cortex in a Luminance Dependent Manner ]]> https://biorxiv.org/content/10.1101/2020.01.20.913160v1?rss=1 Bouvier, G. Senzai, Y. Scanziani, M. 2020-01-21 doi:10.1101/2020.01.20.913160 Cold Spring Harbor Laboratory Press 2020-01-21 <![CDATA[ Overcoming the inhibitory microenvironment surrounding oligodendrocyte progenitor cells following demyelination ]]> https://biorxiv.org/content/10.1101/2020.01.21.906073v1?rss=1 Saraswat, D. Polanco, J. J. Shayya, H. J. Tripathi, A. Welliver, R. Pol, S. U. Broome, J. E. O'Bara, M. A. van Kuppervelt, T. H. Phillips, J. J. Dutta, R. Sim, F. J. 2020-01-21 doi:10.1101/2020.01.21.906073 Cold Spring Harbor Laboratory Press 2020-01-21 <![CDATA[ Fusion of Drosophila oocytes with specified germline sister cells ]]> https://biorxiv.org/content/10.1101/2020.01.22.915736v1?rss=1 Ali-Murthy, Z. Fetter, R. D. Kornberg, T. B. 2020-01-23 doi:10.1101/2020.01.22.915736 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Single cell determination of cardiac microtissue structure and function using light sheet microscopy ]]> https://biorxiv.org/content/10.1101/2020.01.22.915926v1?rss=1 Turaga, D. Matthys, O. B. Hookway, T. A. Joy, D. A. Calvert, M. McDevitt, T. C. 2020-01-23 doi:10.1101/2020.01.22.915926 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ RBMS1 suppresses colon cancer metastasis through targeted stabilization of its mRNA regulon ]]> https://biorxiv.org/content/10.1101/2020.01.22.916205v1?rss=1 Yu, J. Culbertson, B. Asgharian, H. Navickas, A. Fish, L. Olegario, J. P. Hanisch, B. Weinberg, E. Dienstmann, R. Warren, R. Goodarzi, H. 2020-01-23 doi:10.1101/2020.01.22.916205 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Neurons in Visual Cortex are Driven by Feedback Projections when their Feedforward Sensory Input is Missing ]]> https://biorxiv.org/content/10.1101/2020.01.24.919142v1?rss=1 Keller, A. J. Roth, M. M. Scanziani, M. 2020-01-25 doi:10.1101/2020.01.24.919142 Cold Spring Harbor Laboratory Press 2020-01-25 <![CDATA[ MHC*IMP - Imputation of Alleles for Genes in the Major Histocompatibility Complex ]]> https://biorxiv.org/content/10.1101/2020.01.24.919191v1?rss=1 Squire, D. M. Motyer, A. Ahn, R. S. Nitiham, J. Huang, Z.-M. Oksenberg, J. R. Liao, W. Leslie, S. 2020-01-25 doi:10.1101/2020.01.24.919191 Cold Spring Harbor Laboratory Press 2020-01-25 <![CDATA[ Epithelial morphogenesis in the perinatal mouse uterus ]]> https://biorxiv.org/content/10.1101/2020.01.28.922385v1?rss=1 Vue, Z. Behringer, R. 2020-01-28 doi:10.1101/2020.01.28.922385 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ Near-atomic structures of the BBSome reveal a novel mechanism for transition zone crossing ]]> https://biorxiv.org/content/10.1101/2020.01.29.925610v1?rss=1 Bahl, K. Yang, S. Chou, H.-T. Woodsmith, J. Stelzl, U. Walz, T. Nachury, M. V. 2020-01-30 doi:10.1101/2020.01.29.925610 Cold Spring Harbor Laboratory Press 2020-01-30 <![CDATA[ Cytoprotection by a naturally occurring variant of ATP5G1 in Arctic ground squirrels ]]> https://biorxiv.org/content/10.1101/2020.01.31.929018v1?rss=1 Singhal, N. S. Bai, M. Lee, E. M. Luo, S. Cook, K. R. Ma, D. K. 2020-01-31 doi:10.1101/2020.01.31.929018 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ A Disinhibitory Circuit for Contextual Modulation in Primary Visual Cortex ]]> https://biorxiv.org/content/10.1101/2020.01.31.929166v1?rss=1 Keller, A. J. Roth, M. M. Caudill, M. Dipoppa, M. Miller, K. D. Scanziani, M. 2020-01-31 doi:10.1101/2020.01.31.929166 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Poecivirus is present in individuals with beak deformities in seven species of North American birds ]]> https://biorxiv.org/content/10.1101/2020.02.03.927442v1?rss=1 Zylberberg, M. Van Hemert, C. Handel, C. M. Liu, R. DeRisi, J. 2020-02-04 doi:10.1101/2020.02.03.927442 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ ZipSeq : Barcoding for Real-time Mapping of Single Cell Transcriptomes ]]> https://biorxiv.org/content/10.1101/2020.02.04.932988v1?rss=1 Hu, K. H. Eichorst, J. P. McGinnis, C. S. Patterson, D. M. Chow, E. D. Kersten, K. Jameson, S. C. Gartner, Z. J. Rao, A. A. Krummel, M. F. 2020-02-04 doi:10.1101/2020.02.04.932988 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Principles of dengue virus evolvability derived from genotype-fitness maps in human and mosquito cells ]]> https://biorxiv.org/content/10.1101/2020.02.05.936195v1?rss=1 Dolan, P. T. Taguwa, S. Aguilar Rangel, M. Acevedo, A. Andino, R. Frydman, J. 2020-02-07 doi:10.1101/2020.02.05.936195 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ MicroRNA-dependent inhibition of PFN2 orchestrates ERK activation and pluripotent state transitions by regulating endocytosis ]]> https://biorxiv.org/content/10.1101/2020.02.06.936070v1?rss=1 Sangokoya, C. Blelloch, R. 2020-02-06 doi:10.1101/2020.02.06.936070 Cold Spring Harbor Laboratory Press 2020-02-06 <![CDATA[ BET Bromodomain Proteins Regulate Transcriptional Reprogramming in Genetic Dilated Cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2020.02.09.940882v1?rss=1 Antolic, A. Wakimoto, H. Jiao, Z. Gorham, J. M. DePalma, S. R. Conner, D. A. Lee, D. Y. Qi, J. Seidman, J. G. Bradner, J. E. Brown, J. D. Haldar, S. M. Seidman, C. E. Burke, M. A. 2020-02-10 doi:10.1101/2020.02.09.940882 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ Massively Parallel Analysis of Human 3' UTRs Reveals that AU-Rich Element Length and Registration Predict mRNA Destabilization ]]> https://biorxiv.org/content/10.1101/2020.02.12.945063v1?rss=1 Siegel, D. A. Le Tonqueze, O. Biton, A. Zaitlen, N. Erle, D. J. 2020-02-12 doi:10.1101/2020.02.12.945063 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ High-temperature live-cell imaging of cytokinesis, cell motility and cell-cell adhesion in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius ]]> https://biorxiv.org/content/10.1101/2020.02.16.951772v1?rss=1 50{degrees}C) has impeded the study of cell motility and cell division in thermophilic archaea such as model organisms from the genus Sulfolobus. Here we describe a system for imaging samples at 75{degrees}C using high numerical aperture, oil-immersion lenses. With this system we observed and quantified the dynamics of cell division in the model thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. In addition, we observed previously undescribed dynamic cell shape changes, cell motility, and cell-cell interactions, shedding significant new light on the high-temperature lifestyle of this organism. ]]> Charles-Orszag, A. Lord, S. J. Mullins, D. 2020-02-17 doi:10.1101/2020.02.16.951772 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ Oncogenic mutant RAS activity is rescaled by the ERK/MAPK pathway ]]> https://biorxiv.org/content/10.1101/2020.02.17.952093v1?rss=1 Gillies, T. E. Pargett, M. Silva, J. M. Teragawa, C. McCormick, F. Albeck, J. G. 2020-02-17 doi:10.1101/2020.02.17.952093 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ IFN-{lambda}4 increases the risk of gastrointestinal infections and malaria in Malian children ]]> https://biorxiv.org/content/10.1101/2020.02.24.962688v1?rss=1 Prokunina-Olsson, L. Morrison, R. L. Obajemu, A. Mahamar, A. Kim, S. Attaher, O. Florez-Vargas, O. Sidibe, Y. Onabajo, O. O. Hutchinson, A. A. Manning, M. Kwan, J. Brand, N. Dicko, A. Fried, M. Albert, P. S. Mbulaiteye, S. M. Duffy, P. E. 2020-02-25 doi:10.1101/2020.02.24.962688 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ CRISPR Screen in Regulatory T Cells Reveals Ubiquitination Modulators of Foxp3 ]]> https://biorxiv.org/content/10.1101/2020.02.26.966911v1?rss=1 Cortez, J. T. Montauti, E. Shifrut, E. Zhang, Y. Shaked, O. Xu, Y. Roth, T. Simeonov, D. Zhang, Y. Chen, S. Li, Z. Vogel, I. A. Prator, G. Y. Zhang, B. Lee, Y. Sun, Z. Ifergan, I. Van Gool, F. Bluestone, J. A. Marson, A. Fang, D. 2020-02-27 doi:10.1101/2020.02.26.966911 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ Molecular goniometers for single-particle cryo-EM of DNA-binding proteins ]]> https://biorxiv.org/content/10.1101/2020.02.27.968883v1?rss=1 Aksel, T. Yu, Z. Cheng, Y. Douglas, S. M. 2020-02-28 doi:10.1101/2020.02.27.968883 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types ]]> https://biorxiv.org/content/10.1101/2020.02.29.970558v1?rss=1 Yao, Z. Liu, H. Xie, F. Fischer, S. Adkins, R. S. Aldrige, A. I. Ament, S. A. Bartlett, A. Behrens, M. M. Van den Berge, K. Bertagnolli, D. Biancalani, T. Booeshaghi, A. S. Corrada Bravo, H. Casper, T. Colantuoni, C. Crabtree, J. Creasy, H. Crichton, K. Crow, M. Dee, N. Dougherty, E. L. Doyle, W. I. Dudoit, S. Fang, R. Felix, V. Fong, O. Giglio, M. Goldy, J. Hawrylycz, M. Bezieux, H. R. d. Herb, B. R. Hertzano, R. Hou, X. Hu, Q. Huang, Z. J. Kancherla, J. Kroll, M. Lathia, K. Li, Y. E. Lucero, J. D. Luo, C. Mahurkar, A. McMillen, D. Nadaf, N. M. Ner 2020-03-02 doi:10.1101/2020.02.29.970558 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Fusion pore expansion and contraction during catecholamine release from endocrine cells ]]> https://biorxiv.org/content/10.1101/2020.03.02.972745v1?rss=1 Jackson, M. B. Hsiao, Y.-T. Chang, C.-W. 2020-03-02 doi:10.1101/2020.03.02.972745 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Lysine63-linked ubiquitin chains earmark GPCRs for BBSome-mediated removal from cilia ]]> https://biorxiv.org/content/10.1101/2020.03.04.977090v1?rss=1 Shinde, S. R. Nager, A. R. Nachury, M. V. 2020-03-05 doi:10.1101/2020.03.04.977090 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Hedgehog produced by the Drosophila wing imaginal disc induces distinct expression responses in three target tissues ]]> https://biorxiv.org/content/10.1101/2020.03.05.979799v1?rss=1 Hatori, R. Kornberg, T. B. 2020-03-06 doi:10.1101/2020.03.05.979799 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ Cytoskeletal tension forces mitohormesis ]]> https://biorxiv.org/content/10.1101/2020.03.06.979583v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@1ecdaceorg.highwire.dtl.DTLVardef@1112c32org.highwire.dtl.DTLVardef@6c99a1org.highwire.dtl.DTLVardef@1da1e5f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Tharp, K. M. Higuchi-Sanabria, R. Timblin, G. Garzon-Coral, C. Ford, B. Schneider, C. Muncie, J. M. Stashko, C. Daniele, J. Frankino, P. Manoli, S. Shao, H. Gestwicki, J. Hellerstein, M. Nomura, D. K. Saijo, K. Dunn, A. Dillin, A. Weaver, V. M. 2020-03-07 doi:10.1101/2020.03.06.979583 Cold Spring Harbor Laboratory Press 2020-03-07 <![CDATA[ An emergent population code in primary auditory cortex supports selective attention to spectral and temporal sound features ]]> https://biorxiv.org/content/10.1101/2020.03.09.984773v1?rss=1 Downer, J. D. Verhein, J. R. Rapone, B. C. O'Connor, K. N. Sutter, M. L. 2020-03-10 doi:10.1101/2020.03.09.984773 Cold Spring Harbor Laboratory Press 2020-03-10 <![CDATA[ ZENITH: A flow cytometry based method for functional profiling energy metabolism with single cell resolution ]]> https://biorxiv.org/content/10.1101/2020.03.10.985796v1?rss=1 ARGUELLO, R. J. COMBES, A. J. CHAR, R. BOUSIQUOT, E. GIGAN, J. P. CAMOSSETO, V. SAMAD, B. TSUI, J. YAN, P. BOISSONNEAU, S. FIGARELLA-BRANGER, D. TABOURET, E. GATTI, E. Krummel, M. F. PIERRE, P. 2020-03-11 doi:10.1101/2020.03.10.985796 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Hierarchical effects of choice related activity and neural encoding during feature selective attention ]]> https://biorxiv.org/content/10.1101/2020.03.10.986349v1?rss=1 Mohn, J. L. Downer, J. O'Connor, K. N. Johnson, J. S. Sutter, M. L. 2020-03-11 doi:10.1101/2020.03.10.986349 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Scalable method for micro-CT analysis enables large scale quantitative characterization of brain lesions and implants ]]> https://biorxiv.org/content/10.1101/2020.03.12.989871v1?rss=1 Kastner, D. B. Kharazia, V. Nevers, R. Astudillo Maya, D. Williams, G. M. Yang, Z. Smyth, C. Della Santina, L. Parkinson, D. Y. Frank, L. M. 2020-03-14 doi:10.1101/2020.03.12.989871 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ Histone dynamics within the nucleosome octamer play a critical role in SNF2h-mediated nucleosome sliding ]]> https://biorxiv.org/content/10.1101/2020.03.14.992073v1?rss=1 Gamarra, N. Narlikar, G. 2020-03-16 doi:10.1101/2020.03.14.992073 Cold Spring Harbor Laboratory Press 2020-03-16 <![CDATA[ Evolution of an enzyme conformational ensemble guides design of an efficient biocatalyst ]]> https://biorxiv.org/content/10.1101/2020.03.19.999235v1?rss=1 Broom, A. Rakotoharisoa, R. V. Thompson, M. C. Zarifi, N. Nguyen, E. Mukhametzhanov, N. Liu, L. Fraser, J. S. Chica, R. A. 2020-03-20 doi:10.1101/2020.03.19.999235 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ K2P channel C-type gating involves asymmetric selectivity filter order-disorder transitions ]]> https://biorxiv.org/content/10.1101/2020.03.20.000893v1?rss=1 Lolicato, M. Natale, A. Aberemane-Ali, F. Crottes, D. Capponi, S. Duman, R. Wagner, A. Rosenberg, J. M. Grabe, M. Minor, D. L. 2020-03-21 doi:10.1101/2020.03.20.000893 Cold Spring Harbor Laboratory Press 2020-03-21 <![CDATA[ A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing ]]> https://biorxiv.org/content/10.1101/2020.03.22.002386v1?rss=1 Gordon, D. E. Jang, G. M. Bouhaddou, M. Xu, J. Obernier, K. O'Meara, M. J. Guo, J. Z. Swaney, D. L. Tummino, T. A. Huttenhain, R. Kaake, R. Richards, A. L. Tutuncuoglu, B. Foussard, H. Batra, J. Haas, K. Modak, M. Kim, M. Haas, P. Polacco, B. J. Braberg, H. Fabius, J. M. Eckhardt, M. Soucheray, M. Brewer, M. Cakir, M. McGregor, M. J. Li, Q. Naing, Z. Z. C. Zhou, Y. Peng, S. Kirby, I. T. Melnyk, J. E. Chorba, J. S. Lou, K. Dai, S. A. Shen, W. Shi, Y. Zhang, Z. Barrio-Hernandez, I. Memon, D. Hernandez-Armenta, C. Mathy, C. J. P. Perica, T. Pilla, K. B. 2020-03-22 doi:10.1101/2020.03.22.002386 Cold Spring Harbor Laboratory Press 2020-03-22 <![CDATA[ Coordinate genomic association of transcription factors controlled by an imported quorum sensing peptide in Cryptococcus neoformans ]]> https://biorxiv.org/content/10.1101/2020.03.30.016329v1?rss=1 Summers, D. K. Perry, D. S. Rao, B. Madhani, H. D. 2020-03-30 doi:10.1101/2020.03.30.016329 Cold Spring Harbor Laboratory Press 2020-03-30 <![CDATA[ A negative feedback loop mediated by the NR4A family of nuclear hormone receptors restrains expansion of B cells that receive signal one in the absence of signal two ]]> https://biorxiv.org/content/10.1101/2020.03.31.017434v1?rss=1 Tan, C. Hiwa, R. Mueller, J. L. Vykunta, V. Hibiya, K. Noviski, M. Huizar, J. Brooks, J. F. Garcia, J. Heyn, C. Li, Z. Marson, A. Zikherman, J. 2020-04-01 doi:10.1101/2020.03.31.017434 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Lateralized role of prefrontal cortex in guiding orienting behavior ]]> https://biorxiv.org/content/10.1101/2020.04.12.038356v1?rss=1 Mohebi, A. Oweiss, K. G. 2020-04-13 doi:10.1101/2020.04.12.038356 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ Rapid, precise quantification of large DNA excisions and inversions by ddPCR ]]> https://biorxiv.org/content/10.1101/2020.04.13.039297v1?rss=1 20 kb) excisions and inversions, while also revealing a surprisingly low dependence on linear distance, up to 170 kb. We further modified the method to measure precise repair of excision junctions and allele-specific excision, with important implications for disease modeling and therapeutic gene editing. ]]> Watry, H. L. Feliciano, C. M. Gjoni, K. Takahashi, G. Miyaoka, Y. Conklin, B. R. Judge, L. M. 2020-04-14 doi:10.1101/2020.04.13.039297 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Small molecule cognitive enhancer reverses age-related memory decline in mice. ]]> https://biorxiv.org/content/10.1101/2020.04.13.039677v1?rss=1 Krukowski, K. Nolan, A. Frias, E. S. Boone, M. Ureta, G. Grue, K. Paladini, M.-S. Elizarraras, E. Delgado, L. Bernales, S. Walter, P. Rosi, S. 2020-04-15 doi:10.1101/2020.04.13.039677 Cold Spring Harbor Laboratory Press 2020-04-15 <![CDATA[ Blood RNA Profiles are Diagnostic for Severity in Human Acute Spinal Cord Injury ]]> https://biorxiv.org/content/10.1101/2020.04.15.037325v1?rss=1 Kyritsis, N. Torres-Espin, A. Schupp, P. G. Huie, J. R. Chou, A. Duong Fernandez, X. Thomas, L. H. Tsolinas, R. E. Hemmerle, D. Pascual, L. U. Singh, V. Pan, J. Z. Talbott, J. F. Whetstone, W. D. Burke, J. F. DiGiorgio, A. M. Weinstein, P. R. Manley, G. T. Dhall, S. S. Ferguson, A. R. Oldham, M. C. Bresnahan, J. C. Beattie, M. S. 2020-04-17 doi:10.1101/2020.04.15.037325 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ Continuous lineage recording reveals rapid, multidirectional metastasis in a lung cancer xenograft model in mouse ]]> https://biorxiv.org/content/10.1101/2020.04.16.045245v1?rss=1 Quinn, J. J. Jones, M. G. Okimoto, R. A. Yosef, N. Bivona, T. G. Weissman, J. S. 2020-04-17 doi:10.1101/2020.04.16.045245 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ SMARCA4 supports the oncogenic landscape of KRAS-driven lung tumors ]]> https://biorxiv.org/content/10.1101/2020.04.18.043927v1?rss=1 Collisson, E. 2020-04-20 doi:10.1101/2020.04.18.043927 Cold Spring Harbor Laboratory Press 2020-04-20 <![CDATA[ Role of c-Met/β1 integrin complex in the metastatic cascade ]]> https://biorxiv.org/content/10.1101/2020.04.20.051888v1?rss=1 Lau, D. Wadhwa, H. Sudhir, S. Jain, S. Chandra, A. Nguyen, A. Spatz, J. Shah, S. S. Cheng, J. Safaee, M. Yagnik, G. Jahangiri, A. Aghi, M. K. 2020-04-22 doi:10.1101/2020.04.20.051888 Cold Spring Harbor Laboratory Press 2020-04-22 <![CDATA[ G protein-regulated endocytic trafficking of adenylyl cyclase type 9 ]]> https://biorxiv.org/content/10.1101/2020.04.23.057026v1?rss=1 Lazar, A. M. Irannejad, R. Baldwin, T. A. Sundaram, A. B. Gutkind, J. S. Inoue, A. Dessauer, C. W. Von Zastrow, M. 2020-04-25 doi:10.1101/2020.04.23.057026 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ A splicing isoform of GPR56 mediates microglial synaptic refinement via phosphatidylserine binding ]]> https://biorxiv.org/content/10.1101/2020.04.24.059840v1?rss=1 Li, T. Chiou, B. Gilman, C. K. Luo, R. Koshi, T. Yu, D. Oak, H. C. Giera, S. Johnson-Venkatesh, E. Muthukumar, A. K. Stevens, B. Umemori, H. Piao, X. 2020-04-25 doi:10.1101/2020.04.24.059840 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Sex-Specific Cross Tissue Meta-Analysis Identifies Immune Dysregulation in Women with Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2020.04.24.060558v1?rss=1 Paranjpe, M. D. Belonwu, S. Wang, J. K. Oskotsky, T. Gupta, A. Taubes, A. Zalocusky, K. Paranjpe, I. Glicksberg, B. S. Huang, Y. Sirota, M. 2020-04-25 doi:10.1101/2020.04.24.060558 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ The mitotic protein NuMA plays a spindle-independent role in nuclear formation and mechanics ]]> https://biorxiv.org/content/10.1101/2020.05.02.070680v1?rss=1 Serra-Marques, A. Houtekamer, R. Hintzen, D. Canty, J. T. Yildiz, A. Dumont, S. 2020-05-03 doi:10.1101/2020.05.02.070680 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ Immunodietica: interrogating the role of diet in autoimmune disease ]]> https://biorxiv.org/content/10.1101/2020.05.05.079418v1?rss=1 Gershteyn, I. M. Burov, A. A. Miao, B. Y. Morais, V. H. Ferreira, L. M. R. 2020-05-07 doi:10.1101/2020.05.05.079418 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries ]]> https://biorxiv.org/content/10.1101/2020.05.09.086264v1?rss=1 Zhou, J. Li, S. Leung, K. K. ODonovan, B. K. Zou, J. DeRisi, J. Wells, J. A. 2020-05-10 doi:10.1101/2020.05.09.086264 Cold Spring Harbor Laboratory Press 2020-05-10 <![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[ Androgen regulates SARS-CoV-2 receptor levels and is associated with severe COVID-19 symptoms in men ]]> https://biorxiv.org/content/10.1101/2020.05.12.091082v1?rss=1 Ghazizadeh, Z. Majd, H. Richter, M. Samuel, R. Zekavat, S. M. Asgharian, H. Farahvashi, S. Kalantari, A. Ramirez, J. Zhao, H. Natarajan, P. Goodarzi, H. Fattahi, F. 2020-05-12 doi:10.1101/2020.05.12.091082 Cold Spring Harbor Laboratory Press 2020-05-12 <![CDATA[ A Molecular Mechanism for Probabilistic Bet-hedging and its Role in Viral Latency ]]> https://biorxiv.org/content/10.1101/2020.05.14.096560v1?rss=1 Chaturvedi, S. Klein, J. Vardi, N. Bolovan-Fritts, C. Wolf, M. Du, K. Mlera, L. Calvert, M. Moorman, N. J. Goodrum, F. Huang, B. Weinberger, L. S. 2020-05-15 doi:10.1101/2020.05.14.096560 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Polarized endosome dynamics engage cytosolic Par-3 and dynein during asymmetric division ]]> https://biorxiv.org/content/10.1101/2020.05.15.098012v1?rss=1 Zhao, X. Tong, K. Chen, x. Yang, B. Li, Q. Dai, Z. Shi, X. Seiple, I. Huang, B. Guo, S. 2020-05-16 doi:10.1101/2020.05.15.098012 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Hsp70 chaperone blocks α-synuclein oligomer formation via a novel engagement mechanism ]]> https://biorxiv.org/content/10.1101/2020.05.15.098699v1?rss=1 Tao, J. Berthet, A. Citron, R. Stanley, R. Gestwicki, J. Agard, D. A. McConlogue, L. 2020-05-16 doi:10.1101/2020.05.15.098699 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Massively multiplex single-molecule oligonucleosome footprinting ]]> https://biorxiv.org/content/10.1101/2020.05.20.105379v1?rss=1 Abdulhay, N. J. McNally, C. P. Hsieh, L. J. Kasinathan, S. Keith, A. Estes, L. S. Karimzadeh, M. Underwood, J. G. Goodarzi, H. Narlikar, G. J. Ramani, V. 2020-05-22 doi:10.1101/2020.05.20.105379 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Structure and reconstitution of a hydrolase complex that releases peptidoglycan from the membrane after polymerization ]]> https://biorxiv.org/content/10.1101/2020.05.21.109470v1?rss=1 Schaefer, K. Owens, T. W. Page, J. E. Santiago, M. Kahne, D. Walker, S. 2020-05-22 doi:10.1101/2020.05.21.109470 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Discovery of multiple anti-CRISPRs uncovers anti-defense gene clustering in mobile genetic elements ]]> https://biorxiv.org/content/10.1101/2020.05.22.110304v1?rss=1 Pinilla-Redondo, R. Shehreen, S. Marino, N. D. Fagerlund, R. D. Brown, C. M. Soerensen, S. J. Fineran, P. C. Bondy-Denomy, J. 2020-05-22 doi:10.1101/2020.05.22.110304 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Single cell analysis of human site-specific melanocyte differentiation and the decoding of developmental programs in melanoma ]]> https://biorxiv.org/content/10.1101/2020.05.25.115287v1?rss=1 Belote, R. L. Le, D. Maynard, A. Lang, U. E. Sinclair, A. Planells-Palop, V. Baskin, L. S. Tward, A. D. Darmanis, S. Judson-Torres, R. L. 2020-05-28 doi:10.1101/2020.05.25.115287 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Cellular-scale silicon probes for high-density, precisely-localized neurophysiology ]]> https://biorxiv.org/content/10.1101/2020.05.26.117572v1?rss=1 Egert, D. Pettibone, J. R. Lemke, S. Patel, P. R. Caldwell, C. M. Cai, D. Ganguly, K. Chestek, C. A. Berke, J. 2020-05-29 doi:10.1101/2020.05.26.117572 Cold Spring Harbor Laboratory Press 2020-05-29 <![CDATA[ Complement factor C1q mediates chronic neuron loss and inflammation post-brain injury ]]> https://biorxiv.org/content/10.1101/2020.05.29.120220v1?rss=1 Holden, S. S. Aboubakr, O. Higashikubo, B. Cho, F. S. Chang, A. H. Morningstar, A. Mathur, V. Kuhn, L. J. Suri, P. Sankaranarayanan, S. Andrews-Zwilling, Y. Aronica, E. Yednock, T. Paz, J. T. 2020-05-31 doi:10.1101/2020.05.29.120220 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Scalp EEG interictal high frequency oscillations as an objective EEG biomarker of infantile spasms ]]> https://biorxiv.org/content/10.1101/2020.05.31.126573v1?rss=1 Nariai, H. Hussain, S. A. Bernardo, D. Motoi, H. Sonoda, M. Kuroda, N. Asano, E. Nguyen, J. Elashoff, D. Sankar, R. Bragin, A. Staba, R. J. Wu, J. Y. 2020-06-01 doi:10.1101/2020.05.31.126573 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ NMDA receptors control cortical axonal projections via EPHRIN-B/EPHB signaling ]]> https://biorxiv.org/content/10.1101/2020.06.03.130559v1?rss=1 Zhou, J. Lin, Y. Huynh, T. Noguchi, H. Bush, J. Pleasure, S. 2020-06-04 doi:10.1101/2020.06.03.130559 Cold Spring Harbor Laboratory Press 2020-06-04 <![CDATA[ pHLARE: A Genetically Encoded Ratiometric Lysosome pH Biosensor ]]> https://biorxiv.org/content/10.1101/2020.06.03.132720v1?rss=1 Webb, B. A. Cook, J. Wittmann, T. Barber, D. L. 2020-06-04 doi:10.1101/2020.06.03.132720 Cold Spring Harbor Laboratory Press 2020-06-04 <![CDATA[ Human Induced Pluripotent Stem Cell Derived Sensory Neurons are Sensitive to the Neurotoxic Effects of Paclitaxel ]]> https://biorxiv.org/content/10.1101/2020.06.04.134262v1?rss=1 Xiong, C. Chua, K. C. Stage, T. B. Kim, J. Altman-Merino, A. Chan, D. Saraf, K. Ferracini, A. C. Fattahi, F. Kroetz, D. L. 2020-06-05 doi:10.1101/2020.06.04.134262 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Distinct genetic pathways define pre-leukemic and compensatory clonal hematopoiesis in Shwachman-Diamond syndrome ]]> https://biorxiv.org/content/10.1101/2020.06.04.134692v1?rss=1 Kennedy, A. L. Myers, K. C. Bowman, J. Gibson, C. J. Camarda, N. D. Furutani, E. M. Muscato, G. M. Klein, R. H. Ballotti, K. Liu, S. Harris, C. E. Galvin, A. Malsch, M. Dale, D. Gansner, J. M. Nakano, T. A. Bertuch, A. Vlachos, A. Lipton, J. M. Castillo, P. Connelly, J. Churpek, J. Edwards, J. R. Hijiya, N. Ho, R. H. Hofmann, I. Huang, J. N. Keel, S. Lamble, A. Lau, B. W. Norkin, M. Stieglitz, E. Stock, W. Walkovich, K. Boettcher, S. Brendel, C. Fleming, M. D. Davies, S. M. Weller, E. A. Bahl, C. Carter, S. L. Shimamura, A. Lindsley, R. C. 2020-06-05 doi:10.1101/2020.06.04.134692 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Donor-derived mitochondrial DNA variant peptides elicit allo-specific immune response in transplant patients ]]> https://biorxiv.org/content/10.1101/2020.06.04.134965v1?rss=1 Marishta, A. Yang, Y. Hu, X. Jang, M. K. Cuttin, K. Jackson, A. M. Luikart, H. Deuse, T. Khush, K. K. Schrepfer, S. Agbor-Enoh, S. Valantine, H. 2020-06-05 doi:10.1101/2020.06.04.134965 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Satellite repeat transcripts modulate heterochromatin condensates and safeguard chromosome stability in mouse embryonic stem cells ]]> https://biorxiv.org/content/10.1101/2020.06.08.139642v1?rss=1 Novo, C. L. Wong, E. Hockings, C. Poudel, C. Sheekey, E. Walker, S. Kaminski Schierle, G. S. Narlikar, G. Rugg-Gunn, P. 2020-06-08 doi:10.1101/2020.06.08.139642 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ Identification of compounds producing non-visual photosensation via TrpA1 in zebrafish ]]> https://biorxiv.org/content/10.1101/2020.06.10.111203v1?rss=1 Cheng, D. McCarroll, M. Taylor, J. Wu, T. S. KOKEL, D. 2020-06-10 doi:10.1101/2020.06.10.111203 Cold Spring Harbor Laboratory Press 2020-06-10 <![CDATA[ Sentinel p16INK4a+ cells in the basement membrane form a reparative niche in the lung ]]> https://biorxiv.org/content/10.1101/2020.06.10.142893v1?rss=1 Reyes de Mochel, N. Cheong, K. N. Cassandras, M. Wang, C. Krasilnikov, M. Matatia, P. Molofsky, A. Campisi, J. PENG, T. 2020-06-10 doi:10.1101/2020.06.10.142893 Cold Spring Harbor Laboratory Press 2020-06-10 <![CDATA[ Mobile element warfare via CRISPR and anti-CRISPR in Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2020.06.15.151498v1?rss=1 Leon, L. M. Park, A. E. Borges, A. L. Zhang, J. Bondy-Denomy, J. 2020-06-15 doi:10.1101/2020.06.15.151498 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Pain and itch processing by subpopulations of molecularly diverse spinal and trigeminal projection neurons ]]> https://biorxiv.org/content/10.1101/2020.06.17.156091v1?rss=1 Wercberger, R. Braz, J. M. Weinrich, J. A. Basbaum, A. I. 2020-06-19 doi:10.1101/2020.06.17.156091 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Reward processing electrophysiology in schizophrenia: Effects of age and illness phase ]]> https://biorxiv.org/content/10.1101/2020.06.18.158469v1?rss=1 Abram, S. V. Roach, B. Holroyd, C. B. Paulus, M. Ford, J. Mathalon, D. H. Fryer, S. L. 2020-06-20 doi:10.1101/2020.06.18.158469 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Human Prostate Cancer-Associated Macrophage Subtypes with Prognostic Potential Revealed by Single-cell Transcriptomics ]]> https://biorxiv.org/content/10.1101/2020.06.19.160770v1?rss=1 Siefert, J. C. Cioni, B. Muraro, M. J. Alshalalfa, M. Vivie, J. van der Poel, H. Feng, F. Y. Wessels, L. Zwart, W. Bergman, A. M. 2020-06-20 doi:10.1101/2020.06.19.160770 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Female reproductive tract has low concentration of SARS-CoV2 receptors ]]> https://biorxiv.org/content/10.1101/2020.06.20.163097v1?rss=1 Goad, J. Rudolph, J. Rajkovic, A. 2020-06-22 doi:10.1101/2020.06.20.163097 Cold Spring Harbor Laboratory Press 2020-06-22 <![CDATA[ Increased baseline RASGRP1 signals Enhance Stem Cell Fitness during Native Hematopoiesis ]]> https://biorxiv.org/content/10.1101/2020.06.24.169631v1?rss=1 Karra, L. Romero-Moya, D. Ksionda, O. Krush, M. Gu, Z. Mues, M. Depeille, P. Mullighan, C. Roose, J. 2020-06-25 doi:10.1101/2020.06.24.169631 Cold Spring Harbor Laboratory Press 2020-06-25 <![CDATA[ Recording of DNA binding events during gut commensalism reveals the action of a repurposed Candida albicans regulatory network ]]> https://biorxiv.org/content/10.1101/2020.06.24.169920v1?rss=1 Witchley, J. N. Brimacombe, C. A. Abon, N. A. Noble, S. 2020-06-24 doi:10.1101/2020.06.24.169920 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Non-canonical activation of the ER stress sensor ATF6 by Legionella pneumophila effectors ]]> https://biorxiv.org/content/10.1101/2020.06.26.174185v1?rss=1 Ibe, N. U. Mukherjee, S. 2020-06-27 doi:10.1101/2020.06.26.174185 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Phosphorylation modulates liquid-liquid phase separation of the SARS-CoV-2 N protein ]]> https://biorxiv.org/content/10.1101/2020.06.28.176248v1?rss=1 Carlson, C. R. Asfaha, J. B. Ghent, C. M. Howard, C. J. Hartooni, N. Morgan, D. O. 2020-06-29 doi:10.1101/2020.06.28.176248 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ The deubiquitinase Usp9x regulates PRC2-mediated chromatin reprogramming during mouse development ]]> https://biorxiv.org/content/10.1101/2020.06.28.176412v1?rss=1 Macrae, T. A. Ramalho-Santos, M. 2020-06-29 doi:10.1101/2020.06.28.176412 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Discovery of a Cellular Mechanism Regulating Transcriptional Noise ]]> https://biorxiv.org/content/10.1101/2020.06.29.128439v1?rss=1 Desai, R. Hansen, M. M. K. Martin, B. Yu, C. Ding, S. Thomson, M. Weinberger, L. S. 2020-06-30 doi:10.1101/2020.06.29.128439 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ High-content Imaging-based Pooled CRISPR Screens in Mammalian Cells ]]> https://biorxiv.org/content/10.1101/2020.06.30.179648v1?rss=1 Yan, X. Stuurman, N. Ribeiro, S. A. Tanenbaum, M. E. Horlbeck, M. A. Liem, C. R. Jost, M. Weissman, J. S. Vale, R. 2020-07-01 doi:10.1101/2020.06.30.179648 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Biomolecular condensates amplify mRNA decapping by coupling protein interactions with conformational changes in Dcp1/Dcp2 ]]> https://biorxiv.org/content/10.1101/2020.07.09.195057v1?rss=1 Ryan W Tibble Anaïs Depaix Joanna Kowalska Jacek Jemielity John D Gross 2020-07-09 doi:10.1101/2020.07.09.195057 Cold Spring Harbor Laboratory Press 2020-07-09 <![CDATA[ A Transcriptional Switch Governing Fibroblast Plasticity Underlies Reversibility of Chronic Heart Disease ]]> https://biorxiv.org/content/10.1101/2020.07.21.214874v1?rss=1 Alexanian, M. Przytycki, P. F. Micheletti, R. Padmanabhan, A. Ye, L. Travers, J. G. Gonzalez Teran, B. Duan, Q. Ranade, S. S. Felix, F. Linares-Saldana, R. Huang, Y. Andreoletti, G. Yang, J. Ivey, K. N. Jain, R. McKinsey, T. A. Rosenfeld, M. G. Gifford, C. Pollard, K. S. Haldar, S. M. Srivastava, D. 2020-07-22 doi:10.1101/2020.07.21.214874 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Ventral Tegmental Area GABA, glutamate, and glutamate-GABA neurons are heterogenous in their electrophysiological and pharmacological properties ]]> https://biorxiv.org/content/10.1101/2020.07.22.216093v1?rss=1 Miranda-Barrientos, J. A. Chambers, I. Mongia, S. Liu, B. Wang, H.-L. Mateo-Semidey, G. E. Margolis, E. B. Zhang, S. Morales, M. 2020-07-23 doi:10.1101/2020.07.22.216093 Cold Spring Harbor Laboratory Press 2020-07-23 <![CDATA[ T cell subset-selective IL2RA enhancers shape autoimmune diabetes risk ]]> https://biorxiv.org/content/10.1101/2020.07.22.216564v1?rss=1 Simeonov, D. R. Wong, H. S. Cortez, J. T. Young, A. Li, Z. Nguyen, V. Park, K. Umhoefer, J. Indart, A. C. Woo, J. M. Anderson, M. S. Germain, R. N. Marson, A. 2020-07-22 doi:10.1101/2020.07.22.216564 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Machine intelligence identifies soluble TNFa as a therapeutic target for spinal cord injury ]]> https://biorxiv.org/content/10.1101/2020.07.22.216572v1?rss=1 Huie, J. R. Ferguson, A. R. Kyritsis, N. Pan, J. Irvine, K.-A. Nielson, J. L. Schupp, P. Oldham, M. C. Gensel, J. C. Lin, A. Segal, M. R. Ratan, R. Bresnahan, J. C. Beattie, M. 2020-07-24 doi:10.1101/2020.07.22.216572 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ An atlas of lamina-associated chromatin across thirteen human cell types reveals cell-type-specific and multiple subtypes of peripheral heterochromatin ]]> https://biorxiv.org/content/10.1101/2020.07.23.218768v1?rss=1 Keough, K. C. Shah, P. P. Wickramasinghe, N. M. Dundes, C. E. Chen, A. Salomon, R. E. A. Whalen, S. Loh, K. M. Dubois, N. Pollard, K. S. Jain, R. 2020-07-24 doi:10.1101/2020.07.23.218768 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Cell-free DNA as a biomarker for prostate cancer: elevated concentration and decreased fragment size ]]> https://biorxiv.org/content/10.1101/2020.07.26.215020v1?rss=1 Chen, E. Cario, C. L. Leong, L. Lopez, K. Marquez, C. Chu, C. Li, P. S. Oropeza, E. Tenggara, I. Cowan, J. Simko, J. P. Chan, J. M. Friedlander, T. Wyatt, A. W. Aggarwal, R. Paris, P. L. Carroll, P. R. Feng, F. Witte, J. S. 2020-07-26 doi:10.1101/2020.07.26.215020 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ Automatic segmentation of dentate nuclei for microstructure assessment: example of application to temporal lobe epilepsy patients ]]> https://biorxiv.org/content/10.1101/2020.07.29.222430v1?rss=1 Gaviraghi, M. Giovanni Savini, G. Castellazzi, G. Palesi, F. Rolandi, N. Sacco, S. Pichiecchio, A. Mariani, V. Tartara, E. Tassi, L. Vitali, P. D'Angelo, E. Gandini Wheeler-Kingshott, C. A. M. 2020-07-30 doi:10.1101/2020.07.29.222430 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ α-Synuclein plasma membrane localization correlates with cellular phosphatidylinositol polyphosphate levels. ]]> https://biorxiv.org/content/10.1101/2020.07.31.224600v1?rss=1 Eichmann, C. Jacob, R. S. Dema, A. Mercadante, D. Selenko, P. 2020-07-31 doi:10.1101/2020.07.31.224600 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ Engineered ACE2 receptor traps potently neutralize SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.07.31.231746v1?rss=1 Glasgow, A. Glasgow, J. E. Limonta, D. Solomon, P. Lui, I. Zhang, Y. Nix, M. A. Rettko, N. J. Lim, S. A. Zha, S. Yamin, R. Kao, K. Rosenberg, O. S. Ravetch, J. V. Wiita, A. P. Leung, K. K. Zhou, X. X. Hobman, T. C. Kortemme, T. K. Wells, J. A. 2020-08-01 doi:10.1101/2020.07.31.231746 Cold Spring Harbor Laboratory Press 2020-08-01 <![CDATA[ Developing Cyclic Peptomers as Broad-Spectrum Gram negative Bacterial Type III Secretion System Inhibitors ]]> https://biorxiv.org/content/10.1101/2020.08.03.235622v1?rss=1 Lam, H. Lau, T. Lentz, A. Sherry, J. Cabrera-Cortez, A. Hug, K. Engel, J. Lokey, S. Auerbach Stone, V. 2020-08-04 doi:10.1101/2020.08.03.235622 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Peptide Antidotes to SARS-CoV-2 (COVID-19) ]]> https://biorxiv.org/content/10.1101/2020.08.06.238915v1?rss=1 Watson, A. Ferreira, L. M. R. Hwang, P. Xu, J. Stroud, R. 2020-08-06 doi:10.1101/2020.08.06.238915 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ Robust Estimation of Noise for Electromagnetic Brain Imaging with the Champagne Algorithm ]]> https://biorxiv.org/content/10.1101/2020.08.07.241943v1?rss=1 Cai, C. Diwakar, M. Hashemi, A. Haufe, S. Sekihara, K. Nagarajan, S. 2020-08-07 doi:10.1101/2020.08.07.241943 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ An ultra-high affinity synthetic nanobody blocks SARS-CoV-2 infection by locking Spike into an inactive conformation ]]> https://biorxiv.org/content/10.1101/2020.08.08.238469v1?rss=1 Schoof, M. Faust, B. Saunders, R. A. Sangwan, S. Rezelj, V. V. Hoppe, N. Boone, M. Billesboelle, C. Zimanyi, M. Deshpande, I. Liang, J. Anand, A. A. Dobzinski, N. Zha, B. S. Barsi-Rhyne, B. Bleyy, V. Barile-Hill, A. W. Gupta, S. Simoneau, C. R. Leon, K. White, K. M. Nock, S. Liu, Y. Krogan, N. J. Ralston, C. Y. Swaney, D. L. Garcia-Sastre, A. Ott, M. Vignuzzi, M. Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, Walter, P. Manglik, A. 2020-08-10 doi:10.1101/2020.08.08.238469 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Durable Control of HIV-1 Using a Staphylococcus aureus Cas9-Expressing Lentivirus Co-Targeting Viral Latency and Host Susceptibility ]]> https://biorxiv.org/content/10.1101/2020.08.10.243329v1?rss=1 Chavez, L. R. Reddy, N. R. Raymond, K. A. Bouzidi, M. S. Desai, S. Dossani, Z. Y. Sperber, H. S. Theiler, J. Korber, B. Pillai, S. K. 2020-08-10 doi:10.1101/2020.08.10.243329 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Regulated delivery controls Drosophila Hedgehog, Wingless and Decapentaplegic signaling ]]> https://biorxiv.org/content/10.1101/2020.08.12.247759v1?rss=1 Kornberg, T. B. Hatori, R. 2020-08-13 doi:10.1101/2020.08.12.247759 Cold Spring Harbor Laboratory Press 2020-08-13 <![CDATA[ Systematic evaluation of genome sequencing as a first-tier diagnostic test for prenatal and pediatric disorders ]]> https://biorxiv.org/content/10.1101/2020.08.12.248526v1?rss=1 Lowther, C. Valkanas, E. Giordano, J. L. Wang, H. Z. Currall, B. B. O'Keefe, K. Collins, R. L. Zhao, X. Austin-Tse, C. A. Evangelista, E. Aggarwal, V. Lucente, D. Gauthier, L. D. Tolonen, C. Sahakian, N. An, J.-Y. Dong, S. Norton, M. E. MacKenzie, T. Devlin, B. Gilmore, K. Powell, B. Brandt, A. Vetrini, F. DiVito, M. Goldstein, D. B. Sanders, S. J. MacArthur, D. G. Hodge, J. C. O'Donnell-Luria, A. Rehm, H. Vora, N. Levy, B. Brand, H. Wapner, R. Talkowski, M. E. 2020-08-13 doi:10.1101/2020.08.12.248526 Cold Spring Harbor Laboratory Press 2020-08-13 <![CDATA[ The conserved ER-transmembrane protein TMEM39 coordinates with vesicular COPII to promote collagen secretion and prevent ER stress ]]> https://biorxiv.org/content/10.1101/2020.08.17.253450v1?rss=1 Zhang, Z. Luo, S. oliveirabarbosa, g. Bai, M. Kornberg, T. Ma, D. K. 2020-08-17 doi:10.1101/2020.08.17.253450 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ 4 β-hydroxycholesterol is a pro-lipogenic factor that promotes SREBP1c expression and activity through Liver X-receptor. ]]> https://biorxiv.org/content/10.1101/2020.08.20.256487v1?rss=1 Moldavski, O. Zushin, P.-J. H. Berdan, C. A. van Eijkeren, R. J. Jiang, X. Qian, M. Ory, D. S. Covey, D. F. Nomura, D. Stahl, A. Weiss, E. Zoncu, R. 2020-08-21 doi:10.1101/2020.08.20.256487 Cold Spring Harbor Laboratory Press 2020-08-21 <![CDATA[ SARS-CoV-2 infection of human iPSC-derived cardiac cells predicts novel cytopathic features in hearts of COVID-19 patients ]]> https://biorxiv.org/content/10.1101/2020.08.25.265561v1?rss=1 Perez-Bermejo, J. A. Kang, S. S. Rockwood, S. J. Simoneau, C. R. Joy, D. A. Ramadoss, G. N. Silva, A. C. Flanigan, W. R. Li, H. Nakamura, K. Whitman, J. D. Ott, M. Conklin, B. R. McDevitt, T. C. 2020-08-25 doi:10.1101/2020.08.25.265561 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Optimization and scaling of patient-derived brain organoids uncovers deep phenotypes of disease ]]> https://biorxiv.org/content/10.1101/2020.08.26.251611v1?rss=1 Shah, K. Bedi, R. Rogozhnikov, A. Ramkumar, P. Tong, Z. Rash, B. Stanton, M. Sorokin, J. Apaydin, C. Batarse, A. Bergamaschi, J. Blattner, R. Brown, S. Bosshardt, A. Castrillo, C. Dang, B. Drusinsky, S. Enriquez, L. Grayson, D. Hilliard, J. Hsu, P.-K. Johnson, C. Jones, R. Lash, A. Lee, E. Li, K. McKay, A. Mount, E. Nicola, J. Oumzil, I. Paek, J. Pascoe, D. Piepho, A. Poust, S. Quang, D. Schultz, M. Sims, J. Taylor, P. Treiman, G. Wueseke, O. Young, N. Pollen, A. A. Flanzer, D. Chao, D. Skibinski, G. Kato, S. Escola, S. 2020-08-27 doi:10.1101/2020.08.26.251611 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ DYRK2 is a ciliary kinase involved 1 in vertebrate Hedgehog signal transduction ]]> https://biorxiv.org/content/10.1101/2020.08.31.275511v1?rss=1 Morante, N. Sigg, M. A. Strauskulage, L. Raleigh, D. R. Reiter, J. F. 2020-08-31 doi:10.1101/2020.08.31.275511 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Ciliary signaling-patterned smooth muscle drives tubular elongation ]]> https://biorxiv.org/content/10.1101/2020.08.31.276295v1?rss=1 Yang, Y. Paivinen, P. Xia, C. Krup, A. L. Makela, T. P. Mostov, K. E. Reiter, J. F. 2020-09-01 doi:10.1101/2020.08.31.276295 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Biological Noise in an Organelle Size Control System ]]> https://biorxiv.org/content/10.1101/2020.08.31.276428v1?rss=1 Bauer, D. Ishikawa, H. Wemmer, K. Marshall, W. F. 2020-09-01 doi:10.1101/2020.08.31.276428 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ miR-200 deficiency promotes lung cancer metastasis by activating cancer-associated fibroblasts ]]> https://biorxiv.org/content/10.1101/2020.09.02.276550v1?rss=1 Xue, B. Chuang, C.-H. Prosser, H. M. Fuziwara, C. S. Chan, C. Sahasrabudhe, N. Kühn, M. Wu, Y. Chen, J. Biton, A. Chen, C. Wilkinson, J. E. McManus, M. T. Bradley, A. Winslow, M. M. Su, B. He, L. 2020-09-03 doi:10.1101/2020.09.02.276550 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Characterizing tissue composition through combined analysis of single-cell morphologies and transcriptional states ]]> https://biorxiv.org/content/10.1101/2020.09.05.284539v1?rss=1 Bao, F. Deng, Y. Wan, S. Wang, B. Dai, Q. Altschuler, S. Wu, L. 2020-09-05 doi:10.1101/2020.09.05.284539 Cold Spring Harbor Laboratory Press 2020-09-05 <![CDATA[ Multivariate pattern analysis of brain structure predicts functional outcome after auditory-based cognitive training interventions ]]> https://biorxiv.org/content/10.1101/2020.09.06.283481v1?rss=1 Kambeitz-Ilankovic, L. Vinogradov, S. Wenzel, J. Fisher, M. Haas, S. Betz, L. Penzel, N. Nagarajan, S. Koutsouleris, N. Subramaniam, K. 2020-09-08 doi:10.1101/2020.09.06.283481 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ Label-free imaging and classification of live P. falciparum ]]> https://biorxiv.org/content/10.1101/2020.09.08.285346v1?rss=1 Lebel, P. M. Dial, R. Vemuri, V. N. P. Garcia, V. E. DeRisi, J. Gomez-Sjoberg, R. 2020-09-09 doi:10.1101/2020.09.08.285346 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Fine-tuning of Epithelial EGFR signals Supports Coordinated Mammary Gland Development ]]> https://biorxiv.org/content/10.1101/2020.09.10.291872v1?rss=1 Samocha, A. Doh, H. Sitarama, V. Nguyen, Q. Gbenedio, O. Rudolf, J. Eckalbar, W. Barczak, A. Miao, Y. Garcia, C. Lawson, D. Werb, Z. Kessenbrock, K. Depeille, P. Roose, J. 2020-09-10 doi:10.1101/2020.09.10.291872 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Single-cell RNA sequencing of Tocilizumab-treated peripheral blood mononuclear cells as an in vitro model of inflammation ]]> https://biorxiv.org/content/10.1101/2020.09.11.281782v1?rss=1 Zarinsefat, A. Hartoularos, G. Ye, C. J. Sarwal, M. M. 2020-09-11 doi:10.1101/2020.09.11.281782 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Zika virus alters centrosome organization to suppress the innate immune response ]]> https://biorxiv.org/content/10.1101/2020.09.15.298083v1?rss=1 Kodani, A. Knopp, K. Di Lullo, E. Retallack, H. Kriegstein, A. DeRisi, J. Reiter, J. 2020-09-15 doi:10.1101/2020.09.15.298083 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ Characterisation of protease activity during SARS-CoV-2 infection identifies novel viral cleavage sites and cellular targets for drug repurposing ]]> https://biorxiv.org/content/10.1101/2020.09.16.297945v1?rss=1 Meyer, B. Chiaravalli, J. Brownridge, P. Bryne, D. P. Daly, L. A. Agou, F. Eyers, C. E. Eyers, P. A. Vignuzzi, M. Emmott, E. 2020-09-16 doi:10.1101/2020.09.16.297945 Cold Spring Harbor Laboratory Press 2020-09-16 <![CDATA[ The CD28-transmembrane domain mediates chimeric antigen receptor heterodimerization with CD28 ]]> https://biorxiv.org/content/10.1101/2020.09.18.296913v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@bcd17aorg.highwire.dtl.DTLVardef@5cbca9org.highwire.dtl.DTLVardef@660eecorg.highwire.dtl.DTLVardef@5db163_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Muller, Y. Nguyen, D. Ferreira, L. M. R. Ho, P. Raffin, C. Beltran Valencia, R. Congrave-Wilson, Z. Roth, T. Eyquem, J. Van Gool, F. Marson, A. M. R. Wells, J. A. Bluestone, J. A. Tang, Q. 2020-09-19 doi:10.1101/2020.09.18.296913 Cold Spring Harbor Laboratory Press 2020-09-19 <![CDATA[ Dscam1 promotes blood cell survival in Drosophila melanogaster through a dual role in blood cells and neurons ]]> https://biorxiv.org/content/10.1101/2020.09.26.314997v1?rss=1 Ouyang, D. Xiao, X. Mase, A. Li, G. Corcoran, S. Wang, F. Brueckner, K. 2020-09-26 doi:10.1101/2020.09.26.314997 Cold Spring Harbor Laboratory Press 2020-09-26 <![CDATA[ Direct observation of genome surveillance by CRISPR-Cas in bacteria ]]> https://biorxiv.org/content/10.1101/2020.09.29.318501v1?rss=1 Bondy-Denomy, J. Borges, A. Govindarajan, S. 2020-09-29 doi:10.1101/2020.09.29.318501 Cold Spring Harbor Laboratory Press 2020-09-29 <![CDATA[ Early growth response 2 (EGR2) is a novel regulator of the senescence program ]]> https://biorxiv.org/content/10.1101/2020.09.30.321190v1?rss=1 Tyler, E. J. Gutierrez Del Arroyo, A. Wallis, R. Hughes, B. K. Garbe, J. C. Stampfer, M. R. Koh, J. Lowe, R. Philpott, M. P. Bishop, C. L. 2020-10-01 doi:10.1101/2020.09.30.321190 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ South Asian patient population genetics reveal strong founder effects and high rates of homozygosity - new resources for precision medicine ]]> https://biorxiv.org/content/10.1101/2020.10.02.323238v1?rss=1 Wall, J. Sathirapongsasuti, J. F. Gupta, R. Barik, A. Rai, R. K. Rasheed, A. Radha, V. Belsare, S. Menon, R. Phalke, S. Mittal, A. Fang, J. Tanneeru, D. Robinson, J. Chaudhary, R. Fuchsberger, C. Forer, L. Schoenherr, S. Bei, Q. Bhangale, T. Tom, J. Gadde, S. G. K. V, P. B. Naik, N. K. Wang, M. Kwok, P.-Y. Khera, A. V. Lakshmi, B. R. Butterworth, A. Danesh, J. Seshagiri, S. Kathiresan, S. Ghosh, A. Mohan, V. Chowdhury, A. Saleheen, D. Stawiski, E. Peterson, A. S. 2020-10-02 doi:10.1101/2020.10.02.323238 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Role for the Na+/K+ ATPase α 3 subunit in folding and lamination of the human neocortex ]]> https://biorxiv.org/content/10.1101/2020.10.03.319137v1?rss=1 Smith, R. S. Florio, M. Akula, S. Neil, J. Wang, Y. Hill, R. S. Goldman, M. Mullally, C. Reed, N. Bello-Espinosa, L. Sarnat, L. F. Monteiro, F. Erasmo, C. Pinto e Vairo, F. Morava, E. Barkovich, A. J. Gonzalez-Heydrich, J. Brownstein, C. McCarroll, S. Walsh, C. A. 2020-10-04 doi:10.1101/2020.10.03.319137 Cold Spring Harbor Laboratory Press 2020-10-04 <![CDATA[ De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families ]]> https://biorxiv.org/content/10.1101/2020.10.06.329011v1?rss=1 Belyeu, J. R. Brand, H. Wang, H. Zhao, X. Pedersen, B. S. Feusier, J. Gupta, M. Nicholas, T. J. Baird, L. Devlin, B. Sanders, S. J. Jorde, L. B. Talkowski, M. E. Quinlan, A. R. 2020-10-08 doi:10.1101/2020.10.06.329011 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Tractography dissection variability: what happens when 42 groups dissect 14 white matter bundles on the same dataset? ]]> https://biorxiv.org/content/10.1101/2020.10.07.321083v1?rss=1 Schilling, K. G. Rheault, F. Petit, L. Hansen, C. B. Nath, V. Yeh, F.-C. Girard, G. Barakovic, M. Rafael-Patino, J. Yu, T. Fischi-Gomez, E. Pizzolato, M. Ocampo-Pineda, M. Schiavi, S. Canales-Rodriguez, E. J. Daducci, A. Granziera, C. Innocenti, G. Thiran, J.-P. Mancini, L. Wastling, S. Cocozza, S. Petracca, M. Pontillo, G. Mancini, M. Vos, S. B. Vakharia, V. N. Duncan, J. S. Melero, H. Manzanedo, L. Sanz-Morales, E. Pena-Melian, A. Calamante, F. Attye, A. Cabeen, R. P. Korobova, L. Toga, A. W. Ambili Vijayakumari, A. Parker, D. Verma, R. Radwan, A. Sun 2020-10-08 doi:10.1101/2020.10.07.321083 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Neural dynamics of semantic categorization in semantic variant of Primary Progressive Aphasia. ]]> https://biorxiv.org/content/10.1101/2020.10.07.329698v1?rss=1 Borghesani, V. Dale, C. L. Lukic, S. Hinkley, L. B. N. Lauricella, M. Shwe, W. Miziuri, D. Honma, S. Miller, Z. Miller, B. L. Houde, J. Gorno-Tempini, M. L. Nagarajan, S. 2020-10-09 doi:10.1101/2020.10.07.329698 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Cytonemes with complex geometries and composition extend into invaginations of target cells ]]> https://biorxiv.org/content/10.1101/2020.10.09.332676v1?rss=1 Kornberg, T. B. Wood, B. Baena, V. Huang, H. Terasaki, M. 2020-10-09 doi:10.1101/2020.10.09.332676 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ CoRa -A general approach for quantifying biological feedback control ]]> https://biorxiv.org/content/10.1101/2020.10.09.334078v1?rss=1 Gomez-Schiavon, M. El-Samad, H. 2020-10-10 doi:10.1101/2020.10.09.334078 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ Single cell transcriptome analysis defines novel heterogeneity within the pancreatic ductal tree ]]> https://biorxiv.org/content/10.1101/2020.10.12.336784v1?rss=1 Hendley, A. M. Rao, A. A. Leonhardt, L. Ashe, S. Smith, J. A. Giacometti, S. Peng, X. L. Jiang, H. Berrios, D. Pawlak, M. Li, L. Y. Lee, J. Collisson, E. A. Anderson, M. Fragiadakis, G. K. Yeh, J. J. Chun, J. Y. Kim, G. E. Weaver, V. M. Hebrok, M. 2020-10-12 doi:10.1101/2020.10.12.336784 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ On the role of photoreceptor identity in controlling accurate wiring of the Drosophila visual circuit ]]> https://biorxiv.org/content/10.1101/2020.10.13.337865v1?rss=1 Altschuler, S. J. Ji, W. Wu, L. F. 2020-10-13 doi:10.1101/2020.10.13.337865 Cold Spring Harbor Laboratory Press 2020-10-13 <![CDATA[ PTBP1 Regulates Injury Responses and Sensory Pathways in Adult Peripheral Neurons ]]> https://biorxiv.org/content/10.1101/2020.10.22.348631v1?rss=1 Alber, S. Di-Matteo, P. Zdradzinski, M. D. Marvaldi, L. Kawaguchi, R. Medzihradszky, K. F. Doron-Mandel, E. Okladnikov, N. Rishal, I. Nevo, R. Lee, S. J. Sahoo, P. K. Burlingame, A. L. Coppola, G. Twiss, J. L. Fainzilber, M. 2020-10-22 doi:10.1101/2020.10.22.348631 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19 ]]> https://biorxiv.org/content/10.1101/2020.10.23.352666v1?rss=1 Le, B. L. Andreoletti, G. Oskotsky, T. Vallejo-Gracia, A. Rosales, R. Yu, K. Z. Kosti, I. Leon, K. E. Bunis, D. G. Li, C. Kumar, G. R. White, K. M. Garcia-Sastre, A. E. Ott, M. Sirota, M. 2020-10-23 doi:10.1101/2020.10.23.352666 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ Cytoplasm Biophysical Properties Madolute Microtubule Dynamics ]]> https://biorxiv.org/content/10.1101/2020.10.27.352716v1?rss=1 Molines, A. T. Lemiere, J. Edrington, C. H. Hsu, C.-T. Steinmark, I. E. Suhling, K. Goshima, G. Holt, L. J. Brouhard, G. Chang, F. T. 2020-10-28 doi:10.1101/2020.10.27.352716 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Ethacridine inhibits SARS-CoV-2 by inactivating viral particles in cellular models ]]> https://biorxiv.org/content/10.1101/2020.10.28.359042v1?rss=1 Li, X. Lidsky, P. Xiao, Y. Wu, C.-T. Garcia-Knight, M. Yang, J. Nakayama, T. Nayak, J. V. Jackson, P. K. Andino, R. Shu, X. 2020-10-28 doi:10.1101/2020.10.28.359042 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Global Absence and Targeting of Protective Immune States in Severe COVID-19. ]]> https://biorxiv.org/content/10.1101/2020.10.28.359935v1?rss=1 Combes, A. J. Courau, T. Kuhn, N. F. Hu, K. H. Ray, A. Chen, W. S. Clearly, S. J. Chew, N. W. Kushnoor, D. Reeder, G. C. Shen, A. Tsui, J. Hiam-Galvez, K. J. Munoz-Sandoval, P. Zhu, W. S. Lee, D. S. Sun, Y. You, R. Magnen, M. Rodriguez, L. Leligdowicz, A. Zamecnik, C. R. Loudermilk, R. P. Wilson, M. R. Ye, C. J. Fragiadakis, G. K. Looney, M. R. Chan, V. Ward, A. Carrillo, S. Matthay, M. Erle, D. J. Woodruff, P. G. Langelier, C. Kangelaris, K. Hendrickson, C. M. Calfee, C. Rao, A. A. Krummel, M. F. 2020-10-29 doi:10.1101/2020.10.28.359935 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ Ethnicity-specific transcriptomic variation in immune cells and correlation with disease activity in systemic lupus erythematosus ]]> https://biorxiv.org/content/10.1101/2020.10.30.362715v1?rss=1 =6) and White-low, Asians-low (SLEDAI < 6). Random forest classification of disease activity in the White and Asian cohorts showed the best classification in CD4+ T cells in White. The results from these analyses will help stratify patients based on their gene expression signatures to enable precision medicine for SLE. ]]> Andreoletti, G. Lanata, C. M. Paranjpe, I. Jain, T. S. Nititham, J. Taylor, K. E. Combes, A. J. Maliskova, L. Jimmie Ye, C. Katz, P. Dall Era, M. Yazdany, J. Criswell, L. A. Sirota, M. 2020-11-01 doi:10.1101/2020.10.30.362715 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ Transcriptional Network Orchestrating Regional Patterning of Cortical Progenitors ]]> https://biorxiv.org/content/10.1101/2020.11.03.366914v1?rss=1 Ypsilanti, A. R. Pattabiraman, K. Catta-Preta, R. Golonzhka, O. Lindtner, S. Tang, K. Jones, I. Abnousi, A. Juric, I. Hu, M. Shen, Y. Dickel, D. E. Visel, A. Pennachio, L. A. Hawrylycz, M. Thompson, C. Zeng, H. Barozzi, I. Nord, A. S. Rubenstein, J. L. R. 2020-11-04 doi:10.1101/2020.11.03.366914 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ Activating Immune Recognition in Pancreatic Ductal Adenocarcinoma Using Autophagy Inhibition, MEK blockade and CD40 Agonism ]]> https://biorxiv.org/content/10.1101/2020.11.05.370569v1?rss=1 Jiang, H. Courau, T. Lupin-Jimenez, L. Borison, J. Ritchie, A. J. Mayer, A. T. Krummel, M. F. Collisson, E. A. 2020-11-06 doi:10.1101/2020.11.05.370569 Cold Spring Harbor Laboratory Press 2020-11-06 <![CDATA[ TSC1 loss-of-function increases risk for tauopathy by inducing tau acetylation and preventing autophagy-mediated tau clearance ]]> https://biorxiv.org/content/10.1101/2020.11.08.371922v1?rss=1 Alquezar, C. Schoch, K. M. Geier, E. G. Ramos, E. M. Scrivo, A. Li, K. Argouarch, A. R. Mlynarski, E. E. Dombroski, B. Yokoyama, J. S. Cuervo, A. M. Burlingame, A. L. Schellenberg, G. D. Miller, T. M. Miller, B. L. Kao, A. W. 2020-11-08 doi:10.1101/2020.11.08.371922 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ The primary cilium is required for MC4R control of food intake and body weight ]]> https://biorxiv.org/content/10.1101/2020.11.13.382234v1?rss=1 Wang, Y. Bernard, A. A. Comblain, F. Yue, X. Paillart, C. Zhang, S. Reiter, J. Vaisse, C. 2020-11-15 doi:10.1101/2020.11.13.382234 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ The single pass membrane protein MRAP2 regulates energy homeostasis by promoting primary cilia localization of the G protein-coupled receptor MC4R ]]> https://biorxiv.org/content/10.1101/2020.11.13.382325v1?rss=1 Bernard, A. A. Ojeda Naharros, I. Bourgain-Guglielmetti, F. Ciprin, J. Yue, X. Zhang, S. McDaid, E. Nachury, M. V. Reiter, J. Vaisse, C. 2020-11-15 doi:10.1101/2020.11.13.382325 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ Functional microstructure of CaV-mediated calcium signaling in the axon initial segment ]]> https://biorxiv.org/content/10.1101/2020.11.13.382374v1?rss=1 Lipkin, A. M. Cunniff, M. M. Spratt, P. W. Lemke, S. M. Bender, K. J. 2020-11-13 doi:10.1101/2020.11.13.382374 Cold Spring Harbor Laboratory Press 2020-11-13 <![CDATA[ GABAergic signaling promotes early-life seizures in epileptic SYNGAP1+/- mice ]]> https://biorxiv.org/content/10.1101/2020.11.14.381749v1?rss=1 Sullivan, B. J. Kipnis, P. A. Ammanuel, S. G. Kadam, S. D. 2020-11-15 doi:10.1101/2020.11.14.381749 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ ATP hydrolysis coordinates the activities of two motors in a dimeric chromatin remodeling enzyme ]]> https://biorxiv.org/content/10.1101/2020.11.17.387662v1?rss=1 Johnson, S. L. Narlikar, G. 2020-11-18 doi:10.1101/2020.11.17.387662 Cold Spring Harbor Laboratory Press 2020-11-18 <![CDATA[ Regulation of Dopamine D1 Receptor Signaling at the Golgi Apparatus by a Low Affinity Dopamine Transporter ]]> https://biorxiv.org/content/10.1101/2020.11.23.394445v1?rss=1 Puri, N. M. Romano, G. R. Mai, Q. N. Irannejad, R. 2020-11-23 doi:10.1101/2020.11.23.394445 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ Sleep is required for odor exposure to consolidate memory and remodel olfactory synapses. ]]> https://biorxiv.org/content/10.1101/2020.11.24.395228v1?rss=1 Munoz-Lobato, F. Benedetti, K. L. Farah, F. Chandra, R. Bokka, A. Brueggemann, C. Saifuddin, F. M. Nordquist, S. K. Li, J. Chang, E. Varshney, A. Jiminez, V. Andersen, K. E. Baradwaj, A. Miller, J. M. Dunn, R. L. Tsujimoto, B. Duong, A. Tran, A. Churgin, M. Fang-Yen, C. Bremer, M. Kato, S. VanHoven, M. L'Etoile, N. 2020-11-25 doi:10.1101/2020.11.24.395228 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ THE TRPV CHANNEL OSM-9 MEDIATES OLFACTORY LONG- TERM MEMORY CONSOLIDATION INDEPENDENT OF SLEEP ]]> https://biorxiv.org/content/10.1101/2020.11.27.400747v1?rss=1 Benedetti, K. L. Chen, A. L'Etoile, N. 2020-11-29 doi:10.1101/2020.11.27.400747 Cold Spring Harbor Laboratory Press 2020-11-29 <![CDATA[ Lyophilized yeast powder for adjuvant free thermostable vaccine delivery ]]> https://biorxiv.org/content/10.1101/2020.11.30.401885v1?rss=1 Kumar, R. Kharbikar, B. N. Desai, T. A. 2020-12-01 doi:10.1101/2020.11.30.401885 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Zika Virus Infection Prevents Host mRNA Nuclear Export by Disrupting UPF1 Function ]]> https://biorxiv.org/content/10.1101/2020.12.03.410837v1?rss=1 Leon, K. E. Flynn, R. E. Khalid, M. M. Fontaine, K. A. Nguyen, T. Kumar, R. Simoneau, C. R. Tomar, S. Jimenez-Morales, D. Dunlap, M. Kaye, J. A. Shah, P. S. Finkbeiner, S. Krogan, N. J. Bertozzi, C. Carette, J. E. Ott, M. 2020-12-04 doi:10.1101/2020.12.03.410837 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ Starvation induces shrinkage of the bacterial cytoplasm ]]> https://biorxiv.org/content/10.1101/2020.12.06.413849v1?rss=1 Shi, H. Westfall, C. S. Kao, J. Odermatt, P. D. Cesar, S. Sievert, M. Moore, J. Gonzalez, C. G. Zhang, L. Elias, J. E. Chang, F. Huang, K. C. Levin, P. A. 2020-12-07 doi:10.1101/2020.12.06.413849 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ Deep Linear Modeling of Hierarchical Functional Connectivity in the Human Brain ]]> https://biorxiv.org/content/10.1101/2020.12.13.422538v1?rss=1 Zhang, W. Palacios, E. M. Mukherjee, P. 2020-12-15 doi:10.1101/2020.12.13.422538 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ How inhibitory neurons increase information transmission under threshold modulation ]]> https://biorxiv.org/content/10.1101/2020.12.13.422611v1?rss=1 Hsu, W.-M. M. Kastner, D. B. Baccus, S. A. Sharpee, T. O. 2020-12-15 doi:10.1101/2020.12.13.422611 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Juvenile exposure to acute traumatic stress leads to long-lasting alterations in grey matter myelination in adult female but not male rats ]]> https://biorxiv.org/content/10.1101/2020.12.14.422686v1?rss=1 Breton, J. M. Barraza, M. Hu, K. Y. Frias, S. J. Long, K. L. P. Kaufer, D. 2020-12-15 doi:10.1101/2020.12.14.422686 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Cyclic gallium-68 labeled peptides for specific detection of human angiotensin-converting enzyme 2 ]]> https://biorxiv.org/content/10.1101/2020.12.15.412809v1?rss=1 View larger version (18K): org.highwire.dtl.DTLVardef@f3047org.highwire.dtl.DTLVardef@12ab9a9org.highwire.dtl.DTLVardef@33f43org.highwire.dtl.DTLVardef@12e77ed_HPS_FORMAT_FIGEXP M_FIG For Table of Contents use only C_FIG ]]> Parker, M. Blecha, J. Rosenberg, O. Ohliger, M. Flavell, R. Wilson, D. M. 2020-12-16 doi:10.1101/2020.12.15.412809 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ Microbiome and Metabolome driven differentiation of TGF-β producing Tregs leads to Senescence and HIV latency ]]> https://biorxiv.org/content/10.1101/2020.12.15.422949v1?rss=1 Sekaly, R.-P. Ghneim, K. Sharma, A. A. Ribeiro, S. P. Fourati, S. Ahlers, J. Kulpa, D. Xu, X. Brehm, J. Talla, A. Arumugam, S. Darko, S. Rodriguez, B. Shive, C. Cristescu, R. Loboda, A. Balderas, R. Wang, I.-m. Hunt, P. Lamarre, D. Douek, D. Hazuda, D. Lederman, M. Deeks, S. 2020-12-15 doi:10.1101/2020.12.15.422949 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Broad transcriptomic dysregulation across the cerebral cortex in ASD ]]> https://biorxiv.org/content/10.1101/2020.12.17.423129v1?rss=1 Haney, J. R. Wamsley, B. Chen, G. T. Parhami, S. Emani, P. S. Chang, N. Hoftman, G. D. de Alba, D. Kale, G. Ramaswami, G. Hartl, C. L. Jin, T. Wang, D. Ou, J. Wu, Y. E. Parikshak, N. N. Swarup, V. Belgard, T. G. Gerstein, M. Pasaniuc, B. Gandal, M. J. Geschwind, D. H. 2020-12-18 doi:10.1101/2020.12.17.423129 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ Interneuron origins in the embryonic porcine medial ganglionic eminence ]]> https://biorxiv.org/content/10.1101/2020.12.18.423526v1?rss=1 Casalia, M. L. Li, T. Ramsay, H. ROSS, P. J. Paredes, M. F. Baraban, S. C. 2020-12-21 doi:10.1101/2020.12.18.423526 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ CTCF is a Barrier for Totipotent-like Reprogramming ]]> https://biorxiv.org/content/10.1101/2020.12.20.423692v1?rss=1 Olbrich, T. Vega-Sendino, M. Tillo, D. Wu, W. Zolnerowich, N. Tran, A. D. Domingo, C. N. Franco, M. Markiewicz Potoczny, M. Pegoraro, G. Fitzgerald, P. Kruhlak, M. Lazzerini, E. Nora, E. Nussenzweig, A. Ruiz Macias, S. 2020-12-22 doi:10.1101/2020.12.20.423692 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Multicohort Analysis of Publicly-available Monocyte Expression Data Identifies Gene Signatures to Accurately Monitor Subset-specific Changes in Human Diseases ]]> https://biorxiv.org/content/10.1101/2020.12.21.423397v1?rss=1 Vallania, F. Zisman, L. Macaubas, C. Hung, S.-C. Rajasekaran, N. Mason, S. Graf, J. Nakamura, M. Mellins, E. Khatri, P. 2020-12-22 doi:10.1101/2020.12.21.423397 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ CRISPR-based functional genomics in human dendritic cells ]]> https://biorxiv.org/content/10.1101/2020.12.22.423985v1?rss=1 93% across >300 genes. Using this method, we perform genetic screens in moDCs, identifying mechanisms by which DCs tune responses to lipopolysaccharides from the human microbiome. In addition, we reveal donor-specific responses to lipopolysaccharides, underscoring the importance of assessing immune phenotypes in donor-derived cells, and identify genes that control this specificity, highlighting the potential of our method to pinpoint determinants of inter-individual variation in immune responses. Our work sets the stage for a systematic dissection of the immune signaling at the host-microbiome interface and for targeted engineering of DCs for neoantigen vaccination. ]]> Jost, M. Jacobson, A. N. Hussmann, J. A. Cirolia, G. Fischbach, M. Weissman, J. S. 2020-12-22 doi:10.1101/2020.12.22.423985 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Elucidation of the molecular interactions that enable stable assembly and structural diversity in multicomponent immune receptors ]]> https://biorxiv.org/content/10.1101/2020.12.22.424036v1?rss=1 Fong, L.-K. Chalkely, M. J. Tan, S. K. Grabe, M. DeGrado, W. 2020-12-22 doi:10.1101/2020.12.22.424036 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Selective Targeting of Ras Mutant Cancers via a New Small Molecule ]]> https://biorxiv.org/content/10.1101/2020.12.23.423300v1?rss=1 Tolani, B. Celli, A. Yao, Y. Tan, Y. Z. Fetter, R. Liem, C. R. de Smith, A. J. Vasanthakumar, T. Bisignano, P. Seiple, I. B. Rubinstein, J. L. Jost, M. Weissman, J. S. 2020-12-23 doi:10.1101/2020.12.23.423300 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ Negative feedback by NUR77/Nr4a1 restrains B cell clonal dominance during early T-dependent immune responses ]]> https://biorxiv.org/content/10.1101/2020.12.25.424409v1?rss=1 Brooks, J. F. Tan, C. Mueller, J. L. Hibiya, K. Hiwa, R. Zikherman, J. 2020-12-26 doi:10.1101/2020.12.25.424409 Cold Spring Harbor Laboratory Press 2020-12-26 <![CDATA[ eIF2B Conformation and Assembly State Regulate the Integrated Stress Response ]]> https://biorxiv.org/content/10.1101/2020.12.28.424567v1?rss=1 Schoof, M. Boone, M. Wang, L. Lawrence, R. E. Frost, A. Walter, P. 2020-12-29 doi:10.1101/2020.12.28.424567 Cold Spring Harbor Laboratory Press 2020-12-29 <![CDATA[ Enhanced Solid Tumor Recognition and T cell Stemness with SynNotch CAR Circuits ]]> https://biorxiv.org/content/10.1101/2021.01.06.425642v1?rss=1 Hyrenius-Wittsten, A. Su, Y. Park, M. Garcia, J. M. Perry, N. Montgomery, G. Liu, B. Roybal, K. T. 2021-01-07 doi:10.1101/2021.01.06.425642 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ GC-1 spg cells are most similar to Leydig cells, a testis somatic cell-type, and not germ cells ]]> https://biorxiv.org/content/10.1101/2021.01.07.425754v1?rss=1 Norman, A. R. Byrnes, L. Reiter, J. R. 2021-01-07 doi:10.1101/2021.01.07.425754 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Caspase inhibition mitigates tau cleavage and neurotoxicity in iPSC-induced neurons with the V337M MAPT mutation ]]> https://biorxiv.org/content/10.1101/2021.01.08.425912v1?rss=1 Theofilas, P. Wang, C. Butler, D. Morales, D. O. Petersen, C. Chin, B. Yang, T. Khan, S. Ng, R. Kayed, R. Karch, C. M. Miller, B. L. Gestwicki, J. E. Gan, L. Temple, S. Arkin, M. R. Grinberg, L. T. 2021-01-09 doi:10.1101/2021.01.08.425912 Cold Spring Harbor Laboratory Press 2021-01-09 <![CDATA[ A global cancer data integrator reveals principles of synthetic lethality, sex disparity and immunotherapy. ]]> https://biorxiv.org/content/10.1101/2021.01.08.425918v1?rss=1 Yogodzinski, C. H. Arab, A. Pritchard, J. R. Goodarzi, H. Gilbert, L. 2021-01-09 doi:10.1101/2021.01.08.425918 Cold Spring Harbor Laboratory Press 2021-01-09 <![CDATA[ Experimental and mathematical insights on the interactions between poliovirus and a defective interfering genome ]]> https://biorxiv.org/content/10.1101/2021.01.11.426198v1?rss=1 Andino, R. Shirogane, Y. Rousseau, E. Voznica, J. Xiao, Y. Su, W. Catching, A. Whitfiled, Z. J. Rouzine, I. M. Bianco, S. 2021-01-11 doi:10.1101/2021.01.11.426198 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ De novo protein fold families expand the designable ligand binding site space ]]> https://biorxiv.org/content/10.1101/2021.01.13.426598v1?rss=1 Pan, X. Kortemme, T. 2021-01-15 doi:10.1101/2021.01.13.426598 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ Tropism of SARS-CoV-2 for Developing Human Cortical Astrocytes ]]> https://biorxiv.org/content/10.1101/2021.01.17.427024v1?rss=1 Andrews, M. G. Mukhtar, T. Eze, U. C. Simoneau, C. R. Perez, Y. Mostajo-Radji, M. A. Wang, S. Velmeshev, D. Salma, J. Kumar, G. R. Pollen, A. A. Crouch, E. E. Ott, M. Kriegstein, A. R. 2021-01-18 doi:10.1101/2021.01.17.427024 Cold Spring Harbor Laboratory Press 2021-01-18 <![CDATA[ Treponema denticola dentilisin triggered TLR2/MyD88 activation upregulates a tissue destructive program involving MMPs via Sp1 in human oral cells ]]> https://biorxiv.org/content/10.1101/2021.01.18.427101v1?rss=1 Ganther, S. Radaic, A. Chang, N.-Y. N. Tafolla, C. Zhan, L. Fenno, J. C. Kapila, Y. 2021-01-18 doi:10.1101/2021.01.18.427101 Cold Spring Harbor Laboratory Press 2021-01-18 <![CDATA[ Molecular programs of fibrotic change in aging human lung ]]> https://biorxiv.org/content/10.1101/2021.01.18.427195v1?rss=1 Lee, J. Islam, M. N. Boostanpour, K. Aran, D. Christenson, S. Matthay, M. A. Eckalbar, W. DePianto, D. J. Arron, J. R. Magee, L. Bhattacharya, S. Matsumoto, R. Kubota, M. Farber, D. L. Bhattacharya, J. Wolters, P. J. Bhattacharya, M. 2021-01-19 doi:10.1101/2021.01.18.427195 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Mechanotaxis directs Pseudomonas aeruginosa twitching motility. ]]> https://biorxiv.org/content/10.1101/2021.01.26.428277v1?rss=1 Tala, L. Kuhn, M. Inclan, Y. Patino, R. Pierrat, X. Vos, I. Al-Mayyah, Z. MacMillan, H. Negrete, J. Engel, J. N. Persat, A. 2021-01-26 doi:10.1101/2021.01.26.428277 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ A Human Accelerated Region is a Leydig cell GLI2 Enhancer that Affects Male-Typical Behavior ]]> https://biorxiv.org/content/10.1101/2021.01.27.428524v1?rss=1 Reiter, J. Norman, A. R. Ahituv, N. R. Ryu, A. H. Jamieson, K. Shen, Y. Pollard, K. S. Thomas, S. 2021-01-27 doi:10.1101/2021.01.27.428524 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ NR2F1 is a barrier to dissemination of early-evolved mammary cancer cells ]]> https://biorxiv.org/content/10.1101/2021.01.29.428822v1?rss=1 Rodriguez Tirado, C. A. Kale, N. Carlini, M. J. Shrivastava, N. Khalil, B. D. Bravo-Cordero, J. J. Alexander, M. Ji, J. Sosa, M. S. 2021-01-29 doi:10.1101/2021.01.29.428822 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ Cofilin pathology is a new player on α-synuclein-induced spine impairment in models of hippocampal synucleinopathy ]]> https://biorxiv.org/content/10.1101/2021.02.02.425931v1?rss=1 Oliveira da Silva, M. I. Santejo, M. Babcock, I. W. Magalhaes, A. Minamide, L. S. Castillo, E. Gerhardt, E. Fahlbusch, C. Swanson, R. A. Outeiro, T. F. Bamburg, J. R. Liz, M. A. 2021-02-02 doi:10.1101/2021.02.02.425931 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Deep Proteome Profiling of Human Mammary Epithelia at Lineage and Age Resolution ]]> https://biorxiv.org/content/10.1101/2021.02.02.429276v1?rss=1 9,000 total proteins, and >15,000 phosphopeptides, from normal primary human mammary epithelia at lineage resolution from ten women ranging in age from 19 to 68. Data were quality controlled, and results were biologically validated with cell-based assays. Age-dependent protein signatures were identified using differential expression analyses and weighted protein co-expression network analyses. Up-regulation of basal markers in luminal cells, including KRT14 and AXL, were a prominent consequence of aging. PEAK1 was identified as an age-dependent signaling kinase in luminal cells, which revealed a potential age-dependent vulnerability for targeted ablation. Correlation analyses between transcriptome and proteome revealed age-associated loss of proteostasis regulation. Protein expression and phosphorylation changes in the aging breast epithelium identify potential therapeutic targets for reducing breast cancer susceptibility. ]]> Hinz, S. Manousopoulou, A. Miyano, M. Sayaman, R. W. Aguilera, K. Y. Todhunter, M. E. Lopez, J. C. Sohn, L. L. Wang, L. D. LaBarge, M. A. 2021-02-02 doi:10.1101/2021.02.02.429276 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Paradoxical hyperexcitability from NaV1.2 sodium channel loss in neocortical pyramidal cells ]]> https://biorxiv.org/content/10.1101/2021.02.02.429423v1?rss=1 Spratt, P. W. Ben-Shalom, R. Sahagun, A. Keeshen, C. M. Sanders, S. J. Bender, K. J. 2021-02-02 doi:10.1101/2021.02.02.429423 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Integrated plasma proteomic and single-cell immune signaling network signatures demarcate mild, moderate, and severe COVID-19 ]]> https://biorxiv.org/content/10.1101/2021.02.09.430269v1?rss=1 Feyaerts, D. Hedou, J. Gillard, J. Chen, H. Tsai, E. S. Peterson, L. S. Ando, K. Manohar, M. Do, E. Dhondalay, G. K. R. Fitzpatrick, J. Artandi, M. Chang, I. Snow, T. T. Chinthrajah, R. S. Warren, C. M. Wittman, R. Meyerowitz, J. G. Ganio, E. A. Stelzer, I. A. Han, X. Verdonk, F. Gaudilliere, D. K. Mukherjee, N. Tsai, A. S. Rumer, K. K. Jiang, S. J. Valdes-Ferrer, S. I. Kelly, J. D. Furman, D. Aghaeepour, N. Angst, M. S. Boyd, S. D. Pinsky, B. A. Nolan, G. P. Nadeau, K. C. Gaudilliere, B. McIlwain, D. R. 2021-02-12 doi:10.1101/2021.02.09.430269 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ Identifying the genetic basis and molecular mechanisms underlying phenotypic correlation between complex human traits using a gene-based approach ]]> https://biorxiv.org/content/10.1101/2021.02.09.430368v1?rss=1 Gu, J. Fuller, C. K. Zheng, J. Li, H. 2021-02-10 doi:10.1101/2021.02.09.430368 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Phenotypic analysis of catastrophic childhood epilepsy genes: The Epilepsy Zebrafish Project ]]> https://biorxiv.org/content/10.1101/2021.02.11.430844v1?rss=1 Griffin, A. Carpenter, C. Liu, J. Grone, B. Hamling, K. Moog, M. Dinday, M. T. Figueroa, F. Anvar, M. Ononuju, C. Qu, T. Baraban, S. C. 2021-02-12 doi:10.1101/2021.02.11.430844 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ Multisite phosphorylation by Cdk1 initiates delayed negative feedback to control mitotic transcription ]]> https://biorxiv.org/content/10.1101/2021.02.14.431158v1?rss=1 Asfaha, J. Ord, M. Loog, M. Morgan, D. O. 2021-02-14 doi:10.1101/2021.02.14.431158 Cold Spring Harbor Laboratory Press 2021-02-14 <![CDATA[ Glioblastoma remodeling of neural circuits in the human brain decreases survival ]]> https://biorxiv.org/content/10.1101/2021.02.18.431915v1?rss=1 Krishna, S. Choudhury, A. Seo, K. Ni, L. Kakaizada, S. Lee, A. Aabedi, A. Cao, C. Sudharshan, R. Egladyous, A. Almeida, N. Venkatesh, H. Findlay, A. Nagarajan, S. Raleigh, D. Brang, D. Monje, M. Hervey-Jumper, S. 2021-02-19 doi:10.1101/2021.02.18.431915 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Microglial NF-κB drives tau spreading and toxicity in a mouse model of tauopathy ]]> https://biorxiv.org/content/10.1101/2021.02.22.432272v1?rss=1 Wang, C. Fan, L. Zhan, L. Kodama, L. Liu, B. Chin, M. Y. Li, Y. Le, D. Zhou, Y. Condello, C. Grinberg, L. T. Seeley, W. W. Miller, B. L. Mok, S.-A. Gestwicki, J. E. Gan, L. 2021-02-22 doi:10.1101/2021.02.22.432272 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ The type 2 asthma mediator IL-13 inhibits SARS-CoV-2 infection of bronchial epithelium ]]> https://biorxiv.org/content/10.1101/2021.02.25.432762v1?rss=1 1.5-fold change, FDR < 0.05). Many IL-13-regulated SARS-CoV-2-associated genes were also altered in type 2 high asthma and COPD. IL-13 pretreatment reduced viral RNA recovered from SARS-CoV-2 infected cells and decreased dsRNA, a marker of viral replication, to below the limit of detection in our assay. Mucus also inhibited viral infection. ConclusionsIL-13 markedly reduces susceptibility of HBECs to SARS-CoV-2 infection through mechanisms that likely differ from those activated by type I interferons. Our findings may help explain reports of relatively low prevalence of asthma in patients diagnosed with COVID-19 and could lead to new strategies for reducing SARS-CoV-2 infection. ]]> Bonser, L. R. Eckalbar, W. L. Rodriguez, L. Shen, J. Koh, K. D. Zlock, L. T. Christenson, S. Woodruff, P. G. Finkbeiner, W. E. Erle, D. J. 2021-02-25 doi:10.1101/2021.02.25.432762 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ A unicellular walker embodies a finite state machine ]]> https://biorxiv.org/content/10.1101/2021.02.26.433123v1?rss=1 Larson, B. T. Garbus, J. Pollack, J. B. Marshall, W. F. 2021-02-27 doi:10.1101/2021.02.26.433123 Cold Spring Harbor Laboratory Press 2021-02-27 <![CDATA[ Infusion of CCR5 Gene-Edited T Cells Allows Immune Reconstitution, HIV Reservoir Decay, and Long-Term Virological Control ]]> https://biorxiv.org/content/10.1101/2021.02.28.433290v1?rss=1 Zeidan, J. Sharma, A. A. Lee, G. Raad, A. Fromentin, R. Fourati, S. Ghneim, K. Sanchez, G. P. Benne, C. Canderan, G. Procopio, F. A. Balderas, R. Monette, G. Lalezari, J. P. Heffernan, J. M. Sabbagh, L. Chomont, N. Ando, D. Deeks, S. G. Sekaly, R.-P. 2021-03-01 doi:10.1101/2021.02.28.433290 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Ribosomal RNA methylation by GidB is a capacitor for discrimination of mischarged tRNA ]]> https://biorxiv.org/content/10.1101/2021.03.02.433644v1?rss=1 Bi, Z. Su, H. Hong, J. Javid, B. 2021-03-03 doi:10.1101/2021.03.02.433644 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ Opposing motors provide mechanical and functional robustness in the human spindle ]]> https://biorxiv.org/content/10.1101/2021.03.02.433652v1?rss=1 Neahring, L. Cho, N. H. Dumont, S. 2021-03-02 doi:10.1101/2021.03.02.433652 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[ Large-scale placenta DNA methylation mega-analysis reveals fetal sex-specific differentially methylated CpG sites and regions ]]> https://biorxiv.org/content/10.1101/2021.03.04.433985v1?rss=1 Andrews, S. V. Yang, I. J. Froehlich, K. Oskotsky, T. Sirota, M. 2021-03-05 doi:10.1101/2021.03.04.433985 Cold Spring Harbor Laboratory Press 2021-03-05 <![CDATA[ Elevated N-glycosylation of immunoglobulin G variable regions in myasthenia gravis highlights a commonality across autoantibody-associated diseases ]]> https://biorxiv.org/content/10.1101/2021.03.06.434199v1?rss=1 Mandel-Brehm, C. Fichtner, M. L. Jiang, R. Winton, V. J. Vazquez, S. E. Pham, M. C. Hoehn, K. B. Kelleher, N. L. Nowak, R. J. Kleinstein, S. H. Wilson, M. R. DeRisi, J. L. OConnor, K. C. 2021-03-08 doi:10.1101/2021.03.06.434199 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Stromal inflammation is a targetable driver of hematopoietic aging ]]> https://biorxiv.org/content/10.1101/2021.03.08.434485v1?rss=1 Verovskaya, E. V. Mitchell, C. A. Calero-Nieto, F. J. Herault, A. Dellorusso, P. D. Wang, X. Zhang, S. Y. Flohr Svendsen, A. Pietras, E. M. Bakker, S. T. Ho, T. T. Gottgens, B. Passegue, E. 2021-03-09 doi:10.1101/2021.03.08.434485 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19 ]]> https://biorxiv.org/content/10.1101/2021.03.09.434529v1?rss=1 van der Wijst, M. G. P. Vazquez, S. E. Hartoularos, G. C. Bastard, P. Grant, T. Bueno, R. Lee, D. S. Greenland, J. R. Sun, Y. Perez, R. Ogorodnikov, A. Ward, A. Mann, S. A. Lynch, K. L. Yun, C. Havlir, D. V. Chamie, G. Marquez, C. Greenhouse, B. Lionakis, M. S. Norris, P. J. Dumont, L. J. Kelly, K. Zhang, P. Zhang, Q. Gervais, A. Le Voyer, T. Whatley, A. Si, Y. Byrne, A. Combes, A. J. Arkal, A. Song, Y. S. Fragiadakis, G. K. UCSF COMET consortium, Kangelaris, K. Calfee, C. S. Erle, D. J. Hendrickson, C. Krummel, M. F. Woodruff, P. G. Langelier, C. R. 2021-03-10 doi:10.1101/2021.03.09.434529 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Massively parallel reporter perturbation assay uncovers temporal regulatory architecture during neural differentiation ]]> https://biorxiv.org/content/10.1101/2021.03.12.435197v1?rss=1 Kreimer, A. Ashuach, T. Inoue, F. Khodaverdian, A. Yosef, N. Ahituv, N. 2021-03-12 doi:10.1101/2021.03.12.435197 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Community Evaluation of Glycoproteomics Informatics Solutions Reveals High-Performance Search Strategies of Glycopeptide Data ]]> https://biorxiv.org/content/10.1101/2021.03.14.435332v1?rss=1 Kawahara, R. Alagesan, K. Bern, M. Cao, W. Chalkley, R. J. Cheng, K. Choo, M. S. Edwards, N. Goldman, R. Hoffmann, M. Hu, Y. Huang, Y. Kim, J. Y. Kletter, D. Liquet-Weiland, B. Liu, M. Mechref, Y. Meng, B. Neelamegham, S. Nguyen-Khuong, T. Nilsson, J. Pap, A. Park, G. W. Parker, B. L. Pegg, C. L. Penninger, J. M. Phung, T. K. Pioch, M. Rapp, E. Sakalli, E. Sanda, M. Shulz, B. L. Scott, N. E. Sofronov, G. Stadlmann, J. Vakhrushev, S. Y. Woo, C. M. Wu, H.-Y. Yang, P. Ying, W. Zhang, H. Zhang, Y. Zhao, J. Zaia, J. Haslam, S. M. Palmisano, G. Yoo, J. S 2021-03-15 doi:10.1101/2021.03.14.435332 Cold Spring Harbor Laboratory Press 2021-03-15 <![CDATA[ Noncanonical mRNA decay by the endoplasmic-reticulum stress sensor IRE1α promotes cancer-cell survival ]]> https://biorxiv.org/content/10.1101/2021.03.16.435520v1?rss=1 Le Thomas, A. Ferri, E. Marsters, S. Harnoss, J. M. Modrusan, Z. Li, W. Rudolph, J. Wang, W. Wu, T. D. Walter, P. Ashkenazi, A. 2021-03-16 doi:10.1101/2021.03.16.435520 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Tight nanoscale clustering of Fc gamma-receptors using DNA origami promotes phagocytosis ]]> https://biorxiv.org/content/10.1101/2021.03.18.436011v1?rss=1 Kern, N. Dong, R. Douglas, S. M. Vale, R. D. Morrissey, M. A. 2021-03-18 doi:10.1101/2021.03.18.436011 Cold Spring Harbor Laboratory Press 2021-03-18 <![CDATA[ Ciliary Hedgehog signaling regulates cell survival to build the facial midline ]]> https://biorxiv.org/content/10.1101/2021.03.18.436057v1?rss=1 Abrams, S. R. Reiter, J. F. 2021-03-18 doi:10.1101/2021.03.18.436057 Cold Spring Harbor Laboratory Press 2021-03-18 <![CDATA[ Intraflagellar transport trains can turn around without the ciliary tip complex ]]> https://biorxiv.org/content/10.1101/2021.03.19.436138v1?rss=1 Nievergelt, A. P. Zykov, I. Diener, D. R. Buchholz, T.-O. Delling, M. Diez, S. Jug, F. Stepanek, L. Pigino, G. 2021-03-19 doi:10.1101/2021.03.19.436138 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Coupling of spliceosome complexity to intron diversity ]]> https://biorxiv.org/content/10.1101/2021.03.19.436190v1?rss=1 Sales-Lee, J. Perry, D. S. Bowser, B. A. Diedrich, J. K. Rao, B. Beusch, I. Yates, J. R. Roy, S. W. Madhani, H. D. 2021-03-20 doi:10.1101/2021.03.19.436190 Cold Spring Harbor Laboratory Press 2021-03-20 <![CDATA[ Anti-GD2 antibody disrupts GD2:Siglec-7 interactions and synergizes with CD47 blockade to mediate tumor eradication ]]> https://biorxiv.org/content/10.1101/2021.03.19.436221v1?rss=1 Theruvath, J. Menard, M. Smith, B. A. Linde, M. H. Coles, G. Wu, W. Kiru, L. Delaidelli, A. Silberstein, J. L. Banuelos, A. Dhingra, S. Sotillo, E. Heitzeneder, S. Tousley, A. Lattin, J. Xu, P. Huang, J. Nasholm, N. Dalton, G. N. He, A. Kuo, T. C. Sangalang, E. R. B. Pons, J. Barkal, A. Brewer, R. Marjon, K. D. Marshall, P. L. Fernandes, R. Cochran, J. Sorensen, P. Daldrup-Link, H. E. Weissman, I. L. Sage, J. Majeti, R. Bertozzi, C. R. Weiss, W. A. Mackall, C. L. Majzner, R. G. 2021-03-21 doi:10.1101/2021.03.19.436221 Cold Spring Harbor Laboratory Press 2021-03-21 <![CDATA[ Proteome plasticity in response to persistent environmental change ]]> https://biorxiv.org/content/10.1101/2021.03.22.436511v1?rss=1 Domnauer, M. Zheng, F. Li, L. Zhang, Y. Chang, C. E. Unruh, J. Conkright-Fincham, J. McCroskey, S. Florens, L. Zhang, Y. Seidel, C. Fong, B. Schilling, B. Sharma, R. Ramanathan, A. Si, K. Zhou, C. 2021-03-22 doi:10.1101/2021.03.22.436511 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.03.23.436694v1?rss=1 Jimenez, D. S. Kim, J. Ragipani, B. Zhang, B. Street, L. A. Kramer, M. Albritton, S. E. Winterkorn, L. Ercan, S. 2021-03-24 doi:10.1101/2021.03.23.436694 Cold Spring Harbor Laboratory Press 2021-03-24 <![CDATA[ Time-varying Dynamic Network Model For Dynamic Resting State Functional Connectivity in fMRI and MEG imaging ]]> https://biorxiv.org/content/10.1101/2021.04.01.438060v1?rss=1 Jiang, F. Jin, H. Bao, Y. Xie, X. Cummings, J. Raj, A. Nagarajan, S. 2021-04-02 doi:10.1101/2021.04.01.438060 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ TDP-43 represses cryptic exon inclusion in FTD/ALS gene UNC13A ]]> https://biorxiv.org/content/10.1101/2021.04.02.438213v1?rss=1 Ma, X. R. Prudencio, M. Koike, Y. Vatsavayai, S. C. Kim, G. Harbinski, F. Rodriguez, C. M. Schmidt, H. B. Cummings, B. B. Wyatt, D. W. Kurylo, K. Miller, G. Mekhoubad, S. Sallee, N. Jansen-West, K. Cook, C. Pickles, S. Oskarsson, B. Graff-Radford, N. R. Boeve, B. F. Knopman, D. S. Petersen, R. C. Dickson, D. W. Green, E. M. Seeley, W. W. Petrucelli, L. Gitler, A. D. 2021-04-04 doi:10.1101/2021.04.02.438213 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Comprehensive Proteomic Quantification of Bladder Stone Progression in a Cystinuric Mouse Model Using Data-Independent Acquisitions ]]> https://biorxiv.org/content/10.1101/2021.04.06.438573v1?rss=1 Rose, J. Basisty, N. Zee, T. Wehrfritz, C. Bose, N. Desprez, P.-Y. Kapahi, P. Stoller, M. Schilling, B. 2021-04-06 doi:10.1101/2021.04.06.438573 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Ligand Strain Energy in Large Library Docking ]]> https://biorxiv.org/content/10.1101/2021.04.06.438722v1?rss=1 Gu, S. Smith, M. S. Yang, Y. Irwin, J. J. Shoichet, B. K. 2021-04-08 doi:10.1101/2021.04.06.438722 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Autism risk gene POGZ promotes chromatin accessibility and expression of clustered synaptic genes ]]> https://biorxiv.org/content/10.1101/2021.04.07.438852v1?rss=1 Markenscoff, E. Binyameen, F. Whalen, S. Price, J. Lim, K. Catta-Preta, R. Pai, E. L.-L. Mu, X. Xu, D. Pollard, K. S. Nord, A. State, M. W. Rubenstein, J. L. R. 2021-04-08 doi:10.1101/2021.04.07.438852 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ An Engineered Contact Lens for Passive and Sustained Release of Lifitegrast, an Anti-Dry Eye Syndrome Drug ]]> https://biorxiv.org/content/10.1101/2021.04.10.439289v1?rss=1 View larger version (75K): org.highwire.dtl.DTLVardef@1049076org.highwire.dtl.DTLVardef@a83fceorg.highwire.dtl.DTLVardef@1f52c4borg.highwire.dtl.DTLVardef@12f0ead_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mu, C. Lee, V. Liu, Y. Han, Y. marriott, g. 2021-04-11 doi:10.1101/2021.04.10.439289 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ A Pan-Cancer Census of Dominant Tumor Immune Archetypes ]]> https://biorxiv.org/content/10.1101/2021.04.26.441344v1?rss=1 View larger version (77K): org.highwire.dtl.DTLVardef@55a5ccorg.highwire.dtl.DTLVardef@f8205corg.highwire.dtl.DTLVardef@1480b8org.highwire.dtl.DTLVardef@eb94e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Combes, A. J. Samad, B. Tsui, J. Chew, N. W. Yan, P. Reeder, G. C. Kushnoor, D. Shen, A. Davidson, B. Barczac, A. J. Adkisson, M. Edwards, A. Naser, M. Barry, K. C. Courau, T. Hammoudi, T. Arguello, R. J. Rao, A. A. Olshen, A. B. Immunoprofiler Consortium, Cai, C. Zhan, J. Davis, K. C. Kelley, R. K. Chapman, J. S. Attreya, C. E. Patel, A. Daud, A. I. Ha, P. Diaz, A. Kratz, J. R. Collisson, E. A. Fragiadakis, G. K. Erle, D. J. Boissonnas, A. Asthana, S. Chan, V. Krummel, M. F. 2021-04-27 doi:10.1101/2021.04.26.441344 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Protracted yet coordinated differentiation of long-lived SARS-CoV-2-specific CD8+ T cells during COVID-19 convalescence ]]> https://biorxiv.org/content/10.1101/2021.04.28.441880v1?rss=1 Ma, T. Ryu, H. McGregor, M. Babcock, B. Neidleman, J. Xie, G. George, A. F. Frouard, J. Murray, V. Gill, G. Ghosn, E. Newell, E. Lee, S. Roan, N. 2021-04-29 doi:10.1101/2021.04.28.441880 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Regulation of layered T cell tolerance mechanisms by the NR4A family is essential to preserve immune homeostasis and suppress autoimmunity ]]> https://biorxiv.org/content/10.1101/2021.04.28.441904v1?rss=1 Hiwa, R. Nielsen, H. V. Mueller, J. L. Zikherman, J. 2021-04-29 doi:10.1101/2021.04.28.441904 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ A type I interferon response defines a conserved microglial state required for effective phagocytosis ]]> https://biorxiv.org/content/10.1101/2021.04.29.441889v1?rss=1 Dorman, L. C. Nguyen, P. T. Escoubas, C. C. Vainchtein, I. D. Xiao, Y. Lidsky, P. V. Wang, E. Y. Taloma, S. E. Nakao-Inoue, H. Rivera, B. M. Condello, C. Andino, R. Nowakowski, T. J. Molofsky, A. V. 2021-04-30 doi:10.1101/2021.04.29.441889 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Active Surveillance Characterizes Human Intratumoral T Cell Exhaustion ]]> https://biorxiv.org/content/10.1101/2021.05.06.443033v1?rss=1 You, R. Artichoker, J. Fries, A. Edwards, A. Combes, A. J. Reeder, G. Samad, B. Krummel, M. F. 2021-05-07 doi:10.1101/2021.05.06.443033 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ Combinatorial immunotherapies overcome MYC-driven immune evasion ]]> https://biorxiv.org/content/10.1101/2021.05.07.442684v1?rss=1 Lee, J. V. Houseley, F. Yau, C. Van de Mark, D. Nakagawa, R. Hemmati, G. Hernandez, G. A. Winkler, J. Zhang, Y. Samson, S. Baas, C. Esserman, L. J. Van't Veer, L. J. Rugo, H. S. Matloubian, M. Goga, A. 2021-05-08 doi:10.1101/2021.05.07.442684 Cold Spring Harbor Laboratory Press 2021-05-08 <![CDATA[ ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress ]]> https://biorxiv.org/content/10.1101/2021.05.07.443199v1?rss=1 Teng, Y.-C. Sundaresan, A. O'Hara, R. Gant, V. U. Li, M. Martire, S. Warshaw, J. N. Basu, A. Banaszynski, L. 2021-05-07 doi:10.1101/2021.05.07.443199 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ Assessing chromatin relocalization in 3D using the patient rule induction method ]]> https://biorxiv.org/content/10.1101/2021.05.08.443243v1?rss=1 Segal, M. R. 2021-05-10 doi:10.1101/2021.05.08.443243 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Identification of Cancer-Associated Fibroblasts in Glioblastoma and Defining Their Pro-tumoral Effects ]]> https://biorxiv.org/content/10.1101/2021.05.08.443250v1?rss=1 Jain, S. Rick, J. Joshi, R. Beniwal, A. Spatz, J. Chang, A. C.-C. Nguyen, A. T. Sudhir, S. Chandra, A. Haddad, A. Wadhwa, H. Shah, S. S. Choi, S. Hayes, J. L. Wang, L. Yagnik, G. Costello, J. F. Diaz, A. Aghi, M. K. 2021-05-10 doi:10.1101/2021.05.08.443250 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ In situ and transcriptomic identification of synapse-associated microglia in the developing zebrafish brain ]]> https://biorxiv.org/content/10.1101/2021.05.08.443268v1?rss=1 Silva, N. J. Dorman, L. C. vainchtein, i. Horneck, N. C. Molofsky, A. V. 2021-05-10 doi:10.1101/2021.05.08.443268 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. ]]> https://biorxiv.org/content/10.1101/2021.05.10.443524v1?rss=1 Gupta, M. Azumaya, C. M. Moritz, M. Pourmal, S. Diallo, A. Merz, G. E. Jang, G. M. Bouhaddou, M. Fossati, A. Brilot, A. F. Diwanji, D. Hernandez, E. Herrera, N. Kratochvil, H. T. Lam, V. L. Li, F. Li, Y. Nguyen, H. C. Nowotny, C. Owens, T. W. Peters, J. K. Rizo, A. N. Schulze-Gahmen, U. Smith, A. M. Young, I. D. Yu, Z. Asarnow, D. Billesbolle, C. Campbell, M. G. Chen, J. Chen, K.-H. Chio, U. S. Dickinson, M. S. Doan, L. Jin, M. Kim, K. Li, J. Li, Y.-L. Linossi, E. Liu, Y. Lo, M. Lopez, J. Lopez, K. E. Mancino, A. Moss, F. R. Paul, M. D. Pawar, K. I 2021-05-12 doi:10.1101/2021.05.10.443524 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ CRISPR activation and interference screens in primary human T cells decode cytokine regulation ]]> https://biorxiv.org/content/10.1101/2021.05.11.443701v1?rss=1 Schmidt, R. Steinhart, Z. Layeghi, M. Freimer, J. W. Nguyen, V. Q. Blaeschke, F. Marson, A. 2021-05-12 doi:10.1101/2021.05.11.443701 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ mRNA vaccine-induced SARS-CoV-2-specific T cells recognize B.1.1.7 and B.1.351 variants but differ in longevity and homing properties depending on prior infection status ]]> https://biorxiv.org/content/10.1101/2021.05.12.443888v1?rss=1 Neidleman, J. Luo, X. McGregor, M. Xie, G. Murray, V. Greene, W. C. Lee, S. A. Roan, N. R. 2021-05-12 doi:10.1101/2021.05.12.443888 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ Molecular diversity and lineage commitment of human interneuron progenitors ]]> https://biorxiv.org/content/10.1101/2021.05.13.444045v1?rss=1 Velmeshev, D. Chavali, M. Nowakowski, T. J. Bhade, M. Mayer, S. Goyal, N. Alvarado, B. Mancia, W. Wang, S. Speir, M. Haeussler, M. J. Rowitch, D. Alvarez-Buylla, A. Huang, E. Paredes, M. Kriegstein, A. 2021-05-14 doi:10.1101/2021.05.13.444045 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ When rare meets common: Treatable genetic diseases are enriched in the general psychiatric population ]]> https://biorxiv.org/content/10.1101/2021.05.13.444051v1?rss=1 Sriretnakumar, V. Harripaul, R. Kennedy, J. L. So, J. 2021-05-18 doi:10.1101/2021.05.13.444051 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ An Atlas of Cortical Arealization Identifies Dynamic Molecular Signatures ]]> https://biorxiv.org/content/10.1101/2021.05.17.444528v1?rss=1 Bhaduri, A. Sandoval-Espinosa, C. Otero-Garcia, M. Oh, I. Yin, R. Eze, U. C. Nowakowski, T. J. Kriegstein, A. R. 2021-05-17 doi:10.1101/2021.05.17.444528 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ A systematic comparison of fibroblasts derived from postmortem human dura mater versus dermal epithelium for neurodegenerative disease modeling ]]> https://biorxiv.org/content/10.1101/2021.05.17.444554v1?rss=1 Argouarch, A. R. Cosme, C. G. Garcia, K. Corrales, C. I. Nana, A. L. Karydas, A. M. Spina, S. Grinberg, L. T. Miller, B. Goodarzi, H. Seeley, W. W. Kao, A. W. 2021-05-18 doi:10.1101/2021.05.17.444554 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ The molecular mechanism of load adaptation by branched actin networks ]]> https://biorxiv.org/content/10.1101/2021.05.24.445507v1?rss=1 Li, T.-D. Bieling, P. Weichsel, J. Mullins, R. D. Fletcher, D. A. 2021-05-25 doi:10.1101/2021.05.24.445507 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Assembly and levels of P-TEFb depend on reversiblephosphorylation of cyclinT1 ]]> https://biorxiv.org/content/10.1101/2021.05.25.445695v1?rss=1 Huang, F. Nguyen, T. N. N. Echeverria, I. Ramachandran, R. Cary, D. C. Paculova, H. Sali, A. Weiss, A. Peterlin, B. M. Fujinaga, K. 2021-05-25 doi:10.1101/2021.05.25.445695 Cold Spring Harbor Laboratory Press 2021-05-25 <![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[ Mechanical Forces during Lymph Node Expansion Govern Fibroblastic Reticular Network Remodeling ]]> https://biorxiv.org/content/10.1101/2021.05.27.446027v1?rss=1 Horsnell, H. L. Tetley, R. J. de Belly, H. Makris, S. Benjamin, A. C. Paluch, E. Mao, Y. Acton, S. E. 2021-05-27 doi:10.1101/2021.05.27.446027 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Glucocorticoid receptor collaborates with pioneer factors and AP-1 to execute genome-wide regulation ]]> https://biorxiv.org/content/10.1101/2021.06.01.444518v1?rss=1 Wissink, E. M. Martinez, D. M. Ehmsen, K. T. Yamamoto, K. R. Lis, J. T. 2021-06-01 doi:10.1101/2021.06.01.444518 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ SARS-CoV-2 infection studies in lung organoids identify TSPAN8 as novel mediator ]]> https://biorxiv.org/content/10.1101/2021.06.01.446640v1?rss=1 Hysenaj, L. Little, S. Kulhanek, K. R. Gbenedio, O. Rodriguez, L. Shen, A. Lone, J.-C. Lupin-Jimenez, L. C. Bonser, L. Serwas, N. K. Bahl, K. Mick, E. Li, J. Z. Ding, V. Matsumoto, S. Maishan, M. l. Fragiadakis, G. Jablons, D. M. Langelier, C. R. Matthay, M. Ott, M. Sil, A. Krummel, M. Combes, A. J. Erle, D. M. Kratz, J. R. Roose, J. P. 2021-06-02 doi:10.1101/2021.06.01.446640 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ High activity and high functional connectivity are mutually exclusive in resting state zebrafish and human brains ]]> https://biorxiv.org/content/10.1101/2021.06.02.446741v1?rss=1 12,000 neurons in the forebrain. By classifying their activity and functional connectivity into three levels (high, medium, low), we find that highly active neurons have low functional connections and highly connected neurons are of low activity. Intriguingly, deploying the same analytical methods on functional magnetic resonance imaging (fMRI) data from the resting state human brain, we uncover a similar relationship between activity and functional connectivity, that is, regions of high activity are non-overlapping with those of high connectivity. These findings reveal a previously unknown and evolutionarily conserved brain organizational principle that have implications for understanding disease states and designing artificial neuronal networks. ]]> Zarei, M. Xie, D. Jiang, F. Bagirov, A. Huang, B. Raj, A. Nagarajan, S. Guo, S. 2021-06-02 doi:10.1101/2021.06.02.446741 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Single-cell RNA-sequencing reveals widespread personalized, context-specific gene expression regulation in immune cells. ]]> https://biorxiv.org/content/10.1101/2021.06.04.447088v1?rss=1 Oelen, R. de Vries, D. H. Brugge, H. Gordon, G. Vochteloo, M. Ye, C. J. Westra, H.-J. Franke, L. van der Wijst, M. G. P. 2021-06-06 doi:10.1101/2021.06.04.447088 Cold Spring Harbor Laboratory Press 2021-06-06 <![CDATA[ Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant ]]> https://biorxiv.org/content/10.1101/2021.06.06.446826v1?rss=1 Thorne, L. G. Bouhaddou, M. Reuschl, A.-K. Zuliani-Alvarez, L. Polacco, B. J. Pelin, A. Batra, J. Whelan, M. V. X. Ummadi, M. Roic, A. Turner, J. Obernier, K. Braberg, H. Soucheray, M. Richards, A. L. Chen, K.-H. Harjai, B. Memon, D. Hosmillo, M. Hiatt, J. Jahun, A. S. Goodfellow, I. G. Noursadeghi, M. Fabius, J. Shokat, K. Jura, N. Verba, K. A. Beltrao, P. Swaney, D. L. Garcia-Sastre, A. Jolly, C. Towers, G. J. Krogan, N. J. 2021-06-07 doi:10.1101/2021.06.06.446826 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Viral Evasion of the Integrated Stress Response Through Antagonistic eIF2-P Mimicry ]]> https://biorxiv.org/content/10.1101/2021.06.07.447473v1?rss=1 Schoof, M. Wang, L. Cogan, J. Z. Lawrence, R. Boone, M. Wuerth, J. D. Frost, A. Walter, P. 2021-06-08 doi:10.1101/2021.06.07.447473 Cold Spring Harbor Laboratory Press 2021-06-08 <![CDATA[ Allele-specific gene editing rescues pathology in a human model of Charcot-Marie-Tooth disease type 2E ]]> https://biorxiv.org/content/10.1101/2021.06.09.447796v1?rss=1 Feliciano, C. M. Wu, K. Watry, H. L. Marley, C. B. E. Ramadoss, G. N. Ghanim, H. Y. Liu, A. Z. Zholudeva, L. V. McDevitt, T. C. Saporta, M. A. Conklin, B. R. Judge, L. M. 2021-06-09 doi:10.1101/2021.06.09.447796 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ Expansion of RNA sequence diversity and RNA editing rates throughout human cortical development ]]> https://biorxiv.org/content/10.1101/2021.06.10.447947v1?rss=1 Cuddleston, R. Sloofman, L. Liang, L. Mossotto, E. Fan, X. Wang, M. Zhang, B. Wang, J. Sestan, N. Devlin, B. Roeder, K. Buxbaum, J. D. Sanders, S. Breen, M. S. 2021-06-10 doi:10.1101/2021.06.10.447947 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Allosteric Inhibition of a Vesicular Glutamate Transporter by an Isoform-Specific Antibody ]]> https://biorxiv.org/content/10.1101/2021.06.16.447601v1?rss=1 Eriksen, J. Li, F. Stroud, R. M. Edwards, R. H. 2021-06-16 doi:10.1101/2021.06.16.447601 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ CUB domain containing protein 1 (CDPC1) is a target for radioligand therapy in castration resistant prostate cancer ]]> https://biorxiv.org/content/10.1101/2021.06.17.448569v1?rss=1 Zhao, N. Trepka, k. Wang, Y.-h. Chopra, S. Hooshdaran, N. Kim, H. Yang, J. Zhuo, J. Lim, S. Leung, K. K. Egusa, E. Zhang, L. K. Foye, A. Chou, J. Feng, F. Y. Small, E. J. Evans, M. J. Wells, J. A. Aggarwal, R. 2021-06-17 doi:10.1101/2021.06.17.448569 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Modular, Cascade-like Transcriptional Program of Regeneration in Stentor ]]> https://biorxiv.org/content/10.1101/2021.06.23.449623v1?rss=1 Sood, P. Lin, A. McGillivary, R. Marshall, W. F. 2021-06-23 doi:10.1101/2021.06.23.449623 Cold Spring Harbor Laboratory Press 2021-06-23 <![CDATA[ Aberrant FGF signaling promotes granule neuron precursor expansion in SHH subgroup infantile medulloblastoma ]]> https://biorxiv.org/content/10.1101/2021.06.23.449636v1?rss=1 Yabut, O. R. Gomez, H. Arela, J. Castillo, J. G. Ngo, T. Pleasure, S. J. 2021-06-24 doi:10.1101/2021.06.23.449636 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ An acetyl-click screening platform identifies a small molecule inhibitor of Histone Acetyltransferase 1 (HAT1) with anti-tumor activity ]]> https://biorxiv.org/content/10.1101/2021.06.25.449993v1?rss=1 Gruber, J. J. Rangarajan, A. Chou, T. Geller, B. S. Banuelos, S. Greenhouse, R. Snyder, M. Lipchik, A. M. 2021-06-26 doi:10.1101/2021.06.25.449993 Cold Spring Harbor Laboratory Press 2021-06-26 <![CDATA[ Origins and timing of emerging lesions in advanced renal cell carcinoma ]]> https://biorxiv.org/content/10.1101/2021.06.27.450111v1?rss=1 Wallace, A. Porten, S. Lo, A. A. Oreper, D. Lounsbury, N. Havnar, C. Pechuan-Jorge, X. Zill, O. Meng, M. 2021-06-28 doi:10.1101/2021.06.27.450111 Cold Spring Harbor Laboratory Press 2021-06-28 <![CDATA[ Innate, translation-dependent silencing of an invasive transposon in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2021.06.29.450179v1?rss=1 Oberlin, S. Rajeswaran, R. Trasser, M. Barragan-Borrero, V. Schon, M. A. Plotnikova, A. Loncsek, L. Nodine, M. D. Mari-Ordonez, A. Voinnet, O. 2021-06-29 doi:10.1101/2021.06.29.450179 Cold Spring Harbor Laboratory Press 2021-06-29 <![CDATA[ Short homology-directed repair using optimized Cas9 in the pathogen Cryptococcus neoformans enables rapid gene deletion and tagging ]]> https://biorxiv.org/content/10.1101/2021.06.30.450566v1?rss=1 Huang, M. Y. Joshi, M. B. Boucher, M. J. Lee, S. Loza, L. C. Gaylord, E. A. Doering, T. L. Madhani, H. D. 2021-06-30 doi:10.1101/2021.06.30.450566 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ Fly Cell Atlas: a single-cell transcriptomic atlas of the adult fruit fly ]]> https://biorxiv.org/content/10.1101/2021.07.04.451050v1?rss=1 250 distinct cell types across all tissues. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types that are shared between tissues, such as blood and muscle cells, allowed the discovery of rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the entire Drosophila community and serves as a comprehensive reference to study genetic perturbations and disease models at single cell resolution. ]]> Li, H. Janssens, J. De Waegeneer, M. Kolluru, S. S. Davie, K. Gardeux, V. Sealens, W. David, F. Brbic, M. Leskovec, J. McLaughlin, C. Xie, Q. Jones, R. Brueckner, K. Shim, J. Tattikota, S. G. Schnorrer, F. Rust, K. Nystul, T. Carvalho-Santos, Z. Ribeiro, C. Pal, S. Przytycka, T. M. Allen, A. Goodwin, S. Berry, C. Fuller, M. T. White-Cooper, H. Matunis, E. DiNardo, S. Galenza, A. O'Brien, L. E. Dow, J. A. T. FCA Consortium, Jasper, H. Oliver, B. Perrimon, N. Deplancke, B. Quake, S. Luo, L. Aerts, S. 2021-07-05 doi:10.1101/2021.07.04.451050 Cold Spring Harbor Laboratory Press 2021-07-05 <![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[ High-resolution estimates of crossover and noncrossover recombination from a captive baboon colony ]]> https://biorxiv.org/content/10.1101/2021.07.10.451667v1?rss=1 1 Kb) NCO tracts. We fit a mixture-of-two-geometric distributions model to the NCO tract length distribution and estimate that >99% of all NCO tracts are very short (mean 24 bp), but the remaining tracts can be quite long (mean 11 Kb). A single geometric distribution model for NCO tract lengths is incompatible with the data, suggesting that LD-based methods for estimating NCO recombination rates that make this assumption may need to be modified. SignificanceMost homologous recombination events are noncrossovers (NCO), but little is known about NCO conversion tract lengths. Here we utilize whole-genome sequence data from large baboon pedigrees to estimate the NCO tract length distribution and to study other aspects of recombination. ]]> Wall, J. Robinson, J. A. Cox, L. A. 2021-07-12 doi:10.1101/2021.07.10.451667 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Pooled screening of CAR T cells identifies non-native signaling domains for next- generation immunotherapies ]]> https://biorxiv.org/content/10.1101/2021.07.11.451980v1?rss=1 Goodman, D. B. Azimi, C. S. Kearns, K. Garakani, K. Garcia, J. Patel, N. Hwang, B. Lee, D. Park, E. Ye, C. J. Marson, A. Bluestone, J. Roybal, K. 2021-07-12 doi:10.1101/2021.07.11.451980 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Functional and Structural Segregation of Overlapping Helices in HIV-1 ]]> https://biorxiv.org/content/10.1101/2021.07.15.452440v1?rss=1 Safari, M. Jayaraman, B. Yang, S. Smith, C. Fernandes, J. D. Frankel, A. D. 2021-07-15 doi:10.1101/2021.07.15.452440 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ Data-independent acquisition protease-multiplexing enables increased proteome sequence coverage across multiple fragmentation modes ]]> https://biorxiv.org/content/10.1101/2021.07.15.452565v1?rss=1 Richards, A. L. Chen, K.-H. Wilburn, D. B. Stevenson, E. Polacco, B. Searle, B. C. Swaney, D. L. 2021-07-15 doi:10.1101/2021.07.15.452565 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ Deep neural language modeling enables functional protein generation across families ]]> https://biorxiv.org/content/10.1101/2021.07.18.452833v1?rss=1 Madani, A. Krause, B. Greene, E. R. Subramanian, S. Mohr, B. P. Holton, J. M. Olmos, J. L. Xiong, C. Sun, Z. Z. Socher, R. Fraser, J. S. Naik, N. 2021-07-18 doi:10.1101/2021.07.18.452833 Cold Spring Harbor Laboratory Press 2021-07-18 <![CDATA[ Single-cell genomics reveals region-specific developmental trajectories underlying neuronal diversity in the prenatal human hypothalamus ]]> https://biorxiv.org/content/10.1101/2021.07.20.453090v1?rss=1 Herb, B. Glover, H. J. Bhaduri, A. Casella, A. M. Bale, T. L. Kriegstein, A. Doege, C. Ament, S. A. 2021-07-20 doi:10.1101/2021.07.20.453090 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ Internet of Things Architecture for High Throughput Biology ]]> https://biorxiv.org/content/10.1101/2021.07.29.453595v1?rss=1 Parks, D. F. Voitiuk, K. Geng, J. Elliott, M. A. T. Keefe, M. G. Jung, E. A. Robbins, A. Baudin, P. V. Ly, V. T. Hawthorne, N. Yong, D. Sanso, S. E. Rezaee, N. Sevetson, J. L. Seiler, S. T. Currie, R. Hengen, K. B. Nowakowski, T. J. Salama, S. R. Teodorescu, M. Haussler, D. 2021-08-01 doi:10.1101/2021.07.29.453595 Cold Spring Harbor Laboratory Press 2021-08-01 <![CDATA[ Xenotransplantation of porcine progenitor cells in an epileptic California sea lion (Zalophus californianus) ]]> https://biorxiv.org/content/10.1101/2021.07.30.454497v1?rss=1 Simeone, C. A. Andrews, J. P. Johnson, S. P. Casalia, M. Kochanski, R. Chang, E. F. Cameron, D. Dennison, S. Inglis, B. Scott, G. Kruse-Elliott, K. Okonski, F. F. Calvo, E. Goulet, K. Robles, D. Griffin-Stence, A. Kuiper, E. Krasovec, L. Field, C. L. Hoard, V. F. Baraban, S. C. 2021-07-31 doi:10.1101/2021.07.30.454497 Cold Spring Harbor Laboratory Press 2021-07-31 <![CDATA[ Interleukin-33 coordinates a microglial phagocytic response and limits corticothalamic excitability and seizure susceptibility ]]> https://biorxiv.org/content/10.1101/2021.08.05.455250v1?rss=1 Han, R. T. Vainchtein, I. D. Schlachetzki, J. C. M. Cho, F. S. Dorman, L. C. Johung, T. Ahn, E. Barron, J. T. Inoue, H. N. Joshi, A. Molofsky, A. B. Glass, C. K. Paz, J. T. Molofsky, A. V. 2021-08-06 doi:10.1101/2021.08.05.455250 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Visual modulation of spectrotemporal receptive fields in mouse auditory cortex ]]> https://biorxiv.org/content/10.1101/2021.08.06.455445v1?rss=1 Bigelow, J. Morrill, R. J. Olsen, T. Bazarini, S. N. Hasenstaub, A. R. 2021-08-07 doi:10.1101/2021.08.06.455445 Cold Spring Harbor Laboratory Press 2021-08-07 <![CDATA[ Autophagy cargo receptors are secreted via extracellular vesicles and particles in response to endolysosomal inhibition or impaired autophagosome maturation ]]> https://biorxiv.org/content/10.1101/2021.08.12.456045v1?rss=1 Solvik, T. A. Nguyen, T. A. Lin, Y.-H. T. Marsh, T. Huang, E. J. Wiita, A. P. Debnath, J. Leidal, A. M. 2021-08-12 doi:10.1101/2021.08.12.456045 Cold Spring Harbor Laboratory Press 2021-08-12 <![CDATA[ Respiratory Alkalosis Provokes Spike-Wave Discharges in Seizure- Prone Rats ]]> https://biorxiv.org/content/10.1101/2021.08.15.456408v1?rss=1 Salvati, K. Souza, G. M. P. R. Lu, A. C. Ritger, M. L. Guyenet, P. Abbott, S. B. Beenhakker, M. P. 2021-08-15 doi:10.1101/2021.08.15.456408 Cold Spring Harbor Laboratory Press 2021-08-15 <![CDATA[ Columnar localization and laminar origin of cortical surface electrical potentials ]]> https://biorxiv.org/content/10.1101/2021.08.16.456540v1?rss=1 Baratham, V. L. Dougherty, M. E. Ledochowitsch, P. Maharbiz, M. M. Bouchard, K. 2021-08-17 doi:10.1101/2021.08.16.456540 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Precision engineering of an anti-HLA-A2 chimeric antigen receptor in regulatory T cells for transplant immune tolerance ]]> https://biorxiv.org/content/10.1101/2021.08.16.456548v1?rss=1 Muller, Y. D. Ferreira, L. M. R. Ronin, E. Ho, P. Nguyen, V. Faleo, G. Zhou, Y. Lee, K. Leung, K. K. Skartsis, N. Kaul, A. M. Mulder, A. Claas, F. H. J. Wells, J. A. Bluestone, J. A. Tang, Q. 2021-08-17 doi:10.1101/2021.08.16.456548 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Imaging-guided fine tuning of CAR synapse dynamics and T cell triggering ]]> https://biorxiv.org/content/10.1101/2021.08.18.456686v1?rss=1 Beppler, C. Eichorst, J. Marchuk, K. Cai, E. Castellanos, C. A. Sriram, V. Roybal, K. T. Krummel, M. F. 2021-08-19 doi:10.1101/2021.08.18.456686 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ The B.1.427/1.429 (epsilon) SARS-CoV-2 variants are more virulent than ancestral B.1 (614G) in Syrian hamsters ]]> https://biorxiv.org/content/10.1101/2021.08.25.457626v1?rss=1 Carroll, T. Fox, D. van Doremalen, N. Ball, E. Morris, M. K. Sotomayor-Gonzalez, A. Servellita, V. Rustagi, A. Yinda, C. K. Fritts, L. Port, J. R. Ma, Z.-M. Holbrook, M. Schulz, J. Blish, C. A. Hanson, C. Chiu, C. Y. Munster, V. Stanley, S. Miller, C. J. 2021-08-25 doi:10.1101/2021.08.25.457626 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ IDENTIFICATION OF A NOVEL BDNF-SPECIFIC CORTICOSTRIATAL CIRCUITRY ]]> https://biorxiv.org/content/10.1101/2021.08.26.457842v1?rss=1 Ehinger, Y. Soneja, D. Phamluong, K. Ron, D. 2021-08-26 doi:10.1101/2021.08.26.457842 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ Colloidal aggregators in biochemical SARS-CoV-2 repurposing screens ]]> https://biorxiv.org/content/10.1101/2021.08.31.458413v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@bfe5a2org.highwire.dtl.DTLVardef@7d05a1org.highwire.dtl.DTLVardef@1fcc3a5org.highwire.dtl.DTLVardef@190a153_HPS_FORMAT_FIGEXP M_FIG Table of Contents Graphic C_FIG ]]> O'Donnell, H. R. Tummino, T. A. Bardine, C. Craik, C. S. Shoichet, B. K. 2021-08-31 doi:10.1101/2021.08.31.458413 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Mechanism of innate immune reprogramming by a fungal meningitis pathogen ]]> https://biorxiv.org/content/10.1101/2021.09.02.458767v1?rss=1 Dang, E. V. Lei, S. Radkov, A. Madhani, H. 2021-09-02 doi:10.1101/2021.09.02.458767 Cold Spring Harbor Laboratory Press 2021-09-02 <![CDATA[ Biosynthesis of linear protein nanoarrays using the flagellar axoneme ]]> https://biorxiv.org/content/10.1101/2021.09.02.458790v1?rss=1 Ishikawa, H. Tian, J. L. Yu, J. E. Marshall, W. F. Qin, H. 2021-09-02 doi:10.1101/2021.09.02.458790 Cold Spring Harbor Laboratory Press 2021-09-02 <![CDATA[ Hybrid ssDNA repair templates enable high yield genome engineering in primary cells for disease modeling and cell therapy manufacturing ]]> https://biorxiv.org/content/10.1101/2021.09.02.458799v1?rss=1 5-fold and live cell yields by >7-fold relative to dsDNA HDRTs with CTS. Knock-in efficiency and yield with ssCTS HDRTs were increased further with small molecule inhibitor combinations to improve HDR. We demonstrate application of these methods across a variety of target loci, knock-in constructs, and primary human cell types to reach ultra-high HDR efficiencies (>80-90%) which we use for pathogenic gene variant modeling and universal gene replacement strategies for IL2RA and CTLA4 mutations associated with mendelian immune disorders. Finally, we develop a GMP-compatible method for fully non-viral CAR-T cell manufacturing, demonstrating knock-in efficiencies of 46-62% and generating yields of >1.5 x 109 CAR+ T cells, well above current doses for adoptive cellular therapies. Taken together, we present a comprehensive non-viral approach to model disease associated mutations and re-write targeted genome sequences to program immune cell therapies at a scale compatible with future clinical application. ]]> Shy, B. R. Vykunta, V. Ha, A. Roth, T. L. Talbot, A. Nguyen, D. N. Chen, Y. Y. Blaeschke, F. Vedova, S. Mamedov, M. Chung, J.-Y. Li, H. Wolf, J. Martin, T. G. Ye, L. Eyquem, J. Esensten, J. Marson, A. 2021-09-04 doi:10.1101/2021.09.02.458799 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ Allosteric mechanism of signal transduction in the two-component system histidine kinase PhoQ ]]> https://biorxiv.org/content/10.1101/2021.09.03.458835v1?rss=1 Mensa, B. Polizzi, N. F. Molnar, K. S. Natale, A. M. Lemmin, T. DeGrado, W. F. 2021-09-05 doi:10.1101/2021.09.03.458835 Cold Spring Harbor Laboratory Press 2021-09-05 <![CDATA[ A unique form of collective epithelial migration is crucial for tissue fusion in the secondary palate and can overcome loss of epithelial apoptosis ]]> https://biorxiv.org/content/10.1101/2021.09.07.459343v1?rss=1 Teng, T. Teng, C. Kaartinen, V. Bush, J. O. 2021-09-08 doi:10.1101/2021.09.07.459343 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ Spatio-temporal coordination at the maternal-fetal interface promotes trophoblast invasion and vascular remodeling in the first half of human pregnancy ]]> https://biorxiv.org/content/10.1101/2021.09.08.459490v1?rss=1 Greenbaum, S. Averbukh, I. Soon, E. Rizzuto, G. Baranski, A. Greenwald, N. Bosse, M. Jaswa, E. G. Khair, Z. Kwok, S. Warshawsky, S. Miller, G. Schwartz, M. Graf, W. Van Valen, D. Keren, L. Hollmann, T. van de Rijn, M. Angelo, M. 2021-09-10 doi:10.1101/2021.09.08.459490 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ Stimulation related artifacts and a multipurpose template-based offline removal solution for a novel sensing-enabled deep brain stimulation device ]]> https://biorxiv.org/content/10.1101/2021.09.10.457001v1?rss=1 Hammer, L. H. Kochanski, R. B. Starr, P. Little, S. 2021-09-11 doi:10.1101/2021.09.10.457001 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Integrated gene analyses of de novo mutations from 46,612 trios with autism and developmental disorders ]]> https://biorxiv.org/content/10.1101/2021.09.15.460398v1?rss=1 Wang, T. Kim, C. Bakken, T. E. Gillentine, M. A. Henning, B. Mao, Y. Gilissen, C. Consortium, S. Nowakowski, T. J. Eichler, E. E. 2021-09-16 doi:10.1101/2021.09.15.460398 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ Divergent encoding of active avoidance behavior in corticostriatal and corticolimbic projections ]]> https://biorxiv.org/content/10.1101/2021.09.15.460552v1?rss=1 Kajs, B. L. Loewke, A. C. Dorsch, J. M. Vinson, L. T. Gunaydin, L. A. 2021-09-16 doi:10.1101/2021.09.15.460552 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ Genome-wide mapping implicates R-loops in lineage-specific processes and formation of DNA break hotspots in neural stem/progenitor cells ]]> https://biorxiv.org/content/10.1101/2021.09.20.460546v1?rss=1 Thongthip, S. Carlson, A. Crossley, M. P. Schwer, B. 2021-09-20 doi:10.1101/2021.09.20.460546 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ Ligand binding remodels protein side chain conformational heterogeneity ]]> https://biorxiv.org/content/10.1101/2021.09.21.461269v1?rss=1 Wankowicz, S. A. de Oliveira, S. H. P. Hogan, D. W. van den Bedem, H. Fraser, J. S. 2021-09-21 doi:10.1101/2021.09.21.461269 Cold Spring Harbor Laboratory Press 2021-09-21 <![CDATA[ The nuclear transport factor CSE1 drives macronuclear volume increase and macronuclear node condensation in Stentor coeruleus ]]> https://biorxiv.org/content/10.1101/2021.09.21.461284v1?rss=1 McGillivary, R. M. Sood, P. Hammar, K. Marshall, W. F. 2021-09-22 doi:10.1101/2021.09.21.461284 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ Perilacunar bone tissue exhibits sub-micrometer modulus gradation which depends on the recency of osteocyte bone formation ]]> https://biorxiv.org/content/10.1101/2021.09.21.461298v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@1fe5a68org.highwire.dtl.DTLVardef@1e17e90org.highwire.dtl.DTLVardef@13c2e3corg.highwire.dtl.DTLVardef@1ff9f38_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Rux, C. J. Vahidi, G. Darabi, A. Cox, L. M. Heveran, C. M. 2021-09-24 doi:10.1101/2021.09.21.461298 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Multi-context genetic modeling of transcriptional regulation resolves novel disease loci ]]> https://biorxiv.org/content/10.1101/2021.09.23.461579v1?rss=1 Thompson, M. Gordon, M. G. Lu, A. Tandon, A. Halperin, E. Gusev, A. Ye, C. J. Balliu, B. Zaitlen, N. 2021-09-23 doi:10.1101/2021.09.23.461579 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/2021.09.24.461597v1?rss=1 Zhang, M. J. Hou, K. Dey, K. K. Jagadeesh, K. A. Weinand, K. Sakaue, S. Taychameekiatchai, A. Rao, P. Pisco, A. O. Zou, J. Wang, B. Gandal, M. Raychaudhuri, S. Pasaniuc, B. Price, A. L. 2021-09-28 doi:10.1101/2021.09.24.461597 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ Single-molecule analysis of specificity and multivalency in binding of short linear substrate motifs to the APC/C ]]> https://biorxiv.org/content/10.1101/2021.09.25.461797v1?rss=1 Hartooni, N. Sung, J. Jain, A. Morgan, D. O. 2021-09-26 doi:10.1101/2021.09.25.461797 Cold Spring Harbor Laboratory Press 2021-09-26 <![CDATA[ The short flagella 1 (SHF1) gene in Chlamydomonas encodes a Crescerin TOG-domain protein required for late stages of flagellar growth. ]]> https://biorxiv.org/content/10.1101/2021.09.27.462016v1?rss=1 Perlaza, K. Mirvis, M. Ishikawa, H. Marshall, W. F. 2021-09-27 doi:10.1101/2021.09.27.462016 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ Optogenetic EB1 inactivation shortens metaphase spindles by disrupting cortical force-producing interactions with astral microtubules ]]> https://biorxiv.org/content/10.1101/2021.09.29.462463v1?rss=1 Dema, A. van Haren, J. Wittmann, T. 2021-10-01 doi:10.1101/2021.09.29.462463 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Endoplasmic reticulum stress activates human IRE1α through reversible assembly of inactive dimers into small oligomers ]]> https://biorxiv.org/content/10.1101/2021.09.29.462487v1?rss=1 Belyy, V. Zuazo-Gaztelu, I. Alamban, A. Ashkenazi, A. Walter, P. 2021-09-30 doi:10.1101/2021.09.29.462487 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Structural basis of ATP-dependent high-fidelity epigenome maintenance ]]> https://biorxiv.org/content/10.1101/2021.10.01.462825v1?rss=1 Wang, J. Catania, S. Wang, C. de la Cruz, M. J. Rao, B. Madhani, H. D. Patel, D. J. 2021-10-01 doi:10.1101/2021.10.01.462825 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Robust T cell activation requires an eIF3-driven burst in T cell receptor translation ]]> https://biorxiv.org/content/10.1101/2021.10.04.463005v1?rss=1 DeSilva, D. Ferguson, L. Chin, G. Smith, B. Apathy, R. Roth, T. Blaeschke, F. Kudla, M. Marson, A. Ingolia, N. T. Cate, J. H. 2021-10-04 doi:10.1101/2021.10.04.463005 Cold Spring Harbor Laboratory Press 2021-10-04 <![CDATA[ Pan-cancer imaging of TERT expression using deuterium magnetic resonance spectroscopy-based assessment of pyruvate metabolism ]]> https://biorxiv.org/content/10.1101/2021.10.05.462047v1?rss=1 Batsios, G. Taglang, C. Tran, M. Stevers, N. Barger, C. Gillespie, A. M. Ronen, S. Costello, J. Viswanath, P. 2021-10-06 doi:10.1101/2021.10.05.462047 Cold Spring Harbor Laboratory Press 2021-10-06 <![CDATA[ Aberrant Functional Connectivity between Reward and Inhibitory Control Networks in Pre-Adolescent Binge Eating Disorder ]]> https://biorxiv.org/content/10.1101/2021.10.06.463386v1?rss=1 Murray, S. Alba, C. Duval, C. Nagata, J. Cabeen, R. Lee, D. Toga, A. W. Siegel, S. Jann, K. 2021-10-08 doi:10.1101/2021.10.06.463386 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ A sense-antisense RNA interaction promotes breast cancer metastasis via regulation of NQO1 expression ]]> https://biorxiv.org/content/10.1101/2021.10.08.463652v1?rss=1 Culbertson, B. Garcia, K. Markett, D. Asgharian, H. Chen, L. Fish, L. Navickas, A. Yu, J. Woo, B. Nanda, S. Rabinowitz, J. Goodarzi, H. 2021-10-09 doi:10.1101/2021.10.08.463652 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ SARS-CoV-2 spike protein induces abnormal inflammatory blood clots neutralized by fibrin immunotherapy ]]> https://biorxiv.org/content/10.1101/2021.10.12.464152v1?rss=1 Ryu, J. K. Sozmen, E. G. Dixit, K. Montano, M. Matsui, Y. Liu, Y. Helmy, E. Deerinck, T. J. Yan, Z. Schuck, R. Acevedo, R. M. Spencer, C. M. Thomas, R. Pico, A. R. Zamvil, S. S. Lynch, K. L. Ellisman, M. H. Greene, W. C. Akassoglou, K. 2021-10-13 doi:10.1101/2021.10.12.464152 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Mapping enzyme catalysis with metabolomic biosensing ]]> https://biorxiv.org/content/10.1101/2021.10.15.464597v1?rss=1 Xu, L. Chang, K.-C. Payne, E. M. Modavi, C. Liu, L. Palmer, C. Tao, N. Alper, H. S. Kennedy, R. T. Cornett, D. S. Abate, A. R. 2021-10-16 doi:10.1101/2021.10.15.464597 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ The ESX-1 secretion system senses bacterial contact and prepares mycobacteria for environmental adaptation ]]> https://biorxiv.org/content/10.1101/2021.10.17.464699v1?rss=1 Herrera, N. Odermatt, P. D. Voorhies, M. Nakagawa, R. Sil, A. Chang, F. Rosenberg, O. S. 2021-10-17 doi:10.1101/2021.10.17.464699 Cold Spring Harbor Laboratory Press 2021-10-17 <![CDATA[ Multi-model Order ICA: A Data-driven Method for Evaluating Brain Functional Network Connectivity Within and Between Multiple Spatial Scales ]]> https://biorxiv.org/content/10.1101/2021.10.24.465635v1?rss=1 Meng, X. Iraji, A. Fu, Z. Kochunov, P. Belger, A. Ford, J. McEwen, S. Mathalon, D. H. Mueller, B. A. Pearlson, G. D. Potkin, S. G. Preda, A. Turner, J. van Erp, T. G. M. Sui, J. Calhoun, V. 2021-10-27 doi:10.1101/2021.10.24.465635 Cold Spring Harbor Laboratory Press 2021-10-27 <![CDATA[ Aldehyde dehydrogenase 3A1 deficiency leads to mitochondrial dysfunction and impacts salivary gland stem cell self-renewal, differentiation and survival ]]> https://biorxiv.org/content/10.1101/2021.10.25.461994v1?rss=1 Viswanathan, V. Cao, H. Saiki, J. Jiang, D. Mattingly, A. Nambiar, D. K. Bloomstein, J. Li, Y. Jiang, S. Chamoli, M. Sirjani, D. Kaplan, M. Holsinger, F. C. Liang, R. Feng, Z. Eyben, R. V. Lagory, E. Guan, L. Jiang, H. Ye, J. Nolan, G. P. Denko, N. Knox, S. Rosen, D. M. Le, Q. T. 2021-10-26 doi:10.1101/2021.10.25.461994 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Deep Phenotypic Analysis of Blood and Lymphoid T and NK Cells from HIV+ Controllers and Non-Controllers ]]> https://biorxiv.org/content/10.1101/2021.10.27.466175v1?rss=1 George, A. F. Luo, X. Neidleman, J. Hoh, R. Vohra, P. Thomas, R. Shin, M.-G. Lee, M. J. Blish, C. A. Deeks, S. G. Greene, W. C. Lee, S. A. Roan, N. R. 2021-10-28 doi:10.1101/2021.10.27.466175 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Chlamydomonas ARMC2/PF27 is an obligate cargo adapter for IFT of radial spokes ]]> https://biorxiv.org/content/10.1101/2021.10.31.466660v1?rss=1 Lechtreck, K. F. Liu, Y. Dai, J. Alkhofash, R. Butler, J. Alford, L. Yang, P. 2021-10-31 doi:10.1101/2021.10.31.466660 Cold Spring Harbor Laboratory Press 2021-10-31 <![CDATA[ Host Variation in Interferon, MHC Class I, Glycosylation, and Viral Transcription Genes Predict HIV Persistence ]]> https://biorxiv.org/content/10.1101/2021.10.31.466670v1?rss=1 Siegel, D. A. Thanh, C. Wan, E. Hoh, R. Hobbs, K. Pan, T. Gibson, E. A. Kroetz, D. L. Hunt, P. W. Marin, J. Hecht, F. Pilcher, C. Milush, J. Martin, M. Carrington, M. Pillai, S. Busch, M. P. Stone, M. Huang, M.-L. Roychoundhury, P. Haworth, K. Jerome, K. R. Kiem, H.-P. Heinrich, T. J. Deeks, S. G. Lee, S. 2021-11-03 doi:10.1101/2021.10.31.466670 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Single-Cell Multiomics Defines Tolerogenic Extrathymic Aire-Expressing Populations with Unique Homology to Thymic Epithelium ]]> https://biorxiv.org/content/10.1101/2021.11.05.467513v1?rss=1 Wang, J. Lareau, C. A. Bautista, J. L. Gupta, A. R. Sandor, K. Germino, J. Yin, Y. Arvedson, M. P. Reeder, G. C. Cramer, N. T. Xie, F. Ntranos, V. Satpathy, A. T. Anderson, M. S. Gardner, J. M. 2021-11-06 doi:10.1101/2021.11.05.467513 Cold Spring Harbor Laboratory Press 2021-11-06 <![CDATA[ CRISPR-Cas9 mediated nuclear transport and genomic integration of nanostructured genes in human primary cells ]]> https://biorxiv.org/content/10.1101/2021.11.08.467750v1?rss=1 Lin Shiao, E. Pfeifer, W. G. Shy, B. R. Doost, M. S. Chen, E. Vykunta, V. S. Hamilton, J. R. Stahl, E. C. Lopez, D. M. Espinoza, C. R. S. Dejanov, A. E. Lew, R. J. Poirer, M. G. Marson, A. Castro, C. E. Doudna, J. A. 2021-11-09 doi:10.1101/2021.11.08.467750 Cold Spring Harbor Laboratory Press 2021-11-09 <![CDATA[ Prevalent mouse phenotypes in the unexplored druggable genome ]]> https://biorxiv.org/content/10.1101/2021.11.08.467777v1?rss=1 Gulyaeva, O. Hu, Z. Oprea, T. I. Lloyd, K. Gomez, S. M. Roth, B. L. McManus, M. 2021-11-08 doi:10.1101/2021.11.08.467777 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ Microbial signals and lymphotoxin drive TNF-independent death of A20 and ABIN-1 deficient epithelium ]]> https://biorxiv.org/content/10.1101/2021.11.08.467808v1?rss=1 Rusu, I. Mennillo, E. Bain, J. L. Li, Z. Sun, X. Ly, K. Rosli, Y. Y. Naser, M. Wang, Z. Advincula, R. Achacoso, P. Shao, L. Razani, B. Klein, O. D. Marson, A. Turnbaugh, J. Turnbaugh, P. Malynn, B. A. Ma, A. Kattah, M. G. 2021-11-08 doi:10.1101/2021.11.08.467808 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ Nucleolar-based Dux repression is essential for 2-cell stage exit ]]> https://biorxiv.org/content/10.1101/2021.11.11.468235v1?rss=1 Xie, S. Q. Leeke, B. J. Whilding, C. Wagner, R. T. Garcia-Llagostera, F. Chammas, P. Cheung, N. T.-F. Dormann, D. McManus, M. Percharde, M. 2021-11-12 doi:10.1101/2021.11.11.468235 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ The Astrin/SKAP Complex Reduces Friction at the Kinetochore-Microtubule Interface ]]> https://biorxiv.org/content/10.1101/2021.11.29.469773v1?rss=1 Rosas Salvans, M. Sutanto, R. Suresh, P. Dumont, S. 2021-11-30 doi:10.1101/2021.11.29.469773 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Adolescent rats extend help to outgroup members, highlighting a neural network for group identity categorization. ]]> https://biorxiv.org/content/10.1101/2021.11.29.470434v1?rss=1 Breton, J. Eisner, J. S. Gandhi, V. S. Musick, N. Zhang, A. Long, K. L. P. Perloff, O. S. Hu, K. Y. Pham, C. M. Lalchandani, P. Barraza, M. K. Kantor, B. Kaufer, D. Ben-Ami Bartal, I. 2021-12-01 doi:10.1101/2021.11.29.470434 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ 15N metabolic labeling quantification workflow in Arabidopsis using Protein Prospector ]]> https://biorxiv.org/content/10.1101/2021.11.30.470624v1?rss=1 Shrestha, R. Reyes, A. V. Baker, P. R. Wang, Z.