bioRxiv Channel: Weizmann Institute of Science https://biorxiv.org This feed contains articles for bioRxiv Channel "Weizmann Institute of Science" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Neutralizing Gatad2a-Chd4-Mbd3 Axis within the NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency ]]> https://biorxiv.org/content/10.1101/192781v1?rss=1 Mor, N. Rais, Y. Peles, S. Sheban, D. Aguilera-Castrejon, A. Zviran, A. Elinger, D. Viukov, S. Geula, S. Krupalnik, V. Zerbib, M. Chomsky, E. Lasman, L. Shani, T. Bayerl, J. Gafni, O. Hanna, S. Buenrostro, J. Hagai, T. Masika, H. Bergman, Y. Greenleaf, W. J. Esteban, M. A. Levin, Y. Massarwa, R. Merbl, Y. Novershtern, N. Hanna, J. H. 2018-02-09 doi:10.1101/192781 Cold Spring Harbor Laboratory Press 2018-02-09 <![CDATA[ Neutralizing Gatad2a-Chd4-Mbd3 Axis within the NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency ]]> https://biorxiv.org/content/10.1101/192781v1?rss=1 Mor, N. Rais, Y. Peles, S. Sheban, D. Aguilera-Castrejon, A. Zviran, A. Elinger, D. Viukov, S. Geula, S. Krupalnik, V. Zerbib, M. Chomsky, E. Lasman, L. Shani, T. Bayerl, J. Gafni, O. Hanna, S. Buenrostro, J. Hagai, T. Masika, H. Bergman, Y. Greenleaf, W. J. Esteban, M. A. Levin, Y. Massarwa, R. Merbl, Y. Novershtern, N. Hanna, J. H. 2018-02-09 doi:10.1101/192781 Cold Spring Harbor Laboratory Press 2018-02-09 <![CDATA[ Neutralizing Gatad2a-Chd4-Mbd3 Axis within the NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency ]]> https://biorxiv.org/content/10.1101/192781v1?rss=1 Mor, N. Rais, Y. Peles, S. Sheban, D. Aguilera-Castrejon, A. Zviran, A. Elinger, D. Viukov, S. Geula, S. Krupalnik, V. Zerbib, M. Chomsky, E. Lasman, L. Shani, T. Bayerl, J. Gafni, O. Hanna, S. Buenrostro, J. Hagai, T. Masika, H. Bergman, Y. Greenleaf, W. J. Esteban, M. A. Levin, Y. Massarwa, R. Merbl, Y. Novershtern, N. Hanna, J. H. 2018-02-09 doi:10.1101/192781 Cold Spring Harbor Laboratory Press 2018-02-09 <![CDATA[ Chronic inflammation partially recapitulates the gene expression signature of aging ]]> https://biorxiv.org/content/10.1101/2022.09.26.509471v1?rss=1 Landsberger, T. Amit, I. Alon, U. 2022-09-27 doi:10.1101/2022.09.26.509471 Cold Spring Harbor Laboratory Press 2022-09-27 <![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[ Regulation of chromatin microphase separation by adsorbed protein complexes ]]> https://biorxiv.org/content/10.1101/2022.09.29.510124v1?rss=1 Adame-Arana, O. Bajpai, G. Lorber, D. Volk, T. Safran, S. A. 2022-09-30 doi:10.1101/2022.09.29.510124 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Biogenic plate-like guanine crystals form via templated nucleation of thin crystal leaflets on amyloid scaffolds ]]> https://biorxiv.org/content/10.1101/2022.09.29.510168v1?rss=1 Eyal, Z. Deis, R. Varsano, N. Dezorella, N. Rechav, K. Houben, L. Gur, D. 2022-09-30 doi:10.1101/2022.09.29.510168 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ The cellular states and fates of shed intestinal cells ]]> https://biorxiv.org/content/10.1101/2022.10.03.510592v1?rss=1 Bahar Halpern, K. Biram, A. Egozi, A. Korem Kohanim, Y. Shulman, Z. Itzkovitz, S. 2022-10-04 doi:10.1101/2022.10.03.510592 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ MTCH2 cooperates with MFN2 and lysophosphatidic acid synthesis to sustain mitochondrial fusion ]]> https://biorxiv.org/content/10.1101/2022.10.04.510812v1?rss=1 Goldman, A. Mullokandov, M. Zaltsman, Y. Regev, L. Zaidman, S. Gross, A. 2022-10-05 doi:10.1101/2022.10.04.510812 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ UV irradiation remodels the specificity landscape of transcription factors ]]> https://biorxiv.org/content/10.1101/2022.10.07.511343v1?rss=1 Mielko, Z. Zhang, Y. Liu, Y. Schaich, M. A. Schnable, B. Burdinski, D. Adar, S. Pufall, M. Van Houten, B. Gordan, R. Afek, A. 2022-10-08 doi:10.1101/2022.10.07.511343 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ Designed active-site library reveals thousands of functional GFP variants ]]> https://biorxiv.org/content/10.1101/2022.10.11.511732v1?rss=1 16,000 unique designs encoding as many as eight active-site mutations. Many designs exhibit substantial and useful diversity in functional thermostability (up to 96 {degrees}C), fluorescence lifetime, and quantum yield. By eliminating incompatible active-site mutations, htFuncLib generates a large diversity of functional sequences. We envision that htFuncLib will be useful for one-shot optimization of activity in enzymes, binders, and other proteins. ]]> Weinstein, J. Y. Aldaravi, C. M. G. Lipsh-Sokolik, R. Hoch, S. Y. Liebermann, D. Nevo, R. Weissman, H. Petrovich-Kopitman, E. Margulies, D. Ivankov, D. McCandlish, D. Fleishman, S. J. 2022-10-11 doi:10.1101/2022.10.11.511732 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Daily turnover of active giant virus infection during algal blooms revealed by single-cell transcriptomics ]]> https://biorxiv.org/content/10.1101/2022.10.15.512338v1?rss=1 Hevroni, G. Vincent, F. J. Ku, C. Sheyn, U. Vardi, A. 2022-10-15 doi:10.1101/2022.10.15.512338 Cold Spring Harbor Laboratory Press 2022-10-15 <![CDATA[ Disparate patterns of genetic divergence in three widespread corals across a pan-Pacific environmental gradient highlights species-specific adaptation trajectories. ]]> https://biorxiv.org/content/10.1101/2022.10.13.512013v1?rss=1 Hume, B. C. Voolstra, C. R. Armstrong, E. Mitushasi, G. Porro, B. Oury, N. Agostini, S. Boissin, E. Poulain, J. Carradec, Q. Paz-Garcia, D. A. Zoccola, D. Magalon, H. Moulin, C. Bourdin, G. Iwankow, G. Romac, S. Banaigs, B. Boss, E. Bowler, C. de Vargas, C. Douville, E. Flores, M. Furla, P. Galand, P. Gilson, E. Lombard, F. Pesant, S. Reynaud, S. Sullivan, M. B. Shinichi, S. Thomas, O. Trouble, R. Vega Thurber, R. Wincker, P. Planes, S. Allemand, D. Forcioli, D. 2022-10-17 doi:10.1101/2022.10.13.512013 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Damage dynamics in single E. coli and the role of chance in the timing of cell death ]]> https://biorxiv.org/content/10.1101/2022.10.17.512406v1?rss=1 Yang, Y. Karin, O. Mayo, A. Song, X. Chen, P. Lindner, A. B. Alon, U. 2022-10-17 doi:10.1101/2022.10.17.512406 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ From genome wide SNPs to genomic islands of differentiation: the quest for species diagnostic markers in two scleractinian corals, Pocillopora and Porites ]]> https://biorxiv.org/content/10.1101/2022.10.21.513203v1?rss=1 Deshuraud, R. Ottaviani, A. Poulain, J. Lepretre, M. Beluche, O. Mahieu, E. Lebled, S. Belser, C. Rouan, A. Moulin, C. Boissin, E. Bourdin, G. Iwankow, G. Romac, S. Agostini, S. Banaigs, B. Boss, E. S. Bowler, C. de Vargas, C. Douville, E. Flores, M. Furla, P. Galand, P. Lombard, F. Pesant, S. Reynaud, S. Sullivan, M. B. Sunagawa, S. Thomas, O. Trouble, R. Thurber, R. V. Voolstra, C. R. Wincker, P. Zoccola, D. Planes, S. Allemand, D. Gilson, E. Forcioli, D. 2022-10-21 doi:10.1101/2022.10.21.513203 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Modulation of type I interferon responses potently inhibits SARS-CoV-2 replication and inflammation in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2022.10.21.512606v1?rss=1 Hoang, T. N. Viox, E. G. Upadhyay, A. A. Strongin, Z. Tharp, G. K. Pino, M. Nchioua, R. Hirschenberger, M. Gagne, M. Nguyen, K. Harper, J. L. Marciano, S. Boddapati, A. K. Pellegrini, K. L. Tisoncik-Go, J. Whitmore, L. S. Karunakaran, K. A. Roy, M. Kirejczyk, S. Curran, E. H. Wallace, C. Wood, J. S. Connor-Stroud, F. Kasturi, S. P. Levit, R. D. Gale, M. Vanderford, T. H. Silvestri, G. Busman-Sahay, K. Estes, J. D. Vaccari, M. Douek, D. C. Sparrer, K. M. J. Kirchhoff, F. Johnson, R. P. Schreiber, G. Bosinger, S. E. Paiardini, M. 2022-10-24 doi:10.1101/2022.10.21.512606 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ The effects of drought and inter-plant competition on the ectomycorrhizal interaction between fungi and Aleppo pine seedlings ]]> https://biorxiv.org/content/10.1101/2022.10.25.513645v1?rss=1 Herol, L. Shemesh, H. Avidar, M. Yirmiahu, S. Zach, Y. klein, T. Livne- Luzon, S. 2022-10-26 doi:10.1101/2022.10.25.513645 Cold Spring Harbor Laboratory Press 2022-10-26 <![CDATA[ Tell me who your neighbors are: The role of spatial location and tree species identity in determining the ectomycorrhizal community composition of saplings and mature trees in a mixed conifer forest ]]> https://biorxiv.org/content/10.1101/2022.10.27.514003v1?rss=1 Livne- Luzon, S. Avidar, M. Herol, L. Rog, I. Klein, T. Shemesh, H. 2022-10-28 doi:10.1101/2022.10.27.514003 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ How do Vampires Suck Blood? ]]> https://biorxiv.org/content/10.1101/2022.10.31.514445v1?rss=1 Gou, M. Duan, X. Li, J. Wang, Y. Li, Q. Pang, Y. Dong, Y. 2022-10-31 doi:10.1101/2022.10.31.514445 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ The molecular principles governing HCMV infection outcome ]]> https://biorxiv.org/content/10.1101/2022.10.31.514490v1?rss=1 Schwartz, M. Shnayder, M. Nachshon, A. Arazi, T. Kitsberg, Y. Levi Samia, R. Lavi, M. Kuint, R. Tsabari, R. Stern-Ginossar, N. 2022-10-31 doi:10.1101/2022.10.31.514490 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ e-cone and d-cone singularities drive submucosal collagen fiber remodeling in intestinal anastomotic surgery ]]> https://biorxiv.org/content/10.1101/2022.10.31.514540v1?rss=1 Fleischer, B. Nguyen, N. Pal, A. Khabaz, K. Tsamis, A. Efrati, E. Witten, T. Alverdy, J. Pocivavsek, L. 2022-11-01 doi:10.1101/2022.10.31.514540 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ CellSighter - A neural network to classify cells in highly multiplexed images ]]> https://biorxiv.org/content/10.1101/2022.11.07.515441v1?rss=1 Amitay, Y. Bussi, Y. Feinstein, B. Bagon, S. Milo, I. Keren, L. 2022-11-08 doi:10.1101/2022.11.07.515441 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ Large clones of pre-existing T cells drive early immunity against SARS-COV-2 and LCMV infection. ]]> https://biorxiv.org/content/10.1101/2022.11.08.515436v1?rss=1 Milighetti, M. Peng, Y. Tan, C. C. S. Mark, M. Nageswaran, G. Byrne, S. Ronel, T. Peacock, T. Mayer, A. Chandran, A. Rosenheim, J. Wheelan, M. Yao, X. Liu, G. Felce, S. L. Dong, T. Mentzer, A. J. Knight, J. C. Balloux, F. Greenstein, E. Reich-Zeliger, S. Pade, C. Gibbons, J. M. Semper, A. Brooks, T. Otter, A. Altmann, D. M. Boyton, R. J. Maini, M. K. McKnight, A. Manisty, C. Treibel, T. A. Moon, J. C. COVIDsortium Investigators, Noursadeghi, M. Chain, B. 2022-11-08 doi:10.1101/2022.11.08.515436 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ Ex vivo intestinal permeability assay (X-IPA) for tracking barrier function dynamics ]]> https://biorxiv.org/content/10.1101/2022.11.08.515584v1?rss=1 Bootz-Maoz, H. Simon, A. Del Mare-Roumani, S. Bennet, Y. Zheng, D. Amidror, S. Elinav, E. Yissachar, N. 2022-11-08 doi:10.1101/2022.11.08.515584 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation ]]> https://biorxiv.org/content/10.1101/2022.11.11.516100v1?rss=1 Ben-Tov Perry, R. Tsoory, M. Tolmasov, M. Ulitsky, I. 2022-11-11 doi:10.1101/2022.11.11.516100 Cold Spring Harbor Laboratory Press 2022-11-11 <![CDATA[ Motion-Induced Blindness as a Noisy Excitable System ]]> https://biorxiv.org/content/10.1101/2022.11.12.516289v1?rss=1 katkov, m. Cooperman, A. Meital-Kfir, N. Sagi, D. 2022-11-13 doi:10.1101/2022.11.12.516289 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Forgetting Dynamics For Items of Different Categories ]]> https://biorxiv.org/content/10.1101/2022.11.14.516480v1?rss=1 Georgiou, A. katkov, m. Tsodyks, M. 2022-11-14 doi:10.1101/2022.11.14.516480 Cold Spring Harbor Laboratory Press 2022-11-14 <![CDATA[ Time-Aligned Hourglass Gastrulation Models in Rabbit and Mouse ]]> https://biorxiv.org/content/10.1101/2022.11.13.516304v1?rss=1 Mayshar, Y. Raz, O. Cheng, S. Ben-Yair, R. Hadas, R. Reines, N. Mittnenzweig, M. Ben-Kiki, O. Lifshitz, A. Tanay, A. Stelzer, Y. 2022-11-15 doi:10.1101/2022.11.13.516304 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells ]]> https://biorxiv.org/content/10.1101/2022.11.16.516734v1?rss=1 Dunjic, M. Jonas, F. Yaakov, G. More, R. Mayshar, Y. Rais, Y. Barkai, N. Stelzer, Y. 2022-11-17 doi:10.1101/2022.11.16.516734 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ A cell circuit approach to dissect fibroblast-macrophage interactions in the tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2022.11.17.516850v1?rss=1 Mayer, S. Milo, T. Isaacson, A. Halperin, C. Miyara, S. Stein, Y. Pevsner-Fischer, M. Tzahor, E. Alon, U. Scherz-Shouval, R. 2022-11-17 doi:10.1101/2022.11.17.516850 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Evolutionarily conserved waves of tooth replacement in the gecko are dependent on local signaling ]]> https://biorxiv.org/content/10.1101/2022.11.17.513312v1?rss=1 Brink, K. S. Cytrynbaum, E. N. Grieco, T. M. Henriquez, J. I. Zhitnitsky, A. Richman, J. M. 2022-11-18 doi:10.1101/2022.11.17.513312 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ Bridging the light-electron resolution gap with correlative cryo-SRRF and dual-axis cryo-STEM tomography ]]> https://biorxiv.org/content/10.1101/2022.11.19.517200v1?rss=1 Kirchweger, P. Mullick, D. Sawin, P. P. Wolf, S. G. Elbaum, M. 2022-11-19 doi:10.1101/2022.11.19.517200 Cold Spring Harbor Laboratory Press 2022-11-19 <![CDATA[ Multi-site assessment of reproducibility in high-content live cell imaging data ]]> https://biorxiv.org/content/10.1101/2022.11.18.516878v1?rss=1 Hu, J. Serra-Picamal, X. Bakker, G.-J. Troys, M. V. Winograd-katz, S. Ege, N. Gong, X. Didan, Y. Grosheva, I. Polansky, O. Bakkali, K. Hamme, E. V. Erp, M. v. Vullings, M. Weiss, F. Clucas, J. Dowbaj, A. M. Sahai, E. Ampe, C. Geiger, B. Friedl, P. Bottai, M. Stromblad, S. 2022-11-20 doi:10.1101/2022.11.18.516878 Cold Spring Harbor Laboratory Press 2022-11-20 <![CDATA[ Allosteric communication between ligand binding domains modulates substrate inhibition in adenylate kinase ]]> https://biorxiv.org/content/10.1101/2022.11.21.517316v1?rss=1 Scheerer, D. Adkar, B. V. Bhattacharyya, S. Levy, D. Iljina, M. Riven, I. Dym, O. Haran, G. Shakhnovich, E. 2022-11-21 doi:10.1101/2022.11.21.517316 Cold Spring Harbor Laboratory Press 2022-11-21 <![CDATA[ Inhibiting a promiscuous GPCR: iterative discovery of bitter taste receptor ligands ]]> https://biorxiv.org/content/10.1101/2022.11.24.517821v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@30bd42org.highwire.dtl.DTLVardef@1d94fbforg.highwire.dtl.DTLVardef@2858borg.highwire.dtl.DTLVardef@18d9af2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Fierro, F. Peri, L. Huebner, H. Tabor-Schkade, A. Waterloo, L. Loeber, S. Pfeiffer, T. Dingjan, T. Margulis, E. Gmeiner, P. Niv, M. Y. 2022-11-25 doi:10.1101/2022.11.24.517821 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ A Possible Unitary Mechanism for General Anesthesia ]]> https://biorxiv.org/content/10.1101/2022.11.29.518334v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@4a5b8aorg.highwire.dtl.DTLVardef@1bfc961org.highwire.dtl.DTLVardef@3e002corg.highwire.dtl.DTLVardef@7d74f0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gupta, A. Sang, Y. Fontanesi, C. Turin, L. Naaman, R. 2022-11-30 doi:10.1101/2022.11.29.518334 Cold Spring Harbor Laboratory Press 2022-11-30 <![CDATA[ Metacell projection for interpretable and quantitative use of transcriptional atlases ]]> https://biorxiv.org/content/10.1101/2022.12.01.518678v1?rss=1 Ben-Kiki, O. Bercovich, A. Lifshitz, A. Tanay, A. 2022-12-02 doi:10.1101/2022.12.01.518678 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Convergent evolution of the SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant ]]> https://biorxiv.org/content/10.1101/2022.12.05.519085v1?rss=1 Ito, J. Suzuki, R. Uriu, K. Itakura, Y. Zahradnik, J. Deguchi, S. Wang, L. Lytras, S. Tamura, T. Kida, I. Nasser, H. Shofa, M. Begum, M. M. Tsuda, M. Oda, Y. Fujita, S. Yoshimatsu, K. Ito, H. Nao, N. Asakura, H. Nagashima, M. Sadamasu, K. Yoshimura, K. Yamamoto, Y. Nagamoto, T. Schreiber, G. The Genotype to Phenotype Japan (G2P-Japan) Consortium, Saito, A. Matsuno, K. Takayama, K. Tanaka, S. Fukuhara, T. Ikeda, T. Sato, K. 2022-12-05 doi:10.1101/2022.12.05.519085 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ Regulatory heterogeneity of Vegf- and Wnt7-dependent angiogenesis drives phenotypic diversity of brain vasculature ]]> https://biorxiv.org/content/10.1101/2022.12.08.519692v1?rss=1 Parab, S. Card, O. A. Chen, Q. Buck, L. D. Quick, R. E. Horrigan, W. F. Levkowitz, G. Vanhollebeke, B. Matsuoka, R. L. 2022-12-09 doi:10.1101/2022.12.08.519692 Cold Spring Harbor Laboratory Press 2022-12-09 <![CDATA[ Actomyosin remodeling regulates biomineral formation, growth and morphology during eukaryote skeletogenesis ]]> https://biorxiv.org/content/10.1101/2022.12.21.521381v1?rss=1 Hijaze, E. Gildor, T. Seidel, R. Winter, M. Bertinetti, L. Layous, M. Politi, Y. de-Leon, S. B.-T. 2022-12-21 doi:10.1101/2022.12.21.521381 Cold Spring Harbor Laboratory Press 2022-12-21 <![CDATA[ Early excitatory and inhibitory modifications in the motor cortex following skill learning support motor memory consolidation and cortical plasticity overnight ]]> https://biorxiv.org/content/10.1101/2022.12.27.521981v1?rss=1 Eisenstein, T. Furman-Haran, E. Tal, A. 2022-12-27 doi:10.1101/2022.12.27.521981 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants ]]> https://biorxiv.org/content/10.1101/2022.12.27.521986v1?rss=1 Tamura, T. Ito, J. Uriu, K. Zahradnik, J. Kida, I. Nasser, H. Shofa, M. Oda, Y. Lytras, S. Nao, N. Itakura, Y. Deguchi, S. Suzuki, R. Wang, L. Begum, M. M. Tsuda, M. Kosugi, Y. Fujita, S. Yoshimatsu, K. Suzuki, S. Asakura, H. Nagashima, M. Sadamasu, K. Yoshimura, K. Yamamoto, Y. Nagamoto, T. Schreiber, G. The Genotype to Phenotype Japan (G2P-Japan) Consortium, Ikeda, T. Fukuhara, T. Saito, A. Tanaka, S. Matsuno, K. Takayama, K. Sato, K. 2022-12-27 doi:10.1101/2022.12.27.521986 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ One-shot design elevates functional expression levels of a voltage-gated potassium channel ]]> https://biorxiv.org/content/10.1101/2022.12.28.522065v1?rss=1 Weinstein, J. J. Saikia, C. Karbat, I. Goldenzweig, A. Reuveny, E. Fleishman, S. J. 2022-12-29 doi:10.1101/2022.12.28.522065 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Human TRMT2A methylates different components of the translation machinery and contributes to translation fidelity ]]> https://biorxiv.org/content/10.1101/2022.12.28.522094v1?rss=1 Witzenberger, M. Burczyk, S. Welp, L. M. Wagner, M. Monecke, T. Janowski, R. Carell, T. Urlaub, H. Hauck, S. M. Voigt, A. Niessing, D. 2022-12-29 doi:10.1101/2022.12.28.522094 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Circuit to target approach defines an autocrine myofibroblast loop that drives cardiac fibrosis ]]> https://biorxiv.org/content/10.1101/2023.01.01.522422v1?rss=1 Miyara, S. Adler, M. Bassat, E. Divinsky, Y. Umansky, K. B. Elkahal, J. Genzelinakh, A. Kain, D. Lendengolts, D. Shalit, T. Gershovits, M. Shakked, A. Zhang, L. Wang, J. Kimchi, D. M. Baehr, A. Sarig, R. Kupatt, C. Tanaka, E. M. Medzhitov, R. Mayo, A. Alon, U. Tzahor, E. 2023-01-03 doi:10.1101/2023.01.01.522422 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Metabolic rewiring of the probiotic bacterium Lacticaseibacillus rhamnosus GG contributes to cell wall remodeling and antimicrobials production ]]> https://biorxiv.org/content/10.1101/2023.01.03.522566v1?rss=1 Suissa, R. Olender, T. Malitsky, S. Golani, O. Turjeman, S. Meijler, M. M. Koren, O. Kolodkin-Gal, I. 2023-01-03 doi:10.1101/2023.01.03.522566 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Comment on 'Connexins evolved after early chordates lost innexin diversity' ]]> https://biorxiv.org/content/10.1101/2023.01.05.522624v1?rss=1 Kelmanson, I. V. Bakin, E. A. Karbat, I. Slivko-Koltchik, G. A. Reuveny, E. Panchin, Y. V. 2023-01-06 doi:10.1101/2023.01.05.522624 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ DNA G-quadruplex is a transcriptional control device that regulates memory ]]> https://biorxiv.org/content/10.1101/2023.01.09.523337v1?rss=1 Marshall, P. R. Zhao, Q. Davies, J. Liau, W.-S. Lee, Y. Basic, D. Periyakaruppiah, A. Zajaczkowski, E. Leighton, L. J. Madugalle, S. U. Musgrove, M. Kielar, M. Gong, H. Ren, H. Kaczmarczyk, L. Jackson, W. S. Chen, A. Spitale, R. Bredy, T. 2023-01-10 doi:10.1101/2023.01.09.523337 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Uncovering the Dynamics of Precise Repair at CRISPR/Cas9-induced Double-Strand Breaks ]]> https://biorxiv.org/content/10.1101/2023.01.10.523377v1?rss=1 Ben-Tov, D. Mafessoni, F. Cucuy, A. Honig, A. Bessudo, C. Levy, A. A. 2023-01-10 doi:10.1101/2023.01.10.523377 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Enhanced transmissibility, infectivity and immune resistance of the SARS-CoV-2 Omicron XBB.1.5 variant ]]> https://biorxiv.org/content/10.1101/2023.01.16.524178v1?rss=1 Uriu, K. Ito, J. Zahradnik, J. Fujita, S. Kosugi, Y. Schreiber, G. The Genotype to Phenotype Japan (G2P-Japan) Consortium, Sato, K. 2023-01-17 doi:10.1101/2023.01.16.524178 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ Dissecting the basis for differential substrate specificity of ADAR1 and ADAR2 ]]> https://biorxiv.org/content/10.1101/2023.01.16.524339v1?rss=1 Zambrano-Mila, M. S. Witzenberger, M. Uzonyi, A. Nir, R. Ben-Aroya, S. Levanon, E. Schwartz, S. 2023-01-17 doi:10.1101/2023.01.16.524339 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ FcyRIIB is a novel immune checkpoint in the tumor microenvironment limiting activity of Treg-targeting antibodies ]]> https://biorxiv.org/content/10.1101/2023.01.19.522856v1?rss=1 Knorr, D. A. Leidner, R. Jensen, S. Meng, R. Jones, A. Ballesteros-Merino, C. Bell, R. B. Baez, M. Sprott, D. Bifulco, C. Piening, B. D. Dahan, R. Fox, B. Ravetch, J. 2023-01-20 doi:10.1101/2023.01.19.522856 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Integration of spatially opposing cues by a single interneuron guides decision making in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.01.23.525194v1?rss=1 Gat, A. Pechuk, V. Peedikayil-Kurien, S. Goldman, G. Lubliner, J. Karimi, S. Krieg, M. Oren-Suissa, M. 2023-01-23 doi:10.1101/2023.01.23.525194 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ A conserved family of immune effectors cleaves cellular ATP upon viral infection ]]> https://biorxiv.org/content/10.1101/2023.01.24.525353v1?rss=1 Rousset, F. Yirmiya, E. Nesher, S. Brandis, A. Mehlman, T. Itkin, M. Malitsky, S. Millman, A. Melamed, S. Sorek, R. 2023-01-24 doi:10.1101/2023.01.24.525353 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ Carotenoid retention during post-harvest storage of Capsicum annuum: the role of the fruit surface structure. ]]> https://biorxiv.org/content/10.1101/2023.01.27.525890v1?rss=1 Holden, A. C. Cohen, H. Rickett, D. V. Aharoni, A. Fraser, P. D. 2023-01-28 doi:10.1101/2023.01.27.525890 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ Theoretical model of membrane protrusions driven by curved active proteins ]]> https://biorxiv.org/content/10.1101/2023.01.31.526240v1?rss=1 Ravid, Y. Penic, S. Mimori-Kiyosue, Y. Suetsugu, S. Iglic, A. Gov, N. 2023-02-03 doi:10.1101/2023.01.31.526240 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Isolating objective and subjective filling-in using the Drift Diffusion Model ]]> https://biorxiv.org/content/10.1101/2023.02.01.526391v1?rss=1 Dekel, R. Sagi, D. Zomet, A. Levi, D. M. Polat, U. 2023-02-03 doi:10.1101/2023.02.01.526391 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Single-molecule FRET probes the allosteric effect of ATP on the protein-translocating pore loops of a AAA+ machine ]]> https://biorxiv.org/content/10.1101/2023.02.02.526786v1?rss=1 Iljina, M. Mazal, H. Dayananda, A. Zhang, Z. Stan, G. Riven, I. Haran, G. 2023-02-03 doi:10.1101/2023.02.02.526786 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ A simple cognitive model explains movement decisions during schooling in zebrafish ]]> https://biorxiv.org/content/10.1101/2023.02.05.527161v1?rss=1 Oscar, L. Li, L. Gorbonos, D. Couzin, I. Gov, N. 2023-02-05 doi:10.1101/2023.02.05.527161 Cold Spring Harbor Laboratory Press 2023-02-05 <![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[ Decoupling cell size homeostasis in diatoms from the geometrical constraints of the silica cell-wall ]]> https://biorxiv.org/content/10.1101/2023.02.08.527611v1?rss=1 de Haan, D. Ramos, N.-H. Gal, A. 2023-02-08 doi:10.1101/2023.02.08.527611 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ TRAF3 Suppression Encourages B Cell Recruitment and Prolongs Survival of Microbiome-Intact Mice with Ovarian Cancer ]]> https://biorxiv.org/content/10.1101/2023.02.09.527814v1?rss=1 Zorea, J. Motro, Y. Mazor, R. Carmi, Y. Shulman, Z. Mahajna, J. Moran-Gilad, J. Elkabets, M. 2023-02-09 doi:10.1101/2023.02.09.527814 Cold Spring Harbor Laboratory Press 2023-02-09 <![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[ The yeast RNA methylation complex consists of conserved yet reconfigured components with m6A-dependent and independent roles ]]> https://biorxiv.org/content/10.1101/2023.02.10.528004v1?rss=1 Ensinck, I. Maman, A. Albihlal, W. Lassandro, M. Salzano, G. Sideri, T. Howell, S. Calvani, E. Patel, H. Bushkin, G. G. Snijders, A. P. Ralser, M. Skehel, M. Casanal, A. Schwartz, S. van Werven, F. 2023-02-10 doi:10.1101/2023.02.10.528004 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Rab7 dependent regulation of goblet cell protein CLCA1 modulates gastrointestinal homeostasis ]]> https://biorxiv.org/content/10.1101/2023.02.13.528320v1?rss=1 Gaur, P. Rajendran, Y. Srivastava, B. Markandey, M. Yoskovitz, V.-R. Mohapatra, G. Suhail, A. Choudhary, S. Tyagi, S. Yadav, S. C. Pandey, A. K. Merbl, Y. Bajaj, A. Ahuja, V. Srikanth, C. 2023-02-13 doi:10.1101/2023.02.13.528320 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ A comparative study of low-pH tolerance and chitinase activity between toxigenic and non-toxigenic strains of Vibrio cholerae ]]> https://biorxiv.org/content/10.1101/2023.02.13.528346v1?rss=1 Jayaraman, V. Khan, S. A. Perinbam, K. Rakheja, I. Vadakkepat, A. K. Chaudhary, S. K. Pandey, A. K. Mitra, J. 2023-02-13 doi:10.1101/2023.02.13.528346 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ Spatio-temporal coherence of circadian clocks and gating of differentiation in Anabaena filaments ]]> https://biorxiv.org/content/10.1101/2023.02.15.528611v1?rss=1 Arbel-Goren, R. Dassa, B. Zhitnitsky, A. Valladares, A. Herrero, A. Flores, E. Stavans, J. 2023-02-15 doi:10.1101/2023.02.15.528611 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Acetylation-dependent coupling between G6PD activity and apoptotic signaling ]]> https://biorxiv.org/content/10.1101/2023.02.19.529048v1?rss=1 Wu, F. Muskat, N. H. Dvilansky, I. Koren, O. Shahar, A. Gazit, R. Elia, N. Arbely, E. 2023-02-19 doi:10.1101/2023.02.19.529048 Cold Spring Harbor Laboratory Press 2023-02-19 <![CDATA[ Machine learning inference of continuous single-cell state transitions during myoblast differentiation and fusion ]]> https://biorxiv.org/content/10.1101/2023.02.19.529100v1?rss=1 Shakarchy, A. Zarfati, G. Hazak, A. Mealem, R. Huk, K. Avinoam, O. Zaritsky, A. 2023-02-19 doi:10.1101/2023.02.19.529100 Cold Spring Harbor Laboratory Press 2023-02-19 <![CDATA[ Human Arm Redundancy - A New Approach for the Inverse Kinematics Problem ]]> https://biorxiv.org/content/10.1101/2023.02.20.528995v1?rss=1 Barliya, A. Krausz, N. Naaman, H. Chiovetto, E. Giese, M. A. Flash, T. 2023-02-21 doi:10.1101/2023.02.20.528995 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Increased cortical inhibition immediately following brief motor memory reactivation supports reconsolidation and overnight offline learning gains ]]> https://biorxiv.org/content/10.1101/2023.02.21.529358v1?rss=1 Eisenstein, T. Furman-Haran, E. Tal, A. 2023-02-21 doi:10.1101/2023.02.21.529358 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Modulation of proximity to criticality enhances slow activity fluctuations during free recall ]]> https://biorxiv.org/content/10.1101/2023.02.24.529043v1?rss=1 Yellin, D. Siegel, N. Malach, R. Shriki, O. 2023-02-27 doi:10.1101/2023.02.24.529043 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ EnCPdock: a web-interface for direct conjoint comparative analyses of complementarity and binding energetics in inter-protein associations ]]> https://biorxiv.org/content/10.1101/2023.02.26.530084v1?rss=1 Biswas, G. Mukherjee, D. Dutta, N. Ghosh, P. Basu, S. 2023-02-27 doi:10.1101/2023.02.26.530084 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Respiration-Triggered Olfactory Stimulation ReducesObstructive Sleep Apnea Symptoms Severity: A Prospective Pilot Study ]]> https://biorxiv.org/content/10.1101/2023.02.28.530439v1?rss=1 Perl, O. Kemer, L. Green, A. Arish, N. Corcos, Y. Arzi, A. Dagan, Y. 2023-03-01 doi:10.1101/2023.02.28.530439 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Physiological stress drives the emergence of a Salmonella subpopulation through ribosomal RNA regulation ]]> https://biorxiv.org/content/10.1101/2023.03.02.530801v1?rss=1 Avraham, R. Ciolli Mattioli, C. Eisner, K. Rosenbaum, A. Wang, M. Amir, A. Golding, I. 2023-03-02 doi:10.1101/2023.03.02.530801 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ SifA SUMOylation governs Salmonella intracellular survival via modulation of lysosomal function ]]> https://biorxiv.org/content/10.1101/2023.03.02.530793v1?rss=1 Srikanth, C. V. Chandrasekhar, H. Mohapatra, G. Singh, M. Rana, S. Kaur, N. Sharma, S. Tuli, A. Das, P. 2023-03-03 doi:10.1101/2023.03.02.530793 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Antibody-directed extracellular proximity biotinylation reveals Contactin-1 regulates axo-axonic innervation of axon initial segments. ]]> https://biorxiv.org/content/10.1101/2023.03.06.531378v1?rss=1 Ogawa, Y. Lim, B. George, S. Oses-Prieto, J. Rasband, J. Eshed-Eisenbach, Y. Nair, S. Boata, F. Peles, E. Burlingame, A. Van Aelst, L. Rasband, M. N. 2023-03-06 doi:10.1101/2023.03.06.531378 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Functional Ambidexterity of an Ancient Nucleic Acid-Binding Domain ]]> https://biorxiv.org/content/10.1101/2023.03.06.531422v1?rss=1 Weil-Ktorza, O. Fridmann-Sirkis, Y. Despotovic, D. Naveh-Tassa, S. Levy, Y. Metanis, N. Longo, L. M. 2023-03-07 doi:10.1101/2023.03.06.531422 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Clustering predicted structures at the scale of the known protein universe ]]> https://biorxiv.org/content/10.1101/2023.03.09.531927v1?rss=1 Barrio-Hernandez, I. Yeo, J. Jänes, J. Wein, T. Varadi, M. Velankar, S. Beltrao, P. Steinegger, M. 2023-03-10 doi:10.1101/2023.03.09.531927 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Single-molecule acceptor rise time (smART) FRET for nanoscale distance sensitivity ]]> https://biorxiv.org/content/10.1101/2023.03.15.532809v1?rss=1 Guo, J. Chen, X. Manna, P. Lin, X. Scott, M. N. Chen, W. J. Hoffman, M. Zhang, B. Schlau-Cohen, G. S. 2023-03-16 doi:10.1101/2023.03.15.532809 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Statistical modeling and analysis of multiplexed imaging data ]]> https://biorxiv.org/content/10.1101/2023.03.17.533200v1?rss=1 Bost, P. Casanova, R. Mor, U. Bodenmiller, B. 2023-03-21 doi:10.1101/2023.03.17.533200 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ TREM2-dependent senescent microglia conserved in aging and Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2023.03.20.533401v1?rss=1 Rachmian, N. Medina, S. Cherqui, U. Akiva, H. Deitch, D. Edilbi, D. Croese, T. Salame, T. M. Peralta Ramos, J. M. Cahalon, L. Krizhanovsky, V. Schwartz, M. 2023-03-21 doi:10.1101/2023.03.20.533401 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Cytoskeletal networks are adaptive active elastic filamentous materials that design their own shape in response to system geometry ]]> https://biorxiv.org/content/10.1101/2023.03.21.533327v1?rss=1 Livne, G. Gat, S. Armon, S. Bernheim-Groswasser, A. 2023-03-23 doi:10.1101/2023.03.21.533327 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ From Microstates to Macrostates in the Conformational Dynamics of GroEL: a Single-Molecule FRET Study ]]> https://biorxiv.org/content/10.1101/2023.03.23.533937v1?rss=1 Liebermann, D. G. Jungwirth, J. Riven, I. Barak, Y. Levy, D. Horovitz, A. Haran, G. 2023-03-25 doi:10.1101/2023.03.23.533937 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Modelling how curved active proteins and shear flow pattern cellular shape and motility ]]> https://biorxiv.org/content/10.1101/2023.03.27.534326v1?rss=1 Sadhukhan, S. Penic, S. Iglic, A. Gov, N. 2023-03-27 doi:10.1101/2023.03.27.534326 Cold Spring Harbor Laboratory Press 2023-03-27 <![CDATA[ Stable mammalian serum albumins designed for bacterial expression ]]> https://biorxiv.org/content/10.1101/2023.03.28.534334v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@71ef93org.highwire.dtl.DTLVardef@27a975org.highwire.dtl.DTLVardef@1e657fforg.highwire.dtl.DTLVardef@19b3de3_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- Computational design stabilized human and bovine serum albumins - Designs express solubly in E. coli and exhibit up to 40 {degrees}C increased thermostability - Some designs exhibit identical ligand binding properties - Crystal structure confirms design accuracy - Designs can be used in cell culture and in vitro applications ]]> Khersonsky, O. Fleishman, S. J. Goldsmith, M. Zaretsky, I. Hamer-Rogotner, S. Dym, O. 2023-03-28 doi:10.1101/2023.03.28.534334 Cold Spring Harbor Laboratory Press 2023-03-28 <![CDATA[ Self-eating while being eaten: Elucidating the relationship between aphid feeding and the plant autophagy machinery in Arabidopsis leaves ]]> https://biorxiv.org/content/10.1101/2023.03.28.534380v1?rss=1 Hao, L. K. Dangol, A. Shavit, R. Pitt, W. J. Nalam, V. Brotman, Y. Michaeli, S. Peled-Zehavi, H. Tzin, V. 2023-03-29 doi:10.1101/2023.03.28.534380 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ High-resolution tracking of unconfined zebrafish behavior reveals stimulatory and anxiolytic effects of psilocybin ]]> https://biorxiv.org/content/10.1101/2023.04.13.536830v1?rss=1 Braun, D. Rosenberg, A. Haruvi, R. Malamud, D. Barbara, R. Kawashima, T. 2023-04-14 doi:10.1101/2023.04.13.536830 Cold Spring Harbor Laboratory Press 2023-04-14 <![CDATA[ Reversing protonation of weakly basic drugs greatly enhances intracellular diffusion and decreases lysosomal sequestration ]]> https://biorxiv.org/content/10.1101/2023.04.19.537456v1?rss=1 DEY, D. Marciano, S. Poryvai, A. Groborz, O. wohlrabova, L. Slanina, T. Schreiber, G. 2023-04-21 doi:10.1101/2023.04.19.537456 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Energetic driving force for LHCII clustering in plant membranes ]]> https://biorxiv.org/content/10.1101/2023.04.19.537479v1?rss=1 Manna, P. Hoffmann, M. Davies, T. Richardson, K. H. Johnson, M. P. Schlau-Cohen, G. S. 2023-04-21 doi:10.1101/2023.04.19.537479 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ A minimal physical model for curvotaxis driven by curved protein complexes at the cell's leading edge ]]> https://biorxiv.org/content/10.1101/2023.04.19.537490v1?rss=1 Sadhu, R. K. Luciano, M. Xi, W. Torres, C. M. Schroder, M. Blum, C. Tarantola, M. Penic, S. Iglic, A. Beta, C. Steinbock, O. Bodenschatz, E. Ladoux, B. GABRIELE, S. Gov, N. 2023-04-21 doi:10.1101/2023.04.19.537490 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Non-canonical D1-D2 rearrangements are bimodal and represent a conservative hidden stage of VDJ recombination in TCR beta locus ]]> https://biorxiv.org/content/10.1101/2023.04.21.537904v1?rss=1 Smirnova, A. O. Miroshnichenkova, A. M. Belyaeva, L. D. Kelmanson, I. V. Lebedev, Y. B. Mamedov, I. Z. Chudakov, D. M. Komkov, A. Y. 2023-04-25 doi:10.1101/2023.04.21.537904 Cold Spring Harbor Laboratory Press 2023-04-25 <![CDATA[ Excitable dynamics of flares and relapses in autoimmune diseases ]]> https://biorxiv.org/content/10.1101/2023.05.03.539265v1?rss=1 Lebel, Y. Milo, T. Bar, A. Mayo, A. Alon, U. 2023-05-04 doi:10.1101/2023.05.03.539265 Cold Spring Harbor Laboratory Press 2023-05-04 <![CDATA[ Conserved cardiolipin-mitochondrial ADP/ATP carrier interactions assume distinct structural and functional roles that are clinically relevant ]]> https://biorxiv.org/content/10.1101/2023.05.05.539595v1?rss=1 Senoo, N. Chinthapalli, D. K. Baile, M. G. Golla, V. K. Saha, B. Ogunbona, O. B. Saba, J. A. Munteanu, T. Valdez, Y. Whited, K. Chorev, D. Alder, N. May, E. R. Robinson, C. V. Claypool, S. M. 2023-05-06 doi:10.1101/2023.05.05.539595 Cold Spring Harbor Laboratory Press 2023-05-06 <![CDATA[ Dissecting the impact of somatic hypermutation on SARS-CoV-2 neutralization and viral escape ]]> https://biorxiv.org/content/10.1101/2023.05.09.539943v1?rss=1 Korenkov, M. Zehner, M. Cohen-Dvashi, H. Borenstein-Katz, A. Kottege, L. Janicki, H. Vanshylla, K. Weber, T. Gruell, H. Koch, M. Diskin, R. Kreer, C. Klein, F. 2023-05-09 doi:10.1101/2023.05.09.539943 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Pregnancy and postpartum dynamics revealed by an atlas of millions of lab tests ]]> https://biorxiv.org/content/10.1101/2023.05.11.540359v1?rss=1 Bar, A. Mendelson Cohen, N. Korem Kohanim, Y. Mayo, A. Toledano, Y. Alon, U. 2023-05-14 doi:10.1101/2023.05.11.540359 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Allochthonous groundwater microorganisms affect coastal seawater microbial abundance, activity and diversity ]]> https://biorxiv.org/content/10.1101/2023.05.14.540660v1?rss=1 Yanuka-Golub, K. Belkin, N. Weber, N. Mayyani, M. Levy, Y. Reznik, I. J. Rubin-Blum, M. Rahav, E. Kiro, Y. 2023-05-14 doi:10.1101/2023.05.14.540660 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Tracking global changes induced in the CD4 T cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence. ]]> https://biorxiv.org/content/10.1101/001883v1?rss=1 Niclas Thomas Katharine Best Mattia Cinelli Shlomit Reich-Zeliger Hila Gal Eric Shifrut Asaf Madi Nir Friedman John Shawe-Taylor Benny Chain 2014-01-17 doi:10.1101/001883 Cold Spring Harbor Laboratory Press 2014-01-17 <![CDATA[ Frequent and Transient Acquisition of Pluripotency During Somatic Cell Trans-differentiation with iPSC Reprogramming Factors ]]> https://biorxiv.org/content/10.1101/008284v1?rss=1 90%), are attained after transient acquisition of pluripotency, and followed by rapid differentiation. Our findings underscore a molecular and functional coupling between inducing pluripotency and obtaining "trans-differentiated" somatic cells via OSKM induction, and have implications on defining molecular trajectories assumed during different cell reprogramming methods. ]]> Itay Maza Inbal Casoi Sergey Viukov Yoach Rais Asaf Zviran Shay Geula Vladislav Krupalnik Mirie Zerbib Rada Massarwa Noa Novershtern Jacob Hanna 2014-08-23 doi:10.1101/008284 Cold Spring Harbor Laboratory Press 2014-08-23 <![CDATA[ Mbd3/NuRD is a Key Inhibitory Module During the Induction and Maintenance of Naïve Pluripotency ]]> https://biorxiv.org/content/10.1101/013961v1?rss=1 Asaf Zviran Yoach Rais Nofar Mor Noa Novershtern Jacob H Hanna 2015-03-06 doi:10.1101/013961 Cold Spring Harbor Laboratory Press 2015-03-06 <![CDATA[ A minimalistic resource allocation model to explain ubiquitous increase in protein expression with growth rate ]]> https://biorxiv.org/content/10.1101/015180v1?rss=1 Uri Barenholz Leeat Keren Eran Segal Ron Milo 2015-02-13 doi:10.1101/015180 Cold Spring Harbor Laboratory Press 2015-02-13 <![CDATA[ Novel APC-like properties of human NK cells directly regulate T cell activation ]]> https://biorxiv.org/content/10.1101/016816v1?rss=1 Jacob Hanna Ofer Mandelboim 2015-03-30 doi:10.1101/016816 Cold Spring Harbor Laboratory Press 2015-03-30 <![CDATA[ Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs ]]> https://biorxiv.org/content/10.1101/017889v1?rss=1 Gali Housman Igor Ulitsky 2015-04-10 doi:10.1101/017889 Cold Spring Harbor Laboratory Press 2015-04-10 <![CDATA[ Dynamic stem cell states: naive to primed pluripotency in rodents and humans ]]> https://biorxiv.org/content/10.1101/030676v1?rss=1 Leehee Weinberger Muneef Ayyash Noa Novershtern Jacob H. Hanna 2015-11-06 doi:10.1101/030676 Cold Spring Harbor Laboratory Press 2015-11-06 <![CDATA[ Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs ]]> https://biorxiv.org/content/10.1101/031385v1?rss=1 Jenny Chen Alexander A. Shishkin Xiaopeng Zhu Sabah Kadri Itay Maza Jacob H Hanna Aviv Regev Manuel Garber 2015-11-11 doi:10.1101/031385 Cold Spring Harbor Laboratory Press 2015-11-11 <![CDATA[ A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells ]]> https://biorxiv.org/content/10.1101/033423v1?rss=1 Ailone Tichon Noa Gil Yoav Lubelsky Tal Havkin Solomon Doron Lemze Shalev Itzkovitz Noam Stern-Ginossar Igor Ulitsky 2015-12-02 doi:10.1101/033423 Cold Spring Harbor Laboratory Press 2015-12-02 <![CDATA[ Gene body H2B monoubiquitylation regulates gene-selective RNA Polymerase II pause release and is not rate limiting for transcription elongation ]]> https://biorxiv.org/content/10.1101/035386v1?rss=1 Gilad Fuchs Eran Rosenthal Debora-Rosa Bublik Tommy Kaplan Moshe Oren 2015-12-25 doi:10.1101/035386 Cold Spring Harbor Laboratory Press 2015-12-25 <![CDATA[ Revised estimates for the number of human and bacteria cells in the body ]]> https://biorxiv.org/content/10.1101/036103v1?rss=1 Ron Sender Shai Fuchs Ron Milo 2016-01-06 doi:10.1101/036103 Cold Spring Harbor Laboratory Press 2016-01-06 <![CDATA[ Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq ]]> https://biorxiv.org/content/10.1101/054387v1?rss=1 Michele Busby Catherine Xue Yossi Farjoun Elizabeth Gienger Ido Yofe Adrianne Gladden Chad Nusbaum Alon Goren 2016-05-19 doi:10.1101/054387 Cold Spring Harbor Laboratory Press 2016-05-19 <![CDATA[ Local and thalamic origins of ongoing and sensory evoked cortical correlations ]]> https://biorxiv.org/content/10.1101/058727v1?rss=1 Katayun Cohen-Kashi Malina Boaz Mohar Akiva N Rappaport Ilan Lampl 2016-06-13 doi:10.1101/058727 Cold Spring Harbor Laboratory Press 2016-06-13 <![CDATA[ Short Tandem Repeat stutter model inferred from direct measurement of in vitro stutter noise ]]> https://biorxiv.org/content/10.1101/065110v1?rss=1 Ofir Raz Tamir Biezuner Adam Spiro Shiran Amir Lilach Milo Alon Titelman Amos Onn Uriel Feige Ehud Shapiro 2016-07-21 doi:10.1101/065110 Cold Spring Harbor Laboratory Press 2016-07-21 <![CDATA[ Design principles of autocatalytic cycles constrain enzyme kinetics and force over-expression at flux branch points ]]> https://biorxiv.org/content/10.1101/074641v1?rss=1 Uri Barenholz Dan Davidi Ed Reznik Yinon Bar-On Niv Antonovsky Elad Noor Ron Milo 2016-09-11 doi:10.1101/074641 Cold Spring Harbor Laboratory Press 2016-09-11 <![CDATA[ The PhytoClust Tool for Metabolic Gene Clusters Discovery in Plant Genomes ]]> https://biorxiv.org/content/10.1101/079343v1?rss=1 Nadine Toepfer Lisa-Maria Fuchs Asaph Aharoni 2016-10-07 doi:10.1101/079343 Cold Spring Harbor Laboratory Press 2016-10-07 <![CDATA[ Darwinian Selection Induces Lamarckian Adaptation in a Holobiont Model ]]> https://biorxiv.org/content/10.1101/093120v1?rss=1 Osmanovic, D. Kessler, D. A. Rabin, Y. Soen, Y. 2016-12-11 doi:10.1101/093120 Cold Spring Harbor Laboratory Press 2016-12-11 <![CDATA[ Cell cycle dynamics of chromosomal organisation at single-cell resolution ]]> https://biorxiv.org/content/10.1101/094466v1?rss=1 Nagano, T. Lubling, Y. Varnai, C. Dudley, C. Leung, W. Baran, Y. Mandelson Cohen, N. Wingett, S. Fraser, P. Tanay, A. 2016-12-15 doi:10.1101/094466 Cold Spring Harbor Laboratory Press 2016-12-15 <![CDATA[ Large-scale rewiring in a yeast hybrid ]]> https://biorxiv.org/content/10.1101/100263v1?rss=1 Herbst, R. Bar-Zvi, D. Reikhav, S. Soifer, I. Breker, M. Jona, G. Shimoni, E. Schuldiner, M. Levy, A. Barkai, N. 2017-01-13 doi:10.1101/100263 Cold Spring Harbor Laboratory Press 2017-01-13 <![CDATA[ T-DNA integration is rapid and influenced by the chromatin state of the host genome. ]]> https://biorxiv.org/content/10.1101/104372v1?rss=1 Shilo, S. Tripathi, P. Melamed-Bessudo, C. Tzfadia, O. Muth, T. R. Levy, A. A. 2017-01-31 doi:10.1101/104372 Cold Spring Harbor Laboratory Press 2017-01-31 <![CDATA[ The Human Cell Atlas ]]> https://biorxiv.org/content/10.1101/121202v1?rss=1 Regev, A. Teichmann, S. Lander, E. S. Amit, I. Benoist, C. Birney, E. Bodenmiller, B. Campbell, P. Carninci, P. Clatworthy, M. Clevers, H. Deplancke, B. Dunham, I. Eberwine, J. Eils, R. Enard, W. Farmer, A. Fugger, L. Gottgens, B. Hacohen, N. Haniffa, M. Hemberg, M. Kim, S. K. Klenerman, P. Kriegstein, A. Lein, E. Linnarsson, S. Lundeberg, J. Majumder, P. Marioni, J. Merad, M. Mhlanga, M. Nawijn, M. Netea, M. Nolan, G. Pe'er, D. Philipakis, A. Ponting, C. P. Quake, S. R. Reik, W. Rozenblatt-Rosen, O. Sanes, J. R. Satija, R. Shumacher, T. Shalek, A. K 2017-05-08 doi:10.1101/121202 Cold Spring Harbor Laboratory Press 2017-05-08 <![CDATA[ A Note On Dynamical Compensation And Its Relation To Parameter Identifiability ]]> https://biorxiv.org/content/10.1101/123489v1?rss=1 Karin, O. Alon, U. Sontag, E. 2017-04-03 doi:10.1101/123489 Cold Spring Harbor Laboratory Press 2017-04-03 <![CDATA[ Principles Of Cellular Resource Allocation Revealed By Condition-Dependent Proteome Profiling ]]> https://biorxiv.org/content/10.1101/124370v1?rss=1 Metzl-Raz, E. Kafri, M. Yaakov, G. Soifer, I. Gurvich, Y. Barkai, N. 2017-04-05 doi:10.1101/124370 Cold Spring Harbor Laboratory Press 2017-04-05 <![CDATA[ Increasing Suppression Of Saccade-Related Transients Along The Human Visual Hierarchy ]]> https://biorxiv.org/content/10.1101/124867v1?rss=1 Golan, T. Davidesco, I. Meshulam, M. Groppe, D. M. Megevand, P. Yeagle, E. M. Goldfinger, M. S. Harel, M. Melloni, L. Schroeder, C. E. Deouell, L. Y. Mehta, A. D. Malach, R. 2017-04-20 doi:10.1101/124867 Cold Spring Harbor Laboratory Press 2017-04-20 <![CDATA[ Intercellular mRNA Trafficking Via Membrane Nanotubes In Mammalian Cells ]]> https://biorxiv.org/content/10.1101/137836v1?rss=1 Haimovich, G. Ecker, C. M. Dunagin, M. C. Eggan, E. Raj, A. Gerst, J. E. Singer, R. H. 2017-05-14 doi:10.1101/137836 Cold Spring Harbor Laboratory Press 2017-05-14 <![CDATA[ NQO1 Binds And Supports SIRT1 Function ]]> https://biorxiv.org/content/10.1101/139907v1?rss=1 Tsvetkov, P. Adler, J. Adamovich, Y. Asher, G. Reuven, N. Shaul, Y. 2017-05-19 doi:10.1101/139907 Cold Spring Harbor Laboratory Press 2017-05-19 <![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[ Coupling Of Tactile LFP Signals Between Mouse Cortex And Olfactory Bulb ]]> https://biorxiv.org/content/10.1101/144279v1?rss=1 Parabucki, A. Lampl, I. 2017-05-31 doi:10.1101/144279 Cold Spring Harbor Laboratory Press 2017-05-31 <![CDATA[ Environmental factors dominate over host genetics in shaping human gut microbiota composition ]]> https://biorxiv.org/content/10.1101/150540v1?rss=1 Rothschild, D. Weissbrod, O. Barkan, E. Korem, T. Zeevi, D. Costea, P. I. Godneva, A. Kalka, I. N. Bar, N. Zmora, N. Pevsner-Fischer, M. Israeli, D. Kosower, N. Malka, G. Wolf, B. C. Avnit-Sagi, T. Lotan-Pompan, M. Weinberger, A. Halpern, Z. Carmi, S. Elinav, E. Segal, E. 2017-06-16 doi:10.1101/150540 Cold Spring Harbor Laboratory Press 2017-06-16 <![CDATA[ Dual role of E-cadherin in the regulation of invasive collective migration of mammary carcinoma cells ]]> https://biorxiv.org/content/10.1101/151613v1?rss=1 Elisha, Y. Kalchenko, V. Kuznetsov, Y. Geiger, B. 2017-06-18 doi:10.1101/151613 Cold Spring Harbor Laboratory Press 2017-06-18 <![CDATA[ DddY is a bacterial dimethylsulfoniopropionate lyase representing a new cupin enzyme superfamily with unknown primary function ]]> https://biorxiv.org/content/10.1101/161257v1?rss=1 107 tons annually and plays a key role in the oceanic sulfur cycle and ecology. Marine bacteria, algae, and possibly other organisms, release DMS via cleavage of dimethylsulfoniopropionate (DMSP). Different genes encoding proteins with DMSP lyase activity are known belonging to different superfamilies and exhibiting highly variable levels of DMSP lyase activity. DddY shows the highest activity among all reported bacterial lyases yet is poorly characterized. Here, we describe the characterization of recombinant DddY is from different marine bacteria. We found that DddY activity demands a transition metal ion cofactor. DddY also shares two sequence motifs with other bacterial lyases assigned as cupin-like enzymes, DddQ, DddL, DddK, and DddW. These cupin motif residues are essential for DddY activity, as for the other cupin DMSP lyases, and all these enzymes are characterized by a common metal-chelator inhibitor (TPEN). Analysis of all sequences carrying these cupin motifs defined a superfamily: Cupin-DLL (DMSP lyases and lyase-like). The DMSP lyase families are sporadically distributed suggesting that DMSP lyases evolved within this superfamily independently along multiple lineages. However, the specific activity levels, genomic context analysis, and systematic profiling of substrate selectivity as described in the accompanying paper, indicate that for only some of these families, most distinctly DddY and DddL, DMSP lyase is the primary, native activity. In other families, foremost DddQ, DMSP lyase seems to be merely a promiscuous activity. The native function of DddQ, and of nearly all members of this newly identified Cupin-DLL superfamily, remains unknown.nnAbbreviationsnnFundingFinancial support by the Estate of Mark Scher, and the Sasson & Marjorie Peress Philanthropic Fund, are gratefully acknowledged. D.S.T. is the Nella and Leon Benoziyo Professor of Biochemistry. ]]> Lei, L. Alcolombri, U. Tawfik, D. S. 2017-07-09 doi:10.1101/161257 Cold Spring Harbor Laboratory Press 2017-07-09 <![CDATA[ Native or promiscuous? Analyzing putative dimethylsulfoniopropionate lyases using a substrate proofing approach ]]> https://biorxiv.org/content/10.1101/168930v1?rss=1 Lei, L. Cherukuri, K. P. Meltzer, D. Alcolombri, U. Tawfik, D. 2017-07-27 doi:10.1101/168930 Cold Spring Harbor Laboratory Press 2017-07-27 <![CDATA[ Evolution of chalcone isomerase from a non-catalytic ancestor ]]> https://biorxiv.org/content/10.1101/174128v1?rss=1 Kaltenbach, M. Burke, J. R. Dindo, M. Pabis, A. Munsberg, F. S. Rabin, A. Kamerlin, S. C. L. Noel, J. P. Tawfik, D. S. 2017-08-10 doi:10.1101/174128 Cold Spring Harbor Laboratory Press 2017-08-10 <![CDATA[ Deciphering Transcriptional Regulation of Human Core Promoters ]]> https://biorxiv.org/content/10.1101/174904v1?rss=1 Weingarten-Gabbay, S. Nir, R. Lubliner, S. Sharon, E. Kalma, Y. Weinberger, A. Segal, E. 2017-08-10 doi:10.1101/174904 Cold Spring Harbor Laboratory Press 2017-08-10 <![CDATA[ Prestimulus Activity in the Cingulo-Opercular Network Predicts Memory for Naturalistic Episodic Experience ]]> https://biorxiv.org/content/10.1101/176057v1?rss=1 Cohen, N. Ben-Yakov, A. Weber, J. Edelson, M. Paz, R. Dudai, Y. 2017-08-14 doi:10.1101/176057 Cold Spring Harbor Laboratory Press 2017-08-14 <![CDATA[ Conformational states during vinculin unlocking differentially regulate focal adhesion properties ]]> https://biorxiv.org/content/10.1101/176586v1?rss=1 Chorev, D. S. Volberg, T. Livne, A. Eisenstein, M. Martins, B. Kam, Z. Jockusch, B. Medalia, O. Sharon, M. Geiger, B. 2017-08-16 doi:10.1101/176586 Cold Spring Harbor Laboratory Press 2017-08-16 <![CDATA[ High-Resolution Dissection of Conducive Reprogramming Trajectory to Ground State Pluripotency ]]> https://biorxiv.org/content/10.1101/184135v1?rss=1 Zviran, A. Mor, N. Rais, Y. Gingold, H. Peles, S. Chomsky, E. Viukov, S. Buenrostro, J. D. Weinberger, L. Manor, Y. S. Krupalnik, V. Zerbib, M. Hezroni, H. Jaitin, D. A. Larastiaso, D. Gilad, S. Benjamin, S. Mousa, A. Ayyash, M. Sheban, D. Bayerl, J. Aguilera Castrejon, A. Massarwa, R. Maza, I. Hanna, S. Amit, I. Stelzer, Y. Ulitsky, I. Greenleaf, W. J. Pilpel, Y. Novershtern, N. Hanna, J. H. 2017-09-07 doi:10.1101/184135 Cold Spring Harbor Laboratory Press 2017-09-07 <![CDATA[ Oscillations synchronize amygdala-to-prefrontal primate circuits during aversive learning ]]> https://biorxiv.org/content/10.1101/184531v1?rss=1 Taub, A. H. Paz, R. 2017-09-05 doi:10.1101/184531 Cold Spring Harbor Laboratory Press 2017-09-05 <![CDATA[ Rescue of Conformational Dynamics in Enzyme Catalysis by Directed Evolution ]]> https://biorxiv.org/content/10.1101/185009v1?rss=1 Otten, R. Liu, L. Kenner, L. R. Clarkson, M. W. Mavor, D. Tawfik, D. S. Kern, D. Fraser, J. S. 2017-09-05 doi:10.1101/185009 Cold Spring Harbor Laboratory Press 2017-09-05 <![CDATA[ Comparison of seven single cell Whole Genome Amplification commercial kits using targeted sequencing ]]> https://biorxiv.org/content/10.1101/186940v1?rss=1 Biezuner, T. Raz, O. Amir, S. Milo, L. Adar, R. Fried, Y. Ainbinder, E. Shapiro, E. 2017-09-11 doi:10.1101/186940 Cold Spring Harbor Laboratory Press 2017-09-11 <![CDATA[ SHAMAN: bin-free randomization, normalization and screening of Hi-C matrices ]]> https://biorxiv.org/content/10.1101/187203v1?rss=1 Mendelson Cohen, N. Olivares-Chauvet, P. Lubling, Y. Baran, Y. Lifshitz, A. Hoichman, M. Tanay, A. 2017-09-12 doi:10.1101/187203 Cold Spring Harbor Laboratory Press 2017-09-12 <![CDATA[ Repeated performance in problem-solving tasks attenuates human cortical responses ]]> https://biorxiv.org/content/10.1101/189217v1?rss=1 Meshulam, M. Golan, T. Harel, M. Groppe, D. Keller, C. Megevand, P. Mehta, A. Malach, R. 2017-09-15 doi:10.1101/189217 Cold Spring Harbor Laboratory Press 2017-09-15 <![CDATA[ Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells ]]> https://biorxiv.org/content/10.1101/189746v1?rss=1 Lubelsky, Y. Ulitsky, I. 2017-09-16 doi:10.1101/189746 Cold Spring Harbor Laboratory Press 2017-09-16 <![CDATA[ Salient Experiences are Represented by Unique Transcriptional Signatures in the Brain ]]> https://biorxiv.org/content/10.1101/192278v1?rss=1 Mukherjee, D. Ignatowska-Jankowska, B. M. Itskovits, E. Gonzales, B. J. Turm, H. Izakson, L. Haritan, D. Bleistein, N. Cohen, C. Amit, I. Shay, T. Grueter, B. Zaslaver, A. Citri, A. 2017-09-21 doi:10.1101/192278 Cold Spring Harbor Laboratory Press 2017-09-21 <![CDATA[ Resolving ESCRT-III spirals at the intercellular bridge of dividing cells using 3D STORM imaging ]]> https://biorxiv.org/content/10.1101/194613v1?rss=1 Goliand, I. Dadosh, T. Elia, N. 2017-09-27 doi:10.1101/194613 Cold Spring Harbor Laboratory Press 2017-09-27 <![CDATA[ Force dependence of filopodia adhesion: involvement of myosin II and formins ]]> https://biorxiv.org/content/10.1101/195420v1?rss=1 Alieva, N. O. Efremov, A. K. Hu, S. Oh, D. Chen, Z. Natarajan, M. Ong, H. T. Jegou, A. Romet-Lemonne, G. Groves, J. T. Sheetz, M. P. Yan, J. Bershadsky, A. D. 2017-09-28 doi:10.1101/195420 Cold Spring Harbor Laboratory Press 2017-09-28 <![CDATA[ Microtubule regulation of integrin-based adhesions is mediated by myosin-IIA ]]> https://biorxiv.org/content/10.1101/195495v1?rss=1 Nishimura, Y. Mohd Rafiq, N. Plotnikov, S. V. Zhang, Z. Thiagarajan, V. Natarajan, M. Jones, G. E. Kanchanawong, P. Bershadsky, A. D. 2017-09-28 doi:10.1101/195495 Cold Spring Harbor Laboratory Press 2017-09-28 <![CDATA[ Temporal profiling of redox-dependent heterogeneity in single cells ]]> https://biorxiv.org/content/10.1101/198408v1?rss=1 Radzinski, M. Fassler, R. Yogev, O. Breuer, W. Gutin, J. Ravid, T. Friedman, N. Schuldiner, M. Shai, N. Reichmann, D. 2017-10-04 doi:10.1101/198408 Cold Spring Harbor Laboratory Press 2017-10-04 <![CDATA[ The role of m6A-RNA methylation in stress response regulation ]]> https://biorxiv.org/content/10.1101/200402v1?rss=1 Engel, M. Roeh, S. Eggert, C. Kaplick, P. M. Tietze, L. Arloth, J. Weber, P. Rex-Haffner, M. Jakovcevski, M. Uhr, M. Eder, M. Wotjak, C. T. Schmidt, M. V. Deussing, J. M. Binder, E. B. Chen, A. 2017-10-09 doi:10.1101/200402 Cold Spring Harbor Laboratory Press 2017-10-09 <![CDATA[ Cnidarian cell type diversity revealed by whole-organism single-cell RNA-seq analysis ]]> https://biorxiv.org/content/10.1101/201103v1?rss=1 Sebe-Pedros, A. Chomsky, E. Saudemont, B. Mailhe, M.-P. Pleisser, F. Renno, J. Loe-Mie, Y. Lifshitz, A. Mukamel, Z. Schmutz, S. Nouvault, S. Spitz, F. Tanay, A. Marlow, H. 2017-10-11 doi:10.1101/201103 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ BACH family members regulate angiogenesis and lymphangiogenesis by modulating VEGFC expression ]]> https://biorxiv.org/content/10.1101/2019.12.13.876268v1?rss=1 Cohen, B. Tempelhof, H. Raz, T. Oren, R. Nicenboim, J. Bochner, F. Even, R. Jelinski, A. Eilam, R. Ben-Dor, S. Addadi, Y. Golani, O. Lazar, S. Yaniv, K. Neeman, M. 2019-12-15 doi:10.1101/2019.12.13.876268 Cold Spring Harbor Laboratory Press 2019-12-15 <![CDATA[ Transcription-factor binding to replicated DNA ]]> https://biorxiv.org/content/10.1101/2019.12.15.877035v1?rss=1 Bar-Ziv, R. Brodsky, S. Chapal, M. Barkai, N. 2019-12-15 doi:10.1101/2019.12.15.877035 Cold Spring Harbor Laboratory Press 2019-12-15 <![CDATA[ Model balancing: consistent in-vivo kinetic constants and metabolic states obtained by convex optimisation ]]> https://biorxiv.org/content/10.1101/2019.12.23.887166v1?rss=1 Liebermeister, W. 2019-12-23 doi:10.1101/2019.12.23.887166 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ The predictive power of the microbiome exceeds that of genome-wide association studies in the discrimination of complex human disease ]]> https://biorxiv.org/content/10.1101/2019.12.31.891978v1?rss=1 Tierney, B. T. He, Y. Church, G. M. Segal, E. J. Kostic, A. D. Patel, C. J. 2020-01-02 doi:10.1101/2019.12.31.891978 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ Recurrent pre-leukemic deletions in myeloid malignancies are the result of DNA double-strand breaks followed by microhomology-mediated end joining ]]> https://biorxiv.org/content/10.1101/2020.01.01.888610v1?rss=1 Feldman, T. Bercovich, A. Moskovitz, Y. Chapal-Ilani, N. Mitchell, A. Medeiros, J. J. Kaushansky, N. Biezuner, T. Minden, M. D. Gupta, V. Tanay, A. Shlush, L. I. 2020-01-02 doi:10.1101/2020.01.01.888610 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ Hormonal dysregulation after prolonged HPA axis activation can be explained by changes of adrenal and corticotroph masses ]]> https://biorxiv.org/content/10.1101/2020.01.01.892596v1?rss=1 Karin, O. Raz, M. Tendler, A. Bar, A. Korem Kohanim, Y. Milo, T. Alon, U. 2020-01-02 doi:10.1101/2020.01.01.892596 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ ERBB2 drives YAP activation and EMT-like processes during cardiac regeneration ]]> https://biorxiv.org/content/10.1101/2020.01.07.897199v1?rss=1 Aharonov, A. Shakked, A. Umansky, K. B. Savidor, A. Kain, D. Lendengolts, D. Revach, O.-Y. Morikawa, Y. Dong, J. Levin, Y. Geiger, B. Martin, J. F. Tzahor, E. 2020-01-08 doi:10.1101/2020.01.07.897199 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ A novel calcium-concentrating compartment drives biofilm formation and persistent infections ]]> https://biorxiv.org/content/10.1101/2020.01.08.898569v1?rss=1 Keren-Paz, A. Cohen-Cymberknoh, M. Kolodkin-Gal, D. Karunker, I. Dersch, S. Wolf, S. G. Olender, T. Kartvelishvily, E. Kapishnikov, S. Green-Zelinger, P. Shteinberg, M. Zamir, G. Gal, A. Graumann, P. Kerem, E. Kolodkin-Gal, I. 2020-01-09 doi:10.1101/2020.01.08.898569 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ The conformational distribution of a major facilitator superfamily peptide transporter is modulated by the membrane composition ]]> https://biorxiv.org/content/10.1101/2020.01.09.900316v1?rss=1 Lasitza Male, T. Bartels, K. Wiggers, F. Rosenblum, G. Jungwirth, J. Hofmann, H. Loew, C. 2020-01-09 doi:10.1101/2020.01.09.900316 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Division of labor between YAP and TAZ in non-small cell lung cancer ]]> https://biorxiv.org/content/10.1101/2020.01.12.894733v1?rss=1 Shaked, M. Oren, M. Dassa, B. Sinha, S. Di Agostino, S. Azuri, I. Aylon, Y. Blandino, G. Ruppin, E. 2020-01-13 doi:10.1101/2020.01.12.894733 Cold Spring Harbor Laboratory Press 2020-01-13 <![CDATA[ Cancer-associated fibroblast compositions change with breast cancer progression linking S100A4 and PDPN ratios with clinical outcome ]]> https://biorxiv.org/content/10.1101/2020.01.12.903039v1?rss=1 Friedman, G. Levi-Galibov, O. David, E. Bornstein, C. Giladi, A. Dadiani, M. Mayo, A. Halperin, C. Pevsner-Fischer, M. Lavon-Pashot, H. Nevo, R. Stein, Y. Ali, H. R. Caldas, C. Nili-Gal-Yam, E. Alon, U. Amit, I. Scherz-Shouval, R. 2020-01-13 doi:10.1101/2020.01.12.903039 Cold Spring Harbor Laboratory Press 2020-01-13 <![CDATA[ Glucocorticoid Receptor ablation promotes cardiac regeneration by hampering cardiomyocyte terminal differentiation ]]> https://biorxiv.org/content/10.1101/2020.01.15.901249v1?rss=1 Pianca, N. Pontis, F. Chirivi, M. Papa, V. Braga, L. Patnala, R. S. Bongiovanni, C. Mazzeschi, M. Umansky, K. B. Cenacchi, G. Lauriola, M. Giacca, M. Rizzi, R. Tzahor, E. D'Uva, G. 2020-01-15 doi:10.1101/2020.01.15.901249 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Modular and distinct PlexinA4/Farp2/Rac1 signaling controls dendrite morphogenesis ]]> https://biorxiv.org/content/10.1101/2020.01.15.908434v1?rss=1 Danelon, V. Goldner, R. Martinez, E. Gokhman, I. Wang, K. Yaron, A. Tran, T. S. 2020-01-16 doi:10.1101/2020.01.15.908434 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ Primordial emergence of a nucleic acid binding protein via phase separation and statistical ornithine to arginine conversion ]]> https://biorxiv.org/content/10.1101/2020.01.18.911073v1?rss=1 Longo, L. M. Despotovic, D. Weil-Ktorza, O. Walker, M. J. Jablonska, J. Fridmann-Sirkis, Y. Varani, G. Norman Metanis, N. Tawfik, D. S. 2020-01-18 doi:10.1101/2020.01.18.911073 Cold Spring Harbor Laboratory Press 2020-01-18 <![CDATA[ Independent evolution of transcript abundance and gene regulatory dynamics ]]> https://biorxiv.org/content/10.1101/2020.01.22.915033v1?rss=1 Krieger, G. Lupo, O. Levy, A. A. Barkai, N. 2020-01-23 doi:10.1101/2020.01.22.915033 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Splice-specific deficiency of the PTSD-associated gene PAC1 leads to a paradoxical age-dependent stress behavior ]]> https://biorxiv.org/content/10.1101/2020.01.24.918185v1?rss=1 Biran, J. Gliksberg, M. Shirat, I. Swaminathan, A. Levitas-Djerbi, T. Appelbaum, L. Levkowitz, G. 2020-01-25 doi:10.1101/2020.01.24.918185 Cold Spring Harbor Laboratory Press 2020-01-25 <![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[ Bi-fated tendon-to-bone attachment cells are regulated by shared enhancers and KLF transcription factors ]]> https://biorxiv.org/content/10.1101/2020.01.29.924654v1?rss=1 Kult, S. Zelzer, E. Olender, T. Osterwalder, M. Krief, S. Blecher-Gonen, R. Ben-Moshe, S. Farack, L. Keren-Shaul, H. Leshkowitz, D. Salame, T.-M. Capellini, T. D. Itzkovitz, S. Amit, I. Visel, A. 2020-01-30 doi:10.1101/2020.01.29.924654 Cold Spring Harbor Laboratory Press 2020-01-30 <![CDATA[ ATG8-interacting (ATI) 1 and 2 define a plant starvation-induced ER-phagy pathway and serve as MSBP1 (MAPR5) cargo-receptors ]]> https://biorxiv.org/content/10.1101/2020.01.29.924886v1?rss=1 Wu, J. Michaeli, S. Galili, G. Zehavi, H. 2020-01-30 doi:10.1101/2020.01.29.924886 Cold Spring Harbor Laboratory Press 2020-01-30 <![CDATA[ Altered conformational sampling along an evolutionary trajectory changes the catalytic activity of an enzyme ]]> https://biorxiv.org/content/10.1101/2020.02.03.932491v1?rss=1 Kaczmarski, J. A. Mahawaththa, M. C. Feintuch, A. Clifton, B. E. Adams, L. A. Goldfarb, D. Otting, G. Jackson, C. J. 2020-02-04 doi:10.1101/2020.02.03.932491 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Sexually divergent effects of social dominance on chronic stress outcomes in mice ]]> https://biorxiv.org/content/10.1101/2020.02.04.933481v1?rss=1 Karamihalev, S. Brivio, E. Flachskamm, C. Stoffel, R. Schmidt, M. V. Chen, A. 2020-02-04 doi:10.1101/2020.02.04.933481 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Unexplained Repeated Pregnancy Loss is Associated with Altered Perceptual and Brain Responses to Men's Body-Odor ]]> https://biorxiv.org/content/10.1101/2020.02.06.937029v1?rss=1 Sobel, N. Rozenkrantz, L. Weissgross, R. Weiss, T. Ravrebi, I. Frumin, I. Shushan, S. Gorodisky, L. Reshef, N. Holzman, Y. Pinchover, L. Endevelt-Shapi, Y. Mishor, E. Furman-Haran, E. Carp, H. 2020-02-07 doi:10.1101/2020.02.06.937029 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[ Small-molecule inhibition of Lats kinases promotes Yap-dependent proliferation in postmitotic mammalian tissues ]]> https://biorxiv.org/content/10.1101/2020.02.11.944157v1?rss=1 Kastan, N. Gnedeva, K. Alisch, T. Petelski, A. Huggins, D. Chiaravalli, J. Aharanov, A. Shakked, A. Tzahor, E. Nagiel, A. Segil, N. Hudspeth, A. J. 2020-02-12 doi:10.1101/2020.02.11.944157 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Human hormone seasonality ]]> https://biorxiv.org/content/10.1101/2020.02.13.947366v1?rss=1 Tendler, A. Bar, A. Mendelson Cohen, N. Karin, O. Korem Kohanim, Y. Maimon, L. Milo, T. Raz, M. Mayo, A. Tanay, A. Alon, U. 2020-02-14 doi:10.1101/2020.02.13.947366 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[ Genome-scale conserved molecular principles of mRNA half-life regulation ]]> https://biorxiv.org/content/10.1101/2020.02.17.952267v1?rss=1 Basu, S. Mallik, S. Hait, S. Kundu, S. 2020-02-17 doi:10.1101/2020.02.17.952267 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ Cell substrate patterns driven by curvature-sensitive actin polymerization: waves and podosomes. ]]> https://biorxiv.org/content/10.1101/2020.02.17.953018v1?rss=1 Naoz, M. Gov, N. 2020-02-17 doi:10.1101/2020.02.17.953018 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ Differential tissue stiffness of body column facilitates locomotion of Hydra on solid substrates ]]> https://biorxiv.org/content/10.1101/2020.02.29.971044v1?rss=1 Naik, S. Unni, M. K. Sinha, D. Rajput, S. S. Puli, C. R. Chatterji, A. Patil, S. Galande, S. 2020-03-03 doi:10.1101/2020.02.29.971044 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ Space-time logic of liver gene expression at sublobular scale ]]> https://biorxiv.org/content/10.1101/2020.03.05.976571v1?rss=1 Droin, C. El Kholtei, J. Bahar Halpern, K. Hurni, C. Rozenberg, M. Muvkadi, S. Itzkovitz, S. Naef, F. 2020-03-06 doi:10.1101/2020.03.05.976571 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ Assembly Mechanism of Mucin and von Willebrand Factor Polymers ]]> https://biorxiv.org/content/10.1101/2020.03.08.982447v1?rss=1 Javitt, G. Khmelnitsky, L. Albert, L. Elad, N. Ilani, T. Diskin, R. Fass, D. 2020-03-09 doi:10.1101/2020.03.08.982447 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ Dynamic changes in tRNA modifications and abundance during T-cell activation ]]> https://biorxiv.org/content/10.1101/2020.03.14.991901v1?rss=1 Rak, R. Polonsky, M. Eizenberg, I. Dahan, O. Friedman, N. Pilpel, Y. T. 2020-03-15 doi:10.1101/2020.03.14.991901 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ Optimization of skeletal protein preparation for LC-MS/MS sequencing yields additional coral skeletal proteins in Stylophora pistillata ]]> https://biorxiv.org/content/10.1101/2020.03.16.991273v1?rss=1 Peled, Y. Drake, J. L. Malik, A. Almuly, R. Lalzar, M. Morgenstern, D. Mass, T. 2020-03-18 doi:10.1101/2020.03.16.991273 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ Sulfopin, a selective covalent inhibitor of Pin1, blocks Myc-driven tumor initiation and growth in vivo ]]> https://biorxiv.org/content/10.1101/2020.03.20.998443v1?rss=1 Dubiella, C. Pinch, B. J. Zaidman, D. Manz, T. D. Poon, E. He, S. Resnick, E. Langer, E. M. Daniel, C. J. Seo, H.