bioRxiv Channel: Georgia Institute of Technology https://biorxiv.org This feed contains articles for bioRxiv Channel "Georgia Institute of Technology" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Novel Approach Explains Spatio-Spectral Interactions in Raw Electroencephalogram Deep Learning Classifiers ]]> https://biorxiv.org/content/10.1101/2023.02.26.530118v1?rss=1 Ellis, C. A. Sattiraju, A. Miller, R. L. Calhoun, V. D. 2023-02-27 doi:10.1101/2023.02.26.530118 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Pairing Explainable Deep Learning Classification with Clustering to Uncover Effects of Schizophrenia Upon Whole Brain Functional Network Connectivity Dynamics ]]> https://biorxiv.org/content/10.1101/2023.03.01.530708v1?rss=1 Ellis, C. A. Miller, R. L. Calhoun, V. D. 2023-03-02 doi:10.1101/2023.03.01.530708 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Brain rhythms control microglial response and cytokine expression via NFkappaB signaling ]]> https://biorxiv.org/content/10.1101/2023.03.03.530908v1?rss=1 Prichard, A. Garza, K. M. Shridhar, A. He, C. Bitfaran, S. Wang, Y. Goodson, M. C. Jaeger, D. Wood, L. B. Singer, A. C. 2023-03-03 doi:10.1101/2023.03.03.530908 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Simulations suggest walking with reduced propulsive force would not mitigate the energetic consequences of lower tendon stiffness ]]> https://biorxiv.org/content/10.1101/2023.03.03.530931v1?rss=1 Pimentel, R. Sawicki, G. Franz, J. R. 2023-03-03 doi:10.1101/2023.03.03.530931 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Design and characterization of porous poly(glycerol-dodecanedioate) scaffolds for cartilage repair ]]> https://biorxiv.org/content/10.1101/2023.03.03.531009v1?rss=1 Qin, Y. Ramaraju, H. Hollister, S. J. Coleman, R. M. 2023-03-03 doi:10.1101/2023.03.03.531009 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ An expanded GCaMP reporter toolkit for functional imaging in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.03.06.531342v1?rss=1 Ding, J. Peng, L. Moon, S. Lee, H. J. Patel, D. S. Lu, H. 2023-03-08 doi:10.1101/2023.03.06.531342 Cold Spring Harbor Laboratory Press 2023-03-08 <![CDATA[ GABAergic synaptic scaling is triggered by changes in spiking activity rather than transmitter receptor activation. ]]> https://biorxiv.org/content/10.1101/2023.03.08.531789v1?rss=1 Gonzalez-Islas, C. E. Sabra, Z. Fong, M.-f. Bulow, P. Au Yong, N. Engisch, K. Wenner, P. 2023-03-09 doi:10.1101/2023.03.08.531789 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Manipulation of the nucleoscaffold potentiates cellular reprogramming kinetics ]]> https://biorxiv.org/content/10.1101/2023.03.12.532246v1?rss=1 Yang, B. A. Monteiro da Rocha, A. Newton, I. Shcherbina, A. Wong, S.-W. Fraczek, P. M. Larouche, J. A. Hiraki, H. L. Baker, B. M. Shin, J.-W. Takayama, S. Thouless, M. D. Aguilar, C. A. 2023-03-13 doi:10.1101/2023.03.12.532246 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ Division of labor promotes the entrenchment of multicellularity ]]> https://biorxiv.org/content/10.1101/2023.03.15.532780v1?rss=1 Conlin, P. L. Goldsby, H. J. Libby, E. Skocelas, K. G. Ratcliff, W. C. Ofria, C. Kerr, B. 2023-03-16 doi:10.1101/2023.03.15.532780 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ A Framework for Systematically Evaluating the Representations Learned by A Deep Learning Classifier from Raw Multi-Channel Electroencephalogram Data ]]> https://biorxiv.org/content/10.1101/2023.03.20.533467v1?rss=1 Ellis, C. A. Sattiraju, A. Miller, R. L. Calhoun, V. D. 2023-03-21 doi:10.1101/2023.03.20.533467 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ The timing of confidence computations in human prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2023.03.21.533662v1?rss=1 Xue, K. Zheng, Y. Rafiei, F. Rahnev, D. 2023-03-21 doi:10.1101/2023.03.21.533662 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Constitutive expression of the Type VI secretion system carries no measurable fitness cost in Vibrio cholerae ]]> https://biorxiv.org/content/10.1101/2023.03.24.534098v1?rss=1 Zhang, C. Ratcliff, W. C. Hammer, B. K. 2023-03-24 doi:10.1101/2023.03.24.534098 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Spinal sensorimotor circuits play a prominent role in hindlimb locomotor recovery after staggered thoracic lateral hemisections but cannot restore posture and interlimb coordination during quadrupedal locomotion in adult cats ]]> https://biorxiv.org/content/10.1101/2023.03.23.533936v1?rss=1 Audet, J. Yassine, S. Lecomte, C. G. Mari, S. Soucy, F. Morency, C. Merlet, A. N. Harnie, J. Beaulieu, C. Gendron, L. Rybak, I. A. Prilutsky, B. I. Frigon, A. 2023-03-25 doi:10.1101/2023.03.23.533936 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Beyond the reference: gene expression variation and transcriptional response to RNAi in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.03.24.533964v1?rss=1 Bell, A. D. Chou, H. T. Paaby, A. B. 2023-03-25 doi:10.1101/2023.03.24.533964 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Spatiotemporal coordination of Rac1 and Cdc42 at the whole cell level during cell ruffling ]]> https://biorxiv.org/content/10.1101/2023.03.31.535147v1?rss=1 Hladyshau, S. Stoop, J. P. Kamada, K. Nie, S. Tsygankov, D. V. 2023-03-31 doi:10.1101/2023.03.31.535147 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ Synergistic Integration of Deep Neural Networks and Finite Element Method with Applications for Biomechanical Analysis of Human Aorta ]]> https://biorxiv.org/content/10.1101/2023.04.03.535423v1?rss=1 Liang, L. Liu, M. Elefteriades, J. Sun, W. 2023-04-05 doi:10.1101/2023.04.03.535423 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ Dynein-Powered Cell Locomotion Guides Metastasis of Breast Cancer ]]> https://biorxiv.org/content/10.1101/2023.04.04.535605v1?rss=1 Tagay, Y. Kheirabadi, S. Ataie, Z. Singh, R. Prince, O. Nguyen, A. Zhovmer, A. S. Ma, X. Sheikhi, A. Tsygankov, D. Tabdanov, E. D. 2023-04-06 doi:10.1101/2023.04.04.535605 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Genetic modifiers of APOBEC-induced mutagenesis ]]> https://biorxiv.org/content/10.1101/2023.04.05.535598v1?rss=1 Mertz, T. M. Rice-Reynolds, E. Nguyen, L. Wood, A. Bray, N. Mitchell, D. Lobachev, K. Roberts, S. 2023-04-06 doi:10.1101/2023.04.05.535598 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Enriched zones of embedded ribonucleotides are associated with DNA replication and coding sequences in the human mitochondrial genome ]]> https://biorxiv.org/content/10.1101/2023.04.05.535745v1?rss=1 Xu, P. Yang, T. Kundnani, D. L. Sun, M. Marsili, S. Gombolay, A. L. Jeon, Y. Newnam, G. Balachander, S. Bazzani, V. Baccarani, U. Park, V. S. Tao, S. Lori, A. Schinazi, R. F. Kim, B. Pursell, Z. F. Tell, G. F. Vascotto, C. Storici, F. 2023-04-06 doi:10.1101/2023.04.05.535745 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Multiple brain activation patterns for the same task ]]> https://biorxiv.org/content/10.1101/2023.04.08.536107v1?rss=1 Nakuci, J. Yeon, J. Kim, J.-H. Kim, S.-P. Rahnev, D. 2023-04-08 doi:10.1101/2023.04.08.536107 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Microtubule search-and-capture model evaluates the effect of chromosomal volume conservation on spindle assembly during mitosis ]]> https://biorxiv.org/content/10.1101/2023.04.08.536118v1?rss=1 Nayak, P. Chatterjee, S. Paul, R. 2023-04-08 doi:10.1101/2023.04.08.536118 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ LinRace: single cell lineage reconstruction using paired lineage barcode and gene expression data ]]> https://biorxiv.org/content/10.1101/2023.04.12.536601v1?rss=1 Pan, X. Li, H. Putta, P. Zhang, X. 2023-04-13 doi:10.1101/2023.04.12.536601 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Rapid bacteria-phage coevolution drives the emergence of multi-scale networks ]]> https://biorxiv.org/content/10.1101/2023.04.13.536812v1?rss=1 Borin, J. M. Lee, J. J. Lucia-Sanz, A. Gerbino, K. R. Weitz, J. M. Meyer, J. R. 2023-04-14 doi:10.1101/2023.04.13.536812 Cold Spring Harbor Laboratory Press 2023-04-14 <![CDATA[ Cross-subject Mapping of Neural Activity with Restricted Boltzmann Machines ]]> https://biorxiv.org/content/10.1101/2023.04.14.536854v1?rss=1 Angjelichinoski, M. Wu, S. Putney, J. Sponberg, S. Tarokh, V. 2023-04-14 doi:10.1101/2023.04.14.536854 Cold Spring Harbor Laboratory Press 2023-04-14 <![CDATA[ High prevalence of LPS mutants and R2-Pyocin susceptible variants in Pseudomonas aeruginosa populations sourced from cystic fibrosis lung infections ]]> https://biorxiv.org/content/10.1101/2023.04.26.538445v1?rss=1 Mei, M. Pheng, P. Kurzeja-Edwards, D. Diggle, S. P. 2023-04-27 doi:10.1101/2023.04.26.538445 Cold Spring Harbor Laboratory Press 2023-04-27 <![CDATA[ A multiadjuvant polysaccharide-amino acid-lipid (PAL) subunit nanovaccine generates robust systemic and lung-specific mucosal immune responses against SARS-CoV-2 in mice ]]> https://biorxiv.org/content/10.1101/2023.05.05.539395v1?rss=1 Pandey, B. Wang, Z. Jimenez, A. Bhatia, E. Jain, R. Beach, A. Maniar, D. Hosten, J. O'Farrell, L. Vantucci, C. Hur, D. Noel, R. K. Ringquist, R. M. Smith, C. Ochoa, M. A. Roy, K. 2023-05-08 doi:10.1101/2023.05.05.539395 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Using CRISPR/Cas9 to identify genes required for mechanosensory neuron development and function ]]> https://biorxiv.org/content/10.1101/2023.05.08.539861v1?rss=1 Johnson, C. J. Kulkarni, A. Buxton, W. J. Hui, T. Y. Kayastha, A. Khoja, A. A. Leandre, J. Mehta, V. Ostrowski, L. Pareizs, E. G. Scotto, R. L. Vargas, V. Vellingiri, R. M. Verzino, G. Vohra, R. Wakade, S. C. Winkeljohn, V. M. Winkeljohn, V. M. Rotterman, T. M. Stolfi, A. 2023-05-08 doi:10.1101/2023.05.08.539861 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Attenuation of muscle spindle firing with artificially increased series compliance during stretch of relaxed muscle ]]> https://biorxiv.org/content/10.1101/2023.05.08.539853v1?rss=1 Abbott, E. M. Stephens, J. D. Simha, S. N. Wood, L. Nardelli, P. Cope, T. C. Ting, L. H. Sawicki, G. S. 2023-05-09 doi:10.1101/2023.05.08.539853 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Quantitative flow cytometric selection of tau conformational nanobodies specific for pathological aggregates ]]> https://biorxiv.org/content/10.1101/2023.05.13.540640v1?rss=1 Zupancic, J. M. Smith, M. D. Trzeciakiewicz, H. Skinner, M. E. Ferris, S. P. Makowski, E. K. Lucas, M. J. McArthur, N. Kane, R. S. Paulson, H. L. Tessier, P. M. 2023-05-14 doi:10.1101/2023.05.13.540640 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Geometry shapes evolution of early multicellularity ]]> https://biorxiv.org/content/10.1101/003673v1?rss=1 Eric Libby Will Ratcliff Mike Travisano Ben Kerr 2014-03-30 doi:10.1101/003673 Cold Spring Harbor Laboratory Press 2014-03-30 <![CDATA[ Excess False Positive Rates in Methods for Differential Gene Expression Analysis using RNA-Seq Data ]]> https://biorxiv.org/content/10.1101/020784v1?rss=1 David M Rocke Luyao Ruan Yilun Zhang J. Jared Gossett Blythe Durbin-Johnson Sharon Aviran 2015-06-11 doi:10.1101/020784 Cold Spring Harbor Laboratory Press 2015-06-11 <![CDATA[ Whole genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection ]]> https://biorxiv.org/content/10.1101/022194v1?rss=1 PingHsun Hsieh Krishna R Veeramah Joseph Lachance Sarah A Tishkoff Jeffrey D Wall Michael F Hammer Ryan N Gutenkunst 2015-07-08 doi:10.1101/022194 Cold Spring Harbor Laboratory Press 2015-07-08 <![CDATA[ Re-examining the relationship between virus and microbial cell abundances in the global oceans ]]> https://biorxiv.org/content/10.1101/025544v1?rss=1 Charles H. Wigington Derek L. Sonderegger Corina P.D. Brussaard Alison Buchan Jan F. Finke Jed Fuhrman Jay T. Lennon Mathias Middelboe Curtis A. Suttle Charles Stock William H. Wilson K. Eric Wommack Steven W. Wilhelm Joshua S. Weitz 2015-08-26 doi:10.1101/025544 Cold Spring Harbor Laboratory Press 2015-08-26 <![CDATA[ Microbiome engineering could select for more virulent pathogens ]]> https://biorxiv.org/content/10.1101/027854v1?rss=1 Luke McNally Pedro F Vale Sam P Brown 2015-09-30 doi:10.1101/027854 Cold Spring Harbor Laboratory Press 2015-09-30 <![CDATA[ Apoptosis in snowflake yeast: novel trait, or side effect of toxic waste? ]]> https://biorxiv.org/content/10.1101/029918v1?rss=1 Jennifer Pentz Bradford P Taylor William C Ratcliff 2015-10-26 doi:10.1101/029918 Cold Spring Harbor Laboratory Press 2015-10-26 <![CDATA[ Trait Heritability in Major Transitions ]]> https://biorxiv.org/content/10.1101/041830v1?rss=1 Matthew D Herron William C Ratcliff 2016-02-29 doi:10.1101/041830 Cold Spring Harbor Laboratory Press 2016-02-29 <![CDATA[ Replicator Dynamics with Feedback-Evolving Games: Towards a Co-Evolutionary Game Theory ]]> https://biorxiv.org/content/10.1101/043299v1?rss=1 Joshua S Weitz Sam P Brown Ceyhun Eksin Keith Paarporn William C Ratcliff 2016-03-11 doi:10.1101/043299 Cold Spring Harbor Laboratory Press 2016-03-11 <![CDATA[ Wolbachia confers sex-specific resistance and tolerance to enteric but not systemic bacterial infection in Drosophila ]]> https://biorxiv.org/content/10.1101/045757v1?rss=1 Radhakrishnan B Vasanthakrishnan Gupta Vanika Jonathon A Siva-Jothy Katy M Monteith Sam P Brown Pedro F Vale 2016-04-02 doi:10.1101/045757 Cold Spring Harbor Laboratory Press 2016-04-02 <![CDATA[ Emergence of increased frequency and severity of multiple infections by viruses due to spatial clustering of hosts ]]> https://biorxiv.org/content/10.1101/048876v1?rss=1 Bradford P Taylor Catherine J Penington Joshua S Weitz 2016-04-15 doi:10.1101/048876 Cold Spring Harbor Laboratory Press 2016-04-15 <![CDATA[ The Pseudomonas aeruginosa PSL polysaccharide is a social but non-cheatable trait in biofilms ]]> https://biorxiv.org/content/10.1101/049783v1?rss=1 Yasuhiko Irie Aled Roberts Kasper N Kragh Vernita D Gordon Jamie Hutchison Rosalind J Allen Gavin Melaugh Thomas Bjarnsholt Stuart A West Stephen P Diggle 2016-04-22 doi:10.1101/049783 Cold Spring Harbor Laboratory Press 2016-04-22 <![CDATA[ Inferring phage-bacteria infection networks from time series data ]]> https://biorxiv.org/content/10.1101/051581v1?rss=1 Luis Jover Justin Romberg Joshua S Weitz 2016-05-03 doi:10.1101/051581 Cold Spring Harbor Laboratory Press 2016-05-03 <![CDATA[ Lysis, Lysogeny, and Virus-Microbe Ratios ]]> https://biorxiv.org/content/10.1101/051805v1?rss=1 Joshua Weitz Stephen J Beckett Jennifer R Brum B. B. Cael Jonathan Dushoff 2016-05-05 doi:10.1101/051805 Cold Spring Harbor Laboratory Press 2016-05-05 <![CDATA[ The evolution of coercive policing in genetically mixed groups: the case of plasmid copy number control ]]> https://biorxiv.org/content/10.1101/053579v1?rss=1 Kyriakos Kentzoglanakis Sam Brown Richard Goldstein 2016-05-22 doi:10.1101/053579 Cold Spring Harbor Laboratory Press 2016-05-22 <![CDATA[ Environmental modification via a quorum sensing molecule influences the social landscape of siderophore production ]]> https://biorxiv.org/content/10.1101/053918v1?rss=1 Roman Popat Freya Harrison Luke McNally Paul Williams Stephen P Diggle 2016-05-17 doi:10.1101/053918 Cold Spring Harbor Laboratory Press 2016-05-17 <![CDATA[ Time-dependent fitness effects can drive bet-hedging populations extinct ]]> https://biorxiv.org/content/10.1101/054007v1?rss=1 Eric Libby William C Ratcliff 2016-05-18 doi:10.1101/054007 Cold Spring Harbor Laboratory Press 2016-05-18 <![CDATA[ Synergistic elimination of bacteria by phage and the immune system ]]> https://biorxiv.org/content/10.1101/057927v1?rss=1 Chung Yin (Joey) Leung Joshua S. Weitz 2016-06-08 doi:10.1101/057927 Cold Spring Harbor Laboratory Press 2016-06-08 <![CDATA[ Programmed cell death can increase the efficacy of microbial bet-hedging ]]> https://biorxiv.org/content/10.1101/059071v1?rss=1 Eric Libby William W. Driscoll William C. Ratcliff 2016-06-15 doi:10.1101/059071 Cold Spring Harbor Laboratory Press 2016-06-15 <![CDATA[ Killing by Type VI secretion drives clonal phase separation and the evolution of cooperation ]]> https://biorxiv.org/content/10.1101/063487v1?rss=1 Luke McNally Eryn Bernardy Jacob Thomas Arben Kalziqi Jennifer T Pentz Sam Brown Brian Hammer Peter Yunker William Ratcliff 2016-07-14 doi:10.1101/063487 Cold Spring Harbor Laboratory Press 2016-07-14 <![CDATA[ A revised dilution methodology and implications for estimates of rates of plankton mortality ]]> https://biorxiv.org/content/10.1101/072231v1?rss=1 Stephen J Beckett Joshua S Weitz 2016-08-30 doi:10.1101/072231 Cold Spring Harbor Laboratory Press 2016-08-30 <![CDATA[ Genetic correlations with climate variables suggest Caenorhabditis elegans natural niche preferences ]]> https://biorxiv.org/content/10.1101/075960v1?rss=1 Kathryn S. Evans Yuehui Zhao Lijiang Long Shannon C. Brady Patrick T. McGrath Erik C. Andersen 2016-09-19 doi:10.1101/075960 Cold Spring Harbor Laboratory Press 2016-09-19 <![CDATA[ Biophysical Attributes of CpG Presentation Control TLR9 Signaling to Differentially Polarize Systemic Immune-Responses ]]> https://biorxiv.org/content/10.1101/076935v1?rss=1 Jardin A Leleux Pallab Pradhan Krishnendu Roy 2016-09-23 doi:10.1101/076935 Cold Spring Harbor Laboratory Press 2016-09-23 <![CDATA[ Using the Price equation to analyze multi-level selection on the reproductive policing mechanism of bacterial plasmids ]]> https://biorxiv.org/content/10.1101/079574v1?rss=1 Kyriakos Kentzoglanakis Sam P Brown Richard A Goldstein 2016-10-12 doi:10.1101/079574 Cold Spring Harbor Laboratory Press 2016-10-12 <![CDATA[ Constraints on eQTL fine mapping in the presence of multi-site local regulation of gene expression ]]> https://biorxiv.org/content/10.1101/084293v1?rss=1 Zeng, B. Lloyd-Jones, L. Holloway, A. Marigorta, U. M. Metspalu, A. Montgomery, G. W. Esko, T. Brigham, K. L. Quyyumi, A. A. Idaghdour, Y. Yang, J. Visscher, P. M. Powell, J. E. Gibson, G. 2016-10-29 doi:10.1101/084293 Cold Spring Harbor Laboratory Press 2016-10-29 <![CDATA[ Cobalt enrichment in anaerobic microbial cocultures revealed by synchrotron X-ray fluorescence imaging ]]> https://biorxiv.org/content/10.1101/087585v1?rss=1 Glass, J. B. Chen, S. Dawson, K. S. Horton, D. R. Vogt, S. Ingall, E. D. Twining, B. S. Orphan, V. J. 2016-11-14 doi:10.1101/087585 Cold Spring Harbor Laboratory Press 2016-11-14 <![CDATA[ Shifting microbial communities sustain multi-year iron reduction and methanogenesis in ferruginous sediment incubations ]]> https://biorxiv.org/content/10.1101/087783v1?rss=1 Bray, M. S. Wu, J. Reed, B. C. Kretz, C. B. Simister, R. L. Henny, C. Stewart, F. J. DiChristina, T. J. Brandes, J. A. Fowle, D. A. Crowe, S. A. Glass, J. B. 2016-11-15 doi:10.1101/087783 Cold Spring Harbor Laboratory Press 2016-11-15 <![CDATA[ DeeperBind: Enhancing Prediction of Sequence Specificities of DNA Binding Proteins ]]> https://biorxiv.org/content/10.1101/099754v1?rss=1 Wang, M. D. Hassanzadeh, H. R. 2017-01-12 doi:10.1101/099754 Cold Spring Harbor Laboratory Press 2017-01-12 <![CDATA[ Division of labor, bet hedging, and the evolution of mixed biofilm investment strategies ]]> https://biorxiv.org/content/10.1101/107102v1?rss=1 Lowery, N. V. McNally, L. Ratcliff, W. C. Brown, S. P. 2017-02-08 doi:10.1101/107102 Cold Spring Harbor Laboratory Press 2017-02-08 <![CDATA[ High-Throughput Controlled Mechanical Stimulation and Functional Imaging In Vivo ]]> https://biorxiv.org/content/10.1101/107318v1?rss=1 Cho, Y. Porto, D. A. Hwang, H. Grundy, L. J. Schafer, W. R. Lu, H. 2017-02-10 doi:10.1101/107318 Cold Spring Harbor Laboratory Press 2017-02-10 <![CDATA[ Infants’ neural oscillatory processing of theta-rate speech patterns exceeds adults’ ]]> https://biorxiv.org/content/10.1101/108852v1?rss=1 Leong, V. Byrne, E. Clackson, K. Harte, N. Lam, S. de Barbaro, K. Wass, S. 2017-02-15 doi:10.1101/108852 Cold Spring Harbor Laboratory Press 2017-02-15 <![CDATA[ Genome-wide protein phylogenies for four African cichlid species ]]> https://biorxiv.org/content/10.1101/110510v1?rss=1 Varadarajan, A. R. Mopuri, R. Streelman, J. T. McGrath, P. T. 2017-02-21 doi:10.1101/110510 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[ Alphaproteobacteria fix nitrogen in a Sphagnum-dominated peat bog using molybdenum-dependent nitrogenase ]]> https://biorxiv.org/content/10.1101/114918v1?rss=1 Warren, M. J. Lin, X. Gaby, J. C. Kretz, C. B. Morton, P. L. Pett-Ridge, J. Weston, D. J. Schadt, C. W. Kostka, J. E. Glass, J. B. 2017-03-07 doi:10.1101/114918 Cold Spring Harbor Laboratory Press 2017-03-07 <![CDATA[ Horizontal Gene Transfer of Functional Type VI Killing Genes by Natural Transformation ]]> https://biorxiv.org/content/10.1101/122499v1?rss=1 Thomas, J. Watve, S. S. Ratcliff, W. C. Hammer, B. K. 2017-03-30 doi:10.1101/122499 Cold Spring Harbor Laboratory Press 2017-03-30 <![CDATA[ Transcriptome-Wide Prediction Of lncRNA-RNA Interactions By A Thermodynamics Algorithm ]]> https://biorxiv.org/content/10.1101/126946v1?rss=1 Antonov, I. Marakhonov, A. Zamkova, M. Skoblov, M. Medvedeva, Y. 2017-04-12 doi:10.1101/126946 Cold Spring Harbor Laboratory Press 2017-04-12 <![CDATA[ Systemic Activation Coordinates The Heat Shock Response Of The Insulin/IGF-1 Pathway In Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/131375v1?rss=1 Kopito, R. B. Watkins, K. Levine, E. 2017-05-06 doi:10.1101/131375 Cold Spring Harbor Laboratory Press 2017-05-06 <![CDATA[ MotifMark: Finding Regulatory Motifs in DNA Sequences ]]> https://biorxiv.org/content/10.1101/134296v1?rss=1 Hassanzadeh, H. R. 2017-05-05 doi:10.1101/134296 Cold Spring Harbor Laboratory Press 2017-05-05 <![CDATA[ DeepDeath: Learning To Predict The Underlying Cause Of Death With Big Data ]]> https://biorxiv.org/content/10.1101/134965v1?rss=1 Hassanzadeh, H. R. Sha, Y. Wang, M. D. 2017-05-06 doi:10.1101/134965 Cold Spring Harbor Laboratory Press 2017-05-06 <![CDATA[ Wireless Implantable Sensor For Non-Invasive, Longitudinal Quantification Of Axial Strain Across Rodent Long Bone Defects ]]> https://biorxiv.org/content/10.1101/142778v1?rss=1 Klosterhoff, B. S. Ong, K. G. Krishnan, L. Hetzendorfer, K. M. Chang, Y.-H. Allen, M. G. Guldberg, R. E. Willett, N. J. 2017-05-26 doi:10.1101/142778 Cold Spring Harbor Laboratory Press 2017-05-26 <![CDATA[ Reverse-Correlation Analysis of Mechanosensation Circuit in C. elegans Reveals Temporal and Spatial Encoding ]]> https://biorxiv.org/content/10.1101/147363v1?rss=1 Porto, D. A. Giblin, J. Zhao, Y. Lu, H. 2017-06-09 doi:10.1101/147363 Cold Spring Harbor Laboratory Press 2017-06-09 <![CDATA[ Mapping-free variant calling using haplotype reconstruction from k-mer frequencies ]]> https://biorxiv.org/content/10.1101/153619v1?rss=1 Audano, P. Ravishankar, S. Vannberg, F. 2017-06-22 doi:10.1101/153619 Cold Spring Harbor Laboratory Press 2017-06-22 <![CDATA[ Structure and misfolding of the flexible tripartite coiled coil domain of glaucoma-associated myocilin ]]> https://biorxiv.org/content/10.1101/154112v1?rss=1 Hill, S. E. Nguyen, E. Donegan, R. K. Hazel, A. Gumbart, J. C. Lieberman, R. L. 2017-06-23 doi:10.1101/154112 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ A Deep Learning Approach to Estimate Collagenous Tissue Nonlinear Anisotropic Stress-Strain Responses from Microscopy Images ]]> https://biorxiv.org/content/10.1101/154161v1?rss=1 Liang, L. Liu, M. Sun, W. 2017-06-23 doi:10.1101/154161 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ mRNA detection in budding yeast with single fluorophores ]]> https://biorxiv.org/content/10.1101/155143v1?rss=1 Wadsworth, G. Parikh, R. Choy, J. Kim, H. 2017-06-24 doi:10.1101/155143 Cold Spring Harbor Laboratory Press 2017-06-24 <![CDATA[ Instantaneous Brain Dynamics Mapped to a Continuous State Space ]]> https://biorxiv.org/content/10.1101/157115v1?rss=1 Billings, J. Medda, A. Shakil, S. Shen, X. Kashyap, A. Chen, S. Abbas, A. Zhang, X. Nezafati, M. Pan, W.-J. Berman, G. Keilholz, S. 2017-06-28 doi:10.1101/157115 Cold Spring Harbor Laboratory Press 2017-06-28 <![CDATA[ Obstruction of pilus retraction stimulates bacterial surface sensing ]]> https://biorxiv.org/content/10.1101/157727v1?rss=1 Ellison, C. K. Kan, J. Dillard, R. S. Kysela, D. T. Hampton, C. M. Ke, Z. Wright, E. R. Biais, N. Dalia, A. B. Brun, Y. V. 2017-06-30 doi:10.1101/157727 Cold Spring Harbor Laboratory Press 2017-06-30 <![CDATA[ Correlations, interactions, and predictability in virus-microbe networks ]]> https://biorxiv.org/content/10.1101/176628v1?rss=1 Coenen, A. R. Weitz, J. S. 2017-08-15 doi:10.1101/176628 Cold Spring Harbor Laboratory Press 2017-08-15 <![CDATA[ Assortative mating on ancestry-variant traits in admixed Latin American populations ]]> https://biorxiv.org/content/10.1101/177634v1?rss=1 Norris, E. T. Rishishwar, L. Wang, L. Conley, A. B. Chande, A. T. Dabrowski, A. M. Valderrama-Aguirre, A. Jordan, I. K. 2017-08-17 doi:10.1101/177634 Cold Spring Harbor Laboratory Press 2017-08-17 <![CDATA[ Quasi-Periodic Patterns of Intrinsic Brain Activity in Individuals and their Relationship to Global Signal ]]> https://biorxiv.org/content/10.1101/180596v1?rss=1 Yousefi, B. Shin, J. Schumacher, E. H. Keilholz, S. D. 2017-08-25 doi:10.1101/180596 Cold Spring Harbor Laboratory Press 2017-08-25 <![CDATA[ A Mathematical Model of the Phosphoinositide Pathway ]]> https://biorxiv.org/content/10.1101/182634v1?rss=1 Olivenca, D. V. Uliyakina, I. Fonseca, L. L. Amaral, M. Voit, E. Pinto, F. R. 2017-08-30 doi:10.1101/182634 Cold Spring Harbor Laboratory Press 2017-08-30 <![CDATA[ Pharmacodynamic Considerations of Collateral Sensitivity in Design of Antibiotic Treatment Regimen ]]> https://biorxiv.org/content/10.1101/189381v1?rss=1 Udekwu, K. I. Weiss, H. 2017-09-20 doi:10.1101/189381 Cold Spring Harbor Laboratory Press 2017-09-20 <![CDATA[ Improved Prokaryotic Gene Prediction Yields Insights into Transcription and Translation Mechanisms on Whole Genome Scale ]]> https://biorxiv.org/content/10.1101/193490v1?rss=1 Lomsadze, A. Gemayel, K. Tang, S. Borodovsky, M. 2017-09-26 doi:10.1101/193490 Cold Spring Harbor Laboratory Press 2017-09-26 <![CDATA[ A synthetic stroma-free germinal center niche using material-surface driven polyvalent signaling efficiently induces antigen-specific humoral immunity ex vivo ]]> https://biorxiv.org/content/10.1101/194456v1?rss=1 Roh, K.-H. Wilson, H. K. Pradhan, P. Bai, K. Bohannon, C. D. Dale, G. Leleux, J. A. Jacob, J. Roy, K. 2017-09-27 doi:10.1101/194456 Cold Spring Harbor Laboratory Press 2017-09-27 <![CDATA[ Motility in multicellular Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/201194v1?rss=1 Boyd, M. Herron, M. D. Rosenzweig, F. 2017-10-10 doi:10.1101/201194 Cold Spring Harbor Laboratory Press 2017-10-10 <![CDATA[ A Multi-Niche Microvascularized Human Bone-Marrow-on-a-Chip ]]> https://biorxiv.org/content/10.1101/2019.12.15.876813v1?rss=1 Nelson, M. R. Ghoshal, D. Mejias, J. C. Frey Rubio, D. Keith, E. Roy, K. 2019-12-15 doi:10.1101/2019.12.15.876813 Cold Spring Harbor Laboratory Press 2019-12-15 <![CDATA[ A portable, low-cost device for precise control of specimen temperature under stereomicroscopes ]]> https://biorxiv.org/content/10.1101/2019.12.19.882605v1?rss=1 Testa, N. D. Kaul, S. Le, K. N. Zhan, M. Lu, H. Paaby, A. B. 2019-12-19 doi:10.1101/2019.12.19.882605 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Eukaryotic-like ribosomal RNA region in Lokiarchaeota ]]> https://biorxiv.org/content/10.1101/2019.12.25.888164v1?rss=1 100 nt) compared to all other prokaryotes studied to date. Asgard ESs have distinct structures from eukaryotic ESs, but share a common three-way junction out of which the ES grew. Our findings raise the possibility that supersized ESs existed on the ribosomal surface before the last eukaryotic common ancestor, opening the question of whether ribosomal complexity is more deeply rooted than previously thought. ]]> Penev, P. I. Fakhretaha-Aval, S. Patel, V. J. Cannone, J. J. Gutell, R. R. Petrov, A. S. Williams, L. D. Glass, J. B. 2019-12-27 doi:10.1101/2019.12.25.888164 Cold Spring Harbor Laboratory Press 2019-12-27 <![CDATA[ GeneMark-EP and -EP+: automatic eukaryotic gene prediction supported by spliced aligned proteins ]]> https://biorxiv.org/content/10.1101/2019.12.31.891218v1?rss=1 Bruna, T. Lomsadze, A. Borodovsky, M. 2020-01-02 doi:10.1101/2019.12.31.891218 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ Community lifespan, niche expansion and the evolution of interspecific cooperation ]]> https://biorxiv.org/content/10.1101/2020.01.02.893321v1?rss=1 Rodrigues, A. M. M. Estrela, S. Brown, S. P. 2020-01-03 doi:10.1101/2020.01.02.893321 Cold Spring Harbor Laboratory Press 2020-01-03 <![CDATA[ The challenge of RNA branching prediction: a parametric analysis of multiloop initiation under thermodynamic optimization ]]> https://biorxiv.org/content/10.1101/2020.01.03.893891v1?rss=1 Poznanovic, S. Barrera-Cruz, F. Kirkpatrick, A. Ielusic, M. Heitsch, C. 2020-01-03 doi:10.1101/2020.01.03.893891 Cold Spring Harbor Laboratory Press 2020-01-03 <![CDATA[ Tissue Engineered Vascularized Patient-Specific Temporomandibular Joint Reconstruction in a Yucatan Pig Model ]]> https://biorxiv.org/content/10.1101/2020.01.09.900746v1?rss=1 Abramowicz, S. Hollister, S. Crotts, S. Goudy, S. 2020-01-10 doi:10.1101/2020.01.09.900746 Cold Spring Harbor Laboratory Press 2020-01-10 <![CDATA[ Development of Systemic Immune Dysregulation in a Rat Trauma Model with Biomaterial-Associated Infection ]]> https://biorxiv.org/content/10.1101/2020.01.10.901769v1?rss=1 Vantucci, C. E. Ahn, H. Schenker, M. L. Pradhan, P. Wood, L. B. Guldberg, R. E. Roy, K. Willett, N. 2020-01-11 doi:10.1101/2020.01.10.901769 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Generation of Monophasic Action Potentials and Intermediate Forms ]]> https://biorxiv.org/content/10.1101/2020.01.10.901793v1?rss=1 Iravanian, S. Uzelac, I. Herndon, C. J. Langberg, J. Fenton, F. 2020-01-11 doi:10.1101/2020.01.10.901793 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ A behavioral polymorphism caused by a single gene inside a supergene ]]> https://biorxiv.org/content/10.1101/2020.01.13.897637v1?rss=1 Merritt, J. R. Grogan, K. E. Zinzow-Kramer, W. Sun, D. Ortlund, E. A. Maney, D. Yi, S. 2020-01-14 doi:10.1101/2020.01.13.897637 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ A Pathway and Network Oriented Approach to Enlighten Molecular Mechanisms of Type 2 Diabetes Using Multiple Association Studies ]]> https://biorxiv.org/content/10.1101/2020.01.14.905547v1?rss=1 Bakir-Gungor, B. Unlu Yazici, M. Goy, G. Temiz, M. 2020-01-15 doi:10.1101/2020.01.14.905547 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Mechanical Regulation of Microvascular Angiogenesis ]]> https://biorxiv.org/content/10.1101/2020.01.14.906354v1?rss=1 Ruehle, M. A. Eastburn, E. A. LaBelle, S. A. Krishnan, L. Weiss, J. A. Boerckel, J. D. Wood, L. B. Guldberg, R. E. Willett, N. J. 2020-01-15 doi:10.1101/2020.01.14.906354 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Ultrasound imaging links soleus muscle neuromechanics and energetics during human walking with elastic ankle exoskeletons ]]> https://biorxiv.org/content/10.1101/2020.01.20.909259v1?rss=1 Nuckols, R. W. Dick, T. J. M. Beck, O. N. Sawicki, G. S. 2020-01-20 doi:10.1101/2020.01.20.909259 Cold Spring Harbor Laboratory Press 2020-01-20 <![CDATA[ Evaluation of M2-like macrophage enrichment after diffuse traumatic brain injury through transient interleukin-4 expression from engineered mesenchymal stromal cells ]]> https://biorxiv.org/content/10.1101/2020.01.28.918441v1?rss=1 Enam, S. F. Kader, S. R. Bodkin, N. Lyon, J. G. Calhoun, M. Azrak, C. Tiwari, P. M. Vanover, D. Wang, H. Santangelo, P. J. Bellamkonda, R. V. 2020-01-28 doi:10.1101/2020.01.28.918441 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ Weighted minimizer sampling improves long read mapping ]]> https://biorxiv.org/content/10.1101/2020.02.11.943241v1?rss=1 Jain, C. Rhie, A. Zhang, H. Chu, C. Koren, S. Phillippy, A. 2020-02-11 doi:10.1101/2020.02.11.943241 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ Optical Control of Cytokine Signaling via Bioinspired, Polymer-Induced Latency ]]> https://biorxiv.org/content/10.1101/2020.02.13.948240v1?rss=1 Perdue, L. A. Do, P. David, C. Chyong, A. Kellner, A. Ruggieri, A. Kim, H. R. Salaita, K. Lesinski, G. B. Porter, C. C. Dreaden, E. C. 2020-02-14 doi:10.1101/2020.02.13.948240 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Organoid Polymer Functionality and Mode of Klebsiella Pneumoniae Membrane Antigen Presentation Regulates Ex Vivo Germinal Center Epigenetics in Young and Aged B Cells ]]> https://biorxiv.org/content/10.1101/2020.02.16.947408v1?rss=1 Graney, P. L. Lai, K. Post, S. Brito, I. Cyster, J. Singh, A. 2020-02-17 doi:10.1101/2020.02.16.947408 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ Lower Soil Carbon Loss Due to Persistent Microbial Adaptation to Climate Warming ]]> https://biorxiv.org/content/10.1101/2020.02.23.961300v1?rss=1 Guo, X. Gao, Q. Yuan, M. Wang, G. Zhou, X. Feng, J. Shi, Z. Hale, L. Wu, L. Zhou, A. Tian, R. Liu, F. Wu, B. Chen, L. Gyo Jung, C. Niu, S. Li, D. Xu, X. Jiang, L. Escalas, A. Wu, L. He, Z. Van Nostrand, J. Ning, D. Liu, X. Yang, Y. Schuur, E. Konstantinidis, K. T. Cole, J. R. Penton, C. R. Luo, Y. Tiedje, J. Zhou, J. 2020-02-25 doi:10.1101/2020.02.23.961300 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Automated measurement of long-term bower behaviors in Lake Malawi cichlids using depth sensing and action recognition ]]> https://biorxiv.org/content/10.1101/2020.02.27.968511v1?rss=1 85%) classifies ten sand manipulation behaviors across three different species and distinguishes between scooping and spitting events that occur during bower construction versus feeding. Registration of depth and video data streams enables topographical mapping of these behaviors onto a dynamic 3D sand surface. The hardware required for this setup is inexpensive (<$250 per setup), allowing for the simultaneous recording from many independent aquariums. We further show that bower construction behaviors are non-uniform in time, non-uniform in space, and spatially repeatable across trials. We also quantify a unique behavioral phenotype in interspecies hybrids, wherein males sequentially express both phenotypes of behaviorally-divergent parental species. Our work demonstrates that simultaneously tracking both structure and behavior provides an integrated picture of long-term goal-directed decision-making in a naturalistic, dynamic, and social environment. ]]> Johnson, Z. V. Long, L. Li, J. Arrojwala, M. T. S. Aljapur, V. Lee, T. Lowder, M. C. Gu, K. Lancaster, T. J. Stockert, J. I. Moorman, J. M. Lecesne, R. L. Streelman, J. T. McGrath, P. T. 2020-02-28 doi:10.1101/2020.02.27.968511 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ Adding carbon fiber to shoe soles does not improve running economy: a muscle-level explanation ]]> https://biorxiv.org/content/10.1101/2020.02.28.969584v1?rss=1 Beck, O. N. Golyski, P. R. Sawicki, G. S. 2020-02-29 doi:10.1101/2020.02.28.969584 Cold Spring Harbor Laboratory Press 2020-02-29 <![CDATA[ Shape-to-graph Mapping Method for Efficient Characterization and Classification of Complex Geometries in Biological Images ]]> https://biorxiv.org/content/10.1101/2020.03.02.972786v1?rss=1 Pilcher, W. Yang, X. Zhurikhina, A. Chernaya, O. Xu, Y. Qiu, P. Tsygankov, D. 2020-03-02 doi:10.1101/2020.03.02.972786 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Out-of-register parallel β-sheets and antiparallel β-sheets coexist in 150 kDa oligomers formed by Aβ(1-42) ]]> https://biorxiv.org/content/10.1101/2020.03.03.974394v1?rss=1 Gao, Y. Guo, C. Watzlawik, J. O. Lee, E. J. Huang, D. Zhou, H.-X. Rosenberry, T. L. Paravastu, A. K. 2020-03-04 doi:10.1101/2020.03.03.974394 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ Engineered Heterochronic Parabiosis in 3D Microphysiological System for Identification of Muscle Rejuvenating Factors ]]> https://biorxiv.org/content/10.1101/2020.03.10.975482v1?rss=1 Lee, Y. Choi, J. J. Ahn, S. I. Lee, N. H. Han, W. M. Mohiuddin, M. Shin, E. J. Wood, L. B. Park, K. D. Kim, Y. Jang, Y. C. 2020-03-11 doi:10.1101/2020.03.10.975482 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Automated Annotation of Cell Identities in Dense Cellular Images ]]> https://biorxiv.org/content/10.1101/2020.03.10.986356v1?rss=1 Chaudhary, S. Lee, S. A. Li, Y. Patel, D. S. Lu, H. 2020-03-11 doi:10.1101/2020.03.10.986356 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Mechanism of action of HBV capsid assembly modulators predicted from binding to early assembly intermediates ]]> https://biorxiv.org/content/10.1101/2020.03.23.002527v1?rss=1 Pavlova, A. Bassit, L. Cox, B. Korablyov, M. Chipot, C. Verma, K. Russell, O. O. Schinazi, R. F. Gumbart, J. C. 2020-03-25 doi:10.1101/2020.03.23.002527 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ TMS alters multivoxel patterns in the absence of overall activity changes ]]> https://biorxiv.org/content/10.1101/2020.03.25.008334v1?rss=1 Rafiei, F. Safrin, M. Wokke, M. Lau, H. Rahnev, D. 2020-03-26 doi:10.1101/2020.03.25.008334 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ Population structure and pharmacogenomic risk stratification in the United States ]]> https://biorxiv.org/content/10.1101/2020.03.28.013755v1?rss=1 96% accuracy, and accordingly GA provides only a marginal increase in resolution for PGx risk stratification. PGx variants are highly diverged compared to the genomic background; 82 variants show significant frequency differences among SIRE groups, and genome-wide patterns of PGx variation are almost entirely concordant with SIRE. Nevertheless, 97% of PGx variation is found within rather than between groups. Examples of highly differentiated PGx variants illustrate how SIRE partitions PGx variation based on group-specific ancestry patterns and contains valuable information for risk stratification. Finally, we show that individuals who identify as Black or Hispanic benefit more when SIRE is considered for treatment decisions than individuals from the majority White population. ]]> Nagar, S. D. Conley, A. B. Jordan, I. K. 2020-03-29 doi:10.1101/2020.03.28.013755 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ Optoregulated force application to cellular receptors using molecular motors ]]> https://biorxiv.org/content/10.1101/2020.03.31.015198v1?rss=1 Zheng, Y. Han, M. K. L. Zhao, R. Blass, J. Zhang, J. Zhou, D. W. Colard-Itte, J.-R. Dattler, D. Giuseppone, N. Hoth, M. Garcia, A. J. Qu, B. Bennewitz, R. del Campo, A. 2020-03-31 doi:10.1101/2020.03.31.015198 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ Accumulation of dead cells from contact killing facilitates coexistence in bacterial biofilms ]]> https://biorxiv.org/content/10.1101/2020.04.03.024158v1?rss=1 Steinbach, G. Crisan, C. V. Ng, S. L. Hammer, B. K. Yunker, P. J. 2020-04-05 doi:10.1101/2020.04.03.024158 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Mechanics and energetics of walking and running up and downhill: A joint-level perspective to guide design of lower-limb exoskeletons ]]> https://biorxiv.org/content/10.1101/2020.04.07.029579v1?rss=1 Nuckols, R. W. Takahashi, K. Z. Farris, D. J. Mizrachi, S. Riemer, R. Sawicki, G. S. 2020-04-07 doi:10.1101/2020.04.07.029579 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors ]]> https://biorxiv.org/content/10.1101/2020.04.07.029694v1?rss=1 Lewis, J. E. Forshaw, T. E. Boothman, D. A. Furdui, C. M. Kemp, M. L. 2020-04-08 doi:10.1101/2020.04.07.029694 Cold Spring Harbor Laboratory Press 2020-04-08 <![CDATA[ Human Ribosomal G-Quadruplexes Regulate Heme Bioavailability ]]> https://biorxiv.org/content/10.1101/2020.04.15.042721v1?rss=1 Mestre-Fos, S. Ito, C. Moore, C. M. Reddi, A. R. Williams, L. D. 2020-04-15 doi:10.1101/2020.04.15.042721 Cold Spring Harbor Laboratory Press 2020-04-15 <![CDATA[ Transplantation of muscle stem cell mitochondria rejuvenates the bioenergetic function of dystrophic muscle ]]> https://biorxiv.org/content/10.1101/2020.04.17.017822v1?rss=1 Mohiuddin, M. Choi, J. J. Lee, N. H. Jeong, H. H. Anderson, S. E. Han, W. M. Aliya, B. Peykova, T. Z. Verma, S. Garcia, A. J. Aguilar, C. A. Jang, Y. C. 2020-04-18 doi:10.1101/2020.04.17.017822 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ NFATc acts as a non-canonical phenotypic stability factor for a hybrid epithelial/mesenchymal phenotype ]]> https://biorxiv.org/content/10.1101/2020.04.18.047803v1?rss=1 Subbalakshmi, A. R. Kundnani, D. Biswas, K. Ghosh, A. Hanash, S. Tripathi, S. C. Jolly, M. K. 2020-04-18 doi:10.1101/2020.04.18.047803 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Side-Impact Collision: Mechanics of Obstacle Negotiation in Sidewinding Snakes ]]> https://biorxiv.org/content/10.1101/2020.04.22.055681v1?rss=1 Astley, H. C. Rieser, J. M. Kaba, A. Paez, V. M. Tomkinson, I. Mendelson, J. R. Goldman, D. I. 2020-04-24 doi:10.1101/2020.04.22.055681 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ GRNUlar: Gene Regulatory Network reconstruction using Unrolled algorithm from Single Cell RNA-Sequencing data ]]> https://biorxiv.org/content/10.1101/2020.04.23.058149v1?rss=1 Shrivastava, H. Zhang, X. Aluru, S. Song, L. 2020-04-25 doi:10.1101/2020.04.23.058149 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Treating Influenza and SARS-CoV-2 via mRNA-encoded Cas13a ]]> https://biorxiv.org/content/10.1101/2020.04.24.060418v1?rss=1 Blanchard, E. L. Vanover, D. Bawage, S. S. Tiwari, P. M. Rotolo, L. Beyersdorf, J. Peck, H. E. Bruno, N. C. Hincapie, R. Finn, M. G. Michel, F. Lafontaine, E. R. Hogan, R. J. Zurla, C. Santangelo, P. J. 2020-04-24 doi:10.1101/2020.04.24.060418 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Remote control of CAR T cell therapies by thermal targeting ]]> https://biorxiv.org/content/10.1101/2020.04.26.062703v1?rss=1 Miller, I. C. Sun, L.-K. Harris, A. M. Gamboa, L. Zamat, A. Kwong, G. A. 2020-04-28 doi:10.1101/2020.04.26.062703 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ MSCquartets 1.0: Quartet methods for species trees and networks under the multispecies coalescent model in R ]]> https://biorxiv.org/content/10.1101/2020.05.01.073361v1?rss=1 Rhodes, J. A. Banos, H. Mitchell, J. D. Allman, E. S. 2020-05-03 doi:10.1101/2020.05.01.073361 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ Mechanism and function of root circumnutation ]]> https://biorxiv.org/content/10.1101/2020.05.04.075127v1?rss=1 Taylor, I. W. Lehner, K. R. McCaskey, E. N. Nirmal, N. A. Ozkan-Aydin, Y. Murray-Cooper, M. Jain, R. Hawkes, E. W. Ronald, P. C. Goldman, D. I. Benfey, P. N. 2020-05-05 doi:10.1101/2020.05.04.075127 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Addressing Inaccurate Nosology in Mental Health: A Multi Label Data Cleansing Approach for Detecting Label Noise from Structural Magnetic Resonance Imaging Data in Mood and Psychosis Disorders ]]> https://biorxiv.org/content/10.1101/2020.05.06.081521v1?rss=1 Rokham, H. Pearlson, G. Abrol, A. Falakshahi, H. Plis, S. Calhoun, V. 2020-05-08 doi:10.1101/2020.05.06.081521 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ Rapid Assembly and Screening of Multivalent Immune Cell-Redirecting Therapies for Leukemia ]]> https://biorxiv.org/content/10.1101/2020.05.08.082628v1?rss=1 Do, P. Perdue, L. A. Chyong, A. Hunter, R. Dougan, J. Henry, C. J. Porter, C. C. Dreaden, E. C. 2020-05-10 doi:10.1101/2020.05.08.082628 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Nano-Emulsion Adjuvant Enhances Cross-presentation by Lipid Body Formation Independent of Glycolysis ]]> https://biorxiv.org/content/10.1101/2020.05.08.083790v1?rss=1 Suresh, M. Lee, W. Kingstad-Bakke, B. Paulson, B. Larsen, A. Overmyer, K. Marinaik, C. Dull, K. Toy, R. Vogel, G. Mueller, K. Tweed, K. Walsh, A. Russell, J. Saha, K. Reyes, L. Skala, M. Sauer, J.-D. Shayakhmetov, D. M. Coon, J. Roy, K. 2020-05-12 doi:10.1101/2020.05.08.083790 Cold Spring Harbor Laboratory Press 2020-05-12 <![CDATA[ Microbial helpers allow cyanobacteria to thrive in ferruginous waters ]]> https://biorxiv.org/content/10.1101/2020.05.08.085001v1?rss=1 Szeinbaum, N. Toporek, Y. J. Reinhard, C. T. Glass, J. B. 2020-05-09 doi:10.1101/2020.05.08.085001 Cold Spring Harbor Laboratory Press 2020-05-09 <![CDATA[ Combined pigment and metatranscriptomic analysis reveals synchronized diel patterns of phenotypic light response across domains in the open ocean ]]> https://biorxiv.org/content/10.1101/2020.05.12.091322v1?rss=1 Becker, K. W. Harke, M. J. Mende, D. R. Muratore, D. Weitz, J. S. DeLong, E. F. Dyhrman, S. T. Van Mooy, B. A. S. 2020-05-14 doi:10.1101/2020.05.12.091322 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Polarized endosome dynamics engage cytosolic Par-3 and dynein during asymmetric division ]]> https://biorxiv.org/content/10.1101/2020.05.15.098012v1?rss=1 Zhao, X. Tong, K. Chen, x. Yang, B. Li, Q. Dai, Z. Shi, X. Seiple, I. Huang, B. Guo, S. 2020-05-16 doi:10.1101/2020.05.15.098012 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Community-scale Synchronization and Temporal Partitioning of Gene Expression, Metabolism, and Lipid Biosynthesis in Oligotrophic Ocean Surface Waters ]]> https://biorxiv.org/content/10.1101/2020.05.15.098020v1?rss=1 Muratore, D. Boysen, A. K. Harke, M. J. Becker, K. W. Casey, J. R. Coesel, S. N. Mende, D. R. Wilson, S. T. Aylward, F. O. Eppley, J. M. Vislova, A. Peng, S. Rodriguez-Gonzalez, R. A. Beckett, S. J. Armbrust, E. V. DeLong, E. F. Karl, D. M. White, A. E. Zehr, J. P. Van Mooy, B. A. S. Dyhrman, S. T. Ingalls, A. E. Weitz, J. S. 2020-05-16 doi:10.1101/2020.05.15.098020 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Visualizing the itch-sensing skin arbors ]]> https://biorxiv.org/content/10.1101/2020.05.18.098871v1?rss=1 Xing, Y. Steele, H. R. Hilley, H. B. Niehoff, T. Lawson, K. Han, L. 2020-05-20 doi:10.1101/2020.05.18.098871 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ T cells Mediate Progression of Load-Induced Osteoarthritis ]]> https://biorxiv.org/content/10.1101/2020.05.20.106435v1?rss=1 Wheeler, T. A. Antoinette, A. Y. Kim, M. J. van der Meulen, M. C. H. Singh, A. 2020-05-23 doi:10.1101/2020.05.20.106435 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ A Biphasic Approach for Characterizing Tensile, Compressive, and Hydraulic Properties of the Sclera ]]> https://biorxiv.org/content/10.1101/2020.05.21.108936v1?rss=1 Brown, D. M. Pardue, M. T. Ethier, C. R. 2020-05-25 doi:10.1101/2020.05.21.108936 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ First passage time study of DNA strand displacement ]]> https://biorxiv.org/content/10.1101/2020.05.21.109454v1?rss=1 Broadwater, D. W. B. Cook, A. W. Kim, H. D. 2020-05-22 doi:10.1101/2020.05.21.109454 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ A three-dimensional thalamocortical dataset for characterizing brain heterogeneity ]]> https://biorxiv.org/content/10.1101/2020.05.22.111617v1?rss=1 Prasad, J. A. Balwani, A. H. Johnson, E. C. Miano, J. D. Sampathkumar, V. de Andrade, V. Fezza, K. Du, M. Vescovi, R. Jacobsen, C. Kording, K. P. Gürsoy, D. Gray-Roncal, W. Kasthuri, N. Dyer, E. L. 2020-05-25 doi:10.1101/2020.05.22.111617 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Regenerating motor neurons prime muscle stem cells for myogenesis by enhancing protein synthesis and mitochondrial bioenergetics ]]> https://biorxiv.org/content/10.1101/2020.05.24.113456v1?rss=1 Choi, J. J. Shin, E. J. Han, W. M. Anderson, S. E. Mohiuddin, M. Lee, N. H. Tran, T. Nakhai, S. Jeong, H. Shcherbina, A. Jeong, G. Oh, D. G. Weinstock, L. Sankar, S. B. Ogle, M. E. Katsimpardi, L. Rao, T. N. Wood, L. B. Aguilar, C. A. Wagers, A. J. Jang, Y. C. 2020-05-26 doi:10.1101/2020.05.24.113456 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Collective protection and transport in entangled biological and robotic active matter ]]> https://biorxiv.org/content/10.1101/2020.05.25.114736v1?rss=1 Ozkan Aydin, Y. Goldman, D. I. Bhamla, M. S. 2020-05-27 doi:10.1101/2020.05.25.114736 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ A Deep Feature Learning Approach for Mapping the Brains Microarchitecture and Organization ]]> https://biorxiv.org/content/10.1101/2020.05.26.117473v1?rss=1 Balwani, A. H. Dyer, E. L. 2020-06-01 doi:10.1101/2020.05.26.117473 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ Novel heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase ]]> https://biorxiv.org/content/10.1101/2020.05.27.118968v1?rss=1 Gamiz-Arco, G. Gutierrez-Rus, L. Risso, V. Ibarra-Molero, B. Hoshino, Y. Petrovic, D. Romero-Rivera, A. Seelig, B. Gavira, J. Kamerlin, S. Gaucher, E. Sanchez-Ruiz, J. 2020-05-28 doi:10.1101/2020.05.27.118968 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Single Cell Deconstruction of Muscle Stem Cell Heterogeneity During Aging Reveals Sensitivity to the Neuromuscular Junction ]]> https://biorxiv.org/content/10.1101/2020.05.28.121426v1?rss=1 Ulintz, P. J. Larouche, J. Mohiuddin, M. Castor Macias, J. Kurpiers, S. J. Liu, W. Choi, J. J. Brown, L. A. Markworth, J. F. de Silva, K. Levi, B. D. Merajver, S. D. Chakkalakal, J. V. Jang, Y. C. Brooks, S. V. Aguilar, C. A. 2020-05-29 doi:10.1101/2020.05.28.121426 Cold Spring Harbor Laboratory Press 2020-05-29 <![CDATA[ The evolution of virulence in Pseudomonas aeruginosa during chronic wound infection ]]> https://biorxiv.org/content/10.1101/2020.05.29.124545v1?rss=1 Vanderwoude, J. Fleming, D. Azimi, S. Rumbaugh, K. Diggle, S. P. 2020-05-30 doi:10.1101/2020.05.29.124545 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ TreeMap: A Structured Approach to Fine Mapping of eQTL Variants ]]> https://biorxiv.org/content/10.1101/2020.05.31.125880v1?rss=1 Liu, L. Chandrashekar, P. Zeng, B. Sanderford, M. D. Kumar, S. Gibson, G. 2020-05-31 doi:10.1101/2020.05.31.125880 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ A generative modeling approach for interpreting population-level variability in brain structure ]]> https://biorxiv.org/content/10.1101/2020.06.04.134635v1?rss=1 Liu, R. Subakan, C. Balwani, A. H. Whitesell, J. D. Harris, J. A. Koyejo, S. Dyer, E. 2020-06-05 doi:10.1101/2020.06.04.134635 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Compensation of physiological motion enables high-yield whole-cell recording in vivo ]]> https://biorxiv.org/content/10.1101/2020.06.09.143008v1?rss=1 3 mm below the pial surface) from 26% (n=17/64) to 48% (n=32/66). Whole-cell recording yield improved from 10% (n = 9/88) to 24% (n=18/76) when motion compensation was used during the gigaseal formation. As an example of its application, we utilized this system to investigate the role of the sensory environment and ventral posterior medial region (VPM) projection synchrony on intracellular dynamics in the barrel cortex. This method results in substantially greater subcortical whole-cell recording yield than previously reported and thus makes pan-brain whole-cell electrophysiology practical in the living mouse brain. ]]> Stoy, W. M. Yang, B. Kight, A. Wright, N. C. Borden, P. Y. Stanley, G. B. Forest, C. R. 2020-06-11 doi:10.1101/2020.06.09.143008 Cold Spring Harbor Laboratory Press 2020-06-11 <![CDATA[ Combinatorial phosphorylation modulates the structure and function of the G protein gamma subunit in yeast ]]> https://biorxiv.org/content/10.1101/2020.06.09.143123v1?rss=1 Nassiri Toosi, Z. Su, X. Choudhury, S. Li, W. Pang, Y. T. Gumbart, J. C. Torres, M. P. 2020-06-11 doi:10.1101/2020.06.09.143123 Cold Spring Harbor Laboratory Press 2020-06-11 <![CDATA[ Mainly on the Plane: Deep Subsurface Bacterial Proteins Bind and Alter Clathrate Structure ]]> https://biorxiv.org/content/10.1101/2020.06.15.152181v1?rss=1 Johnson, A. M. Huard, D. J. E. Kim, J. Raut, P. Dai, S. Lieberman, R. L. Glass, J. B. 2020-06-15 doi:10.1101/2020.06.15.152181 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Metagenomic characterization of soil microbial communities in the Luquillo experimental forest (Puerto Rico) and implications for nitrogen cycling ]]> https://biorxiv.org/content/10.1101/2020.06.15.153866v1?rss=1 Karthikeyan, S. Orellana, L. H. Johnston, E. R. Hatt, J. Löffler, F. E. Ayala-del-Rio, H. Gonzalez, G. Konstantinidis, K. T. 2020-06-16 doi:10.1101/2020.06.15.153866 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ Glucose promotes resistance of human commensal Escherichia coli against contact-killing by pandemic Vibrio cholerae ]]> https://biorxiv.org/content/10.1101/2020.06.22.166306v1?rss=1 Crisan, C. Nichols, H. Wiesenfeld, S. Steinbach, G. Yunker, P. J. Hammer, B. K. 2020-06-23 doi:10.1101/2020.06.22.166306 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ A classification-based approach to estimate the number of resting fMRI dynamic functional connectivity states ]]> https://biorxiv.org/content/10.1101/2020.06.24.161745v1?rss=1 Saha, D. K. Damaraju, E. Rashid, B. Abrol, A. Plis, S. Calhoun, V. 2020-06-25 doi:10.1101/2020.06.24.161745 Cold Spring Harbor Laboratory Press 2020-06-25 <![CDATA[ JAGGED1 Stimulates Cranial Neural Crest Cell Osteoblast Commitment Pathways and Bone Regeneration Independent of Canonical NOTCH Signaling ]]> https://biorxiv.org/content/10.1101/2020.06.24.169755v1?rss=1 Kamalakar, A. McKinney, J. M. Salinas Duron, D. Amanso, A. M. Ballestas-Naissir, S. A. Drissi, H. Willett, N. J. Bhattaram, P. Garcia, A. J. Wood, L. B. Goudy, s. 2020-06-24 doi:10.1101/2020.06.24.169755 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ State-space optimal feedback control of optogenetically driven neural activity ]]> https://biorxiv.org/content/10.1101/2020.06.25.171785v1?rss=1 Bolus, M. F. Willats, A. A. Rozell, C. J. Stanley, G. B. 2020-06-29 doi:10.1101/2020.06.25.171785 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Chromosome fusions shape an ancient UV sex chromosome system ]]> https://biorxiv.org/content/10.1101/2020.07.03.163634v1?rss=1 Carey, S. B. Jenkins, J. Payton, A. C. Shu, S. Lovell, J. T. Maumus, F. Sreedasyam, A. Tiley, G. P. Fernandez-Pozo, N. Barry, K. Chen, C. Wang, M. Lipzen, A. Daum, C. Saski, C. A. McBreen, J. C. Conrad, R. E. Kollar, L. M. Olsson, S. Huttunen, S. Landis, J. B. Burleigh, G. Wickett, N. J. Johnson, M. G. Rensing, S. A. Grimwood, J. Schmutz, J. McDaniel, S. 2020-07-04 doi:10.1101/2020.07.03.163634 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Quantitative benzimidazole resistance and fitness effects of parasitic nematode beta-tubulin alleles ]]> https://biorxiv.org/content/10.1101/2020.07.07.191866v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@139cb71org.highwire.dtl.DTLVardef@15b8f53org.highwire.dtl.DTLVardef@1e98feorg.highwire.dtl.DTLVardef@ce8847_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Clayton M. Dilks Steffen R. Hahnel Qicong Sheng Lijiang Long Patrick T. McGrath Erik C. Andersen 2020-07-08 doi:10.1101/2020.07.07.191866 Cold Spring Harbor Laboratory Press 2020-07-08 <![CDATA[ Polymeric Pathogen-like Particles-Based Combination Adjuvants Elicit Potent Mucosal T Cell Immunity to Influenza A Virus ]]> https://biorxiv.org/content/10.1101/2020.07.10.197749v1?rss=1 Brock A Bakke Randall Toy Woojong Lee Pallab Pradhan Gabriela Vogel Chandranaik Marinaik Autumn Larsen Yoshihiro Kawaoka Krishnendu A Roy M Suresh 2020-07-11 doi:10.1101/2020.07.10.197749 Cold Spring Harbor Laboratory Press 2020-07-11 <![CDATA[ Cell-type and cytosine context-specific evolution of DNA methylation in the human brain ]]> https://biorxiv.org/content/10.1101/2020.07.14.203034v1?rss=1 Jeong, H. Mendizabal, I. Berto, S. Chatterjee, P. Layman, T. Usui, N. Toriumi, K. Douglas, C. Singh, D. Huh, I. Preuss, T. M. Konopka, G. Yi, S. V. 2020-07-14 doi:10.1101/2020.07.14.203034 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ Endothelial reprogramming by disturbed flow revealed by single-cell RNA and chromatin accessibility study ]]> https://biorxiv.org/content/10.1101/2020.07.15.205427v1?rss=1 Andueza, A. Kumar, S. Kim, J. Kang, D. W. Mumme, H. L. Perez, J. I. Jo, H. 2020-07-15 doi:10.1101/2020.07.15.205427 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ TRAF6-IRF5 kinetics, TRIF, and biophysical factors drive synergistic innate responses to particle-mediated MPLA-CpG co-presentation ]]> https://biorxiv.org/content/10.1101/2020.07.17.207209v1?rss=1 Pradhan, P. Toy, R. Jhita, N. Blanchard, E. L. Atalis, A. Pandey, B. Santangelo, P. J. Shayakhmetov, D. M. Roy, K. 2020-07-17 doi:10.1101/2020.07.17.207209 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ TLR7 and RIG-I dual-adjuvant loaded nanoparticles drive broadened and synergistic responses in dendritic cells and boost cellular immunity in influenza vaccination ]]> https://biorxiv.org/content/10.1101/2020.07.17.207423v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@1599111org.highwire.dtl.DTLVardef@1431395org.highwire.dtl.DTLVardef@baa40dorg.highwire.dtl.DTLVardef@16877cf_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Toy, R. Keenum, M. C. Pradhan, P. Phang, K. Chen, P. Chukwu, C. Nguyen, A. Liu, J. Jain, S. Kozlowski, G. Hosten, J. Suthar, M. Roy, K. 2020-07-17 doi:10.1101/2020.07.17.207423 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Antifibrotic activity of a rho-kinase inhibitor restores outflow function and intraocular pressure homeostasis ]]> https://biorxiv.org/content/10.1101/2020.07.17.208207v1?rss=1 Li, G. Lee, C. Read, A. T. Wang, K. Navarro, I. Cui, J. Young, K. Gorijavolu, R. Sulchek, T. Kopczynski, C. Farsiu, S. Samples, J. Challa, P. Ethier, C. R. Stamer, W. D. 2020-07-17 doi:10.1101/2020.07.17.208207 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs ]]> https://biorxiv.org/content/10.1101/2020.07.20.211532v1?rss=1 70% similarity in functional pathways. These community-wide patterns were further confirmed by analysis of metagenome-assembled genomes (MAGs), which showed - in addition- that novel species and genera of the chemoautotrophic Campylobacterales order dominated the springs. These MAGs carried different pathways for thiosulfate and/or sulfide oxidation coupled to carbon fixation pathways. Overall, our study showed that even in the long term, functions of microbial communities in a moderately hot terrestrial spring remain stable, driving presumably the corresponding stability in community structure. ]]> Meziti, A. Nikouli, E. Hatt, J. Konstantinidis, K. T. Kormas, K. A. 2020-07-20 doi:10.1101/2020.07.20.211532 Cold Spring Harbor Laboratory Press 2020-07-20 <![CDATA[ MicrobeAnnotator: a user-friendly, comprehensive microbial genome annotation pipeline ]]> https://biorxiv.org/content/10.1101/2020.07.20.211847v1?rss=1 Ruiz Perez, C. A. Conrad, R. E. Konstantinidis, K. T. 2020-07-21 doi:10.1101/2020.07.20.211847 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Genome-wide variation in DNA methylation linked to developmental stage and chromosomal suppression of recombination in white-throated sparrows ]]> https://biorxiv.org/content/10.1101/2020.07.24.220582v1?rss=1 Sun, D. Layman, T. Jeong, H. Chatterjee, P. Grogan, K. Merritt, J. Maney, D. Yi, S. 2020-07-25 doi:10.1101/2020.07.24.220582 Cold Spring Harbor Laboratory Press 2020-07-25 <![CDATA[ Using genetically encoded heme sensors to probe the mechanisms of heme uptake and homeostasis in Candida albicans ]]> https://biorxiv.org/content/10.1101/2020.07.26.221606v1?rss=1 Weissman, Z. Pinsky, M. Donegan, R. K. Reddi, A. R. Kornitzer, D. 2020-07-26 doi:10.1101/2020.07.26.221606 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ The landscape of micro-inversions provides clues for population genetic analysis of humans ]]> https://biorxiv.org/content/10.1101/2020.07.27.218867v1?rss=1 Qu, L. Wang, L. He, F. Han, Y. Yang, L. Wang, M. D. Zhu, H. 2020-07-27 doi:10.1101/2020.07.27.218867 Cold Spring Harbor Laboratory Press 2020-07-27 <![CDATA[ Effects of osteogenic ambulatory mechanical stimulation on early stages of BMP-2mediated bone repair ]]> https://biorxiv.org/content/10.1101/2020.07.28.225870v1?rss=1 Klosterhoff, B. S. Vantucci, C. E. Kaiser, J. Ong, K. G. Wood, L. B. Weiss, J. A. Guldberg, R. E. Willett, N. J. 2020-07-29 doi:10.1101/2020.07.28.225870 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Biomaterial encapsulation of human mesenchymal stromal cells modulates paracrine signaling response and enhances efficacy for treatment of established osteoarthritis ]]> https://biorxiv.org/content/10.1101/2020.07.30.228288v1?rss=1 McKinney, J. M. Pucha, K. A. Doan, T. N. Wang, L. Weinstock, L. D. Tignor, B. T. Fowle, K. L. Levit, R. D. Wood, L. B. Willett, N. J. 2020-07-30 doi:10.1101/2020.07.30.228288 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ Integration of machine learning and genome-scale metabolic modeling identifies multi-omics biomarkers for radiation resistance ]]> https://biorxiv.org/content/10.1101/2020.08.02.233098v1?rss=1 Lewis, J. E. Kemp, M. L. 2020-08-02 doi:10.1101/2020.08.02.233098 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ Heterogenous response to R-pyocin killing in populations of Pseudomonas aeruginosa sourced from cystic fibrosis lungs ]]> https://biorxiv.org/content/10.1101/2020.08.05.238956v1?rss=1 Mei, M. Thomas, J. Diggle, S. P. 2020-08-06 doi:10.1101/2020.08.05.238956 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ A novel method for tri-clustering dynamic functional network connectivity (dFNC) identifies significant schizophrenia effects across multiple states in distinct subgroups of individuals ]]> https://biorxiv.org/content/10.1101/2020.08.06.239152v1?rss=1 Rahaman, M. A. Damaraju, E. Turner, J. van Erp, T. G. M. Mathalon, D. Vaidya, J. Muller, B. Pearlson, G. D. Calhoun, V. D. 2020-08-07 doi:10.1101/2020.08.06.239152 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ BRAKER2: Automatic Eukaryotic Genome Annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database ]]> https://biorxiv.org/content/10.1101/2020.08.10.245134v1?rss=1 Bruna, T. Hoff, K. Stanke, M. Lomsadze, A. Borodovsky, M. 2020-08-11 doi:10.1101/2020.08.10.245134 Cold Spring Harbor Laboratory Press 2020-08-11 <![CDATA[ Wing damage affects flight kinematics but not flower tracking performance in hummingbird hawkmoths ]]> https://biorxiv.org/content/10.1101/2020.08.16.252759v1?rss=1 Kihlström, K. Aiello, B. Warrant, E. J. Sponberg, S. Stoeckl, A. L. 2020-08-18 doi:10.1101/2020.08.16.252759 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Statelets: high dimensional predominant shapes in dynamic functional network connectivity ]]> https://biorxiv.org/content/10.1101/2020.08.16.252999v1?rss=1 Rahaman, M. A. Damaraju, E. Saha, D. K. Plis, S. M. Calhoun, V. 2020-08-17 doi:10.1101/2020.08.16.252999 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ A thermal trade-off between viral production and degradation drives phytoplankton-virus population dynamics ]]> https://biorxiv.org/content/10.1101/2020.08.18.256156v1?rss=1 Demory, D. Weitz, J. Baudoux, A.-C. Touzeau, S. Simon, N. Ranbouille, S. Sciandra, A. Bernard, O. 2020-08-18 doi:10.1101/2020.08.18.256156 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Divergent DNA methylation signatures underlying X chromosome regulation in marsupials and eutherians ]]> https://biorxiv.org/content/10.1101/2020.08.26.269068v1?rss=1 Singh, D. Sun, D. King, A. G. Alquezar-Planas, D. E. Johnson, R. N. Alvarez-Ponce, D. Yi, S. V. 2020-08-27 doi:10.1101/2020.08.26.269068 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Mapping ribonucleotides embedded in genomic DNA to single-nucleotide resolution using Ribose-Map ]]> https://biorxiv.org/content/10.1101/2020.08.27.267153v1?rss=1 Gombolay, A. Storici, F. 2020-08-27 doi:10.1101/2020.08.27.267153 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2020.08.27.270314v1?rss=1 El-Sayed, W. M. M. Gombolay, A. L. Xu, P. Yang, T. Jeon, Y. Balachander, S. Newnam, G. Tao, S. Bowen, N. E. Schinazi, R. F. Kim, B. Chen, Y. Storici, F. 2020-08-27 doi:10.1101/2020.08.27.270314 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Gene co-expression analysis of human RNASEH2A reveals functional networks associated with DNA replication, DNA damage response, and cell cycle regulation ]]> https://biorxiv.org/content/10.1101/2020.08.27.270595v1?rss=1 Marsili, S. Tichon, A. Storici, F. 2020-08-27 doi:10.1101/2020.08.27.270595 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Ribonucleotide incorporation characteristics around yeast autonomously replicating sequences reveal the labor division of replicative DNA polymerases ]]> https://biorxiv.org/content/10.1101/2020.08.27.270728v1?rss=1 Xu, P. Storici, F. 2020-08-28 doi:10.1101/2020.08.27.270728 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ An Approach to Automatically Label & Order Brain Activity/Component Maps ]]> https://biorxiv.org/content/10.1101/2020.08.31.275578v1?rss=1 Salman, M. S. Wager, T. D. Damaraju, E. C. Abrol, A. Calhoun, V. D. 2020-09-01 doi:10.1101/2020.08.31.275578 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Depsipeptide nucleic acids: prebiotic formation, oligomerization, and self-assembly of a new candidate proto-nucleic acid ]]> https://biorxiv.org/content/10.1101/2020.09.01.278838v1?rss=1 Hud, N. V. Fialho, D. M. Karunakaran, S. Greeson, K. W. Martinez, I. Schuster, G. B. Krishnamurthy, R. 2020-09-04 doi:10.1101/2020.09.01.278838 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ Quantitative analysis of transporter activity biosensors ]]> https://biorxiv.org/content/10.1101/2020.09.03.282301v1?rss=1 Park, J. Chavez, T. M. Frommer, W. Cheung, L. S. 2020-09-04 doi:10.1101/2020.09.03.282301 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease ]]> https://biorxiv.org/content/10.1101/2020.09.07.286344v1?rss=1 Pavlova, A. Lynch, D. L. Daidone, I. Zanetti-Polzi, L. Smith, M. D. Chipot, C. Kneller, D. W. Kovalevsky, A. Coates, L. Golosov, A. A. Dickson, C. J. Velez-Vega, C. Duca, J. S. Vermaas, J. V. Pang, Y. T. Acharya, A. Parks, J. M. Smith, J. C. Gumbart, J. C. 2020-09-10 doi:10.1101/2020.09.07.286344 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Identifiability of Tissue Material Parameters from Uniaxial Tests using Multi-start Optimization ]]> https://biorxiv.org/content/10.1101/2020.09.09.289702v1?rss=1 Safa, B. N. Santare, M. H. Ethier, C. R. Elliott, D. M. 2020-09-10 doi:10.1101/2020.09.09.289702 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Single-Cell RNAseq of Out-of-Thaw Mesenchymal Stromal Cells Shows Striking Tissue-of-Origin Differences and Inter-donor Cell-Cycle Variations ]]> https://biorxiv.org/content/10.1101/2020.09.10.290155v1?rss=1 Trochez, C. M. Chatterjee, P. Pradhan, P. Ogle, M. E. Botchwey, E. A. Kurtzberg, J. Yeago, C. Gibson, G. Roy, K. 2020-09-11 doi:10.1101/2020.09.10.290155 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ R2DT: computational framework for template-based RNA secondary structure visualisation across non-coding RNA types ]]> https://biorxiv.org/content/10.1101/2020.09.10.290924v1?rss=1 13 million diagrams, creating the worlds largest RNA 2D structure dataset. The software is freely available at https://github.com/rnacentral/R2DT and a web server is found at https://rnacentral.org/r2dt. ]]> Sweeney, B. A. Hoksza, D. Nawrocki, E. P. Ribas, C. E. Madeira, F. Cannone, J. J. Gutell, R. R. Maddala, A. Meade, C. Williams, L. D. Petrov, A. S. Chan, P. P. Lowe, T. M. Finn, R. D. Petrov, A. I. 2020-09-11 doi:10.1101/2020.09.10.290924 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ TIN2 facilitates TRF1-mediated trans- and cis-interactions on physiologically relevant long telomeric DNA ]]> https://biorxiv.org/content/10.1101/2020.09.12.286559v1?rss=1 Pan, H. Kaur, P. Liu, M. Xu, P. Mahn, C. Barnes, R. Tang, Q. Hao, P. Bhattaram, D. You, C. Piehler, J. Weninger, K. Riehn, R. Smith, S. Opersko, P. L. Wang, H. 2020-09-13 doi:10.1101/2020.09.12.286559 Cold Spring Harbor Laboratory Press 2020-09-13 <![CDATA[ Single-Cell Transcriptomic Attributes and Unbiased Computational Modeling for the Prediction of Immunomodulatory Potency of Mesenchymal Stromal Cells ]]> https://biorxiv.org/content/10.1101/2020.09.12.294850v1?rss=1 Pradhan, P. Chatterjee, P. Stevens, H. Y. Glen, C. Medrano-Trochez, C. Jimenez, A. Kippner, L. Seeto, W. J. Li, Y. Gibson, G. Kurtzberg, J. Kontanchek, T. Yeago, C. Roy, K. 2020-09-12 doi:10.1101/2020.09.12.294850 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ Quantitative and dynamic cell polarity tracking in plant cells ]]> https://biorxiv.org/content/10.1101/2020.09.12.294942v1?rss=1 Gong, Y. Varnau, R. Wallner, E.