bioRxiv Channel: Tel Aviv University https://biorxiv.org This feed contains articles for bioRxiv Channel "Tel Aviv University" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ The evolution of genetic diversity in changing environments ]]> https://biorxiv.org/content/10.1101/004440v1?rss=1 Oana Carja Uri Liberman Marcus W. Feldman 2014-04-23 doi:10.1101/004440 Cold Spring Harbor Laboratory Press 2014-04-23 <![CDATA[ Differential relationships between habitat fragmentation and within-population genetic diversity of three forest-dwelling birds ]]> https://biorxiv.org/content/10.1101/004903v1?rss=1 Benjamin Zuckerberg Matt Carling Roi Dor Elise Ferree Garth Spellman Andrea Townsend 2014-05-08 doi:10.1101/004903 Cold Spring Harbor Laboratory Press 2014-05-08 <![CDATA[ Chromosomal Inversion Symmetry: Generalized Chargaff Rules ]]> https://biorxiv.org/content/10.1101/013789v1?rss=1 Sagi Shporer Benny Chor David Horn 2015-01-14 doi:10.1101/013789 Cold Spring Harbor Laboratory Press 2015-01-14 <![CDATA[ TreeQTL: hierarchical error control for eQTL findings ]]> https://biorxiv.org/content/10.1101/021170v1?rss=1 Christine Peterson Marina Bogomolov Yoav Benjamini Chiara Sabatti 2015-07-07 doi:10.1101/021170 Cold Spring Harbor Laboratory Press 2015-07-07 <![CDATA[ Shift and adapt: the costs and benefits of karyotype variations ]]> https://biorxiv.org/content/10.1101/025171v1?rss=1 Aleeza C Gerstein Judith Berman 2015-08-20 doi:10.1101/025171 Cold Spring Harbor Laboratory Press 2015-08-20 <![CDATA[ The genetics of Bene Israel from India reveals both substantial Jewish and Indian ancestry ]]> https://biorxiv.org/content/10.1101/025809v1?rss=1 Yedael Y. Waldman Arjun Biddanda Natalie R. Davidson Paul Billing-Ross Maya Dubrovsky Christopher L. Campbell Carole Oddoux Eitan Friedman Gil Atzmon Eran Halperin Harry Ostrer Alon Keinan 2015-08-31 doi:10.1101/025809 Cold Spring Harbor Laboratory Press 2015-08-31 <![CDATA[ Recycler: an algorithm for detecting plasmids from de novo assembly graphs ]]> https://biorxiv.org/content/10.1101/029926v1?rss=1 Roye Rozov Aya Brown Kav David Bogumil Naama Shterzer Eran Halperin Itzhak Mizrahi Ron Shamir 2015-10-26 doi:10.1101/029926 Cold Spring Harbor Laboratory Press 2015-10-26 <![CDATA[ Characterization of expression quantitative trait loci in extensively phenotyped pedigrees ascertained for bipolar disorder ]]> https://biorxiv.org/content/10.1101/031427v1?rss=1 Christine Peterson Susan Service Anna Jasinska Fuying Gao Ivette Zelaya Terri Teshiba Carrie Bearden Victor Reus Gabriel Macaya Carlos López-Jaramillo Marina Bogomolov Yoav Benjamini Eleazar Eskin Giovanni Coppola Nelson Freimer Chiara Sabatti 2015-11-12 doi:10.1101/031427 Cold Spring Harbor Laboratory Press 2015-11-12 <![CDATA[ Fast and accurate construction of confidence intervals for heritability ]]> https://biorxiv.org/content/10.1101/031492v1?rss=1 Regev Schweiger Shachar Kaufman Reijo Laaksonen Marcus E Kleber Winfried März Eleazar Eskin Saharon Rosset Eran Halperin 2015-11-24 doi:10.1101/031492 Cold Spring Harbor Laboratory Press 2015-11-24 <![CDATA[ Shared generative rules of locomotor behavior in arthropods and vertebrates ]]> https://biorxiv.org/content/10.1101/031716v1?rss=1 Alex Gomez-Marin Efrat Oron Anna Gakamsky Dan Valente Yoav Benjamini Ilan Golani 2015-11-14 doi:10.1101/031716 Cold Spring Harbor Laboratory Press 2015-11-14 <![CDATA[ On the Apportionment of Population Structure ]]> https://biorxiv.org/content/10.1101/033852v1?rss=1 Yaron Granot Omri Tal Saharon Rosset Karl Skorecki 2015-12-07 doi:10.1101/033852 Cold Spring Harbor Laboratory Press 2015-12-07 <![CDATA[ An Ancestry Based Approach for Detecting Interactions ]]> https://biorxiv.org/content/10.1101/036640v1?rss=1 Danny Park Itamar Eskin Eun Yong Kang Eric R Gamazon Celeste Eng Christopher R Gignoux Joshua M Galanter Esteban Burchard Chun J Ye Hugues Aschard Eleazar Eskin Eran Halperin Noah Zaitlen 2016-01-13 doi:10.1101/036640 Cold Spring Harbor Laboratory Press 2016-01-13 <![CDATA[ Cis-regulatory evolution in prokaryotes revealed by interspecific archaeal hybrids. ]]> https://biorxiv.org/content/10.1101/044362v1?rss=1 Carlo Artieri Adit Naor Israela Turgeman-Grott Yiqi Zhou Ryan York Uri Gophna Hunter Fraser 2016-03-17 doi:10.1101/044362 Cold Spring Harbor Laboratory Press 2016-03-17 <![CDATA[ The Effects of Migration and Assortative Mating on Admixture Linkage Disequilibrium ]]> https://biorxiv.org/content/10.1101/056168v1?rss=1 Noah Zaitlen Scott Huntsman Donglei Hu Melissa Spear Celeste Eng Sam S Oh Marquitta J White Angel Mak Adam Davis Kelly Meade Emerita Brigino-Buenaventura Michael A LeNoir Kirsten Bibbins-Domingo Esteban G Burchard Eran Halperin 2016-05-31 doi:10.1101/056168 Cold Spring Harbor Laboratory Press 2016-05-31 <![CDATA[ With a little help from my friends: Cooperation can accelerate crossing of adaptive valleys ]]> https://biorxiv.org/content/10.1101/062323v1?rss=1 Uri Obolski Ohad Lewin-Epstein Eran Even-Tov Yoav Ram Lilach Hadany 2016-07-06 doi:10.1101/062323 Cold Spring Harbor Laboratory Press 2016-07-06 <![CDATA[ Functional Cliques in Developmentally Correlated Neural Networks ]]> https://biorxiv.org/content/10.1101/064147v1?rss=1 Stefano Luccioli Ari Barzilai Eshel Ben-Jacob Paolo Bonifazi Alessandro Torcini 2016-07-18 doi:10.1101/064147 Cold Spring Harbor Laboratory Press 2016-07-18 <![CDATA[ Genome-wide methylation data mirror ancestry information ]]> https://biorxiv.org/content/10.1101/066340v1?rss=1 Elior Rahmani Liat Shenhav Regev Schweiger Paul Yousefi Karen Huen Brenda Eskenazi Celeste Eng Scott Huntsman Donglei Hu Joshua Galanter Sam Oh Melanie Waldenberger Konstantin Strauch Harald Grallert Thomas Meitinger Christian Gieger Nina Holland Esteban Burchard Noah Zaitlen Eran Halperin 2016-07-27 doi:10.1101/066340 Cold Spring Harbor Laboratory Press 2016-07-27 <![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[ Ploidy tug-of-war: evolutionary and genetic environments influence the rate of ploidy drive in a human fungal pathogen ]]> https://biorxiv.org/content/10.1101/084467v1?rss=1 Gerstein, A. Lim, H. Berman, J. Hickman, M. 2016-10-31 doi:10.1101/084467 Cold Spring Harbor Laboratory Press 2016-10-31 <![CDATA[ Interrogating the Topological Robustness of Gene Regulatory Circuits ]]> https://biorxiv.org/content/10.1101/084962v1?rss=1 Huang, B. Lu, M. Jia, D. Ben-Jacob, E. Levine, H. Onuchic, J. 2016-11-03 doi:10.1101/084962 Cold Spring Harbor Laboratory Press 2016-11-03 <![CDATA[ Histone deacetylase inhibitors reduce the number of herpes simplex virus-1 genomes initiating expression in individual cells. ]]> https://biorxiv.org/content/10.1101/086249v1?rss=1 Shapira, L. Ralph, M. Tomer, E. Cohen, S. Kobiler, O. 2016-11-07 doi:10.1101/086249 Cold Spring Harbor Laboratory Press 2016-11-07 <![CDATA[ Genetic variation and gene expression across multiple tissues and developmental stages in a non-human primate ]]> https://biorxiv.org/content/10.1101/092874v1?rss=1 Jasinska, A. J. Zelaya, I. Service, S. K. Peterson, C. Cantor, R. M. Choi, O.-W. DeYoung, J. Eskin, E. Fairbanks, L. A. Fears, S. Furterer, A. Huang, Y. S. Ramensky, V. Schmitt, C. A. Svardal, H. Jorgensen, M. J. Kaplan, J. R. Villar, D. Aken, B. L. Flicek, P. Nag, R. Wong, E. S. Blangero, J. Dyer, T. D. Bogomolov, M. Benjamini, Y. Weinstock, G. M. Dewar, K. Sabatti, C. Wilson, R. K. Jentsch, J. D. Warren, W. Coppola, G. Woods, R. P. Freimer, N. B. 2016-12-09 doi:10.1101/092874 Cold Spring Harbor Laboratory Press 2016-12-09 <![CDATA[ Genome-wide association study in Collaborative Cross mice revealed a skeletal role for Rhbdf2 ]]> https://biorxiv.org/content/10.1101/094698v1?rss=1 Levy, R. Levet, C. Cohen, K. Freeman, M. Mott, R. Iraqi, F. Gabet, Y. 2016-12-16 doi:10.1101/094698 Cold Spring Harbor Laboratory Press 2016-12-16 <![CDATA[ Neural precursors of decisions that matter--an ERP study of deliberate and arbitrary choice ]]> https://biorxiv.org/content/10.1101/097626v1?rss=1 Maoz, U. Yaffe, G. Koch, C. Mudrik, L. 2017-01-01 doi:10.1101/097626 Cold Spring Harbor Laboratory Press 2017-01-01 <![CDATA[ Small RNAs reflect grandparental environments in apomictic dandelion ]]> https://biorxiv.org/content/10.1101/099572v1?rss=1 Morgado, L. Preite, V. Oplaat, C. Anava, S. Ferreira de Carvalho, J. Rechavi, O. Johannes, F. Verhoeven, K. 2017-01-11 doi:10.1101/099572 Cold Spring Harbor Laboratory Press 2017-01-11 <![CDATA[ Reduced representation optical methylation mapping (R2OM2). ]]> https://biorxiv.org/content/10.1101/108084v1?rss=1 Grunwald, A. Sharim, H. Gabrieli, T. Michaeli, Y. Torchinsky, D. Juhasz, M. Reifenberger, J. Hastie, A. R. Cao, H. Weinhold, E. Ebenstein, Y. 2017-03-06 doi:10.1101/108084 Cold Spring Harbor Laboratory Press 2017-03-06 <![CDATA[ Cas9-Assisted Targeting of CHromosome segments (CATCH) for targeted nanopore sequencing and optical genome mapping ]]> https://biorxiv.org/content/10.1101/110163v1?rss=1 Gabrieli, T. Sharim, H. Michaeli, Y. Ebenstein, Y. 2017-02-20 doi:10.1101/110163 Cold Spring Harbor Laboratory Press 2017-02-20 <![CDATA[ Key Issues Review: Evolution on rugged adaptive landscapes ]]> https://biorxiv.org/content/10.1101/112177v1?rss=1 Obolski, U. Ram, Y. Hadany, L. 2017-03-03 doi:10.1101/112177 Cold Spring Harbor Laboratory Press 2017-03-03 <![CDATA[ A Bayesian Framework for Estimating Cell Type Composition from DNA Methylation Without the Need for Methylation Reference ]]> https://biorxiv.org/content/10.1101/112417v1?rss=1 Rahmani, E. Schweiger, R. Shenhav, L. Eskin, E. Halperin, E. 2017-02-28 doi:10.1101/112417 Cold Spring Harbor Laboratory Press 2017-02-28 <![CDATA[ RecBlast: Cloud-Based Large Scale Orthology Detection ]]> https://biorxiv.org/content/10.1101/112946v1?rss=1 Rapoport, E. Neuhof, M. 2017-03-02 doi:10.1101/112946 Cold Spring Harbor Laboratory Press 2017-03-02 <![CDATA[ Reduced representation optical methylation mapping (R2OM2). ]]> https://biorxiv.org/content/10.1101/113522v1?rss=1 Grunwald, A. Sharim, H. Gabrieli, T. Michaeli, Y. Torchinsky, D. Juhasz, M. Wagner, K. R. Pevsner, J. Reifenberger, J. Hastie, A. R. Cao, H. Weinhold, E. Ebenstein, Y. 2017-03-03 doi:10.1101/113522 Cold Spring Harbor Laboratory Press 2017-03-03 <![CDATA[ Imaging Object-Scene Integration in Visible and Invisible Natural Scenes ]]> https://biorxiv.org/content/10.1101/116111v1?rss=1 Faivre, N. Dubois, J. Schwartz, N. Mudrik, L. 2017-03-12 doi:10.1101/116111 Cold Spring Harbor Laboratory Press 2017-03-12 <![CDATA[ Temporal Niche Expansion In Mammals From A Nocturnal Ancestor After Dinosaur Extinction ]]> https://biorxiv.org/content/10.1101/123273v1?rss=1 Maor, R. Dayan, T. Ferguson-Gow, H. Jones, K. 2017-04-02 doi:10.1101/123273 Cold Spring Harbor Laboratory Press 2017-04-02 <![CDATA[ Faucet: streaming de novo assembly graph construction ]]> https://biorxiv.org/content/10.1101/125658v1?rss=1 Rozov, R. Goldshlager, G. Halperin, E. Shamir, R. 2017-04-08 doi:10.1101/125658 Cold Spring Harbor Laboratory Press 2017-04-08 <![CDATA[ Association mapping and haplotype analysis of the pre-harvest sprouting resistance locus Phs-A1 reveals a causal role of TaMKK3-A in global germplasm ]]> https://biorxiv.org/content/10.1101/131201v1?rss=1 Shorinola, O. Balcarkova, B. Hyles, J. Tibbits, J. F. G. Hayden, M. J. Holusova, K. Valarik, M. Distelfeld, A. Torada, A. Barrero, J. M. Uauy, C. 2017-04-26 doi:10.1101/131201 Cold Spring Harbor Laboratory Press 2017-04-26 <![CDATA[ Human brain-derived Aβ oligomers bind to synapses and disrupt synaptic activity in a manner that requires APP ]]> https://biorxiv.org/content/10.1101/135673v1?rss=1 Walsh, D. Wang, Z. Jackson, R. J. Hong, W. Walter, T. M. Moreno, A. Liu, W. Li, S. Frosch, M. P. Slutsky, I. Young-Pearse, T. Spires-Jones, T. L. 2017-05-09 doi:10.1101/135673 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ The Role Of Diffusion MRI In Neuroscience ]]> https://biorxiv.org/content/10.1101/140459v1?rss=1 Assaf, Y. Johansen-Berg, H. Thiebaut de Schotten, M. 2017-05-22 doi:10.1101/140459 Cold Spring Harbor Laboratory Press 2017-05-22 <![CDATA[ An exact and efficient score test for variance components models ]]> https://biorxiv.org/content/10.1101/140889v1?rss=1 Schweiger, R. Weissbrod, O. Rahmani, E. Müller-Nurasyid, M. Kunze, S. Gieger, C. Waldenberger, M. Rosset, S. Halperin, E. 2017-06-03 doi:10.1101/140889 Cold Spring Harbor Laboratory Press 2017-06-03 <![CDATA[ The processing of dynamic faces in the human brain: Support for an integrated neural framework of face processing. ]]> https://biorxiv.org/content/10.1101/140939v1?rss=1 Bernstein, M. Erez, Y. Blank, I. Yovel, G. 2017-06-05 doi:10.1101/140939 Cold Spring Harbor Laboratory Press 2017-06-05 <![CDATA[ OCT4 Impedes Cell Fate Redirection By The Melanocyte Lineage Master Regulator MITF ]]> https://biorxiv.org/content/10.1101/142943v1?rss=1 Sheinboim, D. Maza, I. Dror, I. Parikh, S. Krupalnik, V. Bell, R. E. Zviran, A. Suita, Y. Hakim, O. Gutfreund, Y. M. Khaled, M. Hanna, J. H. Levy, C. 2017-05-27 doi:10.1101/142943 Cold Spring Harbor Laboratory Press 2017-05-27 <![CDATA[ An anti-cancer binary system activated by bacteriophage HK022 Integrase ]]> https://biorxiv.org/content/10.1101/147736v1?rss=1 Elias, A. Spector, I. Gritsenko, N. Zilberstein, Y. Gorovits, R. Prag, G. Kolot, M. 2017-06-12 doi:10.1101/147736 Cold Spring Harbor Laboratory Press 2017-06-12 <![CDATA[ Reconstructing cancer karyotypes from short read data: the half full and half empty glass ]]> https://biorxiv.org/content/10.1101/152447v1?rss=1 Eitan, R. Shamir, R. 2017-06-20 doi:10.1101/152447 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Does floral herbivory reduce pollination-mediated fitness in shelter rewarding Royal Irises? ]]> https://biorxiv.org/content/10.1101/184382v1?rss=1 Ghara, M. Ewerhardy, C. Yardeni, G. Matzliach, M. Sapir, Y. 2017-09-04 doi:10.1101/184382 Cold Spring Harbor Laboratory Press 2017-09-04 <![CDATA[ An extensive enhancer-promoter map generated by genome-scale analysis of enhancer and gene activity patterns ]]> https://biorxiv.org/content/10.1101/190231v1?rss=1 300,000 cross-validated E-P links spanning ~16K known genes. Our study presents an improved method for inferring regulatory links between enhancers and promoters, and provides an extensive resource of E-P maps that could greatly assist the functional interpretation of the noncoding regulatory genome. FOCS and our predicted E-P map are publicly available at http://acgt.cs.tau.ac.il/focs. ]]> Hait, T. A. Amar, D. Shamir, R. Elkon, R. 2017-09-18 doi:10.1101/190231 Cold Spring Harbor Laboratory Press 2017-09-18 <![CDATA[ Evolutionary rate shifts suggest species-specific adaptation events in HIV-1 and SIV ]]> https://biorxiv.org/content/10.1101/190769v1?rss=1 Gelbart, M. Stern, A. 2017-09-19 doi:10.1101/190769 Cold Spring Harbor Laboratory Press 2017-09-19 <![CDATA[ Precopulatory behavior and sexual conflict in the desert locust ]]> https://biorxiv.org/content/10.1101/190793v1?rss=1 Golov, Y. Rillich, J. Harari, A. Ayali, A. 2017-09-19 doi:10.1101/190793 Cold Spring Harbor Laboratory Press 2017-09-19 <![CDATA[ N6-methyladenosine modification and the YTHDF2 reader protein play cell type specific roles in lytic viral gene expression during Kaposi’s sarcoma-associated herpesvirus infection ]]> https://biorxiv.org/content/10.1101/201475v1?rss=1 Hesser, C. Karijolich, J. Dominissini, D. He, C. Glaunsinger, B. A. 2017-10-11 doi:10.1101/201475 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ A spectral jamming avoidance response does not help bats deal with jamming ]]> https://biorxiv.org/content/10.1101/2019.12.16.876086v1?rss=1 Mazar, O. Yovel, Y. 2019-12-16 doi:10.1101/2019.12.16.876086 Cold Spring Harbor Laboratory Press 2019-12-16 <![CDATA[ Reconstructing the evolutionary origins of extreme halophilic Archaeal lineages ]]> https://biorxiv.org/content/10.1101/2019.12.19.883488v1?rss=1 Feng, Y. Neri, U. Gosselin, S. Louyakis, A. S. Papke, R. T. Gophna, U. Gogarten, J. P. 2019-12-20 doi:10.1101/2019.12.19.883488 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ The functional organization of high-level visual cortex determines the representation of complex visual stimuli ]]> https://biorxiv.org/content/10.1101/2019.12.22.852293v1?rss=1 Kliger, L. Yovel, G. 2019-12-23 doi:10.1101/2019.12.22.852293 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ The rebound response plays a role in the motion mechanisms and perception ]]> https://biorxiv.org/content/10.1101/2019.12.31.891580v1?rss=1 Cohen-Duwek, H. Spitzer, H. 2020-01-02 doi:10.1101/2019.12.31.891580 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ Face recognition depends on specialized mechanisms tuned to view-invariant facial features: Insights from deep neural networks optimized for face or object recognition ]]> https://biorxiv.org/content/10.1101/2020.01.01.890277v1?rss=1 Abudarham, N. Yovel, G. 2020-01-02 doi:10.1101/2020.01.01.890277 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ Prediction of synonymous corrections by the BE-FF computational tool expands the targeting scope of base editing ]]> https://biorxiv.org/content/10.1101/2020.01.06.890244v1?rss=1 View larger version (17K): org.highwire.dtl.DTLVardef@36330borg.highwire.dtl.DTLVardef@514ca0org.highwire.dtl.DTLVardef@17dbc56org.highwire.dtl.DTLVardef@1d7d8d2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Rabinowitz, R. Abadi, S. Almog, S. Offen, D. 2020-01-06 doi:10.1101/2020.01.06.890244 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ Tracing the evolutionary history and global expansion of Candida auris using population genomic analyses ]]> https://biorxiv.org/content/10.1101/2020.01.06.896548v1?rss=1 Chow, N. A. Munoz, J. F. Gade, L. Berkow, E. Li, X. Welsh, R. M. Forsberg, K. Lockhart, S. R. Adam, R. Alanio, A. Alastruey-Izquierdo, A. Althawadi, S. Belen Arauz, A. Ben-Ami, R. Bharat, A. Calvo, B. C. Desnos-Ollivier, M. Escandon, P. Gardam, D. Gunturu, R. Heath, C. H. Kurzai, O. Martin, R. Litvintseva, A. P. Cuomo, C. 2020-01-07 doi:10.1101/2020.01.06.896548 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ Effective psychological treatment for PTSD changes the dynamics of specific large-scale brain networks ]]> https://biorxiv.org/content/10.1101/2020.01.07.891986v1?rss=1 Charquero-Ballester, M. Kleim, B. Vidaurre, D. Ruff, C. Stark, E. Tuulari, J. J. McManners, H. Bar-Haim, Y. Bouquillon, L. Moseley, A. Williams, S. C. R. Woolrich, M. W. Kringelbach, M. L. Ehlers, A. 2020-01-07 doi:10.1101/2020.01.07.891986 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ Three Rules Explain Transgenerational Small RNA Inheritance in C. elegans ]]> https://biorxiv.org/content/10.1101/2020.01.08.899203v1?rss=1 20,000 worms we reveal 3 inheritance rules: (1) Once a response is initiated, each isogenic mother stochastically assumes an "inheritance state", establishing a commitment that determines the fate of the inheritance. (2) The response that each mother transfers is uniform in each generation of her descendants. (3) The likelihood that an RNAi response would transmit to the progeny increases the more generations the response lasts, according to a "hot hand" principle. Mechanistically, the different parental "inheritance states" correspond to global changes in the expression levels of endogenous small RNAs, immune response genes, and targets of the conserved transcription factor HSF-1. We show that these rules predict the descendants developmental rate and resistance to stress. ]]> Houri Zeevi, L. Antonova, O. Rechavi, O. 2020-01-09 doi:10.1101/2020.01.08.899203 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ ModelTeller: model selection for optimal phylogenetic reconstruction using machine learning ]]> https://biorxiv.org/content/10.1101/2020.01.09.899906v1?rss=1 Abadi, S. Avram, O. Rosset, S. Pupko, T. Mayrose, I. 2020-01-09 doi:10.1101/2020.01.09.899906 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ SCAPP: An algorithm for improved plasmid assembly in metagenomes ]]> https://biorxiv.org/content/10.1101/2020.01.12.903252v1?rss=1 Pellow, D. Probst, M. Furman, O. Zorea, A. Segal, A. Mizrahi, I. Shamir, R. 2020-01-14 doi:10.1101/2020.01.12.903252 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Early EEG and behavioral alterations in Dravet mice ]]> https://biorxiv.org/content/10.1101/2020.01.13.904557v1?rss=1 Fadila, S. Quinn, S. Turchetti Maia, A. Yakubovich, D. Anderson, K. L. Rubinstein, M. 2020-01-14 doi:10.1101/2020.01.13.904557 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Evolutionary forces on A-to-I RNA editing revealed by sequencing individual honeybee drones ]]> https://biorxiv.org/content/10.1101/2020.01.15.907287v1?rss=1 Duan, Y. Dou, S. Huang, J. Eisenberg, E. Lu, J. 2020-01-15 doi:10.1101/2020.01.15.907287 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Relating the past with the present: Information integration and segregation during ongoing narrative processing ]]> https://biorxiv.org/content/10.1101/2020.01.16.908731v1?rss=1 Chang, C. H. C. Lazaridi, C. Yeshurun, Y. Norman, K. A. Hasson, U. 2020-01-17 doi:10.1101/2020.01.16.908731 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ An instructive role for IL7RA in the development of human B-cell precursor leukemia. ]]> https://biorxiv.org/content/10.1101/2020.01.27.919951v1?rss=1 Geron, I. Savino, A. M. Tal, N. Fishman, H. Brown, J. Turati, V. James, C. Sarno, J. Lee, Y. N. Rein Gil, A. Birger, Y. Muler, I. Hameiri-Grossman, M. Marcu-Malina, V. Parnas, O. Fischer, U. Muschen, M. Borkhard, A. Kirsch, I. R. Nagler, A. Enver, T. Izraeli, S. 2020-01-28 doi:10.1101/2020.01.27.919951 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ Extracellular ATP released from Candida albicans activates non-peptidergic neurons to augment host defense ]]> https://biorxiv.org/content/10.1101/2020.01.27.921049v1?rss=1 Edwards, T. Zhang, S. Liu, A. Cohen, J. Zhou, P. Mogavero, S. hube, b. berman, j. bougnoux, m.-e. mathers, a. gaffen, s. Albers, K. M. koeber, h. r. davis, b. d'enfert, c. Kaplan, D. H. 2020-01-28 doi:10.1101/2020.01.27.921049 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ Spatio-temporal Proteomic Analysis of Stress Granule disassembly using APEX Reveals Regulation by SUMOylation and links to ALS pathogenesis ]]> https://biorxiv.org/content/10.1101/2020.01.29.830133v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@15899daorg.highwire.dtl.DTLVardef@1dcd399org.highwire.dtl.DTLVardef@c7ef12org.highwire.dtl.DTLVardef@20c096_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hagai, M.-K. Siany, A. Kedersha, N. Knafo, N. Rivkin, N. Danino, Y. M. Cohen, N. Olender, T. Moens, T. Higginbottom, A. Cooper-Knock, J. Eitan, C. Toth Cohen, B. Van Den Bocho, L. Anderson, P. Ivanov, P. Geiger, T. Hornstein, E. 2020-01-29 doi:10.1101/2020.01.29.830133 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ Estimation of the propensity for sexual selection in a cyclical parthenogen ]]> https://biorxiv.org/content/10.1101/2020.02.05.935148v1?rss=1 Duneau, D. Altermatt, F. Ferdy, J.-B. Ben-ami, F. Ebert, D. 2020-02-05 doi:10.1101/2020.02.05.935148 Cold Spring Harbor Laboratory Press 2020-02-05 <![CDATA[ Sex-specific crossover rates did not change with parental age in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2020.02.06.938183v1?rss=1 Baskar, R. Saini, R. Singh, A. K. Hyde, G. J. 2020-02-07 doi:10.1101/2020.02.06.938183 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Hyaluronan-NK cell Interaction Controls the Primary Vascular Barrier during Early Pregnancy ]]> https://biorxiv.org/content/10.1101/2020.02.09.940544v1?rss=1 Hadas, R. Gershon, E. Cohen, A. Stroganov, S. Atrakchi, O. Lazar, S. Golani, O. Dassa, B. Elbaz, M. Cohen, G. Kartvelishvily, E. Eilam, R. Dekel, N. Neeman, M. 2020-02-10 doi:10.1101/2020.02.09.940544 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ mRNA secondary structure stability regulates bacterial translation insulation and re-initiation ]]> https://biorxiv.org/content/10.1101/2020.02.10.941153v1?rss=1 Chemla, Y. Peeri, M. Heltberg, M. L. Eichler, J. Jensen, M. H. Tuller, T. Alfonta, L. 2020-02-10 doi:10.1101/2020.02.10.941153 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ A universal subcuticular bacterial symbiont of a coral predator, the crown-of-thorns starfish ]]> https://biorxiv.org/content/10.1101/2020.02.13.947093v1?rss=1 Wada, N. Yuasa, H. Kajitani, R. Gotoh, Y. Ogura, Y. Yoshimura, D. Toyoda, A. Tang, S.-L. Higashimura, Y. Sweatman, H. Forsman, Z. H. Bronstein, O. Eyal, G. Thongtham, N. Itoh, T. Hayashi, T. Yasuda, N. 2020-02-14 doi:10.1101/2020.02.13.947093 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Exposure to Mites Sensitizes Intestinal Stem Cell Maintenance, Splenic Marginal Zone B Cell Homeostasis, And Heart Development to Notch Dosage and Cooperativity. ]]> https://biorxiv.org/content/10.1101/2020.02.13.948224v1?rss=1 Kobia, F. M. Preusse, K. Dai, Q. Weaver, N. Stein, S. J. Pear, W. Yuan, Z. Kovall, R. Kuang, Y. Eafergen, N. Sprinzak, D. Gebelein, B. Brunskill, E. W. Kopan, R. 2020-02-14 doi:10.1101/2020.02.13.948224 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Anode surface bioaugmentation enhances deterministic biofilm assembly in microbial fuel cells ]]> https://biorxiv.org/content/10.1101/2020.02.17.951574v1?rss=1 Yanuka-Golub, K. Dubinsky, V. Korenblum, E. Reshef, L. Ofek-Lalzar, M. Rishpon, J. Gophna, U. 2020-02-17 doi:10.1101/2020.02.17.951574 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ MONET: Multi-omic patient module detection by omic selection ]]> https://biorxiv.org/content/10.1101/2020.02.21.960062v1?rss=1 Rappoport, N. Safra, R. Shamir, R. 2020-02-24 doi:10.1101/2020.02.21.960062 Cold Spring Harbor Laboratory Press 2020-02-24 <![CDATA[ Hook Shape of Growing Leaves Results from an Active Regulation ]]> https://biorxiv.org/content/10.1101/2020.02.27.967513v1?rss=1 Riviere, M. Corre, Y. Peaucelle, A. Derr, J. Douady, S. 2020-02-27 doi:10.1101/2020.02.27.967513 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ B cells engineered to express an anti-HIV antibody allow memory retention, class switch recombination and clonal selection in mice ]]> https://biorxiv.org/content/10.1101/2020.02.28.970822v1?rss=1 Nahmad, A. D. Raviv, Y. Horovitz-Fried, M. Sofer, I. Akriv, T. Nataf, D. Dotan, I. Burstein, D. Wine, Y. Benhar, I. Barzel, A. 2020-03-03 doi:10.1101/2020.02.28.970822 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ Non-CG methylation is superior to CG methylation in genome regulation ]]> https://biorxiv.org/content/10.1101/2020.03.04.971267v1?rss=1 Domb, K. Katz, A. Yaari, R. Kaisler, E. Nguyen, V. H. Hong, U. V. T. Griess, O. Gitin Heskiau, K. Ohad, N. Zemach, A. 2020-03-05 doi:10.1101/2020.03.04.971267 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ A codon model for associating phenotypic traits with altered selective patterns of sequence evolution ]]> https://biorxiv.org/content/10.1101/2020.03.04.974584v1?rss=1 Halabi, K. Levy Karin, E. Gueguen, L. Mayrose, I. 2020-03-05 doi:10.1101/2020.03.04.974584 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Processive and stochastic CHH methylation by plant DRM2 and CMT2 revealed by single-read methylome analysis ]]> https://biorxiv.org/content/10.1101/2020.03.05.974956v1?rss=1 Harris, K. D. Zemach, A. 2020-03-06 doi:10.1101/2020.03.05.974956 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ Real-time Ratiometric Imaging of Micelles Assembly State in a Microfluidic Cancer-on-a-chip ]]> https://biorxiv.org/content/10.1101/2020.03.08.978783v1?rss=1 Feiner-Gracia, N. Glinkowska Mares, A. Buzhor, M. Rodriguez-Trujillo, R. Samitier, J. Amir, R. Pujals, S. Albertazzi, L. 2020-03-09 doi:10.1101/2020.03.08.978783 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ Exploring Potential Signals of Selection for Disordered Residues in Naturally Occurring Prokaryotic and Eukaryotic Proteins ]]> https://biorxiv.org/content/10.1101/2020.03.10.979443v1?rss=1 Panda, A. Tuller, T. 2020-03-10 doi:10.1101/2020.03.10.979443 Cold Spring Harbor Laboratory Press 2020-03-10 <![CDATA[ Striatin is required for hearing and affects inner hair cells and ribbon synapses ]]> https://biorxiv.org/content/10.1101/2020.03.11.987396v1?rss=1 Nadar Ponniah, P. Taiber, S. Caspi, M. Koffler-Brill, T. Dror, A. A. Rubinstein, M. Lang, R. W. Avraham, K. B. Rosin-Arbesfeld, R. 2020-03-11 doi:10.1101/2020.03.11.987396 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Spontaneous regression of micro-metastases following primary tumor excision: a critical role for primary tumor secretome ]]> https://biorxiv.org/content/10.1101/2020.03.12.986992v1?rss=1 Shaashua, L. Eckerling, A. Israeli, B. Yanovich, G. Rosenne, E. Fichman-Horn, S. Ben Zvi, I. Sorski, L. Satchi-Fainaro, R. Geiger, T. Sloan, E. K. Ben-Eliyahu, S. 2020-03-13 doi:10.1101/2020.03.12.986992 Cold Spring Harbor Laboratory Press 2020-03-13 <![CDATA[ Access to PCNA by Srs2 and Elg1 controls the choice between alternative repair pathways in yeast ]]> https://biorxiv.org/content/10.1101/2020.03.24.006932v1?rss=1 Arbel, M. Bronstein, A. Sau, S. Liefshitz, B. Kupiec, M. 2020-03-25 doi:10.1101/2020.03.24.006932 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Motor-evoked neural responses in auditory cortex are associated with improved sensitivity to self-generated sounds ]]> https://biorxiv.org/content/10.1101/2020.03.25.002485v1?rss=1 Reznik, D. Hacohen, N. Buaron, B. Zion Golumbic, E. Mukamel, R. 2020-03-25 doi:10.1101/2020.03.25.002485 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Anticipatory responses along motion trajectories in awake monkey area V1 ]]> https://biorxiv.org/content/10.1101/2020.03.26.010017v1?rss=1 Benvenuti, G. Chemla, S. Boonman, A. Perrinet, L. Masson, G. S. Chavane, F. 2020-03-29 doi:10.1101/2020.03.26.010017 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ Inhalation: A means to explore and optimize nintedanib's pharmacokinetic/pharmacodynamic relationship ]]> https://biorxiv.org/content/10.1101/2020.03.27.012401v1?rss=1 Epstein-Shochet, G. Pham, S. Beck, S. Naiel, S. Mekhael, O. Revill, S. Hayat, A. Vierhout, M. Bardestein-Wald, B. Shitrit, D. Ask, K. Montgomery, A. B. Kolb, M. Surber, M. 2020-03-29 doi:10.1101/2020.03.27.012401 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ Production of Hyaluronan by the Trophectoderm is a Prerequisite for Mouse Blastocyst Attachment ]]> https://biorxiv.org/content/10.1101/2020.03.27.012880v1?rss=1 Hadas, R. Gershon, E. Cohen, A. Ben-dor, S. Kohen, F. Dekel, N. Neeman, M. 2020-03-29 doi:10.1101/2020.03.27.012880 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ Temporally-precise basolateral amygdala activation is required for the formation of taste memories in the gustatory cortex ]]> https://biorxiv.org/content/10.1101/2020.03.29.013995v1?rss=1 800ms), but not the early epoch (EE, 200-700ms), BLA activation during novel taste experience is essential for normal CTA, for early c-Fos expression in the GC (a marker of TMT formation) and for the subsequent changes in GC ensemble palatability coding. Interestingly, BLA activity was not required for intact taste identity or palatability perceptions. We further show that BLA-LE information is transmitted to GC through the BLA[->]NBM pathway where it affects the formation of taste memories. These results expose the dependence of long-term memory formation on specific temporal windows during sensory responses and the distributed circuits supporting this dependence. SignificanceConsumption of a novel taste may result in malaise and poses a threat to animals. Since the effects of poisoning appear only hours after consumption, animals must store the novel tastes information in memory until they associate it with its value (nutritious or poisonous). Here we elucidate the neuronal activity patterns and circuits that support the processing and creation of novel-taste memories in rats. Our results show that specific patterns of temporal activation in the basolateral amygdala transmitted across brain areas are important for formation of taste memory and taste-malaise association. These findings may shed light on long-term activity-to-memory transformation in other sensory modalities. ]]> Arieli, E. Gerbi, R. Shein-Idelson, M. Moran, A. 2020-03-30 doi:10.1101/2020.03.29.013995 Cold Spring Harbor Laboratory Press 2020-03-30 <![CDATA[ Renewable Fatty Acid Ester Production in Clostridium ]]> https://biorxiv.org/content/10.1101/2020.03.29.014746v1?rss=1 Feng, J. Zhang, J. Wang, P. Jimenez-Bonilla, P. Gu, Y. Zhou, J. Cao, M. Shao, Z. Borovok, I. Wang, Y. 2020-03-30 doi:10.1101/2020.03.29.014746 Cold Spring Harbor Laboratory Press 2020-03-30 <![CDATA[ A bacterial tragedy of the commons that masks the actual frequency of mutants ]]> https://biorxiv.org/content/10.1101/2020.04.02.022889v1?rss=1 Neves, H. I. Trombini, G. Ramos, T. Yang, H. M. Yagil, E. Spira, B. 2020-04-04 doi:10.1101/2020.04.02.022889 Cold Spring Harbor Laboratory Press 2020-04-04 <![CDATA[ Spatial cueing effects are not what we thought: on the timing of attentional deployment ]]> https://biorxiv.org/content/10.1101/2020.04.08.031302v1?rss=1 Yaron, I. Lamy, D. 2020-04-09 doi:10.1101/2020.04.08.031302 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Visual attention modulates the integration of goal-relevant evidence and not value ]]> https://biorxiv.org/content/10.1101/2020.04.14.031971v1?rss=1 Sepulveda, P. Usher, M. Davies, N. Benson, A. Ortoleva, P. De Martino, B. 2020-04-14 doi:10.1101/2020.04.14.031971 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Areas of global importance for terrestrial biodiversity, carbon, and water ]]> https://biorxiv.org/content/10.1101/2020.04.16.021444v1?rss=1 Jung, M. Arnell, A. De Lamo, X. Garcia-Rangel, S. Lewis, M. Mark, J. Merow, C. Miles, L. Ondo, I. Pironon, S. Ravilious, C. Rivers, M. Schepashenko, D. Tallowin, O. van Soesbergen, A. Govaerts, R. Boyle, B. L. Enquist, B. J. Feng, X. Gallagher, R. V. Maitner, B. Meiri, S. Mulligan, M. Ofer, G. Hanson, J. O. Jetz, W. Di Marco, M. McGowan, J. Rinnan, D. S. Sachs, J. D. Lesiv, M. Adams, V. M. Andrew, S. C. Burger, J. R. Hannah, L. Marquet, P. McCarthy, J. K. Morueta-Holme, N. Newman, E. A. Park, D. S. Roehrdanz, P. R. Svenning, J.-C. Violle, C. Wieringa, 2020-04-16 doi:10.1101/2020.04.16.021444 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ A general 3D model for growth dynamics of sensory-growth systems: from plants to robotics ]]> https://biorxiv.org/content/10.1101/2020.04.21.053033v1?rss=1 Porat, A. Tedone, F. Palladino, M. Marcati, P. Meroz, Y. 2020-04-23 doi:10.1101/2020.04.21.053033 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Flexible machine learning prediction of antigen presentation for rare and common HLA-I alleles ]]> https://biorxiv.org/content/10.1101/2020.04.25.061069v1?rss=1 Bravi, B. Tubiana, J. Cocco, S. Monasson, R. Mora, T. Walczak, A. M. 2020-04-25 doi:10.1101/2020.04.25.061069 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Elevated expression of ACE2 in tumor-adjacent normal tissues of cancer patients ]]> https://biorxiv.org/content/10.1101/2020.04.25.061200v1?rss=1 Winkler, T. Ben-David, U. 2020-04-25 doi:10.1101/2020.04.25.061200 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Identification of essential genes and fluconazole resistance genes in Candida glabrata by profiling of Hermes transposon insertions. ]]> https://biorxiv.org/content/10.1101/2020.04.27.064048v1?rss=1 Gale, A. N. Sakhawala, R. M. Levitan, A. Sharan, R. Berman, J. Timp, W. Cunningham, K. W. 2020-04-29 doi:10.1101/2020.04.27.064048 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Oculomotor inhibition precedes temporally expected auditory targets ]]> https://biorxiv.org/content/10.1101/2020.04.28.065839v1?rss=1 Abeles, D. Amit, R. Tal-Perry, N. Carrasco, M. Yuval-Greenberg, S. 2020-04-30 doi:10.1101/2020.04.28.065839 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Tripartite Inhibition of SRC-WNT-PKC Signalling Consolidates Human Naive Pluripotency ]]> https://biorxiv.org/content/10.1101/2020.05.23.112433v1?rss=1 Bayerl, J. Ayyash, M. Shani, T. Manor, Y. Gafni, O. Kalma, Y. Aguilera-Castrejon, A. Zerbib, M. Amir, H. Sheban, D. Geula, S. Mor, N. Weinberger, L. Krupalnik, V. Oldak, B. Livnat, N. Tarazi, S. Tawil, S. Lasman, L. Hanna, S. Novershtern, N. Ben-Yosef, D. Viukov, S. Hanna, J. H. 2020-05-24 doi:10.1101/2020.05.23.112433 Cold Spring Harbor Laboratory Press 2020-05-24 <![CDATA[ Structural basis of SARS-CoV-2 spike protein induced by ACE2 ]]> https://biorxiv.org/content/10.1101/2020.05.24.113175v1?rss=1 Meirson, T. Bomze, D. Markel, G. 2020-05-24 doi:10.1101/2020.05.24.113175 Cold Spring Harbor Laboratory Press 2020-05-24 <![CDATA[ Predicting Individual Variability in Task-Evoked Brain Activity in Schizophrenia ]]> https://biorxiv.org/content/10.1101/2020.05.25.114603v1?rss=1 Tik, N. Livny, A. Gal, S. Gigi, K. Tsarfaty, G. Weiser, M. Tavor, I. 2020-05-25 doi:10.1101/2020.05.25.114603 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Neuronal resonance can be generated independently at distinct levels of organization ]]> https://biorxiv.org/content/10.1101/2020.05.26.117309v1?rss=1 Stark, E. Rotstein, H. G. 2020-05-29 doi:10.1101/2020.05.26.117309 Cold Spring Harbor Laboratory Press 2020-05-29 <![CDATA[ Insulin-like growth factor 2 (IGF2) protects against Huntington's disease through the extracellular disposal of protein aggregates ]]> https://biorxiv.org/content/10.1101/2020.05.28.119164v1?rss=1 Garcia-Huerta, P. Troncoso-Escudero, P. Wu, D. Thiruvalluvan, A. Cisternas, M. Henriquez, D. R. Plate, L. Chana-Cuevas, P. Sequel, C. Thielen, P. Longo, K. A. Geddes, B. J. Lederkremer, G. Sharma, N. Shenkman, M. Naphade, S. Sardi, P. Spichiger, C. Richter, H. G. Court, F. Ellerby, L. Wiseman, L. Gonzalez-Billault, C. Bergink, S. Vidal, R. L. Hetz, C. 2020-05-30 doi:10.1101/2020.05.28.119164 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Mother Brain is Wired for Social Moments ]]> https://biorxiv.org/content/10.1101/2020.05.31.125955v1?rss=1 Shimon-Raz, O. Salomon, R. Bloch, M. Aisenberg Romano, G. Hendler, T. Yeshurun, Y. Ulmer Yaniv, A. Zagoory-Sharon, O. Feldman, R. 2020-06-01 doi:10.1101/2020.05.31.125955 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ Structure of the human heterotetrameric cis-prenyltransferase complex ]]> https://biorxiv.org/content/10.1101/2020.06.02.095570v1?rss=1 Lisnyansky Bar-El, M. Vankova, P. Man, P. Haitin, Y. Giladi, M. 2020-06-02 doi:10.1101/2020.06.02.095570 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ The Impact of Restriction-Modification Systems on Mating in Haloferax volcanii ]]> https://biorxiv.org/content/10.1101/2020.06.06.138198v1?rss=1 Ouellette, M. Makkay, A. M. Louyakis, A. S. Gophna, U. Gogarten, J. P. Papke, R. T. 2020-06-08 doi:10.1101/2020.06.06.138198 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ Spectrum of genes for inherited hearing loss in the Israeli Jewish population, including the novel human deafness gene ATOH1 ]]> https://biorxiv.org/content/10.1101/2020.06.11.144790v1?rss=1 Brownstein, Z. Gulsuner, S. Walsh, T. Martins, F. T. A. Taiber, S. Isakov, O. Lee, M. Bordeynik-Cohen, M. Birkan, M. Chang, W. Casadei, S. Danial-Farran, N. Abu Rayyan, A. Carlson, R. Kamal, L. Arnporsson, A. O. Sokolov, M. Gilony, D. Lipschitz, N. Frydman, M. Davidov, B. Macarov, M. Sagi, M. Vinkler, C. Poran, H. Sharony, R. Samara, N. Zvi, N. Baris-Feldman, H. Singer, A. Handzel, O. Hertzano, R. Ali-Naffaa, D. Ruhrman-Shahar, N. Madgar, O. Sofrin, E. Peleg, A. Khayat, M. Shohat, M. Basel-Salmon, L. Pras, E. Lev, D. Wolf, M. Steingrimsson, E. Shomro 2020-06-12 doi:10.1101/2020.06.11.144790 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Collective motion as a distinct behavioral state of the individual ]]> https://biorxiv.org/content/10.1101/2020.06.15.152454v1?rss=1 Knebel, D. Sha-ked, C. Agmon, N. Ariel, G. Ayali, A. 2020-06-15 doi:10.1101/2020.06.15.152454 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Are we ready to track climate-driven shifts in marine species across international boundaries? - A global survey of scientific bottom trawl data ]]> https://biorxiv.org/content/10.1101/2020.06.18.125930v1?rss=1 Maureaud, A. A. Frelat, R. Pecuchet, L. Shackell, N. Merigot, B. Pinsky, M. L. Amador, K. Anderson, S. C. Arkhipkin, A. Auber, A. Barri, I. Bell, R. Belmaker, J. Beukhof, E. Camara, M. L. Guevara-Carrasco, R. Choi, J. Christensen, H. T. Conner, J. Cubillos, L. A. Diadhiou, H. D. Edelist, D. Emblemsvag, M. Ernst, B. Fairweather, T. P. Fock, H. O. Friedland, K. D. Garcia, C. B. Gascuel, D. Gislason, H. Goren, M. Guitton, J. Jouffre, D. Hattab, T. Hidalgo, M. Kathena, J. N. Knuckey, I. Kide, S. O. Koen-Alonso, M. Koopman, M. Kulik, V. Leon, J. P. Levitt-B 2020-06-20 doi:10.1101/2020.06.18.125930 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Selective vulnerability of aneuploid human cancer cells to inhibition of the spindle assembly checkpoint ]]> https://biorxiv.org/content/10.1101/2020.06.18.159038v1?rss=1 Cohen-Sharir, Y. McFarland, J. M. Abdusamad, M. Marquis, C. Tang, H. Ippolito, M. R. Bernhard, S. V. Laue, K. Malaby, H. L. Jones, A. Kazachkova, M. Lyons, N. Nagaraja, A. Bass, A. J. Beroukhim, R. Santaguida, S. Stumpff, J. Golub, T. R. Storchova, Z. Ben-David, U. 2020-06-19 doi:10.1101/2020.06.18.159038 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Show me your Dufour's gland and I'll tell you who you are: caste and physiology specific signals in Bombus impatiens ]]> https://biorxiv.org/content/10.1101/2020.06.20.163089v1?rss=1 Derstine, N. T. Villar, G. Hefetz, A. Millar, J. Amsalem, E. 2020-06-20 doi:10.1101/2020.06.20.163089 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ The Botrytis cinerea Crh transglycosylae is a cytoplasmic effector triggering plant cell death and defense response ]]> https://biorxiv.org/content/10.1101/2020.06.23.166843v1?rss=1 Bi, K. Scalschi, L. Jaiswal, G. N. Fried, R. Zhu, W. Masrati, G. Mengiste, T. Sharon, A. 2020-06-23 doi:10.1101/2020.06.23.166843 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ Variability of dynamic patterns of cortical excitability in schizophrenia: A test-retest TMS-EEG study ]]> https://biorxiv.org/content/10.1101/2020.06.24.170019v1?rss=1 Naim-Feil, J. Peled, A. Freche, D. Hess, S. Grinshpoon, A. Levit-Binnun, N. Moses, E. 2020-06-25 doi:10.1101/2020.06.24.170019 Cold Spring Harbor Laboratory Press 2020-06-25 <![CDATA[ Aneuploid cells activate NF-κB to promote their immune clearance by NK cells ]]> https://biorxiv.org/content/10.1101/2020.06.25.172239v1?rss=1 Wang, R. W. Vigano', S. Ben-David, U. Amon, A. Santaguida, S. 2020-06-27 doi:10.1101/2020.06.25.172239 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Homozygote loss-of-function variants in the human COCH gene underlie hearing loss ]]> https://biorxiv.org/content/10.1101/2020.06.29.178053v1?rss=1 Danial-Faran, N. Chervinsky, E. Nadar-Ponniah, P. T. Cohen Barak, E. Taiber, S. Khayat, M. Avraham, K. B. Shalev, S. A. 2020-06-30 doi:10.1101/2020.06.29.178053 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ Spatial cueing effects do not always index attentional capture: Evidence for a Priority Accumulation Framework ]]> https://biorxiv.org/content/10.1101/2020.07.01.181826v1?rss=1 Darnell, M. Lamy, D. 2020-07-02 doi:10.1101/2020.07.01.181826 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ More than just a ticket canceller: The mitochondrial processing peptidase matures complex precursor proteins at internal cleavage sites ]]> https://biorxiv.org/content/10.1101/2020.07.02.183996v1?rss=1 Friedl, J. Knopp, M. R. Groh, C. Paz, E. Gould, S. B. Boos, F. Herrmann, J. M. 2020-07-03 doi:10.1101/2020.07.02.183996 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ Deviation from baseline mutation burden provides powerful and robust rare-variants association test for complex diseases ]]> https://biorxiv.org/content/10.1101/2020.07.04.186619v1?rss=1 Jiang, L. Jiang, H. Dai, S. Chen, Y. Song, Y.-Q. Tang, C. Wang, B. Garcia-Barcelo, M.-M. Tam, P. Cherny, S. Sham, P. C. Li, M. 2020-07-04 doi:10.1101/2020.07.04.186619 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Sick Bats Stay Home Alone: Social distancing during the acute phase response in Egyptian fruit bats (Rousettus aegyptiacus) ]]> https://biorxiv.org/content/10.1101/2020.07.06.189357v1?rss=1 Moreno, K. R. Weinberg, M. Harten, L. Salinas Ramos, V. B. Herrera M., L. G. Czirjak, G. A. Yovel, Y. 2020-07-06 doi:10.1101/2020.07.06.189357 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model Archaeon ]]> https://biorxiv.org/content/10.1101/2020.07.06.189845v1?rss=1 Makkay, A. M. Louyakis, A. S. Ram-Mohan, N. Gophna, U. Gogarten, J. P. Papke, R. T. 2020-07-06 doi:10.1101/2020.07.06.189845 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ ATP-Citrate lyase fuels axonal transport across species ]]> https://biorxiv.org/content/10.1101/2020.07.07.192096v1?rss=1 Nguyen, L. Even, A. Morelli, G. Le Bail, R. Shilian, M. Turchetto, S. Broix, L. Brandis, A. Inbar, S. Chariot, A. Saudou, F. Dietrich, P. Dragatsis, I. Brone, B. Rigo, J.-M. Weil, M. 2020-07-07 doi:10.1101/2020.07.07.192096 Cold Spring Harbor Laboratory Press 2020-07-07 <![CDATA[ Species coexistence and overlapping distributions in a metacommunity are compatible with niche differences and competition at a local scale ]]> https://biorxiv.org/content/10.1101/2020.07.10.196758v1?rss=1 Maxime Dubart Patrice David Frida Ben-Ami Christoph R. Haag Ilmari Pajunen Dieter Ebert 2020-07-10 doi:10.1101/2020.07.10.196758 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Identification and characterization of key long non-coding RNAs in the auditory system ]]> https://biorxiv.org/content/10.1101/2020.07.10.197251v1?rss=1 Tal Koffler-Brill Shahar Taiber Alejandro Anaya Mor Bordeynik-Cohen Einat Rosen Likhitha Kolla Naama Messika-Gold Ran Elkon Matthew W. Kelley Igor Ulitsky Karen B. Avraham 2020-07-12 doi:10.1101/2020.07.10.197251 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ Enhancers with cooperative Notch binding sites are more resistant to regulation by the Hairless co-repressor ]]> https://biorxiv.org/content/10.1101/2020.07.12.199422v1?rss=1 Yi Kuang Anna Pyo Natanel Eafergan Brittany Cain Lisa M. Gutzwiller Ofri Axelrod Ellen K. Gagliani Matthew T Weirauch Raphael Kopan Rhett Kovall David Sprinzak Brian Gebelein 2020-07-12 doi:10.1101/2020.07.12.199422 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ On the Emergence of P-Loop NTPase and Rossmann Enzymes from a Beta-Alpha-Beta Ancestral Fragment ]]> https://biorxiv.org/content/10.1101/2020.07.15.204123v1?rss=1 Longo, L. M. Jablonska, J. Vyas, P. Kolodny, R. Ben-Tal, N. Tawfik, D. S. 2020-07-15 doi:10.1101/2020.07.15.204123 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ Dynamic spatiotemporal coordination of neural stem cell fate decisions through local feedback in the adult vertebrate brain ]]> https://biorxiv.org/content/10.1101/2020.07.15.205021v1?rss=1 Dray, N. Mancini, L. Binshtok, U. Cheysson, F. Supatto, W. Mahou, P. Bedu, S. Ortica, S. Krecsmarik, M. Herbert, S. Masson, J.-B. Tinevez, J.