-Y. Chalkley, R. J. Xu, S.-L. 2021-12-01 doi:10.1101/2021.11.30.470624 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Input-specific control of interneuron numbers in nascent striatal networks ]]> https://biorxiv.org/content/10.1101/2021.12.01.470575v1?rss=1 Sreenivasan, V. Serafeimidou-Pouliou, E. Exposito-Alonso, D. Bercsenyi, K. Bernard, C. Bae, S.-E. Oozeer, F. Hanusz-Godoy, A. Edwards, R. Marin, O. 2021-12-02 doi:10.1101/2021.12.01.470575 Cold Spring Harbor Laboratory Press 2021-12-02 <![CDATA[ Application of Parallel Reaction Monitoring in 15N labeled Samples for Quantification ]]> https://biorxiv.org/content/10.1101/2021.12.01.470846v1?rss=1 Reyes, A. V. Shrestha, R. Baker, P. R. Chalkley, R. J. Xu, S.-L. 2021-12-03 doi:10.1101/2021.12.01.470846 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ Control of nuclear size by osmotic forces in Schizosaccharomyces pombe ]]> https://biorxiv.org/content/10.1101/2021.12.05.471221v1?rss=1 Lemiere, J. Real-Calderon, P. Holt, L. Fai, T. Chang, F. 2021-12-07 doi:10.1101/2021.12.05.471221 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Single-fiber nucleosome density shapes the regulatory output of a mammalian chromatin remodeling enzyme ]]> https://biorxiv.org/content/10.1101/2021.12.10.472156v1?rss=1 Abdulhay, N. J. Hsieh, L. J. McNally, C. P. Ketavarapu, M. Kasinathan, S. Nanda, A. S. Ostrowski, M. S. Wu, K. Moore, C. M. Goodarzi, H. Narlikar, G. J. Ramani, V. 2021-12-11 doi:10.1101/2021.12.10.472156 Cold Spring Harbor Laboratory Press 2021-12-11 <![CDATA[ Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq ]]> https://biorxiv.org/content/10.1101/2021.12.16.473013v1?rss=1 2.5 million human cells and present a framework to power biological discovery with the resulting genotype-phenotype map. We use transcriptional phenotypes to predict the function of poorly-characterized genes, uncovering new regulators of ribosome biogenesis (including CCDC86, ZNF236, and SPATA5L1), transcription (C7orf26), and mitochondrial respiration (TMEM242). In addition to assigning gene function, single-cell transcriptional phenotypes allow for in-depth dissection of complex cellular phenomena - from RNA processing to differentiation. We leverage this ability to systematically identify the genetic drivers and consequences of aneuploidy and to discover an unanticipated layer of stress-specific regulation of the mitochondrial genome. Our information-rich genotype-phenotype map reveals a multidimensional portrait of gene function and cellular behavior. ]]> Replogle, J. M. Saunders, R. A. Pogson, A. N. Hussmann, J. A. Lenail, A. Guna, A. Mascibroda, L. Wagner, E. J. Adelman, K. Bonnar, J. L. Jost, M. Norman, T. M. Weissman, J. S. 2021-12-17 doi:10.1101/2021.12.16.473013 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Modeling the dynamics of within-host viral infection and evolution predicts quasispecies distributions and phase boundaries separating distinct classes of infections ]]> https://biorxiv.org/content/10.1101/2021.12.16.473030v1?rss=1 Lewis, G. R. Marshall, W. F. Jones, B. A. 2021-12-20 doi:10.1101/2021.12.16.473030 Cold Spring Harbor Laboratory Press 2021-12-20 <![CDATA[ ICoRD: Iterative Correlation-Based ROI Detection Method for the Extraction of Neural Signals in Calcium Imaging ]]> https://biorxiv.org/content/10.1101/2021.12.16.473055v1?rss=1 Kang, S. Park, J. Kim, K. Lim, S.-H. Choi, J. H. Rah, J.-C. Choi, J.-W. 2021-12-17 doi:10.1101/2021.12.16.473055 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Combination of Mycobacterium tuberculosis RS ratio and CFU improves the ability of murine efficacy experiments to distinguish between drug treatments ]]> https://biorxiv.org/content/10.1101/2021.12.21.473768v1?rss=1 Dide-Agossou, C. Bauman, A. A. Ramey, M. E. Rossmassler, K. Al Mubarak, R. Pauly, S. Voskuil, M. I. Garcia?Cremades, M. Savic, R. M. Nahid, P. Moore, C. M. Tasneen, R. Nuermburger, E. Robertson, G. T. Walter, N. D. 2021-12-24 doi:10.1101/2021.12.21.473768 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ P-TEFb is degraded by Siah1/2 in quiescent cells ]]> https://biorxiv.org/content/10.1101/2021.12.30.474394v1?rss=1 Huang, F. Feng, Y. Peterlin, B. M. Fujinaga, K. 2022-01-01 doi:10.1101/2021.12.30.474394 Cold Spring Harbor Laboratory Press 2022-01-01 <![CDATA[ hPSC-Derived Enteric Ganglioids Model Human ENS Development and Function ]]> https://biorxiv.org/content/10.1101/2022.01.04.474746v1?rss=1 Majd, H. Samuel, R. M. Ramirez, J. T. Kalantari, A. Barber, K. Ghazizadeh, Z. Chemel, A. K. Cesiulis, A. Richter, M. N. Das, S. Keefe, M. G. Wang, J. Shiv, R. McCann, C. J. Bhat, S. Khoroshkin, M. Yu, J. Nowakowski, T. J. Goodarzi, H. Thapar, N. Kaltschmidt, J. A. Fattahi, F. 2022-01-04 doi:10.1101/2022.01.04.474746 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ Exploring the rules of chimeric antigen receptor phenotypic output using combinatorial signaling motif libraries and machine learning ]]> https://biorxiv.org/content/10.1101/2022.01.04.474985v1?rss=1 View larger version (17K): org.highwire.dtl.DTLVardef@8dbf97org.highwire.dtl.DTLVardef@1d8300org.highwire.dtl.DTLVardef@1838ba0org.highwire.dtl.DTLVardef@143d907_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Daniels, K. G. Wang, S. Simic, M. S. Bhargava, H. K. Capponi, S. Tonai, Y. Yu, W. Bianco, S. Lim, W. A. 2022-01-04 doi:10.1101/2022.01.04.474985 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ Proteomic Dissection of a Giant Cell ]]> https://biorxiv.org/content/10.1101/2022.01.06.475287v1?rss=1 Lin, A. Piehowski, P. Tsai, C.-F. Makushok, T. Yi, L. Diaz, U. Yan, C. Summers, D. Sood, P. Smith, R. Liu, T. Marshall, W. F. 2022-01-06 doi:10.1101/2022.01.06.475287 Cold Spring Harbor Laboratory Press 2022-01-06 <![CDATA[ Naive arthritogenic SKG T cells have a defect in anergy and a repertoire pruned by superantigen ]]> https://biorxiv.org/content/10.1101/2022.01.13.476250v1?rss=1 Ashouri, J. F. McCarthy, E. Yu, S. Perlmutter, N. Lin, C. DeRisi, J. Ye, C. J. Weiss, A. 2022-01-16 doi:10.1101/2022.01.13.476250 Cold Spring Harbor Laboratory Press 2022-01-16 <![CDATA[ STAT3 regulates cytokine production downstream of TNFR1 in part by inducing expression of TNFAIP3/A20 ]]> https://biorxiv.org/content/10.1101/2022.01.19.476699v1?rss=1 Antonia, R. J. Karelehto, E. Toriguchi, K. Matli, M. Warren, R. S. Pfeffer, L. M. Donner, D. B. 2022-01-20 doi:10.1101/2022.01.19.476699 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Therapeutic Interruption of T Cell Development Generates High-Affinity T Cells That Escape Exhaustion and Improve Cancer Immunotherapy ]]> https://biorxiv.org/content/10.1101/2022.01.19.476935v1?rss=1 Dhuey, E. Oldridge, O. Ravishankar, R. Dada, H. Yu, Y. Anderson, M. S. Minn, A. J. 2022-01-21 doi:10.1101/2022.01.19.476935 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Synthetic glycans that control gut microbiome structure mitigate colitis in mice ]]> https://biorxiv.org/content/10.1101/2022.01.28.478269v1?rss=1 Tolonen, A. C. Beauchemin, N. Bayne, C. Li, L. Tan, J. Lee, J. Meehan, B. Meisner, J. Millet, Y. Rapp, E. Kottler, R. Murphy, C. Turnbaugh, P. J. von Maltzahn, G. Liu, C. M. van Hylckama Vlieg, J. 2022-01-29 doi:10.1101/2022.01.28.478269 Cold Spring Harbor Laboratory Press 2022-01-29 <![CDATA[ Clemizole and Trazodone are Effective Antiseizure Treatments in a Zebrafish Model of STXBP1 Disorder ]]> https://biorxiv.org/content/10.1101/2022.01.30.478390v1?rss=1 Moog, M. Baraban, S. C. 2022-01-30 doi:10.1101/2022.01.30.478390 Cold Spring Harbor Laboratory Press 2022-01-30 <![CDATA[ Influence of earlier human activity on gut microbiota and immune responses of Darwin's finches in the Galapagos Islands ]]> https://biorxiv.org/content/10.1101/2022.02.07.479384v1?rss=1 Bygrave, J. Zylberberg, M. A. Addesso, A. Knutie, S. A. 2022-02-09 doi:10.1101/2022.02.07.479384 Cold Spring Harbor Laboratory Press 2022-02-09 <![CDATA[ Deep tissue infection by an invasive human fungal pathogen requires novel lipid-based suppression of the IL-17 response ]]> https://biorxiv.org/content/10.1101/2022.02.07.479457v1?rss=1 Basso, P. Dang, E. V. Urisman, A. Madhani, H. D. Cowen, L. E. Noble, S. M. 2022-02-08 doi:10.1101/2022.02.07.479457 Cold Spring Harbor Laboratory Press 2022-02-08 <![CDATA[ Temporal and sequential transcriptional dynamics define lineage shifts in corticogenesis ]]> https://biorxiv.org/content/10.1101/2022.02.10.479992v1?rss=1 Mukhtar, T. Breda, J. Boareto, M. Grobecker, P. Karimaddini, Z. Grison, A. Eschbach, K. Chandrasekhar, R. Vermeul, S. Okoniewski, M. Pachkov, M. Atanasoski, S. Beisel, C. Iber, D. Nimwegen, E. v. Taylor, V. 2022-02-11 doi:10.1101/2022.02.10.479992 Cold Spring Harbor Laboratory Press 2022-02-11 <![CDATA[ Highly efficient generation of isogenic pluripotent stem cell models using prime editing ]]> https://biorxiv.org/content/10.1101/2022.02.15.480601v1?rss=1 Li, H. Busquets, O. Verma, Y. Syed, K. M. Kutnowski, N. Pangilinan, G. R. Gilbert, L. Bateup, H. Rio, D. C. Hockemeyer, D. Soldner, F. 2022-02-15 doi:10.1101/2022.02.15.480601 Cold Spring Harbor Laboratory Press 2022-02-15 <![CDATA[ Tensor decomposition reveals coordinated multicellular patterns of transcriptional variation that distinguish and stratify disease individuals ]]> https://biorxiv.org/content/10.1101/2022.02.16.480703v1?rss=1 Mitchel, J. Gordon, M. G. Perez, R. K. Biederstedt, E. Bueno, R. Ye, C. J. Kharchenko, P. 2022-02-18 doi:10.1101/2022.02.16.480703 Cold Spring Harbor Laboratory Press 2022-02-18 <![CDATA[ Antigen-dependent inducible T cell reporter system for PET imaging of breast cancer and glioblastoma ]]> https://biorxiv.org/content/10.1101/2022.02.16.480729v1?rss=1 10-fold higher [18F]FHBG signals seen in antigen-expressing tumors versus the corresponding controls. The main innovation described is therefore PET detection of T cells via specific antigen-induced signals, in contrast to reporter systems relying on constitutive gene expression. ]]> Shin, J. Parker, M. Zhu, I. Alanizi, A. Rodriguez, C. Liu, R. Watchmaker, P. Kalita, M. Blecha, J. Luu, J. Wright, B. Lapi, S. Flavell, R. Okada, H. Tlsty, T. Wilson, D. Roybal, K. 2022-02-16 doi:10.1101/2022.02.16.480729 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ Inhibition of the tuft cell/ILC2 axis reduces gastric tumor development in mice ]]> https://biorxiv.org/content/10.1101/2022.02.16.480779v1?rss=1 O'Keefe, R. N. Carli, A. Baloyan, D. Sterle, S. Eissmann, M. F. Poh, A. R. Seillet, C. Locksley, R. M. Ernst, M. M. Buchert, M. 2022-02-18 doi:10.1101/2022.02.16.480779 Cold Spring Harbor Laboratory Press 2022-02-18 <![CDATA[ Single-Cell Multi-Omic Roadmap of Human Fetal Pancreatic Development ]]> https://biorxiv.org/content/10.1101/2022.02.17.480942v1?rss=1 de la O, S. Liu, Z. Sun, H. Yu, S. K. Wong, D. M. Chu, E. Rao, S. A. Eng, N. Peixoto, G. Bouza, J. Shen, Y. Knox, S. M. Tward, A. D. Gloyn, A. L. Sneddon, J. B. 2022-02-18 doi:10.1101/2022.02.17.480942 Cold Spring Harbor Laboratory Press 2022-02-18 <![CDATA[ Statistical curve models for inferring 3D chromatin architecture ]]> https://biorxiv.org/content/10.1101/2022.02.19.481149v1?rss=1 Tuzhilina, E. Hastie, T. Segal, M. 2022-02-20 doi:10.1101/2022.02.19.481149 Cold Spring Harbor Laboratory Press 2022-02-20 <![CDATA[ Aberrant cortical development is driven by impaired cell cycle and translational control in a DDX3X syndrome model ]]> https://biorxiv.org/content/10.1101/2022.02.21.481343v1?rss=1 Hoye, M. L. Calviello, L. Poff, A. J. Ejimogu, N.-E. Newman, C. R. ou, j. Floor, S. N. Silver, D. L. 2022-02-21 doi:10.1101/2022.02.21.481343 Cold Spring Harbor Laboratory Press 2022-02-21 <![CDATA[ T cells use distinct topological and membrane receptor scanning strategies that individually coalesce during receptor recognition ]]> https://biorxiv.org/content/10.1101/2022.02.23.481517v1?rss=1 Cai, E. Beppler, C. Eichorst, J. Marchuk, K. Krummel, M. F. 2022-02-25 doi:10.1101/2022.02.23.481517 Cold Spring Harbor Laboratory Press 2022-02-25 <![CDATA[ "Transposon Mutagenesis Reveals RBMS3 as a Promoter of Malignant Progression of BRAFV600E-Driven Lung Tumorigenesis." ]]> https://biorxiv.org/content/10.1101/2022.02.28.482366v1?rss=1 CTNNB1>c-MYC pathway. Finally, analyses of patient samples in The Cancer Genome Atlas (TCGA) revealed that the region of chromosome 3 encompassing RBMS3 is frequently lost in NSCLC and correlates with poor patient prognosis. Collectively, SB-mediated transposon mutagenesis has revealed the ability of a novel tumor suppressor, RBMS3, to cooperate with BRAFV600E to promote lung carcinogenesis, and suggests that RBMS3 silencing may contribute to malignant progression of numerous human lung cancers. SIGNIFICANCEThe BRAFV600E oncoprotein kinase is a potent initiator of benign lung tumorigenesis, but is insufficient to elicit malignant lung adenocarcinoma without additional cooperating alterations. Sleeping Beauty-mediated transposon mutagenesis has revealed a number of genes that cooperate with BRAFV600E to promote lung cancer progression, in particular Rbms3, which encodes an RNA binding protein. Hence, this genetic screen provides a deeper understanding of the molecular mechanisms underlying BRAFV600E-driven lung carcinogenesis, and is an important step improving our ability to successfully target this disease. ]]> Vaishnavi, A. Juan, J. Scherzer, M. T. VanVeen, J. E. Stehn, C. Hackett, C. S. Dupuy, A. Chmura, S. A. van der Weyden, L. Newberg, J. Y. Mann, K. M. Liu, A. Rust, A. G. Weiss, W. A. Adams, D. Grossman, A. Mann, M. B. McMahon, M. 2022-02-28 doi:10.1101/2022.02.28.482366 Cold Spring Harbor Laboratory Press 2022-02-28 <![CDATA[ Sub-harmonic Entrainment of Cortical Gamma Oscillations to Deep Brain Stimulation in Parkinson's Disease: Predictions and Validation of a Patient-Specific Non-Linear Model ]]> https://biorxiv.org/content/10.1101/2022.03.01.482549v1?rss=1 Sermon, J. J. Olaru, M. Anso, J. Little, S. Bogacz, R. Starr, P. A. Denison, T. Duchet, B. 2022-03-04 doi:10.1101/2022.03.01.482549 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication ]]> https://biorxiv.org/content/10.1101/2022.03.06.483172v1?rss=1 Moll, T. Odon, V. Harvey, C. Collins, M. Peden, A. Franklin, J. Graves, E. Marshall, J. dos Santos Souza, C. Zhang, S. Azzouz, M. Gordon, D. Krogan, N. Ferraiuolo, L. Snyder, M. Shaw, P. Rehwinkel, J. Cooper-Knock, J. 2022-03-07 doi:10.1101/2022.03.06.483172 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Demuxafy: Improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods ]]> https://biorxiv.org/content/10.1101/2022.03.07.483367v1?rss=1 Neavin, D. Senabouth, A. Lee, J. Ripoll, A. Franke, L. Prabhakar, S. Ye, C. McCarthy, D. Mele, M. Hemberg, M. Powell, J. 2022-03-08 doi:10.1101/2022.03.07.483367 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Whole brain network analysis of neural synchrony and information flow during transition from wakefulness to light non-rapid eye movement sleep ]]> https://biorxiv.org/content/10.1101/2022.03.09.483562v1?rss=1 Fan, J. M. Kudo, K. Verma, P. Ranasinghe, K. G. Morise, H. Findlay, A. M. Kirsch, H. E. Raj, A. Krystal, A. D. Nagarajan, S. S. 2022-03-11 doi:10.1101/2022.03.09.483562 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ Cohesin erases genomic-proximity biases to drive stochastic Protocadherin expression for proper neural wiring ]]> https://biorxiv.org/content/10.1101/2022.03.09.483674v1?rss=1 Kiefer, L. Servito, G. I. F. Rajkumar, S. M. Langen, J. Chiosso, A. Buckley, A. Cha, E. S. Horta, A. Mui, M. H. Canzio, D. 2022-03-11 doi:10.1101/2022.03.09.483674 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ The maternal X chromosome impairs cognition and accelerates brain aging through epigenetic modulation in female mice ]]> https://biorxiv.org/content/10.1101/2022.03.09.483691v1?rss=1 Abdulai-Saiku, S. Gupta, S. Wang, D. Moreno, A. Huang, Y. Srivastava, D. Panning, B. Dubal, D. 2022-03-12 doi:10.1101/2022.03.09.483691 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ Thermodynamic stabilization of the von Willebrand Factor A1 domain due to loss-of-function disease-related mutations. ]]> https://biorxiv.org/content/10.1101/2022.03.10.483861v1?rss=1 Sandoval-Perez, A. Mejia-Restrepo, V. Aponte-Santamaria, C. 2022-03-11 doi:10.1101/2022.03.10.483861 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ A conserved immune trajectory of recovery in hospitalized COVID-19 patients ]]> https://biorxiv.org/content/10.1101/2022.03.15.484467v1?rss=1 200 longitudinal peripheral blood samples from patients hospitalized with COVID-19, with other respiratory infections, and healthy individuals, using mass cytometry to measure immune cells and signaling states at single cell resolution. COVID-19 patients showed a unique immune composition and an early, coordinated and elevated immune cell signaling profile, which correlated with early hospital discharge. Intra-patient time course analysis tied to clinically relevant events of recovery revealed a conserved set of immunological processes that accompany, and are unique to, disease resolution and discharge. This immunological process, together with additional changes in CD4 regulatory T cells and basophils, accompanies recovery from respiratory failure and is associated with better clinical outcomes at the time of admission. Our work elucidates the biological timeline of immune recovery from COVID-19 and provides insights into the fundamental processes of COVID-19 resolution in hospitalized patients. ]]> Okholm, T. L. H. Burnett, C. E. Tenvooren, I. Marquez, D. M. Tamaki, S. Sandoval, P. M. The UCSF COMET Consortium, Calfee, C. S. Hendrickson, C. M. Kangelaris, K. N. Langelier, C. R. Krummel, M. F. Woodruff, P. G. Erle, D. J. Ansel, K. M. Spitzer, M. H. 2022-03-16 doi:10.1101/2022.03.15.484467 Cold Spring Harbor Laboratory Press 2022-03-16 <![CDATA[ Regionally distinct trophoblast regulate barrier function and invasion in the human placenta ]]> https://biorxiv.org/content/10.1101/2022.03.21.485195v1?rss=1 Marsh, B. P. Zhou, Y. Kapzidic, M. Fisher, S. Blelloch, R. 2022-03-22 doi:10.1101/2022.03.21.485195 Cold Spring Harbor Laboratory Press 2022-03-22 <![CDATA[ mTORC2 coordinates the leading and trailing edge cytoskeletal programs during neutrophil migration ]]> https://biorxiv.org/content/10.1101/2022.03.25.484773v1?rss=1 Saha, S. Town, J. Weiner, O. 2022-03-27 doi:10.1101/2022.03.25.484773 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Transient Water Wires Mediate Selective Proton Conduction in Designed Channel Proteins ]]> https://biorxiv.org/content/10.1101/2022.03.28.485852v1?rss=1 Kratochvil, H. T. Watkins, L. C. Mravic, M. Thomaston, J. L. Nicoludis, J. M. Liu, L. Voth, G. A. DeGrado, W. 2022-03-28 doi:10.1101/2022.03.28.485852 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Long-range inhibition synchronizes and updates prefrontal task activity ]]> https://biorxiv.org/content/10.1101/2022.03.31.486626v1?rss=1 Cho, K. Shi, J. Sohal, V. S. 2022-04-01 doi:10.1101/2022.03.31.486626 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Active emulsions in living cell membranes driven by contractile stresses and transbilayer coupling ]]> https://biorxiv.org/content/10.1101/2022.04.02.486649v1?rss=1 Saha, S. Das, A. Patra, C. Anilkumar, A. A. Sil, P. Mayor, S. Rao, M. 2022-04-04 doi:10.1101/2022.04.02.486649 Cold Spring Harbor Laboratory Press 2022-04-04 <![CDATA[ Microenvironmental engineering improves the self-organization of patterned microvascular networks ]]> https://biorxiv.org/content/10.1101/2022.04.04.487052v1?rss=1 Cabral, K. A. Srivastava, V. Coyle, M. C. Stashko, C. Weaver, V. Gartner, Z. J. 2022-04-05 doi:10.1101/2022.04.04.487052 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Nucleoporins facilitate ORC loading onto chromatin ]]> https://biorxiv.org/content/10.1101/2022.04.05.487200v1?rss=1 Richards, L. Lord, C. Benton, M. L. Capra, J. A. Nordman, J. T. 2022-04-05 doi:10.1101/2022.04.05.487200 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ The {varphi}PA3 Phage Nucleus is Enclosed by a Self-Assembling, 2D Crystalline Lattice ]]> https://biorxiv.org/content/10.1101/2022.04.06.487387v1?rss=1 Nieweglowska, E. S. Brilot, A. F. Mendez, M. Baek, M. Li, J. Kokontis, C. Cheng, Y. Baker, D. Bondy-Denomy, J. Agard, D. A. 2022-04-06 doi:10.1101/2022.04.06.487387 Cold Spring Harbor Laboratory Press 2022-04-06 <![CDATA[ Modeling and mechanical perturbations reveal how spatially regulated anchorage gives rise to spatially distinct mechanics across the mammalian spindle ]]> https://biorxiv.org/content/10.1101/2022.04.08.487649v1?rss=1 Suresh, P. Galstyan, V. Phillips, R. Dumont, S. 2022-04-08 doi:10.1101/2022.04.08.487649 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ An oligogenic inheritance test detects risk genes and their interactions in congenital heart defects and developmental comorbidities ]]> https://biorxiv.org/content/10.1101/2022.04.08.487704v1?rss=1 Pittman, M. Lee, K. Srivastava, D. Pollard, K. S. 2022-04-10 doi:10.1101/2022.04.08.487704 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Estimating Brain Functional Connectivity from Common Subspace Mapping Between Structural and Functional Connectomes ]]> https://biorxiv.org/content/10.1101/2022.04.12.488055v1?rss=1 Ghosh, S. Raj, A. Nagarajan, S. 2022-04-13 doi:10.1101/2022.04.12.488055 Cold Spring Harbor Laboratory Press 2022-04-13 <![CDATA[ The cilia enriched oxysterol 7β,27-DHC is required for polycystin activation ]]> https://biorxiv.org/content/10.1101/2022.04.13.488122v1?rss=1 Ha, K. Mundt, N. Bisignano, P. Pinedo, A. Cao, E. Reiter, J. Raleigh, D. Delling, M. 2022-04-14 doi:10.1101/2022.04.13.488122 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ Chlamydia trachomatis effector Dre1 interacts with dynactin to reposition host organelles during infection ]]> https://biorxiv.org/content/10.1101/2022.04.15.488217v1?rss=1 Sherry, J. Dolat, L. MacMahon, E. Swaney, D. Bastidas, R. Johnson, J. R. Valdivia, R. Krogan, N. J. Elwell, C. Engel, J. 2022-04-18 doi:10.1101/2022.04.15.488217 Cold Spring Harbor Laboratory Press 2022-04-18 <![CDATA[ Microglial inflammatory activation paradoxically improves glucose tolerance during diet-induced obesity ]]> https://biorxiv.org/content/10.1101/2022.04.19.488819v1?rss=1 Douglass, J. D. Valdearcos, M. Ness, K. M. Wyse-Jackson, A. Dorfman, M. D. Frey, J. M. Niraula, A. Banerjee, J. Fasnacht, R. Robblee, M. Koliwad, S. K. Thaler, J. 2022-04-20 doi:10.1101/2022.04.19.488819 Cold Spring Harbor Laboratory Press 2022-04-20 <![CDATA[ Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence ]]> https://biorxiv.org/content/10.1101/2022.04.20.488974v1?rss=1 Belk, J. Yao, W. Ly, N. Freitas, K. Chen, Y.-T. Shi, Q. Valencia, A. Shifrut, E. Kale, N. Yost, K. Duffy, C. Hwee, M. Miao, Z. Ashworth, A. Mackall, C. Marson, A. Carnevale, J. Vardhana, S. Satpathy, A. 2022-04-21 doi:10.1101/2022.04.20.488974 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ Immediate myeloid depot for SARS-CoV-2 in the human lung ]]> https://biorxiv.org/content/10.1101/2022.04.28.489942v1?rss=1 Magnen, M. You, R. Rao, A. A. Davis, R. T. Rodriguez, L. Simoneau, C. R. Hysenaj, L. Hu, K. H. The UCSF COMET Consortium, Love, C. Woodruff, P. G. Erle, D. J. Hendrickson, C. M. Calfee, C. S. Matthay, M. A. Roose, J. P. Sil, A. Ott, M. Langelier, C. R. Krummel, M. F. Looney, M. R. 2022-04-29 doi:10.1101/2022.04.28.489942 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ A transcriptional mechanism involving R-loop, m6A modification and RNA abasic sites regulates an enhancer RNA of APOE. ]]> https://biorxiv.org/content/10.1101/2022.05.01.489793v1?rss=1 Watts, J. A. Grunseich, C. Rodriguez, Y. Liu, Y. Li, D. Burdick, J. T. Bruzel, A. Crouch, R. J. Mahley, R. W. Wilson, S. Cheung, V. G. 2022-05-01 doi:10.1101/2022.05.01.489793 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Ribotoxic collisions on CAG expansions disrupt proteostasis and stress responses in Huntington's Disease ]]> https://biorxiv.org/content/10.1101/2022.05.04.490528v1?rss=1 Aviner, R. Lee, T.-T. Masto, V. B. Gestaut, D. Li, K. H. Andino, R. P. Frydman, J. 2022-05-05 doi:10.1101/2022.05.04.490528 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Multi-tasking Deep Network for Tinnitus Classification and Severity Prediction from Multimodal Structural Images ]]> https://biorxiv.org/content/10.1101/2022.05.07.491000v1?rss=1 Lin, C.-T. Ghosh, S. Hinkley, L. B. Dale, C. L. Souza, A. C. Sabes, J. H. Hess, C. P. Adams, M. E. Cheung, S. W. Nagarajan, S. 2022-05-08 doi:10.1101/2022.05.07.491000 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ Accelerating the clock: Interconnected speedup of energetic and molecular dynamics during aging in cultured human cells ]]> https://biorxiv.org/content/10.1101/2022.05.10.491392v1?rss=1 100-fold hypermetabolic phenotype characterized by increased maintenance costs, and associated with increased mtDNA genome density, upregulation of senescence-associated extracellular secretion, and induction of maintenance-related transcriptional programs. 3) Finally, manipulating MR with mitochondria-targeted metabolic, genetic, and pharmacological perturbations predictably altered the molecular rate of aging, providing experimental evidence for the interplay of MR and aging in a human system. These data highlight the key role that the partitioning of energetic resources between growth and maintenance/repair processes plays in cellular aging, and converge with predictions of cross-species metabolic theory indicating that energy metabolism governs how human cells age. Significance StatementHow cells age is of fundamental importance to understanding the diversity of mammalian lifespans and the wide variation in human aging trajectories. By aging primary human fibroblasts over several months in parallel with multi-omics and energetic profiling, we find that as human cells age and progressively divide more slowly, surprisingly, they progressively consume energy faster. By manipulating cellular metabolic rates, we confirm that the higher the cellular metabolic rate, the faster cells experience telomere shortening and epigenetic aging - a speedup phenotype consistent with allometric scaling theory. By modeling robust energetic and molecular aging trajectories across donors and experimental conditions, we find that independent of cell division rates, molecular aging trajectories are predicted by the partitioning of the energy budget between growth and maintenance processes. These results integrate molecular and energetic drivers of aging and therefore have important long-term implications to understand biological aging phenomena ranging from cellular senescence to human longevity. ]]> Sturm, G. Bobba-Alves, N. Tumasian, R. A. Michelson, J. Ferrucci, L. Kempes, C. P. Picard, M. 2022-05-12 doi:10.1101/2022.05.10.491392 Cold Spring Harbor Laboratory Press 2022-05-12 <![CDATA[ Perturbation of ATP6V0A1 as a Driver and Druggable Target for Renal Proximal Tubular Cellular Injury in Nephropathic Cystinosis ]]> https://biorxiv.org/content/10.1101/2022.05.13.491826v1?rss=1 Sur, S. Kerwin, M. Pineda, S. Sansanwal, P. Sigdel, T. K. Sirota, M. Sarwal, M. M. 2022-05-13 doi:10.1101/2022.05.13.491826 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ MFGE8 links absorption of dietary fatty acids with catabolism of enterocyte lipid stores through HNF4 γ- dependent transcription of CES enzymes ]]> https://biorxiv.org/content/10.1101/2022.05.16.492147v1?rss=1 Datta, R. Gholampour, M. A. Yang, C. D. Volk, R. Lin, S. Podolsky, M. J. Arnold, T. Rieder, F. Zaro, B. W. Verzi, M. Lehner, R. Abumrad, N. Lizama, C. O. Atabai, K. 2022-05-18 doi:10.1101/2022.05.16.492147 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Long-term functional regeneration of radiation damaged salivary glands through delivery of a neurogenic hydrogel ]]> https://biorxiv.org/content/10.1101/2022.05.19.491203v1?rss=1 3 months). Thus, we reveal a novel regenerative approach for restoring epithelial organ structure and function that has significant implications for human patients. TeaserNovel application of an injectable neurogenic-based hydrogel for restoring the structure and function of radiation-damaged tissue. ]]> Li, J. Sudiwala, S. Berthoin, L. May, A. J. Mohabbat, S. Gaylord, E. A. Cruz Pacheco, N. Lombaert, I. A. M. Jeon, O. Alsberg, E. Bahney, C. S. Knox, S. M. 2022-05-19 doi:10.1101/2022.05.19.491203 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Two therapeutic CRISPR/Cas9 gene editing approaches revert FTD/ALS cellular pathology caused by a C9orf72 repeat expansion mutation in patient derived cells ]]> https://biorxiv.org/content/10.1101/2022.05.21.492887v1?rss=1 Sckaff, M. Gill, K. Sachdev, A. Birk, A. M. Aladesuyi Arogundade, O. Watry, H. L. Keough, K. C. Tsai, Y.-C. Ziegle, J. Conklin, B. R. Clelland, C. D. 2022-05-21 doi:10.1101/2022.05.21.492887 Cold Spring Harbor Laboratory Press 2022-05-21 <![CDATA[ Reconstitution of the SARS-CoV-2 ribonucleosome provides insights into genomic RNA packaging and regulation by phosphorylation ]]> https://biorxiv.org/content/10.1101/2022.05.23.493138v1?rss=1 Carlson, C. Adly, A. Bi, M. Cheng, Y. Morgan, D. O. 2022-05-24 doi:10.1101/2022.05.23.493138 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ The transcription regulator Lmo3 is required for cell fate specification in the external globus pallidus. ]]> https://biorxiv.org/content/10.1101/2022.05.24.493171v1?rss=1 Biswas, S. Chan, C. S. Rubenstein, J. L. R. Gan, L. 2022-05-24 doi:10.1101/2022.05.24.493171 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ A preprocessing and functional connectivity analysis pipeline for mesoscale calcium imaging ]]> https://biorxiv.org/content/10.1101/2022.05.24.493310v1?rss=1 O'Connor, D. Mandino, F. Shen, X. Horien, C. Ge, X. Herman, P. Crair, M. Papademetris, X. Lake, E. M. Constable, R. T. 2022-05-25 doi:10.1101/2022.05.24.493310 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Fatty acid synthesis knockdown promotes biofilm wrinkling and inhibits sporulation in Bacillus subtilis ]]> https://biorxiv.org/content/10.1101/2022.05.31.494136v1?rss=1 Arjes, H. A. Gui, H. Porter, R. Atolia, E. Peters, J. Gross, C. Kearns, D. B. Huang, K. A. 2022-05-31 doi:10.1101/2022.05.31.494136 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Physical and functional convergence of the autism risk genes Scn2a and Ank2 in neocortical pyramidal cell dendrites ]]> https://biorxiv.org/content/10.1101/2022.05.31.494205v1?rss=1 Nelson, A. D. Catalfio, A. M. Gupta, J. M. Min, L. Caballero-Floran, R. N. Dean, K. P. Elvira, C. C. Derderian, K. D. Kyoung, H. Sahagun, A. Sanders, S. J. Bender, K. Jenkins, P. M. 2022-05-31 doi:10.1101/2022.05.31.494205 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Male mice carrying the BDNF Val68Met polymorphism exhibit alcohol preferences versus social interaction and acute tolerance through malfunction of BDNF in the ventral hippocampus ]]> https://biorxiv.org/content/10.1101/2022.06.01.494180v1?rss=1 Moffat, J. J. Sakhai, S. Hoisington, Z. W. Ron, D. 2022-06-03 doi:10.1101/2022.06.01.494180 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Quantitative proteomic analysis reveals apoE4-dependent phosphorylation of the actin-regulating protein VASP ]]> https://biorxiv.org/content/10.1101/2022.06.06.495052v1?rss=1 Cakir, Z. Lord, S. J. Jimenez-Morales, D. Jang, G. M. Polacco, B. J. Eckhardt, M. Newton, B. W. Zhou, Y. Orr, A. L. Johnson, J. R. Mullins, D. Krogan, N. J. Swaney, D. L. Mahley, R. W. 2022-06-07 doi:10.1101/2022.06.06.495052 Cold Spring Harbor Laboratory Press 2022-06-07 <![CDATA[ Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-ray Crystallography ]]> https://biorxiv.org/content/10.1101/2022.06.10.495662v1?rss=1 Wolff, A. M. Nango, E. Young, I. D. Brewster, A. S. Kubo, M. Nomura, T. Sugahara, M. Owada, S. Barad, B. A. Ito, K. Bhowmick, A. Carbajo, S. Hino, T. Holton, J. M. Im, D. O'Riordan, L. J. Tanaka, T. Tanaka, R. Sierra, R. G. Yumoto, F. Tono, K. Iwata, S. Sauter, N. K. Fraser, J. S. Thompson, M. C. 2022-06-12 doi:10.1101/2022.06.10.495662 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ A Development-Inspired Niche for Homeostatic Human Mini-Intestines ]]> https://biorxiv.org/content/10.1101/2022.06.12.495827v1?rss=1 Childs, C. J. Holloway, E. M. Sweet, C. W. Tsai, Y.-H. Wu, A. Wu, J. Cardenas, O. P. Capeling, M. M. Eiken, M. Zwick, R. Palikuqi, B. Trentesaux, C. Zhang, C. Glass, I. Loebel, C. Yu, Q. Camp, G. Sexton, J. Z. Klein, O. D. Verzi, M. P. Spence, J. J. 2022-06-12 doi:10.1101/2022.06.12.495827 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Endocytic trafficking determines cellular tolerance of presynaptic opioid signaling ]]> https://biorxiv.org/content/10.1101/2022.06.15.496340v1?rss=1 Jullie, D. Benitez, C. Knight, T. A. Von Zastrow, M. 2022-06-16 doi:10.1101/2022.06.15.496340 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Early and lifelong effects of APOE4 on neuronal gene expression networks relevant to Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2022.06.16.496371v1?rss=1 Grone, B. Zalocusky, K. Hao, Y. Yoon, S. Y. Arriola, P. Huang, Y. 2022-06-17 doi:10.1101/2022.06.16.496371 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Dynamic top-down biasing implements rapid adaptive changes to individual movements ]]> https://biorxiv.org/content/10.1101/2022.06.16.496455v1?rss=1 Tian, L. Y. Warren, T. L. Brainard, M. S. 2022-06-17 doi:10.1101/2022.06.16.496455 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Systems Analysis of de novo Mutations in Congenital Heart Diseases Identified a Molecular Network in Hypoplastic Left Heart Syndrome ]]> https://biorxiv.org/content/10.1101/2022.06.23.496464v1?rss=1 Wang, Y. J. Zhang, X. Lam, C. K. Guo, H. Wang, C. Zhang, S. Wu, J. C. Snyder, M. Li, J. 2022-06-26 doi:10.1101/2022.06.23.496464 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Pitfalls of genotyping microbial communities with rapidly growing genome collections ]]> https://biorxiv.org/content/10.1101/2022.06.30.498336v1?rss=1 Zhao, C. Shi, Z. J. Pollard, K. S. 2022-07-02 doi:10.1101/2022.06.30.498336 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Membrane curvature sensing and symmetry breaking of the M2 proton channel from Influenza A ]]> https://biorxiv.org/content/10.1101/2022.07.02.498578v1?rss=1 Helsell, C. V. M. Marcoline, F. V. Lincoff, J. Natale, A. M. Grabe, M. 2022-07-05 doi:10.1101/2022.07.02.498578 Cold Spring Harbor Laboratory Press 2022-07-05 <![CDATA[ GPCR-dependent spatiotemporal cAMP generation confers functional specificity in cardiomyocytes and cardiac responses ]]> https://biorxiv.org/content/10.1101/2022.07.13.499965v1?rss=1 Irannejad, R. Mai, Q. N. Lin, T.-Y. Zhang, H. Wilson, E. Chien, H.-C. Yee, S. W. Giacomini, K. M. Olgin, J. E. 2022-07-13 doi:10.1101/2022.07.13.499965 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq ]]> https://biorxiv.org/content/10.1101/2022.07.15.500120v1?rss=1 Sunshine, S. Puschnik, A. S. Replogle, J. M. Laurie, M. T. Liu, J. Zha, B. S. Nunez, J. K. Byrum, J. R. McMorrow, A. H. Frieman, M. B. Winkler, J. Qiu, X. Rosenberg, O. S. Leonetti, M. D. Ye, C. J. Weissman, J. S. DeRisi, J. L. Hein, M. Y. 2022-07-17 doi:10.1101/2022.07.15.500120 Cold Spring Harbor Laboratory Press 2022-07-17 <![CDATA[ Evidence for intercellular bridges and radial patterning of meiotic initiation in the human fetal ovary ]]> https://biorxiv.org/content/10.1101/2022.07.18.500281v1?rss=1 Soygur, B. Derpinghaus, A. Cunha, G. R. Baskin, L. S. Laird, D. J. 2022-07-18 doi:10.1101/2022.07.18.500281 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Wireless Measurements Using Electrical Impedance Spectroscopy to Monitor Fracture Healing ]]> https://biorxiv.org/content/10.1101/2022.07.23.501237v1?rss=1 Fukase, N. Duke, V. R. Lin, M. C. Stake, I. K. Huard, M. Huard, J. Marmor, M. T. Maharbiz, M. M. Ehrhart, N. P. Bahney, C. S. Herfat, S. T. 2022-07-23 doi:10.1101/2022.07.23.501237 Cold Spring Harbor Laboratory Press 2022-07-23 <![CDATA[ Neuronal Activity Alters Neuron to OPC Synapses ]]> https://biorxiv.org/content/10.1101/2022.07.25.501254v1?rss=1 Moura, D. S. Parvathaneni, A. Sahagun, A. Noguchi, H. Tilton, I. Brennan, E. Brock, R. M. Halladay, L. R. Pleasure, S. J. Cocas, L. A. 2022-07-25 doi:10.1101/2022.07.25.501254 Cold Spring Harbor Laboratory Press 2022-07-25 <![CDATA[ Allosteric Regulation of a Synaptic Vesicle Glutamate Transporter ]]> https://biorxiv.org/content/10.1101/2022.07.26.501550v1?rss=1 Li, F. Eriksen, J. Oses-Prieto, J. A. Gomez, Y. K. Xu, H. Finer-Moore, J. Nguyen, P. Bowen, A. Nelson, A. Burlingame, A. Grabe, M. Stroud, R. Edwards, R. 2022-07-26 doi:10.1101/2022.07.26.501550 Cold Spring Harbor Laboratory Press 2022-07-26 <![CDATA[ Modular Pooled Discovery of Synthetic Knockin Sequences to Program Durable Cell Therapies ]]> https://biorxiv.org/content/10.1101/2022.07.27.501186v1?rss=1 Blaeschke, F. Chen, Y. Y. Apathy, R. Li, Z. Mowery, C. T. Nyberg, W. A. To, A. Yu, R. Bueno, R. Kim, M. C. Schmidt, R. Goodman, D. B. Feuchtinger, T. Eyquem, J. Ye, C. J. Shifrut, E. Roth, T. L. Marson, A. 2022-07-27 doi:10.1101/2022.07.27.501186 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ Differential Analysis of Stromal-Epithelial Interactions between In Situ and Invasive Breast Cancer using Gene Expression Profiling ]]> https://biorxiv.org/content/10.1101/2022.07.30.502150v1?rss=1 Officer, A. Dempsey, A. M. Murrow, L. M. Gartner, Z. Tamayo, P. Yau, C. Harismendy, O. 2022-08-02 doi:10.1101/2022.07.30.502150 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Profile of the somatic mutational landscape in breast tumors from Hispanic/Latina women ]]> https://biorxiv.org/content/10.1101/2022.08.01.502349v1?rss=1 Ding, Y. C. Song, H. Adamson, A. Schmolze, D. Hu, D. Huntsman, S. Steele, L. Patrick, C. Hernandez, N. Adams, C. D. Fejerman, L. Gardner, K. L. Napoles, A. M. Perez-Stable, E. J. Weitzel, J. N. Bengtsson, H. Huang, F. W. Neuhausen, S. L. Ziv, E. 2022-08-03 doi:10.1101/2022.08.01.502349 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Optogenetic control of RelA reveals effect of transcription factor dynamics on downstream gene expression ]]> https://biorxiv.org/content/10.1101/2022.08.03.502739v1?rss=1 Osimiri, L. C. Bonny, A. R. Takagishi, S. R. Luecke, S. Riehs, N. Hoffmann, A. El-Samad, H. 2022-08-05 doi:10.1101/2022.08.03.502739 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Sensitive multimodal profiling of native DNA by transposase-mediated single-molecule sequencing ]]> https://biorxiv.org/content/10.1101/2022.08.07.502893v1?rss=1 Nanda, A. S. Wu, K. Kasinathan, S. Ostrowski, M. S. Clugston, A. S. Satpathy, A. Sweet-Cordero, E. A. Goodarzi, H. Ramani, V. 2022-08-07 doi:10.1101/2022.08.07.502893 Cold Spring Harbor Laboratory Press 2022-08-07 <![CDATA[ Reliable energy-based antibody humanization and stabilization ]]> https://biorxiv.org/content/10.1101/2022.08.14.503891v1?rss=1 Tennenhouse, A. Khmelnitsky, L. Yeshaya, N. Noronha, A. Lindzen, M. Khalaila, R. Zaretsky, I. Fridmann Sirkis, Y. Galon-Wolfenson, Y. Abramson, J. Yarden, Y. Fass, D. Fleishman, S. J. 2022-08-15 doi:10.1101/2022.08.14.503891 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Single-cell RNA sequencing identifies regulators of differentiation and nutritional cues in Drosophila female germ cells ]]> https://biorxiv.org/content/10.1101/2022.08.15.504025v1?rss=1 Sun, Z. Nystul, T. Zhong, G. 2022-08-15 doi:10.1101/2022.08.15.504025 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Deriving Schwann Cells from hPSCs Enables Disease Modeling and Drug Discovery for Diabetic Peripheral Neuropathy ]]> https://biorxiv.org/content/10.1101/2022.08.16.504209v1?rss=1 Majd, H. Amin, S. Ghazizadeh, Z. Cesiulis, A. Arroyo, E. Lankford, K. Farahvashi, S. Chemel, A. K. Okoye, M. Scantlen, M. D. Tchieu, J. Calder, E. L. LeRouzic, V. Arab, A. Goodarzi, H. Pasternak, G. Kocsis, J. D. Chen, S. Studer, L. Fattahi, F. 2022-08-17 doi:10.1101/2022.08.16.504209 Cold Spring Harbor Laboratory Press 2022-08-17 <![CDATA[ Arrestin-3 agonism at D3 dopamine receptors defines a subclass of second generation antipsychotics that promotes drug tolerance ]]> https://biorxiv.org/content/10.1101/2022.08.17.504324v1?rss=1 Schamiloglu, S. Lewis, E. Hergarden, A. C. Bender, K. Whistler, J. L. 2022-08-18 doi:10.1101/2022.08.17.504324 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ Testing the ion-current model for flagellar length sensing and IFT regulation ]]> https://biorxiv.org/content/10.1101/2022.08.20.504661v1?rss=1 Ishikawa, H. Moore, J. Diener, D. Delling, M. Marshall, W. F. 2022-08-21 doi:10.1101/2022.08.20.504661 Cold Spring Harbor Laboratory Press 2022-08-21 <![CDATA[ A Mesp1-dependent developmental breakpoint in transcriptional and epigenomic specification of early cardiac precursors ]]> https://biorxiv.org/content/10.1101/2022.08.22.504863v1?rss=1 Krup, A. L. Winchester, S. Ranade, S. Agrawal, A. Devine, W. P. Sinha, T. Choudhary, K. Dominguez, M. Thomas, R. Black, B. L. Srivastava, D. Bruneau, B. 2022-08-22 doi:10.1101/2022.08.22.504863 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Defective Ca2+- dependent activation of TRPM4 channels contributes to age-related cerebral small vessel disease in Col4a1 mutant mice ]]> https://biorxiv.org/content/10.1101/2022.08.24.505186v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@11a8cb9org.highwire.dtl.DTLVardef@d00b8org.highwire.dtl.DTLVardef@1aa5b24org.highwire.dtl.DTLVardef@145a9c0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yamasaki, E. Thakore, P. Ali, S. Solano, A. S. Wang, X. Gao, X. Labelle-Dumais, C. Chaumeil, M. M. Gould, D. B. Earley, S. 2022-08-26 doi:10.1101/2022.08.24.505186 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Organ-Specific Fuel Rewiring in Acute and Chronic Hypoxia Redistributes Glucose and Fatty Acid Metabolism ]]> https://biorxiv.org/content/10.1101/2022.08.25.505289v1?rss=1 Midha, A. D. Zhou, Y. Queliconi, B. B. Barrios, A. M. Fong, C. O. Y. Blecha, J. E. VanBrocklin, H. Seo, Y. Jain, I. H. 2022-08-26 doi:10.1101/2022.08.25.505289 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Genome-wide prediction of disease variants with a deep protein language model ]]> https://biorxiv.org/content/10.1101/2022.08.25.505311v1?rss=1 Brandes, N. Goldman, G. Wang, C. H. Ye, C. J. Ntranos, V. 2022-08-26 doi:10.1101/2022.08.25.505311 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Plasma Proteome Perturbation for CMV DNAemia in Kidney Transplantation ]]> https://biorxiv.org/content/10.1101/2022.08.25.505318v1?rss=1 Sigdel, T. Boada, P. Kerwin, M. Rashmi, P. Gjertson, D. Rossetti, M. Sur, S. Munar, D. Cimino, J. Ahn, R. Pickering, H. Sen, S. Parmar, R. Fatou, B. Steen, H. Schaenman, J. Bunnapradist, S. Reed, E. Sarwal, M. M. CMV Systems Immunobiology Group, 2022-08-26 doi:10.1101/2022.08.25.505318 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ LSD-induced increase of Ising temperature and algorithmic complexity of brain dynamics ]]> https://biorxiv.org/content/10.1101/2022.08.27.505518v1?rss=1 Ruffini, G. Damiani, G. Lozano-Soldevilla, D. Deco, N. Rosas, F. Kiani, N. Ponce-Alvarez, A. Kringelbach, M. L. Carhart-Harris, R. Deco, G. L. 2022-08-29 doi:10.1101/2022.08.27.505518 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Genome-wide and high-density CRISPR-Cas9 screens identify point mutations in PARP1 causing PARP inhibitor resistance ]]> https://biorxiv.org/content/10.1101/203224v1?rss=1 Pettitt, S. J. Krastev, D. B. Brandsma, I. Drean, A. Song, F. Aleksandrov, R. Harrell, M. I. Menon, M. Brough, R. Campbell, J. Frankum, J. Ranes, M. Pemberton, H. N. Rafiq, R. Fenwick, K. Swain, A. Guettler, S. Lee, J.-M. Swisher, E. M. Stoynov, S. Yusa, K. Ashworth, A. Lord, C. J. 2017-10-14 doi:10.1101/203224 Cold Spring Harbor Laboratory Press 2017-10-14 <![CDATA[ Light-Activated Cell Identification and Sorting (LACIS): A New Method to Identify and Select Edited Clones on a Microfluidic Device ]]> https://biorxiv.org/content/10.1101/204693v1?rss=1 Mocciaro, A. Roth, T. Bennett, H. Soumillon, M. Shah, A. Hiatt, J. Chapman, K. Marson, A. Lavieu, G. 2017-10-17 doi:10.1101/204693 Cold Spring Harbor Laboratory Press 2017-10-17 <![CDATA[ Hsp90 dictates viral sequence space by balancing the evolutionary tradeoffs between protein stability, aggregation and translation rate ]]> https://biorxiv.org/content/10.1101/208462v1?rss=1 Geller, R. Pechmann, S. Acevedo, A. Andino, R. Frydman, J. 2017-10-24 doi:10.1101/208462 Cold Spring Harbor Laboratory Press 2017-10-24 <![CDATA[ Robust identification of deletions in exome and genome sequence data based on clustering of Mendelian errors ]]> https://biorxiv.org/content/10.1101/209478v1?rss=1 Manheimer, K. B. Patel, N. Richter, F. Gorham, J. Tai, A. C. Homsy, J. Boskovski, M. T. Parfenov, M. Goldmuntz, E. Chung, W. K. Brueckner, M. Tristani-Firouzi, M. Srivastava, D. Seidman, J. G. Seidman, C. E. Gelb, B. D. Sharp, A. J. 2017-10-26 doi:10.1101/209478 Cold Spring Harbor Laboratory Press 2017-10-26 <![CDATA[ A size-invariant bud-length timer enables robustness in yeast cell size control ]]> https://biorxiv.org/content/10.1101/211714v1?rss=1 Allard, C. A. H. Decker, F. Weiner, O. D. Toettcher, J. E. Graziano, B. R. 2017-10-31 doi:10.1101/211714 Cold Spring Harbor Laboratory Press 2017-10-31 <![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[ Protection from epidemics is a driving force for evolution of lifespan setpoints ]]> https://biorxiv.org/content/10.1101/215202v1?rss=1 Lidsky, P. V. Andino, R. 2017-11-06 doi:10.1101/215202 Cold Spring Harbor Laboratory Press 2017-11-06 <![CDATA[ Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly ]]> https://biorxiv.org/content/10.1101/217968v1?rss=1 Parsa, J.-Y. Boudoukha, S. Burke, J. Homer, C. Madhani, H. 2017-11-11 doi:10.1101/217968 Cold Spring Harbor Laboratory Press 2017-11-11 <![CDATA[ New routes for PTP1B allosteric inhibition by multitemperature crystallography, fragment screening and covalent tethering ]]> https://biorxiv.org/content/10.1101/218966v1?rss=1 Keedy, D. A. Hill, Z. B. Biel, J. T. Kang, E. Rettenmaier, T. J. Brandao-Neto, J. Pearce, N. M. von Delft, F. Wells, J. A. Fraser, J. S. 2017-11-13 doi:10.1101/218966 Cold Spring Harbor Laboratory Press 2017-11-13 <![CDATA[ Bringing Diffuse X-ray Scattering Into Focus ]]> https://biorxiv.org/content/10.1101/219113v1?rss=1 Wall, M. Wolff, A. M. Fraser, J. S. 2017-11-13 doi:10.1101/219113 Cold Spring Harbor Laboratory Press 2017-11-13 <![CDATA[ Singleton Variants Dominate the Genetic Architecture of Human Gene Expression ]]> https://biorxiv.org/content/10.1101/219238v1?rss=1 Hernandez, R. D. Uricchio, L. H. Hartman, K. Ye, J. Dahl, A. Zaitlen, N. 2017-11-14 doi:10.1101/219238 Cold Spring Harbor Laboratory Press 2017-11-14 <![CDATA[ Cytoplasmic import and processing of mRNA amplify transcriptional bursts accounting for the majority of cellular noise ]]> https://biorxiv.org/content/10.1101/222901v1?rss=1 Hansen, M. M. K. Desai, R. V. Simpson, M. L. Weinberger, L. S. 2017-11-21 doi:10.1101/222901 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ Spliceosome profiling visualizes the operations of a dynamic RNP in vivo at nucleotide resolution ]]> https://biorxiv.org/content/10.1101/224170v1?rss=1 Burke, J. Longhurst, A. Merkurjev, D. Sales-Lee, J. Rao, B. Moresco, J. Yates, J. Li, J. J. Madhani, H. D. 2017-11-22 doi:10.1101/224170 Cold Spring Harbor Laboratory Press 2017-11-22 <![CDATA[ Tracing cellular heterogeneity in pooled genetic screens via multi-level barcoding ]]> https://biorxiv.org/content/10.1101/224345v1?rss=1 Boettcher, M. Covarrubias, S. Biton, A. Blau, J. A. Wang, H. Zaitlen, N. McManus, M. T. 2017-11-26 doi:10.1101/224345 Cold Spring Harbor Laboratory Press 2017-11-26 <![CDATA[ Developmental loci harbor clusters of accelerated regions that evolved independently in ape lineages ]]> https://biorxiv.org/content/10.1101/226019v1?rss=1 Kostka, D. Holloway, A. K. Pollard, K. 2017-11-28 doi:10.1101/226019 Cold Spring Harbor Laboratory Press 2017-11-28 <![CDATA[ High accuracy measurements of nanometer-scale distances between fluorophores at the single-molecule level ]]> https://biorxiv.org/content/10.1101/234740v1?rss=1 2 nm, using a standard TIRF microscope and open-source software. We applied our two-color localization method to uncover a [~]4 nm conformational change in the "stalk" of the motor protein dynein, revealing unexpected flexibility in this antiparallel coiled-coil domain. These new methods enable high-accuracy distance measurements of single-molecules that can be used over a wide range of length scales. ]]> Niekamp, S. Sung, J. Huynh, W. Vale, R. D. Stuurman, N. 2017-12-15 doi:10.1101/234740 Cold Spring Harbor Laboratory Press 2017-12-15 <![CDATA[ A Comprehensive Evaluation of the Genetic Architecture of Sudden Cardiac Arrest ]]> https://biorxiv.org/content/10.1101/235234v1?rss=1 Ashar, F. N. Mitchell, R. N. Albert, C. M. Newton-Cheh, C. Brody, J. A. Muller-Nurasyid, M. Moes, A. Meitinger, T. Mak, A. Huikuri, H. Junttila, M. J. Goyette, P. Pulit, S. L. Pazoki, R. Tanck, M. W. Blom, M. T. Zhao, X. Hauvlinna, A. S. Jabbari, R. Glinge, C. Tragante, V. Escher, S. A. Chakravarti, A. Ehret, G. Coresh, J. Li, M. Prineas, R. J. Franco, O. H. Kwok, P.-Y. Lumley, T. Dumas, F. McKnight, B. Rotter, J. I. Lemaitre, R. N. Heckbert, S. R. O'Donnell, C. J. Hwang, S.-J. Tardif, J.-C. Kortelainen, M.-L. VanDenburgh, M. Uitterlinden, A. G. Hofman, 2017-12-16 doi:10.1101/235234 Cold Spring Harbor Laboratory Press 2017-12-16 <![CDATA[ Olfactory and Vomeronasal Receptor Feedback Employ Divergent Mechanisms of PERK Activation ]]> https://biorxiv.org/content/10.1101/239830v1?rss=1 Dalton, R. Karagoz, E. Kahiapo, J. Sharma, R. Bashkirova, L. Lyons, D. Matsunami, H. Walter, P. 2018-01-04 doi:10.1101/239830 Cold Spring Harbor Laboratory Press 2018-01-04 <![CDATA[ Rapid Identification and Validation of Novel Rheumatoid Arthritis Drug Treatments using an Integrative Bioinformatics Platform ]]> https://biorxiv.org/content/10.1101/243998v1?rss=1 Daugherty, A. C. Farrington, C. Hakin, I. Mujahid, S. Noblin, E. S. Radin, A. M. Chua, M.-S. Rabe, M. Fernald, G. Ford, D. Sirota, M. Schaevitz, L. Radin, A. A. 2018-01-07 doi:10.1101/243998 Cold Spring Harbor Laboratory Press 2018-01-07 <![CDATA[ Real time genetic compensation operationally defines the dynamic demands of feedback control ]]> https://biorxiv.org/content/10.1101/244020v1?rss=1 Harrigan, P. Madhani, H. El-Samad, H. 2018-01-07 doi:10.1101/244020 Cold Spring Harbor Laboratory Press 2018-01-07 <![CDATA[ Ostreococcus tauri is a high-lipid content green algae that extrudes clustered lipid droplets ]]> https://biorxiv.org/content/10.1101/249052v1?rss=1 Smallwood, C. R. Chrisler, W. Chen, J.-H. Patello, E. Thomas, M. Boudreau, R. Ekman, A. Wang, H. McDermott, G. Evans, J. E. 2018-01-17 doi:10.1101/249052 Cold Spring Harbor Laboratory Press 2018-01-17 <![CDATA[ Next generation CRISPR/Cas9 transcriptional activation in Drosophila using flySAM ]]> https://biorxiv.org/content/10.1101/252031v1?rss=1 Jia, Y. Xu, R.-G. Ren, X. Ewen-Campen, B. Rajakumar, R. Zirin, J. Yang-Zhou, D. Zhao, R. Wang, F. Mao, D. Peng, P. Qiao, H.-H. Wang, X. Liu, L.-P. Xu, B. Ji, J.-Y. Lu, Q. Sun, J. Perrimon, N. Ni, J.-Q. 2018-01-31 doi:10.1101/252031 Cold Spring Harbor Laboratory Press 2018-01-31 <![CDATA[ OGT binds a conserved C-terminal domain of TET1 toregulate TET1 activity and function in development ]]> https://biorxiv.org/content/10.1101/253872v1?rss=1 Hrit, J. Li, C. Martin, E. A. Simental, E. Goll, M. Panning, B. 2018-01-25 doi:10.1101/253872 Cold Spring Harbor Laboratory Press 2018-01-25 <![CDATA[ Conserved Roles of C. elegans and Human MANFs in Sulfatide Binding and Cytoprotection ]]> https://biorxiv.org/content/10.1101/263731v1?rss=1 Bai, M. Vozdek, R. Hnizda, A. Jiang, C. Wang, B. Kuchar, L. Li, T. Zhang, Y. Wood, C. Feng, L. Dang, Y. Ma, D. K. 2018-02-11 doi:10.1101/263731 Cold Spring Harbor Laboratory Press 2018-02-11 <![CDATA[ SOX2 Regulation by Hedgehog Signaling Controls Adult Lingual Epithelium Homeostasis ]]> https://biorxiv.org/content/10.1101/269522v1?rss=1 Castillo-Azofeifa, D. Seidel, K. Gross, L. Jacquez, B. Klein, O. D. Barlow, L. A. 2018-02-22 doi:10.1101/269522 Cold Spring Harbor Laboratory Press 2018-02-22 <![CDATA[ A Genetic Program Mediates Cold-warming Response and Promotes Stress-induced Phenoptosis in C. elegans ]]> https://biorxiv.org/content/10.1101/271106v1?rss=1 Jiang, W. Wei, Y. Long, Y. Owen, A. Wang, B. Wu, X. Luo, S. Dang, Y. Ma, D. 2018-02-24 doi:10.1101/271106 Cold Spring Harbor Laboratory Press 2018-02-24 <![CDATA[ A novel xenograft model reveals invasive mesenchymal transition and ineffective angiogenic response during the evolution of resistance to anti-angiogenic therapy ]]> https://biorxiv.org/content/10.1101/272328v1?rss=1 Jahangiri, A. Chen, W. Chandra, A. Nguyen, A. Weiss, J. Wolf, K. Lin, G. Rick, J. Sidorov, M. Flanigan, P. Yagnik, G. Carbonell, W. S. Kumar, S. Aghi, M. K. 2018-02-28 doi:10.1101/272328 Cold Spring Harbor Laboratory Press 2018-02-28 <![CDATA[ Robotic automation of droplet microfluidics ]]> https://biorxiv.org/content/10.1101/278556v1?rss=1 Tran, T. M. Kim, S. C. Abate, A. R. 2018-03-07 doi:10.1101/278556 Cold Spring Harbor Laboratory Press 2018-03-07 <![CDATA[ Single-cell RNA-seq reveals profibrotic macrophages in lung fibrosis ]]> https://biorxiv.org/content/10.1101/284604v1?rss=1 Aran, D. Looney, A. P. Liu, L. Fong, V. Hsu, A. Wolters, P. J. Abate, A. Butte, A. J. Bhattacharya, M. 2018-03-19 doi:10.1101/284604 Cold Spring Harbor Laboratory Press 2018-03-19 <![CDATA[ Avian keratin disorder of Alaska black-capped chickadees is associated with Poecivirus infection ]]> https://biorxiv.org/content/10.1101/284992v1?rss=1 Zylberberg, M. Van Hemert, C. Handel, C. M. DeRisi, J. 2018-03-19 doi:10.1101/284992 Cold Spring Harbor Laboratory Press 2018-03-19 <![CDATA[ Diverse progenitor cells preserve salivary gland ductal architecture after radiation induced damage ]]> https://biorxiv.org/content/10.1101/295501v1?rss=1 May, A. Cruz Pacheco, N. Emmerson, E. Siedel, K. Nathan, S. Muench, M. O. Klein, O. D. Knox, S. M. 2018-04-05 doi:10.1101/295501 Cold Spring Harbor Laboratory Press 2018-04-05 <![CDATA[ Approaches to maximize sgRNA-barcode coupling in Perturb-seq screens ]]> https://biorxiv.org/content/10.1101/298349v1?rss=1 Adamson, B. Norman, T. M. Jost, M. Weissman, J. S. 2018-04-11 doi:10.1101/298349 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ Construction of a novel phagemid to produce custom DNA origami scaffolds ]]> https://biorxiv.org/content/10.1101/309682v1?rss=1 Nafisi, P. M. Aksel, T. Douglas, S. M. 2018-04-27 doi:10.1101/309682 Cold Spring Harbor Laboratory Press 2018-04-27 <![CDATA[ Mechanistic Origins of Dynamic Instability in Filaments from the Phage Tubulin, PhuZ ]]> https://biorxiv.org/content/10.1101/311498v1?rss=1 Zehr, E. A. Rohu, A. Liu, Y. Verba, K. A. Pogliano, J. Grigorieff, N. Agard, D. A. 2018-04-30 doi:10.1101/311498 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Heart enhancers with deeply conserved regulatory activity are established early in development ]]> https://biorxiv.org/content/10.1101/312611v1?rss=1 Yuan, X. Song, M. Devine, P. Bruneau, B. G. Scott, I. C. Wilson, M. D. 2018-05-04 doi:10.1101/312611 Cold Spring Harbor Laboratory Press 2018-05-04 <![CDATA[ crisprQTL mapping as a genome-wide association framework for cellular genetic screens ]]> https://biorxiv.org/content/10.1101/314344v1?rss=1 Gasperini, M. Hill, A. McFaline-Figueroa, J. L. Martin, B. Trapnell, C. Ahituv, N. Shendure, J. 2018-05-04 doi:10.1101/314344 Cold Spring Harbor Laboratory Press 2018-05-04 <![CDATA[ Chimeric antigen receptors that trigger phagocytosis ]]> https://biorxiv.org/content/10.1101/316323v1?rss=1 Morrissey, M. A. Williamson, A. P. Steinbach, A. M. Roberts, E. W. Kern, N. Headley, M. B. Vale, R. D. 2018-05-07 doi:10.1101/316323 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ Decoupling the impact of microRNAs on translational repression versus RNA degradation in embryonic stem cells ]]> https://biorxiv.org/content/10.1101/316679v1?rss=1 Blelloch, R. Freimer, J. W. Hu, T. 2018-05-07 doi:10.1101/316679 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ The Clinical Imperative for Inclusivity: Race, Ethnicity, and Ancestry (REA) in Genomics ]]> https://biorxiv.org/content/10.1101/317800v1?rss=1 Popejoy, A. B. Ritter, D. I. Crooks, K. Currey, E. Fullerton, S. M. Hindorff, L. A. Koenig, B. Ramos, E. M. Sorokin, E. P. Wand, H. Wright, M. W. Zou, J. Gignoux, C. R. Bonham, V. L. Plon, S. E. Bustamante, C. D. The Clinical Genome Resource (ClinGen) Ancestry and Diversity Working Group (ADWG), 2018-05-09 doi:10.1101/317800 Cold Spring Harbor Laboratory Press 2018-05-09 <![CDATA[ A data mining paradigm for identifying key factors in biological processes using gene expression data ]]> https://biorxiv.org/content/10.1101/327478v1?rss=1 Li, J. Zheng, L. Uchiyama, A. Bin, L. Mauro, T. M. Elias, P. M. Pawelczyk, T. Sakowicz-Burkiewicz, M. Trzeciak, M. Leung, D. Y. M. Morasso, M. I. Yu, P. 2018-05-21 doi:10.1101/327478 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ Cofilin-actin rod formation in neuronal processes after brain ischemia ]]> https://biorxiv.org/content/10.1101/331082v1?rss=1 Won, S. J. Minnella, A. M. Wu, L. Eun, C. H. Rome, E. Shaw, A. E. Herson, P. S. Bamburg, J. R. Swanson, R. A. 2018-05-25 doi:10.1101/331082 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Early projections of Ebola outbreak size and duration with and without vaccine use in Equateur, Democratic Republic of Congo, as of May 21, 2018 ]]> https://biorxiv.org/content/10.1101/331447v1?rss=1 Kelly, J. D. Worden, L. Wannier, R. Hoff, N. A. Mukadi, P. Sinai, C. Ackley, S. Chen, X. Gao, D. Rutherford, G. W. Lietman, T. M. Muyembe-Tamfum, J. J. Rimoin, A. W. Porco, T. C. 2018-05-26 doi:10.1101/331447 Cold Spring Harbor Laboratory Press 2018-05-26 <![CDATA[ A genetically-encoded fluorescent sensor enables rapid and specific detection of dopamine in flies, fish, and mice ]]> https://biorxiv.org/content/10.1101/332528v1?rss=1 Sun, F. Zeng, J. Jing, M. Zhou, J. Feng, J. Owen, S. F. Luo, Y. Li, F. Yamaguchi, T. Yong, Z. Gao, Y. Peng, W. Wang, L. Zhang, S. Du, J. Lin, D. Xu, M. Kreitzer, A. C. Cui, G. Li, Y. 2018-05-31 doi:10.1101/332528 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ Modeling meiotic homolog pairing: increased fidelity from a tug of war between telomere forces and a pairing-based Brownian ratchet ]]> https://biorxiv.org/content/10.1101/332767v1?rss=1 Marshall, W. F. Fung, J. C. 2018-05-28 doi:10.1101/332767 Cold Spring Harbor Laboratory Press 2018-05-28 <![CDATA[ Rapid Therapeutic Recommendations in the Context of a Global Public Health Crisis using Translational Bioinformatics Approaches: A proof-of-concept study using Nipah Virus Infection ]]> https://biorxiv.org/content/10.1101/333021v1?rss=1 Shameer, K. Johnson, K. W. Readhead, B. Glicksberg, B. McCallum, C. R, A. Hirsch, J. Bock, K. Chelico, J. Hajizadeh, N. Oppenheim, M. Dudley, J. 2018-05-29 doi:10.1101/333021 Cold Spring Harbor Laboratory Press 2018-05-29 <![CDATA[ Loss of the Wnt/β-catenin pathway in microglia of the developing brain drives pro-inflammatory activation leading to white matter injury ]]> https://biorxiv.org/content/10.1101/334359v1?rss=1 Van Steenwinckel, J. Schang, A.-L. Krishnan, M. L. Degos, V. Delahaye-Duriez, A. Bokobza, C. Verdonk, F. Montane, A. Sigaut, S. Hennebert, O. Lebon, S. Schwendimann, L. Le Charpentier, T. Hassan-Abdi, R. Ball, G. Aljabar, P. Saxena, A. Holloway, R. K. Birchmeier, W. Miron, V. Rowitch, D. Chretien, F. Leconte, C. Besson, V. C. Petretto, E. G. Edwards, A. D. Hagberg, H. Soussi-Yanicostas, N. Fleiss, B. Gressens, P. 2018-05-31 doi:10.1101/334359 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ CRISPR-Cas9 interrogation of a putative fetal globin repressor in human erythroid cells. ]]> https://biorxiv.org/content/10.1101/335729v1?rss=1 Chung, J. E. Magis, W. Vu, J. Heo, S.-J. Wartiovaara, K. Walters, M. C. Kurita, R. Nakamura, Y. Boffelli, D. Martin, D. I. Corn, J. E. Dewitt, M. A. 2018-05-31 doi:10.1101/335729 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ Deep learning models reveal internal structure and diverse computations in the retina under natural scenes ]]> https://biorxiv.org/content/10.1101/340943v1?rss=1 Maheswaranathan, N. McIntosh, L. T. Kastner, D. B. Melander, J. Brezovec, L. Nayebi, A. Wang, J. Ganguli, S. Baccus, S. A. 2018-06-08 doi:10.1101/340943 Cold Spring Harbor Laboratory Press 2018-06-08 <![CDATA[ New genetic signals for lung function highlight pathways and pleiotropy, and chronic obstructive pulmonary disease associations across multiple ancestries ]]> https://biorxiv.org/content/10.1101/343293v1?rss=1 Shrine, N. Guyatt, A. L. Erzurumluoglu, A. M. Jackson, V. E. Hobbs, B. D. Melbourne, C. Batini, C. Fawcett, K. A. Song, K. Sakornsakolpat, P. Li, X. Boxall, R. Reeve, N. F. Obeidat, M. Zhao, J. H. Wielscher, M. Understanding Society Scientific Group, Weiss, S. Kentistou, K. A. Cook, J. P. Sun, B. B. Zhou, J. Hui, J. Karrasch, S. Imboden, M. Harris, S. E. Marten, J. Enroth, S. Kerr, S. M. Surakka, I. Vitart, V. Lehtimäki, T. Allen, R. J. Bakke, P. S. Beaty, T. H. Bleecker, E. R. Bosse, Y. Brandsma, C.-A. Chen, Z. Crapo, J. D. Danesh, J. DeMeo, 2018-06-12 doi:10.1101/343293 Cold Spring Harbor Laboratory Press 2018-06-12 <![CDATA[ The Evolution of White Matter Microstructural Changes After Mild Traumatic Brain Injury: A Longitudinal DTI and NODDI Study ]]> https://biorxiv.org/content/10.1101/345629v1?rss=1 Palacios, E. Owen, J. P. Yuh, E. L. Wang, M. B. Vassar, M. J. Ferguson, A. R. Diaz-Arrastia, R. Giacino, J. T. Okonkwo, D. O. Robertson, C. S. Stein, M. B. Temkin, N. Jain, S. McCrea, M. Mac Donald, C. L. Manley, G. T. Mukherjee, P. TRACK-TBI Investigators, 2018-06-14 doi:10.1101/345629 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ Direct evidence for prediction signals in frontal cortex independent of prediction error ]]> https://biorxiv.org/content/10.1101/346213v1?rss=1 Duerschmid, S. Reichert, C. Hinrichs, H. Heinze, H.-J. Kirsch, H. E. Knight, R. T. Deouell, L. Y. 2018-06-14 doi:10.1101/346213 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ Sensory Over-Responsivity: Parent Report, Direct Assessment Measures, and Neural Architecture ]]> https://biorxiv.org/content/10.1101/355628v1?rss=1 Tavassoli, T. Brandes-Aitken, A. Chu, R. Porter, L. Schoen, S. Miller, L. J. Gerdes, M. R. Owen, J. Mukherjee, P. Marco, E. J. 2018-06-28 doi:10.1101/355628 Cold Spring Harbor Laboratory Press 2018-06-28 <![CDATA[ Feedback-mediated signal conversion promotes viral fitness ]]> https://biorxiv.org/content/10.1101/361071v1?rss=1 Vardi, N. Chaturvedi, S. Weinberger, L. S. 2018-07-03 doi:10.1101/361071 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Heterogeneity of transposon expression and activation of the repressive network in human fetal germ cells ]]> https://biorxiv.org/content/10.1101/364315v1?rss=1 Reznik, B. Cincotta, S. A. Jaszczak, R. G. Mateo, L. J. Shen, J. Cao, M. Bascin, L. Ye, P. An, W. Laird, D. 2018-07-07 doi:10.1101/364315 Cold Spring Harbor Laboratory Press 2018-07-07 <![CDATA[ Smart bone plates can monitor fracture healing ]]> https://biorxiv.org/content/10.1101/366039v1?rss=1 Lin, M. C. Hu, D. Marmor, M. Herfat, S. T. Bahney, C. S. Maharbiz, M. M. 2018-07-10 doi:10.1101/366039 Cold Spring Harbor Laboratory Press 2018-07-10 <![CDATA[ The autism-associated gene Scn2a plays an essential role in synaptic stability and learning ]]> https://biorxiv.org/content/10.1101/366781v1?rss=1 Spratt, P. Ben-Shalom, R. Keeshen, C. Burke, K. Clarkson, R. Sanders, S. Bender, K. 2018-07-10 doi:10.1101/366781 Cold Spring Harbor Laboratory Press 2018-07-10 <![CDATA[ Multi-omics analysis of AML cells treated with azacitidine reveals highly variable cell surface proteome remodeling ]]> https://biorxiv.org/content/10.1101/369322v1?rss=1 Leung, K. K. Nguyen, A. Shi, T. Tang, L. Ni, X. Escoubet, L. MacBeth, K. J. DiMartino, J. Wells, J. A. 2018-07-14 doi:10.1101/369322 Cold Spring Harbor Laboratory Press 2018-07-14 <![CDATA[ Facile real time detection of membrane colocalization of RAS superfamily GTPase proteins in living cells ]]> https://biorxiv.org/content/10.1101/369587v1?rss=1 Li, Y.-C. Wang, L. Hayes, T. K. Sutton, M. N. Bast, R. C. McCormick, F. Der, C. J. Wahl, G. M. 2018-07-15 doi:10.1101/369587 Cold Spring Harbor Laboratory Press 2018-07-15 <![CDATA[ Massively parallel characterization of regulatory dynamics during neural induction ]]> https://biorxiv.org/content/10.1101/370452v1?rss=1 Inoue, F. Kreimer, A. Ashuach, T. Ahituv, N. Yosef, N. 2018-07-16 doi:10.1101/370452 Cold Spring Harbor Laboratory Press 2018-07-16 <![CDATA[ A nucleus-like compartment shields bacteriophage DNA from CRISPR-Cas and restriction nucleases ]]> https://biorxiv.org/content/10.1101/370791v1?rss=1 Mendoza, S. D. Berry, J. D. Nieweglowska, E. S. Leon, L. M. Agard, D. Bondy-Denomy, J. 2018-07-17 doi:10.1101/370791 Cold Spring Harbor Laboratory Press 2018-07-17 <![CDATA[ Narcolepsy risk loci are enriched in immune cells and suggest autoimmune modulation of the T cell receptor repertoire ]]> https://biorxiv.org/content/10.1101/373555v1?rss=1 Ollila, H. Sharon, E. Lin, L. Sinnott-Armstrong, N. Ambati, A. Hillary, R. P. Jolanki, O. Faraco, J. Einen, M. Luo, G. Zhang, J. Han, F. Yan, H. Dong, X. S. Li, J. Hong, S.-C. Kim, T. W. Dauvilliers, Y. Barateau, L. Lammers, G. J. Fronczek, R. Mayer, G. Santamaria, J. Arnulf, I. Knudsen, S. Lyamouri-Bredahl, M. K. Thorsby, P. M. Plazzi, G. Pizza, F. Moresco, M. Crowe, C. Van-den-Eeden, S. K. Lecendreux, M. Bourgin, P. Kanbayashi, T. Peraita-Adrados, R. Martinez-Orozco, F. J. Beneto, A. Montplaisir, J. Desautels, A. Huang, Y.-S. Jennum, P. Nevsimalova, 2018-07-22 doi:10.1101/373555 Cold Spring Harbor Laboratory Press 2018-07-22 <![CDATA[ A Metagenomic Comparison of Tracheal Aspirate and Mini-Bronchial Alveolar Lavage for Assessment of Respiratory Microbiota ]]> https://biorxiv.org/content/10.1101/375360v1?rss=1 Kalantar, K. Moazed, F. Christenson, S. Wilson, J. Deiss, T. Belzer, A. Vessell, K. Jauregui, A. Boulourchi, S. DeRisi, J. L. Calfee, C. Langelier, C. 2018-07-24 doi:10.1101/375360 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ Lipid associated polygenic enrichment in Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/383844v1?rss=1 500,000 cases and controls) and validated tools to quantify genetic pleiotropy, we systematically identified single nucleotide polymorphisms (SNPs) jointly associated with AD and one or more CV RFs, namely body mass index (BMI), type 2 diabetes (T2D), coronary artery disease (CAD), waist hip ratio (WHR), total cholesterol (TC), low-density (LDL) and high-density lipoprotein (HDL). In fold enrichment plots, we observed robust genetic enrichment in AD as a function of plasma lipids (TC, LDL, and HDL); we found minimal AD genetic enrichment conditional on BMI, T2D, CAD, and WHR. Beyond APOE, at conjunction FDR < 0.05 we identified 57 SNPs on 19 different chromosomes that were jointly associated with AD and CV outcomes including APOA4, ABCA1, ABCG5, LIPG, and MTCH2/SPI1. We found that common genetic variants influencing AD are associated with multiple CV RFs, at times with a different directionality of effect. Expression of these AD/CV pleiotropic genes was enriched for lipid metabolism processes, over-represented within astrocytes and vascular structures, highly co-expressed, and differentially altered within AD brains. Beyond APOE, we show that the polygenic component of AD is enriched for lipid associated RFs. Rather than a single causal link between genetic loci, RF and the outcome, we found that common genetic variants influencing AD are associated with multiple CV RFs. Our collective findings suggest that a network of genes involved in lipid biology also influence Alzheimers risk. ]]> Broce, I. Tan, C. H. Fan, C. C. Witoelar, A. Wen, N. Jansen, I. Hess, C. Dillon, W. Glastonbury, C. Glymour, M. Yokoyama, J. Elahi, F. Rabinovici, G. Miller, B. Mormino, E. Sperling, R. Bennett, D. McEvoy, L. Brewer, J. Feldman, H. Posthuma, D. Hyman, B. Schellenberg, G. Yaffe, K. Andreassen, O. Dale, A. Sugrue, L. Karch, C. Desikan, R. 2018-08-03 doi:10.1101/383844 Cold Spring Harbor Laboratory Press 2018-08-03 <![CDATA[ Minor isozymes tailor yeast metabolism to carbon availability ]]> https://biorxiv.org/content/10.1101/394056v1?rss=1 Bradley, P. H. Gibney, P. A. Botstein, D. Troyanskaya, O. Rabinowitz, J. 2018-08-17 doi:10.1101/394056 Cold Spring Harbor Laboratory Press 2018-08-17 <![CDATA[ Challenge data set for macromolecular multi-microcrystallography ]]> https://biorxiv.org/content/10.1101/394965v1?rss=1 Holton, J. M. 2018-08-18 doi:10.1101/394965 Cold Spring Harbor Laboratory Press 2018-08-18 <![CDATA[ GxEMM: Extending linear mixed models to general gene-environment interactions ]]> https://biorxiv.org/content/10.1101/397638v1?rss=1 Dahl, A. Cai, N. Flint, J. Zaitlen, N. 2018-08-22 doi:10.1101/397638 Cold Spring Harbor Laboratory Press 2018-08-22 <![CDATA[ Multiple Exposures, Reinfection, and Risk of Progression to Active Tuberculosis ]]> https://biorxiv.org/content/10.1101/398271v1?rss=1 Ackley, S. Lee, R. S. Worden, L. Zwick, E. Porco, T. C. Behr, M. A. Pepperell, C. S. 2018-08-24 doi:10.1101/398271 Cold Spring Harbor Laboratory Press 2018-08-24 <![CDATA[ Small molecule inhibition of IRE1α kinase/RNase has anti-fibrotic effects in the lung ]]> https://biorxiv.org/content/10.1101/398552v1?rss=1 Thamsen, M. Ghosh, R. Auyeung, V. C. Brumwell, A. Chapman, H. A. Backes, B. J. Perara, G. Maly, D. J. Sheppard, D. Papa, F. R. 2018-08-23 doi:10.1101/398552 Cold Spring Harbor Laboratory Press 2018-08-23 <![CDATA[ An open-source control system for in vivo fluorescence measurements from deep-brain structures ]]> https://biorxiv.org/content/10.1101/399329v1?rss=1 Owen, S. F. Kreitzer, A. C. 2018-08-23 doi:10.1101/399329 Cold Spring Harbor Laboratory Press 2018-08-23 <![CDATA[ Depletion of microbiome-derived molecules in the host using Clostridium genetics ]]> https://biorxiv.org/content/10.1101/401489v1?rss=1 Guo, C.-J. Allen, B. Hiam, K. Dodd, D. van Treuren, W. Higginbottom, S. Fischer, C. Sonnenburg, J. Spitzer, M. Fischbach, M. 2018-08-27 doi:10.1101/401489 Cold Spring Harbor Laboratory Press 2018-08-27 <![CDATA[ The 22q11 low copy repeats are characterized by unprecedented size and structure variability ]]> https://biorxiv.org/content/10.1101/403873v1?rss=1 Demaerel, W. Mostovoy, Y. Yilmaz, F. Vervoort, L. Pastor, S. Hestand, M. S. Swillen, A. Vergaelen, E. Geiger, E. A. Coughlin, C. R. Chow, S. K. McDonald-McGinn, D. Morrow, B. Kwok, P.-Y. Xiao, M. Emanuel, B. S. Shaikh, T. H. Vermeesch, J. R. 2018-09-12 doi:10.1101/403873 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ Peripartum cardiomyopathy and hypertensive disorders of pregnancy and cardiovascular events among 1.6 million California pregnancies ]]> https://biorxiv.org/content/10.1101/404350v1?rss=1 Arnaout, R. Nah, G. Marcus, G. Tseng, Z. H. Foster, E. Harris, I. Dianji, P. Klein, L. Gonzalez, J. M. Parikh, N. I. 2018-08-30 doi:10.1101/404350 Cold Spring Harbor Laboratory Press 2018-08-30 <![CDATA[ Gelbox - An Interactive Simulation Tool for Gel Electrophoresis ]]> https://biorxiv.org/content/10.1101/406132v1?rss=1 Gingold, C. Douglas, S. M. 2018-09-05 doi:10.1101/406132 Cold Spring Harbor Laboratory Press 2018-09-05 <![CDATA[ Chromatin rewiring mediates programmed evolvability via aneuploidy ]]> https://biorxiv.org/content/10.1101/407841v1?rss=1 Brimmacombe, C. Burke, J. Parsa, J.-Y. Witchley, J. Burrack, L. Madhani, H. Noble, S. 2018-09-03 doi:10.1101/407841 Cold Spring Harbor Laboratory Press 2018-09-03 <![CDATA[ Landscape of stimulation-responsive chromatin across diverse human immune cells ]]> https://biorxiv.org/content/10.1101/409722v1?rss=1 Calderon, D. Nguyen, M. L. T. Mezger, A. Kathiria, A. Nguyen, V. Lescano, N. Wu, B. Trombetta, J. Ribado, J. V. Knowles, D. A. Gao, Z. Parent, A. V. Burt, T. D. Anderson, M. S. Criswell, L. A. Greenleaf, W. J. Marson, A. Pritchard, J. K. 2018-09-05 doi:10.1101/409722 Cold Spring Harbor Laboratory Press 2018-09-05 <![CDATA[ Pediatric Brainstem Encephalitis Outbreak Investigation with Metagenomic Next-Generation Sequencing ]]> https://biorxiv.org/content/10.1101/414979v1?rss=1 Leon, K. E. Casas-Alba, D. Ramesh, A. Khan, L. M. Launes, C. Sample, H. A. Zorn, K. C. Vallero-Rello, A. Langelier, C. Munoz-Almagro, C. DeRisi, J. L. Wilson, M. R. 2018-09-12 doi:10.1101/414979 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ Detection of early stage pancreatic cancer using 5-hydroxymethylcytosine signatures in circulating cell free DNA ]]> https://biorxiv.org/content/10.1101/422675v1?rss=1 Collin, F. Ning, Y. Phillips, T. McCarthy, E. Scott, A. Ellison, C. Ku, C.-J. Guler, G. D. Chau, K. Ashworth, A. Quake, S. R. Levy, S. 2018-09-20 doi:10.1101/422675 Cold Spring Harbor Laboratory Press 2018-09-20 <![CDATA[ Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines ]]> https://biorxiv.org/content/10.1101/424697v1?rss=1 Iacobucci, C. Piotrowski, C. Aebersold, R. Amaral, B. C. Andrews, P. Borchers, C. Brodie, N. I. Bruce, J. E. Chaignepain, S. Chavez, J. D. Claverol, S. Cox, J. Degliesposti, G. Dong, M. Q. Edinger, N. Emanuelsson, C. Gay, M. Goetze, M. Gozzo, F. C. Gutierrez, C. Haupt, C. Heck, A. J. R. Herzog, F. Huang, L. Hoopmann, M. R. Kalisman, N. Klykov, O. Kukacka, Z. Liu, F. MacCoss, M. J. Mechtler, K. Mesika, R. Moritz, R. L. Nagaraj, N. Nesati, V. Ninnis, R. Novak, P. O'Reilly, F. J. Pelzing, M. Petrotchenko, E. Piersimoni, L. Plasencia, M. Pukala, T. Rand, 2018-09-26 doi:10.1101/424697 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ phylogenize: a web tool to identify microbial genes underlying environment associations ]]> https://biorxiv.org/content/10.1101/425231v1?rss=1 Bradley, P. H. Pollard, K. S. 2018-09-24 doi:10.1101/425231 Cold Spring Harbor Laboratory Press 2018-09-24 <![CDATA[ FLASH: A next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences ]]> https://biorxiv.org/content/10.1101/426338v1?rss=1 Quan, J. Langelier, C. Kuchta, A. Batson, J. Teyssier, N. Lyden, A. Caldera, S. McGeever, A. Dimitrov, B. King, R. Wilheim, J. Murphy, M. Pesce Ares, L. Travisano, K. A. Sit, R. Amato, R. Mumbengegwi, D. R. Smith, J. L. Bennett, A. Gosling, R. Mourani, P. M. Calfee, C. S. Neff, N. F. Chow, E. D. Kim, P. S. Greenhouse, B. DeRisi, J. L. Crawford, E. D. 2018-09-27 doi:10.1101/426338 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ The nuclear RNAi factor, NRDE2, prevents the accumulation of DNA damage during mitosis in stressful growth conditions ]]> https://biorxiv.org/content/10.1101/428250v1?rss=1 Asuni, A. Venkataramanan, S. Suzuki, A. Floor, S. N. Goga, A. L'Etoile, N. 2018-09-27 doi:10.1101/428250 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ Light-based tuning of ligand half-life supports kinetic proofreading model of T cell activation ]]> https://biorxiv.org/content/10.1101/432864v1?rss=1 Tischer, D. Weiner, O. D. 2018-10-02 doi:10.1101/432864 Cold Spring Harbor Laboratory Press 2018-10-02 <![CDATA[ Establishing a causal role for medial prefrontal cortex in reality monitoring ]]> https://biorxiv.org/content/10.1101/436907v1?rss=1 Subramaniam, K. Kothare, H. Hinkley, L. Tarapore, P. Nagarajan, S. 2018-10-07 doi:10.1101/436907 Cold Spring Harbor Laboratory Press 2018-10-07 <![CDATA[ Beta-band activity in medial prefrontal cortex predicts source memory encoding and retrieval accuracy ]]> https://biorxiv.org/content/10.1101/437244v1?rss=1 Subramaniam, K. Hinkley, L. Mizuiri, D. Kothare, H. Garrett, C. Findlay, A. Houde, J. Nagarajan, S. 2018-10-07 doi:10.1101/437244 Cold Spring Harbor Laboratory Press 2018-10-07 <![CDATA[ Cell-type-specific resolution epigenetics without the need for cell sorting or single-cell biology ]]> https://biorxiv.org/content/10.1101/437368v1?rss=1 Rahmani, E. Schweiger, R. Rhead, B. Criswell, L. A. Barcellos, L. F. Eskin, E. Rosset, S. Sankararaman, S. Halperin, E. 2018-10-07 doi:10.1101/437368 Cold Spring Harbor Laboratory Press 2018-10-07 <![CDATA[ Suppressor of Fused controls the proliferation of postnatal neural stem and precursor cells via a Gli3-dependent mechanism ]]> https://biorxiv.org/content/10.1101/438705v1?rss=1 Gomez, H. G. Castillo, J. G. Noguchi, H. Aguilar, D. Pleasure, S. J. Yabut, O. R. 2018-10-09 doi:10.1101/438705 Cold Spring Harbor Laboratory Press 2018-10-09 <![CDATA[ Antiviral adaptive immunity and tolerance in the mosquito Aedes aegyti ]]> https://biorxiv.org/content/10.1101/438911v1?rss=1 Andino, R. Tassetto, M. Kunitomi, M. Whitfield, Z. J. Dolan, P. T. Sanchez-Vargas, I. Ribiero, I. Chen, T. Olson, K. E. 2018-10-09 doi:10.1101/438911 Cold Spring Harbor Laboratory Press 2018-10-09 <![CDATA[ Synthetic essentiality of metabolic regulator PDHK1 in PTEN-deficient cells and cancers ]]> https://biorxiv.org/content/10.1101/441295v1?rss=1 Chatterjee, N. Pazarentzos, E. Hrustanovic, G. Lin, L. Verschueren, E. Johnson, J. R. Hofree, M. Yan, J. J. Olivas, V. Newton, B. W. Dollen, J. V. Earnshaw, C. H. Flanagan, J. Chan, E. Asthana, S. Ideker, T. Wu, W. Mayekar, M. K. Suzuki, J. Barad, B. Kirichok, Y. Fraser, J. Weiss, W. A. Krogan, N. J. Tulpule, A. Sabnis, A. J. Bivona, T. G. 2018-10-11 doi:10.1101/441295 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Cyclin B2 is required for progression through meiosis in mouse oocytes ]]> https://biorxiv.org/content/10.1101/441352v1?rss=1 Daldello, E. M. Luong, X. G. Yang, C.-R. Huhn, J. Conti, M. 2018-10-12 doi:10.1101/441352 Cold Spring Harbor Laboratory Press 2018-10-12 <![CDATA[ The glucocorticoid receptor ligand-binding domain confers drug-gated protein regulation in C. elegans ]]> https://biorxiv.org/content/10.1101/445833v1?rss=1 Monsalve, G. C. Yamamoto, K. R. Ward, J. D. 2018-10-17 doi:10.1101/445833 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Reverse GWAS: Using Genetics to Identify and Model Phenotypic Subtypes ]]> https://biorxiv.org/content/10.1101/446492v1?rss=1 Dahl, A. Cai, N. Ko, A. Laakso, M. Pajukanta, P. Flint, J. Zaitlen, N. 2018-10-17 doi:10.1101/446492 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ LC3 and STRAP regulate actin filament assembly by JMY during autophagosome formation ]]> https://biorxiv.org/content/10.1101/451393v1?rss=1 Hu, X. Mullins, R. D. 2018-10-24 doi:10.1101/451393 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ Insertion sequences drive the emergence of a highly adapted human pathogen ]]> https://biorxiv.org/content/10.1101/452334v1?rss=1 Sentausa, E. Basso, P. Berry, A. Adrait, A. Bellement, G. Coute, Y. Lory, S. Elsen, S. Attree, I. 2018-10-25 doi:10.1101/452334 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Building Key Populations HIV Treatment Cascades in Data-Scarce Environments: Towards a participatory stakeholder methodology for cascades construction, adoption, and utilization ]]> https://biorxiv.org/content/10.1101/452417v1?rss=1 Lane, T. Grasso, M. Scheibe, A. Liu, G. Marr, A. Murangandi, P. Aynalem, G. Slabbert, M. Malaka, L. Isdahl, Z. Osmand, T. Nadol, P. 2018-10-24 doi:10.1101/452417 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ Cell-extrinsic mechanical forces restore neutrophil polarization in the absence of branched actin assembly ]]> https://biorxiv.org/content/10.1101/457119v1?rss=1 Graziano, B. R. Town, J. P. Nagy, T. L. Fosnaric, M. Penic, S. Iglic, A. Kralj-Iglic, V. Gov, N. Diz-Munoz, A. Weiner, O. D. 2018-10-30 doi:10.1101/457119 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ Real-time projections of epidemic transmission and estimation of vaccination impact during an Ebola virus disease outbreak in the Eastern region of the Democratic Republic of Congo ]]> https://biorxiv.org/content/10.1101/461285v1?rss=1 Worden, L. Wannier, R. Hoff, N. A. Musene, K. Selo, B. Mossoko, M. Okitolonda-Wemakoy, E. Muyembe-Tamfum, J. J. Rutherford, G. Lietman, T. M. Rimoin, A. W. Porco, T. C. Kelly, J. D. 2018-11-05 doi:10.1101/461285 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ Matrix linear models for high-throughput chemical genetic screens ]]> https://biorxiv.org/content/10.1101/468140v1?rss=1 Liang, J. W. Nichols, R. J. Sen, S. 2018-11-11 doi:10.1101/468140 Cold Spring Harbor Laboratory Press 2018-11-11 <![CDATA[ Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq ]]> https://biorxiv.org/content/10.1101/469635v1?rss=1 Wienert, B. Wyman, S. K. Richardson, C. D. Yeh, C. D. Akcakaya, P. Porritt, M. J. Morlock, M. Vu, J. T. Kazane, K. R. Watry, H. L. Judge, L. M. Conklin, B. R. Maresca, M. Corn, J. E. 2018-11-14 doi:10.1101/469635 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ TFF3 is a ligand for LINGO2 that de-represses EGFR to control disease outcome during colitis and gastrointestinal nematode infection ]]> https://biorxiv.org/content/10.1101/469700v1?rss=1 Ji, Y. Wei, Y. Park, J. Hung, L. Y. Young, T. Herbine, K. Oniskey, T. Pastore, C. Nieves, W. Somsouk, M. Herbert, D. 2018-11-13 doi:10.1101/469700 Cold Spring Harbor Laboratory Press 2018-11-13 <![CDATA[ Transient activation of the UPRER is an essential step in the acquisition of pluripotency during reprogramming ]]> https://biorxiv.org/content/10.1101/472787v1?rss=1 Simic, M. Moehle, E. Schinzel, R. Lorbeer, F. Jullie, D. Halloran, J. Heydari, K. Sanchez, M. Hockemeyer, D. Dillin, A. 2018-11-17 doi:10.1101/472787 Cold Spring Harbor Laboratory Press 2018-11-17 <![CDATA[ Tracing diagnosis trajectories over millions of inpatients reveal an unexpected association between schizophrenia and rhabdomyolysis ]]> https://biorxiv.org/content/10.1101/473082v1?rss=1 Paik, H. Kan, M. J. Rappoport, N. Hadley, D. Sirota, M. Chen, B. Manber, U. Cho, S. B. Butte, A. J. 2018-11-19 doi:10.1101/473082 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Age but not disease progression defines CD4+ and CD8+ T stem cell memory levels in human retroviral infections: contrasting effects of HTLV-1 and HIV-1 ]]> https://biorxiv.org/content/10.1101/473363v1?rss=1 400% increase in elderly HTLV-1 infected individuals (>60 years). A significant correlation between age and TSCM signature genes was validated at the transcriptome level in an independent cohort. CD8+ but not CD4+ TSCM were significantly decreased in untreated HIV-1 infection. Unexpectedly, CD8+ TSCM recovery upon successful antiretroviral treatment was essentially complete (92.2{+/-}11.0%) in younger (<45 years) individuals, but significantly lower (37.3{+/-}6.1%) in older (>45 years) individuals (p=0.0003).nnConclusionIn HTLV-1 infection, an age-dependent accumulation of CD4+ and CD8+ TSCM points towards a possible protective role of CD8 TSCM in the elderly against leukemic but not neuroinflammatory disease. HIV-1-infected individuals lose their ability to restore CD8+ TSCM levels upon successful antiretroviral therapy at later age (>45 years), which might eventually lead to immunological failure and decreased vaccine efficacy. ]]> Menezes, S. M. Leal, F. E. Pereira Ribeiro, S. Dierckx, T. Roederer, M. SenGupta, D. Nixon, D. Van Weyenbergh, J. 2018-11-19 doi:10.1101/473363 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Evaluating Clinical Benefit in I-SPY 2 ]]> https://biorxiv.org/content/10.1101/473447v1?rss=1 Basu, A. Melisko, M. Esserman, L. J. 2018-11-19 doi:10.1101/473447 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Glutamate signaling at cytoneme synapses ]]> https://biorxiv.org/content/10.1101/475665v1?rss=1 Huang, H. Liu, S. Kornberg, T. B. 2018-11-21 doi:10.1101/475665 Cold Spring Harbor Laboratory Press 2018-11-21 <![CDATA[ Temperature-Jump Solution X-ray Scattering Reveals Distinct Motions in a Dynamic Enzyme ]]> https://biorxiv.org/content/10.1101/476432v1?rss=1 Thompson, M. C. Barad, B. A. Wolff, A. M. Cho, H. S. Schotte, F. Schwarz, D. M. C. Anfinrud, P. Fraser, J. S. 2018-11-21 doi:10.1101/476432 Cold Spring Harbor Laboratory Press 2018-11-21 <![CDATA[ Conformational dynamics of the HIV Vif protein complex ]]> https://biorxiv.org/content/10.1101/483099v1?rss=1 Ball, K. A. Chan, L. M. Stanley, D. J. Tierney, E. Thapa, S. Ta, H. M. Burton, L. A. Binning, J. M. Jacobsen, M. Gross, J. 2018-11-29 doi:10.1101/483099 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ Longitudinally persistent cerebrospinal fluid B-cells resist treatment in multiple sclerosis ]]> https://biorxiv.org/content/10.1101/490938v1?rss=1 Greenfield, A. L. Dandekar, R. Ramesh, A. Eggers, E. L. Wu, H. Laurent, S. Harkin, W. Pierson, N. S. Weber, M. S. Henry, R. G. Bischof, A. Cree, B. A. C. Hauser, S. L. Wilson, M. R. von Büdingen, H.- C. 2018-12-09 doi:10.1101/490938 Cold Spring Harbor Laboratory Press 2018-12-09 <![CDATA[ Beyond SNP Heritability: Polygenicity and Discoverability of Phenotypes Estimated with a Univariate Gaussian Mixture Model ]]> https://biorxiv.org/content/10.1101/498550v1?rss=1 1%. We apply the model to diverse phenotypes and validate the implementation with simulations. We find model polygenicities ranging from [~=] 2 x 10-5 to [~=] 4 x 10-3, with discoverabilities similarly ranging over two orders of magnitude. A power analysis allows us to estimate the proportions of phenotypic variance explained additively by causal SNPs at current sample sizes, and map out sample sizes required to explain larger portions of additive SNP heritability. The model also allows for estimating residual inflation. ]]> Holland, D. Frei, O. Desikan, R. Fan, C. C. Shadrin, A. Smeland, O. Sundar, V. S. Thompson, P. Andreassen, O. A. Dale, A. M. 2018-12-17 doi:10.1101/498550 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ Timed inhibition of CDC7 increases CRISPR-Cas9 mediated templated repair ]]> https://biorxiv.org/content/10.1101/500462v1?rss=1 Wienert, B. Feng, S. J. Locke, M. Nguyen, D. N. Wyman, S. K. Kazane, K. R. MARSON, A. Richardson, C. D. Corn, J. E. 2018-12-19 doi:10.1101/500462 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Exploration of Anti-Yo and Anti-Hu paraneoplastic neurological disorders by PhIP-Seq reveals a highly restricted pattern of antibody epitopes ]]> https://biorxiv.org/content/10.1101/502187v1?rss=1 O'Donovan, B. D. Mandel-Brehm, C. Vazquez, S. E. Liu, J. Parent, A. V. Anderson, M. S. Kassimatis, T. Zekeridou, A. Hauser, S. L. Pittock, S. J. Chow, E. Wilson, M. R. DeRisi, J. L. 2018-12-20 doi:10.1101/502187 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ Human, Nonhuman Primate, and Bat Cells Are Broadly Susceptible to Tibrovirus Particle Cell Entry ]]> https://biorxiv.org/content/10.1101/507350v1?rss=1 Cai, Y. Yu, S. Jangra, R. Postnikova, E. Wada, J. Tesh, R. Whelan, S. Lauck, M. Wiley, M. Finch, C. Radoshitzky, S. O'Connor, D. Palacios, G. Chandran, K. Chiu, C. Kuhn, J. 2018-12-27 doi:10.1101/507350 Cold Spring Harbor Laboratory Press 2018-12-27 <![CDATA[ Reversible silencing of endogenous receptors in intact brain tissue using two-photon pharmacology ]]> https://biorxiv.org/content/10.1101/515288v1?rss=1 Pittolo, S. Lee, H. Lladoo, A. Tosi, S. Bosch, M. Bardia, L. Gomez-Santacana, X. Llebaria, A. Soriano, E. Colombelli, J. Poskanzer, K. E. Perea, G. Gorostiza, P. 2019-01-09 doi:10.1101/515288 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ Dynamic Change of Electrostatic Field in TMEM16F Permeation Pathway Shifts Its Ion Selectivity ]]> https://biorxiv.org/content/10.1101/515569v1?rss=1 Ye, W. Han, T. W. He, M. Jan, Y. N. Jan, L. Y. 2019-01-16 doi:10.1101/515569 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ Effects of α-tubulin acetylation on microtubule structure and stability ]]> https://biorxiv.org/content/10.1101/516591v1?rss=1 Eshun-Wilson, L. Zhang, R. Portran, D. Nachury, M. Toso, D. Lohr, T. Vendruscolo, M. Bonomi, M. Fraser, J. Nogales, E. 2019-01-09 doi:10.1101/516591 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ NWB:N 2.0: An Accessible Data Standard for Neurophysiology ]]> https://biorxiv.org/content/10.1101/523035v1?rss=1 Ruebel, O. Tritt, A. Dichter, B. Braun, T. Cain, N. Clack, N. Davidson, T. J. Dougherty, M. Fillion-Robin, J.-C. Graddis, N. Grauer, M. Kiggins, J. T. Niu, L. Ozturk, D. Schroeder, W. Soltesz, I. Sommer, F. T. Svoboda, K. Ng, L. Frank, L. M. Bouchard, K. 2019-01-17 doi:10.1101/523035 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ Regular cycling between representations of alternatives in the hippocampus ]]> https://biorxiv.org/content/10.1101/528976v1?rss=1 Kay, K. Chung, J. E. Sosa, M. Schor, J. S. Karlsson, M. P. Larkin, M. C. Liu, D. F. Frank, L. M. 2019-01-28 doi:10.1101/528976 Cold Spring Harbor Laboratory Press 2019-01-28 <![CDATA[ Microstructure of Ingestive Behaviors in Mus Musculus ]]> https://biorxiv.org/content/10.1101/529198v1?rss=1 Onnis, G. Layco-Bader, E. Tecott, L. 2019-02-19 doi:10.1101/529198 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ Multiplex immunofluorescence methods in neurodegenerative diseases ]]> https://biorxiv.org/content/10.1101/533547v1?rss=1 Ehrenberg, A. J. Morales, D. O. Tejedor, J. S. Mulder, J. Grinberg, L. T. 2019-02-11 doi:10.1101/533547 Cold Spring Harbor Laboratory Press 2019-02-11 <![CDATA[ Population history and gene divergence in Native Mexicans inferred from 76 human exomes ]]> https://biorxiv.org/content/10.1101/534818v1?rss=1 Avila-Arcos, M. C. McManus, K. F. Sandoval, K. Rodriguez-Rodriguez, J. E. Martin, A. R. Luisi, P. Villa-Islas, V. Penaloza-Espinosa, R. I. Eng, C. Huntsman, S. Burchard, E. G. Gignoux, C. R. Bustamante, C. D. Moreno-Estrada, A. 2019-01-30 doi:10.1101/534818 Cold Spring Harbor Laboratory Press 2019-01-30 <![CDATA[ The functional landscape of the human phosphoproteome ]]> https://biorxiv.org/content/10.1101/541656v1?rss=1 Ochoa, D. Jarnuczak, A. F. Gehre, M. Soucheray, M. Kleefeldt, A. A. Vieitez, C. Hill, A. Garcia-Alonso, L. Swaney, D. L. Vizcaino, J. A. A. Noh, K.-M. Beltrao, P. 2019-02-05 doi:10.1101/541656 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Opportunities for improved surveillance and control of infectious diseases from age-specific case data ]]> https://biorxiv.org/content/10.1101/545319v1?rss=1 Rodriguez-Barraquer, I. Salje, H. Cummings, D. A. 2019-02-08 doi:10.1101/545319 Cold Spring Harbor Laboratory Press 2019-02-08 <![CDATA[ A dataset to explore kinase control of environmental stress responsive transcription ]]> https://biorxiv.org/content/10.1101/547356v1?rss=1 Mace, K. Krakowiak, J. El-Samad, H. Pincus, D. 2019-02-12 doi:10.1101/547356 Cold Spring Harbor Laboratory Press 2019-02-12 <![CDATA[ Cryptic inoviruses are pervasive in bacteria and archaea across Earth's biomes ]]> https://biorxiv.org/content/10.1101/548222v1?rss=1 Roux, S. Krupovic, M. Daly, R. A. Borges, A. L. Nayfach, S. Schulz, F. Cheng, J.-F. Ivanova, N. N. Bondy-Denomy, J. Wrighton, K. C. Woyke, T. Visel, A. Kyrpides, N. Eloe-Fadrosh, E. A. 2019-02-15 doi:10.1101/548222 Cold Spring Harbor Laboratory Press 2019-02-15 <![CDATA[ Optogenetic control reveals differential promoter interpretation of transcription factor nuclear translocation dynamics ]]> https://biorxiv.org/content/10.1101/548255v1?rss=1 Chen, S. Y. Osimiri, L. C. Chevalier, M. W. Bugaj, L. J. Ng, A. H. Stewart-Ornstein, J. Neves, L. T. El-Samad, H. 2019-02-13 doi:10.1101/548255 Cold Spring Harbor Laboratory Press 2019-02-13 <![CDATA[ Dynamics of living cells in a cytomorphological state space ]]> https://biorxiv.org/content/10.1101/549246v1?rss=1 Chang, A. Y. Marshall, W. F. 2019-02-13 doi:10.1101/549246 Cold Spring Harbor Laboratory Press 2019-02-13 <![CDATA[ Electron cryo-microscopy structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome. ]]> https://biorxiv.org/content/10.1101/550970v1?rss=1 Armache, J.-P. Gamarra, N. Johnson, S. L. Leonard, J. D. Wu, S. Narlikar, G. J. Cheng, Y. 2019-02-15 doi:10.1101/550970 Cold Spring Harbor Laboratory Press 2019-02-15 <![CDATA[ A high-resolution, chromosome-assigned Komodo dragon genome reveals adaptations in the cardiovascular, muscular, and chemosensory systems of monitor lizards ]]> https://biorxiv.org/content/10.1101/551978v1?rss=1 Lind, A. Lai, Y. Y. Y. Mostovoy, Y. Holloway, A. K. Iannucci, A. Mak, A. C. Fondi, M. Orlandini, V. Eckalbar, W. L. Milan, M. Rovatsos, M. Kichigin, I. G. Makunin, A. I. Trifonov, V. Schijlen, E. Kratochvil, L. Fani, R. Jessop, T. S. Patarnello, T. Hicks, J. W. Ryder, O. A. Mendelson, J. R. Ciofi, C. Kwok, P.-Y. A. Pollard, K. S. Bruneau, B. 2019-02-15 doi:10.1101/551978 Cold Spring Harbor Laboratory Press 2019-02-15 <![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[ Effect of Maxillary Expansion and Protraction on the Oropharyngeal Airway in Individuals with Non-syndromic Cleft Palate with or without Cleft Lip ]]> https://biorxiv.org/content/10.1101/557199v1?rss=1 Oberoi, S. Alrejaye, N. Gao, J. 2019-02-21 doi:10.1101/557199 Cold Spring Harbor Laboratory Press 2019-02-21 <![CDATA[ Brain Aging in Major Depressive Disorder: Results from the ENIGMA Major Depressive Disorder working group ]]> https://biorxiv.org/content/10.1101/560623v1?rss=1 Han, L. K. Dinga, R. Hahn, T. Ching, C. Eyler, L. Aftanas, L. Aghajani, M. Aleman, A. Baune, B. Berger, K. Brak, I. Busatto Filho, G. Carballedo, A. Connolly, C. Couvy-Duchesne, B. Cullen, K. Dannlowski, U. Davey, C. Dima, D. Duran, F. Enneking, V. Filimonova, E. Frenzel, S. Frodl, T. Fu, C. Godlewska, B. Gotlib, I. Grabe, H. Groenewold, N. Grotegerd, D. Gruber, O. Hall, G. Harrison, B. Hatton, S. Hermesdorf, M. Hickie, I. Ho, T. Hosten, N. Jansen, A. Kahler, C. Kircher, T. Klimes-Dougan, B. Kramer, B. Krug, A. Lagopoulos, J. Leenings, R. MacMaster 2019-02-26 doi:10.1101/560623 Cold Spring Harbor Laboratory Press 2019-02-26 <![CDATA[ Chaperone-Mediated Reflux of Secretory Proteins to the Cytosol During Endoplasmic Reticulum Stress ]]> https://biorxiv.org/content/10.1101/562306v1?rss=1 Igbaria, A. Merksamer, P. I. Trusina, A. Tilahun, F. Johnson, J. R. Brandman, O. Krogan, N. J. Weissman, J. S. Papa, F. R. 2019-03-12 doi:10.1101/562306 Cold Spring Harbor Laboratory Press 2019-03-12 <![CDATA[ Dynamic chromatin targeting of BRD4 stimulates cardiac fibroblast activation ]]> https://biorxiv.org/content/10.1101/563445v1?rss=1 Stratton, M. S. Bagchi, R. A. Hirsch, R. A. Riching, A. S. Felisbino, M. B. Enyart, B. Y. Koch, K. A. Cavasin, M. A. Alexanian, M. Song, K. Qi, J. Lemieux, M. E. Lam, M. P. Y. Haldar, S. M. Lin, C. Y. McKinsey, T. 2019-02-28 doi:10.1101/563445 Cold Spring Harbor Laboratory Press 2019-02-28 <![CDATA[ Theta phase synchrony is sensitive to corollary discharge abnormalities in early illness schizophrenia but not in the clinical high-risk syndrome ]]> https://biorxiv.org/content/10.1101/563460v1?rss=1 Ford, J. M. Roach, B. J. Loewy, R. Stuart, B. Mathalon, D. H. 2019-02-28 doi:10.1101/563460 Cold Spring Harbor Laboratory Press 2019-02-28 <![CDATA[ mTORC1 IN THE ORBITOFRONTAL CORTEX PROMOTES HABITUAL ALCOHOL SEEKING ]]> https://biorxiv.org/content/10.1101/564310v1?rss=1 Morisot, N. Berger, A. Phamluong, K. Laguesse, S. Moffat, J. Ron, D. 2019-03-01 doi:10.1101/564310 Cold Spring Harbor Laboratory Press 2019-03-01 <![CDATA[ Mapping the human subcortical auditory system using histology, post mortem MRI and in vivo MRI at 7T ]]> https://biorxiv.org/content/10.1101/568139v1?rss=1 Sitek, K. R. Gulban, O. F. Calabrese, E. Johnson, G. A. Ghosh, S. S. de Martino, F. 2019-03-05 doi:10.1101/568139 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ A non-Dicer RNase III and four other novel factors required for RNAi-mediated transposon suppression in the human pathogenic yeast C. neoformans ]]> https://biorxiv.org/content/10.1101/577924v1?rss=1 Burke, J. E. Longhurst, A. D. Natarajan, P. Rao, B. Liu, S. J. Sales-Lee, J. Mortensen, Y. Moresco, J. Diedrich, J. K. Yates, J. R. Madhani, H. D. 2019-03-14 doi:10.1101/577924 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ The \"sewing machine\" for minimally invasive neural recording ]]> https://biorxiv.org/content/10.1101/578542v1?rss=1 Hanson, T. L. Diaz-Botia, C. A. Kharazia, V. Maharbiz, M. M. Sabes, P. N. 2019-03-14 doi:10.1101/578542 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ Two accessory proteins govern MmpL3 mycolic acid transport in mycobacteria ]]> https://biorxiv.org/content/10.1101/581447v1?rss=1 Fay, A. Czudnochowski, N. Rock, J. Johnson, J. Krogan, N. Rosenberg, O. Glickman, M. 2019-03-27 doi:10.1101/581447 Cold Spring Harbor Laboratory Press 2019-03-27 <![CDATA[ Interleukin 17 and senescence regulate the foreign body response ]]> https://biorxiv.org/content/10.1101/583757v1?rss=1 Chung, L. Maestas, D. Lebid, A. Mageau, A. Rosson, G. D. Wu, X. Wolf, M. T. Tam, A. Wang, X. Vanderzee, I. Andorko, J. I. Narain, R. Sadlter, K. Fan, H. Cihakova, D. Jourdan Le Saux, C. Housseau, F. Pardoll, D. Elisseeff, J. 2019-03-20 doi:10.1101/583757 Cold Spring Harbor Laboratory Press 2019-03-20 <![CDATA[ Whole-genome and RNA sequencing reveal variation and transcriptomic coordination in the developing human prefrontal cortex ]]> https://biorxiv.org/content/10.1101/585430v1?rss=1 Werling, D. Pochareddy, S. Choi, J. An, J. Y. Sheppard, B. Peng, M. Li, Z. Dastmalchi, C. Santperebaro, G. Sousa, A. Tebbenkamp, A. Kaur, N. Gulden, F. Breen, M. Liang, L. Gilson, M. Zhao, X. Dong, S. Klei, L. Cicek, A. E. Buxbaum, J. Adle-Biassette, H. Thomas, J.-L. Aldinger, K. A. O'Day, D. R. Glass, I. Zaitlen, N. Talkowski, M. Roeder, K. State, M. W. Devlin, B. Sanders, S. Sestan, N. 2019-03-22 doi:10.1101/585430 Cold Spring Harbor Laboratory Press 2019-03-22 <![CDATA[ A NOVEL MECHANISM FOR NF-κB-ACTIVATION VIA IκB-AGGREGATION: IMPLICATIONS FOR HEPATIC MALLORY-DENK-BODY INDUCED INFLAMMATION ]]> https://biorxiv.org/content/10.1101/585497v1?rss=1 Liu, Y. Trnka, M. J. Guan, S. Kwon, D. Kim, D.-H. Chen, J.-J. Greer, P. A. Burlingame, A. L. Correia, M. A. 2019-03-21 doi:10.1101/585497 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ A novel high-throughput molecular counting method with single base-pair resolution enables accurate single-gene NIPT ]]> https://biorxiv.org/content/10.1101/597732v1?rss=1 98% and >99%, respectively. Validation of sgNIPT was further performed with maternal blood samples collected during pregnancy, and sgNIPT was 100% concordant with newborn follow-up. ]]> Tsao, D. S. Silas, S. Landry, B. P. Itzep, N. Nguyen, A. B. Kanne, C. K. Sheehan, V. A. Sharma, R. Shukla, R. Arora, P. N. Atay, O. 2019-04-03 doi:10.1101/597732 Cold Spring Harbor Laboratory Press 2019-04-03 <![CDATA[ The RNA binding protein DAZL functions as repressor and activator of maternal mRNA translation during oocyte maturation ]]> https://biorxiv.org/content/10.1101/598805v1?rss=1 Yang, C. Rajkovic, G. Daldello, E. M. Luong, X. G. Chen, J. Conti, M. 2019-04-04 doi:10.1101/598805 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ Apoptosis in the fetal testis eliminates developmentally defective germ cell clones ]]> https://biorxiv.org/content/10.1101/601013v1?rss=1 Nguyen, D. H. Laird, D. J. 2019-04-05 doi:10.1101/601013 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ An integrative analysis of GWAS and intermediate molecular trait data reveals common molecular mechanisms supporting genetic similarity between seemingly unrelated complex traits ]]> https://biorxiv.org/content/10.1101/601229v1?rss=1 Gu, J. Fuller, C. Zheng, J. Li, H. 2019-04-07 doi:10.1101/601229 Cold Spring Harbor Laboratory Press 2019-04-07 <![CDATA[ Rapid discovery of synthetic DNA sequences to rewrite endogenous T cell circuits ]]> https://biorxiv.org/content/10.1101/604561v1?rss=1 Roth, T. L. Li, P. J. Nies, J. Yu, R. Nguyen, M. L. T. Lee, Y. Apathy, R. Truong, A. Hiatt, J. Wu, D. Nguyen, D. N. Goodman, D. Bluestone, J. A. Roybal, K. Shifrut, E. Marson, A. 2019-04-12 doi:10.1101/604561 Cold Spring Harbor Laboratory Press 2019-04-12 <![CDATA[ 2’, 3’, 4’-trihydroxychalcone is an Estrogen Receptor Ligand Which Modulates the Activity of 17β-estradiol ]]> https://biorxiv.org/content/10.1101/607275v1?rss=1 Herber, C. Quirit, J. Firestone, G. Krois, C. 2019-04-13 doi:10.1101/607275 Cold Spring Harbor Laboratory Press 2019-04-13 <![CDATA[ Small molecule inhibitors of a human recombination-associated ATPase, RAD54 ]]> https://biorxiv.org/content/10.1101/614586v1?rss=1 Ehmsen, K. T. Ang, K. K. H. Wright, W. D. Davies, J. L. Younis, Y. Birman, Y. Bryant, C. Gallardo-Godoy, A. Renslo, A. R. Neitz, R. J. Arkin, M. R. Heyer, W.-D. 2019-04-19 doi:10.1101/614586 Cold Spring Harbor Laboratory Press 2019-04-19 <![CDATA[ Modulating pathogenesis with Mobile-CRISPRi ]]> https://biorxiv.org/content/10.1101/618637v1?rss=1 Rosenberg, O. Qu, J.-X. Prasad, N. K. Peters, J. Looney, M. Yu, M. Lyden, A. Chen, S. Crawford, E. Silvis, M. 2019-04-25 doi:10.1101/618637 Cold Spring Harbor Laboratory Press 2019-04-25 <![CDATA[ Bifunctional Small Molecule Ligands of K-Ras Induce Its Association with Immunophilin Proteins ]]> https://biorxiv.org/content/10.1101/619551v1?rss=1 Zhang, Z. Shokat, K. 2019-04-26 doi:10.1101/619551 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Induction via Functional Protein Stabilization of Hepatic Cytochromes P450 upon gp78/ Autocrine Motility Factor Receptor (AMFR) Ubiquitin E3-ligase Genetic Ablation in Mice: Therapeutic and Toxicological Relevance. ]]> https://biorxiv.org/content/10.1101/623041v1?rss=1 Kwon, D. Kim, S.-m. Jacob, P. Liu, Y. Correia, M. A. 2019-04-30 doi:10.1101/623041 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ Predicting neurodevelopmental outcomes in children with perinatal HIV using a novel machine learning algorithm ]]> https://biorxiv.org/content/10.1101/632273v1?rss=1 90%). Dynamic change indices and interactions between mental health and biological indices emerged as key predictors.nnConclusionMachine learning-based regression defined a unique explanatory model of neurocognitive outcomes among children with pHIV. The predictive algorithm included a combination of HIV, physical health, and mental health indices extracted from readily available clinical measures. Studies are needed to explore the clinical relevance of the data-driven explanatory model, including potential to inform targeted interventions aimed at modifiable risk factors. ]]> Paul, R. Mellins, C. Robbins, R. Kerr, S. Malee, K. Sophonphan, J. Jahanshad, N. Auripibul, L. Thongpibul, K. Kosalaraksa, P. Kanjanavanit, S. Ngampiyaskul, C. Luesomboon, W. Wongsawat, J. Vonthanak, S. Chettra, K. Suwanlerk, T. Valcour, V. Balla, L. Salminen, L. Preston, R. Garcia, P. Ananworanich, J. Puthanakit, T. 2019-05-09 doi:10.1101/632273 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ High throughput Characterization of KCNB1 variants Associated with Developmental and Epileptic Encephalopathy ]]> https://biorxiv.org/content/10.1101/637041v1?rss=1 Kang, S. K. Vanoye, C. G. Misra, S. N. Echevarria, D. M. Calhoun, J. D. O'Connor, J. B. Fabre, K. L. McKnight, D. Demmer, L. Goldenberg, P. Grote, L. E. Thiffault, I. Saunders, C. Strauss, K. A. Torkamani, A. van der Smagt, J. van Gassen, K. Carson, R. P. Diaz, J. Leon, E. Jacher, J. E. Hannibal, M. C. Litwin, J. Friedman, N. R. Schreiber, A. Lynch, B. Poduri, A. Marsh, E. D. Goldberg, E. M. Millichap, J. J. George, A. L. Kearney, J. 2019-05-14 doi:10.1101/637041 Cold Spring Harbor Laboratory Press 2019-05-14 <![CDATA[ Unique Transcription Factor Functions Regulate Epigenetic and Transcriptional Dynamics During Cardiac Reprogramming ]]> https://biorxiv.org/content/10.1101/642900v1?rss=1 Stone, N. R. Gifford, C. A. Thomas, R. Pratt, K. J. B. Samse-Knapp, K. Mohamed, T. M. A. Radzinsky, E. M. Schricker, A. Yu, P. Ivey, K. N. Pollard, K. S. Srivastava, D. 2019-05-20 doi:10.1101/642900 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Huntington phosphorylation governs BDNF homeostasis and improves the phenotype of Mecp2 knockout mice ]]> https://biorxiv.org/content/10.1101/643312v1?rss=1 Ehinger, Y. Bruyere, j. Panayotis, N. Abada, Y.-S. Saidi, L. Matagne, V. Scaramuzzino, C. Vitet, H. Benoit Delatour, B. Villard, L. Saudou, F. Roux, J.-C. 2019-05-20 doi:10.1101/643312 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Thymically-derived Foxp3+ regulatory T cells are the primary regulators of type 1 diabetes in the non-obese diabetic mouse model ]]> https://biorxiv.org/content/10.1101/644229v1?rss=1 Holohan, D. R. Van Gool, F. Bluestone, J. A. 2019-05-20 doi:10.1101/644229 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Novel Small Molecules Targeting the Intrinsically Disordered Structural Ensemble of α-Synuclein Protect Against Diverse α-Synuclein Mediated Dysfunctions ]]> https://biorxiv.org/content/10.1101/646505v1?rss=1 Toth, G. Neumann, T. Berthet, A. Masliah, E. Spencer, B. Tao, J. Jobling, M. Gardai, S. Bertoncini, C. Cremades, N. Bova, M. Ballaron, S. Chen, X.-H. Mao, W. Nguyen, P. Tabios, M. Tambe, M. Rochet, J.-C. Junker, H.-D. Schwizer, D. Sekul, R. Ott, I. Anderson, J. Szoke, B. Hoffman, W. Christodoulou, J. Yednock, T. Agard, D. Schenk, D. McConlogue, L. 2019-05-24 doi:10.1101/646505 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Unraveling the functional role of the orphan solute carrier, SLC22A24 in the transport of steroid conjugates through metabolomic and genome-wide association studies ]]> https://biorxiv.org/content/10.1101/648238v1?rss=1 Yee, S. W. Stecula, A. Chien, H.-C. Zou, L. Feofanova, E. V. van Borselen, M. Cheung, K. W. K. Yousri, N. A. Suhre, K. Kinchen, J. M. Boerwinkle, E. Irannejad, R. Yu, B. Giacomini, K. M. 2019-05-23 doi:10.1101/648238 Cold Spring Harbor Laboratory Press 2019-05-23 <![CDATA[ cfrB,cfrC, and a potential new cfr-like gene in Clostridium difficile strains recovered across Latin America ]]> https://biorxiv.org/content/10.1101/649020v1?rss=1 Stojkovic, V. Ulate, M. F. Hidalgo-Villeda, F. Aguilar, E. Monge-Cascante, C. Pizarro-Guajardo, M. Tsai, K. Tzoc, E. Camorlinga-Ponce, M. Paredes-Sabja, D. Quesada-Gomez, C. Fujimori, D. Rodriguez, C. 2019-05-24 doi:10.1101/649020 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Investigating Transfusion-Related Sepsis using Culture-Independent Metagenomic Sequencing ]]> https://biorxiv.org/content/10.1101/653337v1?rss=1 Crawford, E. D. Kamm, J. Miller, S. Li, L. Caldera, S. Lyden, A. D. Yokoe, D. Nichols, A. Ramirez-Avila, L. Tran, N. K. Barnhard, S. Conner, P. M. Nambiar, A. Zinter, M. S. Moayeri, M. Hayakawa Serpa, P. Prince, B. C. Quan, J. Sit, R. Tan, M. Phelps, M. DeRisi, J. S. Tato, C. M. Langelier, C. 2019-05-30 doi:10.1101/653337 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ Serological and metagenomic interrogation of cerebrospinal fluid implicates enteroviruses in pediatric acute flaccid myelitis ]]> https://biorxiv.org/content/10.1101/666230v1?rss=1 Schubert, R. D. Hawes, I. Ramachandran, P. S. Ramesh, A. Crawford, E. D. Pak, J. E. Wu, W. Cheung, C. K. O'Donovan, B. D. Tato, C. M. Lyden, A. Tan, M. Sit, R. Sowa, G. Sample, H. A. Zorn, K. C. Banerji, D. Khan, L. M. Bove, R. Hauser, S. L. Gelfand, A. A. Johnson-Kerner, B. Nash, K. Krishnamoorthy, K. S. Chitnis, T. Ding, J. Z. McMillan, H. J. Chiu, C. Y. Briggs, B. Glaser, C. A. Yen, C. Chu, V. Wadford, D. A. Dominguez, S. R. Ng, T. F. F. Marine, R. L. Lopez, A. S. Nix, W. A. Soldatos, A. Gorman, M. Benson, L. Messacar, K. Konopka-Anstadt, J. L. Ob 2019-06-10 doi:10.1101/666230 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Comparison of Rosetta flexible-backbone computational protein design methods on binding interactions ]]> https://biorxiv.org/content/10.1101/674291v1?rss=1 Loshbaugh, A. L. Kortemme, T. 2019-06-17 doi:10.1101/674291 Cold Spring Harbor Laboratory Press 2019-06-17 <![CDATA[ BOLD Decoding of Individual Pain Anticipation Biases During Uncertainty ]]> https://biorxiv.org/content/10.1101/675645v1?rss=1 Kadlec, M. Tosun, D. Strigo, I. 2019-06-20 doi:10.1101/675645 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ Regulation of community functional composition across taxonomic variation by resource-consumer dynamics ]]> https://biorxiv.org/content/10.1101/677682v1?rss=1 Worden, L. 2019-06-21 doi:10.1101/677682 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Mapping gene regulatory networks of primary CD4+ T cells using single-cell genomics and genome engineering ]]> https://biorxiv.org/content/10.1101/678060v1?rss=1 Gate, R. E. Kim, M. C. Lu, A. Lee, D. Shifrut, E. Subramaniam, M. Marson, A. Ye, C. J. 2019-06-21 doi:10.1101/678060 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Adipocyte JAK2 mediates aging-associated metabolic liver disease and progression to hepatocellular carcinoma ]]> https://biorxiv.org/content/10.1101/681809v1?rss=1 Corbit, K. J. Wilson, C. G. Lowe, D. Tran, J. L. Vera, N. B. Clasquin, M. Mattis, A. N. Weiss, E. J. 2019-06-24 doi:10.1101/681809 Cold Spring Harbor Laboratory Press 2019-06-24 <![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[ 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[ Tumor cell phenotype and heterogeneity differences in IDH1 mutant vs wild-type gliomas ]]> https://biorxiv.org/content/10.1101/690297v1?rss=1 Berens, M. Sood, A. Barnholtz-Sloan, J. Graf, J. F. Cho, S. Kim, S. Kiefer, J. Byron, S. A. Halperin, R. F. Nasser, S. Adkins, J. Cuyugan, L. Devine, K. Ostrom, Q. Couce, M. Wolansky, L. McDonough, E. Schyberg, S. Dinn, S. Sloan, A. E. Prados, M. Phillips, J. J. Nelson, S. J. Liang, W. S. Rusu, M. Zavodszky, M. Ginty, F. 2019-07-02 doi:10.1101/690297 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Mapping Vector Field of Single Cells ]]> https://biorxiv.org/content/10.1101/696724v1?rss=1 Qiu, X. Zhang, Y. Yang, D. Hosseinzadeh, S. Wang, L. Yuan, R. Xu, S. Ma, Y. Replogle, J. Darmanis, S. Xing, J. Weissman, J. 2019-07-09 doi:10.1101/696724 Cold Spring Harbor Laboratory Press 2019-07-09 <![CDATA[ HBMITool: a user-friendly software for labeling Human Brain Microscopy Images ]]> https://biorxiv.org/content/10.1101/699215v1?rss=1 Wang, H. Grinberg, L. T. Alegro, M. 2019-07-11 doi:10.1101/699215 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Multiple Measures Reveal The Value of Both Race And Geographic Ancestry For Self-Identification ]]> https://biorxiv.org/content/10.1101/701698v1?rss=1 Damotte, V. Zhao, C. Lin, C. Williams, E. Louzoun, Y. Madbouly, A. Kotlarz, R. McDaniel, M. Norman, P. J. Lizee, A. Myres, N. M. Ball, C. A. Chahine, K. G. Byrnes, J. Wang, Y. Maiers, M. Hollenbach, J. A. 2019-07-13 doi:10.1101/701698 Cold Spring Harbor Laboratory Press 2019-07-13 <![CDATA[ Aberrant cell segregation in craniofacial primordia and the emergence of facial dysmorphology in craniofrontonasal syndrome ]]> https://biorxiv.org/content/10.1101/704619v1?rss=1 Niethamer, T. K. Percival, C. J. Teng, T. Franco, M. Du, Y. X. Bush, J. O. 2019-07-16 doi:10.1101/704619 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ Mechanistic Insights into the Protective Roles of Polyphosphate Against Amyloid Cytotoxicity ]]> https://biorxiv.org/content/10.1101/704882v1?rss=1 Lempart, J. Tse, E. Lauer, J. A. Ivanova, M. I. Sutter, A. Yoo, N. Huettemann, P. Southworth, D. Jakob, U. 2019-07-16 doi:10.1101/704882 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ Linkage Disequilibrium and Heterozygosity Modulate the Genetic Architecture of Human Complex Phenotypes: Evidence of Natural Selection from GWAS Summary Statistics ]]> https://biorxiv.org/content/10.1101/705285v1?rss=1 Holland, D. Frei, O. Desikan, R. Fan, C. C. Shadrin, A. Smeland, O. Andreassen, O. A. Dale, A. 2019-07-16 doi:10.1101/705285 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ Targeting DNA damage response and Replication Stress in Pancreatic Cancer ]]> https://biorxiv.org/content/10.1101/713545v1?rss=1 nView larger version (47K):norg.highwire.dtl.DTLVardef@106f2b8org.highwire.dtl.DTLVardef@1294d22org.highwire.dtl.DTLVardef@86f5d3org.highwire.dtl.DTLVardef@751e13_HPS_FORMAT_FIGEXP M_FIG C_FIG STATEMENT OF SIGNIFICANCEWe define therapeutic strategies that target subgroups of PC using novel signatures of DNA damage response deficiency and replication stress. This potentially offers patients with DNA repair defects therapeutic options outside standard of care platinum chemotherapy and is being tested in clinical trials on the Precision-Panc platform. ]]> Dreyer, S. Upstill-Goddard, R. Paulus-Hock, V. Paris, C. Maria-Lampraki, E. Dray, E. Serrels, B. Rebus, S. Brunton, H. Nourse, C. Bailey, U.-M. Jones, M. Moran-Jones, K. Wright, D. Duthie, F. Oien, K. Evers, L. McKay, C. McGregor, G. Gulati, A. Brough, R. Bajrami, I. Pettitt, S. Dzubiunski, M. Candido, J. Balkwill, F. Barry, S. Grutzmann, R. Rahib, L. Glasgow Precision Oncology Laboratory, Australian Pancreatic Genome Initiative, Johns, A. Pajic, M. Froeling, F. Beer, P. Musgrove, E. Petersen, G. Ashworth, A. Frame, M. Crawford, H. Simeone, D. Lord, 2019-07-24 doi:10.1101/713545 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Recognition of histone H3 methylation states by the PHD1 domain of histone demethylase KDM5A ]]> https://biorxiv.org/content/10.1101/715474v1?rss=1 Longbotham, J. E. Kelly, M. J. S. Galonic Fujmori, D. 2019-07-26 doi:10.1101/715474 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ State and trait characteristics of anterior insula time-varying functional connectivity ]]> https://biorxiv.org/content/10.1101/716720v1?rss=1 Pasquini, L. Toller, G. Staffaroni, A. Brown, J. A. Deng, J. Lee, A. Kurcyus, K. Shdo, S. M. Allen, I. Sturm, V. E. Cobigo, Y. Borghesani, V. Battistella, G. Gorno-Tempini, M. L. Rankin, K. P. Kramer, J. Rosen, H. H. Miller, B. L. Seeley, W. W. 2019-07-27 doi:10.1101/716720 Cold Spring Harbor Laboratory Press 2019-07-27 <![CDATA[ Telomeric Double Strand Breaks Facilitate Formation of 5’ C-Rich Overhangs in G1 Human Cells ]]> https://biorxiv.org/content/10.1101/720565v1?rss=1 Nelson, C. B. Alturki, T. Taylor, L. Maranon, D. G. Muraki, K. Murnane, J. P. Bailey, S. M. 2019-08-01 doi:10.1101/720565 Cold Spring Harbor Laboratory Press 2019-08-01 <![CDATA[ Structure-function analysis reveals a DNA polymerization-independent role for mitochondrial DNA polymerase IC in African trypanosomes. ]]> https://biorxiv.org/content/10.1101/730523v1?rss=1 Miller, J. C. Delzell, S. B. Concepcion-Acevedo, J. Boucher, M. J. Klingbeil, M. M. 2019-08-09 doi:10.1101/730523 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ BET proteins are required for transcriptional activation of the senescent beta cell secretome in Type 1 Diabetes ]]> https://biorxiv.org/content/10.1101/736231v1?rss=1 Thompson, P. J. Shah, A. Apostolopolou, C.-C. Bhushan, A. 2019-08-15 doi:10.1101/736231 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Aging induces aberrant state transition kinetics in murine muscle stem cells ]]> https://biorxiv.org/content/10.1101/739185v1?rss=1 Kimmel, J. C. Hwang, A. B. Marshall, W. F. Brack, A. S. 2019-08-19 doi:10.1101/739185 Cold Spring Harbor Laboratory Press 2019-08-19 <![CDATA[ The Interaction of LILRB2 with HLA-B is Associated with Psoriasis Susceptibility ]]> https://biorxiv.org/content/10.1101/741983v1?rss=1 Yanovsky, R. L. Chen, H. Leslie, S. Carrington, M. Liao, W. 2019-08-21 doi:10.1101/741983 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Speed and diffusion of kinesin-2 are competing limiting factors in flagellar length control model ]]> https://biorxiv.org/content/10.1101/751990v1?rss=1 Ma, R. Hendel, N. L. Marshall, W. F. Qin, H. 2019-08-30 doi:10.1101/751990 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ Loss of a novel striated muscle-enriched mitochondrial protein Coq10a enhances postnatal cardiac hypertrophic growth ]]> https://biorxiv.org/content/10.1101/755793v1?rss=1 Hirose, K. Chang, S. Yu, H. Wang, J. Barca, E. Chen, X. Khyeam, S. Tajima, K. Yoneshiro, T. Kajimura, S. Quinzii, C. M. Hu, G. Huang, G. N. 2019-09-03 doi:10.1101/755793 Cold Spring Harbor Laboratory Press 2019-09-03 <![CDATA[ In vitro and in vivo roles of glucocorticoid and vitamin D receptors in the control of cardiomyocyte proliferative potential ]]> https://biorxiv.org/content/10.1101/755827v1?rss=1 Cutie, S. Lunn, D. Huang, G. 2019-09-03 doi:10.1101/755827 Cold Spring Harbor Laboratory Press 2019-09-03 <![CDATA[ Defined factors to reactivate cell cycle activity in adult mouse cardiomyocytes ]]> https://biorxiv.org/content/10.1101/755991v1?rss=1 Judd, J. Lovas, J. Huang, G. N. 2019-09-03 doi:10.1101/755991 Cold Spring Harbor Laboratory Press 2019-09-03 <![CDATA[ Complement component 4 genes contribute sex-specific vulnerability in diverse illnesses ]]> https://biorxiv.org/content/10.1101/761718v1?rss=1 Kamitaki, N. Sekar, A. Handsaker, R. E. de Rivera, H. Tooley, K. Morris, D. L. Taylor, K. E. Whelan, C. W. Tombleson, P. Olde Loohuis, L. M. Schizophrenia Working Group of the Psychiatric Genomics Consortium, Boehnke, M. Kimberly, R. P. Kaufman, K. M. Harley, J. B. Langefeld, C. D. Seidman, C. E. Pato, M. T. Pato, C. N. Ophoff, R. A. Graham, R. R. Criswell, L. A. Vyse, T. J. McCarroll, S. A. 2019-09-09 doi:10.1101/761718 Cold Spring Harbor Laboratory Press 2019-09-09 <![CDATA[ Dissecting the chitinolytic activity of mammalian chitinases ]]> https://biorxiv.org/content/10.1101/762336v1?rss=1 Barad, B. A. Liu, L. Diaz, R. E. Basilio, R. Van Dyken, S. J. Locksley, R. M. Fraser, J. S. 2019-09-08 doi:10.1101/762336 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ Transcriptomic profiling of plaque psoriasis and cutaneous T cell subsets during treatment with secukinumab ]]> https://biorxiv.org/content/10.1101/764118v1?rss=1 Liu, J. H. Chang, H.-W. Beck, K. Sekhon, S. Schmidt, T. H. Yan, D. Huang, Z.-M. Yang, E. Sanchez, I. Nakamura, M. Bhattarai, S. Thibodeaux, Q. Ahn, R. S. Bhutani, T. Rosenblum, M. D. Liao, W. 2019-09-10 doi:10.1101/764118 Cold Spring Harbor Laboratory Press 2019-09-10 <![CDATA[ Optimal design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis ]]> https://biorxiv.org/content/10.1101/766972v1?rss=1 Mandric, I. Schwarz, T. Majumdar, A. Perez, R. Subramaniam, M. Ye, C. J. Pasaniuc, B. Halperin, E. 2019-09-12 doi:10.1101/766972 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals ]]> https://biorxiv.org/content/10.1101/767061v1?rss=1 Wolff, A. M. Young, I. D. Sierra, R. G. Brewster, A. S. Martynowycz, M. W. Nango, E. Sugahara, M. Nakane, T. Ito, K. Aquila, A. Bhowmick, A. Biel, J. T. Carbajo, S. Cohen, A. E. Cortez, S. Gonzalez, A. Hino, T. Im, D. Koralek, J. D. Kubo, M. Lazarou, T. S. Nomura, T. Owada, S. Samelson, A. Tanaka, R. Tanaka, T. Thompson, E. M. van den Bedem, H. Woldeyes, R. A. Yumoto, F. Zhao, W. Tono, K. Boutet, S. Iwata, S. Gonen, T. Sauter, N. K. Fraser, J. S. Thompson, M. C. 2019-09-12 doi:10.1101/767061 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Definition of alleles and altered regulatory motifs across Cas9-edited cell populations ]]> https://biorxiv.org/content/10.1101/775361v1?rss=1 Ehmsen, K. T. Knuesel, M. T. Martinez, D. Asahina, M. Aridomi, H. Yamamoto, K. R. 2019-09-19 doi:10.1101/775361 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Differential modulation of ventral tegmental area circuits by the nociceptin/orphanin FQ system ]]> https://biorxiv.org/content/10.1101/776484v1?rss=1 Driscoll, J. R. Wallace, T. L. Martin, W. J. Margolis, E. B. 2019-09-19 doi:10.1101/776484 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Inherited Causes of Clonal Hematopoiesis of Indeterminate Potential in TOPMed Whole Genomes ]]> https://biorxiv.org/content/10.1101/782748v1?rss=1 Bick, A. G. Weinstock, J. Nandakumar, S. K. Fulco, C. P. Leventhal, M. J. Bao, E. L. Nasser, J. Zekavat, S. M. Szeto, M. D. Laurie, C. Taub, M. Mitchell, B. Barnes, K. Moscati, A. Fornage, M. Redline, S. Psaty, B. M. Silverman, E. Weiss, S. Palmer, N. Ramachandran, V. Burchard, E. Kardia, S. He, J. Kaplan, R. Smith, N. L. Arnett, D. Schwartz, D. Correa, A. de Andrade, M. Guo, X. Konkle, B. A. Custer, B. Peralta, J. Gui, H. Meyers, D. McGarvey, S. T. Chen, I. Shoemaker, M. B. Peyser, P. A. Broome, J. Gogarten, S. Wang, F. F. Wong, Q. Montasser, M. Da 2019-09-27 doi:10.1101/782748 Cold Spring Harbor Laboratory Press 2019-09-27 <![CDATA[ Hedgehog pathway activation through conformational blockade of the Patched sterol conduit ]]> https://biorxiv.org/content/10.1101/783290v1?rss=1 Zhang, Y. Lu, W.-J. Bulkley, D. Liang, J. Ralko, A. Roberts, K. J. Li, A. Cho, W. Cheng, Y. Manglik, A. Beachy, P. 2019-09-26 doi:10.1101/783290 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM ]]> https://biorxiv.org/content/10.1101/786285v1?rss=1 Alvarez, M. Rahmani, E. Garske, K. M. Miao, Z. Benhammou, J. N. Ye, C. J. Pisegna, J. R. Pietilainen, K. H. Halperin, E. Pajukanta, P. 2019-09-30 doi:10.1101/786285 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ Human hepatic tryptophan 2,3-dioxygenase ubiquitin-dependent protein degradation: The critical role of its exosite as the molecular lynchpin of its substrate-mediated protein stabilization ]]> https://biorxiv.org/content/10.1101/793380v1?rss=1 Kim, S.-M. Liu, Y. Wang, Y. Karkashon, S. Lewis-Ballester, A. Yeh, S.-R. Correia, M. A. 2019-10-04 doi:10.1101/793380 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ Estrogen Drives Melanocortin Neurons To Reduce Sedentary Behavior ]]> https://biorxiv.org/content/10.1101/794792v1?rss=1 Krause, W. C. Rodriguez, R. Gegenhuber, J. B. Matharu, N. Rodriguez, A. N. Padilla, A. Herber, C. B. Correa, S. M. Ahituv, N. M. Tollkuhn, J. Ingraham, H. A. 2019-10-08 doi:10.1101/794792 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Broadly Conserved Roles of TMEM-131 Family Proteins in Intracellular Collagen Assembly and Secretory Cargo Trafficking ]]> https://biorxiv.org/content/10.1101/794842v1?rss=1 Zhang, Z. Bai, M. Barbosa, G. O. Chen, A. Wei, Y. Luo, S. Wang, X. Wang, B. Tsukui, T. LI, H. Sheppard, D. Kornberg, T. Ma, D. K. 2019-10-05 doi:10.1101/794842 Cold Spring Harbor Laboratory Press 2019-10-05 <![CDATA[ Selectivity and engineering of the sialoglycan-binding spectrum in Siglec-like adhesins ]]> https://biorxiv.org/content/10.1101/796912v1?rss=1 Bensing, B. Loukachevitch, L. V. Agarwal, R. Yamakawa, I. Luong, K. Hadadianpour, A. Yu, H. Fialkowski, K. Castro, M. Wawrzak, Z. Chen, X. Baudry, J. Smith, J. Sullam, P. Iverson, T. M. 2019-10-07 doi:10.1101/796912 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Predicting 3D genome folding from DNA sequence ]]> https://biorxiv.org/content/10.1101/800060v1?rss=1 Fudenberg, G. Kelley, D. R. Pollard, K. S. 2019-10-10 doi:10.1101/800060 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Paralytic, the Drosophila voltage-gated sodium channel, regulates proliferation of neural progenitors ]]> https://biorxiv.org/content/10.1101/803288v1?rss=1 Piggott, B. J. Peters, C. J. He, Y. Huang, X. Younger, S. Jan, L. Jan, Y. N. 2019-10-14 doi:10.1101/803288 Cold Spring Harbor Laboratory Press 2019-10-14 <![CDATA[ Dopamine and risky decision-making in pathological and problem gamblers. ]]> https://biorxiv.org/content/10.1101/805929v1?rss=1 Peters, J. Vega, T. Weinstein, D. Mitchell, J. Kayser, A. 2019-10-16 doi:10.1101/805929 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ High throughput CRISPR screening identifies genes involved in macrophage viability and inflammatory pathways ]]> https://biorxiv.org/content/10.1101/807164v1?rss=1 Covarrubias, S. Vollmers, A. Capili, A. Boettcher, M. Robinson, E. K. O'Briain, L. Vollmers, C. Blau, J. McManus, M. Carpenter, S. 2019-10-16 doi:10.1101/807164 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Opioids depress breathing through two small brainstem sites ]]> https://biorxiv.org/content/10.1101/807297v1?rss=1 Iris, B. Wei, X. P. Kish, E. Yackle, K. 2019-10-17 doi:10.1101/807297 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Dynamic preferences account for inter-animal variability during the continual learning of a cognitive task ]]> https://biorxiv.org/content/10.1101/808006v1?rss=1 Kastner, D. B. Miller, E. A. Yang, Z. Roumis, D. K. Liu, D. F. Frank, L. M. Dayan, P. 2019-10-17 doi:10.1101/808006 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Broad and thematic remodeling of the surface glycoproteome on isogenic cells transformed with driving proliferative oncogenes ]]> https://biorxiv.org/content/10.1101/808139v1?rss=1 Leung, K. K. Wilson, G. M. Kirkemo, L. L. Riley, N. M. Coon, J. J. Wells, J. A. 2019-10-17 doi:10.1101/808139 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ EGFR Oncogenes Expressed In Glioblastoma Are Activated As Covalent Dimers And Paradoxically Stimulated By Erlotinib ]]> https://biorxiv.org/content/10.1101/810721v1?rss=1 Buck, E. O'Connor, M. Romashko, D. Salomatov, A. Ishiyama, N. Epstein, D. Mayweg, A. Flohr, A. Iacone, R. Nicolaides, T. Markovic, S. Zhang, J. 2019-10-21 doi:10.1101/810721 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein ]]> https://biorxiv.org/content/10.1101/811083v1?rss=1 Wych, D. C. Fraser, J. S. Mobley, D. L. Wall, M. 2019-10-18 doi:10.1101/811083 Cold Spring Harbor Laboratory Press 2019-10-18 <![CDATA[ A Chromatin Accessibility Atlas of the Developing Human Telencephalon ]]> https://biorxiv.org/content/10.1101/811620v1?rss=1 Markenscoff-Papadimitriou, E. Whalen, S. Przytycki, P. Thomas, R. Binyameen, F. Nowakowski, T. J. Sanders, S. J. State, M. W. Pollard, K. S. Rubenstein, J. L. 2019-10-21 doi:10.1101/811620 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Amino and PEG-Amino Graphene Oxide Grids Enrich and Protect Samples for High-resolution Single Particle Cryo-electron Microscopy ]]> https://biorxiv.org/content/10.1101/813972v1?rss=1 Wang, F. Yu, Z. Betegon, M. Campbell, M. Aksel, T. Zhao, J. Li, S. Douglas, S. M. Cheng, Y. Agard, D. 2019-10-22 doi:10.1101/813972 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Genetic and clinical analyses of psychosis spectrum symptoms in a large multi-ethnic youth cohort reveal significant link with ADHD. ]]> https://biorxiv.org/content/10.1101/814087v1?rss=1 Olde Loohuis, L. M. Mennigen, E. Ori, A. P. S. Perkins, D. Robinson, E. Addington, J. Cadenhead, K. S. Cornblatt, B. A. Mathalon, D. H. McGlashan, T. H. Seidman, L. J. Keshavan, M. Stone, W. Tsuang, M. T. Walker, E. F. Woods, S. W. Cannon, T. D. Gur, R. C. Gur, R. E. Bearden, C. E. Ophoff, R. A. 2019-10-22 doi:10.1101/814087 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Phenotype-based screening of synthetic cannabinoids in a Dravet Syndrome zebrafish model ]]> https://biorxiv.org/content/10.1101/815811v1?rss=1 Griffin, A. Anvar, M. Hamling, K. Baraban, S. C. 2019-10-23 doi:10.1101/815811 Cold Spring Harbor Laboratory Press 2019-10-23 <![CDATA[ Drug resistant gut bacteria mimic a host mechanism for anticancer drug clearance ]]> https://biorxiv.org/content/10.1101/820084v1?rss=1 Spanogiannopoulos, P. Bradley, P. H. Melamed, J. Malig, Y. N. A. Lam, K. N. Gerona, R. R. Pollard, K. S. Turnbaugh, P. 2019-10-25 doi:10.1101/820084 Cold Spring Harbor Laboratory Press 2019-10-25 <![CDATA[ Obesity Potentiates TH2 Immunopathology via Dysregulation of PPAR ]]> https://biorxiv.org/content/10.1101/825836v1?rss=1 Bapat, S. Liang, Y. Liu, S. Zhang, L.