-S. Bergmann, D. C. Cheung, L. S. 2020-09-13 doi:10.1101/2020.09.12.294942 Cold Spring Harbor Laboratory Press 2020-09-13 <![CDATA[ Constrained brain volume in an efficient coding model explains the fraction of excitatory and inhibitory neurons in sensory cortices ]]> https://biorxiv.org/content/10.1101/2020.09.17.299040v1?rss=1 Alreja, A. Nemenman, I. Rozell, C. J. 2020-09-19 doi:10.1101/2020.09.17.299040 Cold Spring Harbor Laboratory Press 2020-09-19 <![CDATA[ Long-term cellulose enrichment selects for highly cellulolytic consortia and competition for public goods ]]> https://biorxiv.org/content/10.1101/2020.09.18.304485v1?rss=1 Lewin, G. R. Davis, N. M. McDonald, B. R. Book, A. J. Chevrette, M. G. Suh, S. Boll, A. Currie, C. R. 2020-09-19 doi:10.1101/2020.09.18.304485 Cold Spring Harbor Laboratory Press 2020-09-19 <![CDATA[ A Probabilistic and Anisotropic Failure Metric for Ascending Thoracic Aortic Aneurysm Risk Stratification ]]> https://biorxiv.org/content/10.1101/2020.09.28.317255v1?rss=1 Liu, M. Liang, L. Zou, Q. Ismail, Y. Lou, X. Iannucci, G. Chen, E. P. Leshnower, B. G. Elefteriades, J. A. Sun, W. 2020-09-29 doi:10.1101/2020.09.28.317255 Cold Spring Harbor Laboratory Press 2020-09-29 <![CDATA[ Inference of multiple trajectories in single cell RNA-seq data from RNA velocity ]]> https://biorxiv.org/content/10.1101/2020.09.30.321125v1?rss=1 Zhang, Z. Zhang, X. 2020-10-02 doi:10.1101/2020.09.30.321125 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Rapid Cortical Adaptation and the Role of Thalamic Synchrony During Wakefulness ]]> https://biorxiv.org/content/10.1101/2020.10.08.331660v1?rss=1 Wright, N. C. Borden, P. Y. Liew, Y. J. Bolus, M. F. Stoy, W. M. Forest, C. R. Stanley, G. B. 2020-10-08 doi:10.1101/2020.10.08.331660 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Inferring Monosynaptic Connectivity Across Brain Structures In-Vivo ]]> https://biorxiv.org/content/10.1101/2020.10.09.333930v1?rss=1 Liew, Y. J. Pala, A. Whitmire, C. J. Stoy, W. A. Forest, C. R. Stanley, G. B. 2020-10-09 doi:10.1101/2020.10.09.333930 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Genome-enabled inference of functional genetic variants in the face, brain and behavior ]]> https://biorxiv.org/content/10.1101/2020.10.12.336453v1?rss=1 Patil, C. K. Sylvester, J. B. Abdilleh, K. Norsworthy, M. W. Pottin, K. Malinsky, M. Bloomquist, R. Johnson, Z. McGrath, P. T. Streelman, J. T. 2020-10-12 doi:10.1101/2020.10.12.336453 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ Rapid Development of Neutralizing and Diagnostic SARS-COV-2 Mouse Monoclonal Antibodies ]]> https://biorxiv.org/content/10.1101/2020.10.13.338095v1?rss=1 Chapman, A. P. Tang, X. Lee, J. R. Chida, A. Mercer, K. Wharton, R. E. Kainulainen, M. H. Harcourt, J. L. Martines, R. B. Schroeder, M. Zhao, L. Bryksin, A. Zhou, B. Bergeron, E. Bollweg, B. C. Tamin, A. Thornburg, N. Wentworth, D. E. Petway, D. Bagarozzi, D. Finn, M. G. Goldstein, J. M. 2020-10-14 doi:10.1101/2020.10.13.338095 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Gulf of Mexico blue hole harbors high levels of novel microbial lineages ]]> https://biorxiv.org/content/10.1101/2020.10.18.342550v1?rss=1 Patin, N. V. Dietrich, Z. A. Stancil, A. Quinan, M. Beckler, J. Hall, E. R. Culter, J. Smith, C. G. Taillefert, M. Stewart, F. J. 2020-10-19 doi:10.1101/2020.10.18.342550 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ Learning sparse codes from compressed representations with biologically plausible local wiring constraints ]]> https://biorxiv.org/content/10.1101/2020.10.23.352443v1?rss=1 Fallah, K. Willats, A. A. Liu, N. Rozell, C. J. 2020-10-23 doi:10.1101/2020.10.23.352443 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ StartLink+: Prediction of Gene Starts in Prokaryotic Genomes by an Algorithm Integrating Independent Sources of Evidence ]]> https://biorxiv.org/content/10.1101/2020.10.25.352625v1?rss=1 Gemayel, K. Lomsadze, A. Borodovsky, M. 2020-10-26 doi:10.1101/2020.10.25.352625 Cold Spring Harbor Laboratory Press 2020-10-26 <![CDATA[ Spatial modulation of dark versus bright stimulus responses in mouse visual cortex ]]> https://biorxiv.org/content/10.1101/2020.10.27.353573v1?rss=1 Williams, B. Del Rosario, J. Coletta, S. Murlin, E. K. Muzzu, T. Speed, A. Meyer-Baese, L. Saleem, A. B. Haider, B. 2020-10-28 doi:10.1101/2020.10.27.353573 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Wing shape evolution in bombycoid moths reveals two distinct strategies for maneuverable flight ]]> https://biorxiv.org/content/10.1101/2020.10.27.358176v1?rss=1 Aiello, B. R. Sikandar, U. B. Minoguchi, H. Kimball, K. Hamilton, C. A. Kawahara, A. Y. Sponberg, S. 2020-10-28 doi:10.1101/2020.10.27.358176 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Leapfrog dynamics in phage-bacteria coevolution revealed by joint analysis of cross-infection phenotypes and whole genome sequencing ]]> https://biorxiv.org/content/10.1101/2020.10.31.337758v1?rss=1 Gupta, A. Peng, S. Leung, C. Y. Borin, J. M. Weitz, J. Meyer, J. R. 2020-11-01 doi:10.1101/2020.10.31.337758 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ MetaPop: A pipeline for macro- and micro-diversity analyses and visualization of microbial and viral metagenome-derived populations ]]> https://biorxiv.org/content/10.1101/2020.11.01.363960v1?rss=1 Gregory, A. C. Gerhardt, K. Zhong, Z.-P. Bolduc, B. Temperton, B. Konstantinidis, K. T. C. Sullivan, M. B. 2020-11-02 doi:10.1101/2020.11.01.363960 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ Hybrid Clustering of single-cell gene-expression and cell spatial information via integrated NMF and k-means ]]> https://biorxiv.org/content/10.1101/2020.11.15.383281v1?rss=1 Oh, S. Park, H. Zhang, X. 2020-11-15 doi:10.1101/2020.11.15.383281 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ Multidimensional single-cell modeling of cellular signaling ]]> https://biorxiv.org/content/10.1101/2020.11.15.383711v1?rss=1 Wade, J. D. Lun, X. Bodenmiller, B. Voit, E. D. 2020-11-16 doi:10.1101/2020.11.15.383711 Cold Spring Harbor Laboratory Press 2020-11-16 <![CDATA[ Methylation Quantitative Trait Loci are Largely Consistent across Disease States in Crohns disease ]]> https://biorxiv.org/content/10.1101/2020.11.16.385534v1?rss=1 Venkateswaran, S. Somineni, H. K. Kilaru, V. Kartrinli, S. Prince, J. Okou, D. Hyams, J. S. Lee, D. A. Kellermayer, R. Gibson, G. Cutler, D. Smith, A. K. Kugathasan, S. Conneely, K. 2020-11-17 doi:10.1101/2020.11.16.385534 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ Adherent cell remodeling on micropatterns is modulated by Piezo1 channels ]]> https://biorxiv.org/content/10.1101/2020.11.18.389106v1?rss=1 Jetta, D. Bahrani Fard, M. R. Sachs, F. Munechika, K. Hua, S. Z. 2020-11-20 doi:10.1101/2020.11.18.389106 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Spatial heterogeneity of glioblastoma cells reveals sensitivity to NAD+ depletion at tumor edge ]]> https://biorxiv.org/content/10.1101/2020.11.26.399725v1?rss=1 Yamashita, D. Botta, D. Cho, H. J. Guo, X. Ozaki, S. Flanary, V. L. Sirota, I. Gao, M. Yamaguchi, S. Nakano, M. A. Zhou, F. Zhou, H. Kondo, T. Kunieda, T. Crossman, D. Kornblum, H. Gorospe, M. Nam, D.-H. Zamboni, N. Gu, Z. Lund, F. E. Nakano, I. 2020-11-27 doi:10.1101/2020.11.26.399725 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Effect of human synovial fluid from osteoarthritis patients and healthy individuals on lymphatic contractility ]]> https://biorxiv.org/content/10.1101/2020.12.02.408294v1?rss=1 Michalaki, E. Nepiyushchikh, Z. V. Bernard, F. C. Rudd, J. M. Mukherjee, A. McKinney, J. M. Doan, T. N. Willett, N. J. Dixon, J. B. 2020-12-03 doi:10.1101/2020.12.02.408294 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ A Budding Yeast Model for Human Disease Mutations in the EXOSC2 Cap Subunit of the RNA Exosome ]]> https://biorxiv.org/content/10.1101/2020.12.06.413658v1?rss=1 Sterrett, M. C. Enyenihi, L. Leung, S. W. Hess, L. Strassler, S. E. Farchi, D. Lee, R. S. Withers, E. S. Kremsky, I. Baker, R. E. Basrai, M. A. Van Hoof, A. Fasken, M. B. Corbett, A. H. 2020-12-07 doi:10.1101/2020.12.06.413658 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ Hawkmoths use wingstroke-to-wingstroke frequency modulation for aerial recovery to vortex ring perturbations ]]> https://biorxiv.org/content/10.1101/2020.12.07.413781v1?rss=1 Gau, J. Gemilere, R. LDS-VIP FM subteam, Lynch, J. Gravish, N. Sponberg, S. 2020-12-08 doi:10.1101/2020.12.07.413781 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ Activity-based urinary biomarkers of response and resistance to checkpoint blockade immunotherapy ]]> https://biorxiv.org/content/10.1101/2020.12.10.420265v1?rss=1 0.9). Our data supports the use of activity-based biomarkers for early on-treatment response assessment and classification of refractory tumors based on resistance mechanisms. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/420265v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@12ce799org.highwire.dtl.DTLVardef@118fcc5org.highwire.dtl.DTLVardef@17b227eorg.highwire.dtl.DTLVardef@115a7fc_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mac, Q. D. Xu, C. Bowen, J. R. Sivakumar, A. Phuengkham, H. Su, F.-Y. Stentz, S. Z. Sim, H. Harris, A. M. Li, T. T. Qiu, P. Kwong, G. A. 2020-12-11 doi:10.1101/2020.12.10.420265 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Propagating patterns of intrinsic activity along macroscale gradients coordinate functional connections across the whole brain ]]> https://biorxiv.org/content/10.1101/2020.12.11.422071v1?rss=1 Yousefi, B. Keilholz, S. 2020-12-12 doi:10.1101/2020.12.11.422071 Cold Spring Harbor Laboratory Press 2020-12-12 <![CDATA[ Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations ]]> https://biorxiv.org/content/10.1101/2020.12.15.422944v1?rss=1 ter Horst, A. M. Santos-Medellin, C. Sorensen, J. W. Zinke, L. A. Wilson, R. M. Johnston, E. R. Trubl, G. G. Pett-Ridge, J. Blazewicz, S. J. Hanson, P. J. Chanton, J. P. Schadt, C. W. Kostka, J. E. Emerson, J. B. 2020-12-15 doi:10.1101/2020.12.15.422944 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Quantitative Control of Noise in Mammalian Gene Expression by Dynamic Histone Regulations ]]> https://biorxiv.org/content/10.1101/2020.12.20.423693v1?rss=1 Tan, D. Chen, R. Mo, Y. Xu, W. Lu, X. He, H. Gu, S. Jiang, F. Fan, W. Wang, Y. Chen, X. Huang, W. 2020-12-21 doi:10.1101/2020.12.20.423693 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ Multiple overlapping dynamic patterns of the visual sensory network in schizophrenia ]]> https://biorxiv.org/content/10.1101/2020.12.21.423535v1?rss=1 Sendi, M. S. E. Pearlson, G. D. Mathalon, D. H. Ford, J. M. Preda, A. van Erp, T. G. M. Calhoun, V. D. 2020-12-22 doi:10.1101/2020.12.21.423535 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Disrupted dynamic functional network connectivity among cognitive control networks in the progression of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2020.12.31.424877v1?rss=1 Sendi, M. S. E. Zendehrouh, E. Fu, Z. Liu, J. Du, Y. Mormino, E. C. Salat, D. H. Miller, R. L. Calhoun, V. 2021-01-03 doi:10.1101/2020.12.31.424877 Cold Spring Harbor Laboratory Press 2021-01-03 <![CDATA[ Aberrant Dynamic Functional Connectivity of Default Mode Network in Schizophrenia and Links to Symptom Severity ]]> https://biorxiv.org/content/10.1101/2021.01.03.425152v1?rss=1 Sendi, M. S. E. Zendehrouh, E. Ellis, C. A. Liang, Z. Fu, Z. Mathalon, D. H. Ford, J. M. Preda, A. van Erp, T. G. M. Miller, R. L. Pearlson, G. D. Turner, J. A. Calhoun, V. D. 2021-01-04 doi:10.1101/2021.01.03.425152 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ A novel approach to the empirical characterization of learning in biological systems ]]> https://biorxiv.org/content/10.1101/2021.01.10.426118v1?rss=1 Cohen, Y. Cvitanovic, P. Solla, S. A. 2021-01-10 doi:10.1101/2021.01.10.426118 Cold Spring Harbor Laboratory Press 2021-01-10 <![CDATA[ VeloSim: Simulating single cell gene-expression and RNA velocity ]]> https://biorxiv.org/content/10.1101/2021.01.11.426277v1?rss=1 Zhang, Z. Zhang, X. 2021-01-13 doi:10.1101/2021.01.11.426277 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ Periplasm homeostatic regulation maintains spatial constraints essential for cell envelope processes and cell viability ]]> https://biorxiv.org/content/10.1101/2021.01.13.426498v1?rss=1 Mandela, E. Stubenrauch, C. J. Ryoo, D. Hwang, H. Cohen, E. J. Torres, V. V. L. Deo, P. Webb, C. T. Huang, C. Schittenhelm, R. B. Beeby, M. C. Gumbart, J. Lithgow, T. Hay, I. D. 2021-01-13 doi:10.1101/2021.01.13.426498 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ A large-scale neural network training framework for generalized estimation of single-trial population dynamics ]]> https://biorxiv.org/content/10.1101/2021.01.13.426570v1?rss=1 Keshtkaran, M. R. Sedler, A. R. Chowdhury, R. H. Tandon, R. Basrai, D. Nguyen, S. L. Sohn, H. Jazayeri, M. Miller, L. E. Pandarinath, C. 2021-01-15 doi:10.1101/2021.01.13.426570 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ Cell surface hydrophobicity determines Pseudomonas aeruginosa aggregate assembly ]]> https://biorxiv.org/content/10.1101/2021.01.14.426723v1?rss=1 Azimi, S. Thomas, J. Cleland, S. Curtis, J. E. Goldberg, J. B. Diggle, S. P. 2021-01-14 doi:10.1101/2021.01.14.426723 Cold Spring Harbor Laboratory Press 2021-01-14 <![CDATA[ Representation learning for neural population activity with Neural Data Transformers ]]> https://biorxiv.org/content/10.1101/2021.01.16.426955v1?rss=1 Ye, J. Pandarinath, C. 2021-01-19 doi:10.1101/2021.01.16.426955 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ RNAStructViz: Graphical base pairing analysis ]]> https://biorxiv.org/content/10.1101/2021.01.20.427505v1?rss=1 Schmidt, M. D. Kirkpatrick, A. E. Heitsch, C. D. 2021-01-21 doi:10.1101/2021.01.20.427505 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ PrismExp: Predicting Human Gene Function by Partitioning Massive RNA-seq Co-expression Data ]]> https://biorxiv.org/content/10.1101/2021.01.20.427528v1?rss=1 Lachmann, A. Rizzo, K. Bartal, A. Jeon, M. Clarke, D. J. B. Ma'ayan, A. 2021-01-21 doi:10.1101/2021.01.20.427528 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Spatiotemporal Trajectories in Resting-state FMRI Revealed by Convolutional Variational Autoencoder ]]> https://biorxiv.org/content/10.1101/2021.01.25.427841v1?rss=1 Zhang, X. Maltbie, E. Keilholz, S. 2021-01-26 doi:10.1101/2021.01.25.427841 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Machine learning to extract muscle fascicle length changes from dynamic ultrasound images in real-time ]]> https://biorxiv.org/content/10.1101/2021.01.25.428061v1?rss=1 Rosa, L. G. Zia, J. S. Inan, O. T. Sawicki, G. S. 2021-01-25 doi:10.1101/2021.01.25.428061 Cold Spring Harbor Laboratory Press 2021-01-25 <![CDATA[ Generating novel protein sequences using Gibbs sampling of masked language models ]]> https://biorxiv.org/content/10.1101/2021.01.26.428322v1?rss=1 Johnson, S. R. Massie, K. Monaco, S. Sayed, Z. 2021-01-27 doi:10.1101/2021.01.26.428322 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Adaptive Behavior and the Role of Primary Somatosensory Cortex ]]> https://biorxiv.org/content/10.1101/2021.01.29.428886v1?rss=1 Waiblinger, C. Borden, P. Y. Stanley, G. B. 2021-01-30 doi:10.1101/2021.01.29.428886 Cold Spring Harbor Laboratory Press 2021-01-30 <![CDATA[ Synthetic Antigen-Presenting Cells for Adoptive T Cell Therapy ]]> https://biorxiv.org/content/10.1101/2021.02.01.429167v1?rss=1 Dahotre, S. N. Romanov, A. M. Su, F.-Y. Kwong, G. A. 2021-02-02 doi:10.1101/2021.02.01.429167 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Lateral Undulation Aids Biological and Robotic Earthworm Anchoring and Locomotion ]]> https://biorxiv.org/content/10.1101/2021.02.02.429151v1?rss=1 Ozkan-Aydin, Y. Liu, B. Carruthers Ferrero, A. Seidel, M. Hammond, F. L. Goldman, D. I. 2021-02-03 doi:10.1101/2021.02.02.429151 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ A variant selection framework for genome graphs ]]> https://biorxiv.org/content/10.1101/2021.02.02.429378v1?rss=1 Jain, C. Tavakoli, N. Aluru, S. 2021-02-03 doi:10.1101/2021.02.02.429378 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Knockdown of Dnmt1 links Gene body DNA methylation to regulation of gene expression and maternal-zygotic transition in the wasp Nasonia ]]> https://biorxiv.org/content/10.1101/2021.02.02.429402v1?rss=1 Arsala, D. Wu, X. Yi, S. V. Lynch, J. A. 2021-02-02 doi:10.1101/2021.02.02.429402 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Improving RNA branching predictions: advances and limitations ]]> https://biorxiv.org/content/10.1101/2021.02.04.429782v1?rss=1 Poznanovic, S. Wood, C. Cloer, M. Heitsch, C. 2021-02-06 doi:10.1101/2021.02.04.429782 Cold Spring Harbor Laboratory Press 2021-02-06 <![CDATA[ Deep learning for robust and flexible tracking in behavioral studies for C. elegans ]]> https://biorxiv.org/content/10.1101/2021.02.08.430359v1?rss=1 Lu, H. Bates, K. Le, K. 2021-02-10 doi:10.1101/2021.02.08.430359 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Relatively Shorter Muscle Lengths Increase the Metabolic Rate of Cyclic Force Production ]]> https://biorxiv.org/content/10.1101/2021.02.10.430661v1?rss=1 Beck, O. N. Schroeder, J. N. Trejo, L. H. Franz, J. R. Sawicki, G. S. 2021-02-11 doi:10.1101/2021.02.10.430661 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ Protocell Arrays for Simultaneous Detection of Diverse Analytes ]]> https://biorxiv.org/content/10.1101/2021.02.13.431022v1?rss=1 Zhang, Y. Kojima, T. Kim, G.-A. McNerney, M. P. Takayama, S. Styczynski, M. P. 2021-02-15 doi:10.1101/2021.02.13.431022 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ The relationship between dynamic functional network connectivity and spatial orientation in healthy young adults ]]> https://biorxiv.org/content/10.1101/2021.02.14.431143v1?rss=1 Sendi, M. S. E. Ellis, C. A. Miller, R. L. Salat, D. H. Calhoun, V. D. 2021-02-16 doi:10.1101/2021.02.14.431143 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Multiple Sites on SARS-CoV-2 Spike Protein are Susceptible to Proteolysis by Cathepsins B, K, L, S, and V ]]> https://biorxiv.org/content/10.1101/2021.02.17.431617v1?rss=1 Bollavaram, K. Leeman, T. Kulkarni, A. Upshaw, S. Lee, M. Yang, J. Song, H. Platt, M. O. 2021-02-17 doi:10.1101/2021.02.17.431617 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Frequency of quorum sensing mutations in Pseudomonas aeruginosa strains isolated from different environments ]]> https://biorxiv.org/content/10.1101/2021.02.22.432365v1?rss=1 O'Connor, K. Zhao, C. Y. Diggle, S. P. 2021-02-23 doi:10.1101/2021.02.22.432365 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Conformational changes in twitchin kinase in vivo revealed by FRET imaging of freely moving C. elegans ]]> https://biorxiv.org/content/10.1101/2021.03.01.433414v1?rss=1 Porto, D. Matsunaga, Y. Franke, B. Williams, R. Qadota, H. Mayans, O. Benian, G. M. Lu, H. 2021-03-01 doi:10.1101/2021.03.01.433414 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Sod1 Integrates Oxygen Availability to Redox Regulate NADPH Production and the Thiol Redoxome ]]> https://biorxiv.org/content/10.1101/2021.03.04.433951v1?rss=1 Montllor-Albalate, C. Kim, H. Jonke, A. P. Torres, M. P. Reddi, A. 2021-03-04 doi:10.1101/2021.03.04.433951 Cold Spring Harbor Laboratory Press 2021-03-04 <![CDATA[ Multichromatic Near-Infrared Imaging to Assess Interstitial Lymphatic and Venous Uptake In Vivo ]]> https://biorxiv.org/content/10.1101/2021.03.07.434298v1?rss=1 Bernard, F. C. Kaiser, J. Raval, S. K. Nepiyushchikh, Z. V. Doan, T. N. Willett, N. J. Dixon, J. B. 2021-03-08 doi:10.1101/2021.03.07.434298 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ A low-cost, long-term underwater camera trap network coupled with deep residual learning image analysis ]]> https://biorxiv.org/content/10.1101/2021.03.08.434472v1?rss=1 Bilodeau, S. M. Schwartz, A. W. H. Xu, B. Pauca, V. P. Silman, M. R. 2021-03-09 doi:10.1101/2021.03.08.434472 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Osteoarthritis Early-, Mid- and Late-Stage Progression in the Rat Medial Meniscus Transection Model ]]> https://biorxiv.org/content/10.1101/2021.03.11.434909v1?rss=1 Doan, T. N. McKinney, J. Pucha, K. Bernard, F. Willett, N. 2021-03-12 doi:10.1101/2021.03.11.434909 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ A minimal robophysical model of quadriflagellate self-propulsion ]]> https://biorxiv.org/content/10.1101/2021.03.14.434582v1?rss=1 Diaz, K. Robinson, T. L. Ozkan Aydin, Y. Aydin, E. Goldman, D. I. Wan, K. Y. 2021-03-15 doi:10.1101/2021.03.14.434582 Cold Spring Harbor Laboratory Press 2021-03-15 <![CDATA[ Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations ]]> https://biorxiv.org/content/10.1101/2021.03.15.435471v1?rss=1 Conrad, R. E. Viver, T. Gago, J. F. Hatt, J. K. Venter, F. Rossello-Mora, R. Konstantinidis, K. T. 2021-03-17 doi:10.1101/2021.03.15.435471 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae ]]> https://biorxiv.org/content/10.1101/2021.03.16.435725v1?rss=1 Lindsey, C. R. Rosenzweig, F. Herron, M. D. 2021-03-17 doi:10.1101/2021.03.16.435725 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ A Weighted Network Analysis Framework for the Hourglass Effect - and its Application in the C. Elegans Connectome ]]> https://biorxiv.org/content/10.1101/2021.03.19.436224v1?rss=1 Batta, I. Yao, Q. Sabrin, K. M. Dovrolis, C. 2021-03-20 doi:10.1101/2021.03.19.436224 Cold Spring Harbor Laboratory Press 2021-03-20 <![CDATA[ Critical interactions for SARS-CoV-2 spike protein binding to ACE2 identified by machine learning ]]> https://biorxiv.org/content/10.1101/2021.03.19.436231v1?rss=1 Pavlova, A. Zhang, Z. Acharya, A. Lynch, D. L. Pang, Y. T. Mou, Z. Parks, J. M. Chipot, C. Gumbart, J. C. 2021-03-21 doi:10.1101/2021.03.19.436231 Cold Spring Harbor Laboratory Press 2021-03-21 <![CDATA[ Pseudomonas aeruginosa reaches collective decisions via transient segregation of quorum sensing activities across cells ]]> https://biorxiv.org/content/10.1101/2021.03.22.436499v1?rss=1 Jayakumar, P. Thomas, S. A. Brown, S. P. Kuemmerli, R. 2021-03-22 doi:10.1101/2021.03.22.436499 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ The link between static and dynamic brain functional network connectivity and genetic risk of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2021.03.27.437354v1?rss=1 Sendi, M. S. E. Zendehrouh, E. Ellis, C. A. Chen, J. Miller, R. L. Mormino, E. C. Salat, D. H. Calhoun, V. 2021-03-29 doi:10.1101/2021.03.27.437354 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ Building reusable phage and antibiotic treatments via exploitation of bacteria-phage coevolutionary dynamics. ]]> https://biorxiv.org/content/10.1101/2021.03.31.437900v1?rss=1 Gurney, J. Brown, S. P. 2021-03-31 doi:10.1101/2021.03.31.437900 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Dynamic functional connectivity links with treatment response of electroconvulsive therapy in major depressive disorder ]]> https://biorxiv.org/content/10.1101/2021.03.31.437958v1?rss=1 Sendi, M. S. E. Dini, H. Sui, J. Fu, Z. Espinoza, R. Narr, K. Qi, S. Abbott, C. C. van Rooij, S. Riva-Posse, P. Mayberg, H. S. Calhoun, V. D. 2021-04-02 doi:10.1101/2021.03.31.437958 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ A new contact killing toxin permeabilizes cells and belongs to a large protein family ]]> https://biorxiv.org/content/10.1101/2021.03.31.437997v1?rss=1 Hammer, B. K. Crisan, C. Chandrashekar, H. Everly, C. Steinbach, G. Hill, S. E. Lieberman, R. R. Yunker, P. J. 2021-04-01 doi:10.1101/2021.03.31.437997 Cold Spring Harbor Laboratory Press 2021-04-01 <![CDATA[ A general framework to learn tertiary structure for protein sequence annotation ]]> https://biorxiv.org/content/10.1101/2021.04.01.438098v1?rss=1 Gao, M. Skolnick, J. 2021-04-03 doi:10.1101/2021.04.01.438098 Cold Spring Harbor Laboratory Press 2021-04-03 <![CDATA[ Stratification of Risk of Progression to Colectomy in Ulcerative Colitis using Measured and Predicted Gene Expression ]]> https://biorxiv.org/content/10.1101/2021.04.02.438187v1?rss=1 Mo, A. Nagpal, S. Gettler, K. Haritunians, T. Giri, M. Haberman, Y. Karns, R. Prince, J. Arafat, D. Hsu, N.-Y. Chuang, L.-S. Argmann, C. Kasarskis, A. Suarez-Farinas, M. Gotman, N. Mengesha, E. Venkateswaran, S. Rufo, P. A. Baker, S. S. Sauer, C. G. Markowitz, J. Pfefferkorn, M. D. Rosh, J. R. Boyle, B. M. Mack, D. R. Baldassano, R. N. Shah, S. LeLeiko, N. S. Heyman, M. B. Griffiths, A. M. Patel, A. S. Noe, J. D. Thomas, S. D. Aronow, B. J. Walters, T. D. McGovern, D. P. Hyams, J. S. Kugathasan, S. Cho, J. Denson, L. A. Gibson, G. 2021-04-04 doi:10.1101/2021.04.02.438187 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Impact of an Urban Sanitation Intervention on Enteric Pathogen Detection in Soils ]]> https://biorxiv.org/content/10.1101/2021.04.02.438233v1?rss=1 Capone, D. Berendes, D. Cumming, O. Holcomb, D. A. Knee, J. Konstantinidis, K. T. Levy, K. Nala, R. Risk, B. B. Brown, J. 2021-04-02 doi:10.1101/2021.04.02.438233 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ GNPS Dashboard: Collaborative Analysis of Mass Spectrometry Data in the Web Browser ]]> https://biorxiv.org/content/10.1101/2021.04.05.438475v1?rss=1 Petras, D. Phelan, V. V. Acharya, D. D. Allen, A. E. Aron, A. T. Bandeira, N. Belle-Oudry, D. Boecker, S. Bowen, B. P. Cummings, D. A. Deutsch, J. M. Fahy, E. Garg, N. Gregor, R. Handelsman, J. Navarro-Hoyos, M. Jarmusch, A. K. Jarmusch, S. A. Louie, K. B. Maloney, K. N. Marty, M. T. Meijler, M. M. Mizrahi, I. Molina-Santiago, C. Neve, R. L. Northen, T. R. Panitchpakdi, M. Pullman, B. Puri, A. W. Schmid, R. Subramaniam, S. Thukral, M. Vasquez-Castro, F. Dorrestein, P. C. Wang, M. 2021-04-06 doi:10.1101/2021.04.05.438475 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Emergent myxobacterial behaviors arise from reversal suppression induced by kin contacts ]]> https://biorxiv.org/content/10.1101/2021.04.08.439045v1?rss=1 Balagam, R. Cao, P. Sah, G. P. Zhang, Z. A. Wall, D. Igoshin, O. A. 2021-04-09 doi:10.1101/2021.04.08.439045 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Plasticity of the gastrocnemius elastic system in response to decreased work and power demand during growth ]]> https://biorxiv.org/content/10.1101/2021.04.12.439563v1?rss=1 cox, S. DeBoef, A. Katugam, K. Salzano, M. Q. Piazza, S. Rubenson, J. 2021-04-14 doi:10.1101/2021.04.12.439563 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Correcting artifacts in ratiometric biosensor imaging; an improved approach for dividing noisy signals ]]> https://biorxiv.org/content/10.1101/2021.04.13.439673v1?rss=1 Marston, D. J. Slattery, S. Hahn, K. M. Tsygankov, D. 2021-04-14 doi:10.1101/2021.04.13.439673 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Assessment of the Viscoelastic Mechanical Properties of the Porcine Optic Nerve Head using Micromechanical Testing and Finite Element Modeling ]]> https://biorxiv.org/content/10.1101/2021.04.16.440170v1?rss=1 Safa, B. N. Read, A. T. Ethier, C. R. 2021-04-16 doi:10.1101/2021.04.16.440170 Cold Spring Harbor Laboratory Press 2021-04-16 <![CDATA[ Learning latent embedding of multi-modal single cell data and cross-modality relationship simultaneously ]]> https://biorxiv.org/content/10.1101/2021.04.16.440230v1?rss=1 Zhang, Z. Yang, C. Zhang, X. 2021-04-19 doi:10.1101/2021.04.16.440230 Cold Spring Harbor Laboratory Press 2021-04-19 <![CDATA[ Repair of critical-size porcine craniofacial bone defects using a collagen-polycaprolactone composite biomaterial ]]> https://biorxiv.org/content/10.1101/2021.04.19.440506v1?rss=1 Dewey, M. J. Milner, D. J. Weisgerber, D. Flanagan, C. Rubessa, M. Lotti, S. Polkoff, K. Crotts, S. Hollister, S. J. Wheeler, M. B. Harley, B. 2021-04-20 doi:10.1101/2021.04.19.440506 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Developmental Circadian Disruption Alters Placental Signaling in Mice ]]> https://biorxiv.org/content/10.1101/2021.04.21.440521v1?rss=1 Clarkson-Townsend, D. A. Bales, K. L. Hermetz, K. E. Burt, A. A. Pardue, M. Marsit, C. J. 2021-04-22 doi:10.1101/2021.04.21.440521 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Changes in Cellular Crosstalk between Skeletal Muscle Myoblasts and Bone Osteoblasts with Aging ]]> https://biorxiv.org/content/10.1101/2021.04.26.441458v1?rss=1 Doering, J. A. Britt, C. E. Sawicki, G. S. Cole, J. H. 2021-04-27 doi:10.1101/2021.04.26.441458 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ ACE2 glycans preferentially interact with the RBD of SARS-CoV-2 over SARS-CoV ]]> https://biorxiv.org/content/10.1101/2021.04.29.442038v1?rss=1 Acharya, A. Lynch, D. Pavlova, A. Pang, Y. T. Gumbart, J. 2021-04-30 doi:10.1101/2021.04.29.442038 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ High arsenic levels increase activity rather than diversity or abundance of arsenic metabolism genes in paddy soils ]]> https://biorxiv.org/content/10.1101/2021.05.03.442544v1?rss=1 Zhang, S.-Y. Xiao, X. Chen, S.-C. Zhu, Y. Sun, G.-X. Konstantinidis, K. T. 2021-05-04 doi:10.1101/2021.05.03.442544 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Explainable Sleep Stage Classification with Multimodal Electrophysiology Time-series ]]> https://biorxiv.org/content/10.1101/2021.05.04.442658v1?rss=1 Ellis, C. A. Zhang, R. Carbajal, D. A. Miller, R. L. Calhoun, V. A. Wang, M. D. 2021-05-05 doi:10.1101/2021.05.04.442658 Cold Spring Harbor Laboratory Press 2021-05-05 <![CDATA[ Transcriptomic and rRNA:rDNA signatures of environmental vs. enteric Enterococcus faecalis isolates under oligotrophic freshwater conditions ]]> https://biorxiv.org/content/10.1101/2021.05.04.442698v1?rss=1 Suttner, B. Kim, M. Johnston, E. R. Orellana, L. Ruiz-Perez, C. A. Rodriguez-R, L. M. Hatt, J. Brown, J. Santo Domingo, J. W. Konstantinidis, K. T. 2021-05-05 doi:10.1101/2021.05.04.442698 Cold Spring Harbor Laboratory Press 2021-05-05 <![CDATA[ Predicting T Cell Quality During Manufacturing Through an Artificial Intelligence-based Integrative Multi-Omics Analytical Platform ]]> https://biorxiv.org/content/10.1101/2021.05.05.442854v1?rss=1 Odeh-Couvertier, V. Y. Dwarshuis, N. J. Colonna, M. B. Levine, B. L. Edison, A. S. Kotanchek, T. Roy, K. Torres-Garcia, W. 2021-05-06 doi:10.1101/2021.05.05.442854 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Multi-omics characterization of mesenchymal stem/stromal cells for the identification of putative critical quality attributes ]]> https://biorxiv.org/content/10.1101/2021.05.10.440010v1?rss=1 Maughon, T. S. Shen, X. Huang, D. Michael, A. O. A. Shockey, W. A. Andrews, S. H. McRae, J. M. Platt, M. O. Fernandez, F. M. Edison, A. S. Stice, S. L. Marklein, R. A. 2021-05-11 doi:10.1101/2021.05.10.440010 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ The terminal heme synthetic enzyme, Coproheme Decarboxylase, coordinates heme synthesis and uptake in response to iron in Mycobacteria ]]> https://biorxiv.org/content/10.1101/2021.05.10.443464v1?rss=1 Donegan, R. K. Copeland, J. Edgha, S. Brown, G. Hale, O. F. Mitra, A. Yang, H. Dailey, H. A. Niederweis, M. Jain, P. Reddi, A. R. 2021-05-10 doi:10.1101/2021.05.10.443464 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ An Explainable Deep Learning Approach for Multimodal Electrophysiology Classification ]]> https://biorxiv.org/content/10.1101/2021.05.12.443594v1?rss=1 Ellis, C. A. Carbajal, D. A. Zhang, R. Miller, R. L. Calhoun, V. D. Wang, M. D. 2021-05-14 doi:10.1101/2021.05.12.443594 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ Improved constraints increase the predictivity and applicability of a linear programming-based dynamic metabolic modeling framework ]]> https://biorxiv.org/content/10.1101/2021.05.13.444091v1?rss=1 Lee, J. Y. Styczynski, M. P. 2021-05-16 doi:10.1101/2021.05.13.444091 Cold Spring Harbor Laboratory Press 2021-05-16 <![CDATA[ Leveraging the mass balances of cellular metabolism to infer absolute concentrations from relative abundance metabolomics data ]]> https://biorxiv.org/content/10.1101/2021.05.13.444095v1?rss=1 Lee, J. Y. Styczynski, M. P. 2021-05-16 doi:10.1101/2021.05.13.444095 Cold Spring Harbor Laboratory Press 2021-05-16 <![CDATA[ SCOUR: A stepwise machine learning framework for predicting metabolite-dependent regulatory interactions ]]> https://biorxiv.org/content/10.1101/2021.05.14.444159v1?rss=1 Lee, J. Y. Nguyen, B. Orosco, C. Styczynski, M. P. 2021-05-17 doi:10.1101/2021.05.14.444159 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Metabolic Dynamics in Escherichia coli-based Cell-Free Systems ]]> https://biorxiv.org/content/10.1101/2021.05.16.444339v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@1afbfc3org.highwire.dtl.DTLVardef@156a23aorg.highwire.dtl.DTLVardef@b494adorg.highwire.dtl.DTLVardef@18d03dc_HPS_FORMAT_FIGEXP M_FIG Abstract Figure C_FIG ]]> Miguez, A. M. Zhang, Y. Piorino, F. Styczynski, M. P. 2021-05-17 doi:10.1101/2021.05.16.444339 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Maturation of Human Long-lived Plasma Cells Results in Resistance to Apoptosis by Transcriptional and Epigenetic Regulation ]]> https://biorxiv.org/content/10.1101/2021.05.22.445269v1?rss=1 Joyner, C. J. Ley, A. Nguyen, D. Ali, M. Corrado, A. Tipton, C. Scharer, C. Mi, T. Woodruff, M. C. Hom, J. Boss, J. M. Duan, M. Gibson, G. Roberts, D. Andrews, J. Lonial, S. Sanz, I. Lee, F. E.-H. 2021-05-23 doi:10.1101/2021.05.22.445269 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ Identifying dysregulated immune cell subsets following critical volumetric muscle loss with pseudo-time trajectories ]]> https://biorxiv.org/content/10.1101/2021.05.25.445480v1?rss=1 Hymel, L. A. Anderson, S. E. Turner, T. C. York, W. Y. Lim, H. S. Qiu, P. Jang, Y. C. Willett, N. J. Botchwey, E. A. 2021-05-26 doi:10.1101/2021.05.25.445480 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ Characterizing Human Mesenchymal Stromal Cells Immune Modulatory Potency Using Targeted Lipidomic Profiling of Sphingolipids ]]> https://biorxiv.org/content/10.1101/2021.06.01.446428v1?rss=1 DeVeaux, S. A. Ogle, M. E. Vyshnya, S. Chiappa, N. F. Leitmann, B. Rudy, R. Day, A. Mortensen, L. J. Kurtzberg, J. Roy, K. Botchwey, E. 2021-06-02 doi:10.1101/2021.06.01.446428 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Mitochondrial Contact Site and Cristae Organizing System (MICOS) Machinery Supports Heme Biosynthesis by Enabling Optimal Performance of Ferrochelatase ]]> https://biorxiv.org/content/10.1101/2021.06.01.446600v1?rss=1 Dietz, J. V. Willoughby, M. M. Piel, R. B. Ross, T. A. Bohovych, I. Addis, H. G. Fox, J. L. Lanzilotta, W. N. Dailey, H. A. Wohlschlegel, J. A. Reddi, A. R. Medlock, A. E. Khalimonchuk, O. 2021-06-01 doi:10.1101/2021.06.01.446600 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ Heme oxygenase-2 (HO-2) binds and buffers labile heme, which is largely oxidized, in human embryonic kidney cells ]]> https://biorxiv.org/content/10.1101/2021.06.06.447256v1?rss=1 Hanna, D. A. Moore, C. M. Liu, L. Yuan, X. Fleischhacker, A. S. Hamza, I. Ragsdale, S. W. Reddi, A. R. 2021-06-07 doi:10.1101/2021.06.06.447256 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ TSEBRA: Transcript Selector for BRAKER ]]> https://biorxiv.org/content/10.1101/2021.06.07.447316v1?rss=1 Gabriel, L. Hoff, K. J. Bruna, T. Borodovsky, M. Stanke, M. 2021-06-07 doi:10.1101/2021.06.07.447316 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Treadmill exercise promotes retinal astrocyte plasticity and protects against retinal degeneration ]]> https://biorxiv.org/content/10.1101/2021.06.07.447392v1?rss=1 Bales, K. L. Chacko, A. S. Nickerson, J. M. Pardue, M. T. Boatright, J. H. Pardue, M. 2021-06-07 doi:10.1101/2021.06.07.447392 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Phenotyping the tumor-immune microenvironment (TiME) in vivo by cellular-level optical imaging reveals unique combination phenotypes with variable inflammation and endothelial anergy ]]> https://biorxiv.org/content/10.1101/2021.06.10.447835v1?rss=1 Sahu, A. Tembo, T. Kose, K. Santella, A. Alfonso, A. Li, M. Cordova, M. Gill, M. Fox, C. Gonzalez, S. Wang, A. W. Kurtansky, N. R. Chandrani, P. Kumar, P. Yin, S. Jilani, H. Mehta, P. Navarrete-Dechent, C. Peterson, G. King, K. Dusza, S. Yang, N. Liu, S. Phillip, W. Rossi, A. Halpern, A. Deng, L. Pulitzer, M. Marghoob, A. Chen, C.-S. J. Rajadhyaksha, M. 2021-06-10 doi:10.1101/2021.06.10.447835 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ A Novel Local Explainability Approach for Spectral Insight into Raw EEG-Based Deep Learning Classifiers ]]> https://biorxiv.org/content/10.1101/2021.06.10.447983v1?rss=1 Ellis, C. A. Miller, R. L. Calhoun, V. 2021-06-11 doi:10.1101/2021.06.10.447983 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ A Novel Local Ablation Approach for Explaining Multimodal Classifiers ]]> https://biorxiv.org/content/10.1101/2021.06.10.447986v1?rss=1 Ellis, C. A. Carbajal, D. A. Zhang, R. Sendi, M. S. E. Miller, R. L. Calhoun, V. Wang, M. D. 2021-06-11 doi:10.1101/2021.06.10.447986 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Diel population dynamics and mortality of Prochlorococcus in the North Pacific Subtropical Gyre ]]> https://biorxiv.org/content/10.1101/2021.06.15.448546v1?rss=1 Beckett, S. J. Demory, D. Coenen, A. R. Casey, J. R. Dugenne, M. Follett, C. L. Connell, P. Carlson, M. C. G. Hu, S. K. Wilson, S. T. Muratore, D. Rodriguez-Gonzalez, R. A. Peng, S. Becker, K. W. Mende, D. R. Armbrust, E. V. Caron, D. A. Lindell, D. Follows, M. J. White, A. E. Ribalet, F. Weitz, J. S. 2021-06-16 doi:10.1101/2021.06.15.448546 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ Metagenome-based comparisons of decay rates and host-specificity of fecal microbial communities for improved microbial source tracking ]]> https://biorxiv.org/content/10.1101/2021.06.17.448865v1?rss=1 Suttner, B. Lindner, B. G. Kim, M. Conrad, R. E. Rodriguez, L. M. Orellana, L. H. Johnston, E. R. Hatt, J. K. Zhu, K. J. Brown, J. Konstantinidis, K. T. 2021-06-17 doi:10.1101/2021.06.17.448865 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Fast alignment and preprocessing of chromatin profiles with Chromap ]]> https://biorxiv.org/content/10.1101/2021.06.18.448995v1?rss=1 Zhang, H. Song, L. Wang, X. Cheng, H. Wang, C. Meyer, C. Liu, T. Tang, M. Aluru, S. Yue, F. Liu, X. S. Li, H. 2021-06-18 doi:10.1101/2021.06.18.448995 Cold Spring Harbor Laboratory Press 2021-06-18 <![CDATA[ Large-Scale Intrinsic Functional Brain Organization Emerges from Three Canonical Spatiotemporal Patterns ]]> https://biorxiv.org/content/10.1101/2021.06.20.448984v1?rss=1 Bolt, T. S. Nomi, J. Bzdok, D. Chang, C. Yeo, B. T. T. Uddin, L. Q. Keilholz, S. 2021-06-20 doi:10.1101/2021.06.20.448984 Cold Spring Harbor Laboratory Press 2021-06-20 <![CDATA[ Antibiotics drive expansion of rare pathogens in a chronic infection microbiome model ]]> https://biorxiv.org/content/10.1101/2021.06.21.449018v1?rss=1 Varga, J. J. Zhao, C. Davis, J. D. Hao, Y. Farrell, J. M. Gurney, J. R. Voit, E. Brown, S. P. 2021-06-21 doi:10.1101/2021.06.21.449018 Cold Spring Harbor Laboratory Press 2021-06-21 <![CDATA[ TedSim: temporal dynamics simulation of single cell RNA-sequencing data and cell division history ]]> https://biorxiv.org/content/10.1101/2021.06.21.449283v1?rss=1 Pan, X. Li, H. Zhang, X. 2021-06-22 doi:10.1101/2021.06.21.449283 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Time-scales modulate optimal lysis-lysogeny decision switches and near-term phage fitness ]]> https://biorxiv.org/content/10.1101/2021.06.21.449334v1?rss=1 Shivam, S. Li, G. Lucia-Sanz, A. Weitz, J. S. 2021-06-22 doi:10.1101/2021.06.21.449334 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Point-of-care analyte quantification and digital readout via lysate-based cell-free biosensors interfaced with personal glucose monitors ]]> https://biorxiv.org/content/10.1101/2021.06.22.449464v1?rss=1 View larger version (18K): org.highwire.dtl.DTLVardef@100532forg.highwire.dtl.DTLVardef@554ac4org.highwire.dtl.DTLVardef@19fa9d4org.highwire.dtl.DTLVardef@146c729_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Zhang, Y. Steppe, P. L. Kazman, M. W. Styczynski, M. P. 2021-06-22 doi:10.1101/2021.06.22.449464 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Adaptive shifts underlie the divergence in wing morphology in bombycoid moths ]]> https://biorxiv.org/content/10.1101/2021.06.23.449655v1?rss=1 Aiello, B. R. Tan, M. Bin Sikandar, U. Alvey, A. J. Bhinderwala, B. Kimball, K. Barber, J. Hamilton, C. A. Kawahara, A. Y. Sponberg, S. 2021-06-24 doi:10.1101/2021.06.23.449655 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Clinical recovery of Macaca fascicularis infected with Plasmodium knowlesi ]]> https://biorxiv.org/content/10.1101/2021.06.28.448877v1?rss=1 Peterson, M. S. Joyner, C. J. Brady, J. A. Wood, J. S. Cabrera-Mora, M. Saney, C. L. Fonseca, L. L. Cheng, W. T. Jang, J. Lapp, S. A. Soderberg, S. R. Nural, M. V. Humphrey, J. C. Hankus, A. Machiah, D. Karpuzoglu, E. DeBarry, J. D. MaHPIC-Consortium, Tirouvanziam, R. Kissinger, J. C. Moreno, A. Gumber, S. Voit, E. O. Gutierrez, J. B. Cordy, R. J. Galinski, M. R. 2021-06-28 doi:10.1101/2021.06.28.448877 Cold Spring Harbor Laboratory Press 2021-06-28 <![CDATA[ Mechanistic model-driven exometabolomic characterisation of human dopaminergic neuronal metabolism ]]> https://biorxiv.org/content/10.1101/2021.06.30.450562v1?rss=1 Preciat, G. Moreno, E. L. Wegrzyn, A. Willacey, C. C. W. Modamio, J. Monteiro, F. L. El Assal, D. Schurink, A. Oliveira, M. A. P. Zhang, Z. Cousins, B. Zach, S. Vempala, S. Hengerer, B. Harms, A. Schwamborn, J. C. Thiele, I. Hankemeier, T. Fleming, R. M. 2021-07-01 doi:10.1101/2021.06.30.450562 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ RNA and the Goldilocks Zone: Where Mg2+ concentration is just right ]]> https://biorxiv.org/content/10.1101/2021.07.01.450745v1?rss=1 Guth-Metzler, R. Mohamed, A. M. Cowan, E. T. Frenkel-Pinter, M. Wartell, R. Glass, J. B. Williams, L. D. 2021-07-01 doi:10.1101/2021.07.01.450745 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ Gradient-mixing LEGO robots for purifying DNA origami nanostructures of multiple components rate-zonal centrifugation ]]> https://biorxiv.org/content/10.1101/2021.07.02.450731v1?rss=1 Sentosa, J. Horne, B. Djutanta, F. Showkeir, D. Rezvani, R. Hariadi, R. F. 2021-07-03 doi:10.1101/2021.07.02.450731 Cold Spring Harbor Laboratory Press 2021-07-03 <![CDATA[ The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA ]]> https://biorxiv.org/content/10.1101/2021.07.06.451362v1?rss=1 Rolando, J. L. Kolton, M. Song, T. Kostka, J. E. 2021-07-07 doi:10.1101/2021.07.06.451362 Cold Spring Harbor Laboratory Press 2021-07-07 <![CDATA[ A DEEP LEARNING APPROACH TO ESTIMATING INITIAL CONDITIONS OF BRAIN NETWORK MODELS IN REFERENCE TO MEASURED FMRI DATA ]]> https://biorxiv.org/content/10.1101/2021.07.07.451431v1?rss=1 Kashyap, A. Plis, S. Schirner, M. Ritter, P. Keilholz, S. 2021-07-08 doi:10.1101/2021.07.07.451431 Cold Spring Harbor Laboratory Press 2021-07-08 <![CDATA[ Emergent collective locomotion in an active polymer model of entangled worm blobs ]]> https://biorxiv.org/content/10.1101/2021.07.08.451507v1?rss=1 Nguyen, C. Ozkan-Aydin, Y. Tuazon, H. Goldman, D. I. Bhamla, M. S. Peleg, O. 2021-07-09 doi:10.1101/2021.07.08.451507 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Thalamic state controls timing and synchronization of primary somatosensory cortical representations in the awake mouse ]]> https://biorxiv.org/content/10.1101/2021.07.09.451656v1?rss=1 Borden, P. Y. Wright, N. C. Morissette, A. R. Jaeger, D. Haider, B. Stanley, G. B. 2021-07-10 doi:10.1101/2021.07.09.451656 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ Consistent coordination patterns provide near perfect behavior decoding in a comprehensive motor program for insect flight ]]> https://biorxiv.org/content/10.1101/2021.07.13.452211v1?rss=1 Putney, J. Angjelichinoski, M. Ravier, R. Ferrari, S. Tarokh, V. Sponberg, S. 2021-07-14 doi:10.1101/2021.07.13.452211 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ A Gradient-based Spectral Explainability Method for EEG Deep Learning Classifiers ]]> https://biorxiv.org/content/10.1101/2021.07.14.452360v1?rss=1 Ellis, C. A. Sendi, M. S. E. Miller, R. L. Calhoun, V. D. 2021-07-14 doi:10.1101/2021.07.14.452360 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ An information theoretic method to resolve millisecond-scale spike timing precision in a comprehensive motor program ]]> https://biorxiv.org/content/10.1101/2021.07.14.452403v1?rss=1 Putney, J. Niebur, T. Barker, R. Sponberg, S. 2021-07-15 doi:10.1101/2021.07.14.452403 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ Novel municipal sewage-associated bacterial genomes and their potential in source tracking ]]> https://biorxiv.org/content/10.1101/2021.07.15.452399v1?rss=1 Lindner, B. G. Suttner, B. Conrad, R. E. Rodriguez-R, L. M. Hatt, J. K. Zhu, K. J. Brown, J. Konstantinidis, K. T. 2021-07-15 doi:10.1101/2021.07.15.452399 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ TIGAR-V2: Efficient TWAS Tool with Nonparametric Bayesian eQTL Weights of 49 Tissue Types from GTEx V8 ]]> https://biorxiv.org/content/10.1101/2021.07.16.452700v1?rss=1 Parrish, R. L. Gibson, G. C. Epstein, M. P. Yang, J. 2021-07-16 doi:10.1101/2021.07.16.452700 Cold Spring Harbor Laboratory Press 2021-07-16 <![CDATA[ Ipsilateral stimulus encoding in primary and secondary somatosensory cortex of awake mice ]]> https://biorxiv.org/content/10.1101/2021.07.16.452704v1?rss=1 Pala, A. Stanley, G. B. 2021-07-18 doi:10.1101/2021.07.16.452704 Cold Spring Harbor Laboratory Press 2021-07-18 <![CDATA[ Spontaneous emergence of multicellular heritability ]]> https://biorxiv.org/content/10.1101/2021.07.19.452990v1?rss=1 Zamani-Dahaj, S. A. Burnetti, A. Day, T. Ratcliff, w. C. Yunker, P. J. Herron, M. D. 2021-07-20 doi:10.1101/2021.07.19.452990 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ Drop, Swap, and Generate: A Self-Supervised Approach for Generating Neural Activity ]]> https://biorxiv.org/content/10.1101/2021.07.21.453285v1?rss=1 Liu, R. Azabou, M. Dabagia, M. Lin, C.-H. Azar, M. G. Hengen, K. B. Valko, M. Dyer, E. L. 2021-07-23 doi:10.1101/2021.07.21.453285 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Evolution of a chordate-specific mechanism for myoblast fusion ]]> https://biorxiv.org/content/10.1101/2021.07.24.453587v1?rss=1 Zhang, H. Shang, R. Kim, K. Zheng, W. Johnson, C. J. Sun, L. Niu, X. Liu, L. Uyeno, T. A. Zhou, J. Liu, L. Pei, J. Fissette, S. D. Green, S. A. Samudra, S. P. Wen, J. Zhang, J. Eggenschwiler, J. Menke, D. Bronner, M. E. Grishin, N. V. Li, W. Ye, K. Zhang, Y. Stolfi, A. Bi, P. 2021-07-25 doi:10.1101/2021.07.24.453587 Cold Spring Harbor Laboratory Press 2021-07-25 <![CDATA[ Comprehensive multi-omics single-cell data integration reveals greater heterogeneity in the human immune system ]]> https://biorxiv.org/content/10.1101/2021.07.25.453651v1?rss=1 Xu, C. Yang, J. Kosters, A. Babcock, B. R. Qiu, P. Ghosn, E. 2021-07-26 doi:10.1101/2021.07.25.453651 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry ]]> https://biorxiv.org/content/10.1101/2021.07.26.453787v1?rss=1 Wang, D. Zhou, B. Keppel, T. Solano, M. Baudys, J. Goldstein, J. Finn, M. G. Fan, X. Chapman, A. P. Bundy, J. Woolfitt, A. R. Osman, S. Pirkle, J. L. Wentworth, D. E. Barr, J. R. 2021-07-26 doi:10.1101/2021.07.26.453787 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ Cellular organization in lab-evolved and extant multicellular species obeys a maximum entropy law ]]> https://biorxiv.org/content/10.1101/2021.07.29.454238v1?rss=1 Day, T. C. Höhn, S. S. Zamani-Dahaj, S. A. Yanni, D. Burnetti, A. Pentz, J. Honerkamp-Smith, A. R. Wioland, H. Sleath, H. R. Ratcliff, W. C. Goldstein, R. E. Yunker, P. J. 2021-07-29 doi:10.1101/2021.07.29.454238 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ An age-depth model and revised stratigraphy of vertebrate-bearing units in Natural Trap Cave, Wyoming ]]> https://biorxiv.org/content/10.1101/2021.07.30.454390v1?rss=1 Lovelace, D. M. Redman, C. M. Minckley, T. A. Schubert, B. W. Mahan, S. Wood, J. R. McGuire, J. L. Laden, J. Bitterman, K. Heiniger, H. Fenderson, L. Cooper, A. Mitchell, K. Meachen, J. A. 2021-08-01 doi:10.1101/2021.07.30.454390 Cold Spring Harbor Laboratory Press 2021-08-01 <![CDATA[ Inhibition of the H3K27 demethylase UTX enhances the epigenetic silencing of HIV proviruses and induces HIV-1 DNA hypermethylation but fails to permanently block HIV reactivation ]]> https://biorxiv.org/content/10.1101/2021.08.02.454353v1?rss=1 Nguyen, K. Karn, J. Kyung, W. Dobrowolski, C. Shukla, M. 2021-08-02 doi:10.1101/2021.08.02.454353 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ Cell type-specific biotin labeling in vivo resolves regional neuronal proteomic differences in mouse brain ]]> https://biorxiv.org/content/10.1101/2021.08.03.454921v1?rss=1 Rayaprolu, S. Bitarafan, S. Betarbet, R. Sunna, S. N. Cheng, L. Xiao, H. Bagchi, P. Duong, D. M. Nelson, R. Goettemoeller, A. M. Olah, V. J. Rowan, M. J. Levey, A. I. Wood, L. B. Seyfried, N. T. Rangaraju, S. 2021-08-04 doi:10.1101/2021.08.03.454921 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ De novo evolution of macroscopic multicellularity ]]> https://biorxiv.org/content/10.1101/2021.08.03.454982v1?rss=1 Bozdag, G. O. Zamani-Dahaj, S. A. Kahn, P. C. Day, T. C. Tong, K. Balwani, A. H. Dyer, E. L. Yunker, P. J. Ratcliff, W. C. 2021-08-05 doi:10.1101/2021.08.03.454982 Cold Spring Harbor Laboratory Press 2021-08-05 <![CDATA[ Stable Flow-induced Expression of KLK10 Inhibits Endothelial Inflammation and Atherosclerosis ]]> https://biorxiv.org/content/10.1101/2021.08.10.455857v1?rss=1 Williams, D. Mahmoud, M. Liu, R. Andueza, A. Kumar, S. Kang, D.-W. Zhang, J. Tamargo, I. Villa-Roel, N. Baek, K.-I. Lee, H. An, Y. Zhang, L. Tate, E. W. Bagchi, P. Pohl, J. Mosnier, L. Diamandis, E. P. Mihara, K. Hollenberg, M. Dai, Z. Jo, H. 2021-08-10 doi:10.1101/2021.08.10.455857 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact ]]> https://biorxiv.org/content/10.1101/2021.08.12.456168v1?rss=1 Pang, Y. T. Acharya, A. Lynch, D. Pavlova, A. Gumbart, J. 2021-08-13 doi:10.1101/2021.08.12.456168 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Inference and Validation of the Structure of Lotka-Volterra Models ]]> https://biorxiv.org/content/10.1101/2021.08.14.456346v1?rss=1 Voit, E. Davis, J. Olivenca, D. 2021-08-15 doi:10.1101/2021.08.14.456346 Cold Spring Harbor Laboratory Press 2021-08-15 <![CDATA[ Metabolomics of healthy and stony coral tissue loss disease affected Montastraea cavernosa corals ]]> https://biorxiv.org/content/10.1101/2021.08.18.456681v1?rss=1 Deutsch, J. M. Jaiyesimi, O. Pitts, K. Houk, J. Ushijima, B. Walker, B. K. Paul, V. J. Garg, N. 2021-08-19 doi:10.1101/2021.08.18.456681 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Diversification of small RNA pathways underlies germline RNAi incompetence in wild C. elegans strains ]]> https://biorxiv.org/content/10.1101/2021.08.21.457212v1?rss=1 Chou, H. T. Valencia, F. Alexander, J. C. Bell, A. D. Deb, D. Pollard, D. A. Paaby, A. B. 2021-08-22 doi:10.1101/2021.08.21.457212 Cold Spring Harbor Laboratory Press 2021-08-22 <![CDATA[ Emergence and Enhancement of Ultrasensitivity through Posttranslational Modulation of Protein Stability ]]> https://biorxiv.org/content/10.1101/2021.08.22.457287v1?rss=1 Kumbale, C. Voit, E. Zhang, Q. 2021-08-23 doi:10.1101/2021.08.22.457287 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ The ultrafast snap of a finger is mediated by skin friction ]]> https://biorxiv.org/content/10.1101/2021.08.25.457533v1?rss=1 Acharya, R. Challita, E. J. Ilton, M. Bhamla, M. S. 2021-08-26 doi:10.1101/2021.08.25.457533 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ Dissociating the Neural Correlates of Planning and Executing Hierarchical Task Sets ]]> https://biorxiv.org/content/10.1101/2021.08.26.457791v1?rss=1 Cookson, S. L. Schumacher, E. H. 2021-08-28 doi:10.1101/2021.08.26.457791 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Microbial habitability of the early Mars lacustrine environment sustained by iron redox cycling ]]> https://biorxiv.org/content/10.1101/2021.09.07.459191v1?rss=1 Moore, R. A. Carr, C. E. 2021-09-07 doi:10.1101/2021.09.07.459191 Cold Spring Harbor Laboratory Press 2021-09-07 <![CDATA[ Freeze-thaw Cycles Enable a Prebiotically Plausible and Continuous Pathway from Nucleotide Activation to Nonenzymatic RNA Copying ]]> https://biorxiv.org/content/10.1101/2021.09.07.459201v1?rss=1 Zhang, S. J. Duzdevich, D. Carr, C. E. Szostak, J. W. 2021-09-07 doi:10.1101/2021.09.07.459201 Cold Spring Harbor Laboratory Press 2021-09-07 <![CDATA[ Comammox Nitrospira bacteria outnumber canonical nitrifiers irrespective of electron donor mode and availability ]]> https://biorxiv.org/content/10.1101/2021.09.27.461883v1?rss=1 Vilardi, K. J. Cotto, I. Rivera, M. S. Dai, Z. Anderson, C. L. Pinto, A. 2021-09-29 doi:10.1101/2021.09.27.461883 Cold Spring Harbor Laboratory Press 2021-09-29 <![CDATA[ Seascape genomics reveals metapopulation connectivity network of Paramuricea biscaya in the northern Gulf of Mexico ]]> https://biorxiv.org/content/10.1101/2021.10.06.463359v1?rss=1 200 meters deep) are largely understudied. In this study, we investigated the spatial diversity patterns and metapopulation connectivity of the octocoral Paramuricea biscaya throughout the northern Gulf of Mexico (GoM). Paramuricea biscaya is one of the most abundant corals on the lower continental slope (between 1200 and 2500 m) in the GoM. The 2010 Deepwater Horizon oil spill (DWH) directly impacted populations of this species and thus are considered primary targets for restoration. We used a combination of seascape genomic analyses, high-resolution ocean circulation modeling, and larval dispersal simulations to quantify the degree of population structuring and connectivity among P. biscaya populations. Evidence supports the hypotheses that the genetic diversity of P. biscaya is predominantly structured by depth, and that larval dispersal among connected populations is asymmetric due to dominant ocean circulation patterns. Our results suggest that there are intermediate unsampled populations in the central GoM that serve as stepping stones for dispersal. The data suggest that the DeSoto Canyon area, and possibly the West Florida Escarpment, critically act as sources of larvae for areas impacted by the DWH oil spill in the Mississippi Canyon. This work illustrates that the management of deep-sea marine protected areas should incorporate knowledge of connectivity networks and depth-dependent processes throughout the water column. ]]> Galaska, M. Liu, G. Quattrini, A. West, D. Bracco, A. Erickson, K. Herrera, S. 2021-10-08 doi:10.1101/2021.10.06.463359 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ Kilometer-scale larval dispersal processes predict metapopulation connectivity pathways for Paramuricea biscaya in the northern Gulf of Mexico ]]> https://biorxiv.org/content/10.1101/2021.10.06.463363v1?rss=1 Liu, G. Bracco, A. B. Quattrini, A. M. Herrera, S. 2021-10-08 doi:10.1101/2021.10.06.463363 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ A Snapshot of the Global Drinking Water Virome: Diversity and Metabolic Potential Vary with Residual Disinfectant Use ]]> https://biorxiv.org/content/10.1101/2021.10.07.463401v1?rss=1 Hegarty, B. E. Dai, Z. Raskin, L. Pinto, A. J. Wigginton, K. Duhaime, M. B. 2021-10-08 doi:10.1101/2021.10.07.463401 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ Comparison between Lotka-Volterra and Multivariate Autoregressive models of ecological interaction systems ]]> https://biorxiv.org/content/10.1101/2021.10.07.463461v1?rss=1 Olivenca, D. V. Davis, J. D. Voit, E. O. 2021-10-09 doi:10.1101/2021.10.07.463461 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ A Novel Activation Maximization-based Approach for Insight into Electrophysiology Classifiers ]]> https://biorxiv.org/content/10.1101/2021.10.10.463830v1?rss=1 Ellis, C. A. Sendi, M. S. E. Miller, R. L. Calhoun, V. D. 2021-10-12 doi:10.1101/2021.10.10.463830 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ In vivo mRNA delivery to virus-specific T cells by light-induced ligand exchange of MHC class I antigen-presenting nanoparticles ]]> https://biorxiv.org/content/10.1101/2021.10.14.464373v1?rss=1 Su, F.-Y. Zhao, Q. Dahotre, S. N. Gamboa, L. Bawage, S. S. Silva Trenkle, A. D. Zamat, A. Phuengkham, H. Ahmed, R. Santangelo, P. Kwong, G. A. 2021-10-15 doi:10.1101/2021.10.14.464373 Cold Spring Harbor Laboratory Press 2021-10-15 <![CDATA[ Dynamic Brain Network States during Suspenseful Film Viewing ]]> https://biorxiv.org/content/10.1101/2021.10.19.465030v1?rss=1 Bezdek, M. A. Keilholz, S. D. Schumacher, E. H. 2021-10-19 doi:10.1101/2021.10.19.465030 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex ]]> https://biorxiv.org/content/10.1101/2021.10.29.466335v1?rss=1 Akey, C. Singh, D. Ouch, C. Echeverria, I. Nudelman, I. Varberg, J. M. Yu, Z. Fang, F. Shi, Y. Wang, J. Saltzberg, D. Song, K. Xu, C. Gumbart, J. Suslov, S. Unruh, J. Jaspersen, S. L. Chait, B. Sali, A. Menendez-Martinez, J. Ludke, S. J. Villa, E. Rout, M. 2021-10-29 doi:10.1101/2021.10.29.466335 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator ]]> https://biorxiv.org/content/10.1101/2021.11.09.467909v1?rss=1 Abdelfattah, A. S. Zheng, J. Reep, D. Tsegaye, G. Tsang, A. Arthur, B. J. Rehorova, M. Olson, C. V. Huang, Y.-C. Shuai, Y. Koyama, M. Moya, M. V. Weber, T. D. Lemire, A. L. Baker, C. A. Falco, N. Zheng, Q. Grimm, J. B. Yip, M. C. Walpita, D. Forest, C. R. Chase, M. Campagnola, L. Murphy, G. Wong, A. M. Mertz, J. Economo, M. N. Turner, G. Lin, B.-J. Chen, T.-W. Novak, O. Lavis, L. D. Svoboda, K. Korff, W. Schreiter, E. R. Hasseman, J. P. Kolb, I. 2021-11-11 doi:10.1101/2021.11.09.467909 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Predicting direct physical interactions in multimeric proteins with deep learning ]]> https://biorxiv.org/content/10.1101/2021.11.09.467949v1?rss=1 Gao, M. An, D. N. Parks, J. M. Skolnick, J. 2021-11-11 doi:10.1101/2021.11.09.467949 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ α-Synuclein pre-formed fibrils induce prion-like protein aggregation and neurotoxicity in C. elegans models of Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2021.11.11.468276v1?rss=1 Chen, M. Vincent, J. Ezeanii, A. Wakade, S. Yerigenahally, S. Mor, D. E. 2021-11-13 doi:10.1101/2021.11.11.468276 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ A deep learning framework for inference of single-trial neural population activity from calcium imaging with sub-frame temporal resolution ]]> https://biorxiv.org/content/10.1101/2021.11.21.469441v1?rss=1 Zhu, F. Grier, H. A. Tandon, R. Cai, C. Giovannucci, A. Kaufman, M. T. Pandarinath, C. 2021-11-21 doi:10.1101/2021.11.21.469441 Cold Spring Harbor Laboratory Press 2021-11-21 <![CDATA[ Uncovering Xenobiotics in the Dark Metabolome using Ion Mobility Spectrometry, Mass Defect Analysis and Machine Learning ]]> https://biorxiv.org/content/10.1101/2021.11.21.469449v1?rss=1 Foster, M. Rainey, M. Watson, C. Dodds, J. N. Fernandez, F. Baker, E. 2021-11-21 doi:10.1101/2021.11.21.469449 Cold Spring Harbor Laboratory Press 2021-11-21 <![CDATA[ Cooperative binding of TCR and CD4 to pMHC enhances TCR sensitivity ]]> https://biorxiv.org/content/10.1101/2021.11.22.469547v1?rss=1 Rushdi, M. N. Pan, V. Li, K. Travaglino, S. Choi, H.-K. Hong, J. Griffitts, F. Agnihotri, P. Mariuzza, R. A. Ke, Y. Zhu, C. 2021-11-22 doi:10.1101/2021.11.22.469547 Cold Spring Harbor Laboratory Press 2021-11-22 <![CDATA[ Comparison of neuromuscular junction dynamics following ischemic and aged skeletal muscle ]]> https://biorxiv.org/content/10.1101/2021.11.23.469760v1?rss=1 Aliya, B. Mohiuddin, M. Choi, J. Jeong, G. Kang, I. Castels, H. Jones, C. Jang, Y. C. 2021-11-23 doi:10.1101/2021.11.23.469760 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ Sensitizing solid tumors to CAR-mediated cytotoxicity using synthetic antigens ]]> https://biorxiv.org/content/10.1101/2021.12.11.472238v1?rss=1 Gamboa, L. Zamat, A. H. Vanover, D. Thiveaud, C. A. Peck, H. E. Phuengkham, H. Sivakumar, A. Harris, A. M. Dahotre, S. N. Su, F.-Y. Santangelo, P. J. Kwong, G. A. 2021-12-12 doi:10.1101/2021.12.11.472238 Cold Spring Harbor Laboratory Press 2021-12-12 <![CDATA[ A Model Visualization-based Approach for Insight into Waveforms and Spectra Learned by CNNs ]]> https://biorxiv.org/content/10.1101/2021.12.16.473028v1?rss=1 Ellis, C. A. Miller, R. L. Calhoun, V. D. 2021-12-19 doi:10.1101/2021.12.16.473028 Cold Spring Harbor Laboratory Press 2021-12-19 <![CDATA[ Novel Methods for Elucidating Modality Importance in Multimodal Electrophysiology Classifiers ]]> https://biorxiv.org/content/10.1101/2022.01.01.474276v1?rss=1 Ellis, C. A. Sendi, M. S. Zhang, R. Carbajal, D. A. Wang, M. D. Miller, R. L. Calhoun, V. D. 2022-01-02 doi:10.1101/2022.01.01.474276 Cold Spring Harbor Laboratory Press 2022-01-02 <![CDATA[ Embracing enzyme promiscuity with activity-based compressed biosensing ]]> https://biorxiv.org/content/10.1101/2022.01.04.474983v1?rss=1 Holt, B. A. Lim, H. S. Su, M. Tuttle, M. Liakakos, H. Qiu, P. Kwong, G. A. 2022-01-04 doi:10.1101/2022.01.04.474983 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ Evolution of a cis-acting SNP that controls Type VI Secretion in Vibrio cholerae ]]> https://biorxiv.org/content/10.1101/2022.01.11.475911v1?rss=1 Ng, S. L. Kammann, S. A. Steinbach, G. Hoffmann, T. Yunker, P. J. Hammer, B. K. 2022-01-12 doi:10.1101/2022.01.11.475911 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Which lower-limb joints compensate for destabilising energy during walking in humans ]]> https://biorxiv.org/content/10.1101/2022.01.11.475955v1?rss=1 Golyski, P. R. Sawicki, G. S. 2022-01-12 doi:10.1101/2022.01.11.475955 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ In vivo Biomechanical Assessment of Iridial Deformations and Muscle Contractions in Human Eyes ]]> https://biorxiv.org/content/10.1101/2022.01.14.476393v1?rss=1 100%) and essentially spatially uniform radial strains in the iris in vivo, consistent with previous findings. Inverse finite element modeling showed that sphincter muscle tractions were c. 5-fold greater than iridial stroma stiffness (range 4- to 13-fold, depending on sphincter muscle size). This muscle traction is greater than has been previously estimated, which may be due to methodological differences and/or to different patient populations in our study (European descent) vs. previous studies (Asian); the latter possibility is of particular interest due to differential incidence rates of PACG in these populations. Our methodology is fast and inexpensive and may be a useful tool in understanding biomechanical factors contributing to PACG. ]]> Safa, B. N. Bahrani Fard, M. R. Ethier, C. R. 2022-01-17 doi:10.1101/2022.01.14.476393 Cold Spring Harbor Laboratory Press 2022-01-17 <![CDATA[ Catch bond models explain how force amplifies TCR signaling and antigen discrimination ]]> https://biorxiv.org/content/10.1101/2022.01.17.476694v1?rss=1 Choi, H.