-Y. Lang, G. Beaurepaire, E. Sprinzak, D. Bally-Cuif, L. 2020-07-16 doi:10.1101/2020.07.15.205021 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ Modelling cortical laminar connectivity in the macaque brain ]]> https://biorxiv.org/content/10.1101/2020.07.19.210526v1?rss=1 Shamir, I. Assaf, Y. 2020-07-19 doi:10.1101/2020.07.19.210526 Cold Spring Harbor Laboratory Press 2020-07-19 <![CDATA[ Prokaryotic rRNA-mRNA interactions are involved in all translation steps and shape bacterial transcripts ]]> https://biorxiv.org/content/10.1101/2020.07.24.220731v1?rss=1 Bahiri Elitzur, S. Cohen-Kupiec, R. Yacobi, D. Fine, L. Apt, B. Diament, A. Tuller, T. 2020-07-25 doi:10.1101/2020.07.24.220731 Cold Spring Harbor Laboratory Press 2020-07-25 <![CDATA[ Establishing live-cell single-molecule localization microscopy imaging and single-particle tracking in the archaeon Haloferax volcanii ]]> https://biorxiv.org/content/10.1101/2020.07.27.222935v1?rss=1 Turkowyd, B. Schreiber, S. Wörtz, J. Shtifman Segal, E. Mevarech, M. Duggin, I. G. Marchfelder, A. Endesfelder, U. 2020-07-27 doi:10.1101/2020.07.27.222935 Cold Spring Harbor Laboratory Press 2020-07-27 <![CDATA[ Quantifying the dynamics of long-range cell-cell mechanical communication ]]> https://biorxiv.org/content/10.1101/2020.07.30.223149v1?rss=1 Nahum, A. Koren, Y. Natan, S. Goren, S. Lesman, A. Zaritsky, A. 2020-07-30 doi:10.1101/2020.07.30.223149 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ Early birds, late owls, and the ecological role of intra-population chronotype variation ]]> https://biorxiv.org/content/10.1101/2020.08.09.243261v1?rss=1 Royzrakh-Pasternak, E. Dayan, T. Levy, O. Kronfeld-Schor, N. 2020-08-10 doi:10.1101/2020.08.09.243261 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Characterization of a new Leishmania major isolate for use in a controlled human infection model ]]> https://biorxiv.org/content/10.1101/2020.08.12.245936v1?rss=1 Ashwin, H. Sadlova, J. Vojtkova, B. Becvar, T. Lypaczewski, P. Schwartz, E. Greensted, E. Van Bocxlaer, K. Pasin, M. Lipinski, K. Parkash, V. Matlashewski, G. Layton, A. Lacey, C. Jaffe, C. Volf, P. Kaye, P. 2020-08-12 doi:10.1101/2020.08.12.245936 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ A Sub-Minute Resolution Prediction of Brain Temperature Based on Sleep-Wake State in the Mouse ]]> https://biorxiv.org/content/10.1101/2020.08.12.246405v1?rss=1 Sela, Y. Hoekstra, M. M. B. Franken, P. 2020-08-12 doi:10.1101/2020.08.12.246405 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ The Mehler reaction site is the Phylloquinone within Photosystem I ]]> https://biorxiv.org/content/10.1101/2020.08.13.249367v1?rss=1 Kozuleva, M. Petrova, A. Milrad, Y. Semenov, A. Ivanov, B. Redding, K. E. Yacoby, I. 2020-08-14 doi:10.1101/2020.08.13.249367 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ A power amplification dyad in seahorses ]]> https://biorxiv.org/content/10.1101/2020.08.13.249466v1?rss=1 Avidan, C. Day, S. W. Holzman, R. 2020-08-14 doi:10.1101/2020.08.13.249466 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ A lesson from COVID-19 on inaccessibility of web-based information for disabled populations worldwide ]]> https://biorxiv.org/content/10.1101/2020.08.16.252676v1?rss=1 Dror, A. A. Layous, E. Mizrachi, M. Daoud, A. Eisenbach, N. Morozov, N. G. Srouji, S. Avraham, K. B. Sela, E. 2020-08-17 doi:10.1101/2020.08.16.252676 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Value Certainty in Diffusion Decision Models ]]> https://biorxiv.org/content/10.1101/2020.08.22.262725v1?rss=1 Lee, D. Usher, M. 2020-08-24 doi:10.1101/2020.08.22.262725 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Estimating encounter location distributions from animal tracking data ]]> https://biorxiv.org/content/10.1101/2020.08.24.261628v1?rss=1 Noonan, M. J. Martinez-Garcia, R. Davis, G. H. Crofoot, M. C. Kays, R. Hirsch, B. T. Payne, E. Sih, A. Sinn, D. L. Spiegel, O. Fagan, W. F. Fleming, C. H. Calabrese, J. 2020-08-25 doi:10.1101/2020.08.24.261628 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Transcutaneous vagus nerve stimulation in humans induces pupil dilation and attenuates alpha oscillations ]]> https://biorxiv.org/content/10.1101/2020.08.25.265876v1?rss=1 Sharon, O. Fahoum, F. Nir, Y. 2020-08-25 doi:10.1101/2020.08.25.265876 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Growth-laws and invariants from ribosome biogenesis in lower Eukarya ]]> https://biorxiv.org/content/10.1101/2020.08.26.268680v1?rss=1 Kostinski, S. Reuveni, S. 2020-08-27 doi:10.1101/2020.08.26.268680 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Brain volumetric changes in the general population following the COVID-19 outbreak and lockdown ]]> https://biorxiv.org/content/10.1101/2020.09.08.285007v1?rss=1 Salomon, T. Cohem, A. Ben-Zvi, G. Gera, R. Oren, S. Roll, D. Rozic, G. Saliy, A. Tik, N. Tsarfati, G. Tavor, I. Schonberg, T. Assaf, Y. 2020-09-09 doi:10.1101/2020.09.08.285007 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Transient cell-in-cell formation underlies tumor resistance to immunotherapy ]]> https://biorxiv.org/content/10.1101/2020.09.10.287441v1?rss=1 Gutwillig, A. Santana-Magal, N. Farhat-Younis, L. Rasoulouniriana, D. Madi, A. Luxenburg, C. Cohen, J. Padmanabhan, K. Shomron, N. Shapira, G. Feinmesser, M. Zlotnik, O. Debets, R. Reticker-Flynn, N. E. Rider, P. Carmi, Y. 2020-09-10 doi:10.1101/2020.09.10.287441 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Conserved interactions required for in vitro inhibition of the main protease of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ]]> https://biorxiv.org/content/10.1101/2020.09.10.288720v1?rss=1 Shitrit, A. Zaidman, D. Kalid, O. Bloch, I. Doron, D. Yarnizky, T. Buch, I. Segev, I. Ben-Zeev, E. Segev, E. Kobiler, O. 2020-09-10 doi:10.1101/2020.09.10.288720 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ A chemiluminescent protease probe for rapid, sensitive, and inexpensive detection of live Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2020.09.14.296772v1?rss=1 Babin, B. M. Fernandez-Cuervo, G. Sheng, J. Green, O. Ordonez, A. A. Turner, M. L. Keller, L. J. Jain, S. K. Shabat, D. Bogyo, M. 2020-09-14 doi:10.1101/2020.09.14.296772 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ The maternal foam plug constitutes a reservoir for the desert locust's bacterial symbionts ]]> https://biorxiv.org/content/10.1101/2020.09.15.296319v1?rss=1 Lavy, O. Gophna, U. Ayali, A. Gihaz, S. Fishman, A. Gefen, E. 2020-09-15 doi:10.1101/2020.09.15.296319 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ Disruption of Glial Ca2+ Oscillations at the Drosophila Blood-Brain Barrier Predisposes to Seizure-Like Behavior ]]> https://biorxiv.org/content/10.1101/2020.09.16.285841v1?rss=1 Weiss, S. Clamon, L. C. Manoim, J. E. Ormerod, K. G. Parnas, M. Littleton, J. T. 2020-09-16 doi:10.1101/2020.09.16.285841 Cold Spring Harbor Laboratory Press 2020-09-16 <![CDATA[ Microbiome-related aspects of locust density-dependent phase transition ]]> https://biorxiv.org/content/10.1101/2020.09.17.301010v1?rss=1 Lavy, O. Lewin-Epstein, O. Bendett, Y. Gophna, U. Gefen, E. Hadany, L. Ayali, A. 2020-09-17 doi:10.1101/2020.09.17.301010 Cold Spring Harbor Laboratory Press 2020-09-17 <![CDATA[ Within-host competition modulates pneumococcal antibiotic resistance in the pre-vaccination era ]]> https://biorxiv.org/content/10.1101/2020.09.24.311340v1?rss=1 Lourenco, J. Daon, Y. Gori, A. Obolski, U. 2020-09-25 doi:10.1101/2020.09.24.311340 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Aneuploidy-driven genome instability triggers resistance to chemotherapy ]]> https://biorxiv.org/content/10.1101/2020.09.25.313924v1?rss=1 Ippolito, M. R. Martis, V. Hong, C. Wardenaar, R. Zerbib, J. Spierings, D. C. J. Ben-David, U. Foijer, F. Santaguida, S. 2020-09-26 doi:10.1101/2020.09.25.313924 Cold Spring Harbor Laboratory Press 2020-09-26 <![CDATA[ The value of the whole or the sum of the parts: The role of ventromedial prefrontal cortex in multi-attribute object evaluation ]]> https://biorxiv.org/content/10.1101/2020.09.29.319293v1?rss=1 Pelletier, G. Aridan, N. Fellows, L. K. Schonberg, T. 2020-10-01 doi:10.1101/2020.09.29.319293 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Harnessing machine learning to unravel protein degradation in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2020.10.04.325795v1?rss=1 Pupko, T. Nagar, N. Ecker, N. Loewenthal, G. Avram, O. Ben-Meir, D. Biran, D. Ron, E. 2020-10-05 doi:10.1101/2020.10.04.325795 Cold Spring Harbor Laboratory Press 2020-10-05 <![CDATA[ Model Adequacy Tests for Likelihood Models of Chromosome-Number Evolution ]]> https://biorxiv.org/content/10.1101/2020.10.05.326231v1?rss=1 Rice, A. Mayrose, I. 2020-10-07 doi:10.1101/2020.10.05.326231 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ Multi-Clonal Live SARS-CoV-2 In Vitro Neutralization by Antibodies Isolated from Severe COVID-19 Convalescent Donors ]]> https://biorxiv.org/content/10.1101/2020.10.06.323634v1?rss=1 Mor, M. Werbner, M. Alter, J. Safra, M. Chomsky, E. Hada-Neeman, S. Polonsky, K. Nowell, C. Clark, A. Roitburd-Berman, A. Ben-Shalom, N. Navon, M. Rafael, D. Sharim, H. Kiner, E. Griffis, E. Gershoni, J. M. Kobiler, O. Leibel, S. L. Zimhony, O. Carlin, A. F. Yaari, G. Dassau, M. Gal-Tanamy, M. Hagin, D. Croker, B. A. Freund, N. 2020-10-06 doi:10.1101/2020.10.06.323634 Cold Spring Harbor Laboratory Press 2020-10-06 <![CDATA[ Bi-directional electron transfer between H2 and NADPH mitigates the response to light fluctuations in green algae ]]> https://biorxiv.org/content/10.1101/2020.10.08.331504v1?rss=1 Milrad, Y. Schweitzer, S. Feldman, Y. Yacoby, I. 2020-10-08 doi:10.1101/2020.10.08.331504 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ A mobile genetic element increases bacterial host fitness by manipulating development ]]> https://biorxiv.org/content/10.1101/2020.10.09.328104v1?rss=1 Jones, J. M. Grinberg, I. Eldar, A. Grossman, A. D. 2020-10-09 doi:10.1101/2020.10.09.328104 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Evidence integration and decision-confidence are modulated by stimulus consistency ]]> https://biorxiv.org/content/10.1101/2020.10.12.335943v1?rss=1 Glickman, M. Moran, R. Usher, M. 2020-10-12 doi:10.1101/2020.10.12.335943 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ Multi-Modal Single-Molecule Imaging with Continuously Controlled Spectral-resolution (CoCoS) Microscopy ]]> https://biorxiv.org/content/10.1101/2020.10.13.330910v1?rss=1 Jeffet, J. Michaeli-Hoch, Y. Torchinsky, D. Israel-Elgali, I. Shomron, N. Craggs, T. D. Ebenstein, Y. 2020-10-13 doi:10.1101/2020.10.13.330910 Cold Spring Harbor Laboratory Press 2020-10-13 <![CDATA[ Design of SARS-CoV-2 RBD mRNA Vaccine Using Novel Ionizable Lipids ]]> https://biorxiv.org/content/10.1101/2020.10.15.341537v1?rss=1 Elia, U. Srinivas, R. Dammes, N. Bar-Haim, E. Naidu, G. S. Makdasi, E. Cohen, O. Peer, D. 2020-10-15 doi:10.1101/2020.10.15.341537 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Mutation-specific pathophysiological mechanisms define different neurodevelopmental disorders associated with SATB1 dysfunction ]]> https://biorxiv.org/content/10.1101/2020.10.23.352278v1?rss=1 den Hoed, J. Boer, E. d. Voisin, N. Dingemans, A. Guex, N. Wiel, L. Nellaker, C. Amudhavalli, S. Banka, S. Bena, F. Ben-Zeev, B. Bonagura, V. Bruel, A.-L. Brunet, T. Brunner, H. Chew, H. Chrast, J. Cimbalistien, L. Coon, H. Study, T. D. Delot, E. Demurger, F. Denomme-Pichon, A.-S. Depienne, C. Donnai, D. Dyment, D. Elpeleg, O. Faivre, L. Gilissen, C. Granger, L. Haber, B. Hachiya, Y. Hamzavi Abedi, Y. Hanebeck, J. Hehir-Kwa, J. Horist, B. Itai, T. Jackson, A. Jewell, R. Jones, K. Joss, S. Kashii, H. Kato, M. Kattentidt-Mouravieva, A. Kok, F. Kotzaer 2020-10-24 doi:10.1101/2020.10.23.352278 Cold Spring Harbor Laboratory Press 2020-10-24 <![CDATA[ Multi-Scale Modeling of Intensive Macroalgae Cultivation and Marine Nitrogen Sequestration ]]> https://biorxiv.org/content/10.1101/2020.10.25.338798v1?rss=1 Zollmann, M. Rubinsky, B. Liberzon, A. Golberg, A. 2020-10-25 doi:10.1101/2020.10.25.338798 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ Lamin regulates the dietary restriction response via the mTOR pathway in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2020.10.27.357913v1?rss=1 Charar, C. Metsuyanim-Cohen, S. Gruenbaum, Y. Bar, D. Z. 2020-10-27 doi:10.1101/2020.10.27.357913 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells ]]> https://biorxiv.org/content/10.1101/2020.10.30.362947v1?rss=1 Sumida, T. S. Dulberg, S. Schupp, J. Stillwell, H. A. Axisa, P.-P. Comi, M. Lincoln, M. Unterman, A. Kaminski, N. Madi, A. Kuchroo, V. K. Hafler, D. A. 2020-10-31 doi:10.1101/2020.10.30.362947 Cold Spring Harbor Laboratory Press 2020-10-31 <![CDATA[ Cytokinin inhibits fungal development and virulence by targeting cellular trafficking ]]> https://biorxiv.org/content/10.1101/2020.11.04.369215v1?rss=1 Gupta, R. Pizarro, L. Anand, G. Laor, D. Kovetz, N. Yehuda, T. Gazit, E. Bar, M. 2020-11-05 doi:10.1101/2020.11.04.369215 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Testing the masculinization hypothesis in a sample of 23,935 human brains ]]> https://biorxiv.org/content/10.1101/2020.11.09.373258v1?rss=1 Alon, N. Meilijson, I. Joel, D. 2020-11-10 doi:10.1101/2020.11.09.373258 Cold Spring Harbor Laboratory Press 2020-11-10 <![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[ A probabilistic model for indel evolution: differentiating insertions from deletions ]]> https://biorxiv.org/content/10.1101/2020.11.22.393108v1?rss=1 Loewenthal, G. Rapoport, D. Avram, O. Moshe, A. Itzkovitch, A. Israeli, O. Azouri, D. Cartwright, R. A. Mayrose, I. Pupko, T. 2020-11-22 doi:10.1101/2020.11.22.393108 Cold Spring Harbor Laboratory Press 2020-11-22 <![CDATA[ Two Parallel Pathways Mediate Olfactory-Driven Backward Locomotion ]]> https://biorxiv.org/content/10.1101/2020.11.23.393819v1?rss=1 Israel, S. Rozenfeld, E. Weber, D. Huetteroth, W. Parnas, M. 2020-11-23 doi:10.1101/2020.11.23.393819 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ Reconstitution of β-adrenergic regulation of CaV1.2: Rad-dependent and Rad-independent protein kinase A mechanisms. ]]> https://biorxiv.org/content/10.1101/2020.11.30.403964v1?rss=1 2-fold increase in CaV1.2 current, a hyperpolarizing shift in activation curve, and a high constitutive activity of {beta}2-AR. ConclusionsThe adrenergic modulation of CaV1.2 is composed of two distinct pathways, Rad-independent and Rad-dependent. The latter contributes most of the {beta}-AR-induced enhancement of CaV1.2 activity, crucially depends on CaV{beta} subunit, and is differently regulated by {beta}1-AR and {beta}2-AR. The reconstitution of the full {beta}-AR cascade provides the means to address central unresolved issues related to roles of auxiliary proteins in the cascade, CaV1.2 isoforms, and will help to develop therapies for catecholamine-induced cardiac pathologies. ]]> Katz, M. Subramaniam, S. Chomsky-Hecht, O. Tsemakhovich, V. Belkacemi, A. Flockerzi, V. Klussmann, E. Hirsch, J. Weiss, S. Dascal, N. 2020-12-01 doi:10.1101/2020.11.30.403964 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Leukodystrophy resembling Vanishing White Matter Disease is recapitulated by brain-specific depletion of apoptosis regulator MCL-1 ]]> https://biorxiv.org/content/10.1101/2020.12.02.408138v1?rss=1 Cleveland, A. H. Romero, A. Alfonso Azcona, L. Herrero, M. Elroy-Stein, O. Gama, V. Gershon, T. R. 2020-12-03 doi:10.1101/2020.12.02.408138 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Light-harvesting in mesophotic corals is powered by a spatially efficient photosymbiotic system between coral host and microalgae ]]> https://biorxiv.org/content/10.1101/2020.12.04.411496v1?rss=1 Kramer, N. Tamir, R. Ben-Zvi, O. Jacques, S. L. Loya, Y. Wangpraseurt, D. 2020-12-06 doi:10.1101/2020.12.04.411496 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Marine Bacteria Associated with the Green Seaweed Ulva sp. for the Production of Polyhydroxyalkanoates ]]> https://biorxiv.org/content/10.1101/2020.12.05.413369v1?rss=1 Gnaim, R. Polikovsky, M. Unis, R. Sheviryov, J. Gozin, M. Golberg, A. 2020-12-06 doi:10.1101/2020.12.05.413369 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Overt visual attention and value computation in complex risky choice ]]> https://biorxiv.org/content/10.1101/2020.12.08.416313v1?rss=1 Fan, X. Elsey, J. Wyngaard, A. Yang, Y.-P. Sampson, A. Emeric, E. E. Glickman, M. Usher, M. Levy, D. Stuphorn, V. Niebur, E. 2020-12-09 doi:10.1101/2020.12.08.416313 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Global Age-Specific Patterns of Cyclic Gene Expression Revealed by Tunicate Transcriptome Atlas ]]> https://biorxiv.org/content/10.1101/2020.12.08.417055v1?rss=1 Voskoboynik, Y. Glina, A. Kowarsky, M. Anselmi, C. Neff, N. F. Ishizuka, K. J. Palmeri, K. J. Rosental, B. Gordon, T. Quake, S. R. Weissman, I. L. Ben-Shlomo, R. Sahoo, D. Voskoboynik, A. 2020-12-09 doi:10.1101/2020.12.08.417055 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Oblique Transmission, Conformity, and Preference in the Evolution of Altruism ]]> https://biorxiv.org/content/10.1101/2020.12.10.420513v1?rss=1 Denton, K. K. Ram, Y. Feldman, M. W. 2020-12-11 doi:10.1101/2020.12.10.420513 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Distributional changes in myelin-specific MRI markers uncover dynamics in the fornix following spatial navigation training ]]> https://biorxiv.org/content/10.1101/2020.12.13.422557v1?rss=1 Anaby, D. Tendler, B. C. Treder, M. S. Hametner, S. Koeck, U. Tax, C. M. W. Parker, G. D. Barazany, D. Assaf, Y. Jones, D. K. 2020-12-13 doi:10.1101/2020.12.13.422557 Cold Spring Harbor Laboratory Press 2020-12-13 <![CDATA[ A Guide to Pre-Processing High-Throughput Animal Tracking Data ]]> https://biorxiv.org/content/10.1101/2020.12.15.422876v1?rss=1 Gupte, P. R. Beardsworth, C. E. Spiegel, O. Lourie, E. Toledo, S. Nathan, R. Bijleveld, A. I. 2020-12-16 doi:10.1101/2020.12.15.422876 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ Effect of Deletion of the Ribonucleotide Reductase Gene in Wild Type and Virion Associated Host Shutoff (vhs-1) Mutant Herpes Simplex Virus-1 on Viral Proliferation and Infected-Carcinoma Cell Cultures Growth ]]> https://biorxiv.org/content/10.1101/2020.12.18.423438v1?rss=1 Schlesinger, P. Frenkel, N. 2020-12-19 doi:10.1101/2020.12.18.423438 Cold Spring Harbor Laboratory Press 2020-12-19 <![CDATA[ Bridging themes: short protein segments found in different architectures ]]> https://biorxiv.org/content/10.1101/2020.12.22.424031v1?rss=1 Kolodny, R. Nepomnyachiy, S. Tawfik, D. S. Ben-Tal, N. 2020-12-22 doi:10.1101/2020.12.22.424031 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Narratives: fMRI data for evaluating models of naturalistic language comprehension ]]> https://biorxiv.org/content/10.1101/2020.12.23.424091v1?rss=1 Nastase, S. A. Liu, Y.-F. Hillman, H. Zadbood, A. Hasenfratz, L. Keshavarzian, N. Chen, J. Honey, C. J. Yeshurun, Y. Regev, M. Nguyen, M. Chang, C. H. C. Baldassano, C. Lositsky, O. Simony, E. Chow, M. A. Leong, Y. C. Brooks, P. P. Micciche, E. Choe, G. Goldstein, A. Vanderwal, T. Halchenko, Y. O. Norman, K. A. Hasson, U. 2020-12-23 doi:10.1101/2020.12.23.424091 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ STORM-Net: Simple and Timely Optode Registration Method for Functional Near-Infrared Spectroscopy (fNIRS) ]]> https://biorxiv.org/content/10.1101/2020.12.29.424683v1?rss=1 Erel, Y. Jaffe-Dax, S. Yeshurun, Y. Bermano, A. 2020-12-29 doi:10.1101/2020.12.29.424683 Cold Spring Harbor Laboratory Press 2020-12-29 <![CDATA[ Microtubule-associated ROP interactors both delimit and transduce ROP signaling and regulate microtubule dynamics ]]> https://biorxiv.org/content/10.1101/2021.01.08.425872v1?rss=1 Feiguelman, G. Cui, X. Sternberg, H. Fu, Y. Yalovsky, S. 2021-01-08 doi:10.1101/2021.01.08.425872 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Simultaneous association of grip effort with snack food items does not change preferences ]]> https://biorxiv.org/content/10.1101/2021.01.10.426077v1?rss=1 Aridan, N. Schonberg, T. 2021-01-10 doi:10.1101/2021.01.10.426077 Cold Spring Harbor Laboratory Press 2021-01-10 <![CDATA[ ApoE4 attenuates cortical neuronal activity and impairs memory in young apoE4 rats ]]> https://biorxiv.org/content/10.1101/2021.01.14.426651v1?rss=1 Har-Paz, I. Arieli, E. Moran, A. 2021-01-14 doi:10.1101/2021.01.14.426651 Cold Spring Harbor Laboratory Press 2021-01-14 <![CDATA[ DNA-based copy number analysis confirms genomic evolution of PDX models ]]> https://biorxiv.org/content/10.1101/2021.01.15.426865v1?rss=1 Hoge, A. Getz, M. Beroukhim, R. Golub, T. Ha, G. Ben-David, U. 2021-01-17 doi:10.1101/2021.01.15.426865 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Induced neural differentiation of human mesenchymal stem cells affects lipid metabolism pathways ]]> https://biorxiv.org/content/10.1101/2021.01.17.427010v1?rss=1 Green, P. Kan, I. Mesilati-Stahy, R. Argov-Argamann, N. Offen, D. 2021-01-18 doi:10.1101/2021.01.17.427010 Cold Spring Harbor Laboratory Press 2021-01-18 <![CDATA[ An elongated COI fragment to discriminate botryllid species and as an improved ascidian DNA barcode ]]> https://biorxiv.org/content/10.1101/2021.01.20.427448v1?rss=1 Salonna, M. Gasparini, F. Huchon, D. Montesanto, F. Haddas-Sasson, M. Ekins, M. McNamara, M. Mastrototaro, F. Gissi, C. 2021-01-21 doi:10.1101/2021.01.20.427448 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ The fitness costs and benefits of trisomy of each Candida albicanschromosome ]]> https://biorxiv.org/content/10.1101/2021.01.21.427689v1?rss=1 Yang, F. Jiang, Y. Cao, Y. Berman, J. 2021-01-22 doi:10.1101/2021.01.21.427689 Cold Spring Harbor Laboratory Press 2021-01-22 <![CDATA[ Long Reads Capture Simultaneous Enhancer-Promoter Methylation Status for Cell-type Deconvolution ]]> https://biorxiv.org/content/10.1101/2021.01.28.428654v1?rss=1 Margalit, S. Abramson, Y. Sharim, H. Manber, Z. Bhattacharya, S. Chen, Y. W. Vilain, E. Barseghyan, H. Elkon, R. Sharan, R. Ebenstein, Y. 2021-01-29 doi:10.1101/2021.01.28.428654 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ Evolution of the bread wheat D-subgenome and enriching it with diversity from Aegilops tauschii ]]> https://biorxiv.org/content/10.1101/2021.01.31.428788v1?rss=1 Gaurav, K. Arora, S. Silva, P. Sanchez-Martin, J. Horsnell, R. Gao, L. Brar, G. S. Widrig, V. Raupp, J. Singh, N. Wu, S. Kale, S. M. Chinoy, C. Nicholson, P. Quiroz-Chavez, J. Simmonds, J. Hayta, S. Smedley, M. A. Harwood, W. Pearce, S. Gilbert, D. Kangara, N. Gardener, C. Forner-Martinez, M. Liu, J. Yu, G. Boden, S. Pascuccci, A. Ghosh, S. Hafeez, A. N. O'Hara, T. Waites, J. Cheema, J. Steuernagel, B. Patpour, M. Justesen, A. F. Liu, S. Rudd, J. Avni, R. Sharon, A. Steiner, B. Kirana, R. P. Buerstmayr, H. Mehrabi, A. A. Nasyrova, F. Y. Chayut, N. 2021-02-01 doi:10.1101/2021.01.31.428788 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Therapeutic antibodies, targeting the SARS-CoV-2 spike N-terminal domain, protect lethally infected K18-hACE2 mice ]]> https://biorxiv.org/content/10.1101/2021.02.02.428995v1?rss=1 Noy-Porat, T. Mechaly, A. Levy, Y. Makdasi, E. Alcalay, R. Gur, D. Aftalion, M. Falach, R. Leviatan Ben-Arye, S. Lazar, S. Zauberman, A. Epstein, E. Chitlaru, T. Weiss, S. Achdout, H. Edgeworth, J. D. Kikkeri, R. Yu, H. Chen, X. Yitzhaki, S. Shapira, S. C. Padler-Karavani, V. Mazor, O. Rosenfeld, R. 2021-02-02 doi:10.1101/2021.02.02.428995 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Structure of plant PSI-plastocyanin complex reveals strong hydrophobic interactions. ]]> https://biorxiv.org/content/10.1101/2021.02.03.429574v1?rss=1 Caspy, I. Fadeeva, M. Kuhlgert, S. Borovikova-Sheinker, A. Klaiman, D. Masrati, G. Drepper, F. Ben-Tal, N. Hippler, M. Nelson, N. 2021-02-03 doi:10.1101/2021.02.03.429574 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Expanding the MECP2 network using comparative genomics reveals potential therapeutic targets for Rett syndrome ]]> https://biorxiv.org/content/10.1101/2021.02.14.431162v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@1d7e0f8org.highwire.dtl.DTLVardef@1f2c602org.highwire.dtl.DTLVardef@1a5dd7dorg.highwire.dtl.DTLVardef@7071c8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Unterman, I. Bloch, I. Cazacu, S. Kazimirsky, G. Berman, B. P. Ben-Zeev, B. Brodie, C. Tabach, Y. 2021-02-15 doi:10.1101/2021.02.14.431162 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ Calling differential DNA methylation at cell-type resolution: addressing misconceptions and best practices ]]> https://biorxiv.org/content/10.1101/2021.02.14.431168v1?rss=1 Rahmani, E. Jew, B. Schweiger, R. Rhead, B. Criswell, L. A. Barcellos, L. F. Eskin, E. Rosset, S. Sankararaman, S. Halperin, E. 2021-02-15 doi:10.1101/2021.02.14.431168 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ Effectiveness of Joint Species Distribution Models in the Presence of Imperfect Detection ]]> https://biorxiv.org/content/10.1101/2021.02.16.431325v1?rss=1 Wang, Y. Stone, L. Hogg, S. E. 2021-02-17 doi:10.1101/2021.02.16.431325 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Probe the effect of clustering on EphA2 receptor signaling efficiency by subcellular control of ligand-receptor mobility ]]> https://biorxiv.org/content/10.1101/2021.02.16.431455v1?rss=1 Chen, Z. Oh, D. Biswas, K. H. Zaidel-Bar, R. Groves, J. T. 2021-02-17 doi:10.1101/2021.02.16.431455 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Biomolecular recognition of the glycan neoantigen CA19-9 by distinct antibodies ]]> https://biorxiv.org/content/10.1101/2021.02.17.431565v1?rss=1 Borenstein-Katz, A. Warszawski, S. Amon, R. Tasnima, N. Yu, H. Chen, X. Padler-Karavani, V. Fleishman, S. J. Diskin, R. 2021-02-17 doi:10.1101/2021.02.17.431565 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Gram-negative outer membrane proteins with multiple β-barrel domains ]]> https://biorxiv.org/content/10.1101/2021.02.17.431615v1?rss=1 Solan, R. Pereira, J. Lupas, A. N. Kolodny, R. Ben-Tal, N. 2021-02-17 doi:10.1101/2021.02.17.431615 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ PredictProtein - Predicting Protein Structure and Function for 29 Years ]]> https://biorxiv.org/content/10.1101/2021.02.23.432527v1?rss=1 Bernhofer, M. Dallago, C. Karl, T. Satagopam, V. Heinzinger, M. Littmann, M. Olenyi, T. Qiu, J. Schuetze, K. Yachdav, G. Ashkenazy, H. Ben-Tal, N. Bromberg, Y. Goldberg, T. Kajan, L. O'Donoghue, S. Sander, C. Schafferhans, A. Schlessinger, A. Vriend, G. Mirdita, M. Gawron, P. Gu, W. Jarosz, Y. Trefois, C. Steinegger, M. Schneider, R. Rost, B. 2021-02-24 doi:10.1101/2021.02.23.432527 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ Chemoenzymatic labeling of DNA methylation patterns for single-molecule epigenetic mapping ]]> https://biorxiv.org/content/10.1101/2021.02.24.432628v1?rss=1 Gabrieli, T. Michaeli, Y. Avraham, S. Torchinsky, D. Juhasz, M. Coruh, C. Arbib, N. Zhou, Z. S. Law, J. A. Weinhold, E. Ebenstein, Y. 2021-02-24 doi:10.1101/2021.02.24.432628 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ Effect of SARS-CoV-2 proteins on vascular permeability ]]> https://biorxiv.org/content/10.1101/2021.02.27.433186v1?rss=1 Rauti, R. Shahoha, M. Leichtmann-Bardoogo, Y. Nasser, R. Tamir, R. Miller, V. Babich, T. Shaked, K. Ehrlich, A. Ioannidis, K. Nahmias, Y. Sharan, R. Ashery, U. Maoz, B. M. 2021-03-01 doi:10.1101/2021.02.27.433186 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Meta-Research: Citation needed? Wikipedia and the COVID-19 pandemic ]]> https://biorxiv.org/content/10.1101/2021.03.01.433379v1?rss=1 Benjakob, O. Aviram, R. Sobel, J. A. 2021-03-01 doi:10.1101/2021.03.01.433379 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Antibody repertoire analysis of tumor-infiltrating B cells reveals distinct signatures and distributions across tissues ]]> https://biorxiv.org/content/10.1101/2021.03.17.435773v1?rss=1 Aizik, L. Dror, Y. Taussig, D. Barzel, A. Carmi, Y. Wine, Y. 2021-03-17 doi:10.1101/2021.03.17.435773 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Distance decay 2.0 - a global synthesis of taxonomic and functional turnover in ecological communities. ]]> https://biorxiv.org/content/10.1101/2021.03.17.435827v1?rss=1 Graco-Roza, C. Aarnio, S. Abrego, N. Acosta, A. T. R. Alahuhta, J. Altman, J. Angiolini, C. Aroviita, J. Attorre, F. Baastrup-Spohr, L. Barrera-Alba, J. J. Belmaker, J. Biurrun, I. Bonari, G. Bruelheide, H. Burrascano, S. Carboni, M. Cardoso, P. Carvalho, J. C. Castaldelli, G. Christensen, M. Correa, G. Dembicz, I. Dengler, J. Dolezal, J. Domingos, P. Eros, T. Ferreira, C. E. L. Filibeck, G. Floeter, S. R. Friedlander, A. Gammal, J. Gavioli, A. Gossner, M. M. Granot, I. Guarino, R. Gustafsson, C. Hayden, B. He, S. Heilmann-Clausen, J. Heino, J. Hunter, 2021-03-19 doi:10.1101/2021.03.17.435827 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ A new drug candidate for glycogen storage disorders enhances glycogen catabolism: Lessons from Adult Polyglucosan Body Disease models ]]> https://biorxiv.org/content/10.1101/2021.03.18.436069v1?rss=1 Vaknin, H. Mishra, K. D'Souza, J. Marisat, M. Sprecher, U. Wald-Altman, S. Dukhovny, A. Raviv, Y. Da'adoosh, B. Engel, H. Benhamron, S. Nitzan, K. Permyakova, A. Rosenmann, H. Lossos, A. Tam, J. Minassian, B. A. Kakhlon, O. Weil, M. 2021-03-19 doi:10.1101/2021.03.18.436069 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Optical Nanosensors for Real-time Feedback on Insulin Secretion by β-Cells ]]> https://biorxiv.org/content/10.1101/2021.03.21.435763v1?rss=1 Ehrlich, R. Hendler-Neumark, A. Wulf, V. Amir, D. Bisker, G. 2021-03-22 doi:10.1101/2021.03.21.435763 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ The lifetime cost of reproductive potential, who spends the most? ]]> https://biorxiv.org/content/10.1101/2021.03.22.432784v1?rss=1 Fuchs, S. Goldenfeld, M. Dviri, M. Librach, C. L. Baum, M. 2021-03-23 doi:10.1101/2021.03.22.432784 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ On-off transition and ultrafast decay of amino acid luminescence driven by modulation of supramolecular packing ]]> https://biorxiv.org/content/10.1101/2021.03.23.436384v1?rss=1 Arnon, Z. A. Kreiser, T. Yakimov, B. Brown, N. Aizen, R. Shaham-Niv, S. Makam, P. Qaisrani, M. N. Poli, E. Ruggiero, A. Slutsky, I. Hassanali, A. Shirshin, E. Levy, D. Gazit, E. 2021-03-23 doi:10.1101/2021.03.23.436384 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ A lipid nanoparticle RBD-hFc mRNA vaccine protects hACE2 transgenic mice against lethal SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2021.03.29.436639v1?rss=1 Elia, U. Rotem, S. Bar-Haim, E. Ramishetti, S. Naidu, G. S. Gur, D. Aftalion, M. Israeli, M. Bercovich-Kinori, A. Alcalay, R. Makdasi, E. Chitlaru, T. Rosenfeld, R. Israely, T. Melamed, S. Abutbul Ionita, I. Danino, D. Peer, D. Cohen, O. 2021-03-29 doi:10.1101/2021.03.29.436639 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ Structural heterogeneity in biliverdin modulates spectral properties of Sandercyanin fluorescent protein ]]> https://biorxiv.org/content/10.1101/2021.04.02.438172v1?rss=1 Ghosh, S. Mondal, S. Yadav, K. Aggarwal, S. Schaefer, W. F. Narayana, C. Subramanian, R. 2021-04-02 doi:10.1101/2021.04.02.438172 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ Impaired top-down auditory processing despite extensive single-neuron responses during human sleep ]]> https://biorxiv.org/content/10.1101/2021.04.03.438283v1?rss=1 Hayat, H. Marmelshtein, A. Krom, A. J. Sela, Y. Tankus, A. Strauss, I. Fahoum, F. Fried, I. Nir, Y. 2021-04-04 doi:10.1101/2021.04.03.438283 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Small but complete: liquid-liquid phase separation in minimalistic peptides ]]> https://biorxiv.org/content/10.1101/2021.04.03.438298v1?rss=1 Tang, Y. Bera, S. Yao, Y. Zeng, J. Lao, Z. Dong, X. Gazit, E. Wei, G. 2021-04-04 doi:10.1101/2021.04.03.438298 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Genetic and phenotypic heterogeneity in PNPT1, MYO15A, PTPRQ and SLC12A2 variants detected among hearing impaired assortative mating families in Southern India ]]> https://biorxiv.org/content/10.1101/2021.04.06.438557v1?rss=1 Vanniya. S, P. Chandru, J. Jeffrey, J. M. Rabinowitz, T. Brownstein, Z. Krishnamoorthy, M. Avraham, K. B. Cheng, L. Shomron, N. Srisailapathy, C. R. S. 2021-04-06 doi:10.1101/2021.04.06.438557 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ In vivo engineered B cells retain memory and secrete high titers of anti-HIV antibodies in mice ]]> https://biorxiv.org/content/10.1101/2021.04.08.438900v1?rss=1 Nahmad, A. D. Lazzarotto, C. R. Zelikson, N. Kustin, T. Tenuta, M. Huang, D. Reuveni, I. Horovitz-Fried, M. Dotan, I. Rosin-Arbesfeld, R. Nemazee, D. Voss, J. E. Stern, A. Tsai, S. Q. Barzel, A. 2021-04-09 doi:10.1101/2021.04.08.438900 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Males perceive honest information from female released sex pheromone in a moth ]]> https://biorxiv.org/content/10.1101/2021.04.14.439460v1?rss=1 Golov, Y. Gonzalez-Karlsson, A. Steinitz, H. Moncaz, A. Halon, E. Horowitz, R. Goldenberg, I. Gurka, R. Liberzon, A. Soroker, V. Jurenka, R. Harari, A. 2021-04-15 doi:10.1101/2021.04.14.439460 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ Same Action, Different Meaning: Neural substrates of Semantic Goal Representation ]]> https://biorxiv.org/content/10.1101/2021.04.18.440307v1?rss=1 Aberbach, S. Buaron, B. Mudrik, L. Mukamel, R. 2021-04-18 doi:10.1101/2021.04.18.440307 Cold Spring Harbor Laboratory Press 2021-04-18 <![CDATA[ Dual reference method for high precision infrared measurement of leaf surface temperature under field conditions ]]> https://biorxiv.org/content/10.1101/2021.04.25.440729v1?rss=1 Muller, J. D. Rotenberg, E. Tatarinov, F. Vishnevetsky, I. Dingjan, T. Kribus, A. Yakir, D. 2021-04-26 doi:10.1101/2021.04.25.440729 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Development of a 3D atlas of the embryonic pancreas for topological and quantitative analysis of heterologous cell interactions ]]> https://biorxiv.org/content/10.1101/2021.04.28.441857v1?rss=1 Glorieux, L. Sapala, A. Willnow, D. Moulis, M. Edri, S. Darrigrand, J.-F. Schonblum, A. Sakhneny, L. Schaumann, L. Gomez, H. F. Lang, C. Conrad, L. Guillemot, F. Levenberg, S. Landsman, L. Iber, D. Pierreux, C. Spagnoli, F. M. 2021-04-29 doi:10.1101/2021.04.28.441857 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ The effects of epistasis and linkage on the invasion of locally beneficial mutations and the evolution of genomic islands ]]> https://biorxiv.org/content/10.1101/2021.04.30.442097v1?rss=1 Pontz, M. Bürger, R. 2021-04-30 doi:10.1101/2021.04.30.442097 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Engineering a customizable antibacterial T6SS-based platform in Vibrio natriegens ]]> https://biorxiv.org/content/10.1101/2021.05.04.439770v1?rss=1 Jana, B. Keppel, K. Salomon, D. 2021-05-04 doi:10.1101/2021.05.04.439770 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Whole-genome duplication shapes the aneuploidy landscape of human cancers ]]> https://biorxiv.org/content/10.1101/2021.05.05.442712v1?rss=1 25% of human tumors during the early stages of tumorigenesis. Although tumors that have undergone WGD are reported to be more permissive to aneuploidy than tumors that have not, it remains unknown whether WGD affects aneuploidy recurrence patterns in human cancers. Here we analyzed clinical tumor samples from 449 WGD- tumors and 157 WGD+ tumors across 22 tumor types. We found distinct recurrence patterns of aneuploidy in WGD- and WGD+ tumors. The relative prevalence of recurrent aneuploidies decreased in WGD+ tumors, in line with increased aneuploidy tolerance. Moreover, the genetic interactions between chromosome arms differed between WGD- and WGD+ tumors, giving rise to distinct co-occurrence and mutual exclusivity aneuploidy patterns. The proportion of whole-chromosome aneuploidy vs. arm-level aneuploidy was significantly higher in WGD+ tumors, indicating distinct dominant mechanisms for aneuploidy formation in WGD- and WGD+ tumors. Human cancer cell lines successfully reproduced these WGD/aneuploidy interactions, confirming the relevance of studying this phenomenon in culture. Lastly, we induced WGD in human colon cancer cell lines, and followed aneuploidy formation in the isogenic WGD+/WGD-cells under standard or selective conditions. These experiments validated key findings from the clinical tumor analysis, and revealed a causal link between WGD and altered aneuploidy landscapes. We conclude that WGD shapes the aneuploidy landscape of human tumors, and propose that the interaction between WGD and aneuploidy is a major contributor to tumor evolution. ]]> Prasad, K. Bloomfield, M. Levi, H. Keuper, K. Bernhard, S. V. Baudoin, N. C. Leor, G. Giam, M. Wong, C. K. Rancati, G. Storchova, Z. Cimini, D. Ben-David, U. 2021-05-05 doi:10.1101/2021.05.05.442712 Cold Spring Harbor Laboratory Press 2021-05-05 <![CDATA[ Simultaneous Morphology, Motility and Fragmentation Analysis of Live Individual Sperm Cells for Male Fertility Evaluation ]]> https://biorxiv.org/content/10.1101/2021.05.11.443542v1?rss=1 Ben-Yehuda, K. Mirsky, S. K. Levi, M. Barnea, I. Meshulach, I. Kontente, S. Benvaish, D. Cur-Cycowicz, R. Nygate, Y. N. Shaked, N. T. 2021-05-12 doi:10.1101/2021.05.11.443542 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ ABA homeostasis and long-distance translocation is redundantly regulated by ABCG ABA importers ]]> https://biorxiv.org/content/10.1101/2021.05.12.443788v1?rss=1 Zhang, Y. Vasuki, H. Liu, J. Bar, H. Lazary, S. Egbaria, A. Ripper, D. Charrier, L. Mussa, Z. Wulff, N. Nour-Eldin, H. H. Aharoni, A. Ragni, L. Strader, L. Sade, N. Weinstain, R. Geisler, M. Shani, E. 2021-05-13 doi:10.1101/2021.05.12.443788 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ Mitochondria serve as axonal shuttle for Cox7c mRNA through mechanism that involves its mitochondrial targeting signal ]]> https://biorxiv.org/content/10.1101/2021.05.19.444640v1?rss=1 Cohen, B. Golani-Armon, A. Altman, T. Savulescu, A. F. Mhlanga, M. M. Perlson, E. Arava, Y. S. 2021-05-20 doi:10.1101/2021.05.19.444640 Cold Spring Harbor Laboratory Press 2021-05-20 <![CDATA[ Formylglycine-generating enzyme-like proteins constitute a novel family of widespread type VI secretion system immunity proteins ]]> https://biorxiv.org/content/10.1101/2021.05.21.445229v1?rss=1 Lopez, J. Nguyen-Hung, L. Moon, K. H. Salomon, D. Bosis, E. Feldman, M. F. 2021-05-22 doi:10.1101/2021.05.21.445229 Cold Spring Harbor Laboratory Press 2021-05-22 <![CDATA[ A role for ecologically-tuned chunking in the evolution of advanced cognition demonstrated by modelling the cleaner fish market problem ]]> https://biorxiv.org/content/10.1101/2021.05.30.446324v1?rss=1 Prat, Y. Bshary, R. Lotem, A. 2021-05-30 doi:10.1101/2021.05.30.446324 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ Characterizing Hydrogen Bonds in Intact RNA from MS2 Bacteriophage Using Solid State Magic Angle Spinning NMR ]]> https://biorxiv.org/content/10.1101/2021.06.02.446732v1?rss=1 Lusky, O. S. Meir, M. Goldbourt, A. 2021-06-02 doi:10.1101/2021.06.02.446732 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Carboxypeptidase E is efficiently secreted and internalized via lysosomes ]]> https://biorxiv.org/content/10.1101/2021.06.06.447232v1?rss=1 Armoza-Eilat, S. Caspi, M. Shomron, O. Hirschberg, K. Rosin-Arbesfeld, R. 2021-06-06 doi:10.1101/2021.06.06.447232 Cold Spring Harbor Laboratory Press 2021-06-06 <![CDATA[ The payoffs and tradeoffs of hygienic behavior: A large-scale field study on a local population of honey bees ]]> https://biorxiv.org/content/10.1101/2021.06.07.447383v1?rss=1 Seltzer, R. Kahanov, P. Kamer, Y. Hetzroni, A. Bienkowska, M. Hefetz, A. Soroker, V. 2021-06-08 doi:10.1101/2021.06.07.447383 Cold Spring Harbor Laboratory Press 2021-06-08 <![CDATA[ The Consciousness Theories Studies (ConTraSt) database: analyzing and comparing empirical studies of consciousness theories ]]> https://biorxiv.org/content/10.1101/2021.06.10.447863v1?rss=1 Yaron, I. Melloni, L. Pitts, M. Mudrik, L. 2021-06-10 doi:10.1101/2021.06.10.447863 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ A quantitative gibberellin signalling biosensor reveals a role for gibberellins in internode specification at the shoot apical meristem ]]> https://biorxiv.org/content/10.1101/2021.06.11.448154v1?rss=1 Shi, B. Felipo-Benavent, A. Cerutti, G. Galvan-Ampudia, C. Jilli, L. Brunoud, G. Mutterer, J. Sakvarelidze-Achard, L. Daviere, J.-M. Navarro-Galiano, A. Walia, A. Lazary, S. Legrand, J. Weinstain, R. Jones, A. M. Prat, S. Achard, P. VERNOUX, T. 2021-06-11 doi:10.1101/2021.06.11.448154 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ COVID-eVax, an electroporated plasmid DNA vaccine candidate encoding the SARS-CoV-2 Receptor Binding Domain, elicits protective immune responses in animal models of COVID-19 ]]> https://biorxiv.org/content/10.1101/2021.06.14.448343v1?rss=1 Conforti, A. Marra, E. Palombo, F. Roscilli, G. Rava, M. Fumagalli, V. Muzi, A. Maffei, M. Luberto, L. Lione, L. Salvatori, E. Compagnone, M. Pinto, E. Pavoni, E. Bucci, F. Vitagliano, G. Stoppoloni, D. Pacello, M. L. Cappelletti, M. Ferrara, F. F. D'Acunto, E. Chiarini, V. Arriga, R. Nyska, A. Di Lucia, P. Marotta, D. Bono, E. Giustini, L. Sala, E. Perucchini, C. Paterson, J. Ryan, K. A. Challis, A. Matusali, G. Colavita, F. Caselli, G. Criscuolo, E. Clementi, N. A. Mancini, N. Gross, R. Siedel, A. Wettstein, L. Munch, J. Donnici, L. Conti, M. De F 2021-06-14 doi:10.1101/2021.06.14.448343 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ Claustral Projections to Anterior Cingulate Cortex Modulate Engagement with the External World ]]> https://biorxiv.org/content/10.1101/2021.06.17.448649v1?rss=1 80,000 trials, we characterize claustrum recruitment during salient behavioral events, and find that a moderate level of activity in claustro-cingulate projections defines optimal engagement. Low activity of this pathway is associated with impulsive actions, while high activity is associated with behavioral lapses. Chemogenetic activation of cingulate-projecting claustrum neurons suppressed impulsive behavior and reduced the engagement of mice in the task. This relationship became even clearer upon addressing individual variability in the strategy mice employed during the ENGAGE task. Furthermore, this association of claustrum activity and engagement extends into sleep. Using simultaneous EEG and photometry recordings in the claustrum, we find that cingulate projecting claustrum neurons are most active during deep unresponsive slow-wave sleep, when mice are less prone to awakening by sensory stimuli. ]]> Atlan, G. Matosevich, N. Peretz-Rivlin, N. Yvgi, I. Chen, E. Kleinman, T. Bleistein, N. Sheinbach, E. Groysman, M. Nir, Y. Citri, A. 2021-06-19 doi:10.1101/2021.06.17.448649 Cold Spring Harbor Laboratory Press 2021-06-19 <![CDATA[ Nanopore callers for epigenetics from limited supervised data ]]> https://biorxiv.org/content/10.1101/2021.06.17.448800v1?rss=1 Yao, B. Hsu, C. Goldner, G. Michaeli, Y. Ebenstein, Y. Listgarten, J. 2021-06-17 doi:10.1101/2021.06.17.448800 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Deconvolution of the epigenetic age discloses distinct inter-personal variability in epigenetic aging patterns ]]> https://biorxiv.org/content/10.1101/2021.06.20.449142v1?rss=1 Shahal, T. Segev, E. Konstantinovsky, T. Marcus, Y. Shefer, G. Pasmanik-Chor, M. Buch, A. Ebenstein, Y. Zimmet, P. Stern, N. 2021-06-22 doi:10.1101/2021.06.20.449142 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Promoter architecture links gene duplication with transcriptional divergence ]]> https://biorxiv.org/content/10.1101/2021.07.03.450995v1?rss=1 Hagai, T. Fraimovitch, E. 2021-07-04 doi:10.1101/2021.07.03.450995 Cold Spring Harbor Laboratory Press 2021-07-04 <![CDATA[ Nonclinical Safety and Immunogenicity of an rVSV-ΔG-SARS-CoV-2-S vaccine in mice, hamsters, rabbits and pigs ]]> https://biorxiv.org/content/10.1101/2021.07.06.451119v1?rss=1 Madar-Balakirski, N. Rosner, A. Melamed, S. Politi, B. Steiner, M. Tamir, H. Yahalom Ronen, Y. Bar-David, E. Ben-Shmuel, A. Sittner, A. Glinert, I. Weiss, S. Bar-Haim, E. Cohen, H. Elia, U. Achdout, H. Erez, N. Rotem, S. Lazar, S. Nyska, A. Yitzhaki, S. Beth-Din, A. Levy, H. Paran, N. Israely, T. Marcus, H. 2021-07-07 doi:10.1101/2021.07.06.451119 Cold Spring Harbor Laboratory Press 2021-07-07 <![CDATA[ A gene coevolution network provides insight into eukaryotic cellular and genomic structure and function ]]> https://biorxiv.org/content/10.1101/2021.07.09.451830v1?rss=1 Steenwyk, J. L. Phillips, M. A. Yang, F. Date, S. S. Graham, T. berman, j. Hittinger, C. T. Rokas, A. 2021-07-10 doi:10.1101/2021.07.09.451830 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ Inulin nanostructures: The sweet-spot of carbohydrate self-assembly ]]> https://biorxiv.org/content/10.1101/2021.07.13.451276v1?rss=1 Arnon, Z. A. Grabarics, M. Kreiser, T. Raveh, A. Pagel, K. Gazit, E. 2021-07-13 doi:10.1101/2021.07.13.451276 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ Epigenetically Inherited Mutation Rates Predicted to Maximize Adaptation Rates ]]> https://biorxiv.org/content/10.1101/2021.07.14.452333v1?rss=1 Ram, Y. Pilpel, Y. T. Lobinska, G. A. 2021-07-14 doi:10.1101/2021.07.14.452333 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ Heterogeneity in the transcriptional response of the human pathogen Aspergillus fumigatus to the antifungal agent caspofungin ]]> https://biorxiv.org/content/10.1101/2021.07.15.452449v1?rss=1 Colabardini, A. C. Wang, F. Dong, Z. Pardeshi, L. Rocha, M. C. Costa, J. H. dos Reis, T. F. Brown, A. Jaber, Q. Z. Fridman, M. Fill, T. Rokas, A. Malavazi, I. Wong, K. H. Goldman, G. H. 2021-07-15 doi:10.1101/2021.07.15.452449 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ Botrytis cinerea BcPTP1 is a late infection phase, cysteine rich protein cytotoxic effector ]]> https://biorxiv.org/content/10.1101/2021.07.18.452873v1?rss=1 Zhu, W. Yu, M. Xu, R. Bi, K. Xiong, C. Liu, Z. Sharon, A. Jiang, D. Wu, M. Gu, Q. Gong, L. Chen, W. Wei, W. 2021-07-19 doi:10.1101/2021.07.18.452873 Cold Spring Harbor Laboratory Press 2021-07-19 <![CDATA[ Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record ]]> https://biorxiv.org/content/10.1101/2021.07.19.453013v1?rss=1 Mongiardino Koch, N. Thompson, J. R. Hatch, A. S. McCowin, M. F. Armstrong, F. Coppard, S. E. Aguilera, F. Bronstein, O. Kroh, A. Mooi, R. Rouse, G. 2021-07-20 doi:10.1101/2021.07.19.453013 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ Neural Collision Detection: an open source library to study the three-dimensional interactions of neurons and other tree-like structures ]]> https://biorxiv.org/content/10.1101/2021.07.20.452894v1?rss=1 Har-Gil, H. Jacobson, Y. Proenneke, A. Staiger, J. F. Tomer, O. Halperin, D. Blinder, P. 2021-07-21 doi:10.1101/2021.07.20.452894 Cold Spring Harbor Laboratory Press 2021-07-21 <![CDATA[ How clustered protocadherin binding specificity is tuned for neuronal self/non-self-recognition ]]> https://biorxiv.org/content/10.1101/2021.07.22.453400v1?rss=1 Goodman, K. M. Katsamba, P. S. Rubinstein, R. Ahlsen, G. Bahna, F. Mannepalli, S. Dan, H. Sampogna, R. Shapiro, L. Honig, B. 2021-07-23 doi:10.1101/2021.07.22.453400 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ m6A is required for resolving progenitor identity during planarian stem cell differentiation ]]> https://biorxiv.org/content/10.1101/2021.07.27.453979v1?rss=1 20,000 cells following perturbation of the pathway, we discovered that m6A negatively regulates transcription of histone variants, and that inhibition of the pathway resulted in accumulation of undifferentiated cells throughout the animal in an abnormal transcriptional state. Analysis of >1000 planarian gene expression datasets revealed that the inhibition of the chromatin modifying complex NuRD had almost indistinguishable consequences, unraveling an unappreciated link between m6A and chromatin modifications. Our findings reveal that m6A is critical for planarian stem cell homeostasis and gene regulation in regeneration. ]]> Dagan, Y. Yesharim, Y. Bonneau, A. R. Schwartz, S. Reddien, P. W. Wurtzel, O. 2021-07-28 doi:10.1101/2021.07.27.453979 Cold Spring Harbor Laboratory Press 2021-07-28 <![CDATA[ A binary effector module secreted by a type VI secretion system ]]> https://biorxiv.org/content/10.1101/2021.07.29.453783v1?rss=1 Dar, Y. Jana, B. Bosis, E. Salomon, D. 2021-07-29 doi:10.1101/2021.07.29.453783 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Proteomic landscape of multi-layered breast cancer internal tumor heterogeneity ]]> https://biorxiv.org/content/10.1101/2021.08.05.455361v1?rss=1 Mardamshina, M. Shenoy, A. Necula, D. Krol, K. Pirak, D. Itzhacky, N. Marin, I. Shalmon, B. Sharan, R. Gal-Yam, E. N. Barshack, I. Geiger, T. 2021-08-06 doi:10.1101/2021.08.05.455361 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Distinct progressions of neuronal activity changes underlie the formation and consolidation of a gustatory associative memory ]]> https://biorxiv.org/content/10.1101/2021.08.08.455552v1?rss=1 Arieli, E. Younis, N. Moran, A. 2021-08-08 doi:10.1101/2021.08.08.455552 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ Genome sequences of Aegilops species of section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement ]]> https://biorxiv.org/content/10.1101/2021.08.09.455628v1?rss=1 Avni, R. Lux, T. Minz-Dub, A. Millet, E. Sela, H. Distelfeld, A. Deek, J. Yu, G. Steuernagel, B. Pozniak, C. Ens, J. Gundlach, H. Mayer, K. F. X. Himmelbach, A. Stein, N. Mascher, M. Spannagl, M. Wulff, B. B. Sharon, A. 2021-08-09 doi:10.1101/2021.08.09.455628 Cold Spring Harbor Laboratory Press 2021-08-09 <![CDATA[ Repair of Noise-Induced Damage to Stereocilia F-actin Cores is Facilitated by XIRP2 ]]> https://biorxiv.org/content/10.1101/2021.08.10.455815v1?rss=1 Wagner, E. L. Im, J.