-S. Chen, Y. Ficarro, S. B. Jamin, Y. Lian, X. Kibe, S. Kozono, S. Koikawa, K. Doctor, Z. M. Nabet, B. Browne, C. M. Yang, A. Stoler-Barak, L. Shah, R. B. Vangos, N. E. Geffken, E. A. Oren, R. Sidi, S. Shulman, Z. Wang, C. Marto, J. A. Dhe-Paganon, S. Look, T. Zhou, X. Z. Lu, K. P. Sears, R. C. Chesler, L. Gray, N. S. London, N. 2020-03-21 doi:10.1101/2020.03.20.998443 Cold Spring Harbor Laboratory Press 2020-03-21 <![CDATA[ Integrated metabolomics and proteomics of symptomatic and early pre-symptomatic states of colitis ]]> https://biorxiv.org/content/10.1101/2020.03.22.002196v1?rss=1 Shimshoni, E. Ghini, V. Solomonov, I. Luchinat, C. Sagi, I. Turano, P. 2020-03-23 doi:10.1101/2020.03.22.002196 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ BCKDK regulates the TCA cycle through PDC to ensure embryonic development in the absence of PDK family ]]> https://biorxiv.org/content/10.1101/2020.03.22.002360v1?rss=1 Heinemann-Yerushalmi, L. Bentovim, L. Felsenthal, N. Michaeli, N. Krief, S. Haffner-Krausz, R. Ben-Dor, S. Itkin, M. Malitsky, S. Silberman, A. Erez, A. Zelzer, E. 2020-03-24 doi:10.1101/2020.03.22.002360 Cold Spring Harbor Laboratory Press 2020-03-24 <![CDATA[ Genetic variation in the social environment affects behavioral phenotypes of oxytocin receptor mutants in zebrafish ]]> https://biorxiv.org/content/10.1101/2020.03.23.002873v1?rss=1 Nunes, A. R. Teles, M. Anbalagan, S. Blechman, J. Levkowitz, G. Oliveira, R. F. 2020-03-26 doi:10.1101/2020.03.23.002873 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ The transcription factor TRF2 has a unique function in regulating cell cycle and apoptosis ]]> https://biorxiv.org/content/10.1101/2020.03.27.011288v1?rss=1 Kedmi, A. Sloutskin, A. Epstein, N. Gasri-Plotnitsky, L. Ickowicz, D. Shoval, I. Doniger, T. Darmon, E. Ideses, D. Porat, Z. Yaron, O. Juven-Gershon, T. 2020-03-28 doi:10.1101/2020.03.27.011288 Cold Spring Harbor Laboratory Press 2020-03-28 <![CDATA[ In-cell destabilization of a homo-dimeric protein complex detected by DEER spectroscopy ]]> https://biorxiv.org/content/10.1101/2020.03.27.011510v1?rss=1 Yang, Y. Chen, S.-N. Yang, F. Li, X. Y. Feintuch, A. Su, X.-C. Goldfarb, D. 2020-03-27 doi:10.1101/2020.03.27.011510 Cold Spring Harbor Laboratory Press 2020-03-27 <![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[ Cystoliths in Ficus leaves: increasing carbon fixation in saturating light by light scattering off a mineral substrate ]]> https://biorxiv.org/content/10.1101/2020.04.08.030999v1?rss=1 Pierantoni, M. Paudel, I. Raphael, B. Tenne, R. Brumfeld, V. Slomka, S. Oron, D. Addadi, L. Weiner, S. Klein, T. 2020-04-09 doi:10.1101/2020.04.08.030999 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Loss of homomeric interactions and heteromers formation is the long-term fate of duplicated homomers ]]> https://biorxiv.org/content/10.1101/2020.04.08.031351v1?rss=1 Mallik, S. Tawfik, D. S. 2020-04-09 doi:10.1101/2020.04.08.031351 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Proteomic analysis of necroptotic extracellular vesicles ]]> https://biorxiv.org/content/10.1101/2020.04.11.037192v1?rss=1 Shlomovitz, I. Yanovich-Arad, G. Erlich, Z. Edry-Botzer, L. Zargarian, S. Cohen, H. Ofir-Birin, Y. Regev-Rudzki, N. Gerlic, M. 2020-04-12 doi:10.1101/2020.04.11.037192 Cold Spring Harbor Laboratory Press 2020-04-12 <![CDATA[ Identification and enrichment of SECReTE cis-acting RNA elements in the Coronaviridae and other (+) single-strand RNA viruses ]]> https://biorxiv.org/content/10.1101/2020.04.20.050088v1?rss=1 Haimovich, G. Olender, T. Baez, C. Gerst, J. E. 2020-04-20 doi:10.1101/2020.04.20.050088 Cold Spring Harbor Laboratory Press 2020-04-20 <![CDATA[ Learned SPARCOM: Unfolded Deep Super-Resolution Microscopy ]]> https://biorxiv.org/content/10.1101/2020.04.20.050294v1?rss=1 Dardikman-Yoffe, G. Eldar, Y. C. 2020-04-20 doi:10.1101/2020.04.20.050294 Cold Spring Harbor Laboratory Press 2020-04-20 <![CDATA[ Sequence determinants and evolution of splicing in budding yeast and related species ]]> https://biorxiv.org/content/10.1101/2020.04.20.050609v1?rss=1 Schirman, D. Yakhini, Z. Dahan, O. Pilpel, Y. 2020-04-21 doi:10.1101/2020.04.20.050609 Cold Spring Harbor Laboratory Press 2020-04-21 <![CDATA[ Half of the world's tree biodiversity is unprotected and is increasingly threatened by human activities ]]> https://biorxiv.org/content/10.1101/2020.04.21.052464v1?rss=1 Guo, W.-Y. Serra-Diaz, J. M. Schrodt, F. Eiserhardt, W. L. Maitner, B. S. Merow, C. Violle, C. Anand, M. Belluau, M. Bruun, H. H. Byun, C. Catford, J. A. Cerabolini, B. E. L. Chacon-Madrigal, E. Ciccarelli, D. Cornelissen, J. H. C. Dang-Le, A. T. de Frutos, A. Dias, A. S. Giroldo, A. B. Guo, K. Gutierrez, A. G. Hattingh, W. He, T. Hietz, P. Hough-Snee, N. Jansen, S. Kattge, J. Klein, T. Komac, B. Kraft, N. Kramer, K. Lavorel, S. Lusk, C. H. Martin, A. R. Mencuccini, M. Michaletz, S. T. Minden, V. Mori, A. S. Niinemets, U. Onoda, Y. Onstein, R. E. Penue 2020-04-23 doi:10.1101/2020.04.21.052464 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Interacting evolutionary pressures drive mutation dynamics and health outcomes in aging blood ]]> https://biorxiv.org/content/10.1101/2020.04.25.058677v1?rss=1 Skead, K. Ang Houle, A. Abelson, S. Agbessi, M. Bruat, V. Lin, B. Soave, D. Shlush, L. Wright, S. Dick, J. Morris, Q. Awadalla, P. 2020-04-27 doi:10.1101/2020.04.25.058677 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ Learning the architectural features that predict functional similarity of neural networks ]]> https://biorxiv.org/content/10.1101/2020.04.27.057752v1?rss=1 Haber, A. Schneidman, E. 2020-04-28 doi:10.1101/2020.04.27.057752 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Bistability in oxidative stress response determines the migration behavior of phytoplankton in turbulence ]]> https://biorxiv.org/content/10.1101/2020.04.28.064980v1?rss=1 Carrara, F. Sengupta, A. Behrendt, L. Vardi, A. Stocker, R. 2020-04-29 doi:10.1101/2020.04.28.064980 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Transcriptional profiling reveals a subset of human breast tumors that retain wt TP53 but display mutant p53-associated features ]]> https://biorxiv.org/content/10.1101/2020.04.30.070037v1?rss=1 Oren, M. Domany, E. Benor, G. Fuks, G. Rueda, O. Chin, S.-F. Caldas, C. mukherjee, s. Arankar, S. Aylon, Y. 2020-05-02 doi:10.1101/2020.04.30.070037 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ Manipulation of the human tRNA pool reveals distinct tRNA sets that act in cellular proliferation or cell cycle arrest ]]> https://biorxiv.org/content/10.1101/2020.04.30.070789v1?rss=1 Aharon-Heferz, N. Frumkin, I. Mayshar, Y. Dahan, O. Pilpel, Y. T. Rak, R. 2020-05-02 doi:10.1101/2020.04.30.070789 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ The coding capacity of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.05.07.082909v1?rss=1 Finkel, Y. Mizrahi, O. Nachshon, A. Weingarten-Gabbay, S. Yahalom-Ronen, Y. Tamir, H. Achdout, H. Melamed, S. Weiss, S. Isrealy, T. Paran, N. Schwartz, M. Stern-Ginossar, N. 2020-05-07 doi:10.1101/2020.05.07.082909 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Surface display of designer protein scaffolds on genome-reduced strains of Pseudomonas putida ]]> https://biorxiv.org/content/10.1101/2020.05.13.093500v1?rss=1 Dvorak, P. Bayer, E. de Lorenzo, V. 2020-05-14 doi:10.1101/2020.05.13.093500 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ What influences selection of native phosphorelay architectures? ]]> https://biorxiv.org/content/10.1101/2020.05.21.108001v1?rss=1 Alves, R. Salvado, B. Milo, R. Vilaprinyo, E. Sorribas, A. 2020-05-26 doi:10.1101/2020.05.21.108001 Cold Spring Harbor Laboratory Press 2020-05-26 <![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[ Mapping the architecture of regulatory variation provides insights into the evolution of complex traits ]]> https://biorxiv.org/content/10.1101/2020.05.24.113217v1?rss=1 Lupo, O. Krieger, G. Jonas, F. Barkai, N. 2020-05-27 doi:10.1101/2020.05.24.113217 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease ]]> https://biorxiv.org/content/10.1101/2020.05.27.118117v1?rss=1 Douangamath, A. Fearon, D. Gehrtz, P. Krojer, T. Lukacik, P. Owen, C. D. Resnick, E. Strain-Damerell, C. aimon, A. Abranyi-Balogh, P. Brandao-Neto, J. Carberry, A. Davison, G. Dias, A. Downes, T. D. Dunnett, L. Fairhead, M. Firth, J. D. Jones, S. P. Keely, A. Keserü, G. M. Klein, H. F. Martin, M. P. Noble, M. E. M. O'Brien, P. Powell, A. Reddi, R. Skyner, R. Snee, M. Waring, M. J. Wild, C. London, N. von Delft, F. Walsh, M. A. 2020-05-27 doi:10.1101/2020.05.27.118117 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ PRosettaC: Rosetta based modeling of PROTAC mediated ternary complexes ]]> https://biorxiv.org/content/10.1101/2020.05.27.119354v1?rss=1 Zaidman, D. London, N. 2020-05-30 doi:10.1101/2020.05.27.119354 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Functional reconstitution of a bacterial CO2 concentrating mechanism in E. coli ]]> https://biorxiv.org/content/10.1101/2020.05.27.119784v1?rss=1 Flamholz, A. I. Dugan, E. Blikstad, C. Gleizer, S. Ben-Nissan, R. Amram, S. Antonovsky, N. Ravishankar, S. Noor, E. Bar-Even, A. Milo, R. Savage, D. 2020-05-27 doi:10.1101/2020.05.27.119784 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ An atlas of robust microbiome associations with phenotypic traits based on large-scale cohorts from two continents ]]> https://biorxiv.org/content/10.1101/2020.05.28.122325v1?rss=1 Rothschild, D. Leviatan, S. Hanemann, A. Cohen, Y. Weissbrod, O. Segal, E. 2020-05-30 doi:10.1101/2020.05.28.122325 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Decision-making in a synthetic cell: the limits of biological computation ]]> https://biorxiv.org/content/10.1101/2020.05.29.116467v1?rss=1 Greiss, F. Daube, S. S. Noireaux, V. Bar-Ziv, R. 2020-05-30 doi:10.1101/2020.05.29.116467 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Paleoclimate and current climate collectively shape the phylogenetic and functional diversity of trees worldwide ]]> https://biorxiv.org/content/10.1101/2020.06.02.128975v1?rss=1 107 years) paleoclimate as important co-determinants, and, notably, with past cold and drought stress being linked to reduced current diversity. These findings demonstrate that tree diversity is affected by paleoclimate millions of years back in time and highlight the potential for tree diversity losses from future climate change. ]]> Guo, W.-Y. Serra-Diaz, J. M. Schrodt, F. Eiserhardt, W. L. Maitner, B. S. Merow, C. Violle, C. Blach-Overgaard, A. Zhang, J. Anand, M. Belluau, M. Bruun, H. H. Byun, C. Catford, J. A. Cerabolini, B. E. L. Chacón-Madrigal, E. Ciccarelli, D. Cornelissen, J. H. C. Dang-Le, A. T. de Frutos, A. Dias, A. S. Giroldo, A. B. Hattingh, W. He, T. Hietz, P. Hough-Snee, N. Jansen, S. Kattge, J. klein, t. Komac, B. Kraft, N. Kramer, K. Lavorel, S. Lusk, C. H. Martin, A. R. Mencuccini, M. Michaletz, S. T. Minden, V. Mori, A. S. Niinemets, Ülo Onoda, Y. Onste 2020-06-03 doi:10.1101/2020.06.02.128975 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Designer protein assemblies with tunable phase diagrams in living cells ]]> https://biorxiv.org/content/10.1101/2020.06.03.131433v1?rss=1 Heidenreich, M. Georgeson, J. Locatelli, E. Rovigatti, L. Nandi, S. K. Steinberg, A. Nadav, Y. Shimoni, E. Safran, S. A. Doye, J. P. K. Levy, E. D. 2020-06-03 doi:10.1101/2020.06.03.131433 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Context-dependent functional compensation between Ythdf m6A readers ]]> https://biorxiv.org/content/10.1101/2020.06.03.131441v1?rss=1 Lasman, L. Krupalnik, V. Geula, S. Zerbib, M. Viukov, S. Mor, N. Aguilera, A. Mizrahi, O. Shashank, S. Nachshon, A. Schneir, D. Aigner, S. Shankar, A. Mueller, J. Stern-Ginossar, N. Yeo, G. W. Novershtern, N. Hanna, J. H. 2020-06-03 doi:10.1101/2020.06.03.131441 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Time-resolved profiling reveals ATF3 as a novel mediator of endocrine resistance in breast cancer ]]> https://biorxiv.org/content/10.1101/2020.06.08.139659v1?rss=1 Borgoni, S. Sofyali, E. Soleimani Dodaran, M. Wilhelm, H. Mueller-Decker, K. Will, R. Noronha, A. Verschure, P. J. Yarden, Y. Magnani, L. van Kampen, A. H. C. Moerland, P. D. Wiemann, S. 2020-06-08 doi:10.1101/2020.06.08.139659 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ On the evolution of chaperones and co-chaperones and the exponential expansion of proteome complexity ]]> https://biorxiv.org/content/10.1101/2020.06.08.140319v1?rss=1 Rebeaud, M. Mallik, S. Goloubinoff, P. A. Tawfik, D. S. 2020-06-09 doi:10.1101/2020.06.08.140319 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Microvillar cartography: a super-resolution single-molecule imaging method to map the positions of membrane proteins with respect to cellular surface topography ]]> https://biorxiv.org/content/10.1101/2020.06.11.145383v1?rss=1 Ghosh, S. Alon, R. Alcover, A. Haran, G. 2020-06-11 doi:10.1101/2020.06.11.145383 Cold Spring Harbor Laboratory Press 2020-06-11 <![CDATA[ Differential cellular responses to adhesive interactions with galectin-8 and fibronectin coated substrates ]]> https://biorxiv.org/content/10.1101/2020.06.14.127076v1?rss=1 Li, W. Sancho, A. E. Groll, J. Zick, Y. Bershadsky, A. Geiger, B. 2020-06-15 doi:10.1101/2020.06.14.127076 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Epithelial Tissues as Active Solids: From Nonlinear Contraction Pulses to Rupture Resistance ]]> https://biorxiv.org/content/10.1101/2020.06.15.153163v1?rss=1 Armon, S. Bull, M. S. Moriel, A. Aharoni, H. Prakash, M. 2020-06-16 doi:10.1101/2020.06.15.153163 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ A molecular lid mechanism for K+ channel blockers revealed by a cone peptide ]]> https://biorxiv.org/content/10.1101/2020.06.15.153577v1?rss=1 Saikia, C. Dym, O. Altma-Gueta, H. Gordon, D. Reuveny, E. Karbat, I. 2020-06-16 doi:10.1101/2020.06.15.153577 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ VEGFC induced cell cycle arrest mediates sprouting and differentiation of venous and lymphatic endothelial cells ]]> https://biorxiv.org/content/10.1101/2020.06.17.155028v1?rss=1 Jerafi-Vider, A. Moshe, N. Hen, G. Splittstoesser, D. Shin, M. Lawson, N. Yaniv, K. 2020-06-19 doi:10.1101/2020.06.17.155028 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Bacterial retrons function in anti-phage defense ]]> https://biorxiv.org/content/10.1101/2020.06.21.156273v1?rss=1 Millman, A. Bernheim, A. Stokar-Avihail, A. Fedorenko, T. Voichek, M. Leavitt, A. Sorek, R. 2020-06-22 doi:10.1101/2020.06.21.156273 Cold Spring Harbor Laboratory Press 2020-06-22 <![CDATA[ Live imaging of chromatin distribution in muscle nuclei reveals novel principles of nuclear architecture and chromatin compartmentalization ]]> https://biorxiv.org/content/10.1101/2020.06.21.163360v1?rss=1 Amiad Pavlov, D. Lorber, D. Bajpai, G. Safran, S. Volk, T. 2020-06-21 doi:10.1101/2020.06.21.163360 Cold Spring Harbor Laboratory Press 2020-06-21 <![CDATA[ Modeling heterogeneity of Triple-Negative Breast Cancer highlights potency of WEE1 and BCL-XL targeting ]]> https://biorxiv.org/content/10.1101/2020.06.22.164418v1?rss=1 Lamballe, F. Ahmad, F. Vinik, Y. Castellanet, O. Daian, F. Mueller, A. Koehler, U. Bailly, A.-L. Josselin, E. Castellano, R. Cayrou, C. Charafe-Jauffret, E. Mills, G. B. Geli, V. Borg, J.-P. Lev, S. Maina, F. 2020-06-22 doi:10.1101/2020.06.22.164418 Cold Spring Harbor Laboratory Press 2020-06-22 <![CDATA[ Reduced nuclear lamin A/C enhances cancer cell squeezing through rigid barriers, does not facilitate endothelial crossing, and impairs experimental metastasis ]]> https://biorxiv.org/content/10.1101/2020.06.23.167130v1?rss=1 Roncato, F. Regev, O. Feigelson, S. W. Yadav, S. K. Kaczmarczyk, L. Levi, N. Drago-Garcia, D. Ovadia, S. Kizner, M. Addadi, Y. Sabino, J. C. Ovadya, Y. de Almeida, S. F. Feldmesser, E. Gerlitz, G. Alon, R. 2020-06-24 doi:10.1101/2020.06.23.167130 Cold Spring Harbor Laboratory Press 2020-06-24 <![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[ Genetics of human gut microbiome composition ]]> https://biorxiv.org/content/10.1101/2020.06.26.173724v1?rss=1 Kurilshikov, A. Medina-Gomez, C. Bacigalupe, R. Radjabzadeh, D. Wang, J. Demirkan, A. Le Roy, C. I. Raygoza Garay, J. A. Finnicum, C. Liu, X. Zhernakova, D. Bonder, M. J. Hansen, T. H. Frost, F. Ruhlemann, M. C. Turpin, W. Moon, J.-Y. Kim, H.-N. Lull, K. Barkan, E. Shah, S. A. Fornage, M. Szopinska-Tokov, J. Wallen, Z. Borisevich, D. Agreus, L. Andreasson, A. Bang, C. Bedrani, L. Bell, J. T. Bisgaard, H. Boehnke, M. Boomsma, D. I. Burk, R. D. Claringbould, A. Croitoru, K. Davies, G. Van Duijn, C. Duijts, L. Falony, G. Fu, J. van der Graaf, A. Hansen, T 2020-06-28 doi:10.1101/2020.06.26.173724 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ Multiplexed mRNA assembly into ribonucleoprotein particles plays an operon-like role in the control of yeast cell physiology ]]> https://biorxiv.org/content/10.1101/2020.06.28.175851v1?rss=1 Nair, R. R. Zabezhinsky, D. Gelin-Licht, R. Haas, B. J. Dyhr, M. C. A. Sperber, H. S. Nusbaum, C. Gerst, J. E. 2020-06-28 doi:10.1101/2020.06.28.175851 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ Visualizing active viral infection reveals diverse cell fates in synchronized algal bloom demise ]]> https://biorxiv.org/content/10.1101/2020.06.28.176719v1?rss=1 Vincent, F. J. Sheyn, U. Porat, Z. Vardi, A. 2020-06-29 doi:10.1101/2020.06.28.176719 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Line-FRAP, a versatile method based on fluorescence recovery after photobleaching to measure diffusion rates in vitro and in vivo ]]> https://biorxiv.org/content/10.1101/2020.07.01.181750v1?rss=1 Dey, D. Marciano, S. Schreiber, G. 2020-07-02 doi:10.1101/2020.07.01.181750 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Allostery through DNA drives phenotype switching ]]> https://biorxiv.org/content/10.1101/2020.07.04.187450v1?rss=1 Rosenblum, G. Elad, N. Rozenberg, H. Wiggers, F. Hofmann, H. 2020-07-04 doi:10.1101/2020.07.04.187450 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Decoding ribosomal RNA modification dynamics at single molecule resolution ]]> https://biorxiv.org/content/10.1101/2020.07.06.189969v1?rss=1 Begik, O. Lucas, M. C. Ramirez, J. M. Cruciani, S. Novoa, E. M. Cruciani, S. Vieira, H. G. S. Medina, R. Liu, H. Sas-Chen, A. Mattick, J. S. Schwartz, S. 2020-07-06 doi:10.1101/2020.07.06.189969 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[ 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[ Insight into the autosomal-dominant inheritance pattern of SOD1-associated ALS from native mass spectrometry ]]> https://biorxiv.org/content/10.1101/2020.07.13.199976v1?rss=1 cveticanin, j. Mondal, T. Meiering, E. M. Sharon, M. Horovitz, A. 2020-07-13 doi:10.1101/2020.07.13.199976 Cold Spring Harbor Laboratory Press 2020-07-13 <![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[ Single cell characterization of a synthetic bacterial clock with a hybrid feedback loop containing dCas9-sgRNA ]]> https://biorxiv.org/content/10.1101/2020.07.16.206722v1?rss=1 Henningsen, J. Schwarz-Schilling, M. Leibl, A. Guttierez, J. A. M. Sagredo, S. Simmel, F. C. 2020-07-16 doi:10.1101/2020.07.16.206722 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner ]]> https://biorxiv.org/content/10.1101/2020.07.21.214932v1?rss=1 1/2 log10 increased infectivity in human cells expressing the human ACE2 protein as the viral receptor. The increased binding/fusion activity of the D614G Spike protein was corroborated in a cell fusion assay using Spike and ACE2 proteins expressed in different cells. These results are consistent with the possibility that the Spike D614G mutant increases the infectivity of SARS-CoV2. ]]> Ogawa, J. Zhu, W. Tonnu, N. Singer, O. Hunter, T. Ryan (Firth), A. L. Pao, G. M. 2020-07-22 doi:10.1101/2020.07.21.214932 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Megadalton-sized dityrosine aggregates of α-synuclein retain high degrees of structural disorder and internal dynamics. ]]> https://biorxiv.org/content/10.1101/2020.07.26.202358v1?rss=1 Verzini, S. Shah, M. Theillet, F.-X. Belsom, A. Bieschke, J. Wanker, E. E. Rappsilber, J. Binolfi, A. Selenko, P. 2020-07-26 doi:10.1101/2020.07.26.202358 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ 3D MAPs discovers the morphological sequence chondrocytes undergo in the growth plate and the regulatory role of GDF5 in this process ]]> https://biorxiv.org/content/10.1101/2020.07.28.225409v1?rss=1 Rubin, S. Agrawal, A. Stegmaier, J. Svorai, J. Addadi, Y. Villoutreix, P. Stern, T. Zelzer, E. 2020-07-28 doi:10.1101/2020.07.28.225409 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Systemic sterile induced-co-expression of IL-12 and IL-18 drives IFN-γ-dependent activation of microglia and recruitment of MHC-II-expressing inflammatory monocytes into the brain. ]]> https://biorxiv.org/content/10.1101/2020.07.30.228098v1?rss=1 Gaviglio, E. A. Peralta Ramos, J. M. Arroyo, D. S. Bussi, C. Iribarren, P. Rodriguez-Galan, M. C. 2020-07-30 doi:10.1101/2020.07.30.228098 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ Helicase-Like Functions in Phosphate Loop Containing Beta-Alpha Polypeptides ]]> https://biorxiv.org/content/10.1101/2020.07.30.228619v1?rss=1 Vyas, P. Trofimyuk, O. Longo, L. M. Deshmukh, F. K. Sharon, M. Tawfik, D. S. 2020-07-30 doi:10.1101/2020.07.30.228619 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ α-Synuclein plasma membrane localization correlates with cellular phosphatidylinositol polyphosphate levels. ]]> https://biorxiv.org/content/10.1101/2020.07.31.224600v1?rss=1 Eichmann, C. Jacob, R. S. Dema, A. Mercadante, D. Selenko, P. 2020-07-31 doi:10.1101/2020.07.31.224600 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ Nonlinear delay differential equations and their application to modeling biological network motifs ]]> https://biorxiv.org/content/10.1101/2020.08.02.233619v1?rss=1 Glass, D. S. Jin, X. Riedel-Kruse, I. H. 2020-08-04 doi:10.1101/2020.08.02.233619 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Clump sequencing exposes the spatial expression programs of intestinal secretory cells ]]> https://biorxiv.org/content/10.1101/2020.08.05.237917v1?rss=1 Manco, R. Averbukh, I. Porat, Z. Bahar Halpern, K. Amit, I. Itzkovitz, S. 2020-08-06 doi:10.1101/2020.08.05.237917 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ Coronacept - a potent immunoadhesin against SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.08.12.247940v1?rss=1 Cohen-Dvashi, H. Weinstein, J. Katz, M. Eilon, M. Mor, Y. Shimon, A. Strobelt, R. Shemesh, M. Fleishman, S. J. Diskin, R. 2020-08-12 doi:10.1101/2020.08.12.247940 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Phosphorylation of Serine114 of the transcription factor ABSCISIC ACID INSENSITIVE 4 is essential for activity ]]> https://biorxiv.org/content/10.1101/2020.08.14.250936v1?rss=1 Eisner, N. Maymon, T. Cancho Sanchez, E. Bar-Zvi, D. Brodsky, S. Finkelstein, R. R. Bar-Zvi, D. 2020-08-14 doi:10.1101/2020.08.14.250936 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Cellular pathways of calcium transport and concentration towards mineral formation in sea urchin larvae ]]> https://biorxiv.org/content/10.1101/2020.08.17.244137v1?rss=1 Kahil, K. Varsano, N. Sorrentino, A. Pereiro, E. Rez, P. Weiner, S. Addadi, L. 2020-08-17 doi:10.1101/2020.08.17.244137 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ A computationally designed fluorescent biosensor for D-serine ]]> https://biorxiv.org/content/10.1101/2020.08.18.255380v1?rss=1 Vongsouthi, V. Whitfield, J. H. Unichenko, P. Mitchell, J. A. Breithausen, B. Khersonsky, O. Kremers, L. Monai, H. Hirase, H. Fleishman, S. J. Henneberger, C. Jackson, C. J. 2020-08-19 doi:10.1101/2020.08.18.255380 Cold Spring Harbor Laboratory Press 2020-08-19 <![CDATA[ Alternative splicing of SLAMF6 in human T cells creates a co-stimulatory isoform that counteracts the inhibitory effect of the full-length receptor ]]> https://biorxiv.org/content/10.1101/2020.08.21.262238v1?rss=1 Hajaj, E. Zisman, E. Tzaban, S. Merims, S. Cohen, J. E. Klein, S. Frankenburg, S. Sade-Feldman, M. Tabach, Y. Yizhak, K. Navon, A. Stepensky, P. Hacohen, N. Peretz, T. Veillette, A. Karni, R. Eisenberg, G. Lotem, M. 2020-08-22 doi:10.1101/2020.08.21.262238 Cold Spring Harbor Laboratory Press 2020-08-22 <![CDATA[ 3D Deconvolution Processing for STEM Cryo-Tomography ]]> https://biorxiv.org/content/10.1101/2020.08.26.267732v1?rss=1 Waugh, B. Wolf, S. G. Fass, D. Branlund, E. Kam, T. Sedat, J. Elbaum, M. 2020-08-27 doi:10.1101/2020.08.26.267732 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ The Formin Inhibitor, SMIFH2, Inhibits Members of the Myosin Superfamily ]]> https://biorxiv.org/content/10.1101/2020.08.30.274613v1?rss=1 Nishimura, Y. Shi, S. Zhang, F. Liu, R. Takagi, Y. Bershadsky, A. D. viasnoff, v. Sellers, J. R. 2020-08-31 doi:10.1101/2020.08.30.274613 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Head-Direction Coding in the Hippocampal Formation of Birds ]]> https://biorxiv.org/content/10.1101/2020.08.31.274928v1?rss=1 2,100 neurons from 23 birds). Whereas spatially-modulated cells (place-cells, border-cells, etc.) were generally not encountered, the firing-rate of 12% of the neurons was unimodally and significantly modulated by the head-azimuth - i.e. these were head-direction cells (HD cells). Typically, HD cells were maximally active at one preferred-direction and minimally at the opposite null-direction, with preferred-directions spanning all 360{degrees}. The HD tuning was relatively broad (mean width [~]130{degrees}), independent of the animals position and speed, and was stable during the recording-session. Similarly to findings in rodents, the HD tuning usually rotated with the rotation of a salient visual cue in the arena. These findings support the existence of an allocentric head-direction representation in the quail hippocampal formation, and provide the first demonstration of head-direction cells in birds. ]]> Ben-Yishay, E. Krivoruchko, K. Ron, S. Ulanovsky, N. Derdikman, D. Gutfreund, Y. 2020-08-31 doi:10.1101/2020.08.31.274928 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Drug binding sites in the multidrug transporter MdfA in detergent solution and in lipid nanodiscs ]]> https://biorxiv.org/content/10.1101/2020.08.31.275321v1?rss=1 Goldfarb, D. Bahrenberg, T. Yardeni, E. H. Feintuch, A. Bibi, E. 2020-08-31 doi:10.1101/2020.08.31.275321 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Self-Supervised Natural Image Reconstruction and Rich Semantic Classification from Brain Activity ]]> https://biorxiv.org/content/10.1101/2020.09.06.284794v1?rss=1 Gaziv, G. Beliy, R. Granot, N. Hoogi, A. Strappini, F. Golan, T. Irani, M. 2020-09-08 doi:10.1101/2020.09.06.284794 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ B Cell Division Capacity in Germinal Centers Depends on Myc Transcript Stabilization Through m6A mRNA Methylation and IGF2BP3 Functions ]]> https://biorxiv.org/content/10.1101/2020.09.08.287433v1?rss=1 Grenov, A. C. Moss, L. Edelheit, S. Cordiner, R. Schmiedel, D. Biram, A. Hanna, J. H. Heick Jensen, T. Schwartz, S. Shulman, Z. 2020-09-09 doi:10.1101/2020.09.08.287433 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Viral infection of algal blooms leaves a halogenated footprint on the dissolved organic matter in the ocean ]]> https://biorxiv.org/content/10.1101/2020.09.08.287805v1?rss=1 Kuhlisch, C. Schleyer, G. Shahaf, N. Vincent, F. Schatz, D. Vardi, A. 2020-09-08 doi:10.1101/2020.09.08.287805 Cold Spring Harbor Laboratory Press 2020-09-08 <![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[ Mechanistic basis for motor-driven membrane constriction by dynamin ]]> https://biorxiv.org/content/10.1101/2020.09.10.289546v1?rss=1 Ganichkin, O. Vancraenenbroeck, R. Rosenblum, G. Hofmann, H. Mikhailov, A. S. Daumke, O. Noel, J. K. 2020-09-11 doi:10.1101/2020.09.10.289546 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Effects of order on episodic memory of event times ]]> https://biorxiv.org/content/10.1101/2020.09.11.289058v1?rss=1 Naim, M. Katkov, M. Tsodyks, M. 2020-09-11 doi:10.1101/2020.09.11.289058 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Single-molecule spectroscopy reveals dynamic allostery mediated by the substrate-binding domain of a AAA+ machine ]]> https://biorxiv.org/content/10.1101/2020.09.13.295345v1?rss=1 Iljina, M. Mazal, H. Goloubinoff, P. Riven, I. Haran, G. 2020-09-14 doi:10.1101/2020.09.13.295345 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ The mitochondrial surface receptor Tom70 protects the cytosol against mitoprotein-induced stress ]]> https://biorxiv.org/content/10.1101/2020.09.14.296194v1?rss=1 Backes, S. Bykov, Y. S. Raeschle, M. Zhou, J. Lenhard, S. Kraemer, L. Muehlhaus, T. Bibi, C. Jann, C. Smith, J. D. Steinmetz, L. M. Rapaport, D. Storchova, Z. Schuldiner, M. Boos, F. Herrmann, J. M. 2020-09-15 doi:10.1101/2020.09.14.296194 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ Behavioral elements and neural circuits underlying exploratory decisions in normative anxiety ]]> https://biorxiv.org/content/10.1101/2020.09.16.300525v1?rss=1 Aberg, K. C. Toren, I. Paz, R. 2020-09-19 doi:10.1101/2020.09.16.300525 Cold Spring Harbor Laboratory Press 2020-09-19 <![CDATA[ An automatic pipeline for the design of irreversible derivatives identifies a potent SARS-CoV-2 Mpro inhibitor. ]]> https://biorxiv.org/content/10.1101/2020.09.21.299776v1?rss=1 Zaidman, D. Gehrtz, P. Filep, M. Fearon, D. Prilusky, J. Duberstein, S. Cohen, G. Owen, D. Resnick, E. Strain-Damerell, C. Lukacik, P. Covid-Moonshot Consortium, Barr, H. A. Walsh, M. von Delft, F. London, N. 2020-09-22 doi:10.1101/2020.09.21.299776 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Insufficient Eye Tracking Data Leads to Errors in Evaluating Typical and Atypical Fixation Preferences ]]> https://biorxiv.org/content/10.1101/2020.09.21.306621v1?rss=1 Reimann, G. E. Walsh, C. Csumitta, K. McClure, P. Pereira, F. Martin, A. Ramot, M. 2020-09-22 doi:10.1101/2020.09.21.306621 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Peripheral sgp130-mediated trans-signaling blockade induces obesity and insulin resistance in mice via PPARα suppression ]]> https://biorxiv.org/content/10.1101/2020.09.24.309716v1?rss=1 Lanton, T. Levkovitch-Siany, O. Udi, S. Tam, J. Abramovich, R. Perles, S. Williams, E. Rachmilewitz, J. Mor, U. Elinav, E. Schmidt-Arras, D. Rehman, A. Rosenstiel, P. Giannou, A. Huber, S. Rose-John, S. Galun, E. Axelrod, J. H. 2020-09-24 doi:10.1101/2020.09.24.309716 Cold Spring Harbor Laboratory Press 2020-09-24 <![CDATA[ The extracellular matrix protein agrin is essential for epicardial epithelial-to-mesenchymal transition during heart development ]]> https://biorxiv.org/content/10.1101/2020.09.25.313742v1?rss=1 Sun, X. Malandraki-Miller, S. Kennedy, T. Bassat, E. Klaourakis, K. Zhou, J. Gamen, E. Vieira, J. M. Tzahor, E. Riley, P. 2020-09-26 doi:10.1101/2020.09.25.313742 Cold Spring Harbor Laboratory Press 2020-09-26 <![CDATA[ Tissue topography steers migrating Drosophila border cells ]]> https://biorxiv.org/content/10.1101/2020.09.27.316117v1?rss=1 Dai, W. Guo, X. Cao, Y. S. Mondo, J. A. Campanale, J. P. Montell, B. J. Burrous, H. Streichan, S. Gov, N. Rappel, W.-J. Montell, D. 2020-09-28 doi:10.1101/2020.09.27.316117 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ A Human Aggression Pheromone Elicits a Sexually Dimorphic Behavioral and Brain Response ]]> https://biorxiv.org/content/10.1101/2020.09.29.318287v1?rss=1 Mishor, E. Amir, D. Weiss, T. Honigstein, D. Weissbrod, A. Livne, E. Gorodisky, L. Karagach, S. Ravia, A. Snitz, K. Karawani, D. Zirler, R. Weissgross, R. soroka, T. Endevelt-Shapira, Y. Agron, S. Rozenkrantz, L. Reshef, N. Furman-Haran, E. Breer, H. Strotmann, J. Sobel, N. 2020-09-30 doi:10.1101/2020.09.29.318287 Cold Spring Harbor Laboratory Press 2020-09-30 <![CDATA[ Polyamines Mediate Folding of Primordial Hyper-Acidic Helical Proteins ]]> https://biorxiv.org/content/10.1101/2020.10.01.321877v1?rss=1 Despotovic, D. Longo, L. M. Aharon, E. Kahana, A. Scherf, T. Gruic-Sovulj, I. Tawfik, D. S. 2020-10-01 doi:10.1101/2020.10.01.321877 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs ]]> https://biorxiv.org/content/10.1101/2020.10.02.324145v1?rss=1 Weingarten-Gabbay, S. Klaeger, S. Sarkizova, S. Pearlman, L. R. Chen, D.-Y. Bauer, M. R. Taylor, H. B. Conway, H. L. Tomkins-Tinch, C. H. Finkel, Y. Nachshon, A. Gentili, M. Rivera, K. D. Keskin, D. B. Rice, C. M. Clauser, K. R. Hacohen, N. Carr, S. A. Abelin, J. G. Saeed, M. Sabeti, P. C. 2020-10-02 doi:10.1101/2020.10.02.324145 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Representational drift in the mouse visual cortex ]]> https://biorxiv.org/content/10.1101/2020.10.05.327049v1?rss=1 Deitch, D. Rubin, A. Ziv, Y. 2020-10-05 doi:10.1101/2020.10.05.327049 Cold Spring Harbor Laboratory Press 2020-10-05 <![CDATA[ Developmental effects of oxytocin neurons on social affiliation and processing of social information ]]> https://biorxiv.org/content/10.1101/2020.10.08.330993v1?rss=1 Nunes, A. R. Gliksberg, M. Varela, S. A. M. Teles, M. Wircer, E. Blechman, J. Petri, G. Levkowitz, G. Oliveira, R. F. 2020-10-08 doi:10.1101/2020.10.08.330993 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Reducing SAR in 7T brain fMRI by circumventing fat suppression while removing the lipid signal through a parallel acquisition approach ]]> https://biorxiv.org/content/10.1101/2020.10.13.337691v1?rss=1 Seginer, A. Furman-Haran, E. Goldberg, I. Schmidt, R. 2020-10-14 doi:10.1101/2020.10.13.337691 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Climbing up and down binding landscapes: a high-throughput study of mutational effects in homologous protein-protein complexes ]]> https://biorxiv.org/content/10.1101/2020.10.14.338756v1?rss=1 Heyne, M. Shirian, J. Cohen, I. Peleg, Y. Radisky, E. S. Papo, N. Shifman, J. M. 2020-10-14 doi:10.1101/2020.10.14.338756 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Mechanosensitive calcium signaling in filopodia ]]> https://biorxiv.org/content/10.1101/2020.10.21.346247v1?rss=1 Efremov, A. K. Yao, M. Sheetz, M. P. Bershadsky, A. D. Martinac, B. Yan, J. 2020-10-21 doi:10.1101/2020.10.21.346247 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ PTBP1 Regulates Injury Responses and Sensory Pathways in Adult Peripheral Neurons ]]> https://biorxiv.org/content/10.1101/2020.10.22.348631v1?rss=1 Alber, S. Di-Matteo, P. Zdradzinski, M. D. Marvaldi, L. Kawaguchi, R. Medzihradszky, K. F. Doron-Mandel, E. Okladnikov, N. Rishal, I. Nevo, R. Lee, S. J. Sahoo, P. K. Burlingame, A. L. Coppola, G. Twiss, J. L. Fainzilber, M. 2020-10-22 doi:10.1101/2020.10.22.348631 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ Mesoscale phase separation of chromatin in the nucleus ]]> https://biorxiv.org/content/10.1101/2020.10.23.338079v1?rss=1 Bajpai, G. Amiad-Pavlov, D. Lorber, D. Volk, T. Safran, S. 2020-10-24 doi:10.1101/2020.10.23.338079 Cold Spring Harbor Laboratory Press 2020-10-24 <![CDATA[ Active palpation underlying shape perception is shaped by physiological thresholds and experience. ]]> https://biorxiv.org/content/10.1101/2020.10.27.356584v1?rss=1 Mizrachi, N. Nelinger, G. Ahissar, E. Arieli, A. 2020-10-27 doi:10.1101/2020.10.27.356584 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ COVID Moonshot: Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine Learning ]]> https://biorxiv.org/content/10.1101/2020.10.29.339317v1?rss=1 18,000 designs), crystallographic data (>840 ligand-bound X-ray structures), assay data (>10,000 measurements), and synthesized molecules (>2,400 compounds) for this campaign were shared rapidly and openly, creating a rich open and IP-free knowledgebase for future anti-coronavirus drug discovery. ]]> The COVID Moonshot Consortium, Achdout, H. Aimon, A. Bar-David, E. Barr, H. Ben-Shmuel, A. Bennett, J. Bobby, M. L. Brun, J. BVNBS, S. Calmiano, M. Carbery, A. Cattermole, E. Chodera, J. D. Clyde, A. Coffland, J. E. Cohen, G. Cole, J. Contini, A. Cox, L. Cvitkovic, M. Dias, A. Douangamath, A. Duberstein, S. Dudgeon, T. Dunnett, L. Eastman, P. K. Erez, N. Fairhead, M. Fearon, D. Fedorov, O. Ferla, M. Foster, H. Foster, R. Gabizon, R. Gehrtz, P. Gileadi, C. Giroud, C. Glass, W. G. Glen, R. Glinert, I. Gorichko, M. Gorrie-Stone, T. Griffen, E. J. Heer 2020-10-30 doi:10.1101/2020.10.29.339317 Cold Spring Harbor Laboratory Press 2020-10-30 <![CDATA[ Highly conserved and cis-acting lncRNAs produced from paralogous regions in the center of HOXA and HOXB clusters in the endoderm lineage ]]> https://biorxiv.org/content/10.1101/2020.11.03.366716v1?rss=1 Degani, N. Ainbinder, E. Ulitsky, I. 2020-11-04 doi:10.1101/2020.11.03.366716 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ Localized Chemogenetic Silencing of Inhibitory Neurons: A novel Mouse Model of Focal Cortical Seizures ]]> https://biorxiv.org/content/10.1101/2020.11.04.367862v1?rss=1 Goldenberg, A. M. Schmidt, S. Mitelman, R. Rubi Levy, D. Katz, Y. Yizhar, O. Beck, H. Lampl, I. 2020-11-05 doi:10.1101/2020.11.04.367862 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ A functional pre-screening platform for identifying points of vulnerability in the cell death map of human melanoma tumors ]]> https://biorxiv.org/content/10.1101/2020.11.11.377671v1?rss=1 Dekel-Bird, N. P. Bialik, S. Itzhaki, O. Salame, T. M. Yaeli-Slonim, N. Levin-Salomon, V. Dasari, S. K. Besser, M. Kimchi, A. 2020-11-11 doi:10.1101/2020.11.11.377671 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ The effect of soil potassium and carbohydrates on xylem conductivity and embolism in an evergreen angiosperm tree and a gymnosperm tree before and after drought ]]> https://biorxiv.org/content/10.1101/2020.11.11.379156v1?rss=1 Wagner, Y. Brumfeld, V. Gruenzweig, J. klein, t. 2020-11-12 doi:10.1101/2020.11.11.379156 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Tetramerization of Phosphoprotein is essential for Respiratory Syncytial virus budding while its N terminal region mediates direct interactions with the Matrix protein. ]]> https://biorxiv.org/content/10.1101/2020.11.17.387951v1?rss=1 Bajorek, M. Galloux, M. Richard, C.-A. Szekely, O. Rosenzweig, R. Sizun, C. Elcouët, J.-F. 2020-11-19 doi:10.1101/2020.11.17.387951 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ Ultrafast Brownian-ratchet mechanism for protein translocation by a AAA+ machine ]]> https://biorxiv.org/content/10.1101/2020.11.19.384313v1?rss=1 Mazal, H. A. Iljina, M. Riven, I. Haran, G. 2020-11-19 doi:10.1101/2020.11.19.384313 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ SARS-CoV-2 utilizes a multipronged strategy to suppress host protein synthesis ]]> https://biorxiv.org/content/10.1101/2020.11.25.398578v1?rss=1 Finkel, Y. Gluck, A. Winkler, R. Nachshon, A. Mizrahi, O. Lubelsky, Y. Zuckerman, B. Slobodin, B. Yahalom-Ronen, Y. Tamir, H. Ulitsky, I. Israely, T. Paran, N. Schwartz, M. Stern-Ginossar, N. 2020-11-25 doi:10.1101/2020.11.25.398578 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ Tumor irradiation combined with vascular-targeted photodynamic therapy enhances anti-tumor effects in preclinical prostate cancer. ]]> https://biorxiv.org/content/10.1101/2020.11.26.400283v1?rss=1 Sjoberg, H. T. Philippou, Y. J. Magnussen, A. L. Tullis, I. D. Bridges, E. Chatrian, A. Loefebvre, J. Tam, K. H. Murphy, E. A. Rittscher, J. Preise, D. Agemy, L. Yechezkel, T. Smart, S. C. Kinchesh, P. Gilchrist, S. Allen, D. P. Scheiblin, D. A. Lockett, S. J. Wink, D. A. Lamb, A. D. Mills, I. G. Harris, A. Muschel, R. J. Vojnovic, B. Scherz, A. Hamdy, F. C. Bryant, R. J. 2020-11-26 doi:10.1101/2020.11.26.400283 Cold Spring Harbor Laboratory Press 2020-11-26 <![CDATA[ Bringing BOS to light: Uncovering the key enzyme in the biosynthesis of the neurotoxin β-ODAP in Grass Pea (Lathyrus sativus L.) ]]> https://biorxiv.org/content/10.1101/2020.11.29.402396v1?rss=1 Goldsmith, M. Barad, S. Knafo, M. Savidor, A. Ben-Dor, S. Brandis, A. Mehlman, T. Peleg, Y. Albeck, S. Dym, O. Benzeev, E. Reich, Z. 2020-11-29 doi:10.1101/2020.11.29.402396 Cold Spring Harbor Laboratory Press 2020-11-29 <![CDATA[ Hypothalamic glucocorticoid receptor in CRF neurons is essential for HPA axis habituation to repeated stressor ]]> https://biorxiv.org/content/10.1101/2020.11.30.402024v1?rss=1 Dournes, C. Dine, J. Lopez, J.-P. Brivio, E. Anderzhanova, E. Roeh, S. Kuehne, C. Holzapfel, M. Huettl, R.-E. Stoffel, R. Tietze, L. Eggert, C. Schieven, M. Jakovcevski, M. Deussing, J. M. Chen, A. 2020-11-30 doi:10.1101/2020.11.30.402024 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ A Novel Role for Nucleolin in Splice Site Selection ]]> https://biorxiv.org/content/10.1101/2020.12.02.402354v1?rss=1 Shefer, K. Boulos, A. Gotea, V. Chaim, Y. B. Sperling, J. Elnitski, L. Sperling, R. 2020-12-03 doi:10.1101/2020.12.02.402354 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ TENT4A poly(A) polymerase regulates translesion DNA synthesis and is mutated in endometrial cancer ]]> https://biorxiv.org/content/10.1101/2020.12.03.409367v1?rss=1 Swain, U. Sehrawat, U. Sarusi-Portuguez, A. Friedlander, G. Rotkopf, R. Ebert, C. Paz-Elizur, T. Dikstein, R. Carell, T. Geacintov, N. Livneh, Z. 2020-12-03 doi:10.1101/2020.12.03.409367 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ An opponent process for alcohol addiction based on changes in endocrine gland mass ]]> https://biorxiv.org/content/10.1101/2020.12.03.410365v1?rss=1 Karin, O. Raz, M. Alon, U. 2020-12-03 doi:10.1101/2020.12.03.410365 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Canonical Wnt signaling exerts bidirectional control on choroid plexus epithelial development ]]> https://biorxiv.org/content/10.1101/2020.12.08.415588v1?rss=1 Parichha, A. Suresh, V. Chatterjee, M. Khsirsagar, A. Ben-Reuven, L. Olender, T. Taketo, M. M. Radosevic, V. Bobic-Rasonja, M. Trinski, S. Jovanov Milosevic, N. Reiner, O. Tole, S. 2020-12-09 doi:10.1101/2020.12.08.415588 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ The context-dependent, combinatorial logic of BMP signaling ]]> https://biorxiv.org/content/10.1101/2020.12.08.416503v1?rss=1 Klumpe, H. E. Langley, M. A. Linton, J. M. Su, C. J. Antebi, Y. E. Elowitz, M. B. 2020-12-08 doi:10.1101/2020.12.08.416503 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ Translational control as a novel regulator of gradient sensing and chemotropism in yeast ]]> https://biorxiv.org/content/10.1101/2020.12.13.422562v1?rss=1 20 novel positive and negative regulators of pheromone gradient sensing, chemotropism, shmoo development, and mating. Aside from known regulators of exocytosis and endocytosis, genes involved in translational control downstream of the G-protein-regulated pheromone and filamentous growth MAPK pathways were identified. These include the Scp160 RNA-binding protein and the Asc1, Rpl12b, and Rpl19b ribosomal proteins (RPs). Importantly, we demonstrate that pheromone treatment and G (Gpa1) activation stimulate Scp160 binding to (and inhibition of) Asc1, which acts downstream of glucose-activated G (Gpa2) on the filamentous growth pathway. Moreover, we identify both Rpl12b and Rpl19b as RP paralog-specific positive regulators of translation of mating components, including Scp160. Thus, opposing MAPK pathways may converge at the level of translational control to regulate signaling output. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC="FIGDIR/small/422562v2_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@3944e1org.highwire.dtl.DTLVardef@1d9204eorg.highwire.dtl.DTLVardef@1d7e902org.highwire.dtl.DTLVardef@2bfc6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gelin-Licht, R. Conlon, P. J. Singh, R. Baez, C. Gal, L. Schuldiner, M. Levchenko, A. Gerst, J. E. 2020-12-13 doi:10.1101/2020.12.13.422562 Cold Spring Harbor Laboratory Press 2020-12-13 <![CDATA[ Coordinating the morphogenesis-differentiation balance by tweaking the cytokinin-gibberellin equilibrium ]]> https://biorxiv.org/content/10.1101/2020.12.14.422551v1?rss=1 Israeli, A. Burko, Y. Shleizer-Burko, S. Daphne Zelnik, I. Sela, N. R. Hajirezaei, M. Fernie, A. R. Tohge, T. Ori, N. Bar, M. 2020-12-15 doi:10.1101/2020.12.14.422551 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Frequency matters: Up- and Down-Regulation of Dopamine Tone Induces Similar Frequency Shifts in Cortico-Basal Ganglia Beta Oscillations ]]> https://biorxiv.org/content/10.1101/2020.12.14.422621v1?rss=1 Iskhakova, L. Rappel, P. Fonar, G. Marmor, O. Paz, R. Israel, Z. Eitan, R. Bergman, H. 2020-12-14 doi:10.1101/2020.12.14.422621 Cold Spring Harbor Laboratory Press 2020-12-14 <![CDATA[ A nuclear role for ARGONAUTE-2 in regulation of neuronal alternative polyadenylation ]]> https://biorxiv.org/content/10.1101/2020.12.15.422806v1?rss=1 Ravid, R. Siany, A. Rivkin, N. Eitan, C. Marmor-Kollet, H. Yanowski, E. Savidor, A. Levin, Y. Rot, G. Meister, G. Hornstein, E. 2020-12-15 doi:10.1101/2020.12.15.422806 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ DNA demethylation switches the drivers of Foxp3 expression to maintain regulatory T cell identity ]]> https://biorxiv.org/content/10.1101/2020.12.16.423137v1?rss=1 Li, J. Xu, B. Zong, X. He, M. Fan, Y. Cross, R. Hanna, J. H. Feng, Y. 2020-12-16 doi:10.1101/2020.12.16.423137 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ An enhanced yeast display platform demonstrates the binding plasticity under various selection pressures ]]> https://biorxiv.org/content/10.1101/2020.12.16.423176v1?rss=1 Zahradnik, J. Dey, D. Marciano, S. Schreiber, G. 2020-12-17 doi:10.1101/2020.12.16.423176 Cold Spring Harbor Laboratory Press 2020-12-17 <![CDATA[ Artificial Antigen Presenting Cells for Detection and Desensitisation of Auto-reactive T cells Associated with Type 1 Diabetes ]]> https://biorxiv.org/content/10.1101/2020.12.26.424333v1?rss=1 Artzy-Schnirman, A. Abu-Shah, E. Chandrawati, R. Altman, E. Yusuf, N. Wang, S.-T. Ramos, J. Hansel, C. Haus-cohen, M. Dahan, R. Arif, S. Dustin, M. L. Peakman, M. Reiter, Y. Stevens, M. M. 2020-12-27 doi:10.1101/2020.12.26.424333 Cold Spring Harbor Laboratory Press 2020-12-27 <![CDATA[ Neuronal regulated Ire1-dependent mRNA decay controls germline differentiation in C. elegans ]]> https://biorxiv.org/content/10.1101/2020.12.29.424718v1?rss=1 Levi-Ferber, M. Shalash, R. Le-Thomas, A. Salzberg, Y. Shurgi, M. Ashkenazi, A. Henis-Korenblit, S. 2020-12-29 doi:10.1101/2020.12.29.424718 Cold Spring Harbor Laboratory Press 2020-12-29 <![CDATA[ Modelling cellular spreading and emergence of motility in the presence of curved membrane proteins and active cytoskeleton forces ]]> https://biorxiv.org/content/10.1101/2021.01.02.425086v1?rss=1 Sadhu, R. K. Penic, S. Iglic, A. Gov, N. S. 2021-01-04 doi:10.1101/2021.01.02.425086 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ scRNA-seq Reveals A Macrophage Subset That Provides A Splenic Replication Niche For Intracellular Salmonella ]]> https://biorxiv.org/content/10.1101/2021.01.04.425175v1?rss=1 Hoffman, D. Avraham, R. Tevet, Y. Rosenberg, G. Vainman, L. Solomon, A. Hen-Avivi, S. Bossel Ben-Moshe, N. 2021-01-04 doi:10.1101/2021.01.04.425175 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Cholesteryl Hemiazelate Induces Lysosome Dysfunction and Exocytosis in Macrophages ]]> https://biorxiv.org/content/10.1101/2021.01.05.422575v1?rss=1 Domingues, N. Calado, R. D. A. Brito, P. Matthiesen, R. Ramalho, J. Soares, M. I. L. Pereira, T. Oliveira, L. Vicente, J. Wong, L. H. Cho, S. M. Simoes, I. Sampaio, J. Klose, C. Surma, M. A. Almeida, M. S. Rodrigues, G. Goncalves, P. A. Ferreira, J. Simons, K. Melo, T. Peden, A. Guimas Almeida, C. Futter, C. E. Futerman, A. H. Vaz, W. Vieira, O. V. 2021-01-05 doi:10.1101/2021.01.05.422575 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Physical theory of biological noise buffering by multi-component phase separation ]]> https://biorxiv.org/content/10.1101/2021.01.05.425486v1?rss=1 Deviri, D. Safran, S. 2021-01-06 doi:10.1101/2021.01.05.425486 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Antiviral activity of bacterial TIR domains via signaling molecules that trigger cell death ]]> https://biorxiv.org/content/10.1101/2021.01.06.425286v1?rss=1 Ofir, G. Herbst, E. Baroz, M. Cohen, D. Millman, A. Doron, S. Tal, N. Malheiro, D. B. A. Malitsky, S. Amitai, G. Sorek, R. 2021-01-06 doi:10.1101/2021.01.06.425286 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ SARS-CoV-2 RBD in vitro evolution follows contagious mutation spread, yet generates an able infection inhibitor ]]> https://biorxiv.org/content/10.1101/2021.01.06.425392v1?rss=1 Zahradnik, J. Marciano, S. Shemesh, M. Zoler, E. Chiaravalli, J. Meyer, B. Dym, O. Elad, N. Schreiber, G. 2021-01-06 doi:10.1101/2021.01.06.425392 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Dynamics on the web: spiders use physical rules to solve complex tasks in mate search and competition ]]> https://biorxiv.org/content/10.1101/2021.01.10.426127v1?rss=1 Haluts, A. Garza Reyes, S. F. Gorbonos, D. Jordan, A. Gov, N. S. 2021-01-11 doi:10.1101/2021.01.10.426127 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Mutants libraries reveal negative design shielding proteins from mis-assembly and re-localization in cells ]]> https://biorxiv.org/content/10.1101/2021.01.20.427404v1?rss=1 Garcia-Seisdedos, H. Levin, T. Shapira, G. Freud, S. Levy, E. D. 2021-01-21 doi:10.1101/2021.01.20.427404 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Evidence for efficient non-evaporative leaf-to-air heat dissipation in a pine forest under drought conditions ]]> https://biorxiv.org/content/10.1101/2021.02.01.429145v1?rss=1 Muller, J. D. Rotenberg, E. Tatarinov, F. Oz, I. Yakir, D. 2021-02-02 doi:10.1101/2021.02.01.429145 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Diffusion of the disordered E-cadherin tail on β-catenin ]]> https://biorxiv.org/content/10.1101/2021.02.03.429507v1?rss=1 Wiggers, F. Wohl, S. Dubovetskyi, A. Rosenblum, G. Zheng, W. Hofmann, H. 2021-02-03 doi:10.1101/2021.02.03.429507 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Resolving the conflict between antibiotic production and rapid growth by recognition of peptidoglycan of susceptible competitors ]]> https://biorxiv.org/content/10.1101/2021.02.07.430110v1?rss=1 Maan, H. Friedman, J. Kolodkin-Gal, I. 2021-02-07 doi:10.1101/2021.02.07.430110 Cold Spring Harbor Laboratory Press 2021-02-07 <![CDATA[ Consistent population activity on the scale of minutes in the mouse hippocampus ]]> https://biorxiv.org/content/10.1101/2021.02.07.430172v1?rss=1 Liu, Y. Levy, S. J. Mau, W. Geva, N. Rubin, A. Ziv, Y. Hasselmo, M. Howard, M. 2021-02-08 doi:10.1101/2021.02.07.430172 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ The ecological significance of extracellular vesicles in modulating host-virus interactions during algal blooms ]]> https://biorxiv.org/content/10.1101/2021.02.10.430559v1?rss=1 Schatz, D. Schleyer, G. Saltvedt, M. R. Sandaa, R.-A. Feldmesser, E. Vardi, A. 2021-02-10 doi:10.1101/2021.02.10.430559 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Substrates modulate charge-reorganization allosteric effects in protein-protein association ]]> https://biorxiv.org/content/10.1101/2021.02.11.430712v1?rss=1 Banerjee-Ghosh, K. Ghosh, S. Levy, D. Riven, I. Naaman, R. Haran, G. 2021-02-12 doi:10.1101/2021.02.11.430712 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ Local thermodynamics governs the formation and dissolution of protein condensates in living cells ]]> https://biorxiv.org/content/10.1101/2021.02.11.430794v1?rss=1 Fritsch, A. W. Diaz-Delgadillo, A. F. Adame-Arana, O. Hoege, C. Kreysing, M. Mittasch, M. Leaver, M. Hyman, A. A. Julicher, F. Weber, C. A. 2021-02-12 doi:10.1101/2021.02.11.430794 Cold Spring Harbor Laboratory Press 2021-02-12 <![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[ The Serine Protease HtrA2 mediates radiation-induced senescence in cancer cells ]]> https://biorxiv.org/content/10.1101/2021.02.17.431668v1?rss=1 Hammer, L. Levin-Salomon, V. Yaeli-Slonim, N. Weiss, M. Dekel-Bird, N. P. Olender, T. Porat, Z. Winograd-Katz, S. Savidor, A. Levin, Y. Bialik, S. Geiger, B. Kimchi, A. 2021-02-17 doi:10.1101/2021.02.17.431668 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Optogenetic silencing of neurotransmitter release with a naturally occurring invertebrate rhodopsin ]]> https://biorxiv.org/content/10.1101/2021.02.18.431673v1?rss=1 Mahn, M. Saraf-Sinik, I. Patil, P. Pulin, M. Bitton, E. Karalis, N. Bruentgens, F. Palgi, S. Gat, A. Dine, J. Wietek, J. Davidi, I. Levy, R. Litvin, A. Zhou, F. Sauter, K. Soba, P. Schmitz, D. Luthi, A. Rost, B. R. Wiegert, J. S. Yizhar, O. 2021-02-18 doi:10.1101/2021.02.18.431673 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Physically interacting beta-delta pairs in the regenerating pancreas revealed by single cell sequencing ]]> https://biorxiv.org/content/10.1101/2021.02.22.432216v1?rss=1 Yanowski, E. Yacovzada, N. S. David, E. Giladi, A. Jaitin, D. Farack, L. Egozi, A. Ben-Zvi, D. Itzkovitz, S. Amit, I. Hornstein, E. 2021-02-22 doi:10.1101/2021.02.22.432216 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ Automatic recognition of macaque facial expressions for detection of affective states ]]> https://biorxiv.org/content/10.1101/2021.02.24.432760v1?rss=1 Morozov, A. Parr, L. Gothard, K. M. Paz, R. Pryluk, R. 2021-02-25 doi:10.1101/2021.02.24.432760 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning ]]> https://biorxiv.org/content/10.1101/2021.03.01.431313v1?rss=1 1 million paired whole-cell and nuclear annotations for tissue images from nine organs and six imaging platforms. We created Mesmer, a deep learning-enabled segmentation algorithm trained on TissueNet that performs nuclear and whole-cell segmentation in tissue imaging data. We demonstrated that Mesmer has better speed and accuracy than previous methods, generalizes to the full diversity of tissue types and imaging platforms in TissueNet, and achieves human-level performance for whole-cell segmentation. Mesmer enabled the automated extraction of key cellular features, such as subcellular localization of protein signal, which was challenging with previous approaches. We further showed that Mesmer could be adapted to harness cell lineage information present in highly multiplexed datasets. We used this enhanced version to quantify cell morphology changes during human gestation. All underlying code and models are released with permissive licenses as a community resource. ]]> Greenwald, N. F. Miller, G. Moen, E. Kong, A. Kagel, A. Fullaway, C. C. McIntosh, B. J. Leow, K. Schwartz, M. S. Dougherty, T. Pavelchek, C. Cui, S. Camplisson, I. Bar-Tal, O. Singh, J. Fong, M. Chaudhry, G. Abraham, Z. Moseley, J. Warshawsky, S. Soon, E. Greenbaum, S. Risom, T. Hollmann, T. Keren, L. Graf, W. Angelo, M. Van Valen, D. 2021-03-02 doi:10.1101/2021.03.01.431313 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ FAM57B is a modulator of ceramide synthesis that regulates sphingolipid homeostasis and synaptic composition in the developing brain ]]> https://biorxiv.org/content/10.1101/2021.03.02.433619v1?rss=1 Tomasello, D. L. Kim, J. L. Khodour, Y. McCammon, J. M. Mitalipova, M. Jaenisch, R. Futerman, A. H. Sive, H. 2021-03-02 doi:10.1101/2021.03.02.433619 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance ]]> https://biorxiv.org/content/10.1101/2021.03.12.435202v1?rss=1 Tsai, K. Stojkovic, V. Noda-Garcia, L. Young, I. D. Myasnikov, A. G. Kleinman, J. Palla, A. Floor, S. N. Frost, A. Fraser, J. S. Tawfik, D. S. Galonic Fujimori, D. 2021-03-13 doi:10.1101/2021.03.12.435202 Cold Spring Harbor Laboratory Press 2021-03-13 <![CDATA[ Contrast adaptation improves spatial integration ]]> https://biorxiv.org/content/10.1101/2021.03.14.435290v1?rss=1 Pinchuk Yacobi, N. Sagi, D. 2021-03-15 doi:10.1101/2021.03.14.435290 Cold Spring Harbor Laboratory Press 2021-03-15 <![CDATA[ In-situ fiducial markers for 3D correlative cryo- fluorescence and FIB-SEM imaging ]]> https://biorxiv.org/content/10.1101/2021.03.14.435311v1?rss=1 Scher, N. Rechav, K. Paul-Gilloteaux, P. Avinoam, O. 2021-03-15 doi:10.1101/2021.03.14.435311 Cold Spring Harbor Laboratory Press 2021-03-15 <![CDATA[ Cytoplasmic forces functionally reorganize nuclear condensates in oocytes ]]> https://biorxiv.org/content/10.1101/2021.03.15.434387v1?rss=1 Al Jord, A. Letort, G. Eichmuller, A. Chanet, S. HUYNH, J.-R. Gov, N. Voituriez, R. Terret, M.-E. Verlhac, M.-H. 2021-03-16 doi:10.1101/2021.03.15.434387 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ BCL-XL blockage in TNBC models confers vulnerability to inhibition of specific cell cycle regulators ]]> https://biorxiv.org/content/10.1101/2021.03.16.435600v1?rss=1 Castellanet, O. Ahmad, F. Vinik, Y. Mills, G. B. Habermann, B. H. Borg, J.-P. H. Lev, S. Lamballe, F. Maina, F. 2021-03-17 doi:10.1101/2021.03.16.435600 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Sacsin cotranslational degradation causes autosomal recessive spastic ataxia of Charlevoix-Saguenay ]]> https://biorxiv.org/content/10.1101/2021.03.16.435646v1?rss=1 Maltecca, F. Longo, F. De Ritis, D. Miluzio, A. Fraticelli, D. Baets, J. Scarlato, M. Santorelli, F. M. Biffo, S. 2021-03-17 doi:10.1101/2021.03.16.435646 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ A novel theoretical framework for simultaneous measurement of excitatory and inhibitory conductances ]]> https://biorxiv.org/content/10.1101/2021.03.30.437555v1?rss=1 Muller-Komorowska, D. Parabucki, A. Elyasaf, G. Katz, Y. Beck, H. Lampl, I. 2021-03-30 doi:10.1101/2021.03.30.437555 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ Inhibition of MRN activity by a telomere protein motif ]]> https://biorxiv.org/content/10.1101/2021.03.30.437761v1?rss=1 Bianchi, A. Carr, A. Cejka, P. Cannavo, E. Foster, W. Smith, C. Maddalena, M. Chahwan, C. Watson, A. Khayat, F. Alshmery, M. 2021-03-31 doi:10.1101/2021.03.30.437761 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ RNA-controlled nucleocytoplasmic shuttling of mRNA decay factors regulates mRNA synthesis and initiates a novel mRNA decay pathway ]]> https://biorxiv.org/content/10.1101/2021.04.01.437949v1?rss=1 Chattopadhyay, S. Garcia-Martinez, J. Haimovich, G. Khwaja, A. Barkai, O. Ghosh, A. Chuarzman, S. G. Schuldiner, M. Elran, R. Rosenberg, M. Bohnsack, K. Bohnsack, M. Perez-Ortin, J. E. Choder, M. 2021-04-01 doi:10.1101/2021.04.01.437949 Cold Spring Harbor Laboratory Press 2021-04-01 <![CDATA[ Novel zebrafish mutants reveal new roles for Apolipoprotein B during embryonic development and pathological conditions ]]> https://biorxiv.org/content/10.1101/2021.04.01.437990v1?rss=1 Tempelhof, H. Moshe, N. Avraham-Davidi, I. Yaniv, K. 2021-04-02 doi:10.1101/2021.04.01.437990 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ The neutralization potency of anti-SARS-CoV-2 therapeutic human monoclonal antibodies is retained against novel viral variants ]]> https://biorxiv.org/content/10.1101/2021.04.01.438035v1?rss=1 Rosenfeld, R. Mazor, O. Makdasi, E. Zvi, A. Alcalay, R. Noy-Porat, T. Peretz, E. Mechaly, A. Levy, Y. Epstein, E. Chitlaru, T. Paran, N. Tamir, H. Zimhony, O. Weiss, S. Mandelboim, M. Mendelson, E. Zuckerman, N. Nemet, I. Kliker, L. Yitzhaki, S. Shapira, S. C. Israely, T. 2021-04-01 doi:10.1101/2021.04.01.438035 Cold Spring Harbor Laboratory Press 2021-04-01 <![CDATA[ An emerging SARS-CoV-2 mutant evading cellular immunity and increasing viral infectivity ]]> https://biorxiv.org/content/10.1101/2021.04.02.438288v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@153428forg.highwire.dtl.DTLVardef@136ca5aorg.highwire.dtl.DTLVardef@1ee490org.highwire.dtl.DTLVardef@2fe478_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Motozono, C. Toyoda, M. Zahradnik, J. Ikeda, T. Saito, A. Tan, T. S. Ngare, I. Nasser, H. Kimura, I. Uriu, K. Kosugi, Y. Torii, S. Yonekawa, A. Shimono, N. Nagasaki, Y. Minami, R. Toya, T. Sekiya, N. Fukuhara, T. Matsuura, Y. Schreiber, G. The Genotype to Phenotype Japan (G2P-Japan) consortium, Nakagawa, S. Ueno, T. Sato, K. 2021-04-05 doi:10.1101/2021.04.02.438288 Cold Spring Harbor Laboratory Press 2021-04-05 <![CDATA[ Spatial expression programs of the intestinal follicle-associated epithelium ]]> https://biorxiv.org/content/10.1101/2021.04.06.438564v1?rss=1 Cohen, N. Massalha, H. Ben-Moshe, S. Egozi, A. Rozenberg, M. Bahar Halpern, K. Itzkovitz, S. 2021-04-07 doi:10.1101/2021.04.06.438564 Cold Spring Harbor Laboratory Press 2021-04-07 <![CDATA[ Uncovering the modified immunopeptidome reveals insights into principles of PTM-driven antigenicity ]]> https://biorxiv.org/content/10.1101/2021.04.10.438991v1?rss=1 Kacen, A. Javitt, A. Kramer, M. P. Morgenstern, D. Tsaban, T. Solomon, A. Teo, G. C. da Veiga Leprevost, F. Barnea, E. Yu, F. Admon, A. Eisenbach, L. Cafri, G. Schueler-Furman, O. Levin, Y. Nesvizhskii, A. I. Merbl, Y. 2021-04-11 doi:10.1101/2021.04.10.438991 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Hsp40s display class-specific binding profiles, serving complementary roles in the prevention of tau amyloid formation ]]> https://biorxiv.org/content/10.1101/2021.04.11.439324v1?rss=1 Irwin, R. Faust, O. Petrovic, I. Wolf, S. G. Hofmann, H. Rosenzweig, R. 2021-04-11 doi:10.1101/2021.04.11.439324 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis ]]> https://biorxiv.org/content/10.1101/2021.04.12.439528v1?rss=1 Jayaraman, V. Lee, D. J. Elad, N. Vimer, S. Sharon, M. Fraser, J. S. Tawfik, D. S. 2021-04-12 doi:10.1101/2021.04.12.439528 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Inhibition of gibberellin accumulation by water deficiency promotes fast and long-term 'drought avoidance' responses in tomato ]]> https://biorxiv.org/content/10.1101/2021.04.13.439675v1?rss=1 Shohat, H. Cheriker, H. Vasuki, H. Illouz-Eliaz, N. Blum, S. Amsellem, Z. Tarkowska, D. Aharoni, A. Eshed, Y. Weiss, D. 2021-04-14 doi:10.1101/2021.04.13.439675 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Actin polymerization and crosslinking drive left-right asymmetry in single cell and cell collectives ]]> https://biorxiv.org/content/10.1101/2021.04.22.440942v1?rss=1 Tee, Y. H. Goh, W. J. Yong, X. Ong, H. T. Hu, J. Tay, I. Y. Y. Shi, S. Jalal, S. Barnett, S. F. H. Kanchanawong, P. Huang, W. Yan, J. Thiagarajan, V. Bershadsky, A. D. 2021-04-22 doi:10.1101/2021.04.22.440942 Cold Spring Harbor Laboratory Press 2021-04-22 <![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[ Synthetic cell-based materials extract positional information from morphogen gradients ]]> https://biorxiv.org/content/10.1101/2021.04.25.441320v1?rss=1 Dupin, A. Aufinger, L. Styazhkin, I. Rothfischer, F. Kaufmann, B. Schwarz, S. Galensowske, N. Clausen-Schaumann, H. Simmel, F. C. 2021-04-26 doi:10.1101/2021.04.25.441320 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Antiviral defense via nucleotide depletion in bacteria ]]> https://biorxiv.org/content/10.1101/2021.04.26.441389v1?rss=1 Tal, N. Millman, A. Stokar-Avihail, A. Fedorenko, T. Leavitt, A. Melamed, S. Yirmiya, E. Abraham, C. Amitai, G. Sorek, R. 2021-04-26 doi:10.1101/2021.04.26.441389 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Mitochondrial ribosomal proteins developed unconventional mitochondrial targeting signals due to structural constraints ]]> https://biorxiv.org/content/10.1101/2021.04.26.441393v1?rss=1 Bykov, Y. Flohr, T. Boos, F. Herrmann, J. M. Schuldiner, M. 2021-04-26 doi:10.1101/2021.04.26.441393 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Entropy Regularized Deconvolution of Cellular Cryo-Transmission Electron Tomograms ]]> https://biorxiv.org/content/10.1101/2021.04.26.441469v1?rss=1 Croxford, M. Elbaum, M. Arigovindan, M. Kam, Z. Agard, D. A. Villa, E. Sedat, J. 2021-04-26 doi:10.1101/2021.04.26.441469 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Generation of specialized blood vessels through transdifferentiation of lymphatic endothelial cells ]]> https://biorxiv.org/content/10.1101/2021.04.28.441726v1?rss=1 Das, R. N. Bassi, I. Han, Y. Lambiase, G. Tevet, Y. Moshe, N. Safriel, S. R. Nicenboim, J. Brueckner, M. Hirsch, D. Eilam-Altstadter, R. Herzog, W. Poss, K. D. Yaniv, K. 2021-04-29 doi:10.1101/2021.04.28.441726 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Covalent Flexible Peptide Docking in Rosetta ]]> https://biorxiv.org/content/10.1101/2021.05.06.441297v1?rss=1 Tivon, B. Gabizon, R. Somsen, B. A. Cossar, P. J. Ottmann, C. London, N. 2021-05-06 doi:10.1101/2021.05.06.441297 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Coordinated regulation of WNT/β-catenin, c-Met, and Integrin signalling pathways by miR-193b controls triple negative breast cancer metastatic traits ]]> https://biorxiv.org/content/10.1101/2021.05.10.443372v1?rss=1 Giacomelli, C. Jung, J. Wachter, A. Ibing, S. Will, R. Mannsperger, H. Uhlmann, S. Sahin, O. Yarden, Y. Beissbarth, T. Korf, U. Körner, C. Wiemann, S. 2021-05-10 doi:10.1101/2021.05.10.443372 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation ]]> https://biorxiv.org/content/10.1101/2021.05.10.443517v1?rss=1 Lopez, R. Li, B. Keren-Shaul, H. Boyeau, P. Kedmi, M. Pilzer, D. Jelinski, A. David, E. Wagner, A. Addadi, Y. Jordan, M. I. Amit, I. Yosef, N. 2021-05-11 doi:10.1101/2021.05.10.443517 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ Generation and timing of graded responses to morphogen gradients ]]> https://biorxiv.org/content/10.1101/2021.05.11.443662v1?rss=1 Carmon, S. Jonas, F. Barkai, N. Schejter, E. D. Shilo, B.-Z. 2021-05-12 doi:10.1101/2021.05.11.443662 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ A chemotactic sensor controls Salmonella-host cell interaction ]]> https://biorxiv.org/content/10.1101/2021.05.14.443827v1?rss=1 Hoffmann, S. Gendera, K. Schmidt, C. Kirchweger, P. Imhof, A. Bogdan, C. Muller, Y. A. Hensel, M. Gerlach, R. G. 2021-05-15 doi:10.1101/2021.05.14.443827 Cold Spring Harbor Laboratory Press 2021-05-15 <![CDATA[ Positive Selection and Heat-Response Transcriptomes Reveal Adaptive Features of the Arabidopsis Desert Relative, Anastatica hierochuntica ]]> https://biorxiv.org/content/10.1101/2021.05.23.445339v1?rss=1 Eshel, G. Duppen, N. Wang, G. Oh, D.