-K. Li, K. Rushdi, M. N. Ge, C. Chen, W. Lou, J. Zhu, C. 2022-01-18 doi:10.1101/2022.01.17.476694 Cold Spring Harbor Laboratory Press 2022-01-18 <![CDATA[ Septin-Mediated Mechanobiological Reprogramming of T Cell Transmigration and 3D Motility ]]> https://biorxiv.org/content/10.1101/2022.01.18.476840v1?rss=1 Zhovmer, A. S. Manning, A. Smith, C. Vishweshwarayah, Y. Wang, J. Saez, P. J. Ma, X. Cartagena-Rivera, A. X. Singh, R. K. Dokholyan, N. V. Tabdanov, E. D. 2022-01-20 doi:10.1101/2022.01.18.476840 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Antibodies targeting conserved non-canonical antigens and endemic coronaviruses associate with favorable outcomes in severe COVID-19 ]]> https://biorxiv.org/content/10.1101/2022.01.24.477545v1?rss=1 Peddireddy, S. P. Rahman, S. A. Cillo, A. R. Vijay, G. M. Somasundaram, A. Workman, C. J. Bain, W. McVerry, B. J. Methe, B. Lee, J. S. Ray, P. Ray, A. Bruno, T. C. Vignali, D. A. Kitsios, G. D. Morris, A. Singh, H. Sarkar, A. Das, J. 2022-01-27 doi:10.1101/2022.01.24.477545 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ Methacrylate-Modified Gold Nanoparticles Enable Non-Invasive Monitoring of Photocrosslinked Hydrogel Scaffolds ]]> https://biorxiv.org/content/10.1101/2022.01.26.477960v1?rss=1 Li, L. Gil, C. J. Finamore, T. A. Evans, C. J. Tomov, M. L. Ning, L. Theus, A. Kabboul, G. Serpooshan, V. Roeder, R. K. 2022-01-28 doi:10.1101/2022.01.26.477960 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Nanoparticle-delivered TLR4 and RIG-I agonists enhance immune response to SARS-CoV-2 subunit vaccine ]]> https://biorxiv.org/content/10.1101/2022.01.31.478507v1?rss=1 View larger version (18K): org.highwire.dtl.DTLVardef@7b8174org.highwire.dtl.DTLVardef@701721org.highwire.dtl.DTLVardef@feb860org.highwire.dtl.DTLVardef@fae094_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Atalis, A. M. Keenum, M. C. Pandey, B. Beach, A. Pradhan, P. Vantucci, C. E. Jain, R. Hosten, J. Smith, C. Kramer, L. L. Jimenez, A. C. Armenta-Ochoa, M. A. Frey, D. A. Roy, K. 2022-02-02 doi:10.1101/2022.01.31.478507 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ High-performance Flexible Microelectrode Array with PEDOT:PSS Coated 3D Micro-cones for Electromyographic Recording ]]> https://biorxiv.org/content/10.1101/2022.02.03.479004v1?rss=1 > 100). The charge storage capacity was measured to be 34.2 mC/cm2, indicating suitability of the electrodes for stimulation applications as well. ]]> Lu, J. Zia, M. Williams, M. J. Jacob, A. L. Chung, B. Sober, S. J. Bakir, M. S. 2022-02-05 doi:10.1101/2022.02.03.479004 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ A Systematic Approach for Explaining Time and Frequency Features Extracted by CNNs from Raw EEG Data ]]> https://biorxiv.org/content/10.1101/2022.02.08.479555v1?rss=1 Ellis, C. A. Miller, R. L. Calhoun, V. D. 2022-02-10 doi:10.1101/2022.02.08.479555 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Experimental and analytical framework for ''mix-and-read'' assays based on split luciferase ]]> https://biorxiv.org/content/10.1101/2022.02.13.480265v1?rss=1 McArthur, N. Cruz-Teran, C. Thatavarty, A. Reeves, G. T. Rao, B. M. 2022-02-15 doi:10.1101/2022.02.13.480265 Cold Spring Harbor Laboratory Press 2022-02-15 <![CDATA[ Dynamic molecular evolution of a supergene with suppressed recombination in white-throated sparrows ]]> https://biorxiv.org/content/10.1101/2022.02.28.481145v1?rss=1 Jeong, H. Baran, N. M. Sun, D. Chatterjee, P. Layman, T. S. Balakrishnan, C. M. Maney, D. L. Yi, S. V. 2022-03-02 doi:10.1101/2022.02.28.481145 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Inferring cell-specific gene regulatory networks from single cell gene expression data ]]> https://biorxiv.org/content/10.1101/2022.03.03.482887v1?rss=1 Zhang, Z. Jongseok, H. Le, S. Zhang, X. 2022-03-04 doi:10.1101/2022.03.03.482887 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Global phylogeography of marine Synechococcus in coastal areas reveals strikingly different communities than in the open ocean ]]> https://biorxiv.org/content/10.1101/2022.03.07.483242v1?rss=1 Dore, H. Leconte, J. Guyet, U. Breton, S. Farrant, G. K. Demory, D. Ratin, M. Hoebeke, M. Corre, E. Pitt, F. D. Ostrowski, M. Scanlan, D. J. Partensky, F. Six, C. Garczarek, L. 2022-03-07 doi:10.1101/2022.03.07.483242 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Evaluating the "cost of generating force" hypothesis across frequency in human running and hopping ]]> https://biorxiv.org/content/10.1101/2022.03.09.483693v1?rss=1 Allen, S. P. Beck, O. N. Grabowski, A. M. 2022-03-12 doi:10.1101/2022.03.09.483693 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ Deletion of can1/cat1 genes and expression of a dominant any1 mutation establish an effective canavanine selection in fission yeast ]]> https://biorxiv.org/content/10.1101/2022.03.11.484000v1?rss=1 T allele. The strong canavanine-resistance conferred by this allele arises from an inability to deposit basic amino acid transporters on the cellular membrane. any1-523C>T leads to reduced post-translational modifications of Any1 regulated by the Tor2 kinase. We also demonstrate that any1-523C>T is a dominate allele. Our results uncover the mechanisms of canavanine-resistance in fission yeast and open the opportunity of using cat1, can1 and any1 mutant alleles in genetic assays. ]]> Ait Saada, A. Costa, A. B. Lobachev, K. S. 2022-03-13 doi:10.1101/2022.03.11.484000 Cold Spring Harbor Laboratory Press 2022-03-13 <![CDATA[ Overlap across psychotic disorders: A functional network connectivity analysis ]]> https://biorxiv.org/content/10.1101/2022.03.13.484190v1?rss=1 Dini, H. Bruni, L. Ramsoy, T. Calhoun, V. Sendi, M. S. E. 2022-03-15 doi:10.1101/2022.03.13.484190 Cold Spring Harbor Laboratory Press 2022-03-15 <![CDATA[ iSparse kmeans: a two-step clustering approach for big dynamic functional network connectivity data ]]> https://biorxiv.org/content/10.1101/2022.03.13.484193v1?rss=1 Sendi, M. S. E. Salat, D. Miller, R. Calhoun, V. 2022-03-16 doi:10.1101/2022.03.13.484193 Cold Spring Harbor Laboratory Press 2022-03-16 <![CDATA[ Volatile hydrogen cyanide released by Pseudomonas aeruginosa provides a competitive advantage over Staphylococcus aureus in biofilm and in vivo lung environments ]]> https://biorxiv.org/content/10.1101/2022.03.24.484598v1?rss=1 Letoffe, S. Wu, Y. Darch, S. E. Beloin, C. Whiteley, M. Touqui, L. Ghigo, J.-M. 2022-03-24 doi:10.1101/2022.03.24.484598 Cold Spring Harbor Laboratory Press 2022-03-24 <![CDATA[ Extended longevity geometrically-inverted proximal tubule organoids for protein uptake studies ]]> https://biorxiv.org/content/10.1101/2022.03.24.485493v1?rss=1 Parigoris, E. Lee, J.-H. Liu, A. Y. Zhao, X. Takayama, S. 2022-03-27 doi:10.1101/2022.03.24.485493 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ An anchored experimental design and meta-analysis approach to address batch effects in large-scale metabolomics ]]> https://biorxiv.org/content/10.1101/2022.03.25.485859v1?rss=1 View larger version (47K): org.highwire.dtl.DTLVardef@84abe1org.highwire.dtl.DTLVardef@3066fforg.highwire.dtl.DTLVardef@1ba166corg.highwire.dtl.DTLVardef@164cf0_HPS_FORMAT_FIGEXP M_FIG C_FIG Fourteen C. elegans strains are used in three individual studies. PD1074, the anchor control strain (orange), is grown alongside test strains (green, yellow, purple). Multiple biological replicates of PD1074 captures environmental variation in growth conditions. Non-polar and polar metabolic data across the three studies (i.e., natural strains, central metabolism mutants, and UGT mutants) were collected by nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS). Data acquisition controls in each block included biological reference material and pooled PD1074 samples. Biological replicates of PD1074 (n = 42 for LC-MS, n = 52 for NMR) were included in all batches. Meta-analysis provided comparable inferences to mixed effects models, and the estimated relative effects of each test strain to PD1074 and straightforward comparisons of test strains across experiments. ]]> Shaver, A. O. Garcia, B. M. Gouveia, G. J. Morse, A. M. Liu, Z. Borges, R. M. Asef, C. K. Leach, F. E. Andersen, E. C. Amster, I. J. Fernandez, F. M. Edison, A. S. McIntyre, L. M. 2022-03-27 doi:10.1101/2022.03.25.485859 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Fold Evolution by Creative Destruction ]]> https://biorxiv.org/content/10.1101/2022.03.30.486258v1?rss=1 Alvarez-Carreno, C. Gupta, R. J. Petrov, A. S. Williams, L. D. 2022-04-01 doi:10.1101/2022.03.30.486258 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Neural systems underlying RDoC social constructs: An activation likelihood estimation meta-analysis ]]> https://biorxiv.org/content/10.1101/2022.04.04.487016v1?rss=1 Lobo, R. P. Bottenhorn, K. L. Riedel, M. C. Toma, A. I. Hare, M. M. Smith, D. D. Moor, A. C. Cowan, I. K. Valdes, J. A. Bartley, J. E. Salo, T. Boeving, E. R. Pankey, B. Sutherland, M. T. Musser, E. D. Laird, A. R. 2022-04-05 doi:10.1101/2022.04.04.487016 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Stabilizing brain-computer interfaces through alignment of latent dynamics ]]> https://biorxiv.org/content/10.1101/2022.04.06.487388v1?rss=1 Karpowicz, B. M. Ali, Y. H. Wimalasena, L. N. Sedler, A. R. Keshtkaran, M. R. Bodkin, K. Ma, X. Miller, L. E. Pandarinath, C. 2022-04-08 doi:10.1101/2022.04.06.487388 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Fast, Efficient, and Accurate Neuro-Imaging Denoising via Deep Learning ]]> https://biorxiv.org/content/10.1101/2022.04.13.488233v1?rss=1 Chaudhary, S. Moon, S. Lu, H. 2022-04-14 doi:10.1101/2022.04.13.488233 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ Cooperative ectodomain interaction among TCRαβ, CD3γε, and CD3δε enhances TCR mechanotransduction ]]> https://biorxiv.org/content/10.1101/2022.04.14.488403v1?rss=1 10 nm gap, requiring the two events to be coupled through the TCR-CD3 interface, thus involving conformational allostery and being regulatable by force. Although weak ECD cis-interactions between TCR{beta} and CD3 have been proposed to contribute to this coupling, their kinetics and mechanical competence remain elusive. Here, we quantify TCR{beta}-CD3 ECD cis-interactions in a pseudo-cis configuration using two-dimensional binding and single-bond force spectroscopy, finding that TCR{beta}-CD3{gamma}{varepsilon} and TCR{beta}-CD3{delta}{varepsilon} interactions have low affinity and rapid kinetics, yet form catch bonds. Critically, concurrent engagement of CD3{gamma}{varepsilon} and CD3{delta}{varepsilon} produces high cis-cooperativity, yielding a stronger and longer-lasting CD3{gamma}{varepsilon}-TCR{beta}-CD3{delta}{varepsilon} trimolecular catch bond than the sum of the two dimeric bonds, with force-stabilized lifetimes matching those of agonist TCR-pMHC trans-interaction. Molecular dynamics simulations reveal an expanded, cooperative, and asymmetric contact network, making CD3{delta}{varepsilon} more force-responsive and susceptible to conformational change than CD3{gamma}{varepsilon}. Interface mutations do not alter force-free affinities but remodel cooperative cis-bond profiles, leading to an inverse correlation with trans-bond profiles and T cell signaling. These results identify cooperative ECD cis-interaction as a mechanically regulatable allosteric coupling element at the TCR-CD3 junction important to antigen recognition and signal initiation. ]]> Yuan, Z. Cong, P. Natarajan, A. Ge, C. Travaglino, S. Beesam, S. Grazette, D. Krogsgaard, M. Zhu, C. 2022-04-15 doi:10.1101/2022.04.14.488403 Cold Spring Harbor Laboratory Press 2022-04-15 <![CDATA[ The rhizodynamics robot: Automated imaging system for studying long-term dynamic root growth ]]> https://biorxiv.org/content/10.1101/2022.04.15.488424v1?rss=1 McCaskey, E. Taylor, I. Pierce, C. Ligon, J. Aydin, E. Hunner, C. Carmichael, A. Eserman, L. Coffey, E. E. D. Benfey, P. N. Goldman, D. I. 2022-04-16 doi:10.1101/2022.04.15.488424 Cold Spring Harbor Laboratory Press 2022-04-16 <![CDATA[ Rye: genetic ancestry inference at biobank scale ]]> https://biorxiv.org/content/10.1101/2022.04.15.488477v1?rss=1 Conley, A. B. Rishishwar, L. Ahmad, M. Sharma, S. Norris, E. T. Jordan, I. K. Marino-Ramirez, L. 2022-04-16 doi:10.1101/2022.04.15.488477 Cold Spring Harbor Laboratory Press 2022-04-16 <![CDATA[ Severe drought events trigger long-term salt marsh dieback in the Southeastern and Gulf of Mexico USA ]]> https://biorxiv.org/content/10.1101/2022.04.18.488673v1?rss=1 Rolando, J. L. Hodges, M. Garcia, K. D. Krueger, G. Williams, N. Carr, J. Robinson, J. George, A. Morris, J. T. Kostka, J. E. 2022-04-18 doi:10.1101/2022.04.18.488673 Cold Spring Harbor Laboratory Press 2022-04-18 <![CDATA[ Weak tension accelerates hybridization and dehybridization of short oligonucleotides ]]> https://biorxiv.org/content/10.1101/2022.04.19.488836v1?rss=1 Hart, D. R. Jeong, J. Gumbart, J. Kim, H. D. 2022-04-20 doi:10.1101/2022.04.19.488836 Cold Spring Harbor Laboratory Press 2022-04-20 <![CDATA[ Bridging scales from spiking activity to the local field potential through latent dynamics ]]> https://biorxiv.org/content/10.1101/2022.04.21.489039v1?rss=1 Sederberg, A. Pala, A. Stanley, G. B. 2022-04-22 doi:10.1101/2022.04.21.489039 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ StandardRat: A multi-center consensus protocol to enhance functional connectivity specificity in the rat brain ]]> https://biorxiv.org/content/10.1101/2022.04.27.489658v1?rss=1 Grandjean, J. Desrosiers-Gregoire, G. Anckaerts, C. Angeles-Valdez, D. Ayad, F. Barriere, D. A. Blockx, I. Bortel, A. B. Broadwater, M. Cardoso, B. M. Celestine, M. Chavez-Negrete, J. E. Choi, S. Christiaen, E. Clavijo, P. Colon-Perez, L. Cramer, S. Daniele, T. Dempsey, E. Diao, Y. Doelemeyer, A. Dopfel, D. Dvorakova, L. Falfan-Melgoza, C. Fernandes, F. F. Fowler, C. F. Fuentes-Ibanez, A. Garin, C. Gelderman, E. Golden, C. E. Guo, C. C. Henckens, M. J. Hennessy, L. A. Herman, P. Hofwijks, N. Horien, C. Ionescu, T. M. Jones, J. Kaesser, J. Kim, E. Lambers 2022-04-28 doi:10.1101/2022.04.27.489658 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. Hillquist) ]]> https://biorxiv.org/content/10.1101/2022.04.28.489789v1?rss=1 Bruna, T. Aryal, R. Dudchenko, O. Sargent, D. J. Mead, D. Buti, M. Cavallini, A. Hytönen, T. Andres, J. Pham, M. Weisz, D. Mascagni, F. Usai, G. Natali, L. Bassil, N. Fernandez, G. E. Lomsadze, A. Armour, M. Olukolu, B. A. Poorten, T. J. Britton, C. Davik, J. Ashrafi, H. Aiden, E. L. Borodovsky, M. Worthington, M. L. 2022-04-30 doi:10.1101/2022.04.28.489789 Cold Spring Harbor Laboratory Press 2022-04-30 <![CDATA[ Within- and between-subject reproducibility and variability in multi-modal, longitudinal brain networks ]]> https://biorxiv.org/content/10.1101/2022.05.03.490544v1?rss=1 Nakuci, J. Wasylyshyn, N. Cieslak, M. Elliot, J. C. Bansal, K. Giesbrecht, B. Grafton, S. T. Vettel, J. M. Garcia, J. O. Muldoon, S. F. 2022-05-04 doi:10.1101/2022.05.03.490544 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Single trial variability in neural activity during a working memory task: A window into multiple distinct information processing sequences ]]> https://biorxiv.org/content/10.1101/2022.05.03.490545v1?rss=1 Nakuci, J. Covey, T. J. Shucard, J. L. Shucard, D. W. Muldoon, S. F. 2022-05-04 doi:10.1101/2022.05.03.490545 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Transformation of coral communities subjected to an unprecedented heatwave is modulated by local disturbance ]]> https://biorxiv.org/content/10.1101/2022.05.10.491220v1?rss=1 Baum, J. K. Claar, D. C. Tietjen, K. L. Magel, J. M. T. Maucieri, D. G. Cobb, K. M. McDevitt-Irwin, J. M. 2022-05-11 doi:10.1101/2022.05.10.491220 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Blockade of TGF-β signaling reactivates HIV-1/SIV reservoirs and immune responses in vivo ]]> https://biorxiv.org/content/10.1101/2022.05.13.489595v1?rss=1 Samer, S. Thomas, Y. Arainga, M. Carter, C. Shirreff, L. M. Arif, M. S. Avitia, J. M. Frank, I. McRaven, M. D. Thuruthiyil, C. T. Heybeli, V. B. Anderson, M. R. Owen, B. Gaisin, A. Bose, D. Simons, L. M. Hultquist, J. F. Arthos, J. Cicala, C. Sereti, I. Santangelo, P. Lorenzo-Redondo, R. Hope, T. J. Villinger, F. J. Marinelli, E. 2022-05-13 doi:10.1101/2022.05.13.489595 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Machine Learning Predicts Treatment Response in Bipolar & Major Depressive Disorders ]]> https://biorxiv.org/content/10.1101/2022.05.13.491903v1?rss=1 Salman, M. S. Verner, E. Bockholt, H. J. Fu, Z. Misiura, M. B. Baker, B. T. Osuch, E. Sui, J. Calhoun, V. D. 2022-05-17 doi:10.1101/2022.05.13.491903 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ Single cell kinetic modeling of redox-based drug metabolism in head and neck squamous cell carcinoma ]]> https://biorxiv.org/content/10.1101/2022.05.17.492281v1?rss=1 Raddatz, A. D. Furdui, C. M. Bey, E. Kemp, M. L. 2022-05-18 doi:10.1101/2022.05.17.492281 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ scMoMaT: Mosaic integration of single cell multi-omics matrices using matrix trifactorization ]]> https://biorxiv.org/content/10.1101/2022.05.17.492336v1?rss=1 Zhang, Z. Sun, H. Chen, X. Mariappan, R. Chen, X. Jain, M. Efremova, M. Rajan, V. Teichmann, S. Zhang, X. 2022-05-19 doi:10.1101/2022.05.17.492336 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ The Effects of Negative Periocular Pressure on Biomechanics of the Optic Nerve Head and Cornea: A Computational Modeling Study ]]> https://biorxiv.org/content/10.1101/2022.05.17.492338v1?rss=1 Safa, B. N. Bleeker, A. Berdahl, J. P. Ethier, C. R. 2022-05-19 doi:10.1101/2022.05.17.492338 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Narrowband gamma oscillations propagate and synchronize throughout the mouse thalamocortical visual system ]]> https://biorxiv.org/content/10.1101/2022.05.19.491028v1?rss=1 Shin, D. Peelman, K. Del Rosario, J. Haider, B. 2022-05-20 doi:10.1101/2022.05.19.491028 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ BOA: A Partitioned View of Genome Assembly ]]> https://biorxiv.org/content/10.1101/2022.05.22.492973v1?rss=1 Ghosh, P. An, X. Keppler, P. Emre Kurt, S. Catalyurek, U. V. Krishnamoorthy, S. Sadayappan, P. Rajam, A. S. Kalyanaraman, A. 2022-05-24 doi:10.1101/2022.05.22.492973 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ An Approach for Estimating Explanation Uncertainty in fMRI dFNC Classification ]]> https://biorxiv.org/content/10.1101/2022.05.23.493148v1?rss=1 Ellis, C. A. Miller, R. L. Calhoun, V. D. 2022-05-25 doi:10.1101/2022.05.23.493148 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Integration of imaging modalities with lipidomic characterization to investigate MSCs potency metrics ]]> https://biorxiv.org/content/10.1101/2022.05.25.493259v1?rss=1 Mortensen, L. J. Priyadarshani, P. Van Grouw, A. R. Liversage, A. R. Nikitina, A. A. Tehrani, K. F. Kemp, M. L. Fernandez, F. 2022-05-26 doi:10.1101/2022.05.25.493259 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ UNDESRTANDING MESENCHYMAL STEM CELL IMMUNE POTENCY:A MORPHOLOMIC AND LIPIDOMIC PERSPECTIVE ]]> https://biorxiv.org/content/10.1101/2022.05.25.493514v1?rss=1 PRIYADARSHANI, P. DeVeaux, S. Leitmann, B. Rui, K. Botchwey, E. Mortensen, L. J. 2022-05-26 doi:10.1101/2022.05.25.493514 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ Examining Effects of Schizophrenia on EEG with Explainable Deep Learning Models ]]> https://biorxiv.org/content/10.1101/2022.05.26.493659v1?rss=1 Ellis, C. A. Sattiraju, A. Miller, R. L. Calhoun, V. 2022-05-29 doi:10.1101/2022.05.26.493659 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Seeing the forest and the tree: Building representations of both individual and collective dynamics with transformers ]]> https://biorxiv.org/content/10.1101/2022.06.10.495595v1?rss=1 Liu, R. Azabou, M. Dabagia, M. Xiao, J. Dyer, E. L. 2022-06-13 doi:10.1101/2022.06.10.495595 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ Distinguishing discrete and continuous behavioral variability using warped autoregressive HMMs ]]> https://biorxiv.org/content/10.1101/2022.06.10.495690v1?rss=1 Costacurta, J. C. Duncker, L. Sheffer, B. Williams, A. H. Gillis, W. Weinreb, C. Markowitz, J. E. Datta, S. R. Linderman, S. W. 2022-06-13 doi:10.1101/2022.06.10.495690 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ Low diversity and microdiversity of comammox bacteria in wastewater systems suggests wastewater-specific adaptation within the Ca. Nitrospira nitrosa cluster. ]]> https://biorxiv.org/content/10.1101/2022.06.11.495745v1?rss=1 Cotto, I. Vilardi, K. J. Huo, L. Fogarty, E. C. Khunjar, W. Wilson, C. De Clippeleir, H. Gilmore, K. Bailey, E. Lücker, S. J. Pinto, A. J. 2022-06-11 doi:10.1101/2022.06.11.495745 Cold Spring Harbor Laboratory Press 2022-06-11 <![CDATA[ Plate-Q: A Frugal Microplate-Reader for Bacterial Signal Quantification ]]> https://biorxiv.org/content/10.1101/2022.06.11.495768v1?rss=1 Sendilraj, V. Gulati, M. Standeven, J. Bhamla, M. S. 2022-06-13 doi:10.1101/2022.06.11.495768 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ Distinct neurotoxic TDP-43 fibril polymorphs can be generated by heterotypic interactions with α-synuclein ]]> https://biorxiv.org/content/10.1101/2022.06.14.496041v1?rss=1 Dhakal, S. Robang, A. S. Bhatt, N. Pungamalai, N. Fung, L. Kayed, R. Paravastu, A. K. Rangachari, V. 2022-06-16 doi:10.1101/2022.06.14.496041 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Active and passive mechanics for rough terrain traversal in centipedes ]]> https://biorxiv.org/content/10.1101/2022.06.17.496557v1?rss=1 Diaz, K. Erickson, E. Chong, B. Soto, D. Goldman, D. I. 2022-06-17 doi:10.1101/2022.06.17.496557 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks ]]> https://biorxiv.org/content/10.1101/2022.06.19.496734v1?rss=1 Guo, Z. Liu, J. Skolnick, J. Cheng, J. 2022-06-20 doi:10.1101/2022.06.19.496734 Cold Spring Harbor Laboratory Press 2022-06-20 <![CDATA[ A natural definition for a bacterial strain and clonal complex ]]> https://biorxiv.org/content/10.1101/2022.06.27.497766v1?rss=1 95% among themselves and ANI <90% to members of other species, while genomes showing ANI 90-95% are comparatively rare. However, it remains unclear if such "discontinuities" or gaps in ANI values can be observed within species and thus, used to advance and standardize intra-species units such as strains and sequence types. By analyzing 18,123 complete isolate genomes from 330 bacterial species with at least ten genome representatives each as well as available long-read metagenomes, we show that such a discontinuity exists between 99.2-99.8% (mean 99.5%) ANI. The 99.5% ANI threshold is largely consistent with how sequence types have been defined in previous epidemiological studies but provides clusters with [~]20% higher accuracy in terms of evolutionary and gene-content relatedness of the grouped genomes, while strains should be consequently defined at higher ANI values (>99.99% proposed). Collectively, our results should facilitate future micro-diversity studies across clinical or environmental settings because they provide a more natural definition of intra-species units of diversity. ]]> Rodriguez-R, L. M. Conrad, R. E. Feistel, D. J. Viver, T. Rossello-Mora, R. Konstantinidis, K. T. 2022-06-27 doi:10.1101/2022.06.27.497766 Cold Spring Harbor Laboratory Press 2022-06-27 <![CDATA[ Annotation of Phage Genomes with Multiple Genetic Codes ]]> https://biorxiv.org/content/10.1101/2022.06.29.495998v1?rss=1 Pfennig, A. Lomsadze, A. Borodovsky, M. 2022-07-02 doi:10.1101/2022.06.29.495998 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Transcriptomic cell type structures in vivo neuronal activity across multiple time scales. ]]> https://biorxiv.org/content/10.1101/2022.07.10.499487v1?rss=1 30 min). We show that transcriptomic cell class information is robustly embedded in the timing of single neuron activity recorded in the intact brain of behaving animals (calcium imaging and extracellular electrophysiology), as well as in a bio-realistic model of visual cortex. In contrast, we were unable to reliably extract cell identity from summary measures of rate, variance, and interevent interval statistics. We applied our analyses to the question of whether transcriptomic subtypes of excitatory neurons represent functionally distinct classes. In the calcium imaging dataset, which contains a diverse set of excitatory Cre lines, we found that a subset of excitatory cell types are computationally distinguishable based upon their Cre lines, and that excitatory types can be classified with higher accuracy when considering their cortical layer and projection class. Here we address the fundamental question of whether a neuron, within a complex cortical network, embeds a fingerprint of its transcriptomic identity into its activity. Our results reveal robust computational fingerprints for transcriptomic types and classes across diverse contexts, defined over multiple timescales. ]]> Schneider, A. Azabou, M. McDougall-Vigier, L. Parks, D. B. Ensley, S. Bhaskaran-Nair, K. Nowakowski, T. J. Dyer, E. L. Hengen, K. B. 2022-07-11 doi:10.1101/2022.07.10.499487 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ A Toxin-Antidote Selfish Element Increases Fitness of its Host ]]> https://biorxiv.org/content/10.1101/2022.07.15.500229v1?rss=1 Long, L. Xu, W. Paaby, A. B. McGrath, P. T. 2022-07-15 doi:10.1101/2022.07.15.500229 Cold Spring Harbor Laboratory Press 2022-07-15 <![CDATA[ Quantifying Cell-type-specific Differences of Single-cell Datasets using UMAP and SHAP ]]> https://biorxiv.org/content/10.1101/2022.07.15.500285v1?rss=1 Lim, H. S. Qiu, P. 2022-07-18 doi:10.1101/2022.07.15.500285 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ MCPNet : A parallel maximum capacity-based genome-scale gene network construction framework ]]> https://biorxiv.org/content/10.1101/2022.07.19.500603v1?rss=1 Pan, T. C. Chockalingam, S. P. Aluru, M. Aluru, S. 2022-07-20 doi:10.1101/2022.07.19.500603 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Clonal development, not aggregation, drives the transition to multicellularity in an isogenic model system ]]> https://biorxiv.org/content/10.1101/2022.07.21.500805v1?rss=1 Pentz, J. T. MacGillivray, K. DuBose, J. G. Conlin, P. L. Reinhardt, E. Libby, E. Ratcliff, W. C. 2022-07-22 doi:10.1101/2022.07.21.500805 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Metabolic activity organizes olfactory representations ]]> https://biorxiv.org/content/10.1101/2022.07.21.500995v1?rss=1 Qian, W. W. Wei, J. N. Sanchez-Lengeling, B. Lee, B. K. Luo, Y. Vlot, M. Dechering, K. Peng, J. Gerkin, R. C. Wiltschko, A. B. 2022-07-22 doi:10.1101/2022.07.21.500995 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Exploring Relationships between Functional Network Connectivity and Cognition with an Explainable Clustering Approach ]]> https://biorxiv.org/content/10.1101/2022.07.23.501266v1?rss=1 Ellis, C. A. Lapera Sancho, M. Miller, R. L. Calhoun, V. 2022-07-24 doi:10.1101/2022.07.23.501266 Cold Spring Harbor Laboratory Press 2022-07-24 <![CDATA[ MetaGeneMark-2: Improved Gene Prediction in Metagenomes ]]> https://biorxiv.org/content/10.1101/2022.07.25.500264v1?rss=1 Gemayel, K. Lomsadze, A. Borodovsky, M. 2022-07-27 doi:10.1101/2022.07.25.500264 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ Idiosyncratic relation between human brain activity and behavior ]]> https://biorxiv.org/content/10.1101/2022.08.01.502338v1?rss=1 Nakuci, J. Yeon, J. Xue, K. Kim, J.-H. Kim, S.-P. Rahnev, D. 2022-08-02 doi:10.1101/2022.08.01.502338 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Subcellular spatially resolved gene neighborhood networks in single cells ]]> https://biorxiv.org/content/10.1101/2022.08.03.502409v1?rss=1 Fang, Z. Form, A. J. Hu, T. K. Zhang, N. Mantalaris, A. Coskun, A. F. 2022-08-05 doi:10.1101/2022.08.03.502409 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ A Universal Language for Finding Mass Spectrometry Data Patterns ]]> https://biorxiv.org/content/10.1101/2022.08.06.503000v1?rss=1 Jarmusch, A. K. Aron, A. T. Petras, D. Phelan, V. V. Bittremieux, W. Acharya, D. D. Ahmed, M. M. A. Bauermeister, A. Bertin, M. J. Boudreau, P. D. Borges, R. M. Bowen, B. P. Brown, C. J. Chagas, F. O. Clevenger, K. D. Correia, M. S. P. Crandall, W. J. Crusemann, M. Damiani, T. Fiehn, O. Garg, N. Gerwick, W. H. Gilbert, J. R. Globisch, D. Gomes, P. W. P. Heuckeroth, S. James, C. A. Jarmusch, S. A. Kakhkhorov, S. A. Kang, K. B. Kersten, R. D. Kim, H. Kirk, R. D. Kohlbacher, O. Kontou, E. E. Liu, K. Lizama-Chamu, I. Luu, G. T. Luzzatto Knaan, T. Marty, M. T. 2022-08-07 doi:10.1101/2022.08.06.503000 Cold Spring Harbor Laboratory Press 2022-08-07 <![CDATA[ CCS Predictor 2.0: An Open-Source Jupyter Notebook Tool for Filtering Out False Positives in Metabolomics ]]> https://biorxiv.org/content/10.1101/2022.08.09.503345v1?rss=1 Rainey, M. A. Watson, C. A. Asef, C. K. Foster, M. R. Baker, E. Fernandez, F. M. 2022-08-09 doi:10.1101/2022.08.09.503345 Cold Spring Harbor Laboratory Press 2022-08-09 <![CDATA[ Cellular profiling of a recently-evolved social behavior ]]> https://biorxiv.org/content/10.1101/2022.08.09.503380v1?rss=1 Johnson, Z. V. Hegarty, B. E. Gruenhagen, G. W. Lancaster, T. J. McGrath, P. T. Streelman, J. T. 2022-08-10 doi:10.1101/2022.08.09.503380 Cold Spring Harbor Laboratory Press 2022-08-10 <![CDATA[ Nanopore Translocation of Topologically Linked DNA Catenanes ]]> https://biorxiv.org/content/10.1101/2022.08.10.503522v1?rss=1 Rheaume, S. Klotz, A. 2022-08-12 doi:10.1101/2022.08.10.503522 Cold Spring Harbor Laboratory Press 2022-08-12 <![CDATA[ Vertical growth dynamics of biofilms ]]> https://biorxiv.org/content/10.1101/2022.08.11.503641v1?rss=1 Bravo, P. Ng, S. L. MacGillivray, K. A. Hammer, B. K. Yunker, P. J. 2022-08-12 doi:10.1101/2022.08.11.503641 Cold Spring Harbor Laboratory Press 2022-08-12 <![CDATA[ Mass spectrometry imaging reveals early metabolic priming of cell lineage in differentiating human induced pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2022.08.16.504020v1?rss=1 Nikitina, A. A. Van Grouw, A. Roysam, T. Huang, D. Fernandez, F. M. Kemp, M. L. 2022-08-16 doi:10.1101/2022.08.16.504020 Cold Spring Harbor Laboratory Press 2022-08-16 <![CDATA[ Examining Reproducibility of EEG Schizophrenia Biomarkers Across Explainable Machine Learning Models ]]> https://biorxiv.org/content/10.1101/2022.08.16.504159v1?rss=1 Ellis, C. A. Sattiraju, A. Miller, R. L. Calhoun, V. D. 2022-08-17 doi:10.1101/2022.08.16.504159 Cold Spring Harbor Laboratory Press 2022-08-17 <![CDATA[ Supraorbital whiskers act as wind-antennae in rat anemotaxis ]]> https://biorxiv.org/content/10.1101/2022.08.18.504295v1?rss=1 Mugnaini, M. Mehrotra, D. Davoine, F. Sharma, V. Mendes, A. R. Brecht, M. Clemens, A. M. 2022-08-18 doi:10.1101/2022.08.18.504295 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ RiboXYZ: A comprehensive database for visualizing and analyzing ribosomestructures ]]> https://biorxiv.org/content/10.1101/2022.08.22.504886v1?rss=1 Kushner, A. Petrov, A. S. Dao Duc, K. 2022-08-23 doi:10.1101/2022.08.22.504886 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ RTNet: A neural network that exhibits the signatures of human perceptual decision making ]]> https://biorxiv.org/content/10.1101/2022.08.23.505015v1?rss=1 Rafiei, F. Rahnev, D. 2022-08-25 doi:10.1101/2022.08.23.505015 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Systems-wide dissection of organic acid assimilation in Pseudomonas aeruginosa reveals a novel path to underground metabolism ]]> https://biorxiv.org/content/10.1101/2022.08.25.505149v1?rss=1 Dolan, S. K. Wijaya, A. Kohlstedt, M. Gläser, L. Brear, P. Silva-Rocha, R. K. Wittmann, C. Welch, M. 2022-08-25 doi:10.1101/2022.08.25.505149 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Deep learning-driven insights into super protein complexes for outer membrane protein biogenesis in bacteria ]]> https://biorxiv.org/content/10.1101/2022.08.25.505253v1?rss=1 Gao, M. Nakajima An, D. Skolnick, J. 2022-08-25 doi:10.1101/2022.08.25.505253 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Ion Mobility for Unknown Metabolite Identification: Hope or Hype? ]]> https://biorxiv.org/content/10.1101/2022.08.26.505158v1?rss=1 Asef, C. K. Rainey, M. Garcia, B. M. Gouveia, G. J. Shaver, A. O. Leach, F. E. Morse, A. M. Edison, A. S. McIntyre, L. Fernandez, F. 2022-08-26 doi:10.1101/2022.08.26.505158 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Solid-State Single-Molecule Sensing with the Electronic Life-detection Instrument for Enceladus/Europa (ELIE) ]]> https://biorxiv.org/content/10.1101/2022.08.31.505913v1?rss=1 Carr, C. E. Ramirez-Colon, J. L. Duzdevich, D. E. Lee, S. Taniguchi, M. Ohshiro, T. Komoto, Y. Soderblom, J. M. Zuber, M. T. 2022-09-02 doi:10.1101/2022.08.31.505913 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Machine learning identification of Pseudomonas aeruginosa strains from colony image data ]]> https://biorxiv.org/content/10.1101/2022.09.02.506375v1?rss=1 Rattray, J. B. Walden, R. Marquez Zacarias, P. Molotkova, E. Perron, G. Solis-Lemus, C. Pimentel-Alarcon, D. Brown, S. P. 2022-09-02 doi:10.1101/2022.09.02.506375 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Trade-offs constrain adaptive pathways to T6 survival ]]> https://biorxiv.org/content/10.1101/2022.09.02.506412v1?rss=1 MacGillivray, K. A. Ng, S. L. Wiesenfeld, S. Guest, R. L. Jubery, T. Silhavy, T. J. Ratcliff, W. C. Hammer, B. K. 2022-09-05 doi:10.1101/2022.09.02.506412 Cold Spring Harbor Laboratory Press 2022-09-05 <![CDATA[ Reduction of the HIV-1 reservoir in T cells from persons with HIV-1 on suppressive antiretroviral therapy using expanded natural killer cells ex vivo ]]> https://biorxiv.org/content/10.1101/2022.09.05.506592v1?rss=1 Checkley Luttge, M. A. LUTTGE, B. G. Dobrowolski, C. Wald, D. N. McMahon, D. Haidar, G. Sobolewski, M. D. Enick, P. N. Cyktor, J. Mellors, J. W. Karn, J. 2022-09-06 doi:10.1101/2022.09.05.506592 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ Tumor microenvironments impair T cell receptor affinity and function ]]> https://biorxiv.org/content/10.1101/2022.09.11.507496v1?rss=1 Yuan, Z. O'Melia, M. J. Li, K. Lyu, J. Zhou, F. Jothikumar, P. Rohner, N. A. Manspeaker, M. P. Francis, D. M. Bai, K. Ge, C. Rushdi, M. N. Chingozha, L. Ruiperez-Campillo, S. Lu, H. Thomas, S. N. Zhu, C. 2022-09-13 doi:10.1101/2022.09.11.507496 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ The dynamic response of quorum-sensing to density is robust to signal supplementation and signal synthase knockouts ]]> https://biorxiv.org/content/10.1101/2022.09.12.507654v1?rss=1 Rattray, J. B. Kramer, P. Gurney, J. Thomas, S. A. Brown, S. P. 2022-09-13 doi:10.1101/2022.09.12.507654 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Screening and Development of Constitutively Synergistic Combination Drug Formulations for T Cell Acute Lymphoblastic Leukemia ]]> https://biorxiv.org/content/10.1101/2022.09.21.508196v1?rss=1 Kelvin, J. M. Zhang, D. Y. Williams, E. K. Moore, S. G. Birnbaum, L. A. Zecca, H. Wang, X. Jain, J. Qui, M. Jui, N. T. Fu, H. Du, Y. Kemp, M. L. Lam, W. A. DeRyckere, D. Graham, D. K. Dreaden, E. C. 2022-09-22 doi:10.1101/2022.09.21.508196 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Temporal dynamics of the multi-omic response to endurance exercise training across tissues ]]> https://biorxiv.org/content/10.1101/2022.09.21.508770v1?rss=1 MoTrPAC Study Group, Amar, D. Gay, N. R. Jean Beltran, P. M. Adkins, J. N. Almagro Armenteros, J. J. Ashley, E. Avila-Pacheco, J. Bae, D. Bararpour, N. Burant, C. Clish, C. Cutter, G. Dasari, S. Dennis, C. Evans, C. R. Fernandez, F. M. Gaul, D. Ge, Y. Gerszten, R. Goodyear, L. J. Hou, Z. Ilkayeva, O. Ivanova, A. A. Jimenez-Morales, D. Kachman, M. T. Keshishian, H. Kraus, W. E. Lanza, I. R. Li, J. Lindholm, M. E. Lira, A. C. Many, G. M. Marwaha, S. Miller, M. E. Muehlbauer, M. J. Nair, K. S. Nair, V. D. Natarajan Raja, A. Newgard, C. Ortlund, E. A. Pie 2022-09-23 doi:10.1101/2022.09.21.508770 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Irregular optogenetic stimulation waveforms can induce naturalistic patterns of hippocampal spectral activity ]]> https://biorxiv.org/content/10.1101/2022.09.21.508935v1?rss=1 Cole, E. R. Eggers, T. E. Weiss, D. Connolly, M. J. Gombolay, M. C. Laxpati, N. G. Gross, R. E. 2022-09-22 doi:10.1101/2022.09.21.508935 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Discovery of homogentisic acid as a precursor in trimethoprim metabolism and natural product biosynthesis ]]> https://biorxiv.org/content/10.1101/2022.09.22.509022v1?rss=1 Mcavoy, A. C. Threatt, P. H. Kapcia, J. Garg, N. 2022-09-25 doi:10.1101/2022.09.22.509022 Cold Spring Harbor Laboratory Press 2022-09-25 <![CDATA[ A 1D Model Characterizing the Role of Spatiotemporal Contraction Distributions on Lymph Transport ]]> https://biorxiv.org/content/10.1101/2022.09.26.508881v1?rss=1 Sedaghati, F. Dixon, B. gleason, R. 2022-09-28 doi:10.1101/2022.09.26.508881 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Effect of Nonlinear Hyperelastic Property of Arterial Tissues on the Pulse Wave Velocity based on the Unified-Fiber-Distribution (UFD) Model ]]> https://biorxiv.org/content/10.1101/2022.09.27.509711v1?rss=1 Dong, H. Liu, M. Woodall, J. Leshnower, B. Gleason, R. L. 2022-09-28 doi:10.1101/2022.09.27.509711 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Cellular proteomic profiling using proximity labelling by TurboID-NES in microglial and neuronal cell lines. ]]> https://biorxiv.org/content/10.1101/2022.09.27.509765v1?rss=1 500 differentially-abundant proteins) including increased canonical pro-inflammatory proteins (Il1a, Irg1, Oasl1) and decrease anti-inflammatory proteins (Arg1, Mgl2). ]]> Sunna, S. Bowen, C. Zeng, H. Rayaprolu, S. Kumar, P. Bagchi, P. Guo, Q. Duong, D. M. Bitarafan, S. Natu, A. Wood, L. Seyfried, N. T. Rangaraju, S. 2022-09-28 doi:10.1101/2022.09.27.509765 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Memory in Repetitive Protein-Protein Interaction Series -- in Memory of the Late Professor Robert M. Nerem ]]> https://biorxiv.org/content/10.1101/2022.10.01.510459v1?rss=1 Rosado, A. M. Zhang, Y. Choi, H.-K. Elrich, S. M. Jin, F. Grakoui, A. Evavold, B. D. Zhu, C. 2022-10-03 doi:10.1101/2022.10.01.510459 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ Towards Greater Neuroimaging Classification Transparency via the Integration of Explainability Methods and Confidence Estimation Approaches ]]> https://biorxiv.org/content/10.1101/2022.10.06.511164v1?rss=1 Ellis, C. A. Miler, R. L. Calhoun, V. D. 2022-10-08 doi:10.1101/2022.10.06.511164 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ Elephants have an adaptable prehensile grip ]]> https://biorxiv.org/content/10.1101/2022.10.06.511214v1?rss=1 Schulz, A. K. Reidenberg, J. Wu, J. Tang, C. Y. Seleb, B. Mancebo, J. Elgart, N. Hu, D. L. 2022-10-08 doi:10.1101/2022.10.06.511214 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ Stromal STAT5-mediated trophic activity regulates hematopoietic multipotent progenitor niche factors ]]> https://biorxiv.org/content/10.1101/2022.10.07.511255v1?rss=1 Wang, Z. Emmel, G. Lim, H. S. Zhu, W. Kosters, A. Ghosn, E. Qiu, P. Bunting, K. 2022-10-07 doi:10.1101/2022.10.07.511255 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Depletion Assisted Hemin Affinity (DAsHA) Proteomics Reveals an Expanded Landscape of Heme Binding Proteins ]]> https://biorxiv.org/content/10.1101/2022.10.11.511733v1?rss=1 Kim, H. Moore, C. M. Mestre-Fos, S. Hanna, D. A. Williams, L. D. Reddi, A. Torres, M. P. 2022-10-11 doi:10.1101/2022.10.11.511733 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ A unified model for the dynamics of ATP-independent ultrafast contraction ]]> https://biorxiv.org/content/10.1101/2022.10.14.512304v1?rss=1 Floyd, C. Molines, A. T. Lei, X. Honts, J. E. Chang, F. Elting, M. W. Vaikuntanathan, S. Dinner, A. R. Bhamla, M. S. 2022-10-16 doi:10.1101/2022.10.14.512304 Cold Spring Harbor Laboratory Press 2022-10-16 <![CDATA[ scMultiSim: simulation of multi-modality single cell data guided by cell-cell interactions and gene regulatory networks ]]> https://biorxiv.org/content/10.1101/2022.10.15.512320v1?rss=1 Li, H. Zhang, Z. Squires, M. Chen, X. Zhang, X. 2022-10-18 doi:10.1101/2022.10.15.512320 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ GSearch: Ultra-Fast and Scalable Microbial Genome Search by combining Kmer Hashing with Hierarchical Navigable Small World Graphs ]]> https://biorxiv.org/content/10.1101/2022.10.21.513218v1?rss=1 Zhao, J. Pierre-both, J. Rodriguez-R, L. M. Konstantinidis, K. T. 2022-10-21 doi:10.1101/2022.10.21.513218 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response ]]> https://biorxiv.org/content/10.1101/2022.10.24.513517v1?rss=1 Patel, A. Kumar, S. Lai, L. Chakravarthy, C. Valanparambil, R. Reddy, E. S. Gottimukkala, K. Bajpai, P. Raju, D. R. Edara, V. V. Davis-Gardner, M. E. Linderman, S. Dixit, K. Sharma, P. Mantus, G. Cheedarla, N. Verkerke, H. P. Frank, F. Neish, A. S. Roback, J. D. Davis, C. W. Wrammert, J. Ahmed, R. Suthar, M. Sharma, A. Murali-Krishna, K. Chandele, A. Ortlund, E. A. 2022-10-24 doi:10.1101/2022.10.24.513517 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Optimal dormancy strategies in fluctuating environments given delays in phenotypic switching ]]> https://biorxiv.org/content/10.1101/2022.10.25.513531v1?rss=1 Magalie, A. Schwartz, D. Lennon, J. T. Weitz, J. 2022-10-27 doi:10.1101/2022.10.25.513531 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ A Robust Bayesian Approach to Bulk Gene Expression Deconvolution withNoisy Reference Signatures ]]> https://biorxiv.org/content/10.1101/2022.10.25.513800v1?rss=1 Ghaffari, S. Bouchonville, K. J. Saleh, E. Schmidt, R. E. Offer, S. M. Sinha, S. 2022-10-27 doi:10.1101/2022.10.25.513800 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Highlight Results, Don't Hide Them: Enhance interpretation, reduce biases and improve reproducibility ]]> https://biorxiv.org/content/10.1101/2022.10.26.513929v1?rss=1 Taylor, P. A. Reynolds, R. C. Calhoun, V. Gonzalez-Castillo, J. Handwerker, D. A. Bandettini, P. A. Mejia, A. F. Chen, G. 2022-10-27 doi:10.1101/2022.10.26.513929 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Identifying Neuropsychiatric Disorder Subtypes and Subtype-dependent Variation in Diagnostic Deep Learning Classifier Performance ]]> https://biorxiv.org/content/10.1101/2022.10.27.514124v1?rss=1 Ellis, C. A. Miller, R. L. Calhoun, V. D. 2022-10-28 doi:10.1101/2022.10.27.514124 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Different genetic architectures of complex traits and their relevance to polygenic score performance ]]> https://biorxiv.org/content/10.1101/2022.10.29.514295v1?rss=1 Carvalho, N. R. G. Harris, A. M. Lachance, J. 2022-10-31 doi:10.1101/2022.10.29.514295 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ High-Throughput Library Transgenesis in Caenorhabditis elegans via Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS) ]]> https://biorxiv.org/content/10.1101/2022.10.30.514301v1?rss=1 Stevenson, Z. C. Moerdyk-Schauwecker, M. J. Banse, S. A. Patel, D. S. Lu, H. Phillips, P. C. 2022-10-31 doi:10.1101/2022.10.30.514301 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ RNA-mediated double-strand break repair in human cells ]]> https://biorxiv.org/content/10.1101/2022.11.01.514688v1?rss=1 Jeon, Y. Ferrari, M. M. Channagiri, T. Xu, P. Balachander, S. Park, V. S. Marsili, S. Pursell, Z. F. Jonoska, N. Storici, F. 2022-11-01 doi:10.1101/2022.11.01.514688 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ A Model of High-Speed Endovascular Sonothrombolysis with Vortex Ultrasound-Induced Shear Stress to Treat Cerebral Venous Sinus Thrombosis ]]> https://biorxiv.org/content/10.1101/2022.11.02.514936v1?rss=1 Zhang, B. Wu, H. Kim, H. Welch, P. J. Cornett, A. Stocker, G. Nogueira, R. G. Kim, J. Owens, G. Dayton, P. A. Xu, Z. Shi, C. Jiang, X. 2022-11-03 doi:10.1101/2022.11.02.514936 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ Microbial and Viral Genome and Proteome Nitrogen Demand Varies Across Multiple Spatial Scales Within a Marine Oxygen Minimum Zone ]]> https://biorxiv.org/content/10.1101/2022.11.11.516076v1?rss=1 Muratore, D. J. Bertagnolli, A. Bristow, L. Thamdrup, B. Weitz, J. S. Stewart, F. J. 2022-11-11 doi:10.1101/2022.11.11.516076 Cold Spring Harbor Laboratory Press 2022-11-11 <![CDATA[ Circuit-specific selective vulnerability in the DMN persists in the face of widespread amyloid burden. ]]> https://biorxiv.org/content/10.1101/2022.11.14.516510v1?rss=1 Brunwasser, S. J. Farris, C. Elmore, H. Dyer, E. L. Nair, K. B. Whitesell, J. D. Harris, J. A. Hengen, K. B. 2022-11-14 doi:10.1101/2022.11.14.516510 Cold Spring Harbor Laboratory Press 2022-11-14 <![CDATA[ Modular gene interactions drive modular pan-genome evolution in bacteria. ]]> https://biorxiv.org/content/10.1101/2022.11.15.516554v1?rss=1 Castro, J. Brown, S. P. 2022-11-15 doi:10.1101/2022.11.15.516554 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Understanding Lesion Progression in a Chronic Model of Cerebral Cavernous Malformations through Combined MRI and Histology ]]> https://biorxiv.org/content/10.1101/2022.11.15.516639v1?rss=1 Fisher, D. G. Sharifi, K. A. Ulutas, E. Z. Kumar, J. S. Kalani, M. Y. S. Miller, G. W. Price, R. J. Tvrdik, P. 2022-11-15 doi:10.1101/2022.11.15.516639 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Ultrastructural characterization of a viral RNA and G-protein containing, membranous organelle formed in respiratory syncytial virus infected cells ]]> https://biorxiv.org/content/10.1101/2022.11.28.517999v1?rss=1 Vijayakrishnan, S. Burns, A. M. Blanchard, E. L. Spink, M. C. Gilchrist, J. Howe, A. Darrow, M. C. Harkiolaki, M. Wu, C.-Y. Dutch, R. E. Santangelo, P. Fearns, R. Bhella, D. 2022-11-28 doi:10.1101/2022.11.28.517999 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Single-Cell Epitope-Transcriptomics Reveal Lung Stromaland Immune Cell Response Kinetics to Nanoparticle delivered RIG-I and TLR4 Agonists ]]> https://biorxiv.org/content/10.1101/2022.11.29.518316v1?rss=1 Keenum, M. C. Chatterjee, P. Atalis, A. M. Pandey, B. Jimenez, A. C. Roy, K. 2022-11-29 doi:10.1101/2022.11.29.518316 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ Identifying eukaryotes in drinking water metagenomes and factors influencing their biogeography. ]]> https://biorxiv.org/content/10.1101/2022.11.29.518372v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@1ae8423org.highwire.dtl.DTLVardef@653471org.highwire.dtl.DTLVardef@5606b7org.highwire.dtl.DTLVardef@1d30cde_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gabrielli, M. Dai, Z. Delafont, V. Timmers, P. van der Wielen, P. Antonelli, M. Pinto, A. J. 2022-11-29 doi:10.1101/2022.11.29.518372 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ Contrastive learning of protein representations with graph neural networks for structural and functional annotations ]]> https://biorxiv.org/content/10.1101/2022.11.29.518451v1?rss=1 Luo, J. Luo, Y. 2022-12-02 doi:10.1101/2022.11.29.518451 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Cortical networks relating to arousal are differentially coupled to neural activity and hemodynamics ]]> https://biorxiv.org/content/10.1101/2022.12.01.518759v1?rss=1 Meyer-Baese, L. Morrissette, A. E. Wang, Y. Le Chatelier, B. Borden, P. Y. Keilholz, S. Stanley, G. B. Jaeger, D. 2022-12-01 doi:10.1101/2022.12.01.518759 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Coordinated Regulation of Cdc42ep1, Actin, and Septin Filaments during Neural Crest Cell Migration ]]> https://biorxiv.org/content/10.1101/2022.12.04.519046v1?rss=1 Kho, M. Hladyshau, S. Tsygankov, D. Nie, S. 2022-12-04 doi:10.1101/2022.12.04.519046 Cold Spring Harbor Laboratory Press 2022-12-04 <![CDATA[ Co-occurrence and cooperation between comammox and anammox bacteria in a full-scale attached growth municipal wastewater treatment process. ]]> https://biorxiv.org/content/10.1101/2022.12.05.519185v1?rss=1 Vilardi, K. J. Cotto, I. Bachmann, M. Parsons, M. Klaus, S. Wilson, C. Bott, C. Pieper, K. Pinto, A. 2022-12-06 doi:10.1101/2022.12.05.519185 Cold Spring Harbor Laboratory Press 2022-12-06 <![CDATA[ Spatial and Spectral Components of the BOLD Global Signal in Rat Resting-State Functional MRI ]]> https://biorxiv.org/content/10.1101/2022.12.06.519194v1?rss=1 Anumba, N. Maltbie, E. Pan, W.-J. LaGrow, T. J. Xu, N. Keilholz, S. 2022-12-09 doi:10.1101/2022.12.06.519194 Cold Spring Harbor Laboratory Press 2022-12-09 <![CDATA[ The effect of random and systematic visual stimulation on entrained infraslow quasi-periodic global waves in human brain activity ]]> https://biorxiv.org/content/10.1101/2022.12.06.519337v1?rss=1 Xu, N. Smith, D. M. Jeno, G. Seeburger, D. T. Schumacher, E. H. Keilholz, S. D. 2022-12-07 doi:10.1101/2022.12.06.519337 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Structural Model for Self-Limiting β-strand Arrangement Within an Alzheimer's Amyloid-β Oligomer ]]> https://biorxiv.org/content/10.1101/2022.12.06.519347v1?rss=1 Gao, Y. Prasad, R. Randolph, P. S. Watzlawik, J. O. Roband, A. S. Guo, C. Stagg, S. M. Zhou, H.-X. Rosenberry, T. L. Paravastu, A. K. 2022-12-06 doi:10.1101/2022.12.06.519347 Cold Spring Harbor Laboratory Press 2022-12-06 <![CDATA[ Using light for energy: examining the evolution of phototrophic metabolism via synthetic construction ]]> https://biorxiv.org/content/10.1101/2022.12.06.519405v1?rss=1 Peterson, A. Baskett, C. Ratcliff, W. C. Burnetti, A. J. 2022-12-08 doi:10.1101/2022.12.06.519405 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ 13C ENDOR Spectroscopy-Guided MD Computations Reveals the Structure of the Enzyme-Substrate Complex of an Active, N-linked Glycosylated Lipoxygenase ]]> https://biorxiv.org/content/10.1101/2022.12.07.519351v1?rss=1 Sharma, A. Whittington, C. Jabed, M. Hill, S. G. Kostenko, A. Yu, T. Li, P. Hoffman, B. M. Offenbacher, A. R. 2022-12-07 doi:10.1101/2022.12.07.519351 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Task learning is subserved by a domain-general brain network ]]> https://biorxiv.org/content/10.1101/2022.12.07.519504v1?rss=1 Yeon, J. Larson, A. S. Rahnev, D. D'Esposito, M. 2022-12-07 doi:10.1101/2022.12.07.519504 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Conformational restriction shapes inhibition of a multidrug efflux adaptor protein ]]> https://biorxiv.org/content/10.1101/2022.12.09.519754v1?rss=1 Russell Lewis, B. Uddin, M. R. Moniruzzaman, M. Kuo, K. M. Higgins, A. J. Shah, L. M. N. Sobott, F. Parks, J. M. Hammerschmid, D. Gumbart, J. C. Zgurskaya, H. I. Reading, E. 2022-12-09 doi:10.1101/2022.12.09.519754 Cold Spring Harbor Laboratory Press 2022-12-09 <![CDATA[ Neuropsychiatric Disorder Subtyping Via Clustered Deep Learning Classifier Explanations ]]> https://biorxiv.org/content/10.1101/2022.12.14.520428v1?rss=1 Ellis, C. A. Miller, R. L. Calhoun, V. D. 2022-12-15 doi:10.1101/2022.12.14.520428 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Biologically-informed deep neural networks provide quantitative assessment of intratumoral heterogeneity in post-treatment glioblastoma ]]> https://biorxiv.org/content/10.1101/2022.12.20.521086v1?rss=1 Wang, H. Argenziano, M. G. Yoon, H. Boyett, D. Save, A. Petridis, P. Savage, W. Jackson, P. Hawkins-Daarud, A. Tran, N. Hu, L. Al-Dalahmah, O. Bruce, J. N. Grinband, J. Swanson, K. Canoll, P. Li, J. 2022-12-20 doi:10.1101/2022.12.20.521086 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Structural damping renders the insect exoskeleton mechanically insensitive to non-sinusoidal deformations ]]> https://biorxiv.org/content/10.1101/2022.12.27.522009v1?rss=1 Wold, E. Lynch, J. Gravish, N. Sponberg, S. 2022-12-27 doi:10.1101/2022.12.27.522009 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ dcSBM: A federated constrained source-based morphometry approach for multivariate brain structure mapping ]]> https://biorxiv.org/content/10.1101/2022.12.29.522266v1?rss=1 Saha, D. K. Silva, R. F. Baker, B. T. Saha, R. Calhoun, V. 2022-12-30 doi:10.1101/2022.12.29.522266 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ Tail wags the dog is unsupported by biomechanical Modeling of Canidae Tails Use during Terrestrial Motion ]]> https://biorxiv.org/content/10.1101/2022.12.30.522334v1?rss=1 Rottier, T. Schulz, A. Sohnel, K. McCarthy, K. Fischer, M. Jusufi, A. 2022-12-31 doi:10.1101/2022.12.30.522334 Cold Spring Harbor Laboratory Press 2022-12-31 <![CDATA[ Machine Learning Reveals Lipidome Remodeling Dynamics in a Mouse Model of Ovarian Cancer ]]> https://biorxiv.org/content/10.1101/2023.01.04.520434v1?rss=1 Bifarin, O. O. Sah, S. Gaul, D. A. Moore, S. G. Chen, R. Palaniappan, M. Kim, J. Matzuk, M. M. Fernandez, F. O. 2023-01-04 doi:10.1101/2023.01.04.520434 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ A Convolutional Autoencoder-based Explainable Clustering Approach for Resting-State EEG Analysis ]]> https://biorxiv.org/content/10.1101/2023.01.04.522805v1?rss=1 Ellis, C. A. Miller, R. Calhoun, V. 2023-01-05 doi:10.1101/2023.01.04.522805 Cold Spring Harbor Laboratory Press 2023-01-05 <![CDATA[ Antigen-dependent IL-12 signaling in CAR T cells promotes regional to systemic disease targeting ]]> https://biorxiv.org/content/10.1101/2023.01.06.522784v1?rss=1 Lee, E. Cullen, C. Murad, J. P. Gumber, D. Park, A. Yang, J. Stern, L. Adkins, L. Dhapola, G. Gittins, B. Chang, W.-C. Martinez, C. Woo, Y. Cristea, M. Rodriguez, L. Ishihara, J. Lee, J. K. Forman, S. J. Wang, L. Priceman, S. J. 2023-01-07 doi:10.1101/2023.01.06.522784 Cold Spring Harbor Laboratory Press 2023-01-07 <![CDATA[ Native Triboelectric Nanogenerator Ion Mobility-Mass Spectrometry of Egg Proteins Relevant to Objects of Cultural Heritage at Picoliter and Nanomolar Quantities. ]]> https://biorxiv.org/content/10.1101/2023.01.09.523258v1?rss=1 Vallejo, D. D. Popowich, A. Arslanoglu, J. Tokarski, C. Fernandez, F. 2023-01-10 doi:10.1101/2023.01.09.523258 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Force-regulated spontaneous conformational changes of integrins α5β1 and αVβ3 ]]> https://biorxiv.org/content/10.1101/2023.01.09.523308v1?rss=1 Chen, Y. Kong, F. Li, Z. Ju, L. A. Zhu, C. 2023-01-09 doi:10.1101/2023.01.09.523308 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ On the physiological and structural contributors to the dynamic balance of excitation and inhibition in local cortical networks ]]> https://biorxiv.org/content/10.1101/2023.01.10.523489v1?rss=1 Shirani, F. Choi, H. 2023-01-10 doi:10.1101/2023.01.10.523489 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Brain signatures indexing variation in internal processing during perceptual decision-making ]]> https://biorxiv.org/content/10.1101/2023.01.10.523502v1?rss=1 View larger version (42K): org.highwire.dtl.DTLVardef@e6e448org.highwire.dtl.DTLVardef@95512eorg.highwire.dtl.DTLVardef@104a976org.highwire.dtl.DTLVardef@11191e2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Nakuci, J. Samaha, J. Rahnev, D. 2023-01-12 doi:10.1101/2023.01.10.523502 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ The mitochondrial multi-omic response to exercise training across tissues ]]> https://biorxiv.org/content/10.1101/2023.01.13.523698v1?rss=1 Amar, D. Gay, N. R. Jimenez-Morales, D. Jean Beltran, P. M. Ramaker, M. E. Natarajan Raja, A. Zhao, B. Sun, Y. Marwaha, S. Gaul, D. Hershman, S. G. Xia, A. Lanza, I. Fernandez, F. M. Montgomery, S. B. Hevener, A. L. Ashley, E. Walsh, M. J. Sparks, L. M. Burant, C. F. Rector, R. S. Thyfault, J. Wheeler, M. T. Goodpaster, B. H. Coen, P. M. Schenk, S. Bodine, S. C. Lindholm, M. E. MoTrPAC Study Group, 2023-01-13 doi:10.1101/2023.01.13.523698 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ GeneMark-ETP: Automatic Gene Finding in Eukaryotic Genomes in Consistence with Extrinsic Data ]]> https://biorxiv.org/content/10.1101/2023.01.13.524024v1?rss=1 Bruna, T. Lomsadze, A. Borodovsky, M. 2023-01-15 doi:10.1101/2023.01.13.524024 Cold Spring Harbor Laboratory Press 2023-01-15 <![CDATA[ Metacommunity Structure Preserves Genome Diversity in the Presence of Gene-specific Selective Sweeps. ]]> https://biorxiv.org/content/10.1101/2023.01.17.524383v1?rss=1 Pompei, S. Bella, E. Weitz, J. Grilli, J. Cosentino Lagomarsino, M. 2023-01-19 doi:10.1101/2023.01.17.524383 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Human Bone Marrow Plasma Cell Atlas: Maturation and Survival Pathways Unraveled by Single Cell Analyses ]]> https://biorxiv.org/content/10.1101/2023.01.18.524601v1?rss=1 Duan, M. Nguyen, D. C. Joyner, C. J. Saney, C. Tipton, C. Andrews, J. Lonial, S. Kim, C. Hentenaar, I. Kosters, A. Ghosn, E. Jackson, A. Knechtle, S. Maruthamuthu, S. Chandran, S. Martin, T. Rajalingam, R. Vincenti, F. Breeden, C. Sanz, I. Gibson, G. Lee, F. E.-H. 2023-01-20 doi:10.1101/2023.01.18.524601 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Emergent Simplicities in Stochastic Intergenerational Homeostasis ]]> https://biorxiv.org/content/10.1101/2023.01.18.524627v1?rss=1 Joshi, K. Wright, C. S. Ziegler, K. F. Spiers, E. M. Crosser, J. T. Eschker, S. Biswas, R. R. Iyer-Biswas, S. 2023-01-20 doi:10.1101/2023.01.18.524627 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Emergence and maintenance of stable coexistence during a long-term multicellular evolution experiment ]]> https://biorxiv.org/content/10.1101/2023.01.19.524803v1?rss=1 Pineau, R. Demory, D. Libby, E. Lac, D. T. Day, T. Bravo, P. Weitz, J. Yunker, P. J. Bozdag, G. O. Ratcliff, W. C. 2023-01-21 doi:10.1101/2023.01.19.524803 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ A Unified Physiological Process Links Global Patterns of Functional MRI, Respiratory Activity, and Autonomic Signaling ]]> https://biorxiv.org/content/10.1101/2023.01.19.524818v1?rss=1 Bolt, T. S. Wang, S. Nomi, J. S. Setton, R. Gold, B. Frederick, B. Spreng, R. N. Keilholz, S. Uddin, L. Chang, C. 2023-01-20 doi:10.1101/2023.01.19.524818 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Global analysis of aging-related protein structural changes uncovers enzyme polymerization-based control of longevity ]]> https://biorxiv.org/content/10.1101/2023.01.23.524173v1?rss=1 Paukstyte, J. Lopez Cabezas, R. M. Feng, Y. Tong, K. Schnyder, D. Elomaa, E. Gregorova, P. Doudin, M. Sarkka, M. Sarameri, J. Lippi, A. Vihinen, H. Juutila, J. Nieminen, A. Toronen, P. Holm, L. Jokitalo, E. Krisko, A. Huiskonen, J. T. Sarin, P. Hietakangas, V. Picotti, P. Barral, Y. Saarikangas, J. 2023-01-23 doi:10.1101/2023.01.23.524173 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ PIC recruitment by synthetic reader-actuators to polycomb-silenced genes blocks triple-negative breast cancer invasion ]]> https://biorxiv.org/content/10.1101/2023.01.23.525196v1?rss=1 Williams, N. L. Hong, L. Jaffe, M. Shields, C. E. Haynes, K. A. 2023-01-23 doi:10.1101/2023.01.23.525196 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Cleo: a testbed for bridging model and experiment by simulating closed-loop stimulation, electrode recording, and optogenetics ]]> https://biorxiv.org/content/10.1101/2023.01.27.525963v1?rss=1 Johnsen, K. A. Cruzado, N. A. Willats, A. A. Rozell, C. J. 2023-01-28 doi:10.1101/2023.01.27.525963 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ A Novel Explainable Fuzzy Clustering Approach for fMRI Dynamic Functional Network Connectivity Analysis ]]> https://biorxiv.org/content/10.1101/2023.01.29.526110v1?rss=1 Ellis, C. A. Miller, R. L. Calhoun, V. D. 2023-01-31 doi:10.1101/2023.01.29.526110 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ The unknown lipids project: harmonized methods improve compound identification and data reproducibility in an inter-laboratory untargeted lipidomics study ]]> https://biorxiv.org/content/10.1101/2023.02.01.526566v1?rss=1 Shen, T. Conway, C. Rempfert, K. R. Kyle, J. E. Colby, S. M. Gaul, D. A. Habra, H. Kong, F. Bloodsworth, K. J. Allen, D. Evans, B. Du, X. Fernandez, F. Metz, T. O. Fiehn, O. Evans, C. R. 2023-02-03 doi:10.1101/2023.02.01.526566 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Development of a Robust Consensus Modeling Approach for Identifying Cellular and Media Metabolites Predictive of Mesenchymal Stromal Cell Potency ]]> https://biorxiv.org/content/10.1101/2023.02.03.526990v1?rss=1 Van Grouw, A. Colonna, M. B. Maughon, T. S. Shen, X. Larey, A. M. Moore, S. G. Carolyn, Y. Facundo, F. M. Arthur, E. S. Stice, S. L. Annie, B.