bioRxiv Channel: The Rockefeller University https://biorxiv.org This feed contains articles for bioRxiv Channel "The Rockefeller University" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ RNA-Rocket: An RNA-Seq Analysis Resource for Infectious Disease Research ]]> https://biorxiv.org/content/10.1101/007963v1?rss=1 Andrew S. Warren Cristina Aurrecoechea Brian Brunk Prerak Desai Scott Emrich Gloria I. Giraldo-Calderón Omar Harb Deborah Hix Daniel Lawson Dustin Machi Chunhong Mao Michael McClelland Eric Nordberg Maulik Shukla Leslie B. Vosshall Alice R. Wattam Rebecca Will Hyun Seung Yoo Bruno Sobral 2014-08-14 doi:10.1101/007963 Cold Spring Harbor Laboratory Press 2014-08-14 <![CDATA[ Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants ]]> https://biorxiv.org/content/10.1101/010363v1?rss=1 Aziz Belkadi Alexandre Bolze Yuval Itan Aurelie Cobat Quentin B Vincent Alexander Antipenko Lei Shang Bertrand Boisson Jean-Laurent Casanova Laurent Abel 2014-10-14 doi:10.1101/010363 Cold Spring Harbor Laboratory Press 2014-10-14 <![CDATA[ High-field Functional Magnetic Resonance Imaging of Vocalization Processing in Marmosets ]]> https://biorxiv.org/content/10.1101/010561v1?rss=1 Srivatsun Sadagopan Nesibe Z Temiz Henning U Voss 2014-10-20 doi:10.1101/010561 Cold Spring Harbor Laboratory Press 2014-10-20 <![CDATA[ Genome-engineering with CRISPR-Cas9 in the mosquito Aedes aegypti ]]> https://biorxiv.org/content/10.1101/013276v1?rss=1 Kathryn E Kistler Leslie B Vosshall Benjamin J Matthews 2014-12-27 doi:10.1101/013276 Cold Spring Harbor Laboratory Press 2014-12-27 <![CDATA[ On the dimensionality of olfactory space ]]> https://biorxiv.org/content/10.1101/022103v1?rss=1 Marcelo O Magnasco Andreas Keller Leslie B Vosshall 2015-07-06 doi:10.1101/022103 Cold Spring Harbor Laboratory Press 2015-07-06 <![CDATA[ Fundamental Structure and Modulation of Neuronal Excitability: Synaptic Control of Coding, Resonance, and Network Synchronization ]]> https://biorxiv.org/content/10.1101/022475v1?rss=1 Christoph Kirst Julian Ammer Felix Felmy Andreas Herz Martin Stemmler 2015-07-13 doi:10.1101/022475 Cold Spring Harbor Laboratory Press 2015-07-13 <![CDATA[ The neurotranscriptome of the Aedes aegypti mosquito ]]> https://biorxiv.org/content/10.1101/026823v1?rss=1 Benjamin J Matthews Carolyn S McBride Matthew DeGennaro Orion Despo Leslie B Vosshall 2015-09-15 doi:10.1101/026823 Cold Spring Harbor Laboratory Press 2015-09-15 <![CDATA[ Tying down loose ends in the Chlamydomonas genome ]]> https://biorxiv.org/content/10.1101/027797v1?rss=1 Frederick R. Cross 2015-09-29 doi:10.1101/027797 Cold Spring Harbor Laboratory Press 2015-09-29 <![CDATA[ TRPA1 tunes mosquito thermotaxis to host temperatures ]]> https://biorxiv.org/content/10.1101/027896v1?rss=1 Roman A Corfas Leslie B Vosshall 2015-09-30 doi:10.1101/027896 Cold Spring Harbor Laboratory Press 2015-09-30 <![CDATA[ Dynamic information routing in complex networks ]]> https://biorxiv.org/content/10.1101/029405v1?rss=1 Christoph Kirst Marc Timme Demian Battaglia 2015-10-18 doi:10.1101/029405 Cold Spring Harbor Laboratory Press 2015-10-18 <![CDATA[ Patching holes in the Chlamydomonas genome ]]> https://biorxiv.org/content/10.1101/030163v1?rss=1 Frej Tulin Frederick R. Cross 2015-10-29 doi:10.1101/030163 Cold Spring Harbor Laboratory Press 2015-10-29 <![CDATA[ Sensitive red protein calcium indicators for imaging neural activity ]]> https://biorxiv.org/content/10.1101/041780v1?rss=1 Hod Dana Boaz Mohar Yi Sun Sujatha Narayan Andrew Gordus Jeremy P Hasseman Getahun Tsegaye Graham T Holt Amy Hu Deepika Walpita Ronak Patel John J Macklin Cornelia I Bargmann Misha B Ahrens Eric R Schreiter Vivek Jayaraman Loren L Looger Karel Svoboda Douglas S Kim 2016-02-29 doi:10.1101/041780 Cold Spring Harbor Laboratory Press 2016-02-29 <![CDATA[ Prevalent Presence of Periodic Actin-spectrin-based Membrane Skeleton in a Broad Range of Neuronal Cell Types and Animal Species ]]> https://biorxiv.org/content/10.1101/045856v1?rss=1 Jiang He Ruobo Zhou Zhuhao Wu Monica Carrasco Peri Kurshan Jonathan Farley David Simon Guiping Wang Boran Han Junjie Hao Evan Heller Marc Freeman Kang Shen Tom Maniatis Marc Tessier-Lavigne Xiaowei Zhuang 2016-04-08 doi:10.1101/045856 Cold Spring Harbor Laboratory Press 2016-04-08 <![CDATA[ Transcriptional bursting explains the noise-versus-mean relationship in mRNA and protein levels ]]> https://biorxiv.org/content/10.1101/049528v1?rss=1 Roy D. Dar Sydney M. Schaffer Siddarth S. Dey Jonathan E. Foley Abhyudai Singh Brandon S. Razooky Adam P. Arkin David V. Schafer Michael L. Simpson Arjun Raj Leor S. Weinberger 2016-04-21 doi:10.1101/049528 Cold Spring Harbor Laboratory Press 2016-04-21 <![CDATA[ Olfactory perception of chemically diverse molecules ]]> https://biorxiv.org/content/10.1101/049999v1?rss=1 Andreas Keller Leslie B Vosshall 2016-04-23 doi:10.1101/049999 Cold Spring Harbor Laboratory Press 2016-04-23 <![CDATA[ Physical model of the sequence-to-function map of proteins ]]> https://biorxiv.org/content/10.1101/069039v1?rss=1 Tsvi Tlusty Albert Libchaber Jean-Pierre Eckmann 2016-08-12 doi:10.1101/069039 Cold Spring Harbor Laboratory Press 2016-08-12 <![CDATA[ Occipital white matter tracts in human and macaque ]]> https://biorxiv.org/content/10.1101/069443v1?rss=1 Hiromasa Takemura Franco Pestilli Kevin S Weiner Georgios A Keliris Sofia M Landi Julia Sliwa Frank Q Ye Michael A Barnett David A Leopold Winrich A Freiwald Nikos K Logothetis Brian A Wandell 2016-08-27 doi:10.1101/069443 Cold Spring Harbor Laboratory Press 2016-08-27 <![CDATA[ Reproducibility and replicability of rodent phenotyping in preclinical studies ]]> https://biorxiv.org/content/10.1101/079350v1?rss=1 Neri Kafkafi Joseph Agassi Elissa J Chesler John C Crabbe Wim E Crusio David Eilam Robert Gerlai Ilan Golani Alex Gomez-Marin Ruth Heller Fuad Iraqi Iman Jaljuli Natasha A Karp Hugh Morgan George Nicholson Donald W Pfaff Helene S Richter Philip B Stark Oliver Stiedl Victoria Stodden Lisa M Tarantino Valter Tucci William Valdar Robert W Williams Hanno Wurbel Yoav Benjamini 2016-10-05 doi:10.1101/079350 Cold Spring Harbor Laboratory Press 2016-10-05 <![CDATA[ Reverse-engineering human olfactory perception from chemical features of odor molecules ]]> https://biorxiv.org/content/10.1101/082495v1?rss=1 Keller, A. Gerkin, R. C. Guan, Y. Dhurandhar, A. Turu, G. Szalai, B. Mainland, J. D. Ihara, Y. Yu, C. W. Wolfinger, R. Vens, C. Schietgat, L. De Grave, K. Norel, R. DREAM Olfaction Prediction Challenge Consortium, Stolovitzky, G. Cecchi, G. Vosshall, L. B. Meyer, P. 2016-10-21 doi:10.1101/082495 Cold Spring Harbor Laboratory Press 2016-10-21 <![CDATA[ The structured diversity of specialized gut symbionts of the New World army ants ]]> https://biorxiv.org/content/10.1101/084376v1?rss=1 Lukasik, P. Newton, J. A. Sanders, J. G. Hu, Y. Moreau, C. Kronauer, D. O'Donnell, S. Koga, R. Russell, J. A. 2016-10-30 doi:10.1101/084376 Cold Spring Harbor Laboratory Press 2016-10-30 <![CDATA[ The adaptive significance of phasic colony cycles in army ants ]]> https://biorxiv.org/content/10.1101/091934v1?rss=1 Garnier, S. Kronauer, D. J. C. 2016-12-06 doi:10.1101/091934 Cold Spring Harbor Laboratory Press 2016-12-06 <![CDATA[ Resolving the Functional Significance of BRCA1 RING Domain Missense Substitutions ]]> https://biorxiv.org/content/10.1101/092619v1?rss=1 Paquette, A. Tao, K. Stark, A. W. Rosenthal, J. Bell, R. Thompson, B. A. Milash, B. A. Gertz, J. Varley, K. E. Thomas, A. Boucher, K. Foulkes, W. D. Goldgar, D. E. Tavtigian, S. V. 2016-12-08 doi:10.1101/092619 Cold Spring Harbor Laboratory Press 2016-12-08 <![CDATA[ Histone gene expression is regulated by histone H2B ubiquitylation in fission yeast ]]> https://biorxiv.org/content/10.1101/094565v1?rss=1 Page, V. Grabowski, D. Allis, C. D. Tanny, J. 2016-12-22 doi:10.1101/094565 Cold Spring Harbor Laboratory Press 2016-12-22 <![CDATA[ Validated Bayesian differentiation of causative and passenger mutations ]]> https://biorxiv.org/content/10.1101/097931v1?rss=1 Cross, F. R. Breker, M. Lieberman, K. L. 2017-01-03 doi:10.1101/097931 Cold Spring Harbor Laboratory Press 2017-01-03 <![CDATA[ De Novo PacBio long-read and phased avian genome assemblies correct and add to genes important in neuroscience research ]]> https://biorxiv.org/content/10.1101/103911v1?rss=1 Korlach, J. Gedman, G. King, S. Chin, J. Howard, J. Cantin, L. Jarvis, E. D. 2017-01-28 doi:10.1101/103911 Cold Spring Harbor Laboratory Press 2017-01-28 <![CDATA[ Evidence for time division multiplexing of multiple simultaneous itemsin a sensory coding bottleneck ]]> https://biorxiv.org/content/10.1101/107185v1?rss=1 Caruso, V. C. Mohl, J. T. Glynn, C. Lee, J. Willett, S. M. Zaman, A. Estrada, R. Tokdar, S. Groh, J. M. 2017-02-09 doi:10.1101/107185 Cold Spring Harbor Laboratory Press 2017-02-09 <![CDATA[ orco mutagenesis causes loss of antennal lobe glomeruli and impaired social behavior in ants ]]> https://biorxiv.org/content/10.1101/112532v1?rss=1 Trible, W. Chang, N.-C. Matthews, B. J. McKenzie, S. K. Olivos-Cisneros, L. Oxley, P. R. Saragosti, J. Kronauer, D. J. 2017-02-28 doi:10.1101/112532 Cold Spring Harbor Laboratory Press 2017-02-28 <![CDATA[ Quantitative evaluation of two-photon calcium imaging modalities for high-speed volumetric calcium imaging in scattering brain tissue ]]> https://biorxiv.org/content/10.1101/115659v1?rss=1 Weisenburger, S. Prevedel, R. Vaziri, A. 2017-03-10 doi:10.1101/115659 Cold Spring Harbor Laboratory Press 2017-03-10 <![CDATA[ Physiological Preparation Of Hair Cells From The Sacculus Of The American Bullfrog (Rana catesbeiana) ]]> https://biorxiv.org/content/10.1101/121582v1?rss=1 Azimzadeh, J. B. Salvi, J. D. 2017-03-29 doi:10.1101/121582 Cold Spring Harbor Laboratory Press 2017-03-29 <![CDATA[ Methicillin resistant Staphylococcus aureus emerged long before the introduction of methicillin in to clinical practice ]]> https://biorxiv.org/content/10.1101/122408v1?rss=1 Harkins, C. P. Pichon, B. Doumith, M. Parkhill, J. Westh, H. Tomasz, A. de Lencastre, H. Bentley, S. D. Kearns, A. M. Holden, M. T. 2017-03-30 doi:10.1101/122408 Cold Spring Harbor Laboratory Press 2017-03-30 <![CDATA[ A multicenter, randomized study of decitabine as epigenetic priming with induction chemotherapy in children with AML ]]> https://biorxiv.org/content/10.1101/124263v1?rss=1 Gore, L. Triche, T. J. Farrar, J. E. Wai, D. Legendre, C. Gooden, G. C. Liang, W. S. Carpten, J. Lee, D. W. Alvaro, F. Macy, M. E. Arndt, C. Barnette, P. Cooper, T. Martin, L. Narendran, A. Pollard, J. Meshinchi, S. Boklan, J. Arceci, R. J. Salhia, B. 2017-06-14 doi:10.1101/124263 Cold Spring Harbor Laboratory Press 2017-06-14 <![CDATA[ Comprehensive characterization of pediatric acute myeloid leukemia reveals novel molecular features and age-specific interactions ]]> https://biorxiv.org/content/10.1101/125609v1?rss=1 2% of cases. In contrast, somatic structural variants, including novel gene fusions and focal MBNL1, ZEB2, and ELF1 deletions, were disproportionately prevalent in young as compared to adult patients. Conversely, DNMT3A and TP53 mutations, common in adults, are conspicuously absent from virtually all pediatric cases. Novel GATA2, FLT3, and CBL mutations, recurrent MYC-ITD, NRAS, KRAS, and WT1 mutations are frequent in pediatric AML. Deletions, mutations, and promoter DNA hypermethylation convergently impact Wnt signaling, Polycomb repression, innate immune cell interactions, and a cluster of zinc finger genes associated with KMT2A rearrangements. These results highlight the need for, and facilitate the development of age-tailored targeted therapies for the treatment of pediatric AML. ]]> Bolouri, H. Farrar, J. E. Triche, T. J. Ries, R. E. Lim, E. L. Alonzo, T. A. Ma, Y. Moore, R. Mungall, A. Marra, M. A. Zhang, J. Ma, X. Liu, Y. Liu, Y. Guidry Auvil, J. M. Davidsen, T. M. Gesuwan, P. Hermida, L. C. Salhia, B. Capone, S. Ramsingh, G. Zwaan, C. M. Noort, S. Piccolo, S. Kolb, E. A. Gamis, A. S. Smith, M. A. Gerhard, D. S. Meshinchi, S. 2017-06-13 doi:10.1101/125609 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ Tissue adaptation: implications for gut immunity and tolerance ]]> https://biorxiv.org/content/10.1101/125641v1?rss=1 Faria, A. M. C. Reis, B. S. Mucida, D. 2017-04-08 doi:10.1101/125641 Cold Spring Harbor Laboratory Press 2017-04-08 <![CDATA[ Morphogen And Community Effects Determine Cell Fates In Response To BMP4 Signaling In Human Embryonic Stem Cells ]]> https://biorxiv.org/content/10.1101/125989v1?rss=1 Nemashkalo, A. Ruzo, A. Heemskerk, I. Warmflash, A. 2017-04-10 doi:10.1101/125989 Cold Spring Harbor Laboratory Press 2017-04-10 <![CDATA[ Dengue virus hijacks a noncanonical oxidoreductase function of a cellular oligosaccharyltransferase complex ]]> https://biorxiv.org/content/10.1101/130914v1?rss=1 Lin, D. L. Cherepanova, N. A. Bozzacco, L. Macdonald, M. R. Gilmore, R. Tai, A. 2017-04-25 doi:10.1101/130914 Cold Spring Harbor Laboratory Press 2017-04-25 <![CDATA[ A Neuropeptide Signaling System That Rapidly Enforces Paternity In The Aedes aegypti Mosquito ]]> https://biorxiv.org/content/10.1101/136150v1?rss=1 500 eggs she will produce during her [~]4-6 week lifespan in the laboratory (2). Successful mating is capable of inducing lifetime refractoriness to subsequent insemination by other males, enforcing the paternity of the first male (3-5). In other species, males use diverse strategies to assure the paternity of their offspring, for instance physical barriers such as mating plugs found in mice (6) and Anopheline mosquitoes (7), and anti-aphrodisiac pheromones used by Drosophila melanogaster males to tag female flies as non-virgin (8). Another widely used strategy in insects is the transfer of biologically active male seminal proteins, produced by the male accessory gland and secreted into the ejaculatory duct along with sperm during insemination, to affect the sexual receptivity of the female (3, 9-13). Perhaps the best-characterized male seminal fluid protein in insects is the Drosophila fly sex peptide (11), which acts on the sex peptide receptor in the female to suppress receptivity and trigger egg production (12). Drosophila sex peptide receptor mutant females will readily remate with multiple males, and wild-type females that mate with sex peptide mutant males remain sexually receptive. ]]> Duvall, L. B. Basrur, N. S. Molina, H. McMeniman, C. J. Vosshall, L. B. 2017-05-09 doi:10.1101/136150 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ De novo indels within introns contribute to ASD incidence ]]> https://biorxiv.org/content/10.1101/137471v1?rss=1 Munoz, A. Yamrom, B. Lee, Y.-h. Andrews, P. Marks, S. Lin, K.-T. Wang, Z. Krainer, A. R. Darnell, R. B. Wigler, M. Iossifov, I. 2017-05-24 doi:10.1101/137471 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ Cooperation And Liaison Between Universities And Editors (CLUE): Recommendations On Best Practice ]]> https://biorxiv.org/content/10.1101/139170v1?rss=1 Wager, E. Kleinert, S. Garfinkel, M. Bahr, V. Baždarić, K. Farthing, M. Graf, C. Hammatt, Z. Horn, L. King, S. Parrish, D. Pulverer, B. Taylor, P. van Meer, G. 2017-05-19 doi:10.1101/139170 Cold Spring Harbor Laboratory Press 2017-05-19 <![CDATA[ Olfactory Receptors Are Required For Social Behavior And Neural Plasticity In Ants, As Evidenced By CRISPR-Mediated Gene Knockout ]]> https://biorxiv.org/content/10.1101/142232v1?rss=1 Yan, H. Opachaloemphan, C. Mancini, G. Yang, H. Gallitto, M. Mlejnek, J. Haight, K. Ghaninia, M. Huo, L. Leibholz, A. Slone, J. Zhou, X. Traficante, M. Penick, C. A. Dolezal, K. Gokhale, K. Stevens, K. Fetter-Pruneda, I. Bonasio, R. Zwiebel, L. J. Berger, S. Liebig, J. Reinberg, D. Desplan, C. 2017-05-25 doi:10.1101/142232 Cold Spring Harbor Laboratory Press 2017-05-25 <![CDATA[ Non-latching positive feedback enables robust bimodality by de-coupling expression noise from the mean ]]> https://biorxiv.org/content/10.1101/144964v1?rss=1 Razooky, B. S. Cao, Y. Perelson, A. S. Simpson, M. L. Weinberger, L. S. 2017-06-13 doi:10.1101/144964 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ Mcm10 functions to isomerize CMG-DNA for replisome bypass of DNA blocks ]]> https://biorxiv.org/content/10.1101/146837v1?rss=1 Langston, L. D. Mayle, R. Schauer, G. D. Yurieva, O. Zhang, D. Yao, N. Y. Georgescu, R. E. O'Donnell, M. E. 2017-06-06 doi:10.1101/146837 Cold Spring Harbor Laboratory Press 2017-06-06 <![CDATA[ LINE-1 and the cell cycle: protein localization and functional dynamics ]]> https://biorxiv.org/content/10.1101/147587v1?rss=1 Mita, P. Wudzinska, A. Sun, X. Andrade, J. Nayak, S. Kahler, D. Badri, S. LaCava, J. Ueberheide, B. Yun, C. Fenyo, D. Boeke, J. 2017-06-30 doi:10.1101/147587 Cold Spring Harbor Laboratory Press 2017-06-30 <![CDATA[ Suppression of non-homologous end joining does not rescue DNA repair defects in Fanconi anemia patient cells ]]> https://biorxiv.org/content/10.1101/151472v1?rss=1 Thongthip, S. Conti, B. A. Lach, F. P. Smogorzewska, A. 2017-06-17 doi:10.1101/151472 Cold Spring Harbor Laboratory Press 2017-06-17 <![CDATA[ Complex polymorphisms in endocytosis genes suggest alpha-cyclodextrin against metastases in breast cancer ]]> https://biorxiv.org/content/10.1101/152405v1?rss=1 Wittkowski, K. M. Dadurian, C. Kim, H. S. Hoshino, A. Lyden, D. 2017-06-20 doi:10.1101/152405 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Type III CRISPR-Cas systems generate cyclic oligoadenylate second messengers to activate Csm6 RNases ]]> https://biorxiv.org/content/10.1101/153262v1?rss=1 Niewoehner, O. Garcia-Doval, C. Rostol, J. T. Berk, C. Schwede, F. Bigler, L. Hall, J. Marraffini, L. Jinek, M. 2017-06-23 doi:10.1101/153262 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ Intestinal epithelial and intraepithelial T cell crosstalk mediates a dynamic response to infection ]]> https://biorxiv.org/content/10.1101/154237v1?rss=1 Hoytema van Konijnenburg, D. P. Reis, B. S. Pedicord, V. Farache, J. Victora, G. D. Mucida, D. 2017-06-23 doi:10.1101/154237 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ Video rate volumetric Ca2+ imaging across cortical layersusing Seeded Iterative Demixing (SID) microscopy ]]> https://biorxiv.org/content/10.1101/155572v1?rss=1 Noebauer, T. Skocek, O. Pernia-Andrade, A. J. Weilguny, L. Martinez Traub, F. Molodtsov, M. I. Vaziri, A. 2017-06-27 doi:10.1101/155572 Cold Spring Harbor Laboratory Press 2017-06-27 <![CDATA[ Dissection of purified LINE-1 reveals distinct nuclear and cytoplasmic intermediates ]]> https://biorxiv.org/content/10.1101/157818v1?rss=1 Molloy, K. R. Taylor, M. S. Altukhov, I. Mita, P. Jiang, H. Adney, E. M. Wudzinska, A. Ischenko, D. Burns, K. H. Fenyo, D. Chait, B. T. Alexeev, D. Rout, M. P. Boeke, J. LaCava, J. 2017-06-30 doi:10.1101/157818 Cold Spring Harbor Laboratory Press 2017-06-30 <![CDATA[ SMELL-S and SMELL-R: olfactory tests not influenced by odor-specific insensitivity or prior olfactory experience ]]> https://biorxiv.org/content/10.1101/161000v1?rss=1 Hsieh, J. W. Keller, A. Wong, M. Jiang, R.-S. Vosshall, L. B. 2017-07-08 doi:10.1101/161000 Cold Spring Harbor Laboratory Press 2017-07-08 <![CDATA[ Rapid isolation of functionally intact nuclei from the yeast Saccharomyces ]]> https://biorxiv.org/content/10.1101/162388v1?rss=1 Niepel, M. Farr, J. Rout, M. P. Strambio De Castillia, C. 2017-07-12 doi:10.1101/162388 Cold Spring Harbor Laboratory Press 2017-07-12 <![CDATA[ Qinichelins, novel catecholate-hydroxamate siderophores synthesized via a multiplexed convergent biosynthesis pathway ]]> https://biorxiv.org/content/10.1101/163170v1?rss=1 Gubbens, J. Wu, C. Zhu, H. Filippov, D. V. Florea, B. I. Rigali, S. Overkleeft, H. S. van Wezel, G. P. 2017-07-13 doi:10.1101/163170 Cold Spring Harbor Laboratory Press 2017-07-13 <![CDATA[ The cytoplasmic DNA sensor cGAS promotes mitotic cell death ]]> https://biorxiv.org/content/10.1101/168070v1?rss=1 Zierhut, C. Funabiki, H. 2017-07-25 doi:10.1101/168070 Cold Spring Harbor Laboratory Press 2017-07-25 <![CDATA[ Experience-dependent translational state defined by cell type-specific ribosome profiling ]]> https://biorxiv.org/content/10.1101/169425v1?rss=1 Eacker, S. M. Crawford, K. Brichta, L. Riessland, M. Ingolia, N. T. Greengard, P. Dawson, T. M. Dawson, V. L. 2017-07-28 doi:10.1101/169425 Cold Spring Harbor Laboratory Press 2017-07-28 <![CDATA[ Tau directs intracellular trafficking by regulating the forces exerted by kinesin and dynein teams ]]> https://biorxiv.org/content/10.1101/173609v1?rss=1 nView larger version (31K):norg.highwire.dtl.DTLVardef@8ba4e0org.highwire.dtl.DTLVardef@1f5945corg.highwire.dtl.DTLVardef@1df2f47org.highwire.dtl.DTLVardef@198f5d8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chaudhary, A. R. Berger, F. Berger, C. L. Hendricks, A. G. 2017-08-08 doi:10.1101/173609 Cold Spring Harbor Laboratory Press 2017-08-08 <![CDATA[ Sniff invariant odor coding ]]> https://biorxiv.org/content/10.1101/174417v1?rss=1 Shusterman, R. Sirotin, Y. B. Smear, M. C. Ahmadian, Y. Rinberg, D. 2017-08-09 doi:10.1101/174417 Cold Spring Harbor Laboratory Press 2017-08-09 <![CDATA[ The complete structure of the small subunit processome ]]> https://biorxiv.org/content/10.1101/175547v1?rss=1 Barandun, J. Chaker-Margot, M. Hunziker, M. Molloy, K. R. Chait, B. T. Klinge, S. 2017-08-13 doi:10.1101/175547 Cold Spring Harbor Laboratory Press 2017-08-13 <![CDATA[ Diverse modes of synaptic signaling, regulation, and plasticity distinguish two classes of C. elegans glutamatergic neurons ]]> https://biorxiv.org/content/10.1101/175836v1?rss=1 Ventimiglia, D. Bargmann, C. 2017-08-13 doi:10.1101/175836 Cold Spring Harbor Laboratory Press 2017-08-13 <![CDATA[ LIM Protein Ajuba associates with the RPA complex through direct and cell cycle-dependent interaction with the RPA70 subunit. ]]> https://biorxiv.org/content/10.1101/177840v1?rss=1 Fowler, S. Maguin, P. Kalan, S. Loayza, D. 2017-08-18 doi:10.1101/177840 Cold Spring Harbor Laboratory Press 2017-08-18 <![CDATA[ Nitrogen conservation, conserved: 46 million years of N-recycling by the core symbionts of turtle ants ]]> https://biorxiv.org/content/10.1101/185314v1?rss=1 Hu, Y Sanders, J Łukasik, P D'Amelio, C Millar, J Vann, D Lan, Y Newton, J Schotanus, M Wertz, J Kronauer, D Pierce, N Moreau, C Engel, P Russell, J 2017-09-07 doi:10.1101/185314 Cold Spring Harbor Laboratory Press 2017-09-07 <![CDATA[ DNAJB1-PRKACA fusion kinase drives tumorigenesis and interacts with β-catenin and the liver regenerative response. ]]> https://biorxiv.org/content/10.1101/192104v1?rss=1 Kastenhuber, E. R. Lalazar, G. Tschaharganeh, D. F. Houlihan, S. L. Baslan, T. Chen, C.-C. Requena, D. Tian, S. Bosbach, B. Wilkinson, J. E. Simon, S. M. Lowe, S. W. 2017-09-21 doi:10.1101/192104 Cold Spring Harbor Laboratory Press 2017-09-21 <![CDATA[ ATRX, DAXX or MEN1 mutant pancreatic neuroendocrine tumors are a distinct alpha-cell signature subgroup ]]> https://biorxiv.org/content/10.1101/195214v1?rss=1 Chan, C. Laddha, S. Lewis, P. Koletsky, M. Robzyk, K. Da Silva, E. Torres, P. Untch, B. Bose, P. Chan, T. Klimstra, D. Allis, C. D. Tang, L. 2017-09-28 doi:10.1101/195214 Cold Spring Harbor Laboratory Press 2017-09-28 <![CDATA[ IRF4 haploinsufficiency in a family with Whipples disease ]]> https://biorxiv.org/content/10.1101/197145v1?rss=1 Guerin, A. Kerner, G. Marr, N. Markle, J. G. Fenollar, F. Wong, N. Boughorbel, S. Avery, D. T. Ma, C. Bougarn, S. Bouaziz, M. Beziat, V. Della Mina, E. Lazarovt, T. Worley, L. Nguyen, T. Patin, E. Deswarte, C. Martinez-Barricarte, R. Boucherit, S. Ayral, X. Edouard, S. Boisson-Dupuis, S. Rattina, V. Bigio, B. Vogt, G. Geissmann, F. Quintana-Murci, L. Chaussabel, D. Tangye, S. Raoult, D. Abel, L. Bustamante, J. Casanova, J.-L. 2017-10-03 doi:10.1101/197145 Cold Spring Harbor Laboratory Press 2017-10-03 <![CDATA[ A natural variant and an engineered mutation in a GPCR promote DEET resistance in C. elegans ]]> https://biorxiv.org/content/10.1101/198705v1?rss=1 Dennis, E. J. Jin, X. Dobosiewicz, M. Duvall, L. B. Hartman, P. S. Bargmann, C. I. Vosshall, L. B. 2017-10-05 doi:10.1101/198705 Cold Spring Harbor Laboratory Press 2017-10-05 <![CDATA[ Hox-logic of preadaptations for social insect symbiosis in rove beetles ]]> https://biorxiv.org/content/10.1101/198945v1?rss=1 Parker, J. Eldredge, K. T. Thomas, I. Coleman, R. Davis, S. 2017-10-05 doi:10.1101/198945 Cold Spring Harbor Laboratory Press 2017-10-05 <![CDATA[ Molecular structure of human KATP in complex with ATP and ADP ]]> https://biorxiv.org/content/10.1101/199034v1?rss=1 Lee, K. Chen, J. MacKinnon, R. 2017-10-12 doi:10.1101/199034 Cold Spring Harbor Laboratory Press 2017-10-12 <![CDATA[ Homozygous STAT2 gain-of-function mutation by loss of USP18 activity in a patient with type I interferonopathy ]]> https://biorxiv.org/content/10.1101/2019.12.12.874123v1?rss=1 Gruber, C. N. Martin-Fernandez, M. Ailal, F. Qiu, X. Taft, J. Altman, J. Rosain, J. Buta, S. Bousfiha, A. Casanova, J.-L. Bustamante, J. Bogunovic, D. 2019-12-16 doi:10.1101/2019.12.12.874123 Cold Spring Harbor Laboratory Press 2019-12-16 <![CDATA[ Intellectual disability-associated factor Zbtb11 cooperates with NRF-2/GABP to control mitochondrial function ]]> https://biorxiv.org/content/10.1101/2019.12.13.875708v1?rss=1 Wilson, B. C. Boehme, L. Annibali, A. Hodgkinson, A. Carroll, T. S. Oakey, R. J. Seitan, V. C. 2019-12-13 doi:10.1101/2019.12.13.875708 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ HIV-1 Vpr induces cell cycle arrest and enhances viral gene expression by depleting CCDC137 ]]> https://biorxiv.org/content/10.1101/2019.12.24.888230v1?rss=1 Zhang, F. Bieniasz, P. D. D. 2019-12-26 doi:10.1101/2019.12.24.888230 Cold Spring Harbor Laboratory Press 2019-12-26 <![CDATA[ Novel genetic features of human and mouse Purkinje cell differentiation defined by comparative transcriptomics. ]]> https://biorxiv.org/content/10.1101/2020.01.07.897371v1?rss=1 Buchholz, D. E. Carroll, T. S. Kocabas, A. Zhu, X. Behesti, H. Faust, P. L. Stalbow, L. Fang, Y. Hatten, M. E. 2020-01-08 doi:10.1101/2020.01.07.897371 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Antigen responsive CD4+ T cell clones contribute to the HIV-1 latent reservoir ]]> https://biorxiv.org/content/10.1101/2020.01.10.902155v1?rss=1 Mendoza, P. Jackson, J. R. Oliveira, T. Gaebler, C. Ramos, V. Caskey, M. Jankovic, M. Nussenzweig, M. C. Cohn, L. B. 2020-01-11 doi:10.1101/2020.01.10.902155 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Nigro-Thalamic Projection Controls Timing of Action Initiation ]]> https://biorxiv.org/content/10.1101/2020.01.12.903500v1?rss=1 Catanese, J. Jaeger, D. 2020-01-14 doi:10.1101/2020.01.12.903500 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Genetic interactions shaping evolutionary trajectories in an RNA virus population ]]> https://biorxiv.org/content/10.1101/2020.01.16.908129v1?rss=1 Chang, C. Bianco, S. Acevedo, A. Tang, C. Andino, R. 2020-01-17 doi:10.1101/2020.01.16.908129 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ Lung type II alveolar epithelial cells collaborate with CCR2+ inflammatory monocytes in host defense against an acute vaccinia infection in the lungs ]]> https://biorxiv.org/content/10.1101/2020.01.20.910927v1?rss=1 Yang, N. Luna, J. M. Dai, P. Wang, Y. Rice, C. M. Deng, L. 2020-01-21 doi:10.1101/2020.01.20.910927 Cold Spring Harbor Laboratory Press 2020-01-21 <![CDATA[ Taking population stratification into account by local permutations in rare-variant association studies on small samples ]]> https://biorxiv.org/content/10.1101/2020.01.29.924977v1?rss=1 Mullaert, J. Bouaziz, M. Seeleuthner, Y. Bigio, B. Casanova, J.-L. Alcais, A. Abel, L. Cobat, A. 2020-01-30 doi:10.1101/2020.01.29.924977 Cold Spring Harbor Laboratory Press 2020-01-30 <![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[ Structural asymmetry governs the assembly and GTPase activity of McrBC restriction complexes ]]> https://biorxiv.org/content/10.1101/2020.01.30.927467v1?rss=1 Niu, Y. Suzuki, H. Hosford, C. J. Walz, T. Chappie, J. S. 2020-01-31 doi:10.1101/2020.01.30.927467 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ A Combination of Two Human Monoclonal Antibodies Limits Fetal Damage by Zika Virus in Macaques ]]> https://biorxiv.org/content/10.1101/2020.01.31.926899v1?rss=1 Van Rompay, K. K. A. Coffey, L. L. Kapoor, T. Gazumyan, A. Keesler, R. I. Jurado, A. Peace, A. Agudelo, M. Watanabe, J. Usachenko, J. Singapuri, A. Immareddy, R. Ardeshir, A. Stuart, J. B. Bournazos, S. Ravetch, J. V. Balderes, P. J. Lorenz, I. C. Esswein, S. R. Keeffe, J. Bjorkman, P. J. Wang, Q. Rice, C. M. MacDonald, M. R. Nussenzweig, M. C. Robbiani, D. F. 2020-02-02 doi:10.1101/2020.01.31.926899 Cold Spring Harbor Laboratory Press 2020-02-02 <![CDATA[ A genome-wide case-only test for the detection of digenic inheritance in human exomes ]]> https://biorxiv.org/content/10.1101/2020.02.06.936922v1?rss=1 Kerner, G. Bouaziz, M. Cobat, A. Bigio, B. Timberlake, A. T. Bustamante, J. Lifton, R. P. Casanova, J.-L. Abel, L. 2020-02-07 doi:10.1101/2020.02.06.936922 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Negative selection on human genes causing severe inborn errors depends on disease outcome and both the mode and mechanism of inheritance ]]> https://biorxiv.org/content/10.1101/2020.02.07.938894v1?rss=1 Rapaport, F. Boisson, B. Gregor, A. Beziat, V. Boisson-Dupuis, S. Bustamante, J. Jouanguy, E. Puel, A. Rosain, J. Zhang, Q. Zhang, S.-Y. Gleeson, J. Quintana-Murci, L. Casanova, J.-L. Abel, L. Patin, E. 2020-02-08 doi:10.1101/2020.02.07.938894 Cold Spring Harbor Laboratory Press 2020-02-08 <![CDATA[ Brown Adipose Tissue is Associated with Improved Cardiometabolic Health and Regulates Blood Pressure ]]> https://biorxiv.org/content/10.1101/2020.02.08.933754v1?rss=1 Becher, T. Palanisamy, S. Kramer, D. J. Marx, S. J. Wibmer, A. G. Del Gaudio, I. Butler, S. D. Jiang, C. S. Vaughan, R. Schoder, H. Di Lorenzo, A. Mark, A. Cohen, P. 2020-02-10 doi:10.1101/2020.02.08.933754 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ Small-molecule inhibition of Lats kinases promotes Yap-dependent proliferation in postmitotic mammalian tissues ]]> https://biorxiv.org/content/10.1101/2020.02.11.944157v1?rss=1 Kastan, N. Gnedeva, K. Alisch, T. Petelski, A. Huggins, D. Chiaravalli, J. Aharanov, A. Shakked, A. Tzahor, E. Nagiel, A. Segil, N. Hudspeth, A. J. 2020-02-12 doi:10.1101/2020.02.11.944157 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Central vestibular tuning arises from patterned convergence of otolith afferents ]]> https://biorxiv.org/content/10.1101/2020.02.14.948356v1?rss=1 Liu, Z. Kimura, Y. Higashijima, S.-i. Hildebrand, D. Morgan, J. Holy, T. Bagnall, M. W. 2020-02-15 doi:10.1101/2020.02.14.948356 Cold Spring Harbor Laboratory Press 2020-02-15 <![CDATA[ Molecular mechanism for direct actin force-sensing by α-catenin ]]> https://biorxiv.org/content/10.1101/2020.02.18.954735v1?rss=1 Mei, L. Espinosa de los Reyes, S. Reynolds, M. J. Liu, S. Alushin, G. M. 2020-02-19 doi:10.1101/2020.02.18.954735 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Activation and self-inactivation mechanisms of the cyclic oligoadenylate-dependent CRISPR ribonuclease Csm6 ]]> https://biorxiv.org/content/10.1101/2020.02.19.952960v1?rss=1 Garcia-Doval, C. Schwede, F. Berk, C. Rostol, J. T. Niewoehner, O. Tejero, O. Hall, J. Marraffini, L. A. Jinek, M. 2020-02-19 doi:10.1101/2020.02.19.952960 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Bacterial immune evasion proteins: The therapeutic potential of CHIPS ]]> https://biorxiv.org/content/10.1101/2020.02.25.964908v1?rss=1 Tromp, A. Zhao, Y. Jongerius, I. Heezius, E. C. Abrial, P. Ruyken, M. van Strijp, J. de Haas, C. J. C. Spaan, A. van Kessel, K. P. M. Henry, T. Haas, P.-J. A. 2020-02-28 doi:10.1101/2020.02.25.964908 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ The Taste of Blood in Mosquitoes ]]> https://biorxiv.org/content/10.1101/2020.02.27.954206v1?rss=1 Jove, V. Gong, Z. Hol, F. J. Zhao, Z. Sorrells, T. R. Carroll, T. S. Prakash, M. McBride, C. S. Vosshall, L. B. 2020-02-27 doi:10.1101/2020.02.27.954206 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ Controlling for Human Population Stratification in Rare Variant Association Studies ]]> https://biorxiv.org/content/10.1101/2020.02.28.969477v1?rss=1 Bouaziz, M. Mullaert, J. Bigio, B. Seeleuthner, Y. Casanova, J.-L. Alcais, A. Abel, L. Cobat, A. 2020-02-28 doi:10.1101/2020.02.28.969477 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ Transcriptional down-regulation of metabolic genes by Gdown1 ablation induces quiescent cell re-entry into the cell cycle ]]> https://biorxiv.org/content/10.1101/2020.03.01.971945v1?rss=1 Jishage, M. Ito, K. Chu, C.-S. Wang, X. Yamaji, M. Roeder, R. G. 2020-03-03 doi:10.1101/2020.03.01.971945 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ Public broadly neutralizing antibodies against hepatitis B virus in individuals with elite serologic activity ]]> https://biorxiv.org/content/10.1101/2020.03.04.976159v1?rss=1 Wang, Q. Michailidis, E. Yu, Y. Wang, Z. Hurley, A. M. Oren, D. A. Mayer, C. T. Gazumyan, A. Liu, Z. Zhou, Y. Schoofs, T. Yao, K.-h. Nieke, J. Wu, J. Jiang, Q. Zou, C. Kabbani, M. Quirk, C. Oliveira, T. Chhosphel, K. Zhang, Q. Schneider, W. M. Jahan, C. Ying, T. Horowitz, J. Caskey, M. Jankovic, M. Robbiani, D. F. Wen, Y. de Jong, Y. P. Rice, C. M. Nussenzweig, M. C. 2020-03-05 doi:10.1101/2020.03.04.976159 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Emergent behavioral organization in heterogeneous groups of a social insect ]]> https://biorxiv.org/content/10.1101/2020.03.05.963207v1?rss=1 Ulrich, Y. Kawakatsu, M. Tokita, C. K. Saragosti, J. Chandra, V. Tarnita, C. E. Kronauer, D. J. 2020-03-06 doi:10.1101/2020.03.05.963207 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ LY6E impairs coronavirus fusion and confers immune control of viral disease ]]> https://biorxiv.org/content/10.1101/2020.03.05.979260v1?rss=1 Pfaender, S. Mar, K. B. Michailidis, E. Kratzel, A. Hirt, D. V'kovski, P. Fan, W. Ebert, N. Stalder, H. Kleine-Weber, H. Hoffmann, M. Hoffmann, H. H. Saeed, M. Dijkman, R. Steinmann, E. Wight-Carter, M. Hanners, N. W. Pohlmann, S. Gallagher, T. Todt, D. Zimmer, G. Rice, C. M. Schoggins, J. W. Thiel, V. 2020-03-07 doi:10.1101/2020.03.05.979260 Cold Spring Harbor Laboratory Press 2020-03-07 <![CDATA[ Mechanosensing through direct binding of tensed F-actin by LIM domains ]]> https://biorxiv.org/content/10.1101/2020.03.06.979245v1?rss=1 Sun, X. Phua, D. Y. Z. Axiotakis, L. Smith, M. A. Blankman, E. Gong, R. Cail, R. C. Espinosa de los Reyes, S. Beckerle, M. C. Waterman, C. M. Alushin, G. M. 2020-03-07 doi:10.1101/2020.03.06.979245 Cold Spring Harbor Laboratory Press 2020-03-07 <![CDATA[ Microbiota-modulated enteric neuron translational profiling uncovers a CART+ glucoregulatory subset ]]> https://biorxiv.org/content/10.1101/2020.03.09.983841v1?rss=1 Muller, P. A. Schneeberger, M. Matheis, F. Kerner, Z. Mucida, D. 2020-03-13 doi:10.1101/2020.03.09.983841 Cold Spring Harbor Laboratory Press 2020-03-13 <![CDATA[ AGO HITS-CLIP in Adipose Tissue Reveals miR-29 as a Post-Transcriptional Regulator of Leptin ]]> https://biorxiv.org/content/10.1101/2020.03.13.991422v1?rss=1 O'Connor, S. Murphy, E. Szwed, S. K. Kanke, M. Marchildon, F. Darnell, R. B. Sethupathy, P. Cohen, P. 2020-03-14 doi:10.1101/2020.03.13.991422 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ Population dynamics of decision making in temperate bacteriophages ]]> https://biorxiv.org/content/10.1101/2020.03.18.996918v1?rss=1 Lang, M. Pleska, M. Guet, C. C. 2020-03-20 doi:10.1101/2020.03.18.996918 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ FcRn, but not FcgRs, drives maternal-fetal transplacental transport of human IgGantibodies ]]> https://biorxiv.org/content/10.1101/2020.03.22.999243v1?rss=1 Borghi, S. Bournazos, S. Thulin, N. Li, C. Gajewski, A. Sherwood, R. Zhang, S. Harris, E. Jagannathan, P. Wang, L.-X. Ravetch, J. V. Wang, T. T. 2020-03-25 doi:10.1101/2020.03.22.999243 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Vpr Co-assembles with Gag during HIV-1 Assembly ]]> https://biorxiv.org/content/10.1101/2020.03.23.004689v1?rss=1 Bredbenner, K. Simon, S. 2020-03-25 doi:10.1101/2020.03.23.004689 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Estrogen and sex-dependent loss of the vocal learning system in female zebra finches ]]> https://biorxiv.org/content/10.1101/2020.03.28.011932v1?rss=1 Choe, H. N. Tewari, J. Zhu, K. W. Davenport, M. Matsunami, H. Jarvis, E. D. 2020-03-29 doi:10.1101/2020.03.28.011932 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ Face selective patches in marmoset frontal cortex ]]> https://biorxiv.org/content/10.1101/2020.04.03.023960v1?rss=1 Schaeffer, D. J. Selvanayagam, J. Johnston, K. D. Menon, R. S. Freiwald, W. A. Everling, S. 2020-04-05 doi:10.1101/2020.04.03.023960 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ De novo protein synthesis in distinct centrolateral amygdala interneurons is required for associative emotional memories ]]> https://biorxiv.org/content/10.1101/2020.04.08.028233v1?rss=1 Shrestha, P. Shan, Z. Marmarcz, M. San Agustin Ruiz, K. Zerihoun, A. T. Juan, C.-Y. Herrero-Vidal, P. M. Pelletier, J. Heintz, N. Klann, E. 2020-04-09 doi:10.1101/2020.04.08.028233 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Cell-Type-Specific Expression of Renin-Angiotensin-System Components in the Human Body and Its Relevance to SARS-CoV-2 Infection ]]> https://biorxiv.org/content/10.1101/2020.04.11.034603v1?rss=1 Suryawanshi, H. Morozov, P. Tuschl, T. Muthukumar, T. tenOever, B. R. Yamaji, M. Williams, Z. 2020-04-11 doi:10.1101/2020.04.11.034603 Cold Spring Harbor Laboratory Press 2020-04-11 <![CDATA[ Relevance of enriched expression of SARS-CoV-2 binding receptor ACE2 in gastrointestinal tissue with pathogenesis of digestive symptoms, diabetes-associated mortality, and disease recurrence in COVID-19 patients ]]> https://biorxiv.org/content/10.1101/2020.04.14.040204v1?rss=1 Etiologically Elusive Disorders Research Network (EEDRN), Kumar, A. Faiq, M. A. Pareek, V. Raza, K. Narayan, R. K. Prasoon, P. Kumar, P. Kulandhasamy, M. Kumari, C. Kant, K. Singh, H. N. Qadri, R. Pandey, S. N. Kumar, S. 2020-04-15 doi:10.1101/2020.04.14.040204 Cold Spring Harbor Laboratory Press 2020-04-15 <![CDATA[ The evolution of sex-biased gene expression in the Drosophila brain ]]> https://biorxiv.org/content/10.1101/2020.04.14.041624v1?rss=1 Khodursky, S. Svetec, N. Durkin, S. Zhao, L. 2020-04-16 doi:10.1101/2020.04.14.041624 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Defining the transcriptional responses of Aspergillus nidulans to cation/alkaline pH stress and the role of the transcription factor SltA. ]]> https://biorxiv.org/content/10.1101/2020.04.16.044396v1?rss=1 Picazo, I. Etxebeste, O. Requena, E. Garzia, A. Espeso, E. A. 2020-04-18 doi:10.1101/2020.04.16.044396 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Affinity proteomic dissection of the human nuclear cap-binding-complex interactome ]]> https://biorxiv.org/content/10.1101/2020.04.20.048470v1?rss=1 Dou, Y. Kalmykova, S. Pashkova, M. Oghbaie, M. Jiang, H. Molloy, K. R. Chait, B. T. Rout, M. P. Fenyo, D. Jensen, T. H. Altukhov, I. LaCava, J. 2020-04-21 doi:10.1101/2020.04.20.048470 Cold Spring Harbor Laboratory Press 2020-04-21 <![CDATA[ Time-resolved cryoEM using Spotiton ]]> https://biorxiv.org/content/10.1101/2020.04.20.050518v1?rss=1 Dandey, V. P. Budell, W. C. Wei, H. Bobe, D. Maruthi, K. Kopylov, M. Eng, E. T. Kahn, P. A. Hinshaw, J. E. Kundu, N. Nimigean, C. M. Fan, C. Sukomon, N. Darst, S. Saecker, R. Chen, J. Malone, B. Potter, C. S. Carragher, B. 2020-04-21 doi:10.1101/2020.04.20.050518 Cold Spring Harbor Laboratory Press 2020-04-21 <![CDATA[ Iterative inhibition of commissural growth cone exploration, not post-crossing barrier, ensures forward midline navigation through SlitC-PlxnA1 signaling ]]> https://biorxiv.org/content/10.1101/2020.04.21.051359v1?rss=1 Ducuing, H. Gardette, T. Pignata, A. Kindbeiter, K. Bozon, M. Thoumine, O. Delloye-Bourgeois, C. Tauszig-Delamasure, S. Castellani, V. 2020-04-23 doi:10.1101/2020.04.21.051359 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Conservation and divergence of DNA replication control in Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2020.04.26.061929v1?rss=1 Ikui, A. E. Ueki, N. Pecani, K. Cross, F. R. 2020-04-27 doi:10.1101/2020.04.26.061929 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ anTraX: high throughput video tracking of color-tagged insects ]]> https://biorxiv.org/content/10.1101/2020.04.29.068478v1?rss=1 Gal, A. Saragosti, J. Kronauer, D. J. 2020-05-01 doi:10.1101/2020.04.29.068478 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ Single Cell RNA Profiling Reveals Adipocyte to Macrophage Signaling Sufficient to Enhance Thermogenesis ]]> https://biorxiv.org/content/10.1101/2020.05.04.077529v1?rss=1 Henriques, F. Bedard, A. H. Guilherme, A. Kelly, M. Chi, J. Zhang, P. Lifshitz, L. M. Bellve, K. Rowland, L. Yenilmez, B. Kumar, S. Wang, Y. Luban, J. Weinstein, L. S. Lin, J. D. Cohen, P. Czech, M. P. 2020-05-05 doi:10.1101/2020.05.04.077529 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ A histone-like motif in yellow fever virus contributes to viral replication ]]> https://biorxiv.org/content/10.1101/2020.05.05.078782v1?rss=1 Mourao, D. Chen, S. Schaefer, U. Bozzacco, L. Carneiro, L. A. Gerber, A. Adura, C. Dill, B. D. Molina, H. Carroll, T. Paul, M. Bhanu, N. V. Garcia, B. A. Joberty, G. Rioja, I. Prinjha, R. K. Roeder, R. G. Rice, C. M. MacDonald, M. R. Patel, D. J. Tarakhovsky, A. 2020-05-06 doi:10.1101/2020.05.05.078782 Cold Spring Harbor Laboratory Press 2020-05-06 <![CDATA[ PI31 expression prevents neuronal degeneration in a mouse Parkinson Disease model ]]> https://biorxiv.org/content/10.1101/2020.05.05.078832v1?rss=1 Steller, H. Minis, A. 2020-05-06 doi:10.1101/2020.05.05.078832 Cold Spring Harbor Laboratory Press 2020-05-06 <![CDATA[ RTEL1 Influences the Abundance and Localization of TERRA RNA ]]> https://biorxiv.org/content/10.1101/2020.05.12.088583v1?rss=1 Ghisays, F. Garzia, A. Wang, H. Canasto-Chibuque, C. Hohl, M. Savage, S. A. Tuschl, T. Petrini, J. H. J. 2020-05-14 doi:10.1101/2020.05.12.088583 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Convergent Antibody Responses to SARS-CoV-2 Infection in Convalescent Individuals ]]> https://biorxiv.org/content/10.1101/2020.05.13.092619v1?rss=1 1:5000. Antibody cloning revealed expanded clones of RBD-specific memory B cells expressing closely related antibodies in different individuals. Despite low plasma titers, antibodies to three distinct epitopes on RBD neutralized at half-maximal inhibitory concentrations (IC50s) as low as single digit ng/mL. Thus, most convalescent plasmas obtained from individuals who recover from COVID-19 do not contain high levels of neutralizing activity. Nevertheless, rare but recurring RBD-specific antibodies with potent antiviral activity were found in all individuals tested, suggesting that a vaccine designed to elicit such antibodies could be broadly effective. ]]> Robbiani, D. F. Gaebler, C. Muecksch, F. Cetrulo Lorenzi, J. Wang, Z. Cho, A. Agudelo, M. Barnes, C. Finkin, S. Hagglof, T. Oliveira, T. Viant, C. Hurley, A. Millard, K. Kost, R. Cipolla, M. Gazumyan, A. Gordon, K. Bianchini, F. Chen, S. Ramos, V. Patel, R. Dizon, J. Shimeliovich, I. Mendoza, P. Hartweger, H. Nogueira, L. Pack, M. Horowitz, J. Schmidt, F. Weisblum, Y. Hoffmann, H.-H. Michailidis, E. Ashbrook, A. Waltari, E. F. Pak, J. Huey-Tubman, K. Koranda, N. Hoffman, P. West, A. Rice, C. Hatziioannou, T. Bjorkman, P. Bieniasz, P. Caskey, M. Nuss 2020-05-15 doi:10.1101/2020.05.13.092619 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Genome-wide landscape of RNA-binding protein dysregulation reveals a major impact on psychiatric disorder risk ]]> https://biorxiv.org/content/10.1101/2020.05.19.102319v1?rss=1 Park, C. Y. Zhou, J. Wong, A. K. Chen, K. M. Theesfeld, C. L. Darnell, R. Troyanskaya, O. G. 2020-05-20 doi:10.1101/2020.05.19.102319 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Trimeric SARS-CoV-2 Spike interacts with dimeric ACE2 with limited intra-Spike avidity ]]> https://biorxiv.org/content/10.1101/2020.05.21.109157v1?rss=1 Lui, I. Zhou, X. X. Lim, S. A. Elledge, S. Solomon, P. Rettko, N. J. Zha, B. S. Kirkemo, L. L. Gramespacher, J. A. Liu, J. Muecksch, F. Lorenzi, J. C. C. Schmidt, F. Weisblum, Y. Robbiani, D. F. Nussenzweig, M. C. Hatziioannou, T. Bieniasz, P. D. Rosenberg, O. Leung, K. K. Wells, J. A. 2020-05-21 doi:10.1101/2020.05.21.109157 Cold Spring Harbor Laboratory Press 2020-05-21 <![CDATA[ Towards complete and error-free genome assemblies of all vertebrate species ]]> https://biorxiv.org/content/10.1101/2020.05.22.110833v1?rss=1 Rhie, A. McCarthy, S. A. Fedrigo, O. Damas, J. Formenti, G. Koren, S. Uliano-Silva, M. Chow, W. Fungtammasan, A. Gedman, G. L. Cantin, L. J. Thibaud-Nissen, F. Haggerty, L. Lee, C. Ko, B. J. Kim, J. Bista, I. Smith, M. Haase, B. Mountcastle, J. Winkler, S. Paez, S. Howard, J. Vernes, S. C. Lama, T. M. Grutzner, F. C. Warren, W. C. Balakrishnan, C. Burt, D. George, J. M. Biegler, M. Iorns, D. Digby, A. Eason, D. Edwards, T. Wilkinson, M. Turner, G. F. Meyer, A. Kautt, A. F. Franchini, P. Detrich, H. W. Svardal, H. Wagner, M. Naylor, G. J. P. Pippel, M 2020-05-23 doi:10.1101/2020.05.22.110833 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ Reference genome and demographic history of the most endangered marine mammal, the vaquita ]]> https://biorxiv.org/content/10.1101/2020.05.27.098582v1?rss=1 Morin, P. A. Archer, F. I. Avila, C. D. Balacco, J. R. Bukhman, Y. V. Chow, W. Fedrigo, O. Formenti, G. Fronczek, J. A. Fungtammasan, A. Gulland, F. M. D. Haase, B. Heide-Jorgensen, M. P. Houck, M. Howe, K. Misuraca, A. C. Mountcastle, J. Musser, W. Paez, S. Pelan, S. Phillippy, A. M. Rhie, A. Robinson, J. A. Rojas-Bracho, L. Rowles, T. K. Ryder, O. A. Smith, C. R. Stevenson, S. Taylor, B. L. Teilmann, J. Torrance, J. Wells, R. S. Westgate, A. Jarvis, E. 2020-05-28 doi:10.1101/2020.05.27.098582 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Functional reconstitution of a bacterial CO2 concentrating mechanism in E. coli ]]> https://biorxiv.org/content/10.1101/2020.05.27.119784v1?rss=1 Flamholz, A. I. Dugan, E. Blikstad, C. Gleizer, S. Ben-Nissan, R. Amram, S. Antonovsky, N. Ravishankar, S. Noor, E. Bar-Even, A. Milo, R. Savage, D. 2020-05-27 doi:10.1101/2020.05.27.119784 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Neural Plate Targeting by in Utero NanoinjEction (NEPTUNE) reveals a role for Sptbn2 in neurulation and abdominal wall closure ]]> https://biorxiv.org/content/10.1101/2020.05.28.115972v1?rss=1 95% of cells in the brain enabled long-term gain- or loss-of-function, and conditional expression was achieved using mini-promotors for cell types of interest. Using NEPTUNE, we silenced Sptbn2, a gene associated with Spinocerebellar ataxia type 5 (SCA5) in humans. Silencing of Sptbn2 induced severe neural tube defects and embryo resorption, suggesting that SPTBN2 in-frame and missense deletions in SCA5 reflect hypomorphic or neomorphic functions, not loss of function. In conclusion, NEPTUNE offers a novel, rapid and cost-effective technique to test gene function in brain development, and can reveal loss of function phenotypes incompatible with life. ]]> Mangold, K. Masek, J. He, J. Lendahl, U. Fuchs, E. Andersson, E. R. 2020-05-28 doi:10.1101/2020.05.28.115972 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies ]]> https://biorxiv.org/content/10.1101/2020.05.28.121533v1?rss=1 Barnes, C. O. West, A. P. Huey-Tubman, K. Hoffmann, M. A. G. Sharaf, N. G. Hoffman, P. R. Koranda, N. Gristick, H. B. Gaebler, C. Muecksch, F. Cetrulo Lorenzi, J. C. Finkin, S. Hagglof, T. Hurley, A. Millard, K. G. Weisblum, Y. Schmidt, F. Hatziioannou, T. Bieniasz, P. D. Caskey, M. Robbiani, D. Nussenzweig, M. C. Bjorkman, P. J. 2020-05-29 doi:10.1101/2020.05.28.121533 Cold Spring Harbor Laboratory Press 2020-05-29 <![CDATA[ C. elegans REMO-1, a glial GPCR, regulates stress-induced nervous system remodeling and behavior ]]> https://biorxiv.org/content/10.1101/2020.06.03.127894v1?rss=1 Lee, I. H. Procko, C. Lu, Y. Shaham, S. 2020-06-04 doi:10.1101/2020.06.03.127894 Cold Spring Harbor Laboratory Press 2020-06-04 <![CDATA[ T cell receptor is required for differentiation but not maintenance of intestinal intraepithelial lymphocytes ]]> https://biorxiv.org/content/10.1101/2020.06.04.134510v1?rss=1 Bilate, A. M. London, M. Castro, T. B. R. Mesin, L. Kongthong, S. Harnagel, A. Victora, G. D. Mucida, D. 2020-06-05 doi:10.1101/2020.06.04.134510 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Stepwise chromatin and transcriptional acquisition of an intraepithelial lymphocyte program ]]> https://biorxiv.org/content/10.1101/2020.06.04.134650v1?rss=1 London, M. Bilate, A. M. Castro, T. B. R. Mucida, D. 2020-06-05 doi:10.1101/2020.06.04.134650 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Elucidating the diversity and potential function of nonribosomal peptide and polyketide biosynthetic gene clusters in the root microbiome ]]> https://biorxiv.org/content/10.1101/2020.06.07.138487v1?rss=1 Dror, B. Wang, Z. Brady, S. F. Jurkevitch, E. Cytryn, E. 2020-06-07 doi:10.1101/2020.06.07.138487 Cold Spring Harbor Laboratory Press 2020-06-07 <![CDATA[ Measuring SARS-CoV-2 neutralizing antibody activity using pseudotyped and chimeric viruses ]]> https://biorxiv.org/content/10.1101/2020.06.08.140871v1?rss=1 Schmidt, F. Weisblum, Y. Muecksch, F. Hoffmann, H.-H. Michailidis, E. Lorenzi, J. C. C. Mendoza, P. Rutkowska, M. Bednarski, E. Gaebler, C. Agudelo, M. Cho, A. Wang, Z. Gazumyan, A. Cipolla, M. Caskey, M. Robbiani, D. F. Nussenzweig, M. C. Rice, C. M. Hatziioannou, T. Bieniasz, P. D. 2020-06-09 doi:10.1101/2020.06.08.140871 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Functional Analysis of Distinct Populations of Subthalamic Nucleus Neurons on Parkinson Disease and OCD-like Behaviors in Mice ]]> https://biorxiv.org/content/10.1101/2020.06.10.137679v1?rss=1 Parolari, L. Schneeberger, M. Heintz, N. Friedman, J. 2020-06-11 doi:10.1101/2020.06.10.137679 Cold Spring Harbor Laboratory Press 2020-06-11 <![CDATA[ Phylogenomics of Ichneumonoidea (Hymenoptera) and implications for evolution of mode of parasitism and viral endogenization ]]> https://biorxiv.org/content/10.1101/2020.06.17.157719v1?rss=1 Sharanowski, B. J. Ridenbaugh, R. D. Piekarski, P. K. Broad, G. R. Burke, G. R. Deans, A. R. Lemmon, A. R. Moriarty Lemmon, E. Diehl, G. J. Whitfield, J. B. Hines, H. M. 2020-06-18 doi:10.1101/2020.06.17.157719 Cold Spring Harbor Laboratory Press 2020-06-18 <![CDATA[ Endemic human coronaviruses induce distinct antibody repertoires in adults and children ]]> https://biorxiv.org/content/10.1101/2020.06.21.163394v1?rss=1 Khan, T. Rahman, M. Al Ali, F. Huang, S. S. Y. Sayeed, A. Nasrallah, G. K. Hasan, M. R. Marr, N. 2020-06-22 doi:10.1101/2020.06.21.163394 Cold Spring Harbor Laboratory Press 2020-06-22 <![CDATA[ Rewiring the specificity of extra-cytoplasmic function sigma factors ]]> https://biorxiv.org/content/10.1101/2020.06.23.168245v1?rss=1 Todor, H. Osadnik, H. Campbell, E. A. Myers, K. S. Donohue, T. J. Gross, C. A. 2020-06-24 doi:10.1101/2020.06.23.168245 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ LINE-1 expression in cancer correlates with DNA damage response, copy number variation, and cell cycle progression ]]> https://biorxiv.org/content/10.1101/2020.06.26.174052v1?rss=1 McKerrow, W. H. Wang, X. Mita, P. Cao, S. Grivainis, M. Ding, L. LaCava, J. Boeke, J. Fenyö, D. H. 2020-06-27 doi:10.1101/2020.06.26.174052 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Heh2/Man1 may be an evolutionarily conserved sensor of NPC assembly state ]]> https://biorxiv.org/content/10.1101/2020.06.29.178129v1?rss=1 Lusk, C. P. Borah, S. Thaller, D. J. Hakhverdyan, Z. Rodriguez, E. C. Rout, M. P. King, M. C. 2020-06-29 doi:10.1101/2020.06.29.178129 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Complete vertebrate mitogenomes reveal widespread gene duplications and repeats ]]> https://biorxiv.org/content/10.1101/2020.06.30.177956v1?rss=1 10 kbp, PacBio or Nanopore) and short (100-300 bp, Illumina) reads. Our pipeline led to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We have observed that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we have identified errors, missing sequences, and incomplete genes in those references, particularly in repeat regions. Our assemblies have also identified novel gene region duplications, shedding new light on mitochondrial genome evolution and organization. ]]> Formenti, G. Rhie, A. Balacco, J. Haase, B. Mountcastle, J. Fedrigo, O. Brown, S. Capodiferro, M. Al-Ajli, F. O. The Vertebrate Genomes Project Consortium, Ambrosini, R. Houde, P. Koren, S. Oliver, K. Smith, M. Skelton, J. Betteridge, E. Dolucan, J. Corton, C. Bista, I. Torrance, J. Tracey, A. Uliano-Silva, M. Howe, K. McCarthy, S. Winkler, S. Kwak, W. Korlach, J. Fungtammasan, A. Fordham, D. Costa, V. Mayes, S. Chiara, M. Horner, D. S. Myers, E. W. Durbin, R. Achilli, A. Braun, E. L. Phillippy, A. M. Jarvis, E. D. 2020-07-01 doi:10.1101/2020.06.30.177956 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ NCBP3 is a productive mRNP component ]]> https://biorxiv.org/content/10.1101/2020.07.04.184861v1?rss=1 Dou, Y. Barbosa, I. Jiang, H. Iasillo, C. Molloy, K. R. Schulze, W. M. Cusack, S. Schmid, M. Le Hir, H. LaCava, J. Jensen, T. H. 2020-07-04 doi:10.1101/2020.07.04.184861 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Measurement of hindered diffusion in complex geometries for high-speed single-molecule experiments ]]> https://biorxiv.org/content/10.1101/2020.07.04.187948v1?rss=1 Bartsch, T. F. Villasante, C. M. Touré, A. Firester, D. M. Hengel, F. E. Oswald, A. Hudspeth, A. J. 2020-07-04 doi:10.1101/2020.07.04.187948 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Screening predictors of weight loss: an Integromics Approach ]]> https://biorxiv.org/content/10.1101/2020.07.06.188284v1?rss=1 Joel Correa da Rosa Jose O. Aleman Jason Mohabir Yupu Liang Jan L Breslow Peter R. Holt 2020-07-10 doi:10.1101/2020.07.06.188284 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex ]]> https://biorxiv.org/content/10.1101/2020.07.08.194084v1?rss=1 James Chen Brandon Malone Eliza Llewellyn Michael Grasso Patrick M. M. Shelton Paul Dominic B. Olinares Kashyap Maruthi Ed Eng Hasan Vatandaslar Brian T. Chait Tarun Kapoor Seth A. Darst Elizabeth A. Campbell 2020-07-08 doi:10.1101/2020.07.08.194084 Cold Spring Harbor Laboratory Press 2020-07-08 <![CDATA[ Obesity causes irreversible mitochondria failure in visceral adipose tissue despite successful anti-obesogenic lifestyle-based interventions ]]> https://biorxiv.org/content/10.1101/2020.07.08.194167v1?rss=1 Alba Gonzalez-Franquesa Pau Gama-Perez Marta Kulis Norma Dahdah Sonia Moreno-Gomez Ana Latorre-Pellicer Rebeca Fernandez-Ruiz Antoni Aguilar-Mogas Erika Monelli Sara Samino Joan Miro Gregor Oemer Xavier Duran Estrella Sanchez-Rebordelo Marc Schneeberger Merce Obach Joel Montane Giancarlo Castellano Vicente Chapaprieta Lourdes Navarro Ignacio Prieto Carlos Castano Anna Novials Ramon Gomis Maria Monsalve Marc Claret Mariona Graupera Guadalupe Soria Joan Vendrell Sonia Fernandez-Veledo Jose Antonio Enriquez Angel Carracedo Jose Carlos Perales Ruben Nogueiras Laur 2020-07-11 doi:10.1101/2020.07.08.194167 Cold Spring Harbor Laboratory Press 2020-07-11 <![CDATA[ SARS-CoV-2 induces activation and diversification of human plasmacytoid pre-dendritic cells. ]]> https://biorxiv.org/content/10.1101/2020.07.10.197343v1?rss=1 Fanny Onodi Lucie Bonnet-Madin Léa Karpf Laurent Meertens Justine Poirot Jerôme LeGoff Constance Delaugerre Ali AMARA Vassili Soumelis 2020-07-10 doi:10.1101/2020.07.10.197343 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Multi-batch cytometry data integration for optimal immunophenotyping ]]> https://biorxiv.org/content/10.1101/2020.07.14.202432v1?rss=1 Ogishi, M. Yang, R. Gruber, C. Pelham, S. Spaan, A. N. Rosain, J. Chbihi, M. Han, J. E. Rao, V. K. Kainulainen, L. Bustamante, J. Boisson, B. Bogunovic, D. Boisson-Dupuis, S. Casanova, J.-L. 2020-07-15 doi:10.1101/2020.07.14.202432 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ Constancy and Change in the 5'UTR of Yellow Fever Virus ]]> https://biorxiv.org/content/10.1101/2020.07.17.207902v1?rss=1 Seligman, S. J. 2020-07-17 doi:10.1101/2020.07.17.207902 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants ]]> https://biorxiv.org/content/10.1101/2020.07.21.214759v1?rss=1 Weisblum, Y. Schmidt, F. Zhang, F. DaSilva, J. Poston, D. Lorenzi, J. C. C. Muecksch, F. Rutkowska, M. Hoffmann, H.