-H. Kazachkova, Y. Herzyk, P. Amtmann, A. Gordon, M. Chalifa-Caspi, V. Oscar, M. A. Bar-David, S. Marshall-Colon, A. Dassanayake, M. Barak, S. 2021-05-23 doi:10.1101/2021.05.23.445339 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ SARS-CoV-2 convergent evolution as a guide to explore adaptive advantage ]]> https://biorxiv.org/content/10.1101/2021.05.24.445534v1?rss=1 Zahradnik, J. Nunvar, J. Schreiber, G. 2021-05-25 doi:10.1101/2021.05.24.445534 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ The geometry of decision-making ]]> https://biorxiv.org/content/10.1101/2021.05.26.445795v1?rss=1 Sridhar, V. H. Li, L. Gorbonos, D. Nagy, M. Schell, B. R. Sorochkin, T. Gov, N. S. Couzin, I. D. 2021-05-27 doi:10.1101/2021.05.26.445795 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Using a recently approved tumor mutational burden biomarker to stratify patients for immunotherapy may introduce a sex bias ]]> https://biorxiv.org/content/10.1101/2021.05.28.446208v1?rss=1 Sinha, N. Sinha, S. Cheng, K. Madan, S. Erez, A. Ryan, B. Schaffer, A. A. Aldape, K. Ruppin, E. 2021-05-29 doi:10.1101/2021.05.28.446208 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ Pseudo-mutant p53 as a targetable phenotype of DNMT3A-mutated pre-leukemia ]]> https://biorxiv.org/content/10.1101/2021.05.30.446347v1?rss=1 Tuval, A. Brilon, Y. Ezogy, H. Moskovitz, Y. Biezuner, T. Leshkowitz, D. Salame, T. M. Minden, M. D. Tal, P. Rotter, V. Oren, M. Kaushansky, N. Shlush, L. I. 2021-05-30 doi:10.1101/2021.05.30.446347 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ Mediobasal hypothalamic FKBP51 acts as a molecular switch linking autophagy to whole-body metabolism ]]> https://biorxiv.org/content/10.1101/2021.05.31.445775v1?rss=1 Haeusl, A. S. Brix, L. M. Bajaj, T. Poehlmann, M. L. Hafner, K. De Angelis, M. Nagler, J. Balsevich, G. Schramm, K.-W. Giavalisco, P. Chen, A. Schmidt, M. V. Gassen, N. C. 2021-05-31 doi:10.1101/2021.05.31.445775 Cold Spring Harbor Laboratory Press 2021-05-31 <![CDATA[ Identification of Pex34p as a component of the peroxisomal de novo biogenesis machinery in yeast ]]> https://biorxiv.org/content/10.1101/2021.05.31.446392v1?rss=1 Radke, J. Nagotu, S. Girzalsky, W. Chakraborty, A. Deckers, M. Schuldiner, M. Zalckvar, E. Erdmann, R. 2021-05-31 doi:10.1101/2021.05.31.446392 Cold Spring Harbor Laboratory Press 2021-05-31 <![CDATA[ Non-Coding Genetic Analysis Implicates Interleukin 18 Receptor Accessory Protein 3'UTR in Amyotrophic Lateral Sclerosis ]]> https://biorxiv.org/content/10.1101/2021.06.03.446863v1?rss=1 25,000 variants in untranslated regions of 6,139 amyotrophic lateral sclerosis (ALS) whole-genomes and 70,403 non-ALS controls. We identified Interleukin-18 Receptor Accessory Protein (IL18RAP) 3'UTR variants significantly enriched in non-ALS genomes, replicated in an independent cohort, and associated with a five-fold reduced risk of developing ALS. Variant IL18RAP 3'UTR reduces mRNA stability and the binding of RNA-binding proteins. Variant IL18RAP 3'UTR further dampens neurotoxicity of human iPSC-derived C9orf72-ALS microglia that depends on NF-{kappa}B signaling. Therefore, the variant IL18RAP 3'UTR provides survival advantage for motor neurons co-cultured with C9-ALS microglia. The study reveals direct genetic evidence and therapeutic targets for neuro-inflammation, and emphasizes the importance of non-coding genetic association studies. One Sentence SummaryNon-coding genetic variants in IL-18 receptor 3UTR decrease ALS risk by modifying IL-18-NF-{kappa}B signaling in microglia. ]]> Eitan, C. Barkan, E. Olender, T. van Eijk, K. R. Moisse, M. Farhan, S. M. K. Siany, A. Hung, S.-T. Yacovzada, N. Cooper-Knock, J. Kenna, K. P. van der Spek, R. A. A. Sproviero, W. Al Khleifat, A. Iacoangeli, A. Shatunov, A. S. Jones, A. R. Chapnik, E. Rothschild, D. Weissbrod, O. Werneburg, S. Schafer, D. P. Brown, R. H. Shaw, P. J. Van Damme, P. van den Berg, L. H. Phatnani, H. P. Segal, E. Ichida, J. K. Al-Chalabi, A. Veldink, J. H. Project MinE ALS Sequencing Consortium, NYGC ALS Consortium, Hornstein, E. 2021-06-05 doi:10.1101/2021.06.03.446863 Cold Spring Harbor Laboratory Press 2021-06-05 <![CDATA[ Quantifying the effects of the plant root on antibiotic production in the beneficial bacterium B. subtilis ]]> https://biorxiv.org/content/10.1101/2021.06.03.446890v1?rss=1 Maan, H. Gilhar, O. Porath, Z. Kolodkin-Gal, I. 2021-06-03 doi:10.1101/2021.06.03.446890 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ Airborne bacteria over oceans shed light on global biogeodiversity patterns ]]> https://biorxiv.org/content/10.1101/2021.06.06.445733v1?rss=1 Lang-Yona, N. Flores, J. M. Haviv, R. Alberti, A. Poulain, J. Belser, C. Trainic, M. Gat, D. Ruscheweyh, H. J. Wincker, P. Sunagawa, S. Rudich, Y. Koren, I. Vardi, A. 2021-06-06 doi:10.1101/2021.06.06.445733 Cold Spring Harbor Laboratory Press 2021-06-06 <![CDATA[ Insulin is expressed by enteroendocrine cells during human fetal development ]]> https://biorxiv.org/content/10.1101/2021.06.07.447234v1?rss=1 Egozi, A. Llivichuzhca-Loja, D. McCourt, B. Farack, L. An, X. Wang, F. Chen, K. Konnikova, L. Itzkovitz, S. 2021-06-07 doi:10.1101/2021.06.07.447234 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Bacterial gasdermins reveal an ancient mechanism of cell death ]]> https://biorxiv.org/content/10.1101/2021.06.07.447441v1?rss=1 200 [A] pores that form a mesh-like structure and disrupt membrane integrity. These results demonstrate that caspase-mediated activation of gasdermins is an ancient form of regulated cell death shared between bacteria and animals. ]]> Johnson, A. G. Wein, T. Mayer, M. L. Duncan-Lowey, B. Yirmiya, E. Oppenheimer-Shaanan, Y. Amitai, G. Sorek, R. Kranzusch, P. J. 2021-06-07 doi:10.1101/2021.06.07.447441 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Cuticular Wax Composition is Essential for Plant Recovery Following Drought with Little Effect under Optimal Conditions ]]> https://biorxiv.org/content/10.1101/2021.06.08.447487v1?rss=1 Negin, B. Hen-Avivi, S. Almekias-Siegl, E. Shachar, L. Aharoni, A. 2021-06-09 doi:10.1101/2021.06.08.447487 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ A late-stage assembly checkpoint of the human mitochondrial ribosome large subunit ]]> https://biorxiv.org/content/10.1101/2021.06.09.447755v1?rss=1 Rebelo-Guiomar, P. Pellegrino, S. Dent, K. Sas- Chen, A. Miller-Fleming, L. Garone, C. Van Haute, L. Rogan, J. F. Dinan, A. M. Firth, A. E. Andrews, B. Whitworth, A. J. Schwartz, S. Warren, A. J. Minczuk, M. 2021-06-09 doi:10.1101/2021.06.09.447755 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ Enteric glial cells favour accumulation of anti-inflammatory macrophages during the resolution of muscularis inflammation ]]> https://biorxiv.org/content/10.1101/2021.06.10.447700v1?rss=1 Stakenborg, M. Abdurahiman, S. De Simone, V. Goverse, G. Stakenborg, N. Van Baarle, L. Wu, Q. Pirottin, D. Kim, J.-S. Maor, L. Pintelon, I. Thys, S. Boon, L. Hao, M. Van Ginderachter, J. Boeckxstaens, G. E. Timmermans, J.-P. Jung, S. Marichal, T. Ibiza, S. Matteoli, G. 2021-06-10 doi:10.1101/2021.06.10.447700 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Sniffing Out New Friends: Similarity in Body-Odor Predicts the Quality of Same-Sex None-Romantic Dyadic Interactions ]]> https://biorxiv.org/content/10.1101/2021.06.14.448352v1?rss=1 Ravreby, I. Snitz, K. Sobel, N. 2021-06-15 doi:10.1101/2021.06.14.448352 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ Genome instability drives epistatic adaptation in the human pathogen Leishmania ]]> https://biorxiv.org/content/10.1101/2021.06.15.448517v1?rss=1 Bussotti, G. Piel, L. Pescher, P. Domagalska, M. A. Rajan, K. S. Doniger, T. Hiregange, D. G. Myler, P. J. Unger, R. Michaeli, S. J. Spaeth, G. F. 2021-06-15 doi:10.1101/2021.06.15.448517 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ SPEAR: a proteomics approach for simultaneous protein expression and redox analysis ]]> https://biorxiv.org/content/10.1101/2021.06.17.448798v1?rss=1 Doron, S. Lampl, N. Savidor, A. Katina, C. Gabashvili, A. Levin, Y. Rosenwasser, S. 2021-06-17 doi:10.1101/2021.06.17.448798 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Emotion increases the similarity between neural representations of pictures, but not their perceived similarity. ]]> https://biorxiv.org/content/10.1101/2021.06.21.449164v1?rss=1 Riberto, M. Paz, R. Pobric, G. Talmi, D. 2021-06-22 doi:10.1101/2021.06.21.449164 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Realistic retinal modeling unravels the differential role of excitation and inhibition to starburst amacrine cells in direction selectivity ]]> https://biorxiv.org/content/10.1101/2021.06.22.449374v1?rss=1 Ezra-Tsur, E. Amsalem, O. Ankri, L. Patil, P. Segev, I. Rivlin, M. 2021-06-22 doi:10.1101/2021.06.22.449374 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Macrophage metabolism in the intestine is compartment-specific and regulated by the microbiota ]]> https://biorxiv.org/content/10.1101/2021.06.24.449804v1?rss=1 Scott, N. A. Lawson, M. Hodgetts, R. Hall, L. J. Mann, E. 2021-06-25 doi:10.1101/2021.06.24.449804 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Genome sequences of the five Sitopsis species of Aegilops and the origin of polyploid wheat B-subgenome ]]> https://biorxiv.org/content/10.1101/2021.07.05.444401v1?rss=1 Li, L. Zhang, Z. Wang, Z. Li, N. Sha, Y. Wang, X. Ding, N. Li, Y. Zhao, J. Wu, Y. Gong, L. Mafessoni, F. Levy, A. Liu, B. 2021-07-06 doi:10.1101/2021.07.05.444401 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Spontaneous pauses in firing of external pallidum neurons are associated with exploratory behavior ]]> https://biorxiv.org/content/10.1101/2021.07.06.451269v1?rss=1 Kaplan, A. Mizrahi-Kliger, A. D. Rappel, P. Iskhakova, L. Fonar, G. Israel, Z. Bergman, H. 2021-07-07 doi:10.1101/2021.07.06.451269 Cold Spring Harbor Laboratory Press 2021-07-07 <![CDATA[ Hippocampal Astrocytes Encode Reward Location ]]> https://biorxiv.org/content/10.1101/2021.07.07.451434v1?rss=1 Doron, A. Rubin, A. Benmelech-Chovav, A. Benaim, N. Carmi, T. Kreisel, T. Ziv, Y. Goshen, I. 2021-07-08 doi:10.1101/2021.07.07.451434 Cold Spring Harbor Laboratory Press 2021-07-08 <![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[ Fatty Alcohols, a Minor Component of the Tree Tobacco Surface Wax, Reduce Insect Herbivory ]]> https://biorxiv.org/content/10.1101/2021.07.15.452450v1?rss=1 Negin, B. Shachar, L. Meir, S. Ramirez, C. C. Horowitz, A. R. Jander, G. Aharoni, A. 2021-07-15 doi:10.1101/2021.07.15.452450 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ CRISPR screens for host factors critical for infection by SARS-CoV-2 variants of concern identify GATA6 as a central modulator of ACE2. ]]> https://biorxiv.org/content/10.1101/2021.07.19.452809v1?rss=1 Israeli, M. Finkel, Y. Israeli, O. Beth-Din, A. Cohen-Gihon, I. Yahalom-Rone, Y. Paran, N. Israely, T. Chitlaru, T. Elia, U. Cohen, O. Nemet, I. Kliker, L. Mandelboim, M. Stern-Ginossar, N. Bercovich-Kinori, A. 2021-07-20 doi:10.1101/2021.07.19.452809 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ A distinct CD115- erythro-myeloid precursor present at the maternal-embryonic interface and in the bone marrow of adult mice ]]> https://biorxiv.org/content/10.1101/2021.07.24.453629v1?rss=1 Tikoo, S. Jain, R. Martinez, B. Song, R. Wielscher, M. Rizzetto, S. Shaw, L. E. Mitchell, A. J. Torres-Pacheco, M. E. Luciani, F. Farlik, M. Wong, J. Jung, S. Fraser, S. T. Weninger, W. 2021-07-25 doi:10.1101/2021.07.24.453629 Cold Spring Harbor Laboratory Press 2021-07-25 <![CDATA[ Temporal Dynamics of HCMV Gene Expression in Lytic and Latent Infections ]]> https://biorxiv.org/content/10.1101/2021.07.26.453763v1?rss=1 Rozman, B. Kitsberg, Y. Nachshon, A. Schwartz, M. Stern-Ginossar, N. 2021-07-26 doi:10.1101/2021.07.26.453763 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ Evolution of binding preferences among whole-genome duplicated transcription factors ]]> https://biorxiv.org/content/10.1101/2021.07.27.453962v1?rss=1 Gera, T. Jonas, F. More, R. Barkai, N. 2021-07-27 doi:10.1101/2021.07.27.453962 Cold Spring Harbor Laboratory Press 2021-07-27 <![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 divide and conquer metacell algorithm for scalable scRNA-seq analysis ]]> https://biorxiv.org/content/10.1101/2021.08.08.453314v1?rss=1 Ben-Kiki, O. Bercovitch, A. Lifshitz, A. Tanay, A. 2021-08-08 doi:10.1101/2021.08.08.453314 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ H3-K27M-Mutant Nucleosomes Interact with MLL1 to Shape the Glioma Epigenetic Landscape ]]> https://biorxiv.org/content/10.1101/2021.08.09.455680v1?rss=1 Furth, N. Algranati, D. Dassa, B. Beresh, O. Fedyuk, V. Morris, N. Kasper, L. Jones, D. Monje, M. Baker, S. Shema, E. 2021-08-10 doi:10.1101/2021.08.09.455680 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ The spatio-temporal program of liver zonal regeneration ]]> https://biorxiv.org/content/10.1101/2021.08.11.455924v1?rss=1 Ben-Moshe, S. Veg, T. Manco, R. Dan, S. Kolodziejczyk, A. A. Bahar Halpern, K. Elinav, E. Itzkovitz, S. 2021-08-12 doi:10.1101/2021.08.11.455924 Cold Spring Harbor Laboratory Press 2021-08-12 <![CDATA[ Crosstalk between myosin II and formin functions in the regulation of force generation and actomyosin dynamics in stress fibers ]]> https://biorxiv.org/content/10.1101/2021.08.15.456175v1?rss=1 Nishimura, Y. Shi, S. Li, Q. Bershadsky, A. D. Viasnoff, V. 2021-08-15 doi:10.1101/2021.08.15.456175 Cold Spring Harbor Laboratory Press 2021-08-15 <![CDATA[ Desolvation Energy Explains Partitioning of Client Proteins into Condensates ]]> https://biorxiv.org/content/10.1101/2021.08.16.456554v1?rss=1 Villegas, J. Levy, E. D. 2021-08-17 doi:10.1101/2021.08.16.456554 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ BRCA mutational status shapes the stromal microenvironment of pancreatic cancer linking CLU+ CAF expression with HSF1 signaling ]]> https://biorxiv.org/content/10.1101/2021.08.18.456576v1?rss=1 Shaashua, L. Pevsner-Fischer, M. Friedman, G. Levi-Galibov, O. Nandakumar, S. Nevo, R. Brown, L. E. Zhang, W. Stein, Y. Kim, H. S. Bojmar, L. Jarnagin, W. R. Lecomte, N. Stok, R. Bishara, H. Hamodi, R. Levy-Lahad, E. Golan, T. Porco, J. A. Iacobuzio-Donahue, C. A. Schultz, N. Lyden, D. Tuveson, D. Kelsen, D. Scherz-Shouval, R. 2021-08-19 doi:10.1101/2021.08.18.456576 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Cap-independent translation and a precisely localized RNA sequence enable SARS-CoV-2 to control host translation and escape anti-viral response ]]> https://biorxiv.org/content/10.1101/2021.08.18.456855v1?rss=1 Slobodin, B. Sehrawat, U. Lev, A. Ogran, A. Fraticelli, D. Hayat, D. Zuckerman, B. Ulitsky, I. Ben-Shmuel, A. Levy, H. Bar-David, E. Dikstein, R. 2021-08-18 doi:10.1101/2021.08.18.456855 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ Voltage imaging identifies spinal circuits that modulate locomotor adaptation in zebrafish ]]> https://biorxiv.org/content/10.1101/2021.08.20.457089v1?rss=1 Böhm, U. L. Kimura, Y. Kawashima, T. Ahrens, M. Higashijima, S.-I. Engert, F. Cohen, A. E. 2021-08-20 doi:10.1101/2021.08.20.457089 Cold Spring Harbor Laboratory Press 2021-08-20 <![CDATA[ A dynamic rhizosphere interplay between tree roots and soil bacteria under drought ]]> https://biorxiv.org/content/10.1101/2021.08.24.457490v1?rss=1 Oppenheimer-Shaanan, Y. Jakoby, G. Starr, M. Karliner, R. Eilon, G. Itkin, M. Malitsky, S. klein, t. 2021-08-25 doi:10.1101/2021.08.24.457490 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ Sex biases in cancer and autoimmune disease incidence are correlated across human tissues ]]> https://biorxiv.org/content/10.1101/2021.09.07.459207v1?rss=1 Crawford, D. R. Sinha, S. Nair, N. U. Ryan, B. M. Barnholtz-Sloan, J. S. Mount, S. M. Erez, A. Aldape, K. Castle, P. E. Rajagopal, P. S. Day, C.-P. Schäffer, A. A. Ruppin, E. 2021-09-08 doi:10.1101/2021.09.07.459207 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ OCT4 activates a Suv39h1-repressive antisense lncRNA to couple histone H3 Lysine 9 methylation to pluripotency ]]> https://biorxiv.org/content/10.1101/2021.09.07.459323v1?rss=1 Bernard, L. D. DUBOIS, A. Heurtier, V. Chervova, A. Tachtsidi, A. Gil, N. Owens, N. Vandormael-Pournin, S. Ulitsky, I. Cohen-Tannoudji, M. Navarro, P. 2021-09-07 doi:10.1101/2021.09.07.459323 Cold Spring Harbor Laboratory Press 2021-09-07 <![CDATA[ The spliced leader RNA silencing (SLS) pathway in Trypanosoma brucei is induced by perturbations of endoplasmic reticulum, Golgi, or mitochondrial proteins factors and functional analysis of SLS inducing kinase, PK3 ]]> https://biorxiv.org/content/10.1101/2021.09.07.459367v1?rss=1 Okalang, U. Mualem Bar-Ner, B. Rajan, K. S. Friedman, N. Aryal, S. Egarmina, K. Hope, R. Khazanov, N. Senderowitz, H. Alon, A. Fass, D. Michaeli, S. 2021-09-08 doi:10.1101/2021.09.07.459367 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ Unique features of transcription termination and initiation at closely spaced tandem human genes ]]> https://biorxiv.org/content/10.1101/2021.09.10.459726v1?rss=1 Nissani, N. Ulitsky, I. 2021-09-11 doi:10.1101/2021.09.10.459726 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Controls on the isotopic composition of microbial methane ]]> https://biorxiv.org/content/10.1101/2021.09.14.460204v1?rss=1 Gropp, J. Jin, Q. Halevy, I. 2021-09-14 doi:10.1101/2021.09.14.460204 Cold Spring Harbor Laboratory Press 2021-09-14 <![CDATA[ Exocytosis of the silicified cell wall of diatoms involves extensive membrane disintegration ]]> https://biorxiv.org/content/10.1101/2021.09.14.460270v1?rss=1 de Haan, D. Peled-Zehavi, H. Addadi, Y. Ben Joseph, O. Aram, L. Gal, A. 2021-09-14 doi:10.1101/2021.09.14.460270 Cold Spring Harbor Laboratory Press 2021-09-14 <![CDATA[ Isolation and characterization of a highly specific monoclonal antibody targeting the botulinum neurotoxin type E exposed SNAP-25 neoepitope ]]> https://biorxiv.org/content/10.1101/2021.09.16.460610v1?rss=1 Mechaly, A. Diamant, E. Alcalay, R. Ben-David, A. Dor, E. Torgeman, A. Barnea, A. Girshengorn, M. Levin, L. Epstein, E. Tennenhouse, A. Fleishman, s. Zichel, R. Mazor, O. 2021-09-16 doi:10.1101/2021.09.16.460610 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ Nitrogen partitioning between branched-chain amino acids and urea cycle enzymes sustains renal cancer progression ]]> https://biorxiv.org/content/10.1101/2021.09.17.460635v1?rss=1 Sciacovelli, M. Dugourd, A. Valcarcel Jimenez, L. Yang, M. Nikitopoulou, E. Costa, A. S. Tronci, L. Caraffini, V. Rodrigues, P. Schmidt, C. Ryan, D. G. Young, T. Zecchini, V. Rossi, S. H. Massie, C. Lohoff, C. Masid, M. Hatzimanikatis, V. Kuppe, C. Von Kriegsheim, A. Kramann, R. Gnanapragasam, V. Warren, A. Y. Stewart, G. D. Erez, A. Vanharanta, S. Saez-Rodriguez, J. Frezza, C. 2021-09-18 doi:10.1101/2021.09.17.460635 Cold Spring Harbor Laboratory Press 2021-09-18 <![CDATA[ DNA dynamics dictates p53 functional outcome ]]> https://biorxiv.org/content/10.1101/2021.09.18.460898v1?rss=1 Safieh, J. Chazan, A. Vyas, P. Saleem, H. Danin-Poleg, Y. Ron, D. Haran, T. E. 2021-09-19 doi:10.1101/2021.09.18.460898 Cold Spring Harbor Laboratory Press 2021-09-19 <![CDATA[ Imaging Flow Cytometry reveals a dual role for exopolysaccharides in biofilms: To promote self-adhesion while repelling non-self-community members ]]> https://biorxiv.org/content/10.1101/2021.09.22.461363v1?rss=1 Maan, H. Povolotsky, T. L. Porat, Z. Kolodkin-Gal, I. 2021-09-22 doi:10.1101/2021.09.22.461363 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ Fitness landscape analysis reveals that the wild type allele is sub-optimal and mutationally robust ]]> https://biorxiv.org/content/10.1101/2021.09.27.461914v1?rss=1 Gabzi, T. Pilpel, Y. T. Friedlander, T. 2021-09-27 doi:10.1101/2021.09.27.461914 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ The DarTG toxin-antitoxin system provides phage defense by ADP-ribosylating viral DNA ]]> https://biorxiv.org/content/10.1101/2021.09.27.462013v1?rss=1 LeRoux, M. Srikant, S. Littlehale, M. L. Teodoro, G. Doron, S. Badiee, M. Leung, A. Sorek, R. Laub, M. T. 2021-09-27 doi:10.1101/2021.09.27.462013 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ Transcriptional interference in toehold switch-based RNA circuits ]]> https://biorxiv.org/content/10.1101/2021.09.29.462367v1?rss=1 Falgenhauer, E. Mückl, A. Schwarz-Schilling, M. Simmel, F. C. 2021-09-29 doi:10.1101/2021.09.29.462367 Cold Spring Harbor Laboratory Press 2021-09-29 <![CDATA[ Balance of osmotic pressures determines the volume of the cell nucleus ]]> https://biorxiv.org/content/10.1101/2021.10.01.462771v1?rss=1 Deviri, D. Safran, S. 2021-10-01 doi:10.1101/2021.10.01.462771 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Oxytocin regulation of social transmission of fear in zebrafish reveals its evolutionary conserved role in emotional contagion ]]> https://biorxiv.org/content/10.1101/2021.10.06.463413v1?rss=1 Akinrinade, I. Kareklas, K. Gliksberg, M. Petri, G. Levkowitz, G. Oliveira, R. 2021-10-06 doi:10.1101/2021.10.06.463413 Cold Spring Harbor Laboratory Press 2021-10-06 <![CDATA[ A Proposed Unified Interphase Nucleus Chromosome Structure: Preliminary Preponderance of Evidence ]]> https://biorxiv.org/content/10.1101/2021.10.08.463051v1?rss=1 Sedat, J. McDonald, A. Cang, H. Lucas, J. S. Arigovindan, M. Kam, Z. Murre, C. Elbaum, M. 2021-10-09 doi:10.1101/2021.10.08.463051 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ Superresolution microscopy reveals partial preassembly and subsequent bending of the clathrin coat during endocytosis ]]> https://biorxiv.org/content/10.1101/2021.10.12.463947v1?rss=1 Mund, M. Tschanz, A. Wu, Y.-L. Frey, F. Mehl, J. L. Kaksonen, M. Avinoam, O. Schwarz, U. S. Ries, J. 2021-10-13 doi:10.1101/2021.10.12.463947 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Control of protein activity by photoinduced spin polarized charge reorganization ]]> https://biorxiv.org/content/10.1101/2021.10.12.464058v1?rss=1 Ghosh, S. Ghosh, K. B. Levy, D. Scheerer, D. Riven, I. Shin, J. Gray, H. Naaman, R. Haran, G. 2021-10-13 doi:10.1101/2021.10.12.464058 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ A Proposed Unified Mitotic Chromosome Architecture ]]> https://biorxiv.org/content/10.1101/2021.10.14.464227v1?rss=1 Sedat, J. McDonald, A. Kasler, H. G. Verdin, E. Cang, H. Murre, C. Elbaum, M. 2021-10-14 doi:10.1101/2021.10.14.464227 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ SURFMAP: a software for mapping in two dimensions protein surface features ]]> https://biorxiv.org/content/10.1101/2021.10.15.464543v1?rss=1 Schweke, H. Mucchielli, M.-H. Chevrollier, N. Gosset, S. Lopes, A. 2021-10-16 doi:10.1101/2021.10.15.464543 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ Systematic analysis of membrane contact sites in Saccharomyces cerevisiae uncovers modulators of cellular lipid distribution ]]> https://biorxiv.org/content/10.1101/2021.10.17.464712v1?rss=1 Castro, I. G. Shortill, S. P. Dziurdzik, S. K. Cadou, A. Ganesan, S. Fenech, E. J. Meyer, H. Fadel, A. David, Y. Davey, M. Mattes, C. Valenti, R. Ernst, R. Zaremberg, V. Levine, T. P. Stefan, C. Conibear, E. Schuldiner, M. 2021-10-19 doi:10.1101/2021.10.17.464712 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Widespread Utilization of Diverse Organophosphate Pollutants by Marine Bacteria ]]> https://biorxiv.org/content/10.1101/2021.10.18.464763v1?rss=1 Despotovic, D. Aharon, E. Trofimyuk, O. Dubovetskyi, A. Cherukuri, K. P. Ashani, Y. Leader, H. Castelli, A. Fumagalli, L. Savidor, A. Levin, Y. Longo, L. M. Segev, E. Tawfik, D. S. 2021-10-18 doi:10.1101/2021.10.18.464763 Cold Spring Harbor Laboratory Press 2021-10-18 <![CDATA[ Massively parallel identification of zipcodes in primary cortical neurons ]]> https://biorxiv.org/content/10.1101/2021.10.21.465275v1?rss=1 von Kuegelgen, N. Mendonsa, S. Dantsuji, S. Ron, M. Kirchner, M. Zerna, N. Bujanic, L. Mertins, P. Ulitsky, I. Chekulaeva, M. 2021-10-21 doi:10.1101/2021.10.21.465275 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[ Spatial coding in the hippocampus of flying owls ]]> https://biorxiv.org/content/10.1101/2021.10.24.465553v1?rss=1 Agarwal, A. Sarel, A. Derdikman, D. Ulanovsky, N. Gutfreund, Y. 2021-10-24 doi:10.1101/2021.10.24.465553 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during algal blooms ]]> https://biorxiv.org/content/10.1101/2021.10.25.465659v1?rss=1 Vincent, F. Gralka, M. Schleyer, G. Schatz, D. J. Cabrera-Brudau, M. Kuhlisch, C. Sichert, A. Vidal-Melgosa, S. Mayers, K. Barak-Gavish, N. Flores, M. Masdeu-Navarro, M. Egge, J. K. Larsen, A. Heheman, J.-H. Marrase, C. Simo, R. Cordero, O. X. Vardi, A. 2021-10-26 doi:10.1101/2021.10.25.465659 Cold Spring Harbor Laboratory Press 2021-10-26 <![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[ Dendritic cell ICAM-1 strengthens immune synapses but is dispensable for effector and memory responses ]]> https://biorxiv.org/content/10.1101/2021.10.27.466043v1?rss=1 Sapoznikov, A. Kozlovski, S. Feigelson, S. W. Davidzohn, N. Wigoda, N. Feldmesser, E. Petrovich-Kopitman, E. Grafen, A. Biton, M. Alon, R. 2021-10-28 doi:10.1101/2021.10.27.466043 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Coccolith Sr/Ca is a Robust Temperature and Growth Rate Indicator that Withstands Dynamic Microbial Interactions ]]> https://biorxiv.org/content/10.1101/2021.10.28.466229v1?rss=1 Segev, E. Eliason, O. 2021-10-28 doi:10.1101/2021.10.28.466229 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Silencing neuronal activity is required for developmental circuit remodeling ]]> https://biorxiv.org/content/10.1101/2021.10.31.466652v1?rss=1 Mayseless, O. Rachad, E.-Y. Shapira, G. Fiala, A. Schuldiner, O. 2021-11-02 doi:10.1101/2021.10.31.466652 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Multiplexed Single-Molecule Epigenetic Analysis of Plasma-Isolated Nucleosomes for Cancer Diagnostics ]]> https://biorxiv.org/content/10.1101/2021.11.01.466724v1?rss=1 Fedyuk, V. Erez, N. Furth, N. Beresh, O. Jones, D. Shinde, A. Andreishcheva, K. Zakai, B. B. Mavor, Y. Peretz, T. Hubert, A. Cohen, J. E. Salah, A. Temper, M. Grinshpun, A. Maoz, M. Zick, A. Ron, G. Shema, E. 2021-11-03 doi:10.1101/2021.11.01.466724 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Single-cell epigenetic analysis reveals principles of chromatin states in H3.3-K27M gliomas ]]> https://biorxiv.org/content/10.1101/2021.11.02.466907v1?rss=1 Harpaz, N. Mittelman, T. Beresh, O. Salame, T. M. Furth, N. Ron, G. Shema, E. 2021-11-04 doi:10.1101/2021.11.02.466907 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Assessing and enhancing foldability in designed proteins ]]> https://biorxiv.org/content/10.1101/2021.11.09.467863v1?rss=1 Fleishman, S. J. Listov, D. Lipsh-Sokolik, R. Yang, C. Correia, B. E. 2021-11-09 doi:10.1101/2021.11.09.467863 Cold Spring Harbor Laboratory Press 2021-11-09 <![CDATA[ Aerobic Bacteria Produce Nitric Oxide via Denitrification and Trigger Algal Population Collapse ]]> https://biorxiv.org/content/10.1101/2021.11.14.468512v1?rss=1 Abada, A. Sperfeld, M. Carmieli, R. Ben-Dor, S. Huang Zhang, I. Babbin, A. R. Segev, E. 2021-11-14 doi:10.1101/2021.11.14.468512 Cold Spring Harbor Laboratory Press 2021-11-14 <![CDATA[ Doppler Slicing for Ultrasound Super-Resolution Without Contrast Agents ]]> https://biorxiv.org/content/10.1101/2021.11.19.469083v1?rss=1 Bar-Zion, A. Solomon, O. Rabut, C. Maresca, D. Eldar, Y. C. Shapiro, M. G. 2021-11-20 doi:10.1101/2021.11.19.469083 Cold Spring Harbor Laboratory Press 2021-11-20 <![CDATA[ Structural features within the NORAD long noncoding RNA underlie efficient repression of Pumilio activity ]]> https://biorxiv.org/content/10.1101/2021.11.19.469243v1?rss=1 Ziv, O. Farberov, S. Lau, J. Y. Miska, E. A. Kudla, G. Ulitsky, I. 2021-11-19 doi:10.1101/2021.11.19.469243 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ CLASS-II KNOX genes coordinate spatial and temporal patterns of the tomato ripening ]]> https://biorxiv.org/content/10.1101/2021.11.19.469310v1?rss=1 Keren-Keiserman, A. Shtern, A. Chalupowicz, D. Furumizu, C. Alvarez, J. p. Amsellem, Z. Arazi, T. Tuvia-Alkalai, S. Efroni, I. Fallik, E. Goldshmidt, A. 2021-11-20 doi:10.1101/2021.11.19.469310 Cold Spring Harbor Laboratory Press 2021-11-20 <![CDATA[ Mitotic Outcomes in Fibrous Environments ]]> https://biorxiv.org/content/10.1101/2021.11.21.469470v1?rss=1 Jana, A. Zhang, H. Wang, J. Kapania, R. Gov, N. Deluca, J. Nain, A. 2021-11-22 doi:10.1101/2021.11.21.469470 Cold Spring Harbor Laboratory Press 2021-11-22 <![CDATA[ Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning ]]> https://biorxiv.org/content/10.1101/2021.11.22.469552v1?rss=1 Leonard, A. C. Weinstein, J. Steiner, P. J. Erbse, A. Fleishman, S. J. Whitehead, T. A. 2021-11-24 doi:10.1101/2021.11.22.469552 Cold Spring Harbor Laboratory Press 2021-11-24 <![CDATA[ Stable and functionally diverse versatile peroxidases by computational design directly from sequence ]]> https://biorxiv.org/content/10.1101/2021.11.25.469886v1?rss=1 Barber-Zucker, S. Mindel, V. Garcia-Ruiz, E. Weinstein, J. J. Alcalde, M. Fleishman, S. J. 2021-11-25 doi:10.1101/2021.11.25.469886 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ Global analysis of human-to-mouse intercellular RNA transfer in cell culture ]]> https://biorxiv.org/content/10.1101/2021.11.28.470233v1?rss=1 View larger version (44K): org.highwire.dtl.DTLVardef@13a7176org.highwire.dtl.DTLVardef@1ef1c75org.highwire.dtl.DTLVardef@1355eeforg.highwire.dtl.DTLVardef@ebc275_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Dasgupta, S. Dyagi, D. Y. Haimovich, G. Wyler, E. Olender, T. Singer, R. H. Landthaler, M. Gerst, J. E. 2021-11-28 doi:10.1101/2021.11.28.470233 Cold Spring Harbor Laboratory Press 2021-11-28 <![CDATA[ Chaperones drive in vitro evolution of uracil glycosylase towards misfolded states ]]> https://biorxiv.org/content/10.1101/2021.11.30.470542v1?rss=1 Melanker, O. Goloubinoff, P. A. Schreiber, G. 2021-12-01 doi:10.1101/2021.11.30.470542 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Neighbor-specific gene expression revealed from physically interacting cells during mouse embryonic development ]]> https://biorxiv.org/content/10.1101/2021.12.02.470916v1?rss=1 Kim, J. Rothov, M. M. Liao, L. Rhee, S. Weng, G. David, E. Amit, I. Hajkarim, M. C. Brickman, J. M. Won, K. J. 2021-12-03 doi:10.1101/2021.12.02.470916 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ Receptor binding and escape from Beta antibody responses drive Omicron-B.1.1.529 evolution ]]> https://biorxiv.org/content/10.1101/2021.12.03.471045v1?rss=1 Zahradnik, J. Tuekprakhon, A. Ginn, H. M. Duyvesteyn, H. M. E. Bahar, M. Khan, S. Avinoam, O. Zhou, D. Nutalai, R. Supasa, P. Wang, B. Dejnirattisai, W. Liu, C. Dijokaite, A. Temperton, N. Mongkolsapaya, J. Fry, E. E. Ren, J. Screaton, G. R. Schreiber, G. Stuart, D. I. 2021-12-07 doi:10.1101/2021.12.03.471045 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ A spatiotemporally resolved single cell atlas of the Plasmodium liver stage ]]> https://biorxiv.org/content/10.1101/2021.12.03.471111v1?rss=1 Afriat, A. Zuzarte-Luis, V. Bahar Halpern, K. Buchauer, L. Marques, S. Lahree, A. Amit, I. Mota, M. M. Itzkovitz, S. 2021-12-03 doi:10.1101/2021.12.03.471111 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ Chronic kidney disease alters Pin1 phosphorylation and parathyroid hormone mRNA binding proteins leading to secondary hyperparathyroidism ]]> https://biorxiv.org/content/10.1101/2021.12.06.470227v1?rss=1 Hassan, A. Pollak, Y. E. Kilav-Levin, R. Silver, J. London, N. Nechama, M. Ben-Dov, I. Z. Naveh, T. 2021-12-06 doi:10.1101/2021.12.06.470227 Cold Spring Harbor Laboratory Press 2021-12-06 <![CDATA[ Genetic, environmental and intrinsic determinants of the human antibody epitope repertoire ]]> https://biorxiv.org/content/10.1101/2021.12.07.471553v1?rss=1 Andreu-Sanchez, S. Bourgonje, A. R. Vogl, T. Kurilshikov, A. Leviatan, S. Ruiz Moreno, A. J. Hu, S. Sinha, T. Vich Vila, A. Klompus, S. Kalka, I. de Leeuw, K. Arends, S. Jonkers, I. H. Withoff, S. Lifelines cohort study, Brouwer, E. Weinberger, A. Wijmenga, C. Segal, E. Weersma, R. K. Fu, J. Zhernakova, A. 2021-12-08 doi:10.1101/2021.12.07.471553 Cold Spring Harbor Laboratory Press 2021-12-08 <![CDATA[ In-depth characterization of the serum antibody epitope repertoire in inflammatory bowel disease using phage-displayed immunoprecipitation sequencing ]]> https://biorxiv.org/content/10.1101/2021.12.07.471581v1?rss=1 Bourgonje, A. R. Andreu-Sanchez, S. Vogl, T. Hu, S. Vila, A. V. Gacesa, R. Leviatan, S. Kurilshikov, A. Klompus, S. Kalka, I. N. van Dullemen, H. M. Weinberger, A. Visschedijk, M. C. Festen, E. A. M. Faber, K. N. Wijmenga, C. Dijkstra, G. Segal, E. Fu, J. Zhernakova, A. Weersma, R. K. 2021-12-09 doi:10.1101/2021.12.07.471581 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Systematic multi-level analysis of an organelle proteome reveals new peroxisomal functions ]]> https://biorxiv.org/content/10.1101/2021.12.08.471723v1?rss=1 Yifrach, E. Holbrook-Smith, D. Bürgi, J. Othman, A. Eisenstein, M. Van Roermund, C. W. T. Visser, W. Tirosh, A. Bibi, C. Galor, S. Weil, U. Fadel, A. Peleg, Y. Waterham, H. Wanders, R. J. Wilmanns, M. Zamboni, N. Schuldiner, M. Zalckvar, E. 2021-12-11 doi:10.1101/2021.12.08.471723 Cold Spring Harbor Laboratory Press 2021-12-11 <![CDATA[ Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma ]]> https://biorxiv.org/content/10.1101/2021.12.14.471886v1?rss=1 Rosenberg, M. I. Greenstein, E. Buchkovich, M. Mikl, M. Peres, A. Santoni-Rugiu, E. Reshef, D. Salovin, A. J. Gibbs, D. L. Irwin, M. S. Naranjo, A. Ulitsky, I. de Alarcon, P. A. Weigman, V. Yaari, G. Panzer, J. A. Friedman, N. Maris, J. M. 2021-12-14 doi:10.1101/2021.12.14.471886 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ Sex-specific topology of the nociceptive circuit shapes dimorphic behavior in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.12.14.472335v1?rss=1 Pechuk, V. Goldman, G. Salzberg, Y. Chaubey, A. H. Bola, R. A. Hoffman, J. R. Endreson, M. L. Miller, R. M. Reger, N. J. Portman, D. S. Ferkey, D. M. Schneidman, E. Oren-Suissa, M. 2021-12-15 doi:10.1101/2021.12.14.472335 Cold Spring Harbor Laboratory Press 2021-12-15 <![CDATA[ Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion ]]> https://biorxiv.org/content/10.1101/2021.12.14.472415v1?rss=1 Garb, J. Lopatina, A. Bernheim, A. Zaremba, M. Siksnys, V. Melamed, S. Leavitt, A. Millman, A. Amitai, G. Sorek, R. 2021-12-14 doi:10.1101/2021.12.14.472415 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ Sir2-domain associated short prokaryotic Argonautes provide defence against invading mobile genetic elements through NAD+ depletion ]]> https://biorxiv.org/content/10.1101/2021.12.14.472599v1?rss=1 Zaremba, M. Dakineviciene, D. Golovinas, E. Stankunas, E. Lopatina, A. Sorek, R. Manakova, E. Ruksenaite, A. Silanskas, A. Asmontas, S. Grigaitis, R. Timinskas, K. Venclovas, C. Siksnys, V. 2021-12-14 doi:10.1101/2021.12.14.472599 Cold Spring Harbor Laboratory Press 2021-12-14 <![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 transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors ]]> https://biorxiv.org/content/10.1101/2021.12.19.473368v1?rss=1 Gavish, A. Tyler, M. Simkin, D. Kovarsky, D. Gonzalez Castro, L. N. Halder, D. Chanoch-Myers, R. Laffy, J. Mints, M. Greenwald, A. R. Weider, A. Tal, R. Spitzer, A. Hara, T. Tirosh, A. Puram, S. V. Suva, M. L. Tirosh, I. 2021-12-20 doi:10.1101/2021.12.19.473368 Cold Spring Harbor Laboratory Press 2021-12-20 <![CDATA[ Oxytocin Signaling Regulates the Homeostatic Response to Cold Stress in Poikilothermic Vertebrates ]]> https://biorxiv.org/content/10.1101/2021.12.20.472748v1?rss=1 Segev, A. Krispin, S. Olthof, A. M. Hyatt, K. Haller, L. Barki, A. Nitzan, T. Levkowitz, G. Kanadia, R. N. Cnaani, A. Biran, J. 2021-12-21 doi:10.1101/2021.12.20.472748 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Neonatal enthesis healing involves non-inflammatory formation of acellular scar through ECM secretion by resident cells ]]> https://biorxiv.org/content/10.1101/2021.12.20.473454v1?rss=1 Vinestock, R. C. Felsenthal, N. Assaraf, E. Katz, E. Rubin, S. Heinemann-Yerushalmi, L. Krief, S. Dezorella, N. Levin-Zaidman, S. Tsoory, M. Thomopoulos, S. Zelzer, E. 2021-12-20 doi:10.1101/2021.12.20.473454 Cold Spring Harbor Laboratory Press 2021-12-20 <![CDATA[ The effects of protein crowders on small molecule drug diffusion ]]> https://biorxiv.org/content/10.1101/2021.12.30.474528v1?rss=1 Dey, D. Nunes-Alves, A. Wade, R. C. Schreiber, G. 2021-12-30 doi:10.1101/2021.12.30.474528 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ Intestinal Mucin Is a Chaperone of Multivalent Copper ]]> https://biorxiv.org/content/10.1101/2022.01.02.474741v1?rss=1 Reznik, N. Gallo, A. D. Rush, K. W. Javitt, G. Fridmann-Sirkis, Y. Ilani, T. Nairner, N. A. Chacon, K. Franz, K. J. Fass, D. 2022-01-02 doi:10.1101/2022.01.02.474741 Cold Spring Harbor Laboratory Press 2022-01-02 <![CDATA[ Theoretical model of efficient phagocytosis driven by curved membrane proteins and active cytoskeleton forces ]]> https://biorxiv.org/content/10.1101/2022.01.04.474893v1?rss=1 Sadhu, R. K. Barger, S. R. Penic, S. Iglic, A. Krendel, M. Gauthier, N. Gov, N. 2022-01-05 doi:10.1101/2022.01.04.474893 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Regulation of major bacterial survival strategies by transcript sequestration in a membraneless organelle ]]> https://biorxiv.org/content/10.1101/2022.01.06.475198v1?rss=1 Szoke, T. Albocher, N. Goldberger, O. Barsheshet, M. Nussbaum-Shochat, A. Wiener, R. Schuldiner, M. Amster-Choder, O. 2022-01-06 doi:10.1101/2022.01.06.475198 Cold Spring Harbor Laboratory Press 2022-01-06 <![CDATA[ The genetic structure of a wild wheat population has remained associated with microhabitats over 36 years ]]> https://biorxiv.org/content/10.1101/2022.01.10.475641v1?rss=1 Dahan-Meir, T. Ellis, T. J. Mafessoni, F. Sela, H. Manisterski, J. Avivi-Ragolsky, N. Raz, A. Feldman, M. Anikster, Y. Nordborg, M. Levy, A. A. 2022-01-11 doi:10.1101/2022.01.10.475641 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ Bacterial lifestyle switch in response to algal metabolites ]]> https://biorxiv.org/content/10.1101/2022.01.10.475657v1?rss=1 Barak-Gavish, N. Dassa, B. Kuhlisch, C. Nussbaum, I. Rosenberg, G. Avraham, R. Vardi, A. 2022-01-10 doi:10.1101/2022.01.10.475657 Cold Spring Harbor Laboratory Press 2022-01-10 <![CDATA[ Ontogenetic Color Switching in Lizards as a by-Product of Guanine Cell Development ]]> https://biorxiv.org/content/10.1101/2022.01.12.475993v1?rss=1 Zhang, G. Yallapragada, V. J. Shemesh, M. Wagner, A. Upcher, A. Pinkas, I. McClelland, H. L. O. Hawlena, D. Palmer, B. A. 2022-01-12 doi:10.1101/2022.01.12.475993 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Inflammatory signals from fatty bone marrow supports the early stages of DNMT3a driven clonal hematopoiesis ]]> https://biorxiv.org/content/10.1101/2022.01.13.476218v1?rss=1 Zioni, N. Bercovich, A. Chapal-Ilani, N. Solomon, A. Petrovich, E. .Sacma, M. Geiger, H. Scheller, M. Müller-Tidow, C. Lipka, D. Shlush, E. Minden, M. Kaushansky, N. Shlush, L. 2022-01-14 doi:10.1101/2022.01.13.476218 Cold Spring Harbor Laboratory Press 2022-01-14 <![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[ Structure and Protein-Protein Interactions of Ice Nucleation Proteins Drive Their Activity ]]> https://biorxiv.org/content/10.1101/2022.01.21.477219v1?rss=1 Hartmann, S. Ling, M. Dreyer, L. S. A. Zipori, A. Finster, K. W. Grawe, S. Jensen, L. Z. Borck, S. Reicher, N. Drace, T. Niedermeier, D. Jones, N. C. Hoffmann, S. V. Wex, H. Rudich, Y. Boesen, T. Santl-Temkiv, T. 2022-01-22 doi:10.1101/2022.01.21.477219 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ The scotopic band: primate detailed scotopic vision and perceptual uncertainty ]]> https://biorxiv.org/content/10.1101/2022.01.25.477659v1?rss=1 Barash, S. Spivak, O. Thier, P. 2022-01-25 doi:10.1101/2022.01.25.477659 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Two AGO proteins with transposon-derived sRNA cargo mark the germline in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2022.01.25.477718v1?rss=1 Bradamante, G. Nguyen, V. H. Incarbone, M. Meir, Z. Bente, H. Dona, M. Lettner, N. Mittelsten Scheid, O. Gutzat, R. 2022-01-25 doi:10.1101/2022.01.25.477718 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Stress resilience is established during development and is regulated by complement factors ]]> https://biorxiv.org/content/10.1101/2022.01.31.478444v1?rss=1 View larger version (59K): org.highwire.dtl.DTLVardef@359261org.highwire.dtl.DTLVardef@11d1e62org.highwire.dtl.DTLVardef@b5d346org.highwire.dtl.DTLVardef@141bae1_HPS_FORMAT_FIGEXP M_FIG C_FIG Why some individual individuals recover better than others from stressful situations is unclear. We show that resilience to stress is established during zebrafish development as a stable and heritable trait. Resilience is augmented by brain-derived neuropeptides and attenuated by innate immune complement factors specifically expressed in the liver. HighlightsO_LIWildtype zebrafish larvae show differences in their dynamics of recovering from stress, with some being more resilient than others. C_LIO_LIResilience is a stable and heritable trait. C_LIO_LIResilient fish show specific stress-responsive transcriptional changes. C_LIO_LINeuropeptide Y and miRNA218 positively affect resilience, while innate immune complement factors attenuate resilience. C_LI ]]> Swaminathan, A. Gliksberg, M. Anbalagan, S. Wigoda, N. Levkowitz, G. 2022-01-31 doi:10.1101/2022.01.31.478444 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ Active site center redesign increases protein stability preserving catalysis ]]> https://biorxiv.org/content/10.1101/2022.01.31.478513v1?rss=1 Romero-Romero, M. L. Garcia-Seisdedos, H. Ibarra-Molero, B. 2022-01-31 doi:10.1101/2022.01.31.478513 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ Determining the targeting specificity of the selective peroxisomal targeting factor Pex9 ]]> https://biorxiv.org/content/10.1101/2022.02.02.478779v1?rss=1 Yifrach, E. Ruowitz, M. Cruz Zaragoza, L. D. Tirosh, A. Gazi, Z. Peleg, Y. Kunze, M. Eisenstein, M. Schliebs, W. Schuldiner, M. Erdmann, R. Zalckvar, E. 2022-02-02 doi:10.1101/2022.02.02.478779 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ Accelerated cognitive decline in obese mouse model of Alzheimer's disease is linked to sialic acid-driven immune deregulation ]]> https://biorxiv.org/content/10.1101/2022.02.05.479219v1?rss=1 Suzzi, S. Croese, T. Ravid, A. Gold, O. Clark, A. R. Medina, S. Kitsberg, D. Adam, M. Vernon, K. A. Kohnert, E. Shapira, I. Malitsky, S. Itkin, M. Colaiuta, S. P. Cahalon, L. Slyper, M. Greka, A. Habib, N. Schwartz, M. 2022-02-08 doi:10.1101/2022.02.05.479219 Cold Spring Harbor Laboratory Press 2022-02-08 <![CDATA[ Tongue immune compartment analysis reveals spatial macrophage heterogeneity ]]> https://biorxiv.org/content/10.1101/2022.02.09.479699v1?rss=1 Mildner, A. Lyras, E. M. Zimmermann, K. Wagner, L. K. Dörr, D. Fischer, C. Jung, S. Yona, S. Hovav, A.-H. Stenzel, W. Dommerich, S. Conrad, T. Leutz, A. 2022-02-11 doi:10.1101/2022.02.09.479699 Cold Spring Harbor Laboratory Press 2022-02-11 <![CDATA[ Functional LINC complex maintains epigenetic landscape and decondenses DNA in mature muscles ]]> https://biorxiv.org/content/10.1101/2022.02.09.479725v1?rss=1 Amiad Pavlov, D. Unnikannan, C. Lorber, D. Stoops, E. Volk, T. 2022-02-10 doi:10.1101/2022.02.09.479725 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Rtt109 promotes nucleosome replacement ahead of the replicating fork ]]> https://biorxiv.org/content/10.1101/2022.02.09.479766v1?rss=1 Jonas, F. Yaakov, G. Barkai, N. 2022-02-09 doi:10.1101/2022.02.09.479766 Cold Spring Harbor Laboratory Press 2022-02-09 <![CDATA[ PyZebrascope: an open-source platform for brain-wide neural activity imaging in zebrafish ]]> https://biorxiv.org/content/10.1101/2022.02.13.480249v1?rss=1 Barbara, R. Kantharaju, M. N. Haruvi, R. Harrington, K. Kawashima, T. 2022-02-15 doi:10.1101/2022.02.13.480249 Cold Spring Harbor Laboratory Press 2022-02-15 <![CDATA[ Virological characteristics of SARS-CoV-2 BA.2 variant ]]> https://biorxiv.org/content/10.1101/2022.02.14.480335v1?rss=1 Yamasoba, D. Kimura, I. Nasser, H. Morioka, Y. Nao, N. Ito, J. Uriu, K. Tsuda, M. Zahradnik, J. Shirakawa, K. Suzuki, R. Kishimoto, M. Kosugi, Y. Kobiyama, K. Hara, T. Toyoda, M. Tanaka, Y. L. Butlertanaka, E. P. Shimizu, R. Ito, H. Wang, L. Oda, Y. Orba, Y. Sasaki, M. Nagata, K. Yoshimatsu, K. Asakura, H. Nagashima, M. Sadamasu, K. Yoshimura, K. Kuramochi, J. Seki, M. Fujiki, R. Kaneda, A. Shimada, T. Nakada, T.-a. Sakao, S. Suzuki, T. Ueno, T. Takaori-Kondo, A. Ishii, K. J. Schreiber, G. The Genotype to Phenotype Japan (G2P-Japan) Consortium, Sawa 2022-02-15 doi:10.1101/2022.02.14.480335 Cold Spring Harbor Laboratory Press 2022-02-15 <![CDATA[ Rock inhibitors target SRSF2 leukemia by disrupting cell mitosis and nuclear morphology ]]> https://biorxiv.org/content/10.1101/2022.02.15.479934v1?rss=1 Su, M. Fleisher, T. Grosheva, I. Horev, M. B. Olszewska, M. Haim, B. Plotnikov, A. Carvalho, S. Moskovitz, Y. Minden, M. Chapal-Ilani, N. Papapetrou, E. P. Dezorella, N. Cheng, T. Kaushansky, N. Geiger, B. Shlush, L. I. 2022-02-17 doi:10.1101/2022.02.15.479934 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ Emergent regulation of ant foraging frequency through a computationally inexpensive forager movement rule ]]> https://biorxiv.org/content/10.1101/2022.02.15.480539v1?rss=1 Baltiansky, L. Frankel, G. Feinerman, O. 2022-02-19 doi:10.1101/2022.02.15.480539 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Polysome-CAGE of TCL1-driven chronic lymphocytic leukemia revealed multiple N-terminally altered epigenetic regulators and a translation stress signature ]]> https://biorxiv.org/content/10.1101/2022.02.15.480558v1?rss=1 Ogran, A. Havkin-Solomon, T. Becker-Herman, S. David, K. Shachar, I. Dikstein, R. 2022-02-15 doi:10.1101/2022.02.15.480558 Cold Spring Harbor Laboratory Press 2022-02-15 <![CDATA[ A unique mineralizing pool of Gli1+ stem cells builds the tendon enthesis and demonstrates therapeutic potential ]]> https://biorxiv.org/content/10.1101/2022.02.17.480929v1?rss=1 Fang, F. Xiao, Y. Zelzer, E. Leong, K. W. Thomopoulos, S. 2022-02-18 doi:10.1101/2022.02.17.480929 Cold Spring Harbor Laboratory Press 2022-02-18 <![CDATA[ Sexually dimorphic architecture and function of a mechanosensory circuit in C. elegans ]]> https://biorxiv.org/content/10.1101/2022.02.18.481005v1?rss=1 Setty, H. Salzberg, Y. Karimi, S. Berent-Barzel, E. Krieg, M. Oren-Suissa, M. 2022-02-19 doi:10.1101/2022.02.18.481005 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ A conditional null allele of Dync1h1 enables targeted analyses of dynein roles in neuronal length sensing and neurological disorders ]]> https://biorxiv.org/content/10.1101/2022.02.20.481176v1?rss=1 Di Pizio, A. Marvaldi, L. Birling, M.-C. Okladnikov, N. Dupuis, L. Fainzilber, M. Rishal, I. 2022-02-20 doi:10.1101/2022.02.20.481176 Cold Spring Harbor Laboratory Press 2022-02-20 <![CDATA[ Redifferentiated cardiomyocytes retain residual dedifferentiation signatures and are protected against ischaemic injury ]]> https://biorxiv.org/content/10.1101/2022.02.22.481415v1?rss=1 Shakked, A. Petrover, Z. Aharonov, A. Ghiringhelli, M. Umansky, K.-B. Nguyen, P. D. Kain, D. Elkahal, J. Divinsky, Y. Miyara, S. Friedlander, G. Savidor, A. Zhang, L. Perez, D. Kastan, N. Lendengolts, D. Levin, Y. Bakkers, J. Gepstein, L. Tzahor, E. 2022-02-22 doi:10.1101/2022.02.22.481415 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Single cell atlas of the neonatal small intestine with necrotizing enterocolitis ]]> https://biorxiv.org/content/10.1101/2022.03.01.482508v1?rss=1 Egozi, A. Olaloye, O. Werner, L. Silva, T. McCourt, B. Pierce, R. An, X. Wang, F. Chen, K. Pober, J. Shouval, D. Itzkovitz, S. Konnikova, L. 2022-03-02 doi:10.1101/2022.03.01.482508 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Sexual deprivation induces a CRF independent stress response and decreases resistance to stressors in Drosophila via a subpopulation of Neuropeptide F receptor-expressing neurons ]]> https://biorxiv.org/content/10.1101/2022.03.02.482596v1?rss=1 Ryvkin, J. Shmueli, A. Jacob, A. Shalit, T. Bentzur, A. Agranovich, B. Abramovich, I. Gottlieb, E. Nassel, D. R. Shohat-Ophir, G. 2022-03-04 doi:10.1101/2022.03.02.482596 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ A Duplex Structure of SARM1 Octamers Induced by a New Inhibitor ]]> https://biorxiv.org/content/10.1101/2022.03.02.482641v1?rss=1 Khazma, T. Golan-Vaishenker, Y. Guez-Haddad, J. Grossman, A. Sain, R. Plotnikov, A. Zalk, R. Yaron, A. Hons, M. Opatowsky, Y. 2022-03-02 doi:10.1101/2022.03.02.482641 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ The role of TGFβ signaling in Gli1+ tendon and enthesis cells ]]> https://biorxiv.org/content/10.1101/2022.03.03.482926v1?rss=1 Song, L. Golman, M. Abraham, A. C. Zelzer, E. Thomopoulos, S. 2022-03-04 doi:10.1101/2022.03.03.482926 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ An amphipathic helix in Brl1 is required for membrane fusion during nuclear pore complex biogenesis in S. cerevisiae ]]> https://biorxiv.org/content/10.1101/2022.03.04.483005v1?rss=1 Kralt, A. Wojtynek, M. Fischer, J. S. Agote-Aran, A. Mancini, R. Dultz, E. Noor, E. Uliana, F. Tatarek-Nossol, M. Antonin, W. Onischenko, E. Medalia, O. Weis, K. 2022-03-04 doi:10.1101/2022.03.04.483005 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Anthroponumbers.org: A Quantitative Database Of Human Impacts on Planet Earth ]]> https://biorxiv.org/content/10.1101/2022.03.04.483053v1?rss=1 Chure, G. Banks, R. A. Flamholz, A. I. Sarai, N. S. Kamb, M. Lopez-Gomez, I. Bar-On, Y. Milo, R. Phillips, R. 2022-03-07 doi:10.1101/2022.03.04.483053 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks ]]> https://biorxiv.org/content/10.1101/2022.03.06.483158v1?rss=1 Heyman, O. Yehezkel, D. Blumberger, N. Rosenberg, G. Ciolli Mattioli, C. Solomon, A. Hoffman, D. Bossel Ben-Moshe, N. Avraham, R. 2022-03-06 doi:10.1101/2022.03.06.483158 Cold Spring Harbor Laboratory Press 2022-03-06 <![CDATA[ LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways ]]> https://biorxiv.org/content/10.1101/2022.03.08.483407v1?rss=1 Kshirsagar, A. Gorelik, A. Olender, T. Sapir, T. Tsuboi, D. Rosenhek-Goldian, I. Malitsky, S. Itkin, M. Argoetti, A. Mandel-Gutfreund, Y. Cohen, S. R. Hanna, J. H. Ulitsky, I. Kaibuchi, K. Reiner, O. 2022-03-08 doi:10.1101/2022.03.08.483407 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Tradeoffs in bacterial physiology determine the efficiency of antibiotic killing ]]> https://biorxiv.org/content/10.1101/2022.03.09.483592v1?rss=1 Bren, A. Glass, D. S. Korem Kohanim, Y. Mayo, A. Alon, U. 2022-03-09 doi:10.1101/2022.03.09.483592 Cold Spring Harbor Laboratory Press 2022-03-09 <![CDATA[ Evolutionary safety of death by mutagenesis ]]> https://biorxiv.org/content/10.1101/2022.03.10.483790v1?rss=1 Lobinska, G. A. Pilpel, Y. T. Nowak, M. A. 2022-03-10 doi:10.1101/2022.03.10.483790 Cold Spring Harbor Laboratory Press 2022-03-10 <![CDATA[ Dimensionality reduction of calcium-imaged neuronal population activity ]]> https://biorxiv.org/content/10.1101/2022.03.11.480682v1?rss=1 Koh, T. H. Bishop, W. E. Kawashima, T. Jeon, B. B. Srinivasan, R. Kuhlman, S. J. Ahrens, M. B. Chase, S. M. Yu, B. M. 2022-03-14 doi:10.1101/2022.03.11.480682 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Genome-wide CRISPR screens identify novel regulators of wild-type and mutant p53 stability ]]> https://biorxiv.org/content/10.1101/2022.03.13.483372v1?rss=1 Lu, Y. Cho, T. Mukherjee, S. Malik, A. A. Gonzlez-Foutel, N. Oh, R. Langille, E. Al-Zahrani, K. Lin, Z. Rotter, V. Ashton-Prolla, P. Chemes, L. B. Moffat, J. Gingras, A.-C. Oren, M. Durocher, D. Schramek, D. 2022-03-14 doi:10.1101/2022.03.13.483372 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events ]]> https://biorxiv.org/content/10.1101/2022.03.14.484207v1?rss=1 Allen, G. Weiss, B. Panasenko, O. O. Huch, S. Villanyi, Z. Albert, B. Dilg, D. Zagatti, M. Schaughency, P. Liao, S. Corden, J. Polte, C. Shore, D. Ignatova, Z. Pelechano, V. Collart, M. A. 2022-03-14 doi:10.1101/2022.03.14.484207 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Parsing the role of NSP1 in SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2022.03.14.484208v1?rss=1 Fisher, T. Gluck, A. Narayanan, K. Kuroda, M. Nachshon, A. C Hsu, J. J Halfmann, P. Yahalom-Ronen, Y. Finkel, Y. Schwartz, M. Weiss, S. K Tseng, C.-T. Israely, T. Paran, N. Kawaoka, Y. Makino, S. Sternn-Ginnosar, N. 2022-03-14 doi:10.1101/2022.03.14.484208 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Adaptive Magnetic Resonance ]]> https://biorxiv.org/content/10.1101/2022.03.16.484410v1?rss=1 Beracha, I. Seginer, A. Tal, A. 2022-03-18 doi:10.1101/2022.03.16.484410 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ TATTOO-seq delineates spatial and cell type-specific regulatory programs during limb patterning ]]> https://biorxiv.org/content/10.1101/2022.03.20.482385v1?rss=1 Bastide, S. Chomsky, E. Saudemont, B. Loe-Mie, Y. Schmutz, S. Novault, S. Marlow, H. Tanay, A. Spitz, F. 2022-03-20 doi:10.1101/2022.03.20.482385 Cold Spring Harbor Laboratory Press 2022-03-20 <![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[ A new monoclonal antibody enables BAR analysis of subcellular importin β1 interactomes ]]> https://biorxiv.org/content/10.1101/2022.03.23.485495v1?rss=1 Song, D.-A. Alber, S. Doron-Mandel, E. Schmid, V. Albus, C. A. Leitner, O. Hamawi, H. Oses-Prieto, J. A. Burlingame, A. Fainzilber, M. Rishal, I. 2022-03-26 doi:10.1101/2022.03.23.485495 Cold Spring Harbor Laboratory Press 2022-03-26 <![CDATA[ Genetically engineered MRI-trackable extracellular vesicles as SARS-CoV-2 mimetics for mapping ACE2 binding in vivo ]]> https://biorxiv.org/content/10.1101/2022.03.27.485958v1?rss=1 Galisova, A. Zahradnik, J. Allouche-Arnon, H. Morandi, M. I. Abou Karam, P. Avinoam, O. Regev-Rudzki, N. Schreiber, G. Bar-Shir, A. 2022-03-28 doi:10.1101/2022.03.27.485958 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Extracellular vesicle fusion visualized by cryo-EM ]]> https://biorxiv.org/content/10.1101/2022.03.28.486013v1?rss=1 Morandi, M. I. Busko, P. Ozer-Partuk, E. Khan, S. Zarfati, G. Elbaz-Alon, Y. Abou Karam, P. Napso Shogan, T. Ginini, L. Gil, Z. Regev-Rudzki, N. Avinoam, O. 2022-03-28 doi:10.1101/2022.03.28.486013 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Protein Quaternary Structures in Solution are a Mixture of Multiple forms ]]> https://biorxiv.org/content/10.1101/2022.03.30.486392v1?rss=1 Marciano, S. Debabrata, D. Listov, D. Fleishman, S. J. Sonn-Segev, A. Mertens, H. Busch, F. Kim, Y. Harvey, S. R. Wysocki, V. H. Schreiber, G. 2022-03-31 doi:10.1101/2022.03.30.486392 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ Combined drought resistance strategies and the hydraulic limit in co-existing Mediterranean woody species ]]> https://biorxiv.org/content/10.1101/2022.04.01.486704v1?rss=1 Alon, A. Cohen, S. Burlett, R. Hochberg, U. Lukyanov, V. Rog, I. Klein, T. Cochard, H. Delzon, S. David-Schwartz, R. 2022-04-04 doi:10.1101/2022.04.01.486704 Cold Spring Harbor Laboratory Press 2022-04-04 <![CDATA[ SARS-CoV-2 spike S375F mutation characterizes the Omicron BA.1 variant ]]> https://biorxiv.org/content/10.1101/2022.04.03.486864v1?rss=1 Kimura, I. Yamasoba, D. Nasser, H. Zahradnik, J. Kosugi, Y. Wu, J. Nagata, K. Uriu, K. Tanaka, Y. L. Ito, J. Shimizu, R. Tan, T. S. Butlertanaka, E. P. Asakura, H. Sadamasu, K. Yoshimura, K. Ueno, T. Takaori-Kondo, A. Schreiber, G. The Genotype to Phenotype Japan (G2P-Japan) Consortium, Toyoda, M. Shirakawa, K. Irie, T. Saito, A. Nakagawa, S. Ikeda, T. Sato, K. 2022-04-03 doi:10.1101/2022.04.03.486864 Cold Spring Harbor Laboratory Press 2022-04-03 <![CDATA[ Perivascular SPP1 Mediates Microglial Engulfment of Synapses in Alzheimers Disease Models ]]> https://biorxiv.org/content/10.1101/2022.04.04.486547v1?rss=1 De Schepper, S. Ge, J. Z. Crowley, G. Ferreira, L. S. Garceau, D. Toomey, C. E. Sokolova, D. Childs, T. Lashley, T. Burden, J. J. Jung, S. Sasner, M. Frigerio, C. S. Hong, S. 2022-04-05 doi:10.1101/2022.04.04.486547 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Information theory characteristics improve the prediction of lithium response in bipolar disorder patients using an SVM classifier ]]> https://biorxiv.org/content/10.1101/2022.04.04.486856v1?rss=1 Tripathi, U. Mizrahi, L. Alda, M. Falkovich, G. Stern, S. 2022-04-05 doi:10.1101/2022.04.04.486856 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains ]]> https://biorxiv.org/content/10.1101/2022.04.10.487755v1?rss=1 Seal, M. Weil-Ktorza, O. Despotovic, D. S Tawfik, D. Levy, Y. Metanis, N. M Longo, L. Goldfarb, D. 2022-04-10 doi:10.1101/2022.04.10.487755 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors ]]> https://biorxiv.org/content/10.1101/2022.04.11.487859v1?rss=1 Hör, J. Jung, J. Đurica-Mitic, S. Barquist, L. Vogel, J. 2022-04-11 doi:10.1101/2022.04.11.487859 Cold Spring Harbor Laboratory Press 2022-04-11 <![CDATA[ Top-down modulation of the retinal code via histaminergic neurons of the hypothalamus ]]> https://biorxiv.org/content/10.1101/2022.04.26.489509v1?rss=1 Warwick, R. A. Riccitelli, S. Heukamp, A. S. Yaakov, H. Ankri, L. Mayzel, J. Gilead, N. Parness-Yossifon, R. Rivlin-Etzion, M. 2022-04-26 doi:10.1101/2022.04.26.489509 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ A toolbox for systematic discovery of stable and transient protein interactors in baker's yeast ]]> https://biorxiv.org/content/10.1101/2022.04.27.489741v1?rss=1 Fenech, E. J. Cohen, N. Kupervaser, M. Gazi, Z. Schuldiner, M. 2022-04-28 doi:10.1101/2022.04.27.489741 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ In-situ energy budget of needle-leaves reveals shift from evaporative to 'air cooling' under drought ]]> https://biorxiv.org/content/10.1101/2022.04.29.489999v1?rss=1 Muller, J. D. Rotenberg, E. Tatarinov, F. Oz, I. Yakir, D. 2022-05-01 doi:10.1101/2022.04.29.489999 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Cellular orientational fluctuations, rotational diffusion and nematic order under periodic driving ]]> https://biorxiv.org/content/10.1101/2022.04.30.490160v1?rss=1 Moriel, A. Livne, A. Bouchbinder, E. 2022-05-01 doi:10.1101/2022.04.30.490160 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Viruses inhibit TIR gcADPR signaling to overcome bacterial defense ]]> https://biorxiv.org/content/10.1101/2022.05.03.490397v1?rss=1 Leavitt, A. Yirmiya, E. Amitai, G. Lu, A. Garb, J. Morehouse, B. R. Hobbs, S. J. Kranzusch, P. J. Sorek, R. 2022-05-03 doi:10.1101/2022.05.03.490397 Cold Spring Harbor Laboratory Press 2022-05-03 <![CDATA[ The Colon Mucosal Sialylglycome Is Redox-Regulated by the Golgi Enzyme QSOX1 ]]> https://biorxiv.org/content/10.1101/2022.05.03.490496v1?rss=1 Ilani, T. Reznik, N. Yeshaya, N. Feldman, T. Vilela, P. Lansky, Z. Javitt, G. Shemesh, M. Brenner, O. Elkis, Y. Varsano, N. Murray, N. Azadi, P. Jaramillo, A. M. Evans, C. M. Fass, D. 2022-05-04 doi:10.1101/2022.05.03.490496 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ A systematic approach to study protein-substrate specificity enables the identification of Ssh1 substrate range ]]> https://biorxiv.org/content/10.1101/2022.05.04.490583v1?rss=1 Cohen, N. Aviram, N. Schuldiner, M. 2022-05-04 doi:10.1101/2022.05.04.490583 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Single-cell atlas of mouse limb development reveals a complex spatiotemporal dynamics of skeleton formation ]]> https://biorxiv.org/content/10.1101/2022.05.07.490557v1?rss=1 Markman, S. Zada, M. David, E. Giladi, A. Amit, I. Zelzer, E. 2022-05-07 doi:10.1101/2022.05.07.490557 Cold Spring Harbor Laboratory Press 2022-05-07 <![CDATA[ An expanding arsenal of immune systems that protect bacteria from phages ]]> https://biorxiv.org/content/10.1101/2022.05.11.491447v1?rss=1 Millman, A. Melamed, S. Leavitt, A. Doron, S. Bernheim, A. Hör, J. Lopatina, A. Ofir, G. Hochhauser, D. Stokar-Avihail, A. Tal, N. Sharir, S. Voichek, M. Erez, Z. Ferrer, J. L. M. Dar, D. Kacen, A. Amitai, G. Sorek, R. 2022-05-11 doi:10.1101/2022.05.11.491447 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ The homodimeric structure of the LARGE1 dual glycosyltransferase ]]> https://biorxiv.org/content/10.1101/2022.05.11.491581v1?rss=1 Katz, M. Diskin, R. 2022-05-12 doi:10.1101/2022.05.11.491581 Cold Spring Harbor Laboratory Press 2022-05-12 <![CDATA[ Partner-assisted artificial selection of a secondary function for efficient bioremediation ]]> https://biorxiv.org/content/10.1101/2022.05.12.491680v1?rss=1 Zaccaria, M. Sandlin, N. Soen, Y. Momeni, B. 2022-05-12 doi:10.1101/2022.05.12.491680 Cold Spring Harbor Laboratory Press 2022-05-12 <![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[ Diffraction contrast in cryo-scanning transmission electron tomography reveals the boundary of hemozoin crystals in situ ]]> https://biorxiv.org/content/10.1101/2022.05.13.491750v1?rss=1 Mullick, D. Rechav, K. Leiserowitz, L. Dzikowski, R. Regev-Rudzki, N. Elbaum, M. 2022-05-13 doi:10.1101/2022.05.13.491750 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Kynurenic acid, a key L-tryptophan-derived metabolite, protects the heart from an ischemic damage ]]> https://biorxiv.org/content/10.1101/2022.05.17.492275v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@f2a49aorg.highwire.dtl.DTLVardef@14a501org.highwire.dtl.DTLVardef@15d016aorg.highwire.dtl.DTLVardef@10800e7_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Bigelman, E. Pasmanik-Chor, M. Dassa, B. Itkin, M. Malitsky, S. Dorot, O. Pichinuk, E. Levin-Zaidman, S. Dezorella, N. Abashidze, A. Kleinberg, Y. Keren, G. Entin Meer, M. 2022-05-17 doi:10.1101/2022.05.17.492275 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ ER translocation of suboptimal targeting sequences depends on Sec61β/Sbh1 and its phosphorylation ]]> https://biorxiv.org/content/10.1101/2022.05.18.492448v1?rss=1 Barbieri, G. Simon, J. Lupusella, C. R. Pereira, F. Elia, F. Meyer, H. Schuldiner, M. Hanes, S. D. Nguyen, D. Helms, V. Romisch, K. 2022-05-19 doi:10.1101/2022.05.18.492448 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Human primed and naive PSCs are both competent indifferentiating into bona fide trophoblast stem cells ]]> https://biorxiv.org/content/10.1101/2022.05.20.492766v1?rss=1 Viukov, S. Shani, T. Bayerl, J. Sheban, d. Stelzer, Y. Novershtern, N. Hanna, J. H. 2022-05-20 doi:10.1101/2022.05.20.492766 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ The petrous bone contains high concentrations of osteocytes: one possible reason why ancient DNA is better preserved in this bone. ]]> https://biorxiv.org/content/10.1101/2022.05.20.492830v1?rss=1 Ibrahim, J. Brumfeld, V. Addadi, Y. Rubin, S. Weiner, S. Boaretto, E. 2022-05-20 doi:10.1101/2022.05.20.492830 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Actin filaments couple the protrusive tips to the nucleus through the I-BAR domain protein IRSp53 for migration of elongated cells on 1D fibers ]]> https://biorxiv.org/content/10.1101/2022.05.20.492840v1?rss=1 Mukherjee, A. Ron, J. Hu, H. T. Nishimura, T. Hanawa-Suetsugu, K. Behkam, B. Gov, N. Suetsugu, S. Nain, A. 2022-05-20 doi:10.1101/2022.05.20.492840 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Coiling of cellular protrusions around extracellular fibers ]]> https://biorxiv.org/content/10.1101/2022.05.24.493192v1?rss=1 Sadhu, R. K. Hernandez-Padilla, C. Eisenbach, Y. E. Zhang, L. Vishwasrao, H. D. Behkam, B. Shroff, H. Igli\v{c}, A. Peles, E. Nain, A. Gov, N. 2022-05-25 doi:10.1101/2022.05.24.493192 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems ]]> https://biorxiv.org/content/10.1101/2022.05.25.493210v1?rss=1 lombard, f. Bourdin, G. Pesant, S. Agostini, S. Baudena, A. Boissin, E. Cassar, N. Clampitt, M. Conan, P. da Silva, O. Dimier, C. Douville, E. Elineau, A. Fin, J. Flores, J. M. Ghiglione, J. F. Hume, B. C. C. Jalabert, L. John, S. G. Kelly, R. L. Koren, I. Lin, Y. Marie, D. McMinds, R. Meriguet, Z. Metzl, N. Paz Garciax, D. A. Pedrotti, M. L. Poulain, J. Pujo Pay, M. Ras, J. Reverdin, G. Romac, S. Rouan, A. Rottinger, E. Vardi, A. Voolstra, C. R. Moulin, C. Iwankow, G. Banaigs, B. Bowler, C. Forcioli, D. Furla, P. Galand, P. E. Gilson, E. Reynaud, S 2022-05-25 doi:10.1101/2022.05.25.493210 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Virological characteristics of the novel SARS-CoV-2 Omicron variants including BA.2.12.1, BA.4 and BA.5 ]]> https://biorxiv.org/content/10.1101/2022.05.26.493539v1?rss=1 Kimura, I. Yamasoba, D. Tamura, T. Nao, N. Oda, Y. Mitoma, S. Ito, J. Nasser, H. Zahradnik, J. Uriu, K. Fujita, S. Kosugi, Y. Wang, L. Tsuda, M. Kishimoto, M. Ito, H. Suzuki, R. Shimizu, R. Begum, M. M. Yoshimatsu, K. Sasaki, J. Sasaki-Tabata, K. Yamamoto, Y. Nagamoto, T. Kanamune, J. Kobiyama, K. Asakura, H. Nagashima, M. Sadamasu, K. Yoshimura, K. Kuramochi, J. Schreiber, G. Ishii, K. J. Hashiguchi, T. The Genotype to Phenotype Japan (G2P-Japan) Consortium, Ikeda, T. Saito, A. Fukuhara, T. Tanaka, S. Matsuno, K. Sato, K. 2022-05-26 doi:10.1101/2022.05.26.493539 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ Arabidopsis thaliana induces multigenerational stress tolerance against biotic and abiotic stressors and memorization of host colonization in Bacillus subtilis ]]> https://biorxiv.org/content/10.1101/2022.05.29.493878v1?rss=1 Gilhar, O. Olender, T. Aharoni, A. Friedman, J. Kolodkin-Gal, I. 2022-05-30 doi:10.1101/2022.05.29.493878 Cold Spring Harbor Laboratory Press 2022-05-30 <![CDATA[ PGRL1A redox states alleviate photoinhibition in Arabidopsis during step changes in light intensity ]]> https://biorxiv.org/content/10.1101/2022.06.07.492398v1?rss=1 Chaturvedi, A. K. Dym, O. Fluhr, R. 2022-06-09 doi:10.1101/2022.06.07.492398 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ From pseudotime to true dynamics: reconstructing a real-time axis for T cells differentiation ]]> https://biorxiv.org/content/10.1101/2022.06.09.495431v1?rss=1 Gavish, A. Chain, B. Salame, T. M. Antebi, Y. E. Katz, S. Reich-Zeliger, S. Friedman, N. 2022-06-12 doi:10.1101/2022.06.09.495431 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ The defence island repertoire of the Escherichia coli pan-genome ]]> https://biorxiv.org/content/10.1101/2022.06.09.495481v1?rss=1 1,300 strains of Escherichia coli, the most widely studied organism in terms of phage-bacteria interactions. We found that defence islands preferentially integrate at several dozens of dedicated integration hotspots in the E. coli genome. Defence islands are usually carried on mobile genetic elements including prophages, integrative conjugative elements and transposons, as well as on other genetic elements whose nature of mobilisation is unclear. Each type of mobile genetic element has a preferred integration position but can carry a diverse variety of defensive cargo. On average, an E. coli genome has 4.5 genomic hotspots occupied by a defence system-containing mobile element, with some strains possessing up to eight defensively occupied hotspots. Our data show that the overwhelming majority of the E. coli pan-immune system is carried on mobile genetic elements that integrate at a discrete set of genomic hotspots, and explains why the immune repertoire substantially varies between different strains of the same species. ]]> Hochhauser, D. Millman, A. Sorek, R. 2022-06-09 doi:10.1101/2022.06.09.495481 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ The evolutionary history of class I aminoacyl-tRNA synthetases indicates early statistical translation ]]> https://biorxiv.org/content/10.1101/2022.06.09.495570v1?rss=1 Jablonska, J. Chun-Chen, Y. Longo, L. M. Tawfik, D. S. Gruic-Sovulj, I. 2022-06-11 doi:10.1101/2022.06.09.495570 Cold Spring Harbor Laboratory Press 2022-06-11 <![CDATA[ Chiral growth of adherent filopodia ]]> https://biorxiv.org/content/10.1101/2022.06.09.495577v1?rss=1 Li, W. Chung, W.