bioRxiv Channel: University of Ottawa https://biorxiv.org This feed contains articles for bioRxiv Channel "University of Ottawa" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Biocompatibility of Subcutaneously Implanted Plant-Derived Cellulose Biomaterials ]]> https://biorxiv.org/content/10.1101/039644v1?rss=1 Daniel J Modulevsky Charles M Cuerrier Andrew E Pelling 2016-02-12 doi:10.1101/039644 Cold Spring Harbor Laboratory Press 2016-02-12 <![CDATA[ Widespread Historical Contingency in Influenza Viruses ]]> https://biorxiv.org/content/10.1101/070094v1?rss=1 Jean Claude Nshogozabahizi Jonathan Dench Stephane Aris-Brosou 2016-08-19 doi:10.1101/070094 Cold Spring Harbor Laboratory Press 2016-08-19 <![CDATA[ Viral outbreaks involve destabilised viruses: evidence from Ebola, Influenza and Zika ]]> https://biorxiv.org/content/10.1101/070102v1?rss=1 Stephane Aris-Brosou Neke Ibeh Jessica Noël 2016-08-18 doi:10.1101/070102 Cold Spring Harbor Laboratory Press 2016-08-18 <![CDATA[ Estimation of sub-epidemic dynamics by means of Sequential Monte Carlo Approximate Bayesian Computation: an application to the Swiss HIV Cohort Study ]]> https://biorxiv.org/content/10.1101/085993v1?rss=1 Ibeh, N. Aris-Brosou, S. 2016-11-07 doi:10.1101/085993 Cold Spring Harbor Laboratory Press 2016-11-07 <![CDATA[ Sexually satiated male Drosophila melanogaster uses gustatory-to-neuropeptide integrative circuits to reduce time investment for mating ]]> https://biorxiv.org/content/10.1101/088724v1?rss=1 Kim, W. J. Lee, S. G. Auge, A.-C. Jan, L. Y. Jan, Y. N. 2016-11-22 doi:10.1101/088724 Cold Spring Harbor Laboratory Press 2016-11-22 <![CDATA[ A Novel DNA-binding Protein Coordinates Asymmetric Chromosome Replication and Chromosome Partitioning ]]> https://biorxiv.org/content/10.1101/091496v1?rss=1 Taylor, J. Panis, G. Viollier, P. Marczynski, G. 2016-12-04 doi:10.1101/091496 Cold Spring Harbor Laboratory Press 2016-12-04 <![CDATA[ Cell Mechanosensing and Avoidance of Strain Gradients ]]> https://biorxiv.org/content/10.1101/095976v1?rss=1 Chagnon-Lessard, S. Jean-Ruel, H. Godin, M. Pelling, A. E. 2016-12-21 doi:10.1101/095976 Cold Spring Harbor Laboratory Press 2016-12-21 <![CDATA[ Approximate Bayesian Computation Algorithms for Estimating Network Model Parameters ]]> https://biorxiv.org/content/10.1101/106450v1?rss=1 Zheng, Y. Aris-Brosou, S. 2017-02-07 doi:10.1101/106450 Cold Spring Harbor Laboratory Press 2017-02-07 <![CDATA[ Resolving Rapid Radiations Within Families Using Anchored Phylogenomics ]]> https://biorxiv.org/content/10.1101/110296v1?rss=1 Leveille-Bourret, E. Starr, J. R. Ford, B. A. Lemmon, E. M. Lemmon, A. R. 2017-02-21 doi:10.1101/110296 Cold Spring Harbor Laboratory Press 2017-02-21 <![CDATA[ Rational design of proteins that exchange on functional timescales ]]> https://biorxiv.org/content/10.1101/113845v1?rss=1 Davey, J. A. Damry, A. M. Goto, N. K. Chica, R. A. 2017-03-03 doi:10.1101/113845 Cold Spring Harbor Laboratory Press 2017-03-03 <![CDATA[ ARSDA: A new approach for storing, transmitting and analyzing high-throughput sequencing data ]]> https://biorxiv.org/content/10.1101/114470v1?rss=1 Xia, X. 2017-03-06 doi:10.1101/114470 Cold Spring Harbor Laboratory Press 2017-03-06 <![CDATA[ Secretogranin-II Plays A Critical Role In Zebrafish Neurovascular Modeling ]]> https://biorxiv.org/content/10.1101/123125v1?rss=1 Tao, B. Hu, H. Mitchell, K. Chen, J. Jia, H. Zhu, Z. Trudeau, V. Hu, W. 2017-04-01 doi:10.1101/123125 Cold Spring Harbor Laboratory Press 2017-04-01 <![CDATA[ Neural Correlates of human cognitive abilities during sleep ]]> https://biorxiv.org/content/10.1101/130500v1?rss=1 Fang, Z. Ray, L. B. Owen, A. M. Fogel, S. 2017-04-25 doi:10.1101/130500 Cold Spring Harbor Laboratory Press 2017-04-25 <![CDATA[ Burst Ensemble Multiplexing: A Neural Code Connecting Dendritic Spikes with Microcircuits ]]> https://biorxiv.org/content/10.1101/143636v1?rss=1 Naud, R. Sprekeler, H. 2017-06-30 doi:10.1101/143636 Cold Spring Harbor Laboratory Press 2017-06-30 <![CDATA[ A vacuum-actuated microtissue stretcher for long-term exposure to oscillatory strain within a 3D matrix ]]> https://biorxiv.org/content/10.1101/149336v1?rss=1 Walker, M. J. Godin, M. Pelling, A. 2017-06-13 doi:10.1101/149336 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ Amyloid accumulation drives proteome-wide alterations in mouse models of Alzheimers disease like pathology ]]> https://biorxiv.org/content/10.1101/150623v1?rss=1 Savas, J. N. Wang, Y.-Z. DeNardo, L. A. Martinez-Bartolome, S. McClatchy, D. B. Hark, T. J. Shanks, N. F. Cozzolino, K. A. Lavallee-Adam, M. Smukowski, S. N. Park, S. K. Kelly, J. W. Koo, E. H. Nakagawa, T. Masliah, E. Ghosh, A. Yates, J. R. 2017-06-15 doi:10.1101/150623 Cold Spring Harbor Laboratory Press 2017-06-15 <![CDATA[ Spontaneous Phase Separation of Cocultured Cell Mixtures In vitro ]]> https://biorxiv.org/content/10.1101/152819v1?rss=1 Hadjiantoniou, S. V. Leblanc-Latour, M. Ignacio, M. Lefevbre, C. Slater, G. Pelling, A. E. 2017-06-20 doi:10.1101/152819 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ The emergence, maintenance and demise of diversity in a spatially variable antibiotic regime ]]> https://biorxiv.org/content/10.1101/158337v1?rss=1 Leale, A. M. Kassen, R. 2017-06-30 doi:10.1101/158337 Cold Spring Harbor Laboratory Press 2017-06-30 <![CDATA[ Noise Gated by Dendrosomatic Interactions Increases Information Transmission ]]> https://biorxiv.org/content/10.1101/163261v1?rss=1 Naud, R. Payeur, A. Longtin, A. 2017-07-14 doi:10.1101/163261 Cold Spring Harbor Laboratory Press 2017-07-14 <![CDATA[ Enhancing the Representational Similarity Between Execution and Imagination of Movement Using Network-Based Brain Computer Interfacing ]]> https://biorxiv.org/content/10.1101/166603v1?rss=1 Kordjazi, N. Koravand, A. Sveistrup, H. 2017-07-21 doi:10.1101/166603 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ Identifying the genetic determinants of particular phenotypes in microbial genomes with very small training sets ]]> https://biorxiv.org/content/10.1101/181222v1?rss=1 Long, G. S. Hussen, M. Dench, J. Aris-Brosou, S. 2017-08-26 doi:10.1101/181222 Cold Spring Harbor Laboratory Press 2017-08-26 <![CDATA[ Translational profiling of macrophages infected with Leishmania donovani identifies mTOR- and eIF4A-sensitive immune-related transcripts ]]> https://biorxiv.org/content/10.1101/2019.12.20.884338v1?rss=1 Chaparro, V. Leroux, L.-P. Masvidal, L. Lorent, J. Graber, T. E. Zimmermann, A. Arango Duque, G. Descoteaux, A. Alain, T. Larsson, O. Jaramillo, M. 2019-12-20 doi:10.1101/2019.12.20.884338 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ An overview of the quality assurance and quality control of magnetic resonance imaging data for the Ontario Neurodegenerative Disease Research Initiative (ONDRI): pipeline development and neuroinformatics ]]> https://biorxiv.org/content/10.1101/2020.01.10.896415v1?rss=1 Scott, C. J. M. Arnott, S. R. Chemparathy, A. Dong, F. Solovey, I. Gee, T. Schmah, T. Chavez, S. Lobaugh, N. Nanayakkara, N. Liang, S. Zamyadi, M. Ozzoude, M. Holmes, M. F. Szilagyi, G. M. Ramirez, J. Symons, S. Black, S. E. Bartha, R. Strother, S. The ONDRI investigators, 2020-01-16 doi:10.1101/2020.01.10.896415 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ PAX2 Induces Tubular-Like Structures in Normal and Ovarian Cancer Cells ]]> https://biorxiv.org/content/10.1101/2020.01.14.906438v1?rss=1 Alwosaibai, K. S. Alamri, S. Garson, K. Vanderhyden, B. 2020-01-15 doi:10.1101/2020.01.14.906438 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ More filtering on SNP calling does not remove evidence of inter-nucleus recombination in dikaryotic arbuscular mycorrhizal fungi ]]> https://biorxiv.org/content/10.1101/2020.01.15.906412v1?rss=1 Chen, E. Mathieu, S. Hoffrichter, A. Ropars, J. Dreissig, S. Fuchs, J. Brachmann, A. Corradi, N. 2020-01-15 doi:10.1101/2020.01.15.906412 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Plant-derived Cellulose Scaffolds for Bone Tissue Engineering. ]]> https://biorxiv.org/content/10.1101/2020.01.15.906677v1?rss=1 Leblanc Latour, M. Tarar, M. Hickey, R. J. Cuerrier, C. M. Catelas, I. Pelling, A. E. 2020-01-15 doi:10.1101/2020.01.15.906677 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Time dependencies in the dynamic mechanical behavior of 3D microtissue cell cultures ]]> https://biorxiv.org/content/10.1101/2020.01.25.916874v1?rss=1 Walker, M. Godin, M. Harden, J. Pelling, A. 2020-01-26 doi:10.1101/2020.01.25.916874 Cold Spring Harbor Laboratory Press 2020-01-26 <![CDATA[ Mechanical stretch sustains myofibroblast phenotype and function in microtissues through latent TGF-β1 activation ]]> https://biorxiv.org/content/10.1101/2020.01.25.917179v1?rss=1 Walker, M. Godin, M. Pelling, A. 2020-01-26 doi:10.1101/2020.01.25.917179 Cold Spring Harbor Laboratory Press 2020-01-26 <![CDATA[ Evolution and variation of 2019-novel coronavirus ]]> https://biorxiv.org/content/10.1101/2020.01.30.926477v1?rss=1 Xiong, C. Jiang, L. Chen, Y. Jiang, Q. 2020-01-30 doi:10.1101/2020.01.30.926477 Cold Spring Harbor Laboratory Press 2020-01-30 <![CDATA[ Direct reprogramming of astrocytes to neurons leads to functional recovery after stroke ]]> https://biorxiv.org/content/10.1101/2020.02.02.929091v1?rss=1 Livingston, J. Lee, T. Daniele, E. Phillips, C. Krassikova, A. Enbar, T. Kortebi, I. Bang, K. W. A. Donville, B. Ibragimov, O. Sachewsky, N. Morshead, C. Faiz, M. 2020-02-03 doi:10.1101/2020.02.02.929091 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ A Comprehensive Assessment of Human Natural Killer Cell Phenotype and Function in Whole Blood ]]> https://biorxiv.org/content/10.1101/2020.02.03.932640v1?rss=1 Market, M. Tennakoon, G. Ng, J. Scaffidi, M. Tanese de Souza, C. Kennedy, M. A. Auer, R. C. 2020-02-04 doi:10.1101/2020.02.03.932640 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ High contiguity long read assembly of Brassica nigra allows localization of active centromeres and provides insights into the ancestral Brassica genome. ]]> https://biorxiv.org/content/10.1101/2020.02.03.932665v1?rss=1 Perumal, S. Koh, C. S. Jin, L. Buchwaldt, M. Higgins, E. Zheng, C. Sankoff, D. Robinson, S. J. Kagale, S. Navabi, Z.-K. Tang, L. Horner, K. N. He, Z. Bancroft, I. Chalhoub, B. Sharpe, A. G. Parkin, I. A. 2020-02-04 doi:10.1101/2020.02.03.932665 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Growth phase-dependent responses of an in vitro gut microbiome to metformin ]]> https://biorxiv.org/content/10.1101/2020.02.05.936500v1?rss=1 log phase > stationary phase. Our results showed that metformin added at lag phase resulted in a significantly reduced abundance of the Clostridiales order as well as an increased abundance of the Bacteroides genus, which was different from stimulation during the rest of the growth phase. Metformin also resulted in alterations of several pathways, including energy production and conversion, lipid transport and metabolism, translation, ribosomal structure and biogenesis. Our results indicate that the timing for drug stimulation should be considered when studying drug-microbiome interactions in vitro. ]]> Hao, Z. Li, L. Ning, Z. Zhang, X. Mayne, J. Cheng, K. Walker, K. Liu, H. Figeys, D. 2020-02-06 doi:10.1101/2020.02.05.936500 Cold Spring Harbor Laboratory Press 2020-02-06 <![CDATA[ Activation of Rab11a and endocytosis by Phosphatidylinositol 4-kinase III beta promotes oncogenic signaling in breast cancer ]]> https://biorxiv.org/content/10.1101/2020.02.10.942177v1?rss=1 MacDonald, S. Harding, K. Bilodeau, P. de Souza, C. Campa, C. Hirsch, E. Auer, R. Lee, J. 2020-02-11 doi:10.1101/2020.02.10.942177 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ Expression of dlx genes in the normal and regenerating brain of adult zebrafish. ]]> https://biorxiv.org/content/10.1101/2020.02.11.943605v1?rss=1 Weinschutz Mendes, H. TAKTEK, M. DURET, T. Ekker, M. 2020-02-11 doi:10.1101/2020.02.11.943605 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ PCR procedures to amplify GC-rich DNA sequences of Mycobacterium bovis ]]> https://biorxiv.org/content/10.1101/2020.02.18.953695v1?rss=1 60%, in comparison to amplifying a gene from the Listeria monocytogenes genome, a genome with a 37.8% GC content. Three PCR protocols were designed and experimented at various conditions with two M. bovis genes, Mb0129, a large gene of 1794 bp with 77.5% GC content, mpb83, a smaller gene of 663 bp in length with moderate GC content of 63%, together with LMHCC_RS00060, a large L.monocytogenes gene of 1617 bp with a lower GC content of 41.53%. The result demonstrated the superiority of the 2-step PCR protocol over other protocols in PCR amplification of Mb0129 when specific high fidelity DNA polymerases were used in the presence of an enhancer. The study highlighted the importance of manipulating the cycling conditions to perform the annealing and extension steps at higher temperatures for a successful PCR amplification of a large GC-rich DNA template. The PCR protocols developed in this study can be valuable tools for the amplification of long GC-rich DNA sequences for various downstream applications. ]]> Assal, N. Lin, M. 2020-02-18 doi:10.1101/2020.02.18.953695 Cold Spring Harbor Laboratory Press 2020-02-18 <![CDATA[ Oxidative Modifications of Parkin Underlie its Selective Neuroprotection in Adult Human Brain ]]> https://biorxiv.org/content/10.1101/2020.02.19.953034v1?rss=1 60 control specimens, we found that in adult human brain - but not in skeletal muscle- parkin is mostly aggregated and insoluble due to oxidative modifications, such as at C253. In vitro, parkins oxidation directly reduces hydrogen peroxide (H2O2) to water. In parkin-deficient human brain, H2O2 concentrations are elevated. In dopamine toxicity studies, wild-type parkin -but not disease-associated mutants-prevents neural death by lowering H2O2 and sequestering radicals within insoluble aggregates. Parkin conjugates dopamine metabolites at the human-specific residue C95 and augments melanin formation in vitro. Using epitope-mapped antibodies, we found that in adult Substantia nigra neurons parkin localizes to neuromelanin within LAMP-3/CD63-positive lysosomes. We conclude that parkins own oxidation, previously considered a loss-of-function event, underlies three neuroprotective effects in adult midbrain: its cysteines participate in H2O2 reduction, dopamine radical conjugation and the formation of neuromelanin. ]]> Tokarew, J. M. El-Kodsi, D. N. Lengacher, N. A. Fehr, T. K. Nguyen, A. P. O'Nuallain, B. Jin, M. Khan, J. M. Ng, A. C.-H. Li, J. Jiang, Q. Zhang, M. Wang, L. Sengupta, R. Barber, K. R. Tran, A. Zandee, S. Dong, X. Scherzer, C. R. Prat, A. Tsai, E. Takanashi, M. Hattori, N. Chan, J. A. West, A. B. Holmgren, A. Puente, L. Shaw, G. S. Toth, G. Woulfe, J. M. Taylor, P. Tomlinson, J. J. Schlossmacher, M. G. 2020-02-20 doi:10.1101/2020.02.19.953034 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Decellularized Plant-Based Scaffolds for Guided Alignment of Myoblast Cells ]]> https://biorxiv.org/content/10.1101/2020.02.23.958686v1?rss=1 Campuzano, S. Mogilever, N. B. Pelling, A. 2020-02-24 doi:10.1101/2020.02.23.958686 Cold Spring Harbor Laboratory Press 2020-02-24 <![CDATA[ Metaproteomic responses of in vitro gut microbiomes to resistant starches: the role of resistant starch type and inter-individual variations ]]> https://biorxiv.org/content/10.1101/2020.02.28.970186v1?rss=1 Li, L. Ryan, J. Ning, Z. Zhang, X. Mayne, J. Lavallee-Adam, M. Stintzi, A. Figeys, D. 2020-03-03 doi:10.1101/2020.02.28.970186 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ Studying the dynamics of the gut microbiota using metabolically stable isotopic labeling and metaproteomics. ]]> https://biorxiv.org/content/10.1101/2020.03.09.982884v1?rss=1 Smyth, P. Zhang, X. Ning, Z. Mayne, J. Moore, J. I. Walker, K. Lavallée-Adam, M. Figeys, D. 2020-03-10 doi:10.1101/2020.03.09.982884 Cold Spring Harbor Laboratory Press 2020-03-10 <![CDATA[ Establishment of a pig influenza challenge model for evaluation of monoclonal antibody delivery platforms ]]> https://biorxiv.org/content/10.1101/2020.03.12.988808v1?rss=1 McNee, A. Smith, T. Holzer, B. Becky, C. Bessell, E. Guibinga, G. Brown, H. Schultheis, K. Fisher, P. Ramos, S. Nunez, A. Bernard, M. Martini, V. Chrun, T. Xiao, Y. Kash, J. C. Taubenberger, J. K. Elliott, S. Patel, A. Beverley, P. Rijal, P. Weiner, D. Townsend, A. Broderick, K. Tchilian, E. 2020-03-13 doi:10.1101/2020.03.12.988808 Cold Spring Harbor Laboratory Press 2020-03-13 <![CDATA[ An easily adopted murine model of distal pancreatectomy for investigating immunotherapy efficacy in resectable pancreatic adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2020.03.17.990903v1?rss=1 Baxter, K. E. Tanese de Souza, C. Tai, L.-H. Yaghini, P. Daneshmand, M. Bell, J. C. Lichty, B. D. Kennedy, M. A. Auer, R. C. 2020-03-18 doi:10.1101/2020.03.17.990903 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ Evolution of an enzyme conformational ensemble guides design of an efficient biocatalyst ]]> https://biorxiv.org/content/10.1101/2020.03.19.999235v1?rss=1 Broom, A. Rakotoharisoa, R. V. Thompson, M. C. Zarifi, N. Nguyen, E. Mukhametzhanov, N. Liu, L. Fraser, J. S. Chica, R. A. 2020-03-20 doi:10.1101/2020.03.19.999235 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Self-cutting and integrating CRISPR plasmids (SCIPs) enable targeted genomic integration of large genetic payloads for rapid cell engineering ]]> https://biorxiv.org/content/10.1101/2020.03.25.008276v1?rss=1 Bloemberg, D. Sosa-Miranda, D. Nguyen, T. Weeratna, R. D. McComb, S. 2020-03-25 doi:10.1101/2020.03.25.008276 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Burst-dependent synaptic plasticity can coordinate learning in hierarchical circuits ]]> https://biorxiv.org/content/10.1101/2020.03.30.015511v1?rss=1 Payeur, A. Guerguiev, J. Zenke, F. Richards, B. Naud, R. 2020-03-31 doi:10.1101/2020.03.30.015511 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ Mapping shifts in nanopore signal to changes in protein and protein-DNA conformation ]]> https://biorxiv.org/content/10.1101/2020.04.01.020420v1?rss=1 Carlsen, A. T. Tabard-Cossa, V. 2020-04-02 doi:10.1101/2020.04.01.020420 Cold Spring Harbor Laboratory Press 2020-04-02 <![CDATA[ Cre-mediated deletion of SMARCA5 disrupts pluripotency in mouse embryonic stem cells ]]> https://biorxiv.org/content/10.1101/2020.04.02.022285v1?rss=1 Cook, D. P. Vanderhyden, B. C. 2020-04-03 doi:10.1101/2020.04.02.022285 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ A new model for vertebrate mineralization via stabilized amorphous calcium carbonate for avian eggshell formation ]]> https://biorxiv.org/content/10.1101/2020.04.08.031989v1?rss=1 Stapane, L. Le Roy, N. Ezagal, J. Rodriguez-Navarro, A. B. Labas, V. Combes-Soia, L. Hincke, M. T. Gautron, J. 2020-04-10 doi:10.1101/2020.04.08.031989 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ Genomics of experimental diversification of Pseudomonas aeruginosa in cystic fibrosis lung-like conditions ]]> https://biorxiv.org/content/10.1101/2020.04.14.041954v1?rss=1 Schick, A. Kassen, R. 2020-04-15 doi:10.1101/2020.04.14.041954 Cold Spring Harbor Laboratory Press 2020-04-15 <![CDATA[ Parkinson Disease-Linked Parkin Mediates Redox Reactions That Lower Oxidative Stress In Mammalian Brain ]]> https://biorxiv.org/content/10.1101/2020.04.26.062380v1?rss=1 El Kodsi, D. N. Tokarew, J. M. Sengupta, R. Lengacher, N. A. Ng, A. C. Boston, H. Jiang, Q. Palmberg, C. Pileggi, C. Shutinoski, B. Li, J. Nguyen, A. P. Fehr, T. K. Im, D. S. Callaghan, S. Park, D. S. LaVoie, M. J. Chan, J. A. Takanashi, M. Hattori, N. Ratan, R. R. Zecca, L. Puente, L. Shaw, G. S. Harper, M.-E. Holmgren, A. Tomlinson, J. J. Schlossmacher, M. G. 2020-04-27 doi:10.1101/2020.04.26.062380 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ A mouse model for spinal muscular atrophy provides insights into non-alcoholic fatty liver disease pathogenesis ]]> https://biorxiv.org/content/10.1101/2020.04.29.051938v1?rss=1 Deguise, M.-O. Pileggi, C. Beauvais, A. Tierney, A. Chehade, L. De Repentigny, Y. Michaud, J. Llavero-Hurtado, M. Lamont, D. Atrih, A. Wishart, T. M. Gillingwater, T. H. Schneider, B. L. Harper, M.-E. Parson, S. H. Kothary, R. 2020-04-30 doi:10.1101/2020.04.29.051938 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ A broad response to intracellular long-chain polyphosphate in human cells ]]> https://biorxiv.org/content/10.1101/2020.05.01.056192v1?rss=1 Bondy-Chorney, E. Abramchuk, I. Nasser, R. Holinier, C. Denoncourt, A. Baijal, K. McCarthy, L. Khacho, M. Lavallee-Adam, M. Downey, M. 2020-05-03 doi:10.1101/2020.05.01.056192 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ The Evolution and Fate of Diversity Under Hard and Soft Selection ]]> https://biorxiv.org/content/10.1101/2020.05.13.091124v1?rss=1 Chen, P. J. Kassen, R. 2020-05-15 doi:10.1101/2020.05.13.091124 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Cadherin-11 is required for neural crest determination and survival ]]> https://biorxiv.org/content/10.1101/2020.05.18.066613v1?rss=1 Manohar, S. Camacho-Magallanes, A. Rogers, C. D. 2020-05-19 doi:10.1101/2020.05.18.066613 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ MealTime-MS: A Machine Learning-Guided Real-Time Mass SpectrometryAnalysis for Protein Identification and Efficient DynamicExclusion ]]> https://biorxiv.org/content/10.1101/2020.05.22.110726v1?rss=1 Pelletier, A. R. Chung, Y.-E. Ning, Z. Wong, N. Figeys, D. Lavallee-Adam, M. 2020-05-23 doi:10.1101/2020.05.22.110726 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ NMR Analysis of the Correlation of Metabolic Changes in Blood and Cerebrospinal Fluid in Alzheimer Model Male and Female Mice ]]> https://biorxiv.org/content/10.1101/2020.05.26.116525v1?rss=1 Stojanovic, F. Taktek, M. Khieu, N. H. Huang, J. Jiang, S. Rennie, K. Chakravarthy, B. Costain, W. J. Cuperlovic-Culf, M. 2020-06-01 doi:10.1101/2020.05.26.116525 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ Synaptic dynamics as convolutional units ]]> https://biorxiv.org/content/10.1101/2020.06.04.133892v1?rss=1 Rossbroich, J. Trotter, D. Toth, K. Naud, R. 2020-06-05 doi:10.1101/2020.06.04.133892 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Transcriptional heterogeneity of stemness phenotypes in the ovarian epithelium ]]> https://biorxiv.org/content/10.1101/2020.06.10.145045v1?rss=1 Carter, L. E. Cook, D. P. McCloskey, C. W. Dang, T. Collins, O. Gamwell, L. F. Dempster, H. A. Vanderhyden, B. C. 2020-06-11 doi:10.1101/2020.06.10.145045 Cold Spring Harbor Laboratory Press 2020-06-11 <![CDATA[ Time meets space: brain dynamics drive spatial topography ]]> https://biorxiv.org/content/10.1101/2020.06.11.106476v1?rss=1 Golesorkhi, M. Tumati, S. Gomez-Pilar, J. Stamatakis, E. Northoff, G. 2020-06-12 doi:10.1101/2020.06.11.106476 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Temporal hierarchy converges with spatial hierarchy: Intrinsic neural timescales follow core-periphery organization ]]> https://biorxiv.org/content/10.1101/2020.06.12.148866v1?rss=1 Golesorkhi, M. Gomez-Pilar, J. Tumati, S. Fraser, M. Northoff, G. 2020-06-13 doi:10.1101/2020.06.12.148866 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ Coronavirus genomes carry the signatures of their habitats ]]> https://biorxiv.org/content/10.1101/2020.06.13.149591v1?rss=1 Wei, Y. Silke, J. R. Aris, P. Xia, X. 2020-06-13 doi:10.1101/2020.06.13.149591 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ Autumn larval cold tolerance does not predict the northern range limit of a widespread butterfly species ]]> https://biorxiv.org/content/10.1101/2020.06.14.151266v1?rss=1 Tremblay, P. MacMillan, H. A. Kharouba, H. M. 2020-06-16 doi:10.1101/2020.06.14.151266 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ Dynamics of a neuronal pacemaker in the weakly electric fish Apteronotus ]]> https://biorxiv.org/content/10.1101/2020.06.26.173088v1?rss=1 Shifman, A. Sun, Y. Benoit, C. Lewis, J. 2020-06-26 doi:10.1101/2020.06.26.173088 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ NK cells acquire PD-1 from the membrane of tumor cells. ]]> https://biorxiv.org/content/10.1101/2020.06.26.174342v1?rss=1 Hasim, M. S. Vulpis, E. Sciume, G. Shih, H.-Y. Scheer, A. MacMillan, O. Petrucci, M. T. Santoni, A. Zingoni, A. Ardolino, M. 2020-06-27 doi:10.1101/2020.06.26.174342 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ PCB126-mediated effects on adipocyte energy metabolism and adipokine secretion may result in abnormal glucose uptake in muscle cells ]]> https://biorxiv.org/content/10.1101/2020.07.07.192245v1?rss=1 Caron, A. Ahmed, F. Peshdary, V. Garneau, L. Atlas, E. Aguer, C. 2020-07-07 doi:10.1101/2020.07.07.192245 Cold Spring Harbor Laboratory Press 2020-07-07 <![CDATA[ MARCKS domain phosphorylation regulates the differential interaction of Diacylglycerol Kinase ζ with Rac1, RhoA and Syntrophin ]]> https://biorxiv.org/content/10.1101/2020.07.08.194100v1?rss=1 Ryan Ard Jean-Christian Maillet Elias Daher Michael Phan Radoslav Zinoviev Robin J. Parks Stephen H. Gee 2020-07-08 doi:10.1101/2020.07.08.194100 Cold Spring Harbor Laboratory Press 2020-07-08 <![CDATA[ SMPD3-mediated extracellular vesicle biogenesis inhibits oligodendroglioma growth ]]> https://biorxiv.org/content/10.1101/2020.07.14.202200v1?rss=1 Balakrishnan, A. Adnani, L. Chinchalongporn, V. Vasan, L. Prokopchuk, O. Chen, M. El-Sehemy, A. Olender, T. Touahri, Y. Ahmad, S. T. Islam, R. Sujanthan, S. Zinyk, D. Comanita, L. C. Kan, B. Fleming, T. Leong, H. S. Morshead, C. M. Brand, M. Wallace, V. A. Chan, J. A. Schuurmans, C. 2020-07-14 doi:10.1101/2020.07.14.202200 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ Myeloid deletion and therapeutic activation of AMP-activated protein kinase (AMPK) do not alter atherosclerosis in male or female mice ]]> https://biorxiv.org/content/10.1101/2020.07.15.204487v1?rss=1 LeBlond, N. D. Ghorbani, P. O'Dwyer, C. Ambursley, N. Nunes, J. R. Smith, T. K. Trzaskalski, N. A. Mulvihill, E. E. Benoit, V. Foretz, M. Fullerton, M. D. 2020-07-15 doi:10.1101/2020.07.15.204487 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ Identification of SARS-CoV2-mediated suppression of NRF2 signaling reveals a potent antiviral and anti-inflammatory activity of 4-octyl-itaconate and dimethyl fumarate ]]> https://biorxiv.org/content/10.1101/2020.07.16.206458v1?rss=1 Olagnier, D. Farahani, E. Thyrsted, J. Cadanet, J. B. Herengt, A. Idorn, M. Hait, A. Hernaez, B. Knudsen, A. Iversen, M. B. Schilling, M. Jorgensen, S. E. Thomsen, M. Reinert, L. Lappe, M. Hoang, H.-D. Gilchrist, V. H. Hansen, A.-L. Ottosen, R. Gunderstofte, C. Moller, C. van der Horst, D. Peri, S. Balachandran, S. Huang, J. Jakobsen, M. Svenningsen, E. B. Poulsen, T. B. Bartsch, L. Thielke, A. L. Luo, Y. Alain, T. Rehwinkel, J. Alcami, A. Hiscott, J. Mogensen, T. Paludan, S. R. Holm, C. K. 2020-07-17 doi:10.1101/2020.07.16.206458 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ SMAD2 promotes myogenin expression and terminal myogenic differentiation. ]]> https://biorxiv.org/content/10.1101/2020.07.28.225888v1?rss=1 Lamarche, E. AlSudais, H. Rajgara, R. Fu, D. Omaiche, S. Wiper-Bergeron, N. 2020-07-29 doi:10.1101/2020.07.28.225888 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Genetically-encoded fluorescent biosensor for rapid detection of protein expression ]]> https://biorxiv.org/content/10.1101/2020.07.30.229633v1?rss=1 30 min that causes delays in real-time detection of protein expression. Here, we engineer a genetically-encoded fluorescent biosensor to enable detection of protein expression within seconds in live cells. This sensor for transiently-expressed proteins (STEP) is based on a fully matured but dim green fluorescent protein in which pre-existing fluorescence increases 11-fold in vivo following the specific and rapid binding of a protein tag (Kd 120 nM, kon 1.7 x 105 M-1s-1). In live E. coli cells, our STEP biosensor enables detection of protein expression twice as fast as the use of standard fluorescent protein fusions. Our biosensor opens the door to the real-time study of short-timescale processes in research model animals with high spatiotemporal resolution. ]]> Eason, M. G. Pandelieva, A. T. Mayer, M. M. Khan, S. T. Garcia, H. G. Chica, R. A. 2020-07-30 doi:10.1101/2020.07.30.229633 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ A Facile Method for Simultaneous Visualization of Wet Cells and Nanostructured Biomaterials in SEM using Ionic Liquids ]]> https://biorxiv.org/content/10.1101/2020.08.05.238246v1?rss=1 Lee, B. E. J. DiCecco, L.