-S. Nakahata, M. I. Imbery, T. E. Li, S. Chen, D. B. Noy, Y. Archer, D. W. Xu, W. Hashisaki, G. T. Avraham, K. B. Shin, J.-B. 2021-08-10 doi:10.1101/2021.08.10.455815 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Frequent Aneuploidy in Primary Human T Cells Following CRISPR-Cas9 cleavage ]]> https://biorxiv.org/content/10.1101/2021.08.20.457092v1?rss=1 Nahmad, A. D. Reuveni, E. Goldschmidt, E. Tenne, T. Liberman, M. Horovitz-Fried, M. Khosravi, R. Kobo, H. Reinstein, E. Madi, A. Ben-David, U. Barzel, A. 2021-08-20 doi:10.1101/2021.08.20.457092 Cold Spring Harbor Laboratory Press 2021-08-20 <![CDATA[ MEK1/2 inhibition transiently alters the tumor immune microenvironment to enhance immunotherapy efficacy against head and neck cancer ]]> https://biorxiv.org/content/10.1101/2021.08.22.457244v1?rss=1 View larger version (42K): org.highwire.dtl.DTLVardef@1c65286org.highwire.dtl.DTLVardef@1541becorg.highwire.dtl.DTLVardef@f557f3org.highwire.dtl.DTLVardef@16134dc_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG ]]> Prasad, M. Zorea, J. Jagadeeshan, S. Shnerb, A. Bouaoud, J. Michon, L. Novoplansky, O. Badarni, M. Cohen, L. Yagodayev, K. Tzadok, S. Rotblat, B. Brezina, L. Mock, A. Karabajakian, A. Fayette, J. Cohen, I. Cooks, T. Allon, I. Dimitstei, O. Joshua, B. Kong, D. Voronov, E. Scaltriti, M. Carmi, Y. Hess, J. Morris, L. G. T. Saintigny, P. Elkabets, M. 2021-08-22 doi:10.1101/2021.08.22.457244 Cold Spring Harbor Laboratory Press 2021-08-22 <![CDATA[ An ultra-low dose of {triangleup}9-tetrahydrocannabinol improves Alzheimer's Disease-related cognitive deficits ]]> https://biorxiv.org/content/10.1101/2021.08.22.457252v1?rss=1 nitzan, k. Ellenbogen, L. Beniamin, T. Sarne, Y. Doron, R. 2021-08-23 doi:10.1101/2021.08.22.457252 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ Policy-relevant indicators for invasive alien species assessment and reporting ]]> https://biorxiv.org/content/10.1101/2021.08.26.457851v1?rss=1 McGeoch, M. A. Arle, E. Belmaker, J. Buba, Y. Clarke, D. A. Essl, F. Garcia-Berthou, E. Groom, Q. Henriksen, M. V. Jetz, W. Kuhn, I. Lenzner, B. Meyer, C. Pagad, S. Pili, A. Roige, M. Seebens, H. Tingley, R. Vicente, J. R. Wilson, J. R. Winter, M. 2021-08-30 doi:10.1101/2021.08.26.457851 Cold Spring Harbor Laboratory Press 2021-08-30 <![CDATA[ Balancing growth amidst salinity stress-lifestyle perspectives from the extremophyte model Schrenkiella parvula ]]> https://biorxiv.org/content/10.1101/2021.08.27.457575v1?rss=1 Tran, K.-N. Pantha, P. Wang, G. Kumar, N. Wijesinghege, C. Hong, H. Johnson, J. Kelt, R. Matherne, M. G. Clement, A. Crain, C. Tran, D. Oh, D.-H. Adhikari, P. Foroozani, M. Finnegan, P. Longstreth, D. Larkin, J. C. Smith, A. P. Dassanayake, M. 2021-08-28 doi:10.1101/2021.08.27.457575 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Mapping interindividual dynamics of innate immune response at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2021.09.01.457774v1?rss=1 Kumasaka, N. Rostom, R. Huang, N. Polanski, K. Meyer, K. Patel, S. Boyd, R. Gomez, C. Barnett, S. Panousis, N. Schwartzentruber, J. Ghoussaini, M. Lyons, P. A. Calero-Nieto, F. J. Göttgens, B. Barnes, J. L. Worlock, K. B. Yoshida, M. Nikolic, M. Stephenson, E. Reynolds, G. Haniffa, M. Marioni, J. Stegle, O. Hagai, T. Teichmann, S. A. 2021-09-01 doi:10.1101/2021.09.01.457774 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ ScanNet: An interpretable geometric deep learning model for structure-based protein binding site prediction ]]> https://biorxiv.org/content/10.1101/2021.09.05.459013v1?rss=1 Tubiana, J. Schneidman-Duhovny, D. Wolfson, H. J. 2021-09-06 doi:10.1101/2021.09.05.459013 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ TTYH family members form tetrameric complexes within the cell membrane ]]> https://biorxiv.org/content/10.1101/2021.09.05.459021v1?rss=1 Melvin, E. Shlush, E. Giladi, M. Haitin, Y. 2021-09-05 doi:10.1101/2021.09.05.459021 Cold Spring Harbor Laboratory Press 2021-09-05 <![CDATA[ Listeria monocytogenes TcyKLMN cystine/cysteine transporter facilitates glutathione synthesis and virulence gene expression ]]> https://biorxiv.org/content/10.1101/2021.09.07.459368v1?rss=1 Herskovits, A. A. Brenner, M. Freidman, S. Haber, A. Borovok, I. Sigal, N. Lewinson, O. 2021-09-08 doi:10.1101/2021.09.07.459368 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ MIMOSA2: A metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data ]]> https://biorxiv.org/content/10.1101/2021.09.14.459910v1?rss=1 Noecker, C. Eng, A. Borenstein, E. 2021-09-14 doi:10.1101/2021.09.14.459910 Cold Spring Harbor Laboratory Press 2021-09-14 <![CDATA[ Dormant phages communicate to control exit from lysogeny ]]> https://biorxiv.org/content/10.1101/2021.09.20.460909v1?rss=1 Aframian, N. Omer Bendori, S. Hen, S. Guler, P. Stokar-Avihail, A. Manor, E. Msaeed, k. Lipsman, V. Grinberg, I. Mahagna, A. Eldar, A. 2021-09-20 doi:10.1101/2021.09.20.460909 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ Characterization of morpho-functional traits in mesophotic corals reveals optimized light capture and photosynthesis ]]> https://biorxiv.org/content/10.1101/2021.09.29.462347v1?rss=1 Kramer, N. Guan, J. Chen, S. Wangpraseurt, D. Loya, Y. 2021-10-01 doi:10.1101/2021.09.29.462347 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Simulation-based inference of evolutionary parameters from adaptation dynamics using neural networks ]]> https://biorxiv.org/content/10.1101/2021.09.30.462581v1?rss=1 Avecilla, G. Chuong, J. Li, F. Sherlock, G. J. Gresham, D. Ram, Y. 2021-10-01 doi:10.1101/2021.09.30.462581 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Actin capping protein regulates actomyosin contractility to maintain germline architecture in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.10.03.462551v1?rss=1 Ray, S. Agarwal, P. Zaidel-Bar, R. 2021-10-03 doi:10.1101/2021.10.03.462551 Cold Spring Harbor Laboratory Press 2021-10-03 <![CDATA[ A nesprin-4/kinesin-1 cargo model for nucleus positioning in cochlear outer hair cells ]]> https://biorxiv.org/content/10.1101/2021.10.10.463824v1?rss=1 Taiber, S. Gozlan, O. Cohen, R. Andrade, L. Moran, Y. Hipp, R. Kelley, M. W. Manor, U. Sprinzak, D. Avraham, K. B. 2021-10-10 doi:10.1101/2021.10.10.463824 Cold Spring Harbor Laboratory Press 2021-10-10 <![CDATA[ Decoding of human identity by computer vision and neuronal vision ]]> https://biorxiv.org/content/10.1101/2021.10.10.463839v1?rss=1 Zhang, Y. M. Aghajan, Z. Ison, M. Lu, Q. Tang, H. Kalender, G. Monsoor, T. Zheng, J. Kreiman, G. Roychowdhury, V. Fried, I. 2021-10-12 doi:10.1101/2021.10.10.463839 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ Predicting Individual Traits from Unperformed Tasks ]]> https://biorxiv.org/content/10.1101/2021.10.12.464045v1?rss=1 Gal, S. Tik, N. Bernstein-Eliav, M. Tavor, I. 2021-10-13 doi:10.1101/2021.10.12.464045 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Escherichia coli strains from patients with inflammatory bowel diseases have disease-specific genomic adaptations ]]> https://biorxiv.org/content/10.1101/2021.10.19.464957v1?rss=1 Dubinsky, V. Reshef, L. Rabinowitz, K. Wasserberg, N. Dotan, I. Gophna, U. 2021-10-20 doi:10.1101/2021.10.19.464957 Cold Spring Harbor Laboratory Press 2021-10-20 <![CDATA[ Structural basis for long-chain isoprenoids synthesis by cis-prenyltransferases ]]> https://biorxiv.org/content/10.1101/2021.10.21.465316v1?rss=1 C10,000) fail to conform to this paradigm. Here, to resolve the structural basis for long-chain isoprenoid synthesis, we focused on the human cis-prenyltransferase complex (hcis-PT). This enzyme, peripheral to the endoplasmic reticulum membrane, produces the precursor for dolichol phosphate, a membrane residing glycosyl carrier. In line with its crucial role in the cellular protein glycosylation machinery, disease-causing mutations in hcis-PT were shown to result in a wide spectrum of clinical phenotypes. The crystallographic structures of hcis-PT in four different substrate/product-bound conformations revealed an outlet enabling product elongation into the bulk solvent. Moreover, hydrogen-deuterium exchange mass spectrometry analysis in solution showed that the hydrophobic active site core is flanked by dynamic regions consistent with separate inlet and outlet orifices. Finally, using a fluorescent substrate analog and a fluorescently-labeled lipid nanodiscs, we show that product elongation and membrane association are closely correlated. Together, our results support directional product synthesis in long-chain enzymes and rubber synthases, with a distinct substrate inlet and product outlet, allowing direct membrane insertion of the elongating isoprenoid during catalysis. This mechanism uncouples active site volume from product length and circumvents the need to expulse hydrophobic product into a polar environment prior to membrane insertion. ]]> Giladi, M. Lisnyansky Bar-El, M. Vankova, P. Ferofontov, A. Melvin, E. Kavan, D. Redko, B. Haimov, E. Wiener, R. Man, P. Haitin, Y. 2021-10-21 doi:10.1101/2021.10.21.465316 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ The proteasome regulator PSME4 drives immune evasion and abrogates anti-tumor immunity in NSCLC ]]> https://biorxiv.org/content/10.1101/2021.10.24.464690v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@e87910org.highwire.dtl.DTLVardef@641843org.highwire.dtl.DTLVardef@175092corg.highwire.dtl.DTLVardef@ad34c2_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMapping the degradation landscape in Non-Small Cell Lung Cancer (NSCLC) uncovers altered proteasome activity and composition C_LIO_LIProteasome regulator PSME4 plays an anti-inflammatory role in NSCLC by attenuating immunoproteasome activity C_LIO_LIPSME4 restricts tumor antigen presentation and cytokine secretion, defining a cold tumor environment C_LIO_LIPSME4 drives tumor immune evasion and is associated with resistance to immunotherapy C_LI ]]> Javitt, A. Shmueli, M. D. Kramer, M. P. Kolodziejczyk, A. A. Cohen, I. J. Kamer, I. Litchfield, K. Bab-Dinitz, E. Zadok, O. Neiens, V. Ulman, A. Radomir, L. Wolf-Levy, H. Eisenberg-Lerner, A. Kacen, A. Alon, M. Toste Rego, A. Stacher-Priehse, E. Linder, M. Koch, I. Bar, J. Swanton, C. Samuels, Y. Levin, Y. C. A. da Fonseca, P. Elinav, E. Friedman, N. Meiners, S. Merbl, Y. 2021-10-24 doi:10.1101/2021.10.24.464690 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ Stemness activity underlying whole brain regeneration in a basal chordate ]]> https://biorxiv.org/content/10.1101/2021.10.24.465595v1?rss=1 Gordon, T. Zaquin, T. Kowarsky, M. A. Voskoboynik, Y. Hendin, N. Wurtzel, O. Caicci, F. Manni, L. Voskoboynik, A. Shenkar, N. 2021-10-24 doi:10.1101/2021.10.24.465595 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ Antigen experience relaxes the organisational structure of the T cell receptor repertoire ]]> https://biorxiv.org/content/10.1101/2021.10.26.465870v1?rss=1 Mark, M. Reich-Zeliger, S. Greenstein, E. Reshef, D. Madi, A. Chain, B. Friedman, N. 2021-10-26 doi:10.1101/2021.10.26.465870 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Pan-cancer mapping of single T cell profiles reveals a TCF1:CXCR6-CXCL16 regulatory axis essential for effective anti-tumor immunity ]]> https://biorxiv.org/content/10.1101/2021.10.31.466532v1?rss=1 Jerby, L. Tooley, K. Escobar, G. Dandekar, G. Madi, A. Goldschmidt, E. Lambden, C. Rozenblatt-Rosen, O. Anderson, A. C. Regev, A. 2021-10-31 doi:10.1101/2021.10.31.466532 Cold Spring Harbor Laboratory Press 2021-10-31 <![CDATA[ Act Natural: Functional Connectivity from Naturalistic Stimuli fMRI Outperforms Resting-State in Predicting Brain Activity ]]> https://biorxiv.org/content/10.1101/2021.11.01.466749v1?rss=1 Gal, S. Coldham, Y. Bernstein-Eliav, M. Tavor, I. 2021-11-03 doi:10.1101/2021.11.01.466749 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ 3CAC: improving the classification of phages and plasmids from metagenomic assemblies using assembly graphs ]]> https://biorxiv.org/content/10.1101/2021.11.05.467408v1?rss=1 Pu, L. Shamir, R. 2021-11-05 doi:10.1101/2021.11.05.467408 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ Compositional Restricted Boltzmann Machines Unveil the Brain-Wide Organization of Neural Assemblies ]]> https://biorxiv.org/content/10.1101/2021.11.09.467900v1?rss=1 van der Plas, T. L. Tubiana, J. Le Goc, G. Migault, G. Kunst, M. Baier, H. Bormuth, V. Englitz, B. Debregeas, G. 2021-11-11 doi:10.1101/2021.11.09.467900 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Sequence learning attenuates cortical responses in both frontal and perceptual cortices in early infancy ]]> https://biorxiv.org/content/10.1101/2021.11.10.468062v1?rss=1 Jaffe-Dax, S. Herbolzheimer, A. Bejjanki, V. R. Emberson, L. L. 2021-11-11 doi:10.1101/2021.11.10.468062 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Causation without correlation: parasite-mediated frequency-dependent selection and infection prevalence ]]> https://biorxiv.org/content/10.1101/2021.11.13.468422v1?rss=1 Lively, C. M. Xu, J. Ben-Ami, F. 2021-11-14 doi:10.1101/2021.11.13.468422 Cold Spring Harbor Laboratory Press 2021-11-14 <![CDATA[ TWIST1 methylation by SETD6 selectively antagonizes LINC-PINT expression in Glioblastoma multiforme ]]> https://biorxiv.org/content/10.1101/2021.11.18.469142v1?rss=1 Admoni-Elisha, L. Feldman, M. Elbaz, T. Chopra, A. Shapira, G. Fry, C. J. Shomron, N. Biggar, K. Levy, D. 2021-11-18 doi:10.1101/2021.11.18.469142 Cold Spring Harbor Laboratory Press 2021-11-18 <![CDATA[ Model for ring closure in ER tubular network dynamics ]]> https://biorxiv.org/content/10.1101/2021.11.18.469198v1?rss=1 Zucker, B. Golani, G. Kozlov, M. M. 2021-11-20 doi:10.1101/2021.11.18.469198 Cold Spring Harbor Laboratory Press 2021-11-20 <![CDATA[ Fine-tuning of deep language models as a computational framework of modeling listeners' perspective during language comprehension ]]> https://biorxiv.org/content/10.1101/2021.11.22.469596v1?rss=1 Tikochinski, R. Goldstein, A. Yeshurun, Y. Hasson, U. Reichart, R. 2021-11-23 doi:10.1101/2021.11.22.469596 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ Deeper than you think: partisan-dependent brain response ]]> https://biorxiv.org/content/10.1101/2021.11.23.469735v1?rss=1 Katabi, N. Simon, H. Yakim, S. Ravreby, I. Yeshurun, Y. 2021-11-27 doi:10.1101/2021.11.23.469735 Cold Spring Harbor Laboratory Press 2021-11-27 <![CDATA[ The DOMINO web-server for active module identification analysis ]]> https://biorxiv.org/content/10.1101/2021.11.25.469692v1?rss=1 Levi, H. Rahmanian, N. Elkon, R. Shamir, R. 2021-11-25 doi:10.1101/2021.11.25.469692 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ Structure of Dunaliella Photosystem II reveals conformational flexibility of stacked and unstacked supercomplexes ]]> https://biorxiv.org/content/10.1101/2021.11.29.470333v1?rss=1 Caspy, I. Fadeeva, M. Mazor, Y. Nelson, N. 2021-11-30 doi:10.1101/2021.11.29.470333 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Adolescent rats extend help to outgroup members, highlighting a neural network for group identity categorization. ]]> https://biorxiv.org/content/10.1101/2021.11.29.470434v1?rss=1 Breton, J. Eisner, J. S. Gandhi, V. S. Musick, N. Zhang, A. Long, K. L. P. Perloff, O. S. Hu, K. Y. Pham, C. M. Lalchandani, P. Barraza, M. K. Kantor, B. Kaufer, D. Ben-Ami Bartal, I. 2021-12-01 doi:10.1101/2021.11.29.470434 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Imaging analysis to quantitate the Interplay of membrane and cytoplasm protein dynamics ]]> https://biorxiv.org/content/10.1101/2021.12.01.470244v1?rss=1 Kislev, N. Egozi, M. Benayahu, D. 2021-12-03 doi:10.1101/2021.12.01.470244 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ A novel PSII photosynthetic control is activated in anoxic cultures of green algae ]]> https://biorxiv.org/content/10.1101/2021.12.01.470728v1?rss=1 Milrad, Y. Nagy, V. Toth, S. Yacoby, I. 2021-12-01 doi:10.1101/2021.12.01.470728 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Dataset-adaptive minimizer order reduces memory usage in k-mer counting ]]> https://biorxiv.org/content/10.1101/2021.12.02.470910v1?rss=1 Flomin, D. Pellow, D. Shamir, R. 2021-12-03 doi:10.1101/2021.12.02.470910 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ A dynamic antibacterial T6SS in Pantoea agglomerans pv. betae delivers a lysozyme-like effector to antagonize competitors ]]> https://biorxiv.org/content/10.1101/2021.12.03.471080v1?rss=1 Carobbi, A. Di Nepi, S. Fridman, C. M. Dar, Y. Ben-Yaakov, R. Barash, I. Salomon, D. Sessa, G. 2021-12-03 doi:10.1101/2021.12.03.471080 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ Improving replicability using interaction with laboratories: a multi-lab experimental assessment ]]> https://biorxiv.org/content/10.1101/2021.12.05.471264v1?rss=1 Jaljuli, I. Kafkafi, N. Giladi, E. Golani, I. Gozes, I. Chesler, E. Bogue, M. A. Bemjamini, Y. 2021-12-07 doi:10.1101/2021.12.05.471264 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Molecular Mechanisms of Neurotransmitter Release Control Distinct Features of Sensory Coding Reliability ]]> https://biorxiv.org/content/10.1101/2021.12.06.471391v1?rss=1 Rozenfeld, E. Ehmann, N. Manoim, J. E. Kittel, R. Parnas, M. 2021-12-07 doi:10.1101/2021.12.06.471391 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ MYH10 governs adipocyte function and adipogenesis through its interaction with GLUT4 ]]> https://biorxiv.org/content/10.1101/2021.12.07.471535v1?rss=1 Kislev, N. Mor-Yossef Moldovan, L. Barak, R. Egozi, M. Benayahu, D. 2021-12-07 doi:10.1101/2021.12.07.471535 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ IGF1 Receptor Regulates Upward Firing Rate Homeostasis via the Mitochondrial Calcium Uniporter ]]> https://biorxiv.org/content/10.1101/2021.12.11.469196v1?rss=1 Katsenelson, M. Shapira, I. Abbas, E. Styr, B. Aid, S. Holzenberger, M. Rizzoli, S. Slutsky, I. 2021-12-12 doi:10.1101/2021.12.11.469196 Cold Spring Harbor Laboratory Press 2021-12-12 <![CDATA[ LY6S, a New Interferon-Inducible Human Member of the Ly6a-Subfamily Expressed by Spleen Cells and Associated with Inflammation and Viral Resistance ]]> https://biorxiv.org/content/10.1101/2021.12.16.472998v1?rss=1 Shmerling, M. Chalik, M. Smorodinsky, N. I. Meeker, A. Roy, S. Sagi-Assif, O. Meshel, T. Danilevsky, A. Shomron, N. Levinger, S. Nishry, B. Baruchi, D. Shargorodsky, A. Ziv, R. Sarusi-Portuguez, A. Lahav, M. Ehrlich, M. Braschi, B. Bruford, E. Witz, I. P. Wreschner, D. H. 2021-12-17 doi:10.1101/2021.12.16.472998 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ The Biomechanics of the Locust Ovipositor Valves: a Unique Digging Apparatus ]]> https://biorxiv.org/content/10.1101/2021.12.22.473831v1?rss=1 Das, R. Gershon, S. Bar-On, B. Tadayon, M. Ayali, A. Pinchasik, B.-E. 2021-12-23 doi:10.1101/2021.12.22.473831 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Seasonal challenges of tropical bats (Rousettus aegyptiacus) in temperate zones ]]> https://biorxiv.org/content/10.1101/2021.12.31.473712v1?rss=1 Weinberg, M. Mazar, O. Goutnik, S. Harten, L. Handel, M. Czirjak, G. A. Yovel, Y. 2022-01-01 doi:10.1101/2021.12.31.473712 Cold Spring Harbor Laboratory Press 2022-01-01 <![CDATA[ Using syncmers improves long-read mapping ]]> https://biorxiv.org/content/10.1101/2022.01.10.475696v1?rss=1 Pellow, D. Dutta, A. Shamir, R. 2022-01-11 doi:10.1101/2022.01.10.475696 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ OrganoID: a versatile deep learning platform for organoid image analysis ]]> https://biorxiv.org/content/10.1101/2022.01.13.476248v1?rss=1 Matthews, J. M. Schuster, B. Kashaf, S. S. Liu, P. Bilgic, M. Rzhetsky, A. Tay, S. 2022-01-16 doi:10.1101/2022.01.13.476248 Cold Spring Harbor Laboratory Press 2022-01-16 <![CDATA[ De-tensioning of collagen fibers optimizes endometrial receptivity and improves the rate of embryo implantation ]]> https://biorxiv.org/content/10.1101/2022.01.18.476712v1?rss=1 Zehorai, E. Gross, T. Shimshoni, E. Hadas, R. Adir, I. Golani, O. Molodij, G. Eitan, R. Kadler, K. Neeman, M. Dakel, N. Solomonov, I. Sagi, I. 2022-01-18 doi:10.1101/2022.01.18.476712 Cold Spring Harbor Laboratory Press 2022-01-18 <![CDATA[ Automated assessment reveals extinction risk of reptiles is widely underestimated across space and phylogeny ]]> https://biorxiv.org/content/10.1101/2022.01.19.477028v1?rss=1 de Oliveira Caetano, G. H. Chapple, D. G. Grenyer, R. Raz, T. Rosenblatt, J. Tingley, R. Böhm, M. Meiri, S. Roll, U. 2022-01-22 doi:10.1101/2022.01.19.477028 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ Mechano-signaling feedback underlies precise inner hair cell patterning in the organ of Corti ]]> https://biorxiv.org/content/10.1101/2022.01.24.477468v1?rss=1 Sprinzak, D. Cohen, R. Taiber, S. Loza, O. Kasirer, S. Woland, S. 2022-01-24 doi:10.1101/2022.01.24.477468 Cold Spring Harbor Laboratory Press 2022-01-24 <![CDATA[ SNTA1 GeneRescues Ion Channel Function in Cardiomyocytes Derived from Induced Pluripotent Stem Cells Reprogrammed from Muscular Dystrophy Patients with Arrhythmias ]]> https://biorxiv.org/content/10.1101/2022.01.25.477696v1?rss=1 Jalife, J. Jimenez-Vazquez, E. N. Arad, M. Macias, A. Vera-Pedrosa, M. L. Cruz, F. M. Cuttita, A. J. Monteiro da Rocha, A. Herron, T. J. Ponce-Balbuena, D. Guerrero-Serna, G. Binah, O. Michele, D. E. 2022-01-26 doi:10.1101/2022.01.25.477696 Cold Spring Harbor Laboratory Press 2022-01-26 <![CDATA[ Lactate Signaling Mediated by AMD3100 Ameliorates Astrocyte Pathology and Remyelination Without Additional Extension of SOD1G93A Mice' Life-Span ]]> https://biorxiv.org/content/10.1101/2022.01.28.478264v1?rss=1 Rabinovich-Nikitin, I. Solomon, B. 2022-01-29 doi:10.1101/2022.01.28.478264 Cold Spring Harbor Laboratory Press 2022-01-29 <![CDATA[ Rapidly evolving viral motifs target biophysically constrained binding pockets of host proteins ]]> https://biorxiv.org/content/10.1101/2022.01.29.478279v1?rss=1 Shuler, G. Hagai, T. 2022-01-31 doi:10.1101/2022.01.29.478279 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ Real-time neurofeedback to alter interpretations of a naturalistic narrative ]]> https://biorxiv.org/content/10.1101/2022.01.30.478388v1?rss=1 Mennen, A. C. Nastase, S. A. Yeshurun, Y. Hasson, U. Norman, K. A. 2022-01-31 doi:10.1101/2022.01.30.478388 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ Molecular mechanics underlying flat-to-round membrane budding in live secretory cells ]]> https://biorxiv.org/content/10.1101/2022.02.02.478826v1?rss=1 Shin, W. Zucker, B. Kundu, N. Lee, S. H. Shi, B. Guo, X. Chan, C. Y. Harrison, J. T. Turechek, J. M. Hinshaw, J. E. Kozlov, M. Wu, L.-G. 2022-02-03 doi:10.1101/2022.02.02.478826 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Specific Peptides Predict Protein Classification. ]]> https://biorxiv.org/content/10.1101/2022.02.04.479085v1?rss=1 Horn, D. Weingart, U. 2022-02-08 doi:10.1101/2022.02.04.479085 Cold Spring Harbor Laboratory Press 2022-02-08 <![CDATA[ A five-fold expansion of the global RNA virome reveals multiple new clades of RNA bacteriophages ]]> https://biorxiv.org/content/10.1101/2022.02.15.480533v1?rss=1 2.5 million RNA viral contigs. Via analysis of the 330k novel RNA-dependent RNA polymerases (RdRP), this expansion corresponds to a five-fold increase of RNA virus diversity. Extended RdRP phylogeny supports monophyly of the five established phyla, reveals two putative new bacteriophage phyla and numerous putative novel classes and orders. The dramatically expanded Lenarviricota phylum, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome diversity. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts. Gene content analysis revealed multiple domains previously not found in RNA viruses and implicated in virus-host interactions. This vast collection of new RNA virus genomes provides insights into RNA virus evolution and should become a major resource for RNA virology. ]]> Neri, U. Wolf, Y. I. Roux, S. Camargo, A. P. Lee, B. D. Kazlauskas, D. Chen, I. M. Ivanova, N. Allen, L. Z. Paez-Espino, D. Bryant, D. A. Bhaya, D. Krupovic, M. RNA Virus Discovery Consortium, Dolja, V. V. Kyrpides, N. C. Koonin, E. V. Gophna, U. 2022-02-17 doi:10.1101/2022.02.15.480533 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ Reduced antigenicity of Omicron lowers host serologic response ]]> https://biorxiv.org/content/10.1101/2022.02.15.480546v1?rss=1 Tubiana, J. Xiang, Y. Fan, L. Wolfson, H. J. Chen, K. Schneidman-Duhovny, D. Shi, Y. 2022-02-15 doi:10.1101/2022.02.15.480546 Cold Spring Harbor Laboratory Press 2022-02-15 <![CDATA[ Integrating phylogenetic and functional data in microbiome studies ]]> https://biorxiv.org/content/10.1101/2022.02.21.480893v1?rss=1 Douglas, G. M. Hayes, M. G. Langille, M. G. I. Borenstein, E. 2022-02-22 doi:10.1101/2022.02.21.480893 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Spatiotemporal growth pattern during plant nutation implies fast dynamics for cell wall mechanics and chemistry: a multiscale study in Averrhoa carambola ]]> https://biorxiv.org/content/10.1101/2022.02.22.481493v1?rss=1 Riviere, M. Peaucelle, A. Derr, J. Douady, S. 2022-02-24 doi:10.1101/2022.02.22.481493 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Saliva metabolome alterations after acute stress ]]> https://biorxiv.org/content/10.1101/2022.02.24.480641v1?rss=1 Morgan, L. Birkler, R. I. D. Shaham-Niv, S. Dong, Y. Wachsman, T. Carmi, L. Yakobson, B. Adler-Abramovich, L. Cohen, H. Zohar, J. Bateson, M. Gazit, E. 2022-02-24 doi:10.1101/2022.02.24.480641 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Clinically oriented prediction of patient response to targeted and immunotherapies from the tumor transcriptome ]]> https://biorxiv.org/content/10.1101/2022.02.27.481627v1?rss=1 Dinstag, G. Shulman, E. D. Elis, E. Ben-Zvi, D. S. Tirosh, O. Maimon, E. Meilijson, I. Elalouf, E. Schiff, E. Hoang, D.-T. Sinha, S. Nair, N. U. Sang Lee, J. Schaffer, A. A. Ronai, Z. Juric, D. Apolo, A. B. Dahut, W. L. Lipkowitz, S. Berger, R. Kurzrock, R. Papanicolau-Sengos, A. Karzai, F. Gilbert, M. R. Aldape, K. Rajagopal, P. S. Beker, T. Ruppin, E. Aharonov, R. 2022-03-01 doi:10.1101/2022.02.27.481627 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Sleep-like changes in neural processing emerge during sleep deprivation in early auditory cortex ]]> https://biorxiv.org/content/10.1101/2022.03.06.483154v1?rss=1 Marmelshtein, A. Nir, Y. 2022-03-07 doi:10.1101/2022.03.06.483154 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Loss of tumor suppressor WWOX enhances RAS activity in pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2022.03.10.483835v1?rss=1 Husanie, H. Abu-Remaileh, M. Abu-Tair, L. Safadi, H. Atlan, K. Golan, T. Aqeilan, R. I. 2022-03-12 doi:10.1101/2022.03.10.483835 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ A connectomics-based taxonomy of mammals ]]> https://biorxiv.org/content/10.1101/2022.03.11.483995v1?rss=1 Suarez, L. E. Yovel, Y. van den Heuvel, M. E. Sporns, O. Assaf, Y. Lajoie, G. Misic, B. 2022-03-12 doi:10.1101/2022.03.11.483995 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ A passive computational marker for individual differences in non-reinforced learning ]]> https://biorxiv.org/content/10.1101/2022.03.20.484477v1?rss=1 Salomon, T. Itzkovitch, A. Daw, N. D. Schonberg, T. 2022-03-21 doi:10.1101/2022.03.20.484477 Cold Spring Harbor Laboratory Press 2022-03-21 <![CDATA[ Distinct gene programs underpinning 'disease tolerance' and 'resistance' in influenza virus infection ]]> https://biorxiv.org/content/10.1101/2022.03.22.485254v1?rss=1 Cohn, O. Yankovitz, G. Peshes-Yaloz, N. Steuerman, Y. Frishberg, A. Brandes, R. Mandelboim, M. R. Hamilton, J. Hagai, T. Amit, I. G. Netea, M. Hacohen, N. A. Iraqi, F. Bacharach, E. Gat-Viks, I. 2022-03-22 doi:10.1101/2022.03.22.485254 Cold Spring Harbor Laboratory Press 2022-03-22 <![CDATA[ S6K1 phosphorylates Cdk1 and MSH6 to regulate DNA repair. ]]> https://biorxiv.org/content/10.1101/2022.03.25.485744v1?rss=1 Amar-Schwartz, A. Ben Hur, V. Jbara, A. Cohen, Y. Barnabas, G. D. Siegfried, Z. Mashahreh, B. Hassouna, F. Shilo, A. Abu-Odeh, M. Berger, M. Wiener, R. Aqeilan, R. I. Geiger, T. Karni, R. 2022-03-27 doi:10.1101/2022.03.25.485744 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Differences in homologous recombination and maintenance of heteropolyploidy between Haloferax volcanii and Haloferax mediterranei ]]> https://biorxiv.org/content/10.1101/2022.03.26.485934v1?rss=1 Altman, N. Dattani, A. Sharon, I. Shtifman-Segal, E. Robinzon, S. Gophna, U. Allers, T. 2022-03-27 doi:10.1101/2022.03.26.485934 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Convergent epitope specificities, V gene usage and public clones elicited by primary exposure to SARS-CoV-2 variants ]]> https://biorxiv.org/content/10.1101/2022.03.28.486152v1?rss=1 Lima, N. S. Mukhamedova, M. Johnston, T. S. Wagner, D. A. Henry, A. R. Wang, L. Yang, E. S. Zhang, Y. Birungi, K. Black, W. P. O'Dell, S. Schmidt, S. D. Moon, D. Lorang, C. G. Zhao, B. Chen, M. Boswell, K. Roberts-Torres, J. Davis, R. L. Peyton, L. Narpala, S. R. O'Connell, S. Wang, J. Schrager, A. Talana, C. A. Leung, K. Shi, W. Khashab, R. Biber, A. Zilberman, T. Rhein, J. Vetter, S. Ahmed, A. Novik, L. Widge, A. Gordon, I. Guech, M. Teng, I.-T. Phung, E. Ruckwardt, T. Pegu, A. Misasi, J. Doria-Rose, N. A. Gaudinski, M. Koup, R. A. Kwong, P. D. M 2022-03-29 doi:10.1101/2022.03.28.486152 Cold Spring Harbor Laboratory Press 2022-03-29 <![CDATA[ Mechano-redox control of Mac-1 de-adhesion from ICAM-1 by protein disulfide isomerase promotes directional movement of neutrophils under flow ]]> https://biorxiv.org/content/10.1101/2022.03.29.486223v1?rss=1 Dupuy, A. Aponte Santamaria, C. Yeheskel, A. Gräter, F. Hogg, P. J. Passam, F. H. Chiu, J. 2022-03-30 doi:10.1101/2022.03.29.486223 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ Perturbed actin cap and nuclear morphology in primary fibroblasts of Huntington's disease patients as a new phenotypic marker for personalized drug evaluation ]]> https://biorxiv.org/content/10.1101/2022.04.03.486386v1?rss=1 Gharaba, S. Paz, O. Feld, L. Abashidze, A. Weinrab, M. Wolfenson, H. Weil, M. 2022-04-04 doi:10.1101/2022.04.03.486386 Cold Spring Harbor Laboratory Press 2022-04-04 <![CDATA[ Conformational Flexibility in Neutralization of SARS-CoV-2 by Naturally Elicited Anti-SARS-CoV-2 Antibodies ]]> https://biorxiv.org/content/10.1101/2022.04.03.486854v1?rss=1 Li, R. Mor, M. Ma, B. Clark, A. E. Alter, J. Werbner, M. Lee, J. Leibel, S. L. Carlin, A. F. Dassau, M. Gal-Tanamy, M. Croker, B. A. Xiang, Y. Freund, N. T. 2022-04-03 doi:10.1101/2022.04.03.486854 Cold Spring Harbor Laboratory Press 2022-04-03 <![CDATA[ Non-cancer stem cell-derived Fibromodulin activates Integrin-dependent Notch signaling in endothelial cells to promote tumor angiogenesis and growth ]]> https://biorxiv.org/content/10.1101/2022.04.03.486893v1?rss=1 Somasundaram, K. Sengupta, S. Mondal, M. Prasasvi, K. R. Mukherjee, A. Magod, P. Urbach, S. Friedmann-Morvinski, D. Marin, P. 2022-04-06 doi:10.1101/2022.04.03.486893 Cold Spring Harbor Laboratory Press 2022-04-06 <![CDATA[ The natural diversity of the yeast proteome reveals chromosome-wide dosage compensation in aneuploids ]]> https://biorxiv.org/content/10.1101/2022.04.06.487392v1?rss=1 Muenzner, J. Trebulle, P. Agostini, F. Messner, C. B. Steger, M. Lehmann, A. Caudal, E. Egger, A.-S. Amari, F. Barthel, N. De Chiara, M. Muelleder, M. Demichev, V. Liti, G. Schacherer, J. Gossmann, T. Berman, J. Ralser, M. 2022-04-08 doi:10.1101/2022.04.06.487392 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ COP I and II dependent trafficking controls ER-associated degradation ]]> https://biorxiv.org/content/10.1101/2022.04.07.487480v1?rss=1 Ogen-Shtern, N. Chang, C. Saad, H. Mazkereth, N. Patel, C. Shenkman, M. Lederkremer, G. Z. 2022-04-08 doi:10.1101/2022.04.07.487480 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Quantitative analysis of C. elegans transcripts by Nanopore direct-cDNA sequencing reveals terminal hairpins in non trans-spliced mRNAs ]]> https://biorxiv.org/content/10.1101/2022.04.14.488332v1?rss=1 Bernard, F. Dargere, D. Rechavi, O. Dupuy, D. 2022-04-14 doi:10.1101/2022.04.14.488332 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ 3D printed SAXS chamber for controlled in-situ dialysis and optical characterization ]]> https://biorxiv.org/content/10.1101/2022.04.19.488724v1?rss=1 Ehm, T. Philipp, J. Barkey, M. Ober, M. Brinkop, A. T. Simml, D. von Westphalen, M. Nickel, B. Beck-Barkai, R. Raedler, J. O. 2022-04-19 doi:10.1101/2022.04.19.488724 Cold Spring Harbor Laboratory Press 2022-04-19 <![CDATA[ Matrix stiffness regulates Notch signaling activity in endothelial cells ]]> https://biorxiv.org/content/10.1101/2022.04.20.488899v1?rss=1 Kretschmer, M. Mamistvalov, R. Sprinzak, D. Vollmar, A. M. Zahler, S. 2022-04-20 doi:10.1101/2022.04.20.488899 Cold Spring Harbor Laboratory Press 2022-04-20 <![CDATA[ Functional Comparison Between Endogenous and Synthetic Notch Systems ]]> https://biorxiv.org/content/10.1101/2022.04.24.489295v1?rss=1 Khamaisi, B. Luca, V. C. Blacklow, S. C. Sprinzak, D. 2022-04-24 doi:10.1101/2022.04.24.489295 Cold Spring Harbor Laboratory Press 2022-04-24 <![CDATA[ Predicting individual skill learning, a cautionary tale ]]> https://biorxiv.org/content/10.1101/2022.04.24.489296v1?rss=1 Abeles, D. Herszage, J. Shahar, M. Censor, N. 2022-04-26 doi:10.1101/2022.04.24.489296 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ Hippocampal cAMP-dependent synaptic potentiation, ERK-dependent immediate-early gene activation, and context-dependent fear conditioning in mice are linked through dependence on the guanine nucleotide exchange factor RapGEF2 ]]> https://biorxiv.org/content/10.1101/2022.04.30.490162v1?rss=1 Jiang, S. Z. Shahoha, M. Tejeda, H. A. Ashery, U. Eiden, L. E. 2022-05-01 doi:10.1101/2022.04.30.490162 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Hybrid offspring of C57BL/6J mice exhibit improved properties for neurobehavioral research ]]> https://biorxiv.org/content/10.1101/2022.05.03.490527v1?rss=1 Sloin, H. E. Bikovski, L. Levi, A. Amber-Vitos, O. Katz, T. Spivak, L. Someck, S. Gattegno, R. Sivroni, S. Sjulson, L. Stark, E. 2022-05-04 doi:10.1101/2022.05.03.490527 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ The MIX domain is required for T6SS-mediated effector secretion ]]> https://biorxiv.org/content/10.1101/2022.05.04.489851v1?rss=1 Fridman, C. M. Jana, B. Ben-Yaakov, R. Bosis, E. Salomon, D. 2022-05-04 doi:10.1101/2022.05.04.489851 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ A versatile, chemically-controlled DNA binding switch enables temporal modulation of Cas9-based effectors ]]> https://biorxiv.org/content/10.1101/2022.05.10.491425v1?rss=1 Wei, C. T. Peleg, O. Borenstein, E. Maly, D. J. Fowler, D. 2022-05-11 doi:10.1101/2022.05.10.491425 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Antisense pairing and SNORD13 structure guide RNA cytidine acetylation ]]> https://biorxiv.org/content/10.1101/2022.05.12.491732v1?rss=1 Thalalla Gamage, S. Bortolin-Cavaille, M.-L. Link, C. N. Bryson, K. M. Sas-Chen, A. Schwartz, S. Cavaille, J. Meier, J. L. 2022-05-13 doi:10.1101/2022.05.12.491732 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Melanocyte-secreted Fibromodulin constrains skin inflammation in mice injected with lupus serum ]]> https://biorxiv.org/content/10.1101/2022.05.13.491848v1?rss=1 Halasi, M. Nyska, A. Rubin, L. Tal, Y. Tsokos, G. C. Adini, I. 2022-05-14 doi:10.1101/2022.05.13.491848 Cold Spring Harbor Laboratory Press 2022-05-14 <![CDATA[ Aspergillus fumigatus can exhibit persistence to the fungicidal drug voriconazole ]]> https://biorxiv.org/content/10.1101/2022.05.16.491816v1?rss=1 Scott, J. Valero, C. Mato-Lopez, A. Donaldson, I. J. Roldan, A. Chown, H. Van-Rhijn, N. Gago, S. Furukawa, T. Mogorovsky, A. Ben Ami, R. Bowyer, P. Osherov, N. Fontaine, T. Goldman, G. H. Mellado, E. Bromley, M. Amich, J. 2022-05-16 doi:10.1101/2022.05.16.491816 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ Engineered Riboswitch Nano-carriers as a Possible Disease-Modifying Treatment for Metabolic Disorders ]]> https://biorxiv.org/content/10.1101/2022.05.16.492066v1?rss=1 Zilberzwige-Tal, S. Gazit, D. Adsi, H. Gartner, M. Behl, R. Laor, D. Gazit, E. 2022-05-16 doi:10.1101/2022.05.16.492066 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ Investigating And Modeling the Factors that Effects the Performance of Genetic Circuits ]]> https://biorxiv.org/content/10.1101/2022.05.16.492150v1?rss=1 Zilberzwige-Tal, S. Fontanarrosa, P. Bychenko, D. Dorfan, Y. Gazit, E. Myers, C. J. 2022-05-17 doi:10.1101/2022.05.16.492150 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ S. cerevisiae cells can grow without the Pds5 cohesin subunit ]]> https://biorxiv.org/content/10.1101/2022.05.21.492904v1?rss=1 Choudhary, K. Itzkovich, Z. Alonso-Perez, E. Bishara, H. Dunn, B. Sherlock, G. Kupiec, M. 2022-05-21 doi:10.1101/2022.05.21.492904 Cold Spring Harbor Laboratory Press 2022-05-21 <![CDATA[ Pleural macrophages promote recovery from influenza virus infection ]]> https://biorxiv.org/content/10.1101/2022.05.25.493482v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@1e8880borg.highwire.dtl.DTLVardef@13b987dorg.highwire.dtl.DTLVardef@19856f9org.highwire.dtl.DTLVardef@76277d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Stumpff, J. P. Kim, S. Y. Forero, A. Nishida, A. Steuerman, Y. Gat-Viks, I. Nair, M. G. Morrison, J. 2022-06-03 doi:10.1101/2022.05.25.493482 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Autophagy controls mucus secretion from intestinal goblet cells by alleviating ER stress ]]> https://biorxiv.org/content/10.1101/2022.05.26.493604v1?rss=1 Naama, M. Telpaz, S. Awad, A. Ben-Simon, S. Harshuk-Shabso, S. Modilevsky, S. Rubin, E. Sawaed, J. Zelik, L. Zigdon, M. Asulin, N. Turjeman, S. Werbner, M. Wongkuna, S. Schroeder, B. Nyska, A. Nuriel-Ohayon, M. Bel, S. 2022-05-29 doi:10.1101/2022.05.26.493604 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Acute expression of human APOBEC3B in mice causes lethality associated with RNA editing ]]> https://biorxiv.org/content/10.1101/2022.06.01.494353v1?rss=1 Alonso de la Vega, A. Temiz, N. A. Tasakis, R. Somogyi, K. Reuveni, E. Ben-David, U. Stenzinger, A. Poth, T. Papavasiliou, F. N. Harris, R. S. Sotillo, R. 2022-06-01 doi:10.1101/2022.06.01.494353 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ Tomato brassinosteroid-signaling kinase Bsk830 is a component of flagellin signaling that regulates pre-invasion immunity ]]> https://biorxiv.org/content/10.1101/2022.06.01.494411v1?rss=1 Sobol, G. Majhi, B. B. Pasmanik-Chor, M. Zhang, N. Roberts, H. M. Martin, G. B. Sessa, G. 2022-06-03 doi:10.1101/2022.06.01.494411 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Transmembrane proteins tetraspanin 4 and CD9 sense membrane curvature ]]> https://biorxiv.org/content/10.1101/2022.06.02.494291v1?rss=1 Dharan, R. Goren, S. Cheppali, S. K. Shendrik, P. Brand, G. Yu, L. Kozlov, M. M. Sorkin, R. 2022-06-03 doi:10.1101/2022.06.02.494291 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Lateral Axonal Modulation is Required for Stimulus-Specific Olfactory Conditioning in Drosophila ]]> https://biorxiv.org/content/10.1101/2022.06.02.494466v1?rss=1 Manoim, J. E. Davidson, A. M. Weiss, S. Hige, T. Parnas, M. 2022-06-03 doi:10.1101/2022.06.02.494466 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Alcohol-specific transcriptional dynamics of memory reconsolidation ]]> https://biorxiv.org/content/10.1101/2022.06.09.495161v1?rss=1 Goltseker, K. Garay, P. Iwase, S. Barak, S. 2022-06-12 doi:10.1101/2022.06.09.495161 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ MHC class II-restricted antigen presentation is required to prevent dysfunction of cytotoxic T cells by blood-borne myeloids in brain tumors ]]> https://biorxiv.org/content/10.1101/2022.06.10.495502v1?rss=1 View larger version (46K): org.highwire.dtl.DTLVardef@1fbedc7org.highwire.dtl.DTLVardef@b7dc3aorg.highwire.dtl.DTLVardef@db7fe6org.highwire.dtl.DTLVardef@aa06b7_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kilian, M. Sheinin, R. Tan, C. L. Kraemer, C. Friedrich, M. Kaminitz, A. Sanghvi, K. Lindner, K. Cichon, F. Jung, S. Jaehne, K. Ratliff, M. Prins, R. von Deimling, A. Wick, W. Madi, A. Bunse, L. Platten, M. 2022-06-12 doi:10.1101/2022.06.10.495502 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Exogenous Nav1.1 activity in excitatory and inhibitory neurons reverts Dravet syndrome comorbidities when delivered post-symptom onset in mice with Dravet ]]> https://biorxiv.org/content/10.1101/2022.06.10.495591v1?rss=1 Fadila, S. Beucher, B. Dopeso-Reyes, I. G. Mavashov, A. Brusel, M. Anderson, K. Goldberg, E. M. Ricobaraza, A. Hernandez-Alcoceba, R. Kremer, E. J. Rubinstein, M. 2022-06-12 doi:10.1101/2022.06.10.495591 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Genomic alterations drive brain metastases formation in colorectal cancer: The role of IRS2 ]]> https://biorxiv.org/content/10.1101/2022.06.10.495658v1?rss=1 Greenberg, I. Sokol, E. Klein Goldberg, A. Simkin, D. Benhamou, M. Bar-Shira, S. Raz, M. Grossman, R. Yeini, E. Ofek, P. Liang, B. Satchi-Fainaro, R. Reuveni, H. Rubinek, T. Wolf, I. 2022-06-12 doi:10.1101/2022.06.10.495658 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Noise-mediated self-organization in mutually shading sunflowers ]]> https://biorxiv.org/content/10.1101/2022.06.11.495747v1?rss=1 Nguyen, C. Dromi, I. Kempinski, A. Gall, G. E. C. Peleg, O. Meroz, Y. 2022-06-13 doi:10.1101/2022.06.11.495747 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ Distributing task-related neural activity across a cortical networkthrough task-independent connections ]]> https://biorxiv.org/content/10.1101/2022.06.17.496618v1?rss=1 Kim, C. Finkelstein, A. Chow, C. C. Svoboda, K. Darshan, R. 2022-06-18 doi:10.1101/2022.06.17.496618 Cold Spring Harbor Laboratory Press 2022-06-18 <![CDATA[ Molecular origins of genome instability following a single chromosome mis-segregation event ]]> https://biorxiv.org/content/10.1101/2022.06.19.496702v1?rss=1 De Feudis, G. Garribba, L. Martis, V. Galli, M. Dumont, M. Eliezer, Y. Wardenaar, R. Ippolito, M. R. Iyer, D. R. Tijhuis, A. E. Spierings, D. C. Schubert, M. Rhind, N. Foijer, F. Ben-David, U. Fachinetti, D. Doksani, Y. Santaguida, S. 2022-06-19 doi:10.1101/2022.06.19.496702 Cold Spring Harbor Laboratory Press 2022-06-19 <![CDATA[ Polyalanine disease mutations impair UBA6-dependent ubiquitination ]]> https://biorxiv.org/content/10.1101/2022.06.20.496786v1?rss=1 Amer-Sarsour, F. Falik, D. Berdichevsky, Y. Kordonsky, A. Prag, G. Vatine, G. Ashkenazi, A. 2022-06-20 doi:10.1101/2022.06.20.496786 Cold Spring Harbor Laboratory Press 2022-06-20 <![CDATA[ De Novo, Post-Zygotic, Inter-Tissue Mosaicism of Cell Autonomous ADNP Mutations in Autistic Individuals: Restricted Environmental Contribution ]]> https://biorxiv.org/content/10.1101/2022.06.21.496616v1?rss=1 Mohiuddin, M. Marusic, Z. Anicic, M. Anke, V. D. Cappuyns, E. Ludovico, R. Vitriolo, A. Kleiman, G. H. Grigg, I. Testa, G. Gozes, I. Kooy, R. F. Pearson, C. E. 2022-06-24 doi:10.1101/2022.06.21.496616 Cold Spring Harbor Laboratory Press 2022-06-24 <![CDATA[ Mapping molecular determinants of Cav2.2 inhibition by RGK proteins and homologs in Xenopus oocytes ]]> https://biorxiv.org/content/10.1101/2022.06.21.496996v1?rss=1 Sasson, Y. Subramaniam, S. Buki, T. Almagor, L. Chomsky-Hecht, O. Katz, M. Puhl, H. Ikeda, S. R. Dascal, N. Hirsch, J. 2022-06-24 doi:10.1101/2022.06.21.496996 Cold Spring Harbor Laboratory Press 2022-06-24 <![CDATA[ Regulation of heme utilization and homeostasis in Candida albicans ]]> https://biorxiv.org/content/10.1101/2022.06.22.497059v1?rss=1 Andrawes, N. Weissman, Z. Pinsky, M. Moshe, S. Berman, J. Kornitzer, D. 2022-06-22 doi:10.1101/2022.06.22.497059 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ Intense sexual conflict affects the female choice strategy in the gregarious desert locust ]]> https://biorxiv.org/content/10.1101/2022.06.26.497525v1?rss=1 Golov, Y. Lavy, O. Halon, E. Rillich, J. Ayali, A. Harari, A. 2022-06-29 doi:10.1101/2022.06.26.497525 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Identification of factors mediating the signaling convergenceof multiple receptors following cell-cell interaction ]]> https://biorxiv.org/content/10.1101/2022.06.27.497758v1?rss=1 Sheinin, R. Dulberg, S. Kaminitz, A. Madi, A. Sharan, R. 2022-06-29 doi:10.1101/2022.06.27.497758 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Polymorphisms Predicting Phylogeny in Hepatitis B Virus (HBV) ]]> https://biorxiv.org/content/10.1101/2022.07.05.498824v1?rss=1 Lourenco, J. McNaughton, A. L. Pley, C. Obolski, U. L. Gupta, S. Matthews, P. C. 2022-07-05 doi:10.1101/2022.07.05.498824 Cold Spring Harbor Laboratory Press 2022-07-05 <![CDATA[ Tetraspanin 4 mediates migrasome formation via a two-stage mechanism ]]> https://biorxiv.org/content/10.1101/2022.07.11.499540v1?rss=1 Dharan, R. Huang, Y. Cheppali, S. K. Goren, S. Shendrik, P. Kozlov, M. M. Yu, L. Sorkin, R. 2022-07-11 doi:10.1101/2022.07.11.499540 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Correspondence between the layered structure of deep language models and temporal structure of natural language processing in the human brain ]]> https://biorxiv.org/content/10.1101/2022.07.11.499562v1?rss=1 Goldstein, A. Ham, E. Nastase, S. A. Zada, Z. Dabush, A. Bobbi Aubrey, B. Schain, M. Gazula, H. Feder, A. Doyle, W. Devore, S. Dugan, P. Friedman, D. Brenner, M. Hassidim, A. Devinsky, O. Flinker, A. Levy, O. Hasson, U. 2022-07-11 doi:10.1101/2022.07.11.499562 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ KDM6A loss sensitizes human acute myeloid leukemia to PARP and BCL2 inhibition ]]> https://biorxiv.org/content/10.1101/2022.07.12.498585v1?rss=1 Boila, L. D. Ghosh, S. Bandyopadhyay, S. K. Jin, L. Murison, A. Zeng, A. G. X. Shaikh, W. Bhowmik, S. Muddineni, S. S. N. A. Biswas, M. Sinha, S. Chatterjee, S. S. Mbong, N. Gan, O. I. Bose, A. Chakraborty, S. Arruda, A. Kennedy, J. A. Mitchell, A. Lechman, E. R. Banerjee, D. Milyavsky, M. Minden, M. D. Dick, J. E. Sengupta, A. 2022-07-13 doi:10.1101/2022.07.12.498585 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Choice-Induced Preference Change under a Sequential Sampling Model Framework ]]> https://biorxiv.org/content/10.1101/2022.07.15.500254v1?rss=1 Lee, D. G. Pezzulo, G. 2022-07-18 doi:10.1101/2022.07.15.500254 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Sensory neurons safeguard from mutational inheritance by controlling the CEP-1/p53-mediated DNA damage response in primordial germ cells ]]> https://biorxiv.org/content/10.1101/2022.07.19.500657v1?rss=1 Uszkoreit, S. Meyer, D. H. Rechavi, O. Schumacher, B. 2022-07-20 doi:10.1101/2022.07.19.500657 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ A vast world of viroid-like circular RNAs revealed by mining metatranscriptomes ]]> https://biorxiv.org/content/10.1101/2022.07.19.500677v1?rss=1 Lee, B. D. Neri, U. Roux, S. Wolf, Y. I. Camargo, A. P. Krupovic, M. Simmonds, P. Kyrpides, N. Gophna, U. Dolja, V. V. Koonin, E. V. 2022-07-20 doi:10.1101/2022.07.19.500677 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Cis-inhibition suppresses basal Notch signalling during sensory organ precursor selection ]]> https://biorxiv.org/content/10.1101/2022.07.19.500683v1?rss=1 Troost, T. Binshtok, U. Sprinzak, D. Klein, T. 2022-07-20 doi:10.1101/2022.07.19.500683 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Candida albicans exhibits heterogeneous and adaptive cytoprotective responses to anti-fungal compounds ]]> https://biorxiv.org/content/10.1101/2022.07.20.500774v1?rss=1 Dumeaux, V. Massahi, S. Bettauer, V. Khurdia, S. S. Costa, A. C. B. P. Omran, R. P. Simpson, S. Xie, J. L. Whiteway, M. Berman, J. Hallett, M. T. 2022-07-21 doi:10.1101/2022.07.20.500774 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Harnessing machine translation methods for sequence alignment ]]> https://biorxiv.org/content/10.1101/2022.07.22.501063v1?rss=1 Dotan, E. Belinkov, Y. Avram, O. Wygoda, E. Ecker, N. Alburquerque, M. Keren, O. Loewenthal, G. Pupko, T. 2022-07-23 doi:10.1101/2022.07.22.501063 Cold Spring Harbor Laboratory Press 2022-07-23 <![CDATA[ The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns ]]> https://biorxiv.org/content/10.1101/2022.07.25.501396v1?rss=1 Loewenthal, G. Wygoda, E. Nagar, N. Glick, L. Mayrose, I. Pupko, T. 2022-07-25 doi:10.1101/2022.07.25.501396 Cold Spring Harbor Laboratory Press 2022-07-25 <![CDATA[ Proteins with multiple G protein-coupled receptor domains ]]> https://biorxiv.org/content/10.1101/2022.07.26.501653v1?rss=1 Isildayancan, K. Kessel, A. Solan, R. Kolodny, R. Ben-Tal, N. 2022-07-28 doi:10.1101/2022.07.26.501653 Cold Spring Harbor Laboratory Press 2022-07-28 <![CDATA[ The hidden secrets of the dental calculus: Calibration of a mass spectrometry protocol for dental calculus protein analysis ]]> https://biorxiv.org/content/10.1101/2022.07.27.501661v1?rss=1 Bender, O. Tzabag, D. Gavish, T. Meyrom, N. Zamir, N. May, H. Sarig, R. Bar, D. Z. 2022-07-27 doi:10.1101/2022.07.27.501661 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ Antibody recognition of CD4-induced open HIV-1 Env trimers ]]> https://biorxiv.org/content/10.1101/2022.07.27.501785v1?rss=1 Yang, Z. Dam, K.