-L. Kozlov, M. M. Medalia, O. Geiger, B. Bershadsky, A. 2022-06-10 doi:10.1101/2022.06.09.495577 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Neural plate progenitors give rise to both anterior and posterior pituitary cells ]]> https://biorxiv.org/content/10.1101/2022.06.12.495791v1?rss=1 Chen, Q. Leshkowitz, D. Li, H. van Impel, A. Schulte-Merker, S. Amit, I. Levkowitz, G. 2022-06-12 doi:10.1101/2022.06.12.495791 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Glucocorticoid-sensitive period of corticotroph development -- implications in early life stress ]]> https://biorxiv.org/content/10.1101/2022.06.13.495881v1?rss=1 Peles, G. Swaminathan, A. Levkowitz, G. 2022-06-14 doi:10.1101/2022.06.13.495881 Cold Spring Harbor Laboratory Press 2022-06-14 <![CDATA[ Epigenetic inheritance of gene-silencing is maintained by a self-tuning mechanism based on resource competition ]]> https://biorxiv.org/content/10.1101/2022.06.15.496123v1?rss=1 Karin, O. Miska, E. A. Simons, B. D. 2022-06-15 doi:10.1101/2022.06.15.496123 Cold Spring Harbor Laboratory Press 2022-06-15 <![CDATA[ Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide is dependent on the resident microbiota ]]> https://biorxiv.org/content/10.1101/2022.06.19.496708v1?rss=1 Hoces, D. Greter, G. Arnoldini, M. Moresi, C. Berent, S. Kolinko, I. Bansept, F. Woller, A. Häfliger, J. Martens, E. Hardt, W.-D. Loverdo, C. Slack, E. 2022-06-19 doi:10.1101/2022.06.19.496708 Cold Spring Harbor Laboratory Press 2022-06-19 <![CDATA[ Designed high-redox potential laccases exhibit high functional diversity ]]> https://biorxiv.org/content/10.1101/2022.06.22.497129v1?rss=1 Barber-Zucker, S. Mateljak, I. Goldsmith, M. Kupervaser, M. Alcalde, M. Fleishman, S. J. 2022-06-23 doi:10.1101/2022.06.22.497129 Cold Spring Harbor Laboratory Press 2022-06-23 <![CDATA[ The Future is 2D: Spectral-Temporal Fitting of Dynamic Magnetic Resonance Spectroscopy Data Provides Exponential Gains in Precision Over Conventional Approaches ]]> https://biorxiv.org/content/10.1101/2022.06.23.497318v1?rss=1 Tal, A. 2022-06-26 doi:10.1101/2022.06.23.497318 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Deciphering the involvement of the Hippo pathway co-regulators, YAP/TAZ in invadopodia formation and matrix degradation ]]> https://biorxiv.org/content/10.1101/2022.06.28.497902v1?rss=1 Venghateri, J. B. Dassa, B. Morgenstern, D. Shreberk-Shaked, M. Oren, M. Geiger, B. 2022-07-01 doi:10.1101/2022.06.28.497902 Cold Spring Harbor Laboratory Press 2022-07-01 <![CDATA[ Exon-intron architecture determines mRNA stability by dictating m6A deposition ]]> https://biorxiv.org/content/10.1101/2022.06.29.498130v1?rss=1 Uzonyi, A. Slobodin, B. Schwartz, S. 2022-06-29 doi:10.1101/2022.06.29.498130 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ RORc expressing immune cells support pro-tumorigenic functions of tertiary lymphoid structures ]]> https://biorxiv.org/content/10.1101/2022.07.02.498540v1?rss=1 View larger version (21K): org.highwire.dtl.DTLVardef@385067org.highwire.dtl.DTLVardef@126c45corg.highwire.dtl.DTLVardef@25ad06org.highwire.dtl.DTLVardef@1829326_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cinnamon, E. Stein, I. Zino, E. Rabinovich, S. Shovman, Y. Schlesinger, Y. Salame, T. M. Reich-Zeliger, S. Lotem, M. Ben-Neriah, Y. Parnas, O. Pikarsky, E. 2022-07-03 doi:10.1101/2022.07.02.498540 Cold Spring Harbor Laboratory Press 2022-07-03 <![CDATA[ Assembly of von Willebrand Factor Tubules with in Vivo Helical Parameters Requires A1 Domain Insertion ]]> https://biorxiv.org/content/10.1101/2022.07.05.498862v1?rss=1 Javitt, G. Fass, D. 2022-07-05 doi:10.1101/2022.07.05.498862 Cold Spring Harbor Laboratory Press 2022-07-05 <![CDATA[ Solanum lycopersicum CLASS-II KNOX genes regulate fruit anatomy via gibberellin-dependent and independent pathways. ]]> https://biorxiv.org/content/10.1101/2022.07.06.498955v1?rss=1 Shtern, A. Keren-Keiserman, A. Mauxion, J.-P. Furumizu, C. Alvarez, J. P. Amsellem, Z. Gil, N. Motenko, E. Alkalai-Tuvia, S. Fallik, E. Gonzalez, N. Goldshmidt, A. 2022-07-06 doi:10.1101/2022.07.06.498955 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ Identification of a multipotent lung progenitor for lung regeneration ]]> https://biorxiv.org/content/10.1101/2022.07.07.498730v1?rss=1 Rosen, C. Shetzen, E. Milman -Krentsis, I. Orgad, R. Su, X. Yadav, R. Shemesh, M. Biram, A. Shulman, Z. Eventov-Friedman, S. Maharjan, M. Qi, Y. Wang, J. Reisner, Y. 2022-07-07 doi:10.1101/2022.07.07.498730 Cold Spring Harbor Laboratory Press 2022-07-07 <![CDATA[ Modulating the proliferative and cytotoxic properties of human TIL by a synthetic immune niche of immobilized CCL21 and ICAM1 ]]> https://biorxiv.org/content/10.1101/2022.07.07.499105v1?rss=1 Yunger, S. Geiger, B. Friedman, N. Besser, M. J. Lieber, S. A. 2022-07-07 doi:10.1101/2022.07.07.499105 Cold Spring Harbor Laboratory Press 2022-07-07 <![CDATA[ Yeast Mitochondrial Derived Vesicles (MDVs) have membrane potential and contain a functional ATP synthase ]]> https://biorxiv.org/content/10.1101/2022.07.10.499450v1?rss=1 Hazan (Ben-Menachem), R. Lintzer, D. Ziv, T. Das, K. Rosenhek-Goldian, I. Porat, Z. Ben Ami Pilo, H. Karniely, S. Saada, A. Regev-Rudzki, N. Pines, O. 2022-07-10 doi:10.1101/2022.07.10.499450 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Machine learning reveals conserved chromatin patterns determining meiotic recombination sites in plants ]]> https://biorxiv.org/content/10.1101/2022.07.11.499557v1?rss=1 Wang, M. Shilo, S. Zhou, A. Zelkowski, M. Olson, M. A. Azuri, I. Shoshani-Hechel, N. Melamed-Bessudo, C. Marand, A. P. Jiang, J. Schnable, J. C. Underwood, C. J. Henderson, I. R. Sun, Q. Pillardy, J. Kianian, P. M. A. Kianian, S. F. Chen, C. Levy, A. A. Pawlowski, W. P. 2022-07-13 doi:10.1101/2022.07.11.499557 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Context-dependent differences in the functional responses of Lactobacillaeca strains to fermentable sugars ]]> https://biorxiv.org/content/10.1101/2022.07.11.499608v1?rss=1 Suissa, R. Oved, R. Maan, H. Gilhar, O. Meijler, M. Koren, O. Kolodkin-Gal, I. 2022-07-11 doi:10.1101/2022.07.11.499608 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Molecular characterization of the intact muscle spindle using a multi-omics approach ]]> https://biorxiv.org/content/10.1101/2022.07.13.499888v1?rss=1 Bornstein, B. Heinemann-Yerushalmi, L. Krief, S. Adler, R. Dassa, B. Leshkowitz, D. Kim, M. Bewick, G. Banks, R. W. Zelzer, E. 2022-07-14 doi:10.1101/2022.07.13.499888 Cold Spring Harbor Laboratory Press 2022-07-14 <![CDATA[ Isolated correlates of somatosensory perception in the mouse posterior cortex ]]> https://biorxiv.org/content/10.1101/2022.07.16.498499v1?rss=1 Sokoletsky, M. Ungarish, D. Katz, Y. Lampl, I. 2022-07-18 doi:10.1101/2022.07.16.498499 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ The C-terminal tail of CSNAP attenuates the CSN complex ]]> https://biorxiv.org/content/10.1101/2022.07.18.500399v1?rss=1 Füzesi-Levi, M. G. Ben-Nissan, G. Listov, D. Hayouka, Z. Fleishman, S. Sharon, M. 2022-07-19 doi:10.1101/2022.07.18.500399 Cold Spring Harbor Laboratory Press 2022-07-19 <![CDATA[ Acanthamoeba polyphaga de novo transcriptome and its dynamics during Mimivirus infection ]]> https://biorxiv.org/content/10.1101/2022.07.20.500700v1?rss=1 Nuri, R. Feldmesser, E. Fridmann-Sirkis, Y. Keren-Shaul, H. Nevo, R. Minsky, A. Reich, Z. 2022-07-20 doi:10.1101/2022.07.20.500700 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Polymer dynamics relates chromosome mixing to temporal changes in biological contact maps ]]> https://biorxiv.org/content/10.1101/2022.07.20.500905v1?rss=1 Bajpai, G. Safran, S. 2022-07-22 doi:10.1101/2022.07.20.500905 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ DNA Methylation is stable after MMEJ and NHEJ double strand break repair ]]> https://biorxiv.org/content/10.1101/2022.07.21.500965v1?rss=1 Bnaya, E. Shilo, S. Feldman, T. Bacharach, T. Moskovitz, Y. Kadam, A. Yedidim, P. Azogy, H. Kaushansky, N. Chapal-Ilani, N. Shlush, L. I. 2022-07-22 doi:10.1101/2022.07.21.500965 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Dually targeted proteins regulate proximity between peroxisomes and partner organelles ]]> https://biorxiv.org/content/10.1101/2022.07.29.501968v1?rss=1 Stehlik, T. Bittner, E. Lam, J. Dimitrov, L. Schöck, I. Harberding, J. Heymons, N. Schuldiner, M. Zalckvar, E. Bölker, M. Schekman, R. Freitag, J. 2022-07-31 doi:10.1101/2022.07.29.501968 Cold Spring Harbor Laboratory Press 2022-07-31 <![CDATA[ How talin allosterically activates vinculin ]]> https://biorxiv.org/content/10.1101/2022.08.01.502287v1?rss=1 Franz, F. Tapia-Rojo, R. Winograd-Katz, S. E. Boujemaa-Paterski, R. Li, W. Unger, T. Albeck, S. Aponte-Santamaria, C. Garcia-Manyes, S. Medalia, O. Geiger, B. Grater, F. 2022-08-02 doi:10.1101/2022.08.01.502287 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[ Mouse-embryo model derived exclusively from embryonic stem cells undergo neurulation and heart development ]]> https://biorxiv.org/content/10.1101/2022.08.01.502371v1?rss=1 Lau, K. Y. C. Rubinstein, H. Gantner, C. W. Amadei, G. Stelzer, Y. Zernicka-Goetz, M. 2022-08-02 doi:10.1101/2022.08.01.502371 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Perceptual stability reflected in neuronal pattern similarities in human visual cortex ]]> https://biorxiv.org/content/10.1101/2022.08.02.502429v1?rss=1 Broday-Dvir, R. Norman, Y. Harel, M. Mehta, A. Malach, R. 2022-08-03 doi:10.1101/2022.08.02.502429 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Do Newly Born Orphan Proteins Resemble Never Born Proteins?A Study using Deep Learning Algorithms ]]> https://biorxiv.org/content/10.1101/2022.08.02.502493v1?rss=1 Liu, J. Yuan, R. Shao, W. Wang, J. Silman, I. Sussman, J. L. 2022-08-02 doi:10.1101/2022.08.02.502493 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Store-operated Ca2+ entry regulatory factor (SARAF) alters murine metabolic state in an age-dependent manner via hypothalamic pathways. ]]> https://biorxiv.org/content/10.1101/2022.08.03.500424v1?rss=1 Gataulin, D. Kuperman, Y. Tsoory, M. Biton, I. Karbat, I. Meshcheriakova, A. Reuveny, E. 2022-08-05 doi:10.1101/2022.08.03.500424 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Genetic drivers of chromosomal integron stability ]]> https://biorxiv.org/content/10.1101/2022.08.03.502626v1?rss=1 Richard, E. Darracq, B. Littner, E. Vit, C. Whiteway, C. Bos, J. Fournes, F. Garriss, G. Conte, V. Lapaillerie, D. Parissi, V. Rousset, F. Skovgaard, O. Bikard, D. Rocha, E. Mazel, D. Loot, C. 2022-08-05 doi:10.1101/2022.08.03.502626 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 ]]> https://biorxiv.org/content/10.1101/2022.08.07.503115v1?rss=1 Saito, A. Tamura, T. Zahradnik, J. Deguchi, S. Tabata, K. Kimura, I. Ito, J. Nasser, H. Toyoda, M. Nagata, K. Uriu, K. Kosugi, Y. Fujita, S. Yamasoba, D. Shofa, M. Begum, M. M. Oda, Y. Suzuki, R. Ito, H. Nao, N. Wang, L. Tsuda, M. Yoshimatsu, K. Yamamoto, Y. Nagamoto, T. Asakura, H. Nagashima, M. Sadamasu, K. Yoshimura, K. Ueno, T. Schreiber, G. Takaori-Kondo, A. The Genotype to Phenotype Japan (G2P-Japan) Consortium, Shirakawa, K. Sawa, H. Irie, T. Takayama, K. Matsuno, K. Tanaka, S. Ikeda, T. Fukuhara, T. Sato, K. 2022-08-08 doi:10.1101/2022.08.07.503115 Cold Spring Harbor Laboratory Press 2022-08-08 <![CDATA[ Reliable energy-based antibody humanization and stabilization ]]> https://biorxiv.org/content/10.1101/2022.08.14.503891v1?rss=1 Tennenhouse, A. Khmelnitsky, L. Yeshaya, N. Noronha, A. Lindzen, M. Khalaila, R. Zaretsky, I. Fridmann Sirkis, Y. Galon-Wolfenson, Y. Abramson, J. Yarden, Y. Fass, D. Fleishman, S. J. 2022-08-15 doi:10.1101/2022.08.14.503891 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ A local sequence signature defines a subset of heterochromatin-associated CpGs with minimal loss of methylation in healthy tissues but extensive loss in cancer ]]> https://biorxiv.org/content/10.1101/2022.08.16.504069v1?rss=1 Bar, D. Fishman, L. Zheng, Y. Unterman, I. Schlesinger, D. Eden, A. Lin, D.-C. Berman, B. P. 2022-08-17 doi:10.1101/2022.08.16.504069 Cold Spring Harbor Laboratory Press 2022-08-17 <![CDATA[ Characteristic energy scales of active fluctuations in adherent cells ]]> https://biorxiv.org/content/10.1101/2022.08.17.504239v1?rss=1 Moriel, A. Wolfenson, H. Bouchbinder, E. 2022-08-17 doi:10.1101/2022.08.17.504239 Cold Spring Harbor Laboratory Press 2022-08-17 <![CDATA[ Cryo-EM structure of the RADAR supramolecular anti-phage defense complex ]]> https://biorxiv.org/content/10.1101/2022.08.17.504323v1?rss=1 Duncan-Lowey, B. Tal, N. Johnson, A. G. Rawson, S. Mayer, M. L. Doron, S. Millman, A. Melamed, S. Fedorenko, T. Kacen, A. Amitai, G. Sorek, R. Kranzusch, P. J. 2022-08-18 doi:10.1101/2022.08.17.504323 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ Epithelial antigen presentation controls commensal-specific intraepithelial T-cells in the gut ]]> https://biorxiv.org/content/10.1101/2022.08.21.504672v1?rss=1 Brabec, T. Schwarzer, M. Kovacova, K. Dobesova, M. Schierova, D. Brezina, J. Pacakova, I. Srutkova, D. Ben-Nun, O. Goldfarb, Y. Splichalova, I. Kolar, M. Abramson, J. Filipp, D. Dobes, J. 2022-08-22 doi:10.1101/2022.08.21.504672 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Energy transfer in ubiquitous rhodopsin pumps with xanthophyll antennas ]]> https://biorxiv.org/content/10.1101/2022.08.24.505090v1?rss=1 Chazan, A. Das, I. Fujiwara, T. Murakoshi, S. Shihoya, W. Rozenberg, A. Molina-Marquez, A. Larom, S. Pushkarev, A. Malakar, P. Ruhman, S. Hasegawa, M. Tsukamoto, Y. Ishizuka, T. Konno, M. Nagata, T. Inoue, K. Mizuno, Y. Katayama, K. Abe-Yoshizumi, R. Kandori, H. Leon, R. M. Yoshizawa, S. Sheves, M. Nureki, O. Beja, O. 2022-08-24 doi:10.1101/2022.08.24.505090 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ A network of mixed actin polarity in the leading edge of spreading cells ]]> https://biorxiv.org/content/10.1101/2022.08.26.505326v1?rss=1 Chung, W.-L. Eibauer, M. Li, W. Boujemaa-Paterski, R. Geiger, B. Medalia, O. 2022-08-26 doi:10.1101/2022.08.26.505326 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Discovery of phage determinants that confer sensitivity to bacterial immune systems ]]> https://biorxiv.org/content/10.1101/2022.08.27.505566v1?rss=1 Stokar-Avihail, A. Fedorenko, T. Garb, J. Leavitt, A. Millman, A. Shulman, G. Wojtania, N. Melamed, S. Amitai, G. Sorek, R. 2022-08-28 doi:10.1101/2022.08.27.505566 Cold Spring Harbor Laboratory Press 2022-08-28 <![CDATA[ gUMI-BEAR, a modular, unsupervised population barcoding method to track variants and evolution at high resolution ]]> https://biorxiv.org/content/10.1101/2022.09.01.506035v1?rss=1 Rezenman, S. Knafo, M. Tsigalnitski, I. Barad, S. Jona, G. Levi, D. Dym, O. Reich, Z. kapon, r. 2022-09-01 doi:10.1101/2022.09.01.506035 Cold Spring Harbor Laboratory Press 2022-09-01 <![CDATA[ Global profiling of the RNA and protein complexes of Escherichia coli by size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq) ]]> https://biorxiv.org/content/10.1101/2022.09.02.506378v1?rss=1 Chihara, K. Gerovac, M. Hör, J. Vogel, J. 2022-09-02 doi:10.1101/2022.09.02.506378 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Novel lipid biomarkers for algal resistance to viral infection in the ocean ]]> https://biorxiv.org/content/10.1101/2022.09.14.507897v1?rss=1 Schleyer, G. Kuhlisch, C. Ziv, C. Ben-Dor, S. Malitsky, S. Schatz, D. Vardi, A. 2022-09-14 doi:10.1101/2022.09.14.507897 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ The trophic pyramid revisited: most animal classes have more predator than herbivore species ]]> https://biorxiv.org/content/10.1101/2022.09.14.507913v1?rss=1 Klein, T. Livne-Luzon, S. Moran, U. 2022-09-16 doi:10.1101/2022.09.14.507913 Cold Spring Harbor Laboratory Press 2022-09-16 <![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[ 3D electron diffraction reveals the chiral nature of the malaria pigment crystal hemozoin ]]> https://biorxiv.org/content/10.1101/2022.09.15.507960v1?rss=1 Klar, P. B. Waterman, D. Gruene, T. Mullick, D. Song, Y. Gilchrist, J. B. Wen, W. Biran, I. Houben, L. Regev-Rudzki, N. Dzikowski, R. Palatinus, L. Zhang, P. Leiserowitz, L. Elbaum, M. 2022-09-16 doi:10.1101/2022.09.15.507960 Cold Spring Harbor Laboratory Press 2022-09-16 <![CDATA[ A new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress ]]> https://biorxiv.org/content/10.1101/2022.09.15.508072v1?rss=1 Reinhard, J. Starke, L. Klose, C. Haberkant, P. Hammaren, H. Stein, F. Klein, O. Berhorst, C. Stumpf, H. Saenz, J. P. Hub, J. Schuldiner, M. Ernst, R. 2022-09-16 doi:10.1101/2022.09.15.508072 Cold Spring Harbor Laboratory Press 2022-09-16 <![CDATA[ AlphaFold2-based fusion design deciphers crucial role of the E3 UFL1 N-terminal helix in E2 UFC1 binding and ufmylation ]]> https://biorxiv.org/content/10.1101/2022.09.15.508077v1?rss=1 Banerjee, S. Varga, J. K. Kumar, M. Schueler-Furman, O. Wiener, R. 2022-09-15 doi:10.1101/2022.09.15.508077 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Modularly designed protein fragments combine into thousands of active and structurally diverse enzymes ]]> https://biorxiv.org/content/10.1101/2022.09.17.508230v1?rss=1 10,000 active enzymes. This design-test-learn loop can be applied, in principle, to any modular protein family, yielding huge diversity and general lessons on protein design principles. ]]> Lipsh-Sokolik, R. Khersonsky, O. Schroder, S. P. de Boer, C. Hoch, S. Y. Davies, G. J. Overkleeft, H. S. Fleishman, S. J. 2022-09-18 doi:10.1101/2022.09.17.508230 Cold Spring Harbor Laboratory Press 2022-09-18 <![CDATA[ Large variations in afforestation-related climate cooling and warming effects across short distances ]]> https://biorxiv.org/content/10.1101/2022.09.18.508428v1?rss=1 200 years in the driest sites to [~]70 years in the intermediate and [~]40 years in the wettest sites. Climate-related benefits of forestation, previously considered at large-spatial scales, should be considered at high-spatial resolutions in climate-change mitigation programs aimed at taking advantage of the vast non-forested dry regions. TeaserClimate-related effects of afforestation can vary between cooling and warming effects across 200 km. ]]> Rohatyn, S. Rotenberg, E. Tatarinov, F. Carmel, Y. Yakir, D. 2022-09-19 doi:10.1101/2022.09.18.508428 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Multi-Dimensional Structure and Dynamics Landscape of Proteins in Mammalian Cells Revealed by In-cell NMR ]]> https://biorxiv.org/content/10.1101/2022.09.20.508803v1?rss=1 Kadavath, H. Prymaczok, N. Eichmann, C. Riek, R. Gerez, J. 2022-09-21 doi:10.1101/2022.09.20.508803 Cold Spring Harbor Laboratory Press 2022-09-21 <![CDATA[ Integrative single cell and spatial transcriptomics of colorectal cancer reveals multicellular functional units that support tumor progression ]]> https://biorxiv.org/content/10.1101/2022.10.02.508492v1?rss=1 Avraham-Davidi, I. Mages, S. Klughammer, J. Moriel, N. Imada, S. Hofree, M. Murray, E. Chen, J. Pelka, K. Mehta, A. Boland, G. M. Delorey, T. M. Caplan, L. Dionne, D. Tirosh, I. Hacohen, N. Chen, F. Yilmaz, O. H. Roper, J. Rozenblatt-Rosen, O. Nitzan, M. Regev, A. 2022-10-02 doi:10.1101/2022.10.02.508492 Cold Spring Harbor Laboratory Press 2022-10-02 <![CDATA[ Emergent oscillations during cellular directional decision-making on junctions ]]> https://biorxiv.org/content/10.1101/2022.10.14.512239v1?rss=1 Ron, J. E. Crestani, M. Kux, J.-M. Liu, J. Al-Dam, N. Monzo, P. Gauthier, N. C. Saez, P. J. Gov, N. S. 2022-10-14 doi:10.1101/2022.10.14.512239 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ Computational design of BclxL inhibitors that target transmembrane domain interactions ]]> https://biorxiv.org/content/10.1101/2022.11.09.515782v1?rss=1 Duart, G. Elazar, A. Weinstein, J. Gadea-Salom, L. Ortiz-Mateu, J. Fleishman, S. Mingarro, I. Martinez-Gil, L. 2022-11-09 doi:10.1101/2022.11.09.515782 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ Fragment-Based Hit Discovery via Unsupervised Learning of Fragment-Protein Complexes ]]> https://biorxiv.org/content/10.1101/2022.11.21.517375v1?rss=1 McCorkindale, W. J. Ahel, I. Barr, H. Correy, G. J. Fraser, J. S. London, N. Schuller, M. Shurrush, K. Lee, A. A. 2022-11-24 doi:10.1101/2022.11.21.517375 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Optimization-Based Decoding of Imaging Spatial Transcriptomics Data ]]> https://biorxiv.org/content/10.1101/2022.11.22.517523v1?rss=1 Bryan, J. P. Binan, L. McCann, C. Eldar, Y. C. Farhi, S. L. Cleary, B. 2022-11-24 doi:10.1101/2022.11.22.517523 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ The lncRNA landscape of cardiac resident macrophages and identification of Schlafenlnc as a regulator of macrophage migratory function ]]> https://biorxiv.org/content/10.1101/2022.11.30.518576v1?rss=1 Dueck, A. Althaus, L. Heise, K. Esfandyari, D. Bayguen, S. Brandes, R. P. Gagneur, J. Jae, N. Knolle, P. Leisegang, M. S. Maegdefessel, L. Meitinger, T. Petzold, N. Ramanujam, D. Sager, H. Schulz, C. Theodorakis, E. Uzonyi, A. Weinberger, T. Bader, M. Schmidt-Supprian, M. Engelhardt, S. 2022-12-01 doi:10.1101/2022.11.30.518576 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Phylogeny and biogeography of the algal DMS-releasing enzyme ]]> https://biorxiv.org/content/10.1101/2022.12.01.518734v1?rss=1 Shemi, A. Ben-Dor, S. Rotkopf, R. Dym, O. Vardi, A. 2022-12-01 doi:10.1101/2022.12.01.518734 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Mega-scale experimental analysis of protein folding stability in biology and protein design ]]> https://biorxiv.org/content/10.1101/2022.12.06.519132v1?rss=1 Tsuboyama, K. Dauparas, J. Chen, J. Mangan, N. M. Ovchinnikov, S. Rocklin, G. J. 2022-12-06 doi:10.1101/2022.12.06.519132 Cold Spring Harbor Laboratory Press 2022-12-06 <![CDATA[ p16-dependent upregulation of PD-L1 impairs immunosurveillance of senescent cells ]]> https://biorxiv.org/content/10.1101/2023.01.30.524522v1?rss=1 Majewska, J. Agrawal, A. Mayo, A. Roitman, L. Chatterjee, R. Kralova, J. Landsberger, T. Katzenelenbogen, Y. Salame, T. M. Hagai, E. Stanojevic, N. Amit, I. Alon, U. Krizhanovsky, V. 2023-02-01 doi:10.1101/2023.01.30.524522 Cold Spring Harbor Laboratory Press 2023-02-01 <![CDATA[ Antibiotic hyper-resistance in a class I aminoacyl-tRNA synthetase with altered active site signature motif ]]> https://biorxiv.org/content/10.1101/2023.01.31.526100v1?rss=1 Brkic, A. Leibundgut, M. Jablonska, J. Zanki, V. Car, Z. Petrovic-Perokovic, V. Marsavelski, A. Ban, N. Gruic-Sovulj, I. 2023-01-31 doi:10.1101/2023.01.31.526100 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Homeostatic synaptic scaling optimizes learning in network models of neural population codes ]]> https://biorxiv.org/content/10.1101/2023.03.05.530392v1?rss=1 Mayzel, J. Schneidman, E. 2023-03-05 doi:10.1101/2023.03.05.530392 Cold Spring Harbor Laboratory Press 2023-03-05 <![CDATA[ The structure and function of neural connectomes are shaped by a small number of design principles ]]> https://biorxiv.org/content/10.1101/2023.03.15.532611v1?rss=1 Haber, A. Wanner, A. Friedrich, R. W. Schneidman, E. 2023-03-15 doi:10.1101/2023.03.15.532611 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Defining the Transcriptional Landscape during Cytomegalovirus Latency with Single-Cell RNA Sequencing ]]> https://biorxiv.org/content/10.1101/208603v1?rss=1 Shnayder, M. Nachshon, A. Krishna, B. Poole, E. Boshkov, A. Binyamin, A. Maza, I. Sinclair, J. Schwartz, M. Stern-Ginossar, N. 2017-10-25 doi:10.1101/208603 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ Development of migrating entheses involves replacement of progenitor populations ]]> https://biorxiv.org/content/10.1101/210799v1?rss=1 Felsenthal, N. Rubin, S. Stern, T. Krief, S. Pal, D. Pryce, B. A. Schweitzer, R. Zelzer, E. 2017-10-29 doi:10.1101/210799 Cold Spring Harbor Laboratory Press 2017-10-29 <![CDATA[ A 20S proteasome receptor for degradation of intrinsically disordered proteins ]]> https://biorxiv.org/content/10.1101/210898v1?rss=1 Biran, A. Myers, N. Adler, J. Broennimann, K. Reuven, N. Shaul, Y. 2017-10-29 doi:10.1101/210898 Cold Spring Harbor Laboratory Press 2017-10-29 <![CDATA[ Oncogenic addiction to high 26S proteasome levels ]]> https://biorxiv.org/content/10.1101/211300v1?rss=1 Tsvetkov, P. Adler, J. Myers, N. Biran, A. Reuven, N. Shaul, Y. 2017-10-30 doi:10.1101/211300 Cold Spring Harbor Laboratory Press 2017-10-30 <![CDATA[ Efficient CRISPR/Cas-mediated homologous recombination in the model diatom Thalassiosira pseudonana ]]> https://biorxiv.org/content/10.1101/215582v1?rss=1 Belshaw, N. Grouneva, I. Aram, L. Gal, A. Hopes, A. Mock, T. 2017-11-09 doi:10.1101/215582 Cold Spring Harbor Laboratory Press 2017-11-09 <![CDATA[ Formation and disassembly of a contractile actomyosin network mediates content release from large secretory vesicles ]]> https://biorxiv.org/content/10.1101/216044v1?rss=1 Segal, D. Zaritsky, A. Schejter, E. D. Shilo, B. Z. 2017-11-08 doi:10.1101/216044 Cold Spring Harbor Laboratory Press 2017-11-08 <![CDATA[ Optimizing gene expression by adapting splicing ]]> https://biorxiv.org/content/10.1101/220228v1?rss=1 Frumkin, I. Yofe, I. Bar-Ziv, R. Voichek, Y. Pilpel, Y. 2017-11-15 doi:10.1101/220228 Cold Spring Harbor Laboratory Press 2017-11-15 <![CDATA[ High-efficiency optogenetic silencing with soma-targeted anion-conducting channelrhodopsins ]]> https://biorxiv.org/content/10.1101/225847v1?rss=1 Mahn, M. Gibor, L. Cohen-Kashi Malina, K. Patil, P. Printz, Y. Oring, S. Levy, R. Lampl, I. Yizhar, O. 2017-12-08 doi:10.1101/225847 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ A genome-wide resource for high-throughput genomic tagging of yeast ORFs ]]> https://biorxiv.org/content/10.1101/226811v1?rss=1 Meurer, M. Duan, Y. Sass, E. Kats, I. Herbst, K. Buchmuller, B. C. Dederer, V. Huber, F. Kirrmaier, D. Stefl, M. Van Laer, K. Dick, T. P. Lemberg, M. K. Khmelinskii, A. Levy, E. D. Knop, M. 2017-11-30 doi:10.1101/226811 Cold Spring Harbor Laboratory Press 2017-11-30 <![CDATA[ AWARENESS OF THE OUTCOME OF SELF-INITIATED POINTING ACTIONS ]]> https://biorxiv.org/content/10.1101/234369v1?rss=1 Gorea, A. Granjon, L. Sagi, D. 2017-12-15 doi:10.1101/234369 Cold Spring Harbor Laboratory Press 2017-12-15 <![CDATA[ Simplifying the combined use of CRISPR-Cas9 and Cre-loxP technologies for the efficient generation of targeted conditional gene knockouts in mammalian cells ]]> https://biorxiv.org/content/10.1101/236679v1?rss=1 Noiman, T. Kahana, C. 2017-12-19 doi:10.1101/236679 Cold Spring Harbor Laboratory Press 2017-12-19 <![CDATA[ Real-time visual interactions across the boundary of awareness ]]> https://biorxiv.org/content/10.1101/237917v1?rss=1 Meital-Kfir, N. Sagi, D. 2017-12-21 doi:10.1101/237917 Cold Spring Harbor Laboratory Press 2017-12-21 <![CDATA[ Development of High-Order Organization of Guanine-Based Reflectors Underlies the Dual Functionality of the Zebrafish Iris ]]> https://biorxiv.org/content/10.1101/240028v1?rss=1 Gur, D. Nicolas, J.-D. Brumfeld, V. Bar-Elli, O. Oron, D. Levkowitz, G. 2017-12-28 doi:10.1101/240028 Cold Spring Harbor Laboratory Press 2017-12-28 <![CDATA[ Isoxanthopterin: An Optically Functional Biogenic Crystal in the Eyes of Decapod Crustaceans ]]> https://biorxiv.org/content/10.1101/240366v1?rss=1 Palmer, B. A. Hirsch, A. Brumfeld, V. Aflalo, E. D. Pinkas, I. Sagi, A. Rozenne, S. Oron, D. Leiserowitz, L. Kronik, L. Weiner, S. Addadi, L. 2017-12-28 doi:10.1101/240366 Cold Spring Harbor Laboratory Press 2017-12-28 <![CDATA[ On a non-trivial application of Algebraic Topology to Molecular Biology ]]> https://biorxiv.org/content/10.1101/240499v1?rss=1 Braslavsky, I. Stavans, J. 2017-12-30 doi:10.1101/240499 Cold Spring Harbor Laboratory Press 2017-12-30 <![CDATA[ Membrane potential correlates of network decorrelation and improved SNR by cholinergic activation in the somatosensory cortex. ]]> https://biorxiv.org/content/10.1101/240853v1?rss=1 Meir, I. Katz, Y. Lampl, I. 2017-12-29 doi:10.1101/240853 Cold Spring Harbor Laboratory Press 2017-12-29 <![CDATA[ Evolutionary tradeoffs and the structure of allelic polymorphisms ]]> https://biorxiv.org/content/10.1101/244210v1?rss=1 Sheftel, H. Szekely, P. Mayo, A. Sella, G. Alon, U. 2018-01-06 doi:10.1101/244210 Cold Spring Harbor Laboratory Press 2018-01-06 <![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[ A bacterial growth law out of steady-state ]]> https://biorxiv.org/content/10.1101/257709v1?rss=1 Korem Kohanim, Y. Levi, D. Jona, G. Bren, A. Alon, U. 2018-01-31 doi:10.1101/257709 Cold Spring Harbor Laboratory Press 2018-01-31 <![CDATA[ Reprogramming protein abundance fluctuations in single cells by degradation ]]> https://biorxiv.org/content/10.1101/260695v1?rss=1 Matalon, O. Steinberg, A. Sass, E. Hausser, J. Levy, E. D. 2018-02-05 doi:10.1101/260695 Cold Spring Harbor Laboratory Press 2018-02-05 <![CDATA[ The interplay of synaptic plasticity and scaling enables the self-organized allocation of multiple memory representations ]]> https://biorxiv.org/content/10.1101/260950v1?rss=1 Auth, J. M. Nachstedt, T. Tetzlaff, C. 2018-02-06 doi:10.1101/260950 Cold Spring Harbor Laboratory Press 2018-02-06 <![CDATA[ Spatial reconstruction of single enterocytes uncovers broad zonation along the intestinal villus axis ]]> https://biorxiv.org/content/10.1101/261529v1?rss=1 Moor, A. E. Harnik, Y. Ben-Moshe, S. Massasa, E. E. Bahar Halpern, K. Itzkovitz, S. 2018-02-07 doi:10.1101/261529 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ Long time-scales in primate amygdala neurons support aversive learning ]]> https://biorxiv.org/content/10.1101/263889v1?rss=1 Taub, A. H. Stolero, T. Livneh, U. Shohat, Y. Paz, R. 2018-02-11 doi:10.1101/263889 Cold Spring Harbor Laboratory Press 2018-02-11 <![CDATA[ Tradeoffs and cultural diversity ]]> https://biorxiv.org/content/10.1101/263905v1?rss=1 Karin, O. Alon, U. 2018-02-14 doi:10.1101/263905 Cold Spring Harbor Laboratory Press 2018-02-14 <![CDATA[ Central dogma rates and the trade-off between precision and economy ]]> https://biorxiv.org/content/10.1101/276139v1?rss=1 Hausser, J. Mayo, A. Alon, U. 2018-03-04 doi:10.1101/276139 Cold Spring Harbor Laboratory Press 2018-03-04 <![CDATA[ Polyamines support myogenesis by facilitating myoblast migration ]]> https://biorxiv.org/content/10.1101/280206v1?rss=1 Brenner, S. Feiler, Y. Kahana, C. 2018-03-11 doi:10.1101/280206 Cold Spring Harbor Laboratory Press 2018-03-11 <![CDATA[ Roles of G1 cyclins in the temporal organization of yeast cell cycle - a transcriptome-wide analysis ]]> https://biorxiv.org/content/10.1101/287573v1?rss=1 Teufel, L. Tummler, K. Flöttmann, M. Herrmann, A. Barkai, N. Klipp, E. 2018-03-23 doi:10.1101/287573 Cold Spring Harbor Laboratory Press 2018-03-23 <![CDATA[ Fast calcium transients in neuronal spines is driven by extreme statistics ]]> https://biorxiv.org/content/10.1101/290734v1?rss=1 Basnayake, K. Korkotian, E. Holcman, D. 2018-03-28 doi:10.1101/290734 Cold Spring Harbor Laboratory Press 2018-03-28 <![CDATA[ Monkeys use the rod-dense retinal region rather than the fovea to visually fixate small targets in scotopic vision ]]> https://biorxiv.org/content/10.1101/290759v1?rss=1 Spivak, O. Thier, P. Barash, S. 2018-03-28 doi:10.1101/290759 Cold Spring Harbor Laboratory Press 2018-03-28 <![CDATA[ Identification of a secretion-enhancing cis regulatory targeting element (SECReTE) involved in mRNA localization and protein synthesis ]]> https://biorxiv.org/content/10.1101/303156v1?rss=1 Cohen-Zontag, O. Lim, L. Q. J. Dahary, D. Olender, T. Pilpel, Y. Gerst, J. 2018-04-17 doi:10.1101/303156 Cold Spring Harbor Laboratory Press 2018-04-17 <![CDATA[ M1A within cytoplasmic mRNAs at single nucleotide resolution: A reconciled transcriptome-wide map ]]> https://biorxiv.org/content/10.1101/308437v1?rss=1 470 sites, in dozens of which at relatively high levels, and in the vast majority of cases these sites were highly unlikely to be substrates of TRMT6/61A, suggesting that additional methyltransferases are active on cytosolic mRNAs. Here we aim to reconcile the contradictions between the two studies, primarily by reanalyzing and re-annotating the set of sites identified in the latter study. We find that the vast majority of sites detected in this study originate from duplications, misannotations, mismapping, SNPs, sequencing errors, and a set of sites originating from the very first transcribed base ( TSS sites). We raise concerns as to whether the TSS sites truly reflect m1A originating from the first transcribed base. We find that only 53 of the sites detected in this study likely reflect bona-fide internal modifications of cytoplasmically encoded mRNA molecules. The vast majority of these are likely to be TRMT6/TRMT61A substrates, and are typically modified at low to undetectable levels. We conclude that within cytosolic mRNAs, m1A is a rare internal modification where it is typically catalyzed at ultra-low stoichiometries via TRMT6/TRMT61A. Our findings offer a clear and consistent view on the abundance and whereabouts of this modification, and lays out key directions for future studies in the field. ]]> Schwartz, S. 2018-04-30 doi:10.1101/308437 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ On the Development of Sesamoid Bones ]]> https://biorxiv.org/content/10.1101/316901v1?rss=1 Eyal, S. Rubin, S. Krief, S. Levin, L. Zelzer, E. 2018-05-08 doi:10.1101/316901 Cold Spring Harbor Laboratory Press 2018-05-08 <![CDATA[ \"In plaque-mass spectrometry imaging\" reveals a major metabolic shift towards odd-chain fatty acid lipids induced by host-virus interactions ]]> https://biorxiv.org/content/10.1101/317206v1?rss=1 Schleyer, G. Shahaf, N. Ziv, C. Dong, Y. Meoded, R. A. Helfrich, E. J. N. Schatz, D. Rosenwasser, S. Rogachev, I. Aharoni, A. Piel, J. Vardi, A. 2018-05-08 doi:10.1101/317206 Cold Spring Harbor Laboratory Press 2018-05-08 <![CDATA[ Actin cytoskeleton self-organization in single epithelial cells and fibroblasts under isotropic confinement ]]> https://biorxiv.org/content/10.1101/318022v1?rss=1 Jalal, S. Huang, R. Y.-J. Viasnoff, V. Tee, Y. H. Bershadsky, A. 2018-05-09 doi:10.1101/318022 Cold Spring Harbor Laboratory Press 2018-05-09 <![CDATA[ Inhibitory and excitatory mechanisms in the human cingulate-cortex support reinforcement learning ]]> https://biorxiv.org/content/10.1101/318659v1?rss=1 Bezalel, V. Paz, R. Tal, A. 2018-05-10 doi:10.1101/318659 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Production of spliced long noncoding RNAs specifies regions with increased enhancer activity ]]> https://biorxiv.org/content/10.1101/319400v1?rss=1 Gil, N. Ulitsky, I. 2018-05-10 doi:10.1101/319400 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Phenotypic variability in chloroplast redox state predicts cell fate in a marine diatom ]]> https://biorxiv.org/content/10.1101/319517v1?rss=1 Mizrachi, A. Graff van Creveld, S. Shapiro, O. H. Rosenwasser, S. Vardi, A. 2018-05-10 doi:10.1101/319517 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Dynamics of social representation in the mouse prefrontal cortex ]]> https://biorxiv.org/content/10.1101/321182v1?rss=1 Levy, D. R. Tamir, T. Kaufman, M. Weissbrod, A. Schneidman, E. Yizhar, O. 2018-05-14 doi:10.1101/321182 Cold Spring Harbor Laboratory Press 2018-05-14 <![CDATA[ Bacterial virulence against an oceanic bloom-forming phytoplankter is mediated by algal DMSP ]]> https://biorxiv.org/content/10.1101/321398v1?rss=1 Barak-Gavish, N. Frada, M. J. Lee, P. A. DiTullio, G. R. Ku, C. Malitsky, S. Aharoni, A. Green, S. J. Rotkopf, R. Kartvelishvily, E. Sheyn, U. Schatz, D. Vardi, A. 2018-05-15 doi:10.1101/321398 Cold Spring Harbor Laboratory Press 2018-05-15 <![CDATA[ Bone Morphology is Regulated Modularly by Global and Regional Genetic Programs ]]> https://biorxiv.org/content/10.1101/324293v1?rss=1 Eyal, S. Kult, S. Rubin, S. Krief, S. Pineault, K. M. Wellik, D. Zelzer, E. 2018-05-16 doi:10.1101/324293 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Dynamic interactions of type I cohesin modules fine-tune the structure of the cellulosome of Clostridium thermocellum ]]> https://biorxiv.org/content/10.1101/328088v1?rss=1 Barth, A. Hendrix, J. Fried, D. Barak, Y. Bayer, E. Lamb, D. C. 2018-05-22 doi:10.1101/328088 Cold Spring Harbor Laboratory Press 2018-05-22 <![CDATA[ Structural Basis for Receptor Recognition by Lujo Virus ]]> https://biorxiv.org/content/10.1101/329482v1?rss=1 Cohen-Dvashi, H. Kilimnik, I. Diskin, R. 2018-05-24 doi:10.1101/329482 Cold Spring Harbor Laboratory Press 2018-05-24 <![CDATA[ Bistable bacterial growth dynamics in the presence of antimicrobial agents ]]> https://biorxiv.org/content/10.1101/330035v1?rss=1 Frenkel, N. Saar Dover, R. Titon, E. Shai, Y. Rom-Kedar, V. 2018-05-24 doi:10.1101/330035 Cold Spring Harbor Laboratory Press 2018-05-24 <![CDATA[ Massive osteopetrosis caused by giant, non-functional osteoclasts in R51Q SNX10 mutant mice ]]> https://biorxiv.org/content/10.1101/332551v1?rss=1 Barnea, M. Stein, M. Winograd-Katz, S. Shalev, M. Arman, E. Brenner, O. Thalji, F. Kanaan, M. Elinav, H. Stepensky, P. Geiger, B. Tuckermann, J. Elson, A. 2018-05-28 doi:10.1101/332551 Cold Spring Harbor Laboratory Press 2018-05-28 <![CDATA[ Chance and pleiotropy dominate genetic diversity in complex bacterial environments ]]> https://biorxiv.org/content/10.1101/340828v1?rss=1 Noda-Garcia, L. Davidi, D. Korenblum, E. Elazar, A. Putintseva, E. Aharoni, A. Tawfik, D. S. 2018-06-07 doi:10.1101/340828 Cold Spring Harbor Laboratory Press 2018-06-07 <![CDATA[ A matrix protein acts as a cue to preserve collective motility of B. subtilis biofilm cells ]]> https://biorxiv.org/content/10.1101/346494v1?rss=1 Steinberg, N. Doron, S. Jain, R. Rosenberg, G. van Teeffelen, S. Kolodkin-Gal, I. 2018-06-14 doi:10.1101/346494 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ TIAM-1/GEF can shape somatosensory dendrites independently of its GEF activity by regulating F-actin localization ]]> https://biorxiv.org/content/10.1101/347567v1?rss=1 Tang, L. T. H. Diaz-Balzac, C. A. Rahman, M. Ramirez-Suarez, N. J. Salzberg, Y. Lazaro-Pena, M. I. Bülow, H. E. 2018-06-14 doi:10.1101/347567 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ A repressor-decay timer for robust temporal patterning in embryonic Drosophila neuroblast lineages ]]> https://biorxiv.org/content/10.1101/354969v1?rss=1 Averbukh, I. Lai, S.-L. Doe, C. Q. Barkai, N. 2018-06-25 doi:10.1101/354969 Cold Spring Harbor Laboratory Press 2018-06-25 <![CDATA[ Systematic assessment of GFP tag position on protein localization and growth fitness in yeast ]]> https://biorxiv.org/content/10.1101/360636v1?rss=1 Davidi, D. Weill, U. Krieger, G. Avihou, Z. Milo, R. Schuldiner, M. 2018-07-02 doi:10.1101/360636 Cold Spring Harbor Laboratory Press 2018-07-02 <![CDATA[ Engrafted parenchymal brain macrophages differ from host microglia in transcriptome, epigenome and responsiveness to challenge ]]> https://biorxiv.org/content/10.1101/369942v1?rss=1 Shemer, A. Grozovski, J. Leng Tay, T. Tao, J. Volaski, A. Suess, P. Ardura-Fabregat, A. Gross, M. Kim, J.-S. David, E. Chappell-Maor, L. Thielecke, L. Glass, C. K. Cornils, K. Prinz, M. Jung, S. 2018-07-16 doi:10.1101/369942 Cold Spring Harbor Laboratory Press 2018-07-16 <![CDATA[ Illuminating spatial A-to-I RNA editing signatures within the Drosophila brain ]]> https://biorxiv.org/content/10.1101/370296v1?rss=1 Sapiro, A. L. Shmueli, A. Henry, G. L. Li, Q. Shalit, T. Yaron, O. Paas, Y. Li, J. B. Shohat-Ophir, G. 2018-07-16 doi:10.1101/370296 Cold Spring Harbor Laboratory Press 2018-07-16 <![CDATA[ The correlated state in balanced neuronal networks ]]> https://biorxiv.org/content/10.1101/372607v1?rss=1 Baker, C. Ebsch, C. Lampl, I. Rosenbaum, R. 2018-07-19 doi:10.1101/372607 Cold Spring Harbor Laboratory Press 2018-07-19 <![CDATA[ An alternative membrane topology permits lipid droplet localization of peroxisomal fatty acyl-CoA reductase 1 ]]> https://biorxiv.org/content/10.1101/373530v1?rss=1 Exner, T. Romero-Brey, I. Yifrach, E. Rivera-Monroy, J. Schrul, B. Zouboulis, C. C. Stremmel, W. Honsho, M. Bartenschlager, R. Zalckvar, E. Poppelreuther, M. Fuellekrug, J. 2018-07-20 doi:10.1101/373530 Cold Spring Harbor Laboratory Press 2018-07-20 <![CDATA[ Multiscale analysis of 3D nuclear morphology reveals new insights into growth plate organization in mice ]]> https://biorxiv.org/content/10.1101/375949v1?rss=1 Rubin, S. Stern, T. Villoutreix, P. Stegmaier, J. Addadi, Y. Zelzer, E. 2018-07-24 doi:10.1101/375949 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ Universal cancer tasks, evolutionary tradeoffs, and the functions of driver mutations ]]> https://biorxiv.org/content/10.1101/382291v1?rss=1 Hausser, J. Szekely, P. Bar, N. Zimmer, A. Sheftel, H. Caldas, C. Alon, U. 2018-08-01 doi:10.1101/382291 Cold Spring Harbor Laboratory Press 2018-08-01 <![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[ Dissecting splicing decisions and cell-to-cell variability with designed sequence libraries ]]> https://biorxiv.org/content/10.1101/392605v1?rss=1 32,000 splicing events to dissect the complexity of splicing regulation through systematicsequence alterations. Measuring RNA and protein splice isoforms allowed us to investigate bothcause and effect of splicing decisions, quantify diverse regulatory inputs and accurately predict (R2=0.75-0.85) isoform ratios from sequence and secondary structure. By profiling individual cells, we measure the cell-to-cell variability of splicing decisions and show that it can be encoded in the DNA and influenced by regulatory inputs, opening the door for a novel,single-cell perspective on splicing regulation. ]]> Mikl, M. Hamburg, A. Pilpel, Y. Segal, E. 2018-08-16 doi:10.1101/392605 Cold Spring Harbor Laboratory Press 2018-08-16 <![CDATA[ Identity domains in complex behavior: Toward a biology of personality ]]> https://biorxiv.org/content/10.1101/395111v1?rss=1 Forkosh, O. Karamihalev, S. Roeh, S. Engel, M. Alon, U. Anpilov, S. Nussbaumer, M. Flachskamm, C. Kaplick, P. Shemesh, Y. Chen, A. 2018-08-20 doi:10.1101/395111 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ Expression of a recombinant, 4’-Phosphopantetheinylated, active M. tuberculosis Fatty acid Synthase I in E. coli ]]> https://biorxiv.org/content/10.1101/400622v1?rss=1 Baron, S. Peleg, Y. Grunwald, J. Morgenstern, D. Elad, N. Peretz, M. Albeck, S. Levin, Y. Welch, J. T. Deweerd, K. A. Schwartz, A. Burstein, Y. Diskin, R. Shakked, Z. Zimhony, O. 2018-08-28 doi:10.1101/400622 Cold Spring Harbor Laboratory Press 2018-08-28 <![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[ Cross-talk between the receptor tyrosine kinases AXL and ERBB3 regulates invadopodia formation in melanoma cells ]]> https://biorxiv.org/content/10.1101/412379v1?rss=1 Revach, O.-Y. Sandler, O. Samuels, Y. Geiger, B. 2018-09-09 doi:10.1101/412379 Cold Spring Harbor Laboratory Press 2018-09-09 <![CDATA[ The physiological butyrylcholinesterase tetramer is a dimer of dimers stabilized by a superhelical assembly ]]> https://biorxiv.org/content/10.1101/431288v1?rss=1 Leung, M. R. Bezouwen, L. S. Schopfer, L. M. Sussman, J. L. Silman, I. Lockridge, O. Zeev-Ben-Mordehai, T. 2018-09-30 doi:10.1101/431288 Cold Spring Harbor Laboratory Press 2018-09-30 <![CDATA[ CSNAP, the smallest CSN subunit, modulates proteostasis through cullin-RING ubiquitin ligases ]]> https://biorxiv.org/content/10.1101/433532v1?rss=1 Füzesi-Levi, M. G. Enchev, R. I. Ben-Nissan, G. Levin, Y. Kupervaser, M. Friedlander, G. Salame, T. M. Nevo, R. Peter, M. Sharon, M. 2018-10-02 doi:10.1101/433532 Cold Spring Harbor Laboratory Press 2018-10-02 <![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[ MetaCell: analysis of single cell RNA-seq data using k-NN graph partitions ]]> https://biorxiv.org/content/10.1101/437665v1?rss=1 Baran, Y. Sebe-Pedros, A. Lubling, Y. Giladi, A. Chomsky, E. Meir, Z. Hoichman, M. Lifshitz, A. Tanay, A. 2018-10-08 doi:10.1101/437665 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ Rapid covalent-probe discovery by electrophile fragment screening ]]> https://biorxiv.org/content/10.1101/442806v1?rss=1 resnick, e. Bradley, A. Gan, J. Douangamath, A. Krojer, T. Sethi, R. Aimon, A. Amitai, G. Belini, D. Bennett, J. Fairhead, M. Fedorov, O. Geurink, P. P. Guo, J. Plotnikov, A. Reznik, N. Ruda, G. F. Diaz Saez, L. Straub, V. M. Szommer, T. Velupillai, r. Zaidman, D. Coker, A. R. Dowson, C. G. Barr, H. Huber, K. V. M. Brennan, P. E. Ovaa, H. von Delft, F. London, N. 2018-10-14 doi:10.1101/442806 Cold Spring Harbor Laboratory Press 2018-10-14 <![CDATA[ A redox-regulated type III metacaspase controls cell death in a marine diatom ]]> https://biorxiv.org/content/10.1101/444109v1?rss=1 Graff van Creveld, S. Ben-Dor, S. Mizrachi, A. Alcolombri, U. Hopes, A. Mock, T. Rosenwasser, S. Vardi, A. 2018-10-17 doi:10.1101/444109 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Deep Convolutional modeling of human face selective columns reveals their role in pictorial face representation ]]> https://biorxiv.org/content/10.1101/444323v1?rss=1 Grossman, S. Gaziv, G. Yeagle, E. M. Harel, M. Megevand, P. Groppe, D. M. Khuvis, S. Herrero, J. L. Irani, M. Mehta, A. D. Malach, R. 2018-10-19 doi:10.1101/444323 Cold Spring Harbor Laboratory Press 2018-10-19 <![CDATA[ Widespread suppression of high-order visual cortex during blinks and external predictable visual interruptions ]]> https://biorxiv.org/content/10.1101/456566v1?rss=1 Golan, T. Grossman, S. Deouell, L. Y. Malach, R. 2018-11-01 doi:10.1101/456566 Cold Spring Harbor Laboratory Press 2018-11-01 <![CDATA[ In-Cell Structural Dynamics of an EGF Receptor during Ligand-induced Dimer-Oligomer Transition. ]]> https://biorxiv.org/content/10.1101/458265v1?rss=1 Clayton, A. Kozer, N. 2018-10-31 doi:10.1101/458265 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ A short HBV RNA region induces RNR-R2 expression in non-cycling cells and in primary human hepatocytes ]]> https://biorxiv.org/content/10.1101/458679v1?rss=1 Ricardo-Lax, I. Broennimann, K. Adler, J. Michailidis, E. De Jong, Y. P. Reuven, N. Shaul, Y. 2018-10-31 doi:10.1101/458679 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ Single cell analysis reveals dynamics of transposable element transcription following epigenetic de-repression ]]> https://biorxiv.org/content/10.1101/462853v1?rss=1 Brocks, D. Chomsky, E. Mukamel, Z. Lifshitz, A. Tanay, A. 2018-11-06 doi:10.1101/462853 Cold Spring Harbor Laboratory Press 2018-11-06 <![CDATA[ Potassium channel regulators are differentially expressed in hippocampi of Ts65Dn and Tc1 Down syndrome mouse models ]]> https://biorxiv.org/content/10.1101/467522v1?rss=1 Stern, S. Keren, R. Kim, Y. Moses, E. 2018-11-11 doi:10.1101/467522 Cold Spring Harbor Laboratory Press 2018-11-11 <![CDATA[ Extensive programmed ribosomal frameshifting in human as revealed by a massively parallel reporter assay ]]> https://biorxiv.org/content/10.1101/469692v1?rss=1 12,000 sequences based on 15 viral and human frameshifting events, allowing us to elucidate the rules governing ribosomal frameshifting in a systematic way and to discover novel regulatory inputs based on amino acid properties and tRNA availability. We assessed the natural variation in HIV gag-pol frameshifting rates by testing >500 clinical isolates and identified subtype-specific differences as well as associations between viral load in patients and the optimality of gag-pol frameshifting rates. We further devised computational models that accurately predict frameshifting potential (up to auROC=0.93) and frameshifting rates (up to Pearson r=0.81) of novel variants, including subtle differences between HIV clinical isolates (r=0.60). Taken together, this systematic approach can contribute to the development of antiviral agents acting on programmed ribosomal frameshifting. ]]> Mikl, M. Alon, A. Mordret, E. Pilpel, Y. Segal, E. 2018-11-14 doi:10.1101/469692 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ Revisiting tradeoffs in Rubisco kinetic parameters ]]> https://biorxiv.org/content/10.1101/470021v1?rss=1 Flamholz, A. Prywes, N. Moran, U. Davidi, D. Bar-On, Y. Oltrogge, L. Savage, D. Milo, R. 2018-11-14 doi:10.1101/470021 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ Senescent cells and the dynamics of aging ]]> https://biorxiv.org/content/10.1101/470500v1?rss=1 Karin, O. Agrawal, A. Porat, Z. Krizhanovsky, V. Alon, U. 2018-11-14 doi:10.1101/470500 Cold Spring Harbor Laboratory Press 2018-11-14 <![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[ Learning probabilistic representations with randomly connected neural circuits ]]> https://biorxiv.org/content/10.1101/478545v1?rss=1 100 neurons in the monkey visual and prefrontal cortices is comparable or better than that of current models. Importantly, the model can be learned using a small number of samples, and using a local learning rule that utilizes noise intrinsic to neural circuits. Slower, structural changes in random connectivity, consistent with rewiring and pruning processes, further improve the efficiency and sparseness of the resulting neural representations. Our results merge insights from neuroanatomy, machine learning, and theoretical neuroscience to suggest random sparse connectivity as a key design principle for neuronal computation. ]]> Maoz, O. Esteki, M. S. Tkacik, G. Kiani, R. Schneidman, E. 2018-11-27 doi:10.1101/478545 Cold Spring Harbor Laboratory Press 2018-11-27 <![CDATA[ Organ transformation by environmental disruption of epigenetic memory ]]> https://biorxiv.org/content/10.1101/482216v1?rss=1 Snir, O. Elgart, M. Ciabrelli, F. Dagan, S. Aviezer, I. Stoops, E. Cavalli, G. Soen, Y. 2018-11-29 doi:10.1101/482216 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ Recruitment of the protein phosphatase-1 catalytic subunit to promoters by the dual-function transcription factor RFX1 ]]> https://biorxiv.org/content/10.1101/493429v1?rss=1 Lubelsky, Y. Shaul, Y. 2018-12-12 doi:10.1101/493429 Cold Spring Harbor Laboratory Press 2018-12-12 <![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[ Dynamics of Spaetzle morphogen shuttling in the Drosophila embryo shapes pattern ]]> https://biorxiv.org/content/10.1101/505925v1?rss=1 Rahimi, N. Averbukh, I. Carmon, S. Schejter, E. D. Barkai, N. Shilo, B.-Z. 2018-12-26 doi:10.1101/505925 Cold Spring Harbor Laboratory Press 2018-12-26 <![CDATA[ Fundamental Law of Memory Recall ]]> https://biorxiv.org/content/10.1101/510750v1?rss=1 Naim, M. Katkov, M. Tsodyks, M. 2019-01-03 doi:10.1101/510750 Cold Spring Harbor Laboratory Press 2019-01-03 <![CDATA[ Orientation-selective adaptation improves perceptual grouping ]]> https://biorxiv.org/content/10.1101/519561v1?rss=1 Pinchuk-Yacobi, N. Sagi, D. 2019-01-13 doi:10.1101/519561 Cold Spring Harbor Laboratory Press 2019-01-13 <![CDATA[ Disease-causing mutations in subunits of OXPHOS complex I affect their physical interactions ]]> https://biorxiv.org/content/10.1101/526020v1?rss=1 Barshad, G. Zlotinkov-Poznianski, N. Gal, L. Schuldiner, M. Mishmar, D. 2019-01-22 doi:10.1101/526020 Cold Spring Harbor Laboratory Press 2019-01-22 <![CDATA[ Spatial sorting enables comprehensive characterization of liver zonation ]]> https://biorxiv.org/content/10.1101/529784v1?rss=1 Ben-Moshe, S. Shapira, Y. Moor, A. E. Bahar Halpern, K. Itzkovitz, S. 2019-01-26 doi:10.1101/529784 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Centering based on active diffusion in mouse oocytes is non-specific ]]> https://biorxiv.org/content/10.1101/531657v1?rss=1 Verlhac, M.-H. Colin, A. Ratzin, N. Almonacid, M. Ahmed, W. Betz, T. Terret, M.-E. Gov, N. Voituriez, R. Gueroui, Z. 2019-01-27 doi:10.1101/531657 Cold Spring Harbor Laboratory Press 2019-01-27 <![CDATA[ Molecular Dynamics Simulations of the Interaction of Mouse and Torpedo Acetylcholinesterase with Covalent Inhibitors Explain Their Differential Reactivity: Implications for Drug Design ]]> https://biorxiv.org/content/10.1101/532754v1?rss=1 Chandar, N. B. Efremenko, I. Silman, I. Martin, J. M. L. Sussman, J. L. 2019-01-28 doi:10.1101/532754 Cold Spring Harbor Laboratory Press 2019-01-28 <![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[ Regulation of CHD2 expression by the Chaserr long noncoding RNA is essential for viability ]]> https://biorxiv.org/content/10.1101/536771v1?rss=1 Rom, A. Melamed, L. Goldrich, M. J. Kadir, R. Golan, M. Biton, I. Ben-Tov Perry, R. Ulitsky, I. 2019-01-31 doi:10.1101/536771 Cold Spring Harbor Laboratory Press 2019-01-31 <![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[ Visual closed-loop dynamics via ocular drift ]]> https://biorxiv.org/content/10.1101/539445v1?rss=1 Gruber, L. Z. Ahissar, E. 2019-02-03 doi:10.1101/539445 Cold Spring Harbor Laboratory Press 2019-02-03 <![CDATA[ Stereotactic system for accurately targeting deep brain structures in awake head-fixed mice ]]> https://biorxiv.org/content/10.1101/539957v1?rss=1 The Deep Target, new system for accurately targeting deep nuclei in head-fixed animals for electrophysiology and optogenetics. > Accurate and precise to within 100 m following a one-time alignment. > Validation: Opto-tagged Vm recordings in the amygdala of awake mice. > Validation: Targeting multiple deep brain structures in the same mouse. ]]> Katz, Y. Sokoletsky, M. Lampl, I. 2019-02-10 doi:10.1101/539957 Cold Spring Harbor Laboratory Press 2019-02-10 <![CDATA[ Revealing neural correlates of behavior without behavioral measurements ]]> https://biorxiv.org/content/10.1101/540195v1?rss=1 Rubin, A. Sheintuch, L. Brande-Eilat, N. Pinchasof, O. Rechavi, Y. Geva, N. Ziv, Y. 2019-02-05 doi:10.1101/540195 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Emergence of hierarchical organization in memory for random material ]]> https://biorxiv.org/content/10.1101/541490v1?rss=1 Naim, M. Katkov, M. Recanatesi, S. Tsodyks, M. 2019-02-05 doi:10.1101/541490 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Inter-thinker consistency of language activations during abstract thoughts ]]> https://biorxiv.org/content/10.1101/546085v1?rss=1 95%. Surprisingly, the activated networks remained the same regardless of changes in thought content. Finally, we found a remarkably consistent activation map across individuals engaged in abstract thinking. The activation to abstract thinking bordered, but strictly avoided visual and motor networks. On the other hand, it partly overlapped with left lateralized language networks. These observations were supported by a quantitative neuronal distance metric analysis. Our results reveal that despite its high level, and varied content nature-abstract thinking activates surprisingly precise and consistent networks in the participants brains. Thinker refers to: The agent of thought; Intellectual, one who tries to use his or her intellect to work, study, reflect, speculate on, or ask and answer questions with regard to a variety of different ideas" (Wikipedia). ]]> Berkovich-Ohana, A. Noy, N. Harel, M. Furman-Haran, E. Arieli, A. Malach, R. 2019-02-10 doi:10.1101/546085 Cold Spring Harbor Laboratory Press 2019-02-10 <![CDATA[ Robo2 regulates synaptic oxytocin content by affecting actin state ]]> https://biorxiv.org/content/10.1101/553198v1?rss=1 Anbalagan, S. Blechman, J. Gliksberg, M. Rotkopf, R. Dadosh, T. Levkowitz, G. 2019-02-17 doi:10.1101/553198 Cold Spring Harbor Laboratory Press 2019-02-17 <![CDATA[ Seeing, fast and slow: the effects of processing time on perceptual bias ]]> https://biorxiv.org/content/10.1101/556944v1?rss=1 median. C_LI ]]> Dekel, R. Sagi, D. 2019-02-21 doi:10.1101/556944 Cold Spring Harbor Laboratory Press 2019-02-21 <![CDATA[ A geometric representation unveils rule-learning dynamics in primate neurons ]]> https://biorxiv.org/content/10.1101/561670v1?rss=1 Cohen, Y. Schneidman, E. Paz, R. 2019-02-28 doi:10.1101/561670 Cold Spring Harbor Laboratory Press 2019-02-28 <![CDATA[ Fenestrae-associated protein Plvap regulates the rate of blood-borne proteins passage into the hypophysis ]]> https://biorxiv.org/content/10.1101/571299v1?rss=1 Gordon, L. Blechman, J. Shimoni, E. Gur, D. Anand-Apte, B. Levkowitz, G. 2019-03-07 doi:10.1101/571299 Cold Spring Harbor Laboratory Press 2019-03-07 <![CDATA[ Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution ]]> https://biorxiv.org/content/10.1101/571679v1?rss=1 Garcia-Campos, M. A. Edelheit, S. Toth, U. Shachar, R. Nir, R. Lasman, L. Brandis, A. Hanna, J. H. Rossmanith, W. Schwartz, S. 2019-03-08 doi:10.1101/571679 Cold Spring Harbor Laboratory Press 2019-03-08 <![CDATA[ Colony entropy - Allocation of goods in ant colonies ]]> https://biorxiv.org/content/10.1101/572032v1?rss=1 Greenwald, E. Eckmann, J.-P. Feinerman, O. 2019-03-08 doi:10.1101/572032 Cold Spring Harbor Laboratory Press 2019-03-08 <![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[ Sex differences in chronic social stress models in mice ]]> https://biorxiv.org/content/10.1101/605527v1?rss=1 Furman, O. Tsoory, M. Chen, A. 2019-04-11 doi:10.1101/605527 Cold Spring Harbor Laboratory Press 2019-04-11 <![CDATA[ Integrative analysis identifies key molecular signatures underlying neurodevelopmental deficits in Fragile X Syndrome ]]> https://biorxiv.org/content/10.1101/606038v1?rss=1 Utami, K. H. Skotte, N. H. Colaco, A. R. Yusof, N. A. B. M. Sim, B. Yeo, X. Y. Bae, H.-G. Garcia-Miralles, M. Radulescu, C. I. Chen, Q. Chaldaiopoulou, G. Liany, H. Nama, S. Sampath, P. Jung, S. Mann, M. Pouladi, M. A. 2019-04-15 doi:10.1101/606038 Cold Spring Harbor Laboratory Press 2019-04-15 <![CDATA[ Regulation of the 20S proteasome by a novel family of inhibitory proteins ]]> https://biorxiv.org/content/10.1101/617415v1?rss=1 Olshina, M. A. Kumar-Deshmukh, F. Arkind, G. Fainer, I. Taranavsky, M. Hayat, D. Ben-Dor, S. Ben-Nissqan, G. Sharon, M. 2019-04-24 doi:10.1101/617415 Cold Spring Harbor Laboratory Press 2019-04-24 <![CDATA[ Signaling via GABAB receptors regulates early development and neurogenesis in the basal metazoan Nematostella vectensis ]]> https://biorxiv.org/content/10.1101/621060v1?rss=1 Levy, S. Brekhman, V. Bakhman, A. Sebe-Pedros, A. Kosloff, M. Lotan, T. 2019-04-27 doi:10.1101/621060 Cold Spring Harbor Laboratory Press 2019-04-27 <![CDATA[ Gene transcription as a limiting factor in protein production and cell growth ]]> https://biorxiv.org/content/10.1101/626242v1?rss=1 Metzl-Raz, E. Kafri, M. Yaakov, G. Barkai, N. 2019-05-02 doi:10.1101/626242 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Individual variation of the dark-background-contingent upshift of gaze: effect of past habituation ]]> https://biorxiv.org/content/10.1101/628610v1?rss=1 Spivak, O. Thier, P. Barash, S. 2019-05-05 doi:10.1101/628610 Cold Spring Harbor Laboratory Press 2019-05-05 <![CDATA[ Electroporated recombinant proteins as tools for in vivo functional complementation, imaging, and chemical biology ]]> https://biorxiv.org/content/10.1101/631358v1?rss=1 Alex, A. Piano, V. Polley, S. Stuiver, M. Voss, S. Ciossani, G. Overlack, K. Voss, B. Wohlgemuth, S. Petrovic, A. Wu, Y.-W. Selenko, P. Musacchio, A. Maffini, S. 2019-05-08 doi:10.1101/631358 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Resolving noise-control conflict by gene duplication ]]> https://biorxiv.org/content/10.1101/634741v1?rss=1 Chapal, M. Mintzer, S. Brodsky, S. Carmi, M. Barkai, N. 2019-05-10 doi:10.1101/634741 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Gateway mechanism confers ultrasensitivity on motor’s function ]]> https://biorxiv.org/content/10.1101/642140v1?rss=1 Afanzar, O. Di Paolo, D. Eisenstein, M. Levi, K. Plochowietz, A. Kapanidis, A. N. Berry, R. M. Eisenbach, M. 2019-05-19 doi:10.1101/642140 Cold Spring Harbor Laboratory Press 2019-05-19 <![CDATA[ In vivo imaging of myonuclei during spontaneous muscle contraction reveals non-uniform nuclear mechanical dynamics in Nesprin/klar mutants ]]> https://biorxiv.org/content/10.1101/643015v1?rss=1 Lorber, D. Rotkopf, R. Volk, T. 2019-05-20 doi:10.1101/643015 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Huntington phosphorylation governs BDNF homeostasis and improves the phenotype of Mecp2 knockout mice ]]> https://biorxiv.org/content/10.1101/643312v1?rss=1 Ehinger, Y. Bruyere, j. Panayotis, N. Abada, Y.-S. Saidi, L. Matagne, V. Scaramuzzino, C. Vitet, H. Benoit Delatour, B. Villard, L. Saudou, F. Roux, J.-C. 2019-05-20 doi:10.1101/643312 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Age-Related Changes in Neural Networks Supporting Complex Visual and Social Processing in Adolescence ]]> https://biorxiv.org/content/10.1101/650887v1?rss=1 Lerner, Y. Scherf, S. Katkov, M. Hasson, U. Behrmann, M. 2019-05-27 doi:10.1101/650887 Cold Spring Harbor Laboratory Press 2019-05-27 <![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[ Defining the Energetic Costs of Cellular Structures ]]> https://biorxiv.org/content/10.1101/666040v1?rss=1 Mahmoudabadi, G. Phillips, R. Lynch, M. Milo, R. 2019-06-10 doi:10.1101/666040 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ The inter-dimeric interface controls function and stability of Ureaplasma urealiticum methionine S-adenosyltransferase ]]> https://biorxiv.org/content/10.1101/669069v1?rss=1 Kleiner, D. Shmulevich, F. Zarivach, R. Shahar, A. Sharon, M. Ben-Nissan, G. Bershtein, S. 2019-06-12 doi:10.1101/669069 Cold Spring Harbor Laboratory Press 2019-06-12 <![CDATA[ Principles for simultaneous measurement of excitatory and inhibitory conductances of single cells in a single trial ]]> https://biorxiv.org/content/10.1101/690719v1?rss=1 Lampl, I. 2019-07-02 doi:10.1101/690719 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Strongly correlated spatiotemporal encoding and simple decoding in the prefrontal cortex ]]> https://biorxiv.org/content/10.1101/693192v1?rss=1 Karpas, E. D. Maoz, O. Kiani, R. Schneidman, E. 2019-07-18 doi:10.1101/693192 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ Defining Monocyte Differentiation into Colonic and Ileal Macrophages ]]> https://biorxiv.org/content/10.1101/695262v1?rss=1 Gross-Vered, M. Shemer, A. Bernshtein, B. Curato, C. Trzebanski, S. Salame, T.-M. David, E. Boura-Halfon, S. Chappell-Maor, L. Jung, S. 2019-07-08 doi:10.1101/695262 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Multiple timescales account for adaptive responses across sensory cortices ]]> https://biorxiv.org/content/10.1101/700062v1?rss=1 Latimer, K. Barbera, D. Sokoletsky, M. Awwad, B. Katz, Y. Nelken, I. Lampl, I. Fairhall, A. Priebe, N. J. 2019-07-14 doi:10.1101/700062 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping ]]> https://biorxiv.org/content/10.1101/700864v1?rss=1 Ramilowski, J. A. Yip, C. W. Agrawal, S. Chang, J.-C. Ciani, Y. Kulakovskiy, I. V. Mendez, M. Ooi, J. L. C. Petri, A. Roos, L. Severin, J. Yasuzawa, K. Ouyang, J. F. Parkinson, N. Abugessaisa, I. Akalin, A. Antonov, I. Arner, E. Bonetti, A. Bono, H. Borsari, B. Brombacher, F. Cannistraci, C. Cardenas, R. Cardon, M. Chang, H. Dostie, J. Ducoli, L. Favorov, A. Fort, A. Garrido, D. Gil, N. Gimenez, J. Guler, R. Handoko, L. Harshbarger, J. Hasegawa, A. Hasegawa, Y. Hashimoto, K. Hayatsu, N. Heutink, P. Hirose, T. Imada, E. L. Itoh, M. Kaczkowski, B. Kan 2019-07-14 doi:10.1101/700864 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ Principles of Cell Circuits for Tissue Repair and Fibrosis ]]> https://biorxiv.org/content/10.1101/710012v1?rss=1 Adler, M. Mayo, A. Zhou, X. Franklin, R. Meizlish, M. Medzhitov, R. Kallenberger, S. Alon, U. 2019-07-24 doi:10.1101/710012 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Retroactive Interference Model of Power-Law Forgetting ]]> https://biorxiv.org/content/10.1101/710269v1?rss=1 Georgiou, A. Katkov, M. Tsodyks, M. 2019-07-22 doi:10.1101/710269 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Comparative analysis of CreER transgenic mice for the study of brain macrophages - a case study ]]> https://biorxiv.org/content/10.1101/725218v1?rss=1 Jung, S. Chappell-Maor, L. Kolesnikov, M. Grozovski, J. Kim, J.-S. Shemer, A. Haimon, Z. Boura-Halfon, S. Prinz, M. Masuda, T. 2019-08-05 doi:10.1101/725218 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ Comprehensive Annotations of Human Herpesvirus 6A and 6B Genomes Reveal Novel and Conserved Genomic Features ]]> https://biorxiv.org/content/10.1101/730028v1?rss=1 Finkel, Y. Schmiedel, D. Tai-Schmiedel, J. Nachshon, A. Schwartz, M. Mandelboim, O. Stern-Ginossar, N. 2019-08-08 doi:10.1101/730028 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ Dynamic control of cortical head-direction signal by angular velocity ]]> https://biorxiv.org/content/10.1101/730374v1?rss=1 Finkelstein, A. Rouault, H. Romani, S. Ulanovsky, N. 2019-08-08 doi:10.1101/730374 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ MKPV (aka MuCPV) and related chapparvoviruses are nephro-tropic and encode novel accessory proteins p15 and NS2 ]]> https://biorxiv.org/content/10.1101/732537v1?rss=1 60% amino acid identity to MKPV. We show that MKPV is kidney-tropic and that the bat chapparvovirus DrPV-1 and a non-human primate chapparvovirus, CKPV, are also found in the kidneys of their hosts. We propose, therefore, that chapparvoviruses with >60% VP1 amino acid identity to MKPV be classified into a genus dubbed Nephroparvovirus, which is consistent with nomenclature for the genus Erythroparvovirus. ]]> Jolly, C. J. Lee, Q. Padula, M. P. Pinello, N. Williams, S. H. O'Rourke, M. B. Fumagalli, M. J. Orkin, J. D. Shaban, B. Brenner, O. Weninger, W. Souza, W. M. d. Melin, A. D. Wong, J. J.