-A. Exir, H. Weck, A. Sask, K. Grandfield, K. 2020-08-06 doi:10.1101/2020.08.05.238246 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ Foam cell induction activates AMPK but uncouples its regulation of autophagy and lysosomal homeostasis ]]> https://biorxiv.org/content/10.1101/2020.08.13.244640v1?rss=1 LeBlond, N. D. Nunes, J. R. C. Smith, T. K. T. Robichaud, S. Gadde, S. Cote, M. Kemp, B. E. Ouimet, M. Fullerton, M. D. 2020-08-13 doi:10.1101/2020.08.13.244640 Cold Spring Harbor Laboratory Press 2020-08-13 <![CDATA[ Synchronization and resilience in the Kuramotowhite matter network model with adaptivestate-dependent delays ]]> https://biorxiv.org/content/10.1101/2020.08.25.266841v1?rss=1 Park, S. H. Lefebvre, J. 2020-08-25 doi:10.1101/2020.08.25.266841 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ The lysosomal TRPML1 channel promotes breast cancer survival by supporting mitochondrial function and cellular metabolism ]]> https://biorxiv.org/content/10.1101/2020.09.04.283242v1?rss=1 Almasi, S. Kennedy, B. E. Yoast, R. E. Emrich, S. M. Trebak, M. El Hiani, Y. 2020-09-04 doi:10.1101/2020.09.04.283242 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ Chronic low-dose dioxin exposure accelerates high fat diet-induced hyperglycemia in female mice ]]> https://biorxiv.org/content/10.1101/2020.09.12.294587v1?rss=1 Matteo, G. Hoyeck, M. P. Blair, H. Zebarth, J. Rick, K. R. Williams, A. Gagne, R. Buick, J. K. Yauk, C. Bruin, J. E. 2020-09-13 doi:10.1101/2020.09.12.294587 Cold Spring Harbor Laboratory Press 2020-09-13 <![CDATA[ Wheat transcriptome profiling reveals abscisic and gibberellic acid treatments regulate early-stage phytohormone defense signaling, cell wall fortification, and metabolic switches following Fusarium graminearum-challenge ]]> https://biorxiv.org/content/10.1101/2020.09.17.302737v1?rss=1 Buhrow, L. M. Liu, Z. Cram, D. Sharma, T. Foroud, N. A. Pan, Y. Loewen, M. C. 2020-09-20 doi:10.1101/2020.09.17.302737 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ Pioglitazone improves deficits of Fmr1-KO mouse model of Fragile X syndrome by interfering with excessive diacylglycerol signaling ]]> https://biorxiv.org/content/10.1101/2020.09.22.301762v1?rss=1 Geoffroy, A. Habbas, K. Zambo, B. Schramm, L. Duchon, A. Flatter, E. Fouillen, L. Zumsteg, J. Heintz, D. Mandel, J.-L. Herault, Y. Moine, H. 2020-09-22 doi:10.1101/2020.09.22.301762 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Computational identification of human biological processes and protein sequence motifs putatively targeted by SARS-CoV-2 proteins using protein-protein interaction networks ]]> https://biorxiv.org/content/10.1101/2020.09.29.318931v1?rss=1 Nadeau, R. Shahryari Fard, S. Scheer, A. Hashimoto-Roth, E. Nygard, D. Abramchuk, I. Chung, Y.-E. Bennett, S. A. L. Lavallee-Adam, M. 2020-09-30 doi:10.1101/2020.09.29.318931 Cold Spring Harbor Laboratory Press 2020-09-30 <![CDATA[ Connectivity for Rapid Synchronization in a Neural Pacemaker Network ]]> https://biorxiv.org/content/10.1101/2020.10.05.325613v1?rss=1 Williams, E. Shifman, A. R. Lewis, J. E. 2020-10-07 doi:10.1101/2020.10.05.325613 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ Transmembrane polar relay drives the allosteric regulation for ABCG5/G8 sterol transporter ]]> https://biorxiv.org/content/10.1101/2020.10.06.327825v1?rss=1 Xavier, B. M. Zein, A. A. Venes, A. Wang, J. Lee, J.-Y. 2020-10-06 doi:10.1101/2020.10.06.327825 Cold Spring Harbor Laboratory Press 2020-10-06 <![CDATA[ Common physiological processes control mercury reduction during photosynthesis and fermentation ]]> https://biorxiv.org/content/10.1101/2020.10.08.332528v1?rss=1 Gregoire, D. S. Janssen, S. E. Lavoie, N. C. Tate, M. T. Poulain, A. J. 2020-10-12 doi:10.1101/2020.10.08.332528 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ High-throughput transcriptomic evaluation of per- and polyfluoroalkyl substances (PFAS) in primary human liver spheroids to inform read-across ]]> https://biorxiv.org/content/10.1101/2020.10.15.341362v1?rss=1 Rowan-Carroll, A. Readon, A. Leingartner, K. Gagne, R. Williams, A. Kuo, B. Bourdon-lacombe, J. Moffat, I. Carrier, R. Nong, A. lorusso, l. Ferguson, S. S. Atlas, E. Yauk, C. 2020-10-15 doi:10.1101/2020.10.15.341362 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Physical activity and general cognitive functioning: A Mendelian Randomization study ]]> https://biorxiv.org/content/10.1101/2020.10.16.342675v1?rss=1 Cheval, B. Darrous, L. Choi, K. Klimentidis, Y. Raichlen, D. Alexander, G. Cullati, S. Kutalik, Z. Boisgontier, M. P. 2020-10-16 doi:10.1101/2020.10.16.342675 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ High-throughput transcriptomics and benchmark concentration modeling for potency ranking of per- and polyfluoroalkyl substances (PFAS) in exposed human liver cell spheroids ]]> https://biorxiv.org/content/10.1101/2020.10.20.347328v1?rss=1 Reardon, A. J. F. Rowan-Carroll, A. Ferguson, S. S. Leingartner, K. Gagne, R. Kuo, B. Williams, A. Lorusso, L. Bourdon-Lacombe, J. Carrier, R. Moffat, I. Yauk, C. L. Atlas, E. 2020-10-21 doi:10.1101/2020.10.20.347328 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Impact of the expectation on memory reconsolidation using a post retrieval extinction paradigm ]]> https://biorxiv.org/content/10.1101/2020.10.26.354977v1?rss=1 Marinos, J. Ashbaugh, A. 2020-10-26 doi:10.1101/2020.10.26.354977 Cold Spring Harbor Laboratory Press 2020-10-26 <![CDATA[ Immunopeptidomics for Dummies: Detailed Experimental Protocols and Rapid, User-Friendly Visualization of MHC I and II Ligand Datasets with MhcVizPipe ]]> https://biorxiv.org/content/10.1101/2020.11.02.360958v1?rss=1 Sirois, I. Caron, E. Kovalchik, K. A. Wessling, L. Saab, F. Ma, Q. Despault, J. Kubiniok, P. Hamelin, D. Faridi, P. Li, C. Purcell, A. W. Tognetti, M. Reiter, L. Bruderer, R. Lanoix, J. Bonneil, E. Courcelles, M. Thibault, P. 2020-11-03 doi:10.1101/2020.11.02.360958 Cold Spring Harbor Laboratory Press 2020-11-03 <![CDATA[ Challenges in Undergraduate Synthetic Biology Training: Insights from a Canadian iGEM Student Perspective ]]> https://biorxiv.org/content/10.1101/2020.11.04.365999v1?rss=1 Diep, P. Boucinha, A. Yeung, B.-r. A. Kell, B. Chen, X. Tsyplenkov, D. Serra, D. Escobar, A. Gnanapragasam, A. Emond, C. A. Sajtovich, V. A. Mahadevan, R. Kilkenny, D. M. Gini-Newman, G. Kaern, M. Ingalls, B. 2020-11-05 doi:10.1101/2020.11.04.365999 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Homemade Bread: Repurposing an Ancient Technology for Low Cost in vitro Tissue Engineering ]]> https://biorxiv.org/content/10.1101/2020.11.13.353698v1?rss=1 Holmes, J. T. Jaberansari, Z. Collins, W. Leblanc Latour, M. Modulevsky, D. J. Pelling, A. 2020-11-13 doi:10.1101/2020.11.13.353698 Cold Spring Harbor Laboratory Press 2020-11-13 <![CDATA[ The Pump-Leak/Donnan ion homeostasis strategies of skeletal muscle fibers and neurons ]]> https://biorxiv.org/content/10.1101/2020.11.20.391813v1?rss=1 Joos, B. Morris, C. E. 2020-11-20 doi:10.1101/2020.11.20.391813 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Donnan dominated ion homeostasis and the longevity of ischemic Na+-loaded dystrophic skeletal muscle ]]> https://biorxiv.org/content/10.1101/2020.11.20.391839v1?rss=1 Morris, C. E. Wheeler, J. J. Joos, B. 2020-11-20 doi:10.1101/2020.11.20.391839 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Age-Associated Insolubility of Parkin in Human Midbrain is Linked to Redox Balance and Sequestration of Reactive Dopamine Metabolites ]]> https://biorxiv.org/content/10.1101/2020.11.20.392175v1?rss=1 Tokarew, J. M. El Kodsi, D. N. Lengacher, N. A. Fehr, T. K. Nguyen, A. P. Shutinoski, B. O'Nuallain, B. Jin, M. Khan, J. Ng, A. C. H. Li, J. Jiang, Q. Zhang, M. Wang, L. Sengupta, R. Barber, K. Tran, A. Zandee, S. Dong, X. Scherzer, C. R. Prat, A. Tsai, E. Takanashi, M. Hattori, N. Chan, J. A. Zecca, L. West, A. Holmgren, A. Puente, L. Shaw, G. S. Toth, G. Woulfe, J. Taylor, P. Tomlinson, J. J. Schlossmacher, M. G. 2020-11-21 doi:10.1101/2020.11.20.392175 Cold Spring Harbor Laboratory Press 2020-11-21 <![CDATA[ Rac guanine nucleotide exchange factors promoting Lgl1 phosphorylation ]]> https://biorxiv.org/content/10.1101/2020.12.01.406538v1?rss=1 Lavictoire, S. J. Jomaa, D. Gont, A. Jardine, K. Cook, D. P. Lorimer, I. A. J. 2020-12-02 doi:10.1101/2020.12.01.406538 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Consistent and High-Frequency Identification of an Intra-Sample Genetic Variant of SARS-CoV-2 with Elevated Fusogenic Properties ]]> https://biorxiv.org/content/10.1101/2020.12.03.409714v1?rss=1 U and G->U, were consistent with errors due to heat-induced DNA damage during sample processing and/or sequencing protocols. Despite high mutational background, we identified recurrent intra-variable positions in the samples analyzed, including several positions at the end of the gene encoding the viral Spike (S) protein. Strikingly, we observed a high-frequency C->A missense mutations resulting in the S protein lacking the last 20 amino acids (S{Delta}20). We found that this truncated S protein undergoes increased processing and increased syncytia formation, presumably due to escaping M protein retention in intracellular compartments. Our findings suggest the emergence of a high-frequency viral sublineage that is not horizontally transmitted but potentially involved in intra-host disease cytopathic effects. IMPORTANCEThe mutation rate and evolution of RNA viruses correlate with viral adaptation. While most mutations do not have significant contributions to viral molecular evolution, some are naturally selected and cause a genetic drift through positive selection. Many recent SARS-CoV-2 variants have been recently described and show phenotypic selection towards more infectious viruses. Our study describes another type of variant that does not contribute to inter-host heterogeneity but rather phenotypic selection toward variants that might have increased cytopathic effects. We identified that a C-terminal truncation of the Spike protein removes an important ER-retention signal, which consequently results in a Spike variant that easily travels through the Golgi toward the plasma membrane in a pre-activated conformation, leading to increased syncytia formation. ]]> Rocheleau, L. Laroche, G. Fu, K. Cote, M. Giguere, P. M. Langlois, M.-A. Pelchat, M. 2020-12-03 doi:10.1101/2020.12.03.409714 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Normal aging affects unconstrained three-dimensional reaching against gravity with reduced vertical precision and increased co-contraction ]]> https://biorxiv.org/content/10.1101/2020.12.03.410001v1?rss=1 Wittenberg, G. F. Tian, J. Kortzog, N. Wyers, L. Van Halewyck, F. Boisgontier, M. Levin, O. Swinnen, S. P. Jonkers, I. 2020-12-03 doi:10.1101/2020.12.03.410001 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ The hybrid nature of task-evoked activity: Inside-out neural dynamics in intracranial EEG and Deep Learning ]]> https://biorxiv.org/content/10.1101/2020.12.09.417774v1?rss=1 Wolff, A. Chen, L. Tumati, S. Golesorkhi, M. Gomez-Pilar, J. Hu, J. Jiang, S. Mao, Y. Longtin, A. Northoff, G. 2020-12-11 doi:10.1101/2020.12.09.417774 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Regional and age-dependent Effects of Cortical Magnetic Stimulation on Unconstrained Reaching Behavior ]]> https://biorxiv.org/content/10.1101/2020.12.14.422725v1?rss=1 Urbin, M. A. Tian, J. McKernan, G. P. Kortzorg, N. Wyers, L. Van Halewyck, F. Boisgontier, M. P. Levin, O. Swinnen, S. P. Jonkers, I. Wittenberg, G. F. 2020-12-15 doi:10.1101/2020.12.14.422725 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Exploring the microbiome-wide lysine acetylation, succinylation and propionylation in human gut microbiota ]]> https://biorxiv.org/content/10.1101/2020.12.14.422746v1?rss=1 60,000 acetylated, and ~20,000 propionylated and succinylated gut microbial peptides. Characterization of these identified modification-specific metaproteomes, i.e. meta-PTMomes, demonstrates that lysine acylations are differentially distributed in microbial species with different metabolic capabilities. ConclusionThis study provides an analytical framework, consisting of a serial immunoaffinity enrichment and an open database search strategy, for the study of lysine acylations in microbiome, which enables functional microbiome studies at the post-translational level. ]]> Zhang, X. Cheng, K. Ning, Z. Mayne, J. Walker, K. Chi, H. Farnsworth, C. Lee, K. Figeys, D. 2020-12-14 doi:10.1101/2020.12.14.422746 Cold Spring Harbor Laboratory Press 2020-12-14 <![CDATA[ Mutation of a conserved Gln residue does not abolish desensitization of acid-sensing ion channel 1 ]]> https://biorxiv.org/content/10.1101/2020.12.19.423606v1?rss=1 Rook, M. L. Miaro, M. Couch, T. Kneisley, D. L. Musgaard, M. MacLean, D. M. 2020-12-20 doi:10.1101/2020.12.19.423606 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ A hypothesis for theta rhythm frequency control in CA1 microcircuits ]]> https://biorxiv.org/content/10.1101/2020.12.23.424154v1?rss=1 Skinner, F. Rich, S. Lunyov, A. Lefebvre, J. Chatzikalymniou, A. 2020-12-24 doi:10.1101/2020.12.23.424154 Cold Spring Harbor Laboratory Press 2020-12-24 <![CDATA[ Spinal V1 neurons inhibit motor targets locally and sensory targets distally to coordinate locomotion ]]> https://biorxiv.org/content/10.1101/2021.01.22.427836v1?rss=1 Sengupta, M. Daliparthi, V. Roussel, Y. Bui, T. V. Bagnall, M. W. 2021-01-24 doi:10.1101/2021.01.22.427836 Cold Spring Harbor Laboratory Press 2021-01-24 <![CDATA[ Longitudinal analysis of humoral immunity against SARS-CoV-2 Spike in convalescent individuals up to 8 months post-symptom onset ]]> https://biorxiv.org/content/10.1101/2021.01.25.428097v1?rss=1 Anand, S. P. Prevost, J. Nayrac, M. Beaudoin-Bussieres, G. Benlarbi, M. Gasser, R. Brassard, N. Laumaea, A. Gong, S. Y. Bourassa, C. Brunet-Ratnasingham, E. Medjahed, H. Gendron-Lepage, G. Goyette, G. Gokool, L. Morrisseau, C. Begin, P. Martel-Laferriere, V. Tremblay, C. Richard, J. Bazin, R. Duerr, R. Kaufmann, D. E. Finzi, A. 2021-01-25 doi:10.1101/2021.01.25.428097 Cold Spring Harbor Laboratory Press 2021-01-25 <![CDATA[ The effects of maternal social connectivity and integration on offspring survival in a marmot ]]> https://biorxiv.org/content/10.1101/2021.01.28.428660v1?rss=1 Montero, A. P. Williams, D. M. Martin, J. G. A. Blumstein, D. T. 2021-01-29 doi:10.1101/2021.01.28.428660 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ Characterization of Critical Determinants of ACE2-RBD Interaction ]]> https://biorxiv.org/content/10.1101/2021.01.29.428773v1?rss=1 Brown, E. E. F. Rezaei, R. Jamieson, T. Dave, J. Martin, N. T. Singaravelu, R. Crupi, M. J. F. Boulton, S. Tucker, S. Duong, J. Poutou, J. Pelin, A. Yasavoli-Sharahi, H. Taha, Z. Arulanandam, R. Surendran, A. Ghahremani, M. Austin, B. Matar, C. Diallo, J.-S. Bell, J. C. Ilkow, C. S. Azad, T. 2021-01-29 doi:10.1101/2021.01.29.428773 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ Chemical defense and tonic immobility in early life stages of the Harlequin cabbage bug, Murgantia histrionica (Heteroptera: Pentatomidae) ]]> https://biorxiv.org/content/10.1101/2021.01.29.428818v1?rss=1 Guerra-Grenier, E. Liu, R. Arnason, J. T. Sherratt, T. N. 2021-01-31 doi:10.1101/2021.01.29.428818 Cold Spring Harbor Laboratory Press 2021-01-31 <![CDATA[ Viral evolutionary dynamics predict Influenza-Like-Illnesses in patients ]]> https://biorxiv.org/content/10.1101/2021.01.31.429026v1?rss=1 Wallbank, C. Aris-Brosou, S. 2021-02-01 doi:10.1101/2021.01.31.429026 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Sleeping at the Switch ]]> https://biorxiv.org/content/10.1101/2021.02.02.429396v1?rss=1 Bouchard, M. Lina, J.-M. Gaudreault, P.-O. Lafreniere, A. Dube, J. Gosselin, N. Carrier, J. 2021-02-03 doi:10.1101/2021.02.02.429396 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ PIGNON: A protein-protein interaction-guided functional enrichment analysis for quantitative proteomics ]]> https://biorxiv.org/content/10.1101/2021.02.03.429592v1?rss=1 Nadeau, R. Byvsheva, A. Lavallee-Adam, M. 2021-02-04 doi:10.1101/2021.02.03.429592 Cold Spring Harbor Laboratory Press 2021-02-04 <![CDATA[ A viral protein utilizes the NDP52/CALCOCO2 selective autophagy receptor to disassemble processing bodies ]]> https://biorxiv.org/content/10.1101/2021.02.07.430164v1?rss=1 Robinson, C.-A. Singh, G. K. Castle, E. L. Boudreau, B. Q. Corcoran, J. 2021-02-08 doi:10.1101/2021.02.07.430164 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Development and validation of a deep learning algorithm and open-source platform for the automatic labelling of motion capture markers ]]> https://biorxiv.org/content/10.1101/2021.02.08.429993v1?rss=1 Clouthier, A. L. Ross, G. B. Mavor, M. P. Coll, I. Boyle, A. Graham, R. B. 2021-02-10 doi:10.1101/2021.02.08.429993 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Modelling spinal locomotor circuits for movements in developing zebrafish ]]> https://biorxiv.org/content/10.1101/2021.02.10.430671v1?rss=1 Roussel, Y. Gaudreau, S. F. Sengupta, M. Bui, T. V. 2021-02-11 doi:10.1101/2021.02.10.430671 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ Parasite co-opts a ubiquitin receptor to induce a plethora of developmental changes ]]> https://biorxiv.org/content/10.1101/2021.02.15.430920v1?rss=1 Huang, W. MacLean, A. Sugio, A. Maqbool, A. Busscher, M. Cho, S.-T. Kamoun, S. Kuo, C.-H. Immink, R. G. H. Hogenhout, S. A. 2021-02-15 doi:10.1101/2021.02.15.430920 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ Cerebellar tDCS alters the perception of optic flow ]]> https://biorxiv.org/content/10.1101/2021.02.15.431326v1?rss=1 Nankoo, J.-F. Madan, C. R. Medina, O. Makepeace, T. Striemer, C. L. 2021-02-17 doi:10.1101/2021.02.15.431326 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Burst coding despite unimodal interval distributions ]]> https://biorxiv.org/content/10.1101/2021.02.18.431851v1?rss=1 Williams, E. Payeur, A. Gidon, A. Naud, R. 2021-02-18 doi:10.1101/2021.02.18.431851 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ The last battle of Anne of Brittany: solving mass grave through an interdisciplinary approach (paleopathology, anthropobiology, history, multiple isotopes and radiocarbon dating) ]]> https://biorxiv.org/content/10.1101/2021.02.22.432237v1?rss=1 Colleter, R. Bataille, C. Milano, S. Dabernat, H. Trost, M. Marchal, M. Guilbeau-Frugier, C. Pichot, D. Hamon, P. Labaune-Jean, F. Jean, S. Le Cloirec, G. Steinbrenner, S. Duchesne, S. Telmon, N. Crubezy, E. Jaouen, K. 2021-02-22 doi:10.1101/2021.02.22.432237 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ Resilience through diversity: Loss of neuronal heterogeneity in epileptogenic human tissue renders neural networks more susceptible to sudden changes in synchrony ]]> https://biorxiv.org/content/10.1101/2021.03.02.433627v1?rss=1 Rich, S. Moradi Chameh, H. Lefebvre, J. Valiante, T. A. 2021-03-03 doi:10.1101/2021.03.02.433627 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ Transcriptional census of epithelial-mesenchymal plasticity in cancer ]]> https://biorxiv.org/content/10.1101/2021.03.05.434142v1?rss=1 Cook, D. P. Vanderhyden, B. C. 2021-03-07 doi:10.1101/2021.03.05.434142 Cold Spring Harbor Laboratory Press 2021-03-07 <![CDATA[ Hibernation slows epigenetic aging in yellow-bellied marmots ]]> https://biorxiv.org/content/10.1101/2021.03.07.434299v1?rss=1 Pinho, G. M. Martin, J. G. A. Farrell, C. Haghani, A. Zoller, J. A. Zhang, J. Snir, S. Pellegrini, M. Wayne, R. K. Blumstein, D. T. Horvath, S. 2021-03-08 doi:10.1101/2021.03.07.434299 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Vtc5 is localized to the vacuole membrane by the conserved AP-3 complex to regulate polyphosphate synthesis in budding yeast ]]> https://biorxiv.org/content/10.1101/2021.03.15.434853v1?rss=1 Bentley-DeSousa, A. Downey, M. 2021-03-16 doi:10.1101/2021.03.15.434853 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ BATL: Bayesian annotations for targeted lipidomics ]]> https://biorxiv.org/content/10.1101/2021.03.18.435788v1?rss=1 Chitpin, J. G. Taylor, G. P. Xu, H. Nguyen, T. T. Ortega, R. Tomlinson, J. J. Schlossmacher, M. G. Saunders-Pullman, R. Bennett, S. A. L. Perkins, T. J. 2021-03-19 doi:10.1101/2021.03.18.435788 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Live imaging of SARS-CoV-2 infection in mice reveals neutralizing antibodies require Fc function for optimal efficacy ]]> https://biorxiv.org/content/10.1101/2021.03.22.436337v1?rss=1 Ullah, I. Prevost, J. Ladinsky, M. S. Stone, H. Lu, M. Anand, S. P. Beaudoin-Bussieres, G. Benlarbi, M. Ding, S. Gasser, R. Fink, C. Chen, Y. Tauzin, A. Goyette, G. Bourassa, C. Medjahed, H. Mack, M. Chung, K. Wilen, C. B. Dekaban, G. A. Dikeakos, J. D. Bruce, E. A. Kaufmann, D. E. Stamatatos, L. McGuire, A. Richard, J. Pazgier, M. Bjorkman, P. Mothes, W. Finzi, A. Kumar, P. Uchil, P. D. 2021-03-22 doi:10.1101/2021.03.22.436337 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Brain virtual histology with X-ray phase-contrast tomography Part II: 3D morphologies of amyloid-β plaques in Alzheimer's disease models ]]> https://biorxiv.org/content/10.1101/2021.03.25.436908v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@7c3167org.highwire.dtl.DTLVardef@18f689eorg.highwire.dtl.DTLVardef@1d9c72org.highwire.dtl.DTLVardef@a027a_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG ]]> Chourrout, M. Roux, M. Boisvert, C. Gislard, C. Legland, D. Arganda-Carreras, I. Olivier, C. Peyrin, F. Boutin, H. Rama, N. Baron, T. Meyronet, D. Brun, E. Rositi, H. Wiart, M. Chauveau, F. 2021-03-25 doi:10.1101/2021.03.25.436908 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Parallel and recurrent cascade models as a unifying force for understanding sub-cellular computation ]]> https://biorxiv.org/content/10.1101/2021.03.25.437091v1?rss=1 Harkin, E. F. Shen, P. R. Richards, B. A. Naud, R. 2021-03-26 doi:10.1101/2021.03.25.437091 Cold Spring Harbor Laboratory Press 2021-03-26 <![CDATA[ GCN5 Maintains Muscle Integrity by Acetylating YY1 to Promote Dystrophin Expression ]]> https://biorxiv.org/content/10.1101/2021.03.29.436986v1?rss=1 Addicks, G. C. Zhang, H. Ryu, D. Vasam, G. Marshall, P. L. Green, A. E. Patel, S. Kang, B. E. Kim, D. Katsyuba, E. Williams, E. G. Renaud, J.-M. Auwerx, J. Menzies, K. J. 2021-03-30 doi:10.1101/2021.03.29.436986 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ Self-organization of a doubly asynchronous irregular network state for spikes and bursts ]]> https://biorxiv.org/content/10.1101/2021.03.29.437548v1?rss=1 Vercruysse, F. Naud, R. Sprekeler, H. 2021-03-30 doi:10.1101/2021.03.29.437548 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ MetaProClust-MS1: A tool for clustering metaproteomes using rapid MS1 profiling ]]> https://biorxiv.org/content/10.1101/2021.03.31.437863v1?rss=1 Simopoulos, C. M. A. Ning, Z. Li, L. Khamis, M. M. Zhang, X. Lavallee-Adam, M. Figeys, D. 2021-04-01 doi:10.1101/2021.03.31.437863 Cold Spring Harbor Laboratory Press 2021-04-01 <![CDATA[ Mixed selectivity coding of sensory and motor social signals in the thalamus of a weakly electric fish ]]> https://biorxiv.org/content/10.1101/2021.04.04.438391v1?rss=1 Wallach, A. Melanson, A. Longtin, A. Maler, L. 2021-04-04 doi:10.1101/2021.04.04.438391 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ CRISPR Knock-in Designer: automatic oligonucleotide design software to introduce point mutations using CRISPR/Cas9 ]]> https://biorxiv.org/content/10.1101/2021.04.11.439384v1?rss=1 Prykhozhij, S. V. Rajan, V. Ban, K. Berman, J. 2021-04-12 doi:10.1101/2021.04.11.439384 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Isolation of the side population from adult neurogenic niches enriches for endothelial cells ]]> https://biorxiv.org/content/10.1101/2021.04.16.440120v1?rss=1 Kalinina, A. Xue, Y. Gnyra, C. Lagace, D. 2021-04-16 doi:10.1101/2021.04.16.440120 Cold Spring Harbor Laboratory Press 2021-04-16 <![CDATA[ Transcriptomic Changes During Stage Progression of Mycosis Fungoides ]]> https://biorxiv.org/content/10.1101/2021.04.20.440708v1?rss=1 Xiao, M. Hennessey, D. Iyer, A. O'Keefe, S. Zhang, F. Sivanand, A. Gniadecki, R. 2021-04-21 doi:10.1101/2021.04.20.440708 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ The cortical hubs related to recovery of consciousness ]]> https://biorxiv.org/content/10.1101/2021.04.25.441310v1?rss=1 Wu, H. Qi, Z. Zhang, J. Wu, C. Wu, X. Huang, Z. Zang, D. Fogel, S. Tanabe, S. Hudetz, A. G. Northoff, G. Mao, Y. Qin, P. 2021-04-26 doi:10.1101/2021.04.25.441310 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ ROMO1 is essential for glucose coupling in the pancreatic beta cell of male mice ]]> https://biorxiv.org/content/10.1101/2021.04.28.441811v1?rss=1 Wells, L. Iorio, C. Ng, A. C.-H. Reeks, C. Yee, S.-P. Screaton, R. A. 2021-04-28 doi:10.1101/2021.04.28.441811 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Retention Time Standardization and Registration (RTStaR): An algorithm that matches corresponding and identifies unique species in nanoliquid chromatography-nanoelectrospray ionization-mass spectrometry lipidomic datasets ]]> https://biorxiv.org/content/10.1101/2021.05.01.442266v1?rss=1 Blanchard, A. P. Wang, Y. Taylor, G. P. Granger, M. W. Fai, S. Figeys, D. Paus, T. Pausova, Z. Xu, H. Bennett, S. A. L. 2021-05-02 doi:10.1101/2021.05.01.442266 Cold Spring Harbor Laboratory Press 2021-05-02 <![CDATA[ Mechanosensitive Osteogenesis on Native Cellulose Scaffolds for Bone Tissue Engineering. ]]> https://biorxiv.org/content/10.1101/2021.05.26.444470v1?rss=1 Leblanc Latour, M. Pelling, A. E. 2021-05-27 doi:10.1101/2021.05.26.444470 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells. ]]> https://biorxiv.org/content/10.1101/2021.05.27.443845v1?rss=1 DURAND, S. BRUELLE, M. BOURDELAIS, F. BENNYCHEN, B. BLIN-GONTHIER, J. ISAAC, C. HUYGHE, A. SEYVE, A. VANBELLE, C. MEYRONET, D. CATEZ, F. DIAZ, J. J. Lavial, F. Ricci, E. P. DUCRAY, F. GABUT, M. 2021-05-29 doi:10.1101/2021.05.27.443845 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ Elevated colonic microbiota-associated paucimannosidic and truncated N-glycans in pediatric ulcerative colitis ]]> https://biorxiv.org/content/10.1101/2021.05.27.446002v1?rss=1 Li, H. Zhang, X. Chen, R. Cheng, K. Ning, Z. Li, J. Twine, S. Stintzi, A. Mack, D. Figeys, D. 2021-05-28 doi:10.1101/2021.05.27.446002 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Single-cell RNA sequencing-based characterization of resident lung mesenchymal stromal cells in bronchopulmonary dysplasia ]]> https://biorxiv.org/content/10.1101/2021.06.18.448928v1?rss=1 Mizikova, I. Lesage, F. Cyr-Depauw, C. Cook, D. P. Hurskainen, M. Hanninen, S. Vadivel, A. Bardin, P. Zhong, S. Carpen, O. Vanderhyden, B. C. Thebaud, B. 2021-06-18 doi:10.1101/2021.06.18.448928 Cold Spring Harbor Laboratory Press 2021-06-18 <![CDATA[ Temporal derivative computation in the dorsal raphe network revealed by an experimentally-driven augmented integrate-and-fire modeling framework ]]> https://biorxiv.org/content/10.1101/2021.06.25.449907v1?rss=1 Harkin, E. F. Payeur, A. Lynn, M. B. Boucher, J.-F. Caya-Bissonnette, L. Cyr, D. Stewart, C. Longtin, A. Naud, R. Beïque, J.