-M. A. Gershoni, J. M. Zolla-Pazner, S. Bjorkman, P. J. 2022-07-28 doi:10.1101/2022.07.27.501785 Cold Spring Harbor Laboratory Press 2022-07-28 <![CDATA[ Clearing the Fungal FoG: Perseverance, a property distinct from resistance, is associated with clinical persistence ]]> https://biorxiv.org/content/10.1101/206359v1?rss=1 Rosenberg, A. Ene, I. V. Dahan, A. Segal, E. S. Colombo, A. L. Bennett, R. J. Berman, J. G. 2017-10-20 doi:10.1101/206359 Cold Spring Harbor Laboratory Press 2017-10-20 <![CDATA[ Redundancy principle for optimal random search in biology ]]> https://biorxiv.org/content/10.1101/210443v1?rss=1 Schuss, Z. Basnayake, K. Holcman, D. 2017-10-27 doi:10.1101/210443 Cold Spring Harbor Laboratory Press 2017-10-27 <![CDATA[ WorMachine: Machine Learning-Based Phenotypic Analysis Tool for Worms ]]> https://biorxiv.org/content/10.1101/211359v1?rss=1 Hakim, A. Mor, Y. Toker, I. A. Levine, A. Markovitz, Y. Rechavi, O. 2017-10-31 doi:10.1101/211359 Cold Spring Harbor Laboratory Press 2017-10-31 <![CDATA[ Using experimental data as a voucher for study pre-registration ]]> https://biorxiv.org/content/10.1101/213439v1?rss=1 Mazor, M. Mazor, N. Mukamel, R. 2017-11-04 doi:10.1101/213439 Cold Spring Harbor Laboratory Press 2017-11-04 <![CDATA[ CRISPys: Optimal sgRNA design for editing multiple members of a gene family using the CRISPR system ]]> https://biorxiv.org/content/10.1101/221341v1?rss=1 Hyams, G. Abadi, S. Avni, A. Halperin, E. Shani, E. Mayrose, I. 2017-11-17 doi:10.1101/221341 Cold Spring Harbor Laboratory Press 2017-11-17 <![CDATA[ The feasibility and stability of large complex biological networks: a random matrix approach ]]> https://biorxiv.org/content/10.1101/223651v1?rss=1 Stone, L. 2017-11-24 doi:10.1101/223651 Cold Spring Harbor Laboratory Press 2017-11-24 <![CDATA[ The Functional Connectivity between the Locust Leg Pattern Generating Networks and the Subesophageal Ganglion Higher Motor Center ]]> https://biorxiv.org/content/10.1101/226167v1?rss=1 Knebel, D. Rillich, J. Nadler, L. Pflueger, H. J. Ayali, A. 2017-11-28 doi:10.1101/226167 Cold Spring Harbor Laboratory Press 2017-11-28 <![CDATA[ A-to-I RNA editing uncovers hidden signals of adaptive genome evolution in animals ]]> https://biorxiv.org/content/10.1101/228734v1?rss=1 Popitsch, N. Huber, C. D. Buchumenski, I. Eisenberg, E. Jantsch, M. von Haeseler, A. Gallach, M. 2017-12-04 doi:10.1101/228734 Cold Spring Harbor Laboratory Press 2017-12-04 <![CDATA[ Evolution of vertical and oblique transmission under fluctuating selection ]]> https://biorxiv.org/content/10.1101/229179v1?rss=1 Ram, Y. Liberman, U. Feldman, M. W. 2017-12-04 doi:10.1101/229179 Cold Spring Harbor Laboratory Press 2017-12-04 <![CDATA[ Generation of Variation and Mean Fitness Increase: Necessity is the Mother of Genetic Invention ]]> https://biorxiv.org/content/10.1101/229351v1?rss=1 Ram, Y. Altenberg, L. Liberman, U. Feldman, M. W. 2017-12-05 doi:10.1101/229351 Cold Spring Harbor Laboratory Press 2017-12-05 <![CDATA[ Pivotal roles of PCNA loading and unloading on heterochromatin function ]]> https://biorxiv.org/content/10.1101/232181v1?rss=1 Janke, R. King, G. Kupiec, M. Rine, J. 2017-12-11 doi:10.1101/232181 Cold Spring Harbor Laboratory Press 2017-12-11 <![CDATA[ Who is the host of the host-associated microbiome? Colony-level dynamics overshadow individual-level characteristics in the fur microbiome of a social mammal, the Egyptian fruit-bat ]]> https://biorxiv.org/content/10.1101/232934v1?rss=1 kolodny, o. Weinberg, M. Reshef, L. Harten, L. Hefetz, A. Gophna, U. Feldman, M. W. Yovel, Y. 2017-12-12 doi:10.1101/232934 Cold Spring Harbor Laboratory Press 2017-12-12 <![CDATA[ Exposure to the oral host niche yields rapid phenotypic and genotypic diversification in Candida albicans ]]> https://biorxiv.org/content/10.1101/254201v1?rss=1 Forche, A. Cromie, G. Gerstein, A. C. Solis, N. V. Pisithkul, T. Srifa, W. Jeffery, E. Filler, S. G. Dudley, A. Berman, J. 2018-01-25 doi:10.1101/254201 Cold Spring Harbor Laboratory Press 2018-01-25 <![CDATA[ Systematic detection of amino acid substitutions in proteome reveals a mechanistic basis of ribosome errors ]]> https://biorxiv.org/content/10.1101/255943v1?rss=1 Mordret, E. Yehonadav, A. Barnabas, G. D. Cox, J. Dahan, O. Geiger, T. Lindner, A. B. Pilpel, Y. 2018-01-29 doi:10.1101/255943 Cold Spring Harbor Laboratory Press 2018-01-29 <![CDATA[ Estimating Heritability and Genetic Correlation in Case Control Studies Directly and with Summary Statistics ]]> https://biorxiv.org/content/10.1101/256388v1?rss=1 Weissbrod, O. Flint, J. Rosset, S. 2018-02-03 doi:10.1101/256388 Cold Spring Harbor Laboratory Press 2018-02-03 <![CDATA[ Asymmetric Overlap in Neuronal Sensation Constraints Rational Choice in C. elegans ]]> https://biorxiv.org/content/10.1101/257535v1?rss=1 Cohen, D. Volovich, M. Zeevi, Y. Louie, K. Levy, D. J. Rechavi, O. 2018-01-31 doi:10.1101/257535 Cold Spring Harbor Laboratory Press 2018-01-31 <![CDATA[ Candida albicans dispersed cells signify a developmental state distinct from biofilm and planktonic phases ]]> https://biorxiv.org/content/10.1101/258608v1?rss=1 Uppuluri, P. Acosta Zakvidar, M. Anderson, M. Dunn, M. Berman, J. Lopez Ribot, J. L. Koehler, J. 2018-02-01 doi:10.1101/258608 Cold Spring Harbor Laboratory Press 2018-02-01 <![CDATA[ Genome-wide epigenetic profiling of 5-hydroxymethylcytosine by long-read optical mapping ]]> https://biorxiv.org/content/10.1101/260166v1?rss=1 Gabrieli, T. Sharim, H. Nifker, G. Jeffet, J. Shahal, T. Arielly, R. Levy-Sakin, M. Hoch, L. Arbib, N. Michaeli, Y. Ebenstein, Y. 2018-02-05 doi:10.1101/260166 Cold Spring Harbor Laboratory Press 2018-02-05 <![CDATA[ The subesophageal ganglion modulates locust inter-leg sensory-motor interactions via contralateral pathways ]]> https://biorxiv.org/content/10.1101/261164v1?rss=1 Knebel, D. Woerner, J. Rillich, J. Nadler, L. Ayali, A. Couzin-Fuchs, E. 2018-02-07 doi:10.1101/261164 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ A T7 phage factor required for managing RpoS in Escherichia coli ]]> https://biorxiv.org/content/10.1101/262279v1?rss=1 Tabib-Salazar, A. Liu, B. Barkar, D. Burchell, L. Qimron, U. Matthews, S. Wigneshweraraj, R. 2018-02-08 doi:10.1101/262279 Cold Spring Harbor Laboratory Press 2018-02-08 <![CDATA[ DNA methylation dynamics during embryonic development and postnatal maturation of the mouse auditory organ of Corti ]]> https://biorxiv.org/content/10.1101/262832v1?rss=1 Avraham, K. B. Yizhar-Barnea, O. Valensisi, C. Kishore, K. Jayavelu, N. D. Andrus, C. Koffler-Brill, T. Ushakov, K. Perl, K. Noy, Y. Bhonker, Y. Pelizzola, M. Hawkins, R. D. 2018-02-10 doi:10.1101/262832 Cold Spring Harbor Laboratory Press 2018-02-10 <![CDATA[ Efflux Pumps Represent Possible Evolutionary Convergence onto the Beta Barrel Fold ]]> https://biorxiv.org/content/10.1101/268029v1?rss=1 Franklin, M. W. Nepomnyachiy, S. Feehan, R. Ben-Tal, N. Kolodny, R. Slusky, J. S. G. 2018-02-19 doi:10.1101/268029 Cold Spring Harbor Laboratory Press 2018-02-19 <![CDATA[ Spacing of Cue-approach Training Leads to Better Maintenance of Behavioral Change ]]> https://biorxiv.org/content/10.1101/268821v1?rss=1 Bakkour, A. Botvinik Nezer, R. Cohen, N. Hover, A. M. Poldrack, R. A. Schonberg, T. 2018-02-21 doi:10.1101/268821 Cold Spring Harbor Laboratory Press 2018-02-21 <![CDATA[ Big data analysis of mitochondrial DNA substitution models: A regression approach elucidating the effects of codon position and neighboring nucleotides ]]> https://biorxiv.org/content/10.1101/272922v1?rss=1 Levinstein Hallak, K. Tzur, S. Rosset, S. 2018-02-27 doi:10.1101/272922 Cold Spring Harbor Laboratory Press 2018-02-27 <![CDATA[ Gut microbiota density influences host physiology and is shaped by host and microbial factors ]]> https://biorxiv.org/content/10.1101/277095v1?rss=1 Contijoch, E. Britton, G. J. Yang, C. Mogno, I. Li, Z. Ng, R. Llewellyn, S. R. Hira, S. Johnson, C. Rabinowitz, K. M. Barkan, R. Dotan, I. Hirten, R. P. Fu, S.-C. Luo, Y. Yang, N. Luong, T. Labrias, P. R. Lira, S. Peter, I. Grinspan, A. Clemente, J. C. Kosoy, R. Kim-Schulze, S. Qin, X. Castillo, A. Hurley, A. Atreja, A. Rogers, J. Fasihuddin, F. Saliaj, M. Nolan, A. Reyes-Mercedes, P. Rodriguez, C. Aly, S. Santa-Cruz, K. Peters, L. A. Suarez-Farinas, M. Huang, R. Hao, K. Zhu, J. Zhang, B. Losic, B. Irizar, H. Song, W.-M. Di Narzo, A. Wang, W. Cohe 2018-03-08 doi:10.1101/277095 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy ]]> https://biorxiv.org/content/10.1101/284240v1?rss=1 Sahu, A. Sang Lee, J. Zhang, G. Wang, Z. Tian, T. Moll, T. Kasumova, G. Miao, B. Wei, Z. Nair, N. U. Ponomarova, O. Friedman, A. Amzallag, A. Greninger, P. Egan, R. Damon, L. Frederick, D. Jerby-Arnon, L. Wagner, A. Cheng, K. Robinson, W. Park, S. G. Gardner, K. Hannenhalli, S. Gutkind, S. Boland, G. Flaherty, K. Benes, C. Herlyn, M. Bartolome, R. Ruppin, E. 2018-03-18 doi:10.1101/284240 Cold Spring Harbor Laboratory Press 2018-03-18 <![CDATA[ ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules ]]> https://biorxiv.org/content/10.1101/288399v1?rss=1 Silverbush, D. Cristea, S. Yanovich, G. Geiger, T. Beerenwinkel, N. Sharan, R. 2018-03-24 doi:10.1101/288399 Cold Spring Harbor Laboratory Press 2018-03-24 <![CDATA[ Decline in pneumococcal disease in unimmunized adults is associated with vaccine-associated protection against colonization in toddlers and preschool-aged children ]]> https://biorxiv.org/content/10.1101/293266v1?rss=1 Weinberger, D. M. Pitzer, V. E. Regev-Yochay, G. Givon-Lavi, N. Dagan, R. 2018-04-05 doi:10.1101/293266 Cold Spring Harbor Laboratory Press 2018-04-05 <![CDATA[ Evolution of Environmentally-Enforced, Repeat Protein Topology in the Outer Membrane ]]> https://biorxiv.org/content/10.1101/309393v1?rss=1 Franklin, M. W. Nepomnyaciy, S. Feehan, R. Ben-Tal, N. Kolodny, R. Slusky, J. 2018-04-27 doi:10.1101/309393 Cold Spring Harbor Laboratory Press 2018-04-27 <![CDATA[ Multisite phosphorylation regulates phenotypic variability in antibiotic tolerance ]]> https://biorxiv.org/content/10.1101/315085v1?rss=1 Libby, E. Reuveni, S. Dworkin, J. 2018-05-04 doi:10.1101/315085 Cold Spring Harbor Laboratory Press 2018-05-04 <![CDATA[ PySight: plug and play photon counting for fast intravital microscopy ]]> https://biorxiv.org/content/10.1101/316125v1?rss=1 Har-Gil, H. Golgher, L. Israel, S. Kain, D. Cheshnovksy, O. Parnas, M. Blinder, P. 2018-05-09 doi:10.1101/316125 Cold Spring Harbor Laboratory Press 2018-05-09 <![CDATA[ More is Better: Using Machine Learning Techniques and Multiple EEG Metrics to Increase Preference Prediction Above and Beyond Traditional Measurements ]]> https://biorxiv.org/content/10.1101/317073v1?rss=1 Hakim, A. Klorfeld, S. Sela, T. Friedman, D. Shabat-Simon, M. Levy, D. J. 2018-05-09 doi:10.1101/317073 Cold Spring Harbor Laboratory Press 2018-05-09 <![CDATA[ Genomic meta-analysis of the interplay between 3D chromatin organization and gene expression programs under basal and stress conditions ]]> https://biorxiv.org/content/10.1101/337766v1?rss=1 Nurick, I. Shamir, R. Elkon, R. 2018-06-03 doi:10.1101/337766 Cold Spring Harbor Laboratory Press 2018-06-03 <![CDATA[ H3K9me3 is Required for Transgenerational Inheritance of Small RNAs that Target a Unique Subset of Newly Evolved Genes ]]> https://biorxiv.org/content/10.1101/338582v1?rss=1 Lev, I. Gingold, H. Rechavi, O. 2018-06-04 doi:10.1101/338582 Cold Spring Harbor Laboratory Press 2018-06-04 <![CDATA[ Recombination between co-infecting herpesviruses occurs where replication compartments coales ]]> https://biorxiv.org/content/10.1101/345918v1?rss=1 Tomer, E. Cohen, E. M. Drayman, N. Afriaat, A. Weitzman, M. D. Zaritsky, A. Kobiler, O. 2018-06-13 doi:10.1101/345918 Cold Spring Harbor Laboratory Press 2018-06-13 <![CDATA[ Reticulate Evolutionary History of a Western Palaearctic Bat Complex Explained by Multiple mtDNA Introgressions in Secondary Contacts ]]> https://biorxiv.org/content/10.1101/348235v1?rss=1 Coraman, E. Dietz, C. Hempel, E. Gazaryan, A. Levin, E. Presetnik, P. Zagmajster, M. Mayer, F. 2018-06-15 doi:10.1101/348235 Cold Spring Harbor Laboratory Press 2018-06-15 <![CDATA[ AccuNGS: a sequencing protocol for detection of ultra-rare variants reveals extensive variation in HIV during first days of infection ]]> https://biorxiv.org/content/10.1101/349498v1?rss=1 Gelbart, M. Harari, S. Ben-Ari, Y. Kustin, T. Meir, M. Miller, D. Mor, O. Stern, A. 2018-06-18 doi:10.1101/349498 Cold Spring Harbor Laboratory Press 2018-06-18 <![CDATA[ Exploration in the Presence of Mother in Typically and Non-Typically Developing Pre-Walking Human Infants ]]> https://biorxiv.org/content/10.1101/350736v1?rss=1 Frostig, T. Alonim, H. Scheingesicht, G. Benjamini, Y. Golani, I. 2018-06-19 doi:10.1101/350736 Cold Spring Harbor Laboratory Press 2018-06-19 <![CDATA[ Neural correlates of effort-based valuation with prospective choices ]]> https://biorxiv.org/content/10.1101/357327v1?rss=1 Aridan, N. Malecek, N. Poldrack, R. Schonberg, T. 2018-06-28 doi:10.1101/357327 Cold Spring Harbor Laboratory Press 2018-06-28 <![CDATA[ Visual features contribute differently to preferences for different item categories ]]> https://biorxiv.org/content/10.1101/360172v1?rss=1 Oren, S. Sela, T. Levy, D. J. Schonberg, T. 2018-07-03 doi:10.1101/360172 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Ancestral fitness and genetic background influence diversity acquired during adaptation to low drug concentration in Candida albicans ]]> https://biorxiv.org/content/10.1101/360347v1?rss=1 Gerstein, A. C. Berman, J. 2018-07-03 doi:10.1101/360347 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Doppler-Based Algorithm for Mapping Cardiac Rotors by Induced Temperature Perturbations ]]> https://biorxiv.org/content/10.1101/362897v1?rss=1 Malki, G. Barnea, O. Tuller, T. 2018-07-05 doi:10.1101/362897 Cold Spring Harbor Laboratory Press 2018-07-05 <![CDATA[ Cardiac Spiral Wave Drifting Due to Spatial Temperature Gradients: A Numerical Study ]]> https://biorxiv.org/content/10.1101/362913v1?rss=1 Malki, G. Zlochiver, S. 2018-07-05 doi:10.1101/362913 Cold Spring Harbor Laboratory Press 2018-07-05 <![CDATA[ Perceptual and memory neural processes underlie short and long-term non-reinforced behavioral change ]]> https://biorxiv.org/content/10.1101/363044v1?rss=1 Botvinik-Nezer, R. Salomon, T. Schonberg, T. 2018-07-05 doi:10.1101/363044 Cold Spring Harbor Laboratory Press 2018-07-05 <![CDATA[ Multi-omic and multi-view clustering algorithms: review and cancer benchmark ]]> https://biorxiv.org/content/10.1101/371120v1?rss=1 Rappoport, N. Shamir, R. 2018-07-19 doi:10.1101/371120 Cold Spring Harbor Laboratory Press 2018-07-19 <![CDATA[ Ventromedial prefrontal cortex is not critical for behavior change without external reinforcement ]]> https://biorxiv.org/content/10.1101/372185v1?rss=1 Aridan, N. Pelletier, G. Fellows, L. Schonberg, T. 2018-07-19 doi:10.1101/372185 Cold Spring Harbor Laboratory Press 2018-07-19 <![CDATA[ A retrieval-counterconditioning procedure diminishes reinstatement of appetitive memories in humans ]]> https://biorxiv.org/content/10.1101/376392v1?rss=1 Gera, R. Barak, S. Schonberg, T. 2018-07-25 doi:10.1101/376392 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ Sexual behavior of the desert locust during intra- and inter-phase interactions ]]> https://biorxiv.org/content/10.1101/377903v1?rss=1 Golov, Y. Rillich, J. Douek, M. Harari, A. R. Ayali, A. 2018-07-26 doi:10.1101/377903 Cold Spring Harbor Laboratory Press 2018-07-26 <![CDATA[ Migration rather than proliferation transcriptomic signatures are strongly associated with breast cancer patient survival ]]> https://biorxiv.org/content/10.1101/379123v1?rss=1 Nair, N. U. Das, A. Rogkoti, V.-M. Fokkelman, M. Marcotte, R. Jong, C. Lee, J. S. Meilijson, I. Hannenhalli, S. Neel, B. Water, B. v. d. Devedec, S. E. L. Ruppin, E. 2018-07-29 doi:10.1101/379123 Cold Spring Harbor Laboratory Press 2018-07-29 <![CDATA[ Inhibitory muscarinic acetylcholine receptors enhance aversive olfactory conditioning in adult Drosophila ]]> https://biorxiv.org/content/10.1101/382440v1?rss=1 Bielopolski, N. Amin, H. Apostolopoulou, A. A. Rozenfeld, E. Lerner, H. Huetteroth, W. Lin, A. C. Parnas, M. 2018-08-01 doi:10.1101/382440 Cold Spring Harbor Laboratory Press 2018-08-01 <![CDATA[ A Framework for Cortical Layer Composition Analysis using Low Resolution T1 MRI Images ]]> https://biorxiv.org/content/10.1101/390112v1?rss=1 Shamir, I. Tomer, O. Baratz, Z. Tsarfaty, G. Faraggi, M. Horowitz, A. Assaf, Y. 2018-08-13 doi:10.1101/390112 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ Demography and behavior of polygyne nests of the supercolonial Cataglyphis niger: Does kinship matter? ]]> https://biorxiv.org/content/10.1101/392522v1?rss=1 Reiner Brodetzki, T. Feinerman, O. Brodetzki, G. Hefetz, A. 2018-08-16 doi:10.1101/392522 Cold Spring Harbor Laboratory Press 2018-08-16 <![CDATA[ Hidden Markov Models Lead to Higher Resolution Maps of Mutation Signature Activity in Cancer ]]> https://biorxiv.org/content/10.1101/392639v1?rss=1 Huang, X. Sason, I. Wojtowicz, D. Kim, Y.-A. Leiserson, M. Przytycka, T. M. Sharan, R. 2018-08-16 doi:10.1101/392639 Cold Spring Harbor Laboratory Press 2018-08-16 <![CDATA[ Increased frequency of travel may act to decrease the chance of a global pandemic ]]> https://biorxiv.org/content/10.1101/404871v1?rss=1 Thompson, R. Thompson, C. Pelerman, O. Gupta, S. Obolski, U. 2018-08-31 doi:10.1101/404871 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ Specific detection of cell-free DNA derived from intestinal epithelial cells using methylation patterns ]]> https://biorxiv.org/content/10.1101/409219v1?rss=1 Lehmann-Werman, R. Zick, A. Paweletz, C. Welch, M. Hubert, A. Maoz, M. Davidy, T. Magenheim, J. Piyanzin, S. Neiman, D. Moss, J. Golan, H. Israeli, E. Fischer, M. Segal, E. Grompe, M. Pikarsky, A. Golan, T. Glaser, B. Shemer, R. Wolpin, B. Dor, Y. 2018-09-05 doi:10.1101/409219 Cold Spring Harbor Laboratory Press 2018-09-05 <![CDATA[ Comparison of early effects of PCV7, PCV10 and PCV13 on S. pneumoniae (SP) nasopharyngeal carriage in a population based study; the Palestinian-Israeli Collaborative Research (PICR) ]]> https://biorxiv.org/content/10.1101/409359v1?rss=1 Abu Seir, R. Azmi, K. Hamdan, A. Namouz, H. Jaar, F. Jaber, H. Rubin, C. Doron, D. Rahav, G. Abdeen, Z. Regev-Yochay, G. 2018-09-07 doi:10.1101/409359 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ The emergence of dynamical instantaneous memory in the spontaneous activity of spatially confined neuronal assemblies in vitro ]]> https://biorxiv.org/content/10.1101/412320v1?rss=1 Piasetzky, Y. Bisio, M. Kanner, S. Goldin, M. Olivenboim, M. Ben-Jacob, E. Hanein, Y. Chiappalone, M. Barzilai, A. Bonifazi, P. 2018-09-10 doi:10.1101/412320 Cold Spring Harbor Laboratory Press 2018-09-10 <![CDATA[ Chemical signatures of honey bee group membership develop via a socially-modulated innate process ]]> https://biorxiv.org/content/10.1101/412353v1?rss=1 Vernier, C. Krupp, J. Marcus, K. Hefetz, A. Levine, J. Ben-Shahar, Y. 2018-09-09 doi:10.1101/412353 Cold Spring Harbor Laboratory Press 2018-09-09 <![CDATA[ NEMO: Cancer subtyping by integration of partial multi-omic data ]]> https://biorxiv.org/content/10.1101/415224v1?rss=1 Rappoport, N. Shamir, R. 2018-09-12 doi:10.1101/415224 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ Genome based QTL and meta-QTL analyses of thousand-kernel weight in tetraploid wheat ]]> https://biorxiv.org/content/10.1101/415240v1?rss=1 8% increase in GW compared to Svevo. Using the reference sequence for the 6A QTL region, we identified a wheat ortholog to OsGRF4, a rice gene previously associated with GW. The coding sequence of this gene (TtGRF4-A) contains four SNPs between Zavitan and Svevo, one of which reveals the Zavitan allele to be rare in a core collection of wild emmer and completely absent from the domesticated emmer genepool. Similarly, another wild emmer accession (G18-16) was found to carry a rare allele of TtGRF4-A that also positively affects GW and is characterized by a unique SNP absent from the entire core collection. These results exemplify the rich genetic diversity of wild wheat, posit TtGRF4-A as a candidate gene underlying the 6A GW QTL, and suggest that the natural Zavitan and G18-16 alleles of TtGRF4-A have potential to increase wheat yields in breeding programs. ]]> Avni, R. Oren, L. Shabtai, G. Assili, S. Pozniak, C. Hale, I. Ben-David, R. Peleg, Z. Distelfeld, A. 2018-09-12 doi:10.1101/415240 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ A seed resource for screening functionally redundant genes and isolation of new mutants impaired in CO2 and ABA responses ]]> https://biorxiv.org/content/10.1101/415976v1?rss=1 Hauser, F. Ceciliato, P. H. d. O. Lin, Y.-C. Guo, D. Gregerson, J. Abbasi, N. Youhanna, D. Park, J. Dubeaux, G. Shani, E. Poomchongkho, N. Schroeder, J. 2018-09-16 doi:10.1101/415976 Cold Spring Harbor Laboratory Press 2018-09-16 <![CDATA[ Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia ]]> https://biorxiv.org/content/10.1101/422295v1?rss=1 Feldman, M. Fernandez-Dominguez, E. Reynolds, L. Baird, D. Pearson, J. Hershkovitz, I. May, H. Goring-Morris, N. Benz, M. Gresky, J. Bianco, R. A. Fairbairn, A. Mustafaoglu, G. Stockhammer, P. W. Posth, C. Haak, W. Jeong, C. Krause, J. 2018-09-20 doi:10.1101/422295 Cold Spring Harbor Laboratory Press 2018-09-20 <![CDATA[ Disentangling unspecific and specific transgenerational immune priming components inhost-parasite interactions ]]> https://biorxiv.org/content/10.1101/429498v1?rss=1 Ben-Ami, F. Orlic, C. Regoes, R. R. 2018-09-27 doi:10.1101/429498 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ Cell-type-specific resolution epigenetics without the need for cell sorting or single-cell biology ]]> https://biorxiv.org/content/10.1101/437368v1?rss=1 Rahmani, E. Schweiger, R. Rhead, B. Criswell, L. A. Barcellos, L. F. Eskin, E. Rosset, S. Sankararaman, S. Halperin, E. 2018-10-07 doi:10.1101/437368 Cold Spring Harbor Laboratory Press 2018-10-07 <![CDATA[ Inferring Population Genetics Parameters of Evolving Viruses Using Time-series Data ]]> https://biorxiv.org/content/10.1101/437483v1?rss=1 Zinger, T. Pennings, P. S. Stern, A. 2018-10-07 doi:10.1101/437483 Cold Spring Harbor Laboratory Press 2018-10-07 <![CDATA[ Cortical microinfarcts caused by single penetrating vessel occlusion lead to widespread reorganization across the entire brain in a CX3CR1 dependent manner ]]> https://biorxiv.org/content/10.1101/437509v1?rss=1 Lubart, A. Benbenishty, A. Har-Gil, H. Laufer, H. Gdalyahu, A. Assaf, Y. Blinder, P. 2018-10-08 doi:10.1101/437509 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ NAP (davunetide) preferential interaction with dynamic 3-repeat Tau explains differential protection in selected tauopathies ]]> https://biorxiv.org/content/10.1101/440941v1?rss=1 Ivashko-Pachima, Y. Maor, M. Gozes, I. 2018-10-11 doi:10.1101/440941 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Directing voluntary temporal attention increases fixational stability ]]> https://biorxiv.org/content/10.1101/449264v1?rss=1 Denison, R. N. Yuval-Greenberg, S. Carrasco, M. 2018-10-22 doi:10.1101/449264 Cold Spring Harbor Laboratory Press 2018-10-22 <![CDATA[ PRODIGY: personalized prioritization of driver genes ]]> https://biorxiv.org/content/10.1101/456723v1?rss=1 2500 patients and comparison to validated driver genes, Prodigy outperformed extant methods and ranking based on network centrality measures. Our results pinpoint the pleiotropic effect of driver genes and show that Prodigy is capable of identifying even very rare drivers. Hence, Prodigy takes a step further towards personalized medicine and treatment. AvailabilityThe Prodigy R package is available at: https://github.com/Shamir-Lab/PRODIGY. ]]> Dinstag, G. Shamir, R. 2018-10-30 doi:10.1101/456723 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ New players in the regulatory network of Vibrio parahaemolyticus type VI secretion system 1 ]]> https://biorxiv.org/content/10.1101/464727v1?rss=1 Ben-Yaakov, R. Salomon, D. 2018-11-08 doi:10.1101/464727 Cold Spring Harbor Laboratory Press 2018-11-08 <![CDATA[ Inter-generational Consequences for Growing C. elegans in Liquid ]]> https://biorxiv.org/content/10.1101/467837v1?rss=1 Lev, I. Bril, R. Liu, Y. Cere, L. I. Rechavi, O. 2018-11-11 doi:10.1101/467837 Cold Spring Harbor Laboratory Press 2018-11-11 <![CDATA[ The Flowering Hormone Florigen Accelerates Secondary Cell Wall Biogenesis to Harmonize Vascular Maturation with Reproductive Development ]]> https://biorxiv.org/content/10.1101/476028v1?rss=1 Shalit-Kaneh, A. Eviatar-Ribak, T. Horev, G. Suss, N. Aloni, R. Eshed, Y. Lifschitz, E. 2018-11-27 doi:10.1101/476028 Cold Spring Harbor Laboratory Press 2018-11-27 <![CDATA[ Engineering Brain Parasites for Intracellular Delivery of Therapeutic Proteins ]]> https://biorxiv.org/content/10.1101/481192v1?rss=1 Bracha, S. Hassi, K. Ross, P. D. Cobb, S. Sheiner, L. Rechavi, O. 2018-12-03 doi:10.1101/481192 Cold Spring Harbor Laboratory Press 2018-12-03 <![CDATA[ Wind drives drought responses of green roof vegetation in two substrates ]]> https://biorxiv.org/content/10.1101/486241v1?rss=1 Przybysz, A. Sonkin, K. Saebo, A. Hanslin, H. M. Konstantin Sonkin, Arne Saebo, Hans Martin Hanslin, 2018-12-03 doi:10.1101/486241 Cold Spring Harbor Laboratory Press 2018-12-03 <![CDATA[ The Ca2+ sensor protein CMI1 fine tunes root development, auxin distribution and responses ]]> https://biorxiv.org/content/10.1101/488536v1?rss=1 Hazak, O. Mamon, E. Lavy, M. Sternberg, H. Behera, S. Schmitz-Thom, I. Bloch, D. Dementiev, O. Gutman, I. Danziger, T. Schwarz, N. Abuzeineh, A. Mockaitis, K. Estelle, M. Hirsch, J. Kudla, J. Yalovsky, S. 2018-12-05 doi:10.1101/488536 Cold Spring Harbor Laboratory Press 2018-12-05 <![CDATA[ Consensus interpretation of the Met34Thr and Val37Ile variants in GJB2 by the ClinGen Hearing Loss Expert Panel ]]> https://biorxiv.org/content/10.1101/493130v1?rss=1 C/p.Met34Thr and c.109G>A/p.Val37Ile in GJB2 are controversial. Therefore, an expert consensus is required for the interpretation of these two variants.nnMETHODSThe ClinGen Hearing Loss Expert Panel (HL-EP) collected published data and shared unpublished information from participating laboratories regarding the two variants. Functional, computational, allelic, and segregation data were also obtained.nnRESULTSThe panel reviewed the synthesized information, and classified the Met34Thr and Val37Ile variants according to professional variant interpretation guidelines. We found that Met34Thr and Val37Ile are significantly overrepresented in hearing loss patients, compared to the general population. Met34Thr or Val37Ile homozygotes or compound heterozygotes typically manifest mild to moderate hearing loss. Several other types of evidence also support pathogenic roles for those two variants.nnCONCLUSIONResolving controversies in variant classification requires coordinated effort among a panel of international multi-institutional experts to share data, standardize classification rules, review evidence, and reach a consensus. The ClinGen HL-EP concluded that Met34Thr and Val37Ile variants in GJB2 are pathogenic for autosomal recessive nonsyndromic hearing loss with variable expressivity and age-dependent penetrance. ]]> Shen, J. Oza, A. del Castillo, I. Duzkale, H. Matsunaga, T. Pandya, A. Kang, H. Mar-Heyming, R. Guha, S. Moyer, K. Lo, C. Kenna, M. Alexander, J. Zhang, Y. Hirsch, Y. Luo, M. Cao, Y. Wai Choy, K. Cheng, Y.-F. Avraham, K. Hu, X. Garrido, G. Moreno-Pelayo, M. Greinwald, J. Zhang, K. Zeng, Y. Brownstein, Z. Basel-Vanagaite, L. Davidov, B. Frydman, M. Weiden, T. Nagan, N. Willis, A. Hemphill, S. Grant, A. Siegert, R. DiStefano, M. Amr, S. Rehm, H. Abou Tayoun, A. The ClinGen Hearing Loss Working Group, 2018-12-11 doi:10.1101/493130 Cold Spring Harbor Laboratory Press 2018-12-11 <![CDATA[ Forces and constraints controlling podosome assembly and disassembly ]]> https://biorxiv.org/content/10.1101/495176v1?rss=1 Mohd Rafiq, N. Grenci, G. Kozlov, M. M. Jones, G. E. Viasnoff, V. Bershadsky, A. D. 2018-12-13 doi:10.1101/495176 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Depopulation of α-synuclein aggregates is associated with rescue of dopamine neuron dysfunction and death in a new Parkinson disease model ]]> https://biorxiv.org/content/10.1101/500629v1?rss=1 Wegrzynowicz, M. Bar-On, D. Calo, L. Anichtchik, O. Iovino, M. Xia, J. Ryazanov, S. Leonov, A. Giese, A. Dalley, J. Griesinger, C. Ashery, U. Spillantini, M. G. 2018-12-19 doi:10.1101/500629 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Incipient species or social polymorphism? Diversity in the desert ant Cataglyphis ]]> https://biorxiv.org/content/10.1101/501270v1?rss=1 Reiner Brodetzki, T. Inbar, S. Cohen, P. Aron, S. Privman, E. Hefetz, A. 2018-12-19 doi:10.1101/501270 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Anesthesia-induced loss of consciousness disrupts auditory responses beyond primary cortex ]]> https://biorxiv.org/content/10.1101/502385v1?rss=1 Krom, A. J. Marmelshtein, A. Gelbard-Sagiv, H. Tankus, A. Hayat, D. Matot, I. Strauss, I. Fahoum, F. Soehle, M. Boström, J. Mormann, F. Fried, I. Nir, Y. 2018-12-21 doi:10.1101/502385 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ Spatiotemporal Integration in Plant Tropisms ]]> https://biorxiv.org/content/10.1101/506147v1?rss=1 Meroz, Y. Bastien, R. Mahadevan, L. 2018-12-26 doi:10.1101/506147 Cold Spring Harbor Laboratory Press 2018-12-26 <![CDATA[ Prediction and control of symmetry breaking in embryoid bodies by environment and signal integration ]]> https://biorxiv.org/content/10.1101/506543v1?rss=1 Sagy, N. Slovin, S. Allalouf, M. Pour, M. Savyon, G. Boxman, J. Nachman, I. 2018-12-26 doi:10.1101/506543 Cold Spring Harbor Laboratory Press 2018-12-26 <![CDATA[ The Molecular Landscape of Anti-Drug Antibodies Reveals the Mechanism of the Immune Response Following Treatment with TNF-alpha Antagonist ]]> https://biorxiv.org/content/10.1101/509489v1?rss=1 Vaisman-Mentesh, A. Rosenstein, S. Yavzori, M. Dror, Y. Fudim, E. Ungar, B. Kopylov, U. Picard, O. Kigel, A. Ben-Horin, S. Benhar, I. Wine, Y. 2019-01-02 doi:10.1101/509489 Cold Spring Harbor Laboratory Press 2019-01-02 <![CDATA[ A neuroprosthetic system to restore neuronal communication in modular networks ]]> https://biorxiv.org/content/10.1101/514836v1?rss=1 Buccelli, S. Bornat, Y. Colombi, I. Ambroise, M. Martines, L. Pasquale, V. Bisio, M. Tessadori, J. Nowak, P. Grassia, F. Averna, A. Tedesco, M. Bonifazi, P. Difato, F. Massobrio, P. Levi, T. Chiappalone, M. 2019-01-09 doi:10.1101/514836 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ A genetic system for generating single-sex progeny in mice ]]> https://biorxiv.org/content/10.1101/515064v1?rss=1 Yosef, I. Shlomovitz, I. Globus, R. Edry-Botzer, L. Munitz, A. Gerlic, M. Qimron, U. 2019-01-10 doi:10.1101/515064 Cold Spring Harbor Laboratory Press 2019-01-10 <![CDATA[ A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals ]]> https://biorxiv.org/content/10.1101/523936v1?rss=1 6,000 RADSeq loci. DAPC and Structure analyses also supported morphospecies assignments, but indicated the potential for two additional cryptic species. Three morphologically distinct species pairs could not, however, be distinguished genetically. ABBA-BABA tests demonstrated significant admixture between some of those species, suggesting that hybridization may confound species delimitation in Sinularia.nnConclusionsA genomic approach can help to guide species delimitation while simultaneously elucidating the processes generating diversity in corals. Results support the hypothesis that hybridization is an important mechanism in the evolution of Anthozoa, including octocorals, and future research should examine the contribution of this mechanism in generating diversity across the coral tree of life. ]]> Quattrini, A. M. Wu, T. Soong, K. Jeng, M.-S. Benayahu, Y. McFadden, C. S. 2019-01-17 doi:10.1101/523936 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ Combinatorial Treatment Increases IKAP Levels in Human Cells Generated from Familial Dysautonomia Patients ]]> https://biorxiv.org/content/10.1101/524587v1?rss=1 Ast, G. Yanai, S. Zonszain, J. Donyo, M. 2019-01-19 doi:10.1101/524587 Cold Spring Harbor Laboratory Press 2019-01-19 <![CDATA[ Ultra-rare genetic variation in the epilepsies: a whole-exome sequencing study of 17,606 individuals ]]> https://biorxiv.org/content/10.1101/525683v1?rss=1 Epi25 Collaborative, Feng, Y.-C. A. Howrigan, D. P. Abbott, L. E. Tashman, K. Cerrato, F. Singh, T. Heyne, H. Byrnes, A. Churchhouse, C. Lal, D. Heinzen, E. L. Cavalleri, G. L. Hakonarson, H. Helbig, I. Krause, R. May, P. Weckhuysen, S. Petrovski, S. Kamalakaran, S. Sisodiya, S. M. Cossette, P. Cotsapas, C. De Jonghe, P. Dixon-Salazar, T. Guerrini, R. Kwan, P. Marson, A. G. Stewart, R. Depondt, C. Dlugos, D. J. Scheffer, I. E. Striano, P. Freyer, C. McKenna, K. Regan, B. M. Bellows, S. T. Leu, C. Bennett, C. A. Johns, E. M. C. Macdonald, A. Shilling, 2019-01-21 doi:10.1101/525683 Cold Spring Harbor Laboratory Press 2019-01-21 <![CDATA[ Global phylogeography and ancient evolution of the widespread human gut virus crAssphage ]]> https://biorxiv.org/content/10.1101/527796v1?rss=1 Edwards, R. Vega, A. Norman, H. Ohaeri, M. C. Levi, K. Dinsdale, E. Cinek, O. Aziz, R. McNair, K. Barr, J. Bibby, K. Brouns, S. Cazares, A. de Jonge, P. A. Desnues, C. Diaz-Munoz, S. Fineran, P. Kurilshikov, A. Lavigne, R. Mazankova, K. McCarthy, D. Nobrega, F. Reyes, A. Tapia, G. Trefault, N. Tyakht, A. Vinuesa, P. Wagemans, J. Zhernakova, A. Aarestrup, F. Ahmadov, G. Alassaf, A. Anton, J. Asangba, A. Billings, E. Cantu, A. Carlton, J. Cazares Lopez, D. Cho, G.-S. Condeff, T. Cortes, P. Cranfield, M. Cuevas, D. De la Iglesia, R. Decewicz, P. Doane, 2019-01-26 doi:10.1101/527796 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Prophylactic TLR9 stimulation reduces brain metastasis through microglia activation ]]> https://biorxiv.org/content/10.1101/533927v1?rss=1 Benbenishty, A. Gadrich, M. Cottarelli, A. Lubart, A. Kain, D. Amer, M. Shaashua, L. Glasner, A. Erez, N. Agalliu, D. Mayo, L. Ben-Eliyahu, S. Blinder, P. 2019-01-31 doi:10.1101/533927 Cold Spring Harbor Laboratory Press 2019-01-31 <![CDATA[ Selection of Candida albicans Trisomy during Oropharyngeal Infection Results in a Commensal-Like Phenotype ]]> https://biorxiv.org/content/10.1101/537340v1?rss=1 Forche, A. Solis, N. V. Swidergall, M. Thomas, R. Guyer, A. Beach, A. Cromie, G. A. Le, G. T. Lowell, E. Pavelka, N. Berman, J. Dudley, A. Selmecki, A. Filler, S. 2019-02-05 doi:10.1101/537340 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Local Targeted Memory Reactivation in Human Sleep ]]> https://biorxiv.org/content/10.1101/539114v1?rss=1 Bar, E. Arzi, A. Perl, O. Livne, E. Sobel, N. Dudai, Y. Nir, Y. 2019-02-07 doi:10.1101/539114 Cold Spring Harbor Laboratory Press 2019-02-07 <![CDATA[ Locus-coeruleus norepinephrine activity gates sensory-evoked awakenings from sleep ]]> https://biorxiv.org/content/10.1101/539502v1?rss=1 Hayat, H. Regev, N. Matosevich, N. Sales, A. Paredes-Rodriguez, E. Krom, A. J. Bergman, L. Li, Y. Lavigne, M. Kremer, E. J. Yizhar, O. Pickering, A. E. Nir, Y. 2019-02-03 doi:10.1101/539502 Cold Spring Harbor Laboratory Press 2019-02-03 <![CDATA[ GNI-A1 mediates trade-off between grain number and grain weight in tetraploid wheat ]]> https://biorxiv.org/content/10.1101/540096v1?rss=1 Golan, G. Ayalon, I. Perry, A. Zimran, G. Ade-Ajayi, T. Mosquna, A. Distelfeld, A. Peleg, Z. 2019-02-05 doi:10.1101/540096 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Respiratory gas levels interact to control ventilatory motor patterns in isolated locust ganglia ]]> https://biorxiv.org/content/10.1101/543793v1?rss=1 Talal, S. Ayali, A. Gefen, E. 2019-02-08 doi:10.1101/543793 Cold Spring Harbor Laboratory Press 2019-02-08 <![CDATA[ Isolation and characterization of live yeast cells from ancient vessels as a tool in bio-archeology ]]> https://biorxiv.org/content/10.1101/549840v1?rss=1 Aouizerat, T. Gutman, I. Paz, Y. Maeir, A. M. Gadot, Y. Gelman, D. Szitenberg, A. Drori, E. Pinkus, A. Schoemann, M. Kaplan, R. Ben-Gedalya, T. Coppenhagen-Glazer, S. Reich, E. Saragovi, A. S. Lipschits, O. Klutstein, M. Hazan, R. 2019-02-14 doi:10.1101/549840 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ Autonomously replicating linear plasmids facilitate the analysis of replication origin function in Candida albicans ]]> https://biorxiv.org/content/10.1101/551127v1?rss=1 Bijlani, S. Thevandavakkam, M. A. Tsai, H.-J. Berman, J. 2019-02-15 doi:10.1101/551127 Cold Spring Harbor Laboratory Press 2019-02-15 <![CDATA[ Short-Term Plasticity Following Motor Sequence Learning Revealed by Diffusion MRI ]]> https://biorxiv.org/content/10.1101/553628v1?rss=1 Tavor, I. Botvinik-Nezer, R. Bernstein-Eliav, M. Tsarfaty, G. Assaf, Y. 2019-02-18 doi:10.1101/553628 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ The benefits of insect-swarm hunting in echolocating bats, and its influence on the evolution of bat echolocation signals ]]> https://biorxiv.org/content/10.1101/554055v1?rss=1 Boonman, A. Yovel, Y. Fenton, B. 2019-02-18 doi:10.1101/554055 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ A Framework for Collective Behavior in Plant Inspired Growth-Driven Systems, Based on Kinematics of Allotropism ]]> https://biorxiv.org/content/10.1101/566364v1?rss=1 Bastien, R. Porat, A. Meroz, Y. 2019-03-03 doi:10.1101/566364 Cold Spring Harbor Laboratory Press 2019-03-03 <![CDATA[ Network-based approaches elucidate differences within APOBEC and clock-like signatures in breast cancer ]]> https://biorxiv.org/content/10.1101/568568v1?rss=1 Kim, Y.-A. Wojtowicz, D. Sarto Basso, R. Sason, I. Robinson, W. Hochbaum, D. S. Leiserson, M. D. M. Sharan, R. Vandin, F. Przytycka, T. M. 2019-03-05 doi:10.1101/568568 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Frequent sugar feeding behavior by Aedes aegypti in Bamako, Mali makes them ideal candidates for control with attractive toxic sugar baits (ATSB) ]]> https://biorxiv.org/content/10.1101/574095v1?rss=1 Sisoko, F. Junnila, A. Traore, M. Traore, S. F. Doumbia, S. Dembele, S. M. Schlein, Y. Gergely, P. Xue, R.-d. Arheart, K. L. Revay, E. E. Kravchenko, V. D. Beier, J. C. Muller, G. C. 2019-03-11 doi:10.1101/574095 Cold Spring Harbor Laboratory Press 2019-03-11 <![CDATA[ Flow arrest in the plasma membrane ]]> https://biorxiv.org/content/10.1101/575456v1?rss=1 Chein, M. Perlson, E. Roichman, Y. 2019-03-12 doi:10.1101/575456 Cold Spring Harbor Laboratory Press 2019-03-12 <![CDATA[ Pore-modulating toxins exploit inherent slow inactivation to block K+ channels ]]> https://biorxiv.org/content/10.1101/576132v1?rss=1 Karbat, I. Altman-Gueta, H. Fine, S. Szanto, T. Hamer-Rogotner, S. Dym, O. Frolow, F. Gordon, D. Panyi, G. Gurevitz, M. Reuveny, E. 2019-03-13 doi:10.1101/576132 Cold Spring Harbor Laboratory Press 2019-03-13 <![CDATA[ Coordinated development of the mouse extrahepatic bile duct: implications for neonatal susceptibility to biliary injury ]]> https://biorxiv.org/content/10.1101/576256v1?rss=1 nView larger version (27K):norg.highwire.dtl.DTLVardef@1685e52org.highwire.dtl.DTLVardef@1086478org.highwire.dtl.DTLVardef@1fc3f55org.highwire.dtl.DTLVardef@1a20a5f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Khandekar, G. Llewellyn, J. Kriegermeier, A. Waisbourd-Zinman, O. Johnson, N. Du, Y. Giwa, R. Liu, X. Kisseleva, T. Russo, P. A. Theise, N. D. Wells, R. G. 2019-03-13 doi:10.1101/576256 Cold Spring Harbor Laboratory Press 2019-03-13 <![CDATA[ Germ Granules Functions are Memorized by Transgenerationally Inherited Small RNAs ]]> https://biorxiv.org/content/10.1101/576934v1?rss=1 16) generations, although their germ granules are intact. Importantly, while P granules are maternally deposited, wild type progeny derived from meg-3/4 male mutants also show reduced RNAi inheritance. Unlike germ granules, small RNAs are inherited also from the sperm. Moreover, we find that the transgenerational effects that depend on the ancestral germ granules require the argonaute protein HRDE-1, which carries heritable small RNAs in the germline. Indeed, small RNA sequencing reveals imbalanced levels of many endogenous small RNAs in germ granules mutants. Strikingly, we find that hrde-1;meg-3/4 triple mutants inherit RNAi, although hrde-1 was previously thought to be essential for heritable silencing. We propose that germ granules sort and shape the RNA pool, and that small RNA inheritance memorizes this activity for multiple generations. ]]> Lev, I. Toker, I. A. Mor, Y. Nitzan, A. Weintraub, G. Bhonkar, O. Ben Shushan, I. Seroussi, U. Claycomb, J. Gingold, H. Zaidel-Bar, R. Rechavi, O. 2019-03-14 doi:10.1101/576934 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ The Distributed Engram ]]> https://biorxiv.org/content/10.1101/583195v1?rss=1 Feldesh, R. 2019-03-20 doi:10.1101/583195 Cold Spring Harbor Laboratory Press 2019-03-20 <![CDATA[ Global Modulation in DNA Epigenetics during Pro-Inflammatory Macrophage Activation ]]> https://biorxiv.org/content/10.1101/587311v1?rss=1 JAIN, N. Shahal, T. Gabrieli, T. Gilat, N. Torchinsky, D. Michaeli, Y. VOGEL, V. Ebenstein, Y. 2019-03-24 doi:10.1101/587311 Cold Spring Harbor Laboratory Press 2019-03-24 <![CDATA[ Single particle diffusion characterization by deep learning ]]> https://biorxiv.org/content/10.1101/588533v1?rss=1 Granik, N. Weiss, L. E. Levine, M. Chein, M. Perlson, E. Roichman, Y. Shechtman, Y. 2019-03-26 doi:10.1101/588533 Cold Spring Harbor Laboratory Press 2019-03-26 <![CDATA[ Contribution of self- and other-regarding motives to (dis)honesty ]]> https://biorxiv.org/content/10.1101/590208v1?rss=1 Shuster, A. Levy, D. J. 2019-03-28 doi:10.1101/590208 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ Mammillothalamic disconnection alters hippocampo-cortical oscillatory activity and microstructure: Implications for diencephalic amnesia ]]> https://biorxiv.org/content/10.1101/590901v1?rss=1 Dillingham, C. M. Milczarek, M. M. Perry, J. C. Frost, B. E. Parker, G. D. Assaf, Y. Sengpiel, F. O'Mara, S. M. Vann, S. 2019-03-27 doi:10.1101/590901 Cold Spring Harbor Laboratory Press 2019-03-27 <![CDATA[ Suction feeding performance and prey escape response interact to determine feeding success in larval fish ]]> https://biorxiv.org/content/10.1101/603316v1?rss=1 Sommerfeld, N. Holzman, R. 2019-04-09 doi:10.1101/603316 Cold Spring Harbor Laboratory Press 2019-04-09 <![CDATA[ Structural integrity following focused ultrasound thalamotomy and its correlation with tremor relief ]]> https://biorxiv.org/content/10.1101/620369v1?rss=1 Zur, G. Lesman-Segev, O. Schlesinger, I. Goldsher, D. Sinai, A. Zaaroor, M. Assaf, Y. Eran, A. Kahn, I. 2019-05-03 doi:10.1101/620369 Cold Spring Harbor Laboratory Press 2019-05-03 <![CDATA[ Memory for Individual Items is Related to Non-Reinforced Preference Change ]]> https://biorxiv.org/content/10.1101/621292v1?rss=1 Botvinik-Nezer, R. Bakkour, A. Salomon, T. Shohamy, D. Schonberg, T. 2019-04-29 doi:10.1101/621292 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ Video-based motion-resilient reconstruction of 3D position for fNIRS/EEG head mounted probes ]]> https://biorxiv.org/content/10.1101/621615v1?rss=1 Jaffe-Dax, S. Bermano, A. H. Emberson, L. L. 2019-05-02 doi:10.1101/621615 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Light environment drives the shallow to mesophotic coral community transition ]]> https://biorxiv.org/content/10.1101/622191v1?rss=1 Tamir, R. Eyal, G. Kramer, N. Laverick, J. Loya, Y. 2019-04-29 doi:10.1101/622191 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ Discovery of tumoricidal DNA aptamers by effect-directed in-vitro evolution ]]> https://biorxiv.org/content/10.1101/629105v1?rss=1 Mamet, N. Amir, Y. Lavi, E. Bassali, L. Harari, G. Rusinek, I. Skalka, N. Debby, E. Greenberg, M. Zamir, A. Paz, A. Reiss, N. Loewenthal, G. Avivi, I. Shimoni, A. Neev, G. Abu-Horowitz, A. Bachelet, I. 2019-05-07 doi:10.1101/629105 Cold Spring Harbor Laboratory Press 2019-05-07 <![CDATA[ PROMO: An interactive tool for analyzing clinically-labeled multi-omic cancer datasets ]]> https://biorxiv.org/content/10.1101/629584v1?rss=1 Netanely, D. Stern, N. Laufer, I. Shamir, R. 2019-05-06 doi:10.1101/629584 Cold Spring Harbor Laboratory Press 2019-05-06 <![CDATA[ Lithium-ATP: structure characterization and lithium binding ]]> https://biorxiv.org/content/10.1101/637900v1?rss=1 Haimovich, A. Goldbourt, A. 2019-05-16 doi:10.1101/637900 Cold Spring Harbor Laboratory Press 2019-05-16 <![CDATA[ Scale-eating specialists evolved adaptive feeding kinematics within a microendemic radiation of San Salvador Island pupfishes ]]> https://biorxiv.org/content/10.1101/648451v1?rss=1 St. John, M. E. Martin, C. H. 2019-05-24 doi:10.1101/648451 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Live cell single molecule tracking and localization microscopy of bioorthogonally labeled plasma membrane proteins ]]> https://biorxiv.org/content/10.1101/660118v1?rss=1 König, A. I. Sorkin, R. Alon, A. Nachmias, D. Dhara, K. Brand, G. Yifrach, O. Roichman, Y. Arbely, E. Elia, N. 2019-06-05 doi:10.1101/660118 Cold Spring Harbor Laboratory Press 2019-06-05 <![CDATA[ Multidimensional extracellular-matrix analysis reveals a silent pre-clinical signature in inflammatory disease ]]> https://biorxiv.org/content/10.1101/665653v1?rss=1 Shimshoni, E. Afik, R. Shenoy, A. Adler, M. Puricelli, L. Ghini, V. Mouhadeb, O. Gluck, N. Fishman, S. Werner, L. Shouval, D. S. Varol, C. Podesta, A. Turano, P. Geiger, T. Milani, P. Luchinat, C. Alon, U. Sagi, I. 2019-06-10 doi:10.1101/665653 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Stress Resets Transgenerational Small RNA Inheritance ]]> https://biorxiv.org/content/10.1101/669051v1?rss=1 Houri-Ze'evi, L. Teichman, G. Gingold, H. Rechavi, O. 2019-06-13 doi:10.1101/669051 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Phase separation of TAZ compartmentalizes the transcription machinery to promote gene expression ]]> https://biorxiv.org/content/10.1101/671230v1?rss=1 Wu, T. Lu, Y. Gutman, O. Lu, H. Zhou, Q. Henis, Y. I. Luo, K. 2019-06-14 doi:10.1101/671230 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ Show me your secret(ed) weapons: a multifaceted approach reveals novel type III-secreted effectors of a plant pathogenic bacterium ]]> https://biorxiv.org/content/10.1101/679126v1?rss=1 Jimenez guerrero, I. Perez-Montano, F. da Silva, G. M. Wagner, N. Shkedy, D. Zhao, M. Pizarro, L. Bar, M. Walcott, R. Sessa, G. Pupko, T. Burdman, S. 2019-06-21 doi:10.1101/679126 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ De novo Transcriptome Characterization of Royal Iris (Iris section Oncocyclus) and