-j. Vogel, I. Marr, D. J. Zhou, C. Choi, E. J. Chang, C. He, N. LeBlanc, M. Lee, I.-k. Suh, J. M. Crotty Alexander, L. E. Liddle, C. Atkins, A. R. Yu, R. T. Downes, M. Ansel, K. M. Marson, A. Gallo, R. L. Evans, R. M. Zheng, Y. 2019-10-31 doi:10.1101/825836 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Recurrent loss of abaA, a master regulator of asexual development in filamentous fungi, correlates with changes in genomic and morphological traits ]]> https://biorxiv.org/content/10.1101/829465v1?rss=1 Mead, M. E. Borowsky, A. T. Joehnk, B. Steenwyk, J. L. Shen, X.-X. Sil, A. Rokas, A. 2019-11-04 doi:10.1101/829465 Cold Spring Harbor Laboratory Press 2019-11-04 <![CDATA[ PCK1 and DHODH drive colorectal cancer liver metastatic colonization and hypoxic pyrimidine nucleotide anabolic biosynthesis ]]> https://biorxiv.org/content/10.1101/833186v1?rss=1 Yamaguchi, N. Weinberg, E. Nguyen, A. Liberti, M. V. Goodarzi, H. Janjigian, Y. Y. Paty, P. B. Saltz, L. B. Kingham, T. P. Loo, J. M. Stanchina, E. d. Tavazoie, S. F. 2019-11-06 doi:10.1101/833186 Cold Spring Harbor Laboratory Press 2019-11-06 <![CDATA[ α-synuclein aggregates induce c-Abl activation and neurodegeneration by a redox stress mechanism ]]> https://biorxiv.org/content/10.1101/840306v1?rss=1 Ghosh, S. Won, S. J. Fong, R. Butler, N. J. M. Moss, A. Wong, C. Pan, J. Sanchez, J. Wu, L. Wang, J. Manfredsson, F. P. Swanson, R. A. 2019-11-13 doi:10.1101/840306 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ Combined modulation of SHH and FGF signaling is crucial for maintenance of the neocortical progenitor specification program ]]> https://biorxiv.org/content/10.1101/841932v1?rss=1 Yabut, O. R. Ng, H.-X. Yoon, K. Gomez, H. G. Arela, J. C. Pleasure, S. 2019-11-14 doi:10.1101/841932 Cold Spring Harbor Laboratory Press 2019-11-14 <![CDATA[ Regional and hemispheric susceptibility of the temporal lobe to FTLD-TDP-43-C pathology ]]> https://biorxiv.org/content/10.1101/847582v1?rss=1 Borghesani, V. Battistella, G. Mandelli, M. L. Welch, A. Weis, E. Younes, K. Neuhaus, J. Grinberg, L. T. Seeley, W. W. Spina, S. Miller, B. L. Miller, Z. Gorno-Tempini, M. L. 2019-11-20 doi:10.1101/847582 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Taking the sub-lexical route: brain dynamics of reading in the semantic variant of Primary Progressive Aphasia. ]]> https://biorxiv.org/content/10.1101/847798v1?rss=1 Borghesani, V. Hinkley, L. B. Ranasinghe, K. G. Thompson, M. Shwe, W. Mizuiri, D. Lauricella, M. Europa, E. Honma, S. Miller, Z. Miller, B. L. Vossel, K. Houde, J. F. Gorno-Tempini, M. L. Nagarajan, S. 2019-11-21 doi:10.1101/847798 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Lgr5+ telocytes are a signaling hub at the intestinal villus tip ]]> https://biorxiv.org/content/10.1101/850909v1?rss=1 Bahar Halpern, K. Massalha, H. Zwick, R. K. Moor, A. E. Castillo-Azofeifa, D. Rozenberg, M. Farack, L. Egozi, A. Miller, D. R. Averbukh, I. Harnik, Y. Weinberg-Corem, N. de Sauvage, F. J. Amit, I. Klein, O. D. Shoshkes-Carmel, M. Itzkovitz, S. 2019-11-21 doi:10.1101/850909 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Extended Recognition of the Histone H3 Tail by Histone Demethylase KDM5A ]]> https://biorxiv.org/content/10.1101/854265v1?rss=1 Petronikolou, N. Longbotham, J. E. Fujimori, D. 2019-11-25 doi:10.1101/854265 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ A minimal CRISPR-Cas3 system for genome engineering ]]> https://biorxiv.org/content/10.1101/860999v1?rss=1 Csorgo, B. Leon, L. M. Chau-Ly, I. J. Vasquez-Rifo, A. Berry, J. D. Mahendra, C. Crawford, E. Lewis, J. D. Bondy-Denomy, J. 2019-12-03 doi:10.1101/860999 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ A discrete mode of endosomal GPCR signaling that does not require β-arrestin ]]> https://biorxiv.org/content/10.1101/2022.09.07.506997v1?rss=1 Blythe, E. E. Von Zastrow, M. 2022-09-08 doi:10.1101/2022.09.07.506997 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Actin-driven protrusions generate rapid long-range membrane tension propagation in cells ]]> https://biorxiv.org/content/10.1101/2022.09.07.507005v1?rss=1 De Belly, H. Yan, S. Borja da Rocha, H. Ichbiah, S. Town, J. P. Turlier, H. Bustamante, C. J. Weiner, O. D. 2022-09-08 doi:10.1101/2022.09.07.507005 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Potentiation of Adipogenesis by Reactive Oxygen Species is a Unifying Mechanism in the Pro-adipogenic Properties of Bisphenol A and its New Structural Analogues. ]]> https://biorxiv.org/content/10.1101/2022.09.08.507176v1?rss=1 Singh, R. D. Wager, J. L. Scheidl, T. B. Connors, L. T. Easson, S. Callaghan, M. A. Alatorre-hinojosa, S. Swift, L. H. Colarusso, P. Jadli, A. SHUTT, T. Patel, V. Thompson, J. 2022-09-08 doi:10.1101/2022.09.08.507176 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Mediator 1 ablation induces enamel-to-hair lineage conversion through enhancer dynamics ]]> https://biorxiv.org/content/10.1101/2022.09.08.507153v1?rss=1 Thaler, R. Yoshizaki, K. Nguyen, T. Fukumoto, S. DenBesten, p. Bikle, D. D. Oda, Y. 2022-09-09 doi:10.1101/2022.09.08.507153 Cold Spring Harbor Laboratory Press 2022-09-09 <![CDATA[ Beta spectral power during sleep is associated with impaired recall of extinguished fear ]]> https://biorxiv.org/content/10.1101/2022.09.08.506006v1?rss=1 0.92). Individuals with PTSD were found to have increased beta PSD compared to healthy controls (ps < .039), and beta PSD correlated with extinction recall in the PTSD group at a similar magnitude to controls (r=.39). Results suggest beta band PSD is elevated in PTSD, and is specifically implicated in difficulties recalling extinguished fear. Significance statementDisturbed sleep is a hallmark feature of posttraumatic stress disorder (PTSD). Certain neural oscillations that occur during sleep have been shown to be altered in PTSD. These include increased 15-30Hz beta oscillations, which are believed to index cortical hyperarousal. Alongside sleep disturbances, patients also show difficulty in recalling extinguished fear. Although prior studies have linked sleep with extinction retention, no studies have investigated the role that neural oscillations during sleep play in this process. Here, we show in both healthy participants and PTSD patients, that increased beta oscillatory power during sleep is associated with impaired extinction retention. Therefore, this study provides new evidence that electrophysiological changes in the sleep EEG of PTSD patients is also implicated in extinction recall processes. ]]> Denis, D. Bottary, R. Cunningham, T. J. Drummond, S. P. A. Straus, L. D. 2022-09-10 doi:10.1101/2022.09.08.506006 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Heterogeneous migration of neuronal progenitors to the insula shapes the human brain ]]> https://biorxiv.org/content/10.1101/2022.09.09.507371v1?rss=1 Mallela, A. N. Deng, H. Gholipour, A. Warfield, S. K. Goldschmidt, E. 2022-09-10 doi:10.1101/2022.09.09.507371 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Perturbations in podocyte transcriptome and biological pathways induced by FSGS associated circulating factors. ]]> https://biorxiv.org/content/10.1101/2022.09.08.507168v1?rss=1 Rashmi, P. Sigdel, T. K. Rychkov, D. Damm, I. da Silva, A. A. Vincenti, F. Lourenco, A. L. Craik, C. S. Reiser, J. Sarwal, M. M. 2022-09-12 doi:10.1101/2022.09.08.507168 Cold Spring Harbor Laboratory Press 2022-09-12 <![CDATA[ Genetic deletion and pharmacologic inhibition of FcER1 reduces renal injury in mouse models of diabetic nephropathy. ]]> https://biorxiv.org/content/10.1101/2022.09.10.507433v1?rss=1 Rashmi, P. Silva, A. A. Sigdel, T. Damm, I. Gouvea, A. L. F. Koliwad, S. Walavalkar, V. Hakroush, S. Sarwal, M. M. 2022-09-13 doi:10.1101/2022.09.10.507433 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Microcosm cultures of a complex synthetic community reveal ecology and genetics of gut microbial organization ]]> https://biorxiv.org/content/10.1101/2022.09.13.507837v1?rss=1 Jin, X. Yu, F. B. Yan, J. Weakley, A. Pollard, K. S. 2022-09-13 doi:10.1101/2022.09.13.507837 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Vowel and formant representation in human auditory speech cortex ]]> https://biorxiv.org/content/10.1101/2022.09.13.507547v1?rss=1 Oganian, Y. Bhaya-Grossman, I. Johnson, K. Chang, E. F. 2022-09-14 doi:10.1101/2022.09.13.507547 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ The landscape of antibody binding affinity in SARS-CoV-2 Omicron BA.1 evolution ]]> https://biorxiv.org/content/10.1101/2022.09.13.507781v1?rss=1 Moulana, A. Dupic, T. Phillips, A. M. Chang, J. Roffler, A. A. Greaney, A. J. Starr, T. N. Bloom, J. D. Desai, M. M. 2022-09-14 doi:10.1101/2022.09.13.507781 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ Pbp1 stabilizes and promotes the translation of Puf3-target mRNAs involved in mitochondrial biogenesis ]]> https://biorxiv.org/content/10.1101/2022.09.14.507933v1?rss=1 van de Poll, F. Sutter, B. M. Lee, C.-D. Yang, Y.-S. Tu, B. P. 2022-09-14 doi:10.1101/2022.09.14.507933 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ OpenPBTA: An Open Pediatric Brain Tumor Atlas ]]> https://biorxiv.org/content/10.1101/2022.09.13.507832v1?rss=1 Shapiro, J. A. Gaonkar, K. S. Savonen, C. L. Spielman, S. J. Bethell, C. J. Jin, R. Rathi, K. S. Zhu, Y. Egolf, L. E. Farrow, B. K. Miller, D. P. Yang, Y. Koganti, T. Noureen, N. Koptyra, M. P. Duong, N. Kraya, A. A. Kline, C. N. Guo, Y. Storm, P. B. Nazarian, J. Mack, S. C. Raman, P. Zheng, S. Madsen, P. J. Van Kuren, N. Robins, S. Huang, X. Waanders, A. J. Kim, J. Hanson, D. Koschmann, C. J. Diskin, S. J. Lulla, R. R. Brown, M. A. Wong, J. Mason, J. L. Scolaro, L. Kim, M. C. Xie, H. M. Rood, B. R. Cole, K. A. Margol, A. S. Vaksman, Z. Kaufman, R. S 2022-09-16 doi:10.1101/2022.09.13.507832 Cold Spring Harbor Laboratory Press 2022-09-16 <![CDATA[ GPCR Signaling Promotes a Stress-induced Genetic Program for Phenoptosis in C. elegans ]]> https://biorxiv.org/content/10.1101/2022.09.16.508223v1?rss=1 Wang, C. Long, Y. Wang, B. Zhang, C. Ma, D. K. 2022-09-17 doi:10.1101/2022.09.16.508223 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Quotidian Profile of Vergence Angle in Ambulatory Subjects Monitored with Wearable Eye Tracking Glasses ]]> https://biorxiv.org/content/10.1101/2022.09.14.506830v1?rss=1 Dilbeck, M. D. Gentry, T. N. Economides, J. R. Horton, J. C. 2022-09-18 doi:10.1101/2022.09.14.506830 Cold Spring Harbor Laboratory Press 2022-09-18 <![CDATA[ A family of novel immune systems targets early infection of nucleus-forming jumbo phages ]]> https://biorxiv.org/content/10.1101/2022.09.17.508391v1?rss=1 200 kb) and the remarkable ability to assemble a proteinaceous nucleus-like structure. The nucleus protects the phage genome from canonical DNA-targeting immune systems, such as CRISPR-Cas and restriction-modification. We hypothesized that the failure of common bacterial defenses creates selective pressure for immune systems that target the unique jumbo phage biology. Here, we identify the "jumbo phage killer" (Juk) immune system that is deployed by a clinical isolate of Pseudomonas aeruginosa to resist [ovbar]KZ. Juk immunity rescues the cell by preventing early phage transcription, DNA replication, and nucleus assembly. Phage infection is first sensed by JukA (formerly YaaW), which localizes rapidly to the site of phage infection at the cell pole, triggered by ejected phage factors. The effector protein JukB is recruited by JukA, which is required to enable immunity and the subsequent degradation of the phage DNA. JukA homologs are found in several bacterial phyla and are associated with numerous other putative effectors, many of which provided specific anti-[ovbar]KZ activity when expressed in P. aeruginosa. Together, these data reveal a novel strategy for immunity whereby immune factors are recruited to the site of phage protein and DNA ejection to prevent phage progression and save the cell. ]]> Li, Y. Guan, J. Hareendranath, S. Crawford, E. Agard, D. A. Makarova, K. S. Koonin, E. V. Bondy-Denomy, J. 2022-09-18 doi:10.1101/2022.09.17.508391 Cold Spring Harbor Laboratory Press 2022-09-18 <![CDATA[ Genetic, clinical underpinnings of subtle early brain change along Alzheimer's dimensions ]]> https://biorxiv.org/content/10.1101/2022.09.16.508329v1?rss=1 WEN, J. Yang, Z. Nasrallah, I. Cui, Y. Erus, G. Srinivasan, D. Abdulkadir, A. Mamourian, E. Hwang, G. Singh, A. Bergman, M. Bao, J. Varol, E. Zhou, Z. Boquet-Pujadas, A. Chen, J. Toga, A. W. Saykin, A. J. Hohman, T. Thompson, P. Villeneuve, S. Gollub, R. Sotiras, A. Wittfeld, K. Grabe, H. Tosun, D. Bilgel, M. An, Y. Marcus, D. LaMontagne, P. J. Heckbert, S. Austin, T. Launer, L. Espeland, M. Masters, C. Maruff, P. Fripp, J. Johnson, S. C. Morris, j. Albert, M. Nick, R. Resnick, S. M. Ferrucci, L. Fan, Y. Mohamad, H. Wolk, D. Shen, L. Shou, H. Dav 2022-09-19 doi:10.1101/2022.09.16.508329 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Homeostatic cytokines reciprocally modulate the emergence of prenatal effector PLZF+CD4+ T cells in humans ]]> https://biorxiv.org/content/10.1101/2022.09.19.508328v1?rss=1 Locher, V. Park, S. Bunis, D. Makredes, S. Burt, T. D. Fragiadakis, G. K. Halkias, J. 2022-09-19 doi:10.1101/2022.09.19.508328 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Systems biology illuminates alternative metabolic niches in the human gut microbiome ]]> https://biorxiv.org/content/10.1101/2022.09.19.508335v1?rss=1 Noecker, C. Sanchez, J. Bisanz, J. E. Escalante, V. Alexander, M. Trepka, K. Heinken, A. Liu, Y. Dodd, D. Thiele, I. DeFelice, B. Turnbaugh, P. J. 2022-09-19 doi:10.1101/2022.09.19.508335 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Hierarchical sequence-affinity landscapes shape the evolution of breadth in an anti-influenza receptor binding site antibody ]]> https://biorxiv.org/content/10.1101/2022.09.21.508900v1?rss=1 Phillips, A. M. Maurer, D. P. Brooks, C. Dupic, T. Schmidt, A. G. Desai, M. M. 2022-09-21 doi:10.1101/2022.09.21.508900 Cold Spring Harbor Laboratory Press 2022-09-21 <![CDATA[ T cell-instructed inflammation drives immune checkpoint inhibitor therapy resistance ]]> https://biorxiv.org/content/10.1101/2022.09.20.508732v1?rss=1 Cho, N. W. Guldberg, S. M. Kim, E. J. Hiam-Galvez, K. J. Wai, K. Levine, L. S. Nabet, B. Y. DeBarge, R. Yee, J. L. Ashitey, N. A. Tenvooren, I. Spitzer, M. H. 2022-09-22 doi:10.1101/2022.09.20.508732 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ The Phosphate Deprivation Response is Mediated by an Interaction between Brassinosteroid Signaling and Zinc in Tomato ]]> https://biorxiv.org/content/10.1101/2022.09.21.508943v1?rss=1 Demirer, G. S. Gibson, D. J. Yue, X. Pan, K. Elishav, E. Khandal, H. Horev, G. Tarkowska, D. Canto-Pastor, A. Kong, S. Maloof, J. Savaldi-Goldstein, S. Brady, S. 2022-09-22 doi:10.1101/2022.09.21.508943 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Pharmacological inhibition of bromodomain and extra-terminal proteins induces NRF-2-mediated inhibition of SARS-CoV-2 replication and is subject to viral antagonism ]]> https://biorxiv.org/content/10.1101/2022.09.22.508962v1?rss=1 Mhlekude, B. Postmus, D. Weiner, J. Stenzel, S. Zapatero-Belinchon, F. J. Olmer, R. Jansen, J. Richter, A. Heinze, J. Heinemann, N. Muhlemann, B. Schroeder, S. Jones, T. C. Muller, M. A. Drosten, C. Pich, A. Thiel, V. Martin, U. Niemeyer, D. Gerold, G. Beule, D. Goffinet, C. 2022-09-23 doi:10.1101/2022.09.22.508962 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Growth cone advance requires EB1 as revealed by genomic replacement with a light-sensitive variant ]]> https://biorxiv.org/content/10.1101/2022.09.22.509085v1?rss=1 Dema, A. Charafeddine, R. A. Rahgozar, S. van Haren, J. Wittmann, T. 2022-09-23 doi:10.1101/2022.09.22.509085 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ The ancestral ESCRT protein TOM1L2 selects ubiquitinated cargoes for retrieval from cilia ]]> https://biorxiv.org/content/10.1101/2022.09.23.509287v1?rss=1 Shinde, S. R. Mick, D. U. Aoki, E. Nachury, M. V. 2022-09-25 doi:10.1101/2022.09.23.509287 Cold Spring Harbor Laboratory Press 2022-09-25 <![CDATA[ Small-molecule ketone esters treat brain network abnormalities in an Alzheimer's disease mouse model ]]> https://biorxiv.org/content/10.1101/2022.09.24.509337v1?rss=1 Newman, J. C. Ma, K. Kroll, F. Higgins, E. Ulrich, S. Palop, J. J. Verdin, E. 2022-09-26 doi:10.1101/2022.09.24.509337 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ A non-ligand surrogate agonist antibody that enhances canonical Wnt signaling and bone regeneration ]]> https://biorxiv.org/content/10.1101/2022.09.25.509440v1?rss=1 Lee, N.-K. Bidlingmaier, S. Su, Y. Seo, Y. Liu, B. 2022-09-27 doi:10.1101/2022.09.25.509440 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Cell circuits between leukemic cells and mesenchymal stem cells block lymphopoiesis by activating lymphotoxin-beta receptor signaling ]]> https://biorxiv.org/content/10.1101/2022.09.23.509256v1?rss=1 Feng, X. Sun, R. Lee, M. Chen, X. Guo, S. Geng, H. Müschen, M. Choi, J. Pereira, J. P. 2022-09-28 doi:10.1101/2022.09.23.509256 Cold Spring Harbor Laboratory Press 2022-09-28 <![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[ A scalable screening platform for phenotypic subtyping of ALS patient-derived fibroblasts ]]> https://biorxiv.org/content/10.1101/2022.09.27.509770v1?rss=1 Kumbier, K. Roth, M. Li, Z. Lazzari-Dean, J. Waters, C. Huang, P. Korobeynikov, V. Consortium, N. Y. G. C. Phatnani, H. Schneider, N. Jacobson, M. Wu, L. Altschuler, S. 2022-09-28 doi:10.1101/2022.09.27.509770 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Genetic Regulators of Sputum Mucin Concentration and Their Associations with COPD Phenotypes ]]> https://biorxiv.org/content/10.1101/2022.09.28.509838v1?rss=1 Van Buren, E. Radicioni, G. Lester, S. O'Neal, W. Dang, H. Kasela, S. Gardadri, S. Curtis, J. Han, M. Krishnan, J. Wan, E. Silverman, E. Hastie, A. Ortega, V. Lappalainen, T. Christenson, S. Li, Y. Cho, M. Kesimer, M. Kelada, S. 2022-09-28 doi:10.1101/2022.09.28.509838 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ A host defense peptide mimetic, brilacidin, potentiates caspofungin antifungal activity against human pathogenic fungi ]]> https://biorxiv.org/content/10.1101/2022.09.28.509882v1?rss=1 dos Reis, T. F. de Castro, P. A. Bastos, R. Pinzan, C. F. Souza, P. F. Ackloo, S. Hossain, M. A. Drewry, D. Alkhazraji, S. Ibrahim, A. Jo, H. deGrado, W. F. Goldman, G. 2022-09-28 doi:10.1101/2022.09.28.509882 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ DASH/Dam1 complex mutants stabilize ploidy by weakening kinetochore-microtubule attachments ]]> https://biorxiv.org/content/10.1101/2022.09.28.509901v1?rss=1 Haase, M. A. B. Olafsson, G. Flores, R. L. Boakye-Ansah, E. Zelter, A. Dickinson, M. S. Stefanita, L. L. Truong, D. M. Asbury, C. L. Davis, T. N. Boeke, J. D. 2022-09-28 doi:10.1101/2022.09.28.509901 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ De novo protein identification in mammalian sperm using high-resolution in situ cryo-electron tomography ]]> https://biorxiv.org/content/10.1101/2022.09.28.510016v1?rss=1 Chen, Z. Shiozaki, M. Haas, K. M. Zhao, S. Guo, C. Polacco, B. J. Yu, Z. Krogan, N. J. Kaake, R. M. Vale, R. D. Agard, D. A. 2022-09-29 doi:10.1101/2022.09.28.510016 Cold Spring Harbor Laboratory Press 2022-09-29 <![CDATA[ A tradeoff between enterovirus A71 particle stability and cell entry ]]> https://biorxiv.org/content/10.1101/2022.09.28.506941v1?rss=1 Catching, A. Yeh, M. T. Bianco, S. Capponi, S. Andino, R. 2022-09-30 doi:10.1101/2022.09.28.506941 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Single-cell sequencing identifies novel atypical B cell subsets with distinct effector functions ]]> https://biorxiv.org/content/10.1101/2022.09.28.509955v1?rss=1 Reyes, R. A. Batugedara, G. Dutta, P. Reers, A. Garza, R. Ssewanyana, I. Feeney, M. E. Greenhouse, B. Bol, S. Bunnik, E. M. 2022-09-30 doi:10.1101/2022.09.28.509955 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ mTOR inhibitor-independent Autophagy Activator Ameliorates Cellular Tauopathy and Prionopathy Neurodegeneration Phenotypes ]]> https://biorxiv.org/content/10.1101/2022.09.29.509997v1?rss=1 Yoon, L. Botham, R. C. Verhelle, A. Cole, C. Tan, E. P. Wu, Y. Sanz-Martinez, P. Xu, J. Cuoco, C. A. Chou, C. C. Labra, S. Elia, L. P. Massey, L. A. Lee, K. Xiao, Q. Kline, G. M. Ta, A. Ardejani, M. S. Cano-Franco, S. Lyang, N. J. Hou, W. C. Yu, A. Fox, S. Ko, Y. Chen, W. Wulkop-Gil, C. Ibrahim, L. H. Jiang, S. Meneses, A. Nelson, L. T. Peng, H. Lipton, S. A. Bollong, M. J. Hansen, M. Morimoto, R. I. Finley, D. Petrassi, H. M. Wiseman, R. L. Powers, E. T. Finkbeiner, S. Garza, D. Prado, M. A. Dikic, I. Frydman, J. Johnson, K. A. Silva, M. C. Haggar 2022-09-30 doi:10.1101/2022.09.29.509997 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Role of intraflagellar transport in transcriptional control during flagellar regeneration in Chlamydomonas ]]> https://biorxiv.org/content/10.1101/2022.09.29.510156v1?rss=1 Perlaza, K. Zamora, I. Marshall, W. F. 2022-09-30 doi:10.1101/2022.09.29.510156 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Stacked binding of a small molecule PET tracer to Alzheimer's tau paired helical filaments ]]> https://biorxiv.org/content/10.1101/2022.09.30.510175v1?rss=1 Merz, G. E. Chalkley, M. J. Tan, S. K. Tse, E. Lee, J. Prusiner, S. B. Paras, N. A. DeGrado, W. F. Southworth, D. R. 2022-10-03 doi:10.1101/2022.09.30.510175 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ Pharmacologic Inhibition of DYRK1A Results in MYC Hyperactivation and ERK Hyperphosphorylation rendering KMT2A-R ALL Cells Sensitive to BCL2 Inhibition ]]> https://biorxiv.org/content/10.1101/2022.10.02.510349v1?rss=1 Hurtz, C. Ayyadevara, V. S. S. A. Wertheim, G. Chukinas, J. Loftus, J. P. Lee, S. J. Kumar, A. Bhansali, R. S. Swaminathan, S. Geng, H. Milne, T. Hua, X. Bernt, K. M. Besson, T. Shi, J. Crispino, J. D. Carroll, M. Tasian, S. K. 2022-10-04 doi:10.1101/2022.10.02.510349 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ Proteomic analysis of flagella from Chlamydomonas mutants lacking the central pair apparatus reveals loss of radial spoke head proteins ]]> https://biorxiv.org/content/10.1101/2022.10.02.510551v1?rss=1 Wemmer, K. A. AZIMZADEH, J. F. Marshall, W. F. 2022-10-04 doi:10.1101/2022.10.02.510551 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ The cellular states and fates of shed intestinal cells ]]> https://biorxiv.org/content/10.1101/2022.10.03.510592v1?rss=1 Bahar Halpern, K. Biram, A. Egozi, A. Korem Kohanim, Y. Shulman, Z. Itzkovitz, S. 2022-10-04 doi:10.1101/2022.10.03.510592 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ EMC holdase:CaV1.2/CaVβ3 complex and CaV1.2 channel structures reveal CaV assembly and drug binding mechanisms ]]> https://biorxiv.org/content/10.1101/2022.10.03.510667v1?rss=1 Chen, Z. Mondal, A. Abderemane-Ali, F. Montano, J. Zaro, B. Minor, D. L. 2022-10-05 doi:10.1101/2022.10.03.510667 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Three-dimensional genome re-wiring in loci with Human Accelerated Regions ]]> https://biorxiv.org/content/10.1101/2022.10.04.510859v1?rss=1 Keough, K. C. Whalen, S. Inoue, F. Przytycki, P. F. Fair, T. Deng, C. Steyert, M. Ryu, H. Lindblad-Toh, K. Karlsson, E. Zoonomia Consortium, Nowakowski, T. J. Ahituv, N. J. Pollen, A. A. Pollard, K. S. 2022-10-05 doi:10.1101/2022.10.04.510859 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Opposing transcription factors MYCL and HEY1 mediate the Notch-dependent airway stem cell fate decision ]]> https://biorxiv.org/content/10.1101/2022.10.05.511009v1?rss=1 Byrnes, L. E. Deleon, R. Reiter, J. F. Choksi, S. P. 2022-10-05 doi:10.1101/2022.10.05.511009 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Circularization of rv0678 for genotypic bedaquiline resistance testing of Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2022.10.05.511060v1?rss=1 Limberis, J. Nalyvayko, A. Ernst, J. Metcalfe, J. Z. 2022-10-06 doi:10.1101/2022.10.05.511060 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ Epigenomic and chromosomal architectural reconfiguration in developing human frontal cortex and hippocampus ]]> https://biorxiv.org/content/10.1101/2022.10.07.511350v1?rss=1 Heffel, M. G. Zhou, J. Zhang, Y. Lee, D.-S. Hou, K. Pastor Alonso, O. Abuhanna, K. Schmitt, A. D. Li, T. Haeussler, M. Wick, B. Zhang, M. J. Xie, F. Ziffra, R. S. Mukamel, E. A. Eskin, E. Pasaniuc, B. Ecker, J. R. Dixon, J. Nowakowski, T. J. Paredes, M. F. Luo, C. 2022-10-08 doi:10.1101/2022.10.07.511350 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ An unbiased screen identified the Hsp70-BAG3 complex as a regulator of myosin binding protein C3 stability. ]]> https://biorxiv.org/content/10.1101/2022.10.08.511444v1?rss=1 Thompson, A. D. Wagner, M. J. Rodriguez, J. Malhotra, A. Vander Roest, S. Lilienthal, U. Shao, H. Yob, J. Prosser, B. L. Helms, A. S. Gestwicki, J. E. Ginsburg, D. E. Day, S. M. 2022-10-08 doi:10.1101/2022.10.08.511444 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ Structural Genomics of the Human Dopamine Receptor System ]]> https://biorxiv.org/content/10.1101/2022.10.09.511478v1?rss=1 Xu, P. Huang, S. Krumm, B. E. Zhuang, Y. Mao, C. Zhang, Y. Wang, Y. Huang, X.-P. Liu, Y.-F. He, X. Li, H. Yin, W. Jiang, Y. Zhang, Y. Roth, B. L. Xu, H. E. 2022-10-10 doi:10.1101/2022.10.09.511478 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ Structural surfaceomics reveals an AML-specific conformation of Integrin-β2 as a CAR-T therapy target ]]> https://biorxiv.org/content/10.1101/2022.10.10.511511v1?rss=1 Mandal, K. Wicaksono, G. Yu, C. Adams, J. J. Hoopmann, M. R. Temple, W. C. Escobar, B. P. Gorelik, M. Ihling, C. H. Nix, M. A. Naik, A. Ramos, E. Kasap, C. Steri, V. Serrano, J. A. C. Salangsang, F. Phojanakong, P. McMillan, M. Gavallos, V. Leavitt, A. D. Sinz, A. Huang, B. J. Stieglitz, E. Smith, C. C. Moritz, R. L. Sidhu, S. S. Huang, L. Wiita, A. P. 2022-10-11 doi:10.1101/2022.10.10.511511 Cold Spring Harbor Laboratory Press 2022-10-11 <![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[ Therapeutic trial of anle138b in mouse models of genetic prion disease ]]> https://biorxiv.org/content/10.1101/2022.10.11.511739v1?rss=1 20 months of age. Vacuolization and PrP deposition were observed in some brain regions in a subset of mutant animals, but appeared unable to carry the weight of a primary endpoint in a therapeutic study. We conclude that not all animal models of prion disease are suited to well-powered therapeutic efficacy studies, and care should be taken in choosing the models that will support drug development programs. ]]> Vallabh, S. M. Zou, D. Pitstick, R. O'Moore, J. Peters, J. Silvius, D. Kriz, J. Jackson, W. S. Carlson, G. A. Minikel, E. V. Cabin, D. E. 2022-10-12 doi:10.1101/2022.10.11.511739 Cold Spring Harbor Laboratory Press 2022-10-12 <![CDATA[ Essential role of the amino-terminal region of Drosha for the Microprocessor function ]]> https://biorxiv.org/content/10.1101/2022.10.12.509557v1?rss=1 Hata, A. Prabhakar, A. Jiang, X. Hu, S. Tang, J. Ghatpande, P. Lagna, G. 2022-10-13 doi:10.1101/2022.10.12.509557 Cold Spring Harbor Laboratory Press 2022-10-13 <![CDATA[ A unified model for the dynamics of ATP-independent ultrafast contraction ]]> https://biorxiv.org/content/10.1101/2022.10.14.512304v1?rss=1 Floyd, C. Molines, A. T. Lei, X. Honts, J. E. Chang, F. Elting, M. W. Vaikuntanathan, S. Dinner, A. R. Bhamla, M. S. 2022-10-16 doi:10.1101/2022.10.14.512304 Cold Spring Harbor Laboratory Press 2022-10-16 <![CDATA[ Innate immune cell-intrinsic ketogenesis is dispensable for organismal metabolism and age-related inflammation ]]> https://biorxiv.org/content/10.1101/2022.10.14.512312v1?rss=1 Goldberg, E. L. Letian, A. Dlugos, T. Leveau, C. Dixit, V. D. L. 2022-10-16 doi:10.1101/2022.10.14.512312 Cold Spring Harbor Laboratory Press 2022-10-16 <![CDATA[ Physiological Condition Dependent Changes in Ciliary GPCR Localization in the Brain ]]> https://biorxiv.org/content/10.1101/2022.10.13.512090v1?rss=1 Brewer, K. M. Engle, S. E. Bansal, R. Brewer, K. K. Jasso, K. R. McIntyre, J. C. Vaisse, C. Reiter, J. F. Berbari, N. F. 2022-10-17 doi:10.1101/2022.10.13.512090 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Neurofeedback training can modulate task-relevant memory replay in rats ]]> https://biorxiv.org/content/10.1101/2022.10.13.512183v1?rss=1 Gillespie, A. K. Astudillo Maya, D. A. Denovellis, E. L. Desse, S. Frank, L. M. 2022-10-17 doi:10.1101/2022.10.13.512183 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Decoding of YAP levels and dynamics by pluripotency factors ]]> https://biorxiv.org/content/10.1101/2022.10.17.512504v1?rss=1 Meyer, K. Lammers, N. C. Bugaj, L. J. Garcia, H. H. Weiner, O. D. 2022-10-17 doi:10.1101/2022.10.17.512504 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Tracking the online construction of linguistic meaning through negation ]]> https://biorxiv.org/content/10.1101/2022.10.14.512299v1?rss=1 Zuanazzi, A. Ripolles, P. Lin, W. M. Gwilliams, L. King, J.-R. Poeppel, D. 2022-10-18 doi:10.1101/2022.10.14.512299 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ CD46 targeted 212Pb alpha particle radioimmunotherapy for prostate cancer treatment ]]> https://biorxiv.org/content/10.1101/2022.10.14.512321v1?rss=1 Li, J. Huang, T. Hua, J. Wang, Q. Su, Y. Chen, P. Bidlingmaier, S. Li, A. Xie, Z. Bidkar, A. Shen, S. Shi, W. Seo, Y. Flavell, R. R. Gioeli, D. Dreicer, R. Li, H. Liu, B. He, J. 2022-10-18 doi:10.1101/2022.10.14.512321 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Autism-associated transcriptional regulators target shared loci proximal to brain-expressed genes. ]]> https://biorxiv.org/content/10.1101/2022.10.17.512583v1?rss=1 Fazel Darbandi, S. An, J. Y. Lim, K. Page, N. F. Liang, L. Ypsilanti, A. Markenscoff-Papadimitriou, E. State, M. W. Nord, A. S. Sanders, S. J. Rubenstein, J. L. R. 2022-10-18 doi:10.1101/2022.10.17.512583 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ 7SK methylation Promotes Transcriptional Activity upon Growth Factor Stimulation ]]> https://biorxiv.org/content/10.1101/2022.10.17.512631v1?rss=1 Alarcon, C. R. Perez-Pepe, M. Desotell, A. W. Li, H. Li, W. Han, B. Lin, Q. Klein, D. E. Liu, Y. Goodarzi, H. 2022-10-18 doi:10.1101/2022.10.17.512631 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis. ]]> https://biorxiv.org/content/10.1101/2022.10.18.512708v1?rss=1 Kehrer, T. Cupic, A. Ye, C. Yildiz, S. Bouhhadou, M. Crossland, N. A. Barrall, E. Cohen, P. Tseng, A. Cagatay, T. Rathnasinghe, R. Flores, D. Jangra, S. Alam, F. Mena, N. Aslam, S. Saqi, A. Marin, A. Rutkowska, M. Ummadi, M. R. Pisanelli, G. Richardson, R. B. Veit, E. C. Fabius, J. M. A. Soucheray, M. Polacco, B. J. Evans, M. J. Swaney, D. L. Gonzalez-Reiche, A. S. Sordillo, E. M. van Bakel, H. Simon, V. Zuliani-Alvarez, L. Fontoura, B. M. A. Rosenberg, B. R. Krogan, N. J. Martinez-Sobrido, L. Garcia-Sastre, A. Miorin, L. 2022-10-19 doi:10.1101/2022.10.18.512708 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ Long-term, super-resolution HIDE imaging of the inner mitochondrial membrane in live cells with a cell-permeant lipid probe ]]> https://biorxiv.org/content/10.1101/2022.10.19.512772v1?rss=1 Zheng, S. Dadina, N. Mozumdar, D. Lesiak, L. Martinez, K. Miller, E. Schepartz, A. 2022-10-19 doi:10.1101/2022.10.19.512772 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ Global landscape of the host response to SARS-CoV-2 variants reveals viral evolutionary trajectories ]]> https://biorxiv.org/content/10.1101/2022.10.19.512927v1?rss=1 Bouhaddou, M. Reuschl, A.-K. Polacco, B. J. Thorne, L. G. Ummadi, M. R. Ye, C. Ramirez, R. R. Pelin, A. Batra, J. Jang, G. M. Xu, J. Moen, J. M. Richards, A. L. Zhou, Y. Harjai, B. Stevenson, E. Rojc, A. Ragazzini, R. Whelan, M. V. X. Furnon, W. De Lorenzo, G. Cowton, V. Syed, A. M. Ciling, A. Deutsch, N. Pirak, D. Dowgier, G. Mesner, D. Turner, J. L. McGovern, B. L. Rodriguez, M. L. Leiva-Rebollo, R. Dunham, A. S. Zhong, X. Eckhardt, M. Fossati, A. Liotta, N. Kehrer, T. Cupic, A. Rutkowska, M. Mena, N. Aslam, S. Hoffert, A. Foussard, H. Pham, J. Ly 2022-10-21 doi:10.1101/2022.10.19.512927 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ The IRE1α-XBP1 signaling axis promotes glycolytic reprogramming in response to inflammatory stimuli ]]> https://biorxiv.org/content/10.1101/2022.10.19.512943v1?rss=1 English, B. C. Savage, H. P. Mahan, S. P. Diaz-Ochoa, V. E. Young, B. M. Abuaita, B. H. Sule, G. J. Knight, J. S. O'Riordan, M. X. Baumler, A. J. Tsolis, R. M. 2022-10-21 doi:10.1101/2022.10.19.512943 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Species-specific roles for the MAFA and MAFB transcription factors in regulatingislet β cell identity ]]> https://biorxiv.org/content/10.1101/2022.10.20.512880v1?rss=1 Cha, J. Tong, X. Walker, E. M. Dahan, T. Cochrane, V. Ashe, S. Russell, R. Osipovich, A. B. Mawla, A. M. Guo, M. Liu, J.-h. Huising, M. O. Magnuson, M. A. Hebrok, M. Dor, Y. Stein, R. 2022-10-21 doi:10.1101/2022.10.20.512880 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ A reversible SRC-relayed COX2-inflammatory program drives therapeutic resistance in BRAF(V600E) colorectal tumors ]]> https://biorxiv.org/content/10.1101/2022.10.20.512885v1?rss=1 Ruiz-Saenz, A. Atreya, C. E. Wang, C. Pan, B. Dreyer, C. A. Brunen, D. Prahallad, A. Munoz, D. P. Ramms, D. J. Burghi, V. Spassov, D. S. Fewings, E. Hwang, Y. C. Cowdrey, C. Moelders, C. Schwarzer, C. Wolf, D. M. Hann, B. VandenBerg, S. R. Shokat, K. Moasser, M. M. Bernards, R. Gutkind, J. S. van't Veer, L. J. Coppe, J.-P. 2022-10-21 doi:10.1101/2022.10.20.512885 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Rubella virus tropism and single cell responses in human primary tissue and microglia-containing organoids ]]> https://biorxiv.org/content/10.1101/2022.10.24.513565v1?rss=1 Popova, G. Retallack, H. Kim, C. N. Shin, D. Wang, A. DeRisi, J. J. Nowakowski, T. J. 2022-10-24 doi:10.1101/2022.10.24.513565 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ A general approach to discover conformational epitope-directed binders for selective inhibition of protein proteolytic activation ]]> https://biorxiv.org/content/10.1101/2022.10.24.513434v1?rss=1 Zhou, J. 2022-10-25 doi:10.1101/2022.10.24.513434 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ A cross-species proteomic map of synapse development reveals neoteny during human postsynaptic density maturation ]]> https://biorxiv.org/content/10.1101/2022.10.24.513541v1?rss=1 1,000 postsynaptic density (PSD) proteins from midgestation to young adulthood, we found that PSD maturation in humans separates into three major phases that are dominated by distinct pathways. Cross-species comparisons reveal that the human PSD matures about two to three times slower than other species and contains higher levels of Rho guanine nucleotide exchange factors (RhoGEFs) in the perinatal period. Enhancement of the RhoGEF signaling in human neurons delays the morphological maturation of dendritic spines and the functional maturation of synapses, potentially contributing to the neotenic traits of human brain development. In addition, PSD proteins can be divided into four modules that exert stage- and cell type-specific functions, possibly explaining their differential associations with cognitive functions and diseases. Together, our proteomic map of synapse development provides a blueprint for studying the molecular basis and evolutionary changes of synapse maturation. ]]> Wang, L. Pang, K. Zhou, L. Cebrian-Silla, A. Gonzalez-Granero, S. Wang, S. Bi, Q. White, M. L. Ho, B. Li, J. Li, T. Perez, Y. Huang, E. J. Winkler, E. A. Paredes, M. F. Kovner, R. Sestan, N. Pollen, A. A. Liu, P. Li, J. Piao, X. Garcia-Verdugo, J. M. Alvarez-Buylla, A. Liu, Z. Kriegstein, A. R. 2022-10-25 doi:10.1101/2022.10.24.513541 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Single-cell analysis of prenatal and postnatal human cortical development ]]> https://biorxiv.org/content/10.1101/2022.10.24.513555v1?rss=1 Velmeshev, D. Perez, Y. Yan, Z. Valencia, J. E. Castaneda-Castellanos, D. R. Schirmer, L. Mayer, S. Wick, B. Wang, S. Nowakowski, T. J. Paredes, M. Huang, E. J. J. Kriegstein, A. 2022-10-25 doi:10.1101/2022.10.24.513555 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Granulin Loss of Function in Human Mature Brain Organoids Implicates Astrocytes in TDP-43 Pathology ]]> https://biorxiv.org/content/10.1101/2022.10.24.513566v1?rss=1 de Majo, M. Koontz, M. Marsan, E. Salinas, N. Ramsey, A. Kuo, Y.-M. Seo, K. Li, H. Draeger, N. M. Leng, K. Kurnellas, M. Miyaoka, Y. Klim, J. R. Kampmann, M. Ward, M. E. Huang, E. J. Ullian, E. M. 2022-10-25 doi:10.1101/2022.10.24.513566 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Loss of MLL3/4 decouples enhancer H3K4 monomethylation, H3K27 acetylation, and gene activation during ESC differentiation ]]> https://biorxiv.org/content/10.1101/2022.10.24.513607v1?rss=1 Blelloch, R. Boileau, R. M. Chen, K. X. 2022-10-25 doi:10.1101/2022.10.24.513607 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ The global anaerobic metabolism regulator fnr is necessary for the degradation of food dyes and drugs by Escherichia coli ]]> https://biorxiv.org/content/10.1101/2022.10.25.513779v1?rss=1 Pieper, L. M. Spanogiannopoulos, P. Volk, R. Miller, C. Wright, A. Turnbaugh, P. J. 2022-10-25 doi:10.1101/2022.10.25.513779 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Dissecting the effects of GTPase and kinase domain mutations on LRRK2 endosomal localization and activity ]]> https://biorxiv.org/content/10.1101/2022.10.25.513743v1?rss=1 Rinaldi, C. Waters, C. S. Kumbier, K. Rao, L. Nichols, R. J. Jacobson, M. P. Wu, L. F. Altschuler, S. J. 2022-10-27 doi:10.1101/2022.10.25.513743 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ A deficiency screen of the 3rd chromosome for dominant modifiers of the Drosophila ER integral membrane protein, Jagunal ]]> https://biorxiv.org/content/10.1101/2022.10.26.513935v1?rss=1 Ascencio, G. de Cruz, M. A. Abuel, J. Alvarado, S. Arriaga, Y. Conrad, E. A. Castro, A. Eichelberger, K. Galvan, L. Gundy, G. Inojoza, J. A. Jimenez, A. D. Lu, N. T. Lugar, C. Marania, R. Mendsaikhan, T. Ortega, J. Nand, N. Rodrigues, N. S. Shabazz, K. Tam, C. Valenciano, E. Hayzelden, C. Eritano, A. S. Riggs, B. 2022-10-28 doi:10.1101/2022.10.26.513935 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Membrane-active peptides escape drug-resistance in cancer ]]> https://biorxiv.org/content/10.1101/2022.10.27.513961v1?rss=1 Benfield, A. H. Vernen, F. Young, R. S. E. Bufi, F. N. Hammerlindl, H. Craik, D. J. Schaider, H. Lawrence, N. Blanksby, S. J. Henriques, S. T. 2022-10-28 doi:10.1101/2022.10.27.513961 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Linking Choroid Plexus Enlargement with Plasma Analyte and Structural Phenotypes in Clinical High Risk for Psychosis: A Multisite Neuroimaging Study ]]> https://biorxiv.org/content/10.1101/2022.10.28.514160v1?rss=1 Bannai, D. Reuter, M. Hegde, R. Hoang, D. Adhan, I. Gandu, S. Pong, S. Zeng, A. Raymond, N. Zeng, V. Chung, Y. He, G. Sun, D. van Erp, T. G. M. Addington, J. Bearden, C. E. Cadenhead, K. Cornblatt, B. Mathalon, D. H. McGlashan, T. Jeffries, C. Stone, W. Tsuang, M. Walker, E. Woods, S. W. Cannon, T. D. Perkins, D. Keshavan, M. Lizano, P. 2022-10-30 doi:10.1101/2022.10.28.514160 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ Single-cell RNA-seq reveals alterations in peripheral CX3CR1 and nonclassical monocytes in familial tauopathy ]]> https://biorxiv.org/content/10.1101/2022.10.28.514304v1?rss=1 Sirkis, D. W. Warly Solsberg, C. Johnson, T. P. Bonham, L. W. Sturm, V. E. Lee, S. E. Rankin, K. P. Rosen, H. J. Boxer, A. L. Seeley, W. W. Miller, B. L. Geier, E. G. Yokoyama, J. S. 2022-10-30 doi:10.1101/2022.10.28.514304 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ Robust expression of transgenes in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2022.10.30.514414v1?rss=1 40-fold increase in its levels. ]]> Lidsky, P. V. Dmitriev, S. E. Andino, R. 2022-10-31 doi:10.1101/2022.10.30.514414 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ Excessive Firing of Dyskinesia-Associated Striatal Direct Pathway Neurons is Gated By Dopamine and Excitatory Synaptic Input ]]> https://biorxiv.org/content/10.1101/2022.10.31.514594v1?rss=1 Ryan, M. B. Girasole, A. E. McGregor, M. M. Brakaj, R. Paletzki, R. F. Gerfen, C. R. Nelson, A. B. 2022-11-01 doi:10.1101/2022.10.31.514594 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ A Semi-Supervised Ensemble Approach to Rank Potential Causal Variants and Their Target Genes in Microglia for Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2022.11.01.514771v1?rss=1 Khaire, A. Wen, J. Yang, X. Shen, Y. Li, Y. 2022-11-03 doi:10.1101/2022.11.01.514771 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B ]]> https://biorxiv.org/content/10.1101/2022.11.02.514751v1?rss=1 Mehlman, T. S. Biel, J. T. Azeem, S. M. Nelson, E. R. Hossain, S. Dunnett, L. E. Paterson, N. G. Douangamath, A. Talon, R. Axford, D. Orins, H. von Delft, F. Keedy, D. A. 2022-11-03 doi:10.1101/2022.11.02.514751 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ Eos promotes TH2 differentiation by propagating the IL-2/STAT5 signaling pathway. ]]> https://biorxiv.org/content/10.1101/2022.11.02.514868v1?rss=1 Tuazon, J. A. Read, K. A. Sreekumar, B. K. Yaeger, M. J. Varikuti, S. Jones, D. M. Warren, R. T. Powell, M. D. Rasheed, M. N. Duncan, E. G. Childs, L. M. Gowdy, K. M. Oestreich, K. J. 2022-11-03 doi:10.1101/2022.11.02.514868 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ Ras-dependent RAF-MAPK hyperactivation by pathogenic RIT1 is a therapeutic target in Noonan syndrome-associated cardiac hypertrophy ]]> https://biorxiv.org/content/10.1101/2022.11.02.514888v1?rss=1 Cuevas-Navarro, A. Wagner, M. Van, R. Swain, M. Allison, M. R. Cheng, A. Messing, S. Simanshu, D. K. Sale, M. J. McCormick, F. Stephen, A. G. Castel, P. 2022-11-03 doi:10.1101/2022.11.02.514888 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ Parabolic avalanche scaling in the synchronization of cortical cell assemblies ]]> https://biorxiv.org/content/10.1101/2022.11.02.514938v1?rss=1 Capek, E. Lins-Ribeiro, T. Srinivasan, K. Miller, S. R. Victor, M. Geist, E. Vakili, A. Pajevic, S. Chialvo, D. R. Plenz, D. 2022-11-03 doi:10.1101/2022.11.02.514938 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ Multi-model order spatially constrained ICA reveals highly replicable group differences and consistent predictive results from fMRI data ]]> https://biorxiv.org/content/10.1101/2022.11.02.514809v1?rss=1 1,600) study of schizophrenia divided into separate validation and replication sets. A multi-scale ICN template was estimated and labeled, then used as input into spatially constrained ICA which was computed on an individual subject level. We then performed a subsequent analysis of multiscale functional network connectivity (msFNC) to evaluate the patient data, including group differences and classification. Results showed highly consistent group differences in msFNC in regions including cerebellum, thalamus, and motor/auditory networks. Importantly, multiple msFNC pairs linking different spatial scales were implicated. We also used the msFNC features as input to a classification model in cross-validated hold-out data and also in an independent test data. Visualization of predictive features was performed by evaluating their feature weights. Finally, we evaluated the relationship of the identified patterns to positive symptoms and found consistent results across datasets. The results verified the robustness of our framework in evaluating brain functional connectivity of schizophrenia at multiple spatial scales, implicated consistent and replicable brain networks, and highlighted a promising approach for leveraging resting fMRI data for brain biomarker development. ]]> Meng, X. Iraji, A. Fu, Z. Kochunov, P. Belger, A. Ford, J. McEwen, S. Mathalon, D. H. Mueller, B. A. Pearlson, G. D. Potkin, S. G. Preda, A. Turner, J. Erp, T. G. M. v. Sui, J. Calhoun, V. 2022-11-04 doi:10.1101/2022.11.02.514809 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Cellpanelr: identify predictive biomarkers from cell line panel response data ]]> https://biorxiv.org/content/10.1101/2022.11.02.514913v1?rss=1 Wassarman, D. R. Wu, T. Shokat, K. 2022-11-04 doi:10.1101/2022.11.02.514913 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Astrocyte-like CEPsh glia responds to the stressful environments ]]> https://biorxiv.org/content/10.1101/2022.11.03.515075v1?rss=1 Chien, E. Garcia, A. J. CHANDRA, R. L'Etoile, N. 2022-11-04 doi:10.1101/2022.11.03.515075 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Integrative single-cell characterization of hypothalamus sex-differential and obesity-associated genes and regulatory elements ]]> https://biorxiv.org/content/10.1101/2022.11.06.515311v1?rss=1 Nguyen, H. P. Chan, C. S. Cintron, D. L. Sheng, R. Harshman, L. Nobuhara, M. Ushiki, A. Biellak, C. An, K. Gordon, G. M. Mifsud, F. Blake, A. Huang, E. J. Hemberg, M. Vaisse, C. Ahituv, N. 2022-11-06 doi:10.1101/2022.11.06.515311 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ Cholinergic Interneurons Drive Motivation by Promoting Dopamine Release in the Nucleus Accumbens ]]> https://biorxiv.org/content/10.1101/2022.11.06.515335v1?rss=1 Mohebi, A. Collins, V. L. Berke, J. D. 2022-11-06 doi:10.1101/2022.11.06.515335 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ Cell-subtype specific effects of genetic variation in the aging and Alzheimer cortex ]]> https://biorxiv.org/content/10.1101/2022.11.07.515446v1?rss=1 Fujita, M. Gao, Z. Zeng, L. McCabe, C. White, C. C. Ng, B. Green, G. S. Rozenblatt-Rosen, O. Phillips, D. Amir-Zilberstein, L. Lee, H. Pearse, R. V. Khan, A. Vardarajan, B. N. Kiryluk, K. Ye, C. J. Klein, H.-U. Wang, G. Regev, A. Habib, N. Schneider, J. A. Wang, Y. Young-Pearse, T. Mostafavi, S. Bennett, D. A. Menon, V. De Jager, P. L. 2022-11-08 doi:10.1101/2022.11.07.515446 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ Dynamic CD8+ T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted by metastasis ]]> https://biorxiv.org/content/10.1101/2022.11.08.513062v1?rss=1 Rahim, M. K. Okholm, T. L. H. Jones, K. B. McCarthy, E. E. Liu, C. C. Yee, J. L. Tamaki, S. J. Marquez, D. M. Tenvooren, I. Wai, K. Cheung, A. Davidson, B. R. Johri, V. Samad, B. O'Gorman, W. E. Krummel, M. F. Combes, A. J. Angelo, M. Fong, L. Algazi, A. P. Ha, P. Spitzer, M. H. 2022-11-08 doi:10.1101/2022.11.08.513062 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ memento: Generalized differential expression analysis of single-cell RNA-seq with method of moments estimation and efficient resampling ]]> https://biorxiv.org/content/10.1101/2022.11.09.515836v1?rss=1 Kim, M. C. Gate, R. E. Lee, D. S. Chun, A. L. Gordon, E. Shifrut, E. Marson, A. Ntranos, V. Ye, C. J. 2022-11-10 doi:10.1101/2022.11.09.515836 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ Core Defense Hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems ]]> https://biorxiv.org/content/10.1101/2022.11.11.516204v1?rss=1 180,000 genomes available on NCBI, revealing Pseudomonas aeruginosa to possess the most diverse anti-phage arsenal of any species with >200 sequenced genomes. Using network analysis to identify the common neighbors of anti-phage systems, we surprisingly identified two highly conserved core defense hotspot loci (cDHS1 and cDHS2). Across more than 1,000 P. aeruginosa strains, cDHS1 is up to 224 kb (mean: 34 kb) with varied arrangements of at least 31 immune systems while cDHS2 has 24 distinct systems (mean: 15.4 kb). cDHS1/2 are present in most P. aeruginosa isolates, in contrast to highly variable mobile DHSs. Most cDHS genes are of unknown function potentially representing new anti-phage systems, which we validated by identifying a novel anti-phage system (Shango) commonly encoded in cDHS1. Identification of core gene markers that flank immune islands could be a simple approach for immune system discovery and may represent popular landing spots for diverse MGEs carrying anti-phage systems. ]]> Johnson, M. C. Laderman, E. Huiting, E. C. Zhang, C. Davidson, A. R. Bondy-Denomy, J. R. 2022-11-11 doi:10.1101/2022.11.11.516204 Cold Spring Harbor Laboratory Press 2022-11-11 <![CDATA[ Circuit dissection and functional validation of a cross-species emotional biomarker ]]> https://biorxiv.org/content/10.1101/2022.11.11.516218v1?rss=1 Jackson, A. Cohen, J. Phensy, A. Chang, E. F. Dawes, H. Sohal, V. 2022-11-11 doi:10.1101/2022.11.11.516218 Cold Spring Harbor Laboratory Press 2022-11-11 <![CDATA[ An RFX transcription factor regulated ciliogenesis in the progenitors of choanoflagellates and animals ]]> https://biorxiv.org/content/10.1101/2022.11.11.515474v1?rss=1 Coyle, M. Tajima, A. Leon, F. Choksi, S. P. Yang, A. Espinoza, S. Hughes, T. R. Reiter, J. F. Booth, D. S. King, N. 2022-11-14 doi:10.1101/2022.11.11.515474 Cold Spring Harbor Laboratory Press 2022-11-14 <![CDATA[ Pseudomonas aeruginosa mechanosensing controls cell polarity during twitching by activating two antagonistic response regulators ]]> https://biorxiv.org/content/10.1101/2022.11.15.516588v1?rss=1 Kuhn, M. J. Macmillan, H. Tala, L. Inclan, Y. Patino, R. Pierrat, X. Al-Mayyah, Z. Engel, J. N. Persat, A. 2022-11-15 doi:10.1101/2022.11.15.516588 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Targeted high throughput mutagenesis of the human spliceosome reveals its in vivo operating principles ]]> https://biorxiv.org/content/10.1101/2022.11.13.516350v1?rss=1 150 proteins. We scaled haploid CRISPR-Cas9 base editing to target the entire human spliceosome and interrogated the mutants using the U2 snRNP/SF3b inhibitor, pladienolide B. Hypersensitive substitutions define functional sites in the U1/U2-containing A-complex but also in components that act as late as the second chemical step after SF3b is dissociated. Viable resistance substitutions map not only to the pladienolide B binding site but also to the G-patch (ATPase activator) domain of SUGP1, which lacks orthologs in yeast. We used these mutants and biochemical approaches to identify the spliceosomal disassemblase DHX15/hPrp43 as the ATPase ligand for SUGP1. These and other data support a model in which SUGP1 promotes splicing fidelity by triggering early spliceosome disassembly in response to kinetic blocks. Our approach provides a template for the analysis of essential cellular machines in humans. ]]> Beusch, I. Rao, B. Studer, M. Luhovska, T. Sukyte, V. Lei, S. Oses-Prieto, J. A. SeGraves, E. Burlingame, A. Jonas, S. Madhani, H. D. 2022-11-16 doi:10.1101/2022.11.13.516350 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Uptake of tumor-derived microparticles induces metabolic reprogramming of macrophages in the early metastatic lung. ]]> https://biorxiv.org/content/10.1101/2022.11.15.516217v1?rss=1 Kersten, K. You, R. Liang, S. Tharp, K. Pollack, J. Weaver, V. M. Krummel, M. F. Headley, M. B. 2022-11-17 doi:10.1101/2022.11.15.516217 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Innate immune response to SARS-1 CoV-2 infection contributes to neuronal damage in human iPSC-derived peripheral neurons ]]> https://biorxiv.org/content/10.1101/2022.11.18.517047v1?rss=1 Passos, V. Henkel, L. M. Wang, J. Zapatero-Belinchon, F. J. Moeller, R. Sun, G. Waltl, I. Ritter, B. Kropp, K. A. Zhu, S. Deleidi, M. Kalinke, U. Hoeglinger, G. Gerold, G. Wegner, F. Viejo-Borbolla, A. 2022-11-18 doi:10.1101/2022.11.18.517047 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ Tracing the origin of pathologic pulmonary fibroblasts ]]> https://biorxiv.org/content/10.1101/2022.11.18.517147v1?rss=1 Tsukui, T. Sheppard, D. 2022-11-18 doi:10.1101/2022.11.18.517147 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ Human endometrial KISS1R inhibits stromal cell decidualization in a manner associated with a reduction in ESR1 levels ]]> https://biorxiv.org/content/10.1101/2022.11.20.517219v1?rss=1 Schaefer, J. Chadchan, S. George, A. Roan, N. Bhattacharya, M. Kommagaini, R. Babwah, A. 2022-11-20 doi:10.1101/2022.11.20.517219 Cold Spring Harbor Laboratory Press 2022-11-20 <![CDATA[ Robust and Highly Efficient Extractions of Proteins from Bones enable Deep, High-Throughput Proteomic Quantification to Gain Insights into Bone Biology ]]> https://biorxiv.org/content/10.1101/2022.11.20.517228v1?rss=1 Rose, J. P. Schurman, C. A. King, C. D. Bons, J. Burton, J. B. Patel, S. K. O'Broin, A. Alliston, T. Schilling, B. 2022-11-20 doi:10.1101/2022.11.20.517228 Cold Spring Harbor Laboratory Press 2022-11-20 <![CDATA[ Systematic Approach Identifies Multiple Transcription Factor Perturbations That Rejuvenate Replicatively Aged Human Skin Fibroblasts ]]> https://biorxiv.org/content/10.1101/2022.11.20.517270v1?rss=1 Sengstack, J. Zheng, J. Mobaraki, M. Lin, J. Deng, C. Li, H. 2022-11-20 doi:10.1101/2022.11.20.517270 Cold Spring Harbor Laboratory Press 2022-11-20 <![CDATA[ Fragment-Based Hit Discovery via Unsupervised Learning of Fragment-Protein Complexes ]]> https://biorxiv.org/content/10.1101/2022.11.21.517375v1?rss=1 McCorkindale, W. J. Ahel, I. Barr, H. Correy, G. J. Fraser, J. S. London, N. Schuller, M. Shurrush, K. Lee, A. A. 2022-11-24 doi:10.1101/2022.11.21.517375 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Anti-integrin αvβ6 autoantibodies are a novel predictive biomarker in ulcerative colitis ]]> https://biorxiv.org/content/10.1101/2022.11.21.517399v1?rss=1 Livanos, A. E. Dunn, A. Fischer, J. Ungaro, R. C. Turpin, W. Lee, S.-H. Rui, S. Del Valle, D. M. Julia, J. J. Martinez-Delgado, G. Riddle, M. S. Murray, J. A. Laird, R. M. Torres, J. Agrawal, M. Magee, J. S. Dervieux, T. Gnjatic, S. Sheppard, D. Sands, B. E. Porter, C. K. Croitoru, K. Petralia, F. Colombel, J.-F. Mehandru, S. 2022-11-24 doi:10.1101/2022.11.21.517399 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Kinetochore-fiber lengths are maintained locally but coordinated globally by poles in the mammalian spindle ]]> https://biorxiv.org/content/10.1101/2022.11.26.517738v1?rss=1 Richter, M. Neahring, L. Tao, J. Sutanto, R. Cho, N. H. Dumont, S. 2022-11-26 doi:10.1101/2022.11.26.517738 Cold Spring Harbor Laboratory Press 2022-11-26 <![CDATA[ Evidence that SPIO Chain Formation is Essential for High-Resolution MPI ]]> https://biorxiv.org/content/10.1101/2022.11.27.518061v1?rss=1 Colson, C. Fung, K. L. B. Bryan, J. Tay, Z. W. Fellows, B. D. Sayuujya, C. Kuo, R. Chandrasekharan, P. Conolly, S. M. 2022-11-28 doi:10.1101/2022.11.27.518061 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Global Endometrial DNA Multi-omics Analysis Reveals Insights into mQTL Regulation and Associated Endometriosis Disease Risk ]]> https://biorxiv.org/content/10.1101/2022.11.27.518106v1?rss=1 Mortlock, S. Houshdaran, S. Kosti, I. Rahmioglu, N. Nezhat, C. Vitonis, A. F. Andrews, S. V. Grosjean, P. Paranjpe, M. Horne, A. W. Jacoby, A. Lager, J. Opoku-Anane, J. Vo, K. C. Manvelyan, E. Sen, S. Ghukasyan, Z. Collins, F. Santamaria, X. Saunders, P. Kober, K. McRae, A. F. Terry, K. L. Vallve-Juanico, J. Becker, C. Rogers, P. A. W. Irwin, J. C. Zondervan, K. Montgomery, G. W. Missmer, S. Sirota, M. Giudice, L. 2022-11-28 doi:10.1101/2022.11.27.518106 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ The connectome of an insect brain ]]> https://biorxiv.org/content/10.1101/2022.11.28.516756v1?rss=1 Winding, M. Pedigo, B. D. Barnes, C. L. Patsolic, H. G. Park, Y. Kazimiers, T. Fushiki, A. Andrade, I. V. Li, F. Valdes-Aleman, J. Khandelwal, A. Randel, N. Barsotti, E. Correia, A. Fetter, R. D. Hartenstein, V. Priebe, C. E. Vogelstein, J. T. Cardona, A. Zlatic, M. 2022-11-28 doi:10.1101/2022.11.28.516756 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Translation-dependent downregulation of Cas12a mRNA by an anti-CRISPR protein ]]> https://biorxiv.org/content/10.1101/2022.11.29.518452v1?rss=1 Marino, N. D. Talaie, A. Carion, H. Zhang, Y. Silas, S. Li, Y. Bondy-Denomy, J. 2022-11-30 doi:10.1101/2022.11.29.518452 Cold Spring Harbor Laboratory Press 2022-11-30 <![CDATA[ Acute adenoviral cardiac infection elicits an arrhythmogenic substrate prior to inflammatory myocardial remodeling and myocarditis ]]> https://biorxiv.org/content/10.1101/2022.11.29.518421v1?rss=1 Padget, R. L. Blair, G. A. North, M. D. Zeitz, M. J. Tanenbaum, M. T. King, D. R. Hoeker, G. S. Swanger, S. A. Poelzing, S. Smyth, J. W. 2022-12-02 doi:10.1101/2022.11.29.518421 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ An ESCRT-dependent pathway of Nuclear and Cytoplasmic Spatial PQC is coordinated at Nuclear Vacuolar Junctions ]]> https://biorxiv.org/content/10.1101/2022.12.01.518779v1?rss=1 Sontag, E. M. Morales-Polanco, F. Chen, J.-H. McDermott, G. Dolan, P. T. Gestaut, D. R. LeGros, M. A. Larabell, C. Frydman, J. 2022-12-02 doi:10.1101/2022.12.01.518779 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Allosteric SHP2 Inhibition Increases Apoptotic Dependency on BCL2 and Synergizes with Venetoclax in FLT3- and KIT- Mutant AML ]]> https://biorxiv.org/content/10.1101/2022.12.01.518665v1?rss=1 Popescu, B. Stahlhut, C. Tarver, T. C. Wishner, S. Lee, B. J. Peretz, C. A. C. Luck, C. Phojanakong, P. Camara Serrano, J. A. Hongo, H. Rivera, J. M. Xirenayi, S. Chukinas, J. A. Steri, V. Tasian, S. K. Stieglitz, E. Smith, C. C. 2022-12-03 doi:10.1101/2022.12.01.518665 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ Generation of adult hippocampal neural stem cells occurs in the early postnatal dentate gyrus and depends on cyclin D2 ]]> https://biorxiv.org/content/10.1101/2022.12.05.518892v1?rss=1 Pastor-Alonso, O. Syeda Zahra, A. Kaske, B. Garcia-Moreno, F. Tetzlaff, F. Bockelmann, E. Grunwald, V. Martin-Suarez, S. Riecken, K. Witte, O. W. Encinas, J. M. Urbach, A. 2022-12-05 doi:10.1101/2022.12.05.518892 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ Structural basis for CaVα2δ:gabapentin binding ]]> https://biorxiv.org/content/10.1101/2022.12.05.519047v1?rss=1 Minor, D. L. Chen, Z. Mondal, A. 2022-12-05 doi:10.1101/2022.12.05.519047 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ Visualizing somatic alterations in spatial transcriptomics data of skin cancer ]]> https://biorxiv.org/content/10.1101/2022.12.05.519162v1?rss=1 Chen, L. Chang, D. Tandukar, B. Deivendran, D. Cho, R. Cheng, J. Bastian, B. C. Ji, A. L. Shain, A. H. 2022-12-07 doi:10.1101/2022.12.05.519162 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ RNA conformational propensities determine cellular activity ]]> https://biorxiv.org/content/10.1101/2022.12.05.519207v1?rss=1 Kelly, M. L. Roy, R. Geng, A. Ganser, L. R. Manghrani, A. Cullen, B. R. Schulze-Gahmen, U. Herschlag, D. Al-Hashimi, H. M. 2022-12-07 doi:10.1101/2022.12.05.519207 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Pleiotropy of autism-associated chromatin regulators ]]> https://biorxiv.org/content/10.1101/2022.12.07.519375v1?rss=1 Lasser, M. Sun, N. Xu, Y. Law, K. Gonzalez, S. Wang, B. Drury, V. Drake, S. Zaltsman, Y. Dea, J. Bader, E. McCluskey, K. E. State, M. W. Willsey, A. J. Willsey, H. R. 2022-12-07 doi:10.1101/2022.12.07.519375 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Mega-scale movie-fields in the mouse visuo-hippocampal network ]]> https://biorxiv.org/content/10.1101/2022.12.07.519455v1?rss=1 Purandare, C. Mehta, M. 2022-12-07 doi:10.1101/2022.12.07.519455 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Mild SARS-CoV-2 infection results in long-lasting microbiota instability ]]> https://biorxiv.org/content/10.1101/2022.12.07.519508v1?rss=1 Upadhyay, V. Suryawanshi, R. Tasoff, P. McCavitt-Malvido, M. Kumar, G. R. Murray, V. Noecker, C. Bisanz, J. E. Hswen, Y. Ha, C. Sreekumar, B. Chen, I. P. Lynch, S. V. Ott, M. Lee, S. Turnbaugh, P. J. 2022-12-08 doi:10.1101/2022.12.07.519508 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ Novel Peptide Inhibitor of Human Tumor Necrosis Factor-α has Antiarthritic Activity ]]> https://biorxiv.org/content/10.1101/2022.12.06.519274v1?rss=1 Sahu, D. Gupta, C. Yennamalli, R. Sharma, S. Roy, S. Hasan, S. Gupta, P. Sharma, V. K. Kashyap, S. Kumar, S. Dwivedi, V. P. Panda, A. K. Das, H. R. Liu, C.-J. 2022-12-10 doi:10.1101/2022.12.06.519274 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ Increased mRNA expression of CDKN2A is a transcriptomic marker of clinically aggressive meningiomas ]]> https://biorxiv.org/content/10.1101/2022.12.07.519545v1?rss=1 Wang, J. Z. Patil, V. Liu, J. Dogan, H. Behling, F. Skardelly, M. Tatagiba, M. Hoffman, E. Bunda, S. Yakubov, R. Kaloti, R. Brandner, S. Gao, A. Cohen-Gadol, A. Barnholtz-Sloan, J. Raleigh, D. Sahm, F. Boutros, P. C. Tabatabai, G. Aldape, K. Nassiri, F. Zadeh, G. International Consortium on Meningiomas (ICOM), 2022-12-10 doi:10.1101/2022.12.07.519545 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ Bulk and Mosaic Deletions of Egfr Reveal Regionally Defined Gliogenesis in the Developing Mouse Forebrain ]]> https://biorxiv.org/content/10.1101/2022.12.10.519926v1?rss=1 Zhang, X. Xiao, G. Johnson, C. A. Cai, Y. Horowitz, Z. Mennicke, C. Coffey, R. Haider, M. Threadgill, D. W. Eliscu, R. Oldham, M. C. Greenbaum, A. C. Ghashghaei, H. T. 2022-12-11 doi:10.1101/2022.12.10.519926 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ 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[ Neural circuit-wide analysis of gene expression during deafening-induced destabilization ofbirdsong ]]> https://biorxiv.org/content/10.1101/2022.12.13.520194v1?rss=1 Colquitt, B. M. Li, K. Green, F. Veline, R. J. Brainard, M. S. 2022-12-14 doi:10.1101/2022.12.13.520194 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation ]]> https://biorxiv.org/content/10.1101/2022.12.14.518457v1?rss=1 Ge, A. Y. Arab, A. Dai, R. Navickas, A. Fish, L. Garcia, K. Asgharian, H. Goodarzi, H. Gilbert, L. 2022-12-14 doi:10.1101/2022.12.14.518457 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ Effects of DNA extraction, DNA integrity, and laboratory on the precision of qPCR-based telomere length measurement - a multi-lab impartial study ]]> https://biorxiv.org/content/10.1101/2022.12.14.520438v1?rss=1 Lin, J. Verhulst, S. Fernandez Alonso, C. Dagnall, C. Gadalla, S. Hastings, W. Lai, T.-P. Zheng, Y.-L. Wang, Y. Shalev, I. Epel, E. Drury, S. 2022-12-14 doi:10.1101/2022.12.14.520438 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ Functional network organization of the mouse cortex determined by wide-field fluorescence imaging shares some --but not all-- properties revealed with simultaneous fMRI-BOLD ]]> https://biorxiv.org/content/10.1101/2022.12.13.520297v1?rss=1 Vafaii, H. Mandino, F. Desrosiers-Gregoire, G. O'Connor, D. Shen, X. Ge, X. Herman, P. Hyder, F. Papademetris, X. Chakravarty, M. Crair, M. Constable, R. T. Lake, E. M. Pessoa, L. 2022-12-15 doi:10.1101/2022.12.13.520297 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ The FMRF-NH2 Gated Sodium Channel of Biomphalaria glabrata: Localization and Expression Following Infection by Schistosoma mansoni ]]> https://biorxiv.org/content/10.1101/2022.12.15.520648v1?rss=1 Miller, M. W. Vicente, L. C. Behra, M. Torres, A. Mendez, P. Rosa-Casillas, M. Bracho, D. P. Rosenthal, J. J. 2022-12-15 doi:10.1101/2022.12.15.520648 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Direct neural perturbations reveal a dynamical mechanism for robust computation ]]> https://biorxiv.org/content/10.1101/2022.12.16.520768v1?rss=1 O'Shea, D. J. Duncker, L. Goo, W. Sun, X. Vyas, S. Trautmann, E. M. Diester, I. Ramakrishnan, C. Deisseroth, K. Sahani, M. Shenoy, K. V. 2022-12-16 doi:10.1101/2022.12.16.520768 Cold Spring Harbor Laboratory Press 2022-12-16 <![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[ Structural basis of odorant recognition by a human odorant receptor ]]> https://biorxiv.org/content/10.1101/2022.12.20.520951v1?rss=1 Billesboelle, C. B. de March, C. A. van der Velden, W. J. C. Ma, N. Tewari, J. Linas del Torrent, C. Li, L. Faust, B. Vaidehi, N. Matsunami, H. Manglik, A. 2022-12-20 doi:10.1101/2022.12.20.520951 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ O-GlcNAc glycosylation orchestrates fate decision and niche function of bone marrow stromal progenitors ]]> https://biorxiv.org/content/10.1101/2022.12.21.521379v1?rss=1 Zhang, Z. Huang, Z. Awad, M. Elsalanty, M. Cray, J. Ball, L. E. Maynard, J. Burlingame, A. L. Zeng, H. Mansky, K. C. Ruan, H.-B. 2022-12-21 doi:10.1101/2022.12.21.521379 Cold Spring Harbor Laboratory Press 2022-12-21 <![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[ A central helical fulcrum in eIF2B coordinates allosteric regulation of Integrated Stress Response signaling ]]> https://biorxiv.org/content/10.1101/2022.12.22.521453v1?rss=1 Lawrence, R. Shoemaker, S. Deal, A. Sangwan, S. Anand, A. Wang, L. Marqusee, S. Walter, P. 2022-12-22 doi:10.1101/2022.12.22.521453 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Structural Basis of Prostaglandin Efflux by MRP4 ]]> https://biorxiv.org/content/10.1101/2022.12.22.521501v1?rss=1 Pourmal, S. Green, E. Bajaj, R. Chemmama, I. Knudsen, G. Gupta, M. Sali, A. Cheng, Y. Craik, C. Kroetz, D. Stroud, R. 2022-12-22 doi:10.1101/2022.12.22.521501 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Optimized CRISPR guide RNA library cloning reduces skew and enables more compact genetic screens ]]> https://biorxiv.org/content/10.1101/2022.12.22.521524v1?rss=1 Heo, S.-J. Enriquez, L. D. Federman, S. Chang, A. Y. Mace, R. Sevade, K. Nguyen, P. Litterman, A. J. Shafer, S. Przybyla, L. Chow, E. D. 2022-12-23 doi:10.1101/2022.12.22.521524 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ Uncovering context-specific genetic-regulation of gene expression from single-cell RNA-sequencing using latent-factor models ]]> https://biorxiv.org/content/10.1101/2022.12.22.521678v1?rss=1 Strober, B. J. Tayeb, K. Popp, J. Qi, G. Gordon, M. G. Perez, R. Ye, C. J. Battle, A. 2022-12-23 doi:10.1101/2022.12.22.521678 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ Epigenetic reprogramming shapes the cellular landscape of schwannoma ]]> https://biorxiv.org/content/10.1101/2022.12.23.521842v1?rss=1 Liu, S. J. Casey-Clyde, T. Cho, N. W. Swinderman, J. Pekmezci, M. Dougherty, M. C. Foster, K. Chen, W. C. Villanueva-Meyer, J. E. Swaney, D. L. Vasudevan, H. N. Choudhury, A. Breshears, J. D. Lang, U. E. Eaton, C. D. Hiam-Galvez, K. J. Stevenson, E. Chen, K.-H. Lien, B. V. Wu, D. Braunstein, S. E. Sneed, P. K. Magill, S. T. Lim, D. A. McDermott, M. W. Berger, M. S. Perry, A. Krogan, N. J. Hansen, M. Spitzer, M. H. Gilbert, L. A. Theodosopoulos, P. V. Raleigh, D. R. 2022-12-24 doi:10.1101/2022.12.23.521842 Cold Spring Harbor Laboratory Press 2022-12-24 <![CDATA[ A 3D Clinical Face Phenotype Space of Genetic Syndromes using a Triplet-Based Singular Geometric Autoencoder ]]> https://biorxiv.org/content/10.1101/2022.12.27.521999v1?rss=1 Mahdi, S. S. Matthews, H. Vanneste, M. Nauwelaers, N. Gong, S. Bouritsas, G. Baynam, G. S. Hammond, P. Spritz, R. Klein, O. D. Hallgrimsson, B. D. Peeters, H. Claes, P. 2022-12-27 doi:10.1101/2022.12.27.521999 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Deficiency in Galectin-3, -8, and -9 impairs immunity to chronic Mycobacterium tuberculosis infection but not acute infection with multiple intracellular pathogens ]]> https://biorxiv.org/content/10.1101/2022.12.29.522180v1?rss=1 Morrison, H. M. Craft, J. Rivera-Lugo, R. Johnson, J. R. Golovkine, G. R. Dodd, C. E. Van Dis, E. Beatty, W. L. Margolis, S. R. Repasy, T. Shaker, I. Lee, A. Y. Vance, R. E. Stanley, S. A. Krogan, N. J. Portnoy, D. A. Penn, B. H. Cox, J. S. 2022-12-29 doi:10.1101/2022.12.29.522180 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Rac negative feedback links local PIP3 rate-of-change to dynamic control of neutrophil guidance ]]> https://biorxiv.org/content/10.1101/2022.12.30.521706v1?rss=1 Town, J. P. Weiner, O. P. 2022-12-31 doi:10.1101/2022.12.30.521706 Cold Spring Harbor Laboratory Press 2022-12-31 <![CDATA[ Highly multiplexed ddPCR-amplicon sequencing reveals strong Plasmodium falciparum population structure and isolated populations amenable to local elimination efforts in Zanzibar ]]> https://biorxiv.org/content/10.1101/2023.01.05.522832v1?rss=1 Holzschuh, A. Lerch, A. Gerlovina, I. Fakih, B. S. Al-Mafazy, A.-W. Reaves, E. J. Ali, A. Abbas, F. Ali, M. H. Ali, M. A. Hetzel, M. W. Yukich, J. O. Koepfli, C. 2023-01-06 doi:10.1101/2023.01.05.522832 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Phenotypic subtyping via contrastive learning ]]> https://biorxiv.org/content/10.1101/2023.01.05.522921v1?rss=1 Gorla, A. Sankararaman, S. Burchard, E. Flint, J. Zaitlen, N. Rahmani, E. 2023-01-06 doi:10.1101/2023.01.05.522921 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Graph Convolutional learning of Multimodal Brain Connectome Data for Schizophrenia Classification ]]> https://biorxiv.org/content/10.1101/2023.01.05.522960v1?rss=1 Ghosh, S. Bhargava, E. Lin, C.-T. Nagarajan, S. S. 2023-01-06 doi:10.1101/2023.01.05.522960 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Chromatin Remodeling Drives Immune-Fibroblast Crosstalk in Heart Failure Pathogenesis ]]> https://biorxiv.org/content/10.1101/2023.01.06.522937v1?rss=1 Alexanian, M. Padmanabhan, A. Nishino, T. Travers, J. G. Ye, L. Lee, C. Y. Sadagopan, N. Huang, Y. Pelonero, A. Auclair, K. Zhu, A. Gonzalez Teran, B. Flanigan, W. Kim, C. K.-S. Lumbao-Conradson, K. Costa, M. Jain, R. Charo, I. Haldar, S. M. Pollard, K. S. Vagnozzi, R. J. McKinsey, T. A. Przytycki, P. F. Srivastava, D. 2023-01-07 doi:10.1101/2023.01.06.522937 Cold Spring Harbor Laboratory Press 2023-01-07 <![CDATA[ M. tuberculosis antigen-responsive IL17+ CD4 T cells are disproportionately spared in ART-suppressed HIV ]]> https://biorxiv.org/content/10.1101/2023.01.06.523027v1?rss=1 Ogongo, P. Tran, A. Marzan, F. Gingrich, D. Krone, M. Aweeka, F. Lindestam Arlehamn, C. S. Martin, J. N. Deeks, S. Hunt, P. W. Ernst, J. D. 2023-01-07 doi:10.1101/2023.01.06.523027 Cold Spring Harbor Laboratory Press 2023-01-07 <![CDATA[ INKILN is a novel long noncoding RNA promoting vascular smooth muscle inflammation ]]> https://biorxiv.org/content/10.1101/2023.01.07.522948v1?rss=1 Zhang, W. Zhao, J. Deng, L. Ishimwe, N. Pauli, J. Wu, W. Shan, S. Kempf, W. Ballantyne, M. D. Kim, D. Lyu, Q. Bennett, M. Rodor, J. Turner, A. W. Lu, Y. W. Gao, P. Choi, M. Warthi, G. Kim, H. W. Barroso, M. M. Bryant, W. B. Miller, C. L. Weintraub, N. L. Maegdefessel, L. Miano, J. M. Baker, A. H. Long, X. 2023-01-08 doi:10.1101/2023.01.07.522948 Cold Spring Harbor Laboratory Press 2023-01-08 <![CDATA[ Oncogene-like addiction to aneuploidy in human cancers ]]> https://biorxiv.org/content/10.1101/2023.01.09.523344v1?rss=1 Girish, V. Lakhani, A. A. Scaduto, C. M. Thompson, S. L. Brown, L. M. Hagenson, R. A. Sausville, E. L. Mendelson, B. E. Lukow, D. A. Yuan, M. L. Kandikuppa, P. K. Stevens, E. C. Lee, S. N. Salovska, B. Li, W. Smith, J. C. Taylor, A. M. Martienssen, R. A. Liu, Y. Sun, R. Sheltzer, J. M. 2023-01-10 doi:10.1101/2023.01.09.523344 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Genome wide-analysis of anterior-posterior mRNA localization in Stentor coeruleus reveals a role for the microtubule cytoskeleton ]]> https://biorxiv.org/content/10.1101/2023.01.09.523364v1?rss=1 Albright, A. R. Angeles-Albores, D. Marshall, W. F. 2023-01-10 doi:10.1101/2023.01.09.523364 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Cryo-EM reveals how Hsp90 and FKBP immunophilins co-regulate the Glucocorticoid Receptor ]]> https://biorxiv.org/content/10.1101/2023.01.10.523504v1?rss=1 Noddings, C. M. Johnson, J. L. Agard, D. A. 2023-01-11 doi:10.1101/2023.01.10.523504 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ Differences in expression of tumor suppressor, innate immune, inflammasome, and potassium/gap junction channel host genes significantly predict viral reservoir size during treated HIV infection ]]> https://biorxiv.org/content/10.1101/2023.01.10.523535v1?rss=1 Dwivedi, A. K. Siegel, D. A. Thanh, C. Hoh, R. Hobbs, K. S. Pan, T. Gibson, E. A. Martin, J. Hecht, F. Pilcher, C. Milush, J. Busch, M. P. Stone, M. Huang, M.-L. Levy, C. N. Roychoudhury, P. Hladik, F. Jerome, K. R. Henrich, T. J. Deeks, S. G. Lee, S. A. 2023-01-11 doi:10.1101/2023.01.10.523535 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ Cooperative hydrodynamics accompany multicellular-like colonial organization in the unicellular ciliate Stentor ]]> https://biorxiv.org/content/10.1101/2023.01.10.523506v1?rss=1 Shekhar, S. Guo, H. Colin, S. P. Marshall, W. F. Kanso, E. A. Costello, J. H. 2023-01-12 doi:10.1101/2023.01.10.523506 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ Selection of optimal cell lines for high-content phenotypic screening ]]> https://biorxiv.org/content/10.1101/2023.01.11.523662v1?rss=1 Heinrich, L. Kumbier, K. Li, L. Altschuler, S. Wu, L. 2023-01-12 doi:10.1101/2023.01.11.523662 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ Structure-based discovery of inhibitors of the SARS-CoV-2 Nsp14 N7-methyltransferase ]]> https://biorxiv.org/content/10.1101/2023.01.12.523677v1?rss=1 Singh, I. Li, F. Fink, E. Chau, I. Li, A. Rodriguez-Hernandez, A. Glenn, I. Zapatero-Belinchon, F. J. Rodriguez, M. Devkota, K. Deng, Z. White, K. Wan, X. Tolmachova, N. A. Moroz, Y. S. Kaniskan, H. U. Ott, M. Gastia-Sastre, A. Jin, J. Fujimori, D. G. Irwin, J. J. Vedadi, M. Shoichet, B. K. 2023-01-13 doi:10.1101/2023.01.12.523677 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Genome-wide screens identify SEL1L as an intracellular rheostat controlling collagen turnover ]]> https://biorxiv.org/content/10.1101/2023.01.13.523943v1?rss=1 Podolsky, M. J. Kheyfets, B. Beigh, A. H. Yang, C. D. Lizama Valenzuela, C. Datta, R. Wolters, P. J. McManus, M. Qi, L. Atabai, K. 2023-01-14 doi:10.1101/2023.01.13.523943 Cold Spring Harbor Laboratory Press 2023-01-14 <![CDATA[ Assembly of gut-derived bacterial communities follows "early-bird" resource utilization dynamics ]]> https://biorxiv.org/content/10.1101/2023.01.13.523996v1?rss=1 Aranda-Diaz, A. Willis, L. Nguyen, T. H. Ho, P.-Y. Vila, J. Thomsen, T. Chavez, T. Yan, R. Yu, F. B. Neff, N. Sanchez, A. Estrela, S. Huang, K. 2023-01-14 doi:10.1101/2023.01.13.523996 Cold Spring Harbor Laboratory Press 2023-01-14 <![CDATA[ Next-generation interaction proteomics for quantitative Jumbophage-bacteria interaction mapping ]]> https://biorxiv.org/content/10.1101/2023.01.13.523954v1?rss=1 6000 unique host-pathogen and >200 pathogen-pathogen interactions for each phage, encompassing >50% of the phage proteome. Interactome-wide comparison across phages showed similar perturbed protein interactions suggesting fundamentally conserved mechanisms of phage predation within the KZ-like phage family. Prediction of novel ORFs revealed a{phi} PA3 complex showing strong structural and sequence similarity to{phi} KZ nvRNAp, suggesting{phi} PA3 also possesses two RNA polymerases acting at different stages of the infection cycle. We further expanded our understanding on the molecular organization of the virion packaged and injected proteome by identifying 23 novel virion components and 5 novel injected proteins, as well as providing the first evidence for interactions between KZ-like phage proteins and the host ribosome. To enable accessibility to this data, we developed PhageMAP, an online resource for network query, visualization, and interaction prediction (https://phagemap.ucsf.edu/). We anticipate this study will lay the foundation for the application of co-fractionation mass spectrometry for the scalable profiling of hostpathogen interactomes and protein complex dynamics upon infection. ]]> Fossati, A. Mozumdar, D. Kokontis, C. Y. Nieweglowska, E. S. Mendez, M. Pelin, A. Li, Y. Guo, B. Krogan, N. J. Agard, D. Bondy-Denomy, J. Swaney, D. L. 2023-01-15 doi:10.1101/2023.01.13.523954 Cold Spring Harbor Laboratory Press 2023-01-15 <![CDATA[ Functional microRNA-Targeting Drug Discovery by Graph-Based Deep Learning ]]> https://biorxiv.org/content/10.1101/2023.01.13.524005v1?rss=1 Keshavarzi Arshadi, A. Salem, M. Karner, H. Garcia, K. Arab, A. Yuan, J. S. Goodarzi, H. 2023-01-16 doi:10.1101/2023.01.13.524005 Cold Spring Harbor Laboratory Press 2023-01-16 <![CDATA[ Arp2/3 Complex Activity Enables Nuclear YAP for Naive Pluripotency of Human Embryonic Stem Cells ]]> https://biorxiv.org/content/10.1101/2023.01.16.524285v1?rss=1 Meyer, N. P. Singh, T. Kutys, M. L. Nystul, T. Barber, D. L. 2023-01-16 doi:10.1101/2023.01.16.524285 Cold Spring Harbor Laboratory Press 2023-01-16 <![CDATA[ The phospho-regulated amphiphysin/endophilin interaction is required for synaptic vesicle endocytosis ]]> https://biorxiv.org/content/10.1101/2023.01.15.524101v1?rss=1 Kontaxi, C. Cousin, M. A. 2023-01-18 doi:10.1101/2023.01.15.524101 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Normative modeling of brain morphometry in Clinical High-Risk for Psychosis ]]> https://biorxiv.org/content/10.1101/2023.01.17.523348v1?rss=1 1.96) scores. ResultsCHR-P and healthy individuals overlapped in the distributions of the observed values, regional z-scores, and all ADS vales. The proportion of CHR-P individuals with infranormal or supranormal values in any metric was low (<12%) and similar to that of healthy individuals. CHR-P individuals who converted to psychosis compared to those who did not convert had a higher percentage of infranormal values in temporal regions (5-7% vs 0.9-1.4%). In the CHR-P group, only the ADSSA showed significant but weak associations (|{beta}|<0.09; PFDR<0.05) with positive symptoms and IQ. Conclusions and RelevanceThe study findings challenge the usefulness of macroscale neuromorphometric measures as diagnostic biomarkers of psychosis risk and suggest that such measures do not provide an adequate explanation for psychosis risk. Key pointsO_ST_ABSQuestionC_ST_ABSIs the risk of psychosis associated with brain morphometric changes that deviate significantly from healthy variation? FindingsIn this study of 1340 individuals high-risk for psychosis (CHR-P) and 1237 healthy participants, individual-level variation in macroscale neuromorphometric measures of the CHR-P group was largely nested within healthy variation and was not associated with the severity of positive psychotic symptoms or conversion to a psychotic disorder. MeaningThe findings suggest the macroscale neuromorphometric measures have limited utility as diagnostic biomarkers of psychosis risk. ]]> Haas, S. S. Ge, R. Agartz, I. Amminger, G. P. Andreassen, O. A. Bachman, P. Baeza, I. Choi, S. Colibazzi, T. Cropley, V. L. de la Fuente-Sandoval, C. Ebdrup, B. H. Fortea, A. Fusar-Poli, P. Glenthoj, B. Y. Glenthoj, L. B. Haut, K. M. Hayes, R. A. Heekeren, K. Hooker, C. I. Hwang, W. J. Jahanshad, N. Kaess, M. Kasai, K. Katagiri, N. Kim, M. Kindler, J. Koike, S. Kristensen, T. D. Kwon, J. S. Lawrie, S. M. Lee, J. Lemmers-Jansen, I. L. Lin, A. Ma, X. Mathalon, D. H. McGuire, P. Michel, C. Mizrahi, R. Mizuno, M. Moller, P. Mora-Duran, R. Nelson, B. Nemot 2023-01-18 doi:10.1101/2023.01.17.523348 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Extensive and Persistent Extravascular Dermal Fibrin Deposition Characterizes Systemic Sclerosis ]]> https://biorxiv.org/content/10.1101/2023.01.16.523256v1?rss=1 Browning, J. L. Bhawan, J. Tseng, A. Crossland, N. Bujor, A. M. Akassoglou, K. Assassi, S. Skaug, B. Ho, J. 2023-01-19 doi:10.1101/2023.01.16.523256 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Molecular Logic of Synaptic Diversity Between Drosophila Tonic and Phasic Motoneurons ]]> https://biorxiv.org/content/10.1101/2023.01.17.524447v1?rss=1 Jetti, S. J. Crane, A. B. Akbergenova, Y. Aponte-Santiago, N. A. Cunningham, K. L. Whittaker, C. W. Littleton, J. T. 2023-01-19 doi:10.1101/2023.01.17.524447 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Human Bone Marrow Plasma Cell Atlas: Maturation and Survival Pathways Unraveled by Single Cell Analyses ]]> https://biorxiv.org/content/10.1101/2023.01.18.524601v1?rss=1 Duan, M. Nguyen, D. C. Joyner, C. J. Saney, C. Tipton, C. Andrews, J. Lonial, S. Kim, C. Hentenaar, I. Kosters, A. Ghosn, E. Jackson, A. Knechtle, S. Maruthamuthu, S. Chandran, S. Martin, T. Rajalingam, R. Vincenti, F. Breeden, C. Sanz, I. Gibson, G. Lee, F. E.-H. 2023-01-20 doi:10.1101/2023.01.18.524601 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Translational predictions of phase 2a first-in patient efficacy studies for antituberculosis drugs ]]> https://biorxiv.org/content/10.1101/2023.01.18.524608v1?rss=1 Savic, R. M. Goh, J. J. N. Ernest, J. P. Strydom, N. Wang, Q. van Wijk, R. C. Zhang, N. Deitchman, A. Nuermberger, E. 2023-01-20 doi:10.1101/2023.01.18.524608 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Frontotemporal Dementia Patient Neurons With Progranulin Deficiency Display Protein Dyshomeostasis ]]> https://biorxiv.org/content/10.1101/2023.01.18.524611v1?rss=1 Elia, L. P. Herting, B. Alijagic, A. Buselli, C. Wong, L. Morrison, G. Prado, M. A. Paolo, J. A. Gygi, S. Finley, D. Finkbeiner, S. 2023-01-20 doi:10.1101/2023.01.18.524611 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Development and characterization of new patient-derived xenograft (PDX) models of osteosarcoma with distinct metastatic capacities ]]> https://biorxiv.org/content/10.1101/2023.01.19.524562v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@17ea2a8org.highwire.dtl.DTLVardef@e8fcc7org.highwire.dtl.DTLVardef@2b9f8corg.highwire.dtl.DTLVardef@1f7b802_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Schott, C. R. Koehne, A. L. Sayles, L. C. Young, E. P. Luck, C. Yu, K. Lee, A. G. Breese, M. R. Leung, S. G. Shah, A. T. Xu, H. Liu, H.-Y. Spillinger, A. Behroozfard, I. H. Marini, K. D. Dinh, P. T. Pons Ventura, M. V. Vanderboon, E. N. Hazard, F. K. Cho, S.-J. Avedian, R. S. Mohler, D. G. Zimel, M. Wustrack, R. Curtis, C. Sirota, M. Sweet-Cordero, E. A. 2023-01-20 doi:10.1101/2023.01.19.524562 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during persistent infection ]]> https://biorxiv.org/content/10.1101/2023.01.19.524758v1?rss=1 Zheng, W. Chang, I.-C. Limberis, J. Budzik, J. M. Zha, B. S. Howard, Z. Ernst, J. D. 2023-01-20 doi:10.1101/2023.01.19.524758 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Dopamine D2 receptors in nucleus accumbens cholinergic interneurons increase impulsive choice ]]> https://biorxiv.org/content/10.1101/2023.01.20.524596v1?rss=1 Cavallaro, J. Yeisley, J. Akdogan, B. Floeder, J. R. Balsam, P. D. Gallo, E. F. 2023-01-20 doi:10.1101/2023.01.20.524596 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Lipopolysaccharide integrity primes bacterial sensitivity to a cell wall-degrading intermicrobial toxin ]]> https://biorxiv.org/content/10.1101/2023.01.20.524922v1?rss=1 Trotta, K. L. Hayes, B. Schneider, J. P. Wang, J. Todor, H. Grimes, P. R. Zhao, Z. Hatleberg, W. Silvis, M. Kim, R. Koo, B.-M. Basler, M. Chou, S. 2023-01-21 doi:10.1101/2023.01.20.524922 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ Single-cell and spatial multi-omics identify innate and stromal modules targeted by anti-integrin therapy in ulcerative colitis. ]]> https://biorxiv.org/content/10.1101/2023.01.21.525036v1?rss=1 Mennillo, E. Kim, Y. J. Rusu, I. Lee, G. Dorman, L. C. Bernard-Vazquez, F. Bain, J. L. Patel, R. Andersen, C. Rao, A. Tamaki, S. Tsui, J. Shen, A. Naser, M. Eckalbar, W. Cho, S.-j. Beck, K. El-Nachef, N. Lewin, S. Selvig, D. R. Terdiman, J. P. Mahadevan, U. Oh, D. Fragiadakis, G. K. Pisco, A. Combes, A. Kattah, M. G. 2023-01-22 doi:10.1101/2023.01.21.525036 Cold Spring Harbor Laboratory Press 2023-01-22 <![CDATA[ Supporting central nervous system neuroprotection and remyelination by specific TLR4 antagonism ]]> https://biorxiv.org/content/10.1101/2023.01.22.524916v1?rss=1 Fernandez-Gomez, B. Marchena, M. A. Pineiro, D. Lao, Y. Valencia, G. Nocera, S. Benitez-Fernandez, R. Gomez-Martin, P. Castano-Leon, A. M. Lagares, A. Hernandez-Jimenez, M. de Castro, F. 2023-01-22 doi:10.1101/2023.01.22.524916 Cold Spring Harbor Laboratory Press 2023-01-22 <![CDATA[ A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens ]]> https://biorxiv.org/content/10.1101/2023.01.22.525086v1?rss=1 Guna, A. Page, K. R. Replogle, J. R. Esantsi, T. K. Wang, M. L. Weissman, J. S. Voorhees, R. M. 2023-01-22 doi:10.1101/2023.01.22.525086 Cold Spring Harbor Laboratory Press 2023-01-22 <![CDATA[ Notch1 cortical signaling regulates epithelial architecture and cell-cell adhesion ]]> https://biorxiv.org/content/10.1101/2023.01.23.524428v1?rss=1 White, M. J. Jacobs, K. A. Singh, T. Kutys, M. L. 2023-01-23 doi:10.1101/2023.01.23.524428 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Insights into the mechanism of oligodendrocyte protection and remyelination enhancement by the integrated stress response ]]> https://biorxiv.org/content/10.1101/2023.01.23.525156v1?rss=1 Chen, Y. Quan, S. Patil, V. Kunjamma, R. B. Tokars, H. M. Leisten, E. D. Chan, J. R. Wong, Y. Popko, B. J. 2023-01-23 doi:10.1101/2023.01.23.525156 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Conformationally Adaptive Dyes Enable Protein-Adaptive Differential Scanning Fluorometry ]]> https://biorxiv.org/content/10.1101/2023.01.23.525251v1?rss=1 Wu, T. S. Yu, J. C. Suresh, A. Gale-Day, Z. J. Alteen, M. G. Woo, A. S. Millbern, Z. Johnson, O. T. Carroll, E. C. Partch, C. L. Fourches, D. Vilnueza, N. R. Vocadlo, D. J. Gestwicki, J. E. 2023-01-24 doi:10.1101/2023.01.23.525251 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ Cholecystokinin-A Signaling Regulates Automaticity of Pacemaker Cardiomyocytes and Shortens Sinus Node Recovery Time ]]> https://biorxiv.org/content/10.1101/2023.01.24.525392v1?rss=1 Ruan, H. Mandla, R. Ravi, N. Galang, G. Soe, A. W. Olgin, J. E. Lang, D. Vedantham, V. 2023-01-24 doi:10.1101/2023.01.24.525392 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ Structural variation across 138,134 samples in the TOPMed consortium ]]> https://biorxiv.org/content/10.1101/2023.01.25.525428v1?rss=1 90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hemotologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression. ]]> Jun, G. English, A. C. Metcalf, G. A. Yang, J. Chaisson, M. J. Pankratz, N. Menon, V. K. Salerno, W. J. Krasheninina, O. Smith, A. V. Lane, J. A. Blackwell, T. Kang, H. M. Salvi, S. Meng, Q. Shen, H. Pasham, D. Bhamidipati, S. Kottapalli, K. Arnett, D. K. Ashley-Koch, A. Auer, P. L. Beutel, K. M. Bis, J. C. Blangero, J. Bowden, D. W. Brody, J. A. Cade, B. E. Chen, Y.-D. I. Cho, M. H. Curran, J. E. Fornage, M. Freedman, B. I. Fingerlin, T. Gelb, B. D. Hou, L. Hung, Y.-J. Kane, J. P. Kaplan, R. Kim, W. Loos, R. J. F. Marcus,, G. M. Mathias, R. A. McGarv 2023-01-26 doi:10.1101/2023.01.25.525428 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ Patterns of within-host spread of Chlamydia trachomatis between vagina, endocervix and rectum revealed by comparative genomic analysis ]]> https://biorxiv.org/content/10.1101/2023.01.25.525576v1?rss=1 Joseph, S. J. Bommona, S. Ziklo, N. Kama, M. Dean, D. Read, T. D. 2023-01-26 doi:10.1101/2023.01.25.525576 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ Mass cytometry identifies dysregulation of circulating and cutaneous immune cells in patients with hidradenitis suppurativa ]]> https://biorxiv.org/content/10.1101/2023.01.27.525867v1?rss=1 Dimitrion, P. Hamzavi, I. Yin, C. Loveless, I. Toor, J. Subedi, K. Khalasawi, N. Miller, A. Huggins, R. Adrianto, I. Veenstra, J. Vellaichamy, G. Hans, A. Daveluy, S. Athar, M. Liao, W. Lim, H. Ozog, D. Zhou, L. Mi, Q.-S. 2023-01-28 doi:10.1101/2023.01.27.525867 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ Structure and dynamics of the essential endogenous mycobacterial polyketide synthasePks13 ]]> https://biorxiv.org/content/10.1101/2023.01.27.525930v1?rss=1 Kim, S. K. Dickinson, M. S. Finer-Moore, J. S. Guan, Z. Kaake, R. M. Echeverria, I. Chen, J. Pulido, E. H. Sali, A. Krogan, N. J. Rosenberg, O. S. Stroud, R. M. 2023-01-28 doi:10.1101/2023.01.27.525930 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ A Systematic Approach to the Discovery of Protein-Protein Inter-action Stabilizers ]]> https://biorxiv.org/content/10.1101/2023.01.29.526112v1?rss=1 Kenanova, D. N. Visser, E. J. Virta, J. M. Sijbesma, E. Centorrino, F. Vickery, H. R. Zhong, M. Neitz, J. R. Brunsveld, L. Ottmann, C. Arkin, M. R. 2023-01-30 doi:10.1101/2023.01.29.526112 Cold Spring Harbor Laboratory Press 2023-01-30 <![CDATA[ Mass Spectrometry Imaging of Hair Identifies Daily Maraviroc Adherence in HPTN 069/ACTG A5305 ]]> https://biorxiv.org/content/10.1101/2023.01.30.526384v1?rss=1 Rosen, E. P. White, N. R. Gilliland, W. M. Gerona, R. Gandhi, M. Amico, K. R. Mayer, K. H. Gulick, R. M. Kashuba, A. D. M. 2023-02-02 doi:10.1101/2023.01.30.526384 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ A thin-film optogenetic visual prosthesis ]]> https://biorxiv.org/content/10.1101/2023.01.31.526482v1?rss=1 Knudsen, E. B. Zappitelli, K. Brown, J. Reeder, J. Smith, K. S. Rostov, M. Choi, J. Rochford, A. Slager, N. Miura, S. K. Rodgers, K. Reed, A. Lewis Israeli, Y. R. Shiraga, S. Seo, K. J. Wolin, C. Dawson, P. Eltaeb, M. Dasgupta, A. Chong, P. Charles, S. Stewart, J. M. Silva, R. A. Kim, T. Kong, Y. Mardinly, A. R. Hodak, M. 2023-02-03 doi:10.1101/2023.01.31.526482 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ EMBER multi-dimensional spectral microscopy enables quantitative determination of disease- and cell-specific amyloid strains ]]> https://biorxiv.org/content/10.1101/2023.02.01.526692v1?rss=1 Yang, H. Yuan, P. Wu, y. Shi, M. caro, C. tengeiji, a. yamanoi, s. Inoue, M. DeGrado, W. Condello, C. 2023-02-03 doi:10.1101/2023.02.01.526692 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Optimizing anesthesia and delivery approaches for dosing into lungs of mice ]]> https://biorxiv.org/content/10.1101/2023.02.01.526706v1?rss=1 View larger version (51K): org.highwire.dtl.DTLVardef@10e90forg.highwire.dtl.DTLVardef@34f8a5org.highwire.dtl.DTLVardef@1b02406org.highwire.dtl.DTLVardef@10d3f33_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Seo, Y. Qiu, L. Magnen, M. Conrad, C. Moussavi-Harami, S. F. Looney, M. R. Cleary, S. J. 2023-02-03 doi:10.1101/2023.02.01.526706 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Clinically relevant concurrent BRAF and MEK inhibition alters differentiation states and sensitizes BRAF V600E-mutated high-grade gliomas to immune checkpoint blockade ]]> https://biorxiv.org/content/10.1101/2023.02.03.526065v1?rss=1 Park, J. Grossauer, S. Wang, W. Xing, Y. L. Koeck, K. Garcia, C. A. Nasajpour, E. Wilson, C. Lancero, H. Harter, P. N. Filipski, K. Daynac, M. Meyer, L. Guinle, M. I. B. Monje, M. Vogel, H. Lim, M. Prolo, L. M. Grant, G. A. Petritsch, C. K. 2023-02-04 doi:10.1101/2023.02.03.526065 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ The Clustered Gamma Protocadherin Pcdhγc4 Isoform Regulates Cortical Interneuron Programmed Cell Death in the Mouse Cortex. ]]> https://biorxiv.org/content/10.1101/2023.02.03.526887v1?rss=1 Mancia Leon, W. R. Steffen, D. M. Dale-Huang, F. Rakela, B. Breevoort, A. Romero-Rodriguez, R. Hasenstaub, A. R. Stryker, M. P. Weiner, J. A. Alvarez-Buylla, A. 2023-02-04 doi:10.1101/2023.02.03.526887 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Neanderthal Introgression Shaped Human Circadian Traits ]]> https://biorxiv.org/content/10.1101/2023.02.03.527061v1?rss=1 Velazquez-Arcelay, K. Colbran, L. L. McArthur, E. Brand, C. M. Siemann, J. K. McMahon, D. G. Capra, J. A. 2023-02-04 doi:10.1101/2023.02.03.527061 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Lung microenvironments harbor Mycobacterium tuberculosis phenotypes with distinct treatment responses ]]> https://biorxiv.org/content/10.1101/2023.02.03.527062v1?rss=1 Walter, N. D. Ernest, J. P. Dide-Agossou, C. Bauman, A. A. Ramey, M. E. Rossmassler, K. Massoudi, L. M. Pauly, S. Al Mubarak, R. Voskuil, M. I. Kaya, F. Sarathy, J. P. Zimmerman, M. D. Dartois, V. Podell, B. K. Savic, R. M. Robertson, G. T. 2023-02-04 doi:10.1101/2023.02.03.527062 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Long lifetime and selective accumulation of the A-type lamins accounts for the tissue specificity of Hutchinson-Gilford progeria syndrome ]]> https://biorxiv.org/content/10.1101/2023.02.04.527139v1?rss=1 Hasper, J. Welle, K. Swovick, K. Hryhorenko, J. Ghaemmaghami, S. Buchwalter, A. 2023-02-04 doi:10.1101/2023.02.04.527139 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Paclitaxel- and vincristine-induced neurotoxicity and drug transport in sensory neurons ]]> https://biorxiv.org/content/10.1101/2023.02.07.527432v1?rss=1 Mortensen, C. Chua, K. C. Hammer, H. S. Nielsen, F. Poetz, O. Svenningsen, A. F. Kroetz, D. L. Stage, T. B. 2023-02-07 doi:10.1101/2023.02.07.527432 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ IVT generation of guideRNAs for Cas9-enrichment Nanopore Sequencing ]]> https://biorxiv.org/content/10.1101/2023.02.07.527484v1?rss=1 Gilpatrick, T. Wang, J. Z. Weiss, D. Norris, A. L. Eshleman, J. R. Timp, W. 2023-02-07 doi:10.1101/2023.02.07.527484 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6 ]]> https://biorxiv.org/content/10.1101/2023.01.31.525914v1?rss=1 80% efficiency. Fully sequenced replicons and infectious viral stocks can be generated in 1 and 3 weeks, respectively. By testing a series of naturally occurring viruses as well as Delta-Omicron chimeric replicons, we show that Omicron nonstructural protein 6 harbors critical attenuating mutations, which dampen viral RNA replication and reduce lipid droplet consumption. Thus, pGLUE overcomes remaining barriers to broadly study SARS-CoV-2 replication and reveals deficits in nonstructural protein function underlying Omicron attenuation. ]]> Taha, T. Y. Chen, I. P. Hayashi, J. M. Tabata, T. Walcott, K. Kimmerly, G. R. Syed, A. M. Ciling, A. Suryawanshi, R. K. Martin, H. S. Bach, B. H. Tsou, C.-L. Montano, M. Khalid, M. M. Sreekumar, B. K. Kumar, G. R. Wyman, S. Doudna, J. A. Ott, M. 2023-02-09 doi:10.1101/2023.01.31.525914 Cold Spring Harbor Laboratory Press 2023-02-09 <![CDATA[ Pharmacodynamic model of PARP1 inhibition and global sensitivity analyses can lead to cancer biomarker discovery ]]> https://biorxiv.org/content/10.1101/2023.02.08.527527v1?rss=1 Mertins, S. D. Isenberg, N. M. Reyes, K.-R. Yoon, B.-J. Urban, N. Jogalekar, M. P. Diolaiti, M. E. Weil, M. R. Stahlberg, E. A. 2023-02-10 doi:10.1101/2023.02.08.527527 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2023.02.09.527892v1?rss=1 Yin, K. Peluso, M. J. Thomas, R. Shin, M.-G. Neidleman, J. Luo, X. Hoh, R. Anglin, K. Huang, B. Argueta, U. Lopez, M. Valdivieso, D. Asare, K. Ibrahim, R. Standker, L. Lu, S. Goldberg, S. A. Lee, S. A. Lynch, K. L. Kelly, J. D. Martin, J. N. Muench, J. Deeks, S. G. Henrich, T. J. Roan, N. R. 2023-02-10 doi:10.1101/2023.02.09.527892 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Unified bursting strategies in ectopic and endogenous even-skipped expression patterns ]]> https://biorxiv.org/content/10.1101/2023.02.09.527927v1?rss=1 Berrocal, A. Lammers, N. C. Garcia, H. G. Eisen, M. B. 2023-02-10 doi:10.1101/2023.02.09.527927 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Integrative single-cell characterization of frugivory adaptations in the bat kidney and pancreas ]]> https://biorxiv.org/content/10.1101/2023.02.12.528204v1?rss=1 Gordon, W. E. Baek, S. Nguyen, H. P. Kuo, Y.-M. Bradley, R. Galazyuk, A. Lee, I. Ingala, M. Simmons, N. B. Schountz, T. Cooper, L. Georgakopoulos-Soares, I. Hemberg, M. Ahituv, N. 2023-02-13 doi:10.1101/2023.02.12.528204 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ Designed Transmembrane Proteins Inhibit the Erythropoietin Receptor in a Custom Binding Topology ]]> https://biorxiv.org/content/10.1101/2023.02.13.526773v1?rss=1 Mravic, M. He, L. Kratochvil, H. Hu, H. Nick, S. E. Bai, W. Edwards, A. Jo, H. Wu, Y. DiMaio, D. DeGrado, W. F. 2023-02-15 doi:10.1101/2023.02.13.526773 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Transmembrane protein CD69 acts as an S1PR1 agonist ]]> https://biorxiv.org/content/10.1101/2023.02.13.528406v1?rss=1 Chen, H. Qin, Y. Chou, M. Cyster, J. G. Li, X. 2023-02-15 doi:10.1101/2023.02.13.528406 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Insulin-mTOR hyperfunction drives C. elegans aging opposed by the megaprotein LPD-3 ]]> https://biorxiv.org/content/10.1101/2023.02.14.528431v1?rss=1 Pandey, T. Wang, B. Zu, J. Deng, H. Shen, K. Vale, G. McDonald, J. G. Ma, D. K. 2023-02-15 doi:10.1101/2023.02.14.528431 Cold Spring Harbor Laboratory Press 2023-02-15 <![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[ Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex ]]> https://biorxiv.org/content/10.1101/2023.02.15.528663v1?rss=1 Deng, C. Whalen, S. Steyert, M. Ziffra, R. Przytycki, P. F. Inoue, F. Pereira, D. A. Capauto, D. Norton, S. Vaccarino, F. M. Pollen, A. A. Nowakowski, T. J. Ahituv, N. A. Pollard, K. S. 2023-02-15 doi:10.1101/2023.02.15.528663 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Generative Molecular Design and Experimental Validation of Selective Histamine H1 Inhibitors ]]> https://biorxiv.org/content/10.1101/2023.02.14.528391v1?rss=1 McLoughlin, K. S. Shi, D. Mast, J. E. Bucci, J. Williams, J. P. Jones, W. D. Miyao, D. Nam, L. Osswald, H. L. Zegelman, L. Allen, J. E. Bennion, B. J. Paulson, A. K. Abagyan, R. Head, M. S. Brase, J. M. 2023-02-16 doi:10.1101/2023.02.14.528391 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Prdm16 and Vcam1 regulate the postnatal disappearance of embryonic radial glia and the ending of cortical neurogenesis ]]> https://biorxiv.org/content/10.1101/2023.02.14.528567v1?rss=1 Li, J. Godoy, M. I. Zhang, A. J. Diamante, G. Ahn, I. S. Cebrian-Silla, A. Alvarez-Buylla, A. Yang, X. Novitch, B. Zhang, Y. 2023-02-16 doi:10.1101/2023.02.14.528567 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Dual credit assignment processes underliedopamine signals in a complex spatialenvironment. ]]> https://biorxiv.org/content/10.1101/2023.02.15.528738v1?rss=1 Krausz, T. A. Comrie, A. E. Frank, L. M. Daw, N. D. Berke, J. D. 2023-02-16 doi:10.1101/2023.02.15.528738 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Molecular basis for potent B cell responses to antigen displayed on particles of viral size ]]> https://biorxiv.org/content/10.1101/2023.02.15.528761v1?rss=1 Brooks, J. F. Riggs, J. Mueller, J. L. Mathenge, R. Wholey, W.-Y. Yoda, S.-T. Vykunta, V. Cheng, W. Zikherman, J. 2023-02-16 doi:10.1101/2023.02.15.528761 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Redox Regulation of m6A Methyltransferase METTL3 in Human β-cells Controls the Innate Immune Response in Type 1 Diabetes ]]> https://biorxiv.org/content/10.1101/2023.02.16.528701v1?rss=1 De Jesus, D. F. Zhang, Z. Brown, N. K. Li, X. Gaffrey, M. J. Kahraman, S. Wei, J. Hu, J. Basile, G. Xiao, L. Rana, T. M. Mathews, C. E. Powers, A. C. Atkinson, M. A. Eizirik, D. L. Dhe-Paganon, S. Parent, A. V. Qian, W.-J. He, C. Kulkarni, R. N. 2023-02-16 doi:10.1101/2023.02.16.528701 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Prospectively predicting BPaMZ Phase IIb outcomes using a translational preclinical mouse to human platform ]]> https://biorxiv.org/content/10.1101/2023.02.16.528876v1?rss=1 Wang, Q. Goh, J. J. N. Zhang, N. Nuermberger, E. Savic, R. M. 2023-02-16 doi:10.1101/2023.02.16.528876 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Broad sensitivity of Candida auris strains to quinolones and mechanisms of resistance ]]> https://biorxiv.org/content/10.1101/2023.02.16.528905v1?rss=1 Lohse, M. B. Laurie, M. T. Levan, S. Ziv, N. Ennis, C. L. Nobile, C. J. DeRisi, J. L. Johnson, A. D. 2023-02-17 doi:10.1101/2023.02.16.528905 Cold Spring Harbor Laboratory Press 2023-02-17 <![CDATA[ DeepHeme: A generalizable, bone marrow classifierwith hematopathologist-level performance ]]> https://biorxiv.org/content/10.1101/2023.02.20.528987v1?rss=1 Goldgof, G. Sun, S. Cleaves, J. Wang, L. Lucas, F. Brown, L. Spectors, J. Boiocchi, L. Baik, J. Zhu, M. Ardon, O. Lu, C. Dogan, A. Goldgof, D. Carmichael, I. Prakash, S. Butte, A. 2023-02-21 doi:10.1101/2023.02.20.528987 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Tracing cancer evolution and heterogeneity using Hi-C ]]> https://biorxiv.org/content/10.1101/2023.02.20.529175v1?rss=1 Erdmann-Pham, D. D. Batra, S. S. Turkalo, T. K. Durbin, J. Blanchette, M. Yeh, I. Shain, H. Bastian, B. Song, Y. S. Rokhsar, D. S. Hockemeyer, D. 2023-02-21 doi:10.1101/2023.02.20.529175 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ TET1 Catalytic Activity is Required for Reprogramming of Imprinting Control Regions and Patterning of Sperm-Specific Hypomethylated Regions ]]> https://biorxiv.org/content/10.1101/2023.02.21.529426v1?rss=1 Prasasya, R. D. Caldwell, B. A. Liu, Z. Wu, S. Leu, N. A. D. Fowler, J. M. Cincotta, S. A. Laird, D. J. Kohli, R. M. Bartolomei, M. 2023-02-21 doi:10.1101/2023.02.21.529426 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ MAP9/MAPH-9 supports axonemal microtubule doublets and modulates motor movement ]]> https://biorxiv.org/content/10.1101/2023.02.23.529616v1?rss=1 Tran, M. V. Ferguson, J. W. Cote, L. E. Khuntsariya, D. Fetter, R. D. Wang, J. T. Wellard, S. R. Sallee, M. D. Eskinazi, S. Genova, M. Magiera, M. M. Janke, C. Stearns, T. Lansky, Z. Shen, K. Magescas, J. Feldman, J. L. 2023-02-23 doi:10.1101/2023.02.23.529616 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Candida albicans stimulates the formation of a multi-receptor complex that mediates epithelial cell invasion during oropharyngeal infection ]]> https://biorxiv.org/content/10.1101/2023.02.23.529756v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@1448372org.highwire.dtl.DTLVardef@111b411org.highwire.dtl.DTLVardef@144f3b8org.highwire.dtl.DTLVardef@1dcf548_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIc-Met is an oral epithelial cell receptor for Candida albicans C_LIO_LIC. albicans infection causes c-Met and the epidermal growth factor receptor (EGFR) to form a complex with E-cadherin, which is required for c-Met and EGFR function C_LIO_LIC. albicans Hyr1 and Als3 interact with c-Met and EGFR, inducing oral epithelial cell endocytosis and virulence during oropharyngeal candidiasis C_LIO_LIDual blockade of c-Met and EGFR ameliorates oropharyngeal candidiasis C_LI ]]> Phan, Q. T. Solis, N. V. Cravener, M. V. Swidergall, M. Lin, J. Huang, M. Y. Liu, H. Singh, S. Ibrahim, A. S. Mazzone, M. Mitchell, A. P. Filler, S. G. 2023-02-23 doi:10.1101/2023.02.23.529756 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Multi-omic screening of invasive GBM cells in engineered biomaterials and patient biopsies reveals targetable transsulfuration pathway alterations ]]> https://biorxiv.org/content/10.1101/2023.02.23.529575v1?rss=1 Garcia, J. H. Akins, E. A. Jain, S. Wolf, K. J. Zhang, J. Choudhary, N. Lad, M. Shukla, P. Gill, S. Carson, W. Carette, L. Zheng, A. Kumar, S. Aghi, M. K. 2023-02-24 doi:10.1101/2023.02.23.529575 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Vagus nerve stimulation using an endovascular electrode array ]]> https://biorxiv.org/content/10.1101/2023.02.23.529747v1?rss=1 Nicolai, E. N. Arturo Larco, J. Madhani, S. I. Asirvatham, S. J. Chang, S.-y. Ludwig, K. A. Savastano, L. E. Worrell, G. A. 2023-02-24 doi:10.1101/2023.02.23.529747 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Fate of telomere entanglements is dictated by the timing of anaphase midregion nuclear envelope breakdown ]]> https://biorxiv.org/content/10.1101/2023.02.24.529917v1?rss=1 Nageshan, R. K. Ortega, R. Krogan, N. Cooper, J. P. 2023-02-25 doi:10.1101/2023.02.24.529917 Cold Spring Harbor Laboratory Press 2023-02-25 <![CDATA[ Dynamic functional connectivity MEG features of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2023.02.23.529813v1?rss=1 Jin, H. Ranasinghe, K. Prahu, P. Dale, C. Gao, Y. Kudo, K. Vossel, K. Raj, A. Nagarajan, S. Jiang, F. 2023-02-26 doi:10.1101/2023.02.23.529813 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ Idioblasts accumulating anticancer alkaloids in Catharanthus roseus leaves are a unique cell type ]]> https://biorxiv.org/content/10.1101/2023.02.24.529939v1?rss=1 Guedes, J. G. Ribeiro, R. Carqueijeiro, I. Guimaraes, A. L. Bispo, C. Archer, J. Azevedo, H. Fonseca, N. A. Sottomayor, M. 2023-02-27 doi:10.1101/2023.02.24.529939 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Acetylcholine engages distinct amygdala microcircuits to gate internal theta rhythm ]]> https://biorxiv.org/content/10.1101/2023.02.26.530135v1?rss=1 Bratsch-Prince, J. X. Warren, J. W. Jones, G. C. McDonald, A. J. Mott, D. D. 2023-02-27 doi:10.1101/2023.02.26.530135 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Uncovering the essential roles of human GCP 2 orthologs in Caenorhabditis elegans. ]]> https://biorxiv.org/content/10.1101/2023.02.27.529682v1?rss=1 Panska, L. Nedvedova, S. Vacek, V. Krivska, D. Konecny, L. Knop, F. Kutil, Z. Skultetyova, L. Leontovyc, A. Ulrychova, L. Sakanari, J. Asahina, M. Barinka, C. Macurkova, M. Dvorak, J. 2023-02-27 doi:10.1101/2023.02.27.529682 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Systematic Identification of Post-Transcriptional Regulatory Modules ]]> https://biorxiv.org/content/10.1101/2023.02.27.530345v1?rss=1 Khoroshkin, M. S. Buyan, A. Dodel, M. Navickas, A. Yu, J. Trejo, F. Doty, A. Baratam, R. Zhou, S. Joshi, T. Miglani, S. Choi, B. Subramanyam, V. Modi, H. Corces, R. Markett, D. Kulakovskiy, I. V. Mardakheh, F. K. Goodarzi, H. 2023-03-01 doi:10.1101/2023.02.27.530345 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Far From Home: Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments ]]> https://biorxiv.org/content/10.1101/2023.02.28.530341v1?rss=1 Chen, V. K. Johnson, M. S. Herissant, L. Humphrey, P. T. Yuan, D. C. Li, Y. Agarwala, A. Hoelscher, S. B. Petrov, D. Desai, M. M. Sherlock, G. J. 2023-03-01 doi:10.1101/2023.02.28.530341 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Inhibitory control of speech production in the human premotor frontal cortex ]]> https://biorxiv.org/content/10.1101/2023.03.01.530698v1?rss=1 Zhao, L. Silva, A. B. Kurteff, G. L. Chang, E. F. 2023-03-01 doi:10.1101/2023.03.01.530698 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Bayesian Inference of a Spectral Graph Model for Brain Oscillations ]]> https://biorxiv.org/content/10.1101/2023.03.01.530704v1?rss=1 Jin, H. Verma, P. Jiang, F. Nagarajan, S. Raj, A. 2023-03-02 doi:10.1101/2023.03.01.530704 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Structure-based discovery of cannabinoid-1 receptor agonists with reduced side effects ]]> https://biorxiv.org/content/10.1101/2023.02.27.530254v1?rss=1 Tummino, T. A. Iliopoulos-Tsoutsouvas, C. Braz, J. M. O'Brien, E. S. Stein, R. M. Craik, V. Tran, N. K. Ganapathy, S. Shiimura, Y. Tong, F. Ho, T. C. Radchenko, D. S. Moroz, Y. S. Liu, F. Rosado, S. R. Bhardwaj, K. Benitez, J. Liu, Y. Kandasamy, H. Normand, C. Semache, M. Sabbagh, L. Glenn, I. Irwin, J. J. Kumar, K. K. Makriyannis, A. Basbaum, A. I. Shoichet, B. K. 2023-03-03 doi:10.1101/2023.02.27.530254 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Multivariate prediction of cognitive performance from the sleep electroencephalogram ]]> https://biorxiv.org/content/10.1101/2023.02.28.530401v1?rss=1 Ujma, P. P. Bodizs, R. Dresler, M. Simor, P. Purcell, S. Stone, K. Yaffe, K. Redline, S. 2023-03-03 doi:10.1101/2023.02.28.530401 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Zfp106 binds to G-quadruplex RNAs and inhibits RAN translation and formation of RNA foci caused by G4C2 repeats ]]> https://biorxiv.org/content/10.1101/2023.03.05.531055v1?rss=1 Celona, B. Wu, H. Dang, B. Kratochvil, H. T. DeGrado, W. F. Black, B. L. 2023-03-05 doi:10.1101/2023.03.05.531055 Cold Spring Harbor Laboratory Press 2023-03-05 <![CDATA[ PI3K block restores age-dependent neurovascular coupling defects associated with cerebral small vessel disease ]]> https://biorxiv.org/content/10.1101/2023.03.03.531032v1?rss=1 Thakore, P. Yamasaki, E. Ali, S. Sanchez Solano, A. Labelle-Dumais, C. Gao, X. Chaumeil, M. M. Gould, D. B. Earley, S. 2023-03-06 doi:10.1101/2023.03.03.531032 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types ]]> https://biorxiv.org/content/10.1101/2023.03.05.531189v1?rss=1 Agarwal, V. Inoue, F. Schubach, M. Martin, B. Dash, P. Zhang, Z. Sohota, A. Noble, W. Yardimci, G. Kircher, M. Shendure, J. Ahituv, N. 2023-03-06 doi:10.1101/2023.03.05.531189 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ KSHV uses viral IL6 to expand infected immunosuppressive macrophages ]]> https://biorxiv.org/content/10.1101/2023.03.05.531224v1?rss=1 Shimoda, M. Inagaki, T. Davis, R. R. Merleev, A. Tepper, C. Maverakis, E. M. Izumiya, Y. 2023-03-06 doi:10.1101/2023.03.05.531224 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Transcriptional adaptation of drug-tolerant Mycobacterium tuberculosis in mice ]]> https://biorxiv.org/content/10.1101/2023.03.06.531356v1?rss=1 Wynn, E. A. Dide-Agossou, C. Reichlen, M. Rossmassler, K. Al Mubarak, R. Reid, J. J. Tabor, S. T. Born, S. E. Ransom, M. R. Davidson, R. M. Walton, K. N. Benoit, J. B. Bauman, A. A. Massoudi, L. M. Dolganov, G. Nahid, P. Voskuil, M. I. Robertson, G. T. Moore, C. M. Walter, N. D. 2023-03-06 doi:10.1101/2023.03.06.531356 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Generation of Schwann cell derived melanocytes from hPSCs identifies pro-metastatic factors in melanoma ]]> https://biorxiv.org/content/10.1101/2023.03.06.531220v1?rss=1 Samuel, R. M. Navickas, A. Maynard, A. Gaylord, E. A. Garcia, K. Bhat, S. Majd, H. Richter, M. N. Elder, N. Le, D. Nguyen, P. Shibata, B. Losa Llabata, M. Selleri, L. Laird, D. J. Darmanis, S. Goodarzi, H. Fattahi, F. 2023-03-07 doi:10.1101/2023.03.06.531220 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ DNAJB8 oligomerization is mediated by an aromatic-rich motif that is dispensable for substrate activity ]]> https://biorxiv.org/content/10.1101/2023.03.06.531355v1?rss=1 Ryder, B. D. Boyer, D. R. Ustyantseva, E. Mendoza-Oliva, A. Kuska, M. Wydorski, P. M. Sawaya, M. Diamond, M. I. Eisenberg, D. Kampinga, H. H. Joachimiak, L. A. 2023-03-07 doi:10.1101/2023.03.06.531355 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Evolutionary constraint and innovation across hundreds of placental mammals ]]> https://biorxiv.org/content/10.1101/2023.03.09.531574v1?rss=1 Christmas, M. J. Kaplow, I. M. Genereux, D. P. Dong, M. X. Hughes, G. M. Li, X. Sullivan, P. F. Hindle, A. G. Andrews, G. Armstrong, J. C. Bianchi, M. Breit, A. M. Diekhans, M. Fanter, C. Foley, N. M. Goodman, D. B. Goodman, L. Keough, K. C. Kirilenko, B. Kowalczyk, A. Lawless, C. Lind, A. L. Meadows, J. R. S. Moreira, L. R. Redlich, R. W. Ryan, L. Swofford, R. Valenzuela, A. Wagner, F. Wallerman, O. Brown, A. R. Damas, J. Fan, K. Gatesy, J. Grimshaw, J. Johnson, J. Kozyrev, S. V. Lawler, A. J. Marinescu, V. D. Morrill, K. M. Osmanski, A. Paulat, N. S. 2023-03-09 doi:10.1101/2023.03.09.531574 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Aberrant phase separation is a common killing strategy of positively charged peptides in biology and human disease ]]> https://biorxiv.org/content/10.1101/2023.03.09.531820v1?rss=1 Boeynaems, S. Ma, X. R. Yeong, V. Ginell, G. M. Chen, J.-H. Blum, J. A. Nakayama, L. Sanyal, A. Briner, A. Van Haver, D. Pauwels, J. Ekman, A. Schmidt, H. B. Sundararajan, K. Porta, L. Lasker, K. Larabell, C. Hayashi, M. A. F. Kundaje, A. Impens, F. Obermeyer, A. Holehouse, A. S. Gitler, A. D. 2023-03-09 doi:10.1101/2023.03.09.531820 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Torch-eCpG: A fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units ]]> https://biorxiv.org/content/10.1101/2023.03.07.531597v1?rss=1 Kober, K. M. Berger, L. G. Roy, R. Olshen, A. 2023-03-10 doi:10.1101/2023.03.07.531597 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Inhibition of muscarinic receptor signaling protects human enteric inhibitory neurons against platin chemotherapy toxicity ]]> https://biorxiv.org/content/10.1101/2023.03.08.531806v1?rss=1 Richter, M. N. Farahvashi, S. Samuel, R. M. Majd, H. Chemel, A. K. Ramirez, J. T. Majd, A. Scantlen, M. D. Elder, N. Cesiulis, A. Garcia, K. Joshi, T. Keefe, M. G. Samiakalantari, B. Turkalj, E. M. Yu, J. Arab, A. Yin, K. Culbertson, B. Vora, B. Xiong, C. Kattah, M. G. Irannejad, R. Kroetz, D. L. Nowakowski, T. J. Goodarzi, H. Fattahi, F. 2023-03-10 doi:10.1101/2023.03.08.531806 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Title: Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease ]]> https://biorxiv.org/content/10.1101/2023.03.10.531987v1?rss=1 Sullivan, P. F. Meadows, J. R. S. Gazal, S. Phan, B. N. Li, X. Genereux, D. P. Dong, M. X. Bianchi, M. Andrews, G. Sakthikumar, S. Nordin, J. Roy, A. Christmas, M. J. Marinescu, V. D. Wang, C. Wallerman, O. Xue, J. R. Li, Y. Yao, S. Sun, Q. Szatkiewicz, J. Wen, J. Huckins, L. M. Lawler, A. J. Keough, K. C. Zheng, Z. Zeng, J. Wray, N. R. Johnson, J. Chen, J. Zoonomia Consortium, Paten, B. Reilly, S. K. Hughes, G. M. Weng, Z. Pollard, K. S. Pfenning, A. R. Forsberg-Nilsson, K. Karlsson, E. K. Lindblad-Toh, K. 2023-03-10 doi:10.1101/2023.03.10.531987 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Cyclone: an accessible pipeline to analyze, evaluate and optimize multiparametric cytometry data ]]> https://biorxiv.org/content/10.1101/2023.03.08.531782v1?rss=1 Patel, R. K. Jaszczak, R. G. Kwok, I. Carey, N. D. Courau, T. Bunis, D. Samad, B. Avanesyan, L. Chew, N. W. Stenske, S. Jespersen, J. M. Publicover, J. Edwards, A. Naser, M. Rao, A. A. Lupin-Jimenez, L. Krummel, M. F. Cooper, S. Baron, J. Combes, A. J. Fragiadakis, G. K. 2023-03-11 doi:10.1101/2023.03.08.531782 Cold Spring Harbor Laboratory Press 2023-03-11 <![CDATA[ Unsupervised pattern discovery in spatial gene expression atlas reveals mouse brain regions beyond established ontology ]]> https://biorxiv.org/content/10.1101/2023.03.10.531984v1?rss=1 Cahill, R. Wang, Y. Lee, A. Zeng, H. Yu, B. Tasic, B. Abbasi-Asl, R. 2023-03-12 doi:10.1101/2023.03.10.531984 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ A systematic search for RNA structural switches across the human transcriptome ]]> https://biorxiv.org/content/10.1101/2023.03.11.532161v1?rss=1 Khoroshkin, M. Asarnow, D. Navickas, A. Winters, A. Yu, J. Zhou, S. K. Zhou, S. Palka, C. Fish, L. Ansel, K. M. Cheng, Y. Gilbert, L. A. Goodarzi, H. 2023-03-12 doi:10.1101/2023.03.11.532161 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Pharmacologic Activation of an Integrated Stress Response Kinase Promotes Mitochondrial Remodeling ]]> https://biorxiv.org/content/10.1101/2023.03.11.532186v1?rss=1 Perea, V. Baron, K. R. Dolina, V. Aviles, G. Rosarda, J. D. Guo, X. Kampmann, M. Wiseman, L. 2023-03-12 doi:10.1101/2023.03.11.532186 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ A molecular glue approach to control the half-life of CRISPR-based technologies ]]> https://biorxiv.org/content/10.1101/2023.03.12.531757v1?rss=1 230 amino acids), utilize expensive controllers with poor pharmacological attributes, and cannot be implemented in vivo on several CRISPR-based technologies. We report a general platform for half-life control using the molecular glue, pomalidomide, that binds to a ubiquitin ligase complex and a response-element bearing CRISPR-based technology, thereby causing the latters rapid ubiquitination and degradation. Using pomalidomide, we were able to control the half-life of large CRISPR-based technologies (e.g., base editors, CRISPRi) and small anti-CRISPRs that inhibit such technologies, allowing us to build the first examples of on-switch for base editors. The ability to switch on, fine-tune and switch-off CRISPR-based technologies with pomalidomide allowed complete control over their activity, specificity, and genome editing outcome. Importantly, the miniature size of the response element and favorable pharmacological attributes of the drug pomalidomide allowed control of activity of base editor in vivo using AAV as the delivery vehicle. These studies provide methods and reagents to precisely control the dosage and half-life of CRISPR-based technologies, propelling their therapeutic development. ]]> Sreekanth, V. Jan, M. Zhao, K. T. Lim, D. Davis, J. R. McConkey, M. Kovalcik, V. Barkal, S. Law, B. K. Fife, J. Tian, R. Vinyard, M. E. Becerra, B. Kampmann, M. E. Sherwood, R. I. Pinello, L. Liu, D. R. Ebert, B. L. Choudhary, A. 2023-03-12 doi:10.1101/2023.03.12.531757 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Aversive experience drives offline ensemble reactivation to link memories across days ]]> https://biorxiv.org/content/10.1101/2023.03.13.532469v1?rss=1 Zaki, Y. Pennington, Z. T. Morales-Rodriguez, D. Francisco, T. R. LaBanca, A. R. Dong, Z. Segura, S. C. Silva, A. J. Shuman, T. Fenton, A. Rajan, K. Cai, D. J. 2023-03-14 doi:10.1101/2023.03.13.532469 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Comparative analysis between RNA-seq and single-molecule RNA FISH indicates that the pyrimidine nucleobase idoxuridine (IdU) globally amplifies transcriptional noise ]]> https://biorxiv.org/content/10.1101/2023.03.14.532632v1?rss=1 Calia, G. P. Chen, X. Zuckerman, B. Weinberger, L. 2023-03-15 doi:10.1101/2023.03.14.532632 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Hox genes modulate physical forces to differentially shape small and large intestinal epithelia ]]> https://biorxiv.org/content/10.1101/2023.03.15.532602v1?rss=1 Gill, H. K. Yin, S. Nerurkar, N. L. Lawlor, J. C. Huycke, T. R. Mahadevan, L. Tabin, C. J. 2023-03-15 doi:10.1101/2023.03.15.532602 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ A protein hydroxylase couples epithelial membrane biology to nucleolar ribosome biogenesis ]]> https://biorxiv.org/content/10.1101/2023.03.15.532818v1?rss=1 Hendrix, E. Andrijes, R. Boora, U. Kaur, A. Bundred, J. R. Zayer, A. Heilig, R. Westrip, C. A. E. Fletcher, S. F. Eaton, C. D. Kennedy, T. J. Piasecka, S. Fischer, R. Smerdon, S. J. Coleman, M. L. 2023-03-16 doi:10.1101/2023.03.15.532818 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ HBV rewires liver cancer signaling by altering PP2A complexes ]]> https://biorxiv.org/content/10.1101/2023.03.15.532845v1?rss=1 Pitea, A. Turnham, R. Eckhardt, M. Jang, G. M. Xu, Z. Lim, H. C. Choi, A. Von Dollen, J. Levin, R. S. Webber, J. T. McCarthy, E. Hu, J. Li, X. Che, L. Chan, G. Kelley, R. K. Swaney, D. Zhang, W. Bandyopadhyay, S. Theis, F. J. Chen, X. Shokat, K. Ideker, T. Krogan, N. J. Gordan, J. 2023-03-16 doi:10.1101/2023.03.15.532845 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Group 2 innate lymphoid cells promote inhibitory synapse development and social behavior ]]> https://biorxiv.org/content/10.1101/2023.03.16.532850v1?rss=1 Barron, J. J. Mroz, N. M. Taloma, S. E. Dahlgren, M. W. Ortiz-Carpena, J. F. Dorman, L. C. Vainchtein, I. D. Escoubas, C. C. Molofsky, A. B. Molofsky, A. V. 2023-03-17 doi:10.1101/2023.03.16.532850 Cold Spring Harbor Laboratory Press 2023-03-17 <![CDATA[ Sensory cortical ensembles exhibit differential coupling to ripples in distinct hippocampal subregions ]]> https://biorxiv.org/content/10.1101/2023.03.17.533028v1?rss=1 Jeong, H. K Namboodiri, V. M. Jung, M. W. Andermann, M. L. 2023-03-18 doi:10.1101/2023.03.17.533028 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ Cryo-EM structure of the human Sirtuin 6-nucleosome complex ]]> https://biorxiv.org/content/10.1101/2023.03.17.533206v1?rss=1 Chio, U. S. Rechiche, O. Bryll, A. R. Zhu, J. Feldman, J. Peterson, C. Tan, S. Armache, J.-P. 2023-03-18 doi:10.1101/2023.03.17.533206 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 ]]> https://biorxiv.org/content/10.1101/2023.03.17.533220v1?rss=1 Abini-Agbomson, S. Gretarsson, K. Shih, R. M. Hsieh, L. Lou, T. De Ioannes, P. Vasilyev, N. Lee, R. Wang, M. Simon, M. Armache, J.-P. Nudler, E. Narlikar, G. Liu, S. Lu, C. Armache, K.-J. 2023-03-18 doi:10.1101/2023.03.17.533220 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ Comparative landscape of genetic dependencies in human and chimpanzee stem cells ]]> https://biorxiv.org/content/10.1101/2023.03.19.533346v1?rss=1 She, R. Fair, T. Schaefer, N. K. Saunders, R. A. Pavlovic, B. J. Weissman, J. S. Pollen, A. A. 2023-03-20 doi:10.1101/2023.03.19.533346 Cold Spring Harbor Laboratory Press 2023-03-20 <![CDATA[ A Spatiotemporal Map of Co-Receptor Signaling Networks Underlying B Cell Activation ]]> https://biorxiv.org/content/10.1101/2023.03.17.533227v1?rss=1 Susa, K. J. Bradshaw, G. A. Eisert, R. J. Schillling, C. M. Kalocsay, M. Blacklow, S. C. Kruse, A. C. 2023-03-21 doi:10.1101/2023.03.17.533227 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells ]]> https://biorxiv.org/content/10.1101/2023.03.22.533709v1?rss=1 Tsuchida, C. A. Brandes, N. Bueno, R. Trinidad, M. Mazumder, T. Yu, B. Hwang, B. Chang, C. Liu, J. Sun, Y. Hopkins, C. R. Parker, K. R. Qi, Y. Satpathy, A. Stadtmauer, E. Cate, J. H. D. Eyquem, J. Fraietta, J. A. June, C. H. Chang, H. Y. Ye, C. J. Doudna, J. A. 2023-03-22 doi:10.1101/2023.03.22.533709 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ Bayesian Inference for Brain Source Imaging with Joint Estimation of Structured Low-rank Noise ]]> https://biorxiv.org/content/10.1101/2023.03.19.533348v1?rss=1 Ghosh, S. Cai, C. Gao, Y. Hashemi, A. Haufe, S. Sekihara, K. Raj, A. Nagarajan, S. 2023-03-23 doi:10.1101/2023.03.19.533348 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Functional identification of language-responsive channels in individual participants in MEG investigations ]]> https://biorxiv.org/content/10.1101/2023.03.23.533424v1?rss=1 Bruffaerts, R. Pongos, A. Shain, C. Lipkin, B. Siegelman, M. Wens, V. Sjogard, M. Pantazis, D. Blank, I. Goldman, S. De Tiege, X. Fedorenko, E. 2023-03-23 doi:10.1101/2023.03.23.533424 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ A Comprehensive Enumeration of the Human Proteostasis Network. 2. Components of the Autophagy-Lysosome Pathway ]]> https://biorxiv.org/content/10.1101/2023.03.22.533675v1?rss=1 The Proteostasis Consortium, Elsasser, S. Elia, L. P. Morimoto, R. I. Powers, E. T. Finley, D. Costa, B. Budron, M. Tokuno, Z. Wang, S. Iyer, R. G. Barth, B. Mockler, E. Finkbeiner, S. Gestwicki, J. E. Richardson, R. A. K. Stoeger, T. Tan, E. P. Xiao, Q. Cole, C. M. Massey, L. A. Garza, D. Kelly, J. W. Rainbolt, T. K. Chou, C.-C. Masto, V. B. Frydman, J. Nixon, R. A. 2023-03-24 doi:10.1101/2023.03.22.533675 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ DIP-MS: A novel ultra-deep interaction proteomics for the deconvolution of protein complexes ]]> https://biorxiv.org/content/10.1101/2023.03.22.533843v1?rss=1 Frommelt, F. Fossati, A. Uliana, F. Wendt, F. Xue, P. Heusel, M. Wollscheid, B. Aebersold, R. Ciuffa, R. Gstaiger, M. 2023-03-24 doi:10.1101/2023.03.22.533843 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Analysis of evolutionary dynamics and clonal architecture in prostate cancer ]]> https://biorxiv.org/content/10.1101/2023.03.23.533974v1?rss=1 Conway, J. Tewari, A. K. Camp, S. Y. Han, S. Crowdis, J. He, M. X. Nyame, Y. A. AlDubayan, S. H. Schultz, N. Szallasi, Z. Pomerantz, M. M. Freedman, M. L. Fong, L. Nelson, P. S. Brown, M. Salari, K. Van Allen, E. 2023-03-25 doi:10.1101/2023.03.23.533974 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Continuous Multiplexed Phage Genome Editing Using Recombitrons ]]> https://biorxiv.org/content/10.1101/2023.03.24.534024v1?rss=1 Fishman, C. B. Crawford, K. D. Bhattarai-Kline, S. Zhang, K. A. Delgado-Gonzalez, A. Shipman, S. L. 2023-03-25 doi:10.1101/2023.03.24.534024 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Glioblastoma induces the recruitment and differentiation of hybrid neutrophils from skull bone marrow ]]> https://biorxiv.org/content/10.1101/2023.03.24.534105v1?rss=1 Lad, M. Beniwal, A. Jain, S. Shukla, P. Jung, J. Shah, S. Yagnik, G. Babikir, H. Nguyen, A. T. Gill, S. Young, J. S. Lui, A. Salha, D. Diaz, A. Aghi, M. K. 2023-03-25 doi:10.1101/2023.03.24.534105 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ An essential role for miR-15/16 in Treg suppression and restriction of proliferation ]]> https://biorxiv.org/content/10.1101/2023.03.26.533356v1?rss=1 Johansson, K. Gagnon, J. D. Zhou, S. Fassett, M. S. Schroeder, A. W. Kageyama, R. Bautista, R. A. Pham, H. Woodruff, P. G. Ansel, K. M. 2023-03-26 doi:10.1101/2023.03.26.533356 Cold Spring Harbor Laboratory Press 2023-03-26 <![CDATA[ SLAPSHOT reveals rapid dynamics of extracellularly exposed proteome in response to calcium-activated plasma membrane phospholipid scrambling ]]> https://biorxiv.org/content/10.1101/2023.03.26.534250v1?rss=1 Tuomivaara, S. T. Teo, C. F. Jan, Y. N. Jan, L. Y. Wiita, A. P. 2023-03-26 doi:10.1101/2023.03.26.534250 Cold Spring Harbor Laboratory Press 2023-03-26 <![CDATA[ A dual, catalytic role for the fission yeast Ccr4-Not complex in gene silencing and heterochromatin spreading ]]> https://biorxiv.org/content/10.1101/2023.03.27.534317v1?rss=1 Challal, D. Menant, A. Goksal, C. Leroy, E. Al-Sady, B. Rougemaille, M. 2023-03-27 doi:10.1101/2023.03.27.534317 Cold Spring Harbor Laboratory Press 2023-03-27 <![CDATA[ Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements ]]> https://biorxiv.org/content/10.1101/2023.03.28.534017v1?rss=1 Chardon, F. M. McDiarmid, T. A. Page, N. F. Martin, B. K. Domcke, S. Regalado, S. G. Lalanne, J.