-W. C. Ross, M. A. 2023-02-04 doi:10.1101/2023.02.03.526990 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue ]]> https://biorxiv.org/content/10.1101/2023.02.03.527012v1?rss=1 Many, G. M. Sanford, J. A. Sagendorf, T. J. Hou, Z. Nigro, P. Whytock, K. L. Amar, D. Caputo, T. Gay, N. R. Gaul, D. A. Hirshman, M. F. Jimenez-Morales, D. Lindholm, M. E. Muehlbauer, M. J. Vamvini, M. Bergman, B. C. Fernandez, F. M. Goodyear, L. J. Ortlund, E. A. Sparks, L. M. Xia, A. Adkins, J. N. Bodine, S. C. Newgard, C. B. Schenk, S. Study Group, T. M. 2023-02-04 doi:10.1101/2023.02.03.527012 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ A novel enhancer-AAV approach selectively targeting dentate granule cells ]]> https://biorxiv.org/content/10.1101/2023.02.03.527045v1?rss=1 Banks, E. Zheng, J. Q. Eaton, A. Olah, V. J. Rowan, M. 2023-02-04 doi:10.1101/2023.02.03.527045 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Coevolution with a seed bank ]]> https://biorxiv.org/content/10.1101/2023.02.08.527722v1?rss=1 Schwartz, D. A. Shoemaker, W. R. Magalie, A. Weitz, J. Lennon, J. T. 2023-02-10 doi:10.1101/2023.02.08.527722 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Ciliary ARL13B inhibits developmental kidney cystogenesis in mouse ]]> https://biorxiv.org/content/10.1101/2023.02.08.527739v1?rss=1 Van Sciver, R. E. Long, A. B. Katz, H. G. Gigante, E. D. Caspary, T. 2023-02-08 doi:10.1101/2023.02.08.527739 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ Explainable Fuzzy Clustering Framework Reveals Divergent Default Mode Network Connectivity Dynamics in Schizophrenia ]]> https://biorxiv.org/content/10.1101/2023.02.13.528329v1?rss=1 Ellis, C. A. Miller, R. L. Calhoun, V. 2023-02-14 doi:10.1101/2023.02.13.528329 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ Stimulus novelty uncovers coding diversity in visual cortical circuits ]]> https://biorxiv.org/content/10.1101/2023.02.14.528085v1?rss=1 Garrett, M. Groblewski, P. Piet, A. Ollerenshaw, D. Yavorska, I. Najafi, F. Amster, A. Bennett, C. Buice, M. Caldejon, S. Casal, L. D'Orazi, F. Daniel, S. de Vries, S. E. Kapner, D. Kiggins, J. Lecoq, J. Ledochowitsch, P. Manavi, S. Mei, N. Morrison, C. B. Naylor, S. Orlova, N. Perkins, J. Ponvert, N. Roll, C. Seid, S. Williams, D. Williford, A. Ahmed, R. Amine, D. Billeh, Y. Bowman, C. Cain, N. Cho, A. Dawe, T. Departee, M. Desoto, M. Feng, D. Gale, S. Gelfand, E. Gradis, N. Grasso, C. Hancock, N. Hu, B. Hytnen, R. Jia, X. Johnson, T. Kato, I. 2023-02-15 doi:10.1101/2023.02.14.528085 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Towards estimating the number of strains that make up a natural bacterial population ]]> https://biorxiv.org/content/10.1101/2023.02.20.529252v1?rss=1 99.8% or <99.2%, revealing a natural "gap" in the sequence space within species. Accordingly, we used this ANI gap to define genomovars and a higher ANI value of >99.99% and shared gene-content >99.0% to define strains. Using these thresholds and extrapolating from how many metagenomic reads each genomovar uniquely recruited, we estimated that -although our 138 isolates represented about 80% of the Sal. ruber population- the total population in one pond is composed of 5,500 to 11,000 genomovars, the great majority of which appear to be rare in situ. These data also revealed that the most frequently recovered isolate in lab media was often not the most abundant genomovar in situ, suggesting that cultivation biases are significant, even in cases that cultivation procedures are thought to be robust. Preliminary analyses of available genomes revealed that the thresholds used for defining strains and distinct intra-species units (genomovars) may be broadly applicable to additional bacterial species. Significance StatementStrains are the smallest distinguishable units within a microbial species. Strains that carry unique gene content often underly the emergence of disease outbreaks and the response of the species to environmental perturbations. Therefore, a major challenge in microbiome research across environmental and clinical settings is to evaluate how many strains of the same species coexist in nature and how dominant strains emerge from this diversity. Unfortunately, the available theoretical concept of strain is not directly applicable to culture-independent surveys. Here, we provide such a practical definition for strain and use it to show that that the number of strains making up a natural bacterial population may be large, in the order of a few thousands, but not infinite. ]]> Viver, T. Conrad, R. E. Rodriguez-R, L. M. Ramirez, A. S. Venter, S. N. Rocha-Cardenas, J. Segura, M. L. Amann, R. Konstantinidis, K. T. Rossello-Mora, R. 2023-02-20 doi:10.1101/2023.02.20.529252 Cold Spring Harbor Laboratory Press 2023-02-20 <![CDATA[ Myomatrix arrays for high-definition muscle recording ]]> https://biorxiv.org/content/10.1101/2023.02.21.529200v1?rss=1 Chung, B. Zia, M. Thomas, K. Michaels, J. A. Jacob, A. Pack, A. Williams, M. Nagapudi, K. Teng, L. H. Arrambide, E. Ouellette, L. Oey, N. Gibbs, R. Anschutz, P. Lu, J. Wu, Y. Kashefi, M. Oya, T. Kersten, R. Mosberger, A. C. O`Connell, S. Wang, R. Marques, H. G. P. Mendes, A. R. Lenschow, C. Kondakath, G. Kim, J. J. Olson, W. Quinn, K. Perkins, P. Gatto, G. Thanawalla, A. R. Coltman, S. K. Kim, T. Smith, T. S. Binder-Markey, B. Zaback, M. Thompson, C. K. Giszter, S. Person, A. Goulding, M. Azim, E. Thakor, N. O`Connor, D. Trimmer, B. Q. Lima, S. Car 2023-02-22 doi:10.1101/2023.02.21.529200 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ The las and rhl Quorum Sensing Systems in Pseudomonas aeruginosa Form a Multi-Signal Reciprocal Network Which Can Tune Reactivity to Variations in Physical and Social Environments ]]> https://biorxiv.org/content/10.1101/2023.02.23.529764v1?rss=1 Thomas, S. A. El-Zayat, A. Gurney, J. Rattray, J. B. Brown, S. P. 2023-02-23 doi:10.1101/2023.02.23.529764 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Constitutively synergistic multiagent drug formulations targeting MERTK, FLT3, and BCL-2 for treatment of AML ]]> https://biorxiv.org/content/10.1101/2023.03.13.531236v1?rss=1 Kelvin, J. M. Jain, J. Thapa, A. Qui, M. Birnbaum, L. A. Moore, S. G. Zecca, H. Summers, R. J. Costanza, E. Uricoli, B. Wang, X. Jui, N. T. Fu, H. Du, Y. DeRyckere, D. Graham, D. K. Dreaden, E. C. 2023-03-15 doi:10.1101/2023.03.13.531236 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ PyTorch-FEA: Autograd-enabled Finite Element Analysis Methods with Applications for Biomechanical Analysis of Human Aorta ]]> https://biorxiv.org/content/10.1101/2023.03.27.533816v1?rss=1 Liang, L. Liu, M. Elefteriades, J. Sun, W. 2023-03-28 doi:10.1101/2023.03.27.533816 Cold Spring Harbor Laboratory Press 2023-03-28 <![CDATA[ Supervised biological network alignment with graph neural networks ]]> https://biorxiv.org/content/10.1101/2023.04.24.538184v1?rss=1 Ding, K. Wang, S. Luo, Y. 2023-04-28 doi:10.1101/2023.04.24.538184 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Translation in a Box: Orthogonal Evolution in the Saccharomyces cerevisiae Mitochondrion ]]> https://biorxiv.org/content/10.1101/2023.04.28.538752v1?rss=1 Rothschild-Mancinelli, B. Alvarez-Carreno, C. Guo, W. Ito, C. Costa, A. Petrov, A. S. Lobachev, K. Williams, L. D. 2023-04-28 doi:10.1101/2023.04.28.538752 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ optSelect: using agent-based modeling and binary PSO techniques for ensemble feature selection and stability assessment ]]> https://biorxiv.org/content/10.1101/206185v1?rss=1 Uppal, K. Lee, E. K. 2017-10-19 doi:10.1101/206185 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ SEACOIN2.0: an interactive mining and visualization tool for information retrieval, summarization, and knowledge discovery ]]> https://biorxiv.org/content/10.1101/206193v1?rss=1 Uppal, K. Lee, E. K. 2017-10-19 doi:10.1101/206193 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ Chemical genomic guided engineering of gamma-valerolactone tolerant yeast ]]> https://biorxiv.org/content/10.1101/213991v1?rss=1 Bottoms, S. Dickinson, Q. McGee, M. Hinchman, L. Higbee, A. Hebert, A. Serate, J. Xie, D. Zhang, Y. Coon, J. J. Myers, C. L. Landick, R. Piotrowski, J. S. 2017-11-04 doi:10.1101/213991 Cold Spring Harbor Laboratory Press 2017-11-04 <![CDATA[ Modified antibiotic adjuvant ratios can slow and steer the evolution of resistance: co-amoxiclav as a case study ]]> https://biorxiv.org/content/10.1101/217711v1?rss=1 Allen, R. C. Brown, S. P. 2017-11-10 doi:10.1101/217711 Cold Spring Harbor Laboratory Press 2017-11-10 <![CDATA[ High-throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries ]]> https://biorxiv.org/content/10.1101/225342v1?rss=1 95% intra-species ANI or <83% inter-species ANI values. We further show that this discontinuity is recovered with or without the most frequently represented species in the database and is robust to historic additions in the public genome databases. Therefore, 95% ANI represents an accurate threshold for demarcating almost all currently named prokaryotic species, and wide species boundaries may exist for prokaryotes. ]]> Jain, C. Rodriguez-R, L. M. Phillippy, A. M. Konstantinidis, K. T. Aluru, S. 2017-11-27 doi:10.1101/225342 Cold Spring Harbor Laboratory Press 2017-11-27 <![CDATA[ The Vibrio cholerae Type VI Secretion System Can Modulate Host Intestinal Mechanics to Displace Commensal Gut Bacteria ]]> https://biorxiv.org/content/10.1101/226472v1?rss=1 Logan, S. L. Thomas, J. Yan, J. Baker, R. P. Shields, D. S. Xavier, J. B. Hammer, B. K. Parthasarathy, R. 2017-11-29 doi:10.1101/226472 Cold Spring Harbor Laboratory Press 2017-11-29 <![CDATA[ A simple mung bean infection model for studying the virulence of Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/229757v1?rss=1 Garge, S. Azimi, S. Diggle, S. P. 2017-12-06 doi:10.1101/229757 Cold Spring Harbor Laboratory Press 2017-12-06 <![CDATA[ Feature-specific awake reactivation in human V1 after visual training ]]> https://biorxiv.org/content/10.1101/231381v1?rss=1 Bang, J. W. Sasaki, Y. Watanabe, T. Rahnev, D. 2017-12-08 doi:10.1101/231381 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ Defining the seafloor microbiome of the Gulf of Mexico and its response to oil perturbation ]]> https://biorxiv.org/content/10.1101/236950v1?rss=1 700 samples. The composition of the seafloor microbiome was broadly consistent across the region and was well approximated by the overlying water depth and depth within the sediment column, while geographic distance played a limited role. Biogeographical distributions were employed to generate predictive models for over 4000 OTU that leverage easy-to-obtain geospatial variables which are linked to measured sedimentary oxygen profiles. Depth stratification and putative niche diversification are evidenced by the distribution of taxa that mediate the microbial nitrogen cycle. Further, these results demonstrate that sediments impacted by the DWH spill had returned to near baseline conditions after two years. The distributions of benthic microorganisms in the Gulf can be constrained, and moreover deviations from these predictions may pinpoint impacted sites and aid in future response efforts or long-term stability studies. ]]> Overholt, W. A. Schwing, P. Hastings, D. Hollander, D. J. Kostka, J. E. 2018-06-06 doi:10.1101/236950 Cold Spring Harbor Laboratory Press 2018-06-06 <![CDATA[ De novo origin of multicellularity in response to predation ]]> https://biorxiv.org/content/10.1101/247361v1?rss=1 Herron, M. D. Borin, J. M. Boswell, J. C. Walker, J. Knox, C. A. Boyd, M. Rosenzweig, F. Ratcliff, W. C. 2018-01-12 doi:10.1101/247361 Cold Spring Harbor Laboratory Press 2018-01-12 <![CDATA[ Ecological advantages and evolutionary limitations of aggregative multicellular development ]]> https://biorxiv.org/content/10.1101/255307v1?rss=1 Pentz, J. T. Marquez-Zacarias, P. Yunker, P. J. Libby, E. Ratcliff, W. C. 2018-01-31 doi:10.1101/255307 Cold Spring Harbor Laboratory Press 2018-01-31 <![CDATA[ Ferrous iron mediates translation ]]> https://biorxiv.org/content/10.1101/256958v1?rss=1 Bray, M. S. Bowman, J. C. Petrov, A. S. Williams, L. D. Glass, J. B. 2018-01-31 doi:10.1101/256958 Cold Spring Harbor Laboratory Press 2018-01-31 <![CDATA[ Haemolymph removal by the parasite Varroa destructor can trigger the proliferation of the Deformed Wing Virus in mite infested bees (Apis mellifera), contributing to enhanced pathogen virulence ]]> https://biorxiv.org/content/10.1101/257667v1?rss=1 Annoscia, D. Brown, S. Di Prisco, G. De Paoli, E. Del Fabbro, S. Zanni, V. Galbraith, D. Caprio, E. Grozinger, C. M. Pennacchio, F. Nazzi, F. 2018-02-05 doi:10.1101/257667 Cold Spring Harbor Laboratory Press 2018-02-05 <![CDATA[ A Fast Adaptive Algorithm for Computing Whole-Genome Homology Maps ]]> https://biorxiv.org/content/10.1101/259986v1?rss=1 97% on multiple datasets. Finally, we performed a sensitive self-alignment of the human genome to compute all duplications of length [≥] 1 Kbp and [≥] 90% identity. The reported output achieves good recall and covers 5% more bases than the current UCSC genome browsers segmental duplication annotation.nnAvailabilityhttps://github.com/marbl/MashMapnnContactadam.phillippy@nih.gov, aluru@cc.gatech.edu ]]> Jain, C. Koren, S. Dilthey, A. Phillippy, A. M. Aluru, S. 2018-02-05 doi:10.1101/259986 Cold Spring Harbor Laboratory Press 2018-02-05 <![CDATA[ Competition in biofilms between Pseudomonas aeruginosa cystic fibrosis isolates is driven by R-pyocins ]]> https://biorxiv.org/content/10.1101/264580v1?rss=1 Oluyombo, O. Diggle, S. P. Penfold, C. N. 2018-02-13 doi:10.1101/264580 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ Hawkmoth flight in the unsteady wakes of flowers ]]> https://biorxiv.org/content/10.1101/264762v1?rss=1 Matthews, M. Sponberg, S. 2018-02-13 doi:10.1101/264762 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ Information sharing for a coordination game in fluctuating environments ]]> https://biorxiv.org/content/10.1101/268268v1?rss=1 Paarporn, K. Eksin, C. Weitz, J. S. 2018-02-20 doi:10.1101/268268 Cold Spring Harbor Laboratory Press 2018-02-20 <![CDATA[ Rapid proteotyping reveals cancer biology and drug response determinants in the NCI-60 cells ]]> https://biorxiv.org/content/10.1101/268953v1?rss=1 Guo, T. Luna, A. Koh, C. C. Rajapakse, V. Wu, Z. Menden, M. P. Cheng, Y. Calzone, L. Martignetti, L. Ori, A. Iskar, M. Gillet, L. Zhong, Q. Varma, S. Schmitt, U. Qiu, P. Sun, Y. zhu, Y. Wild, P. Mathew, G. Bork, P. Beck, M. Saez-Rodriguez, J. Reinhold, W. Sander, C. Pommier, Y. Aebersold, R. 2018-02-21 doi:10.1101/268953 Cold Spring Harbor Laboratory Press 2018-02-21 <![CDATA[ The effect of strain level diversity on robust inference of virus-induced mortality ]]> https://biorxiv.org/content/10.1101/277517v1?rss=1 Beckett, S. J. Weitz, J. S. 2018-03-07 doi:10.1101/277517 Cold Spring Harbor Laboratory Press 2018-03-07 <![CDATA[ Distinguishing the roles of dorsolateral and anterior PFC in visual metacognition ]]> https://biorxiv.org/content/10.1101/280081v1?rss=1 Shekhar, M. Rahnev, D. 2018-03-11 doi:10.1101/280081 Cold Spring Harbor Laboratory Press 2018-03-11 <![CDATA[ ERASE: a novel surface reconditioning strategy for single-molecule experiments ]]> https://biorxiv.org/content/10.1101/282632v1?rss=1 Broadwater, D. W. B. Altman, R. B. Blanchard, S. C. Kim, H. D. 2018-03-15 doi:10.1101/282632 Cold Spring Harbor Laboratory Press 2018-03-15 <![CDATA[ CagY-dependent regulation of type IV secretion in Helicobacter pylori is associated with alterations in integrin binding ]]> https://biorxiv.org/content/10.1101/294769v1?rss=1 Skoog, E. Morikis, V. A. Martin, M. E. Foster, G. A. Cai, L. P. Hansen, L. M. Li, B. Gaddy, J. A. Simon, S. Solnick, J. V. 2018-04-04 doi:10.1101/294769 Cold Spring Harbor Laboratory Press 2018-04-04 <![CDATA[ Viral Fitness Across a Continuum from Lysis to Latency ]]> https://biorxiv.org/content/10.1101/296897v1?rss=1 Weitz, J. S. Li, G. Gulbudak, H. Cortez, M. H. Whitaker, R. J. 2018-04-06 doi:10.1101/296897 Cold Spring Harbor Laboratory Press 2018-04-06 <![CDATA[ Heterogeneous Viral Strategies Promote Coexistence in Virus-Microbe Systems ]]> https://biorxiv.org/content/10.1101/297127v1?rss=1 Gulbudak, H. Weitz, J. 2018-04-07 doi:10.1101/297127 Cold Spring Harbor Laboratory Press 2018-04-07 <![CDATA[ Identification of Significant Computational Building Blocks through Comprehensive Deep Dive of NGS Secondary Analysis Methods ]]> https://biorxiv.org/content/10.1101/301903v1?rss=1 Vasimuddin, M. Misra, S. Aluru, S. 2018-04-16 doi:10.1101/301903 Cold Spring Harbor Laboratory Press 2018-04-16 <![CDATA[ Exploring how generation intervals link strength and speed of epidemics ]]> https://biorxiv.org/content/10.1101/312397v1?rss=1 Park, S. W. Champredon, D. Weitz, J. Dushoff, J. 2018-05-02 doi:10.1101/312397 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Cortical states control visual spatial perception ]]> https://biorxiv.org/content/10.1101/316398v1?rss=1 Speed, A. Del Rosario, J. P. Burgess, C. P. Haider, B. 2018-05-24 doi:10.1101/316398 Cold Spring Harbor Laboratory Press 2018-05-24 <![CDATA[ Single-cell transcriptome profiling of the Ciona larval brain ]]> https://biorxiv.org/content/10.1101/319327v1?rss=1 Sharma, S. Wang, W. Stolfi, A. 2018-05-10 doi:10.1101/319327 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Diversity of active viral infections within the Sphagnum microbiome ]]> https://biorxiv.org/content/10.1101/320002v1?rss=1 Stough, J. M. A. Kolton, M. Kostka, J. E. Weston, D. J. Pelletier, D. A. Wilhelm, S. W. 2018-05-13 doi:10.1101/320002 Cold Spring Harbor Laboratory Press 2018-05-13 <![CDATA[ Developmental system drift in motor ganglion patterning between distantly related tunicates ]]> https://biorxiv.org/content/10.1101/320804v1?rss=1 Lowe, E. K. Stolfi, A. 2018-05-11 doi:10.1101/320804 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Quasi-periodic patterns contribute to functional connectivity in the brain ]]> https://biorxiv.org/content/10.1101/323162v1?rss=1 Abbas, A. Belloy, M. Kashyap, A. Billings, J. Nezafati, M. Keilholz, S. 2018-05-16 doi:10.1101/323162 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Next-generation Sequence-analysis Toolkit (NeST): A standardized bioinformatics framework for analyzing Single Nucleotide Polymorphisms in next-generation sequencing data ]]> https://biorxiv.org/content/10.1101/323535v1?rss=1 Ravishankar, S. Schmedes, S. E. Patel, D. S. Plucinski, M. Talundzic, E. Udhayakumar, V. Vannberg, F. 2018-05-16 doi:10.1101/323535 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Cryptic Native American ancestry recapitulates population-specific migration and settlement of the continental United States ]]> https://biorxiv.org/content/10.1101/333609v1?rss=1 Jordan, I. K. Rishishwar, L. Conley, A. B. 2018-05-30 doi:10.1101/333609 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ Dynamic Properties of Simulated Brain Network Models and Empirical Resting State Data ]]> https://biorxiv.org/content/10.1101/344473v1?rss=1 Kashyap, A. Keilholz, S. 2018-06-12 doi:10.1101/344473 Cold Spring Harbor Laboratory Press 2018-06-12 <![CDATA[ Stress-responsive and metabolic gene regulation are altered in low S-adenosylmethionine ]]> https://biorxiv.org/content/10.1101/346205v1?rss=1 Ding, W. Higgins, D. P. Yadav, D. K. Pukkila-Worley, R. Walker, A. K. 2018-06-13 doi:10.1101/346205 Cold Spring Harbor Laboratory Press 2018-06-13 <![CDATA[ Muscle Stem Cell Niche Dysregulation in Volumetric Muscle Loss Injury ]]> https://biorxiv.org/content/10.1101/346395v1?rss=1 Anderson, S. Han, W. M. Srinivasa, V. Mohiuddin, M. Ruehle, M. A. Moon, A. Shin, E. San Emeterio, C. L. Ogle, M. E. Botchwey, E. A. Willett, N. J. Jang, Y. C. 2018-06-13 doi:10.1101/346395 Cold Spring Harbor Laboratory Press 2018-06-13 <![CDATA[ Re-evaluating the salty divide: phylogenetic specificity of transitions between marine and freshwater systems ]]> https://biorxiv.org/content/10.1101/347021v1?rss=1 Paver, S. Muratore, D. J. Newton, R. J. Coleman, M. 2018-06-14 doi:10.1101/347021 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ Systematic biases in disease forecasting - the role of behavior change ]]> https://biorxiv.org/content/10.1101/349506v1?rss=1 Eksin, C. Paarporn, K. Weitz, J. 2018-06-17 doi:10.1101/349506 Cold Spring Harbor Laboratory Press 2018-06-17 <![CDATA[ Chronic Electrical Stimulation Promotes the Excitability and Plasticity of ESC-derived Neurons following Glutamate-induced Inhibition In vitro ]]> https://biorxiv.org/content/10.1101/354191v1?rss=1 Latchoumane, C.-F. V. Jackson, L. Eslampanah Sendi, M. S. Tehrani, K. F. Mortensen, L. J. Stice, S. L. Ghovanloo, M. Karumbaiah, L. 2018-06-22 doi:10.1101/354191 Cold Spring Harbor Laboratory Press 2018-06-22 <![CDATA[ Pre-stimulus oscillatory activity predicts successful episodic encoding for both young and older adults ]]> https://biorxiv.org/content/10.1101/358721v1?rss=1 Strunk, J. Duarte, A. 2018-06-29 doi:10.1101/358721 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Preparing for the worst: Evidence that older adults proactively downregulate negative affect ]]> https://biorxiv.org/content/10.1101/359901v1?rss=1 Corbett, B. Rajah, M. N. Duarte, A. 2018-07-03 doi:10.1101/359901 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Can we obtain in vivo transmural mean hoop stress of the aortic wall without knowing patient-specific material properties and residual deformations? ]]> https://biorxiv.org/content/10.1101/366849v1?rss=1 Liu, M. Liang, L. Liu, H. Zhang, M. Martin, C. Sun, W. 2018-07-10 doi:10.1101/366849 Cold Spring Harbor Laboratory Press 2018-07-10 <![CDATA[ Estimation of in vivo constitutive parameters of the aortic wall: a machine learning approach ]]> https://biorxiv.org/content/10.1101/366963v1?rss=1 Liu, M. Liang, L. Sun, W. 2018-07-10 doi:10.1101/366963 Cold Spring Harbor Laboratory Press 2018-07-10 <![CDATA[ Synthetic mRNA expressed Cas13a mitigates RNA virus infections ]]> https://biorxiv.org/content/10.1101/370460v1?rss=1 Bawage, S. Tiwari, P. Santangelo, P. 2018-07-23 doi:10.1101/370460 Cold Spring Harbor Laboratory Press 2018-07-23 <![CDATA[ MetaMaps - Strain-level metagenomic assignment and compositional estimation for long reads ]]> https://biorxiv.org/content/10.1101/372474v1?rss=1 12,000 genomes in <30 GB or RAM on a laptop computer. Integrating these mappings with a probabilistic scoring scheme and EM-based estimation of sample composition, MetaMaps achieves >95% accuracy for species-level read assignment and r2 > 0.98 for the estimation of sample composition on both simulated and real data. Uniquely, MetaMaps outputs mapping locations and qualities for all classified reads, enabling functional studies (e.g. gene presence/absence) and the detection of novel species not present in the current database.nnAvailability and ImplementationMetaMaps is implemented in C++/Perl and freely available from https://github.com/DiltheyLab/MetaMaps (GPL v3). ]]> Dilthey, A. Jain, C. Koren, S. Phillippy, A. 2018-07-20 doi:10.1101/372474 Cold Spring Harbor Laboratory Press 2018-07-20 <![CDATA[ Extreme allelic heterogeneity at a Caenorhabditis elegans beta-tubulin locus explains natural resistance to benzimidazoles ]]> https://biorxiv.org/content/10.1101/372623v1?rss=1 Hahnel, S. R. Zdraljevic, S. Rodriguez, B. C. Zhao, Y. McGrath, P. T. Andersen, E. C. 2018-07-19 doi:10.1101/372623 Cold Spring Harbor Laboratory Press 2018-07-19 <![CDATA[ Identifying Gait Phases from Joint Kinematics during Walking with Switched Linear Dynamical Systems ]]> https://biorxiv.org/content/10.1101/378380v1?rss=1 Drnach, L. Essa, I. Ting, L. H. 2018-07-27 doi:10.1101/378380 Cold Spring Harbor Laboratory Press 2018-07-27 <![CDATA[ Microbial Diversity in a Military Impacted Lagoon (Vieques, Puerto Rico) as Revealed by Metagenomics ]]> https://biorxiv.org/content/10.1101/389379v1?rss=1 Davila-Santiago, L. DeLeon-Rodriguez, N. LaSanta-Pagan, K. Hatt, J. Kurt, Z. Massol-Deya, A. Konstantinidis, K. T. 2018-08-10 doi:10.1101/389379 Cold Spring Harbor Laboratory Press 2018-08-10 <![CDATA[ Fast, versatile, and quantitative annotation of complex images ]]> https://biorxiv.org/content/10.1101/391169v1?rss=1 30,000 images, including features of rice root growth and structure, stem cell aggregate morphology, and complex worm (C. elegans) postures, for which we show that the speed of annotation is >130-fold faster than state-of-the-art techniques with similar accuracy. ]]> Bates, K. Jiang, S. Bates, R. Chaudhary, S. Jackson-Holmes, E. Jue, M. McCaskey, E. Goldman, D. Lu, H. 2018-08-13 doi:10.1101/391169 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ Critical Limb Ischemia Induces Remodeling of Skeletal Muscle Motor Unit and Myonuclear- and Mitochondrial-Domains ]]> https://biorxiv.org/content/10.1101/426403v1?rss=1 Mohiuddin, M. Lee, N. H. Moon, J. Y. Han, W. M. Anderson, S. E. Choi, J. J. Nakhai, S. Tran, T. Aliya, B. Kim, D. Y. Gerold, A. Hansen, L. Taylor, W. R. Jang, Y. C. 2018-09-25 doi:10.1101/426403 Cold Spring Harbor Laboratory Press 2018-09-25 <![CDATA[ Leveraging single cell RNA sequencing experiments to model intra-tumor heterogeneity ]]> https://biorxiv.org/content/10.1101/427047v1?rss=1 Ferrall-Fairbanks, M. C. Ball, M. Padron, E. Altrock, P. M. 2018-09-25 doi:10.1101/427047 Cold Spring Harbor Laboratory Press 2018-09-25 <![CDATA[ Effects of BMP-2 dose and delivery of microvascular fragments on healing of bone defects with concomitant volumetric muscle loss ]]> https://biorxiv.org/content/10.1101/428359v1?rss=1 Ruehle, M. Krishnan, L. Vantucci, C. E. Wang, Y. Stevens, H. Y. Roy, K. Guldberg, R. E. Willett, N. J. 2018-09-27 doi:10.1101/428359 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ Collective intercellular communication through ultra-fast hydrodynamic trigger waves ]]> https://biorxiv.org/content/10.1101/428573v1?rss=1 Mathijssen, A. Culver, J. Bhamla, M. S. Prakash, M. 2018-09-26 doi:10.1101/428573 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ Quasi-periodic patterns of brain activity in individuals with Attention-Deficit/Hyperactivity Disorder ]]> https://biorxiv.org/content/10.1101/435347v1?rss=1 Abbas, A. Bassil, Y. Keilholz, S. 2018-10-05 doi:10.1101/435347 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ Dynamic G-quadruplexes on the surface of the human ribosome ]]> https://biorxiv.org/content/10.1101/435594v1?rss=1 Mestre-Fos, S. Penev, P. I. Suttapitugsakul, S. Ito, C. Petrov, A. S. Wartell, R. M. Wu, R. Williams, L. D. 2018-10-05 doi:10.1101/435594 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ A histidine kinase gene is required for large radius root tip circumnutation and surface exploration in rice ]]> https://biorxiv.org/content/10.1101/437012v1?rss=1 Lehner, K. R. Taylor, I. McCaskey, E. N. Jain, R. Ronald, P. C. Goldman, D. I. Benfey, P. N. 2018-10-07 doi:10.1101/437012 Cold Spring Harbor Laboratory Press 2018-10-07 <![CDATA[ Fast, volumetric live-cell imaging using high-resolution light-field microscopy ]]> https://biorxiv.org/content/10.1101/439315v1?rss=1 Li, H. Guo, C. Kim-Holzapfel, D. Li, W. Altshuller, Y. Schroeder, B. Liu, W. Meng, Y. French, J. Takamaru, K.-I. Frohman, M. Jia, S. 2018-10-10 doi:10.1101/439315 Cold Spring Harbor Laboratory Press 2018-10-10 <![CDATA[ Feeding rapidly alters microbiome composition and gene transcription in the clownfish gut ]]> https://biorxiv.org/content/10.1101/440669v1?rss=1 Parris, D. J. Morgan, M. M. Stewart, F. J. 2018-10-11 doi:10.1101/440669 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Adaptive eQTLs reveal the evolutionary impacts of pleiotropy and tissue-specificity, while contributing to health and disease in human populations ]]> https://biorxiv.org/content/10.1101/444737v1?rss=1 Quiver, M. H. Lachance, J. 2018-10-16 doi:10.1101/444737 Cold Spring Harbor Laboratory Press 2018-10-16 <![CDATA[ Cytoarchitecture and Layer Estimation in High-Resolution Neuroanatomical Images ]]> https://biorxiv.org/content/10.1101/445742v1?rss=1 LaGrow, T. J. Moore, M. G. Prasad, J. A. Webber, A. Davenport, M. A. Dyer, E. L. 2018-10-17 doi:10.1101/445742 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ ElectroPen: An ultralow-cost piezoelectric electroporator ]]> https://biorxiv.org/content/10.1101/448977v1?rss=1 Byagathvalli, G. Sinha, S. Zhang, Y. Styczynski, M. Standeven, J. Bhamla, M. S. 2018-12-21 doi:10.1101/448977 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ Resistance diagnostics as a public health tool to combat antibiotic resistance: A model-based evaluation ]]> https://biorxiv.org/content/10.1101/452656v1?rss=1 McAdams, D. Wollein Waldetoft, K. Tedijanto, C. Lipsitch, M. Brown, S. P. 2018-10-26 doi:10.1101/452656 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ The Pseudomonas aeruginosa Wsp pathway undergoes positive evolutionary selection during chronic infection ]]> https://biorxiv.org/content/10.1101/456186v1?rss=1 Gloag, E. S. Marshall, C. Snyder, D. Lewin, G. R. Harris, J. S. Chaney, S. B. Whiteley, M. Cooper, V. S. Wozniak, D. J. 2018-10-29 doi:10.1101/456186 Cold Spring Harbor Laboratory Press 2018-10-29 <![CDATA[ GLaMST: Grow Lineages along Minimum Spanning Tree for B Cell Receptor Sequencing Data ]]> https://biorxiv.org/content/10.1101/465476v1?rss=1 Yang, X. Tipton, C. Woodruff, M. Zhou, E. Lee, F. E.-H. Sanz, I. Qiu, P. 2018-11-08 doi:10.1101/465476 Cold Spring Harbor Laboratory Press 2018-11-08 <![CDATA[ Comparing DNA, RNA and protein levels for measuring microbial activity in nitrogen-amended soils ]]> https://biorxiv.org/content/10.1101/466680v1?rss=1 Orellana, L. H. Hatt, J. Iyer, R. Chourey, K. Hettich, R. L. Spain, J. Yang, W. H. Chee-Sanford, J. Sanford, R. A. Löffler, F. E. Konstantinidis, K. T. 2018-11-10 doi:10.1101/466680 Cold Spring Harbor Laboratory Press 2018-11-10 <![CDATA[ Embracing the dropouts in single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/468025v1?rss=1 Qiu, P. 2018-11-11 doi:10.1101/468025 Cold Spring Harbor Laboratory Press 2018-11-11 <![CDATA[ Noncontractile tissue forces mask muscle fiber forces underlying muscle spindle Ia afferent firing rates in stretch of relaxed rat muscle ]]> https://biorxiv.org/content/10.1101/470302v1?rss=1 Blum, K. P. Nardelli, P. Cope, T. C. Ting, L. H. 2018-11-14 doi:10.1101/470302 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ GRIBCG: A software for selection of sgRNAs in the design of balancer chromosomes ]]> https://biorxiv.org/content/10.1101/484360v1?rss=1 Merritt, B. B. Cheung, L. S. 2018-12-02 doi:10.1101/484360 Cold Spring Harbor Laboratory Press 2018-12-02 <![CDATA[ Why Put-Up with Immunity when there is Resistance: An Excursion into the Population and Evolutionary Dynamics of Restriction-Modification and CRISPR-Cas ]]> https://biorxiv.org/content/10.1101/487132v1?rss=1 Gurney, J. R. Pleska, M. Levin, B. R. 2018-12-04 doi:10.1101/487132 Cold Spring Harbor Laboratory Press 2018-12-04 <![CDATA[ Single-cell membrane potential fluctuations evince network scale-freeness and quasicriticality ]]> https://biorxiv.org/content/10.1101/498477v1?rss=1 Johnson, J. K. Wright, N. C. Xia, J. Wessel, R. 2018-12-17 doi:10.1101/498477 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ State-aware detection of sensory stimuli in the cortex of the awake mouse ]]> https://biorxiv.org/content/10.1101/499269v1?rss=1 Sederberg, A. Pala, A. Zheng, H. J. V. He, B. J. Stanley, G. B. 2018-12-17 doi:10.1101/499269 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ Profiling gene expression of the host response to a Plasmodium vivax irradiated sporozoite immunization and infectious challenge ]]> https://biorxiv.org/content/10.1101/501957v1?rss=1 Rojas-Pena, M. C. Arafat, D. C. Velasquez, J. M. Garimalla, S. C. Arevalo-Herrera, M. Herrera, S. Gibson, G. 2018-12-19 doi:10.1101/501957 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Determinants of cyclization-decyclization kinetics of short DNA with sticky ends ]]> https://biorxiv.org/content/10.1101/503490v1?rss=1 Jeong, J. Kim, H. D. 2018-12-21 doi:10.1101/503490 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ TIGAR: An Improved Bayesian Tool for Transcriptomic Data Imputation Enhances Gene Mapping of Complex Traits ]]> https://biorxiv.org/content/10.1101/507525v1?rss=1 Nagpal, S. Meng, X. Epstein, M. P. Tsoi, L. C. Patrick, M. Gibson, G. De Jager, P. Bennett, D. A. Wingo, A. P. Wingo, T. S. Yang, J. 2018-12-28 doi:10.1101/507525 Cold Spring Harbor Laboratory Press 2018-12-28 <![CDATA[ History-dependent perturbation response in limb muscle ]]> https://biorxiv.org/content/10.1101/509646v1?rss=1 Libby, T. Chukwueke, C. Sponberg, S. 2019-01-02 doi:10.1101/509646 Cold Spring Harbor Laboratory Press 2019-01-02 <![CDATA[ Base-pair mismatch can destabilize small DNA loops through cooperative kinking ]]> https://biorxiv.org/content/10.1101/509711v1?rss=1 Jeong, J. Kim, H. 2019-01-02 doi:10.1101/509711 Cold Spring Harbor Laboratory Press 2019-01-02 <![CDATA[ A comprehensive evaluation of long read error correction methods ]]> https://biorxiv.org/content/10.1101/519330v1?rss=1 Zhang, H. Jain, C. Aluru, S. 2019-01-13 doi:10.1101/519330 Cold Spring Harbor Laboratory Press 2019-01-13 <![CDATA[ A 3D-printed hand-powered centrifuge for molecular biology ]]> https://biorxiv.org/content/10.1101/519835v1?rss=1 Byagathvalli, G. Pomerantz, A. Sinha, S. Standeven, J. Bhamla, M. S. 2019-01-16 doi:10.1101/519835 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ Age-dependent characterization of the carotid and cerebral artery morphologies in a transgenic mouse model of sickle cell anemia using ultrasound and microcomputed tomography ]]> https://biorxiv.org/content/10.1101/522748v1?rss=1 Rivera, C. P. Li, L. Cai, S. Pei, N. McAlear, G. Bollavaram, K. Ariyo, O. V. Omojola, V. O. Song, H. Tan, W. Huo, Y. Platt, M. O. 2019-01-16 doi:10.1101/522748 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ On the Complexity of Sequence to Graph Alignment ]]> https://biorxiv.org/content/10.1101/522912v1?rss=1 Jain, C. Zhang, H. Gao, Y. Aluru, S. 2019-01-17 doi:10.1101/522912 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ Microhabitat predicts species differences in exploratory behavior in Lake Malawi cichlids ]]> https://biorxiv.org/content/10.1101/525378v1?rss=1 Johnson, Z. V. Moore, E. C. Wong, R. Y. Godwin, J. R. Streelman, J. T. Roberts, R. B. 2019-01-22 doi:10.1101/525378 Cold Spring Harbor Laboratory Press 2019-01-22 <![CDATA[ Analysis of Vibrio cholerae genomes using a novel bioinformatic tool identifies new, active Type VI Secretion System gene clusters ]]> https://biorxiv.org/content/10.1101/526723v1?rss=1 Crisan, C. V. Chande, A. T. Williams, K. Raghuram, V. Rishishwar, L. Steinbach, G. Yunker, P. Jordan, K. I. Hammer, B. K. 2019-01-26 doi:10.1101/526723 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ PGCN: Disease gene prioritization by disease and gene embedding through graph convolutional neural networks ]]> https://biorxiv.org/content/10.1101/532226v1?rss=1 Li, Y. Kuwahara, H. Yang, P. Song, L. Gao, X. 2019-01-28 doi:10.1101/532226 Cold Spring Harbor Laboratory Press 2019-01-28 <![CDATA[ Adaptations of Atribacteria to life in methane hydrates: hot traits for cold life ]]> https://biorxiv.org/content/10.1101/536078v1?rss=1 Glass, J. B. Ranjan, P. Kretz, C. B. Nunn, B. L. Johnson, A. M. McManus, J. Stewart, F. J. 2019-01-31 doi:10.1101/536078 Cold Spring Harbor Laboratory Press 2019-01-31 <![CDATA[ The nature of the perceptual representation for decision making ]]> https://biorxiv.org/content/10.1101/537068v1?rss=1 Yeon, J. Rahnev, D. 2019-01-31 doi:10.1101/537068 Cold Spring Harbor Laboratory Press 2019-01-31 <![CDATA[ Mitochondrial-nuclear heme trafficking is regulated by GTPases that control mitochondrial dynamics. ]]> https://biorxiv.org/content/10.1101/539254v1?rss=1 Martinez-Guzman, O. Dietz, J. V. Bohovych, I. Medlock, A. W. Khalimonchuk, O. Reddi, A. R. 2019-02-04 doi:10.1101/539254 Cold Spring Harbor Laboratory Press 2019-02-04 <![CDATA[ Progranulin deficiency leads to reduced glucocerebrosidase activity ]]> https://biorxiv.org/content/10.1101/540450v1?rss=1 Zhou, X. Paushter, D. H. Pagan, M. D. Kim, D. Lieberman, R. L. Overkleeft, H. S. Sun, Y. Smolka, M. B. Hu, F. 2019-02-07 doi:10.1101/540450 Cold Spring Harbor Laboratory Press 2019-02-07 <![CDATA[ Evolutionary dynamics of de novo mutations and mutant lineages arising in a simple, constant environment ]]> https://biorxiv.org/content/10.1101/540625v1?rss=1 Kinnersley, M. Schwartz, K. Boswell, J. Yang, D.-D. Sherlock, G. Rosenzweig, F. 2019-02-04 doi:10.1101/540625 Cold Spring Harbor Laboratory Press 2019-02-04 <![CDATA[ Bacterial defiance as a form of prodrug failure ]]> https://biorxiv.org/content/10.1101/556951v1?rss=1 Holt, B. A. Kwong, G. A. 2019-02-21 doi:10.1101/556951 Cold Spring Harbor Laboratory Press 2019-02-21 <![CDATA[ Marine deep biosphere microbial communities assemble in near-surface sediments in Aarhus Bay ]]> https://biorxiv.org/content/10.1101/557041v1?rss=1 Petro, C. Zaencker, B. Starnawski, P. Jochum, L. M. Ferdelman, T. G. Jorgensen, B. B. Roy, H. Kjeldsen, K. U. Schramm, A. 2019-02-21 doi:10.1101/557041 Cold Spring Harbor Laboratory Press 2019-02-21 <![CDATA[ Multi-omics Integrative Analysis of Acute and Relapsing Malaria in a Non-Human Primate Model of P. vivax infection ]]> https://biorxiv.org/content/10.1101/564195v1?rss=1 Tang, Y. Joyner, C. J. Cordy, R. J. Malaria Host-Pathogen Interaction Center (MaHPIC), Galinski, M. R. Lamb, T. J. Styczynski, M. P. 2019-03-01 doi:10.1101/564195 Cold Spring Harbor Laboratory Press 2019-03-01 <![CDATA[ Deconvolving multiplexed protease signatures with substrate reduction and activity clustering ]]> https://biorxiv.org/content/10.1101/564906v1?rss=1 Zhuang, Q. Holt, B. A. Kwong, G. A. Qiu, P. 2019-03-01 doi:10.1101/564906 Cold Spring Harbor Laboratory Press 2019-03-01 <![CDATA[ A cis-regulatory change underlying the motor neuron-specific loss of terminal selector gene expression in immotile tunicate larvae ]]> https://biorxiv.org/content/10.1101/567719v1?rss=1 Lowe, E. K. Racioppi, C. Peyrieras, N. Ristoratore, F. Christiaen, L. Swalla, B. J. Stolfi, A. 2019-03-05 doi:10.1101/567719 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Wnt7a-releasing synthetic hydrogel enhances local skeletal muscle regeneration and muscle stem cell engraftment ]]> https://biorxiv.org/content/10.1101/569921v1?rss=1 Han, W. M. Mohiuddin, M. Anderson, S. E. Garcia, A. J. Jang, Y. C. 2019-03-06 doi:10.1101/569921 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ Maximum Likelihood Reconstruction of Ancestral Networks by Integer Linear Programming ]]> https://biorxiv.org/content/10.1101/574814v1?rss=1 Rajan, V. Kingsford, C. Zhang, X. 2019-03-13 doi:10.1101/574814 Cold Spring Harbor Laboratory Press 2019-03-13 <![CDATA[ A beneficial genomic rearrangement creates multiple versions of calcipressin in C. elegans ]]> https://biorxiv.org/content/10.1101/578088v1?rss=1 Zhao, Y. Wan, J. Biliya, S. Brady, S. Lee, D. Andersen, E. Vannberg, F. Lu, H. McGrath, P. 2019-03-14 doi:10.1101/578088 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ In silico bacteria evolve robust cooperation via complex quorum-sensing strategies ]]> https://biorxiv.org/content/10.1101/598508v1?rss=1 Wang, Y. Rattray, J. B. Thomas, S. A. Gurney, J. Brown, S. P. 2019-04-03 doi:10.1101/598508 Cold Spring Harbor Laboratory Press 2019-04-03 <![CDATA[ The hourglass organization of the C. elegans connectome ]]> https://biorxiv.org/content/10.1101/600999v1?rss=1 Sabrin, K. Wei, Y. van den Heuvel, M. Dovrolis, C. 2019-04-07 doi:10.1101/600999 Cold Spring Harbor Laboratory Press 2019-04-07 <![CDATA[ Accelerated evolution of oligodendrocytes in human brain ]]> https://biorxiv.org/content/10.1101/601062v1?rss=1 Berto, S. Mendizabal, I. Usui, N. Toriumi, K. Chatterjee, P. Douglas, C. Tamminga, C. Preuss, T. Yi, S. Konopka, G. 2019-04-07 doi:10.1101/601062 Cold Spring Harbor Laboratory Press 2019-04-07 <![CDATA[ Timing is (almost) everything in a comprehensive, spike-resolved flight motor program ]]> https://biorxiv.org/content/10.1101/602961v1?rss=1 Conn, R. Putney, J. Sponberg, S. 2019-04-09 doi:10.1101/602961 Cold Spring Harbor Laboratory Press 2019-04-09 <![CDATA[ Heat-triggered remote control of CRISPR-dCas9 for tunable transcriptional modulation ]]> https://biorxiv.org/content/10.1101/606723v1?rss=1 Gamboa, L. Phung, E. V. Li, H. Meyers, J. P. Kwong, G. 2019-04-12 doi:10.1101/606723 Cold Spring Harbor Laboratory Press 2019-04-12 <![CDATA[ Proteases as Biological Bits for Programmable Medicine ]]> https://biorxiv.org/content/10.1101/607895v1?rss=1 Holt, B. Kwong, G. A. 2019-04-12 doi:10.1101/607895 Cold Spring Harbor Laboratory Press 2019-04-12 <![CDATA[ Morphogenesis and dynamics of slime molds in various environments ]]> https://biorxiv.org/content/10.1101/622662v1?rss=1 Patino-Ramirez, F. Boussard, A. Arson, C. Dussutour, A. 2019-04-29 doi:10.1101/622662 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ Using Earth Mover’s Distance for Viral Outbreak Investigations ]]> https://biorxiv.org/content/10.1101/628859v1?rss=1 Melnyk, A. Knyazev, S. Khudyakov, Y. Vannberg, F. Bunimovich, L. Skums, P. Zelikovsky, A. 2019-05-06 doi:10.1101/628859 Cold Spring Harbor Laboratory Press 2019-05-06 <![CDATA[ Quantitative Models of Phage-Antibiotics Combination Therapy ]]> https://biorxiv.org/content/10.1101/633784v1?rss=1 Rodriguez-Gonzalez, R. A. Leung, C. Y. Chan, B. K. Turner, P. E. Weitz, J. S. 2019-05-10 doi:10.1101/633784 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Discrete Community Assemblages Within Hypersaline Paleolake Sediments of Pilot Valley, Utah ]]> https://biorxiv.org/content/10.1101/634642v1?rss=1 Lynch, K. Rey, K. Bond, R. Biddle, J. Spear, J. Rosenzweig, F. Munakata Marr, J. 2019-05-30 doi:10.1101/634642 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ Neuron subtype-specific effector gene expression in the Motor Ganglion of Ciona ]]> https://biorxiv.org/content/10.1101/641233v1?rss=1 Gibboney, S. Kim, K. Johnson, C. J. Orvis, J. Martinez-Feduchi, P. Lowe, E. K. Sharma, S. Stolfi, A. 2019-05-17 doi:10.1101/641233 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ The Relationship between BOLD and Neural Activity Arises from Temporally Sparse Events ]]> https://biorxiv.org/content/10.1101/644419v1?rss=1 Zhang, X. Pan, W.-J. Keilholz, S. 2019-05-20 doi:10.1101/644419 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Allelic polymorphism shapes collective phenotypes in evolving Pseudomonas aeruginosa populations ]]> https://biorxiv.org/content/10.1101/644724v1?rss=1 Azimi, S. Roberts, A. E. Peng, S. Weitz, J. S. McNally, A. Brown, S. P. Diggle, S. P. 2019-05-21 doi:10.1101/644724 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ Functionalized microcarriers improve T cell manufacturing by facilitating migratory memory T cell production and increasing CD4/CD8 ratio ]]> https://biorxiv.org/content/10.1101/646760v1?rss=1 Dwarshuis, N. J. Song, H. W. Patel, A. Kotanchek, T. Roy, K. 2019-05-23 doi:10.1101/646760 Cold Spring Harbor Laboratory Press 2019-05-23 <![CDATA[ Modification of primary amines to higher order amines reduces in vivo hematological and immunotoxicity of cationic nanocarriers through TLR4 and complement pathways ]]> https://biorxiv.org/content/10.1101/647305v1?rss=1 nView larger version (27K):norg.highwire.dtl.DTLVardef@63c7a7org.highwire.dtl.DTLVardef@c8ac52org.highwire.dtl.DTLVardef@a9589dorg.highwire.dtl.DTLVardef@1f8ec62_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Toy, R. Pradhan, P. Ramesh, V. Di Paolo, N. C. Lash, B. Liu, J. Blanchard, E. L. Santangelo, P. J. Shayakhmetov, D. M. Roy, K. 2019-05-24 doi:10.1101/647305 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ StrainHub: A phylogenetic tool to construct pathogen transmission networks ]]> https://biorxiv.org/content/10.1101/650283v1?rss=1 de Bernardi Schneider, A. Ford, C. T. Hostager, R. Williams, J. Cioce, M. Catalyürek, U. V. Wertheim, J. O. Janies, D. 2019-05-31 doi:10.1101/650283 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Resting brain fluctuations are intrinsically coupled to visual response dynamics ]]> https://biorxiv.org/content/10.1101/650291v1?rss=1 Belloy, M. E. Billings, J. Abbas, A. Kashyap, A. Pan, W.-j. Hinz, R. Vanreusel, V. Vanaudekerke, J. Van der Linden, A. Keilholz, S. D. Verhoye, M. Keliris, G. A. 2019-05-27 doi:10.1101/650291 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ In-vitro and in-vivo Characterization of a Multi-Stage Enzyme-Responsive Nanoparticle-in-Microgel Pulmonary Drug Delivery System ]]> https://biorxiv.org/content/10.1101/650911v1?rss=1 nView larger version (15K):norg.highwire.dtl.DTLVardef@1dcd1dcorg.highwire.dtl.DTLVardef@55e23eorg.highwire.dtl.DTLVardef@788c02org.highwire.dtl.DTLVardef@30161f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mejias, J. C. Roy, K. 2019-05-27 doi:10.1101/650911 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Accelerating Sequence Alignment to Graphs ]]> https://biorxiv.org/content/10.1101/651638v1?rss=1 Jain, C. Misra, S. Zhang, H. Dilthey, A. Aluru, S. 2019-05-27 doi:10.1101/651638 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Neurogenin regulates effectors of migratory neuron cell behaviors in Ciona ]]> https://biorxiv.org/content/10.1101/654798v1?rss=1 Gibboney, S. Kim, K. Razy-Krajka, F. Wang, W. Stolfi, A. 2019-05-30 doi:10.1101/654798 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ Microbiome data enhances predictive models of lung function in people with CF ]]> https://biorxiv.org/content/10.1101/656066v1?rss=1 Zhao, C. Y. Hao, Y. Wang, Y. Varga, J. J. Stecenko, A. A. Goldberg, J. B. Brown, S. P. 2019-05-31 doi:10.1101/656066 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ A nanometer difference in myofilament lattice spacing of two cockroach leg muscles explains their different functions ]]> https://biorxiv.org/content/10.1101/656272v1?rss=1 Tune, T. N. Ma, W. Irving, T. Sponberg, S. N. 2019-05-31 doi:10.1101/656272 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Diminished cortical excitation during perceptual impairments in a mouse model of autism ]]> https://biorxiv.org/content/10.1101/657189v1?rss=1 Del Rosario, J. Speed, A. Arrowood, H. Motz, C. Pardue, M. Haider, B. 2019-06-03 doi:10.1101/657189 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Functional and comparative genomic analysis of integrated prophage-like sequences in Candidatus Liberibacter asiaticus ]]> https://biorxiv.org/content/10.1101/661967v1?rss=1 Dominguez-Mirazo, M. Jin, R. Weitz, J. S. 2019-06-06 doi:10.1101/661967 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Real-time monitoring of mechanical cues in the regenerative niche reveal dynamic strain magnitudes that enhance bone repair ]]> https://biorxiv.org/content/10.1101/663278v1?rss=1 Klosterhoff, B. S. Kaiser, J. Nelson, B. Karipott, S. S. Ruehle, M. A. Hollister, S. J. Weiss, J. Ong, K. G. Willett, N. Guldberg, R. E. 2019-06-06 doi:10.1101/663278 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Optogenetic control of Wnt signaling for modeling early embryogenic patterning with human pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/665695v1?rss=1 500-fold) using an optoWnt optogenetic system, drove broad transcriptional changes and mesendoderm differentiation of human ESCs at high efficiency (>95% cells). Furthermore, activating Wnt signaling in subpopulations of ESCs in 2D and 3D cultures induced cell self-organization and morphogenesis reminiscent of human gastrulation, including changes in cell migration and epithelial to mesenchymal transition. Our findings thus reveal an instructive role for Wnt in directing cell patterning in this ESC model for gastrulation. ]]> Repina, N. A. Bao, X. Zimmermann, J. A. Joy, D. A. Kane, R. S. Schaffer, D. V. 2019-06-10 doi:10.1101/665695 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Cancer Exacerbates Chemotherapy Induced Sensory Neuropathy ]]> https://biorxiv.org/content/10.1101/667105v1?rss=1 Housley, S. Nardelli, P. Carrasco, D. Pfahl, E. Matyunina, L. McDonald, J. F. Cope, T. C. 2019-06-11 doi:10.1101/667105 Cold Spring Harbor Laboratory Press 2019-06-11 <![CDATA[ Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes ]]> https://biorxiv.org/content/10.1101/668343v1?rss=1 Bray, M. S. Wu, J. Padilla, C. C. Stewart, F. J. Fowle, D. A. Henny, C. Simister, R. L. Thompson, K. J. Crowe, S. A. Glass, J. B. 2019-06-13 doi:10.1101/668343 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Infect While the Iron is Scarce: Nutrient Explicit Phage-Bacteria Games ]]> https://biorxiv.org/content/10.1101/674382v1?rss=1 Muratore, D. Weitz, J. S. 2019-06-18 doi:10.1101/674382 Cold Spring Harbor Laboratory Press 2019-06-18 <![CDATA[ The Molecular and Microbial Microenvironments in Chronically Diseased Lungs ]]> https://biorxiv.org/content/10.1101/676148v1?rss=1 Garg, N. Melnik, A. V. Vasquez-Baeza, Y. Aksenov, A. Hyde, E. R. McAvoy, A. C. Wang, M. da Silva, R. Protsyuk, I. Wu, J. V. Bouslimani, A. Lim, Y. W. Luzzatto-Knaan, T. Comstock, W. Quinn, R. A. Wong, R. Humphrey, G. Ackermann, G. Spivey, T. Brouha, S. S. Bandeira, N. Lin, G. Y. Rohwer, F. Conrad, D. Alexandrov, T. Dorrestein, P. C. Knight, R. 2019-06-19 doi:10.1101/676148 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Fitness and productivity increase with ecotypic diversity among E. coli evolved in a simple, constant environment ]]> https://biorxiv.org/content/10.1101/679969v1?rss=1 Yang, D.-D. Alexander, A. Kinnersley, M. Cook, E. Caudy, A. Rosebrock, A. ROSENZWEIG, F. 2019-06-23 doi:10.1101/679969 Cold Spring Harbor Laboratory Press 2019-06-23 <![CDATA[ The anaerobic digestion microbiome: a collection of 1600 metagenome-assembled genomes shows high species diversity related to methane production ]]> https://biorxiv.org/content/10.1101/680553v1?rss=1 50% complete and nearly half were [≥]90% complete with [≤]5% contamination. In most samples, specialized microbial communities were established, while only a few taxa were widespread among the different reactor systems. Metabolic reconstruction of the MAGs enabled the prediction of functional traits related to biomass degradation and methane production from waste biomass. An extensive evaluation of the replication index provided an estimation of the growth rate for microbes involved in different steps of the food chain. The recovery of many MAGs belonging to Candidate Phyla Radiation and other underexplored taxa suggests their specific involvement in the anaerobic degradation of organic matter.nnConclusionsThe outcome of this study highlights a high flexibility of the biogas microbiome. The dynamic composition and adaptability to the environmental conditions, including temperatures and a wide range of substrates, were demonstrated. Our findings enhance the mechanistic understanding of anaerobic digestion microbiome and substantially extend the existing repository of genomes. The established database represents a relevant resource for future studies related to this engineered ecosystem. ]]> Campanaro, S. Treu, L. Rodriguez Rojas, L. M. Kovalovszki, A. Ziels, R. Maus, I. Zhu, X. Kougias, P. G. Basile, A. Luo, G. Schlüter, A. Konstantinidis, K. T. Angelidaki, I. 2019-06-24 doi:10.1101/680553 Cold Spring Harbor Laboratory Press 2019-06-24 <![CDATA[ Validating paired-end read alignments in sequence graphs ]]> https://biorxiv.org/content/10.1101/682799v1?rss=1 Jain, C. Zhang, H. Dilthey, A. Aluru, S. 2019-06-26 doi:10.1101/682799 Cold Spring Harbor Laboratory Press 2019-06-26 <![CDATA[ Expression of extracellular multiheme cytochromes discovered in a betaproteobacterium during Mn(III) reduction ]]> https://biorxiv.org/content/10.1101/695007v1?rss=1 Szeinbaum, N. Nunn, B. L. Cavazos, A. R. Crowe, S. A. Stewart, F. J. DiChristina, T. J. Reinhard, C. T. Glass, J. B. 2019-07-08 doi:10.1101/695007 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Linking light-dependent life history traits with population dynamics for Prochlorococcus and cyanophage ]]> https://biorxiv.org/content/10.1101/696435v1?rss=1 Demory, D. Liu, R. Chen, Y. Zhao, F. Zeng, Q. Weitz, J. 2019-07-11 doi:10.1101/696435 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Extent and context dependence of pleiotropy revealed by high-throughput single-cell phenotyping ]]> https://biorxiv.org/content/10.1101/700716v1?rss=1 Geiler-Samerotte, K. A. Li, S. Lazaris, C. Taylor, A. Ziv, N. Ramjeawan, C. Paaby, A. B. Siegal, M. L. 2019-07-14 doi:10.1101/700716 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ When be Temperate: On the Fitness Benefits of Lysis vs. Lysogeny ]]> https://biorxiv.org/content/10.1101/709758v1?rss=1 Li, G. Cortez, M. H. Weitz, J. S. 2019-07-22 doi:10.1101/709758 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Molecular signature of pruriceptive MrgprA3+ neurons ]]> https://biorxiv.org/content/10.1101/727396v1?rss=1 Xing, Y. Chen, J. Hilley, H. Steele, H. Yang, J. Han, L. 2019-08-06 doi:10.1101/727396 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ Indirect actuation reduces flight power requirements in Manduca sexta via elastic energy exchange ]]> https://biorxiv.org/content/10.1101/727743v1?rss=1 Gau, J. Gravish, N. Sponberg, S. 2019-08-07 doi:10.1101/727743 Cold Spring Harbor Laboratory Press 2019-08-07 <![CDATA[ SAPH-ire TFx: A Machine Learning Recommendation Method and Webtool for the Prediction of Functional Post-Translational Modifications ]]> https://biorxiv.org/content/10.1101/731026v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@4dbe8dorg.highwire.dtl.DTLVardef@1936d5org.highwire.dtl.DTLVardef@15eef8aorg.highwire.dtl.DTLVardef@1c07cea_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure S1.C_FLOATNO ROC curves at different KFSC thresholds. (unfurled in Figure 1E). C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/731026v2_figS4.gif" ALT="Figure 4"> View larger version (20K): org.highwire.dtl.DTLVardef@48e892org.highwire.dtl.DTLVardef@9cf372org.highwire.dtl.DTLVardef@32da4dorg.highwire.dtl.DTLVardef@99fd89_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure S4.C_FLOATNO Model recall and recommendation comparison for PTMs associated with validated functional SLiMs from the ELM resource. C_FIG ]]> English, N. Torres, M. P. 2019-08-09 doi:10.1101/731026 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ Computational search for UV radiation resistance strategies in Deinococcus swuensis isolated from Paramo ecosystems. ]]> https://biorxiv.org/content/10.1101/734129v1?rss=1 95% survival rate). Differentially expressed genes were identified using the R-Bioconductor package NOISeq and compared with other reported resistance strategies reported for this genus. Genes identified as being overexpressed included transcriptional regulators and genes involved in protection against damage by UVR. Non-coding (nc)RNAs were also differentially expressed, some of which have not been previously implicated. This study characterized the early resistance strategy used by D. swuensis and indicates the involvement of ncRNAs in the adaptation to extreme environmental conditions. ]]> Diaz-Riano, J. I. Posada, L. Acosta Garcia, I. C. Ruiz-Perez, C. Garcia-Castillo, C. Reyes, A. Zambrano, M. M. 2019-08-13 doi:10.1101/734129 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ The heme biosynthetic enzyme, 5-aminolevulinic acid synthase (ALAS), and GTPases in control of mitochondrial dynamics and ER contact sites, regulate heme mobilization to the nucleus. ]]> https://biorxiv.org/content/10.1101/734780v1?rss=1 Martinez-Guzman, O. Willoughby, M. M. Saini, A. Dietz, J. V. Bohovych, I. Medlock, A. E. Khalimonchuk, O. Reddi, A. R. 2019-08-13 doi:10.1101/734780 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Metagenomic characterization of creek sediment microbial communities from a major agricultural region in Salinas, California ]]> https://biorxiv.org/content/10.1101/737759v1?rss=1 Suttner, B. Johnston, E. R. Orellana, L. H. Rodriguez-R, L. M. Hatt, J. Carychao, D. Carter, M. Q. Cooley, M. B. Konstantinidis, K. T. 2019-08-16 doi:10.1101/737759 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ Mitigating memory effects during undulatory locomotion on hysteretic materials. ]]> https://biorxiv.org/content/10.1101/748186v1?rss=1 Schiebel, P. E. Astley, H. C. Rieser, J. M. Agarwal, S. Hubicki, C. Hubbard, A. M. Cruz, K. Mendelson, J. R. Kamrin, K. Goldman, D. I. 2019-08-28 doi:10.1101/748186 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields ]]> https://biorxiv.org/content/10.1101/780809v1?rss=1 Medina-Cordoba, L. K. Chande, A. T. Rishishwar, L. Mayer, L. W. Valderrama-Aguirre, L. C. Valderrama-Aguirre, A. Gaby, J. C. Kostka, J. E. Jordan, I. K. 2019-09-24 doi:10.1101/780809 Cold Spring Harbor Laboratory Press 2019-09-24 <![CDATA[ Admixture-enabled selection for rapid adaptive evolution in the Americas ]]> https://biorxiv.org/content/10.1101/783845v1?rss=1 Norris, E. T. Rishishwar, L. Chande, A. T. Conley, A. B. Ye, K. Valderrama-Aguirre, A. Jordan, I. K. 2019-09-28 doi:10.1101/783845 Cold Spring Harbor Laboratory Press 2019-09-28 <![CDATA[ Noninvasive Sleep Scoring in Mice using Electric Field Sensors ]]> https://biorxiv.org/content/10.1101/794552v1?rss=1 93%) and comparable inter- and intra-scorer error as expert EEG/EMG scoring. Novices given an instruction document with examples were able to score sleep comparable to expert scorers (>91% agreement). Additionally, EF sensors were able to quantify 3-state sleep scoring in traditional mouse home cages.nnComparison with existing methodMost noninvasive sleep assessment technology requires animal contact, altered cage environments, and/or can only discern 2 states of arousal (wake or asleep). The EF sensors are able to discriminate REM from non-REM sleep accurately and from outside the animals home cage.nnConclusionsEF sensors provide a simple and reliable method to accurately score 3-state sleep architecture; (i) from outside the typical home cage, (ii) where noninvasive approaches are preferred, or (iii) which EEG/EMG is not possible.nnGraphical AbstractnnO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/794552v1_ufig1.gif" ALT="Figure 1">nView larger version (43K):norg.highwire.dtl.DTLVardef@1b36cf3org.highwire.dtl.DTLVardef@b5fdc9org.highwire.dtl.DTLVardef@28a6dforg.highwire.dtl.DTLVardef@e39a5a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kloefkorn, H. Aiani, L. M. Lakhani, A. Nagesh, S. Moss, A. Goolsby, W. Rehg, J. Pedersen, N. P. Hochman, S. 2019-10-07 doi:10.1101/794552 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ A Novel Droplet Digital PCR Human mtDNA Assay for Global Fecal Source Tracking ]]> https://biorxiv.org/content/10.1101/794891v1?rss=1 Zhu, K. Suttner, B. Konstantinidis, K. T. Brown, J. 2019-10-06 doi:10.1101/794891 Cold Spring Harbor Laboratory Press 2019-10-06 <![CDATA[ Predicting cellular position in the Drosophila embryo from Single-Cell Transcriptomics data ]]> https://biorxiv.org/content/10.1101/796029v1?rss=1 Tanevski, J. Nguyen, T. Truong, B. Karaiskos, N. Ahsen, M. E. Zhang, X. Shu, C. Hu, Y. Pham, H. V. V. Li, X. Le, T. D. Tarca, A. Bhatti, G. Romero, R. Karathanasis, N. Loher, P. Chen, Y. Ouyang, Z. Mao, D. Zhang, Y. Zand, M. Ruan, J. Hafemeister, C. Qiu, P. Tran, D. Nguyen, T. Gabor, A. Yu, T. Glaab, E. Krause, R. Banda, P. Stolovitzky, G. Rajewsky, N. Saez-Rodriguez, J. Meyer, P. 2019-10-10 doi:10.1101/796029 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Microglial ERK activation is a critical regulator of pro-inflammatory immune responses in Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/798215v1?rss=1 Chen, M. J. Ramesha, S. Weinstock, L. D. Gao, T. Ping, L. Xiao, H. Dammer, E. B. Duong, D. D. Levey, A. I. Lah, J. J. Wood, L. B. Rangaraju, S. 2019-10-08 doi:10.1101/798215 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Brain Network Constraints and Recurrent Neural Networks reproduce unique Trajectories and State Transitions seen over the span of minutes in resting state fMRI ]]> https://biorxiv.org/content/10.1101/798520v1?rss=1 Kashyap, A. Keilholz, S. 2019-10-08 doi:10.1101/798520 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Quantitative multiplexed proteomics of mouse microglia by flow-cytometric sorting reveals a core set of highly-abundant microglial proteins ]]> https://biorxiv.org/content/10.1101/802694v1?rss=1 Rayaprolu, S. Xiao, H. Ramesha, S. Duong, D. Dammer, E. B. Lah, J. J. Levey, A. I. Seyfried, N. T. Rangaraju, S. 2019-10-17 doi:10.1101/802694 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Awake reactivation and suppression after brief task exposure depend on task novelty ]]> https://biorxiv.org/content/10.1101/809574v1?rss=1 Bang, J. W. Rahnev, D. 2019-10-17 doi:10.1101/809574 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Addressing age related hearing loss through engineering accessible and affordable hearing technology ]]> https://biorxiv.org/content/10.1101/811828v1?rss=1 Sinha, S. Irani, U. D. Manchaiah, V. Bhamla, M. S. 2019-10-21 doi:10.1101/811828 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Feature-based Molecular Networking in the GNPS Analysis Environment ]]> https://biorxiv.org/content/10.1101/812404v1?rss=1 Nothias, L. F. Petras, D. Schmid, R. Duehrkop, K. Rainer, J. Sarvepalli, A. Protsyuk, I. Ernst, M. Tsugawa, H. Fleischauer, M. Aicheler, F. Aksenov, A. Alka, O. Allard, P.-M. Barsch, A. Cachet, X. Caraballo, M. Da Silva, R. Dang, T. Garg, N. Gauglitz, J. M. Gurevich, A. Isaac, G. Jarmusch, A. K. Kamenik, Z. Kang, K. B. Kessler, N. Koester, I. Korf, A. Le Gouellec, A. Ludwig, M. Martin H., C. McCall, L.-I. McSayles, J. Meyer, S. Mohimani, H. Morsy, M. Moyne, O. Neumann, S. Neuweger, H. Nguyen, N. H. Esposito-Nothias, M. Paolini, J. Phelan, V. Pluskal, 2019-10-20 doi:10.1101/812404 Cold Spring Harbor Laboratory Press 2019-10-20 <![CDATA[ A Multicellular Network Mechanism for Temperature-Robust Food Sensing ]]> https://biorxiv.org/content/10.1101/815373v1?rss=1 Patel, D. S. Diana, G. Entchev, E. V. Zhan, M. Lu, H. Ch'ng, Q. 2019-10-22 doi:10.1101/815373 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Disruption of Redox Balance Enhances the Effects of BRAF-inhibition in Melanoma Cells ]]> https://biorxiv.org/content/10.1101/818989v1?rss=1 Paudel, B. Lewis, J. E. Hardeman, K. N. Hayford, C. E. Robbins, C. J. Codreanu, S. G. Sherrod, S. D. McLean, J. A. Kemp, M. L. Quaranta, V. 2019-10-28 doi:10.1101/818989 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ Impact of substrate-template stability, temperature, phosphate location, and nick-site base pairs on non-enzymatic DNA ligation: Defining parameters for optimization of ligation rates and yields with carbodiimide activation ]]> https://biorxiv.org/content/10.1101/821017v1?rss=1 Hud, N. V. Obianyor, C. Grover, M. A. Clifton, B. Newnam, G. 2019-10-28 doi:10.1101/821017 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ Iterative Subtractive Binning of Freshwater Chronoseries Metagenomes Identifies over Four Hundred Novel Species and their Ecologic Preferences ]]> https://biorxiv.org/content/10.1101/826941v1?rss=1 Rodriguez-R, L. M. Tsementzi, D. Luo, C. Konstantinidis, K. T. 2019-10-31 doi:10.1101/826941 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Experimental control of macrophage pro-inflammatory dynamics using predictive models ]]> https://biorxiv.org/content/10.1101/826966v1?rss=1 Weinstock, L. D. Forsmo, J. E. Wilkinson, A. Ueda, J. Wood, L. B. 2019-11-01 doi:10.1101/826966 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ dSNE: a visualization approach for use with decentralized data ]]> https://biorxiv.org/content/10.1101/826974v1?rss=1 Saha, D. K. Calhoun, V. D. DU, Y. FU, Z. Panta, S. R. Plis, S. M. 2019-11-12 doi:10.1101/826974 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Multi-sensory integration in the mouse cortical connectome using a network diffusion model ]]> https://biorxiv.org/content/10.1101/832485v1?rss=1 Shadi, K. Dyer, E. Dovrolis, C. 2019-11-07 doi:10.1101/832485 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Genome Repository of Oiled Systems (GROS): an interactive and searchable database that expands the catalogued diversity of crude oil-associated microbes ]]> https://biorxiv.org/content/10.1101/838573v1?rss=1 Karthikeyan, S. Rodriguez-R, L. M. Heritier-Robbins, P. Hatt, J. Huettel, M. Kostka, J. E. Konstantinidis, K. T. 2019-11-12 doi:10.1101/838573 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Topological constraints in early multicellularity favor reproductive division of labor ]]> https://biorxiv.org/content/10.1101/842849v1?rss=1 Yanni, D. Jacobeen, S. Marquez-Zacarias, P. Weitz, J. S. Ratcliff, W. C. Yunker, P. J. 2019-11-15 doi:10.1101/842849 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Optimizing the Timing and Composition of Therapeutic Phage Cocktails: A Control-theoretic Approach ]]> https://biorxiv.org/content/10.1101/845172v1?rss=1 Li, G. Leung, C. Y. Wardi, Y. Debarbieux, L. Weitz, J. 2019-11-16 doi:10.1101/845172 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ Bacterial quorum sensing allows graded responses to variations in density, on both individual and population scales ]]> https://biorxiv.org/content/10.1101/850297v1?rss=1 Rattray, J. B. Thomas, S. A. Wang, Y. Brown, S. P. 2019-11-21 doi:10.1101/850297 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Cutting in-line with iron: ribosomal function and non-oxidative RNA cleavage ]]> https://biorxiv.org/content/10.1101/851097v1?rss=1 Guth-Metzler, R. Bray, M. S. Suttapitugsakul, S. Montllor-Albalate, C. Bowman, J. C. Wu, R. Reddi, A. R. Okafor, C. D. Glass, J. B. Williams, L. D. 2019-11-22 doi:10.1101/851097 Cold Spring Harbor Laboratory Press 2019-11-22 <![CDATA[ Biophysical mechanism of ultrafast helical twisting contraction in the giant unicellular ciliate Spirostomum ambiguum ]]> https://biorxiv.org/content/10.1101/854836v1?rss=1 Xinjing, L. X. Bhamla, S. 2019-11-25 doi:10.1101/854836 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ STing: accurate and ultrafast genomic profiling with exact sequence matches ]]> https://biorxiv.org/content/10.1101/855478v1?rss=1 Espitia-Navarro, H. F. Chande, A. T. Nagar, S. D. Smith, H. Jordan, I. K. Rishishwar, L. 2019-11-26 doi:10.1101/855478 Cold Spring Harbor Laboratory Press 2019-11-26 <![CDATA[ HeALTH: An Automated Platform for Long-term Longitudinal Studies of Whole Organisms under Precise Environmental Control ]]> https://biorxiv.org/content/10.1101/863985v1?rss=1 Le, K. N. Zhan, M. Cho, Y. Wan, J. Patel, D. S. Lu, H. 2019-12-04 doi:10.1101/863985 Cold Spring Harbor Laboratory Press 2019-12-04 <![CDATA[ Phage steering of antibiotic-resistance evolution in the bacterial pathogen Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/868661v1?rss=1 Gurney, J. Pradier, L. Griffin, J. S. Gougat-Barbera, C. Chan, B. K. Turner, P. E. Kaltz, O. Hochberg, M. E. 2019-12-10 doi:10.1101/868661 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Brain computation by assemblies of neurons ]]> https://biorxiv.org/content/10.1101/869156v1?rss=1 Vempala, S. Papadimitriou, C. Mitropolsky, D. Collins, M. Maass, W. 2019-12-08 doi:10.1101/869156 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ Experimental evolution of Escherichia coli harboring an ancient translation protein ]]> https://biorxiv.org/content/10.1101/040626v1?rss=1 Betul Kacar Xueliang Ge Suparna Sanyal Eric A. Gaucher 2016-02-22 doi:10.1101/040626 Cold Spring Harbor Laboratory Press 2016-02-22 <![CDATA[ 50-valent inactivated rhinovirus vaccine is broadly immunogenic in rhesus macaques ]]> https://biorxiv.org/content/10.1101/053967v1?rss=1 Sujin Lee Minh Trang Nguyen Michael Currier Joe Jenkins Elizabeth Strobert Adriana Kajon Ranjna Madan-Lala Yury Bochkov James Gern Krishnendu Roy Xiaoyan Lu Dean Erdman Paul Spearman Martin Moore 2016-05-17 doi:10.1101/053967 Cold Spring Harbor Laboratory Press 2016-05-17 <![CDATA[ Predicting Peptide-MHC Binding Affinities With Imputed Training Data ]]> https://biorxiv.org/content/10.1101/054775v1?rss=1 Alex Rubinsteyn Timothy O'Donnell Nandita Damaraju Jeffrey Hammerbacher 2016-05-22 doi:10.1101/054775 Cold Spring Harbor Laboratory Press 2016-05-22 <![CDATA[ Motor control by precisely timed spike patterns ]]> https://biorxiv.org/content/10.1101/056010v1?rss=1 Kyle H. Srivastava Caroline M. Holmes Michiel Vellema Andrea Pack Coen P. H. Elemans Ilya Nemenman Samuel J. Sober 2016-05-30 doi:10.1101/056010 Cold Spring Harbor Laboratory Press 2016-05-30 <![CDATA[ Suboptimality in perception ]]> https://biorxiv.org/content/10.1101/060194v1?rss=1 Dobromir Rahnev Rachel Denison 2016-06-22 doi:10.1101/060194 Cold Spring Harbor Laboratory Press 2016-06-22 <![CDATA[ Dynamics and fate of beneficial mutations under lineage contamination by linked deleterious mutations ]]> https://biorxiv.org/content/10.1101/068429v1?rss=1 Sophie Penisson Tanya Singh Paul D. Sniegowski Philip J Gerrish 2016-08-08 doi:10.1101/068429 Cold Spring Harbor Laboratory Press 2016-08-08 <![CDATA[ Individual- versus group-optimality in the production of secreted bacterial compounds ]]> https://biorxiv.org/content/10.1101/094086v1?rss=1 Schiessl, K. Ross-Gillespie, A. Cornforth, D. M. Weigert, M. Bigosch, C. Brown, S. P. Ackermann, M. Kümmerli, R. 2016-12-14 doi:10.1101/094086 Cold Spring Harbor Laboratory Press 2016-12-14 <![CDATA[ Critical Assessment of Metagenome Interpretation - a benchmark of computational metagenomics software ]]> https://biorxiv.org/content/10.1101/099127v1?rss=1 Sczyrba, A. Hofmann, P. Belmann, P. Koslicki, D. Janssen, S. Droege, J. Gregor, I. Majda, S. Fiedler, J. Dahms, E. Bremges, A. Fritz, A. Garrido-Oter, R. Sparholt Jorgensen, T. Shapiro, N. Blood, P. D. Gurevich, A. Bai, Y. Turaev, D. DeMaere, M. Z. Chikhi, R. Nagarajan, N. Quince, C. Hestbjerg Hansen, L. Sorensen, S. J. Chia, B. K. H. Denis, B. Froula, J. L. Wang, Z. Egan, R. Kang, D. D. Cook, J. J. Deltel, C. Beckstette, M. Lemaitre, C. Peterlongo, P. Rizk, G. Lavenier, D. Wu, Y.-W. Singer, S. W. Jain, C. Strous, M. Klingenberg, H. Meinicke, P. Bart 2017-01-09 doi:10.1101/099127 Cold Spring Harbor Laboratory Press 2017-01-09 <![CDATA[ Spontaneous development of cerebrovascular pathology and microinfarcts in a mouse model of sickle cell disease. ]]> https://biorxiv.org/content/10.1101/103309v1?rss=1 Hyacinth, H. I. Sugihara, C. L. Spencer, T. L. Archer, D. R. Shih, A. Y. 2017-01-27 doi:10.1101/103309 Cold Spring Harbor Laboratory Press 2017-01-27 <![CDATA[ A fast approximate algorithm for mapping long reads to large reference databases ]]> https://biorxiv.org/content/10.1101/103812v1?rss=1 60, 000 genomes. ]]> Jain, C. Dilthey, A. Koren, S. Aluru, S. Phillippy, A. M. 2017-01-27 doi:10.1101/103812 Cold Spring Harbor Laboratory Press 2017-01-27 <![CDATA[ Uncertainty in perceptual representations ]]> https://biorxiv.org/content/10.1101/108944v1?rss=1 Rahnev, D. 2017-02-16 doi:10.1101/108944 Cold Spring Harbor Laboratory Press 2017-02-16 <![CDATA[ Modeling of a negative feedback mechanism explains age-dependent genetic architecture in reproduction in domesticated C. elegans strains ]]> https://biorxiv.org/content/10.1101/114348v1?rss=1 Large, E. E. Padmanabhan, R. Watkins, K. L. Campbell, R. F. Xu, W. McGrath, P. 2017-03-06 doi:10.1101/114348 Cold Spring Harbor Laboratory Press 2017-03-06 <![CDATA[ Predicting clinical outcomes from large scale cancer genomic profiles with deep survival models ]]> https://biorxiv.org/content/10.1101/131367v1?rss=1 Yousefi, S. Amrollahi, F. Amgad, M. Dong, C. Lewis, J. E. Song, C. Gutman, D. A. Halani, S. H. Enrique Velazquez Vega, J. Brat, D. J. Cooper, L. A. 2017-04-27 doi:10.1101/131367 Cold Spring Harbor Laboratory Press 2017-04-27 <![CDATA[ Beyond Autoantibodies: Biological Roles Of Human Autoreactive B Cells In Rheumatoid Arthritis Revealed By Whole Transcriptome Profiling ]]> https://biorxiv.org/content/10.1101/144121v1?rss=1 Mahendra, A. Yang, X. Abnouf, S. Park, D. Soomro, S. Adolacion, J. R. T. Roszik, J. Coarfa, C. Romain, G. Wanzeck, K. Bridges, S. L. Aggarwal, A. Qiu, P. Agarwal, S. K. Mohan, C. Varadarajan, N. 2017-06-01 doi:10.1101/144121 Cold Spring Harbor Laboratory Press 2017-06-01 <![CDATA[ The Genomic Health Of Ancient Hominins ]]> https://biorxiv.org/content/10.1101/145193v1?rss=1 Berens, A. J. Cooper, T. L. Lachance, J. 2017-06-02 doi:10.1101/145193 Cold Spring Harbor Laboratory Press 2017-06-02 <![CDATA[ Widespread signatures of negative selection in the genetic architecture of human complex traits ]]> https://biorxiv.org/content/10.1101/145755v1?rss=1 Zeng, J. de Vlaming, R. Wu, Y. Robinson, M. Lloyd-Jones, L. Yengo, L. Yap, C. Xue, A. Sidorenko, J. McRae, A. Powell, J. Montgomery, G. Metspalu, A. Esko, T. Gibson, G. Wray, N. Visscher, P. Yang, J. 2017-06-03 doi:10.1101/145755 Cold Spring Harbor Laboratory Press 2017-06-03 <![CDATA[ Inferring single-trial neural population dynamics using sequential auto-encoders ]]> https://biorxiv.org/content/10.1101/152884v1?rss=1 Pandarinath, C. O'Shea, D. J. Collins, J. Jozefowicz, R. Stavisky, S. D. Kao, J. C. Trautmann, E. M. Kaufman, M. T. Ryu, S. I. Hochberg, L. R. Henderson, J. M. Shenoy, K. V. Abbott, L. F. Sussillo, D. 2017-06-20 doi:10.1101/152884 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Synthesizing developmental trajectories ]]> https://biorxiv.org/content/10.1101/157834v1?rss=1 Villoutreix, P. Anden, J. Lim, B. Lu, H. Kevrekidis, I. G. Singer, A. Shvartsman, S. Y. 2017-06-30 doi:10.1101/157834 Cold Spring Harbor Laboratory Press 2017-06-30 <![CDATA[ Sensory noise increases metacognitive efficiency ]]> https://biorxiv.org/content/10.1101/189399v1?rss=1 Bang, J. W. Shekhar, M. Rahnev, D. 2017-09-15 doi:10.1101/189399 Cold Spring Harbor Laboratory Press 2017-09-15 <![CDATA[ Experimental warming reduces the diversity and functional potential of the Sphagnum microbiome ]]> https://biorxiv.org/content/10.1101/194761v1?rss=1 Carrell, A. A. Kolton, M. Warren, M. J. Pelletier, D. A. Glass, J. B. Kostka, J. E. Hanson, P. J. Weston, D. J. 2017-09-29 doi:10.1101/194761 Cold Spring Harbor Laboratory Press 2017-09-29 <![CDATA[ Ascertainment bias can create the illusion of genetic health disparities ]]> https://biorxiv.org/content/10.1101/195768v1?rss=1 Kim, M. S. Patel, K. P. Teng, A. K. Berens, A. J. Lachance, J. 2017-09-28 doi:10.1101/195768 Cold Spring Harbor Laboratory Press 2017-09-28 <![CDATA[ Structural brain architectures match intrinsic functional networks and vary across domains: A study from 15000+ individuals ]]> https://biorxiv.org/content/10.1101/2019.12.17.879502v1?rss=1 Luo, N. SUI, J. Abrol, A. Turner, J. A. Damaraju, E. Fu, Z. Fan, L. Chen, J. Lin, D. Zhuo, C. Xu, Y. Glahn, D. C. Rodrigue, A. L. Banich, M. T. Pearlson, G. D. Calhoun, V. D. 2019-12-19 doi:10.1101/2019.12.17.879502 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system ]]> https://biorxiv.org/content/10.1101/2019.12.18.880807v1?rss=1 50% completion, < 10% redundancy), generated nearly four-fold more phage genomes, and improved all associated genome metrics relative to the Illumina only method. The hybrid assemblies yielded MAGs that were on average 7.8% more complete, with 133 fewer contigs and a 14 kbp greater N50. Furthermore, the longer contigs from the hybrid approach generated microbial MAGs that had a higher proportion of rRNA genes. We demonstrate this usefulness by linking microbial MAGs containing 16S rRNA genes with extensive amplicon dataset. This work provides quantitative data to inform a cost-benefit analysis on the decision to supplement shotgun metagenomic projects with long reads towards the goal of recovering genomes from environmentally abundant groups. ]]> Overholt, W. A. Hölzer, M. A. Geesink, P. Diezel, C. Marz, M. Küsel, K. 2019-12-19 doi:10.1101/2019.12.18.880807 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Emergent biases in compensatory mutation can drive gene regulatory network evolution ]]> https://biorxiv.org/content/10.1101/2019.12.18.881276v1?rss=1 Wang, Y. Richards, M. Dorus, S. Priest, N. K. Bryson, J. J. 2019-12-19 doi:10.1101/2019.12.18.881276 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Becoming a better parent: mice learn sounds that improve a stereotyped maternal behavior ]]> https://biorxiv.org/content/10.1101/2019.12.19.883041v1?rss=1 Dunlap, A. G. Besosa, C. Pascual, L. M. Chong, K. K. Walum, H. Kacsoh, D. B. Tankeu, B. B. Lu, K. Liu, R. C. 2019-12-20 doi:10.1101/2019.12.19.883041 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Material-Driven Fibronectin Assembly Rescues Matrix Defects due to Mutations in Collagen IV in Fibroblasts ]]> https://biorxiv.org/content/10.1101/2020.01.06.895839v1?rss=1 Mpoyi, E. N. Cantini, M. Sin, Y. Y. Fleming, L. Zhou, D. W. Costell, M. Lu, Y. Kadler, K. Garcia, A. J. Van Agtmael, T. Salmeron-Sanchez, M. 2020-01-06 doi:10.1101/2020.01.06.895839 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ Sexually dimorphic responses to MPTP found in microglia, inflammation and gut microbiota in a progressive monkey model of Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2020.01.30.925883v1?rss=1 Joers, V. Masilamoni, G. Kempf, D. J. Weiss, A. R. Rotterman, T. Murray, B. Yalcin-Cakmakli, G. Voll, R. Goodman, M. M. Howell, L. Bachevalier, J. Green, S. Naqib, A. Shaikh, M. Engen, P. Keshavarzian, A. Barnum, C. J. Nye, J. A. Smith, Y. Tansey, M. G. 2020-01-31 doi:10.1101/2020.01.30.925883 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ aNy-way Independent Component Analysis ]]> https://biorxiv.org/content/10.1101/2020.02.03.930156v1?rss=1 Duan, K. Silva, R. F. Calhoun, V. D. Liu, J. 2020-02-03 doi:10.1101/2020.02.03.930156 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ Low bias DNA for sustainable and efficient data storage ]]> https://biorxiv.org/content/10.1101/2020.02.09.940411v1?rss=1 Gao, Y. Chen, X. Hao, J. Zhang, C. Qiao, H. Qi, H. 2020-02-10 doi:10.1101/2020.02.09.940411 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ Distinct representations of finger movement and force in human motor and premotor cortices ]]> https://biorxiv.org/content/10.1101/2020.02.18.952945v1?rss=1 Flint, R. D. Tate, M. C. Li, K. Templer, J. W. Rosenow, J. M. Pandarinath, C. Slutzky, M. W. 2020-02-19 doi:10.1101/2020.02.18.952945 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Neuroimaging-based Individualized Prediction of Cognition and Behavior for Mental Disorders and Health: Methods and Promises ]]> https://biorxiv.org/content/10.1101/2020.02.22.961136v1?rss=1 SUI, J. Jiang, R. Bustillo, J. Calhoun, V. D. 2020-02-25 doi:10.1101/2020.02.22.961136 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Effects of Controlled Dual Growth Factor Delivery on Bone Regeneration Following Composite Bone-Muscle Injury ]]> https://biorxiv.org/content/10.1101/2020.03.25.008813v1?rss=1 90%, revealing a strong affinity of VEGF and BMP-2 to heparin and alginate. The system could achieve simultaneous or sequential release of VEGF and BMP-2 by varying the loading strategy. Single growth factor delivery (VEGF or BMP-2 alone) significantly enhanced vascular growth in vitro. However, no synergistic effect was observed for dual growth factor (BMP-2 + VEGF) delivery. Effective bone healing was achieved in all treatment groups (BMP-2, simultaneous or sequential delivery of BMP-2 and VEGF) in the composite injury model. The mechanics of the regenerated bone reached a maximum strength of [~]52% of intact bone with sequential delivery of VEGF and BMP-2. Overall, simultaneous or sequential co-delivery of low-dose BMP-2 and VEGF failed to fully restore the mechanics of bone in this injury model. Given the severity of the composite injury, VEGF alone may not be sufficient to establish mature and stable blood vessels when compared with previous studies co-delivering BMP-2+VEGF enhanced bone tissue regeneration. Hence, future studies are warranted to develop an alternative treatment strategy focusing on better control over growth factor dose, spatiotemporal delivery, and additional growth factors to regenerate fully functional bone tissue. HighlightsO_LIWe developed a smart growth factor delivery system using heparin microparticles and alginate that facilitates tunable delivery of VEGF and BMP-2 in a simultaneous or sequential manner by merely varying the loading strategy. C_LIO_LIIn vitro, both VEGF and BMP-2 alone promoted vascular growth; however, VEGF was significantly more potent, and there was no detectable benefit of co-delivery. C_LIO_LIIn vivo, both BMP-2 alone and co-delivery of VEGF and BMP-2 promoted bone formation in the challenging bone/muscle polytrauma model; however, none of the treatment groups restored biomechanical properties to that of uninjured bone. C_LI ]]> Subbiah, R. Cheng, A. Ruehle, M. A. Hettiaratchi, M. H. Bertassoni, L. E. Guldberg, R. E. 2020-03-26 doi:10.1101/2020.03.25.008813 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ Hype versus hope: Deep learning encodes more predictive and robust brain imaging representations than standard machine learning ]]> https://biorxiv.org/content/10.1101/2020.04.14.041582v1?rss=1 Abrol, A. Fu, Z. Salman, M. Silva, R. Du, Y. Plis, S. Calhoun, V. 2020-04-16 doi:10.1101/2020.04.14.041582 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Spatiotemporal functional interactivity among large-scale brain networks ]]> https://biorxiv.org/content/10.1101/2020.04.14.041830v1?rss=1 Xu, N. Doerschuk, P. C. Keilholz, S. D. Spreng, R. N. 2020-04-16 doi:10.1101/2020.04.14.041830 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Virulent disease epidemics can increase host density by depressing foraging of hosts ]]> https://biorxiv.org/content/10.1101/2020.07.06.189878v1?rss=1 Penczykowski, R. M. Hall, S. R. Shocket, M. S. Housley Ochs, J. Lemanski, B. C. P. Sundar, H. Duffy, M. A. 2020-07-06 doi:10.1101/2020.07.06.189878 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Sparse parallel independent component analysis and its application to identify linked genomic and gray matter alterations underlying working memory impairment in attention-deficit/hyperactivity disorder ]]> https://biorxiv.org/content/10.1101/2020.07.11.198622v1?rss=1 Kuaikuai Duan Jiayu Chen Vince D. Calhoun Wenhao Jiang Kelly Rootes-Murdy Gido Schoenmacker Rogers F. Silva Barbara Franke Jan K. Buitelaar Martine Hoogman Jaap Oosterlaan Pieter J Hoekstra Dirk Heslenfeld Catharina A Hartman Emma Sprooten Alejandro Arias-Vasquez Jessica A. Turner Jingyu Liu 2020-07-12 doi:10.1101/2020.07.11.198622 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ Modular and state-relevant connectivity in high-frequency resting-state BOLD fMRI data: An independent component analysis ]]> https://biorxiv.org/content/10.1101/2020.07.22.212720v1?rss=1 EC) at frequency bins greater than 0.46 Hz, particularly within visual regions. While the effect sizes range from small to large specific to frequency range and resting state (EO vs. EC), with little influence from common artifacts. These differences indicate that unique information can be derived from FNC between BOLD signals at different frequencies relative to a given restingstate acquisition and support the hypothesis meaningful BOLD signal is present at higher frequency ranges. ]]> DeRamus, T. P. Faghiri, A. Iraji, A. Agcaoglu, O. Vergara, V. M. Fu, Z. Silva, R. F. Gazula, H. Stephen, J. M. Wilson, T. W. Wang, Y.