-C. 2021-06-27 doi:10.1101/2021.06.25.449907 Cold Spring Harbor Laboratory Press 2021-06-27 <![CDATA[ Three-dimensional drug screen identifies HDAC inhibitors as therapeutic agents in mTORC1-driven lymphangioleiomyomatosis ]]> https://biorxiv.org/content/10.1101/2021.07.03.451004v1?rss=1 Pietrobon, A. Yockell-Lelievre, J. Melong, N. Smith, L. J. Delaney, S. P. Azzam, N. Xue, C. Merwin, N. Lian, E. Camacho-Magallanes, A. Dore, C. Musso, G. Julian, L. M. Kristof, A. S. Tam, R. Y. Berman, J. N. Shoichet, M. S. Stanford, W. L. 2021-07-04 doi:10.1101/2021.07.03.451004 Cold Spring Harbor Laboratory Press 2021-07-04 <![CDATA[ Examining the effects of an anti-Salmonella bacteriophage preparation, BAFASAL, on ex vivo human gut microbiome composition and function using a multi-omics approach ]]> https://biorxiv.org/content/10.1101/2021.07.04.451072v1?rss=1 Mayne, J. Zhang, X. Butcher, J. Walker, K. Ning, Z. Wojcik, E. Dastych, J. Stintzi, A. Figeys, D. 2021-07-05 doi:10.1101/2021.07.04.451072 Cold Spring Harbor Laboratory Press 2021-07-05 <![CDATA[ Biomechanical study of cellulose scaffolds for bone tissue engineering in vivo and in vitro. ]]> https://biorxiv.org/content/10.1101/2021.07.07.451476v1?rss=1 Leblanc Latour, M. Tarar, M. Hickey, R. J. Cuerrier, C. M. Catelas, I. Pelling, A. 2021-07-07 doi:10.1101/2021.07.07.451476 Cold Spring Harbor Laboratory Press 2021-07-07 <![CDATA[ Impact of temperature on the affinity of SARS-CoV-2 Spike for ACE2 ]]> https://biorxiv.org/content/10.1101/2021.07.09.451812v1?rss=1 Prevost, J. Richard, J. Gasser, R. Ding, S. Fage, C. Anand, S. P. Adam, D. Gupta Vergara, N. Tauzin, A. Benlarbi, M. Gong, S. Y. Goyette, G. Prive, A. Moreira, S. Charest, H. Roger, M. Mothes, W. Pazgier, M. Brochiero, E. Boivin, G. Abrams, C. F. Schon, A. Finzi, A. 2021-07-09 doi:10.1101/2021.07.09.451812 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Newly Emergent Apelin Expressing Endothelial Stem-like Cells Orchestrate Lung Microvascular Repair ]]> https://biorxiv.org/content/10.1101/2021.07.12.452061v1?rss=1 70% of lung ECs, producing severe ALI with near complete resolution by 7 days. At 3 days post injury, a novel gCap population emerged characterized by de novo expression of apelin, together with the stem cell marker, protein C receptor. These stem-like cells transitioned to proliferative ECs, expressing apelin receptor together with the pro-proliferative transcription factor, FoxM1. This progenitor-like cell population was responsible for the rapid replenishment of all depleted EC populations by 7 days post injury, including aerocytes which play a critical role in re-establishment of the air-blood barrier. Treatment with an apelin receptor antagonist prevented recovery and resulted in excessive mortality, consistent with a central role for apelin signaling in EC regeneration and microvascular repair. ConclusionThe lung has a remarkable capacity for microvasculature EC regeneration which is orchestrated by signaling between newly emergent apelin-expressing gCap endothelial stem-like cells and highly proliferative, apelin receptor positive endothelial progenitors. Take-Home messageUsing sublethal lung endothelial cell (EC) ablation, we show for the first that EC regeneration and resolution of acute lung injury is orchestrated by novel apelin-expressing, gCap endothelial stem-like cells by a mechanism requiring apelin signaling. Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY A schematic representation of EC populations contributing to microvascular repair. At baseline (Day 0), there are two main alveolar groups of capillary ECs: larger apelin positive aCap ECs, termed aerocytes, that play a key structural role in forming the air-blood barrier; and smaller apelin receptor (Aplnr) expressing gCap ECs, which are found in the thicker regions at the corners of the alveoli. After DT-induced EC ablation, there is a marked depletion of both EC populations and the appearance of novel transitional and transient populations. At Day 3, there is the appearance of stem-like gCap ECs that paradoxically express apelin, but not its receptor, and are characterized by various stem and progenitor cell markers but show no evidence of proliferation. By Day 5, these transition to ECs expressing Aplnr which have a strong proliferative phenotype, as evidenced by FoxM1 and Ki67 expression, and then rapidly replenish depleted EC pools, including aCap ECs, by Day 7. This transition is orchestrated by the interaction of apelin with its receptor as a critical mechanism in lung microvascular regeneration after EC injury. AT1 = alveolar type -1 epithelial cell; AT2 = alveolar type-2 epithelial cell; APLNR = apelin receptor; ANGPT2 = angiopoietin 2; EPCR = Endothelial protein C receptor. ]]> Godoy, R. S. Cook, D. P. Cober, N. D. Deng, Y. Wang, L. Chakravarti, A. Rowe, K. Stewart, D. J. 2021-07-12 doi:10.1101/2021.07.12.452061 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Experimental evidence that metapopulation structure can accelerate adaptive evolution ]]> https://biorxiv.org/content/10.1101/2021.07.13.452242v1?rss=1 Chakraborty, P. P. Nemzer, L. R. Kassen, R. 2021-07-13 doi:10.1101/2021.07.13.452242 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ Revealing Protein-Level Functional Redundancy in the Human Gut Microbiome using Ultra-deep Metaproteomics ]]> https://biorxiv.org/content/10.1101/2021.07.15.452564v1?rss=1 Li, L. Ning, Z. Zhang, X. Butcher, J. Simopoulos, C. Mayne, J. M. A. Stintzi, A. Mack, D. R. Liu, Y.-Y. Figeys, D. 2021-07-15 doi:10.1101/2021.07.15.452564 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ Delineating Medical Education: Bibliometric Research Approach(es) ]]> https://biorxiv.org/content/10.1101/2021.07.23.453492v1?rss=1 Maggio, L. A. Ninkov, A. Frank, J. R. Costello, J. A. Artino, A. R. 2021-07-26 doi:10.1101/2021.07.23.453492 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ Golden Gate Assembly of Aerobic and Anaerobic Microbial Bioreporters ]]> https://biorxiv.org/content/10.1101/2021.07.23.453609v1?rss=1 Hinz, A. J. Stenzler, B. R. Poulain, A. J. 2021-07-24 doi:10.1101/2021.07.23.453609 Cold Spring Harbor Laboratory Press 2021-07-24 <![CDATA[ Structural Basis and Mode of Action for Two Broadly Neutralizing Antibodies Against SARS-CoV-2 Emerging Variants of Concern ]]> https://biorxiv.org/content/10.1101/2021.08.02.454546v1?rss=1 Mothes, W. Li, W. Chen, Y. Prevost, J. Ullah, I. Lu, M. Gong, S. Y. Tauzin, A. Gasser, R. Vezina, D. Anand, S. P. Goyette, G. Chaterjee, D. Ding, S. Tolbert, W. D. Grunst, M. W. Bo, Y. Zhang, S. Richard, J. Zhou, F. Huang, R. K. Esser, L. Zeher, A. Cote, M. Kumar, P. Sodroski, J. Xia, D. Uchil, P. D. Pazgier, M. Finzi, A. 2021-08-03 doi:10.1101/2021.08.02.454546 Cold Spring Harbor Laboratory Press 2021-08-03 <![CDATA[ Cell-Type Specific Responses to Associative Learning in the Primary Motor Cortex ]]> https://biorxiv.org/content/10.1101/2021.08.08.455571v1?rss=1 Lee, C. Harkin, E. Naud, R. Chen, S. 2021-08-08 doi:10.1101/2021.08.08.455571 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ Long reads and Hi-C sequencing illuminate the two-compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis ]]> https://biorxiv.org/content/10.1101/2021.08.12.456011v1?rss=1 Yildirir, G. Sperschneider, J. Malar, M. C. Chen, E. C. Iwasaki, W. Cornell, C. Corradi, N. 2021-08-12 doi:10.1101/2021.08.12.456011 Cold Spring Harbor Laboratory Press 2021-08-12 <![CDATA[ Learning to be on time: temporal coordination of neural dynamics by activity-dependent myelination ]]> https://biorxiv.org/content/10.1101/2021.08.17.456520v1?rss=1 Talidou, A. Frankland, P. Mabbott, D. Lefebvre, J. 2021-08-19 doi:10.1101/2021.08.17.456520 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Deep Bayesian networks for uncertainty estimation and adversarial resistance of white matter hyperintensity segmentation ]]> https://biorxiv.org/content/10.1101/2021.08.18.456666v1?rss=1 Mojiri Forooshani, P. Biparva, M. Ntiri, E. E. Ramirez, J. Boone, L. Holmes, M. F. Adamo, S. Gao, F. Ozzoude, M. Scott, C. J. M. Dowlatshahi, D. Lawrence-Dewar, J. M. Kwan, D. Lang, A. E. Marcotte, K. Leonard, c. Rochon, E. Heyn, C. Bartha, R. Strother, S. Tardif, J.-C. Symons, S. Masellis, M. Swartz, R. H. Moody, A. Black, S. E. Goubran, M. 2021-08-19 doi:10.1101/2021.08.18.456666 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ A small molecule drug screening identifies colistin sulfate as an enhancer of Natural Killer cell cytotoxicity. ]]> https://biorxiv.org/content/10.1101/2021.08.20.457155v1?rss=1 Cortes-Kaplan, S. Hasim, M. Kaczmarek, S. Taha, Z. Maznyi, G. McComb, S. Lee, S.-H. Diallo, J.-S. Ardolino, M. 2021-08-21 doi:10.1101/2021.08.20.457155 Cold Spring Harbor Laboratory Press 2021-08-21 <![CDATA[ Viral spillover risk in High Arctic increases with melting glaciers ]]> https://biorxiv.org/content/10.1101/2021.08.23.457348v1?rss=1 Lemieux, A. Colby, G. A. Poulain, A. J. Aris-Brosou, S. 2021-08-23 doi:10.1101/2021.08.23.457348 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ Six1 Promotes Skeletal Muscle Thyroid Hormone Response through Regulation of the MCT10 Transporter ]]> https://biorxiv.org/content/10.1101/2021.08.27.457933v1?rss=1 Blais, A. Yang, D. Chakroun, I. Liu, Y. 2021-08-27 doi:10.1101/2021.08.27.457933 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Sex differences in central and peripheral fatigue induced by sustained isometric ankle plantar flexion ]]> https://biorxiv.org/content/10.1101/2021.09.03.458912v1?rss=1 Jo, D. Goubran, M. Bilodeau, M. 2021-09-03 doi:10.1101/2021.09.03.458912 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Sensitivity of discrete symmetry metrics: implications for metric choice ]]> https://biorxiv.org/content/10.1101/2021.09.14.460334v1?rss=1 Hill, A. D. Nantel, J. 2021-09-16 doi:10.1101/2021.09.14.460334 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ Deletion or inhibition of astrocytic transglutaminase 2 promotes functional recovery after spinal cord injury ]]> https://biorxiv.org/content/10.1101/2021.09.15.460455v1?rss=1 Elahi, A. Emerson, J. Rudlong, J. Keillor, J. W. Salois, G. Visca, A. Girardi, P. Johnson, G. V. Proschel, C. 2021-09-17 doi:10.1101/2021.09.15.460455 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ Effects of arm swing amplitude and lower limb asymmetry on motor variability patterns during treadmill gait ]]> https://biorxiv.org/content/10.1101/2021.09.24.461689v1?rss=1 Bailey, C. A. Hill, A. Graham, R. B. Nantel, J. 2021-09-24 doi:10.1101/2021.09.24.461689 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Validity and sensitivity of an inertial measurement unit-driven biomechanical model of motor variability for gait ]]> https://biorxiv.org/content/10.1101/2021.09.27.461967v1?rss=1 Bailey, C. Uchida, T. Nantel, J. Graham, R. 2021-09-27 doi:10.1101/2021.09.27.461967 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ Deficiency of Irx5 protects mice from diet-induced obesity and associated metabolic abnormalities ]]> https://biorxiv.org/content/10.1101/2021.09.27.462004v1?rss=1 Son, J. Kim, K.-H. Hui, C.-c. 2021-09-27 doi:10.1101/2021.09.27.462004 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ Evaluating live microbiota biobanking using an ex vivo microbiome assay and metaproteomics ]]> https://biorxiv.org/content/10.1101/2021.09.30.462621v1?rss=1 Zhang, X. Walker, K. Mayne, J. Li, L. Ning, Z. Stintzi, A. Figeys, D. 2021-09-30 doi:10.1101/2021.09.30.462621 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ tACS competes with ongoing oscillations for control of spike-timing in the primate brain. ]]> https://biorxiv.org/content/10.1101/2021.10.01.462622v1?rss=1 Krause, M. R. Vieira, P. G. Thivierge, J.-P. Pack, C. C. 2021-10-03 doi:10.1101/2021.10.01.462622 Cold Spring Harbor Laboratory Press 2021-10-03 <![CDATA[ Constitutive nuclear accumulation of endogenous alpha-synuclein in mice causes motor dysfunction and cortical atrophy, independent of protein aggregation. ]]> https://biorxiv.org/content/10.1101/2021.10.13.464123v1?rss=1 Geertsma, H. M. Suk, T. R. Ricke, K. M. Horsthuis, K. Parmasad, J.-L. A. Fisk, Z. Callaghan, S. M. Rousseaux, M. W. C. 2021-10-14 doi:10.1101/2021.10.13.464123 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Plant-based production of SARS-CoV-2 antigens for use in a subunit vaccine ]]> https://biorxiv.org/content/10.1101/2021.10.17.464700v1?rss=1 Demone, J. J. Maltseva, M. Nourimand, M. Nasr-Sharif, M. Galipeau, Y. Langlois, M.-A. MacLean, A. M. 2021-10-18 doi:10.1101/2021.10.17.464700 Cold Spring Harbor Laboratory Press 2021-10-18 <![CDATA[ Estimating null and potent modes of feedforward communication in a computational model of cortical activity ]]> https://biorxiv.org/content/10.1101/2021.10.18.464855v1?rss=1 Thivierge, J.-P. Pilzak, A. 2021-10-19 doi:10.1101/2021.10.18.464855 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Plant-based expression of SARS-CoV-2 antigens for use in an oral vaccine ]]> https://biorxiv.org/content/10.1101/2021.12.07.471131v1?rss=1 Power, M. Azad, T. Bell, J. C. MacLean, A. 2021-12-09 doi:10.1101/2021.12.07.471131 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Mesoscale cortex-wide neural dynamics predict self-initiated actions in mice several seconds prior to movement ]]> https://biorxiv.org/content/10.1101/2021.12.17.473193v1?rss=1 Mitelut, C. Zhang, Y. Sekino, Y. Boyd, J. Bolanos, F. Swindale, N. V. Silasi, G. Saxena, S. Murphy, T. H. 2021-12-20 doi:10.1101/2021.12.17.473193 Cold Spring Harbor Laboratory Press 2021-12-20 <![CDATA[ Temporal associations of B and T cell immunity with robust vaccine responsiveness in a 16-week interval BNT162b2 regimen ]]> https://biorxiv.org/content/10.1101/2021.12.18.473317v1?rss=1 Nayrac, M. Dube, M. Sannier, G. Nicolas, A. Marchitto, L. Tastet, O. Tauzin, A. Brassard, N. Beaudoin-Bussieres, G. Vezina, D. Gong, S. Y. Benlarbi, M. Gasser, R. Laumaea, A. Bourassa, C. Gendron-Lepage, G. Medjahed, H. Goyette, G. Ortega-Delgado, G.-G. Laporte, M. Niessl, J. Gokool, L. Morrisseau, C. Arlotto, P. Richard, J. Tremblay, C. Martel-Laferriere, V. Finzi, A. Kaufmann, D. E. 2021-12-21 doi:10.1101/2021.12.18.473317 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Arsenal of Nanobodies for Broad-Spectrum Countermeasures against Current and Future SARS-CoV-2 Variants of Concerns ]]> https://biorxiv.org/content/10.1101/2021.12.20.473401v1?rss=1 Rossotti, M. A. van Faassen, H. Tran, A. Sheff, J. Sandhu, J. A. Duque, D. Hewitt, M. Wen, S. Bavananthasivam, R. Beitari, S. Matte, K. Laroche, G. Giguere, P. M. Gervais, C. Stuible, M. Guimond, J. Perret, S. Hussack, G. Langlois, M.-A. Durocher, Y. Tanha, J. 2021-12-21 doi:10.1101/2021.12.20.473401 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-weeks interval between doses ]]> https://biorxiv.org/content/10.1101/2021.12.21.473679v1?rss=1 Chatterjee, D. Tauzin, A. Marchitto, L. Gong, S. Y. Boutin, M. Bourassa, C. Beaudoin-Bussieres, G. Bo, Y. Ding, S. Laumaea, A. Vezina, D. Perreault, J. Gokool, L. Morrisseau, C. Arlotto, P. Fournier, E. Guilbault, A. Delisle, B. Levade, I. Goyette, G. Gendron-Lepage, G. Medjahed, H. De Serres, G. Tremblay, C. Martel-Laferriere, V. Kaufmann, D. E. Bazin, R. Prevost, J. Moreira, S. Richard, J. Cote, M. Finzi, A. 2021-12-23 doi:10.1101/2021.12.21.473679 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ PFTK1 kinase regulates axogenesis during development via RhoA activation. ]]> https://biorxiv.org/content/10.1101/2022.01.11.475789v1?rss=1 Joselin, A. Rodriguez Gonzalez, Y. Kamkar, F. Jafar-nejad, P. Wang, S. Qu, D. Sanchez Alvarez, L. Hawari, D. Sonnenfeld, M. Slack, R. S. Albert, P. Park, D. S. 2022-01-13 doi:10.1101/2022.01.11.475789 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ Ancestral acetylcholine receptor β-subunit forms homopentamers that prime before opening spontaneously ]]> https://biorxiv.org/content/10.1101/2022.01.12.475990v1?rss=1 Tessier, C. J. G. Sturgeon, R. M. Emlaw, J. R. McCluskey, G. D. Perez-Areales, F. J. daCosta, C. J. B. 2022-01-13 doi:10.1101/2022.01.12.475990 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ Comprehensive assessment of functional effects of commonly used sweeteners on ex vivo human gut microbiome ]]> https://biorxiv.org/content/10.1101/2022.01.15.474735v1?rss=1 Sun, Z. Wang, W. Li, L. Zhang, X. Ning, Z. Mayne, J. Walker, K. Stintzi, A. Figeys, D. 2022-01-16 doi:10.1101/2022.01.15.474735 Cold Spring Harbor Laboratory Press 2022-01-16 <![CDATA[ Pharmacological inhibition of HDAC6 downregulates TGF-β via Smad2/3 acetylation and improves dystrophin-deficient muscles. ]]> https://biorxiv.org/content/10.1101/2022.01.21.477182v1?rss=1 Osseni, A. Ravel-Chapuis, A. Scionti, I. Gangloff, Y.-G. Moncollin, V. Mounier, R. Leblanc, P. Jasmin, B. J. Schaeffer, L. 2022-01-22 doi:10.1101/2022.01.21.477182 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ Becoming metrics literate: An analysis of brief videos that teach about the h-index ]]> https://biorxiv.org/content/10.1101/2022.01.21.477291v1?rss=1 Maggio, L. A. Jeffrey, A. Haustein, S. Samuel, A. 2022-01-24 doi:10.1101/2022.01.21.477291 Cold Spring Harbor Laboratory Press 2022-01-24 <![CDATA[ Ddp1 cooperates with Ppx1 to counter a stress response initiated by non-vacuolar polyphosphate ]]> https://biorxiv.org/content/10.1101/2022.02.02.478728v1?rss=1 McCarthy, L. Abramchuk, I. Wafy, G. Denoncourt, A. Lavallee-Adam, M. Downey, M. 2022-02-02 doi:10.1101/2022.02.02.478728 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ VE607 Stabilizes SARS-CoV-2 Spike In the "RBD-up" Conformation and Inhibits Viral Entry ]]> https://biorxiv.org/content/10.1101/2022.02.03.479007v1?rss=1 Ding, S. Gong, S. Y. Grover, J. Mohammadjavad, M. Chen, Y. Vezina, D. Beaudoin-Bussieres, G. Verma, V. T. Goyette, G. Richard, J. Yang, D. Smith, A. B. Pazgier, M. Cote, M. Abrams, C. Mothes, W. Finzi, A. Baron, C. 2022-02-04 doi:10.1101/2022.02.03.479007 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Identification of a SARS-CoV-2 host metalloproteinase-dependent entry pathway differentially used by SARS-CoV-2 and variants of concern Alpha, Delta, and Omicron ]]> https://biorxiv.org/content/10.1101/2022.02.19.481107v1?rss=1 Benlarbi, M. Laroche, G. Fink, C. Fu, K. Mulloy, R. P. Phan, A. Ariana, A. Stewart, C. M. Prevost, J. Beaudoin-Bussieres, G. Daniel, R. Bo, Y. Yockell-Lelievre, J. Stanford, W. L. Giguere, P. M. Mubareka, S. Finzi, A. Dekaban, G. A. Dikeakos, J. D. Cote, M. 2022-02-22 doi:10.1101/2022.02.19.481107 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Synaptic Location Is a Determinant of the Detrimental Effects of α-Synuclein Pathology to Glutamatergic Transmission in the Basolateral Amygdala ]]> https://biorxiv.org/content/10.1101/2022.02.20.481207v1?rss=1 Nagaraja, C. Chen, L. Daniels, S. Meyerdirk, L. Steiner, J. A. Galvis, M. L. E. Henderson, M. Brundin, P. Chu, H.-y. 2022-02-20 doi:10.1101/2022.02.20.481207 Cold Spring Harbor Laboratory Press 2022-02-20 <![CDATA[ Highly divergent white-tailed deer SARS-CoV-2 with potential deer-to-human transmission ]]> https://biorxiv.org/content/10.1101/2022.02.22.481551v1?rss=1 Pickering, B. Lung, O. Maguire, F. Kruczkiewicz, P. Kotwa, J. D. Buchanan, T. Gagnier, M. Guthrie, J. Jardine, C. Marchand-Austin, A. Masse, A. McClinchey, H. Nirmalarajah, K. Aftanas, P. Blais-Savoie, J. Chee, H.-Y. Chien, E. Yim, W. Goolia, M. Suderman, M. Pinette, M. Smith, G. Sullivan, D. Rudar, J. Adey, E. Nebroski, M. Cote, M. Laroche, G. McGeer, A. Nituch, L. Mubareka, S. Bowman, J. 2022-02-25 doi:10.1101/2022.02.22.481551 Cold Spring Harbor Laboratory Press 2022-02-25 <![CDATA[ SUMOylation of ABCD3 restricts bile acid synthesis and regulates metabolic homeostasis ]]> https://biorxiv.org/content/10.1101/2022.03.03.482848v1?rss=1 Goyon, V. Besse-Patin, A. Zunino, R. Nguyen, M. Coyaud, E. Lee, J. M. Nguyen, B. N. Raught, B. McBride, H. M. 2022-03-04 doi:10.1101/2022.03.03.482848 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Seasonal changes in membrane structure and excitability in central neurons of goldfish (Carassius auratus) under constant environmental conditions ]]> https://biorxiv.org/content/10.1101/2022.03.04.483033v1?rss=1 Country, M. W. Haase, K. Blank, K. Canez, C. R. Roberts, J. A. Campbell, B. F. N. Smith, J. C. Pelling, A. E. Jonz, M. G. 2022-03-07 doi:10.1101/2022.03.04.483033 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Dentate gyrus mossy cells exhibit sparse coding via adaptive spike threshold dynamics ]]> https://biorxiv.org/content/10.1101/2022.03.07.483263v1?rss=1 Trinh, A.-T. Girardi-Schappo, M. Beique, J.-C. Longtin, A. Maler, L. 2022-03-08 doi:10.1101/2022.03.07.483263 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ A comparison of hard and soft direct methods for DNA extraction from soil ]]> https://biorxiv.org/content/10.1101/2022.03.07.483395v1?rss=1 Hill, P. B. Dextraze, M. F. Kroetsch, D. Boddy, C. N. 2022-03-08 doi:10.1101/2022.03.07.483395 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Analyses of Mutational Patterns Induced by Formaldehyde and Acetaldehyde Reveal Similarity to a Common Mutational Signature in Cancers ]]> https://biorxiv.org/content/10.1101/2022.03.08.483495v1?rss=1 Thapa, M. J. Fabros, R. M. Alasmar, S. Chan, K. 2022-03-08 doi:10.1101/2022.03.08.483495 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Improved sensitivity and resolution of ATAC-seq differential DNA accessibility analysis ]]> https://biorxiv.org/content/10.1101/2022.03.16.484118v1?rss=1 Sheikh, A. A. Blais, A. 2022-03-16 doi:10.1101/2022.03.16.484118 Cold Spring Harbor Laboratory Press 2022-03-16 <![CDATA[ The Human Motoneuron Expression Signature is Defined by ALS-Related Genes ]]> https://biorxiv.org/content/10.1101/2022.03.25.485808v1?rss=1 Yadav, A. Matson, K. J. E. Li, L. Hua, I. Gaur, P. Alkaslasi, M. R. Hasan, S. Galuta, A. Dedek, A. Ameri, S. Parnell, J. Alshardan, M. M. Ququmji, F. A. Alhamad, S. M. Wang, A. P. Poulen, G. Lonjon, N. Vachiery-Lahaye, F. Nalls, M. A. Nalls, M. A. Qi, Y. A. Hildebrand, M. E. Mery, P.-F. Bourinet, E. Bauchet, L. Tsai, E. C. Ward, M. E. Le Pichon, C. Menon, V. Levine, A. 2022-03-28 doi:10.1101/2022.03.25.485808 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Separation of NaV Subtypes in the Axon InitialSegment can Impede or Promote Backpropagation ]]> https://biorxiv.org/content/10.1101/2022.04.01.486760v1?rss=1 Barlow, B. S. Longtin, A. Joos, B. 2022-04-05 doi:10.1101/2022.04.01.486760 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ METAbolomics data Balancing with Over-sampling Al-gorithms (META-BOA): an online resource for addressing class imbalance ]]> https://biorxiv.org/content/10.1101/2022.04.21.489108v1?rss=1 Hashimoto-Roth, E. Surendra, A. Lavallee-Adam, M. Bennett, S. A. L. Cuperlovic-Culf, M. 2022-04-22 doi:10.1101/2022.04.21.489108 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ LRRK2 Phosphorylates Neuronal Elav RNA-Binding Proteins to RegulatePhenotypes Relevant to Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2022.04.24.489327v1?rss=1 Pastic, A. Negeri, O. Ravel-Chapuis, A. Savard, A. Trung, M. T. Palidwor, G. Guo, H. Marcogliese, P. Taylor, J. A. Okano, H. Trinkle-Mulcahy, L. Jasmin, B. J. Park, D. Gibbings, D. 2022-04-25 doi:10.1101/2022.04.24.489327 Cold Spring Harbor Laboratory Press 2022-04-25 <![CDATA[ Genetic and pharmacological reduction of CDK14 mitigates synucleinopathy ]]> https://biorxiv.org/content/10.1101/2022.05.02.490309v1?rss=1 Parmasad, J.-L. A. Ricke, K. M. Stykel, M. G. Buchner-Duby, B. Lian, E. Nguyen, B. Lengacher, N. A. Geertsma, H. M. Bruce, A. Callaghan, S. M. Joselin, A. Tomlinson, J. J. Schlossmacher, M. G. Stanford, W. L. Brundin, P. Ryan, S. D. Rousseaux, M. W. C. 2022-05-02 doi:10.1101/2022.05.02.490309 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ More accurate estimation of cell composition in bulk expression through robust integration of single-cell information ]]> https://biorxiv.org/content/10.1101/2022.05.13.491858v1?rss=1 Karimnezhad, A. 2022-05-15 doi:10.1101/2022.05.13.491858 Cold Spring Harbor Laboratory Press 2022-05-15 <![CDATA[ PGC-1β maintains mitochondrial metabolism and restrains inflammatory gene expression ]]> https://biorxiv.org/content/10.1101/2022.05.18.492477v1?rss=1 Guak, H. Sheldon, R. D. Beddows, I. Vander Ark, A. Shen, H. Jones, R. St. Pierre, J. Ma, E. Krawczyk, C. M. 2022-05-19 doi:10.1101/2022.05.18.492477 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Structural analysis of cholesterol binding and sterol selectivity by ABCG5/G8 ]]> https://biorxiv.org/content/10.1101/2022.05.18.492512v1?rss=1 Farhat, D. Rezaei, F. Ristovski, M. Yang, Y. Stancescu, A. Dzimkova, L. Samnani, S. Couture, J.-F. Lee, J.-Y. 2022-05-18 doi:10.1101/2022.05.18.492512 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Homeostatic changes maintain the gain control of spinal motoneurones across the lifetime of C57BL/6J mice ]]> https://biorxiv.org/content/10.1101/2022.05.19.492717v1?rss=1 Goltash, S. Jensen, M. H. Dimintiyanova, K. P. Jensen, D. B. Lehnhoff, J. Moldovan, M. Meehan, C. F. 2022-05-20 doi:10.1101/2022.05.19.492717 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Generation of Functional Human T Cell Development in NOD/SCID/IL2rγnull Humanized Mice Without Using Fetal Tissue: Application as a Model of HIV Infection and Persistence ]]> https://biorxiv.org/content/10.1101/2022.05.30.494009v1?rss=1 Colas, C. Volodina, O. Beland, K. Pham, T. N. Q. Li, Y. Dallaire, F. Soulard, C. Lemieux, W. Colamartino, A. Tremblay-Laganiere, C. Dicaire, R. Guimond, J. Patey, N. Vobecky, S. Poirier, N. Cohen, E. A. Haddad, E. 2022-05-30 doi:10.1101/2022.05.30.494009 Cold Spring Harbor Laboratory Press 2022-05-30 <![CDATA[ Normative values of neuromelanin-sensitive MRI signal in older adults obtained using a standard protocol for acquisition and analysis ]]> https://biorxiv.org/content/10.1101/2022.06.02.493125v1?rss=1 Al Haddad, R. Chamoun, M. Tardif, C. Guimond, S. Horga, G. Rosa-Neto, P. Cassidy, C. 2022-06-05 doi:10.1101/2022.06.02.493125 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ Alterations in neural stem cell quiescence and activation in the 3xTG-AD model of Alzheimers Disease ]]> https://biorxiv.org/content/10.1101/2022.06.08.495344v1?rss=1 Liu, Y. Fong, B. C. Harris, R. A. McNicoll, M.-M. Abdi, A. A. Cuthbert, J. B. Cook, D. P. Figeys, D. Wang, J. Vanderhyden, B. C. Slack, R. S. 2022-06-09 doi:10.1101/2022.06.08.495344 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ The effect of heterospecific and conspecific competition on inter-individual differences in tungara frog tadpole (Engystomops pustulosus) behaviour ]]> https://biorxiv.org/content/10.1101/2022.06.23.497343v1?rss=1 Beyts, C. Cella, M. Colegrave, N. Downie, R. Martin, J. G. A. Walsh, P. 2022-06-26 doi:10.1101/2022.06.23.497343 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Non-invasive quantification of contractile dynamics in cardiac cells, spheroids and organs-on-a-chip using high frequency ultrasound ]]> https://biorxiv.org/content/10.1101/2022.06.28.497094v1?rss=1 Strohm, E. M. Callaghan, N. I. Latifi, N. Rafatian, N. Funakoshi, S. Fernandes, I. Radisic, M. Keller, G. Kolios, M. Simmons, C. A. 2022-07-01 doi:10.1101/2022.06.28.497094 Cold Spring Harbor Laboratory Press 2022-07-01 <![CDATA[ Mutagenesis Induced by Protonation of Single-Stranded DNA is Linked to Glycolytic Sugar Metabolism ]]> https://biorxiv.org/content/10.1101/2022.07.14.500049v1?rss=1 Gelova, S. P. Chan, K. 2022-07-15 doi:10.1101/2022.07.14.500049 Cold Spring Harbor Laboratory Press 2022-07-15 <![CDATA[ Interlimb coordination in Parkinson's disease is affected by a visuospatial dual task ]]> https://biorxiv.org/content/10.1101/2022.07.15.500215v1?rss=1 .12). The LA and MA hip ROM were differently affected by the dual task (p=.023), and intralimb coordination was affected by dual tasking equivalently between sides (p=.004). These results suggest that during normal single-task gait, people with PD use attentional resources to compensate for reduced arm swing. Furthermore, our results indicate that any effect of DT on lower intralimb coordination is not meaningfully different between the LA and MA sides. Statements and DeclarationsThe authors have no relevant financial or non-financial interests to disclose. ]]> Hill, A. Nantel, J. 2022-07-18 doi:10.1101/2022.07.15.500215 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Cell Type Specific DNA Signatures of Transcription Factor Binding ]]> https://biorxiv.org/content/10.1101/2022.07.15.500259v1?rss=1 Awdeh, A. Turcotte, M. Perkins, T. J. 2022-07-18 doi:10.1101/2022.07.15.500259 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ A Markov constraint to uniquely identify elementary flux mode weights in unimolecular metabolic networks ]]> https://biorxiv.org/content/10.1101/2022.07.25.501464v1?rss=1 Chitpin, J. G. Perkins, T. J. 2022-07-27 doi:10.1101/2022.07.25.501464 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ Molecular basis for antiviral activity of pediatric neutralizing antibodies targeting SARS-CoV-2 Spike receptor binding domain ]]> https://biorxiv.org/content/10.1101/2022.07.27.501708v1?rss=1 Chen, Y. Prevost, J. Ullah, I. Romero, H. Lisi, V. Tolbert, W. D. Grover, J. R. Ding, S. Gong, S. Y. Beaudoin-Bussieres, G. Gasser, R. Benlarbi, M. Vezina, D. Anand, S. P. Chatterjee, D. Goyette, G. Grunst, M. W. Yang, Z. Bo, Y. Zhou, F. Beland, K. Bai, X. Zeher, A. R. Huang, R. K. Nguyen, D. N. Sherburn, R. Wu, D. Piszczek, G. Pare, B. Matthies, D. Xia, D. Richard, J. Kumar, P. Mothes, W. Cote, M. Uchil, P. D. Lavallee, V.