-B. Calderon, D. Starita, L. M. Sanders, S. J. Ahituv, N. Shendure, J. 2023-03-28 doi:10.1101/2023.03.28.534017 Cold Spring Harbor Laboratory Press 2023-03-28 <![CDATA[ Ipsilateral restriction of chromosome movement along a centrosome, and apical-basal axis during the cell cycle ]]> https://biorxiv.org/content/10.1101/2023.03.27.534352v1?rss=1 Cai, P. Casas, C. J. Hua, L. L. Mikawa, T. 2023-03-29 doi:10.1101/2023.03.27.534352 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Implantation of engineered adipocytes that outcompete tumors for resources suppresses cancer progression ]]> https://biorxiv.org/content/10.1101/2023.03.28.534564v1?rss=1 Nguyen, H. P. Sheng, R. Murray, E. Ito, Y. Bruck, M. Biellak, C. An, K. Lynce, F. Dillon, D. A. Magbanua, M. J. M. Huppert, L. A. Hammerlindl, H. Esserman, L. Rosenbluth, J. M. Ahituv, N. 2023-03-29 doi:10.1101/2023.03.28.534564 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Coordinated stimulation of axon regenerative and neurodegenerative transcriptional programs by Atf4 following optic nerve injury ]]> https://biorxiv.org/content/10.1101/2023.03.29.534798v1?rss=1 Somasundaram, P. Farley, M. M. Rudy, M. A. Stefanoff, D. G. Shah, M. Goli, P. Heo, J. Wang, S. Tran, N. M. Watkins, T. A. 2023-03-31 doi:10.1101/2023.03.29.534798 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ Few-shot learning: temporal scaling in behavioral and dopaminergic learning ]]> https://biorxiv.org/content/10.1101/2023.03.31.535173v1?rss=1 Burke, D. A. Jeong, H. Wu, B. Lee, S. A. Floeder, J. R. K Namboodiri, V. M. 2023-03-31 doi:10.1101/2023.03.31.535173 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ A Suite of Mouse Reagents for Studying Amelogenesis ]]> https://biorxiv.org/content/10.1101/2023.03.30.534992v1?rss=1 Wald, T. Verma, A. Cooley, V. Marangoni, P. Cazares, O. Sharir, A. Sandoval, E. J. Sung, D. Najibi, H. Drennon, T. Y. Bush, J. O. Joester, D. Klein, O. D. 2023-04-02 doi:10.1101/2023.03.30.534992 Cold Spring Harbor Laboratory Press 2023-04-02 <![CDATA[ Paradoxical increases in anterior cingulate cortex activity during nitrous oxide-induced analgesia reveal a signature of pain affect ]]> https://biorxiv.org/content/10.1101/2023.04.03.534475v1?rss=1 Weinrich, J. A. Liu, C. D. Jewell, M. E. Andolina, C. R. Bernstein, M. X. Benitez, J. Rodriguez-Rosado, S. Braz, J. M. Maze, M. Nemenov, M. I. Basbaum, A. I. 2023-04-03 doi:10.1101/2023.04.03.534475 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ High-throughput colocalization pipeline quantifies efficacy of mitochondrial targeting signals across different protein types ]]> https://biorxiv.org/content/10.1101/2023.04.03.535288v1?rss=1 Lear, S. K. Nunez, J. A. Shipman, S. L. 2023-04-03 doi:10.1101/2023.04.03.535288 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Computational drug repositioning for the identification of new agents to sensitize drug-resistant breast tumors across treatments and receptor subtypes ]]> https://biorxiv.org/content/10.1101/2023.03.30.534178v1?rss=1 Yu, K. Basu, A. Yau, C. Wolf, D. M. Goodarzi, H. Bandyopadhyay, S. Korkola, J. E. Hirst, G. L. Asare, S. I-SPY 2 TRIAL, Demichele, A. Hylton, N. Yee, D. Esserman, L. van 't Veer, L. Sirota, M. 2023-04-04 doi:10.1101/2023.03.30.534178 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ Piezo inhibition prevents and rescues scarring by targeting the adipocyte to fibroblast transition ]]> https://biorxiv.org/content/10.1101/2023.04.03.535302v1?rss=1 Griffin, M. Talbott, H. Guardino, N. Guo, J. Spielman, A. Chen, K. Mascharak, S. Parker, J. Henn, D. Liang, N. King, M. Cotterell, A. Bauer-Rowe, K. Abbas, D. Deleon, N. M. D. Fahy, E. Sivaraj, D. Downer, M. Akras, D. Berry, C. Cook, J. Quarto, N. Klein, O. D. Lorenz, P. Gurtner, G. Januszyk, M. Wan, D. C. Longaker, M. T. 2023-04-04 doi:10.1101/2023.04.03.535302 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ Comparing chromatin contact maps at scale: methods and insights ]]> https://biorxiv.org/content/10.1101/2023.04.04.535480v1?rss=1 Gunsalus, L. M. McArthur, E. Gjoni, K. Kuang, S. Pittman, M. Capra, J. A. Pollard, K. S. 2023-04-04 doi:10.1101/2023.04.04.535480 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ Spatial analysis of human lung cancer reveals organized immune hubs enriched for stem-like CD8 T cells and associated with immunotherapy response ]]> https://biorxiv.org/content/10.1101/2023.04.04.535379v1?rss=1 Chen, J. H. Nieman, L. T. Spurrell, M. Jorgji, V. Richieri, P. M. Xu, K. H. Madhu, R. Parikh, M. Zamora, I. Mehta, A. Nabel, C. S. Freeman, S. S. Pirl, J. D. Lu, C. Meador, C. B. Barth, J. Sakhi, M. Tang, A. L. Sarkizova, S. Price, C. Yizhak, K. Hofree, M. Shih, A. Sade-Feldman, M. Boland, G. M. Pelka, K. Aryee, M. J. Korsunsky, I. Mino-Kenudson, M. Gainor, J. Hacohen, N. 2023-04-06 doi:10.1101/2023.04.04.535379 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Revealing the Grammar of Small RNA Secretion Using Interpretable Machine Learning ]]> https://biorxiv.org/content/10.1101/2023.04.04.535452v1?rss=1 Zirak, B. Naghipourfar, M. Saberi, A. Pouyabahar, D. Zarezadeh, A. Fish, L. Luo, L. Huh, D. Sharifi-Zarchi, A. Goodarzi, H. 2023-04-06 doi:10.1101/2023.04.04.535452 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Parallelized screening of virus accessory genes reveals diverse defense and counter-defense mechanisms ]]> https://biorxiv.org/content/10.1101/2023.04.06.535777v1?rss=1 Silas, S. Carion, H. Makarova, K. S. Laderman, E. Godinez, D. S. Johnson, M. Fossati, A. Swaney, D. Bocek, M. Koonin, E. V. Bondy-Denomy, J. 2023-04-06 doi:10.1101/2023.04.06.535777 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Progranulin inhibits phospholipase sPLA2-IIA to control neuroinflammation ]]> https://biorxiv.org/content/10.1101/2023.04.06.535844v1?rss=1 Du, H. Yang, C. Nana, A. L. Seeley, W. W. Smolka, M. B. Hu, F. 2023-04-06 doi:10.1101/2023.04.06.535844 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ A critical role for PLCG1 in RAS activation by BCR-ABL1 and FLT3-ITD ]]> https://biorxiv.org/content/10.1101/2023.04.07.536070v1?rss=1 Szeto, M. Y. Mase, A. Kulhanek, K. Banerjee, S. Rubio, I. Roose, J. Shah, N. P. 2023-04-10 doi:10.1101/2023.04.07.536070 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ Secreted HLA Fc-Fusion Profiles Immunopeptidome in Hypoxic PDAC and Cellular Senescence ]]> https://biorxiv.org/content/10.1101/2023.04.10.536290v1?rss=1 30,000 unique HLA-associated peptides across two different HLA alleles and seven cell lines. Notably, [~]9,300 of these unique HLA-associated peptides had previously not been identified in the Immune Epitope Database. We believe the sHLA Fc-fusion capture technology will accelerate the study of the immunopeptidome as therapeutic interest in HLA-peptide complexes increases in cancer and beyond. ]]> Rettko, N. J. Kirkemo, L. L. Wells, J. A. 2023-04-12 doi:10.1101/2023.04.10.536290 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Demultiplex2: robust sample demultiplexing for scRNA-seq ]]> https://biorxiv.org/content/10.1101/2023.04.11.536275v1?rss=1 Zhu, Q. Conrad, D. N. Gartner, Z. J. 2023-04-12 doi:10.1101/2023.04.11.536275 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ An automated proximity proteomics pipeline for subcellular proteome and protein interaction mapping ]]> https://biorxiv.org/content/10.1101/2023.04.11.536358v1?rss=1 Huttenhain, R. Krogan, N. J. Eckhardt, M. von Zastrow, M. Roth, B. Foussard, H. Marley, A. Xu, J. Vartak, R. DiBerto, J. F. Patil, T. Polacco, B. J. Zhong, X. Li, Q. 2023-04-12 doi:10.1101/2023.04.11.536358 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Deletion of Pax1 scoliosis-associated regulatory elements leads to a female-biased tail abnormality ]]> https://biorxiv.org/content/10.1101/2023.04.12.536497v1?rss=1 Ushiki, A. Sheng, R. R. Zhang, Y. Zhao, J. Nobuhara, M. Murray, E. Ruan, X. Rios, J. J. Wise, C. A. Ahituv, N. 2023-04-13 doi:10.1101/2023.04.12.536497 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Non-specific recognition of histone modifications by H3K9bhb antibody ]]> https://biorxiv.org/content/10.1101/2023.04.12.536655v1?rss=1 Tsusaka, T. Oses-Prieto, J. A. Lee, C. DeFelice, B. Burlingame, A. Goldberg, E. L. 2023-04-13 doi:10.1101/2023.04.12.536655 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ SEL1L-HRD1 ER-associated degradation is a new ataxia gene ]]> https://biorxiv.org/content/10.1101/2023.04.13.536796v1?rss=1 Lin, L. L. Torres, M. Pederson, B. Wang, H. H. Wei, X. Li, Z. J. Liu, X. Mao, H. Hanzel, M. Govek, E. E. Lu, Y. Wang, H. Zhao, Z. Hatten, M. E. Sun, S. E. Qi, L. 2023-04-14 doi:10.1101/2023.04.13.536796 Cold Spring Harbor Laboratory Press 2023-04-14 <![CDATA[ Total Chemical Synthesis of Glycosylated TREM2 Ectodomain ]]> https://biorxiv.org/content/10.1101/2023.04.14.536909v1?rss=1 Wijegunawardena, G. Castillo, E. Henrickson, B. Davis, R. Condello, C. Wu, H. 2023-04-14 doi:10.1101/2023.04.14.536909 Cold Spring Harbor Laboratory Press 2023-04-14 <![CDATA[ Integrative identification of non-coding regulatory regions driving metastatic prostate cancer ]]> https://biorxiv.org/content/10.1101/2023.04.14.535921v1?rss=1 Woo, B. J. Moussavi-Baygi, R. Karner, H. Karimzadeh, M. Garcia, K. Joshi, T. Yin, K. Navickas, A. Gilbert, L. A. Wang, B. Asgharian, H. Feng, F. Y. Goodarzi, H. 2023-04-16 doi:10.1101/2023.04.14.535921 Cold Spring Harbor Laboratory Press 2023-04-16 <![CDATA[ Axon initial segment GABA inhibits action potential generation throughout periadolescent development ]]> https://biorxiv.org/content/10.1101/2023.04.16.537084v1?rss=1 Lipkin, A. M. Bender, K. J. 2023-04-16 doi:10.1101/2023.04.16.537084 Cold Spring Harbor Laboratory Press 2023-04-16 <![CDATA[ The lncRNA Malat1 Inhibits miR-15/16 to Enhance Cytotoxic T Cell Activation and Memory Cell Formation ]]> https://biorxiv.org/content/10.1101/2023.04.14.536843v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@1ebb1bborg.highwire.dtl.DTLVardef@e19c29org.highwire.dtl.DTLVardef@1d3568forg.highwire.dtl.DTLVardef@1d7d69b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wheeler, B. D. Gagnon, J. D. Zhu, W. S. Munoz-Sandoval, P. Wong, S. K. Simeonov, D. S. Li, Z. Debarge, R. Spitzer, M. Marson, A. Ansel, K. M. 2023-04-17 doi:10.1101/2023.04.14.536843 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Finding the right tool: a comprehensive evaluation of microglial inducible cre mouse models ]]> https://biorxiv.org/content/10.1101/2023.04.17.536878v1?rss=1 Bedolla, A. M. McKinsey, G. Ware, K. Santander, N. Arnold, T. Luo, Y. 2023-04-17 doi:10.1101/2023.04.17.536878 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo ]]> https://biorxiv.org/content/10.1101/2023.04.18.537104v1?rss=1 1000-fold lower levels compared to the wildtype virus while inducing a robust interferon response; all animals infected with the mutant virus survived infection and showed no signs of lung pathology. Our data validate the SARS-CoV-2 NSP3 Mac1 domain as a critical viral pathogenesis factor and a promising target to develop antivirals. ]]> Taha, T. Y. Suryawanshi, R. K. Chen, I. P. Correy, G. J. O'Leary, P. C. Jogalekar, M. P. McCavitt-Malvido, M. Diolaiti, M. Kimmerly, G. R. Tsou, C.-L. Martinez-Sobrido, L. Krogan, N. J. Ashworth, A. Fraser, J. S. Ott, M. 2023-04-18 doi:10.1101/2023.04.18.537104 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ In Vitro Modeling of CD8 T Cell Exhaustion Enables CRISPR Screening to Reveal a Role for BHLHE40 ]]> https://biorxiv.org/content/10.1101/2023.04.17.537229v1?rss=1 Wu, J. E. Manne, S. Ngiow, S. F. Baxter, A. E. Huang, H. Freilich, E. Clark, M. L. Lee, J. H. Chen, Z. Khan, O. Staupe, R. P. Huang, Y. J. Shi, J. Giles, J. R. Wherry, E. J. 2023-04-19 doi:10.1101/2023.04.17.537229 Cold Spring Harbor Laboratory Press 2023-04-19 <![CDATA[ Conserved enhancer logic controls the notochord expression of vertebrate Brachyury ]]> https://biorxiv.org/content/10.1101/2023.04.20.536761v1?rss=1 Kemmler, C. L. Smolikova, J. Moran, H. R. Mannion, B. J. Knapp, D. Lim, F. Czarkwiani, A. Hermosilla Aguayo, V. Rapp, V. Fitch, O. E. Boetschi, S. Selleri, L. Farley, E. Braasch, I. Yun, M. Visel, A. Osterwalder, M. Mosimann, C. Kozmik, Z. Burger, A. 2023-04-20 doi:10.1101/2023.04.20.536761 Cold Spring Harbor Laboratory Press 2023-04-20 <![CDATA[ D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response ]]> https://biorxiv.org/content/10.1101/2023.04.19.537364v1?rss=1 Jiang, J. Chen, S. Tsou, T. McGinnis, C. S. Khazaei, T. Zhu, Q. Park, J. H. Strazhnik, I.-M. Hanna, J. Chow, E. D. Sivak, D. A. Gartner, Z. J. Thomson, M. 2023-04-21 doi:10.1101/2023.04.19.537364 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Disease Tolerance Acquired Through Repeated Plasmodium Infection Involves Epigenetic Reprogramming of Innate Immune Cells ]]> https://biorxiv.org/content/10.1101/2023.04.19.537546v1?rss=1 Nideffer, J. Ty, M. Donato, M. Rek, J. Kajubi, R. Ji, X. Maecker, H. Nankya, F. Musinguzi, K. Press, K. Greenhouse, B. Kamya, M. Feeney, M. E. Dorsey, G. Utz, P. Pulendran, B. Khatri, P. Jagannathan, P. 2023-04-21 doi:10.1101/2023.04.19.537546 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Chemical stimuli override a temperature-dependent morphological program by reprogramming the transcriptome of a fungal pathogen. ]]> https://biorxiv.org/content/10.1101/2023.04.21.537729v1?rss=1 Assa, D. Voorhies, M. Sil, A. 2023-04-22 doi:10.1101/2023.04.21.537729 Cold Spring Harbor Laboratory Press 2023-04-22 <![CDATA[ Codon affinity in mitochondrial DNA shapes evolutionary and somatic fitness ]]> https://biorxiv.org/content/10.1101/2023.04.23.537997v1?rss=1 G) in the mitochondrial DNA (mtDNA) encoded cytochrome c-oxidase subunit 1 gene (MT-CO1, p.Gly391=), which was present at homoplasmy in 47% of immune cells from a healthy donor. Using single-cell multi-omics, we discover highly specific selection against the m.7076G mutant allele in the CD8+ effector memory T cell compartment in vivo, reminiscent of selection observed for pathogenic mtDNA alleles1, 2 and indicative of lineage-specific metabolic requirements. While the wildtype m.7076A allele is translated via Watson-Crick-Franklin base-pairing, the anticodon diversity of the mitochondrial transfer RNA pool is limited, requiring wobble-dependent translation of the m.7076G mutant allele. Notably, mitochondrial ribosome profiling revealed altered codon-anticodon affinity at the wobble position as evidenced by stalled translation of the synonymous m.7076G mutant allele encoding for glycine. Generalizing this observation, we provide a new ontogeny of the 8,482 synonymous variants in the human mitochondrial genome that enables interpretation of functional mtDNA variation. Specifically, via inter- and intra-species evolutionary analyses, population-level complex trait associations, and the occurrence of germline and somatic mtDNA mutations from large-scale sequencing studies, we demonstrate that synonymous variation impacting codon:anticodon affinity is actively evolving across the entire mitochondrial genome and has broad functional and phenotypic effects. In summary, our results introduce a new ontogeny for mitochondrial genetic variation and support a model where organismal principles can be discerned from somatic evolution via single-cell genomics. ]]> Lareau, C. A. Yin, Y. Gutierrez, J. C. Dhindsa, R. S. Gribling-Burrer, A.-S. Hsieh, Y.-H. Nitsch, L. Buquicchio, F. A. Abay, T. Zielinski, S. Stickels, R. R. Ulirsch, J. C. Yan, P. Wang, F. Miao, Z. Sandor, K. Daniel, B. Liu, V. Wang, Q. Hu, F. Smith, K. R. Deevi, S. V. V. Maschmeyer, P. Petrovski, S. Smyth, R. P. Greenleaf, W. J. Kundaje, A. Munschauer, M. Ludwig, L. S. Satpathy, A. T. 2023-04-23 doi:10.1101/2023.04.23.537997 Cold Spring Harbor Laboratory Press 2023-04-23 <![CDATA[ PhIP-Seq uncovers novel autoantibodies and unique endotypes in interstitial lung disease ]]> https://biorxiv.org/content/10.1101/2023.04.24.538091v1?rss=1 Upadhyay, V. Yoon, Y. m. Vazquez, S. E. Velez, T. E. Jones, K. D. Lee, C. T. Law, C. S. Wolters, P. J. Lee, S. Yang, M. M. Farrand, E. Noth, I. Strek, M. E. Anderson, M. DeRisi, J. Sperling, A. I. Shum, A. K. 2023-04-24 doi:10.1101/2023.04.24.538091 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ Transcriptome Analysis Reveals Organ-Specific Effects of 2-Deoxyglucose Treatment in Healthy Mice ]]> https://biorxiv.org/content/10.1101/2023.04.24.537717v1?rss=1 Wells, A. E. Wilson, J. J. Sears, J. D. Wei, J. Heuer, S. Pandey, R. Costa, M. W. Roopenian, D. C. Chang, C.-H. Carter, G. W. 2023-04-25 doi:10.1101/2023.04.24.537717 Cold Spring Harbor Laboratory Press 2023-04-25 <![CDATA[ Tumor cell heterogeneity drives spatial organization of the intratumoral immune response in squamous cell skin carcinoma ]]> https://biorxiv.org/content/10.1101/2023.04.25.538140v1?rss=1 Tanaka, M. Lum, L. Hu, K. H. Ledezma-Soto, C. Superville, D. A. Ng, K. M. Adams, Z. Kersten, K. H. Fong, L. Krummel, M. F. Reeves, M. Q. 2023-04-26 doi:10.1101/2023.04.25.538140 Cold Spring Harbor Laboratory Press 2023-04-26 <![CDATA[ CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions ]]> https://biorxiv.org/content/10.1101/2023.04.26.538498v1?rss=1 Li, E. Benitez, C. Boggess, S. C. Koontz, M. Rose, I. V. L. Draeger, N. Teter, O. M. Samelson, A. J. Ullian, E. M. Kampmann, M. 2023-04-27 doi:10.1101/2023.04.26.538498 Cold Spring Harbor Laboratory Press 2023-04-27 <![CDATA[ Up-regulation of cholesterol synthesis pathways and limited neurodegeneration in a knock-in Sod1 mutant mouse model of ALS. ]]> https://biorxiv.org/content/10.1101/2023.05.05.539444v1?rss=1 Dominov, J. A. Madigan, L. A. Whitt, J. P. Rademacher, K. L. Webster, K. M. Zhang, H. Banno, H. A. Tang, S. Zhang, Y. Wightman, N. Shychuck, E. M. Page, J. Weiss, A. Kelly, K. Kucukural, A. A. Brodsky, M. H. Jaworski, A. Fallon, J. R. Lipscombe, D. Brown, R. H. 2023-05-05 doi:10.1101/2023.05.05.539444 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ Connectome-based prediction of functional impairment in experimental stroke models ]]> https://biorxiv.org/content/10.1101/2023.05.05.539601v1?rss=1 Schmitt, O. Eipert, P. Wang, Y. Kanoke, A. Rabiller, G. Liu, J. 2023-05-05 doi:10.1101/2023.05.05.539601 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ Anatomical registration of intracranial electrodes. Robust model-based localization and deformable smooth brain-shift compensation methods ]]> https://biorxiv.org/content/10.1101/2023.05.08.539503v1?rss=1 Blenkmann, A. O. Leske, S. L. Llorens, A. Lin, J. J. Chang, E. Brunner, P. Schalk, G. Ivanovic, J. Larsson, P. G. Knight, R. T. Endestad, T. Solbakk, A.-K. 2023-05-09 doi:10.1101/2023.05.08.539503 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ The developmental timing of spinal touch processing alterations and its relation to ASD-associated behaviors in mouse models ]]> https://biorxiv.org/content/10.1101/2023.05.09.539589v1?rss=1 Tasnim, A. Alkislar, I. Hakim, R. Turecek, J. Abdelaziz, A. Orefice, L. L. Ginty, D. D. 2023-05-09 doi:10.1101/2023.05.09.539589 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Gene networks reveal stem-cell state convergence during preneoplasia and progression to malignancy in multistage skin carcinogenesis ]]> https://biorxiv.org/content/10.1101/2023.05.08.539863v1?rss=1 Taylor, M. A. Kandyba, E. Halliwell, K. Del Rosario, R. Khoroshkin, M. S. Goodarzi, H. Quigley, D. Li, Y. R. Wu, D. Bollam, S. Mirzoeva, O. Akhurst, R. Balmain, A. 2023-05-10 doi:10.1101/2023.05.08.539863 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ Anatomical and behavioral correlates of auditory perception in developmental dyslexia ]]> https://biorxiv.org/content/10.1101/2023.05.09.539936v1?rss=1 Qi, T. Mandelli, M. L. Watson Pereira, C. L. Wellman, E. Bogley, R. Licata, A. E. Chang, E. F. Oganian, Y. Gorno-Tempini, M. L. 2023-05-10 doi:10.1101/2023.05.09.539936 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ Allosteric regulation of TRPV1 by the inflammatory lipid, LPA ]]> https://biorxiv.org/content/10.1101/2023.05.11.540281v1?rss=1 Arnold, W. R. Julius, D. Cheng, Y. 2023-05-11 doi:10.1101/2023.05.11.540281 Cold Spring Harbor Laboratory Press 2023-05-11 <![CDATA[ Circadian PERIOD complex regulates TC-DSB repair through anchoring to the nuclear envelope ]]> https://biorxiv.org/content/10.1101/2023.05.11.540338v1?rss=1 Le Bozec, B. Guitton-Sert, L. Collins, S. Rocher, V. Guillou, E. Payrault, C. Arnould, C. Guenole, A. Aguirrebengoa, M. Finoux, A.-L. Mangeat, T. Puget, N. Legube, G. 2023-05-11 doi:10.1101/2023.05.11.540338 Cold Spring Harbor Laboratory Press 2023-05-11 <![CDATA[ Respiratory Complex I Regulates Dendritic Cell Maturation in Explant Model of Human Tumor Immune Microenvironment ]]> https://biorxiv.org/content/10.1101/2023.05.10.539944v1?rss=1 Turpin, R. Liu, R. Munne, P. Peura, A. Rannikko, J. H. Philips, G. Boeckx, B. Salmelin, N. Hurskainen, E. Suleymanova, I. Vuorinen, E. M. Lehtinen, L. Mutka, M. Kovanen, P. E. Niinikoski, L. Meretoja, T. Mattson, J. Mustjoki, S. Saavalainen, P. Goga, A. Lambrechts, D. Pouwels, J. Hollmen, M. Klefstrom, J. 2023-05-12 doi:10.1101/2023.05.10.539944 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X ]]> https://biorxiv.org/content/10.1101/2023.05.11.540322v1?rss=1 Jowhar, Z. Xu, A. Venkataramanan, S. Hoye, M. L. Silver, D. L. Floor, S. N. Calviello, L. 2023-05-12 doi:10.1101/2023.05.11.540322 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ Time-resolved network control analysis links reduced control energy under DMT with the serotonin 2a receptor, signal diversity, and subjective experience. ]]> https://biorxiv.org/content/10.1101/2023.05.11.540409v1?rss=1 Singleton, S. P. Timmermann, C. Luppi, A. I. Eckernas, E. Roseman, L. Carhart-Harris, R. L. Kuceyeski, A. 2023-05-12 doi:10.1101/2023.05.11.540409 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ Quantifying the relationship between cell proliferation and morphology during development of the face ]]> https://biorxiv.org/content/10.1101/2023.05.12.540515v1?rss=1 Green, R. M. Lo Vercio, L. Dauter, A. Barretto, E. C. Devine, J. Vidal Garcia, M. Marchini, M. Robertson, S. Zhao, X. Mahika, A. Shakir, M. B. Guo, S. Boughner, J. C. Dean, W. Lander, A. D. Marcucio, R. S. Forkert, N. D. Hallgrimsson, B. 2023-05-12 doi:10.1101/2023.05.12.540515 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ The p97/VCP adapter UBXD1 drives AAA+ remodeling and ring opening through multi-domain tethered interactions ]]> https://biorxiv.org/content/10.1101/2023.05.15.540864v1?rss=1 Braxton, J. R. Altobelli, C. R. Tucker, M. R. Tse, E. Thwin, A. C. Arkin, M. R. Southworth, D. R. 2023-05-15 doi:10.1101/2023.05.15.540864 Cold Spring Harbor Laboratory Press 2023-05-15 <![CDATA[ Asymmetric apical domain states of mitochondrial Hsp60 coordinate substrate engagement and chaperonin assembly ]]> https://biorxiv.org/content/10.1101/2023.05.15.540872v1?rss=1 Braxton, J. R. Shao, H. Tse, E. Gestwicki, J. E. Southworth, D. R. 2023-05-15 doi:10.1101/2023.05.15.540872 Cold Spring Harbor Laboratory Press 2023-05-15 <![CDATA[ Neutrophils actively swell to potentiate rapid migration ]]> https://biorxiv.org/content/10.1101/2023.05.15.540704v1?rss=1 Nagy, T. L. Strickland, J. D. Weiner, O. D. 2023-05-16 doi:10.1101/2023.05.15.540704 Cold Spring Harbor Laboratory Press 2023-05-16 <![CDATA[ Multiomic Single Cell Sequencing Identifies Stemlike Nature of Mixed Phenotype Acute Leukemia and Provides Novel Risk Stratification ]]> https://biorxiv.org/content/10.1101/2023.05.15.540305v1?rss=1 Peretz, C. A. C. Kennedy, V. E. Walia, A. Delley, C. L. Koh, A. Tran, E. Clark, I. Hayford, C. E. D'Amato, C. Xue, Y. Fontanez, K. M. Roy, R. Logan, A. C. Perl, A. E. Abate, A. Olshen, A. Smith, C. C. 2023-05-18 doi:10.1101/2023.05.15.540305 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Multivalent coiled-coil interactions enable full-scale centrosome assembly and strength ]]> https://biorxiv.org/content/10.1101/2023.05.15.540834v1?rss=1 Rios, M. U. Bagnucka, M. A. Ryder, B. D. Gomes, B. F. Familiari, N. Yaguchi, K. Amato, M. Joachimiak, Łukasz A. Woodruff, J. B. 2023-05-18 doi:10.1101/2023.05.15.540834 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ A central helical hairpin in SPD-5 enables centrosome strength and assembly ]]> https://biorxiv.org/content/10.1101/2023.05.16.540868v1?rss=1 Rios, M. U. Ryder, B. D. Familiari, N. Joachimiak, Łukasz A. Woodruff, J. B. 2023-05-18 doi:10.1101/2023.05.16.540868 Cold Spring Harbor Laboratory Press 2023-05-18 <![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[ Engineering Programmable Material-To-Cell Pathways Via Synthetic Notch Receptors To Spatially Control Cellular Phenotypes In Multi-Cellular Constructs ]]> https://biorxiv.org/content/10.1101/2023.05.19.541497v1?rss=1 Garibyan, M. Hoffman, T. Makaske, T. Do, S. March, A. R. Cho, N. Pedroncelli, N. Lima, R. E. Soto, J. Jackson, B. A. Khademhosseini, A. Li, S. McCain, M. Morsut, L. 2023-05-20 doi:10.1101/2023.05.19.541497 Cold Spring Harbor Laboratory Press 2023-05-20 <![CDATA[ The mitochondrial matrix protein cyclophilin D contributes to deficits in parvalbumin interneurons in schizophrenia ]]> https://biorxiv.org/content/10.1101/2023.05.19.541499v1?rss=1 O'Brien, J. T. Jalilvand, S. P. Suji, N. A. Phensy, A. Jupelly, R. K. Mwirigi, J. M. Elahi, H. Price, T. J. Kroener, S. 2023-05-20 doi:10.1101/2023.05.19.541499 Cold Spring Harbor Laboratory Press 2023-05-20 <![CDATA[ Chemoenzymatic syntheses of fluorine-18-labeled disaccharides from FDG yield potent sensors of living bacteria in vivo ]]> https://biorxiv.org/content/10.1101/2023.05.20.541529v1?rss=1 Sorlin, A. Lopez Alvarez, M. Rabbitt, S. Alanizi, A. Shuere, B. Bobba, K. N. Blecha, J. Sakhamuri, S. Evans, M. Bayles, K. J. Flavell, R. Rosenberg, O. Sriram, R. Desmet, T. Nidetzky, B. Engel, J. Ohliger, M. Fraser, J. Wilson, D. M. 2023-05-20 doi:10.1101/2023.05.20.541529 Cold Spring Harbor Laboratory Press 2023-05-20 <![CDATA[ Neurophysiological trajectories in Alzheimer's disease progression ]]> https://biorxiv.org/content/10.1101/2023.05.18.541379v1?rss=1 Kudo, K. Ranasinghe, K. G. Morise, H. Syed, F. Sekihara, K. Rankin, K. P. Miller, B. L. Kramer, J. Rabinovici, G. Vossel, K. Kirsch, H. E. Nagarajan, S. 2023-05-22 doi:10.1101/2023.05.18.541379 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ A Scalable High Throughput Fully Automated Pipeline for the Quantification of Amyloid Pathology in Alzheimer's Disease Using Deep Learning Algorithms ]]> https://biorxiv.org/content/10.1101/2023.05.19.541376v1?rss=1 Gopal Ramaswamy, V. Ahirwar, M. Ryan, G. Signaevski, M. Haroutunian, V. Finkbeiner, S. 2023-05-22 doi:10.1101/2023.05.19.541376 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile ]]> https://biorxiv.org/content/10.1101/2023.05.22.541795v1?rss=1 Muzyukina, P. Shkaruta, A. Guzman, N. M. Andreani, J. Borges, A. L. Bondy-Denomy, J. Maikova, A. Semenova, E. Severinov, K. SOUTOURINA, O. 2023-05-22 doi:10.1101/2023.05.22.541795 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Long-term optical imaging of the spinal cord in awake, behaving animals ]]> https://biorxiv.org/content/10.1101/2023.05.22.541477v1?rss=1 Ahanonu, B. Crowther, A. Kania, A. Casillas, M. R. Basbaum, A. 2023-05-24 doi:10.1101/2023.05.22.541477 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway ]]> https://biorxiv.org/content/10.1101/2023.05.23.540554v1?rss=1 Hoppe, N. Harrison, S. Hwang, S.-H. Chen, Z. Karelina, M. Deshpande, I. Suomivuori, C.-M. Palicharla, V. R. Berry, S. P. Tschaikner, P. Regele, D. Covey, D. F. Stefan, E. Marks, D. S. Reiter, J. Dror, R. O. Evers, A. S. Mukhopadhyay, S. Manglik, A. 2023-05-24 doi:10.1101/2023.05.23.540554 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Comparison of histological delineations of medial temporal lobe cortices by four independent neuroanatomy laboratories ]]> https://biorxiv.org/content/10.1101/2023.05.24.542054v1?rss=1 Wuestefeld, A. Baumeister, H. Adams, J. N. de Flores, R. Hodgetts, C. Mazloum-Farzaghi, N. Olsen, R. K. Puliyadi, V. Tran, T. T. Bakker, A. Canada, K. L. Dalton, M. A. Daugherty, A. M. La Joie, R. Wang, L. Bedard, M. Buendia, E. Denning, A. Irwin, D. J. Ittyerah, R. Lee, E. B. Lim, S. Iniguez de Onzono Martin, M. M. Munoz Lopez, M. Schuck, T. Trotman, W. Vela, A. Yushkevich, P. Amunts, K. Augustinack, J. C. Ding, S.-L. Insausti, R. Kedo, O. Berron, D. Wisse, L. E. M. 2023-05-24 doi:10.1101/2023.05.24.542054 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Type-2 diabetes alters hippocampal neural oscillations and disrupts synchrony between hippocampus and cortex ]]> https://biorxiv.org/content/10.1101/2023.05.25.542288v1?rss=1 Rabiller, G. Ip, Z. Zarrabian, S. Zhang, H. Sato, Y. Yazdan-Shahmorad, A. Liu, J. 2023-05-26 doi:10.1101/2023.05.25.542288 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Contrasting synaptic roles of MDGA1 and MDGA2 ]]> https://biorxiv.org/content/10.1101/2023.05.25.542333v1?rss=1 Bemben, M. A. Sandoval, M. A. Le, A. A. Won, S. Chau, V. N. Lauterborn, J. C. Incontro, S. Li, K. H. Burlingame, A. L. Roche, K. W. Gall, C. M. Nicoll, R. A. Diaz-Alonso, J. 2023-05-26 doi:10.1101/2023.05.25.542333 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Association of an estrogen-sensitive Pax1-Col11a1-Mmp3 signaling axis with adolescent idiopathic scoliosis ]]> https://biorxiv.org/content/10.1101/2023.05.26.542293v1?rss=1 T; p.(Pro1335Leu); P=7.07e-11, OR=1.118). Using CRISPR mutagenesis we generated Pax1 knockout mice (Pax1-/-). In postnatal spines we found that PAX1 and collagen (1) XI protein both localize within the intervertebral disc (IVD)-vertebral junction region encompassing the growth plate, with less collagen (1) XI detected in Pax1-/- spines compared to wildtype. By genetic targeting we found that wildtype Col11a1 expression in costal chondrocytes suppresses expression of Pax1 and of Mmp3, encoding the matrix metalloproteinase 3 enzyme implicated in matrix remodeling. However, this suppression was abrogated in the presence of the AIS-associated COL11A1P1335L mutant. Further, we found that either knockdown of the estrogen receptor gene Esr2, or tamoxifen treatment, significantly altered Col11a1 and Mmp3 expression in chondrocytes. We propose a new molecular model of AIS pathogenesis wherein genetic variation and estrogen signaling increase disease susceptibility by altering a Pax1-Col11a1-Mmp3 signaling axis in spinal chondrocytes. ]]> Wise, C. Yu, H. Khanshour, A. M. Ushiki, A. Otomo, N. Koike, Y. Einarsdottir, E. Fan, Y. Antunes, L. Kidane, Y. H. Sheng, R. Zhang, Y. Pei, J. Grishin, N. V. Evers, B. M. V. Cheung, J. P. Y. Herring, J. A. Terao, C. Song, Y.-Q. Gurnett, C. Gerdhem, P. Ikegawa, S. Rios, J. J. Ahituv, N. 2023-05-27 doi:10.1101/2023.05.26.542293 Cold Spring Harbor Laboratory Press 2023-05-27 <![CDATA[ Expression and purification of the mitochondrial transmembrane protein FAM210A in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2023.05.27.542570v1?rss=1 Hollinger, J. Wu, J. Awayda, K. M. O'Connell, M. R. Yao, P. 2023-05-27 doi:10.1101/2023.05.27.542570 Cold Spring Harbor Laboratory Press 2023-05-27 <![CDATA[ Coupling and uncoupling of midline morphogenesis and cell flow in amniote gastrulation ]]> https://biorxiv.org/content/10.1101/2023.05.26.542486v1?rss=1 Asai, R. Prakash, V. N. Sinha, S. Prakash, M. Mikawa, T. 2023-05-28 doi:10.1101/2023.05.26.542486 Cold Spring Harbor Laboratory Press 2023-05-28 <![CDATA[ Sequential Switching Through IgG1 is Redundant for Allergic Reactivity and Memory to Allergens ]]> https://biorxiv.org/content/10.1101/2023.05.27.542563v1?rss=1 Koenig, J. F. Wade-Vallance, A. K. Jimenez-Saiz, R. Bruton, K. Gadkar, S. Grydziuszko, E. Walker, T. Gordon, M. E. Waserman, S. Jordana, M. 2023-05-28 doi:10.1101/2023.05.27.542563 Cold Spring Harbor Laboratory Press 2023-05-28 <![CDATA[ Exomap1 mouse: a transgenic model for in vivo studies of exosome biology ]]> https://biorxiv.org/content/10.1101/2023.05.29.542707v1?rss=1 5 nm in size. Taken together, these results establish the exomap1 mouse as a useful tool for in vivo studies of exosome biology, and for mapping cell type-specific contributions to biofluid exosome populations. In addition, our data confirm that CD81 is a highly-specific marker for exosomes and is not enriched in the larger microvesicle class of EVs. ]]> Fordjour, F. K. Abuelreich, S. Hong, X. Chatterjee, E. Lallai, V. Ng, M. Saftics, A. Deng, F. Carnel-Amar, N. Wakimoto, H. Shimizu, K. Anh Phu, T. Vu, N. K. Geiger, P. C. Raffai, R. L. Fowler, C. D. Shimizu, K. Das, S. Christenson, L. K. Jovanovic-Talisman, T. Gould, S. 2023-05-29 doi:10.1101/2023.05.29.542707 Cold Spring Harbor Laboratory Press 2023-05-29 <![CDATA[ The oncogene cyclin D1 promotes bipolar spindle integrity under compressive force ]]> https://biorxiv.org/content/10.1101/2023.05.30.542893v1?rss=1 Sutanto, R. Neahring, L. Marques, A. S. Kilinc, S. Goga, A. Dumont, S. 2023-05-31 doi:10.1101/2023.05.30.542893 Cold Spring Harbor Laboratory Press 2023-05-31 <![CDATA[ Reference-free multiplexed single-cell sequencing identifies genetic modifiers of the human immune response ]]> https://biorxiv.org/content/10.1101/2023.05.29.542756v1?rss=1 Hartoularos, G. C. Si, Y. Zhang, F. C. Kathail, P. Lee, D. Ogorodnikov, A. Sun, Y. Song, Y. S. Kang, H. M. Ye, C. J. 2023-06-01 doi:10.1101/2023.05.29.542756 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ MFGE8 inhibits insulin signaling through PTP1B ]]> https://biorxiv.org/content/10.1101/2023.05.30.542928v1?rss=1 Datta, R. Podolsky, M. J. Yang, C. D. Alba, D. Singh, S. Koliwad, S. Lizama, C. O. Atabai, K. 2023-06-01 doi:10.1101/2023.05.30.542928 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Evolution of the mutation spectrum across a mammalian phylogeny ]]> https://biorxiv.org/content/10.1101/2023.05.31.543114v1?rss=1 Beichman, A. C. Robinson, J. A. Lin, M. Moreno-Estrada, A. Nigenda-Morales, S. Harris, K. 2023-06-01 doi:10.1101/2023.05.31.543114 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Phage anti-CBASS protein simultaneously sequesters cyclic trinucleotides and dinucleotides ]]> https://biorxiv.org/content/10.1101/2023.06.01.543220v1?rss=1 Cao, X. Xiao, Y. Huiting, E. Cao, X. Li, D. Ren, J. Guan, L. Wang, Y. Li, L. Bondy-Denomy, J. Feng, Y. 2023-06-01 doi:10.1101/2023.06.01.543220 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Deep learning from harmonized peptide libraries enables retention time prediction of diverse post translational modifications ]]> https://biorxiv.org/content/10.1101/2023.05.30.542978v1?rss=1 2.2 million peptides including 10 common post-translational modification (PTM) types. By linking knowledge learned across diverse peptide chemistries, Chronologer predicts RTs with less than two-thirds the error of other deep learning tools. We show how RT for rare PTMs, such as OGlcNAc, can be learned with high accuracy using as few as 10-100 example peptides in newly harmonized datasets. This iteratively updatable workflow enables Chronologer to comprehensively predict RTs for PTM-marked peptides across entire proteomes. ]]> Wilburn, D. B. Shannon, A. E. Spicer, V. Richards, A. L. Yeung, D. Swaney, D. L. Krokhin, O. V. Searle, B. C. 2023-06-02 doi:10.1101/2023.05.30.542978 Cold Spring Harbor Laboratory Press 2023-06-02 <![CDATA[ Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase ]]> https://biorxiv.org/content/10.1101/2023.06.03.542675v1?rss=1 Diaz, R. E. Ecker, A. K. Correy, G. J. Asthana, P. Young, I. D. Faust, B. Thompson, M. C. Seiple, I. B. Van Dyken, S. J. Locksley, R. M. Fraser, J. S. 2023-06-03 doi:10.1101/2023.06.03.542675 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ DNAJB1-PRKACA fusion protein-regulated LINC00473 promotes tumor growth and alters mitochondrial fitness in fibrolamellar carcinoma ]]> https://biorxiv.org/content/10.1101/2023.06.02.543290v1?rss=1 View larger version (56K): org.highwire.dtl.DTLVardef@20e0f2org.highwire.dtl.DTLVardef@904fbborg.highwire.dtl.DTLVardef@62af84org.highwire.dtl.DTLVardef@f114be_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ma, R. K. Tsai, P.-Y. Farghli, A. R. Shumway, A. J. Kanke, M. Gordan, J. D. Gujral, T. Vakili, K. Nukaya, M. Noetzli, L. Ronnekleiv-Kelly, S. Broom, W. Barrow, J. Sethupathy, P. 2023-06-04 doi:10.1101/2023.06.02.543290 Cold Spring Harbor Laboratory Press 2023-06-04 <![CDATA[ Mechanism of substrate binding and transport in BASS transporters ]]> https://biorxiv.org/content/10.1101/2023.06.02.543391v1?rss=1 Becker, P. Naughton, F. B. Brotherton, D. H. Pacheco-Gomez, R. Beckstein, O. Cameron, A. D. 2023-06-04 doi:10.1101/2023.06.02.543391 Cold Spring Harbor Laboratory Press 2023-06-04 <![CDATA[ A novel small molecule PKC epsilon inhibitor reduces hyperalgesia induced by paclitaxel or opioid withdrawal ]]> https://biorxiv.org/content/10.1101/2023.06.01.543325v1?rss=1 Gregory-Flores, A. Magayewski Bonet, I. J. Desaivre, S. Levine, J. D. McHardy, S. F. de Kraker, H. Russell, N. Fleischer, C. Messing, R. Marinelli, M. 2023-06-05 doi:10.1101/2023.06.01.543325 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Mesostriatal dopamine is sensitive to specific cue-reward contingencies ]]> https://biorxiv.org/content/10.1101/2023.06.05.543690v1?rss=1 Garr, E. Cheng, Y. Jeong, H. Brooke, S. Castell, L. Bal, A. Magnard, R. Namboodiri, V. M. K. Janak, P. H. 2023-06-05 doi:10.1101/2023.06.05.543690 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ NEMO reshapes the protein aggregate interface and promotes aggrephagy by co-condensation with p62 ]]> https://biorxiv.org/content/10.1101/2023.06.05.543428v1?rss=1 Furthmann, N. Angersbach, L. Bader, V. Blusch, A. Goel, S. Sanchez-Vicente, A. Krause, L. J. Grover, P. Trinkaus, V. A. van Well, E. M. Jaugstetter, M. Tschulik, K. Damgaard, R. B. Saft, C. Ellrichmann, G. Gold, R. Koch, A. Englert, B. Glatzel, M. Hartl, F.-U. Nakamura, K. Christine, C. Huang, E. J. Tatzelt, J. Winklhofer, K. F. 2023-06-06 doi:10.1101/2023.06.05.543428 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ Post-acute immunological and behavioral sequelae in mice after Omicron infection ]]> https://biorxiv.org/content/10.1101/2023.06.05.543758v1?rss=1 Ma, T. Suryawanshi, R. K. Miller, S. R. Ly, K. K. Thomas, R. Elphick, N. Yin, K. Luo, X. Kaliss, N. Chen, I. P. Montano, M. Sreekumar, B. Standker, L. Munch, J. Damron, F. H. Palop, J. J. Ott, M. Roan, N. R. 2023-06-07 doi:10.1101/2023.06.05.543758 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Impaired cerebellar plasticity hypersensitizessensory reflexes in SCN2A-associated ASD ]]> https://biorxiv.org/content/10.1101/2023.06.05.543814v1?rss=1 Wang, C. Derderian, K. D. Hamada, E. Zhou, X. Nelson, A. D. Kyoung, H. Ahituv, N. Bouvier, G. Bender, K. 2023-06-07 doi:10.1101/2023.06.05.543814 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ The Neonatal Gyrencephalic Cortex Maintains Regionally Distinct Streams of Neuroblasts ]]> https://biorxiv.org/content/10.1101/2023.06.06.543768v1?rss=1 Kim, J. Sandoval, K. Poddar, A. Chu, J. Horton, E. Cui, D. Nakamura, K. Bartels, T. Wood, C. Rowitch, D. H. Kim, H. Sherwood, C. C. Kramer, B. W. Roberts, A. C. ROSS, P. J. Xu, D. Robertson, N. J. Ji, P. Maga, E. A. Paredes, M. F. 2023-06-07 doi:10.1101/2023.06.06.543768 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Quantifying turgor pressure in budding and fission yeasts based upon osmotic properties ]]> https://biorxiv.org/content/10.1101/2023.06.07.544129v1?rss=1 LEMIERE, J. Chang, F. 2023-06-07 doi:10.1101/2023.06.07.544129 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Neuronal Activation of the Gαq Protein EGL-30/GNAQ Late in Life Rejuvenates Cognition Across Species ]]> https://biorxiv.org/content/10.1101/2023.06.06.543909v1?rss=1 Stevenson, M. E. Bieri, G. Kaletsky, R. Ange, J. S. Remesal, L. Pratt, K. J. B. Zhou, S. Weng, Y. Murphy, C. T. Villeda, S. A. 2023-06-11 doi:10.1101/2023.06.06.543909 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ Neuropathy target esterase activity predicts retinopathy among PNPLA6 disorders ]]> https://biorxiv.org/content/10.1101/2023.06.09.544373v1?rss=1 Liu, J. He, Y. Lwin, C. Han, M. Guan, B. Niak, A. Bender, C. Moore, N. Huryn, L. A. Sergeev, Y. Qian, H. Zeng, Y. Dong, L. Liu, P. Li, J. Haugen, C. J. Prasov, L. Shi, R. Dollfus, H. Aristodemou, P. Laich, Y. Nemeth, A. H. Taylor, J. Downes, S. Krawczynski, M. Meunier, I. Strassberg, M. Tenney, J. Gao, J. Shear, M. A. Moore, A. T. Duncan, J. L. Menendez, B. Hull, S. Vincent, A. Siskind, C. E. Traboulsi, E. I. Blackstone, C. Sisk, R. Utz, V. Webster, A. R. Michaelides, M. Arno, G. Synofzik, M. Hufnagel, R. B. 2023-06-11 doi:10.1101/2023.06.09.544373 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ Homologous chromosome recognition via nonspecific interactions ]]> https://biorxiv.org/content/10.1101/2023.06.09.544427v1?rss=1 Marshall, W. F. Fung, J. C. 2023-06-11 doi:10.1101/2023.06.09.544427 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ KIBRA repairs synaptic plasticity and promotes resilience to tauopathy-related memory loss ]]> https://biorxiv.org/content/10.1101/2023.06.12.543777v1?rss=1 Kauwe, G. Pareja-Navarro, K. Yao, L. Chen, J. Wong, I. Saloner, R. Cifuentes, H. Nana, A. L. Shah, S. Li, Y. Le, D. Spina, S. Grinberg, L. T. Seeley, W. W. Kramer, J. Sacktor, T. Schilling, B. Gan, L. Casaletto, K. B. Tracy, T. E. 2023-06-13 doi:10.1101/2023.06.12.543777 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ Polarized Desmosome and Hemidesmosome Shedding via Exosomes is an Early Indicator of Outer Blood-Retina Barrier Dysfunction ]]> https://biorxiv.org/content/10.1101/2023.06.12.544677v1?rss=1 Hernandez, B. Skiba, N. P. Ploessl, K. Strain, M. Grigsby, D. Kelly, U. Cady, M. A. Manocha, V. Maminishkis, A. Watkins, T. Miller, S. S. Ashley-Koch, A. Stamer, W. D. Weber, B. H. Rickman, C. B. Klingeborn, M. 2023-06-13 doi:10.1101/2023.06.12.544677 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ Scalable, cell type-selective in vivo AAV-based CRISPR screens in mice ]]> https://biorxiv.org/content/10.1101/2023.06.13.544831v1?rss=1 Ramani, B. Rose, I. V. L. Pan, A. Tian, R. Ma, K. Palop, J. J. Kampmann, M. 2023-06-13 doi:10.1101/2023.06.13.544831 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ Intrinsic Homeostatic Plasticity in Mouse and Human Sensory Neurons ]]> https://biorxiv.org/content/10.1101/2023.06.13.544829v1?rss=1 Mcllvried, L. A. Del Rosario, J. S. Pullen, M. Y. Wangzhou, A. Sheahan, T. D. Shepherd, A. J. Slivicki, R. A. Lemen, J. A. Price, T. J. Copits, B. A. Gereau, R. W. 2023-06-14 doi:10.1101/2023.06.13.544829 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ Hyperglycosylation of prosaposin in tumor DCs promotes immune escape in cancer ]]> https://biorxiv.org/content/10.1101/2023.06.14.545005v1?rss=1 Sharma, P. Zhang, X. Ly, K. Kim, J. H. Wan, Q. Kim, J. Lou, M. Kain, L. Teyton, L. Winau, F. 2023-06-14 doi:10.1101/2023.06.14.545005 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ Participant-derived cell line transcriptomic analyses and mouse studies reveal a role for ZNF335 in plasma cholesterol statin response ]]> https://biorxiv.org/content/10.1101/2023.06.14.544860v1?rss=1 Theusch, E. Ting, F. Y. Qin, Y. Stevens, K. Naidoo, D. King, S. M. Yang, N. Orr, J. Han, B. Y. Cyster, J. G. Chen, Y.-D. I. Rotter, J. I. Krauss, R. M. Medina, M. W. 2023-06-15 doi:10.1101/2023.06.14.544860 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis ]]> https://biorxiv.org/content/10.1101/2023.06.16.545386v1?rss=1 Samelson, A. J. Ariqat, N. McKetney, J. Rohanitazangi, G. Parra Bravo, C. Goodness, D. Tian, R. Grosjean, P. Abskharon, R. Eisenberg, D. Kanaan, N. M. Gan, L. Condello, C. Swaney, D. L. Kampmann, M. 2023-06-17 doi:10.1101/2023.06.16.545386 Cold Spring Harbor Laboratory Press 2023-06-17 <![CDATA[ Non-coding sequence variation reveals fragility within interleukin 2 feedback circuitry and shapes autoimmune disease risk ]]> https://biorxiv.org/content/10.1101/2023.06.17.545426v1?rss=1 Simeonov, D. R. Park, K. Cortez, J. T. Young, A. Li, Z. Nguyen, V. Umhoefer, J. Indart, A. C. Woo, J. Anderson, M. S. Tsang, J. S. Germain, R. N. Wong, H. S. Marson, A. 2023-06-18 doi:10.1101/2023.06.17.545426 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Stimulus-specific enhancement of responses in mouse primary visual cortex mediated by GABA release from VIP cells ]]> https://biorxiv.org/content/10.1101/2023.06.19.545641v1?rss=1 Kaneko, M. Hoseini, M. S. Waschek, J. A. Stryker, M. P. 2023-06-20 doi:10.1101/2023.06.19.545641 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking ]]> https://biorxiv.org/content/10.1101/2023.06.20.545796v1?rss=1 Chio, U. S. Palovcak, E. Autzen, A. A. A. Autzen, H. E. Munoz, E. N. Yu, Z. Wang, F. Agard, D. A. Armache, J.-P. Narlikar, G. Cheng, Y. 2023-06-20 doi:10.1101/2023.06.20.545796 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ Human iPSC 4R tauopathy model uncovers modifiers of tau propagation ]]> https://biorxiv.org/content/10.1101/2023.06.19.544278v1?rss=1 Parra Bravo, C. Giani, A. M. Madero-Perez, J. Zhao, Z. Samelson, A. J. Wong, M. Y. Evangelisti, A. Fan, L. Pozner, T. Mercedes, M. Ye, P. Patel, T. Yarahmady, A. Carling, G. Lee, V. M. Y. Sharma, M. Mok, S.-A. Luo, W. Zhao, M. Kampmann, M. Gong, S. Gan, L. 2023-06-22 doi:10.1101/2023.06.19.544278 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ GATA-regulated transcriptional program dictate cell fate equilibrium to establish the maternal-fetal exchange interface and fetal development ]]> https://biorxiv.org/content/10.1101/2023.06.19.545618v1?rss=1 Ghosh, A. Kumar, R. Kumar, R. P. Ray, S. Saha, A. Roy, N. Dasgupta, P. Marsh, C. Paul, S. 2023-06-22 doi:10.1101/2023.06.19.545618 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Small-field visual projection neurons detect translational optic flow and support walking control ]]> https://biorxiv.org/content/10.1101/2023.06.21.546024v1?rss=1 Isaacson, M. D. Eliason, J. L. Nern, A. Rogers, E. M. Lott, G. K. Tabachnik, T. Rowell, W. J. Edwards, A. W. Korff, W. L. Rubin, G. M. Branson, K. Reiser, M. B. 2023-06-22 doi:10.1101/2023.06.21.546024 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Tiny Earth CURE improves student persistence in science ]]> https://biorxiv.org/content/10.1101/2023.06.21.543782v1?rss=1 Miller, S. Aldana, C. C. Du, W. Lee, H. Maldonado, N. Sandoval, P. Vong, J. Young, G. Handelsman, J. Broderick, N. A. Hernandez, P. R. Estrada, M. 2023-06-23 doi:10.1101/2023.06.21.543782 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Activation of Shh/Smo is sufficient to maintain oligodendrocyte precursor cells in an undifferentiated state but is not necessary for differentiation ]]> https://biorxiv.org/content/10.1101/2023.06.23.546285v1?rss=1 Nocera, S. Marchena, M. A. Fernandez-Gomez, B. Lao, Y. Cordano, C. Gomez-Torres, O. Lujan, R. de Castro, F. 2023-06-23 doi:10.1101/2023.06.23.546285 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ The unique microbial diversity, community composition and networks of Pacific Islander endocervical and vaginal microbiomes in the presence or absence of Chlamydia trachomatis infection using metagenomic shotgun sequencing ]]> https://biorxiv.org/content/10.1101/2023.06.23.546186v1?rss=1 Bommana, S. Hu, Y. Kama, M. Wang, R. Kodimerla, R. Jijakli, K. Read, T. Dean, D. 2023-06-24 doi:10.1101/2023.06.23.546186 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ Diverse viral cas genes antagonize CRISPR immunity ]]> https://biorxiv.org/content/10.1101/2023.06.24.545427v1?rss=1 Katz, M. A. Sawyer, E. M. Kozlova, A. Williams, M. C. Margolis, S. R. Oriolt, L. Johnson, M. Bondy-Denomy, J. Meeske, A. J. 2023-06-24 doi:10.1101/2023.06.24.545427 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ Enabling Success Through Transformative Practices in STEM: The Effects of Applying an Anti-Deficit Framework to Diversity and Equity Programming ]]> https://biorxiv.org/content/10.1101/2023.06.22.546152v1?rss=1 Duncan, D. S. Jackson, J. L. Collins, S. Teherani, A. 2023-06-25 doi:10.1101/2023.06.22.546152 Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ The microenvironment dictates glycocalyx construction and immune surveillance ]]> https://biorxiv.org/content/10.1101/2023.06.23.546317v1?rss=1 Tharp, K. Park, S. Timblin, G. A. Richards, A. Berg, J. Twells, N. Riley, N. M. Peltan, E. Shon, D. J. Stevenson, E. Tsui, C. K. Palomba, F. Lefebvre, A. E. Soens, R. Ayad, N. ten Hoeve-Scott, J. Healy, K. Digman, M. Dillin, A. Bertozzi, C. Mahal, L. K. Swaney, D. Cantor, J. R. Paszek, M. Weaver, V. 2023-06-25 doi:10.1101/2023.06.23.546317 Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ Prolonged Kaposi's Sarcoma-associated Herpesvirus vIL-6 Exposure Enhances Inflammatory Responses by Epigenetic Reprogramming ]]> https://biorxiv.org/content/10.1101/2023.06.25.546454v1?rss=1 Inagaki, T. Wang, K.-H. Kumar, A. Izumiya, C. Miura, H. Komaki, S. Davis, R. R. Tepper, C. Katano, H. Shimoda, M. Izumiya, Y. 2023-06-25 doi:10.1101/2023.06.25.546454 Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ Multi-night naturalistic cortico-basal recordings reveal mechanisms of NREM slow wave suppression and spontaneous awakenings in Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2023.06.23.546302v1?rss=1 Anjum, M. F. Smyth, C. Dijk, D.-J. Starr, P. Denison, T. Little, S. 2023-06-26 doi:10.1101/2023.06.23.546302 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ TOMM40 and TOMM22 of the Translocase Outer Mitochondrial Membrane Complex rescue statin-impaired mitochondrial dynamics, morphology, and mitophagy in skeletal myotubes ]]> https://biorxiv.org/content/10.1101/2023.06.24.546411v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@1845842org.highwire.dtl.DTLVardef@1be8a26org.highwire.dtl.DTLVardef@5fd618org.highwire.dtl.DTLVardef@1e0f523_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yang, N. V. Rogers, S. Guerra, R. Pagliarini, D. J. Theusch, E. Krauss, R. M. 2023-06-26 doi:10.1101/2023.06.24.546411 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Patterning and folding of intestinal villi by active mesenchymal dewetting ]]> https://biorxiv.org/content/10.1101/2023.06.25.546328v1?rss=1 Huycke, T. R. Miyazaki, H. Häkkinen, T. Srivastava, V. Barruet, E. McGinnis, C. S. Kalantari, A. Cornwall-Scoones, J. Vaka, D. Zhu, Q. Jo, H. DeGrado, W. F. Thomson, M. Garikipati, K. Boffelli, D. Klein, O. D. Gartner, Z. J. 2023-06-26 doi:10.1101/2023.06.25.546328 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Cross regional coordination of neural activity in the human brain during autobiographical self-referential processing ]]> https://biorxiv.org/content/10.1101/2023.06.26.546582v1?rss=1 Stieger, J. Pinheiro-Chagas, P. Fang, Y. Lusk, Z. Perry, C. Wagner, A. D. Contreras, D. Chen, Q. Huguenard, J. Buch, V. Parvizi, J. 2023-06-27 doi:10.1101/2023.06.26.546582 Cold Spring Harbor Laboratory Press 2023-06-27 <![CDATA[ Population encoding of stimulus features along the visual hierarchy ]]> https://biorxiv.org/content/10.1101/2023.06.27.545450v1?rss=1 Dyballa, L. Rudzite, A. M. Hoseini, M. S. Thapa, M. Stryker, M. P. Field, G. D. Zucker, S. W. 2023-06-27 doi:10.1101/2023.06.27.545450 Cold Spring Harbor Laboratory Press 2023-06-27 <![CDATA[ Self-extinguishing relay waves enable homeostaticcontrol of human neutrophil swarming ]]> https://biorxiv.org/content/10.1101/2023.06.27.546744v1?rss=1 Strickland, J. Pan, D. Godfrey, C. Kim, J. S. Hopke, A. Degrange, M. Villavicencio, B. Mansour, M. K. Zerbe, C. S. Irimia, D. Amir, A. Weiner, O. D. 2023-06-28 doi:10.1101/2023.06.27.546744 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ Recruitment of BAG2 to DNAJ-PKAc scaffolds promotes cell survival and resistance to drug-induced apoptosis in fibrolamellar carcinoma ]]> https://biorxiv.org/content/10.1101/2023.06.28.546958v1?rss=1 Lauer, S. M.-L. Omar, M. H. Golkowski, M. G. Kenerson, H. L. Pascual, B. C. Forbush, K. Smith, F. D. Gordan, J. Ong, S.-E. M. Yeung, R. S. Scott, J. D. 2023-06-28 doi:10.1101/2023.06.28.546958 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ Combinatorial transcription factor binding encodes cis-regulatory wiring of forebrain GABAergic neurogenesis ]]> https://biorxiv.org/content/10.1101/2023.06.28.546894v1?rss=1 Catta-Preta, R. Lindtner, S. Ypsilanti, A. Price, J. Abnousi, A. Su-Feher, L. Wang, Y. Juric, I. Jones, I. Akiyama, J. Hu, M. Shen, Y. Visel, A. Pennacchio, L. Dickel, D. Rubenstein, J. Nord, A. 2023-06-29 doi:10.1101/2023.06.28.546894 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ Discovery of New Broad-Spectrum Anti-Infectives for Eukaryotic Pathogens Using Bioorganometallic Chemistry ]]> https://biorxiv.org/content/10.1101/2023.06.28.546819v1?rss=1 Lin, Y. Jung, H. Bulman, C. A. Ng, J. Vinck, R. O'Beirne, C. Moser, M. S. Tricoche, N. Peguero, R. Li, R. W. Urban, J. F. Le Pape, P. Pagniez, F. Moretto, M. Weil, T. Lustigman, S. Cariou, K. Mitreva, M. Sakanari, J. Gasser, G. 2023-06-30 doi:10.1101/2023.06.28.546819 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Differential susceptibility of male and female germ cells to glucocorticoid-mediated signaling ]]> https://biorxiv.org/content/10.1101/2023.06.30.547215v1?rss=1 Cincotta, S. A. Richardson, N. Foecke, M. H. Laird, D. J. 2023-07-01 doi:10.1101/2023.06.30.547215 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ Single Cell Multi-Omics of an iPSC Model of Human Sinoatrial Node Development Reveals Genetic Determinants of Heart Rate and Arrhythmia Susceptibility ]]> https://biorxiv.org/content/10.1101/2023.07.01.547335v1?rss=1 Engel, J. L. Zhang, X. Lu, D. R. Vila, O. F. Arias, V. Lee, J. Hale, C. Hsu, Y.-H. Li, C.-M. K. Vedantham, V. Ang, Y.-S. 2023-07-01 doi:10.1101/2023.07.01.547335 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ Configurational entropy is an intrinsic driver of tissue structural heterogeneity ]]> https://biorxiv.org/content/10.1101/2023.07.01.546933v1?rss=1 Srivastava, V. Hu, J. L. Garbe, J. C. Veytsman, B. Shalabi, S. F. Yllanes, D. Thomson, M. LaBarge, M. A. Huber, G. Gartner, Z. J. 2023-07-02 doi:10.1101/2023.07.01.546933 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ VTA dopamine neurons drive spatiotemporally heterogeneous striatal dopamine signals during learning ]]> https://biorxiv.org/content/10.1101/2023.07.01.547331v1?rss=1 Engel, L. Wolff, A. R. Blake, M. Collins, V. L. Sinha, S. Saunders, B. T. 2023-07-02 doi:10.1101/2023.07.01.547331 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Chemical alkylation of Asp12 enables mutant selective targeting of K-Ras(G12D) ]]> https://biorxiv.org/content/10.1101/2023.07.01.547359v1?rss=1 Zhang, Z. Zheng, Q. Guiley, K. Z. Shokat, K. 2023-07-02 doi:10.1101/2023.07.01.547359 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Inference for entomological semi-field experiments: Fitting a mathematical model assessing personal and community protection of vector-control interventions ]]> https://biorxiv.org/content/10.1101/2023.06.30.547223v1?rss=1 Fairbanks, E. L. Saeung, M. Pongsiri, A. Vajda, E. Wang, Y. McIver, D. J. Tatarsky, A. Lobo, N. F. Moore, S. J. Ponlawat, A. Chareonviriyaphap, T. Ross, A. Chitnis, N. 2023-07-03 doi:10.1101/2023.06.30.547223 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[ Solute Transport in Engineered Living Materials using Bone Inspired Microscale Channel Networks ]]> https://biorxiv.org/content/10.1101/2023.07.03.547434v1?rss=1 van Wijngaarden, E. W. Bratcher, S. Lewis, K. J. Hernandez, C. J. 2023-07-03 doi:10.1101/2023.07.03.547434 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Activity-Induced MeCP2 Phosphorylation Regulates Retinogeniculate Synapse Refinement ]]> https://biorxiv.org/content/10.1101/2023.07.03.547549v1?rss=1 Tzeng, C. P. Whitwam, T. Boxer, L. D. Li, E. Silberfeld, A. Trowbridge, S. Mei, K. Lin, C. Shamah, R. Griffith, E. C. Renthal, W. Chen, C. Greenberg, M. E. 2023-07-03 doi:10.1101/2023.07.03.547549 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Cryo-EM structure of TMEM63C suggests it functions as a monomer ]]> https://biorxiv.org/content/10.1101/2023.07.04.547736v1?rss=1 Qin, Y. Yu, D. Wu, D. Dong, J. Li, W. T. Ye, C. Cheung, K. C. Zhang, Y. Xu, Y. Wang, Y. Shi, Y. S. Dang, S. 2023-07-04 doi:10.1101/2023.07.04.547736 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ Recyclable CRISPR/Cas9 mediated gene disruption and deletions in Histoplasma ]]> https://biorxiv.org/content/10.1101/2023.07.05.547774v1?rss=1 Joehnk, B. Ali, N. Voorhies, M. Walcott, K. Sil, A. 2023-07-05 doi:10.1101/2023.07.05.547774 Cold Spring Harbor Laboratory Press 2023-07-05 <![CDATA[ SARS-CoV-2 Nsp1 regulates translation start site fidelity to promote infection ]]> https://biorxiv.org/content/10.1101/2023.07.05.547902v1?rss=1 Aviner, R. Lidsky, P. V. Xiao, Y. Tasseto, M. Zhang, L. McAlpine, P. L. Elias, J. Frydman, J. Andino, R. 2023-07-07 doi:10.1101/2023.07.05.547902 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Mapping general anesthesia states based on electro-encephalogram transition phases ]]> https://biorxiv.org/content/10.1101/2023.07.06.547567v1?rss=1 Loison, V. Voskobiynyk, Y. Lindquist, B. Necula, D. Longrois, D. Paz, J. T. Holcman, D. 2023-07-07 doi:10.1101/2023.07.06.547567 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ A meta-analysis of mouse models of tauopathy reveals the cellular underpinnings of selective regional vulnerability ]]> https://biorxiv.org/content/10.1101/2023.07.06.548027v1?rss=1 Torok, J. Maia, P. Anand, C. Raj, A. 2023-07-07 doi:10.1101/2023.07.06.548027 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Using Published Pathway Figures in Enrichment Analysis and Machine Learning ]]> https://biorxiv.org/content/10.1101/2023.07.06.548037v1?rss=1 SHIN, M.-G. Pico, A. 2023-07-07 doi:10.1101/2023.07.06.548037 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Tetracycline transactivator overexpression in keratinocytes triggers a TRPV1 primary sensory neuron-dependent neuropathic itch ]]> https://biorxiv.org/content/10.1101/2023.07.09.548214v1?rss=1 Crowther, A. Kashem, S. Jewell, M. E. Chang, H. L. Casillas, M. R. Midavaine, E. Rodriguez, S. Braz, J. Kania, A. Basbaum, A. 2023-07-10 doi:10.1101/2023.07.09.548214 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ NOTCH3 drives meningioma tumorigenesis and resistance to radiotherapy ]]> https://biorxiv.org/content/10.1101/2023.07.10.548456v1?rss=1 Choudhury, A. Cady, M. A. Lucas, C.-H. G. Najem, H. Phillips, J. J. Palikuqi, B. Zakimi, N. Joseph, T. Birreuta, J. O. Chen, W. C. Bush, N. A. O. Hervey-Jumper, S. L. Klein, O. D. Toedebusch, C. M. Horbinski, C. M. Magill, S. T. Bhaduri, A. Perry, A. Dickinson, P. J. Heimberger, A. B. Ashworth, A. Crouch, E. E. Raleigh, D. R. 2023-07-11 doi:10.1101/2023.07.10.548456 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Resolving Non-identifiability Mitigates Bias in Models of Neural Tuning and Functional Coupling ]]> https://biorxiv.org/content/10.1101/2023.07.11.548615v1?rss=1 Sachdeva, P. Bak, J. H. Livezey, J. A. Frank, L. Kirst, C. Bhattacharyya, S. Bouchard, K. 2023-07-12 doi:10.1101/2023.07.11.548615 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ High throughput PRIME editing screens identify functional DNA variants in the human genome ]]> https://biorxiv.org/content/10.1101/2023.07.12.548736v1?rss=1 Ren, X. Yang, H. Nierenberg, J. L. Sun, Y. Chen, J. Beaman, C. Pham, T. Nobuhara, M. Takagi, M. A. Narayan, V. Li, Y. Ziv, E. Shen, Y. 2023-07-12 doi:10.1101/2023.07.12.548736 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ The h-current controls cortical recurrent network activity through modulation of dendrosomatic communication ]]> https://biorxiv.org/content/10.1101/2023.07.12.548753v1?rss=1 McCormick, D. A. Shu, Y. Hasenstaub, A. R. 2023-07-12 doi:10.1101/2023.07.12.548753 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ Radial glia control microglial differentiation via integrin avb8-dependent trans-activation of TGFB1 ]]> https://biorxiv.org/content/10.1101/2023.07.13.548459v1?rss=1 McKinsey, G. L. Santander, N. Zhang, X. Kleemann, K. Katewa, A. Tran, L. Conant, K. Barraza, M. Lizama, C. O. Koo, H. J. Lee, H. Mukherjee, D. Paidassi, H. Anton, E. S. Atabai, K. Sheppard, D. Butovsky, O. Arnold, T. D. 2023-07-13 doi:10.1101/2023.07.13.548459 Cold Spring Harbor Laboratory Press 2023-07-13 <![CDATA[ Validation of human telomere length trans-ancestry meta-analysis association signals identifies POP5 and KBTBD6 as novel human telomere length regulation genes ]]> https://biorxiv.org/content/10.1101/2023.07.12.548702v1?rss=1 Keener, R. Chhetri, S. B. Connelly, C. J. Taub, M. A. Conomos, M. P. Weinstock, J. S. Ni, B. Strober, B. J. Aslibekyan, S. Auer, P. L. Barwick, L. Becker, L. C. Blangero, J. Bleecker, E. R. Brody, J. A. Cade, B. E. Celedon, J. C. Chang, Y.-C. Cupples, L. A. Custer, B. Freedman, B. I. Gladwin, M. T. Heckbert, S. R. Hou, L. Irvin, M. R. Isasi, C. R. Johnsen, J. M. Kenny, E. E. Kooperberg, C. Minster, R. L. Nekhai, S. Pankratz, N. Peyser, P. A. Rotter, J. I. Taylor, K. D. Telen, M. J. Wu, B. Yanek, L. R. Yang, I. V. Albert, C. Arnett, D. K. Ashley-Koch, A. 2023-07-14 doi:10.1101/2023.07.12.548702 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ Monitoring integrated stress response in live Drosophila ]]> https://biorxiv.org/content/10.1101/2023.07.13.548942v1?rss=1 Lidsky, P. V. Yuan, J. Lashkevich, K. A. Dmitriev, S. E. Andino, R. 2023-07-14 doi:10.1101/2023.07.13.548942 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ Tissue tension permits β-catenin phosphorylation to drive mesoderm specification in human embryonic stem cells. ]]> https://biorxiv.org/content/10.1101/2023.07.14.549074v1?rss=1 Ayad, N. M. E. Lakins, J. N. Ghagre, A. Ehrlicher, A. J. Weaver, V. M. 2023-07-15 doi:10.1101/2023.07.14.549074 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ Distinct senescence mechanisms restrain progression of dysplastic nevi ]]> https://biorxiv.org/content/10.1101/2023.07.14.548818v1?rss=1 Lorbeer, F. K. Rieser, G. Goel, A. Wang, M. Oh, A. Yeh, I. Bastian, B. C. Hockemeyer, D. 2023-07-16 doi:10.1101/2023.07.14.548818 Cold Spring Harbor Laboratory Press 2023-07-16 <![CDATA[ Simultaneous multi-site editing of individual genomes using retron arrays ]]> https://biorxiv.org/content/10.1101/2023.07.17.549397v1?rss=1 Gonzalez-Delgado, A. Lopez, S. C. Rojas-Montero, M. Fishman, C. B. Shipman, S. L. 2023-07-17 doi:10.1101/2023.07.17.549397 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ Interaction with the membrane-anchored protein CHIC2 constrains the ubiquitin ligase activity of CHIP ]]> https://biorxiv.org/content/10.1101/2023.07.17.549407v1?rss=1 Callahan, M. D. Hodul, M. Carroll, E. C. Ravalin, M. Nadel, C. M. de Silva, A. R. Cupo, A. R. McDermott, L. E. Nix, J. C. Page, R. C. Kao, A. W. Gestwicki, J. E. 2023-07-17 doi:10.1101/2023.07.17.549407 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ Sexually dimorphic differences in angiogenesis markers predict brain aging trajectories ]]> https://biorxiv.org/content/10.1101/2023.07.16.549192v1?rss=1 Torres-Espin, A. Rabadaugh, H. Fitzsimons, S. Chou, A. Harvey, D. Lindberg, C. Goldberger, L. Casaletto, K. B. Staffaroni, A. Maillard, P. Miller, B. L. Hinman, J. D. DeCarli, C. Ferguson, A. R. Kramer, J. Elahi, F. M. 2023-07-18 doi:10.1101/2023.07.16.549192 Cold Spring Harbor Laboratory Press 2023-07-18 <![CDATA[ C9orf72 gene networks in the human brain correlate with cortical thickness in C9-FTD and implicate vulnerable cell types ]]> https://biorxiv.org/content/10.1101/2023.07.17.549377v1?rss=1 Broce, I. Sirkis, D. Nillo, R. M. Bonham, L. W. Lee, S. E. Miller, B. L. Sturm, V. Sugrue, L. S. Desikan, R. Yokoyama, J. S. 2023-07-19 doi:10.1101/2023.07.17.549377 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ High-throughput complement component 4 genomic sequence analysis with C4Investigator ]]> https://biorxiv.org/content/10.1101/2023.07.18.549551v1?rss=1 Marin, W. M. Augusto, D. G. Wade, K. J. Hollenbach, J. A. 2023-07-19 doi:10.1101/2023.07.18.549551 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Genome editing induces the transfer of mitochondrial DNA into the nuclear genome ]]> https://biorxiv.org/content/10.1101/2023.07.19.549443v1?rss=1 Wu, J. Liu, Y. Ou, L. Gan, T. Zhangding, Z. Yuan, S. Liu, M. Liu, X. Li, J. Yin, J. Xin, C. Tian, Y. Hu, J. 2023-07-20 doi:10.1101/2023.07.19.549443 Cold Spring Harbor Laboratory Press 2023-07-20 <![CDATA[ Genetic complexity alters drug susceptibility of asexual and gametocyte stages of Plasmodium falciparum to antimalarial candidates ]]> https://biorxiv.org/content/10.1101/2023.07.20.549807v1?rss=1 Greyling, N. van der Watt, M. Gwarinda, H. van Heerden, A. Greenhouse, B. Leroy, D. Niemand, J. Birkholtz, L.-M. 2023-07-21 doi:10.1101/2023.07.20.549807 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ Structure of a tripartite protein complex that targets toxins to the type VII secretion system ]]> https://biorxiv.org/content/10.1101/2023.07.21.550046v1?rss=1 Klein, T. A. Shah, P. Y. Gkragkopoulou, P. Grebenc, D. W. Kim, Y. Whitney, J. C. 2023-07-21 doi:10.1101/2023.07.21.550046 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ APOE4/4 is linked to damaging lipid droplets in Alzheimer's microglia ]]> https://biorxiv.org/content/10.1101/2023.07.21.549930v1?rss=1 Haney, M. Palovics, R. Munson, C. Long, C. Johansson, P. Yip, O. Dong, W. Rawat, E. West, E. Schlachetzki, J. Tsai, A. P.-Y. Guldner, I. Lamichhane, B. Smith, A. Schaum, N. Calcuttawala, K. Shin, A. Wang, Y.-H. Wang, C. Koutsodendris, N. Serrano, G. E. Beach, T. Reiman, E. M. Glass, C. Abu-Remaileh, M. M. Enejder, A. Huang, Y. Wyss-Coray, T. 2023-07-25 doi:10.1101/2023.07.21.549930 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Early-life stress triggers long-lasting organismal resilience and longevity via tetraspanin ]]> https://biorxiv.org/content/10.1101/2023.07.25.550452v1?rss=1 Jiang, W. I. Belly, H. D. Wang, B. K. Wong, A. Kim, M. Oh, F. DeGeorge, J. Huang, X. Guang, S. Weiner, O. K. Ma, D. K. 2023-07-25 doi:10.1101/2023.07.25.550452 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Direct reprogramming of oral epithelial progenitor cells to cancer stem cells at single cell resolution in vivo ]]> https://biorxiv.org/content/10.1101/2023.07.24.550427v1?rss=1 Faraji, F. Ramirez, S. I. Clubb, L. Sato, K. Anguiano Quiroz, P. Y. Galloway, W. M. Mikulski, Z. Hoang, T. S. Medetgul-Ernar, K. Marangoni, P. Jones, K. B. Officer, A. Molinolo, A. A. Kim, K. Sakaguchi, K. Califano, J. A. Smith, Q. Klein, O. D. Tamayo, P. Gutkind, J. S. 2023-07-26 doi:10.1101/2023.07.24.550427 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Human Plasma Proteomic Profile of Clonal Hematopoiesis ]]> https://biorxiv.org/content/10.1101/2023.07.25.550557v1?rss=1 Yu, Z. Vromman, A. Nguyen, N. Q. H. Vellarikkal, S. K. Uddin, M. M. Niroula, A. Griffin, G. Honigberg, M. C. Lin, A. E. Gibson, C. J. Katz, D. H. Tahir, U. Haidermota, S. Ganesh, S. Antoine, T. Weinstock, J. Austin, T. R. Vasan, R. S. peloso, G. M. Hornsby, W. Ganz, P. Manson, J. E. Haring, B. Kooperberg, C. L. Reiner, A. P. Bis, J. C. Psaty, B. M. Min, Y.-I. Correa, A. Lange, L. A. Post, W. Rotter, J. I. Rich, S. S. Wilson, J. G. Ebert, B. L. Yu, B. Ballantyne, C. M. Coresh, J. Sankaran, V. G. Bick, A. G. Jaiswal, S. Libby, P. Gerszten, R. E. NHLBI T 2023-07-27 doi:10.1101/2023.07.25.550557 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Site-specific proximity labeling at single residue resolution for identification of protein partners in vitro and on cells ]]> https://biorxiv.org/content/10.1101/2023.07.27.550738v1?rss=1 Bartholow, T. G. Burroughs, P. Elledge, S. K. Byrnes, J. R. Kirkemo, L. L. Garda, V. Leung, K. K. Wells, J. A. 2023-07-27 doi:10.1101/2023.07.27.550738 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Ribosome subunit attrition and activation of the p53-MDM4 axis dominate the response of MLL-rearranged cancer cells to WDR5 WIN site inhibition ]]> https://biorxiv.org/content/10.1101/2023.07.26.550648v1?rss=1 Howard, G. C. Wang, J. Rose, K. L. Patel, P. Tsui, T. Florian, A. C. Lorey, S. L. Grieb, B. C. Smith, B. N. Slota, M. J. Reynolds, E. M. Goswami, S. Savona, M. R. Lee, T. Fesik, S. W. Liu, Q. Tansey, W. P. 2023-07-29 doi:10.1101/2023.07.26.550648 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ Distinct human stem cell subpopulations drive adipogenesis and fibrosis in musculoskeletal injury ]]> https://biorxiv.org/content/10.1101/2023.07.28.551038v1?rss=1 Garcia, S. M. Diaz, A. Lau, J. Chi, H. M. Lizarraga, M. Davies, M. R. Liu, X. Feeley, B. T. 2023-07-29 doi:10.1101/2023.07.28.551038 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ Computational prediction of protein interactions on single cells by proximity sequencing ]]> https://biorxiv.org/content/10.1101/2023.07.27.550388v1?rss=1 Xia, J. Phan, H. V. Vistain, L. Chen, M. Khan, A. A. Tay, S. 2023-07-30 doi:10.1101/2023.07.27.550388 Cold Spring Harbor Laboratory Press 2023-07-30 <![CDATA[ Conserved long noncoding RNA TILAM promotes liver fibrosis through interaction with PML in hepatic stellate cells ]]> https://biorxiv.org/content/10.1101/2023.07.29.551032v1?rss=1 Sun, C. Zhou, C. Daneshvar, K. Kratkiewicz, A. J. Ben Saad, A. Hess, A. Chen, J. Y. Pondick, J. V. York, S. R. Li, W. Moran, S. P. Gentile, S. Ur Rahman, R. Li, Z. Sparks, R. Habboub, T. Kim, B.-M. Choi, M. Affo, S. Schwabe, R. F. Popov, Y. V. Mullen, A. C. 2023-07-30 doi:10.1101/2023.07.29.551032 Cold Spring Harbor Laboratory Press 2023-07-30 <![CDATA[ EZH2 inhibition sensitizes IDH1R132H mutant gliomas to histone deacetylase inhibitor. ]]> https://biorxiv.org/content/10.1101/2023.07.31.551045v1?rss=1 Sprinzen, L. Garcia, F. G. Mela, A. Lei, L. Upadhyayula, P. Mahajan, A. Humala, N. Manier, L. Caprioli, R. M. Quinones-Hinojosa, A. Casaccia, P. Canoll, P. 2023-08-02 doi:10.1101/2023.07.31.551045 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila ]]> https://biorxiv.org/content/10.1101/2023.08.03.551750v1?rss=1 Steinbach, A. M. Bhadkamkar, V. L. Jimenez-Morales, D. Stevenson, E. Jang, G. M. Krogan, N. J. Swaney, D. L. Mukherjee, S. 2023-08-03 doi:10.1101/2023.08.03.551750 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ Ciliary ARL13B prevents obesity in mice ]]> https://biorxiv.org/content/10.1101/2023.08.02.551695v1?rss=1 Terry, T. T. Gigante, E. D. Alexandre, C. M. Brewer, K. M. Engle, S. E. Yue, X. Berbari, N. F. Vaisse, C. Caspary, T. 2023-08-04 doi:10.1101/2023.08.02.551695 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ Cell growth and nutrient availability control the mitotic exit signaling network in budding yeast ]]> https://biorxiv.org/content/10.1101/2023.08.04.552008v1?rss=1 Talavera, R. A. Prichard, B. E. Sommer, R. A. Leitao, R. M. Sarabia, C. J. Hazir, S. Paulo, J. A. Gygi, S. Kellogg, D. 2023-08-04 doi:10.1101/2023.08.04.552008 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ Using human genetics to develop strategies to increase erythropoietic output from genome-edited hematopoietic stem and progenitor cells ]]> https://biorxiv.org/content/10.1101/2023.08.04.552064v1?rss=1 Camarena, J. Luna, S. E. Hampton, J. P. Majeti, K. R. Charlesworth, C. T. Soupene, E. Sheehan, V. A. Cromer, M. K. Porteus, M. H. 2023-08-04 doi:10.1101/2023.08.04.552064 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ Sulfolobus acidocaldarius adhesion pili power twitching motility in the absence of a dedicated retraction ATPase ]]> https://biorxiv.org/content/10.1101/2023.08.04.552066v1?rss=1 Charles-Orszag, A. van Wolferen, M. Lord, S. J. Albers, S.-V. Mullins, D. 2023-08-04 doi:10.1101/2023.08.04.552066 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ A fibroblast-derived TGFβ/sFRP2 noncanonical Wnt signaling axis underlies epithelial metaplasia in idiopathic pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/2023.08.02.551383v1?rss=1 Cohen, M. L. Brumwell, A. N. Ho, T. C. Montas, G. Golden, J. A. Jones, K. D. Wolters, P. J. Wei, Y. Chapman, H. A. Le Saux, C. J. 2023-08-05 doi:10.1101/2023.08.02.551383 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ Improving rigor and reproducibility in western blot experiments with the blotRig analysis software ]]> https://biorxiv.org/content/10.1101/2023.08.02.551674v1?rss=1 Omondi, C. Chou, A. Fond, K. A. Morioka, K. Joseph, N. R. Sacramento, J. A. Lorio, E. Torres-Espin, A. Radabaugh, H. L. Davis, J. A. Gumbel, J. H. Huie, J. R. Ferguson, A. R. 2023-08-05 doi:10.1101/2023.08.02.551674 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ A semi-automated method for quantifying optokinetic reflex tracking acuity ]]> https://biorxiv.org/content/10.1101/2023.08.03.551461v1?rss=1 Kiraly, J. K. Harris, S. C. Al-Khindi, T. Dunn, F. Kolodkin, A. L. 2023-08-06 doi:10.1101/2023.08.03.551461 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ Glioma-neuronal circuit remodeling induces regional immunosuppression ]]> https://biorxiv.org/content/10.1101/2023.08.04.548295v1?rss=1 Nejo, T. Krishna, S. Jimenez, C. Yamamichi, A. Young, J. S. Lakshmanachetty, S. Chen, T. Phyu, S. S. S. Ogino, H. Watchmaker, P. Diebold, D. Choudhury, A. Daniel, A. G. S. Raleigh, D. R. Hervey-Jumper, S. L. Okada, H. 2023-08-06 doi:10.1101/2023.08.04.548295 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ BAC Transgenic Expression of Human TREM2-R47H Remodels Amyloid Plaques but Unable to Reprogram Plaque-associated Microglial Reactivity in 5xFAD Mice ]]> https://biorxiv.org/content/10.1101/2023.08.03.551881v1?rss=1 Lee, C. Y. D. De La Rocha, A. J. Inouye, K. Langfelder, P. Daggett, A. Gu, X. Jiang, L.-L. Pamonag, Z. Vaca, R. G. Richman, J. Kawaguchi, R. Gao, F. Xu, H. Yang, X. W. 2023-08-07 doi:10.1101/2023.08.03.551881 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Limitations of fluorescent timer proteins toward isolation of developmentally and transcriptionally synchronized populations of human pluripotent stem cells and neural progenitors highlight unique expression and fluorescence maturation kinetics by human cells ]]> https://biorxiv.org/content/10.1101/2023.08.04.552012v1?rss=1 Peter, M. Shipman, S. Macklis, J. D. 2023-08-07 doi:10.1101/2023.08.04.552012 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Epigenetic neural glioblastoma enhances synaptic integration and predicts therapeutic vulnerability ]]> https://biorxiv.org/content/10.1101/2023.08.04.552017v1?rss=1 Drexler, R. Khatri, R. Sauvigny, T. Mohme, M. Maire, C. Ryba, A. Zghaibeh, Y. Duhrsen, L. Salviano-Silva, A. Lamszus, K. Westphal, M. Gempt, J. Wefers, A. K. Neumann, J. Bode, H. Hausmann, F. Huber, T. B. Bonn, S. Jutten, K. Delev, D. Weber, K. J. Harter, P. N. Onken, J. Vajkoczy, P. Capper, D. Wiestler, B. Weller, M. Snijder, B. Buck, A. Weiss, T. Keough, M. B. Ni, L. Monje, M. Silverbush, D. Hovestadt, V. Suva, M. L. Krishna, S. Hervey-Jumper, S. Schueller, U. Heiland, H. D. Haenzelmann, S. Ricklefs, F. L. 2023-08-07 doi:10.1101/2023.08.04.552017 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Two distinct mechanisms of Plexin A function in Drosophila optic lobe lamination and morphogenesis ]]> https://biorxiv.org/content/10.1101/2023.08.07.552282v1?rss=1 Bustillo, M. E. Douthit, J. Astigarraga, S. Treisman, J. E. 2023-08-07 doi:10.1101/2023.08.07.552282 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ The actin binding protein profilin 1 is critical for mitochondria function ]]> https://biorxiv.org/content/10.1101/2023.08.07.552354v1?rss=1 Read, T.-A. Cisterna, B. A. Skruber, K. Ahmadieh, S. Lindamood, H. L. Vitriol, J. Shi, Y. Lefebvre, A. E. Y. T. Black, J. B. Butler, M. T. Bear, J. E. Cherezova, A. Ilatovskaya, D. V. Weintraub, N. L. Vitriol, E. A. 2023-08-07 doi:10.1101/2023.08.07.552354 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Adaptor Protein-3 Produces Synaptic Vesicles that Release Phasic Dopamine ]]> https://biorxiv.org/content/10.1101/2023.08.07.552338v1?rss=1 Jain, S. Yee, A. G. Maas, J. Gierok, S. Xu, H. Stansil, J. Eriksen, J. Nelson, A. Silm, K. Ford, C. P. Edwards, R. H. 2023-08-08 doi:10.1101/2023.08.07.552338 Cold Spring Harbor Laboratory Press 2023-08-08 <![CDATA[ Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina. ]]> https://biorxiv.org/content/10.1101/2023.08.08.552451v1?rss=1 Lyu, P. Iribarne, M. Serjanov, D. Zhai, Y. Hoang, T. Campbell, L. Boyd, P. Palazzo, I. Nagashima, M. Silva, N. J. Hitchcock, P. Qian, J. Hyde, D. Blackshaw, S. 2023-08-08 doi:10.1101/2023.08.08.552451 Cold Spring Harbor Laboratory Press 2023-08-08 <![CDATA[ Environmental challenge rewires functional connections among human genes ]]> https://biorxiv.org/content/10.1101/2023.08.09.552346v1?rss=1 Herken, B. W. Wong, G. Norman, T. Gilbert, L. 2023-08-09 doi:10.1101/2023.08.09.552346 Cold Spring Harbor Laboratory Press 2023-08-09 <![CDATA[ Microbiome single cell atlases generated with a commercial instrument ]]> https://biorxiv.org/content/10.1101/2023.08.08.551713v1?rss=1 Li, X. Xu, L. Demaree, B. Noecker, C. Bisanz, J. E. Weisgerber, D. W. Modavi, C. Turnbaugh, P. J. Abate, A. R. 2023-08-10 doi:10.1101/2023.08.08.551713 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ Plasma Glycomic Markers of Accelerated Biological Aging During Chronic HIV Infection ]]> https://biorxiv.org/content/10.1101/2023.08.09.551369v1?rss=1 Giron, L. B. Liu, Q. Adeniji, O. S. Yin, X. Kannan, T. Ding, J. Lu, D. Y. Langan, S. Zhang, J. Azevedo, J. L. L. C. Hanna, D. B. Ofotokun, I. Lazar, J. Fischl, M. A. Haberlen, S. Macatangay, B. Adimora, A. A. Jamieson, B. D. Rinaldo, C. Merenstein, D. Roan, N. R. Kutsch, O. Gange, S. Wolinsky, S. Witt, M. Post, W. S. Kossenkov, A. Landay, A. Frank, I. Tien, P. C. Gross, R. Brown, T. T. Mohsen, M. A. 2023-08-10 doi:10.1101/2023.08.09.551369 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ Interferon response and epigenetic modulation by SMARCA4 mutations drive ovarian tumor immunogenicity ]]> https://biorxiv.org/content/10.1101/2023.08.08.552544v1?rss=1 Brodeur, M. N. Dopeso, H. Zhu, Y. Longhini, A. L. F. Gazzo, A. Sun, S. Koche, R. Qu, R. Hamard, P.-J. Bykov, Y. Green, H. Chiappinelli, K. B. Ozsoy, M. A. Basili, T. Gardner, R. Walderich, S. De Stanchina, E. Greenbaum, B. D. Gonen, M. Weigelt, B. Zamarin, D. 2023-08-12 doi:10.1101/2023.08.08.552544 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates ]]> https://biorxiv.org/content/10.1101/2023.08.08.552553v1?rss=1 Yee, S. W. Ferrandez-Peral, L. Alentorn, P. Fontsere, C. Ceylan, M. Koleske, M. L. Handin, N. Artegoitia, V. M. Lara, G. Chien, H.-C. Zhou, X. Dainat, J. Zalevsky, A. Sali, A. Brand, C. M. Capra, J. A. Artursson, P. Newman, J. W. Marques-Bonet, T. Giacomini, K. M. 2023-08-12 doi:10.1101/2023.08.08.552553 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ PRDM16 co-operates with LHX2 to shape the human brain ]]> https://biorxiv.org/content/10.1101/2023.08.12.553065v1?rss=1 Suresh, V. Bhattacharya, B. Tshuva, R. Y. Danan Gotthold, M. Olender, T. Bose, M. Ben Zeev, B. Smith, R. S. Pradhan, S. J. Tole, S. Galande, S. Harwell, C. Baizabal, M. Reiner, O. 2023-08-12 doi:10.1101/2023.08.12.553065 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ Flexible regulation of representations on a drifting manifold enables long-term stable complex neuroprosthetic control ]]> https://biorxiv.org/content/10.1101/2023.08.11.551770v1?rss=1 NATRAJ, N. Seko, S. Abiri, R. Yan, H. Graham, Y. Tu-Chan, A. Chang, E. F. Ganguly, K. 2023-08-14 doi:10.1101/2023.08.11.551770 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Characterization of enhancer activity in early human neurodevelopment using Massively parallel reporter assay (MPRA) and forebrain organoids ]]> https://biorxiv.org/content/10.1101/2023.08.14.553170v1?rss=1 Capauto, D. Wang, Y. Wu, F. Norton, S. Mariani, J. Inoue, F. Crawford, G. E. Ahituv, N. Abyzov, A. Vaccarino, F. M. 2023-08-14 doi:10.1101/2023.08.14.553170 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Addressing biases in gene-set enrichment analysis: a case study of Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2023.08.13.553133v1?rss=1 Bakulin, A. Teyssier, N. B. Kampmann, M. Khoroshkin, M. Goodarzi, H. 2023-08-15 doi:10.1101/2023.08.13.553133 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Phosphorylation of a Cleaved Tau Proteoform at a Single Residue Inhibits Binding to the E3 Ubiquitin Ligase, CHIP ]]> https://biorxiv.org/content/10.1101/2023.08.16.553575v1?rss=1 Nadel, C. M. Wucherer, K. Oehler, A. Thwin, A. C. Basu, K. Callahan, M. D. Southworth, D. R. Mordes, D. A. Craik, C. S. Gestwicki, J. E. 2023-08-16 doi:10.1101/2023.08.16.553575 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ Assembly of SARS-CoV-2 ribonucleosomes by truncated N* variant of the nucleocapsid protein ]]> https://biorxiv.org/content/10.1101/2023.08.16.553581v1?rss=1 Adly, A. Bi, M. Carlson, C. Syed, A. M. Ciling, A. Doudna, J. Cheng, Y. Morgan, D. O. 2023-08-17 doi:10.1101/2023.08.16.553581 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ A Hybrid Transistor with Transcriptionally Controlled Computation and Plasticity ]]> https://biorxiv.org/content/10.1101/2023.08.16.553547v1?rss=1 Gao, Y. Zhou, Y. Ji, X. Graham, A. J. Dundas, C. M. Mahfoud, I. E. M. Tibbett, B. M. Tan, B. Partipilo, G. Dodabalapur, A. Rivnay, J. Keitz, B. K. 2023-08-18 doi:10.1101/2023.08.16.553547 Cold Spring Harbor Laboratory Press 2023-08-18 <![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[ Autophagy counters inflammation-driven glycolytic impairment in aging hematopoietic stem cells ]]> https://biorxiv.org/content/10.1101/2023.08.17.553736v1?rss=1 Dellorusso, P. V. Proven, M. A. Calero-Nieto, F. J. Wang, X. Mitchell, C. A. Hartmann, F. Amouzgar, M. Favaro, P. DeVilbiss, A. W. Swann, J. W. Ho, T. T. Zhao, Z. W. Bendall, S. C. Morrison, S. J. Gottgens, B. Passegue, E. 2023-08-19 doi:10.1101/2023.08.17.553736 Cold Spring Harbor Laboratory Press 2023-08-19 <![CDATA[ Consensus prediction of cell type labels with popV ]]> https://biorxiv.org/content/10.1101/2023.08.18.553912v1?rss=1 Ergen, C. Xing, G. Xu, C. Jayasuriya, M. McGeever, E. Pisco, A. O. Streets, A. M. Yosef, N. 2023-08-21 doi:10.1101/2023.08.18.553912 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Designed Endocytosis-Triggering Proteins mediate Targeted Degradation and amplify signaling ]]> https://biorxiv.org/content/10.1101/2023.08.19.553321v1?rss=1 Huang, B. Abedi, M. Ahn, G. Coventry, B. Sappington, I. Wang, R. Schlichthaerle, T. Zhang, J. Z. Wang, Y. Goreshnik, I. Chiu, C. W. Chazin-Gray, A. Chan, S. Gerben, S. Murray, A. Wang, S. O'Neill, J. Yeh, R. Misquith, A. Wolf, A. Tomasovic, L. M. Piraner, D. I. Gonzalez, M. J. D. Bennett, N. R. Venkatesh, P. Ahlrichs, M. Dobbins, C. Yang, W. Wang, X. Vafeados, D. Mout, R. Shivaei, S. Cao, L. Carter, L. Stewart, L. Spangler, J. B. Bernardes, G. J. L. Roybal, K. T. Greisen, P. J. Li, X. Bertozzi, C. Baker, D. 2023-08-21 doi:10.1101/2023.08.19.553321 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Harmonic decomposition of spacetime (HADES) framework characterises the spacetime hierarchy of the DMT brain state ]]> https://biorxiv.org/content/10.1101/2023.08.20.554019v1?rss=1 Vohryzek, J. Cabral, J. Timmermann, C. Atasoy, S. Roseman, L. Nutt, D. Carhart-Harris, R. Deco, G. Kringelbach, M. L. 2023-08-21 doi:10.1101/2023.08.20.554019 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Acquired stress resilience through bacteria-to-nematode horizontal gene transfer ]]> https://biorxiv.org/content/10.1101/2023.08.20.554039v1?rss=1 Pandey, T. Kalluraya, C. Wang, B. Xu, T. Huang, X. Guang, S. Daugherty, M. D. Ma, D. K. 2023-08-21 doi:10.1101/2023.08.20.554039 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Microglia mediate contact-independent neuronal pruning via secreted Neuraminidase-3 associated with extracellular vesicles ]]> https://biorxiv.org/content/10.1101/2023.08.21.554214v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@6842a0org.highwire.dtl.DTLVardef@ee3976org.highwire.dtl.DTLVardef@1fe7ec3org.highwire.dtl.DTLVardef@1345507_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Delaveris, C. S. Wang, C. L. Riley, N. M. Kulkarni, R. U. Bertozzi, C. R. 2023-08-21 doi:10.1101/2023.08.21.554214 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Shh from mossy cells contributes to preventing NSC pool depletion after seizure-induced neurogenesis and in aging ]]> https://biorxiv.org/content/10.1101/2023.08.21.554173v1?rss=1 Noguchi, H. Arela, J. C. Ngo, T. T. Cocas, L. Pleasure, S. 2023-08-22 doi:10.1101/2023.08.21.554173 Cold Spring Harbor Laboratory Press 2023-08-22 <![CDATA[ Spatiotemporal molecular dynamics of the developing human thalamus ]]> https://biorxiv.org/content/10.1101/2023.08.21.554174v1?rss=1 Kim, C. Shin, D. Wang, A. Nowakowski, T. 2023-08-22 doi:10.1101/2023.08.21.554174 Cold Spring Harbor Laboratory Press 2023-08-22 <![CDATA[ Regulation of Lung Immune Tone by the Gut-Lung Axis via Dietary Fiber, Gut Microbiota, and Short-Chain Fatty Acids ]]> https://biorxiv.org/content/10.1101/2023.08.24.552964v1?rss=1 Maruyama, D. Liao, W.-I. Tian, X. Bredon, M. Knapp, J. Doan, T. Tat, C. Chassaing, B. Bhargava, A. Sokol, H. Prakash, A. 2023-08-25 doi:10.1101/2023.08.24.552964 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ Rationally seeded computational protein design ]]> https://biorxiv.org/content/10.1101/2023.08.25.554789v1?rss=1 Albanese, K. I. Petrenas, R. Pirro, F. Naudin, E. A. Borucu, U. Dawson, W. M. Scott, D. A. Leggett, G. J. Weiner, O. D. Oliver, T. Woolfson, D. 2023-08-26 doi:10.1101/2023.08.25.554789 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ Control of microtubules in neuronal processes by profilin 1 and actomyosin ]]> https://biorxiv.org/content/10.1101/2023.08.25.554891v1?rss=1 Cisterna, B. A. Skruber, K. Jane, M. L. Camesi, C. I. Nguyen, I. D. Warp, P. V. Black, J. B. Butler, M. T. Bear, J. E. Read, T.-A. Vitriol, E. A. 2023-08-26 doi:10.1101/2023.08.25.554891 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ CaMKII autophosphorylation but not downstream kinase activity is required for synaptic memory ]]> https://biorxiv.org/content/10.1101/2023.08.25.554912v1?rss=1 CHEN, X. Cai, Q. zhou, j. Pleasure, S. J. Schulman, H. Zhang, M. Nicoll, R. A. 2023-08-26 doi:10.1101/2023.08.25.554912 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ Decreased accuracy of forensic DNA mixture analysis for groups with lower genetic diversity ]]> https://biorxiv.org/content/10.1101/2023.08.25.554311v1?rss=1 View larger version (51K): org.highwire.dtl.DTLVardef@157c28aorg.highwire.dtl.DTLVardef@a4ff05org.highwire.dtl.DTLVardef@62caa0org.highwire.dtl.DTLVardef@1e4ce92_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Flores, M. Ly, C. Ho, E. Ceberio, N. Felix, K. Thorner, H. M. Guardado, M. Paunovich, M. Godek, C. Kalaydjian, C. Rohlfs, R. 2023-08-27 doi:10.1101/2023.08.25.554311 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ S-Nitrosylation of CRTC1 in Alzheimer's disease impairs CREB-dependent gene expression induced by neuronal activity ]]> https://biorxiv.org/content/10.1101/2023.08.25.554320v1?rss=1 Zhang, X. Vlkolinsky, R. Wu, C. Dolatabadi, N. Scott, H. Prikhodko, O. Blanco, M. Lang, N. Pina-Crespo, J. Nakamura, T. Roberto, M. Lipton, S. A. 2023-08-27 doi:10.1101/2023.08.25.554320 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Identification of genetic drivers of plasma lipoproteins in the Diversity Outbred mouse population ]]> https://biorxiv.org/content/10.1101/2023.08.26.554969v1?rss=1 Price, T. R. Emfinger, C. H. Schueler, K. L. King, S. Nicholson, R. Beck, T. Yandell, B. S. Summers, S. Holland, W. L. Krauss, R. M. Keller, M. P. Attie, A. D. 2023-08-27 doi:10.1101/2023.08.26.554969 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Learning chemical sensitivity reveals mechanisms of cellular response ]]> https://biorxiv.org/content/10.1101/2023.08.26.554851v1?rss=1 Connell, W. J. Garcia, K. Goodarzi, H. Keiser, M. J. 2023-08-28 doi:10.1101/2023.08.26.554851 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Brain-Derived CCN3 Is An Osteoanabolic Hormone That Sustains Bone in Lactating Females ]]> https://biorxiv.org/content/10.1101/2023.08.28.554707v1?rss=1 Babey, M. E. Krause, W. C. Herber, C. B. Chen, K. Nikkannen, J. Rodriquez, R. Zhang, X. Castro-Navarro, F. Wang, Y. Villeda, S. Lance, N. E. Scheller, E. L. Chan, C. K. F. Ambrosi, T. H. Ingraham, H. A. 2023-08-28 doi:10.1101/2023.08.28.554707 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Tau fibrils induce nanoscale membrane damage and nucleate cytosolic tau at lysosomes ]]> https://biorxiv.org/content/10.1101/2023.08.28.555157v1?rss=1 Rose, K. Jepson, T. Shukla, S. Maya-Romero, A. Kampmann, M. Xu, K. Hurley, J. H. 2023-08-28 doi:10.1101/2023.08.28.555157 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Neuronal apoE4 induces early hyperexcitability in select populations of hippocampal neurons by altering Nell2 expression ]]> https://biorxiv.org/content/10.1101/2023.08.28.555153v1?rss=1 Jang, S.-S. Tabuena, D. R. Grone, B. Yip, O. Blumenfeld, J. Koutsodendris, N. Ding, L. Xu, Q. Yoon, S. Y. Huang, Y. Zilberter, M. 2023-08-29 doi:10.1101/2023.08.28.555153 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Sex differences in discrimination behavior and orbitofrontal engagement during context-gated reward prediction ]]> https://biorxiv.org/content/10.1101/2023.08.28.555217v1?rss=1 Peterson, S. Maheras, A. Wu, B. Chavira, J. Keiflin, R. 2023-08-29 doi:10.1101/2023.08.28.555217 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Functional characterization of gene regulatory elements and neuropsychiatric disease-associated risk loci in iPSCs and iPSC-derived neurons ]]> https://biorxiv.org/content/10.1101/2023.08.30.555359v1?rss=1 Yang, X. Jones, I. R. Chen, P. B. Yang, H. Ren, X. Zheng, L. Li, B. Li, Y. E. Sun, Q. Wen, J. Beaman, C. Cui, X. Li, Y. Wang, W. Hu, M. Ren, B. Shen, Y. 2023-08-30 doi:10.1101/2023.08.30.555359 Cold Spring Harbor Laboratory Press 2023-08-30 <![CDATA[ PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression ]]> https://biorxiv.org/content/10.1101/2023.08.29.555389v1?rss=1 Schmidt, C. Cohen, S. Gudenas, B. L. Husain, S. Carlson, A. Westelman, S. Wang, L. Phillips, J. J. Northcott, P. A. Weiss, W. A. Schwer, B. 2023-08-31 doi:10.1101/2023.08.29.555389 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ The small G-protein Rac1 in the dorsomedial striatum promotes alcohol-dependent structural plasticity and goal-directed learning in mice ]]> https://biorxiv.org/content/10.1101/2023.08.30.555562v1?rss=1 Hoisington, Z. W. Salvi, A. Laguesse, S. Ehinger, Y. Shukla, C. Phamluong, K. Ron, D. 2023-09-01 doi:10.1101/2023.08.30.555562 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Anionic phospholipids determine G protein coupling selectivity at distinct subcellular membrane compartments ]]> https://biorxiv.org/content/10.1101/2023.08.31.555797v1?rss=1 Hernandez, E. H. Manglik, A. Irannejad, R. 2023-09-01 doi:10.1101/2023.08.31.555797 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Dual α-globin and truncated erythropoietin receptor knock-in restores hemoglobin production in α-thalassemia major-derived hematopoietic stem and progenitor cells ]]> https://biorxiv.org/content/10.1101/2023.09.01.555926v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@1b63dacorg.highwire.dtl.DTLVardef@18b25a1org.highwire.dtl.DTLVardef@53835corg.highwire.dtl.DTLVardef@d52bf5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chu, S. N. Soupene, E. Wienert, B. Yin, H. Sharma, D. Jia, K. Homma, S. Hampton, J. P. Gardner, J. M. Conklin, B. R. MacKenzie, T. C. Porteus, M. H. Cromer, M. K. 2023-09-02 doi:10.1101/2023.09.01.555926 Cold Spring Harbor Laboratory Press 2023-09-02 <![CDATA[ In vivo perturb-seq of cancer and immune cells dissects oncologic drivers and therapy response ]]> https://biorxiv.org/content/10.1101/2023.09.01.555831v1?rss=1 Liu, S. J. Pak, J. Zou, C. Casey-Clyde, T. Borah, A. Wu, D. Seo, K. O'Loughlin, T. Lim, D. Ozawa, T. Berger, M. Weiss, W. Raleigh, D. R. Gilbert, L. A. 2023-09-03 doi:10.1101/2023.09.01.555831 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Reward expectation selectively boosts the firing of accumbens D1+ neurons during motivated approach. ]]> https://biorxiv.org/content/10.1101/2023.09.02.556060v1?rss=1 Faust, T. Mohebi, A. Berke, J. D. 2023-09-03 doi:10.1101/2023.09.02.556060 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Defining RNA oligonucleotides that reverse deleterious phase transitions of RNA-binding proteins with prion-like domains ]]> https://biorxiv.org/content/10.1101/2023.09.04.555754v1?rss=1 Guo, L. Mann, J. R. Mauna, J. C. Copley, K. E. Wang, H. Rubien, J. D. Odeh, H. M. Lin, J. Lee, B. L. Ganser, L. Robinson, E. Kim, K. M. Murthy, A. C. Paul, T. Portz, B. Gleixner, A. M. Diaz, Z. Carey, J. L. Smirnov, A. Padilla, G. Lavorando, E. Espy, C. Shang, Y. Huang, E. J. Chesi, A. Fawzi, N. L. Myong, S. Donnelly, C. J. Shorter, J. 2023-09-04 doi:10.1101/2023.09.04.555754 Cold Spring Harbor Laboratory Press 2023-09-04 <![CDATA[ RNA binding proteins and glycoRNAs form domains on the cell surface for cell penetrating peptide entry ]]> https://biorxiv.org/content/10.1101/2023.09.04.556039v1?rss=1 Perr, J. Langen, A. Almahayni, K. Nestola, G. Chai, P. Lebedenko, C. Volk, R. Caldwell, R. Spiekermann, M. Hemberger, H. Bisaria, N. Tzelepis, K. Calo, E. Mockl, L. Zaro, B. Flynn, R. A. 2023-09-05 doi:10.1101/2023.09.04.556039 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Characterizing tissue structures from spatial omics with spatial cellular graph partition ]]> https://biorxiv.org/content/10.1101/2023.09.05.556133v1?rss=1 Wu, Z. Kondo, A. McGrady, M. Baker, E. A. G. Wu, E. Rahim, M. K. Bracey, N. A. Charu, V. Cho, R. J. Cheng, J. B. Afkarian, M. Zou, J. Mayer, A. T. Trevino, A. E. 2023-09-05 doi:10.1101/2023.09.05.556133 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Causal Genetic Loci for a Motivated Behavior Spectrum Harbor Psychiatric Risk Genes ]]> https://biorxiv.org/content/10.1101/2023.09.06.556529v1?rss=1 Xu, J. Casanave, R. Chitre, A. S. Wang, Q. Nguyen, K.-M. Blake, C. Wagle, M. Cheng, R. Polesskaya, O. Palmer, A. A. Guo, S. 2023-09-06 doi:10.1101/2023.09.06.556529 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ A soybean rust effector protease suppresses host immunity and cleaves a 3-deoxy-7-phosphoheptulonate synthase ]]> https://biorxiv.org/content/10.1101/2023.09.07.556260v1?rss=1 Chicowski, A. S. Qi, M. Variz, H. Bredow, M. Montes-Serey, C. Caiazza, F. Dong, H. Margets, A. C. Mejias, J. Walley, J. Craik, C. Pedley, K. F. Aung, K. Innes, R. W. Whitham, S. 2023-09-08 doi:10.1101/2023.09.07.556260 Cold Spring Harbor Laboratory Press 2023-09-08 <![CDATA[ Endogenous Opioid Signaling Regulates Proliferation of Spinal Cord Ependymal Cells ]]> https://biorxiv.org/content/10.1101/2023.09.07.556726v1?rss=1 Yue, W. W. S. Touhara, K. K. Toma, K. Duan, X. Julius, D. 2023-09-08 doi:10.1101/2023.09.07.556726 Cold Spring Harbor Laboratory Press 2023-09-08 <![CDATA[ Clonal stochasticity in early NK cell response to mouse cytomegalovirus is generated by mature subsets of varying proliferative ability ]]> https://biorxiv.org/content/10.1101/2023.09.07.556760v1?rss=1 Wethington, D. Potempa, M. Giuliani, G. Aguilar, O. A. Grassmann, S. Stewart, W. Adams, N. M. Sun, J. C. Lanier, L. L. Das, J. 2023-09-08 doi:10.1101/2023.09.07.556760 Cold Spring Harbor Laboratory Press 2023-09-08 <![CDATA[ TRPM2-CaMKII signaling drives excessive GABAergic synaptic inhibition following ischemia ]]> https://biorxiv.org/content/10.1101/2023.09.07.556550v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@16ef5f2org.highwire.dtl.DTLVardef@1d51f19org.highwire.dtl.DTLVardef@ecc726org.highwire.dtl.DTLVardef@106cdd0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Burch, A. M. Garcia, J. D. O'Leary, H. Haas, A. Orfila, J. E. Tiemeier, E. Chalmers, N. Smith, K. R. Quillinan, N. Herson, P. S. 2023-09-09 doi:10.1101/2023.09.07.556550 Cold Spring Harbor Laboratory Press 2023-09-09 <![CDATA[ Probing the Mechanisms of Global Brain Reconfiguration after Local Manipulations ]]> https://biorxiv.org/content/10.1101/2023.09.08.556815v1?rss=1 Rabuffo, G. Lokossou, H.-A. Li, Z. Ziaee-Mehr, A. Hashemi, M. Quilichini, P. P. Ghestem, A. Arab, O. Esclapez, M. Verma, P. Raj, A. Gozzi, A. Sorrentino, P. Chuang, K.-H. Perles-Barbacaru, T.-A. Viola, A. Jirsa, V. K. Bernard, C. 2023-09-09 doi:10.1101/2023.09.08.556815 Cold Spring Harbor Laboratory Press 2023-09-09 <![CDATA[ A General Method to Accurately Count Molecular Complexes and Determine the Degree of Labelling in Cells Using Protein Tags ]]> https://biorxiv.org/content/10.1101/2023.09.08.556847v1?rss=1 Tashev, S. A. Euchner, J. Yserentant, K. Hänselmann, S. Hild, F. Chmielewicz, W. Hummert, J. Schwörer, F. Tsopoulidis, N. Germer, S. Sassmannshausen, Z. Fackler, O. T. Klingmüller, U. Herten, D.-P. 2023-09-09 doi:10.1101/2023.09.08.556847 Cold Spring Harbor Laboratory Press 2023-09-09 <![CDATA[ CCR3 inhibition suppresses inflammation-driven recruitment of peripheral immune cells to the eye ]]> https://biorxiv.org/content/10.1101/2023.09.08.556878v1?rss=1 Lopez, Y. Caryotakis, S. Raina, S. Rege, S. V. Harish, R. Ray, R. Kosti, I. Teichert, A. Minami, S. S. Dhande, O. 2023-09-09 doi:10.1101/2023.09.08.556878 Cold Spring Harbor Laboratory Press 2023-09-09 <![CDATA[ Reciprocal inflammatory signals establish profibrotic cross-feeding metabolism ]]> https://biorxiv.org/content/10.1101/2023.09.06.556606v1?rss=1 Yadav, P. Gomez Ortega, J. Chang, K.-C. Pan, S. Biswas, N. Nilsson, J. Yin, X. Bhattacharyya, A. Boostanpour, K. Tsukui, T. Sheppard, D. Li, B. Maishan, M. Taenaka, H. Matthay, M. Muramatsu, R. Naser, M. Molofsky, A. B. Wolters, P. J. Abate, A. R. Tharp, K. Bhattacharya, M. 2023-09-10 doi:10.1101/2023.09.06.556606 Cold Spring Harbor Laboratory Press 2023-09-10 <![CDATA[ Biological and Genetic Determinants of Red Blood Cell Glycolysis ]]> https://biorxiv.org/content/10.1101/2023.09.11.557250v1?rss=1 View larger version (87K): org.highwire.dtl.DTLVardef@1a556b7org.highwire.dtl.DTLVardef@1e02b13org.highwire.dtl.DTLVardef@2bfab1org.highwire.dtl.DTLVardef@15787e3_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIBlood donor age and sex affect glycolysis in stored RBCs from 13,029 volunteers; C_LIO_LIAncestry, genetic polymorphisms in PFKP, HK1, CD38/BST1 influence RBC glycolysis; C_LIO_LIModeled PFKP effects relate to preventing loss of the total AXP pool in stored RBCs; C_LIO_LIATP and hypoxanthine are biomarkers of hemolysis in vitro and in vivo. C_LI ]]> Nemkov, T. Stephenson, D. Earley, E. J. Keele, G. R. Hay, A. Erickson, C. Dzieciatkowska, M. Key, A. M. Moore, A. Stone, M. Deng, X. Kleinman, S. Spitalnik, S. L. Hod, E. A. Hansen, K. Churchill, G. A. Roubinian, N. Norris, P. J. Busch, M. P. Zimring, J. C. Page, G. P. D'Alessandro, A. 2023-09-11 doi:10.1101/2023.09.11.557250 Cold Spring Harbor Laboratory Press 2023-09-11 <![CDATA[ Structure-based discovery of CFTR potentiators and inhibitors ]]> https://biorxiv.org/content/10.1101/2023.09.09.557002v1?rss=1 Liu, F. Kaplan, A. L. Levring, J. Einsiedel, J. Tiedt, S. Distler, K. Omattage, N. Kondratov, I. S. Moroz, Y. S. Pietz, H. L. Irwin, J. J. Gmeiner, P. Shoichet, B. K. Chen, J. 2023-09-12 doi:10.1101/2023.09.09.557002 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Rab35 is required for embryonic development and kidney and ureter homeostasis through regulation of epithelial cell junctions ]]> https://biorxiv.org/content/10.1101/2023.09.11.556924v1?rss=1 Clearman, K. R. Timpratoom, N. Patel, D. Rains, A. B. Haycraft, C. J. R. Croyle, M. J. Reiter, J. F. Yoder, B. K. 2023-09-12 doi:10.1101/2023.09.11.556924 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Disease related changes in ATAC-Seq of more than 450 iPSC-derived motor neuron lines from ALS patients and controls ]]> https://biorxiv.org/content/10.1101/2023.09.11.557005v1?rss=1 Tsitkov, S. Valentine, K. Kozareva, V. Donde, A. Frank, A. Lei, S. Answer ALS Consortium, Van Eyk, J. Finkbeiner, S. Rothstein, J. Thompson, L. Sareen, D. Svendsen, C. N. Fraenkel, E. 2023-09-13 doi:10.1101/2023.09.11.557005 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Plasma membrane abundance dictates phagocytic capacity and functional crosstalk in myeloid cells ]]> https://biorxiv.org/content/10.1101/2023.09.12.556572v1?rss=1 Winer, B. Y. Settle, A. H. Yakimov, A. M. Jeronimo, C. Lazarovt, T. Tipping, M. Saoi, M. Sawh, A. Sepp, A.-L. L. Galiano, M. Perry, J. S. A. Wong, Y. Y. Geissmann, F. Cross, J. Zhou, T. Kam, L. C. Pasoli, H. A. Hohl, T. Cyster, J. G. Weiner, O. Huse, M. 2023-09-13 doi:10.1101/2023.09.12.556572 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Protein phosphatase 1 regulates core PCP signaling ]]> https://biorxiv.org/content/10.1101/2023.09.12.556998v1?rss=1 Song, S. Cho, B. Weiner, A. T. Nissen, S. B. Naharros, I. O. Bosch, P. S. Suyama, K. Hu, Y. He, L. Svinkina, T. Udeshi, N. Carr, S. A. Perrimon, N. Axelrod, J. D. 2023-09-13 doi:10.1101/2023.09.12.556998 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Discovery of a functionally selective serotonin 5-HT1A receptor agonist for the treatment of pain ]]> https://biorxiv.org/content/10.1101/2023.09.11.557127v1?rss=1 Ullrich, A. Schneider, J. Braz, J. M. Neu, E. Staffen, N. Stanek, M. Blahova, J. Hove, T. Albert, T. Allikalt, A. Lober, S. Bhardwaj, K. Rodriguez-Rosado, S. Fink, E. A. Rasmussen, T. Hubner, H. Inoue, A. A. Shoichet, B. K. Basbaum, A. Bottcher, B. Weikert, D. Gmeiner, P. 2023-09-14 doi:10.1101/2023.09.11.557127 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA ]]> https://biorxiv.org/content/10.1101/2023.09.14.557527v1?rss=1 Okholm, T. L. H. Kamstrup, A. B. Nielsen, M. M. Hollensen, A. K. Graversgaard, M. L. Kristensen, L. S. Vang, S. Park, S. S. Yeo, G. W. Dyrskjot, L. Kjems, J. Pedersen, J. S. Damgaard, C. K. 2023-09-14 doi:10.1101/2023.09.14.557527 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Determinants of DDX3X sensitivity uncovered using a helicase activity in translation reporter ]]> https://biorxiv.org/content/10.1101/2023.09.14.557805v1?rss=1 Wilkins, K. Schroeder, T. Gu, S. Revalde, J. Floor, S. N. 2023-09-14 doi:10.1101/2023.09.14.557805 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ CCR2-targeting pepducins reduce T cell-nociceptor interaction driving bone cancer pain ]]> https://biorxiv.org/content/10.1101/2023.09.15.556569v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@15c2d43org.highwire.dtl.DTLVardef@9fa40corg.highwire.dtl.DTLVardef@cb457dorg.highwire.dtl.DTLVardef@13f36e1_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIBreast cancer bone metastases induce pain by activating CCR2 on sensory neurons. C_LIO_LIDRG-infiltrating CD4+ and CD8+ T cells promote the development of bone cancer pain. C_LIO_LICCR2 inhibition by PP101 suppresses DRG neuroinflammation and neuronal excitability. C_LIO_LIPP101 alleviates bone cancer pain without behavioral or physiological side effects. C_LI ]]> Midavaine, E. Brouillette, R. R. Theberge, E. Mona, C. E. Kashem, S. W. Cote, J. Zeugin, V. Besserer-Offroy, E. Longpre, J.-M. Marsault, E. Sarret, P. 2023-09-15 doi:10.1101/2023.09.15.556569 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Ventromedial Prefrontal Cortex and Basolateral Amygdala Projections to Ventromedial Striatum Encode Active Avoidance Behavior ]]> https://biorxiv.org/content/10.1101/2023.09.15.558002v1?rss=1 Bullock, T. E. Gunaydin, L. A. 2023-09-15 doi:10.1101/2023.09.15.558002 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Multiplexed CRISPR gene editing in primary human islet cells with Cas9 ribonucleoprotein ]]> https://biorxiv.org/content/10.1101/2023.09.16.558090v1?rss=1 Bevacqua, R. J. Zhao, W. Merheb, E. Kim, S. H. Marson, A. Gloyn, A. L. Kim, S. K. 2023-09-17 doi:10.1101/2023.09.16.558090 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Gene regulatory network inference from CRISPR perturbations in primary CD4+ T cells elucidates the genomic basis of immune disease ]]> https://biorxiv.org/content/10.1101/2023.09.17.557749v1?rss=1 Weinstock, J. S. Arce, M. M. Freimer, J. W. Ota, M. Marson, A. Battle, A. Pritchard, J. K. 2023-09-17 doi:10.1101/2023.09.17.557749 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Higher-order combinatorial chromatin perturbations by engineered CRISPR-Cas12a for functional genomics ]]> https://biorxiv.org/content/10.1101/2023.09.18.558350v1?rss=1 3) combinatorial targeting of genomic sites with CRISPRi in functional genomics screens, we engineered an Acidaminococcus Cas12a variant -- referred to as multiplexed transcriptional interference AsCas12a (multiAsCas12a). multiAsCas12a incorporates a key mutation, R1226A, motivated by the hypothesis of nicking-induced stabilization of the ribonucleoprotein:DNA complex for improving CRISPRi activity. multiAsCas12a significantly outperforms prior state-of-the-art Cas12a variants in combinatorial CRISPRi targeting using high-order multiplexed arrays of lentivirally transduced CRISPR RNAs (crRNA), including in high-throughput pooled screens using 6-plex crRNA array libraries. Using multiAsCas12a CRISPRi, we discover new enhancer elements and dissect the combinatorial function of cis-regulatory elements. These results instantiate a group testing framework for efficiently surveying potentially numerous combinations of chromatin perturbations for biological discovery and engineering. ]]> Hsiung, C. C.- S. Wilson, C. M. Sambold, N. A. Dai, R. Chen, Q. Misiukiewicz, S. Arab, A. Teyssier, N. O'Loughlin, T. Cofsky, J. Shi, J. Gilbert, L. A. 2023-09-18 doi:10.1101/2023.09.18.558350 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ De novo designed Hsp70 activator dissolves intracellular condensates ]]> https://biorxiv.org/content/10.1101/2023.09.18.558356v1?rss=1 Zhang, J. Z. Greenwood, N. Hernandez, J. Cuperus, J. T. Huang, B. Ryder, B. D. Queitsch, C. Gestwicki, J. E. Baker, D. 2023-09-19 doi:10.1101/2023.09.18.558356 Cold Spring Harbor Laboratory Press 2023-09-19 <![CDATA[ Sex Chromosomes and Gonads Shape the Sex-Biased Transcriptomic Landscape in Tlr7-Mediated Demyelination During Aging ]]> https://biorxiv.org/content/10.1101/2023.09.19.558439v1?rss=1 Lopez-Lee, C. Kodama, L. Fan, L. Wong, M. Y. Foxe, N. R. Ijaz, L. Yu, F. Ye, P. Zhu, J. Norman, K. Torres, E. R. Kim, R. Mousa, G. A. Dubal, D. Liddelow, S. Luo, W. Gan, L. 2023-09-21 doi:10.1101/2023.09.19.558439 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Circulating Platelets Modulate Oligodendrocyte Progenitor Cell Differentiation During Remyelination ]]> https://biorxiv.org/content/10.1101/2023.09.20.558582v1?rss=1 Philp, A. R. Reyes, C. R. Mansilla, J. Sharma, A. Zhao, C. Valenzuela-Krugmann, C. Rawji, K. S. Martinez, G. A. G. Dimas, P. Hinrichsen, B. Ulloa-Leal, C. Waller, A. K. Bessa de Sousa, D. M. Castro, M. A. Aigner, L. Ehrenfeld, P. Silva, M. E. Kazanis, I. Ghevaert, C. Franklin, R. J. M. Rivera, F. J. 2023-09-22 doi:10.1101/2023.09.20.558582 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains ]]> https://biorxiv.org/content/10.1101/2023.09.20.558726v1?rss=1 Zwick, R. K. Kasparek, P. Palikuqi, B. Viragova, S. Weichselbaum, L. McGinnis, C. S. McKinley, K. L. Rathnayake, A. Vaka, D. Nguyen, V. Trentesaux, C. Reyes, E. Gupta, A. Gartner, Z. J. Locksley, R. M. Gardner, J. M. Itzkovitz, S. Boffelli, D. Klein, O. D. 2023-09-22 doi:10.1101/2023.09.20.558726 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ PAI-1 Deficiency Drives Pulmonary Vascular Smooth Muscle Remodeling and Pulmonary Hy-pertension ]]> https://biorxiv.org/content/10.1101/2023.09.21.558893v1?rss=1 Kudryashova, T. V. Zaitsev, S. V. Jiang, L. Buckley, B. J. McGuckin, J. P. Goncharov, D. Zhyvylo, I. Lin, D. Newcomb, G. Piper, B. Bogamuwa, S. Saiyed, A. Teos, L. Ranson, M. Wolters, P. Kelso, M. J. Poncz, M. DeLisser, H. M. Cines, D. B. Goncharova, E. A. Farkas, L. Stepanova, V. 2023-09-22 doi:10.1101/2023.09.21.558893 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Cryo-EM structure of Alzheimer disease tau filaments with PET ligand MK-6240 ]]> https://biorxiv.org/content/10.1101/2023.09.22.558671v1?rss=1 Kunach, P. Vaquer-Alicea, J. Smith, M. S. Hopewell, R. Monistrol, J. Moquin, L. Therriault, J. Tissot, C. Rahmouni, N. Massarweh, G. Soucy, J.-P. Guiot, M.-C. Shoichet, B. K. Rosa-Neto, P. K. Diamond, M. I. Shahmoradian, S. H. 2023-09-22 doi:10.1101/2023.09.22.558671 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Single cell analysis of dup15q syndrome reveals developmental and postnatal molecular changes in autism ]]> https://biorxiv.org/content/10.1101/2023.09.22.559056v1?rss=1 Perez, Y. Velmeshev, D. Wang, L. White, M. Siebert, C. Baltazar, J. Dutton, N. G. Wang, S. Haeussler, M. Chamberlain, S. Kriegstein, A. 2023-09-22 doi:10.1101/2023.09.22.559056 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ GIA: A genome interval arithmetic toolkit for high performance interval set operations ]]> https://biorxiv.org/content/10.1101/2023.09.20.558707v1?rss=1 Teyssier, N. Kampmann, M. Goodarzi, H. 2023-09-23 doi:10.1101/2023.09.20.558707 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ Germline-targeting chimpanzee SIV Envelopes induce V2-apex broadly neutralizing-like B cell precursors in a rhesus macaque infection model ]]> https://biorxiv.org/content/10.1101/2023.09.21.558743v1?rss=1 View larger version (57K): org.highwire.dtl.DTLVardef@17673c8org.highwire.dtl.DTLVardef@1ab61a8org.highwire.dtl.DTLVardef@98781forg.highwire.dtl.DTLVardef@1f63e9b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Musharrafieh, R. Safonova, Y. Song, G. Roark, R. S. Lee, F.-H. Zhang, S. Hurtado, J. Yong, P. Wang, S. Russell, R. M. Ding, W. Li, Y. Rando, J. Murphy, A. I. Lindemuth, E. Zhao, C. Connell, A. J. Lee, W.-H. Mishra, N. Avillion, G. He, W. Callaghan, S. Dueker, K. Vo, A. L. Li, X. Capozzola, T. Joyce, C. Zhao, F. Anzanello, F. Liu, W. Bibollet-Ruche, F. Ramos, A. Li, H. Lewis, M. G. Ozorowski, G. Landais, E. Foley, B. T. Wagh, K. Sok, D. Briney, B. Ward, A. B. Hahn, B. H. Burton, D. R. Shaw, G. M. Andrabi, R. 2023-09-23 doi:10.1101/2023.09.21.558743 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ S100A8/A9 predicts triple-negative breast cancer response to PIM kinase and PD-1/PD-L1 inhibition ]]> https://biorxiv.org/content/10.1101/2023.09.21.558870v1?rss=1 Begg, L. R. Orriols, A. M. Zannikou, M. Yeh, C. Vadlamani, P. Kanojia, D. Bolin, R. Dunne, S. F. Balakrishnan, S. Camarda, R. Roth, D. Zielinski-Mozny, N. A. Yau, C. Vassilopoulos, A. Huang, T.-H. Kim, K.-Y. A. Horiuchi, D. 2023-09-23 doi:10.1101/2023.09.21.558870 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ Predicting Long and Short Duration Beta Bursts from Subthalamic Nucleus Local Field Potential Activity in Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2023.09.22.558764v1?rss=1 150ms) and short (< 150ms) duration beta bursts from subthalamic nucleus local field potential (LFP) recordings. Our approach achieved promising accuracy values of 87% and 85.2% in two patients implanted with a DBS device that was capable of long-term wireless LFP sensing. Our findings highlight the feasibility of prolonged beta burst prediction and could inform the development of a new type of intelligent DBS approach with the capability of delivering stimulation only during the occurrence of prolonged bursts. ]]> Abdi-Sargezeh, B. Shirani, S. Sharma, A. Starr, P. Little, S. Oswal, A. 2023-09-23 doi:10.1101/2023.09.22.558764 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ A developmentally defined population of neurons in the lateral septum controls responses to aversive stimuli ]]> https://biorxiv.org/content/10.1101/2023.09.24.559205v1?rss=1 Turrero Garcia, M. Tran, D. N. Peterson, R. E. Stegmann, S. K. Hanson, S. M. Reid, C. M. Xie, Y. Vu, S. Harwell, C. C. 2023-09-25 doi:10.1101/2023.09.24.559205 Cold Spring Harbor Laboratory Press 2023-09-25 <![CDATA[ Expansion of interferon signaling-associated gene (ISAG)-hi T cells in early-onset Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2023.09.26.559634v1?rss=1 Sirkis, D. W. Solsberg, C. W. Johnson, T. P. Geier, E. G. Bonham, L. W. Miller, B. L. Rabinovici, G. D. Yokoyama, J. S. 2023-09-27 doi:10.1101/2023.09.26.559634 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Distinct transcriptional profiles of maternal and fetal placental macrophages at term are associated with gravidity ]]> https://biorxiv.org/content/10.1101/2023.09.25.559419v1?rss=1 Ozarslan, N. Robinson, J. F. Buarpung, S. Kim, M. Y. Ansbro, M. R. Akram, J. Montoya, D. J. Kamya, M. R. Kakuru, A. Dorsey, G. Rosenthal, P. J. Cheng, G. Feeney, M. E. Fisher, S. J. Gaw, S. L. 2023-09-28 doi:10.1101/2023.09.25.559419 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ Multimodal identification of rare potent effector CD8 T cells in solid tumors ]]> https://biorxiv.org/content/10.1101/2023.09.26.559470v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@4a9429org.highwire.dtl.DTLVardef@4535d9org.highwire.dtl.DTLVardef@1d26e03org.highwire.dtl.DTLVardef@34acd2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ray, A. Bassette, M. Hu, K. H. Pass, L. F. Samad, B. Combes, A. Johri, V. Davidson, B. Hernandez, G. Zaleta-Linares, I. Krummel, M. F. 2023-09-28 doi:10.1101/2023.09.26.559470 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ HybriSeq: Probe-based Device-free Single-cell RNA Profiling ]]> https://biorxiv.org/content/10.1101/2023.09.27.559406v1?rss=1 Foyt, D. Brown, D. Zhou, S. Huang, B. 2023-09-29 doi:10.1101/2023.09.27.559406 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Best practices for perturbation MPRA--a computational evaluation framework of sequence design strategies ]]> https://biorxiv.org/content/10.1101/2023.09.27.559768v1?rss=1 Liu, J. Ashuach, T. Inoue, F. Ahituv, N. Yosef, N. Kreimer, A. 2023-09-29 doi:10.1101/2023.09.27.559768 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Adolescent oligodendrogenesis and myelination restrict experience-dependent neuronal plasticity in adult visual cortex ]]> https://biorxiv.org/content/10.1101/2023.09.29.560231v1?rss=1 Xin, W. Kaneko, M. Roth, R. H. Zhang, A. Nocera, S. Ding, J. B. Stryker, M. P. Chan, J. R. 2023-09-30 doi:10.1101/2023.09.29.560231 Cold Spring Harbor Laboratory Press 2023-09-30 <![CDATA[ BiP/GRP78 is a pro-viral factor for diverse dsDNA viruses that promotes the survival and proliferation of cells upon KSHV infection ]]> https://biorxiv.org/content/10.1101/2023.09.29.560238v1?rss=1 Najarro, G. Brackett, K. Woosley, H. Faeldonea, C. Moreno, O. K. Ramirez Negron, A. Love, C. Ward, R. Langelier, C. Gardner, B. M. Arias, C. 2023-09-30 doi:10.1101/2023.09.29.560238 Cold Spring Harbor Laboratory Press 2023-09-30 <![CDATA[ Disease-specific selective vulnerability and neuroimmune pathways in dementia revealed by single cellgenomics ]]> https://biorxiv.org/content/10.1101/2023.09.29.560245v1?rss=1 Rexach, J. E. Cheng, Y. Chen, L. Polioudakis, D. Lin, L.-C. Mitri, V. Elkins, A. Yin, A. Calini, D. Kawaguchi, R. Ou, J. Huang, J. Williams, C. Robinson, J. Gaus, S. Spina, S. Lee, E. Grinberg, L. Vinters, H. Trojanowski, J. Seeley, W. Molhatra, D. Geschwind, D. 2023-09-30 doi:10.1101/2023.09.29.560245 Cold Spring Harbor Laboratory Press 2023-09-30 <![CDATA[ Transcriptional coupling of telomeric retrotransposons with the cell cycle ]]> https://biorxiv.org/content/10.1101/2023.09.30.560321v1?rss=1 Liu, M. Xie, X.-J. Li, X. Ren, X. Sun, J. Lin, Z. Hemba-Waduge, R.- U.-S. Ji, J.-y. 2023-10-01 doi:10.1101/2023.09.30.560321 Cold Spring Harbor Laboratory Press 2023-10-01 <![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[ Lysosomal proteomics reveals mechanisms of neuronal apoE4-associated lysosomal dysfunction ]]> https://biorxiv.org/content/10.1101/2023.10.02.560519v1?rss=1 Krogsaeter, E. K. McKetney, J. Marquez, A. Cakir, Z. Stevenson, E. Jang, G. M. Rao, A. Zhou, A. Huang, Y. Krogan, N. J. Swaney, D. L. 2023-10-02 doi:10.1101/2023.10.02.560519 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ BNT162b2 mRNA vaccine-induced sex differences in the single-cell transcriptome of peripheral blood mononuclear cells in healthy adults ]]> https://biorxiv.org/content/10.1101/2023.10.02.560569v1?rss=1 Knapp, J. D. Bhargava, A. 2023-10-03 doi:10.1101/2023.10.02.560569 Cold Spring Harbor Laboratory Press 2023-10-03 <![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[ Palatal segment contributions to midfacial growth in three inbred mouse strains ]]> https://biorxiv.org/content/10.1101/2023.10.03.560703v1?rss=1 Welsh, I. C. Feiler, M. Lipman, D. Mormile, I. Hansen, K. Percival, C. J. C. 2023-10-05 doi:10.1101/2023.10.03.560703 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ MOIRE: A software package for the estimation of allele frequenciesand effective multiplicity of infection from polyallelic data ]]> https://biorxiv.org/content/10.1101/2023.10.03.560769v1?rss=1 Murphy, M. Greenhouse, B. 2023-10-05 doi:10.1101/2023.10.03.560769 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Introduction of Dicistrovirus IRESs into UAS/SV40-polyA constructs results in premature polyadenylation and strong overexpression of the upstream ORF in Drosophila animals. ]]> https://biorxiv.org/content/10.1101/2023.10.04.560905v1?rss=1 Lidsky, P. V. Dmitriev, S. E. Andino, R. 2023-10-05 doi:10.1101/2023.10.04.560905 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Structural and molecular basis of choline uptake into the brain by FLVCR2 ]]> https://biorxiv.org/content/10.1101/2023.10.05.561059v1?rss=1 Cater, R. J. Mukherjee, D. Gil Iturbe, E. Erramilli, S. K. Chen, T. Koo, K. Santander, N. G. Reckers, A. R. Kloss, B. Gawda, T. Choy, B. C. Zhang, Z. Clarke, O. B. Yee, S. W. Kossiakoff, A. K. Quick, M. Arnold, T. Mancia, F. 2023-10-05 doi:10.1101/2023.10.05.561059 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Cross-Tissue Specificity of Pediatric DNA Methylation Associated with Cumulative Family Adversity ]]> https://biorxiv.org/content/10.1101/2023.10.04.559423v1?rss=1 Chan, M. H.-M. Merrill, S. M. Fatima, F. MacIsaac, J. L. Obradovic, J. Boyce, W. T. Kobor, M. S. 2023-10-06 doi:10.1101/2023.10.04.559423 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Sexual Differences In The Interaction Between Alcohol And mTORC1 ]]> https://biorxiv.org/content/10.1101/2023.10.04.560781v1?rss=1 Ehinger, Y. Phamluong, K. Ron, D. 2023-10-06 doi:10.1101/2023.10.04.560781 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[ Variants in the DDX6-CXCR5 autoimmune disease risk locus influence the regulatory network in immune cells and salivary gland ]]> https://biorxiv.org/content/10.1101/2023.10.05.561076v1?rss=1 Wiley, M. M. Khatri, B. Joachims, M. L. Tessneer, K. L. Stolarczyk, A. M. Rasmussen, A. Anaya, J.-M. Aqrawi, L. A. Bae, S.-C. Baecklund, E. Bjork, A. Brun, J. G. Bucher, S. M. Dand, N. Eloranta, M.-L. Engelke, F. Forsblad-d'Elia, H. Fugmann, C. Glenn, S. B. Gong, C. Gottenberg, J.-E. Hammenfors, D. Imgenberg-Kreuz, J. Jensen, J. L. Johnsen, S. J. A. Jonsson, M. V. Kelly, J. A. Khanam, S. Kim, K. Kvarnstrom, M. Mandl, T. Martin, J. Morris, D. L. Nocturne, G. Norheim, K. B. Olsson, P. Palm, O. Pers, J.-O. Rhodus, N. L. Sjowall, C. Skarstein, K. Taylor, K. 2023-10-06 doi:10.1101/2023.10.05.561076 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Differential Requirement for Dimerization of the Membrane-Binding PH-TH Module of BTK in B cells and T cells ]]> https://biorxiv.org/content/10.1101/2023.10.05.561114v1?rss=1 Eisen, T. J. Ghaffari-Kashani, S. Weiss, A. Kuriyan, J. 2023-10-06 doi:10.1101/2023.10.05.561114 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Identification of secretory autophagy as a novel mechanism modulating activity-induced synaptic remodeling ]]> https://biorxiv.org/content/10.1101/2023.10.06.560931v1?rss=1 Chang, Y.-C. Gao, Y. Lee, J. Y. Langen, J. Chang, K. T. 2023-10-06 doi:10.1101/2023.10.06.560931 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Structural dynamics of the active HER4 and HER2/HER4 complexes is finely tuned by different growth factors and glycosylation ]]> https://biorxiv.org/content/10.1101/2023.10.06.561161v1?rss=1 Trenker, R. Diwanji, D. Bingham, T. Verba, K. A. Jura, N. 2023-10-06 doi:10.1101/2023.10.06.561161 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ CELL-E 2: Translating Proteins to Pictures and Back with a Bidirectional Text-to-Image Transformer ]]> https://biorxiv.org/content/10.1101/2023.10.05.561066v1?rss=1 Khwaja, E. Song, Y. S. Agarunov, A. Huang, B. 2023-10-07 doi:10.1101/2023.10.05.561066 Cold Spring Harbor Laboratory Press 2023-10-07 <![CDATA[ The Hierarchy of Psychedelic Effects: Three Systematic Reviews and Meta-Analyses ]]> https://biorxiv.org/content/10.1101/2023.10.06.561183v1?rss=1 Shinozuka, K. Jerotic, K. Mediano, P. A. M. Zhao, A. T. Preller, K. H. Carhart-Harris, R. L. Kringelbach, M. L. 2023-10-07 doi:10.1101/2023.10.06.561183 Cold Spring Harbor Laboratory Press 2023-10-07 <![CDATA[ Proteome birthdating reveals age-selectivity of protein ubiquitination ]]> https://biorxiv.org/content/10.1101/2023.10.08.561433v1?rss=1 Meadow, M. E. Broas, S. Hoare, M. Alimohammadi, F. Welle, K. A. Swovick, K. Hryhorenko, J. R. Martinez, J. C. Biashad, S. A. Seluanov, A. Gorbunova, V. Buchwalter, A. Ghaemmaghami, S. 2023-10-08 doi:10.1101/2023.10.08.561433 Cold Spring Harbor Laboratory Press 2023-10-08 <![CDATA[ Exploring the tumor micro-environment in ovarian cancer histotypes and tumor sites ]]> https://biorxiv.org/content/10.1101/2023.10.07.561344v1?rss=1 Xie, B. Olalekan, S. BACK, R. Ashitey, N. A. A. A. Basu, A. 2023-10-10 doi:10.1101/2023.10.07.561344 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Developmental origin and local signals cooperate to determine septal astrocyte identity ]]> https://biorxiv.org/content/10.1101/2023.10.08.561428v1?rss=1 Xie, Y. Reid, C. M. Granados, A. A. Garcia, M. T. Dale-Huang, F. Hanson, S. M. Leon, W. R. M. Liu, J. Adam, M. A. Mosto, O. Pisco, A. O. Alvarez-Buylla, A. Harwell, C. C. 2023-10-10 doi:10.1101/2023.10.08.561428 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ A feasibility study of smartphone sensors to assess the effect of acute high altitude (3,800 m) exposure on cognition and motor function in healthy participants ]]> https://biorxiv.org/content/10.1101/2023.10.09.561578v1?rss=1 Goldman, O. G. Dubowitz, G. Anderson, D. 2023-10-10 doi:10.1101/2023.10.09.561578 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Convergent Epigenetic Evolution Drives Relapse in Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/2023.10.10.561642v1?rss=1 Nuno, K. Azizi, A. Koehnke, T. Lareau, C. Ediriwickrema, A. Corces, M. R. Satpathy, A. T. Majeti, R. 2023-10-10 doi:10.1101/2023.10.10.561642 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Interplay of RAP2 GTPase and the cytoskeleton in Hippo pathway regulation ]]> https://biorxiv.org/content/10.1101/2023.10.10.561687v1?rss=1 Wu, C. Cai, X. Wang, Y. Rodriguez, C. D. Herrmann, L. Zoaldi, G. Huang, C.-Y. Wang, X. Sanghvi, V. R. Lu, R. O. Meng, Z. 2023-10-10 doi:10.1101/2023.10.10.561687 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Control of intestinal stemness and cell lineage by histone variant H2A.Z isoforms ]]> https://biorxiv.org/content/10.1101/2023.10.10.561706v1?rss=1 Rispal, J. Rives, C. Jouffret, V. Leoni, C. Dubois, L. Chevillard-Briet, M. Trouche, D. Escaffit, F. 2023-10-10 doi:10.1101/2023.10.10.561706 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Neurogenesis-mediated circuit remodeling reduces engram reinstatement and promotes forgetting ]]> https://biorxiv.org/content/10.1101/2023.10.10.561722v1?rss=1 Guskjolen, A. Dhaliwal, J. de la Parra, J. Epp, J. R. Ko, S. Chahley, E. de Snoo, M. Solari, M. Panesar, P. Snyder, J. S. Duan, X. Sanes, J. Josselyn, S. Frankland, P. 2023-10-10 doi:10.1101/2023.10.10.561722 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ The single-molecule accessibility landscape of newly replicated mammalian chromatin ]]> https://biorxiv.org/content/10.1101/2023.10.09.561582v1?rss=1 Ostrowski, M. S. Yang, M. G. McNally, C. P. Abdulhay, N. J. Wang, S. Nora, E. P. Goodarzi, H. Ramani, V. 2023-10-11 doi:10.1101/2023.10.09.561582 Cold Spring Harbor Laboratory Press 2023-10-11 <![CDATA[ Population genetic analyses of longitudinal vaginal microbiome reveal racioethnic evolutionary dynamics and prevailing positive selection of Lactobacillus adhesins ]]> https://biorxiv.org/content/10.1101/2023.10.11.561685v1?rss=1 Wei, X. Tsai, M.-S. Liang, L. Jiang, L. Hung, C.-J. Jelliffe-Pawlowski, L. Rand, L. Snyder, M. Jiang, C. 2023-10-11 doi:10.1101/2023.10.11.561685 Cold Spring Harbor Laboratory Press 2023-10-11 <![CDATA[ A Simple Subcortical Feeding Circuit Linking Interoceptive Inputs to Consummatory Behavior ]]> https://biorxiv.org/content/10.1101/2023.10.11.561735v1?rss=1 Kosse, C. Ivanov, J. Knight, Z. Pellegrino, K. Friedman, J. 2023-10-11 doi:10.1101/2023.10.11.561735 Cold Spring Harbor Laboratory Press 2023-10-11 <![CDATA[ Mapping chromatin state and transcriptional response in CIC-DUX4 undifferentiated round cell sarcoma ]]> https://biorxiv.org/content/10.1101/2023.10.11.561932v1?rss=1 Thomas, N. Luck, C. Shlimon, N. Kriska Ponce, R. Kosibaty, Z. Okimoto, R. 2023-10-12 doi:10.1101/2023.10.11.561932 Cold Spring Harbor Laboratory Press 2023-10-12 <![CDATA[ EEG spectral attractors identify a geometric core of resting brain activity ]]> https://biorxiv.org/content/10.1101/2023.10.13.562264v1?rss=1 Pourdavood, P. Jacob, M. 2023-10-13 doi:10.1101/2023.10.13.562264 Cold Spring Harbor Laboratory Press 2023-10-13 <![CDATA[ Cell type specificity of mosaic chromosome 1q gain resolved by snRNA-seq in a case of epilepsy with hyaline protoplasmic astrocytopathy ]]> https://biorxiv.org/content/10.1101/2023.10.16.562560v1?rss=1 Leng, K. Titus, E. Singhal, N. Cadwell, C. R. Devine, W. P. Tihan, T. Qi, Z. Glenn, O. Kamiya, S. Berger, A. Shieh, J. Paredes, M. Upadhyay, V. 2023-10-17 doi:10.1101/2023.10.16.562560 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ The breath shape controls intonation of mouse vocalizations ]]> https://biorxiv.org/content/10.1101/2023.10.16.562597v1?rss=1 MacDonald, A. Yackle, K. 2023-10-17 doi:10.1101/2023.10.16.562597 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Modulating the Unfolded Protein Response with ISRIB Mitigates Cisplatin Ototoxicity ]]> https://biorxiv.org/content/10.1101/2023.10.17.562797v1?rss=1 Li, J. Rouse, S. L. Matthews, I. R. Sherr, E. H. Chan, D. K. 2023-10-17 doi:10.1101/2023.10.17.562797 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Mutant mice lacking alternatively spliced p53 isoforms unveil Ackr4 as a male-specific prognostic factor in Myc-driven B-cell lymphomas ]]> https://biorxiv.org/content/10.1101/2023.10.13.562180v1?rss=1 Fajac, A. Simeonova, I. Leemput, J. Gabriel, M. Morin, A. Lejour, V. Hamon, A. Vaysse-Zinkhofer, W. Eldawra, E. Rakotopare, J. Pinskaya, M. Morillon, A. Bourdon, J.