-P. Calhoun, V. 2020-07-24 doi:10.1101/2020.07.22.212720 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Detection of Prenatal Alcohol Exposure Using Machine Learning Classification of Resting-State Functional Network Connectivity Data ]]> https://biorxiv.org/content/10.1101/2020.08.14.231357v1?rss=1 Rodriguez, C. Vergara, V. Davies, S. Calhoun, V. Savage, D. Hamilton, D. 2020-08-15 doi:10.1101/2020.08.14.231357 Cold Spring Harbor Laboratory Press 2020-08-15 <![CDATA[ Perspectives on the design and performance of upper-limb wearable stimulation devices for stroke survivors with hemiplegia and spasticity ]]> https://biorxiv.org/content/10.1101/2020.08.20.260000v1?rss=1 Seim, C. E. Ritter, B. Starner, T. E. Flavin, K. Lansberg, M. G. Okamura, A. M. 2020-08-22 doi:10.1101/2020.08.20.260000 Cold Spring Harbor Laboratory Press 2020-08-22 <![CDATA[ Tuning of self-renewing capacity in theArabidopsis stomatal lineage by hormonaland nutrition regulation of asymmetric celldivisions ]]> https://biorxiv.org/content/10.1101/2020.09.16.300830v1?rss=1 Gong, Y. Alassimone, J. Varnau, R. Sharma, N. Cheung, L. S. Bergmann, D. C. 2020-09-17 doi:10.1101/2020.09.16.300830 Cold Spring Harbor Laboratory Press 2020-09-17 <![CDATA[ Tractography dissection variability: what happens when 42 groups dissect 14 white matter bundles on the same dataset? ]]> https://biorxiv.org/content/10.1101/2020.10.07.321083v1?rss=1 Schilling, K. G. Rheault, F. Petit, L. Hansen, C. B. Nath, V. Yeh, F.-C. Girard, G. Barakovic, M. Rafael-Patino, J. Yu, T. Fischi-Gomez, E. Pizzolato, M. Ocampo-Pineda, M. Schiavi, S. Canales-Rodriguez, E. J. Daducci, A. Granziera, C. Innocenti, G. Thiran, J.-P. Mancini, L. Wastling, S. Cocozza, S. Petracca, M. Pontillo, G. Mancini, M. Vos, S. B. Vakharia, V. N. Duncan, J. S. Melero, H. Manzanedo, L. Sanz-Morales, E. Pena-Melian, A. Calamante, F. Attye, A. Cabeen, R. P. Korobova, L. Toga, A. W. Ambili Vijayakumari, A. Parker, D. Verma, R. Radwan, A. Sun 2020-10-08 doi:10.1101/2020.10.07.321083 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Cortical beta oscillatory activity evoked during reactive balance recovery scales with perturbation difficulty and individual balance ability ]]> https://biorxiv.org/content/10.1101/2020.10.07.330381v1?rss=1 Ghosn, N. J. Palmer, J. A. Borich, M. R. Ting, L. H. Payne, A. M. 2020-10-09 doi:10.1101/2020.10.07.330381 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Enriching neural stem cell and pro-healing glial phenotypes with electrical stimulation after traumatic brain injury in male rats ]]> https://biorxiv.org/content/10.1101/2020.11.07.372979v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@1bdc466org.highwire.dtl.DTLVardef@1a912c4org.highwire.dtl.DTLVardef@10f269dorg.highwire.dtl.DTLVardef@1b02487_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFIGURE 1.C_FLOATNO C_FIG ]]> Park, E. Lyon, J. G. Alvarado-Velez, M. Betancur, M. I. Mokarram, N. Shin, J. H. Bellamkonda, R. V. 2020-11-08 doi:10.1101/2020.11.07.372979 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ Multilevel Twin Models: Geographical Region as a Third Level Variable ]]> https://biorxiv.org/content/10.1101/2020.11.11.377820v1?rss=1 Tamimy, Z. Kevenaar, S. T. Hottenga, J. J. Hunter, M. D. de Zeeuw, E. L. Neale, M. C. van Beijsterveldt, C. E. M. Dolan, C. V. van Bergen, E. Boomsma, D. I. 2020-11-12 doi:10.1101/2020.11.11.377820 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Representations of local spatial information in the human medial temporal lobe duringmemory-guided navigation ]]> https://biorxiv.org/content/10.1101/2020.11.18.389346v1?rss=1 Wang, S.-F. Carr, V. A. Favila, S. E. Bailenson, J. N. Brown, T. I. Jiang, J. Wagner, A. D. 2020-11-19 doi:10.1101/2020.11.18.389346 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ Establishment of Multi-stage Models of Drug Taking and Seeking in Mice ]]> https://biorxiv.org/content/10.1101/2020.11.25.398503v1?rss=1 Slosky, L. M. Pires, A. Bai, Y. Clark, N. Hauser, E. R. Gross, J. D. Porkka, F. Pogorelov, V. M. Toth, K. Wetsel, W. C. Barak, L. S. Caron, M. G. 2020-11-27 doi:10.1101/2020.11.25.398503 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ A Tunable, Simplified Model for Biological Latch Mediated Spring Actuated Systems ]]> https://biorxiv.org/content/10.1101/2020.12.02.408740v1?rss=1 Cook, A. Pandhigunta, K. Acevedo, M. A. Walker, A. Didcock, R. L. Castro, J. T. Acharya, R. Bhamla, M. S. Anderson, P. S. L. Ilton, M. 2020-12-03 doi:10.1101/2020.12.02.408740 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Building Models of Functional Interactions Among Brain Domains that Encode Varying Information Complexity: A Schizophrenia Case Study ]]> https://biorxiv.org/content/10.1101/2020.12.10.420208v1?rss=1 Batta, I. Abrol, A. Fu, Z. Preda, A. van Erp, T. G. M. Calhoun, V. 2020-12-11 doi:10.1101/2020.12.10.420208 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Competition between bridged dinucleotides and activated mononucleotides determines the error frequency of nonenzymatic RNA primer extension ]]> https://biorxiv.org/content/10.1101/2021.01.02.425068v1?rss=1 Duzdevich, D. Carr, C. E. Ding, D. Zhang, S. J. Walton, T. S. Szostak, J. W. 2021-01-04 doi:10.1101/2021.01.02.425068 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Multi-Spatial Scale Dynamic Interactions between Functional Sources Reveal Sex-Specific Changes in Schizophrenia ]]> https://biorxiv.org/content/10.1101/2021.01.04.425222v1?rss=1 Iraji, A. Faghiri, A. Fu, Z. Rachakonda, S. Kochunov, P. Belger, A. Ford, J. McEwen, S. Mathalon, D. Mueller, B. Pearlson, G. D. Potkin, S. G. Preda, A. Turner, J. Van Erp, T. Calhoun, V. 2021-01-05 doi:10.1101/2021.01.04.425222 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ The Amot/Integrin protein complex transmits mechanical forces required for vascular expansion ]]> https://biorxiv.org/content/10.1101/2021.01.14.426638v1?rss=1 Zhang, Y. Zhang, Y. Kameishi, S. Barutello, G. Zheng, Y. Tobin, N. P. Nicosia, J. Hennig, K. Chiu, D. K.-C. Balland, M. Barker, T. H. Cavallo, F. Holmgren, L. 2021-01-14 doi:10.1101/2021.01.14.426638 Cold Spring Harbor Laboratory Press 2021-01-14 <![CDATA[ Characterization of Poldip2 knockout mice: avoiding incorrect gene targeting ]]> https://biorxiv.org/content/10.1101/2021.02.02.429447v1?rss=1 Lassegue, B. Kumar, S. Mandavilli, R. Wang, K. Tzai, M. Kang, D.-W. Hernandes, M. S. San Martin, A. Jo, H. Taylor, W. R. Griendling, K. K. 2021-02-03 doi:10.1101/2021.02.02.429447 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Bayesian analysis of source tracking markers to estimate the effects of an urban sanitation intervention on human fecal contamination in Mozambique ]]> https://biorxiv.org/content/10.1101/2021.02.19.432000v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@312d2dorg.highwire.dtl.DTLVardef@8cf2caorg.highwire.dtl.DTLVardef@197b549org.highwire.dtl.DTLVardef@fefeb3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Holcomb, D. A. Knee, J. Capone, D. Sumner, T. Adriano, Z. Nala, R. Cumming, O. Brown, J. Stewart, J. R. 2021-02-19 doi:10.1101/2021.02.19.432000 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Multi-Modality Machine Learning Predicting Parkinsons Disease ]]> https://biorxiv.org/content/10.1101/2021.03.05.434104v1?rss=1 Makarious, M. B. Leonard, H. L. Vitale, D. Iwaki, H. Sargent, L. Dadu, A. Violich, I. Hutchins, E. Saffo, D. Bandres-Ciga, S. Kim, J. J. Song, Y. Bookman, M. Nojopranoto, W. Campbell, R. H. Hashemi, S. H. Botia, J. A. Carter, J. F. Maleknia, M. Craig, D. W. Keuren-Jensen, K. V. Morris, H. R. Hardy, J. A. Blauwendraat, C. Singleton, A. B. Faghri, F. Nalls, M. A. Accelerating Medicines Program - Parkinsons Disease (AMP PD), Global Parkinsons Genetics Program (GP2), 2021-03-07 doi:10.1101/2021.03.05.434104 Cold Spring Harbor Laboratory Press 2021-03-07 <![CDATA[ Individualized Spatial Network Predictions Using Siamese Convolutional Neural Networks: A Resting-State fMRI Study of over 11,000 Unaffected Individuals ]]> https://biorxiv.org/content/10.1101/2021.03.22.436403v1?rss=1 Hassanzadeh, R. Silva, R. F. Abrol, A. Salman, M. Bonkhoff, A. Du, Y. Fu, Z. DeRamus, T. Damaraju, E. Baker, B. Calhoun, V. D. 2021-03-22 doi:10.1101/2021.03.22.436403 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Ancient DNA reveals that few GWAS loci have been strongly selected during recent human history ]]> https://biorxiv.org/content/10.1101/2021.04.13.439742v1?rss=1 0.001), including multiple variants that are introgressed from Neanderthals. However, only nine disease-associated variants show a signature of strong selection (|s| > 0.01). Additionally, we find that many risk-associated alleles have increased in frequency during the past 10,000 years. Overall, we find that disease-associated variants from GWAS are governed by nearly neutral evolution. Exceptions to this broad pattern include GWAS loci that protect against asthma and variants in MHC genes. Ancient samples allow us an unprecedented look at how our species has changed over time, and our results represent an important early step in using this new source of data to better understand the evolution of hereditary disease risks. ]]> Simonti, C. N. Lachance, J. 2021-04-14 doi:10.1101/2021.04.13.439742 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Distinct developmental mechanisms influence sexual dimorphisms in the milkweed bug Oncopeltus fasciatus ]]> https://biorxiv.org/content/10.1101/2021.05.12.443917v1?rss=1 Just, J. Laslo, M. Lee, Y. J. Yarnell, M. C. Zhang, Z. Angelini, D. R. 2021-05-14 doi:10.1101/2021.05.12.443917 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ Multiframe Evolving Dynamic Functional Connectivity (EVOdFNCs): A Method for Constructing and Investigating Functional Brain Motifs ]]> https://biorxiv.org/content/10.1101/2021.05.18.444678v1?rss=1 Miller, R. L. Vergara, V. M. Pearlson, G. D. Calhoun, V. D. 2021-05-20 doi:10.1101/2021.05.18.444678 Cold Spring Harbor Laboratory Press 2021-05-20 <![CDATA[ A METHOD FOR INTEGRATIVE ANALYSIS OF LOCAL AND GLOBAL BRAIN DYNAMICS ]]> https://biorxiv.org/content/10.1101/2021.05.18.444698v1?rss=1 Miller, R. L. Vergara, V. M. Calhoun, V. 2021-05-20 doi:10.1101/2021.05.18.444698 Cold Spring Harbor Laboratory Press 2021-05-20 <![CDATA[ Kinetic Monitoring Of Neuronal Stress Response To Proteostasis Dysfunction ]]> https://biorxiv.org/content/10.1101/2021.05.24.445437v1?rss=1 Santiago-Lopez, A. J. Berglund, K. Gross, R. E. Gutekunst, C.-A. N. 2021-05-24 doi:10.1101/2021.05.24.445437 Cold Spring Harbor Laboratory Press 2021-05-24 <![CDATA[ Brain charts for the human lifespan ]]> https://biorxiv.org/content/10.1101/2021.06.08.447489v1?rss=1 Bethlehem, R. A. I. Seidlitz, J. White, S. R. Vogel, J. W. Anderson, K. M. Adamson, C. Adler, S. Alexopoulos, G. S. Anagnostou, E. Areces-Gonzalez, A. Astle, D. E. Auyeung, B. Ayub, M. Ball, G. Baron-Cohen, S. Beare, R. Bedford, S. A. Benegal, V. Beyer, F. Bin Bae, J. Blangero, J. Blesa Cabez, M. Boardman, J. P. Borzage, M. Bosch-Bayard, J. F. Bourke, N. Calhoun, V. D. Chakravarty, M. M. Chen, C. Chertavian, C. Chetelat, G. Chong, Y. S. Cole, J. H. Corvin, A. Courchesne, E. Crivello, F. Cropley, V. L. Crosbie, J. Crossley, N. Delarue, M. Desrivieres, S. 2021-06-10 doi:10.1101/2021.06.08.447489 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Integrative genomic and epigenomic analyses identified IRAK1 as a novel target for chronic inflammation-driven prostate tumorigenesis ]]> https://biorxiv.org/content/10.1101/2021.06.16.447920v1?rss=1 Oseni, S. O. Adebayo, O. Adebayo, A. Kwakye, A. Pavlovic, M. Asghar, W. Hartmann, J. Kumi-Diaka, J. 2021-06-16 doi:10.1101/2021.06.16.447920 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ Moving Beyond the 'CAP' of the Iceberg: Intrinsic Connectivity Networks in fMRI are Continuously Engaging and Overlapping ]]> https://biorxiv.org/content/10.1101/2021.06.23.449485v1?rss=1 Iraji, A. Faghiri, A. Fu, Z. Kochunov, P. Adhikari, B. M. Belger, A. Ford, J. M. McEwen, S. Mathalon, D. H. Pearlson, G. D. Potkin, S. G. Preda, A. Turner, J. A. Van Erp, T. G. M. Chang, C. Calhoun, V. D. 2021-06-24 doi:10.1101/2021.06.23.449485 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ A community-based approach to image analysis of cells, tissues and tumors ]]> https://biorxiv.org/content/10.1101/2021.07.22.451363v1?rss=1 CSBC/PS-ON Image Analysis Working Group, Vizcarra, J. C. Burlingame, E. A. Hug, C. B. Goltsev, Y. White, B. S. Tyson, D. R. Sokolov, A. 2021-07-25 doi:10.1101/2021.07.22.451363 Cold Spring Harbor Laboratory Press 2021-07-25 <![CDATA[ Transcriptomic-based quantification of the epithelial-hybrid-mesenchymal spectrum across biological contexts ]]> https://biorxiv.org/content/10.1101/2021.09.09.458982v1?rss=1 Mandal, S. Tejaswi, T. Janivara, R. Srikrishnan, S. Thakur, P. Sahoo, S. Chakraborty, P. Sohal, S. S. Levine, H. George, J. T. Jolly, M. K. 2021-09-10 doi:10.1101/2021.09.09.458982 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ Differential patterns of change in brain connectivity resulting from traumatic brain injury ]]> https://biorxiv.org/content/10.1101/2021.10.27.466136v1?rss=1 Nakuci, J. McGuire, M. Schweser, F. Poulsen, D. Muldoon, S. F. 2021-10-28 doi:10.1101/2021.10.27.466136 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Consequences of endogenous and virally-induced hyperphosphorylated tau on behavior and cognition in a rat model of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2021.10.30.466530v1?rss=1 Kelberman, M. A. Anderson, C. R. Chlan, E. Rorabaugh, J. M. McCann, K. E. Weinshenker, D. 2021-11-02 doi:10.1101/2021.10.30.466530 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ USPNet: unbiased organism-agnostic signal peptidepredictor with deep protein language model ]]> https://biorxiv.org/content/10.1101/2021.11.04.467361v1?rss=1 Chen, S. Tan, Q. Li, J. Li, Y. 2021-11-05 doi:10.1101/2021.11.04.467361 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ Strict adherence to Mendel's First Law across a large sample of human sperm genomes ]]> https://biorxiv.org/content/10.1101/2021.11.19.469261v1?rss=1 Carioscia, S. A. Weaver, K. J. Bortvin, A. N. Ariad, D. Bell, A. D. McCoy, R. C. 2021-11-20 doi:10.1101/2021.11.19.469261 Cold Spring Harbor Laboratory Press 2021-11-20 <![CDATA[ Estimating muscle activation from EMG using deep learning-based dynamical systems models ]]> https://biorxiv.org/content/10.1101/2021.12.01.470827v1?rss=1 Wimalasena, L. N. Braun, J. F. Keshtkaran, M. R. Hofmann, D. Gallego, J. A. Alessandro, C. Tresch, M. C. Miller, L. E. Pandarinath, C. 2021-12-03 doi:10.1101/2021.12.01.470827 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ Learning Active Multimodal Subspaces in the Brain ]]> https://biorxiv.org/content/10.1101/2021.12.06.471396v1?rss=1 Batta, I. Abrol, A. Fu, Z. Calhoun, V. 2021-12-07 doi:10.1101/2021.12.06.471396 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Pervasive conditional selection of driver mutations and modular epistasis networks in cancer ]]> https://biorxiv.org/content/10.1101/2022.01.10.475617v1?rss=1 2 drivers. Conditionally co-selected genes form modular networks, whose structures challenge the traditional interpretation of within-pathway mutual exclusivity and across-pathway synergy, suggesting a more complex scenario, where gene-specific across-pathway epistasis shapes differentiated cancer subtypes. ]]> Iranzo, J. Gruenhagen, G. Calle-Espinosa, J. Koonin, E. V. 2022-01-11 doi:10.1101/2022.01.10.475617 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ A whole-cell recording database of neuromodulatory action in the adult neocortex ]]> https://biorxiv.org/content/10.1101/2022.01.12.476007v1?rss=1 Yan, X. Calcini, N. Safavi, P. Ak, A. Kole, K. Zeldenrust, F. Celikel, T. 2022-01-13 doi:10.1101/2022.01.12.476007 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ Caenorhabditis nematodes colonize ephemeral resource patches in neotropical forests. ]]> https://biorxiv.org/content/10.1101/2022.01.13.476254v1?rss=1 Sloat, S. A. Noble, L. M. Paaby, A. B. Bernstein, M. Chang, A. Kaur, T. Yuen, J. Tintori, S. C. Jackson, J. L. Martel, A. Salome Correa, J. A. Stevens, L. Blaxter, M. Rockman, M. V. 2022-01-15 doi:10.1101/2022.01.13.476254 Cold Spring Harbor Laboratory Press 2022-01-15 <![CDATA[ Federated analysis in COINSTAC reveals functional network connectivity and spectral links to smoking and alcohol consumption in nearly 2,000 adolescent brains ]]> https://biorxiv.org/content/10.1101/2022.02.02.478847v1?rss=1 Gazula, H. Rootes-Murdy, K. Holla, B. Basodi, S. Zhang, Z. Verner, E. Kelly, R. Murthy, P. Chakrabarti, A. Basu, D. Bhagyalakshmi, S. Lenin, R. Lourembam, R. Kalyanram, K. Kartik, K. Kalyanaraman, K. Ghattu, K. Kuriyan, R. Kurpad, S. S. Barker, G. Bharath, R. D. Desrivieres, S. Purushottam, M. Orfanos, D. P. Sharma, E. Hickman, M. Toledano, M. Vaidya, N. Banaschewski, T. Bokde, A. L. W. Flor, H. Grigis, A. Garavan, H. Gowland, P. Heinz, A. Bruhl, R. Martinot, J.-L. Martinot, M.-L. P. Artiges, E. Nees, F. Paus, T. Poustka, L. Frohner, J. H. Robinson, L 2022-02-04 doi:10.1101/2022.02.02.478847 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Quantitative fate mapping: Reconstructing progenitor field dynamics via retrospective lineage barcoding ]]> https://biorxiv.org/content/10.1101/2022.02.13.480215v1?rss=1 Fang, W. Bell, C. M. Sapirstein, A. Asami, S. Leeper, K. Zack, D. J. Ji, H. Kalhor, R. 2022-02-14 doi:10.1101/2022.02.13.480215 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Aging-regulated TUG1 is dispensable for endothelial cell function ]]> https://biorxiv.org/content/10.1101/2022.02.27.482212v1?rss=1 Gimbel, A. T. Koziarek, S. Theodorou, K. Schulz, J. F. Stanicek, L. Ali, T. Günther, S. Kumar, S. Jo, H. Hübner, N. Maegdefessel, L. Dimmeler, S. van Heesch, S. Boon, R. A. 2022-02-28 doi:10.1101/2022.02.27.482212 Cold Spring Harbor Laboratory Press 2022-02-28 <![CDATA[ Unbreakable DNA tension probes show that cell adhesion receptors detect the molecular force-extension curve of their ligands ]]> https://biorxiv.org/content/10.1101/2022.04.04.487040v1?rss=1 Bender, R. L. Ogasawara, H. Kellner, A. V. Velusamy, A. Salaita, K. 2022-04-04 doi:10.1101/2022.04.04.487040 Cold Spring Harbor Laboratory Press 2022-04-04 <![CDATA[ TITAN: A Toolbox for Information-Theoretic Analysis of Molecular Networks ]]> https://biorxiv.org/content/10.1101/2022.04.18.488630v1?rss=1 Bergmans, T. Celikel, T. 2022-04-18 doi:10.1101/2022.04.18.488630 Cold Spring Harbor Laboratory Press 2022-04-18 <![CDATA[ Defective subviral particles modify ecological equilibria and enhance viral coexistence ]]> https://biorxiv.org/content/10.1101/2022.05.03.490396v1?rss=1 Lucia-Sanz, A. Aguirre, J. Fraile, A. Garcia-Arenal, F. Manrubia, S. 2022-05-03 doi:10.1101/2022.05.03.490396 Cold Spring Harbor Laboratory Press 2022-05-03 <![CDATA[ USP11 promotes endothelial apoptosis-resistance in pulmonary hypertension by deubiquitinating HINT3 ]]> https://biorxiv.org/content/10.1101/2022.05.17.492159v1?rss=1 Jang, A. J. Tseng, V. Kim, J. S. Stearman, R. S. Zhao, Y. Zhao, J. Choi, J. Lister, J. Passineau, M. J. Lam, W. A. Park, C. Benza, R. L. Kang, B.-Y. 2022-05-19 doi:10.1101/2022.05.17.492159 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ PPARγ/ETV2 Axis Regulates Endothelial-to-Mesenchymal Transition in Pulmonary Hypertension ]]> https://biorxiv.org/content/10.1101/2022.05.17.492293v1?rss=1 Lee, D. H. Kim, M. Chang, S. S. Jang, A. J. Kim, J. Ma, J. Passineau, M. J. Benza, R. L. Karmouty-Quintana, H. Lam, W. A. Sutliff, R. L. Hart, C. M. Park, C. Kang, B.-Y. 2022-05-19 doi:10.1101/2022.05.17.492293 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Inhibition of Tgfβ signaling enables durable ventricular pacing by TBX18 gene transfer ]]> https://biorxiv.org/content/10.1101/2022.06.02.493572v1?rss=1 Fan, J. Kim, N. K. Fernandez, N. Kim, T. Y. Li, J. Wolfson, D. Cho, H. C. 2022-06-03 doi:10.1101/2022.06.02.493572 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Fine temporal brain network structure modularizes and localizes differently in men and women: Insights from a novel explainability framework ]]> https://biorxiv.org/content/10.1101/2022.06.09.495551v1?rss=1 Lewis, N. Miller, R. L. Gazula, H. Calhoun, V. 2022-06-12 doi:10.1101/2022.06.09.495551 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Mechanotransductive feedback control of endothelial cell motility and vascular morphogenesis ]]> https://biorxiv.org/content/10.1101/2022.06.15.496293v1?rss=1 Mason, D. E. Goeckel, M. Vega, S. L. Wu, P.-H. Johnson, D. Heo, S.-J. Wirtz, D. Burdick, J. A. Wood, L. Chow, B. Y. Stratman, A. N. Boerckel, J. D. 2022-06-16 doi:10.1101/2022.06.15.496293 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Intrinsic Neural Timescales in Autism Spectrum Disorder and Schizophrenia. A Replication and Direct Comparison Study ]]> https://biorxiv.org/content/10.1101/2022.06.26.497652v1?rss=1 Uscatescu, L. C. Kronbichler, M. Yuerekli, S. S. Kronbichler, L. Calhoun, V. Corbera, S. Bell, M. Pelphrey, K. Pearlson, G. Assaf, M. 2022-06-29 doi:10.1101/2022.06.26.497652 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Decoding Depression During Subcallosal Cingulate Deep Brain Stimulation ]]> https://biorxiv.org/content/10.1101/2022.07.27.501778v1?rss=1 Tiruvadi, V. Veerakumar, A. Smart, O. Crowell, A. Riva-Posse, P. Gross, R. E. McIntyre, C. C. Rozell, C. Butera, R. Mayberg, H. 2022-07-29 doi:10.1101/2022.07.27.501778 Cold Spring Harbor Laboratory Press 2022-07-29 <![CDATA[ SVR-based Multimodal Active Subspace Analysis for the Brain using Neuroimaging Data ]]> https://biorxiv.org/content/10.1101/2022.07.28.501879v1?rss=1 Batta, I. Abrol, A. Calhoun, V. 2022-08-01 doi:10.1101/2022.07.28.501879 Cold Spring Harbor Laboratory Press 2022-08-01 <![CDATA[ Canonical and Replicable Multi-Scale Intrinsic Connectivity Networks in 100k+ Resting-State fMRI Datasets ]]> https://biorxiv.org/content/10.1101/2022.09.03.506487v1?rss=1 Iraji, A. Fu, Z. Faghiri, A. Duda, M. Chen, J. Rachakonda, S. DeRamus, T. P. Kochunov, P. Adhikari, B. M. Belger, A. Ford, J. Mathalon, D. H. Pearlson, G. D. Potkin, S. G. Preda, A. Turner, J. A. Van Erp, T. G. M. Bustillo, J. R. Yang, K. Ishizuka, K. Sawa, A. Hutchison, K. Osuch, E. A. Theberge, J. Abbott, C. Mueller, B. A. Zhi, D. Zhuo, C. Liu, S. Xu, Y. Salman, M. Liu, J. Du, Y. SUI, J. Adali, T. Calhoun, V. 2022-09-05 doi:10.1101/2022.09.03.506487 Cold Spring Harbor Laboratory Press 2022-09-05 <![CDATA[ Motor and cognitive deficits limit the ability to flexibly modulate spatiotemporal gait features in older adults with mild cognitive impairment ]]> https://biorxiv.org/content/10.1101/2022.09.09.507368v1?rss=1 0.9) elicited the largest differences in gait performance in HYA vs. HOA and HOA vs. MCI, respectively. DiscussionThese findings suggest that age-related declines in strength and balance reduce the ability to accurately modulate spatial gait features, while declines in working memory in individuals with MCI may reduce the ability to perform longer temporal gait modification sequences. Differences in rhythmic movement sequence performance highlight motor and cognitive factors potentially underlying deficits in gait modulation capacity, which may guide therapy personalization and provide more sensitive indices to track intervention efficacy. ]]> Rosenberg, M. C. Slusarenko, A. Cao, K. McKay, J. L. Emmery, L. Kesar, T. M. Hackney, M. E. 2022-09-11 doi:10.1101/2022.09.09.507368 Cold Spring Harbor Laboratory Press 2022-09-11 <![CDATA[ Joint cmICA: auto-linking of structural and functional connectivity ]]> https://biorxiv.org/content/10.1101/2022.09.12.507415v1?rss=1 Wu, L. Calhoun, V. 2022-09-14 doi:10.1101/2022.09.12.507415 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ Interpretable machine learning with tree-based Shapley additive explanations: application to metabolomics datasets for binary classification ]]> https://biorxiv.org/content/10.1101/2022.09.19.508550v1?rss=1 Bifarin, O. O. 2022-09-19 doi:10.1101/2022.09.19.508550 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Multicolor Light-Induced Immune Activation via Polymer Photocaged Cytokines ]]> https://biorxiv.org/content/10.1101/2022.10.03.510638v1?rss=1 Birnbaum, L. A. Sullivan, E. C. Do, P. Uricoli, B. Porter, C. C. Henry, C. J. Dreaden, E. C. 2022-10-05 doi:10.1101/2022.10.03.510638 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Gating interactions steer loop conformational changes in the active site of the L1 metallo-β-lactamase ]]> https://biorxiv.org/content/10.1101/2022.10.25.513716v1?rss=1 Zhao, Z. Shen, X. Chen, S. Gu, J. Wang, H. Mojica, M. F. Samanta, M. Bhowmik, D. Vila, A. J. Bonomo, R. A. Haider, S. 2022-10-27 doi:10.1101/2022.10.25.513716 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Sequence-to-expression approach to identify etiological non-coding DNA variations in P53 and cMYC-driven diseases ]]> https://biorxiv.org/content/10.1101/2022.12.05.519089v1?rss=1 Kin, K. Bhogale, S. Zhu, L. Thomas, D. Bertol, J. Zheng, W. J. Sinha, S. Fakhouri, W. D. 2022-12-05 doi:10.1101/2022.12.05.519089 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ Bridging Big Data: Procedures for Combining Non-equivalent Cognitive Measures from the ENIGMA Consortium ]]> https://biorxiv.org/content/10.1101/2023.01.16.524331v1?rss=1 Kennedy, E. Vadlamani, S. Lindsey, H. M. Lei, P.-W. Pugh, M. J. Adamson, M. Alda, M. Alonso-Lana, S. Ambrogi, S. Anderson, T. J. Arango, C. Asarnow, R. Avram, M. Ayesa-Arriola, R. Babikian, T. Banaj, N. Bird, L. J. Borgwardt, S. Brodtmann, A. Brosch, K. Caeyenberghs, K. Calhoun, V. D. Chiaravalloti, N. D. Cifu, D. X. Crespo-Facorro, B. Dalrymple-Alford, J. C. Dams-O'Connor, K. Dannlowski, U. Darby, D. Davenport, N. DeLuca, J. Diaz-Caneja, C. M. Disner, S. G. Dobryakova, E. Ehrlich, S. Esopenko, C. Ferrarelli, F. Frank, L. E. Franz, C. Fuentes-Claramonte, 2023-01-19 doi:10.1101/2023.01.16.524331 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ A machine learning approach to quantify individual gait responses to ankle exoskeletons ]]> https://biorxiv.org/content/10.1101/2023.01.20.524757v1?rss=1 Ebers, M. R. Rosenberg, M. C. Kutz, J. N. Steele, K. M. 2023-01-21 doi:10.1101/2023.01.20.524757 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ Multimodal fusion of multiple rest fMRI networks and MRI gray matter via multilink joint ICA reveals highly significant function/structure coupling in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2023.02.28.530458v1?rss=1 Khalilullah, K. M. I. Agcaoglu, o. Sui, J. Adali, T. Duda, M. Calhoun, V. 2023-03-01 doi:10.1101/2023.02.28.530458 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Dual role of CASP8AP2/FLASH in regulating epithelial-to-mesenchymal (EMT) plasticity ]]> https://biorxiv.org/content/10.1101/2023.03.12.532282v1?rss=1 Catalanotto, M. Vaz, J. M. Abshire, C. Youngblood, R. Chu, M. Levine, H. Jolly, M. K. Dragoi, A.-M. 2023-03-12 doi:10.1101/2023.03.12.532282 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Decentralized Mixed Effects Modeling in COINSTAC ]]> https://biorxiv.org/content/10.1101/2023.05.12.540598v1?rss=1 Basodi, S. Raja, R. Gazula, H. Romero, J. T. Panta, S. Maullin-Sapey, T. J. Nichols, T. E. Calhoun, V. D. 2023-05-13 doi:10.1101/2023.05.12.540598 Cold Spring Harbor Laboratory Press 2023-05-13 <![CDATA[ Engineering a Functional small RNA Negative Autoregulation Network with Model-guided Design ]]> https://biorxiv.org/content/10.1101/227637v1?rss=1 Hu, C. Takahashi, M. Zhang, Y. Lucks, J. 2017-12-01 doi:10.1101/227637 Cold Spring Harbor Laboratory Press 2017-12-01 <![CDATA[ A role for Fibroblast Growth Factor Receptor 1 in the pathogenesis of Neisseria meningitidis ]]> https://biorxiv.org/content/10.1101/283028v1?rss=1 Wooldridge, K. Azimi, S. Wheldon, L. M. Oldfield, N. J. Ala'Aldeen, D. A. A. 2018-03-15 doi:10.1101/283028 Cold Spring Harbor Laboratory Press 2018-03-15 <![CDATA[ Laboratory evolution from social to solitary behavior in the N2 reference strain is unnecessary for its fitness advantages ]]> https://biorxiv.org/content/10.1101/309997v1?rss=1 Zhao, Y. Long, L. Xu, W. Campbell, R. F. Large, E. L. Greene, J. S. McGrath, P. T. 2018-04-30 doi:10.1101/309997 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Selection of horizontal gene transfer through public good production ]]> https://biorxiv.org/content/10.1101/315960v1?rss=1 Dimitriu, T. Misevic, D. Benard Capelle, J. Lindner, A. Brown, S. Taddei, F. 2018-05-07 doi:10.1101/315960 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ Decoding Selective Attention to Context Memory: An Aging Study ]]> https://biorxiv.org/content/10.1101/324384v1?rss=1 Powell, P. S. Strunk, J. James, T. Polyn, S. Duarte, A. 2018-05-16 doi:10.1101/324384 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Parallel multimodal circuits control an innate foraging behavior ]]> https://biorxiv.org/content/10.1101/326405v1?rss=1 Lopez-Cruz, A. Pokala, N. Sordillo, A. Flavell, S. W. McGrath, P. T. Bargmann, C. 2018-05-18 doi:10.1101/326405 Cold Spring Harbor Laboratory Press 2018-05-18 <![CDATA[ Closed-loop coupling of a muscle to a robotic device for dynamic assessment of muscle function ]]> https://biorxiv.org/content/10.1101/337303v1?rss=1 Sundar, K. Ting, L. Deweerth, S. P. 2018-06-02 doi:10.1101/337303 Cold Spring Harbor Laboratory Press 2018-06-02 <![CDATA[ Unilateral optogenetic inhibition and excitation of basal ganglia output show opposing effects on left/right lick choices and movement initiation in mice ]]> https://biorxiv.org/content/10.1101/360818v1?rss=1 Morrissette, A. Chen, P.-H. Bhamani, C. Borden, P. Y. Waiblinger, C. Stanley, G. B. Jaeger, D. 2018-07-02 doi:10.1101/360818 Cold Spring Harbor Laboratory Press 2018-07-02 <![CDATA[ Non-adhesive alginate hydrogels support growth of pluripotent stem cell-derived intestinal organoids ]]> https://biorxiv.org/content/10.1101/364885v1?rss=1 Capeling, M. M. Czerwinski, M. Huang, S. Tsai, Y.-H. Wu, A. Nagy, M. S. Juliar, B. Song, Y. Sundaram, N. Takayama, S. Alsberg, E. Helmrath, M. Putnam, A. J. Spence, J. R. 2018-07-08 doi:10.1101/364885 Cold Spring Harbor Laboratory Press 2018-07-08 <![CDATA[ The Genomic Basis of Arthropod Diversity ]]> https://biorxiv.org/content/10.1101/382945v1?rss=1 Thomas, G. W. C. Dohmen, E. Hughes, D. S. T. Murali, S. C. Poelchau, M. Glastad, K. Anstead, C. A. Ayoub, N. A. Batterham, P. Bellair, M. Binford, G. J. Chao, H. Chen, Y. H. Childers, C. Dinh, H. Doddapaneni, H. Duan, J. J. Dugan, S. Esposito, L. A. Friedrich, M. Garb, J. Gasser, R. B. B. Goodisman, M. A. D. Gundersen-Rindal, D. E. Han, Y. Handler, A. M. Hatakeyama, M. Hering, L. Hunter, W. B. Ioannidis, P. Jayaseelan, J. C. Kalra, D. Khila, A. Korhonen, P. K. Lee, C. E. Lee, S. L. Li, Y. Lindsey, A. R. I. Mayer, G. McGregor, A. P. McKenna, D. D. Misof, 2018-08-04 doi:10.1101/382945 Cold Spring Harbor Laboratory Press 2018-08-04 <![CDATA[ Human genome-edited hematopoietic stem cells phenotypically correct Mucopolysaccharidosis type I ]]> https://biorxiv.org/content/10.1101/408757v1?rss=1 Gomez-Ospina, N. Scharenberg, S. G. Mostrel, N. Bak, R. O. Mantri, S. Quadros, R. M. Gurumurthy, C. B. Lee, C. Bao, G. Aurelian, L. Porteus, M. 2018-09-04 doi:10.1101/408757 Cold Spring Harbor Laboratory Press 2018-09-04 <![CDATA[ The effect of X-linked dosage compensation on complex trait variation ]]> https://biorxiv.org/content/10.1101/433870v1?rss=1 Sidorenko, J. Kassam, I. Kemper, K. Zeng, J. Lloyd-Jones, L. Montgomery, G. W. Gibson, G. Metspalu, A. Esko, T. Yang, J. McRae, A. F. Visscher, P. M. 2018-10-03 doi:10.1101/433870 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ Causal evidence for LTP-based interference in visual learning ]]> https://biorxiv.org/content/10.1101/438598v1?rss=1 Bang, J. W. Milton, D. Sasaki, Y. Watanabe, T. Rahnev, D. 2018-10-08 doi:10.1101/438598 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ Connecting the Microenvironmental Niche to Treatment Response in Ovarian Cancer ]]> https://biorxiv.org/content/10.1101/452052v1?rss=1 Strobl, M. Wicker, M. Adhikarla, V. Shockey, A. Lakatos, E. Pooladvand, P. Schenck, R. Saputro, L. Gatenby, C. Koppens, M. Cruz Garcia, S. Wenham, R. Damaghi, M. Gallaher, J. A. 2018-10-24 doi:10.1101/452052 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ Behavioral evolution drives hindbrain diversification among Lake Malawi cichlid fish ]]> https://biorxiv.org/content/10.1101/467282v1?rss=1 York, R. Byrne, A. Abdilleh, K. Patel, C. Todd, S. Finger, T. Fernald, R. 2018-11-09 doi:10.1101/467282 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ The Medical Genome Reference Bank: Whole genomes and phenotype of 2,570 healthy elderly ]]> https://biorxiv.org/content/10.1101/473348v1?rss=1 Pinese, M. Lacaze, P. Rath, E. M. Stone, A. Brion, M.-J. Ameur, A. Nagpal, S. Puttick, C. Husson, S. Degrave, D. Navin Cristina, T. Silva Kahl, V. F. Statham, A. L. Woods, R. L. McNeil, J. J. Riaz, M. Barr, M. Nelson, M. R. Reid, C. M. Murray, A. M. Shah, R. C. Wolfe, R. Atkins, J. R. Fitzsimmons, C. Cairns, H. M. Green, M. J. Carr, V. J. Cowley, M. J. Pickett, H. A. James, P. A. Powell, J. E. Kaplan, W. Gibson, G. Gyllensten, U. Cairns, M. J. McNamara, M. Dinger, M. E. Thomas, D. M. 2018-11-18 doi:10.1101/473348 Cold Spring Harbor Laboratory Press 2018-11-18 <![CDATA[ The cost of being stable: Trade-offs between effort and stability across a landscape of redundant motor solutions ]]> https://biorxiv.org/content/10.1101/477083v1?rss=1 Sohn, M. H. Ting, L. 2018-11-22 doi:10.1101/477083 Cold Spring Harbor Laboratory Press 2018-11-22 <![CDATA[ Synthetic Biology Research and Innovation Profile 2018: Publications and Patents ]]> https://biorxiv.org/content/10.1101/485805v1?rss=1 Shapira, P. Kwon, S. 2018-12-04 doi:10.1101/485805 Cold Spring Harbor Laboratory Press 2018-12-04 <![CDATA[ Evolution of sperm competition: Natural variation and genetic determinants of Caenorhabditis elegans sperm size ]]> https://biorxiv.org/content/10.1101/501486v1?rss=1 nView larger version (166K):norg.highwire.dtl.DTLVardef@1ff917org.highwire.dtl.DTLVardef@11a5e4corg.highwire.dtl.DTLVardef@250996org.highwire.dtl.DTLVardef@1989580_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gimond, C. Vielle, A. Silva Soares, N. Zdraljevic, S. McGrath, P. Andersen, E. Braendle, C. 2018-12-19 doi:10.1101/501486 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Prefrontal-posterior coupling mediates emotion transitions and their influence on executive function ]]> https://biorxiv.org/content/10.1101/518860v1?rss=1 Hao, Y. Yao, L. Smith, D. M. Sorel, E. Anderson, A. K. Schumacher, E. H. Evans, G. W. 2019-01-11 doi:10.1101/518860 Cold Spring Harbor Laboratory Press 2019-01-11 <![CDATA[ Neanderthal introgression reintroduced functional alleles lost in the human out of Africa bottleneck ]]> https://biorxiv.org/content/10.1101/533257v1?rss=1 Rinker, D. C. Simonti, C. McArthur, E. Shaw, D. Hodges, E. Capra, J. A. 2019-01-29 doi:10.1101/533257 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ PGC-1α overexpression partially rescues impaired oxidative and contractile pathophysiology following volumetric muscle loss injury ]]> https://biorxiv.org/content/10.1101/535328v1?rss=1 Southern, W. M. Nichenko, A. S. Tehrani, K. F. McGranahan, M. J. Krishnan, L. Qualls, A. E. Jenkins, N. J. Mortensen, L. J. Yin, H. Yin, A. Guldberg, R. E. Greising, S. M. Call, J. A. 2019-01-31 doi:10.1101/535328 Cold Spring Harbor Laboratory Press 2019-01-31 <![CDATA[ Cell-type specific epigenetic links to schizophrenia risk in brain ]]> https://biorxiv.org/content/10.1101/609131v1?rss=1 Mendizabal, I. Berto, S. Usui, N. Toriumi, K. Chatterjee, P. Douglas, C. Huh, I. Jeong, H. Layman, T. Tamminga, C. Preuss, T. Konopka, G. Yi, S. 2019-04-16 doi:10.1101/609131 Cold Spring Harbor Laboratory Press 2019-04-16 <![CDATA[ Evolution of Yin and Yang isoforms of a chromatin remodeling subunit results in the creation of two genes ]]> https://biorxiv.org/content/10.1101/616995v1?rss=1 300kD) multidomain subunit of the NURF chromatin remodeling complex. Using CRISPR-Cas9 genome editing and transgenic rescue, we demonstrate that in C. elegans, nurf-1 has split into two, largely non-overlapping isoforms (NURF-1.B and NURF-1.D, which we call Yin and Yang) that share only two of 26 exons. Both isoforms are essential for normal gametogenesis but have opposite effects on male/female gamete differentiation. Reproduction in hermaphrodites, which involves production of both sperm and oocytes, requires a balance of these opposing Yin and Yang isoforms. Transgenic rescue and genetic position of the fixed mutations suggest that different isoforms are modified in each laboratory strain. In a related clade of Caenorhabditis nematodes, the shared exons have duplicated, resulting in the split of the Yin and Yang isoforms into separate genes, each containing approximately 200 amino acids of duplicated sequence that has undergone accelerated protein evolution following the duplication. Associated with this duplication event is the loss of two additional nurf-1 transcripts, including the long-form transcript and a newly identified, highly expressed transcript encoded by the duplicated exons. We propose these lost transcripts are non-functional biproducts necessary to transcribe the Yin and Yang transcripts in the same cells. Our work suggests that evolution of nurf-1 isoforms in nematodes creates adaptive conflict that can be resolved by the creation of new, independent genes. ]]> Xu, W. Long, L. Zhao, Y. Stevens, L. Ellis, R. E. McGrath, P. T. 2019-04-24 doi:10.1101/616995 Cold Spring Harbor Laboratory Press 2019-04-24 <![CDATA[ Hygiene Hampers Competitive Release Of Resistant Bacteria In The Commensal Microbiota ]]> https://biorxiv.org/content/10.1101/639443v1?rss=1 Aspenberg, M. Maad Sasane, S. Nilsson, F. Brown, S. Wollein Waldetoft, K. 2019-05-17 doi:10.1101/639443 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids ]]> https://biorxiv.org/content/10.1101/654756v1?rss=1 Quinn, R. A. Vrbanac, A. Melnik, A. V. Patras, K. A. Christy, M. Nelson, A. T. Aksenov, A. A. Tripathi, A. Humphrey, G. da Silva, R. Bussell, R. Thron, T. Wang, M. Vargas, F. Gauglitz, J. Meehan, M. J. Poulsen, O. Boland, B. S. Chang, J. T. Sandborn, W. J. Lim, M. Garg, N. Lumeng, J. Kazmierczak, B. I. Jain, R. Egan, M. Rhee, K. E. Haddad, G. G. Siegel, D. Mazmanian, S. Nizet, V. Knight, R. Dorrestein, P. C. 2019-06-03 doi:10.1101/654756 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Engineered illumination devices for optogenetic control of cellular signaling dynamics ]]> https://biorxiv.org/content/10.1101/675892v1?rss=1 Repina, N. A. McClave, T. Bao, X. Kane, R. S. Schaffer, D. V. 2019-06-19 doi:10.1101/675892 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Tumor cell-organized fibronectin is required to maintain a dormant breast cancer population ]]> https://biorxiv.org/content/10.1101/686527v1?rss=1 Barney, L. Hall, C. Schwartz, A. Parks, A. Sparages, C. Galarza, S. Platt, M. Mercurio, A. Peyton, S. 2019-07-01 doi:10.1101/686527 Cold Spring Harbor Laboratory Press 2019-07-01 <![CDATA[ A custom genotyping array reveals population-level heterogeneity for the genetic risks of prostate cancer and other cancers in Africa ]]> https://biorxiv.org/content/10.1101/702910v1?rss=1 Harlemon, M. Ajayi, O. Kachambwa, P. Kim, M. S. Simonti, C. N. Quiver, M. H. Petersen, D. C. Mittal, A. Fernandez, P. Hsing, A. W. Baichoo, S. Agalliu, I. Jalloh, M. Gueye, S. M. Snyper, N. Y. Adusei, B. Mensah, J. E. Abrahams, A. O. D. Adebiyi, A. O. Orunmuyi, A. Aisuodionoe-Shadrach, O. I. Nwegbu, M. M. Joffe, M. Chen, W. C. Irusen, H. Neugut, A. I. Quintana, Y. Seutloali, M. Fadipe, M. Warren, C. Woehrmann, M. H. Zhang, P. Ongaco, C. Mawhinney, M. McBride, J. Andrews, C. Adams, M. Pugh, E. Rebbeck, T. R. Petersen, L. Lachance, J. 2019-07-15 doi:10.1101/702910 Cold Spring Harbor Laboratory Press 2019-07-15 <![CDATA[ Development of group-specific nosZ quantification method targeting active nitrous oxide reducing population in complex environmental samples ]]> https://biorxiv.org/content/10.1101/710483v1?rss=1 Kim, D. D. Park, D. Yoon, H. Song, M. J. Yun, T. Yoon, S. 2019-07-22 doi:10.1101/710483 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Darwinian properties and their trade-offs in autocatalytic RNA networks ]]> https://biorxiv.org/content/10.1101/726497v1?rss=1 Ameta, S. Arsene, S. Foulon, S. Saudemont, B. Clifton, B. E. Griffiths, A. D. Nghe, P. 2019-08-08 doi:10.1101/726497 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ Engineering recombination between diverged yeast species reveals genetic incompatibilities ]]> https://biorxiv.org/content/10.1101/755165v1?rss=1 Bozdag, G. O. Ono, J. Denton, J. A. Karakoc, E. Hunter, N. Leu, J.-Y. Greig, D. 2019-09-05 doi:10.1101/755165 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Satellite Imaging of Global Urbanicity relate to Adolescent Brain Development and Behavior ]]> https://biorxiv.org/content/10.1101/781674v1?rss=1 Xu, J. Liu, X. Ing, A. Li, Q. Qin, W. Guo, L. Huang, C. Cheng, J. Wang, M. Geng, Z. Zhu, W. Zhang, B. Liao, W. Qiu, S. Zhang, H. Xu, X. Yu, Y. Gao, B. Han, T. Cui, G. Chen, F. Xian, J. Li, J. Zhang, J. Zuo, X. Wang, D. Shen, W. Miao, Y. Yuan, F. Lui, S. Zhang, X. Xu, K. Zhang, L. Ye, Z. Banaschewski, T. Barker, G. J. Bokde, A. L. W. Quinlan, E. B. Desrivieres, S. Flor, H. Grigis, A. Garavan, H. Gowland, P. Heinz, A. Bruhl, R. Martinot, J.-L. Artiges, E. Nees, F. Orfanos, D. P. Lemaitre, H. Paus, T. Poustka, L. Hohmann, S. Frohner, J. H. Smo 2019-09-25 doi:10.1101/781674 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Single-Cell RNA-Seq Reveals Endocardial Defect in Hypoplastic Left Heart Syndrome ]]> https://biorxiv.org/content/10.1101/809731v1?rss=1 Miao, Y. Tian, L. Martin, M. Paige, S. L. Galdos, F. X. Li, J. Guttman, A. Wei, Y. Moonen, J.-R. Zhang, H. Ma, N. Zhang, B. Grossfeld, P. Mital, S. Chitayat, D. Wu, J. C. Rabinovitch, M. Nelson, T. J. Nie, S. Wu, S. M. Gu, M. 2019-10-17 doi:10.1101/809731 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Age-related Structural and Functional Variations in 5967 Individuals across the Adult Lifespan ]]> https://biorxiv.org/content/10.1101/810101v1?rss=1 Luo, N. Sui, J. Abrol, A. Lin, D. Chen, J. Vergara, V. Fu, Z. Du, Y. Damaraju, E. Xu, Y. Turner, J. Calhoun, V. 2019-10-18 doi:10.1101/810101 Cold Spring Harbor Laboratory Press 2019-10-18 <![CDATA[ A Synthetic Biology Approach to Sequential Stripe Patterning and Somitogenesis ]]> https://biorxiv.org/content/10.1101/825406v1?rss=1 Wu, F. He, C. Fang, X. Baez, J. Ohnmacht, T. Zhang, Q. Chen, X. Allison, K. R. Kuang, Y. Wang, X. 2019-10-31 doi:10.1101/825406 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ WormCat: an online tool for annotation and visualization of Caenorhabditis elegans genome-scale data ]]> https://biorxiv.org/content/10.1101/844928v1?rss=1 Holdorf, A. D. Higgins, D. P. Hart, A. C. Boag, P. R. Pazour, G. Walhout, M. Walker, A. K. 2019-11-15 doi:10.1101/844928 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Diverse muscle spindle firing properties emerge from multiscale muscle mechanics ]]> https://biorxiv.org/content/10.1101/858209v1?rss=1 Blum, K. P. Campbell, K. S. Horslen, B. C. Nardelli, P. Housley, S. N. Cope, T. C. Ting, L. H. 2019-11-29 doi:10.1101/858209 Cold Spring Harbor Laboratory Press 2019-11-29 <![CDATA[ Structural Brain Alterations and Their Association with Cognitive Function and Symptoms in Attention-Deficit/Hyperactivity Disorder Families ]]> https://biorxiv.org/content/10.1101/863605v1?rss=1 Jiang, W. Duan, K. Rootes-Murdy, K. Hoekstra, P. J. Hartman, C. Oosterlaan, J. Heslenfeld, D. Franke, B. Buitelaar, J. Arias-Vasquez, A. Liu, J. Turner, J. 2019-12-04 doi:10.1101/863605 Cold Spring Harbor Laboratory Press 2019-12-04 <![CDATA[ FUNCTIONAL NETWORK CONNECTIVITY (FNC)-BASED GENERATIVE ADVERSARIAL NETWORK (GAN) AND ITS APPLICATIONS IN MENTAL DISORDERS DIAGNOSIS ]]> https://biorxiv.org/content/10.1101/867168v1?rss=1 Zhao, J. Zhi, D. Yan, W. Vince, C. D. Sui, J. 2019-12-06 doi:10.1101/867168 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Riboflow: using deep learning to classify riboswitches with ~99% accuracy ]]> https://biorxiv.org/content/10.1101/868695v1?rss=1 0.99 and macro-averaged F-score of 0.96. A dynamic update functionality is inbuilt to account for the discovery of new riboswitches and extend the predictive modelling to any number of new additional classes. Our work would be valuable in the design and assembly of genetic circuits and the development of the next generation of antibiotics. The software is freely available as a Python package and standalone resource for wide use in genome annotation and biotechnology workflows. AvailabilityPyPi package: riboflow @ https://pypi.org/project/riboflow Repository with Standalone suite of tools: https://github.com/RiboswitchClassifier Language: Python 3.6 with numpy, keras, and tensorflow libraries. Licence: MIT ]]> Premkumar, K. A. R. Bharanikumar, R. Palaniappan, A. 2019-12-08 doi:10.1101/868695 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ Rising daptomycin resistance in Enterococcus faecium across a hospital system occurred via rampant recurrent evolution and occasional transmission between patients. ]]> https://biorxiv.org/content/10.1101/2023.05.09.540070v1?rss=1 Woods, R. Read, A. F. Forstchen, M. Kinnear, C. McKaig, J. Patel, T. Tracy, K. Young, C. L. 2023-05-15 doi:10.1101/2023.05.09.540070 Cold Spring Harbor Laboratory Press 2023-05-15 <![CDATA[ Native-state proteomics of Parvalbumin interneurons identifies novel molecular signatures and metabolic vulnerabilities to early Alzheimer's disease pathology ]]> https://biorxiv.org/content/10.1101/2023.05.17.541038v1?rss=1 Kumar, P. Goettemoeller, A. M. Espinosa-Garcia, C. Tobin, B. R. Tfaily, A. Nelson, R. S. Natu, A. Dammer, E. B. Santiago, J. V. Malepati, S. Cheng, L. Xiao, H. Duong, D. D. Seyfried, N. T. Wood, L. B. Rowan, M. Rangaraju, S. 2023-05-17 doi:10.1101/2023.05.17.541038 Cold Spring Harbor Laboratory Press 2023-05-17 <![CDATA[ Mitochondrial citrate carrier SLC25A1 is a dosage-dependent regulator of metabolic reprogramming and morphogenesis in the developing heart ]]> https://biorxiv.org/content/10.1101/2023.05.22.541833v1?rss=1 Ohanele, C. Peoples, J. N. Karlstaedt, A. Geiger, J. T. Gayle, A. D. Ghazal, N. Sohani, F. Brown, M. E. Davis, M. E. Porter, G. A. Faundez, V. Kwong, J. Q. 2023-05-22 doi:10.1101/2023.05.22.541833 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Liquid plug propagation in computer-controlled microfluidic airway-on-a-chip with semi-circular microchannels ]]> https://biorxiv.org/content/10.1101/2023.05.24.542177v1?rss=1 Viola, H. Vasani, V. Washington, K. Lee, J. H. Selva, C. Li, A. Llorente, C. J. Murayama, Y. Grotberg, J. B. Romano, F. Takayama, S. 2023-05-25 doi:10.1101/2023.05.24.542177 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Low oscillatory shear stress regulates Weibel-Palade body size and vWF release. ]]> https://biorxiv.org/content/10.1101/2023.05.26.542527v1?rss=1 Money, A. Todd, H. J. Jo, H. Beech, D. J. McKeown, L. 2023-05-26 doi:10.1101/2023.05.26.542527 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ An Explainable and Robust Deep Learning Approach for Automated Electroencephalography-based Schizophrenia Diagnosis ]]> https://biorxiv.org/content/10.1101/2023.05.27.542592v1?rss=1 Sattiraju, A. Ellis, C. A. Miller, R. L. Calhoun, V. D. 2023-05-30 doi:10.1101/2023.05.27.542592 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ Common evolutionary origins of the bacterial glycyl tRNA synthetaseand alanyl tRNA synthetase ]]> https://biorxiv.org/content/10.1101/2023.05.29.542759v1?rss=1 Alvarez-Carreno, C. Arciniega, M. Ribas de Pouplana, L. Petrov, A. S. Hernandez-Gonzalez, A. Valencia-Sanchez, M. I. Williams, L. D. Torres-Larios, A. 2023-05-30 doi:10.1101/2023.05.29.542759 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ The Arabidopsis SWEET1 and SWEET2 uniporters recognize similar substrates despite differences in subcellular localization ]]> https://biorxiv.org/content/10.1101/2023.05.30.542931v1?rss=1 Gwon, S. Park, J. Huque, A. K. M. M. Cheung, L. S. 2023-05-30 doi:10.1101/2023.05.30.542931 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ Effect of Aging, Sex, and Gene (Fbln5) on Arterial Stiffness of Mice: 20 Weeks Adult Fbln5-knockout Mice Have Older Arteries than 100 Weeks Wild-Type Mice ]]> https://biorxiv.org/content/10.1101/2023.05.30.542920v1?rss=1 Dong, H. Ferruzzi, J. Liu, M. Brewster, L. P. Leshnower, B. G. Gleason, R. L. 2023-06-01 doi:10.1101/2023.05.30.542920 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ After wounding, a G-protein coupled receptor restores tension to epithelial cells in a dynamic inward-traveling wave ]]> https://biorxiv.org/content/10.1101/2023.05.31.543122v1?rss=1 Han, I. Nassar, L. S. Page-McCaw, A. Hutson, M. S. 2023-06-03 doi:10.1101/2023.05.31.543122 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ Differential encoding of temporal context and expectation under representational drift across hierarchically connected areas ]]> https://biorxiv.org/content/10.1101/2023.06.02.543483v1?rss=1 Wyrick, D. G. Cain, N. Larsen, R. S. Lecoq, J. G. Valley, M. Ahmed, R. Bowlus, J. Boyer, G. Caldejon, S. Casal, L. Chvilicek, M. Departee, M. Groblewski, P. Huang, C. Johnson, K. Kato, I. Larkin, J. D. Lee, E. Liang, E. Mace, K. Nayan, C. Nguyen, T. Reding, M. Seid, S. Sevigny, J. Stoecklin, M. Williford, A. Choi, H. Garrett, M. E. Mazzucato, L. 2023-06-03 doi:10.1101/2023.06.02.543483 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ Proteostatic tuning underpins the evolution of novel multicellular traits ]]> https://biorxiv.org/content/10.1101/2023.05.31.543183v1?rss=1 Montrose, K. Lac, D. T. Burnetti, A. J. Tong, K. Bozdag, G. O. Hukkanen, M. Ratcliff, W. C. Saarikangas, J. 2023-06-05 doi:10.1101/2023.05.31.543183 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Microbial Changes occurring during oronasal fistula wound healing ]]> https://biorxiv.org/content/10.1101/2023.06.02.543508v1?rss=1 Goudy, S. L. Bradley, H. L. Gacasan, C. A. Toma, A. Naudin, C. R. Wuest, W. M. Tomov, M. L. Serpooshan, V. Coskun, A. F. Jones, R. M. 2023-06-06 doi:10.1101/2023.06.02.543508 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ Electrocatalytic on-site oxygenation for transplanted cell-based-therapies ]]> https://biorxiv.org/content/10.1101/2023.06.05.543794v1?rss=1 60k cells/mm3) in hypoxic conditions in vitro and in vivo. Our results demonstrate that exogenous oxygen production devices can be readily integrated into bioelectronic platforms and enable high cell loadings in smaller device footprints with broad applicability. ]]> Lee, I. Surendran, A. Fleury, S. Gimino, I. Curtiss, A. Fell, C. Shiwarski, D. El-Refy, O. Rothrock, B. Jo, S. Schwartzkopff, T. Singh Mehta, A. John, S. Ji, X. Nikiforidis, G. Hester, J. Weber, D. J. Veiseh, O. Feinberg, A. Rivnay, J. Cohen-Karni, T. 2023-06-07 doi:10.1101/2023.06.05.543794 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Automated cell annotation in multi-cell images using an improved CRF_ID algorithm ]]> https://biorxiv.org/content/10.1101/2023.06.07.543949v1?rss=1 Lee, H. J. Liang, J. Chaudhary, S. Moon, S. Yu, Z. Wu, T. Liu, H. Choi, M.-K. Zhang, Y. Lu, H. 2023-06-08 doi:10.1101/2023.06.07.543949 Cold Spring Harbor Laboratory Press 2023-06-08 <![CDATA[ A non-oscillatory, millisecond-scale embedding of brain state provides insight into behavior. ]]> https://biorxiv.org/content/10.1101/2023.06.09.544399v1?rss=1 Parks, D. F. Schneider, A. M. Xu, Y. Brunwasser, S. J. Funderburk, S. Thurber, D. Blanche, T. Dyer, E. L. Haussler, D. Hengen, K. B. 2023-06-09 doi:10.1101/2023.06.09.544399 Cold Spring Harbor Laboratory Press 2023-06-09 <![CDATA[ Common computations in automatic cue combination and metacognitive confidence reports ]]> https://biorxiv.org/content/10.1101/2023.06.07.544029v1?rss=1 Gao, Y. Xue, K. Odegaard, B. Rahnev, D. 2023-06-11 doi:10.1101/2023.06.07.544029 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ BRAKER3: Fully Automated Genome Annotation Using RNA-Seq and Protein Evidence with GeneMark-ETP, AUGUSTUS and TSEBRA ]]> https://biorxiv.org/content/10.1101/2023.06.10.544449v1?rss=1 Gabriel, L. Bruna, T. Hoff, K. J. Ebel, M. Lomsadze, A. Borodovsky, M. Stanke, M. 2023-06-12 doi:10.1101/2023.06.10.544449 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ Entanglement in living systems ]]> https://biorxiv.org/content/10.1101/2023.06.13.544814v1?rss=1 Day, T. C. Zamani-Dahaj, A. Bozdag, G. O. Burnetti, A. J. Bingham, E. P. Conlin, P. L. Ratcliff, W. C. Yunker, P. J. 2023-06-13 doi:10.1101/2023.06.13.544814 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ Native nanoproteomics captures the structure and dynamics of endogenous protein complexes in human heart tissue ]]> https://biorxiv.org/content/10.1101/2023.06.13.544817v1?rss=1 Chapman, E. A. Roberts, D. S. Tiambeng, T. N. Andrews, J. Wang, M.-D. Reasoner, E. A. Melby, J. A. Li, B. H. Kim, D. Alpert, A. J. Jin, S. Ge, Y. 2023-06-13 doi:10.1101/2023.06.13.544817 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ Profiling the neuroimmune cascade in 3xTg mice exposed to successive mild traumatic brain injuries ]]> https://biorxiv.org/content/10.1101/2023.06.13.544838v1?rss=1 Pybus, A. F. Bitarafan, S. Brothers, R. O. Rohrer, A. Khaitan, A. Rivera, F. Udeshi, K. Davies, B. Triplett, S. Dammer, E. B. Rangaraju, S. Buckley, E. M. Wood, L. B. 2023-06-14 doi:10.1101/2023.06.13.544838 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ Acceleration of Large-Scale Single Cell Differential Gene Expression Analysis with FastDE ]]> https://biorxiv.org/content/10.1101/2023.06.15.545003v1?rss=1 Connolly, E. Aluru, M. Chocklingam, S. Dhere, V. Gibson, G. Pan, T. 2023-06-16 doi:10.1101/2023.06.15.545003 Cold Spring Harbor Laboratory Press 2023-06-16 <![CDATA[ Spatial constraints subvert microbial arms race ]]> https://biorxiv.org/content/10.1101/2023.06.16.545151v1?rss=1 Copeland, R. Zhang, C. Hammer, B. K. Yunker, P. J. 2023-06-16 doi:10.1101/2023.06.16.545151 Cold Spring Harbor Laboratory Press 2023-06-16 <![CDATA[ A Common Pathway for Detergent-Assisted Oligomerization of Aβ42 ]]> https://biorxiv.org/content/10.1101/2023.06.22.546091v1?rss=1 Kunnath Muhammedkutty, F. N. Prasad, R. Gao, Y. Rao Sudarshan, T. Robang, A. S. Watzlawik, J. O. Rosenberry, T. L. Paravastu, A. K. Zhou, H.-X. 2023-06-22 doi:10.1101/2023.06.22.546091 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ A Machine Learning Approach for Real-time Cortical State Estimation ]]> https://biorxiv.org/content/10.1101/2023.06.20.545785v1?rss=1 Weiss, D. A. Borsa, A. M. Pala, A. Sederberg, A. J. Stanley, G. B. 2023-06-23 doi:10.1101/2023.06.20.545785 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Spatiotemporal Control of Genomics and Epigenomics by Ultrasound ]]> https://biorxiv.org/content/10.1101/2023.06.21.544125v1?rss=1 Wu, Y. Huang, Z. Liu, Y. Yoon, C.-W. Sun, K. Situ, Y. Ho, P. Yuan, Z. Zhu, L. Eyquem, J. Zhao, Y. Liu, T. Kwong, G. A. Chien, S. Wang, Y. 2023-06-23 doi:10.1101/2023.06.21.544125 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Time-varying Functional Connectivity Predicts Fluctuations in Sustained Attention in a Serial Tapping Task ]]> https://biorxiv.org/content/10.1101/2023.06.22.546092v1?rss=1 Seeburger, D. T. Xu, N. Ma, M. Larson, S. Godwin, C. Keilholz, S. Schumacher, E. H. 2023-06-25 doi:10.1101/2023.06.22.546092 Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ An adversarial collaboration to critically evaluate theories of consciousness ]]> https://biorxiv.org/content/10.1101/2023.06.23.546249v1?rss=1 Cogitate Consortium, Ferrante, O. Gorska-Klimowska, U. Henin, S. Hirschhorn, R. Khalaf, A. Lepauvre, A. Liu, L. Richter, D. Vidal, Y. Bonacchi, N. Brown, T. Sripad, P. Armendariz, M. Bendtz, K. Ghafari, T. Hetenyi, D. Jeschke, J. Kozma, C. Mazumder, D. R. Montenegro, S. Seedat, A. Sharafeldin, A. Yang, S. Baillet, S. Chalmers, D. J. Cichy, R. M. Fallon, F. Panagiotaropoulos, T. I. Blumenfeld, H. Devore, S. Jensen, O. Kreiman, G. de Lange, F. P. Luo, H. Boly, M. Dehaene, S. Koch, C. Tononi, G. Pitts, M. Mudrik, L. Melloni, L. 2023-06-26 doi:10.1101/2023.06.23.546249 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ A sensor complements the steric gate when DNA polymerase ϵ discriminates ribonucleotides. ]]> https://biorxiv.org/content/10.1101/2023.07.01.547322v1?rss=1 Parkash, V. Kulkarni, Y. Bylund, G. Osterman, P. Kamerlin, S. C. L. Johansson, E. 2023-07-01 doi:10.1101/2023.07.01.547322 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ Identifying distinct neural features between the initial and corrective phases of precise reaching using AutoLFADS ]]> https://biorxiv.org/content/10.1101/2023.06.30.547252v1?rss=1 Lee, W.-H. Karpowicz, B. M. Pandarinath, C. Rouse, A. G. 2023-07-02 doi:10.1101/2023.06.30.547252 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Intradisciplinary Growth of Sustainability-Minded Engineers through Conservation Technology ]]> https://biorxiv.org/content/10.1101/2023.07.03.546429v1?rss=1 Schulz, A. K. Shriver, C. Patka, A. Greiner, C. Seleb, B. Watts Hull, R. Subino Sullivan, C. Sonnenberg-Klein, J. Moore, R. 2023-07-03 doi:10.1101/2023.07.03.546429 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Stimulus-dependent functional network topology in mouse visual cortex ]]> https://biorxiv.org/content/10.1101/2023.07.03.547364v1?rss=1 Tang, D. Zylberberg, J. Jia, X. Choi, H. 2023-07-03 doi:10.1101/2023.07.03.547364 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Flow cytometric isolation of drug-like conformational antibodies specific for amyloid fibrils ]]> https://biorxiv.org/content/10.1101/2023.07.04.547698v1?rss=1 Desai, A. A. Zupancic, J. M. Trzeciakiewicz, H. Gerson, J. E. DuBois, K. N. Skinner, M. E. Sharkey, L. M. McArthur, N. Ferris, S. P. Bhatt, N. N. Makowski, E. K. Smith, M. D. Chen, H. Huang, J. Jerez, C. Kane, R. S. Kanaan, N. M. Paulson, H. L. Tessier, P. M. 2023-07-04 doi:10.1101/2023.07.04.547698 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ Exploring Nonlinear Dynamics In Brain Functionality Through Phase Portraits And Fuzzy Recurrence Plots ]]> https://biorxiv.org/content/10.1101/2023.07.06.547922v1?rss=1 Li, Q. Calhoun, V. Pham, T. Iraji, A. 2023-07-07 doi:10.1101/2023.07.06.547922 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Threat expectation does not improve perceptual discrimination despite causing heightened priority processing in the frontoparietal network ]]> https://biorxiv.org/content/10.1101/2023.07.06.547999v1?rss=1 Haddara, N. Rahnev, D. 2023-07-10 doi:10.1101/2023.07.06.547999 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ The Hidden Biocatalytic Potential of the Old Yellow Enzyme Family ]]> https://biorxiv.org/content/10.1101/2023.07.10.548207v1?rss=1 115,000 members of the OYE family were broadly explored to identify phylogenetic and sequence-based trends. From this analysis, 118 novel enzymes were characterized across the family to broadly explore and expand the biocatalytic performance and substrate scope of known OYEs. Over a dozen novel enzymes were identified exhibiting enhanced catalytic activity or altered stereospecificity. Beyond well-established ene reduction, we detected widespread occurrence of oxidative chemistry amongst OYE family members at ambient conditions. Crystallography studies of selected OYEs yielded structures for two enzymes, contributing to a better understanding of their unique performance. Their structures revealed an unusual loop conformation within a novel OYE subclass. Overall, our study significantly expands the known functional and chemical diversity of OYEs while identifying superior biocatalysts for asymmetric reduction and oxidation. ]]> White, D. W. Iamurri, S. Keshavarz-Joud, P. Blue, T. Copp, J. N. Lutz, S. 2023-07-11 doi:10.1101/2023.07.10.548207 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Comammox bacterial preference for urea influences its interactions with aerobic nitrifiers. ]]> https://biorxiv.org/content/10.1101/2023.07.11.548560v1?rss=1 Vilardi, K. J. Johnston, J. Dai, Z. Cotto, I. Tuttle, E. Patterson, A. Stubbins, A. Pieper, K. Pinto, A. 2023-07-11 doi:10.1101/2023.07.11.548560 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ A Vibrating Ingestible BioElectronic Stimulator Modulates Gastric Stretch Receptors for Illusory Satiety ]]> https://biorxiv.org/content/10.1101/2023.07.17.549257v1?rss=1 Srinivasan, S. Alshareef, A. A. Hwang, A. Bryne, C. Kuosmann, J. Ishida, K. Jenkins, J. Liu, S. Madani, W. A. M. Hayward, A. M. Fabian, N. Traverso, G. 2023-07-19 doi:10.1101/2023.07.17.549257 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Spatial Dynamic Subspaces Encode Sex-Specific Schizophrenia Disruptions in Transient Network Overlap and its Links to Genetic Risk ]]> https://biorxiv.org/content/10.1101/2023.07.18.548880v1?rss=1 Iraji, A. Chen, J. Lewis, N. Fu, Z. Agcaoglu, O. Kochunov, P. Adhikari, B. M. Mathalon, D. H. Pearlson, G. D. Macciardi, F. Preda, A. van Erp, T. G. M. Bustillo, J. R. Diaz-Caneja, C. M. Andres-Camazon, P. Dhamala, M. Adali, T. Calhoun, V. D. 2023-07-19 doi:10.1101/2023.07.18.548880 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Dynamic corticothalamic modulation of the somatosensory thalamocortical circuit during wakefulness ]]> https://biorxiv.org/content/10.1101/2023.07.18.549491v1?rss=1 Dimwamwa, E. Pala, A. Chundru, V. Wright, N. C. Stanley, G. B. 2023-07-19 doi:10.1101/2023.07.18.549491 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data ]]> https://biorxiv.org/content/10.1101/2023.07.20.549584v1?rss=1 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms role in ecology and human health. ]]> Zuffa, S. Schmid, R. Bauermeister, A. P. Gomes, P. W. Caraballo-Rodriguez, A. M. El Abiead, Y. Aron, A. T. Gentry, E. C. Zemlin, J. Meehan, M. J. Avalon, N. E. Cichewicz, R. H. Buzun, E. Carrillo Terrazas, M. Hsu, C.