-H. Michailidis, E. Gaebler, C. Agudelo, M. Cho, A. Wang, Z. Gazumyan, A. Cipolla, M. Luchsinger, L. Hillyer, C. D. Caskey, M. Robbiani, D. F. Rice, C. Nussenzweig, M. C. Hatziioannou, T. Bieniasz, P. D. 2020-07-22 doi:10.1101/2020.07.21.214759 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Detection of homozygous and hemizygous partial exon deletions by whole-exome sequencing ]]> https://biorxiv.org/content/10.1101/2020.07.23.217976v1?rss=1 Bigio, B. Seeleuthner, Y. Kerner, G. Migaud, M. Rosain, J. Boisson, B. Nasca, C. Puel, A. Bustamante, J. Casanova, J.-L. Abel, L. Cobat, A. 2020-07-24 doi:10.1101/2020.07.23.217976 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Cargo modulates the conformation of the nuclear pore in living cells ]]> https://biorxiv.org/content/10.1101/2020.07.27.223081v1?rss=1 Pulupa, J. Prior, H. Johnson, D. S. Simon, S. M. 2020-07-28 doi:10.1101/2020.07.27.223081 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ APOBEC2 binds Chromatin and Represses Transcription during Myoblast Differentiation ]]> https://biorxiv.org/content/10.1101/2020.07.29.223594v1?rss=1 Lorenzo, J. P. Molla, L. Ibarra, I. L. Ruf, S. Subramani, P. G. Boulais, J. Harjanto, D. Vonica, A. Di Noia, J. M. Dieterich, C. Zaugg, J. B. Papavasiliou, F. N. 2020-07-29 doi:10.1101/2020.07.29.223594 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Force-dependent stimulation of RNA unwinding by SARS-CoV-2 nsp13 helicase ]]> https://biorxiv.org/content/10.1101/2020.07.31.231274v1?rss=1 Mickolajczyk, K. J. Shelton, P. M. M. Grasso, M. Cao, X. Warrington, S. R. Aher, A. Liu, S. Kapoor, T. M. 2020-07-31 doi:10.1101/2020.07.31.231274 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[ Assembly defects of the human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia ]]> https://biorxiv.org/content/10.1101/2020.08.03.234229v1?rss=1 Sekulovski, S. Devant, P. Panizza, S. Gogakos, T. Pitiriciu, A. Heitmeier, K. Ramsay, E. P. Barth, M. Schmidt, C. Weitzer, S. Tuschl, T. Baas, F. Martinez, J. Trowitzsch, S. 2020-08-03 doi:10.1101/2020.08.03.234229 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Antigen-specific induction of CD4+CD8αα+ intraepithelial T lymphocytes byBacteroidetes species ]]> https://biorxiv.org/content/10.1101/2020.08.05.236513v1?rss=1 Bousbaine, D. Bhagchandani, P. London, M. Mimee, M. Olesen, S. Poyet, M. Cheloha, R. W. Sidney, J. Ling, J. Gupta, A. Lu, T. K. Sette, A. Alm, E. J. Mucida, D. Bilate, A. M. Ploegh, H. L. 2020-08-05 doi:10.1101/2020.08.05.236513 Cold Spring Harbor Laboratory Press 2020-08-05 <![CDATA[ Songbirds can learn flexible contextual control over syllable sequencing ]]> https://biorxiv.org/content/10.1101/2020.08.05.238717v1?rss=1 Veit, L. Tian, L. Y. Monroy Hernandez, C. J. Brainard, M. 2020-08-06 doi:10.1101/2020.08.05.238717 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ A Broadly Neutralizing Macaque Monoclonal Antibody Against the HIV-1 V3-Glycan Patch ]]> https://biorxiv.org/content/10.1101/2020.08.10.244582v1?rss=1 Wang, Z. Barnes, C. O. Gautam, R. Cetrulo Lorenzi, J. C. Mayer, C. T. Oliveira, T. Y. Ramos, V. Cipolla, M. Gordon, K. M. Gristick, H. B. West, A. P. Nishimura, Y. Raina, H. Seaman, M. S. Gazumyan, A. Martin, M. A. Bjorkman, P. J. Escolano, A. Nussenzweig, M. C. 2020-08-10 doi:10.1101/2020.08.10.244582 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Structural basis for transcription complex disruption by the Mfd translocase ]]> https://biorxiv.org/content/10.1101/2020.08.12.248500v1?rss=1 Kang, J. Y. Llewellyn, E. Chen, J. Olinares, P. D. B. Brewer, J. Chait, B. T. Campbell, E. A. Darst, S. A. 2020-08-12 doi:10.1101/2020.08.12.248500 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Inhibition of AlgU by MucA is required for viability in Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2020.08.17.253617v1?rss=1 Schofield, M. C. Rodriguez, D. Kidman, A. A. Michaels, L. A. Campbell, E. A. Jorth, P. A. Tseng, B. S. 2020-08-18 doi:10.1101/2020.08.17.253617 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Respiratory complex and tissue lineage drive mutational patterns in the tumor mitochondrial genome ]]> https://biorxiv.org/content/10.1101/2020.08.18.256362v1?rss=1 Gorelick, A. N. Kim, M. Chatila, W. K. La, K. Hakimi, A. A. Taylor, B. S. Gammage, P. A. Reznik, E. 2020-08-18 doi:10.1101/2020.08.18.256362 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Enterococcus peptidoglycan remodeling promotes immune checkpoint inhibitor therapy ]]> https://biorxiv.org/content/10.1101/2020.08.20.256263v1?rss=1 Griffin, M. E. Espinosa, J. Becker, J. L. Jha, J. K. Fanger, G. R. Hang, H. C. 2020-08-20 doi:10.1101/2020.08.20.256263 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ Colony expansions underlie the evolution of army ant mass raiding ]]> https://biorxiv.org/content/10.1101/2020.08.20.259614v1?rss=1 Chandra, V. Gal, A. Kronauer, D. J. C. 2020-08-20 doi:10.1101/2020.08.20.259614 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ Structural basis for the allosteric regulation of Human Topoisomerase 2α ]]> https://biorxiv.org/content/10.1101/2020.08.23.263558v1?rss=1 Vanden Broeck, A. Lotz, C. Drillien, R. Bedez, C. Lamour, V. 2020-08-24 doi:10.1101/2020.08.23.263558 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development ]]> https://biorxiv.org/content/10.1101/2020.08.27.268730v1?rss=1 Joglekar, A. Przhibelskiy, A. D. Mahfouz, A. Collier, P. Lin, S. Schlusche, A. K. Marrocco, J. Williams, S. R. Haase, B. Hayes, A. Chew, J. G. Weisenfeld, N. I. Wong, M. Y. Stein, A. N. Hardwick, S. Hunt, T. Bent, Z. Fedrigo, O. Sloan, S. A. Risso, D. Jarvis, E. D. Flicek, P. Luo, W. Pitt, G. S. Frankish, A. Smit, A. B. Ross, M. E. Tilgner, H. U. 2020-08-27 doi:10.1101/2020.08.27.268730 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ A giant cell enhancer achieves cell-type specificity through activation via TCP and repression by Dof transcription factors ]]> https://biorxiv.org/content/10.1101/2020.08.28.270454v1?rss=1 Hong, L. Ko, C. S. Kang, S. E. Pruneda-Paz, J. L. Roeder, A. H. K. 2020-08-30 doi:10.1101/2020.08.28.270454 Cold Spring Harbor Laboratory Press 2020-08-30 <![CDATA[ A Duplicated ESCRT-III Factor Blocks Enveloped Virus Budding Without Inhibiting Cellular ESCRT Functions ]]> https://biorxiv.org/content/10.1101/2020.08.30.273656v1?rss=1 Rheinemann, L. Downhour, D. M. Bredbenner, K. Mercenne, G. Davenport, K. A. Schmitt, P. T. McCullough, J. Schmitt, A. P. Simon, S. M. Sundquist, W. I. Elde, N. C. 2020-08-31 doi:10.1101/2020.08.30.273656 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Structural classification of neutralizing antibodies against the SARS-CoV-2 spike receptor-binding domain suggests vaccine and therapeutic strategies ]]> https://biorxiv.org/content/10.1101/2020.08.30.273920v1?rss=1 Barnes, C. O. Jette, C. A. Abernathy, M. E. Dam, K.-M. A. Esswein, S. R. Gristick, H. B. Malyutin, A. G. Sharaf, N. G. Huey-Tubman, K. E. Lee, Y. E. Robbiani, D. F. Nussenzweig, M. C. West, A. P. Bjorkman, P. J. 2020-08-30 doi:10.1101/2020.08.30.273920 Cold Spring Harbor Laboratory Press 2020-08-30 <![CDATA[ Human T-bet governs innate and innate-like adaptive IFN-γ immunity against mycobacteria ]]> https://biorxiv.org/content/10.1101/2020.08.31.274589v1?rss=1 Yang, R. Mele, F. Worley, L. Langlais, D. Rosain, J. Benhsaien, I. Elarabi, H. Croft, C. A. Doisne, J.-M. Zhang, P. Weisshaar, M. Jarrossay, D. Latorre, D. Shen, Y. Han, J. Gruber, C. Markle, J. Ali, F. A. Rahman, M. Khan, T. Seeleuthner, Y. Kerner, G. Husquin, L. T. Maclsaac, J. Jeljeli, M. Ailal, F. Kobor, M. Oleaga-Quintas, C. Roynard, M. Bourgey, M. Baghdadi, J. E. Boisson-Dupuis, S. Puel, A. Batteux, F. Rozenberg, F. Marr, N. Pan-Hammarstrom, Q. Bogunovic, D. Quintana-Murci, L. Carroll, T. Ma, C. Abel, L. Bousfiha, A. Di Santo, J. Glimcher, L. H 2020-08-31 doi:10.1101/2020.08.31.274589 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ An arousal gated visual circuit controls pursuit during Drosophila courtship ]]> https://biorxiv.org/content/10.1101/2020.08.31.275883v1?rss=1 Hindmarsh Sten, T. Li, R. Otopalik, A. Ruta, V. 2020-08-31 doi:10.1101/2020.08.31.275883 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ CENP-A chromatin prevents replication stress at centromeres to avoid structural aneuploidy ]]> https://biorxiv.org/content/10.1101/2020.09.01.277103v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@4e6dc4org.highwire.dtl.DTLVardef@1089c90org.highwire.dtl.DTLVardef@5ee5c2org.highwire.dtl.DTLVardef@3e300d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Giunta, S. Herve, S. White, R. R. Wilhelm, T. Dumont, M. Scelfo, A. Gamba, R. Wong, C. K. Rancati, G. Smogorzewska, A. Funabiki, H. Fachinetti, D. 2020-09-01 doi:10.1101/2020.09.01.277103 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ RecT recombinase expression enables efficient gene editing in Enterococcus ]]> https://biorxiv.org/content/10.1101/2020.09.01.278044v1?rss=1 Chen, V. Griffin, M. E. Hang, H. C. 2020-09-01 doi:10.1101/2020.09.01.278044 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Translational profiling of mouse dopaminoceptive neurons reveals a role of PGE2 in dorsal striatum ]]> https://biorxiv.org/content/10.1101/2020.09.02.279240v1?rss=1 Montalban, E. Giralt, A. Taing, L. Nakamura, Y. Martin, C. de Pins, B. Pelosi, A. Goutebroze, L. Castell, L. Wang, W. Daila Neiburga, K. Vestito, L. Nairn, A. C. Valjent, E. Herve, D. Heintz, N. Gambardella Le Novere, N. Greengard, P. Roussarie, J.-P. Girault, J.-A. 2020-09-03 doi:10.1101/2020.09.02.279240 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Single Cell Transcriptomics of Human Native Kidney and Kidney Allografts and New Insights into the Mechanism of Fibrosis ]]> https://biorxiv.org/content/10.1101/2020.09.03.281733v1?rss=1 Suryawanshi, H. Yang, H. Lubetzky, M. Morozov, P. Lagman, M. Alonso, A. Li, C. Snopkowski, C. Mueller, F. Lee, J. Dadhania, D. Salvatore, S. Seshan, S. Sharma, V. Suthanthiran, M. Tuschl, T. Muthukumar, T. 2020-09-06 doi:10.1101/2020.09.03.281733 Cold Spring Harbor Laboratory Press 2020-09-06 <![CDATA[ Development of Resistance to 4'-Ethynyl-2-Fluoro-2'-Deoxyadenosine (EFdA) by Wild-Type and Nucleoside Reverse Transcriptase Inhibitor Resistant Human Immunodeficiency Virus Type 1 ]]> https://biorxiv.org/content/10.1101/2020.09.04.281485v1?rss=1 Cilento, M. E. Michailidis, E. Ilina, T. V. Nagy, E. Mitsuya, H. Parniak, M. Tedbury, P. R. Sarafianos, S. G. 2020-09-04 doi:10.1101/2020.09.04.281485 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ fruitless mutant male mosquitoes gain attraction to human odor ]]> https://biorxiv.org/content/10.1101/2020.09.04.282434v1?rss=1 Basrur, N. S. De Obaldia, M. E. Morita, T. Herre, M. von Heynitz, R. K. Tsitohay, Y. N. Vosshall, L. B. 2020-09-04 doi:10.1101/2020.09.04.282434 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ Early alphavirus replication dynamics in single cells reveal a passive basis for superinfection exclusion ]]> https://biorxiv.org/content/10.1101/2020.09.07.282053v1?rss=1 Singer, Z. S. Ambrose, P. Danino, T. Rice, C. 2020-09-07 doi:10.1101/2020.09.07.282053 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ Enhanced SARS-CoV-2 Neutralization by Secretory IgA in vitro ]]> https://biorxiv.org/content/10.1101/2020.09.09.288555v1?rss=1 Wang, Z. Lorenzi, J. C. C. Muecksch, F. Finkin, S. Viant, C. Gaebler, C. Cipolla, M. Hoffman, H.-H. Oliveira, T. Y. Oren, D. A. Ramos, V. Nogueira, L. Michailidis, E. Robbiani, D. F. Gazumyan, A. Rice, C. M. Hatziioannou, T. Bieniasz, P. D. Caskey, M. Nussenzweig, M. C. 2020-09-09 doi:10.1101/2020.09.09.288555 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors ]]> https://biorxiv.org/content/10.1101/2020.09.11.291716v1?rss=1 Hoffmann, H.- H. Schneider, W. M. Sanchez-Rivera, F. J. Luna, J. M. Ashbrook, A. W. Soto-Feliciano, Y. M. Leal, A. A. Le Pen, J. Ricardo-Lax, I. Michailidis, E. Hao, Y. Stenzel, A. F. Peace, A. Allis, C. D. Lowe, S. W. MacDonald, M. R. Poirier, J. T. Rice, C. M. 2020-09-11 doi:10.1101/2020.09.11.291716 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Site-specific lipidation enhances IFITM3 membrane interactions and antiviral activity ]]> https://biorxiv.org/content/10.1101/2020.09.11.293324v1?rss=1 Garst, E. H. Lee, H. Das, T. Bhattacharya, S. Percher, A. Wiewiora, R. Witte, I. P. Li, Y. Goger, M. Peng, T. Im, W. Hang, H. C. 2020-09-11 doi:10.1101/2020.09.11.293324 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Time-restricted feeding prolongs lifespan in Drosophila in a peripheral clock-dependent manner ]]> https://biorxiv.org/content/10.1101/2020.09.14.296368v1?rss=1 Cabrera, D. Young, M. W. Axelrod, S. 2020-09-15 doi:10.1101/2020.09.14.296368 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ Antibody potency, effector function and combinations in protection from SARS-CoV-2 infection in vivo ]]> https://biorxiv.org/content/10.1101/2020.09.15.298067v1?rss=1 Schaefer, A. Muecksch, F. Lorenzi, J. C. C. Leist, S. R. Cipolla, M. Bournazos, S. Schmidt, F. Gazumyan, A. Baric, R. S. Robbiani, D. F. Hatziioannou, T. Ravetch, J. V. Bieniasz, P. D. Nussenzweig, M. C. Sheahan, T. P. 2020-09-15 doi:10.1101/2020.09.15.298067 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ Biochemical reconstitutions reveal principles of human γ-TuRC assembly and function ]]> https://biorxiv.org/content/10.1101/2020.09.21.306845v1?rss=1 31 proteins includes{gamma} -tubulin and GCP2-6, as well as MZT1 and an actin-like protein in a "lumenal bridge". The challenge of reconstituting the{gamma} -TuRC has limited dissections of its assembly and function. Here, we report a complete biochemical reconstitution of the human{gamma} -TuRC ({gamma}-TuRC-GFP), a [~]35S complex that nucleates microtubules in vitro. We extend our approach to generate a stable subcomplex,{gamma} -TuRCmini-GFP, which lacks MZT1 and actin. Using mutagenesis, we show that{gamma} -TuRCmini-GFP nucleates microtubules in a guanine nucleotide-dependent manner and proceeds with similar kinetics as reported for native{gamma} -TuRCs. Electron microscopy reveals that{gamma} -TuRC-GFP resembles the native{gamma} -TuRC architecture, while{gamma} -TuRCmini-GFP adopts a partial cone shape presenting only 8-10{gamma} -tubulin subunits and lacks a well-ordered lumenal bridge. Our structure-function analysis suggests that the lumenal bridge facilitates the self-assembly of regulatory interfaces around a microtubule-nucleating "core" in the{gamma} -TuRC. ]]> Wieczorek, M. Ti, S.-C. Urnavicius, L. Molloy, K. R. Aher, A. Chait, B. T. Kapoor, T. M. 2020-09-21 doi:10.1101/2020.09.21.306845 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ Targeting Allostery in the Dynein Motor Domain with Small Molecule Inhibitors ]]> https://biorxiv.org/content/10.1101/2020.09.22.308700v1?rss=1 Santarossa, C. C. Mickolajczyk, K. Steinman, J. B. Urnavicius, L. Chen, N. Fukase, Y. Hirata, Y. Coudray, N. Ekiert, D. C. Bhabha, G. Kapoor, T. M. 2020-09-22 doi:10.1101/2020.09.22.308700 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Lytic bacteriophages facilitate antibiotic sensitization of Enterococcus faecium ]]> https://biorxiv.org/content/10.1101/2020.09.22.309401v1?rss=1 Canfield, G. S. Chatterjee, A. Mangalea, M. R. Sheriff, E. K. Keidan, M. McBride, S. W. McCollister, B. D. Duerkop, B. A. 2020-09-23 doi:10.1101/2020.09.22.309401 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Neutralizing activity of broadly neutralizing anti-HIV-1 antibodies against primary African isolates ]]> https://biorxiv.org/content/10.1101/2020.09.24.310938v1?rss=1 Lorenzi, J. C. C. Mendoza, P. Cohen, Y. Z. Nogueira, L. Lavine, C. Sapiente, J. Seaman, M. Wiatr, M. Mugo, N. R. Mujugira, A. Delany, S. Lingappa, J. R. Celum, C. Caskey, M. Nussenzweig, M. C. 2020-09-25 doi:10.1101/2020.09.24.310938 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Structural variant evolution after telomere crisis ]]> https://biorxiv.org/content/10.1101/2020.09.29.318436v1?rss=1 Dewhurst, S. M. Yao, X. M. Rosiene, J. Tian, H. Behr, J. Bosco, N. Takai, K. de Lange, T. Imielinski, M. 2020-09-29 doi:10.1101/2020.09.29.318436 Cold Spring Harbor Laboratory Press 2020-09-29 <![CDATA[ Fast recovery of disrupted tip links induced by mechanical displacement of hair bundles ]]> https://biorxiv.org/content/10.1101/2020.10.02.324111v1?rss=1 Alonso, R. G. Tobin, M. Martin, P. Hudspeth, A. J. 2020-10-04 doi:10.1101/2020.10.02.324111 Cold Spring Harbor Laboratory Press 2020-10-04 <![CDATA[ SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs ]]> https://biorxiv.org/content/10.1101/2020.10.02.324145v1?rss=1 Weingarten-Gabbay, S. Klaeger, S. Sarkizova, S. Pearlman, L. R. Chen, D.-Y. Bauer, M. R. Taylor, H. B. Conway, H. L. Tomkins-Tinch, C. H. Finkel, Y. Nachshon, A. Gentili, M. Rivera, K. D. Keskin, D. B. Rice, C. M. Clauser, K. R. Hacohen, N. Carr, S. A. Abelin, J. G. Saeed, M. Sabeti, P. C. 2020-10-02 doi:10.1101/2020.10.02.324145 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Genome-scale identification of SARS-CoV-2 and pan-coronavirus host factor networks ]]> https://biorxiv.org/content/10.1101/2020.10.07.326462v1?rss=1 Schneider, W. M. Luna, J. M. Hoffmann, H.- H. Sanchez-Rivera, F. J. Leal, A. A. Ashbrook, A. W. Le Pen, J. Michailidis, E. Ricardo-Lax, I. Peace, A. Stenzel, A. F. Lowe, S. W. MacDonald, M. R. Rice, C. M. Poirier, J. T. 2020-10-08 doi:10.1101/2020.10.07.326462 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Sequence evaluation and comparative analysis of novel assays for intact proviral HIV-1 DNA ]]> https://biorxiv.org/content/10.1101/2020.10.07.330787v1?rss=1 Gaebler, C. Falcinelli, S. D. Stoffel, E. Read, J. Murtagh, R. Oliveira, T. Ramos, V. Lorenzi, J. C. Kirchherr, J. L. James, K. S. Allard, B. Baker, C. Kuruc, J. D. Caskey, M. Archin, N. Siliciano, R. F. Margolis, D. M. Nussenzweig, M. C. 2020-10-09 doi:10.1101/2020.10.07.330787 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ A selectable, plasmid-based system to generate CRISPR/Cas9 gene edited and knock-in mosquito cell lines ]]> https://biorxiv.org/content/10.1101/2020.10.09.333641v1?rss=1 Rozen-Gagnon, K. Yi, S. Jacobson, E. Novack, S. Rice, C. M. 2020-10-10 doi:10.1101/2020.10.09.333641 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ Integration of prophages into CRISPR loci remodels viral immunity in Streptococcus pyogenes ]]> https://biorxiv.org/content/10.1101/2020.10.09.333658v1?rss=1 Varble, A. Campisi, E. Euler, C. W. Fyodorova, J. Rostol, J. Fischetti, V. A. Marraffini, L. A. 2020-10-09 doi:10.1101/2020.10.09.333658 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ TMEM41B is a pan-flavivirus host factor ]]> https://biorxiv.org/content/10.1101/2020.10.09.334128v1?rss=1 Hoffmann, H.- H. Schneider, W. M. Rozen-Gagnon, K. Miles, L. A. Schuster, F. Razooky, B. Jacobson, E. Wu, X. Yi, S. Rudin, C. M. MacDonald, M. R. McMullan, L. K. Poirier, J. T. Rice, C. M. 2020-10-10 doi:10.1101/2020.10.09.334128 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ Behavioral and genomic sensory adaptations underlying the pest activity of Drosophila suzukii ]]> https://biorxiv.org/content/10.1101/2020.10.15.341594v1?rss=1 Durkin, S. M. Chakraborty, M. Abrieux, A. Lewald, K. M. Gadau, A. Svetec, N. Peng, J. Kopyto, M. Chiu, J. C. Emerson, J. J. Zhao, L. 2020-10-15 doi:10.1101/2020.10.15.341594 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Transcriptional silencing of ALDH2 in acute myeloid leukemia confers a dependency on Fanconi anemia proteins ]]> https://biorxiv.org/content/10.1101/2020.10.23.352070v1?rss=1 Yang, Z. Wei, Y. Wu, X. S. Iyer, S. V. Jung, M. Adelman, E. R. Klingbeil, O. Kramer, M. Demerdash, O. E. Chang, K. Goodwin, S. Hodges, E. McCombie, W. R. Figueroa, M. E. Smogorzewska, A. Vakoc, C. R. 2020-10-23 doi:10.1101/2020.10.23.352070 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ Chemical signatures of human odour generate a unique neural code in the brain of Aedes aegypti mosquitoes ]]> https://biorxiv.org/content/10.1101/2020.11.01.363861v1?rss=1 Zhao, Z. Zung, J. L. Kriete, A. L. Iqbal, A. Younger, M. A. Matthews, B. J. Merhof, D. Thiberge, S. Strauch, M. McBride, C. S. 2020-11-02 doi:10.1101/2020.11.01.363861 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ Encoding of facial features by single neurons in the human amygdala and hippocampus ]]> https://biorxiv.org/content/10.1101/2020.11.02.363853v1?rss=1 Cao, R. Li, X. Brandmeir, N. Wang, S. 2020-11-03 doi:10.1101/2020.11.02.363853 Cold Spring Harbor Laboratory Press 2020-11-03 <![CDATA[ Evolution of Antibody Immunity to SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.11.03.367391v1?rss=1 Gaebler, C. Wang, Z. Lorenzi, J. C. C. Muecksch, F. Finkin, S. Tokuyama, M. Ladinsky, M. Cho, A. Jankovic, M. Schaefer-Babajew, D. Oliveira, T. Y. Cipolla, M. Viant, C. Barnes, C. O. Hurley, A. Turroja, M. Gordon, K. Millard, K. G. Ramos, V. Schmidt, F. Weisblum, Y. Jha, D. Tankelevich, M. Yee, J. Shimeliovich, I. Robbiani, D. F. Zhao, Z. Gazumyan, A. Hatziioannou, T. Bjorkman, P. J. Mehandru, S. Bieniasz, P. D. Caskey, M. Nussenzweig, M. C. 2020-11-05 doi:10.1101/2020.11.03.367391 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Non-canonical odor coding ensures unbreakable mosquito attraction to humans ]]> https://biorxiv.org/content/10.1101/2020.11.07.368720v1?rss=1 Younger, M. A. Herre, M. Ehrlich, A. R. Gong, Z. Gilbert, Z. N. Rahiel, S. Matthews, B. J. Vosshall, L. B. 2020-11-08 doi:10.1101/2020.11.07.368720 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ Glia actively sculpt sensory neurons by controlled phagocytosis to tune animal behavior ]]> https://biorxiv.org/content/10.1101/2020.11.11.378893v1?rss=1 Raiders, S. Black, E. C. Bae, A. MacFarlane, S. Shaham, S. Singhvi, A. 2020-11-12 doi:10.1101/2020.11.11.378893 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ GSAP Regulates Amyloid Beta Production through Modulation of Amyloid Precursor Protein Trafficking ]]> https://biorxiv.org/content/10.1101/2020.11.12.379313v1?rss=1 Chang, J. C. Xu, P. Wong, E. Flajolet, M. Li, Y.-M. Greengard, P. 2020-11-13 doi:10.1101/2020.11.12.379313 Cold Spring Harbor Laboratory Press 2020-11-13 <![CDATA[ Near-atomic resolution nucleosome structures and their variations in interphase and metaphase chromosomes ]]> https://biorxiv.org/content/10.1101/2020.11.12.380386v1?rss=1 Arimura, Y. Shih, R. M. Froom, R. Funabiki, H. 2020-11-12 doi:10.1101/2020.11.12.380386 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ As above, so below: Whole transcriptome profiling supports the continuum hypothesis of avian dorsal and ventral pallium organization ]]> https://biorxiv.org/content/10.1101/2020.11.13.375055v1?rss=1 Gedman, G. L. Haase, B. Durieux, G. Biegler, M. Fedrigo, O. Jarvis, E. D. 2020-11-13 doi:10.1101/2020.11.13.375055 Cold Spring Harbor Laboratory Press 2020-11-13 <![CDATA[ Isotropic 3D electron microscopy reference library of whole cells and tissues ]]> https://biorxiv.org/content/10.1101/2020.11.13.382457v1?rss=1 Xu, C. S. Pang, S. Shtengel, G. Müller, A. Ritter, A. T. Hoffman, H. K. Takemura, S.-y. Lu, Z. Pasolli, H. A. Iyer, N. Chung, J. Bennett, D. Weigel, A. V. Walther, T. C. Farese, R. V. van Engelenburg, S. B. Mellman, I. Solimena, M. Hess, H. F. 2020-11-14 doi:10.1101/2020.11.13.382457 Cold Spring Harbor Laboratory Press 2020-11-14 <![CDATA[ GSAP regulates mitochondrial function through the Mitochondria-associated ER membrane in the pathogenesis of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2020.11.17.385245v1?rss=1 Xu, P. Chang, J. C. Zhou, X. Wang, W. Bamkole, M. Wong, E. Bettayeb, K. Jiang, L.-L. Huang, T. Luo, W. Xu, H. Nairn, A. C. Flajolet, M. Ip, N. Li, Y.-M. Greengard, P. 2020-11-18 doi:10.1101/2020.11.17.385245 Cold Spring Harbor Laboratory Press 2020-11-18 <![CDATA[ Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells ]]> https://biorxiv.org/content/10.1101/2020.11.17.385716v1?rss=1 Pae, J. Ersching, J. Castro, T. B. Schips, M. Mesin, L. Allon, S. J. Ordovas-Montanes, J. Mlynarczyk, C. Melnick, A. Efeyan, A. Shalek, A. K. Meyer-Hermann, M. Victora, G. D. 2020-11-17 doi:10.1101/2020.11.17.385716 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ Mosaic RBD nanoparticles elicit neutralizing antibodies against SARS-CoV-2 and zoonotic coronaviruses ]]> https://biorxiv.org/content/10.1101/2020.11.17.387092v1?rss=1 Bjorkman, P. J. Cohen, A. A. Gnanapragasam, P. N. P. Lee, Y. E. Ou, S. Kakutani, L. M. Keeffe, J. R. Barnes, C. O. Nussenzweig, M. C. 2020-11-17 doi:10.1101/2020.11.17.387092 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ Heritable Sexual Attraction under Parental Control ]]> https://biorxiv.org/content/10.1101/2020.11.18.389387v1?rss=1 Toker, I. A. Lev, I. Mor, Y. Gurevich, Y. Fisher, D. Houri-Zeevi, L. Antonova, O. Hadany, L. Shaham, S. Rechavi, O. 2020-11-19 doi:10.1101/2020.11.18.389387 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ Human hepatocyte PNPLA3 148M exacerbates rapid non-alcoholic steatohepatitis development in chimeric mice ]]> https://biorxiv.org/content/10.1101/2020.11.19.387613v1?rss=1 Kabbani, M. Michailidis, E. Steensels, S. Fulmer, C. G. Luna, J. M. Le Pen, J. Tardelli, M. Razooky, B. Ricardo-Lax, I. Zou, C. Zeck, B. Stenzel, A. F. Quirk, C. Foquet, L. Ashbrook, A. W. Schneider, W. M. Belkaya, S. Lalazar, G. Liang, Y. Pittman, M. Devisscher, L. Suemizu, H. Theise, N. D. Chiriboga, L. Cohen, D. E. Copenhaver, R. Grompe, M. Meuleman, P. Ersoy, B. A. Rice, C. M. de Jong, Y. P. 2020-11-20 doi:10.1101/2020.11.19.387613 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ IBEX: A versatile multi-plex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues ]]> https://biorxiv.org/content/10.1101/2020.11.20.390690v1?rss=1 65 parameters in the same tissue section without physical degradation. IBEX can be employed with various types of conventional microscopes and permits use of both commercially available and user-generated antibodies in an open system to allow easy adjustment of staining panels based on ongoing marker discovery efforts. We show how IBEX can also be used with amplified staining methods for imaging strongly fixed tissues with limited epitope retention and with oligonucleotide-based staining, allowing potential cross-referencing between flow cytometry, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq), and IBEX analysis of the same tissue. To facilitate data processing, we provide an open source platform for automated registration of iterative images. IBEX thus represents a technology that can be rapidly integrated into most current laboratory workflows to achieve high content imaging to reveal the complex cellular landscape of diverse organs and tissues. Significance StatementSingle cell flow cytometry and genomic methods are rapidly increasing our knowledge of the diversity of cell types in metazoan tissues. However, suitably robust methods for placing these cells in a spatial context that reveal how their localization and putative interactions contribute to tissue physiology and pathology are still lacking. Here we provide a readily accessible pipeline (IBEX) for highly multi-plex immunofluorescent imaging that enables a fine-grained analysis of cells in their tissue context. Additionally, we describe extensions of the IBEX workflow to handle hard to image tissue preparations and a method to facilitate direct integration of the imaging data with flow cytometry and sequencing technologies. ]]> Radtke, A. J. Kandov, E. Lowekamp, B. Speranza, E. Chu, C. J. Gola, A. Thakur, N. Shih, R. Yao, L. Yaniv, Z. R. Beuschel, R. T. Kabat, J. Croteau, J. Davis, J. Hernandez, J. M. Germain, R. N. 2020-11-21 doi:10.1101/2020.11.20.390690 Cold Spring Harbor Laboratory Press 2020-11-21 <![CDATA[ Origin and evolution of the Zinc Finger Antiviral Protein ]]> https://biorxiv.org/content/10.1101/2020.12.04.412510v1?rss=1 Goncalves Carneiro, D. Takata, M. A. Ong, H. Shilton, A. Bieniasz, P. D. D. 2020-12-05 doi:10.1101/2020.12.04.412510 Cold Spring Harbor Laboratory Press 2020-12-05 <![CDATA[ DOT1L Complex Regulates Transcriptional Initiation 1 in Human Cells ]]> https://biorxiv.org/content/10.1101/2020.12.07.414722v1?rss=1 Yu, M. Roeder, R. Wu, A. Zhi, J. Tian, T. Chen, L. Fu, L. 2020-12-07 doi:10.1101/2020.12.07.414722 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ Persistent Cellular Immunity to SARS-CoV-2 Infection ]]> https://biorxiv.org/content/10.1101/2020.12.08.416636v1?rss=1 Breton, G. Mendoza, P. Hagglof, T. Oliveira, T. Y. Schaefer-Babajew, D. Gaebler, C. Turroja, M. Hurley, A. Caskey, M. Nussenzweig, M. C. 2020-12-09 doi:10.1101/2020.12.08.416636 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Blunting of insulin-stimulated glucose uptake in brown adipose tissue induces systemic metabolic dysregulation in female mice ]]> https://biorxiv.org/content/10.1101/2020.12.09.416685v1?rss=1 Picatoste, B. Yammine, L. Leahey, R. Soares, D. Cohen, P. McGraw, T. E. 2020-12-10 doi:10.1101/2020.12.09.416685 Cold Spring Harbor Laboratory Press 2020-12-10 <![CDATA[ Transcription factors drive opposite relationships between gene age and tissue specificity in male and female Drosophila gonads ]]> https://biorxiv.org/content/10.1101/2020.12.09.418293v1?rss=1 Witt, E. Benjamin, S. Svetec, N. Zhao, L. 2020-12-09 doi:10.1101/2020.12.09.418293 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Distinct expression of select and transcriptome-wide isolated 3'UTRs suggests critical roles in development and transition states ]]> https://biorxiv.org/content/10.1101/2020.12.11.420125v1?rss=1 Hynes, M. Ji, S. Yang, Z. Gozali, L. Kenney, T. Kocabas, A. Park, C. 2020-12-11 doi:10.1101/2020.12.11.420125 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Poly(ADP-ribose) potentiates ZAP antiviral activity ]]> https://biorxiv.org/content/10.1101/2020.12.17.423219v1?rss=1 Pornillos, O. Xue, G. Braczyk, K. Goncalves-Carneiro, D. Ong, H. Dawidziak, D. M. Zawada, K. Yueping, W. Zadrozny, K. K. Ganser-Pornillos, B. K. Bieniasz, P. D. 2020-12-17 doi:10.1101/2020.12.17.423219 Cold Spring Harbor Laboratory Press 2020-12-17 <![CDATA[ Differential compartmentalization of BMP4/NOGGIN requires NOGGIN trans-epithelial transport ]]> https://biorxiv.org/content/10.1101/2020.12.18.423440v1?rss=1 Phan-Everson, T. M.-T. Etoc, F. Brivanlou, A. H. Siggia, E. D. 2020-12-19 doi:10.1101/2020.12.18.423440 Cold Spring Harbor Laboratory Press 2020-12-19 <![CDATA[ A recombinant protein SARS-CoV-2 candidate vaccine elicits high-titer neutralizing antibodies in macaques. ]]> https://biorxiv.org/content/10.1101/2020.12.20.422693v1?rss=1 Baisa, G. Rancour, D. Mansfield, K. Burns, M. Martin, L. Cunha, D. Fischer, J. Muecksch, F. Hatziioannou, T. Bieniasz, P. Schomburg, F. Luke, K. 2020-12-21 doi:10.1101/2020.12.20.422693 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ Linker histone H1.8 inhibits chromatin-binding of condensins and DNA topoisomerase II to tune chromosome compaction and individualization ]]> https://biorxiv.org/content/10.1101/2020.12.20.423657v1?rss=1 Choppakatla, P. Dekker, B. Cutts, E. Vannini, A. Dekker, J. Funabiki, H. 2020-12-20 doi:10.1101/2020.12.20.423657 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ A neuronal circuit for vector computation builds an allocentric traveling-direction signal in the Drosophila fan-shaped body ]]> https://biorxiv.org/content/10.1101/2020.12.22.423967v1?rss=1 Lyu, C. Abbott, L. F. Maimon, G. 2020-12-23 doi:10.1101/2020.12.22.423967 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ Transforming representations of movement from body- to world-centric space ]]> https://biorxiv.org/content/10.1101/2020.12.22.424001v1?rss=1 Lu, J. Westeinde, E. A. Hamburg, L. Dawson, P. M. Lyu, C. Maimon, G. Druckmann, S. Wilson, R. I. 2020-12-23 doi:10.1101/2020.12.22.424001 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ Sustained antibody response to ZIKV infection induced by NS1 protein is accompanied by the progressive appearance of autoreactive antibodies and cross-reactive B cell clones. ]]> https://biorxiv.org/content/10.1101/2020.12.24.423863v1?rss=1 Cavazzoni, C. B. Bozza, V. B. Tostes, L. Maia, B. Mesin, L. Schiepers, A. Ersching, J. Neris, R. L. Conde, J. N. Coleho, D. R. Conde, L. Paula-Neto, H. A. Lima, T. M. Alvim, R. G. F. Castilho, L. R. Mohana-Borges, R. Assuncao-Miranda, I. Nobrega, A. Victora, G. D. Vale, A. M. 2020-12-24 doi:10.1101/2020.12.24.423863 Cold Spring Harbor Laboratory Press 2020-12-24 <![CDATA[ Identification of Discriminative Gene-level and Protein-level Features Associated with Gain-of-Function and Loss-of-Function Mutations ]]> https://biorxiv.org/content/10.1101/2021.01.01.424981v1?rss=1 Sevim Bayrak, C. Jain, A. Stein, D. Chaudhary, K. Nadkarni, G. Van Vleck, T. T. Boisson-Dupuis, S. Stenson, P. Cooper, D. N. Schlessinger, A. N. Itan, Y. 2021-01-04 doi:10.1101/2021.01.01.424981 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Self-organized stem cell-derived human lung buds with proximo-distal patterning and novel targets of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2021.01.06.425622v1?rss=1 Rosado-Olivieri, E. A. Razooky, B. Hoffmann, H.-H. De Santis, R. Rice, C. M. Brivanlou, A. H. 2021-01-06 doi:10.1101/2021.01.06.425622 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Rapid mechanical stimulation of inner-ear hair cells by photonic pressure ]]> https://biorxiv.org/content/10.1101/2021.01.10.426123v1?rss=1 Kozlov, A. Abeytunge, S. Gianoli, F. Hudspeth, A. J. 2021-01-11 doi:10.1101/2021.01.10.426123 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants ]]> https://biorxiv.org/content/10.1101/2021.01.15.426911v1?rss=1 Wang, Z. Schmidt, F. Weisblum, Y. Muecksch, F. Barnes, C. O. Finkin, S. Schaefer-Babajew, D. Cipolla, M. Gaebler, C. Lieberman, J. A. Yang, Z. Abernathy, M. E. Huey-Tubman, K. E. Hurley, A. Turroja, M. West, K. A. Gordon, K. Millard, K. G. Ramos, V. Silva, J. D. Xu, J. Colbert, R. A. Patel, R. Dizon, J. P. Unson-O'Brien, C. Shimeliovich, I. Gazumyan, A. Caskey, M. Bjorkman, P. J. Casellas, R. Hatziioannou, T. Bieniasz, P. D. Nussenzweig, M. C. 2021-01-19 doi:10.1101/2021.01.15.426911 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Altered temporal sequence of transcriptional regulators in the generation of human cerebellar granule cells ]]> https://biorxiv.org/content/10.1101/2021.01.17.427030v1?rss=1 Behesti, H. Kocabas, A. Buchholz, D. E. Carroll, T. S. Hatten, M. E. 2021-01-17 doi:10.1101/2021.01.17.427030 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Bispecific antibody prevents SARS-CoV-2 escape and protects mice from disease ]]> https://biorxiv.org/content/10.1101/2021.01.22.427567v1?rss=1 De Gasparo, R. Pedotti, M. Simonelli, L. Nickl, P. Muecksch, F. Lorenzi, J. C. C. Mazzola, F. Magri, D. Michalcikova, T. Haviernik, J. Honig, V. Cassaniti, I. Percivalle, E. Mrazkova, B. Polakova, N. Fortova, A. Tureckova, J. Iatsiuk, V. Di Girolamo, S. Palus, M. Zudova, D. Bednar, P. Bukova, I. Bianchini, F. Mehn, D. Nencka, R. Strakova, P. Pavlis, O. Rozman, J. Gioria, S. Sammartino, J. C. Giardina, F. Gaiarsa, S. Hammarström, Q. P. Barnes, C. O. Piralla, A. Bjorkman, P. J. Baldanti, F. Calzolai, L. Nussenzweig, M. C. Bieniasz, P. D. Hatziioannou, T. 2021-01-22 doi:10.1101/2021.01.22.427567 Cold Spring Harbor Laboratory Press 2021-01-22 <![CDATA[ The structural basis of odorant recognition in insect olfactory receptors ]]> https://biorxiv.org/content/10.1101/2021.01.24.427933v1?rss=1 del Marmol, J. Yedlin, M. Ruta, V. 2021-01-24 doi:10.1101/2021.01.24.427933 Cold Spring Harbor Laboratory Press 2021-01-24 <![CDATA[ A Developmental Role for Microglial Presenilin 1 in Memory ]]> https://biorxiv.org/content/10.1101/2021.01.26.428181v1?rss=1 Ledo, J. H. Azevedo, E. Medrihan, L. Cheng, J. Silva, H. M. McCabe, K. Bamkole, M. Lafaille, J. J. Friedman, J. M. Stevens, B. Greengard, P. 2021-01-27 doi:10.1101/2021.01.26.428181 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Early therapy with remdesivir and antibody combinations improves COVID-19 disease in mice ]]> https://biorxiv.org/content/10.1101/2021.01.27.428478v1?rss=1 Martinez, D. Schaefer, A. Leist, S. R. Gully, K. Feng, J. Bunyan, E. Porter, D. Cihlar, T. Montgomery, S. Baric, R. S. Nussenzweig, M. C. Sheahan, T. P. 2021-01-28 doi:10.1101/2021.01.27.428478 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Adaptive stimulation of macropinocytosis overcomes aspartate limitation in cancer cells under hypoxia ]]> https://biorxiv.org/content/10.1101/2021.02.02.429407v1?rss=1 Birsoy, K. Bar-Sagi, D. Garcia-Bermudez, J. Prasad, S. Baudrier, L. Badgley, M. A. Liu, Y. La, K. Soula, M. Williams, R. T. Yamaguchi, N. Hwang, R. F. Taylor, L. J. De Stanchina, E. Rostandy, B. Alwaseem, H. Molina, H. 2021-02-03 doi:10.1101/2021.02.02.429407 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Variation in predicted COVID-19 risk among lemurs and lorises ]]> https://biorxiv.org/content/10.1101/2021.02.03.429540v1?rss=1 Melin, A. D. Orkin, J. D. Janiak, M. C. Valenzuela, A. Kuderna, L. F. Marrone, F. Ramangason, H. Horvath, J. E. Roos, C. Kitchener, A. C. Khor, C. C. Lim, W. K. Lee, J. G. Tan, P. Umapathy, G. Raveendran, M. Harris, R. A. Gut, I. Gut, M. Lizano, E. Nadler, T. Zinner, D. Johnson, S. E. Jarvis, E. D. Fedrigo, O. Wu, D. Zhang, G. Farh, K. K.-H. Rogers, J. Marques-Bonet, T. Navarro, A. Juan, D. Arora, P. S. Higham, J. P. 2021-02-03 doi:10.1101/2021.02.03.429540 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Single-cell RNA-sequencing reveals pre-meiotic X-chromosome dosage compensation in Drosophila testis ]]> https://biorxiv.org/content/10.1101/2021.02.05.429952v1?rss=1 Witt, E. Shao, Z. Hu, C. Krause, H. M. Zhao, L. 2021-02-06 doi:10.1101/2021.02.05.429952 Cold Spring Harbor Laboratory Press 2021-02-06 <![CDATA[ Huntingtin CAG expansion impairs germ layer patterning in synthetic human gastruloids through polarity defects. ]]> https://biorxiv.org/content/10.1101/2021.02.06.430005v1?rss=1 Galgoczi, S. Ruzo, A. Markopoulos, C. Yoney, A. Phan-Everson, T. Haremaki, T. Metzger, J. J. Etoc, F. Brivanlou, A. H. 2021-02-07 doi:10.1101/2021.02.06.430005 Cold Spring Harbor Laboratory Press 2021-02-07 <![CDATA[ c-MAF dependent perivascular macrophages regulate diet induced metabolic syndrome ]]> https://biorxiv.org/content/10.1101/2021.02.07.430147v1?rss=1 Moura Silva, H. Kitoko, J. Z. Queiroz, C. P. Kroehling, L. Matheis, F. Lu Yang, K. Ren-Fielding, C. Littman, D. Bozza, M. Mucida, D. Lafaille, J. 2021-02-08 doi:10.1101/2021.02.07.430147 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Intermolecular interactions drive protein adaptive and co-adaptive evolution at both species and population levels ]]> https://biorxiv.org/content/10.1101/2021.02.08.430345v1?rss=1 Peng, J. Zhao, L. 2021-02-10 doi:10.1101/2021.02.08.430345 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ 5-hydroxymethylcytosine mediated active demethylation is required for neuronal differentiation and function ]]> https://biorxiv.org/content/10.1101/2021.02.10.430698v1?rss=1 Stoyanova, E. Riad, M. Rao, A. Heintz, N. 2021-02-11 doi:10.1101/2021.02.10.430698 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ SARS-CoV-2 lineage B.1.526 emerging in the New York region detected by software utility created to query the spike mutational landscape ]]> https://biorxiv.org/content/10.1101/2021.02.14.431043v1?rss=1 West, A. P. Barnes, C. O. Yang, Z. Bjorkman, P. J. 2021-02-15 doi:10.1101/2021.02.14.431043 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ Correlation between structure and function in phosphatidylinositol lipid-dependent Kir2.2 gating ]]> https://biorxiv.org/content/10.1101/2021.02.15.431350v1?rss=1 MacKinnon, R. Zhang, Y. Tao, X. 2021-02-16 doi:10.1101/2021.02.15.431350 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Behavioral control by depolarized and hyperpolarized states of an integrating neuron ]]> https://biorxiv.org/content/10.1101/2021.02.19.431690v1?rss=1 Sordillo, A. Bargmann, C. I. 2021-02-19 doi:10.1101/2021.02.19.431690 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Volumetric Calcium Imaging of 1 Million Neurons Across Cortical Regions at Cellular Resolution Using Light Beads Microscopy ]]> https://biorxiv.org/content/10.1101/2021.02.21.432164v1?rss=1 200,000 neurons at ~5 Hz, recording of populations of ~1 million neurons within ~5.4x6x0.5 mm3 volumes at ~2Hz as well as higher-speed (9.6 Hz) sub-cellular resolution volumetric recordings. LBM provides an unprecedented opportunity for discovering the neurocomputations underlying cortex-wide encoding and processing of information in the mammalian brain. ]]> Vaziri, A. Demas, J. Manley, J. Tejera, F. Barber, K. Kim, H. Martinez Traub, F. Chen, B. 2021-02-22 doi:10.1101/2021.02.21.432164 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ A monocyte/dendritic cell molecular signature of SARS-CoV2-related multisystem inflammatory syndrome in children (MIS-C) with severe myocarditis ]]> https://biorxiv.org/content/10.1101/2021.02.23.432486v1?rss=1 de Cevins, C. Luka, M. Smith, N. Meynier, S. Magerus, A. Carbone, F. Garcia Paredes, V. Barnabei, L. Batignes, M. Boulle, A. Stolzenberg, M.-C. Perot, B. P. Charbit, B. Fali, T. Pirabarakan, V. Sorin, B. Riller, Q. Abdessalem, G. Beretta, M. Grzelak, L. Goncalves, P. Di Santo, J. P. Mouquet, H. Schwartz, O. Zarhrate, M. Parisot, M. Bole-Feysot, C. Masson, C. Cagnard, N. Corneau, A. Bruneau, C. Zhang, S.-Y. Casanova, J.-L. Bader Meunier, B. Haroche, J. Melki, I. Lorrot, M. Oualha, M. Moulin, F. Bonnet, D. Belhadjer, Z. Leruez, M. Allali, S. Gras Leguen 2021-02-23 doi:10.1101/2021.02.23.432486 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ A high-quality Genome and Comparison of Short versus Long Read Transcriptome of the Palaearctic duck Aythya fuligula (Tufted Duck) ]]> https://biorxiv.org/content/10.1101/2021.02.24.432697v1?rss=1 Mueller, R. C. Ellström, P. Howe, K. Uliano-Silva, M. Kuo, R. I. Miedzinska, K. Warr, A. Fedrigo, O. Haase, B. Mountcastle, J. Chow, W. Torrance, J. Wood, J. Järhult, J. D. Naguib, M. M. Olsen, B. Jarvis, E. D. Smith, J. Eöry, L. Kraus, R. H. 2021-02-25 doi:10.1101/2021.02.24.432697 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Derivation and Characterization of an inositol phosphate-independent HIV-1 ]]> https://biorxiv.org/content/10.1101/2021.03.01.433343v1?rss=1 Poston, D. Zang, T. Bieniasz, P. D. 2021-03-01 doi:10.1101/2021.03.01.433343 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Multimeric nanobodies from camelid engineered mice and llamas potently neutralize SARS-CoV-2 variants ]]> https://biorxiv.org/content/10.1101/2021.03.04.433768v1?rss=1 Xu, J. Xu, K. Jung, S. K. Conte, A. Lieberman, J. Muecksch, F. Lorenzi, J. C. C. Park, S. Wang, Z. Tessarollo, L. Bylund, T. Chuang, G.-Y. Olia, A. Teng, I.-T. Zhou, T. Stephens, T. Tsybovsky, Y. Bieniasz, P. D. Hatziioannou, T. Nussenzweig, M. Kwong, P. Casellas, R. 2021-03-04 doi:10.1101/2021.03.04.433768 Cold Spring Harbor Laboratory Press 2021-03-04 <![CDATA[ The Mycobacterium tuberculosis transposon sequencing database (MtbTnDB): a large-scale guide to genetic conditional essentiality ]]> https://biorxiv.org/content/10.1101/2021.03.05.434127v1?rss=1 Jinich, A. Zaveri, A. DeJesus, M. A. Flores-Bautista, E. Smith, C. M. Sassetti, C. M. Rock, J. M. Ehrt, S. Schnappinger, D. Ioerger, T. R. Rhee, K. Y. 2021-03-06 doi:10.1101/2021.03.05.434127 Cold Spring Harbor Laboratory Press 2021-03-06 <![CDATA[ Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies ]]> https://biorxiv.org/content/10.1101/2021.03.07.434227v1?rss=1 Muecksch, F. Weisblum, Y. Barnes, C. Schmidt, F. Schaefer-Babajew, D. Lorenzi, J. Flyak, A. DeLaitsch, A. Huey-Tubman, K. Hou, S. Schiffer, C. Gaebler, C. Wang, Z. Da Silva, J. Poston, D. Finkin, S. Cho, A. Cipolla, M. Oliveira, T. Millard, K. Ramos, V. Gazumyan, A. Rutkowska, M. Caskey, M. Nussenzweig, M. Bjorkman, P. Hatziioannou, T. Bieniasz, P. 2021-03-08 doi:10.1101/2021.03.07.434227 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Cyclodextrins increase membrane tension and are universal activators of mechanosensitive channels ]]> https://biorxiv.org/content/10.1101/2021.03.08.434340v1?rss=1 Cox, C. Zhang, Y. Zhou, Z. Walz, T. Martinac, B. 2021-03-08 doi:10.1101/2021.03.08.434340 Cold Spring Harbor Laboratory Press 2021-03-08 <![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[ The cAMP effector PKA mediates Moody GPCR signaling in Drosophila blood-brain barrier formation and maturation ]]> https://biorxiv.org/content/10.1101/2021.03.10.434865v1?rss=1 Li, X. Fetter, R. Schwabe, T. Jung, C. Steller, H. Gaul, U. 2021-03-11 doi:10.1101/2021.03.10.434865 Cold Spring Harbor Laboratory Press 2021-03-11 <![CDATA[ A quantitative landscape of cell fate transitions identifies principles of cellular decision-making ]]> https://biorxiv.org/content/10.1101/2021.03.11.434982v1?rss=1 Saez, M. Blassberg, R. Camacho-Aguilar, E. Siggia, E. D. Rand, D. A. Briscoe, J. 2021-03-11 doi:10.1101/2021.03.11.434982 Cold Spring Harbor Laboratory Press 2021-03-11 <![CDATA[ Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex ]]> https://biorxiv.org/content/10.1101/2021.03.13.435256v1?rss=1 Malone, B. Chen, J. Wang, Q. Llewellyn, E. Choi, Y. J. Olinares, P. D. B. Cao, X. Hernandez, C. Eng, E. T. Chait, B. T. Shaw, D. E. Landick, R. Darst, S. A. Campbell, E. A. 2021-03-14 doi:10.1101/2021.03.13.435256 Cold Spring Harbor Laboratory Press 2021-03-14 <![CDATA[ Antibody elicited by HIV-1 immunogen vaccination in macaques displaces Env fusion peptide and destroys a neutralizing epitope ]]> https://biorxiv.org/content/10.1101/2021.03.17.435265v1?rss=1 Abernathy, M. E. Gristick, H. B. Vielmetter, J. Keeffe, J. R. Gnanapragasam, P. N. Lee, Y. E. Escolano, A. Gautam, R. Seaman, M. S. Martin, M. A. Nussenzweig, M. C. Bjorkman, P. J. 2021-03-17 doi:10.1101/2021.03.17.435265 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Single-stranded nucleic acid sensing and coacervation by linker histone H1 ]]> https://biorxiv.org/content/10.1101/2021.03.17.435841v1?rss=1 Leicher, R. Osunsade, A. Latham, A. Chua, G. N. L. Watters, J. W. Christodoulou-Rubalcava, S. Zhang, B. David, Y. Liu, S. 2021-03-17 doi:10.1101/2021.03.17.435841 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Mutational escape from the polyclonal antibody response to SARS-CoV-2 infection is largely shaped by a single class of antibodies ]]> https://biorxiv.org/content/10.1101/2021.03.17.435863v1?rss=1 Greaney, A. J. Starr, T. N. Barnes, C. O. Weisblum, Y. Schmidt, F. Caskey, M. Gaebler, C. Agudelo, M. Finkin, S. Wang, Z. Poston, D. Muecksch, F. Hatziioannou, T. Bieniasz, P. D. Robbiani, D. F. Nussenzweig, M. C. Bjorkman, P. J. Bloom, J. D. 2021-03-18 doi:10.1101/2021.03.17.435863 Cold Spring Harbor Laboratory Press 2021-03-18 <![CDATA[ Decreased synthesis and variable gene transcripts of oxytocin in a domesticated avian species ]]> https://biorxiv.org/content/10.1101/2021.03.17.435911v1?rss=1 Tobari, Y. Theofanopoulou, C. Mori, C. Sato, Y. Marutani, M. Fujioka, S. Konno, N. Suzuki, K. Furutani, A. Hakataya, S. Yao, C.-T. Yang, E.-Y. Tsai, C.-R. Tang, P.-C. Chen, C.-F. Boeckx, C. Jarvis, E. Okanoya, K. 2021-03-18 doi:10.1101/2021.03.17.435911 Cold Spring Harbor Laboratory Press 2021-03-18 <![CDATA[ Coagulation factors directly cleave SARS-CoV-2 spike and enhance viral entry ]]> https://biorxiv.org/content/10.1101/2021.03.31.437960v1?rss=1 Kastenhuber, E. R. Jaimes, J. A. Johnson, J. L. Mercadante, M. Muecksch, F. Weisblum, Y. Bram, Y. Schwartz, R. E. Whittaker, G. R. Cantley, L. C. 2021-04-01 doi:10.1101/2021.03.31.437960 Cold Spring Harbor Laboratory Press 2021-04-01 <![CDATA[ Antibody response to SARS-CoV-2 mRNA vaccines in pregnant women and their neonates ]]> https://biorxiv.org/content/10.1101/2021.04.05.438524v1?rss=1 Prabhu, M. Murphy, E. A. Sukhu, A. C. Yee, J. Singh, S. Eng, D. Zhao, Z. Riley, L. E. Yang, Y. J. 2021-04-06 doi:10.1101/2021.04.05.438524 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Advancing quality-control for NGS measurement of actionable mutations in circulating tumor DNA ]]> https://biorxiv.org/content/10.1101/2021.04.06.438497v1?rss=1 Willey, J. C. Morrison, T. Austermiller, B. Crawford, E. L. Craig, D. J. Blomquist, T. M. Jones, W. D. Wali, A. Lococo, J. S. Haseley, N. Richmond, T. A. Novoradovskaya, N. Kusko, R. Chen, G. Li, Q.-Z. Johann, D. Deveson, I. W. Mercer, T. Wu, L. Xu, J. 2021-04-06 doi:10.1101/2021.04.06.438497 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Deep oncopanel sequencing reveals fixation time- and within block position-dependent quality degradation in FFPE processed samples ]]> https://biorxiv.org/content/10.1101/2021.04.06.438687v1?rss=1 Zhang, Y. Blomquist, T. M. Kusko, R. Stetson, D. Zhang, Z. Yin, L. Sebra, R. Gong, B. LoCoco, J. S. Mittal, V. K. Novoradovskaya, N. Yeo, J.-Y. Dominiak, N. Hipp, J. Raymond, A. Qiu, F. Arib, H. Smith, M. L. Brock, J. E. Farkas, D. H. Craig, D. J. Crawford, E. L. Li, D. Morrison, T. Tom, N. Xiao, W. Yang, M. Mason, C. E. Richmond, T. A. Jones, W. Johann, D. J. Shi, L. Tong, W. Willey, J. C. Xu, J. 2021-04-07 doi:10.1101/2021.04.06.438687 Cold Spring Harbor Laboratory Press 2021-04-07 <![CDATA[ Nanobody Repertoires for Exposing Vulnerabilities of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2021.04.08.438911v1?rss=1 Mast, F. D. Fridy, P. C. Ketaren, N. E. Wang, J. Jacobs, E. Y. Olivier, J. P. Sanyal, T. Molloy, K. R. Schmidt, F. Rutkowska, M. Weisblum, Y. Rich, L. M. Vanderwall, E. R. Dambrauskas, N. Vigdorovich, V. Keegan, S. Jiler, J. B. Stein, M. E. Olinares, P. D. B. Hatziioannou, T. Sather, D. N. Debley, J. S. Fenyö, D. Sali, A. Bieniasz, P. D. Aitchison, J. D. Chait, B. T. Rout, M. P. 2021-04-10 doi:10.1101/2021.04.08.438911 Cold Spring Harbor Laboratory Press 2021-04-10 <![CDATA[ Sumoylation of the human histone H4 tail inhibits p300-mediated transcription by RNA polymerase II in cellular extracts ]]> https://biorxiv.org/content/10.1101/2021.04.08.439039v1?rss=1 Leonen, C. J. A. Shimada, M. Weller, C. E. Nakadai, T. Hsu, P. L. Shelton, P. M. M. Sadilek, M. Zheng, N. Roeder, B. Chatterjee, C. 2021-04-08 doi:10.1101/2021.04.08.439039 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ False gene and chromosome losses affected by assembly and sequence errors ]]> https://biorxiv.org/content/10.1101/2021.04.09.438906v1?rss=1 Kim, J. Lee, C. Ko, B. J. Yoo, D. Won, S. Phillippy, A. Fedrigo, O. Zhang, G. Howe, K. Wood, J. Durbin, R. Formenti, G. Brown, S. Cantin, L. Mello, C. V. Cho, S. Rhie, A. Kim, H. Jarvis, E. D. 2021-04-09 doi:10.1101/2021.04.09.438906 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Widespread false gene gains caused by duplication errors in genome assemblies ]]> https://biorxiv.org/content/10.1101/2021.04.09.438957v1?rss=1 Ko, B. J. Lee, C. Kim, J. Rhie, A. Yoo, D. Howe, K. Wood, J. Cho, S. Brown, S. Formenti, G. Jarvis, E. D. Kim, H. 2021-04-09 doi:10.1101/2021.04.09.438957 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Enteric pathogens induce tissue tolerance and prevent neuronal loss from subsequent infections ]]> https://biorxiv.org/content/10.1101/2021.04.09.439221v1?rss=1 Ahrends, T. Aydin, B. Matheis, F. Classon, C. Furtado, G. C. Lira, S. Mucida, D. 2021-04-11 doi:10.1101/2021.04.09.439221 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ An automated workflow for label-free and multiplexed single cell proteomics sample preparation at unprecedented sensitivity. ]]> https://biorxiv.org/content/10.1101/2021.04.14.439828v1?rss=1 Hartlmayr, D. Ctortecka, C. Seth, A. Mendjan, S. Tourniaire, G. Mechtler, K. 2021-04-14 doi:10.1101/2021.04.14.439828 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Deletion of the AMPylase mFICD alters cytokine secretion and affects cognitive plasticity in vivo ]]> https://biorxiv.org/content/10.1101/2021.04.16.440208v1?rss=1 McCaul, N. Porter, C. M. Becker, A. Tang, C.-H. A. Wijne, C. Chatterjee, B. K. Bousbaine, D. Bilate, A. M. Hu, C.-C. A. Ploegh, H. L. Truttmann, M. C. 2021-04-17 doi:10.1101/2021.04.16.440208 Cold Spring Harbor Laboratory Press 2021-04-17 <![CDATA[ Two Isoleucyl tRNAs that Decode 'Synonymous' Codons Divergently Regulate Breast Cancer Progression ]]> https://biorxiv.org/content/10.1101/2021.04.22.440519v1?rss=1 Earnest-Noble, L. B. Hsu, D. Asgharian, H. Mandayam, N. Passarelli, M. C. Goodarzi, H. Tavazoie, S. F. 2021-04-22 doi:10.1101/2021.04.22.440519 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies ]]> https://biorxiv.org/content/10.1101/2021.04.23.441195v1?rss=1 Jette, C. A. Cohen, A. A. Gnanapragasam, P. N. P. Muecksch, F. Lee, Y. E. Huey-Tubman, K. E. Schmidt, F. Hatziioannou, T. Bieniasz, P. D. Nussenzweig, M. C. West, A. P. Keeffe, J. R. Bjorkman, P. Barnes, C. O. 2021-04-26 doi:10.1101/2021.04.23.441195 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model ]]> https://biorxiv.org/content/10.1101/2021.04.25.441198v1?rss=1 Hammer, M. Huisman, M. Rigano, A. Boehm, U. Chambers, J. J. Gaudreault, N. North, A. J. Pimentel, J. A. Sudar, D. Bajcsy, P. Brown, C. M. Corbett, A. D. Faklaris, O. Lacoste, J. Laude, A. Nelson, G. Nitschke, R. Farzam, F. Smith, C. Grunwald, D. Strambio-De-Castillia, C. 2021-04-26 doi:10.1101/2021.04.25.441198 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Therapeutic targeting of SLC6A8 creatine transporter inhibits KRAS mutant and wildtype colon cancer and modulates human creatine levels ]]> https://biorxiv.org/content/10.1101/2021.04.26.441371v1?rss=1 Kurth, I. Yamaguchi, N. Andreu-Agullo, C. Tian, H. S. Sridhar, S. Takeda, S. Gonsalves, F. C. Loo, J. M. Barlas, A. Manova-Todorova, K. Busby, R. Bendell, J. C. Strauss, J. Fakih, M. McRee, A. J. Hendifar, A. E. Rosen, L. S. Cercek, A. Wasserman, R. Spector, S. Raza, S. Tavazoie, M. F. Tavazoie, S. F. 2021-04-26 doi:10.1101/2021.04.26.441371 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ A pro-metastatic tRNA fragment drives Nucleolin oligomerization and stabilization of bound metabolic mRNAs ]]> https://biorxiv.org/content/10.1101/2021.04.26.441477v1?rss=1 Liu, X. Alwaseem, H. Molina, H. Tavora, B. Tavazoie, S. 2021-04-26 doi:10.1101/2021.04.26.441477 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ From musk to body odor: decoding olfaction through genetic variation ]]> https://biorxiv.org/content/10.1101/2021.04.27.441177v1?rss=1 Li, B. Kamarck, M. L. Peng, Q. Lim, F.