-C. Bardot, B. Toledo, F. 2023-10-18 doi:10.1101/2023.10.13.562180 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ Systems-level analyses dissociate genetic regulators of reactive oxygen species and energy production ]]> https://biorxiv.org/content/10.1101/2023.10.14.562276v1?rss=1 Bennett, N. K. Lee, M. Orr, A. L. Nakamura, K. 2023-10-18 doi:10.1101/2023.10.14.562276 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ Development of covalent chemogenetic K2P channel activators ]]> https://biorxiv.org/content/10.1101/2023.10.15.561774v1?rss=1 Deal, P. E. Lee, H. Mondal, A. Lolicato, M. Furtado de Mandonca, P. R. Black, H. El-Hilali, X. Bryant, C. Isacoff, E. Y. Renslo, A. Minor, D. L. 2023-10-18 doi:10.1101/2023.10.15.561774 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ Chromosome size-dependent polar ejection force impairs mammalian mitotic error correction ]]> https://biorxiv.org/content/10.1101/2023.10.16.562637v1?rss=1 Chong, M. K. Rosas Salvans, M. K. Tran, V. Dumont, S. 2023-10-18 doi:10.1101/2023.10.16.562637 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ Multicolor on-chip fluorescence microscopy for real-time surgical guidance ]]> https://biorxiv.org/content/10.1101/2023.10.16.562247v1?rss=1 Roschelle, M. L. Rabbani, R. Papageorgiou, E. Zhang, H. Cooperberg, M. Stohr, B. A. Niknejad, A. Anwar, M. 2023-10-19 doi:10.1101/2023.10.16.562247 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Encoding of melody in the human auditory cortex ]]> https://biorxiv.org/content/10.1101/2023.10.17.562771v1?rss=1 Sankaran, N. Leonard, M. K. Theunissen, F. E. Chang, E. F. 2023-10-19 doi:10.1101/2023.10.17.562771 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ The genetic evolution of acral melanoma ]]> https://biorxiv.org/content/10.1101/2023.10.18.562802v1?rss=1 Wang, M. Fukushima, S. Sheen, Y.-S. Ramelyte, E. Cruz Pacheco, N. Shi, C. Liu, S. Banik, I. Aquino, J. D. Sangueza Acosta, M. Levesque, M. Dummer, R. Liau, J.-Y. Chu, C.-Y. Shain, A. H. Yeh, I. Bastian, B. C. 2023-10-19 doi:10.1101/2023.10.18.562802 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Modeling the consequences of age-linked rDNA hypermethylation with dCas9-directed DNA methylation in human cells ]]> https://biorxiv.org/content/10.1101/2023.10.18.562830v1?rss=1 Blokhina, Y. P. Buchwalter, A. 2023-10-19 doi:10.1101/2023.10.18.562830 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Tumor-wide RNA splicing aberrations generate immunogenic public neoantigens ]]> https://biorxiv.org/content/10.1101/2023.10.19.563178v1?rss=1 Kwok, D. W. Stevers, N. O. Nejo, T. Chen, L. H. Etxeberria, I. Jung, J. Okada, K. Colton Cove, M. Lakshmanachetty, S. Gallus, M. Barpanda, A. Hong, C. Chan, G. K. L. Wu, S. H. Ramos, E. Yamamichi, A. Liu, J. Y. Z. Watchmaker, P. Ogino, H. Saijo, A. Du, A. Grishanina, N. Woo, J. Diaz, A. Chang, S. M. Phillips, J. J. Wiita, A. Klebanoff, C. A. Costello, J. F. Okada, H. 2023-10-20 doi:10.1101/2023.10.19.563178 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Anti-CRISPR proteins trigger a burst of CRISPR-Cas9 expression that enhances phage defense ]]> https://biorxiv.org/content/10.1101/2023.10.22.562561v1?rss=1 Workman, R. E. Stoltzfus, M. J. Keith, N. C. Euler, C. W. Bondy-Denomy, J. Modell, J. W. 2023-10-22 doi:10.1101/2023.10.22.562561 Cold Spring Harbor Laboratory Press 2023-10-22 <![CDATA[ Context-invariant socioemotional encoding by prefrontal ensembles ]]> https://biorxiv.org/content/10.1101/2023.10.19.563015v1?rss=1 Frost, N. A. Donohue, K. C. Sohal, V. 2023-10-23 doi:10.1101/2023.10.19.563015 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Multiomics characterization of cell type repertoires for urine liquid biopsies ]]> https://biorxiv.org/content/10.1101/2023.10.20.563226v1?rss=1 Vorperian, S. K. DeFelice, B. C. Buonomo, J. A. Chinchinian, H. J. Gray, I. J. Yan, J. Mach, K. E. La, V. Lee, T. J. Liao, J. C. Lafayette, R. Loeb, G. B. Bertozzi, C. R. Quake, S. R. 2023-10-23 doi:10.1101/2023.10.20.563226 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Neurophysiological evidence of sensory prediction errors driving speech sensorimotor adaptation ]]> https://biorxiv.org/content/10.1101/2023.10.22.563504v1?rss=1 Kim, K. S. Hinkley, L. B. Dale, C. L. Nagarajan, S. S. Houde, J. F. 2023-10-23 doi:10.1101/2023.10.22.563504 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Micrococcin cysteine-to-thiazole conversion through transient interactions between a scaffolding protein and two modification enzymes ]]> https://biorxiv.org/content/10.1101/2023.10.23.563616v1?rss=1 Calvopina-Chavez, D. G. Bursey, D. M. Tseng, Y.-J. Patil, L. M. Bewley, K. D. Bennallack, P. R. McPhie, J. M. Wagstaff, K. B. Daley, A. Miller, S. M. Moody, J. D. Price, J. C. Griffitts, J. S. 2023-10-23 doi:10.1101/2023.10.23.563616 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning ]]> https://biorxiv.org/content/10.1101/2023.10.22.563498v1?rss=1 Kuang, S. Pollard, K. S. 2023-10-24 doi:10.1101/2023.10.22.563498 Cold Spring Harbor Laboratory Press 2023-10-24 <![CDATA[ Neural signatures of stress susceptibility and resilience in the amygdala-hippocampal network ]]> https://biorxiv.org/content/10.1101/2023.10.23.563652v1?rss=1 Xia, F. Fascianelli, V. Vishwakarma, N. Ghinger, F. G. Fusi, S. Kheirbek, M. 2023-10-24 doi:10.1101/2023.10.23.563652 Cold Spring Harbor Laboratory Press 2023-10-24 <![CDATA[ Pulmonary Ventilation Analysis Using 1H Ultra-Short Echo Time (UTE) Lung MRI: A Reproducibility Study ]]> https://biorxiv.org/content/10.1101/2023.10.22.563196v1?rss=1 Tan, F. Zhu, X. Chan, M. Deveshwar, N. Willmering, M. M. Lustig, M. Larson, P. E. Z. 2023-10-25 doi:10.1101/2023.10.22.563196 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ A Germline Point Mutation in the MYC-FBW7 Phosphodegron Initiates Hematopoietic Malignancies ]]> https://biorxiv.org/content/10.1101/2023.10.23.563660v1?rss=1 Freie, B. Carroll, P. A. Varnum-Finney, B. J. Ramani, V. Bernstein, I. Eisenman, R. N. 2023-10-25 doi:10.1101/2023.10.23.563660 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ The essential chaperone DNAJC17 activates HSP70 to coordinate RNA splicing and G2-M progression. ]]> https://biorxiv.org/content/10.1101/2023.10.25.564066v1?rss=1 Allegakoen, D. V. Kwong, K. Morales, J. Bivona, T. G. Sabnis, A. J. 2023-10-26 doi:10.1101/2023.10.25.564066 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ Designer Fat Cells: Adipogenic Differentiation of CRISPR-Cas9 Genome-Engineered Induced Pluripotent Stem Cells ]]> https://biorxiv.org/content/10.1101/2023.10.26.564206v1?rss=1 Ely, E. V. Kapinski, A. T. Paradi, S. G. Tang, R. Guilak, F. Collins, K. H.-M. 2023-10-26 doi:10.1101/2023.10.26.564206 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees ]]> https://biorxiv.org/content/10.1101/2023.10.26.564272v1?rss=1 Brand, C. M. Kuang, S. Gilbertson, E. N. McArthur, E. Pollard, K. S. Webster, T. H. Capra, J. A. 2023-10-26 doi:10.1101/2023.10.26.564272 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ AlphaMissense is better correlated with functional assays of missense impact than earlier prediction algorithms ]]> https://biorxiv.org/content/10.1101/2023.10.24.562294v1?rss=1 Ljungdahl, A. Kohani, S. Page, N. F. Wells, E. S. Wigdor, E. M. Dong, S. Sanders, S. J. 2023-10-27 doi:10.1101/2023.10.24.562294 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ ZNF397 Loss Triggers TET2-driven Epigenetic Rewiring, Lineage Plasticity, and AR-targeted Therapy Resistance in AR-dependent Cancers ]]> https://biorxiv.org/content/10.1101/2023.10.24.563645v1?rss=1 Mu, P. Xu, Y. Wang, Z. Sjostrom, M. Deng, S. Wang, C. Jonhson, N. Gonzalez, J. Li, X. Metang, L. Rodriguez, C. Mukherji, A. Wainwright, G. Yu, X. Yang, Y. Barnes, S. Hofstad, M. Zhu, H. Hanker, A. He, H. Chen, Y. Wang, Z. Raj, G. Arteaga, C. Feng, F. Wang, Y. Wang, T. 2023-10-27 doi:10.1101/2023.10.24.563645 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Challenges in the discovery of tumor-specific alternative splicing-derived cell-surface antigens in glioma ]]> https://biorxiv.org/content/10.1101/2023.10.26.564156v1?rss=1 Nejo, T. Wang, L. Leung, K. K. Wang, A. Lakshmanachetty, S. Gallus, M. Kwok, D. W. Hong, C. Chen, L. G. Carrera, D. A. Zhang, M. Y. Stevers, N. O. Maldonado, G. C. Yamamichi, A. Watchmaker, P. Naik, A. Shai, A. Phillips, J. Chang, S. M. Wiita, A. P. Wells, J. A. Costello, J. F. Diaz, A. A. Okada, H. 2023-10-27 doi:10.1101/2023.10.26.564156 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Altered PBP4 and GdpP functions synergistically mediate MRSA-like high-level, broad-spectrum β-lactam resistance in Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/2023.10.26.564222v1?rss=1 Lai, L.-Y. Satishkumar, N. Cardozo, S. Hemmadi, V. Marques, L. B. Huang, L. Filipe, S. R. Pinho, M. G. Chambers, H. F. Chatterjee, S. S. 2023-10-28 doi:10.1101/2023.10.26.564222 Cold Spring Harbor Laboratory Press 2023-10-28 <![CDATA[ Rosace: a robust deep mutational scanning analysis framework employing position and mean-variance shrinkage ]]> https://biorxiv.org/content/10.1101/2023.10.24.562292v1?rss=1 Rao, J. Xin, R. Macdonald, C. Howard, M. Estevam, G. O. Yee, S. W. Wang, M. Fraser, J. S. Coyote-Maestas, W. Pimentel, H. 2023-10-29 doi:10.1101/2023.10.24.562292 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ DREDge: robust motion correction for high-density extracellular recordings across species ]]> https://biorxiv.org/content/10.1101/2023.10.24.563768v1?rss=1 Windolf, C. Yu, H. Paulk, A. C. Meszena, D. Munoz, W. Boussard, J. Hardstone, R. Caprara, I. Jamali, M. Kfir, Y. Xu, D. Chung, J. E. Sellers, K. K. Ye, Z. Shaker, J. Lebedeva, A. Raghavan, M. Trautmann, E. Melin, M. D. Couto, J. Garcia, S. Coughlin, B. Horvath, C. Fiath, R. Ulbert, I. Movshon, J. A. Shadlen, M. N. Churchland, M. M. Churchland, A. K. Steinmetz, N. A. Chang, E. F. Schweitzer, J. S. Williams, Z. M. Cash, S. S. Paninski, L. Varol, E. 2023-10-29 doi:10.1101/2023.10.24.563768 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ Structure-Based Discovery of a NPFF1R Antagonist with Analgesic Activity ]]> https://biorxiv.org/content/10.1101/2023.10.25.564029v1?rss=1 Bender, B. J. Pickett, J. E. Braz, J. Kang, H. J. Gahbauer, S. Bhardwaj, K. Rodriguez-Rosado, S. Liu, Y. Jain, M. Basbaum, A. Roth, B. L. Shoichet, B. K. 2023-10-29 doi:10.1101/2023.10.25.564029 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ Docking for molecules that bind in a symmetric stack with SymDOCK ]]> https://biorxiv.org/content/10.1101/2023.10.27.564400v1?rss=1 Smith, M. S. Knight, I. S. Kormos, R. C. Pepe, J. G. Kunach, P. Diamond, M. I. Shahmoradian, S. H. Irwin, J. I. DeGrado, W. F. Shoichet, B. K. 2023-10-29 doi:10.1101/2023.10.27.564400 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells ]]> https://biorxiv.org/content/10.1101/2023.10.28.564055v1?rss=1 20 neighbors using immuno-assays and AlphaFold-Multimer prediction that generated plausible binary interaction models. We further profiled the protein neighborhoods of cell-cell synapses induced by bi-specific T-cell engagers (BiTEs) and chimeric antigen receptor (CAR)T cells at longer length scales. This integrated multi-scale PLP platform maps local and distal protein networks on cell surfaces and between cells. We believe this information will aid in the systematic construction of the cell surface interactome and reveal new opportunities for immunotherapeutics. ]]> Lin, Z. Schaefer, K. Lui, I. Yao, Z. Fossati, A. A. Swaney, D. L. Palar, A. Sali, A. Wells, J. A. 2023-10-29 doi:10.1101/2023.10.28.564055 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ Effects of chronic lithium treatment on neuronal excitability and GABAergic transmission in an Ank3 mutant mouse model ]]> https://biorxiv.org/content/10.1101/2023.10.26.564203v1?rss=1 Caballero-Floran, R. N. Nelson, A. D. Min, L. Jenkins, P. M. 2023-10-30 doi:10.1101/2023.10.26.564203 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ Colloidal aggregation confounds cell-based Covid-19 antiviral screens ]]> https://biorxiv.org/content/10.1101/2023.10.27.564435v1?rss=1 Glenn, I. S. Hall, L. N. Khalid, M. M. Ott, M. Shoichet, B. K. 2023-10-30 doi:10.1101/2023.10.27.564435 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ Immunosuppression is a conserved driver of tuberculosis susceptibility ]]> https://biorxiv.org/content/10.1101/2023.10.27.564420v1?rss=1 Kotov, D. I. Lee, O. V. Ji, D. X. Jaye, D. L. Suliman, S. Gabay, C. Vance, R. E. 2023-11-01 doi:10.1101/2023.10.27.564420 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[ Critical role of CD206+ macrophages in organizing anti-tumor immunity ]]> https://biorxiv.org/content/10.1101/2023.10.31.560822v1?rss=1 Ray, A. Hu, K. H. Kersten, K. Kuhn, N. F. Samad, B. Combes, A. J. Krummel, M. F. 2023-11-02 doi:10.1101/2023.10.31.560822 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Using behavioral biomarkers to redefine epochs of spontaneous recovery following spinal cord injury ]]> https://biorxiv.org/content/10.1101/2023.10.31.564826v1?rss=1 Eisdorfer, J. T. Thackray, J. Theis, T. Vivinetto, A. Ricci, M. T. Lin, S. Oputa, O. Martinez, A. M. Nacht, H. D. Tschang, M. Mahmood, M. Tucker, A. Pusuloori, S. Zmoyro, L. Abraira Lab Computational Group, Popovich, P. Ferguson, A. R. McTigue, D. Tysseling, V. M. Dulin, J. Hollis, E. Datta, S. R. Abraira, V. E. G. 2023-11-02 doi:10.1101/2023.10.31.564826 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Feasibility Study Utilizing NanoString Digital Spatial Profiling (DSP) Technology for Characterizing the Immune Microenvironment in Barrett's Esophagus FFPE Tissues ]]> https://biorxiv.org/content/10.1101/2023.11.02.565001v1?rss=1 Ain, Q. u. Frei, N. Khoshiwal, A. M. Stougie, P. Odze, R. Ferri, L. Duits, L. C. Bergman, J. Stachler, M. D. 2023-11-02 doi:10.1101/2023.11.02.565001 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity ]]> https://biorxiv.org/content/10.1101/2023.11.02.565382v1?rss=1 Alexander, M. Upadhyay, V. Rock, R. Ramirez, L. Puchalska, P. Orellana, D. Ang, Q. Y. Turnbaugh, J. A. Tian, Y. Dumlao, D. Nayak, R. R. Patterson, A. D. Newman, J. C. Crawford, P. A. Turnbaugh, P. J. 2023-11-03 doi:10.1101/2023.11.02.565382 Cold Spring Harbor Laboratory Press 2023-11-03 <![CDATA[ Quantitative Three-dimensional Label-free Digital Holographic Imaging of Cardiomyocyte Size, Ploidy, and Cell Division ]]> https://biorxiv.org/content/10.1101/2023.11.02.565407v1?rss=1 Park, S. Huang, H. Ross, I. Moreno, J. Khyeam, S. Simmons, J. Huang, G. N. Payumo, A. Y. 2023-11-04 doi:10.1101/2023.11.02.565407 Cold Spring Harbor Laboratory Press 2023-11-04 <![CDATA[ MET variants with activating N-lobe mutations identified in hereditary papillary renal cell carcinomas still require ligand stimulation ]]> https://biorxiv.org/content/10.1101/2023.11.03.565283v1?rss=1 Guerin, C. M. Vinchent, A. Damour, I. Laratte, A. Tellier, R. Estevam, G. Meneboo, J.-P. Villenet, C. Descarpentries, C. Fraser, J. S. Figeac, M. Cortot, A. B. Rouleau, E. Tulasne, D. 2023-11-05 doi:10.1101/2023.11.03.565283 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models ]]> https://biorxiv.org/content/10.1101/2023.11.03.565556v1?rss=1 Gjoni, K. Pollard, K. S. 2023-11-05 doi:10.1101/2023.11.03.565556 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Contexts facilitate dynamic value encoding in the mesolimbic dopamine system ]]> https://biorxiv.org/content/10.1101/2023.11.05.565687v1?rss=1 Fraser, K. M. Collins, V. L. Wolff, A. R. Ottenheimer, D. J. Bornhoft, K. N. Pat, F. Chen, B. J. Janak, P. H. Saunders, B. T. 2023-11-05 doi:10.1101/2023.11.05.565687 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants ]]> https://biorxiv.org/content/10.1101/2023.11.03.565292v1?rss=1 Gygi, J. P. Maguire, C. Patel, R. K. Shinde, P. Konstorum, A. Shannon, C. P. Xu, L. Hoch, A. Jayavelu, N. IMPACC Network, Haddad, E. K. Reed, E. F. Kraft, M. McComsey, G. A. Metcalf, J. Ozonoff, A. Esserman, D. Cairns, C. B. Rouphael, N. Bosinger, S. E. Kim-Schulze, S. Krammer, F. Rosen, L. B. Bakel, H. Wilson, M. Eckalbar, W. Maecker, H. Langelier, C. R. Steen, H. Altman, M. C. Montgomery, R. R. Levy, O. Melamed, E. Pulendran, B. Arce, J. Smolen, K. K. Fragiadakis, G. K. Becker, P. M. Augustine, A. D. Sekaly, R. P. Ehrlich, L. I. R. Fourati, S. Pete 2023-11-06 doi:10.1101/2023.11.03.565292 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Single cell transcriptional profiling of benign prostatic hyperplasia reveals a progenitor-like luminal epithelial cell state within an inflammatory microenvironment ]]> https://biorxiv.org/content/10.1101/2023.11.06.565375v1?rss=1 Unno, R. Akutagawa, J. Song, H. Hui, K. Chen, Y.-A. Pham, J. Yang, H. Huang, F. W. Chi, T. 2023-11-07 doi:10.1101/2023.11.06.565375 Cold Spring Harbor Laboratory Press 2023-11-07 <![CDATA[ Gene Expression Meta-Analysis Reveals Aging and Cellular Senescence Signatures in Scleroderma-associated Interstitial Lung Disease ]]> https://biorxiv.org/content/10.1101/2023.11.06.565810v1?rss=1 Yang, M. M. Lee, S. Neely, J. Hinchcliff, M. Wolters, P. J. Sirota, M. 2023-11-07 doi:10.1101/2023.11.06.565810 Cold Spring Harbor Laboratory Press 2023-11-07 <![CDATA[ TBXT dose sensitivity and the decoupling of nascent mesoderm specification from EMT progression in 2D human gastruloids ]]> https://biorxiv.org/content/10.1101/2023.11.06.565933v1?rss=1 Bulger, E. A. Muncie-Vasic, I. Libby, A. R. G. McDevitt, T. C. Bruneau, B. G. 2023-11-07 doi:10.1101/2023.11.06.565933 Cold Spring Harbor Laboratory Press 2023-11-07 <![CDATA[ The entropic heart: Tracking the psychedelic state via heart rate dynamics ]]> https://biorxiv.org/content/10.1101/2023.11.07.566008v1?rss=1 Rosas, F. E. Mediano, P. A. M. Timmermann, C. Luppi, A. I. Candia-Rivera, D. Abbasi-Asl, R. Gazzaley, A. Kringelbach, M. L. Muthukumaraswamy, S. D. Bor, D. Garfinkel, S. Carhart-Harris, R. 2023-11-09 doi:10.1101/2023.11.07.566008 Cold Spring Harbor Laboratory Press 2023-11-09 <![CDATA[ A novel mouse model of cerebral adrenoleukodystrophy highlights NLRP3 activity in lesion pathogenesis ]]> https://biorxiv.org/content/10.1101/2023.11.07.564025v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@1fbfebforg.highwire.dtl.DTLVardef@111e1e8org.highwire.dtl.DTLVardef@10647eborg.highwire.dtl.DTLVardef@15b9af4_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hashemi, E. Srivastava, I. Aguirre, A. Kaushal, E. Yoseph, E. Awani, A. Ryu, J. K. Akassoglou, K. Talebian, S. Chu, P. Pisani, L. Musolino, P. Steinman, L. Doyle, K. Robinson, W. H. Sharpe, O. Cayrol, R. Orchard, P. Lund, T. Vogel, H. Lenail, M. Han, M. Bonkowsky, J. P. Van Haren, K. P. 2023-11-10 doi:10.1101/2023.11.07.564025 Cold Spring Harbor Laboratory Press 2023-11-10 <![CDATA[ Coordinated immune dysregulation in Juvenile Dermatomyositis revealed by single-cell genomics ]]> https://biorxiv.org/content/10.1101/2023.11.07.566033v1?rss=1 Rabadam, G. Wibrand, C. Flynn, E. Hartoularos, G. C. Sun, Y. Ye, C. J. Kim, S. Gartner, Z. J. Sirota, M. Neely, J. 2023-11-10 doi:10.1101/2023.11.07.566033 Cold Spring Harbor Laboratory Press 2023-11-10 <![CDATA[ Light induced expression of gRNA allows for optogenetic gene editing of T lymphocytes in vivo ]]> https://biorxiv.org/content/10.1101/2023.11.09.566272v1?rss=1 Velasquez Pulgarin, D. A. Pelo, N. Ferrandiz, L. Trselic, T. Nyberg, W. A. Bowlin, G. L. Espinosa, A. 2023-11-10 doi:10.1101/2023.11.09.566272 Cold Spring Harbor Laboratory Press 2023-11-10 <![CDATA[ A high-density diffuse optical tomography dataset of naturalistic viewing ]]> https://biorxiv.org/content/10.1101/2023.11.07.565473v1?rss=1 Sherafati, A. Bajracharya, A. Jones, M. Speh, E. Munsi, M. Lin, C.-H. P. Fishell, A. K. Hershey, T. Eggebrecht, A. T. Culver, J. P. Peelle, J. E. 2023-11-11 doi:10.1101/2023.11.07.565473 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ Deletion of sulfate transporter SUL1 extends yeast replicative lifespan via reduced PKA signaling instead of decreased sulfate uptake ]]> https://biorxiv.org/content/10.1101/2023.11.11.566697v1?rss=1 Long, J. Ma, M. Chen, Y. Gong, B. Zheng, Y. Li, H. Yang, J. 2023-11-11 doi:10.1101/2023.11.11.566697 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ Microglia Depletion Reduces Human Neuronal APOE4-Driven Pathologies in a Chimeric Alzheimer's Disease Model ]]> https://biorxiv.org/content/10.1101/2023.11.10.566510v1?rss=1 APOE3). Single-cell RNA-sequencing analysis identified two pro-inflammatory microglial subtypes with high MHC-II gene expression that are enriched in chimeric mice with human APOE4 neuron transplants. These findings highlight the concerted roles of neuronal APOE, especially APOE4, and microglia in AD pathogenesis. HIGHLIGHTSO_LITransplanted human APOE4 neurons generate A{beta} and p-tau aggregates in APOE4-KI mouse hippocampus. C_LIO_LIHuman neuronal APOE4 promotes the formation of dense-core A{beta} plaques and p-tau aggregates. C_LIO_LIMicroglia is required for human neuronal APOE4-driven formation of p-tau aggregates. C_LIO_LIscRNA-seq reveals enrichment of MHC-II microglia in mice with human APOE4 neuron transplants. C_LI ]]> Rao, A. Chen, N. Kim, M. J. Blumenfeld, J. Yip, O. Hao, Y. Liang, Z. Nelson, M. R. Koutsodendris, N. Grone, B. Ding, L. Yoon, S. Y. Arriola, P. Huang, Y. 2023-11-14 doi:10.1101/2023.11.10.566510 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ Proteome-wide base editor screens to assess phosphorylation site functionality in high-throughput ]]> https://biorxiv.org/content/10.1101/2023.11.11.566649v1?rss=1 Kennedy, P. H. Deh Sheikh, A. A. Balakar, M. Jones, A. C. Olive, M. E. Hedge, M. Matias, M. I. Pirete, N. Burt, R. Levy, J. Little, T. Hogan, P. G. Liu, D. R. Doench, J. G. Newton, A. C. Gottschalk, R. A. de Boer, C. Alarcon, S. Newby, G. Myers, S. A. 2023-11-14 doi:10.1101/2023.11.11.566649 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ Lipid metabolism drives allele-specific early-stage hypertrophic cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2023.11.10.564562v1?rss=1 O_LINKSMALLFIG WIDTH=185 HEIGHT=200 SRC="FIGDIR/small/564562v1_ufig2.gif" ALT="Figure 1"> O_LINKSMALLFIG WIDTH=200 HEIGHT=74 SRC="FIGDIR/small/564562v1_ufig3.gif" ALT="Figure 1"> View larger version (90K): org.highwire.dtl.DTLVardef@195b1d7org.highwire.dtl.DTLVardef@cead88org.highwire.dtl.DTLVardef@e2bf35org.highwire.dtl.DTLVardef@776765_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Vaniya, A. Karlstaedt, A. Ates Gulkok, D. Thottakara, T. Liu, Y. Fan, S. Eades, H. Fukunaga, R. Vernon, H. J. Fiehn, O. Abraham, M. R. 2023-11-15 doi:10.1101/2023.11.10.564562 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Testing of putative antiseizure drugs in a preclinical Dravet syndrome zebrafish model ]]> https://biorxiv.org/content/10.1101/2023.11.11.566723v1?rss=1 Whyte-Fagundes, P. Vance, A. Carroll, A. Figueroa, F. Manukyan, C. Baraban, S. C. 2023-11-15 doi:10.1101/2023.11.11.566723 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Enhancing CAR-T Cell Metabolism to Overcome Hypoxic Conditions in the Brain Tumor Microenvironment ]]> https://biorxiv.org/content/10.1101/2023.11.13.566775v1?rss=1 Hatae, R. Kyewalabye, K. Yamamichi, A. Chen, T. Phyu, S. Chuntova, P. Nejo, T. Levine, L. S. Spitzer, M. H. Okada, H. 2023-11-15 doi:10.1101/2023.11.13.566775 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ A Photoactivatable Norepinephrine for Probing Adrenergic Neural Circuits ]]> https://biorxiv.org/content/10.1101/2023.11.13.566764v1?rss=1 Cahill, M. K. Perez, Y. R. Larpthaveesarp, A. Etchenique, R. Poskanzer, K. E. 2023-11-16 doi:10.1101/2023.11.13.566764 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ kmerDB: A Database Encompassing the Set of Genomic and Proteomic Sequence Information for Each Species ]]> https://biorxiv.org/content/10.1101/2023.11.13.566926v1?rss=1 Mouratidis, I. Baltoumas, F. A. Chantzi, N. Chan, C. Montgomery, A. Konnaris, M. A. Georgakopoulos, G. C. Das, A. Chartoumpekis, D. Kovac, J. Pavlopoulos, G. Georgakopoulos-Soares, I. 2023-11-16 doi:10.1101/2023.11.13.566926 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Telomerase reverse transcriptase induces targetable alterations in glutathione and nucleotide biosynthesis in glioblastomas ]]> https://biorxiv.org/content/10.1101/2023.11.14.566937v1?rss=1 Udutha, S. Taglang, C. Batsios, G. Gillespie, A. M. Tran, M. Ronen, S. M. ten Hoeve, J. Graeber, T. G. Viswanath, P. 2023-11-16 doi:10.1101/2023.11.14.566937 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ De novo Design of Peptides that Bind Specific Conformers of α-Synuclein ]]> https://biorxiv.org/content/10.1101/2023.11.14.567090v1?rss=1 Wallace, H. Yang, H. Tan, S. K. Pan, H. Yang, R. Xu, J. Jo, H. Condello, C. Polizzi, N. DeGrado, W. 2023-11-16 doi:10.1101/2023.11.14.567090 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Single phage proteins sequester TIR- and cGAS-generated signaling molecules ]]> https://biorxiv.org/content/10.1101/2023.11.15.567273v1?rss=1 Li, D. Xiao, Y. Xiong, W. Fedorova, I. Wang, Y. Liu, X. Huiting, E. Ren, J. Gao, Z. Zhao, X. Cao, X. Zhang, Y. Bondy-Denomy, J. Feng, Y. 2023-11-16 doi:10.1101/2023.11.15.567273 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Hierarchical annotation of eQTLs enables identification of genes with cell-type divergent regulation ]]> https://biorxiv.org/content/10.1101/2023.11.16.567459v1?rss=1 Przytycki, P. F. Pollard, K. S. 2023-11-16 doi:10.1101/2023.11.16.567459 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Networks extracted from nonlinear fMRI connectivity exhibit unique spatial variation and enhanced sensitivity to differences between individuals with schizophrenia and controls ]]> https://biorxiv.org/content/10.1101/2023.11.16.566292v1?rss=1 Kinsey, S. Kazimierczak, K. Camazon, P. A. Chen, J. Adali, T. Kochunov, P. Adhikari, B. Ford, J. van Erp, T. G. M. Dhamala, M. Calhoun, V. D. Iraji, A. 2023-11-17 doi:10.1101/2023.11.16.566292 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Engineered odorant receptors illuminate structural principles of odor discrimination ]]> https://biorxiv.org/content/10.1101/2023.11.16.567230v1?rss=1 de March, C. A. Ma, N. Billesboelle, C. B. Tewari, J. del Torrent, C. L. van der Velden, W. J. Ojiro, I. Takayama, I. Faust, B. Li, L. Vaidehi, N. Manglik, A. Matsunami, H. 2023-11-17 doi:10.1101/2023.11.16.567230 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Reversible histone deacetylase activity catalyzes lysine acylation ]]> https://biorxiv.org/content/10.1101/2023.11.17.567549v1?rss=1 Tsusaka, T. Najar, M. A. Schwarz, B. Bohrnsen, E. Oses-Prieto, J. A. Lee, C. Burlingame, A. L. Bosio, C. M. Burslem, G. M. Goldberg, E. L. 2023-11-17 doi:10.1101/2023.11.17.567549 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Poc1 is a basal body inner junction protein that promotes triplet microtubule integrity and interconnections ]]> https://biorxiv.org/content/10.1101/2023.11.17.567593v1?rss=1 Ruehle, M. D. Li, S. Agard, D. Pearson, C. G. 2023-11-17 doi:10.1101/2023.11.17.567593 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ An engineered glioblastoma model yields novel macrophage-secreted drivers of invasion ]]> https://biorxiv.org/content/10.1101/2023.11.18.567683v1?rss=1 Akins, E. A. Wilkins, D. Aghi, M. Kumar, S. 2023-11-18 doi:10.1101/2023.11.18.567683 Cold Spring Harbor Laboratory Press 2023-11-18 <![CDATA[ Hybrid assemblies of microbiome Blastocystis protists reveal evolutionary diversification reflecting host ecology ]]> https://biorxiv.org/content/10.1101/2023.11.20.567959v1?rss=1 Lind, A. McDonald, N. A. Gerrick, E. R. Bhatt, A. S. Pollard, K. S. 2023-11-20 doi:10.1101/2023.11.20.567959 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ Insights into Trypanosomiasis Transmission: Age, Infection Rates and Bloodmeal Analysis of Glossina fuscipes fuscipes in N.W. Uganda ]]> https://biorxiv.org/content/10.1101/2023.11.21.568004v1?rss=1 Cunningham, L. J. Esterhuizen, J. Hargrove, J. Lehane, M. Lord, J. Lingley, J. Mangwiro, C. T. N. Opiyo, M. Torr, S. 2023-11-21 doi:10.1101/2023.11.21.568004 Cold Spring Harbor Laboratory Press 2023-11-21 <![CDATA[ Rifampicin tolerance and growth fitness among isoniazid-resistant clinical Mycobacterium tuberculosis isolates: an in-vitro longitudinal study ]]> https://biorxiv.org/content/10.1101/2023.11.22.568240v1?rss=1 Srinivasan, V. Bao, N. L. H. Vinh, D. N. Thanh Hoang Le, N. Thu, D. D. Quang, N. L. Trieu, L. P. T. Nhung, H. N. Ha, V. T. N. Thai, P. V. K. Ha, D. T. M. Lan, N. H. Caws, M. Thwaites, G. E. Javid, B. Thuong, N. T. 2023-11-22 doi:10.1101/2023.11.22.568240 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ ChromaFactor: deconvolution of single-molecule chromatin organization with non-negative matrix factorization ]]> https://biorxiv.org/content/10.1101/2023.11.22.568268v1?rss=1 Gunsalus, L. M. Keiser, M. J. Pollard, K. S. 2023-11-22 doi:10.1101/2023.11.22.568268 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Selective activation of intracellular β1AR using a spatially restricted antagonist ]]> https://biorxiv.org/content/10.1101/2023.11.22.568314v1?rss=1 Liccardo, F. Morstein, J. Lin, T.-Y. Pampel, J. Shokat, K. Irannejad, R. 2023-11-22 doi:10.1101/2023.11.22.568314 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Spatiotemporal dynamics of successive activations across the human brain during simple arithmetic processing ]]> https://biorxiv.org/content/10.1101/2023.11.22.568334v1?rss=1 10,000 sites during arithmetic tasks, as captured by intracranial EEG. We discovered an orderly, successive activation of brain regions, consistent across individuals, and a decrease in functional connectivity as a function of temporal distance between regions. Our findings provide unprecedented insights into the sequence of cognitive processing and regional interactions, offering a novel perspective for enhancing computational models of cognitive symbolic systems. ]]> Pinheiro-Chagas, P. Sava-Segal, C. Akkol, S. Daitch, A. Parvizi, J. 2023-11-22 doi:10.1101/2023.11.22.568334 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Assembly reactions of SARS-CoV-2 nucleocapsid protein with nucleic acid ]]> https://biorxiv.org/content/10.1101/2023.11.22.568361v1?rss=1 Zhao, H. Syed, A. M. Khalid, M. M. Nguyen, A. Ciling, A. Wu, D. Yau, W.-M. Srinivasan, S. Esposito, D. Doudna, J. A. Piszczek, G. Ott, M. Schuck, P. 2023-11-23 doi:10.1101/2023.11.22.568361 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ Gaining Biological Insights through Supervised Data Visualization ]]> https://biorxiv.org/content/10.1101/2023.11.22.568384v1?rss=1 Rhodes, J. S. Aumon, A. Morin, S. Girard, M. Larochelle, C. Lahav, B. Brunet-Ratnasingham, E. Zhang, W. Cutler, A. Zhou, A. Kaufmann, D. E. Zandee, S. Prat, A. Wolf, G. Moon, K. R. 2023-11-23 doi:10.1101/2023.11.22.568384 Cold Spring Harbor Laboratory Press 2023-11-23 <![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[ Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes ]]> https://biorxiv.org/content/10.1101/2023.11.27.567477v1?rss=1 Cutts, Z. Patterson, S. Maliskova, L. Taylor, K. E. Ye, C. J. Dall'Era, M. Yazdany, J. Criswell, L. Fragiadakis, G. K. Langelier, C. Capra, J. A. Sirota, M. Lanata, C. 2023-11-28 doi:10.1101/2023.11.27.567477 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ Reversal of pulmonary veno-occlusive disease phenotypes by inhibition of the integrated stress response ]]> https://biorxiv.org/content/10.1101/2023.11.27.568924v1?rss=1 Prabhakar, A. Kumar, R. Wadhwa, M. Ghatpande, P. Zhang, J. Zhao, Z. Lizama, C. O. Kharbikar, B. N. Graf, S. Treacy, C. M. Morrell, N. W. Graham, B. B. Lagna, G. Hata, A. 2023-11-28 doi:10.1101/2023.11.27.568924 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ Epiregulon: Inference of single-cell transcription factor activity to dissect mechanisms of lineage plasticity and drug response ]]> https://biorxiv.org/content/10.1101/2023.11.27.568955v1?rss=1 Wlodarczyk, T. Lun, A. Wu, D. Menon, S. Toneyan, S. Seidel, K. Wang, L. Tan, J. Chen, S.-Y. Keyes, T. Chlebowski, A. Guo, Y. Metcalfe, C. Hafner, M. Siebel, C. W. Corces, M. R. Yauch, R. Xie, S. Yao, X. 2023-11-28 doi:10.1101/2023.11.27.568955 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ A (Sub)field Guide to Quality Control in Hippocampal Subfield Segmentation on High-resolution T2-weighted MRI ]]> https://biorxiv.org/content/10.1101/2023.11.29.568895v1?rss=1 Canada, K. L. Mazloum-Farzaghi, N. Radman, G. Adams, J. N. Bakker, A. Baumeister, H. Berron, D. Bocchetta, M. Carr, V. Dalton, M. A. de Flores, R. Keresztes, A. LaJoie, R. Mueller, S. Raz, N. Santini, T. Shaw, T. Stark, C. E. L. Tran, T. T. Wang, L. Wisse, L. Wuestefeld, A. Yushkevich, P. A. Olsen, R. Daugherty, A. 2023-12-01 doi:10.1101/2023.11.29.568895 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Paradoxical mTORC1-Dependent microRNA-mediated Translation Repression in the Nucleus Accumbens of Mice Consuming Alcohol Attenuates Glycolysis ]]> https://biorxiv.org/content/10.1101/2023.11.29.569312v1?rss=1 Ehinger, Y. Laguesse, S. Phamluong, K. Salvi, A. Hoisington, Z. W. Soneja, D. Sei, Y. J. Nakamura, K. Ron, D. 2023-12-01 doi:10.1101/2023.11.29.569312 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ The deubiquitinase USP9X regulates RIT1 protein abundance and oncogenic phenotypes ]]> https://biorxiv.org/content/10.1101/2023.11.30.569313v1?rss=1 Riley, A. K. Grant, M. Snell, A. Vichas, A. Moorthi, S. Urisman, A. Castel, P. Wan, L. Berger, A. 2023-12-01 doi:10.1101/2023.11.30.569313 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Time-of-day effects of drugs revealed by high-throughput deep phenotyping ]]> https://biorxiv.org/content/10.1101/2023.11.30.569380v1?rss=1 Ector, C. Schmal, C. Didier, J. De Landtsheer, S. Finger, A.-M. Muller-Marquardt, F. Schulte, J. Sauter, T. Keilholz, U. Herzel, H. Kramer, A. Granada, A. E. 2023-12-01 doi:10.1101/2023.11.30.569380 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Negative feedback control of hunger circuits by the taste of food ]]> https://biorxiv.org/content/10.1101/2023.11.30.569492v1?rss=1 Aitken, T. J. Ly, T. Shehata, S. Sivakumar, N. La Santa Medina, N. Gray, L. A. Dundar, N. Barnes, C. Knight, Z. A. 2023-12-03 doi:10.1101/2023.11.30.569492 Cold Spring Harbor Laboratory Press 2023-12-03 <![CDATA[ A foundational atlas of autism protein interactions reveals molecular convergence ]]> https://biorxiv.org/content/10.1101/2023.12.03.569805v1?rss=1 Wang, B. Vartak, R. Zaltsman, Y. Naing, Z. Z. C. Hennick, K. M. Polacco, B. J. Bashir, A. Eckhardt, M. Bouhaddou, M. Xu, J. Sun, N. Lasser, M. Zhou, Y. Guiley, K. Z. Chan, U. Kaye, J. A. Khare, P. Drake, S. Drury, V. Burke, D. F. Gonzalez, S. Alkhairy, S. Morris, M. Baum, T. Krasnoff, R. Wang, S. Pham, P. Arbalaez, J. Pratt, D. Chag, S. Rolland, T. Bourgeron, T. Finkbeiner, S. Bandyopadhay, S. Ideker, T. Beltrao, P. Willsey, H. R. Obernier, K. Nowakowski, T. J. Huttenhain, R. State, M. W. Willsey, A. J. Krogan, N. J. 2023-12-03 doi:10.1101/2023.12.03.569805 Cold Spring Harbor Laboratory Press 2023-12-03 <![CDATA[ Network-level encoding of local neurotransmitters in cortical astrocytes ]]> https://biorxiv.org/content/10.1101/2023.12.01.568932v1?rss=1 Cahill, M. K. Collard, M. Tse, V. Reitman, M. E. Etchenique, R. Kirst, C. Poskanzer, K. E. 2023-12-04 doi:10.1101/2023.12.01.568932 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ Atrophy-driven functional network collapse in neurodegenerative disease ]]> https://biorxiv.org/content/10.1101/2023.12.01.569654v1?rss=1 Brown, J. A. Lee, A. J. Fernhoff, K. Pistone, T. Pasquini, L. Wise, A. B. Staffaroni, A. M. Mandelli, M. L. Lee, S. E. Boxer, A. L. Rankin, K. P. Rabinovici, G. D. Gorno-Tempini, M. L. Rosen, H. J. Kramer, J. H. Miller, B. L. Seeley, W. W. 2023-12-04 doi:10.1101/2023.12.01.569654 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ Tumor microenvironmental determinants of high-risk DCIS progression ]]> https://biorxiv.org/content/10.1101/2023.12.01.569676v1?rss=1 5cm in size with at least one additional high-risk feature: young age (<45 years), high nuclear grade, hormone receptor negativity, HER2 positivity, the presence of comedonecrosis, or a palpable mass. The tumor immune microenvironment was characterized using multiplex immunofluorescence to identify immune cells and their spatial relationships within the ducts and stroma. Gene copy number analysis and whole exome DNA sequencing identified the mutational burden and driver mutations, and quantitative whole-transcriptome/gene expression analyses were performed. There was no association between the percent of the DCIS genome characterized by copy number variants (CNAs) and recurrence events (DCIS or invasive). Mutations, especially missense mutations, in the breast cancer driver genes PIK3CA and TP53 were common in this high-risk DCIS cohort (47% of evaluated lesions). Tumor infiltrating lymphocyte (TIL) density was higher in DCIS lesions with TP53 mutations (p=0.0079) compared to wildtype lesions, but not in lesions with PIK3CA mutations (p=0.44). Immune infiltrates were negatively associated with hormone receptor status and positively associated with HER2 expression. High levels of CD3+CD8-T cells were associated with good outcomes with respect to any subsequent recurrence (DCIS or invasive cancer), whereas high levels of CD3+Foxp3+ Treg cells were associated with poor outcomes. Spatial proximity analyses of immune cells and tumor cells demonstrated that close proximity of T cells with tumor cells was associated with good outcomes with respect to any recurrence as well as invasive recurrences. Interestingly, we found that myoepithelial continuity (distance between myoepithelial cells surrounding the involved ducts) was significantly lower in DCIS lesions compared to normal tissue (p=0.0002) or to atypical ductal hyperplasia (p=0.011). Gene set enrichment analysis identified several immune pathways associated with low myoepithelial continuity and a low myoepithelial continuity score was associated with better outcomes, suggesting that gaps in the myoepithelial layer may allow access/interactions between immune infiltrates and tumor cells. Our study demonstrates the immune microenvironment of DCIS, in particular the spatial proximity of tumor cells and T cells, and myoepithelial continuity are important determinants for progression of disease. ]]> Glencer, A. Ramalingam, K. Schindler, N. Mori, H. Ghule, P. Lee, K. C. Nachmanson, D. Officer, A. Harismendy, O. Stein, J. L. Stein, G. Weaver, D. Yau, C. Hirst, G. L. Campbell, M. J. Esserman, L. J. Borowsky, A. D. 2023-12-04 doi:10.1101/2023.12.01.569676 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ Msx genes delineate a novel molecular map of the developing cerebellar neuroepithelium. ]]> https://biorxiv.org/content/10.1101/2023.12.03.569760v1?rss=1 Gupta, I. Yeung, J. Rahimi-Balaei, M. Wu, S.-R. Goldowitz, D. 2023-12-04 doi:10.1101/2023.12.03.569760 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ Towards A Wireless Image Sensor for Real-Time Fluorescence Microscopy in Cancer Therapy ]]> https://biorxiv.org/content/10.1101/2023.12.03.569779v1?rss=1 Rabbani, R. Najafiaghdam, H. Roschelle, M. L. Papageorgiou, E. P. Zhao, B. R. Ghanbari, M. M. Muller, R. Stojanovic, V. Anwar, M. 2023-12-05 doi:10.1101/2023.12.03.569779 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Understanding how genetically encoded tags affect phase separation by Heterochromatin Protein HP1α ]]> https://biorxiv.org/content/10.1101/2023.12.04.569983v1?rss=1 Zhou, Z. Narlikar, G. J. 2023-12-05 doi:10.1101/2023.12.04.569983 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ ADPKD-Causing Missense Variants in Polycystin-1 Disrupt Cell Surface Localization or Polycystin Channel Function ]]> https://biorxiv.org/content/10.1101/2023.12.04.570035v1?rss=1 Ha, K. Loeb, G. B. Park, M. Pinedo, A. Park, C. H. Brandes, N. Ritu, F. Ye, C. J. Reiter, J. F. Delling, M. 2023-12-05 doi:10.1101/2023.12.04.570035 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Beta and theta oscillations track effort and previous reward in human basal ganglia and prefrontal cortex during decision making ]]> https://biorxiv.org/content/10.1101/2023.12.05.570285v1?rss=1 Hoy, C. W. de Hemptinne, C. Wang, S. S. Harmer, C. J. Apps, M. A. J. Husain, M. Starr, P. A. Little, S. 2023-12-06 doi:10.1101/2023.12.05.570285 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ Fungi and Bacteria Occupy Distinct Spatial Niches within Carious Dentin ]]> https://biorxiv.org/content/10.1101/2023.12.05.570240v1?rss=1 Sulyanto, R. M. Beall, C. J. Ha, K. Montesano, J. Juang, J. Dickson, J. R. Hashmi, S. B. Bradbury, S. Leys, E. J. Edgerton, M. Ho, S. P. Griffen, A. L. 2023-12-08 doi:10.1101/2023.12.05.570240 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Modeling an ultra-rare epilepsy variant in wildtype mice with in utero prime editing ]]> https://biorxiv.org/content/10.1101/2023.12.06.570164v1?rss=1 Robertson, C. D. Davis, P. Richardson, R. R. Iffland, P. H. Vieira, D. C. O. Steyert, M. McKeon, P. N. Romanowski, A. J. Crutcher, G. Jasarevic, E. Wolff, S. B. E. Mathur, B. N. Crino, P. B. Bale, T. L. Dick, I. E. Poulopoulos, A. 2023-12-08 doi:10.1101/2023.12.06.570164 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ MLL3/MLL4 enzymatic activity shapes DNA replication timing ]]> https://biorxiv.org/content/10.1101/2023.12.07.569680v1?rss=1 Goekbuget, D. Boileau, R. M. Lenshoek, K. Blelloch, R. 2023-12-08 doi:10.1101/2023.12.07.569680 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Syndrome-informed phenotyping identifies a polygenic background for achondroplasia-like facial variation in the general population ]]> https://biorxiv.org/content/10.1101/2023.12.07.570544v1?rss=1 Vanneste, M. Hoskens, H. Goovaerts, S. Matthews, H. Aponte, J. D. Cole, J. Shriver, M. D. Marazita, M. L. Weinberg, S. M. Walsh, S. Richmond, S. Klein, O. D. Spritz, R. A. Peeters, H. Hallgrimsson, B. Claes, P. 2023-12-08 doi:10.1101/2023.12.07.570544 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Somatic mutation as an explanation for epigenetic aging ]]> https://biorxiv.org/content/10.1101/2023.12.08.569638v1?rss=1 Koch, Z. Li, A. Y. Evans, D. Cummings, S. Ideker, T. 2023-12-09 doi:10.1101/2023.12.08.569638 Cold Spring Harbor Laboratory Press 2023-12-09 <![CDATA[ Torques within and outside the human spindle balance twist at anaphase ]]> https://biorxiv.org/content/10.1101/2023.12.10.570990v1?rss=1 Neahring, L. He, Y. Cho, N. H. Liu, G. Fernandes, J. Rux, C. J. Nakos, K. Subramanian, R. Upadhyayula, S. Yildiz, A. Dumont, S. 2023-12-10 doi:10.1101/2023.12.10.570990 Cold Spring Harbor Laboratory Press 2023-12-10 <![CDATA[ Cholesterol Dysregulation Drives Seed-Dependent Tau Aggregation in Patient Stem Cell-Derived Models of Tauopathy ]]> https://biorxiv.org/content/10.1101/2023.12.11.571147v1?rss=1 Lam, M. Kuo, S.-Y. Reis, S. Gestwicki, J. E. Silva, M. C. Haggarty, S. J. 2023-12-12 doi:10.1101/2023.12.11.571147 Cold Spring Harbor Laboratory Press 2023-12-12 <![CDATA[ IGHMBP2 deletion suppresses translation and activates the integrated stress response ]]> https://biorxiv.org/content/10.1101/2023.12.11.571166v1?rss=1 Park, J. Desai, H. Liboy-Lugo, J. Gu, S. Jowhar, Z. Xu, A. Floor, S. N. 2023-12-12 doi:10.1101/2023.12.11.571166 Cold Spring Harbor Laboratory Press 2023-12-12 <![CDATA[ Glioma Cells Secrete Collagen VI to Facilitate Invasion ]]> https://biorxiv.org/content/10.1101/2023.12.12.571198v1?rss=1 Cha, J. Ding, E. A. Carvalho, E. M. Fowler, A. Aghi, M. K. Kumar, S. 2023-12-12 doi:10.1101/2023.12.12.571198 Cold Spring Harbor Laboratory Press 2023-12-12 <![CDATA[ Structure-conditioned masked language models for protein sequence design generalize beyond the native sequence space ]]> https://biorxiv.org/content/10.1101/2023.12.15.571823v1?rss=1 Akpinaroglu, D. Seki, K. Guo, A. Zhu, E. Kelly, M. J. Kortemme, T. 2023-12-15 doi:10.1101/2023.12.15.571823 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ The Primary Cilium and its Hedgehog Signaling in Nociceptors Contribute to Inflammatory and Neuropathic Pain ]]> https://biorxiv.org/content/10.1101/2023.12.27.573420v1?rss=1 Fitzsimons, L. A. Staurengo-Ferrari, L. Bogen, O. Araldi, D. Bonet, I. J. M. Jordan, E. E. Levine, J. D. Tucker, K. L. 2023-12-27 doi:10.1101/2023.12.27.573420 Cold Spring Harbor Laboratory Press 2023-12-27 <![CDATA[ Structure-based discovery of positive allosteric modulators for the calcium sensing receptor ]]> https://biorxiv.org/content/10.1101/2023.12.27.573448v1?rss=1 Liu, F. Wu, C.-G. Tu, C.-L. Glenn, I. Meyerowitz, J. Kaplan, A. L. Lyu, J. Cheng, Z. Tarkhanova, O. O. Moroz, Y. S. Irwin, J. J. Chang, W. Shoichet, B. K. Skiniotis, G. 2023-12-27 doi:10.1101/2023.12.27.573448 Cold Spring Harbor Laboratory Press 2023-12-27 <![CDATA[ Mapping cis- and trans-regulatory target genes of human-specific deletions ]]> https://biorxiv.org/content/10.1101/2023.12.27.573461v1?rss=1 Fair, T. Pavlovic, B. J. Schaefer, N. K. Pollen, A. A. 2023-12-28 doi:10.1101/2023.12.27.573461 Cold Spring Harbor Laboratory Press 2023-12-28 <![CDATA[ Conditioned overconsumption is dependent on reinforcer type in lean, but not obese, mice. ]]> https://biorxiv.org/content/10.1101/2023.12.31.573797v1?rss=1 Lewis-Sanders, D. Bullich, S. Olvera, M. J. Vo, J. Hwang, Y.-S. Stern, S. A. 2024-01-01 doi:10.1101/2023.12.31.573797 Cold Spring Harbor Laboratory Press 2024-01-01 <![CDATA[ Blood immunophenotyping identifies distinct kidney histopathology and outcomes in patients with lupus nephritis ]]> https://biorxiv.org/content/10.1101/2024.01.14.575609v1?rss=1 Horisberger, A. Griffith, A. Keegan, J. Arazi, A. Pulford, J. Murzin, E. Howard, K. Hancock, B. Fava, A. Sasaki, T. Ghosh, T. Inamo, J. Beuschel, R. Cao, Y. Preisinger, K. Gutierrez-Arcelus, M. Eisenhaure, T. M. Guthridge, J. Hoover, P. J. Dall'Era, M. Wofsy, D. Kamen, D. L. Kalunian, K. C. Furie, R. Belmont, M. Izmirly, P. Clancy, R. Hildeman, D. Woodle, E. S. Apruzzese, W. McMahon, M. A. Grossman, J. Barnas, J. L. Payan-Schober, F. Ishimori, M. Weisman, M. Kretzler, M. Berthier, C. C. Hodgin, J. B. Demeke, D. S. Putterman, C. Accelerating Medicines Pa 2024-01-16 doi:10.1101/2024.01.14.575609 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ Host brain environmental influences on transplanted medial ganglionic eminence progenitors ]]> https://biorxiv.org/content/10.1101/2024.01.15.575686v1?rss=1 Paterno, R. Vu, T. Hsieh, C. Baraban, S. C. 2024-01-16 doi:10.1101/2024.01.15.575686 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ Opioid-driven disruption of the septal complex reveals a role for neurotensin- expressing neurons in withdrawal ]]> https://biorxiv.org/content/10.1101/2024.01.15.575766v1?rss=1 Simon, R. Fleming, W. Senthilkumar, P. Briones, B. Ishii, K. Hjort, M. Martin, M. Hashikawa, K. Sanders, A. Golden, S. Stuber, G. 2024-01-16 doi:10.1101/2024.01.15.575766 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ A call for a unified and multimodal definition of cellular identity in the enteric nervous system ]]> https://biorxiv.org/content/10.1101/2024.01.15.575794v1?rss=1 Majd, H. Cesiulis, A. Samuel, R. M. Richter, M. N. Elder, N. Guyer, R. A. Hao, M. Stamp, L. Goldstein, A. Fattahi, F. 2024-01-16 doi:10.1101/2024.01.15.575794 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ Molecular and cellular dynamics of the developing human neocortex at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2024.01.16.575956v1?rss=1 Wang, L. Wang, C. Moriano, J. A. Chen, S. Zhang, S. Mukhtar, T. Wang, S. Cebrian-Silla, A. Bi, Q. Augustin, J. J. de Oliveira, L. G. Song, M. Ge, X. Zuo, G. Paredes, M. F. Huang, E. J. Alvarez-Buylla, A. Duan, X. Li, J. Kriegstein, A. R. 2024-01-16 doi:10.1101/2024.01.16.575956 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ Targeted DNA Sequencing of Cutaneous Melanoma Identifies Prognostic and Predictive Alterations ]]> https://biorxiv.org/content/10.1101/2024.01.18.576113v1?rss=1 5 and <20 mutations/Mb), 40 of 154 (26.0%) were TMB high (>20 and <50 mutations/Mb) and 36 of 154 (23.4%) were classified as TMB very high (>50 mutations/Mb). NRAS mutant melanoma demonstrated significantly decreased overall survival on multivariable analysis (HR for death 2.95, 95% CI 1.13 - 7.69, p = 0.027, log rank test) compared with other TCGA molecular subgroups. Other factors correlated with decreased overall survival included age and ECOG score. Of the 116 patients in our cohort with available treatment data, 36 received combination dual ICI with anti-CTLA4 and anti-PD1 inhibition as first line therapy. Elevated TMB was associated with significantly longer progression-free survival following dual agent ICI (HR 0.26, 95% CI 0.07 - 0.90, p =0.033, log rank test). Conclusions and RelevanceNRAS mutation in CMs correlated with significantly worse overall survival. Elevated TMB was associated with increased progression-free survival for patients treated with combination dual ICI, supporting the potential utility of TMB as a predictive biomarker for ICI response in melanoma. ]]> Vasudevan, H. Haugh, A. M. Osorio, R. C. Francois, R. A. Tawil, M. E. Tsai, K. K. Tetzlaff, M. Daud, A. 2024-01-22 doi:10.1101/2024.01.18.576113 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Ultra-efficient, unified discovery from microbial sequencing with SPLASH and precise statistical assembly ]]> https://biorxiv.org/content/10.1101/2024.01.18.576133v1?rss=1 12% of Earths biomass and profoundly impact human and planetary health.1 Many key biological functions of microbes, and functions differentiating strains, are conferred or modified by genome plasticity including mobilization of genetic elements, phage integration, and CRISPR arrays. Characterizing each of these processes is time-consuming and requires custom bioinformatic workflows ill-suited to enable discovery of new sources of genetic diversity or to uncover which elements are active. Further, strain typing of bacterial species and approaches to discriminate sub-populations remain time-consuming and resource intensive. Here, we show that SPLASH, our published approach for reference-free discovery and analysis directly from raw reads, and an improved statistical assembly algorithm, compactors, unify diverse tasks in microbial sequence analysis: discovering new mobile elements and CRISPR arrays missing from any reference, and generating rapid, metadata-free strain typing of diverse bacteria. SPLASH and compactors together constitute a new general discovery tool for biological discovery in the microbial world. ]]> Henderson, G. Gudys, A. Baharav, T. Sundaramurthy, P. Kokot, M. Wang, P. L. Deorowicz, S. Carey, A. Salzman, J. 2024-01-22 doi:10.1101/2024.01.18.576133 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Maternal n-3 enriched diet reprograms neurovascular transcriptome and blunts inflammation in neonate ]]> https://biorxiv.org/content/10.1101/2024.01.22.576634v1?rss=1 Chumak, T. Jullienne, A. Ek, J. Ardalan, M. Svedin, P. Quan, R. Salehi, A. Salari, S. Obenaus, A. Vexler, Z. Mallard, C. 2024-01-22 doi:10.1101/2024.01.22.576634 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Widespread Peptide Surfactants with Post-translational C-methylations Promote Bacterial Development ]]> https://biorxiv.org/content/10.1101/2024.01.23.576971v1?rss=1 Zhang, C. Seyedsayamdost, M. R. 2024-01-24 doi:10.1101/2024.01.23.576971 Cold Spring Harbor Laboratory Press 2024-01-24 <![CDATA[ High-resolution Inference of Multiplexed Anti-HIV Gene Editing using Single-Cell Targeted DNA Sequencing ]]> https://biorxiv.org/content/10.1101/2024.01.24.576921v1?rss=1 Bouzidi, M. Dossani, Z. Di Benedetto, C. Raymond, K. Desai, S. Chavez, L. Betancur, P. Pillai, S. K. 2024-01-24 doi:10.1101/2024.01.24.576921 Cold Spring Harbor Laboratory Press 2024-01-24 <![CDATA[ Regional specialization manifests in the reliability of neural population codes ]]> https://biorxiv.org/content/10.1101/2024.01.25.576941v1?rss=1 Guidera, J. A. Gramling, D. P. Comrie, A. E. Joshi, A. Denovellis, E. L. Lee, K. H. Zhou, J. Thompson, P. Hernandez, J. Yorita, A. Haque, R. Kirst, C. Frank, L. M. 2024-01-26 doi:10.1101/2024.01.25.576941 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ An experimental census of retrons for DNA production and genome editing ]]> https://biorxiv.org/content/10.1101/2024.01.25.577267v1?rss=1 100 previously untested retrons to identify the natural sequence of RT-DNA they produce, quantify their RT-DNA production, and test the relative efficacy of editing using retron-derived donors to edit bacterial genomes, phage genomes, and human genomes. We add 62 new empirically determined, natural RT-DNAs, which are not predictable from the retron sequence alone. We report a large diversity in RT-DNA production and editing rates across retrons, finding that top performing editors outperform those used in previous studies, and are drawn from a subset of the retron phylogeny. ]]> Khan, A. G. Rojas-Montero, M. Gonzalez-Delgado, A. Lopez, S. C. Fang, R. F. Shipman, S. L. 2024-01-26 doi:10.1101/2024.01.25.577267 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ Oscillatory Hypoxia Induced Unfolded Protein Folding Response Gene Expression Predicts Low Survival in Human Breast Cancer Patients ]]> https://biorxiv.org/content/10.1101/2024.01.25.577274v1?rss=1 Suhail, Y. Liu, Y. Du, W. Afzal, J. Atiq, A. Kshitiz, 2024-01-26 doi:10.1101/2024.01.25.577274 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ CDX2 dose-dependently influences the gene regulatory network underlying human extraembryonic mesoderm development ]]> https://biorxiv.org/content/10.1101/2024.01.25.577277v1?rss=1 Bulger, E. A. McDevitt, T. C. Bruneau, B. G. 2024-01-26 doi:10.1101/2024.01.25.577277 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ Vagus nerve stimulation (VNS) modulates synaptic plasticity in the rat infralimbic cortex via Trk-B receptor activation to reduce drug-seeking ]]> https://biorxiv.org/content/10.1101/2024.01.25.577293v1?rss=1 Driskill, C. M. Childs, J. E. Phensy, A. J. Rodriguez, S. R. O'Brien, J. T. Lindquist, K. L. Naderi, A. O. Bordieanu, B. McGinty, J. F. Kroener, S. 2024-01-26 doi:10.1101/2024.01.25.577293 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ Spyglass: a data analysis framework for reproducible and shareable neuroscience research ]]> https://biorxiv.org/content/10.1101/2024.01.25.577295v1?rss=1 Lee, K. H. Denovellis, E. L. Ly, R. Magland, J. Soules, J. Comrie, A. E. Gramling, D. P. Guidera, J. A. Nevers, R. Adenekan, P. Brozdowski, C. Bray, S. Monroe, E. Bak, J. H. Coulter, M. Sun, X. Tritt, A. Oliver Ruebel, O. Nguyen, T. Yatsenko, D. Chu, J. Kemere, C. Garcia, S. Buccino, A. Frank, L. M. 2024-01-26 doi:10.1101/2024.01.25.577295 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ IgG hexamers initiate acute lung injury ]]> https://biorxiv.org/content/10.1101/2024.01.24.577129v1?rss=1 View larger version (59K): org.highwire.dtl.DTLVardef@15b0346org.highwire.dtl.DTLVardef@33f39eorg.highwire.dtl.DTLVardef@bf0f4dorg.highwire.dtl.DTLVardef@185b5bf_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cleary, S. J. Seo, Y. Tian, J. J. Kwaan, N. Bulkley, D. P. Bentlage, A. E. Vidarsson, G. Boilard, E. Spirig, R. Zimring, J. C. Looney, M. R. 2024-01-27 doi:10.1101/2024.01.24.577129 Cold Spring Harbor Laboratory Press 2024-01-27 <![CDATA[ Field evaluation of a volatile pyrethroid spatial repellent and etofenprox-treated clothing for outdoor protection against forest malaria vectors in Cambodia ]]> https://biorxiv.org/content/10.1101/2024.01.30.577940v1?rss=1 Vajda, E. A. Ross, A. Doum, D. Fairbanks, E. Chitnis, N. A. Hii, J. Moore, S. J. Richardson, J. Macdonald, M. Sovannaroth, S. Kimheng, P. McIver, D. J. Tatarsky, A. Lobo, N. F. 2024-02-02 doi:10.1101/2024.01.30.577940 Cold Spring Harbor Laboratory Press 2024-02-02 <![CDATA[ Sex Differences in the Brain's White Matter Microstructure during Development assessed using Advanced Diffusion MRI Models ]]> https://biorxiv.org/content/10.1101/2024.02.02.578712v1?rss=1 Benavidez, S. M. Abaryan, Z. Kim, G. S. Laltoo, E. McCracken, J. T. Thompson, P. M. Lawrence, K. E. 2024-02-04 doi:10.1101/2024.02.02.578712 Cold Spring Harbor Laboratory Press 2024-02-04 <![CDATA[ MAGIC matrices: freeform bioprinting materials to support complex and reproducible organoid morphogenesis ]]> https://biorxiv.org/content/10.1101/2024.02.01.578324v1?rss=1 Graham, A. J. Khoo, M. W. L. Srivastava, V. Viragova, S. Parekh, K. Morley, C. D. Bird, M. Lebel, P. Kumar, S. Klein, O. D. Gomez-Sjoberg, R. Gartner, Z. J. 2024-02-05 doi:10.1101/2024.02.01.578324 Cold Spring Harbor Laboratory Press 2024-02-05 <![CDATA[ A TBX5-dependent compartment boundary patterns the cardiac interventricular septum ]]> https://biorxiv.org/content/10.1101/2024.02.05.578995v1?rss=1 Kathiriya, I. S. Dominguez, M. H. Rao, K. S. Muncie-Vasic, J. M. Devine, W. P. Hu, K. M. Hota, S. K. Garay, B. I. Quintero, D. Goyal, P. Matthews, M. N. Thomas, R. Sukonnik, T. Miguel-Perez, D. Winchester, S. Brower, E. F. Forjaz, A. Wu, P.-H. Wirtz, D. Kiemen, A. L. Bruneau, B. G. 2024-02-05 doi:10.1101/2024.02.05.578995 Cold Spring Harbor Laboratory Press 2024-02-05 <![CDATA[ Protein-protein interactions with G3BPs drive stress granule condensation and gene expression changes under cellular stress ]]> https://biorxiv.org/content/10.1101/2024.02.06.579149v1?rss=1 Liboy-Lugo, J. M. Espinoza, C. A. Sheu-Gruttadauria, J. Park, J. E. Xu, A. Jowhar, Z. Gao, A. L. Carmona-Negron, J. A. Wittmann, T. Jura, N. Floor, S. N. 2024-02-07 doi:10.1101/2024.02.06.579149 Cold Spring Harbor Laboratory Press 2024-02-07 <![CDATA[ Minimum Effective Dose of Clemastine in a Mouse Model of Preterm White Matter Injury ]]> https://biorxiv.org/content/10.1101/2024.02.08.578953v1?rss=1 Odell, E. P. Jabassini, N. Schniedewind, B. Pease-Raissi, S. E. Frymoyer, A. Christians, U. Green, A. J. Chan, J. R. Ostrem, B. E. L. 2024-02-09 doi:10.1101/2024.02.08.578953 Cold Spring Harbor Laboratory Press 2024-02-09 <![CDATA[ Single Nucleotide Polymorphism (SNP) and Antibody-based Cell Sorting (SNACS): A tool for demultiplexing single-cell DNA sequencing data ]]> https://biorxiv.org/content/10.1101/2024.02.07.579345v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@1e52aaorg.highwire.dtl.DTLVardef@c51d1dorg.highwire.dtl.DTLVardef@fa68a6org.highwire.dtl.DTLVardef@1ec6bd1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kennedy, V. E. Roy, R. Peretz, C. Koh, A. Tran, E. Smith, C. Olshen, A. 2024-02-10 doi:10.1101/2024.02.07.579345 Cold Spring Harbor Laboratory Press 2024-02-10 <![CDATA[ Biochemical, biophysical, and structural investigations of two mutants (C154Y and R312H) of the human Kir2.1 channel involved in the Andersen-Tawil syndrome. ]]> https://biorxiv.org/content/10.1101/2024.02.09.579451v1?rss=1 Zuniga, D. Zoumpoulakis, A. Veloso, R. F. Peverini, L. Shi, S. Pozza, A. Kugler, V. Bonnete, F. Bouceba, T. Wagner, R. Corringer, P.-J. Fernandes, C. A. Venien-Bryan, C. 2024-02-12 doi:10.1101/2024.02.09.579451 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ Alterations in Lysosomal, Glial and Neurodegenerative Biomarkers in Patients with Sporadic and Genetic Forms of Frontotemporal Dementia ]]> https://biorxiv.org/content/10.1101/2024.02.09.579529v1?rss=1 Hsiao-Nakamoto, J. Chiu, C.-L. VandeVrede, L. Ravi, R. Vandenberg, B. De Groot, J. Tsogtbaatar, B. Fang, M. Auger, P. Gould, N. S. Marchioni, F. Powers, C. A. Davis, S. S. Suh, J. H. Alkabsh, J. Heuer, H. W. Lago, A. L. Scearce-Levie, K. Seeley, W. W. Boeve, B. F. Rosen, H. J. Berger, A. Tsai, R. Di Paolo, G. Boxer, A. L. Bhalla, A. Huang, F. 2024-02-12 doi:10.1101/2024.02.09.579529 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ Intercalated amygdala dysfunction drives extinction deficits in the Sapap3 mouse model of obsessive-compulsive disorder ]]> https://biorxiv.org/content/10.1101/2024.02.12.578709v1?rss=1 St. Laurent, R. Kusche, K. M. Kreitzer, A. C. Malenka, R. C. 2024-02-12 doi:10.1101/2024.02.12.578709 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ Prosaposin is cleaved into saposins by multiple cathepsins in a progranulin-regulated fashion ]]> https://biorxiv.org/content/10.1101/2024.02.15.580326v1?rss=1 Hodul, M. Lane-Donovan, C. Mambou, E. A. Yang, Z. Kao, A. W. 2024-02-16 doi:10.1101/2024.02.15.580326 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ Degron-based bioPROTACs for controlling signaling in CAR T cells ]]> https://biorxiv.org/content/10.1101/2024.02.16.580396v1?rss=1 Kim, M. S. Bhargava, H. K. Shavey, G. E. Lim, W. A. El-Samad, H. Ng, A. H. 2024-02-17 doi:10.1101/2024.02.16.580396 Cold Spring Harbor Laboratory Press 2024-02-17 <![CDATA[ High-resolution single particle imaging at 100-200 keV with the Gatan Alpine direct electron detector. ]]> https://biorxiv.org/content/10.1101/2024.02.14.580363v1?rss=1 Chan, L. M. Courteau, B. J. Maker, A. Wu, M. Basanta, B. Mehmood, H. Bulkley, D. Joyce, D. Lee, B. C. Mick, S. Gulati, S. Lander, G. C. Verba, K. A. 2024-02-18 doi:10.1101/2024.02.14.580363 Cold Spring Harbor Laboratory Press 2024-02-18 <![CDATA[ Brain substates induced by DMT relate to sympathetic output and meaningfulness of the experience ]]> https://biorxiv.org/content/10.1101/2024.02.14.580356v1?rss=1 Pasquini, L. Simon, A. Gallen, C. Kettner, H. Roseman, L. Gazzaley, A. Carhart-Harris, R. Timmermann, C. 2024-02-19 doi:10.1101/2024.02.14.580356 Cold Spring Harbor Laboratory Press 2024-02-19 <![CDATA[ Activated STING in the thymus alters T cell development and selection leading to autoimmunity ]]> https://biorxiv.org/content/10.1101/2024.02.17.580803v1?rss=1 Deng, Z. Law, C. S. Kurra, S. Simchoni, N. Shum, A. K. 2024-02-19 doi:10.1101/2024.02.17.580803 Cold Spring Harbor Laboratory Press 2024-02-19 <![CDATA[ Inhibition of Indirect Pathway Activity Causes Abnormal Decision-Making In a Mouse Model of Impulse Control Disorder in Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2024.02.19.581062v1?rss=1 Zhuang, X. Lemak, J. Sridhar, S. Nelson, A. B. 2024-02-22 doi:10.1101/2024.02.19.581062 Cold Spring Harbor Laboratory Press 2024-02-22 <![CDATA[ Microglia are not required for maintenance of blood-brain barrier properties in health, but PLX5622 alters brain endothelial cholesterol metabolism ]]> https://biorxiv.org/content/10.1101/2024.02.20.580754v1?rss=1 Profaci, C. P. Harvey, S. S. Bajc, K. Zhang, T. Z. Zhang, A. Z. Nemec, K. M. McKinsey, G. L. Longworth, A. McMullen, T. P. Arnold, T. D. Lawson, D. A. Bennett, F. C. Davalos, D. Daneman, R. 2024-02-22 doi:10.1101/2024.02.20.580754 Cold Spring Harbor Laboratory Press 2024-02-22 <![CDATA[ Fetal brain response to maternal inflammation requires microglia ]]> https://biorxiv.org/content/10.1101/2024.02.21.581282v1?rss=1 Ostrem, B. Dominguez Iturza, N. Stogsdill, J. Faits, T. Kim, K. Levin, J. Z. Arlotta, P. 2024-02-22 doi:10.1101/2024.02.21.581282 Cold Spring Harbor Laboratory Press 2024-02-22 <![CDATA[ Superoxide enters neurons via LRRC8A-containing volume-regulated anion channels ]]> https://biorxiv.org/content/10.1101/2024.02.20.580732v1?rss=1 Harris, K. Uruk, G. Won, S. J. Mai, N. Baxter, P. Everaerts, K. Sah, R. Swanson, R. A. 2024-02-23 doi:10.1101/2024.02.20.580732 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Molecular and Cellular Mechanisms of Teneurin Signaling in Synaptic Partner Matching ]]> https://biorxiv.org/content/10.1101/2024.02.23.581689v1?rss=1 Xu, C. Li, Z. Lyu, C. Hu, Y. McLaughlin, C. Wong, K. K. L. Xie, Q. Luginbuhl, D. J. Li, H. Udeshi, N. Svinkina, T. Mani, D. R. Carr, S. A. Han, S. Li, T. Li, Y. Guajardo, R. Ting, A. Y. Li, J. Luo, L. 2024-02-23 doi:10.1101/2024.02.23.581689 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ PIKfyve controls dendritic cell function and tumor immunity ]]> https://biorxiv.org/content/10.1101/2024.02.28.582543v1?rss=1 Choi, J. E. Qiao, Y. Kryczek, I. Yu, J. Gurkan, J. Bao, Y. Gondal, M. Tien, J. C.-Y. Maj, T. Yazdani, S. Parolia, A. Xia, H. Zhou, J. Wei, S. Grove, S. Vatan, L. Lin, H. Li, G. Zheng, Y. Zhang, Y. Cao, X. Su, F. Wang, R. He, T. Cieslik, M. Green, M. D. Zou, W. Chinnaiyan, A. M. 2024-03-02 doi:10.1101/2024.02.28.582543 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment ]]> https://biorxiv.org/content/10.1101/2024.03.04.583400v1?rss=1 Zhu, B. Bai, Y. Yeo, Y. Y. Lu, X. Rovira-Clave, X. Chen, H. Yeung, J. Gerber, G. K. Angelo, M. Shalek, A. K. Nolan, G. P. Jiang, S. 2024-03-06 doi:10.1101/2024.03.04.583400 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Regulation of virion production by the ORF8 signal peptide across SARS-CoV-2 variants ]]> https://biorxiv.org/content/10.1101/2024.03.05.583578v1?rss=1 Khalid, M. M. Chen, I. Soveg, F. S. Taha, T. Y. Tabata, T. Suryawanshi, R. Syed, A. M. Ciling, A. McCavitt-Malvido, M. Schulze-Gahmen, U. Hayashi, J. Kim, I.-J. Fong, S. W. Batra, J. Kumar, G. R. Laurent, R. NG, L. F. Krogan, N. J. Doudna, J. A. Verdin, E. Ott, M. 2024-03-06 doi:10.1101/2024.03.05.583578 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Rare Variable M. tuberculosis Antigens induce predominant Th17 responses in human infection ]]> https://biorxiv.org/content/10.1101/2024.03.05.583634v1?rss=1 Ogongo, P. Wassie, L. Tran, A. Columbus, D. Sharling, L. Ouma, G. Ouma, S. G. Bobosha, K. Lindestam Arlehamn, C. S. Gandhi, N. R. Auld, S. C. Rengarajan, J. Day, C. L. Altman, J. D. Blumberg, H. Ernst, J. D. 2024-03-06 doi:10.1101/2024.03.05.583634 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ CD47 is Required for Mesenchymal Progenitor Proliferation and Fracture Repair ]]> https://biorxiv.org/content/10.1101/2024.03.06.583756v1?rss=1 Zondervan, R. L. Capobianco, C. A. Jenkins, D. C. Reicha, J. D. Fredrick, L. M. Lam, C. Isenberg, J. S. Ahn, J. Marcucio, R. S. Hankenson, K. D. 2024-03-06 doi:10.1101/2024.03.06.583756 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Selective vulnerability and resilience to Alzheimer's disease tauopathy as a function of genes and the connectome ]]> https://biorxiv.org/content/10.1101/2024.03.04.583403v1?rss=1 Anand, C. Torok, J. Abdelnour, F. Maia, P. Raj, A. 2024-03-08 doi:10.1101/2024.03.04.583403 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ Lack of TGFβ signaling competency predicts immune poor cancer conversion to immune rich and response to checkpoint blockade ]]> https://biorxiv.org/content/10.1101/2024.03.06.583752v1?rss=1 Moore, J. Gkantalis, J. Guix, I. Chou, W. Yuen, K. Lazar, A. Spitzer, M. H. combes, a. Barcellos-Hoff, M. H. 2024-03-08 doi:10.1101/2024.03.06.583752 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ Combining Cell-Intrinsic and -Extrinsic Resistance to HIV-1 By Engineering Hematopoietic Stem Cells for CCR5 Knockout and B Cell Secretion of Therapeutic Antibodies ]]> https://biorxiv.org/content/10.1101/2024.03.08.583956v1?rss=1 Feist, W. N. Luna, S. E. Ben-Efraim, K. Filsinger Interrante, M. V. Amorin, N. A. Johnston, N. M. Bruun, T. U. J. Ghanim, H. Y. Lesch, B. J. Dudek, A. M. Porteus, M. H. 2024-03-09 doi:10.1101/2024.03.08.583956 Cold Spring Harbor Laboratory Press 2024-03-09 <![CDATA[ Understanding the complex interplay between tau, amyloid and the network in the spatiotemporal progression of Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2024.03.05.583407v1?rss=1 Raj, A. Torok, J. 2024-03-11 doi:10.1101/2024.03.05.583407 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Cell type-specific dynamics of prefrontal gamma synchrony during flexible behavior ]]> https://biorxiv.org/content/10.1101/2024.03.08.584173v1?rss=1 Phensy, A. J. Hagopian, L. L. Sohal, V. S. 2024-03-11 doi:10.1101/2024.03.08.584173 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Bridging Domains in Chronic Lower Back Pain: Large Language Models and Ontology-driven Strategies for Knowledge Graph Construction ]]> https://biorxiv.org/content/10.1101/2024.03.11.584505v1?rss=1 Anderson, P. E. Davidson, J. M. Lin, D. Migler, T. Ho, I. Koenig, C. Bittner, M. Kaplan, S. Paraiso, M. Buhn, N. Stokes, E. Hunt, T. Ropella, G. Lotz, J. 2024-03-14 doi:10.1101/2024.03.11.584505 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Bayesian inference of state feedback control parameters for fo perturbation responses in cerebellar ataxia ]]> https://biorxiv.org/content/10.1101/2024.03.12.584554v1?rss=1 Gaines, J. L. Kim, K. S. Parrell, B. Ramanarayanan, V. Pongos, A. L. Nagarajan, S. S. Houde, J. F. 2024-03-14 doi:10.1101/2024.03.12.584554 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ CDK4 and CDK6 upregulation promotes DNA replication stress, genomic instability and resistance to EGFR targeted therapy in lung cancer ]]> https://biorxiv.org/content/10.1101/2024.03.12.584638v1?rss=1 Gini, B. Gui, P. Wu, W. Kerr, D. L. Tan, L. Barbosa, D. Olivas, V. Gomez, C. Elmes, S. Steri, V. Chakrabarti, T. Bivona, T. G. Blakely, C. M. 2024-03-14 doi:10.1101/2024.03.12.584638 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Eed controls craniofacial osteoblast differentiation and mesenchymal proliferation from the neural crest ]]> https://biorxiv.org/content/10.1101/2024.03.13.584903v1?rss=1 Casey-Clyde, T. Liu, S. J. Serrano, J. A. C. Teng, C. Jang, Y.-G. Vasudevan, H. N. Bush, J. O. Raleigh, D. R. 2024-03-14 doi:10.1101/2024.03.13.584903 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ 5-HT1B receptors mediate dopaminergic inhibition of vesicular fusion and GABA release from striatonigral synapses. ]]> https://biorxiv.org/content/10.1101/2024.03.14.584991v1?rss=1 Molinari, M. Lieberman, O. J. Sulzer, D. Santini, E. Borgkvist, A. 2024-03-14 doi:10.1101/2024.03.14.584991 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Design principles for accurate folding of DNA origami ]]> https://biorxiv.org/content/10.1101/2024.03.18.585609v1?rss=1 Aksel, T. Navarro, E. J. Fong, N. Douglas, S. M. 2024-03-19 doi:10.1101/2024.03.18.585609 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Autonomic Nervous System activity correlates with peak experiences induced by DMT and predicts increases in wellbeing ]]> https://biorxiv.org/content/10.1101/2024.03.19.585567v1?rss=1 Bonnelle, V. Feilding, A. Rosas, F. E. Nutt, D. J. Carhart-Harris, R. L. Timmermann, C. 2024-03-20 doi:10.1101/2024.03.19.585567 Cold Spring Harbor Laboratory Press 2024-03-20 <![CDATA[ Parallel Encoding of Speech in Human Frontal and Temporal Lobes ]]> https://biorxiv.org/content/10.1101/2024.03.19.585648v1?rss=1 Hullett, P. W. Leonard, M. K. Gorno-Tempini, M. L. W. Mandelli, M. L. Chang, E. F. 2024-03-20 doi:10.1101/2024.03.19.585648 Cold Spring Harbor Laboratory Press 2024-03-20 <![CDATA[ Chemoproteomics reveals immunogenic and tumor-associated cell surface substrates of ectokinase CK2α ]]> https://biorxiv.org/content/10.1101/2024.03.20.585970v1?rss=1 Delaveris, C. S. Kong, S. Glasgow, J. Loudermilk, R. P. Kirkemo, L. L. Zhao, F. Salangsang, F. Phojanakong, P. Serrano, J. A. C. Steri, V. Wells, J. A. 2024-03-20 doi:10.1101/2024.03.20.585970 Cold Spring Harbor Laboratory Press 2024-03-20 <![CDATA[ Defining the constituents and functions of a lipid-based jumbo phage compartment ]]> https://biorxiv.org/content/10.1101/2024.03.24.586471v1?rss=1 Mozumdar, D. Fossati, A. Stevenson, E. Guan, J. Nieweglowska, E. S. Rao, S. Agard, D. Swaney, D. L. Bondy-Denomy, J. 2024-03-24 doi:10.1101/2024.03.24.586471 Cold Spring Harbor Laboratory Press 2024-03-24 <![CDATA[ CITE-seq analysis reveals human cytomegalovirus and diabetes-associated adaptive NK cell alterations in cardiovascular disease. ]]> https://biorxiv.org/content/10.1101/2024.03.22.581997v1?rss=1 Armstrong, S. S. Chen, D. G. Kumar, S. Heath, J. R. Feinstein, M. Greenland, J. R. Calabrese, D. R. Lanier, L. L. Ley, K. Shemesh, A. 2024-03-26 doi:10.1101/2024.03.22.581997 Cold Spring Harbor Laboratory Press 2024-03-26 <![CDATA[ Screening and characterization of 133 physiologically-relevant environmental chemicals for reproductive toxicity ]]> https://biorxiv.org/content/10.1101/2024.03.22.584808v1?rss=1 Ulaganathan, G. Jiang, H. Canio, N. Oke, A. Armstrong, S. S. Abrahamsson, D. Varshavsky, J. R. Lam, J. Cooper, C. Robinson, J. F. Fung, J. Woodruff, T. J. Allard, P. 2024-03-27 doi:10.1101/2024.03.22.584808 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Broad therapeutic benefit of myosin inhibition in hypertrophic cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2024.03.22.584986v1?rss=1 Sen Martin, L. Fernandez Trasancos, A. Lopez Unzu, M. A. Pathak, D. Ferrarini, A. Labrador Cantarero, V. Sanchez Ortiz, D. Pricolo, M. R. Vicente, N. Velazquez Carreras, D. Sanchez Garcia, L. Nicolas Avila, J. A. Sanchez Diaz, M. Schlossarek, S. Cusso, L. Desco, M. Villalba Orero, M. Guzman Martinez, G. Calvo, E. Barriales Villa, R. Vazquez, J. Sanchez Cabo, F. Hidalgo, A. Carrier, L. Spudich, J. Ruppel, K. M. Alegre Cebollada, J. 2024-03-27 doi:10.1101/2024.03.22.584986 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Spectral graph model for fMRI: a biophysical, connectivity-based generative model for the analysis of frequency-resolved resting state fMRI ]]> https://biorxiv.org/content/10.1101/2024.03.22.586305v1?rss=1 Raj, A. Sipes, B. S. Verma, P. Mathalon, D. H. Biswal, B. B. Nagarajan, S. S. 2024-03-27 doi:10.1101/2024.03.22.586305 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Mixed clonal-aggregative multicellularity entrained by extreme salinity fluctuations in a close relative of animals ]]> https://biorxiv.org/content/10.1101/2024.03.25.586565v1?rss=1 Ros-Rocher, N. Reyes-Rivera, J. Foroughijabbari, Y. Combredet, C. Larson, B. T. Coyle, M. C. Houtepen, E. A. T. Vermeij, M. J. A. King, N. Brunet, T. 2024-03-27 doi:10.1101/2024.03.25.586565 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Transcript-specific enrichment enables profiling rare cell states via scRNA-seq ]]> https://biorxiv.org/content/10.1101/2024.03.27.587039v1?rss=1 Abay, T. Stickels, R. R. Takizawa, M. T. Nalbant, B. N. Hsieh, Y.-H. Hwang, S. Snopkowski, C. Yu, K. K. H. Abou-Mrad, Z. Tabar, V. Ludwig, L. S. Chaligne, R. Satpathy, A. T. Lareau, C. A. 2024-03-27 doi:10.1101/2024.03.27.587039 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Stable and Oscillatory Hypoxia Differentially Regulate Invasibility of Breast Cancer Associated Fibroblasts ]]> https://biorxiv.org/content/10.1101/2024.03.26.586706v1?rss=1 Du, W. Liu, Y. Afzal, J. Liu, S. Suhail, Y. Kshitiz, 2024-03-28 doi:10.1101/2024.03.26.586706 Cold Spring Harbor Laboratory Press 2024-03-28 <![CDATA[ Conserved jumbo phage factors required for protein import into a phage nucleus ]]> https://biorxiv.org/content/10.1101/2024.03.27.586873v1?rss=1 Kokontis, C. Klein, T. A. Silas, S. Bondy-Denomy, J. 2024-03-28 doi:10.1101/2024.03.27.586873 Cold Spring Harbor Laboratory Press 2024-03-28 <![CDATA[ The Molecular Architecture of the Nuclear Basket ]]> https://biorxiv.org/content/10.1101/2024.03.27.587068v1?rss=1 Singh, D. Soni, N. Hutchings, J. Echeverria, I. Shaikh, F. Duquette, M. Suslov, S. Li, Z. van Eeuwen, T. Molloy, K. Shi, Y. Wang, J. Guo, Q. Chait, B. T. Fernandez-Martinez, J. Rout, M. P. Sali, A. Villa, E. 2024-03-28 doi:10.1101/2024.03.27.587068 Cold Spring Harbor Laboratory Press 2024-03-28 <![CDATA[ py_ped_sim - A flexible forward genetic simulator for complex family pedigree analysis ]]> https://biorxiv.org/content/10.1101/2024.03.25.586501v1?rss=1 Guardado, M. A. Perez, C. Campana, S. Chavez-Rojas, B. Magana, J. Jackson, S. Samperio, E. Syas, K. Hernandez, S. Hernandez, R. Zavala, E. Rohlfs, R. 2024-03-29 doi:10.1101/2024.03.25.586501 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Challenges and Efficacy of Astrocyte-to-Neuron Reprogramming in Spinal Cord Injury: In Vitro Insights and In Vivo Outcomes ]]> https://biorxiv.org/content/10.1101/2024.03.25.586619v1?rss=1 NICEFORO, A. Zholudeva, L. V. Fernandes, S. Lane, M. A. Qiang, L. 2024-03-29 doi:10.1101/2024.03.25.586619 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ COCONUT: An analysis of coiled-coil regions in proteins ]]> https://biorxiv.org/content/10.1101/2024.03.25.586698v1?rss=1 Soni, N. Madhusudhan, M. S. 2024-03-29 doi:10.1101/2024.03.25.586698 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Plasma Proteomics of Genetic Brain Arteriosclerosis and Dementia Syndrome Identifies Signatures of Fibrosis, Angiogenesis, and Metabolic Alterations ]]> https://biorxiv.org/content/10.1101/2024.03.28.587249v1?rss=1 Keller, J. N. Radabaugh, H. Karvelas, N. Fitzsimons, S. Treiman, S. Palafox, M. F. McDonnell, L. Quiroz, Y. T. Lopera, F. J. Banerjee, D. Wang, M. M. Arboleda-Velasquez, J. F. Meschia, J. F. Ferguson, A. R. Elahi, F. M. 2024-03-29 doi:10.1101/2024.03.28.587249 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Epigenomic landscape of the human dorsal root ganglion: sex differences and transcriptional regulation of nociceptive genes ]]> https://biorxiv.org/content/10.1101/2024.03.27.587047v1?rss=1 Franco-Enzastiga, U. Inturi, N. N. Natarajan, K. Mwirigi, J. M. Mazhar, K. Schlachetzki, J. C. Schumacher, M. Price, T. J. 2024-03-30 doi:10.1101/2024.03.27.587047 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ A high-throughput method for quantifying Drosophila fecundity ]]> https://biorxiv.org/content/10.1101/2024.03.27.587093v1?rss=1 Gomez, A. Gonzalez, S. Oke, A. Luo, J. Duong, J. B. Esquerra, R. M. Zimmerman, T. Capponi, S. Fung, J. C. Nystul, T. G. 2024-03-30 doi:10.1101/2024.03.27.587093 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Mesolimbic dopamine ramps reflect environmental timescales ]]> https://biorxiv.org/content/10.1101/2024.03.27.587103v1?rss=1 Floeder, J. R. Jeong, H. Mohebi, A. K Namboodiri, V. M. 2024-03-30 doi:10.1101/2024.03.27.587103 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Differential Roles of Kinetic On- and Off-Rates in T-Cell Receptor Signal Integration Revealed with a Modified Fab'-DNA Ligand ]]> https://biorxiv.org/content/10.1101/2024.04.01.587588v1?rss=1 Wilhelm, K. B. Vissa, A. Groves, J. T. 2024-04-02 doi:10.1101/2024.04.01.587588 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ RosetteArray Platform for Quantitative High-Throughput Screening of Human Neurodevelopmental Risk ]]> https://biorxiv.org/content/10.1101/2024.04.01.587605v1?rss=1 Lundin, B. F. Knight, G. T. Fedorchak, N. J. Krucki, K. Iyer, N. Maher, J. E. Izban, N. R. Roberts, A. Cicero, M. R. Robinson, J. F. Iskandar, B. J. Willett, R. Ashton, R. S. 2024-04-02 doi:10.1101/2024.04.01.587605 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Cryo-EM Structures Reveal Tau Filaments from Down Syndrome Adopt Alzheimer's Disease Fold ]]> https://biorxiv.org/content/10.1101/2024.04.02.587507v1?rss=1 Ghosh, U. Tse, E. Shi, M. Yang, H. Wang, F. Merz, G. E. Prusiner, S. B. Southworth, D. R. Condello, C. 2024-04-03 doi:10.1101/2024.04.02.587507 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ IRF8-driven reprogramming of the immune microenvironment enhances anti-tumor adaptive immunity and reduces immunosuppression in murine glioblastoma ]]> https://biorxiv.org/content/10.1101/2024.04.02.587608v1?rss=1 Montoya, M. Collins, S. A. Chuntova, P. Patel, T. S. Nejo, T. Yamamichi, A. Kasahara, N. Okada, H. 2024-04-03 doi:10.1101/2024.04.02.587608 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Optineurin-facilitated axonal mitochondria delivery promotes neuroprotection and axon regeneration ]]> https://biorxiv.org/content/10.1101/2024.04.02.587832v1?rss=1 Liu, D. Webber, H. C. Bian, F. Xu, Y. Prakash, M. Feng, X. Yang, M. Yang, H. You, I.-J. Li, L. Liu, L. Liu, P. Huang, H. Chang, C.-Y. Liu, L. Shah, S. H. La Torre, A. Welsbie, D. S. Sun, Y. Duan, X. Goldberg, J. L. Braun, M. Lansky, Z. Hu, Y. 2024-04-03 doi:10.1101/2024.04.02.587832 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Structure and function of an intermediate GPCR-G protein complex ]]> https://biorxiv.org/content/10.1101/2024.04.02.587841v1?rss=1 Bi, M. Wang, X. Wang, J. xu, J. Sun, W. Adediwrua, V. A. Miao, Y. Cheng, Y. Ye, L. 2024-04-03 doi:10.1101/2024.04.02.587841 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Chronic hyperactivation of midbrain dopamine neurons causes preferential dopamine neuron degeneration ]]> https://biorxiv.org/content/10.1101/2024.04.05.588321v1?rss=1 Rademacher, K. L. Doric, Z. Haddad, D. Mamaligas, A. Liao, S.-C. Creed, R. Kano, K. Chatterton, Z. Fu, Y. Garcia, J. H. Vance, V. Sei, Y. Kreitzer, A. Halliday, G. Nelson, A. Margolis, E. Nakamura, K. L. 2024-04-10 doi:10.1101/2024.04.05.588321 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC ]]> https://biorxiv.org/content/10.1101/2024.04.10.588779v1?rss=1 Smith, B. J. Zhao, C. Dubinkina, V. Jin, X. Moltzau-Anderson, J. Pollard, K. 2024-04-10 doi:10.1101/2024.04.10.588779 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ A shift from pleiotropic to modular adaptation revealed by a high-resolution two-step adaptive walk ]]> https://biorxiv.org/content/10.1101/2024.04.17.589938v1?rss=1 Kinsler, G. Li, Y. Sherlock, G. J. Petrov, D. 2024-04-18 doi:10.1101/2024.04.17.589938 Cold Spring Harbor Laboratory Press 2024-04-18 <![CDATA[ Molecular basis of proton-sensing by G protein-coupled receptors ]]> https://biorxiv.org/content/10.1101/2024.04.17.590000v1?rss=1 Howard, M. K. Hoppe, N. Huang, X.-P. Macdonald, C. B. Mehrotra, E. Rockefeller Grimes, P. Zahm, A. M. Trinidad, D. D. English, J. G. Coyote-Maestas, W. Manglik, A. 2024-04-18 doi:10.1101/2024.04.17.590000 Cold Spring Harbor Laboratory Press 2024-04-18 <![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[ Depletion of Protein Phosphatase 1 Results in Persistent Activation of the Integrated Stress Response and Age-Associated Exacerbation of Pulmonary Veno-Occlusive Disease ]]> https://biorxiv.org/content/10.1101/2024.04.16.589837v1?rss=1 Prabhakar, A. Wadhwa, M. Ghatpande, P. Kumar, R. Graham, B. B. Lagna, G. Hata, A. 2024-04-20 doi:10.1101/2024.04.16.589837 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Component specific responses of the microbiomes to common chemical stressors in the human food chain ]]> https://biorxiv.org/content/10.1101/2024.04.20.590402v1?rss=1 Wasimuddin, W. Chiaia-Hernandez, A. Terrettaz, C. Thoenen, L. Caggia, V. Matteo, P. Coll-Crespi, M. Notter, M. Mukherjee, M. Chavez-Capilla, T. Ronchi, F. Ganal-Vonarburg, S. C. Grosjean, M. Bigalke, M. Spielvogel, S. Macpherson, A. Mestrot, A. Hapfelmeier, S. Erb, M. Schlaeppi, K. Ramette, A. 2024-04-21 doi:10.1101/2024.04.20.590402 Cold Spring Harbor Laboratory Press 2024-04-21 <![CDATA[ Braf-mutant Schwann cells divert to a repair phenotype to induce congenital demyelinating neuropathy ]]> https://biorxiv.org/content/10.1101/2024.04.24.590951v1?rss=1 Marechal, E. Quintana, P. Aldea, D. A. Mondielli, G. Bernard-Marissal, N. Moreno, M. Delague, V. Weiss, L. Barlier, A. Etchevers, H. C. 2024-04-25 doi:10.1101/2024.04.24.590951 Cold Spring Harbor Laboratory Press 2024-04-25 <![CDATA[ Estrogen Receptor alpha/14-3-3 molecular glues as alternative treatment strategy for endocrine resistant breast cancer ]]> https://biorxiv.org/content/10.1101/2024.04.25.591105v1?rss=1 View larger version (44K): org.highwire.dtl.DTLVardef@173545corg.highwire.dtl.DTLVardef@a78ab7org.highwire.dtl.DTLVardef@183f4b6org.highwire.dtl.DTLVardef@371606_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Visser, E. Donaldson Collier, M. Siefert, J. Konstantinidou, M. Paul, S. Berkhout, J. Virta, J. Somsen, B. Cossar, P. Miley, G. Luzietti, L. Young, L. Vareslija, D. Buluwela, L. Ali, S. Meijer, O. Arkin, M. R. Ottmann, C. O. R. Zwart, W. Brunsveld, L. 2024-04-27 doi:10.1101/2024.04.25.591105 Cold Spring Harbor Laboratory Press 2024-04-27 <![CDATA[ LSD flattens the hierarchy of directed information flow in fast whole-brain dynamics ]]> https://biorxiv.org/content/10.1101/2024.04.25.591130v1?rss=1 Shinozuka, K. Tewarie, P. Luppi, A. Lynn, C. Roseman, L. Muthukumaraswamy, S. D. Nutt, D. J. Carhart-Harris, R. Deco, G. Kringelbach, M. L. 2024-04-28 doi:10.1101/2024.04.25.591130 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Microstructural Mapping of Neural Pathways in Alzheimer's Disease using Macrostructure-Informed Normative Tractometry ]]> https://biorxiv.org/content/10.1101/2024.04.25.591183v1?rss=1 Feng, Y. Chandio, B. Q. Villalon-Reina, J. E. Thomopoulos, S. I. Nir, T. M. Benavidez, S. Laltoo, E. Chattopadhyay, T. Joshi, H. Venkatasubramanian, G. John, J. P. Jahanshad, N. Reid, R. I. Jack, C. R. Weiner, M. M. Thompson, P. M. the Alzheimer's Disease Neuroimaging Initiative, 2024-04-28 doi:10.1101/2024.04.25.591183 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Unifying community-wide whole-brain imaging datasets enables robust automated neuron identification and reveals determinants of neuron positioning in C. elegans ]]> https://biorxiv.org/content/10.1101/2024.04.28.591397v1?rss=1 Sprague, D. Y. Rusch, K. Dunn, R. L. Borchardt, J. Bubnis, G. Chiu, G. Wen, C. Suzuki, R. Chaudhary, S. Dichter, B. Ly, R. Onami, S. Lu, H. Kimura, K. Yemini, E. I. Kato, S. 2024-04-30 doi:10.1101/2024.04.28.591397 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ P66 is a bacterial mimic of CD47 that binds the anti-phagocytic receptor SIRPα and facilitates macrophage evasion by Borrelia burgdorferi ]]> https://biorxiv.org/content/10.1101/2024.04.29.591704v1?rss=1 Tal, M. C. Hansen, P. S. Ogasawara, H. A. Feng, Q. Volk, R. F. Lee, B. Casebeer, S. E. Blacker, G. S. Shoham, M. Galloway, S. D. Sapiro, A. L. Dulgeroff, L.-B. T. Raveh, T. Pothineni, V. R. Potula, H.-H. S. Rajadas, J. Bastounis, E. E. Chou, S. Robinson, W. H. Coburn, J. Weissman, I. L. Zaro, B. W. 2024-04-30 doi:10.1101/2024.04.29.591704 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ An shRNA screen in primary human beta cells identifies the serotonin 1F receptor as a negative regulator of survival during transplant ]]> https://biorxiv.org/content/10.1101/2024.05.01.591950v1?rss=1 Lee, R. A. Chopra, D. G. Nguyen, V. Huang, X.-P. Zhang, Y. Shariati, K. Yiv, N. Schugar, R. Annes, J. Roth, B. L. Ku, G. 2024-05-03 doi:10.1101/2024.05.01.591950 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Genetic variants associated with cell-type-specific intra-individual gene expression variability reveal new mechanisms of genome regulation ]]> https://biorxiv.org/content/10.1101/2024.05.05.592598v1?rss=1 Powell, J. E. Xue, A. Yazar, S. Alquicira, J. Cuomo, A. Senabouth, A. Gordon, G. Kathail, P. Ye, J. Hewitt, A. 2024-05-07 doi:10.1101/2024.05.05.592598 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ Data-driven fine-grained region discovery in the mouse brain with transformers ]]> https://biorxiv.org/content/10.1101/2024.05.05.592608v1?rss=1 Lee, A. J. Yao, S. Lusk, N. Zeng, H. Tasic, B. Abbasi-Asl, R. 2024-05-07 doi:10.1101/2024.05.05.592608 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ NEK1 modulates neurite outgrowth in motor neurons through coordinating retromer formation ]]> https://biorxiv.org/content/10.1101/2024.05.06.592854v1?rss=1 Huang, X. Oses, J. A. Kawaguchi, R. Perrault, L. Frost, D. Chen, K. Guo, F. Zhang, B. Zhao, P. Ho, T. S.-y. Pandey, R. Geschwind, D. H. Burlingame, A. Woolf, C. 2024-05-08 doi:10.1101/2024.05.06.592854 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Closed-loop modulation of remote hippocampal representations with neurofeedback ]]> https://biorxiv.org/content/10.1101/2024.05.08.593085v1?rss=1 Coulter, M. E. Gillespie, A. K. Chu, J. P. Denovellis, E. L. Nguyen, T. T. K. Liu, D. Wadhwani, K. Sharma, B. Wang, K. Deng, X. Eden, U. Kemere, C. Frank, L. M. 2024-05-08 doi:10.1101/2024.05.08.593085 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ A mismatch between striatal cholinergic pauses and dopaminergic reward prediction errors ]]> https://biorxiv.org/content/10.1101/2024.05.09.593336v1?rss=1 Duhne, M. Mohebi, A. Kim, K. Pelattini, L. Berke, J. D. 2024-05-09 doi:10.1101/2024.05.09.593336 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ Indels allow antiviral proteins to evolve functional novelty inaccessible by missense mutations ]]> https://biorxiv.org/content/10.1101/2024.05.07.592993v1?rss=1 Tenthorey, J. del Banco, S. Ramzan, I. Klingenberg, H. Liu, C. Emerman, M. Malik, H. S. 2024-05-10 doi:10.1101/2024.05.07.592993 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Endogenous OptoRhoGEFs reveal biophysical principles of epithelial tissue furrowing ]]> https://biorxiv.org/content/10.1101/2024.05.12.593711v1?rss=1 Countryman, A. D. Doherty, C. A. Herrera-Perez, R. M. Kasza, K. E. 2024-05-12 doi:10.1101/2024.05.12.593711 Cold Spring Harbor Laboratory Press 2024-05-12 <![CDATA[ In Utero Hematopoietic Stem Cell Transplant for Fanconi Anemia ]]> https://biorxiv.org/content/10.1101/2024.05.09.592452v1?rss=1 Swartzrock, L. Dib, C. Denis, M. Willner, H. Ho, K. Haslett, E. Krampf, M. R. Girsen, A. Blumenfeld, Y. J. El-Sayed, Y. Y. Roncarolo, M. G. MacKenzie, T. C. Czechowicz, A. D. 2024-05-14 doi:10.1101/2024.05.09.592452 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Pro-inflammatory macrophage activation does not require inhibition of mitochondrial respiration ]]> https://biorxiv.org/content/10.1101/2024.05.10.593451v1?rss=1 Ball, A. B. Jones, A. E. Nguyen, K. B. Rios, A. Marx, N. Hsieh, W. Y. Yang, K. Desousa, B. R. Kim, K. K. O. Veliova, M. del Mundo, Z. M. Shirihai, O. S. Beninca, C. Stiles, L. Bensinger, S. J. Divakaruni, A. S. 2024-05-14 doi:10.1101/2024.05.10.593451 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Sexually dimorphic regulatory T cell-derived enkephalin imparts pregnancy-induced analgesia ]]> https://biorxiv.org/content/10.1101/2024.05.11.593442v1?rss=1 Midavaine, E. Moraes, B. C. Benitez, J. Rodriguez, S. R. Braz, J. M. Kochhar, N. P. Eckalbar, W. L. Domingos, A. I. Pintar, J. E. Basbaum, A. I. Kashem, S. W. 2024-05-14 doi:10.1101/2024.05.11.593442 Cold Spring Harbor Laboratory Press 2024-05-14 <![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[ Stress hyperglycemia exacerbates inflammatory brain injury after stroke ]]> https://biorxiv.org/content/10.1101/2024.05.14.594195v1?rss=1 Won, S. J. Zhang, Y. Butler, N. J. Kim, K. Mocanu, E. Nzoutchoum, O. T. Lakkaraju, R. Davis, J. Ghosh, S. Swanson, R. A. 2024-05-14 doi:10.1101/2024.05.14.594195 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Likelihood-based interactive local docking into cryo-EM maps in ChimeraX ]]> https://biorxiv.org/content/10.1101/2024.05.16.594509v1?rss=1 Read, R. J. Pettersen, E. F. McCoy, A. J. Croll, T. I. Terwilliger, T. C. Poon, B. K. Meng, E. C. Liebschner, D. Adams, P. D. 2024-05-16 doi:10.1101/2024.05.16.594509 Cold Spring Harbor Laboratory Press 2024-05-16 <![CDATA[ The mitochondrial stress- induced protein carboxyl-terminal alanine and threonine tailing (msiCAT-tailing) promotes glioblastoma tumorigenesis by modulating mitochondrial functions ]]> https://biorxiv.org/content/10.1101/2024.05.15.594447v1?rss=1 Cai, T. Zhang, B. Reddy, E. Wu, Y. Tang, Y. Mondal, I. Wang, J. Ho, W. S. Lu, R. O. Wu, Z. 2024-05-18 doi:10.1101/2024.05.15.594447 Cold Spring Harbor Laboratory Press 2024-05-18 <![CDATA[ Transcriptional control of central T cell tolerance by NR4A family nuclear receptors ]]> https://biorxiv.org/content/10.1101/2024.05.19.594881v1?rss=1 Nielsen, H. V. Mueller, J. L. Hiwa, R. Yang, L. Proekt, I. Rackaityte, E. Aylard, D. Scharer, C. D. Anderson, M. Au-Yeung, B. B. Zikherman, J. 2024-05-21 doi:10.1101/2024.05.19.594881 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Histologic variants in bladder cancer harbor aggressive molecular features including TM4SF1 expression and a CA125+ cell state ]]> https://biorxiv.org/content/10.1101/2024.05.20.595039v1?rss=1 Yang, H. Song, H. Yip, E. Chang, K. Allegakoen, P. Lu, K. L. Hui, K. Pham, J. Kasap, C. Kumar, V. Gayle, J. Stohr, B. A. Ding, C.-K. C. Wiita, A. P. Meng, M. V. Chou, J. Porten, S. P. Huang, F. W. 2024-05-21 doi:10.1101/2024.05.20.595039 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ MHConstructor: A high-throughput, haplotype-informed solution to the MHC assembly challenge ]]> https://biorxiv.org/content/10.1101/2024.05.20.595060v1?rss=1 Wade, K. J. Suseno, R. Kizer, K. Williams, J. Boquett, J. Caillier, S. Pollock, N. R. Renschen, A. Santaniello, A. Oksenberg, J. R. Norman, P. J. Augusto, D. G. Hollenbach, J. A. 2024-05-21 doi:10.1101/2024.05.20.595060 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ A role for pH dynamics regulating transcription factor DNA binding selectivity ]]> https://biorxiv.org/content/10.1101/2024.05.21.595212v1?rss=1 Kisor, K. P. Ruiz, D. G. Jacobson, M. P. Barber, D. L. 2024-05-21 doi:10.1101/2024.05.21.595212 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Norepinephrine Signals Through Astrocytes To Modulate Synapses ]]> https://biorxiv.org/content/10.1101/2024.05.21.595135v1?rss=1 Lefton, K. B. Wu, Y. Yen, A. Okuda, T. Zhang, Y. Dai, Y. Walsh, S. Manno, R. Dougherty, J. Samineni, V. K. Simpson, P. C. Papouin, T. 2024-05-22 doi:10.1101/2024.05.21.595135 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ Analyzing high-throughput assay data to advance the rapid screening of environmental chemicals for human reproductive toxicity ]]> https://biorxiv.org/content/10.1101/2024.05.21.595187v1?rss=1 Varshavsky, J. R. Lam, J. Cooper, C. Allard, P. Fung, J. Oke, A. Kumar, R. Robinson, J. Woodruff, T. 2024-05-22 doi:10.1101/2024.05.21.595187 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ Human neural dynamics of real-world and imagined navigation ]]> https://biorxiv.org/content/10.1101/2024.05.23.595237v1?rss=1 Seeber, M. Stangl, M. Vallejo, M. Topalovic, U. Hiller, S. Halpern, C. H. Langevin, J.-P. Rao, V. R. Fried, I. Eliashiv, D. Suthana, N. 2024-05-23 doi:10.1101/2024.05.23.595237 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ To be unique or blend in: dynamics of male African elephant character durability across time and social contexts ]]> https://biorxiv.org/content/10.1101/2024.05.24.595367v1?rss=1 O'Connell-Rodwell, C. E. Berezin, J. L. Kinzley, C. Freeman, P. T. Sandri, M. N. Kieschnick, D. Abarca, M. Hayssen, V. 2024-05-26 doi:10.1101/2024.05.24.595367 Cold Spring Harbor Laboratory Press 2024-05-26 <![CDATA[ Loss of neutrophil Shp1 produces hemorrhagic and lethal acute lung injury ]]> https://biorxiv.org/content/10.1101/2024.05.23.595575v1?rss=1 Moussavi-Harami, S. F. Cleary, S. J. Magnen, M. Seo, Y. Conrad, C. English, B. C. Qiu, L. Wang, K. M. Abram, C. L. Lowell, C. A. Looney, M. R. 2024-05-28 doi:10.1101/2024.05.23.595575 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ Decellularized biohybrid nerve promotes motor axon projections ]]> https://biorxiv.org/content/10.1101/2024.05.24.595727v1?rss=1 0.2 mS/cm), mechanical alignment, intact mesostructures, and high compatibility with cells and blood. To test the biohybrid nerves effectiveness in promoting motor axon growth, we used human Spinal Cord Spheroids (hSCSs) from HUES 3 Hb9:GFP cells, with motor axons labeled with green fluorescent protein (GFP). Seeding hSCS onto one end of the conduit allowed motor axon outgrowth into the biohybrid nerve. Our construct effectively promoted directed motor axon growth, which improved significantly after seeding the grafts with Schwann cells. This study presents a promising approach for reconstructing axonal tracts in humans. ]]> Mehta, A. S. Zhang, S. L. Xie, X. Khanna, S. Tropp, J. Ji, X. Daso, R. Franz, C. Jordan, S. Rivnay, J. 2024-05-29 doi:10.1101/2024.05.24.595727 Cold Spring Harbor Laboratory Press 2024-05-29 <![CDATA[ Autism gene variants disrupt enteric neuron migration and cause gastrointestinal dysmotility ]]> https://biorxiv.org/content/10.1101/2024.05.28.593642v1?rss=1 McCluskey, K. E. Stovell, K. M. Law, K. Kostyanovskaya, E. Schmidt, J. Exner, C. R. Dea, J. Brimble, E. State, M. W. Willsey, A. J. Willsey, H. R. 2024-05-29 doi:10.1101/2024.05.28.593642 Cold Spring Harbor Laboratory Press 2024-05-29 <![CDATA[ Predicted mechanistic impacts of human protein missense variants ]]> https://biorxiv.org/content/10.1101/2024.05.29.596373v1?rss=1 Janes, J. Muller, M. Selvaraj, S. Manoel, D. Stephenson, J. Goncalves, C. Lafita, A. Polacco, B. Obernier, K. Alasoo, K. Lemos, M. C. Krogan, N. Martin, M. Saraiva, L. R. Burke, D. Beltrao, P. 2024-05-29 doi:10.1101/2024.05.29.596373 Cold Spring Harbor Laboratory Press 2024-05-29 <![CDATA[ Chromatin profiling identifies putative dual roles for H3K27me3 in regulating transposons and cell type specific genes in choanoflagellates ]]> https://biorxiv.org/content/10.1101/2024.05.28.596151v1?rss=1 Gahan, J. M. Helfrich, L. W. Wetzel, L. A. Bhanu, N. V. Yuan, Z.-F. Garcia, B. A. Klose, R. Booth, D. S. 2024-05-30 doi:10.1101/2024.05.28.596151 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Dual Mechanism of Action: Exosomes from Human iPSC-Cardiomyocytes and Mesenchymal Stem Cells Restore Injured Myocardium ]]> https://biorxiv.org/content/10.1101/2024.05.29.596548v1?rss=1 Tzng, E. Bayardo, N. A. Ikeda, G. Takashima, H. Lyons, J. Bennett, M. O'Brien, C. G. Yang, P. C. 2024-05-30 doi:10.1101/2024.05.29.596548 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Targeting complement C3a receptor resolves mitochondrial hyperfusion and subretinal microglial activation in progranulin-deficient frontotemporal dementia ]]> https://biorxiv.org/content/10.1101/2024.05.29.595206v1?rss=1 Tan, L. X. Oertel, F. C. Cheng, A. Cobigo, Y. Keihani, A. Bennett, D. Abdelhak, A. Montes, S. C. Chapman, M. Chen, R. Cordano, C. Ward, M. Casaletto, K. Kramer, J. Rosen, H. H. Boxer, A. L. Miller, B. L. Green, A. Elahi, F. Lakkaraju, A. 2024-06-01 doi:10.1101/2024.05.29.595206 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ CRISPRi-based screen of Autism Spectrum Disorder risk genes in microglia uncovers roles of ADNP in microglia endocytosis and uptake of synaptic material ]]> https://biorxiv.org/content/10.1101/2024.06.01.596962v1?rss=1 Teter, O. M. Draeger, N. M. Sattler, S. M. McQuade, A. Holmes, B. B. Papakis, V. Leng, K. Boggess, S. Shin, D. Nowakowski, T. J. Wells, J. Kampmann, M. 2024-06-01 doi:10.1101/2024.06.01.596962 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Generalized cue reactivity in dopamine neurons after opioids ]]> https://biorxiv.org/content/10.1101/2024.06.02.597025v1?rss=1 Lehmann, C. M. Miller, N. E. Nair, V. S. Costa, K. M. Schoenbaum, G. Moussawi, K. 2024-06-02 doi:10.1101/2024.06.02.597025 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Cross Tissue DNAm Biomarker Prediction using Transfer Learning ]]> https://biorxiv.org/content/10.1101/2024.06.01.596949v1?rss=1 McGreevy, K. M. Chen, B. H. Horvath, S. Telesca, D. 2024-06-03 doi:10.1101/2024.06.01.596949 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Differences in phenotype between long-lived memory B cells against Plasmodium falciparum merozoite antigens and variant surface antigens ]]> https://biorxiv.org/content/10.1101/2024.06.01.596978v1?rss=1 Reyes, R. A. Turner, L. Ssewanyana, I. Jagannathan, P. Feeney, M. E. Lavstsen, T. Greenhouse, B. Bol, S. Bunnik, E. M. 2024-06-03 doi:10.1101/2024.06.01.596978 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Defective interferon signaling in the circulating monocytes of type 2 diabetic mice ]]> https://biorxiv.org/content/10.1101/2024.06.03.597050v1?rss=1 Omodaka, S. Kato, Y. Sato, Y. Falcone-Juengert, J. Zhang, H. Kanoke, A. Eckalbar, W. L. Endo, H. Hsieh, C. L. Aran, D. Liu, J. 2024-06-03 doi:10.1101/2024.06.03.597050 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Molecular effects of indoor tanning ]]> https://biorxiv.org/content/10.1101/2024.06.04.597225v1?rss=1 Gerami, P. Tandukar, B. Deivendran, D. Olivares, S. Chen, L. Tang, J. Tan, T. Sharma, H. Bandari, A. K. Cruz-Pacheco, N. Chang, D. Marty, A. Olshen, A. Murad, N. F. Song, J. Lee, J. Yeh, I. Shain, H. 2024-06-05 doi:10.1101/2024.06.04.597225 Cold Spring Harbor Laboratory Press 2024-06-05 <![CDATA[ At the onset of active whisking, the input layer of barrel cortex exhibits a 24 h window of increased excitability that depends on prior experience. ]]> https://biorxiv.org/content/10.1101/2024.06.04.597353v1?rss=1 Shallow, M. C. Tian, L. Lin, H. Lefton, K. B. Chen, S. Dougherty, J. Culver, J. P. Lambo, M. E. Hengen, K. B. 2024-06-05 doi:10.1101/2024.06.04.597353 Cold Spring Harbor Laboratory Press 2024-06-05 <![CDATA[ PBX1 and PBX3 transcription factors regulate SHH expression in the Frontonasal Ectodermal Zone through complementary mechanisms ]]> https://biorxiv.org/content/10.1101/2024.06.04.597450v1?rss=1 Mok, C. H. Hu, D. Losa, M. Risolino, M. Selleri, L. Marcucio, R. 2024-06-05 doi:10.1101/2024.06.04.597450 Cold Spring Harbor Laboratory Press 2024-06-05 <![CDATA[ Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity ]]> https://biorxiv.org/content/10.1101/2024.06.04.597471v1?rss=1 Trepka, K. Kidder, W. A. Kyaw, T. S. Olson, C. A. Upadhyay, V. Noecker, C. Stanfield, D. Steiding, P. Spanogiannopoulos, P. Dumlao, D. Turnbaugh, J. A. Stachler, M. D. Van Blarigan, E. L. Venook, A. P. Atreya, C. E. Turnbaugh, P. J. 2024-06-06 doi:10.1101/2024.06.04.597471 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Directionality bias is necessary to explain spatiotemporal progression of pathology in mouse models of tauopathy ]]> https://biorxiv.org/content/10.1101/2024.06.04.597478v1?rss=1 Torok, J. Mezias, C. Raj, A. 2024-06-06 doi:10.1101/2024.06.04.597478 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ The disease-causing tau V337M mutation induces tau hypophosphorylation and perturbs axon morphology pathways ]]> https://biorxiv.org/content/10.1101/2024.06.04.597496v1?rss=1 Mohl, G. A. Dixon, G. Marzette, E. McKetney, J. Samelson, A. J. Pereda Serras, C. Jin, J. Li, A. Boggess, S. C. Swaney, D. L. Kampmann, M. 2024-06-06 doi:10.1101/2024.06.04.597496 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Longitudinal Associations Between MicroRNAs and Weight in the Diabetes Prevention Program ]]> https://biorxiv.org/content/10.1101/2024.06.05.597590v1?rss=1 Flowers, E. Stroebel, B. Gong, X. Lewis, K. A. Aouizerat, B. Gadgil, M. Kanaya, A. M. Zhang, L. 2024-06-07 doi:10.1101/2024.06.05.597590 Cold Spring Harbor Laboratory Press 2024-06-07 <![CDATA[ Mapping genes for human face shape: exploration of univariate phenotyping strategies ]]> https://biorxiv.org/content/10.1101/2024.06.06.597731v1?rss=1 Yuan, M. Goovaerts, S. Vanneste, M. Matthews, H. Hoskens, H. Richmond, S. Klein, O. D. Spritz, R. A. Hallgrimsson, B. Walsh, S. Shriver, M. D. Shaffer, J. R. Weinberg, S. M. Peeters, H. Claes, P. 2024-06-07 doi:10.1101/2024.06.06.597731 Cold Spring Harbor Laboratory Press 2024-06-07 <![CDATA[ Insula uses overlapping codes for emotion in self and others ]]> https://biorxiv.org/content/10.1101/2024.06.04.596966v1?rss=1 Xiao, J. Adkinson, J. A. Allawala, A. B. Banks, G. Bartoli, E. Fan, X. Mocchi, M. Pascuzzi, B. Pulapaka, S. Franch, M. C. Mathew, S. J. Mathura, R. K. Myers, J. Pirtle, V. Provenza, N. R. Shofty, B. Watrous, A. J. Pitkow, X. Goodman, W. K. Pouratian, N. Sheth, S. A. Bijanki, K. R. Hayden, B. Y. 2024-06-08 doi:10.1101/2024.06.04.596966 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Noise induces intercellular Ca2+ signaling waves and the unfolded protein response in the hearing cochlea ]]> https://biorxiv.org/content/10.1101/2024.06.05.597671v1?rss=1 Park, Y. Li, J. Ismail Mohamad, N. Matthews, I. R. Santra, P. Sherr, E. H. Chan, D. K. 2024-06-08 doi:10.1101/2024.06.05.597671 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ CLCC1 promotes hepatic neutral lipid flux and nuclear pore complex assembly ]]> https://biorxiv.org/content/10.1101/2024.06.07.597858v1?rss=1 Mathiowetz, A. J. Meymand, E. S. Deol, K. K. Parlakgul, G. Lange, M. Pang, S. P. Roberts, M. A. Torres, E. F. Jorgens, D. M. Zalpuri, R. Kang, M. Boone, C. Zhang, Y. Morgens, D. W. Tso, E. Zhou, Y. Talukdar, S. Levine, T. Ku, G. Arruda, A. P. Olzmann, J. 2024-06-08 doi:10.1101/2024.06.07.597858 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ MITOCHONDRIAL ANTIVIRAL PATHWAYS CONTROL ANTI-HIV RESPONSES AND ISCHEMIC STROKE OUTCOMES VIA THE RIG-1 SIGNALING AND INNATE IMMUNITY MECHANISMS ]]> https://biorxiv.org/content/10.1101/2024.06.07.598027v1?rss=1 Torices, S. Moreno, T. Ramaswamy, S. Naranjo, O. Teglas, T. Osborne, O. M. Park, M. Sun, E. Toborek, M. 2024-06-08 doi:10.1101/2024.06.07.598027 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ The Capicua C1 Domain is Required for Full Activity of the CIC::DUX4 Fusion Oncoprotein ]]> https://biorxiv.org/content/10.1101/2024.06.06.597815v1?rss=1 Luck, C. Jacobs, K. A. Okimoto, R. A. 2024-06-09 doi:10.1101/2024.06.06.597815 Cold Spring Harbor Laboratory Press 2024-06-09 <![CDATA[ GABA production induced by imipridones is a targetable and imageable metabolic alteration in diffuse midline gliomas ]]> https://biorxiv.org/content/10.1101/2024.06.07.597982v1?rss=1 Batsios, G. Udutha, S. Taglang, C. Gillespie, A. M. Lau, B. Ji, S. Phoenix, T. Mueller, S. Venneti, S. Koschmann, C. Viswanath, P. 2024-06-10 doi:10.1101/2024.06.07.597982 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Ferroptosis regulates hemolysis in stored murine and human red blood cells ]]> https://biorxiv.org/content/10.1101/2024.06.11.598512v1?rss=1 View larger version (117K): org.highwire.dtl.DTLVardef@150fec2org.highwire.dtl.DTLVardef@859c43org.highwire.dtl.DTLVardef@1d60156org.highwire.dtl.DTLVardef@f1b91e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> D'Alessandro, A. Keele, G. R. Hay, A. Nemkov, T. Earley, E. J. Stephenson, D. Vincent, M. Deng, X. Stone, M. Dzieciatkowska, M. Hansen, K. Kleinman, S. Spitalnik, S. L. Roubinian, N. Norris, P. J. Busch, M. P. Page, G. P. Stockwell, B. R. Churchill, G. A. Zimring, J. C. 2024-06-11 doi:10.1101/2024.06.11.598512 Cold Spring Harbor Laboratory Press 2024-06-11 <![CDATA[ Prosapip1 in the dorsal hippocampus mediates synaptic protein composition, long-term potentiation, and spatial memory ]]> https://biorxiv.org/content/10.1101/2024.06.13.597459v1?rss=1 Hoisington, Z. W. Gangal, H. Phamluong, K. Shukla, C. Ehinger, Y. Moffat, J. J. Homanics, G. E. Wang, J. Ron, D. 2024-06-13 doi:10.1101/2024.06.13.597459 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Microglia target synaptic sites early during excitatory circuit disassembly in neurodegeneration ]]> https://biorxiv.org/content/10.1101/2024.06.13.598914v1?rss=1 Yu, A. Tan, L. X. Lakkaraju, A. Santina, L. D. Ou, Y. 2024-06-14 doi:10.1101/2024.06.13.598914 Cold Spring Harbor Laboratory Press 2024-06-14 <![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[ Static and Dynamic Cross-Network Functional Connectivity Shows Elevated Entropy in Schizophrenia Patients ]]> https://biorxiv.org/content/10.1101/2024.06.15.599084v1?rss=1 Maksymchuk, N. Bustillo, J. R. Mathalon, D. H. Preda, A. Calhoun, V. D. 2024-06-17 doi:10.1101/2024.06.15.599084 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ The effect of circulating neutralizing antibodies on the replication of SARS-CoV-2 variants following post-vaccination infections. ]]> https://biorxiv.org/content/10.1101/2024.06.18.599357v1?rss=1 Knight, M. A. G. Kelly, J. D. Lu, S. Tassetto, M. A. Goldberg, S. A. Zhang, A. Pineda-Ramirez, J. Anglin, K. Davidson, M. Chen, J. Y. Fortes-Cobby, M. Park, S. Martinez, A. So, M. Donovan, A. Viswanathan, B. Richardson, E. T. McIlwain, D. R. Gaudilliere, B. Rutishauser, R. L. Chenna, A. Petropoulos, C. Wrin, T. Deeks, S. Abedi, G. Saydah, S. Martin, J. Briggs-Hagen, M. Midgley, C. M. Peluso, M. Andino, R. 2024-06-19 doi:10.1101/2024.06.18.599357 Cold Spring Harbor Laboratory Press 2024-06-19 <![CDATA[ ProBASS: a language model with sequence and structural features for predicting the effect of mutations on binding affinity ]]> https://biorxiv.org/content/10.1101/2024.06.21.600041v1?rss=1 Gurusinghe, S. N. S. Wu, Y. DeGrado, W. Shifman, J. M. 2024-06-26 doi:10.1101/2024.06.21.600041 Cold Spring Harbor Laboratory Press 2024-06-26 <![CDATA[ Long-term NMN treatment increases lifespan and healthspan in mice in a sex dependent manner ]]> https://biorxiv.org/content/10.1101/2024.06.21.599604v1?rss=1 Kane, A. E. Chellappa, K. Schultz, M. B. Arnold, M. Li, J. Amorim, J. Diener, C. Zhu, D. Mitchell, S. J. Griffin, P. T. Tian, X. Petty, C. Conway, R. Walsh, K. Shelerud, L. Duesing, C. Mueller, A. Li, K. McNamara, M. Shima, R. T. deCabo, R. Gibbons, S. M. Wu, L. E. Ikeno, Y. Baur, J. A. Rajman, L. Sinclair, D. A. 2024-06-27 doi:10.1101/2024.06.21.599604 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Coordinated Regulation of Renal Glucose Reabsorption and Gluconeogenesis by mTORC2 and Potassium ]]> https://biorxiv.org/content/10.1101/2024.06.22.600201v1?rss=1 Demko, J. Saha, B. Takagi, E. Manis, A. Weber, R. Pearce, D. 2024-06-27 doi:10.1101/2024.06.22.600201 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Scalable intracellular delivery via microfluidic vortex shedding enhances the function of chimeric antigen receptor T-cells ]]> https://biorxiv.org/content/10.1101/2024.06.25.600671v1?rss=1 Sytsma, B. J. Allain, V. Bourke, S. Faizee, F. Fathi, M. Berdeaux, R. Ferreira, L. M. R. Brewer, J. Li, L. Pan, F. L. Rothrock, A. G. Nyberg, W. A. Li, Z. Wilson, L. H. Eyquem, J. Pawell, R. S. 2024-06-27 doi:10.1101/2024.06.25.600671 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Structure of the human K2P13.1(THIK-1) channel reveals a novel hydrophilic pore restriction and lipid cofactor site ]]> https://biorxiv.org/content/10.1101/2024.06.26.600491v1?rss=1 Roy-Chowdhury, S. Jang, S. Abderemane-Ali, F. Naughton, F. Grabe, M. Minor, D. L. 2024-06-27 doi:10.1101/2024.06.26.600491 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Long-term in vitro exposure of Treponema pallidum to sub-bactericidal doxycycline did not induce resistance: Implications for doxy-PEP and syphilis ]]> https://biorxiv.org/content/10.1101/2024.06.27.600921v1?rss=1 Tantalo, L. C. Luetkemeyer, A. Lieberman, N. A. P. Nunley, E. Avendano, C. Greninger, A. L. Celum, C. Giacani, L. 2024-06-27 doi:10.1101/2024.06.27.600921 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ TOMM40 regulates hepatocellular and plasma lipid metabolism via an LXR-dependent pathway ]]> https://biorxiv.org/content/10.1101/2024.06.27.600910v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@17b0c8forg.highwire.dtl.DTLVardef@17599aaorg.highwire.dtl.DTLVardef@1bb6ab2org.highwire.dtl.DTLVardef@15a035f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yang, N. V. Chao, J. Y. Garton, K. A. Tran, T. King, S. Orr, J. Oei, J. H. Kang, M. Zalpuri, R. Jorgens, D. M. Konchadi, P. Chorba, J. S. Theusch, E. Krauss, R. M. 2024-06-29 doi:10.1101/2024.06.27.600910 Cold Spring Harbor Laboratory Press 2024-06-29 <![CDATA[ Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM) ]]> https://biorxiv.org/content/10.1101/2024.06.27.600934v1?rss=1 Goldman, M. Zhao, C. Pollard, K. S. 2024-06-30 doi:10.1101/2024.06.27.600934 Cold Spring Harbor Laboratory Press 2024-06-30 <![CDATA[ Peripheral glia and neurons jointly regulate activity-induced synaptic remodeling at the Drosophila neuromuscular junction ]]> https://biorxiv.org/content/10.1101/2024.06.27.600908v1?rss=1 Chang, Y.-C. Peng, Y.-J. Lee, J. Y. Chang, K. T. 2024-07-02 doi:10.1101/2024.06.27.600908 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Uncovering differential tolerance to deletions versus substitutions with a protein language model ]]> https://biorxiv.org/content/10.1101/2024.06.27.601077v1?rss=1 Goldman, G. Chati, P. Ntranos, V. 2024-07-02 doi:10.1101/2024.06.27.601077 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Neural Stem Cell Relay from B1 to B2 cells in the adult mouse Ventricular-Subventricular Zone ]]> https://biorxiv.org/content/10.1101/2024.06.28.600695v1?rss=1 Cebrian-Silla, A. Assis Nascimento, M. Mancia Leon, W. Gonzalez-Granero, S. Romero-Rodriguez, R. Obernier, K. Steffen, D. M. Lim, D. A. Garcia-Verdugo, J. M. Alvarez-Buylla, A. 2024-07-02 doi:10.1101/2024.06.28.600695 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ HIV-1 control in vivo is related to the number but not the fraction of infected cells with viral unspliced RNA ]]> https://biorxiv.org/content/10.1101/2024.07.01.601579v1?rss=1 Capoferri, A. A. Wiegand, A. Hong, F. Jacobs, J. L. Spindler, J. Musick, A. Bale, M. J. Shao, W. Sobolewski, M. D. Cillo, A. R. Luke, B. T. Fennessey, C. M. Gorelick, R. J. Hoh, R. Halvas, E. K. Deeks, S. G. Coffin, J. M. Mellors, J. W. Kearney, M. F. 2024-07-02 doi:10.1101/2024.07.01.601579 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Multiplatform molecular profiling and functional genomic screens identify prognostic signatures and mechanisms underlying MEK inhibitor response in somatic NF1 mutant glioblastoma ]]> https://biorxiv.org/content/10.1101/2024.07.01.601334v1?rss=1 Pan, S. Mirchia, K. Payne, E. Liu, S. J. Al-Adli, N. Peeran, Z. Shukla, P. Young, J. S. Gupta, R. Wu, J. Pak, J. Seo, K. Ozawa, T. Na, B. Reddy, A. T. Braunstein, S. E. Phillips, J. J. Chang, S. Solomon, D. A. Perry, A. Raleigh, D. R. Berger, M. S. Abate, A. R. Vasudevan, H. N. 2024-07-03 doi:10.1101/2024.07.01.601334 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ The Neurolipid Atlas: a lipidomics resource for neurodegenerative diseases uncovers cholesterol as a regulator of astrocyte reactivity impaired by ApoE4 ]]> https://biorxiv.org/content/10.1101/2024.07.01.601474v1?rss=1 Feringa, F. M. Koppes-den Hertog, S. J. Wang, L. Derks, R. J. E. Kruijff, I. Erlebach, L. Heijneman, J. Miramontes, R. Pömpner, N. Blomberg, N. Olivier-Jimenez, D. Johanson, L. E. Cammack, A. J. Giblin, A. Toomey, C. E. Rose, I. V. L. Yuan, H. Ward, M. E. Isaacs, A. Kampmann, M. Kronenberg-Versteeg, D. Lashley, T. Thompson, L. M. Ori, A. Mohammed, Y. Giera, M. van der Kant, R. H. N. 2024-07-03 doi:10.1101/2024.07.01.601474 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ Structure of a novel α-synuclein filament fold from multiple system atrophy ]]> https://biorxiv.org/content/10.1101/2024.07.01.601365v1?rss=1 Yan, N. L. Candido, F. Tse, E. Melo, A. A. Prusiner, S. B. Mordes, D. A. Southworth, D. R. Paras, N. A. Merz, G. E. 2024-07-04 doi:10.1101/2024.07.01.601365 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ iTome Volumetric Serial Sectioning Apparatus for TEM ]]> https://biorxiv.org/content/10.1101/2024.07.02.601671v1?rss=1 Peale, D. R. Hess, H. Lee, P. R. Cardona, A. Bock, D. Schneider-Mizell, C. M. Fetter, R. D. Lee, W.-P. Robinson, C. G. Iyer, N. Managan, C. 2024-07-04 doi:10.1101/2024.07.02.601671 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ Microglia mediate the early-life programming of adult glucose control ]]> https://biorxiv.org/content/10.1101/2024.07.02.601752v1?rss=1 Valdearcos, M. McGrath, E. R. Brown Mayfield, S. Folick, A. Cheang, R. T. Li, L. Bachor, T. P. Lippert, R. N. Xu, A. W. Koliwad, S. K. 2024-07-04 doi:10.1101/2024.07.02.601752 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ The WAVE complex forms linear arrays at negative membrane curvature to instruct lamellipodia formation. ]]> https://biorxiv.org/content/10.1101/2024.07.08.600855v1?rss=1 Wu, M. Marchando, P. Meyer, K. Tang, Z. Woolfson, D. N. Weiner, O. D. 2024-07-08 doi:10.1101/2024.07.08.600855 Cold Spring Harbor Laboratory Press 2024-07-08 <![CDATA[ Current genomic deep learning models display decreased performance in cell type specific accessible regions ]]> https://biorxiv.org/content/10.1101/2024.07.05.602265v1?rss=1 Kathail, P. Shuai, R. W. Chung, R. Ye, C. J. Loeb, G. Ioannidis, N. M. 2024-07-10 doi:10.1101/2024.07.05.602265 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ The impact of Library Size and Scale of Testing on Virtual Screening ]]> https://biorxiv.org/content/10.1101/2024.07.08.602536v1?rss=1 Liu, F. Mailhot, O. Glenn, I. S. Vigneron, S. F. Bassim, V. Xu, X. Valencia, K. F. Smith, M. S. Radchenko, D. S. Fraser, J. S. Moroz, Y. S. Irwin, J. J. Shoichet, B. K. 2024-07-11 doi:10.1101/2024.07.08.602536 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate ]]> https://biorxiv.org/content/10.1101/2024.07.08.602542v1?rss=1 Marin, H. Simental, E. Allen, C. Martin, E. Panning, B. Al-Sady, B. Buchwalter, A. 2024-07-11 doi:10.1101/2024.07.08.602542 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Acute rapamycin treatment reveals novel mechanisms of behavioral, physiological, and functional dysfunction in a maternal inflammation mouse model of autism and sensory over-responsivity ]]> https://biorxiv.org/content/10.1101/2024.07.08.602602v1?rss=1 Le Belle, J. E. Condro, M. Cepeda, C. Oikonomou, K. D. Tessema, K. Dudley, L. Schoenfield, J. Kawaguchi, R. Geschwind, D. Silva, A. J. Zhang, Z. Shokat, K. Harris, N. G. Kornblum, H. I. 2024-07-11 doi:10.1101/2024.07.08.602602 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ GATA6 regulates WNT and BMP programs to pattern precardiac mesoderm during the earliest stages of human cardiogenesis ]]> https://biorxiv.org/content/10.1101/2024.07.09.602666v1?rss=1 Bisson, J. A. Gordillo, M. Kumar, R. de Silva, N. Yang, E. Banks, K. M. Shi, Z.-D. Lee, K. Yang, D. Chung, W. K. Huangfu, D. Evans, T. 2024-07-11 doi:10.1101/2024.07.09.602666 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Basal p53 maintains a distinct transcriptional program from irradiated p53 in tissue, including tumor suppressors ]]> https://biorxiv.org/content/10.1101/2024.07.11.601367v1?rss=1 Zhou, R. W. Manfredi, J. Silverman, L. Parsons, R. E. 2024-07-11 doi:10.1101/2024.07.11.601367 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Localized in vivo gene editing of murine cancer-associated fibroblasts ]]> https://biorxiv.org/content/10.1101/2024.07.11.603114v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@f375c5org.highwire.dtl.DTLVardef@1b8fad9org.highwire.dtl.DTLVardef@15cfd0aorg.highwire.dtl.DTLVardef@1e8dacc_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kuhn, N. F. Zaleta-Linares, I. Nyberg, W. A. Eyquem, J. Krummel, M. F. 2024-07-16 doi:10.1101/2024.07.11.603114 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Peptide-enabled ribonucleoprotein delivery for CRISPR engineering (PERC) in primary human immune cells and hematopoietic stem cells ]]> https://biorxiv.org/content/10.1101/2024.07.14.603391v1?rss=1 Sahu, S. Castro, M. Muldoon, J. J. Asija, K. Wyman, S. K. Krishnappa, N. Eyquem, J. Nguyen, D. N. Wilson, R. C. 2024-07-16 doi:10.1101/2024.07.14.603391 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Sst- and Vip-Cre mouse lines without age-related hearing loss ]]> https://biorxiv.org/content/10.1101/2024.07.15.603003v1?rss=1 Foss, C. T. Olsen, T. Bigelow, J. Hasenstaub, A. R. 2024-07-18 doi:10.1101/2024.07.15.603003 Cold Spring Harbor Laboratory Press 2024-07-18 <![CDATA[ Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning ]]> https://biorxiv.org/content/10.1101/2024.07.16.603579v1?rss=1 Estevam, G. O. Linossi, E. M. Rao, J. Macdonald, C. B. Ravikumar, A. Chrispens, K. M. Capra, J. A. Coyote-Maestas, W. Pimentel, H. Collisson, E. A. Jura, N. Fraser, J. S. 2024-07-18 doi:10.1101/2024.07.16.603579 Cold Spring Harbor Laboratory Press 2024-07-18 <![CDATA[ PATJ regulates cell stress responses and vascular remodeling post-stroke ]]> https://biorxiv.org/content/10.1101/2024.07.17.603777v1?rss=1 Zhang, M. Jiang, W. Arkelius, K. Swanson, R. A. Ma, D. K. Singhal, N. S. 2024-07-22 doi:10.1101/2024.07.17.603777 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ A Novel Whole Tissue Explant Model of Hidradenitis Suppurativa ]]> https://biorxiv.org/content/10.1101/2024.07.19.603617v1?rss=1 Leboit, P. E. Patel, D. U. Cohen, J. N. Moss, M. I. Naik, H. B. Yates, A. E. Harris, H. W. Klufas, D. M. Kim, E. A. Neuhaus, I. M. Hansen, S. L. Kyle, R. L. Kelly, M. Rosenblum, M. D. Lowe, M. M. 2024-07-23 doi:10.1101/2024.07.19.603617 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ High-yield production of recombinant human myelin oligodendrocyte glycoprotein in SHuffle bacteria without a refolding step ]]> https://biorxiv.org/content/10.1101/2024.07.22.602974v1?rss=1 100 mg/L. Analytical size exclusion chromatography multi-angle light scattering (SEC-MALS) and differential scanning fluorimetry of purified rhMOG reveals a homogeneous monomer with a high melting temperature, indicative of a well-folded protein. An in vitro proliferation assay establishes that purified rhMOG can be processed and recognized by T cells expressing a T cell receptor (TCR) specific for the immunodominant MOG35-55 peptide epitope. Lastly, immunization of wild-type, but not B cell deficient, mice with rhMOG resulted in robust induction of EAE, indicating a B cell-dependent induction. Our SHuffle cell method greatly simplifies rhMOG production by combining the high yield and speed of bacterial cell expression with enhanced disulfide bond formation and folding, which will enable further investigation of B cell-dependent EAE and expand human research of MOG in CNS demyelinating diseases. ]]> Wu, W. Gupta, S. Sagan, S. A. Moseley, C. E. Zamvil, S. S. Pak, J. E. 2024-07-23 doi:10.1101/2024.07.22.602974 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Therapeutic DBS for OCD Suppresses the Default Mode Network ]]> https://biorxiv.org/content/10.1101/2024.07.21.601827v1?rss=1 Slepneva, N. Basich-Pease, G. Reid, L. Frank, A. C. Norbu, T. Krystal, A. D. Sugrue, L. P. Motzkin, J. C. Larson, P. S. Starr, P. A. Morrison, M. A. Lee, A. M. 2024-07-24 doi:10.1101/2024.07.21.601827 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma ]]> https://biorxiv.org/content/10.1101/2024.07.23.604673v1?rss=1 Tandukar, B. Deivendran, D. Chen, L. Cruz-Pacheco, N. Sharma, H. Xu, A. Bandari, A. K. Chen, D. George, C. Marty, A. Cho, R. J. Cheng, J. Saylor, D. Gerami, P. Arron, S. T. Bastian, B. C. Shain, A. H. 2024-07-24 doi:10.1101/2024.07.23.604673 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Mechanism-guided engineering of a minimal biological particle for genome editing ]]> https://biorxiv.org/content/10.1101/2024.07.23.604809v1?rss=1 Ngo, W. Peukes, J. T. Baldwin, A. Xue, Z. W. Hwang, S. Stickels, R. R. Lin, Z. Satpathy, A. Wells, J. A. Schekman, R. Nogales, E. Doudna, J. A. 2024-07-24 doi:10.1101/2024.07.23.604809 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Genetic Architecture and Analysis Practices of Circulating Metabolites in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program ]]> https://biorxiv.org/content/10.1101/2024.07.23.604849v1?rss=1 Wang, N. Ockerman, F. P. Zhou, L. Y. Grove, M. L. Alkis, T. Barnard, J. Bowler, R. P. Clish, C. B. Chung, S. Drzymalla, E. Evans, A. M. Franceschini, N. Gerszten, R. E. Gillman, M. G. Hutton, S. R. Kelly, R. S. Kooperberg, C. Larson, M. G. Lasky-Su, J. A. Meyers, D. A. Woodruff, P. G. Reiner, A. P. Rich, S. S. Rotter, J. Silverman, E. K. Ramachandran, V. S. Weiss, S. T. Wong, K. E. Wood, A. C. Wu, L. NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Yarden, R. Blackwell, T. Smith, A. V. Chen, H. Raffield, L. M. Yu, B. 2024-07-24 doi:10.1101/2024.07.23.604849 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Comparative Analysis of Glycoproteomic Software Using a Tailored Glycan Database ]]> https://biorxiv.org/content/10.1101/2024.07.24.604997v1?rss=1 Hogan, R. A. Pepi, L. E. Riley, N. M. Chalkley, R. J. 2024-07-25 doi:10.1101/2024.07.24.604997 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ A second X chromosome improves cognition in aging male and female mice ]]> https://biorxiv.org/content/10.1101/2024.07.26.605328v1?rss=1 Marino, F. Wang, D. Merrihew, G. E. MacCoss, M. J. Dubal, D. 2024-07-26 doi:10.1101/2024.07.26.605328 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ Proteomic Profiling Reveals Age-Related Changes in Transporter Proteins in the Human Blood-Brain Barrier ]]> https://biorxiv.org/content/10.1101/2024.07.26.604313v1?rss=1 Zhou, X. Azimi, M. Handin, N. Riselli, A. Vora, B. Chun, E. Yee, S. W. Artursson, P. Giacomini, K. M. 2024-07-27 doi:10.1101/2024.07.26.604313 Cold Spring Harbor Laboratory Press 2024-07-27 <![CDATA[ Senescent fibroblasts in the tumor stroma rewire lung cancer metabolism and plasticity ]]> https://biorxiv.org/content/10.1101/2024.07.29.605645v1?rss=1 Lee, J. Nabora, S. R. Woo, S.