-Y. Oles, R. Vasquez Ayala, A. Zhao, J. Chu, H. Kuijpers, M. C. M. Jackrel, S. L. Tugizimana, F. Nephali, L. P. Dubery, I. A. Madala, N. E. Moreira, E. A. Costa-Lotufo, L. V. Lopes, N. P. Rezende-Teixeira, P. Jimenez, P. C. Rimal, B. Patterson, A. D. Traxler, M. F. Pessotti, R. d. C. Alvarado-Villalobos, D. Tamayo-Castillo, G. Chaverri, P. Escud 2023-07-20 doi:10.1101/2023.07.20.549584 Cold Spring Harbor Laboratory Press 2023-07-20 <![CDATA[ Spatially resolved cell atlas of the teleost telencephalon and deep homology of the vertebrate forebrain ]]> https://biorxiv.org/content/10.1101/2023.07.20.549873v1?rss=1 Hegarty, B. E. Gruenhagen, G. W. Johnson, Z. V. Baker, C. M. Streelman, J. T. 2023-07-22 doi:10.1101/2023.07.20.549873 Cold Spring Harbor Laboratory Press 2023-07-22 <![CDATA[ Mechanotransduction governs CD40 function and underlies X-linked Hyper IgM syndrome ]]> https://biorxiv.org/content/10.1101/2023.07.23.550231v1?rss=1 Choi, H.-K. Travaglino, S. Munchhalfen, M. Gorg, R. Zhong, Z. Lyu, J. Reyes-Aguilar, D. M. Wienands, J. Singh, A. Zhu, C. 2023-07-25 doi:10.1101/2023.07.23.550231 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Developmental regulation of zinc homeostasis in differentiating oligodendrocytes ]]> https://biorxiv.org/content/10.1101/2023.07.26.550230v1?rss=1 Elitt, C. M. Ross, M. M. Wang, J. Fahrni, C. J. Rosenberg, P. A. 2023-07-27 doi:10.1101/2023.07.26.550230 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Where top-down meets bottom-up: Cell-type specific connectivity map of the whisker system ]]> https://biorxiv.org/content/10.1101/2023.07.31.551377v1?rss=1 Rault, N. Bergmans, T. Delfstra, N. Kleijnen, B. J. Zeldenrust, F. Celikel, T. 2023-08-02 doi:10.1101/2023.07.31.551377 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Visual Sequence Encoding is Enhanced by Predictable Music Pairing via Modulating Medial Temporal Lobe and Its Connectivity with Frontostriatal Loops ]]> https://biorxiv.org/content/10.1101/2023.08.01.551506v1?rss=1 Ren, Y. Brown, T. 2023-08-03 doi:10.1101/2023.08.01.551506 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ Conductive microgel annealed scaffolds enhance myogenic potential of myoblastic cells ]]> https://biorxiv.org/content/10.1101/2023.08.01.551533v1?rss=1 Casella, A. Lowen, J. Shimamoto, N. Griffin, K. H. Filler, A. C. Panitch, A. Leach, K. 2023-08-03 doi:10.1101/2023.08.01.551533 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ Ciliary ARL13B prevents obesity in mice ]]> https://biorxiv.org/content/10.1101/2023.08.02.551695v1?rss=1 Terry, T. T. Gigante, E. D. Alexandre, C. M. Brewer, K. M. Engle, S. E. Yue, X. Berbari, N. F. Vaisse, C. Caspary, T. 2023-08-04 doi:10.1101/2023.08.02.551695 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ An end-to-end workflow for non-destructive 3D pathology ]]> https://biorxiv.org/content/10.1101/2023.08.03.551845v1?rss=1 Bishop, K. W. Barner, L. A. E. Han, Q. Baraznenok, E. Lan, L. Poudel, C. Gao, G. Serafin, R. B. Chow, S. S. L. Glaser, A. K. Janowczyk, A. Brenes, D. Huang, H. Miyasato, D. True, L. D. Kang, S. Vaughan, J. C. Liu, J. T. C. 2023-08-06 doi:10.1101/2023.08.03.551845 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ Purifying selection and adaptive evolution proximate to the zoonosis of SARS-CoV-1 and SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2023.08.07.552269v1?rss=1 Townsend, J. P. Gaughran, S. Hassler, H. B. Fisk, J. N. Nagib, M. Wu, Y. Wang, Y. Wang, Z. Galvani, A. P. Dornburg, A. 2023-08-07 doi:10.1101/2023.08.07.552269 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ BRAND: A platform for closed-loop experiments with deep network models ]]> https://biorxiv.org/content/10.1101/2023.08.08.552473v1?rss=1 Ali, Y. H. Bodkin, K. Rigotti-Thompson, M. Patel, K. Card, N. S. Bhaduri, B. Nason-Tomaszewski, S. R. Mifsud, D. M. Hou, X. Nicolas, C. Allcroft, S. Hochberg, L. R. Yong, N. A. Stavisky, S. D. Miller, L. E. Brandman, D. M. Pandarinath, C. 2023-08-12 doi:10.1101/2023.08.08.552473 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ Translation as a Biosignature ]]> https://biorxiv.org/content/10.1101/2023.08.10.552839v1?rss=1 McKaig, J. M. Kim, M. Carr, C. E. 2023-08-14 doi:10.1101/2023.08.10.552839 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Second Harmonic Generation Imaging Reveals Entanglement of Collagen Fibers in the Elephant Trunk Skin Dermis ]]> https://biorxiv.org/content/10.1101/2023.08.11.553031v1?rss=1 Schulz, A. Plotczyk, M. Sordilla, S. Boyle, M. Singal, K. Reidenberg, J. Hu, D. Higgins, C. 2023-08-15 doi:10.1101/2023.08.11.553031 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Mechanical force regulates ligand binding and function of PD-1 ]]> https://biorxiv.org/content/10.1101/2023.08.13.553152v1?rss=1 8 pN where force accelerates dissociation. Steered molecular dynamics finds PD-1-PD-L2 complex very sensitive to force due to the two molecules "side-to-side" binding via {beta} sheets. Pulling causes relative rotation and translation between the two molecules by stretching and aligning the complex along the force direction, yielding new atomic contacts not observed in the crystal structure. Compared to wild-type, PD-1 mutants targeting the force-induced new interactions maintain the same binding affinity but display lower rupture force, shorter bond lifetime, reduced tension, and most importantly, impaired capacity to suppress T cell activation. Our results uncover a mechanism for cells to probe the mechanical support of PD-1-PD-Ligand bonds using endogenous forces to regulate PD-1 triggering. ]]> Li, K. Cardenas-Lizana, P. Kellner, A. V. Yuan, Z. Ahn, E. Lyu, J. Li, Z. Salaita, K. Ahmed, R. Zhu, C. 2023-08-15 doi:10.1101/2023.08.13.553152 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Non-invasive canine electroencephalography (EEG): a systematic review ]]> https://biorxiv.org/content/10.1101/2023.08.14.552730v1?rss=1 Kulgod, A. Linden, D. v. d. Franca, L. G. S. Jackson, M. Zamansky, A. 2023-08-16 doi:10.1101/2023.08.14.552730 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ Elephants develop wrinkles through both form & function ]]> https://biorxiv.org/content/10.1101/2023.08.24.554618v1?rss=1 Schulz, A. K. Kaufmann, L. Reveyaz, N. Ritter, C. Hildebrandt, T. Brecht, M. K. 2023-08-25 doi:10.1101/2023.08.24.554618 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ Modulation of cannabinoid receptor 2 alters neuroinflammation and reduces formation of alpha-synuclein aggregates in a rat model of nigral synucleinopathy ]]> https://biorxiv.org/content/10.1101/2023.08.25.554814v1?rss=1 Joers, V. Murray, B. C. McLaughlin, C. Oliver, D. Staley, H. Coronado, J. E. Achat-Mendes, C. Golshani, S. Kelly, S. D. Goodson, M. Lee, D. Manfredsson, F. P. Moore, B. M. Tansey, M. G. 2023-08-27 doi:10.1101/2023.08.25.554814 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Tauopathy severely disrupts homeostatic set-points in emergent neural dynamics but not the activity of individual neurons. ]]> https://biorxiv.org/content/10.1101/2023.09.01.555947v1?rss=1 McGregor, J. N. Farris, C. A. Ensley, S. Schneider, A. Wang, C. Liu, Y. Tu, J. Elmore, H. Ronayne, K. D. Wessel, R. Dyer, E. L. Bhaskaran-Nair, K. Holtzman, D. M. Hengen, K. B. 2023-09-05 doi:10.1101/2023.09.01.555947 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Generative design approach to combine architected Voronoi foams with porous collagen scaffolds to create a tunable composite biomaterial ]]> https://biorxiv.org/content/10.1101/2023.09.05.556448v1?rss=1 Dewey, M. J. Chang, R. S. Nosatov, A. V. Janssen, K. Crotts, S. Hollister, S. Harley, B. 2023-09-07 doi:10.1101/2023.09.05.556448 Cold Spring Harbor Laboratory Press 2023-09-07 <![CDATA[ Targeting YAP mechanosignaling to ameliorate stiffness-induced Schlemm's canal cell pathobiology ]]> https://biorxiv.org/content/10.1101/2023.09.08.556840v1?rss=1 Li, H. Kuhn, M. Kelly, R. A. Singh, A. Palanivel, K. K. Salama, I. De Ieso, M. L. Stamer, W. D. Ganapathy, P. S. Herberg, S. 2023-09-10 doi:10.1101/2023.09.08.556840 Cold Spring Harbor Laboratory Press 2023-09-10 <![CDATA[ Toolkits for detailed and high-throughput interrogation of synapses in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.09.12.557402v1?rss=1 Majeed, M. Han, H. Zhang, K. Liao, C.-P. Hobert, O. Lu, H. 2023-09-13 doi:10.1101/2023.09.12.557402 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Multimodal subspace independent vector analysis captures latent subspace structures in large multimodal neuroimaging studies ]]> https://biorxiv.org/content/10.1101/2023.09.17.558092v1?rss=1 Li, X. Adali, T. Silva, R. F. Calhoun, V. 2023-09-17 doi:10.1101/2023.09.17.558092 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ RATTACA: Genetic predictions in Heterogeneous Stock rats offer a new tool for genetic correlation and experimental design ]]> https://biorxiv.org/content/10.1101/2023.09.18.558279v1?rss=1 Johnson, B. B. Sanches, T. M. Okamoto, M. H. Nguyen, K.-M. Ortez, C. A. Polesskaya, O. Palmer, A. A. 2023-09-19 doi:10.1101/2023.09.18.558279 Cold Spring Harbor Laboratory Press 2023-09-19 <![CDATA[ Fossil-calibrated inference of divergence times among the Volvocine algae enables reconstruction of the steps that led to differentiated multicellularity ]]> https://biorxiv.org/content/10.1101/2023.09.19.558489v1?rss=1 Lindsey, C. R. Knoll, A. H. Herron, M. D. Rosenzweig, F. 2023-09-22 doi:10.1101/2023.09.19.558489 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Estimating multimodal brain variability in schizophreniaspectrum disorders: A worldwide ENIGMA study ]]> https://biorxiv.org/content/10.1101/2023.09.22.559032v1?rss=1 Omlor, W. Rabe, F. Fuchs, S. Cecere, G. Homan, S. Surbeck, W. Kallen, N. Georgiadis, F. Seifritz, E. Weickert, T. Bruggemann, J. Weickert, C. Potkin, S. Hashimoto, R. Sim, K. Rootes-Murdy, K. Quide, Y. Houenou, J. Banaj, N. Vecchio, D. Piras, F. Spalletta, G. Salvador, R. Rodrigue, A. Pearlson, G. Glahn, D. Tomecek, D. Kirschner, M. Kochunov, P. Fan, F.-M. Andreassen, O. Westlye, L. T. A. Berthet, P. Calhoun, V. Howells, F. M. Uhlmann, A. Stein, D. Iasevoli, F. van Erp, T. Turner, J. Homan, P. 2023-09-23 doi:10.1101/2023.09.22.559032 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ OpenCell: A Low-cost, Open-Source, 3-in-1 device for DNA Extraction ]]> https://biorxiv.org/content/10.1101/2023.09.18.558349v1?rss=1 Gupta, A. Yu, J. Challita, E. J. Standeven, J. Bhamla, M. S. 2023-09-25 doi:10.1101/2023.09.18.558349 Cold Spring Harbor Laboratory Press 2023-09-25 <![CDATA[ QPPLab: A generally applicable software package for detecting, analyzing, and visualizing large-scale quasiperiodic spatiotemporal patterns (QPPs) of brain activity ]]> https://biorxiv.org/content/10.1101/2023.09.25.559086v1?rss=1 Xu, N. Yousefi, B. Anumba, N. LaGrow, T. J. Zhang, X. Keilholz, S. 2023-09-25 doi:10.1101/2023.09.25.559086 Cold Spring Harbor Laboratory Press 2023-09-25 <![CDATA[ The impact of phage and phage resistance on microbial community dynamics ]]> https://biorxiv.org/content/10.1101/2023.09.26.559468v1?rss=1 Alseth, E. O. Custodio, R. Sundius, S. A. Kuske, R. A. Brown, S. P. Westra, E. R. 2023-09-26 doi:10.1101/2023.09.26.559468 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Septins Enable T Cell Contact Guidance via Amoeboid-Mesenchymal Switch ]]> https://biorxiv.org/content/10.1101/2023.09.26.559597v1?rss=1 Zhovmer, A. S. Manning, A. Smith, C. Wang, J. Ma, X. Tsygankov, D. Dokholyan, N. V. Cartagena-Rivera, A. X. Singh, R. Tabdanov, E. D. 2023-09-27 doi:10.1101/2023.09.26.559597 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Flight power muscles have a coordinated, causal role in controlling hawkmoth pitch turns ]]> https://biorxiv.org/content/10.1101/2023.09.27.559785v1?rss=1 Wood, L. J. Putney, J. Sponberg, S. 2023-09-27 doi:10.1101/2023.09.27.559785 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Hydrogel-Polyurethane Fiber Composites With Enhanced Microarchitectural Control For Heart Valve Replacement ]]> https://biorxiv.org/content/10.1101/2023.09.29.560202v1?rss=1 Robinson, A. Nkansah, A. Bhat, S. Karnik, S. Jones, S. Fairley, A. Leung, J. Wancura, M. Sacks, M. Dasi, L. Cosgriff-Hernandez, E. 2023-10-01 doi:10.1101/2023.09.29.560202 Cold Spring Harbor Laboratory Press 2023-10-01 <![CDATA[ Context dependent multisensory integration: Mechanosensation depends on luminance for robust performance ]]> https://biorxiv.org/content/10.1101/2023.09.29.560224v1?rss=1 Sharma, V. P. Sponberg, S. 2023-10-02 doi:10.1101/2023.09.29.560224 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutieres syndrome (AGS)-ortholog mutants of Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2023.10.02.560505v1?rss=1 Kundnani, D. L. Yang, T. Gombolay, A. Mukherjee, K. Newnam, G. Meers, C. Mehta, Z. H. Mouawad, C. Storici, F. 2023-10-02 doi:10.1101/2023.10.02.560505 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Spiral NeuroString: High-Density Soft Bioelectronic Fibers for Multimodal Sensing and Stimulation ]]> https://biorxiv.org/content/10.1101/2023.10.02.560482v1?rss=1 Khatib, M. Zhao, E. T. Wei, S. Abramson, A. Bishop, E. B. Chen, C.-H. Thomas, A.-L. Xu, C. Park, J. Lee, Y. Hamnett, R. Yu, W. Root, S. E. Yuan, L. Chakhtoura, D. Kim, K. K. Zhong, D. Nishio, Y. Zhao, C. Wu, C. Jiang, Y. Zhang, A. Li, J. Wang, W. Salimi-Jazi, F. Rafeeqi, T. A. Hemed, N. M. Tok, J. B.-H. Chen, X. Kaltschmidt, J. A. Dunn, J. Bao, Z. 2023-10-03 doi:10.1101/2023.10.02.560482 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Precise cortical contributions to feedback sensorimotor control during reactive balance ]]> https://biorxiv.org/content/10.1101/2023.10.02.560626v1?rss=1 Boebinger, S. Payne, A. Martino, G. Kerr, K. Mirdamadi, J. McKay, J. L. Borich, M. Ting, L. 2023-10-04 doi:10.1101/2023.10.02.560626 Cold Spring Harbor Laboratory Press 2023-10-04 <![CDATA[ Serum Lipidome Profiling Reveals a Distinct Signature of Ovarian Cancer in Korean Women ]]> https://biorxiv.org/content/10.1101/2023.10.05.560751v1?rss=1 Sah, S. Bifarin, O. O. Moore, S. G. Gaul, D. A. Chung, H. Cho, H. Cho, C.-H. Kim, J.-H. Kim, J. Fernandez, F. O. 2023-10-07 doi:10.1101/2023.10.05.560751 Cold Spring Harbor Laboratory Press 2023-10-07 <![CDATA[ Sustained bacterial (N2O) reduction at acidic pH ]]> https://biorxiv.org/content/10.1101/2023.10.06.560748v1?rss=1 He, G. Chen, G. Xie, Y. Swift, C. Cha, G. Konstantinidis, K. T. Radosevich, M. Löffler, F. E. 2023-10-10 doi:10.1101/2023.10.06.560748 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Delivery of A Jagged1-PEG-MAL hydrogel with Pediatric Human Bone Cells Regenerates Critically-Sized Craniofacial Bone Defects ]]> https://biorxiv.org/content/10.1101/2023.10.06.561291v1?rss=1 Kamalakar, A. Tobin, B. Kaimari, S. Toma, A. I. Moriarity, I. Gautam, S. Bhattaram, P. Abramowicz, S. Drissi, H. Garcia, A. Wood, L. Goudy, S. L. 2023-10-10 doi:10.1101/2023.10.06.561291 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ A Histomorphometric and Computational Investigation of the Stabilizing Role of Pectinate Ligaments in the Aqueous Outflow Pathway ]]> https://biorxiv.org/content/10.1101/2023.10.17.562754v1?rss=1 Safa, B. N. Fraticelli Guzman, N. S. Li, G. Stamer, W. D. Feola, A. J. Ethier, C. R. 2023-10-17 doi:10.1101/2023.10.17.562754 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Dual antibacterial properties of copper coated nanotextured stainless steel ]]> https://biorxiv.org/content/10.1101/2023.10.19.563111v1?rss=1 View larger version (44K): org.highwire.dtl.DTLVardef@1d7e8f4org.highwire.dtl.DTLVardef@1feff9borg.highwire.dtl.DTLVardef@3f4224org.highwire.dtl.DTLVardef@10f8207_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Tripathi, A. Park, J. Pho, T. Champion, J. A. 2023-10-19 doi:10.1101/2023.10.19.563111 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Aging and intraocular pressure homeostasis in mice ]]> https://biorxiv.org/content/10.1101/2023.10.17.562768v1?rss=1 Li, G. van Batenburg-Sherwood, J. Safa, B. N. Fraticelli Guzman, N. S. Wilson, A. Bahrani Fard, M. R. Choy, K. de Ieso, M. L. Cui, S. Feola, A. J. Weisz, T. Kuhn, M. Bowes Rickman, C. Farsiu, S. Ethier, C. R. Stamer, W. D. 2023-10-20 doi:10.1101/2023.10.17.562768 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Using an ODE model to separate Rest and Task signals in fMRI ]]> https://biorxiv.org/content/10.1101/2023.10.23.563564v1?rss=1 Kashyap, A. Geenjaar, E. P. T. Bey, P. Dhindsa, J. Glomb, K. Plis, S. Keilholz, S. Ritter, P. 2023-10-23 doi:10.1101/2023.10.23.563564 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Natural variation in oxytocin receptor signaling causes widespread changes in brain transcription: a link to the natural killer gene complex ]]> https://biorxiv.org/content/10.1101/2023.10.26.564214v1?rss=1 Boender, A. J. Johnson, Z. V. Gruenhagen, G. W. Horie, K. Hegarty, B. E. Streelman, J. T. Walum, H. Young, L. J. 2023-10-28 doi:10.1101/2023.10.26.564214 Cold Spring Harbor Laboratory Press 2023-10-28 <![CDATA[ Automated machine learning and explainable AI (AutoML-XAI) for metabolomics: improving cancer diagnostics ]]> https://biorxiv.org/content/10.1101/2023.10.26.564244v1?rss=1 Bifarin, O. O. Fernandez, F. O. 2023-10-31 doi:10.1101/2023.10.26.564244 Cold Spring Harbor Laboratory Press 2023-10-31 <![CDATA[ New information triggers prospective codes to adapt for flexible navigation ]]> https://biorxiv.org/content/10.1101/2023.10.31.564814v1?rss=1 Prince, S. M. Yassine, T. A. Katragadda, N. Roberts, T. C. Singer, A. C. 2023-11-01 doi:10.1101/2023.10.31.564814 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Ultrahigh Resolution Lipid Mass Spectrometry Imaging of High-Grade Serous Ovarian Cancer Mouse Models ]]> https://biorxiv.org/content/10.1101/2023.10.30.564760v1?rss=1 Ma, X. Botros, A. Yun, S. R. Park, E. Y. Kim, O. Park, S. Pham, T.-H. Chen, R. Palaniappan, M. Matzuk, M. M. Kim, J. Fernandez, F. M. 2023-11-02 doi:10.1101/2023.10.30.564760 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Experimental evolution of multicellularity via cuboidal cell packing in fission yeast ]]> https://biorxiv.org/content/10.1101/2023.11.03.565576v1?rss=1 300 million years ago. Our results provide insight into the evolution of cuboidal cell packing, an understudied multicellular morphology, and highlights the deeply convergent potential for a transition to multicellular individuality within fungi. ]]> Pineau, R. Kahn, P. C. Lac, D. T. Denning, M. Wong, W. Ratcliff, W. Bozdag, G. O. 2023-11-05 doi:10.1101/2023.11.03.565576 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ The Vacant Niche Revisited: Using Negative Results to Refine the Limits of Habitability ]]> https://biorxiv.org/content/10.1101/2023.11.06.565904v1?rss=1 Graham, H. V. Ratliff, L. E. Fulford, A. Pozarycki, C. I. Wimp, G. M. Nichols, F. Osburn, M. 2023-11-08 doi:10.1101/2023.11.06.565904 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Enteric Populations of Escherichia coli are Likely to be Resistant to Phages Due to O Antigen Production ]]> https://biorxiv.org/content/10.1101/2023.11.08.566299v1?rss=1 Berryhill, B. A. Burke, K. B. Fontaine, J. Brink, C. E. Harvill, M. G. Goldberg, D. A. Konstantinidis, K. T. Levin, B. R. Woodworth, M. H. 2023-11-08 doi:10.1101/2023.11.08.566299 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ A Method for Analyzing AFM Force Mapping Data Obtained from Soft Tissue Cryosections ]]> https://biorxiv.org/content/10.1101/2023.11.08.566263v1?rss=1 Wong, C. A. Fraticelli Guzman, N. S. Read, A. T. Hedberg-Buenz, A. Anderson, M. G. Feola, A. J. Sulchek, T. Ethier, C. R. 2023-11-13 doi:10.1101/2023.11.08.566263 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Design of parallel ????-sheet nanofibrils using Monte-Carlo search, coarse-grained simulations, and experimental testing ]]> https://biorxiv.org/content/10.1101/2023.11.09.565678v1?rss=1 Sarma, S. Sudarshan, T. R. Nguyen, V. Robang, A. S. Xiao, X. Le, J. V. Helmicki, M. E. Paravastu, A. K. Hall, C. K. 2023-11-13 doi:10.1101/2023.11.09.565678 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ SEAMoD: A fully interpretable neural network for cis-regulatory analysis of differentially expressed genes ]]> https://biorxiv.org/content/10.1101/2023.11.09.565900v1?rss=1 Bhogale, S. Seward, C. H. Stubbs, L. J. Sinha, S. 2023-11-13 doi:10.1101/2023.11.09.565900 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ SPREd: A simulation-supervised neural network tool for gene regulatory network reconstruction ]]> https://biorxiv.org/content/10.1101/2023.11.09.566399v1?rss=1 Wu, Z. Sinha, S. 2023-11-13 doi:10.1101/2023.11.09.566399 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ A non-adaptive explanation for macroevolutionary patterns in the evolution of complex multicellularity ]]> https://biorxiv.org/content/10.1101/2023.11.11.566713v1?rss=1 Bingham, E. P. Ratcliff, W. C. 2023-11-13 doi:10.1101/2023.11.11.566713 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Lateral inhibition in V1 controls neural & perceptual contrast sensitivity ]]> https://biorxiv.org/content/10.1101/2023.11.10.566605v1?rss=1 Del Rosario, J. Coletta, S. Kim, S. H. Mobille, Z. Peelman, K. Williams, B. Otsuki, A. J. Del Castillo Valerio, A. Worden, K. Blanpain, L. T. Lovell, L. Choi, H. Haider, B. 2023-11-14 doi:10.1101/2023.11.10.566605 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ rNMPID: a database for riboNucleoside Mono-Phosphates In DNA ]]> https://biorxiv.org/content/10.1101/2023.11.16.567417v1?rss=1 Yang, J. Sun, M. Ran, Z. Yang, T. Kundnani, D. L. Storici, F. Xu, P. 2023-11-17 doi:10.1101/2023.11.16.567417 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ The biophysical basis of bacterial colony growth ]]> https://biorxiv.org/content/10.1101/2023.11.17.567592v1?rss=1 Pokhrel, A. R. Steinbach, G. Krueger, A. Day, T. C. Tijani, J. Hammer, B. K. Yunker, P. J. 2023-11-17 doi:10.1101/2023.11.17.567592 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Active and abundant alphaproteobacterial nitric oxide transforming enzymes in a marine oxygen deficient zone ]]> https://biorxiv.org/content/10.1101/2023.11.21.568154v1?rss=1 Elbon, C. E. Stewart, F. J. Glass, J. B. 2023-11-22 doi:10.1101/2023.11.21.568154 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Enhanced surface accessibility of SARS-CoV-2 Omicron spike protein due to an altered glycosylation profile ]]> https://biorxiv.org/content/10.1101/2023.11.22.568381v1?rss=1 Wang, D. Zhang, Z. Baudys, J. Haynes, C. A. Osman, S. H. Zhou, B. Barr, J. R. Gumbart, J. C. 2023-11-23 doi:10.1101/2023.11.22.568381 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ EmbedGEM: A framework to evaluate the utility of embeddings for genetic discovery ]]> https://biorxiv.org/content/10.1101/2023.11.24.568344v1?rss=1 Mukherjee, S. McCaw, Z. R. Pei, J. Merkoulovitch, A. Tandon, R. Soare, T. W. Amar, D. Somineni, H. Klein, C. Satapati, S. Lloyd, D. Probert, C. Insitro Research Team, Koller, D. O'Dushlaine, C. Karaletsos, T. 2023-11-25 doi:10.1101/2023.11.24.568344 Cold Spring Harbor Laboratory Press 2023-11-25 <![CDATA[ Polygraph: A Software Framework for the Systematic Assessment of Synthetic Regulatory DNA Elements ]]> https://biorxiv.org/content/10.1101/2023.11.27.568764v1?rss=1 Gupta, A. Lal, A. Gunsalus, L. M. Biancalani, T. Eraslan, G. 2023-11-27 doi:10.1101/2023.11.27.568764 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ Reduced Achilles tendon stiffness in aging persists at matched activations and associates with higher metabolic cost of walking ]]> https://biorxiv.org/content/10.1101/2023.11.27.568808v1?rss=1 Franz, J. R. Krupenevich, R. Gray, A. Batsis, J. A. Sawicki, G. S. 2023-11-27 doi:10.1101/2023.11.27.568808 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ pH selects for distinct N2O-reducing microbiomes in tropical soil microcosms ]]> https://biorxiv.org/content/10.1101/2023.11.29.569236v1?rss=1 Sun, Y. Yin, Y. He, G. Cha, G. Ayala-del-Rio, H. Gonzalez, G. Konstantinidis, K. T. Loeffler, F. E. 2023-11-29 doi:10.1101/2023.11.29.569236 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Examining the role of oxygen-binding proteins on the early evolution of multicellularity ]]> https://biorxiv.org/content/10.1101/2023.12.01.569647v1?rss=1 Wong, W. Bravo, P. Yunker, P. J. Ratcliff, W. C. Burnetti, A. J. 2023-12-04 doi:10.1101/2023.12.01.569647 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ Changes in intra- and interlimb reflexes from hindlimb cutaneous afferents after staggered thoracic lateral hemisections during locomotion in cats ]]> https://biorxiv.org/content/10.1101/2023.12.15.571869v1?rss=1 Mari, S. Lecomte, C. G. Merlet, A. N. Audet, J. Yassine, S. Eddaoui, O. Genois, G. Nadeau, C. Harnie, J. Rybak, I. A. Prilutsky, B. I. Frigon, A. 2023-12-15 doi:10.1101/2023.12.15.571869 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Microscopy-guided subcellular proteomic discovery by high-speed ultra-content photo-biotinylation ]]> https://biorxiv.org/content/10.1101/2023.12.27.573388v1?rss=1 Liao, J.-C. Chen, Y.-D. Chang, C.-W. Cheung, C. H. Y. Chang, H.-J. Sie, Y.-D. Chung, C.-W. Huang, C.-K. Huang, C.-C. Chong, W. M. Liu, Y.-P. Lin, Y.-C. Kai, H.-J. J. Wang, P.-J. 2023-12-27 doi:10.1101/2023.12.27.573388 Cold Spring Harbor Laboratory Press 2023-12-27 <![CDATA[ Community Structure and Function During Periods of High Performance and System Upset in a Full-Scale Mixed Microalgal Wastewater Resource Recovery Facility ]]> https://biorxiv.org/content/10.1101/2024.01.23.576871v1?rss=1 4 months) of stable system performance that achieve robust nutrient recovery, even in winter months in northern latitudes (WI, USA). Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=72 SRC="FIGDIR/small/576871v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@15ef2a4org.highwire.dtl.DTLVardef@8c1de6org.highwire.dtl.DTLVardef@ff1160org.highwire.dtl.DTLVardef@1cded87_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMicrobial dynamics were examined for first full-scale, intensive (small footprint) algal wastewater treatment process (EcoRecover) for advanced P removal. C_LIO_LIMixed microbial communities during stable performance were dominated by Scenedesmus and Cyanobacteria and positively correlated with pH, alkalinity, and influent NH4+, among other parameters. C_LIO_LIBacterial nitrification did not benefit or hinder nutrient recovery, but partial nitrification and NO2- accumulation inhibited algal growth. C_LIO_LITaxa specific pest dynamics are described, with major outbreaks occurring during high temperature in summer months. C_LIO_LIControl of operational parameters, and recovery of stable system performance and algal biomass was achieved following system upsets. C_LI ]]> Alam, M. M. Hodaei, M. Hartnett, E. Gincley, B. Khan, F. Kim, G.-Y. Pinto, A. J. Bradley, I. M. 2024-01-26 doi:10.1101/2024.01.23.576871 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ Nanogap Solid-State Single-Molecule Detection at Mars, Europa, and Microgravity Conditions ]]> https://biorxiv.org/content/10.1101/2024.02.29.582359v1?rss=1 Ramirez-Colon, J. L. Johnson, E. Duzdevich, D. Lee, S. Soderblom, J. Zuber, M. T. Taniguchi, M. Ohshiro, T. Komoto, Y. Carr, C. E. 2024-03-02 doi:10.1101/2024.02.29.582359 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ HyperGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors ]]> https://biorxiv.org/content/10.1101/2024.03.05.583605v1?rss=1 Xu, W. Hsu, P.-K. Moshiri, N. Yu, S. Rosing, T. 2024-03-08 doi:10.1101/2024.03.05.583605 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ Microbial Response to Natural Disturbances: Rare Biosphere often plays a role ]]> https://biorxiv.org/content/10.1101/2024.03.06.583742v1?rss=1 Zhao, J. Brandt, G. Wang, Z. Hunt, D. E. Rodriguez-R, L. M. Hatt, J. K. Konstantinidis, K. T. 2024-03-11 doi:10.1101/2024.03.06.583742 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ A change in cis-regulatory logic underlying obligate versus facultative muscle multinucleation in chordates ]]> https://biorxiv.org/content/10.1101/2024.03.06.583753v1?rss=1 Johnson, C. J. Zhang, Z. Zhang, H. Shang, R. Piekarz, K. M. Bi, P. Stolfi, A. 2024-03-11 doi:10.1101/2024.03.06.583753 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Beyond functional connectivity: deep learning applied to resting-state fMRI time series in the prediction of 58 human traits in the HCP ]]> https://biorxiv.org/content/10.1101/2024.03.07.583858v1?rss=1 Vieira, B. H. Schöttner, M. Calhoun, V. D. Salmon, C. E. G. 2024-03-12 doi:10.1101/2024.03.07.583858 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Local FK506 delivery induces osteogenesis in in vivo rat bone defect and rabbit spine fusion models ]]> https://biorxiv.org/content/10.1101/2024.03.08.584163v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@1b0b690org.highwire.dtl.DTLVardef@a1e032org.highwire.dtl.DTLVardef@1862a55org.highwire.dtl.DTLVardef@1456fc1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Harrer, J. A. Fulton, T. M. Sangadala, S. Kaiser, J. Devereaux, E. J. Oliver, C. Presciutti, S. M. Boden, S. D. Willett, N. J. 2024-03-13 doi:10.1101/2024.03.08.584163 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Insights into Cellular Evolution: Temporal Deep Learning Models and Analysis for Cell Image Classification ]]> https://biorxiv.org/content/10.1101/2024.03.11.584308v1?rss=1 Zhao, X. de Perez, A. R. Dimitrova, E. S. Kemp, M. Anderson, P. E. 2024-03-12 doi:10.1101/2024.03.11.584308 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Behavior can be decoded across the cortex when individual differences are considered ]]> https://biorxiv.org/content/10.1101/2024.03.12.584674v1?rss=1 Nakuci, J. Yeon, J. Kim, J.-H. Kim, S.-P. Rahnev, D. 2024-03-14 doi:10.1101/2024.03.12.584674 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Forelimb movements contribute to hindlimb cutaneous reflexes during locomotion in cats ]]> https://biorxiv.org/content/10.1101/2024.03.13.584812v1?rss=1 Harnie, J. Al Arab, R. Mari, S. Yassine, S. Eddaoui, O. Jehannin, P. Audet, J. Lecomte, C. G. Iorio-Morin, C. Prilutsky, B. I. Rybak, I. A. Frigon, A. 2024-03-14 doi:10.1101/2024.03.13.584812 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ BinDash 2.0: New MinHash Scheme Allows Ultra-fast and Accurate Genome Search and Comparisons ]]> https://biorxiv.org/content/10.1101/2024.03.13.584875v1?rss=1 95% ANI) together. Availability and implementationBinDash is released under the Apache 2.0 license at: https://github.com/zhaoxiaofei/bindash Contactkostas.konstantinidis@gatech.edu Supplementary informationSupplementary data are available at Bioinformatics online. ]]> Zhao, J. Zhao, X. Pierre-Both, J. Konstantinidis, K. T. 2024-03-14 doi:10.1101/2024.03.13.584875 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Identifying EEG Biomarkers of Depression with Novel Explainable Deep Learning Architectures ]]> https://biorxiv.org/content/10.1101/2024.03.19.585728v1?rss=1 Ellis, C. A. Lapera Sancho, M. Miller, R. L. Calhoun, V. D. 2024-03-21 doi:10.1101/2024.03.19.585728 Cold Spring Harbor Laboratory Press 2024-03-21 <![CDATA[ Mitochondrial stress in GABAergic neurons non-cell autonomously regulates organismal health and aging ]]> https://biorxiv.org/content/10.1101/2024.03.20.585932v1?rss=1 Rathor, L. Curry, S. Park, Y. McElroy, T. Robles, B. Yi, S. Chen, W.-W. Min, K. Xiao, R. Lee, M. H. Han, S. M. 2024-03-25 doi:10.1101/2024.03.20.585932 Cold Spring Harbor Laboratory Press 2024-03-25 <![CDATA[ A method for focused ultrasound (FUS) neuromodulation with simultaneous electroencephalogram recordings in awake, head-fixed mice with temporal lobe epilepsy ]]> https://biorxiv.org/content/10.1101/2024.03.20.585988v1?rss=1 Cornelssen, C. Brown, B. Finlinson, E. Blair, S. Senthilkumar, S. Kubanek, J. Wilcox, K. S. 2024-03-25 doi:10.1101/2024.03.20.585988 Cold Spring Harbor Laboratory Press 2024-03-25 <![CDATA[ Parallel Multilink Group Joint ICA: Fusion of 3D Structural and 4D Functional Data Across Multiple Resting fMRI Networks ]]> https://biorxiv.org/content/10.1101/2024.03.21.586091v1?rss=1 Khalilullah, K. M. I. Agcaoglu, O. Sui, J. Duda, M. Adali, T. Calhoun, V. D. 2024-03-27 doi:10.1101/2024.03.21.586091 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Operation regimes of spinal circuits controlling locomotion and role of supraspinal drives and sensory feedback ]]> https://biorxiv.org/content/10.1101/2024.03.21.586122v1?rss=1 Rybak, I. A. Shevtsova, N. A. Markin, S. N. Prilutsky, B. I. Frigon, A. 2024-03-27 doi:10.1101/2024.03.21.586122 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Integrating Chromosome Conformation and DNA Repair in a Computational Framework to Assess Cell Radiosensitivity ]]> https://biorxiv.org/content/10.1101/2024.03.25.586626v1?rss=1 Andriotty, M. Wang, C.-K. C. Kapadia, A. McCord, R. P. Agasthya, G. 2024-03-27 doi:10.1101/2024.03.25.586626 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Multifaceted roles of cohesin in regulating transcriptional loops ]]> https://biorxiv.org/content/10.1101/2024.03.25.586715v1?rss=1 100 kb) loops between distal (super-)enhancers and promoters of cell-type-specific genes. By contrast, the short-range (<50 kb) loops were insensitive to RAD21 depletion and connected genes that are mostly housekeeping. This result explains why only a small fraction of genes are affected by the loss of long-range chromatin interactions due to cohesin depletion. Remarkably, RAD21 depletion appeared to up-regulate genes located in early initiation zones (EIZ) of DNA replication, and the EIZ signals were amplified drastically without RAD21. Our results revealed new mechanistic insights of cohesins multifaceted roles in establishing transcriptional loops, preserving long-range chromatin interactions for cell-specific genes, and maintaining timely order of DNA replication. ]]> Kim, M. Wang, P. Clow, P. Chien, I. Wang, X. Peng, J. Chai, H. Liu, X. Lee, B. Ngan, C. Y. Yue, F. Milenkovic, O. Chuang, J. H. Wei, C.-L. Casellas, R. Cheng, A. Ruan, Y. 2024-03-27 doi:10.1101/2024.03.25.586715 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ A Novel Liver Cancer-Selective Histone Deacetylase Inhibitor Is Effective Against Hepatocellular Carcinoma and Induces Durable Responses with Immunotherapy ]]> https://biorxiv.org/content/10.1101/2024.03.27.587062v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@28281corg.highwire.dtl.DTLVardef@617aa9org.highwire.dtl.DTLVardef@1bc198dorg.highwire.dtl.DTLVardef@31852e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wu, B. Tapadar, S. Ruan, Z. Sun, C. Arnold, R. Olugbami, J. Johnston, A. Arunsi, U. Gaul, D. Petros, J. Kobayashi, T. Duda, D. G. Oyelere, A. K. 2024-03-28 doi:10.1101/2024.03.27.587062 Cold Spring Harbor Laboratory Press 2024-03-28 <![CDATA[ Patch-walking: Coordinated multi-pipette patch clamp for efficiently finding synaptic connections ]]> https://biorxiv.org/content/10.1101/2024.03.30.587445v1?rss=1 Yip, M. C. Gonzalez, M. M. Lewallen, C. F. Landry, C. R. Kolb, I. Yang, B. Stoy, W. M. Fong, M.-f. J Rowan, M. Boyden, E. S. Forest, C. R. 2024-04-01 doi:10.1101/2024.03.30.587445 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ BEAN and HABAS: Polyphyletic insertions in RNAP that point to deep evolutionary divergence of bacteria ]]> https://biorxiv.org/content/10.1101/2024.04.02.587612v1?rss=1 Alvarez-Carreno, C. Huynh, A. T. Orengo, C. Williams, L. D. 2024-04-02 doi:10.1101/2024.04.02.587612 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Tiny amphibious insects use tripod gait for seamless transition across land, water, and duckweed ]]> https://biorxiv.org/content/10.1101/2024.04.02.587757v1?rss=1 O'Neil, J. N. Yung, K. L. Difini, G. Walker, H. Bhamla, M. S. 2024-04-02 doi:10.1101/2024.04.02.587757 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Limb loss and specialized leg dynamics in tiny water-walking insects ]]> https://biorxiv.org/content/10.1101/2024.04.02.587762v1?rss=1 O'Neil, J. N. Yung, K. L. Difini, G. Rohilla, P. Bhamla, M. S. 2024-04-02 doi:10.1101/2024.04.02.587762 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Creative tempo: Spatiotemporal dynamics of the default mode network in improvisational musicians ]]> https://biorxiv.org/content/10.1101/2024.04.07.588391v1?rss=1 Watters, H. N. Fazili, A. Daley, L. Belden, A. LaGrow, T. J. Bolt, T. S. Loui, P. Keilholz, S. 2024-04-09 doi:10.1101/2024.04.07.588391 Cold Spring Harbor Laboratory Press 2024-04-09 <![CDATA[ Analysis of Longitudinal Change Patterns in Developing Brain Using Functional and Structural Magnetic Resonance Imaging via Multimodal Fusion ]]> https://biorxiv.org/content/10.1101/2024.04.07.588473v1?rss=1 Saha, R. Saha, D. K. Fu, Z. Duda, M. Silva, R. F. Calhoun, V. 2024-04-10 doi:10.1101/2024.04.07.588473 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ Multi-Niche Human Bone Marrow On-A-Chip for Studying the Interactions of Adoptive CAR-T Cell Therapies with Multiple Myeloma ]]> https://biorxiv.org/content/10.1101/2024.04.08.588601v1?rss=1 Ghoshal, D. Petersen, I. Ringquist, R. Kramer, L. Bhatia, E. Hu, T. Richard, A. Park, R. Corbin, J. Agarwal, S. Thomas, A. Ramirez, S. Tharayil, J. Downey, E. Ketchum, F. Ochal, A. Sonthi, N. Lonial, S. Kochenderfer, J. N. Tran, R. Zhu, M. Lam, W. A. Coskun, A. F. Roy, K. 2024-04-12 doi:10.1101/2024.04.08.588601 Cold Spring Harbor Laboratory Press 2024-04-12 <![CDATA[ A transcriptome atlas of zygotic and somatic embryogenesis in Norway spruce ]]> https://biorxiv.org/content/10.1101/2024.04.13.589382v1?rss=1 Stojkovic, K. Canovi, C. Le, K.-C. Delhomme, N. Egertsdotter, U. Street, N. R. 2024-04-16 doi:10.1101/2024.04.13.589382 Cold Spring Harbor Laboratory Press 2024-04-16 <![CDATA[ Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands ]]> https://biorxiv.org/content/10.1101/2024.04.15.589101v1?rss=1 Bechtold, E. K. Ellenbogen, J. B. Villa, J. A. de Melo Ferreira, D. K. Oliverio, A. M. Kostka, J. E. Rich, V. I. Varner, R. K. Bansal, S. Ward, E. J. Bohrer, G. Borton, M. A. Wrighton, K. C. Wilkins, M. J. 2024-04-15 doi:10.1101/2024.04.15.589101 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ Wax "tails" enable planthopper nymphs to self-right midair and land on their feet ]]> https://biorxiv.org/content/10.1101/2024.04.15.589523v1?rss=1 McDonald, C. L. Alcalde, G. T. Jones, T. C. Laude, R. A. P. Yap, S. A. Bhamla, M. S. 2024-04-16 doi:10.1101/2024.04.15.589523 Cold Spring Harbor Laboratory Press 2024-04-16 <![CDATA[ DNA methylation differences between the female and male X chromosomes in human brain ]]> https://biorxiv.org/content/10.1101/2024.04.16.589778v1?rss=1 Morgan, R. Loh, E. Singh, D. Mendizabal, I. Yi, S. 2024-04-17 doi:10.1101/2024.04.16.589778 Cold Spring Harbor Laboratory Press 2024-04-17 <![CDATA[ Whole-genome duplication in the Multicellularity Long Term Evolution Experiment ]]> https://biorxiv.org/content/10.1101/2024.04.18.588554v1?rss=1 Tong, K. Datta, S. Cheng, V. Haas, D. J. Gourisetti, S. Yopp, H. L. Day, T. C. Lac, D. T. Conlin, P. L. Bozdag, G. O. Ratcliff, W. C. 2024-04-19 doi:10.1101/2024.04.18.588554 Cold Spring Harbor Laboratory Press 2024-04-19 <![CDATA[ A natural ANI gap that can define intra-species units of bacteriophages and other viruses ]]> https://biorxiv.org/content/10.1101/2024.04.18.590031v1?rss=1 Aldeguer Riquelme, B. Conrad, R. E. Anton, J. Rossello-Mora, R. Konstantinidis, K. T. 2024-04-18 doi:10.1101/2024.04.18.590031 Cold Spring Harbor Laboratory Press 2024-04-18 <![CDATA[ Infraslow dynamic patterns in human cortical networks track a spectrum of external to internal attention ]]> https://biorxiv.org/content/10.1101/2024.04.22.590625v1?rss=1 Watters, H. Davis, A. Fazili, A. Daley, L. LaGrow, T. J. Schumacher, E. H. Keilholz, S. 2024-04-23 doi:10.1101/2024.04.22.590625 Cold Spring Harbor Laboratory Press 2024-04-23 <![CDATA[ Changes in intra- and interlimb reflexes from forelimb cutaneous afferents after staggered thoracic lateral hemisections during locomotion in cats ]]> https://biorxiv.org/content/10.1101/2024.04.23.590723v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@1ef94c1org.highwire.dtl.DTLVardef@f2ec5org.highwire.dtl.DTLVardef@c7c30aorg.highwire.dtl.DTLVardef@d5ce21_HPS_FORMAT_FIGEXP M_FIG C_FIG Contacting an obstacle during locomotion activates cutaneous afferents to maintain balance and coordinate all four limbs. Spinal cord injuries disrupt neural communications between spinal networks controlling the fore- and hindlimbs, impairing balance and limb coordination. Cutaneous reflex pathways can be used to develop therapeutic approaches for restoring ascending and descending transmission to facilitate locomotor recovery. ]]> Mari, S. Lecomte, C. G. Merlet, A. N. Audet, J. Yassine, S. Al Arab, R. Harnie, J. Rybak, I. A. Prilutsky, B. Frigon, A. 2024-04-23 doi:10.1101/2024.04.23.590723 Cold Spring Harbor Laboratory Press 2024-04-23 <![CDATA[ Variation in the Distribution of Large-scale Spatiotemporal Patterns of Activity Across Brain States ]]> https://biorxiv.org/content/10.1101/2024.04.26.591295v1?rss=1 Meyer-Baese, L. Anumba, N. Bolt, T. S. Daley, L. LaGrow, T. J. Zhang, X. Xu, N. Pan, W.-J. Schumacher, E. H. Keilholz, S. 2024-04-29 doi:10.1101/2024.04.26.591295 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Unifying community-wide whole-brain imaging datasets enables robust automated neuron identification and reveals determinants of neuron positioning in C. elegans ]]> https://biorxiv.org/content/10.1101/2024.04.28.591397v1?rss=1 Sprague, D. Y. Rusch, K. Dunn, R. L. Borchardt, J. Bubnis, G. Chiu, G. Wen, C. Suzuki, R. Chaudhary, S. Dichter, B. Ly, R. Onami, S. Lu, H. Kimura, K. Yemini, E. I. Kato, S. 2024-04-30 doi:10.1101/2024.04.28.591397 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ Gait signature changes with walking speed are similar among able-bodied young adults despite persistent individual-specific differences ]]> https://biorxiv.org/content/10.1101/2024.05.01.591976v1?rss=1 Winner, T. S. Rosenberg, M. C. Berman, G. J. Kesar, T. M. Ting, L. H. 2024-05-03 doi:10.1101/2024.05.01.591976 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases ]]> https://biorxiv.org/content/10.1101/2024.05.01.592096v1?rss=1 Corbella, M. Bravo, J. Demkiv, A. O. Calixto, A. R. Sompiyachoke, K. Bergonzi, C. Elias, M. H. Kamerlin, S. C. L. 2024-05-01 doi:10.1101/2024.05.01.592096 Cold Spring Harbor Laboratory Press 2024-05-01 <![CDATA[ Accounting for Cellular-Level Variation in Lysis: Implications for Virus-Host Dynamics ]]> https://biorxiv.org/content/10.1101/2024.05.04.592515v1?rss=1 Dominguez-Mirazo, M. Harris, J. D. Demory, D. Weitz, J. S. 2024-05-07 doi:10.1101/2024.05.04.592515 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ Neuromechanical Phase Lags and Gait Adaptation in the Nematode C. elegans ]]> https://biorxiv.org/content/10.1101/2024.05.06.592744v1?rss=1 Pierce, C. J. Ding, Y. Chong, B. Lu, H. Goldman, D. I. 2024-05-08 doi:10.1101/2024.05.06.592744 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Topological data analysis of pattern formation of human induced pluripotent stem cell colonies ]]> https://biorxiv.org/content/10.1101/2024.05.07.592985v1?rss=1 Hartsock, I. Park, E. Toppen, J. Bubenik, P. Dimitrova, E. S. Kemp, M. L. Cruz, D. A. 2024-05-08 doi:10.1101/2024.05.07.592985 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ The molecular mechanism of on-demand sterol biosynthesis at organelle contact sites ]]> https://biorxiv.org/content/10.1101/2024.05.09.593285v1?rss=1 Zung, N. Aravindan, N. Boshnakovska, A. Valenti, R. Preminger, N. Jonas, F. Yaakov, G. Willoughby, M. Homberg, B. Keller, J. Kupervaser, M. Dezorella, N. Dadosh, T. Wolf, S. G. Itkin, M. Malitsky, S. Brandis, A. Barkai, N. Fernandez-Busnadiego, R. Reddi, A. Rehling, P. Rapaport, D. Schuldiner, M. 2024-05-10 doi:10.1101/2024.05.09.593285 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ HIGH THROUGHPUT QUANTITATION OF HUMAN NEUTROPHIL RECRUITMENT AND FUNCTIONAL RESPONSES IN AN AIR-BLOOD BARRIER ARRAY ]]> https://biorxiv.org/content/10.1101/2024.05.10.593624v1?rss=1 Viola, H. Chen, L. H. Jo, S. Washington, K. Selva, C. Li, A. Feng, D. Giacalone, V. Stephenson, S. Cottrill, K. Mohammed, A. Williams, E. Qu, X. Lam, W. A. Ng, N. L. Fitzpatrick, A. Grunwell, J. Tirouvanziam, R. Takayama, S. 2024-05-14 doi:10.1101/2024.05.10.593624 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Magnetically Steered Cell Therapy For Functional Restoration Of Intraocular Pressure Control In Open-Angle Glaucoma ]]> https://biorxiv.org/content/10.1101/2024.05.13.593917v1?rss=1 Bahrani Fard, M. R. Chan, J. Read, A. T. Li, G. Cheng, L. N Safa, B. Siadat, S. M. Jhunjhunwala, A. Grossniklaus, H. E. Emelianov, S. Y. Stamer, W. D. Kuehn, M. H. Ethier, C. R. 2024-05-15 doi:10.1101/2024.05.13.593917 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Predictive Control of Musculotendon Loads Across Fast and Slow-twitch Muscles in a Simulated System with Parallel Actuation ]]> https://biorxiv.org/content/10.1101/2024.05.14.594110v1?rss=1 Nabipour, M. Sawicki, G. S. Sartori, M. 2024-05-15 doi:10.1101/2024.05.14.594110 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Efficient Federated Learning for distributed NeuroImaging Data ]]> https://biorxiv.org/content/10.1101/2024.05.14.594167v1?rss=1 Thapaliya, B. Ohib, R. Geenjaar, E. P. T. Liu, J. Calhoun, V. Plis, S. 2024-05-15 doi:10.1101/2024.05.14.594167 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Fluctuations and freezing of biofilm-air interfaces ]]> https://biorxiv.org/content/10.1101/2024.05.14.594239v1?rss=1 Bravo, P. J. Yunker, P. J. 2024-05-15 doi:10.1101/2024.05.14.594239 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Leeches Predate on Fast-Escaping and Entangling Blackworms by Spiral Entombment ]]> https://biorxiv.org/content/10.1101/2024.05.14.594257v1?rss=1 Tuazon, H. David, S. W. Ma, K. Bhamla, M. S. 2024-05-15 doi:10.1101/2024.05.14.594257 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma ]]> https://biorxiv.org/content/10.1101/2024.05.15.593193v1?rss=1 Pilcher, W. C. Yao, L. Gonzalez-Kozlova, E. Pita-Juarez, Y. Karagkouni, D. Acharya, C. Michaud, M. E. Hamilton, M. Nanda, S. Song, Y. Sato, K. Wang, J. T. Satpathy, S. Ma, Y. Schulman, J. D'Souza, D. Jayasinghe, R. G. Cheloni, G. Bakhtiari, M. Pabustan, N. Nie, K. Foltz, J. A. Saldarriaga, I. Alaaeldin, R. Lepisto, E. Chen, R. Fiala, M. A. Thomas, B. E. Cook, A. Vieira Dos Santos, J. Chiang, I.-l. Figueiredo De Souza, I. Fortier, J. Slade, M. Oh, S. T. Rettig, M. P. Anderson, E. Li, Y. Dasari, S. Strausbauch, M. A. Simon, V. A. MMRF Immune Atlas Consort 2024-05-17 doi:10.1101/2024.05.15.593193 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ Unexpected events modulate context signaling in VIP and excitatory cells of the visual cortex ]]> https://biorxiv.org/content/10.1101/2024.05.15.594366v1?rss=1 Najafi, F. Russo, S. Lecoq, J. 2024-05-15 doi:10.1101/2024.05.15.594366 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Frequency and duration of sensory flicker controls astrocyte and neuron specific transcriptional profiles in 5xFAD mice ]]> https://biorxiv.org/content/10.1101/2024.05.20.594705v1?rss=1 Bitarafan, S. Pybus, A. F. Rivera Moctezuma, F. G. Adibi, M. H. Franklin, T. Singer, A. C. Wood, L. B. 2024-05-21 doi:10.1101/2024.05.20.594705 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ The Effects of Locus Coeruleus Optogenetic Stimulation on Global Spatiotemporal Patterns in Rats ]]> https://biorxiv.org/content/10.1101/2024.05.23.595327v1?rss=1 Anumba, N. Kelberman, M. A. Pan, W. Marriott, A. Zhang, X. Xu, N. Weinshenker, D. Keilholz, S. 2024-05-23 doi:10.1101/2024.05.23.595327 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Spike Reliability is Cell-Type Specific and Shapes Excitation and Inhibition in the Cortex ]]> https://biorxiv.org/content/10.1101/2024.06.05.597657v1?rss=1 Russo, S. Stanley, G. B. Najafi, F. 2024-06-08 doi:10.1101/2024.06.05.597657 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Multi-modal Spatial-modality Attentive Fusion for Studying Neurodegenerative Disorders ]]> https://biorxiv.org/content/10.1101/2024.06.09.598091v1?rss=1 Rahaman, M. A. Garg, Y. Iraji, A. Fu, Z. Kochunov, P. Hong, L. E. Van Erp, T. G. M. Preda, A. Chen, J. Calhoun, V. 2024-06-09 doi:10.1101/2024.06.09.598091 Cold Spring Harbor Laboratory Press 2024-06-09 <![CDATA[ Reversible kink instability drives ultrafast jumping in nematodes and soft robots ]]> https://biorxiv.org/content/10.1101/2024.06.07.598012v1?rss=1 Kumar, S. Tiwari, I. M. Ortega-Jimenez, V. R. Dillman, A. He, D. Hu, Y. Bhamla, M. S. 2024-06-10 doi:10.1101/2024.06.07.598012 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ SpaDE: Semantic Locality Preserving Biclusteringfor Neuroimaging Data ]]> https://biorxiv.org/content/10.1101/2024.06.08.598092v1?rss=1 Rahaman, M. A. Fu, Z. Iraji, A. Calhoun, V. 2024-06-10 doi:10.1101/2024.06.08.598092 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Multi-parametric thrombus profiling microfluidics detects intensified biomechanical thrombogenesis associated with hypertension and aging ]]> https://biorxiv.org/content/10.1101/2024.06.11.598290v1?rss=1 Din, M. Paul, S. Ullah, S. Yang, H. Xu, R.-G. Abidin, N. A. Z. Chowdhury, B. Zhou, F. Rogers, S. Miller, M. Biswas, A. Hu, L. Fan, Z. Zahner, C. Chen, Z. Berman, M. Xue, L. Ju, L. A. Chen, Y. 2024-06-12 doi:10.1101/2024.06.11.598290 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ Is subjective perceptual similarity metacognitive? ]]> https://biorxiv.org/content/10.1101/2024.06.13.598769v1?rss=1 Moharramipour, A. Zhou, W. Rahnev, D. Lau, H. 2024-06-14 doi:10.1101/2024.06.13.598769 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Advancing source tracking: systematic review and source-specific genome database curation of fecally shed prokaryotes ]]> https://biorxiv.org/content/10.1101/2024.06.14.598882v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@daeadcorg.highwire.dtl.DTLVardef@713d09org.highwire.dtl.DTLVardef@5e538borg.highwire.dtl.DTLVardef@bed833_HPS_FORMAT_FIGEXP M_FIG C_FIG SynopsisWe curate nine prokaryotic genomic databases for fecal source-tracking, summarize their source-specificity, and show their usefulness by bioinformatically testing mock impaired surface water samples. ]]> Lindner, B. G. Choudhury, R. A. Pinamang, P. Bingham, L. D'Amico, I. Hatt, J. K. Konstantinidis, K. T. Graham, K. E. 2024-06-17 doi:10.1101/2024.06.14.598882 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Static and Dynamic Cross-Network Functional Connectivity Shows Elevated Entropy in Schizophrenia Patients ]]> https://biorxiv.org/content/10.1101/2024.06.15.599084v1?rss=1 Maksymchuk, N. Bustillo, J. R. Mathalon, D. H. Preda, A. Calhoun, V. D. 2024-06-17 doi:10.1101/2024.06.15.599084 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Adaptive Wheel Exercise for Mouse Models of Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2024.06.19.598025v1?rss=1 Skelton, H. M. Grogan, D. Kotlure, A. Berglund, K. Gutekunst, C.-A. Gross, R. 2024-06-23 doi:10.1101/2024.06.19.598025 Cold Spring Harbor Laboratory Press 2024-06-23 <![CDATA[ Spinal interneuron population dynamics underlying flexible pattern generation ]]> https://biorxiv.org/content/10.1101/2024.06.20.599927v1?rss=1 Wimalasena, L. N. Pandarinath, C. Au Yong, N. 2024-06-23 doi:10.1101/2024.06.20.599927 Cold Spring Harbor Laboratory Press 2024-06-23 <![CDATA[ Stereotyped spatiotemporal dynamics of spontaneous activity in visual cortex prior to eye-opening ]]> https://biorxiv.org/content/10.1101/2024.06.25.600611v1?rss=1 Kettlewell, L. S. Sederberg, A. Smith, G. B. 2024-06-29 doi:10.1101/2024.06.25.600611 Cold Spring Harbor Laboratory Press 2024-06-29 <![CDATA[ SCEMENT: Scalable and Memory Efficient Integration of Large-scale Single Cell RNA-sequencing Data ]]> https://biorxiv.org/content/10.1101/2024.06.27.601027v1?rss=1 Chockalingam, S. P. Aluru, M. Aluru, S. 2024-07-02 doi:10.1101/2024.06.27.601027 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Microglia Morphological Response to Mesenchymal Stromal Cell Extracellular Vesicles Demonstrates EV Therapeutic Potential for Modulating Neuroinflammation ]]> https://biorxiv.org/content/10.1101/2024.07.01.601612v1?rss=1 Daga, K. R. Larey, A. M. Morfin, M. G. Chen, K. Bitarafan, S. Carpenter, J. M. Hynds, H. M. Hines, K. M. Wood, L. B. Marklein, R. A. 2024-07-03 doi:10.1101/2024.07.01.601612 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ Flexible EMG arrays with integrated electronics for scalable electrode density ]]> https://biorxiv.org/content/10.1101/2024.07.02.601782v1?rss=1 Anschutz, P. M. Zia, M. Lu, J. Williams, M. J. Jacob, A. L. Sober, S. J. Bakir, M. S. 2024-07-03 doi:10.1101/2024.07.02.601782 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ Opto-Myomatrix: μLED integrated microelectrode arrays for optogenetic activation and electrical recording in muscle tissue ]]> https://biorxiv.org/content/10.1101/2024.07.01.601601v1?rss=1 Lu, J. Zia, M. Baig, D. A. Yan, G. Kim, J. J. Nagapudi, K. Anschutz, P. Oh, S. O'Connor, D. H. Sober, S. J. Bakir, M. S. 2024-07-04 doi:10.1101/2024.07.01.601601 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ The WAVE complex forms linear arrays at negative membrane curvature to instruct lamellipodia formation. ]]> https://biorxiv.org/content/10.1101/2024.07.08.600855v1?rss=1 Wu, M. Marchando, P. Meyer, K. Tang, Z. Woolfson, D. N. Weiner, O. D. 2024-07-08 doi:10.1101/2024.07.08.600855 Cold Spring Harbor Laboratory Press 2024-07-08 <![CDATA[ Body oscillations reduce the aerodynamic power requirement of wild silkmoth flight ]]> https://biorxiv.org/content/10.1101/2024.07.07.602433v1?rss=1 Sikandar, U. B. Aiello, B. R. Sponberg, S. 2024-07-10 doi:10.1101/2024.07.07.602433 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Single-cell analysis of pediatric acute myeloid leukemia samples uncovers treatment-resistant stem and mast cells ]]> https://biorxiv.org/content/10.1101/2024.07.09.602801v1?rss=1 Ohlstrom, D. Bakhtia, M. Mumme, H. Michaud, M. Chien, F. Pilcher, W. Satpathy, S. Bhasin, S. Bhasin, M. 2024-07-10 doi:10.1101/2024.07.09.602801 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Body size and light environment modulate flight speed and saccadic behavior in free flying Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2024.07.08.602594v1?rss=1 Barredo, E. Yang, H. Currea, J. P. Sondhi, Y. Palavalli-Nettimi, R. Sponberg, S. Tarokh, V. Theobald, J. 2024-07-11 doi:10.1101/2024.07.08.602594 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Temporal resolution of spike coding in feedforward networks with signal convergence and divergence ]]> https://biorxiv.org/content/10.1101/2024.07.08.602598v1?rss=1 Mobille, Z. Sikandar, U. B. Sponberg, S. Choi, H. 2024-07-11 doi:10.1101/2024.07.08.602598 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ ROLE OF FORELIMB MORPHOLOGY IN MUSCLE SENSORIMOTOR FUNCTIONS DURING LOCOMOTION IN THE CAT ]]> https://biorxiv.org/content/10.1101/2024.07.11.603106v1?rss=1 Rahmati, S. M. Klishko, A. N. Martin, R. S. Bunderson, N. E. Meslie, J. A. Nichols, T. R. Rybak, I. A. Frigon, A. Burkholder, T. J. Prilutsky, B. I. 2024-07-16 doi:10.1101/2024.07.11.603106 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Experimental evolution of gene essentiality in bacteria ]]> https://biorxiv.org/content/10.1101/2024.07.16.600122v1?rss=1 1000 spontaneous suppressor mutations in experimental evolution. Many of these mutations define new gene and pathway relationships, such as F1Fo-ATPase/V1Vo-ATPase/TrkA1-H1 that were demonstrated across multiple Streptococcus species. Patterns of spontaneous mutations occurring in essential gene mutants differed from those found in wildtype. While gene duplications occurred rarely and appeared most often at later stages of evolution, substitutions, deletions, and insertions were prevalent in evolved populations. These essential gene deletion mutants and spontaneous mutations fixed in the mutant populations during evolution establish a foundation for understanding gene essentiality and the interaction of essential genes in networks. ]]> Bao, L. Zhu, Z. Ismail, A. Zhu, B. Anandan, V. Whiteley, M. Kitten, T. Xu, P. 2024-07-19 doi:10.1101/2024.07.16.600122 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Non-Invasive Quality Control of Organoid Cultures Using Mesofluidic CSTR Bioreactors and High-Content Imaging ]]> https://biorxiv.org/content/10.1101/2024.07.19.604365v1?rss=1 Charles, S. Jackson-Holmes, E. Sun, G. Zhou, Y. Siciliano, B. Niu, W. Han, H. Nikitina, A. Kemp, M. L. Wen, Z. Lu, H. 2024-07-23 doi:10.1101/2024.07.19.604365 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ In vivo quantification of anterior and posterior chamber volumes in mice: implications for aqueous humor dynamics ]]> https://biorxiv.org/content/10.1101/2024.07.24.604989v1?rss=1 Kim, D. Fang, R. Zhang, P. Sun, C. Li, G. Montgomery, C. John, S. W. M. Stamer, W. D. Zhang, H. F. Ethier, C. R. 2024-07-25 doi:10.1101/2024.07.24.604989 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ Environmental "Wiggles" as Stabilizers of Species Range Limits Set by Interspecific Competition ]]> https://biorxiv.org/content/10.1101/2024.07.24.605034v1?rss=1 Shirani, F. Freeman, B. G. 2024-07-25 doi:10.1101/2024.07.24.605034 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ Environmental context sculpts spatial and temporal visual processing in thalamus ]]> https://biorxiv.org/content/10.1101/2024.07.26.605345v1?rss=1 Haider, B. Peelman, K. 2024-07-26 doi:10.1101/2024.07.26.605345 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ Structural transitions in kinesin minus-end directed microtubule motility ]]> https://biorxiv.org/content/10.1101/2024.07.29.605428v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@1093cdforg.highwire.dtl.DTLVardef@17b6c99org.highwire.dtl.DTLVardef@16b4a5org.highwire.dtl.DTLVardef@add967_HPS_FORMAT_FIGEXP M_FIG C_FIG Kinesin-14 force productionNew transition states and structural movements in a model for motor energy transduction and force production: {beta}-sheet twisting stores free energy in the microtubule-bound nucleotide-free (NF) state. A fluctuating power stroke is produced in the ATP state with neck mimic docking in the ADP{middle dot}Pi state, resembling the kinesin-1 neck linker. This is followed by {beta}-strand-to-loop transitions in the microtubule-bound ADP + free Pi state. Finally, {beta}-sheet refolding drives the recovery stroke for reversion to the ADP state. ]]> Shibata, S. Wang, M. Y. Imasaki, T. Shigetmatsu, H. Wei, Y. Jobichen, C. Hagio, H. Sivaraman, J. Endow, S. A. Nitta, R. 2024-07-29 doi:10.1101/2024.07.29.605428 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Lymphatic endothelial cell-targeting lipid nanoparticles delivering VEGFC mRNA improve lymphatic function after injury ]]> https://biorxiv.org/content/10.1101/2024.07.31.605343v1?rss=1 Michalaki, E. Chin, R. Jeong, K. Qi, Z. Liebman, L. N. Gonzalez-Vargas, Y. Echeverri, E. S. Paunovska, K. Muramatsu, H. Pardi, N. Tamburini, B. J. Jakus, Z. Dahlman, J. E. Dixon, J. B. 2024-07-31 doi:10.1101/2024.07.31.605343 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Center of mass states render multi-joint torques throughout standing balance recovery ]]> https://biorxiv.org/content/10.1101/2024.08.14.607976v1?rss=1 0.84 & VAF>0.83). Moreover, the hip and knee exhibited feedforward and feedback components, while the ankle only exhibited feedback components. The lack of a feedforward component at the ankle may occur because the compliance of the Achilles tendon attenuates muscle short-range stiffness. Our model may provide a framework for evaluating changes in the feedforward and feedback contributions to balance that occur due to aging, injury, or disease. NEWS AND NOTEWORTHYReactive balance control requires coordination of neurally-mediated feedforward and feedback pathways to generate stabilizing joint torques at the hip, knee, and ankle. Using a sensorimotor response model, we decomposed reactive joint torques into feedforward and feedback contributions based on delays relative to center of mass kinematics. Responses across joints were driven by the same signals, but contributions from feedforward versus feedback pathways differed, likely due to differences in musculotendon properties between proximal and distal muscles. ]]> Jakubowski, K. L. Martino, G. Beck, O. N. Sawicki, G. S. Ting, L. H. 2024-08-19 doi:10.1101/2024.08.14.607976 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Effects of Release of TSG-6 from Heparin Hydrogels on Supraspinatus Muscle Regeneration ]]> https://biorxiv.org/content/10.1101/2024.08.20.608812v1?rss=1 Pearson, J. J. Mao, J. Temenoff, J. S. 2024-08-21 doi:10.1101/2024.08.20.608812 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Characterization, enrichment, and computational modeling of cross-linked actin networks in trabecular meshwork cells ]]> https://biorxiv.org/content/10.1101/2024.08.21.608970v1?rss=1 Li, H. Harvey, D. H. Dai, J. Swingle, S. P. Compton, A. M. Sugali, C. K. Dhamodaran, K. Yao, J. Lin, T.-Y. Sulchek, T. Kim, T. Ethier, C. R. Mao, W. 2024-08-21 doi:10.1101/2024.08.21.608970 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Fornix and Uncinate Fasciculus Support Metacognition-Driven Cognitive Offloading ]]> https://biorxiv.org/content/10.1101/2024.08.24.609527v1?rss=1 Zheng, Y. Bo, B. Wang, D. Liu, Y. Gilbert, S. J. Li, Y. Kwok, S. C. 2024-08-26 doi:10.1101/2024.08.24.609527 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Altered functional connectivity and spatiotemporal dynamics in individuals with sleep disorders ]]> https://biorxiv.org/content/10.1101/2024.08.28.610147v1?rss=1 Daley, L. Saini, P. Watters, H. Bassil, Y. Schumacher, E. Trotti, L. M. Keilholz, S. 2024-08-29 doi:10.1101/2024.08.28.610147 Cold Spring Harbor Laboratory Press 2024-08-29 <![CDATA[ Caveolin assemblies displace one bilayer leaflet to organize and bend membranes ]]> https://biorxiv.org/content/10.1101/2024.08.28.610209v1?rss=1 Doktorova, M. Daum, S. Ebenhan, J. Neudorf, S. Han, B. Sharma, S. Kasson, P. Levental, K. Bacia, K. Kenworthy, A. K. Levental, I. 2024-08-30 doi:10.1101/2024.08.28.610209 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Genetically-encoded phase separation sensors for intracellular probing of biomolecular condensates ]]> https://biorxiv.org/content/10.1101/2024.08.29.610365v1?rss=1 Avecilla, A. R. C. Thomas, J. Quiroz, F. G. 2024-08-30 doi:10.1101/2024.08.29.610365 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Refining Brain Stimulation Therapies: An Active Learning Approach to Personalization ]]> https://biorxiv.org/content/10.1101/2024.09.02.610880v1?rss=1 Sendi, M. S. Core, E. Piallat, B. Ellis, C. A. Eggers, T. E. Laxpati, N. G. Mahmoudi, B. Gutekunst, C.-A. Devergnas, A. D. Mayberg, H. S. Gross, R. E. Calhoun, V. 2024-09-03 doi:10.1101/2024.09.02.610880 Cold Spring Harbor Laboratory Press 2024-09-03 <![CDATA[ Time-on-task-related decrements in performance in the rodent continuous performance test are not caused by physical disengagement from the task ]]> https://biorxiv.org/content/10.1101/2024.09.05.611415v1?rss=1 Li, Y. van Kralingen, T. Masi, M. Villaneuva Sanchez, B. Mitchell, B. Johnson, J. Miranda-Barrientos, J. Rehg, J. J. Martinowich, K. Carr, G. V. 2024-09-10 doi:10.1101/2024.09.05.611415 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ Improving Functional Muscle Regeneration in Volumetric Muscle Loss Injuries by Shifting the Balance of Inflammatory and Pro-Resolving Lipid Mediators ]]> https://biorxiv.org/content/10.1101/2024.09.06.611741v1?rss=1 Turner, T. C. Pittman, F. S. Zhang, H. Hymel, L. A. Zheng, T. Behara, M. Anderson, S. E. Andraca Harrer, J. Link, K. A. Ahammed, M. A. Maner-Smith, K. Liu, X. Yin, X. Lim, H. S. Spite, M. Qiu, P. Garcia, A. J. Mortensen, L. J. Jang, Y. C. Willett, N. J. Botchwey, E. A. 2024-09-12 doi:10.1101/2024.09.06.611741 Cold Spring Harbor Laboratory Press 2024-09-12 <![CDATA[ Adaptive protein synthesis in genetic models of copper deficiency and childhood neurodegeneration ]]> https://biorxiv.org/content/10.1101/2024.09.09.612106v1?rss=1 Lane, A. R. Scher, N. E. Bhattacharjee, S. Zlatic, S. A. Roberts, A. M. Gokhale, A. Singleton, K. S. Duong, D. M. McKenna, M. Liu, W. L. Baiju, A. Moctezuma, F. G. R. Tran, T. Patel, A. Clayton, L. B. Petris, M. J. Wood, L. B. Patgiri, A. Vrailas-Mortimer, A. D. Cox, D. N. Roberts, B. R. Werner, E. Faundez, V. 2024-09-12 doi:10.1101/2024.09.09.612106 Cold Spring Harbor Laboratory Press 2024-09-12 <![CDATA[ Loss of Neurofibromin Induces Inflammatory Macrophage Phenotypic Switch and Retinal Neovascularization via GLUT1 Activation ]]> https://biorxiv.org/content/10.1101/2024.09.13.612509v1?rss=1 ZAIDI, Y. Tritz, R. Zaidi, N. Nabi, F. Zaidi, S. A. H. Morsy, A. Harris, V. Racine, R. Hudson, F. Z. Bordan, Z. Kennard, S. Batori, R. Huo, Y. Csanyi, G. Belin de Chantemele, E. J. Lei, K. Boulis, N. M. Fulton, D. J. Khan, R. H. Caldwell, R. B. Stansfield, B. K. 2024-09-14 doi:10.1101/2024.09.13.612509 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Few-shot Algorithms for Consistent Neural Decoding (FALCON) Benchmark ]]> https://biorxiv.org/content/10.1101/2024.09.15.613126v1?rss=1 Karpowicz, B. M. Ye, J. Fan, C. Tostado-Marcos, P. Rizzoglio, F. Washington, C. Scodeler, T. de Lucena, D. Nason-Tomaszewski, S. R. Mender, M. J. Ma, X. Arneodo, E. M. Hochberg, L. R. Chestek, C. A. Henderson, J. M. Gentner, T. Q. Gilja, V. Miller, L. E. Rouse, A. G. Gaunt, R. A. Collinger, J. L. Pandarinath, C. 2024-09-16 doi:10.1101/2024.09.15.613126 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ High-resolution in vivo kinematic tracking with injectable fluorescent nanoparticles ]]> https://biorxiv.org/content/10.1101/2024.09.17.613529v1?rss=1 Ulutas, E. Z. Pradhan, A. Koveal, D. Markowitz, J. E. 2024-09-17 doi:10.1101/2024.09.17.613529 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ A workflow for microclimate sensor networks: integrating geographic tools, statistics, and local knowledge ]]> https://biorxiv.org/content/10.1101/2024.09.13.612939v1?rss=1 Klinges, D. H. Lembrechts, J. Van de Vondel, S. Greenlee, E. Hayles-Cotton, K. Senior, R. 2024-09-19 doi:10.1101/2024.09.13.612939 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Redefining the Limits of Functional Continuity in the Early Evolution of P-Loop NTPases ]]> https://biorxiv.org/content/10.1101/2024.09.17.613540v1?rss=1 Demkiv, A. O. Toledo-Patino, S. Medina-Carmona, E. Berg, A. Pinto, G. P. Parracino, A. Sanchez-Ruiz, J. M. Hengge, A. C. Laurino, P. Longo, L. M. Kamerlin, S. C. L. 2024-09-19 doi:10.1101/2024.09.17.613540 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ EFFECTS OF SPINAL TRANSECTION AND LOCOMOTOR SPEED ON MUSCLE SYNERGIES OF THE CAT HINDLIMB ]]> https://biorxiv.org/content/10.1101/2024.09.19.613891v1?rss=1 Klishko, A. Harnie, J. Hanson, C. E. Rahmati, S. M. Rybak, I. A. Frigon, A. Prilutsky, B. I. 2024-09-20 doi:10.1101/2024.09.19.613891 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Exercise Evokes Retained Motor Performance without Neuroprotection in a Mouse Model of Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2024.09.20.614034v1?rss=1 Skelton, H. M. Hyman, N. Fernandez, A. Acerbo, E. Scott, M. Berglund, K. Gutekunst, C.