-L. Keller, A. Smeets, M. A. M. Mainland, J. D. Wang, S. 2021-04-28 doi:10.1101/2021.04.27.441177 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Frizzled BRET sensors based on bioorthogonal labeling of unnatural amino acids reveal WNT-induced dynamics of the cysteine-rich domain. ]]> https://biorxiv.org/content/10.1101/2021.05.01.442235v1?rss=1 Kowalski-Jahn, M. Schihada, H. Turku, A. Huber, T. Sakmar, T. P. Schulte, G. 2021-05-01 doi:10.1101/2021.05.01.442235 Cold Spring Harbor Laboratory Press 2021-05-01 <![CDATA[ EOMES is responsible for WNT memory and can substitute for WNT in mesendoderm specification ]]> https://biorxiv.org/content/10.1101/2021.05.01.442278v1?rss=1 Yoney, A. Bai, L. Brivanlou, A. H. Siggia, E. D. 2021-05-01 doi:10.1101/2021.05.01.442278 Cold Spring Harbor Laboratory Press 2021-05-01 <![CDATA[ NOVA2 regulates neural circRNA biogenesis ]]> https://biorxiv.org/content/10.1101/2021.05.02.442201v1?rss=1 Knupp, D. Cooper, D. A. Saito, Y. Darnell, R. B. Miura, P. 2021-05-03 doi:10.1101/2021.05.02.442201 Cold Spring Harbor Laboratory Press 2021-05-03 <![CDATA[ Vaccination boosts naturally enhanced neutralizing breadth to SARS-CoV-2 one year after infection ]]> https://biorxiv.org/content/10.1101/2021.05.07.443175v1?rss=1 Wang, Z. Muecksch, F. Schaefer-Babajew, D. Finkin, S. Viant, C. Gaebler, C. Barnes, C. O. Cipolla, M. Ramos, V. Oliveira, T. Y. Cho, A. Schmidt, F. Silva, J. D. Bednarski, E. Daga, M. Turroja, M. Millard, K. G. Jankovic, M. Gazumyan, A. Bieniasz, P. D. Caskey, M. Hatziioannou, T. Nussenzweig, M. C. 2021-05-09 doi:10.1101/2021.05.07.443175 Cold Spring Harbor Laboratory Press 2021-05-09 <![CDATA[ Single cell analysis of RA synovial B cells reveals a dynamic spectrum of ectopic lymphoid B cell activation and hypermutation characterized by NR4A nuclear receptor expression ]]> https://biorxiv.org/content/10.1101/2021.05.14.443150v1?rss=1 Meednu, N. Rangel-Moreno, J. Zhang, F. Escalera-Rivera, K. Corsiero, E. Prediletto, E. Dicarlo, E. Goodman, S. Donlin, L. Raychaudhuri, S. Bombardieri, M. Pitzalis, C. Orange, D. AMP (RA/SLE) netwrok, McDavid, A. Anolik, J. H. 2021-05-16 doi:10.1101/2021.05.14.443150 Cold Spring Harbor Laboratory Press 2021-05-16 <![CDATA[ Fiberoptic Probe For Hemodynamic Spectroscopy in Freely Moving Mice Shows Cerebrovascular Dysregulation In Alzheimers and Glioma Models ]]> https://biorxiv.org/content/10.1101/2021.05.17.444224v1?rss=1 Gareau, D. S. Snuderl, M. Thomas, C. Bayin, N. S. Placantonakis, D. Zou, J. Yaroslavsky, A. Dietz, M. P. Jacques, S. L. Strickland, S. Krueger, J. G. Ahn, H. J. 2021-05-18 doi:10.1101/2021.05.17.444224 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Unique molecular features and cellular responses differentiate two populations of motor cortical layer 5b neurons in a preclinical model of ALS. ]]> https://biorxiv.org/content/10.1101/2021.05.20.445032v1?rss=1 Moya, M. V. Kim, R. D. Rao, M. N. Cotto, B. A. Pickett, S. B. Sferrazza, C. E. Heintz, N. Schmidt, E. F. 2021-05-21 doi:10.1101/2021.05.20.445032 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ AMP-Kinase mediates regulation of glomerular volume and podocyte survival ]]> https://biorxiv.org/content/10.1101/2021.05.21.445180v1?rss=1 Banu, K. Lin, Q. Basgen, J. M. Planoutene, M. Wei, C. Reghuvaran, A. C. Garzon, F. Garcia, A. Chun, N. Cumpelik, A. Shi, H. Santaneusio, A. Zhang, W. Das, B. Salem, F. Li, L. Cantley, L. G. Ishibe, S. Kaufman, L. Lemley, K. V. Ni, Z. He, J. C. Murphy, B. Menon, M. C. 2021-05-23 doi:10.1101/2021.05.21.445180 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ Entry Pathway for the Inverse Agonist Ligand in the G Protein-Coupled Receptor Rhodopsin ]]> https://biorxiv.org/content/10.1101/2021.05.24.445474v1?rss=1 Tian, H. Gunnison, K. M. Kazmi, M. A. Sakmar, T. P. Huber, T. 2021-05-24 doi:10.1101/2021.05.24.445474 Cold Spring Harbor Laboratory Press 2021-05-24 <![CDATA[ The complete sequence of a human genome ]]> https://biorxiv.org/content/10.1101/2021.05.26.445798v1?rss=1 Nurk, S. Koren, S. Rhie, A. Rautiainen, M. Bzikadze, A. V. Mikheenko, A. Vollger, M. R. Altemose, N. Uralsky, L. Gershman, A. Aganezov, S. Hoyt, S. J. Diekhans, M. Logsdon, G. A. Alonge, M. Antonarakis, S. E. Borchers, M. Bouffard, G. G. Brooks, S. Y. Caldas, G. V. Cheng, H. Chin, C.-S. Chow, W. de Lima, L. G. Dishuck, P. C. Durbin, R. Dvorkina, T. Fiddes, I. T. Formenti, G. Fulton, R. S. Fungtammasan, A. Garrison, E. Grady, P. G. S. Graves-Lindsay, T. A. Hall, I. M. Hansen, N. F. Hartley, G. A. Haukness, M. Howe, K. Hunkapiller, M. W. Jain, C. Jain, M. 2021-05-27 doi:10.1101/2021.05.26.445798 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Loose ends in cancer genome structure ]]> https://biorxiv.org/content/10.1101/2021.05.26.445837v1?rss=1 97% of all large-scale (>10 kbp) cancer structural variation; the rest represent loose ends that require long molecule profiling to unambiguously resolve. Our results have broad relevance for future research and clinical applications of short read WGS and delineate precise directions where long molecule studies might provide transformative insight into cancer genome structure. ]]> Behr, J. M. Yao, X. Hadi, K. Tian, H. Deshpande, A. Rosiene, J. de Lange, T. Imielinski, M. 2021-05-27 doi:10.1101/2021.05.26.445837 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Induction of an immortalized songbird cell line allows for gene characterization and knockout by CRISPR-Cas9 ]]> https://biorxiv.org/content/10.1101/2021.05.27.445896v1?rss=1 Biegler, M. T. Fedrigo, O. Collier, P. Mountcastle, J. Haase, B. Tilgner, H. U. Jarvis, E. D. 2021-05-27 doi:10.1101/2021.05.27.445896 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Inducible and reversible inhibition of miRNA-mediated gene repression in vivo ]]> https://biorxiv.org/content/10.1101/2021.06.01.445680v1?rss=1 La Rocca, G. King, B. Shui, B. Li, X. Zhang, M. Akat, K. Ogrodowski, P. Mastroleo, C. Chen, K. Cavalieri, V. Ma, Y. Anelli, V. Betel, D. Vidigal, J. A. Tuschl, T. Meister, G. Thompson, C. B. Lindsten, T. Haigis, K. M. Ventura, A. 2021-06-01 doi:10.1101/2021.06.01.445680 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ An atomistic model of the coronavirus replication-transcription complex as a hexamer assembled around nsp15 ]]> https://biorxiv.org/content/10.1101/2021.06.08.447516v1?rss=1 Perry, J. K. Appleby, T. C. Bilello, J. P. Feng, J. Y. Schmitz, U. C. Campbell, E. A. 2021-06-08 doi:10.1101/2021.06.08.447516 Cold Spring Harbor Laboratory Press 2021-06-08 <![CDATA[ Systematic reconstruction of the cellular trajectories of mammalian embryogenesis ]]> https://biorxiv.org/content/10.1101/2021.06.08.447626v1?rss=1 Qiu, C. Cao, J. Li, T. Srivatsan, S. Huang, X. Calderon, D. Noble, W. S. Disteche, C. M. Spielmann, M. Moens, C. B. Trapnell, C. Shendure, J. 2021-06-09 doi:10.1101/2021.06.08.447626 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ A landscape model for cell fate decisions during mesoendoderm differentiation in C. elegans based on Wnt dynamics ]]> https://biorxiv.org/content/10.1101/2021.06.09.447780v1?rss=1 Chang, S.-S. Bao, Z. Siggia, E. 2021-06-09 doi:10.1101/2021.06.09.447780 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ Analysis of the Mechanosensor Channel Functionality of TACAN ]]> https://biorxiv.org/content/10.1101/2021.06.11.448078v1?rss=1 Niu, Y. Tao, X. Vaisey, G. Olinares, P. D. B. Alwaseem, H. Chait, B. MacKinnon, R. 2021-06-12 doi:10.1101/2021.06.11.448078 Cold Spring Harbor Laboratory Press 2021-06-12 <![CDATA[ Radiosynthesis and preclinical evaluation of a carbon-11 labeled PDE7 inhibitor for PET neuroimaging ]]> https://biorxiv.org/content/10.1101/2021.06.12.447900v1?rss=1 Xiao, Z. Sun, J. Fujinaga, M. Wei, H. Zhao, C. Haider, A. Van, R. Yamasaki, T. Zhang, Y. Rong, J. Hu, K. Chen, J. Leon, E. C. Hiraishi, A. Wei, J. Xu, Y. Shao, Y. Zhang, H.-T. Lloyd, K. C. K. Wang, L. Zhang, M.-R. Liang, S. H. 2021-06-13 doi:10.1101/2021.06.12.447900 Cold Spring Harbor Laboratory Press 2021-06-13 <![CDATA[ Quantifying concordant genetic effects of de novo mutations on multiple disorders ]]> https://biorxiv.org/content/10.1101/2021.06.13.448234v1?rss=1 Guo, H. Hou, L. Shi, Y. Jin, S. C. Zeng, X. Li, B. Lifton, R. Brueckner, M. Zhao, H.-y. Lu, Q. 2021-06-14 doi:10.1101/2021.06.13.448234 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ Mechanism of CFTR correction by type I folding correctors ]]> https://biorxiv.org/content/10.1101/2021.06.18.449063v1?rss=1 Chen, J. Fiedorczuk, K. 2021-06-18 doi:10.1101/2021.06.18.449063 Cold Spring Harbor Laboratory Press 2021-06-18 <![CDATA[ Control of division and microtubule dynamics in Chlamydomonas by cyclin B/CDKB1 and the anaphase-promoting complex ]]> https://biorxiv.org/content/10.1101/2021.06.29.450376v1?rss=1 Cross, F. Pecani, K. Lieberman, K. Tajima-Shirasaki, N. Onishi, M. 2021-06-29 doi:10.1101/2021.06.29.450376 Cold Spring Harbor Laboratory Press 2021-06-29 <![CDATA[ Genomic Modules and Intramodular Network Convergency of Susceptibility and Resilience in Multimodeled Stress in Male Mice ]]> https://biorxiv.org/content/10.1101/2021.06.30.450390v1?rss=1 Marrocco, J. Caradonna, S. G. Zhang, T.-Y. O'Toole, N. Shen, M.-J. Khalil, H. Einhorn, N. Wen, X. Parent, C. Lee, F. S. Akil, H. McEwen, B. Meaney, M. J. 2021-07-01 doi:10.1101/2021.06.30.450390 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies ]]> https://biorxiv.org/content/10.1101/2021.07.02.450803v1?rss=1 Mc Cartney, A. M. Shafin, K. Alonge, M. Bzikadze, A. V. Formenti, G. Fungtammasan, A. Howe, K. Jain, C. Koren, S. Logsdon, G. A. Miga, K. H. Mikheenko, A. Paten, B. Shumate, A. Soto, D. C. Sovic, I. Wood, J. M. Zook, J. M. Phillippy, A. M. Rhie, A. 2021-07-02 doi:10.1101/2021.07.02.450803 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ Stable Isotope Tracing In Vivo Reveals A Metabolic Bridge Linking The Microbiota To Host Histone Acetylation ]]> https://biorxiv.org/content/10.1101/2021.07.05.450926v1?rss=1 Lund, P. J. Gates, L. A. Leboeuf, M. Smith, S. A. Chau, L. Friedman, E. S. Lopes, M. Saiman, Y. Kim, M. S. Petucci, C. Allis, C. D. Wu, G. D. Garcia, B. A. 2021-07-05 doi:10.1101/2021.07.05.450926 Cold Spring Harbor Laboratory Press 2021-07-05 <![CDATA[ Myosin-driven Nucleation of Actin Filaments Drives Stereocilia Development Critical for Hearing ]]> https://biorxiv.org/content/10.1101/2021.07.09.451618v1?rss=1 Moreland, Z. G. Jiang, F. Aguilar, C. Barzik, M. Gong, R. Shams, A. Faaborg-Andersen, C. Werth, J. C. Harley, R. Sutton, D. C. Cole, S. M. Parker, A. Morse, S. Wilson, E. Takagi, Y. Sellers, J. R. Brown, S. D. Friedman, T. B. Alushin, G. M. Bowl, M. R. Bird, J. E. 2021-07-10 doi:10.1101/2021.07.09.451618 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ The organization of the gravity-sensing system in zebrafish ]]> https://biorxiv.org/content/10.1101/2021.07.09.451839v1?rss=1 Liu, Z. Hildebrand, D. G. C. Morgan, J. L. Slimmon, N. Bagnall, M. W. 2021-07-11 doi:10.1101/2021.07.09.451839 Cold Spring Harbor Laboratory Press 2021-07-11 <![CDATA[ Structural basis for tunable control of actin dynamics by myosin-15 in mechanosensory stereocilia ]]> https://biorxiv.org/content/10.1101/2021.07.09.451843v1?rss=1 Gong, R. Jiang, F. Moreland, Z. G. Reynolds, M. J. Espinosa de los Reyes, S. Gurel, P. S. Shams, A. Bowl, M. R. Bird, J. E. Alushin, G. M. 2021-07-10 doi:10.1101/2021.07.09.451843 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ A sex chromosome drives the emergence of vocal learning following hormonal manipulation in female zebra finches ]]> https://biorxiv.org/content/10.1101/2021.07.12.452102v1?rss=1 Davenport, M. Choe, H. N. Matsunami, H. Jarvis, E. D. 2021-07-12 doi:10.1101/2021.07.12.452102 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing ]]> https://biorxiv.org/content/10.1101/2021.07.13.451380v1?rss=1 Dahn, H. A. Mountcastle, J. Balacco, J. Winkler, S. Bista, I. Schmitt, A. D. Vinnere Pettersson, O. Formenti, G. Oliver, K. Smith, M. Tan, W. Kraus, A. Mac, S. Komoroske, L. M. Lama, T. Crawford, A. J. Murphy, R. W. Brown, S. Scott, A. F. Morin, P. A. Jarvis, E. D. Fedrigo, O. 2021-07-14 doi:10.1101/2021.07.13.451380 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ The myotendinous junction marker collagen XXII enables zebrafish postural control learning and optimal swimming performance through its force transmission activity ]]> https://biorxiv.org/content/10.1101/2021.07.14.452354v1?rss=1 Malbouyres, M. Guiraud, A. Lefrancois, C. Salamito, M. Nauroy, P. Bernard, L. Sohm, F. Allard, B. Ruggiero, F. 2021-07-15 doi:10.1101/2021.07.14.452354 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ Nuclear hormone receptors promote gut and glia detoxifying enzyme induction and protect C. elegans from the mold P. brevicompactum ]]> https://biorxiv.org/content/10.1101/2021.07.15.452486v1?rss=1 Wallace, S. W. Lizzappi, M. C. Hur, H. Liang, Y. Shaham, S. 2021-07-15 doi:10.1101/2021.07.15.452486 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ Merfin: improved variant filtering and polishing via k-mer validation ]]> https://biorxiv.org/content/10.1101/2021.07.16.452324v1?rss=1 Formenti, G. Rhie, A. Walenz, B. P. Thibaud-Nissen, F. Shafin, K. Koren, S. Myers, E. W. Jarvis, E. D. Phillippy, A. M. 2021-07-18 doi:10.1101/2021.07.16.452324 Cold Spring Harbor Laboratory Press 2021-07-18 <![CDATA[ FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons ]]> https://biorxiv.org/content/10.1101/2021.07.18.452839v1?rss=1 Hale, C. R. Sawicka, K. Mora, K. Fak, J. J. Kang, J. J. Cutrim, P. Cialowicz, K. Carroll, T. B. Darnell, R. 2021-07-19 doi:10.1101/2021.07.18.452839 Cold Spring Harbor Laboratory Press 2021-07-19 <![CDATA[ Immunodominant surface epitopes power immune evasion in the African trypanosome ]]> https://biorxiv.org/content/10.1101/2021.07.20.453071v1?rss=1 Gkeka, A. Aresta-Branco, F. Triller, G. Vlachou, E. P. Lilic, M. Olinares, P. D. B. Perez, K. Chait, B. Blatnik, R. Ruppert, T. Stebbins, C. E. Papavasiliou, F. N. 2021-07-20 doi:10.1101/2021.07.20.453071 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ Combination of Antiviral Drugs to Inhibit SARS-CoV-2 Polymerase and Exonuclease as Potential COVID-19 Therapeutics ]]> https://biorxiv.org/content/10.1101/2021.07.21.453274v1?rss=1 Wang, X. Sacramento, C. Q. Jockusch, S. Chaves, O. A. Tao, C. Fintelman-Rodrigues, N. Chien, M. Temerozo, J. R. Li, X. Kumar, S. Xie, W. Patel, D. J. Meyer, C. Garzia, A. Tuschl, T. Bozza, P. T. Russo, J. J. Souza, T. M. L. Ju, J. 2021-07-21 doi:10.1101/2021.07.21.453274 Cold Spring Harbor Laboratory Press 2021-07-21 <![CDATA[ Neuron-Glia Signaling Regulates the Onset of the Antidepressant Response ]]> https://biorxiv.org/content/10.1101/2021.07.23.453443v1?rss=1 Yao, V. Aly, A. Kalik, S. Gresack, J. Wang, W. Handler, A. Schaefer, A. Troyanskaya, O. Greengard, P. Chottekalapanda, R. U. 2021-07-25 doi:10.1101/2021.07.23.453443 Cold Spring Harbor Laboratory Press 2021-07-25 <![CDATA[ Heat-inactivated modified vaccinia virus Ankara boosts Th1-biased cellular and humoral immune responses as a vaccine adjuvant by activating the STING-mediated cytosolic DNA-sensing pathway ]]> https://biorxiv.org/content/10.1101/2021.07.24.453449v1?rss=1 Yang, N. Garzia, A. Meyer, C. Tuschl, T. Merghoub, T. Wolchok, J. Deng, L. 2021-07-26 doi:10.1101/2021.07.24.453449 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ Self-organized morphogenesis of a human neural tube in vitro by geometric constraints ]]> https://biorxiv.org/content/10.1101/2021.07.24.453659v1?rss=1 Karzbrun, E. Khankhel, A. Megale, H. Glasauer, S. Wyle, Y. Britton, G. Warmflash, A. Kosik, K. S. Siggia, E. Shraiman, B. Streichan, S. J. 2021-07-25 doi:10.1101/2021.07.24.453659 Cold Spring Harbor Laboratory Press 2021-07-25 <![CDATA[ Regulatory start-stop elements in 5' untranslated regions pervasively modulate translation ]]> https://biorxiv.org/content/10.1101/2021.07.26.453809v1?rss=1 Rendleman, J. Mohammad, M. P. Pressler, M. Maity, S. Hronova, V. Gao, Z. Herrmannova, A. Lei, A. Allgoewer, K. Sultanov, D. Hinckley, W. E. Szkop, K. Topisirovic, I. Larsson, O. Hatzoglou, M. Valasek, L. S. Vogel, C. 2021-07-26 doi:10.1101/2021.07.26.453809 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ Antibody Evolution after SARS-CoV-2 mRNA Vaccination ]]> https://biorxiv.org/content/10.1101/2021.07.29.454333v1?rss=1 Cho, A. Muecksch, F. Schaefer-Babajew, D. Wang, Z. Finkin, S. Gaebler, C. Ramos, V. Cipolla, M. Agudelo, M. Bednarski, E. DaSilva, J. Shimeliovich, I. Dizon, J. Daga, M. Millard, K. Turroja, M. Schmidt, F. Zhang, F. Ben Tanfous, T. Jankovic, M. Oliveira, T. Gazumyan, A. Caskey, M. Bieniasz, P. D. Hatziioannou, T. Nussenzweig, M. C. 2021-07-29 doi:10.1101/2021.07.29.454333 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ VPS29 exerts opposing effects on endocytic viral entry ]]> https://biorxiv.org/content/10.1101/2021.08.06.455441v1?rss=1 Poston, D. Weisblum, Y. Hobbs, A. Bieniasz, P. D. 2021-08-08 doi:10.1101/2021.08.06.455441 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ High genetic barrier to escape from human polyclonal SARS-CoV-2 neutralizing antibodies ]]> https://biorxiv.org/content/10.1101/2021.08.06.455491v1?rss=1 Schmidt, F. Weisblum, Y. Rutkowska, M. Poston, D. Da Silva, J. Zhang, F. Bednarski, E. Cho, A. Schaefer-Babajew, D. Gaebler, C. Caskey, M. Nussenzweig, M. C. Hatziioannou, T. Bieniasz, P. D. 2021-08-08 doi:10.1101/2021.08.06.455491 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ Role of YAP in early ectodermal specification anda Huntington's Disease model of human neurulation ]]> https://biorxiv.org/content/10.1101/2021.08.11.455964v1?rss=1 Piccolo, F. M. Kastan, N. R. Haremaki, T. Tian, Q. Laundos, T. L. De Santis, R. Carroll, T. S. Luo, J.-D. Gnedeva, K. Etoc, F. Hudspeth, A. J. Brivanlou, A. H. 2021-08-11 doi:10.1101/2021.08.11.455964 Cold Spring Harbor Laboratory Press 2021-08-11 <![CDATA[ Analysis of Mouse Vocal Communication (AMVOC): A deep, unsupervised method for rapid detection, analysis, and classification of ultrasonic vocalizations ]]> https://biorxiv.org/content/10.1101/2021.08.13.456283v1?rss=1 Stoumpou, V. Vargas, C. D. M. Schade, P. F. Giannakopoulos, T. Jarvis, E. D. 2021-08-13 doi:10.1101/2021.08.13.456283 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Fanconi Anemia Pathway Deficiency Drives Copy Number Variation in Squamous Cell Carcinomas ]]> https://biorxiv.org/content/10.1101/2021.08.14.456365v1?rss=1 Webster, A. L. H. Sanders, M. A. Patel, K. Dietrich, R. Noonan, R. J. Lach, F. P. White, R. R. Goldfarb, A. Hadi, K. Edwards, M. M. Donovan, F. X. Jung, M. Sridhar, S. Fedrigo, O. Tian, H. Rosiene, J. Heineman, T. Kennedy, J. A. Bean, L. Rosti, O. Tryon, R. Gonzalez, A.-M. Rosenberg, A. Luo, J.-D. Carrol, T. Velleuer, E. Rastatter, J. C. Wells, S. I. Surralles, J. Bagby, G. MacMillan, M. L. Wagner, J. E. Cancio, M. Boulad, F. Scognamiglio, T. Vaughan, R. Koren, A. Imielinski, M. Chandrasekharappa, S. Auerbach, A. D. Singh, B. Kutler, D. I. Campbell, P. 2021-08-16 doi:10.1101/2021.08.14.456365 Cold Spring Harbor Laboratory Press 2021-08-16 <![CDATA[ Skin stem cells orchestrate de novo generation of extrathymic regulatory T cells to establish a temporary protective niche during wound healing ]]> https://biorxiv.org/content/10.1101/2021.08.16.456570v1?rss=1 Truong, C. Guo, W. Woodside, L. Gang, A. Savage, P. Infarinato, N. Stewart, K. Polak, L. Levorse, J. Pasolli, A. Dikiy, S. Rudensky, A. Fuchs, E. Miao, Y. 2021-08-17 doi:10.1101/2021.08.16.456570 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Systems-wide Analysis Revealed Shared and Unique Responses to Moderate and Acute High Temperatures in the Green Alga Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2021.08.17.456552v1?rss=1 Zhang, N. Mattoon, E. M. McHargue, W. Venn, B. Zimmer, D. Pecani, K. Jeong, J. Anderson, C. M. Chen, C. Berry, J. C. Xia, M. Tzeng, S.-C. Becker, E. Pazouki, L. Evans, B. Cross, F. Cheng, J. Czymmek, K. J. Schroda, M. Muhlhaus, T. Zhang, R. 2021-08-18 doi:10.1101/2021.08.17.456552 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ ORC binds and remodels nucleosomes to specify MCM loading onto DNA ]]> https://biorxiv.org/content/10.1101/2021.08.17.456647v1?rss=1 Li, S. Wasserman, M. R. Yurieva, O. Bai, L. O'Donnell, M. E. Liu, S. 2021-08-18 doi:10.1101/2021.08.17.456647 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ Type I interferon modulates Langerhans cell ADAM17 to promote photosensitivity in lupus ]]> https://biorxiv.org/content/10.1101/2021.08.18.456792v1?rss=1 Li, T. M. Veiga, K. R. Schwartz, N. Chinenov, Y. Oliver, D. J. Lora, J. Jabbari, A. Liu, Y. Shipman, W. D. Sandoval, M. J. Sollohub, I. F. Ambler, W. G. Rashighi, M. Krueger, J. G. Anandasabapathy, N. Blobel, C. P. Lu, T. T. 2021-08-18 doi:10.1101/2021.08.18.456792 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ Self-organization of human dorsal-ventral forebrain structures by light induced SHH ]]> https://biorxiv.org/content/10.1101/2021.08.18.456849v1?rss=1 De Santis, R. Etoc, F. Rosado Olivieri, E. A. Brivanlou, A. H. 2021-08-18 doi:10.1101/2021.08.18.456849 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ C. elegans enteric motor neurons fire synchronized action potentials underlying the defecation motor program ]]> https://biorxiv.org/content/10.1101/2021.08.25.457687v1?rss=1 Jiang, J. Su, Y. Zhang, R. Li, H. Tao, L. Liu, Q. 2021-08-26 doi:10.1101/2021.08.25.457687 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ The MIDAS domain of AAA mechanoenzyme Mdn1 forms catch bonds with two different substrates ]]> https://biorxiv.org/content/10.1101/2021.08.30.458255v1?rss=1 Mickolajczyk, K. J. Olinares, P. D. B. Chait, B. T. Liu, S. Kapoor, T. M. 2021-08-31 doi:10.1101/2021.08.30.458255 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Coherent Gene Assemblies: Example, Yeast Cell Division Cycle, CDC ]]> https://biorxiv.org/content/10.1101/2021.09.05.459023v1?rss=1 Sirovich, L. 2021-09-05 doi:10.1101/2021.09.05.459023 Cold Spring Harbor Laboratory Press 2021-09-05 <![CDATA[ Structural origins of Escherichia coli RNA polymerase open promoter complex stability ]]> https://biorxiv.org/content/10.1101/2021.09.08.459427v1?rss=1 Saecker, R. M. Chen, J. Chiu, C. E. Malone, B. Sortiris, J. Ebrahim, M. Yen, L. Y. Eng, E. T. Darst, S. A. 2021-09-09 doi:10.1101/2021.09.08.459427 Cold Spring Harbor Laboratory Press 2021-09-09 <![CDATA[ Comprehensive analysis of DNA replication timing in genetic diseases and gene knockouts identifies MCM10 as a novel regulator of the replication program ]]> https://biorxiv.org/content/10.1101/2021.09.08.459433v1?rss=1 Caballero, M. Ge, T. Rebelo, A. R. Seo, S. Kim, S. Brooks, K. Zuccaro, M. L. Kanagaraj, R. Vershkov, D. Kim, D. Smogorzewska, A. Smolka, M. B. Benvenisty, N. West, S. C. Egli, D. C. Mace, E. M. Koren, A. 2021-09-09 doi:10.1101/2021.09.08.459433 Cold Spring Harbor Laboratory Press 2021-09-09 <![CDATA[ Molecular and cellular adaptations in hippocampal parvalbumin neurons mediate behavioral responses to chronic social stress ]]> https://biorxiv.org/content/10.1101/2021.09.14.459024v1?rss=1 Bhatti, D. L. Medrihan, L. Chen, M. X. Jin, J. McCabe, K. Wang, W. Azevedo, E. P. Ledo, J. H. Kim, Y. 2021-09-15 doi:10.1101/2021.09.14.459024 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells ]]> https://biorxiv.org/content/10.1101/2021.09.15.460381v1?rss=1 Wang, Y. Yen, F. S. Zhu, X. G. Timson, R. C. Weber, R. Xing, C. Liu, Y. Allwein, B. Luo, H. Yeh, H.-W. Heissel, S. Unlu, G. Gamazon, E. R. Kharas, M. G. Hite, R. Birsoy, K. 2021-09-16 doi:10.1101/2021.09.15.460381 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ HCN2 in cholinergic interneurons of the nucleus accumbens mediates reward response ]]> https://biorxiv.org/content/10.1101/2021.09.21.460269v1?rss=1 Lee, J. Weinberger, M. Kawahara, Y. Cheng, J. Umscweif, G. Medrihan, L. Flajolet, M. Nishi, A. Sagi, Y. 2021-09-21 doi:10.1101/2021.09.21.460269 Cold Spring Harbor Laboratory Press 2021-09-21 <![CDATA[ Structural Mechanics of the Alpha-2-Macroglobulin Transformation ]]> https://biorxiv.org/content/10.1101/2021.09.22.461418v1?rss=1 Arimura, Y. Funabiki, H. 2021-09-24 doi:10.1101/2021.09.22.461418 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ A rise-to-threshold signal for a relative value deliberation ]]> https://biorxiv.org/content/10.1101/2021.09.23.461548v1?rss=1 Vijayan, V. Wang, F. Wang, K. Chakravorty, A. Adachi, A. Akhlaghpour, H. Dickson, B. J. Maimon, G. 2021-09-24 doi:10.1101/2021.09.23.461548 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Parallel systems for social and spatial reasoning within the cortical apex ]]> https://biorxiv.org/content/10.1101/2021.09.23.461550v1?rss=1 Deen, B. Freiwald, W. A. 2021-09-24 doi:10.1101/2021.09.23.461550 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Viral replication in human macrophages enhances an inflammatory cascade and interferon driven chronic COVID-19 in humanized mice. ]]> https://biorxiv.org/content/10.1101/2021.09.27.461948v1?rss=1 Sefik, E. Qu, R. Kaffe, E. Zhao, J. Junqueira, C. Mirza, H. Brewer, R. Han, A. Steach, H. Israelow, B. Chen, Y. G. Halene, S. Iwasaki, A. Meffre, E. Nussenzweig, M. Lieberman, J. Wilen, C. B. Kluger, Y. Flavell, R. A. 2021-09-27 doi:10.1101/2021.09.27.461948 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ An internal expectation guides Drosophila egg-laying decisions ]]> https://biorxiv.org/content/10.1101/2021.09.30.462671v1?rss=1 Vijayan, V. Wang, Z. Chandra, V. Chakravorty, A. Li, R. Sarbanes, S. L. Akhlaghpour, H. Maimon, G. 2021-10-02 doi:10.1101/2021.09.30.462671 Cold Spring Harbor Laboratory Press 2021-10-02 <![CDATA[ Direct Reprogramming of Non-limb Fibroblasts toCells with Properties of Limb Progenitors ]]> https://biorxiv.org/content/10.1101/2021.10.01.462632v1?rss=1 Atsuta, Y. Lee, C. Rodrigues, A. R. Colle, C. Tomizawa, R. R. Lujan, E. G. Tschopp, P. Gorham, J. M. Vannier, J.-P. Seidman, C. Seidman, J. G. Pourquie, O. Tabin, C. 2021-10-01 doi:10.1101/2021.10.01.462632 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Rad24-RFC loads the 9-1-1 clamp by inserting DNA from the top of a wide-open ring, opposite the mechanism of RFC/PCNA ]]> https://biorxiv.org/content/10.1101/2021.10.01.462756v1?rss=1 Zheng, F. Georgescu, R. E. Yao, N. Y. O'Donnell, M. E. Li, H. 2021-10-01 doi:10.1101/2021.10.01.462756 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ A persistent behavioral state enables sustained predation of humans by mosquitoes ]]> https://biorxiv.org/content/10.1101/2021.10.06.463436v1?rss=1 Sorrells, T. R. Pandey, A. Rosas-Villegas, A. Vosshall, L. B. 2021-10-07 doi:10.1101/2021.10.06.463436 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ Evolutionary Dynamics, Evolutionary Forces, and Robustness: A Nonequilibrium Statistical Mechanics Perspective ]]> https://biorxiv.org/content/10.1101/2021.10.10.463854v1?rss=1 Rao, R. Leibler, S. 2021-10-12 doi:10.1101/2021.10.10.463854 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ A molecular switch between mammalian MLL complexes dictates response to Menin-MLL inhibition ]]> https://biorxiv.org/content/10.1101/2021.10.22.465184v1?rss=1 Soto-Feliciano, Y. M. Sanchez-Rivera, F. J. Perner, F. Barrows, D. W. Kastenhuber, E. R. Ho, Y.-J. Carroll, T. Xiong, Y. Soshnev, A. Gates, L. Beytagh, M. C. Cheon, D. Gu, S. Liu, X. S. Krivtsov, A. V. Meneses, M. de Stanchina, E. Stone, R. M. Armstrong, S. A. Lowe, S. W. Allis, C. D. 2021-10-22 doi:10.1101/2021.10.22.465184 Cold Spring Harbor Laboratory Press 2021-10-22 <![CDATA[ Vaccinia E5 is a major inhibitor of the DNA sensor cGAS ]]> https://biorxiv.org/content/10.1101/2021.10.25.465197v1?rss=1 Yang, N. Wang, Y. Dai, P. Li, T. Zierhut, C. Tan, A. Zhang, T. Pan, H. Li, Z. Ordureau, A. Xiang, J. Z. Hendrickson, R. C. Funabiki, H. Chen, Z. Deng, L. 2021-10-26 doi:10.1101/2021.10.25.465197 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Parallel functional subnetworks embedded in the macaque face patch system ]]> https://biorxiv.org/content/10.1101/2021.10.25.465775v1?rss=1 Park, S. H. Koyano, K. W. Russ, B. E. Waidmann, E. N. McMahon, D. B. T. Leopold, D. A. 2021-10-28 doi:10.1101/2021.10.25.465775 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Longitudinal clonal dynamics of HIV-1 latent reservoirs measured by combination quadruplex polymerase chain reaction and sequencing ]]> https://biorxiv.org/content/10.1101/2021.10.28.466316v1?rss=1 Cho, A. Gaebler, C. Olveira, T. Ramos, V. Saad, M. Lorenzi, J. Gazumyan, A. Moir, S. Chun, T.-W. Caskey, M. Nussenzweig, M. 2021-10-28 doi:10.1101/2021.10.28.466316 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Assessing Motivations and Barriers to Science Outreach within Academia: A Mixed-Methods Survey ]]> https://biorxiv.org/content/10.1101/2021.10.28.466319v1?rss=1 Woitowich, N. C. Hunt, G. C. Muhammad, L. N. Garbarino, J. 2021-11-01 doi:10.1101/2021.10.28.466319 Cold Spring Harbor Laboratory Press 2021-11-01 <![CDATA[ Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex ]]> https://biorxiv.org/content/10.1101/2021.10.29.466335v1?rss=1 Akey, C. Singh, D. Ouch, C. Echeverria, I. Nudelman, I. Varberg, J. M. Yu, Z. Fang, F. Shi, Y. Wang, J. Saltzberg, D. Song, K. Xu, C. Gumbart, J. Suslov, S. Unruh, J. Jaspersen, S. L. Chait, B. Sali, A. Menendez-Martinez, J. Ludke, S. J. Villa, E. Rout, M. 2021-10-29 doi:10.1101/2021.10.29.466335 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ The emergence of a collective sensory response threshold in ant colonies ]]> https://biorxiv.org/content/10.1101/2021.10.30.466564v1?rss=1 Gal, A. Kronauer, D. 2021-11-02 doi:10.1101/2021.10.30.466564 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Intratumoral delivery of engineered recombinant modified vaccinia virus Ankara express-ing Flt3L and OX40L generates potent antitumor immunity through activating the cGAS/STING pathway and depleting tumor-infiltrating regulatory T cells ]]> https://biorxiv.org/content/10.1101/2021.10.31.466698v1?rss=1 Yang, N. Wang, Y. Liu, S. Luna, J. M. Mazo, G. Tan, A. Y. Zhang, T. Wang, J. Yan, W. Choi, J. Rossi, A. Xiang, J. Z. Rice, C. M. Merghoub, T. Wolchok, J. D. Deng, L. 2021-11-01 doi:10.1101/2021.10.31.466698 Cold Spring Harbor Laboratory Press 2021-11-01 <![CDATA[ Neutralizing antibodies induced in immunized macaques recognize the CD4-binding site on an occluded-open HIV-1 envelope trimer ]]> https://biorxiv.org/content/10.1101/2021.11.02.466200v1?rss=1 Yang, Z. Dam, K.-M. A. Bridges, M. D. Hoffmann, M. A. G. DeLaitsch, A. T. Gristick, H. B. Escolano, A. Gautam, R. Martin, M. A. Nussenzweig, M. Hubbell, W. Bjorkman, P. J. 2021-11-04 doi:10.1101/2021.11.02.466200 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Protection of nascent DNA at stalled replication forks is mediated by phosphorylation of RIF1 intrinsically disordered region ]]> https://biorxiv.org/content/10.1101/2021.11.04.467328v1?rss=1 Balasubramanian, S. Andreani, M. Andrade, J. G. Saha, T. Garzon, J. Zhang, W. Rahjouei, A. Rosen, D. B. Chait, B. T. Donaldson, A. D. Di Virgilio, M. 2021-11-06 doi:10.1101/2021.11.04.467328 Cold Spring Harbor Laboratory Press 2021-11-06 <![CDATA[ Context-dependent inversion of the response in a single sensory neuron type reverses olfactory preference behavior ]]> https://biorxiv.org/content/10.1101/2021.11.08.467792v1?rss=1 Khan, M. Hartmann, A. H. O'Donnell, M. P. Piccione, M. Chao, P.-H. Dwyer, N. D. Bargmann, C. I. Sengupta, P. 2021-11-09 doi:10.1101/2021.11.08.467792 Cold Spring Harbor Laboratory Press 2021-11-09 <![CDATA[ Newly recruited intraepithelial Ly6A+CCR9+CD4+ T cells protect against enteric viral infection ]]> https://biorxiv.org/content/10.1101/2021.11.10.468106v1?rss=1 Parsa, R. London, M. Rezende de Castro, T. B. Reis, B. Buissant des Amorie, J. Smith, J. G. Mucida, D. 2021-11-10 doi:10.1101/2021.11.10.468106 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ Ensemble cryo-electron microscopy reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex ]]> https://biorxiv.org/content/10.1101/2021.11.10.468168v1?rss=1 Chen, J. Wang, Q. Malone, B. Llewellyn, E. Pechersky, Y. Maruthi, K. Eng, E. T. Perry, J. K. Campbell, E. A. Shaw, D. E. Darst, S. A. 2021-11-12 doi:10.1101/2021.11.10.468168 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ Vγ usage distinguishes pro- and anti-tumor intestinal γδ T cell subsets ]]> https://biorxiv.org/content/10.1101/2021.11.13.468487v1?rss=1 Reis, B. S. Darcy, P. W. Khan, I. Z. Eleso, O. Zhu, C. Schernthanner, M. Lockhart, A. Reed, A. Bortolatto, J. Castro, T. Bilate, A. Grivennikov, S. Mucida, D. 2021-11-13 doi:10.1101/2021.11.13.468487 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ Transcriptional and mutational signatures of the aging germline ]]> https://biorxiv.org/content/10.1101/2021.11.22.469565v1?rss=1 Witt, E. Langer, C. B. Zhao, L. 2021-11-22 doi:10.1101/2021.11.22.469565 Cold Spring Harbor Laboratory Press 2021-11-22 <![CDATA[ A chemical-genetic map of the pathways controlling drug potency in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2021.11.27.469863v1?rss=1 Li, S. Poulton, N. C. Chang, J. S. Azadian, Z. A. Dejusus, M. A. Ruecker, N. Zimmerman, M. D. Eckartt, K. Bosch, B. Engelhart, C. A. Sullivan, D. Gengenbacher, M. Dartois, V. A. Schnappinger, D. Rock, J. M. 2021-11-27 doi:10.1101/2021.11.27.469863 Cold Spring Harbor Laboratory Press 2021-11-27 <![CDATA[ Structural mechanism for bi-directional actin crosslinking by T-plastin ]]> https://biorxiv.org/content/10.1101/2021.12.07.471696v1?rss=1 Mei, L. Reynolds, M. J. Garbett, D. Gong, R. Meyer, T. Alushin, G. M. 2021-12-09 doi:10.1101/2021.12.07.471696 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes ]]> https://biorxiv.org/content/10.1101/2021.12.08.471837v1?rss=1 Toh, H. Yang, C. Formenti, G. Raja, K. Yan, L. Tracey, A. Chow, W. Howe, K. Bergeron, L. A. Zhang, G. Haase, B. Mountcastle, J. Fedrigo, O. Fogg, J. Kirilenko, B. Munegowda, C. Hiller, M. Jain, A. Kihara, D. Rhie, A. Phillippy, A. M. Swanson, S. A. Jiang, P. Clegg, D. O. Jarvis, E. D. Thomson, J. A. Stewart, R. Chaisson, M. J. P. Bukhman, Y. V. 2021-12-10 doi:10.1101/2021.12.08.471837 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ Chemoproteomics of microbiota metabolites reveals small-molecule agonists for orphan receptor GPRC5A ]]> https://biorxiv.org/content/10.1101/2021.12.16.472979v1?rss=1 Zhao, X. Stein, K. R. Chen, V. Griffin, M. E. Hang, H. C. 2021-12-16 doi:10.1101/2021.12.16.472979 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Characterization of sequence determinants of enhancer function using natural genetic variation ]]> https://biorxiv.org/content/10.1101/2021.12.17.473050v1?rss=1 Yang, M. G. Ling, E. Cowley, C. J. Greenberg, M. E. Vierbuchen, T. 2021-12-18 doi:10.1101/2021.12.17.473050 Cold Spring Harbor Laboratory Press 2021-12-18 <![CDATA[ Cryo-EM structure of the human CST·Polα/Primase complex in a recruitment state ]]> https://biorxiv.org/content/10.1101/2021.12.17.473235v1?rss=1 Cai, S. W. Zinder, J. C. Svetlov, V. Bush, M. Nudler, E. Walz, T. de Lange, T. 2021-12-18 doi:10.1101/2021.12.17.473235 Cold Spring Harbor Laboratory Press 2021-12-18 <![CDATA[ Using antibody synergy to engineer a high potency biologic cocktail against C. difficile ]]> https://biorxiv.org/content/10.1101/2021.12.21.473715v1?rss=1 Zhao, H. Tasch, M. Dodds, M. Gewe, M. Martinez, A. Hutton, M. Keeney, K. Pollock, A. Jester, B. Khuong, N. Zhang, M. Brady, C. Heinnickel, M. Tabakh, H. Sanjaya, N. Cruickshank, K. Paddock, T. Ertel, S. Struyvenberg, S. Dang, J. Shanitta, C. Fletcher, D. Goetsch, L. Gamble, C. Mileto, S. Heselpoth, R. Lyras, D. Behnke, C. Fischetti, V. Finrow, B. Roberts, J. M. 2021-12-22 doi:10.1101/2021.12.21.473715 Cold Spring Harbor Laboratory Press 2021-12-22 <![CDATA[ Evolution of Gram+ Streptococcus pyogenes has maximized efficiency of the Sortase A cleavage site ]]> https://biorxiv.org/content/10.1101/2021.12.21.473763v1?rss=1 Readnour, B. M. Ayinuola, Y. A. Russo, B. Liang, Z. Fischetti, V. A. Ploplis, V. Lee, S. W. Castellino, F. J. 2021-12-22 doi:10.1101/2021.12.21.473763 Cold Spring Harbor Laboratory Press 2021-12-22 <![CDATA[ Recombination suppression and selection affect local ancestries in genomes of a migratory songbird ]]> https://biorxiv.org/content/10.1101/2021.12.22.473882v1?rss=1 Ishigohoka, J. Bascon-Cardozo, K. Bours, A. Fuss, J. Rhie, A. Mountcastle, J. Haase, B. Chow, W. Collins, J. Howe, K. Uliano-Silva, M. Fedrigo, O. Jarvis, E. D. Perez-Tris, J. Illera, J. C. Liedvogel, M. 2021-12-23 doi:10.1101/2021.12.22.473882 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Single-nuclei isoform RNA sequencing reveals combination patterns of transcript elements across human brain cell types ]]> https://biorxiv.org/content/10.1101/2021.12.29.474385v1?rss=1 Hardwick, S. A. Hu, W. Joglekar, A. Fan, L. Collier, P. G. Foord, C. Balacco, J. Belchikov, N. Jarroux, J. Prjibelski, A. D. Mikheenko, A. Luo, W. Milner, T. A. Ndhlovu, L. Trojanowski, J. Q. Lee, V. M. Fedrigo, O. Tombacz, D. Ross, M. E. Jarvis, E. Boldogkoi, Z. Gan, L. Tilgner, H. U. 2021-12-30 doi:10.1101/2021.12.29.474385 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ V1 receptive field structure contributes to neuronal response latency ]]> https://biorxiv.org/content/10.1101/2021.12.30.474591v1?rss=1 Vafaei, A. Mohammadi, M. Khadir, A. Zabeh, E. YazdaniBanafsheDaragh, F. Khorasani, M. Lashgari, R. 2022-01-01 doi:10.1101/2021.12.30.474591 Cold Spring Harbor Laboratory Press 2022-01-01 <![CDATA[ Three amphioxus reference genomes reveal gene and chromosome evolution of chordates ]]> https://biorxiv.org/content/10.1101/2022.01.04.475009v1?rss=1 Zhen, H. Xu, L. Cai, C. Zhou, Y. Liu, J. Zhu, Z. Kang, W. Chen, D. Pei, S. Xue, T. Cen, W. Shi, C. Wu, X. Huang, Y. Xu, C. Yan, Y. Yang, Y. He, W. Hu, X. Zhang, Y. Chen, Y. Bi, C. He, C. Xue, L. Xiao, S. Yue, Z. Jiang, Y. Yu, J.-K. Jarvis, E. Li, G. Lin, G. Zhang, Q. Zhou, Q. 2022-01-05 doi:10.1101/2022.01.04.475009 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Differential mosquito attraction to humans is associated with skin-derived carboxylic acid levels ]]> https://biorxiv.org/content/10.1101/2022.01.05.475088v1?rss=1 De Obaldia, M. E. Morita, T. Dedmon, L. C. Boehmler, D. J. Jiang, C. S. Zeledon, E. V. Cross, J. R. Vosshall, L. B. 2022-01-05 doi:10.1101/2022.01.05.475088 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Thermal characterization of the multimeric bacteriophage endolysin PlyC ]]> https://biorxiv.org/content/10.1101/2022.01.06.475266v1?rss=1 Hoopes, J. T. Heselpoth, R. D. Schwarz, F. P. Nelson, D. C. 2022-01-07 doi:10.1101/2022.01.06.475266 Cold Spring Harbor Laboratory Press 2022-01-07 <![CDATA[ Oncogenic role of a developmentally regulated NTRK2 splice variant ]]> https://biorxiv.org/content/10.1101/2022.01.07.475392v1?rss=1 Pattwell, S. S. Arora, S. Nuechterlein, N. Zager, M. Loeb, K. R. Cimino, P. J. Holland, N. C. Reche-Ley, N. Bolouri, H. Bonin, D. A. A. Szulzewsky, F. Phadnis, V. V. Ozawa, T. Wagner, M. J. Haffner, M. C. Cao, J. Shendure, J. Holland, E. C. 2022-01-09 doi:10.1101/2022.01.07.475392 Cold Spring Harbor Laboratory Press 2022-01-09 <![CDATA[ Differential sensory and immune gene evolution in sea turtles with contrasting demographic and life histories ]]> https://biorxiv.org/content/10.1101/2022.01.10.475373v1?rss=1 Bentley, B. P. Carrasco-Valenzuela, T. Ramos, E. K. S. Pawar, H. Arantes, L. S. Alexander, A. Banerjee, S. M. Masterson, P. Kuhlwilm, M. Pippel, M. Mountcastle, J. Haase, B. Silva, M. U. Formenti, G. Howe, K. Chow, W. Tracey, A. Sims, Y. Pelan, S. Wood, J. Perrault, J. R. Stewart, K. Benson, S. Levy, Y. Todd, E. V. Shaffer, H. B. Scott, P. Henen, B. T. Murphy, R. W. Mohr, D. W. Scott, A. F. Gemmell, N. Suh, A. Winkler, S. Thibaud-Nissen, F. Nery, M. F. Marques-Bonet, T. Antunes, A. Tikochinski, Y. Dutton, P. H. Fedrigo, O. Myers, E. W. Jarvis, E. Mazz 2022-01-12 doi:10.1101/2022.01.10.475373 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Basis of narrow-spectrum activity of fidaxomicin on gut pathogen Clostridioides difficile ]]> https://biorxiv.org/content/10.1101/2022.01.17.476619v1?rss=1 Cao, X. Boyaci, H. Chen, J. Bao, Y. Landick, R. Campbell, E. A. 2022-01-17 doi:10.1101/2022.01.17.476619 Cold Spring Harbor Laboratory Press 2022-01-17 <![CDATA[ SARS-CoV-2 impairs interferon production via NSP2-induced repression of mRNA translation ]]> https://biorxiv.org/content/10.1101/2022.01.19.476693v1?rss=1 Choi, J.-H. Zhang, X. Zhang, C. Dai, D. L. Luo, J. Ladak, R. Li, Q. Wiebe, S. Liu, A. C. H. Ran, X. Yang, J. Naeli, P. Garzia, A. Zhou, L. Mahmood, N. Deng, Q. Elaish, M. Lin, R. Hobman, T. Pelletier, J. Alain, T. Vidal, S. Duchaine, T. Mazhab-Jafari, M. Mao, X. Jafarnejad, S. M. Sonenberg, N. 2022-01-20 doi:10.1101/2022.01.19.476693 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Universal guide for skull extraction and custom-fitting of implants to continuous and discontinuous skulls ]]> https://biorxiv.org/content/10.1101/2022.01.22.475298v1?rss=1 Ahmed, Z. Agha, N. S. Trunk, A. Berger, M. Gail, A. 2022-01-23 doi:10.1101/2022.01.22.475298 Cold Spring Harbor Laboratory Press 2022-01-23 <![CDATA[ GABA regulates resonance and spike rate encoding via a universal mechanism that underlies the modulation of action potential generation ]]> https://biorxiv.org/content/10.1101/206581v1?rss=1 Kirst, C. Ammer, J. Felmy, F. Herz, A. Stemmler, M. 2017-10-20 doi:10.1101/206581 Cold Spring Harbor Laboratory Press 2017-10-20 <![CDATA[ Visualization of ligand-induced transmembrane signalling in the full-length human insulin receptor ]]> https://biorxiv.org/content/10.1101/207928v1?rss=1 Gutmann, T. Kim, K. H. Grzybek, M. Walz, T. Coskun, U. 2017-10-23 doi:10.1101/207928 Cold Spring Harbor Laboratory Press 2017-10-23 <![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[ Terminal uridylyltransferases target RNA viruses as part of the innate immune system in animals ]]> https://biorxiv.org/content/10.1101/209114v1?rss=1 Le Pen, J. Jiang, H. Di Domenico, T. Kneuss, E. Kosalka, J. Morgan, M. Much, C. Rudolph, K. L. M. Enright, A. J. O'Carroll, D. Wang, D. Miska, E. A. 2017-10-25 doi:10.1101/209114 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ Molecular basis for the recognition of the human AAUAAA polyadenylation signal ]]> https://biorxiv.org/content/10.1101/209809v1?rss=1 Sun, Y. Zhang, Y. Hamilton, K. Manley, J. L. Shi, Y. Walz, T. Tong, L. 2017-10-27 doi:10.1101/209809 Cold Spring Harbor Laboratory Press 2017-10-27 <![CDATA[ Distinct stimulatory mechanisms regulate the catalytic activity of Polycomb Repressive Complex 2 (PRC2) ]]> https://biorxiv.org/content/10.1101/210542v1?rss=1 Lee, C.-H. Holder, M. Grau, D. Saldana-Meyer, R. Ganai, R. A. Zhang, J. Wang, M. Dobenecker, M.-W. Reinberg, D. Armache, K.-J. 2017-10-28 doi:10.1101/210542 Cold Spring Harbor Laboratory Press 2017-10-28 <![CDATA[ Genetic variation across the human olfactory receptor repertoire alters odor perception ]]> https://biorxiv.org/content/10.1101/212431v1?rss=1 Trimmer, C. Keller, A. Murphy, N. R. Snyder, L. L. Willer, J. R. Nagai, M. Katsanis, N. Vosshall, L. B. Matsunami, H. Mainland, J. D. 2017-11-01 doi:10.1101/212431 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Species and Cell-Type Properties of Classically Defined Human and Rodent Neurons and Glia ]]> https://biorxiv.org/content/10.1101/212696v1?rss=1 Xu, X. Stoyanova, E. Lemiesz, A. Xing, J. Mash, D. C. Heintz, N. 2017-11-01 doi:10.1101/212696 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Knockdown of Liver-Derived C1 Inhibitor Results in Brain Pathology in mice ]]> https://biorxiv.org/content/10.1101/216531v1?rss=1 Farfara, D. Feierman, E. Richards, A. Revenko, A. S. MacLeod, R. A. Norris, E. H. Strickland, S. 2017-11-08 doi:10.1101/216531 Cold Spring Harbor Laboratory Press 2017-11-08 <![CDATA[ One-step generation of monoclonal B cell receptor mice capable of class switch recombination and somatic hypermutation ]]> https://biorxiv.org/content/10.1101/218438v1?rss=1 Jacobsen, J. T. Mesin, L. Markoulaki, S. Cavazzoni, C. B. Bousbaine, D. Jaenisch, R. Victora, G. D. 2017-11-13 doi:10.1101/218438 Cold Spring Harbor Laboratory Press 2017-11-13 <![CDATA[ Cerebellar granule cell precursors can extend processes, undergo short migratory movements and express postmitotic markers before mitosis in the chick EGL ]]> https://biorxiv.org/content/10.1101/220715v1?rss=1 Hanzel, M. Wingate, R. J. 2017-11-16 doi:10.1101/220715 Cold Spring Harbor Laboratory Press 2017-11-16 <![CDATA[ Time course analysis of the brain transcriptome during transitions between brood care and reproduction in the clonal raider ant ]]> https://biorxiv.org/content/10.1101/223255v1?rss=1 Libbrecht, R. Oxley, P. R. Kronauer, D. J. 2017-11-22 doi:10.1101/223255 Cold Spring Harbor Laboratory Press 2017-11-22 <![CDATA[ Modular assembly of the nucleolar large subunit processome ]]> https://biorxiv.org/content/10.1101/223412v1?rss=1 Assur Sanghai, Z. Miller, L. Molloy, K. R. Barandun, J. Hunziker, M. Chaker-Margot, M. Wang, J. Chait, B. T. Klinge, S. 2017-11-21 doi:10.1101/223412 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ Learning to read the imprints of consciousness on global brain dynamics: an application to intra-operative monitoring of anesthesia ]]> https://biorxiv.org/content/10.1101/225813v1?rss=1 Alonso, L. M. Solovey, G. Yanagawa, T. Proekt, A. Cecchi, G. Magnasco, M. O. 2017-11-27 doi:10.1101/225813 Cold Spring Harbor Laboratory Press 2017-11-27 <![CDATA[ Neutrophil adhesion in brain capillaries contributes to cortical blood flow decreases and impaired memory function in a mouse model of Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/226886v1?rss=1 Cruz Hernandez, J. C. Bracko, O. Kersbergen, C. J. Muse, V. Haft-Javaherian, M. Berg, M. Park, L. Vinarcsik, L. K. Ivasyk, I. Kang, Y. Cortes-Canteli, M. Peyrounette, M. Doyeux, V. Smith, A. Zhou, J. Otte, G. Beverly, J. D. Davenport, E. Davit, Y. Strickland, S. Iadecola, C. Lorthois, S. Nishimura, N. Schaffer, C. B. 2017-11-29 doi:10.1101/226886 Cold Spring Harbor Laboratory Press 2017-11-29 <![CDATA[ An open resource for nonhuman primate imaging ]]> https://biorxiv.org/content/10.1101/227462v1?rss=1 Milham, M. Ai, L. Koo, B. Xu, T. Balezeau, F. Baxter, M. G. Croxson, P. L. Damatac, C. G. Harel, N. Freiwald, W. Griffiths, T. D. Everling, S. Jung, B. Kastner, S. Leopold, D. A. Mars, R. B. Menon, R. S. Messinger, A. Morrison, J. H. Nacef, J. Nagy, J. Rios, M. O. Petkov, C. I. Pinsk, M. Poirier, C. Rajimehr, R. Rushworth, M. F. Russ, B. E. Schmid, M. Schwiedrzik, C. M. Sallet, J. Seidlitz, J. Ungerleider, L. Thiele, A. Tsao, D. Yacoub, E. Ye, F. Zarco, W. Margulies, D. S. Schroeder, C. E. 2017-11-30 doi:10.1101/227462 Cold Spring Harbor Laboratory Press 2017-11-30 <![CDATA[ Global phylogenomics of multidrug-resistant Staphylococcus aureus sequence type 772: the Bengal Bay clone ]]> https://biorxiv.org/content/10.1101/233395v1?rss=1 Steinig, E. J. Duchene, S. Robinson, D. A. Monecke, S. Yokoyama, M. Laabei, M. Slickers, P. Andersson, P. Williamson, D. Kearns, A. Goering, R. Dickson, E. Ehricht, R. Ip, M. O'Sullivan, M. V. Coombs, G. W. Petersen, A. Brennan, G. Shore, A. C. Coleman, D. C. Pantosti, A. de Lencastre, H. Westh, H. Kobayashi, N. Heffernan, H. Strommenger, B. Layer, F. Weber, S. Aamot, H. Skakni, L. Peacock, S. J. Sarovich, D. Giffard, P. Harris, S. Parkhill, J. Massey, R. C. Holden, M. T. Bentley, S. D. Tong, S. Y. 2017-12-13 doi:10.1101/233395 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ Self-organization of a functional human organizer by combined WNT and NODAL signalling ]]> https://biorxiv.org/content/10.1101/234633v1?rss=1 Martyn, I. Kanno, T. Ruzo, A. Siggia, E. Brivanlou, A. 2017-12-15 doi:10.1101/234633 Cold Spring Harbor Laboratory Press 2017-12-15 <![CDATA[ Micropattern differentiation of mouse pluripotent stem cells recapitulates embryo regionalized fates and patterning ]]> https://biorxiv.org/content/10.1101/236562v1?rss=1 Hadjantonakis, A.-K. Morgani, S. Siggia, E. D. Metzger, J. J. Nichols, J. 2017-12-19 doi:10.1101/236562 Cold Spring Harbor Laboratory Press 2017-12-19 <![CDATA[ First genome-wide analysis of an endangered lichen reveals isolation by distance and strong population structure ]]> https://biorxiv.org/content/10.1101/237164v1?rss=1 Allen, J. McKenzie, S. Sleith, R. Alter, S. E. 2017-12-21 doi:10.1101/237164 Cold Spring Harbor Laboratory Press 2017-12-21 <![CDATA[ RAB-35 and ARF-6 GTPases Mediate Engulfment and Clearance Following Linker Cell-Type Death ]]> https://biorxiv.org/content/10.1101/237289v1?rss=1 Kutscher, L. M. Keil, W. Shaham, S. 2017-12-20 doi:10.1101/237289 Cold Spring Harbor Laboratory Press 2017-12-20 <![CDATA[ Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons ]]> https://biorxiv.org/content/10.1101/237347v1?rss=1 Yuan, Y. Xie, S. Darnell, J. C. Darnell, A. J. Saito, Y. Phatnani, H. Murphy, E. Zhang, C. Maniatis, T. Darnell, R. 2018-01-07 doi:10.1101/237347 Cold Spring Harbor Laboratory Press 2018-01-07 <![CDATA[ Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control ]]> https://biorxiv.org/content/10.1101/240747v1?rss=1 Matthews, B. J. Dudchenko, O. Kingan, S. Koren, S. Antoshechkin, I. Crawford, J. E. Glassford, W. J. Herre, M. Redmond, S. N. Rose, N. H. Weedall, G. D. Wu, Y. Batra, S. S. Brito-Sierra, C. A. Buckingham, S. D. Campbell, C. L. Chan, S. Cox, E. Evans, B. R. Fansiri, T. Filipovic, I. Fontaine, A. Gloria-Soria, A. Hall, R. Joardar, V. S. Jones, A. K. Kay, R. G. G. Kodali, V. Lee, J. Lycett, G. J. Mitchell, S. N. Muehling, J. Murphy, M. R. Omer, A. Partridge, F. A. Peluso, P. Aiden, A. P. Ramasamy, V. Rasic, G. Roy, S. Saavedra-Rodriguez, K. Sharan, S. Sha 2017-12-29 doi:10.1101/240747 Cold Spring Harbor Laboratory Press 2017-12-29 <![CDATA[ Chromatin Functional States Correlate with HIV Latency Reversal in Infected Primary CD4+ T Cells ]]> https://biorxiv.org/content/10.1101/242958v1?rss=1 Battivelli, E. Dahabieh, M. S. Abdel-Mohsen, M. Svensson, J. P. Tojal Da Silva, I. Cohn, L. B. Gramatica, A. Deeks, S. Greene, W. C. Pillai, S. K. Verdin, E. 2018-01-04 doi:10.1101/242958 Cold Spring Harbor Laboratory Press 2018-01-04 <![CDATA[ Fidaxomicin jams M. tuberculosis RNA polymerase motions needed for initiation via RbpA contacts ]]> https://biorxiv.org/content/10.1101/244533v1?rss=1 Boyaci, H. Chen, J. Lilic, M. Palka, M. Mooney, R. A. Landick, R. Darst, S. A. Campbell, E. A. 2018-01-08 doi:10.1101/244533 Cold Spring Harbor Laboratory Press 2018-01-08 <![CDATA[ Varicella-zoster virus CNS vasculitis and RNA polymerase III gene mutation in identical twins ]]> https://biorxiv.org/content/10.1101/244848v1?rss=1 Carter-Timofte, M. Hansen, A. F. Mardahl, M. Fribourg, S. Rapaport, F. Zhang, S.-Y. Casanova, J.-L. Paludan, S. R. Christiansen, M. Larsen, C. S. Mogensen, T. H. 2018-01-08 doi:10.1101/244848 Cold Spring Harbor Laboratory Press 2018-01-08 <![CDATA[ Neuron-specific cTag-CLIP reveals cell-specific diversity of functional RNA regulation in the brain ]]> https://biorxiv.org/content/10.1101/244905v1?rss=1 Saito, Y. Yuan, Y. Zucker-Scharff, I. Fak, J. J. Tajima, Y. Licatalosi, D. D. Darnell, R. B. 2018-01-08 doi:10.1101/244905 Cold Spring Harbor Laboratory Press 2018-01-08 <![CDATA[ Differential 3’ Processing of Specific Transcripts Expands Regulatory and Protein Diversity Across Neuronal Cell Types ]]> https://biorxiv.org/content/10.1101/245886v1?rss=1 Jereb, S. Hwang, H.-W. Van Otterloo, E. Govek, E.-E. Fak, J. J. Yuan, Y. Hatten, M. E. Darnell, R. B. 2018-01-10 doi:10.1101/245886 Cold Spring Harbor Laboratory Press 2018-01-10 <![CDATA[ A master regulatory network restoring brain glutamate homeostasis is coordinately activated in stroke ]]> https://biorxiv.org/content/10.1101/245928v1?rss=1 Kobayashi, M. Anderson, C. Benakis, C. Moore, M. J. Mele, A. Fak, J. J. Park, C. Y. Zhou, P. Anrather, J. Iadecola, C. Darnell, R. B. 2018-01-10 doi:10.1101/245928 Cold Spring Harbor Laboratory Press 2018-01-10 <![CDATA[ Green function of correlated genes and themechanical evolution of protein ]]> https://biorxiv.org/content/10.1101/246082v1?rss=1 Dutta, S. Eckmann, J.-P. Libchaber, A. Tlusty, T. 2018-01-10 doi:10.1101/246082 Cold Spring Harbor Laboratory Press 2018-01-10 <![CDATA[ ZFP36 RNA-binding proteins restrain T-cell activation and anti-viral immunity ]]> https://biorxiv.org/content/10.1101/247668v1?rss=1 Moore, M. J. Blachere, N. E. Fak, J. J. Park, C. Y. Sawicka, K. Parveen, S. Zucker-Scharff, I. Moltedo, B. Rudensky, A. Darnell, R. 2018-01-14 doi:10.1101/247668 Cold Spring Harbor Laboratory Press 2018-01-14 <![CDATA[ Control of non-homeostatic feeding in sated mice using associative learning of contextual food cues ]]> https://biorxiv.org/content/10.1101/247825v1?rss=1 Stern, S. A. Doerig, K. R. Azevedo, E. P. Stoffel, E. Friedman, J. M. 2018-01-15 doi:10.1101/247825 Cold Spring Harbor Laboratory Press 2018-01-15 <![CDATA[ Anti-HIV-1 B cell responses are dependent on B cell precursor frequency and antigen binding affinity ]]> https://biorxiv.org/content/10.1101/275438v1?rss=1 Dosenovic, P. Kara, E. E. Pettersson, A.-K. McGuire, A. Gray, M. Hartweger, H. Thientosapol, E. S. Stamatatos, L. Nussenzweig, M. C. 2018-03-02 doi:10.1101/275438 Cold Spring Harbor Laboratory Press 2018-03-02 <![CDATA[ Why Should Mitochondria Define Species? ]]> https://biorxiv.org/content/10.1101/276717v1?rss=1 Stoeckle, M. Y. Thaler, D. S. 2018-03-07 doi:10.1101/276717 Cold Spring Harbor Laboratory Press 2018-03-07 <![CDATA[ Zebrafish as a model to investigate the effects of exercise in cancer ]]> https://biorxiv.org/content/10.1101/279232v1?rss=1 Yin, A. Campbell, N. R. Jones, L. W. White, R. M. 2018-03-09 doi:10.1101/279232 Cold Spring Harbor Laboratory Press 2018-03-09 <![CDATA[ Timing of ESCRT-III protein recruitment and membrane scission during HIV-1 assembly ]]> https://biorxiv.org/content/10.1101/281774v1?rss=1 Johnson, D. S. Bleck, M. Simon, S. M. 2018-03-13 doi:10.1101/281774 Cold Spring Harbor Laboratory Press 2018-03-13 <![CDATA[ Efficient inverse graphics in biological face processing ]]> https://biorxiv.org/content/10.1101/282798v1?rss=1 Yildirim, I. Freiwald, W. Tenenbaum, J. 2018-04-02 doi:10.1101/282798 Cold Spring Harbor Laboratory Press 2018-04-02 <![CDATA[ The Genomic Prediction of Disease: Example of type 2 diabetes (T2D) ]]> https://biorxiv.org/content/10.1101/285783v1?rss=1 Sirovich, L. 2018-03-20 doi:10.1101/285783 Cold Spring Harbor Laboratory Press 2018-03-20 <![CDATA[ DNA-Encircled Lipid Bilayers ]]> https://biorxiv.org/content/10.1101/285957v1?rss=1 Iric, K. Subramanian, M. Oertel, J. Agarwal, N. P. Matthies, M. Periole, X. Sakmar, T. P. Huber, T. Fahmy, K. Schmidt, T.-L. 2018-03-21 doi:10.1101/285957 Cold Spring Harbor Laboratory Press 2018-03-21 <![CDATA[ Using a System’s Equilibrium Behavior to Reduce Its Energy Dissipation in Non-Equilibrium Processes ]]> https://biorxiv.org/content/10.1101/291989v1?rss=1 Tafoya, S. Large, S. Liu, S. Bustamante, C. Sivak, D. 2018-03-30 doi:10.1101/291989 Cold Spring Harbor Laboratory Press 2018-03-30 <![CDATA[ Deciphering human ribonucleoprotein regulatory networks ]]> https://biorxiv.org/content/10.1101/295097v1?rss=1 Mukherjee, N. Wessels, H.-H. Lebedeva, S. Sajek, M. Farazi, T. Ghanbari, M. Garzia, A. Munteanu, A. Mihailovic, A. Spitzer, J. Akat, K. Tuschl, T. Ohler, U. 2018-04-05 doi:10.1101/295097 Cold Spring Harbor Laboratory Press 2018-04-05 <![CDATA[ Axin proteolysis by Iduna is required for the regulation of stem cell proliferation and intestinal homeostasis in Drosophila ]]> https://biorxiv.org/content/10.1101/296830v1?rss=1 Gultekin, Y. Steller, H. 2018-04-06 doi:10.1101/296830 Cold Spring Harbor Laboratory Press 2018-04-06 <![CDATA[ Cancer modeling by Transgene Electroporation in Adult Zebrafish (TEAZ) ]]> https://biorxiv.org/content/10.1101/297234v1?rss=1 Callahan, S. J. Tepan, S. Zhang, Y. M. Lindsay, H. Burger, A. Campbell, N. R. Kim, I. S. Hollmann, T. J. Studer, L. Mosimann, C. White, R. M. 2018-04-09 doi:10.1101/297234 Cold Spring Harbor Laboratory Press 2018-04-09 <![CDATA[ Compartmentalized lymph node drainage dictates intestinal adaptive immune responses ]]> https://biorxiv.org/content/10.1101/299628v1?rss=1 Esterhazy, D. Canesso, M. C. Muller, P. A. Lockhart, A. Mesin, L. Faria, A. M. Mucida, D. 2018-04-11 doi:10.1101/299628 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ Enhanced bacterial immunity and mammalian genome editing via RNA polymerase-mediated dislodging of Cas9 from double strand DNA breaks. ]]> https://biorxiv.org/content/10.1101/300962v1?rss=1 Clarke, R. Heler, R. MacDougall, M. S. Yeo, N. C. Chavez, A. Regan, M. Hanakahi, L. Church, G. M. Marraffini, L. A. Merrill, B. 2018-04-13 doi:10.1101/300962 Cold Spring Harbor Laboratory Press 2018-04-13 <![CDATA[ Filamin-A susceptibility to calpain-mediated cleavage as a marker of dynamic conformational changes in intact platelets ]]> https://biorxiv.org/content/10.1101/307397v1?rss=1 Buitrago, L. Coller, B. S. 2018-04-24 doi:10.1101/307397 Cold Spring Harbor Laboratory Press 2018-04-24 <![CDATA[ Rationally designed mimotope library for profiling of the human IgM repertoire ]]> https://biorxiv.org/content/10.1101/308973v1?rss=1 Pashov, A. D. Shivarov, V. Hadzhieva, M. Kostov, V. Ferdinandov, D. Heinz, K.