-H. Goel, S. Stratton, F. Kuang, C. Mansfield, A. LaFave, L. Peng, T. 2024-07-30 doi:10.1101/2024.07.29.605645 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Conservation, alteration, and redistribution of mammalian striatal interneurons ]]> https://biorxiv.org/content/10.1101/2024.07.29.605664v1?rss=1 Corrigan, E. K. DeBerardine, M. Poddar, A. Turrero Garcia, M. Schmitz, M. T. Harwell, C. Paredes, M. Krienen, F. M. Pollen, A. A. 2024-07-30 doi:10.1101/2024.07.29.605664 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Calcium phosphate nanoclusters modify periodontium remodeling and minimize orthodontic relapse ]]> https://biorxiv.org/content/10.1101/2024.07.29.605671v1?rss=1 Cuylear, D. L. Fu, M. L. Chau, J. C. Kharbikar, B. Kazakia, G. Jheon, A. Habelitz, S. Kapila, S. D. Desai, T. A. 2024-07-30 doi:10.1101/2024.07.29.605671 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Ciliary biology intersects autism and congenital heart disease ]]> https://biorxiv.org/content/10.1101/2024.07.30.602578v1?rss=1 Teerikorpi, N. Lasser, M. C. Wang, S. Kostyanovskaya, E. Bader, E. Sun, N. Dea, J. Nowakowski, T. J. Willsey, A. J. Willsey, H. 2024-07-31 doi:10.1101/2024.07.30.602578 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Using virtual patient cohorts to uncover immune response differences in cancer and immunosuppressed COVID-19 patients ]]> https://biorxiv.org/content/10.1101/2024.08.01.605860v1?rss=1 Gazeau, S. Deng, X. Brunet-Ratnasingham, E. Kaufmann, D. E. Larochelle, C. Morel, P. A. Heffernan, J. M. Davis, C. L. Smith, A. M. Jenner, A. L. Craig, M. 2024-08-02 doi:10.1101/2024.08.01.605860 Cold Spring Harbor Laboratory Press 2024-08-02 <![CDATA[ Spatial 3D genome organization controls the activity of bivalent chromatin during human neurogenesis ]]> https://biorxiv.org/content/10.1101/2024.08.01.606248v1?rss=1 7-fold. We further demonstrate that proximity to the nuclear periphery - not the presence of H3K27me3 - is the dominant factor in maintaining the lowly expressed, poised state of bivalent genes embedded in the lamina. In addition to uncovering a critical role of subnuclear genome compartmentalization in neurogenic transcriptional regulation, our results establish a new paradigm in which knowing the spatial location of a gene is necessary to understanding its epigenomic regulation. ]]> Ahanger, S. H. Zhang, C. Semenza, E. R. Gil, E. Cole, M. A. Wang, L. Kriegstein, A. R. Lim, D. 2024-08-02 doi:10.1101/2024.08.01.606248 Cold Spring Harbor Laboratory Press 2024-08-02 <![CDATA[ Phylogeny, morphology, and behavior of the new ciliate species Stentor stipatus ]]> https://biorxiv.org/content/10.1101/2024.08.03.606273v1?rss=1 Rajan, D. H. Lee, B. Albright, A. Tang, E. J. Maravillas, A. Vargas, C. Marshall, W. F. Cortes, D. 2024-08-04 doi:10.1101/2024.08.03.606273 Cold Spring Harbor Laboratory Press 2024-08-04 <![CDATA[ CRISPR-Cas13d as a molecular tool to achieve targeted gene expression knockdown in chick embryos ]]> https://biorxiv.org/content/10.1101/2024.08.03.606488v1?rss=1 Kim, M. Hutchins, E. J. 2024-08-04 doi:10.1101/2024.08.03.606488 Cold Spring Harbor Laboratory Press 2024-08-04 <![CDATA[ Torsional Twist of the SARS-CoV and SARS-CoV-2 SUD-N and SUD-M domains ]]> https://biorxiv.org/content/10.1101/2024.08.13.607777v1?rss=1 Rosas-Lemus, M. Minasov, G. Brunzelle, J. S. Taha, T. Y. Lemak, S. Yin, S. Shuvalova, L. Rosecrans, J. Khanna, K. Seifert, H. S. Savchenko, A. Stogios, P. J. Ott, M. Satchell, K. J. 2024-08-14 doi:10.1101/2024.08.13.607777 Cold Spring Harbor Laboratory Press 2024-08-14 <![CDATA[ The brain simulates actions and their consequences during REM sleep ]]> https://biorxiv.org/content/10.1101/2024.08.13.607810v1?rss=1 Senzai, Y. Scanziani, M. 2024-08-16 doi:10.1101/2024.08.13.607810 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ Perinatal liver inflammation is associated with persistent elevation of CXCL10 and its canonical receptor CXCR3 on common myeloid progenitors ]]> https://biorxiv.org/content/10.1101/2024.08.15.607661v1?rss=1 Alkhani, A. Baskaran, S. Murti, A. Rapp, B. Levy, C. S. Wang, B. Nijagal, A. 2024-08-19 doi:10.1101/2024.08.15.607661 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Quantized multi-task learning for context-specific representations of gene network dynamics ]]> https://biorxiv.org/content/10.1101/2024.08.16.608180v1?rss=1 Chen, H. Venkatesh, M. S. Gomez Ortega, J. Mahesh, S. V. Nandi, T. N. Madduri, R. K. Pelka, K. Theodoris, C. V. 2024-08-19 doi:10.1101/2024.08.16.608180 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ A virtual clinical trial of psychedelics to treat patients with disorders of consciousness ]]> https://biorxiv.org/content/10.1101/2024.08.16.608251v1?rss=1 Alnagger, N. L. N. Cardone, P. Martial, C. Sanz Perl, Y. Mindlin, I. Sitt, J. D. Roseman, L. Carhart-Harris, R. Nutt, D. Mallaroni, P. Mason, N. L. Ramaekers, J. G. Bonhomme, V. Laureys, S. Deco, G. Gosseries, O. Nunez, P. Annen, J. 2024-08-19 doi:10.1101/2024.08.16.608251 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Exploring the diversity of anti-defense systems across prokaryotes, phages, and mobile genetic elements ]]> https://biorxiv.org/content/10.1101/2024.08.21.608784v1?rss=1 Tesson, F. Huiting, E. Wei, L. Ren, J. Johnson, M. C. Planel, R. Cury, J. Feng, Y. Bondy-Denomy, J. Bernheim, A. 2024-08-21 doi:10.1101/2024.08.21.608784 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics ]]> https://biorxiv.org/content/10.1101/2024.08.21.609012v1?rss=1 Bibel, B. Raskar, T. Couvillion, M. Lee, M. Kleinman, J. I. Takeuchi-Tomita, N. Churchman, L. S. Fraser, J. S. Fujimori, D. G. 2024-08-21 doi:10.1101/2024.08.21.609012 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Sensitive and modular amplicon sequencing of Plasmodium falciparum diversity and resistance for research and public health ]]> https://biorxiv.org/content/10.1101/2024.08.22.609145v1?rss=1 Aranda-Diaz, A. Vickers, E. N. Murie, K. Palmer, B. Hathaway, N. Gerlovina, I. Boene, S. Garcia-Ulloa, M. Cistero, P. Katairo, T. Semakuba, F. D. Nsengimaana, B. Gwarinda, H. Garcia-Fernandez, C. Da Silva, C. Datta, D. Kiyaga, S. Wiringilimaana, I. Fekele, S. M. Parr, J. B. Conrad, M. Raman, J. Tukwasibwe, S. 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S. 2024-08-26 doi:10.1101/2024.08.25.609621 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Sustained fertility from first-wave follicle oocytes that pause their growth ]]> https://biorxiv.org/content/10.1101/2024.08.27.609995v1?rss=1 Soygur, B. Gaylord, E. A. Foecke, M. H. Cincotta, S. A. Horan, T. J. Wood, A. Cohen, P. Laird, D. J. 2024-08-28 doi:10.1101/2024.08.27.609995 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Mutant p53 Exploits Enhancers to Elevate Immunosuppressive Chemokine Expression and Impair Immune Checkpoint Inhibitors in Pancreatic Cancer ]]> https://biorxiv.org/content/10.1101/2024.08.28.609802v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@b2354dorg.highwire.dtl.DTLVardef@1c96300org.highwire.dtl.DTLVardef@829f26org.highwire.dtl.DTLVardef@19e7d2e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mahat, D. B. Kumra, H. Castro, S. A. Metcalf, E. Nguyen, K. Morisue, R. Ho, W. W. Chen, I. Sullivan, B. Yim, L. K. Singh, A. Fu, J. Waterton, S. K. Cheng, Y.-C. Roberge, S. Moiso, E. Chauhan, V. P. Moura Silva, H. Spranger, S. Jain, R. K. Sharp, P. A. 2024-08-30 doi:10.1101/2024.08.28.609802 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Coordinated Tbx3 / Tbx5 transcriptional control of the adult ventricular conduction system ]]> https://biorxiv.org/content/10.1101/2024.08.29.610377v1?rss=1 Burnicka-Turek, O. Trampel, K. A. Laforest, B. Broman, M. T. Khan, Z. Rytkin, E. Li, B. Schaffer, E. Gadek, M. Shen, K. M. Efimov, I. R. Moskowitz, I. P. 2024-08-30 doi:10.1101/2024.08.29.610377 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Comprehensive profiling of migratory primordial germ cells reveals niche-specific differences in non-canonical Wnt and Nodal-Lefty signaling in anterior vs posterior migrants ]]> https://biorxiv.org/content/10.1101/2024.08.29.610420v1?rss=1 Jaszczak, R. G. Zussman, J. W. Wagner, D. E. Laird, D. J. 2024-08-30 doi:10.1101/2024.08.29.610420 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ A Novel Approach to Reducing Spinal Implant-Associated Infections ]]> https://biorxiv.org/content/10.1101/2024.08.30.610521v1?rss=1 Nishizawa, M. Hu, D. Serhan, H. Saleh, B. Marcucio, R. S. Morioka, K. 2024-08-31 doi:10.1101/2024.08.30.610521 Cold Spring Harbor Laboratory Press 2024-08-31 <![CDATA[ Deciphering regulation of FOXP3 expression in human conventional T cells ]]> https://biorxiv.org/content/10.1101/2024.08.30.610436v1?rss=1 Umhoefer, J. M. Arce, M. M. Dajani, R. Belk, J. A. Mowery, C. T. Nguyen, V. Gowen, B. G. Simeonov, D. R. Curie, G. L. Corn, J. E. Chang, H. Y. Marson, A. 2024-09-02 doi:10.1101/2024.08.30.610436 Cold Spring Harbor Laboratory Press 2024-09-02 <![CDATA[ Methods for high throughput discovery of fluoroprobes that recognize tau fibril polymorphs ]]> https://biorxiv.org/content/10.1101/2024.09.02.610853v1?rss=1 Carroll, E. C. Yang, H. E. Jones, J. G. Oehler, A. Charvat, A. F. Montgomery, K. M. Yung, A. Millbern, Z. Vinueza, N. R. Degrado, W. F. Mordes, D. A. Condello, C. Gestwicki, J. E. 2024-09-02 doi:10.1101/2024.09.02.610853 Cold Spring Harbor Laboratory Press 2024-09-02 <![CDATA[ The miR-290 and miR-302 clusters are essential for reprogramming of fibroblasts to induced pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2024.09.02.610895v1?rss=1 Ye, J. Boileau, R. M. Parchem, R. J. Judson-Torres, R. L. Blelloch, R. 2024-09-03 doi:10.1101/2024.09.02.610895 Cold Spring Harbor Laboratory Press 2024-09-03 <![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[ Vascular HIF2 signaling prevents cardiomegaly, alveolar congestion and capillary remodeling during chronic hypoxia ]]> https://biorxiv.org/content/10.1101/2024.09.03.610947v1?rss=1 Albendea-Gomez, T. Mendoza-Tamajon, S. Castro-Mecinas, R. Escobar, B. Rocha, S. F. Urra-Balduz, S. Nicolas-Avila, J. A. Oliver, E. Villalba-Orero, M. Martin-Puig, S. 2024-09-06 doi:10.1101/2024.09.03.610947 Cold Spring Harbor Laboratory Press 2024-09-06 <![CDATA[ Identifying deleterious noncoding variation through gain and loss of CTCF binding activity ]]> https://biorxiv.org/content/10.1101/2024.09.04.609712v1?rss=1 Tubbs, C. Benton, M. L. McArthur, E. Capra, J. A. Ruderfer, D. M. 2024-09-08 doi:10.1101/2024.09.04.609712 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ How a pathogenic mutation impairs Hsp60 functional dynamics from monomeric to fully assembled states ]]> https://biorxiv.org/content/10.1101/2024.09.09.611948v1?rss=1 Torielli, L. Guarra, F. Shao, H. Gestwicki, J. E. Serapian, S. A. Colombo, G. 2024-09-09 doi:10.1101/2024.09.09.611948 Cold Spring Harbor Laboratory Press 2024-09-09 <![CDATA[ Ketogenic interventions restore cognition and modulate peripheral metabolic dysfunctions in Alzheimer's disease mouse models ]]> https://biorxiv.org/content/10.1101/2024.09.04.610637v1?rss=1 M'Bra, P. E. H. Hamilton, L. K. Moquin-Beaudry, G. Aubin, M. Lyn-Mangahas, C. Pratesi, F. Brunet, E. Castonguay, A. Mailloux, S. Galoppin, M. Bernier, M. Turri, M. Vachon, A. Mayhue, M. Aumont, A. Tetreault, M. Plourde, M. Fernandes, K. J. L. 2024-09-10 doi:10.1101/2024.09.04.610637 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ ATP-dependent remodeling of chromatin condensates uncovers distinct mesoscale effects of two remodelers ]]> https://biorxiv.org/content/10.1101/2024.09.10.611504v1?rss=1 Moore, C. M. Kaur, U. Wong, E. Chio, U. S. M. Zhou, Z. Ostrowski, M. Wu, K. Irkliyenko, I. Wang, S. Ramani, V. Narlikar, G. 2024-09-10 doi:10.1101/2024.09.10.611504 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ ElixirSeeker: A Machine Learning Framework Utilizing Attention-Driven Fusion of Molecular Fingerprints for the Discovery of Anti-Aging Compounds ]]> https://biorxiv.org/content/10.1101/2024.09.08.611839v1?rss=1 Pan, Y. Cai, H. Ye, F. Xu, W. Huang, Z. Zhu, J. Gong, Y. Li, Y. Ezemaduka, A. N. Gao, S. Liu, S. Li, G. Li, H. Yang, J. Ning, J. Xian, B. 2024-09-13 doi:10.1101/2024.09.08.611839 Cold Spring Harbor Laboratory Press 2024-09-13 <![CDATA[ Leukemia-derived apelin selects endothelial niche clones to promote tumorigenesis ]]> https://biorxiv.org/content/10.1101/2024.09.09.612077v1?rss=1 Baron, C. S. Mitchell, O. Avagyan, S. Menard, R. Yang, S. Robertson, A. L. Potluri, R. Shendure, J. Madelaine, R. McKenna, A. Zon, L. I. 2024-09-13 doi:10.1101/2024.09.09.612077 Cold Spring Harbor Laboratory Press 2024-09-13 <![CDATA[ BST2 induces vascular smooth muscle cell plasticity and phenotype switching during cancer progression ]]> https://biorxiv.org/content/10.1101/2024.09.10.612298v1?rss=1 Bell, C. Baylis, R. Lopez, N. Ma, W. F. Gao, H. Wang, F. Bamezai, S. Fu, C. Kojima, Y. Adkar, S. Luo, L. Miller, C. Leeper, N. L. 2024-09-14 doi:10.1101/2024.09.10.612298 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Intracortical injection of immune checkpoint inhibitor promotes monocyte/macrophage infiltration and restores microglial function and neuronal activity in an AD mouse model ]]> https://biorxiv.org/content/10.1101/2024.09.13.612389v1?rss=1 Park, T. Chang, L. Chung, S. W. Lee, S. Bae, S. Condello, C. Kim, Y. H. Lee, J. Kim, H.-J. Kwon, H.-K. Suh, M. 2024-09-15 doi:10.1101/2024.09.13.612389 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Learning-related oscillatory dynamics in the human cortico-basal ganglia network during motor sequence initiation in Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2024.09.13.612783v1?rss=1 Presbrey, K. N. Wozny, T. A. Louie, K. H. Little, S. Starr, P. A. Abbasi-Asl, R. Wang, D. D. 2024-09-15 doi:10.1101/2024.09.13.612783 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Intravital imaging of pulmonary lymphatics in inflammation and metastatic cancer ]]> https://biorxiv.org/content/10.1101/2024.09.12.612619v1?rss=1 View larger version (64K): org.highwire.dtl.DTLVardef@66dd00org.highwire.dtl.DTLVardef@1373576org.highwire.dtl.DTLVardef@1970dfeorg.highwire.dtl.DTLVardef@17c15c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cleary, S. J. Qiu, L. Seo, Y. Baluk, P. Liu, D. Serwas, N. K. Cyster, J. G. McDonald, D. M. Krummel, M. F. Looney, M. R. 2024-09-17 doi:10.1101/2024.09.12.612619 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ Quantitative Comparison of Monomeric StayGold Variants Using Protein Nanocages in Living Cells ]]> https://biorxiv.org/content/10.1101/2024.09.16.613379v1?rss=1 Viola, G. Jacobs, K. A. Lemiere, J. Kutys, M. L. Wittmann, T. 2024-09-17 doi:10.1101/2024.09.16.613379 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ A dopaminergic basis of behavioral control ]]> https://biorxiv.org/content/10.1101/2024.09.17.613524v1?rss=1 Ballard, I. C. Furman, D. J. Berry, A. S. White, R. L. Jagust, W. J. Kayser, A. S. D'Esposito, M. 2024-09-17 doi:10.1101/2024.09.17.613524 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ Engineered Receptors for Soluble Cell-to-Cell Communication ]]> https://biorxiv.org/content/10.1101/2024.09.17.613377v1?rss=1 Piraner, D. I. Abedi, M. H. Duran Gonzalez, M. J. Chazin-Gray, A. Zhu, I. Ravindran, P. T. Schlichthaerle, T. Huang, B. Lee, D. Baker, D. Roybal, K. T. 2024-09-18 doi:10.1101/2024.09.17.613377 Cold Spring Harbor Laboratory Press 2024-09-18 <![CDATA[ M2 Macrophage Exosomes Reverse Cardiac Functional Decline in Mice with Diet-Induced Myocardial Infarction by Suppressing Type 1 Interferon Signaling in Myeloid Cells ]]> https://biorxiv.org/content/10.1101/2024.09.13.612924v1?rss=1 Ng, M. Gao, A. S. Phu, T. A. Vu, N. K. Raffai, R. 2024-09-19 doi:10.1101/2024.09.13.612924 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN ]]> https://biorxiv.org/content/10.1101/2024.09.16.613176v1?rss=1 Herreros, D. Mata, C. P. Noddings, C. Irene, D. Krieger, J. M. Agard, D. Tsai, M.-D. Sorzano, C. O. S. Carazo, J. M. 2024-09-19 doi:10.1101/2024.09.16.613176 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ The Gq/11 family of Gα subunits is necessary and sufficient for lower jaw development ]]> https://biorxiv.org/content/10.1101/2024.09.17.611698v1?rss=1 Kanai, S. M. Garcia, C. R. Augustus, M. R. Sharafeldeen, S. A. Brooks, E. P. Sucharov, J. Lencer, E. S. Nichols, J. T. Clouthier, D. E. 2024-09-19 doi:10.1101/2024.09.17.611698 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ An integrated view of the structure and function of the human 4D nucleome ]]> https://biorxiv.org/content/10.1101/2024.09.17.613111v1?rss=1 The 4D Nucleome Consortium, Dekker, J. Oksuz, B. A. Zhang, Y. Wang, Y. Minsk, M. K. Kuang, S. Yang, L. Gibcus, J. H. Krietenstein, N. Rando, O. Xu, J. Janssens, D. H. Henikoff, S. Kukalev, A. Willemin, A. Winick-Ng, W. Kempfer, R. Pombo, A. Yu, M. Kumar, P. Zhang, L. Belmont, A. S. Sasaki, T. van Schaik, T. Brueckner, L. Peric-Hupkes, D. van Steensel, B. Wang, P. Chai, H. Kim, M. Ruan, Y. Zhang, R. Quinodoz, S. A. Bhat, P. Guttman, M. Zhao, W. Chien, S. Liu, Y. Venev, S. V. Plewczynski, D. Irastorza Azcarate, I. Szabo, D. Thieme, C. J. Szczepinska, 2024-09-19 doi:10.1101/2024.09.17.613111 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Preventing Inappropriate Signals Pre- and Post-Ligand Perception by a Toggle-Switch Mechanism of ERECTA ]]> https://biorxiv.org/content/10.1101/2024.09.20.612365v1?rss=1 Chen, L. Maes, M. Cochran, A. M. Avila, J. R. Derbyshire, P. Sklenar, J. Haas, K. M. Villen, J. Menke, F. Torii, K. U. 2024-09-21 doi:10.1101/2024.09.20.612365 Cold Spring Harbor Laboratory Press 2024-09-21 <![CDATA[ Extinction of innate floral preferences in the pollinator Eristalis tenax ]]> https://biorxiv.org/content/10.1101/2024.09.20.613821v1?rss=1 Mishra, A. Rajan, D. H. Sharan, M. Gharpure, G. Olsson, S. 2024-09-21 doi:10.1101/2024.09.20.613821 Cold Spring Harbor Laboratory Press 2024-09-21 <![CDATA[ BCR ligation selectively inhibits IgE class switch recombination ]]> https://biorxiv.org/content/10.1101/2024.09.18.613749v1?rss=1 Wade-Vallance, A. K. Yang, Z. Libang, J. B. Krishnapura, A. R. Jung, J. B. Matcham, E. W. Robinson, M. J. Allen, C. D. C. 2024-09-22 doi:10.1101/2024.09.18.613749 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ The HIV-1 Nuclear Export Complex Reveals the Role of RNA in Crm1 Cargo Recognition ]]> https://biorxiv.org/content/10.1101/2024.09.22.614349v1?rss=1 1000 human proteins including ribonucleoprotein (RNP) complexes. The interface between Crm1 and RNP cargos is unknown. The HIV regulatory protein, Rev, was one of the first identified cargos for Crm1 and contains a prototypic nuclear export sequence (NES). We present the cryo-electron microscopy structure of the HIV-1 nuclear export complex (Crm1/Ran-GTP and the Rev/RRE RNP). Rev binds at a previously unseen protein-protein binding site that stabilizes a unique Crm1 dimer and positions two NESs within the Crm1 dimer. The orientation of Rev binding positions the RRE within a charged pocket on the inside of the Crm1 toroid, mediating direct RNA-Ran-GTP contacts, highlighting the significant role of the RRE in the interaction. Structure based mutations, combined with cell-based assays, show that Crm1 has multiple distinct cargo recognition sites and explains how Crm1 can recognize a diverse range of protein and RNP cargos. ]]> Smith, A. M. Li, Y. Velarde, A. Cheng, Y. Frankel, A. D. 2024-09-22 doi:10.1101/2024.09.22.614349 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments ]]> https://biorxiv.org/content/10.1101/2024.09.20.613996v1?rss=1 Flowers, J. Echols, N. Correy, G. Jaishankar, P. Togo, T. Renslo, A. R. van den Bedem, H. Fraser, J. S. Wankowicz, S. A. 2024-09-23 doi:10.1101/2024.09.20.613996 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ Tau P301S Transgenic Mice Develop Gait and Eye Movement Impairments That Mimic Progressive Supranuclear Palsy ]]> https://biorxiv.org/content/10.1101/2024.09.20.614197v1?rss=1 Creed, R. B. Harris, S. C. Sridhar, S. du Lac, S. Zee, D. S. Dunn, F. A. Bouvier, G. Nelson, A. B. 2024-09-23 doi:10.1101/2024.09.20.614197 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ Intracellular diffusion in the cytoplasm increases with cell size in fission yeast ]]> https://biorxiv.org/content/10.1101/2024.09.21.613766v1?rss=1 Tan, C. Lanz, M. Swaffer, M. Skotheim, J. Chang, F. 2024-09-23 doi:10.1101/2024.09.21.613766 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ Super-enhancer profiling reveals ThPOK/ZBTB7B, a CD4+ cell lineage commitment factor, as a master regulator that restricts breast cancer cells to a luminal non-migratory phenotype ]]> https://biorxiv.org/content/10.1101/2024.09.21.614267v1?rss=1 Arcuschin, C. D. Kahrizi, K. Sayaman, R. W. DiBenedetto, C. Shen, Y. Salaberry, P. J. Zakroui, O. Schwarzer, C. Scapozza, A. Betancur, P. Saba, J. D. Coppe, J.-P. Barcellos-Hoff, M. H. Kappes, D. van 't Veer, L. Schor, I. E. Munoz, D. P. 2024-09-24 doi:10.1101/2024.09.21.614267 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Comprehensive proteolytic profiling of Aedes aegypti mosquito midgut extracts: Unraveling the blood meal protein digestion system ]]> https://biorxiv.org/content/10.1101/2024.09.23.614410v1?rss=1 O'Donoghue, A. J. Lui, C. Simington, C. J. Montermoso, S. Moreno-Galvez, E. Serafim, M. S. M. Burata, O. E. Lucero, R. M. Nguyen, J. T. Fong, D. Tran, K. Millan, N. Gallimore, J. M. Parungao, K. A. Fong, J. Suzuki, B. M. Jiang, Z. Isoe, J. Rascon, A. A. 2024-09-24 doi:10.1101/2024.09.23.614410 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Macrophages redeploy functional cancer cell surface proteins following phagocytosis ]]> https://biorxiv.org/content/10.1101/2024.09.23.613776v1?rss=1 Volk, R. F. Casebeer, S. W. Condon, A. C. Zirak, B. Manon, N. Irkliyenko, I. Liao, H. Tao, S. Pollini, T. Ramani, V. Maker, A. Fidler, T. Goodarzi, H. Zaro, B. W. 2024-09-25 doi:10.1101/2024.09.23.613776 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Histone demethylase enzymes KDM5A and KDM5B modulate immune response by suppressing transcription of endogenous retroviral elements ]]> https://biorxiv.org/content/10.1101/2024.09.23.614494v1?rss=1 Chen, H. Sarah, L. Pucciarelli, D. Mao, Y. Diolaiti, M. E. Galonic Fujimori, D. ashworth, A. 2024-09-25 doi:10.1101/2024.09.23.614494 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ nSMase2-mediated exosome secretion shapes the tumor microenvironment to immunologically support pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2024.09.23.614610v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@b6e6d1org.highwire.dtl.DTLVardef@1ebb41eorg.highwire.dtl.DTLVardef@17e4275org.highwire.dtl.DTLVardef@3d31f1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hendley, A. M. Ashe, S. Urano, A. Ng, M. Phu, T. A. Peng, X. L. Luan, C. Finger, A.-M. Jang, G. H. Kerper, N. R. Berrios, D. I. Jin, D. Lee, J. Riahi, I. R. Gbenedio, O. M. Chung, C. Roose, J. Yeh, J. J. Gallinger, S. Biankin, A. V. OKane, G. M. Ntranos, V. Chang, D. Dawson, D. W. Kim, G. E. Weaver, V. M. Raffai, R. L. Hebrok, M. 2024-09-25 doi:10.1101/2024.09.23.614610 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Oxytocin receptor controls distinct components of pair bonding and development in prairie voles ]]> https://biorxiv.org/content/10.1101/2024.09.25.613753v1?rss=1 Sharma, R. Berendzen, K. M. Everitt, A. Wang, B. Williams, G. Wang, S. Quine, K. Larios, R. D. Long, K. L. P. Hoglen, N. Sulaman, B. A. Heath, M. C. Sherman, M. Kinkel, M. Cai, A. Galo, D. Caamal, L. C. Goodwin, N. L. Beery, A. Bales, K. L. Pollard, K. S. Willsey, A. J. Manoli, D. S. 2024-09-26 doi:10.1101/2024.09.25.613753 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ The human ciliopathy protein RSG1 links the CPLANE complex to transition zone architecture ]]> https://biorxiv.org/content/10.1101/2024.09.25.614984v1?rss=1 Vazquez, N. Lee, C. Valenzuela, I. Cusco, I. Codina, M. Martinez-Gil, N. Valverde, D. Lopez-Solarat, C. Bruel, A.-L. Thauvin-Robinet, C. Steichen, E. Filges, I. Joset, P. De Geyter, J. Mooney, N. Gardner, T. Vaidyanathan, K. Marcotte, E. Roberson, E. Phan, T. Derderian, C. Toriyama, M. Demeter, J. Chavez, M. Aziz-Zanjani, M. Jackson, P. Reiter, J. Tizzano, E. Wallingford, J. B. 2024-09-26 doi:10.1101/2024.09.25.614984 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Effect of chronic upregulation of endocannabinoid signaling in vivo with JZL184 on striatal synaptic plasticity and motor learning in YAC128 Huntington disease mice ]]> https://biorxiv.org/content/10.1101/2024.09.25.614804v1?rss=1 Sepers, M. D. Woodard, C. L. Ramandi, D. Vecchiarelli, H. A. Hill, M. N. Raymond, L. A. 2024-09-27 doi:10.1101/2024.09.25.614804 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Robust lipid scrambling by TMEM16 proteins requires an open groove and thin membrane ]]> https://biorxiv.org/content/10.1101/2024.09.25.615027v1?rss=1 90%) occurs at the groove only when TM4 and TM6 have sufficiently separated. Surprisingly, we also observed 60 scrambling events that occurred outside the canonical groove, over 90% of which took place at the dimer-dimer interface in mammalian TMEM16s. This new site suggests an alternative mechanism for lipid scrambling in the absence of an open groove. Impact StatementThe majority of TMEM16 lipid scrambling occurs in the open groove associated with Ca2+-activation, but limited scrambling also occurs in the dimer interface independent of Ca2+. ]]> Stephens, C. A. van Hilten, N. Zheng, L. Grabe, M. 2024-09-27 doi:10.1101/2024.09.25.615027 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Dysregulation of the fluid homeostasis system by aging ]]> https://biorxiv.org/content/10.1101/2024.09.26.615271v1?rss=1 Jang, H. Behne Sharma, A. Dan, U. Wong, J. H. Knight, Z. A. Garrison, J. L. 2024-09-27 doi:10.1101/2024.09.26.615271 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Tumor Cell Spatial Organization Directs EGFR/RAS/RAF Pathway Primary Therapy Resistance through YAP Signaling ]]> https://biorxiv.org/content/10.1101/2024.09.26.615226v1?rss=1 90% following acute EGFRi therapy, and residual tumor cells are associated with dense stroma and have increased nuclear YAP. Interestingly, in vitro EGFRi induced cell cycle arrest in NSCLC cells grown in monolayer, while 3D spheroids preferentially die upon inhibitor treatment. We find differential YAP nuclear localization and activity, driven by the distinct culture conditions, as a common resistance mechanism for selective EGFR/KRAS/BRAF pathway therapies. Forced expression of the YAPS127A mutant partially protects cells from EGFR-mediated cell death in spheroid culture. These studies identify YAP activation in monolayer culture as a non-genetic mechanism of acute EGFR/KRAS/BRAF therapy resistance, highlighting that monolayer vs spheroid cell culture systems can model distinct stages of patient cancer progression. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/615226v3_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1b22ef5org.highwire.dtl.DTLVardef@128ed3corg.highwire.dtl.DTLVardef@1ef1e89org.highwire.dtl.DTLVardef@1bdc0a5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Nakagawa, R. Beardsley, A. Durney, S. Hayward, M.-K. Subramanyam, V. Meyer, N. P. Wismer, H. Goodarzi, H. Weaver, V. M. Van de Mark, D. Goga, A. 2024-09-28 doi:10.1101/2024.09.26.615226 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ Selection promotes age-dependent degeneration of the mitochondrial genome ]]> https://biorxiv.org/content/10.1101/2024.09.27.615276v1?rss=1 Korotkevich, E. Conrad, D. N. Gartner, Z. J. O'Farrell, P. H. 2024-09-28 doi:10.1101/2024.09.27.615276 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ Latent-TGF-β has a domain swapped architecture ]]> https://biorxiv.org/content/10.1101/2024.09.27.615443v1?rss=1 Jin, M. Seed, R. Shing, T. Cheng, Y. Nishimura, S. 2024-09-30 doi:10.1101/2024.09.27.615443 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Engineered Feedback Employing Natural Hypoxia-Responsive Factors Enhances Synthetic Hypoxia Biosensors ]]> https://biorxiv.org/content/10.1101/2024.09.28.615614v1?rss=1 Dreyer, K. S. Donahue, P. S. Boucher, J. D. Chambers, K. M. Ornelas, M. Y. Edelstein, H. I. Leibowitz, B. D. Zhu, K. J. Dray, K. E. Muldoon, J. J. Leonard, J. N. 2024-09-30 doi:10.1101/2024.09.28.615614 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Maintenance of neuronal TDP-43 expression requires axonal lysosome transport ]]> https://biorxiv.org/content/10.1101/2024.09.30.615241v1?rss=1 Ryan, V. H. Lawton, S. Reyes, J. F. Hawrot, J. Frankenfield, A. M. Seddighi, S. Ramos, D. M. Johnson, N. L. Zou, J. Kampmann, M. Replogle, J. Yuan, H. Johnson, K. R. Maric, D. Hao, L. Nalls, M. A. Ward, M. 2024-10-01 doi:10.1101/2024.09.30.615241 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Circulatory proteins shape microglia state and boost phagocytosis ]]> https://biorxiv.org/content/10.1101/2024.09.30.615861v1?rss=1 Lu, N. Moran-Losada, P. Hahn, O. Saksena, A. Tapp, E. Chadarevian, J. P. Dong, W. Shi, S. M. Shuken, S. R. Guldner, I. Zeng, W. To, N.-S. Wong, P. S. Hasselmann, J. Davtyan, H. Sun, J. Li, L. Luo, J. Yang, A. C. Li, Q. Cheung, T. H. Abu-Remaileh, M. Blurton-Jones, M. Wyss-Coray, T. 2024-10-02 doi:10.1101/2024.09.30.615861 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Robust Detection of Brain Stimulation Artifacts in iEEG Using Autoencoder-Generated Signals and ResNet Classification ]]> https://biorxiv.org/content/10.1101/2024.09.30.615930v1?rss=1 Saal, J. Khambhati, A. N. Chang, E. F. Shirvalkar, P. 2024-10-02 doi:10.1101/2024.09.30.615930 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Interrogating the plasma proteome of repetitive head impact exposure and chronic traumatic encephalopathy ]]> https://biorxiv.org/content/10.1101/2024.10.01.616097v1?rss=1 Saloner, R. Casaletto, K. B. Rayaprolu, S. Chakrabarty, P. Abisambra, J. F. Spina, S. Grinberg, L. T. Seeley, W. W. Miller, B. L. Kramer, J. H. Rabinovici, G. D. Asken, B. M. 2024-10-02 doi:10.1101/2024.10.01.616097 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Long range mutual activation establishes Rho and Rac polarity during cell migration ]]> https://biorxiv.org/content/10.1101/2024.10.01.616161v1?rss=1 De Belly, H. Gallen, A. F. Strickland, E. Estrada, D. C. Zager, P. J. Burkhardt, J. K. Turlier, H. Weiner, O. 2024-10-02 doi:10.1101/2024.10.01.616161 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing ]]> https://biorxiv.org/content/10.1101/2024.10.01.616167v1?rss=1 Shin, D. Urbanek, M. E. Larson, H. H. Moussa, A. J. Lee, K. Y. Baker, D. L. Standen-Bloom, E. Ramachandran, S. Bogdanoff, D. Cadwell, C. R. Nowakowski, T. J. 2024-10-02 doi:10.1101/2024.10.01.616167 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Sex differences in the clinical manifestation of autosomal dominant frontotemporal dementia ]]> https://biorxiv.org/content/10.1101/2024.10.01.614851v1?rss=1 Memel, M. Staffaroni, A. Ilan-Gala, I. Garcia Castro, J. Kornak, J. Tartaglia, C. Saloner, R. VandeBunte, A. Paolillo, E. Cadwallader, C. Chen, C. Gorno-Tempini, M. L. Mandelli, M. Apostolova, L. Graff-Radford, N. Litvan, I. Bayram, E. Pressman, P. Miyagawa, T. Mackenzie, I. Goldman, J. Darby, R. Appleby, B. Petrucelli, L. Gendron, T. Heuer, H. Forseberg, L. Rojas, J. Boeve, B. Brushaber, N. Domoto-Reilly, K. Ghoshal, N. Lapid, M. Pascual, B. Lee, S. Ramos, E. Ramanan, V. Rademakers, R. Rascovsky, K. Pantelyat, A. Masdeu, J. Snyder, A. Boxer, A. Rosen 2024-10-03 doi:10.1101/2024.10.01.614851 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Structural basis for saxitoxin congener binding and neutralization by anuran saxiphilins ]]> https://biorxiv.org/content/10.1101/2024.10.01.616181v1?rss=1 Zakrzewska, S. Nixon, S. A. Chen, Z. Hajare, H. S. Park, E. R. Mulcahy, J. V. Arlinghaus, K. M. Neu, E. Konovalov, K. Provasi, D. Leighfield, T. A. Filizola, M. Du Bois, J. Minor, D. L. 2024-10-03 doi:10.1101/2024.10.01.616181 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ microbetag: simplifying microbial network interpretation through annotation, enrichment tests and metabolic complementarity analysis ]]> https://biorxiv.org/content/10.1101/2024.10.01.616208v1?rss=1 Zafeiropoulos, H. Michail Delopoulos, E. I. Erega, A. Schneider, A. Geirnaert, A. Morris, J. Faust, K. 2024-10-03 doi:10.1101/2024.10.01.616208 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Short-term caloric restriction or resveratrol supplementation alters large-scale brain network connectivity in male and female rats ]]> https://biorxiv.org/content/10.1101/2024.10.02.616243v1?rss=1 van Rooij, J. R. A. van den Berg, M. Vasilkosvka, T. Van Audekerke, J. Kosten, L. Bertoglio, D. Adhikari, M. H. Verhoye, M. 2024-10-03 doi:10.1101/2024.10.02.616243 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Coordinate post-transcriptional regulation by microRNAs and RNA binding proteins is critical for early embryonic cell fate decisions ]]> https://biorxiv.org/content/10.1101/2024.10.02.616359v1?rss=1 Sangokoya, C. Blelloch, R. 2024-10-03 doi:10.1101/2024.10.02.616359 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ SPLASH-structure: a statistical approach to identify RNA secondary structures from raw sequencing data, bypassing multiple sequence alignment ]]> https://biorxiv.org/content/10.1101/2024.10.03.616574v1?rss=1 Wang, J. F. Rustagi, A. Salzman, J. 2024-10-04 doi:10.1101/2024.10.03.616574 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function ]]> https://biorxiv.org/content/10.1101/2024.10.04.615095v1?rss=1 Hansen, K. L. Adachi, A. S. Braccioli, L. Kadvani, S. Boileau, R. M. Pokorny, B. Shah, R. Anderson, E. C. Martinovic, M. Zhang, K. Carel, I. Bonitto, K. Blelloch, R. Fudenberg, G. de Wit, E. Nora, E. P. 2024-10-04 doi:10.1101/2024.10.04.615095 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ CRISPR tiling deletion screens reveal functional enhancers of neuropsychiatric risk genes and allelic compensation effects (ACE) on transcription ]]> https://biorxiv.org/content/10.1101/2024.10.08.616922v1?rss=1 Ren, X. Zheng, L. Maliskova, L. Tam, T. W. Sun, Y. Liu, H. Lee, J. Takagi, M. A. Li, B. Ren, B. Wang, W. Shen, Y. 2024-10-10 doi:10.1101/2024.10.08.616922 Cold Spring Harbor Laboratory Press 2024-10-10 <![CDATA[ Proteomic profiling of the local and systemic immune response to pediatric respiratory viral infections ]]> https://biorxiv.org/content/10.1101/2024.10.08.617294v1?rss=1 Lydon, E. Osborne, C. M. Wagner, B. D. Ambroggio, L. Harris, J. K. Reeder, R. W. Carpenter, T. C. Maddux, A. B. Leroue, M. K. Yehya, N. DeRisi, J. L. Hall, M. W. Zuppa, A. Carcillo, J. A. Meert, K. Sapru, A. Pollack, M. M. McQuillen, P. Notterman, D. Langelier, C. R. Mourani, P. M. 2024-10-10 doi:10.1101/2024.10.08.617294 Cold Spring Harbor Laboratory Press 2024-10-10 <![CDATA[ Heterozygous and generalist MxA super-restrictors overcome breadth-specificity tradeoffs in antiviral restriction ]]> https://biorxiv.org/content/10.1101/2024.10.10.617484v1?rss=1 Geiger, R. A. Khera, D. Tenthorey, J. Kochs, G. Graf, L. Emerman, M. Malik, H. S. 2024-10-10 doi:10.1101/2024.10.10.617484 Cold Spring Harbor Laboratory Press 2024-10-10 <![CDATA[ Antibody-Fab and -Fc features promote Mycobacterium tuberculosis restriction. ]]> https://biorxiv.org/content/10.1101/2024.10.07.617070v1?rss=1 Grace, P. S. Peters, J. M. Sixsmith, J. Lu, R. Fenderson, B. A. Vickers, A. Slein, M. D. Irvine, E. B. McKitrick, T. Wei, M.-H. Cummings, R. D. Wallace, A. Cavacini, L. Choudhary, A. K. Proulx, M. K. Sundling, C. Källenius, G. Reljic, R. Ernst, J. D. Casadevall, A. Locht, C. Pinter, A. Sassetti, C. M. Bryson, B. D. Fortune, S. M. Alter, G. 2024-10-11 doi:10.1101/2024.10.07.617070 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Opioid receptors reveal a discrete cellular mechanism of endosomal G protein activation ]]> https://biorxiv.org/content/10.1101/2024.10.07.617095v1?rss=1 Fisher, N. M. Von Zastrow, M. 2024-10-11 doi:10.1101/2024.10.07.617095 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Longitudinal multi-omics reveals pathogenic TSC2 variants disrupt developmental trajectories of human cortical organoids derived from Tuberous Sclerosis Complex ]]> https://biorxiv.org/content/10.1101/2024.10.07.617121v1?rss=1 Niu, W. Yu, S. Li, X. Wang, Z. Chen, R. Michalski, C. Jahangiri, A. Zohdy, Y. Chern, J. J. Whitworth, T. J. Wang, J. Xu, J. Zhou, Y. Qin, Z. Li, B. Gambello, M. J. Peng, J. Wen, Z. 2024-10-11 doi:10.1101/2024.10.07.617121 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Functional screen for mediators of onco-mRNA translation specificity ]]> https://biorxiv.org/content/10.1101/2024.10.10.617637v1?rss=1 Kovalski, J. R. Sarioglu, G. Subramanyam, V. Hernandez, G. Rademaker, G. Oses-Prieto, J. A. Slota, M. Mohan, N. Yiakis, K. Liu, I. Wen, K. W. Kim, G. E. Miglani, S. Burlingame, A. Goodarzi, H. Perera, R. M. Ruggero, D. 2024-10-11 doi:10.1101/2024.10.10.617637 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Striatal lateral inhibition regulates action selection in a mouse model of levodopa-induced dyskinesia ]]> https://biorxiv.org/content/10.1101/2024.10.11.617939v1?rss=1 Twedell, E. L. Bair-Marshall, C. J. Girasole, A. E. Scaria, L. K. Sridhar, S. Nelson, A. B. 2024-10-12 doi:10.1101/2024.10.11.617939 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ A Suite of Foundation Models Captures the Contextual Interplay Between Codons ]]> https://biorxiv.org/content/10.1101/2024.10.10.617568v1?rss=1 Naghipourfar, M. Chen, S. Howard, M. Macdonald, C. Saberi, A. Hagen, T. Mofrad, M. Coyote-Maestas, W. Goodarzi, H. 2024-10-13 doi:10.1101/2024.10.10.617568 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ The kinetics of bedaquiline diffusion in tuberculous cavities opens a window for emergence of resistance. ]]> https://biorxiv.org/content/10.1101/2024.10.09.617456v1?rss=1 Bustion, A. E. Ernest, J. P. Kaya, F. Silva, C. Sarathy, J. Blanc, L. Imperial, M. Gengenbacher, M. Xie, M. Zimmerman, M. Robertson, G. T. Weiner, D. Via, L. E. Barry, C. E. Savic, R. M. Dartois, V. 2024-10-14 doi:10.1101/2024.10.09.617456 Cold Spring Harbor Laboratory Press 2024-10-14 <![CDATA[ Human brain changes after first psilocybin use ]]> https://biorxiv.org/content/10.1101/2024.10.11.617955v1?rss=1 Lyons, T. Spriggs, M. Kerkela, L. Rosas, F. Roseman, L. Timmermann, C. Oestreich, L. Pagni, B. Zeifman, R. Hampshire, A. Trender, W. Douglas, H. Girn, M. Godfrey, K. Kettner, H. Sharif, F. Espasiano, L. Gazzaley, A. Wall, M. Erritzoe, D. Nutt, D. Carhart-Harris, R. 2024-10-14 doi:10.1101/2024.10.11.617955 Cold Spring Harbor Laboratory Press 2024-10-14 <![CDATA[ Immunological Profiling in Knee Osteoarthritis: Treg Dysfunction as Key Driver of Pain ]]> https://biorxiv.org/content/10.1101/2024.10.12.618016v1?rss=1 Binvignat, M. Dubois, J. Marco Salvador, M. Stys, P. Pitoiset, F. Roux, A. Barbie, M. Hassler, S. Lorenzon, R. Ribet, C. Mhanna, V. Vantomme, H. Adda, L. Barennes, P. Coatnoan, N. Legouge, K. Aheng, C. Courties, A. Minssen, L. Butte, A. J. Six, A. Rosenzwajg, M. Tchitchek, N. Berenbaum, F. Klatzmann, D. Mariotti-Ferrandiz, E. Sellam, J. 2024-10-15 doi:10.1101/2024.10.12.618016 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ The Taiwan Precision Medicine Initiative: A Cohort for Large-Scale Studies ]]> https://biorxiv.org/content/10.1101/2024.10.14.616932v1?rss=1 1.4 billion people around the world and serve as a model for developing population-based precision medicine. ]]> Yang, H.-C. Kwok, P.-Y. Li, L.-H. Liu, Y.-M. Jong, Y.-J. Lee, K.-Y. Wang, D.-W. Tsai, M.-F. Yang, J.-H. Chen, C.-H. Yeh, E.-C. Wei, C.-y. Fann, C. S.- J. Huang, Y.-T. Chen, C.-W. Lee, Y.-J. Chu, S.-K. Ho, C.-h. Yang, C.-S. Lee, Y. L. Chen, H.-H. Hou, M.-C. Chiou, J.-F. Yang, S.-F. Wang, C.-H. Huang, C.-Y. Chiu, K.-M. Chen, M. Chiang, F.-T. Lee, S.-L. Chen, S.-S. Yao, W.-J. Chien, C.-C. Lin, S.-Y. Chang, F.-P. Ho, H.-L. Yeh, Y.-C. Tseng, W.-C. Lin, M.-H. Chang, H.-T. Tseng, L.-M. Liang, W.-Y. Chen, P. C.-H. Hang, J.-F. Lin, S.-C. Chan, Y.-J. Kuo, Y. 2024-10-17 doi:10.1101/2024.10.14.616932 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Replicating retroviral delivery of an IL-15 superagonist improves antitumor immunity and long-term survival in poorly immunogenic glioblastoma models ]]> https://biorxiv.org/content/10.1101/2024.10.14.618095v1?rss=1 Haddad, A. F. Saha, A. Spatz, J. Collins, S. Lovalvo, I. Gill, S. Montoya, M. L. Shukla, P. Hong, J. Wang, E. Chuntova, P. Lad, M. Chalif, E. Kasahara, N. Aghi, M. K. 2024-10-17 doi:10.1101/2024.10.14.618095 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Telocytes link epithelial nutrient sensing with amplification of the ILC2-tuft cell circuit ]]> https://biorxiv.org/content/10.1101/2024.10.14.618111v1?rss=1 Liao, C. Ji, M. Wang, Z.-E. Drucker, D. J. Liang, H.-E. Locksley, R. M. 2024-10-17 doi:10.1101/2024.10.14.618111 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Representations of stimulus meaning in the hippocampus ]]> https://biorxiv.org/content/10.1101/2024.10.14.618280v1?rss=1 Biane, J. S. Ladow, M. A. Fan, A. Choi, H. S. Zhou, L. Z. Hassan, S. Apodaca-Montano, D. L. Kwon, A. O. Bratsch-Prince, J. X. Kheirbek, M. A. 2024-10-17 doi:10.1101/2024.10.14.618280 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Dark Microglia Are Abundant in Normal Postnatal Development, where they Remodel Synapses via Phagocytosis and Trogocytosis, and Are Dependent on TREM2 ]]> https://biorxiv.org/content/10.1101/2024.10.15.618087v1?rss=1 Vecchiarelli, H. A. Bisht, K. Sharma, K. P. Weiser Novak, S. Traetta, M. E. Garcia-Segura, M. E. St-Pierre, M.-K. Savage, J. C. Willis, C. Picard, K. Bordeleau, M. Vernoux, N. Khakpour, M. Garg, R. Loewen, S. M. Murray, C. J. Grinberg, Y. Y. Faustino, J. Halvorson, T. Lau, V. Pluchino, S. Vexler, Z. S. Carson, M. J. Manor, U. Peruzzotti-Jametti, L. Tremblay, M.-E. 2024-10-18 doi:10.1101/2024.10.15.618087 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Adhesion G protein-coupled receptor ADGRG1 promotes protective microglial response in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2024.10.15.618329v1?rss=1 Zhu, B. Wangzhou, A. Yu, D. Li, T. Schmidt, R. De Florencio, S. L. Chao, L. Perez, Y. Grinberg, L. T. Spina, S. Ransohoff, R. M. Kriegstein, A. Seeley, W. W. Nowakowski, T. J. Piao, X. 2024-10-18 doi:10.1101/2024.10.15.618329 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ CELL-Diff: Unified diffusion modeling for protein sequences and microscopy images ]]> https://biorxiv.org/content/10.1101/2024.10.15.618585v1?rss=1 Zheng, D. Huang, B. 2024-10-18 doi:10.1101/2024.10.15.618585 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Methylation Clocks Do Not Predict Age or Alzheimer's Disease Risk Across Genetically Admixed Individuals ]]> https://biorxiv.org/content/10.1101/2024.10.16.618588v1?rss=1 2,500 individuals of European and African ancestry from three additional datasets. The clocks also fail to consistently identify age acceleration in admixed AD cases compared to controls. To explore potential causes for the lack of generalization of the clocks, we intersected clock CpGs with methylation, germline genetic variants, and methylation QTL (meQTL) data from global populations. We find differential methylation between African and European ancestry individuals is common for clock CpGs. Genetic variants rarely disrupt clock CpGs between populations, but a substantial fraction of clock CpGs have meQTL with significantly higher frequencies in African genetic ancestries. Our results demonstrate that methylation clocks often fail to predict age and AD risk when applied across populations and suggest avenues for improving their portability by considering differences in genetic and epigenetic patterns across human populations. ]]> Cruz-Gonzalez, S. Gu, E. Gomez, L. Mews, M. Vance, J. M. Cuccaro, M. L. Cornejo-Olivas, M. R. Feliciano-Astacio, B. E. Byrd, G. S. Haines, J. L. Pericak-Vance, M. A. Griswold, A. J. Bush, W. S. Capra, J. A. 2024-10-18 doi:10.1101/2024.10.16.618588 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Microglia regulate GABAergic neurogenesis in prenatal human brain through IGF1 ]]> https://biorxiv.org/content/10.1101/2024.10.19.619180v1?rss=1 Yu, D. Jain, S. Wangzhou, A. De Florencio, S. Zhu, B. Kim, J. Choi, J. Paredes, M. Nowakowski, T. J. Huang, E. J. Piao, X. 2024-10-20 doi:10.1101/2024.10.19.619180 Cold Spring Harbor Laboratory Press 2024-10-20 <![CDATA[ Medicinal chemistry of benzoisoxazole-4,7-dione analogues identifies the ribosomal small subunit as a target for specific mycobacterial translational fidelity ]]> https://biorxiv.org/content/10.1101/2024.10.20.619312v1?rss=1 Wu, J. Chaudhuri, S. Feid, S. C. Pan, M. Kawaji, Q. Liu, G. Javid, B. 2024-10-21 doi:10.1101/2024.10.20.619312 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ Shc1 cooperates with Frs2 and Shp2 to recruit Grb2 in FGF-induced lens development ]]> https://biorxiv.org/content/10.1101/2024.10.20.619055v1?rss=1 Wang, Q. Li, H. Mao, Y. Garg, A. Park, E. S. Wu, Y. Chow, A. Peregrin, J. Zhang, X. 2024-10-22 doi:10.1101/2024.10.20.619055 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Differential enrichment of retinal ganglion cells underlies proposed core neurodegenerative transcription programs ]]> https://biorxiv.org/content/10.1101/2024.10.21.618927v1?rss=1 Watkins, T. A. 2024-10-22 doi:10.1101/2024.10.21.618927 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Phenotypic landscape of a fungal meningitis pathogen reveals its unique biology ]]> https://biorxiv.org/content/10.1101/2024.10.22.619677v1?rss=1 Boucher, M. Banerjee, S. Joshi, M. Wei, A. Huang, M. Lei, S. Ciranni, M. Condon, A. Langen, A. Goddard, T. Caradonna, I. Goranov, A. Homer, C. Mortensen, Y. Petnic, S. Reilly, M. Xiong, Y. Susa, K. Pastore, V. P. Zaro, B. Madhani, H. 2024-10-22 doi:10.1101/2024.10.22.619677 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Multigenerational Proteolytic Inactivation of Restriction Upon Subtle Genomic Hypomethylation ]]> https://biorxiv.org/content/10.1101/2024.10.21.619520v1?rss=1 Shmidov, E. Villani, A. Mendoza, S. D. Avihu, E. Lebenthal-Loinger, I. Karako-Lampert, S. Shoshani, S. Ye, C. Wang, Y. Yan, H. Tang, W. Bondy-Denomy, J. Banin, E. 2024-10-23 doi:10.1101/2024.10.21.619520 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Endogenous neuronal DNA double-strand breaks are not sufficient to drive brain aging and neurodegeneration ]]> https://biorxiv.org/content/10.1101/2024.10.22.619740v1?rss=1 Cohen, S. Cheradame, L. Pratt, K. Collins, S. Barillas, A. Carlson, A. Ramani, V. Legube, G. Villeda, S. Mullins, D. Schwer, B. 2024-10-23 doi:10.1101/2024.10.22.619740 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Type 2 diabetes remodels collateral circulation and promotes leukocyte adhesion following ischemic stroke ]]> https://biorxiv.org/content/10.1101/2024.10.23.619748v1?rss=1 Sato, Y. Li, Y. Kato, Y. Kanoke, A. Sun, Y. J. Nishijima, Y. Wang, R. K. Stryker, M. Endo, H. Liu, J. 2024-10-23 doi:10.1101/2024.10.23.619748 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Single-Nuclei Analysis of the Unfolded Protein Response (SNUPR): A Novel Method revealing bortezomib resistance mechanisms in Multiple Myeloma ]]> https://biorxiv.org/content/10.1101/2024.10.22.617161v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@297668org.highwire.dtl.DTLVardef@1cab0eorg.highwire.dtl.DTLVardef@2238b4org.highwire.dtl.DTLVardef@b8ebf6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Arguello, R. J. Pierre, P. Gigan, J. P. Garcia-Gonzalez, P. Galliot, L. Ghaffar, Y. Flores-Santibanez, F. Seillier, E. Lavignolle-Heguy, R. Fischaux, S. Dos Santos, D. Combes, A. Narita, M. Gatti, E. Nal, B. Rocchi, S. Moreaux, J. 2024-10-25 doi:10.1101/2024.10.22.617161 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Comprehensive structure-function analysis reveals gain- and loss-of-function mechanisms impacting oncogenic KRAS activity ]]> https://biorxiv.org/content/10.1101/2024.10.22.618529v1?rss=1 Kwon, J. Dilly, J. Liu, S. Kim, E. Bian, Y. Dharmaiah, S. Tran, T. H. Kapner, K. S. Ly, S. H. Yang, X. Rabara, D. Waybright, T. J. Giacomelli, A. O. Hong, A. L. Misek, S. L. Wang, B. Ravi, A. Beroukhim, R. Lemke, C. T. Haigis, K. M. Esposito, D. Root, D. E. Nissley, D. V. Stephen, A. G. McCormick, F. Simanshu, D. K. Hahn, W. C. Aguirre, A. J. 2024-10-25 doi:10.1101/2024.10.22.618529 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Sequence-dependent scale for translocon-mediated insertion of interfacial helices in membranes ]]> https://biorxiv.org/content/10.1101/2024.10.23.619793v1?rss=1 Grau, B. Kormos, R. Bano-Polo, M. Chen, K. Garcia-Murria, M. J. Hajredini, F. Sanchez del Pino, M. Jo, H. Martinez-Gil, L. Von Heijne, G. DeGrado, W. Mingarro, I. 2024-10-25 doi:10.1101/2024.10.23.619793 Cold Spring Harbor Laboratory Press 2024-10-25 <![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[ Imaging synaptic density in ageing and Alzheimer's Disease with -SynVesT-1 ]]> https://biorxiv.org/content/10.1101/2024.10.23.619941v1?rss=1 Giorgio, J. Soleimani-Meigooni, D. N. Janabi, M. Baker, S. Chen, X. Toueg, T. N. Weimer, R. Zinnhardt, B. Green, A. Rabinovici, G. D. Jagust, W. 2024-10-26 doi:10.1101/2024.10.23.619941 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ Encoding manifolds constructed from grating responses organize responses to natural scenes in cortical visual areas ]]> https://biorxiv.org/content/10.1101/2024.10.24.620089v1?rss=1 Dyballa, L. Field, G. D. Stryker, M. P. Zucker, S. W. 2024-10-26 doi:10.1101/2024.10.24.620089 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ Differential Sensitivity of Midline Patterning to Mitosis during and after Primitive Streak Extension ]]> https://biorxiv.org/content/10.1101/2024.10.25.620280v1?rss=1 Zhao, Z. Asai, R. Mikawa, T. 2024-10-26 doi:10.1101/2024.10.25.620280 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ APOBEC3A drives metastasis of ovarian cancer by altering epithelial-to-mesenchymal transition ]]> https://biorxiv.org/content/10.1101/2024.10.25.620297v1?rss=1 Devenport, J. M. Tran, T. Harris, B. R. Fingerman, D. F. DeWeerd, R. A. Elkhidir, L. LaVigne, D. A. Fuh, K. Sun, L. Bednarski, J. J. Drapkin, R. Mullen, M. Green, A. M. 2024-10-28 doi:10.1101/2024.10.25.620297 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Restoring the Multiple Sclerosis Associated Imbalance of Gut Indole Metabolites Promotes Remyelination and Suppresses Neuroinflammation ]]> https://biorxiv.org/content/10.1101/2024.10.27.620437v1?rss=1 Jank, L. Singh, S. S. Lee, J. Dhukhwa, A. Siavoshi, F. Joshi, D. Minney, V. Gupta, K. Ghimire, S. Deme, P. Schoeps, V. A. Soman, K. Ladakis, D. Smith, M. Borkowski, K. Newman, J. Baranzini, S. E. Waubant, E. L. Fitzgerald, K. C. Mangalam, A. K. Haughey, N. Kornberg, M. D. Chamling, X. Calabresi, P. A. Bhargava, P. 2024-10-28 doi:10.1101/2024.10.27.620437 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Phosphorylation of HP1/Swi6 relieves competition with Suv39/Clr4 on nucleosomes and enables H3K9 trimethyl spreading. ]]> https://biorxiv.org/content/10.1101/2024.10.25.620326v1?rss=1 Kennedy, D. R. Lemiere, J. Tan, C. Simental, E. Braxton, J. Maxwell, R. A. Amine, A. A. Al-Sady, B. 2024-10-29 doi:10.1101/2024.10.25.620326 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ DNMT3AR882H Is Not Required for Disease Maintenance in Primary Human AML, but Is Associated With Increased Leukemia Stem Cell Frequency ]]> https://biorxiv.org/content/10.1101/2024.10.26.620318v1?rss=1 Koehnke, T. Karigane, D. Hilgart, E. Fan, A. C. Kayamori, K. Miyauchi, M. Collins, C. T. Suchy, F. P. Rangavajhula, A. Feng, Y. Nakauchi, Y. Martinez-Montes, E. Fowler, J. Loh, K. M. Nakauchi, H. Koldobskiy, M. A. Feinberg, A. P. Majeti, R. 2024-10-29 doi:10.1101/2024.10.26.620318 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ A multi-subunit autophagic capture complex facilitates degradation of ER stalled MHC-I in pancreatic cancer. ]]> https://biorxiv.org/content/10.1101/2024.10.27.620516v1?rss=1 Berquez, M. Li, A. L. Luy, M. A. Venida, A. C. O'Loughlin, T. Rademaker, G. Barpanda, A. Hu, J. Yano, J. Wiita, A. Gilbert, L. A. Bruno, P. M. Perera, R. M. 2024-10-29 doi:10.1101/2024.10.27.620516 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ A mitochondrial redox switch licenses the onset of morphogenesis in animals ]]> https://biorxiv.org/content/10.1101/2024.10.28.620733v1?rss=1 Kahlin, U. Dalla Ricca, F. Pillai, S. J. Olivetta, M. Tharp, K. M. Jao, L.-E. Dudin, O. McDonald, K. L. Aydogan, M. G. 2024-10-29 doi:10.1101/2024.10.28.620733 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ eIF4ET regulates meiotic proteome levels to enable oocyte formation and storage ]]> https://biorxiv.org/content/10.1101/2024.10.29.620718v1?rss=1 Bhatia, P. Amin, R. Familiari, N. E. Yaguchi, K. Tran, V. M. Bond, A. Bukulmez, O. Woodruff, J. B. 2024-10-29 doi:10.1101/2024.10.29.620718 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Orexinergic projections to substantia innominata mediate arousal and analgesia ]]> https://biorxiv.org/content/10.1101/2024.10.29.620973v1?rss=1 Xiang, X. Wang, F. Chen, C. Guan, Z. Zhou, W. 2024-10-31 doi:10.1101/2024.10.29.620973 Cold Spring Harbor Laboratory Press 2024-10-31 <![CDATA[ A Novel Human TBCK- Neuronal Cell Model Results in Severe Neurodegeneration and Partial Rescue with Mitochondrial Fission Inhibition ]]> https://biorxiv.org/content/10.1101/2024.10.30.621078v1?rss=1 Angireddy, R. Murali, S. Karisetty, B. C. Kossenkov, A. Katsura, K. Ohl, L. Smith, S. Clark, K. Bhoj, E. Diaz, A. 2024-10-31 doi:10.1101/2024.10.30.621078 Cold Spring Harbor Laboratory Press 2024-10-31 <![CDATA[ A designed Zn2+ sensor domain transmits binding information to transmembrane histidine kinases ]]> https://biorxiv.org/content/10.1101/2024.10.30.621206v1?rss=1 Hatstat, A. K. Kormos, R. Xu, V. DeGrado, W. F. 2024-10-31 doi:10.1101/2024.10.30.621206 Cold Spring Harbor Laboratory Press 2024-10-31 <![CDATA[ Automated segmentation of soft X-ray tomography: native cellular structure with sub-micron resolution at high throughput for whole-cell quantitative imaging in yeast ]]> https://biorxiv.org/content/10.1101/2024.10.31.621371v1?rss=1 Chen, J.-H. F. Mirvis, M. Ekman, A. Vanslembrouck, B. Le Gros, M. Larabell, C. Marshall, W. F. 2024-11-01 doi:10.1101/2024.10.31.621371 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Multi-modal characterization of rodent tooth development ]]> https://biorxiv.org/content/10.1101/2024.11.01.621612v1?rss=1 Jiang, Y. Katsura, K. A. Badt, N. Z. Didziokas, M. Dougherty, S. Goldsby, D. L. Bhoj, E. J. Vining, K. H. 2024-11-01 doi:10.1101/2024.11.01.621612 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Heart tube morphogenesis is regulated by segment-specific gene regulatory networks controlled by MEF2C ]]> https://biorxiv.org/content/10.1101/2024.11.01.621613v1?rss=1 Muncie-Vasic, J. M. Sinha, T. Clark, A. P. Brower, E. F. Saucerman, J. J. Black, B. L. Bruneau, B. G. 2024-11-01 doi:10.1101/2024.11.01.621613 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Hypoxia induces extensive protein and proteolytic remodeling of the cell surface in pancreatic adenocarcinoma (PDAC) cell lines ]]> https://biorxiv.org/content/10.1101/2024.10.30.621099v1?rss=1 Lui, I. Schaefer, K. Kirkemo, L. Zhou, J. Perera, R. M. Leung, K. K. Wells, J. A. 2024-11-02 doi:10.1101/2024.10.30.621099 Cold Spring Harbor Laboratory Press 2024-11-02 <![CDATA[ Site-specific DNA insertion into the human genome with engineered recombinases ]]> https://biorxiv.org/content/10.1101/2024.11.01.621560v1?rss=1 Fanton, A. Bartie, L. J. Martins, J. Q. Tran, V. Q. Goudy, L. Durrant, M. G. Wei, J. Pawluk, A. Konermann, S. Marson, A. Gilbert, L. A. Hsu, P. D. 2024-11-03 doi:10.1101/2024.11.01.621560 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Chromatin mimicry by human JC virus ]]> https://biorxiv.org/content/10.1101/2024.11.04.621823v1?rss=1 Schaefer, U. Miroshnikova, Y. A. Xie, W. Larson, A. G. Lu, Z. Chen, S. Bradic, M. Goldgur, Y. Chen, K. Sharma, V. P. Cao, J. Patel, D. J. Narlikar, G. J. Wickstrom, S. A. Tarakhovsky, A. 2024-11-04 doi:10.1101/2024.11.04.621823 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ Antigen-Specific T Cell Receptor Discovery for Treating Progressive Multifocal Leukoencephalopathy ]]> https://biorxiv.org/content/10.1101/2024.11.04.621904v1?rss=1 Gupta, S. Martinov, T. Thelen, A. Sunahara, M. Mureli, S. Vazquez, A. Gerdts, J. Dandekar, R. Cortese, I. Fouassier, C. Schanzer, E. Urnov, F. D. Marson, A. Shy, B. R. Greenberg, P. D. Wilson, M. R. 2024-11-04 doi:10.1101/2024.11.04.621904 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ Corticonigral projections recruit substantia nigra pars lateralis dopaminergic neurons for auditory threat memories ]]> https://biorxiv.org/content/10.1101/2024.11.04.621665v1?rss=1 Sansalone, L. Evans, R. C. Twedell, E. Zhang, R. Khaliq, Z. M. 2024-11-05 doi:10.1101/2024.11.04.621665 Cold Spring Harbor Laboratory Press 2024-11-05 <![CDATA[ Pseudomonas aeruginosa essential gene perturbations that confer vulnerability to the mammalian host environment ]]> https://biorxiv.org/content/10.1101/2024.11.05.622029v1?rss=1 Prasad, N. K. Ward, R. D. Yu, M. A. Kwon, M. S. Banta, A. B. Rosenberg, O. S. Peters, J. M. 2024-11-05 doi:10.1101/2024.11.05.622029 Cold Spring Harbor Laboratory Press 2024-11-05 <![CDATA[ De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes ]]> https://biorxiv.org/content/10.1101/2024.11.06.621353v1?rss=1 Gjoni, K. Ren, X. Everitt, A. Shen, Y. Pollard, K. S. 2024-11-07 doi:10.1101/2024.11.06.621353 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ Long-term effects of psilocybin on dynamic and effectivity connectivity of fronto-striatal-thalamic circuits ]]> https://biorxiv.org/content/10.1101/2024.11.06.622302v1?rss=1 Pasquini, L. Vohryzek, J. Escrichs, A. Sanz Perl, Y. Alvarez, A. Idesis, S. Girn, M. Roseman, L. Mitchell, J. M. Gazzaley, A. Kringelbach, M. Nutt, D. J. Lyons, T. Carhart-Harris, R. L. Deco, G. 2024-11-07 doi:10.1101/2024.11.06.622302 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ Acetic acid induces osmotic imbalances in drug-resistant bacteria synergistically enhancing cobalt-doped carbon quantum dots bactericidal efficiency ]]> https://biorxiv.org/content/10.1101/2024.11.06.622380v1?rss=1 Truskewycz, A. Choi, B. Pedersen, L. Han, J. Halberg, N. 2024-11-07 doi:10.1101/2024.11.06.622380 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ Integrated, high-dimensional analysis of CD4 T cell epitope specificities and phenotypes reveals unexpected diversity in the response to Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2024.11.05.622086v1?rss=1 Mead, H. L. Kirschman, J. H. Harms, C. E. Kelley, E. J. Soria-Bustos, J. Nelson, G. A. Ogongo, P. Ouma, G. Ouma, S. G. Ernst, J. D. Altin, J. A. 2024-11-08 doi:10.1101/2024.11.05.622086 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome ]]> https://biorxiv.org/content/10.1101/2024.11.06.622278v1?rss=1 Rendina, M. Turnbaugh, P. J. Bradley, P. H. 2024-11-08 doi:10.1101/2024.11.06.622278 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Evolutionarily guided transcription factor design programs novel T cell states ]]> https://biorxiv.org/content/10.1101/2024.11.06.622344v1?rss=1 Takacsi-Nagy, O. Hartman, A. Chen, A. Y. Yin, Y. Reeder, G. C. Kernick, C. Lu, J. McClellan, A. K. Raposo, C. J. Theberath, N. E. Yan, P. K. Eyquem, J. Roth, T. L. Satpathy, A. T. 2024-11-08 doi:10.1101/2024.11.06.622344 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Genetic Basis, Quantitative Nature, and Functional Relevance of Evolutionarily Conserved DNA Methylation ]]> https://biorxiv.org/content/10.1101/2024.11.07.622474v1?rss=1 Dong, Z. Schaffner, S. Fu, M. Whitehead, J. MacIsaac, J. L. Rehkopf, D. H. Boyce, W. T. Rosero-Bixby, L. Quintana-Murci, L. Patin, E. Miller, G. E. Korthauer, K. Kobor, M. S. 2024-11-09 doi:10.1101/2024.11.07.622474 Cold Spring Harbor Laboratory Press 2024-11-09 <![CDATA[ Disease-Linked Regulatory DNA Variants and Homeostatic Transcription Factors in Epidermis ]]> https://biorxiv.org/content/10.1101/2024.11.07.622542v1?rss=1 Porter, D. F. Meyers, R. M. Miao, W. Reynolds, D. Hong, A. W. Yang, X. Mondal, S. Siprashvili, Z. Srinivasan, S. DUCOLI, L. Meyers, J. Nguyen, D. Ko, L. Kellman, L. Elfaki, I. Guo, M. Winge, M. Lopez-Pajares, V. Tao, S. Khavari, P. 2024-11-11 doi:10.1101/2024.11.07.622542 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Single-cell spatial transcriptomics of fixed, paraffin-embedded biopsies reveals colitis-associated cell networks ]]> https://biorxiv.org/content/10.1101/2024.11.11.623014v1?rss=1 Mennillo, E. Lotstein, M. L. Lee, G. Johri, V. Ekstrand, C. Tsui, J. Hou, J. Leet, D. E. He, J. Y. Mahadevan, U. Eckalbar, W. L. Oh, D. Y. Fragiadakis, G. K. Kattah, M. G. Combes, A. 2024-11-11 doi:10.1101/2024.11.11.623014 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ The Impact of Charge Regulation and Ionic Intranuclear Environment on the Nucleosome Core Particle ]]> https://biorxiv.org/content/10.1101/2024.11.11.623012v1?rss=1 Nap, R. J. Gonzalez, P. C. Coraor, A. E. Virk, R. K. A. de Pablo, J. J. Backman, V. Szleifer, I. 2024-11-12 doi:10.1101/2024.11.11.623012 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Loss of TMEM55B modulates lipid metabolism through dysregulated lipophagy and mitochondrial function ]]> https://biorxiv.org/content/10.1101/2024.11.12.623285v1?rss=1 Qin, Y. Teker, S. La Cunza, N. Theusch, E. Yang, N. Venkatesan, L. Su, J. Krauss, R. M. Lakkaraju, A. Mattis, A. N. Medina, M. W. 2024-11-13 doi:10.1101/2024.11.12.623285 Cold Spring Harbor Laboratory Press 2024-11-13 <![CDATA[ Sulfur-species in Zinc-specific Condylar Zones of a Rat Temporomandibular Joint ]]> https://biorxiv.org/content/10.1101/2024.11.11.623079v1?rss=1 Lee, B. H. Yang, Z. Ho, T. J. Wang, Y. Tamura, N. Webb, S. Bone, S. Ho, S. P. 2024-11-14 doi:10.1101/2024.11.11.623079 Cold Spring Harbor Laboratory Press 2024-11-14 <![CDATA[ Interspecies Organoids Reveal Human-Specific Molecular Features of Dopaminergic Neuron Development and Vulnerability ]]> https://biorxiv.org/content/10.1101/2024.11.14.623592v1?rss=1 Nolbrant, S. Wallace, J. L. Ding, J. Zhu, T. Sevetson, J. L. Kajtez, J. Baldacci, I. A. Corrigan, E. K. Hoglin, K. McMullen, R. Schmitz, M. T. Breevoort, A. Swope, D. Wu, F. Pavlovic, B. J. Salama, S. R. Kirkeby, A. Huang, H. Schaefer, N. K. Pollen, A. A. 2024-11-15 doi:10.1101/2024.11.14.623592 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Reduction of DNA Topoisomerase Top2 reprograms the epigenetic landscape and extends health and life span across species ]]> https://biorxiv.org/content/10.1101/2024.11.14.623693v1?rss=1 Zhu, M. Ma, M. Luo, L. Li, F. Zhang, J. Pan, Y. Yang, L. Xiao, Y. Wang, Z. Xian, B. Zheng, Y. Li, H. Yang, J. 2024-11-15 doi:10.1101/2024.11.14.623693 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Inter- and Intrahemispheric Sources of Vestibular Signals to V1 ]]> https://biorxiv.org/content/10.1101/2024.11.18.624137v1?rss=1 Bouvier, G. Sanzeni, A. Hamada, E. Brunel, N. Scanziani, M. 2024-11-19 doi:10.1101/2024.11.18.624137 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ Cellular behavior analysis from live-cell imaging of TCR T cell-cancer cell interactions ]]> https://biorxiv.org/content/10.1101/2024.11.19.624390v1?rss=1 Verma, A. Yu, C. Bachl, S. Lopez, I. Schwartz, M. S. Moen, E. Kale, N. Ching, C. Miller, G. Dougherty, T. Pao, E. Graf, W. Ward, C. Jena, S. G. Marson, A. Carnevale, J. Van Valen, D. A. Engelhardt, B. E. 2024-11-21 doi:10.1101/2024.11.19.624390 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Beta burst characteristics and coupling within the sensorimotor cortical-subthalamic nucleus circuit in Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2024.11.19.624397v1?rss=1 200ms) in both structures displayed temporal overlap (>30%), with an estimated cortico-STN conduction delay of 8ms. Furthermore, approximately 27% of all STN bursts were preceded by a cortical burst. ConclusionCortical beta bursts tend to precede STN beta bursts, with short delays. However, subcortical mechanisms are also likely to contribute to STN burst initiation and propagation. ]]> Yao, P. Abdi-Sargezeh, B. Sharma, A. Liu, T. Tan, H. Hahn, A. Starr, P. Little, S. Oswal, A. 2024-11-21 doi:10.1101/2024.11.19.624397 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Coordinated protein modules define DNA damage responses to carboplatin at single cell resolution in human ovarian carcinoma models ]]> https://biorxiv.org/content/10.1101/2024.11.21.624591v1?rss=1 Bedia, J. S. Huang, Y.-W. Gonzalez, A. D. Gonzalez, V. D. Funingana, I.-G. Rahil, Z. Mike, A. Lowar, A. Vias, M. Ashworth, A. Brenton, J. D. Fantl, W. J. 2024-11-22 doi:10.1101/2024.11.21.624591 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ Dermatopontin-expressing fibroblasts mediate an essential skin macrophage niche ]]> https://biorxiv.org/content/10.1101/2024.11.21.624708v1?rss=1 Vollmers, A. C. Wu, S. Z. Altieri, A. McCartney, E. E. Bender, H. Lee, W. P. Zhang, J. Hu, C. Uttarwar, S. Vander Heiden, J. A. Davidson, C. Chung, Y. Ortiz, W. Long, M. Asuncion, R. Yang, Y. A. Jiang, J. Modrusan, Z. Krishnamurty, A. Fu, W. Müller, S. Buechler, M. B. Turley, S. 2024-11-22 doi:10.1101/2024.11.21.624708 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ Blood draw site and blood matrix influence mineral assessment ]]> https://biorxiv.org/content/10.1101/2024.11.23.625018v1?rss=1 Alejandro, M. G. Schultz, K. Killilea, D. W. 2024-11-24 doi:10.1101/2024.11.23.625018 Cold Spring Harbor Laboratory Press 2024-11-24 <![CDATA[ Replication stress marker phospho-RPA2 predicts response to platinum and PARP inhibitors in homologous recombination-proficient ovarian cancer ]]> https://biorxiv.org/content/10.1101/2024.11.21.624682v1?rss=1 16% of cells had [≥] 2 pRPA2 foci. ResultsIn the discovery cohort, HR-proficient, pRPA2-High tumors demonstrated significantly higher rates of pathologic complete response to platinum chemotherapy than HR-proficient, pRPA2-Low tumors. In the validation cohort, patients with HR-proficient, pRPA2-High tumors had significantly longer survival after platinum treatment than those with HR-proficient, pRPA2-Low tumors. Additionally, the pRPA2 assay effectively predicted survival outcomes in patients treated with PARP inhibitors and in recurrent tumor samples. ConclusionOur study underscores the importance of considering replication stress markers alongside HR status in therapeutic planning. Our work suggest that this assay could be used throughout a patients treatment course to expand the number of patients receiving effective therapy while reducing unnecessary toxicity. ]]> Schab, A. Compadre, A. Drexler, R. Loeb, M. Rodriguez, K. Brill, J. Harrington, S. Sandoval, C. Sanders, B. Kuroki, L. McCourt, C. Hagemann, A. R. Thaker, P. Mutch, D. Powell, M. Serra, V. Hagemann, I. S. Walts, A. E. Karlan, B. Y. Orsulic, S. Fuh, K. Sun, L. Verma, P. Lomonosova, E. Zhao, P. Khabele, D. Mullen, M. M. 2024-11-25 doi:10.1101/2024.11.21.624682 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ 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[ CRISPRa-mediated disentanglement of the Dux-MERVL axis in the 2C-like state, totipotency and cell death ]]> https://biorxiv.org/content/10.1101/2024.11.25.625195v1?rss=1 Chammas, P. Xie, S. Q. Sepulveda-Rincon, L. P. Leeke, B. J. Dore, M. H. Dormann, D. Wagner, R. T. McManus, M. T. Karimi, M. M. Young, G. Percharde, M. 2024-11-25 doi:10.1101/2024.11.25.625195 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ A contextual fear conditioning paradigm in head-fixed mice exploring virtual reality. ]]> https://biorxiv.org/content/10.1101/2024.11.26.625482v1?rss=1 Krishnan, S. Dong, C. Ratigan, H. Morales-Rodriguez, D. Cherian, C. Sheffield, M. 2024-11-27 doi:10.1101/2024.11.26.625482 Cold Spring Harbor Laboratory Press 2024-11-27 <![CDATA[ Programmable epigenome editing by transient delivery of CRISPR epigenome editor ribonucleoproteins ]]> https://biorxiv.org/content/10.1101/2024.11.26.625496v1?rss=1 Nunez, J. K. Xu, D. Besselink, S. Ramadoss, G. N. Dierks, P. H. Lubin, J. P. Pattali, R. K. Brim, J. I. Christenson, A. E. Colias, P. J. Ornelas, I. J. Nguyen, C. D. Chasins, S. E. Conklin, B. R. 2024-11-27 doi:10.1101/2024.11.26.625496 Cold Spring Harbor Laboratory Press 2024-11-27 <![CDATA[ Arterial endothelial deletion of Alk1 causes epistaxis and cerebral microhemorrhage with aberrant arteries and defective smooth muscle coverage. ]]> https://biorxiv.org/content/10.1101/2024.11.25.622742v1?rss=1 Zhang, X. Jacobs, K. A. Raygor, K. P. Li, S. Li, J. Wang, R. A. 2024-11-28 doi:10.1101/2024.11.25.622742 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology ]]> https://biorxiv.org/content/10.1101/2024.11.26.625329v1?rss=1 Sokolowski, D. J. Miclaus, M. Nater, A. Faykoo-Martinez, M. Hoekzema, K. Zuzarte, P. Monis, S. Alvi, S. A. Erdmann, J. Erdmann, A. L. Kumaragurubaran, R. Bayerl, J. Yoo, D. Karimpour, N. Ungerleider, K. Hou, H. Fergal, M. Hourlier, T. Clarke, Z. A. Lischer, H. E. Leordean, D. V. Jiang, Y. Pugh, T. J. Smith, E. S. J. Haggerty, L. Laird, D. J. Lilue, J. Holmes, M. M. Eichler, E. E. Bruggmann, R. Simpson, J. T. Balmus, G. Wilson, M. D. 2024-11-28 doi:10.1101/2024.11.26.625329 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Actin filament assembly driven by distributive polymerases clustered on membrane surfaces ]]> https://biorxiv.org/content/10.1101/2024.11.26.625540v1?rss=1 200 {micro}M). The finite time required for profilin dissociation decreases the advantage conferred by surface-associated polymerases, but only in the absence of force. Load forces enhance the effect of surface polymerases, which can both accelerate elongation and increase the force required to stall filament assembly. ]]> Mullins, D. Skruber, K. 2024-11-28 doi:10.1101/2024.11.26.625540 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Genome Organization with CUT and Tag (GO-CaT) identifies substructure and maturation of lamina-associated domains in neurons of the developing human brain ]]> https://biorxiv.org/content/10.1101/2024.11.27.625786v1?rss=1 Zhang, C. Gil, E. Ahanger, S. H. Li, M. Wang, L. Li, J. Kriegstein, A. Lim, D. 2024-11-28 doi:10.1101/2024.11.27.625786 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Structural and functional insights into activation and regulation of the dynein-dynactin-NuMA complex ]]> https://biorxiv.org/content/10.1101/2024.11.26.625568v1?rss=1 Aslan, M. Cho, N. H. d'Amico, E. A. Taheri, A. Zhao, Y. Zhong, X. Blaauw, M. Carter, A. P. Dumont, S. Yildiz, A. 2024-11-29 doi:10.1101/2024.11.26.625568 Cold Spring Harbor Laboratory Press 2024-11-29 <![CDATA[ NuMA mechanically reinforces the spindle independently of its partner dynein ]]> https://biorxiv.org/content/10.1101/2024.11.29.622360v1?rss=1 Cho, N. H. Aslan, M. Yildiz, A. Dumont, S. 2024-12-01 doi:10.1101/2024.11.29.622360 Cold Spring Harbor Laboratory Press 2024-12-01 <![CDATA[ The GluA1 cytoplasmic tail regulates intracellular AMPA receptor trafficking and synaptic transmission onto dentate gyrus GABAergic interneurons, gating response to novelty ]]> https://biorxiv.org/content/10.1101/2024.12.01.626277v1?rss=1 Leana-Sandoval, G. Kolli, A. V. Chinn, C. A. Madrid, A. Lo, I. Sandoval, M. A. Alizo Vera, V. Simms, J. Wood, M. A. Diaz Alonso, J. 2024-12-02 doi:10.1101/2024.12.01.626277 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ The VGCC auxiliary subunit α2δ1 is an extracellular GluA1 interactor and regulates LTP, spatial memory, and seizure susceptibility ]]> https://biorxiv.org/content/10.1101/2024.12.02.626379v1?rss=1 Leana-Sandoval, G. Kolli, A. V. Sandoval, M. A. Saavedra, E. M. Li, K. H. Chen, L. Y. Burlingame, A. L. Ramirez-Franco, J. J. Diaz-Alonso, J. 2024-12-02 doi:10.1101/2024.12.02.626379 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ Polyfunctional IL-21+ IFNg+ T follicular helper cells contribute to checkpoint inhibitor diabetes mellitus and can be targeted by JAK inhibitor therapy ]]> https://biorxiv.org/content/10.1101/2024.11.27.625710v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@ed4acdorg.highwire.dtl.DTLVardef@c9e062org.highwire.dtl.DTLVardef@1aa81eforg.highwire.dtl.DTLVardef@1388747_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Huang, N. Ortega, J. Kimbrell, K. Lee, J. Scott, L. N. Peluso, E. M. Wang, S. J. Kao, E. Kim, K. Olay, J. Quandt, Z. Angell, T. E. Su, M. A. Lechner, M. G. 2024-12-03 doi:10.1101/2024.11.27.625710 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Coordinated variation in the immune systems and microbiomes of healthy humans is linked to tonic interferon states ]]> https://biorxiv.org/content/10.1101/2024.11.27.625750v1?rss=1 Babdor, J. Patel, R. K. Davidson, B. Noecker, C. Rahim, M. Bisanz, J. E. Tenvooren, I. Marquez, D. Calvo, M. Johri, V. McCarthy, E. Shaheed, A. Ekstrand, C. Weakley, A. M. Yu, F. B. Fiehn, O. Turnbaugh, P. J. Combes, A. J. Fragiadakis, G. K. Spitzer, M. H. 2024-12-03 doi:10.1101/2024.11.27.625750 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Nucleotide GPT: Sequence-Based Deep Learning Prediction of Nuclear Subcompartment-Associated Genome Architecture ]]> https://biorxiv.org/content/10.1101/2024.11.27.625761v1?rss=1 Mclaughlin, S. M. Ahanger, S. H. Lim, D. A. 2024-12-03 doi:10.1101/2024.11.27.625761 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Rebuilding the autoimmune-damaged corneal stroma through topical lubrication ]]> https://biorxiv.org/content/10.1101/2024.11.29.626078v1?rss=1 Efraim, Y. Chen, F. Y. T. Niknezhad, S. V. Pham, D. Cheong, K. N. An, L. Sinada, H. McNamara, N. A. Knox, S. 2024-12-03 doi:10.1101/2024.11.29.626078 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Widespread gene-environment interactions shape the immune response to SARS-CoV-2 infection in hospitalized COVID-19 patients ]]> https://biorxiv.org/content/10.1101/2024.12.03.626676v1?rss=1 Randolph, H. E. Aguirre-Gamboa, R. Brunet-Ratnasingham, E. Nakanishi, T. Locher, V. Ketter, E. Brandolino, C. Larochelle, C. Prat, A. Arbour, N. Dumaine, A. Finzi, A. Durand, M. Richards, J. B. Kaufmann, D. E. Barreiro, L. B. 2024-12-04 doi:10.1101/2024.12.03.626676 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ Epigenetic investigation of multifocal small intestinal neuroendocrine tumours reveals accelerated ageing of tumours and epigenetic alteration of metabolic genes ]]> https://biorxiv.org/content/10.1101/2024.12.02.626017v1?rss=1 Webster, A. P. Makinen, N. Mensah, N. Castignani, C. Larose Cadieux, E. Shivdasani, R. Singh, P. Vaikkinen, H. Dhami, P. Ecker, S. Brown, M. Rimmer, B. Henderson, S. Herrero, J. Suderman, M. Yousefi, P. D. Beck, S. Van Loo, P. Nakakura, E. Thirlwell, C. 2024-12-05 doi:10.1101/2024.12.02.626017 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Prediabetes Phenotype Clusters in the Diabetes Prevention Program Study ]]> https://biorxiv.org/content/10.1101/2024.12.02.626435v1?rss=1 Stroebel, B. M. Gadgil, M. Lewis, K. Longoria, K. Zhang, L. Flowers, E. 2024-12-05 doi:10.1101/2024.12.02.626435 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Target cell tension regulates macrophage trogocytosis ]]> https://biorxiv.org/content/10.1101/2024.12.02.626490v1?rss=1 Cornell, C. E. Chorlay, A. Krishnamurthy, D. Martin, N. R. Baldauf, L. Fletcher, D. A. 2024-12-05 doi:10.1101/2024.12.02.626490 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Convergence of autism proteins at the cilium ]]> https://biorxiv.org/content/10.1101/2024.12.05.626924v1?rss=1 Kostyanovskaya, E. Lasser, M. C. Wang, B. Schmidt, J. Bader, E. Buteo, C. Arbelaez, J. Sindledecker, A. R. McCluskey, K. E. Castillo, O. Wang, S. Dea, J. Helde, K. A. Graglia, J. M. Brimble, E. Kastner, D. B. Ehrlich, A. T. Willsey, A. J. State, M. W. Willsey, H. R. 2024-12-05 doi:10.1101/2024.12.05.626924 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Distinct differentiation trajectories leave lasting impacts on gene regulation and function of V2a interneurons ]]> https://biorxiv.org/content/10.1101/2024.12.03.626573v1?rss=1 Elder, N. H. Majd, A. Bulger, E. A. Samuel, R. M. Zholudeva, L. V. McDevitt, T. C. Fattahi, F. 2024-12-06 doi:10.1101/2024.12.03.626573 Cold Spring Harbor Laboratory Press 2024-12-06 <![CDATA[ In vivo detection of HIV-1 antisense transcripts in untreated and ART-treated individuals ]]> https://biorxiv.org/content/10.1101/2024.12.06.627170v1?rss=1 Capoferri, A. A. Sklutuis, R. Famuyiwa, T. O. Pathak, S. Li, R. Rausch, J. W. Luke, B. T. Hoh, R. Deeks, S. G. Mellors, J. W. Coffin, J. M. Groebner, J. L. Romerio, F. Kearney, M. F. 2024-12-06 doi:10.1101/2024.12.06.627170 Cold Spring Harbor Laboratory Press 2024-12-06 <![CDATA[ High KIR diversity in Uganda and Botswana children living with HIV ]]> https://biorxiv.org/content/10.1101/2024.12.03.626612v1?rss=1 John, M. Kyobe, S. Amujal, M. Katagirya, E. Diphoko, T. Sebetso, G. Mwesigwa, S. Mboowa, G. Retshabile, G. Williams, L. Mogomotsi, M. Mlotshwa, B. Jjingo, D. kateete, D. P. Joloba, M. Mardon, G. Hanchard, N. Hollenbach, J. A. 2024-12-07 doi:10.1101/2024.12.03.626612 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ STING agonists drive recruitment and intrinsic type I interferon responses in monocytic lineage cells for optimal anti-tumor immunity ]]> https://biorxiv.org/content/10.1101/2024.12.08.627385v1?rss=1 Girard, M. Yu, T. Batista, N. V. Yeung, K. K. Lamorte, S. Gao, W. Liu, M. McGaha, T. L. Watts, T. H. 2024-12-11 doi:10.1101/2024.12.08.627385 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Downstream branches of receptor tyrosine kinase signaling act interdependently to shape the face ]]> https://biorxiv.org/content/10.1101/2024.12.10.627829v1?rss=1 Hanne, N. Hu, D. Vidal-Garcia, M. Allen, C. Shakir, M. B. Liu, W. Hallgrimsson, B. Marcucio, R. 2024-12-11 doi:10.1101/2024.12.10.627829 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression between patients ]]> https://biorxiv.org/content/10.1101/2024.12.08.627394v1?rss=1 Smith, A. L. Denny, N. Chahrour, C. Sharp, K. Elliott, N. Harman, J. Jackson, T. Geng, H. Smith, O. Bond, J. Roberts, I. Stam, R. W. Crump, N. T. Davies, J. Roy, A. Milne, T. A. 2024-12-12 doi:10.1101/2024.12.08.627394 Cold Spring Harbor Laboratory Press 2024-12-12 <![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[ spotPCR: A Rapid and Efficient Approach for Indexing Individual Template Molecules using Unique Molecular Identifiers ]]> https://biorxiv.org/content/10.1101/2024.12.11.627791v1?rss=1 Limberis, J. D. Nagel, R. J. Chakravorty, S. Block, D. Dewell, S. Nalyvayko, A. Metcalfe, J. Z. 2024-12-12 doi:10.1101/2024.12.11.627791 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Leucine Aminopeptidase LyLAP enables lysosomal degradation of membrane proteins ]]> https://biorxiv.org/content/10.1101/2024.12.13.628212v1?rss=1 Jain, A. Heremans, I. Rademaker, G. Detomasi, T. Rohweder, P. Anderson, D. Zhang, J. Hernandez, G. Gupta, S. von Linde, T. Lange, M. Spacci, M. Citron, Y. Olzmann, J. Dawson, D. Craik, C. Bommer, G. Perera, R. M. Zoncu, R. 2024-12-14 doi:10.1101/2024.12.13.628212 Cold Spring Harbor Laboratory Press 2024-12-14 <![CDATA[ Multiplexed mosaic tumor models reveal natural phenotypic variations in drug response within and between populations ]]> https://biorxiv.org/content/10.1101/2024.12.13.628239v1?rss=1 Yu, J. X. Suh, J. M. Popova, K. D. Garcia, K. Joshi, T. Culbertson, B. Spinelli, J. B. Subramanyam, V. Lou, K. Shokat, K. M. Weissman, J. Goodarzi, H. 2024-12-16 doi:10.1101/2024.12.13.628239 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Diverse and Location-Specific Roles of PlexinA2, PlexinA4, and NCAM in Developing Hippocampal Mossy Fibers ]]> https://biorxiv.org/content/10.1101/2024.12.15.628586v1?rss=1 Zhao, X.-F. Kohen, R. van Battum, E. Y. Zeng, Y. Zhang, X. Johnson, C. N. Wang, K. Lim, B. C. Oses-Prieto, J. A. Rasband, J. M. Burlingame, A. L. Pasterkamp, R. J. Rasband, M. N. Giger, R. J. 2024-12-16 doi:10.1101/2024.12.15.628586 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Tax1bp1 enhances bacterial virulence and promotes inflammatory responses during Mycobacterium tuberculosis infection of alveolar macrophages ]]> https://biorxiv.org/content/10.1101/2024.12.16.628616v1?rss=1 Chin, J. Abeydeera, N. Repasy, T. Rivera-Lugo, R. Mitchell, G. Nguyen, V. Q. Zheng, W. Richards, A. Swaney, D. L. Krogan, N. J. Ernst, J. D. Cox, J. S. Budzik, J. M. 2024-12-16 doi:10.1101/2024.12.16.628616 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Patient-derived Induced Pluripotent Stem Cells as a Model to Study Frontotemporal Dementia Pathologies ]]> https://biorxiv.org/content/10.1101/2024.12.11.628042v1?rss=1 Barber, D. L. Infante-Tadeo, S. 2024-12-17 doi:10.1101/2024.12.11.628042 Cold Spring Harbor Laboratory Press 2024-12-17 <![CDATA[ Cell cycle-regulated transcriptional pausing of Drosophila replication-dependent histone genes ]]> https://biorxiv.org/content/10.1101/2024.12.16.628706v1?rss=1 Kemp, J. P. Geisler, M. S. Hoover, M. Cho, C.-Y. O'Farrell, P. H. Marzluff, W. F. Duronio, R. J. 2024-12-17 doi:10.1101/2024.12.16.628706 Cold Spring Harbor Laboratory Press 2024-12-17 <![CDATA[ Small molecule activation of the tumor suppressor kinase LKB1 ]]> https://biorxiv.org/content/10.1101/2024.12.17.628051v1?rss=1 Kretschmer, L. S. Mitchell, D. C. Liu, J. Wang, L. Wang, Z. He, C. Ding, L. Adler, M. Turnham, R. E. Kellett, T. Keith, A. Hwang, Y. C. Chan, G. K. L. Li, W. Ramamoorthi, R. Lively, S. Drakas, R. A. Ramani, V. Qing, T. Verba, K. A. Ostrem, J. M. L. Beresis, R. T. Gordan, J. D. 2024-12-20 doi:10.1101/2024.12.17.628051 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ HIV-SEQ REVEALS GLOBAL HOST GENE EXPRESSION DIFFERENCES BETWEEN HIV-TRANSCRIBING CELLS FROM VIREMIC AND SUPPRESSED PEOPLE WITH HIV ]]> https://biorxiv.org/content/10.1101/2024.12.17.629023v1?rss=1 Frouard, J. Telwatte, S. Luo, X. Elphick, N. Thomas, R. Arneson, D. Roychoudhury, P. Butte, A. J. Wong, J. K. Hoh, R. Deeks, S. Lee, S. Roan, N. R. Yukl, S. 2024-12-20 doi:10.1101/2024.12.17.629023 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Differential roles of NaV1.2 and NaV1.6 in neocortical pyramidal cell excitability ]]> https://biorxiv.org/content/10.1101/2024.12.17.629038v1?rss=1 Garcia, J. D. Wang, C. Banks, E. Fenton, T. DeKeyser, J.-M. Abramova, T. V. George, A. L. Ben-Shalom, R. Hackos, D. H. Bender, K. J. 2024-12-20 doi:10.1101/2024.12.17.629038 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ The first comorbidity networks in companion dogs in the Dog Aging Project ]]> https://biorxiv.org/content/10.1101/2024.12.18.629088v1?rss=1 Fang, A. Kumar, L. Creevy, K. E. Promislow, D. E. L. Ma, J. 2024-12-20 doi:10.1101/2024.12.18.629088 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Visualizing Functional Network Connectivity Differences Using an Explainable Machine-learning Method ]]> https://biorxiv.org/content/10.1101/2024.12.18.629283v1?rss=1 Sendi, M. S. E. Itkyal, V. S. Edwards-Swart, S. J. Chun, J. Y. Mathalon, D. H. Ford, J. M. Preda, A. van Erp, T. G. M. Pearlson, G. D. Turner, J. A. Calhoun, V. D. 2024-12-20 doi:10.1101/2024.12.18.629283 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Not all cross-modal responses are explained by face movements ]]> https://biorxiv.org/content/10.1101/2024.12.18.629217v1?rss=1 Olsen, T. R. Hasenstaub, A. R. 2024-12-21 doi:10.1101/2024.12.18.629217 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ The cell biology and genome of Stentor pyriformis, a giant cell that embeds symbiotic algae in a microtubule meshwork ]]> https://biorxiv.org/content/10.1101/2024.12.19.629502v1?rss=1 Boudreau, v. Albright, A. R. Gerbich, T. Fadero, T. Yan, V. Larson, B. Lucas-DeMott, A. Yung, J. Moulin, S. Descovich, C. P. Slabodnick, M. M. Burlacot, A. Wang, J. Niyogi, K. K. Marshall, W. F. 2024-12-21 doi:10.1101/2024.12.19.629502 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ Development and early life stress sensitivity of the rat cortical microstructural similarity network ]]> https://biorxiv.org/content/10.1101/2024.12.20.629759v1?rss=1 Smith, R. L. Sawiak, S. J. Dorfschmidt, L. Dutcher, E. G. Jones, J. A. Hahn, J. D. Sporns, O. Swanson, L. W. Taylor, P. A. Glen, D. R. Dalley, J. W. McMahon, F. J. Raznahan, A. Vertes, P. E. Bullmore, E. T. 2024-12-21 doi:10.1101/2024.12.20.629759 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ Contribution of front-line, standard of care drugs to bactericidal responses, resistance emergence, and cure in murine models of easy- or hard-to-treat tuberculosis disease ]]> https://biorxiv.org/content/10.1101/2024.12.18.629278v1?rss=1 Peroutka-Bigus, N. Brooks, E. J. Ramey, M. E. D'Erasmo, H. Ernest, J. P. Bauman, A. A. Woolhiser, L. K. Savic, R. M. Lenaerts, A. J. Aldridge, B. Sarathy, J. P. Robertson, G. T. 2024-12-22 doi:10.1101/2024.12.18.629278 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ MRS-Sim: Open-Source Framework for Simulating Realistic In Vivo-like MR Spectroscopy Data ]]> https://biorxiv.org/content/10.1101/2024.12.20.629645v1?rss=1 LaMaster, J. T. Oeltzschner, G. Li, Y. 2024-12-22 doi:10.1101/2024.12.20.629645 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Haplotype editing with CRISPR/Cas9 as a therapeutic approach for dominant-negative missense mutations in NEFL ]]> https://biorxiv.org/content/10.1101/2024.12.20.629813v1?rss=1 Dua, P. H. Simon, B. M. Marley, C. B. Feliciano, C. M. Watry, H. L. Steury, D. Abraham, A. Gilbertson, E. N. Ramey, G. D. Capra, J. A. Conklin, B. R. Judge, L. M. 2024-12-22 doi:10.1101/2024.12.20.629813 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Protein CREATE enables closed-loop design of de novo synthetic protein binders ]]> https://biorxiv.org/content/10.1101/2024.12.20.629847v1?rss=1 Lourenco, A. L. Subramanian, A. M. Spencer, R. K. Miao, J. Anaya, M. Fu, W. Chow, E. D. Thomson, M. 2024-12-22 doi:10.1101/2024.12.20.629847 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ The biophysical mechanism of mitochondrial pearling ]]> https://biorxiv.org/content/10.1101/2024.12.21.629509v1?rss=1 Sturm, G. Hake, K. Lefebvre, A. E. Y. T. Rux, C. J. Ivanova, D. Millett-Sikking, A. Tharp, K. M. Rao, B. Closser, M. Waite, A. Precido-Lopez, M. Dumont, S. Lu, W. Manley, S. Landoni, J. C. Marshall, W. F. 2024-12-22 doi:10.1101/2024.12.21.629509 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Collapse of directed functional hierarchy under classical serotonergic psychedelics ]]> https://biorxiv.org/content/10.1101/2024.12.21.629922v1?rss=1 Vohryzek, J. Kringelbach, M. L. Lopez-Sola, E. Garcia Guzman, E. Timmermann, C. Roseman, L. Tagliazucchi, E. Ruffini, G. Carhart-Harris, R. Deco, G. Sanz Perl, Y. 2024-12-22 doi:10.1101/2024.12.21.629922 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Spatiotemporal photocatalytic proximity labeling proteomics reveals ligand-activated extracellular and intracellular EGFR neighborhoods ]]> https://biorxiv.org/content/10.1101/2024.12.21.629933v1?rss=1 Lin, Z. Ngo, W. Chou, Y.-T. Wu, H. Susa, K. J. Jun, Y.-w. Bivona, T. G. Doudna, J. A. Wells, J. A. 2024-12-22 doi:10.1101/2024.12.21.629933 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Gametocyte production and transmission fitness of African and Asian Plasmodium falciparum isolates with differential susceptibility to artemisinins ]]> https://biorxiv.org/content/10.1101/2024.12.23.630038v1?rss=1 Proellochs, N. I. Andolina, C. Ramjith, J. Stoter, R. van Gemert, G.-J. Graumans, W. Campino, S. Vanheer, L. N. Okitwi, M. Tumwebaze, P. K. Conrad, M. D. Clark, T. G. Fidock, D. A. Menard, D. Mok, S. Bousema, T. 2024-12-23 doi:10.1101/2024.12.23.630038 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ Inflammatory Monocytes Increase Prior to Detectable HIV-1 Rebound Viremia ]]> https://biorxiv.org/content/10.1101/2024.12.24.630257v1?rss=1 Farrell-Sherman, A. de la Force, N. Prator, C. Valieris, R. Azam, W. Silva, I. Deeks, S. Thanh, C. Bosch, R. Henrich, T. J. Cohn, L. B. 2024-12-25 doi:10.1101/2024.12.24.630257 Cold Spring Harbor Laboratory Press 2024-12-25 <![CDATA[ Afadin Sorts Different Retinal Neuron Types into Accurate Cellular Layers ]]> https://biorxiv.org/content/10.1101/2024.12.24.630272v1?rss=1 Lum, M. R. Patel, S. Graham, H. K. Zhao, M. Yi, Y. Li, L. Yao, M. La Torre, A. Della Santina, L. Han, Y. Hu, Y. Welsbie, D. S. Duan, X. 2024-12-25 doi:10.1101/2024.12.24.630272 Cold Spring Harbor Laboratory Press 2024-12-25 <![CDATA[ Integration of Transplanted Interneurons Over a New Period of Ocular Dominance Plasticity in Adult Mouse Visual Cortex ]]> https://biorxiv.org/content/10.1101/2024.12.27.630358v1?rss=1 Rakela, B. Sun, J. Marchetta, P. Alvarez-Buylla, A. Hasenstaub, A. R. Stryker, M. P. 2024-12-27 doi:10.1101/2024.12.27.630358 Cold Spring Harbor Laboratory Press 2024-12-27 <![CDATA[ Human precentral gyrus neurons link speech sequences from listening to speaking ]]> https://biorxiv.org/content/10.1101/2024.12.27.630563v1?rss=1 Xu, D. Chung, J. E. Greicius, Q. R. Metzger, S. L. Zhang, Y. Leonard, M. K. Chang, E. F. 2024-12-28 doi:10.1101/2024.12.27.630563 Cold Spring Harbor Laboratory Press 2024-12-28 <![CDATA[ Convergent representations and spatiotemporal dynamics of speech and language in brain and deep neural networks ]]> https://biorxiv.org/content/10.1101/2024.12.28.630582v1?rss=1 Chen, P. Xiang, S. He, L. Chang, E. F. Li, Y. 2024-12-28 doi:10.1101/2024.12.28.630582 Cold Spring Harbor Laboratory Press 2024-12-28 <![CDATA[ Layilin Regulates Treg Motility and Suppressive Capacity in Skin ]]> https://biorxiv.org/content/10.1101/2024.12.30.630730v1?rss=1 Gouirand, V. Clancy, S. Macon, C. Valle, J. Pauli, M. Truong, H.-A. Cohen, J. Kinet, M. Lowe, M. M. Lord, S. J. Skruber, K. Harris, H. Kim, E. Neuhaus, I. Reif, K. Zarrin, A. A. Mullins, R. D. Rosenblum, M. 2024-12-30 doi:10.1101/2024.12.30.630730 Cold Spring Harbor Laboratory Press 2024-12-30 <![CDATA[ A generative framework for enhanced cell-type specificity in rationally designed mRNAs ]]> https://biorxiv.org/content/10.1101/2024.12.31.630783v1?rss=1 Khoroshkin, M. S. Zinkevich, A. Aristova, E. Yousefi, H. Lee, S. B. Mittmann, T. Manegold, K. Penzar, D. Raleigh, D. R. Kulakovskiy, I. V. Goodarzi, H. 2024-12-31 doi:10.1101/2024.12.31.630783 Cold Spring Harbor Laboratory Press 2024-12-31 <![CDATA[ Chronic degenerative failure of salivary glands can be reversed through restoring mitochondrial function ]]> https://biorxiv.org/content/10.1101/2024.12.31.630834v1?rss=1 Li, J. Tan, L. X. Sun, B. Griffin, N. Niknezhad, S. V. Yu, C. Berthoin, L. Cruz Pacheco, N. Mohabbat, S. Sinada, H. Gaylord, E. A. Chen, Y. T. An, L. Efraim, Y. Bahney, C. S. Lombaert, I. M. A. Knox, S. 2025-01-02 doi:10.1101/2024.12.31.630834 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ A20's Linear Ubiquitin Binding Motif Restrains Pathogenic Activation of TH17/22 cells and IL-22 Driven Enteritis ]]> https://biorxiv.org/content/10.1101/2024.12.31.630926v1?rss=1 Bowman, C. J. Stibor, D. Sun, X. Shimizu, H. Yamashita, E. Lenci, N. Advincula, R. Kim, M. C. Turnbaugh, J. A. Sun, Y. Razani, B. Turnbaugh, P. J. Ye, C. J. Malynn, B. A. Ma, A. 2025-01-02 doi:10.1101/2024.12.31.630926 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Aedes aegypti midgut chymotrypsin has no significant role in blood meal protein digestion or fecundity ]]> https://biorxiv.org/content/10.1101/2024.12.31.630969v1?rss=1 Rascon, A. A. Ramirez, A. G. Isoe, J. Serafim, M. S. M. Fong, D. Le, M. A. Nguyen, J. T. Burata, O. E. Lucero, R. M. 2025-01-02 doi:10.1101/2024.12.31.630969 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Perturbing whole-brain models of brain hierarchy: an application for depression following pharmacological treatment ]]> https://biorxiv.org/content/10.1101/2025.01.01.631011v1?rss=1 View larger version (56K): org.highwire.dtl.DTLVardef@7f1b46org.highwire.dtl.DTLVardef@d7a883org.highwire.dtl.DTLVardef@783e39org.highwire.dtl.DTLVardef@3d334d_HPS_FORMAT_FIGEXP M_FIG C_FIG We apply whole-brain models of brain hierarchy based on the Thermodynamics of Mind framework to investigate state transitions in depression. Dynamic sensitivity analysis explores how psilocybin and escitalopram affect susceptibility and drivability to healthier states. Results show that psilocybin increases susceptibility, while escitalopram reduces it, with both enabling optimal transitions. This pipeline demonstrates the promise of in-silico approaches to inform neurostimulation protocols, potentially enhancing or complementing antidepressant therapies. ]]> Socoro Garrigosa, M. Sanz Perl, Y. Kringelbach, M. L. Carhart-Harris, R. Vohryzek, J. Deco, G. 2025-01-02 doi:10.1101/2025.01.01.631011 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ CD38 expression by neonatal human naïve CD4+ T cells shapes their distinct metabolic state and high regulatory T cell potential ]]> https://biorxiv.org/content/10.1101/2025.01.02.631038v1?rss=1 Dwyer, L. R. Clancy, S. Gouirand, V. Chien, C. Rogers, E. E. Oltman, S. P. Jelliffe-Pawlowski, L. L. Lynch, S. V. Wagner, A. Combes, A. J. Scharschmidt, T. C. 2025-01-02 doi:10.1101/2025.01.02.631038 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Identifying a next-generation antimalarial trioxolane in a landscape of artemisinin partial resistance ]]> https://biorxiv.org/content/10.1101/2025.01.02.631109v1?rss=1 Klope, M. T. Talukder, P. Blank, B. R. Chelebieva, S. Chen, J. Fontaine, S. D. Gonciarz, R. L. Jaishankar, P. Lee, G. J. Legac, J. Mathur, V. Narayan, A. Okitwi, M. Orena, S. Settineri, N. S. Tapia, J. Taremwa, Y. Tumwebaze, P. K. Vinod, A. Burrows, J. N. Rosenthal, P. J. Cooper, R. A. Renslo, A. R. 2025-01-03 doi:10.1101/2025.01.02.631109 Cold Spring Harbor Laboratory Press 2025-01-03 <![CDATA[ Targeting Osteosarcoma heterogeneity to improve therapeutic response ]]> https://biorxiv.org/content/10.1101/2025.01.02.631118v1?rss=1 Melano, B. Dinh, T. Zirak, B. Karimzadeh, M. Woo, B. J. Choi, B. Goodarzi, H. Sweet-Cordero, A. 2025-01-03 doi:10.1101/2025.01.02.631118 Cold Spring Harbor Laboratory Press 2025-01-03 <![CDATA[ Lactylation fuels nucleotide biosynthesis and facilitates deuterium metabolic imaging of tumor proliferation in H3K27M-mutant gliomas ]]> https://biorxiv.org/content/10.1101/2025.01.02.631150v1?rss=1 Batsios, G. Taglang, C. udutha, s. Gillespie, A. M. Robinson, S. P. Phoenix, T. Mueller, S. Venneti, S. Koschmann, C. Viswanath, P. 2025-01-03 doi:10.1101/2025.01.02.631150 Cold Spring Harbor Laboratory Press 2025-01-03 <![CDATA[ WormID-Benchmark: Extracting Whole-Brain Neural Dynamics of C. elegans At the Neuron Resolution ]]> https://biorxiv.org/content/10.1101/2025.01.06.631621v1?rss=1 Adhinarta, J. Dong, J. He, T. Sprague, D. Wan, J. Lee, H. J. Yu, Z. Lu, H. Yemini, E. Kato, S. Varol, E. Wei, D. 2025-01-07 doi:10.1101/2025.01.06.631621 Cold Spring Harbor Laboratory Press 2025-01-07 <![CDATA[ MicroRNA signatures of VO2peak in older adult participants of the Study of Muscle, Mobility and Aging ]]> https://biorxiv.org/content/10.1101/2025.01.08.631999v1?rss=1 Karere, G. Hsu, F.-C. Hepple, R. T. Coen, P. M. Cummings, S. Newman, A. Glynn, N. W. Sparks, L. Lane, N. E. Xu, J. Wagner, N. Li, G. Chan, J. Cox, L. A. Kritchevsky, S. 2025-01-09 doi:10.1101/2025.01.08.631999 Cold Spring Harbor Laboratory Press 2025-01-09 <![CDATA[ C12ORF57: a novel principal regulator of synaptic AMPA currents and excitatory neuronal homeostasis ]]> https://biorxiv.org/content/10.1101/2025.01.08.632037v1?rss=1 Jiang, R. Chouchane, M. Moey, C. Bunt, J. Li, J. Allkuraya, F. Alobeid, E. Richards, L. Ullian, E. Sherr, E. 2025-01-10 doi:10.1101/2025.01.08.632037 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ Neural plate pre-patterning enables specification of intermediate neural progenitors in the spinal cord ]]> https://biorxiv.org/content/10.1101/2025.01.09.632276v1?rss=1 Nandagopal, S. Cha, A. Jia, B. Z. Liao, H. Comenho, C. Lahav, G. Wagner, D. E. Tsai, T. Y.-C. Megason, S. G. 2025-01-10 doi:10.1101/2025.01.09.632276 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ Dose-dependent sensitivity of human 3D chromatin to a heart disease-linked transcription factor ]]> https://biorxiv.org/content/10.1101/2025.01.09.632202v1?rss=1 Grant, Z. L. Kuang, S. Zhang, S. Horrillo, A. J. Rao, K. S. Kameswaran, V. Joubran, C. Lau, P. K. Dong, K. Yang, B. Bartosik, W. M. Zemke, N. R. Ren, B. Kathiriya, I. S. Pollard, K. S. Bruneau, B. G. 2025-01-12 doi:10.1101/2025.01.09.632202 Cold Spring Harbor Laboratory Press 2025-01-12 <![CDATA[ Viscoelastic HyA Hydrogel Promotes Recovery of Muscle Quality and Vascularization in a Murine Model of Delayed Rotator Cuff Repair ]]> https://biorxiv.org/content/10.1101/2025.01.08.632047v1?rss=1 Pfaff, M. R. Wague, A. Davies, M. Killaars, A. R. Ning, D. Garcia, S. Nguyen, A. Nuthalapati, P. Liu, M. Liu, X. Feeley, B. T. Healy, K. E. 2025-01-13 doi:10.1101/2025.01.08.632047 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ BDNF in Ventrolateral Orbitofrontal Cortex to Dorsolateral Striatum Circuit Moderates Alcohol Consumption and Gates Alcohol Habit ]]> https://biorxiv.org/content/10.1101/2025.01.09.632255v1?rss=1 Gunasekaran, S. Moffat, J. J. Epstein, J. D. Phamluong, K. Ehinger, Y. Ron, D. 2025-01-13 doi:10.1101/2025.01.09.632255 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Kynurenine Metabolism is Associated with Antidepressant Response to Selective Serotonin Reuptake Inhibitors ]]> https://biorxiv.org/content/10.1101/2025.01.11.632543v1?rss=1 RAMPERSAUD, R. Suneson, K. Wu, G. Lindqvist, D. Ho, T. Myerhoff, D. Reus, V. Irwin, M. Mellon, S. Wolkowitz, O. Brundin, L. 2025-01-13 doi:10.1101/2025.01.11.632543 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Predicting Metabolic Dysfunction Associated Steatotic Liver Disease Risk Using Patient-Derived Induced Pluripotent Stem Cells ]]> https://biorxiv.org/content/10.1101/2025.01.13.632567v1?rss=1 Qin, Y. Chhetri, P. Theusch, E. Lim, G. Teker, S. Kuang, Y.-L. Aziziraftar, S. K. Mehraban, M. H. Munoz-Howell, A. Saxena, V. Le Guillou, D. Mattis, A. N. Maher, J. J. Medina, M. N. 2025-01-15 doi:10.1101/2025.01.13.632567 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Pseudomonas superinfection drives Pf phage transmission within airway infections in patients with cystic fibrosis ]]> https://biorxiv.org/content/10.1101/2025.01.14.632786v1?rss=1 Pourtois, J. D. Haddock, N. L. Gupta, A. Khosravi, A. Martinez, H. Schmidt, A. K. Prakash, P. S. Jain, R. Fleming, P. Chang, T. H. Milla, C. Secor, P. R. De Leo, G. A. Bollyky, P. L. Burgener, E. B. 2025-01-15 doi:10.1101/2025.01.14.632786 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Defining the cell and molecular origins of the primate ovarian reserve ]]> https://biorxiv.org/content/10.1101/2025.01.21.634052v1?rss=1 Wamaitha, S. E. Rojas, E. J. Monticolo, F. Hsu, F.-M. Sosa, E. Mackie, A. M. Oyama, K. Custer, M. Murphy, M. Laird, D. J. Shu, J. Hennebold, J. D. Clark, A. 2025-01-21 doi:10.1101/2025.01.21.634052 Cold Spring Harbor Laboratory Press 2025-01-21 <![CDATA[ Druggable genome CRISPRi screen in 3D hydrogels reveals regulators of cortactin-driven actin remodeling in invading glioblastoma cells ]]> https://biorxiv.org/content/10.1101/2025.01.20.633978v1?rss=1 Hu, M. Weldy, A. Lovalvo, I. Akins, E. Jain, S. Chang, A. Sati, A. Lad, M. Lui, A. Rajidi, A. Kothekar, A. Ding, E. A. Kumar, S. Aghi, M. K. 2025-01-24 doi:10.1101/2025.01.20.633978 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Causal modeling of gene effects from regulators to programs to traits: integration of genetic associations and Perturb-seq ]]> https://biorxiv.org/content/10.1101/2025.01.22.634424v1?rss=1 Ota, M. Spence, J. P. Zeng, T. Dann, E. Marson, A. Pritchard, J. K. 2025-01-24 doi:10.1101/2025.01.22.634424 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Convergent Agonist and Heat Activation of Nociceptor TRPM3 ]]> https://biorxiv.org/content/10.1101/2025.01.23.634542v1?rss=1 Du, J. Lu, W. Kumar, S. Jin, F. Park, S. J. Keuning, S. I. Massimino, R. P. Choi, W. Vu, S. 2025-01-24 doi:10.1101/2025.01.23.634542 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Loss of Fanconi anemia proteins causes a reliance on lysosomal exocytosis ]]> https://biorxiv.org/content/10.1101/2025.01.23.634631v1?rss=1 Fu, B. X. H. X. H. Xu, A. Li, H. Grandis, J. R. Johnson, D. E. Gilbert, L. 2025-01-24 doi:10.1101/2025.01.23.634631 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ URAdime - a tool for analyzing primer sequences in sequencing data to identify dimers and super-amplicons. ]]> https://biorxiv.org/content/10.1101/2025.01.25.634870v1?rss=1 Limberis, J. D. Metcalfe, J. Z. 2025-01-28 doi:10.1101/2025.01.25.634870 Cold Spring Harbor Laboratory Press 2025-01-28 <![CDATA[ Nemo-like kinase disrupts nuclear import and drives TDP43 mislocalization in ALS ]]> https://biorxiv.org/content/10.1101/2025.01.27.635090v1?rss=1 Bekier, M. E. Pinarbasi, E. Mesojedec, J. J. Ghaffari, L. de Majo, M. Ullian, E. Koontz, M. Coleman, S. Li, X. Tank, E. M. Waksmacki, J. Barmada, S. 2025-01-28 doi:10.1101/2025.01.27.635090 Cold Spring Harbor Laboratory Press 2025-01-28 <![CDATA[ Phage defense and genome editing using novel retrons sourced from isolated environmental bacteria ]]> https://biorxiv.org/content/10.1101/2025.01.29.635429v1?rss=1 Nakamura, K. Zhang, K. Mestre, M. R. Rojas-Montero, M. Shipman, S. 2025-01-29 doi:10.1101/2025.01.29.635429 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ Emergence of binding and catalysis from a designed generalist binding protein ]]> https://biorxiv.org/content/10.1101/2025.01.30.635804v1?rss=1 Chen, Y. Bhattacharya, S. Bergmann, L. Correy, G. J. Tan, S. Hou, K. Biel, J. Lu, L. Bakanas, I. Polizzi, N. F. Fraser, J. S. DeGrado, W. F. 2025-01-31 doi:10.1101/2025.01.30.635804 Cold Spring Harbor Laboratory Press 2025-01-31 <![CDATA[ Initial leads to combat streptogramin resistance generated from X-ray fragment screening against VatD ]]> https://biorxiv.org/content/10.1101/2025.01.31.635826v1?rss=1 Asthana, P. - Lee, S. - MacDonald, C. M. Seiple, I. B. Fraser, J. S. 2025-02-02 doi:10.1101/2025.01.31.635826 Cold Spring Harbor Laboratory Press 2025-02-02 <![CDATA[ A scoping study of the whole-cell imaging literature: a foundational corpus, potential for data-mining and research synthesis, and a call for standardization of an emerging field ]]> https://biorxiv.org/content/10.1101/2025.02.03.636363v1?rss=1 Mirvis, M. Weingard, B. Goodman, S. Marshall, W. F. 2025-02-04 doi:10.1101/2025.02.03.636363 Cold Spring Harbor Laboratory Press 2025-02-04 <![CDATA[ Swirling motion of breast cancer cells radially aligns collagen fibers to enable collective invasion ]]> https://biorxiv.org/content/10.1101/2025.01.31.635980v1?rss=1 Saraswathibhatla, A. Rabbi, M. F. Varma, S. Srivastava, V. Ilina, O. Alyafei, N. H. K. Hodgson, L. Gartner, Z. Friedl, P. West, R. Kim, T. B. Chaudhuri, O. 2025-02-06 doi:10.1101/2025.01.31.635980 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ A lateralized pathway for associating nutrients with flavors ]]> https://biorxiv.org/content/10.1101/2025.02.09.637334v1?rss=1 Grove, J. C. R. Li, Q. Backes, H. Kuzmanovic, B. Choi, J. Ubadiah, V. Qiu, L. Zhang, J. Liu, Z. Small, D. M. Tittgemeyer, M. Knight, Z. A. 2025-02-10 doi:10.1101/2025.02.09.637334 Cold Spring Harbor Laboratory Press 2025-02-10 <![CDATA[ Mammalian oocytes receive maternal-effect RNAs from granulosa cells ]]> https://biorxiv.org/content/10.1101/2025.02.10.637575v1?rss=1 1,000 granulosa-transcribed RNAs we identified in the oocyte, those that contribute to proper oocyte maturation and early embryo development were highly enriched. Predicted motifs for two RNA-binding proteins that function in RNA trafficking, FMRP and TDP43, were abundant in the UTRs of the granulosa-derived transcripts. Immunostaining demonstrated that both FMRP and TDP43 co-localize with the actin-rich granulosa cell protrusions that span the zone pellucida and connect to the oocyte, suggesting their role in importing mRNAs. Our results offer the possibility that oocyte failure may not always reflect an intrinsic oocyte deficiency but could arise from insufficient supply of maternal transcripts by granulosa cells during oocyte growth. ]]> Munger, S. C. Tijani, A. Doherty, C. A. Laird, D. J. 2025-02-11 doi:10.1101/2025.02.10.637575 Cold Spring Harbor Laboratory Press 2025-02-11 <![CDATA[ Human Papilloma Virus does not fully inactivate p53 in HNSCC ]]> https://biorxiv.org/content/10.1101/2025.02.11.637252v1?rss=1 Gencel-Augusto, J. Li, H. Woerner, L. C. Borah, A. A. Myers, J. N. Johnson, D. E. Grandis, J. R. 2025-02-14 doi:10.1101/2025.02.11.637252 Cold Spring Harbor Laboratory Press 2025-02-14 <![CDATA[ NF-κB dependent gene expression and plasma IL-1β, TNFα and GCSF drive transcriptomic diversity and CD4:CD8 ratio in people with HIV on ART. ]]> https://biorxiv.org/content/10.1101/2025.02.14.638232v1?rss=1 Wang, Y. Gornalusse, G. Siegel, D. Barbehenn, A. Hoh, R. Martin, J. Hecht, F. Pilcher, C. Semenova, L. Murdoch, D. M. Margolis, D. M. Levy, C. N. Jerome, K. R. Rudin, C. D. Hladik, F. Deeks, S. G. Lee, S. A. Browne, E. P. 2025-02-14 doi:10.1101/2025.02.14.638232 Cold Spring Harbor Laboratory Press 2025-02-14 <![CDATA[ Partial Input Loss Differentially Modifies Neural Pathways ]]> https://biorxiv.org/content/10.1101/2025.02.14.638366v1?rss=1 Lee, J. Y. Kastner, D. B. Harris, S. C. Santina, L. D. John, J. V. Stone, N. S. Dunn, F. A. 2025-02-16 doi:10.1101/2025.02.14.638366 Cold Spring Harbor Laboratory Press 2025-02-16 <![CDATA[ Coordinated macrophage and T cell interactions mediate response to checkpoint blockade in colorectal cancer. ]]> https://biorxiv.org/content/10.1101/2025.02.12.637954v1?rss=1 70% in MMRp CRC. This study identifies key T cell and macrophage subsets mediating the efficacy of immunotherapy in overcoming immune escape in both MMRd and MMRp CRC settings. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/637954v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1778bd6org.highwire.dtl.DTLVardef@17da4e5org.highwire.dtl.DTLVardef@1d4d1d2org.highwire.dtl.DTLVardef@11b58e3_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIAnti-PD-1 therapy leads to the accumulation and colocalization of MHCI/II+ C1Q+ CXCL9+ macrophages and DCs with TCF+ CCL5+ T cells that have high TCR diversity. C_LIO_LIResistance to anti-PD-1 therapy involves multiple T cell checkpoints, TREM2+ macrophages, IL1B+ TREM1+ monocytes and neutrophils, and IFITM+ tumor cells. C_LIO_LISimultaneous blockade of PD-1, LAG3, CTLA-4 and TREM2 dramatically prevents progression of both MMRd and MMRp tumors. C_LIO_LICombination therapy completely eliminates tumors by leveraging MHC+ macrophage, CD4+ and CD8+ T cell interactions, facilitating durable anti-tumor effects. C_LI ]]> Mestrallet, G. Brown, M. Vaninov, N. Cho, N. W. Velazquez, L. Ananthanarayanan, A. Spitzer, M. Vabret, N. Cimen Bozkus, C. Samstein, R. M. Bhardwaj, N. 2025-02-17 doi:10.1101/2025.02.12.637954 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ Near 100% efficient homology-dependent genome engineering in the human fungal pathogen Cryptococcus neoformans ]]> https://biorxiv.org/content/10.1101/2025.02.14.638277v1?rss=1 Nalley, M. Banerjee, S. Huang, M. Y. Madhani, H. D. 2025-02-18 doi:10.1101/2025.02.14.638277 Cold Spring Harbor Laboratory Press 2025-02-18 <![CDATA[ Genome modeling and design across all domains of life with Evo 2 ]]> https://biorxiv.org/content/10.1101/2025.02.18.638918v1?rss=1 Brixi, G. Durrant, M. G. Ku, J. Poli, M. Brockman, G. Chang, D. Gonzalez, G. A. King, S. H. Li, D. B. Merchant, A. T. Naghipourfar, M. Nguyen, E. Ricci-Tam, C. Romero, D. W. Sun, G. Taghibakshi, A. Vorontsov, A. Yang, B. Deng, M. Gorton, L. Nguyen, N. Wang, N. K. Adams, E. Baccus, S. A. Dillmann, S. Ermon, S. Guo, D. Ilango, R. Janik, K. Lu, A. X. Mehta, R. Mofrad, M. R. K. Ng, M. Y. Pannu, J. Re, C. Schmok, J. C. St. John, J. Sullivan, J. Zhu, K. Zynda, G. Balsam, D. Collison, P. Costa, A. B. Hernandez-Boussard, T. Ho, E. Liu, M.-Y. McGrath, T. P 2025-02-21 doi:10.1101/2025.02.18.638918 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ A network of coiled-coil and actin-like proteins controls the cellular organization of magnetosome organelles in deep-branching magnetotactic bacteria ]]> https://biorxiv.org/content/10.1101/2025.02.24.639979v1?rss=1 Russell, V. V. Iavarone, A. T. Ozyamak, E. Grant, C. Komeili, A. 2025-02-24 doi:10.1101/2025.02.24.639979 Cold Spring Harbor Laboratory Press 2025-02-24 <![CDATA[ Natural Killer Cell Receptor Signaling and Activation Depend on Cell Cycle Stages ]]> https://biorxiv.org/content/10.1101/2025.02.24.639882v1?rss=1 Wethington, D. Nayak, I. Jensen, H. Stewart, W. C. Aguilar, O. A. Chen, S.-Y. Nolan, G. P. Behbehani, G. K. Lanier, L. L. Das, J. 2025-02-28 doi:10.1101/2025.02.24.639882 Cold Spring Harbor Laboratory Press 2025-02-28 <![CDATA[ Comparative analysis of human and mouse ovaries across age ]]> https://biorxiv.org/content/10.1101/2025.02.27.640481v1?rss=1 Gaylord, E. A. Foecke, M. F. Samuel, R. M. Soygur, B. Detweiler, A. M. Dorman, L. Borja, M. Laird, A. E. Arjyal, R. Du, J. Gardner, J. M. Neff, N. Fattahi, F. Laird, D. J. 2025-03-03 doi:10.1101/2025.02.27.640481 Cold Spring Harbor Laboratory Press 2025-03-03 <![CDATA[ Single-cell RNA sequencing of peripheral blood defines two immunological subtypes of Sjögren's disease ]]> https://biorxiv.org/content/10.1101/2025.02.27.640483v1?rss=1 Urbanski, G. Taylor, K. E. Flynn, E. Norouzi, A. Chu, C. Davidson, B. Ghosh, A. Nititham, J. Patel, R. K. Poon, A. W. Fragiadakis, G. K. Combes, A. K. Eckalbar, W. L. Criswell, L. A. Ye, C. J. Shiboski, C. H. 2025-03-03 doi:10.1101/2025.02.27.640483 Cold Spring Harbor Laboratory Press 2025-03-03 <![CDATA[ Independent signaling pathways provide a fail-safe mechanism to prevent tumorigenesis ]]> https://biorxiv.org/content/10.1101/2025.02.28.640798v1?rss=1 View larger version (59K): org.highwire.dtl.DTLVardef@762724org.highwire.dtl.DTLVardef@103d1a6org.highwire.dtl.DTLVardef@1b90caforg.highwire.dtl.DTLVardef@1eff5a4_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Rust, K. Schubert, A. Peralta, J. M. Nystul, T. G. 2025-03-06 doi:10.1101/2025.02.28.640798 Cold Spring Harbor Laboratory Press 2025-03-06 <![CDATA[ Searching for influencers among placental immune cells in preeclampsia. ]]> https://biorxiv.org/content/10.1101/2025.03.04.641363v1?rss=1 Paik, H. Ko, T. L. Sirota, M. Park, J.-E. Bunis, D. Lee, S.-K. Heo, H. 2025-03-10 doi:10.1101/2025.03.04.641363 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Assigning Targetable Molecular Pathways to Transdiagnostic Subgroups Across Autism and Related Neurodevelopmental Disorders ]]> https://biorxiv.org/content/10.1101/2025.03.04.641443v1?rss=1 Ellegood, J. Beauchamp, A. Yee, Y. Devenyi, G. Ziolkowski, J. Qiu, L. Askalan, R. Ayub, M. Suetterlin, P. Donovan, A. Basson, M. A. Quesnel, K. M. Berube, N. G. Woo, T. Beversdorf, D. Bjornsson, H. Blakely, R. Crawley, J. Crosbie, J. Orr, B. O. Davis, G. W. Genestine, M. DiCicco-Bloom, E. Egan, S. Fink, K. D. Asbury, S. Lai, J. Rilett, K. Foster, J. A. Vincent, J. B. Frankland, P. Georgiades, S. Penagarikano, O. Geschwind, D. Giger, R. J. Markx, S. Gogos, J. Golzio, C. Pagani, M. Gozzi, A. Pacey, L. K. Hampson, D. Huang, T.-N. Yen, T.-L. Hsueh, Y.-P. 2025-03-10 doi:10.1101/2025.03.04.641443 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ In silico discovery of nanobody binders to a G-protein coupled receptor using AlphaFold-Multimer ]]> https://biorxiv.org/content/10.1101/2025.03.05.640882v1?rss=1 Harvey, E. P. Smith, J. S. Hurley, J. D. Granados, A. Schmid, E. W. Liang-Lin, J. G. Paul, S. Meara, E. M. Ferguson, M. P. Calvillo-Miranda, V. G. Marks, D. S. Walter, J. C. Kruse, A. C. Susa, K. J. 2025-03-10 doi:10.1101/2025.03.05.640882 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Revealing Changes in Linear and Nonlinear Functional Connectivity After Psilocybin and Escitalopram Treatment in Patients with Depression ]]> https://biorxiv.org/content/10.1101/2025.03.05.641592v1?rss=1 Quah, S. K. L. Glick, C. Roseman, L. Pasquini, L. Carhart-Harris, R. L. Saggar, M. 2025-03-10 doi:10.1101/2025.03.05.641592 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Heterocellular and homocellular electrically coupled networks of the thalamus and cortex revealed by focal photomapping ]]> https://biorxiv.org/content/10.1101/2025.03.06.641890v1?rss=1 Vaughn, M. J. Bender, K. Haas, J. 2025-03-10 doi:10.1101/2025.03.06.641890 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Tau-Associated Neuronal Loss in the Intermediate Nucleus of the Human Hypothalamus (VLPO Analog): Unveiling the Basis of NREM Sleep Dysfunction in PSP and Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2025.03.11.642707v1?rss=1 Rastegar-Pouyani, S. Lew, C. Pereira, F. Satpati, A. Paes, V. Leite, R. P. Suemoto, C. Spina, S. Seeley, W. W. Walsh, C. Neylan, T. Grinberg, L. T. 2025-03-13 doi:10.1101/2025.03.11.642707 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ IL-6 underlies microenvironment immunosuppression and resistance to therapy in glioblastoma ]]> https://biorxiv.org/content/10.1101/2025.03.12.642800v1?rss=1 Young, J. Cho, N. W. Lucas, C.-H. G. Najem, H. Mirchia, K. Chen, W. C. Seo, K. Zakimi, N. Daggubati, V. Casey-Clyde, T. Nguyen, M. P. Chen, A. Phillips, J. J. Ozawa, T. Aghi, M. Taylor, J. DeRisi, J. L. Bhaduri, A. Berger, M. S. Heimberger, A. B. Butowski, N. Spitzer, M. H. Raleigh, D. R. 2025-03-14 doi:10.1101/2025.03.12.642800 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Representing Mitochondrial Dynamics with Abstract Algebra ]]> https://biorxiv.org/content/10.1101/2025.03.17.643721v1?rss=1 Mostov, R. Lewis, G. R. Sturm, G. Marshall, W. F. 2025-03-18 doi:10.1101/2025.03.17.643721 Cold Spring Harbor Laboratory Press 2025-03-18 <![CDATA[ Stochastically Emergent Tumors offer in vivo whole genome interrogation of cancer evolution from non-malignant precursors ]]> https://biorxiv.org/content/10.1101/2025.03.17.643814v1?rss=1 Moussavi-Baygi, R. Ryan, M. J. Sim, W. Hoelscher, S. B. Luga, V. Chandrakumar, A. A. Hoes, L. Cha, J. Lee, Y. S. Herm, K. Doron, B. Ding, C. K. C. Stohr, B. A. Jin, P. Nadkarni, T. Fang, X. Haryono, M. Nguyen, A. Karthaus, W. R. Sawyers, C. Feng, F. Y. Goodarzi, H. Bose, R. 2025-03-18 doi:10.1101/2025.03.17.643814 Cold Spring Harbor Laboratory Press 2025-03-18 <![CDATA[ In vivo validation of the palmitoylation cycle as a therapeutic target in NRAS-mutant cancer ]]> https://biorxiv.org/content/10.1101/2025.03.20.644389v1?rss=1 Decker, M. Huang, B. J. Ware, T. Boone, C. Tang, M. Ybarra, J. Ballapuram, A. C. Taran, K. A. Chen, P.-Y. Amendariz, M. Leung, C. J. Harris, M. Tjoa, K. Hongo, H. Abelson, S. Rivera, J. Ngo, N. Herbst, D. M. Suciu, R. M. Guijas, C. Sedighi, K. Andalis, T. Roche, E. Xie, B. Liu, Y. Smith, C. C. Stieglitz, E. Niphakis, M. J. Cravatt, B. Shannon, K. 2025-03-21 doi:10.1101/2025.03.20.644389 Cold Spring Harbor Laboratory Press 2025-03-21 <![CDATA[ LSD reconfigures the frequency-specific network landscape of the human brain ]]> https://biorxiv.org/content/10.1101/2025.03.21.644645v1?rss=1 Shinozuka, K. Rosso, M. Coleman, C. R. Roseman, L. Kaelen, M. Muthukumaraswamy, S. D. Nutt, D. J. Carhart-Harris, R. Vuust, P. Kringelbach, M. L. Bonetti, L. 2025-03-24 doi:10.1101/2025.03.21.644645 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ Membrane-associated polymerases deliver most of the actin subunits to a lamellipodial network ]]> https://biorxiv.org/content/10.1101/2025.03.24.645090v1?rss=1 Skruber, K. Sept, D. Mullins, D. 2025-03-25 doi:10.1101/2025.03.24.645090 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ High-Throughput Screening on Primary Tumor-Associated Microglia and Macrophages Identifies HDAC Inhibitors as Enhancers of Phagocytosis and Potent Partners for Immunotherapy in Glioblastoma ]]> https://biorxiv.org/content/10.1101/2025.03.24.645104v1?rss=1 Khalaj, M. Gutierrez, M. L. Nejad, P. Raveh, T. Fattahi, F. Weissman, I. L. 2025-03-27 doi:10.1101/2025.03.24.645104 Cold Spring Harbor Laboratory Press 2025-03-27 <![CDATA[ A multi-modal cell-free RNA language model for liquid biopsy applications ]]> https://biorxiv.org/content/10.1101/2025.03.26.645557v1?rss=1 Karimzadeh, M. Sababi, A. M. Momen-Roknabadi, A. Chen, N.-C. Cavazos, T. B. Sekhon, S. Wang, J. Hanna, R. Huang, A. Nguyen, D. Chen, S. Lam, T. Hartwig, A. Fish, L. Li, H. Behsaz, B. Hormozdiari, F. Alipanahi, B. Goodarzi, H. 2025-04-01 doi:10.1101/2025.03.26.645557 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Smoothened inhibition of PKA at cilia transduces Hedgehog signals ]]> https://biorxiv.org/content/10.1101/2025.04.01.646243v1?rss=1 Nguyen, T. D. Konjikusic, M. J. Castillo, L. D. Reiter, J. F. 2025-04-01 doi:10.1101/2025.04.01.646243 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Effect of Azithromycin treatment on the microbial composition, functional dynamics and resistomes of endocervical, vaginal and rectal microbiomes of women in Fiji with Chlamydia trachomatis infection ]]> https://biorxiv.org/content/10.1101/2025.04.02.646699v1?rss=1 Bommana, S. Olagoke, S. Hu, Y. Wang, R. Kama, M. Dehdashti, M. Kodimerla, R. Read, T. Dean, D. 2025-04-02 doi:10.1101/2025.04.02.646699 Cold Spring Harbor Laboratory Press 2025-04-02 <![CDATA[ Improving interpretability of transcription factor binding models with DNA shape features ]]> https://biorxiv.org/content/10.1101/2025.04.01.646034v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@b648b6org.highwire.dtl.DTLVardef@15fa931org.highwire.dtl.DTLVardef@15d0d31org.highwire.dtl.DTLVardef@d212e_HPS_FORMAT_FIGEXP M_FIG C_FIG Schematic overview of the DeepShape model. One-hot encoded sequence, and five DNA shape attributes--minor groove width (MGW), helical twist (HelT), propeller twist (ProT), roll, and electrostatic potential (EP)--are input separately to sequence and shape branches of the model, each processed through two convolutional layers and subsequently concatenated for further processing through additional convolutional layers. ]]> Keivanfar, R. L. Yang, F. Pollard, K. S. Ioannidis, N. M. 2025-04-03 doi:10.1101/2025.04.01.646034 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Autism-associated Scn2a haploinsufficiency disrupts in vivo dendritic signaling and impairs flexible decision-making ]]> https://biorxiv.org/content/10.1101/2025.04.08.647866v1?rss=1 Wu, H. Shen, L. Indajang, J. Savalia, N. K. Johnson, T. G. Qu, J. Bender, K. J. Kwan, A. C. 2025-04-09 doi:10.1101/2025.04.08.647866 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ Telomere Orchestrates Encapsulation of Mitotic Chromosomes ]]> https://biorxiv.org/content/10.1101/2025.04.13.648587v1?rss=1 Yang, P. B. Mikawa, T. 2025-04-14 doi:10.1101/2025.04.13.648587 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[ Archaeal SegAB forms a bipolar structure that promotes chromosome segregation in spherical cells ]]> https://biorxiv.org/content/10.1101/2025.04.15.649018v1?rss=1 Charles-Orszag, A. Lord, S. J. Herrera, N. Strauskulage, L. Bhowmick, A. Goddard, T. Wassmer, B. van Wolferen, M. Asper, G. Flis, A. Rodriguez, J. Redding, S. Rosenberg, O. Albers, S.-V. Mullins, D. 2025-04-16 doi:10.1101/2025.04.15.649018 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ Dissociating physiological ripples and epileptiform discharges with vision transformers ]]> https://biorxiv.org/content/10.1101/2025.04.11.648468v1?rss=1 Zhang, D. Kleen, J. 2025-04-18 doi:10.1101/2025.04.11.648468 Cold Spring Harbor Laboratory Press 2025-04-18 <![CDATA[ β-III tubulin identifies anti-fibrotic state of pericytes in pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/2025.04.15.648984v1?rss=1 Sato, R. Imamura, K. Tsukui, T. Yoshida, T. Tomita, Y. Fujino, K. Ikeda, T. Onizawa, K. Sogo, T. Combs, C. A. Murgai, M. Kopp, J. B. Suzuki, M. Sakagami, T. Sheppard, D. Mukouyama, Y.-s. 2025-04-19 doi:10.1101/2025.04.15.648984 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ Survey of hippocampal responses to sound in naive mice reveals widespread activation by broadband noise onsets ]]> https://biorxiv.org/content/10.1101/2025.04.15.649017v1?rss=1 Bigelow, J. Suzuki, T. Wu, Y. Hu, Y. Hasenstaub, A. R. 2025-04-20 doi:10.1101/2025.04.15.649017 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ Improved Injury Detection Through Harmonizing Multi-Site Neuroimaging Data after Experimental TBI: A Translational Outcomes Project in NeuroTrauma (TOP-NT) Consortium Study ]]> https://biorxiv.org/content/10.1101/2025.04.15.649026v1?rss=1 5%) and skewness, which introduced significant variation in non-outlier sites. After removal of one outlier site and harmonization using a global sham population, harmonization displayed an increase in effect size in data that displayed group level effects (p<0.01) in both univariate and voxel-level volumes of pathology. This was characterized by movement toward similar distributions in voxel measurements (Kolmogorov-Smirnov p<<0.001 to >0.01) and statistical power increases within the ipsilateral cortex. Harmonization improved statistical power and frequency of significant differences in areas with existing group differences, thus improving the ability to detect regions affected by injury rather than by other confounds. These findings indicate the utility of NeuroCombat in reproducible data collection, where biological differences can be accurately revealed to allow for greater reliability in multi-site neuroimaging studies. Significance StatementThis project demonstrates the utility of NeuroCombat in reducing site effects in multi-site rodent imaging. We also demonstrate that harmonization improves the ability to distinguish between sham and injured rats at the voxel level and increase statistical power and effect size in areas of injury. Multi-center studies are becoming more common to allow for increased efficiency in data collection, and with conservative approaches and analysis into the datasets, NeuroCombat can be utilized to improve study reliability and reproducibility. ]]> Kislik, G. Fox, R. Korotcov, A. V. Zhou, J. Febo, M. Moghadas, B. Bibic, A. Zou, Y. Wan, J. Koehler, R. C. Adebayo, T. Burns, M. P. McCabe, J. T. Wang, K. K. Huie, J. R. Ferguson, A. R. Harris, N. G. The TOP-NT Investigators, 2025-04-20 doi:10.1101/2025.04.15.649026 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ D3 dopamine receptors implicate a subtype of medium spiny neuron in the aversive effects of antipsychotic medications ]]> https://biorxiv.org/content/10.1101/2025.04.15.649037v1?rss=1 Lewis, E. Muir, J. Li, L. C. Glienke, J. Gooding, S. W. Bender, K. Kim, C. Whistler, J. 2025-04-20 doi:10.1101/2025.04.15.649037 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ Essential Role of Protein Kinase R in the Pathogenesis of Pulmonary Veno-occlusive Disease ]]> https://biorxiv.org/content/10.1101/2025.04.18.649514v1?rss=1 Prabhakar, A. Kumar, R. Wadhwa, M. Barpanda, A. Lyons, J. Gowda, A. Gupta, S. Arvind, A. Ghatpande, P. Wiita, A. Graham, B. B. Lagna, G. Hata, A. 2025-04-23 doi:10.1101/2025.04.18.649514 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Plasma lipidome dysregulation in frontotemporal dementia reveals shared, genotype-specific, and severity-linked alterations ]]> https://biorxiv.org/content/10.1101/2025.04.20.649464v1?rss=1 Ambaw, Y. A. Ljubenkov, P. A. Singh, S. Hamed, A. Boland, S. Boxer, A. L. Walther, T. C. Farese, R. 2025-04-24 doi:10.1101/2025.04.20.649464 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Spatiotemporal Analysis of Remyelination Reveals a Concerted Interferon-Responsive Glial State That Coordinates Immune Infiltration ]]> https://biorxiv.org/content/10.1101/2025.04.22.649486v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@2c7e07org.highwire.dtl.DTLVardef@1063719org.highwire.dtl.DTLVardef@10b8862org.highwire.dtl.DTLVardef@26dd8b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Dolan, M.-J. Rakosi-Schmidt, R. Garcia, E. Lin, Y. Nadaf, N. M. Dixon, J. Guo, S. Morshed, N. Depp, C. Doman, J. Xia, J. Jäntti, H. Stevens, B. Macosko, E. Z. 2025-04-29 doi:10.1101/2025.04.22.649486 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Towards individualized deep brain stimulation: A stereoencephalography-based workflow for unbiased neurostimulation target identification ]]> https://biorxiv.org/content/10.1101/2025.04.22.649607v1?rss=1 Saal, J. Kadlec, K. Allawala, A. B. Johnston, L. Leriche, R. Vatsyayan, R. Han, Y. Kist, A. Di Ianni, T. Dawes, H. E. Chang, E. F. Lee, A. M. Krystal, A. D. Moussawi, K. Shirvalkar, P. Sellers, K. K. 2025-04-29 doi:10.1101/2025.04.22.649607 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Interrupting Elmsan1 repression of nuclear Acetyl-CoA production therapeutically reprograms cancer cells ]]> https://biorxiv.org/content/10.1101/2025.04.25.650293v1?rss=1 Zhao, T. He, L. Wong, L. P. Mei, S. Xia, J. Xu, Y. Van Vranken, J. Mazzola, M. Chen, L. Rhee, C. Fang, T. Fukushima, T. Sayles, L. Diaz, M. Gibbons, J. A. B. Mostoslavsky, R. Gygi, S. P. Dou, Z. Sykes, D. B. Sadreyev, R. Sweet-Cordero, A. Scadden, D. T. 2025-04-29 doi:10.1101/2025.04.25.650293 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Discovery of a tRNA-regulatory transcription factor that suppresses breast cancer metastasis ]]> https://biorxiv.org/content/10.1101/2025.04.26.650725v1?rss=1 Chen, S. Markett, D. Karimzadeh, M. Luo, Y. Khoroshkin, M. S. Boyraz, B. Lee, S. Carpenter, C. Nguyen, P. Garcia, K. Joshi, T. Martin, C. Hanisch, B. Molina, H. Tavazoie, S. Ramani, V. Navickas, A. Goodarzi, H. 2025-04-29 doi:10.1101/2025.04.26.650725 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ ARAP2 regulates responses to interferon-gamma by restricting SOCS1 ]]> https://biorxiv.org/content/10.1101/2025.04.28.650977v1?rss=1 Keating, N. Doggett, K. Bidgood, G. Guzman, L. G. M. Dagley, L. Li, K. Gabrielyan, A. Alvarado, C. Williams, B. Broomfield, B. Duckworth, B. Hockings, C. Youssef, J. Leong, E. Morris, R. Kueh, A. Garnham, A. Casanova, J.-L. Boisson-Dupuis, S. Babon, J. Linossi, E. Tate, M. D. Groom, J. R. Nicholson, S. 2025-04-29 doi:10.1101/2025.04.28.650977 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Transcriptomic analysis reveals immune signatures associated with specific cutaneous manifestations of lupus in systemic lupus erythematosus ]]> https://biorxiv.org/content/10.1101/2025.04.27.649460v1?rss=1 Lee, E. Y. Patterson, S. Cutts, Z. Lanata, C. M. Dall'Era, M. Yazdany, J. Criswell, L. A. Haemel, A. Katz, P. Ye, C. J. Langelier, C. Sirota, M. 2025-04-30 doi:10.1101/2025.04.27.649460 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Regulatory logic of human cortex evolution by combinatorial perturbations ]]> https://biorxiv.org/content/10.1101/2025.04.28.651083v1?rss=1 Skaros, A. Vitriolo, A. Leonardi, O. Finazzi, V. Pereira, M. F. Prazzoli, F. Trattaro, S. Moriano, J. Capocefalo, D. Villa, C. E. Boettcher, M. Boeckx, C. Testa, G. 2025-05-01 doi:10.1101/2025.04.28.651083 Cold Spring Harbor Laboratory Press 2025-05-01 <![CDATA[ Evolutionary Sequence and Structural Basis for the Epistatic Origins of Drug Resistance in HIV ]]> https://biorxiv.org/content/10.1101/2025.04.30.651576v1?rss=1 Biswas, A. Choudhuri, I. Huang, K. Sun, Q. Sali, A. Echeverria, I. Haldane, A. Levy, R. Lyumkis, D. 2025-05-02 doi:10.1101/2025.04.30.651576 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ An intrinsically disordered region of histone demethylase KDM5A activates catalysis through interactions with the nucleosomal acidic patch and DNA ]]> https://biorxiv.org/content/10.1101/2025.05.01.651538v1?rss=1 Palla, A. M. Lin, C.-C. Trnka, M. J. Leao, E. M. Petronikolou, N. Burlingame, A. L. McGinty, R. K. Fujimori, D. G. 2025-05-02 doi:10.1101/2025.05.01.651538 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ Harmonized Protocol for Subfield Segmentation in the Hippocampal Body on High-Resolution in vivo MRI from the Hippocampal Subfields Group (HSG) ]]> https://biorxiv.org/content/10.1101/2025.04.29.651039v1?rss=1 Daugherty, A. M. Carr, V. Canada, K. Radman, G. Brown, T. Augustinack, J. Amunts, K. Bakker, A. Berron, D. Burggren, A. Chetelat, G. de Flores, R. Ding, S.