-P. Smith, M. A. Pazgier, M. Haddad, E. Finzi, A. 2022-07-28 doi:10.1101/2022.07.27.501708 Cold Spring Harbor Laboratory Press 2022-07-28 <![CDATA[ An economic and robust TMT labeling approach for high throughput proteomic and metaproteomic analysis ]]> https://biorxiv.org/content/10.1101/2022.07.30.502163v1?rss=1 Creskey, M. Li, l. Ning, Z. Brown, E. Mayne, J. Walker, K. Ampaw, A. Ben, R. Zhang, X. Figeys, D. 2022-08-02 doi:10.1101/2022.07.30.502163 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ RapidAIM 2.0: a high-throughput assay to study functional response of human gut microbiome to xenobiotics ]]> https://biorxiv.org/content/10.1101/2022.08.03.502618v1?rss=1 Li, L. Mayne, J. Beltran, A. ZHANG, X. Ning, Z. Figeys, D. 2022-08-04 doi:10.1101/2022.08.03.502618 Cold Spring Harbor Laboratory Press 2022-08-04 <![CDATA[ Transcriptome and chromatin accessibility mapping reveals a type I interferon response triggered by Mycobacterium tuberculosis infection ]]> https://biorxiv.org/content/10.1101/2022.08.11.503537v1?rss=1 Madden, K. El Hamra, R. Berton, S. Alvarez, G. G. Blais, A. Sun, J. 2022-08-12 doi:10.1101/2022.08.11.503537 Cold Spring Harbor Laboratory Press 2022-08-12 <![CDATA[ Sphingosine kinases promote Ebola virus infection and can be targeted to inhibit filoviruses, coronaviruses, and arenaviruses using late endocytic trafficking to enter cells ]]> https://biorxiv.org/content/10.1101/2022.08.12.503750v1?rss=1 Stewart, C. M. Bo, Y. Fu, K. Chan, M. Kozak, R. Apperley, K. Y.-P. Laroche, G. Beauchemin, A. Kobinger, G. Kobasa, D. Cote, M. 2022-08-12 doi:10.1101/2022.08.12.503750 Cold Spring Harbor Laboratory Press 2022-08-12 <![CDATA[ A Simplified Function-First Method for the Discovery and Optimization of Bispecific Immune Engaging Antibodies ]]> https://biorxiv.org/content/10.1101/2022.08.17.504342v1?rss=1 McComb, S. Shepherd, A. Bennychen, B. Marcil, A. Bloemberg, D. Pon, R. Weeratna, R. 2022-08-18 doi:10.1101/2022.08.17.504342 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ Neural diversity quenches the dynamic volatility of balanced neural networks ]]> https://biorxiv.org/content/10.1101/2022.08.25.505270v1?rss=1 Hutt, A. Rich, S. Valiante, T. A. Lefebvre, J. 2022-08-26 doi:10.1101/2022.08.25.505270 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ A slow 5-HT1AR-mediated recurrent inhibitory network in raphe computes contextual value through synaptic facilitation ]]> https://biorxiv.org/content/10.1101/2022.08.31.506056v1?rss=1 Lynn, M. B. Geddes, S. Chahrour, M. Maille, S. Harkin, E. Harvey-Girard, E. Haj-Dahmane, S. Naud, R. B. Beique, J.-C. 2022-08-31 doi:10.1101/2022.08.31.506056 Cold Spring Harbor Laboratory Press 2022-08-31 <![CDATA[ More than a ligand: PD-L1 promotes oncolytic virus infection via a metabolic shift that inhibits the type I interferon pathway. ]]> https://biorxiv.org/content/10.1101/2022.08.31.506095v1?rss=1 Hodgins, J. Abou-Hamad, J. Hagerman, A. Yakubovich, E. Tanese De Souza, C. Marotel, M. Buchler, A. Fadel, S. Park, M. Fong-McMaster, C. Crupi, M. J. F. Bell, J. C. Harper, M.-E. Rotstein, B. Auer, R. Vanderhyden, B. Sabourin, L. Bourgeois-Daigneault, M.-C. Cook, D. Ardolino, M. 2022-09-03 doi:10.1101/2022.08.31.506095 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ A third SARS-CoV-2 mRNA vaccine dose in people receiving hemodialysis overcomes B cell defects but elicits a skewed CD4+ T cell profile ]]> https://biorxiv.org/content/10.1101/2022.09.05.506622v1?rss=1 Sannier, G. Nicolas, A. Dube, M. Marchitto, L. Nayrac, M. Tastet, O. Tauzin, A. Lima-Barbosa, R. Laporte, M. Cloutier, R. Flores, A. S. Boutin, M. Gong, S. Y. Benlarbi, M. Ding, S. Bourassa, C. Gendron-Lepage, G. Medjahed, H. Goyette, G. Brassard, N. Ortega-Delgado, G.-G. Niessl, J. Gokool, L. Morrisseau, C. Arlotto, P. Rios, N. Tremblay, C. Martel-Laferriere, V. Prat, A. Belair, J. Beaubien-Souligny, W. Goupil, R. Nadeau-Fredette, A.-C. Lamarche, C. Finzi, A. Suri, R. Kaufmann, D. E. 2022-09-07 doi:10.1101/2022.09.05.506622 Cold Spring Harbor Laboratory Press 2022-09-07 <![CDATA[ Bridging global actin network patterns to local molecular dynamics: a combined modeling and machine learning framework ]]> https://biorxiv.org/content/10.1101/2022.09.06.506753v1?rss=1 Rostami, M. W. Bannish, B. E. Gasior, K. Pinals, R. L. Copos, C. Dawes, A. T. 2022-09-07 doi:10.1101/2022.09.06.506753 Cold Spring Harbor Laboratory Press 2022-09-07 <![CDATA[ Characterizing the differential distribution and targets of Sumo paralogs in the mouse brain ]]> https://biorxiv.org/content/10.1101/2022.09.09.507035v1?rss=1 Suk, T. R. Nguyen, T. T. Fisk, Z. A. Mitkovski, M. Geertsma, H. M. Parmasad, J.-L. A. Heer, M. M. Callaghan, S. M. Brose, N. Tirard, M. Rousseaux, M. W. C. 2022-09-10 doi:10.1101/2022.09.09.507035 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Targeting extracellular vesicle delivery to the lungs by microgel encapsulation ]]> https://biorxiv.org/content/10.1101/2022.09.09.507125v1?rss=1 Cober, N. D. Rowe, K. Deng, Y. Benavente-Babace, A. Courtman, D. W. Godin, M. Stewart, D. J. 2022-09-12 doi:10.1101/2022.09.09.507125 Cold Spring Harbor Laboratory Press 2022-09-12 <![CDATA[ SPECC1L binds MYPT1/PP1β and can regulate its distribution between microtubules and filamentous actin ]]> https://biorxiv.org/content/10.1101/2022.09.09.507377v1?rss=1 Mehta, V. Decan, N. Gaudreau-Lapierre, A. Copeland, J. W. Trinkle-Mulcahy, L. 2022-09-10 doi:10.1101/2022.09.09.507377 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Subcellular distribution of PP1 isoforms in holoenzyme complexes ]]> https://biorxiv.org/content/10.1101/2022.09.09.507380v1?rss=1 Mehta, V. Chamousset, D. Law, J. Ooi, S. Campuzano, D. Nguyen, V. Boisvert, F.-M. Moorhead, G. B. Trinkle-Mulcahy, L. 2022-09-10 doi:10.1101/2022.09.09.507380 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Derepression masquerades as activation in a pentameric ligand-gated ion channel ]]> https://biorxiv.org/content/10.1101/2022.09.13.507804v1?rss=1 Tessier, C. J. G. Emlaw, J. R. Sturgeon, R. M. daCosta, C. J. B. 2022-09-15 doi:10.1101/2022.09.13.507804 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Chronic stress exposure alters the gut barrier: sex-specific effects on microbiota and jejunum tight junctions ]]> https://biorxiv.org/content/10.1101/2022.09.13.507821v1?rss=1 Doney, E. Dion-Albert, L. Coulombe-Rozon, F. Osbourne, N. Bernatchez, R. Paton, S. E. J. Kaufmann, F. N. Agomma, R. O. Solano, J. L. Gaumond, R. Dudek, K. A. Szyszkowicz, J. K. Signature Consortium, Lebel, M. Doyen, A. Durand, A. Lavoie-Cardinal, F. Audet, M.-C. Menard, C. 2022-09-16 doi:10.1101/2022.09.13.507821 Cold Spring Harbor Laboratory Press 2022-09-16 <![CDATA[ Computational remodeling of an enzyme conformational landscape for altered substrate selectivity ]]> https://biorxiv.org/content/10.1101/2022.09.16.508321v1?rss=1 St-Jacques, A. D. Rodriguez, J. M. Eason, M. G. Foster, S. M. Khan, S. T. Damry, A. M. Goto, N. K. Thompson, M. C. Chica, R. A. 2022-09-17 doi:10.1101/2022.09.16.508321 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Multisensory inputs control the regulation of time investment for mating by sexual experience in male Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2022.09.23.509131v1?rss=1 Kim, W. J. Lee, S. G. Kang, C. Saad, B. Nguyen, K.-N. H. Guerra-Phalen, A. Bui, D. Abbas, A.-H. Trinh, B. Malik, A. Zeghal, M. Auge, A.-C. Islam, M. E. Wong, K. Stern, T. Lebedev, E. Sun, D. Miao, H. Wu, Z. Sherratt, T. N. 2022-09-24 doi:10.1101/2022.09.23.509131 Cold Spring Harbor Laboratory Press 2022-09-24 <![CDATA[ From comparative gene content and gene order to ancestral contigs, chromosomes and karyotypes ]]> https://biorxiv.org/content/10.1101/2022.09.28.509880v1?rss=1 Xu, Q. Jin, L. Zheng, C. Zhang, X. Leebens-Mack, J. Sankoff, D. 2022-09-30 doi:10.1101/2022.09.28.509880 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Murine macrophage choline metabolism underpins IL-4 polarization and RELMα up-regulation ]]> https://biorxiv.org/content/10.1101/2022.09.30.510305v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@2f83a3org.highwire.dtl.DTLVardef@16b74b1org.highwire.dtl.DTLVardef@1ba1f8dorg.highwire.dtl.DTLVardef@6da06a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ghorbani, P. Kim, S. Y. Smith, T. K. Minarrieta, L. Kilgour, M. K. Ilijevska, M. Alecu, I. Snider, S. A. Margison, K. D. Nunes, J. R. Woo, D. Pember, C. O'Dwyer, C. St-Pierre, J. Bennett, S. A. Nair, M. G. Fullerton, M. D. 2022-10-01 doi:10.1101/2022.09.30.510305 Cold Spring Harbor Laboratory Press 2022-10-01 <![CDATA[ The TUDOR domain of SMN is an H3K79me1 histone mark reader ]]> https://biorxiv.org/content/10.1101/2022.10.06.511070v1?rss=1 Binda, O. Kimenyi Ishimwe, A. B. Galloy, M. Jacquet, K. Corpet, A. Fradet-Turcotte, A. Cote, J. Lomonte, P. 2022-10-11 doi:10.1101/2022.10.06.511070 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ A ternary neural code resolves error and sharpening signals ]]> https://biorxiv.org/content/10.1101/2022.10.07.511138v1?rss=1 Naud, R. Wang, X. Friedenberger, Z. Shin, J. N. Beique, J.-C. Larkum, M. Doron, G. 2022-10-07 doi:10.1101/2022.10.07.511138 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Surface glia predominantly contribute to the development of ALS/FTD in Drosophila model ]]> https://biorxiv.org/content/10.1101/2022.10.07.511246v1?rss=1 Snow, B. A. Stevenson, C. C. Kaur, J. Lee, S. G. Wei, Y. Miao, H. Kim, W. J. 2022-10-07 doi:10.1101/2022.10.07.511246 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Glia-specific expression of neuropeptide receptor Lgr4 regulates development and adult physiology in Drosophila ]]> https://biorxiv.org/content/10.1101/2022.10.07.511249v1?rss=1 Lee, S. G. Kaur, J. Miao, H. Kim, W. J. 2022-10-07 doi:10.1101/2022.10.07.511249 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Sex-specific acute cerebrovascular response to photothrombotic stroke in mice requires rho-kinase ]]> https://biorxiv.org/content/10.1101/2022.10.07.511301v1?rss=1 Raman-Nair, J. Cron, G. McLeod, K. Lacoste, B. 2022-10-07 doi:10.1101/2022.10.07.511301 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Disturbed trophoblast transition links preeclampsia progression from placenta to the maternal syndrome ]]> https://biorxiv.org/content/10.1101/2022.10.10.511539v1?rss=1 Nonn, O. Debnath, O. Valdes, D. S. Sallinger, K. Secener, A. K. Haider, S. Fischer, C. Tiesmeyer, S. Nimo, J. Kuenzer, T. Maxian, T. Knoefler, M. Karau, P. Bartolomaeus, H. Kroneis, T. Frolova, A. Neuper, L. Haase, N. Kraeker, K. Kedziora, S. Forstner, D. Verlohren, S. Stern, C. Coscia, F. Sugulle, M. Jones, S. Thilaganathan, B. Eils, R. Huppertz, B. El-Heliebi, A. Staff, A. C. Mueller, D. N. Dechend, R. Gauster, M. Ishaque, N. Herse, F. 2022-10-11 doi:10.1101/2022.10.10.511539 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Inhibition of GCN5 decreases skeletal muscle fat metabolism during high fat diet feeding ]]> https://biorxiv.org/content/10.1101/2022.10.18.512735v1?rss=1 Green, A. Perras, B. L. Zhang, H. Katsyuba, E. Haboush, A. Nyarko, K. M. Pandey, D. K. Nik-Akhtar, A. Ryu, D. Menzies, K. J. Auwerx, J. 2022-10-21 doi:10.1101/2022.10.18.512735 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis ]]> https://biorxiv.org/content/10.1101/2022.10.19.511543v1?rss=1 Manley, B. F. Lotharukpong, J. S. Barrera-Redondo, J. Yildirir, G. Sperschneider, J. Corradi, N. Paszkowski, U. Miska, E. A. Dallaire, A. 2022-10-21 doi:10.1101/2022.10.19.511543 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Characterizing Eastern spruce budworm's large-scale dispersal events through flight behavior and stable isotope analyses ]]> https://biorxiv.org/content/10.1101/2022.10.20.513023v1?rss=1 Dargent, F. Candau, J.-N. Studens, K. Perrault, K. Reich, M. Bataille, C. 2022-10-21 doi:10.1101/2022.10.20.513023 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Sex-specific effects of voluntary wheel running on behavior and the gut microbiota-immune-brain axis in mice ]]> https://biorxiv.org/content/10.1101/2022.10.24.513258v1?rss=1 Williams, Z. A. Szyszkowicz, J. K. Osborne, N. Allehyany, B. Nadon, C. Udechukwu, M. C. Santos, A. Audet, M.-C. 2022-10-25 doi:10.1101/2022.10.24.513258 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ GENLIB: new function to simulate haplotype transmission in large complex genealogies ]]> https://biorxiv.org/content/10.1101/2022.10.28.514245v1?rss=1 Rakesh, M. Vezina, H. Laprise, C. Freeman, E. Burkett, K. Roy-Gagnon, M.-H. 2022-10-28 doi:10.1101/2022.10.28.514245 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Comprehensive multi-omics characterization of gut microbiome extracellular vesicles reveals a connection to gut-brain axis signaling ]]> https://biorxiv.org/content/10.1101/2022.10.28.514259v1?rss=1 Sultan, S. Yousuf, B. Yeo, J. Ahmed, T. Bouhlel, N. E. Hassan, H. Minic, Z. Mottawea, W. Hammami, R. 2022-10-28 doi:10.1101/2022.10.28.514259 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Metals and metal isotopes in insect wings: Implications for diet, geolocation and pollution exposure ]]> https://biorxiv.org/content/10.1101/2022.11.02.514901v1?rss=1 Reich, M. S. Kindra, M. Dargent, F. Hu, L. Flockhart, D. T. T. Norris, D. R. Kharouba, H. Talavera, G. Bataille, C. P. 2022-11-03 doi:10.1101/2022.11.02.514901 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ Nucleolar reorganization after cellular stress is orchestrated by SMN shuttling between nuclear compartments ]]> https://biorxiv.org/content/10.1101/2022.11.04.515196v1?rss=1 Musawi, S. Donnio, L.-M. Magnani, C. Binda, O. Cote, J. Lomonte, P. Mari, P.-O. Giglia-Mari, G. 2022-11-04 doi:10.1101/2022.11.04.515196 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Pairing Metagenomics and Metaproteomics to Pinpoint Ecological Niches and Metabolic Essentiality of Microbial Communities ]]> https://biorxiv.org/content/10.1101/2022.11.04.515228v1?rss=1 Wang, T. Li, L. Figeys, D. Liu, Y.-Y. 2022-11-05 doi:10.1101/2022.11.04.515228 Cold Spring Harbor Laboratory Press 2022-11-05 <![CDATA[ Reducing mitochondrial ribosomal gene expression does not alter metabolic health or lifespan in mice ]]> https://biorxiv.org/content/10.1101/2022.11.05.515295v1?rss=1 Reid, K. Daniels, E. G. Vasam, G. Kamble, R. Janssens, G. E. Hu, M. Green, A. E. Houtkooper, R. H. Menzies, K. J. 2022-11-05 doi:10.1101/2022.11.05.515295 Cold Spring Harbor Laboratory Press 2022-11-05 <![CDATA[ Discovery of benzophenanthridine derivatives with potent activity against multidrug resistant Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2022.11.07.515485v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@1536acaorg.highwire.dtl.DTLVardef@1881e83org.highwire.dtl.DTLVardef@18b2f58org.highwire.dtl.DTLVardef@d15f1a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sun, Z. Liang, Y. C. Chen, L. Lupien, A. Xu, Z. Berton, S. Behr, M. Yang, W. Sun, J. 2022-11-08 doi:10.1101/2022.11.07.515485 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ Normalized Semi-Covariance Co-Efficiency Analysis of Spike Proteins from SARS-CoV-2 variant Omicron and Other Coronaviruses for their Infectivity and Virulence ]]> https://biorxiv.org/content/10.1101/2022.11.07.515557v1?rss=1 Zhang, W. Xu, T. Zhou, S. Huang, J. S. 2022-11-08 doi:10.1101/2022.11.07.515557 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ Selective control of synaptic plasticity in heterogeneous networks through transcranial alternating current stimulation (tACS) ]]> https://biorxiv.org/content/10.1101/2022.11.15.516556v1?rss=1 Pariz, A. Trotter, D. Hutt, A. Lefebvre, J. 2022-11-15 doi:10.1101/2022.11.15.516556 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Dendritic excitability primarily controls overdispersion ]]> https://biorxiv.org/content/10.1101/2022.11.18.517108v1?rss=1 Friedenberger, Z. Naud, R. 2022-11-18 doi:10.1101/2022.11.18.517108 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ The Neural Correlates of Arousal: The Ventral Posterolateral Nucleus-Global Transient Co-Activation ]]> https://biorxiv.org/content/10.1101/2022.11.23.517776v1?rss=1 Han, J. Xie, Q. Wu, X. Huang, Z. Tanabe, S. Fogel, S. Hudetz, A. G. Wu, H. Northoff, G. Mao, Y. He, S. Qin, P. 2022-11-24 doi:10.1101/2022.11.23.517776 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Circadian reprogramming of adipose progenitor cells regulates intermittent fasting-mediated adipose tissue remodeling and metabolic improvement ]]> https://biorxiv.org/content/10.1101/2022.12.10.519916v1?rss=1 Lee, J. H. Patel, Y. Yeung, J. L.-H. Pickel, L. Ealey, K. N. Togo, J. Kim, Y.-H. Kim, K.-H. Park, J.-G. Jackson, T. Okrainec, A. Kim, J.-R. Park, S.-Y. Dash, S. Sung, H.-K. 2022-12-11 doi:10.1101/2022.12.10.519916 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Reach corrections toward moving targets are faster than reach corrections toward jumping targets ]]> https://biorxiv.org/content/10.1101/2022.12.24.521682v1?rss=1 Reschechtko, S. Gnanaseelan, C. Pruszynski, J. A. 2022-12-24 doi:10.1101/2022.12.24.521682 Cold Spring Harbor Laboratory Press 2022-12-24 <![CDATA[ Resolving the haplotypes of arbuscular mycorrhizal fungi highlights the role of two nuclear populations in host interactions ]]> https://biorxiv.org/content/10.1101/2023.01.15.524138v1?rss=1 Sperschneider, J. Yildirir, G. Malar C, M. Ariane Mayrand Nicol, A. Sorwar, E. Chen, E. C. Brauer, E. K. Bosnich, W. Corradi, N. 2023-01-18 doi:10.1101/2023.01.15.524138 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ TReSR: A PCR-compatible DNA sequence design method for engineering proteins containing tandem repeats ]]> https://biorxiv.org/content/10.1101/2023.01.19.524698v1?rss=1 Davey, J. A. Goto, N. K. 2023-01-19 doi:10.1101/2023.01.19.524698 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Thermoneutral housing does not accelerate metabolic dysfunction-associated fatty liver disease in male or female mice fed a Western diet ]]> https://biorxiv.org/content/10.1101/2023.01.24.524609v1?rss=1 View larger version (58K): org.highwire.dtl.DTLVardef@9b9c5eorg.highwire.dtl.DTLVardef@36fc5aorg.highwire.dtl.DTLVardef@1f1b244org.highwire.dtl.DTLVardef@eea3df_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Nunes, J. R. Smith, T. K. Ghorbani, P. O'Dwyer, C. Trzaskalski, N. A. Dergham, H. Pember, C. Kilgour, M. K. Mulvihill, E. E. Fullerton, M. D. 2023-01-24 doi:10.1101/2023.01.24.524609 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ A new mouse model of ATR-X syndrome carrying a common patient mutation exhibits neurological and morphological defects ]]> https://biorxiv.org/content/10.1101/2023.01.25.525394v1?rss=1 Tillotson, R. Yan, K. Ruston, J. de Young, T. Cordova, A. Turcotte-Cardin, V. Yee, Y. Taylor, C. Visuvanathan, S. Babbs, C. Ivakine, E. A. Sled, J. G. Nieman, B. J. Picketts, D. J. Justice, M. J. 2023-01-25 doi:10.1101/2023.01.25.525394 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Smartwatch-based prediction of single-stride and stride-to-stride gait outcomes using regression-based machine learning ]]> https://biorxiv.org/content/10.1101/2023.01.30.526246v1?rss=1 Bailey, C. A. Mir-Orefice, A. Uchida, T. K. Nantel, J. Graham, R. B. 2023-02-01 doi:10.1101/2023.01.30.526246 Cold Spring Harbor Laboratory Press 2023-02-01 <![CDATA[ Aberrant light sensing and motility in the green alga Chlamydomonas priscuii from the ice-covered Antarctic Lake Bonney ]]> https://biorxiv.org/content/10.1101/2023.02.02.526531v1?rss=1 Poirier, M. Osmers, P. Wilkins, K. Morgan-Kiss, R. Cvetkovska, M. 2023-02-03 doi:10.1101/2023.02.02.526531 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Development of a multifunctional toolkit of intrabody-based biosensors recognizing the V5 peptide tag: highlighting applications with G protein-coupled receptors ]]> https://biorxiv.org/content/10.1101/2023.02.05.527200v1?rss=1 Zeghal, M. Matte, K. Venes, A. Patel, S. Laroche, G. Sarvan, S. Joshi, M. Couture, J.-F. Giguere, P. M. 2023-02-05 doi:10.1101/2023.02.05.527200 Cold Spring Harbor Laboratory Press 2023-02-05 <![CDATA[ Predicting vertical and shear ground reaction forces during walking and jogging using wearable plantar pressure insoles ]]> https://biorxiv.org/content/10.1101/2023.02.19.529141v1?rss=1 Hajizadeh, M. Clouthier, A. Kendall, M. Graham, R. 2023-02-21 doi:10.1101/2023.02.19.529141 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Error-corrected Duplex Sequencing enables direct detection and quantification of mutations in human TK6 cells with remarkable inter-laboratory consistency ]]> https://biorxiv.org/content/10.1101/2023.02.22.529418v1?rss=1 T:A, T:A>C:G, T:A>A:T, and T:A>G:C mutations increased in consistent, concentration-dependent manners in both laboratories, with high proportions of C:G>T:A at all time points. The target sites responded similarly between the two laboratories and revealed a higher average MF in intergenic regions. These results, demonstrating remarkable reproducibility across time and laboratory for both MF and spectrum, support the high value of DuplexSeq for characterizing chemical mutagenicity in both research and regulatory evaluation. ]]> Cho, E. Swartz, C. D. Williams, A. Rivas, M. Recio, L. Witt, K. L. Schmidt, E. K. Yaplee, J. Smith, T. Van, P. Lo, F. Y. Valentine, C. C. Salk, J. J. Marchetti, F. Smith-Roe, S. Yauk, C. 2023-02-22 doi:10.1101/2023.02.22.529418 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Food availability early in life impacts among and within individual variation in behaviour ]]> https://biorxiv.org/content/10.1101/2023.02.23.529667v1?rss=1 Beyts, C. H. Martin, J. H. Colegrave, N. Walsh, P. 2023-02-23 doi:10.1101/2023.02.23.529667 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Duplex Sequencing Provides Detailed Characterization of Mutation Frequencies and Spectra in the Bone Marrow of MutaMouse Males Exposed to Procarbazine Hydrochloride ]]> https://biorxiv.org/content/10.1101/2023.02.23.529719v1?rss=1 80% power. Overall, we demonstrate several advantages of DS over classical mutagenicity assays and provide data to support efforts to identify optimal study designs for the application of DS as a regulatory test. ]]> Dodge, A. E. LeBlanc, D. P. Zhou, G. Williams, A. Meier, M. Van, P. Lo, F. Y. Valentine, C. C. Salk, J. J. Yauk, C. L. Marchetti, F. 2023-02-23 doi:10.1101/2023.02.23.529719 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Comprehensive interrogation of human skeletal muscle reveals a dissociation between insulin resistance and mitochondrial capacity ]]> https://biorxiv.org/content/10.1101/2023.02.24.529750v1?rss=1 Whytock, K. L. Pino, M. F. Sun, Y. Yu, G. De Carvalho, F. G. Yeo, R. X. Vega, R. B. Parmar, G. S. Divoux, A. Kapoor, N. Yi, F. Cornnell, H. Patten, D. A. Harper, M.-E. Gardell, S. J. Smith, S. R. Walsh, M. J. Sparks, L. M. 2023-02-24 doi:10.1101/2023.02.24.529750 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Mice can learn a cognitive map based on a stable start location and self-motion signals ]]> https://biorxiv.org/content/10.1101/2023.02.24.529984v1?rss=1 Xu, J. Girardi-Schappo, M. Beique, J.-C. Longtin, A. Maler, L. 2023-02-27 doi:10.1101/2023.02.24.529984 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Comparative analysis of syngeneic mouse models of high-grade serous ovarian cancer ]]> https://biorxiv.org/content/10.1101/2023.03.09.531888v1?rss=1 Cook, D. P. Galpin, K. J. Rodriguez, G. M. Shakfa, N. Wilson-Sanchez, J. Pereira, M. Matuszewska, K. Haagsma, J. Murshed, H. Cudmore, A. O. MacDonald, E. Tone, A. Shepherd, T. G. Petrik, J. J. Koti, M. Vanderhyden, B. C. 2023-03-10 doi:10.1101/2023.03.09.531888 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ BCL7 proteins, metazoan-specific subunits of the mammalian SWI/SNF complex, bind the nucleosome core particle ]]> https://biorxiv.org/content/10.1101/2023.03.17.532992v1?rss=1 Diaz, D. Kazrani, A. A. Martin, F. Lafouge, J. Siebert, S. Birck, C. Blais, A. Bergamin, E. 2023-03-17 doi:10.1101/2023.03.17.532992 Cold Spring Harbor Laboratory Press 2023-03-17 <![CDATA[ SKA2 regulated hyperactive secretory autophagy drives neuroinflammation-induced neurodegeneration ]]> https://biorxiv.org/content/10.1101/2023.04.03.534570v1?rss=1 Hartmann, J. Bajaj, T. Otten, J. Klengel, C. Gellner, A.-K. Junglas, E. Hafner, K. Anderzhanova, E. A. Tang, F. Missig, G. Rexrode, L. Li, K. Poehlmann, M. L. Heinz, D. E. Lardenoije, R. Dedic, N. McCullough, K. M. Prochnicki, T. Rhomberg, T. Martinelli, S. Payton, A. Robinson, A. C. Stein, V. Latz, E. Carlezon, W. A. Schmidt, M. V. Murgatroyd, C. Berretta, S. Klengel, T. Pantazopoulos, H. Ressler, K. J. Gassen, N. C. 2023-04-03 doi:10.1101/2023.04.03.534570 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Second-order Citations in Altmetrics: A Case Study Analyzing the Audiences of COVID-19 Research in the News and on Social Media ]]> https://biorxiv.org/content/10.1101/2023.04.05.535734v1?rss=1 Alperin, J. P. Fleerackers, A. Riedlinger, M. Haustein, S. 2023-04-06 doi:10.1101/2023.04.05.535734 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Ionic polyphosphorylation of histidine repeat proteins by inorganic polyphosphate ]]> https://biorxiv.org/content/10.1101/2023.04.10.536149v1?rss=1 View larger version (49K): org.highwire.dtl.DTLVardef@1ed34b7org.highwire.dtl.DTLVardef@200259org.highwire.dtl.DTLVardef@17a2954org.highwire.dtl.DTLVardef@12f5d04_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGRAPHICAL ABSTRACTC_FLOATNO C_FIG ]]> Neville, N. Lehotsky, K. Yang, Z. Klupt, K. A. Denoncourt, A. Downey, M. Jia, Z. 2023-04-10 doi:10.1101/2023.04.10.536149 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ The E3 Ubiquitin Ligase Nedd4L Acts as a Checkpoint Against Activation in Quiescent Muscle Stem Cells ]]> https://biorxiv.org/content/10.1101/2023.05.10.540205v1?rss=1 Blackburn, D. Sahinyan, K. Hernnandez Corchado, A. Lazure, F. Richard, V. Raco, L. Zahedi, R. Borchers, C. Lepper, C. Kawabe, H. Jahani-asl, A. Najafabadi, H. S. Soleimani, V. D. 2023-05-10 doi:10.1101/2023.05.10.540205 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ Combining Bacteriophage and Vancomycin is Efficacious Against MRSA biofilm-like Aggregates Formed in Synovial Fluid ]]> https://biorxiv.org/content/10.1101/2023.05.15.540793v1?rss=1 Taha, M. Arnaud, T. Theriault, S. S. Peters, D. Wang, L. Chen, W. Lightly, T. Cook, B. W. M. Abdelbary, H. 2023-05-15 doi:10.1101/2023.05.15.540793 Cold Spring Harbor Laboratory Press 2023-05-15 <![CDATA[ sncRNAP: Prediction and profiling of full sncRNA repertoires from sRNAseq data ]]> https://biorxiv.org/content/10.1101/2023.05.23.541863v1?rss=1 Gibriel, H. baindoor, S. Slack, R. Prehn, J. 2023-05-24 doi:10.1101/2023.05.23.541863 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Functional Subtypes of Synaptic Dynamics in Mouse and Human ]]> https://biorxiv.org/content/10.1101/2023.05.23.541971v1?rss=1 Beninger, J. Rossbroich, J. Toth, K. Naud, R. 2023-05-24 doi:10.1101/2023.05.23.541971 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ The histone lysine demethylase KDM5C fine-tunes gene expression to regulate dendritic cell heterogeneity and function ]]> https://biorxiv.org/content/10.1101/2023.05.28.542441v1?rss=1 Guak, H. Weiland, M. J. VanderArk, A. R. Zhai, L. Lau, K. Mabvakure, B. Corrado, M. Davidson, P. Compton, S. DeCamp, L. Jones, R. M. Nowinski, S. Krawczyk, C. M. 2023-05-28 doi:10.1101/2023.05.28.542441 Cold Spring Harbor Laboratory Press 2023-05-28 <![CDATA[ Wnt binding to Coatomer proteins directs secretion on exosomes independently of palmitoylation ]]> https://biorxiv.org/content/10.1101/2023.05.30.542914v1?rss=1 Gurriaran-Rodriguez, U. Datzkiw, D. Radusky, L. Esper, M. Xiao, F. Ming, H. Fisher, S. Rojas, M. J. De Repentigny, Y. Kothary, R. Rojas, A. L. Serrano, L. Hierro, A. Rudnicki, M. A. 2023-05-30 doi:10.1101/2023.05.30.542914 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ Identification of signalling pathways involved in gill regeneration in zebrafish ]]> https://biorxiv.org/content/10.1101/2023.06.12.544629v1?rss=1 Cadiz, L. Reed, M. Monis, S. Akimenko, M.-A. Jonz, M. G. 2023-06-12 doi:10.1101/2023.06.12.544629 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ PINK1 Deficiency Alters Muscle Stem Cell Fate Decision And Muscle Regenerative Capacity. ]]> https://biorxiv.org/content/10.1101/2023.06.23.546123v1?rss=1 Cairns, G. Thumiah-Mootoo, M. Abbasi, M. R. Racine, J. Lariovov, N. Prola, A. Khacho, M. Burelle, Y. 2023-06-25 doi:10.1101/2023.06.23.546123 Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ Cardiology researchers' practices and perceived barriers related to open science: an international cross-sectional survey ]]> https://biorxiv.org/content/10.1101/2023.06.29.546350v1?rss=1 Cobey, K. D. Alayche, M. Saba, S. Ebrahimzadeh, S. Barnes, N. Y. Alarcon, E. I. Hibbert, B. Moher, D. 2023-07-03 doi:10.1101/2023.06.29.546350 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Cellular Substrate of Eligibility Traces ]]> https://biorxiv.org/content/10.1101/2023.06.29.547097v1?rss=1 Caya-Bissonnette, L. Naud, R. Beïque, J.