-A. Gross, R. E. 2024-09-20 doi:10.1101/2024.09.20.614034 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Abstinence from cocaine self-administration promotes microglia pruning of astrocytes which drives cocaine-seeking behavior ]]> https://biorxiv.org/content/10.1101/2024.09.20.614128v1?rss=1 Testen, A. VanRyzin, J. W. Bellinger, T. J. Kim, R. W. Wang, H. Gastinger, M. J. Witt, E. A. Franklin, J. P. Vecchiarelli, H. A. Picard, K. Tremblay, M.-E. Reissner, K. J. 2024-09-21 doi:10.1101/2024.09.20.614128 Cold Spring Harbor Laboratory Press 2024-09-21 <![CDATA[ Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle:High-Resolution Sampling Every 4 Hours Over 22 Days ]]> https://biorxiv.org/content/10.1101/2024.09.27.614549v1?rss=1 Nunn, B. L. Timmins-Schiffman, E. Mudge, M. C. Plubell, D. Chebli, G. Kubanek, J. Riffle, M. Noble, W. S. Harvey, E. Nunn, T. A. Huntemann, Clum, Foster, Roux, Palaniappan, Mukherjee, Reddy, Daum, Copeland, Chen, Ivanova, Kyrpides, Glavina del rio, Eloe-Fadrosh, 2024-09-28 doi:10.1101/2024.09.27.614549 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ A Collagen Triple Helix without the Super Helical Twist ]]> https://biorxiv.org/content/10.1101/2024.09.26.615199v1?rss=1 Kreutzberger, M. A. B. Yu, L. T. Hancu, M. C. Purdy, M. D. Osinski, T. Kasson, P. Egelman, E. H. Hartgerink, J. D. 2024-09-29 doi:10.1101/2024.09.26.615199 Cold Spring Harbor Laboratory Press 2024-09-29 <![CDATA[ Bacterial motility patterns adapt smoothly in response to spatial confinement and disorder ]]> https://biorxiv.org/content/10.1101/2024.09.29.615714v1?rss=1 Zhang, H. Wetherington, M. T. Ko, H. FitzGerald, C. E. Nirody, J. A. 2024-09-30 doi:10.1101/2024.09.29.615714 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples ]]> https://biorxiv.org/content/10.1101/2024.10.01.616135v1?rss=1 Brochu, H. N. Zhang, Q. Song, K. Wang, L. Deare, E. A. Williams, J. D. Icenhour, C. R. Iyer, L. K. 2024-10-01 doi:10.1101/2024.10.01.616135 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ An engineered chromatin protein with enhanced preferential binding of H3K27me3 over H3K9me3 ]]> https://biorxiv.org/content/10.1101/2024.10.02.616304v1?rss=1 Franklin, K. A. Priode, J. H. Steppe, P. Haynes, K. A. 2024-10-02 doi:10.1101/2024.10.02.616304 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Nanotextured steel surface exhibits antifungal activity ]]> https://biorxiv.org/content/10.1101/2024.10.02.616307v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@9c037dorg.highwire.dtl.DTLVardef@a93518org.highwire.dtl.DTLVardef@dccc6forg.highwire.dtl.DTLVardef@1f19515_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Tripathi, A. Champion, J. 2024-10-02 doi:10.1101/2024.10.02.616307 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Layer 6 corticothalamic neurons induce high gamma oscillations through cortico-cortical and cortico-thalamo-cortical pathways ]]> https://biorxiv.org/content/10.1101/2024.10.05.616808v1?rss=1 Russo, S. Dimwamwa, E. Stanley, G. B. 2024-10-06 doi:10.1101/2024.10.05.616808 Cold Spring Harbor Laboratory Press 2024-10-06 <![CDATA[ Differences in metagenome coverage may confound abundance-based and diversity conclusions ]]> https://biorxiv.org/content/10.1101/2024.10.10.617679v1?rss=1 Riquelme, B. A. Rodriguez-R, L. M. Konstantinidis, K. T. 2024-10-11 doi:10.1101/2024.10.10.617679 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Metabolomic profiles of stony coral species from the Dry Tortugas National Park display inter- and intraspecies variation ]]> https://biorxiv.org/content/10.1101/2024.10.08.617290v1?rss=1 Deutsch, J. M. Demko, A. M. Jaiyesimi, O. A. Foster, G. Kindler, A. Pitts, K. A. Vekich, T. Williams, G. Walker, B. K. Paul, V. J. Garg, N. 2024-10-12 doi:10.1101/2024.10.08.617290 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Regulatory Changes in the Fatty Acid Elongase eloF Underlie the Evolution of Sex-specific Pheromone Profiles in Drosophila prolongata ]]> https://biorxiv.org/content/10.1101/2024.10.09.617394v1?rss=1 Yige, L. Takau, A. Li, J. Fan, T. Hopkins, B. R. Le, Y. Ramirez, S. R. Matsuo, T. Kopp, A. 2024-10-14 doi:10.1101/2024.10.09.617394 Cold Spring Harbor Laboratory Press 2024-10-14 <![CDATA[ Understanding Neuronal Diversity: Role of Input Dynamics and Selectivity ]]> https://biorxiv.org/content/10.1101/2024.10.16.618657v1?rss=1 Joshi, N. van der Burg, S. Celikel, T. Zeldenrust, F. 2024-10-17 doi:10.1101/2024.10.16.618657 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Stabilizing selection and adaptation shape cis and trans gene expression variation in C. elegans ]]> https://biorxiv.org/content/10.1101/2024.10.15.618466v1?rss=1 Bell, A. D. Valencia, F. Paaby, A. B. 2024-10-18 doi:10.1101/2024.10.15.618466 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ The influence of downstream structured elements within mRNA on the dynamics of intersubunit rotation in ribosomes ]]> https://biorxiv.org/content/10.1101/2024.10.17.618931v1?rss=1 Shebl, B. Pavlova, A. Kellenberger, P. Yu, D. Menke, D. Gumbart, J. C. Cornish, P. V. 2024-10-18 doi:10.1101/2024.10.17.618931 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Template-driven dynamic functional network connectivity predicts medication response for major depression and bipolar disorders ]]> https://biorxiv.org/content/10.1101/2024.10.17.618523v1?rss=1 Baker, B. Osuch, E. Langenecker, S. Fournier, J. Turner, J. A. Youngstrom, E. Calhoun, V. 2024-10-20 doi:10.1101/2024.10.17.618523 Cold Spring Harbor Laboratory Press 2024-10-20 <![CDATA[ Mosaic of Somatic Mutations in the Ancient and Still-Living Aspen Clone, Pando ]]> https://biorxiv.org/content/10.1101/2024.10.19.619233v1?rss=1 Pineau, R. Mock, K. E. Morris, J. L. Kraklow, V. Brunelle, A. Pageot, A. Ratcliff, W. C. Gompert, Z. 2024-10-22 doi:10.1101/2024.10.19.619233 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ 40 Hz sensory stimulation enhances CA3-CA1 coordination and prospective coding during navigation in a mouse model of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2024.10.23.619408v1?rss=1 Paulson, A. L. Zhang, L. Prichard, A. M. Singer, A. C. 2024-10-23 doi:10.1101/2024.10.23.619408 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Super Resolved Single-Cell Spatial Metabolomics from Multimodal Mass Spectrometry Imaging guided by Imaging Mass Cytometry ]]> https://biorxiv.org/content/10.1101/2024.10.21.619323v1?rss=1 Ozturk, E. Venkataraman, A. Moctezuma, F. G. R. Coskun, A. F. 2024-10-24 doi:10.1101/2024.10.21.619323 Cold Spring Harbor Laboratory Press 2024-10-24 <![CDATA[ Endothelial cell stiffness and type drive the formation of biomechanically-induced transcellular pores ]]> https://biorxiv.org/content/10.1101/2024.10.23.619950v1?rss=1 Siadat, S. M. Li, H. Millette, B. A. Safa, B. N. Wong, C. A. Bahrani Fard, M. R. Braakman, S. T. Tay, I. Bertrand, J. A. Read, A. T. Schildmeyer, L. A. Perkumas, K. M. Stamer, W. D. Overby, D. R. Ethier, C. R. 2024-10-28 doi:10.1101/2024.10.23.619950 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Large inversions in Lake Malawi cichlids are associated with habitat preference, lineage, and sex determination ]]> https://biorxiv.org/content/10.1101/2024.10.28.620687v1?rss=1 Kumar, N. M. Cooper, T. L. Kocher, T. D. Streelman, J. T. McGrath, P. T. 2024-10-29 doi:10.1101/2024.10.28.620687 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Promiscuous and unbiased recombination underlies the sequence-discrete species of the SAR11 lineage in the deep ocean ]]> https://biorxiv.org/content/10.1101/2024.10.30.621061v1?rss=1 95% Average Nucleotide Identity (ANI) of shared genes among themselves vs. <83% ANI to members of other species while genome pairs showing between 83-95% ANI are comparatively rare. In these surveys, aquatic bacteria of the ubiquitous SAR11 clade (Class Alphaproteobacteria), which play a major role in carbon cycling, are an outlier and often do not exhibit discrete species boundaries, suggesting the potential for alternate modes of genetic differentiation. To explore evolution in SAR11, we analyzed high-quality, single-cell amplified genomes (SAGs) and companion metagenomes from an oxygen minimum zone (OMZ) in the Eastern Tropical Pacific Ocean, where the SAR11 make up [~]20% of the total microbial community. Our results show that SAR11 do form several sequence-discrete species, but their ANI range of discreteness is shifted to lower identities between 86-91%, with intra-species ANI ranging between 91-100%. Measuring recent gene exchange among these genomes based on a newly developed methodology revealed higher frequency of homologous recombination within compared to between species that affects sequence evolution at least twice as much as diversifying point mutation across the genome. Recombination in SAR-11 appears to be more promiscuous compared to other prokaryotic species and has facilitated the spreading of adaptive mutations within the species, further promoting the high intra-species diversity observed. These results implicate rampant, genome-wide homologous recombination as the mechanism that underlies the evolution of SAR11 into discrete species. SignificanceDistinguishing "species" is a pressing issue in microbiology, partly because the mechanisms that create and maintain clusters of genetically similar microbes are sparsely documented for natural populations. By leveraging high quality single-cell genomic data and a novel method for assessing homologous recombination, we show that rampant homologous recombination maintains species-level clusters of genomes for the most abundant order of marine bacteria, suggesting that these genomes may be evolving sexually to a much greater extent than previously thought. Therefore, our results identify a mechanism explaining the evolution of species in a major microbial group and have implications for understanding microbial diversity and the species concept more broadly. ]]> Zhao, J. Maria Pachiadaki, M. Conrad, R. Hatt, J. Bristow, L. Rodriguez-R, L. Rossello-Mora, R. Stewart, F. J. M. Konstantinidis, K. T. 2024-10-30 doi:10.1101/2024.10.30.621061 Cold Spring Harbor Laboratory Press 2024-10-30 <![CDATA[ Antigen-specific T cell immunotherapy by in vivo mRNA delivery ]]> https://biorxiv.org/content/10.1101/2024.10.29.620946v1?rss=1 Su, F.-Y. Siebart, J. C. Chan, C. S. Wang, M. Y. Yao, X. Trenkle, A. D. S. Sivakumar, A. Su, M. Harandi, R. Shahrawat, N. Nguyen, C. H. Goenka, A. Mun, J. Dhodapkar, M. V. Kwong, G. A. 2024-11-03 doi:10.1101/2024.10.29.620946 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Self-Authenticating Genomic Materials with Advanced Genome Signatures ]]> https://biorxiv.org/content/10.1101/2024.11.02.621633v1?rss=1 Wang, Z. Cui, J. Liu, Q. Li, J. Guo, C. Liu, Y. Jiang, C. Xue, H. Li, J. Ke, Y. Qi, H. 2024-11-03 doi:10.1101/2024.11.02.621633 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Fishnet mesh of centrin-Sfi1 drives ultrafast calcium-activated contraction of the giant cell Spirostomum ambiguum ]]> https://biorxiv.org/content/10.1101/2024.11.07.622534v1?rss=1 Lannan, J. Floyd, C. Xu, L. X. Yan, C. Marshall, W. F. Vaikuntanathan, S. Dinner, A. R. Honts, J. E. Bhamla, S. Elting, M. W. 2024-11-08 doi:10.1101/2024.11.07.622534 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Decoding the Neural Dynamics of Headed Syntactic Structure Building ]]> https://biorxiv.org/content/10.1101/2024.11.07.622560v1?rss=1 Zhao, J. Gao, R. Brennan, J. R. 2024-11-08 doi:10.1101/2024.11.07.622560 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Investigating the Impact of Habitual Sleep Quality on Episodic Memory Performance: An EEG-Based Representational Similarity Analysis ]]> https://biorxiv.org/content/10.1101/2024.11.08.622661v1?rss=1 Seraji, M. Mirjalili, S. Duarte, A. Calhoun, V. D. 2024-11-08 doi:10.1101/2024.11.08.622661 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Resting After Learning Facilitates Memory Consolidation and Reverses Spatial Reorientation Impairments in 'New Surroundings' in 3xTg-AD Mice ]]> https://biorxiv.org/content/10.1101/2024.11.12.622722v1?rss=1 Stimmell, A. C. Alday, L. J. Diaz, J. M. Moseley, S. C. Cushing, S. D. Salvador, E. M. Ragsdale, S. M. Wilber, A. A. 2024-11-14 doi:10.1101/2024.11.12.622722 Cold Spring Harbor Laboratory Press 2024-11-14 <![CDATA[ Mechanism of Arrhythmogenesis Driven by Early After Depolarizations in Cardiac Tissue ]]> https://biorxiv.org/content/10.1101/2024.11.14.623585v1?rss=1 Stein, J. Greene, D. Fenton, F. Shiferaw, Y. 2024-11-14 doi:10.1101/2024.11.14.623585 Cold Spring Harbor Laboratory Press 2024-11-14 <![CDATA[ Integrating Machine Learning with Flow-Imaging Microscopy for Automated Monitoring of Algal Blooms ]]> https://biorxiv.org/content/10.1101/2024.11.12.623192v1?rss=1 97{+/-}2.8% accuracy. Furthermore, a convolutional neural network (CNN), trained to classify distinct classes comprising both taxonomical and morphological categories, achieved 94% accuracy in a closed dataset. Nonetheless, the supervised closed-set classifiers struggled with the accurate classification of objects when challenged with debris and novel particles which are common in complex open environments; this limits real-time monitoring applications by requiring extensive manual oversight. To mitigate this, three methods incorporating classification with rejection were tested to improve model precision by excluding irrelevant or unknown classes. Combined, these advances present a fully integrated, end-to-end solution for real-time HAB monitoring in open environmental systems thus enhancing the scalability of automated detection in dynamic aquatic environments. HighlightsO_LIRandom Forest model is more generalizable than Convolutional Neural Networks to remove out-of-focus particles. C_LIO_LIA two-stage clustering algorithm is effective at removing background particles in flow imaging microscopy. C_LIO_LIClosed-set CNN classifier performance deteriorates when challenged with unknown particles. C_LIO_LIClassification with rejection improves both precision and accuracy for environmental samples. C_LI ]]> Khan, F. Gincley, B. Busch, A. Tolofari, D. L. Norton, J. W. Varga, E. McKay, R. M. L. Fuentes-Cabrera, M. Slawecki, T. Pinto, A. J. 2024-11-15 doi:10.1101/2024.11.12.623192 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Ultrafast elastocapillary fans control agile maneuvering in ripple bugs and robots ]]> https://biorxiv.org/content/10.1101/2024.11.15.623609v1?rss=1 Ortega-Jimenez, V. Kim, D. Kumar, S. Kim, C. Koh, J.-s. Bhamla, M. S. 2024-11-15 doi:10.1101/2024.11.15.623609 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Dual Computational Systems in the Development and Evolution of Mammalian Brains ]]> https://biorxiv.org/content/10.1101/2024.11.19.624321v1?rss=1 Imam, N. Kielo, M. Trude, B. M. Finlay, B. L. 2024-11-19 doi:10.1101/2024.11.19.624321 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ Resolving the Taxonomic Status of the Marbled Toad (Bufonidae: Incilius marmoreus): 2RAD-based Phylogeography Including an Isolated Population in Veracruz, Mexico ]]> https://biorxiv.org/content/10.1101/2024.11.23.624927v1?rss=1 Wang, K. Pierson, T. W. Mendelson, J. R. 2024-11-25 doi:10.1101/2024.11.23.624927 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Carbon-conserving Bioproduction of Malate in an E. coli-based Cell-Free System ]]> https://biorxiv.org/content/10.1101/2024.11.26.623433v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@3c89adorg.highwire.dtl.DTLVardef@72d9b3org.highwire.dtl.DTLVardef@327e2eorg.highwire.dtl.DTLVardef@fa0964_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cardiff, R. Chowdhury, S. Sugianto, W. Tickman, B. I. Alba Burbano, D. Meyer, P. A. Cook, M. King, B. Garenne, D. Beliaev, A. Noireaux, V. Peralta-Yahya, P. Carothers, J. M. 2024-11-26 doi:10.1101/2024.11.26.623433 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ High-resolution profiling reveals coupled transcriptional and translational regulation of transgenes ]]> https://biorxiv.org/content/10.1101/2024.11.26.625483v1?rss=1 Peterman, E. L. Ploessl, D. S. Love, K. S. Sanabria, V. Daniels, R. F. Johnstone, C. P. Godavarti, D. R. Kabaria, S. R. Pai, A. A. Galloway, K. E. 2024-11-26 doi:10.1101/2024.11.26.625483 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Born Connected: Do Infants Already Have Adult-Like Multi-Scale Connectivity Networks? ]]> https://biorxiv.org/content/10.1101/2024.11.27.625681v1?rss=1 Bajracharya, P. Mirzaeian, S. Fu, Z. Calhoun, V. Shultz, S. Iraji, A. 2024-11-27 doi:10.1101/2024.11.27.625681 Cold Spring Harbor Laboratory Press 2024-11-27 <![CDATA[ Identification and cryoEM structure determination of Escherichia phage YDC107 tail found in a bacteria-contaminated buffer ]]> https://biorxiv.org/content/10.1101/2024.12.10.627647v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@1444ae3org.highwire.dtl.DTLVardef@907ec1org.highwire.dtl.DTLVardef@71eebdorg.highwire.dtl.DTLVardef@1f0e6a1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kopylov, M. Bobe, D. Jenkins, M. C. Dutta, T. 2024-12-11 doi:10.1101/2024.12.10.627647 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Modulation of all-trans retinoic acid by light and dopamine in the murine eye ]]> https://biorxiv.org/content/10.1101/2024.12.06.627245v1?rss=1 Talwar, S. Mazade, R. Bentley-Ford, M. Yu, J. Pilli, N. Kane, M. A. Ethier, C. R. Pardue, M. T. 2024-12-12 doi:10.1101/2024.12.06.627245 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Morphotype-Resolved Characterization of Microalgal Communities in a Nutrient Recovery Process with ARTiMiS Flow Imaging Microscopy ]]> https://biorxiv.org/content/10.1101/2024.12.16.628756v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@1023934org.highwire.dtl.DTLVardef@f9b4a0org.highwire.dtl.DTLVardef@1c193a6org.highwire.dtl.DTLVardef@1c48ec1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gincley, B. Khan, F. Alam, M. M. Hartnett, E. Kim, G.-Y. Molitor, H. Fisher, A. Bradley, I. Guest, J. Pinto, A. J. 2024-12-16 doi:10.1101/2024.12.16.628756 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Visualizing Functional Network Connectivity Differences Using an Explainable Machine-learning Method ]]> https://biorxiv.org/content/10.1101/2024.12.18.629283v1?rss=1 Sendi, M. S. E. Itkyal, V. S. Edwards-Swart, S. J. Chun, J. Y. Mathalon, D. H. Ford, J. M. Preda, A. van Erp, T. G. M. Pearlson, G. D. Turner, J. A. Calhoun, V. D. 2024-12-20 doi:10.1101/2024.12.18.629283 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Image Processing in the Acute to Chronic Pain Signatures (A2CPS) Project ]]> https://biorxiv.org/content/10.1101/2024.12.19.627509v1?rss=1 Sadil, P. Arfanakis, K. Bhuiyan, E. H. Caffo, B. Calhoun, V. D. Clauw, D. J. DeLano, M. C. Ford, J. C. Gattu, R. Guo, X. Harris, R. E. Ichesco, E. Johnson, M. A. Jung, H. Kahn, A. B. Kaplan, C. M. Leloudas, N. Lindquist, M. A. Luo, Q. Mulderink, T. A. Peltier, S. J. Prasad, P. V. Sica, C. Urrutia, J. Vance, C. G. Wager, T. D. Xuan, Y. Zhou, X. J. Zhou, Y. Shu, D. C. The Acute to Chronic Pain Signatures Consortium, 2024-12-20 doi:10.1101/2024.12.19.627509 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ The conserved global regulator H-NS has a strain-specific impact on biofilm formation in Vibrio fischeri symbionts ]]> https://biorxiv.org/content/10.1101/2024.12.19.629378v1?rss=1 Zarate, D. Isenberg, R. Y. Pavelsky, M. Speare, L. Jackson, A. Mandel, M. J. Septer, A. N. 2024-12-20 doi:10.1101/2024.12.19.629378 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Genetic ancestry and population structure in the All of Us Research Program cohort ]]> https://biorxiv.org/content/10.1101/2024.12.21.629909v1?rss=1 Sharma, S. Nagar, S. D. Pemu, P. Zuchner, S. SEEC Consortium, Marino-Ramirez, L. Meller, R. Jordan, I. K. 2024-12-22 doi:10.1101/2024.12.21.629909 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Disturbed repolarisation-relaxation coupling during acute ischaemia permits systolic mechano-arrhythmogenesis. ]]> https://biorxiv.org/content/10.1101/2024.12.19.629548v1?rss=1 Cameron, B. A. Baumeister, P. A. Lawen, T. Rafferty, S. Taeb, B. Stoyek, M. R. Greiner, J. Uzelac, I. Fenton, F. H. Peyronnet, R. Kohl, P. Quinn, T. A. 2024-12-23 doi:10.1101/2024.12.19.629548 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ YAP regulates periosteal expansion in fracture repair ]]> https://biorxiv.org/content/10.1101/2024.12.23.630086v1?rss=1 Nijsure, M. P. Tobin, B. R. Jones, D. Lang, A. Hallstrom, G. Baitner, M. Tanner, G. I. Moharrer, Y. Panebianco, C. J. Seidl, E. G. Dyment, N. A. Szeto, G. L. Wood, L. B. Boerckel, J. D. 2024-12-23 doi:10.1101/2024.12.23.630086 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ Motor unit mechanisms of speed control in mouse locomotion ]]> https://biorxiv.org/content/10.1101/2024.12.29.628022v1?rss=1 Thomas, K. Gibbs, R. Marques, H. Carey, M. R. Sober, S. J. 2024-12-29 doi:10.1101/2024.12.29.628022 Cold Spring Harbor Laboratory Press 2024-12-29 <![CDATA[ Mycobacterium abscessus promotes Pseudomonas aeruginosa biofilm formation and antibiotic tolerance ]]> https://biorxiv.org/content/10.1101/2024.12.31.630905v1?rss=1 McDaniel, M. S. Edmonds, S. E. Patel, E. N. Baty, J. J. Scoffield, J. A. 2025-01-02 doi:10.1101/2024.12.31.630905 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Resolving vs. Non-resolving Sphingolipid Dynamics During Macrophage Activation: A Time-resolved Metabolic Analysis ]]> https://biorxiv.org/content/10.1101/2024.12.31.630925v1?rss=1 Chiappa, N. Lal, N. Botchwey, E. 2025-01-02 doi:10.1101/2024.12.31.630925 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Scaly-Tail Organ Enhances Static Stability during Pel's Scaly-tailed Flying Squirrels' Arboreal Locomotion ]]> https://biorxiv.org/content/10.1101/2024.12.31.630952v1?rss=1 Schulz, A. K. Chellapurath, M. Khandelwal, P. Rezaei, S. Merker, S. Jusufi, A. 2025-01-02 doi:10.1101/2024.12.31.630952 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ OPTN protects retinal ganglion cells and ameliorates neuroinflammation in optic neuropathies ]]> https://biorxiv.org/content/10.1101/2025.01.09.632264v1?rss=1 Wang, Q. Wang, Y. Jiang, Y. D. D. Donahue, R. Cao, G. Yan, W. Guo, H. Hao, J. Lu, Y. Wang, Q. Tian, F. 2025-01-12 doi:10.1101/2025.01.09.632264 Cold Spring Harbor Laboratory Press 2025-01-12 <![CDATA[ Constructing Biologically Constrained RNNs via Dale's Backprop and Topologically-Informed Pruning ]]> https://biorxiv.org/content/10.1101/2025.01.09.632231v1?rss=1 Balwani, A. Wang, A. Q. Najafi, F. Choi, H. 2025-01-13 doi:10.1101/2025.01.09.632231 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ CellSP: Module discovery and visualization for subcellular spatial transcriptomics data ]]> https://biorxiv.org/content/10.1101/2025.01.12.632553v1?rss=1 Aggarwal, B. Sinha, S. 2025-01-15 doi:10.1101/2025.01.12.632553 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Identification of novel Kv1.3 channel-interacting proteins using proximity labelling in T-cells ]]> https://biorxiv.org/content/10.1101/2025.01.16.633279v1?rss=1 Kour, D. Bowen, C. A. Srivastava, U. Nguyen, H. M. Kumari, R. Kumar, P. Brandelli, A. D. Bitarafan, S. Tobin, B. R. Wood, L. B. Seyfried, N. Wulff, H. Rangaraju, S. 2025-01-18 doi:10.1101/2025.01.16.633279 Cold Spring Harbor Laboratory Press 2025-01-18 <![CDATA[ Endothelial Cu Uptake Transporter CTR1 Senses Disturbed Flow to Promote Atherosclerosis through Cuproptosis ]]> https://biorxiv.org/content/10.1101/2025.01.27.634587v1?rss=1 Sudhahar, V. Xiao, Z. Das, A. Ash, D. Yadav, S. Matier, C. D. Pezacki, A. T. Chatterjee, B. Antipova, O. A. Vogt, S. McMenamin, M. Kelley, S. Gabor, C. Lee, J. Jo, H. Chang, C. J. Rao, J. Kaplan, J. H. Ushio-Fukai, M. Fukai, T. 2025-01-28 doi:10.1101/2025.01.27.634587 Cold Spring Harbor Laboratory Press 2025-01-28 <![CDATA[ H-NS is a conserved repressor of the type VI secretion system in Vibrio fischeri ]]> https://biorxiv.org/content/10.1101/2025.01.30.634523v1?rss=1 Speare, L. Pavelsky, M. Jackson, A. Septer, A. N. 2025-01-30 doi:10.1101/2025.01.30.634523 Cold Spring Harbor Laboratory Press 2025-01-30 <![CDATA[ Haplotype rather than single causal variants effects contribute to regulatory gene expression associations in human myeloid cells ]]> https://biorxiv.org/content/10.1101/2025.01.30.635675v1?rss=1 Greenwood, E. Cao, M. Lee, C. M. Liu, A. Moyo, B. Bao, G. Gibson, G. 2025-01-30 doi:10.1101/2025.01.30.635675 Cold Spring Harbor Laboratory Press 2025-01-30 <![CDATA[ Neuromark dFNC Patterns: A fully automated pipeline to estimate subject-specific states from rs-fMRI data via constrained ICA of dFNC in +100k Subjects ]]> https://biorxiv.org/content/10.1101/2025.01.29.635539v1?rss=1 Esfahani, M. M. Esaulov, V. Venkateswara, H. D. Calhoun, V. 2025-02-02 doi:10.1101/2025.01.29.635539 Cold Spring Harbor Laboratory Press 2025-02-02 <![CDATA[ All-trans retinoic acid and fluid transport in myopigenesis ]]> https://biorxiv.org/content/10.1101/2025.02.05.636685v1?rss=1 Dvoriashyna, M. Bentley-Ford, M. R. Yu, J. Chatterjee, S. Pardue, M. Kane, M. A. Repetto, R. Ethier, C. R. 2025-02-08 doi:10.1101/2025.02.05.636685 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ SAMCell: Generalized Label-Free Biological Cell Segmentation with Segment Anything ]]> https://biorxiv.org/content/10.1101/2025.02.06.636835v1?rss=1 VandeLoo, A. D. Malta, N. J. Aponte, E. van Zyl, C. Xu, D. Forest, C. 2025-02-08 doi:10.1101/2025.02.06.636835 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Machine learning of molecular dynamics simulations provides insights into modulation of viral capsid assembly ]]> https://biorxiv.org/content/10.1101/2025.02.07.637202v1?rss=1 View larger version (17K): org.highwire.dtl.DTLVardef@b2a910org.highwire.dtl.DTLVardef@1798a02org.highwire.dtl.DTLVardef@539b80org.highwire.dtl.DTLVardef@105f0aa_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pavlova, A. Fan, Z. Lynch, D. Gumbart, J. C. 2025-02-08 doi:10.1101/2025.02.07.637202 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Decay and Solid-Liquid Partitioning of Mpox and Vaccinia Viruses in Primary Influent and Settled Solids to Guide Wastewater-Based Epidemiology Practices ]]> https://biorxiv.org/content/10.1101/2025.02.11.633197v1?rss=1 Phaneuf, J. R. Cha, G. Hatt, J. K. Konstantinidis, K. T. Graham, K. E. 2025-02-12 doi:10.1101/2025.02.11.633197 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Identifying Neurobiological Psychosis Biotypes Using Multi-Scale Functional Network Connectivity and its Latent Independent Subspace ]]> https://biorxiv.org/content/10.1101/2025.02.11.637551v1?rss=1 Ballem, R. Camazon, P. A. Jensen, K. M. Bajracharya, P. Diaz-Caneja, C. M. Bustillo, J. R. Turner, J. A. Pearlson, G. D. Chen, J. Calhoun, V. Iraji, A. 2025-02-12 doi:10.1101/2025.02.11.637551 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ The dynamics of explore-exploit decisions suggest a threshold mechanism for reduced random exploration in older adults ]]> https://biorxiv.org/content/10.1101/2025.02.13.638023v1?rss=1 Phelps, C. E. Frisvold, A. E. Sreeram, M. Antoniou, V. D. Oliveira, L. E. Tooke, S. R. Lu, Y. Z. Lemon, A. C. Fraire, J. U. Delval, A. G. R. Smith, B. K. Spangenberg, D. H. Mithelavage, M. N. Ngo, M. N. Keller, E. M. O. Isaac, L. J. Harader, S. A. Mizell, J.-M. Wang, S. Keung, W. Sundman, M. H. Franchetti, M.-K. Choi, Y.-h. Alexander, G. E. Wilson, R. C. 2025-02-17 doi:10.1101/2025.02.13.638023 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ Rewiring protein sequence and structure generative models to enhance protein stability prediction ]]> https://biorxiv.org/content/10.1101/2025.02.13.638154v1?rss=1 Li, Z. Luo, Y. 2025-02-18 doi:10.1101/2025.02.13.638154 Cold Spring Harbor Laboratory Press 2025-02-18 <![CDATA[ Multiple pathways to the evolution of positive assortment in aggregative multicellularity ]]> https://biorxiv.org/content/10.1101/2025.02.17.638078v1?rss=1 Stoy, K. S. MacGillivray, K. A. Burnetti, A. J. Barrett, C. Ratcliff, W. C. 2025-02-18 doi:10.1101/2025.02.17.638078 Cold Spring Harbor Laboratory Press 2025-02-18 <![CDATA[ The fire ant social chromosome exerts a major influence on genome regulation ]]> https://biorxiv.org/content/10.1101/2025.02.17.638763v1?rss=1 Jones, B. M. Waugh, A. H. Catto, M. A. Kay, S. Glastad, K. M. Goodisman, M. A. Kocher, S. D. Hunt, B. G. 2025-02-18 doi:10.1101/2025.02.17.638763 Cold Spring Harbor Laboratory Press 2025-02-18 <![CDATA[ Explainable machine learning for health disparities: type 2 diabetes in the All of Us research program ]]> https://biorxiv.org/content/10.1101/2025.02.18.638789v1?rss=1 Kambara, M. S. Chukka, O. Choi, K. J. Tsenum, J. Gupta, S. English, N. J. Jordan, I. K. Marino-Ramirez, L. 2025-02-19 doi:10.1101/2025.02.18.638789 Cold Spring Harbor Laboratory Press 2025-02-19 <![CDATA[ Cholesterol efflux protein, ABCA1, supports anti-cancer functions of myeloid immune cells ]]> https://biorxiv.org/content/10.1101/2025.02.19.638515v1?rss=1 Bendre, S. V. Wang, Y. Hajyousif, B. K C, R. Bhogale, S. G. Pradeep, D. Krawczynska, N. Schane, C. P. Weisser, E. Singh, A. Han, S. Kim, H. Kockaya, L. Das Gupta, A. Nelczyk, A. T. Gamage, H. E. V. Fei, Y. Guo, X. Deaton, R. J. Sverdloc, M. Gann, P. H. Sinha, S. Wang, K. Van Bortle, K. T. Tajkhorshid, E. Cho, W. Nelson, E. R. 2025-02-19 doi:10.1101/2025.02.19.638515 Cold Spring Harbor Laboratory Press 2025-02-19 <![CDATA[ Joint linear modeling of transcriptomics and proteomics is predictive of cancer metastasis ]]> https://biorxiv.org/content/10.1101/2025.02.15.638428v1?rss=1 Sharma, R. Meimetis, N. Begzati, A. Nagar, S. D. Kellman, B. Baghdassarian, H. M. 2025-02-20 doi:10.1101/2025.02.15.638428 Cold Spring Harbor Laboratory Press 2025-02-20 <![CDATA[ Building Multivariate Molecular Imaging Brain Atlases Using the NeuroMark PET Independent Component Analysis Framework ]]> https://biorxiv.org/content/10.1101/2025.02.18.638362v1?rss=1 Eierud, C. Norgaard, M. Bilgel, M. Petropoulos, H. Fu, Z. Iraji, A. Matheson, G. J. Ganz, M. Pernet, C. Calhoun, V. 2025-02-23 doi:10.1101/2025.02.18.638362 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ Consequences of training data composition for deep learning models in single-cell biology ]]> https://biorxiv.org/content/10.1101/2025.02.19.639127v1?rss=1 Nadig, A. Thoutam, A. Hughes, M. Gupta, A. Navia, A. W. Fusi, N. Raghavan, S. Winter, P. S. Amini, A. P. Crawford, L. 2025-02-24 doi:10.1101/2025.02.19.639127 Cold Spring Harbor Laboratory Press 2025-02-24 <![CDATA[ DeepPath: Overcoming data scarcity for protein transition pathway prediction using physics-based deep learning ]]> https://biorxiv.org/content/10.1101/2025.02.27.640693v1?rss=1 Pang, Y. T. Kuo, K. M. Yang, L. Gumbart, J. C. 2025-03-02 doi:10.1101/2025.02.27.640693 Cold Spring Harbor Laboratory Press 2025-03-02 <![CDATA[ AF3Complex Yields Improved Structural Predictions of Protein Complexes ]]> https://biorxiv.org/content/10.1101/2025.02.27.640585v1?rss=1 Feldman, J. Skolnick, J. 2025-03-03 doi:10.1101/2025.02.27.640585 Cold Spring Harbor Laboratory Press 2025-03-03 <![CDATA[ Monitoring mutant myocilin secretion and localization in trabecular meshwork cell cultures using a protein complementation-based luminescence assay ]]> https://biorxiv.org/content/10.1101/2025.02.28.640780v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@1647a7aorg.highwire.dtl.DTLVardef@1a4e56dorg.highwire.dtl.DTLVardef@d29165org.highwire.dtl.DTLVardef@477e4f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Youngblood, H. A. Harris, E. F. Lankford, K. P. Garfinkel, V. Hulleman, J. Lieberman, R. L. 2025-03-03 doi:10.1101/2025.02.28.640780 Cold Spring Harbor Laboratory Press 2025-03-03 <![CDATA[ Disturbed Flow Induces Reprogramming of Endothelial Cells to Immune-like and Foam Cells under Hypercholesterolemia during Atherogenesis ]]> https://biorxiv.org/content/10.1101/2025.03.06.641843v1?rss=1 Park, C. Baek, K. I. Jeong, K. Kim, P. Hung, R.-C. Choi, L. Chou, C.-L. Kang, D. W. Song, E. J. Kim, Y. van der Laan, S. W. Pasterkamp, G. Villa-Roel, N. Panitch, A. Jo, H. 2025-03-06 doi:10.1101/2025.03.06.641843 Cold Spring Harbor Laboratory Press 2025-03-06 <![CDATA[ Light-induced reversible assembly and actuation in ultrafast Ca2+-driven chemomechanical protein networks ]]> https://biorxiv.org/content/10.1101/2025.03.03.641304v1?rss=1 Lei, X. Floyd, C. Ferrer, L. C. Chakrabortty, T. Chandrasekharan, N. Dinner, A. Coyle, S. M. Honts, J. Bhamla, S. 2025-03-12 doi:10.1101/2025.03.03.641304 Cold Spring Harbor Laboratory Press 2025-03-12 <![CDATA[ Inhibitory cell type heterogeneity in a spatially structured mean-field model of V1 ]]> https://biorxiv.org/content/10.1101/2025.03.13.643046v1?rss=1 Kim, S. H. Choi, H. 2025-03-13 doi:10.1101/2025.03.13.643046 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Weighted Ensemble Simulations Reveal Novel Conformations and Modulator Effects in Hepatitis B Virus Capsid Assembly ]]> https://biorxiv.org/content/10.1101/2025.03.15.643452v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@a0d760org.highwire.dtl.DTLVardef@19bfdb2org.highwire.dtl.DTLVardef@2cbc33org.highwire.dtl.DTLVardef@f7d307_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lynch, D. L. Fan, Z. Pavlova, A. Gumbart, J. C. 2025-03-17 doi:10.1101/2025.03.15.643452 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ Genome-wide ribonucleotide detection in Archaea ]]> https://biorxiv.org/content/10.1101/2025.03.17.643674v1?rss=1 Moalic, Y. Reveil, M. Kundnani, D. L. Balachander, S. Yang, T. Gombolay, A. Ranjbarian, F. Durand, P. Myllykallio, H. Jebbar, M. Storici, F. Henneke, G. 2025-03-17 doi:10.1101/2025.03.17.643674 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ Biofilm Vertical Growth Dynamics Are Captured by An Active Fluid Framework ]]> https://biorxiv.org/content/10.1101/2025.03.17.643762v1?rss=1 Copeland, R. Yunker, P. J. 2025-03-18 doi:10.1101/2025.03.17.643762 Cold Spring Harbor Laboratory Press 2025-03-18 <![CDATA[ A Large Language Model-Powered Map of Metabolomics Research ]]> https://biorxiv.org/content/10.1101/2025.03.18.643696v1?rss=1 Bifarin, O. O. Yelluru, V. S. Simhadri, A. Fernandez, F. M. 2025-03-19 doi:10.1101/2025.03.18.643696 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ Deep Learning Improves Parameter Estimation in Reinforcement Learning Models ]]> https://biorxiv.org/content/10.1101/2025.03.21.644663v1?rss=1 Xiong, H.-D. Ji-An, L. Mattar, M. G. Wilson, R. C. 2025-03-24 doi:10.1101/2025.03.21.644663 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ Antarctic Krill (Euphausia superba) swimming behaviour changes within a vertical flume under varied light, flow and chemical conditions ]]> https://biorxiv.org/content/10.1101/2025.03.24.645119v1?rss=1 Hellessey, N. G. Fields, D. Weissburg, M. 2025-03-25 doi:10.1101/2025.03.24.645119 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ NeuroCarta: An Automated and Quantitative Approach to Mapping Cellular Networks in the Mouse Brain ]]> https://biorxiv.org/content/10.1101/2025.03.25.645187v1?rss=1 Bergmans, T. Celikel, T. 2025-03-25 doi:10.1101/2025.03.25.645187 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Highly selective visual receptive fields in mouse frontal cortex ]]> https://biorxiv.org/content/10.1101/2025.03.25.645272v1?rss=1 Lien, A. D. Haider, B. 2025-03-26 doi:10.1101/2025.03.25.645272 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Conformational Dynamics and Catalytic Backups in a Hyper-Thermostable Engineered Archaeal Protein Tyrosine Phosphatase ]]> https://biorxiv.org/content/10.1101/2025.03.26.645524v1?rss=1 130 {degrees}C (>8 {degrees}C higher than the highest recorded growth temperature of any archaeal strain). Our combined structural, biochemical, biophysical and computational analysis provides insight both into how small steps in evolutionary space can radically modulate the biophysical properties of an enzyme, and showcase the tremendous potential of archaeal enzymes for biotechnology, to generate novel enzymes capable of operating under extreme conditions. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=68 SRC="FIGDIR/small/645524v3_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@186bfccorg.highwire.dtl.DTLVardef@19a265borg.highwire.dtl.DTLVardef@14c526corg.highwire.dtl.DTLVardef@1b75920_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yehorova, D. Alansson, N. Shen, R. Denson, J. M. Robinson, M. Risso, V. A. Molina, N. R. Loria, J. P. Gaucher, E. Sanchez-Ruiz, J. M. Hengge, A. C. Johnson, S. Kamerlin, S. C. L. 2025-03-26 doi:10.1101/2025.03.26.645524 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ How much is Transcription-associated Mutagenesis Driving tRNA Microevolution? ]]> https://biorxiv.org/content/10.1101/2025.03.26.645593v1?rss=1 Banos, H. Wang, L. Simonti, C. Paaby, A. B. Heitsch, C. E. 2025-03-31 doi:10.1101/2025.03.26.645593 Cold Spring Harbor Laboratory Press 2025-03-31 <![CDATA[ Mechanistic basis for non-exponential bacterial growth ]]> https://biorxiv.org/content/10.1101/2025.03.29.646116v1?rss=1 Cylke, A. Banerjee, S. 2025-04-03 doi:10.1101/2025.03.29.646116 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Regional susceptibility of PV interneurons in an hAPP-KI mouse model of Alzheimer's disease pathology ]]> https://biorxiv.org/content/10.1101/2025.04.01.646485v1?rss=1 Gonzalez, M. M. Magondu, B. J Rowan, M. Forest, C. R. 2025-04-03 doi:10.1101/2025.04.01.646485 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Three-dimensional Tracking Method for Water-Hopping Mudskippers in Natural Habitats ]]> https://biorxiv.org/content/10.1101/2025.04.02.646728v1?rss=1 Choi, D. Yung, K. Bergerson, I. Wallace, H. Grafe, U. Bhamla, S. 2025-04-03 doi:10.1101/2025.04.02.646728 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Stability and Adaptability in Balance: A Dual Mechanism for Metaplasticity in Cortical Networks ]]> https://biorxiv.org/content/10.1101/2025.04.02.646896v1?rss=1 Tompos, T. Zeldenrust, F. Celikel, T. 2025-04-03 doi:10.1101/2025.04.02.646896 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Hexapods shift to increasingly stable gaits when climbing on inclined substrates ]]> https://biorxiv.org/content/10.1101/2025.04.04.647231v1?rss=1 Riiska, C. A. Harrison, J. S. Thompson, R. D. Nina, J. Q. Gallice, G. R. Rieser, J. M. Bhamla, S. 2025-04-05 doi:10.1101/2025.04.04.647231 Cold Spring Harbor Laboratory Press 2025-04-05 <![CDATA[ Method for Extracellular Electrochemical Impedance Spectroscopy on Epithelia ]]> https://biorxiv.org/content/10.1101/2025.04.02.646694v1?rss=1 Chien, A. J. Lewallen, C. F. Khor, H. Vazquez Cegla, A. Guo, R. McCarty, N. A. Bharti, K. Forest, C. R. 2025-04-08 doi:10.1101/2025.04.02.646694 Cold Spring Harbor Laboratory Press 2025-04-08 <![CDATA[ Rhagovelia uses interfacial run-and-tumble locomotionto improve prey capture in flowing environments ]]> https://biorxiv.org/content/10.1101/2025.04.03.647112v1?rss=1 Tiwari, I. Nagappan, N. Harrison, J. S. Bhamla, S. 2025-04-09 doi:10.1101/2025.04.03.647112 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ Solid tumor CAR T cells engineered with fusion proteins targeting PDL1 for localized IL-12 delivery ]]> https://biorxiv.org/content/10.1101/2025.04.04.647304v1?rss=1 Murad, J. P. Christian, L. Rosa, R. Ren, Y. Lee, E. Lopez, L. Park, A. Yang, J. Trac, C. Adkins, L. Chang, W.-C. Martinez, C. June, C. H. Forman, S. Ishihara, J. Lee, J. K. Stern, L. Priceman, S. J. 2025-04-09 doi:10.1101/2025.04.04.647304 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ MENDELSEEK: An algorithm that predicts Mendelian Genes and elucidates what makes them special ]]> https://biorxiv.org/content/10.1101/2025.04.06.647432v1?rss=1 Zhou, H. Skolnick, J. 2025-04-10 doi:10.1101/2025.04.06.647432 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Adhesion and injury cues enhance blackworm captureby freshwater planaria ]]> https://biorxiv.org/content/10.1101/2025.04.09.647989v1?rss=1 Tiwari, I. Chudasama, H. Tuazon, H. Bhamla, S. 2025-04-10 doi:10.1101/2025.04.09.647989 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Sexually distinct multi omic responses to progressive endurance exercise training in the rat lung. Findings from MoTrPAC ]]> https://biorxiv.org/content/10.1101/2025.04.10.647997v1?rss=1 Many, G. Sagendorf, T. J. Mitchell, H. D. Sanford, J. A. Cohen, S. Misra, R. Estevao, I. L. Diaz Ludovico, I. Gaul, D. A. Lindholm, M. E. Ushakumary, M. G. Pino, J. Musi, N. Nie, J. Fernandez, F. Ortlund, E. A. Esser, K. A. Bodine, S. C. Schenk, S. Clair, G. C. Adkins, J. N. 2025-04-16 doi:10.1101/2025.04.10.647997 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ Emergence of coordinated cell division during the evolution of multicellularity ]]> https://biorxiv.org/content/10.1101/2025.04.23.650085v1?rss=1 Cedeno Perez, L. F. Pineau, R. Day, T. C. Ratcliff, W. C. Conlin, P. L. 2025-04-24 doi:10.1101/2025.04.23.650085 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Label-Free In-Line Characterization of Immune Cell Culture using Quantitative Phase Imaging ]]> https://biorxiv.org/content/10.1101/2025.04.22.649403v1?rss=1 Serafini, C. E. Gorti, V. Casteleiro Costa, P. Silva Trenkle, A. D. Kanwar, B. Wang, B. Wicker, B. Kippner, L. E. LeCompte, I. Chen, R. Q. Joffe, B. Li, Y. Bowles-Welch, A. C. Li, J. Brown, C. E. Kwong, G. A. Balakirsky, S. Roy, K. Robles, F. E. 2025-04-29 doi:10.1101/2025.04.22.649403 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Cellular and molecular underpinnings of functional networks in the human brain ]]> https://biorxiv.org/content/10.1101/2025.04.28.651051v1?rss=1 Feng, G. Chen, J. Sui, J. Calhoun, V. D. 2025-04-29 doi:10.1101/2025.04.28.651051 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Power-law memory governs bacterial adaptation and learning in fluctuating environments ]]> https://biorxiv.org/content/10.1101/2025.04.26.650739v1?rss=1 Kratz, J. Wang, H. Si, F. Banerjee, S. 2025-04-30 doi:10.1101/2025.04.26.650739 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Spatial Dynamics and Functional Connectivity in EEG: Insights from Lexical Processing ]]> https://biorxiv.org/content/10.1101/2025.04.29.651245v1?rss=1 Aguilar, O. M. H. Grullon, R. 2025-04-30 doi:10.1101/2025.04.29.651245 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ The Consortium for Genomic Diversity, Ancestry, and Health in Colombia (CODIGO): building local capacity in genomics, bioinformatics, and precision medicine ]]> https://biorxiv.org/content/10.1101/2025.04.28.651081v1?rss=1 Marino-Ramirez, L. Sharma, S. Hamilton, J. M. Nguyen, T. L. Gupta, S. Natarajan, A. V. Nagar, S. D. Menuey, J. L. Chen, W.-A. Sanchez-Gomez, A. Satizabal-Soto, J. M. Martinez, B. Marrugo, J. Medina-Rivas, M. Gallo, J. E. Jordan, I. K. Valderrama-Aguirre, A. 2025-05-01 doi:10.1101/2025.04.28.651081 Cold Spring Harbor Laboratory Press 2025-05-01 <![CDATA[ Neural signaling contributes to heart formation and growth in the invertebrate chordate, Ciona robusta. ]]> https://biorxiv.org/content/10.1101/2025.04.28.651085v1?rss=1 Gruner, H. N. Pickett, C. J. Bao, J. Y. Garcia, R. Hozumi, A. Scully, T. Ning, S. Gao, M. Bautista, G. Maze, K. Lim, K. Osugi, T. Collins-Doijode, M. Cairns, O. Levis, G. Chen, S. Y. Gong, T. Satake, H. Moshe-Klein, A. Gigante, E. D. Sasakura, Y. Davidson, B. 2025-05-02 doi:10.1101/2025.04.28.651085 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ Harmonized Protocol for Subfield Segmentation in the Hippocampal Body on High-Resolution in vivo MRI from the Hippocampal Subfields Group (HSG) ]]> https://biorxiv.org/content/10.1101/2025.04.29.651039v1?rss=1 Daugherty, A. M. Carr, V. Canada, K. Radman, G. Brown, T. Augustinack, J. Amunts, K. Bakker, A. Berron, D. Burggren, A. Chetelat, G. de Flores, R. Ding, S.-L. Huang, Y. Insausti, R. Johnson, E. Kanel, P. Keresztes, A. Kedo, O. Kennedy, K. M. Lee, J. Malykhin, N. Martinez, A. Mueller, S. Mulligan, E. Ofen, N. Palombo, D. Pasquini, L. Pluta, J. Raz, N. Riggins, T. Rodrigue, K. M. Saifullah, S. Schlichting, M. L. Stark, C. Wang, L. Yushkevich, P. La Joie, R. Wisse, L. Olsen, R. the Alzheimers Disease Neuroimaging Initiative, the Hippocampal Subfields Gro 2025-05-04 doi:10.1101/2025.04.29.651039 Cold Spring Harbor Laboratory Press 2025-05-04 <![CDATA[ Data-driven feedback augments ultrasound nanotheranostics in brain tumors ]]> https://biorxiv.org/content/10.1101/2025.05.01.651328v1?rss=1 Lee, H. Menezes, V. Zeng, S. Kim, C. Baseman, C. M. Kim, J. H. Padmanabhan, S. Premdas, P. Djeddar, N. Bryksin, A. V. Pandey, N. Anastasiadis, P. Kim, A. J. MacDonald, T. J. Bettegowda, C. Woodworth, G. F. Hermann, F. J. Arvanitis, C. 2025-05-07 doi:10.1101/2025.05.01.651328 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ NeuroMark-HiFi: A Data-Driven Method for Detecting High-Spatial-Frequency Functional Brain Networks ]]> https://biorxiv.org/content/10.1101/2025.05.02.651877v1?rss=1 Behzadfar, N. Iraji, A. Calhoun, V. 2025-05-08 doi:10.1101/2025.05.02.651877 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Neural rhythms as priors of speech computations ]]> https://biorxiv.org/content/10.1101/2025.05.06.652542v1?rss=1 Chandravadia, N. Imam, N. 2025-05-08 doi:10.1101/2025.05.06.652542 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ CRISPR-Cas is beneficial in plasmid competition, but limited by competitor toxin-antitoxin activity when horizontally transferred ]]> https://biorxiv.org/content/10.1101/2025.05.09.653016v1?rss=1 Sünderhauf, D. Ringger, J. R. Payne, L. J. Pinilla-Redondo, R. Gaze, W. H. Brown, S. P. van Houte, S. 2025-05-09 doi:10.1101/2025.05.09.653016 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Validation of Gentamicin and Streptomycin Stability for On-Orbit Microbial Monitoring ]]> https://biorxiv.org/content/10.1101/2025.05.11.653350v1?rss=1 McKaig, J. M. Carr, C. E. 2025-05-11 doi:10.1101/2025.05.11.653350 Cold Spring Harbor Laboratory Press 2025-05-11 <![CDATA[ Combining structural modeling and deep learning to calculate the E. coli protein interactome and functional networks ]]> https://biorxiv.org/content/10.1101/2025.05.07.652715v1?rss=1 Zhao, H. Velez, C. Naravane, A. C. Saha, A. Feldman, J. Skolnick, J. Murray, D. Honig, B. 2025-05-12 doi:10.1101/2025.05.07.652715 Cold Spring Harbor Laboratory Press 2025-05-12 <![CDATA[ Cell-type-specific encoding of prediction and reward in cortical microcircuits during novelty detection ]]> https://biorxiv.org/content/10.1101/2025.05.13.653877v1?rss=1 Sharafeldin, A. Choi, H. 2025-05-14 doi:10.1101/2025.05.13.653877 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Aberrant Fibro-Adipogenic Progenitor Subpopulations Drive Volumetric Muscle Loss-Induced Fibrosis ]]> https://biorxiv.org/content/10.1101/2025.05.11.653339v1?rss=1 Anderson, S. E. Hymel, L. A. Zhang, H. McKinney, J. M. Turner, T. C. Mohiuddin, M. Han, W. M. Lee, N. H. Choi, J. J. Jeong, G. Greenwood, E. Chatterjee, P. Lee, S. Gibson, G. Wood, L. B. Botchwey, E. A. Jang, Y. C. Willett, N. J. 2025-05-15 doi:10.1101/2025.05.11.653339 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ No Effect of Chronic or Acute Pain on Working Memory in the Sternberg Task ]]> https://biorxiv.org/content/10.1101/2025.05.13.653893v1?rss=1 Phelps, C. E. Oliveira, L. E. Ngo, M. N. Medhi, K. S. Schoone, S. Debrosse, D. Aragundi, L. Delval, A. G. R. Wilson, R. C. 2025-05-15 doi:10.1101/2025.05.13.653893 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Emergent higher-order interactions enable coexistence in phage-bacteria community dynamics ]]> https://biorxiv.org/content/10.1101/2025.05.15.651590v1?rss=1 Dey, R. Coenen, A. R. Solonenko, N. E. Burris, M. N. Mackey, A. I. Galasso, J. Sun, C. L. Demory, D. Muratore, D. Beckett, S. J. Sullivan, M. B. Weitz, J. S. 2025-05-16 doi:10.1101/2025.05.15.651590 Cold Spring Harbor Laboratory Press 2025-05-16 <![CDATA[ Dynamic fusion of structural and functional connectivity via joint connectivity matrix ICA ]]> https://biorxiv.org/content/10.1101/2025.05.15.653851v1?rss=1 Wu, L. Duda, M. Iraji, A. Calhoun, V. 2025-05-19 doi:10.1101/2025.05.15.653851 Cold Spring Harbor Laboratory Press 2025-05-19 <![CDATA[ Machine Learning Matches Human Performance at Segmenting the Human Visual Cortex ]]> https://biorxiv.org/content/10.1101/2025.05.16.654503v1?rss=1 Benson, N. C. Song, B. Chen, S. Miyata, T. Takemura, H. Winawer, J. 2025-05-21 doi:10.1101/2025.05.16.654503 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Unmasking complex kinetics in viral entry by inferring hypoexponential models ]]> https://biorxiv.org/content/10.1101/2025.05.18.654751v1?rss=1 Adenekan, O. Kasson, P. 2025-05-23 doi:10.1101/2025.05.18.654751 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Non-destructive, high-resolution T cell characterization and subtyping via deep-ultraviolet microscopy ]]> https://biorxiv.org/content/10.1101/2025.05.20.655120v1?rss=1 Gorti, V. Serafini, C. E. Silva Trenkle, A. D. McCubbins, K. LeCompte, I. Kwong, G. A. Robles, F. E. 2025-05-26 doi:10.1101/2025.05.20.655120 Cold Spring Harbor Laboratory Press 2025-05-26 <![CDATA[ TRPV4 modulates substrate stiffness mechanosensing and transcellular pore formation in human Schlemm's canal cells ]]> https://biorxiv.org/content/10.1101/2025.05.25.656000v1?rss=1 Li, H. Wong, C. A. Siadat, S. M. Perkumas, K. M. Bertrand, J. A. Overby, D. R. Sulchek, T. Stamer, W. D. Ethier, C. R. 2025-05-26 doi:10.1101/2025.05.25.656000 Cold Spring Harbor Laboratory Press 2025-05-26 <![CDATA[ Effect of Age on Xenobiotic-Induced Autoimmunity ]]> https://biorxiv.org/content/10.1101/2025.05.22.655368v1?rss=1 de Ocampo, C. Peiss, A. K. Leung, H. Y. Janssen, L. M. Kono, D. H. Mayeux, J. M. Pollard, K. M. 2025-05-27 doi:10.1101/2025.05.22.655368 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ An information theory framework for capturing multi-connectivity via spatial network encoding reveals reduced population count (Hamming weight) localized to auditory, visual, and motor networks ]]> https://biorxiv.org/content/10.1101/2025.05.22.655511v1?rss=1 Bostami, B. Lewis, N. Agcaoglu, O. Silva, R. F. Turner, J. A. van Erp, T. Ford, J. Calhoun, V. 2025-05-27 doi:10.1101/2025.05.22.655511 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Inhibition of p38 MAPK after repetitive mild TBI ameliorates immune signaling and behavioral deficits ]]> https://biorxiv.org/content/10.1101/2025.05.29.656410v1?rss=1 Li, C. Triplett, S. E. Griffin, M. Silverio, A. Pettit, E. Rohrer, A. Callaway, J. Munagapati, P. Saah, P. Sanz, P. Rivera Moctezuma, F. Buckley, E. Wood, L. B. 2025-05-30 doi:10.1101/2025.05.29.656410 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Encoding of speech modes and loudness in ventral precentral gyrus ]]> https://biorxiv.org/content/10.1101/2025.05.30.657105v1?rss=1 Srinivasan, A. Wairagkar, M. Iacobacci, C. Hou, X. Card, N. S. Jacques, B. G. Pritchard, A. L. Bechefsky, P. H. Hochberg, L. R. AuYong, N. Pandarinath, C. Brandman, D. M. Stavisky, S. D. 2025-06-01 doi:10.1101/2025.05.30.657105 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Viral adsorption to Moore swabs in passive wastewater sampling ]]> https://biorxiv.org/content/10.1101/2025.05.30.656954v1?rss=1 Rao, G. Purvis, T. Cha, G. Dalton, J. Fisher, M. Graham, K. E. Konstantinidis, K. T. Linden, Y. Bivins, A. Brinton, M. A. Stauber, C. Brown, J. 2025-06-02 doi:10.1101/2025.05.30.656954 Cold Spring Harbor Laboratory Press 2025-06-02 <![CDATA[ An intergenerational lipid memory of the social environment in C. elegans ]]> https://biorxiv.org/content/10.1101/2025.06.03.657568v1?rss=1 Wilhelm, T. Chen, W.-W. Wenzel, A. Tang, W. Cicerone, M. T. Lehner, B. 2025-06-03 doi:10.1101/2025.06.03.657568 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ An artificial nervous system for communication between wearable and implantable therapeutics ]]> https://biorxiv.org/content/10.1101/2025.06.04.657863v1?rss=1 15x greater power efficiencies than Bluetooth and Near Field Communication. In vivo studies in rats demonstrate SWANS ability to wirelessly regulate dual hind leg motor control by connecting electronic-skin sensors to implantable neural interfaces via ionic signaling as well as coordinate bioelectronics throughout the epidermal, subcutaneous, intraperitoneal, and gastrointestinal spaces. ]]> Ghanim, R. Lee, Y. J. Byun, G. Jackson, J. Ding, J. Z. Feller, E. Kim, E. Aygun, D. Kaushik, A. Cig, A. Park, J. Healy, S. Cunin, C. E. Gumyusenge, A. Yeo, W. H. Abramson, A. 2025-06-04 doi:10.1101/2025.06.04.657863 Cold Spring Harbor Laboratory Press 2025-06-04 <![CDATA[ aNy-way ICA and its application to estimate cortico-thalamo-cerebellar functional links in schizophrenia ]]> https://biorxiv.org/content/10.1101/2025.06.02.657541v1?rss=1 Duan, K. Silva, R. F. Rahaman, M. A. Fu, Z. Liu, J. Kochunov, P. van Erp, T. G. M. Shultz, S. Calhoun, V. D. 2025-06-06 doi:10.1101/2025.06.02.657541 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ ProGuide: a flexible framework for modeling global conformational rearrangements in proteins using DEER-derived distance restraints ]]> https://biorxiv.org/content/10.1101/2025.06.05.658127v1?rss=1 Grosskopf, J. D. Kasson, P. Lerch, M. T. 2025-06-09 doi:10.1101/2025.06.05.658127 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Opposing responses of hippocampal theta oscillations to running and a forelimb-dominated sensorimotor behavior ]]> https://biorxiv.org/content/10.1101/2025.06.08.658384v1?rss=1 Holguin, G. Jorgensen, K. Tapia, A. Jordan, G. A. Vishwanath, A. Barnes, C. A. Cowen, S. L. 2025-06-09 doi:10.1101/2025.06.08.658384 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Genes govern metabolism-Enzymes define pathways and metabolic relationships ]]> https://biorxiv.org/content/10.1101/2025.06.16.657199v1?rss=1 Zhan, J. Jarrell, Z. R. Kemp, M. L. Weinberg, J. Go, Y.-M. G. Martin, G. S. Jones, D. P. 2025-06-19 doi:10.1101/2025.06.16.657199 Cold Spring Harbor Laboratory Press 2025-06-19 <![CDATA[ Behavioral Signature of Trihexyphenidyl in The Tor1a (DYT1) Knockin Mouse Model of Dystonia ]]> https://biorxiv.org/content/10.1101/2025.06.17.659360v1?rss=1 Qader, A. A. Donsante, Y. Markowitz, J. E. Jinnah, H. A. Pandarinath, C. Hess, E. J. 2025-06-20 doi:10.1101/2025.06.17.659360 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Label-Free Targeted High Efficiency Electroporation with Single-Cell Feedback Control Using Focused Microscale Electric Fields ]]> https://biorxiv.org/content/10.1101/2025.06.16.659916v1?rss=1 80 %) and high (>90 %) cell viability. Delivery of a range of different cargo sizes (4-500 kDa), GFP mRNA expression, CRISPR-Cas9 based knock-out and delivery to a variety of different cell lines, primary human T cells and peripheral blood mononuclear cells (PBMCs) was also demonstrated. Using heterogenous or mixed samples, selective delivery to both cell lines, and primary immune cell subpopulations, from PBMCs, was demonstrated. SPICy thus provides a label-free, continuous flow, targeted non-viral platform for precision cell engineering. ]]> Rudge, J. Rallapalli, Y. Hoyle, M. Sarkar, A. 2025-06-21 doi:10.1101/2025.06.16.659916 Cold Spring Harbor Laboratory Press 2025-06-21 <![CDATA[ GOLF: A Generative AI Framework for Pathogenicity Prediction of Myocilin OLF Variants ]]> https://biorxiv.org/content/10.1101/2025.06.17.660210v1?rss=1 Walton, T. A. Tsui, D. Fogel, L. Huard, D. Chagas, R. Lieberman, R. L. Aghazadeh, A. 2025-06-24 doi:10.1101/2025.06.17.660210 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ Structural connectivity-informed dynamic estimation (STRiDE): Multimodal connectivity constrained ICA ]]> https://biorxiv.org/content/10.1101/2025.06.18.660402v1?rss=1 Fouladivanda, M. Iraji, A. Wu, L. Chen, J. Camazon, P. A. van Erp, T. Belger, A. Pearlson, G. D. Adali, T. Calhoun, V. 2025-06-24 doi:10.1101/2025.06.18.660402 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ EZ-FRCNN: A Fast, Accessible and Robust Deep Learning Package for Object Detection Applications from Ethology to Cell Biology ]]> https://biorxiv.org/content/10.1101/2025.06.19.660198v1?rss=1 Shappell, E. Wheelock, J. Aubry, G. Lu, H. 2025-06-25 doi:10.1101/2025.06.19.660198 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Flow-sensitive HEG1 controls eNOS activity to prevent endothelial dysfunction, hypertension, and atherosclerosis ]]> https://biorxiv.org/content/10.1101/2025.06.24.660441v1?rss=1 Clark, M. D. Kim, Y. Romero, C. A. Kang, D. W. Baek, K. I. Song, E. J. Kellum, C. E. Bowman-Kirigin, J. A. Park, C. Vapoor, V. Pollock, J. S. Jo, H. 2025-06-27 doi:10.1101/2025.06.24.660441 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Human ribomes reveal DNA-embedded ribonucleotides as a new type of epigenetic mark ]]> https://biorxiv.org/content/10.1101/2025.06.27.661996v1?rss=1 Kundnani, D. L. Yang, T. Channagiri, T. Xu, P. Lee, Y. Sun, M. Martinez-Figueroa, F. Randhawa, S. Gogate, A. Jeon, Y. Marsili, S. Newnam, G. Lu, Y. Park, V. Tao, S. Ling, J. Schinazi, R. Pursell, Z. Mohammed, A. Opresko, P. Freudenthal, B. Kim, B. Yi, S. Jonoska, N. Storici, F. 2025-06-30 doi:10.1101/2025.06.27.661996 Cold Spring Harbor Laboratory Press 2025-06-30 <![CDATA[ Copper-Containing ROS-Scavenging Nanozyme Paradoxically Drives Alpha-Synucleinopathy by Amplifying Nitrosative Stress ]]> https://biorxiv.org/content/10.1101/2025.07.01.661317v1?rss=1 Li, S. Mao, Y. Wang, N. Zhang, J. Zhi, X. Chen, Y. Si, J. Yang, Q. Kumbhar, R. Joeng, D. Song, J.-Y. Yang, X. Kang, B. G. Khandekar, A. Park, J. Gao, Y. Yu, S. Chen, R. Zhang, S. Han, J. Dawson, V. L. Liu, P. Han, S. Dawson, T. He, W. Mao, X. 2025-07-05 doi:10.1101/2025.07.01.661317 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ Long-acting hydrogel-based depot formulations of tirzepatide and semaglutide for the management of type 2 diabetes and weight ]]> https://biorxiv.org/content/10.1101/2025.07.02.662867v1?rss=1 d'Aquino, A. I. Dong, C. Nguyen, L. T. Yan, J. Jons, C. K. Saouaf, O. M. Song, Y. E. Eckman, N. Kapasi, S. Williams, C. M. Doulames, V. M. Sen, S. Manna, M. K. Alakesh, A. Lu, K. Hall, I. Appel, E. A. 2025-07-05 doi:10.1101/2025.07.02.662867 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ A protocadherin mediates cell-cell adhesion and integrity of the oral placode in the tunicate Ciona ]]> https://biorxiv.org/content/10.1101/2025.07.11.664433v1?rss=1 Vedurupaka, S. Jadali, B. Johnson, C. J. Stolfi, A. Popsuj, S. 2025-07-14 doi:10.1101/2025.07.11.664433 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ Cell-substrate friction controls biofilm development ]]> https://biorxiv.org/content/10.1101/2025.07.11.664457v1?rss=1 Pokhrel, A. Copeland, R. Hejri, M. Belpaire, T. E. R. Steinbach, G. Ng, S. L. Hammer, B. K. Yunker, P. J. 2025-07-17 doi:10.1101/2025.07.11.664457 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Sensory neurostimulation promotes stress resilience with frequency-specificity ]]> https://biorxiv.org/content/10.1101/2025.07.12.664223v1?rss=1 Franklin, T. C. Bitarafan, S. King, A. T. Goodson, M. Rutledge, C. Gajelli, T. Prichard, A. M. Zepeda, H. Kye, N. Sloan, S. A. Wood, L. Singer, A. C. 2025-07-17 doi:10.1101/2025.07.12.664223 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Metagenome-based vertical profiling of the Gulf of Mexico highlights its uniqueness and far-reaching effects of freshwater input ]]> https://biorxiv.org/content/10.1101/2025.07.17.665386v1?rss=1 Conrad, R. E. Tsementzi, D. Meziti, A. Hatt, J. Montoya, J. Konstantinidis, K. T. 2025-07-17 doi:10.1101/2025.07.17.665386 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Quality control of single-cell ATAC-seq data without peak calling using Chromap ]]> https://biorxiv.org/content/10.1101/2025.07.15.664951v1?rss=1 Ahmed, O. Zhang, H. Langmead, B. Song, L. 2025-07-18 doi:10.1101/2025.07.15.664951 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Deciphering the evolutionary origin of the stereoselectivity of short-chain dehydrogenases in the oxidation of the monoterpenol 1-borneol ]]> https://biorxiv.org/content/10.1101/2025.07.17.664155v1?rss=1 Zuson, J. Helmer, C. P. O. Di Geronimo, B. Chanique, A. M. Kavciakova, K. Teijeiro, R. J. Drienovska, I. Brickel, S. Kracher, D. Kamerlin, L. Loll, B. Kourist, R. 2025-07-18 doi:10.1101/2025.07.17.664155 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Forced exercise modulates retinal inflammatory response and regulates miRNA expression to promote retinal neuroprotection during degeneration ]]> https://biorxiv.org/content/10.1101/2025.07.16.665187v1?rss=1 Haupt, H. B. Chen, V. S. Palumaa, T. Anderson, T. E. Sanchez Rodriguez, G. Chu-Tan, J. Natoli, R. Feola, A. Nickerson, J. Pardue, M. Boatright, J. H. Bales, K. L. 2025-07-21 doi:10.1101/2025.07.16.665187 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Sphingomyelinase Licensing of Mesenchymal Stromal Cells Alters Lipid and Protein Metabolites for Immunomodulation ]]> https://biorxiv.org/content/10.1101/2025.07.17.665406v1?rss=1 DeVeaux, S. A. Shah, D. C. Rui, K. Chiappa, N. F. Zhang, H. Lal, N. ONeill, R. Jang, Y. C. Mortensen, L. J. Roy, K. Botchwey, E. 2025-07-22 doi:10.1101/2025.07.17.665406 Cold Spring Harbor Laboratory Press 2025-07-22 <![CDATA[ Immunomodulatory endothelial cells contribute to T cell recruitment and activation through antigen presentation on MHC class II ]]> https://biorxiv.org/content/10.1101/2025.07.17.665432v1?rss=1 Cartura, M. Aliraj, B. Szyma?ski, W. Ferrario, G. Rezende, F. Gueven, B. Bleckwehl, T. Dimmeler, S. Mueller, O. J. Jo, H. Offermanns, S. Hayat, S. Brandes, R. P. Muench, C. Graumann, J. Weigert, A. Fleming, I. Siragusa, M. 2025-07-22 doi:10.1101/2025.07.17.665432 Cold Spring Harbor Laboratory Press 2025-07-22 <![CDATA[ Simultaneous ligand binding to intact and partially formed ATP binding sites in the hexameric termination factor Rho ]]> https://biorxiv.org/content/10.1101/2025.07.22.665897v1?rss=1 Billings, T. D. Baker, K. L. Lacey, P. Muzquiz, R. Wysocki, V. H. Foster, M. P. 2025-07-24 doi:10.1101/2025.07.22.665897 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ snATAC-Express infers Gene Expression from Prioritized Chromatin Accessibility Peaks using Machine Learning ]]> https://biorxiv.org/content/10.1101/2025.07.25.666784v1?rss=1 Brown, M. Ferrari, A. Dodd, A. Shi, F. Kolachala, V. L. Kugathasan, S. Wolfinger, R. D. Gibson, G. 2025-07-25 doi:10.1101/2025.07.25.666784 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ High speed functional imaging with a microfluidics-compatible open-top light-sheet microscope enabled by model predictive control of a tunable lens ]]> https://biorxiv.org/content/10.1101/2025.07.23.666439v1?rss=1 Calhoun, W. A. Moon, S. Peng, L. Lu, H. 2025-07-27 doi:10.1101/2025.07.23.666439 Cold Spring Harbor Laboratory Press 2025-07-27 <![CDATA[ ASCENT: Annotation-free Self-supervised Contrastive Embeddings for 3D Neuron Tracking in Fluorescence Microscopy ]]> https://biorxiv.org/content/10.1101/2025.07.23.666425v1?rss=1 Han, H. Pritchard, R. H. Lu, H. 2025-07-28 doi:10.1101/2025.07.23.666425 Cold Spring Harbor Laboratory Press 2025-07-28 <![CDATA[ Human Strategy Adaptation in Reinforcement Learning Resembles Policy Gradient Ascent ]]> https://biorxiv.org/content/10.1101/2025.07.28.667308v1?rss=1 Xiong, H.