- L. Crim, M. J. Monette, S. Roediger, B. 2019-08-15 doi:10.1101/732537 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Cellular contractile forces emerge from time and F-actin dependent non-mechanosensitive displacements ]]> https://biorxiv.org/content/10.1101/733303v1?rss=1 Feld, L. Kellerman, L. Mukherjee, A. Livne, A. Bouchbinder, E. Wolfenson, H. 2019-08-13 doi:10.1101/733303 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ A molecular switch for Cdc48 activity and localization during oxidative stress and aging ]]> https://biorxiv.org/content/10.1101/733709v1?rss=1 Reichmann, D. Radzinski, M. Yogev, O. Yesharim, Y. Brielle, E. S. Israeli, R. Fassler, R. Melamed-Book, N. Shai, N. Arkin, I. T. Pick, E. Ravid, T. Schuldiner, M. 2019-08-13 doi:10.1101/733709 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Shared neural codes for eye-gaze and valence ]]> https://biorxiv.org/content/10.1101/736462v1?rss=1 Pryluk, R. Shohat, Y. Morozov, A. Friedman, D. Taub, A. H. Paz, R. 2019-08-15 doi:10.1101/736462 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Social interactions drive efficient foraging and income equality in groups of fish ]]> https://biorxiv.org/content/10.1101/740886v1?rss=1 Harpaz, R. Schneidman, E. 2019-08-20 doi:10.1101/740886 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ Runx3 prevents spontaneous colitis by directingdifferentiation of anti-inflammatory mononuclear phagocytes ]]> https://biorxiv.org/content/10.1101/742650v1?rss=1 hantisteanu, S. Dicken, Y. Negreanu, V. Goldenberg, D. Brenner, O. Leshkowitz, D. Lotem, J. Levanon, D. Groner, Y. 2019-08-21 doi:10.1101/742650 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Single-cell molecular and cellular architecture of neurohypophyseal cell types in the adult mouse ]]> https://biorxiv.org/content/10.1101/744466v1?rss=1 Chen, Q. Leshkowitz, D. Blechman, J. Levkowitz, G. 2019-08-22 doi:10.1101/744466 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ A mixture of three engineered phosphotriesterases enables rapid detoxification of the entire spectrum of known threat nerve agents ]]> https://biorxiv.org/content/10.1101/748749v1?rss=1 Despotovic, D. Aharon, E. Dubovetskyi, A. Leader, H. Ashani, Y. Tawfik, D. S. 2019-08-28 doi:10.1101/748749 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ AMPK regulates ESCRT-dependent microautophagy of proteasomes concomitant with proteasome storage granule assembly during glucose starvation ]]> https://biorxiv.org/content/10.1101/751420v1?rss=1 Li, J. Breker, M. Graham, M. Schuldiner, M. Hochstrasser, M. 2019-08-29 doi:10.1101/751420 Cold Spring Harbor Laboratory Press 2019-08-29 <![CDATA[ Tracking infection dynamics at single-cell level reveals highly resolved expression programs of a large virus infecting algal blooms ]]> https://biorxiv.org/content/10.1101/757542v1?rss=1 Ku, C. Sheyn, U. Sebe-Pedros, A. Ben-Dor, S. Schatz, D. Tanay, A. Rosenwasser, S. Vardi, A. 2019-09-05 doi:10.1101/757542 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ The nasopalatine ducts of the mouse conserve a functional role in pheromone signaling ]]> https://biorxiv.org/content/10.1101/757930v1?rss=1 Levy, D. R. Sofer, Y. Brumfeld, V. Zilkha, N. Kimchi, T. 2019-09-04 doi:10.1101/757930 Cold Spring Harbor Laboratory Press 2019-09-04 <![CDATA[ Can scientists fill the science journalism void? Online public engagement with science stories authored by scientists ]]> https://biorxiv.org/content/10.1101/760520v1?rss=1 Barel-Ben David, Y. Garty, E. S. Baram-Tsabari, A. 2019-09-06 doi:10.1101/760520 Cold Spring Harbor Laboratory Press 2019-09-06 <![CDATA[ Local network determinants of spontaneously emerging cortical maps ]]> https://biorxiv.org/content/10.1101/764068v1?rss=1 Fekete, T. Omer, D. Grinvald, A. van Leeuwen, C. 2019-09-10 doi:10.1101/764068 Cold Spring Harbor Laboratory Press 2019-09-10 <![CDATA[ ERM-Dependent Assembly of T-Cell Receptor Signaling and Co-stimulatory Molecules on Microvilli Prior to Activation ]]> https://biorxiv.org/content/10.1101/766196v1?rss=1 Ghosh, S. Di Bartolo, V. Tubul, L. Shimoni, E. Kartvelishvily, E. Dadosh, T. W. Feigelson, S. Alon, R. Alcover, A. Haran, G. 2019-09-12 doi:10.1101/766196 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Right on time: prediction-errors bidirectionally bias time perception ]]> https://biorxiv.org/content/10.1101/766204v1?rss=1 Toren, I. Aberg, K. Paz, R. 2019-09-12 doi:10.1101/766204 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Peptide-based quorum sensing systems in Paenibacillus polymyxa ]]> https://biorxiv.org/content/10.1101/767517v1?rss=1 Voichek, M. Maass, S. Kroniger, T. Becher, D. Sorek, R. 2019-09-12 doi:10.1101/767517 Cold Spring Harbor Laboratory Press 2019-09-12 <![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[ Chromatin accessibility variations across pancreatic islet maturation ]]> https://biorxiv.org/content/10.1101/782318v1?rss=1 Sobel, J. A. Guay, C. Rodriguez-Trejo, A. Stoll, L. Menoud, V. Regazzi, R. 2019-09-25 doi:10.1101/782318 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Time-Space Fourier κFormula Filter for Motion Artifacts Compensation during Transcranial Fluorescence Brain Imaging ]]> https://biorxiv.org/content/10.1101/789370v1?rss=1 Molodij, G. Meglinski, I. Sdobnov, A. Kuznetsov, Y. Harmelin, A. Kalchenko, V. 2019-10-01 doi:10.1101/789370 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Energy-based and energy-free food-consumption are correlated in captive non-human-primates: A novel dispenser for feeding and behavioral enrichment ]]> https://biorxiv.org/content/10.1101/803528v1?rss=1 Shohat, Y. Paz, R. Pryluk, R. Taub, A. H. 2019-10-16 doi:10.1101/803528 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Mechanosensitive recruitment of BAF to the nuclear membrane inhibits nuclear E2F1 and Yap levels ]]> https://biorxiv.org/content/10.1101/803932v1?rss=1 Unnikannan, C. P. Reuveny, A. Grunberg, D. T. Volk, T. 2019-10-14 doi:10.1101/803932 Cold Spring Harbor Laboratory Press 2019-10-14 <![CDATA[ {-}{-}{-}{-}{-}Polyglutamine-related aggregates serve as a potent antigen source for cross presentation by dendritic cells ]]> https://biorxiv.org/content/10.1101/806414v1?rss=1 Navon, A. Tabachnick-Cherny, S. Berko, D. Pinto, S. Curato, C. Wolf, Y. Porat, Z. Karmona, R. Tirosh, B. Jung, S. 2019-10-15 doi:10.1101/806414 Cold Spring Harbor Laboratory Press 2019-10-15 <![CDATA[ Interaction of contexts in context-dependent orientation estimation ]]> https://biorxiv.org/content/10.1101/816355v1?rss=1 Dekel, R. Sagi, D. 2019-10-25 doi:10.1101/816355 Cold Spring Harbor Laboratory Press 2019-10-25 <![CDATA[ Studying the precuneus reveals structure-function-affect correlation in long-term meditators ]]> https://biorxiv.org/content/10.1101/822056v1?rss=1 Berkovich-Ohana, A. Furman-Haran, E. Malach, R. Arieli, A. Harel, M. Gilaie-Dotan, S. 2019-10-30 doi:10.1101/822056 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ Antagonistic center-surround mechanisms for direction selectivity in the retina ]]> https://biorxiv.org/content/10.1101/831453v1?rss=1 Ankri, L. Ezra-Tsur, E. Maimon, S. R. Kaushansky, N. Rivlin-Etzion, M. 2019-11-05 doi:10.1101/831453 Cold Spring Harbor Laboratory Press 2019-11-05 <![CDATA[ Vacuolar processing enzyme translocates to the vacuole through the autophagy pathway to induce programmed cell death ]]> https://biorxiv.org/content/10.1101/831982v1?rss=1 Eshel, D. Teper-Bamnolker, P. Danieli, R. Peled-Zehavi, H. Belausov, E. Abu-Abied, M. Avin-Wittenberg, T. Sadot, E. 2019-11-05 doi:10.1101/831982 Cold Spring Harbor Laboratory Press 2019-11-05 <![CDATA[ Segment2P: Parameter-free automated segmentation of cellular fluorescent signals ]]> https://biorxiv.org/content/10.1101/832188v1?rss=1 Dolev, N. Pinkus, L. Rivlin-Etzion, M. 2019-11-06 doi:10.1101/832188 Cold Spring Harbor Laboratory Press 2019-11-06 <![CDATA[ Circulating miR-181 is a prognostic biomarker for amyotrophic lateral sclerosis ]]> https://biorxiv.org/content/10.1101/833079v1?rss=1 2 fold risk of death in discovery cohort (126 patients) and an independent replication cohort (additional 122 patients). miR-181 performance is comparable with the established neurofilament light chain (NfL) biomarker and when combined together, miR-181+NfL establish a novel RNA-protein biomarker pair with superior prediction capacity of ALS prognosis. Therefore, plasma miR-181 predicts ALS disease course, and a novel miRNA-protein biomarker approach, based on miR-181+NfL, boosts precision of patient stratification and may greatly enhance the power of clinical trials. One Sentence Summaryplasma miR-181 levels indicate high mortality risk in ALS patients. ]]> Magen, I. Coenen-Stass, A. M. L. Yacovzada, N. S. Grosskreutz, J. Lu, C.-H. Greensmith, L. Malaspina, A. Fratta, P. Hornstein, E. 2019-11-14 doi:10.1101/833079 Cold Spring Harbor Laboratory Press 2019-11-14 <![CDATA[ Predictive whisker kinematics reveal context-dependent sensorimotor strategies ]]> https://biorxiv.org/content/10.1101/833103v1?rss=1 Wallach, A. Deutsch, D. Oram, T. Ahissar, E. 2019-11-06 doi:10.1101/833103 Cold Spring Harbor Laboratory Press 2019-11-06 <![CDATA[ Transneuronal interactions facilitate axonal compartment formation ]]> https://biorxiv.org/content/10.1101/834515v1?rss=1 Bornstein, B. Alyagor, I. Berkun, V. Meltzer, H. Reh, F. Keren-Shaul, H. David, E. Riemensperger, T. Schuldiner, O. 2019-11-07 doi:10.1101/834515 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Feasibility analysis of semiconductor voltage nanosensors for neuronal membrane potential sensing ]]> https://biorxiv.org/content/10.1101/838342v1?rss=1 Ludwig, A. Serna, P. Morgenstein, L. Yang, G. Bar-Elli, O. Ortiz, G. Miller, E. Oron, D. Grupi, A. Weiss, S. Triller, A. 2019-11-12 doi:10.1101/838342 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Endocrine autoimmune disease as a fragility of immune-surveillance against hypersecreting mutants ]]> https://biorxiv.org/content/10.1101/845750v1?rss=1 Korem Kohanim, Y. Tendler, A. Mayo, A. Friedman, N. Alon, U. 2019-11-17 doi:10.1101/845750 Cold Spring Harbor Laboratory Press 2019-11-17 <![CDATA[ Translational regulation of Pmt1 and Pmt2 by Bfr1 affects unfolded protein O-mannosylation ]]> https://biorxiv.org/content/10.1101/847095v1?rss=1 Castells-Ballester, J. Rinis, N. Kotan, I. Gal, L. Bausewein, D. Kats, I. Zatorska, E. Kramer, G. Bukau, B. Schuldiner, M. Strahl, S. 2019-11-20 doi:10.1101/847095 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Lgr5+ telocytes are a signaling hub at the intestinal villus tip ]]> https://biorxiv.org/content/10.1101/850909v1?rss=1 Bahar Halpern, K. Massalha, H. Zwick, R. K. Moor, A. E. Castillo-Azofeifa, D. Rozenberg, M. Farack, L. Egozi, A. Miller, D. R. Averbukh, I. Harnik, Y. Weinberg-Corem, N. de Sauvage, F. J. Amit, I. Klein, O. D. Shoshkes-Carmel, M. Itzkovitz, S. 2019-11-21 doi:10.1101/850909 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ 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[ INHIBITION OF GONADOTROPIN-STIMULATED STEROIDOGENESIS BY THE ERK CASCADE ]]> https://biorxiv.org/content/10.1101/853648v1?rss=1 Seger, R. Hanoch, T. Rosenberg, R. Dantes, A. Merz, W. Strauss, J. F. Amsterdam, A. 2019-11-25 doi:10.1101/853648 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ A decision-time account of individual variability in context-dependent orientation estimation ]]> https://biorxiv.org/content/10.1101/853754v1?rss=1 Dekel, R. Sagi, D. 2019-11-25 doi:10.1101/853754 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Agrin promotes coordinated therapeutic processes leading to improved cardiac repair in pigs ]]> https://biorxiv.org/content/10.1101/854372v1?rss=1 Baehr, A. Umansky, K. B. Bassat, E. Klett, K. Jurisch, V. Bozoglu, T. Hornaschewitz, N. Solyanik, O. Kain, D. Ferrero, B. Cohen-Rabi, R. Krane, M. Cyran, C. Soehnlein, O. Laugwitz, K. L. Hinkel, R. Kupatt, C. Tzahor, E. 2019-11-25 doi:10.1101/854372 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Diurnal variations in the motility of algal populations ]]> https://biorxiv.org/content/10.1101/854844v1?rss=1 Jin, D. Kotar, J. Silvester, E. Leptos, K. Croze, O. A. 2019-11-25 doi:10.1101/854844 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ The somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa ]]> https://biorxiv.org/content/10.1101/862623v1?rss=1 Hofmeister, B. T. Denkena, J. Colome-Tatche, M. Shahryary Dizaji, Y. Hazarika, R. Grimwood, J. Mamid, S. Jenkins, J. Grabowski, P. P. Sreedasyam, A. Shu, S. Barry, K. Lail, K. Adam, C. Lipzen, A. Sorek, R. Kudrna, D. Talag, J. Wing, R. Hall, D. W. Tuskan, G. A. Schmutz, J. Johannes, F. Schmitz, R. J. 2019-12-03 doi:10.1101/862623 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes define survival threshold in erythroid progenitor cells ]]> https://biorxiv.org/content/10.1101/866871v1?rss=1 Adlung, L. Stapor, P. Schmiester, L. Schwarzmueller, L. Wang, D. Timmer, J. Klingmueller, U. Hasenauer, J. Schilling, M. 2019-12-06 doi:10.1101/866871 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Formation and maintenance of robust long-term information storage in the presence of synaptic turnover ]]> https://biorxiv.org/content/10.1101/023531v1?rss=1 Michael Fauth Florentin Wörgötter Christian Tetzlaff 2015-07-31 doi:10.1101/023531 Cold Spring Harbor Laboratory Press 2015-07-31 <![CDATA[ Sensitive red protein calcium indicators for imaging neural activity ]]> https://biorxiv.org/content/10.1101/041780v1?rss=1 Hod Dana Boaz Mohar Yi Sun Sujatha Narayan Andrew Gordus Jeremy P Hasseman Getahun Tsegaye Graham T Holt Amy Hu Deepika Walpita Ronak Patel John J Macklin Cornelia I Bargmann Misha B Ahrens Eric R Schreiter Vivek Jayaraman Loren L Looger Karel Svoboda Douglas S Kim 2016-02-29 doi:10.1101/041780 Cold Spring Harbor Laboratory Press 2016-02-29 <![CDATA[ Dynamic proteomics of HSV1 infection reveals molecular events that govern non-stochastic infection outcomes ]]> https://biorxiv.org/content/10.1101/081653v1?rss=1 50,000 individual cells as they respond to HSV1 infection, allowing us to model infection kinetics and link infection outcome (productive or not) with the cell state at the time of initial infection. We find that single cells differ in their preexisting susceptibility to HSV1, and that this is partially mediated by their cell-cycle position. We also identify specific changes in protein levels and localization in infected cells, attesting to the power of the dynamic proteomics approach for studying virus-host interactions. ]]> Drayman, N. Karin, O. Mayo, A. Danon, T. Shapira, L. Kobiler, O. Alon, U. 2016-10-19 doi:10.1101/081653 Cold Spring Harbor Laboratory Press 2016-10-19 <![CDATA[ Neuronal components of evaluating the human 1 origin of abstract shapes ]]> https://biorxiv.org/content/10.1101/085902v1?rss=1 Goldberg, H. Hart, Y. Mayo, A. Alon, U. Malach, R. 2016-11-22 doi:10.1101/085902 Cold Spring Harbor Laboratory Press 2016-11-22 <![CDATA[ A theory of working memory without consciousness or sustained activity ]]> https://biorxiv.org/content/10.1101/093815v1?rss=1 Trubutschek, D. Marti, S. Ojeda, A. King, J.-R. Mi, Y. Tsodyks, M. Dehaene, S. 2016-12-14 doi:10.1101/093815 Cold Spring Harbor Laboratory Press 2016-12-14 <![CDATA[ Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling ]]> https://biorxiv.org/content/10.1101/146738v1?rss=1 Fuks, G. Elgart, M. Amir, A. Zeisel, A. Turnbaugh, P. J. Soen, Y. Shental, N. 2017-06-06 doi:10.1101/146738 Cold Spring Harbor Laboratory Press 2017-06-06 <![CDATA[ Overcoming insecticide resistance through computational inhibitor design ]]> https://biorxiv.org/content/10.1101/161430v1?rss=1 Correy, G. Zaidman, D. Carvalho, S. Mabbitt, P. D. James, P. J. Kotze, A. C. London, N. Jackson, C. J. 2017-07-10 doi:10.1101/161430 Cold Spring Harbor Laboratory Press 2017-07-10 <![CDATA[ Unmasking cellular response of a bloom-forming alga to virus infection by resolving expression profiling at a single-cell level ]]> https://biorxiv.org/content/10.1101/186981v1?rss=1 Rosenwasser, S. Frada, M. J. Pilzer, D. Rotkopf, R. Vardi, A. 2017-09-12 doi:10.1101/186981 Cold Spring Harbor Laboratory Press 2017-09-12 <![CDATA[ Mutational signatures reveal the role of RAD52 in p53-independent p21 driven genomic instability ]]> https://biorxiv.org/content/10.1101/195263v1?rss=1 Galanos, P. Pappas, G. Polyzos, A. Kotsinas, A. Svolaki, I. Giakoumakis, N. Glytsou, C. Pateras, I. Swain, U. Souliotis, V. Georgakilas, A. Geacintov, N. Scorrano, L. Lukas, C. Lukas, J. Livneh, Z. Lygerou, Z. Sorensen, C. S. Bartek, J. Gorgoulis, V. 2017-09-28 doi:10.1101/195263 Cold Spring Harbor Laboratory Press 2017-09-28 <![CDATA[ Predicting microRNA targeting efficacy in Drosophila ]]> https://biorxiv.org/content/10.1101/198689v1?rss=1 Agarwal, V. Subtelny, A. O. Thiru, P. Ulitsky, I. Bartel, D. P. 2017-10-05 doi:10.1101/198689 Cold Spring Harbor Laboratory Press 2017-10-05 <![CDATA[ Internal water storage buffering maintains plant function under drought as described by a general hydraulic model ]]> https://biorxiv.org/content/10.1101/2020.02.11.943563v1?rss=1 Kaner, A. Preisler, Y. Grünzweig, J. M. Mau, Y. 2020-02-11 doi:10.1101/2020.02.11.943563 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ Resting state fluctuations underlie free and creative verbal behaviors in the human brain ]]> https://biorxiv.org/content/10.1101/2020.03.01.971705v1?rss=1 Broday-Dvir, R. Malach, R. 2020-03-03 doi:10.1101/2020.03.01.971705 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ In situ differentiation of iridophore crystallotypes underlies zebrafish stripe patterning ]]> https://biorxiv.org/content/10.1101/2020.03.25.008664v1?rss=1 Gur, D. Bain, E. J. Johnson, K. Aman, A. J. Pasoili, A. Flynn, J. D. Allen, M. C. Deheyn, D. D. Lee, J. C. Lippincott-Schwartz, J. Parichy, D. M. 2020-03-25 doi:10.1101/2020.03.25.008664 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses ]]> https://biorxiv.org/content/10.1101/2020.04.15.042127v1?rss=1 Rozenberg, A. Oppermann, J. Wietek, J. Fernandez Lahore, R. G. Sandaa, R.-A. Bratbak, G. Hegemann, P. Beja, O. 2020-04-16 doi:10.1101/2020.04.15.042127 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ On the fitness of informative cues in complex environments ]]> https://biorxiv.org/content/10.1101/2020.04.28.066571v1?rss=1 Mafessoni, F. Lachmann, M. Gokhale, C. 2020-04-30 doi:10.1101/2020.04.28.066571 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Rising through the Ranks: Seasonal and Diel Patterns of Marine Viruses ]]> https://biorxiv.org/content/10.1101/2020.05.07.082883v1?rss=1 Hevroni, G. Flores-Uribe, J. Beja, O. Philosof, A. 2020-05-07 doi:10.1101/2020.05.07.082883 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ An NMR-based biosensor to measure stereo-specific methionine sulfoxide reductase (MSR) activities in vitro and in vivo. ]]> https://biorxiv.org/content/10.1101/2020.05.14.092957v1?rss=1 Sanchez-Lopez, M. C. Labadie, N. Lombardo, V. A. Biglione, F. A. Manta, B. Jacob, R. S. Gladyshev, V. N. Abdelilah-Seyfried, S. Selenko, P. Binolfi, A. 2020-05-15 doi:10.1101/2020.05.14.092957 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ The Surprising Role of the Default Mode Network ]]> https://biorxiv.org/content/10.1101/2020.05.18.101758v1?rss=1 Brandman, T. Malach, R. Simony, E. 2020-05-20 doi:10.1101/2020.05.18.101758 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ High resilience of the mycorrhizal community to prescribed seasonal burnings in a Mediterranean woodland ]]> https://biorxiv.org/content/10.1101/2020.06.10.141671v1?rss=1 Livne- Luzon, S. Shemesh, H. Osem, Y. Carmel, Y. Migael, H. Avidan, Y. Tsafrir, A. Glassman, S. I. Bruns, T. D. Ovadia, O. 2020-06-12 doi:10.1101/2020.06.10.141671 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Longitudinal isolation of potent near-germline SARS-CoV-2-neutralizing antibodies from COVID-19 patients ]]> https://biorxiv.org/content/10.1101/2020.06.12.146290v1?rss=1 Kreer, C. Zehner, M. Weber, T. Rohde, C. Halwe, S. Ercanoglu, M. S. Gieselmann, L. Korenkov, M. Gruell, H. Schommers, P. Vanshylla, K. Di Cristanziano, V. Janicki, H. Brinker, R. Ashurov, A. Kraehling, V. Kupke, A. Cohen-Dvashi, H. Koch, M. Lederer, S. Pfeifer, N. Wolf, T. Vehreschild, M. J. G. T. Wendtner, C. Diskin, R. Becker, S. Klein, F. 2020-06-12 doi:10.1101/2020.06.12.146290 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Dissipation During the Gating Cycle of the Bacterial Mechanosensitive Ion Channel Approaches the Landauer's Limit ]]> https://biorxiv.org/content/10.1101/2020.06.26.174649v1?rss=1 Cetiner, U. Raz, O. Sukharev, S. 2020-06-28 doi:10.1101/2020.06.26.174649 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ Pex14p phosphorylation modulates import of citrate synthase 2 into peroxisomes in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2020.07.03.186833v1?rss=1 Schummer, A. Maier, R. Gabay-Maskit, S. Hansen, T. Muehlhaeuser, W. W. D. Suppanz, I. Fadel, A. Schuldiner, M. Girzalsky, W. Oeljeklaus, S. Zalckvar, E. Erdmann, R. Warscheid, B. 2020-07-03 doi:10.1101/2020.07.03.186833 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ De novo designed receptor transmembrane domains enhance CAR-T cell cytotoxicity and attenuate cytokine release ]]> https://biorxiv.org/content/10.1101/2020.07.26.221598v1?rss=1 Elazar, A. Chandler, N. J. Davey, A. S. Weinstein, J. Y. Nguyen, J. V. Trenker, R. Jenkins, M. R. Call, M. J. Call, M. E. Fleishman, S. J. 2020-07-26 doi:10.1101/2020.07.26.221598 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ PHYTOCHROMES B1/B2 ARE MAJOR REGULATORS OF RIPENING-ASSOCIATED EPIGENOME REPROGRAMMING IN TOMATO FRUITS ]]> https://biorxiv.org/content/10.1101/2020.07.30.227447v1?rss=1 Bianchetti, R. Bellora, N. de Haro, L. Zuccarelli, R. Rosado, D. Freschi, L. Rossi, M. BERMUDEZ, L. F. 2020-07-31 doi:10.1101/2020.07.30.227447 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ A transitory signaling center controls timing of primordial germ cell differentiation ]]> https://biorxiv.org/content/10.1101/2020.08.01.232298v1?rss=1 Lehmann, R. Banisch, T. U. Slaidina, M. Gupta, S. Gilboa, L. 2020-08-03 doi:10.1101/2020.08.01.232298 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ The Structural Basis for SARM1 Inhibition, and Activation Under Energetic Stress ]]> https://biorxiv.org/content/10.1101/2020.08.05.238287v1?rss=1 Sporny, M. Guez-Haddad, J. Khazma, T. Yaron, A. Dessau, M. Mim, C. Isupov, M. N. Zalk, R. Hons, M. Opatowsky, Y. 2020-08-05 doi:10.1101/2020.08.05.238287 Cold Spring Harbor Laboratory Press 2020-08-05 <![CDATA[ Modeling Genetic Epileptic Encephalopathies using Brain Organoids ]]> https://biorxiv.org/content/10.1101/2020.08.23.263236v1?rss=1 Steinberg, D. J. Saleem, A. Repudi, S. R. Banne, E. Mahajnah, M. Hanna, J. H. Carlen, P. L. Aqeilan, R. I. 2020-08-23 doi:10.1101/2020.08.23.263236 Cold Spring Harbor Laboratory Press 2020-08-23 <![CDATA[ Dietary suppression of MHC-II expression in intestinal stem cells enhances intestinal tumorigenesis ]]> https://biorxiv.org/content/10.1101/2020.09.05.284174v1?rss=1 Beyaz, S. Roper, J. Xifaras, M. E. Bauer-Rowe, K. E. Ergin, I. Dohnalova, L. Biton, M. Shekar, K. Mou, H. Eskiocak, O. Ozata, D. M. Chung, C. Papciak, K. Almeqdadi, M. Fein, M. Erdemir, A. Valle-Encinas, E. Dogum, K. Garipcan, A. Meyer, H. Fox, J. G. Elinav, E. Kucukural, A. Kumar, P. McAleer, J. Thaiss, C. A. Regev, A. Orkin, S. H. Yilmaz, O. H. 2020-09-08 doi:10.1101/2020.09.05.284174 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ Single Cell Analysis of Regions of Interest (SCARI) using a novel photoswitchable tag ]]> https://biorxiv.org/content/10.1101/2020.10.02.291096v1?rss=1 van der Leun, A. M. Hoekstra, M. E. Reinalda, L. Scheele, C. L. Toebes, M. van de Graaff, M. J. Li, H. Bercovich, A. Lubling, Y. David, E. Thommen, D. S. Tanay, A. van Rheenen, J. Amit, I. van Kasteren, S. I. Schumacher, T. N. 2020-10-03 doi:10.1101/2020.10.02.291096 Cold Spring Harbor Laboratory Press 2020-10-03 <![CDATA[ Neural inflammation alters synaptic plasticity probed by 10 Hz repetitive magnetic stimulation ]]> https://biorxiv.org/content/10.1101/2020.10.16.336065v1?rss=1 Lenz, M. Eichler, A. Kruse, P. Strehl, A. Rodriguez-Rozada, S. Goren, I. Yogev, N. Frank, S. Waisman, A. Deller, T. Jung, S. Maggio, N. Vlachos, A. 2020-10-16 doi:10.1101/2020.10.16.336065 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Spontaneous emergence of behaviorally relevant motifs in human motor cortex ]]> https://biorxiv.org/content/10.1101/2020.10.25.353326v1?rss=1 Livne, T. Kim, D. Metcalf, N. V. Shulman, G. L. Corbetta, M. 2020-10-26 doi:10.1101/2020.10.25.353326 Cold Spring Harbor Laboratory Press 2020-10-26 <![CDATA[ A conserved superlocus regulates above- and belowground root initiation ]]> https://biorxiv.org/content/10.1101/2020.11.11.377937v1?rss=1 Omary, M. Gil-Yarom, N. Yahav, C. Steiner, E. Efroni, I. 2020-11-12 doi:10.1101/2020.11.11.377937 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Genome-wide Identification of the Genetic Basis of Amyotrophic Lateral Sclerosis ]]> https://biorxiv.org/content/10.1101/2020.11.14.382606v1?rss=1 Zhang, S. Cooper-Knock, J. Weimer, A. K. Shi, M. Moll, T. Harvey, C. Nezhad, H. G. Franklin, J. Souza, C. d. S. Wang, C. Li, J. Eitan, C. Hornstein, E. Kenna, K. P. Project MinE Sequencing Consortium, Veldink, J. Ferraiuolo, L. Shaw, P. J. Snyder, M. P. 2020-11-15 doi:10.1101/2020.11.14.382606 Cold Spring Harbor Laboratory Press 2020-11-15 <![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[ Multiplexed Imaging Analysis of the Tumor-Immune Microenvironment Reveals Predictors of Outcome in Triple-Negative Breast Cancer ]]> https://biorxiv.org/content/10.1101/2021.01.06.425496v1?rss=1 Patwa, A. N. Yamashita, R. Long, J. Keren, L. Angelo, M. Rubin, D. 2021-01-08 doi:10.1101/2021.01.06.425496 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Nanoscale resolution of microbial fiber degradation in action ]]> https://biorxiv.org/content/10.1101/2021.02.16.431430v1?rss=1 Tatli, M. Morais, S. Tovar-Herrera, O. E. Bomble, Y. Bayer, E. A. Medalia, O. Mizrahi, I. 2021-02-16 doi:10.1101/2021.02.16.431430 Cold Spring Harbor Laboratory Press 2021-02-16 <![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[ The global ocean size-spectrum from bacteria to whales ]]> https://biorxiv.org/content/10.1101/2021.04.03.438320v1?rss=1 Hatton, I. A. Heneghan, R. F. Bar-On, Y. M. Galbraith, E. D. 2021-04-04 doi:10.1101/2021.04.03.438320 Cold Spring Harbor Laboratory Press 2021-04-04 <![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[ Learning to represent continuous variables in heterogeneous neural networks ]]> https://biorxiv.org/content/10.1101/2021.06.01.446635v1?rss=1 Darshan, R. Rivkind, A. 2021-06-02 doi:10.1101/2021.06.01.446635 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ SmMIP-tools: a computational toolset for processing and analysis of single-molecule molecular inversion probes derived data ]]> https://biorxiv.org/content/10.1101/2021.06.03.446993v1?rss=1 Medeiros, J. J. F. Capo-Chichi, J.-M. Shlush, L. I. Dick, J. E. Arruda, A. Minden, M. D. Abelson, S. 2021-06-04 doi:10.1101/2021.06.03.446993 Cold Spring Harbor Laboratory Press 2021-06-04 <![CDATA[ Reducing Synchronization to Increase Interest Improves Interpersonal Liking ]]> https://biorxiv.org/content/10.1101/2021.06.30.450608v1?rss=1 Ravreby, I. Shilat, Y. Yeshurun, Y. 2021-07-01 doi:10.1101/2021.06.30.450608 Cold Spring Harbor Laboratory Press 2021-07-01 <![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[ MYCN mediates cysteine addiction and sensitizes to ferroptosis ]]> https://biorxiv.org/content/10.1101/2021.08.10.455675v1?rss=1 Alborzinia, H. Florez, A. F. Gogolin, S. Brueckner, L. M. Shao, C. Gartlgruber, M. Nadler Holly, M. Ziehm, M. Paul, F. Steinhauser, S. Bell, E. Shaikhkarami, M. Hartlieb, S. Dreidax, D. Hess, E. M. Kreth, J. Poschet, G. Buettner, M. Nicke, B. Stresemann, C. Reiling, J. H. Fischer, M. Amit, I. Selbach, M. Herrmann, C. Woelfl, S. Henrich, K. O. Hoefer, T. Westermann, F. 2021-08-10 doi:10.1101/2021.08.10.455675 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Spatio-temporal coordination at the maternal-fetal interface promotes trophoblast invasion and vascular remodeling in the first half of human pregnancy ]]> https://biorxiv.org/content/10.1101/2021.09.08.459490v1?rss=1 Greenbaum, S. Averbukh, I. Soon, E. Rizzuto, G. Baranski, A. Greenwald, N. Bosse, M. Jaswa, E. G. Khair, Z. Kwok, S. Warshawsky, S. Miller, G. Schwartz, M. Graf, W. Van Valen, D. Keren, L. Hollmann, T. van de Rijn, M. Angelo, M. 2021-09-10 doi:10.1101/2021.09.08.459490 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ Systematic Discovery of Antimicrobial Polymorphic Toxins ]]> https://biorxiv.org/content/10.1101/2021.10.19.465003v1?rss=1 Nachmias, N. Dotan, N. Shalom, M. Rivitz, A. Shamash-Halevy, N. Oppenheimer-Shaanan, Y. Levy, A. 2021-10-19 doi:10.1101/2021.10.19.465003 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Probing small ribosomal subunit RNA helix 45 acetylation across eukaryotic evolution ]]> https://biorxiv.org/content/10.1101/2021.11.30.470322v1?rss=1 Bortolin-Cavaille, M.-l. Quillien, A. Thalalla Gamage, S. Thomas, J. M. Sas-Chen, A. Sharma, S. Plisson-Chastang, C. Vandel, L. Blader, P. Lafontaine, D. L. Schwartz, S. Meier, J. L. Cavaille, J. 2021-11-30 doi:10.1101/2021.11.30.470322 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Class I DISARM provides anti-phage and anti-conjugation activity by unmethylated DNA recognition ]]> https://biorxiv.org/content/10.1101/2021.12.28.474362v1?rss=1 Aparicio-Maldonado, C. Ofir, G. Salini, A. Sorek, R. Nobrega, F. L. Brouns, S. J. 2021-12-28 doi:10.1101/2021.12.28.474362 Cold Spring Harbor Laboratory Press 2021-12-28 <![CDATA[ Fine oculomotor knowledge enhances high-acuity vision ]]> https://biorxiv.org/content/10.1101/2022.03.17.483854v1?rss=1 Zhao, Z. Ahissar, E. Victor, J. D. Rucci, M. 2022-03-19 doi:10.1101/2022.03.17.483854 Cold Spring Harbor Laboratory Press 2022-03-19 <![CDATA[ Accounting for cis-regulatory constraint prioritizes genes likely to affect species-specific traits ]]> https://biorxiv.org/content/10.1101/2022.03.29.486301v1?rss=1 Starr, A. L. Gokhman, D. Fraser, H. B. 2022-03-30 doi:10.1101/2022.03.29.486301 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ Retrospective behavioral sampling (RBS): a method to effectively track the cognitive fluctuations driven by naturalistic stimulation ]]> https://biorxiv.org/content/10.1101/2022.05.30.493974v1?rss=1 Brandman, T. Malach, R. Simony, E. 2022-06-01 doi:10.1101/2022.05.30.493974 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ Volume regulation in adhered cells: roles of surface tension and cell swelling ]]> https://biorxiv.org/content/10.1101/2022.08.24.505072v1?rss=1 Adar, R. M. Singh Vishen, A. Joanny, J.-F. Sens, P. Safran, S. A. 2022-08-25 doi:10.1101/2022.08.24.505072 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Revisiting the burden borne by fumarase: enzymatic hydration of an olefin ]]> https://biorxiv.org/content/10.1101/2022.09.03.506457v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@f2f7feorg.highwire.dtl.DTLVardef@1774e6aorg.highwire.dtl.DTLVardef@1bd180eorg.highwire.dtl.DTLVardef@1764941_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Bellur, A. Das, S. Jayaraman, V. Behera, S. Suryavanshi, A. Balasubramanian, S. Balaram, P. Jindal, G. Balaram, H. 2022-09-03 doi:10.1101/2022.09.03.506457 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Co-substrate pools can constrain and regulate pathway fluxes in cell metabolism ]]> https://biorxiv.org/content/10.1101/2022.09.05.506656v1?rss=1 West, R. Delattre, H. Noor, E. Feliu, E. Soyer, O. S. 2022-09-06 doi:10.1101/2022.09.05.506656 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ Recovery of equilibrium free energy from non-equilibrium thermodynamics with mechanosensitive ion channels in E. coli ]]> https://biorxiv.org/content/10.1101/229088v1?rss=1 Cetiner, U. Raz, O. Sukharev, S. Jarzynski, C. 2017-12-04 doi:10.1101/229088 Cold Spring Harbor Laboratory Press 2017-12-04 <![CDATA[ Pre-mature senescence in the oldest leaves of low nitrate-grown Atxdh1 mutant uncovers a role for purine catabolism in plant nitrogen metabolism ]]> https://biorxiv.org/content/10.1101/233569v1?rss=1 Sagi, M. Soltabayeva, A. Srivastava, S. Kurmanbayeva, A. Bekturova, A. Fluhr, R. 2017-12-13 doi:10.1101/233569 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ The transcriptome of Paraphelidium tribonemae illuminates the ancestry of Fungi and Opisthosporidia ]]> https://biorxiv.org/content/10.1101/233882v1?rss=1 Torruella, G. Grau-Bove, X. Moreira, D. Karpov, S. A. Burns, J. Sebe-Pedros, A. Volcker, E. Lopez-Garcia, P. 2017-12-13 doi:10.1101/233882 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ In vivo Effects of Temperature on the Heart and Pyloric Rhythms in the Crab, Cancer borealis ]]> https://biorxiv.org/content/10.1101/249631v1?rss=1 Kushinsky, D. Marder, E. 2018-01-17 doi:10.1101/249631 Cold Spring Harbor Laboratory Press 2018-01-17 <![CDATA[ Phospho-regulation of Atoh1 is required for plasticity of secretory progenitors and tissue regeneration ]]> https://biorxiv.org/content/10.1101/268607v1?rss=1 Tomic, G. Morrissey, E. Kozar, S. Ben-Moshe, S. Hoyle, A. Azzarelli, R. Kemp, R. Chilamakuri, C. S. R. Itzkovitz, S. Philpott, A. Winton, D. 2018-02-26 doi:10.1101/268607 Cold Spring Harbor Laboratory Press 2018-02-26 <![CDATA[ Propagation of information along the cortical hierarchy as a function of attention while reading and listening to stories ]]> https://biorxiv.org/content/10.1101/291526v1?rss=1 Regev, M. Simony, E. Lee, K. Tan, K. M. Chen, J. Hasson, U. 2018-04-08 doi:10.1101/291526 Cold Spring Harbor Laboratory Press 2018-04-08 <![CDATA[ Microscale tracking of coral disease reveals timeline of infection and heterogeneity of polyp fate. ]]> https://biorxiv.org/content/10.1101/302778v1?rss=1 Gavish, A. R. Shapiro, O. H. Kramarsky-Winter, E. Vardi, A. 2018-04-17 doi:10.1101/302778 Cold Spring Harbor Laboratory Press 2018-04-17 <![CDATA[ Molecular evolution of juvenile hormone esterase-like proteins in a socially exchanged fluid ]]> https://biorxiv.org/content/10.1101/337568v1?rss=1 LeBoeuf, A. C. Cohanim, A. B. Stoffel, C. Brent, C. S. Waridel, P. Privman, E. Keller, L. Benton, R. 2018-06-03 doi:10.1101/337568 Cold Spring Harbor Laboratory Press 2018-06-03 <![CDATA[ Mice developing mammary tumors evolve T cell sequences shared with human breast cancer patients ]]> https://biorxiv.org/content/10.1101/371260v1?rss=1 Gordin, M. Philip, H. Zilberberg, A. Cohen Gidon, M. Margalit, R. Clouser, C. Adams, K. Vigneault, F. R. Cohen, I. Yaari, G. Efroni, S. 2018-07-30 doi:10.1101/371260 Cold Spring Harbor Laboratory Press 2018-07-30 <![CDATA[ Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition ]]> https://biorxiv.org/content/10.1101/415661v1?rss=1 Schneidman-Duhovny, D. Khuri, N. Dong, G. Q. Winter, M. B. Shifrut, E. Friedman, N. Craik, C. S. Pratt, K. P. Paz, P. Aswad, F. Sali, A. 2018-09-13 doi:10.1101/415661 Cold Spring Harbor Laboratory Press 2018-09-13 <![CDATA[ Microglial SIRPα regulates the emergence of CD11c+ microglia and demyelination damage in white matter ]]> https://biorxiv.org/content/10.1101/443531v1?rss=1 Sato-Hashimoto, M. Nozu, T. Toriba, R. Horikoshi, A. Akaike, M. Kawamoto, K. Hirose, A. Hayashi, Y. Nagai, H. Shimizu, W. Saiki, A. Ishikawa, T. Elhanbaly, R. Kotani, T. Murata, Y. Saito, Y. Masae, M. Shibasaki, K. Oldenborg, P.-A. Jung, S. Matozaki, T. Fukazawa, Y. Ohnishi, H. 2018-10-24 doi:10.1101/443531 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ Molecular anatomy and plasticity of the long noncoding RNA HOTAIR ]]> https://biorxiv.org/content/10.1101/444331v1?rss=1 Spokoini-Stern, R. Stamov, D. Jessel, H. Aharoni, L. Haschke, H. Giron, J. Unger, R. Segal, E. Abu-Horowitz, A. Bachelet, I. 2018-10-15 doi:10.1101/444331 Cold Spring Harbor Laboratory Press 2018-10-15 <![CDATA[ Decreased Inter Trial Phase Coherence of Steady-State Visual Evoked Responses in Sleep Deprivation ]]> https://biorxiv.org/content/10.1101/471730v1?rss=1 Eidelman-Rothman, M. Ben-Simon, E. Freche, D. Keil, A. Hendler, T. Levit-Binnun, N. 2018-11-15 doi:10.1101/471730 Cold Spring Harbor Laboratory Press 2018-11-15 <![CDATA[ Time-resolved systems analysis reveals a critical role of XCR1+ 1 dendritic cells in the maintenance of effector T cells during chronic viral infection ]]> https://biorxiv.org/content/10.1101/476077v1?rss=1 Argilaguet, J. Pedragosa, M. Esteve-Codina, A. Riera, G. Vidal, E. Peligero-Cruz, C. Andreu, D. Kaisho, T. Bocharov, G. Ludewig, B. Heath, S. Meyerhans, A. 2018-11-22 doi:10.1101/476077 Cold Spring Harbor Laboratory Press 2018-11-22 <![CDATA[ Pooled clone collections by multiplexed CRISPR/Cas12a-assisted gene tagging in yeast ]]> https://biorxiv.org/content/10.1101/476804v1?rss=1 90% of correctly tagged clones. Up to several hundred genes can be tagged in a single step and, on a genomic scale, approximately half of all genes are tagged with only ~10-fold oversampling. We report several parameters that affect tagging success and provide a quantitative targeted next-generation sequencing method to analyze such pooled collections. Thus, CASTLING unlocks new avenues for increased throughput in functional genomics and cell biology research. (max 150 words) ]]> Buchmuller, B. C. Herbst, K. Meurer, M. Kirrmaier, D. Sass, E. Levy, E. D. Knop, M. 2018-11-22 doi:10.1101/476804 Cold Spring Harbor Laboratory Press 2018-11-22 <![CDATA[ Face-selective units in human ventral temporal cortex reactivate during free recall ]]> https://biorxiv.org/content/10.1101/487686v1?rss=1 Khuvis, S. Yeagle, E. M. Norman, Y. Grossman, S. Malach, R. Mehta, A. D. 2018-12-05 doi:10.1101/487686 Cold Spring Harbor Laboratory Press 2018-12-05 <![CDATA[ A metabolic switch from OXPHOS to glycolysis is essential for cardiomyocyte proliferation in the regenerating heart ]]> https://biorxiv.org/content/10.1101/498899v1?rss=1 Honkoop, H. de Bakker, D. Aharonov, A. Kruse, F. Shakked, A. Nguyen, P. de Heus, C. Garric, L. Muraro, M. Shoffner, A. Tessadori, F. Peterson, J. Noort, W. Posthuma, G. Grun, D. van der Laarse, W. Klumperman, J. Jaspers, R. Poss, K. van Oudenaarden, A. Tzahor, E. Bakkers, J. 2018-12-18 doi:10.1101/498899 Cold Spring Harbor Laboratory Press 2018-12-18 <![CDATA[ Where does time go when you blink? ]]> https://biorxiv.org/content/10.1101/506279v1?rss=1 Grossman, S. Guata, C. Pesin, S. Malach, R. Landau, A. N. 2018-12-26 doi:10.1101/506279 Cold Spring Harbor Laboratory Press 2018-12-26 <![CDATA[ Multiplexed electron microscopy by fluorescent barcoding allows screening for ultrastructural phenotype ]]> https://biorxiv.org/content/10.1101/515841v1?rss=1 Bykov, Y. Cohen, N. Gabrielli, N. Manenschijn, H. Welsch, S. Chlanda, P. Kukulski, W. Patil, K. R. R. Schuldiner, M. Briggs, J. A. G. 2019-01-09 doi:10.1101/515841 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ Accurate detection of m6A RNA modifications in native RNA sequences ]]> https://biorxiv.org/content/10.1101/525741v1?rss=1 Liu, H. Begik, O. Lucas, M. C. Mason, C. E. Schwartz, S. Mattick, J. S. Smith, M. A. Novoa, E. M. 2019-01-21 doi:10.1101/525741 Cold Spring Harbor Laboratory Press 2019-01-21 <![CDATA[ Modelling the role of dual specificity phosphatases in Herceptin resistant breast cancer cell lines ]]> https://biorxiv.org/content/10.1101/528315v1?rss=1 Buiga, P. Elson, A. Tabernero, L. Schwartz, J.-M. 2019-01-23 doi:10.1101/528315 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Social context and dominance status contribute to sleep patterns and quality in groups of freely-moving mice ]]> https://biorxiv.org/content/10.1101/529669v1?rss=1 Karamihalev, S. Flachskamm, C. Kimura, M. Chen, A. 2019-01-24 doi:10.1101/529669 Cold Spring Harbor Laboratory Press 2019-01-24 <![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[ Aversive learning strengthens episodic memory in both adolescents and adults ]]> https://biorxiv.org/content/10.1101/547331v1?rss=1 Cohen, A. O. Matese, N. G. Filimontseva, A. Shen, X. Shi, T. C. Livne, E. Hartley, C. A. 2019-02-12 doi:10.1101/547331 Cold Spring Harbor Laboratory Press 2019-02-12 <![CDATA[ Fast dose fractionation using ultra-short laser accelerated proton pulses can increase cancer cell mortality, which relies on functional PARP1 protein ]]> https://biorxiv.org/content/10.1101/571703v1?rss=1 Bayart, E. Flacco, A. Delmas, O. Pommarel, L. Levy, D. Cavallone, M. Megnin-Chanet, F. Deutsch, E. Malka, V. 2019-03-08 doi:10.1101/571703 Cold Spring Harbor Laboratory Press 2019-03-08 <![CDATA[ Auditory and semantic cues facilitate decoding of visual object category in MEG ]]> https://biorxiv.org/content/10.1101/598516v1?rss=1 Brandman, T. Avancini, C. Leticevscaia, O. Peelen, M. V. 2019-04-05 doi:10.1101/598516 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ Novel lead compounds that target the ribosomal peptidyl transferase center ]]> https://biorxiv.org/content/10.1101/604777v1?rss=1 Tam, B. Cohen, S. Sherf, D. Eisdorfer, S. A. Perez, M. Soffer, A. Vilenchik, D. Wagner, G. Akabayov, B. 2019-04-10 doi:10.1101/604777 Cold Spring Harbor Laboratory Press 2019-04-10 <![CDATA[ A lipophilicity-based energy function for membrane-protein modelling and design ]]> https://biorxiv.org/content/10.1101/615658v1?rss=1 Weinstein, J. Y. Elazar, A. Fleishman, S. J. 2019-04-25 doi:10.1101/615658 Cold Spring Harbor Laboratory Press 2019-04-25 <![CDATA[ Point mutations in topoisomerase I alter the mutation spectrum in E. coli and impact the emergence of drug resistance genotypes ]]> https://biorxiv.org/content/10.1101/621045v1?rss=1 Bachar, A. Itzhaki, E. Gleizer, S. Shamshoom, M. Milo, R. Antonovsky, N. 2019-04-28 doi:10.1101/621045 Cold Spring Harbor Laboratory Press 2019-04-28 <![CDATA[ Single-cell RNA sequencing reveals mRNA splice isoform switching during kidney development ]]> https://biorxiv.org/content/10.1101/688564v1?rss=1 Wineberg, Y. Bar-Lev, T. H. Futorian, A. Ben-Haim, N. Armon, L. Ickowicz, D. Oriel, S. Bucris, E. Yehuda, Y. Pode-Shakked, N. Gilad, S. Benjamin, S. Hohenstein, P. Dekel, B. Urbach, A. Kalisky, T. 2019-07-01 doi:10.1101/688564 Cold Spring Harbor Laboratory Press 2019-07-01 <![CDATA[ Non-Canonical Regulation of Phosphatidylserine Metabolism by a Phosphatidylinositol Transfer Protein and a Phosphatidylinositol 4-OH Kinase ]]> https://biorxiv.org/content/10.1101/696336v1?rss=1 Wang, Y. Yuan, P. Tripathi, A. Rodriguez, M. Lonnfors, M. Eisenberg-Bord, M. Schuldiner, M. Bankaitis, V. 2019-07-08 doi:10.1101/696336 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Scale free topology as an effective feedback system ]]> https://biorxiv.org/content/10.1101/696575v1?rss=1 Rivkind, A. Schreier, H. Brenner, N. Barak, O. 2019-07-10 doi:10.1101/696575 Cold Spring Harbor Laboratory Press 2019-07-10 <![CDATA[ Transfer of Septin Rings to Cytokinetic Remnants Directs Age-Sensitive ER stress Surveillance Cell Cycle Re-entry ]]> https://biorxiv.org/content/10.1101/698829v1?rss=1 Chao, J. T. Pina, F. Onishi, M. Cohen, Y. Schuldiner, M. Niwa, M. 2019-07-13 doi:10.1101/698829 Cold Spring Harbor Laboratory Press 2019-07-13 <![CDATA[ Diatoms structure the plankton community based on selective segregation in the world’s ocean ]]> https://biorxiv.org/content/10.1101/704353v1?rss=1 Vincent, F. J. Bowler, C. 2019-07-17 doi:10.1101/704353 Cold Spring Harbor Laboratory Press 2019-07-17 <![CDATA[ BIAFLOWS: A collaborative framework to benchmark bioimage analysis workflows ]]> https://biorxiv.org/content/10.1101/707489v1?rss=1 Rubens, U. Mormont, R. Baecker, V. Michiels, G. Paavolainen, L. Ball, G. Unay, D. Pavie, B. Chessel, A. Scholz, L. A. Maska, M. Hoyoux, R. Vandaele, R. Stanciu, S. G. Golani, O. Sladoje, N. Paul-Gilloteaux, P. Maree, R. Tosi, S. 2019-07-19 doi:10.1101/707489 Cold Spring Harbor Laboratory Press 2019-07-19 <![CDATA[ DYNLRB1 is Essential for Dynein Mediated Transport and Neuronal Survival ]]> https://biorxiv.org/content/10.1101/727016v1?rss=1 Terenzio, M. Di Pizio, A. Rishal, I. Marvaldi, L. Di Matteo, P. Kawaguchi, R. Coppola, G. Schiavo, G. Fisher, E. M. C. Fainzilber, M. 2019-08-06 doi:10.1101/727016 Cold Spring Harbor Laboratory Press 2019-08-06 <![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[ Proteomic analysis reveals the recruitment of intrinsically disordered regions to stress granules ]]> https://biorxiv.org/content/10.1101/758599v1?rss=1 Zhu, M. Kuechler, E. R. Zhang, J. Matalon, O. Dubreuil, B. Hofmann, A. Loewen, C. J. R. Levy, E. Gsponer, J. Mayor, T. 2019-09-05 doi:10.1101/758599 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Stability of excitatory structural connectivity predicts the probability of CA1 pyramidal neurons to become engram neurons ]]> https://biorxiv.org/content/10.1101/759225v1?rss=1 Castello-Waldow, T. P. Weston, G. Chenani, A. Loewenstein, Y. Chen, A. Attardo, A. 2019-09-08 doi:10.1101/759225 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ Community Standards for Open Cell Migration Data ]]> https://biorxiv.org/content/10.1101/803064v1?rss=1 Gonzalez-Beltran, A. N. Masuzzo, P. Ampe, C. Bakker, G.-J. Besson, S. Eibl, R. H. Friedl, P. Gunzer, M. Kittisopikul, M. Le Devedec, S. E. Leo, S. Moore, J. Paran, Y. Prilusky, J. Rocca-Serra, P. Roudot, P. Schuster, M. Sergeant, G. Stromblad, S. Swedlow, J. R. van Erp, M. Van Troys, M. Zaritsky, A. Sansone, S.-A. Martens, L. 2019-10-14 doi:10.1101/803064 Cold Spring Harbor Laboratory Press 2019-10-14 <![CDATA[ Pan-cancer single cell RNA-seq uncovers recurring programs of cellular heterogeneity ]]> https://biorxiv.org/content/10.1101/807552v1?rss=1 Kinker, G. S. Greenwald, A. C. Tal, R. Orlova, Z. Cuoco, M. S. McFarland, J. M. Warren, A. Rodman, C. Roth, J. A. Bender, S. A. Kumar, B. Rocco, J. W. Fernandes, P. A. Mader, C. C. Keren-Shaul, H. Plotnikov, A. Barr, H. Tsherniak, A. Rozenblatt-Rosen, O. Krizhanovsky, V. Puram, S. V. Regev, A. Tirosh, I. 2019-10-21 doi:10.1101/807552 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ The co-chaperone Fkbp5 shapes the acute stress response in the paraventricular nucleus of the hypothalamus ]]> https://biorxiv.org/content/10.1101/824664v1?rss=1 Häusl, A. S. Hartmann, J. Pöhlmann, M. L. Brix, L. M. Lopez, J.-P. Brivio, E. Engelhardt, C. Roeh, S. Rudolph, L. Stoffel, R. Hafner, K. Gross, H. M. Reul, J. M. H. M. Deussing, J. M. Ressler, K. J. Gassen, N. C. Chen, A. Schmidt, M. V. 2019-10-30 doi:10.1101/824664 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ Multiplexed single-cell profiling of post-perturbation transcriptional responses to define cancer vulnerabilities and therapeutic mechanism of action ]]> https://biorxiv.org/content/10.1101/868752v1?rss=1 McFarland, J. M. Paolella, B. R. Warren, A. Geiger-Schuller, K. Shibue, T. Rothberg, M. Kuksenko, O. Jones, A. Chambers, E. Dionne, D. Bender, S. Wolpin, B. M. Ghandi, M. Tirosh, I. Rozenblatt-Rosen, O. Roth, J. A. Golub, T. R. Regev, A. Aguirre, A. J. Vazquez, F. Tsherniak, A. 2019-12-08 doi:10.1101/868752 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ CENTRE: A gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction ]]> https://biorxiv.org/content/10.1101/2023.05.16.541035v1?rss=1 Rapakoulia, T. Lopez, S. R. d. V. Omgba, P. A. Laupert, V. Ulitsky, I. Vingron, M. 2023-05-18 doi:10.1101/2023.05.16.541035 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ GGAssembler: Economical Design of Gene Libraries with Precise Control over Mutations ]]> https://biorxiv.org/content/10.1101/2023.05.18.541394v1?rss=1 105 variants with DNA costs <0.007$ per variant and dropping significantly with increased library complexity. >93% of the desired variants were present in the assembly product and >99% were represented within the expected order of magnitude as verified by deep sequencing. The GGAssembler workflow is, therefore, an accurate approach for generating complex variant libraries that may drastically reduce costs and accelerate discovery and optimization of antibodies, enzymes and other proteins. The workflow is accessible through a web interface at https://github.com/Fleishman-Lab/GGAssembler/blob/master/example/colab_oligos_design.ipynb. ]]> Hoch, S. Y. Weinstein, J. Y. Netzer, R. Hakeny, K. Fleishman, S. J. 2023-05-19 doi:10.1101/2023.05.18.541394 Cold Spring Harbor Laboratory Press 2023-05-19 <![CDATA[ A CRISPR-induced DNA break can trigger crossover, chromosomal loss and chromothripsis-like rearrangements ]]> https://biorxiv.org/content/10.1101/2023.05.22.541757v1?rss=1 Samach, A. Mafessoni, F. Gross, O. Melamed-Bessudo, C. Filler Hayut, S. Dahan-Meir, T. Amsellem, Z. Pawlowski, W. P. Levy, A. A. 2023-05-24 doi:10.1101/2023.05.22.541757 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Liver Receptor Homolog-1 (LRH-1/NR5A2) orchestrates hepatic inflammation and TNF-induced cell death ]]> https://biorxiv.org/content/10.1101/2023.05.24.542039v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@13cd609org.highwire.dtl.DTLVardef@1080012org.highwire.dtl.DTLVardef@3cd9c4org.highwire.dtl.DTLVardef@fd0438_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lambrecht, R. Delgado, M. E. Gloe, V. Schuetz, K. Plazzo, A. P. Franke, B. Phan, T. S. Fleming, J. R. Mayans, O. Brunner, T. 2023-05-24 doi:10.1101/2023.05.24.542039 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ CARD-like domains mediate anti-phage defense in bacterial gasdermin systems ]]> https://biorxiv.org/content/10.1101/2023.05.28.542683v1?rss=1 Wein, T. Johnson, A. G. Millman, A. Lange, K. Yirmiya, E. Hadary, R. Garb, J. Steinruecke, F. Hill, A. B. Kranzusch, P. J. Sorek, R. 2023-05-29 doi:10.1101/2023.05.28.542683 Cold Spring Harbor Laboratory Press 2023-05-29 <![CDATA[ The impact of molecular variants, crystallization conditions and space group on structure-ligand complexes: A case study on Bacterial Phosphotriesterase Variants and complexes ]]> https://biorxiv.org/content/10.1101/2023.05.31.542999v1?rss=1 Dym, O. Aggawal, N. Ashani, Y. Albeck, S. Unger, T. Hamer Rogotner, S. Silman, I. Tawfik, D. S. Sussman, J. L. 2023-06-01 doi:10.1101/2023.05.31.542999 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Rim aperture of autophagic membranesbalances cargo inclusion with vesicle maturation ]]> https://biorxiv.org/content/10.1101/2023.06.01.543228v1?rss=1 Shatz, O. Fraiberg, M. Polyansky, A. Shimoni, E. Wolf, S. G. Elazar, Z. 2023-06-01 doi:10.1101/2023.06.01.543228 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Autotrophic growth of E. coli is achieved by a small number of genetic changes ]]> https://biorxiv.org/content/10.1101/2023.06.03.543535v1?rss=1 Ben Nissan, R. Milshtein, E. Pahl, V. de Pins, B. Jona, G. Levi, D. Yung, H. Nir, N. Ezra, D. Gleizer, S. Link, H. Noor, E. Milo, R. 2023-06-03 doi:10.1101/2023.06.03.543535 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ What fraction of cellular DNA turnover becomes cfDNA? ]]> https://biorxiv.org/content/10.1101/2023.06.03.543527v1?rss=1 Sender, R. Noor, E. Milo, R. Dor, Y. 2023-06-06 doi:10.1101/2023.06.03.543527 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ Fusion pore dynamics of large secretory vesicles define a distinct mechanism of exocytosis ]]> https://biorxiv.org/content/10.1101/2023.06.08.544180v1?rss=1 Biton, T. Scher, N. Carmon, S. Elbaz-Alon, Y. Schejter, E. D. Shilo, B.-Z. Avinoam, O. 2023-06-08 doi:10.1101/2023.06.08.544180 Cold Spring Harbor Laboratory Press 2023-06-08 <![CDATA[ An atlas of protein homo-oligomerization across domains of life ]]> https://biorxiv.org/content/10.1101/2023.06.09.544317v1?rss=1 View larger version (79K): org.highwire.dtl.DTLVardef@1507a12org.highwire.dtl.DTLVardef@7e522aorg.highwire.dtl.DTLVardef@1445410org.highwire.dtl.DTLVardef@eb09f7_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Schweke, H. Levin, T. Pacesa, M. Goverde, C. A. Kumar, P. Duhoo, Y. Dornfeld, L. J. Dubreuil, B. Georgeon, S. Ovchinnikov, S. Woolfson, D. N. Correia, B. E. Dey, S. Levy, E. D. 2023-06-11 doi:10.1101/2023.06.09.544317 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ RBD-based high affinity ACE2 antagonist limits SARS-CoV-2 replication in upper and lower airways ]]> https://biorxiv.org/content/10.1101/2023.06.09.544432v1?rss=1 Gagne, M. Flynn, B. J. Honeycutt, C. C. Flebbe, D. R. Andrew, S. F. Provost, S. J. McCormick, L. Van Ry, A. McCarthy, E. Todd, J.-P. M. Bao, S. Teng, I.-T. Marciano, S. Rudich, Y. Li, C. Pessaint, L. Dodson, A. Cook, A. Lewis, M. G. Andersen, H. Zahradnik, J. Nason, M. C. Foulds, K. E. Kwong, P. D. Roederer, M. Schreiber, G. Seder, R. A. Douek, D. C. 2023-06-12 doi:10.1101/2023.06.09.544432 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ Transgene-Free Ex Utero Derivation of A Human Post-Implantation Embryo Model Solely from Genetically Unmodified Naive PSCs ]]> https://biorxiv.org/content/10.1101/2023.06.14.544922v1?rss=1 Oldak, B. Wildschutz, E. Bondarenko, V. Aguilera-Castrejon, A. Zhao, C. Tarazi, S. Comar, M.-Y. Ashouokhi, S. Lokshtanov, D. Roncato, F. Viukov, S. Ariel, E. Rose, M. Livnat, N. Shani, T. Joubran, C. Cohen, R. Addadi, Y. Kedmi, M. Keren-Shaul, H. Petropoulos, S. Lanner, F. Novershtern, N. Hanna, J. H. 2023-06-15 doi:10.1101/2023.06.14.544922 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ CC + : A Searchable Database of Validated Coiled coils in PDB Structures and AlphaFold2 Models ]]> https://biorxiv.org/content/10.1101/2023.06.16.541900v1?rss=1 Kumar, P. Petrenas, R. Dawson, W. M. Schweke, H. Levy, E. D. Woolfson, D. 2023-06-17 doi:10.1101/2023.06.16.541900 Cold Spring Harbor Laboratory Press 2023-06-17 <![CDATA[ Homing in on the rare virosphere reveals the native host of giant viruses ]]> https://biorxiv.org/content/10.1101/2023.06.27.546645v1?rss=1 Fromm, A. Hevroni, G. Vincent, F. Schatz, D. Martinez-Gutierrez, C. A. Aylward, F. O. Vardi, A. 2023-06-27 doi:10.1101/2023.06.27.546645 Cold Spring Harbor Laboratory Press 2023-06-27 <![CDATA[ Self-extinguishing relay waves enable homeostaticcontrol of human neutrophil swarming ]]> https://biorxiv.org/content/10.1101/2023.06.27.546744v1?rss=1 Strickland, J. Pan, D. Godfrey, C. Kim, J. S. Hopke, A. Degrange, M. Villavicencio, B. Mansour, M. K. Zerbe, C. S. Irimia, D. Amir, A. Weiner, O. D. 2023-06-28 doi:10.1101/2023.06.27.546744 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ The Unexpected Match: STAT3-NORAD Interaction, a Novel Link in Antiviral Defense ]]> https://biorxiv.org/content/10.1101/2023.06.29.546999v1?rss=1 Argoetti, A. Shalev, D. Polyak, G. Shima, N. Biran, H. Lahav, T. Hashimshony, T. Mandel-Gutfreund, Y. 2023-06-29 doi:10.1101/2023.06.29.546999 Cold Spring Harbor Laboratory Press 2023-06-29 <![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[ Optimal enzyme profiles in unbranched metabolic pathways ]]> https://biorxiv.org/content/10.1101/2023.06.30.547243v1?rss=1 Noor, E. Liebermeister, W. 2023-07-03 doi:10.1101/2023.06.30.547243 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Polarization and motility of one-dimensional multi-cellular trains ]]> https://biorxiv.org/content/10.1101/2023.07.02.547405v1?rss=1 Ron, J. E. d'Alesandro, J. Cellerin, V. Voituriez, R. Ladoux, B. Gov, N. S. 2023-07-03 doi:10.1101/2023.07.02.547405 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Longitudinal hair cortisol in bipolar disorder and a mechanism based on HPA dynamics ]]> https://biorxiv.org/content/10.1101/2023.07.03.546860v1?rss=1 Milo, T. Maimon, L. Cohen, B. Haran, D. Segman, D. Danon, T. Bren, A. Mayo, A. Cohen Rappaport, G. McInnis, M. Alon, U. 2023-07-03 doi:10.1101/2023.07.03.546860 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Unifying design principles of endocrine gland mass and its regulatory circuits ]]> https://biorxiv.org/content/10.1101/2023.07.03.547486v1?rss=1 Raz, M. Milo, T. Korem Kohanim, Y. karin, O. Tendler, A. Bar, A. Glass, D. S. Mayo, A. Alon, U. 2023-07-03 doi:10.1101/2023.07.03.547486 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Putting cognitive tasks on trial: A measure of reliability convergence ]]> https://biorxiv.org/content/10.1101/2023.07.03.547563v1?rss=1 Kadlec, J. Walsh, C. Sade, U. Amir, A. Rissman, J. Ramot, M. 2023-07-03 doi:10.1101/2023.07.03.547563 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Mapping interactions between disordered regions reveals promiscuity in biomolecular condensate formation ]]> https://biorxiv.org/content/10.1101/2023.07.04.547715v1?rss=1 View larger version (60K): org.highwire.dtl.DTLVardef@1bc6a1forg.highwire.dtl.DTLVardef@db4325org.highwire.dtl.DTLVardef@1154717org.highwire.dtl.DTLVardef@1ee619e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gilat, A. Dubrueil, B. Levy, E. D. 2023-07-04 doi:10.1101/2023.07.04.547715 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ Antisense transcription and PRC2 repression function in parallel during vernalization ]]> https://biorxiv.org/content/10.1101/2023.07.07.547987v1?rss=1 Nielsen, M. Menon, G. Zhao, Y. Mateo-Bonmati, E. Wolff, P. Zhou, S. Howard, M. Dean, C. 2023-07-07 doi:10.1101/2023.07.07.547987 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Affinity hierarchies underlie the co-assembly of nucleolar and heterochromatin condensates in Drosophila embryos ]]> https://biorxiv.org/content/10.1101/2023.07.06.547894v1?rss=1 Rajshekar, S. Adame-Arana, O. Bajpai, G. Lin, K. Colmenares, S. Safran, S. Karpen, G. H. 2023-07-08 doi:10.1101/2023.07.06.547894 Cold Spring Harbor Laboratory Press 2023-07-08 <![CDATA[ Integrative spatial analysis reveals a multi-layered organization of glioblastoma ]]> https://biorxiv.org/content/10.1101/2023.07.06.547924v1?rss=1 Greenwald, A. C. Darnell, N. G. Hoefflin, R. Simkin, D. Gonzalez-Castro, L. N. Mount, C. Hirsch, D. Nomura, M. Talpir, T. Kedmi, M. Goliand, I. Medici, G. Li, B. Keren-Shaul, H. Weller, M. Addadi, Y. Neidert, M. C. Suva, M. L. Tirosh, I. 2023-07-08 doi:10.1101/2023.07.06.547924 Cold Spring Harbor Laboratory Press 2023-07-08 <![CDATA[ Five inhibitory receptors display distinct vesicular distributions in T cells ]]> https://biorxiv.org/content/10.1101/2023.07.21.550019v1?rss=1 Lu, J. Veler, A. Simonetti, B. Raj, T. Chou, P. H. Cross, S. J. Phillips, A. M. Ruan, X. J. Huynh, L. Dowsey, A. W. Ye, D. Murphy, R. F. Verkade, P. Cullen, P. J. Wuelfing, C. 2023-07-22 doi:10.1101/2023.07.21.550019 Cold Spring Harbor Laboratory Press 2023-07-22 <![CDATA[ Systematic exploration of prokaryotic form I rubisco maximal carboxylation rates ]]> https://biorxiv.org/content/10.1101/2023.07.27.550689v1?rss=1 de Pins, B. Greenspoon, L. Bar-On, Y. M. Shamshoum, M. Ben-Nissan, R. Milshtein, E. Davidi, D. Sharon, I. Mueller-Cajar, O. Noor, E. Milo, R. 2023-07-27 doi:10.1101/2023.07.27.550689 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Murine classical monocyte subsets display distinct functions and fates ]]> https://biorxiv.org/content/10.1101/2023.07.29.551083v1?rss=1 Trzebanski, S. Kim, J.-S. Larrossi, N. Kancheva, D. Bastos, J. Haddad, M. Aizik, D. Kralova, J. Gross-Vered, M. Boura-Halfon, S. Lapidot, T. Alon, R. Movahedi, K. Jung, S. 2023-07-31 doi:10.1101/2023.07.29.551083 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ Highly conserved, positively charged tandem repeats mediate multimerization of ice nucleation proteins ]]> https://biorxiv.org/content/10.1101/2023.08.03.551873v1?rss=1 Hansen, T. Lee, J. C. Reicher, N. Ovadia, G. Guo, S. Guo, W. Liu, J. Braslavsky, I. Rudich, Y. Davies, P. L. 2023-08-03 doi:10.1101/2023.08.03.551873 Cold Spring Harbor Laboratory Press 2023-08-03 <![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[ EasyFlow: An open source, user friendly cytometry analyzer with graphic user interface (GUI) ]]> https://biorxiv.org/content/10.1101/2023.08.07.552387v1?rss=1 Ma, Y. Antebi, Y. 2023-08-09 doi:10.1101/2023.08.07.552387 Cold Spring Harbor Laboratory Press 2023-08-09 <![CDATA[ The SARM1 TIR domain produces glycocyclic ADPR molecules as minor products ]]> https://biorxiv.org/content/10.1101/2023.08.10.552750v1?rss=1 Garb, J. Amitai, G. Lu, A. Ofir, G. Brandis, A. Mehlman, T. Kranzusch, P. Sorek, R. 2023-08-10 doi:10.1101/2023.08.10.552750 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ Metal Ions Guide the Production of Silkworm Fibers ]]> https://biorxiv.org/content/10.1101/2023.08.10.552775v1?rss=1 Brookstein, O. Shimoni, E. Eliaz, D. Kaplan-Ashiri, I. Carmel, I. Shimanovich, U. 2023-08-11 doi:10.1101/2023.08.10.552775 Cold Spring Harbor Laboratory Press 2023-08-11 <![CDATA[ PRDM16 co-operates with LHX2 to shape the human brain ]]> https://biorxiv.org/content/10.1101/2023.08.12.553065v1?rss=1 Suresh, V. Bhattacharya, B. Tshuva, R. Y. Danan Gotthold, M. Olender, T. Bose, M. Ben Zeev, B. Smith, R. S. Pradhan, S. J. Tole, S. Galande, S. Harwell, C. Baizabal, M. Reiner, O. 2023-08-12 doi:10.1101/2023.08.12.553065 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ Toxinome - The Bacterial Protein Toxin Database ]]> https://biorxiv.org/content/10.1101/2023.08.12.553073v1?rss=1 Danov, A. Segev, O. Bograd, A. Ben Eliyahu, Y. Dotan, N. Kaplan, T. Levy, A. 2023-08-12 doi:10.1101/2023.08.12.553073 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ Mammalian olfactory cortex neurons retain molecular signatures of ancestral cell types ]]> https://biorxiv.org/content/10.1101/2023.08.13.553130v1?rss=1 Zeppilli, S. Gurrola, A. O. Demetci, P. Brann, D. Attey, R. Zilkha, N. Kimchi, T. Datta, S. R. Singh, R. Tosches, M. A. Crombach, A. Fleischmann, A. 2023-08-14 doi:10.1101/2023.08.13.553130 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ The evolution of sexual dimorphism in gene expression in response to a manipulation of mate competition ]]> https://biorxiv.org/content/10.1101/2023.08.15.553445v1?rss=1 Mishra, P. Rundle, H. D. Agrawal, A. F. 2023-08-17 doi:10.1101/2023.08.15.553445 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ BMP7 promotes cardiomyocyte regeneration ]]> https://biorxiv.org/content/10.1101/2023.08.17.553475v1?rss=1 Bongiovanni, C. Bueno-Levy, H. Posadas Pena, S. D. Del Bono, I. Redaelli, S. Bergen, M. Da Pra, S. Sacchi, F. Miano, C. Boriati, S. Pontis, F. Romaniello, D. Mazzeschi, M. Petraroia, I. Tassinari, R. Kellerer, L. Lauriola, M. Ventura, C. Heermann, S. Weidinger, G. Tzahor, E. D'Uva, G. 2023-08-17 doi:10.1101/2023.08.17.553475 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Consensus prediction of cell type labels with popV ]]> https://biorxiv.org/content/10.1101/2023.08.18.553912v1?rss=1 Ergen, C. Xing, G. Xu, C. Jayasuriya, M. McGeever, E. Pisco, A. O. Streets, A. M. Yosef, N. 2023-08-21 doi:10.1101/2023.08.18.553912 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Loss-of-function cancer-associated mutations in the EIF4G2 non-canonical translation initiation factor ]]> https://biorxiv.org/content/10.1101/2023.08.22.554280v1?rss=1 Meril, S. Bahlsen, M. Eisenstein, M. Savidor, A. Levin, Y. Bialik, S. Pietrokovski, S. Kimchi, A. 2023-08-25 doi:10.1101/2023.08.22.554280 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ txtools: an R package facilitating analysis of RNA modifications, structures, and interactions ]]> https://biorxiv.org/content/10.1101/2023.08.24.554738v1?rss=1 Garcia-Campos, M. A. Schwartz, S. 2023-08-26 doi:10.1101/2023.08.24.554738 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ The glucocorticoid receptor is a critical regulator of muscle satellite cell quiescence. ]]> https://biorxiv.org/content/10.1101/2023.08.27.555012v1?rss=1 Rajgara, R. AlSudais, H. Saleh, A. Brown, A. Barrakad, I. Blais, A. Wiper-Bergeron, N. 2023-08-28 doi:10.1101/2023.08.27.555012 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ A simple method for developing lysine targeted covalent protein reagents ]]> https://biorxiv.org/content/10.1101/2023.08.28.553348v1?rss=1 Gabizon, R. Tivon, B. Reddi, R. N. Van Den Oetelaar, M. Amartely, H. Cossar, P. J. Ottmann, C. London, N. 2023-08-28 doi:10.1101/2023.08.28.553348 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Sedentary behavior may accelerate aging through impact on epigenome and transcriptome: lessons from muscle inactivation in Drosophila larvae ]]> https://biorxiv.org/content/10.1101/2023.08.28.555053v1?rss=1 Brener, A. Lorber, D. Reuveny, A. Toledano, H. Porat-Kuperstein, L. Lebenthal, Y. Weizman, E. Olender, T. Volk, T. 2023-08-28 doi:10.1101/2023.08.28.555053 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Treatment with a selective histone deacetylase (HDAC) 1 and 2 inhibitor in aged mice rejuvenates multiple organ systems ]]> https://biorxiv.org/content/10.1101/2023.08.29.555280v1?rss=1 Tammaro, A. Daniels, E. G. Hu, I. M. t Hart, K. C. Reid, K. Juni, R. P. Butter, L. Vasam, G. Kamble, R. S. Jongejan, A. Aviv, R. I. Roelofs, J. J. T. H. Aronica, E. Boon, R. A. Menzies, K. J. Houtkooper, R. Janssens, G. E. 2023-08-31 doi:10.1101/2023.08.29.555280 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ CoSMIC - A hybrid approach for large-scale, high-resolution microbial profiling of novel niches ]]> https://biorxiv.org/content/10.1101/2023.09.03.556087v1?rss=1 Knafo, M. Rezenman, S. Idan, T. Elgart, M. Dagan, S. Reich, Z. Kapon, R. Sade, D. Shental, N. 2023-09-03 doi:10.1101/2023.09.03.556087 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Bacteria conjugate ubiquitin-like proteins to interfere with phage assembly ]]> https://biorxiv.org/content/10.1101/2023.09.04.556158v1?rss=1 Hör, J. Wolf, S. G. Sorek, R. 2023-09-04 doi:10.1101/2023.09.04.556158 Cold Spring Harbor Laboratory Press 2023-09-04 <![CDATA[ Emergence of disease specific endothelial and stromal cell populations involved in arterial remodeling during development of pulmonary arterial hypertension ]]> https://biorxiv.org/content/10.1101/2023.09.06.555321v1?rss=1 Cober, N. D. McCourt, E. Soares Godoy, R. Deng, Y. Schlosser, K. Situ, A. Cook, D. P. Lemay, S.-E. Klouda, T. Yuan, K. Bonnet, S. Stewart, D. J. 2023-09-06 doi:10.1101/2023.09.06.555321 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Structured RhoGEF recruitment drives myosin II organization on large exocytotic vesicles ]]> https://biorxiv.org/content/10.1101/2023.09.06.556511v1?rss=1 Kamalesh, K. Segal, D. Avinoam, O. Schejter, E. D. Shilo, B.