-M. Pashova, S. Todorova, M. Vassilev, T. L. Kieber-Emmons, T. Meza-Zepeda, L. A. Hovig, E. 2018-04-26 doi:10.1101/308973 Cold Spring Harbor Laboratory Press 2018-04-26 <![CDATA[ Laboratory evolution from social to solitary behavior in the N2 reference strain is unnecessary for its fitness advantages ]]> https://biorxiv.org/content/10.1101/309997v1?rss=1 Zhao, Y. Long, L. Xu, W. Campbell, R. F. Large, E. L. Greene, J. S. McGrath, P. T. 2018-04-30 doi:10.1101/309997 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Structurally Constrained Effective Brain Connectivity ]]> https://biorxiv.org/content/10.1101/310938v1?rss=1 Crimi, A. Dodero, L. Sambataro, F. Murino, V. Sona, D. 2018-04-30 doi:10.1101/310938 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Cerebellar nuclei neurons dictate growth of the cortex through developmental scaling of presynaptic Purkinje cells ]]> https://biorxiv.org/content/10.1101/310953v1?rss=1 Joyner, A. L. Willett, R. T. Wojcinski, A. Bayin, N. S. Lao, Z. Stephen, D. Dauber-Decker, K. L. Wu, Z. Tessier-Lavigne, M. Saito, H. Suzuki, N. 2018-04-30 doi:10.1101/310953 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Connectomics of the zebrafish’s lateral-line neuromast reveals wiring and miswiring in a simple microcircuit ]]> https://biorxiv.org/content/10.1101/311506v1?rss=1 Dow, E. Jacobo, A. Hossain, S. Siletti, K. Hudspeth, A. J. 2018-04-30 doi:10.1101/311506 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ The ubiquitin ligase CRL3Kelch targets HtsRC to organize the Drosophila ring canal cytoskeleton ]]> https://biorxiv.org/content/10.1101/315077v1?rss=1 Hudson, A. M. Mannix, K. M. Gerdes, J. A. Kottemann, M. C. Cooley, L. 2018-05-04 doi:10.1101/315077 Cold Spring Harbor Laboratory Press 2018-05-04 <![CDATA[ Walking Drosophila aim to maintain a neural heading estimate at an internal goal angle ]]> https://biorxiv.org/content/10.1101/315796v1?rss=1 Green, J. Vijayan, V. Mussells Pires, P. Adachi, A. Maimon, G. 2018-05-07 doi:10.1101/315796 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ Single-neuron interactions between the somatosensory thalamo-cortical circuits during perception ]]> https://biorxiv.org/content/10.1101/315911v1?rss=1 Tauste Campo, A. Vazquez, Y. Alvarez, M. Zainos, A. Rossi-Pool, R. Deco, G. Romo, R. 2018-05-07 doi:10.1101/315911 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ Whole-genome deep learning analysis reveals causal role of noncoding mutations in autism ]]> https://biorxiv.org/content/10.1101/319681v1?rss=1 Zhou, J. Park, C. Theesfeld, C. Yuan, Y. Sawicka, K. Darnell, J. Scheckel, C. Fak, J. Tajima, Y. Darnell, R. Troyanskaya, O. 2018-05-11 doi:10.1101/319681 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia ]]> https://biorxiv.org/content/10.1101/321174v1?rss=1 Minuesa, G. Albanese, S. K. Chow, A. Schurer, A. Park, S.-M. Rotsides, C. Z. Taggart, J. Rizzi, A. Naden, L. N. Chou, T. Gourkanti, S. Cappel, D. Passarelli, M. C. Fairchild, L. Adura, C. Glickman, F. J. Schulman, J. Famulare, C. Patel, M. Eibl, J. K. Ross, G. M. Tan, D. S. Leslie, C. S. Beuming, T. Goldgur, Y. Chodera, J. D. Kharas, M. G. 2018-05-14 doi:10.1101/321174 Cold Spring Harbor Laboratory Press 2018-05-14 <![CDATA[ Structural basis for transcript elongation control by NusG/RfaH universal regulators ]]> https://biorxiv.org/content/10.1101/324400v1?rss=1 Kang, J. Y. Mooney, R. A. Nedialkov, Y. Saba, J. Mishanina, T. V. Artsimovitch, I. Landick, R. Darst, S. 2018-05-16 doi:10.1101/324400 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Analysis of HIV-1 latent reservoir and rebound viruses in a clinical trial of anti-HIV-1 antibody 3BNC117 ]]> https://biorxiv.org/content/10.1101/324509v1?rss=1 Cohen, Y. Z. Lorenzi, J. C. C. Krassnig, L. Barton, J. P. Burke, L. Pai, J. Lu, C.-L. Mendoza, P. Oliveira, T. Y. Sleckman, C. Millard, K. Butler, A. Dizon, J. P. Belblidia, S. Witmer-Pack, M. Shimeliovich, I. Gulick, R. M. Seaman, M. S. Jankovic, M. Caskey, M. Nussenzweig, M. C. 2018-05-25 doi:10.1101/324509 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ A non-canonical-PPARγ/RXRα-binding sequence regulates leptin expression in response to changes in adipose tissue mass ]]> https://biorxiv.org/content/10.1101/325480v1?rss=1 Zhang, Y. Dallner, O. S. Nakadai, T. Fayzikhodjaeva, G. Lu, Y.-H. Lazar, M. A. Roeder, R. G. Friedman, J. M. 2018-05-18 doi:10.1101/325480 Cold Spring Harbor Laboratory Press 2018-05-18 <![CDATA[ Parallel multimodal circuits control an innate foraging behavior ]]> https://biorxiv.org/content/10.1101/326405v1?rss=1 Lopez-Cruz, A. Pokala, N. Sordillo, A. Flavell, S. W. McGrath, P. T. Bargmann, C. 2018-05-18 doi:10.1101/326405 Cold Spring Harbor Laboratory Press 2018-05-18 <![CDATA[ FALCON-Phase: Integrating PacBio and Hi-C data for phased diploid genomes ]]> https://biorxiv.org/content/10.1101/327064v1?rss=1 97%) compared to human (82%). In addition, scaffolding with the same Hi-C chromatin contact data resulted in phased chromosome-scale scaffolds. ]]> Kronenberg, Z. N. Hall, R. J. Hiendleder, S. Smith, T. P. L. Sullivan, S. T. Williams, J. L. Kingan, S. B. 2018-05-21 doi:10.1101/327064 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ Molecular mechanism of symmetry breaking in a 3D model of a human epiblast ]]> https://biorxiv.org/content/10.1101/330704v1?rss=1 Simunovic, M. Metzger, J. J. Etoc, F. Yoney, A. Ruzo, A. Martyn, I. Croft, G. Brivanlou, A. H. Siggia, E. D. 2018-05-29 doi:10.1101/330704 Cold Spring Harbor Laboratory Press 2018-05-29 <![CDATA[ GoFish: A Streamlined Environmental DNA Presence/Absence Assay for Marine Vertebrates ]]> https://biorxiv.org/content/10.1101/331322v1?rss=1 Stoeckle, M. Y. Das Mishu, M. Charlop-Powers, Z. 2018-05-25 doi:10.1101/331322 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ WNT signaling memory is required for ACTIVIN to function as a morphogen in human gastruloids ]]> https://biorxiv.org/content/10.1101/333948v1?rss=1 Yoney, A. Etoc, F. Ruzo, A. Metzger, J. J. Martyn, I. Li, S. Kirst, C. Carroll, T. Siggia, E. D. Brivanlou, A. H. 2018-05-30 doi:10.1101/333948 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ Vasculature-associated adipose tissue macrophages dynamically adapt to inflammatory and metabolic challenges ]]> https://biorxiv.org/content/10.1101/336032v1?rss=1 Moura Silva, H. Bafica, A. Rodrigues-Luiz, G. F. Chi, J. Santos, P. d. A. Sgarbi Reis, B. Hoytema van Konijnenburg, D. Crane, A. Arifa, R. D. N. Martin, P. Gasparin Bueno Mendes, D. A. Mansur, D. S. Torres, V. Cadwell, K. Cohen, P. Mucida, D. Lafaille, J. J. 2018-05-31 doi:10.1101/336032 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ ASTN2 modulates synaptic strength by trafficking and degradation of surface proteins ]]> https://biorxiv.org/content/10.1101/337618v1?rss=1 Behesti, H. Fore, T. Woo, P. Horn, Z. Leppert, M. Hull, C. Hatten, M. E. 2018-06-04 doi:10.1101/337618 Cold Spring Harbor Laboratory Press 2018-06-04 <![CDATA[ The aryl hydrocarbon receptor and interferon gamma generate antiviral states via transcriptional repression ]]> https://biorxiv.org/content/10.1101/353789v1?rss=1 Bieniasz, P. D. Kueck, T. Cassella, E. Holler, J. Kim, B. 2018-06-22 doi:10.1101/353789 Cold Spring Harbor Laboratory Press 2018-06-22 <![CDATA[ ATR repression at telomeres by POT1a and POT1b: RPA exclusion and interference by CST ]]> https://biorxiv.org/content/10.1101/354985v1?rss=1 Kratz, K. de Lange, T. 2018-06-24 doi:10.1101/354985 Cold Spring Harbor Laboratory Press 2018-06-24 <![CDATA[ Incomplete penetrance for isolated congenital asplenia in humans with mutations in translated and untranslated RPSA exons ]]> https://biorxiv.org/content/10.1101/356832v1?rss=1 Bolze, A. Boisson, B. Bosch, B. Antipenko, A. Bouaziz, M. Sackstein, P. Chaker-Margot, M. Barlogis, V. Briggs, T. Colino, E. Elmore, A. C. Fisher, A. Genel, F. Hewlett, A. Jedidi, M. Kelecic, J. Krüger, R. Ku, C.-L. Kumararatne, D. Lefevre-Utile, A. Loughlin, S. Mahlaoui, N. Markus, S. Garcia, J.-M. Nizon, M. Oleastro, M. Pac, M. Picard, C. Pollard, A. J. Rodriguez-Gallego, J.-C. Thomas, C. Von Bernuth, H. Worth, A. Meyts, I. Risolino, M. Selleri, L. Puel, A. Klinge, S. Abel, L. Casanova, J.-L. 2018-06-27 doi:10.1101/356832 Cold Spring Harbor Laboratory Press 2018-06-27 <![CDATA[ N-Cadherin Provides a Cis and Trans Ligand for Astrotactin that Functions in Glial-Guided Neuronal Migration ]]> https://biorxiv.org/content/10.1101/357541v1?rss=1 Horn, Z. Behesti, H. Hatten, M. E. 2018-06-27 doi:10.1101/357541 Cold Spring Harbor Laboratory Press 2018-06-27 <![CDATA[ The C. elegans AWA Olfactory Neuron Fires Calcium-Mediated All-or-None Action Potentials ]]> https://biorxiv.org/content/10.1101/359935v1?rss=1 Liu, Q. Kidd, P. B. Dobosiewicz, M. Bargmann, C. 2018-06-30 doi:10.1101/359935 Cold Spring Harbor Laboratory Press 2018-06-30 <![CDATA[ DEET feet: Aedes aegypti mosquitoes use their tarsi to sense DEET on contact ]]> https://biorxiv.org/content/10.1101/360222v1?rss=1 Dennis, E. J. Vosshall, L. B. 2018-07-01 doi:10.1101/360222 Cold Spring Harbor Laboratory Press 2018-07-01 <![CDATA[ PI31 is an adaptor protein for proteasome transport in axons ]]> https://biorxiv.org/content/10.1101/364463v1?rss=1 Liu, K. Jones, S. Minis, A. Rodriguez, J. Molina, H. Steller, H. 2018-07-07 doi:10.1101/364463 Cold Spring Harbor Laboratory Press 2018-07-07 <![CDATA[ Single-cell isoform RNA sequencing (ScISOr-Seq) across thousands of cells reveals isoforms of cerebellar cell types. ]]> https://biorxiv.org/content/10.1101/364950v1?rss=1 1,000 single cells from bulk tissue without cell sorting by leveraging two technologies in three steps: In step one, we employ microfluidics to produce amplified full-length cDNAs barcoded for their cell of origin. This cDNA is split into two pools: one pool for 3 sequencing to measure gene expression (step 2) and another pool for long-read sequencing and isoform expression (step 3). In step two, short-read 3-sequencing provides molecular counts for each gene and cell, which allows clustering cells and assigning a cell type using cell-type specific markers. In step three, an aliquot of the same cDNAs (each barcoded for the individual cell of origin) is sequenced using Pacific Biosciences ("PacBio")1,2,4,5,26 or Oxford Nanopore3. Since these long reads carry the single-cell barcodes identified in step two, one can determine the individual cell from which each long read originates. Since most single cells are assigned to a named cluster, we can also assign the cells cluster name (e.g. "Purkinje cell" or "astrocyte") to the long read in question (Fig 1A) - without losing the cell of origin of each long read.nnO_FIG O_LINKSMALLFIG WIDTH=180 HEIGHT=200 SRC="FIGDIR/small/364950_fig1.gif" ALT="Figure 1">nView larger version (66K):norg.highwire.dtl.DTLVardef@4df0cdorg.highwire.dtl.DTLVardef@fc4beborg.highwire.dtl.DTLVardef@1dc485forg.highwire.dtl.DTLVardef@1138a3e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO (A) Outline of our ScISOr-Seq approach. (B) TSNE-plot depicting cell clusters, marker genes and names given to clusters, including: Bergman glia (BG), External granule cell layer neurons (EGL), Internal granule cell layer and other neurons in the interior of the cerebellum (IGL), two clusters of Purkinje cell layer neurons (PCL), oligodendrocyte progenitor cells (OPCs), Atoh1+ neuronal progenitors, Ptf1a+ neuronal progenitors and other neuronal progenitors (NPCs) (C) In-situ hybridization images from the Allen Brain Atlas depicting expression of marker genes in specific layers. (D) Expression patterns of selected marker genes across cell types.nnC_FIG ]]> Gupta, I. Collier, P. G. Haase, B. Mahfouz, A. Joglekar, A. Floyd, T. Koopmans, F. Barres, B. Smit, A. B. Sloan, S. Luo, W. Fedrigo, O. Ross, M. E. Tilgner, H. U. 2018-07-08 doi:10.1101/364950 Cold Spring Harbor Laboratory Press 2018-07-08 <![CDATA[ Replisome preservation by a single-stranded DNA gate in the CMG helicase ]]> https://biorxiv.org/content/10.1101/368472v1?rss=1 Wasserman, M. R. Schauer, G. D. O'Donnell, M. E. Liu, S. 2018-07-13 doi:10.1101/368472 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ Dynamics of Cas10 Govern Discrimination between Self and Nonself in Type III CRISPR-Cas Immunity ]]> https://biorxiv.org/content/10.1101/369744v1?rss=1 Wang, L. Mo, C. Y. Wasserman, M. R. Rostol, J. T. Marraffini, L. A. Liu, S. 2018-07-20 doi:10.1101/369744 Cold Spring Harbor Laboratory Press 2018-07-20 <![CDATA[ PIP4Ks Suppress Insulin Signaling Through a Catalytic-Independent Mechanism ]]> https://biorxiv.org/content/10.1101/370544v1?rss=1 Wang, D. G. Paddock, M. N. Lundquist, M. R. Sun, J. Y. Mashadova, O. Amadiume, S. Bumpus, T. W. Hodakoski, C. Hopkins, B. D. Fine, M. Hill, A. Yang, T. J. Baskin, J. M. Dow, L. E. Cantley, L. C. 2018-07-20 doi:10.1101/370544 Cold Spring Harbor Laboratory Press 2018-07-20 <![CDATA[ A unifying model to predict multiple object orienting behaviors in tethered flies ]]> https://biorxiv.org/content/10.1101/379651v1?rss=1 Poehlmann, A. Soselisa, S. Fenk, L. M. Straw, A. D. 2018-07-28 doi:10.1101/379651 Cold Spring Harbor Laboratory Press 2018-07-28 <![CDATA[ Resting state functional connectivity patterns associated with pharmacological treatment resistance in temporal lobe epilepsy ]]> https://biorxiv.org/content/10.1101/382523v1?rss=1 Pressl, C. Brandner, P. Schaffelhofer, S. Blackmon, K. Dugan, P. Holmes, M. Thesen, T. Kuzniecky, R. Devinsky, O. Freiwald, W. A. 2018-08-10 doi:10.1101/382523 Cold Spring Harbor Laboratory Press 2018-08-10 <![CDATA[ Insights from Comparison of the Renal and Skin Single Cell Transcriptomes in Lupus Nephritis ]]> https://biorxiv.org/content/10.1101/382846v1?rss=1 Der, E. Suryawanshi, H. Morozov, P. Kustagi, M. Goilav, B. Ranabathou, S. Izmirly, P. Clancy, R. Belmont, H. M. Koenigsberg, M. Mokrzycki, M. Rominieki, H. Graham, J. Rocca, J. Bornkamp, N. Jordan, N. Schulte, E. Wu, M. Pullman, J. Slowikowski, K. Raychaudhuri, S. Guthridge, J. James, J. Acclerating Medicine Partnership (AMP), Buyon, J. Tuschl, T. Putterman, C. 2018-08-01 doi:10.1101/382846 Cold Spring Harbor Laboratory Press 2018-08-01 <![CDATA[ Resolving Filament Level Mechanics in Collagen Networks using Activity Microscopy ]]> https://biorxiv.org/content/10.1101/382903v1?rss=1 Lissek, E. N. Bartsch, T. F. Florin, E.-L. 2018-08-02 doi:10.1101/382903 Cold Spring Harbor Laboratory Press 2018-08-02 <![CDATA[ Nuclear TARBP2 drives oncogenic dysregulation of RNA splicing and decay ]]> https://biorxiv.org/content/10.1101/389213v1?rss=1 Fish, L. Nguyen, H. C. B. Zhang, S. Hochman, M. Dill, B. D. Molina, H. Najafabadi, H. S. Alarcon, C. Goodarzi, H. 2018-08-17 doi:10.1101/389213 Cold Spring Harbor Laboratory Press 2018-08-17 <![CDATA[ Cell-cell signaling elicits local Ca2+ transients in melanocyte dendrites and dendritic spine-like structures ]]> https://biorxiv.org/content/10.1101/390542v1?rss=1 Belote, R. L. Simon, S. M. 2018-08-12 doi:10.1101/390542 Cold Spring Harbor Laboratory Press 2018-08-12 <![CDATA[ Novel small molecule agonists of an Aedes aegypti neuropeptide Y receptor block mosquito biting behavior ]]> https://biorxiv.org/content/10.1101/393793v1?rss=1 Duvall, L. B. Ramos-Espiritu, L. Barsoum, K. E. Glickman, J. F. Vosshall, L. B. 2018-08-16 doi:10.1101/393793 Cold Spring Harbor Laboratory Press 2018-08-16 <![CDATA[ Cancer archetypes co-opt and adapt the transcriptional programs of existing cellular states ]]> https://biorxiv.org/content/10.1101/396622v1?rss=1 Baron, M. Kim, I. S. Moncada, R. Yan, Y. Campbell, N. R. White, R. M. Yanai, I. 2018-08-22 doi:10.1101/396622 Cold Spring Harbor Laboratory Press 2018-08-22 <![CDATA[ Molecular noise shapes bacteria-phage ecologies ]]> https://biorxiv.org/content/10.1101/399527v1?rss=1 Ruess, J. Pleska, M. Guet, C. Tkacik, G. 2018-08-25 doi:10.1101/399527 Cold Spring Harbor Laboratory Press 2018-08-25 <![CDATA[ SeqTailor: a user-friendly webserver for the extraction of DNA or protein sequences from next-generation sequencing data ]]> https://biorxiv.org/content/10.1101/408625v1?rss=1 Zhang, P. Boisson, B. Casanova, J.-L. Abel, L. Itan, Y. 2018-09-05 doi:10.1101/408625 Cold Spring Harbor Laboratory Press 2018-09-05 <![CDATA[ Glutamate spillover in C. elegans triggers repetitive behavior through presynaptic activation of MGL-2/mGluR5 ]]> https://biorxiv.org/content/10.1101/415828v1?rss=1 Katz, M. Corson, F. Keil, W. Singhal, A. Bae, A. Lu, Y. Liang, Y. Shaham, S. 2018-09-13 doi:10.1101/415828 Cold Spring Harbor Laboratory Press 2018-09-13 <![CDATA[ MITO-Tag Mice enable rapid isolation and multimodal profiling of mitochondria from specific cell types in vivo ]]> https://biorxiv.org/content/10.1101/425454v1?rss=1 Bayraktar, E. C. Baudrier, L. Ozerdem, C. Lewis, C. A. Chen, S. H. Kunchok, T. Abu-Remaileh, M. Cangelosi, A. L. Sabatini, D. M. Birsoy, K. Chen, W. W. 2018-09-24 doi:10.1101/425454 Cold Spring Harbor Laboratory Press 2018-09-24 <![CDATA[ Interactions of nuclear transport factors and surface-conjugated FG nucleoporins: Insights and limitations ]]> https://biorxiv.org/content/10.1101/435651v1?rss=1 Hayama, R. Sorci, M. Keating, J. J. Hecht, L. M. Plawsky, J. L. Belfort, G. Chait, B. T. Rout, M. P. 2018-10-05 doi:10.1101/435651 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ Coherent neuronal dynamics driven by optogenetic stimulation in the primate brain ]]> https://biorxiv.org/content/10.1101/437970v1?rss=1 Shewcraft, R. A. Dean, H. L. Wong, Y. T. Hagan, M. A. Fabiszak, M. M. Pesaran, B. 2018-10-16 doi:10.1101/437970 Cold Spring Harbor Laboratory Press 2018-10-16 <![CDATA[ Encoding of an engram for food location by satiety-promoting Drd2 hippocampal neurons ]]> https://biorxiv.org/content/10.1101/439349v1?rss=1 Hippocampus->Septal high-order circuit that encodes the memory of food location. ]]> Azevedo, E. P. Pomeranz, L. Cheng, J. Schneeberger, M. Stern, S. Doerig, K. Greengard, P. Friedman, J. M. 2018-10-11 doi:10.1101/439349 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ A wave of WNT signalling balanced by secreted inhibitors controls primitive streak formation in micropattern colonies of human embryonic stem cells ]]> https://biorxiv.org/content/10.1101/440602v1?rss=1 Martyn, I. Brivanlou, A. H. Siggia, E. D. 2018-10-10 doi:10.1101/440602 Cold Spring Harbor Laboratory Press 2018-10-10 <![CDATA[ The ion channel ppk301 controls freshwater egg-laying in the mosquito Aedes aegypti ]]> https://biorxiv.org/content/10.1101/441592v1?rss=1 Matthews, B. J. Younger, M. A. Vosshall, L. B. 2018-10-12 doi:10.1101/441592 Cold Spring Harbor Laboratory Press 2018-10-12 <![CDATA[ Loss of SATB1 Induces a p21 Dependent CellularSenescence Phenotype in Dopaminergic Neurons ]]> https://biorxiv.org/content/10.1101/452243v1?rss=1 Riessland, M. Kolisnyk, B. Kim, T. W. Cheng, J. Ni, J. Pearson, J. A. Park, E. J. Dam, K. Acehan, D. Ramos-Espiritu, L. S. Wang, W. Zhang, J. Shim, J.-w. Ciceri, G. Brichta, L. Studer, L. Greengard, P. 2018-10-25 doi:10.1101/452243 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Nuclease dead Cas9 is a programmable roadblock for DNA replication ]]> https://biorxiv.org/content/10.1101/455543v1?rss=1 Whinn, K. Kaur, G. Lewis, J. S. Schauer, G. Müller, S. Jergic, S. Naganbabu, M. Bruchez, M. P. O'Donnell, M. Dixon, N. E. van Oijen, A. M. Ghodke, H. 2018-10-29 doi:10.1101/455543 Cold Spring Harbor Laboratory Press 2018-10-29 <![CDATA[ Characterization of intact proviruses in blood and lymph node from HIV-infected individuals undergoing analytical treatment interruption ]]> https://biorxiv.org/content/10.1101/456020v1?rss=1 Vibholm, L. K. Cetrulo Lorenzi, J. C. Pai, J. Cohen, Y. Z. Oliveira, T. Y. Barton, J. P. Noceda, M. G. Lu, C.-L. Ablanedo-Terrazas, Y. Del Rio Estrada, P. M. Reyes-Teran, G. Tolstrup, M. Denton, P. W. Damsgaard, T. Sogaard, O. S. Nussenzweig, M. C. 2018-11-02 doi:10.1101/456020 Cold Spring Harbor Laboratory Press 2018-11-02 <![CDATA[ Eliminating effects of particle adsorption to the air/water interface in single-particle cryo-electron microscopy: Bacterial RNA polymerase and CHAPSO ]]> https://biorxiv.org/content/10.1101/457267v1?rss=1 Chen, J. Noble, A. J. Kang, J. Y. Darst, S. 2018-10-30 doi:10.1101/457267 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ A short HBV RNA region induces RNR-R2 expression in non-cycling cells and in primary human hepatocytes ]]> https://biorxiv.org/content/10.1101/458679v1?rss=1 Ricardo-Lax, I. Broennimann, K. Adler, J. Michailidis, E. De Jong, Y. P. Reuven, N. Shaul, Y. 2018-10-31 doi:10.1101/458679 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ GSAP modulates γ-secretase specificity by inducing conformational change in PS1 ]]> https://biorxiv.org/content/10.1101/461061v1?rss=1 Wong, E. Liao, G. P. Chang, J. Xu, P. Li, Y.-M. Greengard, P. 2018-11-07 doi:10.1101/461061 Cold Spring Harbor Laboratory Press 2018-11-07 <![CDATA[ FMRP association with and regulation of Fragile X granules exhibit circuit-dependent requirements for the KH2 RNA binding domain ]]> https://biorxiv.org/content/10.1101/462168v1?rss=1 Gingrich, E. C. Shepard, K. A. Mitchell, M. E. Sawicka, K. Darnell, J. C. Akins, M. R. 2018-11-05 doi:10.1101/462168 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ Genetic loss of the ubiquitin ligase RNF126, an AID interacting partner and modifier, affects strand targeting during somatic hypermutation of antibody genes ]]> https://biorxiv.org/content/10.1101/469775v1?rss=1 C bias; strickingly, loss of RNF126 was also associated with tandem indels within the variable region (JH4 intron) but only a slight increase in the types of chromosomal translocations that are characteristic of deregulated AID. Conversely, these findings suggest that mono-ubiquitination of AID, likely in situ, is necessary for the proper removal of the protein from the non-transcribed strand, thus producing both optimal patterns of SHM and also limiting the number of indels within the target locus. ]]> Economos, N. G. Delker, R. K. Stavropoulos, P. Papavasiliou, F. N. 2018-11-14 doi:10.1101/469775 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ Notch-Mediated Polarity Decisions in Mechanosensory Hair Cells ]]> https://biorxiv.org/content/10.1101/480798v1?rss=1 Jacobo, A. Dasgupta, A. Erzberger, A. Siletti, K. Hudspeth, A. J. 2018-11-28 doi:10.1101/480798 Cold Spring Harbor Laboratory Press 2018-11-28 <![CDATA[ Bilateral spontaneous otoacoustic emissions show coupling between active oscillators in the two ears ]]> https://biorxiv.org/content/10.1101/484717v1?rss=1 Roongthumskul, Y. O Maoileidigh, D. Hudspeth, A. 2018-12-03 doi:10.1101/484717 Cold Spring Harbor Laboratory Press 2018-12-03 <![CDATA[ Assembly and early maturation of large subunit precursors ]]> https://biorxiv.org/content/10.1101/486225v1?rss=1 Chaker-Margot, M. Klinge, S. 2018-12-04 doi:10.1101/486225 Cold Spring Harbor Laboratory Press 2018-12-04 <![CDATA[ Why Put-Up with Immunity when there is Resistance: An Excursion into the Population and Evolutionary Dynamics of Restriction-Modification and CRISPR-Cas ]]> https://biorxiv.org/content/10.1101/487132v1?rss=1 Gurney, J. R. Pleska, M. Levin, B. R. 2018-12-04 doi:10.1101/487132 Cold Spring Harbor Laboratory Press 2018-12-04 <![CDATA[ Mutations In PIK3C2A Cause Syndromic Short Stature, Skeletal Abnormalities, and Cataracts Associated With Ciliary Dysfunction ]]> https://biorxiv.org/content/10.1101/488411v1?rss=1 Tiosano, D. Baris Feldman, H. Chen, A. Hitzert, M. M. Schueler, M. Gulluni, F. Wiesener, A. Bergua, A. Mory, A. Copeland, B. Gleeson, J. G. Rump, P. van Meer, H. Sival, D. A. Haucke, V. Kriwinsky, J. Knaup, K. X. Reis, A. Hauer, N. N. Hirsch, E. Roepman, R. Pfundt, R. Thiel, C. T. Wiesener, M. S. Aslanyan, M. G. Buchner, D. A. 2018-12-07 doi:10.1101/488411 Cold Spring Harbor Laboratory Press 2018-12-07 <![CDATA[ Dissociating task acquisition from expression during learning reveals latent knowledge ]]> https://biorxiv.org/content/10.1101/489450v1?rss=1 Kuchibhotla, K. V. Hindmarsh Sten, T. Papadoyannis, E. C. Elnozahy, S. Fogelson, K. Kumar, R. Boubenec, Y. Holland, P. C. Ostojic, S. Froemke, R. C. 2018-12-09 doi:10.1101/489450 Cold Spring Harbor Laboratory Press 2018-12-09 <![CDATA[ Astrotactins 1 and 2 have similar membrane topology and mature via endoproteolytic cleavage catalyzed by signal peptidase ]]> https://biorxiv.org/content/10.1101/493858v1?rss=1 Lara, P. Tellgren-Roth, A. Behesti, H. Horn, Z. Schiller, N. Enquist, K. Cammenberg, M. Liljenström, A. Hatten, M. E. Von Heijne, G. Nilsson, I. 2018-12-11 doi:10.1101/493858 Cold Spring Harbor Laboratory Press 2018-12-11 <![CDATA[ Selective neuronal vulnerability in Alzheimer’s disease: a network-based analysis ]]> https://biorxiv.org/content/10.1101/499897v1?rss=1 Roussarie, J.-P. Yao, V. Plautz, Z. Kasturia, S. Albornoz, C. Schmidt, E. F. Brichta, L. Barnea-Cramer, A. Heintz, N. Hof, P. Heiman, M. Flajolet, M. Troyanskaya, O. Greengard, P. 2018-12-19 doi:10.1101/499897 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ The elasticity of individual protocadherin 15 molecules implicates cadherins as the gating springs for hearing ]]> https://biorxiv.org/content/10.1101/503029v1?rss=1 Bartsch, T. F. Hengel, F. E. Oswald, A. Dionne, G. Chipendo, I. V. Mangat, S. S. El Shatanofy, M. Shapiro, L. Mueller, U. Hudspeth, A. J. 2018-12-20 doi:10.1101/503029 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ Structures of the PKA RIα holoenzyme with the FLHCC driver J-PKAcα or wild type PKAcα ]]> https://biorxiv.org/content/10.1101/505347v1?rss=1 Cao, B. Lu, T.-W. Martinez Fiesco, J. Tomasini, M. Fan, L. Simon, S. Taylor, S. Zhang, P. 2018-12-22 doi:10.1101/505347 Cold Spring Harbor Laboratory Press 2018-12-22 <![CDATA[ Non-FG-Nups, ELYS and Nup35, coordinate an ordered assembly of FG-Nups on the scaffold of the nuclear pore complex ]]> https://biorxiv.org/content/10.1101/506469v1?rss=1 Konishi, H. A. Yoshimura, S. H. 2018-12-26 doi:10.1101/506469 Cold Spring Harbor Laboratory Press 2018-12-26 <![CDATA[ Detection of circulating extracellular mRNAs by modified small RNA-sequencing analysis ]]> https://biorxiv.org/content/10.1101/507681v1?rss=1 Akat, K. M. Lee, Y. A. Hurley, A. Morozov, P. Max, K. E. A. Brown, M. Bogardus, K. Sopeyin, A. Hildner, K. Diacovo, T. Neurath, M. F. Borggrefe, M. Tuschl, T. 2018-12-31 doi:10.1101/507681 Cold Spring Harbor Laboratory Press 2018-12-31 <![CDATA[ Gain-of-function mutations in the UNC-2/CaV2α channel lead to hyperactivity and excitation-dominant synaptic transmission in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/509380v1?rss=1 Huang, Y.-C. Pirri, J. Rayes, D. Gao, S. Mulcahy, B. Grant, J. Saheki, Y. Francis, M. Zhen, M. Alkema, M. 2019-01-01 doi:10.1101/509380 Cold Spring Harbor Laboratory Press 2019-01-01 <![CDATA[ General visual and contingent thermal cues interact to elicit attraction in female Aedes aegypti mosquitoes ]]> https://biorxiv.org/content/10.1101/510594v1?rss=1 nView larger version (38K):norg.highwire.dtl.DTLVardef@1fe3d06org.highwire.dtl.DTLVardef@587addorg.highwire.dtl.DTLVardef@ea6d67org.highwire.dtl.DTLVardef@b49d41_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Liu, M. Z. Vosshall, L. B. 2019-01-03 doi:10.1101/510594 Cold Spring Harbor Laboratory Press 2019-01-03 <![CDATA[ Whole Genome Doubling mitigates Muller’s Ratchet in Cancer Evolution ]]> https://biorxiv.org/content/10.1101/513457v1?rss=1 Lopez, S. Lim, E. Huebner, A. Dietzen, M. Mourikis, T. Watkins, T. B. Rowan, A. Dewhurst, S. M. Birkbak, N. J. Wilson, G. A. Jamal-Hanjani, M. Swanton, C. TRACERx Consortium, McGranahan, N. 2019-01-07 doi:10.1101/513457 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ Mycobacterium tuberculosis hijacks an evolutionary recent IFN-IL-6-CEBP axis linked to monocyte development and disease severity in humans ]]> https://biorxiv.org/content/10.1101/514943v1?rss=1 Delgobo, M. Kozlova, E. Rocha, E. L. Rodrigues-Luis, G. F. Mendes, D. A. Mascarin, L. Dias, G. Patricio, D. O. Dierckx, T. Bicca, M. A. Breton, G. Rovaris, D. Moral, J. D. Mansur, D. S. Weyenbergh, J. V. Bafica, A. 2019-01-09 doi:10.1101/514943 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ C99, not beta-amyloid, is associated with selective death of vulnerable neurons in Alzheimer's disease. ]]> https://biorxiv.org/content/10.1101/527572v1?rss=1 Pulina, M. Hopkins, M. Haroutunian, V. Greengard, P. Bustos, V. 2019-01-22 doi:10.1101/527572 Cold Spring Harbor Laboratory Press 2019-01-22 <![CDATA[ N6-methyladenosine dynamics during early vertebrate embryogenesis ]]> https://biorxiv.org/content/10.1101/528422v1?rss=1 70%) of maternal transcripts harbor m6A, and there is a substantial increase of m6A in the polyadenylated mRNA fraction between 0 and 2 hours post fertilization. Notably, we find strong associations between m6A, cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation (ZGA). Interestingly, the relationship between m6A and translation is strongest for peaks located in the 3UTR, but not overlapping stop codons. Sequence analyses revealed enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. After ZGA, m6A seem to diminish the effect of miR-430 mediated degradation. The reported results improve our understanding of the combinatorial code behind post-transcriptional mRNA regulation during embryonic reprogramming and early differentiation. ]]> Aanes, H. Engelsen, D. Manaf, A. Alemu, E. A. Vagbo, C. B. Martin, L. Lerdrup, M. Hansen, K. Mathavan, S. Winata, C. Darnell, R. B. Alestrom, P. Klungland, A. 2019-01-23 doi:10.1101/528422 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Antigen-specific humoral immune responses by CRISPR/Cas9-edited B cells ]]> https://biorxiv.org/content/10.1101/530832v1?rss=1 Hartweger, H. McGuire, A. T. Horning, M. Taylor, J. J. Dosenovic, P. Yost, D. Gazumyan, A. Seaman, M. S. Stamatatos, L. Jankovic, M. Nussenzweig, M. C. 2019-01-26 doi:10.1101/530832 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Reconstruction of 1,000 projection neurons reveals new cell types and organization of long-range connectivity in the mouse brain ]]> https://biorxiv.org/content/10.1101/537233v1?rss=1 Winnubst, J. Bas, E. Ferreira, T. A. Wu, Z. Economo, M. N. Edson, P. Arthur, B. J. Bruns, C. Rokicki, K. Schauder, D. Olbris, D. J. Murphy, S. D. Ackerman, D. G. Arshadi, C. Baldwin, P. Blake, R. Elsayed, A. Hasan, M. Ramirez, D. Dos Santos, B. Weldon, M. Zafar, A. Dudmann, J. T. Gerfen, C. R. Hantman, A. W. Korff, W. Sternson, S. M. Spruston, N. Svoboda, K. Chandrashekar, J. 2019-02-01 doi:10.1101/537233 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ Microbiota imprint gut-intrinsic neuronal programming and sympathetic activity ]]> https://biorxiv.org/content/10.1101/545806v1?rss=1 Muller, P. A. Kerner, Z. Schneeberger Pane, M. Mucida, D. 2019-02-10 doi:10.1101/545806 Cold Spring Harbor Laboratory Press 2019-02-10 <![CDATA[ The regulatory factor ELF1 triggers a critical wave of transcription in the antiviral response to type I interferon ]]> https://biorxiv.org/content/10.1101/549485v1?rss=1 Seifert, L. L. Si, C. Ballentine, S. Saha, D. de Vries, M. Wang, G. Sadic, M. Briley, A. Schaefer, U. Moulton, H. Garcia-Sastre, A. Tripathi, S. Rosenberg, B. R. Dittmann, M. 2019-02-14 doi:10.1101/549485 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ Principles Governing the Dynamics of GABAergic Interneurons in the Barrel Cortex ]]> https://biorxiv.org/content/10.1101/554949v1?rss=1 Yu, J. Hu, H. Agmon, A. Svoboda, K. 2019-02-19 doi:10.1101/554949 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ Adrenergic signaling in muscularis macrophages limits neuronal death following enteric infection ]]> https://biorxiv.org/content/10.1101/556340v1?rss=1 Matheis, F. Muller, P. A. Graves, C. L. Gabanyi, I. Kerner, Z. J. Costa-Borges, D. Mucida, D. 2019-02-21 doi:10.1101/556340 Cold Spring Harbor Laboratory Press 2019-02-21 <![CDATA[ Discovery of conformation-sensitive anti-amyloid protofibril monoclonal antibodies using an engineered chaperone-like amyloid-binding protein ]]> https://biorxiv.org/content/10.1101/558809v1?rss=1 Graham, W. V. Bonito-Oliva, A. Agostinelli, R. Karim, R. Deguzman, J. Kelleher, K. Petro, M. Lindstrom, A.-K. Graff, C. Wood, K. M. Tchistiakova, L. Marquette, K. Wes, P. D. Sakmar, T. P. 2019-02-24 doi:10.1101/558809 Cold Spring Harbor Laboratory Press 2019-02-24 <![CDATA[ Substrate Affinity and Specificity of the ScSth1p Bromodomain Are Fine-Tuned for Versatile Histone Recognition ]]> https://biorxiv.org/content/10.1101/559005v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@10c54b3org.highwire.dtl.DTLVardef@8cb555org.highwire.dtl.DTLVardef@1d4ef1eorg.highwire.dtl.DTLVardef@9eaf00_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG ]]> Blus, B. Hashimoto, H. Seo, H.-S. Krolak, A. Debler, E. 2019-02-25 doi:10.1101/559005 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ New transcriptional circuit evolved by coding sequence changes in a master regulator followed by cis-regulatory changes in its target genes ]]> https://biorxiv.org/content/10.1101/565234v1?rss=1 Britton, C. S. Sorrells, T. R. Johnson, A. D. 2019-03-01 doi:10.1101/565234 Cold Spring Harbor Laboratory Press 2019-03-01 <![CDATA[ Afucosylated maternal anti-dengue IgGs are a biomarker for susceptibility to dengue disease in their infants ]]> https://biorxiv.org/content/10.1101/565259v1?rss=1 Thulin, N. K. Brewer, R. C. Sherwood, R. Bournazos, S. Edwards, K. G. Ramadoss, N. S. Taubenberger, J. K. Memoli, M. Jagannathan, P. Zhang, S. Libraty, D. H. Wang, T. T. 2019-03-06 doi:10.1101/565259 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ High-Affinity Binding of Chemokine Analogs that Display Ligand Bias at the HIV-1 Co-receptor CCR5 ]]> https://biorxiv.org/content/10.1101/575795v1?rss=1 Rico, C. A. Berchiche, Y. A. Horioka, M. Peeler, J. C. Lorenzen, E. Tian, H. Kazmi, M. A. Furstenberg, A. Gaertner, H. Hartley, O. Sakmar, T. P. Huber, T. 2019-03-16 doi:10.1101/575795 Cold Spring Harbor Laboratory Press 2019-03-16 <![CDATA[ Germline genetic determination of cancer progression and survival ]]> https://biorxiv.org/content/10.1101/576181v1?rss=1 APOE3 > APOE4, revealing causal regulation of progression by APOE variants. Mechanistically, recombinant ApoE protein variants differentially suppressed melanoma cell invasion and endothelial recruitment phenotypes. Moreover, tumors in APOE4 mice exhibited greater immune cell infiltration and activation relative to tumors of APOE2 mice. These findings support the notion that human germline genetic makeup can impact the trajectory of a future malignancy. ]]> Ostendorf, B. N. Tafreshian, K. N. Adaku, N. Bilanovic, J. Tavora, B. Tavazoie, S. F. 2019-03-13 doi:10.1101/576181 Cold Spring Harbor Laboratory Press 2019-03-13 <![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[ MeCP2 nuclear dynamics in live neurons results from low and high affinity chromatin interactions ]]> https://biorxiv.org/content/10.1101/586867v1?rss=1 Piccolo, F. Liu, Z. Dong, P. Hsu, C.-L. Stoyanova, E. I. Rao, A. Tjian, R. Heintz, N. 2019-03-23 doi:10.1101/586867 Cold Spring Harbor Laboratory Press 2019-03-23 <![CDATA[ Statistical Analysis of Variability in TnSeq Data Across Conditions Using Zero-Inflated Negative Binomial Regression ]]> https://biorxiv.org/content/10.1101/590281v1?rss=1 Subramaniyam, S. DeJesus, M. A. Saveri, A. Smith, C. M. Baker, R. E. Ehrt, S. Schnappinger, D. Sassetti, C. M. Ioerger, T. R. 2019-03-28 doi:10.1101/590281 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ Multiplexed Analysis of the Secretin-like GPCR-RAMP Interactome ]]> https://biorxiv.org/content/10.1101/597690v1?rss=1 Lorenzen, E. Dodig-Crnkovic, T. Kotliar, I. B. Pin, E. Ceraudo, E. Vaughan, R. D. Uhlen, M. Huber, T. Schwenk, J. M. Sakmar, T. P. 2019-04-06 doi:10.1101/597690 Cold Spring Harbor Laboratory Press 2019-04-06 <![CDATA[ Single-molecule imaging of eukaryotic replisomes reveals compositional plasticity ]]> https://biorxiv.org/content/10.1101/602086v1?rss=1 Lewis, J. S. Spenkelink, L. M. Schauer, G. D. Yurieva, O. Natarajan, V. Kaur, G. Maher, C. Kay, C. O'Donnell, M. E. van Oijen, A. M. 2019-04-08 doi:10.1101/602086 Cold Spring Harbor Laboratory Press 2019-04-08 <![CDATA[ Natural hypothalamic circuit dynamics underlying object memorization ]]> https://biorxiv.org/content/10.1101/603936v1?rss=1 Kosse, C. Burdakov, D. 2019-04-11 doi:10.1101/603936 Cold Spring Harbor Laboratory Press 2019-04-11 <![CDATA[ Machine Source Localization of Tursiops Truncatus Whistle-like Sounds in a Reverberant Aquatic Environment ]]> https://biorxiv.org/content/10.1101/606673v1?rss=1 Woodward, S. F. Reiss, D. Magnasco, M. 2019-04-11 doi:10.1101/606673 Cold Spring Harbor Laboratory Press 2019-04-11 <![CDATA[ Mapping interactions of microbial metabolites and human receptors ]]> https://biorxiv.org/content/10.1101/614537v1?rss=1 Colosimo, D. A. Kohn, J. A. Luo, P. M. Han, S. M. Pickard, A. J. Rao, A. Cross, J. R. Cohen, L. J. Brady, S. F. 2019-05-02 doi:10.1101/614537 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Mapping cell migrations and fates from a gastruloid model to the human primitive streak ]]> https://biorxiv.org/content/10.1101/616227v1?rss=1 Martyn, I. Siggia, E. Brivanlou, A. 2019-04-23 doi:10.1101/616227 Cold Spring Harbor Laboratory Press 2019-04-23 <![CDATA[ Hindbrain V2a neurons impose rhythmic activity on motor neurons in an in vitro reticulospinal circuit ]]> https://biorxiv.org/content/10.1101/620674v1?rss=1 Bubnys, A. Kandel, H. Kow, L.-M. Pfaff, D. W. Tabansky, I. 2019-04-26 doi:10.1101/620674 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Novel Pure αVβ3 Integrin Antagonists That Do Not Induce Receptor Extension, Prime the Receptor, or Enhance Angiogenesis at Low Concentrations ]]> https://biorxiv.org/content/10.1101/620765v1?rss=1 Li, J. Fukase, Y. Shang, Y. Zou, W. Munoz-Felix, J. Buitrago, L. van Agthoven, J. Zhang, Y. Hara, R. Tanaka, Y. Okamoto, R. Yasui, T. Nakahata, T. Imaeda, T. Aso, K. Zhou, Y. Locuson, C. Nesic, D. Duggan, M. Takagi, J. Vaughan, R. Walz, T. Hodivala-Dilke, K. Teitelbaum, S. L. Arnaout, M. A. Filizola, M. Foley, M. A. Coller, B. S. 2019-05-02 doi:10.1101/620765 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Rewiring of transcriptional networks as a major event leading to the diversity of asexual multicellularity in fungi ]]> https://biorxiv.org/content/10.1101/627414v1?rss=1 Etxebeste, O. Otamendi, A. Garzia, A. Espeso, E. A. Cortese, M. S. 2019-05-07 doi:10.1101/627414 Cold Spring Harbor Laboratory Press 2019-05-07 <![CDATA[ Nonreciprocal and Conditional Cooperativity Directs the Pioneer Activity of Pluripotency Transcription Factors ]]> https://biorxiv.org/content/10.1101/633826v1?rss=1 Li, S. Zheng, E. B. Zhao, L. Liu, S. 2019-05-09 doi:10.1101/633826 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Quadruplex qPCR for qualitative and quantitative analysis of the HIV-1 latent reservoir ]]> https://biorxiv.org/content/10.1101/641951v1?rss=1 Gaebler, C. Cetrulo Lorenzi, J. C. Oliveira, T. Y. Nogueira, L. Ramos, V. Lu, C.-L. Pai, J. A. Mendoza, P. Jankovic, M. Caskey, M. Nussenzweig, M. C. 2019-05-31 doi:10.1101/641951 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Performance Evaluation of Traditional Signal Processing Methods in Localizing Tursiops truncatus Whistles in a Reverberant Aquatic Environment ]]> https://biorxiv.org/content/10.1101/642736v1?rss=1 Woodward, S. F. Magnasco, M. 2019-05-20 doi:10.1101/642736 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ A single light-responsive sizer can control multiple-fission cycles in Chlamydomonas ]]> https://biorxiv.org/content/10.1101/648436v1?rss=1 nView larger version (35K):norg.highwire.dtl.DTLVardef@48f9corg.highwire.dtl.DTLVardef@170625eorg.highwire.dtl.DTLVardef@14a20a0org.highwire.dtl.DTLVardef@1a3ff9a_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIG1-sizer and S/M-oscillator can give rise to multiple-fission cycles in ChlamydomonasnC_LIO_LILight-responsive bistable switch may guard transition between G1 and S/M-cyclesnC_LIO_LIIllumination increases S/M-entry threshold, causing multiple-fission cyclesnC_LIO_LIDark shift lowers S/M-entry threshold, allowing small cells to commit to fewer divisionsnC_LI ]]> Heldt, F. S. Tyson, J. J. Cross, F. R. Novak, B. 2019-05-27 doi:10.1101/648436 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Copulas reveal complex and informative dependencies propagating throughout ecology ]]> https://biorxiv.org/content/10.1101/650838v1?rss=1 Ghosh, S. Sheppard, L. W. Holder, M. T. Loecke, T. E. Reid, P. C. Bever, J. D. Reuman, D. C. 2019-05-27 doi:10.1101/650838 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Uveal Melanoma Oncogene CYSLTR2 Encodes a Constitutively Active GPCR Highly Biased Toward Gq Signaling ]]> https://biorxiv.org/content/10.1101/663153v1?rss=1 Ceraudo, E. Horioka, M. Mattheisen, J. M. Hitchman, T. D. Moore, A. R. Kazmi, M. A. Chi, P. Chen, Y. Sakmar, T. P. Huber, T. 2019-06-06 doi:10.1101/663153 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Vesicular stomatitis virus transcription is inhibited by TRIM69 in the interferon-induced antiviral state ]]> https://biorxiv.org/content/10.1101/683292v1?rss=1 Kueck, T. Bloyet, L.-M. Cassella, E. Zang, T. Schmidt, F. Brusic, V. Tekes, G. Pornillos, O. Whelan, S. Bieniasz, P. D. 2019-06-27 doi:10.1101/683292 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Lateral septum neurotensin neurons link stress and anorexia ]]> https://biorxiv.org/content/10.1101/683946v1?rss=1 Azevedo, E. Tan, B. Pomeranz, L. Schneeberger, M. Fetcho, R. Doerig, K. Liston, C. Friedman, J. Stern, S. 2019-06-27 doi:10.1101/683946 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ A molecularly defined insular cortex --> central amygdala circuit mediates conditioned overconsumption of food. ]]> https://biorxiv.org/content/10.1101/684498v1?rss=1 Stern, S. Pomeranz, L. Azevedo, E. Doerig, K. Friedman, J. 2019-06-27 doi:10.1101/684498 central amygdala circuit mediates conditioned overconsumption of food.]]> Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Molecular tuning of the axonal mitochondrial Ca2+ uniporter ensures metabolic flexability of neurotransmission ]]> https://biorxiv.org/content/10.1101/685859v1?rss=1 Ashrafi, G. de Juan-Sanz, J. Farrell, R. Ryan, T. A. 2019-06-28 doi:10.1101/685859 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Regulation of Numb during planar cell polarity establishment in the Drosophila eye ]]> https://biorxiv.org/content/10.1101/686840v1?rss=1 Domingos, P. M. Jenny, A. del Alamo, D. Mlodzik, M. Steller, H. Mollereau, B. 2019-06-28 doi:10.1101/686840 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Histone methyltransferase MMSET/NSD2 is essential for generation of B1 cell compartment in mice ]]> https://biorxiv.org/content/10.1101/687806v1?rss=1 Dobenecker, M.-W. Yurchenko, V. Marcello, J. Becker, A. Rudensky, E. Bahnu, N. Carrol, T. Garcia, B. Rosenberg, B. Prinjha, R. Tarakhovsky, A. 2019-07-02 doi:10.1101/687806 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila ]]> https://biorxiv.org/content/10.1101/689687v1?rss=1 Witt, E. Benjamin, S. Svetec, N. Zhao, L. 2019-07-02 doi:10.1101/689687 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Metabolic signature in nucleus accumbens for anti-depressant-like effects of acetyl-L-carnitine: An in vivo 1H-magnetic resonance spectroscopy study at 14 T ]]> https://biorxiv.org/content/10.1101/690768v1?rss=1 Cherix, A. Larrieu, T. Grosse, J. Rodrigues, J. McEwen, B. Nasca, C. Gruetter, R. Sandi, C. 2019-07-02 doi:10.1101/690768 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Chemogenetic evidence that rapid neuronal de novo protein synthesis is required for consolidation of long-term memory ]]> https://biorxiv.org/content/10.1101/704965v1?rss=1 Shrestha, P. Ayata, P. Herrero Vidal, P. M. Longo, F. Gastone, A. LeDoux, J. Heintz, N. Klann, E. 2019-07-17 doi:10.1101/704965 Cold Spring Harbor Laboratory Press 2019-07-17 <![CDATA[ The proteasome regulator PI31 is required for protein homeostasis, synapse maintenance and neuronal survival in mice ]]> https://biorxiv.org/content/10.1101/711515v1?rss=1 Minis, A. Rodriguez, J. A. Levin, A. Liu, K. Govek, E.-E. Hatten, M. E. Steller, H. 2019-07-22 doi:10.1101/711515 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ The mechanosensitive ion channel TRAAK is localized to the mammalian node of Ranvier ]]> https://biorxiv.org/content/10.1101/713990v1?rss=1 Brohawn, S. G. Wang, W. Schwarz, J. R. Handler, A. Campbell, E. B. MacKinnon, R. 2019-07-25 doi:10.1101/713990 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ Symmetry breaking during morphogenesis of a mechanosensory organ ]]> https://biorxiv.org/content/10.1101/718502v1?rss=1 Erzberger, A. Jacobo, A. Dasgupta, A. Hudspeth, A. J. 2019-07-30 doi:10.1101/718502 Cold Spring Harbor Laboratory Press 2019-07-30 <![CDATA[ The Habenular Receptor GPR151 Regulates Addiction Vulnerability Across Drug Classes ]]> https://biorxiv.org/content/10.1101/720508v1?rss=1 Antolin-Fontes, B. Li, K. Ables, J. L. Riad, M. H. Gorlich, A. Williams, M. Wang, C. Lipford, S. M. Dao, M. Molina, H. Liu, J. Kenny, P. J. Ibanez-Tallon, I. 2019-07-31 doi:10.1101/720508 Cold Spring Harbor Laboratory Press 2019-07-31 <![CDATA[ APOBEC3B-dependent kataegis and TREX1-driven chromothripsis in telomere crisis ]]> https://biorxiv.org/content/10.1101/725366v1?rss=1 Maciejowski, J. Chatzipli, A. Dananberg, A. de Lange, T. Campbell, P. 2019-08-05 doi:10.1101/725366 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ Reliability of an interneuron response depends on an integrated sensory state ]]> https://biorxiv.org/content/10.1101/726083v1?rss=1 Bargmann, C. I. Dobosiewicz, M. 2019-08-05 doi:10.1101/726083 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ Structural basis for transcription activation by Crl through tethering of σS and RNA polymerase ]]> https://biorxiv.org/content/10.1101/726851v1?rss=1 Cartagena, A. J. Banta, A. B. Sathyan, N. Ross, W. Gourse, R. L. Campbell, E. A. Darst, S. A. 2019-08-06 doi:10.1101/726851 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era ]]> https://biorxiv.org/content/10.1101/730531v1?rss=1 Armstrong, J. Hickey, G. Diekhans, M. Deran, A. Fang, Q. Xie, D. Feng, S. Stiller, J. Genereux, D. Johnson, J. Marinescu, V. D. Haussler, D. Alföldi, J. Lindblad-Toh, K. Karlsson, E. Zhang, G. Paten, B. 2019-08-09 doi:10.1101/730531 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ MKPV (aka MuCPV) and related chapparvoviruses are nephro-tropic and encode novel accessory proteins p15 and NS2 ]]> https://biorxiv.org/content/10.1101/732537v1?rss=1 60% amino acid identity to MKPV. We show that MKPV is kidney-tropic and that the bat chapparvovirus DrPV-1 and a non-human primate chapparvovirus, CKPV, are also found in the kidneys of their hosts. We propose, therefore, that chapparvoviruses with >60% VP1 amino acid identity to MKPV be classified into a genus dubbed Nephroparvovirus, which is consistent with nomenclature for the genus Erythroparvovirus. ]]> Jolly, C. J. Lee, Q. Padula, M. P. Pinello, N. Williams, S. H. O'Rourke, M. B. Fumagalli, M. J. Orkin, J. D. Shaban, B. Brenner, O. Weninger, W. Souza, W. M. d. Melin, A. D. Wong, J. J.- L. Crim, M. J. Monette, S. Roediger, B. 2019-08-15 doi:10.1101/732537 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Early post-zygotic mutations contribute to congenital heart disease ]]> https://biorxiv.org/content/10.1101/733105v1?rss=1 Hsieh, A. Morton, S. U. Willcox, J. A. Gorham, J. M. Tai, A. C. Qi, H. DePalma, S. McKean, D. Griffin, E. Manheimer, K. B. Bernstein, D. Kim, R. W. Newburger, J. W. Porter, G. A. Srivastava, D. Tristani-Firouzi, M. Brueckner, M. Lifton, R. P. Goldmuntz, E. Gelb, B. D. Chung, W. K. Seidman, C. Seidman, J. G. Shen, Y. 2019-08-13 doi:10.1101/733105 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Ctf4 organizes sister replisomes and Pol α into a replication factory ]]> https://biorxiv.org/content/10.1101/735746v1?rss=1 Yuan, Z. Georgescu, R. Almeida Santos, R. d. L. Zhang, D. Bai, L. Yao, N. Y. Zhao, G. O'Donnell, M. E. Li, H. 2019-08-15 doi:10.1101/735746 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ DNA unwinding mechanism of a eukaryotic replicative CMG helicase ]]> https://biorxiv.org/content/10.1101/737015v1?rss=1 Yuan, Z. Georgescu, R. Bai, L. Zhang, D. Li, H. O'Donnell, M. 2019-08-15 doi:10.1101/737015 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Supporting evidence for DNA shearing as a mechanism for origin unwinding in eukaryotes ]]> https://biorxiv.org/content/10.1101/739557v1?rss=1 Langston, L. D. Georgescu, R. O'Donnell, M. E. 2019-08-19 doi:10.1101/739557 Cold Spring Harbor Laboratory Press 2019-08-19 <![CDATA[ LINE-1 ORF2P EXPRESSION IS NEARLY IMPERCEPTIBLE IN HUMAN CANCERS ]]> https://biorxiv.org/content/10.1101/744425v1?rss=1 Ardeljan, D. Wang, X. Oghbaie, M. Taylor, M. S. Husband, D. Deshpande, V. Steranka, J. P. Gorbounov, M. Yang, W. R. Sie, B. Larman, H. B. Jiang, H. Molloy, K. R. Altukhov, I. Li, Z. McKerrow, W. Fenyo, D. Burns, K. H. LaCava, J. 2019-08-22 doi:10.1101/744425 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Complex+: Aided Decision-Making for the Study of Protein Complexes ]]> https://biorxiv.org/content/10.1101/744656v1?rss=1 Oghbaie, M. Sulc, P. Fenyo, D. Pennock, M. LaCava, J. 2019-08-22 doi:10.1101/744656 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ New additions to the CRISPR toolbox: CRISPR-CLONInG and CRISPR-CLIP ]]> https://biorxiv.org/content/10.1101/746826v1?rss=1 Shola, D. T. N. 2019-09-05 doi:10.1101/746826 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Expansion of CRISPR loci with multiple memories of infection enables the survival of structured bacterial communities ]]> https://biorxiv.org/content/10.1101/747212v1?rss=1 Pyenson, N. C. Marraffini, L. A. 2019-08-26 doi:10.1101/747212 Cold Spring Harbor Laboratory Press 2019-08-26 <![CDATA[ Serotonin receptor 4 in mature excitatory hippocampal neurons modulates mood and anxiety ]]> https://biorxiv.org/content/10.1101/758151v1?rss=1 Karayol, R. Medrihan, L. Warner-Schmidt, J. L. Rao, M. N. Holzner, E. B. Greengard, P. Heintz, N. Schmidt, E. F. 2019-09-04 doi:10.1101/758151 Cold Spring Harbor Laboratory Press 2019-09-04 <![CDATA[ Lineage-specific control of convergent cell identity by a Forkhead repressor ]]> https://biorxiv.org/content/10.1101/758508v1?rss=1 Mizeracka, K. Rogers, J. M. Shaham, S. Bulyk, M. L. Heiman, M. G. 2019-09-05 doi:10.1101/758508 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ FMRP binding to a ranked subset of long genes is revealed by coupled CLIP and TRAP in specific neuronal cell types ]]> https://biorxiv.org/content/10.1101/762500v1?rss=1 Van Driesche, S. J. Sawicka, K. Zhang, C. Hung, S. K. Y. Park, C. Y. Fak, J. J. Yang, C. Darnell, R. B. Darnell, J. C. 2019-09-09 doi:10.1101/762500 Cold Spring Harbor Laboratory Press 2019-09-09 <![CDATA[ Induced RPB1 depletion reveals a direct gene-specific control of RNA Polymerase III function by RNA Polymerase II ]]> https://biorxiv.org/content/10.1101/764605v1?rss=1 Gerber, A. Ito, K. Chu, C.-S. Roeder, R. G. 2019-09-10 doi:10.1101/764605 Cold Spring Harbor Laboratory Press 2019-09-10 <![CDATA[ E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation and dynamics ]]> https://biorxiv.org/content/10.1101/766725v1?rss=1 Chen, J. Gopalkrishnan, S. Chiu, C. Chen, A. Y. Campbell, E. A. Gourse, R. L. Ross, W. Darst, S. A. 2019-09-12 doi:10.1101/766725 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Clinical severity in Fanconi anemia correlates with residual function of FANCB missense variants ]]> https://biorxiv.org/content/10.1101/772574v1?rss=1 Jung, M. Ramanagoudr-Bhojappa, R. van Twest, S. Ozgur Rosti, R. Murphy, V. J. Tan, W. Donovan, F. Lach, F. Kimble, D. Jiang, C. Vaughan, R. Mehta, P. Pierri, F. Doufour, C. Auerbach, A. D. Deans, A. J. Smogorzewska, A. Chandrasekharappa, S. C. 2019-09-18 doi:10.1101/772574 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Gene Knock Up via 3’UTR editing to study gene function in vivo ]]> https://biorxiv.org/content/10.1101/775031v1?rss=1 Mätlik, K. Olfat, S. Garton, D. R. Montano-Rodriguez, A. Turconi, G. Porokuokka, L. L. Panhelainen, A. Schweizer, N. Kopra, J. Cowlishaw, M. C. Piepponen, T. P. Zhang, F.-P. Sipilä, P. Jakobsson, J. Andressoo, J.-O. 2019-09-23 doi:10.1101/775031 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ Increasing demand for plasma membrane contributes to the energetic cost of early zebrafish embryogenesis. ]]> https://biorxiv.org/content/10.1101/775114v1?rss=1 Rodenfels, J. Sartori, P. Golfier, S. Nagendra, K. Neugebauer, K. Howard, J. 2019-09-18 doi:10.1101/775114 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Presynaptic developmental plasticity allows robust sparse wiring of the Drosophila mushroom body ]]> https://biorxiv.org/content/10.1101/782961v1?rss=1 Clowney, E. J. Elkahlah, N. A. Rogow, J. A. 2019-09-26 doi:10.1101/782961 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Reduced Kv3.1 Activity in Dentate Gyrus Parvalbumin Cells Induces Vulnerability to Depression. ]]> https://biorxiv.org/content/10.1101/784090v1?rss=1 Medrihan, L. Umschweif, G. Sinha, A. Reed, S. Gindinova, K. Sinha, S. C. Greengard, P. Sagi, Y. 2019-09-26 doi:10.1101/784090 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ KV1.2 channels inactivate through a mechanism similar to C-type inactivation ]]> https://biorxiv.org/content/10.1101/784249v1?rss=1 Suarez-Delgado, E. Rangel-Sandin, T. G. Ishida, I. G. Rangel-Yescas, G. E. Rosenbaum, T. Islas, L. D. 2019-09-26 doi:10.1101/784249 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ An RNA-based system to study hepatitis B virus replication and select drug-resistance mutations ]]> https://biorxiv.org/content/10.1101/787630v1?rss=1 Yu, Y. Schneider, W. M. Michailidis, E. Acevedo, A. Ni, Y. Ambrose, P. Zou, C. Kabbani, M. Quirk, C. Jahan, C. Wu, X. Urban, S. Shlomai, A. de Jong, Y. P. Rice, C. M. 2019-10-02 doi:10.1101/787630 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ SPARC: a method to genetically manipulate precise proportions of cells. ]]> https://biorxiv.org/content/10.1101/788679v1?rss=1 Isaacman-Beck, J. Paik, K. C. Wienecke, C. F. R. Yang, H. H. Fisher, Y. E. Wang, I. E. Ishida, I. G. Maimon, G. Wilson, R. I. Clandinin, T. R. 2019-09-30 doi:10.1101/788679 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ Cleavage-furrow formation without F-actin in Chlamydomonas ]]> https://biorxiv.org/content/10.1101/789016v1?rss=1 Onishi, M. Umen, J. G. Cross, F. R. Pringle, J. R. 2019-10-01 doi:10.1101/789016 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Human blood exposure to Clostridium perfringens epsilon toxin may shed light on erythrocyte fragility during active multiple sclerosis ]]> https://biorxiv.org/content/10.1101/789123v1?rss=1 Fischetti, V. A. eleso, O. E. Rumah, K. R. 2019-10-01 doi:10.1101/789123 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Patterns of purifying selection in marine microbes reveal optimization in the genetic code ]]> https://biorxiv.org/content/10.1101/790345v1?rss=1 Shenhav, L. Zeevi, D. 2019-10-02 doi:10.1101/790345 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ PRC2 bridges non-adjacent nucleosomes to establish heterochromatin ]]> https://biorxiv.org/content/10.1101/795260v1?rss=1 Leicher, R. Ge, E. J. Lin, X. Reynolds, M. J. Walz, T. Zhang, B. Muir, T. W. Liu, S. 2019-10-07 doi:10.1101/795260 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Phosphorylation of the ancestral histone variant H3.3 amplifies stimulation-induced transcription ]]> https://biorxiv.org/content/10.1101/808048v1?rss=1 Armache, A. Yang, S. Robbins, L. E. Durmaz, C. Daman, A. W. Jeong, J. Q. Martinez de Paz, A. Ravishankar, A. Arslan, T. Lin, S. Panchenko, T. Garcia, B. A. Hake, S. Li, H. Allis, C. D. Josefowicz, S. Z. 2019-10-17 doi:10.1101/808048 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Distinct roles of BRCA2 in replication fork protection in response to hydroxyurea and DNA interstrand crosslinks ]]> https://biorxiv.org/content/10.1101/811968v1?rss=1 Rickman, K. A. Noonan, R. Lach, F. P. Sridhar, S. Wang, A. T. Abhyankar, A. Kelly, M. Auerbach, A. D. Smogorzewska, A. 2019-10-28 doi:10.1101/811968 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ Common homozygosity for predicted loss-of-function variants reveals both redundant and advantageous effects of dispensable human genes ]]> https://biorxiv.org/content/10.1101/819615v1?rss=1 Rausell, A. Luo, Y. Lopez, M. Seeleuthner, Y. Rapaport, F. Favier, A. Stenson, P. D. Cooper, D. N. Patin, E. Casanova, J.-L. Quintana-Murci, L. Abel, L. 2019-10-28 doi:10.1101/819615 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ Asymmetric molecular architecture of the human γ-tubulin ring complex ]]> https://biorxiv.org/content/10.1101/820142v1?rss=1 100,000 [A]2) surfaces that could interact with different regulatory factors. We also identify an unanticipated structural bridge that includes an actin-like protein and spans the{gamma} -TuRC lumen. Despite its asymmetric composition and architecture, the human{gamma} -TuRC arranges{gamma} -tubulins into a helical geometry poised to nucleate microtubules. The observed compositional complexity of the{gamma} -TuRC could self-regulate its assembly into a cone-shaped structure to control microtubule formation across diverse contexts, e.g. within biological condensates 8 or alongside existing filaments 9. ]]> Wieczorek, M. Urnavicius, L. Ti, S.