-D. Ji-An, L. Wilson, R. C. Mattar, M. G. 2025-07-31 doi:10.1101/2025.07.28.667308 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Single Capture Quantitative Oblique Back-Illumination Microscopy ]]> https://biorxiv.org/content/10.1101/2025.07.29.667497v1?rss=1 Casteleiro Costa, P. Bharadwaj, S. Li, Z. Kaza, N. Lopez-Esteva, M. Lien, A. Haider, B. Robles, F. E. 2025-08-01 doi:10.1101/2025.07.29.667497 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ An in planta single-cell screen to accelerate functional genetics ]]> https://biorxiv.org/content/10.1101/2025.08.06.668818v1?rss=1 Lowensohn, T. N. Cody, W. B. Tsai, C. Vlahos, A. E. Call, C. C. Gao, X. J. Sattely, E. S. 2025-08-07 doi:10.1101/2025.08.06.668818 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Real-time, High-throughput Super-resolution Microscopy via Panoramic Integration ]]> https://biorxiv.org/content/10.1101/2025.08.07.669117v1?rss=1 Yoon, K. Yoon, H. Tadesse, K. Ling, Z. Mandracchia, B. Datta, S. Bozdag, G. O. Burnetti, A. J. Ratcliff, W. C. Jia, S. 2025-08-11 doi:10.1101/2025.08.07.669117 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ Investigating Bio-Nano Interactions of PEGylated Cationic Polyamidoamine (PAMAM) Dendrimers within Synovial Joints ]]> https://biorxiv.org/content/10.1101/2025.08.09.668990v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@9298ccorg.highwire.dtl.DTLVardef@6d85aeorg.highwire.dtl.DTLVardef@63838dorg.highwire.dtl.DTLVardef@151ca4a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Douglas-Green, S. A. Aleman, J. A. Dampty, V. M. Murthy, B. Johnston, B. M. Park, J. H. Grodzinsky, A. J. Hammond, P. T. 2025-08-12 doi:10.1101/2025.08.09.668990 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Novel combination of irreversible electroporation and allogenic chimeric antigen receptor (CAR) T-cell therapy synergizes therapeutic outcomes in a preclinical human pancreatic cancer mouse model ]]> https://biorxiv.org/content/10.1101/2025.08.10.669537v1?rss=1 Jacobs, E. J. Arroyo, J. Parizi, S. S. Guo, W. Lu, Y. Davalos, R. 2025-08-12 doi:10.1101/2025.08.10.669537 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Commensal taxa in gut microbiota limit antibiotic resistance during extended oral antibiotic use ]]> https://biorxiv.org/content/10.1101/2025.08.13.670183v1?rss=1 Cyphert, E. L. Liu, C. Chu, V. T. Dubey, A. Liu, M. Zhong, Z. Cockey, J. R. Diaz, E. C. G. Morales, A. L. Nixon, J. C. Garcia, M. Zeng, S. Rohatgi, S. Wong, J. Arjyal, R. Mekonen, H. Neff, N. Lee, J. Shea, M. K. Fu, X. Booth, S. L. Leifer, C. A. Singh, A. Langelier, C. R. Hernandez, C. J. 2025-08-13 doi:10.1101/2025.08.13.670183 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ Detection of prostate cancer in 3D pathology datasets via generative immunolabeling ]]> https://biorxiv.org/content/10.1101/2025.08.11.669726v1?rss=1 Serafin, R. B. Salguero-Lopez, J. Chow, S. Wang, R. Zhao, Y. Baraznenok, E. Lan, L. Bishop, K. W. Downes, M. Farre, X. True, L. D. Lal, P. Madabhushi, A. Liu, J. T. C. 2025-08-15 doi:10.1101/2025.08.11.669726 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Cell Geometry Limits Bacterial Metabolic Efficiency ]]> https://biorxiv.org/content/10.1101/2025.08.11.669779v1?rss=1 Cylke, A. Banerjee, S. 2025-08-15 doi:10.1101/2025.08.11.669779 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Layer-by-Layer Nanoparticle Outer Polyion Impacts Protein Corona Formation ]]> https://biorxiv.org/content/10.1101/2025.08.13.670086v1?rss=1 View larger version (50K): org.highwire.dtl.DTLVardef@18a2a66org.highwire.dtl.DTLVardef@1e5b755org.highwire.dtl.DTLVardef@676af2org.highwire.dtl.DTLVardef@19e3b34_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Dacoba, T. Douglas-Green, S. A. Murthy, B. Restrepo, A. D. Strom, Z. Billingsley, M. Pryor, M. Hammond, P. T. 2025-08-18 doi:10.1101/2025.08.13.670086 Cold Spring Harbor Laboratory Press 2025-08-18 <![CDATA[ StrainFacts accurately quantifies both endogenous and live biotherapeutic product strain abundances in simulated and clinical vaginal microbiota samples ]]> https://biorxiv.org/content/10.1101/2025.08.15.670563v1?rss=1 Shih, J. Bloom, S. M. Xu, J. Mitchell, C. M. Elsherbini, J. Kwon, D. S. 2025-08-21 doi:10.1101/2025.08.15.670563 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Screening channelrhodopsins using robotic intracellularelectrophysiology and single cell sequencing ]]> https://biorxiv.org/content/10.1101/2025.08.19.671087v1?rss=1 Ehrlich, S. M. VandeLoo, A. D. Badawy, M. Gonzalez, M. M. M. Stockslager, M. Yang, A. Sinha, S. Bracha, S. Park, D. Magondu, B. Yang, B. Boyden, E. S. Forest, C. R. 2025-08-24 doi:10.1101/2025.08.19.671087 Cold Spring Harbor Laboratory Press 2025-08-24 <![CDATA[ Mechanical energetic contributions of the rectus femoris during perturbed walking ]]> https://biorxiv.org/content/10.1101/2025.08.20.671067v1?rss=1 Golyski, P. R. Sawicki, G. S. 2025-08-25 doi:10.1101/2025.08.20.671067 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ Exogenous Delivery of Sphingomyelinase Mediates Mesenchymal Stromal Cell-Extracellular Vesicle Biogenesis, Alters Cargo Sorting, and Therapeutic Potency in vitro ]]> https://biorxiv.org/content/10.1101/2025.08.21.671536v1?rss=1 Shah, D. C. DeVeaux, S. A. Zhang, H. Liu, A. Y. Adedipe, T. A. Chiappa, N. F. Patel, K. A. Jang, Y. C. Goudy, S. L. Sulchek, T. Roy, K. Botchwey, E. A. 2025-08-26 doi:10.1101/2025.08.21.671536 Cold Spring Harbor Laboratory Press 2025-08-26 <![CDATA[ 40 Hz Audiovisual Stimulation Improves Sustained Attention and Related Brain Oscillations ]]> https://biorxiv.org/content/10.1101/2025.08.25.671937v1?rss=1 Attokaren, M. K. Zhang, L. Mettupalli, S. Singer, A. 2025-08-26 doi:10.1101/2025.08.25.671937 Cold Spring Harbor Laboratory Press 2025-08-26 <![CDATA[ Optimized Mappings from Biological Hip Moment Estimates to Exoskeleton Torque can Personalize Assistance Across Users and Generalize Across Tasks ]]> https://biorxiv.org/content/10.1101/2025.08.29.671780v1?rss=1 Powell, J. C. Schonhaut, E. B. Molinaro, D. D. Young, A. J. 2025-08-30 doi:10.1101/2025.08.29.671780 Cold Spring Harbor Laboratory Press 2025-08-30 <![CDATA[ Enhancing Optical Properties and Stability of DNA-Functionalized Carbon Nanotubes with Cryoprotectant Mediated Lyophilization ]]> https://biorxiv.org/content/10.1101/2025.08.26.672410v1?rss=1 Nadeem, A. Kindopp, A. Junge, E. Rahmani, M. Roxbury, D. 2025-08-31 doi:10.1101/2025.08.26.672410 Cold Spring Harbor Laboratory Press 2025-08-31 <![CDATA[ Brain Mecp2 Gene Dosage and Gene Therapy Shape Multi-Omic Signatures and Biomarkers in Rett Syndrome ]]> https://biorxiv.org/content/10.1101/2025.08.30.673242v1?rss=1 Zlatic, S. A. Dammer, E. Crocker, A. Duong, D. Selfridge, J. Gadalla, K. K. Gokhale, A. Tobin, B. R. Wood, L. B. Zandl-Lang, M. Abela, L. Plecko, B. Patgiri, A. Kaufmann, W. E. Carpenter, R. Cobb, S. Faundez, V. 2025-09-02 doi:10.1101/2025.08.30.673242 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ Electrical stimulation elicits space- and parameter-dependent spiking responses in human cortical organoids ]]> https://biorxiv.org/content/10.1101/2025.09.01.673532v1?rss=1 Nigrisoli, D. Seseri, N. Faraci, F. D'Angelo, A. Freddi, R. Chandran, S. Barbieri, R. Corti, S. Ottoboni, L. Russo, S. 2025-09-02 doi:10.1101/2025.09.01.673532 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ Immune Cell Migration Models Synergize Nuclear Piston, Uropod, and Microenvironment into Hydraulic Cell Engine ]]> https://biorxiv.org/content/10.1101/2025.09.02.673867v1?rss=1 Alawadhi, S. Rutkowski, D. M. Tagay, Y. Cartagena-Rivera, A. X. Zhovmer, A. S. Tsygankov, D. Vavylonis, D. Tabdanov, E. D. 2025-09-06 doi:10.1101/2025.09.02.673867 Cold Spring Harbor Laboratory Press 2025-09-06 <![CDATA[ Partner fidelity and coevolution: Useful but not required for rapidly increased mutualistic benefits ]]> https://biorxiv.org/content/10.1101/2025.09.07.674547v1?rss=1 Stoy, K. S. Lac, D. Ratcliff, W. C. 2025-09-08 doi:10.1101/2025.09.07.674547 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ Phase separation and coexistence in spatial coordination games between microbes ]]> https://biorxiv.org/content/10.1101/2025.09.09.675176v1?rss=1 Li, G. Steinbach, G. Yunker, P. J. Yao, Y. Weitz, J. S. 2025-09-09 doi:10.1101/2025.09.09.675176 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ Endoluminal catheter pulsed field ablation for the treatment of atherosclerotic vascular disease ]]> https://biorxiv.org/content/10.1101/2025.09.06.674641v1?rss=1 95% of severe and thick plaques with irreversible electroporation, with single-cell modeling supporting the electroporation of foam cells within the plaque. The 3D atherosclerosis mimic validated the ability of PFA to completely ablate the foam cells with fibrotic tissue at >1000 V/cm. ConclusionsThis study provides the first demonstration of PFA for the treatment of atherosclerotic vascular disease. By combining experimental validation with computational modeling, we establish proof-of-concept that PFA can selectively ablate diseased cells while preserving extracellular architecture, laying the groundwork for future translational development of this therapy. ]]> Salameh, Z. Jacobs, E. Davalos, R. 2025-09-11 doi:10.1101/2025.09.06.674641 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Mechanism of SARS-CoV-2 Nucleocapsid Protein Phosphorylation-induced Functional Switch ]]> https://biorxiv.org/content/10.1101/2025.09.12.675721v1?rss=1 Sullivan, M. S. Morse, M. Grabarkewitz, K. Bayachou, D. Rouzina, I. Wysocki, V. Williams, M. C. Musier-Forsyth, K. 2025-09-12 doi:10.1101/2025.09.12.675721 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ Gastrointestinal delivery of mRNA lipid nanoparticles selectively targets the pancreas ]]> https://biorxiv.org/content/10.1101/2025.09.15.676190v1?rss=1 Abbas, A. M. Ghanim, R. Rudden, S. Schultz, D. Shakked, A. Kim, H. Dahlman, J. Abramson, A. 2025-09-18 doi:10.1101/2025.09.15.676190 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Frequency-Aware Interpretable Deep Learning Framework for Alzheimer's Disease Classification Using rs-fMRI ]]> https://biorxiv.org/content/10.1101/2025.09.18.677114v1?rss=1 Gao, Y. Miller, R. L. Calhoun, V. D. 2025-09-19 doi:10.1101/2025.09.18.677114 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Metabolic Trajectories During Surgical Stress in Patients Undergoing Cardiac Surgery ]]> https://biorxiv.org/content/10.1101/2025.09.16.676529v1?rss=1 Ku, D. Bartelt, J. Feeley, J. Perez-Guzman, M. C. Guerrero-Arroyo, L. Abraham, A. Kollipara, S. Gonzalez, N. Usman, S. Huneault, H. E. Corujo-Rodriguez, A. Davis, G. M. Kibbey, R. G. Jones, D. P. Ziegler, T. R. Halkos, M. Quyyumi, A. A. Smith, M. R. Li, J. Pasquel, F. J. 2025-09-20 doi:10.1101/2025.09.16.676529 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Label-Free, Real-Time, In Vivo Optical Biopsy with a Handheld Quantitative Phase Microscope ]]> https://biorxiv.org/content/10.1101/2025.09.17.675943v1?rss=1 Guang, Z. Bharadwaj, S. Zhang, Z. Neill, S. Olson, J. J. Robles, F. E. 2025-09-20 doi:10.1101/2025.09.17.675943 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Discovering cell types and states from reference atlases with heterogeneous single-cell ATAC-seq features ]]> https://biorxiv.org/content/10.1101/2025.09.19.677191v1?rss=1 Cheng, Y. Zhang, X. 2025-09-21 doi:10.1101/2025.09.19.677191 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Establishing a continuum of cell types in the visual cortex ]]> https://biorxiv.org/content/10.1101/2025.09.22.677893v1?rss=1 Yoo, J. Xie, F. Butrus, S. Xu, R. Tan, Z. Gorzek, R. Mirshahidi, P. Tring, E. Suresh, S. Kim, J. Fleishman, G. Tan, L. Ringach, D. Trachtenberg, J. Xu, X. Zipursky, S. L. Shekhar, K. Jain, S. 2025-09-22 doi:10.1101/2025.09.22.677893 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ RNAcentral in 2026: Genes and literature integration ]]> https://biorxiv.org/content/10.1101/2025.09.19.677274v1?rss=1 Green, A. F. Ribas, C. E. Jandalala, I. Muston, P. O'Cathail, C. Cochrane, G. Ernst, C. Zhao, L. Madrigal, P. Attrill, H. Marygold, S. Lancet, D. Dobzinski, N. Chan, P. P. Lowe, T. M. Bruford, E. A. Seal, R. L. Hermjakob, H. Panneerselvam, K. Finn, R. D. Gurbich, T. A. Griffiths-Jones, S. Fromm, B. Peterson, K. J. Sordyl, D. Bujnicki, J. M. Velankar, S. Appasamy, S. D. Ganguly, S. Zhang, P. He, S. Rutherford, K. M. Wood, V. Lovering, R. C. Picardi, E. Ontiveros, N. Huang, L. Miao, Z. Petrov, A. S. McCann, H. Cavalleri, E. Mesiti, M. Rivas, E. Szikszai 2025-09-24 doi:10.1101/2025.09.19.677274 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ Preparatory encoding of diverse features of intended movement in the human motor cortex ]]> https://biorxiv.org/content/10.1101/2025.09.24.678356v1?rss=1 Rigotti-Thompson, M. Nason-Tomaszewski, S. R. Bechefsky, P. Acosta, A. Hahn, N. Avansino, D. Richards, B. Nicolas, C. Ali, Y. H. Henderson, J. M. Hochberg, L. R. AuYong, N. Pandarinath, C. 2025-09-25 doi:10.1101/2025.09.24.678356 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Multimodal Fusion Analysis of Florbetapir PET and Multiscale Functional Network Connectivity in Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2025.09.26.678805v1?rss=1 MCI > AD) in white matter and cerebellar regions, reflecting structural degeneration; (2) increased amyloid accumulation in affected individuals in grey matter regions, particularly in frontal, sensorimotor, extended hippocampal, and default mode network (DMN) regions, accompanied by functional connectivity alterations that reflected both compensatory and disruptive network dynamics. We identified PET-derived components that captured distinct stages of disease progression, with the DMN component emerging as a late-stage biomarker and a white matter component showing early-stage changes with limited progression thereafter. Additionally, several components showed significant variation in loadings between APOE{varepsilon} 4 carriers and non-carriers, linking the multimodal signatures to a well-established genetic risk factor for AD. ]]> Bimali, B. Khasayeva, N. Nagaboina, G. Chen, J. Fedorov, A. Lah, J. Levey, A. Calhoun, V. Iraji, A. Ballem, A. R. 2025-09-29 doi:10.1101/2025.09.26.678805 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Multi-omics integration at cell type resolution uncovers gene-metabolite mechanisms underlying osteoarthritis heterogeneity ]]> https://biorxiv.org/content/10.1101/2025.09.26.678886v1?rss=1 Ojha, A. Chatterjee, P. Kippner, L. E. Stevens, H. Y. Yeago, C. Drissi, H. Mautner, K. Boden, S. Roy, K. Sinha, S. 2025-09-29 doi:10.1101/2025.09.26.678886 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Diagnosis-Optimized Dynamic Feature Learning Reveals Altered Default Mode Network Connectivity in Schizophrenia ]]> https://biorxiv.org/content/10.1101/2025.09.30.679557v1?rss=1 Seraji, M. Ellis, C. A. Ma, L. Turner, J. A. Preda, A. Mathalon, D. H. van Erp, T. G. M. Sendi, M. S. E. Calhoun, V. D. 2025-10-01 doi:10.1101/2025.09.30.679557 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Metagenomics reveal allopatric speciation and higher connectivity among coastal vs. inland hypersaline lakes and solar salterns ]]> https://biorxiv.org/content/10.1101/2025.10.01.679725v1?rss=1 99.8%) were also observed, especially for some Haloquadratum species. The findings suggest that coastal hypersaline systems are loosely constrained by geographic isolation, with clear signals of allopatric speciation at the mesoscale (tenths to hundreds of kilometers) that become blurrier at larger scales. ]]> Viver, T. Gago, J. F. Bustos-Caparros, E. Aldeguer-Riquelme, B. Rodriguez-R, L. M. Ramirez, A. S. Albuquerque, L. Amiour, S. Oren, A. Burcin Mutlu, M. Venter, S. N. Baxter, B. K. Llames, M. E. Gonzalez, B. Rodriguez Valdecantos, G. Banciu, H. L. Stott, M. B. Santos, F. Anton, J. Amann, R. Konstantinidis, K. T. Rossello-Mora, R. 2025-10-01 doi:10.1101/2025.10.01.679725 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ γδ17 T cell-stromal networks modulate matrix composition and vascularity in foreign body response ]]> https://biorxiv.org/content/10.1101/2025.09.30.679608v1?rss=1 Ruta, A. Krishnan, K. Woo, J. Mejias, J. C. Gray-Gaillard, E. F. Maestas, D. R. Nguyen, H. H. Rindone, A. N. Cherry, C. Patatanian, M. Yu, F. H. Yang, B. Amelung, C. King, C. D. Schilling, B. Gerecht, S. Fertig, E. J. Huyer, L. D. Pardoll, D. M. Elisseeff, J. H. 2025-10-02 doi:10.1101/2025.09.30.679608 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Neuroinflammatory Stress Preferentially Impacts Synaptic MAPK Signaling and Mitochondria in Excitatory Neurons ]]> https://biorxiv.org/content/10.1101/2025.10.03.680087v1?rss=1 1000 proteins, consistent with neuron-specific biotinylation, also confirmed by immunofluorescence microscopy. Camk2a-specific synaptic proteome revealed molecular signatures related to mitochondrial function, synaptic transmission, protein translation. LPS-treated mice displayed body weight loss and neuroinflammation, characterized by glial activation, increased pro-inflammatory cytokine levels and upregulated expression of Alzheimers disease (AD)-related microglial genes. LPS-induced neuroinflammation exerted distinct effects on the synaptic proteome, including increased mitochondrial and reduced cytoskeletal-synaptic proteins, while suppressed synaptic MAPK signaling. Importantly, these changes were not observed at the whole neuron level, indicating unique vulnerability of the synapse to neuroinflammation. In line with synapse proteomic and signaling changes, LPS altered the ultrastructure of asymmetric synapses, suggesting dysregulation of excitatory neurotransmission. Co-expression network analysis of Camk2a neuronal proteins further resolved mitochondria- and synapse-specific protein modules, some of which were neuroinflammation-dependent. Neuroinflammation increased levels of a mitochondria-enriched module, and decreased levels of a pre-synaptic vesicle module, without impacting a post-synaptic membrane module. LPS-dependent mitochondrial and LPS-independent post-synaptic modules in mouse neurons mapped to post-mortem human AD brain proteomic modules which were decreased in cases with AD dementia and positively correlated to cognitive function, including pro-resilience markers for AD. ConclusionOur findings using native-state proteomics of Camk2a neurons combined with synaptosome enrichment identify proteome-level mechanisms of early synaptic vulnerability to neuroinflammation relevant to AD. ]]> Espinosa-Garcia, C. Srivastava, U. Kumar, P. Kour, D. Malepati, S. Tobin, B. Xiao, H. Sunna, S. Bowen, C. A. Cheng, L. Bagchi, P. Duong, D. M. Whitworth, T. J. Liu, X. Seyfried, N. Wood, L. B. Faundez, V. Rangaraju, S. 2025-10-05 doi:10.1101/2025.10.03.680087 Cold Spring Harbor Laboratory Press 2025-10-05 <![CDATA[ Transcriptomic Signature and PROTAC Strategy Revealed Histone Lysine Demethylase as a Target of Anticancer Activity of Deferiprone. ]]> https://biorxiv.org/content/10.1101/2025.10.13.682199v1?rss=1 Johnston, A. Olugbami, J. O. Walunj, D. Bangaru, A. Wu, B. Kern, R. Yang, R. Nelson, T. J. Clarke, B. J. Murugan, J. Hathaway, N. A. Fan, Y. Oyelere, A. K. 2025-10-15 doi:10.1101/2025.10.13.682199 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Nuclear-encoded tRNA genes harbor substantial allelic diversity in three nematode species ]]> https://biorxiv.org/content/10.1101/2025.10.14.682033v1?rss=1 Bell, A. D. Simonti, C. Banos, H. Wang, L. Heitsch, C. Lachance, J. Paaby, A. B. 2025-10-15 doi:10.1101/2025.10.14.682033 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Skin-conformal electronics for wearable electrogastrography monitoring ]]> https://biorxiv.org/content/10.1101/2025.10.14.682324v1?rss=1 Xing, L. Cai, Y. Zhang, Y. Mottini, V. Heller, L. Li, J. 2025-10-15 doi:10.1101/2025.10.14.682324 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Minimal Perturbation of Activation Loop Dynamics Rewires KinaseSignaling ]]> https://biorxiv.org/content/10.1101/2025.10.15.682502v1?rss=1 Jain, P. Yehorova, D. Febri, R. R. Clifton, B. E. Demkiv, A. Uechi, G.-i. Robinson, M. Kamerlin, S. C. L. Okada, M. Imamoto, A. Laurino, P. 2025-10-15 doi:10.1101/2025.10.15.682502 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ IDBac: an open-access web platform and compendium for the identification of bacteria by MALDI-TOF mass spectrometry. ]]> https://biorxiv.org/content/10.1101/2025.10.15.682631v1?rss=1 1400 strains spanning 6 bacterial phyla. Accompanying the knowledgebase is analysis infrastructure to identify unknown isolates, probe relationships within culture collections using metadata integration, and visualize specialized metabolite differences within groups of closely related bacteria. To highlight this utility and encourage wide community contribution, examples of each are presented. ]]> Krull, N. K. Strobel, M. Saulog, J. Zaroubi, L. Paulo, B. S. Timba, M. Braun, D. R. Mingolelli, G. Raherisoanjato, J. Shepherd, R. A. Scott, A. F. De Silva, C. Fergusson, C. Daniel, Z. Pokharel, S. K. Romanowski, S. Hernandez, A. Monge-Loria, M. Dylla, C. E. Natu, M. M. Petukhova, V. Z. Garg, N. Jensen, P. R. Blachowicz, A. Cassilly, C. D. Guan, L. Stevens, C. D. Winter, J. M. McKinnie, S. M. K. Adaikpoh, B. I. Carlson, S. McCauley, E. P. Metcalf, W. W. Bugni, T. S. Mullowney, M. W. Pamer, E. G. Henke, M. T. Barton, H. Carter, D. O. Eustaquio, A. S. Lini 2025-10-15 doi:10.1101/2025.10.15.682631 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Decellularized Meniscus (MEND) as a biomaterial that supports stem cell invasion and chondrogenesis ]]> https://biorxiv.org/content/10.1101/2025.10.16.682874v1?rss=1 Bonelli, H. M. Klessel, S. E. Barbella, C. Smith, K. W. Y. Gottardi, R. 2025-10-17 doi:10.1101/2025.10.16.682874 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Omega-3 Fatty Acid Derived Neuroactive Lipids - Docosahexaenoyl-Glycine and Its Epoxide Metabolites are Multifunctional Lipid Mediators ]]> https://biorxiv.org/content/10.1101/2025.10.17.681057v1?rss=1 Kim, J. Franchini, L. Yudin, Y. Denissiouk, A. Rohacs, T. Orlandi, C. Das, A. 2025-10-17 doi:10.1101/2025.10.17.681057 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Microparticle-Enabled Single Cell Multiparameter Electronic Immunophenotyping for Selective Electroporation ]]> https://biorxiv.org/content/10.1101/2025.10.17.682894v1?rss=1 5 fold enrichment of lymphocytes in the electroporated cell population. This approach expands the capabilities of EP, offering a promising solution to decrease manufacturing complexity in both research and clinical cell engineering workflows ]]> Hoyle, M. Rudge, J. Rallapalli, Y. Sarkar, A. 2025-10-17 doi:10.1101/2025.10.17.682894 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ GlueFinder: A Data-Driven Framework for the Rational Discovery of Molecular Glues ]]> https://biorxiv.org/content/10.1101/2025.10.17.683126v1?rss=1 Skolnick, J. Srinivasan, B. Zhou, H. 2025-10-17 doi:10.1101/2025.10.17.683126 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Sub-daily Bermuda Atlantic Time Series virus sampling reveals taxonomy, host, and functional differences at the population, but not community level ]]> https://biorxiv.org/content/10.1101/2025.10.20.683370v1?rss=1 Carrillo, A. Hageman, E. Chittick, L. Mackey, A. I. Ndlovu, K. S. Tian, F. Gilbert, N. E. Muratore, D. Vik, D. LeCleir, G. R. Sun, C. Jang, H. B. Pavan, R. R. Weitz, J. S. Wilhelm, S. W. Sullivan, M. B. 2025-10-20 doi:10.1101/2025.10.20.683370 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Sensory Neural Noise as a Limiting Factor in Visual Working Memory Precision in Neurotypicals and Schizophrenia ]]> https://biorxiv.org/content/10.1101/2025.10.20.683426v1?rss=1 Park, W. J. Ichinose, M. Hu, G. Woodman, G. F. Tadin, D. Park, S. 2025-10-20 doi:10.1101/2025.10.20.683426 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ A Feature Learning Model Identifies Predictive Attributes of Mesenchymal Stromal Cell Efficacy ]]> https://biorxiv.org/content/10.1101/2025.10.20.683469v1?rss=1 South, S. M. Pacheco, Y. C. McKinney, J. M. Bitarafan, S. Pucha, K. A. Pancheri, N. M. Link, K. Lin, A. Wood, L. B. Willett, N. 2025-10-21 doi:10.1101/2025.10.20.683469 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Aβ-42 sidechain deamidation at Q15 and N27 modulate protein aggregation and microglial responses via altered cytokine production and CD68 expression ]]> https://biorxiv.org/content/10.1101/2025.10.22.684043v1?rss=1 Griffin, M. N. Dinakarapandian, D. M. Li, C. Ramaswamy, P. Saheba, S. J. Lee, J. C. Sudarshan, T. R. Sajimon, M. Wheeler, C. J. Raskatov, J. A. Paravastu, A. K. Wood, L. B. 2025-10-23 doi:10.1101/2025.10.22.684043 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ MetaboFM: A Foundation Model for Spatial Metabolomics ]]> https://biorxiv.org/content/10.1101/2025.10.23.684227v1?rss=1 Ozturk, E. Moctezuma, F. G. R. Coskun, A. F. 2025-10-24 doi:10.1101/2025.10.23.684227 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ Human-like individual differences emerge from random weight initializations in neural networks ]]> https://biorxiv.org/content/10.1101/2025.10.25.684448v1?rss=1 Fung, H. Ratan Murty, N. A. Rahnev, D. 2025-10-26 doi:10.1101/2025.10.25.684448 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Mechanism of single-strand annealing from native mass spectrometry and cryo-EM structures of RAD52 homolog Mgm101 ]]> https://biorxiv.org/content/10.1101/2025.10.26.684629v1?rss=1 Wheat, C. T. Qi, Z. Hussain, M. Zakharova, K. Wysocki, V. H. Bell, C. E. 2025-10-26 doi:10.1101/2025.10.26.684629 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Tissue surface mechanics constrains proliferation-driven forces to guide mammalian body axis elongation ]]> https://biorxiv.org/content/10.1101/2025.10.27.684710v1?rss=1 Trani-Bustos, M. G. Savill, R. Boutillon, A. Pospisil, P. Conkar, D. Froeb, C. Soltwedel, J. R. van de Wouw, H. L. Sletten, E. M. Veenvliet, J. Campas, O. 2025-10-27 doi:10.1101/2025.10.27.684710 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Quantitative metagenomics using a portable protocol. ]]> https://biorxiv.org/content/10.1101/2025.10.28.684933v1?rss=1 Bian, K. Busch, A. Norton, J. Bott, C. Gonzalez, R. Curtis, K. Tolofari, D. Khunjar, W. Graham, K. E. Pinto, A. J. 2025-10-28 doi:10.1101/2025.10.28.684933 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ Structural modeling reveals the mechanism of motor ATPase coordination during type IV pilus retraction ]]> https://biorxiv.org/content/10.1101/2025.10.30.685630v1?rss=1 Teipen, A. E. Holt, J. D. Lynch, D. L. Peng, Y. Dalia, T. N. Gumbart, J. C. Nadell, C. D. Dalia, A. B. 2025-10-30 doi:10.1101/2025.10.30.685630 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Aversive Learning Induces Context-Gated Global Reorganization of Neural Dynamics in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2025.10.31.685731v1?rss=1 Liang, J. Moon, S. Moza, S. Lee, H. J. Eleftheriadis, P. E. Chen, J. Ge, M. Chen, M. Lu, H. Zhang, Y. 2025-11-01 doi:10.1101/2025.10.31.685731 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ Data-Driven Symbolic Higher-Order Epistasis Discovery with Kolmogorov-Arnold Networks ]]> https://biorxiv.org/content/10.1101/2025.10.31.685894v1?rss=1 Patil, O. R. Shazand, K. Marteau, B. Shen, Y. Wang, M. D. 2025-11-04 doi:10.1101/2025.10.31.685894 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Network modularity reveals context and state-dependent reorganization of time-varying functional connectivity in single-cell resolved neural activity recordings ]]> https://biorxiv.org/content/10.1101/2025.11.02.686048v1?rss=1 Moon, S. Liang, J. Lee, H. J. Maalouf, A. Yu, Z. Moza, S. Zhang, Y. Lu, H. 2025-11-04 doi:10.1101/2025.11.02.686048 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Environmental filtering shapes patch dynamics across isolated mesophotic reefs ]]> https://biorxiv.org/content/10.1101/2025.11.02.686126v1?rss=1 Pittoors, N. C. Tweedt, S. M. McCartin, L. J. Vohsen, S. A. Lopera, L. Mihalek, S. Lai, J. Durkin, K. M. Weigt, L. Nuttall, M. F. Bracco, A. Meyer, C. P. Herrera, S. 2025-11-04 doi:10.1101/2025.11.02.686126 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Microfluidics-Enabled Simultaneous Imaging of Neural Activity and Behavior in Chemically Stimulated, Head-Fixed C. elegans ]]> https://biorxiv.org/content/10.1101/2025.11.03.686171v1?rss=1 Lee, H. J. Vallier, J. Lu, H. 2025-11-04 doi:10.1101/2025.11.03.686171 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Influence of exoskeleton stiffness on primary afferent feedback during stretch perturbations of isolated muscle-tendon unit ]]> https://biorxiv.org/content/10.1101/2025.11.03.686366v1?rss=1 Alshareef, A. A. Nardelli, P. J. Simha, S. N. Cope, T. C. Ting, L. H. Sawicki, G. S. 2025-11-05 doi:10.1101/2025.11.03.686366 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Metabolically driven differentiation of human pluripotent stem cells to generate robust and functional lymphatic endothelial cells ]]> https://biorxiv.org/content/10.1101/2025.11.03.686405v1?rss=1 View larger version (49K): org.highwire.dtl.DTLVardef@1c4caa5org.highwire.dtl.DTLVardef@d42b08org.highwire.dtl.DTLVardef@1554ffcorg.highwire.dtl.DTLVardef@1f64ae6_HPS_FORMAT_FIGEXP M_FIG C_FIG A xeno-free and stepwise differentiation protocol with VEGF-C and sodium acetate induces lymphatic identity in iPSC-derived endothelial cells. Differentiated LECs (dLECs) express key lymphatic markers as verified using bulk RNA-sequencing, qPCR, FACS, and immunostaining. These dLECs secrete important cytokines for lympangiocrine signaling, able to form robust 2D and 3D lymphatic networks, as well as demonstrate in vivo functionality and host integration in murine models. ]]> Jeong, D. P. Saha, S. Montes-Pinzon, D. Taglione, A. Lightsey, N. K. Gamage, R. S. Stein, B. Dixon, J. B. Hanjaya-Putra, D. 2025-11-05 doi:10.1101/2025.11.03.686405 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ When Animals Turn Inside Out: The Eversion of Bloodworms ]]> https://biorxiv.org/content/10.1101/2025.11.05.686822v1?rss=1 Kim, S. Tuma, A. Qin, D. Ryu, Y. J. Kim, D. Abhilash, A. Chintawar, S. Thomas-Holness, C. Fladger, A. Behravesh, E. Zhen, Y. Zhou, Y. Thompson, J. T. Hu, D. L. 2025-11-06 doi:10.1101/2025.11.05.686822 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Epithelial convergent extension as a tuning process ]]> https://biorxiv.org/content/10.1101/2025.11.06.687029v1?rss=1 Arzash, S. Liu, A. J. Manning, M. L. 2025-11-07 doi:10.1101/2025.11.06.687029 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ Intrinsic ion dynamics underlies the temporal nature of resting-state functional connectivity ]]> https://biorxiv.org/content/10.1101/2025.11.08.687387v1?rss=1 Gonzalez, O. C. Sanda, P. Hlinka, J. Bazhenov, M. Krishnan, G. 2025-11-09 doi:10.1101/2025.11.08.687387 Cold Spring Harbor Laboratory Press 2025-11-09 <![CDATA[ CapuchinAI: Leveraging AI to study wild primate cognition ]]> https://biorxiv.org/content/10.1101/2025.11.07.687266v1?rss=1 97% accuracy) YOLOv7-based facial recognition model (Multiple Capuchins v1.0) with a portable Raspberry Pi-driven touchscreen-reward apparatus designed for automated operation in natural habitats. The system detects approaching capuchins, initiates video recording, presents touchscreen stimuli, and dispenses food rewards contingent on task performance. During a two-week presentation to two habituated groups of wild white-faced capuchins (Cebus imitator) at the Taboga Forest Reserve, 16 individuals voluntarily interacted with the apparatus, 10 learned to trigger rewards, and 8 formed and retained robust screen-reward associations. The rapid habituation and learning rates demonstrate the feasibility of deploying AI-mediated cognitive experiments in the wild. CapuchinAI addresses several long-standing challenges in field cognition research by enabling: (1) autonomous, individualized task administration without researcher intervention; (2) standardized, repeatable trials across individuals and sessions; (3) scalable deployment across groups and sites; and (4) parallel data collection on behavior, identity, and performance. This methodology provides a blueprint for integrating machine learning, touchscreen testing, and automated reward delivery to study within- and between-individual cognitive variation under natural conditions. CapuchinAI represents a significant step toward long-term comparative research on primate cognition by making laboratory experimental paradigms accessible in the wild, bridging the gap between lab and field. Research HighlightsO_LIWe present CapuchinAI, a field-ready touchscreen testing station that uses real-time facial recognition to study cognition in wild capuchin monkeys C_LIO_LIWe developed a YOLOv7-based facial recognition model (Multiple Capuchins v1.0) that identifies individual capuchins with >97% precision and recall from static images, video, and live footage, enabling fully automated, individualized testing in the wild. C_LIO_LIWe integrated a version of this model into a closed-loop touchscreen-reward pipeline that detects an approaching monkey, presents a basic learning task, and automatically delivers food rewards based on the monkeys responses. C_LIO_LIWild capuchins rapidly habituated and learned touchscreen-reward associations, showing that AI-enabled touchscreens provide a scalable field method for deploying lab-style cognitive tests and mapping individual differences across tasks, species, and sites. C_LI ]]> Sanchez Vargas, F. Potluri, S. R. Abernethy, J. Benitez, M. E. 2025-11-10 doi:10.1101/2025.11.07.687266 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Impact of early locus coeruleus lesions in the TgF344 Alzheimer's disease rat model ]]> https://biorxiv.org/content/10.1101/2025.11.09.687363v1?rss=1 Marriott, A. E. Schroeder, J. P. Korukonda, A. Pate, B. S. McCann, K. E. Weinshenker, D. Kelberman, M. A. 2025-11-10 doi:10.1101/2025.11.09.687363 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Gene-centric analysis of Raskinella chloraquaticus reveals a functionally conserved taxonomic group in global drinking water distribution systems ]]> https://biorxiv.org/content/10.1101/2025.11.10.687676v1?rss=1 Sudarshan, A. S. Konstantinidis, K. T. Pinto, A. J. 2025-11-11 doi:10.1101/2025.11.10.687676 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ Harnessing Plasmid Crosstalk in Transcription Factor Mediated Cell-Free Biosensors ]]> https://biorxiv.org/content/10.1101/2025.11.11.687754v1?rss=1 Patterson, A. T. Piorino, F. Bronovitskiy, S. S. Godavarti, D. R. Styczynski, M. P. 2025-11-11 doi:10.1101/2025.11.11.687754 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ Elucidating Neurodevelopmental Trajectories in Cancer with Topic Modeling: Revealing Persistent External Granule Layer Lineages in Medulloblastoma ]]> https://biorxiv.org/content/10.1101/2025.11.12.687706v1?rss=1 Rajendran, A. Haldipur, P. Arora, S. Grama, K. Subramanian, S. S. Galan, L. M. Johnson, D. Aldinger, K. A. Shendure, J. Millen, K. J. Gennari, J. H. Pattwell, S. S. 2025-11-13 doi:10.1101/2025.11.12.687706 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Slow waves generation and propagation in a model of brain lesions ]]> https://biorxiv.org/content/10.1101/2025.11.12.688042v1?rss=1 Gaglioti, G. Dalla Porta, L. Colombo, M. A. Russo, S. Nieus, T. R. Deco, G. Corbetta, M. Sarasso, S. Sanchez-Vives, M. V. Massimini, M. 2025-11-13 doi:10.1101/2025.11.12.688042 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Bruch's Membrane Contributes to the Structural Integrity of the Human Eye ]]> https://biorxiv.org/content/10.1101/2025.11.13.688375v1?rss=1 Tan, R. K. Y. Sharma, S. Chan, A. Ho, C. Braeu, F. Jonas, J. Han, L. Wang, X. Zhu, Y. Leo, H. L. Buist, M. Aung, T. Perera, S. Girard, M. J. A. 2025-11-14 doi:10.1101/2025.11.13.688375 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Improved Stability and Interpretability of Motor Modules Computed with an Autoencoder ]]> https://biorxiv.org/content/10.1101/2025.11.11.687901v1?rss=1 Nathella, S. R. Seamon, B. A. Young, A. J. Ting, L. H. 2025-11-16 doi:10.1101/2025.11.11.687901 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ Ephaptic coupling and power fluctuations in depression ]]> https://biorxiv.org/content/10.1101/2025.11.15.688471v1?rss=1 Pinotsis, D. Alagapan, S. Sarikhani, P. Nauvel, T. Rozell, C. Mayberg, H. 2025-11-16 doi:10.1101/2025.11.15.688471 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ Harmonized Protocol for Segmentation of the Hippocampal Tail on High-Resolution in vivo MRI from the Hippocampal Subfields Group (HSG) ]]> https://biorxiv.org/content/10.1101/2025.11.20.689476v1?rss=1 0.98; Averaged Dice Similarity Coefficient = 0.92) and inter-rater reliability (Averaged ICC(2,k) > 0.98; Averaged Dice Similarity Coefficient = 0.86) and offers a practical framework for replicable segmentation. By establishing standardized guidelines, this protocol enhances comparability of findings across developmental, aging, and clinical research and is compatible with ongoing technological advances. ]]> de Flores, R. Canada, K. L. Brown, T. Gervais, N. J. Maass, A. Radman, G. Shine, J. Tucker, H. L. Molloy, E. N. Adams, J. N. Reinke, M. B. Bakker, A. Berron, D. Dalton, M. A. Kennedy, K. M. La Joie, R. Mueller, S. G. Ofen, N. Olsen, R. K. Raz, N. Riggins, T. Rodrigue, K. M. Stark, C. Wang, L. Wisse, L. E. Yushkevich, P. A. Carr, V. A. Daugherty, A. M. Alzheimer's Disease Neuroimaging Initiative, Hippocampal Subfields Group, 2025-11-20 doi:10.1101/2025.11.20.689476 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ Comparative genomics and interactions of vector thysanopterans and transmitted viruses ]]> https://biorxiv.org/content/10.1101/2025.11.21.689785v1?rss=1 Catto, M. A. Labadie, P. E. Kennedy, G. G. Jacobson, A. L. Hunt, B. G. Srinivasan, R. 2025-11-22 doi:10.1101/2025.11.21.689785 Cold Spring Harbor Laboratory Press 2025-11-22 <![CDATA[ Reinforcement learning for adaptive control of phenotypically heterogeneous bacterial populations ]]> https://biorxiv.org/content/10.1101/2025.11.21.689767v1?rss=1 Kratz, J. Wen, Z. Banerjee, S. Carja, O. 2025-11-24 doi:10.1101/2025.11.21.689767 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Anion supercharging enables structural assignment of oxidatively released O-glycans ]]> https://biorxiv.org/content/10.1101/2025.11.23.689986v1?rss=1 Kelly, M. I. Ashwood, C. 2025-11-25 doi:10.1101/2025.11.23.689986 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Quantifying antibiotic susceptibility and inoculum effects using transient dynamics of Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2025.11.26.690803v1?rss=1 Sundius, S. A. Farrell, J. Eick, K. Kuske, R. Brown, S. P. 2025-11-26 doi:10.1101/2025.11.26.690803 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ Longitudinal Changes in Cortical Response Dynamics with Deep Brain Stimulation to the Subcallosal Cingulate for Treatment-Resistant Depression ]]> https://biorxiv.org/content/10.1101/2025.11.26.690543v1?rss=1 Desai, A. Van Bogaert, T. Choi, K. S. Song, H. N. Cha, J. Alagapan, S. Xu, E. Dahill-Fuchel, J. Veerakumar, A. Kopell, B. H. Figee, M. Riva-Posse, P. Rozell, C. J. Mayberg, H. Waters, A. C. 2025-12-01 doi:10.1101/2025.11.26.690543 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Dopamine and serotonin transients predict depressive symptom relief following deep brain stimulation of human subcallosal cingulate cortex ]]> https://biorxiv.org/content/10.64898/2025.11.28.691184v1?rss=1 Shevlin, B. R. K. R. K. Fu, Q. X. Batten, S. R. Kopell, B. H. Neal Davis, A. Heflin, M. Heisig, S. Rozell, C. J. Kato, A. Kulkarni, K. R. Choi, K. S. Song, H. N. ONeil, S. Nauvel, T. Trivedi, I. White, J. P. Lohrenz, T. Figee, M. Twomey, T. Moran, R. Bang, D. Hartle, A. E. Howe, W. M. Kishida, K. T. Barbosa, L. S. Fiore, V. G. Saez, I. Montague, P. R. Mayberg, H. S. Gu, X. 2025-12-02 doi:10.64898/2025.11.28.691184 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ MOSAIC: A scalable framework for fMRI dataset aggregation and modeling of human vision ]]> https://biorxiv.org/content/10.64898/2025.11.28.690060v1?rss=1 Lahner, B. Deb, M. Murty, N. A. R. Oliva, A. 2025-12-03 doi:10.64898/2025.11.28.690060 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Evaluating the effects of CD8/CD4 on T cell function in terms of TCR-pMHC-coreceptor catch and slip bonds ]]> https://biorxiv.org/content/10.64898/2025.12.01.691627v1?rss=1 Travaglino, S. Kazemipour Ashkezari, A. H. Li, M. Watson, V. E. Cong, P. Doudy, L. Choi, H.-K. Zhu, C. 2025-12-03 doi:10.64898/2025.12.01.691627 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ RNA-Binding Protein NF90 Mediates Polycomb-Independent Transactivation by EZH2 to Promote Cancer Growth ]]> https://biorxiv.org/content/10.64898/2025.12.02.691892v1?rss=1 Wang, Y. Peng, L. Lu, x. shi, h. Zheng, M. Senthil, S. Akhtar, J. Lee, Y. Chandonnet, H. Licht, J. D. Yang, X. Zhao, J. C. Yu, J. 2025-12-03 doi:10.64898/2025.12.02.691892 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ The language network responds robustly to sentences across diverse tasks ]]> https://biorxiv.org/content/10.64898/2025.12.02.691902v1?rss=1 nonwords contrast isolated the same set of language-responsive voxels across all tasks; the locations of those voxels were participant-specific, highlighting the value of individual-specific functional localization. We therefore conclude that language localization is robust to task variation. We then examined responses to each task in these language-responsive voxels (the language network) and in the domain-general multiple demand (MD) network, known to respond to task demands. The language network responded robustly to sentences across all tasks, with somewhat higher responses to semantically engaging tasks. In contrast, the MD network responded to both sentences and nonwords in the presence of a demanding task, which warrants caution when examining brain responses to language tasks accompanied by task demands, as such tasks engage two independent systems. A multivariate analysis revealed that stimulus information is more easily decodable in the language network, whereas task information is more decodable in the MD network. These results suggest that the language and MD networks perform complementary functions during task-driven language comprehension, with the language network primarily extracting information from linguistic input and the MD network determining the appropriate response to the task. ]]> Gao, R. Cheung, C. Siegelman, M. Pongos, A. L. A. Kean, H. H. Tanner, A. Fedorenko, E. Ivanova, A. A. 2025-12-05 doi:10.64898/2025.12.02.691902 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ From Skin to Cortex: End-to-End Spiking Neural Network Simulation of Tactile Information Flow ]]> https://biorxiv.org/content/10.64898/2025.12.03.692094v1?rss=1 Rault, N. Tompos, T. Marx, E. F. Zeldenrust, F. Degertekin, L. Celikel, T. 2025-12-08 doi:10.64898/2025.12.03.692094 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ A microgel bone marrow model of mesenchymal stem cell paracrine signaling supporting hematopoietic stem cell retention ]]> https://biorxiv.org/content/10.64898/2025.12.05.692616v1?rss=1 Thompson, G. B. Kuo, K. M. Garcia, A. Harley, B. 2025-12-09 doi:10.64898/2025.12.05.692616 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ The fitness costs of reproductive specialization scale inversely with organismal size ]]> https://biorxiv.org/content/10.64898/2025.12.08.693006v1?rss=1 Zhang, C. Libby, E. Burnetti, A. J. Heron, M. Ratcliff, W. 2025-12-09 doi:10.64898/2025.12.08.693006 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Semantic reasoning takes place largely outside the language network ]]> https://biorxiv.org/content/10.64898/2025.12.07.692873v1?rss=1 Ivanova, A. A. Kauf, C. Gao, R. She, J. S. Kean, H. H. Goldhaber, T. Nieto-Castanon, A. Varley, R. Kanwisher, N. G. Fedorenko, E. 2025-12-10 doi:10.64898/2025.12.07.692873 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Caenorhabditis briggsae ancestral genomic hyper-diversity contrasts with globally distributed genome-wide haplotypes ]]> https://biorxiv.org/content/10.64898/2025.12.08.693002v1?rss=1 Moya, N. D. Wang, B. Tanny, R. E. Sauria, M. E. G. O'Connor, L. M. Khorshidian, A. McKeown, R. Gosse, C. Dilks, C. M. Crombie, T. A. Zhang, G. Rais, E. Frezal, L. Dang, V. D. Haryoso, E. Devi, M. P. Gimond, C. Cook, D. E. Hsu, J.-C. Shaver, A. O. Zdraljevic, S. Richaud, A. Wen, T. Mehraj, A. H, S. Arulprakasam, K. R. Koury, E. J. Roberto, N. M. Schaye, E. S. Singh, V. Tarno, H. Ailion, M. Paaby, A. B. Zhao, Z. Cutter, A. D. Wang, J. Rockman, M. V. Braendle, C. Andersen, E. C. 2025-12-11 doi:10.64898/2025.12.08.693002 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Spatiotemporal Network Dynamics Reveal Alzheimer's Disease Progression ]]> https://biorxiv.org/content/10.64898/2025.12.09.692653v1?rss=1 LaGrow, T. Itkyal, V. S. Watters, H. N. Jensen, K. M. Ballem, R. Pan, W.-j. Irajie, A. Calhoun, V. Keilholz, S. 2025-12-11 doi:10.64898/2025.12.09.692653 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Higher levels of antibiotic resistance are less competitive: the hidden ecological cost of no-metabolic cost resistance ]]> https://biorxiv.org/content/10.64898/2025.12.15.694367v1?rss=1 Wetherington, M. Copeland, R. Zhang, C. Hammer, B. K. Yunker, P. J. 2025-12-15 doi:10.64898/2025.12.15.694367 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Projection-specific Routing of Odor Information in the Olfactory Cortex ]]> https://biorxiv.org/content/10.64898/2025.12.12.694045v1?rss=1 Daste, S. Pham, T. H. Seppo, M. Andre, A. Srinivasan, S. Xiao, J. Sattin, A. Nardin, C. Fellin, T. Franks, K. Dyer, E. Fleischmann, A. 2025-12-16 doi:10.64898/2025.12.12.694045 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Learning Epithelial Elasticity via Local Tension Remodeling ]]> https://biorxiv.org/content/10.64898/2025.12.17.694921v1?rss=1 Arzash, S. Banerjee, S. 2025-12-19 doi:10.64898/2025.12.17.694921 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ A Reinforcement Learning Approach for Modeling Organic 2 Compound-Induced Antimicrobial Resistance Dynamics ]]> https://biorxiv.org/content/10.64898/2025.12.18.695270v1?rss=1 Hedman, H. D. 2025-12-22 doi:10.64898/2025.12.18.695270 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ An NKX2-5 homolog is required downstream of BMP signaling to pattern the sensory-adhesive organ of a tunicate larva ]]> https://biorxiv.org/content/10.64898/2025.12.18.695272v1?rss=1 Johnson, C. J. Kavaler, J. Cota, C. D. Stolfi, A. 2025-12-22 doi:10.64898/2025.12.18.695272 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Non-human primate LIBRA-Seq accelerates neutralizing antibody discovery in RM vaccinated against HIV-1 ]]> https://biorxiv.org/content/10.64898/2025.12.19.695353v1?rss=1 Edwards, C. Silva-Trenkle, A. Sahoo, A. Cruickshank, K. Lapp, S. A. Raju, N. Ton, T. Metz, A. McGhee, E. Mbadugha, F. A. Charles, T. P. Saini, A. Gill, K. Pellegrini, K. L. Kong, R. Wrammert, J. Upadhyay, A. A. Derdeyn, C. A. Amara, R. R. Kwong, G. A. Bosinger, S. E. 2025-12-22 doi:10.64898/2025.12.19.695353 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ A standardized and reproducible behavioral protocol to elicit visual spatial attention in mice ]]> https://biorxiv.org/content/10.64898/2025.12.19.695467v1?rss=1 Peelman, K. Allen, N. Ahn, J. Del Rosario, J. Jacobson, K. C. Kim, E. Lien, A. D. Lopez-Esteva, M. Lovell, L. Worden, K. Yang, Y. Zhuang, J. Haider, B. 2025-12-22 doi:10.64898/2025.12.19.695467 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Identification of DksA as a novel pro-inflammatory mediator of Pseudomonas aeruginosa under conditions mimicking chronic cystic fibrosis lung infection ]]> https://biorxiv.org/content/10.64898/2025.12.21.695867v1?rss=1 Wauters, M. Bolle, L. Van den Bossche, S. Grassi, L. Van Haver, D. Dufour, S. Devos, S. Impens, F. Van Braeckel, E. Hirsch, A. K. H. Whiteley, M. Saelens, X. Crabbe, A. 2025-12-23 doi:10.64898/2025.12.21.695867 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Biophysically Grounded Deep Learning Improves Protein-Protein ΔΔG Prediction ]]> https://biorxiv.org/content/10.64898/2025.12.23.696257v1?rss=1 Feldman, J. Maechler, A. Wang, D. Shakhnovich, E. 2025-12-25 doi:10.64898/2025.12.23.696257 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ Temporal Multi-Omic Analysis Uncovers Sex-Biased Molecular Programs Underlying Skeletal Muscle Adaptation to Endurance Training ]]> https://biorxiv.org/content/10.64898/2025.12.26.696612v1?rss=1 Many, G. Jin, C. Day, N. Smith, G. R. Iyer, G. Sanford, J. A. Bareja, A. Jimenez-Morales, D. Voos, K. Leach, D. T. A. Goodyear, L. Goodpaster, B. Ortlund, E. A. Burant, C. F. Gaul, D. Viggars, M. R. Kohrt, W. Snyder, M. Fernandez, F. Esser, K. A. Bodine, S. Huffman, K. Kraus, W. Newgard, C. Hevener, A. L. Qian, W.-J. Schenk, S. Adkins, J. N. Lindholm, M. E. 2025-12-27 doi:10.64898/2025.12.26.696612 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ HPVarcall: Calling lineages and sublineages for partial DNA sequences of human papillomavirus ]]> https://biorxiv.org/content/10.64898/2025.12.31.697187v1?rss=1 Lomsadze, A. Borodovsky, M. 2026-01-02 doi:10.64898/2025.12.31.697187 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Modulates the Functional Output of Human Taste Bud Cells ]]> https://biorxiv.org/content/10.64898/2025.12.31.697221v1?rss=1 Iyer, S. Montmayeur, J.-P. Hunt, W. D. Dotson, C. D. 2026-01-02 doi:10.64898/2025.12.31.697221 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Real-Time GPU-Accelerated Digital Heart Twin: Integrating Bidirectional Interactions Between Living Optogenetic Monolayers and Computational Simulations ]]> https://biorxiv.org/content/10.64898/2026.01.05.697699v1?rss=1 Valibeigi, Y. Kaboudian, A. Fenton, F. Bub, G. 2026-01-05 doi:10.64898/2026.01.05.697699 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ Regulatory T cells clonally expand and contribute to stromal cell function in fibrotic response to synthetic implants ]]> https://biorxiv.org/content/10.64898/2026.01.05.697727v1?rss=1 Mejias, J. C. Krishnan, K. Ruta, A. Ramanujam, A. S. Gray-Gaillard, E. F. Huyer, L. D. Maestas, D. R. Nagaraj, S. Yu, F. H. Rindone, A. N. Abraham, P. Browne, M. Fertig, E. J. Pardoll, D. M. Elisseeff, J. H. 2026-01-06 doi:10.64898/2026.01.05.697727 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Cellular basis of accelerated whole-tooth regeneration ]]> https://biorxiv.org/content/10.64898/2026.01.06.697137v1?rss=1 3x on the plucked half of the jaw. Then, we used single-nucleus RNA-seq to profile cellular and molecular changes across the first week of post-plucking tooth replacement. This approach allowed us to infer cellular trajectories in dental epithelium and mesenchyme that underlie tooth regeneration. We identifed distinct gene expression profiles and cellular interactions across four time points of accelerated tooth replacement, with divergent involvement of epithelial, mesenchymal and immune cell types. Diferential signaling of Collagen, BMP, MMP, Semaphorin and Slit-Robo pathways was evident after plucking and highlights temporally-sequenced roles of immune response, odontogenesis, vascularization and nerve pathfinding as teeth are constructed anew. Overall, this study provides insight into the trajectory of cellular interactions accompanying whole-tooth replacement and offers a comparative foundation for understanding dental regeneration in vertebrates. ]]> Mubeen, T. He, H. Gruenhagen, G. Satoskar, A. Streelman, J. T. 2026-01-07 doi:10.64898/2026.01.06.697137 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ High performance sorting of motor unit action potentials with EMUsort ]]> https://biorxiv.org/content/10.64898/2026.01.06.697952v1?rss=1 O'Connell, S. Michaels, J. A. Wang, R. Mamidipaka, S. Venkatesh, M. Aresh, N. Pachitariu, M. Pruszynski, J. A. Sober, S. J. Pandarinath, C. 2026-01-07 doi:10.64898/2026.01.06.697952 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ TEDLH: Domain HMMs for sensitive detection of remote homologues ]]> https://biorxiv.org/content/10.64898/2026.01.07.697892v1?rss=1 0.6) and a conserved two-layer /{beta} sandwich core fold. All-against-all HMM-HMM comparisons across TEDLH also reveal sequence similarities across the CATH hierarchy (cross-hits). At low query coverage (<50%), cross-hits are more frequent between CATH classes, whereas at higher coverage thresholds (>70%) they predominantly occur between superfamilies. These cross-hits are not driven by superfamily size or sequence diversity and can provide guidance for CATH curation. As an example, analysis of cross-hits between superfamilies 2.170.130.30 and 3.10.20.30 reveals evolutionary relationships between these groups. Availability and ImplementationTEDLH is compatible with HH-suite3 and is available from FigShare https://doi.org/10.6084/m9.figshare.28531754 for local use. Contactc.carreno@ucl.ac.uk ]]> Alvarez-Carreno, C. Petrov, A. S. Waman, V. P. Sillitoe, I. Orengo, C. 2026-01-08 doi:10.64898/2026.01.07.697892 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ CELLWHISPER: INFERENCE OF DIRECT CELL-CELL COMMUNICATION FROM SPATIAL TRANSCRIPTOMICS ]]> https://biorxiv.org/content/10.64898/2026.01.07.697982v1?rss=1 Kumar, A. Moctezuma, F. R. Aggarwal, B. Zhang, N. Coskun, A. F. Sinha, S. 2026-01-08 doi:10.64898/2026.01.07.697982 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Highly under-actuated dynamic manipulation: Dice stacking is mostly open-loop ]]> https://biorxiv.org/content/10.64898/2026.01.08.698399v1?rss=1 Eckstein, N. I. Lerner, M. Srinivasan, M. 2026-01-09 doi:10.64898/2026.01.08.698399 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ Legionella and Mycobacterium populations exhibit geographic structuring across and within drinking water systems ]]> https://biorxiv.org/content/10.64898/2026.01.13.699378v1?rss=1 He, H. DiLoreto, S. Yang, J. Milne, P. Impellitteri, C. A. Stubbins, A. Pieper, K. Graham, K. Huang, C.-H. Pinto, A. 2026-01-14 doi:10.64898/2026.01.13.699378 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Programming T cells for Early Cancer Detection with Customized Protease-Activatable Receptors ]]> https://biorxiv.org/content/10.64898/2026.01.16.699939v1?rss=1 Phuengkham, H. Chen, Y. Sivakumar, A. Zamat, A. H. Gamboa, L. Mac, Q. D. Lee, H. J. Rogers, L. C. You, J. Steele, S. A. Zhu, S. Gollins, M. S. Blazeck, J. Qiu, P. Kwong, G. A. 2026-01-20 doi:10.64898/2026.01.16.699939 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ SARS-CoV-2 membrane protein biogenesis ]]> https://biorxiv.org/content/10.64898/2026.01.19.700281v1?rss=1 Ortiz Mateu, J. Pearson, G. J. Rius-Salvador, M. Sedighian, S. Pavlova, A. Alonso-Romero, J. Acosta-Caceres, J. M. Metola, A. Garcia-Murria, M. J. Skehel, J. M. Gumbart, J. C. Carlton, J. C. von Heijne, G. Sanchez-del Pino, M. M. Martinez-Gil, L. Mingarro, I. 2026-01-20 doi:10.64898/2026.01.19.700281 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ MANTIS: Analytics toolkit for spatial metabolomics with matching spatial transcriptomics data ]]> https://biorxiv.org/content/10.64898/2026.01.20.700581v1?rss=1 Hao, Y. Kim, Y. Aggarwal, B. Sinha, S. 2026-01-21 doi:10.64898/2026.01.20.700581 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Linking genomic and phenotypic traits to interaction outcomes in a synthetic phyllosphere community ]]> https://biorxiv.org/content/10.64898/2026.01.16.699983v1?rss=1 Batarseh, T. N. Collado, J. O. Mehlferber, E. C. Alvarez-Navarrete, R. M. Wagner, F. J. Koskella, B. N. 2026-01-22 doi:10.64898/2026.01.16.699983 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Integrative Inference of Spatially Resolved Cell Lineage Trees using LineageMap ]]> https://biorxiv.org/content/10.64898/2026.01.19.700383v1?rss=1 Pan, X. Chen, Y. Zhang, X. 2026-01-22 doi:10.64898/2026.01.19.700383 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Neuromark Fusion: A Replicable Multimodal Template for Structure-Function Fusion of Brain MRI ]]> https://biorxiv.org/content/10.64898/2026.01.23.701328v1?rss=1 15,000 subjects to generate a normative model of multimodal structure-function linkages that can be used as a template to guide ICA fusions of new datasets. When applying this template in two datasets, resultant components exhibit high correspondence to the template even in small sample sizes, and subject-level loadings from template-derived ICs show significant associations to age. ]]> Duda, M. Baker, B. Turner, J. A. van Erp, T. Calhoun, V. 2026-01-26 doi:10.64898/2026.01.23.701328 Cold Spring Harbor Laboratory Press 2026-01-26 <![CDATA[ A Primary Central Source Determines Perturbation-Evoked N1 Amplitudes but not Latencies in Younger Adults ]]> https://biorxiv.org/content/10.64898/2026.01.23.701364v1?rss=1 Protzak, J. Mirdamadi, J. L. Borich, M. R. Ting, L. H. 2026-01-26 doi:10.64898/2026.01.23.701364 Cold Spring Harbor Laboratory Press 2026-01-26 <![CDATA[ An integrated platform for simultaneous wide-field voltage/calcium imaging and fMRI (EPI & ZTE) reveals neuronal infraslow dynamics underlying functional connectivity ]]> https://biorxiv.org/content/10.64898/2026.01.26.701889v1?rss=1 98% transmission), a chronically stable optically-fused cranial window, and a subject-conformal RF surface coil compatible with both EPI and zero-echo-time (ZTE) fMRI. The system supports concurrent wide-field imaging of genetically encoded voltage or calcium indicators concurrently with intrinsic hemoglobin signals. In individual mice, wide-field optical and fMRI measures yield concordant functional connectivity, and cross-modal timing analyses demonstrate that neuronal infraslow dynamics (<0.1 Hz) underlie the majority of fMRI connectivity, after removing hemodynamic crosstalk. The platforms sensitivity, chronic stability, and sequence flexibility broaden access to cellular-to-whole-brain investigations across basic and translational neuroimaging. ]]> Pan, W.-J. Daley, L. Watters, H. Meyer-Baese, L. Gopinath, K. Jaeger, D. Keilholz, S. 2026-01-27 doi:10.64898/2026.01.26.701889 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Machine Learning Ensemble Reveals Distinct Molecular Pathways of Retinal Damage in Spaceflown Mice ]]> https://biorxiv.org/content/10.64898/2026.01.22.701181v1?rss=1 Casaletto, J. A. Scott, R. T. Rathod, A. Jain, A. Chandar, A. Adapala, A. Prajapati, A. Nautiyal, A. Jayaraman, A. Boddu, A. Kelam, A. Jain, A. Pham, B. Shastry, D. Narayanan, D. Kosaraju, E. Paley, E. Uribe, F. P. Shahid, I. Ye, I. Wu, J. Lin, J. Srinivas, K. Della Monica, M. P. Hitt, M. Lin, M. Volkan, M. Kharya, M. Kaul, M. Jaffer, M. A. Ali, M. Chang, N. Z. Ashri, N. Couderc, N. B. Paladugu, P. Hiremath, R. Pathak, R. Dogra, S. Srinivas, S. Samaddar, S. Gopinath, S. Sawant, S. Cai, S. Pala, V. Nair, V. Shi, Z. Narayanan, S. Mundackal Thomas, D 2026-01-29 doi:10.64898/2026.01.22.701181 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data ]]> https://biorxiv.org/content/10.64898/2026.01.24.701521v1?rss=1 Mannochio-Russo, H. Goncalves Nunes, W. D. Xing, S. de Oliveira, F. Caraballo-Rodriguez, A. M. Portal Gomes, P. W. Charron-Lamoureux, V. Agongo, J. Avalon, N. E. Bui, T. Cancelada, L. Chevrette, M. G. Cumsille, A. de Araujo, M. B. De Graeve, M. Deleray, V. Donia, M. S. Dzveta, M. B. El Abiead, Y. Ellis, R. J. Franklin, D. Garg, N. Gouda, H. Hamany Djande, C. Y. Hiskia, A. Ho, B. N. Hughes, C. C. Hwang, S. Iliakopoulou, S. Iudicello, J. E. Jarmusch, A. K. Kaloudis, T. Koester, I. Konkel, R. Koolen, H. H. F. Kvitne, K. E. La Rosa, S. L. Lam, A. Lamichhane, S 2026-01-29 doi:10.64898/2026.01.24.701521 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ Machine Learning Identifies Distinct Treg-Mediated Remodeling in HFpEF Hearts Treated with Neonatal Mesenchymal Stem Cells and Their Secretome ]]> https://biorxiv.org/content/10.64898/2026.01.29.702616v1?rss=1 Ge, Z.-D. Han, J. Takaesu, F. Mishra, R. Sharma, S. Chen, L. Fu, X. Filipp, M. Wai, C. M. Shao, N.-Y. Sinha, A. Saha, P. Puvvala, A. Ventura, L. Bileweska, A. Stefenwicz, A. Guru, S. Gunasekaran, M. Yang, E. Dawn, B. Yang, P. Shah, S. Thorp, E. B. Davis, M. Kaushal, S. 2026-01-30 doi:10.64898/2026.01.29.702616 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Interleukin-6 restricts pre-thymic T cell lineage commitment of progenitors driving loss of SIV control ]]> https://biorxiv.org/content/10.64898/2026.01.29.702123v1?rss=1 Anwar, S. Sadek, N. Beusch, C. M. Coskun, A. F. Abdel-Hakeem, M. S. Johnson, R. P. Staal, F. Velu, V. Paiardini, M. Keele, B. F. Silvestri, G. Gordon, D. E. Tomalka, J. A. Rahman, S. A. 2026-02-02 doi:10.64898/2026.01.29.702123 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Serum Proteomic Profiling Implicates a Dysregulated Neurohormonal-Inflammatory Axis in Post-Fontan Tachycardia ]]> https://biorxiv.org/content/10.64898/2026.01.30.702962v1?rss=1 Takaesu, F. Villarreal, D. J. Zhou, A. Jimenez, M. Turner, M. Spiess, J. L. Kievert, J. Deshetler, C. Schwartzman, W. Yates, A. R. Kelly, J. M. Breuer, C. K. Davis, M. 2026-02-02 doi:10.64898/2026.01.30.702962 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Immune checkpoint inhibitors amplify type 2 immune mediated repair bypro-regenerative scaffolds ]]> https://biorxiv.org/content/10.64898/2026.01.31.703034v1?rss=1 Garcia, J. Ruta, A. Yu, F. Mejias, J. Pena, A. Rutkowski, N. Gray-Gaillard, E. Dubois, C. Cherry, C. Browne, M. Stivers, K. Maestas, D. Krishnan, K. Bell, A. Fertig, E. J. Cooney, C. Cooney, D. Byrne, P. Hillel, A. Smith, K. Ji, H. Anders, r. Pardoll, D. Ellisseeff, J. 2026-02-03 doi:10.64898/2026.01.31.703034 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Connectomes across temporal scales with simultaneous wide-field optical imaging and resting-state functional MRI ]]> https://biorxiv.org/content/10.64898/2026.02.01.703149v1?rss=1 Pan, W.-J. Daley, L. Meyer-Baese, L. Keilholz, S. 2026-02-03 doi:10.64898/2026.02.01.703149 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Tissue Injury and Biomaterial Treatment Modulate Tumor Growth and Response to Immunotherapy ]]> https://biorxiv.org/content/10.64898/2026.02.02.703323v1?rss=1 Ruta, A. Gray-Gaillard, E. F. Garcia, J. A. Davenport Huyer, L. Mathkour, Y. Cherry, C. Patatanian, M. Mejias, J. C. Maestas, D. R. Krishnan, K. Abraham, P. Wolf, M. T. Smith, K. N. Pardoll, D. M. Elisseeff, J. H. 2026-02-04 doi:10.64898/2026.02.02.703323 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Cross-Modal Scaffolding: Music Enhances Hippocampal Binding and Separation for Visual Sequential Memory ]]> https://biorxiv.org/content/10.64898/2026.02.03.703550v1?rss=1 Ren, Y. Ahluwalia, V. Arthur, C. Brown, T. 2026-02-05 doi:10.64898/2026.02.03.703550 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ Geometric constraints in the development of primate extrastriate visual cortex ]]> https://biorxiv.org/content/10.64898/2026.02.04.703881v1?rss=1 Kim, H. Arcaro, M. J. Imam, N. 2026-02-07 doi:10.64898/2026.02.04.703881 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ Investigating White Matter Functional Network Connectivity Across the Alzheimers Disease Spectrum Using Resting-State fMRI ]]> https://biorxiv.org/content/10.64898/2026.02.04.703913v1?rss=1 Itkyal, V. S. LaGrow, T. J. Jensen, K. M. Iraji, A. Calhoun, V. 2026-02-07 doi:10.64898/2026.02.04.703913 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ Springtail-inspired compliant hinge enables terrain-adaptable takeoff in insect-scale robots ]]> https://biorxiv.org/content/10.64898/2026.02.04.703923v1?rss=1 Harrison, J. Kim, B. Ko, H. Smith, A. Truong, T. Koh, J.-s. Bhamla, S. 2026-02-07 doi:10.64898/2026.02.04.703923 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ Anaerobic methane oxidation by ANME-2a at two molar chloride in Orca Basin ]]> https://biorxiv.org/content/10.64898/2026.02.09.704686v1?rss=1 Adepoju, L. A. McKaig, J. M. Salcedo, R. S. R. Martinez, A. Buessecker, S. Skoog, E. J. Elbon, C. E. Paris, E. R. Desmarais, M. Sephus, C. D. Pozarycki, C. Hegelein, V. Quartini, E. S. Schartup, A. T. Doran, P. T. Carr, C. E. Ingall, E. D. Bartlett, D. H. Murali, R. Raven, M. R. Dekas, A. E. Bowman, J. S. Schmidt, B. E. Glass, J. B. 2026-02-09 doi:10.64898/2026.02.09.704686 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Large language models unlock the ecology of species interactions ]]> https://biorxiv.org/content/10.64898/2026.02.06.704115v1?rss=1 Zou, H.-X. Yang, X. Hajamaideen, T. H. Stein, O. J. Beltran, R. S. Freeman, B. G. Lindquist, M. Miller, E. T. Mengarelli, S. Probst, C. M. Valdovinos, F. S. Van Berkel, D. B. Zarnetske, P. L. Weeks, B. C. Zhu, K. 2026-02-10 doi:10.64898/2026.02.06.704115 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ DynMoCo: a Novel AI Framework to Reveal Modular Substructures of Protein From Molecular Dynamics ]]> https://biorxiv.org/content/10.64898/2026.02.08.704355v1?rss=1 Mao, L. Kwak, M. Ashkezari, A. H. K. Li, Z. Chen, Y. Cong, P. Phee, J. H. Kang, S. Li, J. Zhu, C. 2026-02-10 doi:10.64898/2026.02.08.704355 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ Spatiotemporal cell type deconvolution leveraging tissue structure ]]> https://biorxiv.org/content/10.64898/2026.02.10.705204v1?rss=1 Lobo, M. M. Zhang, Z. Zhang, X. 2026-02-12 doi:10.64898/2026.02.10.705204 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ Sub-second Extracellular Impedance Measurement of Epithelial Cell Monolayers using Step Excitations and Time-domain Analysis ]]> https://biorxiv.org/content/10.64898/2026.02.17.706376v1?rss=1 Guo, R. Chien, A. J. Hawks, J. Magondu, B. Yang, B. Acevedo, X. O. Watson, A. Lewis, B. Hatcher, C. Forest, C. R. 2026-02-18 doi:10.64898/2026.02.17.706376 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ L-DOPA treatment promotes sustained neurovascular and synaptichomeostasis in the diabetic retina ]]> https://biorxiv.org/content/10.64898/2026.02.17.706466v1?rss=1 Chlan, E. Li, C. Bales, K. Wood, L. B. Pardue, M. 2026-02-18 doi:10.64898/2026.02.17.706466 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Conditioned Graph Reconstruction of Brain Functional Network Connectivity Reveals Interpretable Latent Axes of Sex and Fluid Intelligence ]]> https://biorxiv.org/content/10.64898/2026.02.20.707025v1?rss=1 Batta, I. Ajith, M. Calhoun, V. 2026-02-20 doi:10.64898/2026.02.20.707025 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ PFOA induced metabolic and immune perturbations in a SARS-2 infection model ]]> https://biorxiv.org/content/10.64898/2026.02.21.707085v1?rss=1 Lanier, D. N. Rowe Haas, D. Uchimiya, M. Jones, C. Johnson, S. Sakamoto, K. Chappel, J. R. Fry, A. N. Leach, F. E. DeWitt, J. Woodlief, T. Gaul, D. A. Baker, E. S. Fernandez, F. M. Tompkins, S. M. Edison, A. S. 2026-02-23 doi:10.64898/2026.02.21.707085 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ PantheonOS: An Evolvable Multi-Agent Framework for Automatic Genomics Discovery ]]> https://biorxiv.org/content/10.64898/2026.02.26.707870v1?rss=1 Xu, W. Poussi, E. Zhong, Q. Zeng, Z. Zou, C. Wang, X. Lu, Y. Cui, M. Okamura, D. Huang, C. Ding, J. Zhao, Z. Yang, Y. Pan, X. Vijay, V. Konno, N. Liu, N. Li, L. Ma, X. R. Conley, S. D. Kern, C. Goodyer, W. R. Bintu, B. Zhu, Q. Chi, N. C. He, J. Rognoni, L. Zhang, X. Wu, J. Ellison, D. Rabinovitch, M. Engreitz, J. M. Qiu, X. 2026-02-27 doi:10.64898/2026.02.26.707870 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ Neuronal p38α knockout protects against neurological consequences following repetitive mild traumatic brain injury ]]> https://biorxiv.org/content/10.64898/2026.02.26.708089v1?rss=1 Li, C. Triplett, S. E. Griffin, M. N. Holberton, A. L. Kadragic, A. Moctezuma, F. G. R. Saheba, S. Saah, P. F. Sanz, P. I. Lee, J. C. Wadhwani, R. Dawson, D. Lunt, S. E. Chigurupati, M. Buckley, E. M. Wood, L. B. 2026-02-28 doi:10.64898/2026.02.26.708089 Cold Spring Harbor Laboratory Press 2026-02-28 <![CDATA[ Multi-Omic, Multi-Tissue Responses to Acute Exercise in Sedentary Adults: Findings from the Molecular Transducers of Physical Activity Consortium ]]> https://biorxiv.org/content/10.64898/2026.02.27.702183v1?rss=1 MoTrPAC Study Group, Katz, D. H. Jin, C. A. Many, G. M. Smith, G. R. Keshishian, H. Clark, N. M. Iyer, G. Ahn, C. Lindholm, M. E. Sagendorf, T. J. Amar, D. Barber, J. L. Brandt, A. R. Coen, P. M. Ge, Y. Hart, P. Hsu, F.-C. Jaeger, B. C. Jimenez-Morales, D. Leach, D. T. Mani, D. R. Montalvo, S. Pincas, H. Rao, P. Sanford, J. A. Smith, K. S. Vetr, N. G. Adkins, J. N. Ashley, E. A. Carr, S. A. Miller, M. E. Montgomery, S. B. Nair, V. D. Robbins, J. M. Snyder, M. P. Sparks, L. M. Tracy, R. Walsh, M. J. Wheeler, M. T. Xia, A. Y. Sealfon, S. C. Gerszten, R 2026-03-03 doi:10.64898/2026.02.27.702183 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ An optogenetics-compatible red fluorescent calcium indicator with negligible blue light photoactivation ]]> https://biorxiv.org/content/10.64898/2026.02.28.708321v1?rss=1 Zhang, X. Addison, B. R. Ulutas, E. Z. Deng, C. M. Doshi, S. Nabhan, S. Emanuel, A. J. Markowitz, J. E. Koveal, D. 2026-03-03 doi:10.64898/2026.02.28.708321 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ The limits of Bayesian estimates of divergence times in measurably evolving populations ]]> https://biorxiv.org/content/10.64898/2026.02.28.708707v1?rss=1 Ivanov, S. Fosse, S. dos reis, M. Duchene, S. 2026-03-03 doi:10.64898/2026.02.28.708707 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Cancer-Causing Mutations Alter the Interplay Between Loop Dynamics and Catalysis in the Protein Tyrosine Phosphatases SHP-1 and SHP-2 ]]> https://biorxiv.org/content/10.64898/2026.03.02.708844v1?rss=1 Brownless, A.-L. R. Robinson, M. Kamerlin, S. C. L. 2026-03-03 doi:10.64898/2026.03.02.708844 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Evolutionary profile enhancement improves protein function annotation for remote homologs ]]> https://biorxiv.org/content/10.64898/2026.03.03.709280v1?rss=1 Dai, S. Luo, J. Luo, Y. 2026-03-04 doi:10.64898/2026.03.03.709280 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ PAVR: High-Resolution Cellular Imaging via a Physics-Aware Volumetric Reconstruction Framework ]]> https://biorxiv.org/content/10.64898/2026.03.04.709609v1?rss=1 Hua, X. Han, K. Ling, Z. Reid, O. Gao, Z. Zhang, H. Botchwey, E. Forghani, P. Liu, W. Sawant, M. A. Radmand, A. Kim, H. Dahlman, J. E. Kesarwala, A. Xu, C. Jia, S. 2026-03-06 doi:10.64898/2026.03.04.709609 Cold Spring Harbor Laboratory Press 2026-03-06