-C. 2023-06-30 doi:10.1101/2023.06.29.547097 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Morphological variability may limit single-cell specificity to electric field stimulation ]]> https://biorxiv.org/content/10.1101/2023.06.30.547168v1?rss=1 Trotter, D. Pariz, A. Hutt, A. Lefebvre, J. 2023-07-03 doi:10.1101/2023.06.30.547168 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Plant Cellulose as a Substrate for 3D Neural Stem Cell Culture ]]> https://biorxiv.org/content/10.1101/2023.06.30.547242v1?rss=1 Couvrette, L. Walker, K. Bui, T. Pelling, A. 2023-07-02 doi:10.1101/2023.06.30.547242 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ pUdOs: concise plasmids for bacterial and mammalian cells ]]> https://biorxiv.org/content/10.1101/2023.07.05.547852v1?rss=1 Ourida Manigat, F. Connell, L. B. Stewart, B. N. LePabic, A.-R. Tessier, C. J. G. Emlaw, J. R. Calvert, N. D. Rossl, A. Shuhendler, A. J. daCosta, C. J. B. Campbell-Valois, F.-X. 2023-07-05 doi:10.1101/2023.07.05.547852 Cold Spring Harbor Laboratory Press 2023-07-05 <![CDATA[ Proteomics analysis reveals a role for E. coli polyphosphate kinase in membrane structure and polymyxin resistance during starvation ]]> https://biorxiv.org/content/10.1101/2023.07.06.546892v1?rss=1 Baijal, K. Abrumchuk, I. Herrera, C. Trent, M. S. Lavallee-Adam, M. Downey, M. 2023-07-06 doi:10.1101/2023.07.06.546892 Cold Spring Harbor Laboratory Press 2023-07-06 <![CDATA[ Distinct forms of structural plasticity of adult-born interneuron spines induced by different odor learning paradigms ]]> https://biorxiv.org/content/10.1101/2023.07.20.549882v1?rss=1 Ferreira, A. Constantinescu, V.-S. Malvaut, S. Saghatelyan, A. Hardy, S. V. 2023-07-23 doi:10.1101/2023.07.20.549882 Cold Spring Harbor Laboratory Press 2023-07-23 <![CDATA[ Burstprop for Learning in Spiking Neuromorphic Hardware ]]> https://biorxiv.org/content/10.1101/2023.07.25.550525v1?rss=1 Stuck, M. Naud, R. 2023-07-28 doi:10.1101/2023.07.25.550525 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Interaction of SCoV-2 NSP7 or NSP8 alone may cause constriction of the RNA entry channel in NSP12: Implications for novel RdRp inhibitor drug discovery ]]> https://biorxiv.org/content/10.1101/2023.07.26.550660v1?rss=1 Singh, D. Kushwaha, T. Kulandaisamy, R. Kumar, V. Baswal, K. Tiwari, S. H. Ghorai, A. Kumar, M. Kumar, S. Polamarasetty, A. Sehgal, D. Katika, M. R. Gadde, S. Cote, M. Kayampeta, S. R. Appaiahgari, M. B. Inampudi, K. K. 2023-07-27 doi:10.1101/2023.07.26.550660 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Intrinsic neural timescales attenuate information transfer along the uni-transmodal hierarchy ]]> https://biorxiv.org/content/10.1101/2023.07.28.551047v1?rss=1 Catal, Y. Wolman, A. Abbasi, S. Northoff, G. 2023-07-29 doi:10.1101/2023.07.28.551047 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ Phenological mismatch between trees and wildflowers: Reconciling divergent findings in two recent analyses ]]> https://biorxiv.org/content/10.1101/2023.08.01.551551v1?rss=1 Lee, B. R. Alecrim, E. F. Forrest, J. R. K. Heberling, J. M. Primack, R. B. Sargent, R. D. 2023-08-03 doi:10.1101/2023.08.01.551551 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ Heart-on-a-chip model of immune-induced cardiac dysfunction reveals the involvement of free mitochondrial DNA and therapeutic effects of endothelial exosomes ]]> https://biorxiv.org/content/10.1101/2023.08.09.552495v1?rss=1 Lu, X. Z. Rafatian, N. Zhao, Y. Wagner, K. T. Beroncal, E. L. Li, B. Lee, C. Chen, J. Churcher, E. Vosoughi, D. Wang, Y. Baker, A. Trahtemberg, U. Li, B. Pierro, A. Andreazza, A. dos Santos, C. C. Radisic, M. 2023-08-09 doi:10.1101/2023.08.09.552495 Cold Spring Harbor Laboratory Press 2023-08-09 <![CDATA[ Rapid diversification of Pseudomonas aeruginosa in cystic fibrosis lung-like conditions ]]> https://biorxiv.org/content/10.1101/231050v1?rss=1 Schick, A. Kassen, R. 2017-12-08 doi:10.1101/231050 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ Computational docking reveals evolutionary conservation of a specific interaction between 15d-Prostaglandin-J2 and eIF4A. ]]> https://biorxiv.org/content/10.1101/237610v1?rss=1 Yun, S. J. Kim, H. Lee, S. G. Jung, S.-H. Kim, J. H. Ryu, J. E. Singh, N. J. Jeon, J. Han, J.-K. Kim, C.-H. Kim, S. Kim, K. S. Jang, S. K. Kim, W. J. 2017-12-21 doi:10.1101/237610 Cold Spring Harbor Laboratory Press 2017-12-21 <![CDATA[ How the Central American Seaway and an ancient northern passage affected Flatfish diversification ]]> https://biorxiv.org/content/10.1101/247304v1?rss=1 300 species (out of ca. 800 extant), from 13 of the 14 known families over nine genes, and employed relaxed molecular clocks to uncover their patterns of diversification. As the fossil record of flatfish is contentious, we used sister species distributed on both sides of the American continent to calibrate clock models based on the closure of the Central American Seaway (CAS), and on their current species range. We show that flatfish diversified in two bouts, as species that are today distributed around the Equator diverged during the closure of CAS, while those with a northern range diverged after this, hereby suggesting the existence of a post-CAS closure dispersal for these northern species, most likely along a trans-Arctic northern route, a hypothesis fully compatible with paleogeographic reconstructions. ]]> Byrne, L. Chapleau, F. Aris-Brosou, S. 2018-01-12 doi:10.1101/247304 Cold Spring Harbor Laboratory Press 2018-01-12 <![CDATA[ RECAP reveals the true statistical significance of ChIP-seq peak calls ]]> https://biorxiv.org/content/10.1101/260687v1?rss=1 Chitpin, J. G. Awdeh, A. Perkins, T. J. 2018-02-05 doi:10.1101/260687 Cold Spring Harbor Laboratory Press 2018-02-05 <![CDATA[ Tectal stem cells display diverse regenerative capacities ]]> https://biorxiv.org/content/10.1101/268136v1?rss=1 Lindsey, B. W. Aitkens, G. E. Tang, J. K. Khabooshan, M. Vandestadt, C. Kaslin, J. 2018-02-19 doi:10.1101/268136 Cold Spring Harbor Laboratory Press 2018-02-19 <![CDATA[ An improved method for fitting gamma distribution to substitution rate variation among sites ]]> https://biorxiv.org/content/10.1101/276329v1?rss=1 Xia, X. 2018-03-05 doi:10.1101/276329 Cold Spring Harbor Laboratory Press 2018-03-05 <![CDATA[ Imputing missing distances in molecular phylogenetics ]]> https://biorxiv.org/content/10.1101/276345v1?rss=1 Xia, X. 2018-03-05 doi:10.1101/276345 Cold Spring Harbor Laboratory Press 2018-03-05 <![CDATA[ Expectations may Influence the Effects of Transcranial Direct-Current Stimulation ]]> https://biorxiv.org/content/10.1101/279554v1?rss=1 Rabipour, S. Wu, A. D. Davidson, P. S. R. Iacoboni, M. 2018-03-10 doi:10.1101/279554 Cold Spring Harbor Laboratory Press 2018-03-10 <![CDATA[ A novel time-stamp mechanism transforms egocentric encounters into an allocentric spatial representation ]]> https://biorxiv.org/content/10.1101/285494v1?rss=1 Wallach, A. Harvey-Girard, E. Jun, J. J. Longtin, A. Maler, L. 2018-03-23 doi:10.1101/285494 Cold Spring Harbor Laboratory Press 2018-03-23 <![CDATA[ Accurate prediction of orthologs in the presence of divergence after duplication ]]> https://biorxiv.org/content/10.1101/294405v1?rss=1 Lafond, M. Meghdari Miardan, M. Sankoff, D. 2018-04-04 doi:10.1101/294405 Cold Spring Harbor Laboratory Press 2018-04-04 <![CDATA[ Evidence of a nonadaptive buildup of mutational load in human populations over the past 40,000 years ]]> https://biorxiv.org/content/10.1101/307058v1?rss=1 Aris-Brosou, S. 2018-04-25 doi:10.1101/307058 Cold Spring Harbor Laboratory Press 2018-04-25 <![CDATA[ A synthetic non-histone substrate provides insight into substrate targeting by the Gcn5 HAT and sirtuin HDACs ]]> https://biorxiv.org/content/10.1101/345637v1?rss=1 Rossl, A. Lin, M. Downey, M. 2018-06-12 doi:10.1101/345637 Cold Spring Harbor Laboratory Press 2018-06-12 <![CDATA[ Do city cachers store less? The effect of urbanization and exploration on spatial memory in individual scatter hoarders ]]> https://biorxiv.org/content/10.1101/377143v1?rss=1 Thompson, M. J. Morand-Ferron, J. 2018-07-25 doi:10.1101/377143 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ ULK-mediated phosphorylation of ATG16L1 promotes xenophagy, but destabilizes the ATG16L1 Crohn’s mutant ]]> https://biorxiv.org/content/10.1101/387563v1?rss=1 Alsaadi, R. M. Losier, T. T. Tian, W. Guo, Z. Russell, R. C. 2018-08-08 doi:10.1101/387563 Cold Spring Harbor Laboratory Press 2018-08-08 <![CDATA[ A novel method for comparison of arterial remodeling in hypertension: quantification of arterial trees and recognition of remodeling patterns on histological sections ]]> https://biorxiv.org/content/10.1101/424119v1?rss=1 Gutsol, A. Blanco, P. Samokhina, S. Afanasiev, S. Kennedy, C. Popov, S. Burns, K. 2018-09-21 doi:10.1101/424119 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ Risks of exposure to systemic insecticides in agricultural soil in Ontario, Canada for the hoary squash bee (Peponapis pruinosa) and other ground-nesting bee species ]]> https://biorxiv.org/content/10.1101/434498v1?rss=1 Chan, D. S. W. Prosser, R. S. Rodriguez-Gil, J. L. Raine, N. E. 2018-10-31 doi:10.1101/434498 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ A starless bias in the maximum likelihood phylogenetic methods ]]> https://biorxiv.org/content/10.1101/435412v1?rss=1 10000) when a star tree is imposed, but < 1 (suggesting strong rate heterogeneity over sites) when an (incorrect) resolved tree is imposed. Thus, the dependence of "rate heterogeneity" on tree topology implies that "rate heterogeneity" is not a sequence-specific feature, cautioning against interpreting a small to mean that some sites are under strong purifying selection and others not. Thirdly, because there is no existing (and working) likelihood method for evaluating a star tree with continuous gamma-distributed rate, I have implemented the method for JC69 in a self-contained R script for a four-OTU tree (star or resolved), in addition to another R script assuming a constant rate over sites. These R scripts should be useful for teaching and exploring likelihood methods in phylogenetics. ]]> Xia, X. 2018-10-05 doi:10.1101/435412 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ Targeting MYC Overexpressing Leukemia with Cardiac Glycoside Proscillaridin Through Downregulation of Histone Acetyltransferases ]]> https://biorxiv.org/content/10.1101/444133v1?rss=1 Da Costa, E. M. Armaos, G. McInnes, G. Beaudry, A. Moquin-Beaudry, G. Bertrand-Lehouillier, V. Caron, M. Richer, C. St-Onge, P. Johnson, J. Krogan, N. Sai, Y. Downey, M. Rafei, M. Boileau, M. Eppert, K. Flores-Diaz, E. Haman, A. Hoang, T. Sinnett, D. Beausejour, C. McGraw, S. Raynal, N. J. M. 2018-10-15 doi:10.1101/444133 Cold Spring Harbor Laboratory Press 2018-10-15 <![CDATA[ Cell-autonomous transcriptional mechanism for enhancement of translation capacity in secretory cells ]]> https://biorxiv.org/content/10.1101/454421v1?rss=1 Khetchoumian, K. Balsalobre, A. Mayran, A. Christian, H. Chenard, V. St-Pierre, J. Drouin, J. 2018-10-26 doi:10.1101/454421 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ The idiosyncratic drivers of correlated evolution ]]> https://biorxiv.org/content/10.1101/474536v1?rss=1 Dench, J. Aris-Brosou, S. Kassen, R. 2018-11-19 doi:10.1101/474536 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Neural activity in a hippocampus-like region of the teleost pallium are associated with navigation and active sensing ]]> https://biorxiv.org/content/10.1101/495887v1?rss=1 Fotowat, H. Lee, C. Jun, J. J. Maler, L. 2018-12-13 doi:10.1101/495887 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Human Gene Expression Variability and its Dependence on Methylation and Aging ]]> https://biorxiv.org/content/10.1101/500785v1?rss=1 Bashkeel, N. Perkins, T. Kaern, M. Lee, J. 2018-12-18 doi:10.1101/500785 Cold Spring Harbor Laboratory Press 2018-12-18 <![CDATA[ Spike-Diffuse-Spike Modelling of AxonalPropagation Links Demyelination to CompoundAction Potential Dispersion ]]> https://biorxiv.org/content/10.1101/501379v1?rss=1 Naud, R. Longtin, A. 2018-12-19 doi:10.1101/501379 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ TargetSeeker-MS: A computational method for drug target discovery using protein separation coupled to mass spectrometry ]]> https://biorxiv.org/content/10.1101/513663v1?rss=1 Lavallee-Adam, M. Pelletier, A. Diedrich, J. K. Low, W. Pinto, A. F. Martinez-Bartolome, S. Petrascheck, M. Moresco, J. J. Yates, J. R. 2019-01-07 doi:10.1101/513663 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ Quantitative Analysis of Global Protein Stability Rates in Tissues ]]> https://biorxiv.org/content/10.1101/520494v1?rss=1 McClatchy, D. B. Gao, Y. Lavalle-Adam, M. Yates, J. R. 2019-01-15 doi:10.1101/520494 Cold Spring Harbor Laboratory Press 2019-01-15 <![CDATA[ Induction of an alternative 5’ leader enhances translation of Inpp5e and resistance to oncolytic virus infection ]]> https://biorxiv.org/content/10.1101/522607v1?rss=1 Hoang, H.-D. Graber, T. Jia, J.-J. Vaidya, N. Gilchrist, V. Li, W. Gkogkas, C. Jaramillo, M. Jafarnejad, S. M. Alain, T. 2019-01-17 doi:10.1101/522607 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ Episodic diversifying selection and intragenomic interactions shape the evolution of DNA and RNA viruses ]]> https://biorxiv.org/content/10.1101/539239v1?rss=1 Aris-Brosou, S. Parent, L. Ibeh, N. 2019-02-03 doi:10.1101/539239 Cold Spring Harbor Laboratory Press 2019-02-03 <![CDATA[ Therapeutic Targeting of Casein Kinase 1δ/ε in an Alzheimer's Disease Mouse Model ]]> https://biorxiv.org/content/10.1101/539627v1?rss=1 Adler, P. Mayne, J. Walker, K. Ning, Z. Figeys, D. 2019-02-03 doi:10.1101/539627 Cold Spring Harbor Laboratory Press 2019-02-03 <![CDATA[ Inhibitor of apoptosis, IAP, genes play a critical role in the survival of HIV-infected macrophages ]]> https://biorxiv.org/content/10.1101/543017v1?rss=1 Kumar, A. Caballero, R. E. H. Dong, S. X. M. Gajanayaka, N. Ali, H. Cassol, E. Cameron, W. Korneluk, R. Tremblay, M. Angel, J. 2019-02-06 doi:10.1101/543017 Cold Spring Harbor Laboratory Press 2019-02-06 <![CDATA[ RapidAIM: A culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs ]]> https://biorxiv.org/content/10.1101/543256v1?rss=1 Li, L. Ning, Z. Zhang, X. Mayne, J. Cheng, K. Stintzi, A. Figeys, D. 2019-02-08 doi:10.1101/543256 Cold Spring Harbor Laboratory Press 2019-02-08 <![CDATA[ The distribution of fitness effects among synonymous mutations in a gene under selection ]]> https://biorxiv.org/content/10.1101/553610v1?rss=1 Kassen, R. Lebeuf-Taylor, E. McCloskey, N. Hinz, A. Bailey, S. 2019-02-18 doi:10.1101/553610 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ Few Effects of a 5-week Computerized Cognitive Training Program in Healthy Older Adults ]]> https://biorxiv.org/content/10.1101/570143v1?rss=1 Rabipour, S. Morrison, C. Crompton, J. Petrucelli, M. Germano, M. d. O. G. Popescu, A. Davidson, P. S. R. 2019-03-08 doi:10.1101/570143 Cold Spring Harbor Laboratory Press 2019-03-08 <![CDATA[ Cellular and network mechanisms may generate sparse coding of sequential object encounters in hippocampal-like circuits ]]> https://biorxiv.org/content/10.1101/571414v1?rss=1 Trinh, A.-T. Clarke, S. E. Harvey-Girard, E. Maler, L. 2019-03-09 doi:10.1101/571414 Cold Spring Harbor Laboratory Press 2019-03-09 <![CDATA[ Phytoplasma SAP11 effector destabilization of TCP transcription factors differentially impact development and defence of Arabidopsis versus maize ]]> https://biorxiv.org/content/10.1101/574319v1?rss=1 Pecher, P. Moro, G. Canale, M. C. Capdevielle, S. Singh, A. MacLean, A. Sugio, A. Kuo, C.-H. Lopes, J. R. S. Hogenhout, S. A. 2019-03-12 doi:10.1101/574319 Cold Spring Harbor Laboratory Press 2019-03-12 <![CDATA[ WACS: Improving Peak Calling by Optimally Weighting Controls ]]> https://biorxiv.org/content/10.1101/582650v1?rss=1 Awdeh, A. Turcotte, M. Perkins, T. J. 2019-03-28 doi:10.1101/582650 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ Multicenter preclinical studies as an innovative method to enhance translation: a systematic review of published studies ]]> https://biorxiv.org/content/10.1101/591289v1?rss=1 Hunniford, V. T. Grudniewicz, A. Fergusson, D. A. Grigor, E. Lansdell, C. Lalu, M. 2019-03-27 doi:10.1101/591289 Cold Spring Harbor Laboratory Press 2019-03-27 <![CDATA[ Identification and characterization of OmpT-like proteases in uropathogenic Escherichia coli clinical isolates ]]> https://biorxiv.org/content/10.1101/594564v1?rss=1 Desloges, I. Taylor, J. A. Leclerc, J.-M. Brannon, J. R. Portt, A. Spencer, J. D. Dewar, K. Marczynski, G. T. Manges, A. Gruenheid, S. Le Moual, H. Thomassin, J.-L. 2019-04-04 doi:10.1101/594564 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ The Virulence Index: A Metric for Quantitative Analysis of Phage Virulence ]]> https://biorxiv.org/content/10.1101/606350v1?rss=1 Storms, Z. J. Teel, M. R. Mercurio, K. Sauvageau, D. 2019-04-12 doi:10.1101/606350 Cold Spring Harbor Laboratory Press 2019-04-12 <![CDATA[ Engineered Retroviruses as Fluorescent Biological Reference Particles for Nanoscale Flow Cytometry ]]> https://biorxiv.org/content/10.1101/614461v1?rss=1 Tang, V. A. Fritzsche, A. K. Renner, T. M. Burger, D. Lannigan, J. A. Brittain, G. C. Ouellet, C. V. van der Pol, E. Langlois, M.-A. 2019-04-19 doi:10.1101/614461 Cold Spring Harbor Laboratory Press 2019-04-19 <![CDATA[ An in vitro model maintaining taxon-specific functional activities of the gut microbiome ]]> https://biorxiv.org/content/10.1101/616656v1?rss=1 Li, L. Abou-Samra, E. Ning, Z. Zhang, X. Mayne, J. Wang, J. Cheng, K. Walker, K. Stintzi, A. Figeys, D. 2019-04-23 doi:10.1101/616656 Cold Spring Harbor Laboratory Press 2019-04-23 <![CDATA[ Parsing out the variability of transmission at central synapses using optical quantal analysis ]]> https://biorxiv.org/content/10.1101/624692v1?rss=1 Soares, C. Trotter, D. Longtin, A. Beïque, J.-C. Naud, R. 2019-05-03 doi:10.1101/624692 Cold Spring Harbor Laboratory Press 2019-05-03 <![CDATA[ Efficient and robust NK-Cell transduction with Baboon Envelope pseudotyped lentivector: a major tool for immunotherapy ]]> https://biorxiv.org/content/10.1101/625285v1?rss=1 Colamartino, A. B. L. Lemieux, W. Bifsha, P. Nicoletti, S. Chakravarti, N. Remon, J. S. Romero, H. Selleri, S. Beland, K. Guiot, M. Tremblay-Laganiere, C. Dicaire, R. Barreiro, L. Lee, D. A. Verhoeyen, E. Haddad, E. 2019-05-02 doi:10.1101/625285 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ PP2ACdc55 dephosphorylates Pds1 to inhibit spindle elongation ]]> https://biorxiv.org/content/10.1101/648386v1?rss=1 Khondker, S. Kajjo, S. Chandler-Brown, D. Skotheim, J. Rudner, A. Ikui, A. E. 2019-05-28 doi:10.1101/648386 Cold Spring Harbor Laboratory Press 2019-05-28 <![CDATA[ The Avocado Genome Informs Deep Angiosperm Phylogeny, Highlights Introgressive Hybridization, and Reveals Pathogen Influenced Gene Space Adaptation ]]> https://biorxiv.org/content/10.1101/654285v1?rss=1 Rendon-Anaya, M. Ibarra-Laclette, E. Mendez Bravo, A. Lan, T. Zheng, C. Carretero-Paulet, L. Perez-Torres, C. A. Chacon-Lopez, A. Hernandez-Guzman, G. Chang, T.-H. Farr, K. Barbazuk, W. B. Chamala, S. Mutwil, M. Shivhare, D. Mitter, N. Hayward, A. Fletcher, S. Rozas, J. B. Sanchez Gracia, A. Kuhn, D. Barrientos-Priego, A. F. Salojarvi, J. Librado, P. Sankoff, D. Herrera-Estrella, A. B. Albert, V. A. Herrera-Estrella, L. 2019-05-31 doi:10.1101/654285 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ The effects of arm swing amplitude and lower-limb asymmetry on gait stability ]]> https://biorxiv.org/content/10.1101/664565v1?rss=1 Hill, A. Nantel, J. 2019-06-07 doi:10.1101/664565 Cold Spring Harbor Laboratory Press 2019-06-07 <![CDATA[ Armeniaspirols inhibit the ATP-dependent proteases ClpYQ and ClpXP in Gram-positive bacteria, dysregulating the divisome ]]> https://biorxiv.org/content/10.1101/685669v1?rss=1 Labana, P. Dornan, M. H. Lafreniere, M. Czarny, T. L. Brown, E. D. Pezacki, J. P. Boddy, C. 2019-06-28 doi:10.1101/685669 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Proteins required for vacuolar function are targets of lysine polyphosphorylation in yeast ]]> https://biorxiv.org/content/10.1101/697847v1?rss=1 McCarthy, L. Bentley-DeSousa, A. Denoncourt, A. Tseng, Y.-C. Gabriel, M. Downey, M. 2019-07-10 doi:10.1101/697847 Cold Spring Harbor Laboratory Press 2019-07-10 <![CDATA[ Blue sky’s the limit? Somatic embryogenesis as a means of propagating recalcitrant blue spruce (Picea pungens) cultivar Hoopsii ]]> https://biorxiv.org/content/10.1101/700518v1?rss=1 Demone, J. J. Mao, J. Wan, S. Nourimand, M. Hansen, A. E. Flinn, B. Facchin, O. Prost, A. Altosaar, I. 2019-07-12 doi:10.1101/700518 Cold Spring Harbor Laboratory Press 2019-07-12 <![CDATA[ Host defense responses of CO441 and CL30 maize lines to Fusarium graminearum analyzed by comparative label-free quantitative proteomics ]]> https://biorxiv.org/content/10.1101/700542v1?rss=1 El Bilali, J. Reid, L. Altosaar, I. 2019-07-14 doi:10.1101/700542 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ Climate change lowers diversity and functional potential of microbes in Canada’s high Arctic ]]> https://biorxiv.org/content/10.1101/705178v1?rss=1 Colby, G. A. Ruuskanen, M. St. Pierre, K. St.Louis, V. Poulain, A. Aris-Brosou, S. 2019-07-16 doi:10.1101/705178 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ Arbovirus Vectors of Epidemiological Concern in the Americas: A Scoping Review of Entomological Studies on Zika, Dengue and Chikungunya Virus Vectors ]]> https://biorxiv.org/content/10.1101/713693v1?rss=1 Jones, R. Kulkarni, M. A. Davidson, T. M. V. Research Team, R.-L. Talbot, B. Beate Sander Camila Gonzalez, Marcos Miretti, Maur, 2019-07-25 doi:10.1101/713693 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ Origin of Conformational Dynamics in a Globular Protein ]]> https://biorxiv.org/content/10.1101/724286v1?rss=1 Damry, A. M. Mayer, M. M. Broom, A. Goto, N. K. Chica, R. A. 2019-08-04 doi:10.1101/724286 Cold Spring Harbor Laboratory Press 2019-08-04 <![CDATA[ Comparing transcriptional dynamics of the epithelial-mesenchymal transition ]]> https://biorxiv.org/content/10.1101/732412v1?rss=1 Cook, D. P. Vanderhyden, B. C. 2019-08-13 doi:10.1101/732412 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ An alternative AUG codon that produces an N-terminally extended form of the influenza A virus NP is a virulence factor for a swine-derived virus. ]]> https://biorxiv.org/content/10.1101/738427v1?rss=1 Wise, H. M. Gaunt, E. Ping, J. Holzer, B. Jasim, S. Lycett, S. J. Murphy, L. Livesey, A. Brown, R. Smith, N. Morgan, S. Clark, B. Kudryavtseva, K. Beard, P. M. Nguyen-Van-Tam, J. Salguero, F. J. Tchilian, E. Dutia, B. M. Brown, E. G. Digard, P. 2019-08-19 doi:10.1101/738427 Cold Spring Harbor Laboratory Press 2019-08-19 <![CDATA[ A transient amphipathic helix in the PCSK9 prodomain facilitates low-density lipoprotein binding ]]> https://biorxiv.org/content/10.1101/743195v1?rss=1 5-fold. Modeling studies suggested the transient -helix aligns multiple polar residues to interact with positive-charged residues in the C-terminal domain. Gain-of-function PCSK9 mutations associated with familial hypercholesterolemia (FH) and clustered at the predicted interdomain interface (R469W, R496W, F515L) inhibited LDL binding, which was abolished for the R496W variant. These studies inform on allosteric conformational changes in PCSK9 required for high-affinity binding to LDL particles. Moreover, we report the initial identification of FH-associated mutations that diminish the ability of PCSK9 to bind LDL, supporting that LDL association in the circulation inhibits PCSK9 activity. ]]> Sarkar, S. K. Foo, A. C. Y. Matyas, A. Kosenko, T. Goto, N. K. Vergara-Jaque, A. Lagace, T. 2019-08-22 doi:10.1101/743195 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Seasonal Effects of Environmental Change on Yellow-Bellied Marmot Population Dynamics ]]> https://biorxiv.org/content/10.1101/745620v1?rss=1 Paniw, M. Childs, D. Armitage, K. B. Blumstein, D. T. Martin, J. Oli, M. Ozgul, A. 2019-08-24 doi:10.1101/745620 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ β11-12 linker isomerization governs Acid-sensing ion channel desensitization and recovery ]]> https://biorxiv.org/content/10.1101/746271v1?rss=1 Rook, M. L. Williamson, A. Lueck, J. D. Musgaard, M. Maclean, D. M. 2019-08-24 doi:10.1101/746271 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Atrous Convolution with transfer learning for Skin Lesions Classification ]]> https://biorxiv.org/content/10.1101/746388v1?rss=1 Ratul, M. A. R. Mozaffari, M. H. Parimbelli, E. Lee, W. 2019-08-24 doi:10.1101/746388 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Loss of MLKL Decreases Necrotic Core but Increases Macrophage Lipid Accumulation In Atherosclerosis ]]> https://biorxiv.org/content/10.1101/746644v1?rss=1 Rasheed, A. Robichaud, S. Nguyen, M.-A. Geoffrion, M. Cottee, M. L. Dennison, T. Pietrangelo, A. Lee, R. Ouimet, M. Rayner, K. 2019-08-28 doi:10.1101/746644 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ Fatty acid-induced lipotoxicity inhibits choline metabolism independent of ER stress in mouse primary hepatocytes ]]> https://biorxiv.org/content/10.1101/746750v1?rss=1 nView larger version (42K):norg.highwire.dtl.DTLVardef@1090f2aorg.highwire.dtl.DTLVardef@1c28eedorg.highwire.dtl.DTLVardef@35a80eorg.highwire.dtl.DTLVardef@ac5a53_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> O'Dwyer, C. Yaworski, R. LeBlond, N. D. Ghorbani, P. Nunes, J. R. Margison, K. D. Smith, T. T. Gobeil Odai, K. Han, S. Fullerton, M. D. 2019-08-25 doi:10.1101/746750 Cold Spring Harbor Laboratory Press 2019-08-25 <![CDATA[ In vitro hepatitis C virus infection and hepatic choline metabolism ]]> https://biorxiv.org/content/10.1101/746776v1?rss=1 nView larger version (56K):norg.highwire.dtl.DTLVardef@133a652org.highwire.dtl.DTLVardef@1ec8fa8org.highwire.dtl.DTLVardef@1cb7626org.highwire.dtl.DTLVardef@b9bbc2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gobeil Odai, K. O'Dwyer, C. Steenbergen, R. Shaw, T. A. Renner, T. M. Ghorbani, P. Rezaaifar, M. Han, S. Langlois, M.-A. Crawley, A. M. Russell, R. S. Pezacki, J. P. Tyrrell, D. L. Fullerton, M. D. 2019-08-25 doi:10.1101/746776 Cold Spring Harbor Laboratory Press 2019-08-25 <![CDATA[ Characterization of LXR-activating nanoparticle formulations in primary mouse macrophages ]]> https://biorxiv.org/content/10.1101/746784v1?rss=1 Smith, T. T. Kahiel, Z. LeBlond, N. D. Ghorbani, P. Farah, E. Cote, M. Gadde, S. Fullerton, M. D. 2019-08-25 doi:10.1101/746784 Cold Spring Harbor Laboratory Press 2019-08-25 <![CDATA[ Microbiome-wide characterization of post-translational modifications ]]> https://biorxiv.org/content/10.1101/753996v1?rss=1 Cheng, K. Ning, Z. Zhang, X. Mayne, J. Figeys, D. 2019-09-03 doi:10.1101/753996 Cold Spring Harbor Laboratory Press 2019-09-03 <![CDATA[ Nucleosome positioning sequence patterns as packing or regulatory ]]> https://biorxiv.org/content/10.1101/755272v1?rss=1 Pranckeviciene, E. Hosid, S. Liang, N. Ioshikhes, I. 2019-09-02 doi:10.1101/755272 Cold Spring Harbor Laboratory Press 2019-09-02 <![CDATA[ An analysis of intrinsic base substitution patterns in diverse species reveals connections to cancer and metabolism ]]> https://biorxiv.org/content/10.1101/758540v1?rss=1 1.9 billion variants. We found that the base substitution patterns for many species most closely match mutational signature 5 in cancers. Signature 5 is also ubiquitous in cancers and normal human cells, suggesting similar patterns of mutation across species are likely due to conserved biochemistry. Finally, we present evidence from yeast that sugar metabolism is directly linked to this form of DNA damage. We propose that conserved metabolic processes in cells are coupled to continuous generation of mutations, which are acted upon by genetic selection to drive the evolution of species, and cancers. One Sentence SummaryEnergy metabolism produces DNA damage leading to similar patterns of base substitutions in many species and in human cancers. ]]> Chan, K. Doherty, K. N. Alasmar, S. 2019-09-08 doi:10.1101/758540 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ Long-term metabolic consequences of acute dioxin exposure differ between male and female mice ]]> https://biorxiv.org/content/10.1101/762476v1?rss=1 Hoyeck, M. P. Blair, H. Ibrahim, M. Solanki, S. Elsawy, M. Prakash, A. Rick, K. R. Matteo, G. O'Dwyer, S. Bruin, J. E. 2019-09-09 doi:10.1101/762476 Cold Spring Harbor Laboratory Press 2019-09-09 <![CDATA[ Learning long temporal sequences in spiking networks by multiplexing neural oscillations ]]> https://biorxiv.org/content/10.1101/766758v1?rss=1 Vincent-Lamarre, P. Calderini, M. Thivierge, J.