-L. Huang, Y. Insausti, R. Johnson, E. Kanel, P. Keresztes, A. Kedo, O. Kennedy, K. M. Lee, J. Malykhin, N. Martinez, A. Mueller, S. Mulligan, E. Ofen, N. Palombo, D. Pasquini, L. Pluta, J. Raz, N. Riggins, T. Rodrigue, K. M. Saifullah, S. Schlichting, M. L. Stark, C. Wang, L. Yushkevich, P. La Joie, R. Wisse, L. Olsen, R. the Alzheimers Disease Neuroimaging Initiative, the Hippocampal Subfields Gro 2025-05-04 doi:10.1101/2025.04.29.651039 Cold Spring Harbor Laboratory Press 2025-05-04 <![CDATA[ Antibody response to Aedes aegypti D7L1+2 salivary proteins as marker of aggregate vector exposure and correlate of dengue virus susceptibility ]]> https://biorxiv.org/content/10.1101/2025.05.01.651659v1?rss=1 Bahr, L. Hamins-Puertolas, M. Buddhari, D. Petzlova, I. Oliveira, F. Thomas, S. J. Thangamani, S. Waickman, A. Anderson, K. 2025-05-06 doi:10.1101/2025.05.01.651659 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ A Cluster of Acidic Residues in the Cytoplasmic Domain of SARS-CoV-2 Spike is Required for Virion-Incorporation and Infectivity ]]> https://biorxiv.org/content/10.1101/2025.05.04.652125v1?rss=1 Stoneham, C. A. Singh, R. De Leon, A. Tafelmeyer, P. Acosta, F. Fuori, A. Anderson, M. Ramirez, P. W. Schwartzer-Sperber, H. S. Pillai, S. K. Lewinski, M. K. Guatelli, J. 2025-05-06 doi:10.1101/2025.05.04.652125 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ Investigating Local Negative Feedback of Rac Activity by Mathematical Models and Cell Motility Simulations ]]> https://biorxiv.org/content/10.1101/2025.05.05.651928v1?rss=1 Algorta, J. Town, J. P. Weiner, O. Edelstein-Keshet, L. 2025-05-06 doi:10.1101/2025.05.05.651928 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ Identification of a RIPK2-Regulated Gene Signature as a Candidate Biomarker for RIPK2 Activity and Prognosis in Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2025.04.30.651490v1?rss=1 Elgehama, A. M. Yang, Q. He, Z. Ruegg, L. E. You, S. Yang, W. 2025-05-07 doi:10.1101/2025.04.30.651490 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Detecting neuroplastic effects induced by ketamine in healthy human subjects: a multimodal approach ]]> https://biorxiv.org/content/10.1101/2025.05.01.651686v1?rss=1 Agnorelli, C. Peill, J. Sawicka, G. Kurtin, D. L. Shatalina, E. Ahmad, K. Wall, M. B. Rua, C. Godfrey, K. Ertl, N. Searle, G. Zhou, K. Weiss, B. Fagiolini, A. Carhart-Harris, R. Matthews, P. M. Rabiner, E. Nutt, D. Erritzoe, D. 2025-05-07 doi:10.1101/2025.05.01.651686 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Synaptic vesicles that store monoamines and glutamate differ in protein composition. ]]> https://biorxiv.org/content/10.1101/2025.05.06.651945v1?rss=1 Asmerian, H. Diaz, A. J. Xu, H. Oses-Prieto, J. A. Alberts, J. Sanetra, A. M. Gnanabharathi, B. Carr, N. Burlingame, A. L. Edwards, R. H. Silm, K. 2025-05-07 doi:10.1101/2025.05.06.651945 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Associations between floor material and E. coli contamination in rural Bangladeshi households ]]> https://biorxiv.org/content/10.1101/2025.05.07.652756v1?rss=1 Tazin, S. Islam, M. Pickering, A. J. Kwong, L. H. Mertens, A. Niven, C. Arnold, B. F. Hubbard, A. E. Alam, M. Sen, D. Islam, S. Rahman, M. Unicomb, L. Luby, S. P. Benjamin-Chung, J. Ercumen, A. 2025-05-08 doi:10.1101/2025.05.07.652756 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ BRAFV600E-Driven Lung Tumorigenesis Requires Ligand-Mediated Activation of ERBB Receptor Signaling ]]> https://biorxiv.org/content/10.1101/2025.05.04.652129v1?rss=1 Dacheux, M. Wu, M.-J. Scherzer, M. T. Nillson, M. Murphy, B. Schuman, S. Ju, Z. Bivona, T. Lito, P. Gumbleton, M. Puri, S. Akerley, W. Wang, J. Wang, K. Heymach, J. V. Kinsey, C. G. Negrao, M. V. McMahon, M. Vaishnavi, A. 2025-05-09 doi:10.1101/2025.05.04.652129 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Genome Dynamics and Chromosome Structural Variations in Histoplasma ohiense, a fungal pathogen of humans ]]> https://biorxiv.org/content/10.1101/2025.05.05.652209v1?rss=1 Heater, S. Voorhies, M. Sil, A. 2025-05-09 doi:10.1101/2025.05.05.652209 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ The phosphatases TCPTP, PTPN22, and SHP1 play unique roles in T cell phosphotyrosine maintenance and feedback regulation of the TCR ]]> https://biorxiv.org/content/10.1101/2025.05.05.652301v1?rss=1 Callahan, A. Mojumdar, A. Hu, M. Wang, A. Griffith, A. Huang, N. Chua, X. Y. Mroz, N. M. Puterbaugh, R. Z. Reilly, S. P. Salomon, A. R. 2025-05-09 doi:10.1101/2025.05.05.652301 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Separable global and local beta burst dynamics in motor cortex of primates ]]> https://biorxiv.org/content/10.1101/2025.05.05.652217v1?rss=1 Khanna, P. farrokhi, b. Choi, H. Griffin, S. Heimbuch, I. Novik, L. Thiesen, K. Morrison, J. H. Morecraft, R. Ganguly, K. 2025-05-10 doi:10.1101/2025.05.05.652217 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ Transcription Factor (TF) validation using Dam-IT simultaneously captures genome-wide TF-DNA binding, direct gene regulation, and chromatin accessibility in plant cells ]]> https://biorxiv.org/content/10.1101/2025.05.06.652526v1?rss=1 Hinckley, W. E. Jack, A. Li, A. Frangos, S. Pasquino, A. Huang, S.-s. C. Coruzzi, G. M. 2025-05-11 doi:10.1101/2025.05.06.652526 Cold Spring Harbor Laboratory Press 2025-05-11 <![CDATA[ UNCOVERseq Enables Sensitive and Controlled Gene Editing Off-Target Nomination Across CRISPR-Cas Modalities and Systems ]]> https://biorxiv.org/content/10.1101/2025.05.09.653165v1?rss=1 Kinney, K. J. Jia, K. Zhang, H. Schmaljohn, E. Osborne, T. Thommandru, B. Murugan, K. Sanchez-Pena, A. West, S. Chen, S. Codipilly, R. Sturgeon, M. Turk, R. McNeill, M. Behlke, M. Jacobi, A. M. Cromer, K. Kurgan, G. 2025-05-11 doi:10.1101/2025.05.09.653165 Cold Spring Harbor Laboratory Press 2025-05-11 <![CDATA[ In utero lipid nanoparticle delivery achieves robust editing in hematopoietic stem cells. ]]> https://biorxiv.org/content/10.1101/2025.05.12.652147v1?rss=1 Worthington, A. K. Borges, B. Lum, T. Echeverri, E. S. Zada, F. M. Cordero, M. Kim, H. Zenhausern, R. Celik, O. Shaw, C. Gutierrez-Martinez, P. Omarova, M. Blanchard, C. Burns, S. Cromer, K. Dahlman, J. MacKenzie, T. 2025-05-12 doi:10.1101/2025.05.12.652147 Cold Spring Harbor Laboratory Press 2025-05-12 <![CDATA[ A protective role of REM sleep in the pathological basal ganglia-cortical circuit of Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2025.05.07.652676v1?rss=1 Zhang, J.-X. Smyth, C. Anjum, M. F. Leng, Y. Krystal, A. D. Starr, P. A. Little, S. 2025-05-13 doi:10.1101/2025.05.07.652676 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Conformational biosensors delineate endosomal G protein regulation by GPCRs ]]> https://biorxiv.org/content/10.1101/2025.05.12.653522v1?rss=1 Wysolmerski, B. Blythe, E. E. von Zastrow, M. 2025-05-13 doi:10.1101/2025.05.12.653522 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Transcriptomic comparison of early onset preeclampsia and placenta accreta identifies inverse trophoblast and decidua functions at the maternal-fetal interface ]]> https://biorxiv.org/content/10.1101/2025.05.09.653201v1?rss=1 Yin, O. Almonte-Loya, A. Appierdo, R. Yang, M. Yilmaz, B. D. Oskotsky, T. T. Gonzalez, J. M. Giudice, L. C. Afshar, Y. Sirota, M. 2025-05-14 doi:10.1101/2025.05.09.653201 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ First Generation Tools for the Modeling of Capicua (CIC) - Family Fusion Oncoprotein-Driven Cancers ]]> https://biorxiv.org/content/10.1101/2025.05.13.653825v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@1c1cf27org.highwire.dtl.DTLVardef@1073faforg.highwire.dtl.DTLVardef@e61455org.highwire.dtl.DTLVardef@140e952_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Luck, C. Jacobs, K. A. Riad, J. Macaraig, C. D. Ponce, R. K. M. Okimoto, R. A. 2025-05-14 doi:10.1101/2025.05.13.653825 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Affinity-matured CD72-targeting Nanobody CAR T-cells Enhance Elimination of Antigen-Low B-cell Malignancies ]]> https://biorxiv.org/content/10.1101/2025.05.09.653155v1?rss=1 Izgutdina, A. Rashid, T. Temple, W. C. Patino-Escobar, B. Walunj, S. Geng, H. Takamatsu, H. Gil-Alos, D. Kang, A. S. Ramos, E. Chen, S.-Y. Johnson, H. Nix, M. A. Naik, A. Yuan, C. M. Wang, H.-W. Aminov, S. Sahu, S. Larson, R. C. Carpenter, C. Salangsang, F. Phojanakong, P. Camara Serrano, J. A. Tariq, I. Zakraoui, O. Steri, V. Valeri, A. Martinez-Lopez, J. Maus, M. V. Parekh, S. Verma, A. Shah, N. N. Wiita, A. 2025-05-15 doi:10.1101/2025.05.09.653155 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ GFP-Free Live-Neuron Quantitative Imaging Reveals Compartmentalization and Growth Dynamics of PolyQ Aggregates ]]> https://biorxiv.org/content/10.1101/2025.05.12.653542v1?rss=1 Bi, X. Lin, L.-E. Miao, K. Wei, L. 2025-05-15 doi:10.1101/2025.05.12.653542 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Genetic Surveillance Reveals Differential Evolutionary Dynamic of Anopheles gambiae Under Contrasting Insecticidal Tools used in Malaria control ]]> https://biorxiv.org/content/10.1101/2025.05.12.653619v1?rss=1 Njoroge, H. Namuli, L. Nagi, S. C. Hernandez-Koutoucheva, A. McDermott, D. P. Knight, E. Gonahasa, S. Lynd, A. R. Oruni, A. Maiteki-Sebuguzi, C. Opigo, J. Yeka, A. Katureebe, A. Kyohere, M. Kamya, M. Dorsey, G. hemingway, J. Staedke, S. Clarkson, C. S. Miles, A. Lucas, E. R. Donnelly, M. J. 2025-05-15 doi:10.1101/2025.05.12.653619 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Select azo compounds post-translationally modulate HTRA1 abundance and activity potentially through interactions at the trimer interface ]]> https://biorxiv.org/content/10.1101/2025.05.13.651909v1?rss=1 Hulleman, J. Jeon, S. Bali, S. DiCesare, S. Abbas, A. Daniel, S. Ortega, A. Collier, G. Yang, J. Bhattacharyaa, A. McCoy, M. Joachimiak, L. A. Posner, B. 2025-05-16 doi:10.1101/2025.05.13.651909 Cold Spring Harbor Laboratory Press 2025-05-16 <![CDATA[ Monte Carlo track-structure simulation of the impact of Ultra-Hight Dose Rate and oxygen concentration on the Fenton reaction. ]]> https://biorxiv.org/content/10.1101/2025.05.13.652705v1?rss=1 Chaoui, M. Tayalati, Y. Bouhali, O. ramos mendez, j. 2025-05-16 doi:10.1101/2025.05.13.652705 Cold Spring Harbor Laboratory Press 2025-05-16 <![CDATA[ Benchmarking cerebellar organoids to model autism spectrum disorder and human brain evolution ]]> https://biorxiv.org/content/10.1101/2025.05.14.653684v1?rss=1 Aprile, D. Leonardi, O. Petrella, A. Castaldi, D. Culotta, L. Cheroni, C. Valente, A. Bonfanti, M. Vitriolo, A. Moriano, J. Mirabella, F. Tintori, A. Boeckx, C. Testa, G. 2025-05-16 doi:10.1101/2025.05.14.653684 Cold Spring Harbor Laboratory Press 2025-05-16 <![CDATA[ Oxytocin receptor absence reduces selectivity in peer relationships and alters neurochemical release dynamics in prairie voles ]]> https://biorxiv.org/content/10.1101/2025.05.15.654128v1?rss=1 Black, A. M. Komatsu, N. Zhao, J. Taskey, S. R. Serrano, N. S. Sharma, R. Manoli, D. S. Landry, M. P. Beery, A. 2025-05-16 doi:10.1101/2025.05.15.654128 Cold Spring Harbor Laboratory Press 2025-05-16 <![CDATA[ Single Cell RNA Sequencing Reveals Gene Expression Continuums Along the Spatial Hierarchy of the Pulmonary Circulation ]]> https://biorxiv.org/content/10.1101/2025.05.17.654540v1?rss=1 Sveiven, S. Knutsen, C. Zanini, F. Cornfield, D. Alvira, C. 2025-05-19 doi:10.1101/2025.05.17.654540 Cold Spring Harbor Laboratory Press 2025-05-19 <![CDATA[ Structural basis for Porcupine inhibition ]]> https://biorxiv.org/content/10.1101/2025.05.19.654776v1?rss=1 Black, K. A. Mobbs, J. I. Venugopal, H. Dite, T. A. Leis, A. Wong, L. L. Dagley, L. Thal, D. M. Glukhova, A. 2025-05-19 doi:10.1101/2025.05.19.654776 Cold Spring Harbor Laboratory Press 2025-05-19 <![CDATA[ eIF4G2-Mediated Translation Initiation of Histone Modifiers Is Essential for Intestinal Stem Cell Maintenance and Differentiation ]]> https://biorxiv.org/content/10.1101/2025.05.19.652834v1?rss=1 Kunitomi, H. Khaine, A. M. Jamee, R. Lancero, M. Raychaudhuri, A. Perli, S. D. Sato, Y. Iwasaki, M. Ruivo, P. R. Tomoda, K. Mito, M. Shichino, Y. Iwasaki, S. Yamanaka, S. 2025-05-20 doi:10.1101/2025.05.19.652834 Cold Spring Harbor Laboratory Press 2025-05-20 <![CDATA[ Repetitive Levodopa Treatment Drives Cell Type-Specific Striatal Adaptations Associated With Progressive Dyskinesia in Parkinsonian Mice ]]> https://biorxiv.org/content/10.1101/2025.05.16.654598v1?rss=1 Paz, R. M. Ryan, M. B. Marcott, P. F. Girasole, A. E. Faryean, J. Duong, V. Sridhar, S. Nelson, A. B. 2025-05-21 doi:10.1101/2025.05.16.654598 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Synaptic proteins that aggregate and degrade slower with aging accumulate in microglia ]]> https://biorxiv.org/content/10.1101/2025.05.20.654652v1?rss=1 Guldner, I. H. Wagner, V. P. Moran Losada, P. Shi, S. M. Chen, K. Meese, B. T. Oh, H. Le Guen, Y. Lu, N. Wong, P. S. To, N.-S. Garceau, D. Guo, Z. Luo, J. Sasner, M. Keller, A. Yang, A. C. Cheung, T. Wyss-Coray, T. 2025-05-21 doi:10.1101/2025.05.20.654652 Cold Spring Harbor Laboratory Press 2025-05-21 <![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[ Actionable biological programs to enhance EGFR-targeted therapy response unveiled by single-cell lineage tracing in clinically relevant lung cancer models ]]> https://biorxiv.org/content/10.1101/2025.05.19.654081v1?rss=1 Gini, B. Tamaki, W. Yu, J. X. Barbosa, D. Wu, W. Pourmoghadam, Y. Allegakoen, P. Kim, D. Miglani, S. Elmes, S. Olivas, V. Goodarzi, H. Bivona, T. G. 2025-05-23 doi:10.1101/2025.05.19.654081 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ A catalog of ancient proxies for modern genetic variants ]]> https://biorxiv.org/content/10.1101/2025.05.19.654975v1?rss=1 90% of genotypes were correctly predicted, even in a 45,000 year old individual. We also find that AGVs are significantly older than expected and that many likely are evolving neutrally. We integrate these results in a database that researchers can easily query to identify ancient proxy variants if their variant of interest is not directly genotyped in ancient humans. ]]> Brand, C. M. Capra, J. A. 2025-05-23 doi:10.1101/2025.05.19.654975 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ GABAergic signaling by VIP interneurons gates running-dependent visual recovery in the adult brain ]]> https://biorxiv.org/content/10.1101/2025.05.21.655402v1?rss=1 Lebedeva, A. Kling, F. Rakela, B. Stryker, M. P. Sun, Y. J. 2025-05-23 doi:10.1101/2025.05.21.655402 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ The 1p/19q co-deletion induces targetable and imageable vulnerabilities in glucose metabolism in oligodendrogliomas ]]> https://biorxiv.org/content/10.1101/2025.05.20.655097v1?rss=1 Udutha, S. Batsios, G. Taglang, C. Gillespie, A. M. Viswanath, P. 2025-05-24 doi:10.1101/2025.05.20.655097 Cold Spring Harbor Laboratory Press 2025-05-24 <![CDATA[ Identification and Characterization of PLUTO-201, a Novel Long Non-Coding RNA Associated with Poor Outcomes in Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2025.05.21.655369v1?rss=1 Li, H. Younger, N. S. Malik, B. Shin, H. J. Zhang, C. Niknafs, Y. Zhao, S. Wilder-Romans, K. Pitchiaya, S. Han, S. Barnard, T. J. Lloyd, P. Zhang, M. Chesner, L. N. Calvert, M. Egusa, E. A. Zhu, J. Chou, J. Das, R. Kothari, V. Shenoy, T. Diolaiti, M. E. Malik, R. Prensner, J. R. Burlingame, A. L. Ashworth, A. Chinnaiyan, A. M. Feng, F. Li, H. 2025-05-24 doi:10.1101/2025.05.21.655369 Cold Spring Harbor Laboratory Press 2025-05-24 <![CDATA[ Aperiodic neural dynamics define a novel signature of glioma-induced excitation-inhibition dysregulation ]]> https://biorxiv.org/content/10.1101/2025.05.23.655626v1?rss=1 Sibih, Y. E. Dada, A. O. Cunningham, E. E. Olshausen, N. Kaur, J. Jayabal, V. Oten, S. Herr, S. Gonzales, C. N. Daniel, A. Krishna, S. Ambati, V. S. Aabedi, A. A. Umbach, G. Mirchia, K. Lalwani, P. Chang, E. F. Raleigh, D. R. Nagarajan, S. Brang, D. Hervey-Jumper, S. L. 2025-05-24 doi:10.1101/2025.05.23.655626 Cold Spring Harbor Laboratory Press 2025-05-24 <![CDATA[ Perivascular matrix densification dysregulates angiogenesis and activates pro-inflammatory endothelial cells ]]> https://biorxiv.org/content/10.1101/2025.05.20.655215v1?rss=1 Xia, J. Wang, W. Jacobs, K. Lin, D. Jarman, E. Matera, D. Loesel, K. Davison, C. Hiraki, H. Tan, X. Shikanov, E. Kent, R. Parent, C. Fan, X. Shikanov, A. Kutys, M. L. Baker, B. 2025-05-25 doi:10.1101/2025.05.20.655215 Cold Spring Harbor Laboratory Press 2025-05-25 <![CDATA[ Mapping early patterning events in human neural development usingan in-vitro microfluidic stem cell model ]]> https://biorxiv.org/content/10.1101/2025.05.23.655442v1?rss=1 Rathore, G. S. Ankjaer, M. Rifes, P. Hanninen, E. Calleja, F. S. Rusimbi, C. Kajtez, J. Nygaard, A. H. Piilgaard, L. S. Dubonyte, U. Norgaard, Z. A. Christensen, J. B. Egerod, K. L. Camp, J. G. Pers, T. Treutlein, B. Kirkeby, A. 2025-05-26 doi:10.1101/2025.05.23.655442 Cold Spring Harbor Laboratory Press 2025-05-26 <![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[ An information theory framework for capturing multi-connectivity via spatial network encoding reveals reduced population count (Hamming weight) localized to auditory, visual, and motor networks ]]> https://biorxiv.org/content/10.1101/2025.05.22.655511v1?rss=1 Bostami, B. Lewis, N. Agcaoglu, O. Silva, R. F. Turner, J. A. van Erp, T. Ford, J. Calhoun, V. 2025-05-27 doi:10.1101/2025.05.22.655511 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Chondrocyte-Specific Knockout of Piezo1 and Piezo2 Protects Against Post-Traumatic Osteoarthritis Structural Damage and Pain in Mice ]]> https://biorxiv.org/content/10.1101/2025.05.22.655585v1?rss=1 Ely, E. Lenz, K. Paradi, S. Ack, S. Behrmann, A. Dunivan, S. Braxton, L. Liedtke, W. Chen, Y. Collins, K. H. Guilak, F. 2025-05-27 doi:10.1101/2025.05.22.655585 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Extracellular Ca2+-Sensing Receptor (CaSR) Regulates Hypothalamic Function to Control Energy and Skeletal Metabolism in Mice ]]> https://biorxiv.org/content/10.1101/2025.05.22.655605v1?rss=1 Park-sigal, J. J. Norton, M. Tu, C.-L. Cheng, Z. Fadahunsi, N. Lee, H. Kim, S. Li, A. Grinberg, L. T. Bewick, G. A. Murphy, K. G. Chang, W. A. 2025-05-27 doi:10.1101/2025.05.22.655605 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ A Cellular Basis for Heightened Gut Sensitivity in Females ]]> https://biorxiv.org/content/10.1101/2025.05.23.654927v1?rss=1 Venkataraman, A. Figueroa, E. E. Castro, J. Navarro, F. M. C. Soota, D. Brierley, S. M. Julius, D. Ingraham, H. A. 2025-05-28 doi:10.1101/2025.05.23.654927 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Multivalent Lipid MVL5 Micellar Nanoparticles Exhibit Dramatically Increased Loading of Paclitaxel with PEGylation Enhancing Human Cancer Cell Penetration Depth and Cytotoxicity ]]> https://biorxiv.org/content/10.1101/2025.05.24.655953v1?rss=1 Fisher, W. S. Ghasemizadeh, A. Roshan, S. Goldstein, A. Douglas, J. Perez, R. Li, Y. Ewert, K. K. Safinya, C. R. 2025-05-29 doi:10.1101/2025.05.24.655953 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ Caffeine Impairs Red Blood Cell Storage Quality by Dual Inhibition of ADORA2b Signaling and G6PD Activity ]]> https://biorxiv.org/content/10.1101/2025.05.27.656446v1?rss=1 Dzieciatkowska, M. Hay, A. Issaian, A. Keele, G. R. Bevers, S. Nemkov, T. Reisz, J. A. Maslanka, M. Stephenson, D. Moore, A. Deng, X. Stone, M. Hansen, K. Kleinman, S. Norris, P. J. Busch, M. P. Page, G. P. Roubinian, N. H. Xia, Y. Zimring, J. C. D'Alessandro, A. 2025-05-30 doi:10.1101/2025.05.27.656446 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ A non-spike nucleocapsid R204P mutation in SARS-CoV-2 Omicron XEC enhances inflammation and pathogenicity ]]> https://biorxiv.org/content/10.1101/2025.05.28.656516v1?rss=1 Tsujino, S. Tsuda, M. Ito, J. Deguchi, S. Taha, T. Y. Nasser, H. Wang, L. Rosecrans, J. Suzuki, R. Suzuki, S. Yoshimatsu, K. Ott, M. The Genotype to Phenotype Japan (G2P-Japan) Consortium, Ikeda, T. Takayama, K. Sato, K. Tanaka, S. Tamura, T. Fukuhara, T. 2025-05-30 doi:10.1101/2025.05.28.656516 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ A Transcriptomics-Based Computational Drug Repositioning Pipeline Identifies Simvastatin And Primaquine As Novel Therapeutics For Endometriosis Pain ]]> https://biorxiv.org/content/10.1101/2025.05.28.656743v1?rss=1 Oskotsky, T. T. Tang, X. Arthurs, E. Govil, A. Abbasi, F. Bhoja, A. Bunis, D. J. Lau, A. Einhaus, J. Diop, M. Irwin, J. C. Gaudilliere, B. Stevenson, D. K. Giudice, L. C. McAllister, S. L. Sirota, M. 2025-05-30 doi:10.1101/2025.05.28.656743 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Genome-wide CRISPR screens identify PTGES3 as a novel AR modulator ]]> https://biorxiv.org/content/10.1101/2025.05.29.656244v1?rss=1 Li, H. Melnyk, J. E. Fu, B. X. H. Shrestha, R. Zhang, M. Sjostrom, M. Feng, S. Anderson, J. Han, W. Chesner, L. N. Shin, H. J. Farsh, T. Suarez, H. J. Nath, S. Chou, J. Das, R. Egusa, E. A. Calvert, M. Kishishita, A. Barpanda, A. Zhu, J. Maheshwari, A. Chen, W. S. Alshalalfa, M. Winters, A. Hua, J. T. Liu, T. Davicioni, E. Wiita, A. P. Stohr, B. A. Siddiqui, J. Huang, B. Small, E. J. Shokat, K. M. Nelson, P. Quigley, D. A. Wasmuth, E. V. Gilbert, L. A. Feng, F. Y. 2025-05-30 doi:10.1101/2025.05.29.656244 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Complex I Drives Glutamine-Dependent TCA Cycle to Support Viability of MYChigh Breast Cancer Cells ]]> https://biorxiv.org/content/10.1101/2025.05.27.656356v1?rss=1 Anttila, J. M. Savelius, M. Somani, J. Nicorici, D. Munne, P. M. Id, L. Peura, A. Hiltunen, A. O. Aung, J. Awadhpersad, R. Prajapati, B. Peltonen, M. Ala-Hongisto, H. Gautam, P. Valimaki, M. J. Tervonen, T. A. Sapovalovaite, K. Devarajan, R. Perez, M. V. R. Mutka, M. Kovanen, P. Niinikoski, L. Meretoja, T. Mattson, J. Heikkila, P. Wennerberg, K. Arsenian-Henriksson, M. Westermarck, J. Aittokallio, T. Goga, A. Jackson, C. B. Nieminen, A. I. Klefstrom, J. 2025-05-31 doi:10.1101/2025.05.27.656356 Cold Spring Harbor Laboratory Press 2025-05-31 <![CDATA[ An atlas of TF driven gene programs across human cells ]]> https://biorxiv.org/content/10.1101/2025.05.30.657075v1?rss=1 Pett, J. P. Prete, M. Pham, D. England, N. Yuan, H. Prigmore, E. Tuck, L. Oszlanczi, A. To, K. Xu, C. Suo, C. Dann, E. He, P. Kedlian, V. R. Kanemaru, K. Cranley, J. Yang, L. Elmentaite, R. Oliver, A. J. Cujba, A.-M. Cakir, B. Murray, S. Mahbubani, K. T. Saeb-Parsy, K. Gambardella, L. Kasper, M. Haniffa, M. A. Nawijn, M. C. Teichmann, S. A. Meyer, K. B. 2025-06-01 doi:10.1101/2025.05.30.657075 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Active learnings impact on student course performance in STEM varies by type and intensity ]]> https://biorxiv.org/content/10.1101/2025.06.01.657285v1?rss=1 Xu, S. Velasco, V. Hill, M. J. Tran, E. Agrawal, S. Arroyo, E. N. Behling, S. Chambwe, N. Cintron, D. L. Cooper, J. D. Dunster, G. Grummer, J. A. Hennessey, K. Hsiao, J. Iranon, N. Jones, L. Jordt, H. Keller, M. Lacey, M. E. Littlefield, C. E. Lowe, A. Newman, S. Okolo, V. Olroyd, S. Peecook, B. R. Pickett, S. B. Slager, D. L. Caviedes-Solis, I. W. Stanchak, K. E. Sundaravaradan, V. Valdebenito, C. Williams, C. R. Zinsli, K. A. Freeman, S. Theobald, E. J. 2025-06-02 doi:10.1101/2025.06.01.657285 Cold Spring Harbor Laboratory Press 2025-06-02 <![CDATA[ Clonal Expansion of Alveolar Fibroblast Progeny Drives Pulmonary Fibrosis ]]> https://biorxiv.org/content/10.1101/2025.05.31.657194v1?rss=1 Molina, C. Tsukui, T. Khan, I. Ren, X. Qiu, W. Matthay, M. Wolters, P. Sheppard, D. 2025-06-03 doi:10.1101/2025.05.31.657194 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Clinical Trypanosoma cruzi isolates share a common antigen repertoire that is absent from culture adapted strains ]]> https://biorxiv.org/content/10.1101/2025.06.04.657671v1?rss=1 Hakim, J. M. C. Gutierrez Guarnizo, S. A. Duran, A. Malaga-Machacha, E. Duque, C. Singer, L. Colanzi, R. Sherbuk, J. E. Gilman, R. Bern, C. Messenger, L. A. Mugnier, M. R. Working Group on Chagas Disease in Bolivia and Peru, 2025-06-04 doi:10.1101/2025.06.04.657671 Cold Spring Harbor Laboratory Press 2025-06-04 <![CDATA[ An improved model for prediction of de novo designed proteins with diverse geometries ]]> https://biorxiv.org/content/10.1101/2025.06.02.657515v1?rss=1 Orr, B. Crilly, S. E. Akpinaroglu, D. Zhu, E. Keiser, M. J. Kortemme, T. 2025-06-06 doi:10.1101/2025.06.02.657515 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ IL-18 inhibition enlarges lesions, necrotic cores and thickens fibrous caps in Jak2V617F clonal hematopoiesis-driven atherosclerosis. ]]> https://biorxiv.org/content/10.1101/2025.06.03.657754v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@a93b2forg.highwire.dtl.DTLVardef@6cc057org.highwire.dtl.DTLVardef@1c7afc5org.highwire.dtl.DTLVardef@e4da82_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIInflammasome activation produces active IL-1 and IL-18 and worsens atherosclerosis in clonal hematopoiesis (CH) however the contribution of IL-18 is unknown. C_LIO_LIAntibody inhibition of IL-18 increased plaque collagen but also increased early lesion area and late lesions with large necrotic cores in Jak2VF CH mice. C_LIO_LIThere was a reversal of AIM2 inflammasome activation but a switch to apoptosis which along with reduced efferocytosis increased necrosis C_LIO_LIThese events appeared to be coordinated by reduced IFN-{gamma} which increased collagen but also decreased expression of efferocytotic genes. Our studies call into question whether inhibition of IL-18 would stabilize plaques in CH. C_LI ]]> Tavallaie, M. Hsu, C.-C. Hardaway, B. Dou, H. Fidler, T. Kim, E. Wang, N. Westerterp, M. Tall, A. R. 2025-06-06 doi:10.1101/2025.06.03.657754 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ AlphaFold models of host-pathogen interactions elucidate the prevalence and structural modes of molecular mimicry ]]> https://biorxiv.org/content/10.1101/2025.06.04.657796v1?rss=1 Baptista, D. Gomez-Lucas, L. Jänes, J. Krogan, N. J. Joao Amorim, M. Ivarsson, Y. Beltrao, P. 2025-06-06 doi:10.1101/2025.06.04.657796 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Mechanical force locally damages, remodels and stabilizes the lattice of spindle microtubules ]]> https://biorxiv.org/content/10.1101/2025.06.05.657915v1?rss=1 Rux, C. J. Chong, M. K. Myers, S. Cho, N. H. Dumont, S. 2025-06-06 doi:10.1101/2025.06.05.657915 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Regulators of Interferon-Responsive Microglia Uncovered by Genome-wide CRISPRi Screening ]]> https://biorxiv.org/content/10.1101/2025.06.05.658176v1?rss=1 McQuade, A. Castillo, V. C. Hagan, V. Liang, W. Ta, T. Mishra, R. Teter, O. Teyssier, N. Leng, K. Kampmann, M. 2025-06-06 doi:10.1101/2025.06.05.658176 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Live-cell analyses with unsegmented images to study cancer cell response to modified T cell therapy ]]> https://biorxiv.org/content/10.1101/2025.06.04.657687v1?rss=1 Epstein, L. Weiner, A. C. Verma, A. Saedi, M. Carnevale, J. Marson, A. Engelhardt, B. E. 2025-06-07 doi:10.1101/2025.06.04.657687 Cold Spring Harbor Laboratory Press 2025-06-07 <![CDATA[ Paracrine Signals from HIV-1 Infected Immune Cells Reprogram Cervical Cancer Pathways ]]> https://biorxiv.org/content/10.1101/2025.06.06.658239v1?rss=1 Olwal, C. O. Rathore, U. Makanani, S. Kaushal, P. Ashley, I. A. Ummadi, M. R. Appiah, V. Djomkam Zune, A. L. Blanc, S. Winters, D. Delgado, Y. Muthoka, K. Fabius, J. M. Eckhardt, M. Kaake, R. M. Su, M. Fregoso, O. I. Hultquist, J. F. Orango, E. O. Swaney, D. L. Kyei, G. B. Krogan, N. J. Quashie, P. K. Bediako, Y. Bouhaddou, M. 2025-06-07 doi:10.1101/2025.06.06.658239 Cold Spring Harbor Laboratory Press 2025-06-07 <![CDATA[ Effects of diffusion MRI spatial resolution on human brain short-range association fiber reconstruction and structural connectivity estimation ]]> https://biorxiv.org/content/10.1101/2025.06.04.657810v1?rss=1 Zheng, J. Li, Z. Zhong, W. Wang, Z. Li, Z. Yang, H. Liu, M. Cao, X. Liao, C. David, S. H. Huang, S. Y. Tian, Q. 2025-06-09 doi:10.1101/2025.06.04.657810 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Low-density lipoprotein receptor-targeting chimeras for membrane protein degradation and enhanced drug delivery ]]> https://biorxiv.org/content/10.1101/2025.06.06.658366v1?rss=1 Zhao, F. Wu, Y. Schaefer, K. Zhang, Y. Miao, K. Yao, Z. Ganjave, S. D. Kumru, K. Peters-Clarke, T. M. Inague, A. Olzmann, J. A. Leung, K. K. Wells, J. A. 2025-06-09 doi:10.1101/2025.06.06.658366 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Alterations of the composition and spatial organization of the microenvironment following non-dysplastic Barrett's esophagus through progression to cancer ]]> https://biorxiv.org/content/10.1101/2025.06.09.657642v1?rss=1 Lin, M.-L. Hickey, J. W. Passman, A. Carlotti, E. Devkumar, S. Derwa, Y. H. ChinAleong, J. Hackett, R. J. Evans, J. A. Sangwan, V. Novelli, M. R. Rodriguez-Justo, M. Wright, N. A. Jansen, M. Underwood, T. J. Huang, S. Gascard, P. McLean, M. H. Schurch, C. M. Tlsty, T. M. Ferri, L. Nolan, G. P. McDonald, S. A. 2025-06-12 doi:10.1101/2025.06.09.657642 Cold Spring Harbor Laboratory Press 2025-06-12 <![CDATA[ Multi-selective RAS(ON) Inhibition Targets Oncogenic RAS Mutations and Overcomes RAS/MAPK-Mediated Resistance to FLT3 and BCL2 Inhibitors in Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/2025.06.10.658786v1?rss=1 Popescu, B. Jones, M. F. Piao, M. Tran, E. Koh, A. Lomeli, I. Peretz, C. A. C. Murad, N. Abelson, S. Morales, C. Rivera, J. M. Pikman, Y. Cheng, M. L. Logan, A. C. Stieglitz, E. Smith, C. C. 2025-06-14 doi:10.1101/2025.06.10.658786 Cold Spring Harbor Laboratory Press 2025-06-14 <![CDATA[ A connectomic resource for neural cataloguing and circuit dissection of the larval zebrafish brain ]]> https://biorxiv.org/content/10.1101/2025.06.10.658982v1?rss=1 180,000 segmented soma, >40,000 molecularly annotated neurons, and 30 million synapses, most of which were classified as excitatory, inhibitory, or modulatory. To characterize the directional flow of activity across the brain, we leverage the synaptic and cell body annotations to compute region-wise input and output drive indices at single cell resolution. We illustrate the datasets utility by dissecting and validating circuits in three distinct systems: water flow direction encoding in the lateral line, recurrent excitation and contralateral inhibition in a hindbrain motion integrator, and functionally relevant targeted long-range projections from a tegmental excitatory nucleus, demonstrating that this resource enables rigorous hypothesis testing as well as exploratory-driven circuit analysis. The dataset is integrated into an open-access platform optimized to facilitate community reconstruction and discovery efforts throughout the larval zebrafish brain. ]]> Petkova, M. D. Januszewski, M. Blakely, T. Herrera, K. J. Schuhknecht, G. F. P. Tiller, R. Choi, J. Schalek, R. L. Boulanger-Weil, J. Peleg, A. Wu, Y. Wang, S. Troidl, J. Kumar Vohra, S. Wei, D. Lin, Z. Bahl, A. Tapia, J. C. Iyer, N. Miller, Z. T. Hebert, K. B. Pavarino, E. C. Taylor, M. Deng, Z. Stingl, M. Hockling, D. Hebling, A. Wang, R. C. Zhang, L. L. Dvorak, S. Faik, Z. King, K. I. Goel, P. Wagner-Carena, J. Aley, D. Chalyshkan, S. Contreas, D. Li, X. Muthukumar, A. V. Vernaglia, M. S. Tapia Carrasco, T. Melnychuck, S. Yan, T. Dalal, A. DiMarti 2025-06-15 doi:10.1101/2025.06.10.658982 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ A lipid plug affects K2P6.1(TWIK-2) function ]]> https://biorxiv.org/content/10.1101/2025.06.11.659167v1?rss=1 Mondal, A. Niranjan, S. Minor, D. L. 2025-06-15 doi:10.1101/2025.06.11.659167 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Increased Synapse Elimination by Inflammatory Cells Contributes to Long-lasting Post-Stroke Memory Dysfunction in Old Mice ]]> https://biorxiv.org/content/10.1101/2025.06.13.659591v1?rss=1 Shabani, Z. Pan, P. Li, Q. Wang, Z. Leng, K. Sangras, S. Huo, K. Yadav, A. Wang, C. Shi, J. Chinn, G. Kyritsis, N. Ferguson, A. R. Hellman, J. Su, H. 2025-06-15 doi:10.1101/2025.06.13.659591 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Rapid acquisition of HIV-1 neutralization breadth in a rhesus V2 apex germline antibody mouse model after a single bolus immunization ]]> https://biorxiv.org/content/10.1101/2025.06.12.659380v1?rss=1 Ghosh, A. R. Habib, R. Mishra, N. Roark, R. S. Akauliya, M. Albowaidey, A. A. Allen, J. D. Amereh, K. Avillion, G. Bottermann, M. Liang, B. Chaudhary, N. Callaghan, S. Dye, J. Li, X. Ellis-Pugh, J. R. Chowdhury, R. R. James, N. E. Liu, X. Maiorino, L. Villavicencio, P. M. Nedellec, R. Oberoi, P. Sowers, K. J. Park, Y. Prum, T. Rodriguez, L. Ssozi, M. Torres, J. Walsh, A. A. Warner, J. E. Weldon, S. R. Xu, L. Wiehe, K. Crispin, M. Ward, A. B. Nair, U. Hahn, B. H. Burton, D. R. Shapiro, L. Kwong, P. D. Irvine, D. J. Andrabi, R. Shaw, G. M. Batista, F. 2025-06-17 doi:10.1101/2025.06.12.659380 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Genome editing of phylogenetically distinct bacteria using portable retron-mediated recombineering ]]> https://biorxiv.org/content/10.1101/2025.06.16.660010v1?rss=1 Gonzalez-Delgado, A. Bonillo-Lopez, L. Johnson, M. S. Knoedlseder, N. Ko, C.-C. Lekbach, Y. Oh, J.-H. Selvakumar, H. Wold, M. C. Yu, Z. Aragon, V. Gralnick, J. A. Guell, M. Hatfull, G. Keitz, B. K. Koskella, B. Mutalik, V. K. van Pijkeren, J. P. Shipman, S. 2025-06-17 doi:10.1101/2025.06.16.660010 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ FOXM1 Inhibition Promotes Polyploidization and Metabolic Maturation in Human iPSC-Derived Hepatocytes by Modulating the Wnt/β-Catenin Pathway ]]> https://biorxiv.org/content/10.1101/2025.06.17.660221v1?rss=1 Telles-Silva, K. A. Pacheco, L. Komatsu, S. Chianca, F. Chagas, G. Martins, G. C. Gridina, M. Panchenko, D. Carvalho, V. M. Caldini, E. G. Fishman, V. S. Arkin, M. Goulart, E. Zatz, M. 2025-06-18 doi:10.1101/2025.06.17.660221 Cold Spring Harbor Laboratory Press 2025-06-18 <![CDATA[ Comprehensive Cross-Domain Taxonomic Classification of Microbiotas using Partitioned Amplification Multiplexed Amplicon Sequencing (PAMA-seq) ]]> https://biorxiv.org/content/10.1101/2025.06.18.660470v1?rss=1 Li, X. Trepka, K. R. Song, F. Kyaw, T. S. Turnbaugh, P. J. Abate, A. J. 2025-06-19 doi:10.1101/2025.06.18.660470 Cold Spring Harbor Laboratory Press 2025-06-19 <![CDATA[ Induction of meningioma stem signature via hydrogel reprogramming and application of meningioma stem cell marker CXCR4 to pathological diagnosis and treatment. ]]> https://biorxiv.org/content/10.1101/2025.06.14.659672v1?rss=1 Oda, Y. Tsuda, M. Wang, L. Suzuka, J. Yuzawa, S. Ise, K. Habiba, U. He, J. Tanikawa, S. Sugino, H. Tanei, Z.-i. Mawrin, C. Gong, J. P. Tanaka, S. 2025-06-20 doi:10.1101/2025.06.14.659672 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Transient Dietary Changes Modulate Inflammatory Disease Trajectory in the Lean State ]]> https://biorxiv.org/content/10.1101/2025.06.15.659784v1?rss=1 Jiang, Z. Tayeri, J. M. Tabuchi, C. Gayer, S. G. Yoo, A. Sun, I.-H. Wang, J. Yin, H. Chuah, S. S. Deshpande, P. Johri, V. Davidson, B. Tsui, J. Kuhn, N. F. Courau, T. Combes, A. J. Gardner, J. M. Bapat, S. P. 2025-06-20 doi:10.1101/2025.06.15.659784 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Satb1 integrates cohesin mediated genome organization and transcriptional regulation during T cell development ]]> https://biorxiv.org/content/10.1101/2025.06.19.657327v1?rss=1 Madhok, A. Patta, I. Desai, I. Tayyab, M. Choudhary, V. Vishwakarma, S. Saha, S. Lahesmaa, R. Narlikar, G. Galande, S. 2025-06-20 doi:10.1101/2025.06.19.657327 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ ADAR1 Restricts Poliovirus Infection through dual disruption of translation initiation and protein coding ]]> https://biorxiv.org/content/10.1101/2025.06.19.660622v1?rss=1 Kim, D. McCarthy, F. Li, K. Chalkley, R. J. Pak, J. Elias, J. E. Aviner, R. 2025-06-23 doi:10.1101/2025.06.19.660622 Cold Spring Harbor Laboratory Press 2025-06-23 <![CDATA[ Control of Quiescence and Activation of Human Muscle Stem Cells by Cytokines ]]> https://biorxiv.org/content/10.1101/2025.06.21.660874v1?rss=1 Striedinger, K. Barruet, E. Atamaniauc, E. Linquist, K. Knott, C. Brack, A. Pomerantz, J. H. 2025-06-23 doi:10.1101/2025.06.21.660874 Cold Spring Harbor Laboratory Press 2025-06-23 <![CDATA[ Developmental Plasticity and Stromal Co-option Shape a Pituitary Neuroendocrine Tumor Transcriptional Continuum ]]> https://biorxiv.org/content/10.1101/2025.06.18.659743v1?rss=1 Osorio, R. C. Oh, J. Y. Jung, J. Ehrenberg, A. J. Saha, A. Lad, M. Khela, H. Brennick, N. Giannikopoulos, P. Seeley, W. W. Grinberg, L. T. Diaz, A. Aghi, M. K. 2025-06-24 doi:10.1101/2025.06.18.659743 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ Improving the Scalability of Bayesian Phylodynamic Inference through Efficient MCMC Proposals ]]> https://biorxiv.org/content/10.1101/2025.06.18.660471v1?rss=1 Bouckaert, R. Weidemüller, P. Esquivel Gomez, L. Müller, N. F. 2025-06-24 doi:10.1101/2025.06.18.660471 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ Peroxisomal import is circadian in glia and regulates sleep and lipid metabolism ]]> https://biorxiv.org/content/10.1101/2025.06.23.661129v1?rss=1 Das, A. Serna, I. M. R. Kumar, A. Kalita, H. Sherpa, L. Vaughen, J. P. Bai, H. 2025-06-25 doi:10.1101/2025.06.23.661129 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Plasma Proteomic Profiling Reveals Distinct Signatures of Chest CT Phenotypes in Sarcoidosis ]]> https://biorxiv.org/content/10.1101/2025.06.24.661339v1?rss=1 Shastry, V. Leach, S. M. Elicker, B. M. Koth, L. L. 2025-06-25 doi:10.1101/2025.06.24.661339 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ De novo designed bright, hyperstable rhodamine binders for fluorescence microscopy ]]> https://biorxiv.org/content/10.1101/2025.06.24.661379v1?rss=1 Chen, Y. Yserentant, K. Hong, K. Kuang, Y. Bhowmick, A. Charles-Orszag, A. Lord, S. J. Lu, L. Hou, K. Mann, S. I. Grimm, J. B. Lavis, L. D. Mullins, R. D. DeGrado, W. F. Huang, B. 2025-06-25 doi:10.1101/2025.06.24.661379 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Early transcriptional signatures of MeCP2 positive and negative cells in Rett syndrome ]]> https://biorxiv.org/content/10.1101/2025.06.26.661761v1?rss=1 Li, Y. Anderson, A. G. Qi, G. Wu, S.-R. Revelli, J.-P. Liu, Z. Zoghbi, H. Y. 2025-06-26 doi:10.1101/2025.06.26.661761 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[ Functionalizing hydrogel nanovials with vesicles mimicking antigen-presenting vesicles and cancer exosomes improves T cell capture and activation ]]> https://biorxiv.org/content/10.1101/2025.06.24.661128v1?rss=1 Olson, B. A. Mellody, M. P. Soemardy, C. Mao, Z. Mei, A. Lippert, K. Hoffmann, M. A. G. Di Carlo, D. Mayo, S. L. 2025-06-27 doi:10.1101/2025.06.24.661128 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Accurate variant effect estimation in FACS-based deep mutational scanning data with Lilace ]]> https://biorxiv.org/content/10.1101/2025.06.24.661380v1?rss=1 Freudenberg, J. Rao, J. Howard, M. K. Macdonald, C. Greenwald, N. F. Coyote-Maestas, W. Pimentel, H. 2025-06-27 doi:10.1101/2025.06.24.661380 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ A cell-based scrambling assay reveals phospholipid headgroup preference of TMEM16F on the plasma membrane ]]> https://biorxiv.org/content/10.1101/2025.06.25.661602v1?rss=1 Teo, C. F. Tuomivaara, S. T. van Hilten, N. Crottes, D. Jan, Y. N. Grabe, M. Jan, L. Y. 2025-06-27 doi:10.1101/2025.06.25.661602 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Synaptic plasticity of prefrontal long-range inhibition regulates cognitive flexibility ]]> https://biorxiv.org/content/10.1101/2025.06.27.662040v1?rss=1 Zhu, X. Hagopian, L. L. Wallquist, K. E. Sohal, V. S. 2025-06-28 doi:10.1101/2025.06.27.662040 Cold Spring Harbor Laboratory Press 2025-06-28 <![CDATA[ Dietary restriction promotes neuronal resilience via ADIOL ]]> https://biorxiv.org/content/10.1101/2025.06.25.661551v1?rss=1 View larger version (16K): org.highwire.dtl.DTLVardef@3246f7org.highwire.dtl.DTLVardef@d13dbaorg.highwire.dtl.DTLVardef@12b86f6org.highwire.dtl.DTLVardef@a98d62_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Guijarro-Hernandez, A. Yoo, S. Lemieux, G. A. Komatsu, S. Jiang, W. I. Latiff, A. Q. Patil, R. R. Ma, D. K. Ashrafi, K. 2025-06-29 doi:10.1101/2025.06.25.661551 Cold Spring Harbor Laboratory Press 2025-06-29 <![CDATA[ Photothrombotic Ischemic Thalamic Stroke in Mice Recapitulates Spontaneous Pain Features of Central Post-Stroke Pain in Humans ]]> https://biorxiv.org/content/10.1101/2025.06.26.661797v1?rss=1 Ford, J. B. Tambou, O. N. Weinrich, J. A. Chatterjee, D. Basbaum, A. Paz, J. T. 2025-06-29 doi:10.1101/2025.06.26.661797 Cold Spring Harbor Laboratory Press 2025-06-29 <![CDATA[ Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA ]]> https://biorxiv.org/content/10.1101/2025.06.26.661849v1?rss=1 Zhang, Z. Georgakopoulos Soares, I. Bourque, G. Ahituv, N. Inoue, F. 2025-06-30 doi:10.1101/2025.06.26.661849 Cold Spring Harbor Laboratory Press 2025-06-30 <![CDATA[ Luminal Vascular Dysfunction Drives Rapid Blood Brain Barrier Injury in Hyperglycemic Stroke: Key Roles for Luminal Glycocalyx and Complement ]]> https://biorxiv.org/content/10.1101/2025.06.26.661858v1?rss=1 Chen, H. Frank, J. A. Tan, C. Lee, A. G. Kopchock, R. Chiang, T. Kim, A. Galvan, M. Fraser, J. F. Dornbos, D. Aboul-Nour, H. Millson, N. Tomlinson, S. McCullough, L. D. Pennypacker, K. Cheng, M. Y. Bliss, T. Steinberg, G. K. 2025-06-30 doi:10.1101/2025.06.26.661858 Cold Spring Harbor Laboratory Press 2025-06-30 <![CDATA[ The gut microbiome shapes pharmacology and treatment outcomes for a key anti-inflammatory therapy ]]> https://biorxiv.org/content/10.1101/2025.06.26.661733v1?rss=1 Villa Soto, V. S. Degraeve, A. L. Heath, C. M. Orellana, D. A. Reilly, E. R. Mukherjee, M. Brockert, J. G. Dumlao, D. S. Blank, R. B. Perlmutter, N. Yu, S. Ashouri, J. Scher, J. U. Patterson, A. D. Turnbaugh, P. J. Nayak, R. R. Mukherjee, M. F. 2025-07-01 doi:10.1101/2025.06.26.661733 Cold Spring Harbor Laboratory Press 2025-07-01 <![CDATA[ A mitotic bookmark coordinates transcription and replication ]]> https://biorxiv.org/content/10.1101/2025.06.29.662044v1?rss=1 Cho, C.-Y. O'Farrell, P. H. 2025-07-02 doi:10.1101/2025.06.29.662044 Cold Spring Harbor Laboratory Press 2025-07-02 <![CDATA[ Two parallel lineage-committed progenitors contribute to the developing brain ]]> https://biorxiv.org/content/10.1101/2025.07.02.662771v1?rss=1 Dundes, C. E. Jokhai, R. T. Ahsan, H. Kang, R. S. Salomon-Shulman, R. E. A. Rajan, A. Kim, Y. S. Stanton, L. J. Xu, C. Do, S. McDonald, B. D. Lopez, J. M. A. Urrutia, H. A. Greenfeld, H. Wong, A. Qu, Y. Petkovic, A. S. Miao, Y. Garcia, K. C. Monje, M. Wagner, D. E. Bronner, M. E. Lowe, C. J. Loh, K. M. 2025-07-03 doi:10.1101/2025.07.02.662771 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Multimodal sensory overload in dopamine-deficient larval zebrafish leads to paradoxical kinesia ]]> https://biorxiv.org/content/10.1101/2025.06.30.662454v1?rss=1 Bose, K. Guo, S. Bhardwaj, K. 2025-07-04 doi:10.1101/2025.06.30.662454 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Differential Assembly of Mouse and Human Tumor Microenvironments ]]> https://biorxiv.org/content/10.1101/2025.07.01.661217v1?rss=1 View larger version (71K): org.highwire.dtl.DTLVardef@22bcf7org.highwire.dtl.DTLVardef@a410b7org.highwire.dtl.DTLVardef@1455eb5org.highwire.dtl.DTLVardef@14cc6f5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Courau, T. Jaszczak, R. G. Samad, B. Flynn, E. Reeder, G. C. Chew, N. W. Tsui, J. Ray, A. Wismer, H. Bunis, D. Lupin-Jimenez, L. Gavil, N. V. Masopust, D. Graham, J. P. Skelly, D. A. Vesco, X. Liu, E. T. Fragiadakis, G. K. Combes, A. J. Krummel, M. F. 2025-07-05 doi:10.1101/2025.07.01.661217 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ Labile iron pool dynamics do not drive ferroptosis potentiation in colorectal cancer cells ]]> https://biorxiv.org/content/10.1101/2025.07.01.662602v1?rss=1 Ponnusamy, V. Randall, D. R. Lee, Z. Das, N. K. Zhao, L. Buscher, K. Solanki, S. Renslo, A. Shah, Y. M. Hsu, P. P. 2025-07-05 doi:10.1101/2025.07.01.662602 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ TOMM40 Knockdown in Macrophages Inhibits Oxidized LDL-induced NLRP3 Activation and Promotes LXR-β Mediated Cholesterol Transporter Gene Expression ]]> https://biorxiv.org/content/10.1101/2025.07.01.662675v1?rss=1 Chelluri, S. S. Yang, N. V. Theusch, E. Krauss, R. M. 2025-07-05 doi:10.1101/2025.07.01.662675 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ Electrocorticographic Detection of Speech Networks in Glioma-infiltrated Cortex ]]> https://biorxiv.org/content/10.1101/2025.07.04.663249v1?rss=1 Ambati, V. S. Persad, A. S. Kaur, J. Herr, S. Cunningham, E. Dada, A. Ekert, J. O. Greicius, Q. Silva, A. McMillan Villalobos, P. Olshausen, N. Sibih, Y. Oten, S. Yamada, H. S. Umbach, G. Aabedi, A. A. Al-Holou, W. Young, J. Sushil, M. Chang, E. F. Berger, M. S. Brang, D. Hervey-Jumper, S. L. 2025-07-05 doi:10.1101/2025.07.04.663249 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity ]]> https://biorxiv.org/content/10.1101/2025.07.04.663231v1?rss=1 10 [A] conformational range for the active site loop and that the loop is stabilized by transient contacts. This disorder is significant, as we show that the transient contacts which stabilize this loop in a closed conformation are essential for catalysis both in vitro and in cells. We propose that GS filament formation constitutes a negative-feedback mechanism, directly linking product concentration to the structural and functional remodeling of the enzyme. ]]> Greene, E. Muniz, R. Yamamura, H. Hoff, S. E. Bajaj, P. Lee, D. J. Thompson, E. M. Arada, A. Lee, G. M. Bonomi, M. Kollman, J. M. Fraser, J. S. 2025-07-06 doi:10.1101/2025.07.04.663231 Cold Spring Harbor Laboratory Press 2025-07-06 <![CDATA[ Blocking Osteoprotegerin Reprograms Cancer Associated Fibroblast to Promotes Immune Infiltration into the Tumor Microenvironment ]]> https://biorxiv.org/content/10.1101/2025.07.04.663190v1?rss=1 Wang, Y. Apostolopoulou, H. Sun, I. H. Bains, A. Gibbs, D. Huang, S. Alliston, T. Maker, A. Tlsty, T. Ntranos, V. Gardner, J. M. Bhushan, A. 2025-07-07 doi:10.1101/2025.07.04.663190 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ Beating the gold standard: A review of Mycobacterium tuberculosis lysis using bead beating and the need for standardization. ]]> https://biorxiv.org/content/10.1101/2025.07.07.663234v1?rss=1 Limberis, J. D. Metcalfe, J. Z. 2025-07-07 doi:10.1101/2025.07.07.663234 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ High-throughput multi-camera array microscope platform for automated 3D behavioral analysis of freely swimming zebrafish larvae ]]> https://biorxiv.org/content/10.1101/2025.07.07.661868v1?rss=1 Chen, H. Li, K. Kreiss, L. Reamey, P. Pierce, L. X. Zhang, R. Da Luz, R. Chaware, A. Kim, K. Cook, C. B. Yang, X. Lerner, J. F. Doman, J. Begue, A. Efromson, J. Harfouche, M. Horstmeyer, G. McCarroll, M. N. Horstmeyer, R. 2025-07-08 doi:10.1101/2025.07.07.661868 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ Benchmarking Large Language Models for Predictive Modeling in Biomedical Research With a Focus on Reproductive Health ]]> https://biorxiv.org/content/10.1101/2025.07.07.663529v1?rss=1 Sarwal, R. Tarca, V. Kalavros, N. Bhatti, G. Bhattacharya, S. Butte, A. J. Romero, R. J. Stolovitzky, G. Oskotsky, T. T. Tarca, A. L. Sirota, M. 2025-07-10 doi:10.1101/2025.07.07.663529 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ Clinical and molecular characterisation of primary refractoriness to atezolizumab plus bevacizumab in patients with unresectable hepatocellular carcinoma. ]]> https://biorxiv.org/content/10.1101/2025.07.08.663653v1?rss=1 Lombardi, P. Ramon-Gil, E. Brunetti, L. Manfredi, G. F. Merces, G. Fulgenzi, C. A. M. DAlessio, A. Torkpour, A. Celsa, C. Stefanini, B. Yang, H. Crowley, F. Marron, T. U. Saeed, A. Pinter, M. Scheiner, B. Huang, Y.-H. Lee, P.-C. Nishida, N. Po-Ting Lin, R. Dalbeni, A. Vivaldi, C. Masi, G. Rohlen, N. von Felden, J. Kaseb, A. Galle, P. R. Kudo, M. Hsu, W.-F. Rimassa, L. Parisi, A. Kelley, R. K. Toyoda, H. Pirisi, M. Jabar, R. F. Rakaee, M. Cabibbo, G. Camma, C. Piscaglia, F. Hwang, S. Shin, D. J. Li, M. Daniele, G. Mann, D. Chon, H. J. Leslie, J. Pin 2025-07-10 doi:10.1101/2025.07.08.663653 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ Selective Sensitivity of Ph-like B-ALL to BRG1 Inhibition Reveals a Novel Targeted Therapy Strategy ]]> https://biorxiv.org/content/10.1101/2025.07.08.661805v1?rss=1 View larger version (56K): org.highwire.dtl.DTLVardef@1b0a6cforg.highwire.dtl.DTLVardef@977257org.highwire.dtl.DTLVardef@d3bf7forg.highwire.dtl.DTLVardef@1c12d52_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ayyadevara, V. S. S. A. Gaur, S. Paik, A. Perencsik, R. Toma, M. M. Wertheim, G. Geng, H. Skorski, T. Swaminathan, S. Hurtz, C. 2025-07-11 doi:10.1101/2025.07.08.661805 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ Cell atlas of the developing human meninges reveals a dura origin of meningioma ]]> https://biorxiv.org/content/10.1101/2025.07.08.663122v1?rss=1 Vinsland, E. Marco Salas, S. Kapustova, I. Hu, L. Webb, S. Li, X. He, X. Nilsson, M. Hanifa, M. Barker, R. A. Persson, O. Raleigh, D. R. Sundstrom, E. Lonnerberg, P. Linnarsson, S. 2025-07-11 doi:10.1101/2025.07.08.663122 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ Tim-3 Promotes Early Differentiation of Tbet+ Effector T Cells During Acute Viral Infection ]]> https://biorxiv.org/content/10.1101/2025.07.08.663709v1?rss=1 Manandhar, P. Landy, E. Mori, K. Kane, L. P. 2025-07-11 doi:10.1101/2025.07.08.663709 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ ImmuneFM: Pre-training Foundation Model from Cytometry Data for Immunology Research ]]> https://biorxiv.org/content/10.1101/2025.07.09.664020v1?rss=1 Ding, S. Bhattacharya, S. Butte, A. 2025-07-11 doi:10.1101/2025.07.09.664020 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ A Fibroblast State Choreographs an Epithelial YAP-dependent Regenerative Program Essential to (Pre)malignancy via ECM-mediated Mechanotransduction ]]> https://biorxiv.org/content/10.1101/2025.07.11.661192v1?rss=1 Pan, D. Gascard, P. Caruso, J. A. Chen-Tanyolac, C. Sangwan, V. Bertos, N. Camilleri-Broet, S. Berube, J. Oikonomopoulos, S. Strasser, M. K. Gibbs, D. L. Bons, J. Burton, J. B. Rose, J. P. Shah, S. Bai, R. Lee, S. Fels-Elliott, D. R. Miyara, S. Alon, U. Urisman, A. Ragoussis, I. Huang, S. Schilling, B. Ferri, L. E. Tlsty, T. D. 2025-07-11 doi:10.1101/2025.07.11.661192 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ KIF5A downregulation in spinal muscular atrophy links axonal regeneration defects with ALS ]]> https://biorxiv.org/content/10.1101/2025.07.11.664426v1?rss=1 Akiyama, T. Zeng, Y. Guo, C. Gautier, O. Koepke, L. S. Bombosch, J. Sianto, O. Ross, J. P. Hoang, P. T. Zhao, L. Y. Spencer, C. Monje, M. Day, J. W. Gitler, A. D. 2025-07-13 doi:10.1101/2025.07.11.664426 Cold Spring Harbor Laboratory Press 2025-07-13 <![CDATA[ Cortical organoids reveal human-specific roles of METTL5 in neurodevelopment via regulation of CHCHD2 ]]> https://biorxiv.org/content/10.1101/2025.07.13.664555v1?rss=1 Turkalj, E. M. Kuljanishvili, M. Kang, G. Liu, I. Ghent, C. Waltier Soriano, C. Keyhanvar, N. Brody, D. Oldham, M. Vissers, C. 2025-07-13 doi:10.1101/2025.07.13.664555 Cold Spring Harbor Laboratory Press 2025-07-13 <![CDATA[ The Notch1 intracellular domain orchestrates mechanotransduction of fluid shear stress ]]> https://biorxiv.org/content/10.1101/2025.07.13.663563v1?rss=1 Singh, T. Jacobs, K. A. Polacheck, W. J. Kutys, M. L. 2025-07-14 doi:10.1101/2025.07.13.663563 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[ Auto-MedCalc: Automated Biomarkers Discovery and Risk Score Generation with AI Agents ]]> https://biorxiv.org/content/10.1101/2025.07.10.664265v1?rss=1 Ding, S. Bhattacharya, S. Butte, A. 2025-07-16 doi:10.1101/2025.07.10.664265 Cold Spring Harbor Laboratory Press 2025-07-16 <![CDATA[ Programmable translational inhibition by a molecular glue-oligonucleotide conjugate ]]> https://biorxiv.org/content/10.1101/2025.07.15.664547v1?rss=1 Wang, S. Kovalski, J. R. Zapatero-Belinchon, F. J. Bennett, M. Kuzuoglu-Öztürk, D. Li, Q. Stevenson, E. Liu, J. Krogan, N. J. Ott, M. Swaney, D. L. Ruggero, D. Lou, K. Shokat, K. 2025-07-16 doi:10.1101/2025.07.15.664547 Cold Spring Harbor Laboratory Press 2025-07-16 <![CDATA[ Primary cilia and BBS4 are required for postnatal pituitary development ]]> https://biorxiv.org/content/10.1101/2025.07.15.664994v1?rss=1 Brewer, K. M. Brewer, K. K. Richardson, N. C. Reiter, J. F. Berbari, N. F. Konjikusic, M. J. 2025-07-18 doi:10.1101/2025.07.15.664994 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Tracking tau and cellular responses in human iPSC-microglia from uptake to seedable secretion in extracellular vesicles ]]> https://biorxiv.org/content/10.1101/2025.07.17.664991v1?rss=1 Karabova, M. K. del Ser Badia, A. Hedegaard, A. Washer, S. J. Baykam, Z. O'Brien, D. P. Vendrell, I. Hester, S. S. Fischer, R. Johnson, E. Melia, C. E. Matthews-Palmer, T. R. S. Matadeen, R. Santambrogio, A. Metrick, M. Vendruscolo, M. Keeling, S. Cheam, K. McEwan, W. A. Kosik, K. S. Day, T. A. James, W. S. Cowley, S. A. 2025-07-21 doi:10.1101/2025.07.17.664991 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Programmable microparticles rewire CAR signaling to enable super-physiological expansion of human T cells in vitro ]]> https://biorxiv.org/content/10.1101/2025.07.17.665438v1?rss=1 Zeng, Q. Flemming, L. Chen, Y. Mazumder, T. Hammerlindl, H. Allen, G. M. Almeida, R. Williams, J. Z. Hernandez-Lopez, R. A. Eyquem, J. Ye, C. J. Lim, W. A. Tang, Q. Desai, T. Huang, X. 2025-07-22 doi:10.1101/2025.07.17.665438 Cold Spring Harbor Laboratory Press 2025-07-22 <![CDATA[ Mapping mesenchymal diversity in the developing human intestine and organoids ]]> https://biorxiv.org/content/10.1101/2025.07.22.665939v1?rss=1 View larger version (69K): org.highwire.dtl.DTLVardef@46299borg.highwire.dtl.DTLVardef@55a014org.highwire.dtl.DTLVardef@180a104org.highwire.dtl.DTLVardef@1cb42b2_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIA spatial atlas of fibroblast heterogeneity in the human intestine C_LIO_LIPopulations include subepithelial, submucosal, lamina propria, and CXCL13+ fibroblasts C_LIO_LIFibroblast position in the developing intestine is maintained into adulthood C_LIO_LIOrganoids largely recreate the spatial organization of the human intestine C_LI ]]> Johnson, K. F. Dong, X. Tsai, Y.-H. Wu, A. Clark, S. G. Huang, S. Zwick, R. Glass, I. Walton, K. D. Klein, O. D. Spence, J. 2025-07-22 doi:10.1101/2025.07.22.665939 Cold Spring Harbor Laboratory Press 2025-07-22 <![CDATA[ Receptor-tethered orthogonal IL-2 enhances regulatory T cell therapy ]]> https://biorxiv.org/content/10.1101/2025.07.19.665688v1?rss=1 Indart, A. Lyu, H. Nguyen, V. Rosenthal, W. Jang, S. Chen, Y. Jude, K. Su, L. Garcia, K. C. Bluestone, J. A. Tang, Q. 2025-07-23 doi:10.1101/2025.07.19.665688 Cold Spring Harbor Laboratory Press 2025-07-23 <![CDATA[ Canonical and phosphoribosyl ubiquitination coordinate to stabilize a proteinaceous structure surrounding the Legionella-containing vacuole ]]> https://biorxiv.org/content/10.1101/2025.07.22.666189v1?rss=1 Steinbach, A. Mokkapati, C. Mukherjee, S. 2025-07-23 doi:10.1101/2025.07.22.666189 Cold Spring Harbor Laboratory Press 2025-07-23 <![CDATA[ Integrated single-nuclei and spatial transcriptomic profiling of human sacrococcygeal teratomas reveals heterogeneity in cellular composition and X-chromosome inactivation ]]> https://biorxiv.org/content/10.1101/2025.07.21.665156v1?rss=1 Rojas, E. J. Giannikou, K. Huang, B. J. Cho, S.-J. Cordero, M. Pena, D. Vu, L. Bagrodia, A. Derderian, S. C. MacKenzie, T. C. Laird, D. J. 2025-07-24 doi:10.1101/2025.07.21.665156 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Hippocampal input-driven plasticity of prefrontal interneurons reveals a circuit basis for impaired spatial working memory. ]]> https://biorxiv.org/content/10.1101/2025.07.21.665987v1?rss=1 View larger version (61K): org.highwire.dtl.DTLVardef@29a326org.highwire.dtl.DTLVardef@1964208org.highwire.dtl.DTLVardef@1c94e4corg.highwire.dtl.DTLVardef@1336edb_HPS_FORMAT_FIGEXP M_FIG C_FIG IN BRIEFSilverstein et al. investigated how ventral hippocampus (vHPC) inputs to medial prefrontal cortex (mPFC) interact with mPFC interneuron populations to support spatial working memory (SWM) in mice. They show that repeated vHPC input stimulation that reduces vHPC drive onto vasoactive intestinal peptide (VIP) interneurons also elevates delay-related VIP interneuron activity in early SWM task training, and this enhanced activity correlates with poorer training performance. Mice modelling the 22q11.2 deletion syndrome--known to have SWM learning deficits--recapitulate this altered VIP interneuron activity and show reduced vHPC input targeting of VIP interneurons. HIGHLIGHTSO_LIRepeated stimulation of vHPC inputs to mPFC persistently depresses VIP interneuron activity and enhances SST interneuron activity in mice C_LIO_LIBlunted monosynaptic drive onto mPFC VIP interneurons by repeated vHPC input stimulation plausibly reproduces in vivo activity changes C_LIO_LIStimulated mice show heightened VIP interneuron activity during the delay epoch in early SWM task training that correlates with poorer training performance C_LIO_LIMice modeling the 22q11.2 deletion syndrome with known SWM task learning deficits mirror this aberrant VIP interneuron activity profile and show reduced vHPC input targeting of VIP interneurons C_LI ]]> Silverstein, S. E. Clarity, T. T. Deshpande, M. S. Vaughan, E. Novik, S. Yarur, H. E. Zhang, S. Tsai, V. S. Ye, R. Mikofsky, R. M. Hsiang, M. Bauman, A. Loewinger, G. Pereira, F. Morales, M. Sohal, V. S. Tejeda, H. Gordon, J. A. Kupferschmidt, D. A. 2025-07-24 doi:10.1101/2025.07.21.665987 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ An open-source pipeline for calcium imaging and all-optical physiology in human stem cell-derived neurons ]]> https://biorxiv.org/content/10.1101/2025.07.21.664988v1?rss=1 Afshar-Saber, W. Gasparoli, F. M. Yang, Z. Teaney, N. A. Lalani, L. Srinivasan, G. Whye, D. Buttermore, E. Winden, K. D. Chen, C. Sahin, M. 2025-07-25 doi:10.1101/2025.07.21.664988 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ Single-Cell Profiling Reveals Altered Endometrial Cellular Features Across the Menstrual Cycle in Endometriosis Patients ]]> https://biorxiv.org/content/10.1101/2025.07.21.666016v1?rss=1 Almonte-Loya, A. Wang, W. Houshdaran, S. Tang, X. Flynn, E. Liu, B. Kushnoor, D. Nezhat, C. Vilella, F. Simon, C. Vo, K. C. Casillas, A. Khan, U. Serras, C. P. Oskotsky, T. T. Huang, D. Vallve-Juanico, J. Irwin, J. Combes, A. Sirota, M. Fragiadakis, G. Giudice, L. 2025-07-25 doi:10.1101/2025.07.21.666016 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ Methylation variability and LINE-1 activation in multiple myeloma ]]> https://biorxiv.org/content/10.1101/2025.07.22.666173v1?rss=1 Wan, Q. Leung, A. Y. Bhandari, M. V. Kato, H. Song, J. Y. Schones, D. E. 2025-07-26 doi:10.1101/2025.07.22.666173 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ Targeting RUNX1 in Macrophages Facilitates Cardiac Recovery ]]> https://biorxiv.org/content/10.1101/2025.07.25.665779v1?rss=1 Amrute, J. M. Zhu, A. Pai, Y.-L. Hector-Greene, M. An, Y. Lim, K. R. Sheth, M. Padmanabhan, A. Lee, C. Y. Yamawaki, T. Sicklinger, F. Hartmann, N. Bredemeyer, A. Lee, C. J. M. Xu, V. Bell, L. Harmon, T. Shin, H. Parvathaneni, A. Liu, L. Dutta, A. K. Pruitt, D. Barreda, J. Chen, J. Shroff, U. N. Nadadur, R. Nigro, J. Weinheimer, C. J. Kovacs, A. Cui, J. Wang, C. Li, C.-M. K. Kreisel, D. Liu, Y. Foo, R. S.-Y. Schneider, R. K. Engreitz, J. Mann, D. Rulifson, I. Jackson, S. Ason, B. Kramann, R. Drakos, S. G. Leuschner, F. Alexanian, M. Lavine, K. J. 2025-07-26 doi:10.1101/2025.07.25.665779 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ Aggressive Cholesterol Lowering Normalizes Atherosclerosis Regression in Jak2V617F Clonal Hematopoiesis ]]> https://biorxiv.org/content/10.1101/2025.07.23.666334v1?rss=1 Hardaway, B. D. Fidler, T. P. Tavallaie, M. Avrampou, K. Hsu, C.-C. Schiavone, S. Xiao, T. Wang, N. Tall, A. R. 2025-07-27 doi:10.1101/2025.07.23.666334 Cold Spring Harbor Laboratory Press 2025-07-27 <![CDATA[ Metastasis-associated wound repair promotes reciprocal activation of the lung epithelium and breast cancer metastases during outgrowth ]]> https://biorxiv.org/content/10.1101/2025.07.23.666437v1?rss=1 Christenson, J. L. Spoelstra, N. S. Williams, M. M. O'Neill, K. I. Orlicky, D. J. Wagner, J. A. Goodspeed, A. E. Kuo, L.-W. Crump, L. S. Richer, J. K. 2025-07-27 doi:10.1101/2025.07.23.666437 Cold Spring Harbor Laboratory Press 2025-07-27 <![CDATA[ Ebola virus VP35 NNLNS motif modulates viral RNA synthesis and MIB2-mediated signaling ]]> https://biorxiv.org/content/10.1101/2025.07.27.667045v1?rss=1 Uwase, G. Luthra, P. Vogel, O. A. Batra, J. LaRosa, B. A. Sheehan, K. C. F. Khatavkar, O. Payton, J. Davey, R. A. Krogan, N. J. Basler, C. F. Leung, D. W. Amarasinghe, G. K. 2025-07-27 doi:10.1101/2025.07.27.667045 Cold Spring Harbor Laboratory Press 2025-07-27 <![CDATA[ AlignmentFold and AlignmentPartition: Improving the align-then-fold approach for RNA secondary structure prediction ]]> https://biorxiv.org/content/10.1101/2025.07.23.666478v1?rss=1 Mittal, A. Mathews, D. H. 2025-07-28 doi:10.1101/2025.07.23.666478 Cold Spring Harbor Laboratory Press 2025-07-28 <![CDATA[ Cell Cycle Arrest of a "Zippering" Epithelial Cell Cluster Shapes the Face and is Disrupted in Craniofacial Disorders ]]> https://biorxiv.org/content/10.1101/2025.07.28.667310v1?rss=1 Qu, T. Chacon, B. H. Faure, L. Losa, M. Hernandez-Martinez, R. Robinson, K. Jones, A. Lisgo, S. Risolino, M. De Anda, J. Panagiotakos, G. Leslie-Clarkson, E. J. Adameyko, I. Selleri, L. 2025-07-30 doi:10.1101/2025.07.28.667310 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ Aging-Associated Autoimmunity in Genetically Diverse UM-HET3 Mice Shows a Female Sex Bias ]]> https://biorxiv.org/content/10.1101/2025.07.25.666876v1?rss=1 Guzniczak, N. Makuch, M. Tillett, M. Bagavant, H. Deshmukh, U. S. 2025-07-31 doi:10.1101/2025.07.25.666876 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ A stem cell-based platform for functional analysis of genetic variants in lung disease ]]> https://biorxiv.org/content/10.1101/2025.07.28.667211v1?rss=1 Wallman, D. J. Homma, S. T. Finton, M. Beermann, M. Jacob, A. Choksi, S. Pletcher, S. D. Xu, H. Bawa, P. S. Reiter, J. F. Horani, A. Brody, S. L. Berical, A. Hawkins, F. J. 2025-07-31 doi:10.1101/2025.07.28.667211 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Modulation of the 14-3-3σ/C-RAF autoinhibited complexby molecular glues ]]> https://biorxiv.org/content/10.1101/2025.07.30.667769v1?rss=1 Konstantinidou, M. Vickery, H. R. Pennings, M. A. M. Virta, J. M. Visser, E. J. Bannier, S. D. Srikanth, M. Cismoski, S. Z. Young, L. C. van den Oetelaar, M. C. M. McCromick, F. Ottmann, C. Brunsveld, L. Arkin, M. R. 2025-07-31 doi:10.1101/2025.07.30.667769 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ BBSome-Mediated Clearance of Ubiquitinated IMPG2 Defines a Constitutive Ciliary Retrieval Pathway in Photoreceptors ]]> https://biorxiv.org/content/10.1101/2025.07.29.667331v1?rss=1 Das, T. Bradshaw, G. A. Hyer, J. Masek, M. Kuo, Y.-M. Bachmann-Gagescu, R. Kalocsay, M. Nachury, M. V. 2025-08-01 doi:10.1101/2025.07.29.667331 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Alanine Catabolism as a Targetable Vulnerability for MYC-Driven Liver Cancer ]]> https://biorxiv.org/content/10.1101/2025.07.29.667471v1?rss=1 Montoya, T. Lee, J. V. Qiu, L. Krall, A. V. Matulionis, N. Seo, Y. Finck, B. Kelley, R. K. Christofk, H. Goga, A. 2025-08-01 doi:10.1101/2025.07.29.667471 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ The Lipid Hydrolase ABHD6 is a Therapeutic Target in Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD)-Related Hepatocellular Carcinoma ]]> https://biorxiv.org/content/10.1101/2025.07.29.667509v1?rss=1 Orabi, D. Massey, W. Fung, K. Varadharajan, V. Ramachandiran, I. Banerjee, R. Silver, D. J. Osborn, L. J. Brown, A. L. Marshall, S. Ferguson, D. Cao, S. Schugar, R. C. Finney, C. Neumann, C. Burrows, A. C. Horak, A. J. Pathak, P. Helsley, R. N. Bulfon, D. Zimmermann, R. Leung, Y. H. Madiraju, S. R. M. Prentki, M. Lee, R. G. Mullick, A. E. Zergeeva, O. Dasarathy, S. Lee, Z. Allende, D. S. Aucejo, F. Lathia, J. D. Brown, J. M. 2025-08-02 doi:10.1101/2025.07.29.667509 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ A novel locus associated with decreased susceptibility of Plasmodium falciparum to lumefantrine and dihydroartemisinin has emerged and spread in Uganda ]]> https://biorxiv.org/content/10.1101/2025.07.30.667738v1?rss=1 50% in northern Uganda by 2016 and eastern Uganda by 2023. PIN-carrying parasites showed significantly decreased ex vivo susceptibilities, measured as IC50s, to lumefantrine, mefloquine and dihydroartemisinin, either with or without coincident K13 mutations. Thus, PX1 polymorphisms may impact on the susceptibilities of African malaria parasites to key drugs. ]]> Niare, K. Tafesse, B. Treat, M. Sadler, J. Okitwi, M. Orena, S. Asua, V. Kreutzfeld, O. Legac, J. Samuel, N. L. Yeka, A. Rosenthal, P. J. Juliano, J. J. Bailey, J. A. Conrad, M. D. 2025-08-02 doi:10.1101/2025.07.30.667738 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ The Rpd3 histone deacetylase is critical for temperature-mediated morphogenesis and virulence in the human fungal pathogen Histoplasma ]]> https://biorxiv.org/content/10.1101/2025.08.01.668069v1?rss=1 Ali, N. B. Voorhies, M. Rodriguez, R. A. Sil, A. 2025-08-04 doi:10.1101/2025.08.01.668069 Cold Spring Harbor Laboratory Press 2025-08-04 <![CDATA[ Systemic translocation of S. aureus Drives Anti-CD4 Autoimmunity in Treated HIV Infection ]]> https://biorxiv.org/content/10.1101/2025.08.04.668434v1?rss=1 Jiang, W. Da, C. Luo, Z. Ning, W. Heath, S. L. Gisslen, M. Price, R. W. Adekunle, R. Salman, T. Johnson, D. McKinnon, J. E. Hu, W. Ndhlovu, L. 2025-08-04 doi:10.1101/2025.08.04.668434 Cold Spring Harbor Laboratory Press 2025-08-04 <![CDATA[ Targeting the COP9 signalosome overcomes platinum resistance in ovarian cancer through two distinct genome stability mechanisms ]]> https://biorxiv.org/content/10.1101/2025.08.04.668450v1?rss=1 Lomonosova, E. Loeb, M. Rodriguez, K. van Biljon, L. N. Brill, J. Schab, A. Minett, M. Barron, J. Bittner, M. Park, J. Drexler, R. Sandoval, C. Oplt, A. Gallup, E. Thuthika, P. K. Sadeghipour, N. Wu, S. Oberley, M. J. Sanders, B. Kuroki, L. McCourt, C. Hagemann, A. R. Thaker, P. Mutch, D. Powell, M. Hagemann, I. S. Ilagan, M. Fuh, K. Verma, P. Scharer, O. Mosammaparast, N. Khabele, D. Mullen, M. M. 2025-08-06 doi:10.1101/2025.08.04.668450 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ Reversible therapeutic resistance in EGFR mutant lung cancer caused by RB1 loss induced lineage plasticity ]]> https://biorxiv.org/content/10.1101/2025.08.04.668485v1?rss=1 Zhang, L. Chinnam, M. Balk, B. Zhang, X. Wang, Y. Shaurova, T. Alam, S. Pokharel, S. Singh, P. Jacobi, J. Wang, J. Cortes Gomez, E. Habitzruther, M. Seshadri, M. Atanassov, B. Wu, W. Benevolenskaya, E. Blakely, C. M. Hershberger, P. Long, M. Bivona, T. Goodrich, D. W. 2025-08-06 doi:10.1101/2025.08.04.668485 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ Evidence for the major role of PH4EFB in the prolyl 4-hydroxylation of Drosophila collagen IV ]]> https://biorxiv.org/content/10.1101/2025.08.05.668786v1?rss=1 Ishikawa, Y. Toups, M. A. Elkrewi, M. Zajac, A. L. Horne-Badovinac, S. Matsubayashi, Y. 2025-08-06 doi:10.1101/2025.08.05.668786 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ The Placental Transcriptome Serves as a Mechanistic Link between Prenatal Phthalate Exposure and Placental Efficiency ]]> https://biorxiv.org/content/10.1101/2025.08.05.664214v1?rss=1 Parenti, M. Lapehn, S. MacDonald, J. Bammler, T. Szpiro, A. Hazlehurst, M. Day, D. B. Thoreson, C. Kannan, K. Bush, N. R. LeWinn, K. Z. Zhao, Q. Sathyanarayana, S. Paquette, A. G. 2025-08-07 doi:10.1101/2025.08.05.664214 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Defined human tri-lineage brain microtissues ]]> https://biorxiv.org/content/10.1101/2025.08.05.668605v1?rss=1 Uenaka, T. Jung, S. Kumar, I. Vodehnal, K. Rastogi, M. Yoo, Y. Koontz, M. Thome, C. Li, W. Chan, T. Green, E. M. Chesnov, K. Sun, Z. Zhang, S. Wang, J. Venida, A. Mahul Mellier, A.-L. Atkins, M. Jackrel, M. Skotheim, J. M. Wyss-Coray, T. Abu-Remaileh, M. Lashuel, H. A. Bassik, M. C. Sudhof, T. C. del Sol, A. Ullian, E. Wernig, M. 2025-08-07 doi:10.1101/2025.08.05.668605 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Comparative evaluation of genomic footprinting algorithms for predicting transcription factor binding sites in single-cell data ]]> https://biorxiv.org/content/10.1101/2025.08.07.669008v1?rss=1 Everitt, A. Whalen, S. Pollard, K. S. 2025-08-07 doi:10.1101/2025.08.07.669008 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Circuit inhibition promotes the dynamic reorganization of prefrontal task encoding to support cognitive flexibility ]]> https://biorxiv.org/content/10.1101/2025.08.09.669414v1?rss=1 Johnson-Cruz, C. Cho, K. K. A. Sohal, V. S. 2025-08-11 doi:10.1101/2025.08.09.669414 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ Genetic and Epigenetic Reprogramming of Transposable Elements Drives ecDNA-Mediated Metastatic Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2025.08.08.668693v1?rss=1 Mout, L. Moreno-Rodriguez, T. Grillo, G. Nand, A. Keshavarzian, T. Bahl, S. Kang, K. Bootsma, M. Minnee, E. Zhou, S. Burns, K. H. Corey, E. Nelson, P. Dehm, S. M. Zhao, S. G. Zwart, W. Feng, F. Quigley, D. Lupien, M. 2025-08-12 doi:10.1101/2025.08.08.668693 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ The Hsp40 co-chaperone DNAJC7 modifies polyglutamine but not polyglycine aggregation ]]> https://biorxiv.org/content/10.1101/2025.08.10.669490v1?rss=1 Ramani, B. Ehsani, K. Kampmann, M. 2025-08-12 doi:10.1101/2025.08.10.669490 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Spatiotemporal control of cortical centrin patterning by regionalized Sfi1 family scaffolding proteins in Stentor coeruleus ]]> https://biorxiv.org/content/10.1101/2025.08.11.669701v1?rss=1 Yan, C. J. Steube, N. Dey, G. Marshall, W. F. 2025-08-13 doi:10.1101/2025.08.11.669701 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ Fine needle aspiration biopsy of breast specimens effectively harvests cells for patient-derived organoids modeling breast ductal carcinoma in situ ]]> https://biorxiv.org/content/10.1101/2025.08.12.669895v1?rss=1 Ye, J. Goldhammer, N. Vohra, P. Warhadpande, S. De Castro, G. C. Maldonado Rodas, C. Moasser, M. M. Ramalingam, K. Abe, S. Alvarado, M. Ewing, C. Goodwin, K. Mukhtar, R. Wong, J. Esserman, L. Balassanian, R. Rosenbluth, J. M. 2025-08-13 doi:10.1101/2025.08.12.669895 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ Commensal taxa in gut microbiota limit antibiotic resistance during extended oral antibiotic use ]]> https://biorxiv.org/content/10.1101/2025.08.13.670183v1?rss=1 Cyphert, E. L. Liu, C. Chu, V. T. Dubey, A. Liu, M. Zhong, Z. Cockey, J. R. Diaz, E. C. G. Morales, A. L. Nixon, J. C. Garcia, M. Zeng, S. Rohatgi, S. Wong, J. Arjyal, R. Mekonen, H. Neff, N. Lee, J. Shea, M. K. Fu, X. Booth, S. L. Leifer, C. A. Singh, A. Langelier, C. R. Hernandez, C. J. 2025-08-13 doi:10.1101/2025.08.13.670183 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ A population-scale atlas of blood and tissue in lupus nephritis ]]> https://biorxiv.org/content/10.1101/2025.08.11.669754v1?rss=1 Gurajala, S. Sugiarto, N. W. Curtis, M. Eisenhaure, T. M. Arazi, A. Fava, A. Xiao, Q. Mears, J. Rovin, B. Berthier, C. C. Izmirly, P. M. Barnas, J. L. Hoover, P. J. Peters, M. Raychowdhury, R. Horisberger, A. Sakaue, S. Zhao, Y. Furie, R. A. Belmont, H. M. Hildeman, D. A. Woodle, E. S. Dall'Era, M. Putterman, C. Kamen, D. L. McMahon, M. A. Grossman, J. Kalunian, K. C. Hodgin, J. B. Payan-Schober, F. Apruzzese, W. Perlman, H. Cuda, C. M. Wofsy, D. Guthridge, J. M. Anolik, J. H. James, J. A. Accelerating Medicines Partnerships Rheumatoid Arthritis/Systemic Lu 2025-08-14 doi:10.1101/2025.08.11.669754 Cold Spring Harbor Laboratory Press 2025-08-14 <![CDATA[ Cul5Wsb2 uses BCL2 proteins as co-receptors to target Bim for degradation. ]]> https://biorxiv.org/content/10.1101/2025.08.14.670414v1?rss=1 Vaysse-Zinkhofer, W. Alcindor, E. Garaffo, N. Toczyski, D. P. 2025-08-14 doi:10.1101/2025.08.14.670414 Cold Spring Harbor Laboratory Press 2025-08-14 <![CDATA[ NIPBL dosage shapes genome folding by tuning the rate of cohesin loop extrusion ]]> https://biorxiv.org/content/10.1101/2025.08.14.667581v1?rss=1 Shah, R. Tortora, M. M. C. Louafi, N. Rahmaninejad, H. Hansen, K. L. Anderson, E. C. Wen, D. Giorgetti, L. Fudenberg, G. Nora, E. P. 2025-08-15 doi:10.1101/2025.08.14.667581 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Multiplexed Perturbation Enables Scalable Pooled Screens ]]> https://biorxiv.org/content/10.1101/2025.08.14.669942v1?rss=1 Oberlin, S. Tay, N. Q. Xue, A. Pimentel, H. McManus, M. 2025-08-15 doi:10.1101/2025.08.14.669942 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Design of an ultrabright biosensor for dynamic imaging of kinase activity in cells ]]> https://biorxiv.org/content/10.1101/2025.08.13.669976v1?rss=1 Li, X. Tan, S. K. Chung, C.-I. Hatstat, K. A. Zhao, Q. Luo, J. DeGrado, W. F. shu, X. 2025-08-16 doi:10.1101/2025.08.13.669976 Cold Spring Harbor Laboratory Press 2025-08-16 <![CDATA[ An interneuronal CRH and CRHBP circuit stabilizes birdsong performance ]]> https://biorxiv.org/content/10.1101/2025.08.16.670679v1?rss=1 Colquitt, B. M. Brainard, M. 2025-08-17 doi:10.1101/2025.08.16.670679 Cold Spring Harbor Laboratory Press 2025-08-17 <![CDATA[ Bivalent mRNA booster encoding virus-like particles elicits potent polyclass RBD antibodies in pre-vaccinated mice ]]> https://biorxiv.org/content/10.1101/2025.08.18.670983v1?rss=1 Fan, C. Cohen, A. A. Dam, K.-M. A. Rorick, A. V. Priso Fils, A.-C. I. Yang, Z. Gnanapragasam, P. N. Segovia, L. N. Huey-Tubman, K. E. Moon, W. J. Lin, P. J. Bjorkman, P. J. Hoffmann, M. A. 2025-08-19 doi:10.1101/2025.08.18.670983 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ White Matter Tract Vulnerability to Amyloid Pathology on the Alzheimer's Disease Continuum ]]> https://biorxiv.org/content/10.1101/2025.08.18.670970v1?rss=1 Chandio, B. Q. Nir, T. M. Villalon-Reina, J. E. Thomopoulos, S. I. Feng, Y. Reid, R. I. Jack, C. R. Weiner, M. W. Garyfallidis, E. Jahanshad, N. Braskie, M. N. O'Bryant, S. Thompson, P. M. 2025-08-20 doi:10.1101/2025.08.18.670970 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ Regulated development of cannibalistic supergiant cells ]]> https://biorxiv.org/content/10.1101/2025.08.19.671124v1?rss=1 Larson, B. T. Giannotti, D. Mtawali, M. Lord, S. J. Boscaro, V. Keeling, P. J. 2025-08-20 doi:10.1101/2025.08.19.671124 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ Divergent viral phosphodiesterases for immune signaling evasion ]]> https://biorxiv.org/content/10.1101/2025.08.21.671373v1?rss=1 Doherty, E. E. Nomburg, J. E. Adler, B. A. Lopez, S. Hsieh, K. Price, N. Blount, N. Doudna, J. A. 2025-08-21 doi:10.1101/2025.08.21.671373 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Inhibitory NK receptors regulate the γδ T cell response to malaria ]]> https://biorxiv.org/content/10.1101/2025.08.18.670802v1?rss=1 Olive, M. E. Callaway, P. C. Ilala, M. Levan, J. Acevedo, G. R. Nankya, F. Arinaitwe, E. Rek, J. Jagannathan, P. Dorsey, G. Kamya, M. R. Feeney, M. E. 2025-08-22 doi:10.1101/2025.08.18.670802 Cold Spring Harbor Laboratory Press 2025-08-22 <![CDATA[ Structure-guided engineering of CCL27 enhances natural ligand CAR T-cells against CCR10 for multiple myeloma ]]> https://biorxiv.org/content/10.1101/2025.08.19.670119v1?rss=1 Chilakapati, N. Patino-Escobar, B. Chen, E. Y. Dalal, R. de Montagnac, J. Johnson, H. Kang, A. S. Akagi, N. Ramos, E. Phojanakong, P. Salangsang, F. Zeng, Y. Chari, A. Chung, A. Kumar, A. D. Martin, T. G. Shy, B. R. Steri, V. Karlon, W. J. Kortemme, T. Barwick, B. G. Wiita, A. P. 2025-08-23 doi:10.1101/2025.08.19.670119 Cold Spring Harbor Laboratory Press 2025-08-23 <![CDATA[ PHLDA2 promotes breast cancer metastasis by co-opting a developmental program for placental vascular remodeling ]]> https://biorxiv.org/content/10.1101/2025.08.19.670946v1?rss=1 Halas, P. V. Savage, H. Hachey, S. J. Lev, T. Prem Antony Samy, A. L. Chan, C. Jimenez, S. Domadia, R. M. Lin, I. Mallya, S. Insua-Rodriguez, J. Gonzalez, J. Adam, I. Alshetaiwi, H. Hernandez, G. A. Longworth, A. McMullen, T. P. Kessenbrock, K. Hughes, C. C. Ma, D. Lawson, D. A. 2025-08-23 doi:10.1101/2025.08.19.670946 Cold Spring Harbor Laboratory Press 2025-08-23 <![CDATA[ HP1B and H3K9me3 Regulate Olfactory Receptor Choice and Transcriptional Identity ]]> https://biorxiv.org/content/10.1101/2025.08.21.671605v1?rss=1 Escamilla-del-Arenal, M. Duffie, R. Shayya, H. Loconte, V. Ekman, A. Street, L. A. Horta, A. Canzio, D. Monahan, K. Larabell, C. A. Jovanovic, M. Lomvardas, S. 2025-08-25 doi:10.1101/2025.08.21.671605 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ A fibroblast-centric network drives cold fibrosis in the tumor microenvironment of lung squamous cell carcinoma ]]> https://biorxiv.org/content/10.1101/2025.08.25.668405v1?rss=1 Miyara, S. Frenkel, S. Mayo, A. Gascard, P. Strasser, M. Gibbs, D. Weizman, E. Ben Shalom, I. Stein, Y. Pan, D. Caruso, J. A. Sangwan, V. Bertos, N. Berube, J. Camilleri-Broet, S. Oikonomopoulos, S. Djambazian, H. Umansky, K. B. Elkahal, J. Mayer, S. Fiset, P. O. Adler, M. Tzahor, E. Ragoussis, I. Huang, S. Ferri, L. Tlsty, T. Scherz-Shouval, R. Alon, U. 2025-08-25 doi:10.1101/2025.08.25.668405 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ Integrated ambient modeling and genetic demultiplexing of single-cell RNA+ATAC multiome experiments with Ambimux ]]> https://biorxiv.org/content/10.1101/2025.08.21.671671v1?rss=1 95%) and was able to correctly assign singlets at considerably high ambient fractions (up to 60%) for both RNA and ATAC modalities. In comparison with models that do not consider ambient contamination, these only maintained similar sensitivity levels at considerably lower ambient fractions (up to 25%). We then generated a real data set of seven visceral adipose tissue biopsies run on a single 10x Multiome channel. We ran ambimux and detected 4,986 singlets, capturing similar numbers as other methods. Then, we sought to evaluate the fidelity of the ambient fraction estimates from ambimux. We split singlets into ambient-enriched (>5% contamination in both modalities) or nuclear-enriched (<5% in both) droplets and performed gene-peak linkage analysis. Low ambient droplets resulted in more significant hits with gene-peak links enriched at the transcription start site relative to high ambient droplets, suggesting that the ambient droplets identified by ambimux hamper the identification of biologically meaningful signals. In summary, we developed a joint single-cell multiome demultiplexing method, ambimux, that accurately models and estimates ambient molecule contamination in each modality. ]]> Alvarez, M. Li, T. Lee, S. H. T. Arasu, U. T. Selvarajan, I. Örd, T. Rahmani, E. Chen, Z. J. Avram, O. Kar, A. Kaminska, D. Männistö, V. Halperin, E. Pihlajamäki, J. Luo, C. Kaikkonen, M. U. Zaitlen, N. Pajukanta, P. 2025-08-26 doi:10.1101/2025.08.21.671671 Cold Spring Harbor Laboratory Press 2025-08-26 <![CDATA[ Substitution spectrum and selection at G-quadruplexes in great ape telomere-to-telomere genomes ]]> https://biorxiv.org/content/10.1101/2025.08.24.671323v1?rss=1 Zhang, X. Mohanty, S. K. Chiaromonte, F. Makova, K. 2025-08-27 doi:10.1101/2025.08.24.671323 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Using DNA origami to study nanoscale organization of plasma membranes ]]> https://biorxiv.org/content/10.1101/2025.08.27.672545v1?rss=1 Corradi, E. Shen, K. Karatas, Z. Cercy, M. Schlichthaerle, T. Osouf, M. Vialet, B. Barthelemy, P. Rosendale, M. Radhakrishnan, A. V. Chen, T. Jungmann, R. Gissot, A. Douglas, S. Giannone, G. 2025-08-27 doi:10.1101/2025.08.27.672545 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ DTI versus NODDI White Matter Microstructural Biomarkers of Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2025.08.22.671829v1?rss=1 Liou, K. Thomopoulos, S. I. Yoo, H. Shuai, Y. Chehrzadeh, S. Arani, A. Borowski, B. Reid, R. I. Jack, C. R. Weiner, M. W. Jahanshad, N. Thompson, P. M. Nir, T. M. 2025-08-28 doi:10.1101/2025.08.22.671829 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ Organoid-evaluable clinical biomarkers predict drug responses and guide new breast cancer therapies ]]> https://biorxiv.org/content/10.1101/2025.08.24.671810v1?rss=1 Bui, T. B. V. Wolf, D. M. Bruck, M. C. Moore, K. Lien, J. Choi, S. D. Warhadpande, S. Parizadeh, A. Dillon, D. Overmoyer, B. Lynce, F. I-SPY 2 Investigators, Nijman, I. J. Burgering, B. M. Harris, I. S. Esserman, L. J. Van 't Veer, L. J. Rosenbluth, J. M. 2025-08-28 doi:10.1101/2025.08.24.671810 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ Microtubule Inhibition Triggers MYC-Mediated Immunogenic Cell Death in Breast Cancer ]]> https://biorxiv.org/content/10.1101/2025.08.26.671755v1?rss=1 Aung, J. Liu, R. Peura, A. Hiltunen, A. O. Id, L. J. Savelius, M. Peltonen, M. Turpin, R. J. Salmelin, N. Anttila, J. M. Tervonen, T. A. Suleymanova, I. Nicorici, D. Mutka, M. Mattson, J. Kovanen, P. E. Niinikoski, L. Meretoja, T. Prajapati, B. Goga, A. Munne, P. Pouwels, J. Klefstrom, J. 2025-08-28 doi:10.1101/2025.08.26.671755 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ Long-term dietary interventions fail to mitigate functional connectivity loss and cognitive decline in the TgF344-AD rat model of Alzheimers Disease ]]> https://biorxiv.org/content/10.1101/2025.08.25.672063v1?rss=1 van Rooij, J. R. A. van den Berg, M. Van Vosselen, M. Calus, E. Vasilkovska, T. Kosten, L. Van Spilbeeck, I. Van Audekerke, J. van Dam, D. Bertoglio, D. Adhikari, M. H. Verhoye, M. 2025-08-29 doi:10.1101/2025.08.25.672063 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ Angiopoietin signalling is a central axis of amyloid-driven vascular dysfunction in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.08.25.672093v1?rss=1 Flotho, M. Yang, A. Kern, F. Graf, S. Diks, I. F. Shin, H. Berdnik, D. Agam, M. Channappa, D. Shi, S. Belnap, M. A. Simmons, E. Bradshaw, K. Grandke, F. Bennett, D. A. Buckwalter, M. Keller, A. Wyss-Coray, T. 2025-08-29 doi:10.1101/2025.08.25.672093 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ iPSC-Derived Hepatocytes from Patients with MASLD Exhibit Early Mitochondrial Dysfunction ]]> https://biorxiv.org/content/10.1101/2025.08.27.672733v1?rss=1 Le Guillou, D. Siao, K. Her, C. L. Duwaerts, C. C. Maher, J. J. 2025-08-30 doi:10.1101/2025.08.27.672733 Cold Spring Harbor Laboratory Press 2025-08-30 <![CDATA[ Dynamic neural states underpin bradykinesia severity in Parkinsons disease ]]> https://biorxiv.org/content/10.1101/2025.08.26.672349v1?rss=1 Sharma, A. Sargezeh, B. A. Hahn, A. Shcherbakova, M. Neumann, W. J. Little, S. Starr, P. Oswal, A. 2025-08-31 doi:10.1101/2025.08.26.672349 Cold Spring Harbor Laboratory Press 2025-08-31 <![CDATA[ Cryptic splicing in synaptic and membrane excitability genes links TDP-43 loss to neuronal dysfunction ]]> https://biorxiv.org/content/10.1101/2025.08.28.672801v1?rss=1 Guo, C. Chen, K. Vatsavayai, S. C. Aikyama, T. Zeng, Y. Liu, C. Sianto, O. Yang, E. Bombosch, J. Powell, R. Zhen, S. Mekhoubad, S. Morrie, R. D. Miller, G. Green, E. M. Petrucelli, L. Seeley, W. W. Gitler, A. D. 2025-09-02 doi:10.1101/2025.08.28.672801 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ Atypical developmental remodeling of dopamine neurons involves AKT-GSK3β signaling and glia-mediated axon degeneration ]]> https://biorxiv.org/content/10.1101/2025.08.29.673168v1?rss=1 Zhang, X. Chen, W. Wang, Y. Tu, X. Zhang, X. Davis, R. L. Jan, L. Y. Jan, Y. N. 2025-09-03 doi:10.1101/2025.08.29.673168 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Understanding and imaging PHGDH-driven intrinsic resistance to mutant IDH inhibition in gliomas ]]> https://biorxiv.org/content/10.1101/2025.08.30.673205v1?rss=1 Taglang, C. Batsios, G. Gillespie, A. M. Phillips, J. J. Taylor, J. W. Viswanath, P. 2025-09-04 doi:10.1101/2025.08.30.673205 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Spatiotemporal cellular dynamics of the notochord shape intervertebral disc morphogenesis in the mouse embryo through apoptosis and proliferation ]]> https://biorxiv.org/content/10.1101/2025.09.02.673643v1?rss=1 Warin, J. Balissat, E. Colombier, P. Paillat, L. Dutilleul, M. Camus, A. 2025-09-04 doi:10.1101/2025.09.02.673643 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Spatial Single-Cell Atlas Reveals KSHV-Driven Broad Cellular Reprogramming, Progenitor Expansion, Immune and Vascular Remodeling in Kaposi's Sarcoma ]]> https://biorxiv.org/content/10.1101/2025.09.01.673567v1?rss=1 Meng, W. Das, A. Sinha, H. Naous, R. Bracci, P. McGrath, M. Huang, Y. Gao, S.-J. 2025-09-05 doi:10.1101/2025.09.01.673567 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Incubator-Free Organoid Culture in a Sealed Recirculatory System ]]> https://biorxiv.org/content/10.1101/2025.09.03.673593v1?rss=1 Rosen, Y. Doganyigit, K. Arul, S. Wachtel, E. Ehrlich, D. Venuturimilli, V. Mouzaya, M. Oriaku, S. Ndiforchu, B. Kaurala, G. Hernandez, S. Moarefian, M. Schweiger, H. Cisneros, A. Zeraatkar, M. Geng, J. Mostajo-Radji, M. A. Winkler, E. Haussler, D. Teodorescu, M. 2025-09-05 doi:10.1101/2025.09.03.673593 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Sex differences in the developing human cortex intersect with genetic risk of neurodevelopmental disorders ]]> https://biorxiv.org/content/10.1101/2025.09.04.674293v1?rss=1 Hennick, K. Sui, Y. Karunakaran, D. Nicolella, A. Leonard, R. Meyer-Schuman, R. Berk-Rauch, H. Wang, T. Chakravarti, A. Zoghbi, H. Y. Eichler, E. E. Nowakowski, T. J. 2025-09-05 doi:10.1101/2025.09.04.674293 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ MitoScribe single-cell molecular recorder logs graded signaling dynamics into mitochondrial DNA ]]> https://biorxiv.org/content/10.1101/2025.09.05.674553v1?rss=1 Wang, L. Poulis, N. Srivastava, D. Shipman, S. 2025-09-05 doi:10.1101/2025.09.05.674553 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ BOGO: A Proteome-Wide Gene Overexpression Platform for Discovering Rational Cancer Combination Therapies ]]> https://biorxiv.org/content/10.1101/2025.09.02.673780v1?rss=1 View larger version (56K): org.highwire.dtl.DTLVardef@19d5d7dorg.highwire.dtl.DTLVardef@64f7eborg.highwire.dtl.DTLVardef@d08b75org.highwire.dtl.DTLVardef@173c448_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG Cancer drug resistance remains a major barrier to durable treatment success, often leading to relapse despite advances in precision oncology. While combination therapies are being increasingly investigated, such as chemotherapy with small molecule inhibitors, predicting drug response and identifying rational drug combinations based on resistance mechanisms remain major challenges. Therefore, a proteome-wide, single-gene overexpression screening platform is essential for guiding rational therapy selection. Here, we present BOGO (Bxb1-landing pad human ORFeome-integrated system for a proteome-wide Gene Overexpression), a robust, scalable, and reproducible screening platform that enables single-copy, site-specific integration and overexpression of [~]19,000 human open across cancer cell models. Using BOGO, we identified drug-specific response drivers for 16 chemotherapeutic agents and integrated clinical datasets to uncover proliferation and resistance-associated genes with prognostic potential. Drug response similarity networks revealed both shared and unique mechanisms, highlighting key pathways such as autophagy, apoptosis, and Wnt signaling, and notable resistance-associated genes including BCL2, POLD2, and TRADD. In particular, we proposed a synergistic combination of the BCL2 family inhibitor ABT-263 (Navitoclax(R)) and the DNA analog TAS-102 (Lonsurf(R)), which revealed that lysosomal modulation is a key mechanism driving DNA analog resistance. This combination therapy selectively enhanced cytotoxicity in colorectal and pancreatic cancer cells in vitro, and demonstrated therapeutic benefit in vivo in both cell line-derived xenograft (CDX) and patient-derived xenograft (PDX) models. Together, these findings establish BOGO as a powerful gene overexpression perturbation platform for systematically identifying chemoresistance and chemosensitization drivers, and for discovering rational combination therapies. Its scalability and reproducibility position BOGO as a broadly applicable tool for functional genomics and therapeutic discovery beyond cancer resistance. ]]> Jo, K. B. Alruwaili, M. M. Kim, D.-E. Koh, Y. Kim, H. You, K. Kim, J.-S. Sane, S. Guo, Y. Wright, J. P. Lim, H. J. Naranjo, M. N. Cote, A. G. Roth, F. P. Hill, D. E. Choi, J.-H. Lee, H. Matreyek, K. A. Farh, K. K.- H. Park, J.-E. Kim, H. Bakin, A. V. Kim, D.-K. 2025-09-07 doi:10.1101/2025.09.02.673780 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Targeting p16INK4a reverses alveolar epithelial cell dysfunction and induces lung regeneration in emphysema ]]> https://biorxiv.org/content/10.1101/2025.09.05.674489v1?rss=1 Ribeiro Baptista, B. Toigo, M. Justeau, G. Abou-atmeh, P. De Freitas Castro, T. Zysman, M. Thiebaut De Menonville, C. Audureau, E. Schnyder, K. Wang, H. Hu, Y. Koenigshoff, M. Lanone, S. Chabot, F. Zana-Taieb, E. Jourdan Le Saux, C. Lehmann, M. Derumeaux, G. Boczkowski, J. Gote-Schniering, J. Boyer, L. 2025-09-07 doi:10.1101/2025.09.05.674489 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ De novo design of semisynthetic protein nanopores ]]> https://biorxiv.org/content/10.1101/2025.09.08.674823v1?rss=1 Schnaider, L. Hatstat, A. K. Scott, A. J. Tan, S. K. Hambley, R. G. Dawson, W. M. Griffiths, R. C. Kormos, R. C. Melo, A. A. Tse, E. Polizzi, N. C. Wallace, E. J. Merz, G. E. DeGrado, W. F. 2025-09-08 doi:10.1101/2025.09.08.674823 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ Conserved lipid metabolic reprogramming confers hypoxic and aging resilience ]]> https://biorxiv.org/content/10.1101/2025.09.06.674665v1?rss=1 Jiang, W. I. Vale, G. D. d. Pearce, Q. Kong, K. Zhou, W. McDonald, J. G. Cox, J. E. Singhal, N. S. Ma, D. K. 2025-09-09 doi:10.1101/2025.09.06.674665 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ Redox regulation of neuroinflammatory pathways contributes to damage in Alzheimers disease brain ]]> https://biorxiv.org/content/10.1101/2025.09.08.674963v1?rss=1 Carnevale, L. N. Banerjee, P. Zhang, X. Navarro, J. Raspur, C. K. Nakamura, T. Schahrer, E. Scott, H. Lang, N. Diedrich, J. K. Yates, J. R. Lipton, S. A. 2025-09-09 doi:10.1101/2025.09.08.674963 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ The role of intrinsically disordered domains in regulating G protein coupled receptor signaling ]]> https://biorxiv.org/content/10.1101/2025.09.10.675278v1?rss=1 Xu, J. Qiu, R. Garces, A. M. Hubner, H. Xu, X. Weikert, D. Gmeiner, P. Lerch, M. T. Kobilka, B. 2025-09-11 doi:10.1101/2025.09.10.675278 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals Lactobacillus crispatus accessory genes associated with cervical dysplasia ]]> https://biorxiv.org/content/10.1101/2025.09.11.675634v1?rss=1 Dubin, C. A. Zhao, C. Pollard, K. S. Oskotsky, T. Golob, J. L. Sirota, M. 2025-09-11 doi:10.1101/2025.09.11.675634 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ In situ Proteomics Unveils Specialized Domains for Extrasynaptic Signaling on Neuronal Cilia ]]> https://biorxiv.org/content/10.1101/2025.09.10.675452v1?rss=1 Chang, C.-H. Trinh, V. N. Lokesh, N. R. Montecinos, C. K. Pownall, M. E. Kalocsay, M. Nachury, M. V. 2025-09-12 doi:10.1101/2025.09.10.675452 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ H3N2 influenza virus tropism shifts to glycan receptors on tracheal ciliated cells ]]> https://biorxiv.org/content/10.1101/2025.09.12.675939v1?rss=1 Kikuchi, C. Antonopoulos, A. Wang, S. Biyasheva, A. Chien, Y.-C. Bharat, A. McBride, R. Nycholat, C. M. Thompson, A. J. Dell, A. Khoo, K.-H. Schleimer, R. Haslam, S. M. Paulson, J. C. 2025-09-13 doi:10.1101/2025.09.12.675939 Cold Spring Harbor Laboratory Press 2025-09-13 <![CDATA[ Evaluating the Contribution of Genome 3D Folding to Variation in Human Height Using Machine Learning ]]> https://biorxiv.org/content/10.1101/2025.09.09.675195v1?rss=1 Gu, W. Gilbertson, E. Baranzini, S. E. Salem, R. Capra, J. A. 2025-09-15 doi:10.1101/2025.09.09.675195 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ Anatomical integrity of the human cochlea estimated with optical coherence tomography for future clinical application ]]> https://biorxiv.org/content/10.1101/2025.09.10.675414v1?rss=1 Secchia, P. McHugh, C. I. Cho, N. H. O'Malley, J. T. Zhu, M. Dharmarajan, A. Zosuls, A. Feng, J. J. Cheng, Y. S. Puria, S. Eckhard, A. H. Nakajima, H. H. 2025-09-16 doi:10.1101/2025.09.10.675414 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ The Integrated Cellular and Molecular Landscape of Autoimmunity ]]> https://biorxiv.org/content/10.1101/2025.09.12.675833v1?rss=1 Appierdo, R. Pepe, G. Helmer-Citterich, M. Sirota, M. Vallania, F. Gherardini, P. F. 2025-09-17 doi:10.1101/2025.09.12.675833 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Virtual Reality and Tablet Cognitive Training Improve Attention and Academic Skills Without Dose Effects ]]> https://biorxiv.org/content/10.1101/2025.09.16.676629v1?rss=1 Giannakopoulou, A. Gordon, A. M. Gallen, C. E. Seaman, M. Fedele, D. Anguera, J. A. 2025-09-17 doi:10.1101/2025.09.16.676629 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers ]]> https://biorxiv.org/content/10.1101/2025.09.18.677126v1?rss=1 Eckhardt, B. V. Richter, H. J. Rondeel, I. Renduchintala, K. Mattiroli, F. Ramani, V. 2025-09-18 doi:10.1101/2025.09.18.677126 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Metabolic and transcriptional adaptations to phagocytosis in microglia sustain their functionality and regenerative properties ]]> https://biorxiv.org/content/10.1101/2025.09.18.676800v1?rss=1 Marquez-Ropero, M. Valero, J. Cuesta-Puente, X. Marquez-Galera, A. Pereira-Iglesias, M. Gonzalez-Dominguez, M. Louail, A. Beccari, S. Lopez-Murillo, L. San Juan, A. Arrey, G. Diaz-Aparicio, I. Dubbelaar, M. L. Ribera-Ramos, A. Sarmiento Soto, M. Ruiz, R. Ayerra, L. Vilas-Zornoza, A. Cabrera, D. van Liempd, S. Garcia-Moreno, F. Blomgren, K. Gonzalez-Granero, S. Garcia-Verdugo, J. M. Falcon-Perez, J. M. Aymerich, M. S. Hambardzumyan, D. Casafont, I. Eggen, B. J. L. Venero, J. L. Lopez-Atalaya, J. P. Sierra, A. 2025-09-19 doi:10.1101/2025.09.18.676800 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Single-sequence deep learning delivers crystal-quality models of covalent K-Ras G12 hotspot complexes ]]> https://biorxiv.org/content/10.1101/2025.09.16.676163v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@bcbad5org.highwire.dtl.DTLVardef@8e2baborg.highwire.dtl.DTLVardef@1d507a2org.highwire.dtl.DTLVardef@e851ef_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jung, S. Zheng, Q. Shokat, K. 2025-09-21 doi:10.1101/2025.09.16.676163 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Deep Receptor Scanning Reveals General Sequence Constraints on GPCR Biosynthesis ]]> https://biorxiv.org/content/10.1101/2025.09.19.677468v1?rss=1 Tedman, A. Goel, M. Shah, S. Howard, M. K. Chamness, L. M. Bonifasi, A. Adams, I. Gallagher, J. M. Penn, W. D. Nemec, K. McDonald, E. F. Corman, B. N. Robinson, J. P. Post, C. B. Clark, P. L. Babu, M. M. Manglik, A. Kuntz, C. P. Coyote-Maestas, W. Schlebach, J. P. 2025-09-21 doi:10.1101/2025.09.19.677468 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ An image-based CRISPR screen reveals splicing-mediated control of HP1α condensates ]]> https://biorxiv.org/content/10.1101/2025.09.21.676939v1?rss=1 Wong, M. M.-K. Zhou, S. Carpenter, C. Valbuena, R. Priyadarshini, M. Arya, A. Rizvi, A. Carswell-Crumpton, C. Wileveau, A. Lopez-Lopez, G. Tycko, J. Yao, D. Spees, K. Maynard, J. Bassik, M. C. Goodarzi, H. Sanulli, S. 2025-09-21 doi:10.1101/2025.09.21.676939 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Broad-Spectrum HIV-1 Detection and Neutralization via Multivalent Designer DNA Nanostructures ]]> https://biorxiv.org/content/10.1101/2025.09.21.677611v1?rss=1 Umrao, S. Dwivedy, A. Zheng, M. Anirudhan, V. Parlatan, U. Henrich, T. Cunningham, B. Demirci, U. Wang, X. 2025-09-21 doi:10.1101/2025.09.21.677611 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Bicistronic CAR T-cells Against CD70 & Active Integrin β2 Overcome Antigen Heterogeneity and Preserve Safety in Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/2025.09.21.677627v1?rss=1 Kang, A. S. Johnson, H. Lei, N. Wong, J. Razi, N. Izgutdina, A. Kasap, C. Chilakapati, N. Rivera, J. Phojanakong, P. Serrano, J. A. C. Salangsang, F. Steri, V. Logan, A. C. Eyquem, J. Huang, B. J. Wiita, A. P. 2025-09-21 doi:10.1101/2025.09.21.677627 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Defective proviruses cause T cell reprogramming through promoter exaptation in HIV-1 infection ]]> https://biorxiv.org/content/10.1101/2025.09.22.676989v1?rss=1 Hamann, M. V. Brauckmann, L. Schwarz, C. Spohn, M. Stoeck, R. Leddy, S. Frouard, J. Adiba, M. Thiele, F. Virdi, S. Grundhoff, A. Feschotte, C. Roan, N. R. Tolosa, E. Lange, U. C. 2025-09-22 doi:10.1101/2025.09.22.676989 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ Neuroanatomical Correlates of Negative Symptoms in Schizophrenia ]]> https://biorxiv.org/content/10.1101/2025.09.22.677864v1?rss=1 Kamalakannan, S. M. V. Male, A. G. Yilanli, M. Lella, A. Lee, J. Quide, Y. Green, M. J. Cairns, M. J. Carr, V. J. Catts, S. Henskens, F. A. Jablensky, A. Loughland, C. Michie, P. Mowry, B. Pantelis, C. Shall, U. Scott, R. J. Belger, A. Bustillo, J. Lim, K. Ford, J. M. Mathalon, D. H. Preda, A. Mueller, B. Potkin, S. G. Satterhwaite, T. D. Gur, R. C. Gur, R. E. Banaj, N. Vecchio, D. Piras, F. Piras, F. Ehrlich, S. Bernardoni, F. Borgwardt, S. Cobia, D. Alpert, K. Wang, L. Agartz, I. Jonsson, E. G. Kaiser, S. Clotet, E. P. Salvador, R. Jaramillo, C. L. 2025-09-23 doi:10.1101/2025.09.22.677864 Cold Spring Harbor Laboratory Press 2025-09-23 <![CDATA[ RNAcentral in 2026: Genes and literature integration ]]> https://biorxiv.org/content/10.1101/2025.09.19.677274v1?rss=1 Green, A. F. Ribas, C. E. Jandalala, I. Muston, P. O'Cathail, C. Cochrane, G. Ernst, C. Zhao, L. Madrigal, P. Attrill, H. Marygold, S. Lancet, D. Dobzinski, N. Chan, P. P. Lowe, T. M. Bruford, E. A. Seal, R. L. Hermjakob, H. Panneerselvam, K. Finn, R. D. Gurbich, T. A. Griffiths-Jones, S. Fromm, B. Peterson, K. J. Sordyl, D. Bujnicki, J. M. Velankar, S. Appasamy, S. D. Ganguly, S. Zhang, P. He, S. Rutherford, K. M. Wood, V. Lovering, R. C. Picardi, E. Ontiveros, N. Huang, L. Miao, Z. Petrov, A. S. McCann, H. Cavalleri, E. Mesiti, M. Rivas, E. Szikszai 2025-09-24 doi:10.1101/2025.09.19.677274 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ In vivo genome-wide CRISPR screens in human T cells to enhance T cell therapy for solid tumors ]]> https://biorxiv.org/content/10.1101/2025.09.23.678127v1?rss=1 Liu, Q. Chen, P. A. Urs, E. Zhang, S. Arce, M. Wang, C. Li, Z. Seo, J. Kale, N. LaFlam, T. N. Peng, F. Shifrut, E. Allen, G. Eyquem, J. N. Fuh, K. Dodgson, S. Cyster, J. G. Marson, A. Carnevale, J. 2025-09-24 doi:10.1101/2025.09.23.678127 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ Dissecting Gene Regulatory Networks Governing Human Cortical Cell Fate ]]> https://biorxiv.org/content/10.1101/2025.09.23.678137v1?rss=1 Ding, J. W. Kim, C. N. Ostrowski, M. S. Abeykoon, Y. Pavlovic, B. J. Wallace, J. L. Nowakowski, T. J. Pollen, A. A. 2025-09-24 doi:10.1101/2025.09.23.678137 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ Comparing Neanderthal introgression maps reveals core agreement but substantial heterogeneity ]]> https://biorxiv.org/content/10.1101/2025.09.23.678138v1?rss=1 Chen, Y. Velazquez-Arcelay, K. Capra, J. A. 2025-09-24 doi:10.1101/2025.09.23.678138 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ Identity-stable multi-animal tracking using bidirectional segmentation with object-level memory ]]> https://biorxiv.org/content/10.1101/2025.09.22.677949v1?rss=1 Wang, S. Quine, K. Jordan, A. Dasari, S. Manoli, D. S. Kirst, C. 2025-09-25 doi:10.1101/2025.09.22.677949 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Getting a head start: Craniofacial heterochrony in marsupials involves dynamic changes to molecular and cellular mechanisms underlying neural crest development ]]> https://biorxiv.org/content/10.1101/2025.09.23.678178v1?rss=1 Newton, A. H. Farley, E. R. Major, A. T. Hutchison, J. C. Lawrence, B. M. Sears, K. E. Renfree, M. B. Couzens, A. M. C. Shaw, G. Ord, S. Schneider, R. A. Pask, A. J. 2025-09-25 doi:10.1101/2025.09.23.678178 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Childhood brain tumours instruct cranial haematopoiesis and immunotolerance ]]> https://biorxiv.org/content/10.1101/2025.09.25.678472v1?rss=1 Cooper, E. A. Posner, D. A. Lee, C. Y. C. Hu, L. Bonner, S. Taylor, J. T. Baldwin, O. Jimenez-Guerrero, R. Masih, K. E. Wickham Rahrmann, K. Eigenbrood, J. Ngo, G. Franklin, V. N. R. D'Santos, C. Mair, R. Santarius, T. Craven, C. Jalloh, I. Moreno-Vicente, J. Halim, T. Wang, L. Kriegstein, A. Swartling, F. J. Khan, J. Clatworthy, M. R. Gilbertson, R. J. 2025-09-26 doi:10.1101/2025.09.25.678472 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ Joint Mapping of Chromatin Accessibility and Targeted Proteomics in HER2-expressing Breast Cancer Systems ]]> https://biorxiv.org/content/10.1101/2025.09.25.678463v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@673263org.highwire.dtl.DTLVardef@11d28c5org.highwire.dtl.DTLVardef@15fa336org.highwire.dtl.DTLVardef@1d4426b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Fomitcheva Khartchenko, A. Lam, T. Goldhammer, N. Bont, M. Warhadpande, S. Rosenbluth, J. Herr, A. 2025-09-27 doi:10.1101/2025.09.25.678463 Cold Spring Harbor Laboratory Press 2025-09-27 <![CDATA[ High resolution spatial profiling of the hematopoietic landscape of the murine lung ]]> https://biorxiv.org/content/10.1101/2025.09.25.678618v1?rss=1 Skvir, N. J. Ysasi, A. B. Jarzabek, V. Yeung, A. K. Chen, J. Dries, R. J. Murphy, G. J. 2025-09-27 doi:10.1101/2025.09.25.678618 Cold Spring Harbor Laboratory Press 2025-09-27 <![CDATA[ Daple-FLT3 (CCDC88C-FLT3) gene fusion requires the coiled-coil domain for maximal activation and pericentrosomal localization ]]> https://biorxiv.org/content/10.1101/2025.09.25.678166v1?rss=1 Kao, D. Acquazzino, M. Ibarra, A. Valenzuela, E. Mai, H. Aguilar, K. Stieglitz, E. Ear, J. 2025-09-29 doi:10.1101/2025.09.25.678166 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Perinatal Shifts in Fecal-Derived Metabolites and Associations with Postpartum Depression ]]> https://biorxiv.org/content/10.1101/2025.09.25.678627v1?rss=1 Longoria, K. D. Cassidy, M. L. Lewis, K. A. Garcia, S. R. Franco-Rocha, O. Y. Dube, S. Nguyen, T. C. Flowers, E. Widen, E. M. 2025-09-29 doi:10.1101/2025.09.25.678627 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Hepatic cytochrome P450 endoplasmic reticulum-associated degradation (ERAD): Topological determinants and cellular partnerships that dictate the preferential P450 proteolytic sorting into macroautophagy rather than UPS. ]]> https://biorxiv.org/content/10.1101/2025.09.25.678692v1?rss=1 Hong, X. He, L. Liu, Y. Luo, J. Shu, X. Correia, M. A. 2025-09-29 doi:10.1101/2025.09.25.678692 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ The Integrated Stress Response Pathway Improves Aged Murine Muscle Stem Cell Activation and in vivo Regeneration. ]]> https://biorxiv.org/content/10.1101/2025.09.26.678822v1?rss=1 Brown, A. D. Scaramozza, A. Zhang, H. Mahin, S. Suresh, N. Tsusaka, T. Eliazer, S. Liu, X. Feeley, B. Brack, A. S. 2025-09-29 doi:10.1101/2025.09.26.678822 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Engineering Inducible Cell Fate Transitions by Harnessing Epigenetic Silencing ]]> https://biorxiv.org/content/10.1101/2025.09.29.679324v1?rss=1 Campos, O. A. Migliara, A. Toda, S. Lopez, P. Lim, W. A. Almeida, R. 2025-09-30 doi:10.1101/2025.09.29.679324 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ Accelerated Tempo of Cortical Neurogenesis in Down Syndrome ]]> https://biorxiv.org/content/10.1101/2025.09.29.679346v1?rss=1 Ding, J. W. Kim, C. N. Steyert, M. R. Yuan, A. T. Shin, D. Ivanov, D. Nowakowski, T. J. Pollen, A. A. 2025-09-30 doi:10.1101/2025.09.29.679346 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ Clinical cure of chronic hepatitis B is dependent on activation and perpetuation of robust CD4+ T cell responses ]]> https://biorxiv.org/content/10.1101/2025.09.29.677401v1?rss=1 Jespersen, J. M. Avanesyan, L. Publicover, J. Carey, N. D. Patel, R. K. Edwards, A. W. Stenske, S. Shin, J. Li, J. Simone, M. Chew, N. W. Wong, N. Trilok, S. Erickson, A. Rao, A. Loo, C. P. Stec, M. Anderson, M. Cloherty, G. Sarkar, M. Combes, A. J. Wakil, A. E. Segal, M. R. Fragiadakis, G. K. Cooper, S. Baron, J. L. 2025-10-01 doi:10.1101/2025.09.29.677401 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ A mechanical origin for implantation defects in embryos from aged females ]]> https://biorxiv.org/content/10.1101/2025.09.29.679218v1?rss=1 Cavanaugh, K. E. Franco-Onate, M. Laird, D. J. Oakes, P. W. Alert, R. Weiner, O. D. 2025-10-01 doi:10.1101/2025.09.29.679218 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Single-cell-level digital twins for preterm birth prevention strategies ]]> https://biorxiv.org/content/10.1101/2025.09.29.679252v1?rss=1 Einhaus, J. Neidlinger, P. Fondeur, O. Sato, M. Anronikov, A. Miyazaki, K. Amar, J. N. Ando, K. Badea, V. Gaudilliere, D. K. Sabayev, M. Feyaerts, D. Diop, M. Tsai, A. S. Cambriel, A. Ganio, E. A. Lagarde, R. O'Kelly, E. Stelzer, I. A. Hedou, J. Wong, R. J. Blumenfeld, Y. J. Lyell, D. J. Shaw, G. M. Oskotsky, T. T. Sirota, M. Giudice, L. C. Stevenson, D. K. Aghaeepour, N. Gaudilliere, B. 2025-10-01 doi:10.1101/2025.09.29.679252 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Mechanism of phosphoinositide regulation of lysosomal pH via inhibition of CLC-7 ]]> https://biorxiv.org/content/10.1101/2025.10.01.679551v1?rss=1 Hilton, J. K. Lin, Y. Sefah, E. Deme, J. C. Parker, J. L. Langton, M. J. Grabe, M. Lea, S. M. Newstead, S. Mindell, J. A. 2025-10-02 doi:10.1101/2025.10.01.679551 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ NOVA: a novel R-package enabling multi-parameter analysis and visualization of neural activity in MEA recordings ]]> https://biorxiv.org/content/10.1101/2025.10.01.679841v1?rss=1 Escoubas, C. C. Guney, E. Miravet, A. T. Magee, N. Phua, R. Ruggero, D. Molofsky, A. V. Weiss, W. A. 2025-10-02 doi:10.1101/2025.10.01.679841 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Few-Shot Classification of Cryo-EM Micrographs Using Triplet Loss Embeddings ]]> https://biorxiv.org/content/10.1101/2025.10.01.679860v1?rss=1 Ho, A. Sung, B. Lee, S. Tsai, F. T. F. 2025-10-02 doi:10.1101/2025.10.01.679860 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Cerebellar outputs for rapid directional refinement of forelimb movement ]]> https://biorxiv.org/content/10.1101/2025.10.01.679895v1?rss=1 Thanawalla, A. R. Wilcox, O. Rhee, E. Jiang, J. Huang, K. W. Yusufi, R. Saklaway, D. Nagamori, A. Conner, J. M. Chen, A. I. Azim, E. 2025-10-02 doi:10.1101/2025.10.01.679895 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Directed evolution of a stem-helix targeting antibody enables MERS-CoV cross-neutralization through enhanced binding affinity ]]> https://biorxiv.org/content/10.1101/2025.10.02.680065v1?rss=1 Zhou, P. Yuan, M. Zhang, Y. Limbo, O. Song, G. Zhao, F. Liu, H. He, W.-t. Capozzola, T. Callaghan, S. Avillion, G. Li, X. Beutler, N. Yong, P. Anzanello, F. Rogers, T. F. Burton, D. R. Jardine, J. G. Wilson, I. A. Andrabi, R. 2025-10-02 doi:10.1101/2025.10.02.680065 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency ]]> https://biorxiv.org/content/10.1101/2025.10.02.679816v1?rss=1 Nocente, M. C. Della Rosa, M. Malcom, A. A. Lister, G. Savin, I. Ray-Jones, H. Elderkin, S. Tian, R. Andrews, S. Bendall, A. Semprich, C. I. Kampmann, M. Malysheva, V. Rostovskaya, M. Rugg-Gunn, P. Spivakov, M. 2025-10-03 doi:10.1101/2025.10.02.679816 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Lineage Tracing Reveals a Shared Cellular Origin for Supraclavicular Brown and Inguinal Beige Adipocytes ]]> https://biorxiv.org/content/10.1101/2025.10.02.680118v1?rss=1 Ran, Y. Zhang, K. Shen, Y.-T. Mo, Q. Wang, Z. Yalamanchili, H. K. John, S. Kogiso, M. Gao, X. Wang, C. Sinha, T. Black, B. Chen, M.-H. 2025-10-03 doi:10.1101/2025.10.02.680118 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Minor Cannabinoids CBD, CBG, CBN and CBC differentially modulate sensory neuron activation ]]> https://biorxiv.org/content/10.1101/2025.10.02.680148v1?rss=1 Rabl, K. Gruenke, L. Banfal, A. Eilers, H. Hellman, J. Schumacher, M. A. 2025-10-03 doi:10.1101/2025.10.02.680148 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ S1P induces bleb-based T cell motility via S1PR1-dependent activation of RhoA and WNK1 ]]> https://biorxiv.org/content/10.1101/2025.10.03.680076v1?rss=1 Staback Rodriguez, F. De Belly, H. Zhang, Y. Strickland, E. Frazer, G. L. Ojukwu, J. Williamson, B. J. Weiner, O. D. Burkhardt, J. K. 2025-10-04 doi:10.1101/2025.10.03.680076 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ Macrophage phagocytosis of Coccidioides promotes its differentiation into the parasitic form ]]> https://biorxiv.org/content/10.1101/2025.10.05.680493v1?rss=1 Symington, J. Dabholkar, A. English, B. Voorhies, M. Sil, A. 2025-10-05 doi:10.1101/2025.10.05.680493 Cold Spring Harbor Laboratory Press 2025-10-05 <![CDATA[ Multi-immersion Oblique Plane Microscope (miOPM): A reconfigurable platform for high-resolution Light-Sheet Fluorescence Microscopy. ]]> https://biorxiv.org/content/10.1101/2025.10.04.680473v1?rss=1 Chen, B. Millett-Sikking, A. Galecki, S. Daetwyler, S. Jiou, J. Monistrol, J. Shen, Q. Zhou, F. Y. Lin, H.-Y. Jenkins, E. Stein, M. Marlar-Pavey, M. Sturm, G. Y. Li, A. Tang, Q. Feng, B. Diaz, U. Chen, Y. Shalizi, A. Gillich, A. Friedman, J. R. Tomer, R. R. Chang, B.-J. Marshall, W. Shahmoradian, S. Dean, K. M. Fiolka, R. P. 2025-10-06 doi:10.1101/2025.10.04.680473 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Site-specific genome engineering of primary human natural killer cells for programmable anti-tumor function ]]> https://biorxiv.org/content/10.1101/2025.10.05.680386v1?rss=1 Allain, V. Rothrock, A. G. Bernard, P.-L. Nyberg, W. A. Talbot, A. Muldoon, J. J. Chung, J.-Y. To, A. Chang, C. R. Kimmerly, G. R. Liu, C. Tsao, T. Mortazavi, Y. Seo, J. Li, Z. Shemesh, A. Schmidt, R. Ward, C. C. Marson, A. Lanier, L. L. Aguilar, O. A. Eyquem, J. 2025-10-06 doi:10.1101/2025.10.05.680386 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Base-editing a single missense mutation in A20 enhances CAR-T cell efficacy ]]> https://biorxiv.org/content/10.1101/2025.10.05.680562v1?rss=1 Blaisdell, A. Bachl, S. Sandoval, L. R. Ching, C. Bowman, C. J. Kale, N. Prabandham, M. Diolaiti, M. Havig, C. Advincula, R. Lenci, N. Li, Z. Yamashita, E. Wang, C. H. Zhang, S. Liu, Q. Achacoso, P. Stibor, D. Oynebraten, I. Seo, J. Ashworth, A. Marson, A. Ye, C. J. Malynn, B. A. Eyquem, J. Carnevale, J. Ma, A. 2025-10-06 doi:10.1101/2025.10.05.680562 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ A Dual Inhibitory Network in the Thalamic Reticular Nucleus Delineated by Pallidal and Intra-Reticular Inhibition ]]> https://biorxiv.org/content/10.1101/2025.10.05.680571v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@19035b0org.highwire.dtl.DTLVardef@b4f323org.highwire.dtl.DTLVardef@1c68d8eorg.highwire.dtl.DTLVardef@777c15_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cho, F. S. Huguenard, J. R. Paz, J. T. 2025-10-06 doi:10.1101/2025.10.05.680571 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Consistent Induction of Broadly Neutralizing HIV Antibodies by a Novel Two-Step Mechanism Informs Immunogen Design ]]> https://biorxiv.org/content/10.1101/2025.10.06.680687v1?rss=1 Skelly, A. N. Gristick, H. B. Li, H. Gavor, E. Connell, A. J. Kreider, E. F. Marchitto, L. Hogarty, M. P. Newby, M. L. Allen, J. D. Liu, W. West, A. P. Ayyanathan, K. Campion, M. S. Winters, K. Gordon, C. G. Osbaldeston, R. A. Akeley, M. J. Li, Y. Singh, A. Cruickshank, K. Park, Y. Zhao, C. Li, X. Amereh, K. Van Itallie, E. Carey, J. W. Albertus, A. DeLaitsch, A. T. Keeffe, J. R. Lituchy, M. G. Walsh, A. A. Morris, D. J. Habib, R. Bibollet-Ruche, F. Mishra, N. Avillion, G. Koranda, N. S. Plante, S. J. Martella, C. L. Lora, J. Wang, E. J. D. Lewis, M. G 2025-10-06 doi:10.1101/2025.10.06.680687 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Impaired IFNγ responsiveness of lung monocyte-derived cells limits immunity to Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2025.10.06.680719v1?rss=1 Zheng, W. Limberis, J. D. Howard, Z. P. Mohapatra, A. Takagi, E. Ernst, J. D. 2025-10-06 doi:10.1101/2025.10.06.680719 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Bayesian multi-state multi-condition modeling of a protein structure based on X-ray crystallography data ]]> https://biorxiv.org/content/10.1101/2025.10.07.680994v1?rss=1 Hancock, M. HOLTON, J. M. Fraser, J. S. Adams, P. D. Sali, A. 2025-10-07 doi:10.1101/2025.10.07.680994 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Macrodomain ADP-ribose binding but not ADP-ribosylhydrolase activity is critical for chikungunya virus infection of Aedes mosquitoes ]]> https://biorxiv.org/content/10.1101/2025.10.09.681498v1?rss=1 Bardossy, E. S. Bergmann, L. Lacritick, A. H. Nigg, J. Correy, G. J. Ashworth, A. Fraser, J. S. Saleh, M. C. 2025-10-09 doi:10.1101/2025.10.09.681498 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ Ex Vivo Expanded Regulatory T Cells Inhibit AAA Progression by Limiting CD4+ and CD8+ T Cell Accumulation in Aortic Tissue ]]> https://biorxiv.org/content/10.1101/2025.10.08.681290v1?rss=1 Dasari, C. Lopez, J. L. Shawyan Jan, M. Shaligram, S. Lin, P.-Y. Levy-Lambert, D. Huang, A. G. Lizama Valenzuela, C. Hadley, P. Tang, Q. Oskowitz, A. 2025-10-10 doi:10.1101/2025.10.08.681290 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ Metabolic Alterations driven by PFKFB3 upregulation confer Resistance to Trastuzumab in HER2-Positive Breast Cancer. ]]> https://biorxiv.org/content/10.1101/2025.10.09.681343v1?rss=1 Vincken, R. Pasco, S. T. Steri, V. Bozal-Basterra, L. van Ijcken, W. F. J. Carracedo, A. Huylebroeck, D. Moasser, M. M. Ruiz-Saenz, A. 2025-10-10 doi:10.1101/2025.10.09.681343 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ Sensorimotor Theta Oscillations Coordinate Speech Movements ]]> https://biorxiv.org/content/10.1101/2025.10.09.681482v1?rss=1 Norman, Y. Frank, L. M. Chang, E. F. 2025-10-10 doi:10.1101/2025.10.09.681482 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ IGF2BP3 remodels the microRNA targeting landscape in MLL-AF4 leukemia ]]> https://biorxiv.org/content/10.1101/2025.10.10.681741v1?rss=1 Kabbani, L. E. Kapoor, S. Sharma, G. E. Gutierrez, M. Neeb, Z. T. Jaiswal, A. Ritter, A. J. Katzman, S. Feldman, J. E. Rao, D. S. Sanford, J. S. 2025-10-13 doi:10.1101/2025.10.10.681741 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Transcriptional regulation of disease-relevant microglial activation programs ]]> https://biorxiv.org/content/10.1101/2025.10.12.681832v1?rss=1 McQuade, A. Mishra, R. Hagan, V. Liang, W. Colias, P. Castillo, V. C. Lubin, J. Haage, V. Marshe, V. Fujita, M. Gomes, L. Ta, T. Teter, O. Chasins, S. E. De Jager, P. L. Nunez, J. K. Kampmann, M. 2025-10-13 doi:10.1101/2025.10.12.681832 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Discovery of AVI-6451, a Potent and Selective Inhibitor of the SARS-CoV-2 ADP-Ribosylhydrolase Mac1 with Oral Efficacy in vivo ]]> https://biorxiv.org/content/10.1101/2025.10.11.681833v1?rss=1 Jaishankar, P. Correy, G. J. Matsui, Y. Togo, T. Rachman, M. M. Stevens, M. G. V. Hantz, E. R. Zheng, J. Diolaiti, M. E. Montano, M. Taha, T. Y. Rosecrans, J. Pampel, J. Krogan, N. J. Shoichet, B. K. Ashworth, A. Ott, M. Fraser, J. S. Renslo, A. R. 2025-10-14 doi:10.1101/2025.10.11.681833 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ CNPY4 is a Lipid-Binding Regulator of Sphingolipid Homeostasis ]]> https://biorxiv.org/content/10.1101/2025.10.13.682155v1?rss=1 Paul, M. D. Zbodakova, O. Glenn, I. S. Stotland, A. Klein, O. D. Jura, N. 2025-10-14 doi:10.1101/2025.10.13.682155 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Single-cell transcriptomic profiling of bam mutant tumor reveals germline heterogeneity and gcrf1 as a modulator in Drosophila germ cells ]]> https://biorxiv.org/content/10.1101/2025.10.14.682265v1?rss=1 Sun, Z. Zeng, Y. Nystul, T. G. Zhong, G. 2025-10-15 doi:10.1101/2025.10.14.682265 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ New proteomic biomarkers identified in plasma extracellular vesicles in sarcoidosis: a case-control matched study ]]> https://biorxiv.org/content/10.1101/2025.10.14.682425v1?rss=1 0.75. Of these, the AUC was > 0.90 for 13 proteins. 62 differentially expressed EV proteins strongly correlated with 20 clinical variables of severity, chest X-ray findings, and/or laboratory results. Functional annotation and network analysis suggest that these differentially expressed proteins regulate endocytosis, host responses to external stimuli, and transcription processes. Moreover, the top three ranked pathways were clathrin-mediated endocytosis, Hsp90 chaperone cycle, and spliceosome. CONCLUSIONS. This study demonstrates that plasma EV proteins can serve as biomarkers of various clinical phenotypes of the disease. At a Glance CommentaryCurrent Scientific Knowledge on the Subject: Sarcoidosis is a heterogeneous condition affecting multiple organs. The role of blood extracellular vesicles in the diagnosis and pathogenesis of this condition remains unknown. What This Study Adds to the Field: We identified differentially expressed proteins in plasma EVs by combining proteomics and machine learning algorithms. Top-ranked proteins can serve as diagnostic biomarkers and potential mechanisms for the development of sarcoidosis. ]]> Xi, N. M. Gabby, L. Zhao, R. Vanarsa, K. Qiao, M. Zhang, D. Zhang, J. Mohan, C. Judson, M. A. Koth, L. L. JI, H. 2025-10-16 doi:10.1101/2025.10.14.682425 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ Fine-Tuning Protein Language Models on Human Spatial Constraint Yields State-of-the-Art Variant Effect Prediction ]]> https://biorxiv.org/content/10.1101/2025.10.15.682722v1?rss=1 Bajracharya, G. Capra, J. A. 2025-10-16 doi:10.1101/2025.10.15.682722 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ In silico reconstruction of primary and metastatic tumor architecture using GIS-augmented spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.10.16.682879v1?rss=1 Yoo, J. Y. Akter, S. Zuo, Q. Kazemi, A. Wu, W. Goel, M. Lam, A. Dutta, D. Barnick, B. Pekmezci, M. Grosse Perdekamp, M. Soliman, A. Madak-Erdogan, Z. 2025-10-17 doi:10.1101/2025.10.16.682879 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Antibody Reveals Conformational Latch Controlling Herpesvirus Proteases ]]> https://biorxiv.org/content/10.1101/2025.10.17.683123v1?rss=1 Zimanyi, M. Hulce, K. R. Bohn, M. F. Norman, J. Rohweder, P. J. Cheng, Y. Craik, C. 2025-10-17 doi:10.1101/2025.10.17.683123 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ All-atom protein design via SE(3) flow matching with ProteinZen ]]> https://biorxiv.org/content/10.1101/2025.10.18.683228v1?rss=1 Li, A. J. Kortemme, T. 2025-10-18 doi:10.1101/2025.10.18.683228 Cold Spring Harbor Laboratory Press 2025-10-18 <![CDATA[ The neural basis of emotional generalization in empathy ]]> https://biorxiv.org/content/10.1101/2025.10.18.683207v1?rss=1 Hayden, B. Allawalla, A. Adkinson, J. Fan, X. Franch, M. Gates, V. Mathura, R. Pascuzzi, B. Mocchi, M. Myers, J. Pulapaka, S. Banks, G. Bartoli, E. Goodman, W. Mathew, S. Pitkow, X. Pouratian, N. Provenza, N. Shofty, B. Watrous, A. Bijanki, K. Sheth, S. Yoo, S. B. M. 2025-10-19 doi:10.1101/2025.10.18.683207 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ ANTIPODE Provides a Global View of Cell Type Homology and Transcriptomic Divergence in the Developing Mammalian Brain ]]> https://biorxiv.org/content/10.1101/2025.10.18.683238v1?rss=1 Schmitz, M. T. Ding, J. W. Nolbrant, S. McMullen, R. Kim, C. N. Pavlovic, B. J. Nowakowski, T. J. Bakken, T. E. Ye, C. J. Pollen, A. A. 2025-10-19 doi:10.1101/2025.10.18.683238 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ Autoregulation of the MET Receptor Tyrosine Kinase by its Intracellular Juxtamembrane Domain ]]> https://biorxiv.org/content/10.1101/2025.10.19.683305v1?rss=1 Linossi, E. M. Espinoza, C. A. Estevam, G. O. Fraser, J. S. Jura, N. 2025-10-19 doi:10.1101/2025.10.19.683305 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ Self-supervised learning enables robust microbiome predictions in data-limited and cross-cohort settings ]]> https://biorxiv.org/content/10.1101/2025.10.19.683269v1?rss=1 Zahavi, L. Levine, Z. Godneva, A. Dubinkina, V. Dhir, R. Pollard, K. S. Weinberger, A. Segal, E. 2025-10-20 doi:10.1101/2025.10.19.683269 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Oncogenic and immunomodulatory functions of SUV420H1 in HPV-negative head and neck squamous cell carcinoma. ]]> https://biorxiv.org/content/10.1101/2025.10.20.683419v1?rss=1 Moshiri, A. Luff, M. Kim, S. Jiang, M. Dar, M. S. Patel, M. McKinnon, K. Edmondson, E. Akhtar, J. Cheng, H. Saloura, V. 2025-10-20 doi:10.1101/2025.10.20.683419 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ mRNA delivery of genetically encoded mosaic-8 pan-sarbecovirus RBD vaccines ]]> https://biorxiv.org/content/10.1101/2025.10.21.683747v1?rss=1 Cohen, A. A. Keeffe, J. R. Manasyan, L. Madireddy, I. Fils, A.-C. I. P. Dam, K.-M. A. Stober, H. E. Hills, R. A. Moon, W. J. Lin, P. J. C. Howarth, M. R. Hoffmann, M. A. G. Bjorkman, P. J. 2025-10-22 doi:10.1101/2025.10.21.683747 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ ADAPT-M: A workflow for rapid, quantitative in vitro measurements of enriched protein libraries ]]> https://biorxiv.org/content/10.1101/2025.10.21.683815v1?rss=1 Perez, C. P. DelRosso, N. V. Noland, C. L. Parekh, U. Choe, C. A. Eguchi, R. R. Wen, Q. Fordyce, P. M. Huang, P. 2025-10-22 doi:10.1101/2025.10.21.683815 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Reverse transcribed ssDNA derepresses translation of a retron antiviral protein ]]> https://biorxiv.org/content/10.1101/2025.10.22.683967v1?rss=1 Zhang, K. Rojas-Montero, M. Poola, D. Klas, J. Carabias, A. Zhang, D. Mestre, M. R. Zhao, R. Davila-Hidalgo, A. Montoya, G. Pinilla-Redondo, R. Gonzalez-Delgado, A. Shipman, S. L. 2025-10-22 doi:10.1101/2025.10.22.683967 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Germline-targeting HIV immunogen induces cross-neutralizing antibodies in outbred macaques ]]> https://biorxiv.org/content/10.1101/2025.10.22.684023v1?rss=1 Mishra, N. Liang, B. Roark, R. S. Ghosh, A. Callaghan, S. Lee, W.-H. Li, X. Vo, A. L. Avillion, G. Habib, R. H. Bibollet-Ruche, F. Giese, G. Somanathan, A. Chowdhury, R. R. Oberoi, P. Amereh, K. Zhu, Y. Zhang, Y. Kassab, M. Tjio, L. Andrabi, S. Reyes, R. A. Allen, J. D. James, N. E. Randall, K. N. van der Maas, L. Ben-Akiva, E. Kaczmarek-Michaels, K. plante, S. Martella, C. L. Skelly, A. N. Singh, A. Hurtado, J. Dueker, K. Capozzola, T. Nedellec, R. Ozorowski, G. Lewis, M. Falcone, S. Carfi, A. Himansu, S. Shapiro, L. Crispin, M. Hahn, B. H. Briney, 2025-10-23 doi:10.1101/2025.10.22.684023 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Coupling differential adhesion to cell signaling avoids kinetic traps to yield robust multicellular self-organization ]]> https://biorxiv.org/content/10.1101/2025.10.23.684104v1?rss=1 Pelc, G. McKeithan, W. L. Guo, Y. Brenner, M. P. Lim, W. A. Nitzan, M. 2025-10-24 doi:10.1101/2025.10.23.684104 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ STING activation reshapes the tumor microenvironment leading to tumor regression in osteosarcoma ]]> https://biorxiv.org/content/10.1101/2025.10.24.684275v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@15b1e5corg.highwire.dtl.DTLVardef@12650aaorg.highwire.dtl.DTLVardef@79ef71org.highwire.dtl.DTLVardef@15704c9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Young, E. P. Johnson, C. A. Lee, A. G. Morris, D. Tsui, J. Breese, M. R. Camara Serrano, J. A. Schott, C. R. Abram, C. L. Leung, S. G. Sayles, L. C. Pettiwala, A. M. Gutierrez Vera, V. S. Lowell, C. A. Combes, A. J. McEachron, T. A. Sweet-Cordero, E. A. 2025-10-25 doi:10.1101/2025.10.24.684275 Cold Spring Harbor Laboratory Press 2025-10-25 <![CDATA[ Structure-guided design of native-like HIV Env Single Chain Trimers for enhanced stability, immunogenicity, and versatile vaccine delivery ]]> https://biorxiv.org/content/10.1101/2025.10.25.684215v1?rss=1 Li, X. Krishnamurthy, I. Mishra, N. James, N. E. Roy Chowdhury, R. Callaghan, S. Somanathan, A. Avillion, G. Amereh, K. Sekar, T. Oberoi, P. Zhu, Y. Torres, J. L. Lee, W.-H. Allen, J. D. Liang, B. Giese, G. Vo, A. L. Andrabi, S. Jain, I. Mergiya, A. Capozzola, T. He, W.-t. Anzanello, F. Habib, R. Bibollet-Ruche, F. Nedellec, R. Duttonsackett, S. Ozorowski, G. Burton, D. R. Hahn, B. H. Shaw, G. M. Ward, A. B. Crispin, M. Barnes, C. O. Andrabi, R. 2025-10-26 doi:10.1101/2025.10.25.684215 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ A20 restriction of nitric oxide production restores macrophage bioenergetic balance ]]> https://biorxiv.org/content/10.1101/2025.10.26.684676v1?rss=1 Ma, A. Chan, M.