-Z. 2023-09-06 doi:10.1101/2023.09.06.556511 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars ]]> https://biorxiv.org/content/10.1101/2023.09.06.556570v1?rss=1 Salojarvi, J. Rambani, A. Yu, Z. Guyot, R. Strickler, S. Lepelley, M. Wang, C. Rajaraman, S. Rastas, P. Zheng, C. Munoz, D. S. Meidanis, J. Paschoal, A. R. Bawin, Y. Krabbenhoft, T. Wang, Z. Q. Fleck, S. Aussel, R. Bellanger, L. Charpagne, A. Fournier, C. Kassam, M. Lefebvre, G. Metairon, S. Moine, D. Rigoreau, M. Stolte, J. Hamon, P. Couturon, E. Tranchant-Dubreuil, C. Mukherjee, M. Lan, T. Engelhardt, J. Stadler, P. DeLemos, S. C. Suzuki, S. I. Sumirat, U. ChingMan, W. Dauchot, N. Orozco-Arias, S. Garavito, A. Kiwuka, C. Musoli, P. Nalukenge, A. Gu 2023-09-06 doi:10.1101/2023.09.06.556570 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ NAD+ depletion and altered mitochondrial function are key to the establishment of placental dysfunction in an inflammatory-driven subclass of preeclampsia ]]> https://biorxiv.org/content/10.1101/2023.09.09.556974v1?rss=1 Bainbridge, S. Menzies, K. J. Jahan, F. Cariaco, Y. Akhtar, A. N. Green, A. 2023-09-09 doi:10.1101/2023.09.09.556974 Cold Spring Harbor Laboratory Press 2023-09-09 <![CDATA[ Epidermal barrier dysregulation in atopic skin predisposes for excessive growth of the allergy-associated yeast Malassezia ]]> https://biorxiv.org/content/10.1101/2023.09.11.557156v1?rss=1 Ruchti, F. Zwicky, P. Becher, B. Dubrac, S. LeibundGut-Landmann, S. 2023-09-11 doi:10.1101/2023.09.11.557156 Cold Spring Harbor Laboratory Press 2023-09-11 <![CDATA[ Escalating High-dimensional Imaging using Combinatorial Channel Multiplexing and Deep Learning ]]> https://biorxiv.org/content/10.1101/2023.09.09.556962v1?rss=1 Ben-Uri, R. Ben Shabat, L. Bar-Tal, O. Bussi, Y. Maimon, N. Keidar Haran, T. Milo, I. Elhanani, O. Rochwarger, A. Schürch, C. M. Bagon, S. Keren, L. 2023-09-12 doi:10.1101/2023.09.09.556962 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Fusarium graminearum Ste2 and Ste3 Receptors Undergo Peroxidase Induced Heterodimerization ]]> https://biorxiv.org/content/10.1101/2023.09.14.557733v1?rss=1 Sharma, T. Jomphe, R. Y. Zhang, D. Magalhaes, A. C. Loewen, M. C. 2023-09-14 doi:10.1101/2023.09.14.557733 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Bumblebee occupancy responds to complex interactions between local and landscape land use, climatic niche properties and climate change ]]> https://biorxiv.org/content/10.1101/2023.09.12.557199v1?rss=1 Newbold, T. Kerr, J. T. Soroye, P. Williams, J. J. 2023-09-15 doi:10.1101/2023.09.12.557199 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Sound-mediated nucleation and growth of amyloid fibrils ]]> https://biorxiv.org/content/10.1101/2023.09.16.558053v1?rss=1 Kozell, A. Solomonov, A. Benyamin, D. Greenblatt, H. M. Levy, Y. Rosenhek-Goldian, I. Raviv, U. Shimanovich, U. 2023-09-16 doi:10.1101/2023.09.16.558053 Cold Spring Harbor Laboratory Press 2023-09-16 <![CDATA[ Loss of EIF4G2 Mediates Aggressiveness in Distinct Human Endometrial Cancer Subpopulations with Poorer Survival Outcome in Patients ]]> https://biorxiv.org/content/10.1101/2023.09.14.557672v1?rss=1 Meril, S. Muhlbauer Avni, M. Lior, C. Bhalsen, M. Olender, T. Savidor, A. Krausz, J. Belhanes Peled, H. Birisi, H. David, N. Bialik, S. Scherz-Shouval, R. Ben David, Y. Kimchi, A. 2023-09-17 doi:10.1101/2023.09.14.557672 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ PURA Syndrome-causing mutations impair PUR-domain integrity and affect P-body association ]]> https://biorxiv.org/content/10.1101/2023.09.19.558386v1?rss=1 Proske, M. Janowski, R. Bacher, S. Kang, H.-S. Monecke, T. Koehler, T. Hutten, S. Tretter, J. Crois, A. Molitor, L. Varela-Rial, A. Fino, R. Donati, E. De Fabritiis, G. Dormann, D. Sattler, M. Niessing, D. 2023-09-20 doi:10.1101/2023.09.19.558386 Cold Spring Harbor Laboratory Press 2023-09-20 <![CDATA[ Biomedical researchers perspectives on the reproducibility of research: a cross-sectional international survey ]]> https://biorxiv.org/content/10.1101/2023.09.18.558287v1?rss=1 Cobey, K. D. Ebrahimzadeh, S. Page, M. Thibault, R. Nguyen, P.-Y. Abu-Dalfa, F. Moher, D. 2023-09-21 doi:10.1101/2023.09.18.558287 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Mesoscale molecular assembly is favored by the active, crowded cytoplasm ]]> https://biorxiv.org/content/10.1101/2023.09.19.558334v1?rss=1 Shu, T. Mitra, G. Alberts, J. B. Viana, M. Levy, E. D. Hocky, G. M. Holt, L. J. 2023-09-21 doi:10.1101/2023.09.19.558334 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Serotonin predictively encodes value ]]> https://biorxiv.org/content/10.1101/2023.09.19.558526v1?rss=1 Harkin, E. F. Grossman, C. D. Cohen, J. Y. Beïque, J.-C. Naud, R. 2023-09-21 doi:10.1101/2023.09.19.558526 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Differential and lasting gene expression changes in circulating CD8 T cells in chronic HCV infection with cirrhosis and related insights on the role of Hedgehog signaling ]]> https://biorxiv.org/content/10.1101/2023.09.20.557725v1?rss=1 Li, J. Vranjkovic, A. Read, D. Delaney, S. P. Stanford, W. L. Cooper, C. L. Crawley, A. M. 2023-09-21 doi:10.1101/2023.09.20.557725 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Mapping relationships between glutathione and SLC25 transporters in cancers using hybrid machine learning models ]]> https://biorxiv.org/content/10.1101/2023.09.20.558442v1?rss=1 Kennedy, L. S. Sandhu, J. K. Harper, M.-E. Cuperlovic-Culf, M. 2023-09-21 doi:10.1101/2023.09.20.558442 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ A genetic circuit on a single DNA molecule as autonomous dissipative nanodevice ]]> https://biorxiv.org/content/10.1101/2023.09.21.558768v1?rss=1 Greiss, F. Lardon, N. Schutz, L. Barak, Y. Daube, S. S. Weinhold, E. Noireaux, V. Bar-Ziv, R. 2023-09-21 doi:10.1101/2023.09.21.558768 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Hippocampal Ripples linked to Declarative Memory Judgments in Children ]]> https://biorxiv.org/content/10.1101/2023.09.19.558300v1?rss=1 Norman, Y. Dorfmuller, G. Taussig, D. Dorison, N. Fohlen, M. Chipaux, M. Ferrand-Sorbets, S. Bulteau, C. Harel, M. Malach, R. Levy, M. 2023-09-22 doi:10.1101/2023.09.19.558300 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ CD8 T cell hyperfunction and reduced tumour control in models of advanced liver fibrosis ]]> https://biorxiv.org/content/10.1101/2023.09.20.557752v1?rss=1 Madani, J. Li, J. Vranjkovic, A. Jorritsma, K. Hasim, M. S. Daneshmand, M. Cheung, A. C. Ching, A. M. E. Bruin, J. E. Ardolino, M. Crawley, A. M. 2023-09-22 doi:10.1101/2023.09.20.557752 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains ]]> https://biorxiv.org/content/10.1101/2023.09.20.558726v1?rss=1 Zwick, R. K. Kasparek, P. Palikuqi, B. Viragova, S. Weichselbaum, L. McGinnis, C. S. McKinley, K. L. Rathnayake, A. Vaka, D. Nguyen, V. Trentesaux, C. Reyes, E. Gupta, A. Gartner, Z. J. Locksley, R. M. Gardner, J. M. Itzkovitz, S. Boffelli, D. Klein, O. D. 2023-09-22 doi:10.1101/2023.09.20.558726 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ The Role of Vitamin D in Emiliania huxleyi: A Microalgal Perspective on UV-B Exposure ]]> https://biorxiv.org/content/10.1101/2023.09.21.558789v1?rss=1 Eliason, O. Malitsky, S. Panizel, I. Feldmesser, E. Sperfeld, M. Segev, E. 2023-09-22 doi:10.1101/2023.09.21.558789 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised Blood-Brain Barrier integrity ]]> https://biorxiv.org/content/10.1101/2023.09.24.559123v1?rss=1 Bassi, I. Grunspan, M. Hen, G. Ravichandran, K. A. Moshe, N. Safriel, S. R. Chen, A. Ruiz De Almodovar, C. Yaniv, K. 2023-09-24 doi:10.1101/2023.09.24.559123 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ Bacteria Contribute Exopolysaccharides to an Algal-Bacterial Joint Extracellular Matrix ]]> https://biorxiv.org/content/10.1101/2023.09.27.559704v1?rss=1 Lipsman, V. Shlakhter, O. Rocha, J. Segev, E. 2023-09-27 doi:10.1101/2023.09.27.559704 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Mapping the biochemical landscape of rubisco ]]> https://biorxiv.org/content/10.1101/2023.09.27.559826v1?rss=1 99% of single amino acid mutants across CO2 concentrations, we inferred enzyme velocity and CO2 affinity for thousands of substitutions. We identified many highly conserved positions that tolerate mutation and rare mutations that improve CO2 affinity. These data suggest that non-trivial kinetic improvements are readily accessible and provide a comprehensive sequence-to-function mapping for enzyme engineering efforts. ]]> Prywes, N. Phillips, N. R. Oltrogge, L. M. de Pins, B. Cowan, A. E. Taylor-Kearney, L. J. Chang, H. A. Hall, L. N. Bhatt, A. Shih, P. Milo, R. Savage, D. F. 2023-09-27 doi:10.1101/2023.09.27.559826 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Best practices for perturbation MPRA--a computational evaluation framework of sequence design strategies ]]> https://biorxiv.org/content/10.1101/2023.09.27.559768v1?rss=1 Liu, J. Ashuach, T. Inoue, F. Ahituv, N. Yosef, N. Kreimer, A. 2023-09-29 doi:10.1101/2023.09.27.559768 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Integration of metabolic flux with hepatic glucagon signaling and gene expression profiles in the conscious dog ]]> https://biorxiv.org/content/10.1101/2023.09.28.559999v1?rss=1 Coate, K. C. Ramnanan, C. J. Smith, M. Winnick, J. J. Kraft, G. Irimia, J. M. Farmer, B. Donahue, P. Roach, P. J. Cherrington, A. D. Edgerton, D. S. 2023-10-01 doi:10.1101/2023.09.28.559999 Cold Spring Harbor Laboratory Press 2023-10-01 <![CDATA[ Mapping the tumor stress network reveals dynamic shifts in the stromal oxidative stress response ]]> https://biorxiv.org/content/10.1101/2023.09.29.560126v1?rss=1 Lior, C. Barki, D. Kelsen, D. Iacobuzio-Donahue, C. Scherz-Shouval, R. 2023-10-01 doi:10.1101/2023.09.29.560126 Cold Spring Harbor Laboratory Press 2023-10-01 <![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[ The TMPRSS2 non-protease domains regulating SARS-CoV-2 Spike in mediated virus entry ]]> https://biorxiv.org/content/10.1101/2023.10.01.560357v1?rss=1 Strobelt, R. Adler, J. Shaul, Y. 2023-10-02 doi:10.1101/2023.10.01.560357 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Inferring plasticity rules from single-neuron spiketrains using deep learning methods ]]> https://biorxiv.org/content/10.1101/2023.10.01.560360v1?rss=1 Wang, X. Beique, J.-C. Naud, R. 2023-10-02 doi:10.1101/2023.10.01.560360 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Cell-to-cell heterogeneity drives host-virus coexistence in a bloom-forming alga ]]> https://biorxiv.org/content/10.1101/2023.10.03.560477v1?rss=1 Joffe, N. Kuhlisch, C. Schleyer, G. Ahlers, N. S. Shemi, A. Vardi, A. 2023-10-03 doi:10.1101/2023.10.03.560477 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Specificity and promiscuity of JAK recruitment regulates pleiotropy of cytokine-receptor signaling ]]> https://biorxiv.org/content/10.1101/2023.10.04.560821v1?rss=1 Zoler, E. Meyer, T. Bellon, J. S. Sun, B. Piehler, J. Schreiber, G. 2023-10-04 doi:10.1101/2023.10.04.560821 Cold Spring Harbor Laboratory Press 2023-10-04 <![CDATA[ Compression of sickspan by interventions that steepen the survival curve ]]> https://biorxiv.org/content/10.1101/2023.10.04.560871v1?rss=1 Yang, Y. Mayo, A. Levy, T. Jarosz, D. F. Alon, U. 2023-10-05 doi:10.1101/2023.10.04.560871 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ A topographical atlas of alpha-Synuclein dosage and cell-type expression in the mouse brain and periphery ]]> https://biorxiv.org/content/10.1101/2023.10.05.559770v1?rss=1 Geertsma, H. M. Fisk, Z. A. Sauline, L. Prigent, A. Kurgat, K. Callaghan, S. M. aSCENT PD Consortium, Henderson, M. Rousseaux, M. W. C. 2023-10-07 doi:10.1101/2023.10.05.559770 Cold Spring Harbor Laboratory Press 2023-10-07 <![CDATA[ Differential encoding of odor and place in mouse piriform and entorhinal cortex ]]> https://biorxiv.org/content/10.1101/2023.10.05.561119v1?rss=1 Mena, W. Baker, K. Rubin, A. Kohli, S. Yoo, Y. Ziv, Y. Razaei-Mazinani, C. Fleischmann, A. 2023-10-08 doi:10.1101/2023.10.05.561119 Cold Spring Harbor Laboratory Press 2023-10-08 <![CDATA[ ABTrans: A Transformer-based model for predicting interaction between anti-Abeta antibodies and peptides ]]> https://biorxiv.org/content/10.1101/2023.10.09.561503v1?rss=1 Su, Y. Zhang, L. Wang, Y. Ma, B. 2023-10-11 doi:10.1101/2023.10.09.561503 Cold Spring Harbor Laboratory Press 2023-10-11 <![CDATA[ Repression of mRNA translation initiation by GIGYF1 via blocking the eIF3-eIF4G1 interaction ]]> https://biorxiv.org/content/10.1101/2023.10.14.562322v1?rss=1 Choi, J.-H. Luo, J. Hesketh, G. G. Guo, S. 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Oren-Suissa, M. 2023-10-19 doi:10.1101/2023.10.19.563073 Cold Spring Harbor Laboratory Press 2023-10-19 <![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[ Breast Cancer Macrophage Heterogeneity and Self-renewal are Determined by Spatial Localization ]]> https://biorxiv.org/content/10.1101/2023.10.24.563749v1?rss=1 Ben-Chetrit, N. Niu, X. Sotelo, J. Swett, A. D. Rajasekhar, V. K. Jiao, M. S. Stewart, C. M. Bhardwaj, P. Kottapalli, S. Ganesan, S. Loyher, P.-L. Potenski, C. Hannuna, A. Brown, K. A. Iyengar, N. M. Giri, D. D. Lowe, S. W. Healey, J. H. Geissmann, F. Sagi, I. Joyce, J. A. Landau, D. A. 2023-10-27 doi:10.1101/2023.10.24.563749 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease ]]> https://biorxiv.org/content/10.1101/2023.10.27.561846v1?rss=1 Kilian, C. Ulrich, H. Zouboulis, V. Sprezyna, P. Schreiber, J. Landsberger, T. Büttner, M. Biton, M. Villablanca, E. J. Huber, S. Adlung, L. 2023-10-30 doi:10.1101/2023.10.27.561846 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ A virally encoded high resolution screen of cytomegalovirus host dependencies ]]> https://biorxiv.org/content/10.1101/2023.10.30.564793v1?rss=1 Finkel, Y. Nachshon, A. Aharon, E. Arazi, T. Simonovsky, E. Dobesova, M. Gluck, A. Fisher, T. Stanton, R. J. Schwartz, M. Stern-Ginossar, N. 2023-10-30 doi:10.1101/2023.10.30.564793 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ Leaderless consensus decision-making determines cooperative transport direction in weaver ants ]]> https://biorxiv.org/content/10.1101/2023.10.29.564117v1?rss=1 Carlesso, D. Stewardson, M. Garnier, S. Feinerman, O. Reid, C. 2023-11-01 doi:10.1101/2023.10.29.564117 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Mutational biases contribute to the neutral complexification of protein interaction networks following gene duplication ]]> https://biorxiv.org/content/10.1101/2023.10.31.565025v1?rss=1 Cisneros, A. F. Nielly-Thibault, L. Mallik, S. Levy, E. D. Landry, C. R. 2023-11-02 doi:10.1101/2023.10.31.565025 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Design of efficient artificial enzymes using crystallographically-enhanced conformational sampling ]]> https://biorxiv.org/content/10.1101/2023.11.01.564846v1?rss=1 Rakotoharisoa, R. V. Seifinoferest, B. Zarifi, N. Miller, J. D. M. Rodriguez, J. M. Thompson, M. C. Chica, R. A. 2023-11-02 doi:10.1101/2023.11.01.564846 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Simultaneous multi-transient linear-combination modeling of MRS data improves uncertainty estimation ]]> https://biorxiv.org/content/10.1101/2023.11.01.565164v1?rss=1 Zollner, H. J. Davies-Jenkins, C. B. Simicic, D. B. Tal, A. Sulam, J. Oeltzschner, G. 2023-11-04 doi:10.1101/2023.11.01.565164 Cold Spring Harbor Laboratory Press 2023-11-04 <![CDATA[ Egg MVBs elicit an antimicrobial pathway to degrade paternal mitochondria after fertilization ]]> https://biorxiv.org/content/10.1101/2023.11.05.565307v1?rss=1 Ben-Hur, S. Afar, S. Politi, Y. Gal, L. Golani, O. Sivan, E. Haffner-Krausz, R. Maizenberg, E. Peretz, S. Roth, Z. Kalo, D. Dezorella, N. Morgenstern, D. Pietrokovski, S. Yacobi-Sharon, K. Arama, E. 2023-11-05 doi:10.1101/2023.11.05.565307 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Using large language models to study human memory for meaningful narratives ]]> https://biorxiv.org/content/10.1101/2023.11.03.565484v1?rss=1 Georgiou, A. Can, T. Katkov, M. Tsodyks, M. 2023-11-06 doi:10.1101/2023.11.03.565484 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Circadian coupling of mitochondria in a deep-diving mammal ]]> https://biorxiv.org/content/10.1101/2023.11.06.565796v1?rss=1 Ciccone, C. Kante, F. Folkow, L. P. Hazlerigg, D. West, A. C. Wood, S. H. 2023-11-06 doi:10.1101/2023.11.06.565796 Cold Spring Harbor Laboratory Press 2023-11-06 <![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[ Algal Exudates Promote Conjugation in Marine Roseobacters ]]> https://biorxiv.org/content/10.1101/2023.11.14.567099v1?rss=1 Segev, E. Duchin Rapp, Y. Yuda, L. Matsliyah, D. Kublanov, I. V. 2023-11-14 doi:10.1101/2023.11.14.567099 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ Stereotyped goal-directed activity patterns in the insular cortex ]]> https://biorxiv.org/content/10.1101/2023.11.13.566809v1?rss=1 Talpir, I. Livneh, Y. 2023-11-15 doi:10.1101/2023.11.13.566809 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Convergent evolution of monocyte differentiation in adult skin permits repair of the Langerhans cell network ]]> https://biorxiv.org/content/10.1101/2023.11.13.566862v1?rss=1 Appios, A. Davies, J. Sirvent, S. Henderson, S. Trzebanski, S. Schroth, J. Law, M. L. Boal Carvalho, I. Yuan-Hao Kan, H. Major, C. Vallejo, A. Hall, N. J. Ardern-Jones, M. Henson, S. M. Emmerson, E. Jung, S. Polak, M. E. Bennett, C. L. 2023-11-15 doi:10.1101/2023.11.13.566862 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Bone elongation in the embryo occurs without column formation in the growth plate ]]> https://biorxiv.org/content/10.1101/2023.11.14.567062v1?rss=1 Rubin, S. Agrawal, A. Seewald, A. Villoutreix, P. Baule, A. Zelzer, E. 2023-11-16 doi:10.1101/2023.11.14.567062 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Enhanced efficiency in the bilingual brain through the inter-hemispheric cortico-cerebellar pathway in early second language acquisition ]]> https://biorxiv.org/content/10.1101/2023.11.16.567455v1?rss=1 Gracia-Tabuenca, Z. Barbeau, E. B. Kousaie, S. Chen, J.-K. Chai, X. J. Klein, D. 2023-11-16 doi:10.1101/2023.11.16.567455 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ The Role of Electron Spin-Polarizability and Charge Dynamics in Protein Function ]]> https://biorxiv.org/content/10.1101/2023.11.16.567399v1?rss=1 Vyas, P. Santra, K. Preeyanka, N. Gupta, A. Weil-Ktorza, O. Zhu, Q. Longo, L. M. Fransson, J. Metanis, N. Naaman, R. 2023-11-17 doi:10.1101/2023.11.16.567399 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Monocyte-derived microglia with Dnmt3a mutation cause motor pathology in aging mice ]]> https://biorxiv.org/content/10.1101/2023.11.16.567402v1?rss=1 Kim, J.-S. Trzebanski, S. Shin, S.-H. Ilani, N. C. Kaushansky, N. Scheller, M. Solomon, A. Liu, Z. Aust, O. Boura-Halfon, S. Amann, L. Prinz, M. Ginhoux, F. Avraham, R. Mueller-Tidow, C. Uderhardt, S. Milenkovic, I. Shlush, L. Jung, S. 2023-11-17 doi:10.1101/2023.11.16.567402 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ A liquid-to-solid phase transition of biomolecular condensates drives in vivo formation of yeast amyloids and prions ]]> https://biorxiv.org/content/10.1101/2023.11.17.566816v1?rss=1 Alieva, M. K. Nikishina, S. B. Kireev, I. I. Golyshev, S. A. Tyurin-Kuzmin, P. A. Ivanova, L. V. Alexandrov, A. I. Kushnirov, V. V. Dergalev, A. A. 2023-11-18 doi:10.1101/2023.11.17.566816 Cold Spring Harbor Laboratory Press 2023-11-18 <![CDATA[ PROTACable is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning to Automate the De Novo Design of PROTACs ]]> https://biorxiv.org/content/10.1101/2023.11.20.567951v1?rss=1 Mslati, H. Gentile, F. Pandey, M. Ban, F. Cherkasov, A. 2023-11-21 doi:10.1101/2023.11.20.567951 Cold Spring Harbor Laboratory Press 2023-11-21 <![CDATA[ Seasonal Human Coronaviruses OC43, 229E, and NL63 Induce Cell Surface Modulation of Entry Receptors and Display Host Cell-Specific Viral Replication Kinetics ]]> https://biorxiv.org/content/10.1101/2023.11.20.567923v1?rss=1 Siragam, V. Maltseva, M. Castonguay, N. Galipeau, Y. Srinivasan, M. M. Soto, J. H. Dankar, S. Langlois, M.-A. 2023-11-22 doi:10.1101/2023.11.20.567923 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Cancer-associated fibroblasts serve as decoys to suppress NK cell anti-cancer cytotoxicity ]]> https://biorxiv.org/content/10.1101/2023.11.23.568355v1?rss=1 Ben-Shmuel, A. Gruper, Y. Levi-Galibov, O. Rosenberg-Fogler, H. Carradori, G. Stein, Y. Dadiani, M. Naumova, M. Nevo, R. Morzaev-Sulzbach, D. Yagel, G. Mayer, S. Gal-Yam, E. Scherz-Shouval, R. 2023-11-23 doi:10.1101/2023.11.23.568355 Cold Spring Harbor Laboratory Press 2023-11-23 <![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[ A unique chaperoning mechanism in Class A JDPs recognizes and stabilizes mutant p53. ]]> https://biorxiv.org/content/10.1101/2023.11.28.568993v1?rss=1 Zoltsman, G. Dang, T. L. Kuchersky, M. Faust, O. Silva, M. S. Ilani, T. Wentink, A. S. Bukau, B. Rosenzweig, R. 2023-11-28 doi:10.1101/2023.11.28.568993 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ Differential proteome diversification in yeast populations: modes of short-term adaptation and fitness outcomes ]]> https://biorxiv.org/content/10.1101/2023.11.28.568995v1?rss=1 Knafo, M. Rezenman, S. Tsigalnitski, I. Nevo, R. Reich, Z. Kapon, R. 2023-11-28 doi:10.1101/2023.11.28.568995 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ Cell-mediated cholesterol crystal processing and clearance observed by 3D cryo-imaging in human atherosclerotic plaques ]]> https://biorxiv.org/content/10.1101/2023.11.28.568890v1?rss=1 Shenkar, J. C. Kaestner, A. Rechav, K. Brumfeld, V. Kaplan-Ashiri, I. Avinoam, O. Speter, C. Halak, M. Kruth, H. Addadi, L. 2023-11-29 doi:10.1101/2023.11.28.568890 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Temporal genomic analysis of melanoma rejection identifies regulators of tumor immune evasion ]]> https://biorxiv.org/content/10.1101/2023.11.29.569032v1?rss=1 Shvefel, S. C. Pai, J. Cao, Y. Pal, L. Levy, R. Yao, W. Cheng, K. Zemanek, M. Bartok, O. Weller, C. Yin, Y. Du, P. Yakubovich, E. Orr, I. Ben-Dor, S. Oren, R. Fellus-Alyagor, L. Golani, O. Goliand, I. Ranmar, D. Savchenko, I. Ketrarou, N. Schaffer, A. A. Ruppin, E. Satpathy, A. Samuels, Y. 2023-11-29 doi:10.1101/2023.11.29.569032 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[ Demonstration of Bioplastic Production from CO2 and Formate using the Reductive Glycine Pathway in E. coli ]]> https://biorxiv.org/content/10.1101/2023.12.02.569694v1?rss=1 Fedorova, D. Ben-Nissan, R. Milshtein, E. Jona, G. Dezorella, N. Feiguelman, G. Fedorov, R. Gomaa, A. Lindner, A. B. Noor, E. Milo, R. 2023-12-03 doi:10.1101/2023.12.02.569694 Cold Spring Harbor Laboratory Press 2023-12-03 <![CDATA[ Strain-specific evolution and host-specific regulation of transposable elements in the model plant symbiont Rhizophagus irregularis ]]> https://biorxiv.org/content/10.1101/2023.12.01.569630v1?rss=1 Oliveira, J. I. N. Corradi, N. 2023-12-04 doi:10.1101/2023.12.01.569630 Cold Spring Harbor Laboratory Press 2023-12-04 <![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[ High throughput screening identifies broad-spectrum Coronavirus entry inhibitors ]]> https://biorxiv.org/content/10.1101/2023.12.04.569985v1?rss=1 Khan, S. Partuk, E. O. Chiaravalli, J. Kozer, N. Shurrush, K. A. Elbaz-Alon, Y. Scher, N. Giraud, E. Tran-Rajau, J. Agou, F. Barr, H. M. Avinoam, O. 2023-12-05 doi:10.1101/2023.12.04.569985 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Influence of heterogeneous myelination patterns on axonal conduction and vulnerability to demyelination ]]> https://biorxiv.org/content/10.1101/2023.12.04.570018v1?rss=1 Talidou, A. Lefebvre, J. 2023-12-05 doi:10.1101/2023.12.04.570018 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Multi-variate statistical and machine learning reveals the interplay between sex and age in antibody responses to de novo SARS-CoV-2 infection and vaccination ]]> https://biorxiv.org/content/10.1101/2023.12.05.569965v1?rss=1 60y.o. females. Complex correlation analyses found vaccination induced less antibody isotype switching and neutralization in older persons, especially in females. Sex dependent antibody & neutralization behavior decayed fastest in older males and with vaccination. Such sex and age characterization by machine learning can direct studies integrating cell mediated responses to define yet elusive correlates of protection and inform age and sex precision-focused vaccine design. ]]> Cuperlovic-Culf, M. Bennett, S. Galipeau, Y. McCluskie, P. S. Arnold, C. Bagheri, S. Cooper, C. L. Langlois, M.-A. Fritz, J. A. Piccirillo, C. Crawley, A. M. 2023-12-05 doi:10.1101/2023.12.05.569965 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Self-renewing Sox9+ osteochondral stem cells in the postnatal skeleton ]]> https://biorxiv.org/content/10.1101/2023.12.07.570646v1?rss=1 Farhat, S. Tilouche, B. Short, S. Piron, M. Campbell, T. M. Fernandes, A. Somyk, M. Bandukwala, H. Arezza, E. Sastourne-Arrey, Q. Reilly, K. Chakra, M. A. Bader, G. Kunz, L. Schroeder, T. Carsen, S. Mattar, P. Dilworth, J. Coutu, D. L. 2023-12-08 doi:10.1101/2023.12.07.570646 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ snPATHO-seq: unlocking the pathology archives ]]> https://biorxiv.org/content/10.1101/2023.12.07.570700v1?rss=1 Wang, T. Harvey, K. Escudero Morales, J. Kiedik, B. Al-Eryani, G. Greenwald, A. C. Kalavros, N. SegatovDezem, F. Ma, Y. Pita-Juarez, Y. Wise, K. Degletagne, C. Elz, A. Johanneson, J. Pakiam, F. Ryu, H. Newell, E. W. Tonon, L. Kohlway, A. Drennon, T. Hadadianpour, A. Abousoud, J. Scott, R. Lund, P. Durruthy, J. Vallejos, A. F. Kaczorowski, D. Warren, J. Butler, L. M. O'Toole, S. Plummer, J. T. Vlachos, I. Lundeberg, J. Swarbrick, A. Martelotto, L. G. 2023-12-08 doi:10.1101/2023.12.07.570700 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Rapid long-distance migration of RPA on single stranded DNA occurs through intersegmental transfer utilizing multivalent interactions ]]> https://biorxiv.org/content/10.1101/2023.12.09.570606v1?rss=1 Pangeni, S. Biswas, G. Kaushik, V. Kuppa, S. Yang, O. Lin, C.-T. Mishra, G. Levy, Y. Antony, E. Ha, T. 2023-12-10 doi:10.1101/2023.12.09.570606 Cold Spring Harbor Laboratory Press 2023-12-10 <![CDATA[ High-energy demand and nutrient exhaustion in MTCH2 knockout cells ]]> https://biorxiv.org/content/10.1101/2023.12.15.571941v1?rss=1 Chourasia, S. Petucci, C. Wang, H. Han, X. Sivan, E. Brandis, A. Mehlman, T. Malitsky, S. Itkin, M. Rotkopf, R. Regev, L. Zaltsman, Y. Gross, A. 2023-12-16 doi:10.1101/2023.12.15.571941 Cold Spring Harbor Laboratory Press 2023-12-16 <![CDATA[ From Selfies to Science - Precise 3D Leaf Measurement with iPhone 13 and Its Implications for Plant Development and Transpiration ]]> https://biorxiv.org/content/10.1101/2023.12.30.573617v1?rss=1 Bar-Sella, G. Gavish, M. Moshelion, M. 2023-12-30 doi:10.1101/2023.12.30.573617 Cold Spring Harbor Laboratory Press 2023-12-30 <![CDATA[ Amplifying post-stimulation oscillatory dynamics by engaging synaptic plasticity with periodic stimulation: a modelling study ]]> https://biorxiv.org/content/10.1101/2024.01.25.577245v1?rss=1 Lefebvre, J. Pariz, A. 2024-01-26 doi:10.1101/2024.01.25.577245 Cold Spring Harbor Laboratory Press 2024-01-26 <![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[ Probing PAC1 receptor activation across species with an engineered sensor ]]> https://biorxiv.org/content/10.1101/2024.02.06.579048v1?rss=1 Cola, R. B. Niethammer, S. N. Rajamannar, P. Gresch, A. Bhat, M. A. Assoumou, K. Williams, E. T. Hauck, P. Hartrampf, N. Benke, D. Stoeber, M. Levkowitz, G. Melzer, S. Patriarchi, T. 2024-02-07 doi:10.1101/2024.02.06.579048 Cold Spring Harbor Laboratory Press 2024-02-07 <![CDATA[ Dual Targeting of Histone Deacetylases and MYC as Potential Treatment Strategy for H3-K27M Pediatric Gliomas ]]> https://biorxiv.org/content/10.1101/2024.02.05.578974v1?rss=1 Algranati, D. Oren, R. Dassa, B. Fellus-Alyagor, L. Plotnikov, A. Barr, H. Harmelin, A. London, N. Ron, G. Furth, N. Shema, E. 2024-02-09 doi:10.1101/2024.02.05.578974 Cold Spring Harbor Laboratory Press 2024-02-09 <![CDATA[ Phages reconstitute NAD+ to counter bacterial immunity ]]> https://biorxiv.org/content/10.1101/2024.02.11.579819v1?rss=1 Osterman, I. Samra, H. Rousset, F. Loseva, E. Itkin, M. Malitsky, S. Yirmiya, E. Millman, A. Sorek, R. 2024-02-13 doi:10.1101/2024.02.11.579819 Cold Spring Harbor Laboratory Press 2024-02-13 <![CDATA[ The antifungal activity of cymoxanil is associated with proton pump inhibition and disruption of plasma membrane potential ]]> https://biorxiv.org/content/10.1101/2024.03.01.583004v1?rss=1 Mendes, F. Meyer, H. Amaral, L. Castro, B. Schuldiner, M. Sousa, M. J. Chaves, S. 2024-03-02 doi:10.1101/2024.03.01.583004 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ Particulate Contamination of Human Placenta: Plastic and Non-Plastic ]]> https://biorxiv.org/content/10.1101/2024.03.01.583005v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@9f5b0org.highwire.dtl.DTLVardef@1e13468org.highwire.dtl.DTLVardef@37aa3forg.highwire.dtl.DTLVardef@8a197e_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIBoth plastic and non-plastic foreign particles were observed in term placentas from Canadian women C_LIO_LIPlacenta contamination with most of the non-plastic particle types observed has not previously been reported. C_LIO_LIParticles were observed in similar frequency in placenta regions corresponding to maternal or fetal circulation suggesting that particles pass unhindered through the placenta. C_LI ]]> Zurub, R. W. Bainbridge, S. A. Rahman, L. Halappanavar, S. Wade, M. 2024-03-06 doi:10.1101/2024.03.01.583005 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ IPPK-1 and IP6 contribute to ventral nerve cord assembly in C. elegans ]]> https://biorxiv.org/content/10.1101/2024.03.03.583222v1?rss=1 Noblett, N. Roenspies, T. Flibotte, S. Colavita, A. 2024-03-06 doi:10.1101/2024.03.03.583222 Cold Spring Harbor Laboratory Press 2024-03-06 <![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[ The 3'-untranslated regions of yeast ribosomal protein mRNAs determine paralog incorporation into ribosomes and recruit factors necessary for specialized functions ]]> https://biorxiv.org/content/10.1101/2024.03.18.585503v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@15ba935org.highwire.dtl.DTLVardef@c210b7org.highwire.dtl.DTLVardef@d77b7dorg.highwire.dtl.DTLVardef@ec72f4_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Singh, R. Crawford, R. A. Mall, D. P. Pavitt, G. D. Gerst, J. E. 2024-03-19 doi:10.1101/2024.03.18.585503 Cold Spring Harbor Laboratory Press 2024-03-19 <![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[ 2P-NucTag: on-demand phototagging for molecular analysis of functionally identified cortical neurons ]]> https://biorxiv.org/content/10.1101/2024.03.21.586118v1?rss=1 Shi, J. Nutkovich, B. Kushinsky, D. Rao, B. Y. Herrlinger, S. A. Mihaila, T. S. Malina, K. C.-K. OToole, C. K. Conde Paredes, M. E. Yong, H. C. Varol, E. Losonczy, A. Spiegel, I. 2024-03-26 doi:10.1101/2024.03.21.586118 Cold Spring Harbor Laboratory Press 2024-03-26 <![CDATA[ A new cellular platform for studying autophagy ]]> https://biorxiv.org/content/10.1101/2024.03.28.587157v1?rss=1 Goldin-Azulay, K. Fraiberg, M. Trofimyuk, O. Reuven, N. Levin, Y. Kopitman, E. Elazar, Z. 2024-03-29 doi:10.1101/2024.03.28.587157 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Optogenetics-integrated gut organ culture system connects enteric neurons dynamics and gut homeostasis ]]> https://biorxiv.org/content/10.1101/2024.03.28.587149v1?rss=1 Naim, G. Romano, H. Amidror, S. Jessula Levy, D. Cohen, A. Sochen, C. Yarden, Y. Feng, M. Farah, N. Tsentsarevsky, R. Brodie, Z. Reich, Y. Simon, A. Toister, E. Shoval, I. Mandel, Y. Biton, M. Yissachar, N. 2024-03-30 doi:10.1101/2024.03.28.587149 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Shape dynamics and migration of branched cells on complex networks ]]> https://biorxiv.org/content/10.1101/2024.03.29.585638v1?rss=1 Liu, J. Boix-Campos, J. Ron, J. E. Kux, J. M. Gov, N. Saez, P. J. 2024-03-31 doi:10.1101/2024.03.29.585638 Cold Spring Harbor Laboratory Press 2024-03-31 <![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[ Active state structures of a bistable visual opsin bound to G proteins ]]> https://biorxiv.org/content/10.1101/2024.04.09.588704v1?rss=1 Tejero, O. Pamula, F. K. Koyanagi, M. Nagata, T. Afanasyev, P. Das, I. Deupi, X. Sheves, M. Terakita, A. Schertler, G. F. X. Rodrigues, M. J. Tsai, C.-J. 2024-04-10 doi:10.1101/2024.04.09.588704 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ Intracellular binding pocket revealed in the human bitter taste receptor TAS2R14 ]]> https://biorxiv.org/content/10.1101/2024.04.10.588278v1?rss=1 Peri, L. Matzov, D. Huxley, D. R. Rainish, A. Fierro, F. Sapir, L. Pfeiffer, T. Waterloo, L. Huebner, H. Weikert, D. Peleg, Y. Gmeiner, P. Mccormick, P. Niv, M. Y. Shalev-Benami, M. 2024-04-10 doi:10.1101/2024.04.10.588278 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ Rapid and Sensitive Protein Complex Alignment with Foldseek-Multimer ]]> https://biorxiv.org/content/10.1101/2024.04.14.589414v1?rss=1 Kim, W. Mirdita, M. Karin, E. L. Gilchrist, C. L. M. Schweke, H. Soeding, J. Levy, E. Steinegger, M. 2024-04-14 doi:10.1101/2024.04.14.589414 Cold Spring Harbor Laboratory Press 2024-04-14 <![CDATA[ Confinement in fibrous environments positions and orients mitotic spindles ]]> https://biorxiv.org/content/10.1101/2024.04.12.589246v1?rss=1 Sarkar, A. Jana, A. Agashe, A. Wang, J. Kapania, R. Gov, N. S. DeLuca, J. G. Paul, R. Nain, A. S. 2024-04-15 doi:10.1101/2024.04.12.589246 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ The Natural Material Evolution and Stage-wise Assembly of Silk Along the Silk Gland ]]> https://biorxiv.org/content/10.1101/2024.04.16.589504v1?rss=1 Brookstein, O. Shimoni, E. Eliaz, D. Dezorella, N. Biran, I. Rechav, K. Sivan, E. Kozell, A. Shimanovich, U. 2024-04-16 doi:10.1101/2024.04.16.589504 Cold Spring Harbor Laboratory Press 2024-04-16 <![CDATA[ Pangenomes of Human Gut Microbiota Uncover Links Between Genetic Diversity and Stress Response ]]> https://biorxiv.org/content/10.1101/2024.04.17.589959v1?rss=1 Shoer, S. Reicher, L. Pilpel, Y. Segal, E. 2024-04-18 doi:10.1101/2024.04.17.589959 Cold Spring Harbor Laboratory Press 2024-04-18 <![CDATA[ Profiling the LAM family of contact site tethers provides insights into their regulation and function ]]> https://biorxiv.org/content/10.1101/2024.04.18.590074v1?rss=1 Fenech, E. J. Kupervaser, M. Boshnakovska, A. Ravid, S. Gomes Castro, I. Asraf, Y. Callegari, S. Lenz, C. Rehling, P. Schuldiner, M. 2024-04-18 doi:10.1101/2024.04.18.590074 Cold Spring Harbor Laboratory Press 2024-04-18 <![CDATA[ A systematic bi-genomic split-GFP assay illuminates the mitochondrial matrix proteome and protein targeting routes ]]> https://biorxiv.org/content/10.1101/2024.04.17.589881v1?rss=1 Bykov, Y. S. Zuttion, S. Senger, B. Klein, O. Asraf, Y. Meyer, H. Becker, H. D. Kucharczyk, R. Schuldiner, M. 2024-04-19 doi:10.1101/2024.04.17.589881 Cold Spring Harbor Laboratory Press 2024-04-19 <![CDATA[ Group social dynamics in a semi-natural setup reveal an adaptive value for aggression in male mice ]]> https://biorxiv.org/content/10.1101/2024.04.25.591070v1?rss=1 Anpilov, S. Shemesh, Y. Benjamin, A. Biagini, T. Sztainberg, Y. Richter-Levin, A. Forkosh, O. Chen, A. 2024-04-28 doi:10.1101/2024.04.25.591070 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Essentiality and dynamic expression of the human tRNA pool during viral infection ]]> https://biorxiv.org/content/10.1101/2024.04.25.591047v1?rss=1 Aharon-Hefetz, N. Schwartz, M. Dahan, O. Stern-Ginossar, N. Pilpel, Y. 2024-04-30 doi:10.1101/2024.04.25.591047 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ PEX39 facilitates the peroxisomal import of PTS2 proteins ]]> https://biorxiv.org/content/10.1101/2024.04.30.591961v1?rss=1 Chen, W. W. Rodrigues, T. A. Wendscheck, D. Pedrosa, A. G. Yang, C. Francisco, T. Mocklinghoff, T. Zografakis, A. Nunes-Silva, B. Avraham, R. E. Silva, A. R. Ferreira, M. J. Das, H. Bender, J. Oeljeklaus, S. Sondhi, V. Schuldiner, M. Zalckvar, E. Hofmann, K. Waterham, H. R. DeBerardinis, R. J. Azevedo, J. E. Warscheid, B. 2024-05-03 doi:10.1101/2024.04.30.591961 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ The molecular mechanism of on-demand sterol biosynthesis at organelle contact sites ]]> https://biorxiv.org/content/10.1101/2024.05.09.593285v1?rss=1 Zung, N. Aravindan, N. Boshnakovska, A. Valenti, R. Preminger, N. Jonas, F. Yaakov, G. Willoughby, M. Homberg, B. Keller, J. Kupervaser, M. Dezorella, N. Dadosh, T. Wolf, S. G. Itkin, M. Malitsky, S. Brandis, A. Barkai, N. Fernandez-Busnadiego, R. Reddi, A. Rehling, P. Rapaport, D. Schuldiner, M. 2024-05-10 doi:10.1101/2024.05.09.593285 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Passive shaping of intra- and intercellular m6A dynamics via mRNA metabolism ]]> https://biorxiv.org/content/10.1101/2024.05.09.593376v1?rss=1 Dierks, D. Nir, R. Shachar, R. Uzonyi, A. Garcia-Campos, M. A. Rossmanith, W. Hanna, J. H. Slobodin, B. Antebi, Y. Scherz-Shouval, R. Schwartz, S. 2024-05-14 doi:10.1101/2024.05.09.593376 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation ]]> https://biorxiv.org/content/10.1101/2024.05.22.595375v1?rss=1 DeGroat, W. Inoue, F. Ashuach, T. Yosef, N. Ahituv, N. Kreimer, A. 2024-05-23 doi:10.1101/2024.05.22.595375 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Genesis: A Modular Protein Language Modelling Approach to Immunogenicity Prediction ]]> https://biorxiv.org/content/10.1101/2024.05.22.595296v1?rss=1 O'Brien, H. Salm, M. Morton, L. T. Szukszto, M. O'Farrell, F. Boulton, C. King, L. Bola, S. K. Becker, P. Craig, A. Nielsen, M. Samuels, Y. Swanton, C. Mansour, M. R. Hadrup, S. R. Quezada, S. 2024-05-26 doi:10.1101/2024.05.22.595296 Cold Spring Harbor Laboratory Press 2024-05-26 <![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[ mRNA Vaccine-Induced SARS-CoV-2 Spike-Specific IFN-γ and IL-2 T-cell Responses are Predictive of Serological Neutralization and are Transiently Enhanced by Pre-Existing Cross-Reactive Immunity ]]> https://biorxiv.org/content/10.1101/2024.05.28.596157v1?rss=1 Samaan, P. Korosec, C. Budylowski, P. Chau, S. L. L. Pasculescu, A. Qi, F. Delgado-Brand, M. Tursun, T. R. Mailhot, G. Dayam, R. M. Arnold, C. R. Langlois, M.-A. Patel, A. de Launay, K. Q. Boyd, J. M. Takaoka, A. Colwill, K. McGeer, A. Straus, S. Gingras, A.-C. Heffernen, J. M. Ostrowski, M. 2024-05-29 doi:10.1101/2024.05.28.596157 Cold Spring Harbor Laboratory Press 2024-05-29 <![CDATA[ Data-modeling the interplay between single cell shape, single cell protein expression, and tissue state ]]> https://biorxiv.org/content/10.1101/2024.05.29.595857v1?rss=1 Tamir, Y. Bussi, Y. Owczare, C. Luque, L. Torrisi, G. Rose, L. A. Kliper-Gross, O. Sander, C. Schumacher, L. Parsons, M. Keren, L. Zaritsky, A. 2024-05-30 doi:10.1101/2024.05.29.595857 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ An unconventional interaction interface between the peroxisomal targeting factor Pex5 and Eci1 enables PTS1 independent import ]]> https://biorxiv.org/content/10.1101/2024.06.02.597006v1?rss=1 Peer, L. Elad, N. Dym, O. Tirosh, A. Jacobovitch, J. Albeck, S. Schuldiner, M. Peleg, Y. Zalckvar, E. 2024-06-02 doi:10.1101/2024.06.02.597006 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ TGFβ determines morphology and key cellular processes of activated CD4+ T cells ]]> https://biorxiv.org/content/10.1101/2024.06.02.597009v1?rss=1 Eizenberg-Magar, I. Rimer, J. Miller, S. Elyahu, Y. Mark, M. Porat, Z. Reich-Zeliger, S. Monsonego, A. Antebi, Y. E. Friedman, N. 2024-06-03 doi:10.1101/2024.06.02.597009 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Long-range neuropeptide relay as a central-peripheral communication mechanism for the context-dependent modulation of interval timing behaviors. ]]> https://biorxiv.org/content/10.1101/2024.06.03.597273v1?rss=1 Zhang, T. Wu, Z. Song, Y. Li, W. Sun, Y. Zhang, X. Wong, K. C. Schweizer, J. Nguyen, K.-N. H. Kwan, A. Kim, W. J. 2024-06-04 doi:10.1101/2024.06.03.597273 Cold Spring Harbor Laboratory Press 2024-06-04 <![CDATA[ Peptidergic neurons with extensive branching orchestrate the internal states and energy balance of male Drosophila melanogaster. ]]> https://biorxiv.org/content/10.1101/2024.06.04.597277v1?rss=1 Kim, W. J. Song, Y. Zhang, T. Zhang, X. Ryu, T. H. Wong, K. C. Wu, Z. Wei, Y. Schweizer, J. Nguyen, K.-N. H. kwan, A. Yu, K. 2024-06-05 doi:10.1101/2024.06.04.597277 Cold Spring Harbor Laboratory Press 2024-06-05 <![CDATA[ Centrosomes act as organizing centers to promote Polo kinase-mediated adaptation to persistent DNA damage ]]> https://biorxiv.org/content/10.1101/2024.06.13.598907v1?rss=1 Langlois-Lemay, L. D'Amours, D. 2024-06-15 doi:10.1101/2024.06.13.598907 Cold Spring Harbor Laboratory Press 2024-06-15 <![CDATA[ Single-cell variations of circadian clock and immune gene expression in microglia and neurodegeneration ]]> https://biorxiv.org/content/10.1101/2024.06.16.599193v1?rss=1 Ouk, K. Yalcin, M. Rigat, L. Keren-Shaul, H. David, E. Knop, A. Boettcher, C. Kramer, A. Amit, I. Relogio, A. Priller, J. 2024-06-16 doi:10.1101/2024.06.16.599193 Cold Spring Harbor Laboratory Press 2024-06-16 <![CDATA[ The bacterial Bmt methionine synthase is involved in lag phase shortening ]]> https://biorxiv.org/content/10.1101/2024.06.19.599700v1?rss=1 Segev, E. Narvaez-Barragan, D. A. Sperfeld, M. 2024-06-21 doi:10.1101/2024.06.19.599700 Cold Spring Harbor Laboratory Press 2024-06-21 <![CDATA[ Glial voltage-gated K+ channels modulate the neural abiotic stress tolerance of Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2024.06.28.601156v1?rss=1 Andersen, M. K. Livingston, D. B. H. Robertson, R. M. MacMillan, H. A. 2024-07-02 doi:10.1101/2024.06.28.601156 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Scene context and attention independently facilitate MEG decoding of object category ]]> https://biorxiv.org/content/10.1101/2024.06.30.601374v1?rss=1 Leticevscaia, O. Brandman, T. Peelen, M. V. 2024-07-02 doi:10.1101/2024.06.30.601374 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Building a small brain with a simple stochastic generative model ]]> https://biorxiv.org/content/10.1101/2024.07.01.601562v1?rss=1 Richter, O. Schneidman, E. 2024-07-04 doi:10.1101/2024.07.01.601562 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ Coordinated network of T cells and antigen presenting cells regulate tolerance to food ]]> https://biorxiv.org/content/10.1101/2024.07.11.603064v1?rss=1 Rudnitsky, A. Oh, H. Talmor, J. Kedmi, R. 2024-07-16 doi:10.1101/2024.07.11.603064 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Identification of V. parvula and S. gordonii adhesins mediating co-aggregation and its impact on physiology and mixed biofilm structure ]]> https://biorxiv.org/content/10.1101/2024.07.16.603716v1?rss=1 DORISON, L. BECHON, N. MARTIN-GALLAUSIAUX, C. CHAMORRO RODRIGUEZ, S. V. VITRENKO, Y. OUAZAHROU, R. VILLA, R. DESCHAMPS, J. BRIANDET, R. GRIBALDO, S. GHIGO, J.-M. BELOIN, C. 2024-07-16 doi:10.1101/2024.07.16.603716 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Development of 3-in-1 nanotherapeutic strategies for ovarian cancer ]]> https://biorxiv.org/content/10.1101/2024.07.17.604002v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@1c2d3e3org.highwire.dtl.DTLVardef@1e4e73eorg.highwire.dtl.DTLVardef@109aceeorg.highwire.dtl.DTLVardef@387843_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOTOCC_FLOATNO C_FIG Among gynecological cancers, ovarian cancer causes the most fatality. Platin-based chemotherapy is the primary therapeutic option, but it is limited by a variety of drug resistance mechanisms. Ovarian cancer is a complex and challenging disease to treat, and combination approaches have shown stronger efficacy than a single drug alone. However, they still need to overcome challenges, such as the non-selective distribution of drugs, and side effects caused by each drug in the combination. To overcome these issues, here we explored a 3-in-1 combination nanotherapeutic approach containing cisplatin, olaparib, and metformin for ovarian cancer. To encapsulate hydrophilic cisplatin and metformin inside the nanoparticle (NP) core, we developed cisplatin polymer prodrugs and metformin derivatives. Our results showed successful development of 3-in-1 NPs containing cisplatin, olaparib, and metformin, and they are stable in the physiological conditions. In vitro evaluation showed each agent in the 3-in-1 NPs is active and exerts therapeutic effects, contributing to ovarian cancer cell killing at lower concentrations. These results provide insight into developing novel nanotherapeutic strategies for improving ovarian cancer treatment. ]]> Durocher, E. McGrath, S. Gahunia, E. Matsuura, N. Gadde, S. 2024-07-22 doi:10.1101/2024.07.17.604002 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ Spiking neural network models of sound localisation via a massively collaborative process ]]> https://biorxiv.org/content/10.1101/2024.07.19.604252v1?rss=1 Ghosh, M. Habashy, K. G. De Santis, F. Fiers, T. Ercelik, D. F. Meszaros, B. Friedenberger, Z. Bena, G. Hong, M. Abubacar, U. Byrne, R. T. Riquelme, J. L. Liu, Y. H. Aizenbud, I. Bicknell, B. A. Bormuth, V. Antonietti, A. Goodman, D. F. M. 2024-07-23 doi:10.1101/2024.07.19.604252 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ A Burst-Dependent Algorithm for Neuromorphic On-Chip Learning of Spiking Neural Networks ]]> https://biorxiv.org/content/10.1101/2024.07.19.604308v1?rss=1 Stuck, M. Naud, R. 2024-07-23 doi:10.1101/2024.07.19.604308 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Controlled pH Alteration Enables Guanine Accumulation and Drives Crystallization within Iridosomes ]]> https://biorxiv.org/content/10.1101/2024.07.20.604036v1?rss=1 Eyal, Z. Ggorelick-Ashkenazi, A. Deis, R. Barzilay, Y. Broder, Y. Kellum, A. P. Varsano, N. Hartstein, M. Sorrentino, A. Kaplan-Ashiri, I. Rechav, K. Metzler, R. Houben, L. Kronik, L. Rez, P. Gur, D. 2024-07-23 doi:10.1101/2024.07.20.604036 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ predicTTE: An accessible and optimal tool for time-to-event prediction in neurological diseases ]]> https://biorxiv.org/content/10.1101/2024.07.20.604416v1?rss=1 Weinreich, M. McDonough, H. Yacovzada, N. Magen, I. Cohen, Y. Harvey, C. Gornall, S. Boddy, S. Alix, J. Mohseni, N. Kurz, J. Kenna, K. Zhang, S. Iacoangeli, A. Al-Khleifat, A. Snyder, M. Hobson, E. Al-Chalabi, A. Hornstein, E. Elhaik, E. Shaw, P. McDermott, C. Cooper-Knock, J. 2024-07-23 doi:10.1101/2024.07.20.604416 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Range geographies, not functional traits, explain convergent range and phenology shifts under climate change ]]> https://biorxiv.org/content/10.1101/2024.07.22.604548v1?rss=1 Sirois-Delisle, C. Gordon, S. C. C. Kerr, J. 2024-07-23 doi:10.1101/2024.07.22.604548 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Early and Delayed STAT1-Dependent Responses Drive Local Trained Immunity of Macrophages in the Spleen ]]> https://biorxiv.org/content/10.1101/2024.07.19.604264v1?rss=1 Solomon, A. Bossel Ben-Moshe, N. Hoffman, D. Trzebanski, S. Yehezkel, D. Vainman, L. Netea, M. G. Avraham, R. 2024-07-24 doi:10.1101/2024.07.19.604264 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Preventing plasmid multimer formation in commonly used synthetic biology plasmids ]]> https://biorxiv.org/content/10.1101/2024.07.23.604805v1?rss=1 Vaisbourd, E. Bren, A. Alon, U. Glass, D. S. 2024-07-24 doi:10.1101/2024.07.23.604805 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Transfer RNA acetylation regulates in vivo mammalian stress signaling ]]> https://biorxiv.org/content/10.1101/2024.07.25.605208v1?rss=1 Thalalla Gamage, S. Khoogar, R. Howpay Manage, S. A. Crawford, M. C. Georgeson, J. Polevoda, B. V. Sanders, C. Lee, K. A. Nance, K. D. Iyer, V. Kustanovich, A. Perez, M. Thu, C. T. Nance, S. R. Miller, C. N. Holewinski, R. J. Meyer, T. Koparde, V. Yang, A. Jailwala, P. Nguyen, J. T. Andresson, T. Mock, B. A. Gu, S. Edmondson, E. F. Difilippantonio, S. Chari, R. Schwartz, S. O'Connell, M. R. Wu, C. C.-C. Meier, J. L. 2024-07-26 doi:10.1101/2024.07.25.605208 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ Dose-related Mutagenic and Clastogenic Effects of Benzofluoranthene in Mouse Somatic Tissues Detected by Duplex Sequencing and the Micronucleus Assay ]]> https://biorxiv.org/content/10.1101/2024.07.26.605228v1?rss=1 A:T mutations, followed by C:G>T:A and C:G>G:C, indicating that BbF metabolites mainly target guanines and cytosines. The mutation spectrum of BbF correlates with cancer mutational signatures associated with tobacco exposure, supporting its contribution to the carcinogenicity of combustion-derived PAHs in humans. Overall, BbFs mutagenic effects are similar to benzo[a]pyrene, a well-studied mutagenic PAH. Our work showcases the utility of DS for effective mutagenicity assessment of environmental pollutants. SynopsisWe used Duplex Sequencing to study the mutagenicity of benzo[b]fluoranthene across the mouse genome. Dose-dependent changes in mutation frequency and spectrum quantify its role in PAH-induced carcinogenicity. ]]> Schuster, D. M. LeBlanc, D. P. M. Zhou, G. Meier, M. J. Dodge, A. E. White, P. A. Long, A. S. Williams, A. Hobbs, C. Diesing, A. Smith-Roe, S. L. Salk, J. J. Marchetti, F. Yauk, C. L. 2024-07-26 doi:10.1101/2024.07.26.605228 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ Subtypes and proliferation patterns of small intestine neuroendocrine tumors revealed by single cell RNA sequencing ]]> https://biorxiv.org/content/10.1101/2024.07.29.605642v1?rss=1 Somech, E. Halder, D. Spitzer, A. Barbolin, C. Tyler, M. Halperin, R. Biton, M. Tirosh, A. Tirosh, I. 2024-07-30 doi:10.1101/2024.07.29.605642 Cold Spring Harbor Laboratory Press 2024-07-30 <![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[ tp53 R217H and R242H Mutant Zebrafish Exhibit Dysfunctional p53 Hallmarks and Recapitulate Li-Fraumeni Syndrome Phenotypes ]]> https://biorxiv.org/content/10.1101/2024.07.31.605368v1?rss=1 Kobar, K. Berman, J. N. Fiene, J. A. Tuzi, L. Burnley, E. Galpin, K. J. C. Midgen, C. Laverty, B. Moksa, M. Cao, Q. Subasri, V. Wen, T. T. Shlien, A. Hirst, M. Malkin, D. Prykhozhij, S. Carles, A. 2024-08-03 doi:10.1101/2024.07.31.605368 Cold Spring Harbor Laboratory Press 2024-08-03 <![CDATA[ Hierarchical Working Memory and a New Magic Number ]]> https://biorxiv.org/content/10.1101/2024.08.14.607952v1?rss=1 Zhong, W. Katkov, M. Tsodyks, M. 2024-08-15 doi:10.1101/2024.08.14.607952 Cold Spring Harbor Laboratory Press 2024-08-15 <![CDATA[ The glycolytic reaction PGAM unexpectedly restrains Th17 pathogenicity and Th17-dependent autoimmunity ]]> https://biorxiv.org/content/10.1101/2024.08.18.607992v1?rss=1 Wang, C. Wagner, A. Fessler, J. DeTomaso, D. Zaghouani, S. Zhou, Y. Pierce, K. Sobel, R. A. Clish, C. Yosef, N. Kuchroo, V. K. 2024-08-19 doi:10.1101/2024.08.18.607992 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Multi-Omics Unveils Strain-Specific Neuroactive Metabolite Production Linked to Inflammation Modulation by Bacteroides and Their Extracellular Vesicles ]]> https://biorxiv.org/content/10.1101/2024.08.19.608651v1?rss=1 yousuf, b. Mottawea, W. Esmail, G. A. Nazemof, N. Bouhlel, N. E. Njoku, E. Li, Y. Zhang, X. Minic, Z. Hammami, R. 2024-08-20 doi:10.1101/2024.08.19.608651 Cold Spring Harbor Laboratory Press 2024-08-20 <![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[ Discovery of potent SARS-CoV-2 nsp3 macrodomain inhibitors uncovers lack of translation to cellular antiviral response ]]> https://biorxiv.org/content/10.1101/2024.08.19.608619v1?rss=1 Lee, A. A. Amick, I. Aschenbrenner, J. C. Barr, H. A. Benjamin, J. Brandis, A. Cohen, G. Diaz-Tapia, R. Duberstein, S. Dixon, J. Cousins, D. Fairhead, M. Fearon, D. Frick, J. Gayvert, J. de Godoy, A. S. Griffen, E. J. Huber, K. V. M. Koekemoer, L. Lahav, N. Marples, P. G. McGovern, B. L. Mehlman, T. Robinson, M. C. Singh, U. Szommer, T. Tomlinson, C. W. E. Vargo, T. von Delft, F. Wang, S. White, K. M. Williams, E. Winokan, M. 2024-08-21 doi:10.1101/2024.08.19.608619 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Conserved RNA-binding protein interactions mediate syntologous lncRNA functions ]]> https://biorxiv.org/content/10.1101/2024.08.21.605776v1?rss=1 Sabate-Cadenas, X. Lavalou, P. Ross, C. J. Chen, L. Zielinski, D. Vacher, S. Ledevin, M. Larcher, T. Petitjean, M. Damy, L. Servant, N. Bieche, I. Ulitsky, I. Shkumatava, A. 2024-08-21 doi:10.1101/2024.08.21.605776 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Activation and Evasion of the FEAR Pathway by RNA Viruses ]]> https://biorxiv.org/content/10.1101/2024.08.22.609092v1?rss=1 Rex, E. A. Seo, D. Embry, A. Arulanandam, R. Spinelli, M. M. Diallo, J.-S. Gammon, D. B. 2024-08-22 doi:10.1101/2024.08.22.609092 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Potassium induces conformational changes in the Sabia virus spike complex ]]> https://biorxiv.org/content/10.1101/2024.08.22.609195v1?rss=1 Cohen-Dvashi, H. Katz, M. Diskin, R. 2024-08-22 doi:10.1101/2024.08.22.609195 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ A multi-omics approach to identify deleterious mutations in plants ]]> https://biorxiv.org/content/10.1101/2024.08.22.609273v1?rss=1 Baruch, O. Levy, A. A. Mafessoni, F. 2024-08-23 doi:10.1101/2024.08.22.609273 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining ]]> https://biorxiv.org/content/10.1101/2024.08.27.610007v1?rss=1 Prillo, S. An, K. Wu, W. Kristanto, I. Jones, M. G. Song, Y. S. Yosef, N. 2024-08-28 doi:10.1101/2024.08.27.610007 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Investigating the p21 Ubiquitin-Independent Degron Reveals a Dual Degron Module Regulating p21 Degradation and Function. ]]> https://biorxiv.org/content/10.1101/2024.08.29.610237v1?rss=1 Riutin, M. Erez, P. Adler, J. Biran, A. Myers, N. Shaul, Y. 2024-08-29 doi:10.1101/2024.08.29.610237 Cold Spring Harbor Laboratory Press 2024-08-29 <![CDATA[ The Balanced Mind and its Intrinsic Neural Timescales in Advanced Meditators ]]> https://biorxiv.org/content/10.1101/2024.08.29.609126v1?rss=1 Malipeddi, S. Sasidharan, A. Venugopal, R. Ventura, B. Bauer, C. C. P.N., R. Mehrotra, S. John, J. P. Kutty, B. M. Northoff, G. 2024-08-30 doi:10.1101/2024.08.29.609126 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Transglutaminase 2 function in glioblastoma tumor efferocytosis ]]> https://biorxiv.org/content/10.1101/2024.08.29.610293v1?rss=1 Lui, M. Sevinc, F. Elgafarawi, M. Munoz, D. G. Keillor, J. W. Sinclair, J. Catana, D. Woulfe, J. Lorimer, I. A. 2024-08-30 doi:10.1101/2024.08.29.610293 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ The gut microbiota is a determinant of sexual dimorphism in ALS-linked TDP43 mice ]]> https://biorxiv.org/content/10.1101/2024.08.29.610355v1?rss=1 Beraldi, E. J. Lee, S. Jiang, Y. Rea, I. M. Phull, R. Keenan, C. M. Stephens, M. Bardhi, M. Bankole, O. Pfeffer, G. Biernaskie, J. McCoy, K. D. Elinav, E. Sharkey, K. A. Nguyen, M. D. 2024-08-30 doi:10.1101/2024.08.29.610355 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ The Initiator Caspase Dronc Drives Compensatory Proliferation of Apoptosis-Resistant Cells During Epithelial Tissue Regeneration After Ionizing Radiation ]]> https://biorxiv.org/content/10.1101/2024.09.01.610661v1?rss=1 JNK signaling pathway in DARE cells directly regulates their proliferation, which in turn influences NARE cell proliferation. Consequently, we show that maintaining proliferative homeostasis between DARE and NARE cells is vital for balanced tissue regeneration. Given the widespread use of ionizing irradiation in cancer treatment and prevention, our findings have potential implications for understanding treatment-resistant cells and cancer recurrence. ]]> Braun, T. Afgin, N. Sapozhnikov, L. Sivan, E. Bergmann, A. Baena-Lopez, L. A. Yacobi-Sharon, K. Arama, E. 2024-09-02 doi:10.1101/2024.09.01.610661 Cold Spring Harbor Laboratory Press 2024-09-02 <![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[ Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes ]]> https://biorxiv.org/content/10.1101/2024.09.03.611065v1?rss=1 Lee, H.-o. Stai, J. S. Xu, Q. Hewavithana, T. Batra, R. Liu, A. Jordan, B. D. Walstead, R. Jenkins, J. W. Williams, M. Webber, j. Grimwood, J. Lovell, J. T. Bruna, T. Shu, S. Keymanesh, K. Eichenberger, J. Schmutz, J. Goodstein, D. M. Barry, K. W. Sankoff, D. Jin, L. Leebens-Mack, J. Cannon, S. B. 2024-09-08 doi:10.1101/2024.09.03.611065 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Hematopoietic Tet2 inactivation enhances the response to checkpoint blockade immunotherapy ]]> https://biorxiv.org/content/10.1101/2024.09.09.612140v1?rss=1 Vanner, R. J. Bansal, S. Buttigeig, M. M. Zeng, A. G. X. Rondeau, V. Chan, D. Y. Chan-Seng-Yue, M. Jin, L. McLeod, J. Donato, E. Stelmach, P. Vlasschaert, C. Yang, Y. Gupta, A. Genta, S. Sanz Garcia, E. Shlush, L. Ribeiro, M. Butler, M. O. Abelson, S. Minden, M. Chan, S. M. Rauh, M. J. Trumpp, A. Dick, J. E. 2024-09-11 doi:10.1101/2024.09.09.612140 Cold Spring Harbor Laboratory Press 2024-09-11 <![CDATA[ Functional separation of long-range inputs by intrinsic dynamics of dorsal raphe 5-HT neurons ]]> https://biorxiv.org/content/10.1101/2024.09.09.611991v1?rss=1 Lynn, M. B. Naud, R. Maler, L. Beique, J.-C. 2024-09-13 doi:10.1101/2024.09.09.611991 Cold Spring Harbor Laboratory Press 2024-09-13 <![CDATA[ Ultrastructural analysis of the brain endothelium by electron tomography ]]> https://biorxiv.org/content/10.1101/2024.09.09.612128v1?rss=1 Kotchetkov, P. Lacoste, B. 2024-09-14 doi:10.1101/2024.09.09.612128 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Profiling the physiological impact of aberrant folded-state protein filamentation in cells ]]> https://biorxiv.org/content/10.1101/2024.09.13.612878v1?rss=1 View larger version (84K): org.highwire.dtl.DTLVardef@7136a4org.highwire.dtl.DTLVardef@ba62dborg.highwire.dtl.DTLVardef@b02bbaorg.highwire.dtl.DTLVardef@6cbf9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Levin, T. Garcia-Seisdedos, H. Lobov, A. Wojtynek, M. Alexandrov, A. Jona, G. Levi, D. Medalia, O. Levy, E. D. 2024-09-14 doi:10.1101/2024.09.13.612878 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Voltage imaging reveals circuit computations in the raphe underlying serotonin-mediated motor vigor learning ]]> https://biorxiv.org/content/10.1101/2024.09.15.613083v1?rss=1 Kawashima, T. Wei, Z. Haruvi, R. Shainer, I. Narayan, S. Baier, H. Ahrens, M. B. 2024-09-16 doi:10.1101/2024.09.15.613083 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ Global and compartmentalized serotonergic control of sensorimotor integration underlying motor adaptation ]]> https://biorxiv.org/content/10.1101/2024.09.15.613094v1?rss=1 Haruvi, R. Barbara, R. Shainer, I. Rosenberg, A. M. Moshe, L. Malamud, D. Toledano, J. Braun, D. Baier, H. Kawashima, T. 2024-09-16 doi:10.1101/2024.09.15.613094 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ Elucidating early intestinal stem cell response to bacterial infection ]]> https://biorxiv.org/content/10.1101/2024.09.15.613128v1?rss=1 Lebon, S. Davidzohn, N. Menachem, A. H. Katz, A. Wigoda, N. Rotkopf, R. Dadosh, T. Levin-Zaidman, S. Dezorella, N. Blumberger, N. Hoffman, D. Hofree, M. Biton, M. 2024-09-19 doi:10.1101/2024.09.15.613128 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Neuronal lipid droplets play a conserved and sex-biased role in maintaining whole-body energy homeostasis ]]> https://biorxiv.org/content/10.1101/2024.09.19.613929v1?rss=1 View larger version (54K): org.highwire.dtl.DTLVardef@1936e92org.highwire.dtl.DTLVardef@40478aorg.highwire.dtl.DTLVardef@18d5faorg.highwire.dtl.DTLVardef@882ee9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Manceau, R. Majeur, D. Cherian, C. M. Miller, C. J. Wat, L. W. Fisher, J. D. Labarre, A. Hollman, S. Prakash, S. Audet, S. Chao, C. F. Depaauw-Holt, L. R. Rogers, B. Bosson, A. Xi, J. J. Y. Callow, C. A. S. Yoosefi, N. Shahraki, N. Xia, Y. H. Hui, A. VanderZwaag, J. Bouyakdan, K. Rodaros, D. Kotchetkov, P. Daneault, C. Fallahpour, G. Tetreault, M. Tremblay, M.-E. Ruiz, M. Lacoste, B. Parker, A. Murphy-Royal, C. Huan, T. Fulton, S. Rideout, E. Alquier, T. 2024-09-20 doi:10.1101/2024.09.19.613929 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Monocyte-derived cells but not Microglia cause Oxidative Tissue Damage in Neuroinflammation ]]> https://biorxiv.org/content/10.1101/2024.09.18.612891v1?rss=1 Villar-Vesga, J. De Feo, D. Clement, P. Ingelfinger, F. Ulutekin, C. Kim, J. Pena-Francesch, M. Schmidt, K. W. Meuffels, E. Bugada, V. Greis, D. Pereira, S. A. Oberbichler, L. Seehusen, F. Prisco, F. Dalvi, U. Munz, C. Saab, A. S. Becher, B. Mundt, S. 2024-09-22 doi:10.1101/2024.09.18.612891 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Broadly Reactive Anti-VHH Antibodies for Characterizing, Blocking, or Activating Nanobody-Based CAR-T Cells ]]> https://biorxiv.org/content/10.1101/2024.09.18.613561v1?rss=1 94% CAR purity, with retained CD8/CD4 heterogeneity. Functionally, anti-VHH antibody-expanded CAR-T cells maintained strong antigen specific activity without functional exhaustion. Overall, these data identify a useful new tool for understanding and manipulating VHH-based CAR-T cells. Funding SourceThis work was funded by the National Research Council Canada Disruptive Technology Solutions Cell and Gene Therapy challenge program, and BioCanRx Declaration of interestsThe anti-VHH antibodies reported here are the subject of a provisional patent application by the National Research Council of Canada ]]> McComb, S. Dupont, B. Shepherd, A. Bennychen, B. Marcil, A. Arbabi-Ghahroudi, M. Tamblyn, L. Raphael, S. Sheff, J. Hussack, G. Moraitis, A. Wu, C. Gadoury, C. Fortin, A. Parat, M. Page, M. Lippens, J. Joubert, S. Lamoureux, L. Malenfant, F. Acchione, M. Pohankova, P. Schrag, J. Acel, A. Maurice, R. Lefebvre, J. Coutu, M. Smith, E. El Bakkouri, M. Hill, J. J. Tremblay, T.-L. Faulkes, S. Webb, J. Zafer, A. Zhu, Q. Nguyen, T. Pon, R. A. Weeratna, R. D. 2024-09-22 doi:10.1101/2024.09.18.613561 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Natural killer cell function is regulated by TGF-β signaling in pregnancy and tumor progression ]]> https://biorxiv.org/content/10.1101/2024.09.18.613652v1?rss=1 Yalin, A. Wang, S.-Y. Landsberger, T. Gamliel, M. Elefant, N. Kotzur, R. Goldman-Wohl, D. David, E. Molgora, M. Bhattarai, B. Cella, M. Meir-Salame, T. Gilad, R. Yagel, S. Zuk, O. Colonna, M. Mandelboim, O. Amit, I. 2024-09-22 doi:10.1101/2024.09.18.613652 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Caspase-Activated DNase Localizes to Cancer Causing Translocation Breakpoints During Cell Differentiation ]]> https://biorxiv.org/content/10.1101/2024.09.24.614809v1?rss=1 Alsowaida, D. Larsen, B. D. Hachmer, S. Azimi, M. Arezza, E. Brunette, S. Tur, S. Palii, C. G. Albraidy, B. Sorensen, C. S. Brand, M. Dilworth, F. J. Megeney, L. A. 2024-09-26 doi:10.1101/2024.09.24.614809 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Transcription swells chromosomes in vitro ]]> https://biorxiv.org/content/10.1101/2024.09.25.614905v1?rss=1 Greiss, F. Daube, S. S. Noireaux, V. Bar-Ziv, R. 2024-09-26 doi:10.1101/2024.09.25.614905 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ CCR5 antagonists as neuroprotective and stroke recovery enhancing agents: a preclinical systematic review and meta-analysis ]]> https://biorxiv.org/content/10.1101/2024.09.25.614925v1?rss=1 Sharif, A. Jeffers, M. S. Fergusson, D. A. Bapuji, R. Nicholls, S. G. Humphrey, J. Johnston, W. Mitchell, E. Speirs, M.-A. Stronghill, L. Vuckovic, M. Wulf, S. Shorr, R. Dowlatshahi, D. Corbett, D. Lalu, M. M. 2024-09-27 doi:10.1101/2024.09.25.614925 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ A computationally designed panel of diverse and selective peroxygenases for terpene oxyfunctionalization ]]> https://biorxiv.org/content/10.1101/2024.09.27.615329v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@3f8dceorg.highwire.dtl.DTLVardef@76ee48org.highwire.dtl.DTLVardef@15f2a7org.highwire.dtl.DTLVardef@edba31_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Munch, J. Soler, J. Fleishman, S. Garcia-Borras, M. Weissenborn, M. J. 2024-09-28 doi:10.1101/2024.09.27.615329 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ MetaLab Platform Enables Comprehensive DDA and DIA Metaproteomics Analysis ]]> https://biorxiv.org/content/10.1101/2024.09.27.615406v1?rss=1 Cheng, K. Ning, Z. Zhang, X. Duan, H. Mayne, J. Figeys, D. 2024-09-28 doi:10.1101/2024.09.27.615406 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ Variants in Lrrk2 and Snca deficiency do not alter the course of primary encephalitis due to neurotropic reovirus T3D in newborn mice ]]> https://biorxiv.org/content/10.1101/2024.09.28.615578v1?rss=1 Lunn, M. O. Rousso, C. Tomlinson, J. J. Brown, E. G. Schlossmacher, M. G. 2024-09-28 doi:10.1101/2024.09.28.615578 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ Zebrafish glial-vascular interactions progressively expand over the course of brain development ]]> https://biorxiv.org/content/10.1101/2024.09.27.615488v1?rss=1 Gall, L. G. Stains, C. M. Freitas-Andrade, M. Jia, B. Z. Patel, N. Megason, S. G. Lacoste, B. O'Brown, N. M. 2024-09-30 doi:10.1101/2024.09.27.615488 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ The Deubiquitinating Enzyme Otub2 Modulates Pancreatic Beta-Cells Function and Survival ]]> https://biorxiv.org/content/10.1101/2024.09.30.615641v1?rss=1 Oshry, M. Isaac, R. Boura-Halfon, S. Sampson, S. Lev, S. Zick, Y. Vinik, Y. 2024-10-01 doi:10.1101/2024.09.30.615641 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ A Drosophila screen of schizophrenia-related genes highlights the requirement of neural and glial matrix metalloproteinases for neuronal remodeling ]]> https://biorxiv.org/content/10.1101/2024.10.01.616025v1?rss=1 Keret, S. Meltzer, H. Marmor-Kollet, N. Schuldiner, O. 2024-10-02 doi:10.1101/2024.10.01.616025 Cold Spring Harbor Laboratory Press 2024-10-02 <![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[ EASI-ORC: A Pipeline for the Efficient Analysis and Segmentation of smFISH Images for Organelle-RNA Colocalization Measurements in Yeast ]]> https://biorxiv.org/content/10.1101/2024.10.04.616601v1?rss=1 Garin, S. Levavi, L. Gerst, J. E. 2024-10-04 doi:10.1101/2024.10.04.616601 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Automated, Stress-Free, and Precise Measurement of Songbird Weight in Neuroscience Experiments ]]> https://biorxiv.org/content/10.1101/2024.10.05.616794v1?rss=1 Bonneh, Y. Tuval, A. Ben-Shitrit, I. Goffer, L. Cohen, Y. 2024-10-05 doi:10.1101/2024.10.05.616794 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ Conservation of mRNA operon formation in the control of the heat shock response in mammalian cells ]]> https://biorxiv.org/content/10.1101/2024.10.05.616786v1?rss=1 Pataki, E. Gerst, J. E. 2024-10-06 doi:10.1101/2024.10.05.616786 Cold Spring Harbor Laboratory Press 2024-10-06 <![CDATA[ Canary Mating Season Songs Move Between Order and Disorder ]]> https://biorxiv.org/content/10.1101/2024.10.06.616872v1?rss=1 Levin, S. Cohen, Y. 2024-10-06 doi:10.1101/2024.10.06.616872 Cold Spring Harbor Laboratory Press 2024-10-06 <![CDATA[ Oxygen chemoreceptor inhibition by dopamine D2 receptors in isolated zebrafish gills ]]> https://biorxiv.org/content/10.1101/2024.10.08.617247v1?rss=1 Reed, M. Jonz, M. G. 2024-10-12 doi:10.1101/2024.10.08.617247 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ The Curated Cancer Cell Atlas: comprehensive characterisation of tumours at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2024.10.11.617836v1?rss=1 Tyler, M. Gavish, A. Barbolin, C. Tschernichovsky, R. Hoefflin, R. Mints, M. Puram, S. V. Tirosh, I. 2024-10-12 doi:10.1101/2024.10.11.617836 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene program in bat wing development ]]> https://biorxiv.org/content/10.1101/2024.10.10.617585v1?rss=1 Schindler, M. Feregrino, C. Aldrovandi, S. Lo, B.