Identification of Flower Development Genes ]]> https://biorxiv.org/content/10.1101/680363v1?rss=1 Bar-Lev, Y. Senden, E. Pasjmanik-Chor, M. Sapir, Y. 2019-06-23 doi:10.1101/680363 Cold Spring Harbor Laboratory Press 2019-06-23 <![CDATA[ Analysis of DNM3 and VAMP4 as genetic modifiers of LRRK2 Parkinsons disease ]]> https://biorxiv.org/content/10.1101/686550v1?rss=1 Brown, E. E. Blauwendraat, C. Trinh, J. Rizig, M. Nalls, M. Leveille, E. Ruskey, J. Jonvik, H. Tan, M. Bandres-Ciga, S. Hassin-Baer, S. Brockmann, K. Hardy, J. Singleton, A. Alcalay, R. Gasser, T. Grosset, D. Williams, N. Pittman, A. Gan-Or, Z. Fernandez-Santiago, R. Brice, A. Lesage, S. Farrer, M. Wood, N. Morris, H. R. 2019-06-28 doi:10.1101/686550 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ The little caterpillar that could - Tobacco Hornworm (Manduca sexta) caterpillars as a novel host model for the study of fungal virulence and drug efficacy ]]> https://biorxiv.org/content/10.1101/693226v1?rss=1 1.4 million patients world-wide with mortality rates approaching 75%. It is thus imperative to study fungal virulence mechanisms, efficacy of antifungal drugs, and host response pathways. While this is commonly done in mammalian models, which are afflicted by ethical and practical concerns, invertebrate models, such as wax moth larvae and nematodes have been introduced over the last two decades. To complement existing invertebrate host models, we developed fifth instar caterpillars of the Tobacco Hornworm moth Manduca sexta as a novel host model. These caterpillars can be maintained at 37{degrees}C, are suitable for injections with defined amounts of yeast cells, and are susceptible to the most threatening yeast pathogens, including C. albicans, C. neoformans, C. auris, and C. glabrata. Importantly, fungal burden can be assessed daily throughout the course of infection in a single caterpillars faeces and haemolymph. Infected caterpillars can be rescued by treatment with antifungal drugs. Notably, these animals are large enough for weight to provide a reliable and reproducible measure of fungal disease. M. sexta caterpillars combine a suite of parameters that make them suitable for the study of fungal virulence. ]]> Lyons, N. Softley, I. Balfour, A. Williamson, C. O'Brien, H. Diezmann, S. 2019-07-04 doi:10.1101/693226 Cold Spring Harbor Laboratory Press 2019-07-04 <![CDATA[ G protein-coupled potassium channels implicated in mouse and cellular models of GNB1 Encephalopathy ]]> https://biorxiv.org/content/10.1101/697235v1?rss=1 Colombo, S. Petri, S. Shalomov, B. Reddy, H. P. Tabak, G. Dhindsa, R. S. Gelfman, S. Teng, S. Krizay, D. Rafikian, E. E. Bera, A. K. Yang, M. Boland, M. J. Peng, Y. Frankel, W. N. Dascal, N. Goldstein, D. B. 2019-07-09 doi:10.1101/697235 Cold Spring Harbor Laboratory Press 2019-07-09 <![CDATA[ Astrocyte senescence in an Alzheimer’s disease mouse model is mediated by TGF-β1 and results in neurotoxicity ]]> https://biorxiv.org/content/10.1101/700013v1?rss=1 Amram, S. Iram, T. Lazdon, E. Vassar, R. Ben Porath, I. Frenkel, D. 2019-07-12 doi:10.1101/700013 Cold Spring Harbor Laboratory Press 2019-07-12 <![CDATA[ Shear forces drive precise patterning of hair cells in the mammalian inner ear ]]> https://biorxiv.org/content/10.1101/707422v1?rss=1 Cohen, R. Amir-Zilberstein, L. Hersch, M. Woland, S. Taiber, S. Matsuzaki, F. Bergmann, S. Avraham, K. B. Sprinzak, D. 2019-07-18 doi:10.1101/707422 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ INTERACTION BETWEEN PLOIDY, BREEDING SYSTEM, AND LINEAGE DIVERSIFICATION ]]> https://biorxiv.org/content/10.1101/709329v1?rss=1 Zenil-Ferguson, R. Burleigh, G. Igic, B. Freyman, W. A. Mayrose, I. Goldberg, E. E. 2019-07-22 doi:10.1101/709329 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Global priorities for conservation of reptilian phylogenetic diversity in the face of human impacts ]]> https://biorxiv.org/content/10.1101/723742v1?rss=1 Gumbs, R. Gray, C. L. Bohm, M. Hoffmann, M. Grenyer, R. Jetz, W. Meiri, S. Roll, U. Owen, N. R. Rosindell, J. 2019-08-02 doi:10.1101/723742 Cold Spring Harbor Laboratory Press 2019-08-02 <![CDATA[ The evolution of paternal care: a role for microbes? ]]> https://biorxiv.org/content/10.1101/725192v1?rss=1 Gurevich, Y. Lewin-Epstein, O. Hadany, L. 2019-08-05 doi:10.1101/725192 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ Uncoating of COPII from ER exit site membranes precedes cargo accumulation and membrane fission ]]> https://biorxiv.org/content/10.1101/727107v1?rss=1 Shomron, O. Nevo-Yassaf, I. Aviad, T. Yaffe, Y. Zahavi, E. E. Dukhovny, A. Perlson, E. Brodsky, I. Yeheskel, A. Pasmanik-Chor, M. Mironov, A. Beznoussenko, G. V. Mironov, A. A. Sklan, E. H. Patterson, G. H. Yonemura, Y. Kaether, C. Hirschberg, K. 2019-08-06 doi:10.1101/727107 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ Emergence and patterning dynamics of mouse definitive endoderm ]]> https://biorxiv.org/content/10.1101/728642v1?rss=1 Pour, M. Kumar, A. S. Walther, M. Wittler, L. Meissner, A. Nachman, I. 2019-08-07 doi:10.1101/728642 Cold Spring Harbor Laboratory Press 2019-08-07 <![CDATA[ Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality ]]> https://biorxiv.org/content/10.1101/732552v1?rss=1 Levitan, A. Gale, A. N. Dalton, E. K. Kozan, D. W. Cunningham, K. W. Sharan, R. Berman, J. 2019-08-12 doi:10.1101/732552 Cold Spring Harbor Laboratory Press 2019-08-12 <![CDATA[ Genetic modifiers of risk and age at onset in GBA associated Parkinson disease and Lewy body dementia ]]> https://biorxiv.org/content/10.1101/738351v1?rss=1 10-fold. An outstanding question in the field is what other genetic factors that influence GBA-associated risk for disease, and whether these overlap with known PD risk variants.nnUsing multiple, large case-control datasets, totalling 217,165 individuals (22,757 PD cases, 13,431 PD proxy cases, 622 LBD cases and 180,355 controls), we identified 1,772 PD cases, 711 proxy cases and 7,624 controls with a GBA variant (p.E326K, p.T369M or p.N370S). We performed a genome-wide association study and analysed the most recent PD-associated genetic risk score to detect genetic influences on GBA risk and age at onset. We attempted to replicate our findings in two independent datasets, including the personal genetics company 23andMe, Inc. and whole-genome sequencing data. Our analysis showed that the overall PD genetic risk score modifies risk for disease and decreases age at onset in carriers of GBA variants. Notably, this effect was consistent across all tested GBA risk variants. Dissecting this signal demonstrated that variants in close proximity to SNCA and CTSB (encoding cathepsin B) are the most significant contributors. Risk variants in the CTSB locus were identified to decrease mRNA expression of CTSB. Additional analyses suggest a possible genetic interaction between GBA and CTSB and GBA p.N370S neurons were shown to have decreased Cathepsin B expression compared to controls. These data provide a genetic basis for modification of GBA-associated PD risk and age at onset and demonstrate that variability at genes implicated in lysosomal function exerts the largest effect on GBA associated risk for disease. Further, these results have important implications for selection of GBA carriers for therapeutic interventions. ]]> Blauwendraat, C. Reed, X. Krohn, L. Heilbron, K. Bandres-Ciga, S. Tan, M. Gibbs, J. R. Hernandez, D. G. Kumaran, R. Langston, R. Bonet Ponce, L. Alcalay, R. Hassin-Baer, S. Greenbaum, L. Iwaki, H. Leonard, H. Grenn, F. P. Ruskey, J. A. Sabir, M. Ahmed, S. Makarious, M. B. Pihlstrom, L. Toft, M. van Hilten, J. J. Marinus, J. Schulte, C. Sharma, M. Brockmann, K. Siitonen, A. Majamaa, K. Eerola-Rautio, J. Tienari, P. The 23andMe Research Team, Pantelyat, A. Hillis-Trupe, A. Dawson, T. Rosenthal, L. Albert, M. Resnick, S. M. Ferrucci, L. Morris, C. M. Ple 2019-08-18 doi:10.1101/738351 Cold Spring Harbor Laboratory Press 2019-08-18 <![CDATA[ Phase-amplitude markers of synchrony and noise: A resting-state and TMS-EEG study of schizophrenia ]]> https://biorxiv.org/content/10.1101/740621v1?rss=1 Freche, D. Naim-Feil, J. Hess, S. Peled, A. Grinshpoon, A. Moses, E. Levit-Binnun, N. 2019-08-23 doi:10.1101/740621 Cold Spring Harbor Laboratory Press 2019-08-23 <![CDATA[ Enhancer architecture sensitizes cell specific responses to Notch gene dose via a bind and discard mechanism ]]> https://biorxiv.org/content/10.1101/742908v1?rss=1 Kuang, Y. Golan, O. Preusse, K. Cain, B. Salomone, J. Campbell, I. Okwubido-Williams, F. V. Hass, M. R. Eafergan, N. Moberg, K. H. Kovall, R. Kopan, R. Sprinzak, D. Gebelein, B. 2019-08-22 doi:10.1101/742908 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Sleep differentially affects early and late neuronal responses to sounds in auditory and perirhinal cortices ]]> https://biorxiv.org/content/10.1101/743666v1?rss=1 40ms) responses in all monitored regions diminished during NREM sleep. The robust attenuation of late responses prevalent in PRC represents a novel neural correlate of sensory disconnection during sleep, opening new avenues for investigating the mediating mechanisms.nnSignificance StatementReduced behavioral responsiveness to sensory stimulation is at the core of sleeps definition, but it is still unclear how the sleeping brain responds differently to sensory stimuli. In the current study we recorded neuronal spiking responses to sounds along the cortical processing hierarchy of rats during wakefulness and natural sleep. Responses in auditory cortex only showed modest changes during sleep, whereas sleep robustly attenuated the responses of neurons in high-level perirhinal cortex. We also found that during NREM sleep, the response latency predicts the degree of sleep attenuation in individual neurons above and beyond their anatomical location. These results provide anatomical and temporal signatures of sensory disconnection during sleep and pave the way to understanding the underlying mechanisms. ]]> Sela, Y. Krom, A. J. Bergman, L. Regev, N. Nir, Y. 2019-08-22 doi:10.1101/743666 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Open source computational simulation for a moth-inspired navigation algorithm ]]> https://biorxiv.org/content/10.1101/744912v1?rss=1 Benelli, N. Gurka, R. Golov, Y. Harari, A. Zilman, G. Liberzon, A. 2019-08-22 doi:10.1101/744912 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Hydrodynamic regime drives flow reversals in suction feeding larval fishes during early ontogeny ]]> https://biorxiv.org/content/10.1101/771436v1?rss=1 8%) in slow strikes produced by larger fish. Our modeling explains the observations of "in-and-out" events in larval fish, where prey enters the mouth but is not swallowed. It further highlights the importance of prey transport as an integral part in determining suction feeding success. ]]> Krishnan, K. Nafi, A. S. Gurka, R. Holzman, R. 2019-09-18 doi:10.1101/771436 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Sema3A Facilitates a Retrograde Death Signal via CRMP4-Dynein Complex Formation in ALS Motor Axons ]]> https://biorxiv.org/content/10.1101/774737v1?rss=1 PERLSON, E. Maimon, R. Ankol, L. Weissova, R. Tank, E. Gradus, T. Opatowsky, Y. Barmada, S. Balastik, M. 2019-09-19 doi:10.1101/774737 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Evolution of metastases-associated fibroblasts in the lung microenvironment is driven by stage-specific transcriptional plasticity ]]> https://biorxiv.org/content/10.1101/778936v1?rss=1 Shani, O. Raz, Y. Megides, O. Shacham, H. Cohen, N. Silverbush, D. Monteran, L. Sharan, R. Tsarfaty, I. Erez, N. 2019-09-23 doi:10.1101/778936 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ Systematic identification of functional SNPs interrupting 3’ UTR polyadenylation signals ]]> https://biorxiv.org/content/10.1101/782425v1?rss=1 Shulman, E. D. Elkon, R. 2019-09-25 doi:10.1101/782425 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ PlasClass improves plasmid sequence classification ]]> https://biorxiv.org/content/10.1101/783571v1?rss=1 Pellow, D. Mizrahi, I. Shamir, R. 2019-10-07 doi:10.1101/783571 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Local adaptation to abiotic and biotic stresses and phenotypic selection on flowering time in annual Brachypodium spp. along an aridity gradient ]]> https://biorxiv.org/content/10.1101/783779v1?rss=1 Penner, S. Sapir, Y. 2019-09-26 doi:10.1101/783779 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Integrative modelling of the full-length human dehydrodolichyl diphosphate synthase using a hybrid computational and experimental approach ]]> https://biorxiv.org/content/10.1101/787119v1?rss=1 Lisnyansky Barel, M. Lee, S. Y. Ki, A. Y. Kapelushnik, N. Loewenstein, A. Chung, K. Y. Schneidman-Duhovny, D. Giladi, M. Newman, H. Haitin, Y. 2019-10-07 doi:10.1101/787119 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Early hippocampal hyperexcitability followed by disinhibition in a mouse model of Dravet syndrome ]]> https://biorxiv.org/content/10.1101/790170v1?rss=1 nView larger version (15K):norg.highwire.dtl.DTLVardef@220862org.highwire.dtl.DTLVardef@54840eorg.highwire.dtl.DTLVardef@a9d006org.highwire.dtl.DTLVardef@9854ec_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Almog, Y. Brusel, M. Anderson, K. Rubinstein, M. 2019-10-02 doi:10.1101/790170 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Electroencephalographic evidence for the involvement of mirror neuron and error monitoring related processes in virtual body ownership ]]> https://biorxiv.org/content/10.1101/795773v1?rss=1 Raz, G. Gurevitch, G. Vaknin, T. Aazamy, A. Gefen, I. Grunstein, S. Azouri, G. Goldway, N. 2019-10-07 doi:10.1101/795773 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Molecular and Morphological Signatures of Chordate Development: Two Distinct Pathways, One Tunicate ]]> https://biorxiv.org/content/10.1101/801589v1?rss=1 Kowarsky, M. Anselmi, C. Hotta, K. Burighel, P. Zaniolo, G. Caicci, F. Rosental, B. Neff, N. F. Ishizuka, K. J. Palmeri, K. J. Okamoto, J. Gordon, T. Weissman, I. L. Quake, S. R. Manni, L. Voskoboynik, A. 2019-10-14 doi:10.1101/801589 Cold Spring Harbor Laboratory Press 2019-10-14 <![CDATA[ The Development, Function, and Plasticity of the Immune Macroenvironment in Cancer ]]> https://biorxiv.org/content/10.1101/805473v1?rss=1 Allen, B. M. Hiam, K. J. Burnett, C. E. Venida, A. DeBarge, R. Carmi, Y. Spitzer, M. H. 2019-10-16 doi:10.1101/805473 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Vibrio pore-forming leukocidin activates pyroptotic cell death via the NLRP3 inflammasome ]]> https://biorxiv.org/content/10.1101/816553v1?rss=1 Baram, N. Cohen, H. Edry-Botzer, L. Salomon, D. Gerlic, M. 2019-10-24 doi:10.1101/816553 Cold Spring Harbor Laboratory Press 2019-10-24 <![CDATA[ Resolving the dark matter of ABCA4 for 1,054 Stargardt disease probands through integrated genomics and transcriptomics ]]> https://biorxiv.org/content/10.1101/817767v1?rss=1 A and c.1938-514G>A resulted in dual PE insertions consisting of the same upstream, but different downstream PEs. The intron 44 variant c.6148-84A>T resulted in two PE insertions that were accompanied by flanking exon deletions. Structural variant analysis revealed 11 distinct deletions, two of which contained small inverted segments. Uniparental isodisomy of chromosome 1 was identified in one proband. Integrated complete gene sequencing combined with transcript analysis, identified pathogenic deep-intronic and structural variants in 26% of bi-allelic cases not solved previously by sequencing of coding regions. This strategy serves as a model study that can be applied to other inherited diseases in which only one or a few genes are involved in the majority of cases. ]]> Khan, M. Cornelis, S. S. Pozo-Valero, M. d. Whelan, L. Runhart, E. H. Mishra, K. Bults, F. AlSwaiti, Y. AlTabishi, A. Baere, E. D. Banfi, S. Banin, E. Bauwens, M. Ben-Yosef, T. Boon, C. J. F. Born, L. I. v. d. Defoort, S. Devos, A. Dockery, A. Dudakova, L. Fakin, A. Farrar, G. J. Ferraz Sallum, J. M. Fujinami, K. Gilissen, C. Glavac, D. Gorin, M. B. Greenberg, J. Hayashi, T. Hettinga, Y. Hoischen, A. Hoyng, C. B. Hufendiek, K. Jagle, H. Kamakari, S. Karali, M. Kellner, U. Klaver, C. C. W. Kousal, B. Lamey, T. MacDonald, I. M. Matynia, A. McLaren, T. M 2019-10-25 doi:10.1101/817767 Cold Spring Harbor Laboratory Press 2019-10-25 <![CDATA[ Moving by thoughts alone? Amount of finger movement and pendulum length determine success in the Chevreul Pendulum Illusion ]]> https://biorxiv.org/content/10.1101/841445v1?rss=1 Cantergi, D. Awasthi, B. Friedman, J. 2019-11-14 doi:10.1101/841445 Cold Spring Harbor Laboratory Press 2019-11-14 <![CDATA[ Disruption of relapse to alcohol seeking by aversive counterconditioning following memory retrieval ]]> https://biorxiv.org/content/10.1101/841536v1?rss=1 Goltseker, K. Handrus, H. Barak, S. 2019-11-14 doi:10.1101/841536 Cold Spring Harbor Laboratory Press 2019-11-14 <![CDATA[ Variability in the analysis of a single neuroimaging dataset by many teams ]]> https://biorxiv.org/content/10.1101/843193v1?rss=1 Botvinik-Nezer, R. Holzmeister, F. Camerer, C. Dreber, A. Huber, J. Johannesson, M. Kirchler, M. Nichols, T. E. Poldrack, R. A. Schonberg, T. 2019-11-15 doi:10.1101/843193 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Comprehensive post mortem brain samples analysis detects global reduction of multiple proteasome subunits expression in schizophrenia ]]> https://biorxiv.org/content/10.1101/853226v1?rss=1 Hertzberg, L. Maggio, N. Muler, I. Yitzhaky, A. Majer, M. Haroutunian, V. Katsel, P. Domany, E. Weiser, M. 2019-11-25 doi:10.1101/853226 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ A revised mechanism of action of hyperaldosteronism-linked mutations in cytosolic domains of GIRK4 (KCNJ5). ]]> https://biorxiv.org/content/10.1101/866202v1?rss=1 Shalomov, B. Handklo-Jamal, R. Reddy, H. P. Theodor, N. Bera, A. K. Dascal, N. 2019-12-05 doi:10.1101/866202 Cold Spring Harbor Laboratory Press 2019-12-05 <![CDATA[ Compact attractors of an antithetic integral feedback system have a simple structure ]]> https://biorxiv.org/content/10.1101/868000v1?rss=1 Margaliot, M. Sontag, E. D. 2019-12-08 doi:10.1101/868000 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ Addictions may be driven by competition-induced microbiome dysbiosis ]]> https://biorxiv.org/content/10.1101/2022.08.02.502262v1?rss=1 Lewin-Epstein, O. Jaques, Y. Feldman, M. W. Kaufer, D. Hadany, L. 2022-08-02 doi:10.1101/2022.08.02.502262 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Prosperity of the commons: Generalist mycorrhizal species dominate a mixed forest and may promote forest diversity by mediating resource sharing among trees ]]> https://biorxiv.org/content/10.1101/2022.08.01.502298v1?rss=1 Rog, I. Lewin-Epstein, O. Livne-Luzon, S. Hadany, L. Klein, T. 2022-08-03 doi:10.1101/2022.08.01.502298 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Multiple T6SSs, mobile auxiliary modules, and effectors revealed in a systematic analysis of the Vibrio parahaemolyticus pan-genome ]]> https://biorxiv.org/content/10.1101/2022.08.02.502582v1?rss=1 Jana, B. Keppel, K. Fridman, C. M. Bosis, E. Salomon, D. 2022-08-03 doi:10.1101/2022.08.02.502582 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ An Effective mRNA-LNP Vaccine Against the Lethal Plague Bacterium ]]> https://biorxiv.org/content/10.1101/2022.08.07.503096v1?rss=1 Kon, E. Levy, Y. Elia, U. Cohen, H. Halevy, I. Aftalion, M. Ezra, A. Bar-Haim, E. Naidu, G. S. Diesendruck, Y. Rotem, S. Ad-El, N. Goldsmith, M. Mamroud, E. Peer, D. Cohen, O. 2022-08-07 doi:10.1101/2022.08.07.503096 Cold Spring Harbor Laboratory Press 2022-08-07 <![CDATA[ Post-phagocytosis activation of NLRP3 inflammasome by two novel T6SS effectors ]]> https://biorxiv.org/content/10.1101/2022.08.11.503615v1?rss=1 Cohen, H. Baram, N. Fridman, C. M. Edry-Botzer, L. Salomon, D. Gerlic, M. 2022-08-12 doi:10.1101/2022.08.11.503615 Cold Spring Harbor Laboratory Press 2022-08-12 <![CDATA[ The host transcriptional response to superinfection by influenza virus and streptococcus pneumonia ]]> https://biorxiv.org/content/10.1101/2022.08.15.503953v1?rss=1 Cohn, O. Yankovitz, G. Mandelboim, M. Peshes-Yaloz, N. Bacharach, E. Gat-Viks, I. 2022-08-15 doi:10.1101/2022.08.15.503953 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ eIF3 mRNA selectivity profiling reveals eIF3k as a cancer-relevant regulator of ribosome content ]]> https://biorxiv.org/content/10.1101/2022.08.28.505560v1?rss=1 Wolf, D. A. Duan, H. Zhang, S. Zarai, Y. Oellinger, R. Wu, Y. Sun, L. Hu, C. Tian, G. Tuller, T. Rad, R. Cheng, Y. 2022-08-28 doi:10.1101/2022.08.28.505560 Cold Spring Harbor Laboratory Press 2022-08-28 <![CDATA[ Transcriptional response of circadian clock genes to an 'artificial light at night' pulse in the cricket Gryllus bimaculatus ]]> https://biorxiv.org/content/10.1101/2022.08.31.505991v1?rss=1 Levy, K. Fishman, B. Barnea, A. Ayali, A. Tauber, E. 2022-09-01 doi:10.1101/2022.08.31.505991 Cold Spring Harbor Laboratory Press 2022-09-01 <![CDATA[ mTOR pathway inhibition stimulates pharmacologically induced nonsense suppression ]]> https://biorxiv.org/content/10.1101/2022.08.31.506003v1?rss=1 Wittenstein, A. Caspi, M. Rippin, I. Elroy-Stein, O. Eldar-Finkelmn, H. Thoms, S. Rosin-Arbesfeld, R. 2022-09-01 doi:10.1101/2022.08.31.506003 Cold Spring Harbor Laboratory Press 2022-09-01 <![CDATA[ Probing Local Force Propagation in Tensed Fibrous Gels ]]> https://biorxiv.org/content/10.1101/2022.09.07.506942v1?rss=1 Goren, S. Levin, M. Brand, G. Lesman, A. Sorkin, R. 2022-09-09 doi:10.1101/2022.09.07.506942 Cold Spring Harbor Laboratory Press 2022-09-09 <![CDATA[ Revising the global biogeography of plant life cycles ]]> https://biorxiv.org/content/10.1101/2022.09.13.507878v1?rss=1 Poppenwimer, T. Mayrose, I. DeMalach, N. 2022-09-16 doi:10.1101/2022.09.13.507878 Cold Spring Harbor Laboratory Press 2022-09-16 <![CDATA[ A new high-resolution three-dimensional retinal implant: System design and preliminary human results ]]> https://biorxiv.org/content/10.1101/2022.09.14.507901v1?rss=1 Yanovitch, L. Raz-Prag, D. Hanein, Y. 2022-09-17 doi:10.1101/2022.09.14.507901 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ The differential regulation of placenta trophoblast bisphosphoglycerate mutase in fetal growth restriction: preclinical study in mice and observational histological study of human placenta. ]]> https://biorxiv.org/content/10.1101/2022.09.14.507932v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@500160org.highwire.dtl.DTLVardef@8a68a9org.highwire.dtl.DTLVardef@dd60c3org.highwire.dtl.DTLVardef@1fbb209_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Stroganov, S. Harris, T. Fellus-Alyagor, L. Ben Moyal, L. Plitman Mayo, R. Golani, O. Brandis, A. Mehlman, T. Kovo, M. Biron-Shental, T. Dekel, N. Neeman, M. 2022-09-19 doi:10.1101/2022.09.14.507932 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Visual processing and collective motion-related decision-making in desert locusts ]]> https://biorxiv.org/content/10.1101/2022.09.19.508462v1?rss=1 Bleichman, I. Yadav, P. Ayali, A. 2022-09-19 doi:10.1101/2022.09.19.508462 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Kidney-specific methylation patterns correlate with kidney function and are lost upon kidney disease progression ]]> https://biorxiv.org/content/10.1101/2022.09.19.508466v1?rss=1 Sagy, N. Meyrom, N. Beckerman, P. Pleniceanu, O. Bar, D. Z. 2022-09-19 doi:10.1101/2022.09.19.508466 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ PLANAtools - an interactive gene expression repository for the planarian Schmidtea mediterranea ]]> https://biorxiv.org/content/10.1101/2022.09.21.508730v1?rss=1 Hoffman, M. Wurtzel, O. 2022-09-22 doi:10.1101/2022.09.21.508730 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Integration of Gene Expression and DNA Methylation Data Across Different Experiments ]]> https://biorxiv.org/content/10.1101/2022.09.21.508920v1?rss=1 Itai, Y. Rappoport, N. Shamir, R. 2022-09-22 doi:10.1101/2022.09.21.508920 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Metabolic plasticity of T-cell therapies: multi-omic profiling of interacting human tumor-infiltrating lymphocytes and autologous tumor adoptive cell therapy ]]> https://biorxiv.org/content/10.1101/2022.09.28.509590v1?rss=1 Martinez-Paniagua, M. Haymaker, C. Robinson, J. Harel, M. Creasy, C. Adolacion, J. R. T. An, X. Fathi, M. Rezvan, A. Kumar, M. Amritkar, A. Woodman, S. E. Amaria, R. N. Geiger, T. Hwu, P. Bernatchez, C. Varadarajan, N. 2022-09-30 doi:10.1101/2022.09.28.509590 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Clarifying space use concepts in ecology: range vs. occurrence distributions ]]> https://biorxiv.org/content/10.1101/2022.09.29.509951v1?rss=1 Alston, J. M. Fleming, C. H. Noonan, M. J. Tucker, M. A. Silva, I. Folta, C. Akre, T. S. Ali, A. H. Belant, J. L. Beyer, D. Blaum, N. Boehning-Gaese, K. Cunha de Paula, R. Dekker, J. Drescher-Lehman, J. Farwig, N. Fichtel, C. Fischer, C. Ford, A. T. Janssen, R. Jeltsch, F. Kappeler, P. M. LaPoint, S. D. Markham, A. C. Medici, P. Morato, R. G. Nathan, R. Olson, K. Patterson, B. D. Petroelje, T. Ramalho, E. E. Roesner, S. Santos, L. G. R. O. Schabo, D. G. Selva, N. Sergiel, A. Spiegel, O. Ullman, W. Zieba, F. Zwijacz-Kozica, T. Wittemyer, G. Fagan, W. F. 2022-09-30 doi:10.1101/2022.09.29.509951 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Chromatin regulators in the TBX1 network confer risk for conotruncal heart defects in 22q11.2DS and sporadic congenital heart disease ]]> https://biorxiv.org/content/10.1101/2022.09.30.507111v1?rss=1 Zhao, Y. Wang, Y. Shi, L. McDonald-McGinn, D. M. Crowley, T. B. McGinn, D. E. Tran, O. T. Miller, D. Zackai, E. Johnston, H. R. Chow, E. Vorstman, J. A. S. Vingerhoets, C. van Amelsvoort, T. Gothelf, D. Swillen, A. Breckpot, J. Vermeesch, J. R. Eliez, S. Schneider, M. van den Bree, M. B. Owen, M. J. Kates, W. Repetto, G. M. Shashi, V. Schoch, K. Bearden, C. E. Digilio, M. C. E. Unolt, M. Putotto, C. Marino, B. Pontillo, M. Armando, M. Vicari, S. Angkustsiri, K. Campbell, L. Busa, T. Heine-Suner, D. Murphy, K. C. Murphy, D. Garcia-Minaur, S. Fernandez, L 2022-10-03 doi:10.1101/2022.09.30.507111 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ Epigenetic aging waves:Artificial intelligence detects clustering of switch points in DNA methylation rate in defined sex-dependent age periods ]]> https://biorxiv.org/content/10.1101/2022.10.02.510495v1?rss=1 Segev, E. Shahal, T. Konstantinovsky, T. Marcus, Y. Shefer, G. Ebenstein, Y. Pasmanik-Chor, M. Stern, N. 2022-10-05 doi:10.1101/2022.10.02.510495 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ A data-driven approach for predicting the impact of drugs on the human microbiome ]]> https://biorxiv.org/content/10.1101/2022.10.08.510500v1?rss=1 Algavi, Y. Borenstein, E. 2022-10-08 doi:10.1101/2022.10.08.510500 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ Optical Genome and Epigenome Mapping of Clear Cell Renal Cell Carcinoma ]]> https://biorxiv.org/content/10.1101/2022.10.11.511152v1?rss=1 Margalit, S. Tulpova, Z. Michaeli, Y. Detinis Zur, T. Deek, J. Louzoun-Zada, S. Grunwald, A. Scher, Y. Schutz, L. Weinhold, E. Gnatek, Y. Over, D. Dekel, B. Friedman, E. Ebenstein, Y. 2022-10-12 doi:10.1101/2022.10.11.511152 Cold Spring Harbor Laboratory Press 2022-10-12 <![CDATA[ Deep learning algorithms reveal a new visual-semantic representation of familiar faces in human perception and memory ]]> https://biorxiv.org/content/10.1101/2022.10.16.512398v1?rss=1 Shoham, A. Grosbard, I. Patashnik, O. Cohen-Or, D. Yovel, G. 2022-10-18 doi:10.1101/2022.10.16.512398 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Efficient minimizer orders for large values of k using minimum decycling sets ]]> https://biorxiv.org/content/10.1101/2022.10.18.512682v1?rss=1 13, and thus cannot help in the many applications that require minimizer orders for larger k. Here, we close the gap of efficient minimizer orders for large values of k by introducing decycling-set-based minimizer orders, new orders based on minimum decycling sets. We show that in practice these new minimizer orders select a number of k-mers comparable to that of minimizer orders based on universal k-mer hitting sets, and can also scale up to larger k. Furthermore, we developed a method that computes the minimizers in a sequence on the fly without keeping the k-mers of a decycling set in memory. This enables the use of these minimizer orders for any value of k. We expect the new orders to improve the runtime and memory usage of algorithms and data structures in high-throughput DNA sequencing analysis. ]]> Pellow, D. Pu, L. Ekim, B. Kotlar, L. Berger, B. Shamir, R. Orenstein, Y. 2022-10-21 doi:10.1101/2022.10.18.512682 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Global landscape of the host response to SARS-CoV-2 variants reveals viral evolutionary trajectories ]]> https://biorxiv.org/content/10.1101/2022.10.19.512927v1?rss=1 Bouhaddou, M. Reuschl, A.-K. Polacco, B. J. Thorne, L. G. Ummadi, M. R. Ye, C. Ramirez, R. R. Pelin, A. Batra, J. Jang, G. M. Xu, J. Moen, J. M. Richards, A. L. Zhou, Y. Harjai, B. Stevenson, E. Rojc, A. Ragazzini, R. Whelan, M. V. X. Furnon, W. De Lorenzo, G. Cowton, V. Syed, A. M. Ciling, A. Deutsch, N. Pirak, D. Dowgier, G. Mesner, D. Turner, J. L. McGovern, B. L. Rodriguez, M. L. Leiva-Rebollo, R. Dunham, A. S. Zhong, X. Eckhardt, M. Fossati, A. Liotta, N. Kehrer, T. Cupic, A. Rutkowska, M. Mena, N. Aslam, S. Hoffert, A. Foussard, H. Pham, J. Ly 2022-10-21 doi:10.1101/2022.10.19.512927 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ CWLP and PRP940 form plasma-membrane nanodomain complexes with aquaporins, interact with PP2A and contribute to dehydration tolerance ]]> https://biorxiv.org/content/10.1101/2022.10.20.512913v1?rss=1 Honig, A. Eilenberg, H. Zuther, E. Avisar, D. Erster, O. Eshkol, G. Stein, H. Reznik, N. Schuster, S. Belausov, E. Abu-Abied, M. Hotta, T. Lee, Y.-R. J. Liu, B. Sadot, E. Koncz, C. Zilberstein, A. Fichman, Y. 2022-10-21 doi:10.1101/2022.10.20.512913 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Brain substrates of episodic memory for identity, location, and action information: A lesion-behavior mapping study ]]> https://biorxiv.org/content/10.1101/2022.10.21.512938v1?rss=1 Ben-Zvi Feldman, S. Soroker, N. Levy, D. A. 2022-10-24 doi:10.1101/2022.10.21.512938 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Echolocating bats prefer a high risk-high gain foraging strategy to increase prey profitability ]]> https://biorxiv.org/content/10.1101/2022.10.25.513681v1?rss=1 Stidsholt, L. Hubancheva, A. Greif, S. Goerlitz, H. R. Johnson, M. P. Yovel, Y. Madsen, P. T. 2022-10-26 doi:10.1101/2022.10.25.513681 Cold Spring Harbor Laboratory Press 2022-10-26 <![CDATA[ A new class of polymorphic T6SS effectors and tethers ]]> https://biorxiv.org/content/10.1101/2022.10.27.514009v1?rss=1 Kanarek, K. Fridman, C. M. Bosis, E. Salomon, D. 2022-10-27 doi:10.1101/2022.10.27.514009 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Clustering multilayered cytoarchitectonic surface-based data in the brain ]]> https://biorxiv.org/content/10.1101/2022.10.29.514347v1?rss=1 Shamir, I. Assaf, Y. Shamir, R. 2022-10-30 doi:10.1101/2022.10.29.514347 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ Simultaneous global labeling (SiGL) of 5-methylcytosine and 5-hydroxymethylcytosine by DNA alkylation with a synthetic cofactor and engineered methyltransferase ]]> https://biorxiv.org/content/10.1101/2022.10.31.513813v1?rss=1 Avraham, S. schuetz, L. Kaever, L. Dankers, A. Margalit, S. Michaeli, Y. Zirkin, S. Torchinsky, D. Gilat, N. Bahr, O. Nifker, G. Koren-Michowitz, M. Weinhold, E. Ebenstein, Y. 2022-10-31 doi:10.1101/2022.10.31.513813 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ Self-Assembly of Tunable Intrinsically DisorderedPeptide Amphiphiles ]]> https://biorxiv.org/content/10.1101/2022.10.28.514176v1?rss=1 Ehm, T. Shinar, H. Jacoby, G. Meir, S. Koren, G. Segal Asher, M. Korpanty, J. Thompson, M. P. Gianneschi, N. C. Kozlov, M. M. Azoulay-Ginsbur, S. E. Amir, R. Raedler, J. O. Beck, R. 2022-11-01 doi:10.1101/2022.10.28.514176 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Development and validation of an fMRI-informed EEG model of reward-related ventral striatum activation ]]> https://biorxiv.org/content/10.1101/2022.11.01.514407v1?rss=1 Singer, N. Poker, G. Dunsky, N. Nemni, S. Doron, M. Baker, T. Dagher, A. Zatorre, R. Hendler, T. 2022-11-03 doi:10.1101/2022.11.01.514407 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ DeepOM: Single-molecule optical genome mapping via deep learning ]]> https://biorxiv.org/content/10.1101/2022.11.04.512597v1?rss=1 Nogin, Y. Detinis Zur, T. Margalit, S. Barzilai, I. Alalouf, O. Ebenstein, Y. Shechtman, Y. 2022-11-04 doi:10.1101/2022.11.04.512597 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Analysis of Larval Fish Feeding Behavior under Naturalistic Conditions ]]> https://biorxiv.org/content/10.1101/2022.11.14.516417v1?rss=1 Bar, S. Levy, L. Avidan, S. Holzman, R. 2022-11-16 doi:10.1101/2022.11.14.516417 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Vibrio parahaemolyticus T6SS2 effector repertoires ]]> https://biorxiv.org/content/10.1101/2022.11.17.516722v1?rss=1 Tchelet, D. Keppel, K. Bosis, E. Salomon, D. 2022-11-17 doi:10.1101/2022.11.17.516722 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ The role of vertical and horizontal transmission in the assembly of seed fungal endophyte communities in wheat and wheat wild relatives ]]> https://biorxiv.org/content/10.1101/2022.11.21.517337v1?rss=1 Sharon, O. Sun, X. Ezrati, S. Kagan-Trushina, N. Sharon, A. 2022-11-23 doi:10.1101/2022.11.21.517337 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus ]]> https://biorxiv.org/content/10.1101/2022.11.22.517304v1?rss=1 Steenwyk, J. L. Balamurugan, C. Raja, H. A. Goncalves, C. Li, N. Martin, F. Berman, J. Oberlies, N. H. Gibbons, J. G. Goldman, G. H. Geiser, D. M. Hibbett, D. S. Rokas, A. 2022-11-24 doi:10.1101/2022.11.22.517304 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Calredoxin regulates the chloroplast NADPH-dependent thioredoxin reductase in Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2022.11.22.517551v1?rss=1 Zinzius, K. Marchetti, G. M. Fischer, R. Milrad, Y. Oltmanns, A. Kelterborn, S. Yacoby, I. Hegemann, P. Scholz, M. Hippler, M. 2022-11-25 doi:10.1101/2022.11.22.517551 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ RNAlysis: analyze your RNA sequencing data without writing a single line of code ]]> https://biorxiv.org/content/10.1101/2022.11.25.517851v1?rss=1 Teichman, G. Cohen, D. Ganon, O. Dunsky, N. Shani, S. Gingold, H. Rechavi, O. 2022-11-25 doi:10.1101/2022.11.25.517851 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ What makes eye movements effective retrieval cue: The contribution of visual and the motor components to memory performance ]]> https://biorxiv.org/content/10.1101/2022.11.26.517864v1?rss=1 Taub, K. Goshen-Gottstein, Y. Yuval-Greenberg, S. 2022-11-26 doi:10.1101/2022.11.26.517864 Cold Spring Harbor Laboratory Press 2022-11-26 <![CDATA[ Acute effect of antiseizure drugs on background oscillations in Scn1aA1783V Dravet syndrome mouse model ]]> https://biorxiv.org/content/10.1101/2022.11.29.518351v1?rss=1 Quinn, S. Brusel, M. Ovadia, M. Rubinstein, M. 2022-11-29 doi:10.1101/2022.11.29.518351 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ Antifungal tolerance and resistance emerge at distinct drug concentrations and rely upon different aneuploid chromosomes ]]> https://biorxiv.org/content/10.1101/2022.11.30.518455v1?rss=1 Yang, F. Scopel, E. F. Li, H. Sun, L. Kawar, N. Cao, Y. Jiang, Y. Berman, J. 2022-12-02 doi:10.1101/2022.11.30.518455 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Unprecedented yet gradual nature of first millennium CE intercontinental crop plant dispersal revealed in ancient Negev desert refuse ]]> https://biorxiv.org/content/10.1101/2022.12.01.518650v1?rss=1 Fuks, D. Melamed, Y. Langgut, D. Erickson-Gini, T. Tepper, Y. Bar-Oz, G. Weiss, E. 2022-12-02 doi:10.1101/2022.12.01.518650 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Consilience in disease ecology: FMDV transmission dynamics reflect viral growth and immune response rates. ]]> https://biorxiv.org/content/10.1101/2022.12.02.518883v1?rss=1 Macdonald, J. C. Gulbudak, H. Beechler, B. Gorsich, E. Gubbins, S. Perez-Martin, E. Jolles, A. 2022-12-03 doi:10.1101/2022.12.02.518883 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ Characterizing habit learning in the human brain at the individual and group levels: a multi-modal MRI study ]]> https://biorxiv.org/content/10.1101/2022.12.12.520188v1?rss=1 Gera, R. Bar Or, M. Tavor, I. Roll, D. Cockburn, J. Barak, S. Tricomi, E. O'Doherty, J. P. Schonberg, T. 2022-12-13 doi:10.1101/2022.12.12.520188 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Human intestinal epithelial cells can internalize luminal fungi via LC3-associated phagocytosis ]]> https://biorxiv.org/content/10.1101/2022.12.14.520372v1?rss=1 Cohen-Kedar, S. Shaham Barda, E. Rabinowitz, K. M. Keizer, D. Abu-Taha, H. Schwartz, S. Kaboub, K. Baram, L. Sadot, E. White, I. Wasserberg, N. Wolff-Bar, M. Levy-Barda, A. Dotan, I. 2022-12-15 doi:10.1101/2022.12.14.520372 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Cultural transmission, competition for prey, and the evolution of cooperative hunting ]]> https://biorxiv.org/content/10.1101/2022.12.14.520505v1?rss=1 Borofsky, T. M. Feldman, M. W. Ram, Y. 2022-12-15 doi:10.1101/2022.12.14.520505 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Soaring migrants flexibly respond to sea-breeze in a migratory bottleneck: using first derivatives to identify behavioural adjustments over time ]]> https://biorxiv.org/content/10.1101/2022.12.15.520614v1?rss=1 Becciu, P. Troupin, D. Dinevich, L. Leshem, Y. Sapir, N. 2022-12-15 doi:10.1101/2022.12.15.520614 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Passive identification of subjective preferences towards individual items using eye-tracking in a virtual reality environment ]]> https://biorxiv.org/content/10.1101/2022.12.18.520570v1?rss=1 Gabay, M. Schonberg, T. 2022-12-18 doi:10.1101/2022.12.18.520570 Cold Spring Harbor Laboratory Press 2022-12-18 <![CDATA[ The trembling hand unraveled: the motor dynamics and neural sources of choice inconsistency ]]> https://biorxiv.org/content/10.1101/2022.12.20.521216v1?rss=1 Kurtz-David, V. Madar, A. Hakim, A. Palmon, N. Levy, D. J. 2022-12-20 doi:10.1101/2022.12.20.521216 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Altered somatic hypermutation patterns in COVID-19 patients classifies disease severity ]]> https://biorxiv.org/content/10.1101/2022.12.20.521139v1?rss=1 Safra, M. Tamari, Z. Polak, P. Shiber, S. Matan, M. Karameh, H. Helviz, Y. Levy-Barda, A. Yahalom, V. Peretz, A. Ben-Chetrit, E. Brenner, B. Tuller, T. Gal-Tanamy, M. Yaari, G. 2022-12-21 doi:10.1101/2022.12.20.521139 Cold Spring Harbor Laboratory Press 2022-12-21 <![CDATA[ A novel performance scoring quantification framework for stress test set-ups ]]> https://biorxiv.org/content/10.1101/2022.12.21.521346v1?rss=1 Kozlovski, T. Hausdorff, J. M. Davidov, O. Giladi, N. Mirelman, A. Benjamini, Y. 2022-12-21 doi:10.1101/2022.12.21.521346 Cold Spring Harbor Laboratory Press 2022-12-21 <![CDATA[ Neural Synchronization as a Function of Engagement with the Narrative ]]> https://biorxiv.org/content/10.1101/2023.01.01.522416v1?rss=1 Ohad, T. Yeshurun, Y. 2023-01-02 doi:10.1101/2023.01.01.522416 Cold Spring Harbor Laboratory Press 2023-01-02 <![CDATA[ The online metacognitive control of decisions ]]> https://biorxiv.org/content/10.1101/2023.01.02.522463v1?rss=1 Lee, D. G. Benon, J. Hopper, W. Verdeil, M. Pessiglione, M. Vinckier, F. Bouret, S. Rouault, M. Lebouc, R. Pezzulo, G. Schreiweis, C. Burguiere, E. Daunizeau, J. 2023-01-02 doi:10.1101/2023.01.02.522463 Cold Spring Harbor Laboratory Press 2023-01-02 <![CDATA[ The Labbing Project: A database management application for neuroimaging research ]]> https://biorxiv.org/content/10.1101/2023.01.02.522426v1?rss=1 Baratz, Z. Assaf, Y. 2023-01-03 doi:10.1101/2023.01.02.522426 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Optimizing FreeSurfer's Surface Reconstruction Parameters for Anatomical Feature Estimation ]]> https://biorxiv.org/content/10.1101/2023.01.02.522457v1?rss=1 Baratz, Z. Assaf, Y. 2023-01-03 doi:10.1101/2023.01.02.522457 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Revealing how memory shapes time-dependent computational processes in plant tropisms ]]> https://biorxiv.org/content/10.1101/2023.01.06.522981v1?rss=1 Riviere, M. Meroz, Y. 2023-01-06 doi:10.1101/2023.01.06.522981 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Modeling of growth of Ulva sp. macroalgae in a controlled photobioreactor based on nitrogen accumulation dynamics ]]> https://biorxiv.org/content/10.1101/2023.01.08.523140v1?rss=1 Zollmann, M. Liberzon, A. Golberg, A. 2023-01-08 doi:10.1101/2023.01.08.523140 Cold Spring Harbor Laboratory Press 2023-01-08 <![CDATA[ Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation ]]> https://biorxiv.org/content/10.1101/2023.01.09.523230v1?rss=1 Caspi, I. Meir, M. Ben Nun, N. Stern, A. Ram, Y. 2023-01-09 doi:10.1101/2023.01.09.523230 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ Cultivation of Ulva sp. offshore the Eastern Mediterranean Sea in experimental bioreactors: seasonal growth dynamics and environmental effects ]]> https://biorxiv.org/content/10.1101/2023.01.15.524102v1?rss=1 Zollmann, M. Liberzon, A. Palatnik, R. R. Zilberman, D. Golberg, A. 2023-01-18 doi:10.1101/2023.01.15.524102 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Vision-Based Collective Motion: A Locust-Inspired Reductionist Model ]]> https://biorxiv.org/content/10.1101/2023.01.17.524210v1?rss=1 Krongauz, D. L. Ayali, A. Kaminka, G. A. 2023-01-20 doi:10.1101/2023.01.17.524210 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ C-terminal conformational changes in SCF-D3/MAX2 ubiquitin ligase are required for KAI2-mediated signaling ]]> https://biorxiv.org/content/10.1101/2023.01.19.524830v1?rss=1 Tal, L. Guercio, A. M. Varshney, K. Young, A. Gutjahr, C. Shabek, N. 2023-01-20 doi:10.1101/2023.01.19.524830 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ 4CAC: 4-class classification of metagenome assembliesusing machine learning and assembly graphs ]]> https://biorxiv.org/content/10.1101/2023.01.20.524935v1?rss=1 Pu, L. Shamir, R. 2023-01-21 doi:10.1101/2023.01.20.524935 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ Lost in space(s): multimodal neuroimaging of disorientation along the Alzheimer's disease continuum ]]> https://biorxiv.org/content/10.1101/2023.01.25.525587v1?rss=1 Peters-Founshtein, G. Gazit, L. Naveh, T. Domachevsky, L. Korczyn, A. Bernstine, H. Groshar, D. Marshall, G. Arzy, S. 2023-01-26 doi:10.1101/2023.01.25.525587 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ Human aneuploid cells depend on the RAF/MEK/ERK pathway for overcoming increased DNA damage ]]> https://biorxiv.org/content/10.1101/2023.01.27.525822v1?rss=1 Zerbib, J. Ippolito, M. R. Eliezer, Y. De Feudis, G. Reuveni, E. Kadmon, A. S. Martin, S. Vigano', S. Leor, G. Berstler, J. Laue, K. Cohen-Sharir, Y. Scorzoni, S. Vazquez, F. Ben-David, U. Santaguida, S. 2023-01-27 doi:10.1101/2023.01.27.525822 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Increased RNA and protein degradation is required for counteracting transcriptional burden and proteotoxic stress in human aneuploid cells ]]> https://biorxiv.org/content/10.1101/2023.01.27.525826v1?rss=1 Ippolito, M. R. Zerbib, J. Eliezer, Y. Reuveni, E. Vigano', S. De Feudis, G. Kadmon, A. S. Vigorito, I. Martin, S. Laue, K. Cohen-Sharir, Y. Scorzoni, S. Vazquez, F. Santaguida, S. Ben-David, U. 2023-01-27 doi:10.1101/2023.01.27.525826 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Iron Regulatory Protein 1 is Required for the Propagation of Inflammation in Inflammatory Bowel Disease ]]> https://biorxiv.org/content/10.1101/2023.01.27.525690v1?rss=1 Fahoum, L. Belizowsky, S. Ghatpande, N. Guttmann-Raviv, N. Zhang, W. Kuanyu, L. Wing-Hang, T. Nyska, A. Waterman, M. Weisshof, R. Zukirman, A. Meyron-Holtz, E. 2023-01-28 doi:10.1101/2023.01.27.525690 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ Heat-induced seizures, premature mortality, and hyperactivity in a novel Scn1a nonsense model for Dravet syndrome ]]> https://biorxiv.org/content/10.1101/2023.02.01.526678v1?rss=1 Mavashov, A. Brusel, M. Liu, J. Woytowicz, V. Bae, H. Chen, Y.