-P. 2019-09-12 doi:10.1101/766758 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Plasmid transmitted small multidrug resistant (SMR) efflux pumps differ in gene regulation and enhance tolerance to quaternary ammonium compounds (QAC) when grown as biofilms ]]> https://biorxiv.org/content/10.1101/768630v1?rss=1 500 sequenced proteobacterial plasmids. SMR sequence diversity from plasmid database surveys identified 20 unique SMR sequences annotated as qacE/E{Delta}1/F/G/H/I/L, or sugE. Phylogenetic analysis shows Qac sequences are homologous to archetypical SMR member EmrE, and share a single sequence origin. In contrast, SugE sequences are homologous to archetypical member Gdx/SugE and likely originate from different species. SMR genes, qacE, qacE{Delta}1, qacF, qacG, qacH, and sugE(p), were over-expressed in Escherichia coli to determine their QAC antimicrobial susceptibility as planktonic, colony, and biofilms. SMRs (except qacE{Delta}1/sugE) expressed in biofilms significantly increased its QAC tolerance as compared to planktonic and colony growth. Analysis of upstream SMR nucleotide regions indicate sugE(p) genes are regulated by type II guanidinium riboswitches, whereas qacE and qacE{Delta}1 have a conserved class I integron Pq promoter, and qacF/G/H are regulated by integron Pc promoter in variable cassettes region. Beta-galactosidase assays were used to characterize growth conditions regulating Pq and Pc promoters and revealed that Pq and Pc have different expression profiles during heat, peroxide, and QAC exposure. Altogether, this study reveals that biofilm growth methods are optimal for SMR-mediated QAC susceptibility testing and suggests SMR gene regulation on plasmids is similar to chromosomally inherited SMR members. ]]> Slipski, C. J. Jamieson, T. R. Lam, A. Leung Shing, V. Bell, K. Zhanel, G. G. Bay, D. C. 2019-09-14 doi:10.1101/768630 Cold Spring Harbor Laboratory Press 2019-09-14 <![CDATA[ Mechanotransduction of strain regulates an invasive phenotype in newly transformed epithelial cells ]]> https://biorxiv.org/content/10.1101/770487v1?rss=1 Chagnon-Lessard, S. Jean-Ruel, H. Godin, M. Pelling, A. 2019-09-15 doi:10.1101/770487 Cold Spring Harbor Laboratory Press 2019-09-15 <![CDATA[ Deep characterization of the protein lysine acetylation in human gut microbiome and its alterations in patients with Crohn’s disease ]]> https://biorxiv.org/content/10.1101/772483v1?rss=1 Zhang, X. Ning, Z. Mayne, J. Deeke, S. A. Walker, K. Farnsworth, C. L. Stokes, M. P. Mack, D. Stintzi, A. Figeys, D. 2019-09-18 doi:10.1101/772483 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ DJ-1 (Park7) affects the gut microbiome, metabolites, and development of Innate Lymphoid Cells (ILCs) ]]> https://biorxiv.org/content/10.1101/776005v1?rss=1 Singh, Y. Trautwein, C. Dhariwal, A. Salker, M. S. Alauddin, M. Zizmare, L. Pelzl, L. Feger, M. Matthes, J. Casadei, N. Föller, M. Pachauri, V. Park, D. S. Mak, T. W. Frick, J. S. Wallweiner, D. Brucker, S. Lang, F. Riess, O. 2019-09-19 doi:10.1101/776005 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Structural and mechanical remodeling of the cytoskeleton studied in 3D microtissues under acute dynamic stretch ]]> https://biorxiv.org/content/10.1101/780312v1?rss=1 Walker, M. Rizzuto, P. Godin, M. Pelling, A. 2019-10-06 doi:10.1101/780312 Cold Spring Harbor Laboratory Press 2019-10-06 <![CDATA[ A synthetic likelihood solution to the silent synapse estimation problem ]]> https://biorxiv.org/content/10.1101/781898v1?rss=1 Lynn, M. B. Lee, K. F. H. Soares, C. Naud, R. Beique, J.-C. 2019-09-25 doi:10.1101/781898 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Light scatter and fluorescence calibration allow standard comparisons of small particle data between different instruments. ]]> https://biorxiv.org/content/10.1101/796961v1?rss=1 Welsh, J. A. Tang, V. A. 2019-10-18 doi:10.1101/796961 Cold Spring Harbor Laboratory Press 2019-10-18 <![CDATA[ Gender-specific pathophysiological mGluR5-dependent Aβ oligomer signaling in Alzheimer mice ]]> https://biorxiv.org/content/10.1101/803262v1?rss=1 Abd-Elrahman, K. S. Hamilton, A. de Souza, J. M. Albaker, A. Ribeiro, F. M. Ferguson, S. S. G. 2019-10-13 doi:10.1101/803262 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ A Chemoenzymatic Method for Glycoproteomic N-glycan Type Quantitation ]]> https://biorxiv.org/content/10.1101/803494v1?rss=1 Li, H. Li, L. Cheng, K. Ning, Z. Mayne, J. Zhang, X. Walker, K. Chen, R. Twine, S. Li, J. Figeys, D. 2019-10-15 doi:10.1101/803494 Cold Spring Harbor Laboratory Press 2019-10-15 <![CDATA[ Chlamydomonas sp. UWO241 exhibits high cyclic electron flow and rewired metabolism under high salinity ]]> https://biorxiv.org/content/10.1101/813824v1?rss=1 Kalra, I. Wang, X. Cvetkovska, M. Jeong, J. McHargue, W. Zhang, R. Hüner, N. P. A. Yuan, J. S. Morgan-Kiss, R. M. 2019-10-23 doi:10.1101/813824 Cold Spring Harbor Laboratory Press 2019-10-23 <![CDATA[ Loss of Dnmt3a dependent methylation in inhibitory neurons impairs neural function through a mechanism that impacts Rett syndrome ]]> https://biorxiv.org/content/10.1101/815639v1?rss=1 Lavery, L. A. Ure, K. Wan, Y.-W. Luo, C. Trostle, A. J. Wang, W. Lopez, J. Lucero, J. Durham, M. A. Castanon, R. Nery, J. R. Liu, Z. Goodell, M. A. Ecker, J. R. Behrens, M. M. Zoghbi, H. 2019-10-22 doi:10.1101/815639 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Neuropeptide relay between SIFa signaling controls the experience-dependent mating duration of male Drosophila ]]> https://biorxiv.org/content/10.1101/819045v1?rss=1 Wong, K. C. Schweizer, J. Nguyen, K.-N. H. Atieh, S. Kim, W. J. 2019-10-25 doi:10.1101/819045 Cold Spring Harbor Laboratory Press 2019-10-25 <![CDATA[ A Compendium of Kinetic Cell Death Modulatory Profiles Identifies Ferroptosis Regulators ]]> https://biorxiv.org/content/10.1101/826925v1?rss=1 Conlon, M. Poltorack, C. Forcina, G. C. Wells, A. Mallais, M. Kahanu, A. Magtanong, L. Pratt, D. Dixon, S. J. 2019-10-31 doi:10.1101/826925 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Mitochondria tether to Focal Adhesions during cell migration and regulate their size. ]]> https://biorxiv.org/content/10.1101/827998v1?rss=1 Daniel, R. Mengeta, A. Bilodeau, P. Lee, J. M. 2019-11-01 doi:10.1101/827998 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ Phosphatidylinositol 4-kinase III beta regulates cell shape, migration and focal adhesion number. ]]> https://biorxiv.org/content/10.1101/828046v1?rss=1 Law-Vinh, D. Bilodeau, P. Jacobsen, D. Lee, J. 2019-11-01 doi:10.1101/828046 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ Antiretroviral APOBEC3 Cytidine Deaminases Alter HIV-1 Provirus Integration Site Profiles ]]> https://biorxiv.org/content/10.1101/833475v1?rss=1 Ajoge, H. O. Renner, T. M. Kohio, H. P. Coleman, M. D. Langlois, M.-A. Barr, S. D. 2019-11-07 doi:10.1101/833475 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Astrocyte-like glia-specific gene deathstar is crucial for normal development, adult locomotion and lifespan of male Drosophila ]]> https://biorxiv.org/content/10.1101/839811v1?rss=1 Najafi, H. Wong, K. Kim, W. J. 2019-11-12 doi:10.1101/839811 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ pepFunk, a tool for peptide-centric functional analysis in metaproteomic human gut microbiome studies ]]> https://biorxiv.org/content/10.1101/854976v1?rss=1 Simopoulos, C. M. A. Ning, Z. Zhang, X. Li, L. Walker, K. Lavallee-Adam, M. Figeys, D. 2019-11-25 doi:10.1101/854976 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Skin Lesions Classification Using Deep Learning Based on Dilated Convolution ]]> https://biorxiv.org/content/10.1101/860700v1?rss=1 Ratul, M. A. R. Mozaffari, M. H. Lee, D. W. Parimbelli, D. E. 2019-11-30 doi:10.1101/860700 Cold Spring Harbor Laboratory Press 2019-11-30 <![CDATA[ Multiplexed single-cell transcriptomic analysis of normal and impaired lung development in the mouse ]]> https://biorxiv.org/content/10.1101/868802v1?rss=1 Hurskainen, M. K. Mizikova, I. Cook, D. P. Cyr-Depauw, C. Lesage, F. Andersson, N. Helle, E. Renesme, L. Jankov, R. P. Heikinheimo, M. Vanderhyden, B. Thebaud, B. 2019-12-08 doi:10.1101/868802 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ Prediction of 8-state protein secondary structures by 1D-Inception and BD-LSTM ]]> https://biorxiv.org/content/10.1101/871921v1?rss=1 Ratul, M. A. R. Turcotte, M. Mozaffari, M. H. Lee, W. 2019-12-11 doi:10.1101/871921 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ Notorious Novel Avian Influenza Viruses H10N8 and H7N9 in China in 2013 Co-originated from H9N2 ]]> https://biorxiv.org/content/10.1101/004390v1?rss=1 Liang Chen Feng Zhu Chenglong Xiong Zhijie Zhang Lufang Jiang Rui Li Genming Zhao Yue Chen Qingwu Jiang 2014-04-21 doi:10.1101/004390 Cold Spring Harbor Laboratory Press 2014-04-21 <![CDATA[ The human experience with intravenous levodopa ]]> https://biorxiv.org/content/10.1101/024794v1?rss=1 Shan H Siddiqi Natalia K Abraham Christopher L Geiger Morvarid Karimi Joel S Perlmutter Kevin J Black 2015-08-18 doi:10.1101/024794 Cold Spring Harbor Laboratory Press 2015-08-18 <![CDATA[ Extracellular Forces Cause the Nucleus to Deform in a Highly Controlled Anisotropic Manner ]]> https://biorxiv.org/content/10.1101/027888v1?rss=1 Kristina Haase Joan K. L. Macadangdang Claire H. Edrington Charles M. Cuerrier Sebastian Hadjiantoniou James L. Harden Ilona S. Skerjanc Andrew E. Pelling 2015-10-01 doi:10.1101/027888 Cold Spring Harbor Laboratory Press 2015-10-01 <![CDATA[ Analysis of protein-coding genetic variation in 60,706 humans ]]> https://biorxiv.org/content/10.1101/030338v1?rss=1 Exome Aggregation Consortium Monkol Lek Konrad Karczewski Eric Minikel Kaitlin Samocha Eric Banks Timothy Fennell Anne O'Donnell-Luria James Ware Andrew Hill Beryl Cummings Taru Tukiainen Daniel Birnbaum Jack Kosmicki Laramie Duncan Karol Estrada Fengmei Zhao James Zou Emma Pierce-Hoffman Joanne Berghout David Cooper Nicole Deflaux Mark DePristo Ron Do Jason Flannick Menachem Fromer Laura Gauthier Jackie Goldstein Namrata Gupta Daniel Howrigan Adam Kiezun Mitja Kurki Ami Levy Moonshine Pradeep Natarajan Lorena Orozco Gina Peloso Ryan Poplin Manuel Rivas Valentin Ruano-Rubio Samuel Rose Douglas 2015-10-30 doi:10.1101/030338 Cold Spring Harbor Laboratory Press 2015-10-30 <![CDATA[ Pollinator specialization imposes stronger evolutionary constraints on flower shape ]]> https://biorxiv.org/content/10.1101/041533v1?rss=1 Simon Joly François Lambert Hermine Alexandre Étienne Léveillé-Bourret John L. Clark 2016-02-26 doi:10.1101/041533 Cold Spring Harbor Laboratory Press 2016-02-26 <![CDATA[ Measuring Mechanodynamics using an Unsupported Epithelial Monolayer Grown at an Air-Water Interface ]]> https://biorxiv.org/content/10.1101/052555v1?rss=1 Corinne Gullekson Matthew Walker James L. Harden Andrew Pelling 2016-05-10 doi:10.1101/052555 Cold Spring Harbor Laboratory Press 2016-05-10 <![CDATA[ Utilizing Social Media and Video Games to Control #DIY Microscopes ]]> https://biorxiv.org/content/10.1101/053470v1?rss=1 Maxime Leblanc-Latour Craig Bryan Andrew Pelling 2016-05-15 doi:10.1101/053470 Cold Spring Harbor Laboratory Press 2016-05-15 <![CDATA[ Rapid Dynamics of Cell-Shape Recovery in Response to Local Deformations ]]> https://biorxiv.org/content/10.1101/056143v1?rss=1 Kristina Haase Tyler N Shendruk Andrew E Pelling 2016-05-30 doi:10.1101/056143 Cold Spring Harbor Laboratory Press 2016-05-30 <![CDATA[ Semi-Automated Identification of Ontological Labels in the Biomedical Literature with goldi ]]> https://biorxiv.org/content/10.1101/073460v1?rss=1 Christopher B. Cole Sejal Patel Jo Knight 2016-09-05 doi:10.1101/073460 Cold Spring Harbor Laboratory Press 2016-09-05 <![CDATA[ Sepsis Increases Perioperative Metastases In A Murine Model ]]> https://biorxiv.org/content/10.1101/142083v1?rss=1 Tai, L.-H. Ananth, A. A. Seth, R. Alkayyal, A. Zhang, J. de Souza, C. T. Staibano, P. Kennedy, M. A. Auer, R. C. 2017-05-25 doi:10.1101/142083 Cold Spring Harbor Laboratory Press 2017-05-25 <![CDATA[ Mechanical mismatch between Ras transformed and untransformed epithelial cells. ]]> https://biorxiv.org/content/10.1101/152942v1?rss=1 Gullekson, C. Cojoc, G. Schurmann, M. Guck, J. Pelling, A. 2017-06-20 doi:10.1101/152942 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Cerebral grey matter density is associated with neuroreceptor and neurotransporter availability: A combined PET and MRI study ]]> https://biorxiv.org/content/10.1101/2020.01.29.924530v1?rss=1 Manninen, S. Karjalainen, T. Tuominen, L. Hietala, J. Kaasinen, V. Joutsa, J. Rinne, J. Nummenmaa, L. 2020-01-30 doi:10.1101/2020.01.29.924530 Cold Spring Harbor Laboratory Press 2020-01-30 <![CDATA[ Inhibition and down regulation of the serotonin transporter contribute to the progression of degenerative mitral regurgitation ]]> https://biorxiv.org/content/10.1101/2020.03.10.985382v1?rss=1 Levy, R. J. Fitzpatrick, E. Castillero, E. Shukla,, H. J. Inamdar,, V. V. Aghali, A. E. Grau, J. B. Rioux, N. Salvati, E. Keeney, S. J. Nissim, I. Gorman, R. C. C. Rauova, L. Stachelek, S. J. Brown, C. R. Krieger, A. M. Ferrari, G. 2020-03-11 doi:10.1101/2020.03.10.985382 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Vaccine Elicitation of HIV Broadly Neutralizing Antibodies from Engineered B cells ]]> https://biorxiv.org/content/10.1101/2020.03.17.989699v1?rss=1 Huang, D. Tran, J. T. Olson, A. Vollbrecht, T. Guryleva, M. V. Tenuta, M. Fuller, R. P. Schiffner, T. Abadejos, J. R. Couvrette, L. Blane, T. R. Saye, K. Li, W. Landais, E. Gonzalez-Martin, A. Schief, W. Murrell, B. Burton, D. R. Nemazee, D. Voss, J. E. 2020-03-17 doi:10.1101/2020.03.17.989699 Cold Spring Harbor Laboratory Press 2020-03-17 <![CDATA[ Improved segmentation of the intracranial and ventricular volumes in populations with cerebrovascular lesions and atrophy using 3D CNNs ]]> https://biorxiv.org/content/10.1101/2020.03.23.000844v1?rss=1 Ntiri, E. E. Holmes, M. F. Mojiri, P. Ramirez, J. Gao, F. Ozzoude, M. Adamo, S. Scott, C. Dowlatshahi, D. Lawrence-Dewar, J. M. Kwan, D. Lang, A. E. Symons, S. Bartha, R. Strother, S. Tardif, J.-C. Masellis, M. Swartz, R. H. Moody, A. Black, S. Goubran, M. 2020-03-25 doi:10.1101/2020.03.23.000844 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Tumor invasion as non-equilibrium phase separation ]]> https://biorxiv.org/content/10.1101/2020.04.28.066845v1?rss=1 Kang, W. Ferruzzi, J. Spatarelu, C.-P. Han, Y. L. Sharma, Y. Koehler, S. Butler, J. P. Roblyer, D. Zaman, M. H. Guo, M. Chen, Z. Pegoraro, A. F. Fredberg, J. J. 2020-04-29 doi:10.1101/2020.04.28.066845 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Pathologic α-Synuclein Species Activate LRRK2 in Pro-Inflammatory Monocyte and Macrophage Responses ]]> https://biorxiv.org/content/10.1101/2020.05.04.077065v1?rss=1 Xu, E. Boddu, R. Abdelmotilib, H. A. Kelly, K. Sokratian, A. Harms, A. S. Schonhoff, A. M. Bryant, N. Harmsen, I. E. Schlossmacher, M. Chandra, S. Krendelshchikova, V. Liu, Z. West, A. B. 2020-05-05 doi:10.1101/2020.05.04.077065 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Heat Shock Protein 27 Immune Complex Upregulates LDLR Expression Thereby Reducing Plasma Cholesterol and Atherogenesis ]]> https://biorxiv.org/content/10.1101/2020.05.21.102350v1?rss=1 Chen, Y.-X. Shi, C. Deng, J. Diao, C. Maarouf, N. Rosin, M. Shrivastava, V. Hu, A. Bharadwa, S. Adijiang, A. Ulke-Lemee, A. Gwilym, B. L. Hellmich, A. Malozzi, C. Batulan, Z. Dean, J. L. E. Ramirez, F. D. Liu, J. Gerthoffer, W. T. O'Brien, E. R. 2020-05-25 doi:10.1101/2020.05.21.102350 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Distinguishing within from between individual effects: How to use the within-individual centering method for quadratic pattern ]]> https://biorxiv.org/content/10.1101/2020.05.25.114421v1?rss=1 Fay, R. Martin, J. Plard, F. 2020-05-28 doi:10.1101/2020.05.25.114421 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Cross-sectional evaluation of humoral responses against SARS-CoV-2 Spike ]]> https://biorxiv.org/content/10.1101/2020.06.08.140244v1?rss=1 Prevost, J. Gasser, R. Beaudoin-Bussieres, G. Richard, J. Duerr, R. Laumaea, A. Anand, S. P. Goyette, G. Ding, S. Medjahed, H. Lewin, A. Perreault, J. Tremblay, T. Gendron-Lepage, G. Gauthier, N. Carrier, M. Marcoux, D. Piche, A. Lavoie, M. Benoit, A. Loungnarath, V. Brochu, G. Desforges, M. Talbot, P. J. Gould Maule, G. T. Cote, M. Therrien, C. Serhir, B. Bazin, R. Roger, M. Finzi, A. 2020-06-08 doi:10.1101/2020.06.08.140244 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ Naturalistic coding of working memory in primate prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2020.06.19.162446v1?rss=1 Roussy, M. Luna, R. Duong, L. Corrigan, B. Gulli, R. A. Nogueira, R. Moreno-Bote, R. Sachs, A. J. Palaniyappan, L. Martinez-Trujillo, J. C. 2020-06-22 doi:10.1101/2020.06.19.162446 Cold Spring Harbor Laboratory Press 2020-06-22 <![CDATA[ Bridging the gap - Spontaneous fluctuations shape stimulus-evoked spectral power ]]> https://biorxiv.org/content/10.1101/2020.06.23.166058v1?rss=1 Wainio-Theberge, S. Wolff, A. Northoff, G. 2020-06-24 doi:10.1101/2020.06.23.166058 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease ]]> https://biorxiv.org/content/10.1101/2020.06.25.169573v1?rss=1 Audain, E. Wilsdon, A. Breckpot, J. Izarzugaza, J. M. Fitzgerald, T. W. Anne-Karin, K. Sifrim, A. Wuennemann, F. Perez-Riverol, Y. Abdul-Khaliq, H. Bak, M. Bassett, A. S. Belmont, J. Benson, W. D. Berger, F. Daehnert, I. Devriendt, K. Dittrich, S. Daubeney, P. Garg, V. Hackmann, K. Hoff, K. Hofmann, P. Dombrowsky, G. Pickardt, T. Bauer, U. Keavney, B. Klaassen, S. Kramer, H.-H. Marshall, C. R. Milewicz, D. M. Lemaire, S. Coselli, J. Mitchell, M. E. Tomita-Mitchell, A. Prakash, S. K. Stamm, K. Stewart, A. F. Silversides, C. K. Siebert, R. Stiller, B. Ros 2020-06-25 doi:10.1101/2020.06.25.169573 Cold Spring Harbor Laboratory Press 2020-06-25 <![CDATA[ Cardiomyocyte-specific Srsf3 deletion reveals a mitochondrial regulatory role ]]> https://biorxiv.org/content/10.1101/2020.07.03.186999v1?rss=1 Dumont, A.-A. Dumont, L. Zhou, D. Giguere, H. Pileggi, C. Harper, M.-E. Blondin, D. P. Scott, M. S. Auger-Messier, M. 2020-07-04 doi:10.1101/2020.07.03.186999 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Vascular calcification has a role in acute non-renal phosphate clearance ]]> https://biorxiv.org/content/10.1101/2020.07.29.225532v1?rss=1 Turner, M. E. Lansing, A. P. Jeronimo, P. S. Lee, L. H. Svajger, B. A. Zelt, J. G. Petkovich, M. P. Holden, R. M. Adams, M. A. 2020-07-30 doi:10.1101/2020.07.29.225532 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ Intrinsic neural timescales related to sensory processing: Evidence from abnormal behavioural states ]]> https://biorxiv.org/content/10.1101/2020.07.30.229161v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@1893c45org.highwire.dtl.DTLVardef@d4176dorg.highwire.dtl.DTLVardef@4dfaa8org.highwire.dtl.DTLVardef@183621e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Zilio, F. Gomez-Pilar, J. Cao, S. Zhang, J. Zang, D. Qi, Z. Tan, J. Hiromi, T. Wu, X. Fogel, S. Huang, Z. Hohmann, M. R. Fomina, T. Synofzik, M. Grosse-Wentrup, M. Owen, A. M. Northoff, G. 2020-07-31 doi:10.1101/2020.07.30.229161 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ Cortical thickness estimation in individuals with cerebral small vessel disease, focal atrophy, and chronic stroke lesions. ]]> https://biorxiv.org/content/10.1101/2020.08.04.236760v1?rss=1 Ozzoude, M. Ramirez, J. Raamana, P. R. Holmes, M. F. Walker, K. Scott, C. J. M. Goubran, M. Kwan, D. Tartaglia, M. C. Beaton, D. Strother, S. C. Symons, S. Bartha, R. Swartz, R. H. Black, S. E. on behalf of the ONDRI Investigators, 2020-08-05 doi:10.1101/2020.08.04.236760 Cold Spring Harbor Laboratory Press 2020-08-05 <![CDATA[ The Contributions of the Allopolyploid Parents of the Mesopolyploid Brassiceae are Evolutionarily Distinct but Functionally Compatible ]]> https://biorxiv.org/content/10.1101/2020.08.10.245258v1?rss=1 Hao, Y. Mabry, M. E. Edger, P. Freeling, M. Zheng, C. Jin, L. VanBuren, R. Colle, M. An, H. Abrahams, R. S. Qi, X. Barry, K. Daum, C. Shu, S. Schmutz, J. Sankoff, D. Barker, M. S. Lyons, E. Pires, J. C. Conant, G. C. 2020-08-12 doi:10.1101/2020.08.10.245258 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Higher-order sensorimotor circuit of the brain' global network supports human consciousness ]]> https://biorxiv.org/content/10.1101/2020.09.22.308072v1?rss=1 Qin, P. Wu, X. Wu, C. Wu, H. Zhang, J. Huang, Z. Weng, X. Qi, Z. Tang, W. Hiromi, T. Tan, J. Tanabe, S. Fogel, S. Hudetz, A. G. Yang, Y. Stamatakis, E. A. Mao, Y. Northoff, G. 2020-09-23 doi:10.1101/2020.09.22.308072 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Mis-splicing of Mdm2 leads to increased P53-activity and craniofacial defects in a MFDM Eftud2 mutant mouse model ]]> https://biorxiv.org/content/10.1101/2020.09.22.308205v1?rss=1 Beauchamp, M.-C. Djedid, A. Bareke, E. Merkuri, F. Aber, R. Tam, A. S. Lines, M. A. Boycott, K. M. Stirling, P. C. Fish, J. L. Majewski, J. L. Jerome-Majewska, L. A. 2020-09-22 doi:10.1101/2020.09.22.308205 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Cohesin components Stag1 and Stag2 differentially influence haematopoietic mesoderm development in zebrafish embryos ]]> https://biorxiv.org/content/10.1101/2020.10.19.346122v1?rss=1 Ketharnathan, S. Labudina, A. Horsfield, J. A. 2020-10-19 doi:10.1101/2020.10.19.346122 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ Plant Scaffolds Support Motor Recovery and Regeneration in Rat Spinal Cord Injury ]]> https://biorxiv.org/content/10.1101/2020.10.21.347807v1?rss=1 Modulevsky, D. J. Cuerrier, C. M. Leblanc-Latour, M. Hickey, R. J. Obhi, R.-J. K. Shore, I. Galuta, A. Walker, K. L. A. Tsai, E. C. Pelling, A. E. 2020-10-22 doi:10.1101/2020.10.21.347807 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ The genetic and linguistic structures of Abyssinians and their neighbor reveal the historical demographic dynamics and environmental adaptation in the African Horn region. ]]> https://biorxiv.org/content/10.1101/2020.10.21.348599v1?rss=1 Sertse, D. B.Mersha, T. Z. Habtewold, J. 2020-10-22 doi:10.1101/2020.10.21.348599 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ Engineered Tissue Interfaces for in vitro and in vivo Bioengineering ]]> https://biorxiv.org/content/10.1101/2020.11.06.371278v1?rss=1 Hickey, R. J. Leblanc Latour, M. Harden, J. L. Pelling, A. 2020-11-08 doi:10.1101/2020.11.06.371278 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ YeastNet: Deep Learning Enabled Accurate Segmentation of Budding Yeast Cells in Bright-field Microscopy ]]> https://biorxiv.org/content/10.1101/2020.11.30.402917v1?rss=1 Salem, D. Li, Y. Xi, P. Cuperlovic-Culf, M. Phenix, H. Kaern, M. 2020-12-02 doi:10.1101/2020.11.30.402917 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Mesolimbic opioid-dopamine interaction is disrupted in obesity but recovered by weight loss following bariatric surgery ]]> https://biorxiv.org/content/10.1101/2020.12.10.418764v1?rss=1 Karlsson, H. K. Tuominen, L. Helin, S. Salminen, P. Nuutila, P. Nummenmaa, L. 2020-12-11 doi:10.1101/2020.12.10.418764 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ A unified theory of E/I synaptic balance, quasicritical neuronal avalanches and asynchronous irregular spiking ]]> https://biorxiv.org/content/10.1101/2020.12.17.423201v1?rss=1 Girardi-Schappo, M. Galera, E. F. Carvalho, T. T. A. Brochini, L. Kamiji, N. L. Roque, A. C. Kinouchi, O. 2020-12-17 doi:10.1101/2020.12.17.423201 Cold Spring Harbor Laboratory Press 2020-12-17 <![CDATA[ Rare coding variants in 35 genes associate with circulating lipid levels: a multi-ancestry analysis of 170,000 exomes ]]> https://biorxiv.org/content/10.1101/2020.12.22.423783v1?rss=1 170,000 individuals from multiple ancestries: 97,493 European, 30,025 South Asian, 16,507 African, 16,440 Hispanic/Latino, 10,420 East Asian, and 1,182 Samoan. We identified 35 genes associated with circulating lipid levels. Ten of these: ALB, SRSF2, JAK2, CREB3L3, TMEM136, VARS, NR1H3, PLA2G12A, PPARG and STAB1 have not been implicated for lipid levels using rare coding variation in population-based samples. We prioritize 32 genes identified in array-based genome-wide association study (GWAS) loci based on gene-based associations, of which three: EVI5, SH2B3, and PLIN1, had no prior evidence of rare coding variant associations. Most of the associated genes showed evidence of association in multiple ancestries. Also, we observed an enrichment of gene-based associations for low-density lipoprotein cholesterol drug target genes, and for genes closest to GWAS index single nucleotide polymorphisms (SNP). Our results demonstrate that gene-based associations can be beneficial for drug target development and provide evidence that the gene closest to the array-based GWAS index SNP is often the functional gene for blood lipid levels. ]]> Hindy, G. Dornbos, P. Chaffin, M. D. Liu, D. J. Wang, M. X. Aguilar-Salinas, C. A. Antonacci-Fulton, L. Ardissino, D. Arnett, D. K. Aslibekyan, S. Atzmon, G. Ballantyne, C. M. Barajas-Olmos, F. Barzilai, N. Becker, L. C. Bielak, L. F. Bis, J. C. Blangero, J. Boerwinkle, E. Bonnycastle, L. L. Bottinger, E. Bowden, D. W. Bown, M. J. Brody, J. A. Broome, J. G. Burtt, N. P. Cade, B. E. Centeno-Cruz, F. Chan, E. Chang, Y.-C. Chen, Y.-D. I. Cheng, C.-Y. Choi, W. J. Chowdhury, R. Contreras-Cubas, C. Cordova, E. J. Correa, A. Cupples, L. A. Curran, J. E. Danesh, 2020-12-23 doi:10.1101/2020.12.22.423783 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ A common polymorphism that protects from cardiovascular disease increases fibronectin processing and secretion ]]> https://biorxiv.org/content/10.1101/2021.03.09.434522v1?rss=1 Soubeyrand, S. Lau, P. Nikpay, M. Dang, A.-T. McPherson, R. 2021-03-09 doi:10.1101/2021.03.09.434522 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Increasing role of pyrethroid-resistant Anopheles funestus in malaria transmission in the Lake Zone, Tanzania: implications for the evaluation of novel vector control products ]]> https://biorxiv.org/content/10.1101/2021.04.01.438043v1?rss=1 Matowo, N. S. Martin, J. Kulkarni, M. A. Mosha, J. F. Lukole, E. Isaya, G. Shirima, B. Kaaya, R. Moyes, C. Hancock, P. A. Rowland, M. Manjurano, A. Mosha, F. W. Protopopoff, N. Messenger, L. A. 2021-04-01 doi:10.1101/2021.04.01.438043 Cold Spring Harbor Laboratory Press 2021-04-01 <![CDATA[ The Expression Pattern of miR-17, -24, -124 and -145 as Diagnostic Factor for Metastatic Gastric Cancer; a Lesson from Gastric Cancer Stem cells ]]> https://biorxiv.org/content/10.1101/2021.04.08.439087v1?rss=1 Yasavoli-Sharahi, H. Jahangiri-Tazehkand, S. Iranmehr, Z. Eslahchi, C. Emami Razavi, A. Moradi, S. Shayan Asl, N. Memari, F. Ebrahimi, M. 2021-04-11 doi:10.1101/2021.04.08.439087 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Lhx2 is a progenitor-intrinsic modulator of Sonic Hedgehog signaling during early retinal neurogenesis ]]> https://biorxiv.org/content/10.1101/2021.04.24.441277v1?rss=1 Li, X. Gordon, P. J. Gaynes, J. A. Fuller, A. W. Ringuette, R. Santiago, C. P. Wallace, V. A. Blackshaw, S. Li, P. LEVINE, E. M. 2021-04-26 doi:10.1101/2021.04.24.441277 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Investigating the Contribution of White Matter Hyperintensities and Cortical Thickness to Empathy in Neurodegenerative and Cerebrovascular Diseases ]]> https://biorxiv.org/content/10.1101/2021.08.01.454640v1?rss=1 Ozzoude, M. Varriano, B. Beaton, D. Ramirez, J. Holmes, M. F. Scott, C. J. M. Gao, F. Sunderland, K. M. McLaughlin, P. Rabin, J. Goubran, M. Kwan, D. Roberts, A. Bartha, R. Symons, S. Tan, B. Swartz, R. H. Abrahao, A. Saposnik, G. Masellis, M. Lang, A. E. Marras, C. Zinman, L. Shoesmith, C. Borrie, M. Fischer, C. E. Frank, A. Freedman, M. Montero-Odasso, M. Kumar, S. Pasternak, S. Strother, S. C. Pollock, B. G. Rajji, T. K. Seitz, D. Tang-wai, D. Chum, M. Turnbull, J. Dowlatshahi, D. Hassan, A. Casaubon, L. Mandzia, J. Sahlas, D. Breen, D. P. Grimes, 2021-08-03 doi:10.1101/2021.08.01.454640 Cold Spring Harbor Laboratory Press 2021-08-03 <![CDATA[ Contribution of single mutations to selected SARS-CoV-2 emerging variants Spike antigenicity ]]> https://biorxiv.org/content/10.1101/2021.08.04.455140v1?rss=1 Gong, S. Y. Chatterjee, D. Richard, J. Prevost, J. Tauzin, A. Gasser, R. Bo, Y. Vezina, D. Goyette, G. Gendron-Lepage, G. Medjahed, H. Roger, M. Cote, M. Finzi, A. 2021-08-04 doi:10.1101/2021.08.04.455140 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ Different neural codes serve long and short-term memory functions in primate Hippocampus and Lateral Prefrontal Cortex during virtual navigation ]]> https://biorxiv.org/content/10.1101/2021.08.20.457136v1?rss=1 Corrigan, B. W. Gulli, R. A. Doucet, G. Roussy, M. Luna, R. Sachs, A. J. Martinez-Trujillo, J. C. 2021-08-21 doi:10.1101/2021.08.20.457136 Cold Spring Harbor Laboratory Press 2021-08-21 <![CDATA[ Engineering genetically-encoded synthetic biomarkers for breath-based cancer detection ]]> https://biorxiv.org/content/10.1101/2021.09.01.456741v1?rss=1 Vermesh, O. D'Souza, A. Alam, I. S. Wardak, M. McLaughlin, T. El Rami, F. Sathirachinda, A. Bell, J. C. James, M. L. Hori, S. S. Gross, E. R. Gambhir, S. S. 2021-09-01 doi:10.1101/2021.09.01.456741 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Intrinsic neural activity predisposes susceptibility to a body illusion ]]> https://biorxiv.org/content/10.1101/2021.09.18.460883v1?rss=1 Hsu, T.