-W. Monaco, A. A. Ringel, A. R. Morales, A. Zehnder, T. Behncke, R. Y. Glaser, J. Barclay, A. Andrey, G. Kragesteen, B. K. Hagerling, R. Haas, S. A. Vingron, M. Ulitsky, I. Marti-Renom, M. Hechavarria, J. C. Fasel, N. J. Hiller, M. Lupianez, D. Mundlos, S. Real, F. M. 2024-10-13 doi:10.1101/2024.10.10.617585 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ The ATP-dependent protease ClpYQ degrades cell division proteins DivIVA and Mbl in Bacillus subtilis ]]> https://biorxiv.org/content/10.1101/2024.10.15.618472v1?rss=1 Lasnosky, T. D. Darnowski, M. G. Brazeau-Henrie, J. T. Labana, P. Boddy, C. N. 2024-10-17 doi:10.1101/2024.10.15.618472 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ HP1a promotes chromatin liquidity and drives spontaneous heterochromatin compartmentalization ]]> https://biorxiv.org/content/10.1101/2024.10.18.618981v1?rss=1 Brennan, L. D. Kim, H.-K. Colmenares, S. Ego, T. Kumar, A. Safran, S. Ryu, J.-K. Karpen, G. 2024-10-18 doi:10.1101/2024.10.18.618981 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Developmental changes in the control of primary motoneuron excitability by the M-current in larval zebrafish ]]> https://biorxiv.org/content/10.1101/2024.10.17.618843v1?rss=1 Gaudreau, S. F. Bui, T. 2024-10-21 doi:10.1101/2024.10.17.618843 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ Autonomous biogenesis of the entire protein translation machinery excluding ribosomes ]]> https://biorxiv.org/content/10.1101/2024.10.20.619270v1?rss=1 Schwarz-Schilling, M. Dupin, A. Avidan, N. Barak, Y. Shimizu, Y. Daube, S. S. Bar-Ziv, R. H. 2024-10-21 doi:10.1101/2024.10.20.619270 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ The impact of tropodithietic acid on microbial physiology under varying culture complexities ]]> https://biorxiv.org/content/10.1101/2024.10.23.619853v1?rss=1 Shlakhter, O. Segev, E. 2024-10-23 doi:10.1101/2024.10.23.619853 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumor growth and metastasis ]]> https://biorxiv.org/content/10.1101/2024.10.21.619529v1?rss=1 Jones, M. G. Sun, D. Min, K. H. Colgan, W. N. Tian, L. Weir, J. A. Chen, V. Z. Koblan, L. W. Yost, K. E. Mathey-Andrews, N. Russell, A. J. C. Stickels, R. R. Balderrama, K. S. Rideout, W. M. Chang, H. Y. Jacks, T. Chen, F. Weissman, J. S. Yosef, N. Yang, D. 2024-10-24 doi:10.1101/2024.10.21.619529 Cold Spring Harbor Laboratory Press 2024-10-24 <![CDATA[ TIR signaling activates caspase-like immunity in bacteria ]]> https://biorxiv.org/content/10.1101/2024.10.24.620036v1?rss=1 ROUSSET, F. Osterman, I. Scherf, T. Falkovich, A. Leavitt, A. Amitai, G. Shir, S. Malitsky, S. Itkin, M. Savidor, A. Sorek, R. 2024-10-25 doi:10.1101/2024.10.24.620036 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Virus Entry is a Major Determinant of HCMV Latency in Monocytes ]]> https://biorxiv.org/content/10.1101/2024.10.26.619803v1?rss=1 Kitsberg, Y. Nachshon, A. arazi, t. Fisher, T. Wainstein, A. Finkel, Y. Stern-Ginossar, N. Schwartz, M. 2024-10-27 doi:10.1101/2024.10.26.619803 Cold Spring Harbor Laboratory Press 2024-10-27 <![CDATA[ Insights on macrosynteny, 'rebel' genes, and a new sex-linked region in anurans from comparative genomics and a new chromosome-level genome for the western chorus frog ]]> https://biorxiv.org/content/10.1101/2024.10.27.620512v1?rss=1 Chen, Y. Lougheed, D. R. Sun, Z. Ethier, J. Trudeau, V. L. Lougheed, S. C. 2024-10-28 doi:10.1101/2024.10.27.620512 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Functional interaction between transcription factor Sfp1 and the NuA4 complex in response to nutrient availability ]]> https://biorxiv.org/content/10.1101/2024.10.28.620578v1?rss=1 Xu, K. Joly-Beauparlant, C. Bianco, S. Cote, V. Herrmann, L. Droit, A. Downey, M. Nourani, A. Cote, J. 2024-10-28 doi:10.1101/2024.10.28.620578 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Intracellular amphiregulin is critical for heterochromatin maintenance and genomic stability in response to replication stress in BRCA2mut/+mammary epithelial cells ]]> https://biorxiv.org/content/10.1101/2024.10.27.620431v1?rss=1 Jiang, T. Zein, A. Pratt, C. M. A. 2024-10-29 doi:10.1101/2024.10.27.620431 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Rapid adaptation and increased genetic parallelism in experimental metapopulations of Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2024.10.28.620660v1?rss=1 Chakraborty, P. Kassen, R. 2024-10-29 doi:10.1101/2024.10.28.620660 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ A Protocol for Neuralized Murine Olfactory Organoids ]]> https://biorxiv.org/content/10.1101/2024.10.29.620938v1?rss=1 Ozgun, A. Suman, P. Coulombe, J. aSCENT-PD Investigators, Brown, E. G. Tomlinson, J. J. Woulfe, J. M. Schlossmacher, M. G. 2024-10-31 doi:10.1101/2024.10.29.620938 Cold Spring Harbor Laboratory Press 2024-10-31 <![CDATA[ High throughput single-cell proteomics of in-vivo cells ]]> https://biorxiv.org/content/10.1101/2024.11.01.621461v1?rss=1 Karagach, S. Smollich, J. Atrakchi, O. Mohan, V. Geiger, T. 2024-11-01 doi:10.1101/2024.11.01.621461 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Analyses of transposable elements in arbuscular mycorrhizal fungi support evolutionary parallels with fungal plant pathogens ]]> https://biorxiv.org/content/10.1101/2024.11.04.621924v1?rss=1 Oliveira, J. I. Lane, C. Mugambi, K. Yildirir, G. Nicol, A. M. Kokkoris, V. Banchini, C. Dadej, K. Dettman, J. Stefani, F. Corradi, N. 2024-11-05 doi:10.1101/2024.11.04.621924 Cold Spring Harbor Laboratory Press 2024-11-05 <![CDATA[ Differential Equation Modeling of Cell Population Dynamics in Skeletal Muscle Regeneration from Single-Cell Transcriptomic Data ]]> https://biorxiv.org/content/10.1101/2024.11.06.622368v1?rss=1 Al-Ghazawi, R. Shao, X. Perkins, T. J. 2024-11-08 doi:10.1101/2024.11.06.622368 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Arbuscular mycorrhizal fungal genotype and nuclear organization as driving factors in host plant nutrient acquisition and stable carbon capture ]]> https://biorxiv.org/content/10.1101/2024.11.07.622487v1?rss=1 Ferguson, R. Mugambi, K. M. Villeneuve-Laroche, M. Kallenbach, C. M. Antunes, P. Corradi, N. 2024-11-08 doi:10.1101/2024.11.07.622487 Cold Spring Harbor Laboratory Press 2024-11-08 <![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[ Metaproteomics reveals age-specific alterations of gut microbiome in hamsters with SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2024.11.12.623292v1?rss=1 Creskey, M. Angulo, F. S. Wu, Q. Tamming, L. Fekete, E. Cheng, K. Ning, Z. Wang, A. Rodrigues, P. B. Rodovalho, V. d. R. Vinolo, M. A. R. Figeys, D. Li, X. Trottein, F. Zhang, X. 2024-11-13 doi:10.1101/2024.11.12.623292 Cold Spring Harbor Laboratory Press 2024-11-13 <![CDATA[ Characteristics of early career health researchers and experiences of burnout during the COVID-19 pandemic in Canada ]]> https://biorxiv.org/content/10.1101/2024.11.13.622718v1?rss=1 Hewko, S. Kowalec, K. Anderson, L. Mulvihill, E. E. Aristizabal, M. Ciernia, A. V. Dhillon, S. Dufour, A. Lim, G. E. Rousseaux, M. Saleem, A. Daraz, L. Lam, G. Association of Canadian Early Career Health Researchers, 2024-11-14 doi:10.1101/2024.11.13.622718 Cold Spring Harbor Laboratory Press 2024-11-14 <![CDATA[ Atomic elementary flux modes explain the steady state flow of metabolites in large-scale flux networks ]]> https://biorxiv.org/content/10.1101/2024.11.13.623484v1?rss=1 Chitpin, J. G. Perkins, T. J. 2024-11-15 doi:10.1101/2024.11.13.623484 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Prey movement shapes the acquisition of predator expertise in a virtual bi-trophic system ]]> https://biorxiv.org/content/10.1101/2024.11.15.621573v1?rss=1 Fraser Franco, M. Santostefano, F. Martin, J. G. A. Kelly, C. D. Montiglio, P.-O. 2024-11-17 doi:10.1101/2024.11.15.621573 Cold Spring Harbor Laboratory Press 2024-11-17 <![CDATA[ A novel rhodopsin-based voltage indicator for simultaneous two-photon optical recording with GCaMP in vivo ]]> https://biorxiv.org/content/10.1101/2024.11.15.623698v1?rss=1 Villette, V. Yang, S. Valenti, R. Macklin, J. J. Bradley, J. Mathieu, B. Lombardini, A. Podgorski, K. Dieudonne, S. Schreiter, E. R. Abdelfattah, A. S. 2024-11-17 doi:10.1101/2024.11.15.623698 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[ Understanding the Dynamics of Biomass Deconstruction by the Cellulolytic Anaerobe C. thermocellum ]]> https://biorxiv.org/content/10.1101/2024.11.19.624254v1?rss=1 Yarbrough, J. Stich, D. Hengge, N. Xu, Q. Chung, D. Ziegler, S. Huang, S. Morais, S. Mizrahi, I. Bayer, E. A. Bomble, Y. 2024-11-22 doi:10.1101/2024.11.19.624254 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ H- and m-channel overexpression promotes seizure-like events by impairing the ability of inhibitory neurons to process correlated inputs ]]> https://biorxiv.org/content/10.1101/2024.11.25.625196v1?rss=1 Rich, S. Valiante, T. A. Lefebvre, J. 2024-11-25 doi:10.1101/2024.11.25.625196 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Immune organization in sentinel lymph nodes of melanoma patients is prognostic of distant metastases ]]> https://biorxiv.org/content/10.1101/2024.11.24.625041v1?rss=1 Amitay, Y. Milo, I. Keidar-Haran, T. Deis, S. Truzman, G. Elhanani, O. Salame, T. M. Azimov, M. Stein, I. Cohen, J. Lotem, M. Pikarsky, E. Keren, L. 2024-11-26 doi:10.1101/2024.11.24.625041 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Piezo2 in sensory neurons influences systemic and adipose tissue metabolism ]]> https://biorxiv.org/content/10.1101/2024.11.27.624676v1?rss=1 Passini, F. S. Bornstein, B. Rubin, S. Kuperman, Y. Krief, S. Masschelein, E. Mehlman, T. Brandis, A. Addadi, Y. Huri-Ohev Shalom, S. Richter, E. A. Yardeni, T. Tirosh, A. De Bock, K. Zelzer, E. 2024-11-28 doi:10.1101/2024.11.27.624676 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Design principles of transcription factors with intrinsically disordered regions ]]> https://biorxiv.org/content/10.1101/2024.11.26.625383v1?rss=1 Ji, W. Hachmo, O. Barkai, N. Amir, A. 2024-11-29 doi:10.1101/2024.11.26.625383 Cold Spring Harbor Laboratory Press 2024-11-29 <![CDATA[ Asynchronous subunit transitions precede acetylcholine receptor activation ]]> https://biorxiv.org/content/10.1101/2024.12.02.626350v1?rss=1 Thompson, M. J. Tessier, C. J. G. Ananchenko, A. Emlaw, J. R. Dehez, F. Zarkadas, E. daCosta, C. J. B. Nury, H. Baenziger, J. E. 2024-12-02 doi:10.1101/2024.12.02.626350 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ The RNA-binding protein PRRC2B preserves 5' TOP mRNA during starvation to maintain ribosome biogenesis during nutrient recovery ]]> https://biorxiv.org/content/10.1101/2024.12.04.626744v1?rss=1 Goldberg, N. Bril, D. Eisenstein, M. Olender, T. Savidor, A. Bialik, S. Pietrokovski, S. Kimchi, A. 2024-12-04 doi:10.1101/2024.12.04.626744 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ An Atlas of Cellular Archetypes ]]> https://biorxiv.org/content/10.1101/2024.12.04.626890v1?rss=1 Crowley, G. Alon, U. Quake, S. R. 2024-12-04 doi:10.1101/2024.12.04.626890 Cold Spring Harbor Laboratory Press 2024-12-04 <![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[ Pex3 promotes formation of peroxisome-peroxisome and peroxisome-lipid droplet contact sites ]]> https://biorxiv.org/content/10.1101/2024.12.10.627744v1?rss=1 Amado, L. Franzkoch, R. Percifull, L. Flatemersch, V. Brüggermann, E. J. Psathaki, O. E. Schuldiner, M. Bohnert, M. Gonzalez Montoro, A. 2024-12-12 doi:10.1101/2024.12.10.627744 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Random Tree Model of Meaningful Memory ]]> https://biorxiv.org/content/10.1101/2024.12.11.627835v1?rss=1 Zhong, W. Can, T. Georgiou, A. Shnayderman, I. Katkov, M. Tsodyks, M. 2024-12-16 doi:10.1101/2024.12.11.627835 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Evolutionary dynamics at the leading edge ofbiological invasions ]]> https://biorxiv.org/content/10.1101/2024.12.13.628423v1?rss=1 Poloni, S. Lutscher, F. Lewis, M. 2024-12-16 doi:10.1101/2024.12.13.628423 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ The formin FMNL2 plays a role in the response of melanoma cells to substrate stiffness ]]> https://biorxiv.org/content/10.1101/2024.12.13.628356v1?rss=1 Clugston, J. D. Fox, S. Harden, J. L. Copeland, J. W. 2024-12-17 doi:10.1101/2024.12.13.628356 Cold Spring Harbor Laboratory Press 2024-12-17 <![CDATA[ Wnt/β-Catenin coordinates muscle spindle development by regulating capsule differentiation, intrafusal fiber nuclei aggregation and proprioceptive nerve endings ]]> https://biorxiv.org/content/10.1101/2024.12.18.629133v1?rss=1 Guo, Q. Gatterer, A. Rosner, A. Krief, S. Rotkopf, R. Passini, F. S. Wigoda, N. Bornstein, B. Zelzer, E. 2024-12-20 doi:10.1101/2024.12.18.629133 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ LAG3 marks activated but hyporesponsive NK cells. ]]> https://biorxiv.org/content/10.1101/2024.12.18.629184v1?rss=1 Vasilyeva, V. Makinson, O. Chan, C. Park, M. O'Dwyer, C. Ali, A. Abrar, U. H. K. Tanese de Souza, C. Hasim, M. S. Asif, S. Kurdieh, R. Abou-Hamad, J. Yakubovich, E. Hodgins, J. Al Haddad, P. Pietropaolo, G. Mazzei, J. Seo, H. Huang, Q. Nersesian, S. Chay, D. Jacquelot, N. Cook, D. Lee, S.-H. Sciume, G. Waggoner, S. N. Ardolino, M. Marotel, M. 2024-12-21 doi:10.1101/2024.12.18.629184 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ A widespread family of viral sponge proteins reveals specific inhibition of nucleotide signals in anti-phage defense ]]> https://biorxiv.org/content/10.1101/2024.12.30.630793v1?rss=1 1,300 immune evasion proteins. A 2.1 [A] crystal structure of Acb4 in complex with 3'3'-cGAMP reveals a tetrameric assembly that functions as a sponge to sequester CBASS signals and inhibit immune activation. We demonstrate Acb4 alone is sufficient to disrupt CBASS activation in vitro and enable immune evasion in vivo. Analyzing phages that infect diverse bacteria, we explain how Acb4 selectively targets nucleotide signals in host defense and avoids disruption of cellular homeostasis. Together, our results reveal principles of immune evasion protein evolution and explain a major mechanism phages use to inhibit host immunity. ]]> Chang, R. B. Toyoda, H. C. Hobbs, S. J. Richmond-Buccola, D. Wein, T. Burger, N. Chouchani, E. T. Sorek, R. Kranzusch, P. J. 2024-12-31 doi:10.1101/2024.12.30.630793 Cold Spring Harbor Laboratory Press 2024-12-31 <![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[ Receptor dimerization enables ligand discrimination through tunable response heterogeneity ]]> https://biorxiv.org/content/10.1101/2025.01.01.630981v1?rss=1 Biran, A. Antebi, Y. E. 2025-01-02 doi:10.1101/2025.01.01.630981 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Hypoxia-related immune subsets induced by Salmonella Typhi infection link early bacterial gut invasion to human infection outcomes ]]> https://biorxiv.org/content/10.1101/2025.01.08.631852v1?rss=1 Bossel Ben-Moshe, N. Hen Avivi, S. Levy Efrati, L. Vainman, L. Hill, J. OConnor, D. Verheul, M. Stockdale, L. McLean, F. Pollard, A. Avraham, R. 2025-01-10 doi:10.1101/2025.01.08.631852 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ Single-molecule assay reveals the impact of composition, RNA duplex, and inhibitors on the binding dynamics of SARS-CoV-2 polymerase complex ]]> https://biorxiv.org/content/10.1101/2025.01.10.632212v1?rss=1 Lovell, T. C. Dewling, H. A. Li, C. X. Lee, H. W. Gordon, C. J. Kocincova, D. Badmalia, M. D. Tchesnokov, E. P. Gotte, M. Cosa, G. 2025-01-11 doi:10.1101/2025.01.10.632212 Cold Spring Harbor Laboratory Press 2025-01-11 <![CDATA[ Neural correlates of approach and avoidance tendencies toward physical activity and sedentary stimuli: An fMRI study ]]> https://biorxiv.org/content/10.1101/2025.01.10.632302v1?rss=1 Cheval, B. Ceravolo, L. Igloi, K. Sander, D. Zimmermann, M. Van Ruitenbeek, P. Boisgontier, M. P. 2025-01-12 doi:10.1101/2025.01.10.632302 Cold Spring Harbor Laboratory Press 2025-01-12 <![CDATA[ How Intrinsic Neural Timescales Relate To Event-Related Activity - Key Role For Intracolumnar Connections ]]> https://biorxiv.org/content/10.1101/2025.01.10.632350v1?rss=1 Catal, Y. Wolman, A. Buccellato, A. Keskin, K. Northoff, G. 2025-01-12 doi:10.1101/2025.01.10.632350 Cold Spring Harbor Laboratory Press 2025-01-12 <![CDATA[ Specialized Molecular Pathways Drive the Formation of Light-Scattering Assemblies in Leucophores ]]> https://biorxiv.org/content/10.1101/2025.01.12.632588v1?rss=1 Barzilay, Y. Eyal, Z. Noy, Y. Varsano, N. Olender, T. Bera, S. Lerer-Goldshtein, T. Kedmi, M. Porat, Z. Pinkas, I. Levin-Zaidman, S. Dezorella, N. Gur, D. 2025-01-13 doi:10.1101/2025.01.12.632588 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ TMPRSS2-ERG confers resistance to antiandrogens: mechanism and therapeutic implications ]]> https://biorxiv.org/content/10.1101/2025.01.17.633582v1?rss=1 Sekar, A. Chatterjee, R. Selvadurai, B. R. Ray, L. Verma, A. Nataraj, N. B. Garcia, D. D. Giri, S. Genna, A. Karatekin, F. Gupta, N. Zerbib, M. Vinik, Y. Avioz, T. Weizman, E. David, E. A. Schaffer, A. Pan, Y. Huang, H. M van Weerden, W. Corey, E. Hunt, H. Greenstein, A. Blecher-Gonen, R. Oren, R. Afek, A. Amit, I. Lev, S. Ku, A. Kartal, S. R. Bright, J. T. Lis, R. L. Dahut, W. Sowalsky, A. G. Ruppin, E. Yarden, Y. 2025-01-20 doi:10.1101/2025.01.17.633582 Cold Spring Harbor Laboratory Press 2025-01-20 <![CDATA[ Rubisco is slow across the tree of life ]]> https://biorxiv.org/content/10.1101/2025.01.19.633714v1?rss=1 de Pins, B. Malbranke, C. Jablonska, J. Shmuel, A. Sharon, I. Bitbol, A.-F. Mueller-Cajar, O. Noor, E. Milo, R. 2025-01-22 doi:10.1101/2025.01.19.633714 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Exploring GPCR-mediated optogenetic modulation of seizure network in a pig model of Temporal Lobe Epilepsy ]]> https://biorxiv.org/content/10.1101/2025.01.23.634545v1?rss=1 Chang, S.-y. Bar-Or, K. L. Mivalt, F. Maltais, D. Kfir, Y. Kim, J. Kim, I. Hershko, M. Daily, J. Swissa, E. Levi, O. Yizhar, O. Eldar, Y. Worrell, G. 2025-01-23 doi:10.1101/2025.01.23.634545 Cold Spring Harbor Laboratory Press 2025-01-23 <![CDATA[ ResolVI - addressing noise and bias in spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.01.20.634005v1?rss=1 Ergen, C. Yosef, N. 2025-01-24 doi:10.1101/2025.01.20.634005 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ BAHCC1 promotes gene expression in neuronal cells by antagonizing SIN3A-HDAC1 ]]> https://biorxiv.org/content/10.1101/2025.01.24.634719v1?rss=1 Monziani, A. Ben-Tov Perry, R. Hezroni, H. Ulitsky, I. 2025-01-24 doi:10.1101/2025.01.24.634719 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Distal mutations in a designed retro-aldolase alter loop dynamics to shift and accelerate the rate-limiting step ]]> https://biorxiv.org/content/10.1101/2025.01.26.634918v1?rss=1 Hunt, S. E. Klaus, C. John, A. E. Zarifi, N. Martinez, A. Feixas, F. Garcia-Borras, M. Thompson, M. C. Chica, R. A. 2025-01-26 doi:10.1101/2025.01.26.634918 Cold Spring Harbor Laboratory Press 2025-01-26 <![CDATA[ Avoidance of pyroptosis accounts for the relatively high metastatic potential observed in early hybrid EMT states ]]> https://biorxiv.org/content/10.1101/2025.01.26.634904v1?rss=1 Verma, A. Genna, A. Vinik, Y. Nataraj, N. B. Abedrabbo, M. Selvadurai, B. R. Bhandari, T. Aharoni, N. Ramesh, P. Boguslavski, B. Drago, D. Salame, T. M. Prior, A. Levin, Y. Weizman, E. Zhu, R. Caldas, C. Rueda, O. M. Lev, S. Yarden, Y. 2025-01-27 doi:10.1101/2025.01.26.634904 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ Customizing the Structure of a Minimal TIM Barrel to Craft a De Novo Enzyme ]]> https://biorxiv.org/content/10.1101/2025.01.28.635154v1?rss=1 1,600-fold to 32,000 M-{superscript 1} s-{superscript 1}. These results demonstrate that de novo TIM barrels can be endowed with substrate binding pockets supporting efficient catalytic function, establishing a platform for building enzymes on demand from minimal protein scaffolds. ]]> Beck, J. Smith, B. J. Zarifi, N. Freund, E. Chica, R. A. Hoecker, B. 2025-01-29 doi:10.1101/2025.01.28.635154 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ Visualizing sub-organellar lipid distribution using correlative light and electron microscopy ]]> https://biorxiv.org/content/10.1101/2025.01.28.635245v1?rss=1 Lennartz, H. M. Khan, S. Böhlig, K. Leng, W. Elsner, F. Scher, N. Wilsch-Bräuninger, M. Avinoam, O. Nadler, A. 2025-01-29 doi:10.1101/2025.01.28.635245 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ HIF1α gates tendon response to overload and drives tendinopathy independently of vascular recruitment ]]> https://biorxiv.org/content/10.1101/2025.02.02.635939v1?rss=1 Moschini, G. Mohanan, A. G. Niewczas, I. S. Taylor, D. E. Jaeger, P. K. Hussien, A. A. Wunderli, S. L. Baumberger, O. Wolleb, M. Niederoest, B. Bollhalder, M. Ardicoglu, R. Turiel, G. Masschelein, E. Morice, S. Ardiles, S. Mous, L. Aronoff, M. R. Hilbe, M. Selman, F. Wieser, K. Fucentese, S. F. Passini, F. S. Blache, U. Surdez, D. Wennemers, H. Clark, J. Elewaut, D. De Bock, K. Snedeker, J. G. 2025-02-03 doi:10.1101/2025.02.02.635939 Cold Spring Harbor Laboratory Press 2025-02-03 <![CDATA[ Pupillometry Reveals Autonomic Adjustments During Diving Reflex in Face Immersion Apnea ]]> https://biorxiv.org/content/10.1101/2025.01.31.635967v1?rss=1 0.25 Hz) occurs, together with an increased entropy, contrary to the remaining conditions. This indicates a shift in autonomic balance and an increased complexity of pupil fluctuations during the diving reflex. Our findings present pupil dynamics as a valuable entry point to the exploration of autonomic adjustments for this reflex. ]]> Rizzuto, V. Montanari, R. Mesin, L. Bortolozzo-Gleich, H. Laurino, M. Bonneh, Y. Yellin, D. Laganovska, G. Vanags, J. Gemignani, A. 2025-02-06 doi:10.1101/2025.01.31.635967 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ Poly-L-Ornithine Coated Plant Scaffolds Support Motor Recovery in Rats after Traumatic Spinal Cord Injury ]]> https://biorxiv.org/content/10.1101/2025.02.05.636658v1?rss=1 Couvrette, L. Walker, K. Bayat, A. Modulevsky, D. Laliberte, A. Cuerrier, C. Leblanc Latour, M. Hickey, R. Boudria, R. Monty, R. Obhi, R.-J. Shore, I. Galuta, A. Tsai, E. Bui, T. Pelling, A. E. 2025-02-08 doi:10.1101/2025.02.05.636658 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ The creation and validation of a fully animal component-free media for select adherent cell types ]]> https://biorxiv.org/content/10.1101/2025.02.05.636679v1?rss=1 Mogilever, N. B. Godin Page, M.-H. Solola, A. Pelling, A. E. 2025-02-08 doi:10.1101/2025.02.05.636679 Cold Spring Harbor Laboratory Press 2025-02-08 <![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[ Duplications in the Chlorophyll a oxygenase (CAO) gene across the Viridiplantae ]]> https://biorxiv.org/content/10.1101/2025.02.10.637544v1?rss=1 Poirier, M. C. Wright, R. Cvetkovska, M. 2025-02-11 doi:10.1101/2025.02.10.637544 Cold Spring Harbor Laboratory Press 2025-02-11 <![CDATA[ Time-to-onset and temporal dynamics of EEG during breath-watching meditation ]]> https://biorxiv.org/content/10.1101/2025.02.11.637771v1?rss=1 Malipeddi, S. Sasidharan, A. Venugopal, R. Tewarie, P. K. B. P.N., R. Northoff, G. Laureys, S. Subramaniam, B. Kutty, B. M. 2025-02-12 doi:10.1101/2025.02.11.637771 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Identification of polyphosphate-binding proteins in E. coli uncovers targets involved in translation control and ribosome biogenesis ]]> https://biorxiv.org/content/10.1101/2025.02.12.637445v1?rss=1 Baijal, K. Kore, B. Abramchuck, I. Denoncourt, A. Han, S. Simms, A. Dagenais, A. Long, A. R. Rudner, A. D. Lavallee-Adam, M. Gray, M. J. Downey, M. 2025-02-14 doi:10.1101/2025.02.12.637445 Cold Spring Harbor Laboratory Press 2025-02-14 <![CDATA[ Systematic Metaproteomics Mapping Reveals Functional and Ecological Landscapes of Human Gut Microbiota Responses to Therapeutic Drugs ]]> https://biorxiv.org/content/10.1101/2025.02.13.637346v1?rss=1 Li, L. Simopoulos, C. M. A. Mayne, J. Ning, Z. Zhang, X. Hamada, M. Butcher, J. Serrana, J. M. Wang, L. Cheng, K. M. Qin, H. Walker, K. ZHANG, X. Stintzi, A. Figeys, D. 2025-02-14 doi:10.1101/2025.02.13.637346 Cold Spring Harbor Laboratory Press 2025-02-14 <![CDATA[ Encoded and non-genetic alternative protein variants expand human functional proteome ]]> https://biorxiv.org/content/10.1101/2025.02.17.638604v1?rss=1 Tretyachenko, V. Leiman, T. Dahan, O. Asraf, O. Dahary, D. Pilpel, Y. T. 2025-02-17 doi:10.1101/2025.02.17.638604 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ Cold-induced nucleosome dynamics linked to silencing of Arabidopsis FLC ]]> https://biorxiv.org/content/10.1101/2025.02.17.638618v1?rss=1 Montez, M. Zhu, D. Huertas, J. Maristany, M. J. Rutjens, B. Nielsen, M. L. Collepardo-Guevara, R. Dean, C. 2025-02-20 doi:10.1101/2025.02.17.638618 Cold Spring Harbor Laboratory Press 2025-02-20 <![CDATA[ A spatial transcriptomics atlas of live donors reveals unique zonation patterns in the healthy human liver ]]> https://biorxiv.org/content/10.1101/2025.02.22.639181v1?rss=1 Yakubovsky, O. Afriat, A. Egozi, A. Bahar Halpern, K. Barkai, T. Harnik, Y. Korem Kohanim, Y. Novoselsky, R. Golani, O. Goliand, I. Addadi, Y. Kedmi, M. Keren-Shaul, H. Fellus-Alyagor, L. Hirsch, D. Mayer, C. Peri, R. Pencovich, N. Timucin, T. Nachmany, I. Itzkovitz, S. 2025-02-23 doi:10.1101/2025.02.22.639181 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ Latitudinal phylogenetic and diversity gradients are explained by a tropical-temperate transitional region ]]> https://biorxiv.org/content/10.1101/2025.02.23.639794v1?rss=1 Lerner, D. Weir, J. T. Klein, T. Greenbaum, G. 2025-02-24 doi:10.1101/2025.02.23.639794 Cold Spring Harbor Laboratory Press 2025-02-24 <![CDATA[ Corrections in single cell migration path in vivo are controlled by pulses in polar Rac1 activation ]]> https://biorxiv.org/content/10.1101/2025.02.24.639819v1?rss=1 Hoffmann, D. Agranov, T. Kuehl, L. Simons, B. D. Gov, N. Raz, E. 2025-02-26 doi:10.1101/2025.02.24.639819 Cold Spring Harbor Laboratory Press 2025-02-26 <![CDATA[ A novel integrated framework to identify and characterize regional-scale pest insect dispersal ]]> https://biorxiv.org/content/10.1101/2025.02.26.640127v1?rss=1 Dargent, F. Reich, M. S. Miller, M. Studens, K. Benvidi, N. Perrault, K. Aibueku, J. Holmes, B. Bataille, C. Candau, J.-N. 2025-03-01 doi:10.1101/2025.02.26.640127 Cold Spring Harbor Laboratory Press 2025-03-01 <![CDATA[ Notch-mediated regulation of β-Catenin-TCF activity instructs anteroposterior neuron positioning in C. elegans ]]> https://biorxiv.org/content/10.1101/2025.03.02.641079v1?rss=1 Chan, W. Justin, E. Roenspies, T. Rumley, J. D. Murray, J. I. Colavita, A. 2025-03-03 doi:10.1101/2025.03.02.641079 Cold Spring Harbor Laboratory Press 2025-03-03 <![CDATA[ Differential effects of immobilized CCL21 and ICAM1 on TILs with distinct expansion properties ]]> https://biorxiv.org/content/10.1101/2025.03.02.641030v1?rss=1 Yado, S. Zoabi, R. Brezinger-Dayan, K. Albeck, S. Unger, T. Meiron, M. Nahmad, A. D. Gilat, A. T. Besser, M. J. Geiger, B. 2025-03-10 doi:10.1101/2025.03.02.641030 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ A pharmacological modality to sequester homomeric proteins ]]> https://biorxiv.org/content/10.1101/2025.03.05.641597v1?rss=1 Livnah, E. Suss, O. Rogel, A. Gilat, A. Abdan, Y. Villegas, J. D. Tivon, B. Albeck, S. Unger, T. Golani, O. Goliand, I. Margulies, D. Levy, E. D. London, N. 2025-03-11 doi:10.1101/2025.03.05.641597 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Protein massively parallel binding assay reveals transcription factor binding determinants ]]> https://biorxiv.org/content/10.1101/2025.03.05.641616v1?rss=1 Lupo, O. Brodsky, S. Jana Lang, T. Manadre, W. Valinsky, G. Navon, Y. Mindel, V. Barkai, N. 2025-03-11 doi:10.1101/2025.03.05.641616 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Peptide abundance correlations in metaproteomics enhance taxonomic and functional analysis of the human gut microbiome ]]> https://biorxiv.org/content/10.1101/2025.03.13.642886v1?rss=1 Sun, Z. Ning, Z. Wu, Q. Li, L. Doxey, A. C. Figeys, D. 2025-03-13 doi:10.1101/2025.03.13.642886 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Millisecond bidirectional protein translocation by a HSP100 machine ]]> https://biorxiv.org/content/10.1101/2025.03.13.643017v1?rss=1 Casier, R. Levy, D. Riven, I. Barak, Y. Haran, G. 2025-03-15 doi:10.1101/2025.03.13.643017 Cold Spring Harbor Laboratory Press 2025-03-15 <![CDATA[ SpikeMAP: An unsupervised spike sorting pipeline for cortical excitatory and inhibitory neurons in high-density multielectrode arrays with ground-truth validation ]]> https://biorxiv.org/content/10.1101/2025.03.14.643403v1?rss=1 Giraud, E. Lynn, M. Vincent-Lamarre, P. Beique, J.-C. Thivierge, J.-P. 2025-03-15 doi:10.1101/2025.03.14.643403 Cold Spring Harbor Laboratory Press 2025-03-15 <![CDATA[ Targeted Protein Degradation of NUDT5 Reveals an Unexpected Non-Enzymatic Role in 6-Thioguanine-Mediated Toxicity ]]> https://biorxiv.org/content/10.1101/2025.03.16.643557v1?rss=1 Marques, A.-S. M. C. Bauer, L. G. Nguyen, T.-A. Orta, A. G. Venne, J.-L. Cheng, C. Balikci, E. Tivon, B. London, N. Kubicek, S. Huber, K. V. M. 2025-03-17 doi:10.1101/2025.03.16.643557 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ A Novel Algorithm for the Harmonization of Pan-cancer Proteomics ]]> https://biorxiv.org/content/10.1101/2025.03.17.642820v1?rss=1 Simchi, N. Givton, O. Rinberg, J. Shtrikman, A. Geiger, T. Nesvizhskii, A. I. Seger, E. Pevzner, K. 2025-03-17 doi:10.1101/2025.03.17.642820 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[ MIR192 Upregulates GLP-1 Receptor and Improves Statin-Induced Impairment of Insulin Secretion ]]> https://biorxiv.org/content/10.1101/2025.03.18.643960v1?rss=1 Kuang, Y.-L. Locatelli, C. A. A. Qin, Y. Zhang, Y. Theusch, E. Munoz-Howell, A. Sanchez, G. Lu, M. Nguyen, M.-A. Yalamanchili, T. Wang, X. Nalula, G. Mattis, A. N. Oni-Orisan, A. Iribarren, C. Krauss, R. M. Mulvihill, E. E. Medina, M. W. 2025-03-19 doi:10.1101/2025.03.18.643960 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ State-of-the-art covalent virtual screening with AlphaFold3 ]]> https://biorxiv.org/content/10.1101/2025.03.19.642201v1?rss=1 London, N. Shamir, Y. 2025-03-19 doi:10.1101/2025.03.19.642201 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ The prefusion structure of the HERV-K (HML-2) Env spike complex ]]> https://biorxiv.org/content/10.1101/2025.03.19.644160v1?rss=1 Shaked, R. Katz, M. Cohen-Dvashi, H. Diskin, R. 2025-03-19 doi:10.1101/2025.03.19.644160 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ Early-life gut microbiome and stress-axis perturbations dysregulate systemic, mucosal, and brain immunity ]]> https://biorxiv.org/content/10.1101/2025.03.19.644259v1?rss=1 Arrieta, M. C. Ortega, V. A. Asbury, M. R. Mackenzie, C. Vicentini, F. A. Hafeez, B. Duan, H. Mercer, E. M. vanTilburg Bernardes, E. Kalbfleisch, K. Samara, J. Pettersen, V. K. Figeys, D. Sharkey, K. 2025-03-20 doi:10.1101/2025.03.19.644259 Cold Spring Harbor Laboratory Press 2025-03-20 <![CDATA[ The positionally conserved long non-coding RNA DANCR is an essential regulator of zebrafish development and a human melanoma oncogene ]]> https://biorxiv.org/content/10.1101/2025.03.21.644561v1?rss=1 Jones, S. M. E. Coe, E. A. Shapiro, M. Ulitsky, I. Kelsh, R. N. Vance, K. W. 2025-03-23 doi:10.1101/2025.03.21.644561 Cold Spring Harbor Laboratory Press 2025-03-23 <![CDATA[ Translating the Post-Mortem Brain Multi-Omics Molecular Taxonomy of Alzheimer's Dementia to Living Humans ]]> https://biorxiv.org/content/10.1101/2025.03.20.644323v1?rss=1 Iturria-Medina, Y. Poole, V. N. Zammit, A. R. de Paiva Lopes, K. Vialle, R. A. Yu, L. Tasaki, S. Batalha, C. Hong, J. H. Sanchez-Rodriguez, L. Geddes, M. R. Abadir, P. Ortlund, E. A. De Jager, P. Menon, V. Schnaider Beeri, M. Buchman, A. S. Levin, Y. Morgenstern, D. Schneider, J. A. Kaddurah-Daouk, R. Wyss-Coray, T. Seyfried, N. Poulakis, K. Rosa-Neto, P. Wang, Y. Bennett, D. A. 2025-03-24 doi:10.1101/2025.03.20.644323 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ Temporal coding enables hyperacuity in event based vision ]]> https://biorxiv.org/content/10.1101/2025.03.25.645190v1?rss=1 Assa, E. Rivkind, A. Kreiserman, M. Khan, F. S. Khan, S. Ahissar, E. 2025-03-26 doi:10.1101/2025.03.25.645190 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ ELIP is preferentially expressed in stomatal guard cells and has a role in stomatal opening upon transition to light ]]> https://biorxiv.org/content/10.1101/2025.03.26.645183v1?rss=1 Bednarczyk, D. Cohen, M. Kamara, I. Tiwari, V. Itafa, E. A. Regon, P. Savidor, A. Yadav, D. Belausov, E. Charuvi, D. 2025-03-27 doi:10.1101/2025.03.26.645183 Cold Spring Harbor Laboratory Press 2025-03-27 <![CDATA[ c-Abl Phosphorylates Plk1 in Facilitating DNA Damage-Induced G2/M Checkpoint Release with a Trade-off of Micronuclei Formation ]]> https://biorxiv.org/content/10.1101/2025.03.27.645704v1?rss=1 Meltser, V. Ben-Yehoyada, M. Adler, J. Reuven, N. Shaul, Y. 2025-03-28 doi:10.1101/2025.03.27.645704 Cold Spring Harbor Laboratory Press 2025-03-28 <![CDATA[ Modeling the Controls on Microbial Iron and Manganese Reduction in Methanic Sediments ]]> https://biorxiv.org/content/10.1101/2025.03.30.646147v1?rss=1 Neumann Wallheimer, R. Halevy, I. Sivan, O. 2025-03-31 doi:10.1101/2025.03.30.646147 Cold Spring Harbor Laboratory Press 2025-03-31 <![CDATA[ The molecular and cellular interplay between the osteopetrosis-associated proteins SNX10, OSTM1, and CLC-7 during osteoclastogenesis ]]> https://biorxiv.org/content/10.1101/2025.03.31.646258v1?rss=1 Reuven, N. Winograd-Katz, S. E. Barnea-Zohar, M. Pri-Or, A. Levin, Y. Vacher, J. Geiger, B. Elson, A. 2025-03-31 doi:10.1101/2025.03.31.646258 Cold Spring Harbor Laboratory Press 2025-03-31 <![CDATA[ Two opposing redox signals mediated by 2-Cys peroxiredoxin shape the redox proteome during photosynthetic induction ]]> https://biorxiv.org/content/10.1101/2025.04.02.646757v1?rss=1 Doron, S. Lampl, N. Savidor, A. Pri-Or, A. Katina, C. Cejudo, F. J. Levin, Y. Rosenwasser, S. 2025-04-02 doi:10.1101/2025.04.02.646757 Cold Spring Harbor Laboratory Press 2025-04-02 <![CDATA[ Deciphering the role of the lncRNA TRIBAL in hepatocyte models ]]> https://biorxiv.org/content/10.1101/2025.04.02.646870v1?rss=1 Soubeyrand, S. Lau, P. McPherson, R. 2025-04-03 doi:10.1101/2025.04.02.646870 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Neural stem cell epigenomes and fate bias are temporally coordinated during corticogenesis ]]> https://biorxiv.org/content/10.1101/2025.04.03.647013v1?rss=1 Shapira, Y. Noack, F. Vangelisti, S. Chong, F. Lifshitz, A. Tanay, A. Bonev, B. 2025-04-04 doi:10.1101/2025.04.03.647013 Cold Spring Harbor Laboratory Press 2025-04-04 <![CDATA[ EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology ]]> https://biorxiv.org/content/10.1101/2025.04.08.647803v1?rss=1 Monziani, A. Unfried, J. P. Cvetanovic, T. Ulitsky, I. 2025-04-09 doi:10.1101/2025.04.08.647803 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ Langerhans Cells Regulate Tongue Intraepithelial Innervation in a Microbiota- and Age-Dependent Manner ]]> https://biorxiv.org/content/10.1101/2025.04.03.647024v1?rss=1 Netanely, Y. Saba, Y. Naamneh, R. Yacoub, S. Jaber, Y. Raviv, A. Eli-Berchoer, L. Shapiro, H. Elinav, E. Wilensky, A. Clausen, B. E. Hovav, A.-H. 2025-04-10 doi:10.1101/2025.04.03.647024 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ A structural basis for chaperone repression of stress signalling from the endoplasmic reticulum ]]> https://biorxiv.org/content/10.1101/2025.04.14.648677v1?rss=1 Neidhardt, L. Tung, J. Kuchersky, M. Milczarek, J. Kargas, V. Stott, K. Rosenzweig, R. S. Ron, D. Yan, Y. 2025-04-14 doi:10.1101/2025.04.14.648677 Cold Spring Harbor Laboratory Press 2025-04-14 <![CDATA[ A Rosella-PLIN2 Knock-in Mouse Reveals Lipophagy and Immunometabolic Interplay in Atherosclerosis ]]> https://biorxiv.org/content/10.1101/2025.04.15.647781v1?rss=1 Laval, T. Joyce, N. Boucher, D. Rochon, V. Emerton, C. Dharia, M. Robichaud, S. Lorant, V. Nguyen, M.-A. Geoffrion, M. Rayner, K. J. Gibbings, D. Nutter, L. M. J. Russell, R. C. Ouimet, M. 2025-04-16 doi:10.1101/2025.04.15.647781 Cold Spring Harbor Laboratory Press 2025-04-16 <![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[ Heritability of human lifespan is about 50% when confounding factors are addressed ]]> https://biorxiv.org/content/10.1101/2025.04.20.649385v1?rss=1 Shenhar, B. Pridham, G. de Oliveira, T. L. Yang, Y. Raz, N. Deelen, J. Hagg, S. Alon, U. 2025-04-21 doi:10.1101/2025.04.20.649385 Cold Spring Harbor Laboratory Press 2025-04-21 <![CDATA[ Synaptic Encoding of Time in Working Memory ]]> https://biorxiv.org/content/10.1101/2025.04.21.649874v1?rss=1 Mongillo, G. Misha Tsodyks, M. 2025-04-23 doi:10.1101/2025.04.21.649874 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ TDP-43 toxic gain of function links ALS/FTLD-TDP and Alzheimer's Disease through splicing ]]> https://biorxiv.org/content/10.1101/2025.04.20.648873v1?rss=1 Van Zuiden, W. Meimoun, T. D. Bar, C. Siany, A. Moshe, L. Yacovzada, N. S. Weizman, E. Neumann, M. Buchman, A. S. Wang, Y. Bennett, D. A. Glass, J. D. G. D. Trautwig, A. N. Seyfried, N. Cooper-Knock, J. Hornstein, E. 2025-04-24 doi:10.1101/2025.04.20.648873 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ In Vitro and Viral Evolution Convergence Reveal the Selective Pressures Driving Omicron Emergence ]]> https://biorxiv.org/content/10.1101/2025.04.23.650148v1?rss=1 Shoshany, A. Tian, R. Blanco, M. P. Hruska, A. Konar, A. Baxova, K. Zoler, E. Mokrejs, M. Schreiber, G. Zahradnik, J. 2025-04-24 doi:10.1101/2025.04.23.650148 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ The essential co-chaperone Sgt1 regulates client dwell time in the Hsp90 chaperone cycle ]]> https://biorxiv.org/content/10.1101/2025.04.24.648904v1?rss=1 Engler, S. Delhommel, F. Dodt, C. Lopez, A. Faust, O. Napolitano, V. Popowicz, G. M. Rosenzweig, R. Sattler, M. Buchner, J. 2025-04-24 doi:10.1101/2025.04.24.648904 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Non-duality in brain and experience of advanced meditators - Key role for Intrinsic Neural Timescales ]]> https://biorxiv.org/content/10.1101/2025.04.21.649758v1?rss=1 Malipeddi, S. Sasidharan, A. Ventura, B. Venugopal, R. Bauer, C. C. Tewarie, P. K. B. Ravindra, P. N. Mehrotra, S. John, J. P. Subramaniam, B. Laureys, S. Kutty, B. M. Northoff, G. 2025-04-29 doi:10.1101/2025.04.21.649758 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ A large global soil carbon sink informed by repeated soil samplings ]]> https://biorxiv.org/content/10.1101/2025.04.25.650716v1?rss=1 Jia, R. Fricke, E. Malhotra, A. Bar-On, Y. M. Deng, J. Pineiro, G. Bazzoni, B. Alvarez, R. Findlay, N. te Beest, M. Zhou, Y. Boutton, T. W. Dar, J. A. Kothandaraman, S. MacDougall, A. S. Eisenhauer, N. Peri, P. L. Zheng, J. Power, S. A. Reed, S. C. Macek, P. Haider, S. Sitch, S. O'Sullivan, M. Friedlingstein, P. Bond-Lamberty, B. Hungate, B. Jackson, R. B. Subramanian, M. Patel, K. Terrer, C. 2025-04-29 doi:10.1101/2025.04.25.650716 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Mapping the transcriptional landscape of algal resistance to viral infection reveals a core expression program ]]> https://biorxiv.org/content/10.1101/2025.04.29.650402v1?rss=1 Shaler, T. Fromm, A. Schatz, D. Ben-dor, S. Feldmesser, E. Vardi, A. 2025-04-29 doi:10.1101/2025.04.29.650402 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ A Conserved Venous Remodeling Program Governs Inferior Vena Cava Formation in Zebrafish ]]> https://biorxiv.org/content/10.1101/2025.04.28.650985v1?rss=1 Lambiase, G. Moshe, N. Raanan, C. Das, R. N. Yaniv, K. 2025-05-01 doi:10.1101/2025.04.28.650985 Cold Spring Harbor Laboratory Press 2025-05-01 <![CDATA[ Postoperative Stress Accelerates Atherosclerosis through Inflammatory Remodeling of the HDL Proteome and Impaired Reverse Cholesterol Transport ]]> https://biorxiv.org/content/10.1101/2025.05.02.651357v1?rss=1 Boucher, D. M. Rochon, V. Laval, T. Lorant, V. Carter, A. Emerton, C. Joyce, N. Vinayak, N. Scaffidi, M. Auer, R. C. Gordon, S. M. Ouimet, M. 2025-05-04 doi:10.1101/2025.05.02.651357 Cold Spring Harbor Laboratory Press 2025-05-04 <![CDATA[ Context-dependent spatial multicellular network motifs for single-cell spatial biology ]]> https://biorxiv.org/content/10.1101/2025.05.05.651422v1?rss=1 Zamir, A. Amitay, Y. Tamir, Y. Keren, L. Zaritsky, A. 2025-05-07 doi:10.1101/2025.05.05.651422 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Algal Betaine Triggers Bacterial Hydrogen Peroxide Production that Promotes Algal Demise ]]> https://biorxiv.org/content/10.1101/2025.05.07.652642v1?rss=1 Narvaez-Barragan, D. A. Yuda, L. Lipsman, V. Yahalomi, D. Malitsky, S. Segev, E. 2025-05-07 doi:10.1101/2025.05.07.652642 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ CellTune: An integrative software for accurate cell classification in spatial proteomics ]]> https://biorxiv.org/content/10.1101/2025.05.05.652215v1?rss=1 Bussi, Y. Shainshein, D. Ovits, E. Posner, S. Azulay, N. Maimon, N. Keidar Haran, T. Ben-uri, R. Brown, C. Schuldiner, N. Yaniv, E. Van Valen, D. A. Milo, I. Elhanani, O. Schiemann, R. Keren, L. 2025-05-09 doi:10.1101/2025.05.05.652215 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Pus7 mutation links tRNA dysregulation to aggressive behavior through activation of the integrated stress response and glycolytic reprogramming ]]> https://biorxiv.org/content/10.1101/2025.05.12.653498v1?rss=1 Stock, M. Guillen-Angel, M. Witzenberger, M. Nowak, J. Biela, A. Chramiec-Glabik, A. Mariano, V. Dreos, R. Sklias, A. Quadroni, M. Brummer, A. Gallart-Ayala, H. Ivanisevic, J. Guex, N. Kleenman, L. Leidel, S. Helm, M. Bagni, C. Glatt, S. Gatfield, D. Schwartz, S. Roignant, J.-Y. 2025-05-12 doi:10.1101/2025.05.12.653498 Cold Spring Harbor Laboratory Press 2025-05-12 <![CDATA[ Parkin-dependent ubiquitination of TAX1BP1 directs efficient autophagic removal of defective mitochondria ]]> https://biorxiv.org/content/10.1101/2025.05.16.654474v1?rss=1 Lechado-Terradas, A. Lemke, B. Zittlau, K. Kahle, P. J. Macek, B. 2025-05-19 doi:10.1101/2025.05.16.654474 Cold Spring Harbor Laboratory Press 2025-05-19 <![CDATA[ Rescuing Ischemic Brain Injury by Rewiring Mitochondrial Electron Flow ]]> https://biorxiv.org/content/10.1101/2025.05.19.650489v1?rss=1 Yoval-Sanchez, B. Guerrero, I. Sosunov, S. Chen, Q. Ansari, F. Siragusa, M. Konrad, C. Niatsetskaya, Z. Stepanova, A. Starkov, A. Khruschev, S. Magrane, J. Nikitina, A. A. Bereshchenko, O. Witting, I. Zhou, P. Zhou, L. Szibor, M. Manfredi, G. Gross, S. Ten, V. Galkin, A. 2025-05-23 doi:10.1101/2025.05.19.650489 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Intrinsically disordered regions facilitate Msn2 target search to drive promoter selectivity ]]> https://biorxiv.org/content/10.1101/2025.05.23.654710v1?rss=1 Strugo, N. Burstein, C. Hossain, S. S. Nago, N. Khamis, H. Kaplan, A. 2025-05-27 doi:10.1101/2025.05.23.654710 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Comparative genomic analysis of Cluster AZ Arthrobacter phages ]]> https://biorxiv.org/content/10.1101/2025.05.26.655371v1?rss=1 Freise, A. C. Furlong, K. P. Klyczek, K. K. Beyer, A. R. Chong, R. A. Edgington, N. P. Gibb, B. P. Swerdlow, S. J. Bendele, M. G. Cobb, I. D. Mitchell, Z. J. Cresawn, S. G. Garcia Costas, A. M. Rudner, A. D. 2025-05-27 doi:10.1101/2025.05.26.655371 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Evaluation of network inference algorithms for derivation of metabolic relationships from lipidomic and metabolomic datasets ]]> https://biorxiv.org/content/10.1101/2025.05.23.654112v1?rss=1 Archinuk, F. Greenyer, H. Stege, U. Bennett, S. A. L. Cuperlovic-Culf, M. Jabbari, H. 2025-05-28 doi:10.1101/2025.05.23.654112 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Actin Networking Collapse Under STAT5A Deficiency Drives Mitochondrial Dysfunction and Autocrine IFN-beta Production ]]> https://biorxiv.org/content/10.1101/2025.05.26.656095v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@1cee57aorg.highwire.dtl.DTLVardef@3be0cdorg.highwire.dtl.DTLVardef@123ed52org.highwire.dtl.DTLVardef@1b1bfcc_HPS_FORMAT_FIGEXP M_FIG C_FIG Key pointsSTAT5A deficiency disrupts cytoskeletal integrity via ACTN1 loss. The disrupted actin-cytoskeleton impairs mitochondria organization, causing ROS production and DNA damage. STAT5A knockout activates cGAS-STING signaling and IFN-{beta} production. Restoring ACTN1 rescues cytoskeleton, mitochondrial function, and immune balance. ]]> Sun, B. Krishnamohan, M. Nevo, R. Zoler, E. Geiger, B. Schreiber, G. 2025-05-28 doi:10.1101/2025.05.26.656095 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Chemotaxis of branched cells in complex environments ]]> https://biorxiv.org/content/10.1101/2025.05.27.656457v1?rss=1 Liu, J. Ron, J. E. Rinaldi, G. Williantarra, I. Georgantzoglou, A. de Vries, I. Sixt, M. Sarris, M. Gov, N. 2025-05-29 doi:10.1101/2025.05.27.656457 Cold Spring Harbor Laboratory Press 2025-05-29 <![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[ scVIVA: a probabilistic framework for representation of cells and their environments in spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.06.01.657182v1?rss=1 Levy, N. Ingelfinger, F. Bakulin, A. Cinnirella, G. Boyeau, P. Nadler, B. Ergen, C. Yosef, N. 2025-06-03 doi:10.1101/2025.06.01.657182 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Non-Invasive Mechanical-Functional Analysis of Individual Liver Mitochondria by Atomic Force Microscopy ]]> https://biorxiv.org/content/10.1101/2025.06.01.657242v1?rss=1 Zorikova, E. O. Chourasia, S. Rosenhek-Goldian, I. Cohen, S. R. Nesterov, S. V. Gross, A. 2025-06-03 doi:10.1101/2025.06.01.657242 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Purinergic receptor activation rectifies autism-associated endothelial dysfunction ]]> https://biorxiv.org/content/10.1101/2025.06.02.657522v1?rss=1 Ouellette, J. Warsi, S. Romero, P. Khare, P. Naz, S. Aubert-Tandon, L. Pileggi, C. Yandiev, S. Freitas-Andrade, M. Comin, C. H. Harper, M.-E. Manickam, D. S. Dabertrand, F. Saghatelyan, A. Lacoste, B. 2025-06-03 doi:10.1101/2025.06.02.657522 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Persistent ECM Scarring Reprograms Intestinal Stem Cells to Drive Chronic Inflammation ]]> https://biorxiv.org/content/10.1101/2025.06.08.658481v1?rss=1 Adir, I. Sochen, C. Menachem, A. H. Lebon, S. Toval, B. Holiar, V. Davidzohn, N. Salame, T. M. Rosenhek-Goldian, I. Savickas, S. Sabino, F. auf dem Keller, U. Biton, M. Sagi, I. 2025-06-09 doi:10.1101/2025.06.08.658481 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Metacaspases mediate thermotolerance of diatoms following marine heat waves ]]> https://biorxiv.org/content/10.1101/2025.06.09.658587v1?rss=1 Sadeh, M. Schatz, D. Ben-Dor, S. Mizrachi, A. Graff van Creveld, S. Zafrin, A. Vardi, A. 2025-06-09 doi:10.1101/2025.06.09.658587 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Pcbp1 orchestrates amino acid metabolism burst during the naive-to-primed pluripotency transition ]]> https://biorxiv.org/content/10.1101/2025.06.07.658314v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@1e17b48org.highwire.dtl.DTLVardef@64e940org.highwire.dtl.DTLVardef@10d6b00org.highwire.dtl.DTLVardef@1ec0d23_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Bakhmet, E. I. Potapenko, E. V. Shuvalov, O. Y. Lobov, A. A. Repkin, E. A. Vorobyeva, N. E. Korablev, A. N. Zinovyeva, A. S. Kuzmin, A. A. Aksenov, N. D. Kopylov, A. T. Wu, G. Schoeler, H. R. Tomilin, A. N. 2025-06-10 doi:10.1101/2025.06.07.658314 Cold Spring Harbor Laboratory Press 2025-06-10 <![CDATA[ Hyperpolarization activated cation channel mediated intrinsic plasticity changes underlie the malleability of with-in cell-type electrophysiological heterogeneity ]]> https://biorxiv.org/content/10.1101/2025.06.09.658517v1?rss=1 Chameh, H. M. Falby, M. Yang, Y. Movahed, M. Arbabi, K. Sarathy, C. Tripathy, S. J. Zhang, L. Lefebvre, J. Valiante, T. A. 2025-06-10 doi:10.1101/2025.06.09.658517 Cold Spring Harbor Laboratory Press 2025-06-10 <![CDATA[ Open-science discovery of DNDI-6510, a compound that addresses genotoxic and metabolic liabilities of the COVID Moonshot SARS-CoV-2 Mpro lead inhibitor ]]> https://biorxiv.org/content/10.1101/2025.06.16.660018v1?rss=1 Griffen, E. J. Fearon, D. McGovern, B. L. Koekemoer, L. Balcomb, B. H. Szommer, T. Fate, G. Robinson, R. P. Lefker, B. A. Duberstein, S. Lahav, N. Braillard, S. Vangeel, L. Laporte, M. Charvillon, F. B. MacLeod, A. K. Wells, A. Garner, P. Knight, R. Rees, P. Simon, A. Jochmans, D. Neyts, J. Read, K. D. Barr, H. Robinson, M. Lee, A. A. London, N. Chodera, J. von Delft, F. White, K. M. Perry, B. Sjo, P. von Delft, A. R. 2025-06-17 doi:10.1101/2025.06.16.660018 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Dynamic growth trajectories distinguish bacteriostatic and bactericidal antibiotics at subinhibitory concentrations ]]> https://biorxiv.org/content/10.1101/2025.06.14.659040v1?rss=1 Vaisbourd, E. Glass, D. S. Yang, Y. Mayo, A. Bren, A. Alon, U. 2025-06-19 doi:10.1101/2025.06.14.659040 Cold Spring Harbor Laboratory Press 2025-06-19 <![CDATA[ Metabolite correlation networks reveal complex phenotypes of adaptation-driving mutations ]]> https://biorxiv.org/content/10.1101/2025.06.17.660120v1?rss=1 Samuel, S. Jasinska, W. Sternlicht, E. Nikelshparg, M. Kleiner, D. Pilosof, S. Bershtein, S. 2025-06-20 doi:10.1101/2025.06.17.660120 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Discovery of orally bioavailable Zika and West Nile Virus antiviral compounds targeting the NS2B-NS3 protease ]]> https://biorxiv.org/content/10.1101/2025.06.19.660642v1?rss=1 Kenton, N. T. Barr, H. Cherepakha, A. Coelmont, L. Collard, C. Cousins, D. Davies, G. H. M. Degtyarenko, O. Dirksen, A. Elbrecht, D. Fearon, D. Gayvert, J. Griffen, E. Jochmans, D. Kaptein, S. Kliatskiy, P. Kochetkov, A. Kordubailo, M. Lahav, N. London, N. Maas, E. Marples, P. Nady, N. Neyts, J. Nguyen, L. Ni, X. Ogorodnik, Y. Robinson, M. C. Simpson, C. T. Tarabara, I. Tkachenko, A. von Delft, A. von Delft, F. Yakymenko, O. Lee, A. A. 2025-06-20 doi:10.1101/2025.06.19.660642 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ An advanced head-to-tail mouse embryo model with hypoxia-mediated neural patterning ]]> https://biorxiv.org/content/10.1101/2025.06.17.660116v1?rss=1 Balaskas, A. Kraus, I. Ozguldez, H. O. Omgba, P. A. Buschow, R. Bolondi, A. Berlad, I. Hanna, J. H. Kretzmer, H. Bulut-Karslioglu, A. 2025-06-22 doi:10.1101/2025.06.17.660116 Cold Spring Harbor Laboratory Press 2025-06-22 <![CDATA[ Loss of CHMP2A implicates an ordered assembly of ESCRT-III proteins during cytokinetic abscission ]]> https://biorxiv.org/content/10.1101/2025.06.24.661003v1?rss=1 Kamenetsky, N. Nachmias, D. Khan, S. Avinoam, O. Hazan, I. Upcher, A. Elia, N. 2025-06-24 doi:10.1101/2025.06.24.661003 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ Comprehensive Survey of Gut Microbiome Associations with Health Conditions in the Human Phenotype Project ]]> https://biorxiv.org/content/10.1101/2025.06.26.661672v1?rss=1 Weissglas-Volkov, D. Reisner, Y. Shor, T. Diament, A. Jankelow, A. Godneva, A. Dhir, R. Segal, E. 2025-06-26 doi:10.1101/2025.06.26.661672 Cold Spring Harbor Laboratory Press 2025-06-26 <![CDATA[ Distinct sex differences in the production of steroids and neuropeptides in the adult zebrafish brain-pituitary gonadal axis ]]> https://biorxiv.org/content/10.1101/2025.06.22.660951v1?rss=1 Peng, D. Lu, C. Trudeau, V. L. 2025-06-27 doi:10.1101/2025.06.22.660951 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Sensitizing Immune-Refractory Ovarian Tumors via p53 Mutation-Tailored Immunotherapy ]]> https://biorxiv.org/content/10.1101/2025.06.23.661120v1?rss=1 Chatterjee, R. Simoni-Nieves, A. Truong, A. Lindzen, M. Ozmen, F. Cherry, C. Zwicky, P. Mukherjee, S. Selvadurai, B.-R. Salame, T. M. Gupta, N. Giri, S. Kramarski, L. Avraham, Y. Weizman, E. Ozmen, T. Noronha, A. Chakrabarti, P. Ramesh-Kumar, D. Downward, J. Dahan, R. Amit, I. Velculescu, V. Brenton, J. Mills, G. Oren, M. Yarden, Y. 2025-06-27 doi:10.1101/2025.06.23.661120 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ A Two-Phase Core-Plasma Model for Microvascular Blood Flow: Comparative Analysis of Hemodynamic Models ]]> https://biorxiv.org/content/10.1101/2025.06.25.661657v1?rss=1 Salame, M. Fenech, M. 2025-06-28 doi:10.1101/2025.06.25.661657 Cold Spring Harbor Laboratory Press 2025-06-28 <![CDATA[ Phototactic Decision-Making by Micro-Algae ]]> https://biorxiv.org/content/10.1101/2025.07.02.662716v1?rss=1 Raikwar, S. Al-Kassem, A. Gov, N. S. Pesci, A. Jeanneret, R. Goldstein, R. E. 2025-07-03 doi:10.1101/2025.07.02.662716 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Systematic DNA nicking reveals the structural logic of protein recognition ]]> https://biorxiv.org/content/10.1101/2025.06.30.662289v1?rss=1 Yao, Y. M. O'Hagan, M. P. Onoon, K. Givon, L. Hamer-Rogotner, S. Salinas, R. Kessler, N. Dym, O. Pipatpolkai, T. Schumacher, M. A. Afek, A. 2025-07-04 doi:10.1101/2025.06.30.662289 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Sequence Analysis of P4-ATPases Reveals the Structural Determinants for the Stable Monomeric P4B-ATPase Phospholipid Transporters. ]]> https://biorxiv.org/content/10.1101/2025.07.01.662597v1?rss=1 Sai, K. V. Rajan, S. A. S. Lee, J.-Y. 2025-07-04 doi:10.1101/2025.07.01.662597 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Extracellular Vesicles Mediate Glucose Regulation by GLUT4-Overexpressing Engineered Muscle Tissue in T2D Mice ]]> https://biorxiv.org/content/10.1101/2025.07.08.663248v1?rss=1 Shoyhet, H. Cohen, Y. Bachinsky, Y. H. Rosenhek-Goldian, I. Kamyshinsky, R. Hornstein, E. Levenberg, S. 2025-07-11 doi:10.1101/2025.07.08.663248 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ A Fibroblast State Choreographs an Epithelial YAP-dependent Regenerative Program Essential to (Pre)malignancy via ECM-mediated Mechanotransduction ]]> https://biorxiv.org/content/10.1101/2025.07.11.661192v1?rss=1 Pan, D. Gascard, P. Caruso, J. A. Chen-Tanyolac, C. Sangwan, V. Bertos, N. Camilleri-Broet, S. Berube, J. Oikonomopoulos, S. Strasser, M. K. Gibbs, D. L. Bons, J. Burton, J. B. Rose, J. P. Shah, S. Bai, R. Lee, S. Fels-Elliott, D. R. Miyara, S. Alon, U. Urisman, A. Ragoussis, I. Huang, S. Schilling, B. Ferri, L. E. Tlsty, T. D. 2025-07-11 doi:10.1101/2025.07.11.661192 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ Swidden pollen spectra are unique, having no modern analogues ]]> https://biorxiv.org/content/10.1101/2025.07.14.664661v1?rss=1 Ershova, E. Ponomarenko, E. Pimenov, V. 2025-07-18 doi:10.1101/2025.07.14.664661 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Pollen indicators of slash-and-burn agriculture in forest soils and peatlands: a case study of Zvenigorod biological station (Moscow region, Russia) ]]> https://biorxiv.org/content/10.1101/2025.07.14.664680v1?rss=1 Ershova, E. Pimenov, V. Ponomarenko, E. Krivokorin, I. Bakumenko, V. Krenke, N. 2025-07-18 doi:10.1101/2025.07.14.664680 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Synaptic and intrinsic membrane defects disrupt early neural network dynamics in Down syndrome ]]> https://biorxiv.org/content/10.1101/2025.07.17.665141v1?rss=1 Hannan, S. B. Alic, I. Murray, A. Kwon, J. Mortensen, M. Kang, H. J. Plecas, A. Goh, P. O'Brien, N. Naud, R. Nizetic, D. Smart, T. G. 2025-07-20 doi:10.1101/2025.07.17.665141 Cold Spring Harbor Laboratory Press 2025-07-20 <![CDATA[ Object detection through dynamic motor-sensory convergence ]]> https://biorxiv.org/content/10.1101/2025.07.16.665117v1?rss=1 Nelinger, G. Saraf-Sinik, I. Ahissar, E. 2025-07-21 doi:10.1101/2025.07.16.665117 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Active Conformations of Neuronal Na+,K+-ATPase isoforms and a Disease-Causing Mutant ]]> https://biorxiv.org/content/10.1101/2025.07.27.666930v1?rss=1 Christensen, M. E. Habeck, M. Katz, A. Fruergaard, M. U. Peleg, Y. Pick, U. Karlish, S. J. D. Nissen, P. 2025-07-27 doi:10.1101/2025.07.27.666930 Cold Spring Harbor Laboratory Press 2025-07-27 <![CDATA[ Extracting Value Coding Features from Individual Serotonin Neurons ]]> https://biorxiv.org/content/10.1101/2025.07.28.667134v1?rss=1 Harkin, E. Beique, J.-C. Naud, R. 2025-07-29 doi:10.1101/2025.07.28.667134 Cold Spring Harbor Laboratory Press 2025-07-29 <![CDATA[ Can you trust your reconstructed lineage tree? A homoplasy-based approach for irreversible evolution ]]> https://biorxiv.org/content/10.1101/2025.07.27.667007v1?rss=1 Zilber, P. Prillo, S. Yosef, N. Nadler, B. 2025-07-30 doi:10.1101/2025.07.27.667007 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ Processing and sectioning of organ donor spinal cord tissue for electrophysiology on acute human spinal cord slices ]]> https://biorxiv.org/content/10.1101/2025.07.26.666132v1?rss=1 Dedek, A. Gambeta, E. Shriraam, R. Topcu, E. McDermott, J. S. Krajewski, J. L. Tsai, E. C. Hildebrand, M. E. 2025-07-31 doi:10.1101/2025.07.26.666132 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Ceramide Connects TNF-α Signaling to Organelle Biophysical Remodeling ]]> https://biorxiv.org/content/10.1101/2025.07.26.666759v1?rss=1 Ventura, A. E. Pinto, S. N. Pokorna, S. Laviad, E. L. Thiam, A. R. Prieto, M. Futerman, A. H. Silva, L. C. 2025-07-31 doi:10.1101/2025.07.26.666759 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Dynamic Functional Pathway Development in Type 1 Spinal Interneurons: Stage-specific roles of retinoic acid activity ]]> https://biorxiv.org/content/10.1101/2025.07.29.667367v1?rss=1 Rekler, D. Kagan, S. Krutous, N. R. Friedlander, G. Kalcheim, C. 2025-07-31 doi:10.1101/2025.07.29.667367 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Elevated brain α-synuclein, phosphorylated-tau, and oxidative stress in mice that survived influenza A pneumonitis ]]> https://biorxiv.org/content/10.1101/2025.07.31.667659v1?rss=1 Lunn, M. O. Lengacher, N. A. Hake-Volling, Q. Tomlinson, J. J. aSCENT-PD Investigators, Brown, E. G. Schlossmacher, M. G. 2025-08-01 doi:10.1101/2025.07.31.667659 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Structural basis of an EMC:Spf1 insertase-dislocase complex in the eukaryotic endoplasmic reticulum ]]> https://biorxiv.org/content/10.1101/2025.08.07.669073v1?rss=1 Klose, C. J. Prabu, J. R. Fenech, E. J. Braeuning, B. Baydar, I. Steigenberger, B. von Gronau, S. Arad, S. Langlois, C. R. Schuldiner, M. Schulman, B. A. Feige, M. J. 2025-08-07 doi:10.1101/2025.08.07.669073 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Mutant IDH silences GSX2 to reprogram neural progenitor cell fate and promote gliomagenesis ]]> https://biorxiv.org/content/10.1101/2025.08.12.667486v1?rss=1 Xiao, Y. Shi, D. D. Guo, L. Neumann, E. Levitt, M. M. Kaphle, P. Shipman, T. Li, H. Cai, F. Ramirez, D. M. O. Zacharias, L. Chen, Z. Lin, M. Puliyappadamba, V. T. Chen, T. Savani, M. R. Pena, S. Wansapura, J. Mathews, T. P. Mishra, P. Kim, Y. J. Raj, P. Richardson, T. E. Xu, J. Mack, S. C. Rahme, G. J. Bernstein, B. E. DeBerardinis, R. J. Tirosh, I. Suva, M. L. Xu, L. Abdullah, K. G. McBrayer, S. K. 2025-08-13 doi:10.1101/2025.08.12.667486 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ Spatial proteomics reveals mechanisms of cell-intrinsic tryptophan metabolism controlling ovarian cancer survival ]]> https://biorxiv.org/content/10.1101/2025.08.14.670277v1?rss=1 Xu, T. T. Metousis, A. Kainacher, L. Zhang, X. Steigenberger, B. Madden, K. G. Schweitzer, L. C. Duteil, C. Rossini, S. Lengyel, E. Obermayr, E. Shulman, Z. Nordmann, T. M. Lindberg, E. L. Mann, M. Murray, P. J. 2025-08-18 doi:10.1101/2025.08.14.670277 Cold Spring Harbor Laboratory Press 2025-08-18 <![CDATA[ Transgenic Cowpea Expressing Synthetic BtCry1Ab Confers High Resistance to Legume Pod Borer (Maruca vitrata) ]]> https://biorxiv.org/content/10.1101/2025.08.16.670672v1?rss=1 Jothi, M. Kumar, S. Maravi, D. K. Altosaar, I. Kalia, V. Sahoo, L. 2025-08-20 doi:10.1101/2025.08.16.670672 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ Mapping Leukocyte Dynamics during Neuroinflammation Identifies Meningeal Monocyte-Derived Macrophages as Drivers of Progressive Disease ]]> https://biorxiv.org/content/10.1101/2025.08.15.670462v1?rss=1 Villar-Vesga, J. Clement, P. Van Hove, H. Meuffels, E. Bugada, V. Kim, J. Greis, D. Jorba-Adolff, P. Mayoux, M. Lasne, A. Ashworth, C. Zwicky, P. Scharli, S. Engelenburg, H. J. Hsiao, C.-C. Hamann, J. Smolders, J. Tatsch, L. Kirschenbaum, D. Schreiner, B. Herwerth, M. Tugues, S. Greter, M. DeFeo, D. Becher, B. Ingelfinger, F. Mundt, S. 2025-08-21 doi:10.1101/2025.08.15.670462 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ A Suite of Stains: Characterization of four fluorophores as complementary tools for visualizing neutral lipids in an extremophilic green alga ]]> https://biorxiv.org/content/10.1101/2025.08.18.670973v1?rss=1 Osmers, P. Boisvert, E.-J. Y. Boddy, C. N. Fogg, D. E. Cvetkovska, M. 2025-08-22 doi:10.1101/2025.08.18.670973 Cold Spring Harbor Laboratory Press 2025-08-22 <![CDATA[ A fibroblast-centric network drives cold fibrosis in the tumor microenvironment of lung squamous cell carcinoma ]]> https://biorxiv.org/content/10.1101/2025.08.25.668405v1?rss=1 Miyara, S. Frenkel, S. Mayo, A. Gascard, P. Strasser, M. Gibbs, D. Weizman, E. Ben Shalom, I. Stein, Y. Pan, D. Caruso, J. A. Sangwan, V. Bertos, N. Berube, J. Camilleri-Broet, S. Oikonomopoulos, S. Djambazian, H. Umansky, K. B. Elkahal, J. Mayer, S. Fiset, P. O. Adler, M. Tzahor, E. Ragoussis, I. Huang, S. Ferri, L. Tlsty, T. Scherz-Shouval, R. Alon, U. 2025-08-25 doi:10.1101/2025.08.25.668405 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ The dynamics of episodic recall ]]> https://biorxiv.org/content/10.1101/2025.08.27.671980v1?rss=1 Mizrachi, N. Ahissar, E. 2025-08-28 doi:10.1101/2025.08.27.671980 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ Deciphering the Origin and Plasticity of Circulating Endothelial Cells: A Model for Systemic Angiogenesis Programs in Health and Disease ]]> https://biorxiv.org/content/10.1101/2025.08.26.672338v1?rss=1 Efros, O. Brook, D. Yaniv, Y. Elkahal, J. Furer, N. Dadi, G. Naor, H. Rappoport, N. Milman, O. Kedmi, M. Katz, U. Tavor, S. Duek, A. Maor, E. Sternik, L. Kaushansky, N. Tzahor, E. Yaniv, K. Shlush, L. 2025-08-29 doi:10.1101/2025.08.26.672338 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ Juvenile Hormone Signalling Underlies the Switchpoint and Differentiation of Soldiers in Camponotus floridanus ]]> https://biorxiv.org/content/10.1101/2025.08.25.672237v1?rss=1 MacMillan, O. Singer, J. Perrakis, S. Craig, A. Ntanga, D. Qiu, D. Rajakumar, R. 2025-08-30 doi:10.1101/2025.08.25.672237 Cold Spring Harbor Laboratory Press 2025-08-30 <![CDATA[ Loss of Sox10 in a HER2+ model prevents tumor initiation and induces luminal-to-basal reprograming in cancer cells. ]]> https://biorxiv.org/content/10.1101/2025.08.26.672423v1?rss=1 Garland, B. Delisle, S. Abou-Hamad, J. De Souza, C. Zuccarini, R. Auer, R. C. Sabourin, L. 2025-08-31 doi:10.1101/2025.08.26.672423 Cold Spring Harbor Laboratory Press 2025-08-31 <![CDATA[ Evidence of spinal cord comparator modules for rapid corrections of movements ]]> https://biorxiv.org/content/10.1101/2025.08.27.672590v1?rss=1 Ozyurt, M. G. Chiasson, S. Laliberte, A. M. Nascimento, F. Khan, E. Mayer, W. P. Bhumbra, G. S. Akay, T. Bui, T. V. Beato, M. Brownstone, R. M. Ronzano, R. 2025-09-01 doi:10.1101/2025.08.27.672590 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection ]]> https://biorxiv.org/content/10.1101/2025.09.01.673470v1?rss=1 Garb, J. E. Adams, D. W. Yardeni, E. H. Blokesch, M. Sorek, R. 2025-09-01 doi:10.1101/2025.09.01.673470 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ Structure of Pex8 in complex with peroxisomal receptor Pex5 reveals its essential role in peroxisomal cargo translocation ]]> https://biorxiv.org/content/10.1101/2025.08.30.673231v1?rss=1 Ekal, L. Wendscheck, D. David, Y. Chojnowski, G. Jeffries, C. M. Mullapudi, E. Schuldiner, M. Warscheid, B. Zalckvar, E. Wilmanns, M. 2025-09-02 doi:10.1101/2025.08.30.673231 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ Excitability as a Design Principle in the Immune System ]]> https://biorxiv.org/content/10.1101/2025.08.31.673412v1?rss=1 Lebel, Y. Alon, U. 2025-09-02 doi:10.1101/2025.08.31.673412 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ Extracellular activity of a bacterial protease associated with reduced phage infectivity ]]> https://biorxiv.org/content/10.1101/2025.09.03.674096v1?rss=1 Herbst, E. Rosen Blechman, G. Fedorenko, T. Melamed, S. Amitai, G. Sorek, R. 2025-09-03 doi:10.1101/2025.09.03.674096 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Keeping an Eye on Plasticity Genes: Insulin/TOR Pathway Components Mediating Nutritional Plasticity of Eyes Within and Between Sex ]]> https://biorxiv.org/content/10.1101/2025.08.31.673361v1?rss=1 Heffernan, S. Etchells Foisy, E. Rajakumar, R. 2025-09-04 doi:10.1101/2025.08.31.673361 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ OSDR2.0 infers microenvironment-driven cell-state transitions and population dynamics from a single spatial biopsy ]]> https://biorxiv.org/content/10.1101/2025.09.02.673328v1?rss=1 Ben Shalom, I. Somer, J. Miyara, S. Mayo, A. Mannor, S. Alon, U. 2025-09-05 doi:10.1101/2025.09.02.673328 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Resolving hematopoietic stem versus progenitor cell potential in the mouse dorsal aorta by differential Runx1 +110 enhancer activity ]]> https://biorxiv.org/content/10.1101/2025.09.02.673630v1?rss=1 Anselmi, G. Frontera, V. Rode, C. Jarratt, A. Mehmood, N. T. Nicholls, M. S. Antoniou, S. Azzoni, E. Stamatoyannopoulos, J. Levanon, D. Groner, Y. de Bruijn, M. F. T. R. 2025-09-05 doi:10.1101/2025.09.02.673630 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ TECPR2 maintains mitochondrial homeostasis in neurodegeneration ]]> https://biorxiv.org/content/10.1101/2025.09.04.674193v1?rss=1 Elazar, Z. Chaurasia, M. Fraiberg, M. Subic, N. Shatz, O. Kokabi, K. Gogoi, O. Trofimyuk, O. Tamim-Yecheskel, B. C. Freud, S. Demishtein, A. Kopitman, E. Goliand, I. Chourasia, S. Peleg, Y. Ainbinder, E. Dezorella, N. 2025-09-07 doi:10.1101/2025.09.04.674193 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Structure-based discovery of inhibitors of Mac1 domain of nonstructural protein-3 of SARS-CoV-2 by machine learning-augmented screening of chemical space ]]> https://biorxiv.org/content/10.1101/2025.09.05.674529v1?rss=1 Ban, F. Ravichandran, R. Correy, G. J. Herasymenko, O. Silva, M. Ackloo, S. Bolotokova, A. Chau, I. Gibson, E. Harding, R. Hutchinson, A. Loppnau, P. Fraser, J. S. Schapira, M. Cherkasov, A. Gentile, F. 2025-09-08 doi:10.1101/2025.09.05.674529 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ Elevated surface La promotes hyperfusion and contributes to impaired resorption in osteopetrosis. ]]> https://biorxiv.org/content/10.1101/2025.09.07.674639v1?rss=1 WHITLOCK, J. M. Leikina, E. Wang, H.