-H. Dani, V. S. Cardenal, E. Spinosa, V. Aibar, J. A. Rubinstein, M. 2023-02-02 doi:10.1101/2023.02.01.526678 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ Lifelong tissue memory relies on spatially organised dedicated progenitors located distally from the injury ]]> https://biorxiv.org/content/10.1101/2023.02.02.526841v1?rss=1 Levron, C. L. Watanabe, M. Proserpio, V. Piacenti, G. Lauria, A. Kaltenbach, S. Nohara, T. Anselmi, F. Duval, C. Donna, D. Baev, D. Natsuga, K. Hagai, T. Oliviero, S. Donati, G. 2023-02-03 doi:10.1101/2023.02.02.526841 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Phenotype switching of the mutation rate facilitates adaptive evolution ]]> https://biorxiv.org/content/10.1101/2023.02.06.527392v1?rss=1 Lobinska, G. A. Pilpel, Y. Ram, Y. 2023-02-07 doi:10.1101/2023.02.06.527392 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ Coordination between endoderm progression and gastruloid elongation controls endodermal morphotype choice ]]> https://biorxiv.org/content/10.1101/2023.02.07.527329v1?rss=1 Farag, N. Schiff, C. Nachman, I. 2023-02-08 doi:10.1101/2023.02.07.527329 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ Chemoresistome Mapping in Individual Breast Cancer Patients Unravels Diversity in Dynamic Transcriptional Adaptation ]]> https://biorxiv.org/content/10.1101/2023.02.09.527790v1?rss=1 Dadiani, M. Friedlander, G. Perry, G. Balint-Lahat, N. Gilad, S. Morzaev-Sulzbach, D. Bossel Ben-Moshe, N. Pavlovski, A. Domany, E. Shenoy, A. Barshack, I. Geiger, T. Kaufman, B. Gal-Yam, E. N. 2023-02-10 doi:10.1101/2023.02.09.527790 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Attachment Stimuli Trigger Widespread Synchrony across Multiple Brains ]]> https://biorxiv.org/content/10.1101/2023.02.10.527970v1?rss=1 Shimon-Raz, O. Yeshurun, Y. Ulmer-Yaniv, A. Levinkron, A. Salomon, R. Feldman, R. 2023-02-12 doi:10.1101/2023.02.10.527970 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ A diverse repertoire of anti-defense systems is encoded in the leading region of plasmids ]]> https://biorxiv.org/content/10.1101/2023.02.15.528439v1?rss=1 Samuel, B. Burstein, D. 2023-02-16 doi:10.1101/2023.02.15.528439 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Broad sensitivity of Candida auris strains to quinolones and mechanisms of resistance ]]> https://biorxiv.org/content/10.1101/2023.02.16.528905v1?rss=1 Lohse, M. B. Laurie, M. T. Levan, S. Ziv, N. Ennis, C. L. Nobile, C. J. DeRisi, J. L. Johnson, A. D. 2023-02-17 doi:10.1101/2023.02.16.528905 Cold Spring Harbor Laboratory Press 2023-02-17 <![CDATA[ The contribution of eye movements to memory retrieval depends on the visual input ]]> https://biorxiv.org/content/10.1101/2023.02.19.529117v1?rss=1 Taub, K. Yuval-Greenberg, S. 2023-02-19 doi:10.1101/2023.02.19.529117 Cold Spring Harbor Laboratory Press 2023-02-19 <![CDATA[ Imprinted cell memory in glycogen storage disorder 1a ]]> https://biorxiv.org/content/10.1101/2023.02.20.529109v1?rss=1 Sprecher, U. Dsouza, J. Mishra, K. Miliano, A. C. Mithieux, G. Rajas, F. Avraham, S. Anikster, Y. Kakhlon, O. Weil, M. 2023-02-20 doi:10.1101/2023.02.20.529109 Cold Spring Harbor Laboratory Press 2023-02-20 <![CDATA[ It's all about location: reliance on spatial rather than visual context when trying to remember ]]> https://biorxiv.org/content/10.1101/2023.02.20.529294v1?rss=1 Taub, K. Yuval-Greenberg, S. 2023-02-20 doi:10.1101/2023.02.20.529294 Cold Spring Harbor Laboratory Press 2023-02-20 <![CDATA[ Predicting Individual Traits From T1-weighted Anatomical MRI Using the Xception CNN Architecture ]]> https://biorxiv.org/content/10.1101/2023.02.20.529226v1?rss=1 Baratz, Z. Assaf, Y. 2023-02-21 doi:10.1101/2023.02.20.529226 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Control of telomere length in yeast by SUMOylated PCNA and the Elg1 PCNA unloader ]]> https://biorxiv.org/content/10.1101/2023.02.22.529580v1?rss=1 Singh, P. Gazy, I. Kupiec, M. 2023-02-23 doi:10.1101/2023.02.22.529580 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ White matter properties in fronto-parietal tracts predict maladaptive functional activation and deficient response inhibition in ADHD ]]> https://biorxiv.org/content/10.1101/2023.03.02.530758v1?rss=1 Smullen, D. Bagshaw, A. P. Shalev, L. Tsafrir, S. Mevorach, C. 2023-03-02 doi:10.1101/2023.03.02.530758 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ A Vibrio T6SS-mediated lethality in a marine animal model ]]> https://biorxiv.org/content/10.1101/2023.03.06.530577v1?rss=1 Cohen, H. Gerlic, M. Salomon, D. 2023-03-06 doi:10.1101/2023.03.06.530577 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Alleviating the barrier of adventitious roots formation in recalcitrant mature tissue by slow release of a synthetic auxin ]]> https://biorxiv.org/content/10.1101/2023.03.13.532257v1?rss=1 Roth, O. Yechezkel, S. Serero, O. Eliyahu, A. Vints, I. Tzeela, P. Carignano, A. Janacek, D. P. Peters, V. Kessel, A. Dwivedi, V. Carmeli-Weissberg, M. Shaya, F. Faigenboim-Doron, A. Riov, J. Klavins, E. Dawid, C. Hammes, U. Z. Ben-Tal, N. Napier, R. Sadot, E. Weinstain, R. 2023-03-13 doi:10.1101/2023.03.13.532257 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ Behavioral and neuroimaging correlates of attentional biases to angry faces in individuals in remission from depression: a population-derived study ]]> https://biorxiv.org/content/10.1101/2023.03.13.532400v1?rss=1 Nagrodzki, J. Passamonti, L. Schweizer, S. Stretton, J. Knights, E. Henson, R. N. Cam-CAN, Wolpe, N. 2023-03-14 doi:10.1101/2023.03.13.532400 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Mechanism of tension propagation in cell membranes ]]> https://biorxiv.org/content/10.1101/2023.03.22.533804v1?rss=1 Barnoy, A. Tsaturyan, A. K. Kozlov, M. M. 2023-03-22 doi:10.1101/2023.03.22.533804 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ Serine peptidases and increased amounts of soluble proteins contribute to heat priming of the plant pathogenic fungus Botrytis cinerea ]]> https://biorxiv.org/content/10.1101/2023.03.23.534054v1?rss=1 ZHANG, M. Trushina, N. Lang, T. Hahn, M. Pasmanik-Chor, M. Sharon, A. 2023-03-24 doi:10.1101/2023.03.23.534054 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Positive and biphasic extracellular waveforms correspond to return currents and axonal spikes ]]> https://biorxiv.org/content/10.1101/2023.03.24.534099v1?rss=1 Someck, S. Levi, A. Sloin, H. E. Spivak, L. Gattegno, R. Stark, E. 2023-03-25 doi:10.1101/2023.03.24.534099 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ An efficient, scarless, selection-free technology for phage engineering ]]> https://biorxiv.org/content/10.1101/2023.03.26.534254v1?rss=1 Goren, M. G. Mahata, T. Qimron, U. 2023-03-26 doi:10.1101/2023.03.26.534254 Cold Spring Harbor Laboratory Press 2023-03-26 <![CDATA[ A widespread bacterial mobile genetic element encodes weapons against phages, bacteria, and eukaryotes ]]> https://biorxiv.org/content/10.1101/2023.03.28.534373v1?rss=1 MAHATA, T. Kanarek, K. Goren, M. G. Bosis, E. Qimron, U. Salomon, D. 2023-03-28 doi:10.1101/2023.03.28.534373 Cold Spring Harbor Laboratory Press 2023-03-28 <![CDATA[ A visual paired associate learning (vPAL) paradigm to study memory consolidation during sleep ]]> https://biorxiv.org/content/10.1101/2023.03.28.534494v1?rss=1 Schmidig, F. J. Geva-Sagiv, M. Falach, R. Yakim, S. Gat, Y. Sharon, O. Fried, I. Nir, Y. 2023-03-28 doi:10.1101/2023.03.28.534494 Cold Spring Harbor Laboratory Press 2023-03-28 <![CDATA[ Learning to learn: Single session acquisition of new rules by freely-moving mice ]]> https://biorxiv.org/content/10.1101/2023.03.28.534599v1?rss=1 Levi, A. Aviv, N. Stark, E. 2023-03-28 doi:10.1101/2023.03.28.534599 Cold Spring Harbor Laboratory Press 2023-03-28 <![CDATA[ Conversion of methionine biosynthesis in E. coli from trans- to direct-sulfurylation enhances extracellular methionine levels ]]> https://biorxiv.org/content/10.1101/2023.03.28.534524v1?rss=1 Gruzdev, N. Hacham, Y. Haviv, H. Stern, I. Gabay, M. Bloch, I. Amir, R. Gal, M. Yadid, I. 2023-03-29 doi:10.1101/2023.03.28.534524 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Short-term auditory priming in freely-moving mice ]]> https://biorxiv.org/content/10.1101/2023.04.03.535329v1?rss=1 Sivroni, S. Sloin, H. E. Stark, E. 2023-04-03 doi:10.1101/2023.04.03.535329 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Sequential effect in pre-stimulus oculomotor inhibition ]]> https://biorxiv.org/content/10.1101/2023.04.04.535537v1?rss=1 Tal-Perry, N. Yuval-Greenberg, S. 2023-04-04 doi:10.1101/2023.04.04.535537 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ A quantitative model for spatio-temporal dynamics of root gravitropism ]]> https://biorxiv.org/content/10.1101/2023.04.11.536255v1?rss=1 Porat, A. Riviere, M. Meroz, Y. 2023-04-11 doi:10.1101/2023.04.11.536255 Cold Spring Harbor Laboratory Press 2023-04-11 <![CDATA[ Computationally Engineered CRISPR-SpyCas9 High-Fidelity Variants with Improved Specificity and Reduced Non-specific DNA Damage ]]> https://biorxiv.org/content/10.1101/2023.04.11.536265v1?rss=1 Rabinowitz, R. Shor, O. Zerbib, J. Herman, S. Zelikson, N. Madiwale, S. Yom-Tov, N. Ben-David, U. Benninger, F. Offen, D. 2023-04-11 doi:10.1101/2023.04.11.536265 Cold Spring Harbor Laboratory Press 2023-04-11 <![CDATA[ Immune clustering reveals molecularly distinct subtypes of lung adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2023.04.17.537140v1?rss=1 Lender, Y. 2023-04-17 doi:10.1101/2023.04.17.537140 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Harnessing the flexibility of neural networks to predict dynamic theoretical parameters underlying human choice behavior ]]> https://biorxiv.org/content/10.1101/2023.04.21.537666v1?rss=1 Ger, Y. Nachmani, E. Wolf, L. Shahar, N. 2023-04-21 doi:10.1101/2023.04.21.537666 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Dating ancient humans splits by estimating Poisson rates from mitochondrial DNA parity samples ]]> https://biorxiv.org/content/10.1101/2023.04.21.537838v1?rss=1 Levinstein Hallak, K. Rosset, S. 2023-04-21 doi:10.1101/2023.04.21.537838 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ A comparative analysis of the antiviral response in two bat species reveals conserved and divergent innate immune pathways ]]> https://biorxiv.org/content/10.1101/2023.04.23.537989v1?rss=1 Schneor, L. Kaltenbach, S. Fridman, S. Nissan, Y. Shuler, G. Fraimovitch, E. Weinberg, M. Kolodziejczyk, A. A. Donati, G. Teeling, E. C. Yovel, Y. Hagai, T. 2023-04-23 doi:10.1101/2023.04.23.537989 Cold Spring Harbor Laboratory Press 2023-04-23 <![CDATA[ Temporally correlated active forces drive chromosome structure and dynamics ]]> https://biorxiv.org/content/10.1101/2023.04.23.528410v1?rss=1 Brahmachari, S. Markovich, T. MacKintosh, F. C. Onuchic, J. N. 2023-04-24 doi:10.1101/2023.04.23.528410 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ Arbitrium communication controls phage life-cycle through modulation of a bacterial anti-phage defense system ]]> https://biorxiv.org/content/10.1101/2023.04.27.537455v1?rss=1 Guler, P. Omer Bendori, S. Aframian, N. Kessel, A. Eldar, A. 2023-04-27 doi:10.1101/2023.04.27.537455 Cold Spring Harbor Laboratory Press 2023-04-27 <![CDATA[ CryoEM PSII structure reveals adaptation mechanisms to environmental stress in Chlorella ohadii ]]> https://biorxiv.org/content/10.1101/2023.05.04.539358v1?rss=1 Fadeeva, M. Klaiman, D. Caspy, I. Nelson, N. 2023-05-04 doi:10.1101/2023.05.04.539358 Cold Spring Harbor Laboratory Press 2023-05-04 <![CDATA[ Epigenetic information loss is a common feature of multiple diseases and aging ]]> https://biorxiv.org/content/10.1101/2023.05.07.539727v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@12049e0org.highwire.dtl.DTLVardef@d214c7org.highwire.dtl.DTLVardef@52425forg.highwire.dtl.DTLVardef@839011_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO Tissue unique methylation pattern regress toward the mean upon disease. A single methylation site, showing low methylation in the liver and high in every other tissue, becomes more methylated in diseased livers. C_FIG ]]> Sagy, N. Chang, C. Bar, D. Z. 2023-05-07 doi:10.1101/2023.05.07.539727 Cold Spring Harbor Laboratory Press 2023-05-07 <![CDATA[ On the mechanical origins of waving, coiling and skewing in Arabidopsis thaliana roots ]]> https://biorxiv.org/content/10.1101/2023.05.17.541081v1?rss=1 Porat, A. Tekinalp, A. Bhosale, Y. Gazzola, M. Meroz, Y. 2023-05-19 doi:10.1101/2023.05.17.541081 Cold Spring Harbor Laboratory Press 2023-05-19 <![CDATA[ Wired together, change together: Spike timing modifies transmission in converging assemblies ]]> https://biorxiv.org/content/10.1101/2023.05.22.541797v1?rss=1 Spivak, L. Someck, S. Levi, A. Sivroni, S. Stark, E. 2023-05-24 doi:10.1101/2023.05.22.541797 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Design of optimal labeling patterns for optical genome mapping via information theory ]]> https://biorxiv.org/content/10.1101/2023.05.23.541882v1?rss=1 Nogin, Y. Bar-Lev, D. Hanania, D. Detinis Zur, T. Ebenstein, Y. Yaakobi, E. Weinberger, N. Shechtman, Y. 2023-05-24 doi:10.1101/2023.05.23.541882 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Brainways: An Open-Source AI-based Software For Registration and Analysis of Fluorescent Markers on Coronal Brain Slices ]]> https://biorxiv.org/content/10.1101/2023.05.25.542252v1?rss=1 Kantor, B. Ben-Ami Bartal, I. 2023-05-25 doi:10.1101/2023.05.25.542252 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ The variation and evolution of complete human centromeres ]]> https://biorxiv.org/content/10.1101/2023.05.30.542849v1?rss=1 Logsdon, G. A. Rozanski, A. N. Ryabov, F. Potapova, T. Shepelev, V. A. Mao, Y. Rautiainen, M. Koren, S. Nurk, S. Porubsky, D. Lucas, J. K. Hoekzema, K. Munson, K. M. Gerton, J. L. Phillippy, A. M. Alexandrov, I. A. Eichler, E. E. 2023-05-31 doi:10.1101/2023.05.30.542849 Cold Spring Harbor Laboratory Press 2023-05-31 <![CDATA[ Loss of Lamin A leads to the nuclear translocation of AGO2 and compromised RNA interference ]]> https://biorxiv.org/content/10.1101/2023.06.05.543674v1?rss=1 Lobo, V. Nowak, I. Fernandez, C. Correa Muler, A. I. Westholm, J. O. Huang, H.-C. Fabrik, I. Huynh, H. T. Kanik, M. Hartlova, A. Benhalevy, D. Angeletti, D. Sarshad, A. A. 2023-06-05 doi:10.1101/2023.06.05.543674 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Species and habitat specific changes in bird activity in an urban environment during Covid 19 lockdown ]]> https://biorxiv.org/content/10.1101/2023.06.03.543542v1?rss=1 Sun, C. Hassin, Y. Boonman, A. Shwartz, A. Yovel, Y. 2023-06-06 doi:10.1101/2023.06.03.543542 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ Exposure to temporal randomness promotes subsequent adaptation to new temporal regularities ]]> https://biorxiv.org/content/10.1101/2023.06.04.543595v1?rss=1 Shdeour, O. R. Tal-Perry, N. Glickman, M. Yuval-Greenberg, S. 2023-06-06 doi:10.1101/2023.06.04.543595 Cold Spring Harbor Laboratory Press 2023-06-06 <![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[ An adversarial collaboration to critically evaluate theories of consciousness ]]> https://biorxiv.org/content/10.1101/2023.06.23.546249v1?rss=1 Cogitate Consortium, Ferrante, O. Gorska-Klimowska, U. Henin, S. Hirschhorn, R. Khalaf, A. Lepauvre, A. Liu, L. Richter, D. Vidal, Y. Bonacchi, N. Brown, T. Sripad, P. Armendariz, M. Bendtz, K. Ghafari, T. Hetenyi, D. Jeschke, J. Kozma, C. Mazumder, D. R. Montenegro, S. Seedat, A. Sharafeldin, A. Yang, S. Baillet, S. Chalmers, D. J. Cichy, R. M. Fallon, F. Panagiotaropoulos, T. I. Blumenfeld, H. Devore, S. Jensen, O. Kreiman, G. de Lange, F. P. Luo, H. Boly, M. Dehaene, S. Koch, C. Tononi, G. Pitts, M. Mudrik, L. Melloni, L. 2023-06-26 doi:10.1101/2023.06.23.546249 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ A bistable inhibitory OptoGPCR for multiplexed optogenetic control of neural circuits ]]> https://biorxiv.org/content/10.1101/2023.07.01.547328v1?rss=1 Wietek, J. Nozownik, A. Pulin, M. Saraf-Sinik, I. Matosevich, N. Malan, D. Brown, B. J. Dine, J. Levy, R. Litvin, A. Regev, N. Subramaniam, S. Bitton, E. Benjamin, A. Copits, B. A. Sasse, P. Rost, B. R. Schmitz, D. Soba, P. Nir, Y. Wiegert, J. S. Yizhar, O. 2023-07-02 doi:10.1101/2023.07.01.547328 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Multi-view integration of microbiome data for predicting host disease and identifying disease-associated features ]]> https://biorxiv.org/content/10.1101/2023.07.03.547607v1?rss=1 Muller, E. Shiryan, I. Borenstein, E. 2023-07-04 doi:10.1101/2023.07.03.547607 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ Machine-learning analysis of factors that shape cancer aneuploidy landscapes reveals an important role for negative selection ]]> https://biorxiv.org/content/10.1101/2023.07.05.547626v1?rss=1 Jubran, J. Slutsky, R. Rozenblum, N. Rokach, L. Ben-David, U. Yeger-Lotem, E. 2023-07-05 doi:10.1101/2023.07.05.547626 Cold Spring Harbor Laboratory Press 2023-07-05 <![CDATA[ The reward system plays a role in natural story comprehension ]]> https://biorxiv.org/content/10.1101/2023.07.13.548681v1?rss=1 Kobo, O. Yeshurun, Y. Schonberg, T. 2023-07-13 doi:10.1101/2023.07.13.548681 Cold Spring Harbor Laboratory Press 2023-07-13 <![CDATA[ Peptriever: A Bi-Encoder approach for large-scale protein-peptide binding search ]]> https://biorxiv.org/content/10.1101/2023.07.13.548811v1?rss=1 Gurvich, R. Markel, G. Tanoli, Z. Meirson, T. 2023-07-13 doi:10.1101/2023.07.13.548811 Cold Spring Harbor Laboratory Press 2023-07-13 <![CDATA[ An N-terminal delivery domain defines a new class of polymorphic T6SS effectors in Enterobacterales ]]> https://biorxiv.org/content/10.1101/2023.07.16.549128v1?rss=1 Carobbi, A. di Nepi, S. Bosis, E. Salomon, D. Sessa, G. 2023-07-16 doi:10.1101/2023.07.16.549128 Cold Spring Harbor Laboratory Press 2023-07-16 <![CDATA[ Using big sequencing data to identify chronic SARS-Coronavirus-2 infections ]]> https://biorxiv.org/content/10.1101/2023.07.16.549184v1?rss=1 Harari, S. Miller, D. Fleishon, S. Burstein, D. Stern, A. 2023-07-17 doi:10.1101/2023.07.16.549184 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ Reaching the tumor: mobility of polymeric micelles inside an in vitro tumor-on-a-chip model with dual ECM ]]> https://biorxiv.org/content/10.1101/2023.07.14.548885v1?rss=1 Olea, A. R. Jurado, A. Slor, G. Tevet, S. Pujals, S. De La Rosa, V. R. Hoogenboom, R. Amir, R. J. Albertazzi, L. 2023-07-18 doi:10.1101/2023.07.14.548885 Cold Spring Harbor Laboratory Press 2023-07-18 <![CDATA[ Systematics of harvester ants (Messor) in Israel based on integrated morphological, genetic, and ecological data ]]> https://biorxiv.org/content/10.1101/2023.07.16.549226v1?rss=1 Saar, M. Eyer, P. A. Magory Cohen, T. Ionescu-Hirsch, A. Dor, R. Dorchin, N. 2023-07-18 doi:10.1101/2023.07.16.549226 Cold Spring Harbor Laboratory Press 2023-07-18 <![CDATA[ Methods for cell isolation and analysis of the highly regenerative tunicate Polycarpa mytiligera ]]> https://biorxiv.org/content/10.1101/2023.07.21.549655v1?rss=1 Gordon, T. Hendin, N. Wurtzel, O. 2023-07-22 doi:10.1101/2023.07.21.549655 Cold Spring Harbor Laboratory Press 2023-07-22 <![CDATA[ Migrasome formation is initiated preferentially in tubular junctions by alternations of membrane tension or intracellular pressure ]]> https://biorxiv.org/content/10.1101/2023.08.03.551756v1?rss=1 Zuker, B. Dharan, R. Wang, D. Yu, L. Sorkin, R. Kozlov, M. 2023-08-04 doi:10.1101/2023.08.03.551756 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ Evaluation of the Ability of AlphaFold to Predict the Three-Dimensional Structures of Antibodies and Epitopes ]]> https://biorxiv.org/content/10.1101/2023.08.03.551715v1?rss=1 Polonsky, K. Pupko, T. Freund, N. 2023-08-06 doi:10.1101/2023.08.03.551715 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ Sex-Specific Developmental Gene Expression Atlas Unveils Dimorphic Gene Networks in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.08.05.552096v1?rss=1 Haque, R. Peedikayil-Kurien, S. Setty, H. Salzberg, Y. Stelzer, G. Litvak, E. Gingold, H. Rechavi, O. Oren-Suissa, M. 2023-08-06 doi:10.1101/2023.08.05.552096 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ TGF-β1 inhibits cholesterol metabolism in hepatocytes to facilitate cell death, EMT and signals for HSC activation. ]]> https://biorxiv.org/content/10.1101/2023.08.14.552900v1?rss=1 Wang, S. Link, F. Han, M. Liebe, R. Yao, Y. Hammad, S. Dropmann, A. Chaudhary, R. Asimakopoulos, A. Krizanac, M. Weiskirchen, R. Henis, Y. I. Ehrlich, M. Ebert, M. Dooley, S. 2023-08-15 doi:10.1101/2023.08.14.552900 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Effect of Tokenization on Transformers for Biological Sequences ]]> https://biorxiv.org/content/10.1101/2023.08.15.553415v1?rss=1 Dotan, E. Jaschek, G. Pupko, T. Belinkov, Y. 2023-08-17 doi:10.1101/2023.08.15.553415 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Calcium regulation of the Arabidopsis Na+/K+ transporter HKT1;1 improves seed germination under salt stress ]]> https://biorxiv.org/content/10.1101/2023.08.17.553671v1?rss=1 Chandran, A. E. J. Finkler, A. Hait, T. A. Kiere, Y. David, S. Pasmanik-Chor, M. Shkolnik, D. 2023-08-18 doi:10.1101/2023.08.17.553671 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ Local activation of CA1 pyramidal cells induces theta phase precession ]]> https://biorxiv.org/content/10.1101/2023.08.19.553985v1?rss=1 Sloin, H. Spivak, L. Levi, A. Gattegno, R. Someck, S. Stark, E. 2023-08-21 doi:10.1101/2023.08.19.553985 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Chloride intracellular channel (CLIC) proteins function as fusogens ]]> https://biorxiv.org/content/10.1101/2023.08.27.554981v1?rss=1 Manori, B. Vaknin, A. Vankova, P. Nitzan, A. Zaidel-Bar, R. Man, P. Giladi, M. Haitin, Y. 2023-08-27 doi:10.1101/2023.08.27.554981 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Travelling waves or sequentially activated discrete modules: mapping the granularity of cortical propagation ]]> https://biorxiv.org/content/10.1101/2023.08.27.552978v1?rss=1 Orsher, Y. Rom, A. Perel, R. Lahini, Y. Blinder, P. Shein-Idelson, M. 2023-08-28 doi:10.1101/2023.08.27.552978 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Microbial dispersion in the human gut through the lens of fecal transplant ]]> https://biorxiv.org/content/10.1101/2023.08.29.555267v1?rss=1 Algavi, Y. Borenstein, E. 2023-08-29 doi:10.1101/2023.08.29.555267 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Robust parameterization of a viral-immune kinetics model for sequential Dengue virus (DENV) infections with Antibody-Dependent Enhancement (ADE) ]]> https://biorxiv.org/content/10.1101/2023.08.29.555313v1?rss=1 Macdonald, J. C. Gulbudak, H. 2023-08-31 doi:10.1101/2023.08.29.555313 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Small Extracellular Vesicles from Failing Heart Accelerate Tumor Growth ]]> https://biorxiv.org/content/10.1101/2023.09.03.555686v1?rss=1 Caller, T. Rotem, I. Shaihov Teper, O. Lendengolts, D. Schary, Y. Shai, R. Glick Saar, E. Dominissini, D. Motie, M. Katzir, I. Popovtzer, R. Nahmoud, M. Boomgarden, A. DSouza Schorey, C. Naftali Shani, N. Leor, J. 2023-09-05 doi:10.1101/2023.09.03.555686 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ An experimental approach towards untangling the role of nature versus nurture in shaping the microbiome of social insects ]]> https://biorxiv.org/content/10.1101/2023.09.04.556269v1?rss=1 Cohen, T. M. Bodner, L. Turjeman, S. Sharon, E. Cohen, A. Bouchebti, S. Tikhonov, E. Koren, O. Levin, E. 2023-09-06 doi:10.1101/2023.09.04.556269 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ A Manifold-Based Framework for Studying the Dynamics of the Vaginal Microbiome ]]> https://biorxiv.org/content/10.1101/2023.09.06.556518v1?rss=1 Tsamir-Rimon, M. Borenstein, E. 2023-09-06 doi:10.1101/2023.09.06.556518 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ The Effect of Arm Restriction on Dynamic Stability and Upper Body Responses to Lateral Loss of Balance During Walking: An Observational Study ]]> https://biorxiv.org/content/10.1101/2023.09.11.557158v1?rss=1 Rosenblum, U. Lavi, A. Fischer, A. Parmet, Y. Haim, A. Handelzalts, S. 2023-09-13 doi:10.1101/2023.09.11.557158 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ The CUL4-DDB1-DCAF1 E3 ubiquitin ligase complex regulates PLK4 protein levels to prevent premature centriole duplication ]]> https://biorxiv.org/content/10.1101/2023.09.13.555514v1?rss=1 Hoffmann, I. Grossmann, J. Kratz, A.-S. Kordonsky, A. Prag, G. 2023-09-13 doi:10.1101/2023.09.13.555514 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Nature-Inspired Peptide of MtDef4 C-terminus Tail Enables Protein Delivery in Mammalian Cells ]]> https://biorxiv.org/content/10.1101/2023.09.14.557695v1?rss=1 Adriana-Lifshits, L. Breuer, Y. Sova, M. Gupta, S. Kadosh, D. Weinberg, E. Hayouka, Z. Bar, D. z. Gal, M. 2023-09-15 doi:10.1101/2023.09.14.557695 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Cytogenetic resource enables mechanistic resolution of changing trends in human pluripotent stem cell aberrations linked to feeder-free culture ]]> https://biorxiv.org/content/10.1101/2023.09.21.558777v1?rss=1 Stavish, D. Price, C. J. Gelezauskaite, G. Leonhard, K. A. Taapken, S. M. McIntire, E. M. Laing, O. James, B. M. Riley, J. J. Zerbib, J. Baker, D. Harding, A. L. Jestice, L. H. Eleveld, T. F. Gillis, A. J. M. Hillenius, S. Looijenga, L. H. J. Gokhale, P. J. Ben-David, U. J. Ludwig, T. Barbaric, I. 2023-09-21 doi:10.1101/2023.09.21.558777 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Peripheral Blood Single-Cell Sequencing Uncovers Common and Specific Immune Aberrations in Fibrotic Lung Diseases ]]> https://biorxiv.org/content/10.1101/2023.09.20.558301v1?rss=1 Zhao, A. Y. Unterman, A. Abu Hussein, N. Sharma, P. Flint, J. Yan, X. Adams, T. S. Justet, A. Sumida, T. S. Zhao, J. Schupp, J. C. Raredon, M. S. B. Ahangari, F. C. Zhang, Y. Buendia-Roldan, I. Adegunsoye, A. Sperling, A. I. Prasse, A. Ryu, C. Herzog, E. Selman, M. Pardo, A. Kaminski, N. 2023-09-22 doi:10.1101/2023.09.20.558301 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Expression of modified FcγRI enables myeloid cells to elicit robust tumor-specific cytotoxicity ]]> https://biorxiv.org/content/10.1101/2023.09.30.560338v1?rss=1 Carmi, Y. Farhat-Younis, L. Na, M. Zarfin, A. Santana-Magal, N. Richter, A. Khateeb, A. Gutwillig, A. Rasoulouniriana, D. Gleiberman, A. Beck, L. Giger, T. Ashkenazi, A. Barzel, A. Rider, P. 2023-10-02 doi:10.1101/2023.09.30.560338 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Amniotic Fluid Organoids As Personalized Tools For Real-Time Modeling Of The Developing Fetus ]]> https://biorxiv.org/content/10.1101/2023.10.05.561078v1?rss=1 Babosova, O. Weisz, B. Rabinowitz, G. Avnet, H. Shani, H. Schwartz, A. Batsry, L. Pardo, N. Elkan, T. Stockheim, D. Jubany, T. Frank, D. Barshack, I. Dotan, Z. Levin-Klein, R. Beckerman, P. Pleniceanu, O. 2023-10-07 doi:10.1101/2023.10.05.561078 Cold Spring Harbor Laboratory Press 2023-10-07 <![CDATA[ Association between movement patterns, microbiome diversity, and potential pathogen presence in free-ranging feral pigeons foraging in dairy farms. ]]> https://biorxiv.org/content/10.1101/2023.10.11.561861v1?rss=1 Crafton, M. Spiegel, O. Cahani, S. Lublin, A. Rauer, L. 2023-10-11 doi:10.1101/2023.10.11.561861 Cold Spring Harbor Laboratory Press 2023-10-11 <![CDATA[ Attentional Engagement and Disengagement: Quantifying Attentional Shifts Utilizing the Steady State Visual Evoked Potentials ]]> https://biorxiv.org/content/10.1101/2023.10.21.563393v1?rss=1 Eidelman-Rothman, M. Reuveni, O. Keil, A. Kritzman, L. Freche, D. Okon-Singer, H. Levit-Binnun, N. 2023-10-23 doi:10.1101/2023.10.21.563393 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ The gems of the Middle-East: Unveiling the biodiversity of Monogonont rotifers in temporary waterbodies of Israel ]]> https://biorxiv.org/content/10.1101/2023.10.25.563682v1?rss=1 Hirshberg, O. Paraskevopoulou, S. Kiemel, K. Ben-Ami, F. 2023-10-29 doi:10.1101/2023.10.25.563682 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ Spatial and single-cell transcriptomics illuminate bat immunity and barrier tissue evolution ]]> https://biorxiv.org/content/10.1101/2023.10.30.564705v1?rss=1 Levinger, R. Tussia-Cohen, D. Friedman, S. Lender, Y. Nissan, Y. Fraimovitch, E. Gavriel, Y. Tearle, J. Kolodziejczyk, A. Gomes, T. Kunowska, N. Weinberg, M. Donati, G. James, K. R. Yovel, Y. Hagai, T. 2023-11-02 doi:10.1101/2023.10.30.564705 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ ReptiLearn: A Smart Home Cage for Behavioral Experiments in Reptiles ]]> https://biorxiv.org/content/10.1101/2023.11.02.565252v1?rss=1 Eisenberg, T. Shein-Idelson, M. 2023-11-03 doi:10.1101/2023.11.02.565252 Cold Spring Harbor Laboratory Press 2023-11-03 <![CDATA[ When Night Becomes Day: Artificial Light at Night Alters Insect Behavior under Semi-Natural Conditions ]]> https://biorxiv.org/content/10.1101/2023.11.06.565762v1?rss=1 Levy, K. Wegrzyn, Y. Moaraf, S. Barnea, A. Ayali, A. 2023-11-06 doi:10.1101/2023.11.06.565762 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Advance Glycation End-products induction accelerate amyloid deposits in adipocyte`s lipid droplets ]]> https://biorxiv.org/content/10.1101/2023.11.06.565836v1?rss=1 Izgilov, R. Kislev, N. Omari, E. Benayahu, D. 2023-11-07 doi:10.1101/2023.11.06.565836 Cold Spring Harbor Laboratory Press 2023-11-07 <![CDATA[ Self Fourier shell correlation: properties and application to cryo-ET ]]> https://biorxiv.org/content/10.1101/2023.11.07.565363v1?rss=1 Verbeke, E. J. Gilles, M. A. T. Bendory, T. Singer, A. 2023-11-08 doi:10.1101/2023.11.07.565363 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Mesenchymal Stromal Cells regulate human Hematopoietic Stem Cell survival and regeneration via cAMP/PKA pathway ]]> https://biorxiv.org/content/10.1101/2023.11.09.566361v1?rss=1 Milyavsky, M. MUDDINENI, S. S. N. A. Katz-Even, C. Zipin-Roitman, A. Weizman, E. Nagler, A. Raz, Y. Beider, K. 2023-11-09 doi:10.1101/2023.11.09.566361 Cold Spring Harbor Laboratory Press 2023-11-09 <![CDATA[ Clustered Protocadherin Cis-interactions are Required for Homophilic Combinatorial Cell-Cell Recognition Underlying Neuronal Self-Avoidance ]]> https://biorxiv.org/content/10.1101/2023.11.11.566682v1?rss=1 Wiseglass, G. Boni, N. Smorodinsky-Atias, K. Rubinstein, R. 2023-11-11 doi:10.1101/2023.11.11.566682 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ The Parkinson's disease risk gene cathepsin B promotes fibrillar alpha-synuclein clearance, lysosomal function and glucocerebrosidase activity in dopaminergic neurons ]]> https://biorxiv.org/content/10.1101/2023.11.11.566693v1?rss=1 Jones-Tabah, J. He, K. Senkevich, K. Karpilovsky, N. Deyab, G. Cousineau, Y. Nikanorova, D. Goldsmith, T. del Cid Pellitero, E. Chen, C. X.-Q. Luo, W. You, Z. Abdian, N. Pietrantonio, I. Goiran, T. Ahmad, J. Ruskey, J. A. Asayesh, F. Spiegelman, D. Fahn, S. Waters, C. Monchi, O. Dauvilliers, Y. Dupre, N. Miliukhina, I. Timofeeva, A. Emelyanov, A. Pchelina, S. Greenbaum, L. Hassin-Baer, S. Alcalay, R. N. Milnerwood, A. Durcan, T. M. Gan-Or, Z. Fon, E. A. 2023-11-15 doi:10.1101/2023.11.11.566693 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Visual interpretability of image-based classification models by generative latent space disentanglement applied to in vitro fertilization ]]> https://biorxiv.org/content/10.1101/2023.11.15.566968v1?rss=1 Rotem, O. Schwartz, T. Maor, R. Tauber, Y. Tsarfati Shapiro, M. Meseguer, M. Gilboa, D. Seidman, D. S. Zaritsky, A. 2023-11-17 doi:10.1101/2023.11.15.566968 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Heteroplasmy is rare in plant mitochondria compared to plastids despite similar mutation rates ]]> https://biorxiv.org/content/10.1101/2023.11.15.567200v1?rss=1 Khachaturyan, M. Santer, M. Reusch, T. B. H. Dagan, T. 2023-11-17 doi:10.1101/2023.11.15.567200 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Detecting Protein-DNA Binding in Single Molecules using Antibody Guided Methylation ]]> https://biorxiv.org/content/10.1101/2023.11.20.567792v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@dac365org.highwire.dtl.DTLVardef@522ecaorg.highwire.dtl.DTLVardef@17ddb38org.highwire.dtl.DTLVardef@1c371b0_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO (i) ChAMP is added to fix and permeabilized cells, where it binds (ii) any antibody, and upon the addition of SAM, methylates nearby GpC sites, to be detected by sequencing (iii-iv). C_FIG ]]> Thatavarty, A. Sagy, N. Erdos, M. R. Lee, I. Simpson, J. T. Timp, W. Collins, F. S. Bar, D. Z. 2023-11-20 doi:10.1101/2023.11.20.567792 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ OM2Seq: Learning retrieval embeddings for optical genome mapping ]]> https://biorxiv.org/content/10.1101/2023.11.20.567868v1?rss=1 Nogin, Y. Sapir, D. Detinis Zur, T. Weinberger, N. Belinkov, Y. Ebenstein, Y. Shechtman, Y. 2023-11-21 doi:10.1101/2023.11.20.567868 Cold Spring Harbor Laboratory Press 2023-11-21 <![CDATA[ Engineering mice for female-biased progeny without impacting genetic integrity and litter size ]]> https://biorxiv.org/content/10.1101/2023.11.21.568055v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@5f23b3org.highwire.dtl.DTLVardef@20ed2corg.highwire.dtl.DTLVardef@1b3007dorg.highwire.dtl.DTLVardef@e54cf6_HPS_FORMAT_FIGEXP M_FIG C_FIG One sentence summaryY chromosome manipulation yields mostly female mice, preserving litter size without genetic alteration in females. Significance statementThis study describes a genetic approach for producing predominantly female offspring in mice without altering litter size or transmitting genetic modifications to the progeny. A cassette inserted into the Y chromosome of males induces a strong female bias in offspring through a mechanism that remains unclear. The female offspring do not inherit the transgene and are genetically unmodified. This system provides a simple and conditional platform for sex ratio control in mammals, with potential applications in animal breeding and welfare. ]]> Yosef, I. Mahata, T. Chen, Y. Bar-Joseph, H. Shalgi, R. Munitz, A. Gerlic, M. Qimron, U. 2023-11-22 doi:10.1101/2023.11.21.568055 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Connectivity underlying motor cortex activity during naturalistic goal-directed behavior ]]> https://biorxiv.org/content/10.1101/2023.11.25.568673v1?rss=1 20,000,000 excitatory neuronal pairs revealed fine-scale columnar architecture in layer 2/3 of the motor cortex. Neurons displayed local (< 100 {micro}m) like-to-like connectivity according to target-location tuning, and inhibition over longer spatial scales. Connectivity patterns comprised a continuum, with abundant weakly connected neurons and sparse strongly connected neurons that function as network hubs. Hub neurons were weakly tuned to target-location and reward-outcome but strongly influenced neighboring neurons. This network of neurons, encoding location and outcome of movements to different motor goals, may be a general substrate for rapid learning of complex, goal-directed behaviors. ]]> Finkelstein, A. Daie, K. Rozsa, M. Darshan, R. Svoboda, K. 2023-11-26 doi:10.1101/2023.11.25.568673 Cold Spring Harbor Laboratory Press 2023-11-26 <![CDATA[ Tripartite interactions of PKA catalytic subunit and C-terminal domains of cardiac Ca2+ channel modulate its β-adrenergic regulation ]]> https://biorxiv.org/content/10.1101/2023.11.28.564875v1?rss=1 Oz, S. Sharon, T. Surbramaniam, S. Pallien, T. Katz, M. Tsemakhovich, V. Tripathy, D. R. Sasson, G. Chomsky-Hecht, O. Vysochek, L. Schulz, M. Fecher-Trost, C. Zuhlke, K. Bertinetti, D. Herberg, F. W. Keren-Raifman, T. Flockerzi, V. Hirsch, J. A. Klussmann, E. Weiss, S. Dascal, N. 2023-11-28 doi:10.1101/2023.11.28.564875 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ Origin and evolution of the bread wheat D genome ]]> https://biorxiv.org/content/10.1101/2023.11.29.568958v1?rss=1 Cavalet-Giorsa, E. Gonzalez-Munoz, A. Athiyannan, N. Holden, S. Salhi, A. Gardener, C. Quiroz-Chavez, J. Rustamova, S. M. Elkot, A. F. Patpour, M. Rasheed, A. Mao, L. Lagudah, E. S. Periyannan, S. K. Sharon, A. Himmelbach, A. Reif, J. C. Knauft, M. Mascher, M. Stein, N. Chayut, N. Ghosh, S. Perovic, D. Putra, A. Perera, A. B. Hu, C.-Y. Yu, G. Ahmed, H. I. Laquai, K. D. Rivera, L. F. Chen, R. Wang, Y. Gao, X. Liu, S. Raupp, W. J. Olson, E. L. Lee, J.-Y. Chhuneja, P. Kaur, S. Zhang, P. Park, R. F. Ding, Y. Liu, D.-C. Li, W. Nasyrova, F. Y. Dvorak, J. 2023-11-29 doi:10.1101/2023.11.29.568958 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Natural and age-related variation in circulating human hematopoietic stem cells ]]> https://biorxiv.org/content/10.1101/2023.11.30.569167v1?rss=1 Furer, N. Rappoport, N. Lifshitz, A. bercovich, A. Ben-Kiki, O. Danin, A. Kedmi, M. Shipony, Z. Lipson, D. Meiri, E. Yanai, G. Shapira, S. Arber, N. Berdichevsky, S. Tavor, S. Tyner, J. Joshi, S. K. Landau, D. Ganesan, S. Dusaj, N. Chamely, P. Kaushansky, N. Chapal Ilani, N. Shamir, R. Tanay, A. Shlush, L. 2023-11-30 doi:10.1101/2023.11.30.569167 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ High defense system expression broadens protection range at the cost of increased autoimmunity ]]> https://biorxiv.org/content/10.1101/2023.11.30.569366v1?rss=1 Aframian, N. Omer-Bendori, S. Hen, T. Guler, P. Elder, A. 2023-11-30 doi:10.1101/2023.11.30.569366 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes ]]> https://biorxiv.org/content/10.1101/2023.11.30.569198v1?rss=1 100 great ape individuals. These reference assemblies are expected to inform human evolution and conservation genetics of nonhuman apes, all of which are endangered species. ]]> Makova, K. D. Pickett, B. D. Harris, R. S. Hartley, G. A. Cechova, M. Pal, K. Nurk, S. Yoo, D. Li, Q. Hebbar, P. McGrath, B. C. Antonacci, F. Aubel, M. Biddanda, A. Borchers, M. Bornberg, E. Bouffard, G. G. Brooks, S. Y. Carbone, L. Carrel, L. Carroll, A. Chang, P.-C. Chin, C.-S. Cook, D. E. Craig, S. J. C. de Gennaro, L. Diekhans, M. Dutra, A. Garcia, G. H. Grady, P. G. S. Green, R. E. Haddad, D. Hallast, P. Harvey, W. T. Hickey, G. Hillis, D. A. Hoyt, S. J. Jeong, H. Kamali, K. Pond, S. L. K. LaPolice, T. M. Lee, C. Lewis, A. P. Loh, Y.-H. E. Maste 2023-12-01 doi:10.1101/2023.11.30.569198 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ The SCN8A p.(Gly1625Arg) variant associated with developmental and epileptic encephalopathy causes complex biophysical changes and reduced neuronal firing ]]> https://biorxiv.org/content/10.1101/2023.12.04.569940v1?rss=1 Quinn, S. Zhang, N. Fenton, T. A. Brusel, M. Muruganandam, P. Peleg, Y. Giladi, M. Haitin, Y. Lerche, H. Bassan, H. Liu, Y. Ben-Shalom, R. Rubinstein, M. 2023-12-05 doi:10.1101/2023.12.04.569940 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ The Role of Attention in Multi Attribute Decision Making ]]> https://biorxiv.org/content/10.1101/2023.12.06.570439v1?rss=1 Sampson, A. L. Yang, Y.-P. Usher, M. Levy, D. Niebur, E. Stuphorn, V. 2023-12-08 doi:10.1101/2023.12.06.570439 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Brain-wide activity-identity mapping of neural networks associated with prosocial motivation in rats ]]> https://biorxiv.org/content/10.1101/2023.12.10.570980v1?rss=1 Ruzal, K. Trachtenberg, E. Kantor, B. Flumin, H. Roemer, A. Crespo, A. Kohl, J. Ben-Ami Bartal, I. 2023-12-11 doi:10.1101/2023.12.10.570980 Cold Spring Harbor Laboratory Press 2023-12-11 <![CDATA[ Production of single-cell-protein (SCP)/poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) matrices through fermentation of archaea Haloferax mediterranei ]]> https://biorxiv.org/content/10.1101/2023.12.15.571855v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@773447org.highwire.dtl.DTLVardef@94a96org.highwire.dtl.DTLVardef@1ffdfb8org.highwire.dtl.DTLVardef@1b8e27a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Unis, R. Gnaim, R. Kashyap, M. Shamis, O. Gnayem, N. Gozin, M. Liberzon, A. Gnaim, J. Golberg, A. 2023-12-15 doi:10.1101/2023.12.15.571855 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ The Statistical Building Blocks of Animal Movement Simulations ]]> https://biorxiv.org/content/10.1101/2023.12.27.573450v1?rss=1 Getz, W. M. Salter, R. Sethi, V. Cain, S. Nathan, R. Spiegel, O. Toledo, S. 2023-12-27 doi:10.1101/2023.12.27.573450 Cold Spring Harbor Laboratory Press 2023-12-27 <![CDATA[ Engineering of methionine-auxotroph Escherichia coli via parallel evolution of two enzymes from Corynebacterium glutamicum's direct-sulfurylation pathway enables its recovery in minimal medium ]]> https://biorxiv.org/content/10.1101/2024.01.08.574620v1?rss=1 Gabay, M. Stern, I. Gruzdev, N. Cohen, A. Lifshits, L. A. Ansbacher, T. Yadid, I. Gal, M. 2024-01-08 doi:10.1101/2024.01.08.574620 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ Chromosome 7 to the rescue: overcoming chromosome 10 loss in gliomas ]]> https://biorxiv.org/content/10.1101/2024.01.17.576103v1?rss=1 Nair, N. U. Schaffer, A. A. Gertz, M. E. Cheng, K. Zerbib, J. Sahu, A. D. Leor, G. Shulman, E. D. Aldape, K. D. Ben-David, U. Ruppin, E. 2024-01-22 doi:10.1101/2024.01.17.576103 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Quantification of beta cell carrying capacity in prediabetes ]]> https://biorxiv.org/content/10.1101/2024.01.31.578144v1?rss=1 Woller, A. Tamir, Y. Bar, A. Mayo, A. Rein, M. Godneva, A. Mendelson Cohen, N. Segal, E. Toledano, Y. Shilo, S. Gonze, D. Alon, U. 2024-02-02 doi:10.1101/2024.01.31.578144 Cold Spring Harbor Laboratory Press 2024-02-02 <![CDATA[ Pesticide chemical leads inhibiting protein-protein interactions ]]> https://biorxiv.org/content/10.1101/2024.02.03.578754v1?rss=1 Ben Shushan, R. S. Cohen, E. Ben Naim, N. Amram, E. Gressel, J. Peleg, D. Dotan, N. Bloch, I. Gal, M. 2024-02-04 doi:10.1101/2024.02.03.578754 Cold Spring Harbor Laboratory Press 2024-02-04 <![CDATA[ Changes in responses of auditory cortex neurons upon falling asleep and awakening ]]> https://biorxiv.org/content/10.1101/2024.02.06.579189v1?rss=1 Marmelshtein, A. Lavy, B. Hadad, B. Nir, Y. 2024-02-07 doi:10.1101/2024.02.06.579189 Cold Spring Harbor Laboratory Press 2024-02-07 <![CDATA[ Related PP2C phosphatases Pic3 and Pic12 negatively regulate immunity in tomato to Pseudomonas syringae ]]> https://biorxiv.org/content/10.1101/2024.02.08.579555v1?rss=1 Xia, F. Zhang, N. Smith, R. E. Chakraborty, J. Sobol, G. Tang, X. Fei, Z. Sessa, G. Martin, G. B. 2024-02-12 doi:10.1101/2024.02.08.579555 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ Predicting gene sequences with AI to study evolutionarily selected codon usage patterns ]]> https://biorxiv.org/content/10.1101/2024.02.11.579798v1?rss=1 Sidi, T. Bahiri Elitzur, S. Tuller, T. Kolodny, R. 2024-02-12 doi:10.1101/2024.02.11.579798 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ A new archaeal virus that suppresses the transcription of host immunity genes ]]> https://biorxiv.org/content/10.1101/2024.02.12.579488v1?rss=1 Turgeman-Grott, I. Golan, N. Neri, U. Naki, D. Altman-Price, N. Eizenshtein, K. Choudhary, D. K. Levy, R. Papke, R. T. Himani, H. Reshef, L. Gophna, U. 2024-02-12 doi:10.1101/2024.02.12.579488 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ Adeno-Associated Viral Tools to Trace Neural Development and Connectivity Across Amphibians ]]> https://biorxiv.org/content/10.1101/2024.02.15.580289v1?rss=1 Jaeger, E. C. B. Vijatovic, D. Deryckere, A. Zorin, N. Nguyen, A. L. Ivanian, G. Woych, J. Arnold, R. C. Ortega Gurrola, A. Shvartsman, A. Barbieri, F. Toma, F. A. Gorbsky, G. J. Horb, M. E. Cline, H. T. Shay, T. F. Kelley, D. B. Yamaguchi, A. Shein-Idelson, M. Tosches, M. A. Sweeney, L. B. 2024-02-16 doi:10.1101/2024.02.15.580289 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ High or Low Expectations: Expected intensity of action outcome is embedded in action ‎kinetics ]]> https://biorxiv.org/content/10.1101/2024.02.20.581162v1?rss=1 Buaron, B. Reznik, D. Mukamel, R. 2024-02-23 doi:10.1101/2024.02.20.581162 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Obstacle Negotiation in Female Locust Oviposition Digging ]]> https://biorxiv.org/content/10.1101/2024.03.05.583468v1?rss=1 Klechevski, C. Kats, L. Ayali, A. 2024-03-11 doi:10.1101/2024.03.05.583468 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Expanding and enriching the LncRNA gene landscape using the GeneCaRNA database ]]> https://biorxiv.org/content/10.1101/2024.03.11.584435v1?rss=1 200 bases long), including [~]100,000 novel genes. The latter have sparse functional information, a vast terra incognita for future research. LncRNA genes are uniformly represented on all nuclear chromosomes, with 10 genes on mitochondrial DNA. Data obtained from MalaCards, another GeneCards Suite member, finds 1,547 genes associated with 1 to 50 diseases. [~]15% of the associations portray experimental evidence, with cancers tending to be multigenic. Preliminary text mining within GeneCaRNA discovers interactions of LncRNA transcripts with target gene products, with 25% being ncRNAs and 75% proteins. GeneCaRNA has a biological pathways section, which at present shows 131 pathways for 38 LncRNA genes, a basis for future expansion. Finally, our GeneHancer database provides regulatory elements for [~]110,000 LncRNA genes, offering pointers for co-regulated genes and genetic linkages from enhancers to diseases. We anticipate that the broad vista provided by GeneCaRNA will serve as an essential guide for further LncRNA research in disease decipherment. ]]> Aggarwal, S. Rosenblum, C. Gould, M. Ziman, S. Barshir, R. Zelig, O. Golan, Y. G. Iny-Stein, T. Safran, M. Pietrokovski, S. Lancet, D. 2024-03-13 doi:10.1101/2024.03.11.584435 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Extreme temperatures impede the release success of captive-bred avian scavengers ]]> https://biorxiv.org/content/10.1101/2024.03.14.585025v1?rss=1 Anglister, N. Acacio, M. Vaadia, G. Arnon, E. A. Bruer, M. B. Hatzofe, O. Miller, Y. King, R. Pinter-Wollman, N. Spiegel, O. 2024-03-16 doi:10.1101/2024.03.14.585025 Cold Spring Harbor Laboratory Press 2024-03-16 <![CDATA[ Following The Evolutionary Paths Of Highly Specific Homophilic Adhesion Proteins ]]> https://biorxiv.org/content/10.1101/2024.03.18.585463v1?rss=1 Wiseglass, G. Rubinstein, R. 2024-03-19 doi:10.1101/2024.03.18.585463 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ A T6SS in the coral pathogen Vibrio coralliilyticus secretes an arsenal of anti-eukaryotic effectors and contributes to virulence ]]> https://biorxiv.org/content/10.1101/2024.03.20.584600v1?rss=1 Mass, S. Cohen, H. Gerlic, M. Ushijima, B. van Kessel, J. C. Bosis, E. Salomon, D. 2024-03-20 doi:10.1101/2024.03.20.584600 Cold Spring Harbor Laboratory Press 2024-03-20 <![CDATA[ Bacteria adapt nutrient deprivation by reducing vacant 70S ribosomes via the silencing factor RsfS ]]> https://biorxiv.org/content/10.1101/2024.03.23.586405v1?rss=1 Qin, B. Zhang, H. Nikolay, R. Jiang, L. Brotman, Y. Zhang, G. 2024-03-23 doi:10.1101/2024.03.23.586405 Cold Spring Harbor Laboratory Press 2024-03-23 <![CDATA[ A high-throughput zebrafish screen identifies novel candidate treatments for Kaposiform Lymphangiomatosis (KLA) ]]> https://biorxiv.org/content/10.1101/2024.03.21.586124v1?rss=1 Bassi, I. Jabali, A. Farag, N. Egozi, S. Moshe, N. Leichner, G. S. Geva, P. Levin, L. Barzilai, A. Avivi, C. Long, J. Otterstrom, J. J. Paran, Y. Barr, H. Yaniv, K. Greenberger, S. 2024-03-25 doi:10.1101/2024.03.21.586124 Cold Spring Harbor Laboratory Press 2024-03-25 <![CDATA[ BetaAlign: a deep learning approach for multiple sequence alignment ]]> https://biorxiv.org/content/10.1101/2024.03.24.586462v1?rss=1 Dotan, E. Wygoda, E. Ecker, N. Alburquerque, M. Avram, O. Belinkov, Y. Pupko, T. 2024-03-27 doi:10.1101/2024.03.24.586462 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Text-related functionality of visual human pre-frontal activations revealed through neural network convergence ]]> https://biorxiv.org/content/10.1101/2024.04.02.587774v1?rss=1 Shoham, A. Broday-Dvir, R. Yaron, I. Yovel, G. Malach, R. 2024-04-02 doi:10.1101/2024.04.02.587774 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Comparative genomics of macaques and integrated insights into genetic variation and population history ]]> https://biorxiv.org/content/10.1101/2024.04.07.588379v1?rss=1 Zhang, S. Xu, N. Fu, L. Yang, X. Li, Y. Yang, Z. Feng, Y. Ma, K. Jiang, X. Han, J. Hu, R. Zhang, L. Gennaro, L. d. Ryabov, F. Meng, D. He, Y. Wu, D. Yang, C. Paparella, A. Mao, Y. Bian, X. Lu, Y. Antonacci, F. Ventura, M. Shepelev, V. A. Miga, K. H. Alexandrov, I. A. Logsdon, G. A. Phillippy, A. M. Su, B. Zhang, G. Eichler, E. E. Lu, Q. Shi, Y. Sun, Q. Mao, Y. 2024-04-08 doi:10.1101/2024.04.07.588379 Cold Spring Harbor Laboratory Press 2024-04-08 <![CDATA[ Interpolation of Microbiome Composition in Longitudinal Datasets ]]> https://biorxiv.org/content/10.1101/2024.04.23.590847v1?rss=1 Borenstein, E. Peleg, O. 2024-04-28 doi:10.1101/2024.04.23.590847 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Reproductive and ecological adaptations to climate underpin the evolution of sociality in lizards ]]> https://biorxiv.org/content/10.1101/2024.05.01.592000v1?rss=1 Halliwell, B. O'Connor, E. A. Uller, T. Meiri, S. Holland, B. Cornwallis, C. K. While, G. 2024-05-03 doi:10.1101/2024.05.01.592000 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Helping behavior is associated with increased affiliative behavior, activation of the prosocial brain network and elevated oxytocin receptor expression in the nucleus accumbens ]]> https://biorxiv.org/content/10.1101/2024.05.06.592793v1?rss=1 Hazani, R. Breton, J. M. Trachtenberg, E. Kantor, B. Maman, A. Bigelman, E. Cole, S. Weller, A. Ben-Ami Bartal, I. 2024-05-07 doi:10.1101/2024.05.06.592793 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ Laminar RNNs: using biologically-inspired network topology on the cortical laminar level in memory tasks ]]> https://biorxiv.org/content/10.1101/2024.05.06.592696v1?rss=1 Shamir, I. Assaf, Y. 2024-05-08 doi:10.1101/2024.05.06.592696 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Bile acids activate the antibacterial T6SS1 in the gut pathogen Vibrio parahaemolyticus ]]> https://biorxiv.org/content/10.1101/2024.05.12.593732v1?rss=1 Schiffmann, S. Mass, S. Salomon, D. 2024-05-12 doi:10.1101/2024.05.12.593732 Cold Spring Harbor Laboratory Press 2024-05-12 <![CDATA[ Oligosaccharyltransferase is involved in targeting to ER-associated degradation ]]> https://biorxiv.org/content/10.1101/2024.05.12.593735v1?rss=1 Shenkman, M. Ogen-Shtern, N. Patel, C. Groisman, B. Pasmanik-Chor, M. Schermann, S. M. Korner, R. Lederkremer, G. Z. 2024-05-14 doi:10.1101/2024.05.12.593735 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Biochemical and neurophysiological effects of deficiency of the mitochondrial import protein TIMM50 ]]> https://biorxiv.org/content/10.1101/2024.05.20.594480v1?rss=1 Paz, E. Jain, S. Gottfried, I. Staretz-Chacham, O. Mahajnah, M. Bagchi, P. Seyfried, N. Ashery, U. Azem, A. 2024-05-20 doi:10.1101/2024.05.20.594480 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ Mitochondrial inner membrane remodeling as a driving force of organelle shaping ]]> https://biorxiv.org/content/10.1101/2024.05.27.595707v1?rss=1 Preminger, N. Zucker, B. Hassdenteufel, S. Stephan, T. Jakobs, S. Kozlov, M. Schuldiner, M. 2024-05-28 doi:10.1101/2024.05.27.595707 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ The Fat4 intracellular domain controls turnover of Fat4/Dchs1 planar polarity membrane complexes ]]> https://biorxiv.org/content/10.1101/2024.05.25.595882v1?rss=1 Easa, Y. Loza, O. Cohen, R. Sprinzak, D. 2024-05-30 doi:10.1101/2024.05.25.595882 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Race-dependent variability in the human tumor mycobiome ]]> https://biorxiv.org/content/10.1101/2024.06.01.596924v1?rss=1 Coster, D. Margalit, T. Boursi, B. Shamir, R. 2024-06-03 doi:10.1101/2024.06.01.596924 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Threes a crowd: The relationship among endoparasites, an epibiont and their Daphnia host ]]> https://biorxiv.org/content/10.1101/2024.06.03.597088v1?rss=1 Hirshberg, O. Ben-Ami, F. 2024-06-03 doi:10.1101/2024.06.03.597088 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ PP2C phosphatase Pic14 negatively regulates tomato Pto/Prf-triggered immunity by inhibiting MAPK activation ]]> https://biorxiv.org/content/10.1101/2024.06.03.597203v1?rss=1 Chakraborty, J. Sobol, G. Xia, F. Zhang, N. Martin, G. B. Sessa, G. 2024-06-04 doi:10.1101/2024.06.03.597203 Cold Spring Harbor Laboratory Press 2024-06-04 <![CDATA[ Ethosuximide: subunit- and Gβγ-dependent blocker and reporter of allosteric changes in GIRK channels ]]> https://biorxiv.org/content/10.1101/2024.06.04.597296v1?rss=1 Shalomov, B. Friesacher, T. Yakubovich, D. Combista, J. C. Reddy, H. P. Dabbah, S. Bernsteiner, H. Zangerl-Plessl, E.