-Y. Zhou, J.-F. Northoff, G. Yeh, S.-L. Lane, T. J. 2021-09-20 doi:10.1101/2021.09.18.460883 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ ModelMatcher: A scientist-centric online platform to facilitate collaborations between stakeholders of rare and undiagnosed disease research ]]> https://biorxiv.org/content/10.1101/2021.09.30.462504v1?rss=1 Harnish, J. M. Li, L. Rogic, S. Poirier-Morency, G. Kim, S.-Y. Undiagnosed Diseases Network, Boycott, K. M. Wangler, M. F. Bellen, H. J. Hieter, P. Pavlidis, P. Liu, Z. Yamamoto, S. 2021-10-01 doi:10.1101/2021.09.30.462504 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ BDNF signaling in Hebbian and Stentian structural plasticity in the developing visual system ]]> https://biorxiv.org/content/10.1101/2021.10.07.463583v1?rss=1 Kutsarova, E. Schohl, A. Munz, M. Wang, A. Zhang, Y. Y. Bilash, O. M. Ruthazer, E. S. 2021-10-09 doi:10.1101/2021.10.07.463583 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ 14-3-3ζ constrains insulin secretion in pancreatic β-cells by regulating mitochondrial function ]]> https://biorxiv.org/content/10.1101/2021.10.17.464702v1?rss=1 Mugabo, Y. Zhao, C. Tan, J. J. Ghosh, A. Campbell, S. A. Fadzeyeva, E. Pare, F. Pan, S. S. Galipeau, M. Ast, J. Broichhagen, J. Hodson, D. J. Mulvihill, E. E. Petropoulos, S. Lim, G. E. 2021-10-17 doi:10.1101/2021.10.17.464702 Cold Spring Harbor Laboratory Press 2021-10-17 <![CDATA[ SOCS3-mediated activation of p53-p21-NRF2 axis and cellular adaptation to oxidative stress in SOCS1-deficient hepatocellular carcinoma ]]> https://biorxiv.org/content/10.1101/2021.10.21.465149v1?rss=1 Khan, M. M. Boufaied, N. Yeganeh, M. Ghosh, A. Kandhi, R. Bagheri, R. Petkiewicz, S. Sharma, A. Yoshimura, A. Ferbeyre, G. Labbe, D. P. Ramanathan, S. Ilangumaran, S. 2021-10-21 doi:10.1101/2021.10.21.465149 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ Mapping neurotransmitter systems to the structural and functional organization of the human neocortex ]]> https://biorxiv.org/content/10.1101/2021.10.28.466336v1?rss=1 1 200 healthy individuals to construct a whole-brain 3-D normative atlas of 19 receptors and transporters across 9 different neurotransmitter systems. We find that receptor profiles align with structural connectivity and mediate function, including neurophysiological oscillatory dynamics and resting state hemodynamic functional connectivity. Using the Neurosynth cognitive atlas, we uncover a topographic gradient of overlapping receptor distributions that separates extrinsic and intrinsic psychological processes. Finally, we find both expected and novel associations between receptor distributions and cortical thinning patterns across 13 disorders. We replicate all findings in an independently collected autoradiography dataset. This work demonstrates how chemoarchitecture shapes brain structure and function, providing a new direction for studying multi-scale brain organization. ]]> Hansen, J. Y. Shafiei, G. Markello, R. D. Smart, K. Cox, S. M. Wu, Y. Gallezot, J.-D. Aumont, E. Servaes, S. Scala, S. G. Dubois, J. M. Wainstein, G. Bezgin, G. Funck, T. Schmitz, T. W. Spreng, R. N. Soucy, J.-P. Baillet, S. Guimond, S. Hietala, J. Bedard, M.-A. Leyton, M. Kobayashi, E. Rosa-Neto, P. Palomero-Gallagher, N. Shine, J. Carson, R. E. Tuominen, L. Dagher, A. Misic, B. 2021-10-30 doi:10.1101/2021.10.28.466336 Cold Spring Harbor Laboratory Press 2021-10-30 <![CDATA[ Quality-controlled R-loop meta-analysis reveals the characteristics of R-Loop consensus regions ]]> https://biorxiv.org/content/10.1101/2021.11.01.466823v1?rss=1 Miller, H. Montemayor, D. Abdul, J. Vines, A. Levy, S. Sharma, K. Frost, B. Chedin, F. Bishop, A. J. 2021-11-04 doi:10.1101/2021.11.01.466823 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Central and peripheral delivery of AAV9-SMN target different pathomechanisms in a mouse model of spinal muscular atrophy ]]> https://biorxiv.org/content/10.1101/2021.11.08.467795v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@1e4e882org.highwire.dtl.DTLVardef@15ccf93org.highwire.dtl.DTLVardef@3fe393org.highwire.dtl.DTLVardef@75cc20_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Reilly, A. N. Deguise, M. Beauvais, A. Yaworski, R. Thebault, S. Tessier, D. R. Tabard-Cossa, V. Hensel, N. Schneider, B. L. Kothary, R. 2021-11-08 doi:10.1101/2021.11.08.467795 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ Correspondence between gene expression and neurotransmitter receptor and transporter density in the human brain ]]> https://biorxiv.org/content/10.1101/2021.11.30.469876v1?rss=1 Hansen, J. Y. Markello, R. D. Tuominen, L. Norgaard, M. Kuzmin, E. Palomero-Gallagher, N. Dagher, A. Misic, B. 2021-12-02 doi:10.1101/2021.11.30.469876 Cold Spring Harbor Laboratory Press 2021-12-02 <![CDATA[ Brain responses in aggression-prone individuals: A systematic review and meta-analysis of functional magnetic resonance imaging (fMRI) studies of anger- and aggression-eliciting tasks ]]> https://biorxiv.org/content/10.1101/2022.01.11.475895v1?rss=1 Nikolic, M. Pezzoli, P. Jaworska, N. Seto, M. C. 2022-01-12 doi:10.1101/2022.01.11.475895 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ SARS-CoV-2 impairs interferon production via NSP2-induced repression of mRNA translation ]]> https://biorxiv.org/content/10.1101/2022.01.19.476693v1?rss=1 Choi, J.-H. Zhang, X. Zhang, C. Dai, D. L. Luo, J. Ladak, R. Li, Q. Wiebe, S. Liu, A. C. H. Ran, X. Yang, J. Naeli, P. Garzia, A. Zhou, L. Mahmood, N. Deng, Q. Elaish, M. Lin, R. Hobman, T. Pelletier, J. Alain, T. Vidal, S. Duchaine, T. Mazhab-Jafari, M. Mao, X. Jafarnejad, S. M. Sonenberg, N. 2022-01-20 doi:10.1101/2022.01.19.476693 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Temporal Optimization of Radiation Therapy to Heterogeneous Tumour Populations and Cancer Stem Cells ]]> https://biorxiv.org/content/10.1101/2022.01.26.477741v1?rss=1 Meaney, C. Kohandel, M. Novruzi, A. 2022-01-28 doi:10.1101/2022.01.26.477741 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Ingestion of microplastic fibres, but not microplastic beads, impacts growth rates in the tropical house cricket Gryllodes sigillatus ]]> https://biorxiv.org/content/10.1101/2022.02.07.479438v1?rss=1 Fudlosid, S. Ritchie, M. W. Muzzatti, M. J. Allison, J. E. Provencher, J. MacMillan, H. A. 2022-02-10 doi:10.1101/2022.02.07.479438 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ The Voices of Medical Education Science: Describing the Published Landscape ]]> https://biorxiv.org/content/10.1101/2022.02.10.479930v1?rss=1 Maggio, L. Costello, J. Ninkov, A. Frank, J. Artino, A. R. 2022-02-10 doi:10.1101/2022.02.10.479930 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Stable working memory and perceptual representations in macaque lateral prefrontal cortex during naturalistic vision in virtual environments ]]> https://biorxiv.org/content/10.1101/2022.03.24.485710v1?rss=1 Roussy, M. Corrigan, B. W. Luna, R. Gulli, R. A. Sachs, A. J. Palaniyappan, L. Martinez-Trujillo, J. C. 2022-03-27 doi:10.1101/2022.03.24.485710 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ GliaMorph: A modular image analysis toolkit to quantify Müller glial cell morphology ]]> https://biorxiv.org/content/10.1101/2022.05.05.490765v1?rss=1 View larger version (73K): org.highwire.dtl.DTLVardef@198fca6org.highwire.dtl.DTLVardef@f319fcorg.highwire.dtl.DTLVardef@2f0fadorg.highwire.dtl.DTLVardef@1ae4ce7_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIGlial morphology is complex, making it challenging to accurately quantify 3D cell shape. C_LIO_LIWe developed the GliaMorph toolkit for image pre-processing, glial segmentation, and quantification of Muller glial cells. C_LIO_LIMuller glia elaborate their morphology and rearrange subcellular features during embryonic development. C_LIO_LIGliaMorph accurately identifies subcellular changes in models with disrupted glia cells, including zebrafish cadherin2 loss of function and a mouse glaucoma model. C_LI ]]> Kugler, E. C. Bravo, I. Durmishi, X. Marcotti, S. Beqiri, S. Carrington, A. Stramer, B. C. Mattar, P. MacDonald, R. B. 2022-05-05 doi:10.1101/2022.05.05.490765 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Cholecystokinin-expressing (CCK+) basket cells are key controllers of theta-gamma coupled rhythms in the hippocampus ]]> https://biorxiv.org/content/10.1101/2022.06.01.494440v1?rss=1 Chatzikalymniou, A. Sengupta, S. Lefebvre, J. Skinner, F. 2022-06-03 doi:10.1101/2022.06.01.494440 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ The development of intracytoplasmic membranes in alphaproteobacteria involves the conserved mitochondrial crista-developing Mic60 protein ]]> https://biorxiv.org/content/10.1101/2022.06.14.496148v1?rss=1 Munoz-Gomez, S. A. Cadena, L. R. Gardiner, A. T. Leger, M. M. Sheikh, S. Connell, L. Bily, T. Kopejtka, K. Beatty, J. T. Koblizek, M. Roger, A. J. Slamovits, C. H. Lukes, J. Hashimi, H. 2022-06-17 doi:10.1101/2022.06.14.496148 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ PTEN and BRCA1 tumor suppressor loss associated tumor immune microenvironment exhibits differential response to therapeutic STING pathway activation in a murine model of ovarian cancer ]]> https://biorxiv.org/content/10.1101/2022.06.27.497846v1?rss=1 Shakfa, N. Li, D. Conseil, G. Lightbody, E. D. Wilson-Sanchez, J. Hamade, A. Chenard, S. Laight, B. J. Asante, A. Tyryshkin, K. Köbel, M. Koti, M. 2022-07-01 doi:10.1101/2022.06.27.497846 Cold Spring Harbor Laboratory Press 2022-07-01 <![CDATA[ Early Electrophysiological Aberrations in the Hippocampus of the TgF344-AD Rat Model as a Potential Biomarker for Alzheimer's Disease Prognosis ]]> https://biorxiv.org/content/10.1101/2022.07.01.498373v1?rss=1 Moradi, F. van den Berg, M. Mirjebreili, M. Kosten, L. Verhoye, M. Amiri, M. Keliris, G. A. 2022-07-03 doi:10.1101/2022.07.01.498373 Cold Spring Harbor Laboratory Press 2022-07-03 <![CDATA[ Regulation of TRIB1 abundance in hepatoma models ]]> https://biorxiv.org/content/10.1101/2022.07.07.499132v1?rss=1 Soubeyrand, S. McPherson, R. Lau, P. 2022-07-07 doi:10.1101/2022.07.07.499132 Cold Spring Harbor Laboratory Press 2022-07-07 <![CDATA[ Neural sequences in primate prefrontal cortex encode working memory in naturalistic environments ]]> https://biorxiv.org/content/10.1101/2022.08.18.504406v1?rss=1 Roussy, M. Busch, A. Luna, R. Leavitt, M. Mofrad, M. H. Gulli, R. A. Corrigan, B. Minac, J. Sachs, A. J. Palaniyappan, L. Muller, L. W. Martinez-Trujillo, J. C. 2022-08-18 doi:10.1101/2022.08.18.504406 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ Pten regulates endocytic trafficking of cell adhesion and signaling molecules to pattern the retina ]]> https://biorxiv.org/content/10.1101/2022.08.31.506085v1?rss=1 Touahri, Y. Hanna, J. Tachibana, N. David, L. A. Olender, T. Okawa, S. Chinchalongporn, V. Balakrishnan, A. Cantrup, R. Dixit, R. Mattar, P. Saleh, F. Ilnytskyy, Y. Murshed, M. Mains, P. Kovalchuk, I. Lefebvre, J. Cayouette, M. del Sol, A. Brand, M. Reese, B. E. Schuurmans, C. 2022-09-03 doi:10.1101/2022.08.31.506085 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Irx1 and Irx2 play dose-dependent cooperative functions in mammalian development ]]> https://biorxiv.org/content/10.1101/2022.10.03.510739v1?rss=1 Sheybani-Deloui, S. Xu, L. Hu, L. Yuan, Q. Son, J. E. Son, J. E. Kim, K.-H. Liu, W. Mo, R. Zhang, X. Chi, L. Delgado Olguin, P. Hui, C.-C. 2022-10-04 doi:10.1101/2022.10.03.510739 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ Vector diversity and malaria prevalence: global trends and local determinants ]]> https://biorxiv.org/content/10.1101/2022.10.13.512182v1?rss=1 Hoi, A. G. Gilbert, B. Mideo, N. 2022-10-14 doi:10.1101/2022.10.13.512182 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ Patterns of community science data use in peer-reviewed research on biodiversity ]]> https://biorxiv.org/content/10.1101/2022.10.17.512636v1?rss=1 Binley, A. D. Vincent, J. Rytwinski, T. Proctor, C. Urness, E. Davis, S. Soroye, P. Bennett, J. R. 2022-10-21 doi:10.1101/2022.10.17.512636 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ SARS-CoV-2 vaccine-breakthrough infections (VBIs) by Omicron (B.1.1.529) variant and consequences in structural and functional impact ]]> https://biorxiv.org/content/10.1101/2022.12.12.520021v1?rss=1 Abduljaleel, Z. Melebari, S. Dehlawi, S. Kumar S, U. Aziz, S. A. Dannoun, A. I. Malik, S. M. Doss C, G. P. 2022-12-14 doi:10.1101/2022.12.12.520021 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ Robust hierarchically organized whole-brain patterns of dysconnectivity in schizophrenia spectrum disorders observed after Personalized Intrinsic Network Topography ]]> https://biorxiv.org/content/10.1101/2022.12.13.520333v1?rss=1 Dickie, E. W. Shahab, S. Hawco, C. Miranda, D. Herman, G. Argyelan, M. Ji, J. L. W. Jeyachandra, J. Anticevic, A. Malhotra, A. K. Voineskos, A. N. 2022-12-15 doi:10.1101/2022.12.13.520333 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Base editing as a genetic treatment for spinal muscular atrophy ]]> https://biorxiv.org/content/10.1101/2023.01.20.524978v1?rss=1 Alves, C. R. R. Ha, L. L. Yaworski, R. Lazzarotto, C. R. Christie, K. A. Reilly, A. Beauvais, A. Doll, R. M. de la Cruz, D. Maguire, C. A. Swoboda, K. J. Tsai, S. Q. Kothary, R. Kleinstiver, B. P. 2023-01-21 doi:10.1101/2023.01.20.524978 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ Functional Connectivity of the Cerebellar Vermis in Bipolar Disorder and Associations with Mood ]]> https://biorxiv.org/content/10.1101/2023.02.02.526878v1?rss=1 Saleem, A. Harmata, G. Jain, S. Voss, M. W. Fiedorowicz, J. G. Williams, A. J. Shaffer, J. J. Richards, J. G. Barsotti, E. J. Sathyaputri, L. Schmitz, S. L. Christensen, G. E. Long, J. D. Xu, J. Wemmie, J. A. Magnotta, V. 2023-02-02 doi:10.1101/2023.02.02.526878 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ Cerebellar Morphological Differences in Bipolar Disorder Type I ]]> https://biorxiv.org/content/10.1101/2023.02.20.528549v1?rss=1 Harmata, G. I. S. Barsotti, E. J. Casten, L. G. Fiedorowicz, J. G. Williams, A. J. Shaffer, J. J. Richards, J. G. Sathyaputri, L. Schmitz, S. L. Christensen, G. E. Long, J. D. Gaine, M. E. Xu, J. Michaelson, J. J. Wemmie, J. A. Magnotta, V. A. 2023-02-21 doi:10.1101/2023.02.20.528549 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Genetic dysregulation of an endothelial Ras signaling network in vein of Galen malformations ]]> https://biorxiv.org/content/10.1101/2023.03.18.532837v1?rss=1 Zhao, S. Mekbib, K. Y. van der Ent, M. A. Allington, G. Prendergast, A. Chau, J. E. Smith, H. Shohfi, J. Ocken, J. Duran, D. Furey, C. G. Le, H. T. Duy, P. Q. Reeves, B. C. Zhang, J. Nelson-Williams, C. Chen, D. Li, B. Nottoli, T. Bai, S. Rolle, M. Zeng, X. Dong, W. Fu, P.-Y. Wang, Y.-C. Mane, S. Piwowarczyk, P. Fehnel, K. P. See, A. P. Iskandar, B. J. Aagaard-Kienitz, B. Kundishora, A. J. DeSpenza, T. Greenberg, A. B. W. Kidanemariam, S. M. Prendergast, A. Johnston, J. M. Jackson, E. Storm, P. B. Lang, S.-S. Butler, W. E. Carter, B. S. Chapman, P. St 2023-03-22 doi:10.1101/2023.03.18.532837 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ Expanding Interdisciplinarity: A bibliometric study of medical education using the MEJ-24 ]]> https://biorxiv.org/content/10.1101/2023.03.22.533841v1?rss=1 Maggio, L. Costello, J. A. Ninkov, A. Frank, J. Artino, A. R. 2023-03-24 doi:10.1101/2023.03.22.533841 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ A common flanking variant is associated with enhanced meiotic stability of the FGF14-SCA27B locus ]]> https://biorxiv.org/content/10.1101/2023.05.11.540430v1?rss=1 Pellerin, D. Del Gobbo, G. Couse, M. Dolzhenko, E. Dicaire, M.-J. Rebelo, A. Roth, V. Wandzel, M. Bonnet, C. Ashton, C. Lamont, P. J. Laing, N. G. Renaud, M. Ravenscroft, G. Houlden, H. Synofzik, M. Eberle, M. A. Boycott, K. M. Pastinen, T. Brais, B. Zuchner, S. Danzi, M. C. 2023-05-14 doi:10.1101/2023.05.11.540430 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ The variable domain from the mitochondrial fission mechanoenzyme Drp1 promotes liquid-liquid phase separation ]]> https://biorxiv.org/content/10.1101/2023.05.29.542732v1?rss=1 Posey, A. E. Bagheri, M. Ross, K. A. Lanum, E. N. Khan, M. A. Jennings, C. M. Harwig, M. C. Kennedy, N. W. Hilser, V. J. Harden, J. L. Hill, R. B. 2023-05-29 doi:10.1101/2023.05.29.542732 Cold Spring Harbor Laboratory Press 2023-05-29 <![CDATA[ Preserved striatal innervation and motor function despite severe loss of nigral dopamine neurons following mitochondrial dysfunction induced by mtDNA mutations ]]> https://biorxiv.org/content/10.1101/2023.07.07.547791v1?rss=1 Pass, T. Ricke, K. M. Hofmann, P. Chowdhury, R. Nie, Y. Chinnery, P. F. Endepols, H. Neumaier, B. Carvalho, A. Rigoux, L. Steculorum, S. Prudent, J. Riemer, T. Aswendt, M. Brachvogel, B. Wiesner, R. J. 2023-07-08 doi:10.1101/2023.07.07.547791 Cold Spring Harbor Laboratory Press 2023-07-08 <![CDATA[ Registered report: Age-preserved semantic memory and the CRUNCH effect manifested as differential semantic control networks: an fMRI study ]]> https://biorxiv.org/content/10.1101/2023.07.19.549657v1?rss=1 Haitas, N. Dubuc, J. Masse-Leblanc, C. Chamberland, V. Amiri, M. Glatard, T. Wilson, M. Joanette, Y. Steffener, J. 2023-07-19 doi:10.1101/2023.07.19.549657 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ C24 sphingolipids play a surprising and central role in governing cholesterol and lateral organization of the live cell plasma membrane ]]> https://biorxiv.org/content/10.1101/212142v1?rss=1 Courtney, K. C. Pezeshkian, W. Raghupathy, R. Zhang, G. Darbyson, A. Ipsen, J. H. Ford, D. A. Khandelia, H. Presley, J. F. Zha, X. 2017-10-31 doi:10.1101/212142 Cold Spring Harbor Laboratory Press 2017-10-31 <![CDATA[ Niche separation increases with genetic distance among bloom-forming cyanobacteria ]]> https://biorxiv.org/content/10.1101/226860v1?rss=1 Tromas, N. Taranu, Z. E. Martin, B. D. Willis, A. Fortin, N. Greer, C. W. Shapiro, B. J. 2017-11-29 doi:10.1101/226860 Cold Spring Harbor Laboratory Press 2017-11-29 <![CDATA[ Regulation of ATR activity by the RNA polymerase II phosphatase PNUTS-PP1 ]]> https://biorxiv.org/content/10.1101/267013v1?rss=1 Landsverk, H. B. Sandquist, L. E. Rodland, G. E. Grallert, B. Trinkle-Mulcahy, L. Syljuasen, R. G. 2018-02-16 doi:10.1101/267013 Cold Spring Harbor Laboratory Press 2018-02-16 <![CDATA[ ProtaBank: A repository for protein design and engineering data ]]> https://biorxiv.org/content/10.1101/272211v1?rss=1 Wang, C. Y. Chang, P. M. Ary, M. L. Allen, B. D. Chica, R. A. Mayo, S. L. Olafson, B. D. 2018-02-26 doi:10.1101/272211 Cold Spring Harbor Laboratory Press 2018-02-26 <![CDATA[ Microbiome inhibition of IRAK-4 by trimethylamine mediates metabolic and immune benefits in high-fat-diet-induced insulin resistance ]]> https://biorxiv.org/content/10.1101/277434v1?rss=1 Chilloux, J. Brial, F. Everard, A. Smyth, D. Zhang, L. Plovier, H. Myridakis, A. Hoyles, L. Fuchs, J. E. Blancher, C. Gencer, S. Martinez-Gili, L. Fearnside, J. F. Barton, R. H. Neves, A. L. Rothwell, A. R. Gerard, C. Calderari, S. Boulange, C. L. Patel, S. Scott, J. Glen, R. C. Gooderham, N. J. Nicholson, J. K. Gauguier, D. Liu, P. P. Cani, P. D. Dumas, M.-E. E. 2018-03-07 doi:10.1101/277434 Cold Spring Harbor Laboratory Press 2018-03-07 <![CDATA[ Time dependence of cellular responses to dynamic and complex strain fields ]]> https://biorxiv.org/content/10.1101/286625v1?rss=1 Chagnon-Lessard, S. Godin, M. Pelling, A. E. 2018-03-22 doi:10.1101/286625 Cold Spring Harbor Laboratory Press 2018-03-22 <![CDATA[ Biallelic Mutations in LRRC56 encoding a protein associated with intraflagellar transport, cause mucociliary clearance and laterality defects ]]> https://biorxiv.org/content/10.1101/288852v1?rss=1 Bonnefoy, S. Watson, C. Kernohan, K. Lemos, M. Hutchinson, S. Poulter, J. Crinion, L. O'Callaghan, C. Hirst, R. Rutman, A. Huang, L. Hartley, T. Grynspan, D. Moya, E. Li, C. Carr, I. Bonthron, D. Leroux, M. Care4Rare Canada Consortium, Boycott, K. Bastin, P. Sheridan, E. 2018-03-27 doi:10.1101/288852 Cold Spring Harbor Laboratory Press 2018-03-27 <![CDATA[ The Growth Hormone Secretagogue Receptor, Ghrelin and Biochemical Signaling Molecules in Human Heart Failure ]]> https://biorxiv.org/content/10.1101/362525v1?rss=1 Sullivan, R. Randhawa, V. Stokes, A. Wu, D. Lalonde, T. Kiaii, B. Luyt, L. Wisenberg, G. Dhanvantari, S. 2018-07-04 doi:10.1101/362525 Cold Spring Harbor Laboratory Press 2018-07-04 <![CDATA[ Identification of rare-disease genes in diverse undiagnosed cases using whole blood transcriptome sequencing and large control cohorts ]]> https://biorxiv.org/content/10.1101/408492v1?rss=1 Fresard, L. Smail, C. Smith, K. S. Ferraro, N. M. Teran, N. A. Kernohan, K. D. Bonner, D. Li, X. Marwaha, S. Zappala, Z. Balliu, B. Davis, J. R. Liu, B. Prybol, C. J. Kholer, J. N. Zastrow, D. B. Fisk, D. G. Grove, M. E. Davidson, J. M. Hartley, T. Joshi, R. Strober, B. J. Utiramerur, S. Care4Rare Canada Consortium, Undiagnosed Diseases Network, Lind, L. Ingelsson, E. Battle, A. Bejerano, G. Bernstein, J. A. Ashley, E. A. Boycott, K. M. Merker, J. D. Wheeler, M. T. Montgomery, S. B. 2018-09-04 doi:10.1101/408492 Cold Spring Harbor Laboratory Press 2018-09-04 <![CDATA[ Process-specific somatic mutation distributions vary with three-dimensional genome structure ]]> https://biorxiv.org/content/10.1101/426080v1?rss=1 Akdemir, K. C. Le, V. T. Killcoyne, S. King, D. A. Li, Y.-P. Lian, Y. Inoue, A. Amin, S. Robinson, F. S. Herrera, R. E. Lynn, E. J. Chan, K. Seth, S. Klimczak, L. J. Gerstung, M. Gordenin, D. A. O'Brien, J. Li, L. Verhaak, R. G. Campbell, P. Fitzgerald, R. Morrison, A. J. Dixon, J. R. Futreal, A. 2018-09-25 doi:10.1101/426080 Cold Spring Harbor Laboratory Press 2018-09-25 <![CDATA[ Cell-type-specific methylome-wide association studies implicate neurodegenerative processes and neuroimmune communication in major depressive disorder ]]> https://biorxiv.org/content/10.1101/432088v1?rss=1 Chan, R. F. Turecki, G. Shabalin, A. A. Guintivano, J. Zhao, M. Xie, L. Y. van Grootheest, G. Kaminsky, Z. A. Dean, B. Penninx, B. W. J. H. Aberg, K. A. van den Oord, E. J. C. G. 2018-10-03 doi:10.1101/432088 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ Would conserving natural land cover in landscapes conserve biodiversity? ]]> https://biorxiv.org/content/10.1101/436410v1?rss=1 De Camargo, R. X. Currie, D. 2018-10-05 doi:10.1101/436410 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ TCF7L1 and TCF7 differentially regulate specific mouse ES cell genes in response to GSK-3 inhibition ]]> https://biorxiv.org/content/10.1101/473801v1?rss=1 Moreira, S. Seo, C. Polena, E. Mahendram, S. Mercier, E. Blais, A. Doble, B. 2018-11-21 doi:10.1101/473801 Cold Spring Harbor Laboratory Press 2018-11-21 <![CDATA[ Genetic association analyses highlight IL6, ALPL, and NAV1 as three new susceptibility genes underlying calcific aortic valve stenosis ]]> https://biorxiv.org/content/10.1101/515494v1?rss=1 Theriault, S. Dina, C. Messika-Zeitoun, D. Le Scouarnec, S. Capoulade, R. Gaudreault, N. Rigade, S. Li, Z. Simonet, F. Lamontagne, M. Clavel, M.-A. Arsenault, B. J. Boureau, A.-S. Lecointe, S. Baron, E. Bonnaud, S. Karakachoff, M. Charpentier, E. Fellah, I. Roussel, J.-C. Verhoye, J. P. Baufreton, C. Probst, V. Roussel, R. D.E.S.I.R. Study Group, Redon, R. Dagenais, F. Pibarot, P. Mathieu, P. Le Tourneau, T. Bosse, Y. Schott, J.-J. 2019-01-11 doi:10.1101/515494 Cold Spring Harbor Laboratory Press 2019-01-11 <![CDATA[ A large-scale multivariate pQTL study sheds light on the genetic architecture of obesity ]]> https://biorxiv.org/content/10.1101/524405v1?rss=1 80% replicate in the second independent cohort and have significant enrichment with functional genomic elements and disease risk loci. Moreover, 78% of the pQTLs whose protein abundance was quantified by both proteomic techniques are confirmed across assays. Our thorough comparisons with standard univariate QTL mapping on (1) these data and (2) synthetic data emulating the real data show how LOCUS borrows strength across correlated protein levels and markers on a genome-wide scale to effectively increase statistical power. Notably, 15% of the pQTLs uncovered by LOCUS would be missed by the univariate approach, including several trans and pleiotropic hits with successful independent validation. Finally, the analysis of extensive clinical data from the two cohorts indicates that the genetically-driven proteins identified by LOCUS are enriched in associations with low-grade inflammation, insulin resistance and dyslipidemia and might therefore act as endophenotypes for metabolic diseases. While considerations on the clinical role of the pQTLs are beyond the scope of our work, these findings generate useful hypotheses to be explored in future research; all results are accessible online from our searchable database. Thanks to its efficient variational Bayes implementation, LOCUS can analyse jointly thousands of traits and millions of markers. Its applicability goes beyond pQTL studies, opening new perspectives for large-scale genome-wide association and QTL analyses. Author summaryExploring the functional mechanisms between the genotype and disease endpoints in view of identifying innovative therapeutic targets has prompted molecular quantitative trait locus studies, which assess how genetic variants (single nucleotide polymorphisms, SNPs) affect intermediate gene (eQTL), protein (pQTL) or metabolite (mQTL) levels. However, conventional univariate screening approaches do not account for local dependencies and association structures shared by multiple molecular levels and markers. Conversely, the current joint modelling approaches are restricted to small datasets by computational constraints. We illustrate and exploit the advantages of our recently introduced Bayesian framework LOCUS in a fully multivariate pQTL study, with {approx} 300K tag SNPs (capturing information from 4M markers) and 100 - 1,000 plasma protein levels measured by two distinct technologies. LOCUS identifies novel pQTLs that replicate in an independent cohort, confirms signals documented in studies 2 - 18 times larger, and detects more pQTLs than a conventional two-stage univariate analysis of our datasets. Moreover, some of these pQTLs might be of biomedical relevance and would therefore deserve dedicated investigation. Our extensive numerical experiments on these data and on simulated data demonstrate that the increased statistical power of LOCUS over standard approaches is largely attributable to its ability to exploit shared information across outcomes while efficiently accounting for the genetic correlation structures at a genome-wide level. ]]> Ruffieux, H. Carayol, J. Harper, M. E. Dent, R. Saris, W. Astrup, A. Davison, A. Hager, J. Valsesia, A. 2019-01-18 doi:10.1101/524405 Cold Spring Harbor Laboratory Press 2019-01-18 <![CDATA[ A missense variant in Mitochondrial Amidoxime Reducing Component 1 gene and protection against liver disease ]]> https://biorxiv.org/content/10.1101/594523v1?rss=1 Emdin, C. A. Haas, M. Khera, A. V. Aragam, K. Chaffin, M. Jiang, L. Wei, W.