-Y. Zhang, W. Katz, G. Reuven, N. Elson, A. Geiger, B. Chernomordik, L. V. 2025-09-08 doi:10.1101/2025.09.07.674639 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ Subcellular mRNA localization patterns across tissues resolved with spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.09.07.674688v1?rss=1 Novoselsky, R. Golani, O. Barkai, T. Kedmi, M. Goliand, I. Fine, M. Kent, I. Nachmany, I. Itzkovitz, S. 2025-09-09 doi:10.1101/2025.09.07.674688 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ The impact of rearing environment on C. elegans: Phenotypic, transcriptomic and intergenerational responses to 3D enriched habitats ]]> https://biorxiv.org/content/10.1101/2025.09.07.674770v1?rss=1 Guisnet, A. Halaby, N. Rivest, M. Romero Quineche, B. Hendricks, M. 2025-09-09 doi:10.1101/2025.09.07.674770 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ Inter-individual variability of neurotransmitter receptor and transporter density in the human brain ]]> https://biorxiv.org/content/10.1101/2025.09.09.674944v1?rss=1 Hansen, J. Y. Tuisku, J. Johansson, J. Chang, Z. McGinnity, C. Beliveau, V. Guimond, S. Ganz, M. Norgaard, M. Galovic, M. Bezgin, G. Cox, S. M. Hietala, J. Leyton, M. Kobayashi, E. Rosa-Neto, P. Funck, T. Palomero-Gallagher, N. Knudsen, G. M. Marsden, P. Hammers, A. Nummenmaa, L. Tuominen, L. Misic, B. 2025-09-10 doi:10.1101/2025.09.09.674944 Cold Spring Harbor Laboratory Press 2025-09-10 <![CDATA[ H3.3 De Novo Mutations Alter Lysine 36 Methylation via Distinct Mechanisms ]]> https://biorxiv.org/content/10.1101/2025.09.09.674984v1?rss=1 Morcos, S. M. Sarvan, S. Saettone, A. Wong, C. J. Vo, S. C. Milo, A. Bayoumy, O. H. Angireddy, R. Burke, G. L. Greenblatt, J. F. Jabado, N. Chen, C. C. Bhoj, E. Gingras, A.-C. Couture, J.-F. Campos, E. I. 2025-09-10 doi:10.1101/2025.09.09.674984 Cold Spring Harbor Laboratory Press 2025-09-10 <![CDATA[ Disruption of the developmental factor Otp in the adult forebrain reveals its diverse physiological functions ]]> https://biorxiv.org/content/10.1101/2025.09.09.675064v1?rss=1 Tahor, M. Kuperman, Y. Nahum, T. Tsoory, M. Bejar, B. Regev, E. Blechman, J. Biran, J. Chen, A. Levkowitz, G. 2025-09-10 doi:10.1101/2025.09.09.675064 Cold Spring Harbor Laboratory Press 2025-09-10 <![CDATA[ Shadow Montage and Cone-Beam Reconstruction in 4D-STEM Tomography ]]> https://biorxiv.org/content/10.1101/2025.09.06.674643v1?rss=1 Seifer, S. Houben, L. Elbaum, M. 2025-09-11 doi:10.1101/2025.09.06.674643 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ CytoVI: Deep generative modeling of antibody-based single cell technologies ]]> https://biorxiv.org/content/10.1101/2025.09.07.674699v1?rss=1 Ingelfinger, F. Levy, N. Ergen, C. Bakulin, A. Becker, A. Boyeau, P. Kim, M. Ditz, D. Dirks, J. Maaskola, J. Wertheimer, T. Zeiser, R. Widmer, C. C. Amit, I. Yosef, N. 2025-09-12 doi:10.1101/2025.09.07.674699 Cold Spring Harbor Laboratory Press 2025-09-12 <![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[ Resynchronization of the biological clock using exposure to low oxygen levels in humans: an exploratory study ]]> https://biorxiv.org/content/10.1101/2025.09.09.674331v1?rss=1 Morin, R. Forest, G. Nolet, K. I. Bourgon, V. Duval, F.-G. Mauger, J.-F. Imbeault, P. 2025-09-15 doi:10.1101/2025.09.09.674331 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ Vsb1, Ypq1 and Ypq2 control dynamic cationic amino acid storage in the yeast vacuole ]]> https://biorxiv.org/content/10.1101/2025.09.11.675521v1?rss=1 Zaremba, E. Vierendeels, F. Dutoit, R. Bodo, E. Bifulco, E. Tricot, C. Noor, E. Andre, B. Onischenko, E. Cools, M. 2025-09-16 doi:10.1101/2025.09.11.675521 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Age-based approach to characterize the dynamics of cellular processes ]]> https://biorxiv.org/content/10.1101/2025.09.14.676129v1?rss=1 Noor, E. Jefimov, K. Bifulco, E. Onishchenko, E. 2025-09-17 doi:10.1101/2025.09.14.676129 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Comparative developmental transcriptomics of Drosophila mushroom body neurons highlights the mevalonate pathway as a regulator of axon growth ]]> https://biorxiv.org/content/10.1101/2025.09.17.676757v1?rss=1 Fahdan, L. Meltzer, H. Wigoda, N. Rotkopf, R. Schuldiner, O. 2025-09-17 doi:10.1101/2025.09.17.676757 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ IRF1 Tunes Basal Immunity and Antiviral Readiness in a Context-Dependent Manner ]]> https://biorxiv.org/content/10.1101/2025.09.16.676475v1?rss=1 Zoler, E. Miodownik, I. Ben-dor, S. Harari, D. Zahradnik, J. Afek, A. Schreiber, G. 2025-09-18 doi:10.1101/2025.09.16.676475 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ TDP-43 pathology triggers SRRM4-dependent cryptic splicing of G3BP1 in ALS/FTD ]]> https://biorxiv.org/content/10.1101/2025.09.17.676845v1?rss=1 Fakim, H. Ghosh, A. Amzallag, E. Danino, Y. M. Triassi, V. Brown, A.-L. Pal, N. Deshaies, J.-E. Dubinski, A. Lacombe, A. Fauchon, C. Esfahani, A. M. Ling, K. Rigo, F. Jafar-nejad, P. NYGC ALS Consortium, Francis, N. J. Trempe, J.-F. Fratta, P. Coyne, A. N. Hornstein, E. Velde, C. V. 2025-09-18 doi:10.1101/2025.09.17.676845 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Parsing the Functions of Immediate Early Proteins in HCMV Infection Outcome ]]> https://biorxiv.org/content/10.1101/2025.09.19.676120v1?rss=1 Kitsberg, Y. Nachshon, A. Ginossar, N. Schwartz, M. 2025-09-19 doi:10.1101/2025.09.19.676120 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Implicit processes do not contribute to learning to reach in small mirror reversed environments ]]> https://biorxiv.org/content/10.1101/2025.09.17.676913v1?rss=1 Heirani Moghaddam, S. Cressman, E. K. Manson, G. A. 2025-09-20 doi:10.1101/2025.09.17.676913 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Aberrant inheritance of extrachromosomal DNA amplifications promotes cancer evolution ]]> https://biorxiv.org/content/10.1101/2025.09.19.677276v1?rss=1 Marom, S. Lifshits Dayan, I. Narasimha Kadali, V. Giurgiu-Kraljic, M. Koifman, G. Hakeny, K. Chaurasia, M. Benamozig, O. Nevo, R. Azuri, I. Ryvkin, J. Rotkopf, R. Stelzer, G. Oniashvili, N. Mardoukh, J. Pollock, S. Iremadze, N. Shipony, Z. Kupervaser, M. Wigoda, N. Leshkowitz, D. Elazar, Z. Berko, E. Henssen, A. Shoshani, O. 2025-09-21 doi:10.1101/2025.09.19.677276 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Cardiomyocyte-expressed TGFβ signals to fibroblasts to program early heart maturation and adult myocyte identity ]]> https://biorxiv.org/content/10.1101/2025.09.22.677845v1?rss=1 Minerath, R. A. Kasam, R. K. Swoboda, C. O. Prasad, V. Grimes, K. M. Blair, N. S. Khalil, H. Alfieri, C. M. Eads, L. Saviola, A. A. Azhar, M. Miao, L. Wu, M. Tallquist, M. V. Hansen, K. Weirauch, M. T. Yutzey, K. Millay, D. Molkentin, J. D. 2025-09-22 doi:10.1101/2025.09.22.677845 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ Spinal dI3 neurons are involved in sustained motor adaptation elicited by low-threshold cutaneous afferents ]]> https://biorxiv.org/content/10.1101/2025.09.22.677841v1?rss=1 Khan, E. U. Nasiri, S. Chiasson, S. A. Couvrette, L. J. Laliberte, A. M. Bui, T. V. 2025-09-23 doi:10.1101/2025.09.22.677841 Cold Spring Harbor Laboratory Press 2025-09-23 <![CDATA[ RNAcentral in 2026: Genes and literature integration ]]> https://biorxiv.org/content/10.1101/2025.09.19.677274v1?rss=1 Green, A. F. Ribas, C. E. Jandalala, I. Muston, P. O'Cathail, C. Cochrane, G. Ernst, C. Zhao, L. Madrigal, P. Attrill, H. Marygold, S. Lancet, D. Dobzinski, N. Chan, P. P. Lowe, T. M. Bruford, E. A. Seal, R. L. Hermjakob, H. Panneerselvam, K. Finn, R. D. Gurbich, T. A. Griffiths-Jones, S. Fromm, B. Peterson, K. J. Sordyl, D. Bujnicki, J. M. Velankar, S. Appasamy, S. D. Ganguly, S. Zhang, P. He, S. Rutherford, K. M. Wood, V. Lovering, R. C. Picardi, E. Ontiveros, N. Huang, L. Miao, Z. Petrov, A. S. McCann, H. Cavalleri, E. Mesiti, M. Rivas, E. Szikszai 2025-09-24 doi:10.1101/2025.09.19.677274 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ AMICI: Attention Mechanism Interpretation of Cell-cell Interactions ]]> https://biorxiv.org/content/10.1101/2025.09.22.677860v1?rss=1 Hong, J. Desai, K. Nguyen, T. D. Nazaret, A. Levy, N. Ergen, C. Plitas, G. Azizi, E. 2025-09-24 doi:10.1101/2025.09.22.677860 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ Hemodynamic and electrophysiological progression of the Rose Bengal photothrombotic stroke model in mice: vasoactive properties of Rose Bengal, tissue heating, wavelength optimization, and sex differences in lesion volume ]]> https://biorxiv.org/content/10.1101/2025.09.22.677889v1?rss=1 Chary, P. Rehmani, S. Davidson, S. Li, X. Chen, S. Silasi, G. 2025-09-24 doi:10.1101/2025.09.22.677889 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ Conservation and divergence of transcriptional heterogeneity in the cardiac conduction system ]]> https://biorxiv.org/content/10.1101/2025.09.23.678069v1?rss=1 Bakr, M. Dababneh, S. Tibbits, G. F. Oh, Y. Kim, K.-H. 2025-09-25 doi:10.1101/2025.09.23.678069 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Functional and metabolomic analyses of brown adipose tissue during cold-deacclimation reveal rapid adaptations in N-acetylated amino acid metabolism ]]> https://biorxiv.org/content/10.1101/2025.09.23.678072v1?rss=1 Pileggi, C. A. McIlroy, E. Hamilton, L. M. Kuksal, N. Kennedy, L. S. Vasilyeva, V. Kanaan, M. El Hankouri, Z. Burelle, Y. S. Cuperlovic-Culf, M. Harper, M.-E. 2025-09-25 doi:10.1101/2025.09.23.678072 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Intrinsic Neural Oscillations Predict Verbal Learning Performance and Encoding Strategy Use ]]> https://biorxiv.org/content/10.1101/2025.09.27.678958v1?rss=1 Oswald, V. Landry, M. abdelhedi, H. Lippe, S. Robaey, P. Jerbi, K. 2025-09-28 doi:10.1101/2025.09.27.678958 Cold Spring Harbor Laboratory Press 2025-09-28 <![CDATA[ A synthetic bacterium that degrades and assimilates poly(ethylene terephthalate) ]]> https://biorxiv.org/content/10.1101/2025.09.28.673679v1?rss=1 Freund, D. Cherukuri, K. P. Mireles, R. Kippen, J. Shossel, M. Noda-Garcia, L. 2025-09-28 doi:10.1101/2025.09.28.673679 Cold Spring Harbor Laboratory Press 2025-09-28 <![CDATA[ Dynamic Ribosomal RNA Methylation Regulates Translation in the Hematopoietic System and is Essential for Stem Cell Fitness ]]> https://biorxiv.org/content/10.1101/2025.09.29.679281v1?rss=1 Rabany, O. Ben-Dror, S. Arafat, M. Aharoni, H. Halperin, Y. Marchand, V. Romanovski, N. Ussishkin, N. Livneh, M. Reches, A. Wexler, J. Mayorek, N. Monderer-Rothkoff, G. Shifman, S. Mammer, W. VanInsberghe, M. Pauli, C. Muller-Tidow, C. Karmi, O. Livneh, Y. van Oudenaarden, A. Motorin, Y. Nachmani, D. 2025-09-30 doi:10.1101/2025.09.29.679281 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ Learning the DNA syntax of human microbiomes to infer health and disease ]]> https://biorxiv.org/content/10.1101/2025.09.30.679483v1?rss=1 Mejia-Fleisacher, A. Bossel Ben-Moshe, N. Antman, T. Zeevi, D. Avraham, R. 2025-09-30 doi:10.1101/2025.09.30.679483 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ MECP2 Mutations Rewire Human ESC Fate and Bias Cortical Lineage Commitment ]]> https://biorxiv.org/content/10.1101/2025.09.30.679576v1?rss=1 Guillon, M. Brin, M. Gabet, E. Gromaire, J. Bernard, M. Laurent, L. Rabin, T. Asali, L. Liu, Y. Flamier, A. 2025-10-02 doi:10.1101/2025.09.30.679576 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Ca2+ Plateau Potentials Reflect Cross-Theta Cortico-Hippocampal Input Dynamics and Acetylcholine for Rapid Formation of Efficient Place-Cell Code ]]> https://biorxiv.org/content/10.1101/2025.10.01.676159v1?rss=1 Wang, H.-Y. Hsu, Y.-C. Huang, H.-P. Chen, C.-T. Huang, X.-B. Wang, C.-T. Naud, R. Hsu, C.-L. 2025-10-02 doi:10.1101/2025.10.01.676159 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Electrospectrometry of the Mouse Brain ]]> https://biorxiv.org/content/10.1101/2025.10.01.679820v1?rss=1 Wang, X. Beique, J.-C. Naud, R. 2025-10-02 doi:10.1101/2025.10.01.679820 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ BRCA mutation alters the stromal landscape in normal ovaries ]]> https://biorxiv.org/content/10.1101/2025.10.01.679597v1?rss=1 Vaishnav, H. T. Murray, A. Piccolo, O. R. McCloskey, C. W. Yakubovich, E. Macdonald, E. Echaibi, M. Trudel, D. Mes-Masson, A.-M. Drapkin, R. Landry, D. A. Vanderhyden, B. C. 2025-10-03 doi:10.1101/2025.10.01.679597 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Differential effects of aging and Alzheimer's disease on microemboli clearance in a mouse model of microinfarction ]]> https://biorxiv.org/content/10.1101/2025.09.30.679680v1?rss=1 View larger version (17K): org.highwire.dtl.DTLVardef@760ec2org.highwire.dtl.DTLVardef@c2e2caorg.highwire.dtl.DTLVardef@b76011org.highwire.dtl.DTLVardef@1040eec_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Haugen, F. O. Silasi, G. 2025-10-04 doi:10.1101/2025.09.30.679680 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ RamanBot: Versatile high throughput Raman system ]]> https://biorxiv.org/content/10.1101/2025.10.03.680377v1?rss=1 Atia, K. Hunter, R. Asare-Werehene, M. K. Tsang, B. Anis, H. 2025-10-06 doi:10.1101/2025.10.03.680377 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Preselection CD4+CD8+ thymocytes modulate TCR responsiveness following TCRβ selection ]]> https://biorxiv.org/content/10.1101/2025.10.03.680384v1?rss=1 Kim, E. Aylard, D. A. Steier, Z. Ortiz, D. Choi, J. Chen, S. Streets, A. M. Yosef, N. Robey, E. 2025-10-06 doi:10.1101/2025.10.03.680384 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Alzheimer's disease causes bone marrow myelopoiesis dysfunction ]]> https://biorxiv.org/content/10.1101/2025.10.06.680030v1?rss=1 Abellanas, M. A. Basurco, L. Purnapatre, M. Burgaletto, C. Castellani, G. Phoebeluc Colaiuta, S. Peralta-Ramos, J. M. Ibraheem, A. Murad, S. Antonello, P. Kovacs, M. Androsova, Y. Nathansohn, B. Partney, H. Cahalon, L. Valdes-Mas, R. Josephides, J. M. Salame, T. M. Espelosin, M. Cuadrado-Tejedor, M. Garcia-Osta, A. Deczkowska, A. Schwartz, M. 2025-10-07 doi:10.1101/2025.10.06.680030 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Neuromodulation of zebrafish primary motoneuron firing is shaped by developmental changes in the M-current ]]> https://biorxiv.org/content/10.1101/2025.10.06.680750v1?rss=1 Bui, T. V. Gaudreau, S. F. 2025-10-07 doi:10.1101/2025.10.06.680750 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ DNMT3A-R882 mutations intrinsically drive dysfunctional neutropoiesis from human haematopoietic stem cells ]]> https://biorxiv.org/content/10.1101/2025.10.08.679225v1?rss=1 Mantica, G. Vedi, A. Tuval, A. Huerga Encabo, H. Hayler, D. Krzywon, A. Mitchell, E. Dunn, W. G. Biezuner, T. Bastos, H. P. Sham, K. Santoro, A. Lee, J. Williams, N. Danin, A. Chapal, N. Moskovitz, Y. Arruda, A. Fiorillo, E. Orru, V. Marongiu, M. McKinney, E. Cucca, F. Collin, M. Minden, M. Campbell, P. Vassiliou, G. S. Fabre, M. A. Nangalia, J. Bonnet, D. Shlush, L. Laurenti, E. 2025-10-08 doi:10.1101/2025.10.08.679225 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ VASP regulates the polar organization of adhesion-associated actin filaments ]]> https://biorxiv.org/content/10.1101/2025.10.08.681099v1?rss=1 Chung, W.-L. Boujemaa-Paterski, R. Winograd-Katz, S. Eibauer, M. Geiger, B. Medalia, O. 2025-10-08 doi:10.1101/2025.10.08.681099 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Chryseobacterium indologenes mediates resistance to osimertinib by activating the IGF1R pathway in EGFR-mutant lung adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2025.10.08.681060v1?rss=1 Li, W. Zhang, K. Raul, M. Rotter-Maskowitz, A. Nejman, D. Potempa, J. Straussman, R. Raz, D. 2025-10-09 doi:10.1101/2025.10.08.681060 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ Methane Cycling Microbes are Important Predictors of Methylmercury Accumulation in Rice Paddies ]]> https://biorxiv.org/content/10.1101/2025.10.09.681528v1?rss=1 Zhang, R. Poulain, A. J. Pu, Q. Liu, J. Abdelhafiz, M. A. Feng, X. Meng, B. Gregoire, D. S. 2025-10-11 doi:10.1101/2025.10.09.681528 Cold Spring Harbor Laboratory Press 2025-10-11 <![CDATA[ An open CAR-T single-cell atlas to enable in-depth characterization and rational engineering of CAR-T products ]]> https://biorxiv.org/content/10.1101/2025.10.11.681788v1?rss=1 Camara-Pena, S. Rodriguez-Marquez, P. Planell, N. Calleja-Cervantes, M. E. Jordana-Urriza, L. Cinnirella, G. Reich-Zeliger, S. Rodriguez-Otero, P. Tamariz, E. Ochoa, I. Yosef, N. Rodriguez-Madoz, J. R. Prosper, F. Hernaez, M. 2025-10-13 doi:10.1101/2025.10.11.681788 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ A Mechanistic Model for the HPA Axis Cortisol Paradox in PTSD ]]> https://biorxiv.org/content/10.1101/2025.10.13.681561v1?rss=1 Danan, D. Grosskopf, Y. Hayut, Y. Toledano, Y. Doenyas-Barak, K. Mayo, A. Alon, U. 2025-10-14 doi:10.1101/2025.10.13.681561 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Lineage origin and microenvironment shape neuroblastoma transcriptional state and plasticity ]]> https://biorxiv.org/content/10.1101/2025.10.13.682025v1?rss=1 Fresmann, N. Koeppke, J. Gauert, A. Senoussi, A. Olivares-Chauvet, P. Schott, M. Hoefer, L. Henssen, A. G. Rajewsky, N. Spanjaard, B. Hagemann, A. I. H. Junker, J. P. 2025-10-14 doi:10.1101/2025.10.13.682025 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Mucinolysome in gut microbiomes of farm animals and humans ]]> https://biorxiv.org/content/10.1101/2025.10.14.682383v1?rss=1 Akresi, J. E. Do, T. V. T. Cui, Z. Shanmugam, N. R. S. Morais, S. Mizrahi, I. Bayer, E. Yin, Y. 2025-10-15 doi:10.1101/2025.10.14.682383 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Ubiquitination regulates granulostasis and DRiP accumulation in SGs under heat stress via the E3 ligase MKRN2 ]]> https://biorxiv.org/content/10.1101/2025.10.15.682570v1?rss=1 Amzallag, E. Danino, Y. M. Secco, V. Carra, S. Hornstein, E. 2025-10-16 doi:10.1101/2025.10.15.682570 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ Micro-C in Solanum Uncovers Conserved Genome Folding and Epigenetically Defined Loops with Bifunctional Enhancer-Silencer Activity ]]> https://biorxiv.org/content/10.1101/2025.10.16.682740v1?rss=1 Filler-Hayut, S. Hansen, A. S. 2025-10-16 doi:10.1101/2025.10.16.682740 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ Co-targeting MERTK and EGFR with a Bispecific Antibody Overcomes Drug Resistance Across Mutations in Exons 19, 20, and 21 ]]> https://biorxiv.org/content/10.1101/2025.10.16.681972v1?rss=1 Giri, S. Selvadurai, B.-R. Simoni-Nieves, A. Gupta, N. Lindzen, M. Chatterjee, R. Genna, A. Van-Daele, M. Ramesh-Kumar, D. Zerbib, M. Oren, R. Meijer, I. S. Wippich, E. F. Avraham, Y. Dahan, R. Kilpatrick, L. E. Platt, S. Hill, S. J. Pal, L. R. Ruppin, E. Romaniello, D. Lauriola, M. Yarden, Y. 2025-10-17 doi:10.1101/2025.10.16.681972 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ GLYATL1 is associated with metabolic and epigenetic changes and with endocrine resistance in luminal breast cancer ]]> https://biorxiv.org/content/10.1101/2025.10.17.682994v1?rss=1 Mueller, J. Sofyali, E. Schwarzmueller, L. Aylon, Y. Weizman, E. Schlicker, L. Kelly, K. Borgoni, S. Oz, S. Stocker, C. Burmester, S. Woerner, A. Karolus, S. Michels, B. E. Heiss, D. Will, R. Rodrigues de Melo Costa, V. Lutsik, P. Weichenhan, D. Hofmann, I. Belugali Nataraj, N. Yarden, Y. Magnani, L. Plass, C. Schulze, A. Koerner, C. Oren, M. Wiemann, S. 2025-10-17 doi:10.1101/2025.10.17.682994 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Computational modelling of functional maturation of primary motoneuron firing properties in developing zebrafish ]]> https://biorxiv.org/content/10.1101/2025.10.17.683092v1?rss=1 Gaudreau, S. F. Bui, T. 2025-10-17 doi:10.1101/2025.10.17.683092 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Self-supervised learning enables robust microbiome predictions in data-limited and cross-cohort settings ]]> https://biorxiv.org/content/10.1101/2025.10.19.683269v1?rss=1 Zahavi, L. Levine, Z. Godneva, A. Dubinkina, V. Dhir, R. Pollard, K. S. Weinberger, A. Segal, E. 2025-10-20 doi:10.1101/2025.10.19.683269 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ OASIS: in vivo AAV-mediated transduction and genome editing of adult oligodendrocytes ]]> https://biorxiv.org/content/10.1101/2025.10.20.683551v1?rss=1 Ding, X. Curtis, J. Xing, Y. Wu, Y. Peles, E. Rasband, M. N. 2025-10-21 doi:10.1101/2025.10.20.683551 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ HDCluster: High-Degree Graph Clustering for Robust Analysis of Single Molecule Localization Microscopy ]]> https://biorxiv.org/content/10.1101/2025.10.23.684134v1?rss=1 Khater, I. M. Nabi, I. R. Hamarneh, G. 2025-10-24 doi:10.1101/2025.10.23.684134 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ Synthetic Mimetics of Exosomal Lipid Profile Enhance Gemcitabine Delivery in Pancreatic Cancer ]]> https://biorxiv.org/content/10.1101/2025.10.24.684306v1?rss=1 Napso Shogan, T. Gil, Z. Schroeder, A. Ginini, L. Amer, M. Regev-Rudzki, N. Avinoam, O. Wolfenson, H. 2025-10-25 doi:10.1101/2025.10.24.684306 Cold Spring Harbor Laboratory Press 2025-10-25 <![CDATA[ Serotonin stimulates proliferation of ionocytes via the 5-HT2A receptor in zebrafish larvae ]]> https://biorxiv.org/content/10.1101/2025.10.24.684416v1?rss=1 MacDonald, W. M. Jonz, M. G. 2025-10-26 doi:10.1101/2025.10.24.684416 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Silk fibroin as a modulator of the amyloidogenic α-synuclein aggregation ]]> https://biorxiv.org/content/10.1101/2025.10.25.684501v1?rss=1 Miali, M. E. Shimanovich, U. Barak, Y. sirkis, Y. f. Goldian, I. Brookstein, O. 2025-10-26 doi:10.1101/2025.10.25.684501 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Mapping Functional Dynamics Hotspots for Protein Engineering with NMR Peak Intensity Analysis ]]> https://biorxiv.org/content/10.1101/2025.10.26.684639v1?rss=1 Damry, A. M. Hunt, S. E. Legault, S. Thompson, M. C. Goto, N. K. Chica, R. A. 2025-10-26 doi:10.1101/2025.10.26.684639 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Temporal control of axonal floor plate crossing through a combination of incoherent feedforward and feedback loops of gene regulatory network regulating Robo3 expression ]]> https://biorxiv.org/content/10.1101/2025.10.26.684599v1?rss=1 Sudakevitz-Merzbach, R. Majumder, M. Elberg, G. Bakhtan, M. Rekler, D. Khazanov, S. Wheaton, B. J. Ben-Arie, N. Friedlander, G. Kalchiem, C. Ivy Wilson, S. Jaworski, A. Adler, M. Klar, A. 2025-10-27 doi:10.1101/2025.10.26.684599 Cold Spring Harbor Laboratory Press 2025-10-27 <![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[ Decoding the Oral Microbiome: Metagenomic Insights into Host Metabolic Health ]]> https://biorxiv.org/content/10.1101/2025.10.28.685004v1?rss=1 XUE, H. Godneva, A. Tang, F. Li, H. Li, Y. Hu, M. Li, R. Su, J. Segal, E. Razzak, I. 2025-10-30 doi:10.1101/2025.10.28.685004 Cold Spring Harbor Laboratory Press 2025-10-30 <![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[ Temporal dynamics of noradrenaline release at fine spatial scales during motor learning ]]> https://biorxiv.org/content/10.1101/2025.10.29.685016v1?rss=1 Yin, X. Jones, N. Jumarang, A. Patriarchi, T. Chen, S. S. 2025-10-30 doi:10.1101/2025.10.29.685016 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Inherent coupling of perceptual judgments to actions in the mouse cortex ]]> https://biorxiv.org/content/10.1101/2025.10.30.685660v1?rss=1 Sokoletsky, M. Nikitina, A. A. Waychal, K. Katz, Y. Lampl, I. 2025-10-31 doi:10.1101/2025.10.30.685660 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Biotope-dependent High Level Resistance to Reactive Oxygen Species, Antibiotic Tolerance, and Virulence of Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/2025.10.31.685911v1?rss=1 Leguillier, V. Gloux, K. Khalife, M. D'Mello, R. Minic, Z. Sentic, M. Catto, M. Manzano, M. Pechoux, C. Truchet, S. Gaudu, P. Nielsen-Leroux, C. Heddi, B. Gruss, A. Vidic, J. 2025-11-03 doi:10.1101/2025.10.31.685911 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Multimerin1, not Galectin-8, Promotes Gastric Chief Cell Differentiation by Tempering WNT Signaling ]]> https://biorxiv.org/content/10.1101/2025.11.04.685347v1?rss=1 Lin, X. Nicolazzi, G. A. Liu, X. Nwokolo, C. Zick, Y. Saenz, J. Brown, J. W. 2025-11-05 doi:10.1101/2025.11.04.685347 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Acute AMPK activation does not adequately stimulate insulin signaling in skeletal muscle models of Myotonic Dystrophy Type 1 ]]> https://biorxiv.org/content/10.1101/2025.11.04.686135v1?rss=1 Adjei-Afriyie, O. Spendiff, S. Carmona-Martinez, R. Manta, A. Hentschel, A. Ho, K. O'Neil, D. Dawe, L. Roos, A. Ljubicic, V. MacKenzie, A. Ravel-Chapuis, A. Lochmuller, H. 2025-11-05 doi:10.1101/2025.11.04.686135 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Bacteria sense virus-induced genome degradation via methylated mononucleotides ]]> https://biorxiv.org/content/10.1101/2025.11.05.686725v1?rss=1 Osterman, I. Hurieve, B. Moses, S. Falkovich, A. H. Itkin, M. Malitsky, S. Yirmiya, E. Sorek, R. 2025-11-05 doi:10.1101/2025.11.05.686725 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Widespread DNA off-targeting confounds studies of RNA chromatin occupancy ]]> https://biorxiv.org/content/10.1101/2025.11.11.687850v1?rss=1 Goldrich, M. J. Delhaye, L. Bekaert, S.-L. Decaesteker, B. Van Nieuwerburgh, F. Speleman, F. Eyckerman, S. Mestdagh, P. Ulitsky, I. 2025-11-11 doi:10.1101/2025.11.11.687850 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ Metabolic zonation and characterization of tissue slices with spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.11.11.687271v1?rss=1 Etxezarreta Arrastoa, O. Pirona, A.-C. Wagner, A. Yosef, N. 2025-11-12 doi:10.1101/2025.11.11.687271 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Redefining Ovarian Fibrosis Through Comparative Analysis of Collagen Architecture ]]> https://biorxiv.org/content/10.1101/2025.11.12.688021v1?rss=1 Aitken, C. J. Kadhim, L. Murray, A. Landry, D. A. 2025-11-13 doi:10.1101/2025.11.12.688021 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ No rest for the rodent: energy management strategies in the naked mole-rat ]]> https://biorxiv.org/content/10.1101/2025.11.12.688094v1?rss=1 1. Despite their high lifetime energy expenditure and resistance to age-related metabolic decline, energy management is yet to be explored in the African naked mole-rat (NMR, Heterocephalus glaber). To investigate metabolic strategies in the NMR, repeated metabolic and activity measurements were taken in 32 individual NMRs using a multiplexed metabolic system. DEE was not repeatable, thus the DEE-RMR covariance at the among-individual level could not be fitted. At the within-individual level, however, the positive correlation between RMR and activity and the DEE-RMR relationship with b > 1 indicated support for the performance model. Hence, our results indicate that within-individual changes in activity and RMR are associated, suggesting that when a NMR increases activity on a given day, the impact on DEE are disproportionate because of a concurrent increase RMR. ]]> Chan, P. V. Turchyn, D. M. Careau, V. Pamenter, M. E. 2025-11-13 doi:10.1101/2025.11.12.688094 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Single-cell quantification of senescence burden reveals cell type-specific ageing dynamics across organs ]]> https://biorxiv.org/content/10.1101/2025.11.14.688272v1?rss=1 Cherqui, U. Sopher, I.-R. Akiva, H. Menahem, O. Kopitman, E. Blecher-Gonen, R. Keren-Shaul, H. Rachmian, N. Mayo, A. Alon, U. Gal, H. Krizhanovsky, V. 2025-11-14 doi:10.1101/2025.11.14.688272 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ A multiplexed approach for genetic screening of human cells by electron microscopy uncovers a critical effector of mitochondrial cristae shape ]]> https://biorxiv.org/content/10.1101/2025.11.15.688601v1?rss=1 Hassdenteufel, S. Bykov, Y. S. Dubreuil, B. Noll, K. Faust, O. Kamyshinsky, R. Itkin, M. Cohen, N. Malitsky, S. Peleg, Y. Albeck, S. von der Malsburg, K. Fass, D. van der Laan, M. Schuldiner, M. 2025-11-16 doi:10.1101/2025.11.15.688601 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ Sex- and ketogenesis-dependent effects of intermittent fasting against diet-induced obesity and fatty liver disease ]]> https://biorxiv.org/content/10.1101/2025.11.17.688915v1?rss=1 Aslani, T. Asif, S. Oh, Y. Lee, H. Stocker, C. Kwon, S. Pan, J. Dababneh, S. Zhao, X. Taylor, L. Mullick, A. E. Tibbits, G. F. Kim, R. Y. Fullerton, M. D. Mulvihill, E. E. Son, J. E. Kim, K.-H. 2025-11-18 doi:10.1101/2025.11.17.688915 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ TurboID-based proximity labeling enables in vivo mapping of Plasmodiophora brassicae secretome in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2025.11.18.684874v1?rss=1 Kalinger, K. S. Gallipeau-Burns, E. Hossain, M. M. Nourimand, M. Mietkiewska, E. Talasila, M. Uhrig, R. G. Todd, C. D. MacLean, A. M. 2025-11-18 doi:10.1101/2025.11.18.684874 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ Global warming drives the evolutionary rate of H1N1 and H3N2 influenza viruses ]]> https://biorxiv.org/content/10.1101/2025.11.20.689475v1?rss=1 Vilain, M. Mghabghab, R. Aris-Brosou, S. 2025-11-20 doi:10.1101/2025.11.20.689475 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ Reconstructing the network of horizontal gene exchange in bacteria to differentiate direct and indirect transfers ]]> https://biorxiv.org/content/10.1101/2025.11.20.689518v1?rss=1 Sheinman, M. Stentella, T. Etheimer, P. Massip, F. Arndt, P. F. 2025-11-21 doi:10.1101/2025.11.20.689518 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Ferroptosis governs lymphatic vessel growth and regression ]]> https://biorxiv.org/content/10.1101/2025.11.18.689033v1?rss=1 Drekolia, M.-K. Wang, D. Chen, Y. Du, Y. Wittig, J. Xu, R. Schilling, D. Aliraj, B. Mettner, J. Gupta, L. Xu, C. Guenther, S. Cetic, R. Matthess, Y. Fleming, I. Kaulich, M. Dobreva, G. Weigert, A. Dick, T. P. Dikic, I. Stolz, A. Yaniv, K. Linkermann, A. Hu, J. Bibli, S.-I. 2025-11-24 doi:10.1101/2025.11.18.689033 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Subanesthetic Ketamine Disrupts Predictive Signaling in the Prefrontal Cortex ]]> https://biorxiv.org/content/10.1101/2025.11.24.690250v1?rss=1 Corrigan, B. W. Roussy, M. Luna, R. Gulli, R. A. Schall, J. D. Sachs, A. J. Palaniyappan, L. Martinez-Trujillo, J. C. 2025-11-28 doi:10.1101/2025.11.24.690250 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ ClsDiff-AMP30: Generating Antimicrobial Peptides by a Classifier Guidance Noise Predictor ]]> https://biorxiv.org/content/10.1101/2025.11.25.690620v1?rss=1 Yan, J. Cai, J. Li, Y. Lin, Z. Xian, W. Wei, X. Lei, I. F. Zhou, M. Campbell-Valois, F.-X. Siu, S. W. I. 2025-11-29 doi:10.1101/2025.11.25.690620 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Azimuthal Segment Imaging in cryo-STEM Tomography ]]> https://biorxiv.org/content/10.1101/2025.11.26.690630v1?rss=1 Kirchweger, P. Seifer, S. Wolf, S. G. Varsano, N. Zens, B. Schur, F. K. Elbaum, M. 2025-11-29 doi:10.1101/2025.11.26.690630 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Reverse-engineering B-Arrestin Bias in the d-Opioid Receptor ]]> https://biorxiv.org/content/10.1101/2025.11.27.690850v1?rss=1 Stepniewski, T. M. Zeghal, M. Szabo, I. Solano, M. M. Rodriguez-Espigares, I. Korchevaya, E. Torrens-Fontanals, M. de Fabritiis, G. Filipek, S. Giguere, P. M. Selent, J. 2025-12-01 doi:10.1101/2025.11.27.690850 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Cell surface ATP6V1B2 marks a subset of persistent senescent cells with increased resistance to apoptosis ]]> https://biorxiv.org/content/10.1101/2025.11.30.691415v1?rss=1 Freizus, N. Majewska, J. M. Ovadya, Y. Kopitman, E. Porat, Z. Mayo, A. Meir-Salame, T. Dassa, B. Stelzer, G. Alon, U. Krizhanovsky, V. 2025-12-01 doi:10.1101/2025.11.30.691415 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Bacterial strains in the human gut associate with host physiology ]]> https://biorxiv.org/content/10.1101/2025.11.30.691432v1?rss=1 Shoer, S. Godneva, A. Weinberger, A. Pollard, K. S. Pilpel, Y. Segal, E. 2025-12-01 doi:10.1101/2025.11.30.691432 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Damselflies Overcome Color Saturation Barriers of Photonic Glasses via Structural Dispersion and Pigment Loading ]]> https://biorxiv.org/content/10.64898/2025.11.29.691096v1?rss=1 Lemcoff, T. Alus, L. Batushansky, A. Fishman, Y. Theodor, N. Shavit, K. Hyitner, L. Kelber, A. Haataja, J. Oron, D. Palmer, B. A. 2025-12-02 doi:10.64898/2025.11.29.691096 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Systematic discovery of TIR-based immune signaling systems in bacteria ]]> https://biorxiv.org/content/10.64898/2025.12.03.692087v1?rss=1 Yirmiya, E. Leavitt, A. Hurieva, B. alkovich, A. H. Bechon, N. Rousset, F. Osterman, I. Sorek, R. 2025-12-03 doi:10.64898/2025.12.03.692087 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ An extended structure of the intracellular domain of the Torpedo nicotinic acetylcholine receptor and its proposed interactions with rapsyn ]]> https://biorxiv.org/content/10.64898/2025.12.03.692134v1?rss=1 Henault, C. M. Habes, M. Tessier, C. J. G. Baenziger, J. E. 2025-12-04 doi:10.64898/2025.12.03.692134 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ Nucleic acid strand length governs mitochondrial reprogramming and mtROS-associated antiviral responses following TLR3 engagement ]]> https://biorxiv.org/content/10.64898/2025.12.03.691914v1?rss=1 LMW). Further, selectively targeting the mtROS derived from Complex I leads to augmented type I IFN production. Overall, these findings highlight that targeting specific sources of mtROS without affecting electron flow may be a potential avenue for specific augmentation of antiviral responses during viral infections. ]]> Ahmed, D. Al Daraawi, M. Humphrey, A. Abdo, O. Roy, D. Sheridan, M.-E. Versey, Z. Mejlaoui, R. Jaworski, A. Edwards, A. Abizaid, A. Kumar, A. Golshani, A. Cassol, E. 2025-12-05 doi:10.64898/2025.12.03.691914 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ In form for a swarm: programmable neutrophil swarming impacts infection outcome ]]> https://biorxiv.org/content/10.64898/2025.12.03.692046v1?rss=1 Borbora, S. M. Williantarra, I. Rinaldi, G. Cui, C. Luo, E. Y. Walker, H. A. Craven, H. M. Desrentes, A. Gov, N. Sarris, M. 2025-12-05 doi:10.64898/2025.12.03.692046 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Metabolic Rewiring by alpha-Synuclein Enables Mitohormetic Protection ]]> https://biorxiv.org/content/10.64898/2025.12.05.692538v1?rss=1 Gross, A. Geula, S. Grosheva, I. Zaltsmann, Y. Regev, L. Chourasia, S. 2025-12-07 doi:10.64898/2025.12.05.692538 Cold Spring Harbor Laboratory Press 2025-12-07 <![CDATA[ Structure-based design of antibody repertoires with drug-like properties ]]> https://biorxiv.org/content/10.64898/2025.12.10.693474v1?rss=1 Tennenhouse, A. Wilen, R. Gaiduk, S. Borni, S. Yardeni, E. H. Goldsmith, M. Albeck, S. Unger, T. Diskin, R. Fleishman, S. J. 2025-12-10 doi:10.64898/2025.12.10.693474 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Polar ecosystems harbor highly divergent DNA viruses underrepresented in current reference databases ]]> https://biorxiv.org/content/10.64898/2025.12.09.693195v1?rss=1 Kulkarni, V. Aris-Brosou, S. 2025-12-11 doi:10.64898/2025.12.09.693195 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Funders' expectations for open science in cardiovascular research: A Scoping review of the largest cardiovascular research funders ]]> https://biorxiv.org/content/10.64898/2025.12.11.693828v1?rss=1 Vieira Armond, A. C. Alaoui, A. M. Moher, D. Rouleau, J. Cobey, K. D. 2025-12-16 doi:10.64898/2025.12.11.693828 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Pharmacological Inhibition of FKBP51 Mitigates Early Life Adversity-Induced Social Deficits ]]> https://biorxiv.org/content/10.64898/2025.12.13.694102v1?rss=1 Bordes, J. Ji, X. Gasperoni, S. Sudre-Chinsky, C. Harbich, D. Flachskamm, C. Fontanet, P. Narayan, S. Uhr, M. Namendorf, C. Chen, A. Hausch, F. Lopez, J. P. Schmidt, M. V. 2025-12-16 doi:10.64898/2025.12.13.694102 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ High-Fidelity Tuning of Olfactory Mixture Distances in the Perceptual Space of Smell Through a Community Effort ]]> https://biorxiv.org/content/10.64898/2025.12.13.694160v1?rss=1 Satarifard, V. Sisson, L. Han, Y. Ilidio, P. Hladis, M. Lalis, M. Song, X. Yin, W. Ravia, A. Zheng, C. X. Andreoletti, G. Albrecht, J. Pellegrino, R. Wang, Z. Yang, S. D'hondt, R. Ghinis, A. de Boer, J. Nakano, F. K. Gharahighehi, A. DREAM Olfactory Mixtures Prediction Consortium, Sanchez-Lengeling, B. Keller, A. Vosshall, L. B. Fiorucci, S. Tewari, A. Topin, J. Vens, C. Bjorkman, M. Kragic, D. Sobel, N. Christakis, N. A. Mainland, J. D. Meyer, P. 2025-12-16 doi:10.64898/2025.12.13.694160 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Metabolic, epigenetic and transcriptomic alterations in postnatal 16p11.2 deficient murine astrocytes ]]> https://biorxiv.org/content/10.64898/2025.12.16.694710v1?rss=1 Blakeley, N. Naz, S. Liu, Z. Renner, T. Leclerc, S. Comin, C. H. da Silva, M. V. Vergette, C. Porter, C. J. Perkins, T. J. Lacoste, B. 2025-12-17 doi:10.64898/2025.12.16.694710 Cold Spring Harbor Laboratory Press 2025-12-17 <![CDATA[ Reinke crystals are immunoreactive for purine-synthesizing metabolic enzymes ]]> https://biorxiv.org/content/10.64898/2025.12.18.695235v1?rss=1 Woulfe, J. Flood, T. Faulkes, S. Munoz, D. G. 2025-12-22 doi:10.64898/2025.12.18.695235 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Systemic administration of PD-L1 blocking antibodies leads to removal of senescent microglia ]]> https://biorxiv.org/content/10.64898/2025.12.22.695923v1?rss=1 Androsova, Y. Kertser, A. Partney, H. Nathansohn, B. Ibraheem, A. Abellanas, M. A. Croese, T. Salame, T. M. Akiva, H. Krizhanovsky, V. Schwartz, M. 2025-12-24 doi:10.64898/2025.12.22.695923 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ Myelin Supports Cortical Circuit Function Underlying Skilled Movement ]]> https://biorxiv.org/content/10.64898/2025.12.23.696289v1?rss=1 Gagon, K. Della Flora Nunes, G. Nettles, D. Nguyen, T. Carter, E. R. Lins, A. Williams, R. Lefebvre, J. Denman, D. Hughes, E. G. Welle, C. G. 2025-12-24 doi:10.64898/2025.12.23.696289 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ The Two Frontiers Project Field Handbook and OpenTools: Standardizing microbial fieldwork for biobank-scale sequencing and culturomics ]]> https://biorxiv.org/content/10.64898/2025.12.25.695958v1?rss=1 Ryon, K. A. Henriksen, J. R. Johns, A. Diana, S. Boddy, V. Carpenter, G. Miller, E. Kent, B. Peixoto, R. Tierney, B. T. 2025-12-25 doi:10.64898/2025.12.25.695958 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ Cell-type-specific adaptations to mitochondrial stress underly the neurological presentations of MTRFR mutations ]]> https://biorxiv.org/content/10.64898/2025.12.30.696998v1?rss=1 Zarate-Mendez, M. O'Connor, K. Malig, N. Podmanicky, O. Kleniuk, J. Spendiff, S. Reid, E. Lochmüller, H. Hathazi, D. Horvath, R. 2025-12-31 doi:10.64898/2025.12.30.696998 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Changes in microhabitat structure around amphibian breeding ponds in the northern Rocky Mountains following severe wildfire ]]> https://biorxiv.org/content/10.64898/2026.01.03.697496v1?rss=1 Skretting, T. Smith, A. M. McCune, J. L. Lee-Yaw, J. A. 2026-01-03 doi:10.64898/2026.01.03.697496 Cold Spring Harbor Laboratory Press 2026-01-03 <![CDATA[ A panoramic view of the expression and function of the Doublesex/DMRT gene family in C. elegans ]]> https://biorxiv.org/content/10.64898/2026.01.01.697290v1?rss=1 Wang, C. Salzberg, Y. Oren-Suissa, M. Hobert, O. 2026-01-05 doi:10.64898/2026.01.01.697290 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ Lysosome-Related Organelles Orchestrate Guanine Crystal Formation in Pigment Cells ]]> https://biorxiv.org/content/10.64898/2026.01.05.697611v1?rss=1 Gorelick-Ashkenazi, A. Barzilay, Y. Lerer-Goldshtein, T. Olender, T. Eyal, Z. Glaser, M. Broder, Y. Mishol, N. Deis, R. Kedmi, M. Gur, D. 2026-01-05 doi:10.64898/2026.01.05.697611 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ Features affecting Cas9-Induced Editing Efficiency and Patterns in Tomato: Evidence from a Large CRISPR Dataset ]]> https://biorxiv.org/content/10.64898/2026.01.06.696182v1?rss=1 Cucuy, A. Ben-Tov, D. Melamed-Bessudo, C. Honig, A. Cohen, B. A. Levy, A. A. 2026-01-07 doi:10.64898/2026.01.06.696182 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ IL-12R signaling promotes type 1 regulatory T cell specialization by sustaining T-bet ]]> https://biorxiv.org/content/10.64898/2026.01.10.698646v1?rss=1 Estrada Brull, A. Carlen, Y. M. Revert Rubio, L. Zwicky, P. Mundt, S. Becher, B. Joller, N. 2026-01-11 doi:10.64898/2026.01.10.698646 Cold Spring Harbor Laboratory Press 2026-01-11 <![CDATA[ Eco-evolutionary dynamics in competitive systems: Rescue or murder? ]]> https://biorxiv.org/content/10.64898/2026.01.14.699340v1?rss=1 Leoz, S. Lutscher, F. Allhoff, K. T. Govaert, L. 2026-01-14 doi:10.64898/2026.01.14.699340 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ The 3D Genome of Gigaspora margarita Unveils Stable Chromatin and Nucleolar Organization and Symbiont-Dependent Genome Dynamics ]]> https://biorxiv.org/content/10.64898/2026.01.14.699541v1?rss=1 Mugambi, K. M. Oliveira, J. I. N. Magurno, F. Salviolo, A. Lanfranco, L. Novero, M. Ghignone, S. Yildirir, G. Wang, Y. Bonfante, P. Corradi, N. 2026-01-15 doi:10.64898/2026.01.14.699541 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ A Multiomic Analysis of Cachectic Mice Reveals Cancer Driven Suppression of Muscle Stem Cell Differentiation ]]> https://biorxiv.org/content/10.64898/2026.01.12.699072v1?rss=1 Blackburn, D. M. Hernandez-Corchado, A. Sahinyan, K. Khorasani, H. H. Lazure, F. Richard, V. Qu, D. Wang, S. Borchers, C. H. Jahani-Asl, A. Najafabadi, H. S. Koromilas, A. E. Soleimani, V. D. 2026-01-16 doi:10.64898/2026.01.12.699072 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ Mitigating Bias in Spatial Transcriptomic Pipelines via Human Feedback ]]> https://biorxiv.org/content/10.64898/2026.01.15.699786v1?rss=1 Boyeau, P. Bates, S. Ergen, C. Jordan, M. I. Yosef, N. 2026-01-16 doi:10.64898/2026.01.15.699786 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ Chemical control of CSA geometry enables relaxation-optimized 19F-13C NMR probes ]]> https://biorxiv.org/content/10.64898/2026.01.19.700399v1?rss=1 Shim, J.-G. Georgieva, N. N. Robson, S. A. Burdzhiev, N. T. Petrov, O. I. Cui, J. Acharya, A. Kuprov, I. Gelev, V. Ziarek, J. J. 2026-01-20 doi:10.64898/2026.01.19.700399 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ dna-parser: a Python library written in Rust for fast encoding of DNA and RNA sequences ]]> https://biorxiv.org/content/10.64898/2026.01.20.700656v1?rss=1 Vilain, M. Aris-Brosou, S. 2026-01-21 doi:10.64898/2026.01.20.700656 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ The causes and consequences of human-specific DNA methylation ]]> https://biorxiv.org/content/10.64898/2026.01.20.700710v1?rss=1 Ma, Z. Starr, A. L. Gokhman, D. Fraser, H. 2026-01-21 doi:10.64898/2026.01.20.700710 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ MetaTree: an interactive web platform for hierarchical data visualization and multi-group comparison ]]> https://biorxiv.org/content/10.64898/2026.01.22.701099v1?rss=1 Wu, Q. Zhang, A. Ning, Z. Figeys, D. 2026-01-23 doi:10.64898/2026.01.22.701099 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Pex9 regulates TORC2 during the cellular response to oxidative stress ]]> https://biorxiv.org/content/10.64898/2026.01.25.701303v1?rss=1 Angel, M. Szitenberg, A. Carmi, M. Asraf, Y. Barkai, N. Schuldiner, M. 2026-01-25 doi:10.64898/2026.01.25.701303 Cold Spring Harbor Laboratory Press 2026-01-25 <![CDATA[ Chemoproteomics discovery of a CNS-penetrant covalent inhibitor of PIKfyve ]]> https://biorxiv.org/content/10.64898/2026.01.26.701341v1?rss=1 Burton, A. J. Chupak, L. S. Davis, A. J. Mady, A. S. Meniconi, M. Teobald, B. Dorsey, B. W. Byrne, L. R. Mulhern, R. Lundeen, B. Sorensen, E. W. Patel, B. Brennan, S. Kormocha, D. Tommasi, R. Simpson, G. L. Keillor, J. W. D'Agostino, L. Huang, P. S. Penebre, E. 2026-01-28 doi:10.64898/2026.01.26.701341 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ A Genome-wide Visual Screen Identifies Lysophosphatidylcholine as Counter Spatial Regulator of DAG and Sterols in Yeast ]]> https://biorxiv.org/content/10.64898/2026.01.27.702077v1?rss=1 Henderson, A. Lalani, A. Ganesan, S. Mesa-Galloso, H. Zung, N. Portela, P. Sosa Ponce, L. Baetz, K. Schuldiner, M. Zaremberg, V. 2026-01-28 doi:10.64898/2026.01.27.702077 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ Bacterial defense via RES-mediated NAD+ depletion is countered by phage phosphatases ]]> https://biorxiv.org/content/10.64898/2026.01.28.702374v1?rss=1 Osterman, I. Hurieva, B. Yirmiya, E. Hochhauser, D. Itkin, M. Malitsky, S. Sorek, R. 2026-01-28 doi:10.64898/2026.01.28.702374 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ FOXA2 potently represses viral gene expression by targeting NF-kB-dependent transcription in liver cells ]]> https://biorxiv.org/content/10.64898/2026.01.27.701993v1?rss=1 Suleiman, T. Walker, M. D. 2026-01-29 doi:10.64898/2026.01.27.701993 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ A Chemical-Genetic Interaction Matrix Reveals Drug Mechanism and Genetic Architecture ]]> https://biorxiv.org/content/10.64898/2026.01.28.701823v1?rss=1 12,000 high confidence chemical-genetic interactions (CGIs). This dataset revealed many previously unappreciated off-target effects for well-characterized compounds and novel MOAs for uncharacterized compounds. The CGI matrix uncovered dense genetic modules that yielded new biological insights into phospholipidosis, mitotic regulation, metabolism, the DNA damage response, and mTOR signaling. The dataset allowed identification of multi-drug sensitization and resistance mechanisms, inference of gene function, elaboration of cross-process connectivity, evaluation of the cell type specificity of CGIs, prediction of chemical synergism, and extensive annotation of understudied genes. This resource provides a map of the genetic landscape in human cells and a framework to help guide drug discovery. ]]> Coulombe-Huntington, J. Bertomeu, T. Huard, C. Chatr-aryamontri, A. St-Cyr, D. J. Sanchez-Osuna, M. Papadopoli, D. Normandin, K. Paydar, M. McLaughlan, S. St-Denis, C. Zhang, L. Say, H. Palou, R. Stark, C. Breitkreutz, B.-J. van der Sloot, A. M. Manohar, S. Lavoie, H. Borden, K. L. B. Raught, B. D'Amours, D. Sicheri, F. Verreault, A. Mader, S. Meloche, S. Therrien, M. Thibault, P. Wilhelm, B. Dirks, P. B. Aitchison, J. D. Patton, E. E. King, R. W. Roux, P. P. Sauvageau, G. Hoang, T. Marinier, A. Harrington, L. Kwok, B. Archambault, V. Topisirovic, I. Ty 2026-01-29 doi:10.64898/2026.01.28.701823 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ Catch-and-Display Immunoassay as an Accessible Platform for Digital Biomarker Detection ]]> https://biorxiv.org/content/10.64898/2026.01.27.702166v1?rss=1 Liu, Y. Walker, S. Klaczko, M. Singer, B. Godin, M. Tabard-Cossa, V. Flax, J. McGrath, J. 2026-01-30 doi:10.64898/2026.01.27.702166 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ From biting to engulfment: curvature-actin coupling controls phagocytosis of soft, deformable targets ]]> https://biorxiv.org/content/10.64898/2026.01.28.702248v1?rss=1 Sadhukhan, S. Cornell, C. E. Sandhu, M. K. Peeters, Y. Penic, S. Iglic, A. Fletcher, D. A. Jaumouille, V. Vorselen, D. Gov, N. S. 2026-01-30 doi:10.64898/2026.01.28.702248 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ immgenT: A Comprehensive Reference of Convergent T-cell States in the Mouse ]]> https://biorxiv.org/content/10.64898/2026.01.30.702892v1?rss=1 Magill, I. Casey, O. Mallah, D. Panigrahi, S. S. Zhou, L. Barreiro del Rio, O. Bangs, D. J. Bee, G. C. W. Borys, S. Choi, J. Ergen, C. Ferraj, E. Fiusco, M. Freuchet, A. Galletti, G. Globig, A.-M. Heim, T. Imianowski, C. Lai, R. Liang, Z. Lebron Figueroa, A. Lucas, E. D. Merkenschlager, J. Osum, K. Reilly, S. Shinkawa, T. Thefaine, C. E. Weiss, E. S. Yang, L. Zhang, S. Zorzetto-Fernandes, A. L. Croteau, J. D. Alegre, M.-L. Behar, S. M. Bosselut, R. Brossay, L. Cadwell, K. Chervonsky, A. Gapin, L. Hamilton, S. E. Huh, J. R. Iliev, I. Jabri, B. Jameson, 2026-02-02 doi:10.64898/2026.01.30.702892 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Single-cell transcriptome imaging reveals conserved and virulence-linked phenotypic states in bacteria ]]> https://biorxiv.org/content/10.64898/2026.02.01.703127v1?rss=1 Persky, Z. Ciolli Mattioli, C. Garcia, K. Z. Azran, O. Avraham, R. Dar, D. 2026-02-02 doi:10.64898/2026.02.01.703127 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Intelliwaste: NMR of 13C-labeled Spent Media Enables Non-Invasive Metabolic Fingerprinting of Pluripotent Stem Cells and LIS1-Associated Neuropathology ]]> https://biorxiv.org/content/10.64898/2026.02.04.703261v1?rss=1 95% 13C1-Glucose. Under these conditions, 13C3-lactate emerged as the most abundant labeled product, with 20-50-fold lower fluxes to 13C3-alanine, 13C2-acetate, 13C3-serine, and 13C3-pyruvate, and 100-300-fold lower fluxes to 13C1-formate and multiple 13C-labeled glutamate species. These profiles allow for precise quantification of fractional metabolic isotopic labeling and glucose-derived carbon flow. To demonstrate biological utility, we first examine the effect of L-glutamine omission, which selectively reduces 13C3-alanine/13C3-lactate and 13C4-glutamate/13C3-lactate flux ratios, while the 13C3-Glutamate/13C3-Lactate and 13C2-Glutamate/13C3-Lactate flux ratios remained unchanged. These findings suggest a specific role for extracellular glutamine in modulating the activity of alanine aminotransferase and pyruvate carboxylase. We then characterized LIS1 mutant hESCs--a model of lissencephaly--and observed significantly increased flux ratios involving 13C4-, 13C3-, and 13C2-glutamate relative to 13C3-lactate, indicating enhanced glutamate production via the TCA cycle. These findings establish Intelliwaste as a powerful tool for metabolic profiling in the study of human neurodevelopment and disease. Its non-destructive nature makes it particularly well-suited for tracking metabolic changes during differentiation and in patient-derived organoid models of neurological disorders. ]]> Harris, T. Karlinski Zur, M. Sapir, T. Reiner, O. Schmidt, R. 2026-02-06 doi:10.64898/2026.02.04.703261 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ A framework for reparative CAR T engineering in the CNS ]]> https://biorxiv.org/content/10.64898/2026.02.09.703122v1?rss=1 Shalita, R. Ben Yehuda, M. Boskovic, P. Frid, Y. Kuznetsov, Y. Tsoory, M. Kalchenko, V. Brenner, O. David, E. Mazuz, K. Majzner, R. G. Kipnis, J. Amit, I. 2026-02-11 doi:10.64898/2026.02.09.703122 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ 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[ A cortical basis for perception of internal gut sensations ]]> https://biorxiv.org/content/10.64898/2026.02.11.705298v1?rss=1 Rafael, O. Shtiglitz, S. Miller, J. Prilutski, Y. Talpir, I. Lavi, A. Livneh, Y. 2026-02-12 doi:10.64898/2026.02.11.705298 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ Spatial Rewiring of Enterocyte Identity in Celiac Disease ]]> https://biorxiv.org/content/10.64898/2026.02.14.705877v1?rss=1 Barkai, T. Frieman-Sharabi, R. Bahar Halpern, K. Novoselsky, R. Korem Kohanim, Y. Shir, S. Golani, O. Goliand, I. Addadi, Y. Kedmi, M. Keren-Shaul, H. Prichislov, L. Guz-Mark, A. Nissim, H. Shamir, R. Shouval, D. Itzkovitz, S. 2026-02-17 doi:10.64898/2026.02.14.705877 Cold Spring Harbor Laboratory Press 2026-02-17 <![CDATA[ Fusion of lipid membranes: an alternative pathway ]]> https://biorxiv.org/content/10.64898/2026.02.19.706911v1?rss=1 Jin, D. Li, Z. Roke, S. Klein, J. 2026-02-20 doi:10.64898/2026.02.19.706911 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Linking biochemical and cellular efficacy of MERS coronavirus main protease inhibitors ]]> https://biorxiv.org/content/10.64898/2026.02.20.707097v1?rss=1 La, V. N. T. Lahav, N. Rodriguez, M. Diaz-Tapia, R. McGovern, B. Benjamin, J. Barr, H. Kang, L. Chodera, J. D. Minh, D. 2026-02-21 doi:10.64898/2026.02.20.707097 Cold Spring Harbor Laboratory Press 2026-02-21 <![CDATA[ Cilia beating of ependymal cells regulates adult neural stem cell quiescence via mechanical forces mediated by PKD1/2-TRPM3 ]]> https://biorxiv.org/content/10.64898/2026.02.26.708348v1?rss=1 Bressan, C. Gengatharan, A. Rodriguez-Aller, R. Richter, M. L. Snapyan, M. Fischer-Sternjak, J. Rezaeezadeh Roukerd, M. Roisin, N. Cherinet, A. Biernaskie, J. Habibi, E. Gotz, M. Saghatelyan, A. 2026-03-02 doi:10.64898/2026.02.26.708348 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ Universal functionalization of extracellular vesicles with nanobody adapters ]]> https://biorxiv.org/content/10.64898/2026.02.28.708726v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@189c052org.highwire.dtl.DTLVardef@b14f76org.highwire.dtl.DTLVardef@d7dab1org.highwire.dtl.DTLVardef@156b9ab_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Galisova, A. Zahradnik, J. Merunkova, E. Havlicek, D. Uskoba, J. Porat, Z. Jirak, D. 2026-03-03 doi:10.64898/2026.02.28.708726 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Diffusion-ACP39: A Decoder-Adaptive Latent Diffusion Framework for Generative Anticancer Peptide Discovery ]]> https://biorxiv.org/content/10.64898/2026.03.04.709539v1?rss=1 Yan, J. Wu, Q. Li, Y. Cai, J. Zhou, M. CACPbell-Valois, F.-X. Siu, S. W. 2026-03-06 doi:10.64898/2026.03.04.709539 Cold Spring Harbor Laboratory Press 2026-03-06 <![CDATA[ Invasion histories reveal most North American introduced plants have not yet reached climatic stasis. ]]> https://biorxiv.org/content/10.64898/2026.03.05.709936v1?rss=1 Roach-Krajewski, M. Smith, T. W. Kharouba, H. M. 2026-03-07 doi:10.64898/2026.03.05.709936 Cold Spring Harbor Laboratory Press 2026-03-07 <![CDATA[ Chromatin tethering to the nuclear envelope enhances its accessibility to RNAPII and promotes chromatin asymmetric organization ]]> https://biorxiv.org/content/10.64898/2026.03.06.710131v1?rss=1 Lorber, D. Azuri, I. Kumar, A. Rotkopf, R. Safran, S. Volk, T. 2026-03-07 doi:10.64898/2026.03.06.710131 Cold Spring Harbor Laboratory Press 2026-03-07 <![CDATA[ A Ubiquitin network safeguards cell identity by continuously degrading stem-cell related translational machinery ]]> https://biorxiv.org/content/10.64898/2026.03.06.709266v1?rss=1 Daniel, S. Ghanem, R. Makhzumy, M. Bitman-Lotan, E. Soffers, J. Henriksen, J. c. Sarusi-Portuguez, A. Rissland, O. S. Mohan, R. D. Shiber, A. Orian, A. M. 2026-03-08 doi:10.64898/2026.03.06.709266 Cold Spring Harbor Laboratory Press 2026-03-08 <![CDATA[ A bacterial extracellular matrix protein forms a supramolecular metallogel ]]> https://biorxiv.org/content/10.64898/2026.03.09.710396v1?rss=1 97% water content. Electron- and atomic force-microscopies as well as small angle X-ray scattering measurements show that cross-linking with zinc ions induces a transition in TasA morphology from one-dimensional fibers to two-dimensional sheets. Electron paramagnetic resonance measurements then show that such a significant morphological shift is associated with molecular changes in the coordination environment of zinc ions, which lead to structural changes at the protein level. When assembling into macroscopic networks, TasA-Zn metallogels exhibit viscoelastic properties and a fast recovery following an excessive strain. These metallogels represent a novel class of bacterially-derived ECMs that form easily at room temperature without covalent crosslinking, and may be used as a natural matrix-mimics in biofilm models for infection studies. ]]> Ghrayeb, M. Ashman, A. Mukhopadhyay, S. Felig, A. Joppf, J. Levy-Kalisman, Y. Raviv, U. Bertinetti, L. Politi, Y. Zaburdaev, V. Ruthstein, S. Chai, L. 2026-03-09 doi:10.64898/2026.03.09.710396 Cold Spring Harbor Laboratory Press 2026-03-09 <![CDATA[ Synaptic Input Triggers On-Demand Spine-Specific Mitochondrial ATP Production and Delivery ]]> https://biorxiv.org/content/10.64898/2026.03.09.708229v1?rss=1 Paquin-Lefebvre, F. Kushnireva, L. Xu, Z. Kubler, S. Feofilaktova, T. Laughlin, S. Rouach, N. Korkotian, E. Holcman, D. 2026-03-11 doi:10.64898/2026.03.09.708229 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Multimodal reference brain atlas of adult Danionella cerebrum ]]> https://biorxiv.org/content/10.64898/2026.03.09.710483v1?rss=1 Kadobianskyi, M. Henninger, J. Markov, D. Groneberg, A. Veith, J. Renz, M. A. Atabay, K. D. Reddien, P. Maler, L. Judkewitz, B. 2026-03-11 doi:10.64898/2026.03.09.710483 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Contributions of error correction and the spindle assembly checkpoint to mitotic timing and fidelity ]]> https://biorxiv.org/content/10.64898/2026.03.10.710927v1?rss=1 Ha, G. Qiu, L. Amir, A. Needleman, D. 2026-03-13 doi:10.64898/2026.03.10.710927 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Plasma β-hydroxybutyrate Concentrations in Young Adult Females After a High-Fat Meal Under Normoxemia, Intermittent Hypoxemia, and Continuous Hypoxemia ]]> https://biorxiv.org/content/10.64898/2026.03.11.711039v1?rss=1 Goulet, N. Larocque, A. Marcoux, C. Bourgon, V. Mauger, J.-F. Amaratunga, R. Imbeault, P. 2026-03-13 doi:10.64898/2026.03.11.711039 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Spatial analysis reveals the evolving organization of low-grade and high-grade IDH-mutant glioma ]]> https://biorxiv.org/content/10.64898/2026.03.12.709536v1?rss=1 Hoefflin, R. Greenwald, A. C. Galili Darnell, N. Mount, C. W. Tiomkin, Y. Simkin, D. Patterson, A. B. Gonzalez Castro, L. N. Goliand, I. Golani, O. Joseph, K. Beck, J. Ravi, V. M. Kedmi, M. Keren-Shaul, H. Addadi, Y. Neidert, M. C. Suva, M. L. Tirosh, I. 2026-03-13 doi:10.64898/2026.03.12.709536 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ A stress-function tradeoff organizes epithelial heterogeneity across spatial scales in the human thyroid ]]> https://biorxiv.org/content/10.64898/2026.03.12.711294v1?rss=1 Korem Kohanim, Y. Barkai, T. Novoselsky, R. Shir, S. Bahar Halpern, K. Reich-Zeliger, S. Elkahal, J. Tessler, I. Shivatzki, S. Schwartz, I. Remer, E. Avior, G. Hoefllin, R. Kedmi, M. Keren-Shaul, H. Goliand, I. Addadi, Y. Golani, O. Alon, E. Itzkovitz, S. Medzhitov, R. 2026-03-16 doi:10.64898/2026.03.12.711294 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ Lipid droplets accumulate and delay regulated cell death execution ]]> https://biorxiv.org/content/10.64898/2026.03.16.712084v1?rss=1 Shan, Y. Stopa, K. B. Rouchidane Eyitayo, A. Jollivet, F. Girard, V. Jamard, C. Sapozhnikov, L. Arama, E. Szecsi, J. Bendahmane, M. Davoust-Nataf, N. Walter, L. Liu, M. Aznar, N. Ichim, G. Mollereau, B. 2026-03-17 doi:10.64898/2026.03.16.712084 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Protein disorder controls allostery in DNA ]]> https://biorxiv.org/content/10.64898/2026.03.17.710445v1?rss=1 Rosenblum, G. Terterov, I. Mishra, S. K. Elad, N. Gianga, T.-M. Hussain, R. Siligardi, G. Hofmann, H. 2026-03-18 doi:10.64898/2026.03.17.710445 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[ Epithelial MHC II antigen presentation dynamically informs intestinal homeostasis and injury ]]> https://biorxiv.org/content/10.64898/2026.03.18.712348v1?rss=1 Holiar, V. Rudenko, V. Weller, C. Naumova, M. Lebon, S. Canella, M. Busko, P. Sarusi-Portuguez, A. Shalit, T. Habshush Menachem, A. Adir, I. Petrover, Z. Greenberg, P. Katina, C. Gradchenko, P. Toval, B. Yissachar, N. Sagi, I. Tzahor, E. Levin, Y. Samuels, Y. Biton, M. 2026-03-20 doi:10.64898/2026.03.18.712348 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ LOSS OF PARKIN DISRUPTS NUCLEAR AND MITOCHONDRIAL PROGRAMS REQUIRED FOR MUSCLE REGENERATION ]]> https://biorxiv.org/content/10.64898/2026.03.20.712989v1?rss=1 Gourlay, M. Abbasi, M. R. Cairns, G. Thumiah-Mootoo, M. Racine, J. Ly, H. M. Wang, A. Larionov, N. Blais, A. Khacho, M. Burelle, Y. 2026-03-23 doi:10.64898/2026.03.20.712989 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ Multiple mTOR RNA localization signals regulate subcellular protein synthesis and axonal growth ]]> https://biorxiv.org/content/10.64898/2026.03.22.713398v1?rss=1 Samra, N. Sahoo, P. K. Di Pizio, A. Buchanan, C. N. Okladnikov, N. Abraham, O. Ben-Dor, S. Haffner-Krausz, R. Rishal, I. Twiss, J. L. Fainzilber, M. 2026-03-24 doi:10.64898/2026.03.22.713398 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Intracellular carbon storage enables starvation survival in marine bacteria ]]> https://biorxiv.org/content/10.64898/2026.03.25.714165v1?rss=1 Shlakhter, O. Talmor, Y. Malitsky, S. Otikovs, L. Szitenberg, A. Segev, E. 2026-03-25 doi:10.64898/2026.03.25.714165 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Cancer resistance to therapy by tissue-level homeostatic feedback ]]> https://biorxiv.org/content/10.64898/2026.03.25.714177v1?rss=1 Somer, J. Straussman, R. Alon, U. Mannor, S. 2026-03-27 doi:10.64898/2026.03.25.714177 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ A stapled peptide inhibitor of MDM2 enables pharmacological activation of p53 in zebrafish ]]> https://biorxiv.org/content/10.64898/2026.03.26.714438v1?rss=1 Kheder, S. Krkoska, M. Mihalic, F. Kobar, K. Andrysik, Z. Bräutigam, L. Lindström, S. Berman, J. N. Lane, D. P. Lama, D. Kannan, P. 2026-03-30 doi:10.64898/2026.03.26.714438 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[ Branch-specific axon pruning induced by Dpr4/DIP-{Theta} transneuronal interactions ]]> https://biorxiv.org/content/10.64898/2026.03.29.715068v1?rss=1 Meltzer, H. Shachar, S. Sergeeva, A. Bornstein, B. Shapira, G. Katsamba, P. S. Mannepalli, S. M. Bahna, F. Moreno, N. Alyagor, I. Berkun, V. Currier, T. A. Shapiro, L. Honig, B. Schuldiner, O. 2026-03-31 doi:10.64898/2026.03.29.715068 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Population genomics reveals multi-scale mechanisms sustaining schistosomiasis re-emergence in a near-elimination setting ]]> https://biorxiv.org/content/10.64898/2026.03.30.715205v1?rss=1 Guss, H. Francioli, Y. Grover, E. Hill, A. Zou, W. Wade, K. Pike, H. Gopalan, S. S. Yang, L. Bo, Z. Pollock, D. Carlton, E. Castoe, T. A. 2026-04-01 doi:10.64898/2026.03.30.715205 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Metabolostasis failure thresholds are linked with network topology, metabolite solubility, and translational control ]]> https://biorxiv.org/content/10.64898/2026.03.31.715129v1?rss=1 A. Levkovich, S. M Lim, C. A. Marzini, E. Adsi, H. Lahav, M. Sogolovsky-Bard, I. Gartner, M. Kaplan, K. DeRowe, Y. Pasmanik-Chor, M. Brandis, A. Vendruscolo, M. Gazit, E. Laor Bar-Yosef, D. 2026-04-02 doi:10.64898/2026.03.31.715129 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ The U-method: Leveraging expression probability for robust biological marker detection ]]> https://biorxiv.org/content/10.64898/2026.03.31.715470v1?rss=1 Stein, Y. Lavon, H. Hindi Malowany, M. Arpinati, L. Scherz-Shouval, R. 2026-04-02 doi:10.64898/2026.03.31.715470 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ Histone Modification Metapeaks are Epigenetic Landmarks Predictive of Cell State ]]> https://biorxiv.org/content/10.64898/2026.03.31.715657v1?rss=1 Tanner, R. M. Perkins, T. J. 2026-04-02 doi:10.64898/2026.03.31.715657 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ Removing head ganglia in amphibious centipedes unveils descending contribution to versatile locomotor repertoire ]]> https://biorxiv.org/content/10.64898/2026.04.02.716080v1?rss=1 Yasui, K. Standen, E. M. Kano, T. Aonuma, H. Ishiguro, A. 2026-04-06 doi:10.64898/2026.04.02.716080 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ ATP13A2 Loss of Function-Driven Polyamine Dysregulation Induces SAM Depletion and Epigenetic Astrocyte Toxicity ]]> https://biorxiv.org/content/10.64898/2026.04.02.716164v1?rss=1 Coccia, E. Morrone Parfitt, G. Ijaz, S. Sati, A. Gesner, J. Perez Arevalo, A. Strong, J. Bright, A. Sohail, S. Meimoun, T. Ahfeldt, T. Vangheluwe, P. Blanchard, J. 2026-04-06 doi:10.64898/2026.04.02.716164 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ Temperature stress resilience in polar Chlamydomonas is regulated by acclimation to light and salinity: implications for survival in a changing world ]]> https://biorxiv.org/content/10.64898/2026.04.03.716389v1?rss=1 Osmers, P. Szenasi, A. Kostyniuk, L. Caputo, S. Bradette, N. Cvetkovska, M. 2026-04-07 doi:10.64898/2026.04.03.716389 Cold Spring Harbor Laboratory Press 2026-04-07 <![CDATA[ Single-section multiplexed imaging enables comprehensive lung cancer diagnosis ]]> https://biorxiv.org/content/10.64898/2026.04.05.716628v1?rss=1 Ben-uri, R. Keidar Haran, T. Bussi, Y. Vainer, G. Arnon, J. Pillar, N. Sourikh, H. Fuchs, I. Elhanani, O. Neuman, T. Pikarsky, E. Keren, L. 2026-04-08 doi:10.64898/2026.04.05.716628 Cold Spring Harbor Laboratory Press 2026-04-08