-M. Stary-Weinzinger, A. Dascal, N. 2024-06-05 doi:10.1101/2024.06.04.597296 Cold Spring Harbor Laboratory Press 2024-06-05 <![CDATA[ Amygdala Self-Neuromodulation Capacity as a Window for Process-Related Network Recruitment ]]> https://biorxiv.org/content/10.1101/2024.06.06.592364v1?rss=1 Gurevitch, G. Lubianiker, N. Markovits, T. Or-Borichev, A. Fine, N. B. Fruchtman-Steinbok, T. Keynan, J. N. Friedman, A. Singer, N. Hendler, T. 2024-06-08 doi:10.1101/2024.06.06.592364 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Concurrent emergence of view invariance, sensitivity to critical features, and identity face classification through visual experience: Insights from deep learning algorithms ]]> https://biorxiv.org/content/10.1101/2024.06.08.597949v1?rss=1 Rosemblaum, M. Guy, N. Grosbard, I. Abudarham, N. Yovel, G. 2024-06-08 doi:10.1101/2024.06.08.597949 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ A tool for CRISPR-Cas9 gRNA evaluation based on computational models of gene expression ]]> https://biorxiv.org/content/10.1101/2024.06.08.598047v1?rss=1 Cohen, S. Bergman, S. Lynn, N. Tuller, T. 2024-06-08 doi:10.1101/2024.06.08.598047 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ High-order Michaelis-Menten equations allow inference of hidden kinetic parameters in enzyme catalysis ]]> https://biorxiv.org/content/10.1101/2024.06.12.598609v1?rss=1 Singh, D. Robin, T. Urbakh, M. Reuveni, S. 2024-06-14 doi:10.1101/2024.06.12.598609 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ PreyTouch: An Automated System for Prey Capture Experiments Using a Touch Screen ]]> https://biorxiv.org/content/10.1101/2024.06.16.599188v1?rss=1 Eyal, R. Shein-Idelson, M. 2024-06-17 doi:10.1101/2024.06.16.599188 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Dynamics in the intact fd bacteriophage revealed by pseudo 3D REDOR-based magic angle spinning NMR ]]> https://biorxiv.org/content/10.1101/2024.06.17.598843v1?rss=1 Lusky, O. S. Sherer, D. Goldbourt, A. 2024-06-19 doi:10.1101/2024.06.17.598843 Cold Spring Harbor Laboratory Press 2024-06-19 <![CDATA[ Density-dependent network structuring within and across wild animal systems ]]> https://biorxiv.org/content/10.1101/2024.06.28.601262v1?rss=1 58,000 individual animals, spanning 30 species of fish, reptiles, birds, mammals, and insects. 80% of systems exhibited strong positive relationships between local density and network centrality. However, >80% of relationships were nonlinear and 75% became shallower at higher values, signifying that demographic and behavioural processes counteract densitys effects, thereby producing saturating trends [11-15]. Densitys effect was much stronger and less saturating for spatial than social networks, such that individuals become disproportionately spatially connected rather than socially at higher densities. Consequently, ecological processes that depend on spatial connections (e.g. indirect pathogen transmission, resource competition, and territory formation) are likely more density-dependent than those involving social interactions (e.g. direct pathogen transmission, aggression, and social learning). These findings reveal fundamental ecological rules governing societal structuring, with widespread implications. Identifying scaling rules based on processes that generalise across systems, such as these patterns of density dependence, might provide the ability to predict network structures in novel systems. ]]> Albery, G. F. Becker, D. J. Firth, J. A. Silk, M. Sweeny, A. R. Wal, E. V. Webber, Q. Allen, B. Babayan, S. A. Barve, S. Begon, M. Birtles, R. J. Block, T. A. Block, B. A. Bradley, J. E. Budischak, S. Buesching, C. Burthe, S. J. Carlisle, A. B. Caselle, J. E. Cattuto, C. Chaine, A. S. Chapple, T. Cheney, B. J. Clutton-Brock, T. Collier, M. Curnick, D. J. Delahay, R. J. Farine, D. R. Fenton, A. Ferretti, F. Fielding, H. Foroughirad, V. Frere, C. Gardner, M. G. Geffen, E. Godfrey, S. S. Graham, A. L. Hammond, P. S. Henrich, M. Heurich, M. Hopwood, P. Ila 2024-07-02 doi:10.1101/2024.06.28.601262 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Hair Cells Loss Estimation from Audiograms ]]> https://biorxiv.org/content/10.1101/2024.07.07.602394v1?rss=1 Furst, M. Koral, Y. Zorea, A. 2024-07-10 doi:10.1101/2024.07.07.602394 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ The interpretation attributed to observed gaze shifts affects their social-cueing effect ]]> https://biorxiv.org/content/10.1101/2024.07.18.603902v1?rss=1 Zehngut, A. Yuval-Greenberg, S. 2024-07-22 doi:10.1101/2024.07.18.603902 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ Inhibitory mechanisms in the prefrontal-cortex differentially mediate Putamen activity during valence-based learning ]]> https://biorxiv.org/content/10.1101/2024.07.29.605168v1?rss=1 Finkelman, T. Aberg, K. C. Furman-Haran, E. Paz, R. Tal, A. 2024-08-02 doi:10.1101/2024.07.29.605168 Cold Spring Harbor Laboratory Press 2024-08-02 <![CDATA[ Seeing the Future: Anticipatory Eye Gaze as a Marker of Memory ]]> https://biorxiv.org/content/10.1101/2024.08.14.607869v1?rss=1 Yamin, D. Schmidig, F. J. Sharon, O. Nadu, Y. Nir, J. Ranganath, C. Nir, Y. 2024-08-19 doi:10.1101/2024.08.14.607869 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Genetic underpinnings of predicted changes in cardiovascular function using self supervised learning ]]> https://biorxiv.org/content/10.1101/2024.08.15.608061v1?rss=1 Levine, Z. Lutsker, G. Godneva, A. Weinberger, A. Lotan-Pompan, M. Talmor-Barkan, Y. Reisner, Y. Rossman, H. Segal, E. 2024-08-21 doi:10.1101/2024.08.15.608061 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ WHIX is a T6SS secretion domain found in polymorphic double-edged sword effectors ]]> https://biorxiv.org/content/10.1101/2024.08.21.608442v1?rss=1 Fridman, C. M. Keppel, K. Rudenko, V. Altuna-Alvarez, J. Albesa-Jove, D. Bosis, E. Salomon, D. 2024-08-22 doi:10.1101/2024.08.21.608442 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon ]]> https://biorxiv.org/content/10.1101/2024.08.29.610280v1?rss=1 Hartley, G. A. Okhovat, M. Hoyt, S. J. Fuller, E. Pauloski, N. Alexandre, N. Alexandrov, I. A. Drennan, R. S. Dubocanin, D. Gilbert, D. M. Mao, Y. McCann, C. Neph, S. Ryabov, F. Sasaki, T. Storer, J. M. Svendsen, D. Troy, W. Wells, J. Core, L. Stergachis, A. Carbone, L. O'Neill, R. J. 2024-08-30 doi:10.1101/2024.08.29.610280 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ A spatial atlas of human gastro-intestinal acute GVHD reveals epithelial and immune dynamics underlying disease pathophysiology ]]> https://biorxiv.org/content/10.1101/2024.09.02.610085v1?rss=1 Azulay, N. Milo, I. Bussi, Y. Ben Uri, R. Keidar Haran, T. Eldar, M. Elhanani, O. Harnik, Y. Yakubovsky, O. Nachmany, I. Salame, T. M. Wartenberg, M. Bertheau, P. Michonneau, D. Socie, G. Keren, L. 2024-09-03 doi:10.1101/2024.09.02.610085 Cold Spring Harbor Laboratory Press 2024-09-03 <![CDATA[ Engineered chitosan-derived nanocarrier for efficient siRNA delivery to peripheral and central neurons ]]> https://biorxiv.org/content/10.1101/2024.09.05.611434v1?rss=1 Spencer, A. P. Vilaca, A. Xavier, M. Santos, R. Ionescu, A. Lazaro, M. Leiro, V. Perlson, E. Guimaraes, S. C. Maoz, B. M. Pego, A. P. 2024-09-10 doi:10.1101/2024.09.05.611434 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ Unveiling the potential of neuron-targeted dendriplexes for siRNA delivery using a PNS-CNS-on-Chip ]]> https://biorxiv.org/content/10.1101/2024.09.05.611457v1?rss=1 Spencer, A. P. Xavier, M. Guimaraes, S. C. Vilaca, A. Ionescu, A. Santos, R. Lazaro, M. Perlson, E. Leiro, V. Maoz, B. M. Pego, A. P. 2024-09-10 doi:10.1101/2024.09.05.611457 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ An archaeal CBASS system eliminates viruses without killing the host cells ]]> https://biorxiv.org/content/10.1101/2024.09.12.612678v1?rss=1 Choudhary, D. K. Singla, H. Vassover, D. Golan, N. Reshef, L. Dubunsky, V. Gophna, U. 2024-09-12 doi:10.1101/2024.09.12.612678 Cold Spring Harbor Laboratory Press 2024-09-12 <![CDATA[ Navigating a fine balance: point-mutant cheater viruses disrupt the viral replication cycle ]]> https://biorxiv.org/content/10.1101/2024.09.18.613812v1?rss=1 Meir, M. Kahn, A. Farage, C. Maoz, Y. Harel, N. Ben Zvi, A. Segev, S. Volkov, M. Yahud, R. Gophna, U. Stern, A. 2024-09-22 doi:10.1101/2024.09.18.613812 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Identification of a novel mycovirus belonging to the ''flexivirus''-related family with icosahedral virion ]]> https://biorxiv.org/content/10.1101/2024.09.25.614901v1?rss=1 Wu, C.-F. Okada, R. Neri, U. Chang, Y.-C. Ogawara, T. Kitaura, K. Komatsu, K. Moriyama, H. 2024-09-25 doi:10.1101/2024.09.25.614901 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Internal in-frame translation generates Cas11b, which is important for effective interference in an archaeal CRISPR-Cas system ]]> https://biorxiv.org/content/10.1101/2024.10.02.616218v1?rss=1 Sailer, A.-L. Brendel, J. Chernev, A. Koenig, S. Bischler, T. Graefenhan, T. Urlaub, H. Gophna, U. Marchfelder, A. 2024-10-02 doi:10.1101/2024.10.02.616218 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Aging at scale: Younger dogs and larger breeds from the Dog Aging Project show accelerated epigenetic aging. ]]> https://biorxiv.org/content/10.1101/2024.10.03.616519v1?rss=1 McCoy, B. M. Mariner, B. L. Cheng, C. F. Silkas, E. Adjangba, C. Greenier, A. Brassington, L. Marye, A. Harrison, B. R. Partida-Aguilar, M. Bamberger, T. Algavi, Y. Muller, E. Harris, A. Rout, E. Avery, A. Promislow, D. Borenstein, E. The Dog Aging Project Consortium, Snyder-Mackler, N. 2024-10-04 doi:10.1101/2024.10.03.616519 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Design of bacterial DNT sensors based on computational models ]]> https://biorxiv.org/content/10.1101/2024.10.04.616532v1?rss=1 Bahiri Elitzur, S. Shpigel, E. Katzir, I. Alon, U. Belkin, S. Tuller, T. 2024-10-04 doi:10.1101/2024.10.04.616532 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Genetically encoded biosensor for fluorescence lifetime imaging of PTEN dynamics in the intact brain ]]> https://biorxiv.org/content/10.1101/2024.10.04.616644v1?rss=1 Kagan, T. Gabay, M. Levi, Y. Eid, S. Malchenko, N. Maman, M. Nitzan, A. Ravotto, L. Zaidel-Bar, R. Gal, M. Laviv, T. 2024-10-06 doi:10.1101/2024.10.04.616644 Cold Spring Harbor Laboratory Press 2024-10-06 <![CDATA[ DNA methylation of transposons pattern aging differences across a diverse cohort of dogs from the Dog Aging Project ]]> https://biorxiv.org/content/10.1101/2024.10.08.617286v1?rss=1 Mariner, B. L. McCoy, B. M. Greenier, A. Brassington, L. Silkas, E. Adjangba, C. Marye, A. Harrison, B. R. Bamberger, T. Algavi, Y. Muller, E. Harris, A. Rout, E. The Dog Aging Project Consortium, Avery, A. Borenstein, E. Promislow, D. Snyder-Mackler, N. 2024-10-11 doi:10.1101/2024.10.08.617286 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Early experience affects foraging behavior of wild fruit-bats more than their original behavioral predispositions ]]> https://biorxiv.org/content/10.1101/2024.10.10.617636v1?rss=1 Rachum, A. Harten, L. M. Assa, R. Goldshtein, A. Chen, X. Gonceer, N. Yovel, Y. 2024-10-12 doi:10.1101/2024.10.10.617636 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Spectrin coordinates cortical actomyosin organization and differentiation essential for a functional epithelial barrier ]]> https://biorxiv.org/content/10.1101/2024.10.17.618796v1?rss=1 Soffer, A. Bhosale, A. Matsui, T. Niessen, C. M. Luxenburg, C. Rubsam, M. 2024-10-18 doi:10.1101/2024.10.17.618796 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ A new phylogenetic framework for the genus Kalanchoe (Crassulaceae) and implications for infrageneric classification ]]> https://biorxiv.org/content/10.1101/2024.10.17.618389v1?rss=1 Rodewald, S. E. Klein, D.-P. Shtein, R. Smith, G. F. Joyce, E. Morales-Briones, D. F. Bernhard, S. Letsara, R. Mertes, H. Huehn, P. Kadereit, G. 2024-10-19 doi:10.1101/2024.10.17.618389 Cold Spring Harbor Laboratory Press 2024-10-19 <![CDATA[ Protein catabolites as blood-based biomarkers of aging physiology: Findings from the Dog Aging Project ]]> https://biorxiv.org/content/10.1101/2024.10.17.618956v1?rss=1 Harrison, B. R. Partida-Aguilar, M. Marye, A. Djukovic, D. Kauffman, M. Dunbar, M. D. Mariner, B. L. McCoy, B. M. Algavi, Y. M. Muller, E. Baum, S. Bamberger, T. Raftery, D. Creevy, K. E. Dog Aging Project Consortium, Avery, A. Borenstein, E. Snyder-Mackler, N. Promislow, D. E. 2024-10-21 doi:10.1101/2024.10.17.618956 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ Antarctic biosecurity policy effectively manages the rates of alien introductions ]]> https://biorxiv.org/content/10.1101/2024.10.26.620391v1?rss=1 Leihy, R. I. McGeoch, M. A. Clarke, D. A. Peake, L. Buba, Y. Belmaker, J. Chown, S. L. 2024-10-29 doi:10.1101/2024.10.26.620391 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Drugs Commonly Used in Fungal Infection Risk Conditions Promote Drug Tolerance or Resistance in Candida albicans ]]> https://biorxiv.org/content/10.1101/2024.11.09.622705v1?rss=1 Obermeier, M. Esparza Mora, M. A. Heese, O. Cohen, N. Varma, S. J. Tober-Lau, P. Hartl, J. Kurth, F. Berman, J. Ralser, M. 2024-11-09 doi:10.1101/2024.11.09.622705 Cold Spring Harbor Laboratory Press 2024-11-09 <![CDATA[ Potential for Biodiversity in Shared Residential Yards ]]> https://biorxiv.org/content/10.1101/2024.11.11.622952v1?rss=1 Livne, H. Gruntman, M. Blumenfeld Lieberthal, E. 2024-11-11 doi:10.1101/2024.11.11.622952 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ The organization of high-level visual cortex is aligned with visual rather than abstract linguistic information ]]> https://biorxiv.org/content/10.1101/2024.11.12.623145v1?rss=1 Shoham, A. Broday-Dvir, R. Malach, R. Yovel, G. 2024-11-12 doi:10.1101/2024.11.12.623145 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Optimized Plaque Assay for Detecting Chronically Infecting Viruses of Haloarchaea ]]> https://biorxiv.org/content/10.1101/2024.11.12.619373v1?rss=1 Navok, S. Cohen, L. Ron, E. Z. Gophna, U. 2024-11-13 doi:10.1101/2024.11.12.619373 Cold Spring Harbor Laboratory Press 2024-11-13 <![CDATA[ AI-assisted imaging screening reveals mechano-molecular tissue organizers and network of signaling hubs. ]]> https://biorxiv.org/content/10.1101/2024.11.14.623670v1?rss=1 Bertocchi, C. Alegria, J. J. Vasquez-Sepulveda, S. Ibanez-Prat, R. Srinivasan, A. Arrano-Valenzuela, I. Castro-Pereira, B. Soto-Montandon, C. Trujillo-Espergel, A. Owen, G. I. Kanchanawong, P. Cerda, M. Motta, G. Zaidel-Bar, R. Ravasio, A. 2024-11-15 doi:10.1101/2024.11.14.623670 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Modality-Specific and Amodal Language Processing by Single Neurons ]]> https://biorxiv.org/content/10.1101/2024.11.16.623907v1?rss=1 Yair, L. Friedmann, N. King, J.-R. Mankin, E. Rangel, A. Tankus, A. Dehaene, S. Fried, I. 2024-11-17 doi:10.1101/2024.11.16.623907 Cold Spring Harbor Laboratory Press 2024-11-17 <![CDATA[ Integrated Ising Model with global inhibition for decision making ]]> https://biorxiv.org/content/10.1101/2024.11.18.624088v1?rss=1 Tapinova, O. Finkelman, T. Reitich-Stolero, T. Paz, R. Tal, A. Gov, N. 2024-11-19 doi:10.1101/2024.11.18.624088 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ Whole-Genome Sequencing of the Wild Barley Diversity Collection: A Resource for Identifying and Exploiting Genetic Variation for Cultivated Barley Improvement ]]> https://biorxiv.org/content/10.1101/2024.11.18.624148v1?rss=1 Sallam, A. H. Guo, Y. Jayakodi, M. Himmelbach, A. Fiebig, A. Simmons, J. Bethke, G. Lee, Y. Spanner, R. Badea, A. Baum, M. Belzile, F. Ben-David, R. Brueggeman, R. Case, A. Cattivelli, L. Davis, M. Dockter, C. Dolezel, J. Dreiseitl, A. Gavin, R. Glick, L. Greiner, S. Hamilton, R. Hayes, P. M. Heisel, S. Henson, C. Kilian, B. Komatsuda, T. Li, C. Liu, C. Mahalingam, R. Maruschewski, M. Matny, O. Maurer, A. Mayer, K. F. X. Mayrose, I. Morrell, P. Moscou, M. Muehlbauer, G. J. Oono, Y. Ordon, F. Ozkan, H. Pecinka, A. Perovic, D. Pillen, K. Pourkheirand 2024-11-20 doi:10.1101/2024.11.18.624148 Cold Spring Harbor Laboratory Press 2024-11-20 <![CDATA[ Alanine-scanning of the yeast killer toxin K2 reveals key residues for activity, gain-of-function variants, and supports prediction of precursor processing and 3D structure. ]]> https://biorxiv.org/content/10.1101/2024.11.22.624868v1?rss=1 Prins, R. C. Marinus, T. Dafni, E. Yacoby, I. Billerbeck, S. 2024-11-22 doi:10.1101/2024.11.22.624868 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ Six-legged-bound: a newly-described insect gait ]]> https://biorxiv.org/content/10.1101/2024.11.22.624955v1?rss=1 Amir, A. Yuval, O. Ayali, A. 2024-11-23 doi:10.1101/2024.11.22.624955 Cold Spring Harbor Laboratory Press 2024-11-23 <![CDATA[ Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients ]]> https://biorxiv.org/content/10.1101/2024.11.23.624482v1?rss=1 Rutsinsky, N. Ben Zvi, A. Fabian, I. Segev, S. T. Jacobi, B. Harari, S. Meijers, S. Paran, Y. Stern, A. 2024-11-25 doi:10.1101/2024.11.23.624482 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Comparative transcriptomic profile reveals candidate genes manipulated by type III effectors of Pantoea agglomerans pv. betae leading to gall formation in beet ]]> https://biorxiv.org/content/10.1101/2024.11.24.624952v1?rss=1 Gupta, P. Pasmanik-Chor, M. Zemach, H. Barash, I. Teper, D. Sessa, G. 2024-11-26 doi:10.1101/2024.11.24.624952 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Mapping the canine microbiome: Insights from the Dog Aging Project ]]> https://biorxiv.org/content/10.1101/2024.12.02.625632v1?rss=1 Bamberger, T. Muller, E. Algavi, Y. M. Greenier, A. Adjangba, C. Slikas, E. Brassington, L. Mariner, B. McCoy, B. Harrison, B. R. Partida-Aguilar, M. Marye, A. Harris, A. Rout, E. DAP Consortium, Avery, A. Promislow, D. E. L. Snyder-Mackler, N. Borenstein, E. 2024-12-02 doi:10.1101/2024.12.02.625632 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ Dynamic Control of Argonautes by a Rapidly Evolving Immunological Switch ]]> https://biorxiv.org/content/10.1101/2024.11.30.626165v1?rss=1 Ewe, C. K. Teichman, G. Knott, M. M. Anava, S. Gingold, H. Bardan Sarmiento, M. Troemel, E. Rechavi, O. 2024-12-05 doi:10.1101/2024.11.30.626165 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Thermosensory neurons control genetic inheritance through regulation of germline transposons ]]> https://biorxiv.org/content/10.1101/2024.12.02.626368v1?rss=1 Szanto, P. Meyer, D. H. Teichman, G. Perez-Llanos, F. Rickert, D. Koehrer, K. Rechavi, O. Schumacher, B. 2024-12-05 doi:10.1101/2024.12.02.626368 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Perception of Temperature Even in the Absence of Actual Change is Sufficient to Drive Transgenerational Epigenetic Inheritance ]]> https://biorxiv.org/content/10.1101/2024.12.02.626416v1?rss=1 Teichman, G. Sela, M. Ewe, C. K. Rieger, I. Anava, S. Mor, Y. Szanto, P. Meyer, D. H. Doron, H. Shachar, O. Pechuk, V. Gingold, H. Oren-Suissa, M. McGee, M. Shapira, M. Schumacher, B. Rechavi, O. 2024-12-05 doi:10.1101/2024.12.02.626416 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ From Pigments to Precision: Exploring Genetic Transformation and Genome Editing in Wheat and Barley ]]> https://biorxiv.org/content/10.1101/2024.12.03.626565v1?rss=1 Prusty, M. R. Shatil-Cohen, A. Kumar, R. Sharma, D. Minz-Dub, A. Ezrati, S. Hihinashvili, A. Sharon, A. 2024-12-06 doi:10.1101/2024.12.03.626565 Cold Spring Harbor Laboratory Press 2024-12-06 <![CDATA[ Protein2Text: Providing Rich Descriptions for Protein Sequences ]]> https://biorxiv.org/content/10.1101/2024.12.04.626777v1?rss=1 Dotan, E. Lyubman, I. Bacharach, E. Pupko, T. Belinkov, Y. 2024-12-07 doi:10.1101/2024.12.04.626777 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ Bayesian Perspective for Orientation Estimation in Cryo-EM and Cryo-ET ]]> https://biorxiv.org/content/10.1101/2024.12.04.626841v1?rss=1 Xu, S. Balanov, A. Bendory, T. 2024-12-07 doi:10.1101/2024.12.04.626841 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ Novel immunotherapy for multiple solid cancers using an Anti-HVEM blocking monoclonal antibody ]]> https://biorxiv.org/content/10.1101/2024.12.16.627913v1?rss=1 Galore-Haskel, G. Merhavi-Shoham, E. Shapiro, M. Bareli, R. Dror, N. Seliktar-Ofir, S. Shamalov, K. Levy-Barda, A. Hout-Siloni, G. Schachter, J. Sadot, E. Eitan, R. Barshack, I. Golan, S. Feferman, Y. Yeoshoua, E. Eyadat, S. Greenberg, E. Markel, G. 2024-12-16 doi:10.1101/2024.12.16.627913 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ How bats exit a crowded colony when relying on echolocation only - a modeling approach ]]> https://biorxiv.org/content/10.1101/2024.12.16.628648v1?rss=1 Mazar, O. Yovel, Y. 2024-12-17 doi:10.1101/2024.12.16.628648 Cold Spring Harbor Laboratory Press 2024-12-17 <![CDATA[ A haplotype-based evolutionary history of barley domestication ]]> https://biorxiv.org/content/10.1101/2024.12.18.628695v1?rss=1 Guo, Y. Jayakodi, M. Himmelbach, A. Ben-Yosef, E. Davidovich, U. David, M. Hartmann-Shenkman, A. Kislev, M. Fahima, T. Schuenemann, V. Reiter, E. Krause, J. Steffenson, B. J. Stein, N. Weiss, E. Mascher, M. 2024-12-21 doi:10.1101/2024.12.18.628695 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ A somatic multiple myeloma mutation unravels a mechanism of oligomerization-mediated product inhibition in GGPPS ]]> https://biorxiv.org/content/10.1101/2024.12.25.628878v1?rss=1 Yehia, R. Portasikova, J. M. Mor Yosef, R. Da'adoosh, B. Kadek, A. Man, P. Giladi, M. Haitin, Y. 2024-12-25 doi:10.1101/2024.12.25.628878 Cold Spring Harbor Laboratory Press 2024-12-25 <![CDATA[ Enhancing Collagen Biosynthesis in Mammalian Cells Through Hypoxia-Mimetic Prolyl Hydroxylase Inhibition ]]> https://biorxiv.org/content/10.1101/2024.12.25.630305v1?rss=1 Shahar, B. Kilimnik, I. Adriana Lifshits, L. Netti, F. Sova, M. Rosin-Grunewald, D. Gal, M. Adler-Abramovich, L. 2024-12-25 doi:10.1101/2024.12.25.630305 Cold Spring Harbor Laboratory Press 2024-12-25 <![CDATA[ T cell-derived IFN-γ Suppresses T Follicular Helper Cell Differentiation and Antibody Responses during Viral Infections ]]> https://biorxiv.org/content/10.1101/2024.12.31.630815v1?rss=1 Sala, E. Nelli, M. Laura, C. Di Lucia, P. Beccaria, C. G. Bono, E. B. Mangione, M. Marotta, D. Sperto, V. Grillo, M. Giustini, L. Nie, J. Furiato, G. Malpighi, C. Consolo, E. David, E. Cohen, M. Giladi, A. Amit, I. Bosselut, R. Guidotti, L. G. Iannacone, M. Kuka, M. 2025-01-01 doi:10.1101/2024.12.31.630815 Cold Spring Harbor Laboratory Press 2025-01-01 <![CDATA[ Assessing Garmin Stress Level Score Against Heart Rate Variability Measurements ]]> https://biorxiv.org/content/10.1101/2025.01.06.630177v1?rss=1 Rosenbach, H. Itzkovitch, A. Gidron, Y. Schonberg, T. 2025-01-09 doi:10.1101/2025.01.06.630177 Cold Spring Harbor Laboratory Press 2025-01-09 <![CDATA[ Self-supervision deep learning models are better models of human high-level visual cortex: The roles of multi-modality and dataset training size ]]> https://biorxiv.org/content/10.1101/2025.01.09.632216v1?rss=1 Grosbard, I. D. Yovel, G. 2025-01-13 doi:10.1101/2025.01.09.632216 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ High Cognitive Violation of Expectations is Compromised in Cerebellar Ataxia ]]> https://biorxiv.org/content/10.1101/2025.01.11.632539v1?rss=1 Daniel, L. A. Vakil, E. Saban, W. 2025-01-13 doi:10.1101/2025.01.11.632539 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Stable, Easy-to-Handle, Fully Autologous Electrospun Polymer-Peptide Skin Equivalent for Severe Burn Injuries ]]> https://biorxiv.org/content/10.1101/2025.01.12.632550v1?rss=1 Cohen-Gerassi, D. BenShoshan, M. Liiani, A. Reuveni, T. Loboda, O. Haratz, M. Haik, J. Binderman, I. Shacham-Diamand, Y. Sitt, A. Di Segni, A. Adler-Abramovich, L. 2025-01-15 doi:10.1101/2025.01.12.632550 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Low-frequency ultrasound-mediated blood-brain barrier opening enables non-invasive lipid nanoparticle RNA delivery to glioblastoma ]]> https://biorxiv.org/content/10.1101/2025.01.23.634427v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@cad2bdorg.highwire.dtl.DTLVardef@1d1936corg.highwire.dtl.DTLVardef@259d83org.highwire.dtl.DTLVardef@1883aed_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Elbaz, M. Ad-El, N. Chulanova, Y. Brier, D. Goldsmith, M. Bismuth, M. Brosque, A. Sher, D. Gutkin, A. Bar-On, D. Friedmann-Morvinski, D. Peer, D. Ilovitsh, T. 2025-01-26 doi:10.1101/2025.01.23.634427 Cold Spring Harbor Laboratory Press 2025-01-26 <![CDATA[ A brainstem map of orofacial rhythms ]]> https://biorxiv.org/content/10.1101/2025.01.27.635041v1?rss=1 Kaku, H. Liu, L. D. Gao, R. West, S. Liao, S.-M. Finkelstein, A. Kleinfeld, D. Thomas, A. Tipparaju, S. L. Svoboda, K. Li, N. 2025-01-27 doi:10.1101/2025.01.27.635041 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ Eye movement patterns under exposure to spatial disorientation illusions during simulated flight ]]> https://biorxiv.org/content/10.1101/2025.01.28.635199v1?rss=1 Harel, M. Nakdimon, I. Schonberg, T. 2025-01-29 doi:10.1101/2025.01.28.635199 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ An early surge of norepinephrine along brainstem pathways drives sensory-evoked awakening ]]> https://biorxiv.org/content/10.1101/2025.01.29.635485v1?rss=1 PRN and LC->BF circuits. Extracellular NE dynamics in BF and PRN exhibited distinct sound-evoked activation during sleep, including a fast sound-evoked NE peak specific to PRN. Causal optogenetic interrogation of LC efferent pathways, by retro-ChR2 activation or PdCO silencing of synapses in target regions, revealed a pivotal role for early LC->PRN activity in driving arousal and sound-evoked awakenings. Together, our results uncover a prominent role for early LC-NE PRN activity in connecting sensory and arousal pathways and establish LC heterogeneity in regulating arousal. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/635485v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@eb7b3eorg.highwire.dtl.DTLVardef@1e85006org.highwire.dtl.DTLVardef@ddfa7eorg.highwire.dtl.DTLVardef@1687606_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Matosevich, N. Regev, N. Kimchy, E. Zelinger, N. Kabaha, S. Gabay, N. Marmelshtein, A. Nir, Y. 2025-01-29 doi:10.1101/2025.01.29.635485 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ Inferring binding rates from enzymatic turnover time statistics ]]> https://biorxiv.org/content/10.1101/2025.02.04.636412v1?rss=1 Singh, D. Urbakh, M. Reuveni, S. 2025-02-05 doi:10.1101/2025.02.04.636412 Cold Spring Harbor Laboratory Press 2025-02-05 <![CDATA[ Microbiota Dynamics in Lionfish (Pterois): Insights into Invasion and Establishment in the Mediterranean Sea ]]> https://biorxiv.org/content/10.1101/2025.02.03.635474v1?rss=1 Meron, D. Lalzar, M. Rothman, S. B.-S. Kroin, Y. Kaufman, E. Kitson-Walters, K. Zvi-Kedem, T. Shemesh, E. Tsadok, R. Nativ, H. Einbinder, S. Tchernov, D. 2025-02-07 doi:10.1101/2025.02.03.635474 Cold Spring Harbor Laboratory Press 2025-02-07 <![CDATA[ The Winner Takes It All: a single genotype of Kalanchoe xhoughtonii is a global invader ]]> https://biorxiv.org/content/10.1101/2025.02.03.636197v1?rss=1 Pascual-Diaz, J. P. Besoli, N. Lopez-Pujol, J. Nualart, N. Perez-Lorenzo, I. Shtein, R. Valenzuela, L. Vitales, D. Garcia, S. 2025-02-07 doi:10.1101/2025.02.03.636197 Cold Spring Harbor Laboratory Press 2025-02-07 <![CDATA[ Inducible re-epithelialization of cancer cells increases autophagy and DNA damage: implications for breast cancer dormancy ]]> https://biorxiv.org/content/10.1101/2025.02.09.636592v1?rss=1 Drago, D. Giri, S. Chattaerjee, R. Simoni Nieves, A. Abedrabbo, M. Genna, A. Uribe Rios, M. L. Lindzen, M. Sekar, A. Gupta, N. Aharoni, N. Bhandari, T. Mayalagu, A. Schwarzmuller, L. Tarade, N. Zhu, R. Mohan-Raju, H.-R. Karatekin, F. Roncato, F. Eyal-Lubling, Y. Keidar, T. Nof, Y. Belugali Nataraj, N. Bernshtein, K. S. Wagner, B. Ulhas Nair, N. Sanghvi, N. Alon, R. Seger, R. Pikarsky, E. Donzelli, S. Blandino, G. Wiemann, S. Lev, S. Prywes, R. Barkan, D. Rueda, O. Caldas, C. Ruppin, E. Shiloh, Y. Dahlhoff, M. Yarden, Y. 2025-02-10 doi:10.1101/2025.02.09.636592 Cold Spring Harbor Laboratory Press 2025-02-10 <![CDATA[ AI-directed gene fusing prolongs the evolutionary half-life of synthetic gene circuits ]]> https://biorxiv.org/content/10.1101/2025.02.10.637495v1?rss=1 Menuhin-Gruman, I. Arbel, M. Naki, D. Bergman, S. Tuller, T. 2025-02-12 doi:10.1101/2025.02.10.637495 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Calcium signaling is a universal carbon source signal transducer and effects an ionic memory of past carbon sources ]]> https://biorxiv.org/content/10.1101/2025.02.11.637612v1?rss=1 Simpson-Lavy, K. Kupiec, M. 2025-02-12 doi:10.1101/2025.02.11.637612 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Distinct roles for thymic stromal lymphopoietin (TSLP) and IL-33 in experimental eosinophilic esophagitis ]]> https://biorxiv.org/content/10.1101/2025.02.25.640192v1?rss=1 Dsilva, A. Wagner, A. Itan, M. Rhone, N. Avlas, S. Gordon, Y. Davidian, N. Sharma, S. Razrvarina, E. Zan-Bar, I. Parnes, J. R. Gorski, K. S. Sherrill, J. D. Varol, C. Ziegler, S. F. Rothenberg, M. Munitz, A. 2025-03-01 doi:10.1101/2025.02.25.640192 Cold Spring Harbor Laboratory Press 2025-03-01 <![CDATA[ Preserving clusters and correlations: a dimensionality reduction method for exceptionally high global structure preservation ]]> https://biorxiv.org/content/10.1101/2025.03.09.642213v1?rss=1 Gildenblat, J. Pahnke, J. 2025-03-13 doi:10.1101/2025.03.09.642213 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Novel Driver Mutations in GCB Lymphoma Patients That Affect Transcription Factors Binding ]]> https://biorxiv.org/content/10.1101/2025.03.15.643417v1?rss=1 Shami-Schnitzer, O. Tuller, T. 2025-03-17 doi:10.1101/2025.03.15.643417 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ Alterations in background ECoG activity and behavioral deficits in a mouse model of CHD2-related developmental delay ]]> https://biorxiv.org/content/10.1101/2025.03.18.643778v1?rss=1 Mavashov, A. Turk, S. Sarusi, Y. Brusel, M. Ben Tov Perry, R. Quinn, S. Almog, Y. Vilian, K. Ulitsky, I. Rubinstein, M. 2025-03-18 doi:10.1101/2025.03.18.643778 Cold Spring Harbor Laboratory Press 2025-03-18 <![CDATA[ MSI-VISUAL: New visualization methods for mass spectrometry imaging and tools for interactive mapping and exploration of m/z values ]]> https://biorxiv.org/content/10.1101/2025.03.18.643852v1?rss=1 Gildenblat, J. Pahnke, J. 2025-03-19 doi:10.1101/2025.03.18.643852 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ Auditory Perception Induces Cortical and Thalamic Event-Related Desynchronization in the Mouse ]]> https://biorxiv.org/content/10.1101/2025.03.21.644604v1?rss=1 McGill, S. H. Xin, Q. Yadav, T. Zhao, C. W. Paszkowski, P. Darby, F. Guha, M. Nguyen, T. Jin, D. S. Nir, Y. Liu, J. Sieu, L.-A. Blumenfeld, H. 2025-03-22 doi:10.1101/2025.03.21.644604 Cold Spring Harbor Laboratory Press 2025-03-22 <![CDATA[ Decoding host responses: How a freshwater invertebrate defends against a parasitic bacterium ]]> https://biorxiv.org/content/10.1101/2025.03.28.645445v1?rss=1 Gattis, S. Paraskevopoulou, S. Marcus, J. R. Ben-Ami, F. 2025-03-29 doi:10.1101/2025.03.28.645445 Cold Spring Harbor Laboratory Press 2025-03-29 <![CDATA[ Transcriptomic landscape reveals immunity related trade-offs in an invertebrate-fungal host-parasite system ]]> https://biorxiv.org/content/10.1101/2025.03.28.645961v1?rss=1 Paraskevopoulou, S. Gattis, S. Ben-Ami, F. 2025-04-02 doi:10.1101/2025.03.28.645961 Cold Spring Harbor Laboratory Press 2025-04-02 <![CDATA[ Cell and nuclear size are associated with chromosomal instability and tumorigenicity in cancer cells that undergo whole genome doubling ]]> https://biorxiv.org/content/10.1101/2025.03.28.645986v1?rss=1 Bloomfield, M. Huth, S. McCausland, D. Saad, R. Bano, N. Chau, T. N. Sweet, M. Baudoin, N. C. McCaffrey, A. Fluet, K. Schmelz, E. M. Ben-David, U. Cimini, D. 2025-04-02 doi:10.1101/2025.03.28.645986 Cold Spring Harbor Laboratory Press 2025-04-02 <![CDATA[ Mechanisms of long term non-reinforced preference change: functional connectivity changes in a longitudinal functional MRI study ]]> https://biorxiv.org/content/10.1101/2025.04.08.647732v1?rss=1 Itzkovitch, A. Oren, S. Chopra, S. Fornito, A. Schonberg, T. 2025-04-14 doi:10.1101/2025.04.08.647732 Cold Spring Harbor Laboratory Press 2025-04-14 <![CDATA[ Nucleotide insufficiency induced by p53 deficiency leads to replication stress driving genomic instability ]]> https://biorxiv.org/content/10.1101/2025.04.17.649416v1?rss=1 Zaatra, W. Philippos, G. Smirnov, P. Cochavi, S. M. Otonicar, J. Chan, M. Harel, M. Devens, F. Eliassaf, A. Grimes, K. Irony-Tur Sinai, M. Sigismondo, G. Gieiger, T. Korbel, J. Krijgsveld, J. Shalev, O. Kerem, B. Ernst, A. 2025-04-18 doi:10.1101/2025.04.17.649416 Cold Spring Harbor Laboratory Press 2025-04-18 <![CDATA[ Write and read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing. ]]> https://biorxiv.org/content/10.1101/2025.04.14.648727v1?rss=1 Bertocchi, U. Grunwald, A. Goldner, G. Eitan, E. Avraham, S. Deek, J. Michaeli, Y. Yao, B. Listgarten, J. Simpson, J. T. Timp, W. Ebenstein, Y. 2025-04-19 doi:10.1101/2025.04.14.648727 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ Latent dimensions in neural representations predict choice context effects ]]> https://biorxiv.org/content/10.1101/2025.04.15.648989v1?rss=1 Madar, A. Zemer, T. Tavor, I. Levy, D. J. 2025-04-20 doi:10.1101/2025.04.15.648989 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ Photobiological Hydrogen Production at Scale: Integrating Bioprocess Optimization and Techno-Economic Modeling ]]> https://biorxiv.org/content/10.1101/2025.04.27.650233v1?rss=1 Elman, T. Isaac, S. Yacoby, I. 2025-04-30 doi:10.1101/2025.04.27.650233 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Human biliary atresia extrahepatic cholangiocyte organoids express increased ER and oxidative stress, altered drug metabolism and cell polarity changes ]]> https://biorxiv.org/content/10.1101/2025.05.04.649927v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@150ab7org.highwire.dtl.DTLVardef@172953forg.highwire.dtl.DTLVardef@1a46e4eorg.highwire.dtl.DTLVardef@45c5c6_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIFirst transcriptomic profiling of extrahepatic cholangiocyte organoids (EHCOs) from BA patients, C_LIO_LIrevealing distinct molecular alterations compared to controls. C_LIO_LIBA EHCOs exhibit disrupted epithelial polarity, with downregulation of E-cadherin and Sox17 and upregulation of CFTR. C_LIO_LIER stress is a hallmark of BA cholangiocytes, with elevated PERK, BiP, and ATF4, and C_LIO_LIdysregulation of downstream effectors including CHOP, ERO1A, and SOD3. C_LIO_LIBA EHCOs are more susceptible to biliatresone-induced injury, with enhanced ER stress and structural damage. C_LIO_LIInhibition of cytochrome P450 activity (CYP4A) reduces ER stress markers. C_LI ]]> Har-Zahav, A. Hamody, Y. Danan, K. Tobar, A. Basphelchik, M. Gurevich, M. Shamir, R. Gat-Viks, I. Waisbourd-Zinman, O. 2025-05-04 doi:10.1101/2025.05.04.649927 Cold Spring Harbor Laboratory Press 2025-05-04 <![CDATA[ A Spectral Image Scanning Microscope for Multi-Color High-Resolution Imaging ]]> https://biorxiv.org/content/10.1101/2025.05.14.653993v1?rss=1 Bram, L. Tal-Friedman, O. Fibeesh, N. Bar-Sinai, Y. Flaxer, E. Roichman, Y. Ebenstein, Y. Jeffet, J. 2025-05-18 doi:10.1101/2025.05.14.653993 Cold Spring Harbor Laboratory Press 2025-05-18 <![CDATA[ NaviGraph ]]> https://biorxiv.org/content/10.1101/2025.05.18.654725v1?rss=1 Koren Iton, A. Iton, E. Michaelson, D. M. Blinder, P. 2025-05-21 doi:10.1101/2025.05.18.654725 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Dual-Axial Force Measurements of Non-Tethered Plants ]]> https://biorxiv.org/content/10.1101/2025.05.29.656568v1?rss=1 Ohad, A. Meroz, Y. 2025-05-30 doi:10.1101/2025.05.29.656568 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ A Plasma Membrane Vesicle Imaging-Based Platform for Studying Membrane Fusion ]]> https://biorxiv.org/content/10.1101/2025.05.29.656808v1?rss=1 Yosibash, I. Khan, S. Lichtenstein, A. Dharan, R. Vaknin, A. Daniel, S. Avinoam, O. Sorkin, R. 2025-05-30 doi:10.1101/2025.05.29.656808 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Twist and Snout: Head and Body Morphologies Determine Feeding Kinematics in Substrate-Biting Fishes ]]> https://biorxiv.org/content/10.1101/2025.05.28.656629v1?rss=1 Perevolotsky, T. Brotman-Krass, J. M. Ratner, Y. Avigad, Y. Summers, A. P. Donatelli, C. M. Holzman, R. 2025-06-01 doi:10.1101/2025.05.28.656629 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ A social bee can learn a novel queen pheromone ]]> https://biorxiv.org/content/10.1101/2025.05.30.657092v1?rss=1 Amsalem, E. Hefetz, A. 2025-06-02 doi:10.1101/2025.05.30.657092 Cold Spring Harbor Laboratory Press 2025-06-02 <![CDATA[ Measurements and simulations of transmembrane water exchange by diffusion NMR methods: From yeast cells to optic nerve ex vivo ]]> https://biorxiv.org/content/10.1101/2025.06.01.657299v1?rss=1 Scher, Y. Reuveni, S. Cohen, Y. 2025-06-03 doi:10.1101/2025.06.01.657299 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Organellar data sets confirm overall angiosperm relationships if problematic RNA-edit sites are accounted for in mitochondrial genomes ]]> https://biorxiv.org/content/10.1101/2025.06.09.658674v1?rss=1 Gerelle, W. K. Jost, M. Marques, I. Les, D. Vallejos, R. Little, S. Sinn, B. T. Sokoloff, D. D. Macfarlane, T. D. Iles, W. Feild, T. Mathews, S. Moore, M. Couvreur, T. L. P. Sauquet, H. Wanke, S. Graham, S. W. 2025-06-12 doi:10.1101/2025.06.09.658674 Cold Spring Harbor Laboratory Press 2025-06-12 <![CDATA[ Annotating the X-ray diffraction pattern of vertebrate striated muscle ]]> https://biorxiv.org/content/10.1101/2025.06.11.659175v1?rss=1 Koubassova, N. A. Dutta, D. Ma, W. Tsaturyan, A. K. Irving, T. Padron, R. Craig, R. 2025-06-16 doi:10.1101/2025.06.11.659175 Cold Spring Harbor Laboratory Press 2025-06-16 <![CDATA[ Image-Based Meta- and Mega-Analysis (IBMMA): A Unified Framework for Large-Scale, Multi-Site, Neuroimaging Data Analysis ]]> https://biorxiv.org/content/10.1101/2025.06.16.657725v1?rss=1 Steele, N. Morey, R. Hussain, A. Russell, C. Suarez-Jimenez, B. Pozzi, E. Jameei, H. Schmaal, L. Veer, I. Waller, L. Jahanshad, N. Thomopoulos, S. Salminen, L. Olff, M. Frijling, J. Veltman, D. Koch, S. Nawijn, L. van Zuiden, M. Wang, L. Zhu, Y. Li, G. Stein, D. Ipser, J. Neria, Y. Zhu, X. Ravid, O. Zilcha-Mano, S. Lazarov, A. Huggins, A. Stevens, J. Ressler, K. Jovanovic, T. van Rooij, S. Fani, N. Mueller, S. Hudson, A. Daniels, J. Sierk, A. Manthey, A. Walter, H. van der Wee, N. van der Werff, S. Vermeiren, R. Schmahl, C. Herzog, J. Rektor, I. i 2025-06-17 doi:10.1101/2025.06.16.657725 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Evolutionary insights into provirus-encoded CRISPR-Cas systems in halophilic archaea ]]> https://biorxiv.org/content/10.1101/2025.06.17.660064v1?rss=1 Naki, D. Gophna, U. 2025-06-17 doi:10.1101/2025.06.17.660064 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Twinfilin is a potent uncapper of actin capping protein and modulates actomyosin contractility in the C. elegans spermatheca ]]> https://biorxiv.org/content/10.1101/2025.06.17.660173v1?rss=1 Saini, A. Kreizman, S. Towsif, E. Martinez-Lopez, J. Maimon Zielonka, I. Nitzan, A. Rudnik, L. Shekhar, S. Zaidel-Bar, R. 2025-06-18 doi:10.1101/2025.06.17.660173 Cold Spring Harbor Laboratory Press 2025-06-18 <![CDATA[ REMI: Reconstructing Episodic Memory During Intrinsic Path Planning ]]> https://biorxiv.org/content/10.1101/2025.07.02.662824v1?rss=1 Wang, Z. Morris, G. Derdikman, D. Chaudhari, P. Balasubramanian, V. 2025-07-03 doi:10.1101/2025.07.02.662824 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ The complex interaction between megaherbivores, climate and fire has shaped the evolution and distribution of plant spinescence across biogeographical realms ]]> https://biorxiv.org/content/10.1101/2025.07.02.662719v1?rss=1 10 kg. Using structural equation models, we assessed how herbivores, climate and fire directly and indirectly affected the proportion of spinescent mimosoids across global and continental assemblages. C_LIO_LIThe proportion of spinescent mimosoids in assemblages increased with extant and extinct herbivore richness, drought and heat, while fire influenced spinescence indirectly, by affecting herbivore richness. Notably, correlations of spinescence differed between Africa and America, with increasing importance of extinct herbivores in Africa, illustrating legacy effects on spinescence. C_LIO_LIMegaherbivores have shaped spinescence in mimosoids, especially in dry environments, where losing plant tissues is costly. Spinescence originated [~]35 Mya, with the transition of mimosoids to seasonally dry environments, pre-dating the Miocene expansion of savannas. Our study suggests that both long-term climatic transitions and the emergence of open, herbivore-rich landscapes played crucial roles in the evolution and distribution of spinescence. C_LI ]]> Souza Ferreira, R. Ringelberg, J. Hughes, C. Arle, E. Woelke, F. Tomlinson, K. Onstein, R. 2025-07-05 doi:10.1101/2025.07.02.662719 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ PHOSPHATIDYLSERINE EXPOSURE AND EXTRACELLULAR ANNEXIN A5 WEAKEN THE ACTIN CORTEX IN OSTEOCLAST FUSION ]]> https://biorxiv.org/content/10.1101/2025.07.16.663971v1?rss=1 Leikina, E. Tsaturyan, A. Melikov, K. Whitlock, J. M. Cunanan, J. Roegner, M. Katz, G. Kozlov, M. Chernomordik, L. 2025-07-18 doi:10.1101/2025.07.16.663971 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Psoriasin inhibits microbial growth in food by metal sequestering ]]> https://biorxiv.org/content/10.1101/2025.07.20.665715v1?rss=1 Gitler, M. Sivan, G. Breuer, Y. Chang, C. Sova, M. Hayouka, Z. Gal, M. 2025-07-20 doi:10.1101/2025.07.20.665715 Cold Spring Harbor Laboratory Press 2025-07-20 <![CDATA[ Genomic signatures of increasing disease burden in recent prehistory ]]> https://biorxiv.org/content/10.1101/2025.07.22.666087v1?rss=1 Harris, K. D. Talmor, Y. Nof, M. B. Y. Marom, N. Jaffe, Y. Slon, V. Greenbaum, G. 2025-07-24 doi:10.1101/2025.07.22.666087 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Volumetric Differences of Thalamic Nuclei are Associated with Post-Trauma Psychopathology ]]> https://biorxiv.org/content/10.1101/2025.07.24.666644v1?rss=1 Steele, N. Hussain, A. Baird, C. L. Haswell, C. C. Sun, D. Rangel-Jimenez, L. Abdallah, C. G. Angstadt, M. August, G. Berg, H. Blackford, J. U. Cisler, J. Daniels, J. K. Davenport, N. D. Davidson, R. J. Densmore, M. Disner, S. G. El-Hage, W. Etkin, A. Fani, N. Frijling, J. L. Gordon, E. M. Grupe, D. W. Herringa, R. J. Hudson, A. R. Jahanshad, N. Jovanovic, T. King, A. Koch, S. B. J. Lanius, R. Lazarov, A. Li, G. Liberzon, I. Lissek, S. Lu, G. M. Manthey, A. Maron-Katz, A. Nawijn, L. Nelson, S. M. Neria, Y. Neufeld, R. W. J. Nitschke, J. B. Olatunji, B. 2025-07-25 doi:10.1101/2025.07.24.666644 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ The Analgesic and Dissociative Properties of Ketamine are Separate and Correspond to Distinct Neural Mechanisms ]]> https://biorxiv.org/content/10.1101/2025.07.25.666594v1?rss=1 Goldway, N. Hendler, T. Jalon, I. Pasternak, Y. Sar-El, R. Mirelman, D. Sarna, N. Green, N. Agbaria, Y. Sharon, H. 2025-07-31 doi:10.1101/2025.07.25.666594 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ ABCA7 deficiency exacerbates glutamate excitotoxicity in Alzheimer's disease mice -- a new pharmacological target for Glu-related neurotoxicity ]]> https://biorxiv.org/content/10.1101/2025.07.25.666774v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@1491b86org.highwire.dtl.DTLVardef@ae3bb3org.highwire.dtl.DTLVardef@d1716dorg.highwire.dtl.DTLVardef@6dd7a2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gorska, A. M. Santos-Garcia, I. Kvasnicka, A. Dobesova, D. Friedecky, D. Gildenblat, J. Pahnke, J. 2025-07-31 doi:10.1101/2025.07.25.666774 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Liposomal iron bisglycinate hydrochloride, but not free iron bisglycinate, enhances serum iron restoration in a mouse model of inflammation-induced anemia ]]> https://biorxiv.org/content/10.1101/2025.07.28.667108v1?rss=1 Kahana Sela, M. Agbaria, A. Omari Knani, N. Awida, R. Weizman, A. Gavish, M. 2025-07-31 doi:10.1101/2025.07.28.667108 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ CD33 and Clusterin Interact Biophysically and Genetically to Modulate Alzheimer Risk ]]> https://biorxiv.org/content/10.1101/2025.07.29.667318v1?rss=1 Dodd, R. B. Enomoto, M. Zhou, Y. Sato, K. Zhang, Y. Chen, F. Acheson, B. Ghaffari, D. Sayn-Wittgenstein, E. Manning, J. J. Dukas, G. V. Patel, R. Schweizer Burguete, A. Kralovec, M. J. Rashid, M. Hall, J. L. Tamucci, K. A. Chatila, Z. K. Liu, M. Lee, A. J. Vardarajan, B. N. Taga, M. Pollari, S. Rabinovitch, A. Rillahan, C. D. Bobkov, A. A. Sergienko, E. Meadows, W. Qamar, S. S. Randle, S. J. Johnson, C. M. Sevalle, J. Griffen, J. Bohm, C. Ikura, M. Xian, X. Herz, J. Kelly, M. A. West, J. Satapathy, S. Wilson, M. R. Javitch, J. A. Fraser, P. Bennett, D 2025-07-31 doi:10.1101/2025.07.29.667318 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ The role of plant polyploidy in the structure of plant-pollinator communities ]]> https://biorxiv.org/content/10.1101/2025.08.04.668489v1?rss=1 Halabi, K. Ecker, N. Susin Streher, N. Pupko, T. Ashman, T.