-Q. Feng, Q. Karjalainen, J. Havulinna, A. Kiiskinen, T. Bick, A. Ardissino, D. Wilson, J. G. Schunkert, H. McPherson, R. Watkins, H. Elosua, R. Bown, M. J. Samani, N. J. Baber, U. Erdmann, J. Gupta, N. Danesh, J. Saleheen, D. Daly, M. Denny, J. Gabriel, S. Kathiresan, S. 2019-03-31 doi:10.1101/594523 Cold Spring Harbor Laboratory Press 2019-03-31 <![CDATA[ Infection-driven activation of transglutaminase 2 boosts glucose uptake and hexosamine biosynthesis ]]> https://biorxiv.org/content/10.1101/634501v1?rss=1 Maffei, B. Laverriere, M. Wu, Y. Triboulet, S. Perrinet, S. Duchateau, M. Matondo, M. Hollis, R. L. Gourley, C. Rupp, J. Keillor, J. W. Subtil, A. 2019-05-10 doi:10.1101/634501 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ An improved method for culturing myotubes on laminins for the robust clustering of postsynaptic machinery ]]> https://biorxiv.org/content/10.1101/664268v1?rss=1 Pezinski, M. Daszczuk, P. Pradhan, B. S. Lochmuller, H. Proszynski, T. J. 2019-06-07 doi:10.1101/664268 Cold Spring Harbor Laboratory Press 2019-06-07 <![CDATA[ Serological and metagenomic interrogation of cerebrospinal fluid implicates enteroviruses in pediatric acute flaccid myelitis ]]> https://biorxiv.org/content/10.1101/666230v1?rss=1 Schubert, R. D. Hawes, I. Ramachandran, P. S. Ramesh, A. Crawford, E. D. Pak, J. E. Wu, W. Cheung, C. K. O'Donovan, B. D. Tato, C. M. Lyden, A. Tan, M. Sit, R. Sowa, G. Sample, H. A. Zorn, K. C. Banerji, D. Khan, L. M. Bove, R. Hauser, S. L. Gelfand, A. A. Johnson-Kerner, B. Nash, K. Krishnamoorthy, K. S. Chitnis, T. Ding, J. Z. McMillan, H. J. Chiu, C. Y. Briggs, B. Glaser, C. A. Yen, C. Chu, V. Wadford, D. A. Dominguez, S. R. Ng, T. F. F. Marine, R. L. Lopez, A. S. Nix, W. A. Soldatos, A. Gorman, M. Benson, L. Messacar, K. Konopka-Anstadt, J. L. Ob 2019-06-10 doi:10.1101/666230 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Adding MASP1 to the lectin pathway - leprosy association puzzle: hints from gene polymorphisms and protein levels. ]]> https://biorxiv.org/content/10.1101/666909v1?rss=1 A and rs13064994*C>T, exon 12 3-untranslated rs72549262*C>G, rs1109452*C>T and rs850314*G>A) and measured MASP-1, MASP-3 and MAp44 serum levels in 196 leprosy patients (60%, lepromatous) and 193 controls.nnPrincipal findingsLower MASP-3 and MAp44 levels were observed in patients, compared with controls (P=0.0002 and P<0.0001, respectively) and in lepromatous, compared with non-lepromatous patients (P=0.008 and P=0.002, respectively). Higher MASP-3 levels occurred in controls carrying variants/haplotypes associated with leprosy resistance (rs13064994*T, rs1109452_rs850314*CG within GT_CCG and rs850314*A: OR=0.5-0.6, Pcorr=0.01-0.04). Controls with rs1109452*T, included in susceptibility haplotypes (GT_GTG/GT_CTG: OR=2.0, Pcorr=0.03), had higher MASP-1 and lower MASP-3 levels (P[≤]0.009). Those with GC_CCG, presented increasing susceptibility (OR=1.7, Pcorr=0.006) and had higher MAp44 levels (P=0.015). MASP-3 expression decreased in patients, compared with controls carrying rs1109452_rs850314*CA or CG (P[≤]0.02), which may rely on exon 12 CpG methylation and/or miR-2861/miR-3181 mRNA binding.nnConclusionPolymorphisms regulating MASP-3/MAp44 availability in serum modulate leprosy susceptibility, underlining the importance of lectin pathway regulation against pathogens that exploit phagocytosis to parasitize host macrophages.nnAuthor summarySince immemorial times, Mycobacterium leprae inflicts permanent injuries in human kind, within a wide symptomatic spectrum ranging from insensitive skin patches to disabling physical lesions. Innate resistance to this parasite is well recognized, but poorly understood. The complement system is one of the most important arms of the innate response, and several lines of evidence indicate that it may be usurped by the parasite to enhance its entrance into host cells. These include our recent work on genetic association of the disease with lectin pathway components and the complement receptor CR1, whose polymorphisms modulate susceptibility to infection and clinical presentation. Here, we add another pivotal piece in the leprosy parasite-host interaction puzzle: polymorphisms and serum levels of three different lectin pathway proteins, all encoded by the same gene, namely mannan-binding lectin-associated serine protease 1 (MASP1). We found lower levels of two of these proteins, MASP-3 and MAp44, in leprosy patients. Higher MASP-3/lower MASP-1 levels were associated with protective haplotypes, containing two side-by-side polymorphisms located in the exclusive untranslated region of MASP-3 exon 12, which may regulate exon splicing and/or translation efficiency. The associations revealed in this study reflect the pleiotropic nature of this gene. They further illustrate the complexity of the response mounted against the parasite, which places MASP1 products in the regulatory crossroad between the innate and adaptive arms of the immunological system, modulating leprosy susceptibility. ]]> Weinschutz Mendes, H. C. Boldt, A. W. Stahlke, E. R. S. Jensenius, J. C. Thiel, S. Messias-Reason, I. J. T. 2019-06-11 doi:10.1101/666909 Cold Spring Harbor Laboratory Press 2019-06-11 <![CDATA[ Mathematics and the brain - a category theoretic approach to go beyond the neural correlates of consciousness ]]> https://biorxiv.org/content/10.1101/674242v1?rss=1 Northoff, G. Tsuchiya, N. Saigo, H. 2019-06-20 doi:10.1101/674242 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ The evolution of biotic and abiotic realized niches within freshwater Synechococcus ]]> https://biorxiv.org/content/10.1101/678375v1?rss=1 Tromas, N. Castelli, M. Taranu, Z. E. Pimentel, J. S. M. Pereira, D. A. Marcoz, R. Giani, A. Shapiro, B. J. 2019-06-21 doi:10.1101/678375 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ TSC2-deficiency potentiates a catabolic signaling switch that differentiates neural and neural crest lineage development and progressive disease manifestations ]]> https://biorxiv.org/content/10.1101/683359v1?rss=1 Delaney, S. P. Julian, L. M. Pietrobon, A. Yockell-Lelievre, J. Dore, C. Wang, T. T. Doyon, V. C. Raymond, A. Patten, D. A. Harper, M.-E. Sun, H. Stanford, W. L. 2019-06-27 doi:10.1101/683359 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Myf6/MRF4 is a Myogenic Niche Regulator Required for the Maintenance of the Muscle Stem Cell Pool ]]> https://biorxiv.org/content/10.1101/691386v1?rss=1 Lazure, F. Blackburn, D. M. Karam, N. Sahinyan, K. Nguyen, D. Sharanak, A. Corchado, A. H. Lepper, C. Najafabadi, H. S. Perkins, T. J. Jahani-Asl, A. Soleimani, V. 2019-07-03 doi:10.1101/691386 Cold Spring Harbor Laboratory Press 2019-07-03 <![CDATA[ High Resolution Genome Wide Expression Analysis of Single Myofibers Using SMART-Seq ]]> https://biorxiv.org/content/10.1101/724393v1?rss=1 Blackburn, D. M. Lazure, F. Perkins, T. J. Soleimani, V. D. 2019-08-05 doi:10.1101/724393 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ Microbial genomes retrieved from High Arctic lake sediments provision their microbes with genes to strive in cold and oligotrophic environments ]]> https://biorxiv.org/content/10.1101/724781v1?rss=1 Ruuskanen, M. Colby, G. St. Pierre, K. St. Louis, V. Aris-Brosou, S. Poulain, A. 2019-08-05 doi:10.1101/724781 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ The Secretome of Liver X Receptor Agonist Treated Early Outgrowth Cells Decreases Atherosclerosis in Ldlr-/- Mice ]]> https://biorxiv.org/content/10.1101/757435v1?rss=1 Rasheed, A. Shawky, S. Tsai, R. Jung, R. G. Simard, T. Hibbert, B. Rayner, K. J. Cummins, C. L. 2019-09-04 doi:10.1101/757435 Cold Spring Harbor Laboratory Press 2019-09-04 <![CDATA[ Heterozygous ATP-binding Cassette Transporter G5 Gene Deficiency and Risk of Coronary Artery Disease ]]> https://biorxiv.org/content/10.1101/780734v1?rss=1 Nomura, A. Emdin, C. A. Won, H.-H. Peloso, G. M. Natarajan, P. Ardissino, D. Danesh, J. Schunkert, H. Correa, A. Bown, M. J. Samani, N. J. Erdmann, J. McPherson, R. Watkins, H. Saleheen, D. Elosua, R. Kawashiri, M.-a. Tada, H. Gupta, N. Shah, S. H. Rader, D. J. Gabriel, S. Khera, A. V. Kathiresan, S. 2019-09-26 doi:10.1101/780734 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Deposition of Polycyclic Aromatic Hydrocarbons (PAHs) into Northern Ontario Lake Sediments ]]> https://biorxiv.org/content/10.1101/786913v1?rss=1 Colby, G. A. 2019-09-30 doi:10.1101/786913 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ Intrinsic Architecture of Global Signal Topography and Its Modulation by Tasks ]]> https://biorxiv.org/content/10.1101/798819v1?rss=1 Zhang, J. Huang, Z. Tumati, S. Northoff, G. 2019-10-09 doi:10.1101/798819 Cold Spring Harbor Laboratory Press 2019-10-09 <![CDATA[ Fatty acid oxidation impairs macrophage effector functions that control Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/799619v1?rss=1 Chandra, P. He, L. Zimmerman, M. Yang, G. Koster, S. Ouimet, M. Wang, H. Moore, K. J. Dartois, V. Schilling, J. D. Philips, J. A. 2019-10-10 doi:10.1101/799619 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Climate change and local host availability drive the northern range boundary in the rapid northward expansion of the eastern giant swallowtail butterfly ]]> https://biorxiv.org/content/10.1101/868125v1?rss=1 Wilson, J. K. Casajus, N. Hutchinson, R. A. McFarland, K. P. Kerr, J. T. Berteaux, D. Larrivee, M. Prudic, K. L. 2019-12-06 doi:10.1101/868125 Cold Spring Harbor Laboratory Press 2019-12-06 <![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[ 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[ Discovery of 2-amide-3-methylester thiophenes inhibiting SARS-CoV-2 ADP-ribosyl hydrolysing macrodomain and coronavirus replication ]]> https://biorxiv.org/content/10.1101/2023.08.28.555062v1?rss=1 Wazir, S. Parviainen, T. A. O. Maksimainen, M. M. Duong, M. T. H. Pfannenstiel, J. J. Cluff, D. Sowa, S. T. Galera-Prat, A. Ferraris, D. V. Fehr, A. Heiskanen, J. P. Lehtiö, L. 2023-08-29 doi:10.1101/2023.08.28.555062 Cold Spring Harbor Laboratory Press 2023-08-29 <![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[ 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[ 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[ 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[ 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[ 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[ 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[ Autophagy-dependent alternative splicing event produces a more stable ribosomal protein S24 isoform that aids in hypoxic cell survival ]]> https://biorxiv.org/content/10.1101/2023.09.25.559338v1?rss=1 Kerry, J. Specker, E. J. Mizzoni, M. Brumwell, A. Fell, L. Goodbrand, J. Rosen, M. N. Uniacke, J. 2023-09-25 doi:10.1101/2023.09.25.559338 Cold Spring Harbor Laboratory Press 2023-09-25 <![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[ 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[ 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[ Multiunit frontal eye field activity codes the visuomotor transformation, but not gaze prediction or target memory, in a delayed saccade task ]]> https://biorxiv.org/content/10.1101/2023.10.08.560888v1?rss=1 Seo, S. Bharmauria, V. Schuetz, A. Yan, X. Wang, H. Crawford, J. D. 2023-10-10 doi:10.1101/2023.10.08.560888 Cold Spring Harbor Laboratory Press 2023-10-10 <![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. Pistofidis, A. Ladak, R. J. An, Y. Alain, T. Schmeing, M. Gingras, A.-C. Duchaine, T. Zhang, X. Sonenberg, N. Jafarnejad, S. M. 2023-10-15 doi:10.1101/2023.10.14.562322 Cold Spring Harbor Laboratory Press 2023-10-15 <![CDATA[ Vicious cycle of hemodynamic perturbation and endothelial injury in development and progression of pulmonary arterial hypertension ]]> https://biorxiv.org/content/10.1101/2023.10.16.562339v1?rss=1 Deng, Y. Chaudhary, K. R. Yang, A. Kesavan, K. Wang, L. Chathely, K. Stewart, D. J. 2023-10-19 doi:10.1101/2023.10.16.562339 Cold Spring Harbor Laboratory Press 2023-10-19 <![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[ 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[ 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[ 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[ 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[ 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[ 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[ Cell-type specific contributions to theta-gamma coupled rhythms in the hippocampus ]]> https://biorxiv.org/content/10.1101/2024.03.05.583493v1?rss=1 Sengupta, S. Talidou, A. Lefebvre, J. Skinner, F. 2024-03-07 doi:10.1101/2024.03.05.583493 Cold Spring Harbor Laboratory Press 2024-03-07 <![CDATA[ Assessing fecal metaproteomics workflow and small protein recovery using DDA and DIA PASEF mass spectrometry ]]> https://biorxiv.org/content/10.1101/2024.03.13.584844v1?rss=1 Wang, A. Fekete, E. E. Creskey, M. Cheng, K. Ning, Z. Pfeifle, A. Li, X. Figeys, D. Zhang, X. 2024-03-14 doi:10.1101/2024.03.13.584844 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ MetaDIA: A Novel Database Reduction Strategy for DIA Human Gut Metaproteomics ]]> https://biorxiv.org/content/10.1101/2024.03.14.585104v1?rss=1 Duan, H. Ning, Z. Sun, Z. Guo, T. Sun, Y. Figeys, D. 2024-03-16 doi:10.1101/2024.03.14.585104 Cold Spring Harbor Laboratory Press 2024-03-16 <![CDATA[ GABA-ergic inhibition in human MT predicts visuo-spatial intelligence mediated by reverberation with frontal cortex ]]> https://biorxiv.org/content/10.1101/2024.03.20.585863v1?rss=1 Gao, Y. Cai, Y.-C. Liu, D.-Y. Yu, J. Wang, J. Li, M. Xu, B. Wang, T. Chen, G. Northoff, G. Bai, R. Song, X. 2024-03-22 doi:10.1101/2024.03.20.585863 Cold Spring Harbor Laboratory Press 2024-03-22 <![CDATA[ Identification of stress specific autophagy regulators from tandem CRISPR screens ]]> https://biorxiv.org/content/10.1101/2024.03.27.587008v1?rss=1 Losier, T. T. Rousseaux, M. W. C. Russell, R. C. 2024-03-27 doi:10.1101/2024.03.27.587008 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ The ER-phagy receptor FAM134B is targeted by Salmonella Typhimurium to promote infection ]]> https://biorxiv.org/content/10.1101/2024.03.28.587227v1?rss=1 Gatica, D. Alsaadi, R. M. El Hamra, R. Mueller, R. Miyazaki, M. Sad, S. Russell, R. 2024-03-29 doi:10.1101/2024.03.28.587227 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ A stress-dependent TDP-43 SUMOylation program preserves neuronal function ]]> https://biorxiv.org/content/10.1101/2024.04.12.589206v1?rss=1 Suk, T. R. Part, C. E. Nguyen, T. T. Zhang, J. L. Heer, M. M. Caballero-Gomez, A. Grybas, V. S. McKeever, P. M. Nguyen, B. Callaghan, S. M. Woulfe, J. M. Robertson, J. Rousseaux, M. W. C. 2024-04-13 doi:10.1101/2024.04.12.589206 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ Loss of VHL-mediated pRb regulation promotes clear cell renal cell carcinoma ]]> https://biorxiv.org/content/10.1101/2024.04.14.589424v1?rss=1 Russell, R. Akuma, M. Kim, M. Zhu, C. Wiljer, E. Gaudreau-Lapierre, A. Patterson, L. Trinkle-Mulcahy, L. Stanford, W. L. Riazalhosseini, Y. 2024-04-17 doi:10.1101/2024.04.14.589424 Cold Spring Harbor Laboratory Press 2024-04-17 <![CDATA[ Stabilizing transglutaminase 2 in the open conformation results in reactive astrocytes being more neurosupportive ]]> https://biorxiv.org/content/10.1101/2024.04.15.589192v1?rss=1 Emerson, J. Delgado, T. Hong, M. Keillor, J. W. Johnson, G. V. 2024-04-19 doi:10.1101/2024.04.15.589192 Cold Spring Harbor Laboratory Press 2024-04-19 <![CDATA[ Aldehydic load as an objective imaging biomarker of mild traumatic brain injury ]]> https://biorxiv.org/content/10.1101/2024.04.16.589820v1?rss=1 Kirby, A. Ward, C. Calvert, N. D. Daniel, R. Leung, J. W.-H. Shawma, A. Suchy, M. Donatelli, C. Wang, J. Standen, E. Shuhendler, A. J. 2024-04-16 doi:10.1101/2024.04.16.589820 Cold Spring Harbor Laboratory Press 2024-04-16 <![CDATA[ MetaX: A peptide centric metaproteomic data analysis platform using Operational Taxa-Functions (OTF) ]]> https://biorxiv.org/content/10.1101/2024.04.19.590315v1?rss=1 Wu, Q. Ning, Z. Zhang, A. Zhang, X. Sun, Z. Figeys, D. 2024-04-24 doi:10.1101/2024.04.19.590315 Cold Spring Harbor Laboratory Press 2024-04-24 <![CDATA[ Cellular and molecular changes in the human osteoarthritic and aging hip pulvinar ]]> https://biorxiv.org/content/10.1101/2024.04.21.590119v1?rss=1 Tilouche, B. Farhat, S. Short, S. Somyk, M. Beaule, P. Carsen, S. Grammatopoulos, G. Coutu, D. L. 2024-04-26 doi:10.1101/2024.04.21.590119 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ Delineating the functional activity of antibodies with cross-reactivity to SARS-CoV-2, SARS-CoV-1 and related sarbecoviruses ]]> https://biorxiv.org/content/10.1101/2024.04.24.590836v1?rss=1 Ruiz, F. Foreman, W. Lilly, M. Baharani, V. A. Depierreux, D. M. Chohan, V. Taylor, A. L. Guenthoer, J. Ralph, D. Matsen, F. A. Chu, H. Y. Bieniasz, P. D. Cote, M. Starr, T. N. Overbaugh, J. 2024-04-25 doi:10.1101/2024.04.24.590836 Cold Spring Harbor Laboratory Press 2024-04-25 <![CDATA[ Ancestral sequence reconstruction of Mic60 reveals a residue signature supporting respiration in yeast ]]> https://biorxiv.org/content/10.1101/2024.04.26.591372v1?rss=1 Benning, F. M. C. Bell, T. A. Nguyen, T. H. Syau, D. Connell, L. B. daCosta, C. J. B. Chao, L. H. 2024-04-29 doi:10.1101/2024.04.26.591372 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Dopey-dependent regulation of extracellular vesicles maintains neuronal morphology ]]> https://biorxiv.org/content/10.1101/2024.05.07.591898v1?rss=1 Park, S. Noblett, N. Pitts, L. Colavita, A. Wehman, A. M. Jin, Y. Chisholm, A. D. 2024-05-08 doi:10.1101/2024.05.07.591898 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Effect Of Ayahuasca on Experimental Models of Ethanol Addiction and Immunohistochemistry Analysis in Rodents ]]> https://biorxiv.org/content/10.1101/2024.05.07.592962v1?rss=1 0.05). ConclusionsAyahuasca was well tolerated at ceremonies-equivalent doses and blocked ethanol-induced-CPP across all doses, while {Delta}FosB levels in NAc were unchanged at 24h. Limitations on the CPP baseline and {Delta}FosB results may limit sensitivity, generalisability and interpretation. Findings provide preliminary evidence that ayahuasca-pretreatment may blunt ethanol-context preference, reinforcing the need of replication with stronger reward baselines, naive controls and complementary molecular markers. ]]> Distefano Wiltenburg, V. Morales-Lima, G. Sousa Santos, A. V. Echeverry Bermudez, M. Cardoso Cruz, F. de Oliveira Silveira, G. Yonamine, M. Ayako Tiba, P. Rieli Mendes, F. 2024-05-10 doi:10.1101/2024.05.07.592962 Cold Spring Harbor Laboratory Press 2024-05-10 <![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[ PhyloFunc: Phylogeny-informed Functional Distance as a New Ecological Metric for Metaproteomic Data Analysis ]]> https://biorxiv.org/content/10.1101/2024.05.28.596184v1?rss=1 Wang, L. Simopoulos, C. M. A. Serrana, J. M. Ning, Z. Sun, B. Yuan, J. Figeys, D. Li, L. 2024-06-02 doi:10.1101/2024.05.28.596184 Cold Spring Harbor Laboratory Press 2024-06-02 <![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[ Enhancing oncolytic virotherapy by exosome-mediated microRNA reprograming of the tumour microenvironment. ]]> https://biorxiv.org/content/10.1101/2024.06.07.597913v1?rss=1 Jennings, V. Rumbold-Hall, R. Migneco, G. Barr, T. Reilly, K. Ingram, N. St Hilare, I. Heaton, S. Alzamel, N. Jackson, D. Ralph, C. McNeish, I. Bell, J. C. Melcher, A. Ilkow, C. S. Cook, G. P. Errington-Mais, F. 2024-06-09 doi:10.1101/2024.06.07.597913 Cold Spring Harbor Laboratory Press 2024-06-09 <![CDATA[ Palytoxin Evokes Reversible Spreading Depolarization in the Locust CNS ]]> https://biorxiv.org/content/10.1101/2024.06.11.598415v1?rss=1 wang, y. Van Dusen, R. A. McGuire, C. Andrew, R. D. Robertson, M. 2024-06-11 doi:10.1101/2024.06.11.598415 Cold Spring Harbor Laboratory Press 2024-06-11 <![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[ 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[ CACHE Challenge #1: targeting the WDR domain of LRRK2, a Parkinson's Disease associated protein. ]]> https://biorxiv.org/content/10.1101/2024.07.18.603797v1?rss=1 Ackloo, S. Arrowsmith, C. H. Ban, F. Barden, C. J. Beck, H. Beranek, J. Berenger, F. Bolotokova, A. Bret, G. Breznik, M. Carosati, E. Chau, I. Chen, Y. Cherkasov, A. Della Corte, D. Denzinger, K. Dong, A. Draga, S. Dunn, I. Edfeldt, K. Edwards, A. Eguida, M. Eisenhuth, P. Friedrich, L. Fuerll, A. Gardiner, S. Gentile, F. Ghiabi, P. Gibson, E. Glavatskikh, M. Gorgulla, C. Guenther, J. Gunnarsson, A. Guseve, F. Gutkin, E. Hillisch, A. Hoffer, L. Hogner, A. Irwin, J. J. Isayev, O. Ivanova, A. Jacquemard, C. Jarrett, A. J. Jensen, J. H. Kireev, D. Klebe 2024-07-18 doi:10.1101/2024.07.18.603797 Cold Spring Harbor Laboratory Press 2024-07-18 <![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[ 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[ 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[ 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[ 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[ Mitochondrial Dysfunction alters Early Endosome Distribution and Cargo Trafficking via ROS-Mediated Microtubule Reorganization ]]> https://biorxiv.org/content/10.1101/2024.08.21.608999v1?rss=1 Vishwakarma, A. Chikhi, L. Todkar, K. Ouellet, M. Germain, M. 2024-08-22 doi:10.1101/2024.08.21.608999 Cold Spring Harbor Laboratory Press 2024-08-22 <![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[ 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[ Mitochondrial transplantation: a novel therapy for liver ischemia/reperfusion injury ]]> https://biorxiv.org/content/10.1101/2024.09.04.608457v1?rss=1 Mukkala, A. N. David, B. A. Ailenberg, M. Liang, J. Vaswani, C. M. Karakas, D. Goldfarb, R. Barbour, W. Gasner, A. Wu, R. S. Petrut, R. Jerkic, M. Andreazza, A. dos Santos, C. Ni, H. Zhang, H. Kapus, A. Kubes, P. Rotstein, O. 2024-09-05 doi:10.1101/2024.09.04.608457 Cold Spring Harbor Laboratory Press 2024-09-05 <![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[ 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[ 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[ 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[ 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[ 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[ 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[ 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 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[ 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[ 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[ 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[ Canadian science graduate stipends lie below the poverty line ]]> https://biorxiv.org/content/10.1101/2024.11.06.622240v1?rss=1 Fraass, A. J. Bailey, T. J. Karunakumar, K. Wishart, A. E. 2024-11-08 doi:10.1101/2024.11.06.622240 Cold Spring Harbor Laboratory Press 2024-11-08 <![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[ 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[ Smc5/6 association with microtubules controls dynamic pericentromeric chromatin folding ]]> https://biorxiv.org/content/10.1101/2024.11.13.623393v1?rss=1 Carre-Simon, A. Batrin, R. Isler, S. Dahl Pinholt, H. Foldes, T. Laflamme, G. Barbi, M. Mirny, L. D'Amours, D. Fabre, E. 2024-11-15 doi:10.1101/2024.11.13.623393 Cold Spring Harbor Laboratory Press 2024-11-15 <![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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ Proteomic Signatures of Podocyte Injury Are Reflected in Urinary Extracellular Vesicles in Pediatric Nephrotic Syndrome. ]]> https://biorxiv.org/content/10.1101/2025.08.19.670903v1?rss=1 Cooper, T. T. Hovey, O. Lajoie, G. A. Kennedy, C. Burger, D. Myette, R. L. 2025-08-23 doi:10.1101/2025.08.19.670903 Cold Spring Harbor Laboratory Press 2025-08-23 <![CDATA[ IRP1 deficiency alters mitochondrial metabolism and protects against metabolic syndrome pathologies ]]> https://biorxiv.org/content/10.1101/2025.08.19.671129v1?rss=1 Gu, W. Wilkinson, N. Fillebeen, C. Blackburn, D. M. Sahinyan, K. Bonneil, E. Zhao, T. Luo, Z. Soleimani, V. Richard, V. R. Borchers, C. H. Koulman, A. Jenkins, B. Michalke, B. Zischka, H. Sailer, J. Venkataramani, V. Iliopoulos, O. Sweeney, G. Pantopoulos, K. 2025-08-25 doi:10.1101/2025.08.19.671129 Cold Spring Harbor Laboratory Press 2025-08-25 <![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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ Isolation of Extracellular Vesicles from Minimal Volume Ascites Fluid Using Strong Anion Exchange Magnetic Beads ]]> https://biorxiv.org/content/10.1101/2025.09.24.678291v1?rss=1 2-fold increase in proteomic depth compared to raw ascites. Notably, this study was able to identify 1000 proteins not previously annotated in Vesiclepedia for OC-derived EVs, alongside distinct SERS signatures, highlighting the potential for multiomic analysis. Comparative analysis with UC revealed enhanced proteomic depth obtained with Mag-Net beads, albeit we also observed differential detection of canonical markers (e.g., CD9, CD81) between input volumes of ascites fluid. These findings establish Mag-Net as a scalable, low-input platform for EV-based biomarker discovery, paving the way for improved early detection and molecular insights into OC progression. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=155 HEIGHT=200 SRC="FIGDIR/small/678291v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@2a23a5org.highwire.dtl.DTLVardef@8a2ce6org.highwire.dtl.DTLVardef@189e9c2org.highwire.dtl.DTLVardef@15200f8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cooper, T. T. Veliz, L. Afzali, F. Hovey, O. F. J. Myette, R. L. Johnston, T. P. Wells, C. Robertson, T. Burger, D. Abraham, S. A. Shepherd, T. G. Craig, A. Lagugne-Labarthet, F. Lajoie, G. A. Postovit, L.-M. 2025-09-26 doi:10.1101/2025.09.24.678291 Cold Spring Harbor Laboratory Press 2025-09-26 <![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[ 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[ 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[ 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[ Heart-On-a-Chip with Integrated Ultrasoft Mechanosensors for Continuous Measurement of Cell- and Tissue-scale Contractile Stresses ]]> https://biorxiv.org/content/10.1101/2025.10.16.682609v1?rss=1 Mousavi, A. Boghdady, C.-M. Cui, S. Rostami, S. Shakeri, A. Rafatian, N. Aurousseau, M. Andelfinger, G. Radisic, M. Moraes, C. Savoji, H. 2025-10-16 doi:10.1101/2025.10.16.682609 Cold Spring Harbor Laboratory Press 2025-10-16 <![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[ 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[ 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 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ Patient-Specific 3D Heart-On-a-Chip Model of Dilated Cardiomyopathy with Embedded Bead-Based Mapping of Tissue Contractility ]]> https://biorxiv.org/content/10.64898/2025.12.20.695633v1?rss=1 Mousavi, A. Mouttet, L. Cui, S. Hekmatnia, Y. Mottahedi, M. Derish, I. Rafatian, N. Aurousseau, M. Andelfinger, G. Cecere, R. Savoji, H. 2025-12-23 doi:10.64898/2025.12.20.695633 Cold Spring Harbor Laboratory Press 2025-12-23 <![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[ 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[ 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[ 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[ 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 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[ 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[ Genomic selection for seed yield enhances flax breeding efficiency ]]> https://biorxiv.org/content/10.64898/2026.03.01.707406v1?rss=1 You, F. M. Zheng, C. Zagariah Daniel, J. J. Li, P. Jackle, K. House, M. Tar'an, B. Cloutier, S. 2026-03-03 doi:10.64898/2026.03.01.707406 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[ 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[ 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[ 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[ Cardiac defects in spinal muscular atrophy and the role of SMN in cardiomyocyte homeostasis ]]> https://biorxiv.org/content/10.64898/2026.03.20.713246v1?rss=1 Garner, R. Ha, L. L. Nery, F. C. Spellman, R. G. Chehade, L. Eichelberger, E. J. Duarte Lepez, S. D. S. Johnstone, A. J. Kothary, R. Swoboda, K. J. Alves, C. R. R. 2026-03-24 doi:10.64898/2026.03.20.713246 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Haplotype-resolved Genome Assemblies of Hybrid Wheatgrass and Bluebunch Wheatgrass Reveal the Stepwise Polyploid Origin and Biased Subgenome Dominance ]]> https://biorxiv.org/content/10.64898/2026.03.27.714782v1?rss=1 Ji, Y. Chaudhary, R. Khan, N. Perumal, S. Wang, Z. Moghanloo, L. Hucl, P. Biligetu, B. Sharpe, A. G. Jin, L. 2026-03-27 doi:10.64898/2026.03.27.714782 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[ 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[ Disentangling shape and size in a population of unusually large Threespine Stickleback (Gasterosteus aculeatus) from Vancouver Island, British Columbia ]]> https://biorxiv.org/content/10.64898/2026.04.01.715936v1?rss=1 Perry, S. Duclos, K. K. Jamniczky, H. 2026-04-03 doi:10.64898/2026.04.01.715936 Cold Spring Harbor Laboratory Press 2026-04-03