-C. Molloy, K. R. Chait, B. T. Kapoor, T. M. 2019-10-25 doi:10.1101/820142 Cold Spring Harbor Laboratory Press 2019-10-25 <![CDATA[ Allosteric coupling between alpha-rings of the 20S proteasome ]]> https://biorxiv.org/content/10.1101/832113v1?rss=1 Yu, Z. Yu, Y. Wang, F. Myasnikov, A. G. Coffino, P. Cheng, Y. 2019-11-07 doi:10.1101/832113 Cold Spring Harbor Laboratory Press 2019-11-07 <![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[ Cerebellar neurodynamics during motor planning predict decision timing and outcome on single-trial level ]]> https://biorxiv.org/content/10.1101/833889v1?rss=1 Lin, Q. Helmreich, M. Schlumm, F. Li, J. Robson, D. Engert, F. Schier, A. Noebauer, T. Vaziri, A. 2019-11-11 doi:10.1101/833889 Cold Spring Harbor Laboratory Press 2019-11-11 <![CDATA[ Novel patterns of complex structural variation revealed across thousands of cancer genome graphs ]]> https://biorxiv.org/content/10.1101/836296v1?rss=1 Hadi, K. Yao, X. Behr, J. M. Deshpande, A. Xanthopoulakis, C. Rosiene, J. Darmofal, M. Tian, H. DeRose, J. Mortensen, R. Adney, E. Gajic, Z. Eng, K. Wala, J. A. Wrzeszczynski, K. O. Arora, K. Shah, M. Emde, A.-K. Felice, V. Frank, M. O. Darnell, R. Ghandi, M. Huang, F. Maciejowski, J. De Lange, T. Setton, J. Riaz, N. Reis-Filho, J. S. Powell, S. Knowles, D. Reznik, E. Mishra, B. Beroukhim, R. Zody, M. Robine, N. Oman, K. Sanchez, C. A. Kuhner, M. K. Smith, L. P. Galipeau, P. C. Paulson, T. G. Reid, B. J. Li, X. Wilkes, D. Sboner, A. Mosquera, J. M. 2019-11-09 doi:10.1101/836296 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Six new reference-quality bat genomes illuminate the molecular basis and evolution of bat adaptations ]]> https://biorxiv.org/content/10.1101/836874v1?rss=1 99%) mammalian BUSCO genes. Phylogenetic analyses of 12,931 protein coding-genes and 10,857 conserved non-coding elements identified across 48 mammalian genomes helped to resolve bats closest extant relatives within Laurasiatheria, supporting a basal position for bats within Scrotifera. Genome-wide screens along the bat ancestral branch revealed (a) selection on hearing-involved genes (e.g LRP2, SERPINB6, TJP2), which suggest that laryngeal echolocation is a shared ancestral trait of bats; (b) selection (e.g INAVA, CXCL13, NPSR1) and loss of immunity related proteins (e.g. LRRC70, IL36G), including pro-inflammatory NF-kB signalling; and (c) expansion of the APOBEC family, associated with restricting viral infection, transposon activity and interferon signalling. We also identified unique integrated viruses, indicating that bats have a history of tolerating viral pathogens, lethal to other mammal species. Non-coding RNA analyses identified variant and novel microRNAs, revealing regulatory relationships that may contribute to phenotypic diversity in bats. Together, our reference-quality genomes, high-quality annotations, genome-wide screens and in-vitro tests revealed previously unknown genomic adaptations in bats that may explain their extraordinary traits. ]]> Jebb, D. Huang, Z. Pippel, M. Hughes, G. M. Lavrichenko, K. Devanna, P. Winkler, S. Jermiin, L. S. Skirmuntt, E. C. Katzourakis, A. Burkitt-Gray, L. Ray, D. A. Sullivan, K. A. Roscito, J. G. Kirilenko, B. M. Davalos, L. M. Corthals, A. P. Power, M. Jones, G. Ransome, R. D. Dechmann, D. Locatelli, A. G. Puechmaille, S. J. Fedrigo, O. Jarvis, E. D. Springer, M. S. Hiller, M. Vernes, S. C. Myers, E. W. Teeling, E. C. 2019-11-09 doi:10.1101/836874 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Nova proteins direct synaptic integration of somatostatin interneurons through activity-dependent alternative splicing ]]> https://biorxiv.org/content/10.1101/845230v1?rss=1 Fishell, G. Wamsley, B. Ibrahim, L. A. Yusuf, N. Fisher, E. Jaglin, X. H. Xu, Q. Gao, L. Khodadadi-Jamayran, A. Favuzzi, E. Yuan, Y. Darnell, R. Dimidschstein, J. 2019-11-16 doi:10.1101/845230 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ A lymphatic-stem cell interactome regulates intestinal stem cell activity ]]> https://biorxiv.org/content/10.1101/2022.01.29.478341v1?rss=1 Niec, R. Chu, T. Gur-Cohen, S. Schernthanner, M. Hidalgo, L. Pasolli, H. A. Kataru, R. Mehrara, B. Pe'er, D. Fuchs, E. 2022-01-30 doi:10.1101/2022.01.29.478341 Cold Spring Harbor Laboratory Press 2022-01-30 <![CDATA[ Conserved Neutralizing Epitopes on the N-Terminal Domain of Variant SARS-CoV-2 Spike Proteins ]]> https://biorxiv.org/content/10.1101/2022.02.01.478695v1?rss=1 Wang, Z. Muecksch, F. Cho, A. Gaebler, C. Hoffmann, H.-H. Ramos, V. Zong, S. Cipolla, M. Johnson, B. Schmidt, F. DaSilva, J. Bednarski, E. Tanfous, T. B. Raspe, R. Yao, K. Lee, Y. E. Chen, T. Turroja, M. Millard, K. G. Dizon, J. Kaczynska, A. Gazumyan, A. Oliveira, T. Y. Rice, C. M. Caskey, M. Bieniasz, P. D. Hatziioannou, T. Barnes, C. O. Nussenzweig, M. C. 2022-02-01 doi:10.1101/2022.02.01.478695 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Chromatin sequesters pioneer transcription factor Sox2 from exerting force on DNA ]]> https://biorxiv.org/content/10.1101/2022.02.02.478883v1?rss=1 Nguyen, T. Li, S. Chang, J. Watters, J. Ng, H. Osunsade, A. David, Y. Liu, S. 2022-02-03 doi:10.1101/2022.02.02.478883 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Cryomilling Tethered Chromatin Conformation Capture reveal new insights into inter-chromosomal interactions ]]> https://biorxiv.org/content/10.1101/2022.02.03.478915v1?rss=1 Xu, J. Kumar, S. Hua, N. Kou, Y. Lei, X. Aitchison, J. Rout, M. Alber, F. Chen, L. 2022-02-04 doi:10.1101/2022.02.03.478915 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ A novel 5' DNA binding site in RFC facilitates PCNA loading for gap DNA repair ]]> https://biorxiv.org/content/10.1101/2022.02.04.479194v1?rss=1 Zhang, F. Georgescue, R. Yao, N. Y. Li, H. O'Donnell, M. E. 2022-02-05 doi:10.1101/2022.02.04.479194 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ Metabolic-scale gene activation screens identify SLCO2B1 as a heme transporter that enhances cellular iron availability ]]> https://biorxiv.org/content/10.1101/2022.02.06.479330v1?rss=1 Unlu, G. Prizer, B. Erdal, R. Yeh, H.-W. Bayraktar, E. C. Birsoy, K. 2022-02-07 doi:10.1101/2022.02.06.479330 Cold Spring Harbor Laboratory Press 2022-02-07 <![CDATA[ Antiviral DExD/H-box helicase 60 selectively inhibits translation from type II internal ribosome entry sites ]]> https://biorxiv.org/content/10.1101/2022.02.08.479557v1?rss=1 Sadic, M. Schneider, W. M. Katsara, O. Medina, G. N. Mogulothu, A. Yu, Y. Gu, M. de los Santos, T. Schneider, R. J. Dittmann, M. 2022-02-08 doi:10.1101/2022.02.08.479557 Cold Spring Harbor Laboratory Press 2022-02-08 <![CDATA[ Epigenetic Memory of COVID-19 in Innate Immune Cells and Their Progenitors ]]> https://biorxiv.org/content/10.1101/2022.02.09.479588v1?rss=1 View larger version (54K): org.highwire.dtl.DTLVardef@1ffe42dorg.highwire.dtl.DTLVardef@dd4868org.highwire.dtl.DTLVardef@1bcae8borg.highwire.dtl.DTLVardef@674e85_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cheong, J. G. Ravishankar, A. Sharma, S. Parkhurst, C. Nehar-Belaid, D. Ma, S. Paddock, L. Fatou, B. Karakaslar, E. Thibodeau, A. Bale, M. Kartha, V. Yee, J. Mays, M. Y. Leyre, L. Martinez de Paz, A. Daman, A. Alvarez-Mulett, S. Robbins, L. LaFond, E. Weidman, K. Racine-Brzostek, S. Yang, H. Price, D. Jones, R. B. Schenck, E. Kaner, R. Chadburn, A. Zhao, Z. Steen, H. Pascual, V. Buenrostro, J. Niec, R. Lief, L. Ucar, D. Josefowicz, S. 2022-02-10 doi:10.1101/2022.02.09.479588 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Selective integration of diverse taste inputs within a single taste modality ]]> https://biorxiv.org/content/10.1101/2022.02.09.479727v1?rss=1 Deere, J. U. Uttley, H. A. Martinez Santana, N. Devineni, A. V. 2022-02-10 doi:10.1101/2022.02.09.479727 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ The integrated stress response remodels the microtubule organizing center to clear unfolded proteins following proteotoxic stress ]]> https://biorxiv.org/content/10.1101/2022.02.13.480280v1?rss=1 Fuchs, E. Hurwitz, B. Guzzi, N. Gola, A. Fiore, V. F. Sendoel, A. Nikolova, M. Barrows, D. Carroll, T. S. Pasolli, H. A. 2022-02-14 doi:10.1101/2022.02.13.480280 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Increased Potency and Breadth of SARS-CoV-2 Neutralizing Antibodies After a Third mRNA Vaccine Dose ]]> https://biorxiv.org/content/10.1101/2022.02.14.480394v1?rss=1 Muecksch, F. Wang, Z. Cho, A. Gaebler, C. Ben Tanfous, T. DaSilva, J. Bednarski, E. Ramos, V. Zong, S. Johnson, B. Raspe, R. Schaefer-Babajew, D. Shimeliovich, I. Daga, M. Yao, K.-H. Schmidt, F. Millard, K. G. Turroja, M. Jankovic, M. Oliveira, T. Y. Gazumyan, A. Caskey, M. Hatziioannou, T. Bieniasz, P. D. Nussenzweig, M. 2022-02-15 doi:10.1101/2022.02.14.480394 Cold Spring Harbor Laboratory Press 2022-02-15 <![CDATA[ Insulin/IGF Signaling Regulates Presynaptic Glutamate Release in Aversive Olfactory Learning ]]> https://biorxiv.org/content/10.1101/2022.02.14.480437v1?rss=1 Bargmann, C. I. Cheng, D. Lee, J. Ebert, M. Brown, M. Tomioka, M. Iino, Y. 2022-02-15 doi:10.1101/2022.02.14.480437 Cold Spring Harbor Laboratory Press 2022-02-15 <![CDATA[ Allosteric interactions prime androgen receptor dimerization and activation ]]> https://biorxiv.org/content/10.1101/2022.02.20.481229v1?rss=1 Wasmuth, E. Vanden Broeck, A. LaClair, J. R. Hoover, E. A. Lawrence, K. E. Paknejad, N. Pappas, K. J. Matthies, D. Wang, B. Feng, W. Watson, P. A. Zinder, J. C. Karthaus, W. de la Cruz, M. J. Hite, R. K. Manova-Todorova, K. Yu, Z. Weintraub, S. T. Klinge, S. Sawyers, C. 2022-02-21 doi:10.1101/2022.02.20.481229 Cold Spring Harbor Laboratory Press 2022-02-21 <![CDATA[ HIV-1 Vpu restricts Fc-mediated effector functions in vivo ]]> https://biorxiv.org/content/10.1101/2022.02.21.481308v1?rss=1 Prevost, J. Anand, S. P. Rajashekar, J. K. Richard, J. Goyette, G. Medjahed, H. Gendron-Lepage, G. Chen, H.-C. Chen, Y. Horwitz, J. A. Grunst, M. W. Zolla-Pazner, S. Haynes, B. F. Burton, D. R. Flavell, R. A. Kirchhoff, F. Hahn, B. H. Smith, A. B. Pazgier, M. Nussenzweig, M. C. Kumar, P. Finzi, A. 2022-02-22 doi:10.1101/2022.02.21.481308 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ A novel lineage of RORγt+Aire+ antigen presenting cells promotes peripheral generation of intestinal regulatory T cells and tolerance during early life ]]> https://biorxiv.org/content/10.1101/2022.02.26.481148v1?rss=1 Akagbosu, B. Tayyebi, Z. Shibu, G. Paucar Iza, Y. A. Deep, D. Franco Parisotto, Y. Pasolli, H. A. Elmentaite, R. Knott, M. Hemmers, S. Jahn, L. Friedrich, C. Verter, J. van den Brink, M. Gasteiger, G. Grünewald, T. G. P. Leslie, C. Rudensky, A. Y. Brown, C. C. 2022-03-01 doi:10.1101/2022.02.26.481148 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Rapidly evolving genes underlie Aedes aegypti mosquito reproductive resilience during drought ]]> https://biorxiv.org/content/10.1101/2022.03.01.482582v1?rss=1 Venkataraman, K. Shai, N. Lakhiani, P. Zylka, S. Zhao, J. Herre, M. Zeng, J. Neal, L. A. Molina, H. Zhao, L. Vosshall, L. B. 2022-03-02 doi:10.1101/2022.03.01.482582 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Distinct gene expression by expanded clones of quiescent memory CD4+ T cells harboring intact latent HIV-1 proviruses ]]> https://biorxiv.org/content/10.1101/2022.03.02.482683v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@19e89d2org.highwire.dtl.DTLVardef@16a5685org.highwire.dtl.DTLVardef@563a97org.highwire.dtl.DTLVardef@120a224_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Weymar, G. H. Bar-On, Y. Oliveira, T. Y. Gaebler, C. Ramos, V. Hartweger, H. Breton, G. Caskey, M. Cohn, L. B. Jankovic, M. Nussenzweig, M. C. 2022-03-02 doi:10.1101/2022.03.02.482683 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Automated assembly of high-quality diploid human reference genomes ]]> https://biorxiv.org/content/10.1101/2022.03.06.483034v1?rss=1 Jarvis, E. D. Formenti, G. Rhie, A. Guarracino, A. Yang, C. Wood, J. Tracey, A. Thibaud-Nissen, F. Vollger, M. R. Porubsky, D. Cheng, H. Asri, M. Logsdon, G. A. Carnevali, P. Chaisson, M. Chin, C.-S. Cody, S. Collins, J. Ebert, P. Escalona, M. Fedrigo, O. Fulton, R. S. Fulton, L. L. Garg, S. Ghurye, J. Green, E. Hall, I. M. Harvey, W. H. Hasenfeld, P. Hastie, A. Haukness, M. Jain, M. Kirsche, M. Kolmogorov, M. Korbel, J. O. Koren, S. Korlach, J. Lee, J. Li, D. Lindsay, T. Lucas, J. Luo, F. Marschall, T. McDaniel, J. Nie, F. Olsen, H. E. Olson, N. 2022-03-06 doi:10.1101/2022.03.06.483034 Cold Spring Harbor Laboratory Press 2022-03-06 <![CDATA[ Reprogrammed Schwann cells organize into dynamic tracks that promote pancreatic cancer invasion ]]> https://biorxiv.org/content/10.1101/2022.03.08.481473v1?rss=1 Deborde, S. Gusain, L. Powers, A. Marcadis, A. Yu, Y. Chen, C.-H. Frants, A. Kao, E. Omelchenko, T. Tang, L. Vakiani, E. Calo, A. Reva, B. Jessen, K. R. Wong, R. J. 2022-03-08 doi:10.1101/2022.03.08.481473 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Assembly and phylogeographic analysis of novel Taenia solium mitochondrial genomes reveal further differentiation between and within Asian and African-American genotypes ]]> https://biorxiv.org/content/10.1101/2022.03.10.483888v1?rss=1 Jimenez-Avalos, G. Soto Obando, A. Solis, M. Gilman, R. H. Cama, V. Garcia, H. H. Sheen, P. Requena, D. Zimic, M. 2022-03-11 doi:10.1101/2022.03.10.483888 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ A naturally arising broad and potent CD4-binding site antibody with low somatic mutation ]]> https://biorxiv.org/content/10.1101/2022.03.16.484662v1?rss=1 Barnes, C. O. Schoofs, T. Gnanapragasam, P. N. P. Golijanin, J. Huey-Tubman, K. E. Gruell, H. Schommers, P. Suh-Toma, N. Lee, Y. E. Lorenzi, J. C. C. Piechocka-Trocha, A. Scheid, J. F. West, A. P. Walker, B. D. Seaman, M. S. Klein, F. Nussenzweig, M. C. Bjorkman, P. J. 2022-03-18 doi:10.1101/2022.03.16.484662 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq ]]> https://biorxiv.org/content/10.1101/2022.03.23.485509v1?rss=1 Vazquez, S. E. Mann, S. A. Bodansky, A. Kung, A. F. Quandt, Z. Ferre, E. M. N. Landegren, N. Eriksson, D. Bastard, P. Zhang, S.-Y. Liu, J. Mitchell, A. Mandel-Brehm, C. Miao, B. Sowa, G. Zorn, K. Chan, A. Y. Shimizu, C. Tremoulet, A. Lynch, K. Wilson, M. R. Kämpe, O. Dobbs, K. Delmonte, O. M. Notarangelo, L. D. Burns, J. C. Casanova, J.-L. Lionakis, M. S. Torgerson, T. R. Anderson, M. S. DeRisi, J. L. 2022-03-25 doi:10.1101/2022.03.23.485509 Cold Spring Harbor Laboratory Press 2022-03-25 <![CDATA[ A cell cycle-linked mechanism for the glutamine driven establishment of stem cell fate ]]> https://biorxiv.org/content/10.1101/2022.03.24.485713v1?rss=1 Xiao, M. J. Wu, C.-H. Meek, G. Kelly, B. Young, L. E. A. Martire, S. Castillo, D. B. Saha, P. Dube, A. L. Gentry, M. Banaszynski, L. A. Sun, R. C. KIKANI, C. 2022-03-25 doi:10.1101/2022.03.24.485713 Cold Spring Harbor Laboratory Press 2022-03-25 <![CDATA[ HIV-1 CD4-binding site germline antibody-Env structures inform vaccine design ]]> https://biorxiv.org/content/10.1101/2022.03.25.485873v1?rss=1 Dam, K.-M. A. Barnes, C. O. Gristick, H. B. Schoofs, T. Nussenzweig, M. C. Bjorkman, P. J. 2022-03-26 doi:10.1101/2022.03.25.485873 Cold Spring Harbor Laboratory Press 2022-03-26 <![CDATA[ Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs ]]> https://biorxiv.org/content/10.1101/2022.03.24.485682v1?rss=1 Formenti, G. Abueg, L. Brajuka, A. Brajuka, N. Gallardo, C. Giani, A. Fedrigo, O. Jarvis, E. D. 2022-03-27 doi:10.1101/2022.03.24.485682 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Sperm mosaicism predicts transmission of de novo mutations to human blastocysts ]]> https://biorxiv.org/content/10.1101/2022.03.28.486034v1?rss=1 Yang, X. Stanley, V. McEvoy-Venneri, J. Xu, X. Morales, A. J. Gleeson, J. G. Breuss, M. W. 2022-03-28 doi:10.1101/2022.03.28.486034 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Pangenomics provides insights into the role of synanthropy in barn swallow evolution ]]> https://biorxiv.org/content/10.1101/2022.03.28.486082v1?rss=1 Secomandi, S. Gallo, G. R. Sozzoni, M. Iannucci, A. Galati, E. Abueg, L. Balacco, J. Caprioli, M. Chow, W. Ciofi, C. Collins, J. Fedrigo, O. Ferretti, L. Fungtammasan, A. Haase, B. Howe, K. Kwak, W. Lombardo, G. Masterson, P. Messina, G. Moller, A. P. Mountcastle, J. Mousseau, T. A. Ferrer-Obiol, J. Olivieri, A. Rhie, A. Rubolini, D. Saclier, M. Stanyon, R. Stucki, D. Thibaud-Nissen, F. Torrance, J. Torroni, A. Weber, K. Ambrosini, R. Bonisoli-Alquati, A. Jarvis, E. D. Gianfranceschi, L. Formenti, G. 2022-03-29 doi:10.1101/2022.03.28.486082 Cold Spring Harbor Laboratory Press 2022-03-29 <![CDATA[ Antibody evolution to SARS-CoV-2 after single-dose Ad26.COV2.S vaccine ]]> https://biorxiv.org/content/10.1101/2022.03.31.486548v1?rss=1 Cho, A. Muecksch, F. Wang, Z. Ben Tanfous, T. DaSilva, J. Raspe, R. Johnson, B. Bednarski, E. Ramos, V. Schaefer-Babajew, D. Shimeliovich, I. Dizon, J. Yao, K.-H. Schmidt, F. Millard, K. G. Turroja, M. Jankovic, M. Oliveira, T. Y. Gazumyan, A. Gaebler, C. Caskey, M. Hatziioannou, T. Bieniasz, P. D. Nussenzweig, M. C. 2022-04-01 doi:10.1101/2022.03.31.486548 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Systematic identification of unannotated ORFs in Drosophila reveals evolutionary heterogeneity ]]> https://biorxiv.org/content/10.1101/2022.04.04.486978v1?rss=1 Zheng, E. B. Zhao, L. 2022-04-05 doi:10.1101/2022.04.04.486978 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Development of an improved inhibitor of Lats kinases to promote regeneration of mammalian organs ]]> https://biorxiv.org/content/10.1101/2022.04.07.487521v1?rss=1 Kastan, N. R. Oak, S. Liang, R. Baxt, L. Myers, R. W. Ginn, J. Liverton, N. Huggins, D. J. Pichardo, J. Paul, M. Carroll, T. S. Nagiel, A. Gnedeva, K. Hudspeth, A. J. 2022-04-08 doi:10.1101/2022.04.07.487521 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Violation of the fluctuation-response relation from a linear model of hair bundle oscillations ]]> https://biorxiv.org/content/10.1101/2022.04.15.488459v1?rss=1 Berger, F. Hudspeth, A. J. 2022-04-15 doi:10.1101/2022.04.15.488459 Cold Spring Harbor Laboratory Press 2022-04-15 <![CDATA[ Peptidergic signaling controls the dynamics of sickness behavior in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2022.04.16.488560v1?rss=1 Marquina-Solis, J. Vandewyver, E. Hawk, J. Colon-Ramos, D. Beets, I. Bargmann, C. 2022-04-17 doi:10.1101/2022.04.16.488560 Cold Spring Harbor Laboratory Press 2022-04-17 <![CDATA[ Genome-wide detection of human variants that disrupt intronic branchpoints ]]> https://biorxiv.org/content/10.1101/2022.04.18.488668v1?rss=1 Zhang, P. Philippot, Q. Ren, W. Lei, W.-T. Li, J. Stenson, P. D. Palacin, P. S. Colobran, R. Boisson, B. Zhang, S.-Y. Puel, A. Pan-Hammarström, Q. Zhang, Q. Cooper, D. N. Abel, L. Casanova, J.-L. 2022-04-18 doi:10.1101/2022.04.18.488668 Cold Spring Harbor Laboratory Press 2022-04-18 <![CDATA[ Glutamatergic projections from ventral hippocampus to nucleus accumbens cholinergic neurons are altered in a mouse model of depression ]]> https://biorxiv.org/content/10.1101/2022.04.20.488950v1?rss=1 Milosevic, A. Medrihan, L. Knudsens, M. Ferraro, T. Vasques, P. D. C. Romin, Y. Fujisawa, S. Greengard, P. 2022-04-20 doi:10.1101/2022.04.20.488950 Cold Spring Harbor Laboratory Press 2022-04-20 <![CDATA[ Interspecific allometric scaling in eDNA production in fishes reflects physiological and surface area allometry ]]> https://biorxiv.org/content/10.1101/2022.04.22.489177v1?rss=1 Yates, M. C. Wilcox, T. Stoeckle, M. Heath, D. 2022-04-22 doi:10.1101/2022.04.22.489177 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Depicting pseudotime-lagged causality across single-cell trajectories for accurate gene-regulatory inference ]]> https://biorxiv.org/content/10.1101/2022.04.25.489377v1?rss=1 Reagor, C. C. Velez-Angel, N. Hudspeth, A. J. 2022-04-26 doi:10.1101/2022.04.25.489377 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ The swan genome and transcriptome: its not all black and white ]]> https://biorxiv.org/content/10.1101/2022.05.02.490350v1?rss=1 Karawita, A. C. Cheng, Y. Chew, K. Y. Challgula, A. Kraus, R. Mueller, R. C. Tong, M. Z. W. Hulme, K. D. Beielefeldt-Ohmann, H. Steele, L. E. Wu, M. Sng, J. D. Noye, E. Bruxner, T. J. Au, G. G. Lowthe, S. Blommaert, J. Suh, A. McCauley, A. J. Kaur, P. Olga, D. Aiden, E. Fedrigo, O. Formenti, G. Mountcastle, J. Chow, W. Martin, F. J. Ogeh, D. N. Thiaud-Nissen, F. Howe, K. Collins, J. Tracey, A. Smith, J. Kuo, R. I. Renfree, M. b. Kimura, T. Sakoda, Y. McDougall, M. Spencer, H. G. Pyne, M. Tolf, C. Waldenstrom, J. Jarvis, E. D. Baker, M. L. Burt, D. W. 2022-05-03 doi:10.1101/2022.05.02.490350 Cold Spring Harbor Laboratory Press 2022-05-03 <![CDATA[ A systematic approach to study protein-substrate specificity enables the identification of Ssh1 substrate range ]]> https://biorxiv.org/content/10.1101/2022.05.04.490583v1?rss=1 Cohen, N. Aviram, N. Schuldiner, M. 2022-05-04 doi:10.1101/2022.05.04.490583 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Dynamic HIV-1 spike motion creates vulnerability for its membrane-bound tripod to antibody attack ]]> https://biorxiv.org/content/10.1101/2022.05.09.491169v1?rss=1 Yang, S. Hiotis, G. Wang, Y. Chen, J. Wang, J.-h. Kim, M. Reinherz, E. L. Walz, T. 2022-05-09 doi:10.1101/2022.05.09.491169 Cold Spring Harbor Laboratory Press 2022-05-09 <![CDATA[ Epitope-Evaluator: an interactive web application to study predicted T-cell epitopes ]]> https://biorxiv.org/content/10.1101/2022.05.09.491119v1?rss=1 Soto, L. F. Requena, D. Fuxman Bass, J. I. 2022-05-10 doi:10.1101/2022.05.09.491119 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Context-dependent transcriptional regulation by Drosophila Polycomb Response Elements ]]> https://biorxiv.org/content/10.1101/2022.05.11.491498v1?rss=1 Coleman, R. T. Struhl, G. 2022-05-11 doi:10.1101/2022.05.11.491498 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Tethering distinct molecular profiles of single cells by their lineage histories to investigate sources of cell state heterogeneity ]]> https://biorxiv.org/content/10.1101/2022.05.12.491602v1?rss=1 Minkina, A. Cao, J. Shendure, J. 2022-05-12 doi:10.1101/2022.05.12.491602 Cold Spring Harbor Laboratory Press 2022-05-12 <![CDATA[ Humoral immunity to SARS-CoV-2 elicited by combination COVID-19 vaccination regimens ]]> https://biorxiv.org/content/10.1101/2022.05.13.491823v1?rss=1 Wang, Z. Muecksch, F. Muenn, F. Cho, A. Zong, S. Raspe, R. Ramos, V. Johnson, B. Tanfous, T. B. DaSilva, J. Bednarski, E. Guzman-Cardozo, C. Tober-Lau, P. Hillus, D. Yao, K. Shimeliovich, I. Turroja, M. Millard, K. G. Dizon, J. Kaczynska, A. Gazumyan, A. Jankovic, M. Oliveira, T. Y. Caskey, M. Bieniasz, P. D. Hatziioannou, T. Kurth, F. Sander, L. Nussenzweig, M. C. Gaebler, C. 2022-05-13 doi:10.1101/2022.05.13.491823 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ The proto-oncogene DEK regulates neuronal excitability and tau accumulation in Alzheimer's disease vulnerable neurons ]]> https://biorxiv.org/content/10.1101/2022.05.14.491965v1?rss=1 Rodriguez-Rodriguez, P. Arroyo-Garcia, L. E. Li, L. Tsagkogianni, C. Wang, W. Salas-Allende, I. Plautz, Z. Cedazo-Minguez, A. Sinha, S. Troyanskaya, O. G. Flajolet, M. Yao, V. Roussarie, J.-P. 2022-05-15 doi:10.1101/2022.05.14.491965 Cold Spring Harbor Laboratory Press 2022-05-15 <![CDATA[ Structural basis for substrate selection by the SARS-CoV-2 replicase ]]> https://biorxiv.org/content/10.1101/2022.05.20.492815v1?rss=1 Malone, B. F. Perry, J. K. Olinares, P. D. B. Chen, J. Appleby, T. K. Feng, J. Y. Bilello, J. P. Ng, H. Sotiris, J. Ebrahim, M. Chua, E. Y. D. Mendez, J. H. Eng, E. T. Landick, R. Chait, B. T. Campbell, E. A. Darst, S. A. 2022-05-20 doi:10.1101/2022.05.20.492815 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Inhibition of major histocompatibility complex-I antigen presentation by sarbecovirus ORF7a proteins ]]> https://biorxiv.org/content/10.1101/2022.05.25.493467v1?rss=1 Zhang, F. Zang, T. Stevenson, E. M. Lei, X. Copertino, D. C. Mota, T. M. Boucau, J. Garcia-Beltran, W. F. Jones, R. B. F. Bieniasz, P. D. 2022-05-26 doi:10.1101/2022.05.25.493467 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ ALDH9A1 Deficiency as a Source of Endogenous DNA Damage that Requires Repair by the Fanconi Anemia Pathway ]]> https://biorxiv.org/content/10.1101/2022.05.26.493623v1?rss=1 Jung, M. Ilyashov, I. Park, Y. Donovan, F. X. Ramanagoudr Bhojappa, R. Keahi, D. Durmaz, J. A. Choijilsuren, H. B. Goldfarb, A. Stein, M. Kim, J. White, R. R. Sridhar, S. Noonan, R. Wiley, T. Carroll, T. S. Lach, F. P. Auerbach, A. D. Miranda, I. Chandrasekharappa, S. C. Smogorzewska, A. 2022-05-27 doi:10.1101/2022.05.26.493623 Cold Spring Harbor Laboratory Press 2022-05-27 <![CDATA[ PAF1 and FACT cooperate with MLL-AF4 to drive enhancer activity in leukemia ]]> https://biorxiv.org/content/10.1101/2022.05.27.493676v1?rss=1 Crump, N. T. Smith, A. Godfrey, L. Jackson, N. Rice, S. Kim, J. Basrur, V. Fermin, D. Elenitoba-Johnson, K. Roeder, R. G. Allis, C. D. Roberts, I. Roy, A. Milne, T. 2022-05-27 doi:10.1101/2022.05.27.493676 Cold Spring Harbor Laboratory Press 2022-05-27 <![CDATA[ A developmental pathway for epithelial-to-motoneuron transformation in C. elegans ]]> https://biorxiv.org/content/10.1101/2022.05.27.493712v1?rss=1 Rashid, A. Tevlin, M. Lu, Y. Shaham, S. 2022-05-29 doi:10.1101/2022.05.27.493712 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Modeling the effects of genetic and diet induced obesity on melanoma progression in zebrafish. ]]> https://biorxiv.org/content/10.1101/2022.05.27.493792v1?rss=1 Montal, E. Lumaquin, D. Ma, Y. Suresh, S. White, R. 2022-05-29 doi:10.1101/2022.05.27.493792 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Actin nucleotide state modulates the F-actin structural landscape evoked by bending forces ]]> https://biorxiv.org/content/10.1101/2022.06.02.494606v1?rss=1 Reynolds, M. J. Hachicho, C. Carl, A. G. Gong, R. Alushin, G. M. 2022-06-02 doi:10.1101/2022.06.02.494606 Cold Spring Harbor Laboratory Press 2022-06-02 <![CDATA[ All-optical closed-loop voltage clamp for precise control of muscles and neurons in live animals ]]> https://biorxiv.org/content/10.1101/2022.06.03.494532v1?rss=1 Bergs, A. C. Liewald, J. F. Rodriguez-Rozada, S. Liu, Q. Wirt, C. Bessel, A. Zeitzschel, N. Durmaz, H. Nozownik, A. Vierock, J. Bargmann, C. Hegemann, P. Wiegert, J. S. Gottschalk, A. 2022-06-04 doi:10.1101/2022.06.03.494532 Cold Spring Harbor Laboratory Press 2022-06-04 <![CDATA[ MLL3 regulates the CDKN2A tumor suppressor locus in liver cancer ]]> https://biorxiv.org/content/10.1101/2022.06.07.495174v1?rss=1 Soto-Feliciano, Y. M. Zhu, C. Morris, J. P. Huang, C.-h. Koche, R. P. Ho, Y.-j. Banito, A. Chen, C.-w. Shroff, A. Tian, S. Geulah, L. Chen, C.-c. Fennell, M. Armstrong, S. Allis, C. D. Tschaharganeh, D. Lowe, S. W. 2022-06-09 doi:10.1101/2022.06.07.495174 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Regulated extracellular matrix trafficking shapes cell growth during cartilage morphogenesis ]]> https://biorxiv.org/content/10.1101/2022.06.08.495337v1?rss=1 Levic, D. S. Unlu, G. Melville, D. B. Knapik, E. W. 2022-06-10 doi:10.1101/2022.06.08.495337 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Molecular and functional mechanisms of long-term visual habituation in larval zebrafish ]]> https://biorxiv.org/content/10.1101/2022.06.17.496451v1?rss=1 Lamire, L.-A. Haesemeyer, M. Engert, F. Granato, M. Randlett, O. 2022-06-17 doi:10.1101/2022.06.17.496451 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ The nucleoporin Nup170 mediates subtelomeric gene silencing through the Ctf18-RFC complex and PCNA ]]> https://biorxiv.org/content/10.1101/2022.06.17.496627v1?rss=1 Kumar, S. Neal, M. L. Li, S. Navare, A. T. Mast, F. D. Rout, M. P. Aitchison, J. D. 2022-06-17 doi:10.1101/2022.06.17.496627 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Aromatase Inhibitor Induced Musculoskeletal Inflammation is Observed Independent of Oophorectomy in a Novel Mouse Model ]]> https://biorxiv.org/content/10.1101/2022.06.22.497263v1?rss=1 Young, N. A. Hampton, J. Sharma, J. Jablonski, K. DeVries, A. C. Bratasz, A. Wu, L.-C. Lustberg, M. Reinbolt, R. Jarjour, W. N. 2022-06-26 doi:10.1101/2022.06.22.497263 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Mex67 paralogs mediate division of labor in trypanosome RNA processing and export. ]]> https://biorxiv.org/content/10.1101/2022.06.27.497849v1?rss=1 Obado, S. O. Stein, M. Hegedusova, E. Zhang, W. Hutchinson, S. Glover, L. Paris, Z. Chait, B. T. Field, M. C. Rout, M. P. 2022-06-28 doi:10.1101/2022.06.27.497849 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ Quantitative prediction and measurement of Piezo's membrane footprint ]]> https://biorxiv.org/content/10.1101/2022.06.28.497996v1?rss=1 Haselwandter, C. A. MacKinnon, R. Guo, Y. Fu, Z. 2022-06-29 doi:10.1101/2022.06.28.497996 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Mutations in rv0678 confer low-level resistance to benzothiazinone DprE1 inhibitors in M. tuberculosis ]]> https://biorxiv.org/content/10.1101/2022.06.29.498178v1?rss=1 Poulton, N. C. Azadian, Z. A. DeJesus, M. A. Rock, J. M. 2022-06-29 doi:10.1101/2022.06.29.498178 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Elastic properties and shape of the Piezo dome underlying its mechanosensory function ]]> https://biorxiv.org/content/10.1101/2022.07.01.498002v1?rss=1 Haselwandter, C. A. Guo, Y. Fu, Z. MacKinnon, R. 2022-07-01 doi:10.1101/2022.07.01.498002 Cold Spring Harbor Laboratory Press 2022-07-01 <![CDATA[ Convergent gene expression highlights shared vocal motor microcircuitry in songbirds and humans ]]> https://biorxiv.org/content/10.1101/2022.07.01.498177v1?rss=1 Gedman, G. L. Biegler, M. T. Haase, B. Wirthlin, M. Fedrigo, O. Pfenning, A. R. Jarvis, E. D. 2022-07-02 doi:10.1101/2022.07.01.498177 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe ]]> https://biorxiv.org/content/10.1101/2022.07.02.498543v1?rss=1 Kerner, G. Neehus, A.-L. Abel, L. Casanova, J.-L. Patin, E. Laval, G. Quintana-Murci, L. 2022-07-03 doi:10.1101/2022.07.02.498543 Cold Spring Harbor Laboratory Press 2022-07-03 <![CDATA[ Cyclic AMP is a critical mediator of intrinsic drug resistance and fatty acid metabolism in M. tuberculosis ]]> https://biorxiv.org/content/10.1101/2022.07.07.499113v1?rss=1 Wong, A. I. Beites, T. Planck, K. A. Li, S. Poulton, N. C. Rhee, K. Schnappinger, D. Ehrt, S. Rock, J. M. 2022-07-07 doi:10.1101/2022.07.07.499113 Cold Spring Harbor Laboratory Press 2022-07-07 <![CDATA[ A Draft Human Pangenome Reference ]]> https://biorxiv.org/content/10.1101/2022.07.09.499321v1?rss=1 Liao, W.-W. Asri, M. Ebler, J. Doerr, D. Haukness, M. Hickey, G. Lu, S. Lucas, J. K. Monlong, J. Abel, H. J. Buonaiuto, S. Chang, X. H. Cheng, H. Chu, J. Colonna, V. Eizenga, J. M. Feng, X. Fischer, C. Fulton, R. S. Garg, S. Groza, C. Guarracino, A. Harvey, W. T. Heumos, S. Howe, K. Jain, M. Lu, T.-Y. Markello, C. Martin, F. J. Mitchell, M. W. Munson, K. M. Mwaniki, M. N. Novak, A. M. Olsen, H. E. Pesout, T. Porubsky, D. Prins, P. Sibbesen, J. A. Tomlinson, C. Villani, F. Vollger, M. R. Human Pangenome Reference Consortium, Bourque, G. Chaisson, M. 2022-07-09 doi:10.1101/2022.07.09.499321 Cold Spring Harbor Laboratory Press 2022-07-09 <![CDATA[ Encoding of Dynamic Facial Information in the Middle Dorsal Face Area ]]> https://biorxiv.org/content/10.1101/2022.07.24.501335v1?rss=1 Yang, Z. Freiwald, W. A. 2022-07-25 doi:10.1101/2022.07.24.501335 Cold Spring Harbor Laboratory Press 2022-07-25 <![CDATA[ Single neurons in thalamus and subthalamic nucleus process cardiac and respiratory signals in humans ]]> https://biorxiv.org/content/10.1101/2022.07.25.501133v1?rss=1 De Falco, E. Solca, M. Bernasconi, F. Babo-Rebelo, M. Young, N. Sammartino, F. Rezai, A. Krishna, V. Blanke, O. 2022-07-25 doi:10.1101/2022.07.25.501133 Cold Spring Harbor Laboratory Press 2022-07-25 <![CDATA[ 12S Gene Metabarcoding with DNA Standard Quantifies Marine Bony FishEnvironmental DNA, Identifies Threshold for Reproducible Amplification, and Overcomes Distortion Due to Non-Fish Vertebrate DNA ]]> https://biorxiv.org/content/10.1101/2022.07.29.502053v1?rss=1 Stoeckle, M. Y. Ausubel, J. H. Coogan, M. 2022-08-02 doi:10.1101/2022.07.29.502053 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Single cell, whole embryo phenotyping of pleiotropic disorders of mammalian development ]]> https://biorxiv.org/content/10.1101/2022.08.03.500325v1?rss=1 Huang, X. Henck, J. Qiu, C. Sreenivasan, V. K. A. Balachandran, S. Behncke, R. Chan, W.-L. Despang, A. Dickel, D. E. Haag, N. Hagerling, R. Hansmeier, N. Hennig, F. Marshall, C. Rajderkar, S. Ringel, A. Robson, M. Saunders, L. Srivatsan, S. R. Ulferts, S. Wittler, L. Zhu, Y. Kalscheuer, V. M. Ibrahim, D. Kurth, I. Kornak, U. Beier, D. R. Visel, A. Pennacchio, L. A. Trapnell, C. Cao, J. Shendure, J. Spielmann, M. 2022-08-04 doi:10.1101/2022.08.03.500325 Cold Spring Harbor Laboratory Press 2022-08-04 <![CDATA[ FGF21 Counteracts Alcohol Intoxication by Activating Noradrenergic Neurons ]]> https://biorxiv.org/content/10.1101/2022.08.09.502667v1?rss=1 Choi, M. Schneeberger, M. Fan, W. Bugde, A. Gautron, L. Vale, K. Zhang, Y. Friedman, J. M. Mangelsdorf, D. J. Kliewer, S. A. 2022-08-11 doi:10.1101/2022.08.09.502667 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Sex differences in inter-individual gene expression variability across human tissues ]]> https://biorxiv.org/content/10.1101/2022.08.09.503366v1?rss=1 Khodursky, S. Jiang, C. S. Zheng, E. B. Vaughan, R. Schrider, D. R. Zhao, L. 2022-08-11 doi:10.1101/2022.08.09.503366 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Piezo1 as a force-through-membrane sensor in red blood cells. ]]> https://biorxiv.org/content/10.1101/2022.08.10.503510v1?rss=1 Vaisey, G. Banerjee, P. North, A. J. Haselwandter, C. A. MacKinnon, R. 2022-08-11 doi:10.1101/2022.08.10.503510 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Memory B cell responses to Omicron subvariants after SARS-CoV-2 mRNA breakthrough infection ]]> https://biorxiv.org/content/10.1101/2022.08.11.503601v1?rss=1 Wang, Z. Zhou, P. Muecksch, F. Cho, A. Tanfous, T. B. Canis, M. Witte, L. Johnson, B. Raspe, R. Schmidt, F. Bednarski, E. DaSilva, J. Ramos, V. Zong, S. Turroja, M. Millard, K. G. Yao, K. Shimeliovich, I. Dizon, J. Kaczynska, A. Jankovic, M. Gazumyan, A. Oliveira, T. Y. Caskey, M. Gaebler, C. Bieniasz, P. D. Hatziioannou, T. Nussenzweig, M. C. 2022-08-12 doi:10.1101/2022.08.11.503601 Cold Spring Harbor Laboratory Press 2022-08-12 <![CDATA[ Structure of the pre-mRNA leakage 39-kDa proteinreveals a single domain of integrated zf-C3HC and Rsm1 modules ]]> https://biorxiv.org/content/10.1101/2022.08.11.503642v1?rss=1 Hashimoto, H. Ramirez, D. H. Lautier, O. Pawlak, N. Blobel, G. PALANCADE, B. Debler, E. W. 2022-08-12 doi:10.1101/2022.08.11.503642 Cold Spring Harbor Laboratory Press 2022-08-12 <![CDATA[ Lipids Maintain Genomic Stability and Developmental Potency of Murine Pluripotent Stem Cells ]]> https://biorxiv.org/content/10.1101/2022.08.12.503780v1?rss=1 Wen, D. Zhong, L. Gordillo, M. Wang, X. Qin, Y. Huang, Y. Soshnev, A. Kumar, R. Nanjangud, G. James, D. Allis, C. D. Evans, T. Carey, B. 2022-08-15 doi:10.1101/2022.08.12.503780 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ An evolutionarily conserved pacemaker role for HCN ion channels in smooth muscle ]]> https://biorxiv.org/content/10.1101/2022.08.14.503722v1?rss=1 Yang, L. Arbona, R. J. R. Smith, C. Banks, K. M. Thomas, V. K. Palmer, L. Evans, T. Hurtado, R. 2022-08-15 doi:10.1101/2022.08.14.503722 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Epistasis lowers the genetic barrier to SARS-CoV-2 neutralizing antibody escape ]]> https://biorxiv.org/content/10.1101/2022.08.17.504313v1?rss=1 Witte, L. Baharani, V. Schmidt, F. Wang, Z. Cho, A. Raspe, R. Guzman-Cardozo, M. C. Muecksch, F. Gaebler, C. Caskey, M. Nussenzweig, M. C. Hatziioannou, T. Bieniasz, P. D. 2022-08-19 doi:10.1101/2022.08.17.504313 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ Human anti-ACE2 monoclonal antibodies as pan-sarbecovirus prophylactic agents ]]> https://biorxiv.org/content/10.1101/2022.08.24.505169v1?rss=1 Zhang, F. Jenkins, J. de Carvalho, R. V. H. Nakandakari-Higa, S. Chen, T. Abernathy, M. E. Nyakatura, E. Andrew, D. Lebedeva, I. V. Lorenz, I. C. Hoffmann, H.- H. Rice, C. M. Victora, G. D. Barnes, C. O. Hatziioannou, T. Bieniasz, P. D. 2022-08-24 doi:10.1101/2022.08.24.505169 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ MicroRNA-218 instructs proper assembly of hippocampal networks ]]> https://biorxiv.org/content/10.1101/2022.08.24.505085v1?rss=1 Taylor, S. Kobayashi, M. Vilella, A. Tiwari, D. Zolboot, N. Hartzell, A. Girgiss, C. Abaci, Y. De Sanctis, C. Bellenchi, G. C. Darnell, R. B. Gross, C. Zoli, M. Berg, D. K. Lippi, G. 2022-08-25 doi:10.1101/2022.08.24.505085 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Antigen presentation dynamics shape the response to emergent variants like SARS-CoV-2 Omicron strain after multiple vaccinations with wild type strain ]]> https://biorxiv.org/content/10.1101/2022.08.24.505127v1?rss=1 Yang, L. Van Beek, M. Wang, Z. Muecksch, F. Canis, M. Hatziioannou, T. Bieniasz, P. D. Nussenzweig, M. C. Chakraborty, A. K. 2022-08-25 doi:10.1101/2022.08.24.505127 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Molecular fate-mapping of serum antibodies reveals the effects of antigenic imprinting on repeated immunization ]]> https://biorxiv.org/content/10.1101/2022.08.29.505743v1?rss=1 Schiepers, A. van 't Wout, M. F. Greaney, A. J. Zang, T. Muramatsu, H. Lin, P. J. Tam, Y. K. Mesin, L. Starr, T. N. Bieniasz, P. D. Pardi, N. Bloom, J. D. Victora, G. D. 2022-08-30 doi:10.1101/2022.08.29.505743 Cold Spring Harbor Laboratory Press 2022-08-30 <![CDATA[ Motion of single molecular tethers reveals dynamic subdomains at ER-mitochondria contact sites ]]> https://biorxiv.org/content/10.1101/2022.09.03.505525v1?rss=1 Obara, C. J. Nixon-Abell, J. Moore, A. S. Riccio, F. Hoffman, D. P. Shtengel, G. Xu, C. S. Schaefer, K. Pasolli, H. A. Masson, J.-B. Hess, H. F. Calderon, C. P. Blackstone, C. Lippincott-Schwartz, J. 2022-09-03 doi:10.1101/2022.09.03.505525 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Reorganizing Niche Architecture Still Preserves Organ Function in the Hair Follicle ]]> https://biorxiv.org/content/10.1101/2022.09.06.506764v1?rss=1 Wei, H. Du, S. Parksong, J. Pasolli, H. A. Regot, S. Gonzalez, L. E. Xin, T. Greco, V. 2022-09-08 doi:10.1101/2022.09.06.506764 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ CD4-binding site immunogens elicit heterologous anti-HIV-1 neutralizing antibodies in transgenic and wildtype animals ]]> https://biorxiv.org/content/10.1101/2022.09.08.507086v1?rss=1 Gristick, H. B. Hartweger, H. Loewe, M. van Schooten, J. Ramos, V. Oliviera, T. Y. Nishimura, Y. Koranda, N. S. Wall, A. Yao, K.-H. Poston, D. Gazumyan, A. Wiatr, M. Horning, M. Keeffe, J. R. Hoffmann, M. A. Yang, Z. Abernathy, M. E. Dam, K.-M. A. Gao, H. Gnanapragasam, P. N. Kakutani, L. M. Pavlovitch-Bedzyk, A. J. Seaman, M. S. Howarth, M. McGuire, A. T. Stamatatos, L. Martin, M. A. West, A. P. Nussenzweig, M. C. Bjorkman, P. J. 2022-09-12 doi:10.1101/2022.09.08.507086 Cold Spring Harbor Laboratory Press 2022-09-12 <![CDATA[ Fanconi anemia-isogenic head and neck cancer cell line pairs - a basic and translational science resource ]]> https://biorxiv.org/content/10.1101/2022.09.11.507488v1?rss=1 Nguyen, H. T. Tang, W. Webster, A. L. H. Whiteaker, J. R. Chandler, C. M. Errazquin, R. Sullivan, L. B. Jonlin, E. Hoskins, E. E. Chen, E. Y. Fritzke, M. Paulovich, A. G. Wells, S. I. Roohollahi, K. Dorsman, J. Brakenhoff, R. Garcia-Escudero, R. Smogorzewska, A. Wakefield, L. Grompe, M. Monnat, R. J. 2022-09-13 doi:10.1101/2022.09.11.507488 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Microbiota-stimulated Interleukin-22 regulates brain neurons and protects against stress-induced anxiety ]]> https://biorxiv.org/content/10.1101/2022.09.16.508224v1?rss=1 Ilanges, A. Xia, M. Lu, J. Chen, L. Shiao, R. Wang, C. Feng, R. Jin, Z. Yi, H. Qi, Q. Li, J. Schneeberger, M. Lu, B. Friedman, J. M. Yu, X. 2022-09-19 doi:10.1101/2022.09.16.508224 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Corticothalamic Neurons in Motor Cortex Have a Permissive Role in Motor Execution ]]> https://biorxiv.org/content/10.1101/2022.09.20.508799v1?rss=1 Carmona, L. M. Tun, L. T. Kim, A. Shiao, R. Kissner, M. D. Menon, V. Costa, R. M. 2022-09-22 doi:10.1101/2022.09.20.508799 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Control of lipolysis by a population of oxytocinergic sympathetic neurons ]]> https://biorxiv.org/content/10.1101/2022.09.27.509745v1?rss=1 Li, E. Wang, L. Wang, D. Chi, J. Smith, G. Klein, S. Cohen, P. Rosen, E. 2022-09-28 doi:10.1101/2022.09.27.509745 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ A global view of aging and Alzheimer's pathogenesis-associated cell population dynamics and molecular signatures in the human and mouse brains ]]> https://biorxiv.org/content/10.1101/2022.09.28.509825v1?rss=1 300 cell subtypes and deciphered their underlying molecular programs and spatial locations especially for rare cell types (e.g., pinealocytes, tanycytes). Leveraging these data, we generated a global readout of age-dependent changes at cell subtype resolution, providing insights into cell types that expand (e.g., rare astrocytes and vascular leptomeningeal cells in the olfactory bulb, reactive microglia, and oligodendrocytes) or are depleted (e.g., neuronal progenitors, neuroblasts, committed oligodendrocyte precursors) as age progresses. Furthermore, we explored cell-type-specific responses to genetic perturbations associated with Alzheimers disease (AD) and identified rare cell types depleted (e.g., mt-Cytb+, mt-Rnr2+ choroid plexus epithelial cells) or enriched (e.g., Col25a1+, Ndrg1+ interbrain and midbrain neurons) in both AD models. Key findings are consistent between males and females, validated across the transcriptome, chromatin accessibility, and spatial analyses. Finally, we profiled a total of 118,240 single-nuclei transcriptomes from twenty-four post-mortem human brain samples derived from control and AD patients, revealing highly cell-type-specific and region-specific gene expression changes associated with AD pathogenesis. Critical AD-associated gene signatures were validated in both human and mice. In summary, these data comprise a rich resource for exploring cell-type-specific dynamics and the underlying molecular mechanisms in normal and pathological mammalian aging. ]]> Sziraki, A. Lu, Z. Lee, J. Banyai, G. Anderson, S. Abdulraouf, A. Metzner, E. Liao, A. Epstein, A. Xu, Z. Zhang, Z. Gan, L. Nelson, P. T. Zhou, W. Cao, J. 2022-09-30 doi:10.1101/2022.09.28.509825 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Microbiota-dependent histone butyrylation in the mammalian intestine ]]> https://biorxiv.org/content/10.1101/2022.09.29.510184v1?rss=1 Gates, L. A. Reis, B. S. Lund, P. J. Paul, M. R. Leboeuf, M. Nadeem, Z. Carroll, T. S. Garcia, B. Mucida, D. Allis, C. D. 2022-09-30 doi:10.1101/2022.09.29.510184 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ A comprehensive view of cell-type-specific temporal dynamics in human and mouse brains ]]> https://biorxiv.org/content/10.1101/2022.10.01.509820v1?rss=1 Lu, Z. Zhang, M. Lee, J. Sziraki, A. Anderson, S. Ge, S. Nelson, P. T. Zhou, W. Cao, J. 2022-10-05 doi:10.1101/2022.10.01.509820 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Apolipoprotein E2 Promotes Melanoma Growth, Metastasis, and Protein Synthesis via the LRP1 Receptor ]]> https://biorxiv.org/content/10.1101/2022.10.03.510632v1?rss=1 Adaku, N. Ostendorf, B. N. Tavazoie, S. F. 2022-10-05 doi:10.1101/2022.10.03.510632 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Integrative genetic analysis identifies FLVCR1 as an essential component of choline transport in mammals ]]> https://biorxiv.org/content/10.1101/2022.10.05.509986v1?rss=1 Kenny, T. C. Khan, A. Son, Y. Yue, L. Heissel, S. Gamazon, E. R. Alwaseem, H. Hite, R. K. Birsoy, K. 2022-10-05 doi:10.1101/2022.10.05.509986 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Inhibition of the SARS-CoV-2 helicase at single-nucleotide resolution. ]]> https://biorxiv.org/content/10.1101/2022.10.07.511351v1?rss=1 Marx, S. K. Mickolajczyk, K. J. Craig, J. M. Thomas, C. A. Pfeffer, A. M. Abell, S. J. Carrasco, J. D. Franzi, M. C. Huang, J. R. Kim, H. C. Brinkerhoff, H. D. Kapoor, T. M. Gundlach, J. H. Laszlo, A. H. 2022-10-08 doi:10.1101/2022.10.07.511351 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ Initiation of HIV-1 Gag lattice assembly is required for cytoplasmic recognition of the viral genome packaging signal ]]> https://biorxiv.org/content/10.1101/2022.10.06.511082v1?rss=1 Lei, X. Goncalves-Carneiro, D. Zang, T. M. Bieniasz, P. D. 2022-10-10 doi:10.1101/2022.10.06.511082 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ An in vivo avian model of human melanoma to perform rapid and robust preclinical studies ]]> https://biorxiv.org/content/10.1101/2022.10.12.511927v1?rss=1 Jarrosson, L. Dalle, S. Costechareyre, C. Tang, Y. Grimont, M. Plaschka, M. Lacourrege, M. Teinturier, R. Le Bouar, M. Maucort-Boulch, D. Eberhardt, A. Castellani, V. Caramel, J. Delloye-Bourgeois, C. 2022-10-13 doi:10.1101/2022.10.12.511927 Cold Spring Harbor Laboratory Press 2022-10-13 <![CDATA[ High-throughput screening identifies small molecule inhibitors of thioesterase superfamily member 1: Implications for the management of non-alcoholic fatty liver disease ]]> https://biorxiv.org/content/10.1101/2022.10.15.512369v1?rss=1 Krumm, C. S. Ramos-Espiritu, L. Landzberg, R. S. Adura, C. Liu, X. Acuna, M. Xie, Y. Xu, X. Tillman, M. C. Li, Y. Glickman, F. Ortlund, E. A. Ginn, J. D. Cohen, D. E. 2022-10-18 doi:10.1101/2022.10.15.512369 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ A tissue injury repair pathway distinct but parallel to host pathogen defense ]]> https://biorxiv.org/content/10.1101/2022.10.18.509515v1?rss=1 Liu, S. Hur, Y. H. Cai, X. Cong, Q. Yang, Y. Xu, C. Bilate, A. M. Gonzales, K. A. U. Cowley, C. J. Hurwitz, B. Luo, J.-D. Tseng, T. Gur-Cohen, S. Sribour, M. Omelchenko, T. Levorse, J. Pasolli, H. A. Thompson, C. B. Mucida, D. Fuchs, E. 2022-10-19 doi:10.1101/2022.10.18.509515 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ DISRUPTION OF SYMPATHETIC OUTFLOW TO INTRA-ABDOMINAL ORGANS EMULATES THE METABOLIC EFFECTS OF SLEEVE GASTRECTOMY IN OBESE MICE ]]> https://biorxiv.org/content/10.1101/2022.10.17.512615v1?rss=1 Emiliano, A. Kraljevic, M. Lopatinsky, N. R. Batista, R. Jiang, C. Schwartz, G. J. 2022-10-21 doi:10.1101/2022.10.17.512615 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Structural and functional basis of the universal transcription factor NusG pro-pausing activity in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2022.10.21.513233v1?rss=1 Delbeau, M. Omollo, E. O. Froom, R. Koh, S. Mooney, R. A. Lilic, M. Brewer, J. J. Rock, J. Darst, S. A. Campbell, E. A. Landick, R. 2022-10-22 doi:10.1101/2022.10.21.513233 Cold Spring Harbor Laboratory Press 2022-10-22 <![CDATA[ Head-on and co-directional RNA polymerase collisions orchestrate bidirectional transcription termination ]]> https://biorxiv.org/content/10.1101/2022.10.23.513370v1?rss=1 Wang, L. Watters, J. W. Ju, X. Liu, S. 2022-10-23 doi:10.1101/2022.10.23.513370 Cold Spring Harbor Laboratory Press 2022-10-23 <![CDATA[ Species-wide genomics of kakapo provides transformational tools to accelerate recovery ]]> https://biorxiv.org/content/10.1101/2022.10.22.513130v1?rss=1 Guhlin, J. G. Le Lec, M. F. Wold, J. Koot, E. Winter, D. Biggs, P. Galla, S. J. Urban, L. Foster, Y. Cox, M. P. Digby, A. Uddstrom, L. Eason, D. Vercoe, D. Davis, T. Kakapo Recovery Team, Howard, J. T. Jarvis, E. J. Robertson, F. E. Robertson, B. C. Gemmell, N. Steeves, T. E. Santure, A. W. Dearden, P. 2022-10-24 doi:10.1101/2022.10.22.513130 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Proximity-dependent labeling identifies dendritic cells that prime the antitumor CD4+ T cell response ]]> https://biorxiv.org/content/10.1101/2022.10.25.513771v1?rss=1 Chudnovskiy, A. Nakandakari-Higa, S. Castro, T. B. Cui, A. Lin, C.-H. Sade-Feldman, M. Phillips, B. K. Pae, J. Mesin, L. Bortolatto, J. Schweitzer, L. D. Pasqual, G. Lu, L.-F. Hacohen, N. Victora, G. D. 2022-10-25 doi:10.1101/2022.10.25.513771 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Identification of dendritic cell-T cell interactions driving immune responses to food ]]> https://biorxiv.org/content/10.1101/2022.10.26.513772v1?rss=1 Canesso, M. C. C. Castro, T. B. Nakandakari-Higa, S. Lockhart, A. Esterhazy, D. Reis, B. S. Victora, G. D. Mucida, D. 2022-10-27 doi:10.1101/2022.10.26.513772 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Antibody-lectin chimeras for glyco-immune checkpoint blockade ]]> https://biorxiv.org/content/10.1101/2022.10.26.513931v1?rss=1 Stark, J. C. Gray, M. A. Wisnovsky, S. Ibarlucea-Benitez, I. Riley, N. M. Ribi, M. K. Lustig, M. Errington, W. J. Bruncsics, B. Sarkar, C. A. Valerius, T. Ravetch, J. V. Bertozzi, C. R. 2022-10-27 doi:10.1101/2022.10.26.513931 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Neotelomere formation by human telomerase ]]> https://biorxiv.org/content/10.1101/2022.10.31.514589v1?rss=1 Kinzig, C. G. Zakusilo, G. Takai, K. K. de Lange, T. 2022-11-01 doi:10.1101/2022.10.31.514589 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Human FcγRIIIa activation on splenic macrophages drives the in vivo pathogenesis of dengue disease ]]> https://biorxiv.org/content/10.1101/2022.11.02.514909v1?rss=1 Yamin, R. Kao, K. S. MacDonald, M. R. Cantaert, T. Rice, C. M. Ravetch, J. V. Bournazos, S. 2022-11-03 doi:10.1101/2022.11.02.514909 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ Converting an allocentric goal into an egocentric steering signal ]]> https://biorxiv.org/content/10.1101/2022.11.10.516026v1?rss=1 Mussells Pires, P. Abbott, L. F. Maimon, G. 2022-11-13 doi:10.1101/2022.11.10.516026 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Systematic identification and characterization of novel genes in the regulation and biogenesis of photosynthetic machinery ]]> https://biorxiv.org/content/10.1101/2022.11.12.515357v1?rss=1 Kafri, M. Patena, W. Martin, L. Wang, L. Gomer, G. Sirkejyan, A. K. Goh, A. Wilson, A. T. Gavrilenko, S. E. Breker, M. Roichman, A. McWhite, C. D. Rabinowitz, J. D. Cross, F. R. Wuhr, M. Jonikas, M. C. 2022-11-15 doi:10.1101/2022.11.12.515357 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Identifying genes and pathways linking astrocyte regional specificity to Alzheimer's disease susceptibility ]]> https://biorxiv.org/content/10.1101/2022.11.16.515390v1?rss=1 Zhang, R. Knudsen, M. Vasques, P. D. C. Tadych, A. Rodriguez-Rodriguez, P. Greengard, P. Roussarie, J.-P. Milosevic, A. Troyanskaya, O. G. 2022-11-17 doi:10.1101/2022.11.16.515390 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Semaphorin7A patterns neural circuitry in the lateral line of the zebrafish ]]> https://biorxiv.org/content/10.1101/2022.11.17.516962v1?rss=1 Dasgupta, A. Hudspeth, A. 2022-11-17 doi:10.1101/2022.11.17.516962 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Environmental and genetic drivers of population differences in SARS-CoV-2 immune responses ]]> https://biorxiv.org/content/10.1101/2022.11.22.517073v1?rss=1 Aquino, Y. Bisiaux, A. Li, Z. O'Neill, M. Mendoza-Revilla, J. Merkling, S. H. Kerner, G. Hasan, M. Libri, V. Bondet, V. Smith, N. de Cevins, C. Menager, M. M. Luca, F. Pique-Regi, R. Barba-Spaeth, G. Pietropaoli, S. Schwartz, O. Leroux-Roels, G. Lee, C.-K. Leung, K. Wu, J. T. K. Peiris, J. S. M. Bruzzone, R. Abel, L. Casanova, J.