-L. Mayrose, I. 2025-08-05 doi:10.1101/2025.08.04.668489 Cold Spring Harbor Laboratory Press 2025-08-05 <![CDATA[ Muscle power output reflects elevated viscosity in the propulsion system of flying miniature wasps ]]> https://biorxiv.org/content/10.1101/2025.08.07.668836v1?rss=1 Sarig, A. Engels, T. Lehmann, F. Ribak, G. 2025-08-07 doi:10.1101/2025.08.07.668836 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Neuronal oversight of germline small RNAs prevents heat-induced sterility in lab-domesticated Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2025.08.07.669182v1?rss=1 Ewe, C. K. Achache, H. Weiss, S. Mogilevskaya, A. Valenski, M. Teichman, G. Anava, S. Gingold, H. Posner, R. Antonova, O. Tzur, Y. B. Rechavi, O. 2025-08-10 doi:10.1101/2025.08.07.669182 Cold Spring Harbor Laboratory Press 2025-08-10 <![CDATA[ Monoclonal Antibodies from COVID-19 Convalescent Patients Target Cryptic Epitopes for Universal SARS-CoV-2 Neutralization ]]> https://biorxiv.org/content/10.1101/2025.08.17.670707v1?rss=1 Harit, A. Mor, M. Yefet, R. Izhaki-Tavor, L. S. Gal-Tanamy, M. Freund, N. Dessau, M. 2025-08-19 doi:10.1101/2025.08.17.670707 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ Competitive pre-ordering during planning persists in kinematically fused sequential movements ]]> https://biorxiv.org/content/10.1101/2025.08.18.670892v1?rss=1 Wright-Wieckowski, H. Friedman, J. Galea, J. Kornysheva, K. M. 2025-08-19 doi:10.1101/2025.08.18.670892 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ Mutations in VPS18 lead to a neutrophil maturation defect associated with disturbed vesicle homeostasis ]]> https://biorxiv.org/content/10.1101/2025.08.15.670286v1?rss=1 Gao, J. Bader, A. Linder, M. I. Cheng, J. Richter, M. Zehrer, A. Mitt, K. Popper, B. Meissner, F. Tatematsu, M. Rohlfs, M. Frenz-Wiessner, S. Somekh, I. Yacobovich, J. Steinberg-Shemer, O. Somech, R. Soehnlein, O. Schmid, B. Klein, C. Walzog, B. Maier-Begandt, D. 2025-08-21 doi:10.1101/2025.08.15.670286 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Mono-allelic p.R37H Dehydrodolichyl Diphosphate Synthase variants lead to protein glycosylation defects, aberrant lipid profiles and interneuron scarcity in a novel mouse model of progressive epileptic encephalopathy. ]]> https://biorxiv.org/content/10.1101/2025.08.15.670547v1?rss=1 A:p.R37H pathogenic variant. DhddsR37H+/- mice present with seizures, myoclonus and memory deficits associated with reduced density or/and maturity of inhibitory interneurons in the cortex. Multiomics analyses of mouse CNS tissues, together with the enzymatic/structural characterization of the R37H DHDDS mutant protein, reveal that the variant produces a catalytically inactive enzyme and results in a brain dolichol deficit, aberrant glycosylation of brain glycoproteins, including those involved in synaptic transmission, and major perturbations in the CNS proteome and lipidome. Acetazolamide, a carbonic anhydrase inhibitor clinically approved for treatment of glaucoma, epilepsy, and intracranial hypertension, and successfully used "off-label" to treat genetic movement disorders, drastically reduces seizure susceptibility to pentylenetetrazol in DhddsR37H+/- mice, suggesting potential therapeutic value of using this drug in human DHDDS-CDG patients. Together, our results define cis-PTase as a master regulator of CNS development and function and establish that its monoallelic debilitating variants cause a novel Congenital Disorder of Glycosylation, associated with aberrant levels of neuronal proteins and lipids. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=113 HEIGHT=200 SRC="FIGDIR/small/670547v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@6d7260org.highwire.dtl.DTLVardef@1701fb8org.highwire.dtl.DTLVardef@32a129org.highwire.dtl.DTLVardef@1f2ba08_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Da Silva, A. Tene Tadoum, S. B. Muffels, I. J. J. Budhraja, R. Sturiale, L. Messina, A. Giladi, M. Taherzadeh, M. Fazeli, M. Bonneil, E. Khan, S. te Vruchte, D. Yamanaka, Y. Di Cristo, G. Hamdan, F. F. Platt, F. M. Tomatsu, S. Haitin, Y. Kozicz, T. Thibault, P. Garozzo, D. Pandey, A. Morava, E. Rossignol, E. Pshezhetsky, A. V. 2025-08-21 doi:10.1101/2025.08.15.670547 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Integrated ambient modeling and genetic demultiplexing of single-cell RNA+ATAC multiome experiments with Ambimux ]]> https://biorxiv.org/content/10.1101/2025.08.21.671671v1?rss=1 95%) and was able to correctly assign singlets at considerably high ambient fractions (up to 60%) for both RNA and ATAC modalities. In comparison with models that do not consider ambient contamination, these only maintained similar sensitivity levels at considerably lower ambient fractions (up to 25%). We then generated a real data set of seven visceral adipose tissue biopsies run on a single 10x Multiome channel. We ran ambimux and detected 4,986 singlets, capturing similar numbers as other methods. Then, we sought to evaluate the fidelity of the ambient fraction estimates from ambimux. We split singlets into ambient-enriched (>5% contamination in both modalities) or nuclear-enriched (<5% in both) droplets and performed gene-peak linkage analysis. Low ambient droplets resulted in more significant hits with gene-peak links enriched at the transcription start site relative to high ambient droplets, suggesting that the ambient droplets identified by ambimux hamper the identification of biologically meaningful signals. In summary, we developed a joint single-cell multiome demultiplexing method, ambimux, that accurately models and estimates ambient molecule contamination in each modality. ]]> Alvarez, M. Li, T. Lee, S. H. T. Arasu, U. T. Selvarajan, I. Örd, T. Rahmani, E. Chen, Z. J. Avram, O. Kar, A. Kaminska, D. Männistö, V. Halperin, E. Pihlajamäki, J. Luo, C. Kaikkonen, M. U. Zaitlen, N. Pajukanta, P. 2025-08-26 doi:10.1101/2025.08.21.671671 Cold Spring Harbor Laboratory Press 2025-08-26 <![CDATA[ Understanding Shape and Residual Stress Dynamics in Rod-Like Plant Organs ]]> https://biorxiv.org/content/10.1101/2025.08.25.672092v1?rss=1 Porat, A. Routier-Kierzkowska, A.-L. Meroz, Y. 2025-08-28 doi:10.1101/2025.08.25.672092 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ A Spatially Resolved Atlas of Alternative Polyadenylation Across 18 Human Tissues and 76 Disease States ]]> https://biorxiv.org/content/10.1101/2025.08.27.672753v1?rss=1 Jiang, Z. Min, Z. Wu, Z. Chen, Y. Wu, Z. Wen, H. Wu, C. Guo, J. Si, K. Li, D. Wang, G. Mao, S. Li, W. Zeng, B. Zhang, W. 2025-09-01 doi:10.1101/2025.08.27.672753 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ Separating error from bias: A new framework for facial age estimation in humans and AIs ]]> https://biorxiv.org/content/10.1101/2025.08.28.672503v1?rss=1 Ganel, T. Mazuz, Y. Algom, D. Goodale, M. A. 2025-09-01 doi:10.1101/2025.08.28.672503 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ United we stand: Plants that physically touch each other are more resilient to stress ]]> https://biorxiv.org/content/10.1101/2025.09.02.673745v1?rss=1 Pelaez-Vico, M. A. Fichman, Y. Ghani, A. Dhakal, S. Karpinski, S. M. Joshi, T. Mittler, R. 2025-09-05 doi:10.1101/2025.09.02.673745 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Ca2+-calmodulin regulates Kv7.1 channel gating by allosterically interfering with its inactivation path ]]> https://biorxiv.org/content/10.1101/2025.09.02.673758v1?rss=1 Daus, N. costa, F. Guardiani, C. Lipinsky, M. Ben-Bassat, A. Haitin, Y. Giacomello, A. Attali, B. 2025-09-06 doi:10.1101/2025.09.02.673758 Cold Spring Harbor Laboratory Press 2025-09-06 <![CDATA[ Phage-encoded homing endonucleases attenuate bacterial immunity ]]> https://biorxiv.org/content/10.1101/2025.09.07.674715v1?rss=1 Mahata, T. Kanarek, K. Ragavan, R. M. Haldar, A. Shur, G. Yehia, R. Burstein, D. Haitin, Y. Qimron, U. Salomon, D. 2025-09-07 doi:10.1101/2025.09.07.674715 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Contrastive learning unites sequence and structure in a global representation of protein space ]]> https://biorxiv.org/content/10.1101/2025.09.05.674454v1?rss=1 Yanai, G. Axel, G. Longo, L. M. Ben-Tal, N. Kolodny, R. 2025-09-08 doi:10.1101/2025.09.05.674454 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ A Bioelectronic Scaffold for Label-Free, Real-Time Monitoring of Wound Healing ]]> https://biorxiv.org/content/10.1101/2025.09.04.674270v1?rss=1 Cohen-Gerassi, D. C. Loboda, O. Jog, A. Messer, O. Goldstein, D. A. Reuveni, T. Aviv, M. Sitt, A. Shacham-Diamand, Y. Sokol, M. Adler-Abramovich, L. 2025-09-09 doi:10.1101/2025.09.04.674270 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ The tufted ghost crab (Ocypode cursor) feeding on stranded loggerhead turtles (Caretta caretta) in the southeastern Mediterranean ]]> https://biorxiv.org/content/10.1101/2025.09.06.674680v1?rss=1 Goren, M. Galil, B. S. Bronstein, O. 2025-09-11 doi:10.1101/2025.09.06.674680 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ RNA splicing dynamics in CD8 T cells uncovers isoforms that impact T cell-mediated cancer immunotherapy ]]> https://biorxiv.org/content/10.1101/2025.09.07.674706v1?rss=1 Tzaban, S. appasamy, p. Zisman, E. Klein, S. Lewis, R. Yu, H. Khorgade, A. Schwartz, M. A. Sade-Feldman, M. Eisenhaure, T. Parnas, O. Popovtzer, A. Cohen, C. Shifrut, E. AlKhafaji, A. M. Karni, R. Eisenberg, G. Hacohen, N. Lotem, M. 2025-09-11 doi:10.1101/2025.09.07.674706 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ TREM2 macrophages are associated with enhanced response to PD-1 blockade in human hepatocellular carcinoma ]]> https://biorxiv.org/content/10.1101/2025.09.09.675071v1?rss=1 Hamon, P. Park, M. D. Le Berichel, J. Cohen, M. Soong, B. Y. Buckup, M. Hennequin, C. Lindblad, K. E. Mattiuz, R. Figueiredo, I. Tabachnikova, A. Dawson, T. D'souza, D. Troncoso, L. Ioannou, G. Price, C. Fernandez, N. Giladi, A. Barboy, O. Zhao, Z. Ozbey, S. Cappuyns, S. Reid, A. Hamel, S. Kim, J. Donne, R. Chang, C. Marvin, R. Stefanos, H. Chung, G. Merand, R. Halasz, L. Hegde, S. Guerin, L. M. Ni, M. Wei, Y. Atwal, G. Lansky, A. Jamal, H. Yi, N. Chin, T. James, N. Malissen, N. Desland, F. Lavin, Y. Ward, S. C. Fiel, M. I. Brody, R. Dekervel, J. 2025-09-12 doi:10.1101/2025.09.09.675071 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ Repurposed hnRNPC binds mature mRNAs and safeguards the mitotic transcriptome ]]> https://biorxiv.org/content/10.1101/2025.09.11.675670v1?rss=1 Lev-Ari, L. Laster, S. Atzmon, A. Blumenkrants, D. Benhalevy, D. Elroy-Stein, O. 2025-09-12 doi:10.1101/2025.09.11.675670 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ 3D-Printed Titanium Implants with Bioactive Peptide-polysaccharide Scaffolds for Personalized Bone Reconstruction ]]> https://biorxiv.org/content/10.1101/2025.09.08.674817v1?rss=1 Rattner, N. Perlis, V. Golden, E. Pokhojaev, A. Sarig, R. Binderman, I. Halperin-Sternfeld, M. Dadia, S. Adler-Abramovich, L. 2025-09-13 doi:10.1101/2025.09.08.674817 Cold Spring Harbor Laboratory Press 2025-09-13 <![CDATA[ Partial Inhibition of Viral Replication Machinery Enhances Recombination in Herpes Simplex Viruses ]]> https://biorxiv.org/content/10.1101/2025.09.15.676234v1?rss=1 Altman, M. Avhar, D. Altman, Y. Cohen, I. Azulay, H. Korner, T. Sweed, S. Tomer, E. Kobiler, O. 2025-09-15 doi:10.1101/2025.09.15.676234 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ The legacy of past heatwaves on 'off-host' parasite stages: Reduced infection risk and costs in the Daphnia-Pasteuria system ]]> https://biorxiv.org/content/10.1101/2025.09.10.675284v1?rss=1 BOUTRY, J. Lavi Shasha, N. Ben-Ami, F. 2025-09-16 doi:10.1101/2025.09.10.675284 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ MSI-ATLAS: Mass spectrometry imaging and explainable machine learning uncover the brain's lipid landscapes ]]> https://biorxiv.org/content/10.1101/2025.09.12.675752v1?rss=1 Gildenblat, J. Stamnaes, J. Pahnke, J. 2025-09-17 doi:10.1101/2025.09.12.675752 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ In vivo genome-wide CRISPR screens in human T cells to enhance T cell therapy for solid tumors ]]> https://biorxiv.org/content/10.1101/2025.09.23.678127v1?rss=1 Liu, Q. Chen, P. A. Urs, E. Zhang, S. Arce, M. Wang, C. Li, Z. Seo, J. Kale, N. LaFlam, T. N. Peng, F. Shifrut, E. Allen, G. Eyquem, J. N. Fuh, K. Dodgson, S. Cyster, J. G. Marson, A. Carnevale, J. 2025-09-24 doi:10.1101/2025.09.23.678127 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ Super-Resolved Spatial Transcriptomics Reveals Early Changes in RNA Localization in the 5xFAD Hippocampus ]]> https://biorxiv.org/content/10.1101/2025.09.24.678295v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@1b46cf2org.highwire.dtl.DTLVardef@5cc55eorg.highwire.dtl.DTLVardef@a1ade4org.highwire.dtl.DTLVardef@9f833e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Diamant Karasik, Y. Eger, H. Goldberg, T. Seri, Y. Schottlender, N. Ben Mor, T. Safra, M. Shenhav, M. Zak, H. Danino, M. Rosenberg, Y. Glick, A. Feldman, N. Slater, N. Gottfried, I. Ashery, U. Alon, S. 2025-09-26 doi:10.1101/2025.09.24.678295 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ Spatial and Single-cell Transcriptomics Reveal Programs Governing Fibroblastic Foci Fibroblasts ]]> https://biorxiv.org/content/10.1101/2025.09.26.678416v1?rss=1 Stein, Y. Freund, O. Borsekofsky, S. Cohn-Schwartz, D. Levy, L. Ofek, E. Spitzer, A. Adams, T. S. Schupp, J. C. Kaminski, N. Bar-Shai, A. Unterman, A. 2025-09-29 doi:10.1101/2025.09.26.678416 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Stage-specific transcriptomics of a leader cell reveals cell machineries driving collective invasion ]]> https://biorxiv.org/content/10.1101/2025.09.29.679269v1?rss=1 Agarwal, P. Maimon Zielonka, I. Gingold, H. Stolzenbach, V. Anava, S. Antonova, O. Cram, E. J. Rechavi, O. Zaidel-Bar, R. 2025-10-01 doi:10.1101/2025.09.29.679269 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ A switch in collagen expression regulates cessation of distal tip cell migration in C. elegans ]]> https://biorxiv.org/content/10.1101/2025.10.03.680101v1?rss=1 Stolzenbach, V. Griffin, S. S. Agarwal, P. Zaidel-Bar, R. Cram, E. J. 2025-10-03 doi:10.1101/2025.10.03.680101 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Structural basis for ATP-driven double-ring assembly of the human mitochondrial Hsp60 chaperonin ]]> https://biorxiv.org/content/10.1101/2025.10.04.680452v1?rss=1 Tascon, I. Lopez-Alonso, J. P. Shkolnisky, Y. Gil-Carton, D. Vilchez-Garcia, J. Berruezo, A. G. Gomez-Llorente, Y. Malik, R. Jebara, F. Patra, M. Hirsch, J. A. Azem, A. Ubarretxena-Belandia, I. 2025-10-05 doi:10.1101/2025.10.04.680452 Cold Spring Harbor Laboratory Press 2025-10-05 <![CDATA[ Structural remodeling of the mitochondrial protein biogenesis machinery under proteostatic stress ]]> https://biorxiv.org/content/10.1101/2025.10.06.680693v1?rss=1 Ehses, K. L. Lopez-Alonso, J. P. Antico, O. Azem, A. Muqit, M. Ubarretxena-Belandia, I. Fernandez-Busnadiego, R. 2025-10-06 doi:10.1101/2025.10.06.680693 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Light pollution affects the behavior and life history traits of aquatic invertebrates ]]> https://biorxiv.org/content/10.1101/2025.10.09.679630v1?rss=1 Bereza, E. Rotter, I. Paraskevopoulou, S. Ben-Ami, F. 2025-10-10 doi:10.1101/2025.10.09.679630 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ Single cell transcriptomics reveals enrichment of aggregation-prone alpha-synuclein isoforms across synucleinopathies ]]> https://biorxiv.org/content/10.1101/2025.10.13.682119v1?rss=1 Shwab, E. K. Pierson, W. Gingerich, D. C. Man, Z. Margalit, S. Yona, D. Sivan, A. Gamache, J. Serrano, G. E. E. Beach, T. Ebenstein, Y. Beck, R. Chiba-Falek, O. 2025-10-14 doi:10.1101/2025.10.13.682119 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ BDNF-induced axonal mTOR activation promotes Rab5 translation, axonal transport, and CREB phosphorylation in cortical neurons. ]]> https://biorxiv.org/content/10.1101/2025.10.14.682461v1?rss=1 Tiburcio-Felix, R. Tapia- Peralta, C. Arriagada, G. Perlson, E. Bronfman, F. C. 2025-10-15 doi:10.1101/2025.10.14.682461 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Live-cell quantitative monitoring reveals distinct, high-affinity Gβγ regulations of GIRK2 and GIRK1/2 channels ]]> https://biorxiv.org/content/10.1101/2025.10.15.682510v1?rss=1 250 {micro}M) G{beta}{gamma}-GIRK interaction affinity, contradicting earlier sub-{micro}M estimates and implying low signaling efficiency. We show that G{gamma} prenylation, which mediates G{beta}{gamma} membrane attachment required for GIRK activation, also contributes to the G{beta}{gamma}-GIRK interaction, explaining the poor affinity obtained with non-prenylated G{beta}{gamma}. Using quantitative protein titration and electrophysiology in live Xenopus oocytes, G{beta}{gamma} affinity for homotetrameric GIRK2 ranged from 4-30 {micro}M. Heterotetrameric GIRK1/2 showed a higher G{beta}{gamma} apparent affinity due to unique G{beta}{gamma}-docking site (anchor) in GIRK1, which enriches G{beta}{gamma} at the channel. Biochemical approaches and molecular dynamic simulations revealed that the G{beta}{gamma} anchor is formed by interacting N-terminal and distal C-terminal domains of the GIRK1 subunits, distinct from the G{beta}{gamma}-binding "activation" site(s) underlying channel opening. Thus, the affinity of G{beta}{gamma}-GIRK interaction is within the expected physiological range, while dynamic pre-coupling of G{beta}{gamma} to GIRK1-containing channels through high-affinity interactions further enhances the GPCR-Gi/o-GIRK signaling efficiency. ]]> Handklo-Jamal, R. Keren-Raifman, T. Shalomov, B. Hofer, P. Kahanovitch, U. Friesacher, T. Tabak, G. Tsemakhovich, V. Reddy, H. P. Chomsky-Hecht, O. Ranjan Tripathy, D. Zuhlke, K. Dessauer, C. W. Klussmann, E. Haitin, Y. Hirsch, J. Weinzinger, A. S. Yakubovich, D. Dascal, N. 2025-10-15 doi:10.1101/2025.10.15.682510 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Evolutionary history, ecological divergence, and introgression in the Oncocyclus irises species complex in the Southern Levant ]]> https://biorxiv.org/content/10.1101/2025.10.16.682823v1?rss=1 Bar-Lev, Y. Lozada-Gobilard, S. Xavier, A. Glick, L. Mayrose, I. Sapir, Y. 2025-10-16 doi:10.1101/2025.10.16.682823 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ Auditory network persistence of stimulus representation in awake and naturally sleeping mice ]]> https://biorxiv.org/content/10.1101/2025.10.22.683945v1?rss=1 Hadad, B. Regev, N. Kimchy, U. Rechnitz, O. Abramson, S. Finkelstein, A. Derdikman, D. Nir, Y. 2025-10-23 doi:10.1101/2025.10.22.683945 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ The evolutionary origin of host association and polycistronic transcription in trypanosomatids ]]> https://biorxiv.org/content/10.1101/2025.10.27.684775v1?rss=1 Mallik, S. Sylman, M. Dahary, D. Dahan, O. Michaeli, S. Spaeth, G. F. Pilpel, Y. T. 2025-10-27 doi:10.1101/2025.10.27.684775 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Counterproductive: coinfection of a water flea by a fungus and a microsporidium reduces the reproductive outputs of all parties. ]]> https://biorxiv.org/content/10.1101/2025.10.29.685260v1?rss=1 Halle, S. Sofer, A. Ben-Ami, F. 2025-10-29 doi:10.1101/2025.10.29.685260 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ Acetylation of Axonal G3BP1 through ELP3 Accelerates Axon Regeneration ]]> https://biorxiv.org/content/10.1101/2025.10.28.685144v1?rss=1 Dalla Costa, I. Michenfelder, E. Siciliano, S. Tapita, A. Buchanan, C. N. Vaughn, L. S. Lee, J. Oses-Prieto, J. A. Ma, C. Thames, E. Samra, N. Ben-Dor, S. Haffner-Krausz, R. McElveen, M. Smith, T. P. Nawar, N. Manaswiyoungkul, P. Gunning, P. T. Fainzilber, M. Burlingame, A. Zhu, H. Perlson, E. Sahoo, P. K. Twiss, J. L. 2025-10-30 doi:10.1101/2025.10.28.685144 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Multimodal profiling reveals a Notch-responsive regenerative subpopulation of cochlear supporting cells ]]> https://biorxiv.org/content/10.1101/2025.11.04.686551v1?rss=1 Khalaily, L. Kasirer, S. Domb, K. Zhou, M. Shao, B. Taiber, S. Elkon, R. Tao, L. Sprinzak, D. Avraham, K. B. 2025-11-05 doi:10.1101/2025.11.04.686551 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Unconscious switching of dorsal and medial pathways for plasticity and stability during NREM and REM sleep ]]> https://biorxiv.org/content/10.1101/2025.11.04.686485v1?rss=1 Yamada, T. Labonte-Clark, T. Censor, N. Watanabe, T. Sasaki, Y. 2025-11-06 doi:10.1101/2025.11.04.686485 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Helical charge distribution at the transmembrane-luminal interface determines subcellular localization ]]> https://biorxiv.org/content/10.1101/2025.11.12.688035v1?rss=1 Saad, H. Benyair, R. Mazor, T. Lederkremer, G. Z. 2025-11-13 doi:10.1101/2025.11.12.688035 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Biologically-constrained insect models enable realistic simulations and improve biomechanical predictions of locomotion ]]> https://biorxiv.org/content/10.1101/2025.11.13.687989v1?rss=1 Yuval, O. Amir, A. Ozeri, E. Ayali, A. 2025-11-14 doi:10.1101/2025.11.13.687989 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Evaluating rapid extraction methods for recovering ancient DNA from archaeological sediments ]]> https://biorxiv.org/content/10.1101/2025.11.13.688359v1?rss=1 Dagtas, N. D. Jabareen, A. Cyrek, K. Krajcarz, M. T. Krajcarz, M. Rojo-Guerra, M. A. Sanchez-Yustos, P. Sudoł-Procyk, M. Safra, S. Slon, V. 2025-11-14 doi:10.1101/2025.11.13.688359 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Context-dependent benefits of training and reminders in visual skill learning ]]> https://biorxiv.org/content/10.1101/2025.11.14.688438v1?rss=1 Kolken, Y. J. T. Roberts, M. J. Naseri, P. Martino, F. D. Censor, N. Weerd, P. D. 2025-11-14 doi:10.1101/2025.11.14.688438 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Neural dynamics outside task-coding dimensions drive decision trajectories through transient amplification ]]> https://biorxiv.org/content/10.1101/2025.11.20.689599v1?rss=1 Pereira-Obilinovic, U. Daie, K. Chen, S. Svoboda, K. Darshan, R. 2025-11-22 doi:10.1101/2025.11.20.689599 Cold Spring Harbor Laboratory Press 2025-11-22 <![CDATA[ Arbitrium systems control lysis/lysogeny through the regulation of small antirepressor proteins ]]> https://biorxiv.org/content/10.1101/2025.11.23.689978v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@63dd49org.highwire.dtl.DTLVardef@54e7ecorg.highwire.dtl.DTLVardef@466235org.highwire.dtl.DTLVardef@d98ef2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kabel, S. Bendori, S. O. Borenstein, T. Guler, P. del Sol, F. G. Mancheno-Bonilla, J. Marina, A. Eldar, A. 2025-11-24 doi:10.1101/2025.11.23.689978 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Immunological Differences in Atopic Dermatitis Across Age Groups: Insights from Single-Cell Multi-Omics ]]> https://biorxiv.org/content/10.1101/2025.11.22.689843v1?rss=1 Baldonado, G. C. L. Kumar, S. Jin, J. Fang, X. Ildardashty, A. Braun, M. Neuhaus, I. M. Mathes, E. Bhutani, T. Liao, W. 2025-11-25 doi:10.1101/2025.11.22.689843 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Identification of a putative RBOHD-FERONIA-CRK10-PIP2;6 plasma membrane complex that interacts with phyB to regulate ROS production in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2025.11.23.689998v1?rss=1 Mohanty, D. Fichman, Y. Pelaez-Vico, M. A. Myers, R. J. Sealander, M. Sinha, R. Morrow, J. Eckstein, R. Olson, K. Xu, C. An, H. Yoo, C. Y. Zhu, J.-K. Zhao, C. Zandalinas, S. I. Liscum, E. Mittler, R. 2025-11-26 doi:10.1101/2025.11.23.689998 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ TAGINE: Fast Taxonomy-based Feature Engineering for Microbiome Analysis ]]> https://biorxiv.org/content/10.1101/2025.11.25.689983v1?rss=1 Baum, S. Meshulam, I. Peleg, O. Algavi, Y. Borenstein, E. 2025-11-27 doi:10.1101/2025.11.25.689983 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ A developmentally inspired computational model of face recognition that learns continuously through generative memory replay ]]> https://biorxiv.org/content/10.1101/2025.11.25.690208v1?rss=1 Abudarham, N. Yovel, G. 2025-11-28 doi:10.1101/2025.11.25.690208 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ A model of transcriptional bursting dynamics based on coupling between chromatin and enhancer states ]]> https://biorxiv.org/content/10.1101/2025.11.29.691276v1?rss=1 Axelrod, O. Binshtok, U. Gebelein, B. Garcia, H. Sprinzak, D. 2025-12-01 doi:10.1101/2025.11.29.691276 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Real-Time Sensing of Food Spoilage Using a Recombinant mVenus-Tolles FRET pH Biosensor ]]> https://biorxiv.org/content/10.64898/2025.11.30.691354v1?rss=1 Gabay, M. Sova, M. Laviv, T. Gal, M. 2025-12-02 doi:10.64898/2025.11.30.691354 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Chromosome-arm 17p Loss Renders Breast Cancer Cells Vulnerable to AURKB Inhibition ]]> https://biorxiv.org/content/10.64898/2025.12.01.691489v1?rss=1 Winkler, T. Sdeor, E. Saad, R. Okada, H. Laue, K. J. Leor, G. Wolf, G. Struluv Shachar, S. Ben-David, U. 2025-12-02 doi:10.64898/2025.12.01.691489 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ From Big Data to Small Scales: Machine Learning Enhances Microclimate Model Predictions ]]> https://biorxiv.org/content/10.64898/2025.12.01.691551v1?rss=1 Itzkovitch, A. Sulami, I. Doron Efroni, R. Shahar, M. Levy, O. 2025-12-02 doi:10.64898/2025.12.01.691551 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Tolerance to the antifungal drug fluconazole is mediated by tuning cytoplasmic fluidity ]]> https://biorxiv.org/content/10.64898/2025.12.03.691994v1?rss=1 Plumb, E. Serrano, A. Chevalier, L. Elferich, J. Sinn, L. R. Grigorieff, N. Ralser, M. Berman, J. Bassilana, M. Arkowitz, R. A. 2025-12-03 doi:10.64898/2025.12.03.691994 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ A Cytoplasmic Index for Quantifying Immune-Related A-to-I RNA Editing ]]> https://biorxiv.org/content/10.64898/2025.12.03.692070v1?rss=1 25,000 RNA-seq samples demonstrates CEI outperforms the global editing index in sensitivity and specificity, resolving tissue- and infection-linked editing patterns. An open-source, cloud-native pipeline enables scalable, low-cost deployment. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/692070v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@159ae9org.highwire.dtl.DTLVardef@6d6119org.highwire.dtl.DTLVardef@101b4a1org.highwire.dtl.DTLVardef@f9d96b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cohen-Fultheim, R. Twersky, I. Krupkin, H. Roth, S. H. Levanon, E. Y. Eisenberg, E. 2025-12-04 doi:10.64898/2025.12.03.692070 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ Phenotype-driven parallel embedding for microbiome multi-omic data integration ]]> https://biorxiv.org/content/10.64898/2025.12.05.692119v1?rss=1 Bamberger, T. consortium, D. Borenstein, E. 2025-12-06 doi:10.64898/2025.12.05.692119 Cold Spring Harbor Laboratory Press 2025-12-06 <![CDATA[ Nanobubble based sonobiopsy reveals circulating protein signatures of BBB opening and glioblastoma ]]> https://biorxiv.org/content/10.64898/2025.12.04.692317v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@d0186aorg.highwire.dtl.DTLVardef@1f2fe8borg.highwire.dtl.DTLVardef@25921forg.highwire.dtl.DTLVardef@9c3566_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gattegno, R. Sher, D. Zohar, O. Moskov, K. Morvinski, D. F. Ilovitsh, T. 2025-12-08 doi:10.64898/2025.12.04.692317 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ A Site-Specific Organometallic Approach for Installing Tyrosine Phosphorylation Mimics to Decipher the Role of Phosphorylation in Alpha-Synuclein (aSyn) Aggregation and Seeding ]]> https://biorxiv.org/content/10.64898/2025.12.05.692498v1?rss=1 Mandal, S. Lin, X. Gemelli, A. V. Singh, M. Mahul-Mellier, A.-L. Jasiqi, Y. Bouri, B. Jbara, M. Lashuel, H. 2025-12-08 doi:10.64898/2025.12.05.692498 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Pan-cancer analysis reveals genomic fidelity and evolution of patient-derived organoids ]]> https://biorxiv.org/content/10.64898/2025.12.10.693393v1?rss=1 Raz, L. Ben-Yishay, T. Khoury, H. Saad, R. Zoabi, A. Orlandi, G. Donzelli, S. Blandino, G. Ben-David, U. 2025-12-11 doi:10.64898/2025.12.10.693393 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Title: You Are What You Sync: Neural Synchronization Predicts Religious Affiliation ]]> https://biorxiv.org/content/10.64898/2025.12.03.692126v1?rss=1 Zvi, Y. Kerem, N. Yeshurun, Y. 2025-12-12 doi:10.64898/2025.12.03.692126 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ RBProximity-CLIP Enables Subcellular Mapping of RNA-Binding Protein Interactions at Nucleotide Resolution ]]> https://biorxiv.org/content/10.64898/2025.12.12.693770v1?rss=1 Nowak, I. Polash, A. H. Huynh, H. T. Kaur, M. Lobo, V. Scutenaire, J. Fong, M. Alluhaibi, G. Anastasakis, D. G. Hafner, M. Benhalevy, D. Sarshad, A. 2025-12-15 doi:10.64898/2025.12.12.693770 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Colon-Specific Epigenetic Clocks from Minimal Features Reveal Disease-Driven Aging ]]> https://biorxiv.org/content/10.64898/2025.12.15.694318v1?rss=1 Sagy, N. Bender, O. Bar, D. Z. 2025-12-17 doi:10.64898/2025.12.15.694318 Cold Spring Harbor Laboratory Press 2025-12-17 <![CDATA[ Minimally invasive delivery of optical nanosensors using injectable hydrogels ]]> https://biorxiv.org/content/10.64898/2025.12.21.695747v1?rss=1 Kleiner, S. Bisker, G. 2025-12-23 doi:10.64898/2025.12.21.695747 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ A food chain of ribozymes built on an ancestral strand ]]> https://biorxiv.org/content/10.64898/2025.12.22.695801v1?rss=1 Weiss, R. Farage, C. Mellul, N. Levy-Zamir, A. Svirskaya, Y. Ben-Dov, O. Vernia, N. Ittah, S. Ionescu, A. Ionescu, D. Bachelet, I. 2025-12-23 doi:10.64898/2025.12.22.695801 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ B-PPI: A Cross-Attention Model for Large-Scale Bacterial Protein-Protein Interaction Prediction ]]> https://biorxiv.org/content/10.64898/2025.12.23.696145v1?rss=1 Agassy, C. Samuel, B. Mayo, S. Zorea, A. Burstein, D. 2025-12-25 doi:10.64898/2025.12.23.696145 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ Fluorescence lifetime-based biosensor for monitoring compartmentalized autophagy dynamics in the intact mammalian brain ]]> https://biorxiv.org/content/10.64898/2025.12.25.693346v1?rss=1 Maman, M. Bond, G. Malchenko, N. Desbois, M. Kagan, T. Levy, Y. Eid, S. Orovan, S. Naftachi, G. Lapidot, M. Rapaport, R. Break, E. P. Grill, B. Scholl, B. Laviv, T. 2025-12-25 doi:10.64898/2025.12.25.693346 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ Quantifying Population Reversibility of Sensor Performance inMulti-Cycle Single-Sensor Recovery Assay ]]> https://biorxiv.org/content/10.64898/2025.12.25.696491v1?rss=1 Rosenberg, G. Bisker, G. 2025-12-26 doi:10.64898/2025.12.25.696491 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ High dimensional tissue specific regulatory codes embedded in viral coding regions ]]> https://biorxiv.org/content/10.64898/2025.12.27.696677v1?rss=1 Davidson, A. Parr, M. Totzeck, F. Churkin, A. Barash, D. Frishman, D. Tuller, T. 2025-12-27 doi:10.64898/2025.12.27.696677 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ A multi-ring shifter network computes head direction in zebrafish ]]> https://biorxiv.org/content/10.64898/2025.12.29.696831v1?rss=1 Mei, S. Lavian, H. Wu, Y. K. Stemmler, M. B. Portugues, R. Herz, A. V. M. 2025-12-29 doi:10.64898/2025.12.29.696831 Cold Spring Harbor Laboratory Press 2025-12-29 <![CDATA[ Smarcc1 is essential for the patterning of the optic stalk and differentiation of the optic nerve head astrocytes ]]> https://biorxiv.org/content/10.64898/2025.12.30.697056v1?rss=1 Zuk-Bar, N. Ovadia, S. Cui, G. Obolensky, A. Banin, E. Ofri, R. Jing, N. Ashery-Padan, R. 2025-12-30 doi:10.64898/2025.12.30.697056 Cold Spring Harbor Laboratory Press 2025-12-30 <![CDATA[ Cryoablation temperature monitoring with dense ultrasonic speed-of-sound shift imaging ]]> https://biorxiv.org/content/10.64898/2026.01.04.697528v1?rss=1 Lamm, G. Grutman, T. Bismuth, M. Ilovitsh, T. 2026-01-04 doi:10.64898/2026.01.04.697528 Cold Spring Harbor Laboratory Press 2026-01-04 <![CDATA[ When exploration replaces storage: how eye movements shape visual working memory ]]> https://biorxiv.org/content/10.64898/2026.01.04.697560v1?rss=1 Qais, R. Knight, R. Yuval-Greenberg, S. 2026-01-04 doi:10.64898/2026.01.04.697560 Cold Spring Harbor Laboratory Press 2026-01-04 <![CDATA[ A personalized eye-tracking system reveals complex state-dependent visual acquisition in lizards ]]> https://biorxiv.org/content/10.64898/2026.01.06.697876v1?rss=1 Leberstein, N. Remenick, T. Becker, M. Shein-Idelson, M. 2026-01-06 doi:10.64898/2026.01.06.697876 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Epigenetic Liquid Biopsy Enables Universal Mutation-Agnostic Molecular Surveillance for High-Risk Neuroblastoma ]]> https://biorxiv.org/content/10.64898/2026.01.15.699217v1?rss=1 Gal Mark, N. Grunwald, A. Gahramanov, V. Hameiri-Grossman, M. Shinderman-Maman, E. Gaas, D. Shichrur, K. Chausky Barzakh, E. Sever, A. Amar, S. Ash, S. Birger, Y. Izraeli, S. Ebenstein, Y. Berko, E. R. 2026-01-16 doi:10.64898/2026.01.15.699217 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ Ribosome Quality Control Mitigates Proteotoxic Stress in Aneuploid Cells ]]> https://biorxiv.org/content/10.64898/2026.01.19.700285v1?rss=1 Vigano, S. Ippolito, M. R. Scorzoni, S. Barrio, L. Loffreda, A. Rodriguez-Munoz, M. Donzel, D. Eliezer, Y. Pontano Vaites, L. Paulo, J. Marenda, M. Palma, A. Ben-David, U. Viero, G. Milan, M. Santaguida, S. 2026-01-20 doi:10.64898/2026.01.19.700285 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Mitochondrial cardiolipin sequestration of caspofungin underlies Cryptococcus neoformans inherent resistance and may contribute to cardiotoxicity ]]> https://biorxiv.org/content/10.64898/2026.01.20.700633v1?rss=1 Loksztejn, A. K. Upadhya, R. Caro, E. A. Gooden, D. M. Yona, A. Ellis, P. K. Fridman, M. Schumacher, M. A. Brennan, R. G. Donlin, M. J. Lodge, J. K. 2026-01-20 doi:10.64898/2026.01.20.700633 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Ancestral sequence reconstruction using generative models ]]> https://biorxiv.org/content/10.64898/2026.01.18.700141v1?rss=1 Dotan, E. Wygoda, E. Schers, A. Lyubman, I. Belinkov, Y. Pupko, T. 2026-01-21 doi:10.64898/2026.01.18.700141 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Single-cell and spatial transcriptomics unveils key regulators governing cell differentiation for Schistosoma sexual development ]]> https://biorxiv.org/content/10.64898/2026.01.20.700708v1?rss=1 Lu, Z. Wang, X. Li, S. Li, X. Du, P. Zheng, Y. Liu, L. Zhang, Y. Wurtzel, O. Cheng, G. 2026-01-21 doi:10.64898/2026.01.20.700708 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ LocAlign: Local Protein Structural Alignment with Geometric Deep Learning ]]> https://biorxiv.org/content/10.64898/2026.01.24.701262v1?rss=1 Ravid, H. Tubiana, J. Wolfson, H. J. 2026-01-26 doi:10.64898/2026.01.24.701262 Cold Spring Harbor Laboratory Press 2026-01-26 <![CDATA[ Collective Posterior Inference from Highly Variable Empirical Replicates ]]> https://biorxiv.org/content/10.64898/2026.01.26.701673v1?rss=1 Ben Nun, N. Rosset, S. Gresham, D. Ram, Y. 2026-01-27 doi:10.64898/2026.01.26.701673 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Aeromonas adhesins facilitate kin and non-kin attachment to enable T6SS-mediated antagonism in liquid ]]> https://biorxiv.org/content/10.64898/2026.01.27.701733v1?rss=1 Fridman, C. M. Cohen, H. Keppel, K. Tejada-Arranz, A. Basler, M. Gerlic, M. Salomon, D. 2026-01-27 doi:10.64898/2026.01.27.701733 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Isolation and characterization of novel banana rhizosphere bacteria for the control of Fusarium oxysporum f. sp. cubense TR4 ]]> https://biorxiv.org/content/10.64898/2026.01.29.702532v1?rss=1 Cohen, D.-d. Doron-Faigenboim, A. Cohen, J. Maymon, M. Freeman, S. Carmeli, S. Minz, D. 2026-01-29 doi:10.64898/2026.01.29.702532 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ Dynamic Regulation of CD300b, and CD300f on Myeloid Cells in Oral Immunotherapy ]]> https://biorxiv.org/content/10.64898/2026.01.28.702205v1?rss=1 Epstein-Rigbi, N. Itan, M. Avlas, S. Damari, E. Nachshon, L. Koren, Y. Levy, M. Goldberg, M. R. Elizur, A. Munitz, A. 2026-01-30 doi:10.64898/2026.01.28.702205 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Analysis of the assembly, stabilization and maturation of the multiphasic TAZ biomolecular condensates ]]> https://biorxiv.org/content/10.64898/2026.01.29.702607v1?rss=1 Shapira, K. E. Zhu, Q. Grig, E. Chen, X. Jing, Y. Li, X. D. Wolfenson, H. Henis, Y. I. Luo, K. 2026-02-02 doi:10.64898/2026.01.29.702607 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Evaluating the applicability of kinship analyses for sedimentary ancient DNA datasets ]]> https://biorxiv.org/content/10.64898/2026.02.02.703194v1?rss=1 Cohen, P. Johnson, S. Zavala, E. I. Moorjani, P. Slon, V. 2026-02-02 doi:10.64898/2026.02.02.703194 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ A deep-learning-based score to evaluate multiple sequence alignments ]]> https://biorxiv.org/content/10.64898/2026.02.02.703429v1?rss=1 Serok, N. Polonsky, K. Ashkenazy, H. Mayrose, I. Thorne, J. L. Pupko, T. 2026-02-05 doi:10.64898/2026.02.02.703429 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ ER-associated protein degradation initiates by retrotranslocation from the ER quality control compartment ]]> https://biorxiv.org/content/10.64898/2026.02.04.703732v1?rss=1 Patel, C. Ogen-Shtern, N. Saad, H. Burrone, O. R. Petris, G. Lederkremer, G. Z. 2026-02-06 doi:10.64898/2026.02.04.703732 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ Adaptive spatio-temporal phase retrieval for ultra-short pulse wavefront shaping ]]> https://biorxiv.org/content/10.64898/2026.02.04.703770v1?rss=1 Shaul, O. Ilovitsh, T. 2026-02-06 doi:10.64898/2026.02.04.703770 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ Identification of protein secretion systems and type III effectors in wood-associated bacteria of the genus Xylophilus ]]> https://biorxiv.org/content/10.64898/2026.02.05.703958v1?rss=1 Roux, Z. Wagner, N. Brottier, L. Pupko, T. Koebnik, R. 2026-02-09 doi:10.64898/2026.02.05.703958 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Optimizing Protein Tokenization: Reduced Amino Acid Alphabets for Efficient and Accurate Protein Language Models ]]> https://biorxiv.org/content/10.64898/2026.02.08.701987v1?rss=1 Rannon, E. Burstein, D. 2026-02-10 doi:10.64898/2026.02.08.701987 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ CytoLight: A Rapid and Versatile Fluorescent-Based Labeling Method for Extracellular Vesicle Characterization and Tracking ]]> https://biorxiv.org/content/10.64898/2026.02.10.705037v1?rss=1 Rosen, I. Itzhaki, E. Gover-Proaktor, A. Shapira, S. Partouche, S. Qassim, L. Grinshpan-Langman, S. Qasim, A. Levy-Erez, D. John, F. Porat, Z. Moskovits, N. Zemel, R. Ben Zur, T. Raanani, P. Offen, D. Granot, G. Samara, A. 2026-02-11 doi:10.64898/2026.02.10.705037 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ Chromosomal instability and chromosome 17p loss drive convergentNDE1 synthetic lethality in metastatic cancer cells ]]> https://biorxiv.org/content/10.64898/2026.02.10.704921v1?rss=1 Teddy, C. M. Hoj, J. P. Caci, J. Lu, M. Killarney, S. T. Ben-Yishay, T. Ben-David, U. M. Wood, K. C. 2026-02-12 doi:10.64898/2026.02.10.704921 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ The mitochondrial chaperone HSPD1 folds MTHFD2 independently of its co-chaperone HSPE1 ]]> https://biorxiv.org/content/10.64898/2026.02.16.706072v1?rss=1 Gabbay, S. Ben-David, H. Alassam, S. S. Cohen, L. Levy, T. Levin, L. Tickotsky-Moskovitz, N. Abramovich, I. Batushansky, A. Dror, S. Elkabets, M. Alon, N. Brotman, Y. Kaluski-Kopatch, S. Nikelshparg, E. Sued-Hendrickson, S. Bershtein, S. Ben-Zvi, A. Rotblat, B. 2026-02-17 doi:10.64898/2026.02.16.706072 Cold Spring Harbor Laboratory Press 2026-02-17 <![CDATA[ The Sniffbot: A biohybrid robot for active sensing-based odor localization and discrimination ]]> https://biorxiv.org/content/10.64898/2026.02.17.706375v1?rss=1 Shvil, N. Gozin, N. Sheinin, A. Yuval, O. Yovel, Y. Maoz, B. M. Ayali, A. 2026-02-18 doi:10.64898/2026.02.17.706375 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Mega-frequency mutagenesis: generation of non-random precise mutations with extremely high frequency upon adaptation of cancer cells to drugs and stress ]]> https://biorxiv.org/content/10.64898/2026.02.20.707073v1?rss=1 Oleynik, V. Edathil Kadangodan, A. Gahramanov, V. Das, S. R. Levi, B. Yaglom, J. Anoshkin, K. Kumar, S. Steinberg, B. G. Reizel, Y. Polonsky, P. Koman, I. Levitt, V. Pinhasov, A. Marusyk, A. Nesher, E. Sherman, M. Y. 2026-02-23 doi:10.64898/2026.02.20.707073 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Specialization of independently acquired flagellar FliC proteins in plant-associated Sphingomonas balances swimming and immunogenicity ]]> https://biorxiv.org/content/10.64898/2026.02.23.707200v1?rss=1 Russ, D. Saha, C. Paul, K. Zheng, Z. Law, T. F. Anguita-Maeso, M. Lundberg, D. S. Fitzpatrick, C. R. Dangl, J. L. 2026-02-24 doi:10.64898/2026.02.23.707200 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ Neural Evidence of Early Sensitivity to Text in Pre-reading Toddlers ]]> https://biorxiv.org/content/10.64898/2026.02.24.707347v1?rss=1 Kherbawy, N. Potter, C. E. Jaffe-Dax, S. 2026-02-26 doi:10.64898/2026.02.24.707347 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Stretching drives Membrane Homogenization of Phase-Separated Supported Lipid Bilayers ]]> https://biorxiv.org/content/10.64898/2026.02.26.708304v1?rss=1 Perlman Illouz, A. Meyer, R. Köster, S. Golani, G. Sorkin, R. 2026-02-28 doi:10.64898/2026.02.26.708304 Cold Spring Harbor Laboratory Press 2026-02-28 <![CDATA[ Quiescence improves Candida albicans survival of fungicidal drug exposure ]]> https://biorxiv.org/content/10.64898/2026.02.27.708532v1?rss=1 Gresham, D. Imir, O. Druseikis, M. Xie, Y. Ji, Y. Holt, L. Berman, J. 2026-02-28 doi:10.64898/2026.02.27.708532 Cold Spring Harbor Laboratory Press 2026-02-28 <![CDATA[ Multi-Omic, Multi-Tissue Responses to Acute Exercise in Sedentary Adults: Findings from the Molecular Transducers of Physical Activity Consortium ]]> https://biorxiv.org/content/10.64898/2026.02.27.702183v1?rss=1 MoTrPAC Study Group, Katz, D. H. Jin, C. A. Many, G. M. Smith, G. R. Keshishian, H. Clark, N. M. Iyer, G. Ahn, C. Lindholm, M. E. Sagendorf, T. J. Amar, D. Barber, J. L. Brandt, A. R. Coen, P. M. Ge, Y. Hart, P. Hsu, F.-C. Jaeger, B. C. Jimenez-Morales, D. Leach, D. T. Mani, D. R. Montalvo, S. Pincas, H. Rao, P. Sanford, J. A. Smith, K. S. Vetr, N. G. Adkins, J. N. Ashley, E. A. Carr, S. A. Miller, M. E. Montgomery, S. B. Nair, V. D. Robbins, J. M. Snyder, M. P. Sparks, L. M. Tracy, R. Walsh, M. J. Wheeler, M. T. Xia, A. Y. Sealfon, S. C. Gerszten, R 2026-03-03 doi:10.64898/2026.02.27.702183 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Blood Biochemical Responses to Acute Exercise: Findings from the Molecular Transducers of Physical Activity Consortium (MoTrPAC) ]]> https://biorxiv.org/content/10.64898/2026.03.02.704798v1?rss=1 Robbins, J. M. Katz, D. H. Many, G. Rao, P. Smith, G. R. Tiwari, G. Spielmann, G. Montalvo, S. Iyer, G. Amar, D. Leach, D. T. Coyne, B. J. Lindholm, M. E. Goodpaster, B. H. Walsh, M. J. Clish, C. B. Burant, C. F. Gerszten, R. E. MoTrPAC Study Group, 2026-03-04 doi:10.64898/2026.03.02.704798 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Robust self-organization of livestock pluripotent stem cells into post-gastrulation embryo models with advanced neuronal and mesodermal structures ]]> https://biorxiv.org/content/10.64898/2026.03.02.709113v1?rss=1 Hauser, M. Berkowicz, P. Namestnikov, M. Dekel, B. Schlesinger, S. Nachman, I. 2026-03-04 doi:10.64898/2026.03.02.709113 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Exploring per-base quality scores as a surrogate marker of cell-free DNA fragmentome ]]> https://biorxiv.org/content/10.64898/2026.03.08.710357v1?rss=1 Volkov, H. H. V. Raitses-Gurevich, M. Grad, M. Shlayem, R. Leibowitz, D. Rubinek, T. Golan, T. Shomron, N. 2026-03-10 doi:10.64898/2026.03.08.710357 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ FAMUS: A Few-Shot Learning Framework for Large-Scale Protein Annotation ]]> https://biorxiv.org/content/10.64898/2026.03.08.710366v1?rss=1 Shur, G. Burstein, D. 2026-03-10 doi:10.64898/2026.03.08.710366 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Scavenger Cells Failure to Maintain Systemic RNA Homeostasis Causes Epigenetically Inherited Germline Tumors ]]> https://biorxiv.org/content/10.64898/2026.03.09.710559v1?rss=1 Rieger, I. Mor, Y. Lev, I. Nitzan, A. Kong, C. B. Anava, S. Gingold, H. Zaidel-Bar, R. Rechavi, O. 2026-03-11 doi:10.64898/2026.03.09.710559 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Trans-regenerational RNAi Memory in Planarians ]]> https://biorxiv.org/content/10.64898/2026.03.11.711021v1?rss=1 Cherian, P. V. Aviram, I. Weill, U. Shapira, T. Anava, S. Gingold, H. Rink, J. C. Rechavi, O. Wurtzel, O. 2026-03-13 doi:10.64898/2026.03.11.711021 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Segment Any Plant (SAP): Foundation-Model Segmentation for Plant Time-Series Phenotyping ]]> https://biorxiv.org/content/10.64898/2026.03.11.711099v1?rss=1 Abbey, A. Meroz, Y. 2026-03-13 doi:10.64898/2026.03.11.711099 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Circumnutations drive embodied mechanical sensing and support selection in twining plants ]]> https://biorxiv.org/content/10.64898/2026.03.16.712031v1?rss=1 Ohad, A. Porat, A. Meroz, Y. 2026-03-18 doi:10.64898/2026.03.16.712031 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Sustained exposure to CAR-T cell secretome impairs human Hematopoietic Stem Cell function and is reversible by dual TNFα-IFNγ blockade ]]> https://biorxiv.org/content/10.64898/2026.03.17.712280v1?rss=1 Muddineni, S. S. N. A. Rasoulouniriana, D. Meir, A. Geller, D. Singha Roy, D. Tako, E. Solomon, N. Avraham, T. Raz, Y. Chen, R. Shifrut, E. Jacoby, E. Milyavsky, M. 2026-03-18 doi:10.64898/2026.03.17.712280 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Context-dependent determinants of CRISPR-Cas9 editing efficiency revealed through cross-species endogenous editing analysis ]]> https://biorxiv.org/content/10.64898/2026.03.18.712093v1?rss=1 Cohen, S. Bergman, S. Burghardt, M. Menuhin-Gruman, I. Eyal, E. Arbel, N. Emmanuel, E. Kapel, M. Rabinovich, L. Avital, G. Maoz, A. Avitzour, M. Bogen, M. Orenstein, Y. Rahimi, M. Yaish, O. Veksler-Lublinsky, I. Cohen, L. Malul, T. Mayrose, I. Rice, A. Landau, E. Burstein, D. Arias, O. Gertz, D. Kutchinsky, O. Aharoni, A. Li, D. Parnas, O. Mol Jaya Prakashan, M. Shovman, Y. Izhiman, T. Kunis, G. Wiener, A. Barhum, Y. Steinberg Shemer, O. Izraeli, S. Birger, Y. Markovich, O. Furest, D. Moshkovitz, S. Yahalom, A. Dominissini, D. Brezinger-Dayan, K. J. 2026-03-18 doi:10.64898/2026.03.18.712093 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Disruption of the Brain-Spleen Axis Impairs Monocyte-Microglia Communication and Accelerates Disease Progression in a Model of Amyloidosis ]]> https://biorxiv.org/content/10.64898/2026.03.18.712196v1?rss=1 Croese, T. Abellanas, M. A. Polonsky, H. Arad, M. Peralta Ramos, J. M. Androsova, Y. Riccitelli, S. Medina, S. Palmas, F. Strobel, R. Castellani, G. Kviatcovsky, D. Phoebeluc-Colaiuta, S. Adam, M. Murad, S. Partney, H. Kitsberg, D. Dieter, A. Salame, T.-M. Brandis, A. Mehlman, T. Singer, O. Rivlin-Etzion, M. Wiegert, S. Shaul, Y. Kobiler, O. Yizhar, O. Habib, N. Schwartz, M. 2026-03-20 doi:10.64898/2026.03.18.712196 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Capping protein regulates the balance of assembly among diverse actin networks in C. elegans zygotes ]]> https://biorxiv.org/content/10.64898/2026.03.23.713757v1?rss=1 Yde, S. E. Suarez, C. Ray, S. Zaidel-Bar, R. Kadzik, R. S. Munro, E. Kovar, D. R. 2026-03-24 doi:10.64898/2026.03.23.713757 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Delusions Emerge from Generative Model Reorganisation rather than Faulty Inference: Insights from Hybrid Predictive Coding ]]> https://biorxiv.org/content/10.64898/2026.03.23.713603v1?rss=1 Navarro, V. M. Brugger, S. Wolpe, N. Harding, J. Fletcher, P. Teufel, C. 2026-03-25 doi:10.64898/2026.03.23.713603 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Notch mediated lateral inhibition is shaped by morphological differences to reinforce bias toward signal-sending or receiving roles ]]> https://biorxiv.org/content/10.64898/2026.03.27.712410v1?rss=1 Richa, P. Roussos, C. Zhu, C. Lenz, M. O. Kasirer, S. Sprinzak, D. Bray, S. 2026-03-28 doi:10.64898/2026.03.27.712410 Cold Spring Harbor Laboratory Press 2026-03-28 <![CDATA[ MAAMOUL: Metabolic network-based discovery of microbiome-metabolome shifts in disease ]]> https://biorxiv.org/content/10.64898/2026.03.27.714614v1?rss=1 Muller, E. Baum, S. Borenstein, E. 2026-03-30 doi:10.64898/2026.03.27.714614 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Neurofilament Light Disordered Tail Mutations Reshape Its Self-Assembled Network Structure ]]> https://biorxiv.org/content/10.64898/2026.03.27.714705v1?rss=1 Aodeh, R. Dan, Y. Yona, D. Shalabi, M. Sivan, A. Kravicas, M. Aharoni, H. Koren, G. Adler-Abramovich, L. Beck, R. 2026-03-30 doi:10.64898/2026.03.27.714705 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Haplotype-resolved centromeric chromatin organization from a complete diploid human genome ]]> https://biorxiv.org/content/10.64898/2026.03.27.714900v1?rss=1 Xu, Y. Loucks, H. Menendez, J. Ryabov, F. Lucas, J. K. Cechova, M. 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