-P. Advincula, R. Achacoso, P. Grossman, E. Nomura, D. Malynn, B. 2025-10-27 doi:10.1101/2025.10.26.684676 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Mutating different α-tubulin acetylation sites has distinct effects on axon terminal morphogenesis in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2025.10.27.684845v1?rss=1 Than, H. Welch, C. J. Schauer, E. Trujillo, S. P. Wildonger, J. 2025-10-27 doi:10.1101/2025.10.27.684845 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Development and validation of an ultra-low-cost, open source normothermic ex vivo organ perfusion platform ]]> https://biorxiv.org/content/10.1101/2025.10.27.684886v1?rss=1 Yang, H. Higgins, N. Chu, S. Lee, J. Meyer, N. R. Hansen, K. Saeed, M. Ferreira, R. Sorrentino, T. A. Mena, J. Suarez, P. Maluf, F. C. Sui, W. Escobar, M. C. Mann, U. Braun, H. Du, J. Elmer, J. R. Chi, T. L. Roy, S. Flake, A. Gardner, J. M. Stoller, M. 2025-10-28 doi:10.1101/2025.10.27.684886 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ Macrophage EHD1 promotes inflammation and stabilizes sortilin to accelerate atherosclerosis ]]> https://biorxiv.org/content/10.1101/2025.10.27.684958v1?rss=1 Cai, B. Ma, F. Liu, Y. Xu, Y. Liu, W. Gupta, N. Zhu, Y. Xiao, L. Traylor, J. Rom, O. Kovacic, J. Fidler, T. Yurdagul, A. Orr, A. W. Huang, X. 2025-10-28 doi:10.1101/2025.10.27.684958 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ Repeated evolutionary turnover of vertebrate skeletal muscle myosins ]]> https://biorxiv.org/content/10.1101/2025.10.28.684953v1?rss=1 Harvey, C. M. Schuppe, E. R. Brainard, M. S. Fuxjager, M. J. Pease, J. B. 2025-10-28 doi:10.1101/2025.10.28.684953 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ Hippo signaling differentially regulates distal progenitor subpopulations and their transitional states to construct the mammalian lungs ]]> https://biorxiv.org/content/10.1101/2025.10.28.684989v1?rss=1 Zhang, K. Basak, M. Zaher, Y. Yao, E. Wang, S.-A. Aung, T. Chuang, P.-T. 2025-10-28 doi:10.1101/2025.10.28.684989 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ A proteomic signature of vascular dysfunction linked to tauopathy and degeneration in the aging brain ]]> https://biorxiv.org/content/10.1101/2025.10.27.684881v1?rss=1 Radabaugh, H. L. Keller, J. N. Radtke, C. H. Kunney, C. Karvelas, N. Chan, H. W. Brathaban, N. Meyer-Franke, A. Casaletto, K. Zetterberg, H. Miller, B. L. Cruchaga, C. Kramer, J. Akassoglou, K. Ferguson, A. R. Elahi, F. M. 2025-10-29 doi:10.1101/2025.10.27.684881 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ Pitavastatin counteracts venetoclax resistance mechanisms in acute myeloid leukemia ]]> https://biorxiv.org/content/10.1101/2025.10.27.684888v1?rss=1 Fruman, D. Buono, R. Juarez, D. Paul, M. Skuli, S. J. Wong, I. B. Tarnekar, I. Ying, Z. Le, I. Wertheim, G. Bakayoko, A. Kruidenier, M. Sebti, S. Konopleva, M. Fleischman, A. G. Jang, C. Carroll, M. 2025-10-29 doi:10.1101/2025.10.27.684888 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ Acetylation of Axonal G3BP1 through ELP3 Accelerates Axon Regeneration ]]> https://biorxiv.org/content/10.1101/2025.10.28.685144v1?rss=1 Dalla Costa, I. Michenfelder, E. Siciliano, S. Tapita, A. Buchanan, C. N. Vaughn, L. S. Lee, J. Oses-Prieto, J. A. Ma, C. Thames, E. Samra, N. Ben-Dor, S. Haffner-Krausz, R. McElveen, M. Smith, T. P. Nawar, N. Manaswiyoungkul, P. Gunning, P. T. Fainzilber, M. Burlingame, A. Zhu, H. Perlson, E. Sahoo, P. K. Twiss, J. L. 2025-10-30 doi:10.1101/2025.10.28.685144 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Plasmodium falciparum exploits NUAK1 to establish infection in human erythrocytes ]]> https://biorxiv.org/content/10.1101/2025.10.30.685469v1?rss=1 Navarrete, D. J. Kim, C. Y. McLelland, K. Gonzalez Ramirez, M. Baro, B. Salinas, N. D. Tolia, N. H. Doerig, C. Ong, S.-E. Golkowski, M. G. Egan, E. S. 2025-10-30 doi:10.1101/2025.10.30.685469 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Engineered orthogonal translation systems from metagenomic libraries expand the genetic code ]]> https://biorxiv.org/content/10.1101/2025.10.30.685624v1?rss=1 200 tRNAs, test >1,250 combinations of aaRS:tRNA pairs, and identify the AP1 TrpRS:tRNATrpUCA as an orthogonal pair that natively encodes tryptophan at the UGA codon. We demonstrate that the AP1 TrpRS:tRNATrpUCA is highly active in cell-free and cellular contexts. We then use Ochre, a genomically recoded Escherichia coli strain that lacks UAG and UGA codons, to engineer an AP1 TrpRS variant capable of 5-hydroxytryptophan incorporation at an open UGA codon. We anticipate that our strategy of integrating metagenomic bioprospecting with cell-free screening and cell-based engineering will accelerate the discovery and optimization of orthogonal translation systems for genetic code expansion. ]]> Seki, K. Nguyen, M. T. A. Penev, P. I. Isaacs, F. J. Banfield, J. F. Jewett, M. C. 2025-10-30 doi:10.1101/2025.10.30.685624 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ PCSK9 and High-Fat Diet Synergistically Induce Neurovascular Dysfunction and Neuroinflammation ]]> https://biorxiv.org/content/10.1101/2025.10.29.685380v1?rss=1 Zhang, M. Letian, A. Mohl, G. A. Kroke, B. Arkelius, K. Clelland, C. D. Goldberg, E. L. Singhal, N. S. 2025-10-31 doi:10.1101/2025.10.29.685380 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Cohesin Acetylation and ATPase Activity Control Cohesion and Loop Architecture through Distinct Mechanisms ]]> https://biorxiv.org/content/10.1101/2025.10.30.685539v1?rss=1 Costantino, L. Ye, T. Boardman, K. Xiang, S. Luo, J. Mu, Y. Ma, W. Koshland, D. 2025-10-31 doi:10.1101/2025.10.30.685539 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Single-cell, multi-region profiling of the macaque brain across the lifespan ]]> https://biorxiv.org/content/10.1101/2025.10.31.685880v1?rss=1 Yang, W. Watkins, K. L. DeCasien, A. R. O'Neill, M. B. Bohlen, M. O. O'Day, D. R. Duran, M. Qiu, C. Meleshko, A. Vo, A. Menke, M. Calderon, D. Cayo Biobank Research Unit, Sallet, J. Higham, J. P. Martinez, M. I. Trapnell, C. Starita, L. M. Montague, M. J. Platt, M. Chiou, K. L. Shendure, J. Snyder-Mackler, N. 2025-11-01 doi:10.1101/2025.10.31.685880 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ Structural Mechanism of Prestin-Membrane Mechanotransduction ]]> https://biorxiv.org/content/10.1101/2025.10.31.685930v1?rss=1 Bavi, N. Haller, P. Homma, K. Lin, X. Milewski, W. Zhao, M. Sosnick, T. Perozo, E. 2025-11-01 doi:10.1101/2025.10.31.685930 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ TOMM40 suppression promotes neuronal cholesterol imbalance and molecular and behavioral phenotypes of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.10.31.685963v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@e3e3e2org.highwire.dtl.DTLVardef@1861f67org.highwire.dtl.DTLVardef@77a813org.highwire.dtl.DTLVardef@1bb9a83_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yang, N. V. Wang, S. Li, B. Simms, J. Dinh, L. Huang, A. Oei, J. H. Yassine, H. N. Krauss, R. M. 2025-11-01 doi:10.1101/2025.10.31.685963 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ Rapid generation of ventral A9-like dopaminergic neurons from patterned iPSCs ]]> https://biorxiv.org/content/10.1101/2025.10.31.685897v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@1d83eb3org.highwire.dtl.DTLVardef@1fc7fa5org.highwire.dtl.DTLVardef@2033e3org.highwire.dtl.DTLVardef@2e8fa3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chaplot, K. Zhang, L. Wessman, J. Rivera, M. Wang, Z. Wang, F. Duan, X. England, P. M. Clark, I. C. Ullian, E. M. 2025-11-02 doi:10.1101/2025.10.31.685897 Cold Spring Harbor Laboratory Press 2025-11-02 <![CDATA[ Spatial Attention and Session Day Independently Modulate Human Visual Cortical Plasticity ]]> https://biorxiv.org/content/10.1101/2025.10.31.685945v1?rss=1 Limon, P. N. Norcia, A. M. Ash, R. T. 2025-11-03 doi:10.1101/2025.10.31.685945 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Epigenetic control of microglial developmental milestones from proliferative progenitors to efficient phagocytes ]]> https://biorxiv.org/content/10.1101/2025.11.03.685577v1?rss=1 Pereira-Iglesias, M. Martinson, D. Falco, C. Maldonado-Teixido, J. Gonzalez-Rodriguez, M. Senovilla-Ganzo, R. Benito, E. Beccari, S. Valero, J. Mora-Romero, B. Ballasch, I. Viguier, S. Haene, P. Boettiger, M. Reisz, J. A. Manso, Y. Parkkinen, L. Aransay, A. M. Soria, F. N. D'Alessandro, A. Soriano, E. Thion, M. Garel, S. Greter, M. Giralt, A. Pascual, A. Garcia-Moreno, F. Menassa, D. A. Carrillo, J. A. Sierra, A. 2025-11-04 doi:10.1101/2025.11.03.685577 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ NINJ1 is activated by Mycobacterium tuberculosis ESX-1 secreted effector EsxA and mediates necrosis of infected human macrophages ]]> https://biorxiv.org/content/10.1101/2025.11.04.685750v1?rss=1 Saetra, R. S. R. Hansen, M. Kappelhoff, S. Bugge, M. Marstad, A. Ryan, L. Devant, P. Kagan, J. C. Freude, K. K. Beckwith, K. S. FLO, T. H. 2025-11-04 doi:10.1101/2025.11.04.685750 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ A role for the Stentor syntaxin protein in post-wound cell survival ]]> https://biorxiv.org/content/10.1101/2025.11.04.686591v1?rss=1 Nadkarni, A. V. Diaz, U. Zhang, K. F. Tang, S. K. Y. Marshall, W. F. 2025-11-05 doi:10.1101/2025.11.04.686591 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Large-scale discovery of neural enhancers for cis-regulation therapies ]]> https://biorxiv.org/content/10.1101/2025.11.04.686611v1?rss=1 McDiarmid, T. A. Page, N. F. Chardon, F. M. Daza, R. M. Chen, G. T. Kosicki, M. James, L. M. Nourie, H. C. Laboy-Cintron, D. Lee, A. S. Vij, P. Calderon, D. Lalanne, J.-B. Martin, B. K. Fink, K. Talkowski, M. E. Muotri, A. R. Philpot, B. D. Pennacchio, L. A. Geschwind, D. H. Sanders, S. J. Ahituv, N. Shendure, J. 2025-11-05 doi:10.1101/2025.11.04.686611 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ RainBar: Optical Barcoding for Pooled Live-Cell Imaging with Single-Cell Resolution ]]> https://biorxiv.org/content/10.1101/2025.11.04.686676v1?rss=1 Mosadeghi, R. Foyt, D. Sharp, L. Taylor, C. A. Tay, N. Oberlin, S. Fan, J. Bourke, S. Kattah, M. G. Huang, B. Q. McManus, M. T. 2025-11-05 doi:10.1101/2025.11.04.686676 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ A spatial transcriptomic atlas of autism-associated genes identifies convergence in the developing human thalamus ]]> https://biorxiv.org/content/10.1101/2025.11.05.685843v1?rss=1 Aivazidis, A. Memi, F. Rademaker, K. Koko, M. Roberts, K. Trinh, A. Petryszak, R. Kleshchevnikov, V. Tuck, E. Lisgo, S. Li, T. Makarchuk, S. Prete, M. Nowakowski, T. J. Martin, H. C. Bayraktar, O. A. 2025-11-06 doi:10.1101/2025.11.05.685843 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ An InDel Genomic Variant within a Bifunctional Super-Enhancer for LINC00636 and CD47 Regulation in Breast Cancer ]]> https://biorxiv.org/content/10.1101/2025.11.05.684493v1?rss=1 Di Benedetto, C. Tsark, A. Acenas, D. D. Thach, A. Singal, A. Opazo-Medallo, V. Rodriguez, A. El Zeini, M. Zhang, H. Park, C. Gonzales-Velozo, H. Weissman, I. L. Betancur, P. 2025-11-07 doi:10.1101/2025.11.05.684493 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ Disruption of Cell-Type-Specific Molecular Programs of Medium Spiny Neurons in Autism ]]> https://biorxiv.org/content/10.1101/2025.11.05.686845v1?rss=1 Yuan, G. Suresh, V. Wigdor, E. Hao, Y. Leonard, R. Steyert, M. Griffiths, M. Evans, C. Rohani, N. Weiss, J. Lassen, F. H. Schafer, N. Dong, S. Palmer, D. S. Sanders, S. J. Nowakowski, T. J. 2025-11-07 doi:10.1101/2025.11.05.686845 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ SPARK: in silico simulations for benchmarking nascent RNA sequencing experiments ]]> https://biorxiv.org/content/10.1101/2025.11.06.687082v1?rss=1 Calvo-Roitberg, E. Lehman, J. W. Tam, E. Elhajjajy, S. Engelhardt, B. E. Pai, A. A. 2025-11-08 doi:10.1101/2025.11.06.687082 Cold Spring Harbor Laboratory Press 2025-11-08 <![CDATA[ Structural basis and physiological significance of non-canonical Gs coupling to the prototypical Gi-coupled melatonin MT1 receptor ]]> https://biorxiv.org/content/10.1101/2025.11.08.687348v1?rss=1 Okamoto, H. Oishi, A. Ikegami, K. McHugh, R. Masri, B. Kusakizako, T. Kobayashi, K. Karamitri, A. Cecon, E. Dam, J. Nagase, M. Tikhonova, I. Nureki, O. Jockers, R. 2025-11-08 doi:10.1101/2025.11.08.687348 Cold Spring Harbor Laboratory Press 2025-11-08 <![CDATA[ TriLeukeVax: A CD80/IL-15/IL-15Rα Expressing Autologous AML Cell Vaccine Elicits Robust Anti-Leukemic Cytolytic Activity ]]> https://biorxiv.org/content/10.1101/2025.11.07.687000v1?rss=1 80% of leukemic mice with serial administration of TLV. In the current studies, TLV was generated from 59/60 cryopreserved, diagnostic bone marrow-derived patient AML samples. Ex vivo priming of post-remission patient T-cells by ex vivo co-culture with autologous TLV stimulated robust proliferative and cytotoxic responses. In secondary co-cultures, T-cells previously primed by initial co-culture with TLV, showed greater clonal expansion and leukemia-specific cytolytic activity towards de novo autologous AML blasts than did control, unprimed T-cells. The enhanced anti-leukemic activity of TLV-primed T-cells against de novo AML confirms the potential for vaccine administration to effectively target minimal residual disease (MRD) persisting after chemotherapy and reduce relapse. Key PointsO_LITriLeukeVax induces proliferation, activation, and effective anti-leukemic cytolytic responses in remission T-cells. C_LIO_LIPrimed T-cells show polyclonal expansion and transcription profiles associated with proliferation, memory, and cytotoxicity. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/687000v2_ufig1.gif" ALT="Figure UFIG"> View larger version (38K): org.highwire.dtl.DTLVardef@5c1827org.highwire.dtl.DTLVardef@35b2e2org.highwire.dtl.DTLVardef@1732914org.highwire.dtl.DTLVardef@18df655_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOVisual Abstract.C_FLOATNO TriLeukeVax (TLV) workflow and mechanism of action. Diagnostic AML patient bone marrow aspirates are collected, purified in Ficoll and cryopreserved. Samples are thawed and lentivirally transduced to produce TLV. Vaccination of AML patients in remission with TLV will stimulate the activation and expansion of leukemia-specific T-cells, effector memory cells, and NK cells by combining the co-stimulatory effects of CD80 with immune stimulation by the IL-15/IL-15R heterodimer expressed by the transduced AML cells, thereby targeting MRD and potentially increasing relapse-free survival in AML patients. C_FIG ]]> Du, J. Wijayaratna, U. N. Wang, X. Fung, J. P. Huang, B. Farzaneh, F. Kohn, D. B. Combes, A. J. Gaensler, K. M. L. 2025-11-09 doi:10.1101/2025.11.07.687000 Cold Spring Harbor Laboratory Press 2025-11-09 <![CDATA[ Parvalbumin interneurons gate and shape striatal sequences ]]> https://biorxiv.org/content/10.1101/2025.11.08.687375v1?rss=1 Duhne, M. Gonzalez Montalvo, I. Zheng, C. S. Pelattini, L. Berke, J. D. 2025-11-09 doi:10.1101/2025.11.08.687375 Cold Spring Harbor Laboratory Press 2025-11-09 <![CDATA[ Dissecting mammalian cortical circuit development at single-cell resolution using inducible barcoded rabies virus ]]> https://biorxiv.org/content/10.1101/2025.11.07.687321v1?rss=1 Zhang, Z. D'Arcy, B. He, L. Arroyo, D. Deasy, S. Matthews, E. Yan, Z. Rastogi, N. Mancia Leon, W. Kaur, K. S. Southwell, D. G. Huang, Z. J. Silver, D. Velmeshev, D. 2025-11-10 doi:10.1101/2025.11.07.687321 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ A conserved sRNA regulates mucin adhesion and gut colonization across the Enterococcaceae ]]> https://biorxiv.org/content/10.1101/2025.11.10.687296v1?rss=1 Bowden, S. Jennings, K. C. Zlitni, S. Brooks, E. F. Davin, M. E. Natarajan, A. Asare, L. Fremin, B. J. Wilmes, P. Hettich, R. L. Salzman, N. H. Bhatt, A. S. 2025-11-11 doi:10.1101/2025.11.10.687296 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ Scalable imaging-based profiling of CRISPR perturbations with protein barcodes ]]> https://biorxiv.org/content/10.1101/2025.11.11.687767v1?rss=1 Choudhary, K. McManus, M. 2025-11-11 doi:10.1101/2025.11.11.687767 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ Lactate dehydrogenase-induced DNA Topoisomerase 1 is a novel regulator of smooth muscle cell proliferation and remodeling in pulmonary arterial hypertension ]]> https://biorxiv.org/content/10.1101/2025.11.10.687749v1?rss=1 Jiang, L. Zhyvylo, I. Goncharov, D. Dey, T. Kelly, N. Teos, L. Franzi, L. Saiyed, A. Kenyon, N. J. Greenland, J. R. Wolters, P. J. Chen, S. Y. Delisser, H. Kudryashova, T. V. Goncharova, E. A. 2025-11-12 doi:10.1101/2025.11.10.687749 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Putative azithromycin-resistance mutations in Chlamydia trachomatis are globally distributed but arose before azithromycin was discovered ]]> https://biorxiv.org/content/10.1101/2025.11.10.687758v1?rss=1 Sharma, P. Dean, D. Read, T. D. 2025-11-12 doi:10.1101/2025.11.10.687758 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Fast-conducting mechanonociceptors uniquely engage reflexive and affective pain circuitry to drive protective responses ]]> https://biorxiv.org/content/10.1101/2025.11.11.687663v1?rss=1 Lezgiyeva, K. Liu, J. Nguyen, K. DeLisle, M. M. Ko, F. C. Fullam, S. Obeidat, A. M. Turecek, J. Alkislar, I. Lehnert, B. P. Martinez-Garcia, R. I. Sivakumar, R. Choi, J. Mazor, O. Garibyan, L. Sharma, N. Emanuel, A. J. Malfait, A.-M. Miller, R. E. Ginty, D. D. 2025-11-12 doi:10.1101/2025.11.11.687663 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ APOE4-Aβ synergy drives brain network dysfunction and neuronal lysosomal-ER proteostasis dysregulation in preclinical Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.11.11.687887v1?rss=1 Shin, J. Brady, E. Chen, C. Lauderdale, K. Agrawal, A. Zhang, Y. Jiang, X. Herbert, J. Mallen, D. D. Ly, K. K. Honma, P. S. Guo, Z. Sant, C. Thomas, R. Miller, S. R. Cobos, I. Palop, J. J. 2025-11-12 doi:10.1101/2025.11.11.687887 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Co-Hyperpolarized Dehydroascorbate and Pyruvate MRI Predicts Radiation Response in Glioblastoma Models ]]> https://biorxiv.org/content/10.1101/2025.11.11.687898v1?rss=1 Coffee, E. Porcari, P. Patel, S. Figlioli, G. Berishaj, M. Rahimi-Keshari, K. 2025-11-13 doi:10.1101/2025.11.11.687898 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Class-I myosin responds to change in membrane tension during clathrin-mediated endocytosis in human induced pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2025.11.12.688091v1?rss=1 Smith, S. L. Zhan, T. Li, W. De Belly, H. Zhang, Q. Xu, K. Weiner, O. Drubin, D. G. 2025-11-13 doi:10.1101/2025.11.12.688091 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Pre-existing and emergent cortical neuronal assembly sequences during learning ]]> https://biorxiv.org/content/10.1101/2025.11.12.688154v1?rss=1 Pemberton, L. Jeong, H. K Namboodiri, V. M. 2025-11-13 doi:10.1101/2025.11.12.688154 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Acute Myeloid Leukemia Relapse after Bromodomain Inhibitor Treatment or Chemotherapy is Characterized by Myc-Ras Transcriptional Remodeling ]]> https://biorxiv.org/content/10.1101/2025.11.13.688312v1?rss=1 Huang, B. J. D'Souza, J. Batingana, A. R. Harris, M. D. Wang, X. Hwang, E. Wandler, A. M. Burgess, M. R. Li, Q. Meshinchi, S. Bollag, G. Shannon, K. 2025-11-14 doi:10.1101/2025.11.13.688312 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Decoding hidden goal-directed navigational states and their neuronal representations using a novel labyrinth paradigm and probabilistic modeling framework ]]> https://biorxiv.org/content/10.1101/2025.11.13.688348v1?rss=1 Honma, P. S. Bangera, S. C. Thomas, R. R. Kaliss, N. Xia, D. Palop, J. J. 2025-11-14 doi:10.1101/2025.11.13.688348 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ The phenotypic landscape of the mycobacterial cell ]]> https://biorxiv.org/content/10.1101/2025.11.14.688347v1?rss=1 35 antibiotics, detergents, and other anti-microbials predominantly targeting the cell envelope of Mycobacterium smegmatis, a saprophytic model Mycobacterium. We highlight new information derived from this screen, including the identification of novel functions for previously uncharacterized conserved and essential genes (in mycolic acid and arabinogalactan synthesis), the discovery of a new drug scaffold/protein target pair, and insights into the mechanism of action of two commonly used antibiotics. These data are also a valuable resource for the mycobacterial research community, as they provide thousands of novel phenotypes for uncharacterized genes and meaningful phenotypic correlations between annotated and uncharacterized genes. ]]> Herrera, N. Todor, H. Kim, L. M. Burkhart, H. N. Billings, E. Warner, T. C. Lee, S. Y. Sayegh, N. Y. Bosch, B. Kiessling, L. L. Mancia, F. Rock, J. M. Gross, C. A. 2025-11-15 doi:10.1101/2025.11.14.688347 Cold Spring Harbor Laboratory Press 2025-11-15 <![CDATA[ Model of ocular surface ion and water transport predicts efficacy of dry eye therapeutics targeting epithelial transport and tear fluid dynamics ]]> https://biorxiv.org/content/10.1101/2025.11.17.688783v1?rss=1 Verma, V. Lindgren, E. S. Levin, M. H. Cil, O. Tradtrantip, L. Yan, R. Pasricha, N. D. Verkman, A. S. 2025-11-17 doi:10.1101/2025.11.17.688783 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ TAF15 amyloids propagate via defined motifs in a prion-like fashion ]]> https://biorxiv.org/content/10.1101/2025.11.17.688886v1?rss=1 Konstantoulea, K. Gadhe, L. Goodavish, F. GUPTA, A. Tagad, H. Vaquer-Alicea, J. Ghayal, N. B. Roemer, S. F. DeTure, M. A. Nana, A. L. Spina, S. Grinberg, L. T. Seeley, W. W. Dickson, D. W. White, C. L. Diamond, M. I. Louros, N. N. 2025-11-18 doi:10.1101/2025.11.17.688886 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ Scalable Human Cellular Models of Parkinson Disease Reveal A Druggable Link Between the Angiotensin Receptor 1 and Alpha-Synuclein Pathology ]]> https://biorxiv.org/content/10.1101/2025.11.18.689137v1?rss=1 Daynac, M. Mouilleau, V. Liu, Y. Yang, X. Shen, Y. Guo, S. 2025-11-19 doi:10.1101/2025.11.18.689137 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ Harmonized Protocol for Segmentation of the Hippocampal Tail on High-Resolution in vivo MRI from the Hippocampal Subfields Group (HSG) ]]> https://biorxiv.org/content/10.1101/2025.11.20.689476v1?rss=1 0.98; Averaged Dice Similarity Coefficient = 0.92) and inter-rater reliability (Averaged ICC(2,k) > 0.98; Averaged Dice Similarity Coefficient = 0.86) and offers a practical framework for replicable segmentation. By establishing standardized guidelines, this protocol enhances comparability of findings across developmental, aging, and clinical research and is compatible with ongoing technological advances. ]]> de Flores, R. Canada, K. L. Brown, T. Gervais, N. J. Maass, A. Radman, G. Shine, J. Tucker, H. L. Molloy, E. N. Adams, J. N. Reinke, M. B. Bakker, A. Berron, D. Dalton, M. A. Kennedy, K. M. La Joie, R. Mueller, S. G. Ofen, N. Olsen, R. K. Raz, N. Riggins, T. Rodrigue, K. M. Stark, C. Wang, L. Wisse, L. E. Yushkevich, P. A. Carr, V. A. Daugherty, A. M. Alzheimer's Disease Neuroimaging Initiative, Hippocampal Subfields Group, 2025-11-20 doi:10.1101/2025.11.20.689476 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ Analyses of bent spindles reveal the mechanics of anaphase B in fission yeast ]]> https://biorxiv.org/content/10.1101/2025.11.20.689516v1?rss=1 Real-Calderon, P. Fai, T. Daga, R. Lemiere, J. Chang, F. 2025-11-20 doi:10.1101/2025.11.20.689516 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ Congenital CMV infection drives oligoclonal expansion of cytotoxic γδ T cells from early fetal progenitors ]]> https://biorxiv.org/content/10.1101/2025.11.20.689355v1?rss=1 Levan, J. Vaaben, A. V. Tsui, J. Davidson, B. R. Olive, M. E. Callaway, P. C. Nguyen, C. B. T. Ilala, M. Patel, R. K. Hunter, R. D. Fragiadakis, G. K. Combes, A. J. Nankya, F. Dorsey, G. Kakuru, A. Muhindo, M. Feeney, M. E. 2025-11-21 doi:10.1101/2025.11.20.689355 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ "Awe-scillations": EEG spectral and complexity representations of awe ]]> https://biorxiv.org/content/10.1101/2025.11.20.689403v1?rss=1 Chen, J. C. C. Mace, G. Ostrand, A. Valtierra, C. Griffith, S. Campusano, R. Li, A. Vinson, E. Schlomberg, J. Eshel, M. Suntay, J. M. Rahim, S. Anguera, R. Brown, D. A. Swann, N. C. Mazzucato, L. Hu, X. Zhang, D. Timmermann, C. Carhart-Harris, R. Zanto, T. Ziegler, D. Gazzaley, A. Pasquini, L. 2025-11-21 doi:10.1101/2025.11.20.689403 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Drug-induced phospholipidosis as an artifact in antiviral drug repurposing ]]> https://biorxiv.org/content/10.1101/2025.11.20.689520v1?rss=1 Glenn, I. S. Paris, L. White, A. D. Garda, V. G. Montano, M. Khalid, M. M. Kao, A. W. Ott, M. Shoichet, B. K. 2025-11-21 doi:10.1101/2025.11.20.689520 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Saxiphilin functions as a "toxin sponge" protein that counteracts the effects of saxitoxin poisoning ]]> https://biorxiv.org/content/10.1101/2025.11.20.689596v1?rss=1 Nixon, S. A. Zakrzewska, S. Jang, S. Huang, K. Barra, A. Chen, Z. Goss, D. R. Park, E. Du Bois, J. Minor, D. L. 2025-11-21 doi:10.1101/2025.11.20.689596 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Increased mannosylation of extracellular vesicles in Long COVID plasma provides a potential therapeutic target for Galanthus nivalis agglutinin (GNA) affinity resin ]]> https://biorxiv.org/content/10.1101/2025.11.21.689519v1?rss=1 Pesqueira Sanchez, M. A. de Necochea Campion, R. Dalhuisen, T. Fehrman, E. A. Chhabra, P. S. Kelly, J. D. Martin, J. N. Deeks, S. G. Henrich, T. J. Peluso, M. J. LaRosa, S. P. 2025-11-21 doi:10.1101/2025.11.21.689519 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ High extraversion enhances attentional control through dynamic network reorganization ]]> https://biorxiv.org/content/10.1101/2025.11.20.689570v1?rss=1 Chen, J. C. C. Nandi, B. Campusano, R. Jiang, F. Ziegler, D. Gazzaley, A. Zanto, T. 2025-11-22 doi:10.1101/2025.11.20.689570 Cold Spring Harbor Laboratory Press 2025-11-22 <![CDATA[ Genetic variation of human G6PD impacts Red Blood Cell transfusion efficacy ]]> https://biorxiv.org/content/10.1101/2025.11.21.689741v1?rss=1 View larger version (76K): org.highwire.dtl.DTLVardef@1897489org.highwire.dtl.DTLVardef@1420587org.highwire.dtl.DTLVardef@178e8ddorg.highwire.dtl.DTLVardef@1003b44_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Karafin, M. S. Issaian, A. V. Bevers, S. Reisz, J. A. Hay, A. Keele, G. R. Dzieciatkowska, M. Cendali, F. I. Haiman, Z. B. Key, A. M. Nemkov, T. Stephenson, D. Marsh, E. Moore, A. Palha, M. S. Legenzov, E. A. Lamb, D. R. Deng, X. Stone, M. Hansen, K. Kleinman, S. Norris, P. J. Busch, M. P. Vallese, F. Palsson, B. O. Spitalnik, S. Kao, J. P. Roubinian, N. H. Janetzko, J. Page, G. P. Eisenmesser, E. Z. Zimring, J. C. Buehler, P. W. D'Alessandro, A. 2025-11-22 doi:10.1101/2025.11.21.689741 Cold Spring Harbor Laboratory Press 2025-11-22 <![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[ Bacteriophage genome-wide transposon mutagenesis ]]> https://biorxiv.org/content/10.1101/2025.11.23.690004v1?rss=1 Chan, A. W. Yee, W.-X. Mozumdar, D. Kokontis, C. Y. Rojas-Montero, M. Yuping, L. Bondy-Denomy, J. Yang, Y. 2025-11-24 doi:10.1101/2025.11.23.690004 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ A geothermal amoeba sets a new upper temperature limit for eukaryotes ]]> https://biorxiv.org/content/10.1101/2025.11.24.690213v1?rss=1 Rappaport, H. B. Petek-Seoane, N. A. Tyml, T. Mikus, F. Labutti, K. Ani, G. Niblo, J. K. MacVicar, E. Shepherd, R. M. de la Higuera, I. Lord, S. J. Dey, G. Wolfe, G. V. Dudin, O. Sukenik, S. Katz, L. A. Stedman, K. M. Skruber, K. Schulz, F. Mullins, R. D. Oliverio, A. M. 2025-11-24 doi:10.1101/2025.11.24.690213 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Steady-state epithelial apical flatness is characterized by MLCK morphodynamics and asynchronous Ca2+ oscillations, but not underlying ECM geometry ]]> https://biorxiv.org/content/10.1101/2025.11.21.688964v1?rss=1 Wu, H. Herrmann, E. G. Hyer, J. M. Hua, L. L. Mikawa, T. 2025-11-25 doi:10.1101/2025.11.21.688964 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Modifications to the gut microbiome alter bone matrix proteomics and fracture toughness at the cellular scale ]]> https://biorxiv.org/content/10.1101/2025.11.21.689836v1?rss=1 Hunt, N. K. Liu, C. Liu, J. Tang, Q. Stephen, S. J. Wang, B. Schurman, C. A. King, C. D. Liu, Q. Vashishth, D. Schilling, B. Hassani, M. Hernandez, C. J. 2025-11-25 doi:10.1101/2025.11.21.689836 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Injury-induced tau pathology promotes aggressive behavior in Drosophila without neurodegeneration. ]]> https://biorxiv.org/content/10.1101/2025.11.22.689595v1?rss=1 Maxson, R. Smoyer, C. J. Hampton, M. F. Shen, Y. Wiese, K. Yee, C. Singh, A. Funtila, A. McKenney, R. J. Ori-McKenney, K. M. 2025-11-25 doi:10.1101/2025.11.22.689595 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Immunological Differences in Atopic Dermatitis Across Age Groups: Insights from Single-Cell Multi-Omics ]]> https://biorxiv.org/content/10.1101/2025.11.22.689843v1?rss=1 Baldonado, G. C. L. Kumar, S. Jin, J. Fang, X. Ildardashty, A. Braun, M. Neuhaus, I. M. Mathes, E. Bhutani, T. Liao, W. 2025-11-25 doi:10.1101/2025.11.22.689843 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Crystallographic Ensembles Reveal the Structural Basis of Binding Entropy in SARS-CoV2 Macrodomain ]]> https://biorxiv.org/content/10.1101/2025.11.25.690589v1?rss=1 Seo, L. Farran, I. Aslam, A. Li, X. Jaishankar, P. Fraser, J. S. Renslo, A. Wankowicz, S. A. 2025-11-26 doi:10.1101/2025.11.25.690589 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ Spatial Transcriptomics Reveals CXCL12+ Fibroblasts as Central Immune Organizers through CXCR4 Signaling in Abdominal Aortic Aneurysm ]]> https://biorxiv.org/content/10.1101/2025.11.24.690328v1?rss=1 580,000 cells identified from aortic tissue sections C_LIO_LIWe identified CXCL12+ fibroblasts as central stromal hubs that organize adaptive immune niches through CXCR4-mediated crosstalk with B and T cells C_LIO_LIWe discovered that stromal populations carry the strongest genetic enrichment for AAA risk, notably fibroblast and modulated smooth muscle cell populations C_LI What Are The Clinical Implications? O_LIThese findings position stromal-immune interactions, particularly the CXCL12-CXCR4 axis, as a potential therapeutic target to slow AAA progression C_LIO_LIThe spatial atlas provides a framework for mechanistic studies and drug-discovery efforts, guiding future interventions aimed at modifying the microenvironment that destabilizes the aneurysmal aortic wall C_LI ]]> Levy-Lambert, D. Ramirez, J. L. Shaikh, S. De Jeronimo Diaz, C. Huang, A. G. Combes, A. Fragiadakis, G. Fidler, T. Oskowitz, A. 2025-11-29 doi:10.1101/2025.11.24.690328 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Neuronal APOE4 alone is sufficient to drive tau pathology, neurodegeneration, and neuroinflammation in an Alzheimer's disease mouse model ]]> https://biorxiv.org/content/10.1101/2025.11.25.690488v1?rss=1 Blumenfeld, J. Li, Y. Kim, M. J. Yip, O. Yao, L. De Leon, S. Fulthorpe, R. Shostak, D. Platow, Z. Suan, K. Hao, Y. Koutsodendris, N. Ellis, C. Nguyen, J. Huang, Y. 2025-11-29 doi:10.1101/2025.11.25.690488 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ HDL-associated phosphatidylserine blunts myeloid activation and protects from atherosclerosis ]]> https://biorxiv.org/content/10.1101/2025.11.26.689708v1?rss=1 Bernal, A. Hamid, A. Grao-Roldan, C. Scarpa, A. Sanchez, I. Nicolas-Avila, J. A. Pena-Couso, L. Yaghmour, M. H. Benguria, A. Rosado, A. Sanchez, L. Torroja, C. Dopazo, A. Sanchez-Cabo, F. Hidalgo, A. Senders, M. L. van Leent, M. M. T. Seep, L. Hasenauer, J. Placek, K. Thiele, C. Netea, M. G. Mulder, W. J. M. Riksen, N. P. Perez-Medina, C. 2025-11-30 doi:10.1101/2025.11.26.689708 Cold Spring Harbor Laboratory Press 2025-11-30 <![CDATA[ Uncovering senescent fibroblast heterogeneity connects DNA damage response to idiopathic pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/2025.11.26.690792v1?rss=1 Hughes, J.-W. B. Pujari, A. Sandholm, A. Croll, D. Monk, L. B. Joshua, I. Butterfield, R. Horton, C. Schneider, K. Senchyna, F. Brown, I. Coelho, A. L. Ho, T.-C. Deguchi, H. Le Saux, C. J. Deinhardt-Emmer, S. Ellerby, L. M. Vitari, A. Furman, D. Hogoboam, C. M. Laslavic, A. Desprez, P.-Y. Quarta, M. Campisi, J. 2025-11-30 doi:10.1101/2025.11.26.690792 Cold Spring Harbor Laboratory Press 2025-11-30 <![CDATA[ Beyond Correlation: An Ultra-Large Physics-Driven Vascularized Tumor Model to Bridge Feature Formation with Underlying Biology ]]> https://biorxiv.org/content/10.1101/2025.11.26.690767v1?rss=1 Du, J. Zhou, Y. Jin, L. Sheng, K. 2025-12-01 doi:10.1101/2025.11.26.690767 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ GPR34 regulation of disease-associated microglial states and responses to physiological stimuli ]]> https://biorxiv.org/content/10.1101/2025.11.26.690816v1?rss=1 Geller, A. Kwon, M. J. Simmons, S. K. Xu, Q. Martenis, W. E. Doman, J. Natarajan, S. Stalnaker, K. J. Zhang, J. Adiconis, X. Nguyen, T. Demers, M. Batzli, D. Valle-Tojeiro, A. Biji, C. Aryal, S. Pribiag, H. Depp, C. Morshed, N. Misri, D. Bohannon, D. Longhi, E. Keshishian, H. Carr, S. A. McKinney, D. Gould, A. E. Lebois, E. Weiwer, M. Johnson, M. Levin, J. Z. Zhang, Y.-L. Sheng, M. Kunwar, P. S. 2025-12-01 doi:10.1101/2025.11.26.690816 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ FCHo2, instead of talin, enables inside-out activation of integrin αvβ5 in curved adhesions ]]> https://biorxiv.org/content/10.1101/2025.11.28.691229v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@eb4addorg.highwire.dtl.DTLVardef@1802a01org.highwire.dtl.DTLVardef@145e805org.highwire.dtl.DTLVardef@83d641_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lu, C.-H. Lee, C. E. Zhang, W. Yang, Y. Valencia, L. A. You, H. Tsai, C.-T. Cui, B. 2025-12-01 doi:10.1101/2025.11.28.691229 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Interrogating the Regulatory Function of HAQERs during Human Cortical Development ]]> https://biorxiv.org/content/10.1101/2025.11.30.691411v1?rss=1 Abeykoon, Y. Dzikowski, N. Luo, Y. Sinniah, E. Weaver, S. Pavlovic, B. J. Wallace, J. L. Mangan, R. J. Lowe, C. B. Pollen, A. A. 2025-12-01 doi:10.1101/2025.11.30.691411 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Bacterial strains in the human gut associate with host physiology ]]> https://biorxiv.org/content/10.1101/2025.11.30.691432v1?rss=1 Shoer, S. Godneva, A. Weinberger, A. Pollard, K. S. Pilpel, Y. Segal, E. 2025-12-01 doi:10.1101/2025.11.30.691432 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Need-selective gating of dopamine neuron cue responses by real and virtual hunger ]]> https://biorxiv.org/content/10.64898/2025.11.29.691326v1?rss=1 Mamaligas, A. A. Berke, J. Kreitzer, A. C. Knight, Z. A. 2025-12-02 doi:10.64898/2025.11.29.691326 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ An orthogonal TRAP enables intersectional genetic access to activated neurons in the mouse brain ]]> https://biorxiv.org/content/10.64898/2025.11.30.691330v1?rss=1 Chatziris, N. Jarvie, B. C. Liu, C. Knight, Z. A. 2025-12-02 doi:10.64898/2025.11.30.691330 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Cellular coding of ingestion in the caudal brainstem ]]> https://biorxiv.org/content/10.64898/2025.11.30.691333v1?rss=1 Ly, T. Yi, X. Lee, G. R. Grove, J. C. Sibih, Y. E. Oh, Y. Y. Qiu, L. Sivakumar, N. Knight, Z. A. 2025-12-02 doi:10.64898/2025.11.30.691333 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ A genetic screen in enteroendocrine cells reveals mechanisms that control protein sensing and GLP-1 release ]]> https://biorxiv.org/content/10.64898/2025.11.30.691441v1?rss=1 20,000 sgRNAs identified numerous genes associated with mitochondrial respiration as being necessary for this process. We showed through secondary assays that impairing oxidative phosphorylation (OXPHOS) reduced EEC activation and GLP-1 release in response to nutrients but not in response to a non-nutritive stimulus. On the other hand, boosting OXPHOS increased EEC activation and GLP-1 release. These data reveal that intracellular metabolism within EECs controls the detection of dietary protein, possibly by monitoring the entry of ingested amino acids into the TCA cycle. More broadly, these findings suggest a general strategy to screen for genes and pathways that might be used to boost the nutrient-regulated release of gut peptides such as GLP-1. ]]> Yu, S. Lee, Y. Boggess, S. C. Klein, N. R. Teyssier, N. Kampmann, M. Knight, Z. A. 2025-12-02 doi:10.64898/2025.11.30.691441 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Advancing High-Resolution 7T Diffusion MRI: Evaluating Phase-Encoding Correction Strategies for Distortion Correction from Basic to Four-Way Acquisitions ]]> https://biorxiv.org/content/10.64898/2025.12.01.687254v1?rss=1 Schilling, K. G. Beckett, A. J. S. Amandola, M. Walker, E. B. Feinberg, D. A. Bunge, S. A. Vu, A. T. 2025-12-03 doi:10.64898/2025.12.01.687254 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Female-predominant anti-CD4 IgG autoantibody production and its correlations with plasma levels of progesterone, microbial translocation, and blunted immune reconstitution in HIV-infected patients on suppressive ART ]]> https://biorxiv.org/content/10.64898/2025.12.03.689730v1?rss=1 McKinnon, J. E. Wan, Z. Luo, Z. Hartley, A. Price, R. W. Gisslen, M. Jiang, W. 2025-12-04 doi:10.64898/2025.12.03.689730 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ The Emergence of Novel Versus Known Three-Dimensional Structures from Random Sequences. ]]> https://biorxiv.org/content/10.64898/2025.12.04.691947v1?rss=1 Yang, R. S. Yang, H. Davydenko, A. Mawaldi, Z. Kormos, R. C. Myerscough, D. Wu, Y. DeGrado, W. 2025-12-04 doi:10.64898/2025.12.04.691947 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ Tri-AD: Hippocampal cell-type-specific responses to age, sex and APOE genotype ]]> https://biorxiv.org/content/10.64898/2025.12.03.691944v1?rss=1 Li, Y. Li, Y. Pereda Serras, C. Yao, L. Liang, Z. Almonte-Loya, A. Blumenfeld, J. Suan, K. Yoon, S. Y. Grone, B. Ding, L. Ma, Y. Sun, S. Oskotsky, B. Oskotsky, T. Condello, C. Huang, Y. Sirota, M. 2025-12-08 doi:10.64898/2025.12.03.691944 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Senescence-Linked Fibrosis in the Aging Human Ovary Revealed by p16-Based Histological Profiling and Spatial Transcriptomics ]]> https://biorxiv.org/content/10.64898/2025.12.03.692228v1?rss=1 Watson, M. A. Devrukhkar, P. R. Murad, N. F. Wu, F. Kim, M. J. Anvari, H. Tran, U. Martin, N. Tran, T. Zaza, G. Schneider, K. Soygur, B. Shanes, E. D. Wirtz, D. Pavone, M. G. Melov, S. Wu, P.-H. Furman, D. Duncan, F. E. Schilling, B. 2025-12-08 doi:10.64898/2025.12.03.692228 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Human stem cell models for group 3 medulloblastoma uncover JARID1B as a regulator of the chromatin landscape. ]]> https://biorxiv.org/content/10.64898/2025.12.06.689939v1?rss=1 Qadeer, Z. A. Hou, E. Siegel, D. Westelman, S. Gudenas, B. Smith, K. Ismael, W. M. Wang, L. Johnson, M. O. Grele, S. Phua, R. Hendrikse, L. Guney, E. Huang, M. Gaspar-Maia, A. Northcott, P. A. Taylor, M. D. Weiss, W. A. 2025-12-08 doi:10.64898/2025.12.06.689939 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Neuronal APOE4 drives damaging lipid accumulation via contact-dependent neuron-oligodendrocyte-microglia interaction in Alzheimer's disease ]]> https://biorxiv.org/content/10.64898/2025.12.04.692390v1?rss=1 Kim, M. J. Blumenfeld, J. Li, Y. Yip, O. Yao, L. Ancheta, S. De Leon, S. Platow, Z. Liang, Z. Shostak, D. Suan, K. Hao, Y. Koutsodendris, N. Ellis, C. Nguyen, J. Huang, Y. 2025-12-09 doi:10.64898/2025.12.04.692390 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes ]]> https://biorxiv.org/content/10.64898/2025.12.05.692665v1?rss=1 Judd, J. Spence, J. P. Milind, N. Kachuri, L. Witte, J. S. Pritchard, J. K. 2025-12-09 doi:10.64898/2025.12.05.692665 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Inhibitory potential of autologous neutralizing antibodies sets quantitative limits on the rebound-competent HIV-1 reservoir ]]> https://biorxiv.org/content/10.64898/2025.12.07.692769v1?rss=1 Garcia, M. A. Farrell-Sherman, A. Zhuo, J. Fray, E. J. Zinsser, A. M. Aydin, B. Sowers, K. Li, H. Lopez, B. M. Abeyta-Lopez, A. Chu, T. Lubbeck, D. Chae, M. Varriale, J. Westfall, D. H. Lai, J. Hoh, R. Dalhuisen, T. Simonetti, F. R. Peluso, M. J. Deeks, S. G. Siliciano, R. F. Cohn, L. B. Siliciano, J. D. 2025-12-09 doi:10.64898/2025.12.07.692769 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Alveolar Type II Cell-derived MMP1high basal cells promote destructive microcysts in idiopathic pulmonary fibrosis. ]]> https://biorxiv.org/content/10.64898/2025.12.08.693033v1?rss=1 Garakani, K. Brumwell, A. N. Toigo, M. Jacob, A. Wei, Y. Ho, T. C. Wolters, P. Matthay, M. A. Volk, R. F. Zaro, B. W. Iantorno, S. A. Berhan, A. Sheppard, D. W. Auyeung, V. C. Jourdan Le Saux, C. C. Chapman, H. A. 2025-12-11 doi:10.64898/2025.12.08.693033 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Comparing Multislice Simulations of MD Simulations with CryoEM Exposes Membrane Prediction Errors ]]> https://biorxiv.org/content/10.64898/2025.12.09.693260v1?rss=1 Mohammed, A. Lincoff, J. Natale, A. Ophus, C. Grabe, M. Frost, A. Moss, F. R. 2025-12-11 doi:10.64898/2025.12.09.693260 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[ Poorer physical function is associated with elevated spatial entropy in the aging brain network landscape ]]> https://biorxiv.org/content/10.64898/2025.12.09.693258v1?rss=1 McIntyre, C. C. ODonnell, S. M. Lyday, R. G. Burdette, J. H. Cummings, S. R. Kritchevsky, S. B. Laurienti, P. J. 2025-12-12 doi:10.64898/2025.12.09.693258 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Mapping the circulating proteome across neurodegeneration: A harmonized, consortium-scale framework for uncovering molecular pathophysiology ]]> https://biorxiv.org/content/10.64898/2025.12.09.693329v1?rss=1 Finney, C. A. An, L. Winchester, L. M. Vogel, J. Wilkins, H. M. Burns, J. M. Swerdlow, R. H. Slawson, C. Rothstein, J. D. Global Neurodegeneration Proteomics Consortium, Lutz, M. W. Saloner, R. Shvetcov, A. 2025-12-12 doi:10.64898/2025.12.09.693329 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Bifunctional transcriptional effector domains control gene expression pulses in an occupancy-dependent manner ]]> https://biorxiv.org/content/10.64898/2025.12.10.693551v1?rss=1 Andrews, C. J. Costa, E. J. Janer Carattini, G. L. DelRosso, N. V. Fujimori, T. Shimasawa, M. Bintu, L. 2025-12-12 doi:10.64898/2025.12.10.693551 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Neuronal APOE4 reduction with an APOE-I3-targeting ASO protects against neurodegeneration and neuroinflammation in an Alzheimer's disease mouse model ]]> https://biorxiv.org/content/10.64898/2025.12.10.693468v1?rss=1 Yip, O. Yao, L. Blumenfeld, J. Kim, M. J. Shostak, D. Platow, Z. Suan, K. Li, Y. Ellis, C. An, A. Hao, Y. Xu, Q. De Leon, S. Nguyen, J. Huang, Y. 2025-12-13 doi:10.64898/2025.12.10.693468 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ MechanoMR microparticle (M3) sensors reveal dynamic stress loading as a driver of epithelial-mesenchymal transition ]]> https://biorxiv.org/content/10.64898/2025.12.10.693598v1?rss=1 An, M. Yu, R. Lin, A. Jang, J. Ohk, J. Kim, Y.-J. Jung, H. Kwak, M. Jun, Y.-w. Cheon, J. 2025-12-13 doi:10.64898/2025.12.10.693598 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ Degraded sensory coding in a mouse model of Scn2a-related disorder and its rescue by CRISPRa gene activation ]]> https://biorxiv.org/content/10.64898/2025.12.13.694145v1?rss=1 Vandemark, K. Monday, H. R. Rodriguez, L. Zhao, M. Lee, M. Ahituv, A. Satapathy, A. Page, N. F. An, K. Hamada, E. C. Ahituv, N. Bender, K. J. Feldman, D. E. 2025-12-14 doi:10.64898/2025.12.13.694145 Cold Spring Harbor Laboratory Press 2025-12-14 <![CDATA[ Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells ]]> https://biorxiv.org/content/10.64898/2025.12.14.692434v1?rss=1 Jung, H. Devant, P. Ching, C. Ota, M. Hamilton, J. Steinhart, Z. Ngo, W. Sandoval, L. Jung, J. H. Xu, D. An, M. Urs, E. Chen, P. A. Allain, V. Tada, T. Nunez, J. K. Landau, N. R. Liu, D. R. Eyquem, J. Doudna, J. A. Marson, A. Carnevale, J. 2025-12-14 doi:10.64898/2025.12.14.692434 Cold Spring Harbor Laboratory Press 2025-12-14 <![CDATA[ Rotational settings quantize nucleosome movement by chromatin regulators ]]> https://biorxiv.org/content/10.64898/2025.12.12.693854v1?rss=1 La, V. Trouth, A. Ramani, V. Ramachandran, S. 2025-12-15 doi:10.64898/2025.12.12.693854 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Integrative Genomic and Functional Analyses Reveal NINL as a Modulator of Tau Aggregation ]]> https://biorxiv.org/content/10.64898/2025.12.12.694063v1?rss=1 Swift, S. K. Huang, G. Cochran, J. N. Minaya, M. A. Castruita, P. A. Miller, K. J. Starr, E. Galasso, G. Marsh, J. A. Kao, A. Yokoyama, J. S. Karch, C. M. 2025-12-16 doi:10.64898/2025.12.12.694063 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ The Binding Landscape of an Essential Nuclear Hormone Receptor in C. elegans ]]> https://biorxiv.org/content/10.64898/2025.12.14.694179v1?rss=1 Sinks, A. L. Asahina, M. Yamamoto, K. R. Ward, J. D. Thurtle-Schmidt, D. M. 2025-12-16 doi:10.64898/2025.12.14.694179 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Functional diversification of the cephalopod proteome by RNA-editing ]]> https://biorxiv.org/content/10.64898/2025.12.15.694494v1?rss=1 Moen, J. M. Richards, A. L. Krogsaeter, E. K. Polacco, B. Gordon, M. Stevenson, E. Boyles, R. Burq, M. Stepec, D. Crampton, B. Cimermancic, P. Rosenthal, J. J. C. Krogan, N. J. Swaney, D. L. 2025-12-16 doi:10.64898/2025.12.15.694494 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Mapping of critical prosodic and phonetic networks in post-stroke apraxia of speech ]]> https://biorxiv.org/content/10.64898/2025.12.16.694760v1?rss=1 Kurteff, G. L. Walker, G. M. Fridriksson, J. Hickok, G. 2025-12-19 doi:10.64898/2025.12.16.694760 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ Mu opioid receptor mRNA and protein localization across the rat and mouse habenula ]]> https://biorxiv.org/content/10.64898/2025.12.16.694766v1?rss=1 Popat, A. K. Simon, R. C. Aoyama, B. B. Wokhlu, A. Ehrlich, A. T. Harwell, C. C. Margolis, E. B. 2025-12-19 doi:10.64898/2025.12.16.694766 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ High false sign rates in transcriptome-wide association studies ]]> https://biorxiv.org/content/10.64898/2025.12.19.695550v1?rss=1 Gerlach, P. A. Milind, N. Spence, J. P. Pritchard, J. K. 2025-12-20 doi:10.64898/2025.12.19.695550 Cold Spring Harbor Laboratory Press 2025-12-20 <![CDATA[ Single cell RNA sequencing reveals limited effects of Lrrk2 genotype in a mouse model of acute CNS inflammation ]]> https://biorxiv.org/content/10.64898/2025.12.18.695199v1?rss=1 Cookson, M. R. Kaganovich, A. Horan-Portelance, L. Landeck, N. Acri, D. J. Ding, J. Langston, R. 2025-12-22 doi:10.64898/2025.12.18.695199 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Neocortical temporal patterning by a two-layered regulatory network ]]> https://biorxiv.org/content/10.64898/2025.12.18.695250v1?rss=1 Yuan, G. Zhao, Z. Dong, X. Wang, X.-W. Zhang, Q. Yu, X. Zhu, M. Yu, J. Zhang, D. Zhang, N. Xu, Z. Dai, L. Liu, Y.-Y. Shi, S.-H. Li, Y. 2025-12-22 doi:10.64898/2025.12.18.695250 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Transcriptomic analysis of 40 human and rodent skeletal muscle exerkines ]]> https://biorxiv.org/content/10.64898/2025.12.19.695001v1?rss=1 Taha, H. B. Robbins, N. Zoha, F.-S. Vivek, N. Bogoniewski, A. 2025-12-22 doi:10.64898/2025.12.19.695001 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Ecdysone Receptor autonomously controls germ cell differentiation in the Drosophila ovary ]]> https://biorxiv.org/content/10.64898/2025.12.19.695538v1?rss=1 Jung, L. E. Warren, A. I. Yin, C. Huang, W. Simmons, A. C. McDonald, S. I. Swain, L. A. Garrido, V. E. Phipps, D. N. Cesar, B. Finger, D. S. Sun, Z. Nystul, T. Ables, E. T. 2025-12-22 doi:10.64898/2025.12.19.695538 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Concreteness shapes semantic representations in bilingual brains ]]> https://biorxiv.org/content/10.64898/2025.12.23.696243v1?rss=1 Lamarre, M. Gong, X. L. Chen, C. Deniz, F. 2025-12-24 doi:10.64898/2025.12.23.696243 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits ]]> https://biorxiv.org/content/10.64898/2025.12.23.696273v1?rss=1 Zhu, R. Dann, E. Yan, J. Reyes Retana, J. Goto, R. Guitche, R. C. Petersen, L. K. Ota, M. Pritchard, J. K. Marson, A. 2025-12-24 doi:10.64898/2025.12.23.696273 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ Shifts in the human gut microbiome during cancer chemotherapy are diet-dependent ]]> https://biorxiv.org/content/10.64898/2025.12.23.696294v1?rss=1 Trepka, K. R. Van Blarigan, E. L. Kyaw, T. S. Olson, C. A. Partipilo, G. Ortega, E. F. Noecker, C. Upadhyay, V. Zhang, C. Gempis, D. Steiding, P. Stanfield, D. Venook, A. P. Atreya, C. E. Kidder, W. A. Turnbaugh, P. J. 2025-12-24 doi:10.64898/2025.12.23.696294 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ Mammalian metaphase kinetochores are elastic and require condensin for robust structure and function ]]> https://biorxiv.org/content/10.64898/2025.12.23.696255v1?rss=1 Tran, V. M. Tao, J. Rux, C. J. Gomez Siu, D. Rosas Salvans, M. Dumont, S. 2025-12-25 doi:10.64898/2025.12.23.696255 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ Aging increases ovarian cancer growth, metastasis and immunosuppression that can be alleviated by inhibiting hedgehog signaling ]]> https://biorxiv.org/content/10.64898/2025.12.23.695206v1?rss=1 Kumari, A. Elbahoty, M. H. Rajkarnikar, R. Sureja, K. Monavarian, M. Quintero, L. M. Fuh, K. Tyrrell, D. J. Shevde, L. A. Margaroli, C. Mythreye, K. 2025-12-27 doi:10.64898/2025.12.23.695206 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ Dose-dependent NFI regulation of progenitor lifespan and output underlying human neocortical malformation ]]> https://biorxiv.org/content/10.64898/2025.12.27.696675v1?rss=1 Zhang, Q. Yuan, G. Albizzati, E. Yang, J. Zhao, Z. Yu, X. Chang, X. Lee, C. H. Du, H. Lao, Z. Krishnamurthy, A. Zhang, X. Lv, X. Tang, X. Hu, S. Chi, Y. Ma, J. Gronostajski, R. M. Richards, L. J. Zhang, J. Joyner, A. L. Tchieu, J. Li, Y. Shi, S.-H. 2025-12-27 doi:10.64898/2025.12.27.696675 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ Large scale prospective evaluation of co-folding across 557 Mac1-ligand complexes and three virtual screens ]]> https://biorxiv.org/content/10.64898/2025.12.25.696505v1?rss=1 50% of the Mac1 ligand poses to better than 2 [A] RMSD of experiment. Despite the potential for co-folding to describe protein conformational changes that stabilize ligand binding, we did not find that common conformational rearrangements, including peptide flip and a large loop opening, were recapitulated by the co-folding prediction. For AF3 and Chai-1, ligand pose prediction confidence weakly, but significantly, tracked experimental potency, while DOCK3.7 energies were only weakly correlated. Boltz-2 affinity predictions showed the strongest correlation with measured potency and, after calibration, achieved lower mean absolute error than a baseline predictor. We next assessed whether co-folding scores could rescore docking hit-lists to distinguish true ligands from non-binders among hundreds of molecules prospectively experimentally tested against AmpC {beta}-lactamase, the dopamine D4 and the {sigma}2 receptors. AF3 ligand pose confidence values did not separate true ligands from high-scoring false-positives as effectively as docking scores or Boltz-2 affinity predictions did. Taken together, the modest, but independent correlations of docking score and co-folding confidence or affinity suggests that integrating physics-based and deep-learning and approaches may help with hit prioritization and subsequent optimization in structure-based ligand discovery. ]]> Kim, J. Correy, G. J. Hall, B. W. Rachman, M. M. Mailhot, O. Togo, T. Gonciarz, R. L. Jaishankar, P. Neitz, R. J. Hantz, E. R. Doruk, Y. U. Stevens, M. G. V. Diolaiti, M. E. Reid, R. Gopalkrishnan, S. Krogan, N. J. Renslo, A. R. Ashworth, A. Shoichet, B. K. Fraser, J. S. 2025-12-28 doi:10.64898/2025.12.25.696505 Cold Spring Harbor Laboratory Press 2025-12-28 <![CDATA[ Sleep-Wake Transitions Are Impaired in the AppNL-G-FMouse Model of Early Onset Alzheimers Disease ]]> https://biorxiv.org/content/10.64898/2025.12.29.696818v1?rss=1 260 sec) Wake bouts and were hyperactive at 18-22 months, which undoubtedly contributed to the increased Wake/reduced sleep. Despite this reduced sleep phenotype, AppNL-G-F mice were no sleepier than WT mice and the sleep homeostat was functional in both strains. In the second study, sex differences in these parameters were assessed at 18-24 months. Reduced sleep was evident in both sexes of AppNL-G-F mice but was clearly more evident in females. Wake and REM sleep bout durations were longer in both sexes of AppNL-G-F mice than in WT littermates. EEG spectral power during NREM sleep was reduced in female AppNL-G-F mice between 4.88-10.50 Hz compared to WT mice whereas, during REM sleep, both male and female AppNL-G-F mice exhibited reduced spectral power in the theta range. These results suggest that A{beta} deposition may impair state transition mechanism(s) in AppNL-G-F mice and demonstrate that, as in human AD patients, the long wake/short sleep phenotype was more evident in female AppNL-G-F mice, thus supporting the use of this strain as a model to investigate interventions that mitigate AD burden during early disease stages. ]]> Kilduff, T. S. Tisdale, R. K. Sun, Y. Miller, S. R. Lee, S. M. Park, S. Shin, J. Allocca, G. Palop, J. 2025-12-29 doi:10.64898/2025.12.29.696818 Cold Spring Harbor Laboratory Press 2025-12-29 <![CDATA[ Type 2 diabetes Reprograms Bone Marrow Hematopoiesis and Dysregulates Immune Signaling in Response to Stroke ]]> https://biorxiv.org/content/10.64898/2025.12.29.696958v1?rss=1 Zhang, H. Gu, W. Yu, K. Tu, C.-L. Chang, W. Liu, J. 2025-12-30 doi:10.64898/2025.12.29.696958 Cold Spring Harbor Laboratory Press 2025-12-30 <![CDATA[ The osm-9 mutant strain is defective in the recovery phase of long-term memory dynamics ]]> https://biorxiv.org/content/10.64898/2025.12.30.697040v1?rss=1 Ma, N. I. Saifuddin, M. F. A. Munoz Lobato, F. L'Etoile, N. D. 2025-12-30 doi:10.64898/2025.12.30.697040 Cold Spring Harbor Laboratory Press 2025-12-30 <![CDATA[ Kinematic fields of the visuo-hippocampal circuit ]]> https://biorxiv.org/content/10.64898/2025.12.30.697009v1?rss=1 Purandare, C. mehta, m. R. 2025-12-31 doi:10.64898/2025.12.30.697009 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Multi-modal choroid plexus pathology in aging and Alzheimer's disease ]]> https://biorxiv.org/content/10.64898/2025.12.30.697051v1?rss=1 500 postmortem samples age 16 to 105, spatial transcriptomics, and functional studies in 5xFAD mice. We identify fibrosis, calcification, and macrophage abnormalities as hallmarks of ChP aging, with AD pathology conferring additional effects, including expansion of a pro-inflammatory fibroblast-macrophage signaling niche. In 5xFAD mice, macrophage dysfunction is associated with impaired epithelial barrier maintenance and repair. Together, these data provide a foundational resource for understanding ChP dysfunction in aging and AD and propose the macrophage-fibroblast-epithelial barrier axis as a driver of ChP pathology. ]]> Xu, H. Lotfy, P. Englert, B. Oberhauser, J. Byer, L. I. J. Wihlman, J. Colangelo, K. Okar, S. V. Thommana, A. Puttonen, H. Mäyränpää, M. I. Tuimala, J. Pedrosa, R. Kumar, D. Haberberger, J. F. Atkins, M. E. Alimukhamedov, S. Pragana, A. Benson, J. Gabrielle, M. E. Dong, A. DurantLaforet, V. Lin, P. B.-C. Keene, C. D. Latimer, C. S. Prater, K. E. Holtzman, D. M. Isakova, A. E. Wyss-Coray, T. Schafer, D. P. Reich, D. S. Lehtimäki, T. Karhunen, P. J. Kok, E. Jansson, D. Yang, A. C. Myllykangas, L. Ordovas-Montanes, J. Lehtinen, M. K. 2025-12-31 doi:10.64898/2025.12.30.697051 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Fezf2 regulates differentiation of Aire-expressing and post-Aire mimetic epithelial populations maintaining thymic homeostasis ]]> https://biorxiv.org/content/10.64898/2025.12.31.697099v1?rss=1 Germino, J. Liu, X. Wang, Y. Balolong, J. Tang, V. Sun, I.-H. Nie, Y. Tsyporin, J. Proekt, I. Rattay, K. Ntranos, V. Anderson, M. S. Chen, B. Gardner, J. M. Miller, C. N. 2026-01-01 doi:10.64898/2025.12.31.697099 Cold Spring Harbor Laboratory Press 2026-01-01 <![CDATA[ Progenitor Diversity and Architecture of the Human Ganglionic Eminences Shaping the Basal Ganglia ]]> https://biorxiv.org/content/10.64898/2025.12.31.697063v1?rss=1 Siebert, C. V. Song, M. Moriano, J. A. Li, Z. Silla, A. C. Walker, M. Chen, S. Baltazar, J. Oliveira, L. G. d. Shankar, M. Xie, Y. Suraparaju, P. Wang, S. Bi, Q. Xie, Y. Ren, Y. Garcia, M. T. Wang, L. Zuo, G. Smidt, M. P. Hoekman, M. F. M. Harwell, C. Parent, J. Rubenstein, J. Alvarez-Buylla, A. Kriegstein, A. 2026-01-02 doi:10.64898/2025.12.31.697063 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Single cell RNA-sequencing reveals an association between testosterone treatment and reduced hormone signaling in the human mammary gland ]]> https://biorxiv.org/content/10.64898/2025.12.31.697241v1?rss=1 Phong, K. T. Song, S. Kim, E. A. Conrad, D. N. Gartner, Z. J. 2026-01-02 doi:10.64898/2025.12.31.697241 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Meta-learning is expressed through altered prefrontal cortical dynamics ]]> https://biorxiv.org/content/10.64898/2026.01.01.697272v1?rss=1 Sun, X. Comrie, A. E. Kahn, A. E. Monroe, E. J. Joshi, A. Guidera, J. A. Denovellis, E. L. Krausz, T. A. Zhou, J. Thompson, P. Hernandez, J. Yorita, A. Haque, R. Berke, J. D. Daw, N. D. Frank, L. M. 2026-01-02 doi:10.64898/2026.01.01.697272 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Conformational changes upon pore blocker removal reveal conductive states of TMEM16A ]]> https://biorxiv.org/content/10.64898/2026.01.02.697443v1?rss=1 60 Cl- permeation events and a single-channel conductance matching experiments. Additional electrostatic and kinetic modeling indicated that TMEM16As transition from outward-rectification to Ohmic conductance with increasing Ca2+ results from a weak voltage dependence of Ca2+ binding, which act cooperatively to open the pore. HIGHLIGHTSO_LIRemoval of the inhibitor 1PBC from TMEM16A induces spontaneous transitions to ion conductive and non-conductive states via bending in TM4 at two different locations. C_LIO_LISimulations suggest that the open state is stabilized by a small hydrophobic network between TM3 and 4 and disrupting this network biases channel closure in electrophysiological recordings. C_LIO_LIA kinetic model of conduction based on energetics from the all-atom MD simulations coupled to continuum calculations gives a linear current-voltage curve consistent with the fully open conformation and removal of 1 Ca2+ switches to an outwardly rectifying state via electrostatic influence on the Cl- energy profile. However, the rectification is too weak to match experiment, but a cooperative model of Ca2+ binding with weak voltage-dependence does match experiment. C_LI ]]> Stephens, C. A. Marcoline, F. V. Peters, C. J. Grabe, M. 2026-01-03 doi:10.64898/2026.01.02.697443 Cold Spring Harbor Laboratory Press 2026-01-03 <![CDATA[ Ninhydrin as a covalent warhead for chemical proteomic-enabled discovery and selective engagement of reactive arginines ]]> https://biorxiv.org/content/10.64898/2026.01.05.697388v1?rss=1 Ecker, A. Langen, A. Fields, C. Montano, J. L. Tran, M. Seiple, I. B. Zaro, B. W. 2026-01-05 doi:10.64898/2026.01.05.697388 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ HONeD-in on Brain Activity: Deconvolving Passive Diffusion on the Structural Network from Functional Brain Signals ]]> https://biorxiv.org/content/10.64898/2026.01.05.697753v1?rss=1 Sipes, B. S. Arab, F. Nagarajan, S. Raj, A. 2026-01-05 doi:10.64898/2026.01.05.697753 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ Cellular consequences, citrullination substrates, and antigenicity resulting from wild-type and targeted PAD4 on cell surfaces ]]> https://biorxiv.org/content/10.64898/2026.01.05.696859v1?rss=1 Kong, S. Peters-Clarke, T. M. Delaveris, C. S. Phojanakong, P. Steri, V. Wells, J. A. 2026-01-06 doi:10.64898/2026.01.05.696859 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Protein tyrosine phosphatase receptor type kappa (PTPRκ) regulates Superior ON-Direction Selective Ganglion Cell development, facilitating image stabilization ]]> https://biorxiv.org/content/10.64898/2026.01.07.698158v1?rss=1 Lin, T.-H. Balraj, A. Al-Khindi, T. Kiraly, J. K. Dunn, F. A. Kolodkin, A. L. 2026-01-07 doi:10.64898/2026.01.07.698158 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ A Joint Tau Propagation and Neuroinflammation Model Reinforces Inflammatory Modulation of Network-Driven Spread in Alzheimer's Disease ]]> https://biorxiv.org/content/10.64898/2026.01.07.698214v1?rss=1 Dhaliwal, I. Sandell, R. Raj, A. 2026-01-08 doi:10.64898/2026.01.07.698214 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Targeted Chromosomal Sequencing of Wild Bonobos Identifies a Genetically Distinct Subpopulation East of the Lomami River ]]> https://biorxiv.org/content/10.64898/2026.01.08.698381v1?rss=1 Crego-Walters, M. Cuadros-Espinoza, S. Ruiz-Gartzia, I. Han, S. Hermosilla, N. Helsen, P. Frandsen, P. Brumwell Prats, A. M. Alentorn-Moron, P. Fontsere, C. Alvarez Estape, M. Ngofuna, M. Monghiemo, C. Leendertz, F. Thompson, J. Fasbender, D. Dieguez, P. Lotana Lokasola, A. Brand, C. Ndjango, J.-B. Georgiev, A. V. Giles, J. A. Liu, W. Li, Y. Sharp, P. M. Pereboom, Z. Andres, A. M. Kuhlwilm, M. Gronau, I. Kuehl, H. Wessling, E. G. Narat, V. Surbeck, M. Hart, J. A. Hart, T. B. Hvilsom, C. Krutzen, M. Stevens, J. Hahn, B. H. Lizano, E. Prado-Martinez, J. M 2026-01-09 doi:10.64898/2026.01.08.698381 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ Smoothened turnover regulated by Hedgehog signaling in Drosophila ]]> https://biorxiv.org/content/10.64898/2026.01.08.698469v1?rss=1 Hatori, R. Wang, W. Kornberg, T. 2026-01-09 doi:10.64898/2026.01.08.698469 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ Tumor cell death by ferroptosis contributes to an immunosuppressive tumor microenvironment in syngeneic murine models of cancer ]]> https://biorxiv.org/content/10.64898/2026.01.09.698662v1?rss=1 Mbah, N. E. Sutton, D. Hong, H. S. Singhal, R. Menjivar, R. E. Giza, H. Sajjakulnukit, P. Perricone, M. Nwosu, Z. Alektiar, J. Lin, J. Long, D. Andren, A. C. Zhang, L. Crawford, H. C. Frankel, T. L. Pasca di Magliano, M. Franchi, L. Shah, Y. M. Lyssiotis, C. A. 2026-01-11 doi:10.64898/2026.01.09.698662 Cold Spring Harbor Laboratory Press 2026-01-11 <![CDATA[ Atypical GPCR Activation Resolved by Nanobody Engineering ]]> https://biorxiv.org/content/10.64898/2026.01.10.698836v1?rss=1 Schlimgen, R. R. Jenjak, S. E. De La Sancha, A. Darcis, J. Billesboelle, C. B. Olson, L. J. Peterson, F. C. Smit, M. J. Manglik, A. Szpakowska, M. Chevigne, A. Volkman, B. F. 2026-01-11 doi:10.64898/2026.01.10.698836 Cold Spring Harbor Laboratory Press 2026-01-11 <![CDATA[ Intramolecular loops control SARS-CoV-2 nucleocapsid protein self-association and nucleic acid binding dependent on phosphorylation ]]> https://biorxiv.org/content/10.64898/2026.01.10.698783v1?rss=1 Nguyen, A. Datta, S. A. Trent, C. Wu, D. Saleem, Z. Szczesna, E. Owoborode, F. Li, Y. Adly, A. N. Kalish, H. R. Piszczek, G. Morgan, D. O. Schuck, P. Zhao, H. 2026-01-12 doi:10.64898/2026.01.10.698783 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ PRSS56 acts as an intrinsic retinal signal driving postnatal ocular axial growth and myopia susceptibility ]]> https://biorxiv.org/content/10.64898/2026.01.11.697334v1?rss=1 Gangappa, K. Duraikannu, D. Advani, J. Labelle-Dumais, C. Uludag, E. B. Koli, S. Singh, N. Jiang, C. Kuo, Y.-M. Ishikawa, Y. Choquet, H. Swaroop, A. Nair, K. S. 2026-01-12 doi:10.64898/2026.01.11.697334 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ Osteoprotegerin-Enabled Immune Evasion by Pathological Adipose Stromal Cells Drives Metabolic Dysfunction in Obesity ]]> https://biorxiv.org/content/10.64898/2026.01.12.698936v1?rss=1 Apolostolopoulou, H. Wang, Y. Bolus, W. R. Singh, R. D. Bains, A. Bahadure, P. Gupta, K. Koliwad, S. K. Bhushan, A. 2026-01-13 doi:10.64898/2026.01.12.698936 Cold Spring Harbor Laboratory Press 2026-01-13 <![CDATA[ An engineered nanobody inhibitor for molecular-to-circuit control of opioid receptor function ]]> https://biorxiv.org/content/10.64898/2026.01.12.698943v1?rss=1 Valbret, Z. Lamothe-Molina, P. L. Papadogkonaki, S. Koehl, A. Arafiles, J. V. V. Shapiro Tuchman, Z. Fisher, N. M. Radoux-Mergault, A. Canziani, A. Huang, G. Von Zastrow, M. Kosloff, M. Hackenberger, C. P. Manglik, A. Patriarchi, T. Stoeber, M. 2026-01-14 doi:10.64898/2026.01.12.698943 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ NPEPPS segmental duplication drives position effect expression of TBC1D3 in the human brain ]]> https://biorxiv.org/content/10.64898/2026.01.14.699559v1?rss=1 3-fold higher expression relative to other copies is driven by a 110 kbp segmental duplication that occurred [~]8.9 million years ago, relocating a partial duplication of the puromycin-sensitive aminopeptidase gene (NPEPPS), including its promoter, adjacent to this TBC1D3 locus. Using neurospheres and comparative transcriptomics of iPSC-derived cultures, we show that expression of NPEPPSP1-TBC1D3 increases as neurons differentiate as a result of alternative splicing and differential polyadenylation usage. While the fusion exists in other ape lineages, we show subsequent deletion of the NPEPPSP1 promoter in Gorilla and a separate, lineage-specific duplication in the Pan lineage ablated the production of this fusion product, rendering this position effect of TBC1D3 specific to humans. ]]> Guitart, X. Brunner, J. W. Ren, L. Jeong, H. Yoo, D. Porubsky, D. Vollger, M. R. Hoekzema, K. Munson, K. M. Sun, K. Ayllon, M. Hoglin, K. McMullen, R. Pavlovic, B. Pollen, A. A. Eichler, E. E. 2026-01-15 doi:10.64898/2026.01.14.699559 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ Soluble DLK1 secreted by telomere-shortening-induced senescent microglia impairs oligodendrocyte functions and alters neuronal activity ]]> https://biorxiv.org/content/10.64898/2026.01.14.699608v1?rss=1 Liu, B. Mahoney, M. Feng, Y. Telpoukhovskaia, M. A. Giani, A. Torres, E. R. Zhan, L. Ye, P. Zhu, J. Foxe, N. Zhu, D. Tong, X. Srivastava, D. Theodoris, C. V. Gong, S. Zhao, M. Fan, L. Gan, L. 2026-01-15 doi:10.64898/2026.01.14.699608 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ B7-H3-targeted natural killer cells effectively kill atypical teratoid / rhabdoid tumors and extend survival in orthotopic xenografts ]]> https://biorxiv.org/content/10.64898/2026.01.15.699746v1?rss=1 Choe, T. Chakravarti, S. Holl, N. J. Zinsky, M. T. Jones, D. G. Guchhait, S. Rahnama, R. Vorri, S. C. Amaral, A. Lucas, C.-H. G. Raabe, E. H. Bonifant, C. 2026-01-16 doi:10.64898/2026.01.15.699746 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ In vivo Proximity & Spatial Proteomics with CRISPR Screening Identify STXBP1 as a Protective Modifier of a-synuclein Toxicity in Dopamine Neurons. ]]> https://biorxiv.org/content/10.64898/2026.01.16.699530v1?rss=1 Shonai, D. Kent, J. Okafor, A. Gao, Y. Parameswaran, P. Bustamante, E. Ramani, B. Diao, Y. Kampmann, M. Soderblom, E. J. Soderling, S. H. 2026-01-17 doi:10.64898/2026.01.16.699530 Cold Spring Harbor Laboratory Press 2026-01-17 <![CDATA[ Rigor and Transparency in two neurotrauma-publishing journals: editorial policies improve transparent reporting. ]]> https://biorxiv.org/content/10.64898/2026.01.16.699952v1?rss=1 Bandrowski, A. E. Namburi, A. Ferguson, A. R. Floyd, C. L. Martone, M. E. PRECISE-TBI Authors, T. 2026-01-19 doi:10.64898/2026.01.16.699952 Cold Spring Harbor Laboratory Press 2026-01-19 <![CDATA[ Cancer drives atherosclerotic plaque vulnerability by inducing pathological angiogenesis ]]> https://biorxiv.org/content/10.64898/2026.01.18.700232v1?rss=1 Luo, L. Fu, C. Jarr, K.-U. Baylis, R. Sun, V. H. Heemelaar, J. von Scheidt, M. Ramirez, D. Krefting, J. Sachs, N. Wettich, J. L. Winter, H. Gao, H. Wang, F. Adkar, S. Haas, A. Gonzalez, M. Nead, K. T. Maegdefessel, L. Schunkert, H. Neilan, T. G. Leeper, N. J. 2026-01-20 doi:10.64898/2026.01.18.700232 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Selective Immune Silencing by Targeted TGF-β Agonists ]]> https://biorxiv.org/content/10.64898/2026.01.19.700410v1?rss=1 Sun, Q. Ogishi, M. Jiang, H. Barrett, A. K. Yan, H. Sola, E. Zhang, J. Xiao, P. Lyu, H. Salehi, A. Tang, Q. Lanz, T. V. Davis, M. M. Negrin, R. S. Garcia, K. C. 2026-01-20 doi:10.64898/2026.01.19.700410 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Memory erasure by dopamine-gated retrospective learning ]]> https://biorxiv.org/content/10.64898/2026.01.17.700100v1?rss=1 Jeong, H. Zsembik, L. Farouq, F. Chakraborty, R. Belur, N. Zhou, M. Sanders, A. D. Wang, S. X. Srinivasan, A. Cox, S. M. L. Garr, E. Brooke, S. Janak, P. H. Leyton, M. Chen, R. Namboodiri, V. M. K. 2026-01-21 doi:10.64898/2026.01.17.700100 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Sequence and Structural Alignments Reveal Insights into ANKLE2 Evolution and Function ]]> https://biorxiv.org/content/10.64898/2026.01.21.700886v1?rss=1 Fishburn, A. T. Florio, C. J. Skawinski, C. L. S. Becker, S. S. Holleman, E. Robertson, A. E. Sitchon, R. Chedin, F. Shah, P. S. 2026-01-21 doi:10.64898/2026.01.21.700886 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ MicroRNA regulatory targets of VO2peak in older adult participants of the Study of Muscle Mobility and Aging (SOMMA) ]]> https://biorxiv.org/content/10.64898/2026.01.19.700188v1?rss=1 Karere, G. Hsu, F.-C. Hepple, R. T. Coen, P. M. Cummings, S. R. Newman, A. B. Glynn, N. W. Sparks, L. M. Lane, N. E. Hayward, A. G. Xu, J. Wagner, N. Li, G. Chan, J. Cox, L. Kritchevsky, S. B. 2026-01-22 doi:10.64898/2026.01.19.700188 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ The role of cohesin loading at enhancers in the flux of loop extrusion and long-range transcriptional control ]]> https://biorxiv.org/content/10.64898/2026.01.20.700462v1?rss=1 Anderson, E. C. Rahmaninejad, H. Aljahani, A. Arnold, E. M. Adachi, A. S. Shah, R. Hansen, K. L. Cavka, I. Boettiger, A. N. Fudenberg, G. Nora, E. P. 2026-01-22 doi:10.64898/2026.01.20.700462 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Histone 3 lysine 9 dimethylation by the G9a-GLP heterodimer requires intranucleosomal product reading ]]> https://biorxiv.org/content/10.64898/2026.01.21.700667v1?rss=1 Yousefi, F. Simental, E. A. Du, Y. Whedon, S. D. Trnka, M. J. Darling, D. Jia, S. Panning, B. Cole, P. A. Halic, M. Al-Sady, B. 2026-01-22 doi:10.64898/2026.01.21.700667 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Conserved assembly architecture of the essential herpesvirus packaging accessory factor ]]> https://biorxiv.org/content/10.64898/2026.01.22.701024v1?rss=1 Bailey, E. J. Devarkar, S. C. Szczepaniak, R. Meissner, L. M. Chen, X. Wu, C. Weller, S. K. Xiong, Y. Didychuk, A. L. 2026-01-22 doi:10.64898/2026.01.22.701024 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Federated single-cell QTL meta-analysis reveals novel disease mechanisms ]]> https://biorxiv.org/content/10.64898/2026.01.20.700519v1?rss=1 Kaptijn, D. Michielsen, L. Neavin, D. Ripoll-Cladellas, A. Alquicira-Hernandez, J. E. Korshevniuk, M. Lee, J. T. H. Oelen, R. Vochteloo, M. Warmerdam, R. Ando, Y. Ban, M. Bayaraa, O. Berg, M. van Blokland, I. Considine, D. Dieng, M. M. Edahiro, R. Gordon, M. G. Groot, H. E. van der Harst, P. Heinig, M. Hon, C.-C. Idaghdour, Y. Kathail, P. de Klein, N. Li, W. Li, Y. Losert, C. Manikanda, V. Moody, J. Naeem, H. Mokrab, Y. Nawijn, M. C. Netea, M. Niewold, J. Okada, Y. Sawcer, S. Soulama, I. Stegle, O. Tsepilov, Y. Park, W.-Y. Rajagopalan, D. Shahin, T. 2026-01-23 doi:10.64898/2026.01.20.700519 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Biophysically realistic network-level transport model of tau progression with exosome-mediated release and uptake processes ]]> https://biorxiv.org/content/10.64898/2026.01.21.700898v1?rss=1 Barron, N. Tora, V. Cozzolino, E. Bertsch, M. Raj, A. 2026-01-23 doi:10.64898/2026.01.21.700898 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Heterologous betacoronavirus spike immunization in nonhuman primates elicits cross-reactive antibodies that neutralize both sarbeco- and merbecoviruses ]]> https://biorxiv.org/content/10.64898/2026.01.22.700386v1?rss=1 Dueker, K. Capozzola, T. Feng, Z. Lin, R. N. Hurtado, J. Bangaru, S. Yuan, M. Beutler, N. Garcia, E. He, W.-t. Callaghan, S. Avillion, G. Vo, L. Li, X. Torres, J. L. Musharrafieh, R. Song, G. Mishra, N. Sharma, P. Yong, P. Anzanello, F. Kaczmarek-Michaels, K. Ben-Akiva, E. Silva, M. Melo, M. Makhdoomi, M. Westfall-Gomez, E. Rinaldi, W. Ferguson, M. Safonova, Y. Crotty, S. Irvine, D. J. Rogers, T. Ward, A. B. Briney, B. Wilson, I. A. Burton, D. R. andrabi, R. 2026-01-23 doi:10.64898/2026.01.22.700386 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Synthetic Hybrid Receptors for Safer and Programmable T Cell Therapy ]]> https://biorxiv.org/content/10.64898/2026.01.22.701150v1?rss=1 Foisey, M. Garcia, J. Li, X. Yang, X. Hilburger, C. Thienpont, C. Chaves-Martinez, A. Belkaya, S. Truong, T. Zhu, I. Liu, R. Hyrenius-wittsten, A. Almeida, R. Shy, B. R. Allen, G. M. Wyman, S. Roybal, K. T. 2026-01-23 doi:10.64898/2026.01.22.701150 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Spatially resolved transcriptome-metabolome integration reveals region-specific glial lipid dysregulation associated with Alzheimer's pathology ]]> https://biorxiv.org/content/10.64898/2026.01.23.701345v1?rss=1 Xu, L. Yang, H. Leon, J. Li, X. Oehler, A. Modavi, C. Abate, A. R. Condello, C. 2026-01-25 doi:10.64898/2026.01.23.701345 Cold Spring Harbor Laboratory Press 2026-01-25 <![CDATA[ Dynamic reorganization of Developmental to Adult Genome Topology Controls the Initiation and Stabilization of the Human Muscle Stem Cell State ]]> https://biorxiv.org/content/10.64898/2026.01.23.701436v1?rss=1 Romero, M. A. Chien, P. Nicoletti, C. Liliom, H. L. Cox, G. Skuratovsky, E. Saleh, K. Gibbs, D. Gane, L. Hoang, D.-H. Caputo, L. Massenet, J. Sobreira, D. R. Puri, P. L. Pyle, A. D. 2026-01-25 doi:10.64898/2026.01.23.701436 Cold Spring Harbor Laboratory Press 2026-01-25 <![CDATA[ Cell-Autonomous and Systemic Circadian Regulation of Gene Expression in Adipocytes ]]> https://biorxiv.org/content/10.64898/2026.01.24.701487v1?rss=1 Worthen, J. M. Frederick, A. M. Loros, J. J. Dumesic, P. A. Dunlap, J. C. 2026-01-25 doi:10.64898/2026.01.24.701487 Cold Spring Harbor Laboratory Press 2026-01-25 <![CDATA[ The Heat shock protein 70 machinery is crucial in the production of infectious chikungunya virus progeny ]]> https://biorxiv.org/content/10.64898/2026.01.26.701664v1?rss=1 van der Laan, M. Verwimp, S. Johnson, O. T. Bouma, E. M. Trappeniers, K. Visscher, F. E. van den Ende-Metselaar, H. H. van de Pol, D. P. I. Delang, L. Gestwicki, J. E. Kampinga, H. H. Smit, J. M. 2026-01-26 doi:10.64898/2026.01.26.701664 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[ 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[ LANA-dependent Interaction of Host Factors DAXX and BRD4 Impact KSHV Lytic Replication ]]> https://biorxiv.org/content/10.64898/2026.01.28.699085v1?rss=1 Castro, M. d. C. C. Adavikolanu, R. Haas, K. M. Zhou, Y. Krogan, N. J. Kaake, R. M. Sanchez, E. L. 2026-01-28 doi:10.64898/2026.01.28.699085 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ SUMO2 Deletion Changes Chromatin Accessibility and Enhances Cytotoxic T Cell Activation and Tumor Infiltration ]]> https://biorxiv.org/content/10.64898/2026.01.27.700738v1?rss=1 Don, N. T. M. Chen, D.-H. Amaral, M. L. J. Ren, T. Kuang, Y. Huang, S.-T. Chilakapati, N. Ren, B. Schoenberger, S. P. Zheng, Y. Chen, Y. 2026-01-29 doi:10.64898/2026.01.27.700738 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ LSD Reconfigures Cortical Dynamics Through Faster Brain Rhythms and Increased Fractal Dimension ]]> https://biorxiv.org/content/10.64898/2026.01.28.702361v1?rss=1 Subramani, V. Nest, T. Pascarella, A. Brunel, J. Ramos, Y. J. M. Harel, Y. Muthukumaraswamy, S. D. Carhart-Harris, R. Lioi, G. Farrugia, N. Jerbi, K. 2026-01-29 doi:10.64898/2026.01.28.702361 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons ]]> https://biorxiv.org/content/10.64898/2026.01.28.702385v1?rss=1 Heffel, M. G. Xu, H. Pastor-Alonso, O. Li, X. Baig, M. S. Irfan Ghoor, R. Li, R. Kern, C. Kum, J. Zhang, Y. Paino, J. Tsai, M. J. Tai, C.-Y. Tucker, G. Zhao, Z. Hou, A. von Behren, Z. Bhade, M. Li, S. Sandoval, K. Scholes, J. Codrea, F. Calimlim, J. Liao, E. K. Leung, G. Kim, J. Eskin, E. Flint, J. Cotter, J. A. Pasaniuc, B. Bintu, B. Zhu, Q. Mukamel, E. A. Ernst, J. Paredes, M. F. Luo, C. 2026-01-29 doi:10.64898/2026.01.28.702385 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ A genetically encoded ionic-stress sensor reveals protons as a sleep driver ]]> https://biorxiv.org/content/10.64898/2026.01.27.702131v1?rss=1 Ji, Z. Liu, J. Wang, B. Wei, S. Bian, Y. Zeng, W. Chung, C.-I. Ma, Z. Zhang, J. Shu, X. Ma, D. K. 2026-01-30 doi:10.64898/2026.01.27.702131 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Methionine metabolism and the NOP2 methyltransferase are essential for MYC-Driven liver tumorigenesis. ]]> https://biorxiv.org/content/10.64898/2026.01.28.702329v1?rss=1 Lin, S. Berdan, C. Sandy, M. Lu, X. Ramani, V. Nomura, D. Chen, X. Lee, J. V. Goga, A. 2026-01-30 doi:10.64898/2026.01.28.702329 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ H4K20me3 and CTCF act reciprocally at TAD boundaries to regulate cell state transitions ]]> https://biorxiv.org/content/10.64898/2026.01.29.702647v1?rss=1 Atai, K. Mitra, M. Bohn, E. Hu, R. Corvalan, A. Jelinek, D. Voisin, L. Ambrus, A. Sarathy, K. Sparks, W. M. Bonitto, K. Dunkwu, A. Coller, H. A. 2026-01-30 doi:10.64898/2026.01.29.702647 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Predicting early bactericidal activity of tuberculosis drug combinations using a translational pharmacokinetic-pharmacodynamic modeling approach ]]> https://biorxiv.org/content/10.64898/2026.01.29.702705v1?rss=1 de Castro Suarez, N. Nuermberger, E. L. Ernest, J. Savic, R. M. 2026-02-02 doi:10.64898/2026.01.29.702705 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Hydrogel-imposed boundary conditions guide single-lumen neuroepithelial morphogenesis ]]> https://biorxiv.org/content/10.64898/2026.01.30.702717v1?rss=1 Huang, M. S. Roth, J. G. Kim, D. Pashin, K. P. Pizzarella, D. Yang, T. M. Liu, Y. Navarro, R. S. Palmer, T. D. Heilshorn, S. C. 2026-02-02 doi:10.64898/2026.01.30.702717 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ cGAS-mediated IFN-I signaling contributes to disease progression in drug-refractory epilepsy ]]> https://biorxiv.org/content/10.64898/2026.01.30.702860v1?rss=1 Huang, Y. Fan, L. Wong, M. Y. Lei, Z. Krishnamachary, B. Zhu, D. Cadiz, M. Nagiri, R. K. Ye, P. Norman, K. Bhagwat, M. Lee, Y. J. Li, H. Zhu, J. Amin, S. Lauderdale, K. Chen, H. Luo, W. Gong, S. Liechty, B. L. Palop, J. J. Sinha, S. C. Wu, J. Zhao, M. Gan, L. 2026-02-02 doi:10.64898/2026.01.30.702860 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Cellular diversity of the developing chick trigeminal ganglion at single-cell resolution ]]> https://biorxiv.org/content/10.64898/2026.02.01.702869v1?rss=1 Arul Nambi Rajan, A. Hutchins, E. J. 2026-02-03 doi:10.64898/2026.02.01.702869 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Structure-guided design of a targeted autoantibody degrader for neurologic disease ]]> https://biorxiv.org/content/10.64898/2026.02.01.703132v1?rss=1 Zimanyi, M. Dayao, M. Asencor, A. I. Kondapavulur, S. Asaki, J. McCutcheon, K. Dabaco, C. Bodansky, A. Craik, C. Pleasure, S. DeRisi, J. L. Cheng, Y. Wilson, M. Pluvinage, J. V. 2026-02-03 doi:10.64898/2026.02.01.703132 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ LUCas: Light-Uncaged Cas13a using photocleavable interfering guide RNAs ]]> https://biorxiv.org/content/10.64898/2026.02.02.700737v1?rss=1 Ng, C. F. Krishnamurthy, D. Dextre, A. Chorlay, A. Ott, M. Fletcher, D. A. 2026-02-04 doi:10.64898/2026.02.02.700737 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ The selectivity implications of docking libraries with greater and lesser similarities to bio-like molecules ]]> https://biorxiv.org/content/10.64898/2026.02.02.703317v1?rss=1 Hall, B. W. Sakamoto, K. Huang, X.-P. Irwin, J. J. Shoichet, B. K. Roth, B. L. 2026-02-04 doi:10.64898/2026.02.02.703317 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ NLRP11 promotes non-canonical inflammasome activation in human macrophages by enhancing caspase-4 recognition of cytosolic lipopolysaccharide ]]> https://biorxiv.org/content/10.64898/2026.02.02.703338v1?rss=1 Gil-Marques, M. L. Devant, P. Kagan, J. C. Goldberg, M. B. 2026-02-04 doi:10.64898/2026.02.02.703338 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Platelet Molecular Maturation Links Platelet Aging and the Platelet Storage Lesion ]]> https://biorxiv.org/content/10.64898/2026.02.03.703379v1?rss=1 Bainton, C. M. Santos, Y. Mayer, F. Fields, A. Zoghbi, K. Mayer, N. Williamson, D. Chinn, G. Rahn, K. C. Musgrove, J. M. Thomas, K. A. Sall, J. Shea, S. M. Kornblith, L. Z. Bainton, R. J. 2026-02-05 doi:10.64898/2026.02.03.703379 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ Scalable probe-based single-cell transcriptional profiling for virtual cell perturbation mapping and synthetic biology phenotyping ]]> https://biorxiv.org/content/10.64898/2026.02.04.703058v1?rss=1 Swinderman, J. T. Tung, P.-Y. Winters, A. Goudy, L. Wilson, C. M. Bounds, L. R. Teyssier, N. Agrawal, A. Dobin, A. Hua, T. Goodarzi, H. Feng, F. Y. Marson, A. Burke, D. P. Hsu, P. D. Roohani, Y. H. Konermann, S. Kosicki, M. Li, N. Gilbert, L. A. 2026-02-05 doi:10.64898/2026.02.04.703058 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ Stereoselective methyl-swapping demonstrates target specificity of cognitive enhancer ]]> https://biorxiv.org/content/10.64898/2026.02.04.700910v1?rss=1 Boone, M. Dalwadi, U. Deal, A. Zhu, P. J. Croll, T. I. Yamazaki, M. Prescott, K. Minopoli, R. Biscocho, I. Wang, J. Lee, D. J. Arthur, C. P. Laughlin, T. G. Zhou, H. Klope, M. T. Egea, P. F. Schoof, M. Lawrence, R. Renslo, A. R. Costa-Mattioli, M. Frost, A. Walter, P. 2026-02-07 doi:10.64898/2026.02.04.700910 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ A Large Animal Model of Heritable Pulmonary Arterial Hypertension UsingGene-edited BMPR2 Sheep ]]> https://biorxiv.org/content/10.64898/2026.02.06.704456v1?rss=1 Datar, S. A. Werry, N. Brown, A. R. Fitzpatrick, D. S. Falade, O. Trott, J. F. Hutchings, R. Amin, E. K. Morgan, J. M. Nawaytou, H. Deutsch, G. H. Johnson, E. G. Gonzales Viera, O. A. Bishop, T. F. Urbino, T. McNabb, B. R. Austin, E. D. Fineman, J. R. Van Eenennaam, A. L. 2026-02-07 doi:10.64898/2026.02.06.704456 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ Harnessing Inflammatory Monocytes to Overcome Resistance to Anti-PD-1 Immunotherapy ]]> https://biorxiv.org/content/10.64898/2026.02.05.704029v1?rss=1 Zimmerman, M. P. Huang, A. C. Cox, E. K. Al Abosy, R. Chong, W. L. Bastian, A. G. Vietor, K. Choutri, Y. Collier, J. Zhabotynsky, V. Wang, H. Fung, M. Weiss, S. A. Robitschek, E. J. Lin, J.-R. Vallius, T. Pant, S. Sorger, P. K. HUGO, W. Sen, D. R. Haining, W. N. Sharpe, A. H. Miller, B. C. 2026-02-08 doi:10.64898/2026.02.05.704029 Cold Spring Harbor Laboratory Press 2026-02-08 <![CDATA[ A decline in follicle cell function is a major driver of Drosophila ovarian aging ]]> https://biorxiv.org/content/10.64898/2026.02.05.704044v1?rss=1 Wolfgram, E. A. Nystul, T. G. 2026-02-08 doi:10.64898/2026.02.05.704044 Cold Spring Harbor Laboratory Press 2026-02-08 <![CDATA[ MAMBAxBrain: A Multi-task Neural Framework Linking Brain Functional Dynamics to Individual Fingerprints, Cognitive and Disease States ]]> https://biorxiv.org/content/10.64898/2026.02.08.704658v1?rss=1 Xia, Y. Arab, F. Saha, U. Sipes, B. Gooden, G. Chen, M. Raj, A. 2026-02-10 doi:10.64898/2026.02.08.704658 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ Systemic hypoxia suppresses solid tumor growth ]]> https://biorxiv.org/content/10.64898/2026.02.09.704975v1?rss=1 Midha, A. D. Chew, B. T. L. Choi, B. M. H. Suh, J. M. Carpenter, C. Baik, A. H. Joshi, T. Blume, S. Y. Haribowo, A. G. Ruivo, P. Flanigan, W. R. Garg, A. Zhang, D. D. Subramanyam, V. Shuere, R. Seo, Y. VanBrocklin, H. Goodarzi, H. Jain, I. H. 2026-02-10 doi:10.64898/2026.02.09.704975 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ PRECISE TBI Model Catalog: Increasing Accessibility and Reproducibility in TBI research ]]> https://biorxiv.org/content/10.64898/2026.02.10.704562v1?rss=1 Surles-Zeigler, M. C. Holmes, L. Sincomb, T. Martone, M. E. Grethe, J. Ferguson, A. R. Dixon, C. E. 2026-02-12 doi:10.64898/2026.02.10.704562 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ Shared somatosensory-motor neural population dynamics track motor recovery after stroke ]]> https://biorxiv.org/content/10.64898/2026.02.10.705199v1?rss=1 Heimbuch, I. S. Khanna, P. Novik, L. Morecraft, R. J. Ganguly, K. 2026-02-12 doi:10.64898/2026.02.10.705199 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ Distinct tau filament folds in familial frontotemporal dementia due to the MAPT S305I mutation ]]> https://biorxiv.org/content/10.64898/2026.02.12.705620v1?rss=1 Pan, H. S. Merz, G. E. Li, A. N. Le, M. Q. Jo, H. Quddus, A. Yung, A. Kormos, R. Melo, A. A. Ramos, E. M. Lago, A. L. Spina, S. Grinberg, L. T. Rosen, H. H. Tse, E. Gorno-Tempini, M. L. DeGrado, W. F. Seeley, W. W. Southworth, D. R. 2026-02-14 doi:10.64898/2026.02.12.705620 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Inhibition of the EBF1-ITGB8 Axis in Bone Marrow Niche Ameliorates Hallmarks of Myelofibrosis ]]> https://biorxiv.org/content/10.64898/2026.02.16.706171v1?rss=1 Tsurkan, L. Doute, M. Morchel, N. Konada, L. Mehmood, R. Ling, T. Atakilit, A. Marcellino, B. Hoffman, R. Vogel, P. Sheppard, D. Crispino, J. Derecka, M. 2026-02-17 doi:10.64898/2026.02.16.706171 Cold Spring Harbor Laboratory Press 2026-02-17 <![CDATA[ Age-related Delays in Osteochondral Remodeling of Fracture Healing Illustrated by Mass Spectrometry Imaging ]]> https://biorxiv.org/content/10.64898/2026.02.13.705828v1?rss=1 Schurman, C. A. Chandler, W. Hu, D. Taylor, H. Tao, N. Miclau, T. Angel, P. Marcucio, R. Schilling, B. 2026-02-18 doi:10.64898/2026.02.13.705828 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Structural modification of oxazolidinone antibiotics alters nascent peptide stalling preference and peptide trajectory through the ribosome ]]> https://biorxiv.org/content/10.64898/2026.02.16.706219v1?rss=1 Kleinman, J. I. Raskar, T. Klepacki, D. Szal, T. Vazquez-Laslop, N. Mankin, A. Fraser, J. S. Fujimori, D. G. 2026-02-18 doi:10.64898/2026.02.16.706219 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Structural evolution of the MTCH family of mitochondrial insertases ]]> https://biorxiv.org/content/10.64898/2026.02.17.705849v1?rss=1 Stevens, T. A. Luo, Z. Lee, C. Hazu, M. Galatis, E. G. Inglis, A. J. Guna, A. Voorhees, R. M. 2026-02-18 doi:10.64898/2026.02.17.705849 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ In vivo deuteration reveals pronounced variation in myelin lipid turnover rates and reduced myelin renewal with ageing ]]> https://biorxiv.org/content/10.64898/2026.02.17.706445v1?rss=1 Lee, J. Y. Cai, Y. Westerhausen, M. Michael, J. A. Teo, J. D. Song, H. Watt, G. Ellis, S. R. Don, A. S. 2026-02-18 doi:10.64898/2026.02.17.706445 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Targeted shedding of extracellular membrane proteins by induced protease recruitment ]]> https://biorxiv.org/content/10.64898/2026.02.17.706468v1?rss=1 Yao, Z. Zhao, F. Miao, K. Peters-Clarke, T. M. Zhang, Y. Ganjave, S. D. Vazquez-Maldonado, A. L. Wu, Y. Kumru, K. Jumaa, H. Leung, K. K. Wells, J. A. 2026-02-18 doi:10.64898/2026.02.17.706468 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Reconstitution of Ras-PI3Kγ membrane communication and feedback using light-induced signaling inputs ]]> https://biorxiv.org/content/10.64898/2026.02.17.706477v1?rss=1 Doerr, S. Olavarrieta-Colasurdo, A. Hansen, S. D. 2026-02-18 doi:10.64898/2026.02.17.706477 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Unique mineralization pattern revealed in TBCK syndrome mouse model ]]> https://biorxiv.org/content/10.64898/2026.02.18.706703v1?rss=1 Katsura, K. A. Jiang, Y. Didziokas, M. Badt, N. Z. Dougherty, S. Vining, K. H. Bhoj, E. J. 2026-02-20 doi:10.64898/2026.02.18.706703 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Autoantibody Repertoires in Healthy Individuals Vary According to HLA Class II Genotype ]]> https://biorxiv.org/content/10.64898/2026.02.19.706904v1?rss=1 Suseno, R. Boquett, J. A. Dandekar, R. Ituarte, T. Alvarenga, B. D. Vierra-Green, C. Spellman, S. Maiers, M. Wilson, M. Hollenbach, J. A. 2026-02-20 doi:10.64898/2026.02.19.706904 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Induction and regulation of a reversible form of suspended animation in C. elegans ]]> https://biorxiv.org/content/10.64898/2026.02.19.706910v1?rss=1 Liu, J. Wang, B. Catrow, J. L. Pearce, Q. Ji, Z. Yang, S. W. Balakrishnan, A. Cox, J. Ma, D. K. 2026-02-20 doi:10.64898/2026.02.19.706910 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ A universal platform for simultaneous TCRα/β removal enables safer and more potent TCR therapies and autoimmune modeling ]]> https://biorxiv.org/content/10.64898/2026.02.19.706929v1?rss=1 90% deletion efficiency in Jurkat and primary human T cells, markedly enhancing the expression, pairing fidelity, and functional potency of transgenic receptors. Using a clinically relevant HLA-A*02:01-restricted DMF5 TCR, we show that dual TCR ablation boosts antigen-specific activation and cytotoxicity in vitro and significantly enhances tumor clearance in vivo in human immune system (HIS) mice, while preventing graft-versus-host disease (GVHD). Targeted locus amplification revealed that CRISPR-induced double-strand breaks did not alter lentiviral integration profiles, confirming genomic safety. Extending this approach to four insulin-reactive TCRs demonstrated that removal of endogenous receptors increased transduction efficiency and functional activity, with one (1E6) showing selective activation and infiltration of stem cell-derived islet grafts (SC-islets) in vivo. This study establishes a universal, safe, and scalable genome-editing platform for generating functionally precise human T cells. By integrating cancer immunotherapy and autoimmune disease modelling within a single framework, it provides a strong preclinical rationale for dual endogenous TCR removal as a route to improved specificity, safety, and therapeutic efficacy in TCR-based cell therapies. ]]> Zanetti, G. Legut, M. Chen, A. Fathi, F. Suek, N. Teteloshvili, N. Li, H. W. Ding, X. Traum, D. Kaestner, K. Hoang, R. E. Bremer, E. Sewell, A. K. Parent, A. V. Creusot, R. J. Sykes, M. Khosravi Maharlooei, M. 2026-02-20 doi:10.64898/2026.02.19.706929 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Acid sphingomyelinase inhibition restores RPE homeostasis and photoreceptor function in preclinical Stargardt macular degeneration models ]]> https://biorxiv.org/content/10.64898/2026.02.20.706984v1?rss=1 Germer, C. J. Williams, S. Fernandes, V. Espinosa Lima, R. La Cunza, N. R. Tan, L. X. Panda, S. R. Iorio, E. Elahi, F. Lakkaraju, A. 2026-02-22 doi:10.64898/2026.02.20.706984 Cold Spring Harbor Laboratory Press 2026-02-22 <![CDATA[ The Untangle Challenge for accurate ensemble models ]]> https://biorxiv.org/content/10.64898/2026.02.21.706873v1?rss=1 Hopkins, M. S. Terwilliger, T. C. Afonine, P. Ginn, H. M. HOLTON, J. M. 2026-02-22 doi:10.64898/2026.02.21.706873 Cold Spring Harbor Laboratory Press 2026-02-22 <![CDATA[ Title: Optogenetic WNT signaling drives germ layer self-organization in a human gastruloid model ]]> https://biorxiv.org/content/10.64898/2026.02.23.707602v1?rss=1 Schaffer, D. V. Johnson, H. J. McMullin, D. M. Zimmermann, J. Kim, C. Repina, N. Bhalerao, R. Nowakowski, T. 2026-02-25 doi:10.64898/2026.02.23.707602 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ Benzoxaboroles are structurally unique binders of eukaryotic translation initiation factor 4E ]]> https://biorxiv.org/content/10.64898/2026.02.24.707563v1?rss=1 Combs, J. B. Peacock, D. M. Craven, G. B. Jung, S. Chen, Y. Le, S. M. Taunton, J. Shokat, K. 2026-02-25 doi:10.64898/2026.02.24.707563 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ CBASS limits bacteriophage production while maintaining cell viability in Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.64898/2026.02.24.707611v1?rss=1 Huiting, E. Wang, B. Shmidov, E. Musunuri, S. Gitai, Z. Bondy-Denomy, J. 2026-02-25 doi:10.64898/2026.02.24.707611 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ Bradykinin Contributes to Vasogenic Edema in Murine Experimental Cerebral Malaria ]]> https://biorxiv.org/content/10.64898/2026.02.23.704410v1?rss=1 Pinheiro, A. d. S. Teixeira, D. E. Silva-Aguiar, R. P. Shim, Y. J. Merkulova, A. Silbak, S. Skomorovska-Prokvolit, Y. Midem, D. Ogolla, S. Burckhardt, B. B. Gangnus, T. Scharfstein, J. Caruso-Neves, C. McCarty, O. J. Gailani, D. Bader, M. Rosenthal, P. Dent, A. E. Janse, C. J. McCrae, K. Pinheiro, A. A. d. S. Kazura, J. W. Schmaier, A. H. 2026-02-26 doi:10.64898/2026.02.23.704410 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Unified function of FACT in mammalian chromatin replication and transcription, dissolving and restoring nucleosomes to counteract genome aggregation ]]> https://biorxiv.org/content/10.64898/2026.02.25.707725v1?rss=1 Frater, R. C. M. Jensen, R. R. Olle Lopez, J. Flury, V. van den Berg, J. Lunow Bournonville, A. Alcaraz, N. Wang, S. Richter, H. Yang, M. Du, Q. van Oudenaarden, A. Ramani, V. Krietenstein, N. Groth, A. 2026-02-26 doi:10.64898/2026.02.25.707725 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Protein-guided RNA barcoding links transcriptomes to synaptic architecture ]]> https://biorxiv.org/content/10.64898/2026.02.26.705527v1?rss=1 Urke, A. Dolan, M.-J. Silverman, J. Kim, M. T. Pineda, J. Garcia, S. Luu, J. Buckley, A. Kumar, V. Zhao, B. Chan, K. Nadaf, N. Balderrama, K. S. Arnold, D. B. Stevens, B. Deverman, B. E. Macosko, E. Z. 2026-02-27 doi:10.64898/2026.02.26.705527 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ Power is a major confounder in the analysis of cross-ancestry 'portability' in human eQTLs ]]> https://biorxiv.org/content/10.64898/2026.02.26.708346v1?rss=1 Gibbs, P. M. Beasley, I. J. Del Azodi, C. B. McCarthy, D. J. Gallego Romero, I. 2026-02-27 doi:10.64898/2026.02.26.708346 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ Differential Methylation by Early Life Adversity in the Future of Families Child Wellbeing Study ]]> https://biorxiv.org/content/10.64898/2026.02.27.708594v1?rss=1 Dumas Ang, S. Chin, S. Schneper, L. M. Johnston, R. A. Koss, K. J. Mitchell, C. Notterman, D. A. Engelhardt, B. E. Pena, C. J. 2026-02-28 doi:10.64898/2026.02.27.708594 Cold Spring Harbor Laboratory Press 2026-02-28 <![CDATA[ Blood-brain barrier dysfunction predicts cognitive trajectory after ischemic stroke ]]> https://biorxiv.org/content/10.64898/2026.02.27.708013v1?rss=1 Xue, L. Jones, O. A. Drag, L. Zera, K. A. Zhu, L. Mlynash, M. Carmichael, N. S. Shu, C.-H. Biesiada, Z. Seong, D. Thomas, O. M. Simmons, E. C. Huang, E. Berry, K. Chung, P. Aslan, A. Xue, R. Rutledge, J. E. Oh, H. S.-H. Yang, L. K. James, T. Ghanem, M. Moran-Losada, P. Poston, K. L. Henderson, V. W. Grainger, J. Allan, S. M. Lansberg, M. Mormino, E. C. Wyss-Coray, T. Kapasi, A. Schneider, J. A. Smith, C. J. Parkes, L. M. Aghaeepour, N. Buckwalter, M. S. 2026-03-02 doi:10.64898/2026.02.27.708013 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ Reprogramming mRNA localization by targeted RNA-protein interference ]]> https://biorxiv.org/content/10.64898/2026.02.27.708609v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@14aaf77org.highwire.dtl.DTLVardef@45af51org.highwire.dtl.DTLVardef@f8fd57org.highwire.dtl.DTLVardef@c06cb1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mason, D. Bandyopadhyay, D. Jiwnani, N. Meyer, B. Mili, S. 2026-03-02 doi:10.64898/2026.02.27.708609 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ Structural variants in human congenital heart disease disrupt distal genomic regulatory contacts of developmental genes ]]> https://biorxiv.org/content/10.64898/2026.02.28.708767v1?rss=1 Lee, J. Wu, J. Pittman, M. Grant, Z. Kuang, S. Quait, D. Morton, S. Fudenberg, G. Traglia, M. Hayes, K. Pediatric Cardiac Genomics Consortium, Kumar, R. Bruneau, B. Pollard, K. S. 2026-03-02 doi:10.64898/2026.02.28.708767 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ NMDA receptor-dependent presynaptic homeostatic plasticity? ]]> https://biorxiv.org/content/10.64898/2026.02.28.708706v1?rss=1 dou, t. zhang, j. hong, y. chen, x. nicoll, r. 2026-03-03 doi:10.64898/2026.02.28.708706 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Intestinal intraepithelial lymphocyte migration and tissue homeostasis are dictated by Gα13 ]]> https://biorxiv.org/content/10.64898/2026.03.01.708910v1?rss=1 Earley, Z. M. Rao, A. Knopper, K. Peng, F. Qiu, L. Jo, N. Lisicka, W. Taglinao, H. An, J. Xu, Y. Yang, L. V. Liu, D. Looney, M. R. Cyster, J. G. 2026-03-03 doi:10.64898/2026.03.01.708910 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ NINTEDANIB AND PIRFENIDONE AFFECT GROWTH AND DIFFERENTIATION OF HUMAN ALVEOLAR TYPE 2 CELLS ]]> https://biorxiv.org/content/10.64898/2026.03.02.708135v1?rss=1 Bazarov, A. V. Serra-Marques, A. Protti, G. Yang, M. Naikawadi, R. P. Green, G. Lee, S. Kukreja, J. Matthay, M. Wax, M. Cai, X. Wolters, R. Rock, J. R. Garfield, D. Wolters, P. J. 2026-03-03 doi:10.64898/2026.03.02.708135 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Hormone signaling and immune programs define differential endocrine responsiveness in high-risk breast tissue ]]> https://biorxiv.org/content/10.64898/2026.03.02.709108v1?rss=1 Goldhammer, N. Bont, M. Warhadpande, S. Choi, M. Cedano, J. Greenwood, H. Ye, J. Schwartz, C. Alvarado, M. Ewing, C. Goodwin, K. Mukhtar, R. Wong, J. Abe, S. Chandler, J. Jackson, J. Olopade, O. Campbell, M. Lam, A. Park, C. Vertido, A. van 't Veer, L. Hylton, N. Esserman, L. Rosenbluth, J. 2026-03-04 doi:10.64898/2026.03.02.709108 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Myofibroblast lineage mapping and inhibiting subretinal fibrosis by targeting SMAD3 and MRTF pathways via microRNA-24 functional study ]]> https://biorxiv.org/content/10.64898/2026.03.03.709397v1?rss=1 Wu, Y. Tong, Y. Byrnes, K. G. Zhou, Q. Dong, C. Benjamin, C. Parker, E. Bao, D. Ren, Z. Anderson, C. A. Ufret-Vincenty, R. L. He, Y.-G. Zhang, Z. Hinkle, D. Ma, J. Wang, S. 2026-03-04 doi:10.64898/2026.03.03.709397 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ LSD Relaxes Structural Constraints on Brain Dynamics and Default Mode Decoupling Tracks Ego Dissolution ]]> https://biorxiv.org/content/10.64898/2026.03.02.709138v1?rss=1 Subramani, V. Pascarella, A. Brunel, J. Harel, Y. Muthukumaraswamy, S. D. Carhart-Harris, R. Jerbi, K. Lioi, G. Farrugia, N. 2026-03-05 doi:10.64898/2026.03.02.709138 Cold Spring Harbor Laboratory Press 2026-03-05 <![CDATA[ ENS lineage potential is not intrinsically regionalized but is modulated by PTPRZ1 signaling ]]> https://biorxiv.org/content/10.64898/2026.03.05.709942v1?rss=1 Kalantari, A. Klein, O. Gartner, Z. J. Fattahi, F. 2026-03-07 doi:10.64898/2026.03.05.709942 Cold Spring Harbor Laboratory Press 2026-03-07 <![CDATA[ CEACAM5/6+ Tumor Cells and IL-1β+ Macrophages Drive Resistance to Chemo-immunotherapy in Gastric Cancer ]]> https://biorxiv.org/content/10.64898/2026.03.05.708917v1?rss=1 Chen, J. Zhang, L. Luo, Y. Han, X. Kang, M. Chen, J. Liu, W. Xun, Z. Chen, G. Chen, K. Xu, S. Zhang, C. Wu, Z. Wu, W. Hao, Z. Han, Y. Lin, Q. Xu, Y. Wang, L. Liang, H. 2026-03-08 doi:10.64898/2026.03.05.708917 Cold Spring Harbor Laboratory Press 2026-03-08 <![CDATA[ A population-scale red blood cell proteome reveals genetically encoded aging clocks predictive of hemolysis and blood donor activity ]]> https://biorxiv.org/content/10.64898/2026.03.07.710284v1?rss=1 View larger version (96K): org.highwire.dtl.DTLVardef@15bd46eorg.highwire.dtl.DTLVardef@1d7c107org.highwire.dtl.DTLVardef@1c1d870org.highwire.dtl.DTLVardef@168dc6f_HPS_FORMAT_FIGEXP M_FIG Dzieciatkowska et al. generate the first population-scale atlas of the RBC proteome across 13,000 donors and develop proteomic and metabolomic aging clocks that quantify biological age. Molecular {Delta}Age is reproducible across donations, genetically encoded and accelerated in G6PD deficiency, sickle cell trait/disease, and iron deficiency - yet reset by iron repletion, tracking with cognitive function and brain iron/myelin. RBC aging clocks predict hemolytic fragility, transfusion efficacy, and donor activity 12 years later. C_FIG HighlightsO_LIRBC proteome atlas of 13,091 donors reveals demographic and genetic programs C_LIO_LIGenetically encoded RBC aging clocks identify regulators of molecular {Delta}age C_LIO_LIMolecular aging features predict hemolysis and transfusion response across cohorts C_LIO_LIRBC molecular age forecasts long-term donor activity over a 12-year follow-up C_LI ]]> Dzieciatkowska, M. Issaian, A. V. Keele, G. R. Saviola, A. Stephenson, D. Bevers, S. Reisz, J. A. Haiman, Z. B. Nemkov, T. Fang, F. Moore, A. Deng, X. Stone, M. Kleinman, S. Norris, P. J. Wang, X. Thein, S.-L. Hod, E. A. Busch, M. P. Roubinian, N. H. Page, G. P. Hansen, K. D'Alessandro, A. 2026-03-08 doi:10.64898/2026.03.07.710284 Cold Spring Harbor Laboratory Press 2026-03-08 <![CDATA[ The React & Rebound Model: Capturing Emotion Regulation Dynamics from Passive Wearable Data ]]> https://biorxiv.org/content/10.64898/2026.03.07.710099v1?rss=1 Heusser, A. C. Simon, T. J. Elliot, E. James, C. Gazzaley, A. Gibson, N. 2026-03-10 doi:10.64898/2026.03.07.710099 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ A Dimeric Rocaglate Promotes Multivalent eIF4A-RNA Assembly ]]> https://biorxiv.org/content/10.64898/2026.03.09.710667v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@12b4dbborg.highwire.dtl.DTLVardef@1fc6e23org.highwire.dtl.DTLVardef@1a2c0f4org.highwire.dtl.DTLVardef@29e158_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Shokat, K. Liu, J. Moore, M. K. Lou, K. Wassarman, D. R. Arab, A. Ojeda, S. Karakyriakou, B. Koglin, A.-S. Ott, C. J. Gilbert, L. 2026-03-10 doi:10.64898/2026.03.09.710667 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Metabolic control of drug resistance by a mycobacterial ion channel ]]> https://biorxiv.org/content/10.64898/2026.03.10.710584v1?rss=1 Gouzy, A. Li, S. Chen, J. Na, A. Saleh, A. Azadian, Z. A. Tam, K. Munsamy-Govender, V. Poulton, N. C. DeJesus, M. A. Schnappinger, D. Rhee, K. Y. Ehrt, S. Rock, J. M. 2026-03-10 doi:10.64898/2026.03.10.710584 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Genome-scale mapping of variant, enhancer and gene function in primary human CD4+ T cells ]]> https://biorxiv.org/content/10.64898/2026.03.09.710372v1?rss=1 Moonen, D. P. Claringbould, A. Gschwind, A. R. Schrod, S. Braunger, J. Feng, C. Rauscher, B. Yi, J. Bi, S. Z. Matthess, Y. Kaulich, M. Acob, R. A. Ayer, A. Engreitz, J. M. Velten, B. Stegle, O. Trynka, G. Zaugg, J. B. Schraivogel, D. Steinmetz, L. M. 2026-03-11 doi:10.64898/2026.03.09.710372 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ KMT2C and KMT2D amplify GRHL2-driven enhancer activation ]]> https://biorxiv.org/content/10.64898/2026.03.10.710694v1?rss=1 Boileau, R. M. Chen, K. Blelloch, R. 2026-03-11 doi:10.64898/2026.03.10.710694 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Saxiphilin is a broad-spectrum toxin sponge for C13-modified saxitoxins ]]> https://biorxiv.org/content/10.64898/2026.03.10.710854v1?rss=1 Zakrzewska, S. Chen, Z. Park, E. Bhaskar, R. G. Bedell, T. A. Du Bois, J. Minor, D. L. 2026-03-11 doi:10.64898/2026.03.10.710854 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Interferon-α and -β subtypes have temporally distinct roles in containing viral spread and protecting vital organs. ]]> https://biorxiv.org/content/10.64898/2026.03.09.710658v1?rss=1 Rezende Melo da Silva, C. Roman, M. I. Heath, N. Gelman, M. Keller, M. Choi, J. Tang, L. Taiwo, O. Kafle, S. Torres-Gonzalez, E. Ramage, H. Andino, R. Sigal, L. J. 2026-03-12 doi:10.64898/2026.03.09.710658 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ Hypothalamic Orexin Input to the Medial Amygdala Links Vigilance to Arousal ]]> https://biorxiv.org/content/10.64898/2026.03.09.710682v1?rss=1 Xiang, X. Chen, C. Zhou, W. 2026-03-12 doi:10.64898/2026.03.09.710682 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ BMP antagonism is required for mandible outgrowth in zebrafish ]]> https://biorxiv.org/content/10.64898/2026.03.11.711234v1?rss=1 Chen, H.-J. Dukov, J. Llyod, T. Xu, P. Farmer, D. 2026-03-12 doi:10.64898/2026.03.11.711234 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ GAP mimetic activity of pan-Ras TCI daraxonrasib synergizes with K-Ras Switch-II pocket inhibition ]]> https://biorxiv.org/content/10.64898/2026.03.11.711097v1?rss=1 Pfaff, P. Shokat, K. 2026-03-13 doi:10.64898/2026.03.11.711097 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Biophysical trade-offs in antibody evolution are resolved by conformation-mediated epistasis ]]> https://biorxiv.org/content/10.64898/2026.03.12.711465v1?rss=1 Tharp, C. R. Catalano, C. Khalifeh, A. Ghaffari-Kashani, S. Huang, R. Kang, G. Scapin, G. Phillips, A. M. 2026-03-13 doi:10.64898/2026.03.12.711465 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Robust PHP in Adult Hippocampus: Essential Assay Optimizations ]]> https://biorxiv.org/content/10.64898/2026.03.12.711375v1?rss=1 Chipman, P. H. Fetter, R. D. Ragozzino, F. J. Lee, U. Davis, G. W. 2026-03-16 doi:10.64898/2026.03.12.711375 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ Reinforcement Learning for Antibiotic Stewardship: Optimizing Prescribing Policies Under Antimicrobial Resistance Dynamics ]]> https://biorxiv.org/content/10.64898/2026.03.12.711398v1?rss=1 Lee, J. Blumberg, S. 2026-03-16 doi:10.64898/2026.03.12.711398 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ Survey of the human proteostasis network: the ubiquitin-proteasome system ]]> https://biorxiv.org/content/10.64898/2026.03.13.711689v1?rss=1 Elsasser, S. Powers, E. Stoeger, T. Sui, X. Kurtzbard, R. D. Martinez-Botia, P. Wangaline, M. A. Gama, A. R. Huttlin, E. L. Elia, L. P. Kelly, J. W. Gestwicki, J. E. Frydman, J. E. Finkbeiner, S. Clerico, E. M. Morimoto, R. Prado, M. A. Vertegaal, A. C. O. Hofmann, K. Finley, D. 2026-03-16 doi:10.64898/2026.03.13.711689 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ Single-library chromosome-scale diploid assemblies of vole genomes resolve a species-specific duplication implicated in pair bonding ]]> https://biorxiv.org/content/10.64898/2026.03.13.711624v1?rss=1 Abuelanin, M. Kaya, G. Lake, J. A. Lambert, C. Wu, M. V. Berendzen, K. Krasheninnikova, K. Wood, J. M. Solomon, N. G. Donaldson, Z. R. Bales, K. L. Howe, K. Korlach, J. Manoli, D. S. Tollkuhn, J. Dennis, M. Y. 2026-03-17 doi:10.64898/2026.03.13.711624 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Using image classifiers to predict CMT2A disease-relevant mitochondrial motility phenotypes in iPSC motor neurons ]]> https://biorxiv.org/content/10.64898/2026.03.16.712192v1?rss=1 Epstein, L. Weiner, A. C. Macklin, B. Kelly, K. R. Conklin, B. R. Engelhardt, B. E. 2026-03-17 doi:10.64898/2026.03.16.712192 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Preferential formation of NUP98-KDM5A condensates at specific H3K4me3-rich loci drives leukemogenic gene expression ]]> https://biorxiv.org/content/10.64898/2026.03.16.712262v1?rss=1 Berrocal, A. Sandoval, J. E. Khetan, N. Ma, A. Wang, T. Moore, C. Narlikar, G. J. Li, H. Galonic Fujimori, D. Huang, B. 2026-03-17 doi:10.64898/2026.03.16.712262 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Genome-scale functional mapping of the mammalian whole brain with in vivo Perturb-seq ]]> https://biorxiv.org/content/10.64898/2026.03.16.711480v1?rss=1 Shi, T. Korshunova, M. Kim, S. DeTomaso, D. Zheng, X. Vishvanath, L. Nyasulu, T. Huynh, N. Sun, A. Thompson, P. C. Zhang, Y. Wigdor, E. M. Rohani, N. Ali, S. Qiu, H. Geralt, M. Zhao, Z. Rabhi, S. Yao, Z. van Velthoven, C. T. Nery, J. R. Castanon, R. G. Dicks, S. Chen, T. J. Ecker, J. R. Zeng, H. Zheng, G. X. Sanders, S. J. Sundaram, L. Jin, X. 2026-03-18 doi:10.64898/2026.03.16.711480 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Female-enriched Eggerthella lenta drives neuroinflammation and IFN-γ via host receptor TLR2 ]]> https://biorxiv.org/content/10.64898/2026.03.16.711194v1?rss=1 Rock, R. R. Alexander, M. Noecker, C. Trepka, K. Upadhyay, V. Ortega, E. Ramirez, L. Siewart, L. Olson, C. Halsey, T. Probstel, A.-K. Baranzini, S. Turnbaugh, P. J. 2026-03-19 doi:10.64898/2026.03.16.711194 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ A Three-dimensional Analytical Framework for Retinal Microvasculature Reveals Layer-associated Vulnerability in Development and Neovascular Remodeling ]]> https://biorxiv.org/content/10.64898/2026.03.16.711909v1?rss=1 Shang, W. Hong, G. Keller, W. E. Morton, R. A. Zeboulon, P. Kenichi, T. Duan, X. Gould, D. B. Kim, T. N. 2026-03-19 doi:10.64898/2026.03.16.711909 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ Gene Expansion and Regulatory Rewiring Shape Sex-Biased Evolution of the Mouse Submandibular Gland Secretome ]]> https://biorxiv.org/content/10.64898/2026.03.18.712472v1?rss=1 Landau, L. J. B. Jain, S. Griffin, N. Saikia, A. Kramer, J. M. Knox, S. Ruhl, S. Gokcumen, O. 2026-03-20 doi:10.64898/2026.03.18.712472 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Library docking for Cannabinoid-2 Receptor ligands ]]> https://biorxiv.org/content/10.64898/2026.03.19.713017v1?rss=1 Rachman, M. M. Iliopoulos-Tsoutsouvas, C. Dominic Sacco, M. Xu, X. Wu, C.-G. Santos, E. Glenn, I. S. Paris, L. Cahill, M. K. Ganapathy, S. Tummino, T. A. Moroz, Y. S. Radchenko, D. S. Okorie, M. Tawfik, V. L. Irwin, J. J. Makriyannis, A. Skiniotis, G. Shoichet, B. K. 2026-03-21 doi:10.64898/2026.03.19.713017 Cold Spring Harbor Laboratory Press 2026-03-21 <![CDATA[ Neurogenin-2 Reprograms Human Microglial Lineage Cells into Neurons In Vitro and in Chimeric Brains ]]> https://biorxiv.org/content/10.64898/2026.03.19.712907v1?rss=1 Jin, M. Ma, Z. Dang, R. Zhang, H. Xue, H. Finkbeiner, S. Liu, Y. Jiang, P. 2026-03-22 doi:10.64898/2026.03.19.712907 Cold Spring Harbor Laboratory Press 2026-03-22 <![CDATA[ Human ancestors interbred with two distinct populations of distant relatives ]]> https://biorxiv.org/content/10.64898/2026.03.22.713509v1?rss=1 Rogers, A. R. Islam, M. T. Brand, C. M. Webster, T. H. 2026-03-23 doi:10.64898/2026.03.22.713509 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ ZMAP: A single-cell meta-atlas of zebrafish embryonic development reveals a consensus hierarchy of cell identities ]]> https://biorxiv.org/content/10.64898/2026.03.23.713599v1?rss=1 Aponte-Santiago, N. A. Su, Y. Wagner, D. E. 2026-03-24 doi:10.64898/2026.03.23.713599 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Genetic architectures of brain-related traits are shaped by strong selective constraints ]]> https://biorxiv.org/content/10.64898/2026.03.22.713538v1?rss=1 Zhu, H. Simons, Y. B. Spence, J. P. Sella, G. Pritchard, J. K. 2026-03-25 doi:10.64898/2026.03.22.713538 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ WTR: A Toolkit for Functional Anterograde Transsynaptic Circuit Mapping ]]> https://biorxiv.org/content/10.64898/2026.03.23.713595v1?rss=1 Wang, T. A. Chen, C. Liu, R. Yi-Luo, A. Cao, X. Hu, J. Guan, S. Chang, S.-y. Cui, X. Zhou, W. Zhao, F. Huang, C.-T. Duan, X. Jan, L. Y. 2026-03-25 doi:10.64898/2026.03.23.713595 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ HIV-1 infection does not confer intrinsic resistance to cell death induced by cytotoxic T lymphocytes ]]> https://biorxiv.org/content/10.64898/2026.03.23.713717v1?rss=1 Bachmann, N. Kim, B. Simonetti, F. R. Kovacs, C. M. Hoh, R. Deeks, S. G. Siliciano, J. D. Siliciano, R. F. 2026-03-25 doi:10.64898/2026.03.23.713717 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Heparan sulfate is essential for Drosophila FGF export ]]> https://biorxiv.org/content/10.64898/2026.03.24.714045v1?rss=1 Barbosa, G. O. Solis-Calero, C. Kornberg, T. 2026-03-26 doi:10.64898/2026.03.24.714045 Cold Spring Harbor Laboratory Press 2026-03-26 <![CDATA[ Requirement for oxidation of neuronal ketone bodies in aging andneurodegeneration ]]> https://biorxiv.org/content/10.64898/2026.03.24.712448v1?rss=1 Yang, J. Nomura, M. Meng, J. X. Garcia, T. Y. Matsuura, T. R. Kelly, D. P. Nakamura, K. Newman, J. C. 2026-03-27 doi:10.64898/2026.03.24.712448 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ A network for self-transcendence derived from patients with brain lesions ]]> https://biorxiv.org/content/10.64898/2026.03.24.713239v1?rss=1 Healey, M. R. Sanchez-Gama, Y. Ding, M. McMahon, J. T. Bourbon, C. Jesani, R. Atwood, G. D. Lord, B. T. Sanguinetti, J. Brewer, J. Vago, D. R. Siddiqi, S. H. Fabbro, F. Urgesi, C. Nielsen, J. A. Ferguson, M. A. 2026-03-27 doi:10.64898/2026.03.24.713239 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Mining functional genes and characterizing cellular transcriptomic profiles in the single-cell atlas of adult Spodoptera litura ovary ]]> https://biorxiv.org/content/10.64898/2026.03.25.713648v1?rss=1 Sun, Z. Jiang, L. Dong, X. Yi, X. Nystul, T. G. Zhong, G. 2026-03-27 doi:10.64898/2026.03.25.713648 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Combinatorial constraints predict that mitochondrial networks contain a large component ]]> https://biorxiv.org/content/10.64898/2026.03.25.714309v1?rss=1 Mostov, R. Lewis, G. R. Das, M. Marshall, W. F. 2026-03-27 doi:10.64898/2026.03.25.714309 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Microenvironmental Determinants of Reaction Kinetics in Biomolecular Condensates Probed with Protein Ligation ]]> https://biorxiv.org/content/10.64898/2026.03.26.714449v1?rss=1 Bae, J. Hong, K. Lee, D. Jun, J. Jung, Y. 2026-03-27 doi:10.64898/2026.03.26.714449 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Tumor Heterogeneity Induces Pro- and Anti-metastatic Myeloid Cell Phenotypes in Breast Cancer Lung Metastasis ]]> https://biorxiv.org/content/10.64898/2026.03.27.714678v1?rss=1 Superville, D. A. Chrenkova, E. Zheng, Y. Combes, A. J. Barozzi, I. Werb, Z. Rendeiro, A. F. McGinnis, C. Goga, A. Winkler, J. 2026-03-27 doi:10.64898/2026.03.27.714678 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Metagenomic strain-resolved DNA modification patterns link extrachromosomal genetic elements to host strains ]]> https://biorxiv.org/content/10.64898/2026.03.27.714056v1?rss=1 1,000 isolate and mock microbiome datasets. Illustrating the approach, we identified 315 strain-resolved, non-redundant ECE-host linkages in environmental and human metagenomes. In infant gut microbiomes, a chromosomal inversion in Enterococcus faecalis alters host and associated plasmid methylation motifs simultaneously. Overall, MODIFI solves a major bottleneck in DNA modification analysis and provides a foundational tool for understanding microbial epigenomics. ]]> Wang, S. Guitor, A. K. Valentin-Alvarado, L. E. Garner, R. Zhang, P. Yan, M. Shi, L.-D. Schoelmerich, M. C. Steininger, H. M. Portik, D. M. Zhang, S. Wilkinson, J. E. Lynch, S. Morowitz, M. J. Hess, M. Diamond, S. Banfield, J. F. Sachdeva, R. 2026-03-28 doi:10.64898/2026.03.27.714056 Cold Spring Harbor Laboratory Press 2026-03-28 <![CDATA[ Spike-in probe-enhanced single-cell RNA-seq reveals post-infusion transcriptomic remodeling of "prime-and-kill" synNotch-CAR-T cells ]]> https://biorxiv.org/content/10.64898/2026.03.26.713760v1?rss=1 Nejo, T. Watchmaker, P. B. Simic, M. S. Yamamichi, A. Lakshmanachetty, S. Zhao, A. Lu, J. Gallus, M. Benway, H. L. Zhu, R. Almeida, R. Lim, W. A. Okada, H. 2026-03-29 doi:10.64898/2026.03.26.713760 Cold Spring Harbor Laboratory Press 2026-03-29 <![CDATA[ StrataChip: a microphysiological system capturing dynamic keratinocyte fate and mechanical transitions during human epidermal morphogenesis ]]> https://biorxiv.org/content/10.64898/2026.03.26.714483v1?rss=1 Amakor, J. K. Rajan, A. A. N. Kamaraj, M. Jacobs, K. A. Hutchins, E. J. Wittmann, T. Kutys, M. L. 2026-03-30 doi:10.64898/2026.03.26.714483 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Prenatal diet buffers infant epigenetic changes linked to pollution and transient wheeze ]]> https://biorxiv.org/content/10.64898/2026.03.26.714555v1?rss=1 Lee, S. A. Konwar, C. Balshaw, R. MacIsaac, J. L. Ramadori, K. Lin, D. T. S. Urtatiz, O. LeWinn, K. Z. Karr, C. J. Smith, A. K. Kobor, M. S. Carroll, K. N. Bush, N. R. Jones, M. J. 2026-03-30 doi:10.64898/2026.03.26.714555 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Multi-cohort Analysis Reveals Microbiome Signatures Associated with Drug Response in New-Onset Rheumatoid Arthritis ]]> https://biorxiv.org/content/10.64898/2026.03.30.715090v1?rss=1 Bodkhe, R. L. Blank, R. B. Trepka, K. R. Orellana, D. A. Scher, J. U. Turnbaugh, P. J. Nayak, R. R. 2026-03-30 doi:10.64898/2026.03.30.715090 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Sleep and emotional memory: translating neural response at encoding to memory accuracy in men and women with and without PTSD ]]> https://biorxiv.org/content/10.64898/2026.03.27.714805v1?rss=1 Santistevan, A. C. Natraj, N. Yack, L. M. Felmingham, K. L. Woodward, S. H. Mathalon, D. H. Neylan, T. C. Richards, A. 2026-03-31 doi:10.64898/2026.03.27.714805 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Cell state-specific metabolic networks govern ferroptosis versus apoptosis in small cell lung cancer ]]> https://biorxiv.org/content/10.64898/2026.03.27.714827v1?rss=1 Kim, J. W. Bebber, C. M. Dai, Y. Bopp, S. Edenhofer, A. Li, A. M. Rosner, T. Berning, L. Yang, M. Leak, L. B. Stroh, J. Shrestha, B. Abdallah, A. Prymidis, D. Olivos, H. Baron, M. Nguyen, T. Shue, Y. T. Nishiga, Y. Drainas, A. Chaikovsky, A. Szylo, K. Li, Y. Kang, Y. P. Manoj, P. Quintanal Villalonga, A. Rudin, C. M. DeNicola, G. M. Dixon, S. J. Frezza, C. Ye, J. von Karstedt, S. Sage, J. 2026-03-31 doi:10.64898/2026.03.27.714827 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Neural correlates of novel word-form learning in developmental language disorder ]]> https://biorxiv.org/content/10.64898/2026.03.28.715039v1?rss=1 Bahar, N. Cler, G. J. Asaridou, S. S. Smith, H. J. Willis, H. E. Healy, M. P. Chughtai, S. Haile, M. Krishnan, S. Watkins, K. E. 2026-03-31 doi:10.64898/2026.03.28.715039 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Resolution of recursive data corruption to transform T-cell epitope discovery ]]> https://biorxiv.org/content/10.64898/2026.03.30.710191v1?rss=1 Preibisch, G. Tyrolski, M. Kucharski, P. Gizinski, S. Grzegorczyk, P. Moon, S. Kim, S. Zaro, B. Gambin, A. 2026-04-01 doi:10.64898/2026.03.30.710191 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ An integrated single cell and spatial omics atlas of human prenatal development ]]> https://biorxiv.org/content/10.64898/2026.03.30.714220v1?rss=1 Webb, S. Rose, A. Xu, C. Steele, L. Kuri, M. A. Stephenson, E. Inecik, K. Jafree, D. Foster, A. R. Basurto-Lozada, D. Chipampe, N.-J. Pournara, A. V. Jacques, M.-A. To, K. Admane, C. Kritikaki, E. Chroscik, M. A. Horsfall, D. Foreman, J. Rademaker, K. Karjalainen, J. Laddach, A. Madad, S. Lawrence, J. E. G. Kleshchevnikov, V. Lisgo, S. Lee, J. T. H. Blevinal, J. Alqahtani, A. Makarchuk, S. Jackson, J. Ucuncu, E. Silva, T. P. Lorenzi, V. Torabi, F. Botting, R. A. Roberts, K. Olabi, B. Chakala, K. P. Dony, L. Dall'Aglio, G. Cujba, A.-M. Whitfield, H. J. 2026-04-01 doi:10.64898/2026.03.30.714220 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Population genomics reveals multi-scale mechanisms sustaining schistosomiasis re-emergence in a near-elimination setting ]]> https://biorxiv.org/content/10.64898/2026.03.30.715205v1?rss=1 Guss, H. Francioli, Y. Grover, E. Hill, A. Zou, W. Wade, K. Pike, H. Gopalan, S. S. Yang, L. Bo, Z. Pollock, D. Carlton, E. Castoe, T. A. 2026-04-01 doi:10.64898/2026.03.30.715205 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Temporal AI model predicts drivers of cell state trajectories across human aging ]]> https://biorxiv.org/content/10.64898/2026.03.30.715396v1?rss=1 Gomez Ortega, J. Nadadur, R. D. Kunitomi, A. Kothen-Hill, S. Wagner, J. U. G. Kurtoglu, S. D. Kim, B. Reid, M. M. Lu, T. Washizu, K. Zanders, L. Chen, H. Zhang, Y. Ancheta, S. Lichtarge, S. Johnson, W. A. Thompson, C. Phan, D. M. Combes, A. J. Yang, A. C. Tadimeti, N. Dimmeler, S. Yamanaka, S. Alexanian, M. Theodoris, C. V. 2026-04-01 doi:10.64898/2026.03.30.715396 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ State-Dependent Organization of Microscale Functional Circuitry in Visual Cortex ]]> https://biorxiv.org/content/10.64898/2026.03.31.715474v1?rss=1 Biswas, R. Wickrama Senevirathne, H. Wang, Y. Zhang, J. Mukherjee, S. Abbasi-Asl, R. 2026-04-01 doi:10.64898/2026.03.31.715474 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Aerobic exercise prevents the loss of endogenous pain modulation in male and female rats with traumatic brain injury. ]]> https://biorxiv.org/content/10.64898/2026.03.31.714901v1?rss=1 Irvine, K.-A. Ferguson, A. R. Clark, D. J. 2026-04-02 doi:10.64898/2026.03.31.714901 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ Epilepsy-associated potassium channel KCNT1 is required for multiciliated cell development in Xenopus ]]> https://biorxiv.org/content/10.64898/2026.03.31.710877v1?rss=1 Chemel, A. K. McCluskey, K. E. Tran, M. N. Ehrlich, A. T. Willsey, H. R. 2026-04-03 doi:10.64898/2026.03.31.710877 Cold Spring Harbor Laboratory Press 2026-04-03 <![CDATA[ Molecular dynamics of Brodmann Area 22 in development and autism ]]> https://biorxiv.org/content/10.64898/2026.03.31.715694v1?rss=1 Suresh, V. Wigdor, E. M. Hao, Y. Leonard, R. Asfouri, J. Griffiths, M. Evans, C. Yuan, G. Rohani, N. Weiss, J. Dema, C. Mukhthar, T. Lassen, F. Schafer, N. Dong, S. Palmer, D. S. Chang, E. F. Sanders, S. J. Nowakowski, T. J. 2026-04-03 doi:10.64898/2026.03.31.715694 Cold Spring Harbor Laboratory Press 2026-04-03 <![CDATA[ Dietary tryptophan mitigates lung ischemia-reperfusion injury via microbiota-derived indole-3-propionate and aryl hydrocarbon receptor signaling ]]> https://biorxiv.org/content/10.64898/2026.04.02.714281v1?rss=1 View larger version (67K): org.highwire.dtl.DTLVardef@112753org.highwire.dtl.DTLVardef@2cdd0eorg.highwire.dtl.DTLVardef@164e413org.highwire.dtl.DTLVardef@b9a34a_HPS_FORMAT_FIGEXP M_FIG A tryptophan-rich diet remodels the gut microbiota and indole metabolite profiles, including IPA, enhances alveolar macrophage AhR signaling, and attenuates sterile lung ischemia-reperfusion injury. C_FIG ]]> Chaki, T. Maruyama, D. Doan, T. N. Tian, X. Prakash, A. 2026-04-06 doi:10.64898/2026.04.02.714281 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ Gain-of-function mutation in SKAP2 leads to type 1 diabetes and broader autoimmunity through hyperactive integrin signaling in myeloid cells ]]> https://biorxiv.org/content/10.64898/2026.04.02.716136v1?rss=1 Tamaki, C. M. Chamberlain, C. E. Abram, C. L. Poojary, S. Bridge, J. Matsuda, J. L. Tamaki, W. Rutsch, N. Spector, L. Dixon, W. Proekt, I. Letourneau-Freiberg, L. R. Philipson, L. H. German, M. S. Anderson, M. S. Lowell, C. A. 2026-04-06 doi:10.64898/2026.04.02.716136 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ FunctionaL Assigning Sequence Homing (FLASH) maps phenotype to sequence with deep and machine learning ]]> https://biorxiv.org/content/10.64898/2026.04.04.715981v1?rss=1 Cotter, D. J. Harrison, M.-C. Rustagi, A. Wang, P. L. Kokot, M. Carey, A. F. Deorowicz, S. Salzman, J. 2026-04-07 doi:10.64898/2026.04.04.715981 Cold Spring Harbor Laboratory Press 2026-04-07 <![CDATA[ Tau-induced mitochondrial reverse electron transport drives neurodegeneration ]]> https://biorxiv.org/content/10.64898/2026.04.04.716514v1?rss=1 Li, W. Rimal, S. Bhurtel, S. Yeung, L. Lu, B. Grinberg, L. T. Spina, S. Cobos, I. Seeley, W. W. Guo, S. Lu, B. 2026-04-07 doi:10.64898/2026.04.04.716514 Cold Spring Harbor Laboratory Press 2026-04-07 <![CDATA[ Gut microbiome-dependent IL-1 signaling is a mediator of ACVR1R206H-driven heterotopic ossification ]]> https://biorxiv.org/content/10.64898/2026.04.05.716562v1?rss=1 95% of FOP patients harbor the ACVR1R206H mutation, patients exhibit significant variability in disease progression, suggesting a role of environmental drivers. Here, we identify the gut microbiome as a regulator of inflammation-driven HO in FOP. Metagenomic profiling of cohabitating FOP/unaffected sibling pairs revealed a pathogenic gut microbiome profile in FOP patients (Bray-Curtis, p < 0.05). In Pdgfr-Cre/Acvr1R206H (FOP) mice, gut microbiome ablation by antibiotics reduced spontaneous HO formation (47.4% reduction, p < 0.05) and reduced plasma IL-1 pathway activity. IL-1{beta} blockade in FOP mice suppressed trauma-induced HO formation. These findings identify a gut microbiome-IL-1-HO axis with modifiable targets for developing treatments for HO and related inflammatory conditions. One Sentence SummaryAntibiotic disruption of the gut microbiome reduces HO in FOP mice via an IL-1 mediated pathway. ]]> Herzog, H. M. Fang, C. Lam, L. Jin, K. Zamarioli, A. Dinh, E. Gupta, C. L. Sharma, A. Moody, T. Pierce, J. L. Hohl, M. S. Takimoto, S. W. Lyalina, S. Wentworth, K. L. Yu, K. Lu, V. F. Isadora Mamikunian, I. Hunt, N. K. Lynch, S. Pollard, K. S. Hernandez, C. J. Perrien, D. S. Hsiao, E. C. 2026-04-08 doi:10.64898/2026.04.05.716562 Cold Spring Harbor Laboratory Press 2026-04-08 <![CDATA[ Successful dendritic cell vaccines require lasting in-situ TNF α secretion to license antitumor CD8 + T cell cytotoxicity ]]> https://biorxiv.org/content/10.64898/2026.04.06.716539v1?rss=1 Khateeb, A. R. Magal, N. S. Inbal, K. Gleiberman, A. Kaminitz, A. Weiss, T. Verbin, G. Richter, A. Zarfin, A. Younis, L. F. Gutwillig, A. Frish, A. Shifrut, E. Reuveni, I. R. Barzel, A. Levi, C. Rider, P. Spitzer, M. H. Engleman, E. G. Madi, A. Carmi, Y. 2026-04-08 doi:10.64898/2026.04.06.716539 Cold Spring Harbor Laboratory Press 2026-04-08