-L. Valkenburg, S. A. Duffy, D. A. Patin, E. Rotival, M. Quintana-Murci, L. 2022-11-22 doi:10.1101/2022.11.22.517073 Cold Spring Harbor Laboratory Press 2022-11-22 <![CDATA[ Multiplexed and scalable cellular phenotyping toward the standardized three-dimensional human neuroanatomy ]]> https://biorxiv.org/content/10.1101/2022.11.23.517711v1?rss=1 Murakami, T. C. Heintz, N. 2022-11-24 doi:10.1101/2022.11.23.517711 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Multiplexed selectivity screening of anti-GPCR antibodies ]]> https://biorxiv.org/content/10.1101/2022.11.24.517810v1?rss=1 400 anti-GPCR Abs from the Human Protein Atlas targeting a customized library of 215 expressed and solubilized GPCRs representing all GPCR subfamilies. We found that ~61% of Abs were selective for their intended target, ~11% to bind off-target, and ~28% not to bind any GPCR. Antigens of on-target Abs were, on average, significantly longer, more disordered, and less likely to be buried in the interior of the GPCR protein than the other Abs. These results provide important insights into the immunogenicity of GPCR epitopes and form a basis for the design of therapeutic Abs and the detection of pathological auto-antibodies. TEASERA multiplexed library-to-library selectivity analysis of 400 anti-GPCR antibodies within subfamilies of 200 solubilized receptors. ]]> Dahl, L. Kotliar, I. Bendes, A. Dodig-Crnkovic, T. Fromm, S. Elofsson, A. Uhlen, M. Sakmar, T. P. Schwenk, J. 2022-11-24 doi:10.1101/2022.11.24.517810 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Autolysosomal exocytosis of lipids protect neurons from ferroptosis ]]> https://biorxiv.org/content/10.1101/2022.11.24.517842v1?rss=1 Ralhan, I. Chang, J. Moulton, M. J. Goodman, L. D. Lee, N. Y. Plummer, G. Pasolli, H. A. Matthies, D. Bellen, H. J. Ioannou, M. S. 2022-11-24 doi:10.1101/2022.11.24.517842 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Microbial symbionts are shared between ants and their associated beetles ]]> https://biorxiv.org/content/10.1101/2022.12.02.518891v1?rss=1 Valdivia, C. Newton, J. A. O'Donnell, S. von Beeren, C. Kronauer, D. J. C. Russell, J. A. Lukasik, P. 2022-12-04 doi:10.1101/2022.12.02.518891 Cold Spring Harbor Laboratory Press 2022-12-04 <![CDATA[ The alarm pheromone and alarm response of the clonal raider ant ]]> https://biorxiv.org/content/10.1101/2022.12.04.518909v1?rss=1 Lopes, L. E. Frank, E. T. Karpati, Z. Schmitt, T. Kronauer, D. J. C. 2022-12-05 doi:10.1101/2022.12.04.518909 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ Assessing Mouse Kidney Parvovirus' Ability to Confound Research by Examining its Effects on Renally Excreted Chemotherapeutics and its Impact on Pathologic Endpoints in the Adenine Model of Chronic Kidney Disease ]]> https://biorxiv.org/content/10.1101/2022.12.09.519764v1?rss=1 Ritter, A. C. Ricart Arbona, R. J. Livingston, R. S. Monette, S. Lipman, N. S. 2022-12-10 doi:10.1101/2022.12.09.519764 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ ohun: an R package for diagnosing and optimizing automatic sound event detection ]]> https://biorxiv.org/content/10.1101/2022.12.13.520253v1?rss=1 Araya-Salas, M. Smith-Vidaurre, G. Chaverri, G. Brenes, J. C. Chirino, F. Elizondo-Calvo, J. Rico-Guevara, A. 2022-12-15 doi:10.1101/2022.12.13.520253 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Gβγ Activates PIP2 Hydrolysis by Recruiting and Orienting PLCβ on the Membrane Surface ]]> https://biorxiv.org/content/10.1101/2022.12.20.521270v1?rss=1 Falzone, M. E. MacKinnon, R. 2022-12-20 doi:10.1101/2022.12.20.521270 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio High Fidelity reads ]]> https://biorxiv.org/content/10.1101/2022.12.23.521667v1?rss=1 Q20). Because of these properties, they have revolutionised genome assembly leading to more accurate and contiguous genomes. In eukaryotes the mitochondrial genome is sequenced alongside the nuclear genome often at very high coverage. A dedicated tool for mitochondrial genome assembly using HiFi reads is still missing. ResultsMitoHiFi was developed within the Darwin Tree of Life Project to assemble mitochondrial genomes from the HiFi reads generated for target species. The input for MitoHiFi is either the raw reads or the assembled contigs, and the tool outputs a mitochondrial genome sequence fasta file along with annotation of protein and RNA genes. Variants arising from heteroplasmy are assembled independently, and nuclear insertions of mitochondrial sequences are identified and not used in organellar genome assembly. MitoHiFi has been used to assemble 374 mitochondrial genomes (369 from 12 phyla and 39 orders of Metazoa and from 6 species of Fungi) for the Darwin Tree of Life Project, the Vertebrate Genomes Project and the Aquatic Symbiosis Genome Project. Inspection of 60 mitochondrial genomes assembled with MitoHiFi for species that already have reference sequences in public databases showed the widespread presence of previously unreported repeats. ConclusionsMitoHiFi is able to assemble mitochondrial genomes from a wide phylogenetic range of taxa from Pacbio HiFi data. MitoHiFi is written in python and is freely available on github (https://github.com/marcelauliano/MitoHiFi). MitoHiFi is available with its dependencies as a singularity image on github (ghcr.io/marcelauliano/mitohifi:master). ]]> Uliano-Silva, M. Gabriel R. N. Ferreira, J. Krasheninnikova, K. Darwin Tree of Life Consortium, Formenti, G. Abueg, L. Torrance, J. W Myers, G. Durbin, R. Blaxter, M. A. McCarthy, S. 2022-12-23 doi:10.1101/2022.12.23.521667 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ Sparse and stereotyped encoding implicates a core glomerulus for ant alarm behavior ]]> https://biorxiv.org/content/10.1101/2022.12.29.522224v1?rss=1 Hart, T. Frank, D. Lopes, L. E. Olivos-Cisneros, L. Lacy, K. D. Trible, W. Ritger, A. Valdes-Rodriguez, S. Kronauer, D. J. C. 2022-12-29 doi:10.1101/2022.12.29.522224 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ An Autoinhibited Conformation of the DnaB-Replicative Helicase phage Lambda P Loader Complex ]]> https://biorxiv.org/content/10.1101/2022.12.30.522210v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@1c44809org.highwire.dtl.DTLVardef@1554deeorg.highwire.dtl.DTLVardef@16f6df9org.highwire.dtl.DTLVardef@9d12dd_HPS_FORMAT_FIGEXP M_FIG C_FIG The DnaB helicase loading pathway at the phage {lambda} replication origin populates two intermediate states, distinguished by the number of {lambda}P loaders present. The DnaB ring in the B6P6 complex is planar and partially open. Although it binds six copies of the {lambda}P loader, the ajar planar state of DnaB yields inchoate interactions with the loader. During the maturation of the complex, the planar state of DnaB is reconfigured into an open spiral in the B6P5 complex, which the pentameric {lambda}P ensemble now grips tightly. This transition required the eviction of one copy of the loader. Although the breach in the DnaB open spiral is sufficiently sized for entry of ssDNA into the internal chamber, the disposition of one {lambda}P chain loader across the single breached interface in DnaB effectively blocks the path to physiological replication origin-derived ssDNA. DnaB is depicted in white/gray ribbon format under a transparent surface. The {lambda}P chains are colored orange and shades of blue. The pink cylinder represents the expected path of ssDNA through DnaB. ]]> Jeruzalmi, D. Brown, D. Shatarupa, A. Olinares, P. D. Chase, J. D. Isiorho, E. Chait, B. 2022-12-30 doi:10.1101/2022.12.30.522210 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ Flexible and scalable control of T cell memory by a reversible epigenetic switch ]]> https://biorxiv.org/content/10.1101/2022.12.31.521782v1?rss=1 Clark, E. Abadie, K. Ukogu, O. Yang, W. Daza, R. Ng, K. K. H. Fathima, J. Wang, A. Bhandoola, A. Nourmohammad, A. Shendure, J. Cao, J. Kueh, H. Y. 2022-12-31 doi:10.1101/2022.12.31.521782 Cold Spring Harbor Laboratory Press 2022-12-31 <![CDATA[ Arginine limitation causes a directed DNA sequence evolution response in colorectal cancer cells ]]> https://biorxiv.org/content/10.1101/2023.01.02.521806v1?rss=1 Hsu, D. Gao, J. Yamaguchi, N. Pinzaru, A. Mandayam, N. Liberti, M. Heissel, S. Alwaseem, H. Tavazoie, S. Tavazoie, S. 2023-01-02 doi:10.1101/2023.01.02.521806 Cold Spring Harbor Laboratory Press 2023-01-02 <![CDATA[ Cooperative NF-κB and Notch1 signaling promotes macrophage-mediated MenaINV expression in breast cancer ]]> https://biorxiv.org/content/10.1101/2023.01.03.522642v1?rss=1 Duran, C. L. Karagiannis, G. S. Chen, X. Sharma, V. P. Entenberg, D. Condeelis, J. S. Oktay, M. H. 2023-01-03 doi:10.1101/2023.01.03.522642 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Control of enhancer activation in the type I interferon response by the histone demethylase Kdm4d/JMJD2d ]]> https://biorxiv.org/content/10.1101/2023.01.14.524033v1?rss=1 Chandwani, R. Fang, T. C. Dewell, S. Tarakhovsky, A. 2023-01-15 doi:10.1101/2023.01.14.524033 Cold Spring Harbor Laboratory Press 2023-01-15 <![CDATA[ Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth ]]> https://biorxiv.org/content/10.1101/2023.01.13.523991v1?rss=1 Liao, J. Shenhav, L. Serrano, M. Zhu, B. Buck, G. A. Korem, T. 2023-01-17 doi:10.1101/2023.01.13.523991 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ Structure and DNA bridging activity of the essential Rec114-Mei4 trimer interface ]]> https://biorxiv.org/content/10.1101/2023.01.18.524603v1?rss=1 Liu, K. Grasso, E. M. Pu, S. Eliezer, D. Liu, S. Keeney, S. 2023-01-18 doi:10.1101/2023.01.18.524603 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ FcyRIIB is a novel immune checkpoint in the tumor microenvironment limiting activity of Treg-targeting antibodies ]]> https://biorxiv.org/content/10.1101/2023.01.19.522856v1?rss=1 Knorr, D. A. Leidner, R. Jensen, S. Meng, R. Jones, A. Ballesteros-Merino, C. Bell, R. B. Baez, M. Sprott, D. Bifulco, C. Piening, B. D. Dahan, R. Fox, B. Ravetch, J. 2023-01-20 doi:10.1101/2023.01.19.522856 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Mechanism of glycoform specificity and protection against antibody dependent enhancement by an anti-afucosylated IgG nanobody ]]> https://biorxiv.org/content/10.1101/2023.01.23.525277v1?rss=1 Gupta, A. Kao, K. S. Yamin, R. Oren, D. A. Golgur, Y. Du, J. Lollar, P. Sundberg, E. Ravetch, J. V. 2023-01-24 doi:10.1101/2023.01.23.525277 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ Ultrasensitive detection of circulating LINE-1 ORF1p as a specific multi-cancer biomarker ]]> https://biorxiv.org/content/10.1101/2023.01.25.525462v1?rss=1 Taylor, M. S. Connie, W. Fridy, P. C. Senussi, Y. Cheng, W.-C. Heaps, J. Mori, K. Cohen, L. Molloy, K. R. Chait, B. T. Goggins, M. Bhan, I. Franses, J. W. Yang, X. Taplin, M.-E. Wang, X. Christiani, D. C. Johnson, B. E. Meyerson, M. Uppaluri, R. Egloff, A. M. Denault, E. N. Spring, L. M. Wang, T.-L. Shih, I.-M. Jung, E. Arora, K. S. Zukerberg, L. R. Yilmaz, O. H. Chi, G. Norden, B. L. Song, Y. Nieman, L. Parikh, A. R. Strickland, M. Mustelin, T. Eng, G. Yilmaz, O. H. Matulonis, U. A. Skates, S. J. Rueda, B. R. Drapkin, R. Klempner, S. J. Deshpande, V. 2023-01-25 doi:10.1101/2023.01.25.525462 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ N-arylpyrazole NOD2 agonists promote immune checkpoint inhibitor therapy ]]> https://biorxiv.org/content/10.1101/2023.01.26.525573v1?rss=1 Griffin, M. E. Tsukidate, T. Hang, H. C. 2023-01-27 doi:10.1101/2023.01.26.525573 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Anteromedial Thalamus Gates the Selection & Stabilization of Long-Term Memories ]]> https://biorxiv.org/content/10.1101/2023.01.27.525908v1?rss=1 Toader, A. C. Regalado, J. M. Li, Y. R. Terceros, A. Yadav, N. Kumar, S. Satow, S. Hollunder, F. Bonito-Oliva, A. Rajasethupathy, P. 2023-01-28 doi:10.1101/2023.01.27.525908 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ Subcortical correlates of consciousness with human single neuron recordings ]]> https://biorxiv.org/content/10.1101/2023.01.27.525684v1?rss=1 Pereira, M. Faivre, N. Bernasconi, F. Brandmeir, N. Suffridge, J. Tran, K. Wang, S. Finomore, V. Konrad, P. Rezai, A. Blanke, O. 2023-01-30 doi:10.1101/2023.01.27.525684 Cold Spring Harbor Laboratory Press 2023-01-30 <![CDATA[ PerturbSci-Kinetics: Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens ]]> https://biorxiv.org/content/10.1101/2023.01.29.526143v1?rss=1 Xu, Z. Sziraki, A. Lee, J. Zhou, W. Cao, J. 2023-01-31 doi:10.1101/2023.01.29.526143 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases ]]> https://biorxiv.org/content/10.1101/2023.01.30.526367v1?rss=1 Funabiki, H. Wassing, I. E. Jia, Q. Luo, J.-D. Carroll, T. 2023-02-02 doi:10.1101/2023.01.30.526367 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ A Chromosome-Level Genome Assembly for the Rock Ptarmigan (Lagopus muta) ]]> https://biorxiv.org/content/10.1101/2023.01.31.526508v1?rss=1 Rodin Morch, P. E. Squires, T. E. Formenti, G. Tracey, A. Abueg, L. A. Brajuka, N. Jarvis, E. D. Melsted, P. Höglund, J. Magnusson, K. P. 2023-02-03 doi:10.1101/2023.01.31.526508 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Histone bivalency regulates the timing of cerebellar granule cell development ]]> https://biorxiv.org/content/10.1101/2023.02.02.526881v1?rss=1 Mätlik, K. Govek, E.-E. Paul, M. R. Allis, C. D. Hatten, M. E. 2023-02-03 doi:10.1101/2023.02.02.526881 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Evolutionary conservation of mechanical strain distributions in functional transitions of protein structures ]]> https://biorxiv.org/content/10.1101/2023.02.07.527482v1?rss=1 Sartori, P. Leibler, S. 2023-02-07 doi:10.1101/2023.02.07.527482 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ Genomic, genetic and phylogenetic evidence for a new falcon species using chromosome-level genome assembly of the gyrfalcon and population genomics ]]> https://biorxiv.org/content/10.1101/2023.02.12.525808v1?rss=1 Al-Ajli, F. O. Formenti, G. Fedrigo, O. Tracey, A. Sims, Y. Howe, K. Karkhi, I. Althani, A. Jarvis, E. Rahman, S. Ayub, Q. 2023-02-13 doi:10.1101/2023.02.12.525808 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ Cooperative super-enhancer inactivation caused by heterozygous loss of CREBBP and KMT2D skews B cell fate decisions and yields T cell-depleted lymphomas ]]> https://biorxiv.org/content/10.1101/2023.02.13.528351v1?rss=1 Li, J. Chin, C. R. Ying, H.-Y. Meydan, C. Teater, M. R. Xia, M. Farinha, P. Takata, K. Chu, C.-S. Rivas, M. A. Chadburn, A. Steidl, C. Scott, D. W. Roeder, R. G. Mason, C. E. Beguelin, W. Melnick, A. M. 2023-02-13 doi:10.1101/2023.02.13.528351 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ LRRC23 loss-of-function impairs radial spoke 3 head assembly and causes defective sperm motility underlying male infertility ]]> https://biorxiv.org/content/10.1101/2023.02.25.530050v1?rss=1 Hwang, J. Y. Chai, P. Nawaz, S. Choi, J. Lopez-Giraldez, F. Hussain, S. Bilguvar, K. Mane, S. Lifton, R. P. Ahmad, W. Zhang, K. Chung, J.-J. 2023-02-26 doi:10.1101/2023.02.25.530050 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ Mobile brain imaging in butoh dancers: from rehearsals to public performance ]]> https://biorxiv.org/content/10.1101/2023.02.26.530087v1?rss=1 Theofanopoulou, C. Paez, S. Huber, D. Todd, E. Ramirez-Moreno, M. A. Khaleghian, B. Sanchez, A. M. Gand, V. Contreras-Vidal, J. L. 2023-02-26 doi:10.1101/2023.02.26.530087 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ A co-transcriptional ribosome assembly checkpoint controls nascent large ribosomal subunit maturation ]]> https://biorxiv.org/content/10.1101/2023.03.02.530842v1?rss=1 Sanghai, Z. Piwowarczyk, R. Vanden Broeck, A. Klinge, S. 2023-03-02 doi:10.1101/2023.03.02.530842 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ A nucleosome switch primes Hepatitis B Virus infection ]]> https://biorxiv.org/content/10.1101/2023.03.03.531011v1?rss=1 Prescott, N. Mansisidor, A. Bram, Y. Lemmon, A. A. Lim, C. Risca, V. I. Schwartz, R. E. David, Y. 2023-03-04 doi:10.1101/2023.03.03.531011 Cold Spring Harbor Laboratory Press 2023-03-04 <![CDATA[ DNA-PK and the TRF2 iDDR inhibit MRN-initiated resection at leading-end telomeres ]]> https://biorxiv.org/content/10.1101/2023.03.06.531339v1?rss=1 Myler, L. R. Toia, B. Vaughan, C. K. Takai, K. Matei, A. M. Wu, P. Paull, T. T. de Lange, T. Lottersberger, F. 2023-03-06 doi:10.1101/2023.03.06.531339 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Bacterial cGAS senses a viral RNA to initiate immunity ]]> https://biorxiv.org/content/10.1101/2023.03.07.531596v1?rss=1 Banh, D. V. Roberts, C. G. Amador, A. M. Brady, S. F. Marraffini, L. A. 2023-03-07 doi:10.1101/2023.03.07.531596 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Operant training for highly palatable food alters translating mRNA in nucleus accumbens D2 neurons and reveals a modulatory role of Neurochondrin ]]> https://biorxiv.org/content/10.1101/2023.03.07.531496v1?rss=1 Montalban, E. Giralt, A. Taing, L. Nakamura, Y. Pelosi, A. Brown, M. de Pins, B. Valjent, E. Martin, M. Nairn, A. C. Greengard, P. Flajolet, M. Herve, D. Gambardella, N. Roussarie, J.-P. Girault, J.-A. 2023-03-09 doi:10.1101/2023.03.07.531496 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Incomplete transcripts dominate the Mycobacterium tuberculosis transcriptome ]]> https://biorxiv.org/content/10.1101/2023.03.10.532058v1?rss=1 Ju, X. Li, S. Froom, R. Wang, L. Lilic, M. Campbell, E. A. Rock, J. M. Liu, S. 2023-03-11 doi:10.1101/2023.03.10.532058 Cold Spring Harbor Laboratory Press 2023-03-11 <![CDATA[ RTF2 controls replication repriming and ribonucleotide excision at the replisome ]]> https://biorxiv.org/content/10.1101/2023.03.13.532415v1?rss=1 Conti, B. A. Ruiz, P. D. Broton, C. Blobel, N. J. Kottemann, M. C. Sridhar, S. Lach, F. P. Wiley, T. Sasi, N. K. Carroll, T. Smogorzewska, A. 2023-03-13 doi:10.1101/2023.03.13.532415 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ Principles of human pre-60S biogenesis ]]> https://biorxiv.org/content/10.1101/2023.03.14.532478v1?rss=1 Vanden Broeck, A. Klinge, S. 2023-03-14 doi:10.1101/2023.03.14.532478 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ The origin and structural evolution of de novo genes in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.03.13.532420v1?rss=1 Peng, J. Zhao, L. 2023-03-15 doi:10.1101/2023.03.13.532420 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ A Genetic Locus Mediating Attentional Processing ]]> https://biorxiv.org/content/10.1101/2023.03.17.533136v1?rss=1 Gershon, Z. Z. Bonito-Oliva, A. Kanke, M. Terceros, A. Fak, J. J. Gebrehemedin, M. De Marco Garcia, N. Iannone, A. F. Sethupathy, P. Rajasethupathy, P. 2023-03-18 doi:10.1101/2023.03.17.533136 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[ Host genetic variation guides hepacivirus clearance, chronicity, and liver fibrosis in mice ]]> https://biorxiv.org/content/10.1101/2023.03.18.533278v1?rss=1 Brown, A. J. Won, J. Wolfisberg, R. Fanhoe, U. Catanzaro, N. West, A. Moreira, F. Nogeuira Batista, M. Ferris, M. T. Linnertz, C. Leist, S. R. Nguyen, C. De la Cruz, G. Midkiff, B. Xia, Y. Montgomery, S. A. Billerbeck, E. Bukh, J. Scheel, T. Rice, C. M. Sheahan, T. P. 2023-03-19 doi:10.1101/2023.03.18.533278 Cold Spring Harbor Laboratory Press 2023-03-19 <![CDATA[ Universal recording of cell-cell contacts in vivo for interaction-based transcriptomics ]]> https://biorxiv.org/content/10.1101/2023.03.16.533003v1?rss=1 Nakandakari-Higa, S. Canesso, M. C. C. Walker, S. Chudnovskiy, A. Jacobsen, J. T. Parigi, S. M. Fiedorczuk, K. Fuchs, E. Bilate, A. M. Pasqual, G. Mucida, D. Pritykin, Y. Victora, G. D. 2023-03-20 doi:10.1101/2023.03.16.533003 Cold Spring Harbor Laboratory Press 2023-03-20 <![CDATA[ Mesoscale volumetric light field (MesoLF) imaging of neuroactivity across cortical areas at 18 Hz ]]> https://biorxiv.org/content/10.1101/2023.03.20.533476v1?rss=1 Nöbauer, T. Zhang, Y. Kim, H. Vaziri, A. 2023-03-21 doi:10.1101/2023.03.20.533476 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Genetic dysregulation of an endothelial Ras signaling network in vein of Galen malformations ]]> https://biorxiv.org/content/10.1101/2023.03.18.532837v1?rss=1 Zhao, S. Mekbib, K. Y. van der Ent, M. A. Allington, G. Prendergast, A. Chau, J. E. Smith, H. Shohfi, J. Ocken, J. Duran, D. Furey, C. G. Le, H. T. Duy, P. Q. Reeves, B. C. Zhang, J. Nelson-Williams, C. Chen, D. Li, B. Nottoli, T. Bai, S. Rolle, M. Zeng, X. Dong, W. Fu, P.-Y. Wang, Y.-C. Mane, S. Piwowarczyk, P. Fehnel, K. P. See, A. P. Iskandar, B. J. Aagaard-Kienitz, B. Kundishora, A. J. DeSpenza, T. Greenberg, A. B. W. Kidanemariam, S. M. Prendergast, A. Johnston, J. M. Jackson, E. Storm, P. B. Lang, S.-S. Butler, W. E. Carter, B. S. Chapman, P. St 2023-03-22 doi:10.1101/2023.03.18.532837 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ TNF-NFkB-p53 axis restricts in vivo survival of hPSC-derived dopamine neuron ]]> https://biorxiv.org/content/10.1101/2023.03.29.534819v1?rss=1 Kim, T. W. Koo, S. Y. Riessland, M. Cho, H. Chaudhry, F. Kolisnyk, B. Russo, M. V. Saurat, N. Mehta, S. Garippa, R. Betel, D. Studer, L. 2023-03-31 doi:10.1101/2023.03.29.534819 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ Dynamic molecular mechanism of the nuclear pore complex permeability barrier ]]> https://biorxiv.org/content/10.1101/2023.03.31.535055v1?rss=1 Kozai, T. Fernandez-Martinez, J. van Eeuwen, T. Gallardo, P. Kapinos, L. E. Mazur, A. Zhang, W. Tempkin, J. Delgado-Izquierdo, M. Raveh, B. Sali, A. Chait, B. T. Veenhoff, L. L. Rout, M. P. Lim, R. Y. H. 2023-04-03 doi:10.1101/2023.03.31.535055 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell types, and development ]]> https://biorxiv.org/content/10.1101/2023.04.02.535281v1?rss=1 Joglekar, A. Hu, W. Zhang, B. Narykov, O. Diekhans, M. Balacco, J. Ndhlovu, L. Milner, T. A. Fedrigo, O. Jarvis, E. D. Sheynkman, G. M. Korkin, D. Ross, M. E. Tilgner, H. U. 2023-04-04 doi:10.1101/2023.04.02.535281 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ Colorectal cancer detection and treatment with engineered probiotics ]]> https://biorxiv.org/content/10.1101/2023.04.03.535370v1?rss=1 Gurbatri, C. R. Radford, G. Vrbanac, L. Coker, C. Im, J. Taylor, S. R. Jang, Y. Sivan, A. Rhee, K. Saleh, A. A. Chien, T. Zandkarimi, F. Lia, I. Lannagan, T. R. Wang, T. Wright, J. A. Thomas, E. Kobayashi, H. Ng, J. Q. Lawrence, M. Sammour, T. Thomas, M. Lewis, M. Papanicolas, L. Perry, J. Fitzsimmons, T. Kaazan, P. Lim, A. Marker, J. Ostroff, C. Rogers, G. Arpaia, N. Worthley, D. L. Woods, S. L. Danino, T. 2023-04-05 doi:10.1101/2023.04.03.535370 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup ]]> https://biorxiv.org/content/10.1101/2023.04.05.535726v1?rss=1 500 million cells. Towards a global framework for exploring mammalian development, we applied single cell combinatorial indexing (sci-*) to profile the transcriptional states of 12.4 million nuclei from 83 precisely staged embryos spanning late gastrulation (embryonic day 8 or E8) to birth (postnatal day 0 or P0), with 2-hr temporal resolution during somitogenesis, 6-hr resolution through to birth, and 20-min resolution during the immediate postpartum period. From these data (E8 to P0), we annotate dozens of trajectories and hundreds of cell types and perform deeper analyses of the unfolding of the posterior embryo during somitogenesis as well as the ontogenesis of the kidney, mesenchyme, retina, and early neurons. Finally, we leverage the depth and temporal resolution of these whole embryo snapshots, together with other published data, to construct and curate a rooted tree of cell type relationships that spans mouse development from zygote to pup. Throughout this tree, we systematically nominate sets of transcription factors (TFs) and other genes as candidate drivers of the in vivo differentiation of hundreds of mammalian cell types. Remarkably, the most dramatic shifts in transcriptional state are observed in a restricted set of cell types in the hours immediately following birth, and presumably underlie the massive changes in physiology that must accompany the successful transition of a placental mammal to extrauterine life. ]]> Qiu, C. Martin, B. K. Welsh, I. C. Daza, R. M. Le, T.-M. Huang, X. Nichols, E. K. Taylor, M. L. Fulton, O. O'Day, D. R. Gomes, A. R. Ilcisin, S. Srivatsan, S. Deng, X. Disteche, C. M. Noble, W. S. Hamazaki, N. Moens, C. B. Kimelman, D. Cao, J. Schier, A. F. Spielmann, M. Murray, S. A. Trapnell, C. Shendure, J. 2023-04-05 doi:10.1101/2023.04.05.535726 Cold Spring Harbor Laboratory Press 2023-04-05 <![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[ Dietary protein shapes the profile and repertoire of intestinal CD4+ T cells ]]> https://biorxiv.org/content/10.1101/2023.04.11.536475v1?rss=1 Lockhart, A. Reed, A. de Castro, T. B. R. Herman, C. Canesso, M. C. C. Mucida, D. 2023-04-13 doi:10.1101/2023.04.11.536475 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[ Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors ]]> https://biorxiv.org/content/10.1101/2023.04.14.536894v1?rss=1 Berenson, A. Lane, R. Soto, L. Patel, M. Ciausu, C. Chen, Y. Shah, S. Santoso, C. Liu, X. Spirohn, K. Hao, T. Hill, D. E. Vidal, M. Fuxman Bass, J. I. 2023-04-14 doi:10.1101/2023.04.14.536894 Cold Spring Harbor Laboratory Press 2023-04-14 <![CDATA[ Sensory neurons couple arousal and foraging decisions in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.04.14.536929v1?rss=1 Scheer, E. Bargmann, C. 2023-04-15 doi:10.1101/2023.04.14.536929 Cold Spring Harbor Laboratory Press 2023-04-15 <![CDATA[ Cell Type Specific CAG Repeat Expansion and Toxicity of Mutant Huntingtin in Human Striatal and Cerebellar Cell Types ]]> https://biorxiv.org/content/10.1101/2023.04.24.538082v1?rss=1 Mätlik, K. Baffuto, M. Kus, L. Davis, D. A. Paul, M. R. Carroll, T. S. Heintz, N. 2023-04-24 doi:10.1101/2023.04.24.538082 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ Layer 5a Corticostriatal Projection Neurons are Selectively Vulnerable in Huntington's Disease ]]> https://biorxiv.org/content/10.1101/2023.04.24.538096v1?rss=1 Pressl, C. Mätlik, K. Kus, L. Darnell, P. Luo, J.-D. Weiss, A. R. Liguore, W. Carroll, T. Davis, D. A. McBride, J. Heintz, N. 2023-04-24 doi:10.1101/2023.04.24.538096 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ Molecular choreography of primer synthesis by the eukaryotic Pol α-primase ]]> https://biorxiv.org/content/10.1101/2023.05.03.539257v1?rss=1 Yuan, Z. Georgescu, R. Li, H. O'Donnell, M. E. 2023-05-03 doi:10.1101/2023.05.03.539257 Cold Spring Harbor Laboratory Press 2023-05-03 <![CDATA[ Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification to biology ]]> https://biorxiv.org/content/10.1101/2023.05.03.539266v1?rss=1 Zheng, F. Georgescu, R. E. Yao, N. Y. O'Donnell, M. E. Li, H. 2023-05-03 doi:10.1101/2023.05.03.539266 Cold Spring Harbor Laboratory Press 2023-05-03 <![CDATA[ ZBTB7A regulates MDD-specific chromatin signatures and astrocyte-mediated stress vulnerability in orbitofrontal cortex ]]> https://biorxiv.org/content/10.1101/2023.05.04.539425v1?rss=1 Fulton, S. L. Bendl, J. Gameiro-Ros, I. Fullard, J. F. Al-Kachak, A. Lepack, A. E. Stewart, A. F. Singh, S. Poller, W. C. Bastle, R. M. Hauberg, M. E. Fakira, A. K. Chen, M. Durand-de Cuttoli, R. Cathomas, F. Ramakrishnan, A. Gleason, K. Shen, L. Tamminga, C. A. Milosevic, A. Russo, S. J. Swirski, F. Blitzer, R. D. Slesinger, P. A. Roussos, P. Maze, I. 2023-05-04 doi:10.1101/2023.05.04.539425 Cold Spring Harbor Laboratory Press 2023-05-04 <![CDATA[ An intrinsically disordered kinetochore protein coordinates mechanical regulation of chromosome segregation by dynein ]]> https://biorxiv.org/content/10.1101/2023.05.07.539709v1?rss=1 McGory, J. M. Barcelos, D. M. Verma, V. Maresca, T. J. 2023-05-09 doi:10.1101/2023.05.07.539709 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Structural basis of CST-Polα/Primase recruitment and regulation by POT1 at telomeres ]]> https://biorxiv.org/content/10.1101/2023.05.08.539880v1?rss=1 Cai, S. W. Takai, H. Walz, T. de Lange, T. 2023-05-09 doi:10.1101/2023.05.08.539880 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Abnormal behavioral episodes associated with sleep and quiescence in Octopus insularis: Possible nightmares in a cephalopod? ]]> https://biorxiv.org/content/10.1101/2023.05.11.540348v1?rss=1 Ramos, E. A. Steinblatt, M. Demsey, R. Reiss, D. Magnasco, M. 2023-05-12 doi:10.1101/2023.05.11.540348 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ The emergence of human gastrulation upon in vitro attachment ]]> https://biorxiv.org/content/10.1101/2023.05.16.541017v1?rss=1 De Santis, R. Rice, E. Croft, G. Yang, M. Rosado-Olivieri, E. A. Brivanlou, A. H. 2023-05-17 doi:10.1101/2023.05.16.541017 Cold Spring Harbor Laboratory Press 2023-05-17 <![CDATA[ Structure of aquaporin-0 arrays in sphingomyelin/cholesterol membranes and implications for lipid rafts ]]> https://biorxiv.org/content/10.1101/2023.05.16.540959v1?rss=1 Chiu, P.-L. Walz, T. 2023-05-18 doi:10.1101/2023.05.16.540959 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Cholesterol mechanically stabilizes aquaporin-0 arrays by strengthening the association of adjacent tetramers ]]> https://biorxiv.org/content/10.1101/2023.05.17.541099v1?rss=1 Orjuela, J. D. Chiu, P.-L. Walz, T. de Groot, B. L. Aponte-Santamaria, C. 2023-05-19 doi:10.1101/2023.05.17.541099 Cold Spring Harbor Laboratory Press 2023-05-19 <![CDATA[ Cancer cells co-evolve with retrotransposons to mitigate viral mimicry ]]> https://biorxiv.org/content/10.1101/2023.05.19.541456v1?rss=1 Sun, S. Hong, J. You, E. Tsanov, K. M. Chacon-Barahona, J. Gioacchino, A. D. Hoyos, D. Li, H. Jiang, H. Ly, H. Marhon, S. A. Murali, R. Chanda, P. Karacay, A. Vabret, N. Carvalho, D. D. LaCava, J. Lowe, S. W. Ting, D. T. Iacobuzio-Donahue, C. A. Solovyov, A. Greenbaum, B. D. 2023-05-20 doi:10.1101/2023.05.19.541456 Cold Spring Harbor Laboratory Press 2023-05-20 <![CDATA[ Quantifying dynamic pro-inflammatory gene expression and heterogeneity in single macrophage cells ]]> https://biorxiv.org/content/10.1101/2023.05.19.541501v1?rss=1 Naigles, B. Narla, A. Soroczynski, J. Tsimring, L. Hao, N. 2023-05-22 doi:10.1101/2023.05.19.541501 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Stem cells tightly regulate dead cell clearance to maintain tissue fitness ]]> https://biorxiv.org/content/10.1101/2023.05.22.541773v1?rss=1 Stewart, K. S. Gonzales, K. A. Yuan, S. Tierney, M. T. Bonny, A. R. Yang, Y. Infarinato, N. R. Cowley, C. J. Levorse, J. M. Pasolli, H. A. Ghosh, S. Rothlin, C. V. Fuchs, E. 2023-05-22 doi:10.1101/2023.05.22.541773 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Formation of a stable RNase Y-RicT (YaaT) complex requires RicA (YmcA) and RicF (YlbF) ]]> https://biorxiv.org/content/10.1101/2023.05.22.541740v1?rss=1 Dubnau, E. DeSantis, M. DUBNAU, D. 2023-05-23 doi:10.1101/2023.05.22.541740 Cold Spring Harbor Laboratory Press 2023-05-23 <![CDATA[ The HLA-II immunopeptidome of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2023.05.26.542482v1?rss=1 Weingarten-Gabbay, S. Chen, D.-Y. Sarkizova, S. Taylor, H. B. Gentili, M. Pearlman, L. R. Bauer, M. R. Rice, C. M. Clauser, K. R. Hacohen, N. Carr, S. A. Abelin, J. G. Saeed, M. Sabeti, P. C. 2023-06-01 doi:10.1101/2023.05.26.542482 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Beyond antibiotic resistance: the whiB7 transcription factor coordinates an adaptive response to alanine starvation in mycobacteria ]]> https://biorxiv.org/content/10.1101/2023.06.02.543512v1?rss=1 Rock, J. M. Poulton, N. C. DeJesus, M. A. Munsamy-Govender, V. Roberts, C. G. Azadian, Z. A. Bosch, B. Lin, K. M. Li, S. 2023-06-03 doi:10.1101/2023.06.02.543512 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ pi_tailtrack: A compact, inexpensive, and open-source behaviour-tracking system for head-restrained zebrafish ]]> https://biorxiv.org/content/10.1101/2023.06.01.543206v1?rss=1 Randlett, O. 2023-06-05 doi:10.1101/2023.06.01.543206 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Differential dynamics specify MeCP2 function at methylated DNA and nucleosomes ]]> https://biorxiv.org/content/10.1101/2023.06.02.543478v1?rss=1 Chua, G. N. L. Watters, J. W. Olinares, P. D. B. Luo, J. A. Chait, B. T. Liu, S. 2023-06-05 doi:10.1101/2023.06.02.543478 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Effects of linker length on phase separation: lessons from the Rubisco-EPYC1 system of the algal pyrenoid ]]> https://biorxiv.org/content/10.1101/2023.06.11.544494v1?rss=1 GrandPre, T. Zhang, Y. Pyo, A. G. T. Weiner, B. Li, J.-L. Jonikas, M. C. Wingreen, N. S. 2023-06-11 doi:10.1101/2023.06.11.544494 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ The principles of peptide selection by the transporter associated with antigen processing ]]> https://biorxiv.org/content/10.1101/2023.06.16.545308v1?rss=1 Lee, J. Oldham, M. L. Manon, V. Chen, J. 2023-06-17 doi:10.1101/2023.06.16.545308 Cold Spring Harbor Laboratory Press 2023-06-17 <![CDATA[ Magnetogenetic cell activation using endogenous ferritin ]]> https://biorxiv.org/content/10.1101/2023.06.20.545120v1?rss=1 Stanley, S. A. Pomeranz, L. E. Li, R. Yu, X. A. Kelly, L. Hassanzadeh, G. Molina, H. Gross, D. Brier, M. I. Vaisey, G. Jimenez-Gonzalez, M. Garcia-Ocana, A. Dordick, J. Friedman, J. M. 2023-06-20 doi:10.1101/2023.06.20.545120 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ Nucleus-Independent Transgenerational Small RNA Inheritance in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.06.20.545749v1?rss=1 Rieger, I. Weintraub, G. Lev, I. Goldstein, K. Bar-Zvi, D. Anava, S. Gingold, H. Shaham, S. Rechavi, O. 2023-06-21 doi:10.1101/2023.06.20.545749 Cold Spring Harbor Laboratory Press 2023-06-21 <![CDATA[ Discovery, Characterization, and Bioactivity of the Achromonodins: Lasso Peptides Encoded by Achromobacter ]]> https://biorxiv.org/content/10.1101/2023.06.21.545946v1?rss=1 Carson, D. V. Zhang, Y. So, L. Cheung-Lee, W. L. Cartagena, A. J. Darst, S. A. Link, A. J. 2023-06-22 doi:10.1101/2023.06.21.545946 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Clonal neural tube organoids self-organise floorplate through BMP-mediated cluster competition ]]> https://biorxiv.org/content/10.1101/2023.06.25.546258v1?rss=1 Krammer, T. Stuart, H. T. Gromberg, E. Ishihara, K. Melchionda, M. Wang, J. Costantini, E. Lehr, S. Cislo, D. Arbanas, L. Hoermann, A. Neumueller, R. A. Elvassore, N. Siggia, E. Briscoe, J. Kicheva, A. Tanaka, E. M. 2023-06-26 doi:10.1101/2023.06.25.546258 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ HD mutation results in a dominant negative effect on HTT function ]]> https://biorxiv.org/content/10.1101/2023.06.26.543767v1?rss=1 Laundos, T. L. Li, S. Cheang, E. De Santis, R. Piccolo, F. M. Brivanlou, A. H. 2023-06-26 doi:10.1101/2023.06.26.543767 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ The evolution and mutational robustness of chromatin accessibility in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.06.26.546587v1?rss=1 Khodursky, S. Zheng, E. B. Svetec, N. Durkin, S. M. Benjamin, S. Gadau, A. Wu, X. Zhao, L. 2023-06-28 doi:10.1101/2023.06.26.546587 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ Inadequate structural constraint on Fab approach rather than paratope elicitation limits HIV-1 MPER vaccine utility ]]> https://biorxiv.org/content/10.1101/2023.06.27.546734v1?rss=1 Tan, K. Chen, J. Kaku, Y. Wang, Y. Donius, L. Khan, R. A. Li, X. Richter, H. Seaman, M. S. Walz, T. Hwang, W. Reinherz, E. L. Kim, M. 2023-06-29 doi:10.1101/2023.06.27.546734 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ The Antitumor Activities of Anti-CD47 Antibodies Require Fc-FcγR interactions ]]> https://biorxiv.org/content/10.1101/2023.06.29.547082v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@1c25202org.highwire.dtl.DTLVardef@960e84org.highwire.dtl.DTLVardef@1930edforg.highwire.dtl.DTLVardef@1b58fcd_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Osorio, J. C. Smith, P. Knorr, D. A. Ravetch, J. 2023-06-29 doi:10.1101/2023.06.29.547082 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy ]]> https://biorxiv.org/content/10.1101/2023.06.28.546576v1?rss=1 Lariviere, D. Abueg, L. Brajuka, N. Gallardo-Alba, C. Gruning, B. Ko, B. J. Ostrovsky, A. Palmada-Flores, M. Pickett, B. D. Rabbani, K. Balacco, J. R. Chaisson, M. Cheng, H. Collins, J. Denisova, A. Fedrigo, O. Gallo, G. R. Giani, A. M. Gooder, G. M. Jain, N. Johnson, C. Kim, H. Lee, C. Marques-Bonet, T. O'Toole, B. Rhie, A. Secomandi, S. Sozzoni, M. Tilley, T. Uliano-Silva, M. van den Beek, M. Waterhouse, R. M. Phillippy, A. M. Jarvis, E. D. Schatz, M. Nekrutenko, A. Formenti, G. 2023-06-30 doi:10.1101/2023.06.28.546576 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ SARS-CoV-2 spike glycosylation affects function and neutralization sensitivity ]]> https://biorxiv.org/content/10.1101/2023.06.30.547241v1?rss=1 Zhang, F. Schmidt, F. Muecksch, F. Wang, Z. Gazumyan, A. Nussenzweig, M. C. Gaebler, C. Caskey, M. Hatziioannou, T. Bieniasz, P. D. 2023-06-30 doi:10.1101/2023.06.30.547241 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus ]]> https://biorxiv.org/content/10.1101/2023.07.14.549041v1?rss=1 Ketaren, N. E. Mast, F. D. Fridy, P. C. Olivier, J. P. Sanyal, T. Sali, A. Chait, B. T. Rout, M. P. Aitchison, J. 2023-07-14 doi:10.1101/2023.07.14.549041 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ Bidirectional Regulation of Motor Circuits Using Magnetogenetic Gene Therapy ]]> https://biorxiv.org/content/10.1101/2023.07.13.548699v1?rss=1 Unda, S. R. Marongiu, R. Pomeranz, L. E. Dyke, J. P. Fung, E. K. Grosenick, L. Zirkel, R. Antoniazzi, A. M. Norman, S. Liston, C. M. Schaffer, C. B. Nishimura, N. Stanley, S. A. Friedman, J. M. Kaplitt, M. G. 2023-07-15 doi:10.1101/2023.07.13.548699 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ Multiple objects evoke fluctuating responses in several regions of the visual pathway ]]> https://biorxiv.org/content/10.1101/2023.07.19.549668v1?rss=1 Schmehl, M. N. Caruso, V. C. Chen, Y. Jun, N. Y. Willett, S. M. Mohl, J. T. Ruff, D. A. Cohen, M. R. Ebihara, A. Freiwald, W. Tokdar, S. T. Groh, J. M. 2023-07-19 doi:10.1101/2023.07.19.549668 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ The SATB1-MIR22-GBA axis mediates glucocerebroside accumulation inducing a cellular senescence-like phenotype in dopaminergic neurons ]]> https://biorxiv.org/content/10.1101/2023.07.19.549710v1?rss=1 Russo, T. Kolisnyk, B. BS, A. Kim, T. W. Martin, J. Plessis-Belair, J. Ni, J. Pearson, J. A. Park, E. J. Sher, R. B. Studer, L. Riessland, M. 2023-07-21 doi:10.1101/2023.07.19.549710 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ A dose-response based model for statistical analysis of chemical genetic interactions in CRISPRi libraries ]]> https://biorxiv.org/content/10.1101/2023.08.03.551759v1?rss=1 Choudhery, S. DeJesus, M. Srinivasan, A. Rock, J. Schnappinger, D. Ioerger, T. 2023-08-05 doi:10.1101/2023.08.03.551759 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ ATRX guards against aberrant differentiation in mesenchymal progenitor cells ]]> https://biorxiv.org/content/10.1101/2023.08.08.552433v1?rss=1 Fang, Y. Barrows, D. Dabas, Y. Carroll, T. S. Tap, W. D. Nacev, B. 2023-08-08 doi:10.1101/2023.08.08.552433 Cold Spring Harbor Laboratory Press 2023-08-08 <![CDATA[ CDK activity at the centrosome regulates the cell cycle ]]> https://biorxiv.org/content/10.1101/2023.08.16.553560v1?rss=1 Roberts, E. L. Kapadia, N. Auchynnikava, T. Basu, S. Nurse, P. 2023-08-16 doi:10.1101/2023.08.16.553560 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ A platform for dissecting force sensitivity and multivalency in actin networks ]]> https://biorxiv.org/content/10.1101/2023.08.15.553463v1?rss=1 Levin, J. T. Pan, A. Barrett, M. T. Alushin, G. M. 2023-08-17 doi:10.1101/2023.08.15.553463 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Dynamics of chromatin accessibility during human first-trimester neurodevelopment ]]> https://biorxiv.org/content/10.1101/2023.08.18.553878v1?rss=1 Mannens, C. C. A. Hu, L. Lonnerberg, P. Schipper, M. Reagor, C. Li, X. He, X. Barker, R. A. Sundstrom, E. Posthuma, D. Linnarsson, S. 2023-08-20 doi:10.1101/2023.08.18.553878 Cold Spring Harbor Laboratory Press 2023-08-20 <![CDATA[ Cellular and Molecular Basis of Leptin Resistance ]]> https://biorxiv.org/content/10.1101/2023.08.24.554526v1?rss=1 Tan, B. Hedbacker, K. Kelly, L. Zhang, Z. Luo, J.-D. Rabinowitz, J. D. Friedman, J. M. 2023-08-26 doi:10.1101/2023.08.24.554526 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ The mechanism of Gαq regulation of PLCβ3-catalyzed PIP2 hydrolysis. ]]> https://biorxiv.org/content/10.1101/2023.08.29.555394v1?rss=1 Falzone, M. E. MacKinnon, R. 2023-08-30 doi:10.1101/2023.08.29.555394 Cold Spring Harbor Laboratory Press 2023-08-30 <![CDATA[ CoSMIC - A hybrid approach for large-scale, high-resolution microbial profiling of novel niches ]]> https://biorxiv.org/content/10.1101/2023.09.03.556087v1?rss=1 Knafo, M. Rezenman, S. Idan, T. Elgart, M. Dagan, S. Reich, Z. Kapon, R. Sade, D. Shental, N. 2023-09-03 doi:10.1101/2023.09.03.556087 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Drugs of abuse hijack a mesolimbic pathway that processes homeostatic need ]]> https://biorxiv.org/content/10.1101/2023.09.03.556059v1?rss=1 Tan, B. Browne, C. J. Nobauer, T. Vaziri, A. Friedman, J. M. Nestler, E. J. 2023-09-05 doi:10.1101/2023.09.03.556059 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Signal-regulated unmasking of the nuclear localization motif in the PAS domain regulates the nuclear translocation of PASK. ]]> https://biorxiv.org/content/10.1101/2023.09.06.556462v1?rss=1 Xiao, M. Dhungel, S. Azad, R. Favaro, D. C. Pushpabai, R. R. Gardner, K. H. KIKANI, C. 2023-09-06 doi:10.1101/2023.09.06.556462 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ A cell atlas of the larval Aedes aegypti ventral nerve cord ]]> https://biorxiv.org/content/10.1101/2023.09.08.556941v1?rss=1 Yin, C. Morita, T. Parrish, J. Z. 2023-09-09 doi:10.1101/2023.09.08.556941 Cold Spring Harbor Laboratory Press 2023-09-09 <![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[ 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[ A modular circuit architecture coordinates the diversification of courtship strategies in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.09.16.558080v1?rss=1 Coleman, R. T. Morantte, I. Koreman, G. T. Cheng, M. L. Ding, Y. Ruta, V. 2023-09-17 doi:10.1101/2023.09.16.558080 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Neural correlates of visual object recognition in rats ]]> https://biorxiv.org/content/10.1101/2023.09.17.555183v1?rss=1 Rhee, J. Y. Echavarria, C. Soucy, E. Greenwood, J. Masis, J. A. Cox, D. D. 2023-09-17 doi:10.1101/2023.09.17.555183 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Inter-organellar nucleic acid communication by a mitochondrial tRNA regulates nuclear metabolic transcription ]]> https://biorxiv.org/content/10.1101/2023.09.21.558912v1?rss=1 Rouya, C. Yambire, K. F. Derbyshire, M. L. Alwaseem, H. Tavazoie, S. F. 2023-09-22 doi:10.1101/2023.09.21.558912 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN Domain ]]> https://biorxiv.org/content/10.1101/2023.09.25.558837v1?rss=1 Small, G. I. Federova, O. Olinares, P. D. B. Chandanani, J. Banerjee, A. Choi, Y. J. Molina, H. Chait, B. Darst, S. A. Campbell, E. A. 2023-09-26 doi:10.1101/2023.09.25.558837 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Using a function-first "scout fragment"-based approach to develop allosteric covalent inhibitors of conformationally dynamic helicase mechanoenzymes ]]> https://biorxiv.org/content/10.1101/2023.09.25.559391v1?rss=1 Ramsey, J. R. Shelton, P. M. M. Heiss, T. K. Olinares, P. D. B. Vostal, L. E. Soileau, H. Grasso, M. Warrington, S. Adaniya, S. Miller, M. Sun, S. Huggins, D. J. Myers, R. W. Chait, B. T. Vinogradova, E. V. Kapoor, T. M. 2023-09-26 doi:10.1101/2023.09.25.559391 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Mixed Multi-Level Visual, Reward, and Motor Signals in Dorsomedial Frontal Cortex Area F7 during Active Naturalistic Video Exploration ]]> https://biorxiv.org/content/10.1101/2023.09.25.559420v1?rss=1 Aboharb, F. Serene, S. Sliwa, J. Freiwald, W. A. 2023-09-27 doi:10.1101/2023.09.25.559420 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ A Window into Mammalian Basement Membrane Development: Insights from the mTurq2-Col4a1 Mouse Model ]]> https://biorxiv.org/content/10.1101/2023.09.27.559396v1?rss=1 Jones, R. A. Trejo, B. Sil, P. Little, K. A. Pasolli, H. A. Joyce, B. Posfai, E. Devenport, D. 2023-09-27 doi:10.1101/2023.09.27.559396 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics ]]> https://biorxiv.org/content/10.1101/2023.09.25.559365v1?rss=1 Mc Cartney, A. M. Formenti, G. Mouton, A. Ciofi, C. Waterhouse, R. M. Mazzoni, C. J. De Panis, D. Schlude Marins, L. S. Leitao, H. G. Diedericks, G. Kirangwa, J. Morselli, M. Salces, J. Escudero, N. Iannucci, A. Natali, C. Svardal, H. Fernandez, R. De Pooter, T. Joris, G. Strazisar, M. Wood, J. Herron, K. E. Seehausen, O. Watts, P. C. Shaw, F. Davey, R. P. Minotto, A. Fernandez Gonzalez, J. M. Bohne, A. Alegria, C. Alioto, T. Alves, P. C. Amorim, I. R. Aury, J.-M. Backstrom, N. Baldrian, P. Ballarin, L. Baltrunaite, L. Barta, E. BedHom, B. Belser, C. B 2023-09-28 doi:10.1101/2023.09.25.559365 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ Pan-viral ORFs discovery using Massively Parallel Ribosome Profiling ]]> https://biorxiv.org/content/10.1101/2023.09.26.559641v1?rss=1 Weingarten-Gabbay, S. Bauer, M. R. Stanton, A. C. Klaeger, S. Verzani, E. K. Lopez, D. Clauser, K. R. Carr, S. A. Abelin, J. G. Rice, C. M. Sabeti, P. C. 2023-09-28 doi:10.1101/2023.09.26.559641 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ Engineered bacteria launch and control an oncolytic virus ]]> https://biorxiv.org/content/10.1101/2023.09.28.559873v1?rss=1 Singer, Z. S. Pabon, J. Huang, H. Rice, C. M. Danino, T. 2023-09-28 doi:10.1101/2023.09.28.559873 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ Advancement in Cellular Topographic and Nanoparticle Capture Imaging by High Resolution Microscopy Incorporating a Freeze-Drying and Gaseous Nitrogen-based Approach ]]> https://biorxiv.org/content/10.1101/2023.09.28.559906v1?rss=1 Uryu, K. Soplop, N. Sheahan, T. P. Catanese, M.-T. Huynh, C. Pena, J. Boudreau, N. Matei, I. Kenific, C. Hashimoto, A. Hoshino, A. Rice, C. M. Lyden, D. 2023-09-28 doi:10.1101/2023.09.28.559906 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ Structural basis of lipid head group entry to the Kennedy pathway by FLVCR1 ]]> https://biorxiv.org/content/10.1101/2023.09.28.560019v1?rss=1 Son, Y. Kenny, T. C. Khan, A. Birsoy, K. Hite, R. K. 2023-09-29 doi:10.1101/2023.09.28.560019 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Altered chromatin occupancy of patient-associated H4 mutants misregulate neuronal differentiation ]]> https://biorxiv.org/content/10.1101/2023.09.29.560141v1?rss=1 Feng, L. Barrows, D. Zhong, L. Matlik, K. Porter, E. G. Djomo, A. M. Yau, I. Soshnev, A. A. Carroll, T. S. Wen, D. Hatten, M. E. Garcia, B. A. Allis, C. D. 2023-09-29 doi:10.1101/2023.09.29.560141 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Allosteric activation of VCP, a AAA unfoldase, by small molecule mimicry ]]> https://biorxiv.org/content/10.1101/2023.10.02.560478v1?rss=1 Jones, N. H. Liu, Q. Urnavicius, L. Dahan, N. E. Vostal, L. E. Kapoor, T. M. 2023-10-02 doi:10.1101/2023.10.02.560478 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Suppression of epithelial proliferation and tumorigenesis by immunoglobulin A ]]> https://biorxiv.org/content/10.1101/2023.10.06.561290v1?rss=1 Donaldson, G. P. Reis, G. L. Saad, M. Mamede, I. Chen, G. DelGaudio, N. L. Zhang, D. Aydin, B. Harrer, C. E. Castro, T. B. R. Grivennikov, S. Reis, B. S. Stadtmueller, B. M. Victora, G. D. Mucida, D. 2023-10-10 doi:10.1101/2023.10.06.561290 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Cross-modal sensory compensation increases mosquito attraction to humans ]]> https://biorxiv.org/content/10.1101/2023.10.10.561721v1?rss=1 Morita, T. Lyn, N. G. von Heynitz, R. K. Goldman, O. V. Sorrells, T. R. DeGennaro, M. Matthews, B. J. Houri-Zeevi, L. Vosshall, L. B. 2023-10-11 doi:10.1101/2023.10.10.561721 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[ Structural basis for CFTR inhibition by CFTRinh-172 ]]> https://biorxiv.org/content/10.1101/2023.10.11.561899v1?rss=1 Young, P. Levring, J. Fiedorczuk, K. Blanchard, S. C. Chen, J. 2023-10-12 doi:10.1101/2023.10.11.561899 Cold Spring Harbor Laboratory Press 2023-10-12 <![CDATA[ Structural identification of a selectivity filter in CFTR ]]> https://biorxiv.org/content/10.1101/2023.10.11.561906v1?rss=1 Levring, J. Chen, J. 2023-10-12 doi:10.1101/2023.10.11.561906 Cold Spring Harbor Laboratory Press 2023-10-12 <![CDATA[ Influence of myosin regulatory light chain and myosin light chain kinase on hair cells of the inner ear ]]> https://biorxiv.org/content/10.1101/2023.10.14.562357v1?rss=1 Oya, R. Woo, K. M. Fabella, B. Alonso, R. G. Hudspeth, A. J. 2023-10-16 doi:10.1101/2023.10.14.562357 Cold Spring Harbor Laboratory Press 2023-10-16 <![CDATA[ A familiar face and person processing area in the human temporal pole ]]> https://biorxiv.org/content/10.1101/2023.10.15.562392v1?rss=1 Deen, B. Husain, G. Freiwald, W. A. 2023-10-16 doi:10.1101/2023.10.15.562392 Cold Spring Harbor Laboratory Press 2023-10-16 <![CDATA[ Neural activity ramps in frontal cortex signal extended motivation during learning ]]> https://biorxiv.org/content/10.1101/2023.10.15.562395v1?rss=1 Regalado, J. M. Corredera Asensio, A. Haunold, T. Toader, A. C. Li, Y. R. Neal, L. A. Rajasethupathy, P. 2023-10-17 doi:10.1101/2023.10.15.562395 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Evolutionary transitions from female to hermaphrodite reproduction remodel olfactory and mating-receptive behaviors ]]> https://biorxiv.org/content/10.1101/2023.10.16.562407v1?rss=1 Ebert, M. S. Bargmann, C. I. 2023-10-17 doi:10.1101/2023.10.16.562407 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Nanomechanics of wild-type and mutant dimers of the tip-link protein protocadherin 15 ]]> https://biorxiv.org/content/10.1101/2023.10.17.562769v1?rss=1 Villasante, C. M. Deng, X. Cohen, J. E. Hudspeth, A. J. 2023-10-19 doi:10.1101/2023.10.17.562769 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Adaptive capacity of a DNA polymerase clamp-loader ATPase complex ]]> https://biorxiv.org/content/10.1101/2023.10.18.562948v1?rss=1 Subramanian, S. Zhang, W. Nimkar, S. Kamel, M. O'Donnell, M. E. Kuriyan, J. 2023-10-19 doi:10.1101/2023.10.18.562948 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Unique Binding and Stabilization Mechanisms Employed By and Engineered Into Nanobodies. ]]> https://biorxiv.org/content/10.1101/2023.10.22.563475v1?rss=1 Ketaren, N. E. Fridy, P. C. Malashkevich, V. Sanyal, T. Brilliantes, M. Thompson, M. K. Orens, D. A. Bonanno, J. B. Sali, a. Almo, S. C. Chait, B. T. Rout, M. P. 2023-10-22 doi:10.1101/2023.10.22.563475 Cold Spring Harbor Laboratory Press 2023-10-22 <![CDATA[ LET-381/FoxF and UNC-30/Pitx2 control the development of C. elegans mesodermal glia that regulate motor behavior. ]]> https://biorxiv.org/content/10.1101/2023.10.23.563501v1?rss=1 Stefanakis, N. Liang, Y. Jiang, J. Shaham, S. 2023-10-23 doi:10.1101/2023.10.23.563501 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ A geometrical model of cell fate specification in the mouse blastocyst ]]> https://biorxiv.org/content/10.1101/2023.10.23.563683v1?rss=1 Raju, A. Siggia, E. 2023-10-25 doi:10.1101/2023.10.23.563683 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ CST--Polymeraseα-primase solves a second telomere end-replication problem ]]> https://biorxiv.org/content/10.1101/2023.10.26.564248v1?rss=1 Takai, H. Aria, V. Borges, P. Yeeles, J. T. P. de Lange, T. 2023-10-26 doi:10.1101/2023.10.26.564248 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ The complete human diploid reference genome of RPE-1 identifies the phased epigenetic landscapes from multi-omics data ]]> https://biorxiv.org/content/10.1101/2023.11.01.565049v1?rss=1 QV60). We mapped the haplotype-specific genomic variation specific to this cell line including t(Xq;10q), a stable 73.18 Mb duplication of chromosome 10 translocated onto the microdeleted chromosome X telomere t(Xq;10q). Polymorphisms between haplotypes of the same genome reveals genetic and epigenetic variation for all chromosomes, especially at centromeres. The RPE-1 assembly as matched reference genome improves mapping quality of multi-omics reads originating from RPE-1 cells with drastic reduction in alignments mismatches compared to using the most complete human reference to date (CHM13). Leveraging the accuracy achieved using a matched reference, we were able to identify the kinetochore sites at base pair resolution and show unprecedented variation between haplotypes. This work showcases the use of matched reference genomes for multi-omics analyses and serves as the foundation for a call to comprehensively assemble experimentally relevant cell lines for widespread application. HighlightsO_LIWe generated the complete phased genome assembly of one of the most widely used non-cancer cell lines (RPE-1) with a stable diploid karyotype C_LIO_LIWe used this genome as a matched reference to analyze sequencing data from RPE-1 C_LIO_LIMapping to the RPE1v1.0 genome improves alignment quality, faithful assignment of reads to each haplotype, and epigenome peak calling accuracy uncovering inter-haplotype variation C_LIO_LIUse of the matched reference genome enables epigenetic precision in identifying for the first time the kinetochore site at base pair resolution for each haplotype C_LIO_LIThe RPE-1 genome represents a new telomere-to-telomere (T2T) human diploid reference for the scientific community that will advance genetic and epigenetic research across fields using this cell line C_LI ]]> Volpe, E. Corda, L. Di Tommaso, E. Pelliccia, F. Ottalevi, R. Licastro, D. Formenti, G. Capulli, M. Guarracino, A. Tassone, E. Giunta, S. 2023-11-03 doi:10.1101/2023.11.01.565049 Cold Spring Harbor Laboratory Press 2023-11-03 <![CDATA[ Ggnbp2 regulates synaptic development and autophagy in motor neurons ]]> https://biorxiv.org/content/10.1101/2023.11.03.565470v1?rss=1 Kerwin, S. K. Carrodus, N. Kewin, A. Lin, T. Qian, X. McRae, A. Yang, J. Collins, B. M. Wray, N. Garton, F. Millard, S. 2023-11-04 doi:10.1101/2023.11.03.565470 Cold Spring Harbor Laboratory Press 2023-11-04 <![CDATA[ Rapid nongenomic estrogen signaling controls alcohol drinking behavior ]]> https://biorxiv.org/content/10.1101/2023.11.02.565358v1?rss=1 Zallar, L. J. Rivera-Irizarry, J. K. Hamor, P. U. Pigulevskiy, I. Liu, D. Welday, J. P. Rico Rozo, A.-S. Bender, R. Asfouri, J. Skelly, M. J. Fecteau, K. M. Hadley, C. K. Levine, O. B. Mehanna, H. Nelson, S. Miller, J. Ghazal, P. Bellotti, P. Erikson, D. W. Geri, J. Pleil, K. E. 2023-11-05 doi:10.1101/2023.11.02.565358 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Male-male interactions shape mate selection in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.11.03.565582v1?rss=1 Hindmarsh Sten, T. Li, R. Hollunder, F. Eleazer, S. Ruta, V. 2023-11-05 doi:10.1101/2023.11.03.565582 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ A reference genome for the Andean cavefish Trichomycterus rosablanca (Siluriformes, Trichomycteridae): building genomic resources to study evolution in cave environments ]]> https://biorxiv.org/content/10.1101/2023.11.11.566715v1?rss=1 Cadena, D. Pabon, L. DoNascimiento, C. Abueg, L. Tiley, T. O-Toole, B. Absolon, D. Sims, Y. Formenti, G. Fedrigo, O. Jarvis, E. Torres, M. 2023-11-13 doi:10.1101/2023.11.11.566715 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Glia detect and mount a protective response to loss of dendrite substructure integrity in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.11.16.567404v1?rss=1 Varandas, K. C. Hodges, B. M. Lubeck, L. Farinas, A. Liang, Y. Lu, Y. Shaham, S. 2023-11-17 doi:10.1101/2023.11.16.567404 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Control of T-shaped Bifurcation by Multiple Guidance Mechanisms during Dorsal Funiculus Development in the Spinal Cord ]]> https://biorxiv.org/content/10.1101/2023.11.17.567638v1?rss=1 Curran, B. M. Nickerson, K. R. Yung, A. R. Goodrich, L. V. Jaworski, A. Tessier-Lavigne, M. Ma, L. 2023-11-18 doi:10.1101/2023.11.17.567638 Cold Spring Harbor Laboratory Press 2023-11-18 <![CDATA[ The Origin and Evolution of Sex Peptide and Sex Peptide Receptor Interactions ]]> https://biorxiv.org/content/10.1101/2023.11.19.567744v1?rss=1 Peng, J. Svetec, N. Molina, H. Zhao, L. 2023-11-19 doi:10.1101/2023.11.19.567744 Cold Spring Harbor Laboratory Press 2023-11-19 <![CDATA[ Structure of the γ-tubulin ring complex-capped microtubule ]]> https://biorxiv.org/content/10.1101/2023.11.20.567916v1?rss=1 Aher, A. Urnavicius, L. Xue, A. Neselu, K. Kapoor, T. 2023-11-20 doi:10.1101/2023.11.20.567916 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ Muscle cofilin alters neuromuscular junction postsynaptic development to strengthen functional neurotransmission ]]> https://biorxiv.org/content/10.1101/2023.11.21.568166v1?rss=1 Christophers, B. Leahy, S. N. Soffar, D. von Saucken, V. Broadie, K. Baylies, M. 2023-11-22 doi:10.1101/2023.11.21.568166 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Fast and accurate disulfide bridge detection ]]> https://biorxiv.org/content/10.1101/2023.11.22.568205v1?rss=1 Heissel, S. He, Y. Jankevics, A. Shi, Y. Molina, H. Viner, R. Scheltema, R. A. 2023-11-22 doi:10.1101/2023.11.22.568205 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Expanding the GPCR-RAMP interactome ]]> https://biorxiv.org/content/10.1101/2023.11.22.568247v1?rss=1 Kotliar, I. B. Bendes, A. Dahl, L. Chen, Y. Saarinen, M. Ceraudo, E. Dodig, T. Uhlen, M. Svenningsson, P. Schwenk, J. Sakmar, T. 2023-11-23 doi:10.1101/2023.11.22.568247 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ Neuronal calcium spikes enable vector inversion in the Drosophila brain ]]> https://biorxiv.org/content/10.1101/2023.11.24.568537v1?rss=1 Ishida, I. G. Sethi, S. Mohren, T. L. Abbott, L. Maimon, G. 2023-11-24 doi:10.1101/2023.11.24.568537 Cold Spring Harbor Laboratory Press 2023-11-24 <![CDATA[ Antiviral innate immune memory in alveolar macrophages following SARS-CoV-2 infection. ]]> https://biorxiv.org/content/10.1101/2023.11.24.568354v1?rss=1 Lercher, A. Cheong, J.-G. Jiang, C. Hoffmann, H.-H. Ashbrook, A. W. Yin, Y. S. Quirk, C. DeGrace, E. J. Chiriboga, L. Rosenberg, B. R. Josefowicz, S. Z. Rice, C. M. 2023-11-27 doi:10.1101/2023.11.24.568354 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ Validation of a heat-inducible Ixodes scapularis HSP70 promoter and developing a tick-specific 3xP3 promoter sequence in ISE6 cells ]]> https://biorxiv.org/content/10.1101/2023.11.29.569248v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@b5ae25org.highwire.dtl.DTLVardef@1bc267borg.highwire.dtl.DTLVardef@1826baborg.highwire.dtl.DTLVardef@16acf4e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pham, M. Hoffmann, H.-h. Kurtti, T. Chana, R. Garcia-Cruz, O. Aliabadi, S. Gulia-Nuss, M. 2023-11-29 doi:10.1101/2023.11.29.569248 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ GeneMAP: A discovery platform for metabolic gene function ]]> https://biorxiv.org/content/10.1101/2023.12.07.570588v1?rss=1 Birsoy, K. Gamazon, E. Khan, A. Unlu, G. Lin, P. Liu, Y. Kilic, E. Kenny, T. C. 2023-12-08 doi:10.1101/2023.12.07.570588 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Opposing effects of pre-existing antibody and memory T cell help on the dynamics of recall germinal centers ]]> https://biorxiv.org/content/10.1101/2023.12.15.571936v1?rss=1 Schiepers, A. van 't Wout, M. F. L. Hobbs, A. Mesin, L. Victora, G. D. 2023-12-15 doi:10.1101/2023.12.15.571936 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Pronounced early differentiation underlies zebra finch gonadal germ cell development. ]]> https://biorxiv.org/content/10.1101/2023.12.30.572255v1?rss=1 Biegler, M. T. Belay, K. Wang, W. Szi, C. Collier, P. G. Luo, J.-D. Haase, B. Gedman, G. L. Sidhu, A. V. Harter, E. Rivera-Lopez, C. Amoako-Boadu, K. Fedrigo, O. Tilgner, H. U. Carroll, T. T. Jarvis, E. D. Keyte, A. L. 2023-12-30 doi:10.1101/2023.12.30.572255 Cold Spring Harbor Laboratory Press 2023-12-30 <![CDATA[ Simultaneous, cortex-wide and cellular-resolution neuronal population dynamics reveal an unbounded scaling of dimensionality with neuron number ]]> https://biorxiv.org/content/10.1101/2024.01.15.575721v1?rss=1 Manley, J. Demas, J. Kim, H. Martinez Traub, F. Vaziri, A. 2024-01-16 doi:10.1101/2024.01.15.575721 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ Lecanemab Blocks the Effects of the Aβ/Fibrinogen Complex on Blood Clots and Synapse Toxicity in Organotypic Culture ]]> https://biorxiv.org/content/10.1101/2024.01.20.576458v1?rss=1 Singh, P. K. Simoes-Pires, E. N. Chen, Z.-L. Torrente, D. Calvano, M. Sharma, A. Strickland, S. Norris, E. H. 2024-01-21 doi:10.1101/2024.01.20.576458 Cold Spring Harbor Laboratory Press 2024-01-21 <![CDATA[ Cryo-EM analysis on magnetic beads for scarce macromolecules in heterogeneous samples ]]> https://biorxiv.org/content/10.1101/2024.01.21.576499v1?rss=1 Arimura, Y. Konishi, H. A. Funabiki, H. 2024-01-22 doi:10.1101/2024.01.21.576499 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Leptin Activated Hypothalamic BNC2 Neurons Acutely Suppress Food Intake ]]> https://biorxiv.org/content/10.1101/2024.01.25.577315v1?rss=1 Tan, H. L. Yin, L. Tan, Y. Ivanov, J. Plucinska, K. Ilanges, A. Herb, B. R. Wang, P. Kosse, C. Cohen, P. Lin, D. Friedman, J. M. 2024-01-26 doi:10.1101/2024.01.25.577315 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ FBM: Freestanding bilayer microscope for single-molecule imaging of membrane proteins ]]> https://biorxiv.org/content/10.1101/2024.01.26.577465v1?rss=1 Perez-Mitta, G. Sezgin, Y. Wang, W. MacKinnon, R. 2024-01-27 doi:10.1101/2024.01.26.577465 Cold Spring Harbor Laboratory Press 2024-01-27 <![CDATA[ Chromosome-scale genome assembly of the rough periwinkle Littorina saxatilis ]]> https://biorxiv.org/content/10.1101/2024.02.01.578480v1?rss=1 De Jode, A. Faria, R. Formenti, G. Sims, Y. Smith, T. Tracey, A. Wood, J. M. D. Zagrodzka, Z. B. Johannesson, K. Butlin, R. K. Leder, E. H. 2024-02-05 doi:10.1101/2024.02.01.578480 Cold Spring Harbor Laboratory Press 2024-02-05 <![CDATA[ Mosaic sarbecovirus vaccination elicits cross-reactive responses in pre-immunized animals ]]> https://biorxiv.org/content/10.1101/2024.02.08.576722v1?rss=1 Cohen, A. A. Keeffe, J. R. Schiepers, A. Dross, S. E. Greaney, A. J. Rorick, A. V. Gao, H. Gnanapragasam, P. N. P. Fan, C. West, A. P. Ramsingh, A. I. Erasmus, J. H. Pata, J. D. Muramatsu, H. Pardi, N. Lin, P. J. C. Baxter, S. Cruz, R. Quintanar-Audelo, M. Robb, E. Serrano-Amatriain, C. Magneschi, L. Fotheringham, I. G. Fuller, D. H. Victora, G. D. Bjorkman, P. J. 2024-02-09 doi:10.1101/2024.02.08.576722 Cold Spring Harbor Laboratory Press 2024-02-09 <![CDATA[ Unselfish meiotic drive maintains heterozygosity in a parthenogenetic ant ]]> https://biorxiv.org/content/10.1101/2024.02.09.579553v1?rss=1 Lacy, K. D. Hart, T. Kronauer, D. J. C. 2024-02-12 doi:10.1101/2024.02.09.579553 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ The Cas10 nuclease activity relieves host dormancy to facilitate spacer acquisition and retention during type III-A CRISPR immunity ]]> https://biorxiv.org/content/10.1101/2024.02.11.579731v1?rss=1 Aviram, N. Shilton, A. Lyn, N. Reis, B. S. Brivanlou, A. Marraffini, L. A. 2024-02-12 doi:10.1101/2024.02.11.579731 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ Molecular switching of a DNA-sliding clamp to a repressor mediates long-range gene silencing ]]> https://biorxiv.org/content/10.1101/2024.02.16.579611v1?rss=1 McLean, T. C. Balaguer-Perez, F. Chandanani, J. Thomas, C. M. Aicart-Ramos, C. Burick, S. Olinares, P. D. B. Gobbato, G. Mundy, J. E. A. Chait, B. T. Lawson, D. M. Darst, S. A. Campbell, E. A. Moreno-Herrero, F. Le, T. B. K. 2024-02-16 doi:10.1101/2024.02.16.579611 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ Mice lacking Astn2 have ASD-like behaviors and altered cerebellar circuit properties ]]> https://biorxiv.org/content/10.1101/2024.02.18.580354v1?rss=1 Hanzel, M. Fernando, K. Maloney, S. E. Gong, S. Mätlik, K. Zhao, J. Pasolli, H. A. Heissel, S. Dougherty, J. D. Hull, C. Hatten, M. E. 2024-02-18 doi:10.1101/2024.02.18.580354 Cold Spring Harbor Laboratory Press 2024-02-18 <![CDATA[ A Genome-Wide Arrayed CRISPR Screen Reveals PLSCR1 as an Intrinsic Barrier to SARS-CoV-2 Entry ]]> https://biorxiv.org/content/10.1101/2024.02.16.580725v1?rss=1 Le Pen, J. Paniccia, G. Bauer, M. Hoffmann, H.- H. Kinast, V. Moncada-Velez, M. Pinharanda, A. Ricardo-Lax, I. Stenzel, A. F. Rosado-Olivieri, E. A. Ashbrook, A. W. Dinnon, K. H. Doyle, W. Freije, C. Hong, S.-H. Lee, D. Lewy, T. Luna, J. M. Peace, A. Schmidt, C. Schneider, W. M. Winkler, R. Larson, C. McGinn, T. Menezes, M.-R. Ramos-Espiritu, L. Banerjee, P. Poirier, J. T. Sanchez-Rivera, F. J. Zhang, Q. Casanova, J.-L. Carroll, T. S. Glickman, J. F. Michailidis, E. Razooky, B. MacDonald, M. R. Rice, C. M. 2024-02-19 doi:10.1101/2024.02.16.580725 Cold Spring Harbor Laboratory Press 2024-02-19 <![CDATA[ A Systematically Optimized Miniaturized Mesoscope (SOMM) for large-scale calcium imaging in freely moving mice ]]> https://biorxiv.org/content/10.1101/2024.02.19.581043v1?rss=1 Zhang, Y. Yuan, L. Wu, J. Noebauer, T. Zhang, R. Xiao, G. Wang, M. Xie, H. Dai, Q. Vaziri, A. 2024-02-22 doi:10.1101/2024.02.19.581043 Cold Spring Harbor Laboratory Press 2024-02-22 <![CDATA[ Next Generation Neuropeptide Y Receptor Small Molecule Agonists Inhibit Mosquito Biting Behavior ]]> https://biorxiv.org/content/10.1101/2024.02.28.582529v1?rss=1 Zeledon, E. V. Baxt, L. A. Khan, T. A. Michino, M. Miller, M. Huggins, D. J. Jiang, C. S. Vosshall, L. B. Duvall, L. B. 2024-03-02 doi:10.1101/2024.02.28.582529 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ Whole-brain neural substrates of behavioral variability in the larval zebrafish ]]> https://biorxiv.org/content/10.1101/2024.03.03.583208v1?rss=1 Manley, J. Vaziri, A. 2024-03-06 doi:10.1101/2024.03.03.583208 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Neuronal substance-P drives breast cancer growth and metastasis via an extracellular RNA/TLR7 axis ]]> https://biorxiv.org/content/10.1101/2024.03.08.584128v1?rss=1 Padmanaban, V. Keller, I. Seltzer, E. S. Ostendorf, B. N. Kerner, Z. Tavazoie, S. F. 2024-03-11 doi:10.1101/2024.03.08.584128 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy ]]> https://biorxiv.org/content/10.1101/2024.03.13.584744v1?rss=1 Saecker, R. M. Mueller, A. U. Malone, B. Chen, J. Budell, W. C. Dandey, V. P. Maruthi, K. Mendez, J. H. Molina, N. Eng, E. T. Yen, L. Y. Potter, C. S. Carragher, B. Darst, S. A. 2024-03-14 doi:10.1101/2024.03.13.584744 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ The lipid droplet protein DHRS3 is a regulator of melanoma cell state ]]> https://biorxiv.org/content/10.1101/2024.03.25.586589v1?rss=1 Johns, E. Ma, Y. Louphrasitthipol, P. Peralta, C. Hunter, M. V. Raymond, J. H. Molina, H. Goding, C. R. White, R. M. 2024-03-28 doi:10.1101/2024.03.25.586589 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[ Neural correlates of individual facial recognition in a social wasp ]]> https://biorxiv.org/content/10.1101/2024.04.11.589095v1?rss=1 Jernigan, C. M. Freiwald, W. A. Sheehan, M. J. 2024-04-15 doi:10.1101/2024.04.11.589095 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ Examining Intercage Transmission of Chlamydia muridarum: Impact of Barrier Husbandry and Cage Sanitization ]]> https://biorxiv.org/content/10.1101/2024.04.19.590256v1?rss=1 Palillo, M. B. Mishkin, N. Mourino, A. Aydin, M. Ricart Arbona, R. J. Lipman, N. S. 2024-04-19 doi:10.1101/2024.04.19.590256 Cold Spring Harbor Laboratory Press 2024-04-19 <![CDATA[ A delta-tubulin/epsilon-tubulin/Ted protein complex is required for centriole architecture ]]> https://biorxiv.org/content/10.1101/2024.04.19.590208v1?rss=1 Pudlowski, R. Xu, L. Milenkovic, L. Hemsworth, K. Stearns, T. Wang, J. T. 2024-04-20 doi:10.1101/2024.04.19.590208 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Delineating the functional activity of antibodies with cross-reactivity to SARS-CoV-2, SARS-CoV-1 and related sarbecoviruses ]]> https://biorxiv.org/content/10.1101/2024.04.24.590836v1?rss=1 Ruiz, F. Foreman, W. Lilly, M. Baharani, V. A. Depierreux, D. M. Chohan, V. Taylor, A. L. Guenthoer, J. Ralph, D. Matsen, F. A. Chu, H. Y. Bieniasz, P. D. Cote, M. Starr, T. N. Overbaugh, J. 2024-04-25 doi:10.1101/2024.04.24.590836 Cold Spring Harbor Laboratory Press 2024-04-25 <![CDATA[ Structure of the Flotillin Complex in a Native Membrane Environment ]]> https://biorxiv.org/content/10.1101/2024.05.09.593390v1?rss=1 Fu, Z. MacKinnon, R. 2024-05-09 doi:10.1101/2024.05.09.593390 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ Force-activated zyxin assemblies coordinate actin nucleation and crosslinking to orchestrate stress fiber repair ]]> https://biorxiv.org/content/10.1101/2024.05.17.594765v1?rss=1 Phua, D. Y. Z. Sun, X. Alushin, G. M. 2024-05-18 doi:10.1101/2024.05.17.594765 Cold Spring Harbor Laboratory Press 2024-05-18 <![CDATA[ Oxydifficidin, a potent Neisseria gonorrhoeae antibiotic due to DedA assisted uptake and ribosomal protein RplL sensitivity ]]> https://biorxiv.org/content/10.1101/2024.05.27.596031v1?rss=1 Kan, J. Morales, A. Hernandez, Y. Ternei, M. A. Lemetre, C. Maclntyre, L. W. Biais, N. Brady, S. F. 2024-05-28 doi:10.1101/2024.05.27.596031 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ The structures of protein kinase A in complex with CFTR: mechanisms of phosphorylation and reversible activation ]]> https://biorxiv.org/content/10.1101/2024.05.28.596263v1?rss=1 Fiedorczuk, K. Iordanov, I. Mihalyi, C. Szollosi, A. Csanady, L. Chen, J. 2024-06-01 doi:10.1101/2024.05.28.596263 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Exploring the energetic and conformational properties of the sequence space connecting naturally occurring RNA tetraloop receptor motifs ]]> https://biorxiv.org/content/10.1101/2024.05.28.596103v1?rss=1 Shin, J. H. Cuevas, L. M. Roy, R. Bonilla, S. L. Al-Hashimi, H. Greenleaf, W. Herschlag, D. 2024-06-02 doi:10.1101/2024.05.28.596103 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Global analysis of protein turnover dynamics in single cells ]]> https://biorxiv.org/content/10.1101/2024.05.30.596745v1?rss=1 1000 cells. Abundance measurements highlighted cell-specific markers of stem cells and various organ-specific cell types. Protein turnover dynamics highlighted differentiation-specific co-regulation of core members of protein complexes with core histone turnover discriminating dividing and non-dividing cells with potential in stem cell and cancer research. Our study represents the most comprehensive SCP analysis to date, offering new insights into cellular diversity and pioneering functional measurements beyond protein abundance. This method distinguishes SCP from other single-cell omics approaches and enhances its scientific relevance in biological research in a multidimensional manner. ]]> Sabatier, P. Ye, Z. Lechner, M. Guzman, U. H. Beusch, C. M. Izaguirre, F. Seth, A. Gritsenko, O. Rodin, S. Grinnemo, K.-H. Olsen, J. V. 2024-06-02 doi:10.1101/2024.05.30.596745 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Contribution of the neuron-specific ATP1A3 to embryonic spinal circuit emergence ]]> https://biorxiv.org/content/10.1101/2024.06.11.598491v1?rss=1 Dinvaut, S. Calvet, S. Comte, J.-C. Gury, R. Pascual, O. Andre, M. Ferrigno, R. Honnorat, J. Moret, F. Marcy, G. Falk, J. Castellani, V. 2024-06-11 doi:10.1101/2024.06.11.598491 Cold Spring Harbor Laboratory Press 2024-06-11 <![CDATA[ Replicative senescence is ATM driven, reversible, and accelerated by hyperactivation of ATM at normoxia ]]> https://biorxiv.org/content/10.1101/2024.06.24.600514v1?rss=1 Stuart, A. J. de Lange, T. 2024-06-26 doi:10.1101/2024.06.24.600514 Cold Spring Harbor Laboratory Press 2024-06-26 <![CDATA[ Epistasis between N-terminal and receptor-binding domains drives cell entry in a bat coronavirus spike ]]> https://biorxiv.org/content/10.1101/2024.06.24.600393v1?rss=1 Tse, A. L. Acreman, C. M. Ricardo-Lax, I. Berrigan, J. Lasso, G. Balogun, T. Kearns, F. L. Casalino, L. McClain, G. L. Chandran, A. M. Lemeunier, C. Amaro, R. E. Rice, C. M. Jangra, R. K. McLellan, J. S. Chandran, K. Miller, E. H. 2024-06-27 doi:10.1101/2024.06.24.600393 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ A Vago-like gene enhances dengue and Zika virus dissemination in Aedes aegypti ]]> https://biorxiv.org/content/10.1101/2024.07.01.601473v1?rss=1 Couderc, E. Crist, A. B. Daron, J. Varet, H. Van Hout, F. A. H. Miesen, P. Palatini, U. Dabo, S. Vial, T. LAMBRECHTS, L. Merkling, S. 2024-07-03 doi:10.1101/2024.07.01.601473 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ G-quadruplexes are a source of vulnerability in BRCA2 deficient granule cell progenitors and medulloblastoma ]]> https://biorxiv.org/content/10.1101/2024.07.20.604431v1?rss=1 Keahi, D. L. Sanders, M. A. Paul, M. R. Webster, A. L. H. Fang, Y. Wiley, T. F. Shalaby, S. Carroll, T. S. Chandrasekharappa, S. C. Sandoval-Garcia, C. MacMillan, M. L. Wagner, J. E. Hatten, M. E. Smogorzewska, A. 2024-07-22 doi:10.1101/2024.07.20.604431 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ Resistance of estrogen receptor function to BET bromodomain inhibition is mediated by transcriptional coactivator cooperativity ]]> https://biorxiv.org/content/10.1101/2024.07.25.605008v1?rss=1 Zhang, S. Roeder, R. G. 2024-07-26 doi:10.1101/2024.07.25.605008 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ Determining mesoscale chromatin structure parameters from spatially correlated cleavage data using a coarse-grained oligonucleosome model ]]> https://biorxiv.org/content/10.1101/2024.07.28.605011v1?rss=1 Clerkin, A. B. Pagane, N. West, D. W. Spakowitz, A. J. Risca, V. I. 2024-07-29 doi:10.1101/2024.07.28.605011 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Mechanism of neurodegeneration mediated by clonal inflammatory microglia ]]> https://biorxiv.org/content/10.1101/2024.07.30.605867v1?rss=1 Vicario, R. Fragkogianni, S. Pokrovskii, M. Mayer, C. Lopez-Rodrigo, E. Hu, Y. Ogishi, M. Alberdi, A. Baako, A. Ay, O. Plu, I. Sazdovitch, V. Heritier, S. Cohen-Aubart, F. Shor, N. Miyara, M. Nguyen-Khac, F. Viale, A. Idbaih, A. Amoura, Z. Rosenblum, M. Zhang, H. Karnoub, E.-R. Sashittal, P. Jakatdar, A. Iacobuzio-Donahue, C. A. Abdel-Wahab, O. Tabar, V. Socci, N. D. Elemento, O. Diamond, E. Boisson, B. Casanova, J.-L. Seilhean, D. Haroche, J. Donadieu, J. Geissmann, F. 2024-07-31 doi:10.1101/2024.07.30.605867 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Complete sequencing of ape genomes ]]> https://biorxiv.org/content/10.1101/2024.07.31.605654v1?rss=1 Yoo, D. Rhie, A. Hebbar, P. Antonacci, F. Logsdon, G. A. Solar, S. J. Antipov, D. Pickett, B. D. Safonova, Y. Montinaro, F. Luo, Y. Malukiewicz, J. Storer, J. M. Lin, J. Sequeira, A. N. Mangan, R. J. Hickey, G. Anez, G. M. Balachandran, P. Bankevich, A. Beck, C. R. Biddanda, A. Borchers, M. Bouffard, G. G. Brannan, E. Brooks, S. Y. Carbone, L. Carrel, L. Chan, A. P. Crawford, J. Diekhans, M. Engelbrecht, E. Feschotte, C. Formenti, G. Garcia, G. H. Gennaro, L. d. Gilbert, D. Green, R. E. Guarracino, A. Gupta, I. Haddad, D. Han, J. Harris, R. S. Hartley 2024-07-31 doi:10.1101/2024.07.31.605654 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ A comparison of super-resolution microscopy techniques for imaging tightly packed microcolonies of an obligate intracellular bacterium ]]> https://biorxiv.org/content/10.1101/2024.08.12.607698v1?rss=1 North, A. Sharma, V. Pyrgaki, C. Lim, J. Atwal, S. Saharat, K. Wright, G. Salje, J. 2024-08-13 doi:10.1101/2024.08.12.607698 Cold Spring Harbor Laboratory Press 2024-08-13 <![CDATA[ Opto-CLIP reveals dynamic FMRP regulation of mRNAs upon CA1 neuronal activation ]]> https://biorxiv.org/content/10.1101/2024.08.13.607210v1?rss=1 Singer, R. A. Rajchin, V. Park, K. Heintz, N. Darnell, R. B. 2024-08-14 doi:10.1101/2024.08.13.607210 Cold Spring Harbor Laboratory Press 2024-08-14 <![CDATA[ Myosin forces elicit an F-actin structural landscape that mediates mechanosensitive protein recognition ]]> https://biorxiv.org/content/10.1101/2024.08.15.608188v1?rss=1 Carl, A. G. Reynolds, M. J. Gurel, P. S. Phua, D. Y. Sun, X. Mei, L. Hamilton, K. Takagi, Y. Noble, A. J. Sellers, J. R. Alushin, G. M. 2024-08-17 doi:10.1101/2024.08.15.608188 Cold Spring Harbor Laboratory Press 2024-08-17 <![CDATA[ Polyunsaturated fatty acid-derived lipid mediator networks characterize COVID-19 severity and risk for critical illness ]]> https://biorxiv.org/content/10.1101/2024.08.28.610123v1?rss=1 View larger version (69K): org.highwire.dtl.DTLVardef@6e406dorg.highwire.dtl.DTLVardef@47c9deorg.highwire.dtl.DTLVardef@1162488org.highwire.dtl.DTLVardef@b86ba3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Papadaki, M. Pavlos, E. Dubourdeau, M. Bailif, V. Badirou, K. Galani, I.-E. Papelis, D. Kamperi, N. Triantafyllia, V. Siouti, L. Salagianni, M. Manioudaki, M. Paschalidis, N. Vatsellas, G. Koukaki, E. Rapti, V. Thanos, D. Rovina, N. Poulakou, G. Cobat, A. Casanova, J.-L. Tamvakopoulos, C. Andreakos, E. 2024-08-28 doi:10.1101/2024.08.28.610123 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Brain Charts for the Rhesus Macaque Lifespan ]]> https://biorxiv.org/content/10.1101/2024.08.28.610193v1?rss=1 Alldritt, S. Ramirez, J. S. B. Vos de Wael, R. Bethlehem, R. Seidlitz, J. Wang, Z. Nenning, K.-H. Esper, N. B. Smallwood, J. Franco, A. R. Byeon, K. Alexander-Bloch, A. Messinger, A. Chen, A. Thiele, A. Weiss, A. R. Shmuel, A. Fox, A. Tusche, A. Brambrink, A. M. Falchier, A. Hiba, B. Jarraya, B. Jung, B. Butler, B. Russ, B. E. Howell, B. R. Drzewiecki, C. M. Guedj, C. Schwiedrzik, C. M. Amiez, C. Wilson, C. R. E. Klink, C. Kroenke, C. Constantinidis, C. Garin, C. M. Poirier, C. Gale, D. J. Leopold, D. A. Rudko, D. A. Amaral, D. G. Tsao, D. Cook, D. J. 2024-08-30 doi:10.1101/2024.08.28.610193 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Estrus-Tracking Cortical Neurons Integrate Social cues and Reproductive states to Adaptively Control Sexually Dimorphic Sociosexual Behaviors ]]> https://biorxiv.org/content/10.1101/2024.08.30.610466v1?rss=1 Wang, Y. Song, X. Chen, X. Zhou, Y. Ma, J. Zhang, F. Wei, L. Qi, G. Yadav, N. Miao, B. Yan, Y. Yuan, G. Mi, D. Rajasethupathy, P. Ibanez-Tallon, I. Jia, X. Heintz, N. Li, K. 2024-08-30 doi:10.1101/2024.08.30.610466 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Spontaneously regenerative corticospinal neurons in mice ]]> https://biorxiv.org/content/10.1101/2024.09.09.612115v1?rss=1 Fait, B. W. Cotto, B. Murakami, T. C. Hagemann-Jensen, M. Zhan, H. Freivald, C. Turbek, I. Gao, Y. Yao, Z. Way, S. W. Zeng, H. Tasic, B. Steward, O. Heintz, N. Schmidt, E. F. 2024-09-12 doi:10.1101/2024.09.09.612115 Cold Spring Harbor Laboratory Press 2024-09-12 <![CDATA[ Hippocampal γCaMKII dopaminylation promotes synaptic-to-nuclear signaling and memory formation ]]> https://biorxiv.org/content/10.1101/2024.09.19.613951v1?rss=1 Stewart, A. F. Fulton, S. L. Durand-de Cuttoli, R. Thompson, R. E. Chen, P.-J. Brindley, E. Cetin, B. Farrelly, L. A. Futamura, R. Claypool, S. Bastle, R. M. Di Salvo, G. Peralta, C. Molina, H. Baljinnyam, E. Marro, S. G. Russo, S. J. Devita, R. J. Muir, T. W. Maze, I. 2024-09-20 doi:10.1101/2024.09.19.613951 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Slit3 Fragments Orchestrate Neurovascular Expansion and Thermogenesis in Brown Adipose Tissue ]]> https://biorxiv.org/content/10.1101/2024.09.24.613949v1?rss=1 Duarte Afonso Serdan, T. Cervantes, H. Frank, B. Tian, Q. Choi, C. H. J. Hoffmann, A. Cohen, P. Bluher, M. Schwartz, G. J. Shamsi, F. 2024-09-26 doi:10.1101/2024.09.24.613949 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Mapping and engineering RNA-controlled architecture of the multiphase nucleolus ]]> https://biorxiv.org/content/10.1101/2024.09.28.615444v1?rss=1 Quinodoz, S. A. Jiang, L. Abu-Alfa, A. A. Comi, T. J. Zhao, H. Yu, Q. Wiesner, L. W. Botello, J. F. Donlic, A. Soehalim, E. Zorbas, C. Wacheul, L. Kosmrlj, A. Lafontaine, D. L. Klinge, S. Brangwynne, C. P. 2024-09-29 doi:10.1101/2024.09.28.615444 Cold Spring Harbor Laboratory Press 2024-09-29 <![CDATA[ RapA opens the RNA polymerase clamp to disrupt post-termination complexes and prevent cytotoxic R-loop formation ]]> https://biorxiv.org/content/10.1101/2024.09.28.614012v1?rss=1 Brewer, J. J. Inlow, K. Mooney, R. A. Bosch, B. Olinares, P. D. B. Marcelino, L. P. Chait, B. T. Landick, R. Gelles, J. Campbell, E. A. Darst, S. A. 2024-09-30 doi:10.1101/2024.09.28.614012 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Heterogeneity and plasticity of the naive CD4+ T cell compartment ]]> https://biorxiv.org/content/10.1101/2024.10.02.615602v1?rss=1 Sajani, A. Schaafsma, E. Croteau, W. Eltanbouly, M. Nowak, E. C. Cheng, C. Burns, C. Turk, M. J. Noelle, R. J. Lines, J. L. 2024-10-03 doi:10.1101/2024.10.02.615602 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ The challenge of chromatin model comparison and validation a project from the first international 4D Nucleome Hackathon ]]> https://biorxiv.org/content/10.1101/2024.10.02.616241v1?rss=1 Kubica, J. Korsak, S. Clerkin, A. B. Kouril, D. Schirman, D. Yadavalli, A. D. Banecki, K. Kadlof, M. Busby, B. Plewczynski, D. 2024-10-03 doi:10.1101/2024.10.02.616241 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Quantifying transcriptome turnover on phylogenies bymodeling gene expression as a binary trait ]]> https://biorxiv.org/content/10.1101/2024.10.03.616564v1?rss=1 Thompson, A. May, M. R. Hopkins, B. Riedl, N. Barmina, O. Liebeskind, B. J. Zhao, L. Begun, D. Kopp, A. 2024-10-04 doi:10.1101/2024.10.03.616564 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Deep mutational scanning identifies variants of Cas1 and Cas2 that increase spacer acquisition in type II-A CRISPR-Cas systems ]]> https://biorxiv.org/content/10.1101/2024.10.10.617623v1?rss=1 Hofmann, R. Herman, C. Mo, C. Mathai, J. Marraffini, L. A. 2024-10-10 doi:10.1101/2024.10.10.617623 Cold Spring Harbor Laboratory Press 2024-10-10 <![CDATA[ Afadin mediates cadherin-catenin complex clustering on F-actin linked to cooperative binding and filament curvature ]]> https://biorxiv.org/content/10.1101/2024.10.08.617332v1?rss=1 Gong, R. Reynolds, M. J. Sun, X. Alushin, G. M. 2024-10-11 doi:10.1101/2024.10.08.617332 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Identification of a specialized lipid barrier for Drosophila metamorphosis ]]> https://biorxiv.org/content/10.1101/2024.10.11.617838v1?rss=1 Lampe, L. Newell, C. L. Wang, B.-J. Makki, R. Alexandre, C. Gilmore, I. S. Zhao, L. Gould, A. P. 2024-10-12 doi:10.1101/2024.10.11.617838 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Enhancing cortico-motoneuronal projections for vocalization in mice ]]> https://biorxiv.org/content/10.1101/2024.10.14.618267v1?rss=1 Boyd, J. L. Kuper, L. Waidmann, E. Yang, V. Jarvis, E. D. 2024-10-16 doi:10.1101/2024.10.14.618267 Cold Spring Harbor Laboratory Press 2024-10-16 <![CDATA[ ybx1 acts upstream of atoh1a to promote the rapid regeneration of hair cells in zebrafish lateral-line neuromasts ]]> https://biorxiv.org/content/10.1101/2024.10.15.618534v1?rss=1 Reagor, C. C. Hudspeth, A. J. 2024-10-18 doi:10.1101/2024.10.15.618534 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Gut bacteria-derived succinate induces enteric nervous system regeneration ]]> https://biorxiv.org/content/10.1101/2024.10.15.618589v1?rss=1 Aydin, B. Mamede, I. Cardoso, J. Deere, J. Alvarez, Y. Qiao, S. Sharma, V. P. Scavuzzo, M. A. Donaldson, G. P. Guo, C.-J. Mucida, D. 2024-10-18 doi:10.1101/2024.10.15.618589 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Exact Continuous Spiking Rate Inference ]]> https://biorxiv.org/content/10.1101/2024.10.18.619111v1?rss=1 Stern, M. 2024-10-21 doi:10.1101/2024.10.18.619111 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ Ybx1 guides C/EBPα and cBAF chromatin-remodeling complex to promote adipogenic gene expression in steatotic hepatocytes ]]> https://biorxiv.org/content/10.1101/2024.10.25.620017v1?rss=1 Jordan, J. M. Qiao, J. Zou, C. Stenseels, S. Haczeyni, F. Fraim, A. Cisneros, A. M. de Jong, Y. P. Ersoy, B. 2024-10-26 doi:10.1101/2024.10.25.620017 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ Identifying Modulators of Cellular Responses by Heterogeneity-sequencing ]]> https://biorxiv.org/content/10.1101/2024.10.28.620481v1?rss=1 Berg, K. Sakellaridi, L. Rummel, T. Hennig, T. Whisnant, A. Lodha, M. Krammer, T. Prusty, B. K. Doelken, L. Saliba, A.-E. Erhard, F. 2024-10-29 doi:10.1101/2024.10.28.620481 Cold Spring Harbor Laboratory Press 2024-10-29 <![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[ Structure of the microtubule anchoring factor NEDD1 bound to the γ-tubulin ring complex ]]> https://biorxiv.org/content/10.1101/2024.11.05.622067v1?rss=1 Munoz Hernandez, H. Xu, Y. Zhang, D. Xue, A. Aher, A. Pellicer Camardiel, A. Walker, E. Maxer, F. Kapoor, T. M. Wieczorek, M. 2024-11-05 doi:10.1101/2024.11.05.622067 Cold Spring Harbor Laboratory Press 2024-11-05 <![CDATA[ DnaB and DciA: Mechanisms of Helicase Loading and Translocation on ssDNA ]]> https://biorxiv.org/content/10.1101/2024.11.09.622779v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@b0641dorg.highwire.dtl.DTLVardef@7caf59org.highwire.dtl.DTLVardef@1dc0fccorg.highwire.dtl.DTLVardef@913ce2_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO The Vibrio cholerae (Vc) DnaB replicative helicase structure bound to single-stranded (ss) DNA is depicted in the ribbon (top left) and sphere-cylinder representation (top right). In the bottom center is a native mass spectrum showing Vc DnaB helicase loading onto single-stranded DNA (ssDNA). C_FIG Replicative helicases are assembled on chromosomes by helicase loaders before initiation of DNA replication. Here, we investigate mechanisms used by the bacterial Vibrio cholerae (Vc) DnaB replicative helicase and the DciA helicase loader. Structural analysis of the ATP{gamma}S form of the VcDnaB-ssDNA complex reveals a configuration distinct from that seen with GDP*AlF4. With ATP{gamma}S, the amino-terminal (NTD) tier, previously found as an open spiral in the GDP*AlF4 complex, adopts a closed planar arrangement. Further, the DnaB subunit at the top of the carboxy-terminal spiral (CTD) tier is displaced by [~]25 [A] between the two forms. We suggest that remodeling the NTD layer between closed planar and open spiral configurations and migration of two distinct CTDs to the top of the DnaB spiral, repeated three times, mediates hand-over-hand translocation. Biochemical analysis suggests that VcDciA leverages its Lasso domain to contact DnaB near its Docking-Linker-Helix interface. Up to three copies of VcDciA bind to VcDnaB and suppress its ATPase activity during loading onto physiological DNA substrates. Our data suggest that DciA loads DnaB onto DNA using the ring-opening mechanism. ]]> Gao, N. Mazzoletti, D. Peng, A. Olinares, P. D. B. Morrone, C. Garavaglia, A. Gouda, N. Tsoy, S. Mendoza, A. Chowdhury, A. Cerullo, A. R. Bhavsar, H. Rossi, F. Rizzi, M. Chait, B. Miggiano, R. Jeruzalmi, D. 2024-11-09 doi:10.1101/2024.11.09.622779 Cold Spring Harbor Laboratory Press 2024-11-09 <![CDATA[ Extensive binding of uncharacterized human transcription factors to genomic dark matter ]]> https://biorxiv.org/content/10.1101/2024.11.11.622123v1?rss=1 Razavi, R. Fathi, A. Yellan, I. Brechalov, A. Laverty, K. U. Jolma, A. Hernandez-Corchado, A. Zheng, H. Yang, A. W. Albu, M. Barazandeh, M. Hu, C. Vorontsov, I. Patel, Z. M. The Codebook Consortium, Kulakovskiy, I. V. Bucher, P. Morris, Q. Najafabadi, H. S. Hughes, T. R. 2024-11-12 doi:10.1101/2024.11.11.622123 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Quantitative guiding of developmental cell fate transitions using gene-free modelling ]]> https://biorxiv.org/content/10.1101/2024.11.16.623539v1?rss=1 Hajji, I. Siggia, E. D. Corson, F. Keil, W. 2024-11-17 doi:10.1101/2024.11.16.623539 Cold Spring Harbor Laboratory Press 2024-11-17 <![CDATA[ ELAVL3 regulates splicing of RNAs encoding synaptic signaling proteins in D1 and D2 striatal medium spiny neurons. ]]> https://biorxiv.org/content/10.1101/2024.11.18.622571v1?rss=1 Irmady, K. Scheckel, C. Singer, R. A. Carroll, T. Darnell, R. B. 2024-11-19 doi:10.1101/2024.11.18.622571 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ Targeted detection of endogenous LINE-1 proteins and ORF2p interactions ]]> https://biorxiv.org/content/10.1101/2024.11.20.624490v1?rss=1 Nielsen, M. I. Wolters, J. C. Rosas Bringas, O. G. Jiang, H. Di Stefano, L. H. Oghbaie, M. Hozeifi, S. Nitert, M. J. van Pijkeren, A. Smit, M. ter Morsche, L. Mourtzinos, A. Deshpande, V. Taylor, M. S. LaCava, J. 2024-11-20 doi:10.1101/2024.11.20.624490 Cold Spring Harbor Laboratory Press 2024-11-20 <![CDATA[ Affinity maturation of antibody responses is mediated by differential plasma cell proliferation ]]> https://biorxiv.org/content/10.1101/2024.11.26.625430v1?rss=1 MacLean, A. J. Deimel, L. P. Zhou, P. ElTanbouly, M. A. Merkenschlager, J. Ramos, V. Santos, G. S. Hagglof, T. Mayer, C. T. Hernandez, B. Gazumyan, A. Nussenzweig, M. C. 2024-11-29 doi:10.1101/2024.11.26.625430 Cold Spring Harbor Laboratory Press 2024-11-29 <![CDATA[ PAG orchestrates T cell immune synapse function by binding to actin ]]> https://biorxiv.org/content/10.1101/2024.11.29.625440v1?rss=1 Moore, E. K. Strazza, M. Hu, X. Tymm, C. Paiola, M. Shannon, M. J. Xie, X. Bukhari, S.-S. Lerrer, S. Mace, E. M. Winchester, R. Mor, A. 2024-12-03 doi:10.1101/2024.11.29.625440 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ EOR-1/PLZF-regulated WAH-1/AIF sequentially promotes early and late stages of non-apoptotic corpse removal ]]> https://biorxiv.org/content/10.1101/2024.12.04.626465v1?rss=1 Rather, N. Williams, M. Elkhalil, A. Sharmin, R. Clark, G. Shaham, S. Ghose, P. 2024-12-05 doi:10.1101/2024.12.04.626465 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ CGC1, a new reference genome for Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2024.12.04.626850v1?rss=1 Ichikawa, K. Shoura, M. J. Artiles, K. L. Jeong, D.-E. Owa, C. Kobayashi, H. Suzuki, Y. Kanamori, M. Toyoshima, Y. Iino, Y. Rougvie, A. E. Wahba, L. Fire, A. Z. Schwarz, E. M. Morishita, S. 2024-12-05 doi:10.1101/2024.12.04.626850 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Modulation of the JAK2-STAT3 pathway promotes expansion and maturation of human iPSCs-derived myogenic progenitor cells ]]> https://biorxiv.org/content/10.1101/2024.12.09.624203v1?rss=1 Caputo, L. Stamenkovic, C. Tierney, M. T. Falzarano, M. S. Bassel-Duby, R. Ferlini, A. Olson, E. N. Puri, P. L. N. Sacco, A. 2024-12-10 doi:10.1101/2024.12.09.624203 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ Persistent genomic erosion in whooping cranes despite demographic recovery ]]> https://biorxiv.org/content/10.1101/2024.12.12.628160v1?rss=1 Fontsere, C. Speak, S. S. Caven, A. J. Rodriguez, J. A. Wang, X. Pacheco, C. Cassatt-Johnstone, M. Femerling, G. Maloney, B. Balacco, J. Collins, J. Sims, Y. Abueg, L. Fedrigo, O. Jarvis, E. D. Hartup, B. K. Shapiro, B. Gilbert, M. T. P. van Oosterhout, C. Morales, H. E. 2024-12-17 doi:10.1101/2024.12.12.628160 Cold Spring Harbor Laboratory Press 2024-12-17 <![CDATA[ The anti-inflammatory activity of IgG requires the co-engagement of types I and II Fc receptors ]]> https://biorxiv.org/content/10.1101/2024.12.16.628704v1?rss=1 Jones, A. T. Martynyuk, T. Marino, A. E. Bournazos, S. Ravetch, J. V. 2024-12-20 doi:10.1101/2024.12.16.628704 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Electric field-induced pore constriction in the human Kv2.1 channel ]]> https://biorxiv.org/content/10.1101/2024.12.18.629208v1?rss=1 Mandala, V. S. MacKinnon, R. 2024-12-20 doi:10.1101/2024.12.18.629208 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Gene regulatory networks and essential transcription factors for de novo originated genes ]]> https://biorxiv.org/content/10.1101/2024.12.19.629391v1?rss=1 Peng, J. Wang, B.-J. Svetec, N. Zhao, L. 2024-12-22 doi:10.1101/2024.12.19.629391 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ C. elegans LET-381/FoxF and DMD-4/DMRT control development of the mesodermal HMC endothelial cell ]]> https://biorxiv.org/content/10.1101/2024.12.23.630164v1?rss=1 Stefanakis, N. Xi, J. Jiang, J. Shaham, S. 2024-12-24 doi:10.1101/2024.12.23.630164 Cold Spring Harbor Laboratory Press 2024-12-24 <![CDATA[ Astrocyte-derived extracellular matrix proteins regulate synapse remodeling in stress-induced depression ]]> https://biorxiv.org/content/10.1101/2024.12.30.630684v1?rss=1 Zhang, R. Rodriguez-Rodriguez, P. Medrihan, L. Chang, J. C. Ferraro, T. Del Cioppo Vasques, P. McCabe, K. Wang, W. Menard, C. Cathomas, F. Chan, K. L. Parise, L. F. Shaham, S. Roussarie, J.-P. Troyanskaya, O. G. Russo, S. Milosevic, A. 2024-12-30 doi:10.1101/2024.12.30.630684 Cold Spring Harbor Laboratory Press 2024-12-30 <![CDATA[ Cell-type specific profiling of human entorhinal cortex at the onset of Alzheimer's disease neuropathology ]]> https://biorxiv.org/content/10.1101/2024.12.31.630881v1?rss=1 Rodriguez-Rodriguez, P. Wang, W. Tsagkogianni, C. Feng, I. Morello-Megias, A. Jain, K. Alanko, V. Kahvecioglu, H. Mohammadi, E. Li, X. Flajolet, M. Sandebring-Matton, A. Maioli, S. Vidal, N. Milosevic, A. Roussarie, J.-P. 2025-01-01 doi:10.1101/2024.12.31.630881 Cold Spring Harbor Laboratory Press 2025-01-01 <![CDATA[ Cross-reactive sarbecovirus antibodies induced by mosaic RBD-nanoparticles ]]> https://biorxiv.org/content/10.1101/2025.01.02.631145v1?rss=1 Fan, C. Keeffe, J. R. Malecek, K. E. Cohen, A. A. West, A. P. Baharani, V. A. Rorick, A. V. Gao, H. Gnanapragasam, P. N. P. Rho, S. Alvarez, J. Segovia, L. N. Hatziioannou, T. Bieniasz, P. D. Bjorkman, P. J. 2025-01-03 doi:10.1101/2025.01.02.631145 Cold Spring Harbor Laboratory Press 2025-01-03 <![CDATA[ Dynamic remodeling of centrioles and the microtubule cytoskeleton in the lifecycle of chytrid fungi ]]> https://biorxiv.org/content/10.1101/2025.01.03.631223v1?rss=1 Long, A. F. Vasudevan, K. Swafford, A. J. M. Venard, C. M. Stajich, J. E. Fritz-Laylin, L. K. Feldman, J. L. Stearns, T. 2025-01-04 doi:10.1101/2025.01.03.631223 Cold Spring Harbor Laboratory Press 2025-01-04 <![CDATA[ C. elegans interprets dietary quality through context-dependent serotonergic modulation ]]> https://biorxiv.org/content/10.1101/2025.01.05.631367v1?rss=1 Feng, L. Marquina-Solis, J. Yue, L. Harnagel, A. Greenfeld, Y. Bargmann, C. 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Ghose, P. 2025-01-13 doi:10.1101/2025.01.08.631976 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Squid primary cell culture as a model system and experimental tool ]]> https://biorxiv.org/content/10.1101/2025.01.12.632648v1?rss=1 Kim, Y. Tanner, H. M. Rosenthal, J. J. Brangwynne, C. P. 2025-01-13 doi:10.1101/2025.01.12.632648 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Heterozygosity at a conserved candidate sex determination locus is associated with female development in the clonal raider ant ]]> https://biorxiv.org/content/10.1101/2025.01.24.634795v1?rss=1 Lacy, K. D. Lee, J. Rozen-Gagnon, K. Wang, W. Carroll, T. S. Kronauer, D. J. C. 2025-01-27 doi:10.1101/2025.01.24.634795 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ The conserved N-terminal SANT1-binding domain (SBD) of EZH2 Regulates PRC2 Activity ]]> https://biorxiv.org/content/10.1101/2025.02.04.636462v1?rss=1 Patriotis, A. L. Soto-Feliciano, Y. Barrows, D. Khan, L. Leboeuf, M. Lund, P. Marunde, M. R. Djomo, A. Keogh, M.-C. Carroll, T. Garcia, B. Soshnev, A. A. Allis, C. D. 2025-02-05 doi:10.1101/2025.02.04.636462 Cold Spring Harbor Laboratory Press 2025-02-05 <![CDATA[ Anti- and Pro-tumor Functions of Distinct Regulatory T Cell Subsets in Colorectal Cancer ]]> https://biorxiv.org/content/10.1101/2025.02.07.637083v1?rss=1 Huang, X. Feng, D. Mitra, S. Andretta, E. S. Hooshdaran, N. B. Ghelani, A. p. Wang, E. Y. Frost, J. N. Lawless, V. R. Vancheswaran, A. Jiang, Q. Leslie, C. S. Rudensky, A. 2025-02-08 doi:10.1101/2025.02.07.637083 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Acetylation of histone H2B on lysine 120 regulates BRD4 binding to intergenic enhancers ]]> https://biorxiv.org/content/10.1101/2025.02.07.637147v1?rss=1 Hamilton, G. A. Ruiz, P. D. Ye, K. Gamble, M. J. 2025-02-08 doi:10.1101/2025.02.07.637147 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Real-time capture of σN transcription initiation intermediates reveals mechanism of ATPase-driven activation by limited unfolding ]]> https://biorxiv.org/content/10.1101/2025.02.07.637174v1?rss=1 Mueller, A. U. Molina, N. Darst, S. A. 2025-02-08 doi:10.1101/2025.02.07.637174 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ A vector-based strategy for olfactory navigation in Drosophila ]]> https://biorxiv.org/content/10.1101/2025.02.15.638426v1?rss=1 Siliciano, A. F. Minni, S. Morton, C. Dowell, C. K. Eghbali, N. B. Rhee, J. Y. Abbott, L. F. Ruta, V. 2025-02-16 doi:10.1101/2025.02.15.638426 Cold Spring Harbor Laboratory Press 2025-02-16 <![CDATA[ Structural Plasticity of RRE Stem-Loop II Modulates Nuclear Export of HIV-1 RNA ]]> https://biorxiv.org/content/10.1101/2025.02.20.639096v1?rss=1 Ojha, M. Hudson, L. Photenhauer, A. Zang, T. Lerew, L. Ekesan, S. Daniels, J. Nguyen, M. 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Freiwald, W. 2025-03-10 doi:10.1101/2025.03.04.641458 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Non-invasive in vivo bidirectional magnetogenetic modulation of pain circuits. ]]> https://biorxiv.org/content/10.1101/2025.03.18.644041v1?rss=1 Antoniazzi, A. M. Unda, S. R. Norman, S. Pomeranz, L. E. Marongiu, R. Stanley, S. A. Friedman, J. M. Kaplitt, M. G. 2025-03-19 doi:10.1101/2025.03.18.644041 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ The Na V1.5 auxiliary subunit FGF13 modulates channels by regulating membrane cholesterol independent of channel binding ]]> https://biorxiv.org/content/10.1101/2025.03.19.644183v1?rss=1 Gade, A. Malvezzi, M. Das, L. T. Matsui, M. Ma, C.-I. J. Mazdisnian, K. Marx, S. O. Maxfield, F. R. Pitt, G. 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Carandini, M. 2025-04-01 doi:10.1101/2025.03.26.645628 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Structural basis for Lamassu-based antiviral immunity and its evolution from DNA repair machinery ]]> https://biorxiv.org/content/10.1101/2025.04.02.646746v1?rss=1 Haudiquet, M. Chakravarti, A. Zhiying, Z. Ramirez, J. L. Herrero del Valle, A. Olinares, P. D. B. Lavenir, R. Aït Ahmed, M. de la Cruz, M. J. Chait, B. Sternberg, S. H. Bernheim, A. Patel, D. 2025-04-02 doi:10.1101/2025.04.02.646746 Cold Spring Harbor Laboratory Press 2025-04-02 <![CDATA[ Aging-dependent dysregulation of EXOSC2 is maintained in cancer as a dependency ]]> https://biorxiv.org/content/10.1101/2025.04.04.647279v1?rss=1 Skamagki, M. Zhang, C. Hacisuleyman, E. Galleti, G. Wu, C. Vinagolu, R. K. Cha, H. Ata, D. Kim, J. Weiskittel, T. Diop, M. Aung, T. Del Latto, M. Kim, A. S. Li, Z. Miele, M. Zhao, R. Tang, L. H. Hendrickson, R. C. Romesser, P. B. Smith, J. J. Giannakakou, P. Darnell, R. B. Bott, M. J. Li, H. Kim, K. 2025-04-07 doi:10.1101/2025.04.04.647279 Cold Spring Harbor Laboratory Press 2025-04-07 <![CDATA[ Mosquito sex under lock and key ]]> https://biorxiv.org/content/10.1101/2025.04.11.648401v1?rss=1 Houri-Zeevi, L. Walker, M. M. Razzauti, J. Sharma, A. Pasolli, H. A. Vosshall, L. B. 2025-04-16 doi:10.1101/2025.04.11.648401 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ Seasonal brain regeneration and chromosome instability are linked to selection on DNA repair in Sorex araneus ]]> https://biorxiv.org/content/10.1101/2025.04.11.648246v1?rss=1 Thomas, W. R. Lama, T. M. Moreno-Santillan, D. Farre, M. Baldoni, C. Abueg, L. Balacco, J. Fedrigo, O. Formenti, G. Jain, N. Mountcastle, J. Tilley, T. Tracey, A. Ray, D. A. Dechmann, D. K. N. von Elverfeldt, D. Nieland, J. Corthals, A. P. Jarvis, E. Davalos, L. M. 2025-04-17 doi:10.1101/2025.04.11.648246 Cold Spring Harbor Laboratory Press 2025-04-17 <![CDATA[ Codon-dependent regulation of mRNA translation and stability by ZC3H7A and ZC3H7B RNA-binding proteins ]]> https://biorxiv.org/content/10.1101/2025.04.21.649502v1?rss=1 Harris Snell, P. L. Naeli, P. Garzia, A. Waldron, J. A. Chatterjee, S. McGirr, T. Ladak, R. J. Choi, J.-H. Luo, J. Leino, S. Jess, N. Shariati, A. Soto Rodriguez, X. Gkogkas, C. G. Sonenberg, N. Tuschl, T. Maguire, S. Jafarnejad, S. M. 2025-04-23 doi:10.1101/2025.04.21.649502 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Short-term gonadal cultures are sufficient for germline transmission in a songbird ]]> https://biorxiv.org/content/10.1101/2025.04.25.650428v1?rss=1 Biegler, M. T. Harter, E. Sidhu, A. V. Szialta, C. Durham, G. Tchernichovski, L. Collier, P. Luo, J.-D. Wang, W. MacIsaac, R. Belay, K. Carroll, T. Keyte, A. L. Jarvis, E. D. 2025-04-29 doi:10.1101/2025.04.25.650428 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[ A CARF-HAD phosphatase effector provides immunity during the type III-A CRISPR-Cas response ]]> https://biorxiv.org/content/10.1101/2025.04.30.651354v1?rss=1 Stella, G. Ye, L. Brady, S. F. Marraffini, L. A. 2025-04-30 doi:10.1101/2025.04.30.651354 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ EnrichSci: Transcript-guided Targeted Cell Enrichment for Scalable Single-Cell RNA Sequencing ]]> https://biorxiv.org/content/10.1101/2025.05.02.651937v1?rss=1 Liao, A. Zhang, Z. Sziraki, A. Abdulraouf, A. Xu, Z. Lu, Z. Zhou, W. Cao, J. 2025-05-08 doi:10.1101/2025.05.02.651937 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Spatiotemporal profiling reveals the impact of caloric restriction on mammalian brain aging ]]> https://biorxiv.org/content/10.1101/2025.05.04.652093v1?rss=1 Zhang, Z. Epstein, A. Schaefer, C. Abdulraouf, A. Jiang, W. Zhou, W. Cao, J. 2025-05-08 doi:10.1101/2025.05.04.652093 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Short chain fatty acids regulate the chromatin landscape and distinct gene expression changes in human colorectal cancer cells ]]> https://biorxiv.org/content/10.1101/2025.05.07.652677v1?rss=1 Kabir, T. Connamacher, C. A. Nadeem, Z. Paul, M. R. Smutny, M. R. Lawler, Z. K. Djomo, A. M. Carroll, T. Gates, L. A. 2025-05-13 doi:10.1101/2025.05.07.652677 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Organism-wide cellular dynamics and epigenomic remodeling in mammalian aging ]]> https://biorxiv.org/content/10.1101/2025.05.12.653376v1?rss=1 Lu, Z. Zhang, Z. Xu, Z. Abdulraouf, A. Zhou, W. Cao, J. 2025-05-15 doi:10.1101/2025.05.12.653376 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Direct interoceptive input to the insular cortex shapes learned feeding behavior ]]> https://biorxiv.org/content/10.1101/2025.05.13.653896v1?rss=1 Zhao, Z. Xu, B. Anthony, S. Subramanian, S. Granger, B. Von-Walter, C. Mizrachi, E. Kidd, M. Srigiriraju, A. McKie, I. Li, Z. Bolton, M. M. Berto, S. Stern, S. A. 2025-05-17 doi:10.1101/2025.05.13.653896 Cold Spring Harbor Laboratory Press 2025-05-17 <![CDATA[ Epigenetic mechanisms governing cell type specific somatic expansion and toxicity in Huntington's disease ]]> https://biorxiv.org/content/10.1101/2025.05.21.653721v1?rss=1 Baffuto, M. Mätlik, K. Ilyashov, I. Siantoputri, M. E. Chetia, H. Harada, Y. Sipos, E. Darnell, P. Kus, L. Carroll, T. Barrows, D. Pressl, C. Didkovsky, N. Heintz, N. 2025-05-26 doi:10.1101/2025.05.21.653721 Cold Spring Harbor Laboratory Press 2025-05-26 <![CDATA[ Sequential transcriptional gates in the thalamo-cortical circuit coordinate memory stabilization ]]> https://biorxiv.org/content/10.1101/2025.05.28.656415v1?rss=1 Terceros, A. Chen, C. Harada, Y. Eilers, T. Gebremedhin, M. Koche, R. P. Hamard, P.-J. Sharma, R. Rajasethupathy, P. 2025-05-28 doi:10.1101/2025.05.28.656415 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Stroke-Related Changes in Tonic and Phasic Muscle Recruitment During Reaching Reveal Pathway-Specific Motor Deficits ]]> https://biorxiv.org/content/10.1101/2025.05.28.656732v1?rss=1 Korol, A. S. Adcock, A. Gritsenko, V. 2025-06-02 doi:10.1101/2025.05.28.656732 Cold Spring Harbor Laboratory Press 2025-06-02 <![CDATA[ Heat-off responses of epidermal cells sensitize Drosophila larvae to noxious inputs ]]> https://biorxiv.org/content/10.1101/2025.05.30.656957v1?rss=1 Yoshino, J. Chiu, A. Morita, T. Yin, C. Tenedini, F. M. Sokabe, T. Emoto, K. Parrish, J. Z. 2025-06-03 doi:10.1101/2025.05.30.656957 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Replaying germinal center evolution on a quantified affinity landscape ]]> https://biorxiv.org/content/10.1101/2025.06.02.656870v1?rss=1 DeWitt, W. S. S. Vora, A. A. Araki, T. Galloway, J. G. Alkutkar, T. Bortolatto, J. Castro, T. B. Dumm, W. Jennings-Schaffer, C. Jia, T. Mesin, L. Ozorowski, G. Pae, J. Ralph, D. K. Bloom, J. D. Nourmohammad, A. Song, Y. S. Ward, A. Starr, T. N. Matsen, F. A. Victora, G. D. 2025-06-05 doi:10.1101/2025.06.02.656870 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ A single factor for safer cellular rejuvenation ]]> https://biorxiv.org/content/10.1101/2025.06.05.657370v1?rss=1 de Lima Camillo, L. P. Gam, R. Maskalenka, K. LeBlanc, F. J. Urrutia, G. A. Mejia, G. M. Miller, H. E. Wardlaw, C. P. Pickles, A. Everton, L. Zaksauskaite, R. Khan, R. B. Welsh, A. Gambo, S. Gallardo, S. Oliynyk, Z. Varankar, S. S. Epstein, A. E. Bendall, A. Mowatt, J. Ives, D. Swain, B. M. 2025-06-06 doi:10.1101/2025.06.05.657370 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Defective plasticity in dermatomyositis patients muscle stem cells is associated with sustained intrinsic inflammatory signaling and disruption of the histone H3.3 chromatin loading pathway ]]> https://biorxiv.org/content/10.1101/2025.06.09.658580v1?rss=1 Bouchereau, W. Chenane, L. Lessard, L. Weiss-Gayet, M. Cardona, Y. Mounier, R. Gallay, L. Allenbach, Y. Benveniste, O. Corpet, A. Chazaud, B. Lomonte, P. 2025-06-11 doi:10.1101/2025.06.09.658580 Cold Spring Harbor Laboratory Press 2025-06-11 <![CDATA[ Neurons, Muscles, and Venom: Identifying Drivers of Cephalopod Predation ]]> https://biorxiv.org/content/10.1101/2025.06.15.659772v1?rss=1 Kirchhoff, K. N. Williams, M. Stambouli, B. Pardo-Blas, J. R. Courtney, A. Sugarman, A. L. Vanselow, D. J. Carrasco, C. Cuddy, C. Schafer, W. R. Cheng, K. C. Seuntjens, E. Holford, M. 2025-06-15 doi:10.1101/2025.06.15.659772 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Ablation of Prdm16 and beige fat causes vascular remodeling and elevated blood pressure ]]> https://biorxiv.org/content/10.1101/2025.06.12.658904v1?rss=1 Koenen, M. Becher, T. Pagano, G. Del Gaudio, I. Barrero, J. A. Montezano, A. C. Ortiz, J. R. Lin, Z. Gomez-Banoy, N. Amblard, R. Kars, M. E. Rubinelli, L. Halix, S. J. Cao, Z. H. Zeng, X. Butler, S. D. Itan, Y. Touyz, R. M. Di Lorenzo, A. Cohen, P. 2025-06-17 doi:10.1101/2025.06.12.658904 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Nucleotide-dependent conformational changes direct peptide export by the transporter associated with antigen processing ]]> https://biorxiv.org/content/10.1101/2025.06.12.659373v1?rss=1 Lee, J. Manon, V. Chen, J. 2025-06-17 doi:10.1101/2025.06.12.659373 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Nucleotide context models outperform protein language models for predicting antibody affinity maturation ]]> https://biorxiv.org/content/10.1101/2025.06.16.659977v1?rss=1 Johnson, M. M. Sung, K. Haddox, H. K. Vora, A. A. Araki, T. Victora, G. D. Song, Y. S. Fukuyama, J. Matsen, F. A. 2025-06-18 doi:10.1101/2025.06.16.659977 Cold Spring Harbor Laboratory Press 2025-06-18 <![CDATA[ The Luminal Ring Protein C2CD3 Acts as a Radial In-to-Out Organizer of the Distal Centriole and Appendages ]]> https://biorxiv.org/content/10.1101/2025.06.17.660204v1?rss=1 Bertiaux, E. Louvel, V. McCafferty, C. van den Hoek, H. Batman, U. Mukherjee, S. Bournonville, L. Mercey, O. Mean, I. Mueller, A. Van der Stappen, P. Buss, G. Daraspe, J. Genoud, C. Stearns, T. Engel, B. D. Hamel, V. Guichard, P. 2025-06-18 doi:10.1101/2025.06.17.660204 Cold Spring Harbor Laboratory Press 2025-06-18 <![CDATA[ A Structural Atlas of TAP Inhibition by Herpesviruses and Poxviruses ]]> https://biorxiv.org/content/10.1101/2025.06.19.660632v1?rss=1 Lee, J. Manon, V. Chen, J. 2025-06-20 doi:10.1101/2025.06.19.660632 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ The end of the American dream: a hard to Swallow reality - How the Barn Swallow (Hirundo rustica) returned from America, a complete mtDNA phylogeny ]]> https://biorxiv.org/content/10.1101/2025.06.23.661004v1?rss=1 Lombardo, G. Gallo, G. R. De Benedictis, A. Cavallini, M. Formenti, G. Ambrosini, R. Gianfranceschi, L. Binelli, G. 2025-06-27 doi:10.1101/2025.06.23.661004 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Centriole biogenesis is seeded by CEP152-CEP63-PCNT aggregates propagating outside the centriole through the Alstrom syndrome protein ALMS1 ]]> https://biorxiv.org/content/10.1101/2025.06.26.661604v1?rss=1 Ozaki, K. Chang, T.-J. B. Yang, W.-Q. Shulman, A. Izquierdo, D. Jane, W.-N. Wang, W.-J. Stearns, T. Luders, J. Yang, T. T. Tsou, M.-F. B. 2025-06-27 doi:10.1101/2025.06.26.661604 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Clonal Expansion and Diversification of Germinal Center and Memory B Cell Responses to Booster Immunization in Primates ]]> https://biorxiv.org/content/10.1101/2025.06.27.661994v1?rss=1 Deimel, L. P. Nishimura, Y. Silva Santos, G. S. Baharani, V. A. Hernandez, B. Oliveira, T. Y. MacLean, A. J. Canis, M. Shawraz, S. Gazumyan, A. Hartweger, H. Bieniasz, P. D. Hatziioannou, T. Martin, M. A. Nussenzweig, M. C. 2025-06-30 doi:10.1101/2025.06.27.661994 Cold Spring Harbor Laboratory Press 2025-06-30 <![CDATA[ DNA polymerase α-primase can function as a translesion DNA polymerase ]]> https://biorxiv.org/content/10.1101/2025.07.02.662785v1?rss=1 20 base hybrid RNA-DNA primer. Interestingly, the DNA Pol1 subunit of Pol lacks a 3-5 proofreading exonuclease, contrary to the high fidelity normally associated with DNA replication. However, Polo and Pol{delta} synthesize the majority of the eukaryotic genome and both contain 3-5 exonuclease activity for high fidelity. None the less, even the small amount of DNA produced by Pol1 in each of the many RNA/DNA primers during chromosome replication adds up to tens of millions of nucleotides in a human genome. Thus it has been a longstanding question why Pol1 lacks a proofreading exonuclease. We show here that Pol is uniquely capable of traversing common oxidized or hydrolyzed template nucleotides and propose that Pol evolved to bypass these common template lesions when they are encountered during chromosome replication. Significance statementEukaryotic Pol-primase contains DNA polymerase (Pol1) and RNA primase subunits that together synthesize a >20 nucleotide hybrid RNA-DNA primer. Bacteria and archaea only require a dozen or less RNA residues to prime DNA synthesis. Therefore, why do eukaryotes require the additional DNA? We propose, and demonstrate here that Pol1, which lacks a proofreading 3-5 exonuclease, is capable of traversing some common template lesions produced in the normal hydrolytic and metabolic oxidative environment of cells. Thus, we hypothesize that Pol1 activity within the eukaryotic primase evolved to help replisomes bypass template damage. Bypassed damaged sites can be dealt with by repair processes after replication has occurred. ]]> Mayle, R. Georgescu, R. O'Donnell, M. E. 2025-07-02 doi:10.1101/2025.07.02.662785 Cold Spring Harbor Laboratory Press 2025-07-02 <![CDATA[ Acute cold exposure in humans shifts the circulating proteome to a cardioprotective and anti-aging profile ]]> https://biorxiv.org/content/10.1101/2025.06.30.662436v1?rss=1 Plucinska, K. Chen, Z.-Z. Xiang, R. Zaman, S. Yan, L. Hurson, C. Peterson, C. Fredrickson, K. Farrell, L. Walker, J. Kars, M. E. Tiwari, G. Pourquie, O. Itan, Y. Carroll, T. Chen, K. Y. Cypess, A. M. Gerszten, R. E. Cohen, P. 2025-07-04 doi:10.1101/2025.06.30.662436 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Fishexplorer: A multimodal cellular atlas platform for neuronal circuit dissection in larval zebrafish ]]> https://biorxiv.org/content/10.1101/2025.07.14.664689v1?rss=1 Vohra, S. K. Eberle, M. Boulanger-Weill, J. Petkova, M. D. Schuhknecht, G. F. P. Herrera, K. J. Kämpf, F. Ruetten, V. M. S. Lichtman, J. W. Engert, F. Randlett, O. Bahl, A. Isoe, Y. Hege, H.-C. Baum, D. 2025-07-15 doi:10.1101/2025.07.14.664689 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ Programmed DNA elimination drives rapid genomic innovation in two thirds of all bird species ]]> https://biorxiv.org/content/10.1101/2025.07.16.664580v1?rss=1 Ruiz-Ruano, F. J. Schlebusch, S. A. Vontzou, N. Moreno, H. Biegler, M. T. Kutschera, V. E. Ekman, D. Borges, I. Pei, Y. Rossini, R. Albrecht, T. Boman, J. Borodin, P. Burri, R. Cain, K. E. Forstmeier, W. Frankl-Vilches, C. Gahr, M. Griffith, S. C. Hill, A. M. Irestedt, M. Joseph, L. Jonsson, K. A. Kawakami, T. Kempenaers, B. Malinovskaya, L. Mueller, J. C. de Oliveira, E. H. C. Palacios-Gimenez, O. M. Palinauskas, V. Qvarnström, A. Reifova, R. Ridl, J. Segami, J. C. Tan, D. J. X. Torgasheva, A. Whibley, A. Suh, A. 2025-07-18 doi:10.1101/2025.07.16.664580 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Global cis-regulatory landscape of double-stranded DNA viruses ]]> https://biorxiv.org/content/10.1101/2025.07.20.665756v1?rss=1 Taslim, T. H. Finkelberg, J. A. Kales, S. Soto-Ugaldi, L. D'Elia, B. Engin, B. Munoz-Esquivel, G. Morara, E. Purinton, J. Chandok, H. Rottenberg, J. T. Castro, R. Martinez-Cuesta, L. Paz, M. A. Tewhey, R. Bass, J. I. F. 2025-07-20 doi:10.1101/2025.07.20.665756 Cold Spring Harbor Laboratory Press 2025-07-20 <![CDATA[ Clonal lineage tracing of innate immune cells in human cancer ]]> https://biorxiv.org/content/10.1101/2025.07.16.665245v1?rss=1 Liu, V. Sandor, K. Yan, P. K. Miao, M. Yin, Y. Stickels, R. R. Chen, A. Y. Hiam-Galvez, K. Gutierrez, J. Zhang, W. Sajjath, S. M. Valbuena, R. Wang, S. Daniel, B. Ludwig, L. S. Howitt, B. E. Lareau, C. A. Satpathy, A. T. 2025-07-21 doi:10.1101/2025.07.16.665245 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Mouse pups lacking a cerebral cortex develop abnormal vocal behavior ]]> https://biorxiv.org/content/10.1101/2025.07.17.665371v1?rss=1 Boyd, J. L. Vargas, C. Jarvis, E. D. 2025-07-22 doi:10.1101/2025.07.17.665371 Cold Spring Harbor Laboratory Press 2025-07-22 <![CDATA[ Axonal defasciculation is restricted to specific branching points during regeneration of the lateral line nerve in zebrafish ]]> https://biorxiv.org/content/10.1101/2025.07.23.666336v1?rss=1 Roy, R. S. Hudspeth, A. J. 2025-07-25 doi:10.1101/2025.07.23.666336 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ Chemogenetic and optogenetic strategies for spatiotemporal control of split-enzyme-based calcium recording ]]> https://biorxiv.org/content/10.1101/2025.07.22.665990v1?rss=1 Zhang, Y. Campmier, B. K. Sharma, A. Eckartt, K. N. Laughlin, S. T. 2025-07-26 doi:10.1101/2025.07.22.665990 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ Human iPSC derived alveolar macrophages reveal macrophage subtype specific functions of itaconate in M. tuberculosis host defense ]]> https://biorxiv.org/content/10.1101/2025.07.23.664455v1?rss=1 Krebs, A. Lazarov, T. Reynolds, A. Dill-McFarland, K. A. Xie, A. Bean, J. Du, M. Levy, O. Buglino, J. Zhong, A. Neehus, A.-L. Boisson-Dupuis, S. Casanova, J.-L. Kroon, E. E. Moller, M. Hawn, T. R. Zhou, T. Finley, L. Juste, M.-A. J. Fitzgerald, D. Geissmann, F. Glickman, M. S. 2025-07-26 doi:10.1101/2025.07.23.664455 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ Compositionality of social gaze in the prefrontal-amygdala circuits ]]> https://biorxiv.org/content/10.1101/2025.07.28.667161v1?rss=1 Qi, G. Dal Monte, O. Fan, S. Chang, S. W. C. 2025-07-29 doi:10.1101/2025.07.28.667161 Cold Spring Harbor Laboratory Press 2025-07-29 <![CDATA[ Recurrent connectivity supports carbon dioxide sensitivity in Aedes aegypti mosquitoes ]]> https://biorxiv.org/content/10.1101/2025.07.29.667487v1?rss=1 Bao, J. Alford, W. Khandelwa, A. Walsh, L. Lantz, G. Poncio, S. Capdevila, L. S. Azatian, Y. DePasquale, B. Hildebrand, D. G. Younger, M. A. Lee, W.-C. A. 2025-07-30 doi:10.1101/2025.07.29.667487 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ Differential Bioenergetic Profile of Human Glioblastoma following Transplantation of Myocyte-derived Mitochondria ]]> https://biorxiv.org/content/10.1101/2025.08.01.668058v1?rss=1 Marshall, K. L. Meadows, E. Mizener, A. Hollander, J. M. Cifarelli, C. P. 2025-08-01 doi:10.1101/2025.08.01.668058 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Murine cytomegalovirus evolved a cell-cycle regulator (m54.5) within the highly conserved viral DNA polymerase gene ]]> https://biorxiv.org/content/10.1101/2025.08.04.668388v1?rss=1 200 aa gene product within a deeply conserved viral gene locus. Author SummarySystems biology approaches have revealed a surprising complexity of herpesvirus gene products. Using advanced sequencing approaches, we discovered a novel gene, m54.5, that independently evolved within a highly conserved region of the murine cytomegalovirus (MCMV) genome. This gene, which shows no conservation in other CMVs, produces a nuclear protein, m54.5p, abundantly expressed early during infection. We show that m54.5p interacts with host cell cycle regulators--the anaphase-promoting complex/cyclosome (APC/C) and phosphatase-6 (PP6)--to arrest cells in G1 phase and block progression into S phase. This function and underlying mechanism are reminiscent of the unrelated UL21a protein in human cytomegalovirus, illustrating how distinct viruses can evolve similar strategies to control host cell division. Despite its role in cell cycle disruption, m54.5p is not required for MCMV replication in cultured cells, suggesting redundant viral mechanisms. Our findings reveal an unexpected plasticity of herpesvirus genomes to evolve new, functional transcripts and proteins even within one of the most highly conserved genomic regions. Our findings thereby reshape our understanding of herpesvirus evolution and virus-host interaction. ]]> Zheng, Y. Juranic Lisnic, V. Lamer, S. Schlosser, A. Dölken, L. Lodha, M. 2025-08-04 doi:10.1101/2025.08.04.668388 Cold Spring Harbor Laboratory Press 2025-08-04 <![CDATA[ O-mannose glycosylations influence E-cadherin functional interactions ]]> https://biorxiv.org/content/10.1101/2025.08.05.668670v1?rss=1 Xie, S. Madunic, K. Rosas Bringas, O. G. Tian, W. Vakhrushev, S. Y. Permentier, H. Horvatovich, P. Halim, A. LaCava, J. 2025-08-06 doi:10.1101/2025.08.05.668670 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ HIV-1 expression is heterogeneous among clones of CD4+ T cells carrying authentic intact latent proviruses ]]> https://biorxiv.org/content/10.1101/2025.08.05.668730v1?rss=1 Bittar, C. Teixeira, A. R. Oliveira, T. Y. Santos, G. S. S. Lenart, K. Fumagalli, M. J. Linden, N. L. Ferreira, I. A. T. M. Caskey, M. Jones, R. B. Jankovic, M. Nussenzweig, M. C. 2025-08-07 doi:10.1101/2025.08.05.668730 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Bottlebrush Polymer Conjugates for Enhanced Antisense Oligonucleotide Therapy in Myotonic Dystrophy Type 1 ]]> https://biorxiv.org/content/10.1101/2025.08.06.668589v1?rss=1 View larger version (21K): org.highwire.dtl.DTLVardef@e3961corg.highwire.dtl.DTLVardef@194225dorg.highwire.dtl.DTLVardef@5c470dorg.highwire.dtl.DTLVardef@3cc46a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Li, Y. Oetheimer, C. Wang, Y. Heo, G. S. Wu, J. Chang, R. Zhang, W. Schneider, E. Chen, J. Fang, Y. Wei, Y. Nian, K. Zhang, H. Sherman, L. Liu, Y. Zhang, K. 2025-08-08 doi:10.1101/2025.08.06.668589 Cold Spring Harbor Laboratory Press 2025-08-08 <![CDATA[ Causal Dynamics of Social Gaze in Primate Prefrontal-Amygdala Networks Revealed by Dynamic Bayesian Modeling ]]> https://biorxiv.org/content/10.1101/2025.08.08.669405v1?rss=1 Xing, F. Fan, S. Dal Monte, O. Jadi, M. Chang, S. Nandy, A. 2025-08-10 doi:10.1101/2025.08.08.669405 Cold Spring Harbor Laboratory Press 2025-08-10 <![CDATA[ A non-catalytic role for RFC in PCNA-mediated processive DNA synthesis ]]> https://biorxiv.org/content/10.1101/2025.08.08.669392v1?rss=1 Chua, G. N. L. Beckwitt, E. C. Miller-Browne, V. Yurieva, O. Zhang, D. Katch, B. J. Watters, J. W. Abrantes, K. Funabiki, R. Zhao, X. O'Donnell, M. E. Liu, S. 2025-08-12 doi:10.1101/2025.08.08.669392 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Reconstructing Waddington's Landscape from Data ]]> https://biorxiv.org/content/10.1101/2025.08.11.669575v1?rss=1 Cislo, D. J. Delas, M. J. Briscoe, J. Siggia, E. D. 2025-08-13 doi:10.1101/2025.08.11.669575 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ Genomic resources for comparative analyses of obligate avian brood parasitism ]]> https://biorxiv.org/content/10.1101/2025.08.12.669747v1?rss=1 97%. Leveraging this new catalog of avian genomes, we constructed clade-level alignments that reveal variation in chromosomal synteny, provide first-time or improved annotations of protein-coding and non-coding genes, and define cross-species ortholog reference sets. We also refine estimates for the timing of the seven independent origins of brood parasitism, ranging from recent events such as 1.6 to 4.5 million years ago in Molothrus cowbirds to much earlier origins over 30 million years ago in two of the three cuckoo lineages. These genomic resources lay the foundation for investigating the genetic and genomic underpinnings of brood parasitism, including the loss of parental care, shifts in mating systems, perhaps resulting in heightened sperm competition, elevated annual fecundity, improved spatial cognition related to nest-finding, and the diverse adaptations shaped by intense coevolution with host species. ]]> Carroll, R. A. Ricemeyer, E. S. Hillier, L. W. DaCosta, J. M. Osipova, E. Smith, S. Jamie, G. Martinez, J. G. Molina-Morales, M. Marques-Bonet, T. Manthey, J. D. Haddad, D. Fuxjager, M. J. Lynch, K. S. Wood, J. M. D. Jarvis, E. Masterson, P. Thibaud-Nissen, F. Hauber, M. Spottiswoode, C. N. Sackton, T. B. Balakrishnan, C. N. Sorenson, M. D. Warren, W. C. 2025-08-15 doi:10.1101/2025.08.12.669747 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Inference of germinal center evolutionary dynamics via simulation-based deep learning ]]> https://biorxiv.org/content/10.1101/2025.08.12.669950v1?rss=1 Ralph, D. K. Bakis, A. G. Galloway, J. Vora, A. A. Araki, T. Song, Y. S. DeWitt, W. S. Matsen, F. A. 2025-08-15 doi:10.1101/2025.08.12.669950 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Temporal Deconvolution of Mesoscale Recordings ]]> https://biorxiv.org/content/10.1101/2025.08.13.670164v1?rss=1 Stern, M. Shea-Brown, E. 2025-08-18 doi:10.1101/2025.08.13.670164 Cold Spring Harbor Laboratory Press 2025-08-18 <![CDATA[ A Toolkit for In Vivo Mapping and Modulating Neurotransmission at Single-Cell Resolution ]]> https://biorxiv.org/content/10.1101/2025.08.18.670838v1?rss=1 Cuentas-Condori, A. Chanaba-Lopez, P. Thomas, M. Feng, L. Wolfe, A. Agoba, P. Schwartz, M. L. Brown, M. Ebert, M. Jorgensen, E. Bargmann, C. I. Colon-Ramos, D. A. 2025-08-18 doi:10.1101/2025.08.18.670838 Cold Spring Harbor Laboratory Press 2025-08-18 <![CDATA[ A predicted structural interactome reveals binding interference from intrinsically disordered regions ]]> https://biorxiv.org/content/10.1101/2025.08.15.670535v1?rss=1 Peng, J. Zhao, L. 2025-08-20 doi:10.1101/2025.08.15.670535 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ Transcriptional Interference Gates Monogenic Odorant Receptor Expression in Ants ]]> https://biorxiv.org/content/10.1101/2025.08.21.671318v1?rss=1 Glotzer, G. L. H. Pastor, P. D. Kronauer, D. J. C. 2025-08-21 doi:10.1101/2025.08.21.671318 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Artificial Intelligence-driven Whole-brain Cell Mapping with Highly Multiplexed In Situ Hybridization ]]> https://biorxiv.org/content/10.1101/2025.08.18.670857v1?rss=1 Murakami, T. Xia, M. Maeda, Y. Yin, Y. Barbano, P. E. Lin, Z. Mano, T. Tainaka, K. Reiter, S. Heintz, N. 2025-08-22 doi:10.1101/2025.08.18.670857 Cold Spring Harbor Laboratory Press 2025-08-22 <![CDATA[ High-Throughput Screening and Initial SAR Studies Identify a Novel Sub-micromolar Potent Human cGAS Inhibitor ]]> https://biorxiv.org/content/10.1101/2025.08.18.670979v1?rss=1 Alarcon-Esposito, J. Nagiri, R. K. Wang, S. Larson, C. Carvallo-Torres, L. Singh, V. K. Gan, L. Sinha, S. C. 2025-08-22 doi:10.1101/2025.08.18.670979 Cold Spring Harbor Laboratory Press 2025-08-22 <![CDATA[ A Nature-Inspired Ion Trap for Parallel Manipulation of Ions on a Massive Scale ]]> https://biorxiv.org/content/10.1101/2025.08.21.671534v1?rss=1 10 ions to be confined and manipulated simultaneously. This architecture enables selective depletion of singly charged ions in real time, greatly improving signal-to-noise ratios and detection sensitivity. The trap also functions as a parallel ion splitter, transmitting ions into multiple m/z-specific beams. We demonstrate scalable ion throughput, real-time charge discrimination, and parallel beam separation, suggesting a path toward truly parallel MS. Our results offer a foundation for next-generation, high-throughput proteomic and metabolomic analyses. ]]> Chait, B. T. Krutchinsky, A. N. 2025-08-25 doi:10.1101/2025.08.21.671534 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ Exaggerated NMDA Receptor-Primed Metaplasticity via SK Channel Dysregulation in Fmr1 Knockout Mice ]]> https://biorxiv.org/content/10.1101/2025.08.26.672454v1?rss=1 Nomura, T. Morton, C. Contractor, A. 2025-08-27 doi:10.1101/2025.08.26.672454 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Tissue-specific clonal selection and differentiation of CD4+ T cells during infection ]]> https://biorxiv.org/content/10.1101/2025.08.25.672130v1?rss=1 Parsa, R. Carvalho de Assis, H. B.R. de Castro, T. Lima dos Reis, G. Hartweger, H. Bilate, A. Mucida, D. 2025-08-28 doi:10.1101/2025.08.25.672130 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ CDK4/6 inhibition induces a DNA damage-independent senescence-associated secretory phenotype driven by delayed activation of NF-κB ]]> https://biorxiv.org/content/10.1101/2025.08.25.672139v1?rss=1 Yeung, J. L.-H. Rendleman, J. Anderson, L. Pressler, M. Pagane, N. Duba, I. Hosuru, R. Tumenbayar, B.-I. Koff, A. Risca, V. I. 2025-08-29 doi:10.1101/2025.08.25.672139 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ Nuclear morphology and chromatin organization modulate T cell cytoskeletal remodeling and immune synapse formation ]]> https://biorxiv.org/content/10.1101/2025.08.25.672234v1?rss=1 Suarez, I. A. R. Pathni, A. Fazekas, F. Connell, M. Upadhyaya, A. 2025-08-29 doi:10.1101/2025.08.25.672234 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ Distinct modes of evolution drive HIV escape from two broadly neutralizing antibodies. ]]> https://biorxiv.org/content/10.1101/2025.08.29.673185v1?rss=1 Romero, E. V. Clyde, A. E. Giorgi, E. E. Westfall, D. H. Azam, W. Taylor, M. L. Caskey, M. Feder, A. F. Cohn, L. B. 2025-08-30 doi:10.1101/2025.08.29.673185 Cold Spring Harbor Laboratory Press 2025-08-30 <![CDATA[ Learning local geometry and nonlinear topology of neural manifolds via spike-timing dependent plasticity ]]> https://biorxiv.org/content/10.1101/2025.08.27.672728v1?rss=1 Schonsheck, N. Giusti, C. 2025-09-01 doi:10.1101/2025.08.27.672728 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ Structural basis for loading of Transcription Repair-Coupling factor Mfd onto stalled elongation complexes ]]> https://biorxiv.org/content/10.1101/2025.09.05.674597v1?rss=1 L2(ADP) -> C1(ATP) -> C2(ATP) -> C3(ADP) -> C4(ADP) -> C5(ATP)]. The first intermediate (L1) was poorly resolved (4.1 [A] nominal resolution) due to low particle occupancy. The pathway is characterized by very large Mfd structural transitions, notably the L1 -> L2 transition. Here, we pre-loaded Mfd with ATP in the presence of the{gamma} -phosphate mimic, BeF3-, limiting rounds of ATP hydrolysis. The resulting accumulation of early intermediates allowed us to resolve the L1 intermediate to 3.5 [A] nominal resolution, revealing bound ADP-BeF3-. We also identified a new intermediate between L1 and L2, L1.5, providing further insight into Mfd conformational changes during loading. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/674597v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@1472098org.highwire.dtl.DTLVardef@acfca3org.highwire.dtl.DTLVardef@fe4424org.highwire.dtl.DTLVardef@12bc521_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Brewer, J. Llewellyn, E. Campbell, E. A. Darst, S. A. 2025-09-06 doi:10.1101/2025.09.05.674597 Cold Spring Harbor Laboratory Press 2025-09-06 <![CDATA[ Biomonitoring in the Anthropocene: Urban estuary environmental DNA tracks marine fish, terrestrial wildlife, and human diet ]]> https://biorxiv.org/content/10.1101/2025.09.04.674353v1?rss=1 Stoeckle, M. Y. Ausubel, J. 2025-09-08 doi:10.1101/2025.09.04.674353 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ Tumor Genotype Dictates Mitochondrial and Immune Vulnerabilities in Liver Cancer ]]> https://biorxiv.org/content/10.1101/2025.09.10.675369v1?rss=1 Unlu, G. Millet, A. Wangdu, K. Donne, R. Erdal, R. DelGaudio, N. L. Uygur, B. Shah, V. Cho, K. Fecke, A. Cansiz, F. Tarcan, Z. C. Isay-Del Viscio, M. Kilic, E. Kurth, I. Molina, H. Sickmann, A. Basturk, O. Patti, G. Beyaz, S. Smith, K. W. Lujambio, A. Tasdogan, A. Tavazoie, S. F. Birsoy, K. 2025-09-11 doi:10.1101/2025.09.10.675369 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Genes required for Mycobacterium tuberculosis to survive the transition from aerosol to pulmonary alveolar lining fluid and early infection in a model of transmission ]]> https://biorxiv.org/content/10.1101/2025.09.15.676370v1?rss=1 Nathan, C. F. Singh, P. R. Mishra, S. Jinich, A. Jiang, X. Tsang, F. DeJesus, M. Rhee, K. Kaner, R. Leopold, P. Crystal, R. G. 2025-09-15 doi:10.1101/2025.09.15.676370 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ Chromosome-level genome assembly of the Brazilian merganser (Mergus octosetaceus), a rare and elusive waterfowl species ]]> https://biorxiv.org/content/10.1101/2025.09.16.676261v1?rss=1 Granger-Neto, H. P. Borges, I. R. F. Cavalcanti, D. B. Campos, D. P. Horan, K. Balacco, J. O'Toole, B. Tilley, T. Jain, N. Abueg, L. Brajuka, N. Formenti, G. P. Fedrigo, O. Jarvis, E. Santos, F. R. 2025-09-19 doi:10.1101/2025.09.16.676261 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ An immunocompetent murine model of virus-elicited liver fibrosis and hepatocellular carcinoma ]]> https://biorxiv.org/content/10.1101/2025.09.19.677076v1?rss=1 Batista, M. N. Bordignon, J. Mosimann, A. L. P. Bobrowski, T. Chen, H.-A. Tobin-Xet, G. Barrall, E. A. Prokhnevska, N. Vaidya, A. B. Lewy, T. Dinnon, K. H. Seifert, L. L. Zeck, B. Quirk, C. Ho, Y.-J. Filiol, A. Wolfisberg, R. Jiang, C. Cogliati, B. Chiriboga, L. Theise, N. MacDonald, M. R. Kamphorst, A. Scheel, T. K. H. Sheahan, T. P. Billerbeck, E. Lowe, S. Rosenberg, B. R. Rice, C. M. 2025-09-21 doi:10.1101/2025.09.19.677076 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Designing signaling environments to modulate neural progenitor cell differentiation with regulatory network models ]]> https://biorxiv.org/content/10.1101/2025.09.20.677552v1?rss=1 Jiang, J. Chen, S. Park, J. H. Tsou, T. Yang, V. Rivaud, P. Thomson, M. 2025-09-21 doi:10.1101/2025.09.20.677552 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ A complete diploid human genome benchmark for personalized genomics ]]> https://biorxiv.org/content/10.1101/2025.09.21.677443v1?rss=1 Hansen, N. F. Dwarshuis, N. Ji, H. J. Rhie, A. Loucks, H. Logsdon, G. A. Vollger, M. R. Storer, J. M. Kim, J. Adam, E. Altemose, N. Antipov, D. Asri, M. Barreira, S. Bohaczuk, S. C. Bzikadze, A. V. Carioscia, S. A. Carroll, A. Chao, K.-H. Chu, Y. Das, A. Ebert, P. English, A. Fleharty, M. Fleming, L. E. Formenti, G. Guarracino, A. Hartley, G. A. Jenike, K. Kalleberg, J. Kang, Y. King, R. Lipovac, J. Mastoras, M. Mitchell, M. W. Negi, S. Olson, N. D. Oshima, K. K. Paulin, L. F. Pickett, B. D. Porubsky, D. Ranchalis, J. Ranjan, D. Rautiainen, M. Riethm 2025-09-21 doi:10.1101/2025.09.21.677443 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ CryoEM of ATP-driven dynamics and itraconazole binding in a fungal ABC pump ]]> https://biorxiv.org/content/10.1101/2025.09.22.677697v1?rss=1 Pata, J. Wiseman, B. Zarkadas, E. Baccouch, R. Samrouth, N. Desbois, C. Moissonier, L. Moreno, A. Banerjee, A. Aguerro, S. Bettler, E. Dujardin, M. Terreux, R. Schoehn, G. Hogbom, M. Boumendjel, A. Lamping, E. Cannon, R. Prasad, R. Chaptal, V. Falson, P. 2025-09-22 doi:10.1101/2025.09.22.677697 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ Korean Natural Farming practices are dominated by a limited number of microbes and decrease fungal diversity ]]> https://biorxiv.org/content/10.1101/2025.09.26.678907v1?rss=1 Thompson, C. Mozeika, S. Paredes, E. Lee, U. 2025-09-27 doi:10.1101/2025.09.26.678907 Cold Spring Harbor Laboratory Press 2025-09-27 <![CDATA[ Distinct genomic architectures but the same gene underlie the convergent evolution of a plant supergene ]]> https://biorxiv.org/content/10.1101/2025.10.01.679701v1?rss=1 Potente, G. Yousefi, N. Choudhury, R. R. Grob, S. Gavrilina, I. A. Keller, B. Mora-Carrera, E. Szovenyi, P. Stubbs, R. L. Weiss-Schneeweiss, H. Temsch, E. M. Schneeweiss, G. M. Hoffmann, M. H. Formenti, G. Mc Cartney, A. M. Mouton, A. Leitao, H. G. Diedericks, G. Svardal, H. Diroma, M. A. Natali, C. Ciofi, C. Leveille-Bourret, E. Conti, E. 2025-10-01 doi:10.1101/2025.10.01.679701 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Memory B cell Development in Response to mRNA SARS-CoV-2 and Nanoparticle Immunization in Mice ]]> https://biorxiv.org/content/10.1101/2025.10.01.679787v1?rss=1 Wiatr, m. wang, z. Canis, M. Gazumyan, A. hernandez, B. Santos, G. S. Shawraz, S. lee, S. Bieniasz, P. D. Hatziioannou, T. Muecksch, F. Nussenzweig, M. C. 2025-10-02 doi:10.1101/2025.10.01.679787 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Persistent interferon signaling and clonal expansion mark early events in DNA methylation damage-induced liver cancer ]]> https://biorxiv.org/content/10.1101/2025.10.01.679856v1?rss=1 Pribyl, L. J. Kay, J. E. Corrigan, J. J. Volk, L. B. Norales, M. Owiti, N. A. Kowal, E. A. Kohale, I. N. Nazari, I. S. Swanson, M. R. Moise, A. C. Ma, D. Levine, S. S. Michelsen, E. Croy, R. G. Ragan, T. Torous, D. K. Avlasevich, S. L. Dertinger, S. D. Carrasco, S. E. Samson, L. D. Essigmann, J. M. White, F. M. Engelward, B. P. 2025-10-03 doi:10.1101/2025.10.01.679856 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Re-infection with SARS-CoV-2 is associated with increased antibody breadth and potency against diverse sarbecovirus strains ]]> https://biorxiv.org/content/10.1101/2025.10.03.679858v1?rss=1 Lilly, M. Ruiz, F. Foreman, W. Chohan, V. Guenthoer, J. Depierreux, D. Baharani, V. Ralph, D. Harteloo, A. Chu, H. Bieniasz, P. D. Starr, T. Overbaugh, J. 2025-10-06 doi:10.1101/2025.10.03.679858 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[ Astrocytes and neurons encode natural stimuli with partially shared but distinct composite receptive fields ]]> https://biorxiv.org/content/10.1101/2025.10.06.680791v1?rss=1 Lu, S. Schultz, S. R. Kozlov, A. S. 2025-10-07 doi:10.1101/2025.10.06.680791 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Ecological cues orchestrate concerted courtship in a Drosophila host specialist ]]> https://biorxiv.org/content/10.1101/2025.10.13.681913v1?rss=1 Brand, P. Keller, K. Coleman, R. T. Eghbali, N. B. Zylka, S. Prieto-Godino, L. L. Ruta, V. 2025-10-14 doi:10.1101/2025.10.13.681913 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ CED-3 caspase promotes dismantling but not onset of non-apoptotic linker cell death in C. elegans ]]> https://biorxiv.org/content/10.1101/2025.10.15.682583v1?rss=1 Yarychkivska, O. Kutscher, L. M. Mamriev, D. Ortiz Bido, B. Lu, Y. Keil, W. Larisch, S. Shaham, S. 2025-10-15 doi:10.1101/2025.10.15.682583 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Exercise intensity modulates the human plasma secretome and interorgan communication ]]> https://biorxiv.org/content/10.1101/2025.10.22.683699v1?rss=1 Olsen, L. Botella, J. Barrows, D. Romero, E. Baird, K. Katayama, M. Kilic, E. Peralta, C. Sanford, H. Farrell, L. Axelrod, C. L. Plucinska, K. Walker, J. Yan, L. Fredrickson, K. Pourquie, O. Robbins, J. M. Vinogradova, E. V. Kirwan, J. P. Zierath, J. R. Krook, A. Gerszten, R. E. Bishop, D. J. Cohen, P. 2025-10-23 doi:10.1101/2025.10.22.683699 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Lipid composition and mechanical force underlie multi-modal regulation of Piezo1 gating ]]> https://biorxiv.org/content/10.1101/2025.10.24.684433v1?rss=1 Vaisey, G. MacKinnon, R. 2025-10-25 doi:10.1101/2025.10.24.684433 Cold Spring Harbor Laboratory Press 2025-10-25 <![CDATA[ B lymphocytes that enter the germinal center late preferentially differentiate into memory cells that recognize subdominant epitopes ]]> https://biorxiv.org/content/10.1101/2025.10.30.685663v1?rss=1 Zhou, P. Hartweger, H. MacLean, A. J. Ramos, V. Yao, K.-h. Hernandez, B. Wang, Z. Gazumyan, A. Nussenzweig, M. C. 2025-11-01 doi:10.1101/2025.10.30.685663 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ A Specialized CD107a+ Macrophage Subset Drives Selective Mycobacterial Phagocytosis ]]> https://biorxiv.org/content/10.1101/2025.10.31.685620v1?rss=1 Eto, C. Luiz, G. Silva, H. M. Munari, E. L. Mendes, D. A. G. B. Beck, B. K. Mascarin, L. Z. Starick, M. Canesso, M. C. C. Reis, B. S. Silveira, G. Bordignon, J. de Menezes, Y. K. T. Mansur, D. S. Lummertz da Rocha, E. Bafica, A. L. B. 2025-11-02 doi:10.1101/2025.10.31.685620 Cold Spring Harbor Laboratory Press 2025-11-02 <![CDATA[ Single Cell Analysis of pBMCs of Psoriasis patients reveals distinct CD4+ T cell phenotypes associated with response to IL-23 blockade. ]]> https://biorxiv.org/content/10.1101/2025.11.04.686122v1?rss=1 Marks, K. E. Sun, A. Y. Adejoorin, I. Chada, L. P. Perillo, A. Barrett, L. Garshick, M. Krueger, J. Merola, J. DiCarli, M. Rao, D. A. Weber, B. N. 2025-11-05 doi:10.1101/2025.11.04.686122 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Identification of distinct cDC2 subpopulations that direct microbiota-specific T cell differentiation ]]> https://biorxiv.org/content/10.1101/2025.11.04.686414v1?rss=1 Carroll, S. L. Ly, A. Liu, A. K. Canesso, M. C. C. Victora, G. D. Mucida, D. Barton, G. M. 2025-11-05 doi:10.1101/2025.11.04.686414 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Mapping unsolved lipidomes accelerates lipid discovery in major bacterial pathogens ]]> https://biorxiv.org/content/10.1101/2025.11.06.685907v1?rss=1 Nair, Y. M. Menon, A. R. Lin, Z. Vossenberg, M. R. L. Munsamy-Govender, V. Young, D. C. Xet-Mull, A. M. Babunovic, G. H. Cheng, T.-Y. Raman, S. Rhee, K. Y. Rock, J. M. de Jong, A. Minnaard, A. J. Mayfield, J. A. Tobin, D. M. Moody, D. B. 2025-11-07 doi:10.1101/2025.11.06.685907 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ Antibody-mediated feedback modulates interclonal competition in the germinal center ]]> https://biorxiv.org/content/10.1101/2025.11.06.686519v1?rss=1 Barbulescu, A. Bilanovic, J. Langelaar, T. Teetz, A. K. Urnavicius, L. Hobbs, A. Shen, J.-J. Abrahamse, N. H. de Carvalho, R. V. Mesin, L. Ferreira, C. L. Bortolatto, J. Victora, G. D. 2025-11-07 doi:10.1101/2025.11.06.686519 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ Proteome-wide in silico screening for human protein-protein interactions ]]> https://biorxiv.org/content/10.1101/2025.11.10.687652v1?rss=1 Schmid, E. Zhu, H. Ryu, E. Lim, Y. Smogorzewska, A. Brown, A. Walter, J. 2025-11-12 doi:10.1101/2025.11.10.687652 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Cap1 forms a cyclic tetra-adenylate-induced membrane pore during the type III-A CRISPR-Cas immune response ]]> https://biorxiv.org/content/10.1101/2025.11.13.688252v1?rss=1 Majumder, P. Cahir, C. W. Roberts, C. G. Patel, D. J. Marraffini, L. A. 2025-11-13 doi:10.1101/2025.11.13.688252 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Genotoxic formaldehyde and lipid aldehydes are sources of DNA damage in keratinocytes ]]> https://biorxiv.org/content/10.1101/2025.11.13.688345v1?rss=1 Blobel, N. J. Yao, Y. Okondo, M. C. Smogorzewska, A. 2025-11-14 doi:10.1101/2025.11.13.688345 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Spatial deconstruction of the plasma membrane ]]> https://biorxiv.org/content/10.1101/2025.11.14.688519v1?rss=1 Mandala, V. S. Zhao, C. Chen, Q. Gross, S. Geri, J. B. MacKinnon, R. 2025-11-14 doi:10.1101/2025.11.14.688519 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[ FERAL: A Video-Understanding System for Direct Video-to-Behavior Mapping ]]> https://biorxiv.org/content/10.1101/2025.11.16.688666v1?rss=1 Skovorodnikov, P. Zhao, J. Buck, F. Kay, T. Frank, D. D. Koger, B. Costelloe, B. R. Couzin, I. D. Razzauti, J. 2025-11-17 doi:10.1101/2025.11.16.688666 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Molecular evolution of CO2-sensing ab1C neurons underlies divergent sensory responses in the Drosophila suzukii species group ]]> https://biorxiv.org/content/10.1101/2025.11.21.689786v1?rss=1 Gadau, A. Mills, S. Jiang, X. Y. Z. Li, C. Svetec, N. Xu, Z. Li, W. Nagel, K. I. Zhao, L. 2025-11-24 doi:10.1101/2025.11.21.689786 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ A cross-species spatial transcriptomic atlas of the human and non-human primate basal ganglia ]]> https://biorxiv.org/content/10.1101/2025.11.22.688128v1?rss=1 Hewitt, M. N. Turner, M. A. Johansen, N. McMillen, D. A. Dan, S. DeBerardine, M. Ruiz, A. Huang, M. Quon, J. Fu, Y. Kapen, I. Barta, S. Martin, N. Cuevas, N. V. Olsen, P. Nagra, J. Campos, J. VanNess, M. M. Ransford, S. Juneau, Z. Hastings, S. Ching, L. Kunst, M. Basu, S. Hollt, T. Li, C. Lelieveldt, B. Yazdani, F. Zhang, Q. Levandowski, K. Feng, G. Rosen, B. Glasser, M. F. Hayashi, T. Garcia, A. D. Kana, O. Maltzer, Z. M. Campagnola, L. Jarsky, T. Kruse, L. Freiwald, W. Keene, C. D. Van Essen, D. C. Ariza, J. Waters, J. Krienen, F. M. Bakken, T. E 2025-11-24 doi:10.1101/2025.11.22.688128 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Molecular interplay between the DNA damage checkpoint kinase Mec1-Ddc2 and its activator Dpb11 on gapped DNA ]]> https://biorxiv.org/content/10.1101/2025.11.28.691181v1?rss=1 Beckwitt, E. C. Chua, G. N. L. Liu, S. O'Donnell, M. E. 2025-11-30 doi:10.1101/2025.11.28.691181 Cold Spring Harbor Laboratory Press 2025-11-30 <![CDATA[ Modeling the Synergetic Dynamics of B cells and TFH cells in Germinal Center Reactions ]]> https://biorxiv.org/content/10.1101/2025.11.27.691027v1?rss=1 Pyo, A. G. T. Merkenschlager, J. Pham, Q. Good, B. H. Nussenzweig, M. C. Wingreen, N. S. 2025-12-01 doi:10.1101/2025.11.27.691027 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Viral transcriptional regulators extensively rewire host pathways through diverse mechanisms ]]> https://biorxiv.org/content/10.64898/2025.12.01.691387v1?rss=1 Rottenberg, J. T. Liu, X. Berenson, A. Soto-Ugaldi, L. F. ElSadec, M. Y. Santoso, C. Corban, J. Dexheimer, P. J. Engin, B. Lane, R. Shah, S. Spirohn-Fitzgerald, K. Khetan, S. Lee, C.-C. Munoz-Esquivel, G. Li, Z. Martinez-Cuesta, L. Lu, Y. Trollmann, P. Hao, T. Yi, S. S. Sahni, N. Bulyk, M. L. Calderwood, M. Weirauch, M. T. Vidal, M. T. Raman, S. Fuxman Bass, J. I. 2025-12-02 doi:10.64898/2025.12.01.691387 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ The germline-restricted chromosome orchestrates germ cell development in passerine birds ]]> https://biorxiv.org/content/10.64898/2025.12.02.691941v1?rss=1 Vontzou, N. Pei, Y. Campo-Bes, I. Forstmeier, W. Hertel, M. Irimia, M. Kempenaers, B. Kuhn, S. Martin, K. Mueller, J. C. Teltscher, K. Mollbrink, A. Abalo, X. Biegler, M. T. Immler, S. Ruiz-Ruano, F. J. Suh, A. 2025-12-05 doi:10.64898/2025.12.02.691941 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Curved Axially Scanned Light-Sheet Microscopy ]]> https://biorxiv.org/content/10.64898/2025.12.03.691599v1?rss=1 Sheppard, S. J. Murakami, T. Shepherd, D. P. 2025-12-09 doi:10.64898/2025.12.03.691599 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Chlorotonils exhibit potent activity against Mycobacterium tuberculosis, while resistance is mediated by MmpR5-MmpL5 ]]> https://biorxiv.org/content/10.64898/2025.12.09.693342v1?rss=1 Deschner, F. Chengalroyen, M. D. Ames, L. Quach, D. Aguilera Olvera, R. Bosch, B. Castro, A. Kim, H. Raman, K. Thornton, N. Wallach, J. Rodrigues da Costa, F. Allen, R. Lupien, A. Zuma, M. Lynch, S. Pogliano, J. Sugie, J. Rock, J. M. Schnappinger, D. Parish, T. Mizrahi, V. DeJesus, M. Mueller, R. Herrmann, J. 2025-12-10 doi:10.64898/2025.12.09.693342 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Signaling induced biophysical disruption of repressed chromatin domains drives immune cell fate ]]> https://biorxiv.org/content/10.64898/2025.12.08.692984v1?rss=1 Martinez de Paz, A. Chin, C. R. Ketavarapu, M. Sun, Y. Marunde, M. R. Chang, J. Khan, L. Cohen, J. Yang, R. Bale, M. J. Daman, A. W. Kumar, V. E. Jiang, C. Ahimovic, D. J. Owyong, M. Ravishankar, A. Wong, W. Shih, R. Graham, B. Smith, C. E. Karagianidis, I. Cerchietti, L. Flowers, C. R. Green, M. R. Mason, C. E. Sun, J. C. Martin-Trujillo, A. Niec, R. E. Long, Y. Keogh, M.-C. Liu, S. Beguelin, W. Leslie, C. S. Melnick, A. M. Josefowicz, S. Z. 2025-12-11 doi:10.64898/2025.12.08.692984 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Non-apoptotic death of the C. elegans linker cell is primed by MYRF-1 activation of pqn-41/polyQ ]]> https://biorxiv.org/content/10.64898/2025.12.08.693091v1?rss=1 Yarychkivska, O. Liu, S. Horowitz, L. B. Newland, S. Wu, P. Mittal, S. Tamura, S. Novosolova, T. Ritter, D. F. Lu, Y. Ercan, S. Hammell, C. Shaham, S. 2025-12-11 doi:10.64898/2025.12.08.693091 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Drosophila maintain a consistent navigational goal angle for days to weeks ]]> https://biorxiv.org/content/10.64898/2025.12.09.693277v1?rss=1 Weisman, J. L. Mohren, T. L. Ryu, J. D. Wyse, M. Z. Dias-Ferreira, E. Maimon, G. 2025-12-11 doi:10.64898/2025.12.09.693277 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Tolerance toward foreigners in ants requires chronic exposure for establishment but only sporadic exposure for maintenance ]]> https://biorxiv.org/content/10.64898/2025.12.10.693507v1?rss=1 Bailly, T. P. M. Rossi, M. Valdes-Rodriguez, S. Schmitt, T. Frank, E. T. Kronauer, D. 2025-12-13 doi:10.64898/2025.12.10.693507 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ Murine CMV Infection Unmasks Macrophage-Driven Inflammatory Cardiomyopathy in Pkp2, but not in Ttn Mutant Mice ]]> https://biorxiv.org/content/10.64898/2025.12.11.693827v1?rss=1 Cirnu, A. Williams, T. D. Noerpel, M. Kammerer, J. Kannt, S. Heil, M. Kimmel, L. Arias-Loza, P.-A. Lhoda, M. Hennig, T. Ashour, D. E. Puhl, S. Rizzo, G. Cochain, C. Krammer, T. Leipold, A. M. Saliba, A.-E. Mack, M. Ziegler, N. Ernst, N. Ludwig, R. J. Campos Ramos, G. Frantz, S. Dölken, L. Gerull, B. 2025-12-15 doi:10.64898/2025.12.11.693827 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Retrotransposon Activation in the Aged and Alzheimer's Disease Brain Examined by Nanopore Long-read DNA Sequencing ]]> https://biorxiv.org/content/10.64898/2025.12.12.693943v1?rss=1 80% methylated), 7% were <50% methylated, 1% were <25%, and the highly demethylated read fraction increased in AD. L1HS 5 UTR methylation was strongly correlated with RNA expression. ConclusionsCpG methylation-mediated repression of young RTEs is compromised in old age - our findings indicate that this is further exacerbated in AD. Amid these failing defenses, we report somatic retrotransposition events in the aging and demented brain. ]]> Kelsey, M. M. G. Chongtham, A. LaCava, J. Taylor, M. S. Boeke, J. D. Gage, F. H. Seluanov, A. Gorbunova, V. Pereira, A. C. Sedivy, J. M. 2025-12-15 doi:10.64898/2025.12.12.693943 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ High-Fidelity Tuning of Olfactory Mixture Distances in the Perceptual Space of Smell Through a Community Effort ]]> https://biorxiv.org/content/10.64898/2025.12.13.694160v1?rss=1 Satarifard, V. Sisson, L. Han, Y. Ilidio, P. Hladis, M. Lalis, M. Song, X. Yin, W. Ravia, A. Zheng, C. X. Andreoletti, G. Albrecht, J. Pellegrino, R. Wang, Z. Yang, S. D'hondt, R. Ghinis, A. de Boer, J. Nakano, F. K. Gharahighehi, A. DREAM Olfactory Mixtures Prediction Consortium, Sanchez-Lengeling, B. Keller, A. Vosshall, L. B. Fiorucci, S. Tewari, A. Topin, J. Vens, C. Bjorkman, M. Kragic, D. Sobel, N. Christakis, N. A. Mainland, J. D. Meyer, P. 2025-12-16 doi:10.64898/2025.12.13.694160 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Cross-species consensus atlas of the primate basal ganglia ]]> https://biorxiv.org/content/10.64898/2025.12.15.694496v1?rss=1 Johansen, N. J. Fu, Y. Schmitz, M. Dubuc, A. Kempynck, N. Wirthlin, M. Garcia, A. D. Hewitt, M. Turner, M. A. Seeman, S. C. Long, B. Liu, X.-P. Dan, S. DeBerardine, M. Kapen, I. Yanny, A. M. Avola, A. Barlow, S. T. Bertagnolli, D. Bhandiwad, A. Budzillo, A. Caballero, V. E. N. Caceres, L. Casper, T. Chakka, A. B. Chakrabarty, R. Clark, M. Daniel, S. Eggermont, J. Ferrer, R. French, L. Gloe, J. Goldy, J. Guilford, N. Guzman, J. Hirschstein, D. Ho, W. James, K. Jones, D. L. Jungert, M. Kannan, M. Kedzierska, K. Z. Kroes, T. Leytze, M. Manning, A. McCu 2025-12-16 doi:10.64898/2025.12.15.694496 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ CAD-C: An engineered nuclease enables repair-free in situ proximity ligation and nucleosome-resolution chromosome walks in human cells ]]> https://biorxiv.org/content/10.64898/2025.12.22.695891v1?rss=1 Soroczynski, J. Westcott, L. A. Zuo, W. Ou, A. Canaj, H. Hickling, J. Yeung, J. L. Konishi, H. A. Campbell, E. B. Whelan, C. Balacco, J. Formenti, G. Risca, V. I. 2025-12-22 doi:10.64898/2025.12.22.695891 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Direct measurement of sub-kilobase chromatin structure reveals that linker histone H1 broadly compacts chromatin, with differential impact amongst epigenetic states ]]> https://biorxiv.org/content/10.64898/2025.12.19.695525v1?rss=1 Canaj, H. Duba, I. Mansisidor, A. Scortea, A. Johnson, R. Pinto, H. Ou, A. Pagane, N. Pae, J. Fyodorov, D. Skoultchi, A. I. Risca, V. I. 2025-12-23 doi:10.64898/2025.12.19.695525 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ PRISM-Seq: An Ultra-sensitive Sequencing Approach For Mapping Lentiviral Integration Sites ]]> https://biorxiv.org/content/10.64898/2025.12.20.695659v1?rss=1 Pal, V. K. Canis, M. Stone, E. Board, N. L. Lenart, K. Fumagalli, M. J. Jones, R. B. Hatziioannou, T. Nussenzweig, M. Muecksch, F. Bieniasz, P. D. Lee, G. Q. 2025-12-23 doi:10.64898/2025.12.20.695659 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ HIV-1 Integration Site Determines the Transcriptional Fate and Persistence of Integrated Proviruses ]]> https://biorxiv.org/content/10.64898/2025.12.26.696579v1?rss=1 Pal, V. Danesh, A. Canis, M. Dilling, T. Miller, I. Huynh, T. T. Copertino, D. Barrows, D. Carroll, T. Hatziioannou, T. Jones, R. B. Lee, G. Q. Muecksch, F. Bieniasz, P. D. 2025-12-26 doi:10.64898/2025.12.26.696579 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Extracellular matrix regulates lineage plasticity in prostate cancer through YAP/TEAD ]]> https://biorxiv.org/content/10.64898/2025.12.30.697072v1?rss=1 Han, T. Sun, Z. Lange, M. Cho, Y. Z. Mcgillivray, P. Buttner, M. Kastan, N. R. Nandakumar, S. Zhao, H. Oak, S. Fong, L. Kang, W. Fan, N. Zhao, J. Salsabeel, N. Kaur, H. Mao, N. Chang, Q. Rosiek, E. Chan, E. Tipping, M. Schultz, N. Hamard, P.-J. De Stanchina, E. Pe'er, D. Koche, R. P. Chen, Z. Hudspeth, A. Sawyers, C. 2025-12-31 doi:10.64898/2025.12.30.697072 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ GCL pruning of PIP3 establishes the soma-germline boundary ]]> https://biorxiv.org/content/10.64898/2025.12.30.697122v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@1efe138org.highwire.dtl.DTLVardef@1ab3b17org.highwire.dtl.DTLVardef@b49412org.highwire.dtl.DTLVardef@1655c5e_HPS_FORMAT_FIGEXP M_FIG Graphical AbstractO_LIMembrane domains with high Torso activity (purple) in the early embryo have a higher PIP3 content. C_LIO_LIAt the posterior pole, GCL-containing germplasm (green) degrades Torso, resulting in a PIP3-low membrane. C_LIO_LIClearing PIP3 enables Myosin II pole bud constriction required for PGC formation. C_LI C_FIG ]]> Saiduddin, M. Pae, J. Vidal, A. M. Alani, M. Lehmann, R. 2025-12-31 doi:10.64898/2025.12.30.697122 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Biological signatures of history: Examination of composite biomes and Y chromosome analysis from da Vinci-associated cultural artifacts ]]> https://biorxiv.org/content/10.64898/2026.01.06.697880v1?rss=1 Singh, H. Rajagopala, S. V. Hart, R. Hallast, P. Loftus, M. Wiscovitch-Russo, R. Conrad, C. R. K. Thaler, D. S. Pinar, G. Aberg, K. C. Lorenzi, R. Lorente, J. A. Ausubel, J. H. Sakmar, T. P. Roby, R. K. Lee, C. Gonzalez-Juarbe, N. 2026-01-06 doi:10.64898/2026.01.06.697880 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ A commensally regulated immune rheostat fine-tunes skin barrier fitness ]]> https://biorxiv.org/content/10.64898/2026.01.07.698149v1?rss=1 Gola, A. Srinivas, R. Rodig, E. G. Schernthanner, M. Abdusselamoglu, M. D. Tierney, M. T. Alexander, N. J. Gonzales, K. A. U. Sajjath, S. M. Soto-Ugaldi, L. F. Bonny, A. R. Fuchs, E. 2026-01-08 doi:10.64898/2026.01.07.698149 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ C. elegans E3 ubiquitin ligase EBAX-1 promotes non-apoptotic linker cell-type death through target-directed miRNA degradation ]]> https://biorxiv.org/content/10.64898/2026.01.07.698237v1?rss=1 Horowitz, L. B. Yarychkivska, O. Lu, Y. Shaham, S. 2026-01-08 doi:10.64898/2026.01.07.698237 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Cell type-specific proximity labeling of organ secretomes reveals energy balance-dependent proteomic remodeling. ]]> https://biorxiv.org/content/10.64898/2026.01.11.698831v1?rss=1 Plucinska, K. Wayne, C. R. Sanford, H. Mathew, B. Ropek, N. Adaniya, S. M. Model, C. Gomez-Banoy, N. Morozova, K. Cao, X. Friedman, J. M. Loh, K. H. Cohen, P. Vinogradova, E. V. 2026-01-12 doi:10.64898/2026.01.11.698831 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ Impact of Amazonian Dance on Speech Performance in People with Parkinson's Disease ]]> https://biorxiv.org/content/10.64898/2026.01.12.699086v1?rss=1 Arigony C. S. Prates, R. A. C. S. P. Espedito Guzzo Junior, C. C. Andreazza Duarte, M. V. Munoz Sanchez, A. Pauli, P. Gomes Martinez, F. Passos-Monteiro, E. Garcia, A. M. Nogueira Haas, A. Theofanopoulou, C. 2026-01-13 doi:10.64898/2026.01.12.699086 Cold Spring Harbor Laboratory Press 2026-01-13 <![CDATA[ Alteration of empathy-related behaviors in two strains of mice expressing mutations of the α5 cholinergic nicotinic receptor subunit ]]> https://biorxiv.org/content/10.64898/2026.01.13.698088v1?rss=1 Tochon, L. Pageze, C. Henkous, N. Guillou, J.-L. David, V. 2026-01-14 doi:10.64898/2026.01.13.698088 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ One-step generation of TCR knock-in mice targeted to the TCRβ locus results in functional mature T lymphocytes ]]> https://biorxiv.org/content/10.64898/2026.01.13.699338v1?rss=1 Bilanovic, J. Bortolatto, J. Duan, S. Bjornsdottir, V. Teetz, A. K. Thoms, A. Fishbach, J. Schmidt, F. Nyberg, W. Hartweger, H. Escolano, A. Thomas, P. Victora, G. D. Bilate, A. M. Jacobsen, J. T. 2026-01-14 doi:10.64898/2026.01.13.699338 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Uncovering the function of Wisp1 in whole-body glucose homeostasis: insights from Wisp1 knockout mice ]]> https://biorxiv.org/content/10.64898/2026.01.15.699691v1?rss=1 Fernandez-Ruiz, R. Garcia-Alaman, A. Fontcuberta-PiSunyer, M. Perea-Atienzar, M. Angulo-Capel, J. Hadley, C. K. Lin, Z. Cohen, P. Vidal, J. Gasa, R. 2026-01-15 doi:10.64898/2026.01.15.699691 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ B Lymphocyte Protein Factories produced by Hematopoietic Stem Cell Gene Editing ]]> https://biorxiv.org/content/10.64898/2026.01.16.699998v1?rss=1 Hartweger, H. Ruprecht, C. Yao, K.-H. Laffont, P. Lima dos Reis, G. Zhou, P. Hägglöf, T. Binet, L. Loewe, M. Hong, J. P. Xiao, T. Sefik, E. Hernandez, B. Gazumyan, A. Jankovic, M. Seaman, M. S. Costa, G. Nelson, S. A. Clark, J. Kanatani, S. Wilson, P. C. Krammer, F. Levashina, E. A. Julien, J.-P. Wardemann, H. Sinnis, P. Stamatatos, L. Flavell, R. A. Nussenzweig, M. C. 2026-01-18 doi:10.64898/2026.01.16.699998 Cold Spring Harbor Laboratory Press 2026-01-18 <![CDATA[ The E. coli clamp loader sharply bends DNA to load β-clamp onto small gaps ]]> https://biorxiv.org/content/10.64898/2026.01.17.700081v1?rss=1 Zheng, F. Yao, N. Y. Georgescu, R. E. Lyu, M. O'Donnell, M. E. Li, H. 2026-01-18 doi:10.64898/2026.01.17.700081 Cold Spring Harbor Laboratory Press 2026-01-18 <![CDATA[ Single-molecule dissection of CFTR folding defects and pharmacological rescue ]]> https://biorxiv.org/content/10.64898/2026.01.26.701897v1?rss=1 Kim, S. A. Levring, J. Chen, J. Yoon, T.-Y. 2026-01-27 doi:10.64898/2026.01.26.701897 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Divergent mitochondrial and metabolic adaptations shape selective vulnerability in ALS ]]> https://biorxiv.org/content/10.64898/2026.01.30.702552v1?rss=1 Cotto, B. A. Zhang, L. Fait, B. W. Peralta, C. Kilic, E. Molina, H. Heintz, N. Schmidt, E. F. 2026-02-02 doi:10.64898/2026.01.30.702552 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ immgenT: A Comprehensive Reference of Convergent T-cell States in the Mouse ]]> https://biorxiv.org/content/10.64898/2026.01.30.702892v1?rss=1 Magill, I. Casey, O. Mallah, D. Panigrahi, S. S. Zhou, L. Barreiro del Rio, O. Bangs, D. J. Bee, G. C. W. Borys, S. Choi, J. Ergen, C. Ferraj, E. Fiusco, M. Freuchet, A. Galletti, G. Globig, A.-M. Heim, T. Imianowski, C. Lai, R. Liang, Z. Lebron Figueroa, A. Lucas, E. D. Merkenschlager, J. Osum, K. Reilly, S. Shinkawa, T. Thefaine, C. E. Weiss, E. S. Yang, L. Zhang, S. Zorzetto-Fernandes, A. L. Croteau, J. D. Alegre, M.-L. Behar, S. M. Bosselut, R. Brossay, L. Cadwell, K. Chervonsky, A. Gapin, L. Hamilton, S. E. Huh, J. R. Iliev, I. Jabri, B. Jameson, 2026-02-02 doi:10.64898/2026.01.30.702892 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Functional border-associated macrophages limit Alzheimer's Disease progression ]]> https://biorxiv.org/content/10.64898/2026.01.31.703045v1?rss=1 Adler, D. Pinheiro Rosa, N. Millet, A. Gajic, Z. Z. cheng, E. Gamallo-Lana, B. Morizawa, Y. Klann, E. Gan, W. Mar, A. C. Ledo, J. H. Moura Silva, H. Lafaille, J. J. 2026-02-03 doi:10.64898/2026.01.31.703045 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ SLC33A1 exports oxidized glutathione to maintain endoplasmic reticulum redox homeostasis ]]> https://biorxiv.org/content/10.64898/2026.02.01.703113v1?rss=1 Birsoy, K. Liu, S. Gad, M. Li, C. Cho, K. Liu, Y. Wangdu, k. Belay, V. Millet, A. Kojima, H. Sanford, H. Wolk, M. Urnavicius, L. Fedorova, M. Patti, G. J. J. Vinogradova, E. V. Hite, R. K. 2026-02-03 doi:10.64898/2026.02.01.703113 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Assessing climate adaptation among Canada lynx (Lynx canadensis) populations at the trailing edge ]]> https://biorxiv.org/content/10.64898/2026.02.04.703807v1?rss=1 Lama, T. M. Bentley, B. P. Johnson, W. E. Komoroske, L. M. DeStefano, S. Vashon, J. Beauclerc, K. Kamilar, J. M. Formenti, G. Batista, A. Spencer, A. G. Federigo, O. Jarvis, E. D. Bowman, J. S. Wilson, P. Organ, J. F. 2026-02-06 doi:10.64898/2026.02.04.703807 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ Th17 effector cytokines induce shared and distinct microglial and endothelial cell responses in post-streptococcal encephalitis ]]> https://biorxiv.org/content/10.64898/2026.02.04.703836v1?rss=1 Wayne, C. R. Akcan, U. Faust, T. E. Duran-Laforet, V. Jamoul, D. Bremner, L. Ampatey, N. Akcan, B. Ho, S. J. Ciric, B. Delaney, S. Vargas, W. S. Swedo, S. Menon, V. Schafer, D. P. Cutforth, T. Agalliu, D. 2026-02-07 doi:10.64898/2026.02.04.703836 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ IFN gamma-induced IRF1 synergizes with TLR7 signals to tune the IRF4-IRF8 axis and drive pathogenic effector B cell fate ]]> https://biorxiv.org/content/10.64898/2026.02.06.704376v1?rss=1 Owiredu, E.-W. Denslow, A. J. Chen, S. Mousseau, B. Foote, J. Yang, G. Peel, J. N. Burnham, R. Browning, K. Scharer, C. D. Randall, T. D. Zumaquero-Martinez, E. Lund, F. E. 2026-02-09 doi:10.64898/2026.02.06.704376 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Functional Reorganization of Motor Subcircuits in Parkinson's disease ]]> https://biorxiv.org/content/10.64898/2026.02.09.704910v1?rss=1 Theofanopoulou, C. Bajaj, N. Sanchez, A. M. Crosson, B. Wolf, S. L. Krishnamurthy, V. McGregor, K. Hackney, M. E. 2026-02-10 doi:10.64898/2026.02.09.704910 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ Cell-Autonomous AR Dependence in Luminal Prostatic Epithelium Governs Survival and Lineage Plasticity ]]> https://biorxiv.org/content/10.64898/2026.02.13.705807v1?rss=1 Chen, Y. Li, D. Wang, N. Guo, W. Owiredu, J. Cho, W. H. Schoeps, D. Cheng, S. Zhang, H. Chan, U. I. Wong, C. K. Callychurn, V. R. Wang, H. Kang, W. Fan, N. Pasolli, H. A. Sharma, A. Gopalan, A. Barbieri, C. E. Gao, D. Chi, P. 2026-02-16 doi:10.64898/2026.02.13.705807 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ Pharmacological Inhibition of SLC33A1 Promotes Endoplasmic Reticulum Hyperoxidation and Induces Adaptive IRE1/XBP1s Signaling ]]> https://biorxiv.org/content/10.64898/2026.02.17.706344v1?rss=1 Kutseikin, S. Rafiq, M. Bora, P. Liu, S. Homan, R. A. Mindrebo, J. T. Holcomb, M. Petrassi, H. M. Qiu, H. Redkina, A. Sosna, J. Lee, T.-T. Hu, X. Forli, S. Parker, C. G. Lander, G. C. Birsoy, K. Saez, E. Wiseman, L. 2026-02-18 doi:10.64898/2026.02.17.706344 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Dynamic Antigen Expression and Intrinsic CTL Resistance in HIV Reservoir Clones ]]> https://biorxiv.org/content/10.64898/2026.02.22.707300v1?rss=1 90%. Notably, a regulatory T-cell ARC displayed pronounced cell-intrinsic resistance to CTL - a longstanding hypothesis we now directly demonstrate - linked to low oxidative stress and reversed with desferoxamine, a hypoxic stress inducer and FDA-approved therapeutic. Overall, we provide novel insights into the vulnerabilities of reservoir clones to potent, sustained CTL pressure and highlight intrinsic resistance pathways as actionable therapeutic targets, opening opportunities for advancing immune-based HIV cure strategies. ]]> Ferreira, I. A. T. M. Herrera, A. Huynh, T. T. Board, N. L. Stone, E. Linden, N. L. Ren, Y. Bittar, C. Pal, V. K. Vedova, S. Naing, E. Sinha, P. Danesh, A. Ovies, C. Liu, F. Leyre, L. Canis, M. Teixeira, A. R. Moir, S. Chun, T.-W. Kovacs, C. Zumbo, P. Betel, D. Halvas, E. K. Lee, G. Q. Caskey, M. Bieniasz, P. D. Nussenzweig, M. C. Jones, R. B. 2026-02-23 doi:10.64898/2026.02.22.707300 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Loss of interruption in the HTT CAG repeat is associated with increased somatic expansion and loss of medium spiny neurons in HD ]]> https://biorxiv.org/content/10.64898/2026.03.02.709181v1?rss=1 150 CAG) somatic expansions are rare in early manifest HD, but accumulate in proportion with duration of disease and inherited CAG repeat length. In patients with the deleterious CAG-CCG loss-of-interruption (CAG-CCG LOI) modifier, the proportion of MSNs with large and very large expansions is increased [~]5-fold despite reduced small somatic expansions in blood, and direct caudate MSN counts are reduced. Our findings suggest that increased somatic CAG expansion contributes to accelerated striatal MSN pathology and hastened onset of HD, but that MSNs with very large genomic CAG expansions can persist among surviving neurons of the HD brain. ]]> Kay, C. Dawson, J. Mätlik, K. Findlay Black, H. Harvey, E. Bortnick, S. Javier, K. Buchanan, C. Soomarooah, T. Bras, I. C. Sequiera, G. Pouladi, M. Arning, L. Nguyen, H. H. Roxburgh, R. Curtis, M. Faull, R. L. Heintz, N. Hayden, M. R. 2026-03-05 doi:10.64898/2026.03.02.709181 Cold Spring Harbor Laboratory Press 2026-03-05 <![CDATA[ An A-rich linker between dengue virus tandem xrRNAs facilitates functional coordination ]]> https://biorxiv.org/content/10.64898/2026.03.04.709395v1?rss=1 Spear, E. O'Donoghue, Z. Bonilla, S. Larsen, K. P. Sherlock, M. E. Kieft, J. S. 2026-03-05 doi:10.64898/2026.03.04.709395 Cold Spring Harbor Laboratory Press 2026-03-05 <![CDATA[ Force-modulated structural landscape of the catch bonding F-actin crosslinker α-actinin-4 ]]> https://biorxiv.org/content/10.64898/2026.03.04.709699v1?rss=1 Chin, A. C. Mukadum, F. Reynolds, M. J. Hocky, G. M. Alushin, G. M. 2026-03-06 doi:10.64898/2026.03.04.709699 Cold Spring Harbor Laboratory Press 2026-03-06 <![CDATA[ Mechanistic Basis for the Selective Recognition of the Fcγ Receptor IIa by Monoclonal Antibody IV.3 ]]> https://biorxiv.org/content/10.64898/2026.03.05.709909v1?rss=1 Wang, J. Novack, S. Li, J. Niejadlik, E. G. Bournazos, S. Coller, B. S. Filizola, M. 2026-03-08 doi:10.64898/2026.03.05.709909 Cold Spring Harbor Laboratory Press 2026-03-08 <![CDATA[ Automatic Generation of Model Sequences for Complex Regions in Assembly Graphs ]]> https://biorxiv.org/content/10.64898/2026.03.06.710180v1?rss=1 Antipov, D. Chen, Y. Sollitto, M. Phillippy, A. M. Formenti, G. Koren, S. 2026-03-10 doi:10.64898/2026.03.06.710180 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[ Optineurin is a gatekeeper of mitochondrial health and proteostasis in Alzheimer's disease vulnerable neurons ]]> https://biorxiv.org/content/10.64898/2026.03.15.711617v1?rss=1 Tsagkogianni, C. Trivisonno, M. Willner, J. S. Garcia-Molinero, C. Tang, Y. Mattina, B. Wang, W. Roussarie, J.-P. Rodriguez, P. 2026-03-16 doi:10.64898/2026.03.15.711617 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ Quinone reductase 2 reads H3 serotonylation to support neuronal maturation ]]> https://biorxiv.org/content/10.64898/2026.03.17.712426v1?rss=1 Chen, M. Yang, C. Li, X. Kong, L. Weekley, B. H. Wei, X. O'Chan, J. C. Vinson, D. A. Cetin, B. Ramakrishnan, A. Shen, L. Zeng, R. Liu, Z. Zhang, J. Cappuccio, K. M. Sokol, J. R. Baljinnyam, E. Hu, R. Rosenblum, K. Molina, H. Zheng, Q. David, Y. Marro, S. G. Muir, T. W. Li, X. D. Li, H. Maze, I. 2026-03-18 doi:10.64898/2026.03.17.712426 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Diverse high-fat diets drive multi-omic reprogramming that persists after dietary reversal ]]> https://biorxiv.org/content/10.64898/2026.03.17.708620v1?rss=1 Van Camp, A. G. Park, J. Ozcelik, E. Eskiocak, O. Ozler, K. A. Papciak, K. Subhash, S. Alwaseem, H. Ergin, I. Chung, C. Shah, V. Yueh, B. Fein, M. R. Durmaz, C. Mozsary, C. Kilic, E. Garipcan, A. Damle, N. Najjar, D. Nelson, T. M. Ryon, K. A. Butler, D. J. Patel, C. J. Thaiss, C. A. Birsoy, K. Mason, C. E. Meydan, C. Tierney, B. T. Beyaz, S. 2026-03-19 doi:10.64898/2026.03.17.708620 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ Zebrafish shoals share leadership during continuous decision-making on the move in a three-room Y-maze ]]> https://biorxiv.org/content/10.64898/2026.03.20.713221v1?rss=1 Seguret, A. Chemtob, Y. Collignon, B. Cazenille, L. Halloy, J. 2026-03-23 doi:10.64898/2026.03.20.713221 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ GPCRs as Targets for Human Brain Modulation: A Multi-omic Atlas of Cell-Type Specific Expression ]]> https://biorxiv.org/content/10.64898/2026.03.23.713764v1?rss=1 Umfress, A. Wertimer, P. Pressl, C. Baffuto, M. Mätlik, K. Fernandez, F. Siantoputri, M. E. Ibanez-Tallon, I. Heintz, N. 2026-03-24 doi:10.64898/2026.03.23.713764 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Homozygosity for rare or common hypomorphic IL23R variants confers a predisposition to tuberculosis in humans ]]> https://biorxiv.org/content/10.64898/2026.03.23.713554v1?rss=1 Olguin Calderon, D. Kilpatrick, L. E. Conil, C. Philippot, Q. Ogishi, M. Vellutini, J. Eun Han, J. Keating, N. Li, H. Rao, G. Bohlen, J. Lay, C. S. Platt, S. Kerner, G. Feredj, E. Peel, J. Momenilandi, M. Seeleuthner, Y. Laine, C. soudee, c. Leloup, C. Debuisson, C. Lanternier, F. Bitoun, S. B. Pavy, S. Mariette, X. Rafik, A. Skhoun, H. EL Ouazzani, H. Abderahmani-Ghorfi, I. EL Baghdadi, J. Baena, A. Tejada-Giraldo, M. Barrera, L. F. Arias, A. A. Fabio, G. Carrabba, M. Emiroglu, M. Bezrodnik, L. EL Zein, L. Hammoud, H. Gregersen, P. Terrier, B. Leon L 2026-03-25 doi:10.64898/2026.03.23.713554 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ MscM uses a novel gating mechanism for bacterial mechanosensitive channels ]]> https://biorxiv.org/content/10.64898/2026.03.24.713958v1?rss=1 Hiotis, G. Walz, T. 2026-03-25 doi:10.64898/2026.03.24.713958 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Fiber optical parametric amplification of low-photon-flux microscopy signals ]]> https://biorxiv.org/content/10.64898/2026.03.25.714345v1?rss=1 50 dB of parametric gain at wavelengths within the third near-infrared transparency window and have similar sensitivity to near-infrared photomultiplier tubes. Furthermore, these amplifiers outperform detection with a photodiode and subsequent electrical amplification, providing a factor of 10-100-fold improvement in sensitivity. We demonstrate amplifier bandwidths up to ~1.6 GHz, a factor of 10 faster than conventional detectors, including near-infrared photo-multiplier tubes, with sensitivity of ~8 nW (corresponding to ~20 photons/pixel). Finally, the increased performance of the optical amplifier is confirmed in diagnostic imaging experiments where >10x less power is required to achieve the same signal-to-noise ratio and contrast as images using electrical amplification. Accordingly, fiber optical parametric amplification is a new path forward for extending the performance of laser scanning microscopes in the near infrared. ]]> Demas, J. Tan, L. Ramachandran, S. 2026-03-30 doi:10.64898/2026.03.25.714345 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ The diploid reference genome of a human embryonic stem cell line ]]> https://biorxiv.org/content/10.64898/2026.03.26.714432v1?rss=1 Pacar, I. Ungaro, M. T. Chen, Y. Dallali, H. Medico, J. A. Hebbar, P. Diekhaus, M. Di Tommaso, E. Geleta, M. Chan, P. P. Lowe, T. M. Balacco, J. Jain, N. Ackerman, F. Mochi, M. Ioannidis, A. G. Sawarkar, N. Diaz, K. Krishna Sudhakar, K. Powell, J. E. Jain, M. Rosa, A. Croft, G. F. Tanzer, A. Jarvis, E. D. Formenti, G. Salama, S. R. Giunta, S. 2026-03-30 doi:10.64898/2026.03.26.714432 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Epigenomic methylome landscape of promoters in vertebrate genomes ]]> https://biorxiv.org/content/10.64898/2026.03.29.715150v1?rss=1 Lee, Y. H. Lee, C. Jarvis, E. Kim, H. 2026-03-30 doi:10.64898/2026.03.29.715150 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Fc receptor dependent and independent mechanisms of antibody-mediatedenhancement of immune responses ]]> https://biorxiv.org/content/10.64898/2026.03.27.714269v1?rss=1 Cipolla, M. MacLean, A. J. Hernandez, B. Silva Santos, G. S. Stamatatos, L. Gazumyan, A. Hartweger, H. Merkenschlager, J. Bournazos, S. Ravetch, J. Nussenzweig, M. 2026-03-31 doi:10.64898/2026.03.27.714269 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Deriving functional network topology from in vivo two-photon calcium imaging: state-dependent graph features in mouse mesoscale motor cortical network ]]> https://biorxiv.org/content/10.64898/2026.03.27.714836v1?rss=1 Peng, G. Sati, N. Latifi, S. 2026-03-31 doi:10.64898/2026.03.27.714836 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Genetic dissection of rapid proteolysis identifies TXNDC15 as a key factor of ERAD and lipid homeostasis ]]> https://biorxiv.org/content/10.64898/2026.04.01.715723v1?rss=1 Liu, Y. Yaochai, M. Y. Liu, S. Alwaseem, H. Birsoy, K. 2026-04-02 doi:10.64898/2026.04.01.715723 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ Human antibodies against West Nile and related orthoflaviviruses ]]> https://biorxiv.org/content/10.64898/2026.04.02.715800v1?rss=1 Cervantes Rincon, T. Frckova, T. Contejean, Z. I. Cantergiani, J. Groen, K. Cena, B. Moro, S. G. Bianchini, F. Simonelli, L. Jarrossay, D. Tosolini, S. Kuratli, R. Robinson, A. R. E. Cizkova, M. Niejadlik, E. G. Moritz, J. Thakur, R. Kratka, Z. Mijatovic, D. Grujic, J. Holoubek, J. Budakov-Obradovic, Z. Salat, J. Honig, V. Vranes, M. Lojpur, Z. Lendak, D. Sevic, S. Bajci, M. Popovic-Dragonjic, L. Popovska Jovicic, B. Gavrilovic, J. Kapoor, T. MacDonald, M. R. Bournazos, S. Varani, L. Palus, M. Hale, B. G. Banovic, P. Ruzek, D. Barnes, C. O. Robbiani, D. 2026-04-06 doi:10.64898/2026.04.02.715800 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ Molecular architecture of the ciliary base in mammalian multiciliated cells ]]> https://biorxiv.org/content/10.64898/2026.04.05.716577v1?rss=1 McCafferty, C. L. Brunet, M. van den Hoek, H. Buss, G. Mercey, O. Van der Stappen, P. Ritz, D. Müller, A. Righetto, R. D. Guichard, P. Hamel, V. Stearns, T. Engel, B. D. 2026-04-07 doi:10.64898/2026.04.05.716577 Cold Spring Harbor Laboratory Press 2026-04-07 <![CDATA[ RNA polymerase inhibitors reveal active-site motions essential for the nucleotide-addition cycle ]]> https://biorxiv.org/content/10.64898/2026.04.06.716786v1?rss=1 Dhingra, Y. Landick, R. Campbell, E. A. Darst, S. A. 2026-04-07 doi:10.64898/2026.04.06.716786 Cold Spring Harbor Laboratory Press 2026-04-07